Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020542.1 Corchorus olitorius cultivar O-4 contig20575, 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: 11140
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Found at i:2114 original size:27 final size:28
Alignment explanation
Indices: 2048--2121 Score: 125
Period size: 28 Copynumber: 2.7 Consensus size: 28
2038 ATGTGAACTT
2048 AAAATGACCAAAATGCCCCTGAACATGC
1 AAAATGACCAAAATGCCCCTGAACATGC
2076 AAAATGACCAAAATGCCCCTG-A-ATGC
1 AAAATGACCAAAATGCCCCTGAACATGC
2102 AAAAATGACCAAAATGCCCC
1 -AAAATGACCAAAATGCCCC
2122 CTAAATGACC
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
26 4 0.09
27 20 0.44
28 21 0.47
ACGTcount: A:0.45, C:0.28, G:0.14, T:0.14
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGAACATGC
Found at i:10989 original size:136 final size:135
Alignment explanation
Indices: 10689--11140 Score: 448
Period size: 139 Copynumber: 3.3 Consensus size: 135
10679 TTGCTGAAGA
* * * * * *
10689 TTTATTTCAGTTGATCCAGGGC-GATCTTTCCTTCCATTTATTTCAGCT-GATCCAGGGCGATTT
1 TTTATTTCAGTTGACCCAGGGCGGTTC-TT-CTTCAATTCATTTTA-ATGGATCCAGGGCGATTT
* * **
10752 TTCTTCAGTTCATTTTAATTGATCCAGGGCGATCTTTC-CTCA-ATTACTTCAGTTGATTCAGGG
63 TTCTTCAG-----TTTACTTGATCCAGGGCGATCTTTCTC-CAGATTATTTCAGTTGACCCAGGG
* * *
10815 TGATCTTTATTTCAG
122 CGGTCTTT-CTTCAG
10830 TTTATTTCAGTTGACCCAGGGCGGTTCTTCTTCAATTCATTTTAATGGATCCAGGGCGATCTTTT
1 TTTATTTCAGTTGACCCAGGGCGGTTCTTCTTCAATTCATTTTAATGGATCCAGGGCGAT-TTTT
* * *
10895 CTTCAGTTTACTTGACCCAGGGCGGTCTTTCTCCAGTTTATTTCAGTTGACCCAGGGCGGTCTTT
65 CTTCAGTTTACTTGATCCAGGGCGATCTTTCTCCAGATTATTTCAGTTGACCCAGGGCGGTCTTT
10960 CTTCAG
130 CTTCAG
* * * * * *
10966 TTGATTTTAGTTGACCCAAGGCGGTCCTTCTTCAATTCATTTTAATTGATCCAAGG-GATTTTTC
1 TTTATTTCAGTTGACCCAGGGCGGTTCTTCTTCAATTCATTTTAATGGATCCAGGGCGATTTTTC
* * * *
11030 TTCAATTTATTTCAGTTGATCCAGGGTGATCTTTCTTCAGAATATTTCAGTTGACCCAGGGCGGT
66 TTCAGTTTA---C--TTGATCCAGGGCGATCTTTCTCCAGATTATTTCAGTTGACCCAGGGCGGT
* *
11095 CTCTCTTCAA
126 CTTTCTTCAG
*
11105 TTTATTTCAGTTGACCCAGGGTGG-TCTTTCTTCAAT
1 TTTATTTCAGTTGACCCAGGGCGGTTC-TTCTTCAAT
Statistics
Matches: 264, Mismatches: 36, Indels: 24
0.81 0.11 0.07
Matches are distributed among these distances:
134 13 0.05
135 3 0.01
136 79 0.30
137 25 0.09
138 1 0.00
139 82 0.31
140 25 0.09
141 33 0.12
142 3 0.01
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (135 bp):
TTTATTTCAGTTGACCCAGGGCGGTTCTTCTTCAATTCATTTTAATGGATCCAGGGCGATTTTTC
TTCAGTTTACTTGATCCAGGGCGATCTTTCTCCAGATTATTTCAGTTGACCCAGGGCGGTCTTTC
TTCAG
Found at i:11131 original size:35 final size:35
Alignment explanation
Indices: 10688--11140 Score: 384
Period size: 35 Copynumber: 13.1 Consensus size: 35
10678 GTTGCTGAAG
*
10688 ATTTATTTCAGTTGATCCAGGGCGATCTTTCCTTCC
1 ATTTATTTCAGTTGATCCAGGGCGATCTTT-CTTCA
* *
10724 ATTTATTTCAGCTGATCCAGGGCGATTTTTCTTCA
1 ATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA
* * * * *
10759 GTTCATTTTAATTGATCCAGGGCGATCTTTCCTCA
1 ATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA
* * * *
10794 A-TTACTTCAGTTGATTCAGGGTGATCTTTATTTCA
1 ATTTATTTCAGTTGATCCAGGGCGATCTTT-CTTCA
* * *
10829 GTTTATTTCAGTTGACCCAGGGCGGT-TCTTCTTCA
1 ATTTATTTCAGTTGATCCAGGGCGATCT-TTCTTCA
* * * *
10864 ATTCATTTTAATGGATCCAGGGCGATCTTTTCTTCA
1 ATTTATTTCAGTTGATCCAGGGCGATC-TTTCTTCA
* * * *
10900 GTTTA---C--TTGACCCAGGGCGGTCTTTCTCCA
1 ATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA
* * *
10930 GTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCA
1 ATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA
* * * * * * *
10965 GTTGATTTTAGTTGACCCAAGGCGGTCCTTCTTCA
1 ATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA
* * * * *
11000 ATTCATTTTAATTGATCCAAGG-GATTTTTCTTCA
1 ATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA
*
11034 ATTTATTTCAGTTGATCCAGGGTGATCTTTCTTCA
1 ATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA
* * * *
11069 GA-ATATTTCAGTTGACCCAGGGCGGTCTCTCTTCA
1 -ATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA
* * *
11104 ATTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCA
1 ATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA
11139 AT
1 AT
Statistics
Matches: 339, Mismatches: 65, Indels: 27
0.79 0.15 0.06
Matches are distributed among these distances:
30 12 0.04
31 13 0.04
33 1 0.00
34 50 0.15
35 202 0.60
36 60 0.18
37 1 0.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (35 bp):
ATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA
Done.