Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021965.1 Corchorus olitorius cultivar O-4 contig21998, 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, 1000
Length: 8187
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:1217 original size:40 final size:39
Alignment explanation
Indices: 1011--1789 Score: 806
Period size: 40 Copynumber: 19.6 Consensus size: 39
1001 GAATTGGCTA
* *
1011 ATAAAGAAATGATCCTAAGCAGGATTTTGAAA-TGA-TTG
1 ATAAA-AAATGATCCTGAGCAGGATTTTGAAATTAATTTG
* * ** * *
1049 ATACAACAACGATCCTGAATAGGA--TGGAAATTGA-TTG
1 ATA-AAAAATGATCCTGAGCAGGATTTTGAAATTAATTTG
* ** ** * *
1086 ATAAAGAAATGGTCCTGAATAGGATTCTAAAAAGT-GTCTTG
1 ATAAA-AAATGATCCTGAGCAGGATT-TTGAAATTAAT-TTG
* * *
1127 ATAAAGCAATGATCCTGAGTAGGATTGTG--ATTAATTTG
1 ATAAA-AAATGATCCTGAGCAGGATTTTGAAATTAATTTG
* *
1165 ATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTG
1 ATAAA-AAATGATCCTGAGCAGGATTTTGAAATTAATTTG
*
1205 ATAAAAAGATGATCCTGAGCAGGATTCTGAAATTAATTTG
1 ATAAAAA-ATGATCCTGAGCAGGATTTTGAAATTAATTTG
* *
1245 ATAAAAACATGATCCTGAGTAGGGTTTTGAAATTAATTTG
1 ATAAAAA-ATGATCCTGAGCAGGATTTTGAAATTAATTTG
* * *
1285 ATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAACTTG
1 ATAAA-AAATGATCCTGAGCAGGATTTTGAAATTAATTTG
* * *
1325 ATAAAACAATGATCCTGAGTAGGGTTTTGAAATTAACTTG
1 ATAAAA-AATGATCCTGAGCAGGATTTTGAAATTAATTTG
*
1365 ATAAAATAATGATCCTGAGCAGGGTTTTGAAATTAATTTG
1 ATAAAA-AATGATCCTGAGCAGGATTTTGAAATTAATTTG
* *
1405 ATAAAAAGATGATCTTGAGCAGGATTCTGAAATTAATTTG
1 ATAAAAA-ATGATCCTGAGCAGGATTTTGAAATTAATTTG
*
1445 ATAAAGTAATGATCCTGAGCAGGATTTTGAAATTAATTTG
1 ATAAA-AAATGATCCTGAGCAGGATTTTGAAATTAATTTG
*
1485 ATAAAAAAGATGATCCTGAGCAGGGTTTCTGAAATTAATTTG
1 AT-AAAAA-ATGATCCTGAGCAGGATTT-TGAAATTAATTTG
* *
1527 ATAAAGCAATGATCTTGAGCAGGATTTTGAAATTAATTTG
1 ATAAA-AAATGATCCTGAGCAGGATTTTGAAATTAATTTG
* * *
1567 ATAAAGCAATGATCCTGAGCAGGATTCTGAAACTAATTTG
1 ATAAA-AAATGATCCTGAGCAGGATTTTGAAATTAATTTG
** *
1607 ATGAAGCAATGATCCTGAGCAGGATTCTGAAATTAATTTG
1 AT-AAAAAATGATCCTGAGCAGGATTTTGAAATTAATTTG
** *
1647 ATGAAGCAATGATCCTGAGCAGGATTCTGAAATTAATTTG
1 AT-AAAAAATGATCCTGAGCAGGATTTTGAAATTAATTTG
**
1687 ATAAAAAGATGATCCTGAGCAGGATTTTGAAAAGAATTTG
1 ATAAAAA-ATGATCCTGAGCAGGATTTTGAAATTAATTTG
* * *
1727 ATAAAGCAATGATCCTGAGCAGGATTCTG--ATTAA-CTG
1 ATAAA-AAATGATCCTGAGCAGGATTTTGAAATTAATTTG
*
1764 GTAAAGAAATGATCCTGAGCAGGATT
1 ATAAA-AAATGATCCTGAGCAGGATT
1790 AAAACCCATA
Statistics
Matches: 651, Mismatches: 67, Indels: 47
0.85 0.09 0.06
Matches are distributed among these distances:
36 7 0.01
37 50 0.08
38 50 0.08
39 8 0.01
40 448 0.69
41 72 0.11
42 16 0.02
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (39 bp):
ATAAAAAATGATCCTGAGCAGGATTTTGAAATTAATTTG
Found at i:2214 original size:153 final size:148
Alignment explanation
Indices: 1839--2245 Score: 491
Period size: 153 Copynumber: 2.8 Consensus size: 148
1829 ATATAGAATT
* * **
1839 CCCGGAGGACTTGTCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACGGAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
* * * *
1904 GC-AA---A-C-TCA-ACCTTGAGCAAGGTTTATTGAAATTTAAACGCAAATTTGATTAACAACA
66 GCAAATTCAGCTTGAGACCTTGAGCAAGGTTTATTGAAACTTAAACACAAATTTGATTAAAAACA
1962 TGATGAAATGAAATGATA
131 TGATGAAATGAAATGATA
* * *
1980 CCTGGAGGTTTTATCATAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
* * **
2045 GCAAATTCTGAATTGAGACCTTGAGCAAGGTTGTGATTTTGAAACTTAAACACAGCTTTGATTAA
66 GCAAATTCAG-CTTGAGACCTTGAGCAAGGTT-T-A--TTGAAACTTAAACACAAATTTGATTAA
*
2110 AAACTTGATGAAATGAAATGATA
126 AAACATGATGAAATGAAATGATA
* * *
2133 CCCGGAGGATTTATTAGAATTAATACCCGGAGGTTTCTGAAATGGTGCCCGAAGGTCTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
*
2198 GCAAATT---C---AG-CCTTGAGCAAGGTTTATTGAAACTTAAACACAACTTTG
66 GCAAATTCAGCTTGAGACCTTGAGCAAGGTTTATTGAAACTTAAACACAAATTTG
2246 TTGAAAGACT
Statistics
Matches: 230, Mismatches: 24, Indels: 24
0.83 0.09 0.09
Matches are distributed among these distances:
141 81 0.35
142 2 0.01
143 1 0.00
144 1 0.00
145 14 0.06
146 2 0.01
148 2 0.01
149 15 0.07
150 1 0.00
151 1 0.00
153 110 0.48
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.29
Consensus pattern (148 bp):
CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
GCAAATTCAGCTTGAGACCTTGAGCAAGGTTTATTGAAACTTAAACACAAATTTGATTAAAAACA
TGATGAAATGAAATGATA
Done.