Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014379.1 Corchorus capsularis cultivar CVL-1 contig14400, 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: 34011
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3275 original size:70 final size:70
Alignment explanation
Indices: 3200--3424 Score: 333
Period size: 70 Copynumber: 3.1 Consensus size: 70
3190 GTTTTTATAG
* * *
3200 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAACTACTTTATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA--TTA---
*
3265 TACCATTTTACTA
61 T---ATTTTACCA
3278 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTT
3343 TACCA
66 TACCA
*
3348 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTGTAACTATTATATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTT
3413 TACCA
66 TACCA
3418 TTTTACT
1 TTTTACT
3425 ATTTTAATTA
Statistics
Matches: 142, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
70 84 0.59
73 1 0.01
76 3 0.02
78 54 0.38
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (70 bp):
TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTT
TACCA
Found at i:3282 original size:78 final size:77
Alignment explanation
Indices: 3192--3430 Score: 350
Period size: 78 Copynumber: 3.2 Consensus size: 77
3182 TTGTTTAGGT
* * *
3192 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAACT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
3256 ACTTTATTTTACCA
65 A-TTTATTTTACCA
3270 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
3335 -TTA---T---A
66 TTTATTTTACCA
* *
3340 TTTTACCATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTGTAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
3405 TTATATTTTACCA
66 TT-TATTTTACCA
3418 TTTTACTATTTTA
1 TTTTACTATTTTA
3431 ATTAAAAAAC
Statistics
Matches: 146, Mismatches: 6, Indels: 18
0.86 0.04 0.11
Matches are distributed among these distances:
70 64 0.44
71 1 0.01
72 2 0.01
73 1 0.01
75 1 0.01
76 3 0.02
78 72 0.49
79 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.01, T:0.49
Consensus pattern (77 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
TTTATTTTACCA
Found at i:5459 original size:2 final size:2
Alignment explanation
Indices: 5452--5476 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5442 AGTGATAAAA
5452 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5477 ACTTTTTGAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11916 original size:14 final size:14
Alignment explanation
Indices: 11897--11926 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11887 TGCATCCTGC
11897 CAAATGTATTTCAT
1 CAAATGTATTTCAT
*
11911 CAAATGTGTTTCAT
1 CAAATGTATTTCAT
11925 CA
1 CA
11927 TCTGGAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (14 bp):
CAAATGTATTTCAT
Found at i:14070 original size:18 final size:18
Alignment explanation
Indices: 14049--14097 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
14039 ATAAGTCACC
14049 AAAAAAAAAAGAACTTCA
1 AAAAAAAAAAGAACTTCA
* ** *
14067 AAAAAATAAAGTCCTTTA
1 AAAAAAAAAAGAACTTCA
*
14085 AAAAAAGAAAGAA
1 AAAAAAAAAAGAA
14098 AATAACAATA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.14
Consensus pattern (18 bp):
AAAAAAAAAAGAACTTCA
Found at i:14553 original size:113 final size:113
Alignment explanation
Indices: 14355--14582 Score: 456
Period size: 113 Copynumber: 2.0 Consensus size: 113
14345 GCCCCTGCAT
14355 TTATTTTTAAAATGAAATTAAGGGTTACCATGCCCTAAAATCCATAACAAATTAGGGGGGTTGTA
1 TTATTTTTAAAATGAAATTAAGGGTTACCATGCCCTAAAATCCATAACAAATTAGGGGGGTTGTA
14420 GTCTCCTACAAGGGTCATGTTTGAACAAGAAATAGTCCATTTTCATCA
66 GTCTCCTACAAGGGTCATGTTTGAACAAGAAATAGTCCATTTTCATCA
14468 TTATTTTTAAAATGAAATTAAGGGTTACCATGCCCTAAAATCCATAACAAATTAGGGGGGTTGTA
1 TTATTTTTAAAATGAAATTAAGGGTTACCATGCCCTAAAATCCATAACAAATTAGGGGGGTTGTA
14533 GTCTCCTACAAGGGTCATGTTTGAACAAGAAATAGTCCATTTTCATCA
66 GTCTCCTACAAGGGTCATGTTTGAACAAGAAATAGTCCATTTTCATCA
14581 TT
1 TT
14583 TAATATGTGA
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 115 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (113 bp):
TTATTTTTAAAATGAAATTAAGGGTTACCATGCCCTAAAATCCATAACAAATTAGGGGGGTTGTA
GTCTCCTACAAGGGTCATGTTTGAACAAGAAATAGTCCATTTTCATCA
Found at i:15476 original size:17 final size:17
Alignment explanation
Indices: 15454--15488 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
15444 ACAAAGCACA
* *
15454 CAACATTAGTCTATGTG
1 CAACATTAATCAATGTG
15471 CAACATTAATCAATGTG
1 CAACATTAATCAATGTG
15488 C
1 C
15489 CCATTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (17 bp):
CAACATTAATCAATGTG
Done.