Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2430
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: 23451
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Found at i:4488 original size:29 final size:27
Alignment explanation
Indices: 4444--4614 Score: 117
Period size: 27 Copynumber: 6.4 Consensus size: 27
4434 GAGATTGGCG
*
4444 CTAAGTGTGCGGGTTTAA-ATTGTACAGCA
1 CTAAGTGTGCGAGTTTAATA-TGT--AGCA
*
4473 CTAAGTGTGCGAGTTTGATATGTAGCA
1 CTAAGTGTGCGAGTTTAATATGTAGCA
*
4500 CTAAGTGTGCGAG-TTGATATGT-G-A
1 CTAAGTGTGCGAGTTTAATATGTAGCA
* *
4524 CTAA--GTGC-A--TTGATAGTGCACAGCA
1 CTAAGTGTGCGAGTTTAATA-TG--TAGCA
* *
4549 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTT-AATATGTAGCA
* * *
4577 CTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAATATGTAGCA
*
4604 CTGAGTGTGCG
1 CTAAGTGTGCG
4615 GACTTAATAT
Statistics
Matches: 121, Mismatches: 9, Indels: 26
0.78 0.06 0.17
Matches are distributed among these distances:
20 6 0.05
21 3 0.02
22 4 0.03
24 6 0.05
25 6 0.05
26 9 0.07
27 42 0.35
28 20 0.17
29 19 0.16
30 4 0.03
31 2 0.02
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (27 bp):
CTAAGTGTGCGAGTTTAATATGTAGCA
Found at i:4507 original size:27 final size:26
Alignment explanation
Indices: 4469--4614 Score: 151
Period size: 27 Copynumber: 5.6 Consensus size: 26
4459 TAAATTGTAC
4469 AGCACTAAGTGTGCGAGTTTGATATGT
1 AGCACTAAGTGTGCGAG-TTGATATGT
4496 AGCACTAAGTGTGCGAGTTGATATGT
1 AGCACTAAGTGTGCGAGTTGATATGT
*
4522 -G-ACTAA--GTGC-A-TTGATAGTGCAC
1 AGCACTAAGTGTGCGAGTTGATA-TG--T
*
4545 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAG-TTGA-TATGT
*
4573 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGA-TATGT
*
4600 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
4615 GACTTAATAT
Statistics
Matches: 104, Mismatches: 4, Indels: 22
0.80 0.03 0.17
Matches are distributed among these distances:
20 6 0.06
21 3 0.03
22 4 0.04
24 6 0.06
25 6 0.06
26 9 0.09
27 45 0.43
28 18 0.17
30 5 0.05
31 2 0.02
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (26 bp):
AGCACTAAGTGTGCGAGTTGATATGT
Found at i:7431 original size:95 final size:97
Alignment explanation
Indices: 7289--7467 Score: 238
Period size: 95 Copynumber: 1.9 Consensus size: 97
7279 AACTAATCTC
* * * *
7289 TCACCTATTGTGAAATGTTACTAGTGTAGTTTAAAAGATTATGAGGGTTTT-CGATGTCCAATTA
1 TCACCTATTGTGAAATGCTACTAGTGTAGTTAAAAAGATCATAAGGGTTTTAC-ATGTCCAATTA
7353 AATATCCAAATAGAAAAGAATACAATTAAGCTA
65 AATATCCAAATAGAAAAGAATACAATTAAGCTA
* * * *
7386 TCACCT-TTGTGCAATGCTA-TGGTGTAGTTAAAAATATCATAAGGGTTTTACATGTCCAATTCA
1 TCACCTATTGTGAAATGCTACTAGTGTAGTTAAAAAGATCATAAGGGTTTTACATGTCCAATTAA
* *
7449 ATATCCAACTAGAGAAGAA
66 ATATCCAAATAGAAAAGAA
7468 AGTAAGTATG
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
95 53 0.75
96 12 0.17
97 6 0.08
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Consensus pattern (97 bp):
TCACCTATTGTGAAATGCTACTAGTGTAGTTAAAAAGATCATAAGGGTTTTACATGTCCAATTAA
ATATCCAAATAGAAAAGAATACAATTAAGCTA
Found at i:13501 original size:19 final size:20
Alignment explanation
Indices: 13470--13536 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 20
13460 TTAAGTTATT
13470 ACAA-CTTACTAAGCTTTAA
1 ACAAGCTTACTAAGCTTTAA
* *
13489 ACAAGCTT-TTAAG-TTTATT
1 ACAAGCTTACTAAGCTTTA-A
*
13508 ACGAGCTTACTAAGC-TTAA
1 ACAAGCTTACTAAGCTTTAA
13527 ACAAGCTTAC
1 ACAAGCTTAC
13537 CTCATTTTGG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
18 4 0.11
19 24 0.63
20 10 0.26
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.33
Consensus pattern (20 bp):
ACAAGCTTACTAAGCTTTAA
Found at i:13527 original size:38 final size:37
Alignment explanation
Indices: 13459--13534 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 37
13449 GTAGTTAAAG
13459 TTTAAGTTATTACAACTTACTAAGCTTTAAACAAGCT
1 TTTAAGTTATTACAACTTACTAAGCTTTAAACAAGCT
*
13496 TTTAAGTTTATTACGAGCTTACTAAGC-TTAAACAAGCT
1 TTTAAG-TTATTAC-AACTTACTAAGCTTTAAACAAGCT
13534 T
1 T
13535 ACCTCATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
37 6 0.17
38 19 0.53
39 11 0.31
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (37 bp):
TTTAAGTTATTACAACTTACTAAGCTTTAAACAAGCT
Found at i:14361 original size:20 final size:20
Alignment explanation
Indices: 14338--14386 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
14328 TTGTTTTCAA
* *
14338 TTTTTTTTCACATT-TTTCT
1 TTTTTTTTCACATTAGTCCT
*
14357 TTTTTATTTCAGATTAGTCCT
1 TTTTT-TTTCACATTAGTCCT
14378 TTTTTTTTC
1 TTTTTTTTC
14387 CAAATTGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 5 0.20
20 12 0.48
21 8 0.32
ACGTcount: A:0.12, C:0.14, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTTTTTTCACATTAGTCCT
Done.