Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014542.1 Corchorus olitorius cultivar O-4 contig14575, 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: 5453
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Found at i:835 original size:194 final size:195
Alignment explanation
Indices: 470--853 Score: 594
Period size: 195 Copynumber: 2.0 Consensus size: 195
460 GTTTAAAGAC
470 TACAAGTTTCAAAAAAAAAAAATCAGGAGGAAAAATGTCCCTTTTGTAAAAATGTACAATTAATT
1 TACAAGTTTCAAAAAAAAAAAATCAGGAGGAAAAATGTCCCTTTTGTAAAAATGTACAATTAATT
*
535 ATATATACATATTGATGCACCCGAGTTGTTAACTCAACTGGTGAGTGCACTATGCTTGAACTGTG
66 ATATATACATATTGATGCACCCGAGTTGTTAACTCAACTGATGAGTGCACTATGCTTGAACTGTG
*
600 AGGTCCTTGGTTCAAATCTCAAGAAATTTGAGTTTAA-TTTTTTGTTTATTTCTTTGGTAAGCAA
131 AGGTCCTGGGTTCAAATCTCAAGAAATTTGAGTTTAATTTTTTTGTTTATTTCTTTGGTAAGCAA
* * * * * * *
664 TACAAG-TTCCAAAATAAAAATTCAGGGGGAAAAATGTTCCTTTTGTAAAAGTGTATAATTAATT
1 TACAAGTTTCAAAAAAAAAAAATCAGGAGGAAAAATGTCCCTTTTGTAAAAATGTACAATTAATT
* * **
728 ACATATATACATATTGATGGACCTGAGTTGTTAACTCAACTGATGAGTGCACTATGCTTG-GTTG
66 --ATATATACATATTGATGCACCCGAGTTGTTAACTCAACTGATGAGTGCACTATGCTTGAACTG
* *
792 TGAGGTCCTGGGTTCAAGTCTCAAGAAATTTGAGTTTAATTTTTTTGTTTATTTGTTTGGTA
129 TGAGGTCCTGGGTTCAAATCTCAAGAAATTTGAGTTTAATTTTTTTGTTTATTTCTTTGGTA
854 GTTTGGTAAG
Statistics
Matches: 172, Mismatches: 15, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
193 51 0.30
194 45 0.26
195 76 0.44
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (195 bp):
TACAAGTTTCAAAAAAAAAAAATCAGGAGGAAAAATGTCCCTTTTGTAAAAATGTACAATTAATT
ATATATACATATTGATGCACCCGAGTTGTTAACTCAACTGATGAGTGCACTATGCTTGAACTGTG
AGGTCCTGGGTTCAAATCTCAAGAAATTTGAGTTTAATTTTTTTGTTTATTTCTTTGGTAAGCAA
Found at i:1736 original size:31 final size:31
Alignment explanation
Indices: 1700--1759 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1690 GTTAATTAAA
*
1700 TCCCTAACGTTATAAATTCGACTCAAATCTG
1 TCCCTAACGTTATAAAATCGACTCAAATCTG
* *
1731 TCCCTAACGTTGTAAAATCGGCTCAAATC
1 TCCCTAACGTTATAAAATCGACTCAAATC
1760 AGTGCCTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.30
Consensus pattern (31 bp):
TCCCTAACGTTATAAAATCGACTCAAATCTG
Found at i:3866 original size:2 final size:2
Alignment explanation
Indices: 3859--3883 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3849 TTCCTATGTA
3859 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3884 ATAACTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3936 original size:41 final size:40
Alignment explanation
Indices: 3875--3952 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 40
3865 ATATATATAT
3875 ATATATATAATAACTAAAATACTTACATTAATTAAATGTA
1 ATATATATAATAACTAAAATACTTACATTAATTAAATGTA
*
3915 ATATACTATAATAACTGAAATACTTACATTAATTAAAT
1 ATATA-TATAATAACTAAAATACTTACATTAATTAAAT
3953 TCTTAGATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 5 0.14
41 31 0.86
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (40 bp):
ATATATATAATAACTAAAATACTTACATTAATTAAATGTA
Found at i:3982 original size:24 final size:23
Alignment explanation
Indices: 3943--3988 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
3933 AATACTTACA
3943 TTAATTAAATTCTTAGATATTTT
1 TTAATTAAATTCTTAGATATTTT
* *
3966 TTAATTCAAATTTTTAGGTATTT
1 TTAATT-AAATTCTTAGATATTT
3989 GTGCGAACGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (23 bp):
TTAATTAAATTCTTAGATATTTT
Found at i:4428 original size:203 final size:202
Alignment explanation
Indices: 4063--4472 Score: 725
Period size: 203 Copynumber: 2.0 Consensus size: 202
4053 TTCCTTAATA
4063 ATAAATAAATCGGATATTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCGGATATTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
*
4128 ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGGTATAGTTCTATATATATAATAGTA
66 ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGGTATAGTTCTATATATATAATAATA
*
4193 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
131 ATGTGTTGTATCTTATTCACTACAACTTTGTTAATAATCTTAGACTTAAAAAATTAATAACATTC
4258 ACCATTG
196 ACCATTG
*
4265 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGAT-ATTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* *
4330 AATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTGTGGTATAGTT-T-TATATATGATA
65 AATTTAATAAATCAACCACTAATGTTCAACTA-ATTTTTT-TGGTATAGTTCTATATATATAATA
*
4393 ATAATGTGTTGTATCTTATTTACTACAACTTTGTTAATAATCTTAGACTTAAAAAATTAATAACA
128 ATAATGTGTTGTATCTTATTCACTACAACTTTGTTAATAATCTTAGACTTAAAAAATTAATAACA
4458 TTCACCATTG
193 TTCACCATTG
4468 ATAAA
1 ATAAA
4473 GTTATTAAGC
Statistics
Matches: 199, Mismatches: 6, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
202 15 0.08
203 167 0.84
204 7 0.04
205 10 0.05
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.44
Consensus pattern (202 bp):
ATAAATAAATCGGATATTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGGTATAGTTCTATATATATAATAATA
ATGTGTTGTATCTTATTCACTACAACTTTGTTAATAATCTTAGACTTAAAAAATTAATAACATTC
ACCATTG
Found at i:5041 original size:36 final size:36
Alignment explanation
Indices: 4994--5063 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
4984 GAGGTTTTGG
* *
4994 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
5030 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
5064 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Done.