Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015344.1 Corchorus olitorius cultivar O-4 contig15377, 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: 3799
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Found at i:109 original size:34 final size:34
Alignment explanation
Indices: 71--160 Score: 171
Period size: 34 Copynumber: 2.6 Consensus size: 34
61 AGCACCACTG
71 TGTCTTCTCGTGTACCTTCGTGTCTGTCTTCCTC
1 TGTCTTCTCGTGTACCTTCGTGTCTGTCTTCCTC
*
105 TGTCTTCTCGTGTACCTTCGTGTCTGTCTTCCTG
1 TGTCTTCTCGTGTACCTTCGTGTCTGTCTTCCTC
139 TGTCTTCTCGTGTACCTTCGTG
1 TGTCTTCTCGTGTACCTTCGTG
161 CCTGCTGGCC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 55 1.00
ACGTcount: A:0.03, C:0.30, G:0.20, T:0.47
Consensus pattern (34 bp):
TGTCTTCTCGTGTACCTTCGTGTCTGTCTTCCTC
Found at i:207 original size:62 final size:62
Alignment explanation
Indices: 132--387 Score: 476
Period size: 62 Copynumber: 4.1 Consensus size: 62
122 TCGTGTCTGT
132 CTTCCTGTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
1 CTTCCTGTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
* *
194 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC
1 CTTCCTGTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
* *
256 CTTCCTTTGTCTTCTCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC
1 CTTCCTGTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
318 CTTCCTGTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
1 CTTCCTGTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
380 CTTCCTGT
1 CTTCCTGT
388 CTTCCTTCCT
Statistics
Matches: 189, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 189 1.00
ACGTcount: A:0.03, C:0.38, G:0.23, T:0.36
Consensus pattern (62 bp):
CTTCCTGTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
Found at i:3610 original size:619 final size:619
Alignment explanation
Indices: 2396--3616 Score: 1459
Period size: 619 Copynumber: 2.0 Consensus size: 619
2386 AAAGACATAA
* *
2396 TTTTTCCACAATTTTTAGCCATAATACTCATAAAAAATTATATAACTCAACGCCAAAAAGATTGA
1 TTTTTCCACAATTTTTAGCCATAATACTCAT--AAAATTATATAACTCAACGCCAAAAAGACTAA
* * * *
2461 ATGTCTTTTCACGCTTCTAATATCGTTTTTCCTATTGTTTTTTCTGTATTAATTTCTAATTAAAT
64 AGGGCTTTTCACGCTTCTAATATCGTTTTTCCTA-T-TTTTTTCAGAATTAATTTCTAATTAAAT
* * * * **
2526 CGAAACAACATTTAGATGCTCATAAAAATATATCCTTAAATCCAATTTGGCTGATATTTGGTTAG
127 CGAAACAACATTCAAATGCTCATAAAAATATATCCTTAAATCCAATGTGGCTGAGACATGGTTAG
* *
2591 ACGGATATAGATATTTCAATTTTCAAGGAGTCTTGCCACAAAAAATCATACAAAACAGAGTCGGG
192 ACGAATATAGA-A-TT-AATTTTCAAGGAGTCTTGCCACAAAAAATCATACAAAACAGAGCCGGG
* *
2656 GCCCCAGAACGCGTTTTTAGCAAAAAACCGCGACGGTTAGTACATGATTTCGGCTAAAATTGACT
254 ACCCCAGAACGCGTTTTTAGCAAAAAACCGCGACGGTTAGTACACGATTTCGGCTAAAATTGACT
* *
2721 CGAAAAGTTTTCCCCTCAATTTTTAGCCAAAATACTCATAAAAATATATAATTCAATGCCAAAAT
319 CGAAAAGTTTTCCCCTCAATTTTTAGCCAAAATACTCATAAAAATATATAACTCAACGCCAAAA-
2786 GATCGAAAGGCTTTTCACGCTTATAATATCGTTTTTCCTATTTTTTTTCTAAATTAATTTCTAAT
383 GA-C-AAA-G--TTTCACGCTTATAATATCGTTTTTCCTATTTTTTTTCTAAATTAATTTCTAAT
**
2851 TAAATCGAAATAGGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTG
443 TAAATCGAAATAACATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTG
** *
2916 GTTAGATGAATATAGATATTTCAAGGAGTCTTGGCCTAAAAAATCATCCAAAACTGAGCTGAGGC
508 GTTAGAAAAATATAGATATTTCAAGGAGTCTTGGCCTAAAAAATCATCCAAAACTGAGCCGAGGC
* *
2981 CCCGGAACGCGTTTTTACAAGATTTTGGCTAAAACTAACCCCAATTT
573 ACCAGAACGCGTTTTTACAAGATTTTGGCTAAAACTAACCCCAATTT
* * * *
3028 TTTTTCCTCAATTTTTGGCCA-AATACTCAT-AAA-TATATAATTCAACGCTAAAAAGACTAAAG
1 TTTTTCCACAATTTTTAGCCATAATACTCATAAAATTATATAACTCAACGCCAAAAAGACTAAAG
* *
3090 GGCTTTTCACGCTTCTAATATTGTTTTTTCTA-TTTTTTCAGAATTAATTTCTAATTAAATCGAA
66 GGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCAGAATTAATTTCTAATTAAATCGAA
* * * *
3154 ACAAGATTCAAATGCTCGTAAAAATA-ATTCCTTAAATCCCATGTGGCTGAGACATGGTTAGATG
131 ACAACATTCAAATGCTCATAAAAATATA-TCCTTAAATCCAATGTGGCTGAGACATGGTTAGACG
* ** * * ***
3218 AATATAG-A-T-A-TTTCAAGGAGTCTTGGCGTAAAAAATCATGCAAAACTGAGCCGGGACCTTG
195 AATATAGAATTAATTTTCAAGGAGTCTTGCCACAAAAAATCATACAAAACAGAGCCGGGACCCCA
* * * * * *
3279 GAACGCGTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTTGGTTAAAATTTTAAAAAAAT
260 GAACGCGTTTTTAGCAAAAAACCGCGACGGTTAGTACACGATTTCGGCTAAAA---T-------T
* ** * *
3344 GAC-CAGTAAA-TTTTTTCTTCAATTTTTAGCCACAATACTCATAAAAATTATATAACTCAACG-
315 GACTC-GAAAAGTTTTCCCCTCAATTTTTAGCCAAAATACTCATAAAAA-TATATAACTCAACGC
* * * **
3406 CAAAA-A-AAA-TTTCATGCTTCTAATATCGTTTTTCCTGTTGTTTTTTCTCTATTAATTTCTAA
378 CAAAAGACAAAGTTTCACGCTTATAATATCGTTTTTCCTATT-TTTTTTCTAAATTAATTTCTAA
* * * *
3468 TTAAATCGGAAATAACATTTAGATGCTCGTAAAAACAAATCCTTAAATCTAATTTGGCTGAGATT
442 TTAAATC-GAAATAACATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATT
* *
3533 TGGTTAGAAAAATATAGATATTTCAAGGAGTCTTGGCAC-AAAAAATCATGCAAAATTGAGCCG-
506 TGGTTAGAAAAATATAGATATTTCAAGGAGTCTTGGC-CTAAAAAATCATCCAAAACTGAGCCGA
*
3596 GGACATCAGAACGCGTTTTTA
570 GG-CACCAGAACGCGTTTTTA
3617 GCCAAAAACT
Statistics
Matches: 506, Mismatches: 66, Indels: 47
0.82 0.11 0.08
Matches are distributed among these distances:
617 114 0.23
618 30 0.06
619 122 0.24
620 3 0.01
621 3 0.01
622 1 0.00
623 1 0.00
624 89 0.18
626 39 0.08
627 73 0.14
628 3 0.01
631 9 0.02
632 19 0.04
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (619 bp):
TTTTTCCACAATTTTTAGCCATAATACTCATAAAATTATATAACTCAACGCCAAAAAGACTAAAG
GGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCAGAATTAATTTCTAATTAAATCGAA
ACAACATTCAAATGCTCATAAAAATATATCCTTAAATCCAATGTGGCTGAGACATGGTTAGACGA
ATATAGAATTAATTTTCAAGGAGTCTTGCCACAAAAAATCATACAAAACAGAGCCGGGACCCCAG
AACGCGTTTTTAGCAAAAAACCGCGACGGTTAGTACACGATTTCGGCTAAAATTGACTCGAAAAG
TTTTCCCCTCAATTTTTAGCCAAAATACTCATAAAAATATATAACTCAACGCCAAAAGACAAAGT
TTCACGCTTATAATATCGTTTTTCCTATTTTTTTTCTAAATTAATTTCTAATTAAATCGAAATAA
CATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGAAAAATAT
AGATATTTCAAGGAGTCTTGGCCTAAAAAATCATCCAAAACTGAGCCGAGGCACCAGAACGCGTT
TTTACAAGATTTTGGCTAAAACTAACCCCAATTT
Found at i:3777 original size:325 final size:317
Alignment explanation
Indices: 2996--3799 Score: 822
Period size: 325 Copynumber: 2.5 Consensus size: 317
2986 AACGCGTTTT
* * * * *
2996 TACAAGATTTTGGCTAAAACTAACCCCAATTTTTTTTCCTCAATTTTTGGCC-AAATACTCAT--
1 TACAAGATTTTGGCTAAAATTTACCCGAAATTTTTTTCCTCAATTTTTAGCCAAAATACTCATAA
* **
3058 AAATATATAATTCAACGCTAAAAAGACTAAAGGGCTTTTCACGCTTCTAATATTGTTTTTTCTA-
66 AAATATATAATTCAACGC-AAAAA-AAT-AAGGGCTTTTCACGCTTCTAATA-TCATTTTTCTAT
* * * *
3122 TTTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAATAATTCCTT
127 TTTTTTCACAATTAATTTCTAATTAAATCGAAACAACATTCAAATGCTCGTAAAAACAAATCCTT
* ** **
3187 AAATCCCATGTGGCTGAGACATGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGTAAAAA
192 AAATCCAATGTGGCTGAGACATGGTTAGAAAAATATAGATATTTCAAGGAGTCTTGGCACAAAAA
* ** *
3252 ATCATGCAAAACTGAGCCGGGACCTTGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAT
257 ATCATGCAAAACTGAGCCGGGACATCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
* * * * *
3313 TACACGATTTTGGTTAAAATTTTAAAAAAATGACCAGTAAA-TTTTTTCTTCAATTTTTAGCCAC
1 TACAAGATTTTGGCTAAAA--TT-------T-ACCCG-AAATTTTTTTCCTCAATTTTTAGCCAA
* * *
3377 AATACTCATAAAAATTATATAACTCAACGC-AAAAAA-AA-----TTTCATGCTTCTAATATCGT
55 AATACTCATAAAAA-TATATAATTCAACGCAAAAAAATAAGGGCTTTTCACGCTTCTAATATCAT
* * * * * *
3435 TTTTCCTGTTGTTTTTTCTCTATTAATTTCTAATTAAATCGGAAATAACATTTAGATGCTCGTAA
119 TTTT-CT-AT-TTTTTTCACAATTAATTTCTAATTAAATC-GAAACAACATTCAAATGCTCGTAA
* * **
3500 AAACAAATCCTTAAATCTAATTTGGCTGAGATTTGGTTAGAAAAATATAGATATTTCAAGGAGTC
180 AAACAAATCCTTAAATCCAATGTGGCTGAGACATGGTTAGAAAAATATAGATATTTCAAGGAGTC
* *
3565 TTGGCACAAAAAATCATGCAAAATTGAGCCGGGACATCAGAACGCGTTTTTAGCCAAAAACTGTG
245 TTGGCACAAAAAATCATGCAAAACTGAGCCGGGACATCAGAACGCGTTTTTAGCCAAAAACCGTG
3630 ATGGTTAG
310 ATGGTTAG
* * *
3638 TACATGATTTCGGCTAAAATTTACCCGAAATTGTTTTTCACCCAATTTTTAGCCAAAATACTCAT
1 TACAAGATTTTGGCTAAAATTTACCCGAAATT-TTTTTC-CTCAATTTTTAGCCAAAATACTCAT
* * * *
3703 AAAAATAAATAATTAAATGACAAAAAAATTTAAGGGCTTTTCACGCTTCTAATATCAATTTTCAT
64 AAAAATATATAATTCAACG-CAAAAAAA--TAAGGGCTTTTCACGCTTCTAATATCATTTTTC-T
* * *
3768 ATCTTTTTTCAAAATTAATTTTTTATTAAATC
125 AT-TTTTTTCACAATTAATTTCTAATTAAATC
Statistics
Matches: 392, Mismatches: 61, Indels: 60
0.76 0.12 0.12
Matches are distributed among these distances:
314 3 0.01
315 5 0.01
316 17 0.04
317 45 0.11
318 6 0.02
319 1 0.00
320 6 0.02
321 19 0.05
323 2 0.01
324 26 0.07
325 183 0.47
326 24 0.06
327 22 0.06
328 12 0.03
329 4 0.01
330 3 0.01
331 14 0.04
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (317 bp):
TACAAGATTTTGGCTAAAATTTACCCGAAATTTTTTTCCTCAATTTTTAGCCAAAATACTCATAA
AAATATATAATTCAACGCAAAAAAATAAGGGCTTTTCACGCTTCTAATATCATTTTTCTATTTTT
TTCACAATTAATTTCTAATTAAATCGAAACAACATTCAAATGCTCGTAAAAACAAATCCTTAAAT
CCAATGTGGCTGAGACATGGTTAGAAAAATATAGATATTTCAAGGAGTCTTGGCACAAAAAATCA
TGCAAAACTGAGCCGGGACATCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
Done.