Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: LOC111275081
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: 3426
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Found at i:2221 original size:54 final size:53
Alignment explanation
Indices: 2163--2525 Score: 244
Period size: 54 Copynumber: 6.7 Consensus size: 53
2153 GTGAGGGAAG
* * *
2163 CATTACTGGAAGTCAGATTCCTAGAAGGGAATCAACCCCAACTTCTGAAGGGAT
1 CATTACTGGAAGTCAAATTTCTAGAAGGGAATCAACCTC-ACTTCTGAAGGGAT
* * **
2217 CATTACTGG-AGATCAAATTTCTACAAGGGAATTAACCTTCACCCCTGATA-GGAT
1 CATTACTGGAAG-TCAAATTTCTAGAAGGGAATCAACC-TCACTTCTGA-AGGGAT
* * * **
2271 CATTACTGGAAATCAAACTTT-GAGAAAGGAATCAACCTTCACCCCTGATA-GGAT
1 CATTACTGGAAGTCAAA-TTTCTAGAAGGGAATCAACC-TCACTTCTGA-AGGGAT
* * ** *
2325 CATTACTGGAAATCAAATTTCTAGAAGGGAATCAAGCTTTGCTTCT--AGTGGCGT
1 CATTACTGGAAGTCAAATTTCTAGAAGGGAATCAA-CCTCACTTCTGAAG-GG-AT
* * *
2379 CATTACTGG-AGATCAAATTTCTAGAAGGGAATCAACTTCTGCTTCTGATGGGAT
1 CATTACTGGAAG-TCAAATTTCTAGAAGGGAATCAACCTC-ACTTCTGAAGGGAT
* * *
2433 CATTACTGGAAACGT--AATTACTAGAAGGGAATCAA-CTGCCATTTCTGATGGGAT
1 CATTACTGG-AA-GTCAAATTTCTAGAAGGGAATCAACCT--CACTTCTGAAGGGAT
* * * * *
2487 CGTTTCTAGAAATCAACTTTCTAGAAGGGAAAT-AACCTC
1 CATTACTGGAAGTCAAATTTCTAGAAGGG-AATCAACCTC
2526 TGCTAATGAT
Statistics
Matches: 252, Mismatches: 34, Indels: 47
0.76 0.10 0.14
Matches are distributed among these distances:
51 1 0.00
52 1 0.00
53 15 0.06
54 216 0.86
55 15 0.06
56 3 0.01
57 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (53 bp):
CATTACTGGAAGTCAAATTTCTAGAAGGGAATCAACCTCACTTCTGAAGGGAT
Found at i:2382 original size:108 final size:108
Alignment explanation
Indices: 2213--2468 Score: 270
Period size: 108 Copynumber: 2.4 Consensus size: 108
2203 ACTTCTGAAG
* * *
2213 GGATCATTACTGGAGATCAAATTTCTACAAGGGAATTAACCTTCACCCCTGATAGGATCATTACT
1 GGATCATTACTGGAAATCAAATTTCTAGAAGGGAATCAACCTTCACCCCTGATAGGATCATTACT
2278 GGAAATCAAACTTT-GAGAAAGGAATCAACCTTC-ACCCCTGATA
66 GGAAATCAAA-TTTCGAGAAAGGAATCAA-CTTCTACCCCTGATA
* ** ** *
2321 GGATCATTACTGGAAATCAAATTTCTAGAAGGGAATCAAGCTTTGCTTCT-AGT-GGCGTCATTA
1 GGATCATTACTGGAAATCAAATTTCTAGAAGGGAATCAACCTTCACCCCTGA-TAGG-ATCATTA
* * * * ** *
2384 CTGGAGATCAAATTTCTAGAAGGGAATCAACTTCTGCTTCTGATG
64 CTGGAAATCAAATTTCGAGAAAGGAATCAACTTCTACCCCTGATA
* *
2429 GGATCATTACTGGAAA-CGTAATTACTAGAAGGGAATCAAC
1 GGATCATTACTGGAAATC-AAATTTCTAGAAGGGAATCAAC
2469 TGCCATTTCT
Statistics
Matches: 124, Mismatches: 19, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
107 11 0.09
108 113 0.91
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (108 bp):
GGATCATTACTGGAAATCAAATTTCTAGAAGGGAATCAACCTTCACCCCTGATAGGATCATTACT
GGAAATCAAATTTCGAGAAAGGAATCAACTTCTACCCCTGATA
Found at i:2466 original size:162 final size:162
Alignment explanation
Indices: 2216--2517 Score: 371
Period size: 162 Copynumber: 1.9 Consensus size: 162
2206 TCTGAAGGGA
*
2216 TCATTACTGGAGATCAAATTTCTACAAGGGAATTAACCTTCACCCCTGATAGGATCATTACTGGA
1 TCATTACTGGAGATCAAATTTCTACAAGGGAATCAACCTTCACCCCTGATAGGATCATTACTGGA
* *
2281 AATCAAACTTTGAGAAAGGAATCAACCT-TCACCCCTGATAGGATCATTACTGGAAATCAAATTT
66 AATCAAACTTTGAGAAAGGAATCAA-CTGCCACCCCTGATAGGATCATTACTAGAAATCAAATTT
2345 CTAGAAGGGAATCAAGCTTTGCTTCTAGTGGCG
130 CTAGAAGGGAATCAAGCTTTGCTTCTAGTGGCG
* * ** *
2378 TCATTACTGGAGATCAAATTTCTAGAAGGGAATCAA-CTTCTGCTTCTGATGGGATCATTACTGG
1 TCATTACTGGAGATCAAATTTCTACAAGGGAATCAACCTTC-ACCCCTGATAGGATCATTACTGG
* * *** * * * *
2442 AAA-CGTAA-TTACT-AGAAGGGAATCAACTGCCATTTCTGATGGGATCGTTTCTAGAAATCAAC
65 AAATC-AAACTT--TGAGAAAGGAATCAACTGCCACCCCTGATAGGATCATTACTAGAAATCAAA
2504 TTTCTAGAAGGGAA
127 TTTCTAGAAGGGAA
2518 ATAACCTCTG
Statistics
Matches: 118, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
161 9 0.08
162 108 0.92
163 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (162 bp):
TCATTACTGGAGATCAAATTTCTACAAGGGAATCAACCTTCACCCCTGATAGGATCATTACTGGA
AATCAAACTTTGAGAAAGGAATCAACTGCCACCCCTGATAGGATCATTACTAGAAATCAAATTTC
TAGAAGGGAATCAAGCTTTGCTTCTAGTGGCG
Done.