Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015432.1 Corchorus olitorius cultivar O-4 contig15465, 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: 2787
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Found at i:603 original size:332 final size:331
Alignment explanation
Indices: 1--1488 Score: 2187
Period size: 333 Copynumber: 4.5 Consensus size: 331
* *
1 TTCATGGAGTTTGGGCGCCAAAAATCAAGCAAAACTGAGTCGAGGCCCCGGAACGCGTTTTTAGC
1 TTCATGGAGTCTGGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCCCCGGAACGCGTTTTTAGC
*
66 CAAAAACTGTGATGGTT-A-A-A--ATTTCGGCTAAAATTTTGCATAAAAATGACCAAAAAAATT
66 CAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAAATT
* * *
126 TTCCTCAATTTTTGGACACAATAATCAGAAAAATATATAATTCAATGTCAAAAAGATTGAAGAGC
131 TTCCTCAATTTTTGGACACAATAATCAGAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGC
*
191 TTTTCAAGCATCTAATATCGCTTTTCCTACTTTTTCTGAATTAATTTCTAATTAAATCGAAACAT
196 TTTTCAAGCATCTAATATCGCTTTTCCTACTTTTTCTGAATTAATTTCTAATAAAATCGAAACAT
*
256 GATTCAGATGCTCGTAAATACAAATTATGAAATCCTTTGTGGCCGAGATTTGGTTAGATGAATAT
261 GATTCAGATGCTCGTAAAAACAAATTATGAAATCCTTTGTGGCCGAGATTTGGTTAGATGAATAT
321 AGATAA
326 AGATAA
* * *
327 TTCATGGAGTCTGGGCGCCAAAAATGAAGCAAAACTGAGTCGGGGCCTCGAAACGCGTTTTTAGC
1 TTCATGGAGTCTGGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCCCCGGAACGCGTTTTTAGC
392 CAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAAAGT
66 CAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAAA-T
457 TTTCCTCAATTTTTGGACACAATAATCAGAAAAATATATAATTCAACGCCAAAAAGATTGAAGGG
130 TTTCCTCAATTTTTGGACACAATAATCAGAAAAATATATAATTCAACGCCAAAAAGATTGAAGGG
* *
522 CTTTTCAAGCATCTAATATCGCTTTTCCTACTTTTTCTGAATTAATTTCTGATAAAATGGAAACA
195 CTTTTCAAGCATCTAATATCGCTTTTCCTACTTTTTCTGAATTAATTTCTAATAAAATCGAAACA
* *
587 TGATT-ATGACGCTCGTAAATACAAATTATGAAATCCTTTGTGGCCGAGATTTGGTTAGATGAAT
260 TGATTCA-GATGCTCGTAAAAACAAATTATGAAATCCTTTGTGGCCGAGATTTGGTTAGATGAAT
651 ATAGATAA
324 ATAGATAA
* ** *
659 TTCATGGAGTCTGGGTGGTAAAAATCAAGCAAAACTGAGTCGAGGGCCCCGAAACGCGTTTTTAG
1 TTCATGGAGTCTGGGCGCCAAAAATCAAGCAAAACTGAGTCG-GGGCCCCGGAACGCGTTTTTAG
724 CCAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAAAT
65 CCAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAAAT
* * *
789 TTTCCTCAATTTTTGGACATAATAATTAGAAAAAATATATAATTCAAAGCCAAAAAGATTGAAGG
130 TTTCCTCAATTTTTGGACACAATAATCAG-AAAAATATATAATTCAACGCCAAAAAGATTGAAGG
* *
854 GCTTTTCAAGCATCTAATATTGCTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAAA-CGAAA
194 GCTTTTCAAGCATCTAATATCGCTTTTCCTACTTTTTCTGAATTAATTTCTAA-TAAAATCGAAA
* *
918 CATGATTCAGATTCTCGTAAAAACAAATTATGAAATCCTTTGTAGCCGAGATTTGGTTAGATGAA
258 CATGATTCAGATGCTCGTAAAAACAAATTATGAAATCCTTTGTGGCCGAGATTTGGTTAGATGAA
*
983 TATAAATAA
323 TATAGATAA
*
992 TTCATGGAGTCTAGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCCCCGGAACGCGTTTTTAGC
1 TTCATGGAGTCTGGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCCCCGGAACGCGTTTTTAGC
* *
1057 CAAAAACTGTAATGGTTAATACACGATTTCGGCTAAAATTTTGCATATAAATGACCCAAAAAAAT
66 CAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCATAAAAATGACCC-AAAAAAT
* *
1122 TTTCCTCAATTTTTGGCCACAATAATCAGAAAAAATATATAATTCAACGCCGAAAAGATTGAAGG
130 TTTCCTCAATTTTTGGACACAATAATCAG-AAAAATATATAATTCAACGCCAAAAAGATTGAAGG
* * * *
1187 GCTTTTCAAGCATATAATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAAC
194 GCTTTTCAAGCATCTAATATCGCTTTTCCTACTTTTTCTGAATTAATTTCTAATAAAATCGAAAC
* ** ** * **
1252 ATGATTCAGATGCTCATAAAAACAAATCCCT-AAATCCAATGTGGCCAAGATTCAGTTAGATGAA
259 ATGATTCAGATGCTCGTAAAAACAAAT-TATGAAATCCTTTGTGGCCGAGATTTGGTTAGATGAA
* **
1316 TATATATTT
323 TATAGATAA
** * * ** * *
1325 TTTTTGGAGTCTGGACGCCAAAAATCAAGCAAAACTAAGTAAGAGCTCCGGAACGCGTTTTTAGC
1 TTCATGGAGTCTGGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCCCCGGAACGCGTTTTTAGC
* * * ** * *
1390 TAAAAACCGTGAAT-G----TACACGATTTCGACTAAAATTTTGCA-AAAAAAAATCCGAAAAAT
66 CAAAAACTGTG-ATGGTTAATACACGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAAAT
* * *
1449 ATTGCCTCAATTTTT-TACCACAATTATCAGAAAAATATAT
130 -TTTCCTCAATTTTTGGA-CACAATAATCAGAAAAATATAT
1489 CTAATATTGT
Statistics
Matches: 1064, Mismatches: 81, Indels: 33
0.90 0.07 0.03
Matches are distributed among these distances:
326 77 0.07
327 17 0.02
328 32 0.03
329 26 0.02
331 38 0.04
332 341 0.32
333 524 0.49
334 9 0.01
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (331 bp):
TTCATGGAGTCTGGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCCCCGGAACGCGTTTTTAGC
CAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAAATT
TTCCTCAATTTTTGGACACAATAATCAGAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGC
TTTTCAAGCATCTAATATCGCTTTTCCTACTTTTTCTGAATTAATTTCTAATAAAATCGAAACAT
GATTCAGATGCTCGTAAAAACAAATTATGAAATCCTTTGTGGCCGAGATTTGGTTAGATGAATAT
AGATAA
Found at i:1385 original size:665 final size:661
Alignment explanation
Indices: 1--1488 Score: 2217
Period size: 665 Copynumber: 2.3 Consensus size: 661
* *
1 TTCATGGAGTTTGGGCGCCAAAAATCAAGCAAAACTGAGTCGAGGCCCCGGAACGCGTTTTTAGC
1 TTCATGGAGTCTGGGCGCCAAAAATCAAGCAAAACTGAGTAGA-GCCCCGGAACGCGTTTTTAGC
*
66 CAAAAACTGTGATGGTTA-A-A--ATTTCGGCTAAAATTTTGCATAAAAATGACCAAAAAAATTT
65 CAAAAACTGTGATGGTTATACACGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAAATTT
* *
127 TCCTCAATTTTTGGACACAATAATCAGAAAAATATATAATTCAATGTCAAAAAGATTGAAGAGCT
130 TCCTCAATTTTTGGACACAATAATCAGAAAAATATATAATTCAAAGCCAAAAAGATTGAAGAGCT
*
192 TTTCAAGCATCTAATATCGCTTTTCCTACTTTTTCTGAATTAATTTCTAATTAAATCGAAACATG
195 TTTCAAGCATCTAATATCGCTTTTCCTACTTTTTCTGAATTAATTTCTAATTAAAACGAAACATG
* *
257 ATTCAGATGCTCGTAAATACAAATTATGAAATCCTTTGTGGCCGAGATTTGGTTAGATGAATATA
260 ATTCAGATGCTCGTAAAAACAAATTATGAAATCCTTTGTAGCCGAGATTTGGTTAGATGAATATA
* * * *
322 GATAATTCATGGAGTCTGGGCGCCAAAAATGAAGCAAAACTGAGTCGGGGCCTCGAAACGCGTTT
325 AATAATTCATGGAGTCTAGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCCCCGAAACGCGTTT
*
387 TTAGCCAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAA
390 TTAGCCAAAAACTGTAATGGTTAATACACGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAA
*
452 AAAGTTTTCCTCAATTTTTGGACACAATAATCAGAAAAATATATAATTCAACGCCAAAAAGATTG
455 AAAATTTTCCTCAATTTTTGGACACAATAATCAGAAAAATATATAATTCAACGCCAAAAAGATTG
* * *
517 AAGGGCTTTTCAAGCATCTAATATCGCTTTTCCTACTTTTTCTGAATTAATTTCTGATAAAATGG
520 AAGGGCTTTTCAAGCATATAATATCGCTTTTCCTACTTTTTCTGAATTAATTTCTAATAAAATCG
* * * ** * **
582 AAACATGATTATGACGCTCGTAAATACAAATTATGAAATCCTTTGTGGCCGAGATTTGGTTAGAT
585 AAACATGATTATGACGCTCATAAAAACAAATCATGAAATCCAATGTGGCCAAGATTCAGTTAGAT
647 GAATATAGATAA
650 GAATATAGATAA
* ** * *
659 TTCATGGAGTCTGGGTGGTAAAAATCAAGCAAAACTGAGTCGAGGGCCCCGAAACGCGTTTTTAG
1 TTCATGGAGTCTGGGCGCCAAAAATCAAGCAAAACTGAGT--AGAGCCCCGGAACGCGTTTTTAG
724 CCAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAAAT
64 CCAAAAACTGTGATGGTT-ATACACGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAAAT
* * *
789 TTTCCTCAATTTTTGGACATAATAATTAGAAAAAATATATAATTCAAAGCCAAAAAGATTGAAGG
128 TTTCCTCAATTTTTGGACACAATAATCAG-AAAAATATATAATTCAAAGCCAAAAAGATTGAAGA
* *
854 GCTTTTCAAGCATCTAATATTGCTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAAACGAAAC
192 GCTTTTCAAGCATCTAATATCGCTTTTCCTACTTTTTCTGAATTAATTTCTAATTAAAACGAAAC
*
919 ATGATTCAGATTCTCGTAAAAACAAATTATGAAATCCTTTGTAGCCGAGATTTGGTTAGATGAAT
257 ATGATTCAGATGCTCGTAAAAACAAATTATGAAATCCTTTGTAGCCGAGATTTGGTTAGATGAAT
*
984 ATAAATAATTCATGGAGTCTAGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCCCCGGAACGCG
322 ATAAATAATTCATGGAGTCTAGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCCCCGAAACGCG
*
1049 TTTTTAGCCAAAAACTGTAATGGTTAATACACGATTTCGGCTAAAATTTTGCATATAAATGACCC
387 TTTTTAGCCAAAAACTGTAATGGTTAATACACGATTTCGGCTAAAATTTTGCATAAAAATGACCC
* *
1114 AAAAAAATTTTCCTCAATTTTTGGCCACAATAATCAGAAAAAATATATAATTCAACGCCGAAAAG
452 AAAAAAATTTTCCTCAATTTTTGGACACAATAATCAG-AAAAATATATAATTCAACGCCAAAAAG
* * *
1179 ATTGAAGGGCTTTTCAAGCATATAATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAA
516 ATTGAAGGGCTTTTCAAGCATATAATATCGCTTTTCCTACTTTTTCTGAATTAATTTCTAATAAA
* *
1244 ATCGAAACATGATTCA-GATGCTCATAAAAACAAATCCCT-AAATCCAATGTGGCCAAGATTCAG
581 ATCGAAACATGATT-ATGACGCTCATAAAAACAAAT-CATGAAATCCAATGTGGCCAAGATTCAG
* **
1307 TTAGATGAATATATATTT
644 TTAGATGAATATAGATAA
** * * *
1325 TTTTTGGAGTCTGGACGCCAAAAATCAAGCAAAACTAAGTAAGAGCTCCGGAACGCGTTTTTAGC
1 TTCATGGAGTCTGGGCGCCAAAAATCAAGCAAAACTGAGT-AGAGCCCCGGAACGCGTTTTTAGC
* * * ** * *
1390 TAAAAACCGTGAAT-G---TACACGATTTCGACTAAAATTTTGCA-AAAAAAAATCCGAAAAATA
65 CAAAAACTGTG-ATGGTTATACACGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAAAT-
* * *
1450 TTGCCTCAATTTTT-TACCACAATTATCAGAAAAATATAT
128 TTTCCTCAATTTTTGGA-CACAATAATCAGAAAAATATAT
1489 CTAATATTGT
Statistics
Matches: 745, Mismatches: 71, Indels: 26
0.88 0.08 0.03
Matches are distributed among these distances:
658 36 0.05
659 37 0.05
660 27 0.04
661 48 0.06
662 1 0.00
664 65 0.09
665 345 0.46
666 184 0.25
667 2 0.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (661 bp):
TTCATGGAGTCTGGGCGCCAAAAATCAAGCAAAACTGAGTAGAGCCCCGGAACGCGTTTTTAGCC
AAAAACTGTGATGGTTATACACGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAAATTTT
CCTCAATTTTTGGACACAATAATCAGAAAAATATATAATTCAAAGCCAAAAAGATTGAAGAGCTT
TTCAAGCATCTAATATCGCTTTTCCTACTTTTTCTGAATTAATTTCTAATTAAAACGAAACATGA
TTCAGATGCTCGTAAAAACAAATTATGAAATCCTTTGTAGCCGAGATTTGGTTAGATGAATATAA
ATAATTCATGGAGTCTAGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTT
TAGCCAAAAACTGTAATGGTTAATACACGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAA
AAATTTTCCTCAATTTTTGGACACAATAATCAGAAAAATATATAATTCAACGCCAAAAAGATTGA
AGGGCTTTTCAAGCATATAATATCGCTTTTCCTACTTTTTCTGAATTAATTTCTAATAAAATCGA
AACATGATTATGACGCTCATAAAAACAAATCATGAAATCCAATGTGGCCAAGATTCAGTTAGATG
AATATAGATAA
Found at i:1675 original size:22 final size:22
Alignment explanation
Indices: 1650--1700 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1640 CCAATATGGG
1650 CCAACTAATATG-AACCTAAGGC
1 CCAACTAATATGTAACCT-AGGC
* *
1672 CCAAATAATATGTATCCTAGGC
1 CCAACTAATATGTAACCTAGGC
*
1694 CCTACTA
1 CCAACTA
1701 TACTAGGCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (22 bp):
CCAACTAATATGTAACCTAGGC
Done.