Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012712.1 Corchorus capsularis cultivar CVL-1 contig12733, 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: 3372
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Found at i:714 original size:11 final size:11
Alignment explanation
Indices: 698--729 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
688 GAAGTTCGTG
698 TTTGAAGATTA
1 TTTGAAGATTA
*
709 TTTGAAGATAA
1 TTTGAAGATTA
720 TTTGAAGATT
1 TTTGAAGATT
730 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:726 original size:22 final size:22
Alignment explanation
Indices: 698--757 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
688 GAAGTTCGTG
*
698 TTTGAAGATTATTTGAAGATAA
1 TTTGAAGATTATTTGAAGACAA
720 TTTGAAG---ATTTGAAGACAA
1 TTTGAAGATTATTTGAAGACAA
*
739 -TTGAAGAATTATTTCAAGA
1 TTTGAAG-ATTATTTGAAGA
758 AGCAAGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
22 15 0.47
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (22 bp):
TTTGAAGATTATTTGAAGACAA
Found at i:732 original size:19 final size:18
Alignment explanation
Indices: 708--745 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
698 TTTGAAGATT
*
708 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
727 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
745 A
1 A
746 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:766 original size:19 final size:19
Alignment explanation
Indices: 742--812 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 19
732 AAGACAATTG
742 AAGAATTATTTCAAGAAGC
1 AAGAATTATTTCAAGAAGC
*
761 AAGAATTGAAGATTTGAAGACAATTG-
1 AAGAATT----ATTTCAAG--AA--GC
787 AAGAATTATTTCAAGAAGC
1 AAGAATTATTTCAAGAAGC
806 AAGAATT
1 AAGAATT
813 GAAGATTTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 18
0.67 0.03 0.30
Matches are distributed among these distances:
18 1 0.02
19 14 0.34
20 2 0.05
22 7 0.17
23 7 0.17
25 2 0.05
26 7 0.17
27 1 0.02
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (19 bp):
AAGAATTATTTCAAGAAGC
Found at i:772 original size:45 final size:45
Alignment explanation
Indices: 721--821 Score: 202
Period size: 45 Copynumber: 2.2 Consensus size: 45
711 TGAAGATAAT
721 TTGAAGATTTGAAGACAATTGAAGAATTATTTCAAGAAGCAAGAA
1 TTGAAGATTTGAAGACAATTGAAGAATTATTTCAAGAAGCAAGAA
766 TTGAAGATTTGAAGACAATTGAAGAATTATTTCAAGAAGCAAGAA
1 TTGAAGATTTGAAGACAATTGAAGAATTATTTCAAGAAGCAAGAA
811 TTGAAGATTTG
1 TTGAAGATTTG
822 GAGCTTATTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.29
Consensus pattern (45 bp):
TTGAAGATTTGAAGACAATTGAAGAATTATTTCAAGAAGCAAGAA
Found at i:802 original size:22 final size:22
Alignment explanation
Indices: 727--802 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
717 TAATTTGAAG
*
727 ATTTGAAGACAATTGAAGAATT
1 ATTTCAAGACAATTGAAGAATT
*
749 ATTTCAAGAAGCAA--GAATTGAA-G
1 ATTTCAAG-A-CAATTGAA--GAATT
*
772 ATTTGAAGACAATTGAAGAATT
1 ATTTCAAGACAATTGAAGAATT
794 ATTTCAAGA
1 ATTTCAAGA
803 AGCAAGAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
21 6 0.14
22 19 0.45
23 11 0.26
24 6 0.14
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.29
Consensus pattern (22 bp):
ATTTCAAGACAATTGAAGAATT
Done.