Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004997.1 Corchorus capsularis cultivar CVL-1 contig05015, 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: 1678
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:967 original size:333 final size:330
Alignment explanation
Indices: 56--1660 Score: 2077
Period size: 333 Copynumber: 4.9 Consensus size: 330
46 TTCGCTAAAC
* * * * *
56 GTACACAATTTCGGCTAAAATTTGGCAAAAATTGACCCGAAGGATTTTTCCTCAAATTTTCGCCC
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTCGCCA
* * *
121 CAATAATCATAGAAAATATATAATTCAAGGCTAAGAAGATTGGAGGGCTTTTCAGGCTTTAAATA
66 CAATAATCATAGAAAATATATAATTCAACGCCAA-AAGATTGGAGGGCTTTTCAGGCTTCAAATA
* * *
186 CCATTTCTCTTATTTTTTCTGAATTAATTTTTATTAAATCGAAATAAGATTCAGATAT-TCGTAA
130 TCATTTTTCTTATTTTTTCTGAATTAATTTTAATTAAATCGAAATAAGATTCAGAT-TCTCGTAA
* * *
250 AAACAAA-TCGTTAAATCCAATGTGGTTAAGATTTGGTTAGATGAATATAGATATCTCAATGACT
194 AAACAAATTC-TTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGACT
* * *
314 CTTGGCAACAAAAATCATGCAAAACTGAGTCGGGGCCCTGGATCGCGTTTTTGGCTAAAACCCGT
258 CTTGGCAACAAAAATCATGCAAAACTGAGTCGGGGCCCAGGAACGCGTTTTTGGCCAAAACCCGT
*
379 GATGATTA
323 GATGGTTA
* * * * ***
387 GTACACAATTTCGGCTAAAATTTTGCAAAAGTTG-CCCGAAGGATTTTTCCTCAATGTTTCATTA
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTCGCCA
* * *
451 CAATACTCGTA-AAATAGATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCAGGCTTCTAAA
66 CAATAATCATAGAAA-ATATATAATTCAACGCC-AAAAGATTGGAGGGCTTTTCAGGCTTC-AAA
* * * *
515 -ATCGTTTTTCTTATTTTTTTCTGAACTAACTTTTAATTAAACCGAAATAAGATTCTA-ATGCTC
128 TATCATTTTTCTTA-TTTTTTCTGAATTAA-TTTTAATTAAATCGAAATAAGATTC-AGATTCTC
* * * *
578 GTAAAAACAAATCCTTAAATCCATTGTAGCTAAGATTTGGTTAGAAGAATATAGATATTTCAAGG
190 GTAAAAACAAATTCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGG
* *
643 ACTATTGGCAACAAAAATCATGCAAAACTGAGCCGGGGCCCAGGAACGCGTTTTTGGCCAAAACC
255 ACTCTTGGCAACAAAAATCATGCAAAACTGAGTCGGGGCCCAGGAACGCGTTTTTGGCCAAAACC
708 CGTGATGGTTA
320 CGTGATGGTTA
* * * *
719 GTACACGATTTCGGCTAAAATTTTACAAAAATTGACCGGAAAGATTTTTCCTCAATTTTTAGCAA
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTCGCCA
* * * *
784 CAATAATCATAGGAAATATATAATTCAACGTCAAAATGATT-GAAGGCTTTTTCACGCTTCAAAT
66 CAATAATCATAGAAAATATATAATTCAACGCCAAAA-GATTGGAGGGC-TTTTCAGGCTTCAAAT
* *
848 ATCATTTTTCTTATGTTTTTCTGAATTAATTTCTAACTAAATCGAAATAAGGTTCAGATTCTCGT
129 ATCATTTTTCTTAT-TTTTTCTGAATTAATTT-TAATTAAATCGAAATAAGATTCAGATTCTCGT
* *
913 AAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGGC
192 AAAAACAAATTCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAC
* *
978 TCTTGGCAACAAAAATTATGTAAAACTGAGTCGGGGCCCAGGAACGCGTTTTTGGCCAAAACCCG
257 TCTTGGCAACAAAAATCATGCAAAACTGAGTCGGGGCCCAGGAACGCGTTTTTGGCCAAAACCCG
*
1043 TGATGCTTA
322 TGATGGTTA
* *
1052 GTACACGATTTCGGC--------TGC-AAAATTGACCCGAAAGATTTTTCCTCAATTATTCGCCC
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTCGCCA
* * * *
1108 CAATACTCA-A-AAAAGTATATAATTCAACGTCAAAATGATT-GAAGGCTTTTTCACGCTTCAAA
66 CAATAATCATAGAAAA-TATATAATTCAACGCCAAAA-GATTGGAGGGC-TTTTCAGGCTTCAAA
* * *
1170 TATCATTTTTCTTATTTTTTTATGAATTAATTTCTAACTAAATCGAAATAAGGTTCAGATTCTCG
128 TATCATTTTTCTTA-TTTTTTCTGAATTAATTT-TAATTAAATCGAAATAAGATTCAGATTCTCG
* *
1235 TAAAAACAAATTCTTAAATCCAATGTGGCTTAGATTTGGTTAGATAAATATAGATATTTCAAGGA
191 TAAAAACAAATTCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGA
* * * * * * *
1300 CTCTTAGCAACAAAATTTATACAAAACAGA-TACTGGGCCCAGGAACGCGTTTTTGGGCCGAAAC
256 CTCTTGGCAACAAAAATCATGCAAAACTGAGT-CGGGGCCCAGGAACGCGTTTTT-GGCCAAAAC
1364 CCGTGATGGTTA
319 CCGTGATGGTTA
* * * *
1376 GTACATGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAGATTTTTCCTCAAATTTTCTCCA
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTCGCCA
* *
1441 CAATAATCATAGAAAATATATAATTCAAGGCCAAGAAGATTGGAGGGCTTTCCAGGCTTCAAATA
66 CAATAATCATAGAAAATATATAATTCAACGCCAA-AAGATTGGAGGGCTTTTCAGGCTTCAAATA
* *
1506 CCATTTCTCTTATTTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTCAGATGT-TCGTA
130 TCATTTTTCTTATTTTTTCTGAATTAA-TTTTAATTAAATCGAAATAAGATTCAGAT-TCTCGTA
* * * *
1570 AAAA-AAA-TCGTTAAATCCAATGTGGTTAAGATTTGCTTAGATGAATATAGATATCTCAATGAC
193 AAAACAAATTC-TTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAC
*
1633 TCTTGGCAACAAAAATCTTGCAAAACTG
257 TCTTGGCAACAAAAATCATGCAAAACTG
1661 CATCAGGGCC
Statistics
Matches: 1121, Mismatches: 117, Indels: 71
0.86 0.09 0.05
Matches are distributed among these distances:
322 4 0.00
323 218 0.19
324 75 0.07
325 2 0.00
329 3 0.00
330 81 0.07
331 53 0.05
332 276 0.25
333 346 0.31
334 52 0.05
335 11 0.01
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (330 bp):
GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTCGCCA
CAATAATCATAGAAAATATATAATTCAACGCCAAAAGATTGGAGGGCTTTTCAGGCTTCAAATAT
CATTTTTCTTATTTTTTCTGAATTAATTTTAATTAAATCGAAATAAGATTCAGATTCTCGTAAAA
ACAAATTCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGACTCTT
GGCAACAAAAATCATGCAAAACTGAGTCGGGGCCCAGGAACGCGTTTTTGGCCAAAACCCGTGAT
GGTTA
Found at i:1549 original size:656 final size:655
Alignment explanation
Indices: 56--1660 Score: 2259
Period size: 656 Copynumber: 2.4 Consensus size: 655
46 TTCGCTAAAC
* * * *
56 GTACACAATTTCGGCTAAAATTTGGCAAAAATTGACCCGAAGGATTTTTCCTCAAATTTTCGCCC
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGA-CCGAAAGATTTTTCCTCAAATTTTCGCCA
* *
121 CAATAATCATAGAAAATATATAATTCAAGGCTAAGAAGATTGGAGGGCTTTTCAGGCTTTAAATA
65 CAATAATCATAGAAAATATATAATTCAAGGCCAAGAAGATTGGAGGGCTTTTCAGGCTTCAAATA
186 CCATTTCTCTTATTTTTTCTGAATTAATTTTT-ATTAAATCGAAATAAGATTCAGATATTCGTAA
130 CCATTTCTCTTATTTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTCAGATATTCGTAA
250 AAACAAATCGTTAAATCCAATGTGGTTAAGATTTGGTTAGATGAATATAGATATCTCAATGACTC
195 AAACAAATCGTTAAATCCAATGTGGTTAAGATTTGGTTAGATGAATATAGATATCTCAATGACTC
* * *
315 TTGGCAACAAAAATCATGCAAAACTGAGTCGGGGCCCTGGATCGCGTTTTTGGCTAAAACCCGTG
260 TTGGCAACAAAAATCATGCAAAACTGAGTCGGGGCCCAGGAACGCGTTTTTGGCCAAAACCCGTG
*
380 ATGATTAGTACACAATTTCGGCTAAAATTTTGCAAAAGTTGCCCGAAGGATTTTTCCTCAATGTT
325 ATGATTAGTACACAATTTCGGC----A---TGCAAAAGTTGCCCGAAAGATTTTTCCTCAATGTT
** * * *
445 TCATTACAATACTCGTAAAATAGATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCAGGCTT
383 TCACCACAATACTCG-AAAAAAGATATAATTCAACGCCAAAAAGATTGGAAGGCTTTTCACGCTT
* * *
510 CTAAAATCGTTTTTCTTATTTTTTTCTGAACTAACTTTTAATTAAACCGAAATAAGATTCTAATG
447 CTAAAATCATTTTTCTTATTTTTTTATGAACTAACTTTTAACTAAACCGAAATAAGATTCTAATG
*
575 CTCGTAAAAACAAATCCTTAAATCCATTGTAGCTAAGATTTGGTTAGAAGAATATAGATATTTCA
512 CTCGTAAAAACAAATCCTTAAATCCAATGTAGCTAAGATTTGGTTAGAAGAATATAGATATTTCA
* * * *
640 AGGACTATTGGCAACAAAAATCATGCAAAACTGAGCCGGGGCCCAGGAACGCGTTTTTGGCCAAA
577 AGGACTATTAGCAACAAAAATCATACAAAACAGAGACGGGGCCCAGGAACGCGTTTTTGGCCAAA
705 ACCCGTGATGGTTA
642 ACCCGTGATGGTTA
* * * *
719 GTACACGATTTCGGCTAAAATTTTACAAAAATTGACCGGAAAGATTTTTCCTCAATTTTTAGCAA
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC-GAAAGATTTTTCCTCAAATTTTCGCCA
* * * * *
784 CAATAATCATAGGAAATATATAATTCAACGTCAA-AATGATT-GAAGGCTTTTTCACGCTTCAAA
65 CAATAATCATAGAAAATATATAATTCAAGGCCAAGAA-GATTGGAGGGC-TTTTCAGGCTTCAAA
* * * * *
847 TATCATTTTTCTTATGTTTTTCTGAATTAATTTCTAACTAAATCGAAATAAGGTTCAGAT-TCTC
128 TACCATTTCTCTTAT-TTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTCAGATAT-TC
* * * *
911 GTAAAAACAAATTC-TTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAG
191 GTAAAAACAAA-TCGTTAAATCCAATGTGGTTAAGATTTGGTTAGATGAATATAGATATCTCAAT
* * *
975 GGCTCTTGGCAACAAAAATTATGTAAAACTGAGTCGGGGCCCAGGAACGCGTTTTTGGCCAAAAC
255 GACTCTTGGCAACAAAAATCATGCAAAACTGAGTCGGGGCCCAGGAACGCGTTTTTGGCCAAAAC
* *
1040 CCGTGATGCTTAGTACACGATTTCGGC-TGCAAAA-TTGACCCGAAAGATTTTTCCTCAAT-TAT
320 CCGTGATGATTAGTACACAATTTCGGCATGCAAAAGTTG-CCCGAAAGATTTTTCCTCAATGT-T
* * * *
1102 TCGCCCCAATACTC-AAAAAAGTATATAATTCAACGTCAAAATGATT-GAAGGCTTTTTCACGCT
383 TCACCACAATACTCGAAAAAAG-ATATAATTCAACGCCAAAAAGATTGGAAGGC-TTTTCACGCT
* * *
1165 TC-AAATATCATTTTTCTTATTTTTTTATGAATTAA-TTTCTAACTAAATCGAAATAAGGTTC-A
446 TCTAAA-ATCATTTTTCTTATTTTTTTATGAACTAACTTT-TAACTAAACCGAAATAAGATTCTA
* * * *
1227 GATTCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTTAGATTTGGTTAGATA-AATATAGATA
509 -ATGCTCGTAAAAACAAATCCTTAAATCCAATGTAGCTAAGATTTGGTTAGA-AGAATATAGATA
* * * * *
1291 TTTCAAGGACTCTTAGCAACAAAATTTATACAAAACAGATACTGGGCCCAGGAACGCGTTTTTGG
572 TTTCAAGGACTATTAGCAACAAAAATCATACAAAACAGAGACGGGGCCCAGGAACGCGTTTTT-G
*
1356 GCCGAAACCCGTGATGGTTA
636 GCCAAAACCCGTGATGGTTA
* *
1376 GTACATGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAGATTTTTCCTCAAATTTTCTCCA
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGA-CCGAAAGATTTTTCCTCAAATTTTCGCCA
*
1441 CAATAATCATAGAAAATATATAATTCAAGGCCAAGAAGATTGGAGGGCTTTCCAGGCTTCAAATA
65 CAATAATCATAGAAAATATATAATTCAAGGCCAAGAAGATTGGAGGGCTTTTCAGGCTTCAAATA
*
1506 CCATTTCTCTTATTTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTCAGATGTTCGTAA
130 CCATTTCTCTTATTTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTCAGATATTCGTAA
*
1571 AAA-AAATCGTTAAATCCAATGTGGTTAAGATTTGCTTAGATGAATATAGATATCTCAATGACTC
195 AAACAAATCGTTAAATCCAATGTGGTTAAGATTTGGTTAGATGAATATAGATATCTCAATGACTC
*
1635 TTGGCAACAAAAATCTTGCAAAACTG
260 TTGGCAACAAAAATCATGCAAAACTG
1661 CATCAGGGCC
Statistics
Matches: 832, Mismatches: 89, Indels: 50
0.86 0.09 0.05
Matches are distributed among these distances:
654 2 0.00
655 93 0.11
656 242 0.29
657 177 0.21
658 9 0.01
662 9 0.01
663 114 0.14
664 19 0.02
665 165 0.20
666 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (655 bp):
GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCGAAAGATTTTTCCTCAAATTTTCGCCAC
AATAATCATAGAAAATATATAATTCAAGGCCAAGAAGATTGGAGGGCTTTTCAGGCTTCAAATAC
CATTTCTCTTATTTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTCAGATATTCGTAAA
AACAAATCGTTAAATCCAATGTGGTTAAGATTTGGTTAGATGAATATAGATATCTCAATGACTCT
TGGCAACAAAAATCATGCAAAACTGAGTCGGGGCCCAGGAACGCGTTTTTGGCCAAAACCCGTGA
TGATTAGTACACAATTTCGGCATGCAAAAGTTGCCCGAAAGATTTTTCCTCAATGTTTCACCACA
ATACTCGAAAAAAGATATAATTCAACGCCAAAAAGATTGGAAGGCTTTTCACGCTTCTAAAATCA
TTTTTCTTATTTTTTTATGAACTAACTTTTAACTAAACCGAAATAAGATTCTAATGCTCGTAAAA
ACAAATCCTTAAATCCAATGTAGCTAAGATTTGGTTAGAAGAATATAGATATTTCAAGGACTATT
AGCAACAAAAATCATACAAAACAGAGACGGGGCCCAGGAACGCGTTTTTGGCCAAAACCCGTGAT
GGTTA
Done.