Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold687
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: 10101
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Warning! 6 characters in sequence are not A, C, G, or T
Found at i:5555 original size:114 final size:114
Alignment explanation
Indices: 5350--6219 Score: 1391
Period size: 114 Copynumber: 7.6 Consensus size: 114
5340 CGCAACCGAT
* *
5350 TGAGTATTAGCAGCGTTTCTATAAAAACGCCGCAAAAACT-AAACCCAGACGACGTCGTTTGGAG
1 TGAGAATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGAG
*
5414 AAACTTCGGTGACATTAGTGGCGTTTTTCGAATAGCGCCGCTAATAATA
66 ACACTTCGGTGACATTAGTGGCGTTTTTCGAATAGCGCCGCTAATAATA
* * * *
5463 TGAGAATTAGCAGCGTTTCTGTAAAAATGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGGG
1 TGAGAATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGAG
* *
5528 ACACTTCGGTGACATTAGTGGCATTTTTTGAATAGCGCCGCTAATAATA
66 ACACTTCGGTGACATTAGTGGCGTTTTTCGAATAGCGCCGCTAATAATA
* *
5577 TGAGAATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAACCCCAGACGACGTCGTCTGGAG
1 TGAGAATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGAG
* *
5642 ACACTTCGGGGCCATTAGTGGCGTTTTTCGAATAGCGCCGCTAATAATA
66 ACACTTCGGTGACATTAGTGGCGTTTTTCGAATAGCGCCGCTAATAATA
* *
5691 TGAGAATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAACCCCAGACGACGTCGTCTGGAG
1 TGAGAATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGAG
* *
5756 ACACTTCGGGGCCATTAGTGGCGTTTTTCGAATAGCGCCGCTAATAATA
66 ACACTTCGGTGACATTAGTGGCGTTTTTCGAATAGCGCCGCTAATAATA
* *
5805 TGAGAATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAACCCCAGACGACGTCGTCTGGAG
1 TGAGAATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGAG
* *
5870 ACACTTCGGTGACATTAGTGGCGTTTTTTGAATAGCGCCGCTAATAATG
66 ACACTTCGGTGACATTAGTGGCGTTTTTCGAATAGCGCCGCTAATAATA
* * * * *
5919 TGAGTATTAGCGGCGTTTTTATAAAAATGCCACAAAAACTAAACCCCAGACGACGTCGTTTGGAG
1 TGAGAATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGAG
* *
5984 ACACTTCGGTGACTTTAGTGGCGTTTTTCTAATAGCGCCGCTAATAATA
66 ACACTTCGGTGACATTAGTGGCGTTTTTCGAATAGCGCCGCTAATAATA
* * * * *
6033 TGAGTATTAGCGGCGTTTCTACAAAAACGCCGGAAAAACTAAAACCCAAACGACTTCGTTTGGAG
1 TGAGAATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGAG
* *
6098 ACACTTCAGTGACATTAGTGGCGTTTTTCGAGTAGCGCCGCTAATAATA
66 ACACTTCGGTGACATTAGTGGCGTTTTTCGAATAGCGCCGCTAATAATA
* *
6147 TGAGTATTAGCGGCGTTTTGTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGA
1 TGAGAATTAGCGGCG-TTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGA
6212 GACACTTC
65 GACACTTC
6220 NNNNNNACTA
Statistics
Matches: 708, Mismatches: 47, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
113 37 0.05
114 619 0.87
115 52 0.07
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (114 bp):
TGAGAATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGAG
ACACTTCGGTGACATTAGTGGCGTTTTTCGAATAGCGCCGCTAATAATA
Found at i:6691 original size:14 final size:15
Alignment explanation
Indices: 6665--6695 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
6655 ACTATATATA
6665 TATGGATTTAGGGAT
1 TATGGATTTAGGGAT
6680 TATGGA-TTAGGGAT
1 TATGGATTTAGGGAT
6694 TA
1 TA
6696 AGGGTTGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (15 bp):
TATGGATTTAGGGAT
Found at i:6778 original size:15 final size:16
Alignment explanation
Indices: 6758--6796 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
6748 ACGTTAGTGG
6758 TTAAGAG-TTAGGGAT
1 TTAAGAGTTTAGGGAT
*
6773 TTAAGAGGTTTAGGGTT
1 TTAAGA-GTTTAGGGAT
6790 TTAAGAG
1 TTAAGAG
6797 GGTCGGGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 2 0.10
17 13 0.62
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (16 bp):
TTAAGAGTTTAGGGAT
Found at i:6787 original size:17 final size:17
Alignment explanation
Indices: 6765--6797 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6755 TGGTTAAGAG
6765 TTAGGGATTTAAGAGGT
1 TTAGGGATTTAAGAGGT
*
6782 TTAGGGTTTTAAGAGG
1 TTAGGGATTTAAGAGG
6798 GTCGGGTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.36, T:0.36
Consensus pattern (17 bp):
TTAGGGATTTAAGAGGT
Found at i:7167 original size:20 final size:20
Alignment explanation
Indices: 7138--7190 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
7128 AAATAAAATT
*
7138 AAAATTAAAATTAAA-ATACA
1 AAAATCAAAATTAAATATA-A
*
7158 AAAATCAAAATGAAATATAA
1 AAAATCAAAATTAAATATAA
*
7178 AAACTCTAAAATT
1 AAAATC-AAAATT
7191 TTTAATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.66, C:0.08, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAATCAAAATTAAATATAA
Found at i:7646 original size:76 final size:79
Alignment explanation
Indices: 7546--7752 Score: 219
Period size: 84 Copynumber: 2.6 Consensus size: 79
7536 GCATTACGCC
* * ** * *
7546 GAAAATGCCGCAAA-TTGTCGGGGTTTTTTTAATGAAACGGTGTCG-TT-T-ACATTAAGGGCAT
1 GAAAATGCCGCAAAGTTTTC-GGGTTTTTTAAACCAAACGGTGTCGTTTCTGACATTAACGACAT
7607 TAGTGGCGCTATGGT
65 TAGTGGCGCTATGGT
7622 -AAAAGTGCCGCAAAGTTTTCGGGTTTTTTAAACCAAACGGTGTCGTTTTCCCTGGCACATTAAC
1 GAAAA-TGCCGCAAAGTTTTCGGGTTTTTTAAACCAAACGGTGTCG-TTT--CT-G-ACATTAAC
7686 GACATTAGTGGCGCTATGGT
60 GACATTAGTGGCGCTATGGT
* * * *
7706 GAAAACGCCGCAAAG-TTTCGGGTTTTTTAAACAAAACGATGCCGTTT
1 GAAAATGCCGCAAAGTTTTCGGGTTTTTTAAACCAAACGGTGTCGTTT
7753 TGCCTTTACG
Statistics
Matches: 110, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
75 4 0.04
76 31 0.28
77 4 0.04
78 2 0.02
81 1 0.01
82 3 0.03
83 26 0.24
84 35 0.32
85 4 0.04
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (79 bp):
GAAAATGCCGCAAAGTTTTCGGGTTTTTTAAACCAAACGGTGTCGTTTCTGACATTAACGACATT
AGTGGCGCTATGGT
Found at i:7771 original size:160 final size:161
Alignment explanation
Indices: 7484--7799 Score: 343
Period size: 160 Copynumber: 2.0 Consensus size: 161
7474 AATTTTATCA
* * * * *
7484 TTTTTGTAAACAAAGCGGTGTCGTTTTGCCTGGCATATTAATGGCATTAGTGGCATTACGCCGAA
1 TTTTTGTAAACAAAGCGGTGTCGTTTTCCCTGGCACATTAACGACATTAGTGGCACTACGCCGAA
* * ** * * * *
7549 AATGCCGCAAATTGTCGGGGTTTTTTTAATGAAACGGTGTCGTTTACATTAAGGGCATTAGTGGC
66 AACGCCGCAAATTGTCGGGGTTTTTTAAACAAAACGATGCCGTTTACATTAACGGCATTAGTGGA
**
7614 GCTATGGTAAAAGTGCCGCAAAGTTTTCGGG
131 GCTATGGTAAAAACGCCGCAAAGTTTTCGGG
* * **
7645 TTTTT-TAAACCAAA-CGGTGTCGTTTTCCCTGGCACATTAACGACATTAGTGGCGCTATGGTGA
1 TTTTTGTAAA-CAAAGCGGTGTCGTTTTCCCTGGCACATTAACGACATTAGTGGCACTACGCCGA
* * * *
7708 AAACGCCGCAAAGTT-TC-GGGTTTTTTAAACAAAACGATGCCGTTTTGCCTTTACGGTATTAGT
65 AAACGCCGCAAA-TTGTCGGGGTTTTTTAAACAAAACGATGCCG-TTTACATTAACGGCATTAGT
* * *
7771 GGAGCTGTGTTAAAAACGCCGCAACGTTT
128 GGAGCTATGGTAAAAACGCCGCAAAGTTT
7800 CATTCTGGTT
Statistics
Matches: 126, Mismatches: 26, Indels: 7
0.79 0.16 0.04
Matches are distributed among these distances:
159 20 0.16
160 95 0.75
161 11 0.09
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (161 bp):
TTTTTGTAAACAAAGCGGTGTCGTTTTCCCTGGCACATTAACGACATTAGTGGCACTACGCCGAA
AACGCCGCAAATTGTCGGGGTTTTTTAAACAAAACGATGCCGTTTACATTAACGGCATTAGTGGA
GCTATGGTAAAAACGCCGCAAAGTTTTCGGG
Found at i:9456 original size:16 final size:16
Alignment explanation
Indices: 9435--9473 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
9425 TAAAGGCAAA
*
9435 TTACATATTAAATAAC
1 TTACATAATAAATAAC
*
9451 TTACATAATACATAAC
1 TTACATAATAAATAAC
9467 TTACATA
1 TTACATA
9474 GCTTAACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (16 bp):
TTACATAATAAATAAC
Done.