Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011724.1 Corchorus olitorius cultivar O-4 contig11757, 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, 686
Length: 1144
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Found at i:573 original size:309 final size:306
Alignment explanation
Indices: 1--1138 Score: 1765
Period size: 309 Copynumber: 3.7 Consensus size: 306
* * * *
1 GCCCAACATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACCAACCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * * *
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTAAGGTTTGCCCAATCGAAGACGATTCAA
66 TTATAGTTAGGCCATAAACAATGAAAAGAAAAGCAATAAGGGTTGCCAAATCGAAGACGATTCAA
* * * *
131 AATGTCACTAATGGGCCCCGATAGGCCGAACATAACAAGTGTTCCAAATGAGCTAAGAACTTCAC
131 AACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
* *
196 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAATAATGGAAAGAAAGGCATTGAGG
196 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
*
261 GTTGCCAAATCGGAGACGATTCAAAACTGAACTAATGGGCCCCGATA
261 GTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGATA
* * *
308 GACCCAAAATAACAAGTGTTACAAATTAGCTAAAAACTTCACAGTGGACTACTCTCACCAAAAAT
1 G-CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC-AAAAT
* * ** * *
373 GATTATAGTTAGGCCATAAACAATGTAAATAAAAGCCTTGAGGGTTGCCCAATCGAAGACGATTC
64 GATTATAGTTAGGCCATAAACAATGAAAAGAAAAGCAATAAGGGTTGCCAAATCGAAGACGATTC
438 AAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
129 AAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
* *
503 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACGATGGAAAGAAAAGCATTAA
194 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA
* * *
568 GGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATTGGCCCTGATA
259 GGGTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGATA
* *
617 GCTCAAAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * * * *
682 TTATAGTTAGGCTATAAATATTGAAAAGAAAAGAAATAAGGATTGCCAAATCGAAGACGATTC-A
66 TTATAGTTAGGCCATAAACAATGAAAAGAAAAGCAATAAGGGTTGCCAAATCGAAGACGATTCAA
* * *
746 AACGTCACTAATGGGCCCCGATAAGCCCAAAACAACAAATGTTCCAAATGAGCTAAAAACTTCAC
131 AACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
* ** *
811 AATGGACTAATCTCACCAAAAAAATTATAGTTAGGCCATAAACAATGGAAGGAAAAGCATTGAGG
196 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
876 GTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATA
261 GTTGCCAAATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGATA
* *
923 GGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCTCAGTGGACTAATCTCACCAAAATG
1 -GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG
* ** *
988 ATTATAATTAGGTAATAAACAATGAAAAGAAAAGCAATGAGGGTTGCCAAATCGAAGACGATTCA
65 ATTATAGTTAGGCCATAAACAATGAAAAGAAAAGCAATAAGGGTTGCCAAATCGAAGACGATTCA
*
1053 AAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGGTAAAAACTTCA
130 AAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
1118 CAGTGGACTAATCTCACCAAA
195 CAGTGGACTAATCTCACCAAA
1139 TCGATT
Statistics
Matches: 757, Mismatches: 68, Indels: 11
0.91 0.08 0.01
Matches are distributed among these distances:
306 164 0.22
307 178 0.24
308 184 0.24
309 231 0.31
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (306 bp):
GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
TTATAGTTAGGCCATAAACAATGAAAAGAAAAGCAATAAGGGTTGCCAAATCGAAGACGATTCAA
AACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
GTTGCCAAATCGAAGACGATTCAAAACGAACTAATGGGCCCCGATA
Found at i:710 original size:153 final size:154
Alignment explanation
Indices: 1--1138 Score: 1751
Period size: 154 Copynumber: 7.4 Consensus size: 154
* * * *
1 GCCCAACATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACCAACCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * *
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTAAGGTTTGCCCAATCGAAGACGATTCAA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAA
*
131 AATGTCACTAATGGGCCCCGATAG
131 AACGTCACTAATGGGCCCCGATAG
* * *
155 GCCGAACATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * *
220 TTATAGTTAGGCCATAAATAATGGAAAGAAAGGCATTGAGGGTTGCCAAATCGGAGACGATTCAA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAA
*
285 AAC-TGAACTAATGGGCCCCGATAG
131 AACGT-CACTAATGGGCCCCGATAG
* * * *
309 ACCCAAAATAACAAGTGTTACAAATTAGCTAAAAACTTCACAGTGGACTACTCTCACCAAAAATG
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC-AAAATG
* * * *
374 ATTATAGTTAGGCCATAAACAATGTAAATAAAAGCCTTGAGGGTTGCCCAATCGAAGACGATTCA
65 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCA
439 AAACGTCACTAATGGGCCCCGATAG
130 AAACGTCACTAATGGGCCCCGATAG
464 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* *
529 TTATAGTTAGGCCATAAACGATGGAAAGAAAAGCATTAAGGGTTGCCAAATCGAAGACGATTCAA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAA
* *
594 AACGTCACTAATTGGCCCTGATA-
131 AACGTCACTAATGGGCCCCGATAG
* *
617 GCTCAAAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* * * * * * * *
682 TTATAGTTAGGCTATAAATATTGAAAAGAAAAGAAATAAGGATTGCCAAATCGAAGACGATTC-A
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAA
*
746 AACGTCACTAATGGGCCCCGATAA
131 AACGTCACTAATGGGCCCCGATAG
* * * **
770 GCCCAAAACAACAAATGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAAAAA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
*
835 TTATAGTTAGGCCATAAACAATGGAAGGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAA
**
900 AACGGAACTAATGGGCCCCGATAG
131 AACGTCACTAATGGGCCCCGATAG
* *
924 GCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCTCAGTGGACTAATCTCACCAAAATGA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
* ** * *
989 TTATAATTAGGTAATAAACAATGAAAAGAAAAGCAATGAGGGTTGCCAAATCGAAGACGATTCAA
66 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAA
1054 AACGTCACTAATGGGCCCCGATAG
131 AACGTCACTAATGGGCCCCGATAG
*
1078 GCCCAAAATAACAAGTGTTCCAAATGAGGTAAAAACTTCACAGTGGACTAATCTCACCAAA
1 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
1139 TCGATT
Statistics
Matches: 892, Mismatches: 87, Indels: 10
0.90 0.09 0.01
Matches are distributed among these distances:
152 22 0.02
153 231 0.26
154 498 0.56
155 140 0.16
156 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (154 bp):
GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAA
AACGTCACTAATGGGCCCCGATAG
Done.