Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011740.1 Corchorus capsularis cultivar CVL-1 contig11761, 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: 46530
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:13976 original size:18 final size:18
Alignment explanation
Indices: 13953--13991 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
13943 TAACACTTAA
13953 CCGCCCTAAGTTTATTTT
1 CCGCCCTAAGTTTATTTT
*
13971 CCGCCCTTAGTTTATTTT
1 CCGCCCTAAGTTTATTTT
13989 CCG
1 CCG
13992 TTAGCAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.13, C:0.31, G:0.13, T:0.44
Consensus pattern (18 bp):
CCGCCCTAAGTTTATTTT
Found at i:15765 original size:2 final size:2
Alignment explanation
Indices: 15758--15783 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15748 CAAGATTTAG
15758 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
15784 GATTAATCGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16647 original size:21 final size:21
Alignment explanation
Indices: 16621--16664 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
16611 TAAAACTGGA
16621 TTGCTAAAT-ACCGCCCCATTT
1 TTGCT-AATCACCGCCCCATTT
*
16642 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
16663 TT
1 TT
16665 TACGCTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.34, G:0.09, T:0.39
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:21435 original size:200 final size:201
Alignment explanation
Indices: 20961--21566 Score: 796
Period size: 200 Copynumber: 3.0 Consensus size: 201
20951 GTAAGCTTTA
* * * * * *
20961 TTATAAGGATTATTGTACAATACACTGTCAATGTAAATTTTGGACTCCATAAGCT-AGTTAAGAA
1 TTAT-AGGATTATTATACAATACACTGTCAGTATAAATTTTGAACTCCATAAG-TGGGTTAAAAA
* * * *
21025 GTTGATACATACCCCCATTTCATAATTAATTAAATATTTAATATTAATACATTTTCCTTAAGGGG
64 GTTGACACATA-CCCCATTTC---A-TAATTAAATATTTAATATTAATACATATTCCCTAAGGGT
** * *
21090 ACACATGTCAACCC------TTAAACCATGTACGTGCAGTCTGCTAAACTCTACTAACGGTGTAT
124 ACACATGTCAACCCTTAAAGTTAAACCCCGTACGTGCAGTCTGCTAAACTCCACTGACGGTGTAT
*
21149 TGTATAATTTTTT
189 TGTATAATTTTTC
* *
21162 TTATAGGATTGTTATACAATACACTGTCAGTATAAATTTTGAACTCCATAAGCGGGTTAAAAAGT
1 TTATAGGATTATTATACAATACACTGTCAGTATAAATTTTGAACTCCATAAGTGGGTTAAAAAGT
* * * * *
21227 TTACACATACCCCATTTCATAATTAAATATTTAACATTAATATATATTCCCTAAGGATACACATC
66 TGACACATACCCCATTTCATAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATG
* * *
21292 TCAACCCTTAAAGTTAAACCCCGTACGTGCAGTCTGCTAAACTCCACGGACGGCGTATTGCATAA
131 TCAACCCTTAAAGTTAAACCCCGTACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAA
21357 TTTTTC
196 TTTTTC
* *
21363 TTATAGGATTATTATA-AATACACTATCAGTATAAATTTTGAACTTCATAAGTGGGTTAAAAAGT
1 TTATAGGATTATTATACAATACACTGTCAGTATAAATTTTGAACTCCATAAGTGGGTTAAAAAGT
*
21427 TGACACATACCCTATTTCATAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATG
66 TGACACATACCCCATTTCATAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATG
* * * *
21492 TCAACCCTTAAAGTTAAACCCCGCACATGTAGTCTGCTAAACTCCACTGACGGTGTATTGTGTAA
131 TCAACCCTTAAAGTTAAACCCCGTACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAA
*
21557 ATTTTC
196 TTTTTC
21563 TTAT
1 TTAT
21567 TTTAAACCAA
Statistics
Matches: 355, Mismatches: 43, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
195 46 0.13
196 1 0.00
199 9 0.03
200 230 0.65
201 69 0.19
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (201 bp):
TTATAGGATTATTATACAATACACTGTCAGTATAAATTTTGAACTCCATAAGTGGGTTAAAAAGT
TGACACATACCCCATTTCATAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATG
TCAACCCTTAAAGTTAAACCCCGTACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAA
TTTTTC
Found at i:21913 original size:19 final size:19
Alignment explanation
Indices: 21889--21927 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
21879 TTTAGACCCA
* *
21889 AAACGGTTGTGAAACGGTT
1 AAACGGTGGTGAAACAGTT
21908 AAACGGTGGTGAAACAGTT
1 AAACGGTGGTGAAACAGTT
21927 A
1 A
21928 CATATAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.10, G:0.31, T:0.23
Consensus pattern (19 bp):
AAACGGTGGTGAAACAGTT
Found at i:36573 original size:13 final size:12
Alignment explanation
Indices: 36543--36575 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
36533 ATATCAAAAT
36543 TAAAACCGACTA
1 TAAAACCGACTA
36555 -AAAACCGACTAA
1 TAAAACCGACT-A
36567 TAAAACCGA
1 TAAAACCGA
36576 AACCGACCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.53
12 1 0.05
13 8 0.42
ACGTcount: A:0.55, C:0.24, G:0.09, T:0.12
Consensus pattern (12 bp):
TAAAACCGACTA
Found at i:36891 original size:1 final size:1
Alignment explanation
Indices: 36844--36871 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
36834 GTTCATGAGT
36844 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
36872 GATACTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:46479 original size:2 final size:2
Alignment explanation
Indices: 46474--46530 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
46464 ATATATATAT
46474 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
46516 -G AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Done.