Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011356.1 Corchorus capsularis cultivar CVL-1 contig11377, 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: 19574
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:6138 original size:19 final size:19
Alignment explanation
Indices: 6114--6158 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
6104 CTCTTTAATT
6114 TTTATTGGGTTGAGAAACA
1 TTTATTGGGTTGAGAAACA
*
6133 TTTATTGGTTTGAGAAACA
1 TTTATTGGGTTGAGAAACA
6152 TATTATT
1 T-TTATT
6159 TTTGCTAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.44
Consensus pattern (19 bp):
TTTATTGGGTTGAGAAACA
Found at i:14476 original size:16 final size:15
Alignment explanation
Indices: 14455--14486 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
14445 AAAACTCACT
14455 TTTTGAGAATTACTAG
1 TTTTGAGAATTA-TAG
14471 TTTTGAGAATTATAG
1 TTTTGAGAATTATAG
14486 T
1 T
14487 AATCTACTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (15 bp):
TTTTGAGAATTATAG
Found at i:15193 original size:21 final size:17
Alignment explanation
Indices: 15154--15188 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
15144 TCAACTTTTG
15154 ATTTGGATTTATAAATA
1 ATTTGGATTTATAAATA
15171 ATTTGGATTTATAAATA
1 ATTTGGATTTATAAATA
15188 A
1 A
15189 CTAATGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (17 bp):
ATTTGGATTTATAAATA
Found at i:16876 original size:6 final size:6
Alignment explanation
Indices: 16866--16910 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
16856 TATATTTCTT
* * *
16866 TTTTCT TTTTCA TTTTCA TTTTCA TTTTCC TTTTCA TTTTTA TTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTT
16911 AGTCTGTTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTTCA
Found at i:17069 original size:30 final size:29
Alignment explanation
Indices: 17033--17089 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 29
17023 TATATATATC
17033 AAGTGAATTGAAAATTTCCCTCAAAAAAAA
1 AAGTGAATTGAAAATTTCCCT-AAAAAAAA
17063 AAGTGAATTGAAAATTTCCCTAAAAAA
1 AAGTGAATTGAAAATTTCCCTAAAAAA
17090 GTGAATTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.53, C:0.12, G:0.11, T:0.25
Consensus pattern (29 bp):
AAGTGAATTGAAAATTTCCCTAAAAAAAA
Found at i:17087 original size:25 final size:26
Alignment explanation
Indices: 17033--17102 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 26
17023 TATATATATC
17033 AAGTGAATTGAAAATTTCCCTCAAAAAAAA
1 AAGTGAATTGAAAATTTCCCT----AAAAA
17063 AAGTGAATTGAAAATTTCCCT-AAAA
1 AAGTGAATTGAAAATTTCCCTAAAAA
17088 AAGTGAATTGAAAAT
1 AAGTGAATTGAAAAT
17103 GAAAGGTCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
25 19 0.47
30 21 0.52
ACGTcount: A:0.51, C:0.10, G:0.13, T:0.26
Consensus pattern (26 bp):
AAGTGAATTGAAAATTTCCCTAAAAA
Found at i:19021 original size:2 final size:2
Alignment explanation
Indices: 19016--19078 Score: 61
Period size: 2 Copynumber: 35.5 Consensus size: 2
19006 TAATAATAAA
*
19016 AT AT AT AT -T AT AT AT AT AT A- AT A- AT AT -T AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19054 A- AT -T AT AT AT AT A- AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19079 ATTATTAAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
1 8 0.16
2 43 0.84
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:19039 original size:28 final size:30
Alignment explanation
Indices: 19001--19074 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 30
18991 TTGTTTAGTA
*
19001 ATATATAATAATA-AAATATATATTA-TAT
1 ATATATAATAATATAAATATATATAATTAT
*
19029 ATATATAATAATATTAGATATATATAATTAT
1 ATATATAATAATA-TAAATATATATAATTAT
19060 ATATATAATAATATA
1 ATATATAATAATATA
19075 TATAATTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 13 0.32
30 12 0.29
31 16 0.39
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (30 bp):
ATATATAATAATATAAATATATATAATTAT
Found at i:19042 original size:19 final size:19
Alignment explanation
Indices: 19015--19085 Score: 72
Period size: 19 Copynumber: 3.5 Consensus size: 19
19005 ATAATAATAA
19015 AATATATATTATATATATAT
1 AATA-ATATTATATATATAT
*
19035 AATAATATTAGATATATAT
1 AATAATATTATATATATAT
*
19054 AATTATA-TATATAATAATAT
1 AATAATATTATAT-AT-ATAT
19074 ATATAATTATTA
1 A-ATAA-TATTA
19086 AACGGTTCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 4 0.10
19 22 0.52
20 9 0.21
21 3 0.07
22 2 0.05
23 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (19 bp):
AATAATATTATATATATAT
Found at i:19077 original size:28 final size:29
Alignment explanation
Indices: 19001--19078 Score: 97
Period size: 28 Copynumber: 2.7 Consensus size: 29
18991 TTGTTTAGTA
* *
19001 ATATATAATAATA-AAATATATATTATAT
1 ATATATAATAATATATATATATAATATAT
19029 ATATATAATAATATTAGATATATATAAT-TAT
1 ATATATAATAATA-T--ATATATATAATATAT
19060 ATATATAATAATATATATA
1 ATATATAATAATATATATA
19079 ATTATTAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
28 18 0.41
30 1 0.02
31 16 0.36
32 9 0.20
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (29 bp):
ATATATAATAATATATATATATAATATAT
Done.