Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018116.1 Corchorus olitorius cultivar O-4 contig18149, 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: 5860
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Found at i:271 original size:28 final size:29
Alignment explanation
Indices: 143--351 Score: 217
Period size: 29 Copynumber: 7.2 Consensus size: 29
133 GACCATACTA
* * * * *
143 CCCCCGGATATGCAAAAATGACAAAAATA
1 CCCCTGGATGTGCAAACATGACCAAAATG
*
172 CCCCTGGATGTGCAAAAATGACCAAAATG
1 CCCCTGGATGTGCAAACATGACCAAAATG
* *
201 CCCCTGGGTGTGCAAACATGATCAAAATG
1 CCCCTGGATGTGCAAACATGACCAAAATG
*
230 CCCCTGAATTGTGCAAACATG-CCAAAATG
1 CCCCTGGA-TGTGCAAACATGACCAAAATG
259 -CCCTCGGATGTGCAAA-ATGACCAAAATG
1 CCCCT-GGATGTGCAAACATGACCAAAATG
* * *
287 CCCCTGGGTGTGCAAACACGATCAAAATG
1 CCCCTGGATGTGCAAACATGACCAAAATG
* * * * *
316 CCCCAGAGTTGTTCAAAAATGACAAAAATG
1 CCCCTG-GATGTGCAAACATGACCAAAATG
346 CCCCTG
1 CCCCTG
352 AGTGTGCGAA
Statistics
Matches: 152, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
27 3 0.02
28 30 0.20
29 85 0.56
30 34 0.22
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (29 bp):
CCCCTGGATGTGCAAACATGACCAAAATG
Found at i:289 original size:86 final size:87
Alignment explanation
Indices: 153--348 Score: 297
Period size: 86 Copynumber: 2.3 Consensus size: 87
143 CCCCCGGATA
*
153 TGCAAAAATGACAAAAATACCCCTGGATGTGCAAAAATGACCAAAATGCCCCTGGGTGTGCAAAC
1 TGCAAAAATGACAAAAAT-GCCCTGGATGTGCAAAAATGACCAAAATGCCCCTGGGTGTGCAAAC
* *
218 ATGATCAAAATGCCCCTGAATTG
65 ACGATCAAAATGCCCCAGAATTG
* *
241 TGCAAACATG-CCAAAATGCCCTCGGATGTGC-AAAATGACCAAAATGCCCCTGGGTGTGCAAAC
1 TGCAAAAATGACAAAAATGCCCT-GGATGTGCAAAAATGACCAAAATGCCCCTGGGTGTGCAAAC
*
304 ACGATCAAAATGCCCCAGAGTTG
65 ACGATCAAAATGCCCCAGAATTG
*
327 TTCAAAAATGACAAAAATGCCC
1 TGCAAAAATGACAAAAATGCCC
349 CTGAGTGTGC
Statistics
Matches: 97, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
86 64 0.66
87 24 0.25
88 9 0.09
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.18
Consensus pattern (87 bp):
TGCAAAAATGACAAAAATGCCCTGGATGTGCAAAAATGACCAAAATGCCCCTGGGTGTGCAAACA
CGATCAAAATGCCCCAGAATTG
Found at i:724 original size:58 final size:58
Alignment explanation
Indices: 595--1048 Score: 700
Period size: 58 Copynumber: 7.9 Consensus size: 58
585 TGAAACATAG
* * * * *
595 ACTCTCGAACAGAGACCTCGACCAAGATTTTAAAAAGCAAGATAAAATTTTGAATTGAAT
1 ACTCTCTAACAGAGACCTCGAACAGGATTTT-AAAA-CAAGATAAGATTTTGAATTGAAA
* * * * *
655 GCTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAGGATGATATTTTAAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
* * *
713 GCTCTCTAACAGAGACCTTGAACAGGATTTTAAAACAAGATAAGATTTTAAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
*
771 ACTCT-TAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTAAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
828 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
886 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
* * *
944 ACTCTCT---AGAGACCCCGAACAGGATTTTAGAACAAGATAAAATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
*
999 ACTCTCTAACAGAGACCTCGAACGGGATTTTAAAACAAGATAAGATTTTG
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTG
1049 TTTTAAACTG
Statistics
Matches: 365, Mismatches: 25, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
55 52 0.14
57 54 0.15
58 228 0.62
59 4 0.01
60 27 0.07
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (58 bp):
ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
Found at i:801 original size:115 final size:116
Alignment explanation
Indices: 595--1048 Score: 700
Period size: 115 Copynumber: 3.9 Consensus size: 116
585 TGAAACATAG
* * * **
595 ACTCTCGAACAGAGACCTCGACCAAGATTTTAAAAAGCAAGATAAAATTTTGAATTGAATGCTCT
1 ACTCTCTAACAGAGACCTCGAACAGGATTTT-AAAA-CAAGATAAAATTTTGAATTGAAAACTCT
* * * *
660 CTAACAGAGACCTCGAACAGGATTTTAAAACAGGATGATATTTTAAATTGAAA
64 CTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
* * * *
713 GCTCTCTAACAGAGACCTTGAACAGGATTTTAAAACAAGATAAGATTTTAAATTGAAAACTCT-T
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAAATTTTGAATTGAAAACTCTCT
*
777 AACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTAAAA
66 AACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
*
828 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCTCT
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAAATTTTGAATTGAAAACTCTCT
893 AACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
66 AACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
* *
944 ACTCTCT---AGAGACCCCGAACAGGATTTTAGAACAAGATAAAATTTTGAATTGAAAACTCTCT
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAAATTTTGAATTGAAAACTCTCT
*
1006 AACAGAGACCTCGAACGGGATTTTAAAACAAGATAAGATTTTG
66 AACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTG
1049 TTTTAAACTG
Statistics
Matches: 313, Mismatches: 22, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
113 94 0.30
115 107 0.34
116 82 0.26
117 4 0.01
118 26 0.08
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (116 bp):
ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAAATTTTGAATTGAAAACTCTCT
AACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
Found at i:893 original size:173 final size:172
Alignment explanation
Indices: 602--1048 Score: 700
Period size: 173 Copynumber: 2.6 Consensus size: 172
592 TAGACTCTCG
* * **
602 AACAGAGACCTCGACCAAGATTTTAAAAAGCAAGATAAAATTTTGAATTGAATGCTCTCTAACAG
1 AACAGAGACCTCGAACAGGATTTT-AAAA-CAAGATAAAATTTTGAATTGAAAACTCTCTAACAG
* * * * * *
667 AGACCTCGAACAGGATTTTAAAACAGGATGATATTTTAAATTGAAAGCTCTCTAACAGAGACCTT
64 AGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAGAGACCTC
732 GAACAGGATTTTAAAACAAGATAAGATTTTAAATTGAAAACTCTT
129 GAACAGGATTTTAAAACAAGATAAGATTTTAAATTGAAAACTC-T
* *
777 AACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTAAAAACTCTCTAACAGAG
1 AACAGAGACCTCGAACAGGATTTTAAAACAAGATAAAATTTTGAATTGAAAACTCTCTAACAGAG
842 ACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAGAGACCTCGA
66 ACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAGAGACCTCGA
*
907 ACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCT
131 ACAGGATTTTAAAACAAGATAAGATTTTAAATTGAAAACTCT
* *
949 --CTAGAGACCCCGAACAGGATTTTAGAACAAGATAAAATTTTGAATTGAAAACTCTCTAACAGA
1 AAC-AGAGACCTCGAACAGGATTTTAAAACAAGATAAAATTTTGAATTGAAAACTCTCTAACAGA
*
1012 GACCTCGAACGGGATTTTAAAACAAGATAAGATTTTG
65 GACCTCGAACAGGATTTTAAAACAAGATAAGATTTTG
1049 TTTTAAACTG
Statistics
Matches: 253, Mismatches: 18, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
170 1 0.00
171 93 0.37
172 1 0.00
173 132 0.52
174 4 0.02
175 22 0.09
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (172 bp):
AACAGAGACCTCGAACAGGATTTTAAAACAAGATAAAATTTTGAATTGAAAACTCTCTAACAGAG
ACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAGAGACCTCGA
ACAGGATTTTAAAACAAGATAAGATTTTAAATTGAAAACTCT
Found at i:1961 original size:36 final size:37
Alignment explanation
Indices: 1871--1968 Score: 117
Period size: 37 Copynumber: 2.7 Consensus size: 37
1861 TAAATTTTTA
*
1871 TGACCTCTCTCTGTTTTAGGTCCAGTTTTTCCTACTC
1 TGACCTCTTTCTGTTTTAGGTCCAGTTTTTCCTACTC
* ** **
1908 TGACCTCTTTCTGTTTTAGGTCCTGTTTTTGTTTTTC
1 TGACCTCTTTCTGTTTTAGGTCCAGTTTTTCCTACTC
* *
1945 -GACCTCTTTCTATTTTAGGCCCAG
1 TGACCTCTTTCTGTTTTAGGTCCAG
1969 CTCTCTTCTT
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
36 21 0.40
37 31 0.60
ACGTcount: A:0.10, C:0.26, G:0.15, T:0.49
Consensus pattern (37 bp):
TGACCTCTTTCTGTTTTAGGTCCAGTTTTTCCTACTC
Done.