Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011262.1 Corchorus capsularis cultivar CVL-1 contig11283, 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: 7743
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:208 original size:21 final size:21
Alignment explanation
Indices: 184--264 Score: 65
Period size: 21 Copynumber: 3.6 Consensus size: 21
174 TGAAATAAAT
184 GTTTTTATTTTGTAAATCTAA
1 GTTTTTATTTTGTAAATCTAA
* * *
205 GTTTTTTTTGTTTCTATGAAAT-AAA
1 G---TTTTTATTT-TGT-AAATCTAA
230 TGTTTTTATTTTGTAAATCTAA
1 -GTTTTTATTTTGTAAATCTAA
*
252 GTTTTTTTTTTGT
1 GTTTTTATTTTGT
265 TTTTTTTTAC
Statistics
Matches: 46, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
21 17 0.37
22 4 0.09
23 8 0.17
24 8 0.17
25 4 0.09
26 5 0.11
ACGTcount: A:0.23, C:0.04, G:0.11, T:0.62
Consensus pattern (21 bp):
GTTTTTATTTTGTAAATCTAA
Found at i:223 original size:47 final size:47
Alignment explanation
Indices: 170--260 Score: 182
Period size: 47 Copynumber: 1.9 Consensus size: 47
160 TATGAAAATC
170 TCTATGAAATAAATGTTTTTATTTTGTAAATCTAAGTTTTTTTTGTT
1 TCTATGAAATAAATGTTTTTATTTTGTAAATCTAAGTTTTTTTTGTT
217 TCTATGAAATAAATGTTTTTATTTTGTAAATCTAAGTTTTTTTT
1 TCTATGAAATAAATGTTTTTATTTTGTAAATCTAAGTTTTTTTT
261 TTGTTTTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.57
Consensus pattern (47 bp):
TCTATGAAATAAATGTTTTTATTTTGTAAATCTAAGTTTTTTTTGTT
Found at i:258 original size:23 final size:23
Alignment explanation
Indices: 185--259 Score: 73
Period size: 23 Copynumber: 3.2 Consensus size: 23
175 GAAATAAATG
185 TTTTTATTTTGTAAATCTAAGTT
1 TTTTTATTTTGTAAATCTAAGTT
* * * *
208 TTTTT-TGTTTCTATGAA-ATAAATG
1 TTTTTAT-TTTGTA--AATCTAAGTT
232 TTTTTATTTTGTAAATCTAAGTT
1 TTTTTATTTTGTAAATCTAAGTT
255 TTTTT
1 TTTTT
260 TTTGTTTTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
22 3 0.08
23 19 0.49
24 14 0.36
25 3 0.08
ACGTcount: A:0.25, C:0.04, G:0.09, T:0.61
Consensus pattern (23 bp):
TTTTTATTTTGTAAATCTAAGTT
Found at i:259 original size:24 final size:24
Alignment explanation
Indices: 185--260 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
175 GAAATAAATG
185 TTTTTATTTTGTAAATCTAAGTTT
1 TTTTTATTTTGTAAATCTAAGTTT
* * * *
209 TTTTTGTTTCTATGAAA--TAA-ATG
1 TTTTTATTT-TGT-AAATCTAAGTTT
232 TTTTTATTTTGTAAATCTAAGTTT
1 TTTTTATTTTGTAAATCTAAGTTT
256 TTTTT
1 TTTTT
261 TTGTTTTTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
21 3 0.08
22 2 0.05
23 12 0.31
24 17 0.44
25 2 0.05
26 3 0.08
ACGTcount: A:0.25, C:0.04, G:0.09, T:0.62
Consensus pattern (24 bp):
TTTTTATTTTGTAAATCTAAGTTT
Found at i:476 original size:32 final size:31
Alignment explanation
Indices: 430--521 Score: 98
Period size: 31 Copynumber: 2.9 Consensus size: 31
420 AAAAAGCCTT
*
430 GCCGCCCTAGTGGGGCAGCT-AGCCGTGGCAGA
1 GCCGTCCTAGTGGGG--GCTCAGCCGTGGCAGA
* *
462 GCCGTCCTAGTGGGGGCTCCGCCGTGGCATA
1 GCCGTCCTAGTGGGGGCTCAGCCGTGGCAGA
*
493 GCCGTCCTAGTGTGGAGGCTCCG-CGTGGC
1 GCCGTCCTAGTG-GG-GGCTCAGCCGTGGC
522 TAAGGATAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
30 3 0.06
31 22 0.41
32 22 0.41
33 7 0.13
ACGTcount: A:0.11, C:0.32, G:0.40, T:0.17
Consensus pattern (31 bp):
GCCGTCCTAGTGGGGGCTCAGCCGTGGCAGA
Found at i:489 original size:31 final size:33
Alignment explanation
Indices: 451--521 Score: 112
Period size: 31 Copynumber: 2.2 Consensus size: 33
441 GGGGCAGCTA
451 GCCGTGGCAGAGCCGTCCTAGTG-GG-GGCTCC
1 GCCGTGGCAGAGCCGTCCTAGTGTGGAGGCTCC
*
482 GCCGTGGCATAGCCGTCCTAGTGTGGAGGCTCC
1 GCCGTGGCAGAGCCGTCCTAGTGTGGAGGCTCC
515 G-CGTGGC
1 GCCGTGGC
522 TAAGGATAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
31 22 0.59
32 8 0.22
33 7 0.19
ACGTcount: A:0.10, C:0.31, G:0.41, T:0.18
Consensus pattern (33 bp):
GCCGTGGCAGAGCCGTCCTAGTGTGGAGGCTCC
Found at i:827 original size:6 final size:6
Alignment explanation
Indices: 818--853 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
808 GAATCAGAAT
*
818 CCCAAA CCCAAA CCCAAA CCCAAA CCCAAT CCCAAA
1 CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA
854 TGGATTTGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.47, C:0.50, G:0.00, T:0.03
Consensus pattern (6 bp):
CCCAAA
Found at i:928 original size:6 final size:6
Alignment explanation
Indices: 917--941 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
907 CAAACCACAA
917 GGAGAT GGAGAT GGAGAT GGAGAT G
1 GGAGAT GGAGAT GGAGAT GGAGAT G
942 AATTGGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.52, T:0.16
Consensus pattern (6 bp):
GGAGAT
Found at i:2877 original size:16 final size:16
Alignment explanation
Indices: 2856--2989 Score: 173
Period size: 16 Copynumber: 8.4 Consensus size: 16
2846 TGCAGTTTTC
2856 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
2872 TCGGGTCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
* *
2888 T-GGGTTATTCGGATT
1 TCGGGTCATTCGGGTT
2903 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
2919 TCAGGTCATACGGGTT
1 TCGGGTCATTCGGGTT
*
2935 TCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
*
2951 TCGGGTCATTTGGGTT
1 TCGGGTCATTCGGGTT
* *
2967 TCGGGTCATTCGGATA
1 TCGGGTCATTCGGGTT
2983 TCGGGTC
1 TCGGGTC
2990 TCGGGTTGGA
Statistics
Matches: 101, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
15 12 0.12
16 89 0.88
ACGTcount: A:0.10, C:0.18, G:0.36, T:0.37
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:3266 original size:42 final size:42
Alignment explanation
Indices: 3219--3300 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
3209 TAGATATTAA
* * *
3219 TTTTGAATATTAAATACATGATTGATTATCATGTGAGGTAGG
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
*
3261 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTA
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTA
3301 TGTGTCAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.40
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
Found at i:3817 original size:16 final size:16
Alignment explanation
Indices: 3761--3832 Score: 67
Period size: 16 Copynumber: 4.5 Consensus size: 16
3751 TTTATAATAT
3761 TCTCGGGTCATAT-GGG
1 TCTCGGGTCAT-TCGGG
* * *
3777 TCTCAGGTCACTCGGA
1 TCTCGGGTCATTCGGG
*
3793 T-TACTGGTCATTCGGG
1 TCT-CGGGTCATTCGGG
3809 TCTCGGGTCATTCGGG
1 TCTCGGGTCATTCGGG
*
3825 TCACGGGT
1 TCTCGGGT
3833 TGGGCGGGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
15 2 0.04
16 42 0.93
17 1 0.02
ACGTcount: A:0.12, C:0.24, G:0.33, T:0.31
Consensus pattern (16 bp):
TCTCGGGTCATTCGGG
Done.