Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015390.1 Corchorus olitorius cultivar O-4 contig15423, 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: 4544
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.32
Found at i:176 original size:57 final size:57
Alignment explanation
Indices: 107--216 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 57
97 AAATAAGTAT
*
107 AATTCAACGCCAAAAATAGTGAA-GGATTTTTCACGCTTCTAATATCGATTTTCATAC
1 AATTCAACGCCAAAAAAAGTGAAGGGA-TTTTCACGCTTCTAATATCGATTTTCATAC
* *
164 AATTCATCGCCAAAAAAATTGAAGGGATTTTCACGCTTCTAATATCGATTTTC
1 AATTCAACGCCAAAAAAAGTGAAGGGATTTTCACGCTTCTAATATCGATTTTC
217 CTATATCTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
57 46 0.94
58 3 0.06
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.34
Consensus pattern (57 bp):
AATTCAACGCCAAAAAAAGTGAAGGGATTTTCACGCTTCTAATATCGATTTTCATAC
Found at i:1481 original size:339 final size:332
Alignment explanation
Indices: 410--1692 Score: 1187
Period size: 328 Copynumber: 3.9 Consensus size: 332
400 TTATCACAGT
* * * * *
410 TTTTGGCTAAAAACGAGTTTCATGG--CCCCGGCTCAGTTTTGAATGATTTTTTGCAGAAAGACT
1 TTTTGGCTAAAAACGCGTTTC--GGAATCCCGGCTCAATTTTAAATGATTTTTGGCAGAAAGACT
* * * *
473 CCTTGAAATATCTATATTCATCTAACCAAATCTCAGTCACAATGGATTTAAGGATTTGTTTTTTA
64 CCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACAATGGATATAAGAATTTG-TTTTTA
* ** ** **
538 CGAGCATCTGAATCTTTATTTCGATTTAATTAGAAA-TAAATTCGG-AAAAA-AAATGGAAAACG
128 CGAGCATCTCAATCTTTATTTCGATTTAATTAGAAATTAAATAGGGAAAAAAGAAAAAGAAAATT
* * * *
600 ATATTAGAAGCGTGAAAATCCCTTCAATTATTTTGGCGTTGAATTTTATATTTTTT-TAAAGTAT
193 ATAATAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCT-AAGTAT
* * * *
664 TGTGGCAAAAAAA-TGAGGAAAAACTTTTGGGGTCAATTTTTGCAAAATTTTCGAAATCGTGTAC
257 TGT-GCAAAAAAATTGAGGAAAAACTTTTCGGGTTAGTTTTTGCAAAATTTTCGAAATCATGTA-
*
728 T-AACTATCACA-G
320 TAAACCATCA-ATG
* * * **
740 TTTTTAGCAAAAAACGCGTTTCGGAGTCCCGGCTCAATTTTGCATGATTTTTGGC-GTAAAGACT
1 -TTTTGGCTAAAAACGCGTTTCGGAATCCCGGCTCAATTTTAAATGATTTTTGGCAG-AAAGACT
* * ** *
804 CCTTCAAATATCTATATTCATCGAACCAAATCTCAGCCACATTTTATATAA-AGATCTGTTTTTA
64 CCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACAATGGATATAAGA-ATTTGTTTTTA
* * * * * *
868 TGAGCATC-CGAA-CCTTATTTCTATTTAATTAGAAATTAATTCGGAAAAGAAATGGAAAAACG-
128 CGAGCATCTC-AATCTTTATTTCGATTTAATTAGAAATTAAATAGGGAAA-AAA--GAAAAA-GA
* * * * * *
930 ATATTAGAATTTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTCTTTCT
188 AAATTATAA--TAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCT
* * * *
995 AAATATTTTGC-AAAAAATTGAGAAAAAACTTTTCGGGTTAGTTTTTAGCCAAAA---TCG-TAT
251 AAGTATTGTGCAAAAAAATTGAGGAAAAACTTTTCGGGTTAGTTTTT-G-CAAAATTTTCGAAAT
* * * *
1055 -AGGT-TACATCA-CGAT-
314 CATGTATAAACCATCAATG
* * *
1070 TTTTGGCTAAAAACGTGTTTCGG-ATCCCGGCTCAGTTTTAAATGATTTTTGGCAGAAAGACTCT
1 TTTTGGCTAAAAACGCGTTTCGGAATCCCGGCTCAATTTTAAATGATTTTTGGCAGAAAGACTCC
* * *
1134 TTGAAATATCTATATTCATCTAACAAAATCTCAGCCACAATGGATTTAAGAATTTGTTTTTACGA
66 TTGAAATATCTATATTCATCGAACCAAATCTCAGCCACAATGGATATAAGAATTTGTTTTTACGA
*
1199 GCATCTCAATCTTTGTTTCGATTTAATTAG-AATTAAATAAGGGAAAAAAGAAAAAGAAAAATTA
131 GCATCTCAATCTTTATTTCGATTTAATTAGAAATTAAAT-AGGGAAAAAAGAAAAAG-AAAATTA
* * * *
1263 TAATAGAAGCGTGAAAAACCATTCAATTTTTTTAGCGTTAAATTATATATTTTTTCTGAGTATTG
194 TAATAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTAAGTATTG
* *
1328 TGCAAAAAAAATTGAGGAAAAACTTGTCAGGTTAGTTTTTGCAAAATTTTAGCCGAAATCAATGT
259 TGC-AAAAAAATTGAGGAAAAACTTTTCGGGTTAGTTTTTGCAAAATTTT---CGAAATC-ATGT
1393 ATAAACCATCAATG
319 ATAAACCATCAATG
* * **
1407 TTATTGGCTAAAAACGCGTTCCGGAACCCCGTTTCAATTTTAAATGATTTTTGGC-GTAAAGACT
1 TT-TTGGCTAAAAACGCGTTTCGGAATCCCGGCTCAATTTTAAATGATTTTTGGCAG-AAAGACT
* * *
1471 CCTTGAAATAT-TCATATTCATCGAACCAAATGTCAGCCAC-ATAGGATATAAGGATTCGTTTTT
64 CCTTGAAATATCT-ATATTCATCGAACCAAATCTCAGCCACAAT-GGATATAAGAATTTGTTTTT
* * * ** *** *
1534 ACGAGCATTTGAATC-TTGTTTCGATTTAATTAGAAATT-AATCCGGAAAAAA-ATGGA-AAAAC
127 ACGAGCATCTCAATCTTTATTTCGATTTAATTAGAAATTAAATAGGGAAAAAAGAAAAAGAAAAT
* * * * * **
1595 GATATTAGAAGCGT-AAAAAGCCGTCAATATTTTTGGCACTGAATTATATATTTTTTCCT-AGTA
192 TATAATAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTT-CTAAGTA
* *
1658 TTGTGGCCAAAAAATTGA-GAATAAACATTTCGGGT
256 TTGT-GCAAAAAAATTGAGGAA-AAACTTTTCGGGT
1693 CAGGCTTTCG
Statistics
Matches: 774, Mismatches: 128, Indels: 98
0.77 0.13 0.10
Matches are distributed among these distances:
325 61 0.08
326 7 0.01
327 39 0.05
328 106 0.14
329 68 0.09
330 22 0.03
331 104 0.13
332 10 0.01
333 64 0.08
334 25 0.03
335 21 0.03
336 32 0.04
337 64 0.08
338 50 0.06
339 101 0.13
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (332 bp):
TTTTGGCTAAAAACGCGTTTCGGAATCCCGGCTCAATTTTAAATGATTTTTGGCAGAAAGACTCC
TTGAAATATCTATATTCATCGAACCAAATCTCAGCCACAATGGATATAAGAATTTGTTTTTACGA
GCATCTCAATCTTTATTTCGATTTAATTAGAAATTAAATAGGGAAAAAAGAAAAAGAAAATTATA
ATAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTAAGTATTGTG
CAAAAAAATTGAGGAAAAACTTTTCGGGTTAGTTTTTGCAAAATTTTCGAAATCATGTATAAACC
ATCAATG
Found at i:1605 original size:659 final size:646
Alignment explanation
Indices: 278--1934 Score: 1865
Period size: 660 Copynumber: 2.5 Consensus size: 646
268 TAAATCGACT
* * * *
278 ACGATATTAGAAGCGTCAAAAGGCCATCAATATTTTTGGCGTTGAATTATAT-TTTTTTTTGTAT
1 ACGATATTAGAAGCGT-AAAAAGCCGTCAATATTTTTGGCGTTGAATTATATATTTTTTCT-AAT
*
342 ATTCTGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATTGTGTACTT--ATC
64 ATTTTGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATTGTGTACTTACATC
*
405 AC-AGTTTTTGGCTAAAAACGAGTTTCATGG-CCCCGGCTCAGTTTTGAATGATTTTTTGCAGAA
129 ACGA-TTTTTGGCTAAAAACG-GTTTC--GGACCCCGGCTCAGTTTTGAATGATTTTTGGCAGAA
*
468 AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGTCACAATGGATTTAAGGATTTGTT
190 AGACTCCTTGAAATATCTATATTCATCTAA-CAAATCTCAGCCACAATGGATTTAAGGATTTG-T
* * * * *
533 TTTTACGAGCATCTGAATCTTTATTTCGATTTAATTAGAAATAAATTCGGAAAAAAAATGGAAAA
253 TTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAATTAAATACGGAAAAAAAAAGAAAAA
* * * * * *
598 CGATATTAGAAGCGTGAAAATCCCTTCAATTATTTTGGCGTTGAATTTTATATTTTTTTAAAGTA
318 CGATAATAGAAGCGTGAAAAACCATTCAATTATTTTAGCGTTAAATTATATATTTTTTTAAAGTA
* ** *
663 TTGTGGCAAAAAAATGAGGAAAAACTTTTGGGGTCAATTTTTGCAAAATTTTCGAAATCGTGTAC
383 TTGTGGCAAAAAAATGAGGAAAAACTTGTCAGGTCAATTTTTGCAAAATTTTCGAAATCATGTAC
* * * ** **
728 TAACTATCACAGTTTTTAGCAAAAAACGCGTTTCGGAGTCCCGGCTCAATTTTGCATGATTTTTG
448 TAACCATCACAGTTATTAGCAAAAAACGCGTTCCGGAACCCCGGCTCAATTTTAAATGATTTTTG
***
793 GCGTAAAGACTCCTTCAAATATCTATATTCATCGAACCAAATCTCAGCCACATTTTATATAAAGA
513 GCGTAAAGACTCCTTCAAATATCTATATTCATCGAACCAAATCTCAGCCACATAGGATATAAAGA
* * *
858 TCTGTTTTTATGAGCATCCGAACCTTATTTCTATTTAATTAGAAATTAATTCGGAAAAGAAATGG
578 TCTGTTTTTACGAGCATCCGAACCTTATTTCGATTTAATTAGAAATTAATCCGGAAAAGAAATGG
923 AAAA
643 AAAA
* * *
927 ACGATATTAGAATTTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTCTT
1 ACG--A-T---A-TTAGAAGCGTAAAAAG-CCGTCAATATTTTTGGCGTTGAATTATATATTTTT
* * * *
992 TCTAAATATTTTGCAAAAAATTGAGAAAAAACTTTTCGGGTTAGTTTTTAGCCAAAATCGTATAG
58 TCT-AATATTTTGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATTGTGTA-
* * *
1057 GTTACATCACGATTTTTGGCTAAAAACGTGTTTCGGATCCCGGCTCAGTTTTAAATGATTTTTGG
121 CTTACATCACGATTTTTGGCTAAAAACG-GTTTCGGACCCCGGCTCAGTTTTGAATGATTTTTGG
* *
1122 CAGAAAGACTCTTTGAAATATCTATATTCATCTAACAAAATCTCAGCCACAATGGATTTAAGAAT
185 CAGAAAGACTCCTTGAAATATCTATATTCATCTAAC-AAATCTCAGCCACAATGGATTTAAGGAT
* *
1187 TTGTTTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAGAATTAAATAAGGGAAAAAAGAAA
249 TTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAATTAAAT-ACGG--AAAA-AAA
** *
1252 AAGAAAAATTATAATAGAAGCGTGAAAAACCATTCAATTTTTTTAGCGTTAAATTATATATTTTT
310 AAGAAAAACGATAATAGAAGCGTGAAAAACCATTCAATTATTTTAGCGTTAAATTATATATTTTT
* * *
1317 TCT-GAGTATTGT-GCAAAAAAAATTGAGGAAAAACTTGTCAGGTTAGTTTTTGCAAAATTTTAG
375 T-TAAAGTATTGTGGC-AAAAAAA-TGAGGAAAAACTTGTCAGGTCAATTTTTGCAAAATTTT--
* * **
1380 CCGAAATCAATGTA-TAAACCATCA-ATGTTATTGGCTAAAAACGCGTTCCGGAACCCCGTTTCA
435 -CGAAATC-ATGTACT-AACCATCACA-GTTATTAGCAAAAAACGCGTTCCGGAACCCCGGCTCA
* *
1443 ATTTTAAATGATTTTTGGCGTAAAGACTCCTTGAAATAT-TCATATTCATCGAACCAAATGTCAG
496 ATTTTAAATGATTTTTGGCGTAAAGACTCCTTCAAATATCT-ATATTCATCGAACCAAATCTCAG
* ** * *
1507 CCACATAGGATATAAGGAT-TCGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAAT
560 CCACATAGGATATAAAGATCT-GTTTTTACGAGCATCCGAACCTTATTTCGATTTAATTAGAAAT
1571 TAATCCGGAAAA-AAATGGAAAA
624 TAATCCGGAAAAGAAATGGAAAA
** *
1593 ACGATATTAGAAGCGTAAAAAGCCGTCAATATTTTTGGCACTGAATTATATATTTTTTCCTAGTA
1 ACGATATTAGAAGCGTAAAAAGCCGTCAATATTTTTGGCGTTGAATTATATATTTTTT-CTAATA
* * * ** * *
1658 TTGTGGCCAAAAAATTGAGAATAAACATTTCGGGTCAGGCTTTCGCCGAAATTGTGTACTAACCA
65 TT-TTG-CAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATTGTGTACTTA-CA
* * * * * * * * * * **
1723 TCACGGTTTTTTAG-TAAAAACGCATTCCGAGGCCACAG-TCTGTTTTGCATGATTTTTGTCACC
127 TCAC-GATTTTTGGCTAAAAACG-GTTTCG-GACCCCGGCTCAGTTTTGAATGATTTTTGGCAGA
* * * * * *
1786 GAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCCCAACCACATTGGATTTAAGGATTTGC
189 AAGACTCCTTGAAATATCTATATTCATCTAA-CAAATCTCAGCCACAATGGATTTAAGGATTTGT
* * * *
1851 TTTTACGTGTATTTGAAT-TTTGTTTCGATTTAATTAGAAATT-AATTC--AAAAAAAATATGAA
253 TTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAG-AATTAAATACGGAAAAAAAA-A-GAA
* * *
1912 AAACGATATTAAAAGCATGAAAA
315 AAACGATAATAGAAGCGTGAAAA
1935 GTCTTCCAAT
Statistics
Matches: 848, Mismatches: 120, Indels: 74
0.81 0.12 0.07
Matches are distributed among these distances:
649 3 0.00
651 1 0.00
652 1 0.00
653 4 0.00
654 5 0.01
655 26 0.03
656 37 0.04
657 60 0.07
658 86 0.10
659 133 0.16
660 179 0.21
661 19 0.02
662 73 0.09
663 35 0.04
664 1 0.00
666 24 0.03
667 161 0.19
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (646 bp):
ACGATATTAGAAGCGTAAAAAGCCGTCAATATTTTTGGCGTTGAATTATATATTTTTTCTAATAT
TTTGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATTGTGTACTTACATCAC
GATTTTTGGCTAAAAACGGTTTCGGACCCCGGCTCAGTTTTGAATGATTTTTGGCAGAAAGACTC
CTTGAAATATCTATATTCATCTAACAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGA
GCATCTGAATCTTTGTTTCGATTTAATTAGAATTAAATACGGAAAAAAAAAGAAAAACGATAATA
GAAGCGTGAAAAACCATTCAATTATTTTAGCGTTAAATTATATATTTTTTTAAAGTATTGTGGCA
AAAAAATGAGGAAAAACTTGTCAGGTCAATTTTTGCAAAATTTTCGAAATCATGTACTAACCATC
ACAGTTATTAGCAAAAAACGCGTTCCGGAACCCCGGCTCAATTTTAAATGATTTTTGGCGTAAAG
ACTCCTTCAAATATCTATATTCATCGAACCAAATCTCAGCCACATAGGATATAAAGATCTGTTTT
TACGAGCATCCGAACCTTATTTCGATTTAATTAGAAATTAATCCGGAAAAGAAATGGAAAA
Found at i:2964 original size:18 final size:18
Alignment explanation
Indices: 2941--2977 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2931 TTGCATATGC
*
2941 AACTACACCCGTTGGTAG
1 AACTACACCCATTGGTAG
2959 AACTACACCCATTGGTAG
1 AACTACACCCATTGGTAG
2977 A
1 A
2978 GTTACCCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (18 bp):
AACTACACCCATTGGTAG
Found at i:3413 original size:60 final size:60
Alignment explanation
Indices: 3320--3437 Score: 227
Period size: 60 Copynumber: 2.0 Consensus size: 60
3310 CTTTACTGGT
*
3320 AAGGAAATTGTACCTCCCAGTTGACTCAACTTTCTACCTCCAACGAAGTGCTAACATGGA
1 AAGGAAATTGTACCTCCCAGTTGACTCAACTTTCTACCTCAAACGAAGTGCTAACATGGA
3380 AAGGAAATTGTACCTCCCAGTTGACTCAACTTTCTACCTCAAACGAAGTGCTAACATG
1 AAGGAAATTGTACCTCCCAGTTGACTCAACTTTCTACCTCAAACGAAGTGCTAACATG
3438 ACATCATGAC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.25
Consensus pattern (60 bp):
AAGGAAATTGTACCTCCCAGTTGACTCAACTTTCTACCTCAAACGAAGTGCTAACATGGA
Done.