Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009816.1 Corchorus capsularis cultivar CVL-1 contig09837, 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: 8546
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:4064 original size:22 final size:22
Alignment explanation
Indices: 4036--4078 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4026 AATTGAATTC
*
4036 GAAGAATTGAAATTGAAGCATG
1 GAAGAATCGAAATTGAAGCATG
4058 GAAGAATCGAAATTGAAGCAT
1 GAAGAATCGAAATTGAAGCAT
4079 TGACATATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.07, G:0.26, T:0.21
Consensus pattern (22 bp):
GAAGAATCGAAATTGAAGCATG
Found at i:4106 original size:58 final size:58
Alignment explanation
Indices: 4000--4191 Score: 226
Period size: 58 Copynumber: 3.3 Consensus size: 58
3990 GAAGGAGGCT
* * * * *
4000 TTGAAGAATTAAAATCGAAACATTGA-A-ATTGAATTCGAAGAATTGAAATTGAAGCA
1 TTGAAGAATTGAAATTGAAGCATTGACATATCGAATTTGAAGAATTGAAATTGAAGCA
* * * * *
4056 TGGAAGAATCGAAATTGAAGCATTGACATATGGATTTTGAAGAATTGAAATTGAAGCG
1 TTGAAGAATTGAAATTGAAGCATTGACATATCGAATTTGAAGAATTGAAATTGAAGCA
* * * * *
4114 TTGAAGAATTGAAACTGAAGCATTGATATTTCGAATTTGAAGAACTGAAATTTAAGCA
1 TTGAAGAATTGAAATTGAAGCATTGACATATCGAATTTGAAGAATTGAAATTGAAGCA
4172 TTGAAGAATTGAAAATTGAA
1 TTGAAGAATTG-AAATTGAA
4192 ATTGAAGCGT
Statistics
Matches: 113, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
56 21 0.19
57 1 0.01
58 84 0.74
59 7 0.06
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.29
Consensus pattern (58 bp):
TTGAAGAATTGAAATTGAAGCATTGACATATCGAATTTGAAGAATTGAAATTGAAGCA
Found at i:4117 original size:22 final size:22
Alignment explanation
Indices: 4092--4139 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
4082 CATATGGATT
* *
4092 TTGAAGAATTGAAATTGAAGCG
1 TTGAAGAATTGAAACTGAAGCA
4114 TTGAAGAATTGAAACTGAAGCA
1 TTGAAGAATTGAAACTGAAGCA
4136 TTGA
1 TTGA
4140 TATTTCGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.27
Consensus pattern (22 bp):
TTGAAGAATTGAAACTGAAGCA
Found at i:4184 original size:8 final size:8
Alignment explanation
Indices: 4150--4271 Score: 51
Period size: 8 Copynumber: 16.0 Consensus size: 8
4140 TATTTCGAAT
4150 TTGAAGAA
1 TTGAAGAA
*
4158 CTG-A-AA
1 TTGAAGAA
* *
4164 TTTAAGCA
1 TTGAAGAA
4172 TTGAAGAA
1 TTGAAGAA
4180 TTGAA-AA
1 TTGAAGAA
4187 TTG-A-AA
1 TTGAAGAA
**
4193 TTGAAGCG
1 TTGAAGAA
** *
4201 TCAAAGAT
1 TTGAAGAA
4209 TTG-A-AA
1 TTGAAGAA
* *
4215 TTGAGGCA
1 TTGAAGAA
*
4223 TTGAATAA
1 TTGAAGAA
*
4231 TTTGAGGAA
1 -TTGAAGAA
*
4240 TTGAAGCA
1 TTGAAGAA
* *
4248 TTAAATAA
1 TTGAAGAA
4256 TTGAAGAA
1 TTGAAGAA
4264 TTGAAGAA
1 TTGAAGAA
4272 AGATCACCCT
Statistics
Matches: 78, Mismatches: 29, Indels: 14
0.64 0.24 0.12
Matches are distributed among these distances:
6 13 0.17
7 9 0.12
8 50 0.64
9 6 0.08
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (8 bp):
TTGAAGAA
Found at i:4248 original size:25 final size:24
Alignment explanation
Indices: 4213--4269 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
4203 AAAGATTTGA
* * *
4213 AATTGAGGCATTGAATAATTTGAGG
1 AATTGAAGCATTAAATAA-TTGAAG
4238 AATTGAAGCATTAAATAATTGAAG
1 AATTGAAGCATTAAATAATTGAAG
4262 AATTGAAG
1 AATTGAAG
4270 AAAGATCACC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 13 0.45
25 16 0.55
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.30
Consensus pattern (24 bp):
AATTGAAGCATTAAATAATTGAAG
Found at i:4435 original size:8 final size:8
Alignment explanation
Indices: 4422--4472 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
4412 AAGAATTGAA
4422 ATTGAAAC
1 ATTGAAAC
*
4430 ATTGAAAT
1 ATTGAAAC
4438 ATTG-AA-
1 ATTGAAAC
4444 ATTGAAAC
1 ATTGAAAC
*
4452 GTTGAATA-
1 ATTGAA-AC
4460 ATTGAAAC
1 ATTGAAAC
4468 ATTGA
1 ATTGA
4473 TGGATTGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
6 4 0.11
7 5 0.14
8 26 0.72
9 1 0.03
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (8 bp):
ATTGAAAC
Found at i:4442 original size:22 final size:21
Alignment explanation
Indices: 4342--4537 Score: 103
Period size: 22 Copynumber: 8.9 Consensus size: 21
4332 AGGATCGAAT
* *
4342 TTGAAGAATTGAAACTGAAGCA
1 TTGAA-AATTGAAATTGAAACA
* *
4364 ATGAAATGTTGAAATTGAAACA
1 TTGAAA-ATTGAAATTGAAACA
* *
4386 TTGAAGGATCG-AATTGGAAGA-A
1 TTGAA-AATTGAAATT-GAA-ACA
*
4408 CTGGAAGAATTGAAATTGAAACA
1 -TTGAA-AATTGAAATTGAAACA
*
4431 TTGAAATATTGAAATTGAAACG
1 TTGAAA-ATTGAAATTGAAACA
***
4453 TTGAATAATTGAAACATTGATGGA
1 TTGAA-AATTG-AA-ATTGAAACA
* *
4477 TTG-AAATTGAATTTGAAGCA
1 TTGAAAATTGAAATTGAAACA
*
4497 TTGAGGAATTGAAATTGAAACA
1 TTGA-AAATTGAAATTGAAACA
*
4519 TT-AAAGGATTGAATTTGAA
1 TTGAAA--ATTGAAATTGAA
4538 GAAACGAAAT
Statistics
Matches: 134, Mismatches: 25, Indels: 30
0.71 0.13 0.16
Matches are distributed among these distances:
20 10 0.07
21 9 0.07
22 86 0.64
23 17 0.13
24 12 0.09
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (21 bp):
TTGAAAATTGAAATTGAAACA
Found at i:4697 original size:58 final size:58
Alignment explanation
Indices: 4610--4955 Score: 471
Period size: 58 Copynumber: 6.1 Consensus size: 58
4600 ATTGAAGCAA
* * * * ** **
4610 TGAAGAATTTGAAGAAAGACCACCTTGGATCATCGAAGTAAATTGAAAAATTGAACGAT
1 TGAAGAA-TTGAAGAAAGATCACCCTGGATCTTTGAAGTAAATTGAAGTATTGAATAAT
* * * *
4669 TGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGGATTGAATGAT
1 TGAAGAATTGAAGAAAGATCACCCTGGATCTTTGAAGTAAATTGAAGTATTGAATAAT
* *
4727 T-AAGGAATTGAAGAAAGATCACCTTGGATCTTTCAAGTAAATTGAAGTATTGAATAAT
1 TGAA-GAATTGAAGAAAGATCACCCTGGATCTTTGAAGTAAATTGAAGTATTGAATAAT
4785 TGAAGAATTGAAGAAAGATCACCCTGGATCTTTGAAGTAAATTGAAGTATTGAATAAT
1 TGAAGAATTGAAGAAAGATCACCCTGGATCTTTGAAGTAAATTGAAGTATTGAATAAT
4843 TGAAGAATTGAAGAAAGATCACCCTGGATC-------T---TTGAAGTATTGAATAAT
1 TGAAGAATTGAAGAAAGATCACCCTGGATCTTTGAAGTAAATTGAAGTATTGAATAAT
4891 TGAAGAATTGAAGAAAGATCACCCTGGATCTTTGAAGTAAATTGAAGTATTGAATAAT
1 TGAAGAATTGAAGAAAGATCACCCTGGATCTTTGAAGTAAATTGAAGTATTGAATAAT
4949 TGAAGAA
1 TGAAGAA
4956 AGACCACCCT
Statistics
Matches: 262, Mismatches: 13, Indels: 25
0.87 0.04 0.08
Matches are distributed among these distances:
48 47 0.18
51 1 0.00
55 1 0.00
57 2 0.01
58 202 0.77
59 9 0.03
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (58 bp):
TGAAGAATTGAAGAAAGATCACCCTGGATCTTTGAAGTAAATTGAAGTATTGAATAAT
Found at i:4798 original size:8 final size:8
Alignment explanation
Indices: 4766--4799 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
4756 CTTTCAAGTA
4766 AATTGAAG
1 AATTGAAG
* *
4774 TATTGAAT
1 AATTGAAG
4782 AATTGAAG
1 AATTGAAG
4790 AATTGAAG
1 AATTGAAG
4798 AA
1 AA
4800 AGATCACCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (8 bp):
AATTGAAG
Found at i:4856 original size:8 final size:8
Alignment explanation
Indices: 4824--4857 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
4814 CTTTGAAGTA
4824 AATTGAAG
1 AATTGAAG
* *
4832 TATTGAAT
1 AATTGAAG
4840 AATTGAAG
1 AATTGAAG
4848 AATTGAAG
1 AATTGAAG
4856 AA
1 AA
4858 AGATCACCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (8 bp):
AATTGAAG
Found at i:4888 original size:48 final size:48
Alignment explanation
Indices: 4826--4965 Score: 228
Period size: 48 Copynumber: 2.9 Consensus size: 48
4816 TTGAAGTAAA
4826 TTGAAGTATTGAATAATTGAAGAATTGAAGAAAGATCACCCTGGATCT
1 TTGAAGTATTGAATAATTGAAGAATTGAAGAAAGATCACCCTGGATCT
4874 TTGAAGTATTGAATAATTGAAGAATTGAAGAAAGATCACCCTGGATCT
1 TTGAAGTATTGAATAATTGAAGAATTGAAGAAAGATCACCCTGGATCT
* *
4922 TTGAAGTAAATTGAAGT-ATTGAATAATTGAAGAAAGACCACCCT
1 TTGAAGT--ATTGAA-TAATTGAAGAATTGAAGAAAGATCACCCT
4966 TTGAAAAATA
Statistics
Matches: 87, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
48 55 0.63
50 31 0.36
51 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.29
Consensus pattern (48 bp):
TTGAAGTATTGAATAATTGAAGAATTGAAGAAAGATCACCCTGGATCT
Found at i:5850 original size:12 final size:10
Alignment explanation
Indices: 5819--5843 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5809 CTTCCTTCTA
5819 TTTTTTCTTT
1 TTTTTTCTTT
5829 TTTTTTCTTT
1 TTTTTTCTTT
5839 TTTTT
1 TTTTT
5844 CATCTTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:6590 original size:15 final size:14
Alignment explanation
Indices: 6566--6595 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
6556 AAATCGTGAC
6566 TCTTTTGAAAACCA
1 TCTTTTGAAAACCA
6580 TCTTGTTGAAAACCA
1 TCTT-TTGAAAACCA
6595 T
1 T
6596 ATTTCAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (14 bp):
TCTTTTGAAAACCA
Done.