Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017554.1 Corchorus olitorius cultivar O-4 contig17587, 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: 4398
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:300 original size:11 final size:12
Alignment explanation
Indices: 276--311 Score: 58
Period size: 11 Copynumber: 3.2 Consensus size: 12
266 CTCCCTCTTG
276 AAACTAGAAGAA
1 AAACTAGAAGAA
288 AAACTAG-AGAA
1 AAACTAGAAGAA
299 AAA-TAGAAGAA
1 AAACTAGAAGAA
310 AA
1 AA
312 GAAATTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.13
11 13 0.57
12 7 0.30
ACGTcount: A:0.69, C:0.06, G:0.17, T:0.08
Consensus pattern (12 bp):
AAACTAGAAGAA
Found at i:1117 original size:327 final size:332
Alignment explanation
Indices: 487--1156 Score: 1003
Period size: 327 Copynumber: 2.0 Consensus size: 332
477 TCTTTCCAAT
* * *
487 TGATTTTTGGCGCCTAGAACCCTTGAAATTTTAATATTCATCTAACCAAATCTCAACCACATTAA
1 TGATTTTTGGCGCCTAGAACCATTGAAATTTCAATATACATCTAACCAAATCTCAACCACATTAA
* *
552 ATTTAAAACTTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATCAGATATTAATTCGGAA
66 ATTTAAAAATTTGATTTTAC-AGCATCTGAATCTTATTTCGATTTAATCAGATATTAATTCGGAA
* * * *
617 AATGATTGGAAAAACGATAGTACAAGCGTGAAAAACCCTTTAATATTTTTGGTGTTGATTTTTAT
130 AATAAATGGAAAAACGATAGTACAAGCGTGAAAAACCCTTCAATATTTTTGGCGTTGATTTTTAT
* *
682 ATTTTTTCTGAGTATTGTGGCCAAATTTTGAGGAAAAATTTATCGGATCATTTTTTGCAAAATTT
195 ATTTTTTCAGAGTATTGTGGCCAAAATTTGAGGAAAAATTTATCGGATCATTTTTTGCAAAATTT
* * * *
747 TAGCCGAAATCGTCTACTATCCATCACGGTTTTGGGCTAAAAACGCGTTCCAGGGACCCGGCTCA
260 TAGCCGAAATCGTCTACTATCCATCACAGTTTTGGCCTAAAAACGCGTTCCAGGGACCCGACACA
812 ATTTTGCA
325 ATTTTGCA
* *
820 TGATTTTTGGCGCCTAGAACCATTGAAATTTCAATATACAATCTAACCAAATCTCAGCCACATTG
1 TGATTTTTGGCGCCTAGAACCATTGAAATTTCAATATAC-ATCTAACCAAATCTCAACCACATTA
* **
885 AATTTAAAAATTTGATTTTAC-G-A-CTGAATCTTATTTCGATTTAATTAGGA-ATTAATTCTTA
65 AATTTAAAAATTTGATTTTACAGCATCTGAATCTTATTTCGATTTAATCA-GATATTAATTCGGA
* * *
946 AAA-AAATGGTAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCGTTGATTTTTA
129 AAATAAATGGAAAAACGATAGTACAAGCGTGAAAAACCCTTCAATATTTTTGGCGTTGATTTTTA
*
1010 TA-TTTTTCAGAGTATTGTGGCCAAAATTTGAGGAAAAATTTTTCGGATC-TTTTTTGCAAAATT
194 TATTTTTTCAGAGTATTGTGGCCAAAATTTGAGGAAAAATTTATCGGATCATTTTTTGCAAAATT
* * * *
1073 TTAGCTGAAATCGTGTACTATCCATCACAGTTTTGGCCTAAAAACGCGTTCCCGGGTCCCGACAC
259 TTAGCCGAAATCGTCTACTATCCATCACAGTTTTGGCCTAAAAACGCGTTCCAGGGACCCGACAC
*
1138 AGTTTTGCA
324 AATTTTGCA
1147 TGATTTTTGG
1 TGATTTTTGG
1157 GGAAAAGTCT
Statistics
Matches: 306, Mismatches: 29, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
327 89 0.29
328 44 0.14
329 56 0.18
330 34 0.11
331 3 0.01
332 1 0.00
333 36 0.12
334 43 0.14
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (332 bp):
TGATTTTTGGCGCCTAGAACCATTGAAATTTCAATATACATCTAACCAAATCTCAACCACATTAA
ATTTAAAAATTTGATTTTACAGCATCTGAATCTTATTTCGATTTAATCAGATATTAATTCGGAAA
ATAAATGGAAAAACGATAGTACAAGCGTGAAAAACCCTTCAATATTTTTGGCGTTGATTTTTATA
TTTTTTCAGAGTATTGTGGCCAAAATTTGAGGAAAAATTTATCGGATCATTTTTTGCAAAATTTT
AGCCGAAATCGTCTACTATCCATCACAGTTTTGGCCTAAAAACGCGTTCCAGGGACCCGACACAA
TTTTGCA
Found at i:1375 original size:183 final size:181
Alignment explanation
Indices: 1027--1381 Score: 446
Period size: 183 Copynumber: 1.9 Consensus size: 181
1017 CAGAGTATTG
* * * *
1027 TGGCCAAAATTTGAGGAAAAATTTTTCGGATCTTTTTTGCAAAATTTTAGCTGAAATCGTGTACT
1 TGGCAAAAAATTGAGGAAAAATTTTTCGGATCTTTTTTGCAAAATTTCAGCCGAAATCGTGTACT
* *
1092 ATCCATCACAGTTTTGGCCTAAAAACGCGTTCCCGGGTCCCGACACAGTTTTGCATGATTTTTGG
66 ATCCATCACAGTTTTGGCCTAAAAACGCGTT-CCGGGCCCCGACACAATTTTGCATGATTTTTGG
* * * * *
1157 GGAAAAGTCTCCTTGAAATATCTATATTGATCTTACCAAATCGGAAAAATTT
130 CGAAAAGACTCCATGAAATATCAATATTCATCTTACCAAATCGGAAAAATTT
1209 TGGCAAAAAATTGAGGAAAAATTTTTCGGAT-TAGTTTTTGCAAAATTTCAGCCGAAATCGTGTA
1 TGGCAAAAAATTGAGGAAAAATTTTTCGGATCT--TTTTTGCAAAATTTCAGCCGAAATCGTGTA
* * * * * *
1273 CTATCCATCACGGTTTTGGGCTAAAAACGCGTT-TGAGGCCCCTGGCTCAATTTTGCTTGATTTT
64 CTATCCATCACAGTTTTGGCCTAAAAACGCGTTCCG-GGCCCC-GACACAATTTTGCATGATTTT
*** *
1337 TGGCGCTTAGAAC-CCATGAAATTTCAATATTCATCTTACCAAATC
127 TGGCGAAAAG-ACTCCATGAAATATCAATATTCATCTTACCAAATC
1382 TCAACCATAT
Statistics
Matches: 147, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
181 2 0.01
182 34 0.23
183 110 0.75
184 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (181 bp):
TGGCAAAAAATTGAGGAAAAATTTTTCGGATCTTTTTTGCAAAATTTCAGCCGAAATCGTGTACT
ATCCATCACAGTTTTGGCCTAAAAACGCGTTCCGGGCCCCGACACAATTTTGCATGATTTTTGGC
GAAAAGACTCCATGAAATATCAATATTCATCTTACCAAATCGGAAAAATTT
Found at i:1836 original size:333 final size:329
Alignment explanation
Indices: 1209--2208 Score: 1251
Period size: 333 Copynumber: 3.0 Consensus size: 329
1199 GGAAAAATTT
* * *
1209 TGGCAAAAAATTGAGGAAAAATTTTTCGGATTAGTTTTTGCAAAATTTCAGCCGAAATCGTGTAC
1 TGGCCAAAAATTGAGGAAAAATTTTTCGGATAAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
* * * *
1274 TATCCATCACGGTTTTGGGCTAAAAACGCGTTTGAGGCCCCTGGCTCAATTTTGCTTGATTTTTG
66 TATCCATCACAGTTTTGGGCTAAAAACGCGTTTCAGGGCCCTGGCTCAATTTTGCATGATTTTTG
* * * *
1339 GCGCTTAGAACCCATGAAATTTCAATATTCATCT-TACCAAATCTCAACCATATTGAATTTAAAA
131 GCGCCTAGAACCCTTGAAATTTCAATATTCATCTAT-CCAAATCTCAGCCACATTGAATTTAAAA
* * *
1403 TTTTGATTTTACGAGCATCTGAATCTTGTTTCGATCTAATTAGGAATTAATTCGGAAAAATATTG
195 ATTTGATTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGGAATTAATTC-GAAAAA-A-TG
* *
1468 GAAAAACGATATTAGAAGCGTGAAAAAT-CCTTCAATATTTTTGGCGTT-AATTTATATATTTTT
257 GAAAAACGATATTAGAAGCG-G-GAAATGCCTTCAATATTTTTGGCGTTGAA-TTATATATATTT
* *
1531 TTCGGGTATTG
319 TCCGAGTATTG
* * *
1542 TGTCCAAAATTTGAGGAAAAATTTTTCGGATCA-TATTTTGCAAAATTTTAGCCGAAATCGTGTA
1 TGGCCAAAAATTGAGGAAAAATTTTTCGGATAAGT-TTTTGCAAAATTTTAGCCGAAATCGTGTA
* * *
1606 CTATCCATCACAGTTTTGGGCTAAAAACGCGTTCCAGGGACCTGACTCAATTTTGCATGATTTTT
65 CTATCCATCACAGTTTTGGGCTAAAAACGCGTTTCAGGGCCCTGGCTCAATTTTGCATGATTTTT
*
1671 GGCGCCTAGAACCCTTGAAATTTCAATATACAATCTATCCAAATCTCAGCCACATTGAATTTAAA
130 GGCGCCTAGAACCCTTGAAATTTCAATATTC-ATCTATCCAAATCTCAGCCACATTGAATTTAAA
*
1736 AATTTGATTTTACGAGCATCTAAATCTTATTTCGATTTAATTAGGAATTAATTCTGAAAAAGATG
194 AATTTGATTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGGAATTAATTC-GAAAAA-ATG
* *
1801 GTAAAACGATATTAGAAGCGGGAAATGCTCTTCAATATTTTTGGTGTTGAATTATATATATTTTC
257 GAAAAACGATATTAGAAGCGGGAAATGC-CTTCAATATTTTTGGCGTTGAATTATATATATTTTC
1866 CGAGTATTG
321 CGAGTATTG
* * *
1875 TGGCCAAAAATTGAGGAAAAATTGTTCGGATAAGTTTTTGCAAAATTTTAGCCAAAATCGAGTA-
1 TGGCCAAAAATTGAGGAAAAATTTTTCGGATAAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
* * * * * * *
1939 TAAACAATCACAGTTTTTGGATAAAAACGCGTTTCAAGGCCCCGGCTCAATTTTGCATGAATTTT
66 T-ATCCATCACAGTTTTGGGCTAAAAACGCGTTTCAGGGCCCTGGCTCAATTTTGCATGATTTTT
* * * * * * * * * *
2004 AGAGTCTAGAGCCCTTGAAATTACTATATTCATCCAACCAAATCTCAGCCACATCGAATTTAAAT
130 GGCGCCTAGAACCCTTGAAATTTCAATATTCATCTATCCAAATCTCAGCCACATTGAATTTAAAA
* * *
2069 ATTTGATTTTAAGAGCATCTGAAA-CTTGTTTCGATTAAATTAGAAATTAATTC-AAGAAAATGG
195 ATTTGATTTTACGAGCATCT-AAATCTTGTTTCGATTTAATTAGGAATTAATTCGAA-AAAATGG
* * * * * * *
2132 AAAAACGATATTAGGAGCGTGAAAAGCCTTTCAATCTTTTTGGCATAGAATTATAAAT-TTCTTC
258 AAAAACGATATTAGAAGCGGGAAATGCC-TTCAATATTTTTGGCGTTGAATTATATATATT-TTC
**
2196 TAAGTATTG
321 CGAGTATTG
2205 TGGC
1 TGGC
2209 AGAGAATTGA
Statistics
Matches: 584, Mismatches: 71, Indels: 27
0.86 0.10 0.04
Matches are distributed among these distances:
329 3 0.01
330 67 0.11
331 7 0.01
332 79 0.14
333 338 0.58
334 89 0.15
335 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (329 bp):
TGGCCAAAAATTGAGGAAAAATTTTTCGGATAAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
TATCCATCACAGTTTTGGGCTAAAAACGCGTTTCAGGGCCCTGGCTCAATTTTGCATGATTTTTG
GCGCCTAGAACCCTTGAAATTTCAATATTCATCTATCCAAATCTCAGCCACATTGAATTTAAAAA
TTTGATTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGGAATTAATTCGAAAAAATGGAAA
AACGATATTAGAAGCGGGAAATGCCTTCAATATTTTTGGCGTTGAATTATATATATTTTCCGAGT
ATTG
Found at i:2797 original size:334 final size:331
Alignment explanation
Indices: 2378--3415 Score: 1296
Period size: 333 Copynumber: 3.1 Consensus size: 331
2368 GGAAAAATTT
* * *
2378 TGGCCAAAAATTGAGGAAATACTTTTCGGATTAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
1 TGGCCAAAAATTGAGGAAATATTTTTCGGATCAGTTTTTGCAAAATTTTAGGCGAAATCGTGTAC
* * *
2443 TATCCATCACGGTGTTTGGCTCAAAACACGTTCCAGGCCCCAGGCTCAATTTTGCTTGATTTTTG
66 TATCCATCACGGTTTTTGGCTAAAAACACGTTCCAGGCCCC-GGCTCAATTTTGCATGATTTTTG
* * *
2508 GCGCCTAGAACCCTTGAAATTTCAATATTCATCTTACCGAATCTCAACCACGTTGAATTTAAAAA
130 GCGCCTAGAACCCTTGAAATTTCAATATTCATCTAACCAAATCTCAACCACATTGAATTTAAAAA
* *
2573 TTTGATTTTACGAGCCTCTGAATCTTGTTTTGATTTAATTAGAAATTATTTCAGAAAGAAAATTG
195 TTTGATTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCAGAAA-AAAATTG
* * * *
2638 GAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCGTTGATTTTTATATCTTTTC
259 GAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATATTTTTGGCGTTGAATTATATAT-TTTTC
2703 TCAGTATTG
323 TCAGTATTG
* * * *
2712 TGGCCAAAATTTGAGGAAAAATTTTTCGGATCATTTTTTGCAAAATTTTAGGCGAAATCGTGTAA
1 TGGCCAAAAATTGAGGAAATATTTTTCGGATCAGTTTTTGCAAAATTTTAGGCGAAATCGTGTAC
* * *
2777 TATCCATCACGGTTTTTGGCTAAAAACACGTTCCAGGGCTCCGACTTAATTTTGCATGATTTTTG
66 TATCCATCACGGTTTTTGGCTAAAAACACGTTCCA-GGCCCCGGCTCAATTTTGCATGATTTTTG
* *
2842 GCGCCCAGAACCCTTGAAATTTCAATATTCATCTAACCAAATCTCAACCACATTGAATTTAAAAC
130 GCGCCTAGAACCCTTGAAATTTCAATATTCATCTAACCAAATCTCAACCACATTGAATTTAAAAA
* * * * * *
2907 TTTGATTTTACGAGCATCTGAATCTTATTTCGATTTAAATAGGAATTAATTCCGGAAAAAATTGG
195 TTTGATTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCAGAAAAAAATTGG
* * * *
2972 GAAAACGATATTAAAAGCATGAAAAGCTCTTCAATATTTTTGGTGTTGAATTATATATTTTT-TC
260 AAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATATTTTTGGCGTTGAATTATATATTTTTCT-
*
3036 CGTGTATTG
324 C-AGTATTG
* * * *
3045 TGGCCAAAAATTGAGGAATTATTTTTCGGATCAGATTTTACAAAATTTTCGGCGAAATCGTGTAC
1 TGGCCAAAAATTGAGGAAATATTTTTCGGATCAGTTTTTGCAAAATTTTAGGCGAAATCGTGTAC
* * * * * ** *
3110 TAACCATCACAGCTTTTGGCTAAAAACGCATTTTAAGGCCCCGGCTCAATTTTGCATGAATTTTG
66 TATCCATCACGGTTTTTGGCTAAAAACAC-GTTCCAGGCCCCGGCTCAATTTTGCATGATTTTTG
* ** * * * *
3175 GCGCCTAGAGCCCTTGAAATTAT-TGTATTCATCTAACAAAATTTCAGCCACATCGAATTTAAAA
130 GCGCCTAGAACCCTTGAAATT-TCAATATTCATCTAACCAAATCTCAACCACATTGAATTTAAAA
* * *
3239 ATTTGATTTTAAGAGCATCTGAATCTTGTTTCT-ATTTAATTAGTAATAAATTCA-AAAAAAA-T
194 ATTTGATTTTACGAGCATCTGAATCTTGTTT-TGATTTAATTAGAAATTAATTCAGAAAAAAATT
** * * * * *
3301 GGAAAAACGATATTATTATCGTGAAAAGCCCTTCAATCTTATTGGCATTGAATTATATATTTACT
258 GGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATATTTTTGGCGTTGAATTATATATTT-TT
*
3366 CTGAGTATTG
322 CTCAGTATTG
* * * ** *
3376 TGG-CAGAGAATTGAGAAAAAAAATTTCGGGTCAGTTTTTG
1 TGGCCA-AAAATTGAGGAAATATTTTTCGGATCAGTTTTTG
3416 GCCGAAAATC
Statistics
Matches: 602, Mismatches: 93, Indels: 21
0.84 0.13 0.03
Matches are distributed among these distances:
330 2 0.00
331 88 0.15
332 12 0.02
333 271 0.45
334 224 0.37
335 5 0.01
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (331 bp):
TGGCCAAAAATTGAGGAAATATTTTTCGGATCAGTTTTTGCAAAATTTTAGGCGAAATCGTGTAC
TATCCATCACGGTTTTTGGCTAAAAACACGTTCCAGGCCCCGGCTCAATTTTGCATGATTTTTGG
CGCCTAGAACCCTTGAAATTTCAATATTCATCTAACCAAATCTCAACCACATTGAATTTAAAAAT
TTGATTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCAGAAAAAAATTGGA
AAAACGATATTAAAAGCGTGAAAAGCCCTTCAATATTTTTGGCGTTGAATTATATATTTTTCTCA
GTATTG
Done.