Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014217.1 Corchorus olitorius cultivar O-4 contig14250, 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: 6973
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Found at i:528 original size:31 final size:30
Alignment explanation
Indices: 493--564 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
483 TACCCAGGAG
*
493 GTCCCTCTACTTACACAAAAA-AATCAATTTA
1 GTCCCTCTACTTA-A-AAAAACAATCAACTTA
*
524 GTCCCTCTAC-TAAAAAAACGATCAACTTA
1 GTCCCTCTACTTAAAAAAACAATCAACTTA
553 GTCCCTCTACTT
1 GTCCCTCTACTT
565 GTAAGATTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
28 5 0.14
29 19 0.51
30 3 0.08
31 10 0.27
ACGTcount: A:0.36, C:0.29, G:0.06, T:0.29
Consensus pattern (30 bp):
GTCCCTCTACTTAAAAAAACAATCAACTTA
Found at i:714 original size:26 final size:28
Alignment explanation
Indices: 664--722 Score: 95
Period size: 26 Copynumber: 2.1 Consensus size: 28
654 GAATCCACCA
664 TAAATTTTCAGAATTTTTTTATAGAAAAT
1 TAAATTTTCAG-ATTTTTTTATAGAAAAT
693 TAAATTTTCAG-TTTTTTT-TAGAAAAT
1 TAAATTTTCAGATTTTTTTATAGAAAAT
719 TAAA
1 TAAA
723 AAAAAAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 12 0.40
27 7 0.23
29 11 0.37
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (28 bp):
TAAATTTTCAGATTTTTTTATAGAAAAT
Found at i:1888 original size:22 final size:25
Alignment explanation
Indices: 1845--1901 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 25
1835 TTCTTTTTAA
1845 TTTTTTTTAAAGATATCGTTTTTCT
1 TTTTTTTTAAAGATATCGTTTTTCT
*
1870 TTTTTTTTAAA-TTA-C-TTTTTCT
1 TTTTTTTTAAAGATATCGTTTTTCT
*
1892 TATTTTTTAA
1 TTTTTTTTAA
1902 TAAAAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 16 0.53
23 1 0.03
24 2 0.07
25 11 0.37
ACGTcount: A:0.21, C:0.07, G:0.04, T:0.68
Consensus pattern (25 bp):
TTTTTTTTAAAGATATCGTTTTTCT
Found at i:2033 original size:31 final size:31
Alignment explanation
Indices: 1992--2065 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
1982 GTCATTAATT
* * *
1992 GGACTCAATTGACCCAATCTGGCAAGTATAG
1 GGACTAAATTGACCCAATCTGACAAGTAGAG
*
2023 GGACTAAATTGACCCAATCTTACAAGTAGAG
1 GGACTAAATTGACCCAATCTGACAAGTAGAG
2054 GGACTAAATTGA
1 GGACTAAATTGA
2066 TTGTTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (31 bp):
GGACTAAATTGACCCAATCTGACAAGTAGAG
Found at i:2117 original size:31 final size:31
Alignment explanation
Indices: 2046--2118 Score: 114
Period size: 30 Copynumber: 2.4 Consensus size: 31
2036 CCAATCTTAC
*
2046 AAGTAGAGGGACTAAATTGATTGTTTTTTTT
1 AAGTAGAGGGACTAAATTGATTGTTTTTTGT
2077 AA-TAGAGGGACTAAATTGATT-TTTTTGTGT
1 AAGTAGAGGGACTAAATTGATTGTTTTT-TGT
2107 AAGTAGAGGGAC
1 AAGTAGAGGGAC
2119 CTCCTTGGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 5 0.13
30 23 0.59
31 11 0.28
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (31 bp):
AAGTAGAGGGACTAAATTGATTGTTTTTTGT
Found at i:6783 original size:25 final size:22
Alignment explanation
Indices: 6750--6799 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
6740 TATCTTAGAT
6750 ATAATATATATTATTAAATAAAAA
1 ATAA-ATATATT-TTAAATAAAAA
*
6774 ATAAATATATTTTAAATAATAA
1 ATAAATATATTTTAAATAAAAA
6796 ATAA
1 ATAA
6800 TGAGTTCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 14 0.56
23 7 0.28
24 4 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAAATATATTTTAAATAAAAA
Done.