Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009416.1 Corchorus capsularis cultivar CVL-1 contig09437, 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: 48518
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3888 original size:19 final size:19
Alignment explanation
Indices: 3866--3927 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
3856 GAATATTGAG
3866 GTTGAGTTTTGTTGGAATT
1 GTTGAGTTTTGTTGGAATT
* *
3885 GTTGA-TTTTGAATATTG-A-G
1 GTTGAGTTTTG--T-TGGAATT
3904 GTTGAGTTTTGTTGGAATT
1 GTTGAGTTTTGTTGGAATT
3923 GTTGA
1 GTTGA
3928 TTAAAATGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
17 2 0.06
18 7 0.21
19 15 0.45
20 7 0.21
21 2 0.06
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (19 bp):
GTTGAGTTTTGTTGGAATT
Found at i:3889 original size:38 final size:38
Alignment explanation
Indices: 3847--3929 Score: 166
Period size: 38 Copynumber: 2.2 Consensus size: 38
3837 TAGTGGGTAA
3847 GTTGATTTTGAATATTGAGGTTGAGTTTTGTTGGAATT
1 GTTGATTTTGAATATTGAGGTTGAGTTTTGTTGGAATT
3885 GTTGATTTTGAATATTGAGGTTGAGTTTTGTTGGAATT
1 GTTGATTTTGAATATTGAGGTTGAGTTTTGTTGGAATT
3923 GTTGATT
1 GTTGATT
3930 AAAATGTTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (38 bp):
GTTGATTTTGAATATTGAGGTTGAGTTTTGTTGGAATT
Found at i:22491 original size:33 final size:33
Alignment explanation
Indices: 22454--22518 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
22444 GACATTCCAA
*
22454 GTGATGTTACCAAATTATTCACTGTCTTTTAAG
1 GTGATGTTACCAAATTATTCACCGTCTTTTAAG
*
22487 GTGATTTTACCAAATTATTCACCGTCTTTTAA
1 GTGATGTTACCAAATTATTCACCGTCTTTTAA
22519 TAATTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (33 bp):
GTGATGTTACCAAATTATTCACCGTCTTTTAAG
Found at i:25052 original size:21 final size:20
Alignment explanation
Indices: 25028--25075 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
25018 TAGATCTAGA
* *
25028 TTTAATTTACTTTGCTTTGTT
1 TTTAATTTAATTT-CTTTCTT
* *
25049 TTTAGTCTAATTTCTTTCTT
1 TTTAATTTAATTTCTTTCTT
25069 TTTAATT
1 TTTAATT
25076 AATCTGTTTA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.17, C:0.10, G:0.06, T:0.67
Consensus pattern (20 bp):
TTTAATTTAATTTCTTTCTT
Found at i:29947 original size:5 final size:5
Alignment explanation
Indices: 29937--29976 Score: 53
Period size: 5 Copynumber: 7.4 Consensus size: 5
29927 TTAAAATTCC
29937 TATTT TATTTT TATTAT TATTAT TATTT TATTT TATTT TA
1 TATTT TA-TTT TATT-T TATT-T TATTT TATTT TATTT TA
29977 AAATTGGGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 17 0.52
6 16 0.48
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (5 bp):
TATTT
Found at i:31396 original size:16 final size:14
Alignment explanation
Indices: 31359--31402 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 14
31349 TATCTTTTTC
31359 TTTT-CTTTGCATTG
1 TTTTGCTTTG-ATTG
31373 TTTTGCTTTGATTG
1 TTTTGCTTTGATTG
31387 ATTATTGCTTTGATTG
1 -TT-TTGCTTTGATTG
31403 CTTGCCTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.30
15 7 0.26
16 12 0.44
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.61
Consensus pattern (14 bp):
TTTTGCTTTGATTG
Found at i:31518 original size:21 final size:21
Alignment explanation
Indices: 31489--31529 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31479 TATGACTCAT
31489 ATGCCTTGAA-TGCTATGATTG
1 ATGCCTTGAATTGCT-TGATTG
*
31510 ATGCTTTGAATTGCTTGATT
1 ATGCCTTGAATTGCTTGATT
31530 TGCTTGATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.44
Consensus pattern (21 bp):
ATGCCTTGAATTGCTTGATTG
Found at i:38375 original size:2 final size:2
Alignment explanation
Indices: 38368--38404 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
38358 TTTGGTTCGT
*
38368 TA TA TA TA TA TA TA TA TA TA TA TT TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38405 GATAGATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:40626 original size:51 final size:51
Alignment explanation
Indices: 40566--40668 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
40556 AAATGGGCTA
*
40566 AGATTATTGAGAAGTATGGTTTGCAGGAAAATAGTTTGCTCAAGAAGTTGC
1 AGATTATTGAGAAGTATGGTTTGCAGGAAAATAGTTGGCTCAAGAAGTTGC
40617 AGATTATTGAGAAGTATGGTTTGCAGGAAAATAGTTGGCTCAAGAAGTTGC
1 AGATTATTGAGAAGTATGGTTTGCAGGAAAATAGTTGGCTCAAGAAGTTGC
40668 A
1 A
40669 TTCCATTCGA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (51 bp):
AGATTATTGAGAAGTATGGTTTGCAGGAAAATAGTTGGCTCAAGAAGTTGC
Found at i:47191 original size:2 final size:2
Alignment explanation
Indices: 47184--47213 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
47174 AATTAAATTA
47184 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47214 GTTTGATCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.