Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007619.1 Corchorus capsularis cultivar CVL-1 contig07640, 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: 10302
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:832 original size:24 final size:24
Alignment explanation
Indices: 784--834 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
774 AAATACTGTG
*
784 AAATTTTAATTATATATAATAATT
1 AAATTTTAATTAAATATAATAATT
*
808 AAATTTTAATTTAAATAT-ATTATT
1 AAATTTTAA-TTAAATATAATAATT
832 AAA
1 AAA
835 AATATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AAATTTTAATTAAATATAATAATT
Found at i:847 original size:27 final size:28
Alignment explanation
Indices: 817--871 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
807 TAAATTTTAA
817 TTTA-AATATATTATTAAAAATAT-TATT
1 TTTATAAT-TATTATTAAAAATATATATT
* *
844 TTTATAATTTTTATTAATAATATATATT
1 TTTATAATTATTATTAAAAATATATATT
872 ACTAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTATAATTATTATTAAAAATATATATT
Found at i:879 original size:20 final size:21
Alignment explanation
Indices: 856--907 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
846 TATAATTTTT
* *
856 ATTAATAATATAT-ATTACTA
1 ATTAATAATATATCAATAATA
*
876 ATTATTAATATATCAATAATA
1 ATTAATAATATATCAATAATA
897 ATTAAATAATA
1 ATT-AATAATA
908 GATGAACGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 12 0.46
21 8 0.31
22 6 0.23
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTAATAATATATCAATAATA
Found at i:4220 original size:114 final size:113
Alignment explanation
Indices: 4071--4333 Score: 437
Period size: 109 Copynumber: 2.3 Consensus size: 113
4061 ACTATTATAG
* *
4071 TTTTATTCTACTAGAAATTCTATTTTTC-TTCAATTAAATTAAATCTAATATCTTTATAATTACT
1 TTTTATTCTACTAAAAACTCTA-TTTTCATTC-ATTAAATTAAATCTAATATCTTTATAATTACT
4135 TTATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
64 TTATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
4185 TTTTATTCTACTAAAAACTCTATTTTCA-T--TT-AATTAAATCTAATATCTTTATAATTACTTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTCATTAAATTAAATCTAATATCTTTATAATTACTTT
*
4246 ATTTTTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 ATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
4294 TTTTATTCTACTAAAAACTCTATTTTCATTCCATTAAATT
1 TTTTATTCTACTAAAAACTCTATTTTCATT-CATTAAATT
4334 CAATATTTTA
Statistics
Matches: 140, Mismatches: 3, Indels: 12
0.90 0.02 0.08
Matches are distributed among these distances:
109 105 0.75
110 3 0.02
113 8 0.06
114 24 0.17
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.49
Consensus pattern (113 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTCATTAAATTAAATCTAATATCTTTATAATTACTTT
ATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:4267 original size:109 final size:109
Alignment explanation
Indices: 4071--4366 Score: 432
Period size: 109 Copynumber: 2.7 Consensus size: 109
4061 ACTATTATAG
* *
4071 TTTTATTCTACTAGAAATTCTATTTTTCTTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTAAATTAAATCTAATATCTTTATAATTACTT
4136 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
*
4185 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTAAATTAAATCTAATATCTTTATAATTACTTTATTT
*
4250 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
** * **
4294 TTTTATTCTACTAAAAACTCTATTTTCATTCCATTAAAT-TCAATATTTTATATAATTTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTAAATTAAATCT-AATATCTT-TATAA-TTACTTTA
4358 TTTTTACCA
63 TTTTTACCA
4367 TTTTAATTTA
Statistics
Matches: 170, Mismatches: 9, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
108 1 0.01
109 124 0.73
110 8 0.05
111 17 0.10
114 20 0.12
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTAAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:6117 original size:126 final size:126
Alignment explanation
Indices: 5892--6145 Score: 508
Period size: 126 Copynumber: 2.0 Consensus size: 126
5882 TTGGAGAGTT
5892 TGGGAAAAGGGACTATGGCATATGTATATCAACCAGAAGAAGTTTCCCCCACTGTCCTTACCAGA
1 TGGGAAAAGGGACTATGGCATATGTATATCAACCAGAAGAAGTTTCCCCCACTGTCCTTACCAGA
5957 ATAATAATGTTATAATGGCAATTGATGAAGCAGGCAGTTGGAGTTTAATGATTCTCTTTCC
66 ATAATAATGTTATAATGGCAATTGATGAAGCAGGCAGTTGGAGTTTAATGATTCTCTTTCC
6018 TGGGAAAAGGGACTATGGCATATGTATATCAACCAGAAGAAGTTTCCCCCACTGTCCTTACCAGA
1 TGGGAAAAGGGACTATGGCATATGTATATCAACCAGAAGAAGTTTCCCCCACTGTCCTTACCAGA
6083 ATAATAATGTTATAATGGCAATTGATGAAGCAGGCAGTTGGAGTTTAATGATTCTCTTTCC
66 ATAATAATGTTATAATGGCAATTGATGAAGCAGGCAGTTGGAGTTTAATGATTCTCTTTCC
6144 TG
1 TG
6146 TTTTTAATTA
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 128 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (126 bp):
TGGGAAAAGGGACTATGGCATATGTATATCAACCAGAAGAAGTTTCCCCCACTGTCCTTACCAGA
ATAATAATGTTATAATGGCAATTGATGAAGCAGGCAGTTGGAGTTTAATGATTCTCTTTCC
Done.