Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011869.1 Corchorus capsularis cultivar CVL-1 contig11890, 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: 32553
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:8554 original size:33 final size:33
Alignment explanation
Indices: 8503--8567 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
8493 GATGAAATAG
*
8503 CCTCACCATATGGTGGGGCGCATTACCCATGCA
1 CCTCACCATATGGCGGGGCGCATTACCCATGCA
* *
8536 CCTCGCCATATGGCGGGGCGCATTATCCATGC
1 CCTCACCATATGGCGGGGCGCATTACCCATGC
8568 GCACTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.18, C:0.34, G:0.26, T:0.22
Consensus pattern (33 bp):
CCTCACCATATGGCGGGGCGCATTACCCATGCA
Found at i:15084 original size:46 final size:46
Alignment explanation
Indices: 15031--15189 Score: 142
Period size: 46 Copynumber: 3.4 Consensus size: 46
15021 TGATTTCTAA
15031 GCCTTCCAGTGGAAATTGATTGTTAAGAATAATAGGGATAGCATAT
1 GCCTTCCAGTGGAAATTGATTGTTAAGAATAATAGGGATAGCATAT
* * ** ** ** ** *
15077 GCCTTCCAGTGAATAATTG-TTCTTAATGCTTTGTTCTTAATGATTTC-TAA
1 GCCTTCCAGTGGA-AATTGATTGTTAA-G----AATAATAGGGATAGCATAT
*
15127 GCCTTCCAGTGGAAATTGATTGTTAAGAATAATAGGGATAGTATAT
1 GCCTTCCAGTGGAAATTGATTGTTAAGAATAATAGGGATAGCATAT
15173 GCCTTCCAGTGGAAATT
1 GCCTTCCAGTGGAAATT
15190 CTATCTAATA
Statistics
Matches: 82, Mismatches: 23, Indels: 16
0.68 0.19 0.13
Matches are distributed among these distances:
45 6 0.07
46 37 0.45
47 6 0.07
49 6 0.07
50 20 0.24
51 7 0.09
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (46 bp):
GCCTTCCAGTGGAAATTGATTGTTAAGAATAATAGGGATAGCATAT
Found at i:15099 original size:96 final size:96
Alignment explanation
Indices: 14989--15183 Score: 381
Period size: 96 Copynumber: 2.0 Consensus size: 96
14979 GTATGCATGT
14989 GTGAATAATTGTTCTTAATGCTTTGTTCTTAATGATTTCTAAGCCTTCCAGTGGAAATTGATTGT
1 GTGAATAATTGTTCTTAATGCTTTGTTCTTAATGATTTCTAAGCCTTCCAGTGGAAATTGATTGT
15054 TAAGAATAATAGGGATAGCATATGCCTTCCA
66 TAAGAATAATAGGGATAGCATATGCCTTCCA
15085 GTGAATAATTGTTCTTAATGCTTTGTTCTTAATGATTTCTAAGCCTTCCAGTGGAAATTGATTGT
1 GTGAATAATTGTTCTTAATGCTTTGTTCTTAATGATTTCTAAGCCTTCCAGTGGAAATTGATTGT
*
15150 TAAGAATAATAGGGATAGTATATGCCTTCCA
66 TAAGAATAATAGGGATAGCATATGCCTTCCA
15181 GTG
1 GTG
15184 GAAATTCTAT
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (96 bp):
GTGAATAATTGTTCTTAATGCTTTGTTCTTAATGATTTCTAAGCCTTCCAGTGGAAATTGATTGT
TAAGAATAATAGGGATAGCATATGCCTTCCA
Found at i:18944 original size:18 final size:18
Alignment explanation
Indices: 18921--18956 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
18911 TATATAAAGG
18921 CTCCCTTTTCCCTAACAC
1 CTCCCTTTTCCCTAACAC
18939 CTCCCTTTTCCCTAACAC
1 CTCCCTTTTCCCTAACAC
18957 ATAGGACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (18 bp):
CTCCCTTTTCCCTAACAC
Found at i:21212 original size:16 final size:18
Alignment explanation
Indices: 21182--21215 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
21172 GAATTCTAAA
21182 ATCAAAATCGTTCGAAAT
1 ATCAAAATCGTTCGAAAT
21200 ATCAAAAT-G-TCGAAAT
1 ATCAAAATCGTTCGAAAT
21216 GTCCGGGTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (18 bp):
ATCAAAATCGTTCGAAAT
Found at i:21858 original size:21 final size:22
Alignment explanation
Indices: 21834--21880 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
21824 TAAGTGAGTC
*
21834 TGATTTGAAT-TTGAAAAC-CTT
1 TGATTTAAATCTTGAAAACTC-T
21855 TGA-TTAAATCTTGAAAACTCT
1 TGATTTAAATCTTGAAAACTCT
21876 TGATT
1 TGATT
21881 ACTAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 5 0.23
21 15 0.68
22 2 0.09
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.43
Consensus pattern (22 bp):
TGATTTAAATCTTGAAAACTCT
Found at i:27299 original size:20 final size:20
Alignment explanation
Indices: 27274--27312 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27264 AAAAAGAGCA
*
27274 CCAATTTGCAAATCAAATGT
1 CCAATTCGCAAATCAAATGT
*
27294 CCAATTCGTAAATCAAATG
1 CCAATTCGCAAATCAAATG
27313 CCTTGTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (20 bp):
CCAATTCGCAAATCAAATGT
Found at i:27859 original size:27 final size:27
Alignment explanation
Indices: 27813--27885 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
27803 AAGTGAACTT
*
27813 AAAATGACCAAAATACCCCCT-AA-ATG
1 AAAATGACCAAAAT-GCCCCTGAACATG
*
27839 CAAAAATGGCCAAAATGCCCCTGAACATG
1 --AAAATGACCAAAATGCCCCTGAACATG
27868 AAAATGACCAAAATGCCC
1 AAAATGACCAAAATGCCC
27886 TTATGTGACC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 22 0.55
28 15 0.38
29 3 0.08
ACGTcount: A:0.47, C:0.27, G:0.12, T:0.14
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAACATG
Found at i:28227 original size:21 final size:21
Alignment explanation
Indices: 28193--28236 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
28183 AGATTTGAGA
28193 AATAATAAAAGAATATAAAAT
1 AATAATAAAAGAATATAAAAT
*
28214 AATAA-AAAACGAATTTAAAAT
1 AATAATAAAA-GAATATAAAAT
28235 AA
1 AA
28237 ATATTTACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (21 bp):
AATAATAAAAGAATATAAAAT
Done.