Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006602.1 Corchorus capsularis cultivar CVL-1 contig06623, 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, 631
Length: 1053
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.23
Found at i:557 original size:154 final size:154
Alignment explanation
Indices: 3--1053 Score: 1690
Period size: 154 Copynumber: 6.8 Consensus size: 154
1 CC
* *
3 AAATCGAAG-CTGATTC-AAACAGCACTAAAGGGCCCCGAAAGGCCGGAAATAACAAGTGTTCTG
1 AAATCGAAGAC-GATTCAAAACAGCACTAATGGGCCCCGAAAGGCCTGAAATAACAAGTGTTCTG
* * *
66 AATGAGCTAAAAACTTCACAATGGACTAATCTTACC-AAATGATTATAGGT-A-GCTCGTAAACA
65 AATGAGCTAAAAACTTCACAGTGTACTAATCTCACCAAAATGATTATA-GTAAGGC-CGTAAACA
* *
128 ATTAGAAAGAAAAGCTTTAGTTGGTTAGCC
128 ATT-GAAAGAAAAGCTTT-G-TGGTTTGCG
* * * * *
158 AAATTGAAGCCGATTTAAAACAGCACTAATGGGCCTCGAAAGGCCCGAAATAACAAGTGTTCTGA
1 AAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCTGAAATAACAAGTGTTCTGA
*
223 ATGAGCTAAAAACTTCACAGTGTACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATT
66 ATGAGCTAAAAACTTCACAGTGTACTAATCTCACCAAAATGATTATAGTAAGGCCGTAAACAATT
*
288 GAAAGAAAAGCTTTGTGGTTTAGCT
131 GAAAGAAAAGCTTTGTGGTTT-GCG
* * * * *
313 AAATCGAAGCCGATTCAATACAGCACTAAAGGGACACGAAAGGCCTGAAATAACAAGTGTTCTGA
1 AAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCTGAAATAACAAGTGTTCTGA
*
378 ATGAGCTAAAAACTTCACAGAGTACTAATCTCACCAAAATGATTATA-TAACGGCCGTAAACAAT
66 ATGAGCTAAAAACTTCACAGTGTACTAATCTCACCAAAATGATTATAGTAA-GGCCGTAAACAAT
*
442 TGAAAGAAAGGCTTTGTGGTTTGCG
130 TGAAAGAAAAGCTTTGTGGTTTGCG
467 AAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCTGAAATAACAAGTGTTCTGA
1 AAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCTGAAATAACAAGTGTTCTGA
532 ATGAGCTAAAAACTTCACAGTGTACTAATCTCACCAAAATGATTATA-TAAAGGCCGTAAACAAT
66 ATGAGCTAAAAACTTCACAGTGTACTAATCTCACCAAAATGATTATAGT-AAGGCCGTAAACAAT
596 TGAAAG-AAAGCTTTAGTGGTTTGCG
130 TGAAAGAAAAGCTTT-GTGGTTTGCG
* *
621 AAATCGAAGACGA-TCCAAACAGCACTAATGGGCCGCGAAAGGCCTGAAATAAACAAGTGTTCTG
1 AAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCTGAAAT-AACAAGTGTTCTG
*
685 AATGAGCTAAAAACTTCACAGTGTACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAAT
65 AATGAGCTAAAAACTTCACAGTGTACTAATCTCACCAAAATGATTATAGTAAGGCCGTAAACAAT
750 TGAAAGAAAAGCTTTGTGGTTTGCG
130 TGAAAGAAAAGCTTTGTGGTTTGCG
775 AAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCTGAAATAACAAGTGTTCTGA
1 AAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCTGAAATAACAAGTGTTCTGA
840 ATGAGCTAAAAACTTCACAGTGTACTAATCTCACCAAAATGATTATA-TAACGGCCGTAAACAAT
66 ATGAGCTAAAAACTTCACAGTGTACTAATCTCACCAAAATGATTATAGTAA-GGCCGTAAACAAT
*
904 TGAAAGAAAAGCTTTGTTGTTTGCG
130 TGAAAGAAAAGCTTTGTGGTTTGCG
929 AAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCTGAAATAACAAGTGTTCTGA
1 AAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCTGAAATAACAAGTGTTCTGA
*
994 ATGAGCTAAAAACTTCACAGTGTACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAA
66 ATGAGCTAAAAACTTCACAGTGTACTAATCTCACCAAAATGATTATAGTAAGGCCGTAAA
Statistics
Matches: 845, Mismatches: 36, Indels: 31
0.93 0.04 0.03
Matches are distributed among these distances:
153 44 0.05
154 481 0.57
155 201 0.24
156 94 0.11
157 23 0.03
158 2 0.00
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (154 bp):
AAATCGAAGACGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCTGAAATAACAAGTGTTCTGA
ATGAGCTAAAAACTTCACAGTGTACTAATCTCACCAAAATGATTATAGTAAGGCCGTAAACAATT
GAAAGAAAAGCTTTGTGGTTTGCG
Done.