Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008571.1 Hibiscus syriacus cultivar Beakdansim tig00111497_pilon, 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: 60014
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4100 original size:29 final size:29
Alignment explanation
Indices: 4066--4124 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
4056 CCTAAATTAA
4066 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
4095 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
4124 T
1 T
4125 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:7560 original size:22 final size:20
Alignment explanation
Indices: 7526--7573 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
7516 TTGAGTAAGT
7526 TTTGATAAGTTAT-TTTGATAA
1 TTTGATAAGTTATGTTT--TAA
*
7547 TTTGAGTATGTTATGTTTTAA
1 TTTGA-TAAGTTATGTTTTAA
7568 TTTGAT
1 TTTGAT
7574 TGATGAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 13 0.54
22 7 0.29
23 3 0.12
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (20 bp):
TTTGATAAGTTATGTTTTAA
Found at i:15363 original size:23 final size:23
Alignment explanation
Indices: 15319--15364 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
15309 ACTAGCTTTA
* *
15319 TGAGTTCATGACCTATTCATTTG
1 TGAGTTCATGACCAATTAATTTG
15342 TGAGTTCAT-AGCCAATTAATTTG
1 TGAGTTCATGA-CCAATTAATTTG
15365 CCATTTCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.41
Consensus pattern (23 bp):
TGAGTTCATGACCAATTAATTTG
Found at i:16274 original size:23 final size:23
Alignment explanation
Indices: 16243--16286 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
16233 AAACAAACAT
*
16243 GAGTATTTTTTAACTTAAAATAA
1 GAGTATTTTTTAACTAAAAATAA
*
16266 GAGTTTTTTTTAACTAAAAAT
1 GAGTATTTTTTAACTAAAAAT
16287 GAAATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (23 bp):
GAGTATTTTTTAACTAAAAATAA
Found at i:16740 original size:21 final size:22
Alignment explanation
Indices: 16715--16755 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
16705 AAAAGCGTCG
*
16715 TAATTTTCAA-ATAAATAAACC
1 TAATTCTCAATATAAATAAACC
*
16736 TAATTCTCAATTTAAATAAA
1 TAATTCTCAATATAAATAAA
16756 TAATATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TAATTCTCAATATAAATAAACC
Found at i:23131 original size:30 final size:30
Alignment explanation
Indices: 23077--23133 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
23067 AATATATCCC
23077 TCAAACTTTTAAAAAAAATCAATTAAGCCT
1 TCAAACTTTTAAAAAAAATCAATTAAGCCT
* * * *
23107 TCAAGCTTTTTAAAAGAATTAATTAAG
1 TCAAACTTTTAAAAAAAATCAATTAAG
23134 TACCTTTACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.33
Consensus pattern (30 bp):
TCAAACTTTTAAAAAAAATCAATTAAGCCT
Found at i:34337 original size:5 final size:6
Alignment explanation
Indices: 34320--34346 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
34310 AATGTTCACT
34320 ATAAAA ATAAAA ATAAAA ATAAAA ATA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATA
34347 TTATTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:37200 original size:20 final size:19
Alignment explanation
Indices: 37177--37215 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
37167 TTAAATGGAA
*
37177 AAATATTATATTTTTAAATT
1 AAATATTA-AATTTTAAATT
*
37197 AAATTTTAAATTTTAAATT
1 AAATATTAAATTTTAAATT
37216 TATATACAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AAATATTAAATTTTAAATT
Found at i:38624 original size:25 final size:25
Alignment explanation
Indices: 38591--38652 Score: 124
Period size: 25 Copynumber: 2.5 Consensus size: 25
38581 TATAAAAACC
38591 TTTTATAAATTAAAATTAGGACAAT
1 TTTTATAAATTAAAATTAGGACAAT
38616 TTTTATAAATTAAAATTAGGACAAT
1 TTTTATAAATTAAAATTAGGACAAT
38641 TTTTATAAATTA
1 TTTTATAAATTA
38653 GGAAAAAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (25 bp):
TTTTATAAATTAAAATTAGGACAAT
Found at i:42477 original size:23 final size:23
Alignment explanation
Indices: 42451--42519 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
42441 CACCACAGCT
*
42451 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
42474 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
42497 CGTAGAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
42520 TATAATATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:42879 original size:2 final size:2
Alignment explanation
Indices: 42872--42909 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
42862 AATCATATGA
42872 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42910 CTTATGCAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45726 original size:16 final size:16
Alignment explanation
Indices: 45707--45761 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
45697 ATTTATAATT
45707 AATATTATAAACAAAA
1 AATATTATAAACAAAA
* **
45723 AATATTATAATA-TACC
1 AATATTATAA-ACAAAA
45739 AATATTATAAACAAAA
1 AATATTATAAACAAAA
45755 AA-ATTAT
1 AATATTAT
45762 GAATTTGATT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 6 0.19
16 24 0.77
17 1 0.03
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (16 bp):
AATATTATAAACAAAA
Found at i:46216 original size:30 final size:31
Alignment explanation
Indices: 46182--46248 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
46172 TTAACGGTAC
* *
46182 AATGATCAACATATTA-T-AATCGATAACATA
1 AATGATCAAAAT-TTAGTAAATCAATAACATA
*
46212 AATGATCAAAATTTAGTAAATCAATAATATA
1 AATGATCAAAATTTAGTAAATCAATAACATA
46243 AATGAT
1 AATGAT
46249 TGAAATGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 3 0.09
30 12 0.38
31 17 0.53
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.31
Consensus pattern (31 bp):
AATGATCAAAATTTAGTAAATCAATAACATA
Found at i:58063 original size:21 final size:21
Alignment explanation
Indices: 58039--58078 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
58029 AATTAATGAT
*
58039 GATACTAACATATTATCATAA
1 GATAATAACATATTATCATAA
58060 GATAATAACATATTATCAT
1 GATAATAACATATTATCAT
58079 TGATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.35
Consensus pattern (21 bp):
GATAATAACATATTATCATAA
Done.