Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011906.1 Corchorus olitorius cultivar O-4 contig11939, 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: 1983
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:675 original size:317 final size:321
Alignment explanation
Indices: 11--781 Score: 873
Period size: 318 Copynumber: 2.4 Consensus size: 321
1 TATAGTTATA
* * * *
11 ATTAAATCGAAACAATATTTAGATG-CTCGTAAAAACAAATGCTTAAATCTAACGTAGCTGAGAG
1 ATTAAATCGAAACAAGATTCAGATGCCTCGTAAAAACAAATACTTAAATCCAAC---G-T--G-G
* * *
75 CCTTGAGA-TTGGTTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAGA
59 CC--GACATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTC-GCCAAAAATCATGCAAAA
* *
139 CTGAGCTGAGGCCCCCGAAACGCATTTTTAGCCCAAAAACCATGATGGTTAGTACACGATTTTCG
121 CTGAGCTCAGGCCCCCGAAACGCATTTTTAGCACAAAAACCATGATGG-T-GTACACGATTTTCG
* * ***
204 GCTAAAATCTGACCTGATTTTTTTTCTAAATTTTTTGCCACAATACTCAGAAAAAATATATAATT
184 GCTAAAAACTGACCGGAAGGTTTTTCTAAATTTTTTGCCACAATACTCAGAAAAAATATATAATT
* *
269 CAACACCAAAAAGATTGAAGGTCTTTTCACACTTTTAATATCATTTTTCCAATTTTTTTCCGAAT
249 CAACACCAAAAAGATTGAAGGGCTTTTCACACTTCTAATATCATTTTTCCAA-TTTTTTCCGAAT
334 TAATTTCTT
313 TAATTTCTT
* * *
343 ATTAAATCGAAACAAGATTCAGATG-CTCGTAAAAATAAATCCTTATATCCAACGTGGCCGACAT
1 ATTAAATCGAAACAAGATTCAGATGCCTCGTAAAAACAAATACTTAAATCCAACGTGGCCGACAT
* *
407 TTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAG-TCA
66 TTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CGCCAAAAATCATGCAAAACTGAGCTCA
* * * *
471 GG-GCTCGAGAACGCGTTTTTAG-ACAAAAACCGTGAT-G-GTACACGA-TTTCGGCTAAAAACT
130 GGCCCCCGA-AACGCATTTTTAGCACAAAAACCATGATGGTGTACACGATTTTCGGCTAAAAACT
* * * * *
531 GATCGGAAAGGTTTTTCTCAATTTTTTTGTCACAATACTTAGAAAAAATATATAATTCAACGCCA
194 GACCGG-AAGGTTTTTCT-AAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACC-
* * *
596 AAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCC-A-TTTTTCCGAATTAATTT-T
256 AAAAAGATTGAAGGGCTTTTCACACTTCTAATATCATTTTTCCAATTTTTTCCGAATTAATTTCT
658 T
321 T
* * ** **
659 AATTAAATTGAAACAAGATTCAGATGCCTCGTAAAAACAAATACTTAAATCGAACGTGGGTGGGA
1 -ATTAAATCGAAACAAGATTCAGATGCCTCGTAAAAACAAATACTTAAATCCAACGTGGCCGACA
* * * * *
724 TTTTGTTCGACGAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGACAAAA
65 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CGCCAAAAATCATG-CAAAA
782 ACAAAAAAAT
Statistics
Matches: 383, Mismatches: 47, Indels: 31
0.83 0.10 0.07
Matches are distributed among these distances:
316 2 0.01
317 59 0.15
318 92 0.24
319 47 0.12
320 38 0.10
321 1 0.00
322 16 0.04
323 19 0.05
324 55 0.14
325 4 0.01
326 1 0.00
328 1 0.00
329 1 0.00
332 47 0.12
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (321 bp):
ATTAAATCGAAACAAGATTCAGATGCCTCGTAAAAACAAATACTTAAATCCAACGTGGCCGACAT
TTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCGCCAAAAATCATGCAAAACTGAGCTCAG
GCCCCCGAAACGCATTTTTAGCACAAAAACCATGATGGTGTACACGATTTTCGGCTAAAAACTGA
CCGGAAGGTTTTTCTAAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAA
GATTGAAGGGCTTTTCACACTTCTAATATCATTTTTCCAATTTTTTCCGAATTAATTTCTT
Found at i:1356 original size:550 final size:549
Alignment explanation
Indices: 300--1668 Score: 1999
Period size: 550 Copynumber: 2.5 Consensus size: 549
290 TCTTTTCACA
* * *
300 CTTTTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTT-ATTAAATCGAAACAAGATTCA
1 CTTTAAATATCATTTTT-CTATTTTTTTCCGAATTTATTT-TTAATTAAATCGAAACAAGATTCA
*
364 GATGCTCGTAAAAA-TAAATCCTTATATCCAACGTGGCCGACATTTGGTTTGATGAATATAGATA
64 GATGCTCGTAAAAACT-AATCCTTATATCCAAGGTGGCCGACATTTGGTTTGATGAATATAGATA
*
428 TTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCAGGGCTCGAGAACGCGTTTTTAG
128 TTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGAGAACGCGTTTTTAG
* * *
493 ACAAAAACCGTGAT-G---GTACACGATTTCGGCTAAAAACTGATCGGAAAGGTTTTTCTCAATT
193 CCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCGGAAAAGTTTTTCTCAATA
* *
554 TTTTTGTCACAATACTTAGAAAAAATATATAATTCAACGCCAAAAAAGATTGACGGGCTTTTCAC
258 TTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAGATTGACGGGCTTTTCAC
*
619 GCTTCTAATATCGTTTTTCCATTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAGAT
323 GCTTCTAATATCGTTTTCCCATTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAGAT
* *
684 GCCTCGTAAAAACAAATACTTAAATCGAACGTGGGTGGGATTTTGTTCGACGAATATAGATATTT
388 GCCTCGTAAAAACAAATACTTAAATCGAACGTGGCTGGGATTGTGTTCGACGAATATAGATATTT
749 CAAGGAGTATTTACGTCAAAAATCATGACAAAAACAAAAAAATATTTTCAGCAAAAAATACACAA
453 CAAGGAGTATTTACGTCAAAAATCATGACAAAAACAAAAAAATATTTTCAGCAAAAAATACACAA
* **
814 TTCAACGCAAAATAAATTGAAATATTTTTCTCG
518 TTCAACGCAAAAAAAATTGAAATA-TAATCTCG
*
847 CTTTAAATATCATTTTTCTATTTTTTTCCAAATTTATTTTTAATTAAATCGAAACAAGATTCAGA
1 CTTTAAATATCATTTTTCTATTTTTTTCCGAATTTATTTTTAATTAAATCGAAACAAGATTCAGA
912 TGCTCGTAAAAACTAATCCTTATATCCAAGGTGGCCGACATTTGGTTTGATGAATATAGATATTT
66 TGCTCGTAAAAACTAATCCTTATATCCAAGGTGGCCGACATTTGGTTTGATGAATATAGATATTT
* *
977 CAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGGAACGCATTTTTAGCCA
131 CAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGAGAACGCGTTTTTAGCCA
1042 AAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCGGAAAAGTTATTTCTCAA-ATT
196 AAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCGGAAAAGTT-TTTCTCAATATT
* * *
1106 TTTGCCACAATACTCAGAAAAAATATATAATTCAACGCC-ATAAAGGTTGACGGGCTTTTCATGC
260 TTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAGATTGACGGGCTTTTCACGC
* *
1170 TTCTAATATCGTTTTCCCATTTTCTTTCGAATTAATTTTTAATTAAATTGAAACTAGATTCAGAT
325 TTCTAATATCGTTTTCCCA-TTT-TTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAGAT
* *
1235 G-CTCGTAAAAACAAATACTTAATTCGAACGTGGCTGGGATTGTGTTCGATGAATATAGATATTT
388 GCCTCGTAAAAACAAATACTTAAATCGAACGTGGCTGGGATTGTGTTCGACGAATATAGATATTT
**
1299 CAAGGAGTATTTACGTCAAAAATCATG-CAAAAAACAAAAAAATATTTTTGGCAAAAAATACACA
453 CAAGGAGTATTTACGTCAAAAATCATGAC-AAAAACAAAAAAATATTTTCAGCAAAAAATACACA
*
1363 GTTCAACGCAAAAAAAATTGAAATATAATCTCG
517 ATTCAACGCAAAAAAAATTGAAATATAATCTCG
* * * *
1396 CTTTAAATATCATTTTTCTATTTTTTTCTGAATTTACTTCTAATTAAATCGAAACAACATTCAGA
1 CTTTAAATATCATTTTTCTATTTTTTTCCGAATTTATTTTTAATTAAATCGAAACAAGATTCAGA
* * * * *
1461 TGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGAGCCTGAGA-TTGGTTAGATGAATAT
66 TGCTCGTAAAAACTAATCCTTATATCCAA---GG-T--G-GCC-GACATTTGGTTTGATGAATAT
* * * * * * *
1525 AGATATTTTAAGGAGTCTTT-CTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCCAAAACCCG
123 AGATATTTCAAGGAGTCTTTGC-GCCAAAAATCATGCAAAATTGAGTCGGGG-CTCGAGAACGCG
* * * * * *
1589 TTTTTAGCCGAAAAACCATGATGGTTAGTTCACGATATTCGGCTAAAAACTGACCCGAATATTTT
186 TTTTTAGCC-AAAAACCGTGATGGTTAGTACACGAT-TTCGGCTAAAAACTGATCGGAAAAGTTT
*
1654 TTCTGAAT-TTTTTGC
249 TTCTCAATATTTTTGC
1669 TCTTTCTGCC
Statistics
Matches: 744, Mismatches: 55, Indels: 35
0.89 0.07 0.04
Matches are distributed among these distances:
545 2 0.00
546 176 0.24
547 18 0.02
549 133 0.18
550 219 0.29
551 48 0.06
552 2 0.00
553 1 0.00
555 2 0.00
556 64 0.09
557 18 0.02
558 38 0.05
559 23 0.03
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (549 bp):
CTTTAAATATCATTTTTCTATTTTTTTCCGAATTTATTTTTAATTAAATCGAAACAAGATTCAGA
TGCTCGTAAAAACTAATCCTTATATCCAAGGTGGCCGACATTTGGTTTGATGAATATAGATATTT
CAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGAGAACGCGTTTTTAGCCA
AAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCGGAAAAGTTTTTCTCAATATTT
TTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAGATTGACGGGCTTTTCACGCT
TCTAATATCGTTTTCCCATTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAGATGCC
TCGTAAAAACAAATACTTAAATCGAACGTGGCTGGGATTGTGTTCGACGAATATAGATATTTCAA
GGAGTATTTACGTCAAAAATCATGACAAAAACAAAAAAATATTTTCAGCAAAAAATACACAATTC
AACGCAAAAAAAATTGAAATATAATCTCG
Found at i:1771 original size:129 final size:129
Alignment explanation
Indices: 1540--1796 Score: 401
Period size: 129 Copynumber: 2.0 Consensus size: 129
1530 TTTTAAGGAG
1540 TCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCCAAAACCCGTTTTTAGCCGAAAAAC
1 TCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCCAAAACCCGTTTTTAGCCGAAAAAC
*
1605 CATGATGGTTAGTTCACGATATTCGGCTAAAAACTGACCCGAATATTTTTTCTG-AATTTTTTGC
66 CATGATGGTTAGTACACGATATTCGGCTAAAAACTGACCCGAAT-TTTTTTCTGTAATTTTTTGC
* * *
1669 TCTTTCTGCCAAAAATCATGTAAAACTGAGCCGGGGCCCCCGAAACGCGTTTTTAGACC-AAAAA
1 TCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCCAAAACCCGTTTTTAG-CCGAAAAA
* * * **
1733 CCATGATGGTTTGTACACGATTTTCGGCTAAAATCTGACCCTTATTTTTTTCTGTAATTTTTTG
65 CCATGATGGTTAGTACACGATATTCGGCTAAAAACTGACCCGAATTTTTTTCTGTAATTTTTTG
1797 TCACAATACT
Statistics
Matches: 117, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
128 9 0.08
129 106 0.91
130 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (129 bp):
TCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCCAAAACCCGTTTTTAGCCGAAAAAC
CATGATGGTTAGTACACGATATTCGGCTAAAAACTGACCCGAATTTTTTTCTGTAATTTTTTGC
Done.