Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2979
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 38926
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:3644 original size:43 final size:43
Alignment explanation
Indices: 3581--3743 Score: 201
Period size: 43 Copynumber: 3.8 Consensus size: 43
3571 ATTTATGGAA
* * *
3581 AAAAACGCCGCTAAAAGTCAA-GCTTTTAGCGGCATTTGTGGG
1 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
*
3623 AAAAGCGCCGCTAAATTGTCAAGGC-TTTAGCGGCCGTTTGT-GG
1 AAAAGCGCCGCTAAA-GGTCAAGGCTTTTAGCGG-CGTTTGTGGG
* *
3666 AAAAGCACAAGCTAAAGGTCAAGGCTTTTAGC-GCGTTTGTGGG
1 AAAAGCGC-CGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
3709 AAAAGCGCCGCTAAACGGT-AAGGCTTTTAGCGGCG
1 AAAAGCGCCGCTAAA-GGTCAAGGCTTTTAGCGGCG
3744 CTGCAAAAAA
Statistics
Matches: 105, Mismatches: 8, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
42 39 0.37
43 46 0.44
44 20 0.19
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
Found at i:9625 original size:9 final size:9
Alignment explanation
Indices: 9611--9703 Score: 96
Period size: 9 Copynumber: 10.0 Consensus size: 9
9601 TGACAACATA
9611 TAAGTTATG
1 TAAGTTATG
9620 TAAGTTATG
1 TAAGTTATG
9629 TAAGTTATG
1 TAAGTTATG
9638 TAAGTTATG
1 TAAGTTATG
*
9647 TAAGTTATA
1 TAAGTTATG
* *
9656 TATTTATTTATA
1 TA---AGTTATG
9668 TAAGTTATG
1 TAAGTTATG
* *
9677 TACGTTTTG
1 TAAGTTATG
*
9686 TAAGTTATA
1 TAAGTTATG
*
9695 TAAATTATG
1 TAAGTTATG
9704 ATATCAAATA
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
9 62 0.89
12 8 0.11
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.48
Consensus pattern (9 bp):
TAAGTTATG
Found at i:9676 original size:48 final size:49
Alignment explanation
Indices: 9615--9707 Score: 134
Period size: 48 Copynumber: 1.9 Consensus size: 49
9605 AACATATAAG
* * *
9615 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTAT-ATATTTAT
1 TTATATAAGTTATGTAAGTTATGTAAGTTATATAAATTATGATATTTAT
* *
9663 TTATATAAGTTATGTACGTTTTGTAAGTTATATAAATTATGATAT
1 TTATATAAGTTATGTAAGTTATGTAAGTTATATAAATTATGATAT
9708 CAAATATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 35 0.90
49 4 0.10
ACGTcount: A:0.34, C:0.01, G:0.15, T:0.49
Consensus pattern (49 bp):
TTATATAAGTTATGTAAGTTATGTAAGTTATATAAATTATGATATTTAT
Found at i:9716 original size:48 final size:48
Alignment explanation
Indices: 9620--9734 Score: 116
Period size: 48 Copynumber: 2.5 Consensus size: 48
9610 ATAAGTTATG
* * * **
9620 TAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATATATTTATTTATA
1 TAAGTTATGTAAGTTATGTAAGTTATATAAATTATATATTCAAATATA
* *
9668 TAAGTTATGTACGTTTTGTAAGTTATATAAATTATGATA-TCAAATATA
1 TAAGTTATGTAAGTTATGTAAGTTATATAAATTAT-ATATTCAAATATA
9716 T---TTATGT-A-TTATGTAAGTT
1 TAAGTTATGTAAGTTATGTAAGTT
9735 TTTTATTTCA
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
43 10 0.18
45 6 0.11
48 38 0.67
49 3 0.05
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.49
Consensus pattern (48 bp):
TAAGTTATGTAAGTTATGTAAGTTATATAAATTATATATTCAAATATA
Found at i:9828 original size:15 final size:15
Alignment explanation
Indices: 9808--9863 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
9798 AAGTAGCGGG
9808 ATTAAATAATATTTA
1 ATTAAATAATATTTA
9823 ATTAAATAATATTT-
1 ATTAAATAATATTTA
9837 A-TAAA-AATTATTTTA
1 ATTAAATAA-TA-TTTA
*
9852 ATTAAGTAATAT
1 ATTAAATAATAT
9864 ACATGTCGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 4 0.11
15 16 0.46
16 5 0.14
17 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
ATTAAATAATATTTA
Found at i:10979 original size:290 final size:290
Alignment explanation
Indices: 10068--11362 Score: 2533
Period size: 290 Copynumber: 4.5 Consensus size: 290
10058 TTGTGATAAA
10068 AAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTA
1 AAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTA
10133 TATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAA
66 TATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAA
*
10198 TATTTAAATATTAAAATTAAACATTATTAATATAAAAAAATAGTAATTTGAATATAATAATATCA
131 TATTTAAATATTAAAATCAAACATTATTAATATAAAAAAATAGTAATTTGAATATAATAATATCA
*
10263 AAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAATGTTATATAAATATTCA
196 AAAAAGAATCGTAGTTTAATTTTTATAAGTAAATCGGAAATAAATTAATGTTATATAAATATTCA
10328 ATAGTAAATGAGCTCGATAGAACTTTTTTC
261 ATAGTAAATGAGCTCGATAGAACTTTTTTC
*
10358 AAGTCTTTTTGAA-TTTTTAAGATTCATTATACGTGGCGTTGTTACACCTAGGGAGGATCCATTA
1 AAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTA
10422 TATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAA
66 TATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAA
10487 TATTTAAATATTAAAATCAAACATTATTAATAT-AAAAAATAGTAATTTGAATATAATAATATC-
131 TATTTAAATATTAAAATCAAACATTATTAATATAAAAAAATAGTAATTTGAATATAATAATATCA
10550 AAAAAGAATCGTAGTTTAATTTTTATAAGTAAATCGGAAATAAATTAATGTTATATAAATATTCA
196 AAAAAGAATCGTAGTTTAATTTTTATAAGTAAATCGGAAATAAATTAATGTTATATAAATATTCA
10615 ATAGTAAATGAGCTCGATAGAACTTTTTTC
261 ATAGTAAATGAGCTCGATAGAACTTTTTTC
10645 AAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTA
1 AAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTA
10710 TATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAA
66 TATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAA
10775 TATTTAAATATTAAAATCAAACATTATTAATATAAAAAAATAGTAATTTGAATATAATAATATCA
131 TATTTAAATATTAAAATCAAACATTATTAATATAAAAAAATAGTAATTTGAATATAATAATATCA
10840 AAAAAGAATCGTAGTTTAATTTTTATAAGTAAATCGGAAATAAATTAATGTTATATAAATATTCA
196 AAAAAGAATCGTAGTTTAATTTTTATAAGTAAATCGGAAATAAATTAATGTTATATAAATATTCA
10905 ATAGTAAATGAGCTCGATAGAACTTTTTTC
261 ATAGTAAATGAGCTCGATAGAACTTTTTTC
10935 AAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTA
1 AAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTA
11000 TATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAA
66 TATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAA
11065 TATTTAAATATTAAAATCAAACATTATTAATATAAAAAAATAGTAATTTGAATATAATAATATCA
131 TATTTAAATATTAAAATCAAACATTATTAATATAAAAAAATAGTAATTTGAATATAATAATATCA
*
11130 AAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAATGTTATATAAATATTCA
196 AAAAAGAATCGTAGTTTAATTTTTATAAGTAAATCGGAAATAAATTAATGTTATATAAATATTCA
11195 ATAGTAAATGAGCTCGATAGAACTTTTTTC
261 ATAGTAAATGAGCTCGATAGAACTTTTTTC
11225 AAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTA
1 AAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTA
11290 TATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAA
66 TATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAA
11355 TATTTAAA
131 TATTTAAA
11363 ATAAGGTTGG
Statistics
Matches: 997, Mismatches: 5, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
287 107 0.11
288 178 0.18
289 177 0.18
290 535 0.54
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (290 bp):
AAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTA
TATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAA
TATTTAAATATTAAAATCAAACATTATTAATATAAAAAAATAGTAATTTGAATATAATAATATCA
AAAAAGAATCGTAGTTTAATTTTTATAAGTAAATCGGAAATAAATTAATGTTATATAAATATTCA
ATAGTAAATGAGCTCGATAGAACTTTTTTC
Found at i:13467 original size:62 final size:61
Alignment explanation
Indices: 13306--13486 Score: 344
Period size: 61 Copynumber: 3.0 Consensus size: 61
13296 ACAAACTAGT
13306 TTTTCCATTTCAGAACAAAAAATCCAAACAACAGACATAAAACTGACAAAAAAGAAATGAA
1 TTTTCCATTTCAGAACAAAAAATCCAAACAACAGACATAAAACTGACAAAAAAGAAATGAA
*
13367 TTTTCCATTTCAGAACAAAAAATCCAAACAACAAACATAAAACTGACAAAAAAGAAATGAA
1 TTTTCCATTTCAGAACAAAAAATCCAAACAACAGACATAAAACTGACAAAAAAGAAATGAA
13428 TTTTCCATTTCAGAACAAAAATATCCAAACAACAGACATAAAACTGACAAAAAAGAAAT
1 TTTTCCATTTCAGAACAAAAA-ATCCAAACAACAGACATAAAACTGACAAAAAAGAAAT
13487 CAAATTTTGG
Statistics
Matches: 117, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
61 81 0.69
62 36 0.31
ACGTcount: A:0.56, C:0.18, G:0.07, T:0.19
Consensus pattern (61 bp):
TTTTCCATTTCAGAACAAAAAATCCAAACAACAGACATAAAACTGACAAAAAAGAAATGAA
Found at i:15864 original size:26 final size:25
Alignment explanation
Indices: 15835--15884 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
15825 GAATTAATCA
15835 TAAACCTTCAAATAC-TAGTTAACTCC
1 TAAACCTT-AAA-ACATAGTTAACTCC
*
15861 TAAACCTTAAACCATAGTTAACTC
1 TAAACCTTAAAACATAGTTAACTC
15885 ATAATTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 13 0.59
26 8 0.36
ACGTcount: A:0.40, C:0.26, G:0.04, T:0.30
Consensus pattern (25 bp):
TAAACCTTAAAACATAGTTAACTCC
Found at i:15919 original size:14 final size:14
Alignment explanation
Indices: 15902--15941 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
15892 ATTAAACATG
* *
15902 CTTAAACCATATAT
1 CTTAAACCATAAAC
15916 CTTAAACCATAAAC
1 CTTAAACCATAAAC
*
15930 CTTAAACTATAA
1 CTTAAACCATAA
15942 TGATAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (14 bp):
CTTAAACCATAAAC
Found at i:16157 original size:41 final size:41
Alignment explanation
Indices: 16098--16481 Score: 565
Period size: 41 Copynumber: 9.4 Consensus size: 41
16088 GGTTATGAGA
* *
16098 TTTTTAGCGGCGTTTTACGAAAAGTGCCGCTGATGCTCTGG
1 TTTTTAGCGGCGTTTTACGAAAAGCGCCGCTAATGCTCTGG
*
16139 TGTTTAGCGGCGTTTTACGAAAAGCGCCGCTAATGCTCTGG
1 TTTTTAGCGGCGTTTTACGAAAAGCGCCGCTAATGCTCTGG
* * * * *
16180 TTTTTTGAGGTGTTTTAGGAAAAGCGCCGCTAATGCTTTGG
1 TTTTTAGCGGCGTTTTACGAAAAGCGCCGCTAATGCTCTGG
*
16221 TTTTTAGCGGCGTTTTA-GGAAAGCGCCGCTAATGCTCTGG
1 TTTTTAGCGGCGTTTTACGAAAAGCGCCGCTAATGCTCTGG
* * *
16261 TTTTTTGCGGCGTTTTACGAGAAGCGTCGCTAATGCTCTGG
1 TTTTTAGCGGCGTTTTACGAAAAGCGCCGCTAATGCTCTGG
16302 TTTTTAGCGGCGTTTTACGAAAAGCGCCGCTAATGCTCTGG
1 TTTTTAGCGGCGTTTTACGAAAAGCGCCGCTAATGCTCTGG
* *
16343 TTTTTTGCGGCGTTTTACGAAAAGCGCCACTAATGCTCTGG
1 TTTTTAGCGGCGTTTTACGAAAAGCGCCGCTAATGCTCTGG
** *
16384 TTTTTAGTTGCGTTTTACGAAAAGCGCCGCTAATGCTCTAGT
1 TTTTTAGCGGCGTTTTACGAAAAGCGCCGCTAATGCTCT-GG
* *
16426 TTTTTTGCGGCGTTTTAGGAAAAGCGCCGCTAATGCTCTGG
1 TTTTTAGCGGCGTTTTACGAAAAGCGCCGCTAATGCTCTGG
*
16467 -TTTTAGCAGCGTTTT
1 TTTTTAGCGGCGTTTT
16482 TTCTAGAACG
Statistics
Matches: 306, Mismatches: 35, Indels: 5
0.88 0.10 0.01
Matches are distributed among these distances:
40 50 0.16
41 220 0.72
42 36 0.12
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.35
Consensus pattern (41 bp):
TTTTTAGCGGCGTTTTACGAAAAGCGCCGCTAATGCTCTGG
Found at i:16378 original size:163 final size:165
Alignment explanation
Indices: 16098--16481 Score: 594
Period size: 163 Copynumber: 2.3 Consensus size: 165
16088 GGTTATGAGA
* * * *
16098 TTTTTAGCGGCGTTTTACGAAAAGTGCCGCTGATGCTCTGGTGTTTAGCGGCGTTTTACGAAAAG
1 TTTTTTGCGGCGTTTTACGAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACGAAAAG
* * * *
16163 CGCCGCTAATGCTCTGGTTTTTTGAGGTGTTTTAGGAAAAGCGCCGCTAATGCTTTGGTTTTTAG
66 CGCCGCTAATGCTCTGGTTTTTTGAGGCGTTTTACGAAAAGCGCCACTAATGCTCTGGTTTTTAG
*
16228 CGGCGTTTTA-GGAAAGCGCCGCTAATGCTCT-GG
131 CGGCGTTTTACGAAAAGCGCCGCTAATGCTCTAGG
* *
16261 TTTTTTGCGGCGTTTTACGAGAAGCGTCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACGAAAAG
1 TTTTTTGCGGCGTTTTACGAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACGAAAAG
*
16326 CGCCGCTAATGCTCTGGTTTTTTGCGGCGTTTTACGAAAAGCGCCACTAATGCTCTGGTTTTTAG
66 CGCCGCTAATGCTCTGGTTTTTTGAGGCGTTTTACGAAAAGCGCCACTAATGCTCTGGTTTTTAG
** *
16391 TTGCGTTTTACGAAAAGCGCCGCTAATGCTCTAGT
131 CGGCGTTTTACGAAAAGCGCCGCTAATGCTCTAGG
* *
16426 TTTTTTGCGGCGTTTTAGGAAAAGCGCCGCTAATGCTCTGG-TTTTAGCAGCGTTTT
1 TTTTTTGCGGCGTTTTACGAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTT
16482 TTCTAGAACG
Statistics
Matches: 200, Mismatches: 19, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
163 127 0.63
164 34 0.17
165 39 0.19
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.35
Consensus pattern (165 bp):
TTTTTTGCGGCGTTTTACGAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACGAAAAG
CGCCGCTAATGCTCTGGTTTTTTGAGGCGTTTTACGAAAAGCGCCACTAATGCTCTGGTTTTTAG
CGGCGTTTTACGAAAAGCGCCGCTAATGCTCTAGG
Found at i:22038 original size:21 final size:20
Alignment explanation
Indices: 22012--22096 Score: 70
Period size: 21 Copynumber: 4.3 Consensus size: 20
22002 TAACTAAATT
22012 CATTTTAATAATTATATTTTA
1 CATTTTAATAATTAT-TTTTA
* **
22033 CATTTT-CT-ATT-TTGATA
1 CATTTTAATAATTATTTTTA
*
22050 -TTTTTAATAATTATTTTTCA
1 CATTTTAATAATTATTTTT-A
*
22070 AATTTTAATAATTATATTTTA
1 CATTTTAATAATTAT-TTTTA
22091 CATTTT
1 CATTTT
22097 CTATTTTGAT
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
16 4 0.08
17 4 0.08
18 4 0.08
19 6 0.12
20 2 0.04
21 25 0.51
22 4 0.08
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (20 bp):
CATTTTAATAATTATTTTTA
Found at i:22080 original size:58 final size:58
Alignment explanation
Indices: 22013--22131 Score: 238
Period size: 58 Copynumber: 2.1 Consensus size: 58
22003 AACTAAATTC
22013 ATTTTAATAATTATATTTTACATTTTCTATTTTGATATTTTTAATAATTATTTTTCAA
1 ATTTTAATAATTATATTTTACATTTTCTATTTTGATATTTTTAATAATTATTTTTCAA
22071 ATTTTAATAATTATATTTTACATTTTCTATTTTGATATTTTTAATAATTATTTTTCAA
1 ATTTTAATAATTATATTTTACATTTTCTATTTTGATATTTTTAATAATTATTTTTCAA
22129 ATT
1 ATT
22132 AAAAATTTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (58 bp):
ATTTTAATAATTATATTTTACATTTTCTATTTTGATATTTTTAATAATTATTTTTCAA
Found at i:26908 original size:3 final size:3
Alignment explanation
Indices: 26900--26942 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
26890 AAACTTTGAG
26900 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
26943 ATGGACGTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:28249 original size:18 final size:19
Alignment explanation
Indices: 28210--28250 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
28200 TATAATTTGG
* *
28210 TAAATTAAAAATTTATGAC
1 TAAAATAAAAATTGATGAC
28229 TAAAATAAAAATTGATG-C
1 TAAAATAAAAATTGATGAC
28247 TAAA
1 TAAA
28251 TTAAGTAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (19 bp):
TAAAATAAAAATTGATGAC
Found at i:32813 original size:17 final size:18
Alignment explanation
Indices: 32791--32826 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
32781 TAAATAATTT
32791 AATATAA-TTATAAATAA
1 AATATAATTTATAAATAA
*
32808 AATATAATTTTTAAATAA
1 AATATAATTTATAAATAA
32826 A
1 A
32827 TGTAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AATATAATTTATAAATAA
Found at i:37891 original size:41 final size:41
Alignment explanation
Indices: 37759--38162 Score: 541
Period size: 41 Copynumber: 10.0 Consensus size: 41
37749 ATTTTAAATT
* * * * *
37759 CAGAGCAATAGCGGCG-TTCTAGAAAAACGCTGCT-AAAAC
1 CAGAGCATTAGCGGCGCTTTTCGTAAAACGCCGCTAAAAAC
* *
37798 CAGAGCATTAGCGGCGCTTTTCCTAAAACGCCGCAAAAAAAC
1 CAGAGCATTAGCGGCGCTTTTCGTAAAACGCCGC-TAAAAAC
* **
37840 TAGAGCATTAGCGGCGCTTTTCGTAAAACGCAACTAAAAAC
1 CAGAGCATTAGCGGCGCTTTTCGTAAAACGCCGCTAAAAAC
* *
37881 CAGAGCATTAGTGGCGCTTTTCGTAAAACGCCGCAAAAAAC
1 CAGAGCATTAGCGGCGCTTTTCGTAAAACGCCGCTAAAAAC
37922 CAGAGCATTAGCGGCGCTTTTCGTAAAACGCCGCTAAAAAC
1 CAGAGCATTAGCGGCGCTTTTCGTAAAACGCCGCTAAAAAC
* *
37963 CAGAGCAATTAGCGACGCTTCTCGTAAAACGCCGC-AAAAAC
1 CAGAGC-ATTAGCGGCGCTTTTCGTAAAACGCCGCTAAAAAC
*
38004 CAGAGCATTAGCGGCG--TTTCCTAAAACGCCGCTAAAAAC
1 CAGAGCATTAGCGGCGCTTTTCGTAAAACGCCGCTAAAAAC
* * * * *
38043 CAAAGCATTAGCGGCGCTTTTCCT-AAACACCTCAAAAAAC
1 CAGAGCATTAGCGGCGCTTTTCGTAAAACGCCGCTAAAAAC
*
38083 CAGAGCATTAGCGGCGCTTTTCGTAAAACGCCGCTAAACAC
1 CAGAGCATTAGCGGCGCTTTTCGTAAAACGCCGCTAAAAAC
* *
38124 CAGAGCATCAGCGGCACTTTTCGTAAAACGCCGCTAAAA
1 CAGAGCATTAGCGGCGCTTTTCGTAAAACGCCGCTAAAA
38163 TCTCATAACC
Statistics
Matches: 320, Mismatches: 37, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
38 14 0.04
39 36 0.11
40 56 0.17
41 153 0.48
42 61 0.19
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (41 bp):
CAGAGCATTAGCGGCGCTTTTCGTAAAACGCCGCTAAAAAC
Found at i:38105 original size:202 final size:203
Alignment explanation
Indices: 37759--38162 Score: 600
Period size: 202 Copynumber: 2.0 Consensus size: 203
37749 ATTTTAAATT
* * *
37759 CAGAGCAATAGCGGCGTTCTAGAAAAACGCTGCTAAAACCAGAGCATTAGCGGCGCTTTTCCTAA
1 CAGAGCAATAGCGACGTTCTAGAAAAACGCCGCAAAAACCAGAGCATTAGCGGCGC-TTTCCTAA
* * * *
37824 AACGCCGCAAAAAAACTAGAGCATTAGCGGCGCTTTTCGTAAAACGCAACTAAAAACCAGAGCAT
65 AACGCCGCAAAAAAACCAAAGCATTAGCGGCGCTTTTCCTAAAACGCAACAAAAAACCAGAGCAT
* * *
37889 TAGTGGCGCTTTTCGTAAAACGCCGCAAAAAACCAGAGCATTAGCGGCGCTTTTCGTAAAACGCC
130 TAGCGGCGCTTTTCGTAAAACGCCGCAAAAAACCAGAGCATCAGCGGCACTTTTCGTAAAACGCC
37954 GCTAAAAAC
195 GCTAAAAAC
* *
37963 CAGAGCAATTAGCGACGCTTCTCGTAAAACGCCGCAAAAACCAGAGCATTAGCGGCG-TTTCCTA
1 CAGAGCAA-TAGCGACG-TTCTAGAAAAACGCCGCAAAAACCAGAGCATTAGCGGCGCTTTCCTA
* *
38027 AAACGCCGC-TAAAAACCAAAGCATTAGCGGCGCTTTTCCTAAACAC-C-TCAAAAAACCAGAGC
64 AAACGCCGCAAAAAAACCAAAGCATTAGCGGCGCTTTTCCTAAA-ACGCAACAAAAAACCAGAGC
* *
38089 ATTAGCGGCGCTTTTCGTAAAACGCCGCTAAACACCAGAGCATCAGCGGCACTTTTCGTAAAACG
128 ATTAGCGGCGCTTTTCGTAAAACGCCGCAAAAAACCAGAGCATCAGCGGCACTTTTCGTAAAACG
38154 CCGCTAAAA
193 CCGCTAAAA
38163 TCTCATAACC
Statistics
Matches: 181, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
202 82 0.45
203 31 0.17
204 26 0.14
205 7 0.04
206 35 0.19
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (203 bp):
CAGAGCAATAGCGACGTTCTAGAAAAACGCCGCAAAAACCAGAGCATTAGCGGCGCTTTCCTAAA
ACGCCGCAAAAAAACCAAAGCATTAGCGGCGCTTTTCCTAAAACGCAACAAAAAACCAGAGCATT
AGCGGCGCTTTTCGTAAAACGCCGCAAAAAACCAGAGCATCAGCGGCACTTTTCGTAAAACGCCG
CTAAAAAC
Found at i:38339 original size:14 final size:14
Alignment explanation
Indices: 38317--38356 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
38307 TTAATTATCA
* *
38317 TTATAGTTTAAGGT
1 TTATGGTTTAAGAT
38331 TTATGGTTTAAGAT
1 TTATGGTTTAAGAT
*
38345 ATATGGTTTAAG
1 TTATGGTTTAAG
38357 CATGTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (14 bp):
TTATGGTTTAAGAT
Found at i:38779 original size:2 final size:2
Alignment explanation
Indices: 38774--38805 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
38764 TAAATTTGAG
38774 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38806 TTCAAACCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.