Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006638.1 Corchorus capsularis cultivar CVL-1 contig06659, 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: 1668
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Found at i:281 original size:154 final size:154
Alignment explanation
Indices: 1--1657 Score: 2366
Period size: 154 Copynumber: 10.8 Consensus size: 154
** * *
1 TTCTTTCAATTGTTTACGACCTAACCGTAATTATTTTGATGAGATTAGACCATTTTGAAGTTTTT
1 TTCTTTCAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTT
* * *
66 AGCACATTCAGAACACTTGTTATTTCGGGCCTTTTGGGGCCCATTACTGCTGTTTTGAATCGTCT
66 AGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCT
*
131 TCGATTTAGCAAACCACAAAGCTT
131 TCGATTTGGCAAACCACAAAGCTT
* * *
155 TTCTTTCAATTGTTTACGACCTAACTATAGTTATTTTGATGAGATTTGTCCATTGTAAAGTTTTT
1 TTCTTTCAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTT
*
220 AGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTACTGCTGTTTTGAATCGTCT
66 AGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCT
285 TCGATTTGGCAAACCACAAAGCTT
131 TCGATTTGGCAAACCACAAAGCTT
* * * * **
309 TTCTTTCCATAGTTTATGGCCTAACTATAATTATTTTGATGAGATTAGTCTTTTGTGAAGTTTTC
1 TTCTTTCAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTT-
* * *
374 TATCTCATTCAGAACACATATTAGTTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGT
65 TAGCTCATTCAGAACACTTGTTA-TTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGT
*
439 CTTCGATTTGCCAAACCACAAAGCTT
129 CTTCGATTTGGCAAACCACAAAGCTT
465 TTCTTTCAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTT
1 TTCTTTCAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTT
* * * *
530 TGCTCATTTAGAACTCTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTACTGTTTTGAATCGTCT
66 AGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCT
**
595 TAAATTTGGCAAACCACAAAGCTT
131 TCGATTTGGCAAACCACAAAGCTT
* * * * *
619 TTCTTTTAATTGTTTACGGCCTAACTATAATCATTTTGTTGAGATTAGTCCACTGTGAAGTTTTT
1 TTCTTTCAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTT
*
684 AGGTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCT
66 AGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCT
* *
749 TCGATTTAGCAAATCACAAAGCTT
131 TCGATTTGGCAAACCACAAAGCTT
* *
773 TTCTTTCAATTGTTTACGACCTAACTATAGTTATTTTGATGAGATTAGTCCATTGTAAAGTTTTT
1 TTCTTTCAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTT
* *
838 AGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGTGGCCCATTACTGCTGTTTTGAATCGTCT
66 AGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCT
903 TCGATTTGGCAAACCACAAAGCTT
131 TCGATTTGGCAAACCACAAAGCTT
* * * * * ** * ** *
927 TACTTTCCATAGTTTATGGCCTATGTATAATTATTTTGATGAGATAAGTCTTTTGTGAAGTTTCT
1 TTCTTTCAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTT
* * * *
992 ATCTCATTCAGAGCACATATTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCT
66 AGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCT
*
1057 TCGATTTAGCAAACCACAAAGCTT
131 TCGATTTGGCAAACCACAAAGCTT
*
1081 TTC-TTCAATTGTTTACGACCTAACTATAATTACTTTGATGAGATTAGTCCATTGTGAAGTTTTT
1 TTCTTTCAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTT
* * * * * *
1145 TGCTCATTTAGAACACTTGTTA---------TTTCGGGGTCCATTAGTACTATTTTGAATCGTAT
66 AGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCT
**
1201 TAAATTTGGCAAACCACAAAGCTT
131 TCGATTTGGCAAACCACAAAGCTT
* * * * *
1225 TTCTTTTAATTGTTTACGGCCTAACTATACTTATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
1 TTCTTTCAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTT
*
1290 AGGTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCT
66 AGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCT
* *
1355 TCGA-TTAGCAAACCACAAAGCAT
131 TCGATTTGGCAAACCACAAAGCTT
* * * * * *
1378 TTCTTTCAATTGTTTACGGCCTAACTATAATCA-TTTGGTGAGACTAGTACACTGTGAAGTTTTT
1 TTCTTTCAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTT
* * * *
1442 CGCTCATTCAGAACACTTGTTATTTCGGGTCTTTCGGGGCCCGTTAGTGCTGTTTTGAATCGGCT
66 AGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCT
1507 TCGATTTGGCAAACCACAAACGTCTT
131 TCGATTTGGCAAACCACAAA-G-CTT
* * * *
1533 TTCCCTTTTAATTGTTTACGACCTAACTATAATCATTTTGGGTGAGATTAGTCCATCGTGAAGTT
1 TT--CTTTCAATTGTTTACGACCTAACTATAATTATTTT-GATGAGATTAGTCCATTGTGAAGTT
*
1598 TTTAGCTCATTCAGAACACTTGTTTTTTCGGGCCTTTCGGGGGCCCATTAGTGCTGTTTT
63 TTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTC-GGGGCCCATTAGTGCTGTTTT
1658 TAGAATCGGC
Statistics
Matches: 1333, Mismatches: 150, Indels: 34
0.88 0.10 0.02
Matches are distributed among these distances:
144 54 0.04
145 74 0.06
152 93 0.07
153 127 0.10
154 713 0.53
155 41 0.03
156 123 0.09
157 29 0.02
158 3 0.00
159 56 0.04
160 20 0.02
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (154 bp):
TTCTTTCAATTGTTTACGACCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTT
AGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCT
TCGATTTGGCAAACCACAAAGCTT
Done.