Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009606.1 Corchorus capsularis cultivar CVL-1 contig09627, 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: 26148
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4935 original size:50 final size:50
Alignment explanation
Indices: 4851--4949 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 50
4841 ATGCAAGGTG
** * * * *
4851 AAATTATATTCTTGGAGGCTTAATTAACCTTTGAAGAAATTAAACCAGAA
1 AAATTATAACCTTGAAGGCTAAATCAACCATTGAAGAAATTAAACCAGAA
*
4901 AAATTATAACCTTGAAGGCTAAATCAACCATTGAAGACATTAAACCAGA
1 AAATTATAACCTTGAAGGCTAAATCAACCATTGAAGAAATTAAACCAGA
4950 GAAACTCATA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.27
Consensus pattern (50 bp):
AAATTATAACCTTGAAGGCTAAATCAACCATTGAAGAAATTAAACCAGAA
Found at i:15058 original size:1 final size:1
Alignment explanation
Indices: 15054--15090 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
15044 AAACTATAGG
15054 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
15091 AACTTATACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:17475 original size:18 final size:20
Alignment explanation
Indices: 17440--17476 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17430 TGACCAATTT
17440 CAATTCTTCTGTGGAATTAA
1 CAATTCTTCTGTGGAATTAA
17460 CAATTCTT-TG-GGAATTA
1 CAATTCTTCTGTGGAATTA
17477 TTTTGACCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 2 0.12
20 8 0.47
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (20 bp):
CAATTCTTCTGTGGAATTAA
Found at i:21405 original size:33 final size:33
Alignment explanation
Indices: 21322--21530 Score: 267
Period size: 33 Copynumber: 6.2 Consensus size: 33
21312 TCTCACGATT
* * *
21322 CTTCCTCTTCTTTTCTTTCCGTATCTCCACCATCTC
1 CTTCCTCTTCTTTTCTTCCCGTATCTCC-GC--CGC
* * *
21358 CTTCCACTTGTTTTCTTCCCGTATCTCAGCCGC
1 CTTCCTCTTCTTTTCTTCCCGTATCTCCGCCGC
*
21391 CTTCCTCTTCTTTTCTTCCCGTATCTCCGCAGTC
1 CTTCCTCTTCTTTTCTTCCCGTATCTCCGCCG-C
21425 C-TCCTCTTCTTTTCTTCCCGTATCTCCGCCGC
1 CTTCCTCTTCTTTTCTTCCCGTATCTCCGCCGC
* *
21457 CTTCCTCTTCTTCTCTTCCCGTAACTCCGCCGC
1 CTTCCTCTTCTTTTCTTCCCGTATCTCCGCCGC
* * *
21490 CTTGCTCTTCTTCTCTTCCCGTAACTCCGCCGC
1 CTTCCTCTTCTTTTCTTCCCGTATCTCCGCCGC
21523 CTTCCTCT
1 CTTCCTCT
21531 GTATCTCCGC
Statistics
Matches: 156, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
32 2 0.01
33 127 0.81
34 2 0.01
35 1 0.01
36 24 0.15
ACGTcount: A:0.06, C:0.44, G:0.09, T:0.41
Consensus pattern (33 bp):
CTTCCTCTTCTTTTCTTCCCGTATCTCCGCCGC
Found at i:22348 original size:11 final size:11
Alignment explanation
Indices: 22332--22356 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
22322 ATACAATCCA
22332 GAGTTAATTTG
1 GAGTTAATTTG
22343 GAGTTAATTTG
1 GAGTTAATTTG
22354 GAG
1 GAG
22357 GATAATCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.32, T:0.40
Consensus pattern (11 bp):
GAGTTAATTTG
Found at i:23953 original size:53 final size:53
Alignment explanation
Indices: 23873--23980 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
23863 AATGCACCTT
23873 GACACCTTGAACACTCTCTTCCTCCACCTTCCACTCCAATGATTTCACTCTAG
1 GACACCTTGAACACTCTCTTCCTCCACCTTCCACTCCAATGATTTCACTCTAG
*
23926 GACACCTTGAACACTCTCTTCCTCCACCTTCCACTCCAATGCTTTCACTCTAG
1 GACACCTTGAACACTCTCTTCCTCCACCTTCCACTCCAATGATTTCACTCTAG
23979 GA
1 GA
23981 TCATGAATTC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.22, C:0.40, G:0.08, T:0.30
Consensus pattern (53 bp):
GACACCTTGAACACTCTCTTCCTCCACCTTCCACTCCAATGATTTCACTCTAG
Found at i:25666 original size:153 final size:150
Alignment explanation
Indices: 25417--25694 Score: 477
Period size: 153 Copynumber: 1.8 Consensus size: 150
25407 TGGGATTGAC
*
25417 TCACCACGTTATCAATGAGATCAAACCAATAATAGGATGACAAATTAGAAGGAAAAAAAAGCATT
1 TCACCACGTCATCAATGAGATCAAACCAATAATAGGATGACAAATTAGAAGGAAAAAAAAGCATT
* * *
25482 TTAATACTTGACTTTGTATAAATTGCTAACTCTACTTTTGAAATTGGTCATATGTTAGGATGAGA
66 TTAATACTGGACTTAGTATAAATTGCTAACTCTACTTTTGAAATTGGTCATATATTAGGATGAGA
25547 AATTATTATATTGACTGGAT
131 AATTATTATATTGACTGGAT
25567 TCACCACGTCATCAATGAGATC-AACCAATAATAGGATGACAAATTAGAAGGATAAAAAAATATG
1 TCACCACGTCATCAATGAGATCAAACCAATAATAGGATGACAAATTAGAAGG--AAAAAAA-A-G
25631 CATTTTAATACTGGACTTAGTATAAATTGCTAACTCTACTTTTGAAATTGGTCATATATTAGGA
62 CATTTTAATACTGGACTTAGTATAAATTGCTAACTCTACTTTTGAAATTGGTCATATATTAGGA
25695 CGATAATTTA
Statistics
Matches: 120, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
149 29 0.24
150 21 0.17
151 7 0.06
152 1 0.01
153 62 0.52
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (150 bp):
TCACCACGTCATCAATGAGATCAAACCAATAATAGGATGACAAATTAGAAGGAAAAAAAAGCATT
TTAATACTGGACTTAGTATAAATTGCTAACTCTACTTTTGAAATTGGTCATATATTAGGATGAGA
AATTATTATATTGACTGGAT
Found at i:25736 original size:21 final size:21
Alignment explanation
Indices: 25712--25754 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
25702 TTATTGGGGA
25712 TTACTAAATACCGCCCCCCTT
1 TTACTAAATACCGCCCCCCTT
** *
25733 TTACTAGGTACCGCCTCCCTT
1 TTACTAAATACCGCCCCCCTT
25754 T
1 T
25755 GGACTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.40, G:0.09, T:0.33
Consensus pattern (21 bp):
TTACTAAATACCGCCCCCCTT
Done.