Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011799.1 Corchorus capsularis cultivar CVL-1 contig11820, 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: 61613
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:37724 original size:65 final size:64
Alignment explanation
Indices: 37596--37783 Score: 333
Period size: 65 Copynumber: 2.9 Consensus size: 64
37586 CCATATAATA
* **
37596 ATTTGTTTCTGAAAC-CCTTTTTCAAGGATTATGAAACTTTTTTATATATATTTGAGGTTTATC
1 ATTTATTTCTGAAACATTTTTTTCAAGGATTATGAAACTTTTTTATATATATTTGAGGTTTATC
37659 ATTTATTTCTGAAACATTTTTTTCAAGGATTATGAAACTTTTTTTATATATATTTGAGGTTTATC
1 ATTTATTTCTGAAACATTTTTTTCAAGGATTATGAAAC-TTTTTTATATATATTTGAGGTTTATC
37724 ATTTATTTCTGAAACATTTTTTTCAAGGATTATGAAACTTTTTTATATATATTTGAGGTT
1 ATTTATTTCTGAAACATTTTTTTCAAGGATTATGAAACTTTTTTATATATATTTGAGGTT
37784 ATACGAATTG
Statistics
Matches: 120, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
63 14 0.12
64 42 0.35
65 64 0.53
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.51
Consensus pattern (64 bp):
ATTTATTTCTGAAACATTTTTTTCAAGGATTATGAAACTTTTTTATATATATTTGAGGTTTATC
Found at i:49863 original size:12 final size:12
Alignment explanation
Indices: 49846--49915 Score: 76
Period size: 12 Copynumber: 6.0 Consensus size: 12
49836 CCTTGCTTCT
49846 CTTCTCTTTTAG
1 CTTCTCTTTTAG
*
49858 CTTCTCTGCTT-G
1 CTTCTCT-TTTAG
*
49870 CTTGTC-TTT--
1 CTTCTCTTTTAG
49879 CTTCTCTTTTAG
1 CTTCTCTTTTAG
49891 CTTCTCTTTTTAG
1 CTTCTC-TTTTAG
49904 CTTCTCTTTTAG
1 CTTCTCTTTTAG
49916 ACCGTAGTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
9 5 0.10
10 5 0.10
12 25 0.51
13 14 0.29
ACGTcount: A:0.06, C:0.26, G:0.10, T:0.59
Consensus pattern (12 bp):
CTTCTCTTTTAG
Found at i:49903 original size:13 final size:13
Alignment explanation
Indices: 49879--49913 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
49869 GCTTGTCTTT
49879 CTTCTC-TTTTAG
1 CTTCTCTTTTTAG
49891 CTTCTCTTTTTAG
1 CTTCTCTTTTTAG
49904 CTTCTCTTTT
1 CTTCTCTTTT
49914 AGACCGTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 6 0.27
13 16 0.73
ACGTcount: A:0.06, C:0.26, G:0.06, T:0.63
Consensus pattern (13 bp):
CTTCTCTTTTTAG
Found at i:50753 original size:18 final size:18
Alignment explanation
Indices: 50730--50764 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
50720 TAACATATTA
*
50730 TGCATTTGTGAAAATTTT
1 TGCATTTCTGAAAATTTT
50748 TGCATTTCTGAAAATTT
1 TGCATTTCTGAAAATTT
50765 GTGTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.49
Consensus pattern (18 bp):
TGCATTTCTGAAAATTTT
Found at i:51154 original size:31 final size:31
Alignment explanation
Indices: 51116--51178 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
51106 CTTCTCCTCA
51116 TGGATGACCAAAGACGAGGGTGAAAATATAG
1 TGGATGACCAAAGACGAGGGTGAAAATATAG
51147 TGGATGACCAAAGACGAGGGTGAAAATATAG
1 TGGATGACCAAAGACGAGGGTGAAAATATAG
51178 T
1 T
51179 TTATGCTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.10, G:0.32, T:0.17
Consensus pattern (31 bp):
TGGATGACCAAAGACGAGGGTGAAAATATAG
Found at i:51749 original size:16 final size:13
Alignment explanation
Indices: 51715--51746 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
51705 GATACAGATG
51715 ATTATTCTAATCT
1 ATTATTCTAATCT
51728 ATTATTCTAATCT
1 ATTATTCTAATCT
51741 ATTATT
1 ATTATT
51747 ATTAATTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTATTCTAATCT
Found at i:53210 original size:20 final size:18
Alignment explanation
Indices: 53172--53207 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
53162 GTGGCTCGGC
*
53172 TATTTTTTTTTAAATAAT
1 TATTTTTTTTTAAAAAAT
53190 TATTATTTTTTTAAAAAA
1 TATT-TTTTTTTAAAAAA
53208 ATTTGTCTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTTTTTTTTAAAAAAT
Found at i:53264 original size:33 final size:33
Alignment explanation
Indices: 53216--53303 Score: 131
Period size: 33 Copynumber: 2.7 Consensus size: 33
53206 AAATTTGTCT
*
53216 AGCCGCCCTAGTGGGGCGGCTCCGCCATGGCTG
1 AGCCGCCCTAGTGGGGAGGCTCCGCCATGGCTG
* * * *
53249 AGCCGTCCTATTGGGGAGGCTACGCCGTGGCTG
1 AGCCGCCCTAGTGGGGAGGCTCCGCCATGGCTG
53282 AGCCGCCCTAGTGGGGAGGCTC
1 AGCCGCCCTAGTGGGGAGGCTC
53304 AGTGTAAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.11, C:0.32, G:0.40, T:0.17
Consensus pattern (33 bp):
AGCCGCCCTAGTGGGGAGGCTCCGCCATGGCTG
Found at i:55857 original size:20 final size:20
Alignment explanation
Indices: 55832--55873 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
55822 CTAGCCCTAT
*
55832 TCCCAACTTCACCTCAAACC
1 TCCCAACCTCACCTCAAACC
*
55852 TCCCAACCTCACTTCAAACC
1 TCCCAACCTCACCTCAAACC
55872 TC
1 TC
55874 ATTTGAACGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.50, G:0.00, T:0.21
Consensus pattern (20 bp):
TCCCAACCTCACCTCAAACC
Done.