Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012294.1 Corchorus capsularis cultivar CVL-1 contig12315, 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: 12413
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Found at i:603 original size:10 final size:10
Alignment explanation
Indices: 588--612 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
578 TAACTCCAAT
588 TATGGACTTA
1 TATGGACTTA
598 TATGGACTTA
1 TATGGACTTA
608 TATGG
1 TATGG
613 GCTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (10 bp):
TATGGACTTA
Found at i:765 original size:19 final size:18
Alignment explanation
Indices: 732--768 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
722 TTGAAATAGT
732 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
750 TCTTCAAATTATCTTCAAG
1 TCTTC-AATGATCTTCAAG
769 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:8578 original size:44 final size:44
Alignment explanation
Indices: 8524--8616 Score: 141
Period size: 44 Copynumber: 2.1 Consensus size: 44
8514 CATCCATAAT
* * * *
8524 TAAACACATAGTCTGGACACATCATCCACTGCTGAATAATACCA
1 TAAACACATAGTCTGAAAACAGCATACACTGCTGAATAATACCA
*
8568 TAAACACATAGTCTGAAAATAGCATACACTGCTGAATAATACCA
1 TAAACACATAGTCTGAAAACAGCATACACTGCTGAATAATACCA
8612 TAAAC
1 TAAAC
8617 TCCGAATACA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.23
Consensus pattern (44 bp):
TAAACACATAGTCTGAAAACAGCATACACTGCTGAATAATACCA
Found at i:8613 original size:20 final size:20
Alignment explanation
Indices: 8550--8613 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 20
8540 ACACATCATC
8550 CACTGCTGAATAATACCATAAA
1 CACTGCTGAATAATACCAT--A
*
8572 CACATAGTCTGAA-AATAGCATA
1 CAC-T-G-CTGAATAATACCATA
8594 CACTGCTGAATAATACCATA
1 CACTGCTGAATAATACCATA
8614 AACTCCGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
19 5 0.14
20 9 0.25
21 1 0.03
22 7 0.19
23 1 0.03
24 8 0.22
25 5 0.14
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.23
Consensus pattern (20 bp):
CACTGCTGAATAATACCATA
Found at i:8663 original size:80 final size:77
Alignment explanation
Indices: 8568--8713 Score: 220
Period size: 77 Copynumber: 1.9 Consensus size: 77
8558 AATAATACCA
* *
8568 TAAACACATAGTCTGAAAATAGCATACACTGCTGAATAATACCATAAACTCCGAATACAAGTACT
1 TAAACACATAGTCTGAAAATA-C-CA-ACTACTGAATAATACCATAAACTCCGAATACAAGTACT
8633 GAATAATAACATAAT
63 GAATAATAACATAAT
* * *
8648 TAAACACATTGTCTGAAAATACCAACTACTGAGTGATACCATAAACTCCGAATACAAGTACTGAA
1 TAAACACATAGTCTGAAAATACCAACTACTGAATAATACCATAAACTCCGAATACAAGTACTGAA
8713 T
66 T
8714 GATGATTAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
77 39 0.64
78 1 0.02
79 1 0.02
80 20 0.33
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.24
Consensus pattern (77 bp):
TAAACACATAGTCTGAAAATACCAACTACTGAATAATACCATAAACTCCGAATACAAGTACTGAA
TAATAACATAAT
Found at i:8702 original size:77 final size:72
Alignment explanation
Indices: 8568--8756 Score: 216
Period size: 77 Copynumber: 2.5 Consensus size: 72
8558 AATAATACCA
* * *
8568 TAAACACATAGTCTGAAAATAGCATACACTGCTGAATAATACCATAAACTCCGAATACAAGTACT
1 TAAACACATTGTCTGAAAATA-C-CA-ACTACTGAATAATACCATAAACTCCGAATACAAGTACT
8633 GAATAATAACATAAT
63 G---AAT--CATAAT
* *
8648 TAAACACATTGTCTGAAAATACCAACTACTGAGTGATACCATAAACTCCGAATACAAGTACTGAA
1 TAAACACATTGTCTGAAAATACCAACTACTGAATAATACCATAAACTCCGAATACAAGTACTGAA
* *
8713 TGATGAT
66 TCATAAT
8720 TAAACACATTGTCTGAGAATACTACCAACTACTGAAT
1 TAAACACATTGTCTGA-AA-A-TACCAACTACTGAAT
8757 GAAACCGAAT
Statistics
Matches: 98, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
72 20 0.20
73 2 0.02
74 4 0.04
75 14 0.14
77 36 0.37
78 1 0.01
79 1 0.01
80 20 0.20
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.25
Consensus pattern (72 bp):
TAAACACATTGTCTGAAAATACCAACTACTGAATAATACCATAAACTCCGAATACAAGTACTGAA
TCATAAT
Found at i:12287 original size:43 final size:43
Alignment explanation
Indices: 12239--12326 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
12229 ATTCTTAATC
* *
12239 GACTACTAGGTTAAGCCATTTATTTACTTAGTTACACCGAATT
1 GACTACTACGTTAAGCCATTTATTTACTTAATTACACCGAATT
*
12282 GACTACTACGTTAAGCCATTTATTTACTTAATTGCACCGAATT
1 GACTACTACGTTAAGCCATTTATTTACTTAATTACACCGAATT
12325 GA
1 GA
12327 GTTAATTACT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (43 bp):
GACTACTACGTTAAGCCATTTATTTACTTAATTACACCGAATT
Found at i:12354 original size:21 final size:21
Alignment explanation
Indices: 12330--12383 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
12320 GAATTGAGTT
12330 AATTACTTAATTTAATTACCA
1 AATTACTTAATTTAATTACCA
*
12351 AATTACTTAACTTAATTACCA
1 AATTACTTAATTTAATTACCA
* *
12372 ATTTTCTTAATT
1 AATTACTTAATT
12384 GCACCGAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTACTTAATTTAATTACCA
Done.