Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022426.1 Corchorus olitorius cultivar O-4 contig22459, 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: 34182
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:566 original size:22 final size:22
Alignment explanation
Indices: 536--579 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
526 TATGGGGTTC
* * *
536 AATGTAGCTCGATTTCAGATTA
1 AATGCAGCTAGATTCCAGATTA
558 AATGCAGCTAGATTCCAGATTA
1 AATGCAGCTAGATTCCAGATTA
580 GTCAGAGTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (22 bp):
AATGCAGCTAGATTCCAGATTA
Found at i:11239 original size:14 final size:14
Alignment explanation
Indices: 11220--11255 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
11210 CATTGAAAAG
11220 TGGGAGCATCACAA
1 TGGGAGCATCACAA
11234 TGGGAGCATCACAA
1 TGGGAGCATCACAA
11248 TGGGAGCA
1 TGGGAGCA
11256 CCGAAGTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.19, G:0.33, T:0.14
Consensus pattern (14 bp):
TGGGAGCATCACAA
Found at i:16369 original size:7 final size:7
Alignment explanation
Indices: 16359--16383 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16349 TTACAGTTGC
16359 TCTTGAT
1 TCTTGAT
16366 TCTTGAT
1 TCTTGAT
16373 TCTTGAT
1 TCTTGAT
16380 TCTT
1 TCTT
16384 TGGACCTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.16, G:0.12, T:0.60
Consensus pattern (7 bp):
TCTTGAT
Found at i:32805 original size:636 final size:628
Alignment explanation
Indices: 31538--33751 Score: 2731
Period size: 636 Copynumber: 3.5 Consensus size: 628
31528 ATGTACTAAC
* * * **
31538 AATCACGGTTTTTGGACTAAAAACGCGTTTTGGGGA-CTCGGCTTAGTTTTGCATGATTTTTGGC
1 AATCAC-G-TTTTGGACTAAAATCGCGTTTCGGGGATC-CGACGCAGTTTTGCATGATTTTTGGC
* * *
31602 AGAAAGCCTCCTTGAAAAATCTGTAATCATCGAACCAAATCTCAGCCACAATGGATTTAAGAATT
63 AGAAAGCCTCCTTGAAATATCTGTATTCATCGAACCAAATCTCAGCCACAATGGATTTAAGGATT
** * *
31667 TGTTTTTACGAGCATCTGAATTTGTTTCGGTTTAATTAGAAATAAATTCAGAAAAAAATGGAAAA
128 TACTTTTACGAGCATCTGAATTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAATGAAAAA
31732 CGATATTGGAAGCGTGAAAAACCCATCAATTTTTTTTTTTTGCGTTGAATTATATATTTTTTCCG
193 CGATATTGGAAGCGTGAAAAACCCATC-A--TTTTTTTTTTGCGTTGAATTATATATTTTTTCCG
* * * *
31797 AGTATTGTGTCAAAAAATTCATAAAAAGTTTCTTTGGGTC-TCTTTTTTGGCGAAATCATGT-TC
255 AGTATTGTGTCAAAAAATTCATAAAAAATTT-TTTGGGTCAT-TTTTTAGCCGAAATCGTGTAT-
* * *
31860 CAACCATCATAATTTTTGGGCTAAAAACGCGTTTTGGGGATCCAGCTTAGTTTTGCATGATTTTT
317 CAACCATCATAGTTTTTGGGCTAAAAACGCGTTTCGGGGATCCGGCTTAGTTTTGCATGATTTTT
31925 GGGAGAAAGCCTCCTTGAAATATCTGTATTCATCGAACCAAATCTCAGCCACAATGGGTTTAAGA
382 GGGAGAAAGCCTCCTTGAAATATCTGTATTCATCGAACCAAATCTCAGCCACAATGGGTTTAAGA
* * * *
31990 ATTTGTTTTTACGAGTATCTGAATTTGTTTCAATTTAATTAGAAATAAATTCGTGAAAAAATGGA
447 ATTTGTTTTTACGAGCATCAGAATTTGTTTCGATTTAATAAGAAATAAATTCG-GAAAAAATGGA
* * *
32055 AAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTTGCGTTGACTTGTATATTTTTACC
511 AAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTTGCGTTGAATTATATATTTTTTCC
* * *
32120 GAGTACTGTGGCAAAAGTTTCAGAAAAAA-TTTTCGGGTAATTTTTTTTAGCTGT
576 GAGTATTGTGGCAAAAATTTCAGAAAAAATTTTTCGGGTAA--TTTTTTAGCCGT
* * * *
32174 CATCACGCATTTTGGGCTAAAATCGCGTTTCGGGGATCCGGCCCAGTTTTGCATGATTTTTGGCA
1 AATCACG--TTTTGGACTAAAATCGCGTTTCGGGGATCCGACGCAGTTTTGCATGATTTTTGGCA
* * * *
32239 GAAAGTCTCCTTGAAATATCTGTATTCATCGAACCAAATCTCAACCACCATGGATTTAAGGGTTT
64 GAAAGCCTCCTTGAAATATCTGTATTCATCGAACCAAATCTCAGCCACAATGGATTTAAGGATTT
* * *
32304 ACTTTTACGAGCATCTGAATTTTGTTTCGATTTAGTTAGAAATAAATTCGGGAAAAAAAAGAAAA
129 ACTTTTACGAGCATCTGAA-TTTGTTTCGATTTAATTAGAAATAAATTC-AGAAAAAAATGAAAA
** *
32369 ACGATATTGGAAGCGTGAAAAACCTTTCAATTTTTTTTTTGCGTTGAATTATATATTTTTTCTGA
192 ACGATATTGGAAGCGTGAAAAACCCATC-ATTTTTTTTTTGCGTTGAATTATATATTTTTTCCGA
* * * * * *
32434 GTATTGTGAT-AGATAATTCAGAAACAAAATTTTCGGGTCATTTTTTAGCCGAAATCGTGTATTA
256 GTATTGTG-TCAAAAAATTCATAAA-AAATTTTTTGGGTCATTTTTTAGCCGAAATCGTGTATCA
** * *
32498 ACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGACCCGGCTTAGTTTTGCATGATTATTGG
319 ACCATCATAGTTTTTGGGCTAAAAACGCGTTTCGGGGATCCGGCTTAGTTTTGCATGATTTTTGG
*
32563 CAGAAAGCCTCCTTGAAATATCTGTATTCATCGAACCAAATCTCAGCCACAATGGAG-TTAAGAA
384 GAGAAAGCCTCCTTGAAATATCTGTATTCATCGAACCAAATCTCAGCCACAATGG-GTTTAAGAA
* * *
32627 TATGTTTTTAGGAGCATCAGAATTTAGTTTTGA-TTAATAAGAAATAAATTCGGAAAAAATGGAA
448 TTTGTTTTTACGAGCATCAGAATTT-GTTTCGATTTAATAAGAAATAAATTCGGAAAAAATGGAA
* * * *
32691 AAACAATATTGAAAGAGTGAAAAAACCCTTCAATTTTTTTTTGTGTTGAATTATATATTTTTTTC
512 AAACGATATTGGAAGCGTG-AAAAACCCTTCAATTTTTTTTTGCGTTGAATTATATA-TTTTTTC
* * * *
32756 CGAGTATTGTGGCAAAAATTTCAGAAAAAATTTTTCGAGTCACTTTTTAGCCGA
575 CGAGTATTGTGGCAAAAATTTCAGAAAAAATTTTTCGGGTAATTTTTTAGCCGT
* ** ** ** * *** * **
32810 AAT--CGTGTATAAACTATCA-CG-GTTTTAGGGCTAAAAACGC-GTTTCG-GGGA-----GAGC
1 AATCACGT-TTTGGACTAAAATCGCGTTTCGGGGAT-CCGACGCAGTTTTGCATGATTTTTG-GC
* * *
32864 AGAAAGCCTCCATGAAATATCTGTATTCATCGAACTAAATCTCAGCCACAATGGATTGAAGGATT
63 AGAAAGCCTCCTTGAAATATCTGTATTCATCGAACCAAATCTCAGCCACAATGGATTTAAGGATT
* * * *
32929 T-GTTTTCACGAGCATCTGAATTTGTTTTGGTTTAATTAGAAATAAATTCGGAAAAAAATGGAAA
128 TACTTTT-ACGAGCATCTGAATTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAAT-GAAA
* * * *
32993 AACAATATTGGAAGCGTG-AAAACCCATCA-CTTTTTTTTGTGTTGCATTATATATTTTTTCCGA
191 AACGATATTGGAAGCGTGAAAAACCCATCATTTTTTTTTTGCGTTGAATTATATATTTTTTCCGA
* * *
33056 GTATTGTGTCAAAAAAATTCATAAAAAATTTTTTTGGTCACTTTTTAGCCGAAAATCGTGTACCA
256 GTATTGTGTC-AAAAAATTCATAAAAAATTTTTTGGGTCATTTTTTAGCCG-AAATCGTGTATCA
* * *
33121 ACCATCATAGTTTTTGGGCTAAAAACGCGTTTCGAGGATCCGGCTCAGTCTTGCATGATTTTTGG
319 ACCATCATAGTTTTTGGGCTAAAAACGCGTTTCGGGGATCCGGCTTAGTTTTGCATGATTTTTGG
* *
33186 GAGAAAGCCTCCTTGAAATATCTGTATGCATCGAATCAAATCTCAGCCACAATGGGTTTAAGAAT
384 GAGAAAGCCTCCTTGAAATATCTGTATTCATCGAACCAAATCTCAGCCACAATGGGTTTAAGAAT
*
33251 TTGTTTTTACGAGCATCTA-AATTTGTTTCGATTTAATTAA-AAATAAATTCGGGTAAAAATGGA
449 TTGTTTTTACGAGCATC-AGAATTTGTTTCGATTTAA-TAAGAAATAAATTC-GGAAAAAATGGA
*
33314 AAAACGATATTGGAAGCGTGAAAAACCCTTCAA-TTTTTTTTGCGTTGAATTATATATTTTTTCT
511 AAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTTGCGTTGAATTATATATTTTTTCC
* * * *
33378 GAATATTGTGGCAAAAATTTTAGAAAAATTTTTTCGGGTAAATTTTTTAGCCGA
576 GAGTATTGTGGCAAAAATTTCAGAAAAAATTTTTCGGGT-AATTTTTTAGCCGT
* * * *
33432 AATTGTCACAGTTTTTGGGCTAAAATCGCGTTTCTGGCACCCGACGCAGTTTTGCATGATTTTTG
1 AA---TCAC-G-TTTTGGACTAAAATCGCGTTTCGGGGATCCGACGCAGTTTTGCATGATTTTTG
*
33497 TCAGAAAGCCTCCTTGAAATA-CTTGTATTCATCGAACCAAATCTCAGCCACAATGGATTTAAGG
61 GCAGAAAGCCTCCTTGAAATATC-TGTATTCATCGAACCAAATCTCAGCCACAATGGATTTAAGG
*
33561 ATTTACTTTTACGAGCATCTGAATTT-TTTCGATTTAGTTAGAAATAAATTCAGAAAAAAATGAG
125 ATTTACTTTTACGAGCATCTGAATTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAATGA-
* * * * *
33625 AAAACTATATTGGAAACGTGAAAAACCCTTCATTTTTTTTCTGCGTTGAATTATATA-TTTTTAC
189 AAAACGATATTGGAAGCGTGAAAAACCCATCATTTTTTTTTTGCGTTGAATTATATATTTTTTCC
* * * * * * *
33689 GTAGTATTAAG-GT-AAAAAATTTAGAAAAAATTTTTCGGGTAACTTTTTATCCGAAATTGTGTA
254 G-AGTATT--GTGTCAAAAAATTCATAAAAAATTTTTTGGGTCATTTTTTAGCCGAAATCGTGTA
33752 CTAAAATGCG
Statistics
Matches: 1352, Mismatches: 175, Indels: 104
0.83 0.11 0.06
Matches are distributed among these distances:
621 43 0.03
622 103 0.08
623 188 0.14
624 49 0.04
625 53 0.04
626 74 0.05
627 1 0.00
628 7 0.01
629 7 0.01
630 13 0.01
631 15 0.01
632 5 0.00
633 8 0.01
634 61 0.05
635 158 0.12
636 440 0.33
637 77 0.06
638 50 0.04
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (628 bp):
AATCACGTTTTGGACTAAAATCGCGTTTCGGGGATCCGACGCAGTTTTGCATGATTTTTGGCAGA
AAGCCTCCTTGAAATATCTGTATTCATCGAACCAAATCTCAGCCACAATGGATTTAAGGATTTAC
TTTTACGAGCATCTGAATTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAATGAAAAACGA
TATTGGAAGCGTGAAAAACCCATCATTTTTTTTTTGCGTTGAATTATATATTTTTTCCGAGTATT
GTGTCAAAAAATTCATAAAAAATTTTTTGGGTCATTTTTTAGCCGAAATCGTGTATCAACCATCA
TAGTTTTTGGGCTAAAAACGCGTTTCGGGGATCCGGCTTAGTTTTGCATGATTTTTGGGAGAAAG
CCTCCTTGAAATATCTGTATTCATCGAACCAAATCTCAGCCACAATGGGTTTAAGAATTTGTTTT
TACGAGCATCAGAATTTGTTTCGATTTAATAAGAAATAAATTCGGAAAAAATGGAAAAACGATAT
TGGAAGCGTGAAAAACCCTTCAATTTTTTTTTGCGTTGAATTATATATTTTTTCCGAGTATTGTG
GCAAAAATTTCAGAAAAAATTTTTCGGGTAATTTTTTAGCCGT
Done.