Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold289
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: 700734
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:671732 original size:12 final size:12
Alignment explanation
Indices: 671715--671739 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
671705 TGCTTGCTTT
671715 TACTTTCATGCA
1 TACTTTCATGCA
671727 TACTTTCATGCA
1 TACTTTCATGCA
671739 T
1 T
671740 TTTGTGCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (12 bp):
TACTTTCATGCA
Found at i:671785 original size:43 final size:43
Alignment explanation
Indices: 671737--671835 Score: 144
Period size: 43 Copynumber: 2.3 Consensus size: 43
671727 TACTTTCATG
* * **
671737 CATTTTGTGCATTACATTTCATGCATGCCTTTCATGTAATTTT
1 CATTTTATGCATTACATTTCATGCATGCATTTCACATAATTTT
*
671780 CATTTTATGGATTACATTTCATGCATGCATTTCACATAATTTT
1 CATTTTATGCATTACATTTCATGCATGCATTTCACATAATTTT
*
671823 CATTTCATGCATT
1 CATTTTATGCATT
671836 TCTTACATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.47
Consensus pattern (43 bp):
CATTTTATGCATTACATTTCATGCATGCATTTCACATAATTTT
Found at i:671833 original size:25 final size:25
Alignment explanation
Indices: 671803--671888 Score: 77
Period size: 25 Copynumber: 3.4 Consensus size: 25
671793 ACATTTCATG
671803 CATGCATTTCACATAATTTTCATTT
1 CATGCATTTCACATAATTTTCATTT
*
671828 CATGCATTTCTTACATTACA-TTTCA-TG
1 CATGCATTTC--ACA-TA-ATTTTCATTT
* * **
671855 CATGCATTTCACGTGATGCTCATTT
1 CATGCATTTCACATAATTTTCATTT
671880 CATGCATTT
1 CATGCATTT
671889 TGTTTCATGC
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
23 1 0.02
24 4 0.08
25 22 0.45
27 14 0.29
28 7 0.14
29 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.44
Consensus pattern (25 bp):
CATGCATTTCACATAATTTTCATTT
Found at i:671850 original size:29 final size:25
Alignment explanation
Indices: 671790--671866 Score: 95
Period size: 25 Copynumber: 3.0 Consensus size: 25
671780 CATTTTATGG
671790 ATTACATTTCATGCATGCATTTCAC
1 ATTACATTTCATGCATGCATTTCAC
*
671815 A-TA-ATTTTCATTTCATGCATTTCTTAC
1 ATTACA-TTTCA-TGCATGCATTTC--AC
671842 ATTACATTTCATGCATGCATTTCAC
1 ATTACATTTCATGCATGCATTTCAC
671867 GTGATGCTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
23 1 0.02
24 7 0.16
25 14 0.32
27 14 0.32
28 7 0.16
29 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.06, T:0.44
Consensus pattern (25 bp):
ATTACATTTCATGCATGCATTTCAC
Found at i:671850 original size:52 final size:56
Alignment explanation
Indices: 671790--671915 Score: 170
Period size: 52 Copynumber: 2.3 Consensus size: 56
671780 CATTTTATGG
**
671790 ATTACATTTCATGCATGCATTTCACATAATTTTCATTTCATGCA-TTT-CTT-A-C
1 ATTACATTTCATGCATGCATTTCACATAATGCTCATTTCATGCATTTTGCTTCAGC
* * *
671842 ATTACATTTCATGCATGCATTTCACGTGATGCTCATTTCATGCATTTTGTTTCATGC
1 ATTACATTTCATGCATGCATTTCACATAATGCTCATTTCATGCATTTTGCTTCA-GC
671899 ATTACATTTCATGCATG
1 ATTACATTTCATGCATG
671916 TTTTCTTTCA
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
52 40 0.62
53 3 0.05
54 2 0.03
55 1 0.02
57 18 0.28
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.44
Consensus pattern (56 bp):
ATTACATTTCATGCATGCATTTCACATAATGCTCATTTCATGCATTTTGCTTCAGC
Found at i:671895 original size:95 final size:96
Alignment explanation
Indices: 671730--671909 Score: 229
Period size: 95 Copynumber: 1.9 Consensus size: 96
671720 TCATGCATAC
* * * ** * *
671730 TTTCATGCATTTTGTGCATTACATTTCATGCATGCCTTTCATGTAATTTTCATTTTATGGATTAC
1 TTTCATGCATTTTGTACATTACATTTCATGCATGCATTTCACGTAATGCTCATTTCATGCATTAC
*
671795 ATTTCATGCA-TGCATTTCACATAATTTTCA
66 ATTTCATGCATTACATTTCACATAATTTTCA
* *
671825 TTTCATGCATTTCT-TACATTACATTTCATGCATGCATTTCACGTGATGCTCATTTCATGCATTT
1 TTTCATGCATTT-TGTACATTACATTTCATGCATGCATTTCACGTAATGCTCATTTCATGCATTA
**
671889 TGTTTCATGCATTACATTTCA
65 CATTTCATGCATTACATTTCA
671910 TGCATGTTTT
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
95 62 0.87
96 9 0.13
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.47
Consensus pattern (96 bp):
TTTCATGCATTTTGTACATTACATTTCATGCATGCATTTCACGTAATGCTCATTTCATGCATTAC
ATTTCATGCATTACATTTCACATAATTTTCA
Found at i:671987 original size:14 final size:14
Alignment explanation
Indices: 671968--672008 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
671958 ATTTCAAAAA
671968 CATTTCATGCATTG
1 CATTTCATGCATTG
671982 CATTTCATTGCATTG
1 CATTTCA-TGCATTG
671997 C-TTTCATGCATT
1 CATTTCATGCATT
672009 AAAACTGCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.23
14 12 0.46
15 8 0.31
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.46
Consensus pattern (14 bp):
CATTTCATGCATTG
Found at i:672674 original size:34 final size:32
Alignment explanation
Indices: 672611--672677 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 32
672601 AAAAAAAGGG
*
672611 GAATCGAATCAAGCAAAAGAAAAGTAAAAAACA
1 GAATCGAATCAACCAAAAGAAAAG-AAAAAACA
672644 GAATCGAATCAAACCAAAGGAGAAAA-AAAAAACA
1 GAATCGAATC-AACCAAA--AGAAAAGAAAAAACA
672678 AAGCAAGGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 10 0.33
34 14 0.47
36 6 0.20
ACGTcount: A:0.64, C:0.13, G:0.15, T:0.07
Consensus pattern (32 bp):
GAATCGAATCAACCAAAAGAAAAGAAAAAACA
Found at i:673557 original size:26 final size:26
Alignment explanation
Indices: 673521--673572 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
673511 GATGACCTCA
673521 AGCTGATTTGGAAATTCGATTATATG
1 AGCTGATTTGGAAATTCGATTATATG
673547 AGCTGATTTGGAAATTCGATTATATG
1 AGCTGATTTGGAAATTCGATTATATG
673573 CTTGTTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (26 bp):
AGCTGATTTGGAAATTCGATTATATG
Found at i:676456 original size:19 final size:20
Alignment explanation
Indices: 676411--676460 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
676401 CACCTTCAGA
* *
676411 TGTATTGATACATAATGCAC
1 TGTATCGATACATAATCCAC
*
676431 AGTATCGATACATAA-CCAC
1 TGTATCGATACATAATCCAC
676450 TGTATCGATAC
1 TGTATCGATAC
676461 TTGCAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATAATCCAC
Found at i:680330 original size:52 final size:52
Alignment explanation
Indices: 680245--680390 Score: 222
Period size: 52 Copynumber: 2.8 Consensus size: 52
680235 ATATGAAATT
*** *
680245 TTGCCTGCATGTATCGATACATTTCAT-ATTGTATCGATACATCTGGGCAAAG
1 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACATCTGGGCAAAG
* *
680297 TTGCCTGCATGTATCGATACAAAGATCGGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACATCTGGGCAAAG
680349 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAT
1 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAT
680391 TGTATCGATA
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.32
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACATCTGGGCAAAG
Found at i:680396 original size:13 final size:13
Alignment explanation
Indices: 680378--680404 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
680368 CAAAGATCAG
680378 TGTATCGATACAT
1 TGTATCGATACAT
680391 TGTATCGATACAT
1 TGTATCGATACAT
680404 T
1 T
680405 TGAGTAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:688998 original size:15 final size:14
Alignment explanation
Indices: 688978--689010 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
688968 ATATCGATAC
688978 ATACAAGATGTATCG
1 ATACAA-ATGTATCG
688993 ATAC-AATGTATCG
1 ATACAAATGTATCG
689006 ATACA
1 ATACA
689011 TGACCAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 12 0.71
14 1 0.06
15 4 0.24
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (14 bp):
ATACAAATGTATCG
Found at i:689003 original size:13 final size:13
Alignment explanation
Indices: 688985--689010 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
688975 TACATACAAG
688985 ATGTATCGATACA
1 ATGTATCGATACA
688998 ATGTATCGATACA
1 ATGTATCGATACA
689011 TGACCAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:689029 original size:34 final size:32
Alignment explanation
Indices: 688969--689031 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 32
688959 TAACTATTTA
688969 TATCGATACATACAAGATGTATCGATACAATG
1 TATCGATACATACAAGATGTATCGATACAATG
689001 TATCGATACATGACCAA-ATTGTATCGATACA
1 TATCGATACAT-A-CAAGA-TGTATCGATACA
689032 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 11 0.39
33 2 0.07
34 15 0.54
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (32 bp):
TATCGATACATACAAGATGTATCGATACAATG
Found at i:692109 original size:2 final size:2
Alignment explanation
Indices: 692102--692133 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
692092 CACATAAGAA
692102 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
692134 TAATGAGCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:697993 original size:20 final size:21
Alignment explanation
Indices: 697958--698000 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
697948 CAGATTATTT
697958 TTAAATTTATATTATTTTAAA
1 TTAAATTTATATTATTTTAAA
697979 TTAAATTTA-ATTATTTTAAA
1 TTAAATTTATATTATTTTAAA
697999 TT
1 TT
698001 TAGATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAAATTTATATTATTTTAAA
Found at i:698012 original size:36 final size:38
Alignment explanation
Indices: 697951--698023 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 38
697941 TTCAAATCAG
*
697951 ATTATTTTTAAATTTATATTATTTTA-AATTAAATTTA
1 ATTATTTTTAAATTTAGATTATTTTAGAATTAAATTTA
*
697988 ATTA-TTTTAAATTTAGA-TATTTTTAGATTTAAATTT
1 ATTATTTTTAAATTTAGATTA-TTTTAGAATTAAATTT
698024 TTTTAGATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 2 0.06
36 17 0.53
37 13 0.41
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (38 bp):
ATTATTTTTAAATTTAGATTATTTTAGAATTAAATTTA
Found at i:698017 original size:16 final size:16
Alignment explanation
Indices: 697983--698032 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
697973 TTTAAATTAA
* *
697983 ATTTAATTA-TTTTAA
1 ATTTAAATATTTTTAG
*
697998 ATTTAGATATTTTTAG
1 ATTTAAATATTTTTAG
*
698014 ATTTAAATTTTTTTAG
1 ATTTAAATATTTTTAG
698030 ATT
1 ATT
698033 CGAGTTATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 7 0.24
16 22 0.76
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTTAAATATTTTTAG
Found at i:698242 original size:18 final size:18
Alignment explanation
Indices: 698219--698257 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
698209 TACTAAAATT
698219 AAAATTT-TAAAAATAATA
1 AAAATTTATAAAAAT-ATA
*
698237 AAAATTTATATAAATATA
1 AAAATTTATAAAAATATA
698255 AAA
1 AAA
698258 TTATATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATTTATAAAAATATA
Found at i:698261 original size:16 final size:16
Alignment explanation
Indices: 698204--698265 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 16
698194 ATGTAATGAC
698204 AAAATTACTA-AAAT-T
1 AAAATTA-TATAAATAT
* *
698219 AAAATTTTAAAAATAAT
1 AAAATTATATAAAT-AT
698236 AAAAATTTATATAAATAT
1 -AAAA-TTATATAAATAT
698254 AAAATTATATAA
1 AAAATTATATAA
698266 TAATTGTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 2 0.05
15 10 0.26
16 8 0.21
17 5 0.13
18 6 0.15
19 8 0.21
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATTATATAAATAT
Found at i:700239 original size:15 final size:14
Alignment explanation
Indices: 700213--700259 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
700203 AGATTATTTC
700213 GAATTAAAATTTTTT
1 GAATT-AAATTTTTT
*
700228 GAA-TATATATTTTT
1 GAATTAAAT-TTTTT
700242 GAATTAAATTTTTT
1 GAATTAAATTTTTT
700256 -AATT
1 GAATT
700260 TAAAACTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 7 0.25
14 14 0.50
15 7 0.25
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
GAATTAAATTTTTT
Found at i:700527 original size:41 final size:40
Alignment explanation
Indices: 700429--700531 Score: 140
Period size: 38 Copynumber: 2.6 Consensus size: 40
700419 CCAACATGCG
*
700429 AAAAAGGAAGCAGACAAGTATCA-TTGAAGTTAACATTGATT
1 AAAAAGG-AGCAGACAAG-ATCATTTGAAGGTAACATTGATT
*
700470 --AAAGGAGCGGACAAGATCATTTGAAGGTAACATTGATT
1 AAAAAGGAGCAGACAAGATCATTTGAAGGTAACATTGATT
700508 AAAAAAGGAGCAGACAAGATCATT
1 -AAAAAGGAGCAGACAAGATCATT
700532 AAACTTAAGC
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
37 4 0.07
38 26 0.47
39 5 0.09
41 20 0.36
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.21
Consensus pattern (40 bp):
AAAAAGGAGCAGACAAGATCATTTGAAGGTAACATTGATT
Done.