Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009921.1 Corchorus olitorius cultivar O-4 contig09953, 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: 2066
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:931 original size:329 final size:323
Alignment explanation
Indices: 1--1598 Score: 1432
Period size: 329 Copynumber: 4.9 Consensus size: 323
* * *
1 AAACAATTTCGACTAAAATTTTG-CAAAACAAACCCGAAAAAGTTTTTCCTCAATTCTTTGCCAC
1 AAAC-ATTTC-ACTAAAATTTTGTAAAAACTAACCCG-AAAAGTTTTTCCTCAATT-TTTGCCAA
* * *
65 AATACTC-AGAAAAAATATATAAATTCAAGGCCAAAAAGATTGAAGGGTTTATTCACGCCTCTAA
62 AATACTCGA-AAAAAATATAT-AATTCAACGCCAAAAAGATTGAAGGGCTT-TTCACGCTTCTAA
* * * *
129 TATCGTTTTT-C-TTTTTTTCCGAATTTATTTCTAATTATATCGAAACATGATTCAGATGCTTGT
124 TATCGTTTTTCCTTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * * *
192 -AAAA-AAATCCTTTAGTCCATTGTGGCTGAGATTTGGTTAGATGAATATAAATATTTCAAAGAG
189 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAAGAG
* * * *
255 TCTTTATGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGTAACGCGTTTTTAGCCAAAAACTG
254 TCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGG-CCAG-AACGCGTTTTTAGCCAAAAACCG
320 T-AT-G-
317 TGATGGT
* * * * * * *
324 ----ATTT--C--------GGCTAAAAACTTACTCGAAGAGTTTTTTTCTC-ATTTTTTCGTAAA
1 AAACATTTCACTAAAATTTTG-TAAAAACTAACCCGAAAAG-TTTTTCCTCAATTTTTGC-CAAA
* * *
374 ATATTC-AGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATAT
63 ATACTCGA-AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATAT
* * *
438 CGTTTAT-CTATTTTTTTCCGAATTAATTTCTAAATAAATCGAAACAAGATTCAGATTCTCGTAA
127 CGTTTTTCCT-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* * * *
502 AAACAAATCGTTAAATCCAGTGTGCCTGAGATTTGGTTCA-ATGAATATAGATA-TTCCAAGCAG
191 AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTT-AGATGAATATAGATATTTCAAAG-AG
* * * * **
565 TCTTTACGACAAATATCATTCAAAACTGAGCCGGGGCCTTAGAACGCATTTTTAGCCAAAAATAG
254 TCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGGCC--AGAACGCGTTTTTAGCCAAAAACCG
630 TGATGAGT
317 TGATG-GT
* * *
638 AAACAATTTCGACTAAAATTTTGTAAAAACAAACCCGAAAAATTTTTCCTCAATTCTTTGCCATA
1 AAAC-ATTTC-ACTAAAATTTTGTAAAAACTAACCCGAAAAGTTTTTCCTCAATT-TTTGCCAAA
* * *
703 ATACTCGAAAAAAATATATAAGTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCCTCTAATATC
63 ATACTCGAAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATC
* * * * * *
768 GTTTTTCCTTTTTTTTCCGAATTTATTTCTAATTATATCGAGACATGATTCAGATGCTTGTGAAA
128 GTTTTTCCTTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* * * * *
833 ACAAATCCTTTAGTCCATTGTGGTTGAGATTTGGTTAGATGAATATAAATATTTCAAAGAGTCTT
193 ACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAAGAGTCTT
* *
898 TATGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCAGTAACGCGTTTTTAGCCAAAAACCGTGA
258 TACGCCAAAAATCATGCAAAACTGAGCCGGGG--CCAG-AACGCGTTTTTAGCCAAAAACCGTGA
963 TGGT
320 TGGT
* * * * * * *
967 ----A-GT-AC-ATAATTTCGGCTAAAAACTGACTCGAAGAGTTTTTTCTC-ATTTTT-CGCAAA
1 AAACATTTCACTAAAATTT-TG-TAAAAACTAACCCGAAAAGTTTTTCCTCAATTTTTGC-CAAA
* * * *
1023 ATATTC-AGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCACGCTTCCAATAT
63 ATACTCGA-AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATAT
* * * ** **
1087 CGTTTTTTC-ATTTTTTCCGAATTAATTTATAATTAAATTTAAACAAGATTGGGATGCTCGTAAA
127 CGTTTTTCCTTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* * * * * * *
1151 ATCAAATTCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATATATATTTTC-AATAGTG
192 AACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATA-TTTCAAAGAGTC
* * ** * *
1215 TTTGCGCCAAAAATCATTG-AAAATTGAGCCGGAATCCAG-ACTGGGTTTTTAGGCAAAAACCGT
256 TTTACGCCAAAAATCA-TGCAAAACTGAGCCGG-GGCCAGAAC-GCGTTTTTAGCCAAAAACCGT
1278 GATGGTT
318 GATGG-T
* * *
1285 AATGCACGATTTCAGCTACAATTTTGCAAAAACTAACCCGAAAGGTTTTTCCTCAATTTTTTGCC
1 AA---AC-ATTTCA-CTAAAATTTTGTAAAAACTAACCCGAAAAGTTTTTCCTCAA-TTTTTGCC
* * * * *
1350 ACAATACTCAGAAAAAAATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAA
60 AAAATACTC-GAAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAA
* * * * * * *
1415 TATCTTTTTTCGTTTTTCTT-CAAATTAGTTT-TCAATTAAATCAAAACAATACTT-AGATGCTC
124 TATCGTTTTTCCTTTTTTTTCCGAATTAATTTCT-AATTAAATCGAAACAAGA-TTCAGATGCTC
* ** *
1477 GTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTTCTTAGATGAATATAGATATTTCAAGG
187 GTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAAG
* * * * * *
1542 AGTCTTTATGCCAAAAACCATACAAAACTGAGACGAGGCCCCGAAACGCGTTTTTAG
252 AGTCTTTACGCCAAAAATCATGCAAAACTGAGCCG-GGGCCAG-AACGCGTTTTTAG
1599 GGAAAAAAAA
Statistics
Matches: 1022, Mismatches: 178, Indels: 141
0.76 0.13 0.11
Matches are distributed among these distances:
306 22 0.02
307 31 0.03
308 73 0.07
309 29 0.03
310 95 0.09
311 4 0.00
313 1 0.00
315 1 0.00
316 2 0.00
317 24 0.02
318 9 0.01
319 122 0.12
320 81 0.08
321 6 0.01
322 23 0.02
323 1 0.00
324 1 0.00
326 1 0.00
327 1 0.00
328 32 0.03
329 211 0.21
330 64 0.06
331 168 0.16
332 18 0.02
333 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (323 bp):
AAACATTTCACTAAAATTTTGTAAAAACTAACCCGAAAAGTTTTTCCTCAATTTTTGCCAAAATA
CTCGAAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTT
TTTCCTTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
AATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAAGAGTCTTTAC
GCCAAAAATCATGCAAAACTGAGCCGGGGCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGT
Found at i:1513 original size:650 final size:636
Alignment explanation
Indices: 1--1598 Score: 2136
Period size: 650 Copynumber: 2.5 Consensus size: 636
1 AAACAATTTCGACTAAAATTTTGC-AAAACAAACCCGAAAAAGTTTTTCCTCAATTCTTTGCCAC
1 AAACAATTTCGACTAAAATTTTGCAAAAACAAACCCG-AAAAGTTTTTCCTCAATTCTTTGCCAC
*
65 AATACTCAG-AAAAAATATATAAATTCAAGGCCAAAAAGATTGAAGGGTTTATTCACGCCTCTAA
65 AATACTCAGAAAAAAATATAT-AATTCAACGCCAAAAAGATTGAAGGGTTT-TTCACGCCTCTAA
129 TATCGTTTTTCTTTTTTTCCGAATTTATTTCTAATTATATCGAAACATGATTCAGATGCTTGTAA
128 TATCGTTTTTCTTTTTTTCCGAATTTATTTCTAATTATATCGAAACATGATTCAGATGCTTGTAA
194 AA-AAATCCTTTAGTCCATTGTGGCTGAGATTTGGTTAGATGAATATAAATATTTCAAAGAGTCT
193 AACAAATCCTTTAGTCCATTGTGGCTGAGATTTGGTTAGATGAATATAAATATTTCAAAGAGTCT
258 TTATGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGTAACGCGTTTTTAGCCAAAAACTGTAT
258 TTATGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGTAACGCGTTTTTAGCCAAAAACTGTAT
* * *
323 GATTTCGGCTAAAAACTTACTCGAAGAGTTTTTTTCTCATTTTTTCGTAAAATATTCAGAAAAAA
323 AATTTCGGCTAAAAACTGACTCGAAGAGTTTTTTTCTCATTTTTTCGCAAAATATTCAGAAAAAA
*
388 TATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTATCTATTTTT
388 TATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCACGCTTCCAATATCGTTTATCTATTTTT
* *
453 TTCCGAATTAATTTCTAAATAAATCGAAACAAGATTCAGATTCTCGTAAAAACAAATCGTTAAAT
453 TTCCGAATTAATTTATAAATAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCGTTAAAT
* *
518 CCAGTGTGCCTGAGATTTGGTTCAATGAATATAGATATTCCAAGCAGTCTTTACGACAAATATCA
518 CCAATGTGCCTGAGATTTGGTTCAATGAATATAGATATTCCAAGCAGTCTTTACGACAAAAATCA
* *
583 TTCAAAACTGAGCCGGGGCCTTAGAACGCATTTTTAGCCAAAAATAGTGATGAGT
583 TTCAAAACTGAGCCGGAGCC-TAGAACGCATTTTTAGCCAAAAACAGTGATGAGT
* * *
638 AAACAATTTCGACTAAAATTTTGTAAAAACAAACCCGAAAAATTTTTCCTCAATTCTTTGCCATA
1 AAACAATTTCGACTAAAATTTTGCAAAAACAAACCCGAAAAGTTTTTCCTCAATTCTTTGCCACA
*
703 ATACTC-GAAAAAAATATATAAGTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCCTCTAATAT
66 ATACTCAGAAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCCTCTAATAT
*
767 CGTTTTTCCTTTTTTTTCCGAATTTATTTCTAATTATATCGAGACATGATTCAGATGCTTGTGAA
131 CGTTTTT-C-TTTTTTTCCGAATTTATTTCTAATTATATCGAAACATGATTCAGATGCTTGT-AA
*
832 AACAAATCCTTTAGTCCATTGTGGTTGAGATTTGGTTAGATGAATATAAATATTTCAAAGAGTCT
193 AACAAATCCTTTAGTCCATTGTGGCTGAGATTTGGTTAGATGAATATAAATATTTCAAAGAGTCT
897 TTATGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCAGTAACGCGTTTTTAGCCAAAAACCGTG
258 TTATGCCAAAAATCATGCAAAACTGAGTCGGGGCCCC-GTAACGCGTTTTTAGCCAAAAA-C---
962 ATGGTAGTACATAATTTCGGCTAAAAACTGACTCGAAGAG-TTTTTTCTCA-TTTTTCGCAAAAT
318 ----T-GT--ATAATTTCGGCTAAAAACTGACTCGAAGAGTTTTTTTCTCATTTTTTCGCAAAAT
1025 ATTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCACGCTTCCAATATCGT
376 ATTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCACGCTTCCAATATCGT
* * ** ** *
1090 TT-TTTCA-TTTTTTCCGAATTAATTTATAATTAAATTTAAACAAGATTGGGATGCTCGTAAAAT
441 TTATCT-ATTTTTTTCCGAATTAATTTATAAATAAATCGAAACAAGATTCAGATGCTCGTAAAAA
* * * * * * *
1153 CAAATTC-TTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATATATATTTTCAA-TAGTGT
505 CAAA-TCGTTAAATCCAATGTGCCTGAGATTTGGTTCAATGAATATAGATA-TTCCAAGCAGTCT
* * * * * ** * *
1216 TTGCGCCAAAAATCATTGAAAATTGAGCCGGAATCC-AG-ACTGGGTTTTTAGGCAAAAACCGTG
568 TTACGACAAAAATCATTCAAAACTGAGCCGG-AGCCTAGAAC-GCATTTTTAGCCAAAAACAGTG
1279 ATG-GTT
631 ATGAG-T
* * * * *
1285 AATGCACGATTTC-AGCTACAATTTTGCAAAAACTAACCCGAAAGGTTTTTCCTCAATTTTTTGC
1 AA---ACAATTTCGA-CTAAAATTTTGCAAAAACAAACCCGAAAAGTTTTTCCTCAATTCTTTGC
* * * *
1349 CACAATACTCAGAAAAAAATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTA
62 CACAATACTCAGAAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCCTCTA
* * * *
1414 ATATCTTTTTTCGTTTTTCTT-C-AAATTAGTTT-TCAATTAAATCAAAACAAT-ACTT-AGATG
127 ATATCGTTTTTC-TTTTT-TTCCGAATTTA-TTTCT-AATTATATCGAAAC-ATGA-TTCAGATG
* * * * * ** *
1474 CTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTTCTTAGATGAATATAGATATTTCA
186 CTTGT-AAAACAAATCCTTTAGTCCATTGTGGCTGAGATTTGGTTAGATGAATATAAATATTTCA
* * * * * *
1539 AGGAGTCTTTATGCCAAAAACCATACAAAACTGAGACGAGGCCCCGAAACGCGTTTTTAG
250 AAGAGTCTTTATGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGTAACGCGTTTTTAG
1599 GGAAAAAAAA
Statistics
Matches: 852, Mismatches: 75, Indels: 56
0.87 0.08 0.06
Matches are distributed among these distances:
635 23 0.03
636 29 0.03
637 117 0.14
638 16 0.02
639 98 0.12
640 22 0.03
641 1 0.00
646 3 0.00
647 25 0.03
648 123 0.14
649 111 0.13
650 191 0.22
651 93 0.11
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (636 bp):
AAACAATTTCGACTAAAATTTTGCAAAAACAAACCCGAAAAGTTTTTCCTCAATTCTTTGCCACA
ATACTCAGAAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCCTCTAATAT
CGTTTTTCTTTTTTTCCGAATTTATTTCTAATTATATCGAAACATGATTCAGATGCTTGTAAAAC
AAATCCTTTAGTCCATTGTGGCTGAGATTTGGTTAGATGAATATAAATATTTCAAAGAGTCTTTA
TGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGTAACGCGTTTTTAGCCAAAAACTGTATAAT
TTCGGCTAAAAACTGACTCGAAGAGTTTTTTTCTCATTTTTTCGCAAAATATTCAGAAAAAATAT
ATAATTCAATGCCAAAAAGATTGACGGGCTTTTCACGCTTCCAATATCGTTTATCTATTTTTTTC
CGAATTAATTTATAAATAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCGTTAAATCCA
ATGTGCCTGAGATTTGGTTCAATGAATATAGATATTCCAAGCAGTCTTTACGACAAAAATCATTC
AAAACTGAGCCGGAGCCTAGAACGCATTTTTAGCCAAAAACAGTGATGAGT
Done.