Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006644.1 Corchorus capsularis cultivar CVL-1 contig06665, 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, 682
Length: 1137
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Found at i:519 original size:154 final size:153
Alignment explanation
Indices: 1--1137 Score: 1592
Period size: 154 Copynumber: 7.4 Consensus size: 153
* *
1 CACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTAAATGTGCTAAAAACTTCACAATGG
1 CACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGG
* *
66 ACTAATCTCATCAAAATAATTATAGTTAGGCCAGAAACAGTAGG-AAGAAAAGCTTTGTGGTTTG
66 ACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACA-AAGGAAAGAAAAGCTTTGTGGTTT-
130 GCAAATCGAAGACGATTCAAAACAG
129 GCAAATCGAAGACGATTCAAAACAG
*
155 CACTAATGGTCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGG
1 CACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGG
* * * * **
220 ACTAATCTCACCAAAATGGAATTATAGCTAGGTCGTAAACAATTGAAAGAAAAGCTTTGTTGG-T
66 ACTAATCTCATCAAAAT--AATTATAGTTAGGCCATAAACAAAGGAAAGAAAAGCTTTG-TGGTT
* * * *
284 TGCAAATTGAAGCCGATTTAACACAG
128 TGCAAATCGAAGACGATTCAAAACAG
* *
310 CACTAATGGGCCTCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTATAAACTTCACAATGG
1 CACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGG
*
375 ACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGATAAGCTTTGTGGTTTGC
66 ACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGAAAAGCTTTGTGGTTTG-
440 CAAATCGAAGACGATTCAAAACAG
130 CAAATCGAAGACGATTCAAAACAG
464 CACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGG
1 CACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGG
* * * * * **
529 ACTAATCTCACCAAAATGATTATAGCTAGGTCGTAAACAATTGAAAGAAAAGCTTTGTTGG-TTG
66 ACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGAAAAGCTTTG-TGGTTTG
* * * *
593 CAAATTGAAGCCGATTTAACACAG
130 CAAATCGAAGACGATTCAAAACAG
* *
617 CACTAATGGGCCTCGAAAGGCCCGAAATAACAAGTGTTCTGAATGTGCTAAAAACTTCACAATGG
1 CACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGG
* * *
682 ACTAATCTCATCAAAATAATTATAGTTAGGCCAGAAACAATAGG-TAGAAAAGGTTTGTGGTTTG
66 ACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAA-AGGAAAGAAAAGCTTTGTGGTTT-
746 GCAAATCGAAGACGATTCAAAACAG
129 GCAAATCGAAGACGATTCAAAACAG
* * *
771 CACTAAT-GG-CCCG-AA-GCCCAAAATAACATGTTTTCTGAATGAGCTAAAAACTTCACAATGG
1 CACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGG
* * * * * * ** *
832 ACCAATCTCACCAAAATGATTATAGCTAGGTCGTAAACAATTGAAATAAAAGCTTTGTTGG-TTG
66 ACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGAAAAGCTTTG-TGGTTTG
* * * *
896 CAAATTGAAGCCGATTTAACACAG
130 CAAATCGAAGACGATTCAAAACAG
* * *
920 CACTAATGGGCCTCGAAAGGCCCGAAATAACAAGTGTTCTGAATGTGCTAAAATCTTCACAATGG
1 CACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGG
* * *
985 ACTAATCTCATCAAAATAACTATAGTAAGGCCAGAAACAATAGG-AAGAAAAGCTTTGTGGTTTG
66 ACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAA-AGGAAAGAAAAGCTTTGTGGTTT-
1049 GCAAATCGAAGACGATTCAAAACAG
129 GCAAATCGAAGACGATTCAAAACAG
1074 CACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATG
1 CACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATG
Statistics
Matches: 859, Mismatches: 105, Indels: 38
0.86 0.10 0.04
Matches are distributed among these distances:
149 29 0.03
150 89 0.10
151 8 0.01
152 14 0.02
153 255 0.30
154 325 0.38
155 103 0.12
156 33 0.04
157 3 0.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (153 bp):
CACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGG
ACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAAAGGAAAGAAAAGCTTTGTGGTTTGC
AAATCGAAGACGATTCAAAACAG
Found at i:968 original size:303 final size:307
Alignment explanation
Indices: 1--1137 Score: 2041
Period size: 303 Copynumber: 3.7 Consensus size: 307
* *
1 CACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTAAATGTGCTAAAAACTTCACAATGG
1 CACTAATGGGCCTCGAAAGGCCCGAAATAACAAGTGTTCTGAATGTGCTAAAAACTTCACAATGG
*
66 ACTAATCTCATCAAAATAATTATAGTTAGGCCAGAAACAGTAGGAAGAAAAGCTTTGTGGTTTGG
66 ACTAATCTCATCAAAATAATTATAGTTAGGCCAGAAACAATAGGAAGAAAAGCTTTGTGGTTTGG
*
131 CAAATCGAAGACGATTCAAAACAGCACTAATGGTCCCCGAAAGGCCCGAAATAACAAGTGTTCTG
131 CAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTG
196 AATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGGAATTATAGCTAGGTCGTAAACA
196 AATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAAT-G-ATTATAGCTAGGTCGTAAACA
261 ATTGAAAGAAAAGCTTTGTTGGTTGCAAATTGAAGCCGATTTAACACAG
259 ATTGAAAGAAAAGCTTTGTTGGTTGCAAATTGAAGCCGATTTAACACAG
* *
310 CACTAATGGGCCTCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTATAAACTTCACAATGG
1 CACTAATGGGCCTCGAAAGGCCCGAAATAACAAGTGTTCTGAATGTGCTAAAAACTTCACAATGG
* *
375 ACTAATCTCATCAAAATAATTATAGTTAGGCCATAAACAA-AGGAAAGATAAGCTTTGTGGTTTG
66 ACTAATCTCATCAAAATAATTATAGTTAGGCCAGAAACAATAGG-AAGAAAAGCTTTGTGGTTTG
*
439 CCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCT
130 GCAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCT
504 GAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGCTAGGTCGTAAACAA
195 GAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGCTAGGTCGTAAACAA
569 TTGAAAGAAAAGCTTTGTTGGTTGCAAATTGAAGCCGATTTAACACAG
260 TTGAAAGAAAAGCTTTGTTGGTTGCAAATTGAAGCCGATTTAACACAG
617 CACTAATGGGCCTCGAAAGGCCCGAAATAACAAGTGTTCTGAATGTGCTAAAAACTTCACAATGG
1 CACTAATGGGCCTCGAAAGGCCCGAAATAACAAGTGTTCTGAATGTGCTAAAAACTTCACAATGG
* *
682 ACTAATCTCATCAAAATAATTATAGTTAGGCCAGAAACAATAGGTAGAAAAGGTTTGTGGTTTGG
66 ACTAATCTCATCAAAATAATTATAGTTAGGCCAGAAACAATAGGAAGAAAAGCTTTGTGGTTTGG
* * *
747 CAAATCGAAGACGATTCAAAACAGCACTAAT-GG-CCCG-AA-GCCCAAAATAACATGTTTTCTG
131 CAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTG
*
808 AATGAGCTAAAAACTTCACAATGGACCAATCTCACCAAAATGATTATAGCTAGGTCGTAAACAAT
196 AATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGCTAGGTCGTAAACAAT
*
873 TGAAATAAAAGCTTTGTTGGTTGCAAATTGAAGCCGATTTAACACAG
261 TGAAAGAAAAGCTTTGTTGGTTGCAAATTGAAGCCGATTTAACACAG
*
920 CACTAATGGGCCTCGAAAGGCCCGAAATAACAAGTGTTCTGAATGTGCTAAAATCTTCACAATGG
1 CACTAATGGGCCTCGAAAGGCCCGAAATAACAAGTGTTCTGAATGTGCTAAAAACTTCACAATGG
* *
985 ACTAATCTCATCAAAATAACTATAGTAAGGCCAGAAACAATAGGAAGAAAAGCTTTGTGGTTTGG
66 ACTAATCTCATCAAAATAATTATAGTTAGGCCAGAAACAATAGGAAGAAAAGCTTTGTGGTTTGG
1050 CAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTG
131 CAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTG
1115 AATGAGCTAAAAACTTCACAATG
196 AATGAGCTAAAAACTTCACAATG
Statistics
Matches: 793, Mismatches: 29, Indels: 14
0.95 0.03 0.02
Matches are distributed among these distances:
303 285 0.36
304 4 0.01
305 8 0.01
306 4 0.01
307 262 0.33
308 7 0.01
309 223 0.28
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (307 bp):
CACTAATGGGCCTCGAAAGGCCCGAAATAACAAGTGTTCTGAATGTGCTAAAAACTTCACAATGG
ACTAATCTCATCAAAATAATTATAGTTAGGCCAGAAACAATAGGAAGAAAAGCTTTGTGGTTTGG
CAAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCTG
AATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGCTAGGTCGTAAACAAT
TGAAAGAAAAGCTTTGTTGGTTGCAAATTGAAGCCGATTTAACACAG
Done.