Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1985
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: 37932
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:1435 original size:40 final size:40
Alignment explanation
Indices: 1373--1553 Score: 222
Period size: 40 Copynumber: 4.5 Consensus size: 40
1363 ACCCAAGTAT
* * *
1373 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCAGATATAGTC-ACTAGCACAAATGC
* * **
1412 CTTCGGGTCTTAACCCAGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCAGATATAGTCACTAGCACAAATGC
*
1452 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCAGATATAGTCACTAGCACAAATGC
* * * *
1492 CTTCGGGACTTAGCCCAGACATAGTAACTTGCAAAAATGC
1 CTTCGGGACTTAGCCCAGATATAGTCACTAGCACAAATGC
*
1532 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCAGATAT
1554 CATCCGAATA
Statistics
Matches: 121, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
39 10 0.08
40 110 0.91
41 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCAGATATAGTCACTAGCACAAATGC
Found at i:1509 original size:80 final size:80
Alignment explanation
Indices: 1373--1553 Score: 258
Period size: 80 Copynumber: 2.3 Consensus size: 80
1363 ACCCAAGTAT
* * * *
1373 CTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAACCCAGATATAGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGACTTAACCCAGACATAGT
* **
1437 CACTAGCATGAATGC
66 AACTAGCAAAAATGC
*
1452 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCCAGACATAG
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGCCTTCGGGACTTAACCCAGACATAG
*
1516 TAACTTGCAAAAATGC
65 TAACTAGCAAAAATGC
1532 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
1554 CATCCGAATA
Statistics
Matches: 91, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
79 12 0.13
80 78 0.86
81 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGACTTAACCCAGACATAGT
AACTAGCAAAAATGC
Found at i:11107 original size:21 final size:20
Alignment explanation
Indices: 11083--11128 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
11073 CGAAATGCAA
11083 TCAACCTAACA-TGAATTAAAT
1 TCAACCTAA-ATTG-ATTAAAT
*
11104 TCAAGCTAAATTGATTAAAT
1 TCAACCTAAATTGATTAAAT
11124 T-AACC
1 TCAACC
11129 ATTCCAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (20 bp):
TCAACCTAAATTGATTAAAT
Found at i:11986 original size:12 final size:12
Alignment explanation
Indices: 11969--12004 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
11959 GAAAATTAAT
11969 TAAAATTTATTA
1 TAAAATTTATTA
11981 TAAAATTTATTA
1 TAAAATTTATTA
*
11993 TAAAATTAATTA
1 TAAAATTTATTA
12005 AAATTCATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TAAAATTTATTA
Found at i:11986 original size:22 final size:22
Alignment explanation
Indices: 11950--12015 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
11940 TAATTCTGTC
* *
11950 AAAAATAATGAAAATTAATTA-
1 AAAATTAATTAAAATTAATTAT
* * *
11971 AAATTTATTATAAAATTTATTAT
1 AAAATTAAT-TAAAATTAATTAT
*
11994 AAAATTAATTAAAATTCATTAT
1 AAAATTAATTAAAATTAATTAT
12016 TTTAATAATT
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 6 0.17
22 22 0.63
23 7 0.20
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
AAAATTAATTAAAATTAATTAT
Found at i:23862 original size:82 final size:81
Alignment explanation
Indices: 23746--23901 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
23736 AAATTGTAAA
* * * *
23746 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
23810 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
23827 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
23892 TGCGAGTTGA
65 TGCGAATTGA
23902 TTGTATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:23869 original size:55 final size:52
Alignment explanation
Indices: 23745--23898 Score: 175
Period size: 55 Copynumber: 2.9 Consensus size: 52
23735 TAAATTGTAA
* *
23745 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * *
23798 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* * *
23853 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT
23899 TGATTGTATA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
53 3 0.03
54 36 0.42
55 46 0.53
56 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:23903 original size:27 final size:27
Alignment explanation
Indices: 23746--23901 Score: 163
Period size: 27 Copynumber: 5.7 Consensus size: 27
23736 AAATTGTAAA
*
23746 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
23773 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
23800 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
23827 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
23855 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
23882 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
23902 TTGTATAGCA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
27 83 0.77
28 25 0.23
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:23912 original size:27 final size:27
Alignment explanation
Indices: 23738--23922 Score: 101
Period size: 27 Copynumber: 6.8 Consensus size: 27
23728 GCGGGATTAA
*
23738 ATTGTAAAGCACTAAGTGTGCG-ATTCG
1 ATTGTATAGCACTAAGTGTGCGAATT-G
*
23765 ACTATGT-T-GCACTAAGTGTGCGAAATG
1 A-T-TGTATAGCACTAAGTGTGCGAATTG
23792 AATATG-AT-GCACTAAGTGTGCGAATTG
1 -AT-TGTATAGCACTAAGTGTGCGAATTG
*** *** * *
23819 ACCATGCGGCACTAAGTGTGCGAGTCTA
1 ATTGTATAGCACTAAGTGTGCGAAT-TG
* * * *
23847 ACTATGTAGCACTAAGTGTGCGATTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*** * *
23874 ATTACGTGGCACTAAGTGTGCGAGTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*
23901 ATTGTATAGCACTGAGTGTGCG
1 ATTGTATAGCACTAAGTGTGCG
23923 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 96 0.76
28 26 0.21
29 3 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
ATTGTATAGCACTAAGTGTGCGAATTG
Found at i:23913 original size:82 final size:81
Alignment explanation
Indices: 23738--23922 Score: 201
Period size: 82 Copynumber: 2.3 Consensus size: 81
23728 GCGGGATTAA
* * * *
23738 ATTGTAAAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCA
1 ATTGTAAAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
23803 CTAAGTGTGCGAATTG
66 CTAAGTGTGCGAATTG
*** *** ** *
23819 ACCATGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGG
1 ATTGTAAAGCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-G
*
23883 CACTAAGTGTGCGAGTTG
64 CACTAAGTGTGCGAATTG
* *
23901 ATTGTATAGCACTGAGTGTGCG
1 ATTGTAAAGCACTAAGTGTGCG
23923 GGCTCAATAT
Statistics
Matches: 81, Mismatches: 21, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
81 20 0.25
82 61 0.75
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
ATTGTAAAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
CTAAGTGTGCGAATTG
Found at i:26960 original size:40 final size:40
Alignment explanation
Indices: 26882--27102 Score: 329
Period size: 40 Copynumber: 5.5 Consensus size: 40
26872 ACCCAAGTAT
* *
26882 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
26921 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
26961 CTTCGGGACTTAGCCCGGATATAGTCACGAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
27001 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
27041 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
27081 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
27103 CATCCGAATA
Statistics
Matches: 168, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
39 11 0.07
40 156 0.93
41 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:31547 original size:80 final size:80
Alignment explanation
Indices: 31436--31616 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
31426 CTCATTCAAT
* * *
31436 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
31499 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
31515 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
31579 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
31596 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
31617 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:31576 original size:40 final size:40
Alignment explanation
Indices: 31433--31616 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
31423 TAACTCATTC
* *
31433 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
31473 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
31513 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
31553 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
31594 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
31617 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:37204 original size:39 final size:40
Alignment explanation
Indices: 37128--37305 Score: 267
Period size: 40 Copynumber: 4.5 Consensus size: 40
37118 ACCCAAGTAT
* *
37128 CTTC-GGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
*
37166 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCAC-AATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
37205 CTTCGGGACTTAGCCCGG-TATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
37244 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
37284 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
37306 CCGAATAATC
Statistics
Matches: 129, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
38 19 0.15
39 51 0.40
40 58 0.45
41 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:37265 original size:78 final size:79
Alignment explanation
Indices: 37156--37301 Score: 258
Period size: 78 Copynumber: 1.9 Consensus size: 79
37146 ATAGCAACTC
* *
37156 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCAC-AATGCCTTCGGGACTTAGCC
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCC
37220 CGGTATAGTCACTA
66 CGGTATAGTCACTA
*
37234 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCC
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCC
37299 CGG
66 CGG
37302 ATATCCGAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
78 41 0.64
79 23 0.36
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCC
CGGTATAGTCACTA
Done.