Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006606.1 Corchorus capsularis cultivar CVL-1 contig06627, 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, 936
Length: 1561
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Found at i:947 original size:447 final size:446
Alignment explanation
Indices: 1--1550 Score: 2488
Period size: 447 Copynumber: 3.4 Consensus size: 446
* * *
1 ACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTAATGGGATCAGGTGCATTAATGCTGGTATGA
1 ACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGA
* *
66 TCGCACCCAATGGT-TTTTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCATT
66 TCGCACCCATTGGTCTTCTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCATT
130 GTTGCCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATGACT
131 GTTGCCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATG---
*
195 ACCCAAAAAATTTTCGAAAGAAGAAGAAAAAATTATTTCTCTTTGGAAACCTTACCGAGCGAACA
193 -------AAATTTTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCGAACA
260 TAAACGGCCTTTGATCCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCAT
251 TAAACGGCCTTTGATCCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCAT
*
325 ACTAAGACGTAATGCTTACATGAACCGATTGCTTCCCATAAGAAATTCCGAAAGTAGAAGAAAAT
316 ACTAAGACGTAATGCTTACATGAACCGATTGCTTCTCATAAGAAATTCCGAAAGTAGAAGAAAAT
390 TAAAAGAAAAAAAATGAAAAAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTA
381 TAAAAGAAAAAAAATGAAAAAGGGGTGCAACACGAGGACTTCCCAGGAGGTCA-CCATCCTAGTA
455 CT
445 CT
* *
457 ACTCTCGCCCAAGCACGTTTACCGTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATG
1 ACTCTCGCCCAAGCACGCTTAAC-TGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATG
*
522 ATCGCACCCATTGGTCTTCTGCATGATAAATCTATACAAGCCACGTCTCATTGGATCCGGTGCAT
65 ATCGCACCCATTGGTCTTCTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCAT
* *
587 TGTTGCAAACATATGATCGTATACATCATACGTACTAAGACTTAATACTTACTTCAACCGATG-A
130 TGTTGCCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATGAA
*
651 ATTTTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCGAACATAAATGGCC
195 ATTTTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCGAACATAAACGGCC
*
716 TTTGATCCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATACTAAGGCG
260 TTTGATCCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATACTAAGACG
781 TAATGCTTACATGAACCGATTGCTTCTCATAAG-AATTACCGAAAGTAGAA-AGAAATTAAAAGA
325 TAATGCTTACATGAACCGATTGCTTCTCATAAGAAATT-CCGAAAGTAGAAGA-AAATTAAAAG-
* *
844 AAAAAAAATGAAAAAGGGGTGCAACACGAAGACTTCCCAAGAGGTCACCAATCCTAGTACT
387 AAAAAAAATGAAAAAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACC-ATCCTAGTACT
* * * *
905 ACTCTCGCCCAAGCACGCTTAACTACGGAATTCTGTTGGGATCCGATGCATTAGTGCTGGTATGA
1 ACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGA
* *
970 TTGCACCCATTGGTCTT-TG-ATTGATAAATCTATACAAGCCACATCTCATTGGATACGGTGCAT
66 TCGCACCCATTGGTCTTCTGCA-TGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCAT
1033 TGTTGCCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATGAC
130 TGTTGCCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATG--
1098 TACCCAAAAGTTTTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCGAACA
193 ------AAA-TTTTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCGAACA
* * *
1163 TAAACGGCCTTTGATCCAGATTGTTCATGTGCCGTTCATAGAACATGTTGTTCATTCGCAGCCAT
251 TAAACGGCCTTTGATCCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCAT
*
1228 ACTAAGACGTAATGCTTACATGAACCGATTGCTT-TCCAAAAGAAATTCCGAAAGTAGAAGAAAA
316 ACTAAGACGTAATGCTTACATGAACCGATTGCTTCT-CATAAGAAATTCCGAAAGTAGAAGAAAA
*
1292 TTAAAAG-AAAAAAAGGAAAAAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACGCATCCTAGT
380 TTAAAAGAAAAAAAATGAAAAAGGGGTGCAACACGAGGACTTCCCAGGAGGTCAC-CATCCTAGT
1356 ACT
444 ACT
* * *
1359 ACTCTCGTCCAAGCACGCTTCACTGCGGAGTTCTGATGGGATCCGGTGCATTCGTGCTGGTATGA
1 ACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGA
1424 TCGCACCCATTGGTC-TCTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCATT
66 TCGCACCCATTGGTCTTCTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCATT
* * *
1488 GTTGCCAACATATGATCGTATACGCCATACGTACTAAGATTTAATACTTACTTCAACCAATGA
131 GTTGCCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATGA
1551 CTACCCAAAA
Statistics
Matches: 1023, Mismatches: 48, Indels: 56
0.91 0.04 0.05
Matches are distributed among these distances:
445 1 0.00
446 109 0.11
447 238 0.23
448 77 0.08
453 1 0.00
454 230 0.22
455 5 0.00
456 197 0.19
457 57 0.06
458 108 0.11
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (446 bp):
ACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGA
TCGCACCCATTGGTCTTCTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCATT
GTTGCCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATGAAA
TTTTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCGAACATAAACGGCCT
TTGATCCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATACTAAGACGT
AATGCTTACATGAACCGATTGCTTCTCATAAGAAATTCCGAAAGTAGAAGAAAATTAAAAGAAAA
AAAATGAAAAAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCATCCTAGTACT
Found at i:1224 original size:456 final size:453
Alignment explanation
Indices: 1--1560 Score: 2599
Period size: 454 Copynumber: 3.4 Consensus size: 453
* * *
1 ACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTAATGGGATCAGGTGCATTAATGCTGGTATGA
1 ACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGA
* *
66 TCGCACCCAATGGTTTTTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCATTG
66 TCGCACCCATTGGTCTTTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCATTG
131 TTGCCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATGACTA
131 TTGCCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATGACTA
*
196 CCCAAAAAATTTTCGAAAGAAGAAGAAAAAATTATTTCTCTTTGGAAACCTTACCGAGCGAACAT
196 CCC--AAAATTTTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCGAACAT
261 AAACGGCCTTTGATCCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATA
259 AAACGGCCTTTGATCCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATA
*
326 CTAAGACGTAATGCTTACATGAACCGATTGCTTCCCATAAGAAATTCCGAAAGTAGAAGAAAATT
324 CTAAGACGTAATGCTTACATGAACCGATTGCTTCTCATAAGAAATTCCGAAAGTAGAAGAAAATT
391 AAAAGAAAAAAAATGAAAAAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTAC
389 AAAAGAAAAAAAATGAAAAAGGGGTGCAACACGAGGACTTCCCAGGAGGTCA-CCATCCTAGTAC
456 T
453 T
* *
457 ACTCTCGCCCAAGCACGTTTACCGTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATG
1 ACTCTCGCCCAAGCACGCTTAAC-TGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATG
*
522 ATCGCACCCATTGGTCTTCTGCATGATAAATCTATACAAGCCACGTCTCATTGGATCCGGTGCAT
65 ATCGCACCCATTGGTCTT-TGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCAT
* *
587 TGTTGCAAACATATGATCGTATACATCATACGTACTAAGACTTAATACTTACTTCAACCGATG--
129 TGTTGCCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATGAC
650 -------AATTTTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCGAACAT
194 TACCCAAAATTTTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCGAACAT
*
708 AAATGGCCTTTGATCCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATA
259 AAACGGCCTTTGATCCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATA
*
773 CTAAGGCGTAATGCTTACATGAACCGATTGCTTCTCATAAG-AATTACCGAAAGTAGAA-AGAAA
324 CTAAGACGTAATGCTTACATGAACCGATTGCTTCTCATAAGAAATT-CCGAAAGTAGAAGA-AAA
* *
836 TTAAAAGAAAAAAAAATGAAAAAGGGGTGCAACACGAAGACTTCCCAAGAGGTCACCAATCCTAG
387 TTAAAAG-AAAAAAAATGAAAAAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACC-ATCCTAG
901 TACT
450 TACT
* * * *
905 ACTCTCGCCCAAGCACGCTTAACTACGGAATTCTGTTGGGATCCGATGCATTAGTGCTGGTATGA
1 ACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGA
* *
970 TTGCACCCATTGGTCTTTG-ATTGATAAATCTATACAAGCCACATCTCATTGGATACGGTGCATT
66 TCGCACCCATTGGTCTTTGCA-TGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCATT
1034 GTTGCCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATGACT
130 GTTGCCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATGACT
1099 ACCCAAAAGTTTTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCGAACAT
195 ACCCAAAA-TTTTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCGAACAT
* * *
1164 AAACGGCCTTTGATCCAGATTGTTCATGTGCCGTTCATAGAACATGTTGTTCATTCGCAGCCATA
259 AAACGGCCTTTGATCCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATA
*
1229 CTAAGACGTAATGCTTACATGAACCGATTGCTT-TCCAAAAGAAATTCCGAAAGTAGAAGAAAAT
324 CTAAGACGTAATGCTTACATGAACCGATTGCTTCT-CATAAGAAATTCCGAAAGTAGAAGAAAAT
*
1293 TAAAAG-AAAAAAAGGAAAAAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACGCATCCTAGTA
388 TAAAAGAAAAAAAATGAAAAAGGGGTGCAACACGAGGACTTCCCAGGAGGTCAC-CATCCTAGTA
1357 CT
452 CT
* * *
1359 ACTCTCGTCCAAGCACGCTTCACTGCGGAGTTCTGATGGGATCCGGTGCATTCGTGCTGGTATGA
1 ACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGA
*
1424 TCGCACCCATTGGTCTCTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCATTG
66 TCGCACCCATTGGTCTTTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCATTG
* * *
1489 TTGCCAACATATGATCGTATACGCCATACGTACTAAGATTTAATACTTACTTCAACCAATGACTA
131 TTGCCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATGACTA
1554 CCCAAAA
196 CCCAAAA
1561 A
Statistics
Matches: 1033, Mismatches: 49, Indels: 46
0.92 0.04 0.04
Matches are distributed among these distances:
445 1 0.00
446 108 0.10
447 238 0.23
448 77 0.07
454 242 0.23
455 5 0.00
456 197 0.19
457 59 0.06
458 106 0.10
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (453 bp):
ACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGA
TCGCACCCATTGGTCTTTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCATTG
TTGCCAACATATGATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATGACTA
CCCAAAATTTTCGAAAGAAGAAGAAAAATTTATTTCTCTTTGGAAACCTTACCGAGCGAACATAA
ACGGCCTTTGATCCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATACT
AAGACGTAATGCTTACATGAACCGATTGCTTCTCATAAGAAATTCCGAAAGTAGAAGAAAATTAA
AAGAAAAAAAATGAAAAAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCATCCTAGTACT
Done.