Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3271
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: 41662
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:3158 original size:13 final size:13
Alignment explanation
Indices: 3113--3149 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
3103 AATGGAAACA
3113 AATTTTTTTTTTG
1 AATTTTTTTTTTG
3126 AATTTTTTTTTTG
1 AATTTTTTTTTTG
3139 AATTTTTTTTT
1 AATTTTTTTTT
3150 CGAGTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.78
Consensus pattern (13 bp):
AATTTTTTTTTTG
Found at i:4806 original size:45 final size:45
Alignment explanation
Indices: 4738--4828 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
4728 ACAAAGAAAG
*
4738 ACCTCGACCACTATCAAGAATGATAGGAACCGTGGTATATGATGA
1 ACCTCGACCACTATCAAGAATGATAAGAACCGTGGTATATGATGA
*
4783 ACCTCGACCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCACTATCAA-GAATGATAAGAACCGTGGTATATGATGA
4828 A
1 A
4829 TGCCACACTA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 42 0.98
46 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (45 bp):
ACCTCGACCACTATCAAGAATGATAAGAACCGTGGTATATGATGA
Found at i:6401 original size:21 final size:23
Alignment explanation
Indices: 6356--6402 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
6346 TCACCTGCAA
* *
6356 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
6379 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
6400 TAA
1 TAA
6403 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:6985 original size:46 final size:46
Alignment explanation
Indices: 6932--7025 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
6922 CAAAGAAAAG
*
6932 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
6978 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
7024 AC
1 AC
7026 GCCACACTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:13991 original size:24 final size:25
Alignment explanation
Indices: 13958--14005 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
13948 AATCGTATAT
13958 CAAGAATTTTCT-TTGAGTTTTCTC
1 CAAGAATTTTCTCTTGAGTTTTCTC
*
13982 CAAGATTTTTCTCTTGAGTTTTCT
1 CAAGAATTTTCTCTTGAGTTTTCT
14006 TTAGAAGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.52
Consensus pattern (25 bp):
CAAGAATTTTCTCTTGAGTTTTCTC
Found at i:14199 original size:617 final size:616
Alignment explanation
Indices: 13343--14565 Score: 2293
Period size: 617 Copynumber: 2.0 Consensus size: 616
13333 TGTTGAGAGC
13343 AGAATTTTCTTTGAGTTTTCTCCAAGATTTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAA
1 AGAATTTTCTTTGAGTTTTCTCCAAGATTTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAA
13408 TCTTGTGATTGTGGGAGCCATCTTCAACCTTCTTCTTGCCATTGATATTCTTTGGAGGGGAGATT
66 TCTTGTGATTGTGGGAGCCATCTTCAACCTTCTTCTTGCCATTGATATTCTTTGGAGGGGAGATT
13473 AGAGCCGTTTGAAGGGAGTTGTGAGATCTTTCGAGATTTCAAGACTTCTTAGGACTTATCTTTTA
131 AGAGCCGTTTGAAGGGAGTTGTGAGATCTTTCGAGATTTCAAGACTTCTTAGGACTTATCTTTTA
13538 ATTTCTTACTGTCAATTCTTTCTTTATTTCTACTTGTACTGAATCATTATCTAATCTATTTTCTG
196 ATTTCTTACTGTCAATTCTTTCTTTATTTCTACTTGTACTGAATCATTATCTAATCTATTTTCTG
13603 TTCTTATTGTGTTTTCAGCCTTTTTCTATCTTAAGGAATCAGCCCAAAAATCCCCAATTTCTAGG
261 TTCTTATTGTGTTTTCAGCCTTTTTCTATCTTAAGGAATCAGCCCAAAAATCCCCAATTTCTAGG
13668 GTTTTTCCATACTCTTTTTGGGTGAAATTAGATTGTCGAAATTTGGGAAAAACTATCTTGGTGTT
326 GTTTTTCCATACTCTTTTTGGGTGAAATTAGATTGTCGAAATTTGGGAAAAACTATCTTGGTGTT
13733 CAATTGGGCAGAATCACAATCTCCTTGAGGGTTTCAAGAACCCTAACACTTATTTCTATTCTCAA
391 CAATTGGGCAGAATCACAATCTCCTTGAGGGTTTCAAGAACCCTAACACTTATTTCTATTCTCAA
* * **
13798 TTTGATTCTTTGCTGATTTGGGGATTTTATTTCAGATCTGGAAATTCAAAGTTCCAATCTTTTAA
456 TTTGATTCCTTGCTGATTTGGGGATTTTATTTCAGATCTGAAAATTCAAAAATCCAATCTTTTAA
* *
13863 TTTTTCTGTTTCGTTTCGGATCTGATTATTTAGGGTTTTCGTAGGAGTTTCCCATGACTTGGCAA
521 -TTTTCTGTTTCGTTTCAGATCTAATTATTTAGGGTTTTCGTAGGAGTTTCCCATGACTTGGCAA
*
13928 CTCGATCTTGGTCTGCGCGCAATCGTATATCA
585 CTCGATCTTGGTCCGCGCGCAATCGTATATCA
*
13960 AGAATTTTCTTTGAGTTTTCTCCAAGATTTTTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAA
1 AGAATTTTCTTTGAGTTTTCTCCAAGATTTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAA
14025 TCTTGTGATTGTGGGAGCCATCTTCAACCTTCTTCTTGCCATTGATATTCTTTGGAGGGGAGATT
66 TCTTGTGATTGTGGGAGCCATCTTCAACCTTCTTCTTGCCATTGATATTCTTTGGAGGGGAGATT
*
14090 AGAGCCGTTTGAAGGGAGTTGTGAGATCTTTCGAGATTTCAAGGCTTCTTAGGACTTATCTTTTA
131 AGAGCCGTTTGAAGGGAGTTGTGAGATCTTTCGAGATTTCAAGACTTCTTAGGACTTATCTTTTA
*
14155 ATTTCTTACTGTCAATTCTTTCTTTATTTCTACTTGTGCTGAATCATTATCTAATCTATTTTCTG
196 ATTTCTTACTGTCAATTCTTTCTTTATTTCTACTTGTACTGAATCATTATCTAATCTATTTTCTG
14220 TTCTTATTGTGTTTTCAGCCTTTTTCTATCTTAAGGAATCAGCCCAAAAATCCCCAATTTCTAGG
261 TTCTTATTGTGTTTTCAGCCTTTTTCTATCTTAAGGAATCAGCCCAAAAATCCCCAATTTCTAGG
14285 GTTTTTCCATACTCTTTTTGGGTGAAATTAGATTGTCGAAATTTGGGAAAAACTATCTTGGTGTT
326 GTTTTTCCATACTCTTTTTGGGTGAAATTAGATTGTCGAAATTTGGGAAAAACTATCTTGGTGTT
* *
14350 TAATTGGGCAGAATCACAATCTCCTTGAGGGTTTCAAGAACCCTAACACTTATTTTTATTCTCAA
391 CAATTGGGCAGAATCACAATCTCCTTGAGGGTTTCAAGAACCCTAACACTTATTTCTATTCTCAA
*
14415 TTTGATTCCTTGCTGATTTGGGGATTTTATTTCAGATCTGAAAATTCAAAAATCTAATCTTTTAA
456 TTTGATTCCTTGCTGATTTGGGGATTTTATTTCAGATCTGAAAATTCAAAAATCCAATCTTTTAA
* * *
14480 TTTTCTGTTTCGTTTCAGATCTAATTGTTTAGGGTTTTCGTAGGAGTTTCTCGTGACTTGGCAAC
521 TTTTCTGTTTCGTTTCAGATCTAATTATTTAGGGTTTTCGTAGGAGTTTCCCATGACTTGGCAAC
14545 TCGATCTTGGTCCGCGCGCAA
586 TCGATCTTGGTCCGCGCGCAA
14566 CCCCGTATCA
Statistics
Matches: 590, Mismatches: 16, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
616 80 0.14
617 510 0.86
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (616 bp):
AGAATTTTCTTTGAGTTTTCTCCAAGATTTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAA
TCTTGTGATTGTGGGAGCCATCTTCAACCTTCTTCTTGCCATTGATATTCTTTGGAGGGGAGATT
AGAGCCGTTTGAAGGGAGTTGTGAGATCTTTCGAGATTTCAAGACTTCTTAGGACTTATCTTTTA
ATTTCTTACTGTCAATTCTTTCTTTATTTCTACTTGTACTGAATCATTATCTAATCTATTTTCTG
TTCTTATTGTGTTTTCAGCCTTTTTCTATCTTAAGGAATCAGCCCAAAAATCCCCAATTTCTAGG
GTTTTTCCATACTCTTTTTGGGTGAAATTAGATTGTCGAAATTTGGGAAAAACTATCTTGGTGTT
CAATTGGGCAGAATCACAATCTCCTTGAGGGTTTCAAGAACCCTAACACTTATTTCTATTCTCAA
TTTGATTCCTTGCTGATTTGGGGATTTTATTTCAGATCTGAAAATTCAAAAATCCAATCTTTTAA
TTTTCTGTTTCGTTTCAGATCTAATTATTTAGGGTTTTCGTAGGAGTTTCCCATGACTTGGCAAC
TCGATCTTGGTCCGCGCGCAATCGTATATCA
Found at i:15235 original size:11 final size:11
Alignment explanation
Indices: 15219--15247 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
15209 TTAAACTAAG
15219 TAAATAAATAA
1 TAAATAAATAA
15230 TAAATAAATAA
1 TAAATAAATAA
15241 -AAATAAA
1 TAAATAAA
15248 ACTTTACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:16273 original size:21 final size:23
Alignment explanation
Indices: 16228--16274 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
16218 TCACCTGCAA
* *
16228 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
16251 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
16272 TAA
1 TAA
16275 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:16857 original size:46 final size:46
Alignment explanation
Indices: 16804--16897 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
16794 CAAAGAAAAG
*
16804 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
16850 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
16896 AC
1 AC
16898 GCCACACTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:18460 original size:21 final size:23
Alignment explanation
Indices: 18415--18461 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
18405 TCACCTGCAA
* *
18415 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
18438 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
18459 TAA
1 TAA
18462 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:22319 original size:15 final size:14
Alignment explanation
Indices: 22283--22337 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
22273 TCTATTGATC
22283 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
22297 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
22311 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
22326 GAAAGAAAAGAA
1 GAGA-AAAAGAA
22338 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:27176 original size:46 final size:46
Alignment explanation
Indices: 27123--27216 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
27113 CAAAGAAAAG
*
27123 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
27169 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
27215 AC
1 AC
27217 GCCACACTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:29371 original size:56 final size:55
Alignment explanation
Indices: 29255--29372 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
29245 TGCATGCTTT
* * * *
29255 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
29309 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
29365 CATTAAAT
1 CATTAAAT
29373 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:30021 original size:20 final size:20
Alignment explanation
Indices: 29996--30050 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
29986 ACGAGTTAAA
* *
29996 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
30016 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
30036 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
30051 TTGAACCACA
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:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:30656 original size:21 final size:23
Alignment explanation
Indices: 30611--30657 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
30601 TCACCTGCAA
* *
30611 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
30634 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
30655 TAA
1 TAA
30658 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:36353 original size:24 final size:25
Alignment explanation
Indices: 36300--36353 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
36290 AACAAATTCT
* *
36300 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
36325 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
36348 TTTTTT
1 TTTTTT
36354 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:38621 original size:14 final size:14
Alignment explanation
Indices: 38602--38628 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38592 CTAGACCGTA
38602 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
38616 TGCAATTTTTTTT
1 TGCAATTTTTTTT
38629 CGATTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.70
Consensus pattern (14 bp):
TGCAATTTTTTTTT
Found at i:38666 original size:12 final size:13
Alignment explanation
Indices: 38633--38667 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
38623 TTTTTTCGAT
38633 TTTTTTTTTAAAAC
1 TTTTTTTTT-AAAC
38647 TTTTTTTTT-AAC
1 TTTTTTTTTAAAC
38659 TTTTTTTTT
1 TTTTTTTTT
38668 TCGAAGCTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
14 9 0.43
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTAAAC
Found at i:38668 original size:14 final size:14
Alignment explanation
Indices: 38631--38668 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
38621 TTTTTTTTCG
38631 ATTTTTTTTTTAAA
1 ATTTTTTTTTTAAA
*
38645 ACTTTTTTTTT-AA
1 ATTTTTTTTTTAAA
*
38658 CTTTTTTTTTT
1 ATTTTTTTTTT
38669 CGAAGCTACG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (14 bp):
ATTTTTTTTTTAAA
Done.