Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019116.1 Corchorus olitorius cultivar O-4 contig19149, 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: 4732
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Found at i:983 original size:15 final size:16
Alignment explanation
Indices: 958--987 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
948 AATAATTAAT
958 TTTAGATTATAATATA
1 TTTAGATTATAATATA
974 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
988 TATTATTTAT
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:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:1519 original size:8 final size:8
Alignment explanation
Indices: 1492--1531 Score: 62
Period size: 8 Copynumber: 4.8 Consensus size: 8
1482 CTGCACGTGA
1492 TTACTATC
1 TTACTATC
1500 TTATCTTATC
1 TTA-C-TATC
1510 TTACTATC
1 TTACTATC
1518 TTACTATC
1 TTACTATC
1526 TTACTA
1 TTACTA
1532 CTATATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 21 0.70
9 2 0.07
10 7 0.23
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.53
Consensus pattern (8 bp):
TTACTATC
Found at i:1836 original size:19 final size:18
Alignment explanation
Indices: 1796--1831 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1786 AATAATTAAT
1796 TTTAGATTATAATATATA
1 TTTAGATTATAATATATA
1814 TTTA-ATTATAATAT-TA
1 TTTAGATTATAATATATA
1830 TT
1 TT
1832 ATTTATAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 10 0.56
18 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTAGATTATAATATATA
Found at i:3920 original size:685 final size:659
Alignment explanation
Indices: 2189--4727 Score: 2292
Period size: 674 Copynumber: 3.8 Consensus size: 659
2179 ATACTTTACA
* * * * * * *
2189 TCATCAAACCAAATCTCAACAACATTGGGTTTAAGAATTTATTTTTACGAGCATC---TGAATCT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAG-GTTTGTTTTTAC-AGCATCATTTGAATCT
* *
2251 TGTTTCGATTTAATTAGAAATTAATTTAGAAATAATAAGAAATACGATATTA-ACAGCATAAAAA
64 TGTTTCGATTTAATTAGAAATTAATTTAGAAA-AAT-AGAAAAACGATATTAGA-AGCGTAAAAA
* ** *
2315 GCCCTCCAATCTTTATGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGA
126 -TCCTCCAAAATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGA
* * * * * * *
2379 GAAATCTTTCGTGTCAATTTTTGTAAAATTTTAGCCGAAATCATGTACTAACAAACCATCACGGT
190 AAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC--GT-GTAA-TAATCATAACGGT
* * * * *
2444 TTTTTGGCTAAAACCGCGTT-CTGGAGACCCAGCTCAATTTTGCATGATTTTTGGCTCCGAGACT
251 TTTTTGGCTAAAACCGCGTTCCAGG-GACCCAGGTCAGTTTTGCATGATTTTTGGC-GCAAGACT
* * * * * *
2508 ACTTGAAATATCTATATTCATCTAATCAAGTCTCAGTCACATTGGATTTAAAGATTAGTCTTTAC
314 CCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTAC
*
2573 GAGCATCTGAATCTTGTTTCGA-TTAATTAGAAATTAATTTGAAAAAAA-ATAGAAAAAACGATA
379 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTAGAAAAAAATAT-G-AAAAACGATA
* * * ** * * *
2636 TTAGAAA-CGTCAAAAGACCTTCAGTCTTTTTTCCGTTCAATTATATAATTTTTATGTGTATTTT
442 TTA-AAAGCGTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATAT-ATTTTTATGAGTATGTT
* * * * * *
2700 AGCCAAAAATTGAGGAAATAGCTTTCGAGTCAA-TTTTTACAAAATTTTAGTCGAAATCCTGTAA
505 AGCTAAAAATTGAAGAAATATCTTTCGGGTCAATTTTTTGCAAAATTTTAGCCGAAAT-CTGTAA
* * * * * * * * *
2764 TAACCATCA-CAGTTTTTGGCTAAAAAAGCTTTCTGGGGCTCCGACTCAGTTTTACATGATTTTT
569 TAA-CA-CAGTATTTTTTTGCTAAAAACGCGTTCCGGGGC-CTGGCTCAGTTTTGCATGATTTTT
* * *
2828 GGCGCCAAGACTCCTTGAGATATCCATAT
631 GGCGTCAAGACTCCTTGAAATATCTATAT
* * *
2857 TCATCTAATCAAATCTCAGCCACATTAGATTTAAGAATTTGTTTTTACA--AGCATTTGAATCTT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAG-GTTTGTTTTTACAGCATCATTTGAATCTT
* *
2920 GTTTCGATTTAATTAGAAATTAATTTAGAAAAATATGAAAAGCGATATT-GAAAGCGTGAAAAGT
65 GTTTCGATTTAATTAGAAATTAATTTAGAAAAATA-GAAAAACGATATTAG-AAGCGT-AAAAAT
* * *
2984 CCTCCAATATTTTTGGCGTTAAATTATATATATATATAAATTATGAGTATTTTATCCAAAAATTG
127 CCTCCAAAATTTTTGGCGTTGAATTATATAT-T-T-T---TTATGAGTATTTTAGCCAAAAATTG
* * * * *** *
3049 ATGAAAAATTTTTCGGGTCATTTTATTTGCAAAATTTTAGCCAAAATCGTGTACCCATCATGGAT
186 AGGAAAAATCTTTCGGGTCA-ATT-TTTGCAAAATTTTAGCCGAAATCGTGTAATAATCAT--AA
*** * * ** * * * *
3114 TTTTTTTTTGGCAAAAAACGCGTTTTAGGGTCCC-GGCTCAGTTTTGCATAATTTTTGGCACGGA
247 CGGTTTTTTGGCTAAAACCGCGTTCCAGGGACCCAGG-TCAGTTTTGCATGATTTTTGGCGC-AA
* * *
3178 CACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGTG-TTTAAGGATTTGTT
310 GACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTG-GATTTAAGGATTTGTT
* * *
3242 TTTACTAGCATCTGAATCTTGTTTCTATTTAATTAAAAATTAATTCAGAAAAAAATATGAAAAAC
374 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT-AGAAAAAAATATGAAAAAC
* * * * *
3307 TATATTAAAAGTGTGAAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTATGTGTATG
438 GATATTAAAAGCGTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATG
* * * *
3372 ATGGCTAAAAATTGAAGAAATATCTTTCGGGTCAATTTTTTGCAAAATTTTAGCCAAAAGCGTGT
503 TTAGCTAAAAATTGAAGAAATATCTTTCGGGTCAATTTTTTGCAAAATTTTAGCCGAAATC-TGT
* * * * *
3437 AATATCACAGTTTTTTTTTTTTTGCTGAAAACGCGTTCCGGGGCCATGGGTCAGTTGTGCATGAT
567 AATAACACAG----TATTTTTTTGCTAAAAACGCGTTCCGGGGCC-TGGCTCAGTTTTGCATGAT
* *
3502 TTTTAGTGTCAAGACTCCTTGAAATATATATCTATAT
627 TTTTGGCGTCAAGACTCCTTG--A-A-ATATCTATAT
* * * * *
3539 TCATTTAATCAAATATCAGCCATATTGGATCTAAGGTTTTTTTTTACGAGCATCTAAATTTTGAA
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGTTTGTTTTTAC-AGCATC---A-TTT---
*
3604 AAAGAATCTTGTTTCGATTTAATTAGAAATT-ATTTCGAAAAATGTAGGAAAAACGATATTAGAA
58 ---GAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAA--TA-GAAAAACGATATTAGAA
* * * *
3668 GCGTAAAAATCCCTTCAAAAGTTTTGGTGTTGAATTATATATTTTTTATGAGTATTTTACCCAAA
117 GCGTAAAAAT-CCTCCAAAATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAA
* * * ** *
3733 CATTAAGGAAATATCTTTCCAGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTAATAATCATA
181 AATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATA
* *
3798 ACGGCTTTTTGGCTAAAACCGCGTTCCAGGGCCCCAGGTCAGTTTTGCATGATTTTTGGCGCTAA
246 ACGGTTTTTTGGCTAAAACCGCGTTCCAGGGACCCAGGTCAGTTTTGCATGATTTTTGGCGC-AA
* * *
3863 GACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCTACATTGGATTTAAGGATTTGTTT
310 GACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTT
* * *
3928 TTACGAGCATATGAATCTCGTTTCGATTTAATTAGAAATTAATTCAG-AAAAAATATGAAAAAAA
375 TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT-AGAAAAAAATATG-AAAAAC
* * * * * * *
3992 GATA-TGAAAGCGTGAAAAGTACTCCAATATTTTTGGCGTTAAATTATATATATTTCATGAATAT
438 GATATTAAAAGCGTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTAT
* * * * *
4056 TTTAG-TCAAAAATTGATGGAAAAATGTTTCGGGTC-ATTTTTTGTAAAATTTTAGCCGAAATC-
502 GTTAGCT-AAAAATTGA-AGAAATATCTTTCGGGTCAATTTTTTGCAAAATTTTAGCCGAAATCT
* * * * * *
4118 G---TACCAC-G-GTTTTTTTGCTAAAAACGTGTTTCGGGACCTCGGCTTAGTTTTGCATGATTT
565 GTAATAACACAGTATTTTTTTGCTAAAAACGCGTTCCGGGGCCT-GGCTCAGTTTTGCATGATTT
* * *
4178 TTGGCATCGAGACTCCTTCAAATATCTATAT
629 TTGGCGTCAAGACTCCTTGAAATATCTATAT
* *
4209 TCATCTAATCAAATCTCAACCACATTGAATTTAAGGATTTGTTTTTACAAGCATC---TGAATCT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGG-TTTGTTTTTAC-AGCATCATTTGAATCT
* * ** * * *
4271 TGTTTCAATTTAATTAGAAATTAATTCAGAAAAATCTTAAAAACAATATTAAAAGCGTAAAAGTC
64 TGTTTCGATTTAATTAGAAATTAATTTAGAAAAAT-AGAAAAACGATATTAGAAGCGTAAAAATC
** * * * * * *
4336 CTCCAATCTTTTTGCCGTTGAATTATATATATTTTATGAGTATTGTGGCTAAAAATTGAGAAAAA
128 CTCCAAAATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAA
* * * *
4401 ATATTTTGGGTCAATTTTTACAAAATTTTAGCCGAAATC--GT-AT-ATCATCACGGTTTTTTGG
193 ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATAACGGTTTTTTGG
* * ** * * * *
4462 CTAAAACAGTG-TCTC-GGGGTCCGGGTCAGTTTTGCATGATATTTGGTGGCAAAACTCCTTGAA
258 CTAAAACCGCGTTC-CAGGGACCCAGGTCAGTTTTGCATGATTTTTGG-CGCAAGACTCCTTGAA
* * * ** * * *
4525 ATATCTATATTCATCTGACCTAATCTTGGCCACATTGGATTTAAGAATTTATTTTTACGAGCATT
321 ATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
* * * * * * * * *
4590 TAAATCATGTTTTGATTGAATTAGAAATTAATTTGAAAAAGATAAGGAAAAACGATATTAGATGC
386 TGAATCTTGTTTCGATTTAATTAGAAATTAATTAGAAAAAAAT-ATGAAAAACGATATTAAAAGC
* * * *
4655 GTGAGAAGTCCTTCAATTTTTTTGGGGTTGAATTATATATTTTTTATGAGTATTGTGA-CTAAAA
450 GTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTA-TGTTAGCTAAAA
4719 ATTG-AGAAA
513 ATTGAAGAAA
4728 AATAT
Statistics
Matches: 1530, Mismatches: 268, Indels: 164
0.78 0.14 0.08
Matches are distributed among these distances:
650 5 0.00
651 138 0.09
652 84 0.05
653 7 0.00
654 2 0.00
656 84 0.05
657 24 0.02
658 27 0.02
659 9 0.01
664 1 0.00
665 2 0.00
666 1 0.00
667 46 0.03
668 85 0.06
669 1 0.00
670 41 0.03
671 18 0.01
672 5 0.00
673 7 0.00
674 270 0.18
675 91 0.06
676 30 0.02
677 3 0.00
678 54 0.04
679 1 0.00
680 6 0.00
681 10 0.01
682 40 0.03
683 1 0.00
684 53 0.03
685 200 0.13
686 17 0.01
687 32 0.02
688 5 0.00
689 37 0.02
692 1 0.00
693 11 0.01
694 34 0.02
695 46 0.03
696 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (659 bp):
TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGTTTGTTTTTACAGCATCATTTGAATCTTG
TTTCGATTTAATTAGAAATTAATTTAGAAAAATAGAAAAACGATATTAGAAGCGTAAAAATCCTC
CAAAATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATC
TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATAACGGTTTTTTGGCTA
AAACCGCGTTCCAGGGACCCAGGTCAGTTTTGCATGATTTTTGGCGCAAGACTCCTTGAAATATC
TATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAT
CTTGTTTCGATTTAATTAGAAATTAATTAGAAAAAAATATGAAAAACGATATTAAAAGCGTGAAA
AGTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATGTTAGCTAAAAATTGAAGA
AATATCTTTCGGGTCAATTTTTTGCAAAATTTTAGCCGAAATCTGTAATAACACAGTATTTTTTT
GCTAAAAACGCGTTCCGGGGCCTGGCTCAGTTTTGCATGATTTTTGGCGTCAAGACTCCTTGAAA
TATCTATAT
Done.