Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014291.1 Corchorus capsularis cultivar CVL-1 contig14312, 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: 17679
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1951 original size:18 final size:18
Alignment explanation
Indices: 1928--1965 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1918 TTAACGATGA
1928 ACTAAACCGGATTAAACT
1 ACTAAACCGGATTAAACT
1946 ACTAAACCGGATTAAACT
1 ACTAAACCGGATTAAACT
1964 AC
1 AC
1966 CACAAAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.24, G:0.11, T:0.21
Consensus pattern (18 bp):
ACTAAACCGGATTAAACT
Found at i:2181 original size:28 final size:29
Alignment explanation
Indices: 2149--2223 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 29
2139 AAGTGACCTT
* *
2149 AAAATGACCAAAATGCCCCCTAAATGT-G
1 AAAATGACCAAAATGCCCCATAAATGTAA
* *
2177 AAAATGACCAAAATG-CCCATTAGTGTAA
1 AAAATGACCAAAATGCCCCATAAATGTAA
2205 AAAATGACCAAAATGCCCC
1 AAAATGACCAAAATGCCCC
2224 TAGATGACCC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
27 8 0.20
28 30 0.73
29 3 0.07
ACGTcount: A:0.45, C:0.24, G:0.13, T:0.17
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCATAAATGTAA
Found at i:2641 original size:63 final size:61
Alignment explanation
Indices: 2572--2857 Score: 239
Period size: 63 Copynumber: 4.7 Consensus size: 61
2562 TTGGAATCGA
*
2572 AACAAGAAACTCTCGACTAGAGACCTCAAGCATGG-TTTGAAACCAACGAGATTTTGAAATTGG
1 AACAAGAAACTCTCGACTAGAGACCTCAAGCA-GGATTTGAAACAAACGAGATTTTG-AATT-G
* * * *
2635 AACAAGAAACTCTCGATTAGAAACCTCAAACAGGATTTGAAACTAAC-ACGATTTTG-A---
1 AACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAACAAACGA-GATTTTGAATTG
* *
2692 AACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAATAGAAACGAGACTTTGAATTG
1 AACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAA-ACAAACGAGATTTTGAATTG
* * * * * ** * *
2754 ACACTAGAGACCCTCAACTAGAGACCTTAATTAGGATTTGGAAATGAAACTG-GATTTAG-ATTG
1 A-ACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTT-GAAA-CAAAC-GAGATTTTGAATTG
* * *
2817 ATACAA-AAGACTCTCAACTAGAGACCTAAAACAGGATTTGA
1 A-ACAAGAA-ACTCTCGACTAGAGACCTCAAGCAGGATTTGA
2858 GATGAACGAG
Statistics
Matches: 184, Mismatches: 26, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
57 38 0.21
58 10 0.05
59 2 0.01
61 1 0.01
62 7 0.04
63 112 0.61
64 13 0.07
65 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.23
Consensus pattern (61 bp):
AACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAACAAACGAGATTTTGAATTG
Found at i:2879 original size:63 final size:62
Alignment explanation
Indices: 2700--2880 Score: 170
Period size: 63 Copynumber: 2.9 Consensus size: 62
2690 GAAACAAGAA
* * * * * * *
2700 ACTCTCGACTAGAGACCTCAAGCAGGATTTGAATAGAAACGAGACTTTGAATTGACACTAGAG
1 ACTCTCAACTAGAGACCTAAAACAGGATTTGAAT-GAAACGAGAATTTGGATTGACACAAAAG
* * ** * *
2763 ACCCTCAACTAGAGACCTTAATTAGGATTTGGAAATGAAACTG-G-ATTTAGATTGATACAAAAG
1 ACTCTCAACTAGAGACCTAAAACAGGATTT-G-AATGAAAC-GAGAATTTGGATTGACACAAAAG
2826 ACTCTCAACTAGAGACCTAAAACAGGATTTGAGATG-AACGAGAATTTGGGATTGA
1 ACTCTCAACTAGAGACCTAAAACAGGATTTGA-ATGAAACGAGAATTT-GGATTGA
2881 AACTCTAATA
Statistics
Matches: 95, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
60 1 0.01
61 5 0.05
62 8 0.08
63 70 0.74
64 7 0.07
65 4 0.04
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (62 bp):
ACTCTCAACTAGAGACCTAAAACAGGATTTGAATGAAACGAGAATTTGGATTGACACAAAAG
Found at i:17248 original size:5 final size:6
Alignment explanation
Indices: 17219--17245 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
17209 CCTAACATAG
17219 AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
17246 TAATCTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:17493 original size:62 final size:61
Alignment explanation
Indices: 17377--17507 Score: 140
Period size: 62 Copynumber: 2.1 Consensus size: 61
17367 AAACCAGTCT
* ** **
17377 TAAATTGAAGCAAATTAACATGAACAGGCCTCAAATCGCAGAGATCTACCATAATCAAGCAA
1 TAAATTGAAGCAAATCAACATGAACAGGCCTCAAATCGCAGAGAAATAAAATAAT-AAGCAA
* * * *
17439 TAAATTGTAA-CAAATCAACATGAACATGCCTCAAATCGTAGTA-AAATAAAATAATAAGGAG
1 TAAATTG-AAGCAAATCAACATGAACAGGCCTCAAATCGCAG-AGAAATAAAATAATAAGCAA
17500 TAAATTGA
1 TAAATTGA
17508 GAAGGGAAGG
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
60 1 0.02
61 11 0.19
62 43 0.74
63 3 0.05
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (61 bp):
TAAATTGAAGCAAATCAACATGAACAGGCCTCAAATCGCAGAGAAATAAAATAATAAGCAA
Done.