Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016691.1 Corchorus olitorius cultivar O-4 contig16724, 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: 20686
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:2726 original size:21 final size:21
Alignment explanation
Indices: 2701--2741 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2691 ACATCATTGT
*
2701 TTTGGTACCCTAAACCATCAA
1 TTTGGAACCCTAAACCATCAA
* *
2722 TTTGGAACCCTTAACTATCA
1 TTTGGAACCCTAAACCATCA
2742 GATATCCCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.32
Consensus pattern (21 bp):
TTTGGAACCCTAAACCATCAA
Found at i:2888 original size:50 final size:50
Alignment explanation
Indices: 2834--2942 Score: 218
Period size: 50 Copynumber: 2.2 Consensus size: 50
2824 CTCTTGAGTA
2834 TCATTTGTAAATGTAATCAACATATTTGCCTACTCTCTTGAGTAGGGGCT
1 TCATTTGTAAATGTAATCAACATATTTGCCTACTCTCTTGAGTAGGGGCT
2884 TCATTTGTAAATGTAATCAACATATTTGCCTACTCTCTTGAGTAGGGGCT
1 TCATTTGTAAATGTAATCAACATATTTGCCTACTCTCTTGAGTAGGGGCT
2934 TCATTTGTA
1 TCATTTGTA
2943 GCAGCTTGCC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (50 bp):
TCATTTGTAAATGTAATCAACATATTTGCCTACTCTCTTGAGTAGGGGCT
Found at i:6303 original size:15 final size:15
Alignment explanation
Indices: 6279--6313 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6269 TCATCCCCAA
* *
6279 CACCAGCAGCTTCTT
1 CACCACCAGCTTCAT
6294 CACCACCAGCTTCAT
1 CACCACCAGCTTCAT
6309 CACCA
1 CACCA
6314 TCACCCGCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.46, G:0.09, T:0.20
Consensus pattern (15 bp):
CACCACCAGCTTCAT
Found at i:14105 original size:29 final size:31
Alignment explanation
Indices: 14061--14130 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
14051 TCTATCTTTC
*
14061 AATTG-TTGATTCGAATTGC-CATATCTTGTT
1 AATTGATTGATTCGAATTGCAAATAT-TTGTT
14091 -ATTGATTGATT-GAATTGCAAATATTTGTT
1 AATTGATTGATTCGAATTGCAAATATTTGTT
14120 AATTGATTGAT
1 AATTGATTGAT
14131 AGATTGTTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
29 16 0.44
30 20 0.56
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (31 bp):
AATTGATTGATTCGAATTGCAAATATTTGTT
Found at i:14125 original size:30 final size:31
Alignment explanation
Indices: 14053--14130 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 31
14043 TTGCTTATTC
* *
14053 TATCTT-TCAATTG-TTGATTCGAATTGCCA
1 TATCTTGTTAATTGATTGATTCGAATTGCAA
14082 TATCTTGTT-ATTGATTGATT-GAATTGCAAA
1 TATCTTGTTAATTGATTGATTCGAATTGC-AA
14112 TAT-TTGTTAATTGATTGAT
1 TATCTTGTTAATTGATTGAT
14131 AGATTGTTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
29 22 0.51
30 21 0.49
ACGTcount: A:0.27, C:0.09, G:0.15, T:0.49
Consensus pattern (31 bp):
TATCTTGTTAATTGATTGATTCGAATTGCAA
Found at i:19182 original size:15 final size:17
Alignment explanation
Indices: 19146--19185 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
19136 CAATTTTTTG
19146 TTTTTTGAAAACAATGAC
1 TTTTTTGAAAAC-ATGAC
19164 TTTTTTGAAAAC-T-AC
1 TTTTTTGAAAACATGAC
19179 TTTTTTG
1 TTTTTTG
19186 GACTCCTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.41
16 1 0.05
18 12 0.55
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (17 bp):
TTTTTTGAAAACATGAC
Done.