Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1084
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: 23350
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:10059 original size:40 final size:40
Alignment explanation
Indices: 10014--10126 Score: 158
Period size: 40 Copynumber: 2.9 Consensus size: 40
10004 TTATTTGATG
10014 TGGAATTGTATCCGGGCTTAAAGACCTGCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCTGCAGGCTTCGTGC
*
10054 TGGAATTGTATCCGGGCTTAAAGACCTGCAGGCTTCGTGT
1 TGGAATTGTATCCGGGCTTAAAGACCTGCAGGCTTCGTGC
* * * *
10094 TAGAA-TGACATTCGGG-TTAAAAACCTGCAGGCT
1 TGGAATTG-TATCCGGGCTTAAAGACCTGCAGGCT
10127 ATGCTAGATA
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
39 18 0.27
40 49 0.73
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TGGAATTGTATCCGGGCTTAAAGACCTGCAGGCTTCGTGC
Found at i:15353 original size:28 final size:27
Alignment explanation
Indices: 15296--15447 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
15286 TAAATTGTGC
*
15296 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
15323 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
15351 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
15378 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
15406 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
15433 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
15448 GACTTAATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:15360 original size:55 final size:55
Alignment explanation
Indices: 15296--15447 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
15286 TAAATTGTGC
*
15296 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
15351 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
15406 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
15448 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:19666 original size:37 final size:39
Alignment explanation
Indices: 19625--19836 Score: 211
Period size: 40 Copynumber: 5.5 Consensus size: 39
19615 GCTACTCGTT
* * *
19625 CAAATG-CTTCGGACATAGCCCGG-TTTAGTAACTTGCA
1 CAAATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCA
*
19662 CAAATGCCTTCGGGGCTTAACCCGGATTTAGTAACTCGC-
1 CAAATGCCTTC-GGACTTAACCCGGATTTAGTAACTCGCA
19701 CACAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CA-AATGCCTTC-GGACTTAACCCGGATTTAGTAACTCGCA
* * * *
19742 CCAATGCCTTCGG-C-TAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
19779 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAACCCGGATTTAGTAAC-TCGCA
19820 CAAA-GCCTTCGGACTTA
1 CAAATGCCTTCGGACTTA
19837 GCCGGAATCA
Statistics
Matches: 149, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
37 38 0.26
38 5 0.03
39 19 0.13
40 78 0.52
41 9 0.06
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:19804 original size:77 final size:77
Alignment explanation
Indices: 19625--19844 Score: 218
Period size: 77 Copynumber: 2.9 Consensus size: 77
19615 GCTACTCGTT
* *
19625 CAAATG-CTTCGGACATAGCCCGG-TTTAGTAACTTGCACAAATGCCTTCGGGGCTTAACCCGGA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTC-GGGCTTAACCCGGA
*
19688 TTTAGTAACTCGC
65 ATTAGTAACTCGC
* * *
19701 CACAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTC-GGC-TAGCCCGG
1 CA-AATGCCTTC-GGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGCTTAACCCGG
*
19764 AATTAGTATCTCGC
64 AATTAGTAACTCGC
* * * * * * *
19778 ACAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGACTT-AGCCG
1 -CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAAC-TCGCACAAATGCCTTCGGGCTTAACCCG
19841 GAAT
63 GAAT
19845 CATTCGAATA
Statistics
Matches: 118, Mismatches: 17, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
76 5 0.04
77 53 0.45
78 25 0.21
79 12 0.10
80 23 0.19
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (77 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGCTTAACCCGGAA
TTAGTAACTCGC
Found at i:19822 original size:117 final size:116
Alignment explanation
Indices: 19627--19836 Score: 255
Period size: 117 Copynumber: 1.8 Consensus size: 116
19617 TACTCGTTCA
* * * *
19627 AATGCTTCGGACATAGCCCGGTTTAGTAACTTGCACAAATGCCTTCGGGGCTTAACCCGGATTTA
1 AATGCTTCGGACATAGCCCGGATTAGTAACTCGCACAAATGCCTTCGGAGCTTAACCCGGATATA
* *
19692 GTAACTCGCCACAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 GTAACTAGCCACAAAGCCTTC-GGACTTAACCCGGATTTAGTAACTCGCACC
* * **
19744 AATGCCTTCGG-C-TAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGATA
1 AATG-CTTCGGACATAGCCCGG-ATTAGTAACTCGCACAAATGCCTTCGGAGCTTAACCCGGATA
* *
19807 TGGTCACTTAG-CACAAAGCCTTCGGACTTA
64 TAGTAAC-TAGCCACAAAGCCTTCGGACTTA
19837 GCCGGAATCA
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
116 15 0.19
117 55 0.71
118 8 0.10
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (116 bp):
AATGCTTCGGACATAGCCCGGATTAGTAACTCGCACAAATGCCTTCGGAGCTTAACCCGGATATA
GTAACTAGCCACAAAGCCTTCGGACTTAACCCGGATTTAGTAACTCGCACC
Done.