Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016135.1 Corchorus capsularis cultivar CVL-1 contig16156, 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: 14182
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2122 original size:28 final size:28
Alignment explanation
Indices: 2090--2146 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
2080 TAACATTTAA
2090 TTTAAAATCTAAAACTTTTTAATAACTT
1 TTTAAAATCTAAAACTTTTTAATAACTT
* * *
2118 TTTAAAATTTAAAGCTTTTTAATCACTT
1 TTTAAAATCTAAAACTTTTTAATAACTT
2146 T
1 T
2147 AAGTAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.49
Consensus pattern (28 bp):
TTTAAAATCTAAAACTTTTTAATAACTT
Found at i:3685 original size:26 final size:25
Alignment explanation
Indices: 3656--3708 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
3646 GATTTGTTTC
* *
3656 TTTTTGATATTATTTATAAAAATTAA
1 TTTTTCATATTATAT-TAAAAATTAA
*
3682 TTTTTCATATTATATTACAAATTAA
1 TTTTTCATATTATATTAAAAATTAA
3707 TT
1 TT
3709 AATATGCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (25 bp):
TTTTTCATATTATATTAAAAATTAA
Found at i:3797 original size:2 final size:2
Alignment explanation
Indices: 3790--3818 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3780 CAATTACTAG
3790 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3819 GTATTAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5948 original size:39 final size:39
Alignment explanation
Indices: 5904--6003 Score: 200
Period size: 39 Copynumber: 2.6 Consensus size: 39
5894 GCCTTGGAAA
5904 GTTAACTTTCCCACAGATTACCTCCTCTTCTTGGTGATC
1 GTTAACTTTCCCACAGATTACCTCCTCTTCTTGGTGATC
5943 GTTAACTTTCCCACAGATTACCTCCTCTTCTTGGTGATC
1 GTTAACTTTCCCACAGATTACCTCCTCTTCTTGGTGATC
5982 GTTAACTTTCCCACAGATTACC
1 GTTAACTTTCCCACAGATTACC
6004 GCCCCTATGG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 61 1.00
ACGTcount: A:0.20, C:0.31, G:0.12, T:0.37
Consensus pattern (39 bp):
GTTAACTTTCCCACAGATTACCTCCTCTTCTTGGTGATC
Found at i:6482 original size:12 final size:12
Alignment explanation
Indices: 6465--6490 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6455 CTTGAGATGG
6465 AAGCATGTGCTC
1 AAGCATGTGCTC
6477 AAGCATGTGCTC
1 AAGCATGTGCTC
6489 AA
1 AA
6491 ACATTTAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (12 bp):
AAGCATGTGCTC
Found at i:10046 original size:31 final size:31
Alignment explanation
Indices: 9975--10046 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
9965 GTCTATCAAC
*
9975 TTTTAATTTGTTTAATTTAAAGCTTTCATTT
1 TTTTAATTTGTTTAATTTAAAGCTTTAATTT
* *
10006 TAATT-ATTTGTTTAATTTAATG-TTTAATTT
1 T-TTTAATTTGTTTAATTTAAAGCTTTAATTT
10036 GTTTTAATTTG
1 -TTTTAATTTG
10047 CAATAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 9 0.26
31 23 0.68
32 2 0.06
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.62
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAAGCTTTAATTT
Found at i:11650 original size:15 final size:16
Alignment explanation
Indices: 11625--11663 Score: 57
Period size: 13 Copynumber: 2.6 Consensus size: 16
11615 CCGCGTCAGG
11625 ATAATTTTTAAAAAAA
1 ATAATTTTTAAAAAAA
11641 ATAA-TTTT--AAAAA
1 ATAATTTTTAAAAAAA
11654 ATAATTTTTA
1 ATAATTTTTA
11664 TGTTAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 9 0.43
14 4 0.19
15 4 0.19
16 4 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATTTTTAAAAAAA
Found at i:11814 original size:45 final size:45
Alignment explanation
Indices: 11763--11857 Score: 190
Period size: 45 Copynumber: 2.1 Consensus size: 45
11753 GTTTGTGTCG
11763 ATATTAGTATTATTATTTATTATGTATTGTTAGTATTAAGTCAAA
1 ATATTAGTATTATTATTTATTATGTATTGTTAGTATTAAGTCAAA
11808 ATATTAGTATTATTATTTATTATGTATTGTTAGTATTAAGTCAAA
1 ATATTAGTATTATTATTTATTATGTATTGTTAGTATTAAGTCAAA
11853 ATATT
1 ATATT
11858 TTTTTTAAGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.52
Consensus pattern (45 bp):
ATATTAGTATTATTATTTATTATGTATTGTTAGTATTAAGTCAAA
Found at i:11923 original size:12 final size:12
Alignment explanation
Indices: 11887--11925 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
11877 CAGAGACATG
*
11887 TTTGTAATTATT
1 TTTGTAAGTATT
* *
11899 ATTGTATGTATT
1 TTTGTAAGTATT
11911 TTTGTAAGTATT
1 TTTGTAAGTATT
11923 TTT
1 TTT
11926 TTATGTTAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.64
Consensus pattern (12 bp):
TTTGTAAGTATT
Found at i:11936 original size:41 final size:44
Alignment explanation
Indices: 11891--11971 Score: 141
Period size: 41 Copynumber: 1.9 Consensus size: 44
11881 GACATGTTTG
11891 TAATTATTATTGTATGT-ATTTTTGTAAGT-AT-TTTTTTATGT
1 TAATTATTATTGTATGTAATTTTTGTAAGTAATATTTTTTATGT
11932 TAATTATTATTGTATGTAATTTTTGTAAGTAATATTTTTT
1 TAATTATTATTGTATGTAATTTTTGTAAGTAATATTTTTT
11972 GTAAGTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
41 17 0.46
42 12 0.32
43 2 0.05
44 6 0.16
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.62
Consensus pattern (44 bp):
TAATTATTATTGTATGTAATTTTTGTAAGTAATATTTTTTATGT
Found at i:11970 original size:16 final size:16
Alignment explanation
Indices: 11951--11984 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
11941 TTGTATGTAA
11951 TTTTTGTAAGTAATAT
1 TTTTTGTAAGTAATAT
11967 TTTTTGTAAGTAATAT
1 TTTTTGTAAGTAATAT
11983 TT
1 TT
11985 GCCGTCCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (16 bp):
TTTTTGTAAGTAATAT
Found at i:13164 original size:23 final size:22
Alignment explanation
Indices: 13138--13182 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
13128 ATAAAATATG
*
13138 TTTTGAAAAATTTATGTTTTAAA
1 TTTTCAAAAATTTAT-TTTTAAA
* *
13161 TTTTCCAAAGTTTATTTTTAAA
1 TTTTCAAAAATTTATTTTTAAA
13183 AAGTTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (22 bp):
TTTTCAAAAATTTATTTTTAAA
Found at i:13932 original size:21 final size:22
Alignment explanation
Indices: 13906--13948 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
13896 AAAAAGTGAA
13906 TTACTAAATACCGCCC-CCTTT
1 TTACTAAATACCGCCCTCCTTT
**
13927 TTACTAGGTACCGCCCTCCTTT
1 TTACTAAATACCGCCCTCCTTT
13949 GTACAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.19, C:0.37, G:0.09, T:0.35
Consensus pattern (22 bp):
TTACTAAATACCGCCCTCCTTT
Done.