Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011830.1 Corchorus capsularis cultivar CVL-1 contig11851, 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: 1709
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Found at i:1423 original size:655 final size:648
Alignment explanation
Indices: 1--1709 Score: 1760
Period size: 655 Copynumber: 2.6 Consensus size: 648
* *
1 GAAGGG-TTTTCACGCTTCTAATATCATTTTTC-TTGCATTTTTTCCGAATAAATTTC---TTAA
1 GAAGGGTTTTTCACGCTTCTAATATCTTTTTTCATT---TTTTTTCCGAATTAATTTCTAATTAA
* * * *
61 ATCGAAACAAGATTCAGATACTCATAAAAACAAATTCTTAAATCCAATATGACTGCGATTTT-GT
63 ATCGAAACATGATTCAGATGCTCATAAAAACAAATTCTTAAATCCAATGTGGCTGCG-TTTTGGT
*
125 TAGAT-GAGTATATATATTTT-AAGAACACTTTCTGCCAAAAATCATGCAAAATTGAGTCGGAGC
127 TAGATGGA-TATATAT-TTTTCAAGAACTCTTTCTGCCAAAAATCATG-AAAATTGAGTCGGAGC
*
188 CCCAAAACACGTTTTTAGCCAAAAACCAG-GATGGTTAGTACACGATTTCGGC-----TAAAAAC
189 CCCAAATCACGTTTTTAGCCAAAAACC-GTGATGGTTAGTACACGATTTCGGCTAAAATAAAAAC
* * * *
247 TGTCCCGAAAATATTTTTCTCAATTTTTTGCCACAATACTAAAAAAAAATATATAATTCAATGCC
253 TGACCCGAAAATATTTTCCTCAATTTTTTGCCACAATACTAAAAAAAAATATATAATTCAAAGAC
* * ** *
312 AAAGAGATTGAAGGGGTTTTCACACTTCTAATATCGTTTTTTTCATTTTTTTTCCGAATTAATTT
318 AAAAAGATTAAAGACGTTTTCACACTTCTAATATCG-TTTTTTCATTTTTTTCCCGAATTAATTT
* *
377 CTAATTAAATCGAAACAAGATTCATATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAG
382 CCAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAG
* * *
442 ATTTAGTTAGATGAATATATATATTTCAAGAAGTCTTTCTGTAAAAAAATCATACAAAACTGAGC
447 ATTTAGTTAGATGAATATAGATATATCAAGAAGTCTTTCTGTAAAAAAACCATACAAAACTGAGC
* *
507 CCGAGCCCTGAAACGCAGTTTTAGCCAGAAACCGTGATGGAACATACACGATTTCGGCTAAAATC
512 ACGAGCCCGGAAACGCAGTTTTAGCCAGAAACCGTGATGGAACATACACGATTTCGGCTAAAATC
* *
572 TGACCTAAAATTTATTCTAATTTGTTTACCACAATACTAAGAAAAACTAAATAAATTAACGCAAA
577 TGACCGAAAATTTATTCTAATTTGTTTACCACAATACTAAGAAAAACTAAATAAATTAACACAAA
637 AAACATT
642 AAACATT
* *
644 GAAAGGTTTTTCACGCTTCTAATATCATTTTTTGCA----TTTTCCGAATTAATTTCTAATTGAA
1 GAAGGGTTTTTCACGCTTCTAATATC-TTTTTT-CATTTTTTTTCCGAATTAATTTCTAATTAAA
* * * * *
705 TCGAACCAAT-ATTCAAATGCTCATAAAAACAAATTTTTAAATCCAATGCGGCTGCGATTTGGTT
64 TCGAAAC-ATGATTCAGATGCTCATAAAAACAAATTCTTAAATCCAATGTGGCTGCGTTTTGGTT
* *
769 AGATGGATATATATTTTTCAAAAATTCTTTCTGCCAAAAATCATGAAAAATTGAGTCGGAGCCCC
128 AGATGGATATATATTTTTCAAGAACTCTTTCTGCCAAAAATCATG-AAAATTGAGTCGGAGCCCC
* *
834 AAATCACGTTTTTAGCCAAAAACCGTGATTGTTTGTACACGATTTCGGCTAAAATTTTGCAAAAA
192 AAATCACGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA---T--AAAAA
* *
899 CTGACCCGAAAAGT-TTTTCCTCAATTTTTTGCGACAATACTTGGAAAAAAAATATATAATTCAA
252 CTGACCCGAAAA-TATTTTCCTCAATTTTTTGCCACAATAC-T-AAAAAAAAATATATAATTCAA
* * *
963 AGACAAAAAGTTTAAAGACTTTTTCACATTTCTAATATCG-TTTTTCA-TTTTTTCCCGAAATT-
314 AGACAAAAAGATTAAAGACGTTTTCACACTTCTAATATCGTTTTTTCATTTTTTTCCCG-AATTA
* * * * *
1025 ATTTCCAATTAAATTGAAATAAGATTGAGATGCTCGTAAAAAGAAA-TCTCTAAATCCAATGTGT
378 ATTTCCAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCT-TAAATCCAATGTGG
* * * *
1089 CTGAGATTTGGTTAGATGAATATAGATATCAT-AAGGAGTCTTTAC-GT-CAAAAACCATGCAAA
442 CTGAGATTTAGTTAGATGAATATAGATAT-ATCAAGAAGTCTTT-CTGTAAAAAAACCATACAAA
* * * * *
1151 ACTGTGGCATG-GCCCGGAAACGC-GTTTTTAG-CTGAACACCGTGATGGTTAGA-ACACGATTT
505 ACTG-AGCACGAGCCCGGAAACGCAG-TTTTAGCCAGAA-ACCGTGATGG-AACATACACGATTT
* * * * * * *
1212 CGGCTAAAAAT-TGGCCCGAAAATTTTTTTCTCAA-TT-TTTGCCATAATACTCATAAAAA-TAT
566 CGGCT-AAAATCT-GACCGAAAA-TTTATTCT-AATTTGTTTACCACAATACTAAGAAAAACTAA
* * *
1273 AT-AATTCAATAC-CAAAATATT
627 ATAAATT-AACACAAAAAACATT
*
1294 GAAGGGTTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTTTTCCAAATTAATTTCTAATTAA
1 GAAGGGTTTTTCACGCTTCTAATATC-TTTTTTCA--TTTTTTTTCCGAATTAATTTCTAATTAA
* * *
1359 ACCGAAACATGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGTTTTGGTT
63 ATCGAAACATGATTCAGATGCTCATAAAAACAAATTCTTAAATCCAATGTGGCTGCGTTTTGGTT
* * * * * * * *
1424 AGAAGAATATATATATTTCAAGAAGTCTTTCTGCAAAAAATCATGCAAATCTGAGCCCGAGCCCT
128 AGATGGATATATATTTTTCAAGAACTCTTTCTGCCAAAAATCATGAAAAT-TGAGTCGGAGCCC-
* *
1489 GAAATGCA-G-TTTTAGCCAGAAACCGTGATGGTTAGTACACGATTTCGGC-----TAAAAACTG
191 CAAAT-CACGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATAAAAACTG
*** * ** * * *
1547 ATTTGAAAAT-TTTATTCTCAATTTTTCACCACAATACTAAAAAAAACTAAATAAATT-AATG-C
255 ACCCGAAAATATTT-TCCTCAATTTTTTGCCACAATACTAAAAAAAAATATAT-AATTCAAAGAC
* * * * * *
1609 AAAAAACATTGAAG-GGTTTTCACGCTTCTAATATCATTTTTCTTGCA-TTTTTT-CCGAATAAA
318 -AAAAAGATTAAAGACGTTTTCACACTTCTAATATC-GTTTT-TT-CATTTTTTTCCCGAATTAA
* *
1671 TTT-C--TTAAATCGAAACAAGATTCAGATACTCATAAAAAC
379 TTTCCAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
Statistics
Matches: 892, Mismatches: 118, Indels: 113
0.79 0.11 0.10
Matches are distributed among these distances:
640 16 0.02
642 55 0.06
643 179 0.20
644 38 0.04
645 47 0.05
646 9 0.01
647 1 0.00
649 2 0.00
650 47 0.05
651 69 0.08
652 136 0.15
653 62 0.07
654 10 0.01
655 214 0.24
656 5 0.01
657 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (648 bp):
GAAGGGTTTTTCACGCTTCTAATATCTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATC
GAAACATGATTCAGATGCTCATAAAAACAAATTCTTAAATCCAATGTGGCTGCGTTTTGGTTAGA
TGGATATATATTTTTCAAGAACTCTTTCTGCCAAAAATCATGAAAATTGAGTCGGAGCCCCAAAT
CACGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATAAAAACTGACCCGA
AAATATTTTCCTCAATTTTTTGCCACAATACTAAAAAAAAATATATAATTCAAAGACAAAAAGAT
TAAAGACGTTTTCACACTTCTAATATCGTTTTTTCATTTTTTTCCCGAATTAATTTCCAATTAAA
TCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTAGTTA
GATGAATATAGATATATCAAGAAGTCTTTCTGTAAAAAAACCATACAAAACTGAGCACGAGCCCG
GAAACGCAGTTTTAGCCAGAAACCGTGATGGAACATACACGATTTCGGCTAAAATCTGACCGAAA
ATTTATTCTAATTTGTTTACCACAATACTAAGAAAAACTAAATAAATTAACACAAAAAACATT
Found at i:1424 original size:322 final size:317
Alignment explanation
Indices: 1--1709 Score: 1581
Period size: 322 Copynumber: 5.3 Consensus size: 317
* *
1 GAAGGG-TTTTCACGCTTCTAATATCATTTTTCTTGCA-TTTTTTCCGAATAAATTTC---TTAA
1 GAAGGGTTTTTCACGCTTCTAATATC-GTTTT-TT-CATTTTTTTCCGAATTAATTTCTAATTAA
* * * * *
61 ATCGAAACAAGATTCAGATACTCATAAAAACAAATTCTTAAATCCAATATGACTGCGATTTTGTT
63 ATCGAAACAAGATTCAGATGCTCATAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTT
* ** * * * * *
126 AGATGAGTATATATATTTTAAGAACACTTTCTGCCAAAAATCATGCAAAATTGAGTCGGAGCCCC
128 AGATGAATATATATA-TTTAAGAAGTCTTTCTGTCAAAAATCATGCAAAACTG-GGCCGAGCCCT
* * * * *
191 AAAACACGTTTTTAGCCAAAAACCAG-GATGGTTAGTACACGATTTCGGCTAAAAACTGTCCCGA
191 GAAACGCGTTTTTAG-CAGAAACC-GTGATGGTTAGTACACGATTTCGGCTAAAAATTGGCCCGA
* * *
255 AAATATTTTTCTCAATTTTTTGCCACAATACTAAAAAAAAATATATAATTCAATGCCAAAGAGAT
254 AAATTTTTTTCTCAATTTTTTGCCACAATACT-AAAAAAAATATATAATTCAATG-CAAAAACAT
320 T
317 T
* *
321 GAAGGGGTTTTCACACTTCTAATATCGTTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAA
1 GAAGGGTTTTTCACGCTTCTAATATCG-TTTTTTCA-TTTTTTTCCGAATTAATTTCTAATTAAA
* * *
386 TCGAAACAAGATTCATATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTAGTTA
64 TCGAAACAAGATTCAGATGCTCATAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTTA
* * *
451 GATGAATATATATATTTCAAGAAGTCTTTCTGTAAAAAAATCATACAAAACTGAGCCCGAGCCCT
129 GATGAATATATATATTT-AAGAAGTCTTTCTGT-CAAAAATCATGCAAAACTG-GGCCGAGCCCT
* * *
516 GAAACGCAG-TTTTAGCCAGAAACCGTGATGG-AACATACACGATTTCGGCT-AAAATCT-GACC
191 GAAACGC-GTTTTTAG-CAGAAACCGTGATGGTTA-GTACACGATTTCGGCTAAAAAT-TGGCCC
* * * * * *
577 TAAAA-TTTATTCT-AATTTGTTTACCACAATACTAAGAAAAACTAAATAAATT-AACGCAAAAA
252 GAAAATTTTTTTCTCAATTT-TTTGCCACAATACTAA-AAAAAATATAT-AATTCAATGC-AAAA
639 ACATT
313 ACATT
* * *
644 GAAAGGTTTTTCACGCTTCTAATATCATTTTTTGCA---TTTTCCGAATTAATTTCTAATTGAAT
1 GAAGGGTTTTTCACGCTTCTAATATCGTTTTTT-CATTTTTTTCCGAATTAATTTCTAATTAAAT
* * * * * *
706 CGAACCAATATTCAAATGCTCATAAAAACAAATTTTTAAATCCAATGCGGCTGCGATTTGGTTAG
65 CGAAACAAGATTCAGATGCTCATAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTTAG
* * * * * * * * * *
771 ATGGATATATATTTTTCAAAAATTCTTTCTGCCAAAAATCATGAAAAATTGAGTCGGAGCCC-CA
130 ATGAATATATATATTT-AAGAAGTCTTTCTGTCAAAAATCATGCAAAACTG-GGCCGAGCCCTGA
* * * * *
835 AATCACGTTTTTAGCCAAAAACCGTGATTGTTTGTACACGATTTCGGCTAAAATTTTGCAAAAAC
193 AA-CGCGTTTTTAG-CAGAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA-ATTG-------
* * * *
900 TGACCCGAAAAGTTTTTCCTCAATTTTTTGCGACAATACTTGGAAAAAAAATATATAATTCAAAG
248 -G-CCCGAAAATTTTTTTCTCAATTTTTTGCCACAATAC-T--AAAAAAAATATATAATTCAATG
**
965 ACAAAAAGTTT
308 -CAAAAACATT
* ** ** * *
976 AAAGACTTTTTCACATTTCTAATATCG-TTTTTCATTTTTTCCCGAAATT-ATTTCCAATTAAAT
1 GAAGGGTTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTCCG-AATTAATTTCTAATTAAAT
* * * * * *
1039 TGAAATAAGATTGAGATGCTCGTAAAAAGAAA-TCTCTAAATCCAATGTGTCTGAGATTTGGTTA
65 CGAAACAAGATTCAGATGCTCATAAAAACAAATTCT-TAAATCCAATGTGGCTGAGATTTGGTTA
* * * * *
1103 GATGAATATAGATATCATAAGGAGTCTTTAC-GTCAAAAACCATGCAAAACTGTGGCATG-GCCC
129 GATGAATATATATAT-TTAAGAAGTCTTT-CTGTCAAAAATCATGCAAAACTG-GGC-CGAGCCC
* * *
1166 GGAAACGCGTTTTTAGCTGAACACCGTGATGGTTAGAACACGATTTCGGCTAAAAATTGGCCCGA
190 TGAAACGCGTTTTTAGCAGAA-ACCGTGATGGTTAGTACACGATTTCGGCTAAAAATTGGCCCGA
* * * * * *
1231 AAATTTTTTTCTCAA-TTTTTGCCATAATACTCATAAAAATATATAATTCAATACCAAAATATT
254 AAATTTTTTTCTCAATTTTTTGCCACAATACTAAAAAAAATATATAATTCAATGCAAAAACATT
*
1294 GAAGGGTTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTTTTCCAAATTAATTTCTAATTAA
1 GAAGGGTTTTTCACGCTTCTAATATCGTTTTTTCA---TTTTTTTCCGAATTAATTTCTAATTAA
* * * *
1359 ACCGAAACATGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGTTTTGGTT
63 ATCGAAACAAGATTCAGATGCTCATAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTT
* * *
1424 AGAAGAATATATATATTTCAAGAAGTCTTTCTG-CAAAAAATCATGCAAATCTGAGCCCGAGCCC
128 AGATGAATATATATATTT-AAGAAGTCTTTCTGTC-AAAAATCATGCAAAACTG-GGCCGAGCCC
* * ****
1488 TGAAATGCAG-TTTTAGCCAGAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATTTG
190 TGAAACGC-GTTTTTAG-CAGAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAATTGGCCCG
* ** *
1552 AAAATTTTATTCTCAATTTTTCACCACAATACTAAAAAAAACTAAATAAATT-AATGCAAAAAAC
253 AAAATTTTTTTCTCAATTTTTTGCCACAATACTAAAAAAAA-TATAT-AATTCAATGC-AAAAAC
1616 ATT
315 ATT
* *
1619 GAAGGG-TTTTCACGCTTCTAATATCATTTTTCTTGCA-TTTTTTCCGAATAAATTTC---TTAA
1 GAAGGGTTTTTCACGCTTCTAATATC-GTTTT-TT-CATTTTTTTCCGAATTAATTTCTAATTAA
*
1679 ATCGAAACAAGATTCAGATACTCATAAAAAC
63 ATCGAAACAAGATTCAGATGCTCATAAAAAC
Statistics
Matches: 1134, Mismatches: 186, Indels: 138
0.78 0.13 0.09
Matches are distributed among these distances:
317 4 0.00
318 90 0.08
319 140 0.12
320 40 0.04
321 49 0.04
322 209 0.18
323 128 0.11
324 132 0.12
325 86 0.08
326 3 0.00
327 2 0.00
328 1 0.00
329 6 0.01
330 19 0.02
331 15 0.01
332 47 0.04
333 153 0.13
334 10 0.01
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (317 bp):
GAAGGGTTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTCCGAATTAATTTCTAATTAAATC
GAAACAAGATTCAGATGCTCATAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTTAGA
TGAATATATATATTTAAGAAGTCTTTCTGTCAAAAATCATGCAAAACTGGGCCGAGCCCTGAAAC
GCGTTTTTAGCAGAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAATTGGCCCGAAAATTTT
TTTCTCAATTTTTTGCCACAATACTAAAAAAAATATATAATTCAATGCAAAAACATT
Done.