Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012472.1 Corchorus olitorius cultivar O-4 contig12505, 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: 44495
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:566 original size:22 final size:22
Alignment explanation
Indices: 511--567 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
501 TAAAAATGGA
* * *
511 TCGTGCTGCGTCGGCACGTGGG
1 TCGTGCTGTGCCGACACGTGGG
* *
533 TCGTGTTATGCCGACACGTGGG
1 TCGTGCTGTGCCGACACGTGGG
555 TCGTGCTGTGCCG
1 TCGTGCTGTGCCG
568 TGCCATTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.07, C:0.26, G:0.40, T:0.26
Consensus pattern (22 bp):
TCGTGCTGTGCCGACACGTGGG
Found at i:582 original size:28 final size:28
Alignment explanation
Indices: 551--621 Score: 124
Period size: 28 Copynumber: 2.5 Consensus size: 28
541 TGCCGACACG
551 TGGGTCGTGCTGTGCCGTGCCATTTTGA
1 TGGGTCGTGCTGTGCCGTGCCATTTTGA
*
579 TGGGTTGTGCTGTGCCGTGCCATTTTGA
1 TGGGTCGTGCTGTGCCGTGCCATTTTGA
*
607 TGGGTCGTGCCGTGC
1 TGGGTCGTGCTGTGC
622 TAGCCCATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.06, C:0.21, G:0.38, T:0.35
Consensus pattern (28 bp):
TGGGTCGTGCTGTGCCGTGCCATTTTGA
Found at i:1091 original size:13 final size:13
Alignment explanation
Indices: 1073--1135 Score: 94
Period size: 13 Copynumber: 5.0 Consensus size: 13
1063 ACAAATATCC
1073 ACGGATATATCGA
1 ACGGATATATCGA
1086 ACGGATATATCG-
1 ACGGATATATCGA
*
1098 ACGAATATATCGA
1 ACGGATATATCGA
1111 ACGGATATATCG-
1 ACGGATATATCGA
*
1123 ACGAATATATCGA
1 ACGGATATATCGA
1136 GGTATCGATG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
12 22 0.49
13 23 0.51
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.24
Consensus pattern (13 bp):
ACGGATATATCGA
Found at i:1105 original size:25 final size:25
Alignment explanation
Indices: 1067--1135 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 25
1057 TTTAATACAA
* *
1067 ATATCCACGGATATATCGAACGGAT
1 ATATCGACGAATATATCGAACGGAT
1092 ATATCGACGAATATATCGAACGGAT
1 ATATCGACGAATATATCGAACGGAT
1117 ATATCGACGAATATATCGA
1 ATATCGACGAATATATCGA
1136 GGTATCGATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (25 bp):
ATATCGACGAATATATCGAACGGAT
Found at i:1107 original size:12 final size:12
Alignment explanation
Indices: 1067--1135 Score: 93
Period size: 12 Copynumber: 5.6 Consensus size: 12
1057 TTTAATACAA
*
1067 ATATCCACGGAT
1 ATATCGACGGAT
1079 ATATCGAACGGAT
1 ATATCG-ACGGAT
*
1092 ATATCGACGAAT
1 ATATCGACGGAT
1104 ATATCGAACGGAT
1 ATATCG-ACGGAT
*
1117 ATATCGACGAAT
1 ATATCGACGGAT
1129 ATATCGA
1 ATATCGA
1136 GGTATCGATG
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
12 28 0.55
13 23 0.45
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (12 bp):
ATATCGACGGAT
Found at i:2100 original size:20 final size:19
Alignment explanation
Indices: 2065--2122 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
2055 TGAATATTTA
2065 CGGATATATCGA--GATAT
1 CGGATATATCGACGGATAT
*
2082 C-GATAAATATCGACGGATACA
1 CGGAT--ATATCGACGGATA-T
2103 CGGATATATCGACGGATAT
1 CGGATATATCGACGGATAT
2122 C
1 C
2123 CGGTGACATT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
16 3 0.09
17 1 0.03
18 7 0.21
19 1 0.03
20 17 0.52
21 1 0.03
22 3 0.09
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.24
Consensus pattern (19 bp):
CGGATATATCGACGGATAT
Found at i:3074 original size:17 final size:17
Alignment explanation
Indices: 3023--3074 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
3013 ATAATCTCAT
3023 AAATCATACCTCAAAGA
1 AAATCATACCTCAAAGA
** * *
3040 ATTTCA-A-CACAAAAA
1 AAATCATACCTCAAAGA
3055 AAATCATACCTCAAAGA
1 AAATCATACCTCAAAGA
3072 AAA
1 AAA
3075 AAAAGTTCAT
Statistics
Matches: 25, Mismatches: 8, Indels: 4
0.68 0.22 0.11
Matches are distributed among these distances:
15 10 0.40
16 2 0.08
17 13 0.52
ACGTcount: A:0.58, C:0.21, G:0.04, T:0.17
Consensus pattern (17 bp):
AAATCATACCTCAAAGA
Found at i:3084 original size:23 final size:21
Alignment explanation
Indices: 3050--3094 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
3040 ATTTCAACAC
**
3050 AAAAAAAATCATACCTCAAAG
1 AAAAAAAATCATAAATCAAAG
3071 AAAAAAAAGTTCATAAATCAAAG
1 AAAAAAAA--TCATAAATCAAAG
3094 A
1 A
3095 CTAAAGTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
23 12 0.60
ACGTcount: A:0.64, C:0.13, G:0.07, T:0.16
Consensus pattern (21 bp):
AAAAAAAATCATAAATCAAAG
Found at i:11702 original size:6 final size:6
Alignment explanation
Indices: 11691--11727 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
11681 CTCACCTTTA
11691 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT A-CTAT AT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT AT
11728 TAAAAAGTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (6 bp):
ATCTAT
Found at i:12061 original size:131 final size:132
Alignment explanation
Indices: 11815--12050 Score: 311
Period size: 131 Copynumber: 1.8 Consensus size: 132
11805 TTGTTTAAAG
* *
11815 TTTTACAATTTTACTTAACTAAAAACTCAATTTTTATTTAATTAAGTCTAATATCCTTATAAATA
1 TTTTACAATTTTACTCAACTAAAAACT-AATTTTTATTTAATTAAATCTAATATCCTTATAAATA
* *
11880 TTTTATTTTTACCAGTTTACTATTTTATTTTAATTAAAAACTTAAATATT-AGAATTGTTTAAAT
65 TTTTATTTTTACCAGTTTACTAATTTATATTAA-TAAAAACTTAAATATTAAGAATTGTTTAAAT
11944 ATAC
129 ATAC
* * * ** **
11948 TTTTATAATTTTACTCAATTAAAAACT-ATTTTTATTTTATTAAATCTAATATTTTTATACCTA-
1 TTTTACAATTTTACTCAACTAAAAACTAATTTTTATTTAATTAAATCTAATATCCTTATAAATAT
*
12011 TTTATTTTTACCATTTTACTAATTTA-ATTAA-AAAAACTTA
66 TTTATTTTTACCAGTTTACTAATTTATATTAATAAAAACTTA
12051 TAAAGTTATT
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
127 9 0.10
129 4 0.04
130 24 0.26
131 30 0.33
133 24 0.26
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (132 bp):
TTTTACAATTTTACTCAACTAAAAACTAATTTTTATTTAATTAAATCTAATATCCTTATAAATAT
TTTATTTTTACCAGTTTACTAATTTATATTAATAAAAACTTAAATATTAAGAATTGTTTAAATAT
AC
Found at i:19811 original size:2 final size:2
Alignment explanation
Indices: 19804--19828 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19794 AACGAGTATA
19804 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
19829 AAGGGCATCT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31644 original size:17 final size:19
Alignment explanation
Indices: 31613--31647 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
31603 ACTTATAATT
31613 TATATATGGTATATTATTA
1 TATATATGGTATATTATTA
31632 TATATAT-GT-TATTATT
1 TATATATGGTATATTATT
31648 TGATTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (19 bp):
TATATATGGTATATTATTA
Found at i:31743 original size:40 final size:40
Alignment explanation
Indices: 31676--31754 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
31666 ACTAAACTAA
* * *
31676 ATTGACATCCTAGTTTTTTTTTAAATATAAATTTTTTAAT
1 ATTGACATCCTAGTTTTCTTATAAATATAAATTATTTAAT
* *
31716 ATTGATATCCTAGTTTTACTTAT-AATATATATTATTTAA
1 ATTGACATCCTAGTTTT-CTTATAAATATAAATTATTTAA
31755 AATAATTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 30 0.91
41 3 0.09
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (40 bp):
ATTGACATCCTAGTTTTCTTATAAATATAAATTATTTAAT
Found at i:32916 original size:18 final size:17
Alignment explanation
Indices: 32883--32916 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
32873 AAAATAAAAA
*
32883 TTTTCAATGCTTTAATT
1 TTTTCAATACTTTAATT
32900 TTTTCAATACGTTTAAT
1 TTTTCAATAC-TTTAAT
32917 AATTAAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTTCAATACTTTAATT
Done.