Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005969.1 Corchorus capsularis cultivar CVL-1 contig05987, 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: 10340
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:6199 original size:2 final size:2
Alignment explanation
Indices: 6192--6232 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
6182 ACTACTGAGT
6192 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6233 ACTTAAAGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6215 original size:19 final size:19
Alignment explanation
Indices: 6191--6229 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
6181 AACTACTGAG
6191 TTATATATATATATATATA
1 TTATATATATATATATATA
6210 TTATATATATATATATATA
1 TTATATATATATATATATA
6229 T
1 T
6230 ATAACTTAAA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTATATATATATATATATA
Found at i:6526 original size:31 final size:30
Alignment explanation
Indices: 6455--6536 Score: 76
Period size: 31 Copynumber: 2.6 Consensus size: 30
6445 GTCTATCAAC
* *
6455 TTTTGATTTGTTTAATTTAAGGCTTTCATT
1 TTTTTATTTGTTTAATTTAAGGCTTTAATT
* *
6485 TTAATTATTTGTTTAATTTAATGC-TTAATT
1 TT-TTTATTTGTTTAATTTAAGGCTTTAATT
*
6515 TGTTTTAATTTGTAATAATTTA
1 T-TTTT-ATTTGT-TTAATTTA
6537 GAATTGATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
30 10 0.24
31 25 0.60
32 7 0.17
ACGTcount: A:0.27, C:0.04, G:0.10, T:0.60
Consensus pattern (30 bp):
TTTTTATTTGTTTAATTTAAGGCTTTAATT
Found at i:9664 original size:85 final size:84
Alignment explanation
Indices: 9557--9899 Score: 429
Period size: 85 Copynumber: 4.0 Consensus size: 84
9547 CCAGTGTTAC
* * * * * *
9557 ATGTGTTTAGGGACTTTGATATAGATGCTTCTGTGTTATAAATGTGCTTGGGGCCTTTGAGAGAG
1 ATGTCTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTTAGAGAG
9622 AGTTGCCCCTGTGTTATAA
66 AGTTGCCCCTGTGTTATAA
* * * * * *
9641 TTGTACTTTGGGGACTTTAATATAAATGCCTTTGTGTTATAAATGTGTTTGAGGACTTTTAAAGA
1 ATGT-CTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTTAGAGA
*
9706 GAATTGCCCCTGTGTTATAA
65 GAGTTGCCCCTGTGTTATAA
* * * * *
9726 ATGTGTTTGGGGACACTTTGATATGGATGCCTCTGTGTTATAAGTGTGCTTGAGAACTTTAAAGA
1 ATGTCTTTGGGG--ACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTT-TAGA
9791 GAGAGTTGCCCCTGTGTTATAA
63 GAGAGTTGCCCCTGTGTTATAA
*
9813 ATGTGC-TTGGGGACTTTGATATAGATACCTCTGTGTTATAAATGTGCTTGAGGA-TTTTAGAGA
1 ATGT-CTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTTAGAGA
* * *
9876 GAGTTGCCCATGTGCTATAT
65 GAGTTGCCCCTGTGTTATAA
9896 ATGT
1 ATGT
9900 GCTTGAGGAT
Statistics
Matches: 220, Mismatches: 34, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
83 26 0.12
84 13 0.06
85 109 0.50
86 39 0.18
87 33 0.15
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (84 bp):
ATGTCTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTTAGAGAG
AGTTGCCCCTGTGTTATAA
Found at i:9854 original size:171 final size:168
Alignment explanation
Indices: 9557--9900 Score: 465
Period size: 171 Copynumber: 2.0 Consensus size: 168
9547 CCAGTGTTAC
* * ** *
9557 ATGTGTTTAGGGACTTTGATATAGATGCTTCTGTGTTATAAATGTGCTTGGGGCCTTTGAGAGAG
1 ATGTGTTTAGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGAACTTTAAGAGAG
* * *
9622 AGTTGCCCCTGTGTTATAATTGTACTTTGGGGACTTTAATATAAATGCCTTTGTGTTATAAATGT
66 AGTTGCCCCTGTGTTATAAATGTACTTTGGGGACTTTAATATAAATACCTCTGTGTTATAAATGT
* * *
9687 GTTTGAGGACTTTTAAAGAGAATTGCCCCTGTGTTATAA
131 GCTTGAGGA-TTTTAAAGAGAATTGCCCATGTGCTATAA
* * *
9726 ATGTGTTTGGGGACACTTTGATATGGATGCCTCTGTGTTATAAGTGTGCTTGAGAACTTTAAAGA
1 ATGTGTTTAGGG--ACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGAACTTT-AAGA
* * *
9791 GAGAGTTGCCCCTGTGTTATAAATGTGC-TTGGGGACTTTGATATAGATACCTCTGTGTTATAAA
63 GAGAGTTGCCCCTGTGTTATAAATGTACTTTGGGGACTTTAATATAAATACCTCTGTGTTATAAA
* * *
9855 TGTGCTTGAGGATTTTAGAGAGAGTTGCCCATGTGCTATAT
128 TGTGCTTGAGGATTTTAAAGAGAATTGCCCATGTGCTATAA
9896 ATGTG
1 ATGTG
9901 CTTGAGGATT
Statistics
Matches: 152, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
169 11 0.07
170 29 0.19
171 83 0.55
172 29 0.19
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (168 bp):
ATGTGTTTAGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGAACTTTAAGAGAG
AGTTGCCCCTGTGTTATAAATGTACTTTGGGGACTTTAATATAAATACCTCTGTGTTATAAATGT
GCTTGAGGATTTTAAAGAGAATTGCCCATGTGCTATAA
Found at i:9962 original size:42 final size:42
Alignment explanation
Indices: 9588--9954 Score: 233
Period size: 42 Copynumber: 8.6 Consensus size: 42
9578 TAGATGCTTC
* * * *
9588 TGTGTTATAAATGTGCTTGGGGCCTTTGAGAGAGAGTTGCCCC
1 TGTGCTATAAATGTGCTTGAGGACTTT-AGAGAGAGTTGCCCA
* * * * * * ** **
9631 TGTGTTATAATTGTACTTTGGGGACTTTA-ATATAAATGCCTT
1 TGTGCTATAAATGTGC-TTGAGGACTTTAGAGAGAGTTGCCCA
* * * * *
9673 TGTGTTATAAATGTGTTTGAGGACTTTTAAAGAGAATTGCCCC
1 TGTGCTATAAATGTGCTTGAGGAC-TTTAGAGAGAGTTGCCCA
* * * * *
9716 TGTGTTATAAATGTGTTTGGGGACACTTT-GATATG-GATGCCTC-
1 TGTGCTATAAATGTGCTTGAGG--ACTTTAGAGA-GAGTTGCC-CA
* * * *
9759 TGTGTTATAAGTGTGCTTGAGAACTTTAAAGAGAGAGTTGCCCC
1 TGTGCTATAAATGTGCTTGAGGACTTT--AGAGAGAGTTGCCCA
* * * * * *
9803 TGTGTTATAAATGTGCTTGGGGACTTT-GATATAGATACCTC-
1 TGTGCTATAAATGTGCTTGAGGACTTTAGAGAGAGTTGCC-CA
* *
9844 TGTGTTATAAATGTGCTTGAGGATTTTAGAGAGAGTTGCCCA
1 TGTGCTATAAATGTGCTTGAGGACTTTAGAGAGAGTTGCCCA
* * *
9886 TGTGCTATATATGTGCTTGAGGATTTTAGAGAGAGTTGCTCA
1 TGTGCTATAAATGTGCTTGAGGACTTTAGAGAGAGTTGCCCA
* *
9928 TGTGCTATATATGTGCTTGGGGACTTT
1 TGTGCTATAAATGTGCTTGAGGACTTT
9955 GGGGAGAGAG
Statistics
Matches: 262, Mismatches: 47, Indels: 31
0.77 0.14 0.09
Matches are distributed among these distances:
41 46 0.18
42 97 0.37
43 70 0.27
44 47 0.18
45 2 0.01
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.38
Consensus pattern (42 bp):
TGTGCTATAAATGTGCTTGAGGACTTTAGAGAGAGTTGCCCA
Done.