Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010159.1 Corchorus olitorius cultivar O-4 contig10191, 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: 31513
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2104 original size:334 final size:333
Alignment explanation
Indices: 1542--2363 Score: 939
Period size: 336 Copynumber: 2.5 Consensus size: 333
1532 ATATATATAT
* * * **
1542 ATATATATATTCATCTAACAAAATTTCAGCCACATTGTATTTAAGGATTTGTTTGTACGAGTTTC
1 ATATTTATATTCATCTAACCAAATTTCAGCCACATTG-ATTTAAGGATTTGTTTTTACGAGCATC
* * * *** *
1607 TAAATCCTGTTTCGATTTAATCAA-AAGTTAATTTTTAAATAAAATAGGAAAAACGATATTAGAA
65 TGAATCTTGTTTCGATTTAAT-AAGAAATTAATTAGGAAATAAAATAGGAAAAACAATATTAGAA
* * * ** * * * *
1671 GCGTGAAAAAGACTTTCAATTTTTTTGTGTTGAATTATTTATTTTTTATGATTATTTTCGATAGA
129 GCGTGAAAAAGACCTTCAATCTTTTTGTATCAAATTATATATTTTTTATGAGTATTTTAGACAGA
* *
1736 AAATAAGGAAAAATCTTTCATGTCAATTTTTGCAAAA-TTCAGCCGAAATCGTGTAGTAACCATC
194 AAATAAGGAAAAATCTTTCAGGTCAATTTTTGCAAAATTTCAGCCGAAATCGTGTACTAACCATC
* * *
1800 GCGGTTTTCGGCTAAAAACGCGTTTC-GCGACC-CGGCTCA-GTTTTGCATGATTTTTGGTGCCA
259 ACGGTTTTCGGCTAAAAACGCGTTACAG-GACCACGGCT-ATGTTTTGCATGATTTTTGGCGCCA
1862 AGAATCCTTGAA
322 AGAATCCTTGAA
*
1874 ATATTTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATC
1 ATATTTATATTCATCTAACCAAATTTCAGCCACATT-GATTTAAGGATTTGTTTTTACGAGCATC
* *
1939 TGAATCTTGTTTCGATTCAATTAGAAATTAATTAGGAAA-AAATATATTGGAAAAACAATATTAG
65 TGAATCTTGTTTCGATTTAATAAGAAATTAATTAGGAAATAAA-ATA--GGAAAAACAATATTAG
* * * *
2003 AAGTGT-TAAAAGGCCTTCAATCTTTTTGATATCAAATTATATATTTTTTATGAGTATTTTAGCC
127 AAGCGTGAAAAAGACCTTCAATCTTTTTG-TATCAAATTATATATTTTTTATGAGTATTTTAGAC
* * * * *
2067 A-AAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCTGAAATCGTGTACTAAC
191 AGAAAA-TAAGGAAAAATCTTTCAGGTCAATTTTTGCAAAATTTCAGCCGAAATCGTGTACTAAC
*
2131 CATCACGGTTTTTGGCTAAAAACGCGTTACAGGACCACGGCTATGTTTTGCATGATTTTTGGCGC
255 CATCACGGTTTTCGGCTAAAAACGCGTTACAGGACCACGGCTATGTTTTGCATGATTTTTGGCGC
** *
2196 CGGGACTCCTTGAA
320 CAAGAATCCTTGAA
* * * * * *
2210 ATATTTTTATTTATCTTACCAAATTTCAGTCACATTCGATTTAAGGATTTGTTTTTATGTGCATC
1 ATATTTATATTCATCTAACCAAATTTCAGCCACATT-GATTTAAGGATTTGTTTTTACGAGCATC
* * * * *
2275 TGAATCTTATTTCGATTTAATAAGAACTTAATTCA-G-AAT-AAATATGAAAAACGATATTAAAA
65 TGAATCTTGTTTCGATTTAATAAGAAATTAATT-AGGAAATAAAATAGGAAAAACAATATTAGAA
* * *
2337 TCGTG-AAAAGTCCTCCAATCGTTTTTG
129 GCGTGAAAAAGACCTTCAATC-TTTTTG
2364 GCATCTTTTC
Statistics
Matches: 414, Mismatches: 61, Indels: 29
0.82 0.12 0.06
Matches are distributed among these distances:
331 4 0.01
332 119 0.29
333 29 0.07
334 81 0.20
335 56 0.14
336 124 0.30
337 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (333 bp):
ATATTTATATTCATCTAACCAAATTTCAGCCACATTGATTTAAGGATTTGTTTTTACGAGCATCT
GAATCTTGTTTCGATTTAATAAGAAATTAATTAGGAAATAAAATAGGAAAAACAATATTAGAAGC
GTGAAAAAGACCTTCAATCTTTTTGTATCAAATTATATATTTTTTATGAGTATTTTAGACAGAAA
ATAAGGAAAAATCTTTCAGGTCAATTTTTGCAAAATTTCAGCCGAAATCGTGTACTAACCATCAC
GGTTTTCGGCTAAAAACGCGTTACAGGACCACGGCTATGTTTTGCATGATTTTTGGCGCCAAGAA
TCCTTGAA
Found at i:6954 original size:12 final size:12
Alignment explanation
Indices: 6937--6961 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6927 AGCCGCTTAC
6937 CACTTGATCCAA
1 CACTTGATCCAA
6949 CACTTGATCCAA
1 CACTTGATCCAA
6961 C
1 C
6962 CATTGTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.36, G:0.08, T:0.24
Consensus pattern (12 bp):
CACTTGATCCAA
Found at i:30193 original size:665 final size:657
Alignment explanation
Indices: 28371--30525 Score: 2162
Period size: 665 Copynumber: 3.2 Consensus size: 657
28361 ACCCATGATG
* * * * *
28371 GTAAAAATT-ACCCGAAAGATTTTCCTCATTTTTTTTGGCAAAACTACTCATAAATATATATAAT
1 GTAAAAATTGACTCGAAAGATTTTCCTCA-ATTTTTAGCCAAAA-TACTCATAAAAATATATAAT
* * * * * *
28435 TCAACACCAAAAGGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTTCGGA
64 TCAACGCCAAAAAGATTGAAGGTCTTTTCACGCTTCTAATATCG-TTTTCATA--TTTTTTCCGA
* *
28500 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACATAAAAACAAATCCTTGAATCCAATG
126 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTCAATCCAATG
* * * * *
28565 TGCCTGAGATTTGATTAGATGAATAAATATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCAAA
191 TGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCAGCG-CAAAAATCATGCAAA
* * * * * * *
28630 ACAGAGCTGTGGTCCTGAAACGCGTTTTTACCCAAAAACCGTGATGGTTA-GTATACGATTTCGG
255 ACTGAAC-CTGGACCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTACGTACACGATTTCGG
* *
28694 CTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGT-TAAAATACTCATAAA
319 CT-AAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAA-TTTT-GTCTAAAATACTCATAAA
* * * ** * * * *
28758 AAATATATAATTCGACATCAAAAAGATTAAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCAAA
381 ATATATATAATTCAAC-TCAAAAATATTGGAGGACTTTTCACGCTTTTAATATTGTTTTT-CATA
* * * * *
28823 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCACATACTCGAAAAAAGAAATCCTT
444 -TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* * ** * * * *
28888 AAATCTAATGTGTCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGA--TTG-CACCAAAAA
508 AAATCCAATCTAACTGAAATTTGATTAGATGAATATAGATATTTCAAAGATCTTGACGCCAAAAA
* * * * * * *
28950 TCATGCAATACTGACTTGGGTCCCGGAACGCGTTTTTAGCCGAAAACCGTGATGGTCAGTACACG
573 TCATGCAAAACTGAATTGGGGCCCAGAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACG
*
29015 A-TT--TCGGCTAAAATTTC
638 ATTTCATCGGCTAAAATTTT
* ** * * * *
29032 GGAAAAATTGA-TCCGAAAGATTTTTCCTCGGTTTCTAACGAAAATACTCATAAAAACATATAAT
1 GTAAAAATTGACT-CGAAAGA-TTTTCCTCAATTTTTAGCCAAAATACTCATAAAAATATATAAT
* * * * * *
29096 TCAATGCCAAAAAAATTGAAAGCCTTTTTCACGCTTTTAATATCGTTTTCATATTTTTTCAGAAT
64 TCAACGCCAAAAAGATTGAAGGTC-TTTTCACGCTTCTAATATCGTTTTCATATTTTTTCCGAAT
* * * *
29161 TAATTTCTTATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTCAATTCAATGTG
128 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTCAATCCAATGTG
* * *
29226 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCCGCACCAAAAAATTATGCAAAA
193 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCAGC-GC-AAAAATCATGCAAAA
* * * * * *
29291 CT-AAGTCGGGGCCCTGAAATGCGTTTTTAGCTAAAAAAAAAAAACGTGATGGTTAC-TACACGA
256 CTGAA-CCTGGACCC-GAAACGCGTTTTTAGC------CAAAAACCGTGATGGTTACGTACACGA
* * * *
29354 TTTCGGCTAAAATTTACAAAAAATGACCCGAAAAATTATTCCATCAATTTT-TCGCTAAAATACT
313 TTTCGGCTAAATTTTGCAAAAATTGACCCGAAAAATTTTTCC-TCAATTTTGT--CTAAAATACT
* *
29418 CATAAAATATATATATAATTCAATTCCAAAAATATTGGAGGACTTTTCAAGCTTTTAATATTGTT
375 CAT-AAA-ATATATATAATTCAACT-CAAAAATATTGGAGGACTTTTCACGCTTTTAATATTGTT
*
29483 TTTCATATTTTT-TCGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
437 TTTCATATTTTTCT-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
* * * * *
29547 AATTCTTAAATCCAATTTAACTGAAATTTGATTAAATGAATATGGATATATCAAAGATTCTTGAC
501 AATCCTTAAATCCAATCTAACTGAAATTTGATTAGATGAATATAGATATTTCAAAGA-TCTTGAC
* *
29612 GCCAAAAATCATGCAAAACTTAGTTGGGGCCCTAGAACGCGTTTTTAGCCAAAAACCGTGATGAT
565 GCCAAAAATCATGCAAAACTGAATTGGGGCCC-AGAACGCGTTTTTAGCCAAAAACCGTGATGAT
* *
29677 TATTACACGATTTCGATCGGCTAGAATTTT
629 TAGTACACGATTTC-ATCGGCTAAAATTTT
* *
29707 GTAAAAATTGACTCGAAAGTTATTTCCTCAATTTTTAGCCACAATACTCATAAAAATTATATAAT
1 GTAAAAATTGACTCGAAAGAT-TTTCCTCAATTTTTAGCCAAAATACTCATAAAAA-TATATAAT
* * *
29772 TCAACGCCAAAAAGTTTGAAGGTCTTTTCATGCTTCTAATATCGTTTTCCCTATTATTTTCCGAA
64 TCAACGCCAAAAAGATTGAAGGTCTTTTCACGCTTCTAATATCGTTTT-CATATT-TTTTCCGAA
* * ** *** * *
29837 TTAATTTCTAATTAAATCGAAACATGATTCATATTTTTC-T-TTTACAAATCCTT-AAACCAATT
127 TTAATTTCTAATTAAATCGAAACAAGATTCAGA-TGCTCATAAAAACAAATCCTTCAATCCAATG
* * * * *
29899 TGGCTGAAATTTGGTTAGATGAATGTAGATATTT-AAGGACTCTCAGCGCAAAAATCATGCAACA
191 TGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCAGCGCAAAAATCATGCAAAA
* * * * * * *
29963 TTGAACCTAGACCCGGAACG-GGTTTTAGCCAAAAACCGTGATTTCGACTAACGTACACGATATC
256 CTGAACCTGGACCCGAAACGCGTTTTTAGCCAAAAACCGTGA--T-G-GTTACGTACACGATTTC
* * * * **
30027 GGCTAATATTTTGCAAAAATTGACCAGAAATATTTTTTCTCAATTTTGTCTAAAATGCTTGTAAA
317 GGCTAA-ATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTGTCTAAAATACTCATAAA
*
30092 ATATATATAATTCAACTCAAAAATATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATT
381 ATATATATAATTCAACTCAAAAATATTGGAGGACTTTTCACGCTTTTAATATTGTTTTTCATATT
* * *
30157 TTTCTGAATTAATTTCTAATTAAATCGAATCAAGATTCAGATGCACGTAAAACCAAATCCTTAAA
446 TTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAA
* * * * *
30222 TGCAATCTAGA-TGATACTTGATTAGATGAATATAGATATTTC-AAGAAGTCTCGATGCCAAAAA
511 TCCAATCTA-ACTGAAATTTGATTAGATGAATATAGATATTTCAAAG-A-TCTTGACGCCAAAAA
* ** * * * * *
30285 TCTTGCAAAACTGAACCGGGGCCCCGAAATGTGTTTTTAGCAAAGAAAACCGTGATAATTAGTAC
573 TCATGCAAAACTGAATTGGGGCCCAG-AACGCGTTTTTAGC-CA-AAAACCGTGATGATTAGTAC
*
30350 ATGATTTCA---GCTAAAATTTT
635 ACGATTTCATCGGCTAAAATTTT
* * * *
30370 GCAAAAAATGAC-CAGCAAAAATTTTCCTCAATTTTTAGCCACAAT-CTCATAAAAAATATATAA
1 GTAAAAATTGACTC-G-AAAGATTTTCCTCAATTTTTAGCCAAAATACTCAT-AAAAATATATAA
*
30433 TTCAACGCTAAAAAGATTGAAGGGT-TTTTCACGCTTCTAATATCG----C-T-TTTTTTCCGAA
63 TTCAACGCCAAAAAGATTGAA-GGTCTTTTCACGCTTCTAATATCGTTTTCATATTTTTTCCGAA
* * *
30491 TTAATTTCTAATTAAAACGAAATATGATTCAGATG
127 TTAATTTCTAATTAAATCGAAACAAGATTCAGATG
30526 TTTGTAAATA
Statistics
Matches: 1245, Mismatches: 193, Indels: 120
0.80 0.12 0.08
Matches are distributed among these distances:
653 1 0.00
654 39 0.03
655 2 0.00
656 1 0.00
657 1 0.00
659 117 0.09
660 29 0.02
661 51 0.04
662 87 0.07
663 61 0.05
664 18 0.01
665 214 0.17
666 163 0.13
667 36 0.03
668 61 0.05
669 27 0.02
670 62 0.05
671 41 0.03
672 21 0.02
673 3 0.00
674 12 0.01
675 115 0.09
676 42 0.03
677 38 0.03
678 3 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (657 bp):
GTAAAAATTGACTCGAAAGATTTTCCTCAATTTTTAGCCAAAATACTCATAAAAATATATAATTC
AACGCCAAAAAGATTGAAGGTCTTTTCACGCTTCTAATATCGTTTTCATATTTTTTCCGAATTAA
TTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTCAATCCAATGTGGCT
GAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCAGCGCAAAAATCATGCAAAACTGAA
CCTGGACCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTACGTACACGATTTCGGCTAAATT
TTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTGTCTAAAATACTCATAAAATATATATAA
TTCAACTCAAAAATATTGGAGGACTTTTCACGCTTTTAATATTGTTTTTCATATTTTTCTGAATT
AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATCTAA
CTGAAATTTGATTAGATGAATATAGATATTTCAAAGATCTTGACGCCAAAAATCATGCAAAACTG
AATTGGGGCCCAGAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCATCGGCTA
AAATTTT
Done.