Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold276
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: 36971
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:6635 original size:24 final size:24
Alignment explanation
Indices: 6603--6655 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
6593 ATTTTTAGTC
*
6603 GGCGCTGCCCCTTCAGCCGGAGCT
1 GGCGCTGCCCCTTCACCCGGAGCT
6627 GGCGCTGCCCCTTCACCCGGAGCT
1 GGCGCTGCCCCTTCACCCGGAGCT
6651 GGCGC
1 GGCGC
6656 ATTACTCTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.08, C:0.43, G:0.34, T:0.15
Consensus pattern (24 bp):
GGCGCTGCCCCTTCACCCGGAGCT
Found at i:9237 original size:46 final size:44
Alignment explanation
Indices: 9094--9237 Score: 123
Period size: 46 Copynumber: 3.1 Consensus size: 44
9084 CCCGCCCCTA
*
9094 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT
* * * *
9141 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAGCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCT
*
9187 AGTGAACTCAGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CT
9233 AGTGA
1 AGTGA
9238 CATGTCACTT
Statistics
Matches: 78, Mismatches: 11, Indels: 16
0.74 0.10 0.15
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 32 0.41
47 30 0.38
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCT
Found at i:10551 original size:16 final size:16
Alignment explanation
Indices: 10530--10572 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
10520 ATGTATCGGC
*
10530 AAAAGTCGAAATACTG
1 AAAAGTCGAAATACCG
* *
10546 AAAAGTCTAAATGCCG
1 AAAAGTCGAAATACCG
10562 AAAAGTCGAAA
1 AAAAGTCGAAA
10573 GTTCGGCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.51, C:0.14, G:0.19, T:0.16
Consensus pattern (16 bp):
AAAAGTCGAAATACCG
Found at i:18031 original size:39 final size:40
Alignment explanation
Indices: 17923--18147 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
17913 TTGAATGATG
* * * *
17923 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
17963 TCCGGACTAAGAT-CCAAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
18003 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
18042 TCCGGGTTAAGTCCCGATGGCATTTGTGCGACTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
18082 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
18123 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
18148 AACGAGGAGC
Statistics
Matches: 159, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
39 33 0.21
40 116 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:19744 original size:46 final size:46
Alignment explanation
Indices: 19677--19852 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
19667 TGTAACCCGC
* *
19677 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTTGTAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACGTTAGTAT
* * *
19723 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGT-T
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACG-TTAGTAT
* * * * *
19769 ACATCTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCA--TAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTAGTAT
*
19816 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
19853 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
45 4 0.04
46 67 0.62
47 35 0.32
48 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTAGTAT
Found at i:19796 original size:93 final size:93
Alignment explanation
Indices: 19684--19855 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
19674 CGCCCATAAG
* * *
19684 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTTGTATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
19748 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
19777 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
19842 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
19856 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:19871 original size:46 final size:44
Alignment explanation
Indices: 19728--19871 Score: 141
Period size: 46 Copynumber: 3.1 Consensus size: 44
19718 TGTATCCATA
19728 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT
* * * *
19775 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCT
19821 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CT
19867 AGTGA
1 AGTGA
19872 CATATCACTT
Statistics
Matches: 80, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
44 9 0.11
45 1 0.01
46 33 0.41
47 31 0.39
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCT
Found at i:21281 original size:29 final size:28
Alignment explanation
Indices: 21212--21297 Score: 102
Period size: 28 Copynumber: 3.0 Consensus size: 28
21202 GCGAGCATGA
*
21212 ATATGAATGTGACTGGGCCTAATGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
*
21240 ATA-GACAGGTGATTTGGGCCTAATGGGCC
1 ATATGA-ATGTGA-TTGGGCCTAATGGGCC
* * *
21269 ATATGAATATGATTGGACTTAATGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
21297 A
1 A
21298 GATACAGGTA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
27 2 0.04
28 23 0.47
29 22 0.45
30 2 0.04
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (28 bp):
ATATGAATGTGATTGGGCCTAATGGGCC
Found at i:29599 original size:27 final size:27
Alignment explanation
Indices: 29568--29745 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29558 TAAATTGTAC
29568 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
29595 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29621 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
29649 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
29677 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29704 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
29731 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
29746 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:29682 original size:82 final size:81
Alignment explanation
Indices: 29569--29724 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29559 AAATTGTACA
* *
29569 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
29633 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
29650 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
29715 TGCGAGTTGA
65 TGCGAATTGA
29725 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:29736 original size:82 final size:81
Alignment explanation
Indices: 29565--29745 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
29555 GATTAAATTG
* *
29565 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
29630 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
29646 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
29710 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
29728 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
29746 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.