Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006647.1 Corchorus capsularis cultivar CVL-1 contig06668, 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, 606
Length: 1011
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.40
Found at i:379 original size:154 final size:154
Alignment explanation
Indices: 4--1005 Score: 1457
Period size: 154 Copynumber: 6.5 Consensus size: 154
1 TTC
4 TGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACAC
1 TGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACAC
* ** * *
69 TTGTTATTTCGGGCCTTTCGAGGCCCATTAAGTGCTGTGTTAAAATCGGCTTCAATTT-GC-AAC
66 TTGTTATTTCGGGCCTTTCGGGGCCCATT-AGTGCTGT-TTTGAATCGTCTTCGATTTGGCAAAC
** *
132 CAACAAAGCTT-TCTTTCAATTGTATA
129 C-ACAAAGCTTATCTTTCCTTTGTTTA
* * * *
158 CGACCTAGCTATAATCTATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACA
1 TGGCCTAACTATAAT-TATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACA
223 CTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACC
65 CTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACC
288 ACAAAGCTTATCTTTCCTTTGTTTA
130 ACAAAGCTTATCTTTCCTTTGTTTA
*
313 TGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCACATTCAGAACAC
1 TGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACAC
* * * * * *
378 TTGTTATTTCGGGCCTTTCGAGGCCTATTAGTGCTGTGTTAAATCGGCTTCAATTT-GC-AACCA
66 TTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACC-
* **
441 ACTAAAGTCTTTTTCTTTCAATTGTTTA
130 AC-AAAG-C-TTATCTTTCCTTTGTTTA
* * * * *
469 CGACCTAGCTATAATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACAC
1 TGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACAC
*
534 TTGTTATTTTGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCA
66 TTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCA
599 CAAAGCTTATCTTTCCTTTGTTTA
131 CAAAGCTTATCTTTCCTTTGTTTA
*
623 TGGCCTAAATATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTATG-TCATTCAGAACA
1 TGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTA-GCTCATTCAGAACA
* * * * *
687 CTTGTTATTT-TGCCCTTTCGGGTCTCATTAGTGCTGTTTTGAATCGTCTTCGATTTGCCAAACC
65 CTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACC
* *
751 ACAAAGCTTTTC-TTCCTATTGTTTC
130 ACAAAGCTTATCTTTCCT-TTGTTTA
* *
776 TGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCACATTTAGAACAC
1 TGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACAC
841 TTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCA
66 TTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCA
906 CAAAGCTTATCTTTCC-TTGTTTAA
131 CAAAGCTTATCTTTCCTTTGTTT-A
** * *
930 TGGCAGAACTATAATTATTTTGATGATATTAGTCCATTGTGAAG-TTTTAGGTCATTCAGAACAC
1 TGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACAC
994 TTGTTATTTCGG
66 TTGTTATTTCGG
1006 CTTCGG
Statistics
Matches: 761, Mismatches: 71, Indels: 33
0.88 0.08 0.04
Matches are distributed among these distances:
152 10 0.01
153 189 0.25
154 315 0.41
155 112 0.15
156 127 0.17
157 4 0.01
158 4 0.01
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (154 bp):
TGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACAC
TTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCA
CAAAGCTTATCTTTCCTTTGTTTA
Found at i:574 original size:310 final size:307
Alignment explanation
Indices: 4--1005 Score: 1624
Period size: 307 Copynumber: 3.3 Consensus size: 307
1 TTC
4 TGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACAC
1 TGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACAC
*
69 TTGTTATTTCGGGCCTTTCGAGGCCCATTAAGTGCTGTGTTAAAATCGGCTTCAATTTGCAACCA
66 TTGTTATTTCGGGCCTTTCGAGGCCTATT-AGTGCTGTGTT-AAATCGGCTTCAATTTGCAACCA
*
134 ACAAAGC-TTTCTTTCAATTGTATACGACCTAGCTATAATCTATTTTGGTGAGATTAGTCCATTG
129 ACAAAGCTTTTCTTTCAATTGTTTACGACCTAGCTATAATC-ATTTTGGTGAGATTAGTCCATTG
198 TGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTT
193 TGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTT
263 TGAATCGTCTTCGATTTGGCAAACCACAAAGCTTATCTTTCCTTTGTTTA
258 TGAATCGTCTTCGATTTGGCAAACCACAAAGCTTATCTTTCCTTTGTTTA
*
313 TGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCACATTCAGAACAC
1 TGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACAC
378 TTGTTATTTCGGGCCTTTCGAGGCCTATTAGTGCTGTGTTAAATCGGCTTCAATTTGCAACCAAC
66 TTGTTATTTCGGGCCTTTCGAGGCCTATTAGTGCTGTGTTAAATCGGCTTCAATTTGCAACCAAC
443 TAAAGTCTTTTTCTTTCAATTGTTTACGACCTAGCTATAATCATTTTGGTGAGATTAGTCCATTG
131 -AAAG-C-TTTTCTTTCAATTGTTTACGACCTAGCTATAATCATTTTGGTGAGATTAGTCCATTG
*
508 TGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTGCTGTTT
193 TGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTT
573 TGAATCGTCTTCGATTTGGCAAACCACAAAGCTTATCTTTCCTTTGTTTA
258 TGAATCGTCTTCGATTTGGCAAACCACAAAGCTTATCTTTCCTTTGTTTA
*
623 TGGCCTAAATATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTATG-TCATTCAGAACA
1 TGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTA-GCTCATTCAGAACA
* * * * * * *
687 CTTGTTATTT-TGCCCTTTCG-GGTCTCATTAGTGCTGTTTTGAATCGTCTTCGATTTGCCAAAC
65 CTTGTTATTTCGGGCCTTTCGAGGCCT-ATTAGTGCTGTGTTAAATCGGCTTCAATTTG-C-AAC
* * * * * *
750 C-ACAAAGCTTTTCTTCCTATTGTTT-CTGGCCTAACTATAATTATTTTGATGAGATTAGTCCAT
127 CAACAAAGCTTTTCTTTCAATTGTTTAC-GACCTAGCTATAATCATTTTGGTGAGATTAGTCCAT
* *
813 TGTGAAGTTTTTAGCACATTTAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGT
191 TGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGT
878 TTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTATCTTTCC-TTGTTTAA
256 TTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTATCTTTCCTTTGTTT-A
** * *
930 TGGCAGAACTATAATTATTTTGATGATATTAGTCCATTGTGAAG-TTTTAGGTCATTCAGAACAC
1 TGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACAC
994 TTGTTATTTCGG
66 TTGTTATTTCGG
1006 CTTCGG
Statistics
Matches: 654, Mismatches: 27, Indels: 26
0.93 0.04 0.04
Matches are distributed among these distances:
305 1 0.00
306 34 0.05
307 220 0.34
308 20 0.03
309 132 0.20
310 210 0.32
311 37 0.06
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (307 bp):
TGGCCTAACTATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACAC
TTGTTATTTCGGGCCTTTCGAGGCCTATTAGTGCTGTGTTAAATCGGCTTCAATTTGCAACCAAC
AAAGCTTTTCTTTCAATTGTTTACGACCTAGCTATAATCATTTTGGTGAGATTAGTCCATTGTGA
AGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGA
ATCGTCTTCGATTTGGCAAACCACAAAGCTTATCTTTCCTTTGTTTA
Done.