Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017416.1 Corchorus olitorius cultivar O-4 contig17449, 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: 13302
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3153 original size:49 final size:48
Alignment explanation
Indices: 3057--3200 Score: 166
Period size: 49 Copynumber: 3.0 Consensus size: 48
3047 GAGCGTGCCA
* * * *
3057 ATCAATTTTGTCAAAAAAAATTGATAAAAAGTGCGATGAAAATTAAAAG
1 ATCAATTTTGTC-ATAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
*
3106 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAG
1 ATCAATTTTGTCATAAAAATTGAGAAAAAG-TGCAATG-AAAAATAAAAG
* * *
3155 TTCAATTTTGT-AGTAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
1 ATCAATTTTGTCA-TAAAAATTGAGAAAAAGTGCAATGAAAAATAAA
3201 GGATTGCTTG
Statistics
Matches: 82, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
48 28 0.34
49 54 0.66
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (48 bp):
ATCAATTTTGTCATAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
Found at i:4492 original size:9 final size:9
Alignment explanation
Indices: 4474--4511 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
4464 TTAATTCATT
4474 TAATTT-CA
1 TAATTTCCA
4482 TAATTTCCA
1 TAATTTCCA
*
4491 TAATTTCCT
1 TAATTTCCA
4500 TAATTTCCA
1 TAATTTCCA
4509 TAA
1 TAA
4512 GTAATTTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 6 0.22
9 21 0.78
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.47
Consensus pattern (9 bp):
TAATTTCCA
Found at i:7713 original size:11 final size:11
Alignment explanation
Indices: 7693--7727 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
7683 TTGACAGCGC
7693 AACAAAAACAA
1 AACAAAAACAA
*
7704 AACGAAAACAA
1 AACAAAAACAA
7715 AACAAAAACAA
1 AACAAAAACAA
7726 AA
1 AA
7728 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:9181 original size:31 final size:32
Alignment explanation
Indices: 9125--9194 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
9115 GAAAGTAACT
*
9125 TTCTATAAGCATGTTACTTGGTGTTAGCATTAG
1 TTCT-TAAGCATGTTACTTGGTGTTAGCACTAG
*
9158 TTCTTAAGTATGTTAC-TGGTGTTAGCACTAG
1 TTCTTAAGCATGTTACTTGGTGTTAGCACTAG
9189 TTCTTA
1 TTCTTA
9195 GATCAACCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 20 0.57
32 11 0.31
33 4 0.11
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.44
Consensus pattern (32 bp):
TTCTTAAGCATGTTACTTGGTGTTAGCACTAG
Found at i:11090 original size:31 final size:30
Alignment explanation
Indices: 11052--11125 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
11042 TTATAAATTT
11052 GGACTCAATTGAC-CCAATCTGACAAGTAGAG
1 GGACTCAATTGACACCAAT-T-ACAAGTAGAG
* *
11083 GGACTCAATTGACATCGAATTTCAAGTAGAG
1 GGACTCAATTGACA-CCAATTACAAGTAGAG
*
11114 AGACTCAATTGA
1 GGACTCAATTGA
11126 TAGTTTTTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 33 0.87
32 1 0.03
33 4 0.11
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (30 bp):
GGACTCAATTGACACCAATTACAAGTAGAG
Found at i:12338 original size:23 final size:23
Alignment explanation
Indices: 12312--12356 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12302 TCAAATCTAA
*
12312 TATCCTTATACCT-ATTTTATTTT
1 TATCATTATA-CTAATTTTATTTT
*
12335 TATCATTTTACTAATTTTATTT
1 TATCATTATACTAATTTTATTT
12357 AAAAACTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.62
Consensus pattern (23 bp):
TATCATTATACTAATTTTATTTT
Done.