Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1463
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: 41292
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:3588 original size:329 final size:329
Alignment explanation
Indices: 2990--3612 Score: 1237
Period size: 329 Copynumber: 1.9 Consensus size: 329
2980 AGTGGGCCTT
*
2990 TTTTTTTTCTTTCCTGGCCCTAATTTTTTTGGATGGAAAACTCTTTAATTATAATTTTCTCGGCC
1 TTTTTTTTCTTTCCTGGCCCTAATTTTTTTGGATGGAAAACTCTTTAATTATAATTTTCTCGACC
3055 TTTACAGTCATTTTAATCATCTCTCTAGAAATTACAAGATCAACAAAATTCTTGTTGCATTTTCT
66 TTTACAGTCATTTTAATCATCTCTCTAGAAATTACAAGATCAACAAAATTCTTGTTGCATTTTCT
3120 ACTAACTTTTCATGATAGGAGGATAAAGGGTATTCACGAATAGCATTAAGGTTTCTTTCTTAATC
131 ACTAACTTTTCATGATAGGAGGATAAAGGGTATTCACGAATAGCATTAAGGTTTCTTTCTTAATC
3185 AAAAGAGGTCGGACCTGAGAGGCCATTTTTCTCTATTTTTGTGTATATTCCTTAAAAGATTTCAT
196 AAAAGAGGTCGGACCTGAGAGGCCATTTTTCTCTATTTTTGTGTATATTCCTTAAAAGATTTCAT
3250 GGACTTCTTTTCCATGCTCTGAAGGGTTAGTTTACAGTCATTTTAAAAGAGGTCGGACCTGAGAG
261 GGACTTCTTTTCCATGCTCTGAAGGGTTAGTTTACAGTCATTTTAAAAGAGGTCGGACCTGAGAG
3315 GCCA
326 GCCA
3319 TTTTTTTTCTTTCCTGGCCCTAATTTTTTTGGATGGAAAACTCTTTAATTATAATTTTCTCGACC
1 TTTTTTTTCTTTCCTGGCCCTAATTTTTTTGGATGGAAAACTCTTTAATTATAATTTTCTCGACC
3384 TTTACAGTCATTTTAATCATCTCTCTAGAAATTACAAGATCAACAAAATTCTTGTTGCATTTTCT
66 TTTACAGTCATTTTAATCATCTCTCTAGAAATTACAAGATCAACAAAATTCTTGTTGCATTTTCT
3449 ACTAACTTTTCATGATAGGAGGATAAAGGGTATTCACGAATAGCATTAAGGTTTCTTTCTTAATC
131 ACTAACTTTTCATGATAGGAGGATAAAGGGTATTCACGAATAGCATTAAGGTTTCTTTCTTAATC
3514 AAAAGAGGTCGGACCTGAGAGGCCATTTTTCTCTATTTTTGTGTATATTCCTTAAAAGATTTCAT
196 AAAAGAGGTCGGACCTGAGAGGCCATTTTTCTCTATTTTTGTGTATATTCCTTAAAAGATTTCAT
3579 GGACTTCTTTTCCATGCTCTGAAGGGTTAGTTTA
261 GGACTTCTTTTCCATGCTCTGAAGGGTTAGTTTA
3613 TCAGGCAACC
Statistics
Matches: 293, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
329 293 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (329 bp):
TTTTTTTTCTTTCCTGGCCCTAATTTTTTTGGATGGAAAACTCTTTAATTATAATTTTCTCGACC
TTTACAGTCATTTTAATCATCTCTCTAGAAATTACAAGATCAACAAAATTCTTGTTGCATTTTCT
ACTAACTTTTCATGATAGGAGGATAAAGGGTATTCACGAATAGCATTAAGGTTTCTTTCTTAATC
AAAAGAGGTCGGACCTGAGAGGCCATTTTTCTCTATTTTTGTGTATATTCCTTAAAAGATTTCAT
GGACTTCTTTTCCATGCTCTGAAGGGTTAGTTTACAGTCATTTTAAAAGAGGTCGGACCTGAGAG
GCCA
Found at i:4662 original size:19 final size:19
Alignment explanation
Indices: 4619--4690 Score: 126
Period size: 19 Copynumber: 3.7 Consensus size: 19
4609 ATTTCAACGA
4619 TTTGTATCGATACATAAAGT
1 TTTGTATCGATACAT-AAGT
*
4639 GTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
4658 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
4677 TTTGTATCGATACA
1 TTTGTATCGATACA
4691 ATGTAAGCTA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 36 0.72
20 14 0.28
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:4751 original size:13 final size:13
Alignment explanation
Indices: 4733--4757 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4723 ATTACCCAAA
4733 TGTATCGATACAT
1 TGTATCGATACAT
4746 TGTATCGATACA
1 TGTATCGATACA
4758 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4824 original size:52 final size:52
Alignment explanation
Indices: 4768--4894 Score: 218
Period size: 52 Copynumber: 2.4 Consensus size: 52
4758 CTGATCTTTG
4768 TATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAATA
1 TATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAATA
* * *
4820 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAATA
*
4872 TATTGATACATGCAGGCAAATTT
1 TATCGATACATGCAGGCAAATTT
4895 TCATATTTCG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (52 bp):
TATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAATA
Found at i:9910 original size:20 final size:19
Alignment explanation
Indices: 9884--9956 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
9874 CTACCAGTTT
*
9884 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAA
*
9904 TATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
9923 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
9944 -ATGTATCGATACA
1 CATGTATCGATACA
9957 TCTGGATGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 18 0.38
20 28 0.60
21 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:10659 original size:17 final size:17
Alignment explanation
Indices: 10637--10670 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
10627 TTCTCCCCCT
10637 TTGTCAAATGCCAATGC
1 TTGTCAAATGCCAATGC
10654 TTGTCAAATGCCAATGC
1 TTGTCAAATGCCAATGC
10671 CAAATTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (17 bp):
TTGTCAAATGCCAATGC
Found at i:12360 original size:31 final size:31
Alignment explanation
Indices: 12319--12392 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
12309 GTGTTTTTGT
* *
12319 TGATG-AATTTGAAGAAAAGTG-AAAGGAAT
1 TGATGAAATTTGAAGAAAAGTGAAAAAGAAA
* **
12348 TGATGCAAATTTGATGAAATTTGAAAAAGAAA
1 TGATG-AAATTTGAAGAAAAGTGAAAAAGAAA
12380 TGATGAAATTTGA
1 TGATGAAATTTGA
12393 GATTGAAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 5 0.14
31 21 0.57
32 11 0.30
ACGTcount: A:0.47, C:0.01, G:0.23, T:0.28
Consensus pattern (31 bp):
TGATGAAATTTGAAGAAAAGTGAAAAAGAAA
Found at i:18751 original size:19 final size:19
Alignment explanation
Indices: 18706--18761 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
18696 CTACCAGTTT
*
18706 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAA
*
18726 TATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
18745 CATGTATCGATATAATG
1 CATGTATCGATACAATG
18762 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:18768 original size:32 final size:33
Alignment explanation
Indices: 18727--18789 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
18717 ACAATTGAGT
*
18727 ATGTATCGATACAATG-A-ACATGTATCGATATA
1 ATGTATCGATACAAAGCATA-ATGTATCGATATA
18759 ATGTATCGATACAAAGCATAATGTATCGATA
1 ATGTATCGATACAAAGCATAATGTATCGATA
18790 CATTTGGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.54
33 12 0.43
34 1 0.04
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATGTATCGATATA
Found at i:20452 original size:282 final size:282
Alignment explanation
Indices: 19948--20514 Score: 1116
Period size: 282 Copynumber: 2.0 Consensus size: 282
19938 AACTTTTTCG
*
19948 ATGGTTGTTTCTTGTCTAGAAGCTTAGCCCAAATCTTATTACATGCAGGTGGCTTATGTTCTTTG
1 ATGGTTGTTTCTTGTCTAGAAGCTTAGCCCAAATCTTACTACATGCAGGTGGCTTATGTTCTTTG
*
20013 CAATATATTAGTTCTGGTTTTATAGACTCTACCCTTAACAAAGCTGAGTATTCCTTTATGTTTGG
66 CAATATATTAGTTCTGGTTTTATAGACTCTACCCTTAACAAAGCTGAATATTCCTTTATGTTTGG
20078 TGTCAAATCCTCATTATTAAAAGTAAAACACTTGTATGAAGGATCCCAAAACTCTATGATGGCTC
131 TGTCAAATCCTCATTATTAAAAGTAAAACACTTGTATGAAGGATCCCAAAACTCTATGATGGCTC
20143 AGATCAAAGATCTTCCCTTTGTATTAAGAGCAAGAGGGCCAATTGACCATACTTCTAGATGAATT
196 AGATCAAAGATCTTCCCTTTGTATTAAGAGCAAGAGGGCCAATTGACCATACTTCTAGATGAATT
20208 GATTCCACCTTTGATTGGTCCA
261 GATTCCACCTTTGATTGGTCCA
20230 ATGGTTGTTTCTTGTCTAGAAGCTTAGCCCAAATCTTACTACATGCAGGTGGCTTATGTTCTTTG
1 ATGGTTGTTTCTTGTCTAGAAGCTTAGCCCAAATCTTACTACATGCAGGTGGCTTATGTTCTTTG
20295 CAATATATTAGTTCTGGTTTTATAGACTCTACCCTTAACAAAGCTGAATATTCCTTTATGTTTGG
66 CAATATATTAGTTCTGGTTTTATAGACTCTACCCTTAACAAAGCTGAATATTCCTTTATGTTTGG
20360 TGTCAAATCCTCATTATTAAAAGTAAAACACTTGTATGAAGGATCCCAAAACTCTATGATGGCTC
131 TGTCAAATCCTCATTATTAAAAGTAAAACACTTGTATGAAGGATCCCAAAACTCTATGATGGCTC
20425 AGATCAAAGATCTTCCCTTTGTATTAAGAGCAAGAGGGCCAATTGACCATACTTCTAGATGAATT
196 AGATCAAAGATCTTCCCTTTGTATTAAGAGCAAGAGGGCCAATTGACCATACTTCTAGATGAATT
20490 GATTCCACCTTTGATTGGTCCA
261 GATTCCACCTTTGATTGGTCCA
20512 ATG
1 ATG
20515 ATTCCATATG
Statistics
Matches: 283, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
282 283 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (282 bp):
ATGGTTGTTTCTTGTCTAGAAGCTTAGCCCAAATCTTACTACATGCAGGTGGCTTATGTTCTTTG
CAATATATTAGTTCTGGTTTTATAGACTCTACCCTTAACAAAGCTGAATATTCCTTTATGTTTGG
TGTCAAATCCTCATTATTAAAAGTAAAACACTTGTATGAAGGATCCCAAAACTCTATGATGGCTC
AGATCAAAGATCTTCCCTTTGTATTAAGAGCAAGAGGGCCAATTGACCATACTTCTAGATGAATT
GATTCCACCTTTGATTGGTCCA
Found at i:22899 original size:29 final size:29
Alignment explanation
Indices: 22867--23010 Score: 150
Period size: 29 Copynumber: 5.0 Consensus size: 29
22857 GTACTAAGTT
**
22867 CCTAAACTTTTCAAAATTATGCTTTGACC
1 CCTAAACTTTTCAAAATTACACTTTGACC
* *
22896 CCTAAAC-TTTCTAAAATTGCACTTTGA-T
1 CCTAAACTTTTC-AAAATTACACTTTGACC
*
22924 CCTATAACTTTTCAAAATTGCACTTTGACC
1 CCTA-AACTTTTCAAAATTACACTTTGACC
* * * *
22954 TCTAAAGTTTTCAAAAATGCACTTTG-CC
1 CCTAAACTTTTCAAAATTACACTTTGACC
* *
22982 CTTAAACTTTTCAAAATTACACTTGGACC
1 CCTAAACTTTTCAAAATTACACTTTGACC
23011 TAAAAATGGC
Statistics
Matches: 96, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
28 30 0.31
29 59 0.61
30 7 0.07
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.37
Consensus pattern (29 bp):
CCTAAACTTTTCAAAATTACACTTTGACC
Found at i:22933 original size:58 final size:57
Alignment explanation
Indices: 22866--23010 Score: 170
Period size: 58 Copynumber: 2.5 Consensus size: 57
22856 GGTACTAAGT
** *
22866 TCCTA-AACTTTTCAAAATTATGCTTTGACCCCTAAAC-TTTCTAAAATTGCACTTTG
1 TCCTATAACTTTTCAAAATTACACTTTGACCCCTAAACTTTTC-AAAAATGCACTTTG
* * *
22922 ATCCTATAACTTTTCAAAATTGCACTTTGACCTCTAAAGTTTTCAAAAATGCACTTTG
1 -TCCTATAACTTTTCAAAATTACACTTTGACCCCTAAACTTTTCAAAAATGCACTTTG
* *
22980 CCCT-TAAACTTTTCAAAATTACACTTGGACC
1 TCCTAT-AACTTTTCAAAATTACACTTTGACC
23011 TAAAAATGGC
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
56 1 0.01
57 31 0.41
58 40 0.53
59 4 0.05
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (57 bp):
TCCTATAACTTTTCAAAATTACACTTTGACCCCTAAACTTTTCAAAAATGCACTTTG
Found at i:24192 original size:5 final size:5
Alignment explanation
Indices: 24182--24209 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
24172 GAAACTGTTA
24182 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
24210 TTTTTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:31262 original size:2 final size:2
Alignment explanation
Indices: 31257--31292 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
31247 TTATATAATG
*
31257 CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
31293 TTTATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:31525 original size:21 final size:21
Alignment explanation
Indices: 31488--31611 Score: 96
Period size: 21 Copynumber: 6.0 Consensus size: 21
31478 TTACAAATGT
*
31488 TATTAAAA-TTATTCCAAAGTTA
1 TATTAAAAGTTA--CCAAAATTA
31510 TATTAAAAGTTACCAAAATTA
1 TATTAAAAGTTACCAAAATTA
* *
31531 TTTTAAAAGTTATCAAAATTA
1 TATTAAAAGTTACCAAAATTA
* * *
31552 TATCAAAAGTTATC-TAA--A
1 TATTAAAAGTTACCAAAATTA
* *
31570 -ACTAAAGGTTACCAAAATTA
1 TATTAAAAGTTACCAAAATTA
* *
31590 TATCAAAAGTTATCTAAAATTA
1 TATTAAAAGTTA-CCAAAATTA
31612 AATGTTACCA
Statistics
Matches: 81, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
17 9 0.11
18 3 0.04
20 3 0.04
21 47 0.58
22 16 0.20
23 3 0.04
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (21 bp):
TATTAAAAGTTACCAAAATTA
Found at i:31595 original size:38 final size:38
Alignment explanation
Indices: 31534--31628 Score: 154
Period size: 38 Copynumber: 2.5 Consensus size: 38
31524 AAAATTATTT
*
31534 TAAAAGTTATCAAAATTATATCAAAAGTTATCTAAAAC
1 TAAAAGTTACCAAAATTATATCAAAAGTTATCTAAAAC
* *
31572 TAAAGGTTACCAAAATTATATCAAAAGTTATCTAAAAT
1 TAAAAGTTACCAAAATTATATCAAAAGTTATCTAAAAC
*
31610 TAAATGTTACCAAAATTAT
1 TAAAAGTTACCAAAATTAT
31629 CAAAATTATA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.33
Consensus pattern (38 bp):
TAAAAGTTACCAAAATTATATCAAAAGTTATCTAAAAC
Found at i:33573 original size:18 final size:20
Alignment explanation
Indices: 33552--33592 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
33542 GTATATTTTA
*
33552 TTAATTTTAA-TTT-AATTT
1 TTAATATTAATTTTGAATTT
33570 TTAATATTAATTTTGAATTT
1 TTAATATTAATTTTGAATTT
33590 TTA
1 TTA
33593 CATAGTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 3 0.15
20 8 0.40
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TTAATATTAATTTTGAATTT
Done.