Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015918.1 Corchorus capsularis cultivar CVL-1 contig15939, 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: 1955
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Found at i:1732 original size:35 final size:34
Alignment explanation
Indices: 1688--1796 Score: 112
Period size: 35 Copynumber: 3.1 Consensus size: 34
1678 GTAATTGGAT
*
1688 AATAGTAATCAGTAAAAAGTAATCGGTAAGAGTAA
1 AATAATAATCAGTAAAAAGTAAT-GGTAAGAGTAA
* * *
1723 AATAATAATCAGT-AAGAGCAAAGTGGTAATAGTAA
1 AATAATAATCAGTAAAAAG-TAA-TGGTAAGAGTAA
* * *
1758 AATATTAATCAGTAAAAGGTAATTAGTAAGAGTAA
1 AATAATAATCAGTAAAAAGTAA-TGGTAAGAGTAA
1793 AATA
1 AATA
1797 GTAAAGAGTA
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
34 4 0.07
35 52 0.87
36 4 0.07
ACGTcount: A:0.52, C:0.05, G:0.18, T:0.25
Consensus pattern (34 bp):
AATAATAATCAGTAAAAAGTAATGGTAAGAGTAA
Found at i:1807 original size:35 final size:35
Alignment explanation
Indices: 1688--1902 Score: 107
Period size: 35 Copynumber: 6.0 Consensus size: 35
1678 GTAATTGGAT
* * ***
1688 AATAGTAATCAGTAAAAAGTAATCGGTAAGAGTAA
1 AATAGTAAACAGTAAAAGGTAAAAAGTAAGAGTAA
* * * * ** *
1723 AATAATAATCAGTAAGA-GCAAAGTGGTAATAGTAA
1 AATAGTAAACAGTAAAAGGTAAA-AAGTAAGAGTAA
* * **
1758 AATATTAATCAGTAAAAGGTAATTAGTAAGAGTAA
1 AATAGTAAACAGTAAAAGGTAAAAAGTAAGAGTAA
* * *
1793 AATAGTAAAGAGTAAGATGATAAAAAGTAAAGAGT--
1 AATAGTAAACAGTAA-AAGGTAAAAAGT-AAGAGTAA
*
1828 AATCAGTAAAGAGTAAAATGGTAAAAAGTAA-AG-AA
1 AAT-AGTAAACAGTAAAA-GGTAAAAAGTAAGAGTAA
* *
1863 TAATCAGTAAAAGAGTAAAATGGTAAAAGGTAAAGAGTAA
1 -AAT-AGT-AAACAGTAAAA-GGTAAAAAGT-AAGAGTAA
1903 TCAGTAAAGA
Statistics
Matches: 145, Mismatches: 22, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
34 5 0.03
35 68 0.47
36 39 0.27
37 27 0.19
38 2 0.01
39 2 0.01
40 2 0.01
ACGTcount: A:0.54, C:0.03, G:0.20, T:0.22
Consensus pattern (35 bp):
AATAGTAAACAGTAAAAGGTAAAAAGTAAGAGTAA
Found at i:1823 original size:7 final size:7
Alignment explanation
Indices: 1788--1902 Score: 52
Period size: 7 Copynumber: 15.7 Consensus size: 7
1778 AATTAGTAAG
1788 AGTAAAA
1 AGTAAAA
*
1795 TAGTAAAG
1 -AGTAAAA
*
1803 AGTAAGA
1 AGTAAAA
*
1810 TGATAAAA
1 AG-TAAAA
*
1818 AGTAAAG
1 AGTAAAA
**
1825 AGTAATC
1 AGTAAAA
*
1832 AGTAAAG
1 AGTAAAA
1839 AGTAAAA
1 AGTAAAA
*
1846 TGGTAAAA
1 -AGTAAAA
1854 AGTAAAGA
1 AGTAAA-A
**
1862 A-TAATC
1 AGTAAAA
1868 AGTAAAA
1 AGTAAAA
1875 GAGTAAAA
1 -AGTAAAA
*
1883 TGGTAAAA
1 -AGTAAAA
* *
1891 GGTAAAG
1 AGTAAAA
1898 AGTAA
1 AGTAA
1903 TCAGTAAAGA
Statistics
Matches: 80, Mismatches: 22, Indels: 11
0.71 0.19 0.10
Matches are distributed among these distances:
6 1 0.01
7 47 0.59
8 32 0.40
ACGTcount: A:0.57, C:0.02, G:0.22, T:0.19
Consensus pattern (7 bp):
AGTAAAA
Found at i:1885 original size:37 final size:36
Alignment explanation
Indices: 1796--1927 Score: 201
Period size: 36 Copynumber: 3.6 Consensus size: 36
1786 AGAGTAAAAT
* *
1796 AGTAAAGAGTAAGATGATAAAAAGTAAAGAGTAATC
1 AGTAAAGAGTAAAATGGTAAAAAGTAAAGAGTAATC
*
1832 AGTAAAGAGTAAAATGGTAAAAAGTAAAGAATAATC
1 AGTAAAGAGTAAAATGGTAAAAAGTAAAGAGTAATC
*
1868 AGTAAAAGAGTAAAATGGTAAAAGGTAAAGAGTAATC
1 AGT-AAAGAGTAAAATGGTAAAAAGTAAAGAGTAATC
* *
1905 AGTAAAGAGAAAAATGGCAAAAA
1 AGTAAAGAGTAAAATGGTAAAAA
1928 TATATATATA
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
36 53 0.61
37 34 0.39
ACGTcount: A:0.58, C:0.03, G:0.22, T:0.17
Consensus pattern (36 bp):
AGTAAAGAGTAAAATGGTAAAAAGTAAAGAGTAATC
Done.