Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015003.1 Corchorus capsularis cultivar CVL-1 contig15024, 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: 65140
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:446 original size:17 final size:17
Alignment explanation
Indices: 418--457 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
408 CTCTTCTAGC
418 AATATA-ACCTTA-CCA
1 AATATATACCTTATCCA
433 AATATATACACTTATCCA
1 AATATATAC-CTTATCCA
451 AATATAT
1 AATATAT
458 GGGGGTCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.27
16 2 0.09
17 4 0.18
18 10 0.45
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (17 bp):
AATATATACCTTATCCA
Found at i:8631 original size:12 final size:12
Alignment explanation
Indices: 8614--8655 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
8604 AGCGAGTAAT
*
8614 AGTTTACGAGGG
1 AGTTTAAGAGGG
8626 AGTTTAAGAGGG
1 AGTTTAAGAGGG
*
8638 AGTTTAAGGGGG
1 AGTTTAAGAGGG
8650 AGTTTA
1 AGTTTA
8656 CGATCAGGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.29, C:0.02, G:0.40, T:0.29
Consensus pattern (12 bp):
AGTTTAAGAGGG
Found at i:24385 original size:9 final size:9
Alignment explanation
Indices: 24362--24395 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
24352 TTTCCTTTTC
*
24362 CTTTTTTTT
1 CTTTTCTTT
24371 CTTTTCTTT
1 CTTTTCTTT
*
24380 CTTTTCTTC
1 CTTTTCTTT
24389 CTTTTCT
1 CTTTTCT
24396 CCAACCTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (9 bp):
CTTTTCTTT
Found at i:36668 original size:33 final size:34
Alignment explanation
Indices: 36626--36700 Score: 116
Period size: 34 Copynumber: 2.2 Consensus size: 34
36616 ATAAAGTTTA
* * *
36626 TTTAACATGCATGATCT-CTTCTTCTACCTTTCT
1 TTTATCATGCATAATCTCCTCCTTCTACCTTTCT
36659 TTTATCATGCATAATCTCCTCCTTCTACCTTTCT
1 TTTATCATGCATAATCTCCTCCTTCTACCTTTCT
36693 TTTATCAT
1 TTTATCAT
36701 TAAAATTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 15 0.39
34 23 0.61
ACGTcount: A:0.19, C:0.28, G:0.04, T:0.49
Consensus pattern (34 bp):
TTTATCATGCATAATCTCCTCCTTCTACCTTTCT
Found at i:36777 original size:33 final size:33
Alignment explanation
Indices: 36735--36870 Score: 191
Period size: 33 Copynumber: 4.1 Consensus size: 33
36725 CTATCCTTGA
36735 ATATTAGTGGCACCTGAAGTTGTCACATCAAAC
1 ATATTAGTGGCACCTGAAGTTGTCACATCAAAC
* * *
36768 ATATTAGTGGCACCAGAAGTTGTCGCATCAAGC
1 ATATTAGTGGCACCTGAAGTTGTCACATCAAAC
* * **
36801 ATATCAGTGACACCTGAAGTTGTCACATCAAGT
1 ATATTAGTGGCACCTGAAGTTGTCACATCAAAC
* *
36834 ATATTAGTGGCACCTGAAGTTGTCACATAAAAA
1 ATATTAGTGGCACCTGAAGTTGTCACATCAAAC
36867 ATAT
1 ATAT
36871 AGTATCACTT
Statistics
Matches: 90, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (33 bp):
ATATTAGTGGCACCTGAAGTTGTCACATCAAAC
Found at i:36915 original size:30 final size:29
Alignment explanation
Indices: 36869--36930 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 29
36859 CATAAAAAAT
36869 ATAGTATCACTTTGACACCCGAAGTTGTC
1 ATAGTATCACTTTGACACCCGAAGTTGTC
* *
36898 ATAGTATCATTTTTGACATCCGAAGTTGTC
1 ATAGTATCA-CTTTGACACCCGAAGTTGTC
36928 ATA
1 ATA
36931 TTAAGGATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (29 bp):
ATAGTATCACTTTGACACCCGAAGTTGTC
Found at i:38157 original size:2 final size:2
Alignment explanation
Indices: 38150--38177 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38140 AACATCTATG
38150 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
38178 TGTGGATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40631 original size:64 final size:64
Alignment explanation
Indices: 40530--40657 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
40520 TTGAATAAAT
40530 CCTTGTATGGATTAAAACAATCTGGGCGTATGTGGTATAATCGCCTTAGTGAATATTTGTTGAA
1 CCTTGTATGGATTAAAACAATCTGGGCGTATGTGGTATAATCGCCTTAGTGAATATTTGTTGAA
40594 CCTTGTATGGATTAAAACAATCTGGGCGTATGTGGTATAATCGCCTTAGTGAATATTTGTTGAA
1 CCTTGTATGGATTAAAACAATCTGGGCGTATGTGGTATAATCGCCTTAGTGAATATTTGTTGAA
40658 GGAAGGATAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.36
Consensus pattern (64 bp):
CCTTGTATGGATTAAAACAATCTGGGCGTATGTGGTATAATCGCCTTAGTGAATATTTGTTGAA
Done.