Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014311.1 Corchorus olitorius cultivar O-4 contig14344, 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: 13930
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2170 original size:14 final size:13
Alignment explanation
Indices: 2151--2188 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
2141 TCTTAATGGA
2151 TTTAAATTTAATGT
1 TTTAAATTTAAT-T
2165 TTTAAATTTAAATT
1 TTTAAATTT-AATT
2179 TTTAAATTTA
1 TTTAAATTTA
2189 CTGGTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.04
14 19 0.83
15 3 0.13
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (13 bp):
TTTAAATTTAATT
Found at i:2640 original size:202 final size:192
Alignment explanation
Indices: 2284--2660 Score: 540
Period size: 202 Copynumber: 1.9 Consensus size: 192
2274 TCCACAACCA
* *
2284 AAATGTTGCTACGTAAAGATTTCACTACCAAAACAACGTCAAGGCTTTTGCAACGACATTTAATC
1 AAATGTTGCTACGTAAAGATTTCACAACCAAAACAACGTCAAGGCTTTTGCAACGACACTTAATC
*
2349 GTTTTTAAATTATTTTGACAACTACCTAGAGGTTGTCATGTAAGTGTTTTGGAAACGACATTTAA
66 GTTTTTAAATTATTTTGACAACTACCTAGAGGTTGTCACGTAAGTGTTTTGGAAACGACATTTAA
* *
2414 TCATTTTTAAAAGTTATTCGTAACCAATTAAAAGTGGTTGCAAAAATTATTACACAACCAATC
131 TCATTTTTAAAAGTTATACGTAACCAATT-AAAGTGATTGCAAAAATTATTACACAACCAATC
* *
2477 AAATGTTGCTACGTAAAAGATTTCACAACCAAAACAACAGTGTTGCGTACGGGTTTTCGCAACGA
1 AAATGTTGCTACGT-AAAGATTTCACAACCAAAACAAC---G-T-C--AAGGCTTTT-GCAACGA
* * * *
2542 CACTTAATTGTTTTTAAATTATTTTGGCAACTACCTAGAGGTCT-TTACGTTAGTGTTTTGGAAA
57 CACTTAATCGTTTTTAAATTATTTTGACAACTACCTAGAGGT-TGTCACGTAAGTGTTTTGGAAA
*
2606 CGACATTTAATCATTTTTAAAAGTTATACGTAACCAATTAAAGTGATTGTAAAAA
121 CGACATTTAATCATTTTTAAAAGTTATACGTAACCAATTAAAGTGATTGCAAAAA
2661 AATTTTCGCA
Statistics
Matches: 162, Mismatches: 12, Indels: 12
0.87 0.06 0.06
Matches are distributed among these distances:
193 14 0.09
194 22 0.14
197 1 0.01
198 1 0.01
199 1 0.01
201 21 0.13
202 101 0.62
203 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (192 bp):
AAATGTTGCTACGTAAAGATTTCACAACCAAAACAACGTCAAGGCTTTTGCAACGACACTTAATC
GTTTTTAAATTATTTTGACAACTACCTAGAGGTTGTCACGTAAGTGTTTTGGAAACGACATTTAA
TCATTTTTAAAAGTTATACGTAACCAATTAAAGTGATTGCAAAAATTATTACACAACCAATC
Found at i:2823 original size:20 final size:20
Alignment explanation
Indices: 2795--2839 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
2785 ACAGCGGACA
*
2795 CTTAGGTCGTTGCGTTAGAT
1 CTTAAGTCGTTGCGTTAGAT
2815 CTTAAGTCGTTGCGTTAGAT
1 CTTAAGTCGTTGCGTTAGAT
*
2835 ATTAA
1 CTTAA
2840 ACAACAGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.13, G:0.24, T:0.40
Consensus pattern (20 bp):
CTTAAGTCGTTGCGTTAGAT
Found at i:4547 original size:21 final size:21
Alignment explanation
Indices: 4523--4577 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
4513 GACTTGGAAT
*
4523 GGTGGTGGCACGGGCATAGCC
1 GGTGGTGGCACGGGCATAACC
* *
4544 GGTGGTCGCACGGGCTTAACC
1 GGTGGTGGCACGGGCATAACC
4565 GGTGGTGGCACGG
1 GGTGGTGGCACGG
4578 TGAATGGGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.13, C:0.24, G:0.47, T:0.16
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATAACC
Found at i:8218 original size:15 final size:16
Alignment explanation
Indices: 8194--8233 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
8184 AGAGGTTGAA
*
8194 AGAAAGCAATTA-AAT
1 AGAAAACAATTATAAT
*
8209 AGAAAACAATTATATT
1 AGAAAACAATTATAAT
8225 AGAAAACAA
1 AGAAAACAA
8234 AACAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.20
Consensus pattern (16 bp):
AGAAAACAATTATAAT
Found at i:12452 original size:307 final size:307
Alignment explanation
Indices: 11898--12512 Score: 1149
Period size: 307 Copynumber: 2.0 Consensus size: 307
11888 AAAATTTGCT
* *
11898 TGACTCGGTTTTGGTAACATCCTCCTGCAATTTGCCCGCTTATTTGCTCATTTTTTCCTACTCTT
1 TGACTCGGTTTTGGTAACATCCTCCTGCAATTTGCCCGATTATTTGCTCATATTTTCCTACTCTT
* *
11963 CATGATCTGTTATAGTTGTTGTAATTGGGCTAAAAAAATGAAAATATTTCTGTAAAACGAATGCT
66 CATGATCTGTTATAGCTGTTGTAATTGGGCTAAAAAAATGAAAATATTTATGTAAAACGAATGCT
* *
12028 CTCCTATTTTGACTGGTGACTTGTCTGACTGTTATGCTTGGTTTTGCTTCTGTTTAATGGCACTA
131 CTCCTATTTTGACTGGTGACTTGTCTGACTGTTAAGCTTGGTTTTGCTTATGTTTAATGGCACTA
*
12093 CTTTCTTGCTTTTGCTGCACACTCCATCAAAATTGTTTTGCTTTCTTTGTTCATCTTGTTTAAAT
196 CTATCTTGCTTTTGCTGCACACTCCATCAAAATTGTTTTGCTTTCTTTGTTCATCTTGTTTAAAT
12158 TTGTTTGATCACTTCTTGGAGTTGAGACCTCTTTGTCGCTCCCTGCA
261 TTGTTTGATCACTTCTTGGAGTTGAGACCTCTTTGTCGCTCCCTGCA
12205 TGACTCGGTTTTGGTAACATCCTCCTGCAATTTGCCCGATTATTTGCTCATATTTTCCTACTCTT
1 TGACTCGGTTTTGGTAACATCCTCCTGCAATTTGCCCGATTATTTGCTCATATTTTCCTACTCTT
12270 CATGATCTGTTATAGCTGTTGTAATTGGGCTAAAAAAATGAAAATATTTATGTAAAACGAATGCT
66 CATGATCTGTTATAGCTGTTGTAATTGGGCTAAAAAAATGAAAATATTTATGTAAAACGAATGCT
12335 CTCCTATTTTGACTGGTGACTTGTCTGACTGTTAAGCTTGGTTTTGCTTATGTTTAATGGCACTA
131 CTCCTATTTTGACTGGTGACTTGTCTGACTGTTAAGCTTGGTTTTGCTTATGTTTAATGGCACTA
* *
12400 CTATCTTGCTTTTTCTGCACACTCCATCAAAATTGTTTTGCTTTCTTTGTTCATCTTGTTTGAAT
196 CTATCTTGCTTTTGCTGCACACTCCATCAAAATTGTTTTGCTTTCTTTGTTCATCTTGTTTAAAT
12465 TTGTTTGATCACTTCTTGGAGTTGAGACCTCTTTGTCGCTCCCTGCA
261 TTGTTTGATCACTTCTTGGAGTTGAGACCTCTTTGTCGCTCCCTGCA
12512 T
1 T
12513 CATTGAACTC
Statistics
Matches: 299, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
307 299 1.00
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (307 bp):
TGACTCGGTTTTGGTAACATCCTCCTGCAATTTGCCCGATTATTTGCTCATATTTTCCTACTCTT
CATGATCTGTTATAGCTGTTGTAATTGGGCTAAAAAAATGAAAATATTTATGTAAAACGAATGCT
CTCCTATTTTGACTGGTGACTTGTCTGACTGTTAAGCTTGGTTTTGCTTATGTTTAATGGCACTA
CTATCTTGCTTTTGCTGCACACTCCATCAAAATTGTTTTGCTTTCTTTGTTCATCTTGTTTAAAT
TTGTTTGATCACTTCTTGGAGTTGAGACCTCTTTGTCGCTCCCTGCA
Found at i:13874 original size:27 final size:27
Alignment explanation
Indices: 13811--13875 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
13801 AGTGAACTTA
**
13811 AAATGACCAAAATGCCCCTGAATGTGC
1 AAATGACCAAAATGCCCCTGAATGACC
* *
13838 AGATGACCAAAATGCCCCTGAGTGACC
1 AAATGACCAAAATGCCCCTGAATGACC
13865 ATAATG-CCAAA
1 A-AATGACCAAA
13876 TAAACAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 29 0.91
28 3 0.09
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.17
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAATGACC
Done.