Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3545
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: 30889
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Found at i:1175 original size:65 final size:63
Alignment explanation
Indices: 1066--1194 Score: 222
Period size: 65 Copynumber: 2.0 Consensus size: 63
1056 ACCCTAGGGT
1066 TAAGGTGACCTAAATGCATGTTTGATGTTACTATTTACTACATGCCATGTTATTATTATCTGA
1 TAAGGTGACCTAAATGCATGTTTGATGTTACTATTTACTACATGCCATGTTATTATTATCTGA
* *
1129 TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTGCATGCCATGTTATTATTATCTGA
1 TAAGG-TGACCTAAATGCATGTTTGA-TGTTACTATTTACTACATGCCATGTTATTATTATCTGA
1194 T
1 T
1195 GTATGGACTG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
63 5 0.08
64 19 0.31
65 38 0.61
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (63 bp):
TAAGGTGACCTAAATGCATGTTTGATGTTACTATTTACTACATGCCATGTTATTATTATCTGA
Found at i:5324 original size:40 final size:40
Alignment explanation
Indices: 5261--5406 Score: 217
Period size: 39 Copynumber: 3.6 Consensus size: 40
5251 CTCGTTCAAT
* *
5261 TGCCTTC-GGACATAGCCCGGATTTAACAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAA
5300 TGCCTTCGGGAC-TACACCCGGATTTAACAACTC-CACGAA
1 TGCCTTCGGGACTTA-ACCCGGATTTAACAACTCGCACGAA
*
5339 TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAA
5379 TGCCTTCGGGACTGTAAACCCGGATTTA
1 TGCCTTCGGGACT-T-AACCCGGATTTA
5407 GTATCTCGTC
Statistics
Matches: 99, Mismatches: 2, Indels: 9
0.90 0.02 0.08
Matches are distributed among these distances:
39 44 0.44
40 42 0.42
41 1 0.01
42 12 0.12
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAA
Found at i:13304 original size:40 final size:40
Alignment explanation
Indices: 13206--13468 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
13196 TCCTCGTTCA
* * * * *
13206 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
13245 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
13285 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
13325 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
13365 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
13405 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
13445 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
13469 CAGCATTCAA
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 37 0.19
40 153 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:21237 original size:40 final size:40
Alignment explanation
Indices: 21139--21401 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
21129 TCCTCGTTCA
* * * * *
21139 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
21178 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
21218 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
21258 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
21298 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
21338 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
21378 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
21402 CAGCATTCAA
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 37 0.19
40 153 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:29025 original size:78 final size:81
Alignment explanation
Indices: 28891--29073 Score: 223
Period size: 78 Copynumber: 2.3 Consensus size: 81
28881 TGAATGATGT
* *
28891 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGCCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
*
28955 GTGCGAGATACTA-AT
66 GTGCGAGATACTATAA
* * * * **
28970 TCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 CCGGGCTAAGCCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATT
*
29032 TGTGCGAGTTACTATAA
65 TGTGCGAGATACTATAA
*
29049 CCGGGCTATGCCCCGAAGGCATTTG
1 CCGGGCTAAGCCCCGAAGGCATTTG
29074 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
77 1 0.01
78 49 0.55
79 25 0.28
80 14 0.16
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
CCGGGCTAAGCCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTATAA
Found at i:29035 original size:40 final size:40
Alignment explanation
Indices: 28890--29073 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
28880 TTGAATGATG
* * * *
28890 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
28930 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACT-AA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28969 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
29008 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
29049 -CCGGGCTATGCCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
29074 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 23 0.19
39 21 0.17
40 70 0.56
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:29091 original size:80 final size:77
Alignment explanation
Indices: 28943--29106 Score: 204
Period size: 79 Copynumber: 2.1 Consensus size: 77
28933 GGACTAAGAT
** **
28943 CCGAAGGCATTTGTGCGAGATACTAATTCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 CCGAAGGCATTTGTGCGAGATACTAAACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAA
*
29008 TCCGGGTTAAGTC
66 TCC-GGTTAAATC
* *
29021 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGCCCCGAAGGCATTTGAACGAG-TAGCT
1 CCGAAGGCATTTGTGCGAGATACTA-AACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-CT
* *
29085 ATATCCGGTTAAATT
63 AAATCCGGTTAAATC
29100 CCGAAGG
1 CCGAAGG
29107 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
78 24 0.32
79 25 0.34
80 25 0.34
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (77 bp):
CCGAAGGCATTTGTGCGAGATACTAAACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAA
TCCGGTTAAATC
Done.