Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023853.1 Corchorus olitorius cultivar O-4 contig23886, 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: 10127
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Found at i:3445 original size:334 final size:332
Alignment explanation
Indices: 1062--4091 Score: 2780
Period size: 333 Copynumber: 9.2 Consensus size: 332
1052 CCTGTTTAAT
* * * * * * *
1062 TTAAATCGAAATAAGATTTAGATACTCTTAAAAATAAATCCTTAAATACAATGTGACTGAGATTT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
* * * * * * *
1127 GGTTAGATGAATATAAATATATTTTAAGGAGTCTTGGCGCCGAAAATCATGCAAAACTGA-CCTG
66 GATTAGATGAATAT--AGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGTCGG
** * * * *
1191 GGCCTTAGAACGCGTTTTTAGCCAAAAA-AG-CATGG-TAGTACACGATTTCGGTTAAAATTTTG
129 GGCC-CGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTG
* ** ** * * * * *
1253 C-AAAAGTGTTCCGAATTATTTTT-CT-AATTTTTAGCCACAATAGTCACAAAAAA-A-A-AATT
193 CAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATT
* * * * ** * * * *
1312 CAATGCCAAAAAGGTTGAAGGGCTTCTCACGCTTCCAATATCCTTTTTC-CTATTTTTTC-AAAT
258 CAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCTTTTTTTTTTCTGAAT
1375 TAATTTCTAA
323 TAATTTCTAA
* * * * * * *
1385 TTAAATTGAAACATGATTTTA-ATGCTCGT-AAAA-AAATCTTTAAATCCAATGTGCCTAAAATT
1 TTAAATCGAAACAAGA-TTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATT
* * ***** * **
1447 TGGTTAGATGAATATAGATATTTCAAGGAGTTTTAAAACAAAAAATCATGCAAAACTGACCCGGG
65 TGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGTCGGG
* * * * *
1512 GCCCCAGAACGTGATTTTAGCCAAAAAACCGTGAT-G---GTACACGATTTCGGCTAAAATTTTA
130 G-CCCGGAACGCGTTTTTAGCC-AAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTG
* * * * ** * * *
1573 CAAAAGTTCATCCG----A-TTTTCCTCGATTTTTATCCACAATACTC-TCAAAATATATATAAT
193 CAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTAAAATACTCAT-AAAAAATATATAAT
* * * * * **
1632 TCAACTG-AAAAAAGATTGGAGTACTTTTCACGCTTTTAATATCGTTTTTC--ATATTTTTCAAA
257 TCAAC-GCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCTTTTTTTTTTCTGA
1694 ATTAATTTCTAA
321 ATTAATTTCTAA
* *
1706 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATATGGCTGAGATTT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
* * * *
1771 GATTAGATAAATATAGATATTTCAAGGAGTCTCGACG-CAAAAATCATGCAAAAATGAGTCGAGG
66 GATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGTCGGGG
* * * ** ** * *
1835 CCCTGAAACGCATTATTAGGAAAAAAACCGTGATGGTTAGTACACGATTTTGGCAAAAATTTTAC
131 CCC-GGAACGCGTTTTTA-GCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGC
* * * * * * *
1900 AAAAAATGACCTGAAAAATTTTTCCTTAATTTTTGGCAAAAATACTCATGAAATATATATAATTT
194 AAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
* * * * * ** * *
1965 AATGCCAAAAAGATTGGATGACTTTTCACGCTTTTCATATCATTTTT-TAATATTTTTCTGGATT
259 AACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCTTTTTTTTTTCTGAATT
2029 AATTT-TAA
324 AATTTCTAA
* * * *
2037 TTAAATCGAAACAAGATTCGGATGTTCGCAAAAACAAATCCTTAAATGCAATGTGTGCCTGAGAT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG-G-CTGAGAT
* * * *
2102 TTGATTAGATGAATAT-GAATATCTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGACTCG
64 TTGATTAGATGAATATAG-ATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGTCG
* * * * * * *
2166 GGGCTCTGGAACGCATTTTTA-CCAAAAATCGTGATGATTATTACACAATTTCAACTAAAATTTT
128 GGGC-CCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTT
* * *
2230 GCAAAAATTGACCC-AAAAGATATTTCCTCAATTTTTGGATAAATTACTCATAAAAAATATATAA
192 GCAAAAATTGACCCGAAAA-ATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAA
* * * * * * *
2294 TTCAACACCAAAAATATTAAAGGGA-TTTTTACGGTTCTAATATTGTTTTT-TTTTTACTTTTTC
256 TTCAACGCCAAAAAGATTGAA-GGACTTTTCACGCTTTTAATATCGTTTTTCTTTTT--TTTTTC
* *
2357 CGAATTAATTTGTAA
318 TGAATTAATTTCTAA
* * * *
2372 TTGAATCGAAACAAGATTTATATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAAATTT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
* * * *
2437 TATTAGATGAATATAGATATTTCAAGGAGTCTTGGTGCCAAAAATCATGCAAAACTGACTCGGGG
66 GATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGTCGGGG
* * * * *
2502 CCCGGAACGCGTTTTTAGCAACAAAAACCGT-A---TTGGTACGCAATTTCGGCTAATATTTTGC
131 CCCGGAACGCGTTTTTAGC--CAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGC
* * *
2563 AAAAATTGACCCGAAAATATTTTTCCTCAATTTTTAGCCACAATACTCATAAAAAATATATAATT
194 AAAAATTGACCCGAAAA-ATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATT
* * * *
2628 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTT-ATATCGTTTTTCCTATTTTTTTCCGAA
258 CAACGCCAAAAAGATTGAAGGACTTTTCACGCTT-TTAATATCGTTTTTCTTTTTTTTTTCTGAA
2692 TTAATTTCTAA
322 TTAATTTCTAA
* * * * * *
2703 TTAAATTGAAACATGATTTAAATGCTTGT--------A-----AAA--CAA--TGGCTGGGATTT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
** * * * ** *
2751 GGCTAGATGAATATAGATATTTGAAGGAGTCTCGGCACCAAAAATCATGCAAAGCTGAACCGGGC
66 GATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGTCGGGG
* * * *
2816 CCCGGAACG-GTTTTTAGCCAAAAACCGTGATGATTATTAAACGATTTCGGCTAAAATTTTGCAA
131 CCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAA
* * * * * * *
2880 AAATTGACCCGAAAGATATTTCTTCAAATTTTAGCCACAATACTCATAAAAAATATATAATTCAA
196 AAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAA
* * ** * *
2945 TGCCAAAAATATTGAAGGGTTTTTCACGATTTTAATATCGTTTTTCATATTTTTTTTCTGAATTA
261 CGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTC-TTTTTTTTTTCTGAATTA
*
3010 ATATCTAA
325 ATTTCTAA
* * * * * *
3018 ATAAATCGAAACAAGATTCAGATGCTCGTAAAAATAAATCCTTAAATGCAATGCGGCTAACATTT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
* *
3083 TATTAGATGAATATAGATATTACAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGTCGCGG
66 GATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGTCG-GG
* * * * * *
3148 GCACGAAACGCGTTTTTATCCAAAAACCATGATGGTTAGTACACGATTTTATCTAAAATTTTGCA
130 GCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCA
* * * *
3213 AAAGA-TGACAC-AAAAACTTTTTTCCTCAATTTTTGGATAAAATACTCATTAAATATATATAAT
195 AAA-ATTGACCCGAAAAA--TTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAAT
* * * * *
3276 TTAACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATTTCGTTTTTCTTTTTTTTTTCTAAA
257 TCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCTTTTTTTTTTCTGAA
*
3341 TTAATTTTTAA
322 TTAATTTCTAA
* * * ** *
3352 TTAAATCAAAATAAGATTCAGATACTCGTAAAAACAAATTTTTAAATCCATTGTGGCTGAGATTT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
* * * * * * *
3417 GATTAGATAAATATGGATATCTCAAGGAGGCTTGGGGCTAAAAATCATGCAAAACTGAGTCGGGG
66 GATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGTCGGGG
* * * *
3482 CCCCGGAACAC-TTTGTTAGCCAAAAGCTGTGATGGTTATTACACGATTTC-GACTAAAATTTTG
131 -CCCGGAACGCGTTT-TTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAG-CTAAAATTTTG
* * * * * *
3545 TAAAAATTGACTCGAAAGATATTTCCTCAATTTTTAGCTAAAATAGTCATAAAAAATATATAATT
193 CAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATT
* * *
3610 CAACACCAAAAAGATTGAAGTG-CTTTTCACGCTTTTAATATCGTTTTTCATTTTTTTTTCTGAT
258 CAACGCCAAAAAGATTGAAG-GACTTTTCACGCTTTTAATATCGTTTTTCTTTTTTTTTTCTGAA
3674 TTAATTTCTAA
322 TTAATTTCTAA
* * * *
3685 TTAAATCGAAACACGATTCATATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGC-GAACATT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTG-AGATT
* * * * * * *
3749 TTATTAGATGGATATAGATATTTC-AGGAAGTCTCAGCGCCAAAAATTATG-ATAAATTGAGCCA
65 TGATTAGATGAATATAGATATTTCAAGG-AGTCTCGGCGCCAAAAATCATGCA-AAACTGAGTCG
* *
3812 GGGCCTCGGAATGCGTTTTCT-GCCAAAAATCGTGATGGTTAGTTAGTACACGATTTCAGCTAAA
128 GGGCC-CGGAACGCGTTTT-TAGCCAAAAACCGTGAT-G---GTTAGTACACGATTTCAGCTAAA
* * * * * *
3876 ATTGTGCAAAAATTGACACGAAAGATTTCTACTCAATTTTTGGCTAAAATACTTAT-AAAAATAT
187 ATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATAT
* * * * *
3940 ATAATTCAACGCCAAAAAGATTGGAGGGCTTTTTACGCTTTTAATATCGTATTTC-TTATTTTTT
252 ATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCTTTTTTTTTT
* *
4004 CTAAACTAATTTCTAA
317 CTGAATTAATTTCTAA
* * **
4020 TTAAATCGAAACAAGTTTTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTTACTGAGATT
1 TTAAATCGAAACAAG-ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATT
*
4085 TGGTTAG
65 TGATTAG
4092 TTGATGCACC
Statistics
Matches: 2219, Mismatches: 389, Indels: 185
0.79 0.14 0.07
Matches are distributed among these distances:
311 10 0.00
312 1 0.00
313 11 0.00
314 159 0.07
315 83 0.04
316 7 0.00
317 3 0.00
318 25 0.01
319 36 0.02
320 54 0.02
321 134 0.06
322 53 0.02
323 79 0.04
324 4 0.00
326 32 0.01
328 3 0.00
330 5 0.00
331 214 0.10
332 300 0.14
333 358 0.16
334 298 0.13
335 179 0.08
336 102 0.05
337 68 0.03
338 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (332 bp):
TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
GATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGTCGGGG
CCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAA
AAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAA
CGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCTTTTTTTTTTCTGAATTAA
TTTCTAA
Found at i:4440 original size:15 final size:16
Alignment explanation
Indices: 4422--4451 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4412 ATAAATAATA
4422 ATATTATAAT-TAAAT
1 ATATTATAATATAAAT
4437 ATATTATAATATAAA
1 ATATTATAATATAAA
4452 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATATAAAT
Found at i:4450 original size:35 final size:34
Alignment explanation
Indices: 4411--4476 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
4401 GTTTCATGAC
* *
4411 TATAAATAATAA-TATTATAATTAAATATATTATAA
1 TATAAA-AATAATTATTAGAAGTAAAT-TATTATAA
4446 TATAAAAATAATTATTAGAAGTAAATTATTA
1 TATAAAAATAATTATTAGAAGTAAATTATTA
4477 ATTACAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 10 0.36
35 18 0.64
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (34 bp):
TATAAAAATAATTATTAGAAGTAAATTATTATAA
Found at i:8358 original size:2 final size:2
Alignment explanation
Indices: 8314--8338 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8304 GTGTAATTTC
8314 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
8339 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8909 original size:20 final size:20
Alignment explanation
Indices: 8884--8927 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
8874 GACTAAAACA
8884 TTATATATTTCATGATGAAT
1 TTATATATTTCATGATGAAT
8904 TTATATATTTCATGATGAAT
1 TTATATATTTCATGATGAAT
8924 TTAT
1 TTAT
8928 TAAAAAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.52
Consensus pattern (20 bp):
TTATATATTTCATGATGAAT
Found at i:9433 original size:111 final size:111
Alignment explanation
Indices: 9239--9461 Score: 428
Period size: 111 Copynumber: 2.0 Consensus size: 111
9229 TTGAGATTGT
9239 TATATATATATATAAGAAGAAGAATATATGACCCAAACGCAGGGGCGGATCCTCTTTATGTCAAT
1 TATATATATATATAAGAAGAAGAATATATGACCCAAACGCAGGGGCGGATCCTCTTTATGTCAAT
9304 TTGCTCTATTATCCCCATACATTTCTATATAAATATATTGAAATTC
66 TTGCTCTATTATCCCCATACATTTCTATATAAATATATTGAAATTC
* *
9350 TATATATATATCTAAGAAGAAGAATATATGACTCAAACGCAGGGGCGGATCCTCTTTATGTCAAT
1 TATATATATATATAAGAAGAAGAATATATGACCCAAACGCAGGGGCGGATCCTCTTTATGTCAAT
9415 TTGCTCTATTATCCCCATACATTTCTATATAAATATATTGAAATTC
66 TTGCTCTATTATCCCCATACATTTCTATATAAATATATTGAAATTC
9461 T
1 T
9462 TAAATTGCCC
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 110 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (111 bp):
TATATATATATATAAGAAGAAGAATATATGACCCAAACGCAGGGGCGGATCCTCTTTATGTCAAT
TTGCTCTATTATCCCCATACATTTCTATATAAATATATTGAAATTC
Found at i:9805 original size:25 final size:24
Alignment explanation
Indices: 9757--9805 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
9747 TTGAATGATT
* *
9757 GAGATTTGAAAGTTTGAAGGTTGA
1 GAGAATTGAAAGTTTGAAAGTTGA
*
9781 GAGAATTGAAAAGTTTGAAATTTGA
1 GAGAATTG-AAAGTTTGAAAGTTGA
9806 AGGAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.33
Consensus pattern (24 bp):
GAGAATTGAAAGTTTGAAAGTTGA
Done.