Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024793.1 Corchorus olitorius cultivar O-4 contig24826, 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: 24446
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2909 original size:26 final size:26
Alignment explanation
Indices: 2873--2941 Score: 129
Period size: 26 Copynumber: 2.7 Consensus size: 26
2863 ACAGTAATTT
2873 TGACCAAAATGCCCCTGAGGCGAAAA
1 TGACCAAAATGCCCCTGAGGCGAAAA
*
2899 TGACCAAAATGCCCCTGAGGTGAAAA
1 TGACCAAAATGCCCCTGAGGCGAAAA
2925 TGACCAAAATGCCCCTG
1 TGACCAAAATGCCCCTG
2942 GTGAATTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.36, C:0.28, G:0.22, T:0.14
Consensus pattern (26 bp):
TGACCAAAATGCCCCTGAGGCGAAAA
Found at i:4836 original size:31 final size:31
Alignment explanation
Indices: 4801--4868 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
4791 GATTCAACTC
* * *
4801 AATTGACCCAATTTTTTGAGTACGTGGACTA
1 AATTGACCCAATATTGTGAGTACATGGACTA
*
4832 AATTGACCCAATATTGTGAGTATATGGACTA
1 AATTGACCCAATATTGTGAGTACATGGACTA
4863 AATTGA
1 AATTGA
4869 TTTTTTTTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (31 bp):
AATTGACCCAATATTGTGAGTACATGGACTA
Found at i:5980 original size:101 final size:102
Alignment explanation
Indices: 5769--6011 Score: 280
Period size: 101 Copynumber: 2.4 Consensus size: 102
5759 AGTTTAGCCT
**** *
5769 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAA---TAAAAATATTTTAAGGATAAATTTCAAAA-T
* *
5834 TTAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
62 TTAATATATTGTTATAGGATTTTAGAAATAAAATACAAAAC
*
5875 TAATTTCACTAAGTTTAGCCCCAAATTAAAA-AAAAATATTTTAAGGATAAA-TTCTATAA-TTA
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATAAAAATATTTTAAGGATAAATTTC-AAAATTTA
* *
5937 ATAATATTGTTATAGGATTTTAGAAATAAAATATATAAC
65 AT-ATATTGTTATAGGATTTTAGAAATAAAATACAAAAC
* * *
5976 TAA-TTCACTAAATTTA-ACCCAAATTAAAATTAAAAT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATAAAAAT
6012 TTTATTTTAG
Statistics
Matches: 121, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
99 12 0.10
100 22 0.18
101 38 0.31
102 18 0.15
106 31 0.26
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (102 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATAAAAATATTTTAAGGATAAATTTCAAAATTTAA
TATATTGTTATAGGATTTTAGAAATAAAATACAAAAC
Found at i:9874 original size:19 final size:17
Alignment explanation
Indices: 9834--9874 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
9824 AAATAATGGC
9834 AAAAAAAAAAAAGGAAT
1 AAAAAAAAAAAAGGAAT
*
9851 GAAAAGAAAGAAAAGGAAT
1 -AAAA-AAAAAAAAGGAAT
9870 AAAAA
1 AAAAA
9875 TTTCTTGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 8 0.38
19 12 0.57
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (17 bp):
AAAAAAAAAAAAGGAAT
Found at i:11536 original size:20 final size:21
Alignment explanation
Indices: 11511--11576 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 21
11501 GTTTATATTA
11511 TATATTATATATATA-ATAAT
1 TATATTATATATATATATAAT
* * *
11531 TATATT-TTTATTTATATAAA
1 TATATTATATATATATATAAT
* *
11551 TAT-TTAAATATGTATATAAT
1 TATATTATATATATATATAAT
11571 TATATT
1 TATATT
11577 TTATTCCATA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
19 8 0.22
20 26 0.72
21 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TATATTATATATATATATAAT
Found at i:11601 original size:40 final size:41
Alignment explanation
Indices: 11517--11603 Score: 99
Period size: 40 Copynumber: 2.1 Consensus size: 41
11507 ATTATATATT
* **
11517 ATATATATAATAATTATATTTTTATTTATATAAATATTTAA
1 ATATATATAATAATTATATTTTTATTCATATAAATAAATAA
*
11558 ATATGTAT-ATAATTATA-TTTTATTCCATATAATATAAAT-A
1 ATATATATAATAATTATATTTTTATT-CATATAA-ATAAATAA
11598 ATATAT
1 ATATAT
11604 TTATTCCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
39 7 0.18
40 21 0.54
41 11 0.28
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (41 bp):
ATATATATAATAATTATATTTTTATTCATATAAATAAATAA
Found at i:17427 original size:56 final size:56
Alignment explanation
Indices: 17341--17453 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
17331 GTCAGAAGTG
17341 CAAATATGATCTTGCAAAAAGTCCAGGTTTATTACAACCTATTCCTATTCCTATTC
1 CAAATATGATCTTGCAAAAAGTCCAGGTTTATTACAACCTATTCCTATTCCTATTC
17397 CAAATATGATCTTGCAAAAAGTCCAGGTTTATTACAACCTATTCCTATTCCTATTC
1 CAAATATGATCTTGCAAAAAGTCCAGGTTTATTACAACCTATTCCTATTCCTATTC
17453 C
1 C
17454 TAAAGGAGCT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.35
Consensus pattern (56 bp):
CAAATATGATCTTGCAAAAAGTCCAGGTTTATTACAACCTATTCCTATTCCTATTC
Done.