Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012177.1 Corchorus capsularis cultivar CVL-1 contig12198, 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: 24345
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Found at i:206 original size:6 final size:6
Alignment explanation
Indices: 189--226 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
179 TGCCTTCTTC
*
189 TTTTCT TCTTCT TTTTCT ATTTTCT TTTTCT TTTTCT T
1 TTTTCT TTTTCT TTTTCT -TTTTCT TTTTCT TTTTCT T
227 CCTCTTTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:213 original size:19 final size:19
Alignment explanation
Indices: 189--225 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
179 TGCCTTCTTC
189 TTTTCTTCTTCTTTTTCTA
1 TTTTCTTCTTCTTTTTCTA
*
208 TTTTCTTTTTCTTTTTCT
1 TTTTCTTCTTCTTTTTCT
226 TCCTCTTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTCTTCTTCTTTTTCTA
Found at i:3456 original size:2 final size:2
Alignment explanation
Indices: 3449--3478 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3439 GTTCTCACTA
3449 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3479 GAGCTTATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6033 original size:87 final size:87
Alignment explanation
Indices: 5830--6041 Score: 218
Period size: 87 Copynumber: 2.4 Consensus size: 87
5820 GTAAATTCTG
** * *
5830 TGGAAACTGATAAGATGGAGAATAATTTGAATTC-AATTGATTGTGATCTTCCTAATGGAGTTAT
1 TGGAAACTGATTTGATGGTGGATAATTTGAATTCAAATT-ATTGTGATCTTCCTAATGGAGTTAT
* * *
5894 GGGTGGTTATGTTGCAAAATCTT
65 GGGTAGTAATGATGCAAAATCTT
* * *
5917 TAGAAAAT-A-TT-ATGGTAGATGATAGTTTGAATTCAAATT-TTAGTGATCTTCCTAATGGAGT
1 TGGAAACTGATTTGATGGT-G--GATAATTTGAATTCAAATTATT-GTGATCTTCCTAATGGAGT
* *
5978 TATGGTTAGTAATGATGCAAAATTTT
62 TATGGGTAGTAATGATGCAAAATCTT
* *
6004 TGGAAACTGATTTGATGGTGGATATTTTGAATTGAAAT
1 TGGAAACTGATTTGATGGTGGATAATTTGAATTCAAAT
6042 CGAAGTGGTC
Statistics
Matches: 101, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
84 4 0.04
85 1 0.01
86 3 0.03
87 80 0.79
88 5 0.05
89 3 0.03
90 5 0.05
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.39
Consensus pattern (87 bp):
TGGAAACTGATTTGATGGTGGATAATTTGAATTCAAATTATTGTGATCTTCCTAATGGAGTTATG
GGTAGTAATGATGCAAAATCTT
Found at i:7996 original size:37 final size:37
Alignment explanation
Indices: 7943--8017 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
7933 TAATTTGAGG
* *
7943 TTCCCTTTAATAATTGATATGTTAAGTGGGTTTTTAA
1 TTCCCTTTAATAATTGATATATTAAGTGAGTTTTTAA
*
7980 TTCCCTTTAATTATTGATATATTAAGTGAGTTTTTAA
1 TTCCCTTTAATAATTGATATATTAAGTGAGTTTTTAA
8017 T
1 T
8018 ATGTTATAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.28, C:0.08, G:0.13, T:0.51
Consensus pattern (37 bp):
TTCCCTTTAATAATTGATATATTAAGTGAGTTTTTAA
Found at i:8031 original size:59 final size:59
Alignment explanation
Indices: 7965--8097 Score: 248
Period size: 59 Copynumber: 2.3 Consensus size: 59
7955 ATTGATATGT
7965 TAAGTGGGTTTTTAATTCCCTTTAATTATTGATATATTAAGTGAGTTTTTAATATGTTA
1 TAAGTGGGTTTTTAATTCCCTTTAATTATTGATATATTAAGTGAGTTTTTAATATGTTA
* *
8024 TAAGTGGGTTTTTAATTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAATATGTTA
1 TAAGTGGGTTTTTAATTCCCTTTAATTATTGATATATTAAGTGAGTTTTTAATATGTTA
8083 TAAGTGGGTTTTTAA
1 TAAGTGGGTTTTTAA
8098 GACATCTCAT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 72 1.00
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.50
Consensus pattern (59 bp):
TAAGTGGGTTTTTAATTCCCTTTAATTATTGATATATTAAGTGAGTTTTTAATATGTTA
Found at i:20625 original size:21 final size:22
Alignment explanation
Indices: 20599--20641 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
20589 ATCTCTTCCG
*
20599 CCGCAGCAAA-GGAAGGAGAAA
1 CCGCAGCAAAGGGAAGAAGAAA
20620 CCGCAGCAAAGGGAAGAAGAAA
1 CCGCAGCAAAGGGAAGAAGAAA
20642 GAAATGGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.49, C:0.19, G:0.33, T:0.00
Consensus pattern (22 bp):
CCGCAGCAAAGGGAAGAAGAAA
Done.