Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014370.1 Corchorus capsularis cultivar CVL-1 contig14391, 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: 12753
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Found at i:39 original size:1 final size:1
Alignment explanation
Indices: 1--27 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
28 CAGTGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:490 original size:12 final size:12
Alignment explanation
Indices: 469--498 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
459 GTTATGGTTC
*
469 TTTTTCTTTCTT
1 TTTTTTTTTCTT
481 TTTTTTTTTCTT
1 TTTTTTTTTCTT
493 TTTTTT
1 TTTTTT
499 GTAATGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:490 original size:16 final size:15
Alignment explanation
Indices: 469--498 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
459 GTTATGGTTC
469 TTTTTCTTTCTTTTTT
1 TTTTTCTTT-TTTTTT
485 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
499 GTAATGTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTCTTTTTTTTT
Found at i:1053 original size:14 final size:14
Alignment explanation
Indices: 1028--1062 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
1018 AAAATTAAAG
1028 AAGAACAAGAAAGAA
1 AAGAA-AAGAAAGAA
1043 AAGAAAAGAAAGAA
1 AAGAAAAGAAAGAA
1057 AA-AAAA
1 AAGAAAA
1063 TAGAGAGACG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.20
14 11 0.55
15 5 0.25
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (14 bp):
AAGAAAAGAAAGAA
Found at i:1231 original size:33 final size:33
Alignment explanation
Indices: 1168--1236 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
1158 GATCATGGGT
* *
1168 CGCGCGCGACCCGGACCATGGTGGGCCGCGACC
1 CGCGCGCGACCCAGACCATGGCGGGCCGCGACC
* *
1201 CGCGCGCGACCTAG-CCATGGCCGGGTCGCGACC
1 CGCGCGCGACCCAGACCATGG-CGGGCCGCGACC
1234 CGC
1 CGC
1237 TGTGTTCATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 6 0.19
33 25 0.81
ACGTcount: A:0.12, C:0.43, G:0.38, T:0.07
Consensus pattern (33 bp):
CGCGCGCGACCCAGACCATGGCGGGCCGCGACC
Found at i:2755 original size:18 final size:19
Alignment explanation
Indices: 2732--2768 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2722 ACTGATTTAG
2732 TATTTATTCTT-ATATAAT
1 TATTTATTCTTCATATAAT
*
2750 TATTTATTGTTCATATAAT
1 TATTTATTCTTCATATAAT
2769 GAAATTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (19 bp):
TATTTATTCTTCATATAAT
Found at i:6101 original size:8 final size:8
Alignment explanation
Indices: 6090--6155 Score: 64
Period size: 8 Copynumber: 7.9 Consensus size: 8
6080 ATATTAAATA
6090 AAATCACT
1 AAATCACT
6098 AAATCACT
1 AAATCACT
6106 -AATCAGACT
1 AAATC--ACT
6115 ATAAGTCACT
1 A-AA-TCACT
6125 AAATCACT
1 AAATCACT
6133 AAAATCACT
1 -AAATCACT
*
6142 ATATCACT
1 AAATCACT
6150 -AATCAC
1 AAATCAC
6156 ACATAAGTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
7 9 0.18
8 20 0.40
9 13 0.26
10 4 0.08
11 2 0.04
12 2 0.04
ACGTcount: A:0.47, C:0.24, G:0.03, T:0.26
Consensus pattern (8 bp):
AAATCACT
Found at i:6142 original size:27 final size:24
Alignment explanation
Indices: 6092--6155 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 24
6082 ATTAAATAAA
6092 ATCACTAAATCACTAATCAGACTAT
1 ATCACTAAATCACTAATCA-ACTAT
6117 AAGTCACTAAATCACTAAAATC-ACTAT
1 -A-TCACTAAATCACT--AATCAACTAT
6144 ATCACT-AATCAC
1 ATCACTAAATCAC
6156 ACATAAGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
24 6 0.17
25 5 0.14
26 2 0.06
27 18 0.51
29 4 0.11
ACGTcount: A:0.45, C:0.25, G:0.03, T:0.27
Consensus pattern (24 bp):
ATCACTAAATCACTAATCAACTAT
Done.