Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007186.1 Corchorus capsularis cultivar CVL-1 contig07207, 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: 56896
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:1906 original size:8 final size:8
Alignment explanation
Indices: 1893--1917 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1883 ATAACTATTT
1893 TATTTTAC
1 TATTTTAC
1901 TATTTTAC
1 TATTTTAC
1909 TATTTTAC
1 TATTTTAC
1917 T
1 T
1918 CAGCTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (8 bp):
TATTTTAC
Found at i:1914 original size:78 final size:78
Alignment explanation
Indices: 1825--1991 Score: 262
Period size: 78 Copynumber: 2.1 Consensus size: 78
1815 TTATTTACAC
* * *
1825 TTTTACAATTTTACTCAACTAAAAACTTTATATTTATTTAATTAAATCTAATATCATTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATATTTATTTAATTAAACCTAATATCATTATAACTA
* *
1890 TTTTATTTTACTA
66 TTTTAGTTTACCA
* * *
1903 TTTTACTATTTTACTCAGCTAAAAACTCTATTTTTATTTAATTAAACCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATATTTATTTAATTAAACCTAATATCATTATAACTA
1968 TTTTAGTTTACCA
66 TTTTAGTTTACCA
1981 TTTTACTATTT
1 TTTTACTATTT
1992 CAATTATCAT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 81 1.00
ACGTcount: A:0.35, C:0.14, G:0.01, T:0.50
Consensus pattern (78 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATATTTATTTAATTAAACCTAATATCATTATAACTA
TTTTAGTTTACCA
Found at i:5103 original size:2 final size:2
Alignment explanation
Indices: 5096--5128 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5086 AATACAAGAA
5096 AT AT AT AT 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 AT AT AT AT A
5129 AACATGATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12824 original size:5 final size:5
Alignment explanation
Indices: 12814--12845 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
12804 AAACATATAA
12814 AAAAT AAAAT AAAAT AAAAT -AAAT -AAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
12846 CTTCTACTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:15975 original size:15 final size:15
Alignment explanation
Indices: 15955--15987 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
15945 TAAAAAAAAA
15955 TGATGATTATAACAT
1 TGATGATTATAACAT
15970 TGATGATTATAACAT
1 TGATGATTATAACAT
15985 TGA
1 TGA
15988 AGTTGTGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.39
Consensus pattern (15 bp):
TGATGATTATAACAT
Found at i:17765 original size:150 final size:150
Alignment explanation
Indices: 17494--17802 Score: 618
Period size: 150 Copynumber: 2.1 Consensus size: 150
17484 TATCTCCAAC
17494 TTACTGAAGATCTACTTTTGGTTATTTTGTTTTTGAGGGTGGTAATCTCATCTCACATAAAAGAA
1 TTACTGAAGATCTACTTTTGGTTATTTTGTTTTTGAGGGTGGTAATCTCATCTCACATAAAAGAA
17559 CCAATCAGTGATTGCACGATCCAGTGCAGAAGCAGAGTATCGTGCTATGGCACAAACTACATGTG
66 CCAATCAGTGATTGCACGATCCAGTGCAGAAGCAGAGTATCGTGCTATGGCACAAACTACATGTG
17624 AGTTGATGTGGATCTATGAA
131 AGTTGATGTGGATCTATGAA
17644 TTACTGAAGATCTACTTTTGGTTATTTTGTTTTTGAGGGTGGTAATCTCATCTCACATAAAAGAA
1 TTACTGAAGATCTACTTTTGGTTATTTTGTTTTTGAGGGTGGTAATCTCATCTCACATAAAAGAA
17709 CCAATCAGTGATTGCACGATCCAGTGCAGAAGCAGAGTATCGTGCTATGGCACAAACTACATGTG
66 CCAATCAGTGATTGCACGATCCAGTGCAGAAGCAGAGTATCGTGCTATGGCACAAACTACATGTG
17774 AGTTGATGTGGATCTATGAA
131 AGTTGATGTGGATCTATGAA
17794 TTACTGAAG
1 TTACTGAAG
17803 GAGATTGGTT
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
150 159 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (150 bp):
TTACTGAAGATCTACTTTTGGTTATTTTGTTTTTGAGGGTGGTAATCTCATCTCACATAAAAGAA
CCAATCAGTGATTGCACGATCCAGTGCAGAAGCAGAGTATCGTGCTATGGCACAAACTACATGTG
AGTTGATGTGGATCTATGAA
Found at i:25539 original size:4 final size:4
Alignment explanation
Indices: 25530--25564 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
25520 ATAAAAACAA
*
25530 AAAT AAAT AAAT AGAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
25565 GGAAAAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:35788 original size:3 final size:3
Alignment explanation
Indices: 35780--35809 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
35770 ACAAAGATTC
*
35780 TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35810 CAACAATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:38130 original size:2 final size:2
Alignment explanation
Indices: 38125--38173 Score: 55
Period size: 2 Copynumber: 23.5 Consensus size: 2
38115 TGGAACACAA
*
38125 AT AT AT AT AT AT AT AT AT AT A- ACC ACT AT ACT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T A-T AT A-T AT AT AT AT AT
38167 AT AT AT A
1 AT AT AT A
38174 CTACTTATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
1 1 0.02
2 37 0.86
3 5 0.12
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:39063 original size:2 final size:2
Alignment explanation
Indices: 39053--39104 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
39043 CTTTGTGTGC
*
39053 TA TA T- TA TA TA TA TA TA TA TA TG TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
39093 TA TA TA TG TA TA
1 TA TA TA TA TA TA
39105 ATAAAAGATG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39087 original size:25 final size:25
Alignment explanation
Indices: 39053--39108 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
39043 CTTTGTGTGC
*
39053 TATATTATATATATATATATATGTA
1 TATATAATATATATATATATATGTA
39078 TATATAATATATATATATATATGTA
1 TATATAATATATATATATATATGTA
39103 TA-ATAA
1 TATATAA
39109 AAGATGGGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (25 bp):
TATATAATATATATATATATATGTA
Found at i:50001 original size:7 final size:7
Alignment explanation
Indices: 49991--50016 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
49981 TTTTTCTTTT
49991 TCTTCCA
1 TCTTCCA
49998 TCTTCCA
1 TCTTCCA
50005 TCTTCCA
1 TCTTCCA
50012 TCTTC
1 TCTTC
50017 TTTCTCTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.42, G:0.00, T:0.46
Consensus pattern (7 bp):
TCTTCCA
Done.