Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold815
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: 42351
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:9191 original size:20 final size:20
Alignment explanation
Indices: 9168--9214 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
9158 GGGTTAAGAT
*
9168 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
9188 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
9208 TGAGCTG
1 TGAGCTG
9215 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:14019 original size:15 final size:14
Alignment explanation
Indices: 13983--14037 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
13973 TCTATTGATC
13983 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
13997 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
14011 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
14026 GAAAGAAAAGAA
1 GAGA-AAAAGAA
14038 TGAGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:18978 original size:12 final size:12
Alignment explanation
Indices: 18961--19003 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
18951 GAATACAAAC
*
18961 TTTTTTTTTGAA
1 TTTTTTTTCGAA
18973 TTTTTTTTCGAA
1 TTTTTTTTCGAA
18985 TTTTTTTTCG-A
1 TTTTTTTTCGAA
18996 TTTTTTTT
1 TTTTTTTT
19004 ACAATCTCGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.77
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:23383 original size:15 final size:13
Alignment explanation
Indices: 23363--23412 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 13
23353 ACTCTCATCA
23363 TTCTTTTCTTTCTTT
1 TTCTTTTC--TCTTT
23378 TTCTTTTCACTCTTT
1 TTCTTTT--CTCTTT
*
23393 TTGTTTTCTCTTT
1 TTCTTTTCTCTTT
23406 TTCTTTT
1 TTCTTTT
23413 TCTCGCTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 12 0.39
15 18 0.58
17 1 0.03
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (13 bp):
TTCTTTTCTCTTT
Found at i:23405 original size:13 final size:14
Alignment explanation
Indices: 23373--23412 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
23363 TTCTTTTCTT
23373 TCTTTTTCTTTTCAC
1 TCTTTTTCTTTT-AC
*
23388 TCTTTTTGTTTT-C
1 TCTTTTTCTTTTAC
23401 TCTTTTTCTTTT
1 TCTTTTTCTTTT
23413 TCTCGCTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
15 11 0.48
ACGTcount: A:0.03, C:0.20, G:0.03, T:0.75
Consensus pattern (14 bp):
TCTTTTTCTTTTAC
Found at i:25511 original size:11 final size:11
Alignment explanation
Indices: 25495--25533 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
25485 AATACAAACT
*
25495 TTTTTTTTGAA
1 TTTTTTTCGAA
25506 TTTTTTTCGAA
1 TTTTTTTCGAA
25517 TTTTTTTCG-A
1 TTTTTTTCGAA
25527 TTTTTTT
1 TTTTTTT
25534 AAATCTCGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:27891 original size:21 final size:23
Alignment explanation
Indices: 27846--27892 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
27836 TCACCTGCAA
* *
27846 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
27869 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
27890 TAA
1 TAA
27893 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:28037 original size:65 final size:63
Alignment explanation
Indices: 27958--28124 Score: 219
Period size: 65 Copynumber: 2.6 Consensus size: 63
27948 TTATTCCAGC
* * *
27958 AACTAGTTTAATTAAAGAAGCATAATTTAA-AGAACTTAATTTATGCATCAATAAATAATCCTAG
1 AACTAGATCAATT-AAGAAGCATAATTTAATA-AA-GTAATTTATGCATCAATAAATAATCCTAG
28022 G
63 G
*
28023 AACTAGATCAATTAAGAAGCATCTTATTTAATAAAGTAATTTATGCATCAATAAATAATCCTAGG
1 AACTAGATCAATTAAGAAGCA--TAATTTAATAAAGTAATTTATGCATCAATAAATAATCCTAGG
*
28088 AACTAGATCAATTAAGAAGCATCTTATTTAATAAAGT
1 AACTAGATCAATTAAGAAGCA--TAATTTAATAAAGT
28125 TCAATAACTA
Statistics
Matches: 95, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
64 8 0.08
65 77 0.81
66 9 0.09
67 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (63 bp):
AACTAGATCAATTAAGAAGCATAATTTAATAAAGTAATTTATGCATCAATAAATAATCCTAGG
Found at i:29560 original size:24 final size:22
Alignment explanation
Indices: 29528--29571 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
29518 CTAACTCTAT
29528 ATAAAACAAATATATAAAAATACA
1 ATAAAAC-AATA-ATAAAAATACA
*
29552 ATAATACAATAATAAAAATA
1 ATAAAACAATAATAAAAATA
29572 AGTATGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (22 bp):
ATAAAACAATAATAAAAATACA
Found at i:32671 original size:19 final size:19
Alignment explanation
Indices: 32647--32683 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
32637 TAAGTATGAA
32647 GGAATTT-CTTGATTGGGCT
1 GGAATTTGCTT-ATTGGGCT
32666 GGAATTTGCTTATTGGGC
1 GGAATTTGCTTATTGGGC
32684 CTCGCCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.16, C:0.11, G:0.32, T:0.41
Consensus pattern (19 bp):
GGAATTTGCTTATTGGGCT
Found at i:33890 original size:15 final size:15
Alignment explanation
Indices: 33870--33899 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
33860 AGAGAACGGA
33870 TTCAAGAATAAGATC
1 TTCAAGAATAAGATC
33885 TTCAAGAATAAGATC
1 TTCAAGAATAAGATC
33900 GACATTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (15 bp):
TTCAAGAATAAGATC
Done.