Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019836.1 Corchorus olitorius cultivar O-4 contig19869, 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: 9931
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Found at i:141 original size:59 final size:59
Alignment explanation
Indices: 69--268 Score: 246
Period size: 59 Copynumber: 3.4 Consensus size: 59
59 AAATTAAAAG
* * * * *
69 TGCAAAAACTGACCATAATGCCCCTAGATATGCAAAAATGACAAAAATACCCCTGGATG
1 TGCAAAAAATGACCAAAATGCCCCTAGATATGCAAAAATGACCAAAATGCCCCTGGATA
* * * * *
128 TGCAAAAAATGACCAAAATACCTCTAGATGTGCAAACATGACCAAAATGCCCCTGAATTA
1 TGCAAAAAATGACCAAAATGCCCCTAGATATGCAAAAATGACCAAAATGCCCCTGGA-TA
* *
188 TGCAAAAAATGACCAAAATG-CCCTCGGATATGC-AAAATGACCAAAATGCCCGTGGATA
1 TGCAAAAAATGACCAAAATGCCCCT-AGATATGCAAAAATGACCAAAATGCCCCTGGATA
246 TGC--AAAATGACCAAAATGCCCCT
1 TGCAAAAAATGACCAAAATGCCCCT
269 GAGTGTGCGA
Statistics
Matches: 121, Mismatches: 17, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
56 15 0.12
57 4 0.03
58 5 0.04
59 71 0.59
60 26 0.21
ACGTcount: A:0.42, C:0.24, G:0.15, T:0.18
Consensus pattern (59 bp):
TGCAAAAAATGACCAAAATGCCCCTAGATATGCAAAAATGACCAAAATGCCCCTGGATA
Found at i:233 original size:28 final size:29
Alignment explanation
Indices: 69--269 Score: 228
Period size: 30 Copynumber: 6.9 Consensus size: 29
59 AAATTAAAAG
* *
69 TGCAAAAACTGACCATAATGCCCCTAGATA
1 TGCAAAAA-TGACCAAAATGCCCCTGGATA
* * *
99 TGCAAAAATGACAAAAATACCCCTGGATG
1 TGCAAAAATGACCAAAATGCCCCTGGATA
* * * *
128 TGCAAAAAATGACCAAAATACCTCTAGATG
1 TGC-AAAAATGACCAAAATGCCCCTGGATA
* *
158 TGCAAACATGACCAAAATGCCCCTGAATTA
1 TGCAAAAATGACCAAAATGCCCCTGGA-TA
188 TGCAAAAAATGACCAAAATG-CCCTCGGATA
1 TGC-AAAAATGACCAAAATGCCCCT-GGATA
*
218 TGC-AAAATGACCAAAATGCCCGTGGATA
1 TGCAAAAATGACCAAAATGCCCCTGGATA
246 TGC-AAAATGACCAAAATGCCCCTG
1 TGCAAAAATGACCAAAATGCCCCTG
270 AGTGTGCGAA
Statistics
Matches: 148, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
28 43 0.29
29 41 0.28
30 47 0.32
31 17 0.11
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (29 bp):
TGCAAAAATGACCAAAATGCCCCTGGATA
Found at i:636 original size:58 final size:58
Alignment explanation
Indices: 513--845 Score: 566
Period size: 58 Copynumber: 5.8 Consensus size: 58
503 TGAAACATAG
* * *
513 ACTCTCGAACAGAGACCTCGATCAAGATTTTAAAAAGCAAGATAAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTT-AAAA-CAAGATAAGATTTTGAATTGAAA
* *
573 GCTCTCTAATAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
631 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAG--AAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
*
687 ACTCTCTAACAGAGACCTCGAACACGATTTTAAAACAAG--AAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
743 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
801 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGA
1 ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGA
846 GTCTGTTTTA
Statistics
Matches: 262, Mismatches: 9, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
56 110 0.42
58 122 0.47
59 4 0.02
60 26 0.10
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (58 bp):
ACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAA
Found at i:806 original size:170 final size:173
Alignment explanation
Indices: 513--840 Score: 581
Period size: 170 Copynumber: 1.9 Consensus size: 173
503 TGAAACATAG
* *
513 ACTCTCGAACAGAGACCTCGATCAAGATTTTAAAAAGCAAGATAAGATTTTGAATTGAAAGCTCT
1 ACTCTCGAACAGAGACCTCGAACAAGATTTTAAAAAGCAAGA-AAGATTTTGAATTGAAAACTCT
*
578 CTAATAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAG
65 CTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAG
643 AGACCTCGAACAGGATTTTAAAACAAGAAGATTTTGAATTGAAA
130 AGACCTCGAACAGGATTTTAAAACAAGAAGATTTTGAATTGAAA
* *
687 ACTCTCTAACAGAGACCTCGAACACGATTTT-AAAA-CAAG-AAGATTTTGAATTGAAAACTCTC
1 ACTCTCGAACAGAGACCTCGAACAAGATTTTAAAAAGCAAGAAAGATTTTGAATTGAAAACTCTC
749 TAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAGA
66 TAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAGA
814 GACCTCGAACAGGATTTTAAAACAAGA
131 GACCTCGAACAGGATTTTAAAACAAGA
841 TAAGAGTCTG
Statistics
Matches: 149, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
170 113 0.76
172 4 0.03
173 4 0.03
174 28 0.19
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (173 bp):
ACTCTCGAACAGAGACCTCGAACAAGATTTTAAAAAGCAAGAAAGATTTTGAATTGAAAACTCTC
TAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAGA
GACCTCGAACAGGATTTTAAAACAAGAAGATTTTGAATTGAAA
Done.