Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012228.1 Corchorus olitorius cultivar O-4 contig12261, whole genome shotgun sequence
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: 6488
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Found at i:1236 original size:21 final size:21
Alignment explanation
Indices: 1210--1365 Score: 219
Period size: 21 Copynumber: 7.4 Consensus size: 21
1200 TGCTAGAAGT
1210 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
1231 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
1252 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
1273 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
1294 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
1315 TCATTGGAGAAGGTTCCAAGA
1 TCATTGGAGAAGGTTCCAAGC
*
1336 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
1357 TCATCGGAG
1 TCATTGGAG
1366 TTGCCTAAGA
Statistics
Matches: 129, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
20 2 0.02
21 127 0.98
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:4977 original size:156 final size:156
Alignment explanation
Indices: 4710--6488 Score: 2747
Period size: 156 Copynumber: 11.4 Consensus size: 156
4700 AGATTCGTAT
* * * *
4710 CATTGTGGTTTGTCAAATCGAAGACGA--TTCAAAACCGAACTAATAGACCCCGAATGGTCCAAA
1 CATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAA
*
4773 ATAACAAGTGTTCAAAATGAGCAAAGAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGT
66 ATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGT
*
4838 TAGTCCATAAACAATGGAAAGAAAAG
131 TAGGCCATAAACAATGGAAAGAAAAG
* * * *
4864 CATTGTTGTTTGCCAAACCGAAGACGATTTTTAAAACCTAACTAATGGGCCCCGAATGGCCCAAA
1 CATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAA
* * * * *
4929 ATAACAAGTGTTCAAAATGAGTTAAGAACTTTACAATGGACTAATCTTACCAAAGTGATCATAGT
66 ATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGT
4994 TAGGCCATAAACAATGGAAAGAAAAG
131 TAGGCCATAAACAATGGAAAGAAAAG
*
5020 CATTATGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCC-AA
1 CATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAA
* * **
5084 ATAACAAATGTTCAAATTGAGCTAAGAACTTCACCTTGGACTAGTCTTACCAAAATGATTATAG-
66 ATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGT
* **
5148 TATGAGAT-AACAAATGGAAAGAAAAG
131 TAGGCCATAAAC-AATGGAAAGAAAAG
*
5174 CATTGTTGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAA
1 CATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCC-AA
* *
5239 AATAACAAGTGTTTTAAAATAGAGCTAAAAACTTACACAATGGACTAGTCTTACCAAAATAGATT
65 AATAACAAGTG-TTCAAAAT-GAGCTAAGAACTT-CACAATGGACTAGTCTTACCAAAAT-GATT
*
5304 ATAGTTAGGCCATAAACAATGGAACG-AAAG
126 ATAGTTAGGCCATAAACAATGGAAAGAAAAG
* *
5334 CATTATGGTTTGCCAAATCGAAGACGATTTTTAAAACCG-ACTAATGGGCCCCGAATGGTACAAA
1 CATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAA
* *
5398 ATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACAAGCCTTACCAAAATGATTATAGT
66 ATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGT
5463 TAGGCCATAAACAATGGAAAGAAAAG
131 TAGGCCATAAACAATGGAAAGAAAAG
*
5489 CATTGTTGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAA
1 CATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAA
* * *
5554 ATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTAACAAAAATGATTATAGT
66 ATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGT
5619 TAGGCCATAAACAATGGAAAGAAAAG
131 TAGGCCATAAACAATGGAAAGAAAAG
* **
5645 CAATGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCAAAATGGTCCAAA
1 CATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAA
* * *
5710 ATAACAAGTGTTCAAAATGAGTTAAAAACATCACAATGGACTAGTCTTACCAAAATGATTATAGT
66 ATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGT
5775 TAGGCCATAAACAATGGAAAGAAAAG
131 TAGGCCATAAACAATGGAAAGAAAAG
*
5801 CATTGTTGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAA
1 CATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAA
* * *
5866 ATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTACTCTAACCAAAATGATTATAGT
66 ATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGT
5931 TAGGCCATAAACAATGGAAAGAAAAG
131 TAGGCCATAAACAATGGAAAGAAAAG
* * * *
5957 CATTGTGGTTTGCCAAATCGAAGGCGA--TTCAAAACCGAACT-ATGGACCCCGAATGGCCCAAA
1 CATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAA
* * *
6019 ATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTAACAAAAATGATTATAGT
66 ATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGT
6084 TAGGCCATAAACAATGGAAAGAAAAG
131 TAGGCCATAAACAATGGAAAGAAAAG
* * * * *
6110 CATTGTGGTTTGCCAAATCGAAGACGA--TTCAAAACCGAACAAATAGACCCCGAATGGCCCAAA
1 CATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAA
* * *
6173 ATAACAAGTGTGCAAAATGACCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATTATAGT
66 ATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGT
*
6238 TAGGCCAAAAACAATGGAAAGAAAAG
131 TAGGCCATAAACAATGGAAAGAAAAG
* * *
6264 CATTAT-ATTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAA
1 CATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAA
* * * *
6328 ATAACAAGTGTTCAAAATGAGCTAAGAACTTTACAATGGACTAATCTTACCAAAGTGATCATAGT
66 ATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGT
*
6393 TAGGCCATAAACAATGGAAAGAAAAA
131 TAGGCCATAAACAATGGAAAGAAAAG
*
6419 CATTATGGTTTGCCAAAATCGAAGACGATTTTTTAAAACCGAACTAATGGGCCCCCGAATGGGTC
1 CATTGTGGTTTGCC-AAATCGAAGACGA-TTTTTAAAACCGAACTAATGGG-CCCCGAAT-GGTC
6484 CAAAA
62 CAAAA
Statistics
Matches: 1496, Mismatches: 108, Indels: 36
0.91 0.07 0.02
Matches are distributed among these distances:
153 169 0.11
154 254 0.17
155 243 0.16
156 632 0.42
157 26 0.02
158 47 0.03
159 52 0.03
160 57 0.04
161 13 0.01
162 3 0.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (156 bp):
CATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAA
ATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAAATGATTATAGT
TAGGCCATAAACAATGGAAAGAAAAG
Done.