Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002952.1 Corchorus olitorius cultivar O-4 contig02957, 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, 641
Length: 1069
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Found at i:685 original size:17 final size:17
Alignment explanation
Indices: 665--715 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
655 AACCAATTAA
665 CAATCTAAATTATATAT
1 CAATCTAAATTATATAT
682 CAAT-TCAAA-T-TA-A-
1 CAATCT-AAATTATATAT
695 CAATCTAAATTATATAT
1 CAATCTAAATTATATAT
712 CAAT
1 CAAT
716 TCAAATGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
13 7 0.25
14 3 0.11
15 4 0.14
16 3 0.11
17 11 0.39
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (17 bp):
CAATCTAAATTATATAT
Found at i:693 original size:30 final size:30
Alignment explanation
Indices: 659--721 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
649 CTACTAAACC
659 AATTAACAATCTAAATTATATATCAATTCA
1 AATTAACAATCTAAATTATATATCAATTCA
689 AATTAACAATCTAAATTATATATCAATTCA
1 AATTAACAATCTAAATTATATATCAATTCA
719 AAT
1 AAT
722 GATTATCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.37
Consensus pattern (30 bp):
AATTAACAATCTAAATTATATATCAATTCA
Found at i:721 original size:17 final size:17
Alignment explanation
Indices: 671--733 Score: 66
Period size: 17 Copynumber: 4.0 Consensus size: 17
661 TTAACAATCT
671 AAATTATATATCAATTC
1 AAATTATATATCAATTC
688 AAA-T-TA-A-CAA-TC
1 AAATTATATATCAATTC
700 TAAATTATATATCAATTC
1 -AAATTATATATCAATTC
*
718 AAATGAT-TATCAATTC
1 AAATTATATATCAATTC
734 TTACTATATT
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
12 2 0.05
13 6 0.15
14 2 0.05
15 4 0.10
16 11 0.28
17 12 0.31
18 2 0.05
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.38
Consensus pattern (17 bp):
AAATTATATATCAATTC
Found at i:746 original size:18 final size:18
Alignment explanation
Indices: 723--758 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
713 AATTCAAATG
723 ATTATCAATTCTTACTAT
1 ATTATCAATTCTTACTAT
741 ATTATCAATTCTTACTAT
1 ATTATCAATTCTTACTAT
759 CAATTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTATCAATTCTTACTAT
Found at i:790 original size:20 final size:20
Alignment explanation
Indices: 762--876 Score: 80
Period size: 20 Copynumber: 5.9 Consensus size: 20
752 TTACTATCAA
762 TTATTATTAATTTATATTAG
1 TTATTATTAATTTATATTAG
* * *
782 TTGTTATTAATTTCTATT-T
1 TTATTATTAATTTATATTAG
* *
801 TTATT-CT-ATTT-T-TT-T
1 TTATTATTAATTTATATTAG
* *
816 TTATTATTAAATTTTTATATCAA
1 TTATTATT-AA--TTTATATTAG
839 TTATTATTAATTTATATTAG
1 TTATTATTAATTTATATTAG
* *
859 TTGTTATTAATTTCTATT
1 TTATTATTAATTTATATT
877 TTTATTCTAT
Statistics
Matches: 75, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
15 8 0.11
16 2 0.03
17 4 0.05
18 2 0.03
19 4 0.05
20 43 0.57
21 1 0.01
22 3 0.04
23 8 0.11
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.64
Consensus pattern (20 bp):
TTATTATTAATTTATATTAG
Found at i:821 original size:77 final size:77
Alignment explanation
Indices: 747--926 Score: 324
Period size: 77 Copynumber: 2.3 Consensus size: 77
737 CTATATTATC
*
747 AATTCTTACTATCAATTATTATTAATTTATATTAGTTGTTATTAATTTCTATTTTTATTCTATTT
1 AATTTTTA-TATCAATTATTATTAATTTATATTAGTTGTTATTAATTTCTATTTTTATTCTATTT
812 TTTTTTATTATTA
65 TTTTTTATTATTA
825 AATTTTTATATCAATTATTATTAATTTATATTAGTTGTTATTAATTTCTATTTTTATTCTATTTT
1 AATTTTTATATCAATTATTATTAATTTATATTAGTTGTTATTAATTTCTATTTTTATTCTATTTT
890 TTTTTATTATTA
66 TTTTTATTATTA
* *
902 AATTTTTATATTATTTATTATTAAT
1 AATTTTTATATCAATTATTATTAAT
927 ACTTCTATTT
Statistics
Matches: 99, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
77 92 0.93
78 7 0.07
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.64
Consensus pattern (77 bp):
AATTTTTATATCAATTATTATTAATTTATATTAGTTGTTATTAATTTCTATTTTTATTCTATTTT
TTTTTATTATTA
Found at i:953 original size:16 final size:16
Alignment explanation
Indices: 932--964 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
922 TTAATACTTC
932 TATTTCTATTAGAATA
1 TATTTCTATTAGAATA
*
948 TATTTCTATTATAATA
1 TATTTCTATTAGAATA
964 T
1 T
965 TAATATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (16 bp):
TATTTCTATTAGAATA
Done.