Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006254.1 Corchorus olitorius cultivar O-4 contig06279, 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, 823
Length: 1372
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Found at i:227 original size:13 final size:11
Alignment explanation
Indices: 109--222 Score: 67
Period size: 11 Copynumber: 10.8 Consensus size: 11
99 ATTATGCTAT
*
109 TATATATCAAA
1 TATATATAAAA
* **
120 TATATTTATGA
1 TATATATAAAA
131 TATATATAAAA
1 TATATATAAAA
*
142 TATAT-T-TAA
1 TATATATAAAA
* **
151 T-TATTTATGA
1 TATATATAAAA
161 TATATATAAAA
1 TATATATAAAA
* *
172 TACATGT-AAA
1 TATATATAAAA
*
182 -ATATATAAAT
1 TATATATAAAA
* **
192 TATATTTATGA
1 TATATATAAAA
203 TATATATAAAA
1 TATATATAAAA
214 TATATATAA
1 TATATATAA
223 CAAATTTTTT
Statistics
Matches: 74, Mismatches: 24, Indels: 10
0.69 0.22 0.09
Matches are distributed among these distances:
8 3 0.04
9 8 0.11
10 9 0.12
11 54 0.73
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (11 bp):
TATATATAAAA
Found at i:353 original size:10 final size:10
Alignment explanation
Indices: 338--362 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
328 ATTTCCTATT
338 TTAAAACCGA
1 TTAAAACCGA
348 TTAAAACCGA
1 TTAAAACCGA
358 TTAAA
1 TTAAA
363 TTAAATTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (10 bp):
TTAAAACCGA
Found at i:759 original size:38 final size:40
Alignment explanation
Indices: 688--767 Score: 137
Period size: 38 Copynumber: 2.0 Consensus size: 40
678 ATATATTCCT
688 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
*
728 ATGTAATA-CTATAATAACT-AAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
766 AT
1 AT
768 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 21 0.54
39 10 0.26
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:794 original size:25 final size:24
Alignment explanation
Indices: 758--804 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
748 AATACTTACA
758 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
782 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
805 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Found at i:1256 original size:203 final size:202
Alignment explanation
Indices: 847--1256 Score: 734
Period size: 203 Copynumber: 2.0 Consensus size: 202
837 TTCCTTAATA
*
847 ATAAATAAATTGGATCTTTAATATCTTTTATAATTTTGAAATTTTATTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTATTTGACATTGATCTAATTT
*
912 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATAATAGTA
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATAATAATA
977 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTCAGACTTAAGAAATTAATAACATTC
131 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTCAGACTTAAGAAATTAATAACATTC
1042 ACCATTG
196 ACCATTG
*
1049 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTATTTGACATTGATCTAATTT
*
1114 AATTTAATAATTCAACCACTAATGTTCAACTAATTTTTTTTTGGTATAGTT-TAATATATAATAA
66 AATTTAATAAATCAACCACTAATGTTCAACTAA-TTTTTTTTGGTATAGTTCT-ATATATAATAA
*
1178 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAA-AGAATTAATAACA
129 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTCAGACTTAAGA-AATTAATAACA
1242 TTCACCATTG
193 TTCACCATTG
1252 ATAAA
1 ATAAA
1257 GTTATTAAGC
Statistics
Matches: 200, Mismatches: 5, Indels: 5
0.95 0.02 0.02
Matches are distributed among these distances:
202 97 0.49
203 103 0.51
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (202 bp):
ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTATTTGACATTGATCTAATTT
AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATAATAATA
ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTCAGACTTAAGAAATTAATAACATTC
ACCATTG
Done.