Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023699.1 Corchorus olitorius cultivar O-4 contig23732, 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: 41034
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:11065 original size:3 final size:3
Alignment explanation
Indices: 11057--11121 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
11047 TTACATTAAA
11057 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11105 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
11122 AAATGAAGTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:11499 original size:146 final size:140
Alignment explanation
Indices: 11232--11517 Score: 448
Period size: 146 Copynumber: 2.0 Consensus size: 140
11222 GGCTCATCAA
* *
11232 TATTCAATATTGATAGAACCATTTCTCTAAATTTGCAAGGCATATATAAAATTACTATTATTAAC
1 TATTCAATATTGATAAAACCATTGCTCTAAATTTGCAAGGCATATATAAAATTACTATTATTAAC
* *
11297 AGAATAATATATAAATTATTTATTTCTAATTACATATATTTATTTATTCACCTTTGAAAATTGTT
66 AAAATAATATATAAATTATTTATTTCTAATTACATATATTCATTTATTCACCTTTGAAAATTGTT
11362 GTCCATCCAT
131 GTCCATCCAT
11372 TATTCAATATTGATAAAACCATTGCTCTAAATTTGCAAGGCACCTATATATATAAATTTACTATT
1 TATTCAATATTGATAAAACCATTGCTCTAAATTTGCAAGG---C-ATATATA-AAA-TTACTATT
*
11437 ATTAACAAAATAATATATAAATTATTTATTT-TAATTACATATATTCATTTATTTACCTTTTGAA
60 ATTAACAAAATAATATATAAATTATTTATTTCTAATTACATATATTCATTTATTCACC-TTTGAA
*
11501 GATTGTTGTCCATCCAT
124 AATTGTTGTCCATCCAT
11518 GATAGATTTT
Statistics
Matches: 133, Mismatches: 6, Indels: 8
0.90 0.04 0.05
Matches are distributed among these distances:
140 38 0.29
143 1 0.01
144 7 0.05
145 27 0.20
146 60 0.45
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (140 bp):
TATTCAATATTGATAAAACCATTGCTCTAAATTTGCAAGGCATATATAAAATTACTATTATTAAC
AAAATAATATATAAATTATTTATTTCTAATTACATATATTCATTTATTCACCTTTGAAAATTGTT
GTCCATCCAT
Found at i:12388 original size:21 final size:21
Alignment explanation
Indices: 12364--12405 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12354 GACAAAATCC
*
12364 GTAACCCGAATGACCCGAGAA
1 GTAACCCGAATGACCCAAGAA
* *
12385 GTAACCTGGATGACCCAAGAA
1 GTAACCCGAATGACCCAAGAA
12406 TATTATAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.26, G:0.24, T:0.12
Consensus pattern (21 bp):
GTAACCCGAATGACCCAAGAA
Found at i:14495 original size:3 final size:3
Alignment explanation
Indices: 14487--14516 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
14477 TAGTTATAAA
14487 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
14517 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:19142 original size:126 final size:124
Alignment explanation
Indices: 18937--19195 Score: 344
Period size: 126 Copynumber: 2.1 Consensus size: 124
18927 ATATCATTTA
* * *
18937 AAAAATATATTTTCAAAATTATAATATATCTAAGTTTTTTTAATTAAATTAGTAAAATGATAAAA
1 AAAAATATATTTTAAAAATTATAATATATATAAGTTTTTTTAATTAAATTAATAAAATGATAAAA
* * *
19002 ATAAAATATGTATAAGGATATTAGATTTGATTAAATAAAAAAATAGAGTTTTTAGTTGAGT
66 ATAAAATATGTATAAGGATATTAGATTTAATGAAAT--AAAAATAGAGCTTTTAGTTGAGT
* * *
19063 AAAAGTATATTTTAAAAAATTCTAATATATATAAG-TTTTTTAATT-AATATAATAAAATGGTAA
1 AAAAATATATTTT-AAAAATTATAATATATATAAGTTTTTTTAATTAAAT-TAATAAAATGATAA
* *
19126 AAGTTAAATAAT-TATAAGGATATTAGATTTAATGAAATAAAAATAGAGCTTTTAGTTGAGT
64 AAATAAAAT-ATGTATAAGGATATTAGATTTAATGAAATAAAAATAGAGCTTTTAGTTGAGT
*
19187 AAAACTATA
1 AAAAATATA
19196 AAAGTTTTAA
Statistics
Matches: 118, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
124 30 0.25
125 3 0.03
126 65 0.55
127 20 0.17
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (124 bp):
AAAAATATATTTTAAAAATTATAATATATATAAGTTTTTTTAATTAAATTAATAAAATGATAAAA
ATAAAATATGTATAAGGATATTAGATTTAATGAAATAAAAATAGAGCTTTTAGTTGAGT
Found at i:21747 original size:93 final size:93
Alignment explanation
Indices: 21569--21753 Score: 307
Period size: 93 Copynumber: 2.0 Consensus size: 93
21559 TTGTTTAAAT
* *
21569 TTTTATAGTTTTAGTCAACCAAAAACTCTGTTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACCAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
* *
21634 TTTTATTTTTACCATTTTACTACTTTAC
66 TTTTATTTTTACCATATTACTAATTTAC
* *
21662 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACCAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
*
21727 TTTTATTTTTACGATATTACTAATTTA
66 TTTTATTTTTACCATATTACTAATTTA
21754 ATTAAAAAGC
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 85 1.00
ACGTcount: A:0.32, C:0.14, G:0.03, T:0.51
Consensus pattern (93 bp):
TTTTATAGTTTTACTCAACCAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATATTACTAATTTAC
Found at i:24276 original size:12 final size:12
Alignment explanation
Indices: 24259--24299 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
24249 TAACTAATTA
24259 ATCTATATTTAT
1 ATCTATATTTAT
*
24271 ATCTATATCTAT
1 ATCTATATTTAT
24283 ATCTAT-TTTAT
1 ATCTATATTTAT
24294 A-CTATA
1 ATCTATA
24300 CTAAAAAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 4 0.15
11 5 0.19
12 17 0.65
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (12 bp):
ATCTATATTTAT
Found at i:24277 original size:6 final size:6
Alignment explanation
Indices: 24259--24288 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
24249 TAACTAATTA
*
24259 ATCTAT ATTTAT ATCTAT ATCTAT ATCTAT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT
24289 TTTATACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (6 bp):
ATCTAT
Found at i:24524 original size:123 final size:129
Alignment explanation
Indices: 24386--24626 Score: 341
Period size: 135 Copynumber: 1.9 Consensus size: 129
24376 CATTGTTTAA
* * *
24386 ACTTTTATAGTTTTACTCAACTACAAACTCTA-TT-TTTATTTGATTAAATCTAATATCC-T-TA
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTATTTATTTAATTAAATCTAATATCCTTATA
*
24447 -TA-ATTTTTACCATTTTACTATTTTAATTAAGAAACTTATATATATTAGAATTTTTTAAATAT
66 CTATATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
*
24509 ACTTTTACAGTTTTACTCAACTAAAAACTTTATTTTTATTTATTTAATTAAATCTAATATCCTTA
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTA--TTTATTTATTTAATTAAATCTAATATCCTTA
24574 TACCTATTTTATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATAT
64 TA-CTA---TATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATAT
24627 ATATTAGAAT
Statistics
Matches: 101, Mismatches: 5, Indels: 12
0.86 0.04 0.10
Matches are distributed among these distances:
123 29 0.29
126 2 0.02
127 23 0.23
128 1 0.01
129 2 0.02
131 2 0.02
135 42 0.42
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (129 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTATTTATTTAATTAAATCTAATATCCTTATA
CTATATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:29652 original size:22 final size:22
Alignment explanation
Indices: 29620--29665 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
29610 AAAGGAAGAG
*
29620 TAAGTCGATTCTTGCATTTCTT
1 TAAGTCAATTCTTGCATTTCTT
*
29642 TAAGTCAATTCTTGTATTTCTT
1 TAAGTCAATTCTTGCATTTCTT
29664 TA
1 TA
29666 TTTCACTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.52
Consensus pattern (22 bp):
TAAGTCAATTCTTGCATTTCTT
Found at i:32227 original size:6 final size:6
Alignment explanation
Indices: 32216--32241 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
32206 TATCTACTTG
32216 TATGTA TATGTA TATGTA TATGTA TA
1 TATGTA TATGTA TATGTA TATGTA TA
32242 GATGACTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
TATGTA
Found at i:33060 original size:22 final size:22
Alignment explanation
Indices: 33035--33079 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
33025 ATCTAATTAG
*
33035 ATATGGAC-TTTGAGATTTAATC
1 ATATGGACATTT-AAATTTAATC
*
33057 ATATGGTCATTTAAATTTAATC
1 ATATGGACATTTAAATTTAATC
33079 A
1 A
33080 ACTAGACCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (22 bp):
ATATGGACATTTAAATTTAATC
Done.