Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold9668.1
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: 4295
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Found at i:1477 original size:239 final size:239
Alignment explanation
Indices: 1058--1535 Score: 938
Period size: 239 Copynumber: 2.0 Consensus size: 239
1048 TGTCCCGGGT
1058 GGTAATCAAAGACAAGCTCGTAATCTTTCAACAACTCAAGCCAACGTCTTTGTCGCAGATTCAAG
1 GGTAATCAAAGACAAGCTCGTAATCTTTCAACAACTCAAGCCAACGTCTTTGTCGCAGATTCAAG
1123 TCTCGTTGAGTCATCAAATATTTGAGACTTTTGTGATCCGAAAATACATGGCACTTCTCACCAAA
66 TCTCGTTGAGTCATCAAATATTTGAGACTTTTGTGATCCGAAAATACATGGCACTTCTCACCAAA
1188 CAGATAATGTCGCCATATTTTTAAAGCAAACACGATGGCAGCTAGTTCGAGATCATGGGTCGGAT
131 CAGATAATGTCGCCATATTTTTAAAGCAAACACGATGGCAGCTAGTTCGAGATCATGGGTCGGAT
*
1253 AATTCCTCTCGTGTGGCTTCAATTGTCTCGACGCATAGGCCACG
196 AATTCCTCTCGTGTGGCTTCAATTGCCTCGACGCATAGGCCACG
1297 GGTAATCAAAGACAAGCTCGTAATCTTTCAACAACTCAAGCCAACGTCTTTGTCGCAGATTCAAG
1 GGTAATCAAAGACAAGCTCGTAATCTTTCAACAACTCAAGCCAACGTCTTTGTCGCAGATTCAAG
1362 TCTCGTTGAGTCATCAAATATTTGAGACTTTTGTGATCCGAAAATACATGGCACTTCTCACCAAA
66 TCTCGTTGAGTCATCAAATATTTGAGACTTTTGTGATCCGAAAATACATGGCACTTCTCACCAAA
1427 CAGATAATGTCGCCATATTTTTAAAGCAAACACGATGGCAGCTAGTTCGAGATCATGGGTCGGAT
131 CAGATAATGTCGCCATATTTTTAAAGCAAACACGATGGCAGCTAGTTCGAGATCATGGGTCGGAT
*
1492 AATTTCTCTCGTGTGGCTTCAATTGCCTCGACGCATAGGCCACG
196 AATTCCTCTCGTGTGGCTTCAATTGCCTCGACGCATAGGCCACG
1536 ACTCGACCTT
Statistics
Matches: 237, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
239 237 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (239 bp):
GGTAATCAAAGACAAGCTCGTAATCTTTCAACAACTCAAGCCAACGTCTTTGTCGCAGATTCAAG
TCTCGTTGAGTCATCAAATATTTGAGACTTTTGTGATCCGAAAATACATGGCACTTCTCACCAAA
CAGATAATGTCGCCATATTTTTAAAGCAAACACGATGGCAGCTAGTTCGAGATCATGGGTCGGAT
AATTCCTCTCGTGTGGCTTCAATTGCCTCGACGCATAGGCCACG
Found at i:2476 original size:49 final size:49
Alignment explanation
Indices: 2404--2501 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
2394 GGTCGAGCGA
2404 AACCTCTATCCGTCAGTTCTTGCAACTGAGCTTTCAACTCCTTTAACTC
1 AACCTCTATCCGTCAGTTCTTGCAACTGAGCTTTCAACTCCTTTAACTC
*
2453 AACCTCTATCCGTCAGTTCTTGCAACTGAGCTTTCAACTCTTTTAACTC
1 AACCTCTATCCGTCAGTTCTTGCAACTGAGCTTTCAACTCCTTTAACTC
2502 GGTTGGTGCC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.22, C:0.32, G:0.10, T:0.36
Consensus pattern (49 bp):
AACCTCTATCCGTCAGTTCTTGCAACTGAGCTTTCAACTCCTTTAACTC
Found at i:4208 original size:200 final size:200
Alignment explanation
Indices: 3865--4264 Score: 773
Period size: 200 Copynumber: 2.0 Consensus size: 200
3855 AAATTCCTTC
* *
3865 CGTTTTTGATCAGCAAATCTCTGACTGATATACTTTTTCCGAAACTCAGTTTGGAAAAACTCCCA
1 CGTTTTTGATCAACAAATCTCTGACTGATATACTTTTTCCCAAACTCAGTTTGGAAAAACTCCCA
3930 AGTTACTTGCTCTCGGGGCACAATAGAAGTCAGAGTACTCCACCAATAGTAGGCAGAATCACGTA
66 AGTTACTTGCTCTCGGGGCACAATAGAAGTCAGAGTACTCCACCAATAGTAGGCAGAATCACGTA
*
3995 GCAAGGAGATAGCACACTTTAGGCATTCATCGGGTGTACAAGATAGCTCATCGAGTACCCGGATA
131 GCAAGGAGATAGCACACTTTAGGCATTCATCGGGTGTACAAGATAGCTCATCGAGTACCCGAATA
4060 GTGTT
196 GTGTT
4065 CGTTTTTGATCAACAAATCTCTGACTGATATACTTTTTCCCAAACTCAGTTTGGAAAAACTCCCA
1 CGTTTTTGATCAACAAATCTCTGACTGATATACTTTTTCCCAAACTCAGTTTGGAAAAACTCCCA
4130 AGTTACTTGCTCTCGGGGCACAATAGAAGTCAGAGTACTCCACCAATAGTAGGCAGAATCACGTA
66 AGTTACTTGCTCTCGGGGCACAATAGAAGTCAGAGTACTCCACCAATAGTAGGCAGAATCACGTA
4195 GCAAGGAGATAGCACACTTTAGGCATTCATCGGGTGTACAAGATAGCTCATCGAGTACCCGAATA
131 GCAAGGAGATAGCACACTTTAGGCATTCATCGGGTGTACAAGATAGCTCATCGAGTACCCGAATA
4260 GTGTT
196 GTGTT
4265 GTCCAGCCAA
Statistics
Matches: 197, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
200 197 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (200 bp):
CGTTTTTGATCAACAAATCTCTGACTGATATACTTTTTCCCAAACTCAGTTTGGAAAAACTCCCA
AGTTACTTGCTCTCGGGGCACAATAGAAGTCAGAGTACTCCACCAATAGTAGGCAGAATCACGTA
GCAAGGAGATAGCACACTTTAGGCATTCATCGGGTGTACAAGATAGCTCATCGAGTACCCGAATA
GTGTT
Done.