Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006601.1 Corchorus capsularis cultivar CVL-1 contig06622, 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, 915
Length: 1525
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:847 original size:152 final size:152
Alignment explanation
Indices: 1--1525 Score: 2321
Period size: 153 Copynumber: 10.0 Consensus size: 152
* *
1 TTTCTAGCCTTTCGTGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTTGGCTAAACCACAAA
1 TTTCTGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGA-TTTGGC-AAACCACAAA
* * *
66 GCTTTTCTTTCCATTGTTT-TGGCCTAACTATAATTATTTTGTTGAGATTAGTCCATTATTAAGT
64 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGT
130 TTTTAGCTCATTCAGAACAC-TTT
129 TTTTAGCTCATTCAGAACACTTTT
* *
153 TTT-TGGCCTTTCGGGGCCCAATAGTGCTGTTTTGAATCGTCTTCGATTTGGGAAACCACAAAGC
1 TTTCTGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGC
* * *
217 TTTTCTTTCCATTGTTTATGGCTTAACTATAATTATTTTCATGAGATTAGTCAATTGTGAAGTTT
66 TTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTT
*
282 TTCGCTCATTCAGAACACTTTTT
131 TTAGCTCATTCAGAACAC-TTTT
* ** *
305 TTTCGGGAGTTTCGGGGCCCAGTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGC
1 TTTCTGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGC
*
370 TTTTCTTTCCATTGTTTATGGCCTAACTATAATTA-TTTGATGAGATTAGTCCATTGGTGCGAGT
66 TTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCCATT-GTG-AAGT
*
434 TTTTAGCTCATTTAGAACACTTTT
129 TTTTAGCTCATTCAGAACACTTTT
* * *
458 TTTCTAGCCTTTCGTGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAGACCACAAAGC
1 TTTCTGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGC
* * * *
523 TTTTCTTTCCATTGTTTTTGGCCTAACTATAATTATTTTCATGAGGTTAGTCAATTGTGAAGTTT
66 TTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTT
*
588 TTCGCTCATTCAGAACACTTTT
131 TTAGCTCATTCAGAACACTTTT
** * *
610 TTT-TCGAGAGTTTCGGGGCCCAGTAGTGCTGTTTTTAATCGTCTTCGATTTGGCAAACCACAAA
1 TTTCT-G-GCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAA
*
674 GCTTTTCTTTCCATTGTTTATGGTCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGT
64 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGT
* *
739 TTTTAGCTCATTTAGAACACTTTG
129 TTTTAGCTCATTCAGAACACTTTT
* *
763 TTTCTAGCCTTTCGTGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGC
1 TTTCTGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGC
*
828 TTTTCTTTCCATTGCTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTT
66 TTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTT
893 TTAGCTCATTCAGAACACTTTT
131 TTAGCTCATTCAGAACACTTTT
* * *
915 TTT-TGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAGTCGTCTTCAATTTGGCAAACCACAAAGA
1 TTTCTGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGC
* *
979 TTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTCATGGGATTAGTCCATTGTGAAGTTT
66 TTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTT
* *
1044 TTAGCTCATGCAGAACACTTTA
131 TTAGCTCATTCAGAACACTTTT
* * * * *
1066 TTTCGGGCCGTTCGGAGCACATTAGTGCTGTTTTGAATCGGCTTCGATTTGGCAAACCACAAAGC
1 TTTCTGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGC
* * * *
1131 TTTTCTTTCCATTGTTTATGGCCTAAATATAATCATTTTGGTGAGATTAGTCCATTGCGAAGTTT
66 TTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTT
1196 TTAGCTCATTCAGAACACTTTTT
131 TTAGCTCATTCAGAACAC-TTTT
* ** *
1219 TTTCGGGAGTTTCGGGGCCCAGTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGC
1 TTTCTGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGC
* *
1284 TTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGACCATTGTGAAATTT
66 TTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTT
*
1349 TTAACTCATTCAGAACAC-TTT
131 TTAGCTCATTCAGAACACTTTT
* *
1370 TTTCTGGCCTTTCGTGGCCCATTAGTGCTGTTTTGAATCTTCTTCGATTTGGCAAACCACAAAGC
1 TTTCTGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGC
* *
1435 TTTTCTTTCCATTG-TTATGGCCTAACTNTAATTA-TTTGATGAGATTAGTCCATTGTGCTAGTT
66 TTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTG-AAGTT
*
1498 TTTAGCTTCATTTAGAACTACTTTT
130 TTTAGC-TCATTCAGAAC-ACTTTT
1523 TTT
1 TTT
Statistics
Matches: 1244, Mismatches: 113, Indels: 31
0.90 0.08 0.02
Matches are distributed among these distances:
149 51 0.04
150 90 0.07
151 268 0.22
152 326 0.26
153 470 0.38
154 39 0.03
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (152 bp):
TTTCTGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGC
TTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTT
TTAGCTCATTCAGAACACTTTT
Found at i:1247 original size:456 final size:455
Alignment explanation
Indices: 7--1524 Score: 2357
Period size: 456 Copynumber: 3.3 Consensus size: 455
1 TTTCTA
*
7 GCCTTTCGTGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTTGGCTAAACCACAAAGCTTTT
1 GCCTTTCGTGGCCCATTAGTGCTGTTTTGAATCGTCTTC-AATTTGGC-AAACCACAAAGCTTTT
** * *
72 CTTTCCATTGTTT-TGGCCTAACTATAATTATTTTGTTGAGATTAGTCCATTATTAAGTTTTTAG
64 CTTTCCATTGTTTATGGCCTAACTATAATTATTTTCATGAGATTAGTCCATTGTGAAGTTTTTAG
* *
136 CTCATTCAGAACACTTTTTT-TGGCCTTTCGGGGCCCAATAGTGCTGTTTTGAATCGTCTTCGAT
129 CTCATTCAGAACACTTTTTTCGGGCCGTTCGGGGCCCAATAGTGCTGTTTTGAATCGTCTTCGAT
* * *
200 TTGGGAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCTTAACTATAATTATTTTCATGAGATT
194 TTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATT
* *
265 AGTCAATTGTGAAGTTTTTCGCTCATTCAGAACACTTTTTTTTCGGGAGTTTCGGGGCCCAGTAG
259 AGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTTTTTTTCGGGAGTTTCGGGGCCCAGTAG
330 TGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTA
324 TGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTA
* *
395 ACTATAATTA-TTTGATGAGATTAGTCCATTGGTGCGAGTTTTTAGCTCATTTAGAACACTTTTT
389 ACTATAATTATTTTGATGAGATTAGTCCATT-GTG-AAGTTTTTAGCTCATTCAGAACACTTTTT
*
459 TTCTA
452 TT-TG
* *
464 GCCTTTCGTGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAGACCACAAAGCTTTTCT
1 GCCTTTCGTGGCCCATTAGTGCTGTTTTGAATCGTCTTCAATTTGGCAAACCACAAAGCTTTTCT
* * * *
529 TTCCATTGTTTTTGGCCTAACTATAATTATTTTCATGAGGTTAGTCAATTGTGAAGTTTTTCGCT
66 TTCCATTGTTTATGGCCTAACTATAATTATTTTCATGAGATTAGTCCATTGTGAAGTTTTTAGCT
* * * *
594 CATTCAGAACACTTTTTTTTCGAG-AGTTTCGGGGCCCAGTAGTGCTGTTTTTAATCGTCTTCGA
131 CATTCAGAACAC--TTTTTTCGGGCCG-TTCGGGGCCCAATAGTGCTGTTTTGAATCGTCTTCGA
*
658 TTTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGTCTAACTATAATTATTTTGATGAGAT
193 TTTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGAT
* * ** ** * *
723 TAGTCCATTGTGAAGTTTTTAGCTCATTTAGAACAC-TTTGTTTCTAGCCTTTCGTGGCCCATTA
258 TAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTTTTTTTCGGGAGTTTCGGGGCCCAGTA
*
787 GTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCCATTGCTTATGGCCT
323 GTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCT
852 AACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTTTTT
388 AACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTTTTT
917 TTG
453 TTG
* * *
920 GCCTTTCGGGGCCCATTAGTGCTGTTTTGAGTCGTCTTCAATTTGGCAAACCACAAAGATTTTCT
1 GCCTTTCGTGGCCCATTAGTGCTGTTTTGAATCGTCTTCAATTTGGCAAACCACAAAGCTTTTCT
*
985 TTCCATTGTTTATGGCCTAACTATAATTATTTTCATGGGATTAGTCCATTGTGAAGTTTTTAGCT
66 TTCCATTGTTTATGGCCTAACTATAATTATTTTCATGAGATTAGTCCATTGTGAAGTTTTTAGCT
* * * * *
1050 CATGCAGAACACTTTATTTCGGGCCGTTCGGAGCACATTAGTGCTGTTTTGAATCGGCTTCGATT
131 CATTCAGAACACTTT-TTTCGGGCCGTTCGGGGCCCAATAGTGCTGTTTTGAATCGTCTTCGATT
* * *
1115 TGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAAATATAATCATTTTGGTGAGATTA
195 TGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTA
*
1180 GTCCATTGCGAAGTTTTTAGCTCATTCAGAACACTTTTTTTTCGGGAGTTTCGGGGCCCAGTAGT
260 GTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTTTTTTTCGGGAGTTTCGGGGCCCAGTAGT
1245 GCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAA
325 GCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAA
* * * *
1310 CTATAATTATTTTGATGAGATTAGACCATTGTGAAATTTTTAACTCATTCAGAACACTTTTTTCT
390 CTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTTTTTTT
1375 G
455 G
* *
1376 GCCTTTCGTGGCCCATTAGTGCTGTTTTGAATCTTCTTCGATTTGGCAAACCACAAAGCTTTTCT
1 GCCTTTCGTGGCCCATTAGTGCTGTTTTGAATCGTCTTCAATTTGGCAAACCACAAAGCTTTTCT
* * *
1441 TTCCATTG-TTATGGCCTAACTNTAATTA-TTTGATGAGATTAGTCCATTGTGCTAGTTTTTAGC
66 TTCCATTGTTTATGGCCTAACTATAATTATTTTCATGAGATTAGTCCATTGTG-AAGTTTTTAGC
*
1504 TTCATTTAGAACTACTTTTTT
130 -TCATTCAGAAC-ACTTTTTT
1525 T
Statistics
Matches: 968, Mismatches: 81, Indels: 25
0.90 0.08 0.02
Matches are distributed among these distances:
454 24 0.02
455 190 0.20
456 426 0.44
457 73 0.08
458 105 0.11
459 150 0.15
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.41
Consensus pattern (455 bp):
GCCTTTCGTGGCCCATTAGTGCTGTTTTGAATCGTCTTCAATTTGGCAAACCACAAAGCTTTTCT
TTCCATTGTTTATGGCCTAACTATAATTATTTTCATGAGATTAGTCCATTGTGAAGTTTTTAGCT
CATTCAGAACACTTTTTTCGGGCCGTTCGGGGCCCAATAGTGCTGTTTTGAATCGTCTTCGATTT
GGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAGATTAG
TCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTTTTTTTCGGGAGTTTCGGGGCCCAGTAGTG
CTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAAC
TATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTTTTTTTG
Done.