Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022665.1 Corchorus olitorius cultivar O-4 contig22698, 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: 5513
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Found at i:116 original size:30 final size:31
Alignment explanation
Indices: 43--106 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
33 ACTAAATACT
*
43 AAAAAAATCCCTAATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
74 AAAAAAATCCCTTATGCTTTTT-TTTT-GGAC
1 AAAAAAATCCCTTATG-TTTTTCTTTTGGGAC
104 AAA
1 AAA
107 TTAGTCCCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 7 0.23
31 19 0.61
32 5 0.16
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (31 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
Found at i:292 original size:29 final size:30
Alignment explanation
Indices: 250--319 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 30
240 CTCATTTTTG
* *
250 AAACGTAAGGGATTAATTT-GTCCCGAAA-A
1 AAACATAAGGGATT-ATTTAGTCCCAAAACA
279 AAACATAAGGGATTATTTAGTCCCAAAAGCA
1 AAACATAAGGGATTATTTAGTCCCAAAA-CA
310 AAACATAAGG
1 AAACATAAGG
320 AATTTTTCTG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 4 0.11
29 21 0.58
31 11 0.31
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.21
Consensus pattern (30 bp):
AAACATAAGGGATTATTTAGTCCCAAAACA
Found at i:1170 original size:26 final size:26
Alignment explanation
Indices: 1141--1203 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
1131 TCTACATAAA
*
1141 TTTAGTAACCTCACATTCTTAGAAAT
1 TTTAGTAACCTCACATTCTTACAAAT
* **
1167 TTTAGTAATCTTGCATTCTTACAAAT
1 TTTAGTAACCTCACATTCTTACAAAT
1193 TTTAGTAACCT
1 TTTAGTAACCT
1204 TTCATATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.43
Consensus pattern (26 bp):
TTTAGTAACCTCACATTCTTACAAAT
Found at i:2534 original size:21 final size:21
Alignment explanation
Indices: 2508--2552 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
2498 ACGAGGAAAA
*
2508 ATAGTA-TTTCATTTGGTTCAT
1 ATAGTAGTTT-ATTTGGGTCAT
2529 ATAGTAGTTTATTTGGGTCAT
1 ATAGTAGTTTATTTGGGTCAT
2550 ATA
1 ATA
2553 TAAGTCTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.49
Consensus pattern (21 bp):
ATAGTAGTTTATTTGGGTCAT
Found at i:2661 original size:22 final size:22
Alignment explanation
Indices: 2618--2661 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2608 GGTCCTAACT
* *
2618 TTGGGTCCCTTTCCATCTTTTG
1 TTGGGTCCCTTTCCAACCTTTG
2640 TTGGGTTCCC-TTCCAACCTTTG
1 TTGGG-TCCCTTTCCAACCTTTG
2662 CCATTTGGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.07, C:0.30, G:0.18, T:0.45
Consensus pattern (22 bp):
TTGGGTCCCTTTCCAACCTTTG
Found at i:4612 original size:17 final size:17
Alignment explanation
Indices: 4566--4616 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 17
4556 ATATACAAGC
*
4566 AAAACAGAAAAAAGAAAA
1 AAAACACAAAAAA-AAAA
*
4584 AAAGAGAGCAAAAAAAAAA
1 AAA-ACA-CAAAAAAAAAA
4603 AAAACACAAAAAAA
1 AAAACACAAAAAAA
4617 CAGAGGCACC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 8 0.29
18 5 0.18
19 9 0.32
20 6 0.21
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (17 bp):
AAAACACAAAAAAAAAA
Done.