Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011063.1 Corchorus capsularis cultivar CVL-1 contig11084, 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: 5247
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Found at i:2733 original size:21 final size:21
Alignment explanation
Indices: 2707--2748 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2697 CTACACTGTC
* *
2707 TACTGGAGAGAGGTTGCTGCG
1 TACTGGACAGAGGTTCCTGCG
2728 TACTGGACAGAGGTTCCTGCG
1 TACTGGACAGAGGTTCCTGCG
2749 ATGGAGGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.24
Consensus pattern (21 bp):
TACTGGACAGAGGTTCCTGCG
Found at i:3169 original size:51 final size:51
Alignment explanation
Indices: 3075--3172 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
3065 ATTTACTTTG
*
3075 TCTTGTTATTTTTCTTCTTATTTCTGTGATTTGCATATGCATAGATGATCT
1 TCTTATTATTTTTCTTCTTATTTCTGTGATTTGCATATGCATAGATGATCT
* * * *
3126 TCTTATTATTTTTCTTCTTATTTTTGTGTTTTGGATTTGCATAGATG
1 TCTTATTATTTTTCTTCTTATTTCTGTGATTTGCATATGCATAGATG
3173 TCATGATAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.16, C:0.11, G:0.14, T:0.58
Consensus pattern (51 bp):
TCTTATTATTTTTCTTCTTATTTCTGTGATTTGCATATGCATAGATGATCT
Found at i:3720 original size:9 final size:9
Alignment explanation
Indices: 3706--3732 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
3696 TTATCCCGTA
3706 TATATATAT
1 TATATATAT
3715 TATATATAT
1 TATATATAT
3724 TATATATAT
1 TATATATAT
3733 ATTTAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TATATATAT
Found at i:3720 original size:11 final size:11
Alignment explanation
Indices: 3704--3735 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3694 TTTTATCCCG
3704 TATATATATA-
1 TATATATATAT
3714 T-TATATATAT
1 TATATATATAT
3724 TATATATATAT
1 TATATATATAT
3735 T
1 T
3736 TAATAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 8 0.40
10 2 0.10
11 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATATATAT
Found at i:4557 original size:2 final size:2
Alignment explanation
Indices: 4550--4588 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4540 GAAAGAATAA
4550 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4589 GTGTAATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4696 original size:2 final size:2
Alignment explanation
Indices: 4689--4730 Score: 59
Period size: 2 Copynumber: 20.5 Consensus size: 2
4679 CCTTTTCTGT
4689 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA GTA TA GTA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA T
4731 CCCTTAATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 1 0.03
2 32 0.86
3 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4713 original size:19 final size:20
Alignment explanation
Indices: 4689--4730 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
4679 CCTTTTCTGT
4689 TATATATATATAATATA-TA
1 TATATATATATAATATAGTA
*
4708 TATATATATATAGTATAGTA
1 TATATATATATAATATAGTA
4728 TAT
1 TAT
4731 CCCTTAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (20 bp):
TATATATATATAATATAGTA
Done.