Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011751.1 Corchorus olitorius cultivar O-4 contig11784, 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: 2353
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Found at i:299 original size:154 final size:153
Alignment explanation
Indices: 1--1793 Score: 2533
Period size: 154 Copynumber: 11.7 Consensus size: 153
* * *
1 AATGGAAAGAAAAGCATCGAGGTTTGCCAAATCCAAAACGATTCAAAACAGAGCTAATGGGCCCC
1 AATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCC
* * * * * * **
66 GAAACGGCCTAAAGTAACAAGTGTTCCAAATGATCCAGAAACTTCACAAAGGACTAATCTCACCA
65 GATA-GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA
131 AAATGATTATAGTTAGGCCATAAAC
129 AAATGATTATAGTTAGGCCATAAAC
*
156 AATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
1 AATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCC
* * * * * * *
221 GAAAGGCCTAAAATAGCAAGTATTCCAAATGAGCTAGAAACTTCACAGTGCACAAATCTCACCAA
65 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
286 AATGATTATAGTTAGGCCATAAAC
130 AATGATTATAGTTAGGCCATAAAC
* * * *
310 AATGGAAAGAAAAGCATTGAGATTTCCCAAATCGAAGACGATTCAGAACGACACTAATGGGCCCC
1 AATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAAGACGATTCAAAACGA-ACTAATGGGCCCC
* *
375 GATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAA
65 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
*
440 AATGATTATAGTTAGGCAATAAAC
130 AATGATTATAGTTAGGCCATAAAC
*
464 AATGGAAAGAAAAGCAGT-GAGGTTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCC
1 AATGGAAAGAAAAGCA-TCGAGGTTTGCCAAATCGAAGACGATTCAAAACGA-ACTAATGGGCCC
* * *
528 CGATAGGCCCAAAACAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATTTGACCA
64 CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA
*
593 AAATGATTATAGTTAGGCTATAAAC
129 AAATGATTATAGTTAGGCCATAAAC
** * * * *
618 AATGGAAAGAAAAGCATTTAGGTTTGCCAAATCGTAGACGATTCAAAACGTCACTAAAGGGTCCC
1 AATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCC
* *
683 GATCGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAGCAA
65 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
*
748 AATGATTATAGTTAGGCCATATAC
130 AATGATTATAGTTAGGCCATAAAC
* * *
772 AATGGAAATAAAAGCATCGAGGGTTGCCAAATCGAATACGATTCAAAACGGAACTAAT-GGCCCC
1 AATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCC
* * * * *
836 AAAAGGCCTAAAATAACAAGTGTTCCAAATGAGCT-AAAACTTTACAGTGGACTATTCTCACCAA
65 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
*
900 AATTATTATAGTTAGGCCATAAAC
130 AATGATTATAGTTAGGCCATAAAC
* * * *
924 AGTGGAAAGAAAAGCATCAAGGGTTGCCAAATCGATA-ATGATTCAAAACGACACTAATGGGCCC
1 AATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGA-AGACGATTCAAAACGA-ACTAATGGGCCC
*
988 CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGAACTAATCTCACCA
64 CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA
*
1053 ACATGATTATAGTTAGGCCATAAAC
129 AAATGATTATAGTTAGGCCATAAAC
* * *
1078 AATGGAAAGAAAAGCATCGAGGGTTGCCAAATCCAA-ACGATTCAAAACAGAGCTAATGGGCCCC
1 AATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCC
* * * *
1142 GAAAGGACTAAAATAACAAGTGTTCC-AATGAGC-CAAAACTTCACAGTGGACTAATCTCACCAA
65 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
1205 AATGATTATAGTTAGGCCATAAAC
130 AATGATTATAGTTAGGCCATAAAC
** * * * * **
1229 AATGGAAAGAAAAATATTGAGGTTTACCAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTT
1 AATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCC
* * * *
1294 GAT-GGACACAAAATAACAAGTGTTCCAAAGGAGCTAAGAACTTCACAGTGGACCTAATCTCACG
65 GATAGG-CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA-CTAATCTCACC
1358 AAAATGATTATAGTTAGGCCATAAAC
128 AAAATGATTATAGTTAGGCCATAAAC
* *
1384 AATGGAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCC
1 AATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAAGACGATTCAAAACGA-ACTAATGGGCCCC
1449 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
65 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
*
1514 AATGATTATAGTTAGGCCATAAAT
130 AATGATTATAGTTAGGCCATAAAC
* *
1538 AATGGAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCC
1 AATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAAGACGATTCAAAACGA-ACTAATGGGCCCC
* * *
1603 GATAGGCCTAAAATAACAAGCGTTCCAAATGAGCTAAAAACTTCACATTGGACTAATCTCACCAA
65 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
*
1668 AATGATTATTGTTAGGCCATAAAC
130 AATGATTATAGTTAGGCCATAAAC
* ***
1692 AATGGAAAGAAAAGCATCGAGGGTTGCCAAATC-AATGACGATTCAAAACGTAACTAATGGGTTT
1 AATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAA-GACGATTCAAAACG-AACTAATGGGCCC
** * * *
1756 TTACAGGCGCAAAATAATAAGTGTTCCAAATGAGCTAA
64 CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
1794 TGATACGAAT
Statistics
Matches: 1480, Mismatches: 138, Indels: 41
0.89 0.08 0.02
Matches are distributed among these distances:
151 86 0.06
152 144 0.10
153 133 0.09
154 909 0.61
155 206 0.14
156 2 0.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.21
Consensus pattern (153 bp):
AATGGAAAGAAAAGCATCGAGGTTTGCCAAATCGAAGACGATTCAAAACGAACTAATGGGCCCCG
ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
ATGATTATAGTTAGGCCATAAAC
Found at i:1491 original size:614 final size:616
Alignment explanation
Indices: 1--1752 Score: 2595
Period size: 614 Copynumber: 2.8 Consensus size: 616
* * * * * * *
1 AATGGAAAGAAAAGCATCGAGGTTTGCCAAATCCAAAACGATTCAAAACAG--AGCTAATGGGCC
1 AATGGAAAGAAAAACATTGAGGTTTACCAAATCGAAGACGATTCAAAAC-GTCA-CTAAAGGGTC
* * * * **
64 CCGAAACGGC-CTAAAGTAACAAGTGTTCCAAATGATC-CAGAAACTTCACAAAGGACTAATCTC
64 CCG-ATCGGCAC-AAAATAACAAGTGTTCCAAATGAGCTAAG-AACTTCACAGTGGACTAATCTC
*
127 ACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAA
126 ACGAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAA
* *
192 GACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCTAAAATAGCAAGTATTCCAAATGAGCTA
191 GACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAATGAGCTA
* * *
257 GAAACTTCACAGTGCACAAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
256 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
* *
322 AGCATTGAGATTTCCCAAATCGAAGACGATTCAGAACGACACTAATGGGCCCCGATAGGCCCAAA
321 AGCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAA
* *
387 ATAACAAGTATTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGT
386 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
* * * *
452 TAGGCAATAAACAATGGAAAGAAAAGCAGT-GAGGTTTCCCAAATCGAAGACGATTCAAAACGAC
451 TAGGCCATAAACAATGGAAAGAAAAGCA-TCGAGGGTTGCCAAATCCAAGACGATTCAAAACGAC
* *
516 ACTAATGGGCCCCGATAGGCCCAAAACAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
515 ACTAATGGGCCCCGAAAGGACCAAAACAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* * *
581 CTAATTTGACCAAAATGATTATAGTTAGGCTATAAAC
580 CTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
* * * *
618 AATGGAAAGAAAAGCATTTAGGTTTGCCAAATCGTAGACGATTCAAAACGTCACTAAAGGGTCCC
1 AATGGAAAGAAAAACATTGAGGTTTACCAAATCGAAGACGATTCAAAACGTCACTAAAGGGTCCC
* *
683 GATCGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA-GCA
66 GATCGGCACAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACG-A
* * *
747 AAATGATTATAGTTAGGCCATATACAATGGAAATAAAAGCATCGAGGGTTGCCAAATCGAATACG
130 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACG
*
812 ATTCAAAACGGAACTAAT-GGCCCCAAAAGGCCTAAAATAACAAGTGTTCCAAATGAGCT-AAAA
195 ATTCAAAACGGAACTAATGGGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAA
* * * *
875 CTTTACAGTGGACTATTCTCACCAAAATTATTATAGTTAGGCCATAAACAGTGGAAAGAAAAGCA
260 CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
** * * *
940 TCAAGGGTTGCCAAATCGATA-ATGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAAATA
325 TTGAGGTTTCCCAAATCGA-AGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAAATA
* *
1004 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGAACTAATCTCACCAACATGATTATAGTTAG
389 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
*
1069 GCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCCAA-ACGATTCAAAACAGA-GCT
454 GCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCCAAGACGATTCAAAAC-GACACT
* * *
1132 AATGGGCCCCGAAAGGACTAAAATAACAAGTGTTCC-AATGAGC-CAAAACTTCACAGTGGACTA
518 AATGGGCCCCGAAAGGACCAAAACAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
1195 ATCTCACCAAAATGATTATAGTTAGGCCATAAAC
583 ATCTCACCAAAATGATTATAGTTAGGCCATAAAC
* * *
1229 AATGGAAAGAAAAATATTGAGGTTTACCAAATCGAAGACGATTTAAAACGTCACTAATGGG-CCT
1 AATGGAAAGAAAAACATTGAGGTTTACCAAATCGAAGACGATTCAAAACGTCACTAAAGGGTCC-
* *
1293 TGAT-GGACACAAAATAACAAGTGTTCCAAAGGAGCTAAGAACTTCACAGTGGACCTAATCTCAC
65 CGATCGG-CACAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGA-CTAATCTCAC
* * *
1357 GAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGA
128 GAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGA
* *
1422 CGATTCAAAAC-GACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
193 CGATTCAAAACGGA-ACTAATGGGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAA
*
1486 AAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAATAATGGAAAGAAAA
257 AAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
*
1551 GCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCTAAAA
322 GCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAAA
* * *
1616 TAACAAGCGTTCCAAATGAGCTAAAAACTTCACATTGGACTAATCTCACCAAAATGATTATTGTT
387 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
1681 AGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAAT-CAATGACGATTCAAAACGTA-
452 AGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCCAA-GACGATTCAAAACG-AC
1744 ACTAATGGG
515 ACTAATGGG
1753 TTTTTACAGG
Statistics
Matches: 1027, Mismatches: 89, Indels: 40
0.89 0.08 0.03
Matches are distributed among these distances:
610 4 0.00
611 152 0.15
612 91 0.09
613 90 0.09
614 441 0.43
615 60 0.06
616 131 0.13
617 57 0.06
618 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (616 bp):
AATGGAAAGAAAAACATTGAGGTTTACCAAATCGAAGACGATTCAAAACGTCACTAAAGGGTCCC
GATCGGCACAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACGAA
AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGA
TTCAAAACGGAACTAATGGGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAAC
TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
TGAGGTTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAAATAAC
AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
CATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCCAAGACGATTCAAAACGACACTAAT
GGGCCCCGAAAGGACCAAAACAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
TCACCAAAATGATTATAGTTAGGCCATAAAC
Done.