Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017850.1 Corchorus olitorius cultivar O-4 contig17883, 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: 16332
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:2165 original size:644 final size:634
Alignment explanation
Indices: 1352--3814 Score: 2390
Period size: 644 Copynumber: 3.8 Consensus size: 634
1342 AAATAAATAA
* * *
1352 TTTCATGCTTCTAATATCGTTTTTCCATTATTTTTTTCCGAATTAATTTCTATTTAAATCGAAAC
1 TTTCACGCTTCTAATATCGTTTTTCCA-TATTTTTCTCCGAATTAATTTCTAATTAAATCGAAAC
* ** *
1417 AAGATTTCA-ATGCTCGTAAAACCAAAT-TCTTATATACAATGTGGCTGAGATTTAATTCGATGG
65 AAGATTT-AGATGCTCGTAAAAACAAATCT-TTATATACAATGTGGCTGAGATTTGGTTCGATGA
*
1480 ATATAGATATTTTAATGAGTCTTTGCGCCAAAAATTATGCAAAATTGAGCCGGGGCTCCGTAACG
128 ATATAGATATTTCAATGAGTCTTTGCGCCAAAAATTATGCAAAATTGAGCCGGGGCTCCGTAACG
*
1545 CGTTTTTAACCAAAAGCCGTGATGGTTAGTATACGATTTCGGCTAAAATTTTGCAAAAATTGACC
193 CGTTTTTAACCAAAAGCCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATT-ACC
* *
1610 CGAAAAGTTTTTCCCCATTTTTTTCCACAATACTCAAAAAAATATATAATTCAACGCCAAAAAAA
257 CGAAAAGTTTTTCCCAATTTTTTGCCACAATACTCAAAAAAATATATAATTCAACGCC-AAAAAA
*
1675 ATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCCCCGAATTTATTTCTATT
321 ATTGAAGGGTTTTTCACGCTTCTAATATCG-TTTT-C-TTTTTTT---CCGAATTTATTTCTAAT
* * *
1740 TAAATCAAAATAAAGATTCAGATGCTCGTAAAACCAAATCCTTATATCCATTGTGGTTGAGATTT
380 TAAATCAAAA-AAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTT
* *
1805 GGTTAGTTGAATATAGATATTTC-AGGAGTCTTTCTGCCAAAAATTATTCAAAACTAAG-CGGGA
444 GGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTCAAAACTAAGCCGGGA
*
1868 GCCGCGTTTTTAGCCAAAAATCGTGACGTACATGATTTCGGCTAAAAAATTACCTGAAAAGTTTT
509 GCCGCGTTTTTAGCCAAAAACCGTGA-GTACATGATTTCGGCTAAAAAATTACCTGAAAAG-TTT
* * *
1933 TTCTCAATCTTTTGCAAAATATTCTGAAAAAATATATAATTCAACGCCAAAATATTGATGGCCT
572 TTCTCAAT-TTTTGCAAAATATTCTGAAAAAATATATAATTCAACGCCAAAAAATTGAAGGACT
* * *
1997 TTTCATGCTTCTAATATCGTTTTTCCATTATTTTTTTCC-AATTTATTTCTAATTAAATCGAAAC
1 TTTCACGCTTCTAATATCGTTTTTCCA-TATTTTTCTCCGAATTAATTTCTAATTAAATCGAAAC
2061 AAGATTTAGATGCTCGTAAAAACAAA-CTTTTATATACAATGTGGCTGAGATTTGGTTCGATGAA
65 AAGATTTAGATGCTCGTAAAAACAAATC-TTTATATACAATGTGGCTGAGATTTGGTTCGATGAA
* * *
2125 TATAGATATTTCAATGAGTCTTTGCTCCAAAAATTATGCAAAATTGAGTCGGGGCTCTGTAACGC
129 TATAGATATTTCAATGAGTCTTTGCGCCAAAAATTATGCAAAATTGAGCCGGGGCTCCGTAACGC
* * * **
2190 GTTTTTAGCCAAAAGCCGTGATGGTTAGTACACGATTTCGGTTAAAATTTTGCAAAAACTATCTT
194 GTTTTTAACCAAAAGCCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTA-CCC
* * * ** **
2255 GAAAAGCTTTTCCCAAATTTTTTGCCATAATACTCAGAAAAATATATAATTTTACGCCAAAAATG
258 GAAAAGTTTTTCCC-AATTTTTTGCCACAATACTCAAAAAAATATATAATTCAACGCCAAAAAAA
*
2320 TTGCAGGG-TTTTCACGCTTCTAATATCGTTTT-TTTTTTT-CGAATTTATTTCTAATTAAATCG
322 TTGAAGGGTTTTTCACGCTTCTAATATCGTTTTCTTTTTTTCCGAATTTATTTCTAATTAAATC-
* * * *
2382 AAACAAAGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGTCTGAGATTTGATTAGA
386 AAAAAAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGA
* * * *
2447 TAAATATAGAAATTTCAAGGAGTCTTTCTGCCAAAAATCATTCAAAACTGAGCCGGGACCCGAAA
451 TGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTCAAAACTAAGCCGGGAGCCG---
* * * * *
2512 TGTTTTTTTAG-CAAATAACCGTTAGTACACGATTTCGGCTAAAAACTAACCTGAAAAGTTTTTC
513 CG--TTTTTAGCCAAA-AACCGTGAGTACATGATTTCGGCTAAAAAATTACCTGAAAAGTTTTTC
* ** *
2576 TCAATTTATTGCAAAATATT-TAGAAAAAAATATATAATTCAACGTCAAAAAAATTGGCGGGCT
575 TCAATTT-TTGCAAAATATTCT-G-AAAAAATATATAATTCAACG-CCAAAAAATTGAAGGACT
* * *
2639 TGTCACGCTTCTAATATCGTTTTTCC--A-TTTTCTCCGAATTAATTTCTAATTAAACCGAAATA
1 TTTCACGCTTCTAATATCGTTTTTCCATATTTTTCTCCGAATTAATTTCTAATTAAATCGAAACA
* *
2701 AGATTTAGATGCTCGTAAAAACAAATCCTTATATACAATGTGACTGAGATTTGGTTCGATGAATA
66 AGATTTAGATGCTCGTAAAAACAAATCTTTATATACAATGTGGCTGAGATTTGGTTCGATGAATA
* * * * * * *
2766 CAGATATTTCAAAGAGTCTTTACGCC-AACATCATGCAAAATTGAGCCGGGACTCCGGAACGCGT
131 TAGATATTTCAATGAGTCTTTGCGCCAAAAATTATGCAAAATTGAGCCGGGGCTCCGTAACGCGT
**
2830 TTTTAGCCAAAAAACCATGAAAGTTAGTACACGATTTCGATGGAAAAAAAAAAAGAAGTACACGA
196 TTTT--------AACC---AAA---AG--C-CG---T-GATGG-----------TTAGTACACGA
2895 TTTCGGCTAAAATTTTGCAAAAATATACCCG-AAAGATTTTTCCTCAATTTTTTGCCACAATACT
229 TTTCGGCTAAAATTTTGCAAAAAT-TACCCGAAAAG-TTTTTCC-CAATTTTTTGCCACAATACT
* * *
2959 AAAAAAATATATATATAATTCAACGCCAAAAAAATTGAACGGTTCTTCACGCTTCTAATATC---
291 -CAAAAA-A-ATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTT
* * * * *
3021 -T-TTTTTTCCCAAATTTATTTCTAATTAAATCAAAAGAGAGATTCAGATGCTTGTAAAATCAAA
353 TTCTTTTTTTCCGAATTTATTTCTAATTAAATCAAAA-AAAGATTCAGATGCTCGTAAAAACAAA
* *
3084 TCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATCAATATAGATATTTCAAGGAGTCTTTCTGT
417 TCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGC
* * *
3149 CAAAAATCATTCAAAACTAAGTCGGGACCATGAAACGCGTTTTTAGCGAAAAACCGTGATGGTTA
482 CAAAAATCATTCAAAACTAAGCCGGG---A-G--CCGCGTTTTTAGCCAAAAACC--G-T-G--A
* * *
3214 GTACATAATTTCGGCTAAAATTTTGCAAAAATTGACCTGAAAGGATTTTCCTCAATTTTTTGCCA
535 GTACATGATTTCGGCT---A------AAAAATT-ACCTGAAAAG-TTTTTCTCAA-TTTTTG-CA
* * * *
3279 CAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTTGAAGGATT
587 AAATATTCTGAAAAAATATATAATTCAACGCC-AAAAAA-TTGAAGGACT
* * * * *
3329 TTTCACGCTTCTAATATCGTTTTCCCAT-TTTTTCCCCGAATTTATTTCTAATTAAATCAAAATA
1 TTTCACGCTTCTAATATCGTTTTTCCATATTTTTCTCCGAATTAATTTCTAATTAAATCGAAA-C
* * * * * * *
3393 AAGATTCAGATGCTCGTAAAACCAAATCTTTATATCCATTGTGGTTGAGATTTGGTTAGTTGAAT
65 AAGATTTAGATGCTCGTAAAAACAAATCTTTATATACAATGTGGCTGAGATTTGGTTCGATGAAT
* * * *
3458 ATAGATATTTC-AGGAGTCTTT-CTGCCAAAAATTATTCAAAACTAAG-CGGGAG--CCG---C-
130 ATAGATATTTCAATGAGTCTTTGC-GCCAAAAATTATGCAAAATTGAGCCGGG-GCTCCGTAACG
* ** * * *
3514 C-TTTTTAGCCAAAAATCATGATGGTTAGTAAATGATTTCGG--------TT--AAAAACTTACC
193 CGTTTTTAACCAAAAGCCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAA-TTACC
* * * * * *
3568 CGAAAAGTTTTTTCTCAATCTTTTG-CAAAATATTCATAAAAAATATACAATTCAACACCAAAAA
257 CGAAAAG-TTTTTCCCAATTTTTTGCCACAATACTCA-AAAAAATATATAATTCAACGCCAAAAA
* * * *
3632 GATTG-ATGGTCTTTTCATGCTTCTAATATCGTTTTTCCATTATATTTTCCGAATTAATTTCTAA
320 AATTGAAGGGT-TTTTCACGCTTCTAATATCG-TTTT-C-TT-T-TTTTCCGAATTTATTTCTAA
* * * * * * * * * *
3696 CTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATTC-TAATATACAATATGGCTAAGAAT
379 TTAAATCAAAAAAAGATTCAGATGCTCGTAAAAACAAATCCTTAA-ATCCATTGTGGCTGAGATT
* * *
3760 TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGC-GGCAAAAATCATGCAAAA
443 TGGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CTGCCAAAAATCATTCAAAA
3815 TTGAGCCGAG
Statistics
Matches: 1521, Mismatches: 184, Indels: 221
0.79 0.10 0.11
Matches are distributed among these distances:
635 89 0.06
636 36 0.02
637 8 0.01
638 43 0.03
639 117 0.08
640 30 0.02
641 96 0.06
642 56 0.04
643 33 0.02
644 241 0.16
645 88 0.06
646 6 0.00
649 8 0.01
650 88 0.06
651 27 0.02
652 2 0.00
654 14 0.01
655 2 0.00
658 1 0.00
659 5 0.00
665 5 0.00
666 1 0.00
669 5 0.00
670 67 0.04
671 135 0.09
672 13 0.01
673 29 0.02
674 21 0.01
675 4 0.00
677 2 0.00
678 18 0.01
681 1 0.00
686 5 0.00
687 6 0.00
688 11 0.01
689 38 0.02
690 41 0.03
691 4 0.00
692 45 0.03
693 80 0.05
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (634 bp):
TTTCACGCTTCTAATATCGTTTTTCCATATTTTTCTCCGAATTAATTTCTAATTAAATCGAAACA
AGATTTAGATGCTCGTAAAAACAAATCTTTATATACAATGTGGCTGAGATTTGGTTCGATGAATA
TAGATATTTCAATGAGTCTTTGCGCCAAAAATTATGCAAAATTGAGCCGGGGCTCCGTAACGCGT
TTTTAACCAAAAGCCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTACCCGAA
AAGTTTTTCCCAATTTTTTGCCACAATACTCAAAAAAATATATAATTCAACGCCAAAAAAATTGA
AGGGTTTTTCACGCTTCTAATATCGTTTTCTTTTTTTCCGAATTTATTTCTAATTAAATCAAAAA
AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAAT
ATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTCAAAACTAAGCCGGGAGCCGCGTTTTTA
GCCAAAAACCGTGAGTACATGATTTCGGCTAAAAAATTACCTGAAAAGTTTTTCTCAATTTTTGC
AAAATATTCTGAAAAAATATATAATTCAACGCCAAAAAATTGAAGGACT
Found at i:5261 original size:21 final size:21
Alignment explanation
Indices: 5235--5275 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5225 TTTTAAGCTT
*
5235 TGATACTTATAATTTTTTTCC
1 TGATACTTAGAATTTTTTTCC
5256 TGATACTTAGAATTTTTTTC
1 TGATACTTAGAATTTTTTTC
5276 ATTAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.07, T:0.56
Consensus pattern (21 bp):
TGATACTTAGAATTTTTTTCC
Found at i:15911 original size:25 final size:24
Alignment explanation
Indices: 15883--15944 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 24
15873 GTGGATTGTA
* *
15883 AAATAAATTGAATAATTAAGACTTT
1 AAATAAATTGAAGAATTAA-ACATT
*
15908 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
*
15932 AAA-AAATTCAAGA
1 AAATAAATTGAAGA
15945 CTGACCCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 9 0.27
24 7 0.21
25 17 0.52
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.31
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Done.