Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011422.1 Corchorus capsularis cultivar CVL-1 contig11443, 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: 106976
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:481 original size:2 final size:2
Alignment explanation
Indices: 439--463 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
429 ACATTGGTGT
439 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 T
464 TTTGAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8169 original size:1 final size:1
Alignment explanation
Indices: 8163--8190 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
8153 TGTTCATATC
8163 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
8191 ATTATATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:17120 original size:32 final size:31
Alignment explanation
Indices: 17058--17123 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
17048 GTGGCCTTGC
* *
17058 CACATGTCATTTTGGTCCAATGTAGCATTGT
1 CACATGGCATTTTGATCCAATGTAGCATTGT
* * *
17089 CACATGGCATTTTTGATCCGATGTGGTATTGT
1 CACATGGCA-TTTTGATCCAATGTAGCATTGT
17121 CAC
1 CAC
17124 GTCGACAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 8 0.28
32 21 0.72
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (31 bp):
CACATGGCATTTTGATCCAATGTAGCATTGT
Found at i:22711 original size:23 final size:23
Alignment explanation
Indices: 22680--22734 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
22670 TTTCGTGTTT
*
22680 TAATTGTGTCAACACGAATAAGA
1 TAATCGTGTCAACACGAATAAGA
*
22703 TAATCGTGTCAACACGATTAAGA
1 TAATCGTGTCAACACGAATAAGA
22726 TAATCGTGT
1 TAATCGTGT
22735 TTCATGTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (23 bp):
TAATCGTGTCAACACGAATAAGA
Found at i:29694 original size:48 final size:48
Alignment explanation
Indices: 29636--29776 Score: 246
Period size: 48 Copynumber: 2.9 Consensus size: 48
29626 GGGGTGGCTC
*
29636 AGTGGCAGGAAGCCGAGTGTAAGGTTTACTGTAAGTGTGGTCATGATT
1 AGTGGCAGGAAGCCGAGTGTAAGGTTTACTGCAAGTGTGGTCATGATT
*
29684 AGTGGCAGGAAGCCGAGTGTAAGGTTTTCTGCAAGTGTGGTCATGATT
1 AGTGGCAGGAAGCCGAGTGTAAGGTTTACTGCAAGTGTGGTCATGATT
* *
29732 AGTGGCAAGAAGCCGAGTGTAAGGTTTGCTGCAAGTGTGGTCATG
1 AGTGGCAGGAAGCCGAGTGTAAGGTTTACTGCAAGTGTGGTCATG
29777 GGTTCGAGTC
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 89 1.00
ACGTcount: A:0.24, C:0.12, G:0.36, T:0.28
Consensus pattern (48 bp):
AGTGGCAGGAAGCCGAGTGTAAGGTTTACTGCAAGTGTGGTCATGATT
Found at i:33964 original size:2 final size:2
Alignment explanation
Indices: 33957--33990 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
33947 AAATGTGGCT
33957 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33991 CGTATGTCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39040 original size:1 final size:1
Alignment explanation
Indices: 39034--39064 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
39024 AAGGAGAAAG
39034 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
39065 GAAAGCAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:50878 original size:19 final size:19
Alignment explanation
Indices: 50854--50894 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
50844 CTCATATTCA
*
50854 TTACAATCAGAATCATCTT
1 TTACAATCAAAATCATCTT
50873 TTACAATCAAAATCATCTT
1 TTACAATCAAAATCATCTT
50892 TTA
1 TTA
50895 TATGGCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39
Consensus pattern (19 bp):
TTACAATCAAAATCATCTT
Found at i:77913 original size:75 final size:75
Alignment explanation
Indices: 77790--77929 Score: 253
Period size: 75 Copynumber: 1.9 Consensus size: 75
77780 GAGCATCAAG
*
77790 AAATCATCAAAAACCGACCAACTGACCTGATTAAGTCCCTGTTTGGTGCACCGTTTGGTCCGTTT
1 AAATCATCAAAAACCGACCAACAGACCTGATTAAGTCCCTGTTTGGTGCACCGTTTGGTCCGTTT
77855 AGGAGAAAAC
66 AGGAGAAAAC
* *
77865 AAATCATCAAAAACCGACCAACAGACTTGATTGAGTCCCTGTTTGGTGCACCGTTTGGTCCGTTT
1 AAATCATCAAAAACCGACCAACAGACCTGATTAAGTCCCTGTTTGGTGCACCGTTTGGTCCGTTT
77930 GGGCCTCCCA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 62 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (75 bp):
AAATCATCAAAAACCGACCAACAGACCTGATTAAGTCCCTGTTTGGTGCACCGTTTGGTCCGTTT
AGGAGAAAAC
Found at i:78238 original size:76 final size:76
Alignment explanation
Indices: 78123--78263 Score: 264
Period size: 76 Copynumber: 1.9 Consensus size: 76
78113 ACAGGGTCTA
*
78123 AAACCGAATGATGTCAGTTTCCTTCAGTTCCATGGGAGGTTGGTTGGTGGTCGGTGCTCAATATC
1 AAACCGAACGATGTCAGTTTCCTTCAGTTCCATGGGAGGTTGGTTGGTGGTCGGTGCTCAATATC
78188 CTACCAAACTG
66 CTACCAAACTG
*
78199 AAACCGAACGATGTCTGTTTCCTTCAGTTCCATGGGAGGTTGGTTGGTGGTCGGTGCTCAATATC
1 AAACCGAACGATGTCAGTTTCCTTCAGTTCCATGGGAGGTTGGTTGGTGGTCGGTGCTCAATATC
78264 TTCCATCAGT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 63 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (76 bp):
AAACCGAACGATGTCAGTTTCCTTCAGTTCCATGGGAGGTTGGTTGGTGGTCGGTGCTCAATATC
CTACCAAACTG
Found at i:79150 original size:6 final size:6
Alignment explanation
Indices: 79110--79164 Score: 65
Period size: 6 Copynumber: 9.2 Consensus size: 6
79100 AAGATGATCA
* * * * *
79110 AGCCCC AGACTC AGCCGC AGACCC AGCCCC GGCCCC AGCCCC AGCCCC
1 AGCCCC AGCCCC AGCCCC AGCCCC AGCCCC AGCCCC AGCCCC AGCCCC
79158 AGCCCC A
1 AGCCCC A
79165 TCCTTAGCAG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.20, C:0.58, G:0.20, T:0.02
Consensus pattern (6 bp):
AGCCCC
Found at i:80615 original size:24 final size:24
Alignment explanation
Indices: 80567--80627 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
80557 TTATTTATGC
*
80567 ATTATGTTAAGAA-ATATGGTTTG
1 ATTATGATAAGAATATATGGTTTG
80590 ATTATGATAAGAATACT-TGGTTTG
1 ATTATGATAAGAATA-TATGGTTTG
80614 ATTATGATAAGAAT
1 ATTATGATAAGAAT
80628 CCTTCGTCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
23 12 0.34
24 22 0.63
25 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.20, T:0.41
Consensus pattern (24 bp):
ATTATGATAAGAATATATGGTTTG
Found at i:82393 original size:56 final size:56
Alignment explanation
Indices: 82302--82411 Score: 175
Period size: 56 Copynumber: 2.0 Consensus size: 56
82292 GATTGTTACC
* * *
82302 TCAACTGGTAGGTGTATCGTGGCTGGACCGTGAGGTCCTGGGTTCAAGTCTCACAT
1 TCAACTGGTAGGTGTACCGTGGCTGGACCATGAGGTCCTGGATTCAAGTCTCACAT
* *
82358 TCAATTGGTAGGTGTACCGTGGCTGGACCATGAGGTCTTGGATTCAAGTCTCAC
1 TCAACTGGTAGGTGTACCGTGGCTGGACCATGAGGTCCTGGATTCAAGTCTCAC
82412 GGAATGTGAG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (56 bp):
TCAACTGGTAGGTGTACCGTGGCTGGACCATGAGGTCCTGGATTCAAGTCTCACAT
Done.