Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014307.1 Corchorus capsularis cultivar CVL-1 contig14328, 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: 8086
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Found at i:2834 original size:3 final size:3
Alignment explanation
Indices: 2826--2861 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2816 CAGGGAAATG
2826 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2862 ACAATAGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2893 original size:12 final size:12
Alignment explanation
Indices: 2876--2900 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2866 TAGAATTACC
2876 ATATGATTATAA
1 ATATGATTATAA
2888 ATATGATTATAA
1 ATATGATTATAA
2900 A
1 A
2901 AGTGAATTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
ATATGATTATAA
Found at i:3672 original size:22 final size:22
Alignment explanation
Indices: 3642--3694 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
3632 ATTACACTAT
*
3642 TTTTTATAAC-GTCCTTATGAAA
1 TTTTGATAACAGTCC-TATGAAA
*
3664 TTTTGATAACATTCCTATGAAA
1 TTTTGATAACAGTCCTATGAAA
*
3686 TTATGATAA
1 TTTTGATAA
3695 TTACACTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 24 0.89
23 3 0.11
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.43
Consensus pattern (22 bp):
TTTTGATAACAGTCCTATGAAA
Found at i:3695 original size:62 final size:62
Alignment explanation
Indices: 3598--3749 Score: 250
Period size: 62 Copynumber: 2.5 Consensus size: 62
3588 ATATTCATAC
* * *
3598 GAAATTATGATAACATTTCTATTAAATTATGATAATTACACTATTTTTTATAACGTCCTTAT
1 GAAATTTTGATAACATTCCTATGAAATTATGATAATTACACTATTTTTTATAACGTCCTTAT
* *
3660 GAAATTTTGATAACATTCCTATGAAATTATGATAATTACACTATTTTTTATGACGTTCTTAT
1 GAAATTTTGATAACATTCCTATGAAATTATGATAATTACACTATTTTTTATAACGTCCTTAT
*
3722 GAAATTTTGATAACTTTCCTATGAAATT
1 GAAATTTTGATAACATTCCTATGAAATT
3750 TCAATAACAA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 84 1.00
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.45
Consensus pattern (62 bp):
GAAATTTTGATAACATTCCTATGAAATTATGATAATTACACTATTTTTTATAACGTCCTTAT
Found at i:3744 original size:22 final size:22
Alignment explanation
Indices: 3657--3750 Score: 81
Period size: 22 Copynumber: 4.5 Consensus size: 22
3647 ATAACGTCCT
*
3657 TATGAAATTTTGATAACATTCC
1 TATGAAATTTTGATAACTTTCC
* *
3679 TATGAAATTATGATAA-TTACAC
1 TATGAAATTTTGATAACTTTC-C
* * * *
3701 TAT----TTTTTATGACGTTCT
1 TATGAAATTTTGATAACTTTCC
3719 TATGAAATTTTGATAACTTTCC
1 TATGAAATTTTGATAACTTTCC
3741 TATGAAATTT
1 TATGAAATTT
3751 CAATAACAAT
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
18 9 0.17
19 2 0.04
21 2 0.04
22 40 0.75
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.46
Consensus pattern (22 bp):
TATGAAATTTTGATAACTTTCC
Found at i:3825 original size:22 final size:22
Alignment explanation
Indices: 3715--4148 Score: 114
Period size: 22 Copynumber: 19.8 Consensus size: 22
3705 TTTTATGACG
*
3715 TTCTTATGAAATTTTGATAACT
1 TTCTTATGAAATTTTGATAACC
* ** *
3737 TTCCTATGAAATTTCAATAACAA
1 TTCTTATGAAATTTTGATAAC-C
* * *
3760 TAC-TATGAAATTTCGAAAACC
1 TTCTTATGAAATTTTGATAACC
* *
3781 TTTTTAT-AAATTTT-ATTTGACC
1 TTCTTATGAAATTTTGA--TAACC
*
3803 TTCTTATGAAATTTTGTTAACC
1 TTCTTATGAAATTTTGATAACC
* * * *
3825 TCTCCCTAAGGAATTTTGA-AGATC
1 T-T-CTTATGAAATTTTGATA-ACC
* *
3849 -TCACTATGAAATTTTGATAATC
1 TTC-TTATGAAATTTTGATAACC
** * *
3871 AACACTAT-AAGATGTTGATAACC
1 TTC-TTATGAA-ATTTTGATAACC
* * * *
3894 TCCATATGATATATTGATAACC
1 TTCTTATGAAATTTTGATAACC
* * * * *
3916 ATGTTATGAAAGTTTAAAAACC
1 TTCTTATGAAATTTTGATAACC
* * * *
3938 TCCATATG-AATTGTCAGTAATCAC
1 TTCTTATGAAATTTTGA-TAA-C-C
*
3962 -AC-TATGAAATTTTGATAACC
1 TTCTTATGAAATTTTGATAACC
* * *
3982 -ACACTATGAAATTGTGATAAACC
1 TTC-TTATGAAATTTTGAT-AACC
4005 TTGC-TATGAAATTTTGATAAACC
1 TT-CTTATGAAATTTTGAT-AACC
* * *
4028 TCCCTATAAAATTTTGATAACC
1 TTCTTATGAAATTTTGATAACC
* *
4050 TCCTTATGAAATCTTGATAA--
1 TTCTTATGAAATTTTGATAACC
*
4070 ---TTA-CAAATTTTGATAACC
1 TTCTTATGAAATTTTGATAACC
* ** *
4088 TCCTTATGATTTTTTGATAATC
1 TTCTTATGAAATTTTGATAACC
* *
4110 -ACATTATGTAATTTTGATAACC
1 TTC-TTATGAAATTTTGATAACC
*
4132 TCGCTT-TGAAATTTTGA
1 T-TCTTATGAAATTTTGA
4149 AATTGGACCA
Statistics
Matches: 307, Mismatches: 72, Indels: 66
0.69 0.16 0.15
Matches are distributed among these distances:
16 11 0.04
17 3 0.01
20 4 0.01
21 18 0.06
22 179 0.58
23 76 0.25
24 15 0.05
25 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TTCTTATGAAATTTTGATAACC
Found at i:3990 original size:88 final size:91
Alignment explanation
Indices: 3866--4030 Score: 198
Period size: 88 Copynumber: 1.8 Consensus size: 91
3856 GAAATTTTGA
* * *
3866 TAATCAACACTATAAGATGTTGATAACCTCCATATGATATAT-TGAT-AACCATGTTATGAAAGT
1 TAATCAACACTATAAGATGTTGATAACCACCATATGAAAT-TGTGATAAACCATGCTATGAAAGT
3929 TT-AAAAACCTCCATATGAATTGTCAG
65 TTGAAAAACCTCCATATGAATTGTCAG
* * *
3955 TAATC-ACACTATGAA-ATTTTGATAACCA-CACTATGAAATTGTGATAAACCTTGCTATGAAAT
1 TAATCAACACTAT-AAGATGTTGATAACCACCA-TATGAAATTGTGATAAACCATGCTATGAAAG
*
4017 TTTGATAAACCTCC
64 TTTGAAAAACCTCC
4031 CTATAAAATT
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
87 3 0.05
88 29 0.45
89 23 0.36
90 9 0.14
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.33
Consensus pattern (91 bp):
TAATCAACACTATAAGATGTTGATAACCACCATATGAAATTGTGATAAACCATGCTATGAAAGTT
TGAAAAACCTCCATATGAATTGTCAG
Found at i:4011 original size:23 final size:23
Alignment explanation
Indices: 3961--4069 Score: 125
Period size: 23 Copynumber: 4.8 Consensus size: 23
3951 TCAGTAATCA
*
3961 CACTATGAAATTTTGAT-AACCA
1 CACTATGAAATTTTGATAAACCT
*
3983 CACTATGAAATTGTGATAAACCT
1 CACTATGAAATTTTGATAAACCT
**
4006 TGCTATGAAATTTTGATAAACCT
1 CACTATGAAATTTTGATAAACCT
* *
4029 CCCTATAAAATTTTGAT-AACCT
1 CACTATGAAATTTTGATAAACCT
*
4051 C-CTTATGAAATCTTGATAA
1 CAC-TATGAAATTTTGATAA
4070 TTACAAATTT
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
21 1 0.01
22 34 0.46
23 39 0.53
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (23 bp):
CACTATGAAATTTTGATAAACCT
Found at i:4013 original size:45 final size:43
Alignment explanation
Indices: 3963--4148 Score: 125
Period size: 45 Copynumber: 4.3 Consensus size: 43
3953 AGTAATCACA
* *
3963 CTATGAAATTTTGATAACCACACTATGAAATTGTGATAAACCTTG
1 CTATGAAATTTTGATAACCACACTATAAAATTGTGAT-AACC-TC
* * *
4008 CTATGAAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTC
1 CTATGAAATTTTGAT-AACCACACTATAAAATTGTGATAACCTC
* *
4052 CTTATGAAATCTTGAT----A-A-T-TACAAATTTTGATAACCTC
1 C-TATGAAATTTTGATAACCACACTATA-AAATTGTGATAACCTC
** * * ** *
4090 CTTATGATTTTTTGATAATCACATTATGTAATTTTGATAACCTC
1 C-TATGAAATTTTGATAACCACACTATAAAATTGTGATAACCTC
*
4134 GCTTTGAAATTTTGA
1 -CTATGAAATTTTGA
4149 AATTGGACCA
Statistics
Matches: 114, Mismatches: 16, Indels: 23
0.75 0.10 0.15
Matches are distributed among these distances:
37 2 0.02
38 30 0.26
42 1 0.01
43 1 0.01
44 28 0.25
45 34 0.30
46 18 0.16
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (43 bp):
CTATGAAATTTTGATAACCACACTATAAAATTGTGATAACCTC
Found at i:4117 original size:60 final size:61
Alignment explanation
Indices: 4013--4129 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 61
4003 CCTTGCTATG
* *
4013 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCCTTATGAAATCTTGATAATTAC
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACCACATTATGAAATCTTGATAATTAC
* * ** * * *
4074 AAATTTTGAT-AACCTCCTTATGATTTTTTGATAATCACATTATGTAATTTTGATAA
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACCACATTATGAAATCTTGATAA
4130 CCTCGCTTTG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
60 37 0.79
61 10 0.21
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.42
Consensus pattern (61 bp):
AAATTTTGATAAACCTCCCTATAAAATTTTGATAACCACATTATGAAATCTTGATAATTAC
Found at i:4269 original size:7 final size:7
Alignment explanation
Indices: 4257--4287 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
4247 GGTTGGAAAT
4257 AAAGACA
1 AAAGACA
4264 AAAGACA
1 AAAGACA
4271 AAAGACA
1 AAAGACA
4278 AAAGACA
1 AAAGACA
4285 AAA
1 AAA
4288 TTAAATAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.74, C:0.13, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAGACA
Found at i:4858 original size:14 final size:14
Alignment explanation
Indices: 4839--4867 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4829 TTATTCGTAC
4839 TTTTATATATAGTA
1 TTTTATATATAGTA
4853 TTTTATATATAGTA
1 TTTTATATATAGTA
4867 T
1 T
4868 AGATTATCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTTTATATATAGTA
Found at i:4889 original size:30 final size:30
Alignment explanation
Indices: 4853--4917 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
4843 ATATATAGTA
4853 TTTTATATATAGTATAGATTATCCGT-GTAC
1 TTTTATATATAGTATAGATTATCCGTGGT-C
4883 TTTTATATATAGTATAGATTATCCGTGGTC
1 TTTTATATATAGTATAGATTATCCGTGGTC
4913 TTTTA
1 TTTTA
4918 GGGCTGTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 32 0.94
31 2 0.06
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.49
Consensus pattern (30 bp):
TTTTATATATAGTATAGATTATCCGTGGTC
Found at i:6839 original size:12 final size:11
Alignment explanation
Indices: 6814--6847 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
6804 TTTCTGTTTT
6814 TTTGTTTTTG-
1 TTTGTTTTTGC
6824 TTTGGTTTTTGC
1 TTT-GTTTTTGC
6836 TTTGTTTTTGC
1 TTTGTTTTTGC
6847 T
1 T
6848 GCGCTGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.14
11 16 0.73
12 3 0.14
ACGTcount: A:0.00, C:0.06, G:0.21, T:0.74
Consensus pattern (11 bp):
TTTGTTTTTGC
Done.