annotate test-data/small_dfam.fasta.cat @ 12:39b40a9a6296 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker commit 2f2463888c41a99aec46d4da0eb0ac66cbc20889"

18 0.00 0.00 0.00 scaffold_1 613 632 (13519) (GT)n#Simple_repeat 1 20 (0) m_b1s252i0

  scaffold_1           613 GTGTGTGTGTGTGTGTGTGT 632
                                               
  (GT)n#Simple_          1 GTGTGTGTGTGTGTGTGTGT 20

Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0)

16 18.30 2.22 2.22 scaffold_1 780 824 (13327) (ATAATA)n#Simple_repeat 1 45 (0) m_b1s252i1

  scaffold_1           780 ATATTAAT-ATACTAAATAATGATAATATTAATTCTAATAATGATA 824
                              v    -   v -      i      v    vv       i   
  (ATAATA)n#Sim          1 ATAATAATAATAAT-AATAATAATAATAATAATAATAATAATAATA 45

Matrix = Unknown
Transitions / transversions = 0.40 (2/5)
Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2)

12 23.88 4.55 0.00 scaffold_1 2231 2274 (11877) (CAGA)n#Simple_repeat 1 46 (0) m_b1s252i2

  scaffold_1          2231 CAGA-AAACAGTCAGCCAATCAGA-GGACAGACTCAGAGACAGACA 2274
                               - i    v   v  iv    -i       vv v         
  (CAGA)n#Simpl          1 CAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACA 46

Matrix = Unknown
Transitions / transversions = 0.50 (3/6)
Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2)

15 18.42 10.20 0.00 scaffold_1 4853 4901 (9250) (TC)n#Simple_repeat 1 54 (0) m_b1s252i3

  scaffold_1          4853 TCTATTTTTCTCTCTCTCTCT-TCGGTCAGTTTCTCT-TCT-TCTC-CTC 4898
                              v i i             -  vv  vv i     -   -    -   
  (TC)n#Simple_          1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50

  scaffold_1          4899 -CTC 4901
                           -   
  (TC)n#Simple_         51 TCTC 54

Matrix = Unknown
Transitions / transversions = 0.60 (3/5)
Gap_init rate = 0.10 (5 / 48), avg. gap size = 1.00 (5 / 5)

13 19.07 1.82 7.69 scaffold_1 6230 6284 (7867) (TAATTAA)n#Simple_repeat 1 52 (0) m_b1s252i4

  scaffold_1          6230 TAATGAGT-ATTACTAATTAATAATTGGATGAGTTTATGAATTCATCATT 6278
                               v i -    v            -i  - i  v  -    v  v   
  (TAATTAA)n#Si          1 TAATTAATAATTAATAATTAATAATT-AAT-AATTAAT-AATTAATAATT 47

  scaffold_1          6279 AAATAA 6284
                           -     
  (TAATTAA)n#Si         48 -AATAA 52

Matrix = Unknown
Transitions / transversions = 0.60 (3/5)
Gap_init rate = 0.09 (5 / 54), avg. gap size = 1.00 (5 / 5)

15 28.31 0.00 3.51 scaffold_1 6548 6606 (7545) (GACA)n#Simple_repeat 1 57 (0) m_b1s252i5

  scaffold_1          6548 GACAGAGAGATAAACAGACAGACATGGAAACAGAGGGACATAGAAAACAA 6597
                                 v   i i           viv i     vi    v -v i  - 
  (GACA)n#Simpl          1 GACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGA-CAGAC-A 48

  scaffold_1          6598 GACAGAGAG 6606
                                 v  
  (GACA)n#Simpl         49 GACAGACAG 57

Matrix = Unknown
Transitions / transversions = 0.86 (6/7)
Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2)

180 25.44 1.41 5.88 scaffold_1 8140 8210 (5941) C AmnL2-1#LINE/L2 (11) 2602 2535 m_b1s601i0

  scaffold_1          8140 ACAACATTATTTTGTCTA-CACCCTGCATACAGCACAGTATATTAAATTT 8188
                                v         v  - ii i v      i-  v    vii   ---
C AmnL2-1#LINE/       2602 ACAACTTTATTTTGTATAGCGTCTTTCATACAA-ACTGTATCCCAAA--- 2557

  scaffold_1          8189 AGGTTTTATTAAGTTAAGTAAT 8210
                            v i    ivi      i    
C AmnL2-1#LINE/       2556 ACGCTTTACAGAGTTAAATAAT 2535

Matrix = 25p39g.matrix
Kimura (with divCpGMod) = 29.45
Transitions / transversions = 1.43 (10/7)
Gap_init rate = 0.07 (5 / 70), avg. gap size = 1.00 (5 / 5)

67 2.94 1.43 0.00 scaffold_1 11981 12050 (2170) (CT)n#Simple_repeat 1 71 (0) c_b1s251i0

  scaffold_1         11981 CTCTCTCTCTCTCCCTCTCCCTCTC-CTCTCTCTCTCTCTCTCTCTCTCT 12029
                                        i     i     -                        
  (CT)n#Simple_          1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50

  scaffold_1         12030 CTCTCTCTCTCTCTCTCTCTC 12050
                                                
  (CT)n#Simple_         51 CTCTCTCTCTCTCTCTCTCTC 71

Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1)

19 15.37 2.78 0.00 scaffold_1 12078 12113 (2107) (CT)n#Simple_repeat 1 37 (0) m_b1s252i6

  scaffold_1         12078 CTCGCTCTCTCACTCTCTCCCTCTCTC-CCCACTCTC 12113
                              v       v       i       - i v     
  (CT)n#Simple_          1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 37

Matrix = Unknown
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1)

## Total Sequences: 1
## Total Length: 14220
## Total NonMask ( excluding >20bp runs of N/X bases ): 14220
## Total NonSub ( excluding all non ACGT bases ):14220
RepeatMasker version 4.1.2-p1 , default mode
run with rmblastn version 2.10.0+
RM Library: CONS-Dfam_3.3