Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006944.1 Corchorus capsularis cultivar CVL-1 contig06965, 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: 19326
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Found at i:1807 original size:25 final size:25
Alignment explanation
Indices: 1742--1819 Score: 93
Period size: 25 Copynumber: 3.0 Consensus size: 25
1732 ATCAGTAATG
*
1742 ATCAATCAATAATTATTTACTTTCTCCC
1 ATCAATCAATAATTATTTAC-TT-T-CA
**
1770 ATCAAAAAAATAATTATTTACTTTCA
1 ATC-AATCAATAATTATTTACTTTCA
1796 ATCAATCAATAATTATTTACTTTC
1 ATCAATCAATAATTATTTACTTTC
1820 CATAAACAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
25 19 0.43
26 4 0.09
27 1 0.02
28 5 0.11
29 15 0.34
ACGTcount: A:0.40, C:0.18, G:0.00, T:0.42
Consensus pattern (25 bp):
ATCAATCAATAATTATTTACTTTCA
Found at i:2338 original size:17 final size:18
Alignment explanation
Indices: 2318--2357 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2308 GATACAAAGT
2318 TTTATA-AAAAAATAATA
1 TTTATAGAAAAAATAATA
*
2335 TTTATAGTAAAAATAATA
1 TTTATAGAAAAAATAATA
2353 TTTAT
1 TTTAT
2358 GGGTTGCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
TTTATAGAAAAAATAATA
Found at i:6835 original size:6 final size:6
Alignment explanation
Indices: 6826--6850 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6816 ACACACACAC
6826 AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA A
6851 TTAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:18503 original size:22 final size:22
Alignment explanation
Indices: 18478--18524 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
18468 ATTTATTCAT
18478 TATTAAATAACTATTAATTAGA
1 TATTAAATAACTATTAATTAGA
* *
18500 TATTAATTAGCTATTAATTAGA
1 TATTAAATAACTATTAATTAGA
18522 TAT
1 TAT
18525 AGTATAATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (22 bp):
TATTAAATAACTATTAATTAGA
Found at i:18520 original size:11 final size:11
Alignment explanation
Indices: 18478--18520 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
18468 ATTTATTCAT
* *
18478 TATTAAATAAC
1 TATTAATTAGC
*
18489 TATTAATTAGA
1 TATTAATTAGC
18500 TATTAATTAGC
1 TATTAATTAGC
18511 TATTAATTAG
1 TATTAATTAG
18521 ATATAGTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:18764 original size:22 final size:22
Alignment explanation
Indices: 18738--18784 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
18728 ATTTATTCAT
18738 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
*
18760 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
18782 TAT
1 TAT
18785 AGTATAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:18780 original size:11 final size:11
Alignment explanation
Indices: 18738--18780 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
18728 ATTTATTCAT
*
18738 TATTAATTAAC
1 TATTAATTAGC
*
18749 TATTAATTAGA
1 TATTAATTAGC
18760 TATTAATTAGC
1 TATTAATTAGC
18771 TATTAATTAG
1 TATTAATTAG
18781 ATATAGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:18861 original size:260 final size:260
Alignment explanation
Indices: 18397--18920 Score: 1003
Period size: 260 Copynumber: 2.0 Consensus size: 260
18387 TCTTCTTATG
18397 TAATCAAAAAAATGAGGATGAAGGGAATAATTAGGTATTAATTAGCTATTATTCCCTTTTAATCA
1 TAATCAAAAAAATGAGGATGAAGGGAATAATTAGGTATTAATTAGCTATTATTCCCTTTTAATCA
18462 TATTGAATTTATTCATTATTAAATAACTATTAATTAGATATTAATTAGCTATTAATTAGATATAG
66 TATTGAATTTATTCATTATTAAATAACTATTAATTAGATATTAATTAGCTATTAATTAGATATAG
18527 TATAATGGATGATTAAGGAGGGGCTTTAAATTAATATGTTAGATGTGAGAAATTACCAAAATGGG
131 TATAATGGATGATTAAGGAGGGGCTTTAAATTAATATGTTAGATGTGAGAAATTACCAAAATGGG
*
18592 GCAATAAGGTGGCACCAGGTTAAAAGTTGAAAGGGCTTGTTAGTAATTTCCGTAGAGGACAAAAA
196 GCAATAAGGTGGCACCAGGTTAAAAGTTGAAAGGGCTTGTTAGTAATTTCCATAGAGGACAAAAA
*
18657 TAATCAAAAAAATGAGGTTGAAGGGAATAATTAGGTATTAATTAGCTATTATTCCCTTTTAATCA
1 TAATCAAAAAAATGAGGATGAAGGGAATAATTAGGTATTAATTAGCTATTATTCCCTTTTAATCA
*
18722 TATTGAATTTATTCATTATTAATTAACTATTAATTAGATATTAATTAGCTATTAATTAGATATAG
66 TATTGAATTTATTCATTATTAAATAACTATTAATTAGATATTAATTAGCTATTAATTAGATATAG
18787 TATAATGGATGATTAAGGAGGGGCTTTAAATTAATATGTTAGATGTGAGAAATTACCAAAATGGG
131 TATAATGGATGATTAAGGAGGGGCTTTAAATTAATATGTTAGATGTGAGAAATTACCAAAATGGG
* *
18852 GCGATAAGGTGGCACCAGGTTAAAAGTTGAAAGGGCTTGTTAGTAATTTCCATAGGGGACAAAAA
196 GCAATAAGGTGGCACCAGGTTAAAAGTTGAAAGGGCTTGTTAGTAATTTCCATAGAGGACAAAAA
18917 TAAT
1 TAAT
18921 ATATAGTATA
Statistics
Matches: 259, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
260 259 1.00
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (260 bp):
TAATCAAAAAAATGAGGATGAAGGGAATAATTAGGTATTAATTAGCTATTATTCCCTTTTAATCA
TATTGAATTTATTCATTATTAAATAACTATTAATTAGATATTAATTAGCTATTAATTAGATATAG
TATAATGGATGATTAAGGAGGGGCTTTAAATTAATATGTTAGATGTGAGAAATTACCAAAATGGG
GCAATAAGGTGGCACCAGGTTAAAAGTTGAAAGGGCTTGTTAGTAATTTCCATAGAGGACAAAAA
Found at i:19067 original size:19 final size:18
Alignment explanation
Indices: 19039--19074 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19029 ACAATCTTTT
19039 AAAAAAAATTTAAAAATC
1 AAAAAAAATTTAAAAATC
*
19057 AAAATAAAATTTTAAAAT
1 AAAA-AAAATTTAAAAAT
19075 AATACTCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAAAAATTTAAAAATC
Done.