Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006634.1 Corchorus capsularis cultivar CVL-1 contig06655, 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, 724
Length: 1208
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Found at i:320 original size:154 final size:154
Alignment explanation
Indices: 9--1208 Score: 1847
Period size: 154 Copynumber: 7.8 Consensus size: 154
1 ATTTTGGG
* * * * *
9 GAGATTAGTCCACTGTGAAGATTTTAGCTCATTCAGAACACTTGTTATTTAGGGCTTTTCGGGGC
1 GAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGC
* * * *
74 CCATTATTGTTGTTTTGAATCGGCTTCAATTTGGCAAACCACAAACCTTTTCTTTCCAATTGTTT
66 CCATTAGTGCTGTTTTGAATCGTCTTCAATTTGGCAAACCACAAAGCTTTTCTTT-CAATTGTTT
* *
139 ACGACCTAACTATAATTA-TTTGTT
130 AGGACCTAACTATAATTATTTTGAT
*
163 GAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAAAACACTTGTTATTTCGGGCCTTTCGAGGC
1 GAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGC
* *
228 CCATTACTGCTGTTTTGAATCAG-CTTCAATTTAGCAAACCACAAAGCTTTTCTTTCAATTGTTT
66 CCATTAGTGCTGTTTTGAATC-GTCTTCAATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTT
*
292 AGGACCTAACTATAATCATTTTGAT
130 AGGACCTAACTATAATTATTTTGAT
* *
317 GAGATTAGGCCATTTTGTAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGG
1 GAGATTAGTCCATTGTG-AAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGG
* * *
382 CCCATTTGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATAGTTT
65 CCCATTAGTGCTGTTTTGAATCGTCTTCAATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTT
* *
447 ACGACCTAACTATAATTATTTTGTT
130 AGGACCTAACTATAATTATTTTGAT
* *
472 GAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAAAACATTTGTTATTTCGGGCCTTTCGAGGC
1 GAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGC
* *
537 CCATTACTGCTGTTTTGAATCAG-CTTCAATTTAGCAAACCACAAAGCTTTTCTTTCAATTGTTT
66 CCATTAGTGCTGTTTTGAATC-GTCTTCAATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTT
*
601 AGGACCTAACTATAATTATTTCGAT
130 AGGACCTAACTATAATTATTTTGAT
* *
626 GAGATTAGGCCATTTTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGC
1 GAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGC
* * *
691 CCATTTGTGCTGTTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATAGTTT
66 CCATTAGTGCTG-TTTTGAATCGTCTTCAATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTT
* *
756 ACGACCTAACTATAATTATTTTGTT
130 AGGACCTAACTATAATTATTTTGAT
*
781 GAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAAAACACTTGTTATTTCGGGCCTTTCGAGGC
1 GAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGC
* * *
846 CCATTACTGCTGTTTTGAATCAG-CTTCAATTTGGCAAACCACAAAGGTATTCTTTCAATTGTTT
66 CCATTAGTGCTGTTTTGAATC-GTCTTCAATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTT
910 AGGACCTAACTATAATTATTTTGAT
130 AGGACCTAACTATAATTATTTTGAT
* *
935 GAGATTAAG-CCATTTTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGATG
1 GAGATT-AGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGG
* * * * *
999 CCCATTAGTGCTGTTTTCAATCGTCTTCGATTTCGCAAACCACAAAGCTTTTCTTTCCATAGTTT
65 CCCATTAGTGCTGTTTTGAATCGTCTTCAATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTT
1064 ATGG-CCTAACTATAATTATTTTGAT
130 A-GGACCTAACTATAATTATTTTGAT
* *
1089 GAGATTAGGCCATTTTGAAG-TTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGC
1 GAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGC
*
1153 CCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTC
66 CCATTAGTGCTGTTTTGAATCGTCTTCAATTTGGCAAACCACAAAGCTTTTCTTTC
Statistics
Matches: 961, Mismatches: 73, Indels: 25
0.91 0.07 0.02
Matches are distributed among these distances:
153 125 0.13
154 547 0.57
155 289 0.30
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (154 bp):
GAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGC
CCATTAGTGCTGTTTTGAATCGTCTTCAATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTA
GGACCTAACTATAATTATTTTGAT
Found at i:589 original size:309 final size:308
Alignment explanation
Indices: 9--1208 Score: 2030
Period size: 309 Copynumber: 3.9 Consensus size: 308
1 ATTTTGGG
* * * * * * *
9 GAGATTAGTCCACTGTGAAGATTTTAGCTCATTCAGAACACTTGTTATTTAGGGCTTTTCGGGGC
1 GAGATTAGGCCATTTTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGC
* * * * *
74 CCATTAT-TGTTGTTTTGAATCGGCTTCAATTTGGCAAACCACAAACCTTTTCTTTCCAATTGTT
66 CCATT-TGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTT-CAATAGTT
138 TACGACCTAACTATAATTA-TTTGTTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAAAAC
129 TACGACCTAACTATAATTATTTTGTTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAAAAC
202 ACTTGTTATTTCGGGCCTTTCGAGGCCCATTACTGCTGTTTTGAATCAGCTTCAATTTAGCAAAC
194 ACTTGTTATTTCGGGCCTTTCGAGGCCCATTACTGCTGTTTTGAATCAGCTTCAATTTAGCAAAC
*
267 CACAAAGCTTTTCTTTCAATTGTTTAGGACCTAACTATAATCATTTTGAT
259 CACAAAGCTTTTCTTTCAATTGTTTAGGACCTAACTATAATTATTTTGAT
317 GAGATTAGGCCATTTTGTAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGG
1 GAGATTAGGCCATTTTG-AAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGG
382 CCCATTTGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATAGTTT
65 CCCATTTGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATAGTTT
447 ACGACCTAACTATAATTATTTTGTTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAAAACA
130 ACGACCTAACTATAATTATTTTGTTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAAAACA
*
512 TTTGTTATTTCGGGCCTTTCGAGGCCCATTACTGCTGTTTTGAATCAGCTTCAATTTAGCAAACC
195 CTTGTTATTTCGGGCCTTTCGAGGCCCATTACTGCTGTTTTGAATCAGCTTCAATTTAGCAAACC
*
577 ACAAAGCTTTTCTTTCAATTGTTTAGGACCTAACTATAATTATTTCGAT
260 ACAAAGCTTTTCTTTCAATTGTTTAGGACCTAACTATAATTATTTTGAT
626 GAGATTAGGCCATTTTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGC
1 GAGATTAGGCCATTTTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGC
691 CCATTTGTGCTGTTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATAGTTT
66 CCATTTGTGCTG-TTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATAGTTT
756 ACGACCTAACTATAATTATTTTGTTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAAAACA
130 ACGACCTAACTATAATTATTTTGTTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAAAACA
*
821 CTTGTTATTTCGGGCCTTTCGAGGCCCATTACTGCTGTTTTGAATCAGCTTCAATTTGGCAAACC
195 CTTGTTATTTCGGGCCTTTCGAGGCCCATTACTGCTGTTTTGAATCAGCTTCAATTTAGCAAACC
* *
886 ACAAAGGTATTCTTTCAATTGTTTAGGACCTAACTATAATTATTTTGAT
260 ACAAAGCTTTTCTTTCAATTGTTTAGGACCTAACTATAATTATTTTGAT
* *
935 GAGATTAAGCCATTTTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGATGC
1 GAGATTAGGCCATTTTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGC
* * * *
1000 CCATTAGTGCTGTTTTCAATCGTCTTCGATTTCGCAAACCACAAAGCTTTTCTTTCCATAGTTTA
66 CCATTTGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATAGTTTA
* * * * * *
1065 TGGCCTAACTATAATTATTTTGATGAGATTAGGCCATTTTGAAG-TTTTAGCTCATTCAGAACAC
131 CGACCTAACTATAATTATTTTGTTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAAAACAC
* * *
1129 TTGTTATTTCGGGCCTTTCGAGGCCCATTAGTGCTGTTTTGAATC-GTCTTCGATTTGGCAAACC
196 TTGTTATTTCGGGCCTTTCGAGGCCCATTACTGCTGTTTTGAATCAG-CTTCAATTTAGCAAACC
1193 ACAAAGCTTTTCTTTC
260 ACAAAGCTTTTCTTTC
Statistics
Matches: 851, Mismatches: 36, Indels: 11
0.95 0.04 0.01
Matches are distributed among these distances:
306 1 0.00
307 93 0.11
308 190 0.22
309 567 0.67
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (308 bp):
GAGATTAGGCCATTTTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGC
CCATTTGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATAGTTTA
CGACCTAACTATAATTATTTTGTTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAAAACAC
TTGTTATTTCGGGCCTTTCGAGGCCCATTACTGCTGTTTTGAATCAGCTTCAATTTAGCAAACCA
CAAAGCTTTTCTTTCAATTGTTTAGGACCTAACTATAATTATTTTGAT
Found at i:880 original size:463 final size:461
Alignment explanation
Indices: 9--1208 Score: 1872
Period size: 463 Copynumber: 2.6 Consensus size: 461
1 ATTTTGGG
* * * * *
9 GAGATTAGTCCACTGTGAAGATTTTAGCTCATTCAGAACACTTGTTATTTAGGGCTTTTCGGGGC
1 GAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGC
* * * *
74 CCATTATTGTTGTTTTGAATCGGCTTCAATTTGGCAAACCACAAACCTTTTCTTTCCAATTGTTT
66 CCATTACTGCTGTTTTGAATC-GCTTCAATTTAGCAAACCACAAAGCTTTTCTTT-CAATTGTTT
* * * * *
139 ACGACCTAACTATAATTATTTGTTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAAAACAC
129 AGGACCTAACTATAATTATTTGATGAGATTAGGCCATTTTGAAGTTTTTAGCTCATTCAGAACAC
* * *
204 TTGTTATTTCGGGCCTTTCGAGGCCCATTACTGCTGTTTTGAATCAG-CTTCAATTTAGCAAACC
194 TTGTTATTTCGGGCCTTTCGAGGCCCATTAGTGCTGTTTTGAATC-GTCTTCGATTTGGCAAACC
* * *
268 ACAAAGCTTTTCTTTCAATTGTTTAGGACCTAACTATAATCATTTTGATGAGATTAGGCCATTTT
258 ACAAAGCTTTTCTTTCAATAGTTTACGACCTAACTATAATCATTTTGATGAGATTAGGCCATTGT
* **
333 GTAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGCCCATTTGTGCTGTTT
323 GTAAGTTTTTAGCTCATTCAAAACACTTGTTATTTCGGGCCTTTCGAGGCCCATTACTGCTGTTT
* *
398 TGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATAGTTTACGACCTAACTATAAT
388 TGAATCGTCTTCAATTTGGCAAACCACAAAGCTATTCTTTCAATAGTTTACGACCTAACTATAAT
*
463 TATTTTGTT
453 TATTTTGAT
* *
472 GAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAAAACATTTGTTATTTCGGGCCTTTCGAGGC
1 GAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGC
537 CCATTACTGCTGTTTTGAATCAGCTTCAATTTAGCAAACCACAAAGCTTTTCTTTCAATTGTTTA
66 CCATTACTGCTGTTTTGAATC-GCTTCAATTTAGCAAACCACAAAGCTTTTCTTTCAATTGTTTA
602 GGACCTAACTATAATTATTTCGATGAGATTAGGCCATTTTGAAGTTTTTAGCTCATTCAGAACAC
130 GGACCTAACTATAATTATTT-GATGAGATTAGGCCATTTTGAAGTTTTTAGCTCATTCAGAACAC
*
667 TTGTTATTTCGGGCCTTTCGAGGCCCATTTGTGCTGTTTTTGAATCGTCTTCGATTTGGCAAACC
194 TTGTTATTTCGGGCCTTTCGAGGCCCATTAGTGCTG-TTTTGAATCGTCTTCGATTTGGCAAACC
* * *
732 ACAAAGCTTTTCTTTCAATAGTTTACGACCTAACTATAATTATTTTGTTGAGATTAGTCCATTGT
258 ACAAAGCTTTTCTTTCAATAGTTTACGACCTAACTATAATCATTTTGATGAGATTAGGCCATTGT
797 G-AAGTTTTTAGCTCATTCAAAACACTTGTTATTTCGGGCCTTTCGAGGCCCATTACTGCTGTTT
323 GTAAGTTTTTAGCTCATTCAAAACACTTGTTATTTCGGGCCTTTCGAGGCCCATTACTGCTGTTT
* * *
861 TGAATCAG-CTTCAATTTGGCAAACCACAAAGGTATTCTTTCAATTGTTTAGGACCTAACTATAA
388 TGAATC-GTCTTCAATTTGGCAAACCACAAAGCTATTCTTTCAATAGTTTACGACCTAACTATAA
925 TTATTTTGAT
452 TTATTTTGAT
* *
935 GAGATTAAG-CCATTTTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGATG
1 GAGATT-AGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGG
* * * * * *
999 CCCATTAGTGCTGTTTTCAATCGTCTTCGATTTCGCAAACCACAAAGCTTTTCTTTCCATAGTTT
65 CCCATTACTGCTGTTTTGAATCG-CTTCAATTTAGCAAACCACAAAGCTTTTCTTTCAATTGTTT
1064 ATGG-CCTAACTATAATTATTTTGATGAGATTAGGCCATTTTGAAG-TTTTAGCTCATTCAGAAC
129 A-GGACCTAACTATAATTA-TTTGATGAGATTAGGCCATTTTGAAGTTTTTAGCTCATTCAGAAC
1127 ACTTGTTATTTCGGGCCTTTCGAGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAAC
192 ACTTGTTATTTCGGGCCTTTCGAGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAAC
1192 CACAAAGCTTTTCTTTC
257 CACAAAGCTTTTCTTTC
Statistics
Matches: 682, Mismatches: 47, Indels: 18
0.91 0.06 0.02
Matches are distributed among these distances:
461 44 0.06
462 85 0.12
463 461 0.68
464 92 0.13
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (461 bp):
GAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGAGGC
CCATTACTGCTGTTTTGAATCGCTTCAATTTAGCAAACCACAAAGCTTTTCTTTCAATTGTTTAG
GACCTAACTATAATTATTTGATGAGATTAGGCCATTTTGAAGTTTTTAGCTCATTCAGAACACTT
GTTATTTCGGGCCTTTCGAGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGGCAAACCACA
AAGCTTTTCTTTCAATAGTTTACGACCTAACTATAATCATTTTGATGAGATTAGGCCATTGTGTA
AGTTTTTAGCTCATTCAAAACACTTGTTATTTCGGGCCTTTCGAGGCCCATTACTGCTGTTTTGA
ATCGTCTTCAATTTGGCAAACCACAAAGCTATTCTTTCAATAGTTTACGACCTAACTATAATTAT
TTTGAT
Done.