Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010994.1 Corchorus capsularis cultivar CVL-1 contig11015, 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: 31533
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:63 original size:32 final size:32
Alignment explanation
Indices: 22--95 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
12 AAAATAGCCG
** *
22 AGCCGCCCCACCGGCGCGACCTGCTGTGGCTA
1 AGCCGCCCCACCGGCGCGACCTGCCCTGGCGA
* *
54 AGCCGCCCCACCGGGGCGGCCTGCCCTGGCGA
1 AGCCGCCCCACCGGCGCGACCTGCCCTGGCGA
86 AGCCGCCCCA
1 AGCCGCCCCA
96 GTGGGGCGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.12, C:0.47, G:0.32, T:0.08
Consensus pattern (32 bp):
AGCCGCCCCACCGGCGCGACCTGCCCTGGCGA
Found at i:159 original size:32 final size:32
Alignment explanation
Indices: 52--158 Score: 117
Period size: 32 Copynumber: 3.3 Consensus size: 32
42 CTGCTGTGGC
**
52 TAAGCCGCCCCACCGGGGCGGCCTGCCC-TGG
1 TAAGCCGCCCCAGTGGGGCGGCCTGCCCATGG
* *** *
83 CGAAGCCGCCCCAGTGGGGCGGCCTATTCATAG
1 -TAAGCCGCCCCAGTGGGGCGGCCTGCCCATGG
*
116 TGAAGCCGCCCTAGTGGGGCGGCCTGCCCATGG
1 T-AAGCCGCCCCAGTGGGGCGGCCTGCCCATGG
149 TAAGCCGCCC
1 TAAGCCGCCC
159 TCTTGGGGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
32 31 0.52
33 29 0.48
ACGTcount: A:0.14, C:0.38, G:0.35, T:0.13
Consensus pattern (32 bp):
TAAGCCGCCCCAGTGGGGCGGCCTGCCCATGG
Found at i:166 original size:32 final size:32
Alignment explanation
Indices: 66--170 Score: 106
Period size: 32 Copynumber: 3.2 Consensus size: 32
56 CCGCCCCACC
*
66 GGGGCGGCCTGCCC-TGGCGAAGCCGCCC-CAGT
1 GGGGCGGCCTGCCCATGG-TAAGCCGCCCTC-GT
*** * *
98 GGGGCGGCCTATTCATAGTGAAGCCGCCCTAGT
1 GGGGCGGCCTGCCCATGGT-AAGCCGCCCTCGT
*
131 GGGGCGGCCTGCCCATGGTAAGCCGCCCTCTT
1 GGGGCGGCCTGCCCATGGTAAGCCGCCCTCGT
163 GGGGCGGC
1 GGGGCGGC
171 ACGGGTCATC
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
32 30 0.52
33 28 0.48
ACGTcount: A:0.11, C:0.34, G:0.39, T:0.15
Consensus pattern (32 bp):
GGGGCGGCCTGCCCATGGTAAGCCGCCCTCGT
Found at i:8028 original size:16 final size:17
Alignment explanation
Indices: 8003--8055 Score: 74
Period size: 16 Copynumber: 3.2 Consensus size: 17
7993 GCGGGTCAGG
8003 TTGGGTTCGGGTTAAAT
1 TTGGGTTCGGGTTAAAT
*
8020 TTGGG-TCGGGTT-GAT
1 TTGGGTTCGGGTTAAAT
*
8035 TCGGGTTCGGGTTAAAT
1 TTGGGTTCGGGTTAAAT
8052 TTGG
1 TTGG
8056 ATCAGGTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 6 0.20
16 14 0.47
17 10 0.33
ACGTcount: A:0.13, C:0.08, G:0.40, T:0.40
Consensus pattern (17 bp):
TTGGGTTCGGGTTAAAT
Found at i:8041 original size:32 final size:32
Alignment explanation
Indices: 8005--8109 Score: 147
Period size: 32 Copynumber: 3.3 Consensus size: 32
7995 GGGTCAGGTT
*
8005 GGGTTCGGGTTAAATTTGGGTCGGGTTGATTC
1 GGGTTCGGGTTAAATTTGGGTCAGGTTGATTC
*
8037 GGGTTCGGGTTAAATTTGGATCAGGTTGATTC
1 GGGTTCGGGTTAAATTTGGGTCAGGTTGATTC
* * * * *
8069 AGGTTTGGGTCAAATTTCGGTCAGGTTAATTC
1 GGGTTCGGGTTAAATTTGGGTCAGGTTGATTC
8101 GGGTTCGGG
1 GGGTTCGGG
8110 CTCGGATTGG
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 63 1.00
ACGTcount: A:0.16, C:0.10, G:0.37, T:0.36
Consensus pattern (32 bp):
GGGTTCGGGTTAAATTTGGGTCAGGTTGATTC
Found at i:10751 original size:25 final size:24
Alignment explanation
Indices: 10717--10775 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 24
10707 TTCAAACCCT
*
10717 AAACTTCATTTCTAAGAACTTCTTC
1 AAACTTCATTTCTAAGAA-ATCTTC
* *
10742 AAACTTCATTTTTAATAAATCTTC
1 AAACTTCATTTCTAAGAAATCTTC
10766 AAA-TTCATTT
1 AAACTTCATTT
10776 TCCTTCATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 7 0.23
24 8 0.26
25 16 0.52
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.44
Consensus pattern (24 bp):
AAACTTCATTTCTAAGAAATCTTC
Found at i:10814 original size:26 final size:26
Alignment explanation
Indices: 10785--10902 Score: 111
Period size: 26 Copynumber: 4.7 Consensus size: 26
10775 TTCCTTCATT
10785 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
10811 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
10837 TTAAACATAAACTAA-T-AA-ACTAA
1 TTAATCATAAACTAATTAAATACTAA
* * * * * *
10860 GTAAT-TTTAATTAATTAATTA-AAA
1 TTAATCATAAACTAATTAAATACTAA
*
10884 CTAATCATAAACTAATTAA
1 TTAATCATAAACTAATTAA
10903 TATTAAAAAA
Statistics
Matches: 72, Mismatches: 16, Indels: 9
0.74 0.16 0.09
Matches are distributed among these distances:
22 6 0.08
23 9 0.12
24 8 0.11
25 12 0.17
26 37 0.51
ACGTcount: A:0.54, C:0.09, G:0.02, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:25747 original size:18 final size:18
Alignment explanation
Indices: 25724--25758 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25714 AAATGCATAA
* *
25724 AAAATTTTACATAAAATG
1 AAAATTATACAAAAAATG
25742 AAAATTATACAAAAAAT
1 AAAATTATACAAAAAAT
25759 TCTCACCGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAATTATACAAAAAATG
Done.