Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021575.1 Corchorus olitorius cultivar O-4 contig21608, 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: 28948
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1824 original size:18 final size:18
Alignment explanation
Indices: 1787--1825 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1777 AAAATTTTCA
* *
1787 AAATGGGATTTTCGTTTG
1 AAATGGGATTTTAGTGTG
*
1805 AAATTGGATTTTAGTGTG
1 AAATGGGATTTTAGTGTG
1823 AAA
1 AAA
1826 ACCTTGATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.26, T:0.41
Consensus pattern (18 bp):
AAATGGGATTTTAGTGTG
Found at i:2680 original size:9 final size:9
Alignment explanation
Indices: 2668--2704 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
2658 AAATTCAATC
2668 AAAAA-CAA
1 AAAAATCAA
2676 AAAAATCAA
1 AAAAATCAA
2685 AAAAATCAA
1 AAAAATCAA
2694 AAAAATCAA
1 AAAAATCAA
2703 AA
1 AA
2705 TTAAAATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 5 0.18
9 23 0.82
ACGTcount: A:0.81, C:0.11, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAATCAA
Found at i:4779 original size:30 final size:30
Alignment explanation
Indices: 4743--5542 Score: 995
Period size: 30 Copynumber: 26.8 Consensus size: 30
4733 GCTTCATCAA
* *
4743 TAATCCTGTTTGAGGATCGTTGCTTTGTTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
*
4773 TAATCCTGTTTGAGGAT-ATTTGCTTTGTTT
1 TAATCCTGTTTGAGGATCA-TTGCTTTATTT
* * *
4803 AAATCCTGTTTGAGGATCTTTGCTTTGTTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
* *
4833 TAATCCTGTTTGAGGATCTTTGCTTTGTTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
*
4863 TAATCCTGGTTGAGGATCATTG-TTTATTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
* * *
4892 TAATCCTGGTCGAGGATCATTGCTTCATTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
*
4922 TAATCCTGTTTGAGGATCATTGCTTCATTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
* *
4952 CAATCCTGGTTGAGGATCATTGCTTTATTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
** *
4982 TAATCCTGTTTGAGGATCGCTGCTTCATTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
* *
5012 CAATCCTGGTTGAGGATCATTGCTTTATTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
***
5042 TAATCCTGTTTGAGGATTGCTGCTTTATTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
* * *
5072 CAATACTGGTTGAGGATCATTGCTTTATTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
* *
5102 TAATCCTGTTTGAGGATCTTTGCTTTGTTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
*
5132 TAATCCTGGTTGAGGATCATTG-TTTATTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
* *
5161 TAATCCTGGTTGAGGATCATTGCTTCATTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
*
5191 TAATCCTGTTTGAGGATCATTGCTTCATTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
* *
5221 CAATCCTGATTGAGGATCATTGCTTTATTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
* ** *
5251 CAATCCTGTTTGAGGATCGCTGCTTCATTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
* *
5281 CAATCCTGGTTGAGGATCATTGCTTTATTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
* ***
5311 TAATCATGTTTGAGGATTGCTGCTTTATTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
* * *
5341 CAACCCTGGTTGAGGATCATTGC-TTATTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
**
5370 TAATCCTGTTTGAGGATCGCTGCTTTA-TT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
* * * *
5399 TAATCCTGGTTAAGGATCGTTGCTTTATGT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
* *
5429 CAATCCTGGTTGAGGATCATTGCTTTATTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
*
5459 TAATCCTGGTTGAGGATCATTG-TTTATTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
* *
5488 TAATGCTGATTGAGGATCATTG-TTTATTT
1 TAATCCTGTTTGAGGATCATTGCTTTATTT
5517 TAAATCCTGGTTT-AGGATCATTGCTT
1 T-AATCCT-GTTTGAGGATCATTGCTT
5543 CAGTTAATTT
Statistics
Matches: 674, Mismatches: 87, Indels: 17
0.87 0.11 0.02
Matches are distributed among these distances:
29 140 0.21
30 529 0.78
31 5 0.01
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.46
Consensus pattern (30 bp):
TAATCCTGTTTGAGGATCATTGCTTTATTT
Found at i:5223 original size:269 final size:269
Alignment explanation
Indices: 4744--5544 Score: 1263
Period size: 269 Copynumber: 3.0 Consensus size: 269
4734 CTTCATCAAT
* * * * * *
4744 AATCCTGTTTGAGGATCGTTGCTTTGTTTTAATCCTGTTTGAGGATAT-TTGCTTTGTTTAAATC
1 AATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGAT-TGCTGCTTTATTTCAATC
* * *
4808 CTGTTTGAGGATCTTTGCTTTGTTTTAATCCTGTTTGAGGATCTTTGCTTTGTTTTAATCCTGGT
65 CTGGTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCTTTGCTTTGTTTTAATCCTGGT
*
4873 TGAGGATCATTGTTTATTTTAATCCTGGTCGAGGATCATTGCTTCATTTTAATCCTGTTTGAGGA
130 TGAGGATCATTGTTTATTTTAATCCTGGTTGAGGATCATTGCTTCATTTTAATCCTGTTTGAGGA
*
4938 TCATTGCTTCATTTCAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCGCT
195 TCATTGCTTCATTTCAATCCTGATTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCGCT
5003 GCTTCATTTC
260 GCTTCATTTC
*
5013 AATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATTGCTGCTTTATTTCAATAC
1 AATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATTGCTGCTTTATTTCAATCC
5078 TGGTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCTTTGCTTTGTTTTAATCCTGGTT
66 TGGTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCTTTGCTTTGTTTTAATCCTGGTT
5143 GAGGATCATTGTTTATTTTAATCCTGGTTGAGGATCATTGCTTCATTTTAATCCTGTTTGAGGAT
131 GAGGATCATTGTTTATTTTAATCCTGGTTGAGGATCATTGCTTCATTTTAATCCTGTTTGAGGAT
*
5208 CATTGCTTCATTTCAATCCTGATTGAGGATCATTGCTTTATTTCAATCCTGTTTGAGGATCGCTG
196 CATTGCTTCATTTCAATCCTGATTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCGCTG
5273 CTTCATTTC
261 CTTCATTTC
* *
5282 AATCCTGGTTGAGGATCATTGCTTTATTTTAATCATGTTTGAGGATTGCTGCTTTATTTCAACCC
1 AATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATTGCTGCTTTATTTCAATCC
** *
5347 TGGTTGAGGATCATTGC-TTATTTTAATCCTGTTTGAGGATCGCTGCTTT-ATTTAATCCTGGTT
66 TGGTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCTTTGCTTTGTTTTAATCCTGGTT
* * * * * *
5410 AAGGATCGTTGCTTTATGTCAATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGA
131 GAGGATCATTG-TTTATTTTAATCCTGGTTGAGGATCATTGCTTCATTTTAATCCTGTTTGAGGA
* * * *
5475 TCATTG-TTTATTTTAATGCTGATTGAGGATCATTG-TTTATTTTAAATCCTGGTTT-AGGATCA
195 TCATTGCTTCATTTCAATCCTGATTGAGGATCATTGCTTTATTTT-AATCCT-GTTTGAGGATCG
*
5537 TTGCTTCA
258 CTGCTTCA
5545 GTTAATTTGA
Statistics
Matches: 497, Mismatches: 31, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
266 7 0.01
267 67 0.13
268 90 0.18
269 333 0.67
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.46
Consensus pattern (269 bp):
AATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATTGCTGCTTTATTTCAATCC
TGGTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCTTTGCTTTGTTTTAATCCTGGTT
GAGGATCATTGTTTATTTTAATCCTGGTTGAGGATCATTGCTTCATTTTAATCCTGTTTGAGGAT
CATTGCTTCATTTCAATCCTGATTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCGCTG
CTTCATTTC
Found at i:6017 original size:28 final size:28
Alignment explanation
Indices: 5976--6051 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 28
5966 AAAAAAATCT
* *
5976 AGGGGCATTTTGGTCATTTTTCACATTTC
1 AGGGGCATTTTGGTCATTTTGCAC-GTTC
*
6005 -GGGGCATTTTGGTCGTTTTGCACGTTC
1 AGGGGCATTTTGGTCATTTTGCACGTTC
*
6032 AGGGGCATTTTAGTCATTTT
1 AGGGGCATTTTGGTCATTTT
6052 AGGTTCACTT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 3 0.07
28 38 0.93
ACGTcount: A:0.14, C:0.16, G:0.26, T:0.43
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTGCACGTTC
Found at i:7147 original size:2 final size:2
Alignment explanation
Indices: 7140--7170 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7130 TTTCTTGCAT
7140 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7171 TTGTGATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11165 original size:27 final size:27
Alignment explanation
Indices: 11108--11159 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
11098 TTTTTTTCAA
*
11108 AAAAAAAAAATTGTTTTTGCGTTTTTG
1 AAAAAAAAAAGTGTTTTTGCGTTTTTG
*
11135 AAAAAAAAAAGTGTTTTTGTGTTTT
1 AAAAAAAAAAGTGTTTTTGCGTTTT
11160 CTAAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.15, T:0.44
Consensus pattern (27 bp):
AAAAAAAAAAGTGTTTTTGCGTTTTTG
Found at i:24895 original size:16 final size:18
Alignment explanation
Indices: 24876--24910 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
24866 AAGGGTAGTT
24876 TAAAAA-AA-TGTTTTCA
1 TAAAAAGAAGTGTTTTCA
24892 TAAAAAGAAGTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
24910 T
1 T
24911 GCAAGAGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 2 0.12
18 9 0.53
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (18 bp):
TAAAAAGAAGTGTTTTCA
Done.