Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009539.1 Corchorus capsularis cultivar CVL-1 contig09560, 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: 24643
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--55 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1 ATA
4 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
46 CT CT CT CT CT
1 CT CT CT CT CT
56 TTTTTCCCCC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4975 original size:12 final size:13
Alignment explanation
Indices: 4958--4986 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4948 TGTTAAGAGG
4958 TTTTCTTTTTCT-
1 TTTTCTTTTTCTA
4970 TTTTCTTTTTCTA
1 TTTTCTTTTTCTA
4983 TTTT
1 TTTT
4987 TGCTTTGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTTTTTCTA
Found at i:6480 original size:21 final size:21
Alignment explanation
Indices: 6454--6497 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
6444 AAAGAAGGGG
*
6454 TTGCTAAAT-ACCGTCCTATTT
1 TTGCT-AATCACCGTCCCATTT
*
6475 TTGCTATTCACCGTCCCATTT
1 TTGCTAATCACCGTCCCATTT
6496 TT
1 TT
6498 TACACTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.27, G:0.09, T:0.45
Consensus pattern (21 bp):
TTGCTAATCACCGTCCCATTT
Found at i:6702 original size:33 final size:32
Alignment explanation
Indices: 6643--6726 Score: 105
Period size: 33 Copynumber: 2.6 Consensus size: 32
6633 TAGTACCGGT
* *
6643 GCCGCCCCAGGAGGCGGTCTATCCATGATAGG
1 GCCGCCCCAGGAGGCGGCCTAGCCATGATAGG
* * *
6675 GCCGCCCCAGGGAGGCGGCCTGGCCATGTTAGT
1 GCCGCCCCA-GGAGGCGGCCTAGCCATGATAGG
6708 GCCGCCCCAGGAGGGCGGC
1 GCCGCCCCAGGA-GGCGGC
6727 TGAGCAATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
32 12 0.27
33 33 0.73
ACGTcount: A:0.14, C:0.35, G:0.39, T:0.12
Consensus pattern (32 bp):
GCCGCCCCAGGAGGCGGCCTAGCCATGATAGG
Found at i:6740 original size:33 final size:34
Alignment explanation
Indices: 6641--6740 Score: 102
Period size: 33 Copynumber: 3.1 Consensus size: 34
6631 TTTAGTACCG
* * *
6641 GTGCCGCCCCAGGA-GGCGGTCT-ATCCATGATA
1 GTGCCGCCCCAGGAGGGCGGCCTGAGCCATGTTA
*
6673 GGGCCGCCCCAGG-GAGGCGGCCTG-GCCATGTTA
1 GTGCCGCCCCAGGAG-GGCGGCCTGAGCCATGTTA
* *
6706 GTGCCGCCCCAGGAGGGCGG-CTGAGCAATTTTA
1 GTGCCGCCCCAGGAGGGCGGCCTGAGCCATGTTA
6739 GT
1 GT
6741 AAAAAAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
32 15 0.27
33 40 0.71
34 1 0.02
ACGTcount: A:0.16, C:0.30, G:0.37, T:0.17
Consensus pattern (34 bp):
GTGCCGCCCCAGGAGGGCGGCCTGAGCCATGTTA
Found at i:22272 original size:3 final size:3
Alignment explanation
Indices: 22264--22289 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
22254 AGAGAAGACA
22264 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
22290 AAATCACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:24258 original size:2 final size:2
Alignment explanation
Indices: 24251--24288 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
24241 GAGTGCTGCA
24251 AT AT AT AT 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 AT AT AT AT
24289 TCATAATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.