Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006617.1 Corchorus capsularis cultivar CVL-1 contig06638, 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: 2367
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Found at i:1059 original size:437 final size:441
Alignment explanation
Indices: 1--1658 Score: 2553
Period size: 454 Copynumber: 3.7 Consensus size: 441
*
1 ATCGTATACGCCATACGTACTAAGACTTAATACTTACTTCAACCGATGACTACTCAAAAAATTTT
1 ATCGTATACGCCATACGTACTAAGACTTAATACTTACTTCAACCGATGACTACCCAAAAAATTTT
66 CGAAAGAAG-ATAAAATTATTTCTCTTTGGAAACCTTACCGAGCGAACATAAACGACCTTTGATC
66 CGAAAGAAGAATAAAATTATTTCTCTTTGGAAACCTTACCGAGCGAACATAAACGACCTTTGATC
*
130 CAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATACTAAGACGTAATCCT
131 CAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATACTAAGAC---A---G
*
195 TACATGAACCGATTGCTGCCCATAAGAAATTCCGAAAGTAGAAGAAAATT-AAAGAAAAAAAATG
190 T---T--A-C-ATTGCTTCCCATAAGAAATTCCGAAAGTAGAAGAAAATTAAAAGAAAAAAAATG
259 AAAAAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCG-TCCAAG
248 AAAAAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCT-CAAG
* * * *
323 CACGATTAATTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTAGAATGATCACACCCATTGG
312 CACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGAATGATCGCACCCATTGG
* * *
388 TCTTTGCATGATGAATCTATACAAGCCACATCTAATTGGATCCGGTGCATTGTTGCCAACATATG
377 ACTTTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCATTGTTGCCAACATATG
* * *
453 ATCGTAAACGCCATACGTACTAAGACTTAATACTTACTTCAAACGATGACTAACC-AAAAATTTT
1 ATCGTATACGCCATACGTACTAAGACTTAATACTTACTTCAACCGATGACTACCCAAAAAATTTT
* *
517 CGAAAGAAGAAGAAAAATTATTTCTCTTTGGAAACCTTACCGAGCGAACATAAATGACCTTTGAT
66 CGAAAGAAGAA-TAAAATTATTTCTCTTTGGAAACCTTACCGAGCGAACATAAACGACCTTTGAT
582 CCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATACTAAGAC-G-TA-A
130 CCAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATACTAAGACAGTTACA
644 -TGCTTCCCATAAGAAATTCCGAAAGTAGAAGAAAATTAAAAGAAAAAAAAATG-AAAAGGGGTG
195 TTGCTTCCCATAAGAAATTCCGAAAGTAGAAGAAAATTAAAAG-AAAAAAAATGAAAAAGGGGTG
* * *
707 CAACACGAGGACTACCCAGGAGGTCACCAATCCTAGTACTACTCTCGCTCAAGCACGCTTAACCG
259 CAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCTCAAGCACGCTTAACTG
* *
772 CGGAGTTCTGATGGGATCCTGTGCATTAGTGCTGGAATGATCGCACCCATCGGACTTTGCATGAT
324 CGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGAATGATCGCACCCATTGGACTTTGCATGAT
837 AAATCTATACAAGCCACATCTCATTGGATCCGGTGCATTGTTGCCAACATATG
389 AAATCTATACAAGCCACATCTCATTGGATCCGGTGCATTGTTGCCAACATATG
890 ATCGTATACGCCATACGTACTAAGACTTAATACTTACTTCAACCGATGACTACCCAAAAAATTTT
1 ATCGTATACGCCATACGTACTAAGACTTAATACTTACTTCAACCGATGACTACCCAAAAAATTTT
955 CGAAAGAAGAATAAAATTATTTCTCTTTGGAAACCTTACCGAGCGAACATAAACGACCTTTGATC
66 CGAAAGAAGAATAAAATTATTTCTCTTTGGAAACCTTACCGAGCGAACATAAACGACCTTTGATC
1020 CAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATACTAAGACGTAATGCT
131 CAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATACTAAGAC---A-G--
*
1085 TACATGAACCGATTGCTTCCCATAAGAAATTCCGAAAGTAGAAGGAAATTAAAAGAAAAAAAATG
190 T---T--A-C-ATTGCTTCCCATAAGAAATTCCGAAAGTAGAAGAAAATTAAAAGAAAAAAAATG
* *
1150 AAAAAGGGGTGCAGCACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGC
248 AAAAAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCTCAAGC
** * *
1215 ACGCTTAACTGAAGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCATTGGC
313 ACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGAATGATCGCACCCATTGGA
*
1280 CTTTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGTATTGTTGCCAACATATG
378 CTTTGCATGATAAATCTATACAAGCCACATCTCATTGGATCCGGTGCATTGTTGCCAACATATG
*
1344 ATCGTATACGTCATACGTACTAAGACTTAATACTTACTTCAACCGATGACTACCCAAAAAATTTT
1 ATCGTATACGCCATACGTACTAAGACTTAATACTTACTTCAACCGATGACTACCCAAAAAATTTT
* *
1409 CGAAAGAAGAA-AAAATTATTTCTCTTTGGAAACCTTACCGAGCGAACATAAATGGCCTTTGATC
66 CGAAAGAAGAATAAAATTATTTCTCTTTGGAAACCTTACCGAGCGAACATAAACGACCTTTGATC
*
1473 CAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATACTAAGATGTAATGCT
131 CAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATACTAAGA---CA-G--
*
1538 TACATGAACCGATTGCTTCCCATAAGAAATTCCGAAAGTAGAAGAGAATTAAAAGAAAAAATAAT
190 T---T--A-C-ATTGCTTCCCATAAGAAATTCCGAAAGTAGAAGAAAATTAAAAGAAAAAA-AAT
*
1603 GAATAAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTC
247 GAAAAAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTC
1659 AGGGATCCGG
Statistics
Matches: 1132, Mismatches: 46, Indels: 54
0.92 0.04 0.04
Matches are distributed among these distances:
436 36 0.03
437 345 0.30
438 31 0.03
440 1 0.00
442 2 0.00
448 1 0.00
450 1 0.00
451 18 0.02
452 52 0.05
453 291 0.26
454 354 0.31
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.26
Consensus pattern (441 bp):
ATCGTATACGCCATACGTACTAAGACTTAATACTTACTTCAACCGATGACTACCCAAAAAATTTT
CGAAAGAAGAATAAAATTATTTCTCTTTGGAAACCTTACCGAGCGAACATAAACGACCTTTGATC
CAGCTTGTTCACGTGCCGTTCATCGAACATGTTGTTCATTCGCAGCCATACTAAGACAGTTACAT
TGCTTCCCATAAGAAATTCCGAAAGTAGAAGAAAATTAAAAGAAAAAAAATGAAAAAGGGGTGCA
ACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCTCAAGCACGCTTAACTGCG
GAGTTCTGATGGGATCCGGTGCATTAGTGCTGGAATGATCGCACCCATTGGACTTTGCATGATAA
ATCTATACAAGCCACATCTCATTGGATCCGGTGCATTGTTGCCAACATATG
Done.