Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2402
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: 35835
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Found at i:2037 original size:2 final size:2
Alignment explanation
Indices: 2030--2062 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2020 TTATGAGGTA
2030 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2063 GGGTGCTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:6069 original size:2 final size:2
Alignment explanation
Indices: 6062--6118 Score: 82
Period size: 2 Copynumber: 28.5 Consensus size: 2
6052 CACATTTTGA
6062 AT AT AT AT -T CAT AT AT AT AT AT AT AT AT AT -T CAT AT AT AT AT
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
6104 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
6119 ACTCTTTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.04
2 47 0.92
3 2 0.04
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6090 original size:22 final size:22
Alignment explanation
Indices: 6062--6113 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
6052 CACATTTTGA
6062 ATATATATTCATATATATATAT
1 ATATATATTCATATATATATAT
6084 ATATATATTCATATATATATAT
1 ATATATATTCATATATATATAT
6106 ATATATAT
1 ATATATAT
6114 ATATAACTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATATATTCATATATATATAT
Found at i:9677 original size:20 final size:20
Alignment explanation
Indices: 9652--9695 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
9642 TAATCAATTC
**
9652 AAAAATTTATATTATTATTT
1 AAAAATTTATATTACCATTT
9672 AAAAATTTATATTACCATTT
1 AAAAATTTATATTACCATTT
9692 AAAA
1 AAAA
9696 GAACATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAAATTTATATTACCATTT
Found at i:13491 original size:13 final size:13
Alignment explanation
Indices: 13473--13511 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
13463 AAATTTAATT
13473 TAATTAATTTTTA
1 TAATTAATTTTTA
13486 TAATT-ATTTTTA
1 TAATTAATTTTTA
*
13498 AAATATAATTTTTA
1 TAAT-TAATTTTTA
13512 ATATATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 10 0.43
13 6 0.26
14 7 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAATTAATTTTTA
Found at i:13510 original size:14 final size:14
Alignment explanation
Indices: 13477--13517 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
13467 TTAATTTAAT
*
13477 TAATTTTTATAAT-
1 TAATTTTTAAAATA
13490 T-ATTTTTAAAATA
1 TAATTTTTAAAATA
*
13503 TAATTTTTAATATA
1 TAATTTTTAAAATA
13517 T
1 T
13518 TTAAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 10 0.42
13 2 0.08
14 12 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTTTTAAAATA
Found at i:13520 original size:23 final size:23
Alignment explanation
Indices: 13494--13537 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
13484 TATAATTATT
*
13494 TTTAAAATATAATTTTTAATATA
1 TTTAAAATATAAATTTTAATATA
*
13517 TTTAAAATTTAAATTTTAATA
1 TTTAAAATATAAATTTTAATA
13538 GTTATAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAAAATATAAATTTTAATATA
Found at i:13531 original size:24 final size:24
Alignment explanation
Indices: 13476--13537 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
13466 TTTAATTTAA
* *
13476 TTAATTTTTATAATTATTTTTAAAAT
1 TTAAATTTT-TAA-TATATTTAAAAT
*
13502 AT-AATTTTTAATATATTTAAAAT
1 TTAAATTTTTAATATATTTAAAAT
13525 TTAAA-TTTTAATA
1 TTAAATTTTTAATA
13538 GTTATAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
23 20 0.65
24 5 0.16
25 5 0.16
26 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTAAATTTTTAATATATTTAAAAT
Found at i:13780 original size:2 final size:2
Alignment explanation
Indices: 13773--13804 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
13763 AGTGTTTGGG
13773 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
13805 AAATTGATGA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:14734 original size:21 final size:19
Alignment explanation
Indices: 14704--14754 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
14694 TTATATATAT
* *
14704 ATATATATATCATTATTTAAA
1 ATATAAATATAATTA-TT-AA
*
14725 ATTTAAATATAATTATTAA
1 ATATAAATATAATTATTAA
14744 ATATAAATATA
1 ATATAAATATA
14755 TATTTGATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 12 0.46
20 2 0.08
21 12 0.46
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATAAATATAATTATTAA
Found at i:14829 original size:38 final size:40
Alignment explanation
Indices: 14765--14852 Score: 110
Period size: 38 Copynumber: 2.2 Consensus size: 40
14755 TATTTGATAT
* *
14765 AAATATTTTTATTTTTTATATTTTTAAAAA-ATTTTAAAAA
1 AAATATTTATATTTTTTATA-TTTTAAAAATATATTAAAAA
*
14805 ATAATATTTATA-TTTTTATA-TTTAAAAATATATTAAAAT
1 A-AATATTTATATTTTTTATATTTTAAAAATATATTAAAAA
14844 AAATATTTA
1 AAATATTTA
14853 AAAAATAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
38 16 0.37
39 9 0.21
40 9 0.21
41 9 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (40 bp):
AAATATTTATATTTTTTATATTTTAAAAATATATTAAAAA
Found at i:14869 original size:20 final size:23
Alignment explanation
Indices: 14822--14866 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
14812 TTATATTTTT
14822 ATATTTAAAAATATATTAAAATAA
1 ATATTTAAAAATATA-TAAAATAA
14846 ATATTTAAAAA-ATA-AAAATAA
1 ATATTTAAAAATATATAAAATAA
14867 TATAAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.33
23 3 0.14
24 11 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATATTTAAAAATATATAAAATAA
Found at i:15301 original size:3 final size:3
Alignment explanation
Indices: 15295--15325 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
15285 ATATCTCTTC
*
15295 TTG TTG TTG TTG TTG TTG TTG TTG TTT TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
15326 GTCCATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (3 bp):
TTG
Found at i:16654 original size:369 final size:366
Alignment explanation
Indices: 15922--17034 Score: 1234
Period size: 366 Copynumber: 3.0 Consensus size: 366
15912 AGAGAGAAAA
** * * * ** ** *
15922 AAAATTATGCACACCGGATTAAAATAACAAACCCGATAGATGACACCTTAAGCAAGTGGTTAAAT
1 AAAATTATGCATGCTGGATTTAAATAAAAAACTTGATAGATGACACCTTAAGCAAGT-CCTAAAA
* * * * *
15987 TTTAGTTTGGAATATTTTATTTTATTTTTCTTTTAACAAAAGAGATCTTAGTTTGAGAATAGGAA
65 CTTGGTTTGGAAGATTTTATTTTA--TTT-TTTTAACAAAAGAGATCTCAATTTGAGAAT---AA
* * * *
16052 AAAGAATTATGGATGTTAGATTAAAATACTAAATTTACTGAACCAATAATTTTTTAAAAATGATT
124 AAA-AATTATGGATGTTAGATTAAAATACT-AATCTACTGAA-AAAT-ATTTTTTGAAAATAATT
* *
16117 ATATAAATCAATT-ATTAAATCTTGAA-TTTGAAAGA-TTTGGTTTTTGATAAGTGAAATACGAT
185 ATATAAATCAATTGATTAAATCTT-AAGTTT-AAAAATTTTGGTTTTTGATAAGTGAAATATGAT
16179 TGTGATTGATCATGCATGCAAAGTTGATGCAAACCAAAATATTCCCAAGTTTGTGACTT-TATGT
248 TGTGATTGATCAT--AT--AAAGTTGATGCAAACCAAAATATTCCCAAGTTTGTGA-TTCTATGT
*
16243 AAATAAGGGGAAGTTAATGGGAAGATGAAAAGGAGAGATCCTAATTCAGAACTTACATC
308 AAATAAGGGGAAGTTAATGGGAAGATGAAAAGGAGAGATCCTAATTCAGAACTTACACC
* *
16302 AAAATTATGCATGCTGGATTTAAATAATAAACTTGATAGATGACGCCTTAAGCAAGTCACTAAAA
1 AAAATTATGCATGCTGGATTTAAATAAAAAACTTGATAGATGACACCTTAAGCAAGTC-CTAAAA
* *
16367 CTTGGATTTGGAAGATTTTATTTTA-TTTTTTAACAAAGGAGATCTCAATTCGAGAATAAAAAAA
65 CTTGG-TTTGGAAGATTTTATTTTATTTTTTTAACAAAAGAGATCTCAATTTGAGAATAAAAAAA
* * * *
16431 TTATGGATGTTAGATTAAAATATTGAATCTATTGAAAGAATACTTTTTGAAAGTAATTATATAAA
129 TTATGGATGTTAGATTAAAATACT-AATCTACTGAAA-AATATTTTTTGAAAATAATTATATAAA
16496 TCAATTGATTAAATCTTAAGTTTAAAAATTTTGGTTTTTGATAAGTGAAATATGATTGTGATTGA
192 TCAATTGATTAAATCTTAAGTTTAAAAATTTTGGTTTTTGATAAGTGAAATATGATTGTGATTGA
* *
16561 TCATATAAAGTTGATGCAAATCAAAATATTCCCAAGTTTATGATTCTATGTAAATAAGGGGAAGT
257 TCATATAAAGTTGATGCAAACCAAAATATTCCCAAGTTTGTGATTCTATGTAAATAAGGGGAAGT
* * *
16626 TAGTAGGG-AGATGAAATGGAGAGATCCTAATTGAG-AC---CACC
322 TAAT-GGGAAGATGAAAAGGAGAGATCCTAATTCAGAACTTACACC
* * * *
16667 AAAATTATGCATGCTAGA-TTAAAGTAAAAAAATCTGATAAATGACACCTTAATCAAGTGCCT-A
1 AAAATTATGCATGCTGGATTTAAA-TAAAAAACT-TGATAGATGACACCTTAAGCAAGT-CCTAA
* * * *
16730 AACTTTGGGTTTGGAAGATATTATTTTATTTTTTTAACAAAAAATATTTCAATTTGAGAAT-AAA
63 AAC-TT-GGTTTGGAAGATTTTATTTTATTTTTTTAACAAAAGAGATCTCAATTTGAGAATAAAA
** * *
16794 AAATTAAAGATGTTAGATTAAAATACTAAACTTACTGAATAAATATTTTTTGAAAATAATTGTAT
126 AAATTATGGATGTTAGATTAAAATACTAATC-TACTGAA-AAATATTTTTTGAAAATAATTATAT
* * * * * * * * * *
16859 AAATTAATTGACTAAACCTTGAGTTT-GAAATATTTGATATTTGATAAG-AAAATATGGTTGAGA
189 AAATCAATTGATTAAATCTTAAGTTTAAAAAT-TTTGGTTTTTGATAAGTGAAATATGATTGTGA
* ** ** * * *
16922 TTGGTCATGCAAAGTTGATGCAAACCAAAATATTCTGAAATTTGTGA--CTGTGTAAATAAGGGA
253 TTGATCATATAAAGTTGATGCAAACCAAAATATTCCCAAGTTTGTGATTCTATGTAAATAAGGGG
*
16985 AAGTTAATGGGAAGATGAAAGGGAGAGATCCTAATTCAGAACTTACACC
318 AAGTTAATGGGAAGATGAAAAGGAGAGATCCTAATTCAGAACTTACACC
17034 A
1 A
17035 TTCAATCCTG
Statistics
Matches: 633, Mismatches: 78, Indels: 57
0.82 0.10 0.07
Matches are distributed among these distances:
362 3 0.00
363 46 0.07
364 7 0.01
365 89 0.14
366 133 0.21
367 36 0.06
368 4 0.01
369 82 0.13
370 3 0.00
371 2 0.00
372 32 0.05
373 89 0.14
374 5 0.01
377 26 0.04
378 2 0.00
380 56 0.09
381 18 0.03
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.34
Consensus pattern (366 bp):
AAAATTATGCATGCTGGATTTAAATAAAAAACTTGATAGATGACACCTTAAGCAAGTCCTAAAAC
TTGGTTTGGAAGATTTTATTTTATTTTTTTAACAAAAGAGATCTCAATTTGAGAATAAAAAAATT
ATGGATGTTAGATTAAAATACTAATCTACTGAAAAATATTTTTTGAAAATAATTATATAAATCAA
TTGATTAAATCTTAAGTTTAAAAATTTTGGTTTTTGATAAGTGAAATATGATTGTGATTGATCAT
ATAAAGTTGATGCAAACCAAAATATTCCCAAGTTTGTGATTCTATGTAAATAAGGGGAAGTTAAT
GGGAAGATGAAAAGGAGAGATCCTAATTCAGAACTTACACC
Found at i:20126 original size:3 final size:3
Alignment explanation
Indices: 20118--20150 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
20108 GTTCTGCATA
20118 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20151 TTTACCCTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:20669 original size:3 final size:3
Alignment explanation
Indices: 20661--20685 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20651 GTATTGTAAA
20661 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
20686 GGTTTTATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:22574 original size:26 final size:26
Alignment explanation
Indices: 22540--22604 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
22530 TATTAAAATT
*
22540 ATTAAA-ATAAATTTATGTAAATTT-AA
1 ATTAAATATAAA-TAAT-TAAATTTGAA
22566 ATTTAAATATAAATAATTAAATTTGAA
1 A-TTAAATATAAATAATTAAATTTGAA
22593 ATTAAATATAAA
1 ATTAAATATAAA
22605 AATGAGATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
26 19 0.54
27 11 0.31
28 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (26 bp):
ATTAAATATAAATAATTAAATTTGAA
Found at i:22585 original size:20 final size:20
Alignment explanation
Indices: 22562--22600 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
22552 TTATGTAAAT
22562 TTAAATTT-AAATATAAATAA
1 TTAAATTTGAAAT-TAAATAA
22582 TTAAATTTGAAATTAAATA
1 TTAAATTTGAAATTAAATA
22601 TAAAAATGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
TTAAATTTGAAATTAAATAA
Found at i:22850 original size:2 final size:2
Alignment explanation
Indices: 22843--22873 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
22833 ACTGACTGGG
22843 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
22874 CAGCTGACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:26106 original size:25 final size:27
Alignment explanation
Indices: 26062--26123 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
26052 GTGAAAAAAT
*
26062 ATTTAAAAAATTATTAATAAGA-TTTAA
1 ATTT-AAAAATTATTAATAACATTTTAA
*
26089 ATTTAAAAATT-TTGATAACATTTTAA
1 ATTTAAAAATTATTAATAACATTTTAA
*
26115 ATTAAAAAA
1 ATTTAAAAA
26124 CTAGTTATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.23
26 20 0.65
27 4 0.13
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (27 bp):
ATTTAAAAATTATTAATAACATTTTAA
Found at i:26280 original size:23 final size:22
Alignment explanation
Indices: 26254--26298 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
26244 TTTTACGTTG
*
26254 AAATAAATTTTTAATTTTTAATT
1 AAATAAA-TTTTAATATTTAATT
*
26277 AAATTAATTTTAATATTTAATT
1 AAATAAATTTTAATATTTAATT
26299 TTTACTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATAAATTTTAATATTTAATT
Found at i:26295 original size:29 final size:29
Alignment explanation
Indices: 26263--26318 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
26253 GAAATAAATT
*
26263 TTTAATTTTTAATTAAATTAATTTTAATA
1 TTTAATTTTTAATTAAATAAATTTTAATA
*
26292 TTTAATTTTTACTTAAATAAATTTTAA
1 TTTAATTTTTAATTAAATAAATTTTAA
26319 CTTAATCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTAATTTTTAATTAAATAAATTTTAATA
Found at i:26361 original size:16 final size:16
Alignment explanation
Indices: 26340--26370 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
26330 TTTTTAATAT
26340 ATTATTTAAATAAAAA
1 ATTATTTAAATAAAAA
26356 ATTATTTAAATAAAA
1 ATTATTTAAATAAAA
26371 GTTAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTATTTAAATAAAAA
Found at i:29628 original size:5 final size:5
Alignment explanation
Indices: 29611--29654 Score: 61
Period size: 5 Copynumber: 8.2 Consensus size: 5
29601 AATATTTTGG
29611 ATATA ATTATA ATATA ATATA ATATAA TATATA ATATA ATATA A
1 ATATA A-TATA ATATA ATATA ATAT-A -ATATA ATATA ATATA A
29655 ATTATTAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 25 0.69
6 7 0.19
7 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:29644 original size:12 final size:12
Alignment explanation
Indices: 29611--29653 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
29601 AATATTTTGG
29611 ATATAAT-TATA
1 ATATAATATATA
29622 ATAT-A-ATATA
1 ATATAATATATA
29632 ATATAATATATA
1 ATATAATATATA
29644 ATATAATATA
1 ATATAATATA
29654 AATTATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 9 0.31
11 5 0.17
12 15 0.52
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATAATATATA
Found at i:29644 original size:17 final size:17
Alignment explanation
Indices: 29622--29654 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29612 TATAATTATA
29622 ATATAATATAATATAAT
1 ATATAATATAATATAAT
29639 ATATAATATAATATAA
1 ATATAATATAATATAA
29655 ATTATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATAATATAATATAAT
Found at i:30579 original size:28 final size:28
Alignment explanation
Indices: 30519--30573 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
30509 TATTTAAATT
30519 TAATTATAAATATAAAAATAATATTTTA
1 TAATTATAAATATAAAAATAATATTTTA
30547 TAATTAATAAATA-ATAAAAT-ATATTTT
1 TAATT-ATAAATATA-AAAATAATATTTT
30574 TAAATTCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
TAATTATAAATATAAAAATAATATTTTA
Done.