Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010357.1 Corchorus capsularis cultivar CVL-1 contig10378, 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: 56454
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:8515 original size:2 final size:2
Alignment explanation
Indices: 8508--8549 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
8498 AAATCAAATA
* *
8508 AT AT AT AT AT AT AT AT AT AT AT AT CT AT CT AT ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
8550 AAAGTACGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8872 original size:108 final size:109
Alignment explanation
Indices: 8641--8914 Score: 428
Period size: 108 Copynumber: 2.5 Consensus size: 109
8631 ACTATTATAG
*
8641 TTTTATTCTACTAAAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
***
8706 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAAAAATTTCTAATATACAA
8755 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
8820 TTACC-AAAAATTTGGATATATTAAAAAAATTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAAAAATTTCTAATATACAA
8863 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA
8915 TAGTTTTTTT
Statistics
Matches: 154, Mismatches: 5, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
107 7 0.05
108 78 0.51
109 42 0.27
110 3 0.02
111 2 0.01
114 22 0.14
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.48
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAAAAATTTCTAATATACAA
Found at i:21937 original size:8 final size:8
Alignment explanation
Indices: 21924--21953 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
21914 AATCTCCACT
21924 TTCCAGAC
1 TTCCAGAC
21932 TTCCAGAC
1 TTCCAGAC
*
21940 TTCCAGAG
1 TTCCAGAC
21948 TTCCAG
1 TTCCAG
21954 TCAATGTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.27
Consensus pattern (8 bp):
TTCCAGAC
Found at i:22160 original size:2 final size:2
Alignment explanation
Indices: 22153--22184 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
22143 TTTGGTGAAC
22153 AT AT AT 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 AT AT AT
22185 GAAGCTTGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23380 original size:152 final size:153
Alignment explanation
Indices: 23099--23403 Score: 492
Period size: 152 Copynumber: 2.0 Consensus size: 153
23089 AATTACTAAG
23099 AATAAACTTTCACTGCAAAATGCCGTGTTGAAATACAGTAATCCACCTTATCATGAATTCATGAT
1 AATAAACTTTCACTGCAAAATGCCGTGTTGAAATACAGTAATCCACC-T-T-AT-AATTCATGAT
* *
23164 TAAACCCATAAATTGCCAGCTAATTATGGTAATTTTTTTTTGGGTCAAATATAATTATAGTAATT
62 TAAACCCATAAATAGCCAGCTAATTATAGTAATTTTTTTTTGGGTCAAATATAATTATAGTAATT
23229 TCCCACACTCAAATTATAAAGTATAAA
127 TCCCACACTCAAATTATAAAGTATAAA
23256 AATAAACTTTCACTGCAAAATGCCGTGTTGAAATACAGTAATCCACC-T-T-A-TCATGATTAAA
1 AATAAACTTTCACTGCAAAATGCCGTGTTGAAATACAGTAATCCACCTTATAATTCATGATTAAA
23317 CCCATAATAAATAGCCAGCTAATTATAGTAATTTTTTTTTGGGTCAAATATAATTATAGTAATTT
66 CCC---ATAAATAGCCAGCTAATTATAGTAATTTTTTTTTGGGTCAAATATAATTATAGTAATTT
*
23382 CCCACGCTCAAATTATAAAGTA
128 CCCACACTCAAATTATAAAGTA
23404 CTCCATAAAA
Statistics
Matches: 142, Mismatches: 3, Indels: 11
0.91 0.02 0.07
Matches are distributed among these distances:
149 14 0.10
150 1 0.01
152 79 0.56
154 1 0.01
157 47 0.33
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (153 bp):
AATAAACTTTCACTGCAAAATGCCGTGTTGAAATACAGTAATCCACCTTATAATTCATGATTAAA
CCCATAAATAGCCAGCTAATTATAGTAATTTTTTTTTGGGTCAAATATAATTATAGTAATTTCCC
ACACTCAAATTATAAAGTATAAA
Found at i:24056 original size:19 final size:19
Alignment explanation
Indices: 24020--24058 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
24010 GTAAGAAAGA
* *
24020 TAATTTCTTCATCTCTTTT
1 TAATTTCGTCATCCCTTTT
*
24039 TAATTTCGTCCTCCCTTTT
1 TAATTTCGTCATCCCTTTT
24058 T
1 T
24059 GAAATTTCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.26, G:0.03, T:0.59
Consensus pattern (19 bp):
TAATTTCGTCATCCCTTTT
Found at i:37386 original size:73 final size:73
Alignment explanation
Indices: 37245--37379 Score: 245
Period size: 73 Copynumber: 1.9 Consensus size: 73
37235 CATGTAGACT
* *
37245 TAAGGAGACTCTACCCCTGCTTCCTTCCTAAAGAGAGCAGAAAACCTAGAACCGCTGCATGCTAC
1 TAAGGAGACTCTACCCCTGCTTCCTTCCTAAAGAGAGCAGAAAACCTAGAACCGCTCCATGATAC
37310 TTCCTTCC
66 TTCCTTCC
37318 TAAGGAGACTCTACCCCTGCTTCCTTCCTAAAGAGAGCAGAAAACCTAGAACCGC-CCATGAT
1 TAAGGAGACTCTACCCCTGCTTCCTTCCTAAAGAGAGCAGAAAACCTAGAACCGCTCCATGAT
37380 CCCTTCCCAT
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
72 5 0.08
73 55 0.92
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (73 bp):
TAAGGAGACTCTACCCCTGCTTCCTTCCTAAAGAGAGCAGAAAACCTAGAACCGCTCCATGATAC
TTCCTTCC
Found at i:54434 original size:15 final size:15
Alignment explanation
Indices: 54410--54441 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
54400 TAAATACTAG
*
54410 TATTATCATTATGTT
1 TATTACCATTATGTT
54425 TATTACCATTATGTT
1 TATTACCATTATGTT
54440 TA
1 TA
54442 CATTCTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.09, G:0.06, T:0.56
Consensus pattern (15 bp):
TATTACCATTATGTT
Found at i:54700 original size:17 final size:17
Alignment explanation
Indices: 54680--54712 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
54670 TAAAATATAA
54680 AATATATAGGGTTAAGC
1 AATATATAGGGTTAAGC
54697 AATATATAGGGTTAAG
1 AATATATAGGGTTAAG
54713 GAAAGGCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.24, T:0.30
Consensus pattern (17 bp):
AATATATAGGGTTAAGC
Found at i:56371 original size:21 final size:21
Alignment explanation
Indices: 56328--56371 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
56318 TTCATGGGGG
* * *
56328 TTGCTAAATACCGTCCTAGTT
1 TTGCTAAATACCGCCCCACTT
56349 TTGCTAAATACCGCCCCACTT
1 TTGCTAAATACCGCCCCACTT
56370 TT
1 TT
56372 TACACTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.30, G:0.11, T:0.36
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCACTT
Done.