Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3165
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: 41588
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Found at i:1423 original size:40 final size:40
Alignment explanation
Indices: 1379--1567 Score: 206
Period size: 40 Copynumber: 4.8 Consensus size: 40
1369 ATAACCACAA
* * *
1379 CACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCG
1 CACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTCG
*
1419 CACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
1 CACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTCG
* * *
1459 CACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTAG
1 CACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTCG
* * * * *
1499 CATAAATGCCTTC-GGACTTAGCCCGGATAAAATC-ACTAG
1 CACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTCG
* *
1538 CATAAATGCCTTC-GGACTTAGCCCGGATAT
1 CACAAATGCCTTCGGGTCTTAGCCCGGATAT
1568 CATTCAAATG
Statistics
Matches: 139, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
38 1 0.01
39 53 0.38
40 81 0.58
41 4 0.03
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
CACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTCG
Found at i:1528 original size:39 final size:40
Alignment explanation
Indices: 1422--1566 Score: 215
Period size: 39 Copynumber: 3.7 Consensus size: 40
1412 CAACTCGCAC
* * * *
1422 AAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTCGCAC
1 AAATGCCTTCGGGACTTAGCCCGGATAAAATC-ACTAGCAT
*
1462 AAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCAT
1 AAATGCCTTCGGGACTTAGCCCGGATAAAATCACTAGCAT
1502 AAATGCCTTC-GGACTTAGCCCGGATAAAATCACTAGCAT
1 AAATGCCTTCGGGACTTAGCCCGGATAAAATCACTAGCAT
1541 AAATGCCTTC-GGACTTAGCCCGGATA
1 AAATGCCTTCGGGACTTAGCCCGGATA
1567 TCATTCAAAT
Statistics
Matches: 100, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
39 54 0.54
40 42 0.42
41 4 0.04
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (40 bp):
AAATGCCTTCGGGACTTAGCCCGGATAAAATCACTAGCAT
Found at i:9496 original size:40 final size:40
Alignment explanation
Indices: 9451--9640 Score: 208
Period size: 40 Copynumber: 4.8 Consensus size: 40
9441 ATAACCACAA
* * *
9451 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
9491 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * *
9531 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* * * * *
9571 GCATAAATGCCTTCGGGACTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* *
9611 GCATAAATGCCTTC--GACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
9641 CATTCAAATG
Statistics
Matches: 140, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
37 1 0.01
38 14 0.10
40 121 0.86
41 4 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:15682 original size:17 final size:17
Alignment explanation
Indices: 15660--15695 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
15650 CCAACTAATG
15660 AATGACATATGATGAAC
1 AATGACATATGATGAAC
15677 AATGACATATGATGAAC
1 AATGACATATGATGAAC
15694 AA
1 AA
15696 GCAGAACTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.11, G:0.17, T:0.22
Consensus pattern (17 bp):
AATGACATATGATGAAC
Found at i:23371 original size:21 final size:21
Alignment explanation
Indices: 23345--23385 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
23335 GAAAGACTTG
23345 GGTCAATTGAAGTATTTTTTA
1 GGTCAATTGAAGTATTTTTTA
23366 GGTCAATTGAAGTATTTTTT
1 GGTCAATTGAAGTATTTTTT
23386 TGAGAAGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.05, G:0.20, T:0.49
Consensus pattern (21 bp):
GGTCAATTGAAGTATTTTTTA
Found at i:29035 original size:34 final size:35
Alignment explanation
Indices: 28992--29058 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
28982 GTTGTTTTTT
*
28992 AAATTAATTAAATTAGGGTTTAA-AGTTTTTAAGA
1 AAATTAATTAAATTAGAGTTTAAGAGTTTTTAAGA
*
29026 AAATTAATTAAATTAGAGTTTAAGGGTTTTTAA
1 AAATTAATTAAATTAGAGTTTAAGAGTTTTTAA
29059 AAATAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 22 0.73
35 8 0.27
ACGTcount: A:0.43, C:0.00, G:0.15, T:0.42
Consensus pattern (35 bp):
AAATTAATTAAATTAGAGTTTAAGAGTTTTTAAGA
Found at i:29406 original size:126 final size:126
Alignment explanation
Indices: 29160--29657 Score: 696
Period size: 126 Copynumber: 4.0 Consensus size: 126
29150 GTAGTTTCTG
* * * *
29160 AAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGACAAAAATGCTTCAAGTA-GATGCATT
1 AAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACT
* * * * *
29224 GTTAGCAAAAATACTAAAAAAAGCTCCCAGTTGGACACTCTTTTTCTACAGTAGTTCTTGA
66 GTCAGCAAAAGTACTGAAAAAAGCTCCCACTTGGACGCTCTTTTTCTACAGTAGTTCTTGA
* *
29285 AAAAATAATTTTGAGAAGACGGTTTTGAAAAAATAGTGAT-AAAAACGCTTCAAGCAGGATGCAC
1 AAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTG-TCAAAAACGCTTCAAGCAGGATGCAC
* **
29349 TGTCAGCAAAAGTACTGAAAGAAGCTCCCACTTATACGCTCTTTTTCTACAGTAGTTCTTGA
65 TGTCAGCAAAAGTACTGAAAAAAGCTCCCACTTGGACGCTCTTTTTCTACAGTAGTTCTTGA
** ** * *
29411 AAAAATAATTTTGAGAAGACAAATCCCAAAAAATAATGTCAAAAACGCTTCAAGCAGGATGCATT
1 AAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACT
* * *
29476 GTCAGCAAAAGTACTGAAAAAAGCTCTCACTTGGATGCTCTTTTTCTACAGTAGTTCCT-A
66 GTCAGCAAAAGTACTGAAAAAAGCTCCCACTTGGACGCTCTTTTTCTACAGTAGTTCTTGA
* ** *
29536 AAAAATAATTTTGAGAAGACAGTTCTGAAAGAATAGTGTCAAAAATACTTCAAACAGGATGCACT
1 AAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACT
* * *
29601 GTCAGCAAAAGTACTGAAAAAAACTCTCACGTGGACGCTCTTTTTCTACAGTAGTTC
66 GTCAGCAAAAGTACTGAAAAAAGCTCCCACTTGGACGCTCTTTTTCTACAGTAGTTC
29658 CTGCTTGGCC
Statistics
Matches: 329, Mismatches: 41, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
125 161 0.49
126 168 0.51
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (126 bp):
AAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACT
GTCAGCAAAAGTACTGAAAAAAGCTCCCACTTGGACGCTCTTTTTCTACAGTAGTTCTTGA
Found at i:29603 original size:251 final size:251
Alignment explanation
Indices: 29160--29657 Score: 712
Period size: 251 Copynumber: 2.0 Consensus size: 251
29150 GTAGTTTCTG
** ** * * *
29160 AAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGACAAAAATGCTTCAAGTAGATGCATTG
1 AAAAATAATTTTGAGAAGACAAATCCCAAAAAATAATGACAAAAACGCTTCAAGCAGATGCATTG
* * *
29225 TTAGCAAAAATACTAAAAAAAGCTCCCAGTTGGACACTCTTTTTCTACAGTAGTTCTTGAAAAAA
66 TCAGCAAAAATACTAAAAAAAGCTCCCACTTGGACACTCTTTTTCTACAGTAGTTCCTGAAAAAA
* * * *
29290 TAATTTTGAGAAGACGGTTTTGAAAAAATAGTGATAAAAACGCTTCAAGCAGGATGCACTGTCAG
131 TAATTTTGAGAAGACAGTTCTGAAAAAATAGTGATAAAAACACTTCAAACAGGATGCACTGTCAG
* * * *
29355 CAAAAGTACTGAAAGAAGCTCCCACTTATACGCTCTTTTTCTACAGTAGTTCTTGA
196 CAAAAGTACTGAAAAAAACTCCCACGTAGACGCTCTTTTTCTACAGTAGTTCTTGA
*
29411 AAAAATAATTTTGAGAAGACAAATCCCAAAAAATAATGTCAAAAACGCTTCAAGCAGGATGCATT
1 AAAAATAATTTTGAGAAGACAAATCCCAAAAAATAATGACAAAAACGCTTCAAGCA-GATGCATT
* * * **
29476 GTCAGCAAAAGTACTGAAAAAAGCTCTCACTTGGATGCTCTTTTTCTACAGTAGTTCCT-AAAAA
65 GTCAGCAAAAATACTAAAAAAAGCTCCCACTTGGACACTCTTTTTCTACAGTAGTTCCTGAAAAA
* *
29540 ATAATTTTGAGAAGACAGTTCTGAAAGAATAGTG-TCAAAAATACTTCAAACAGGATGCACTGTC
130 ATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGAT-AAAAACACTTCAAACAGGATGCACTGTC
* *
29604 AGCAAAAGTACTGAAAAAAACTCTCACGTGGACGCTCTTTTTCTACAGTAGTTC
194 AGCAAAAGTACTGAAAAAAACTCCCACGTAGACGCTCTTTTTCTACAGTAGTTC
29658 CTGCTTGGCC
Statistics
Matches: 217, Mismatches: 28, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
250 1 0.00
251 157 0.72
252 59 0.27
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (251 bp):
AAAAATAATTTTGAGAAGACAAATCCCAAAAAATAATGACAAAAACGCTTCAAGCAGATGCATTG
TCAGCAAAAATACTAAAAAAAGCTCCCACTTGGACACTCTTTTTCTACAGTAGTTCCTGAAAAAA
TAATTTTGAGAAGACAGTTCTGAAAAAATAGTGATAAAAACACTTCAAACAGGATGCACTGTCAG
CAAAAGTACTGAAAAAAACTCCCACGTAGACGCTCTTTTTCTACAGTAGTTCTTGA
Found at i:29658 original size:125 final size:126
Alignment explanation
Indices: 29141--29660 Score: 667
Period size: 125 Copynumber: 4.2 Consensus size: 126
29131 ACAAGATGGA
* * *
29141 TTTTTTTA-AGTAGTTTCTG-AAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGACAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAA
* * * * * *
29204 ATGCTTCAAGTA-GATGCATTGTTAGCAAAAATACT-AAAAAAAGCTCCCA-GTTGGACACTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAAGTACTGAAAAAAA-CTCCCACG-TGGACGCTC
* * *
29264 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTTTGAAAAAATAGTGAT-AAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTG-TCAAA
* * * **
29328 AACGCTTCAAGCAGGATGCACTGTCAGCAAAAGTACTGAAAGAAGCTCCCACTTATACGCTC
65 AACGCTTCAAGCAGGATGCACTGTCAGCAAAAGTACTGAAAAAAACTCCCACGTGGACGCTC
* ** ** *
29390 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACAAATCCCAAAAAATAATGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAA
* * * * *
29455 ACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAAAAGCTCTCACTTGGATGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAAGTACTGAAAAAAACTCCCACGTGGACGCTC
*
29516 TTTTTCTACAGTAGTTCCT-AAAAAATAATTTTGAGAAGACAGTTCTGAAAGAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAA
** * *
29580 ATACTTCAAACAGGATGCACTGTCAGCAAAAGTACTGAAAAAAACTCTCACGTGGACGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAAGTACTGAAAAAAACTCCCACGTGGACGCTC
29641 TTTTTCTACAGTAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
29661 CTTGGCCTTA
Statistics
Matches: 345, Mismatches: 44, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
123 7 0.02
124 9 0.03
125 163 0.47
126 161 0.47
127 5 0.01
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAAGTACTGAAAAAAACTCCCACGTGGACGCTC
Found at i:31580 original size:29 final size:27
Alignment explanation
Indices: 31562--31631 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
31552 ATATTAAGTC
31562 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
31589 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
31617 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
31632 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:31625 original size:28 final size:28
Alignment explanation
Indices: 31562--31659 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
31552 ATATTAAGTC
*
31562 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
31589 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
31617 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
31646 CGCACACTTAGTGC
1 CGCACACTTAGTGC
31660 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:39649 original size:27 final size:26
Alignment explanation
Indices: 39631--39700 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 26
39621 ATATTAAGTC
39631 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
39658 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
39686 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
39701 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (26 bp):
CGCACACTCAGTGCTATATATCAACT
Found at i:39694 original size:28 final size:28
Alignment explanation
Indices: 39631--39728 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
39621 ATATTAAGTC
*
39631 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
39658 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
39686 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
39715 CGCACACTTAGTGC
1 CGCACACTTAGTGC
39729 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Done.