Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2442
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: 38983
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:8323 original size:17 final size:17
Alignment explanation
Indices: 8301--8436 Score: 102
Period size: 18 Copynumber: 7.9 Consensus size: 17
8291 TTTTTTTTAA
*
8301 AAAACACGAAAATTTTC
1 AAAACACGAAAATTTTG
*
8318 AAAACACCGAAATTTTTG
1 AAAACA-CGAAAATTTTG
* * *
8336 AAAACAAGAGGATTTTTG
1 AAAACACGA-AAATTTTG
*
8354 -AAATACGAAAAATTTTG
1 AAAACACG-AAAATTTTG
8371 AAAACACGAAAATTTTTG
1 AAAACACGAAAA-TTTTG
*
8389 -AAACACGGAAATTTTTG
1 AAAACAC-GAAAATTTTG
*
8406 AAAACA--AAATTTTTTG
1 AAAACACGAAA-ATTTTG
*
8422 -AAACACAAAAATTTT
1 AAAACACGAAAATTTT
8437 TAGAAGACAC
Statistics
Matches: 98, Mismatches: 11, Indels: 21
0.75 0.08 0.16
Matches are distributed among these distances:
15 8 0.08
16 10 0.10
17 37 0.38
18 43 0.44
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (17 bp):
AAAACACGAAAATTTTG
Found at i:8351 original size:35 final size:35
Alignment explanation
Indices: 8301--8437 Score: 136
Period size: 35 Copynumber: 4.0 Consensus size: 35
8291 TTTTTTTTAA
* **
8301 AAAACACGAAAATTTTCAAAACACCGAAATTTTTG
1 AAAACAAGAAAATTTTTGAAACACCGAAATTTTTG
** * *
8336 AAAACAAGAGGATTTTTGAAATA-CGAAAAATTTTG
1 AAAACAAGAAAATTTTTGAAACACCG-AAATTTTTG
* *
8371 AAAACACGAAAATTTTTGAAACACGGAAATTTTTG
1 AAAACAAGAAAATTTTTGAAACACCGAAATTTTTG
* **
8406 AAAAC-A-AAATTTTTTGAAACACAAAAATTTTT
1 AAAACAAGAAAATTTTTGAAACACCGAAATTTTT
8438 AGAAGACACT
Statistics
Matches: 83, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
33 23 0.28
34 2 0.02
35 57 0.69
36 1 0.01
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (35 bp):
AAAACAAGAAAATTTTTGAAACACCGAAATTTTTG
Found at i:8437 original size:18 final size:17
Alignment explanation
Indices: 8302--8461 Score: 128
Period size: 17 Copynumber: 9.2 Consensus size: 17
8292 TTTTTTTAAA
* **
8302 AAACACGAAAATTTTCA
1 AAACACAAAAATTTTTG
**
8319 AAACACCGAAATTTTTG
1 AAACACAAAAATTTTTG
*
8336 AAA-ACAAGAGGATTTTTG
1 AAACACAA-A-AATTTTTG
*
8354 AAATACGAAAAA-TTTTG
1 AAACAC-AAAAATTTTTG
*
8371 AAAACACGAAAATTTTTG
1 -AAACACAAAAATTTTTG
**
8389 AAACACGGAAATTTTTG
1 AAACACAAAAATTTTTG
*
8406 AAA-ACAAAATTTTTTG
1 AAACACAAAAATTTTTG
8422 AAACACAAAAATTTTTAG
1 AAACACAAAAATTTTT-G
*
8440 AAGACACTAAAAATTTTGG
1 AA-ACAC-AAAAATTTTTG
8459 AAA
1 AAA
8462 ATGGATTTTT
Statistics
Matches: 117, Mismatches: 16, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
16 15 0.13
17 56 0.48
18 25 0.21
19 10 0.09
20 11 0.09
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (17 bp):
AAACACAAAAATTTTTG
Found at i:8640 original size:219 final size:218
Alignment explanation
Indices: 8415--8840 Score: 499
Period size: 219 Copynumber: 1.9 Consensus size: 218
8405 GAAAACAAAA
* * *
8415 TTTTTTGAAACAC-AAAAATTTTTAGAAGACACTAAAAATTTTGGAAAAT-GGATTTTTTTTTTT
1 TTTTTTGAAACACGAAAAATTTTT-GAAGACACGAAAAATTTTGAAAAATAGAATTTTTTTTTTT
* *
8478 GAAAACACTG-GA-TTTTTTTACACAAAATTTTTGATTTTTTATTAAA-CACGTATCG-TATTTA
65 GAAAACA-TGAGACTTTTTTT-CA-AAAATTTTT--TATTTTA-AAAAGCACGTATCGAT-TTTA
* *
8539 ACACGAATCGGTGATATTCACTCAACATAGCAATGAAATCAACGA-ATTAGTGTCAAATCGATTC
123 ACACGAACCGGTGATATTCACCCAACATAGCAATGAAATCAACGATATTA-TGTCAAATCGATTC
*
8603 ATTATCTTATTT-TTAAAAACACGAATATATT
187 ATTACCTTATTTATTAAAAACACGAATATATT
*
8634 TTTTTTGAAACACGAGAAAAATTTTTGAAGGCACGAAAAATTTTGAAAAATAGAATTTTTTTTTT
1 TTTTTTGAAACAC--GAAAAATTTTTGAAGACACGAAAAATTTTGAAAAATAGAATTTTTTTTTT
* * * * ** *
8699 TGTAAATATGAGACTTTTTTTTAAATATTTTTTATTTTAAAAAGGGCGTATCGATTTTAACGCGA
64 TGAAAACATGAGACTTTTTTTCAAAAATTTTTTATTTTAAAAAGCACGTATCGATTTTAACACGA
* * * * * *
8764 ACCGGTGATATTCACCCAACGTAGCGATGAAATCAACGATTTTATGTTAAATCGATTCGTTGCCT
129 ACCGGTGATATTCACCCAACATAGCAATGAAATCAACGATATTATGTCAAATCGATTCATTACCT
8829 TATTTATTAAAA
194 TATTTATTAAAA
8841 TTATCTAAAA
Statistics
Matches: 175, Mismatches: 22, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
218 3 0.02
219 92 0.53
220 10 0.06
221 32 0.18
222 31 0.18
223 7 0.04
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (218 bp):
TTTTTTGAAACACGAAAAATTTTTGAAGACACGAAAAATTTTGAAAAATAGAATTTTTTTTTTTG
AAAACATGAGACTTTTTTTCAAAAATTTTTTATTTTAAAAAGCACGTATCGATTTTAACACGAAC
CGGTGATATTCACCCAACATAGCAATGAAATCAACGATATTATGTCAAATCGATTCATTACCTTA
TTTATTAAAAACACGAATATATT
Found at i:8673 original size:20 final size:19
Alignment explanation
Indices: 8635--8681 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
8625 GAATATATTT
8635 TTTTTGAAACACGAGAAAAA
1 TTTTTGAAACACG-GAAAAA
*
8655 TTTTTGAAGGCAC-GAAAAA
1 TTTTTGAA-ACACGGAAAAA
8674 -TTTTGAAA
1 TTTTTGAAA
8682 AATAGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 7 0.29
19 6 0.25
20 8 0.33
21 3 0.12
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.30
Consensus pattern (19 bp):
TTTTTGAAACACGGAAAAA
Found at i:8699 original size:22 final size:24
Alignment explanation
Indices: 8674--8720 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
8664 GCACGAAAAA
8674 TTTTG-AAAAAT-AGAATTTTTTT
1 TTTTGTAAAAATGAGAATTTTTTT
* *
8696 TTTTGTAAATATGAGACTTTTTTT
1 TTTTGTAAAAATGAGAATTTTTTT
8720 T
1 T
8721 AAATATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.24
23 5 0.24
24 11 0.52
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (24 bp):
TTTTGTAAAAATGAGAATTTTTTT
Found at i:9059 original size:11 final size:11
Alignment explanation
Indices: 9041--9109 Score: 79
Period size: 11 Copynumber: 6.3 Consensus size: 11
9031 GAATTGAACC
9041 TCTTTTTTT-T
1 TCTTTTTTTCT
9051 TCTTTTTTTCCT
1 TCTTTTTTT-CT
*
9063 TCTTTTTTCCT
1 TCTTTTTTTCT
*
9074 TCTCTTTTTCT
1 TCTTTTTTTCT
9085 TCTTTTTCTT-T
1 TCTTTTT-TTCT
*
9096 TCTTTTTTTTT
1 TCTTTTTTTCT
9107 TCT
1 TCT
9110 GCTGGGCCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
10 11 0.22
11 29 0.57
12 11 0.22
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TCTTTTTTTCT
Found at i:9097 original size:14 final size:13
Alignment explanation
Indices: 9043--9107 Score: 50
Period size: 12 Copynumber: 5.3 Consensus size: 13
9033 ATTGAACCTC
9043 TTTTT-TTTTCTT
1 TTTTTCTTTTCTT
*
9055 TTTTTC-CTTCTT
1 TTTTTCTTTTCTT
* *
9067 TTTTCCTTCTCTT
1 TTTTTCTTTTCTT
9080 TTTCTTC-TTT-TT
1 TTT-TTCTTTTCTT
*
9092 CTTTTCTTTT-TT
1 TTTTTCTTTTCTT
9104 TTTT
1 TTTT
9108 CTGCTGGGCC
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
11 3 0.07
12 27 0.66
13 9 0.22
14 2 0.05
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTCTTTTCTT
Found at i:9389 original size:18 final size:18
Alignment explanation
Indices: 9368--9436 Score: 56
Period size: 17 Copynumber: 3.9 Consensus size: 18
9358 ATTTTTATTA
9368 TTTCTTTTCTTT-TTCTTT
1 TTTC-TTTCTTTCTTCTTT
9386 TTTCTTTCTTTCTTC-TT
1 TTTCTTTCTTTCTTCTTT
** *
9403 CCTCTTT-TCTTCTTCCTT
1 TTTCTTTCT-TTCTTCTTT
*
9421 CTTC-TTCTTTCTTCTT
1 TTTCTTTCTTTCTTCTT
9437 CTTCAAAGTC
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
16 1 0.02
17 29 0.67
18 13 0.30
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTCTTTCTTTCTTCTTT
Found at i:9403 original size:3 final size:3
Alignment explanation
Indices: 9369--9440 Score: 62
Period size: 3 Copynumber: 24.0 Consensus size: 3
9359 TTTTTATTAT
* *
9369 TTC TT- TTC TTT TTC TT- TT- TTC TTTC TTTC TTC TTC CTC TT- TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC -TTC -TTC TTC TTC TTC TTC TTC
9412 TTC TTCC TTC TTC TTC TTTC TTC TTC TTC
1 TTC TT-C TTC TTC TTC -TTC TTC TTC TTC
9441 AAAGTCTAGC
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 8 0.14
3 38 0.64
4 13 0.22
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:9413 original size:14 final size:13
Alignment explanation
Indices: 9368--9440 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
9358 ATTTTTATTA
9368 TTTCTT-TT-CTT
1 TTTCTTCTTCCTT
* *
9379 TTTCTTTTTTCTTT
1 TTTC-TTCTTCCTT
9393 CTTTCTTCTTCCTCT
1 -TTTCTTCTTCCT-T
9408 TTTCTTCTTCCTT
1 TTTCTTCTTCCTT
* *
9421 CTTCTTCTTTCTT
1 TTTCTTCTTCCTT
*
9434 CTTCTTC
1 TTTCTTC
9441 AAAGTCTAGC
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
11 4 0.08
12 2 0.04
13 21 0.40
14 20 0.38
15 5 0.10
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTCTTCTTCCTT
Found at i:9438 original size:10 final size:10
Alignment explanation
Indices: 9368--9439 Score: 69
Period size: 10 Copynumber: 7.2 Consensus size: 10
9358 ATTTTTATTA
9368 TTTCTT-TTC
1 TTTCTTCTTC
*
9377 TTT-TTCTTT
1 TTTCTTCTTC
9386 TTTCTTTCTT-
1 TTTC-TTCTTC
*
9396 TCTTCTTCCTC
1 T-TTCTTCTTC
9407 TTTTCTTCTTC
1 -TTTCTTCTTC
*
9418 CTTCTTCTTC
1 TTTCTTCTTC
9428 TTTCTTCTTC
1 TTTCTTCTTC
9438 TT
1 TT
9440 CAAAGTCTAG
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
8 2 0.04
9 8 0.15
10 25 0.48
11 16 0.31
12 1 0.02
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTCTTCTTC
Found at i:9839 original size:29 final size:29
Alignment explanation
Indices: 9806--9907 Score: 91
Period size: 30 Copynumber: 3.4 Consensus size: 29
9796 TGTAATTTTT
*
9806 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
9835 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
9865 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
*
9894 GGAAAAGTTTAGGG
1 AGAAAA-TTTAGGG
9908 GTCAAAATAC
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
29 17 0.29
30 40 0.68
31 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.24, T:0.29
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:9922 original size:30 final size:30
Alignment explanation
Indices: 9821--9915 Score: 129
Period size: 30 Copynumber: 3.2 Consensus size: 30
9811 ATTTAGGATT
*
9821 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
9851 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
9881 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
9911 AAAAT
1 AAAAT
9916 ACAATTTTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.04
30 54 0.96
ACGTcount: A:0.45, C:0.03, G:0.23, T:0.28
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:12721 original size:19 final size:21
Alignment explanation
Indices: 12699--12742 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
12689 CTTTAGCTCT
*
12699 TTCTCTC-TCGATTC-ATTTC
1 TTCTCTCTTAGATTCTATTTC
12718 TTCT-TCTTAGATTCTATTTC
1 TTCTCTCTTAGATTCTATTTC
12738 TTCTC
1 TTCTC
12743 GAGAACATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 2 0.10
19 10 0.48
20 9 0.43
ACGTcount: A:0.11, C:0.27, G:0.05, T:0.57
Consensus pattern (21 bp):
TTCTCTCTTAGATTCTATTTC
Found at i:17675 original size:16 final size:19
Alignment explanation
Indices: 17653--17693 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 19
17643 TATTTTAGAC
17653 GAATAAAAA-AA-GAAAAA
1 GAATAAAAATAAGGAAAAA
17670 -AATAAAAATAAGGAAAAA
1 GAATAAAAATAAGGAAAAA
17688 GAATAA
1 GAATAA
17694 TTGTGAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 8 0.38
17 2 0.10
18 6 0.29
19 5 0.24
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (19 bp):
GAATAAAAATAAGGAAAAA
Found at i:18944 original size:22 final size:21
Alignment explanation
Indices: 18901--18944 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
18891 TATCATATGA
* *
18901 TTATTTAATATTCTTTGTAAG
1 TTATTTAAAATTCTTTGCAAG
*
18922 TTATTTAAAATGTTTTTGCAAG
1 TTATTTAAAAT-TCTTTGCAAG
18944 T
1 T
18945 AAAATAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.55
Consensus pattern (21 bp):
TTATTTAAAATTCTTTGCAAG
Found at i:19376 original size:34 final size:34
Alignment explanation
Indices: 19312--19381 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
19302 TCGAGGGAAA
** *
19312 AGTTATAAAGTGACCTTTCTTGAAATGAGATAAT
1 AGTTATAAAGTGACCTTTCTCCAAACGAGATAAT
19346 AGTTATAAAGTGACCTTT-TCCAATACGAGATAAT
1 AGTTATAAAGTGACCTTTCTCCAA-ACGAGATAAT
19380 AG
1 AG
19382 AGTTTCGGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 3 0.09
34 29 0.91
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (34 bp):
AGTTATAAAGTGACCTTTCTCCAAACGAGATAAT
Found at i:28440 original size:15 final size:15
Alignment explanation
Indices: 28390--28450 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
28380 CTTTTTATTA
*
28390 TTATTATTATTTA-G
1 TTATTATTATTAATG
* *
28404 TTCATTGTT-TTATTG
1 TT-ATTATTATTAATG
*
28419 CTATTATTATTAATG
1 TTATTATTATTAATG
*
28434 TTATTATTATTATTG
1 TTATTATTATTAATG
28449 TT
1 TT
28451 TCTATATTTC
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
14 9 0.25
15 27 0.75
ACGTcount: A:0.25, C:0.03, G:0.08, T:0.64
Consensus pattern (15 bp):
TTATTATTATTAATG
Done.