Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012034.1 Corchorus capsularis cultivar CVL-1 contig12055, 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: 38446
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Found at i:3722 original size:25 final size:25
Alignment explanation
Indices: 3703--3797 Score: 172
Period size: 25 Copynumber: 3.8 Consensus size: 25
3693 TAAACGCTCA
*
3703 TGTGCTTGCGTTTGGCAAACGAGCC
1 TGTGCTTGCGTTTAGCAAACGAGCC
3728 TGTGCTTGCGTTTAGCAAACGAGCC
1 TGTGCTTGCGTTTAGCAAACGAGCC
3753 TGTGCTTGCGTTTAGCAAACGAGCC
1 TGTGCTTGCGTTTAGCAAACGAGCC
*
3778 TGTGCTTGCGTTTAGAAAAC
1 TGTGCTTGCGTTTAGCAAAC
3798 ACATAGGCTA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 68 1.00
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.29
Consensus pattern (25 bp):
TGTGCTTGCGTTTAGCAAACGAGCC
Found at i:4450 original size:34 final size:34
Alignment explanation
Indices: 4411--4475 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
4401 TCACACGAAA
*
4411 TTTCATATCAAATATTATTCTGTCATATTGATCT
1 TTTCATATCAAATATTATTCTATCATATTGATCT
4445 TTTCATATCAAATATTATTCTATCATATTGA
1 TTTCATATCAAATATTATTCTATCATATTGA
4476 ATATTATTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (34 bp):
TTTCATATCAAATATTATTCTATCATATTGATCT
Found at i:15068 original size:2 final size:2
Alignment explanation
Indices: 15061--15091 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15051 TGGGTCTTTA
15061 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 A
15092 GCGTTAAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18344 original size:1 final size:1
Alignment explanation
Indices: 18338--18371 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
18328 GTCATTGGAG
18338 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
18372 GCCCTCGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20171 original size:30 final size:30
Alignment explanation
Indices: 20132--20207 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 30
20122 TTTTTCTTCT
*
20132 TTGATATGTTTTGTTTCTGA-GAAATTACAAC
1 TTGA-ATGTTTTGTTTC-CACGAAATTACAAC
* *
20163 TTGAATG--TTCTTTCCACGAAATTACTAC
1 TTGAATGTTTTGTTTCCACGAAATTACAAC
*
20191 TTGAATTTTTTGTTTCC
1 TTGAATGTTTTGTTTCC
20208 CTTTAATCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
27 1 0.03
28 22 0.59
30 10 0.27
31 4 0.11
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.47
Consensus pattern (30 bp):
TTGAATGTTTTGTTTCCACGAAATTACAAC
Found at i:27059 original size:122 final size:121
Alignment explanation
Indices: 26843--27081 Score: 433
Period size: 122 Copynumber: 2.0 Consensus size: 121
26833 TTATATTTAT
* *
26843 ACATGTAAATCATGATTGAAGTTTTTCAGATATTTTTACTTGCTTTACATTACTTATTTTGAAGG
1 ACATGTAAATCATGATTGAAGTTTTTCAGATATTTTTACTTGCTTTACATTACTAATTATGAAGG
*
26908 GTTACCCATTCATTTGCTTTTGGATCTATAACAATTTTCTCTCTTTAAGCTCTTAA
66 GTTACCCATTCATTTGCTTTTGGATCTATAACAATTGTCTCTCTTTAAGCTCTTAA
*
26964 ACATGTGAATCATGATTGAAGTTTTTCAGATATTTTTCACTTGCTTTACATTACTAATTATGAAG
1 ACATGTAAATCATGATTGAAGTTTTTCAGATATTTTT-ACTTGCTTTACATTACTAATTATGAAG
27029 GGTTACCCATTCATTTGCTTTTGGATCTATAACAATTGTCTCTCTTTAAGCTC
65 GGTTACCCATTCATTTGCTTTTGGATCTATAACAATTGTCTCTCTTTAAGCTC
27082 CTAATAAACC
Statistics
Matches: 113, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
121 36 0.32
122 77 0.68
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (121 bp):
ACATGTAAATCATGATTGAAGTTTTTCAGATATTTTTACTTGCTTTACATTACTAATTATGAAGG
GTTACCCATTCATTTGCTTTTGGATCTATAACAATTGTCTCTCTTTAAGCTCTTAA
Found at i:30875 original size:12 final size:12
Alignment explanation
Indices: 30858--30882 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30848 TTATTTTCAA
30858 ATTATACAAAAC
1 ATTATACAAAAC
30870 ATTATACAAAAC
1 ATTATACAAAAC
30882 A
1 A
30883 ATAATAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
ATTATACAAAAC
Found at i:36393 original size:22 final size:21
Alignment explanation
Indices: 36368--36419 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
36358 CTACTCGGCC
*
36368 TCGACTCGAGAAAAATTCGGG
1 TCGACTCGAGAAAAATTCGAG
36389 TTCGACTC--GAAAAATTCGAG
1 -TCGACTCGAGAAAAATTCGAG
36409 TCGAGCTCGAG
1 TCGA-CTCGAG
36420 TATTTTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 4 0.15
20 14 0.54
22 8 0.31
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (21 bp):
TCGACTCGAGAAAAATTCGAG
Done.