Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023070.1 Corchorus olitorius cultivar O-4 contig23103, 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: 36028
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2130 original size:121 final size:123
Alignment explanation
Indices: 1941--2189 Score: 430
Period size: 122 Copynumber: 2.0 Consensus size: 123
1931 TCATTTAAGA
* * *
1941 AAAATATTTTAAAAGTTCTAATATATCTAAGTTTTTTAATTAAATTAGTAAAATGATAAAAATAA
1 AAAATATTTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATAA
*
2006 AATAG-TATAAGGATATTAGATTTAATTAAATAATAAAAATAGAGTTTTTAGTTGAAT
66 AATAGTTATAAGGATATTAGATTTAATTAAATAATAAAAATAGAGTTTTTAATTGAAT
* *
2063 AAAATATTTTAAAAATTCTAATATATATAAG-TTTTTAATTAAAATAGTAAAATGGTAAAAATTA
1 AAAATATTTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATAA
2127 AATAGTTATAAGGATATTAGATTTAATTAAATAATAAAAATAGAGTTTTTAATTGAAT
66 AATAGTTATAAGGATATTAGATTTAATTAAATAATAAAAATAGAGTTTTTAATTGAAT
2185 AAAAT
1 AAAAT
2190 TATAAAAATT
Statistics
Matches: 120, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
121 35 0.29
122 85 0.71
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.39
Consensus pattern (123 bp):
AAAATATTTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATAA
AATAGTTATAAGGATATTAGATTTAATTAAATAATAAAAATAGAGTTTTTAATTGAAT
Found at i:6753 original size:19 final size:19
Alignment explanation
Indices: 6715--6753 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6705 TGGAGTTAAG
*
6715 AACTTTGAAAAGCACTATT
1 AACTTTGAAAAGCACGATT
6734 AACTTTGAAAATGCA-GATT
1 AACTTTGAAAA-GCACGATT
6753 A
1 A
6754 GCCTGGAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (19 bp):
AACTTTGAAAAGCACGATT
Found at i:14904 original size:59 final size:59
Alignment explanation
Indices: 14788--14900 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 59
14778 ATTTTTTTCT
* ** * *
14788 TTGAAGTTTTAATTTGGAACTTTCACTCCTTTAATTATCAAAATCGGGATAATTTCTCC
1 TTGAACTTTTAATTTGGAACTTTCACTCCTTTAACAATCAAAATCGAGACAATTTCTCC
* *
14847 TTGAACTTTTAATTTGGAATTTTCAC-CCTTTGACAATCAAAATCGAGACAATTT
1 TTGAACTTTTAATTTGGAACTTTCACTCCTTTAACAATCAAAATCGAGACAATTT
14901 TCTCTTTAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
58 23 0.49
59 24 0.51
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.41
Consensus pattern (59 bp):
TTGAACTTTTAATTTGGAACTTTCACTCCTTTAACAATCAAAATCGAGACAATTTCTCC
Found at i:16880 original size:35 final size:34
Alignment explanation
Indices: 16841--16926 Score: 86
Period size: 35 Copynumber: 2.4 Consensus size: 34
16831 TTTAATGATA
16841 TGTTT-TCTAACAAAATAAATATCCCCTGTTTTCC-C
1 TGTTTCTCTAA-AAAA-AAA-ATCCCCTGTTTTCCTC
*
16876 TGTTTCCCTCTAAAGAAAAAATCCCCTGTTTTCCTC
1 TGTTT--CTCTAAAAAAAAAATCCCCTGTTTTCCTC
16912 TGTTTCACTCTAAAA
1 TGTTT--CTCTAAAA
16927 GTTTTTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
35 19 0.43
36 17 0.39
37 3 0.07
38 5 0.11
ACGTcount: A:0.28, C:0.27, G:0.07, T:0.38
Consensus pattern (34 bp):
TGTTTCTCTAAAAAAAAAATCCCCTGTTTTCCTC
Found at i:26334 original size:30 final size:30
Alignment explanation
Indices: 26254--26337 Score: 132
Period size: 30 Copynumber: 2.8 Consensus size: 30
26244 TATTAGCCCT
* * *
26254 TTTTACCCCATGAATTCTTGAAATGAGACA
1 TTTTGCCCCATGAACTCTTGCAATGAGACA
*
26284 TTTTGCCCCATGAACTCTTGCAATGAGATA
1 TTTTGCCCCATGAACTCTTGCAATGAGACA
26314 TTTTGCCCCATGAACTCTTGCAAT
1 TTTTGCCCCATGAACTCTTGCAAT
26338 TTCAAATCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (30 bp):
TTTTGCCCCATGAACTCTTGCAATGAGACA
Found at i:27240 original size:5 final size:5
Alignment explanation
Indices: 27230--27255 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
27220 TGAACGAAAA
27230 AACAG AACAG AACAG AACAG AACAG A
1 AACAG AACAG AACAG AACAG AACAG A
27256 GGCAAGGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.19, G:0.19, T:0.00
Consensus pattern (5 bp):
AACAG
Found at i:32316 original size:128 final size:129
Alignment explanation
Indices: 32087--32357 Score: 388
Period size: 128 Copynumber: 2.1 Consensus size: 129
32077 CATTAACGAG
*
32087 TTAATGCATTTAA-TTTTTTTTTTCATTACAAATGAGGGAAAGGGAAAGAAGGGCAAGGGTTCAA
1 TTAATGCATTTAATTTTTTTTTTTCATTACAAAGGAGGGAAAGGGAAAGAAGGGCAAGGGTTCAA
* *
32151 ATTACCCCTGCCCTCCATGTGAACTTTTGAGGCCTTGGCCACCAGGCCAAAGCCTCACGTTCT-A
66 A-TACCCCTACCCTCCATGTGAACTTTTGAGGCCTTGGCCACCAGGCCAAAGCCTCAAGTT-TGA
32215 A
129 A
** * * * *
32216 TTAATGCATTTAATTTTTTTTTTTCCATTACAAAGGAGGGAGTGGGAAGGGAGGGCAAGTGTT-T
1 TTAATGCATTTAATTTTTTTTTTT-CATTACAAAGGAGGGAAAGGGAAAGAAGGGCAAGGGTTCA
* *
32280 AA-ACCCCTACTCTCCATGTGAACTTTTGAGGCCTTGGCCACCAGGCCAAAGCCTCAAGTTTGAG
65 AATACCCCTACCCTCCATGTGAACTTTTGAGGCCTTGGCCACCAGGCCAAAGCCTCAAGTTTGAA
32344 TTAATGCATTTAAT
1 TTAATGCATTTAAT
32358 AAACTATAGT
Statistics
Matches: 128, Mismatches: 11, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
127 1 0.01
128 70 0.55
129 13 0.10
130 12 0.09
131 32 0.25
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.31
Consensus pattern (129 bp):
TTAATGCATTTAATTTTTTTTTTTCATTACAAAGGAGGGAAAGGGAAAGAAGGGCAAGGGTTCAA
ATACCCCTACCCTCCATGTGAACTTTTGAGGCCTTGGCCACCAGGCCAAAGCCTCAAGTTTGAA
Done.