Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019034.1 Corchorus olitorius cultivar O-4 contig19067, 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: 6229
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Found at i:569 original size:36 final size:36
Alignment explanation
Indices: 522--591 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
512 AAGATTTTGG
* *
522 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
* *
558 AGAAATATGATAACCAAAATCACGAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
592 GGTTATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.59, C:0.09, G:0.11, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:1713 original size:16 final size:16
Alignment explanation
Indices: 1692--1725 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1682 AAATGGTCAC
1692 TGATATGTATTCTTAT
1 TGATATGTATTCTTAT
*
1708 TGATATGTGTTCTTAT
1 TGATATGTATTCTTAT
1724 TG
1 TG
1726 GTTTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.06, G:0.18, T:0.56
Consensus pattern (16 bp):
TGATATGTATTCTTAT
Found at i:1771 original size:19 final size:19
Alignment explanation
Indices: 1747--1785 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1737 AATGGTGCAT
1747 GCTCTGTTTCTGGAAAATA
1 GCTCTGTTTCTGGAAAATA
1766 GCTCTGTTTCTGGAAAATA
1 GCTCTGTTTCTGGAAAATA
1785 G
1 G
1786 GCAGTAGTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (19 bp):
GCTCTGTTTCTGGAAAATA
Found at i:4751 original size:39 final size:40
Alignment explanation
Indices: 4687--4767 Score: 121
Period size: 39 Copynumber: 2.0 Consensus size: 40
4677 TTTAATTCCT
4687 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
4727 ATGTAATACTA-A-AATAACTGAAATACTTACATTGATTAA
1 ATGTAATA-TATATAATAACTAAAATACTTACATTAATTAA
4766 AT
1 AT
4768 TCTTAGGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
39 27 0.71
40 9 0.24
41 2 0.05
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.36
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:5230 original size:203 final size:203
Alignment explanation
Indices: 4877--5287 Score: 727
Period size: 203 Copynumber: 2.0 Consensus size: 203
4867 TTCCTTAATA
* *
4877 ATAAATAAATTGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTATTTGACATTGATCTAATTTA
*
4942 ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTATATATATATAATAGT
66 ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTATATATATATAATAAT
* * *
5007 AATGTGTTGTATCTTATTCACTACAATTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
131 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGCAATCTTAGACTTAAAAAATTAATAACACT
5072 CACCATTG
196 CACCATTG
5080 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTATTTGACATTGATCTAATTT
1 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTATTTGACATTGATCTAATTT
*
5145 AATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTTGGTATAG-T-TATATATATAATA
65 AATTTAATAAATCAACCACTAATGTTCAACTA-ATTTTTTTTGGTATAGTTATATATATATAATA
5208 ATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGCAATCTTAGACTTAAAAAATTAATAACA
129 ATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGCAATCTTAGACTTAAAAAATTAATAACA
5273 CTCACCATTG
194 CTCACCATTG
5283 ATAAA
1 ATAAA
5288 GTTATTAAGC
Statistics
Matches: 199, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
203 104 0.52
204 80 0.40
205 15 0.08
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (203 bp):
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTATTTGACATTGATCTAATTTA
ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTATATATATATAATAAT
AATGTGTTGTATCTTATTCACTACAACTTTGTTAGCAATCTTAGACTTAAAAAATTAATAACACT
CACCATTG
Found at i:5837 original size:36 final size:36
Alignment explanation
Indices: 5790--5859 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
5780 TGAGATTTTG
* *
5790 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
5826 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
5860 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.