Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020381.1 Corchorus olitorius cultivar O-4 contig20414, 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: 51048
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:10856 original size:11 final size:11
Alignment explanation
Indices: 10840--10874 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
10830 AAATGTTCGA
10840 CTCTGTTTTTC
1 CTCTGTTTTTC
*
10851 CTCTGTTTTTG
1 CTCTGTTTTTC
10862 CTCTGTTTTTC
1 CTCTGTTTTTC
10873 CT
1 CT
10875 TCTTTTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.26, G:0.11, T:0.63
Consensus pattern (11 bp):
CTCTGTTTTTC
Found at i:13166 original size:29 final size:29
Alignment explanation
Indices: 13122--13227 Score: 72
Period size: 29 Copynumber: 3.6 Consensus size: 29
13112 GCCAAAGTGC
* *
13122 TCAAATAATGGTCTAATCTTTTAATTTAG
1 TCAAATAAGGGCCTAATCTTTTAATTTAG
**
13151 TCAAATAAGGGCCTAA-CGTTATTGAAAAT-G
1 TCAAATAAGGGCCTAATC-TT-TT-AATTTAG
* * ** *
13181 CTCAGATGAGGATCTGATCTTTTAATTTAG
1 -TCAAATAAGGGCCTAATCTTTTAATTTAG
*
13211 CCAAATAAGGGCCTAAT
1 TCAAATAAGGGCCTAAT
13228 ATTATCGAAA
Statistics
Matches: 54, Mismatches: 17, Indels: 12
0.65 0.20 0.14
Matches are distributed among these distances:
28 1 0.02
29 30 0.56
30 6 0.11
31 16 0.30
32 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (29 bp):
TCAAATAAGGGCCTAATCTTTTAATTTAG
Found at i:13184 original size:60 final size:59
Alignment explanation
Indices: 13119--13251 Score: 185
Period size: 60 Copynumber: 2.2 Consensus size: 59
13109 TTTGCCAAAG
* * *
13119 TGCTCAAATAATGGTCTAATCTTTTAATTTAGTCAAATAAGGGCCTAACGTTATTGAAAA
1 TGCTCAAATAA-GGTCTAATCTTTTAATTTAGCCAAATAAGGGCCTAACATTATCGAAAA
* * * *
13179 TGCTCAGATGAGGATCTGATCTTTTAATTTAGCCAAATAAGGGCCTAATATTATCGAAAA
1 TGCTCAAATAAGG-TCTAATCTTTTAATTTAGCCAAATAAGGGCCTAACATTATCGAAAA
13239 TGCTCAAATAAGG
1 TGCTCAAATAAGG
13252 GTCTGGCGTC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 2 0.03
60 61 0.97
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.32
Consensus pattern (59 bp):
TGCTCAAATAAGGTCTAATCTTTTAATTTAGCCAAATAAGGGCCTAACATTATCGAAAA
Found at i:18085 original size:12 final size:12
Alignment explanation
Indices: 18068--18104 Score: 56
Period size: 12 Copynumber: 2.9 Consensus size: 12
18058 AAGTTATAAT
18068 TAACCATAATTA
1 TAACCATAATTA
18080 TAACCATAATTA
1 TAACCATAATTA
18092 TAATTCCATAATT
1 TAA--CCATAATT
18105 CCGATCCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 15 0.65
14 8 0.35
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (12 bp):
TAACCATAATTA
Found at i:23734 original size:24 final size:26
Alignment explanation
Indices: 23707--23757 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
23697 TCTCTTTCTT
*
23707 CCTT-ATTC-TTTTTACTATTTTTTC
1 CCTTCATTCATTTGTACTATTTTTTC
* *
23731 CCTTCTTTCATTTGTACTTTTTTTTC
1 CCTTCATTCATTTGTACTATTTTTTC
23757 C
1 C
23758 TAGGAAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 4 0.18
25 3 0.14
26 15 0.68
ACGTcount: A:0.10, C:0.24, G:0.02, T:0.65
Consensus pattern (26 bp):
CCTTCATTCATTTGTACTATTTTTTC
Found at i:28636 original size:19 final size:19
Alignment explanation
Indices: 28612--28670 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
28602 CTGTTTAGTA
28612 ACTGTACAGATAAGATTAC
1 ACTGTACAGATAAGATTAC
* *
28631 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATAAGATTA--C
*
28652 ACTGTACAGATGAGATTAC
1 ACTGTACAGATAAGATTAC
28671 TAGAGCAGCG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (19 bp):
ACTGTACAGATAAGATTAC
Found at i:30188 original size:3 final size:3
Alignment explanation
Indices: 30180--30207 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
30170 CTAAGACTCT
30180 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
30208 AAGAGATGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:36153 original size:21 final size:21
Alignment explanation
Indices: 36129--36173 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
36119 AATTTTAGGC
36129 CTACATAGGAGAATGAAAGAT
1 CTACATAGGAGAATGAAAGAT
36150 CTACATAGGAGAATGAAAGAT
1 CTACATAGGAGAATGAAAGAT
36171 CTA
1 CTA
36174 AAACCACAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.47, C:0.11, G:0.22, T:0.20
Consensus pattern (21 bp):
CTACATAGGAGAATGAAAGAT
Found at i:39804 original size:42 final size:42
Alignment explanation
Indices: 39723--39804 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
39713 TGGGAGGAGA
**
39723 GGATTTTAACAATTTACGCACCCAATATAAAAGGGATTAGTG
1 GGATTTTAACAATTTACGCACCCAATATAAAAGACATTAGTG
* *
39765 GGATTTTAACAATTTACTCACCCAATATGAAAGACATTAG
1 GGATTTTAACAATTTACGCACCCAATATAAAAGACATTAG
39805 GGATTAGTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (42 bp):
GGATTTTAACAATTTACGCACCCAATATAAAAGACATTAGTG
Found at i:40016 original size:26 final size:26
Alignment explanation
Indices: 39986--40035 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
39976 GATTAAAATG
* *
39986 TCAAACGGTATCAATAGGTCAATTTA
1 TCAAACGGAATCAAGAGGTCAATTTA
* *
40012 TCAAATGGAATTAAGAGGTCAATT
1 TCAAACGGAATCAAGAGGTCAATT
40036 GGATTGTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (26 bp):
TCAAACGGAATCAAGAGGTCAATTTA
Found at i:40219 original size:13 final size:13
Alignment explanation
Indices: 40169--40212 Score: 88
Period size: 13 Copynumber: 3.4 Consensus size: 13
40159 TACTCACAAA
40169 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
40182 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
40195 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
40208 GGTCA
1 GGTCA
40213 TAATCAATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (13 bp):
GGTCAAAGTCAAC
Found at i:43868 original size:29 final size:29
Alignment explanation
Indices: 43813--43868 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
43803 AAGATATGCA
***
43813 TCTTAATTTCCTAAAATCTTTTTTTGAAG
1 TCTTAATTTCCTAAAATCTTAAGTTGAAG
*
43842 TCTTAGTTTCCTAAAATCTTAAGTTGA
1 TCTTAATTTCCTAAAATCTTAAGTTGA
43869 TTGAAAGGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.48
Consensus pattern (29 bp):
TCTTAATTTCCTAAAATCTTAAGTTGAAG
Found at i:47394 original size:16 final size:16
Alignment explanation
Indices: 47375--47407 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
47365 TATGTTGATG
47375 GCAGTAAAATTTGAAT
1 GCAGTAAAATTTGAAT
47391 GCAGTAAAATTTGAAT
1 GCAGTAAAATTTGAAT
47407 G
1 G
47408 AGTCAGCCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.30
Consensus pattern (16 bp):
GCAGTAAAATTTGAAT
Found at i:49668 original size:29 final size:30
Alignment explanation
Indices: 49629--49686 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
49619 TATAAATAAT
* *
49629 ATAATATAATTAAATAA-TTATATTTATAC
1 ATAATAAAATTAAATAATTTATATGTATAC
*
49658 ATAATAAAATTGAATAATTTATATGTATA
1 ATAATAAAATTAAATAATTTATATGTATA
49687 ATTATATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (30 bp):
ATAATAAAATTAAATAATTTATATGTATAC
Found at i:50961 original size:3 final size:3
Alignment explanation
Indices: 50953--51045 Score: 186
Period size: 3 Copynumber: 31.0 Consensus size: 3
50943 TGGGTTTGAA
50953 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
51001 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
51046 CCA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.