Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012722.1 Corchorus capsularis cultivar CVL-1 contig12743, 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: 15694
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:1068 original size:2 final size:2
Alignment explanation
Indices: 1063--1094 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1053 TAAACATGAA
1063 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1095 GTCTTAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2818 original size:16 final size:16
Alignment explanation
Indices: 2793--2832 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2783 AACCCACCCG
*
2793 AACCCAAAAAAGCTCA
1 AACCCGAAAAAGCTCA
* *
2809 AACCCGAAAAATCTGA
1 AACCCGAAAAAGCTCA
2825 AACCCGAA
1 AACCCGAA
2833 CCTGAAGCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.53, C:0.30, G:0.10, T:0.07
Consensus pattern (16 bp):
AACCCGAAAAAGCTCA
Found at i:3107 original size:32 final size:32
Alignment explanation
Indices: 3037--3143 Score: 133
Period size: 32 Copynumber: 3.3 Consensus size: 32
3027 CCAATCCGAG
* * * * *
3037 CCCGAACCCGAATTAATCAGACCGAAAATTGA
1 CCCGAACCCGAATCAACCAGACCCAAATTTAA
* *
3069 CGCGAACCCGAATCAACCTGACCCAAATTTAA
1 CCCGAACCCGAATCAACCAGACCCAAATTTAA
* *
3101 CCCGAACCCAAATCAACCCGACCCAAATTTAA
1 CCCGAACCCGAATCAACCAGACCCAAATTTAA
3133 CCCGAACCCGA
1 CCCGAACCCGA
3144 TGACCCGAAC
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.38, C:0.36, G:0.12, T:0.13
Consensus pattern (32 bp):
CCCGAACCCGAATCAACCAGACCCAAATTTAA
Found at i:3111 original size:17 final size:17
Alignment explanation
Indices: 3089--3141 Score: 83
Period size: 16 Copynumber: 3.2 Consensus size: 17
3079 AATCAACCTG
3089 ACCCAAATTTAACCCGA
1 ACCCAAATTTAACCCGA
*
3106 ACCCAAA-TCAACCCG-
1 ACCCAAATTTAACCCGA
3121 ACCCAAATTTAACCCGA
1 ACCCAAATTTAACCCGA
3138 ACCC
1 ACCC
3142 GATGACCCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 7 0.22
16 14 0.44
17 11 0.34
ACGTcount: A:0.40, C:0.42, G:0.06, T:0.13
Consensus pattern (17 bp):
ACCCAAATTTAACCCGA
Found at i:3118 original size:16 final size:17
Alignment explanation
Indices: 3071--3141 Score: 78
Period size: 16 Copynumber: 4.4 Consensus size: 17
3061 AAAATTGACG
*
3071 CGAACCCGAA-TCAACC
1 CGAACCCAAATTCAACC
* *
3087 TG-ACCCAAATTTAACC
1 CGAACCCAAATTCAACC
3103 CGAACCCAAA-TCAACC
1 CGAACCCAAATTCAACC
*
3119 CG-ACCCAAATTTAACC
1 CGAACCCAAATTCAACC
3135 CGAACCC
1 CGAACCC
3142 GATGACCCGA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
15 13 0.29
16 21 0.47
17 11 0.24
ACGTcount: A:0.38, C:0.41, G:0.08, T:0.13
Consensus pattern (17 bp):
CGAACCCAAATTCAACC
Found at i:3126 original size:15 final size:15
Alignment explanation
Indices: 3074--3128 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
3064 ATTGACGCGA
* *
3074 ACCCGAATCAACCTG
1 ACCCAAATCAACCCG
*
3089 ACCCAAATTTAACCCG
1 ACCCAAA-TCAACCCG
3105 AACCCAAATCAACCCG
1 -ACCCAAATCAACCCG
3121 ACCCAAAT
1 ACCCAAAT
3129 TTAACCCGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 14 0.41
16 13 0.38
17 7 0.21
ACGTcount: A:0.40, C:0.40, G:0.07, T:0.13
Consensus pattern (15 bp):
ACCCAAATCAACCCG
Found at i:5950 original size:33 final size:33
Alignment explanation
Indices: 5874--5952 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
5864 TAGACAAAGG
* *
5874 GTCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA
1 GTCGCGTGGCCGGTTGTAGCCGGCCATGGCCGA
** *
5907 GTCGTTTGGCCGGTTGTAGCCGGCCATGTCC-A
1 GTCGCGTGGCCGGTTGTAGCCGGCCATGGCCGA
5939 TGTCGCGTGGCCGG
1 -GTCGCGTGGCCGG
5953 ACATTTCCAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 1 0.03
33 37 0.97
ACGTcount: A:0.06, C:0.28, G:0.43, T:0.23
Consensus pattern (33 bp):
GTCGCGTGGCCGGTTGTAGCCGGCCATGGCCGA
Found at i:5961 original size:23 final size:23
Alignment explanation
Indices: 5925--5998 Score: 130
Period size: 23 Copynumber: 3.2 Consensus size: 23
5915 GCCGGTTGTA
* *
5925 GCCGGCCATGTCCATGTCGCGTG
1 GCCGGACATTTCCATGTCGCGTG
5948 GCCGGACATTTCCATGTCGCGTG
1 GCCGGACATTTCCATGTCGCGTG
5971 GCCGGACATTTCCATGTCGCGTG
1 GCCGGACATTTCCATGTCGCGTG
5994 GCCGG
1 GCCGG
5999 TCTTGTGGCC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.23
Consensus pattern (23 bp):
GCCGGACATTTCCATGTCGCGTG
Found at i:11406 original size:5 final size:5
Alignment explanation
Indices: 11396--11429 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
11386 CTGGTCGAAT
11396 TTTTA TTTTA TTTTA TTTTA TTTT- TTTATA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT-TA TTTT
11430 TCGATATAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 3 0.11
5 21 0.78
6 3 0.11
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:11525 original size:17 final size:17
Alignment explanation
Indices: 11503--11536 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11493 GAATCGGCTA
11503 TGAATTTTTGAAGTTTC
1 TGAATTTTTGAAGTTTC
*
11520 TGAATTTTTGAATTTTC
1 TGAATTTTTGAAGTTTC
11537 AAGAAGGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.56
Consensus pattern (17 bp):
TGAATTTTTGAAGTTTC
Found at i:12513 original size:33 final size:33
Alignment explanation
Indices: 12437--12516 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
12427 TAGACAAAGG
* *
12437 GTCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA
1 GTCGCGTGGCCGGTTGTAGCCGGCCATGGCCGA
** *
12470 GTCGTTTGGCCGGTTGTAGCCGGCCATGTCC-A
1 GTCGCGTGGCCGGTTGTAGCCGGCCATGGCCGA
12502 TGTCGCGTGGCCGGT
1 -GTCGCGTGGCCGGT
12517 CTTGTGGCCG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 1 0.03
33 38 0.97
ACGTcount: A:0.06, C:0.28, G:0.42, T:0.24
Consensus pattern (33 bp):
GTCGCGTGGCCGGTTGTAGCCGGCCATGGCCGA
Done.