Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016469.1 Corchorus capsularis cultivar CVL-1 contig16490, 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: 58226
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1645 original size:31 final size:32
Alignment explanation
Indices: 1610--1669 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
1600 CACTTTAAAA
* *
1610 GGCTTGCAACAGGGTATCACACCC-ACGAAAC
1 GGCTTGCAACAAGGTAGCACACCCTACGAAAC
*
1641 GGCTTGCAATAAGGTAGCACACCCTACGA
1 GGCTTGCAACAAGGTAGCACACCCTACGA
1670 CACCCTTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.15
Consensus pattern (32 bp):
GGCTTGCAACAAGGTAGCACACCCTACGAAAC
Found at i:17281 original size:2 final size:2
Alignment explanation
Indices: 17274--17313 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
17264 AATAAACAAA
17274 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
17314 CATTACTTCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18363 original size:27 final size:25
Alignment explanation
Indices: 18333--18384 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
18323 CAAAAGCTGA
*
18333 TCCGAACCCGAGAATTTGTCCAACCCG
1 TCCGAACCC--GAATTCGTCCAACCCG
*
18360 TCCGAACTCGAATTCGTCCAACCCG
1 TCCGAACCCGAATTCGTCCAACCCG
18385 ATTTGATCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 15 0.65
27 8 0.35
ACGTcount: A:0.25, C:0.38, G:0.17, T:0.19
Consensus pattern (25 bp):
TCCGAACCCGAATTCGTCCAACCCG
Found at i:19058 original size:42 final size:42
Alignment explanation
Indices: 18986--19067 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
18976 TGTTGACACA
* * * *
18986 TACCCCACCTGATAATTAATTATGCGTTTAATATTCAAAACC
1 TACCCCACATGATAATCAATTATGCATTTAATATGCAAAACC
* *
19028 TACCTCACATGATAATCAATTATGTATTTAATATGCAAAA
1 TACCCCACATGATAATCAATTATGCATTTAATATGCAAAA
19068 TTAATATCTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (42 bp):
TACCCCACATGATAATCAATTATGCATTTAATATGCAAAACC
Found at i:19327 original size:16 final size:16
Alignment explanation
Indices: 19308--19409 Score: 138
Period size: 16 Copynumber: 6.4 Consensus size: 16
19298 AGAGCCGGTA
*
19308 GACCCGAGACTCGAAT
1 GACCCGAGACCCGAAT
19324 GACCCG-GAACCCGAAT
1 GACCCGAG-ACCCGAAT
19340 GACCCGAGACCCGAAT
1 GACCCGAGACCCGAAT
*
19356 GACCCGAGACCCGTAT
1 GACCCGAGACCCGAAT
19372 GACCCGAGACCCGAAT
1 GACCCGAGACCCGAAT
*
19388 AACCCGA-ACCC-AGAT
1 GACCCGAGACCCGA-AT
19403 GACCCGA
1 GACCCGA
19410 ATGACCCGAG
Statistics
Matches: 78, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
14 1 0.01
15 13 0.17
16 63 0.81
17 1 0.01
ACGTcount: A:0.31, C:0.37, G:0.24, T:0.08
Consensus pattern (16 bp):
GACCCGAGACCCGAAT
Found at i:19346 original size:9 final size:9
Alignment explanation
Indices: 19319--19418 Score: 80
Period size: 9 Copynumber: 12.3 Consensus size: 9
19309 ACCCGAGACT
19319 CGAATGACC
1 CGAATGACC
*
19328 CGGA--ACC
1 CGAATGACC
19335 CGAATGACC
1 CGAATGACC
19344 CG-A-GACC
1 CGAATGACC
19351 CGAATGACC
1 CGAATGACC
19360 CG-A-GACC
1 CGAATGACC
*
19367 CGTATGACC
1 CGAATGACC
19376 CG-A-GACC
1 CGAATGACC
*
19383 CGAATAACC
1 CGAATGACC
19392 CG-A--ACC
1 CGAATGACC
19398 C-AGATGACC
1 CGA-ATGACC
19407 CGAATGACC
1 CGAATGACC
19416 CGA
1 CGA
19419 GAAAACTGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 26
0.72 0.03 0.25
Matches are distributed among these distances:
6 4 0.05
7 25 0.33
8 7 0.09
9 38 0.51
10 1 0.01
ACGTcount: A:0.32, C:0.37, G:0.23, T:0.08
Consensus pattern (9 bp):
CGAATGACC
Found at i:24448 original size:15 final size:15
Alignment explanation
Indices: 24424--24456 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
24414 CTACAGAGCC
24424 CGAGAACGACGGCGA
1 CGAGAACGACGGCGA
*
24439 CGAGATCGACGGCGA
1 CGAGAACGACGGCGA
24454 CGA
1 CGA
24457 TGACGTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.27, G:0.39, T:0.03
Consensus pattern (15 bp):
CGAGAACGACGGCGA
Found at i:27258 original size:17 final size:17
Alignment explanation
Indices: 27231--27263 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
27221 ATTGCACAGA
27231 TGAATTTAAACCAGAAAT
1 TGAATTTAAACC-GAAAT
27249 TGAA-TTAAACCGAAA
1 TGAATTTAAACCGAAA
27264 CCTTTGCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (17 bp):
TGAATTTAAACCGAAAT
Found at i:29632 original size:12 final size:12
Alignment explanation
Indices: 29601--29636 Score: 63
Period size: 13 Copynumber: 2.9 Consensus size: 12
29591 TGGAGTTTAA
29601 GACGGATATATC
1 GACGGATATATC
29613 GAACGGATATATC
1 G-ACGGATATATC
29626 GACGGATATAT
1 GACGGATATAT
29637 ATCGAGGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (12 bp):
GACGGATATATC
Found at i:34289 original size:30 final size:30
Alignment explanation
Indices: 34253--34325 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
34243 GATATATGTG
* *
34253 GATTTTTGTTGTCTTTTTTTTTTGGCC-AGA
1 GATTTTTGTTGTC-TTTTTCTTTGGCCAAAA
34283 GATTTTTGTTGTC-TTTTCTTTGGCCAAAA
1 GATTTTTGTTGTCTTTTTCTTTGGCCAAAA
34312 GATTTTTGTTGTCT
1 GATTTTTGTTGTCT
34326 ACATAATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 11 0.28
29 15 0.38
30 13 0.33
ACGTcount: A:0.12, C:0.11, G:0.19, T:0.58
Consensus pattern (30 bp):
GATTTTTGTTGTCTTTTTCTTTGGCCAAAA
Found at i:34835 original size:70 final size:70
Alignment explanation
Indices: 34752--34906 Score: 231
Period size: 70 Copynumber: 2.2 Consensus size: 70
34742 CTGTTTAGGT
* * *
34752 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACT
*
34816 ATTTTA
65 ATTGTA
* *
34822 TTTTACTATTTTACTCAACTAAAAACTCTTTTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
34887 TTGTA
66 TTGTA
*
34892 TTTTACCATTTTACT
1 TTTTACTATTTTACT
34907 ATTTTAATTA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
70 75 0.97
71 2 0.03
ACGTcount: A:0.35, C:0.12, G:0.01, T:0.52
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
TTGTA
Found at i:35045 original size:83 final size:85
Alignment explanation
Indices: 34951--35125 Score: 302
Period size: 85 Copynumber: 2.1 Consensus size: 85
34941 TTAAAAATAT
34951 ATTTCTTGAATGACATTGTTTAAACTTTTACAA-TTTTTTTAAAATAAACTTTTGCAACTGAAAT
1 ATTTCTTGAATGACATTGTTTAAACTTTTACAATTTTTTTTAAAATAAACTTTTGCAACTGAAA-
35015 A-ACTA-TTTTTATTTAATTG
65 ACACTATTTTTTATTTAATTG
35034 ATTTCTTGAATGACATTGTTTAAACTTTTACAATTTTTTTTTAAAATAAACTTTTGCAACTGAAA
1 ATTTCTTGAATGACATTGTTTAAACTTTTACAA-TTTTTTTTAAAATAAACTTTTGCAACTGAAA
35099 ACACTATTTTTTTATTTAATTG
65 ACACTA-TTTTTTATTTAATTG
35121 ATTTC
1 ATTTC
35126 AATATTTTTA
Statistics
Matches: 87, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
83 33 0.38
84 1 0.01
85 34 0.39
87 19 0.22
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (85 bp):
ATTTCTTGAATGACATTGTTTAAACTTTTACAATTTTTTTTAAAATAAACTTTTGCAACTGAAAA
CACTATTTTTTATTTAATTG
Found at i:35822 original size:13 final size:13
Alignment explanation
Indices: 35806--35830 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35796 ATGGTATTTC
35806 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
35819 AAAAAAGAAAAA
1 AAAAAAGAAAAA
35831 ACGTTCATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:35902 original size:6 final size:6
Alignment explanation
Indices: 35891--35923 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
35881 GCAATTAGGC
35891 AAATAT AAATAT AAATAT AAATAT AAATTAT AA
1 AAATAT AAATAT AAATAT AAATAT AAA-TAT AA
35924 TAATAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AAATAT
Found at i:35925 original size:18 final size:19
Alignment explanation
Indices: 35891--35930 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
35881 GCAATTAGGC
35891 AAATATAAATATAAAT-AT
1 AAATATAAATATAAATAAT
35909 AAATATAAAT-TATAATAAT
1 AAATATAAATATA-AATAAT
35928 AAA
1 AAA
35931 ACACAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 2 0.10
18 13 0.65
19 5 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATATAAATATAAATAAT
Found at i:58194 original size:2 final size:2
Alignment explanation
Indices: 58187--58211 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58177 CAATTATTTA
58187 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 A
58212 ATTACACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.