Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012654.1 Corchorus olitorius cultivar O-4 contig12687, 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: 21212
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:7041 original size:184 final size:186
Alignment explanation
Indices: 6672--7045 Score: 560
Period size: 184 Copynumber: 2.0 Consensus size: 186
6662 ACGTCACTGG
6672 CTTTGGTACTGCAAACCTCTCATGATCATTGATATTGGGCAATTACATGCAATTTGGGATAATTT
1 CTTTGGTACTGCAAACCTCTCATGATCATTGATATTGGGCAATTACATGCAATTTGGGATAATTT
* * ** * *
6737 GTGACATAAAAGGATACCTTTTGCAGTTTTGCTTGATTAACTGTATCTTTTGTGTCGGTTTGGAG
66 GTGACATAAAACGATAACTGGTGCACTTTTGCTTGATTAACTGTATCTTTTGTGTCGGTTTCGAG
* ** * **
6802 GAAGAATAATTGTGTTTTTACTTCTAGAAGACCGAAAACGACAAATGTGTATTTGT
131 GAAGAATAATGGCATTTGTACTTCTAGAAGACCGAAAACGACAAATGCATATTTGT
6858 CTTTGGTACTGCAAACCTCTCATGATCATTGATATTGGGCAATTACATGCAATTTGGGATAATTT
1 CTTTGGTACTGCAAACCTCTCATGATCATTGATATTGGGCAATTACATGCAATTTGGGATAATTT
6923 GTGACAT-AAACGATAAAAC-GGT-C-CTTTTGCTTGATTAACTGTATCCTTTT-TGTCGGTTTC
66 GTGACATAAAACGAT--AACTGGTGCACTTTTGCTTGATTAACTGTAT-CTTTTGTGTCGGTTTC
* *
6983 GAGGAAGAATTATGGCATTTGTACTTCTAGATGACCGAAAACGACAAATGCATATTTGT
128 GAGGAAGAATAATGGCATTTGTACTTCTAGAAGACCGAAAACGACAAATGCATATTTGT
7042 CTTT
1 CTTT
7046 ACTCGATAAT
Statistics
Matches: 171, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
184 84 0.49
185 12 0.07
186 73 0.43
187 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (186 bp):
CTTTGGTACTGCAAACCTCTCATGATCATTGATATTGGGCAATTACATGCAATTTGGGATAATTT
GTGACATAAAACGATAACTGGTGCACTTTTGCTTGATTAACTGTATCTTTTGTGTCGGTTTCGAG
GAAGAATAATGGCATTTGTACTTCTAGAAGACCGAAAACGACAAATGCATATTTGT
Found at i:14145 original size:21 final size:19
Alignment explanation
Indices: 14119--14177 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
14109 CGTTGCTCTA
*
14119 ATAATCTCATCTGTATAGT
1 ATAATCTCATCTGTACAGT
* * *
14138 ACCTAATCTAATATGTACATT
1 A--TAATCTCATCTGTACAGT
14159 ATAATCTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
14178 TGCTAAACAG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
19 16 0.52
21 15 0.48
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39
Consensus pattern (19 bp):
ATAATCTCATCTGTACAGT
Found at i:15382 original size:7 final size:7
Alignment explanation
Indices: 15370--15398 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
15360 GTGTATAAAT
15370 ATTCATA
1 ATTCATA
15377 ATTCATA
1 ATTCATA
15384 ATTCATA
1 ATTCATA
15391 ATTCATA
1 ATTCATA
15398 A
1 A
15399 CGGAGTGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (7 bp):
ATTCATA
Found at i:18228 original size:330 final size:330
Alignment explanation
Indices: 17610--21209 Score: 4840
Period size: 329 Copynumber: 11.0 Consensus size: 330
17600 CCAGTAAGAT
* * * * * * * **
17610 TTTTGTAAAAGTTGACCTGAAAAATTTTTTCC-CATTTTTTAGCCACAATACTTATAAAAAATAT
1 TTTTGCAAAAATTGACCCGAAAGA-TTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATAT
* * * *
17674 ATAATTCAACGTCAAATAGATTGAAGGGCTTTGCACGCTTCTAATATCATTTTTTTTAATTTTCC
65 ATAATTCAATGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAATATCA-TTTTTTTATTTTTCC
* * * *
17739 GAATTAATTTCCAATTAAATGGAAATATGATTCAAATGCTCGTAAAATCAAATTCC-TAAATCCA
129 GAATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCATA-TCCTTAAATCCA
* *
17803 AAGTGGCTGAGATTTGGGATGATGAATATA-GATAAATCAATGAGTCTTGGGGCCAAAAATCATG
193 AAGTGGCTGAGATTTGGGATGATGAATA-AGGATAATTCAATGAGTCTTGGCGCCAAAAATCATG
* * * * *
17867 CAAAACTGAGTCGCGGCTCCGGAACGCGTTTTCAGCTAAAAATCGTGATGCTTAATACACTG-TT
257 CAAAACTGAGCCGGGGCACCGGAACGCGTTTTCAGCCAAAAATCGTGATGGTTAATACAC-GATT
*
17931 TCAGCAAAAA
321 TCGGCAAAAA
* * * * * *
17941 TTTTGTAAACATTGACCTGAAAGATTTTTCCTCAATTTTTAACTGCAATAGTCGTAAGAAATATA
1 TTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATA
* *
18006 TAATTCAATGCCAAAAAGATTGGAGGGCTTTGCACGCTTCTAATATCATTTTTTTATTTTTCTGA
66 TAATTCAATGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAATATCATTTTTTTATTTTTCCGA
* * * * * *
18071 ATTAATTTCCGATTAGATCGAAGCATGATTCAAATGCTCGTAAAATTATATCCGTAAATTCAATG
131 ATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCATATCCTTAAATCCAAAG
* * *
18136 TGGCTGAGATTTGGAATGATGAATAAGGATAATTCAATGAGTCTTGACACCAAAAATCATGCAAA
196 TGGCTGAGATTTGGGATGATGAATAAGGATAATTCAATGAGTCTTGGCGCCAAAAATCATGCAAA
* * * * *
18201 ACTGAGCCGAGGCATCGGAATGCGTTTTCAGCCAAAAATCGTGAAGGGT-ATACACGATTTC-G-
261 ACTGAGCCGGGGCACCGGAACGCGTTTTCAGCCAAAAATCGTGATGGTTAATACACGATTTCGGC
18263 -----
326 AAAAA
*
18263 ----GCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAGAAATATA
1 TTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATA
* * * * * * *
18324 TAATTCAACGCTAAAAAGATTGAAGGGCTTTGCATGCATCTAAAAT-AATTTTTTACTTTTCCGA
66 TAATTCAATGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAATATCATTTTTTTATTTTTCCGA
18388 ATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCATATCCTTAAATCCAAAG
131 ATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCATATCCTTAAATCCAAAG
* * *
18453 TGGCTGAGATTTGGGATGATGAATATA-GATAAATCAATGAGTCTTGGGGCCAAAAATCATTCAA
196 TGGCTGAGATTTGGGATGATGAATA-AGGATAATTCAATGAGTCTTGGCGCCAAAAATCATGCAA
* * * * *
18517 AACTGAGTCGGGGCCCCGGAACGCGTTTTCAGCTAAAAATCGTGATGGTTAGTACACGATTTCAG
260 AACTGAGCCGGGGCACCGGAACGCGTTTTCAGCCAAAAATCGTGATGGTTAATACACGATTTCGG
*
18582 TAAAAA
325 CAAAAA
* * * * * * *
18588 TTATGTAAAAATTGACCCGAAATATTTTTCCCCAATTTTTAACCACAATACACATAAAAAATATA
1 TTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATA
* *
18653 TAATTCAATGTCAAAAAGATTGAAGGGCTTTGCTCGCTTCT-A-AT-A-----TTA-TTTT----
66 TAATTCAATGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAATATCATTTTTTTATTTTTCCGA
* * * *
18705 -TTATTTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATTATATCCCTAAATCCAATG
131 ATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCATATCCTTAAATCCAAAG
* *
18769 TGGCTGAGATTTGGAATGATGAATAAGGATAATTCAATGAGTCTTGGCACCAAAAATCATGCAAA
196 TGGCTGAGATTTGGGATGATGAATAAGGATAATTCAATGAGTCTTGGCGCCAAAAATCATGCAAA
* * * ** * *
18834 ACTGAGCCGAGGCAACGGAATGCGTTTTCAGCCAAAAATCGTGA-AATAACATACATGATTTCGG
261 ACTGAGCCGGGGCACCGGAACGCGTTTTCAGCCAAAAATCGTGATGGTTA-ATACACGATTTCGG
18898 CAAAAA
325 CAAAAA
*
18904 TTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAGAAATATA
1 TTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATA
* * *
18969 TAATTCAATGCCAAAAAGATTGAAGGGCTTTGCTCGCTTCTAATATTATTTTTTAATTTTTCCGA
66 TAATTCAATGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAATATCATTTTTTTATTTTTCCGA
** * * * *
19034 ATTAATTTCATATTAAATCGAAACATGATTCAAATGCTCGTAAAATTATATCCCTAAATTCAATG
131 ATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCATATCCTTAAATCCAAAG
* *
19099 TGGCTGAGATTTGGAATGATGAATAAGGATAATTCAATGAGTCTTGGCACCAAAAATCATGCAAA
196 TGGCTGAGATTTGGGATGATGAATAAGGATAATTCAATGAGTCTTGGCGCCAAAAATCATGCAAA
* * * * * *
19164 ACTGTGTCGGGGCCCCGGAATGCATTTTCAGCCAAAAATCGTGAAGGTT-ATACACGATTTCGGC
261 ACTGAGCCGGGGCACCGGAACGCGTTTTCAGCCAAAAATCGTGATGGTTAATACACGATTTCGGC
19228 AAAAA
326 AAAAA
*
19233 TTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAGAAATATA
1 TTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATA
* *
19298 TAATTCAATGCCAAAAAGATTGAAGGGCTTTGCACGCATCTAATATAATTTTTTTATTTTTCCGA
66 TAATTCAATGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAATATCATTTTTTTATTTTTCCGA
* * *
19363 ATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATTATATCCTTAATTCCAACG
131 ATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCATATCCTTAAATCCAAAG
* *
19428 TGGCTGAGATTTGGAATGATGAATAAGGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAA
196 TGGCTGAGATTTGGGATGATGAATAAGGATAATTCAATGAGTCTTGGCGCCAAAAATCATGCAAA
* *
19493 ACTGAGCCGGGGCATCGGAATGCGTTTTCAGCCAAAAATC------GTTAATACACGATTTCGGC
261 ACTGAGCCGGGGCACCGGAACGCGTTTTCAGCCAAAAATCGTGATGGTTAATACACGATTTCGGC
19552 AAAAA
326 AAAAA
* *
19557 TTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGTAATAGTCGTAAAAAATATA
1 TTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATA
* *
19622 TAATTCAACGCCAAAAAGATTGAAAGGCTTTGCACGCTTCTAATATCATTTTTTTTATTTTTCCG
66 TAATTCAATGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAATATCA-TTTTTTTATTTTTCCG
*
19687 AATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCATATCCTTAAATCCAAG
130 AATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCATATCCTTAAATCCAAA
* *
19752 GTGGCTGAGATTTGGGATGATGAATATA-GATAATTCAATGAGTCTTGGGGCCTAAAATCATGCA
195 GTGGCTGAGATTTGGGATGATGAATA-AGGATAATTCAATGAGTCTTGGCGCCAAAAATCATGCA
* * * * * * * *
19816 AAACTCAGCTGAGGCCCCGGAACGCGTTTTCAGCTAAGAATCGTGATGGTTAGTACACGATTTCA
259 AAACTGAGCCGGGGCACCGGAACGCGTTTTCAGCCAAAAATCGTGATGGTTAATACACGATTTCG
19881 GCAAAAA
324 GCAAAAA
* * * * * * *
19888 TTATGTAAAAATTGACCCGAAATATTTTTCCCCAATTTTTAACCACAATACACATAAAAAATATA
1 TTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATA
* *
19953 TAATTCAATGCCTAAAATATTGAAGGGCTTTGCACGCTTCTAATAT-ATTTTTTTATTTTTCCGA
66 TAATTCAATGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAATATCATTTTTTTATTTTTCCGA
20017 ATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCATATCCTTAAATCCAAAG
131 ATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCATATCCTTAAATCCAAAG
* *
20082 TGGCTGAGATTTGGGATGATGAATATA-GATAAATCAATGAGTCTTGGGGCCAAAAATCATGCAA
196 TGGCTGAGATTTGGGATGATGAATA-AGGATAATTCAATGAGTCTTGGCGCCAAAAATCATGCAA
* * * * * *
20146 AACTAAGTCGGGGCCCCGGAACGCGTTTTCAGCTAAAAATCGTGATGCTTAATACACGATTTCAG
260 AACTGAGCCGGGGCACCGGAACGCGTTTTCAGCCAAAAATCGTGATGGTTAATACACGATTTCGG
20211 CAAAAA
325 CAAAAA
* *
20217 TTTTGCAAAAAATGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAGAAATATA
1 TTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATA
* *
20282 TAATTCAACGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAATATAATTTTTTTA-TTTTCCGA
66 TAATTCAATGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAATATCATTTTTTTATTTTTCCGA
* * *
20346 ATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATTATATCCCTAAATCCAACG
131 ATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCATATCCTTAAATCCAAAG
* *
20411 TGGCTGAGATTTGGAATGATGAATAAAGGATAATTCAATGAGTCTTGGCACCAAAAATCATGCAA
196 TGGCTGAGATTTGGGATGATGAAT-AAGGATAATTCAATGAGTCTTGGCGCCAAAAATCATGCAA
* * *
20476 AACTGAGCCGGGGCATCGGAATGCGTTTTCAGCCAAAAATCGTGAAGGTT-ATACACGATTTCGG
260 AACTGAGCCGGGGCACCGGAACGCGTTTTCAGCCAAAAATCGTGATGGTTAATACACGATTTCGG
20540 CAAAAA
325 CAAAAA
*
20546 TTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATAGTCGTAAAAAATATA
1 TTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATA
*
20611 TAATTCAACGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAATATCA-TTTTTTATTTTTCCGA
66 TAATTCAATGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAATATCATTTTTTTATTTTTCCGA
* * * * *
20675 ATTAATTTCCGATTAAATCGAAACATGATTCAAAAGCTCGTGAAATCAAATCATTAAATCCAAGG
131 ATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCATATCCTTAAATCCAAAG
* * * * * * * *
20740 TGACAGAGATTTGGGATGACGAATATA-GATAATTCAATGAGGCTTGGGGTCTAAAATCATGGAA
196 TGGCTGAGATTTGGGATGATGAATA-AGGATAATTCAATGAGTCTTGGCGCCAAAAATCATGCAA
* * * * * *
20804 AACTCAACTTGAGGC-CCAGGAACGCGTTTTCAGCCAAGAATCGTGATGGTTAGTACACGATTTC
260 AACTGAGC-CGGGGCACC-GGAACGCGTTTTCAGCCAAAAATCGTGATGGTTAATACACGATTTC
20868 GGCAAAAA
323 GGCAAAAA
*** * * ** * *
20876 TCACG-TAAAATTGACCCGAAATATTTTTCC-CTAATTTTTAACCAAAATACTCATAATAAATAT
1 TTTTGCAAAAATTGACCCGAAAGATTTTTCCTC-AATTTTTAACCGCAATACTCGTAAAAAATAT
* * * *
20939 ATAATTTAATGCCAATAAGATTGAAGGGCTTTGCACTCTTCTAATATAATTTTTTTATTTTTCCG
65 ATAATTCAATGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAATATCATTTTTTTATTTTTCCG
* * *
21004 AATTAATTTCTGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAAG
130 AATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCATATCCTTAAATCCAAA
*
21069 GTGGCTGAGATTTGGGATGATGAATAAGGATAATTCAATGAGTCTTGCCG-CAAAAATTCATGCA
195 GTGGCTGAGATTTGGGATGATGAATAAGGATAATTCAATGAGTCTTGGCGCCAAAAA-TCATGCA
* * * * * * *
21133 AAACTCAGCTGGGTCCCCGGAACGCGTTTTCAGTCAAGAATCGTGATAG--AACGTACACGATTT
259 AAACTGAGCCGGGGCACCGGAACGCGTTTTCAGCCAAAAATCGTGATGGTTAA--TACACGATTT
21196 CGGCAAAAA
322 CGGCAAAAA
21205 TTTTG
1 TTTTG
21210 GAA
Statistics
Matches: 2919, Mismatches: 292, Indels: 118
0.88 0.09 0.04
Matches are distributed among these distances:
315 3 0.00
316 269 0.09
317 173 0.06
318 110 0.04
319 2 0.00
321 4 0.00
322 3 0.00
323 3 0.00
324 128 0.04
325 174 0.06
326 1 0.00
327 4 0.00
328 50 0.02
329 1207 0.41
330 577 0.20
331 211 0.07
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (330 bp):
TTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATA
TAATTCAATGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAATATCATTTTTTTATTTTTCCGA
ATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCATATCCTTAAATCCAAAG
TGGCTGAGATTTGGGATGATGAATAAGGATAATTCAATGAGTCTTGGCGCCAAAAATCATGCAAA
ACTGAGCCGGGGCACCGGAACGCGTTTTCAGCCAAAAATCGTGATGGTTAATACACGATTTCGGC
AAAAA
Done.