Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013529.1 Corchorus capsularis cultivar CVL-1 contig13550, 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: 22741
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:67 original size:10 final size:10
Alignment explanation
Indices: 52--97 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
42 ATTGTTAAAT
52 TTAATTA-TGG
1 TTAATTAGT-G
62 TTAATTAGTG
1 TTAATTAGTG
72 TTAATTAGTG
1 TTAATTAGTG
*
82 TT-ATTAATG
1 TTAATTAGTG
91 TTAATTA
1 TTAATTA
98 CTACTCCCTC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
9 8 0.24
10 24 0.73
11 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (10 bp):
TTAATTAGTG
Found at i:92 original size:19 final size:20
Alignment explanation
Indices: 52--97 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
42 ATTGTTAAAT
*
52 TTAATTATGGTTAATTAGTG
1 TTAATTATGGTTAATTAATG
72 TTAATTA-GTGTT-ATTAATG
1 TTAATTATG-GTTAATTAATG
91 TTAATTA
1 TTAATTA
98 CTACTCCCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (20 bp):
TTAATTATGGTTAATTAATG
Found at i:5099 original size:9 final size:9
Alignment explanation
Indices: 5085--5109 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5075 GAGCCCAAGG
5085 CCCAAGTGC
1 CCCAAGTGC
5094 CCCAAGTGC
1 CCCAAGTGC
5103 CCCAAGT
1 CCCAAGT
5110 ACCCTATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.44, G:0.20, T:0.12
Consensus pattern (9 bp):
CCCAAGTGC
Found at i:8164 original size:30 final size:30
Alignment explanation
Indices: 8125--8182 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
8115 TCATGAGGTA
8125 GAATAATGCGCCCAAGG-CTTATCATGGAGG
1 GAATAATGCG-CCAAGGACTTATCATGGAGG
*
8155 GAATGATGCGCCAAGGACTTATCATGGA
1 GAATAATGCGCCAAGGACTTATCATGGA
8183 CTTGAAGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (30 bp):
GAATAATGCGCCAAGGACTTATCATGGAGG
Found at i:10775 original size:30 final size:30
Alignment explanation
Indices: 10731--10787 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
10721 CAAGTCGATA
10731 ATAAGTCCTTGGCGCATCATTCCCTCCATG
1 ATAAGTCCTTGGCGCATCATTCCCTCCATG
10761 ATAAG-CCTTAGGCGCATCATTCCCTCC
1 ATAAGTCCTT-GGCGCATCATTCCCTCC
10788 CCCTTGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.21, C:0.35, G:0.16, T:0.28
Consensus pattern (30 bp):
ATAAGTCCTTGGCGCATCATTCCCTCCATG
Found at i:11252 original size:33 final size:33
Alignment explanation
Indices: 11196--11334 Score: 122
Period size: 33 Copynumber: 4.2 Consensus size: 33
11186 CTATGATCAA
** *
11196 CCAAAACAGA-TT-GTTTTCATCACAATTAGCAT
1 CCAAAACAGATTTAG-TTTCATCACAAACAACAT
11228 CCAAAACAGATTTAGTTTCATCACAAACAACAT
1 CCAAAACAGATTTAGTTTCATCACAAACAACAT
* * * *
11261 TCAAAACATATTTAGTGTCATCGCAAACAACA-
1 CCAAAACAGATTTAGTTTCATCACAAACAACAT
** * * *
11293 CTCAAATTAGGTTTAGTATCATCGCAAACAACAT
1 C-CAAAACAGATTTAGTTTCATCACAAACAACAT
*
11327 CTAAAACA
1 CCAAAACA
11335 CTCTTTGCAA
Statistics
Matches: 87, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
32 10 0.11
33 75 0.86
34 2 0.02
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.27
Consensus pattern (33 bp):
CCAAAACAGATTTAGTTTCATCACAAACAACAT
Found at i:19984 original size:20 final size:21
Alignment explanation
Indices: 19941--19986 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
19931 GGAGATGGCA
19941 AAGATGCCATTTGATCCATTG
1 AAGATGCCATTTGATCCATTG
*
19962 AAGATGCC-TTTAGGTCC-TTG
1 AAGATGCCATTT-GATCCATTG
19982 AAGAT
1 AAGAT
19987 TCAAGGAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (21 bp):
AAGATGCCATTTGATCCATTG
Found at i:20860 original size:17 final size:17
Alignment explanation
Indices: 20835--20868 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20825 CACCCTTCTT
20835 GAAAATTCAAAAATTCA
1 GAAAATTCAAAAATTCA
*
20852 GAAACTTCAAAAATTCA
1 GAAAATTCAAAAATTCA
20869 TAGCCGATTC
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:0.56, C:0.15, G:0.06, T:0.24
Consensus pattern (17 bp):
GAAAATTCAAAAATTCA
Found at i:20959 original size:5 final size:5
Alignment explanation
Indices: 20942--20971 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
20932 GTTATATCGA
20942 AAAAT ATAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAA
20972 AAATTTTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:22459 original size:33 final size:32
Alignment explanation
Indices: 22352--22460 Score: 121
Period size: 33 Copynumber: 3.3 Consensus size: 32
22342 TTAGTTGCAA
*
22352 AAATGTGTTTTAGATGTTGTTTGCGATGATACT
1 AAATCTGTTTTAG-TGTTGTTTGCGATGATACT
* * * *
22385 AAACCTGATTTGAGTGTTG-TTGCAATGACACT
1 AAATCTG-TTTTAGTGTTGTTTGCGATGATACT
* *
22417 AAATATGTTTTAAGTGTTGTTTGTGATGATACT
1 AAATCTGTTTT-AGTGTTGTTTGCGATGATACT
22450 AAATCTGTTTT
1 AAATCTGTTTT
22461 GAATGCTAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
31 3 0.05
32 23 0.38
33 30 0.49
34 5 0.08
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (32 bp):
AAATCTGTTTTAGTGTTGTTTGCGATGATACT
Found at i:22516 original size:33 final size:32
Alignment explanation
Indices: 22479--22560 Score: 102
Period size: 27 Copynumber: 2.7 Consensus size: 32
22469 ATTGTGATGA
22479 AAATAAGTCTGTTTTGGTTGATCATAGCATTAC
1 AAATAA-TCTGTTTTGGTTGATCATAGCATTAC
*
22512 AAATAA----TTTT-GTTGATCATAGCATTGC
1 AAATAATCTGTTTTGGTTGATCATAGCATTAC
22539 AAATAATCCTGTTTTGGTTGAT
1 AAATAAT-CTGTTTTGGTTGAT
22561 GGCATTGAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
27 22 0.52
28 4 0.10
32 4 0.10
33 12 0.29
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.41
Consensus pattern (32 bp):
AAATAATCTGTTTTGGTTGATCATAGCATTAC
Done.