Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012168.1 Corchorus capsularis cultivar CVL-1 contig12189, 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: 11150
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.30
Found at i:364 original size:130 final size:129
Alignment explanation
Indices: 68--324 Score: 325
Period size: 129 Copynumber: 2.0 Consensus size: 129
58 AAGGATAGCT
** * * * * * *
68 CATGTTATAACTTGTCATAACATTCATTCGCATCAATTGCATAAAGGCAAGAACCCTGATTATTC
1 CATGTTATAAAATCTCATAACATACATTGGAAACAATAGCATAAAGGCAAGAACCCTGATTATTC
* *
133 ACAGAATTGTAAATGGTCACGGCTTTTGACTTGTGGAAGTTCCTACCAAATTGTGGAGGGACCC
66 ACAGAATTGTAAATGGTCACGACTTTTGACTTGTGCAAGTTCCTACCAAATTGTGGAGGGACCC
** * * * * *
197 CATGTTATAACTTGTCATAACATTCATTTGCATCAATAGCATAAAGGCAAGAACCCTGATTATTC
1 CATGTTATAAAATCTCATAACATACATTGGAAACAATAGCATAAAGGCAAGAACCCTGATTATTC
* * *
262 ACGGAATTTGTAAATGGTCACGACTTTTGGCTTGTGCAAGTTCTTACCAAATTGTGGAGGGAC
66 ACAGAA-TTGTAAATGGTCACGACTTTTGACTTGTGCAAGTTCCTACCAAATTGTGGAGGGAC
325 TCCACACCTT
Statistics
Matches: 120, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
129 68 0.57
130 52 0.43
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (129 bp):
CATGTTATAAAATCTCATAACATACATTGGAAACAATAGCATAAAGGCAAGAACCCTGATTATTC
ACAGAATTGTAAATGGTCACGACTTTTGACTTGTGCAAGTTCCTACCAAATTGTGGAGGGACCC
Found at i:2985 original size:12 final size:11
Alignment explanation
Indices: 2962--3003 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
2952 GCCGAGTCGT
2962 AAAA-AAAAAA
1 AAAACAAAAAA
2972 AAAACAACAAAA
1 AAAACAA-AAAA
2984 AAAACAAAAAA
1 AAAACAAAAAA
2995 CAAAA-AAAA
1 -AAAACAAAA
3004 CCAAAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.14
11 10 0.34
12 15 0.52
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAA
Found at i:2985 original size:16 final size:16
Alignment explanation
Indices: 2963--3009 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 16
2953 CCGAGTCGTA
*
2963 AAAAAAAAAAAAACAAC
1 AAAAAAAACAAAA-AAC
2980 AAAAAAAACAAAAAAC
1 AAAAAAAACAAAAAAC
2996 AAAAAAAACCAAAA
1 AAAAAAAA-CAAAA
3010 TTTTGCAACG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAACAAAAAAC
Found at i:2986 original size:19 final size:18
Alignment explanation
Indices: 2962--3003 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
2952 GCCGAGTCGT
2962 AAAAAAAAAAAAAACAACA
1 AAAAAAAAAAAAAACAA-A
*
2981 AAAAAAACAAAAAACAAA
1 AAAAAAAAAAAAAACAAA
2999 AAAAA
1 AAAAA
3004 CCAAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAAACAAA
Found at i:5029 original size:20 final size:20
Alignment explanation
Indices: 4990--5029 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4980 AAACAACTAT
* * *
4990 CCACCCCTTCAAACTCCTCC
1 CCACCCCTCCAAAATACTCC
5010 CCACCCCTCCAAAATACTCC
1 CCACCCCTCCAAAATACTCC
5030 AACCAAACAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.57, G:0.00, T:0.17
Consensus pattern (20 bp):
CCACCCCTCCAAAATACTCC
Found at i:7150 original size:2 final size:2
Alignment explanation
Indices: 7138--7185 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
7128 GATTGCTAGC
* *
7138 AT AT AT GT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7179 -T AT AT AT
1 AT AT AT AT
7186 TACATGTTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8753 original size:17 final size:19
Alignment explanation
Indices: 8731--8773 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
8721 TGGCCATCTC
8731 AAGAAAGAC-T-GTCCGAA
1 AAGAAAGACTTGGTCCGAA
* *
8748 AAGAAAGGCTTGGTTCGAA
1 AAGAAAGACTTGGTCCGAA
8767 AAGAAAG
1 AAGAAAG
8774 GTACATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 8 0.36
18 1 0.05
19 13 0.59
ACGTcount: A:0.47, C:0.12, G:0.28, T:0.14
Consensus pattern (19 bp):
AAGAAAGACTTGGTCCGAA
Done.