Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3195
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: 38012
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4313 original size:17 final size:17
Alignment explanation
Indices: 4288--4342 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
4278 TCTCTTTTCA
*
4288 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
4305 TTCTTTTTTTTATCATTT
1 TTCTTTTTTTT-TGAATT
* *
4323 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
4340 TTC
1 TTC
4343 GGTCTTTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 16 0.53
18 14 0.47
ACGTcount: A:0.09, C:0.13, G:0.04, T:0.75
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:6587 original size:14 final size:13
Alignment explanation
Indices: 6569--6618 Score: 91
Period size: 13 Copynumber: 3.8 Consensus size: 13
6559 TATGCAAATT
6569 TTTTTTTTTTCAA
1 TTTTTTTTTTCAA
6582 TTTTTTTTTTCAA
1 TTTTTTTTTTCAA
6595 TTTTTTTTTTCGAA
1 TTTTTTTTTTC-AA
6609 TTTTTTTTTT
1 TTTTTTTTTT
6619 ACGCACCTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 24 0.67
14 12 0.33
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTTTTTTTTCAA
Found at i:6935 original size:24 final size:23
Alignment explanation
Indices: 6881--6958 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
6871 GGATAATTAA
**
6881 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
6904 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
6928 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
6949 GAAATAGTAT
1 GAAATGGTAT
6959 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:6943 original size:21 final size:21
Alignment explanation
Indices: 6917--6983 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
6907 TTGGTATTTG
6917 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
6938 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
6959 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
6982 GG
1 GG
6984 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:9481 original size:72 final size:73
Alignment explanation
Indices: 9398--9545 Score: 192
Period size: 72 Copynumber: 2.0 Consensus size: 73
9388 TTTAATGCTA
* * *
9398 TCCCAAGTCCCATGCACACACTAAATTCGGCTG-GTTGGGAAAATACAACAG-CAACTTTCGCTT
1 TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTT-GCTT
9461 TAAATGCCG
65 TAAATGCCG
* * * * * *
9470 TCCCAAGTCCCATGCACTCAATAAATTCGGCAGCTTTGGAAAAATGCAGCAGCCACCTTTTCTTT
1 TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTTGCTTT
9535 AAATGCCG
66 AAATGCCG
9543 TCC
1 TCC
9546 ATGTACCTGC
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
72 30 0.46
73 29 0.45
74 6 0.09
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (73 bp):
TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTTGCTTT
AAATGCCG
Found at i:9753 original size:16 final size:16
Alignment explanation
Indices: 9732--9763 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9722 CATTCTGCAT
*
9732 TTAAACAATAGCAGCA
1 TTAAACAACAGCAGCA
9748 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
9764 AAACACATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.22, G:0.12, T:0.16
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:10688 original size:11 final size:11
Alignment explanation
Indices: 10672--10723 Score: 86
Period size: 11 Copynumber: 4.6 Consensus size: 11
10662 AGTTTCTTGA
*
10672 AAAAAAAACTC
1 AAAAAAAATTC
10683 AAAAAAAATTC
1 AAAAAAAATTC
10694 AAAAAAAATTC
1 AAAAAAAATTC
10705 AAAAAAAAATTC
1 -AAAAAAAATTC
10717 AAAAAAA
1 AAAAAAA
10724 TTTTTTTTGG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
11 28 0.72
12 11 0.28
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:10725 original size:22 final size:22
Alignment explanation
Indices: 10672--10723 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 22
10662 AGTTTCTTGA
*
10672 AAAAAAAACTCAAAAAAAATTC
1 AAAAAAAATTCAAAAAAAATTC
10694 AAAAAAAATTCAAAAAAAAATTC
1 AAAAAAAATTC-AAAAAAAATTC
10717 AAAAAAA
1 AAAAAAA
10724 TTTTTTTTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (22 bp):
AAAAAAAATTCAAAAAAAATTC
Found at i:10792 original size:14 final size:13
Alignment explanation
Indices: 10767--10822 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 13
10757 GGATATCAAG
10767 TTGTGAAAAAAAATA
1 TTGTG-AAAAAAA-A
*
10782 TTTTGAAAAAAAAA
1 TTGTG-AAAAAAAA
10796 TTGTGAAAAAGAAA
1 TTGTGAAAAA-AAA
10810 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
10823 AGAGAGCTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
13 8 0.21
14 18 0.47
15 12 0.32
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:10799 original size:29 final size:28
Alignment explanation
Indices: 10767--10823 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
10757 GGATATCAAG
*
10767 TTGTGAAAAAAAATATTTTGAAAAAAAAA
1 TTGTGAAAAAAAA-ATTGTGAAAAAAAAA
*
10796 TTGTGAAAAAGAAATTGTGAAAAAAAAA
1 TTGTGAAAAAAAAATTGTGAAAAAAAAA
10824 GAGAGCTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (28 bp):
TTGTGAAAAAAAAATTGTGAAAAAAAAA
Found at i:11773 original size:18 final size:17
Alignment explanation
Indices: 11752--11796 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
11742 GAGTGACGAG
11752 AGAAAAAGAAACTGAAAA
1 AGAAAAA-AAACTGAAAA
*
11770 AGAAACAAAAATTGAAAA
1 AGAAA-AAAAACTGAAAA
11788 AGAGAAAAA
1 AGA-AAAAA
11797 GATTGGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07
Consensus pattern (17 bp):
AGAAAAAAAACTGAAAA
Found at i:11801 original size:18 final size:18
Alignment explanation
Indices: 11750--11801 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
11740 AAGAGTGACG
*
11750 AGAGAAAAAGAAACTGAAAA
1 AGAGAAAAAG--ATTGAAAA
*
11770 AGA-AACAAAAATTGAAAA
1 AGAGAA-AAAGATTGAAAA
11788 AGAGAAAAAGATTG
1 AGAGAAAAAGATTG
11802 GAGAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 17 0.63
19 4 0.15
20 6 0.22
ACGTcount: A:0.67, C:0.04, G:0.19, T:0.10
Consensus pattern (18 bp):
AGAGAAAAAGATTGAAAA
Found at i:12018 original size:20 final size:20
Alignment explanation
Indices: 11993--12047 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
11983 TGTGGTTCAA
*
11993 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
12013 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
12033 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
12048 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:28288 original size:19 final size:18
Alignment explanation
Indices: 28252--28291 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28242 TTTCCACTCG
*
28252 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
28270 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
28289 TTT
1 TTT
28292 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:29355 original size:12 final size:13
Alignment explanation
Indices: 29338--29383 Score: 76
Period size: 14 Copynumber: 3.5 Consensus size: 13
29328 TAGCTTCTTC
29338 TTTTTTTCACAATT
1 TTTTTTTCACAA-T
29352 TTTTTTTCACAAT
1 TTTTTTTCACAAT
29365 TTTTTTTCA-AAT
1 TTTTTTTCACAAT
29377 TTTTTTT
1 TTTTTTT
29384 TCAACTTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.31
13 10 0.31
14 12 0.38
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTTTCACAAT
Found at i:29387 original size:13 final size:14
Alignment explanation
Indices: 29338--29386 Score: 84
Period size: 13 Copynumber: 3.6 Consensus size: 14
29328 TAGCTTCTTC
29338 TTTTTTTCACAATT
1 TTTTTTTCACAATT
29352 TTTTTTTCACAA-T
1 TTTTTTTCACAATT
29365 TTTTTTTCA-AATT
1 TTTTTTTCACAATT
29378 TTTTTTTCA
1 TTTTTTTCA
29387 ACTTGATATC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
12 2 0.06
13 20 0.59
14 12 0.35
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTTTCACAATT
Found at i:29440 original size:12 final size:12
Alignment explanation
Indices: 29423--29466 Score: 74
Period size: 11 Copynumber: 3.8 Consensus size: 12
29413 ATGGAAACCA
29423 AATTTTTTTTTG
1 AATTTTTTTTTG
29435 AA-TTTTTTTTG
1 AATTTTTTTTTG
29446 AATTTTTTTTTG
1 AATTTTTTTTTG
29458 -ATTTTTTTT
1 AATTTTTTTT
29467 GAGAAACTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 20 0.65
12 11 0.35
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:29454 original size:22 final size:22
Alignment explanation
Indices: 29423--29468 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 22
29413 ATGGAAACCA
29423 AATTTTTTTTTGAATTTTTTTTG
1 AATTTTTTTTTG-ATTTTTTTTG
29446 AATTTTTTTTTGATTTTTTTTG
1 AATTTTTTTTTGATTTTTTTTG
29468 A
1 A
29469 GAAACTACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (22 bp):
AATTTTTTTTTGATTTTTTTTG
Found at i:31210 original size:4 final size:4
Alignment explanation
Indices: 31201--31228 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
31191 TACTAGTCTC
31201 TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT
31229 CCATTTATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Done.