Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold636
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: 35558
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:717 original size:21 final size:20
Alignment explanation
Indices: 666--731 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 20
656 TTTGGTTATT
*
666 AAAAGTTGCATTCTTTCATCC
1 AAAAATTGCATTCTTTCAT-C
*
687 AAAAAATGCATTCTTTCATC
1 AAAAATTGCATTCTTTCATC
*
707 AAACTATTGCA-TCATTTCATC
1 AAA-AATTGCATTC-TTTCATC
728 AAAA
1 AAAA
732 TACATATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
20 6 0.16
21 32 0.84
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (20 bp):
AAAAATTGCATTCTTTCATC
Found at i:4542 original size:58 final size:58
Alignment explanation
Indices: 4424--4554 Score: 142
Period size: 58 Copynumber: 2.3 Consensus size: 58
4414 TTTTTTTGTA
* * * *
4424 AATTT-TCATGATTTAGGACCATTTATGCATTCTCATGTATTTTAGAGTCATTCTATT
1 AATTTGTCATGATTTAGAACCATTTATGCATTCTCATGCATTTCAGAGTCATTCTAGT
* * *
4481 AATTTGTCATGATTTAGAACCGTTTATGCAATT-TCATGCATTTCATGGGT-ATTTTAGT
1 AATTTGTCATGATTTAGAACCATTTATGC-ATTCTCATGCATTTCA-GAGTCATTCTAGT
* *
4539 AATTTGCCATGCTTTA
1 AATTTGTCATGATTTA
4555 AGGATTTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
57 5 0.08
58 51 0.82
59 6 0.10
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.46
Consensus pattern (58 bp):
AATTTGTCATGATTTAGAACCATTTATGCATTCTCATGCATTTCAGAGTCATTCTAGT
Found at i:4720 original size:29 final size:30
Alignment explanation
Indices: 4672--4763 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 30
4662 TTATGTATGT
*
4672 TAGA-GTCATCTTA-GTTATTTTTCATGATC
1 TAGAGGTCAT-TTACGTAATTTTTCATGATC
*
4701 TAGAGGT-TTTTACGTAA-TTTT-ATGAATGC
1 TAGAGGTCATTTACGTAATTTTTCATG-AT-C
* * *
4730 T-GAGGTCATTTAGGTCATTTTTCATAATC
1 TAGAGGTCATTTACGTAATTTTTCATGATC
4759 TAGAG
1 TAGAG
4764 ACTTTCATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 15
0.70 0.09 0.21
Matches are distributed among these distances:
27 3 0.06
28 14 0.29
29 19 0.39
30 11 0.22
31 2 0.04
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (30 bp):
TAGAGGTCATTTACGTAATTTTTCATGATC
Found at i:20242 original size:15 final size:15
Alignment explanation
Indices: 20224--20273 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
20214 GATTTAATTT
20224 AAAAATTTAATTAAA
1 AAAAATTTAATTAAA
* *
20239 AAAAATTAAAATTTAA
1 AAAAATT-TAATTAAA
*
20255 AAAAGTTTAATTTAAA
1 AAAAATTTAA-TTAAA
20271 AAA
1 AAA
20274 GTTTGAATCA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 9 0.32
16 19 0.68
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (15 bp):
AAAAATTTAATTAAA
Found at i:20274 original size:15 final size:15
Alignment explanation
Indices: 20216--20277 Score: 74
Period size: 15 Copynumber: 4.2 Consensus size: 15
20206 TTTAATTTGA
20216 TTTAATTT-AAAAA-
1 TTTAATTTAAAAAAG
* *
20229 TTTAATTAAAAAAAA
1 TTTAATTTAAAAAAG
*
20244 TTAAAATTTAAAAAAG
1 TT-TAATTTAAAAAAG
20260 TTTAATTTAAAAAAG
1 TTTAATTTAAAAAAG
20275 TTT
1 TTT
20278 GAATCAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
13 7 0.17
14 5 0.12
15 17 0.41
16 12 0.29
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
TTTAATTTAAAAAAG
Found at i:20413 original size:19 final size:19
Alignment explanation
Indices: 20389--20433 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
20379 ATTATAATAT
*
20389 ATATTTTATTTA-AAATAAA
1 ATATTTAATTTATAAA-AAA
*
20408 ATATTTAATTTATAAAAAT
1 ATATTTAATTTATAAAAAA
20427 ATATTTA
1 ATATTTA
20434 TAACTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTAATTTATAAAAAA
Found at i:20462 original size:17 final size:17
Alignment explanation
Indices: 20424--20465 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
20414 AATTTATAAA
*
20424 AATATATTTATAACTAT
1 AATATATTTATAACAAT
* *
20441 TATATATTTATATCAAT
1 AATATATTTATAACAAT
20458 AATATATT
1 AATATATT
20466 ATTAATAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATATTTATAACAAT
Found at i:21572 original size:15 final size:15
Alignment explanation
Indices: 21550--21586 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
21540 TTAATCGCTG
*
21550 TAAT-ATTATTTTTT
1 TAATAATTATATTTT
21564 TAATAATTATATTTT
1 TAATAATTATATTTT
21579 TAATAATT
1 TAATAATT
21587 GCATTTCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TAATAATTATATTTT
Found at i:23495 original size:14 final size:14
Alignment explanation
Indices: 23476--23511 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
23466 TGTATTGTAT
23476 TGATACAACACTTA
1 TGATACAACACTTA
23490 TGATACAACACTTA
1 TGATACAACACTTA
23504 TGATACAA
1 TGATACAA
23512 TGTATTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.28
Consensus pattern (14 bp):
TGATACAACACTTA
Found at i:23564 original size:19 final size:20
Alignment explanation
Indices: 23540--23592 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
23530 TAACATTTAT
23540 TGTATCGATACAATACT-TA
1 TGTATCGATACAATACTGTA
* * *
23559 TGTATCAATACATTTACTGTT
1 TGTATCGATACA-ATACTGTA
23580 TGTATCGATACAA
1 TGTATCGATACAA
23593 ATTGTTGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 11 0.41
20 4 0.15
21 12 0.44
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (20 bp):
TGTATCGATACAATACTGTA
Found at i:24378 original size:20 final size:21
Alignment explanation
Indices: 24341--24379 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
24331 AACTAAGCTT
*
24341 GTCACATTAGCAAAATCAATG
1 GTCACATTAACAAAATCAATG
24362 GTCACATTAAC-AAATCAA
1 GTCACATTAACAAAATCAA
24380 CATTTATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.23
Consensus pattern (21 bp):
GTCACATTAACAAAATCAATG
Found at i:29927 original size:21 final size:21
Alignment explanation
Indices: 29903--29942 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29893 TAAGTTTTGT
29903 AAATAAAATTTATA-ATAATTA
1 AAAT-AAATTTATATATAATTA
*
29924 AAATTAATTTATATATAAT
1 AAATAAATTTATATATAAT
29943 GCTACTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATAAATTTATATATAATTA
Found at i:30210 original size:15 final size:15
Alignment explanation
Indices: 30174--30216 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
30164 AATTTTATTT
*
30174 AATTATTAA-AATTA
1 AATTATTAATAATAA
*
30188 ATTTATTAATAATAA
1 AATTATTAATAATAA
30203 AATTATTAATAATA
1 AATTATTAATAATA
30217 GGATTTTGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTATTAATAATAA
Found at i:31943 original size:74 final size:75
Alignment explanation
Indices: 31865--32013 Score: 291
Period size: 75 Copynumber: 2.0 Consensus size: 75
31855 GTTGCCCTAT
31865 CCTTTTTATC-AAAAAAATAAAAAAATTTGCAGCTGCGTTGATATTTTTAATTGTTATGGAATTA
1 CCTTTTTATCAAAAAAAATAAAAAAATTTGCAGCTGCGTTGATATTTTTAATTGTTATGGAATTA
31929 AAATTATTTA
66 AAATTATTTA
31939 CCTTTTTATCAAAAAAAATAAAAAAATTTGCAGCTGCGTTGATATTTTTAATTGTTATGGAATTA
1 CCTTTTTATCAAAAAAAATAAAAAAATTTGCAGCTGCGTTGATATTTTTAATTGTTATGGAATTA
32004 AAATTATTTA
66 AAATTATTTA
32014 TAGAAAAGAT
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 10 0.14
75 64 0.86
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.42
Consensus pattern (75 bp):
CCTTTTTATCAAAAAAAATAAAAAAATTTGCAGCTGCGTTGATATTTTTAATTGTTATGGAATTA
AAATTATTTA
Found at i:32406 original size:9 final size:9
Alignment explanation
Indices: 32394--32427 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
32384 AACATTATAT
32394 AATTTCTTC
1 AATTTCTTC
32403 AATTTCTTC
1 AATTTCTTC
*
32412 ACTTTCTTC
1 AATTTCTTC
32421 AAATTTC
1 -AATTTC
32428 AAATTTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.77
10 5 0.23
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (9 bp):
AATTTCTTC
Done.