view newtests/cap3stdout.txt @ 1:a36a1acd5807 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 commit 3bb28761a3768b3b84616be41efc40683653da60

Number of segment pairs = 342; number of pairwise comparisons = 14
'+' means given segment; '-' means reverse complement

Overlaps            Containments  No. of Constraints Supporting Overlap

******************* Contig 1 ********************
2+
                    9+ is in 2+
                    6+ is in 2+
15+
                    1+ is in 15+
                    17+ is in 15+
13+
******************* Contig 2 ********************
7+
                    10+ is in 7+
******************* Contig 3 ********************
11+
4+
******************* Contig 4 ********************
18+
12+

DETAILED DISPLAY OF CONTIGS
******************* Contig 1 ********************
                          .    :    .    :    .    :    .    :    .    :    .    :
2+                    GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG
9+                    GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG
15+                   GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG
                      ____________________________________________________________
consensus             GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG

                          .    :    .    :    .    :    .    :    .    :    .    :
2+                    GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG
9+                    GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG
15+                   GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG
                      ____________________________________________________________
consensus             GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG

                          .    :    .    :    .    :    .    :    .    :    .    :
2+                    TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG
9+                    TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG
6+                                                                       ACATCCTGG
15+                   TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG
                      ____________________________________________________________
consensus             TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG

                          .    :    .    :    .    :    .    :    .    :    .    :
2+                    GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC
9+                    GTATGGTGGCTGTGGGC                                           
6+                    GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC
15+                   GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC
                      ____________________________________________________________
consensus             GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC

                          .    :    .    :    .    :    .    :    .    :    .    :
2+                    TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC
6+                    TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC
15+                   TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC
                      ____________________________________________________________
consensus             TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC

                          .    :    .    :    .    :    .    :    .    :    .    :
2+                    ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA
6+                    ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA
15+                   ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA
17+                                                                     TACTCCTGCA
                      ____________________________________________________________
consensus             ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA

                          .    :    .    :    .    :    .    :    .    :    .    :
2+                    ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTAC                         
6+                    ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTAC                         
15+                   ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT
1+                             TTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT
17+                   ACGTCCAGATTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT
                      ____________________________________________________________
consensus             ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT

                          .    :    .    :    .    :    .    :    .    :    .    :
15+                   CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG
1+                    CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG
17+                   CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG
                      ____________________________________________________________
consensus             CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG

                          .    :    .    :    .    :    .    :    .    :    .    :
15+                   TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA
1+                    TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA
17+                   TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA
                      ____________________________________________________________
consensus             TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA

                          .    :    .    :    .    :    .    :    .    :    .    :
15+                   TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT
1+                    TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT
17+                   TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT
                      ____________________________________________________________
consensus             TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT

                          .    :    .    :    .    :    .    :    .    :    .    :
15+                   CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA
1+                    CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA
17+                   CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA
                      ____________________________________________________________
consensus             CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA

                          .    :    .    :    .    :    .    :    .    :    .    :
15+                   ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC
1+                    ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC
17+                   ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC
                      ____________________________________________________________
consensus             ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC

                          .    :    .    :    .    :    .    :    .    :    .    :
15+                   CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCC
1+                    CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGT         
17+                   CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGT         
13+                                            GTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCC
                      ____________________________________________________________
consensus             CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCC

                          .    :    .    :    .    :    .    :    .    :    .    :
15+                   TCAAACACTTTGTACTCATCATTCAGATTCGCCTCAGGAGGAGGAGGGCATCCTACAACC
13+                   TCAAACACTTTGTACTCATCATTCAGATTCGCCTCAGGAGGAGGAGGGCATCCTACAACC
                      ____________________________________________________________
consensus             TCAAACACTTTGTACTCATCATTCAGATTCGCCTCAGGAGGAGGAGGGCATCCTACAACC

                          .    :    .    :    .    :    .    :    .    :    .    :
15+                   TCCTTGACATCATAGTCGTTGGATTGGACTGTCAAATTTATCTGCCTCACAGCCACTCTC
13+                   TCCTTGACATCATAGTCGTTGGATTGGACTGTCAAATTTATCTGCCTCACAGCCACTCTC
                      ____________________________________________________________
consensus             TCCTTGACATCATAGTCGTTGGATTGGACTGTCAAATTTATCTGCCTCACAGCCACTCTC

                          .    :    .    :    .    :    .    :    .    :    .    :
15+                   TGCTCCCTCTTAAACTCGTCCAGGAATCCTGACAATGTGGGGAACAGATTAATCCATCCC
13+                   TGCTCCCTCTTAAACTCGTCCAGGAATCCTGACAATGTGGGGAACAGATTAATCCATCCC
                      ____________________________________________________________
consensus             TGCTCCCTCTTAAACTCGTCCAGGAATCCTGACAATGTGGGGAACAGATTAATCCATCCC

                          .    :    .    :    .    :    .    :    .    :    .    :
15+                   GCTTTGTCATCCTCTCCATCTGAATAGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCT
13+                   GCTTTGTCATCCTCTCCATCTGAATAGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCT
                      ____________________________________________________________
consensus             GCTTTGTCATCCTCTCCATCTGAATAGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCT

                          .    :    .    :    .    :    .    :    .    :    .    :
15+                   GACGAATCTGGATATTCAAAGTCCTGGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGC
13+                   GACGAATCTGGATATTCAAAGTCCTGGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGC
                      ____________________________________________________________
consensus             GACGAATCTGGATATTCAAAGTCCTGGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGC

                          .    :    .    :    .    :    .    :    .    :    .    :
15+                   TCTTGCGTTTGCATGACAATAATCTCGCCGGGGATTGTGTTAACCACAGCGTGTATTGTC
13+                   TCTTGCGTTTGCATGACAATAATCTCGCCGGGGATTGTGTTAACCACAGCGTGTATTGTC
                      ____________________________________________________________
consensus             TCTTGCGTTTGCATGACAATAATCTCGCCGGGGATTGTGTTAACCACAGCGTGTATTGTC

                          .    :    .    :    .    :    .    :    .    :    .    :
15+                   TCTTCGATCCGAGGTATGCTGAATCCCATTGTTATCATTAAACCCCTCATACGGTCATAC
13+                   TCTTCGATCCGAGGTATGCTGAATCCCATTGTTATCATTAAACCCCTCATACGGTCATAC
                      ____________________________________________________________
consensus             TCTTCGATCCGAGGTATGCTGAATCCCATTGTTATCATTAAACCCCTCATACGGTCATAC

                          .    :    .    :    .    :    .    :    .    :    .    :
15+                   AGAGTTCTTTGGCGTGCCGTTCTAGATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAG
13+                   AGAGTTCTTTGGCGTGCCGTTCTAGATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAG
                      ____________________________________________________________
consensus             AGAGTTCTTTGGCGTGCCGTTCTAGATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAG

                          .    :    .    :    .    :    .    :    .    :    .    :
15+                   AGCATCATCTCAAGAGCATCGCTCTCAGGCATTGTGGGGACATGTATCACACGGTGTCTG
13+                   AGCATCATCTCAAGAGCATCGCTCTCAGGCATTGTGGGGACATGTATCACACGGTGTCTG
                      ____________________________________________________________
consensus             AGCATCATCTCAAGAGCATCGCTCTCAGGCATTGTGGGGACATGTATCACACGGTGTCTG

                          .    :    .    :    .    :    .    :    .    :    .    :
15+                   TGGTACACTCCCATAATTTGTACGCCAAGAAATTTGTGGTCCGTAATTAGAC
13+                   TGGTACACTCCCATAATTTGTACGCCAAGAAATTTGTGGTCCGTAATTAGAC
                      ____________________________________________________________
consensus             TGGTACACTCCCATAATTTGTACGCCAAGAAATTTGTGGTCCGTAATTAGAC

******************* Contig 2 ********************
                          .    :    .    :    .    :    .    :    .    :    .    :
7+                    TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC
10+                   TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC
                      ____________________________________________________________
consensus             TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC

                          .    :    .    :    .    :    .    :    .    :    .    :
7+                    AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA
10+                   AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA
                      ____________________________________________________________
consensus             AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA

                          .    :    .    :    .    :    .    :    .    :    .    :
7+                    GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA
10+                   GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA
                      ____________________________________________________________
consensus             GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA

                          .    :    .    :    .    :    .    :    .    :    .    :
7+                    GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA
10+                   GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA
                      ____________________________________________________________
consensus             GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA

                          .    :    .    :    .    :    .    :    .    :    .    :
7+                    GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC
10+                   GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC
                      ____________________________________________________________
consensus             GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC

                          .    :    .    :    .    :    .    :    .    :    .    :
7+                    CCACTTTATCGTGGATGGTAAAACTGTTTACAAGAAGAAGAACCCCCATGGACTCATGAC
10+                   CCACTTTATCGTGGATGGTAAAACTGTTTACAAGAAGAAGAACCCCCATGGACTCATGAC
                      ____________________________________________________________
consensus             CCACTTTATCGTGGATGGTAAAACTGTTTACAAGAAGAAGAACCCCCATGGACTCATGAC

                          .    :    .    :    .    :    .    :    .    :    .    :
7+                    TGGAGTTCCAGGAACAACCCTATTTGACACTGTGAAATCTGTAATAGTCTGGAATGAAAT
10+                   TGGAGTTCCAGGAACAACCCTATTTGACACTGTGAAATCTGTAATAGTCTGGAATGAAAT
                      ____________________________________________________________
consensus             TGGAGTTCCAGGAACAACCCTATTTGACACTGTGAAATCTGTAATAGTCTGGAATGAAAT

                          .    :    .    :    .    :    .    :    .    :    .    :
7+                    GTTGGATCAGGCTGGTGCAGGTTCCATAGACCTTTTAAATGAAGCTCAAGTAGTTGAATG
10+                   GTTGGATCAGGCTGGTGCAGGTTCCATAGACCTTTTAAATGAAGCTCAAGTAGTTGAATG
                      ____________________________________________________________
consensus             GTTGGATCAGGCTGGTGCAGGTTCCATAGACCTTTTAAATGAAGCTCAAGTAGTTGAATG

                          .    :    .    :    .    :    .    :    .    :    .    :
7+                    GATGAAGAGACAAGGCTTGGTTGTCAAAGAGGGAA
10+                   GATGAAGAGACAAGGCTTAGTTGTCA         
                      ____________________________________________________________
consensus             GATGAAGAGACAAGGCTTAGTTGTCAAAGAGGGAA

******************* Contig 3 ********************
                          .    :    .    :    .    :    .    :    .    :    .    :
11+                   AACGTAAAACAAACGACATGGATGCATCTAACCCTATTATTTCAAGCGATAGAAGCACTG
4+                                                                    ATAGAAGCACTG
                      ____________________________________________________________
consensus             AACGTAAAACAAACGACATGGATGCATCTAACCCTATTATTTCAAGCGATAGAAGCACTG

                          .    :    .    :    .    :    .    :    .    :    .    :
11+                   TGAATCAGGTTTATGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG
4+                    TGAATCAGGTTTACGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG
                      ____________________________________________________________
consensus             TGAATCAGGTTTACGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG

                          .    :    .    :    .    :    .    :    .    :    .    :
11+                   AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG
4+                    AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG
                      ____________________________________________________________
consensus             AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG

                          .    :    .    :    .    :    .    :    .    :    .    :
11+                   AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG
4+                    AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG
                      ____________________________________________________________
consensus             AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG

                          .    :    .    :    .    :    .    :    .    :    .    :
11+                   TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT
4+                    TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT
                      ____________________________________________________________
consensus             TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT

******************* Contig 4 ********************
                          .    :    .    :    .    :    .    :    .    :    .    :
18+                   TACGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA
12+                      GGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA
                      ____________________________________________________________
consensus             TACGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA

                          .    :    .    :    .    :    .    :    .    :    .    :
18+                   CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA
12+                   CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA
                      ____________________________________________________________
consensus             CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA

                          .    :    .    :    .    :    .    :    .    :    .    :
18+                   ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC
12+                   ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC
                      ____________________________________________________________
consensus             ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC

                          .    :    .    :    .    :    .    :    .    :    .    :
18+                   GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA
12+                   GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA
                      ____________________________________________________________
consensus             GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA

                          .    :    .    :    .    :    .    :    .    :    .    :
18+                   ACAGTTCTTGTTA
12+                   ACAGTTCTTGTTA
                      ____________________________________________________________
consensus             ACAGTTCTTGTTA