Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006613.1 Hibiscus syriacus cultivar Beakdansim tig00016229_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: 70009
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4712 original size:22 final size:21
Alignment explanation
Indices: 4682--4727 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
4672 TAAAGTTCTT
* *
4682 TTTTCTTTTCTTTCTTTCAAG
1 TTTTCTTTTATTTATTTCAAG
*
4703 TTTTCATTTTATTTATTTTAAG
1 TTTTC-TTTTATTTATTTCAAG
4725 TTT
1 TTT
4728 ATTTTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.15, C:0.11, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTCTTTTATTTATTTCAAG
Found at i:11240 original size:25 final size:23
Alignment explanation
Indices: 11206--11260 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 23
11196 AAGTTCTTTC
*
11206 TTTTA-TTTTATTTTCTTTTCAAG
1 TTTTATTTTTATTTTATTTT-AAG
11229 TTTTCATTTTTATTTTATTTTAAG
1 TTTT-ATTTTTATTTTATTTTAAG
11253 TTTTATTT
1 TTTTATTT
11261 GTTAAAATGC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 8 0.28
24 8 0.28
25 13 0.45
ACGTcount: A:0.18, C:0.05, G:0.04, T:0.73
Consensus pattern (23 bp):
TTTTATTTTTATTTTATTTTAAG
Found at i:17571 original size:24 final size:25
Alignment explanation
Indices: 17518--17569 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
17508 TTTTCTTTTC
* *
17518 TTTTCTTTTATTTTCAAGTTTTCAT
1 TTTTATTTTATATTCAAGTTTTCAT
17543 TTTTATTTTATATT-AAGTTTT-AT
1 TTTTATTTTATATTCAAGTTTTCAT
17566 TTTT
1 TTTT
17570 TAAAAAATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.24
24 7 0.28
25 12 0.48
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (25 bp):
TTTTATTTTATATTCAAGTTTTCAT
Found at i:23979 original size:24 final size:24
Alignment explanation
Indices: 23937--23988 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
23927 AAGTTCTTTA
*
23937 TTTTATTCTCTTTTCAAGTCTTCAT
1 TTTTATTCTATTTTCAAGT-TTCAT
* *
23962 TTTTATTTTATTTT-AAGTTTTAT
1 TTTTATTCTATTTTCAAGTTTCAT
23985 TTTT
1 TTTT
23989 TAAAATGCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 8 0.33
24 4 0.17
25 12 0.50
ACGTcount: A:0.17, C:0.10, G:0.04, T:0.69
Consensus pattern (24 bp):
TTTTATTCTATTTTCAAGTTTCAT
Found at i:24691 original size:16 final size:16
Alignment explanation
Indices: 24670--24703 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
24660 TTTAATGAGA
24670 TTAAGGATAAATTTAT
1 TTAAGGATAAATTTAT
24686 TTAAGGATAAATTTAT
1 TTAAGGATAAATTTAT
24702 TT
1 TT
24704 GACAGTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (16 bp):
TTAAGGATAAATTTAT
Found at i:27225 original size:22 final size:22
Alignment explanation
Indices: 27194--27245 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
27184 TTATTTTTTG
*
27194 GTCAAAGTCAATGCTAGTCAAA
1 GTCAACGTCAATGCTAGTCAAA
* *
27216 GTCAACGTCAATTCTGGTCAAA
1 GTCAACGTCAATGCTAGTCAAA
27238 GTCAACGT
1 GTCAACGT
27246 TTAATCAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (22 bp):
GTCAACGTCAATGCTAGTCAAA
Found at i:34247 original size:24 final size:24
Alignment explanation
Indices: 34215--34261 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
34205 TAGTTGAATC
*
34215 AGTACCACCTTGGAAGTTAGAGTT
1 AGTACCACCTTGGAAGCTAGAGTT
* *
34239 AGTATCACCTTGGATGCTAGAGT
1 AGTACCACCTTGGAAGCTAGAGT
34262 CAGCACCATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (24 bp):
AGTACCACCTTGGAAGCTAGAGTT
Found at i:40754 original size:32 final size:32
Alignment explanation
Indices: 40718--40782 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
40708 AGTTCTAGGT
40718 ACCTTCAACGGGTATGAAATGAGATGGAAAGA
1 ACCTTCAACGGGTATGAAATGAGATGGAAAGA
40750 ACCTTCAACGGGTATGAAATGAGATGGAAAGA
1 ACCTTCAACGGGTATGAAATGAGATGGAAAGA
40782 A
1 A
40783 AGAAAGTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.42, C:0.12, G:0.28, T:0.18
Consensus pattern (32 bp):
ACCTTCAACGGGTATGAAATGAGATGGAAAGA
Found at i:45869 original size:17 final size:16
Alignment explanation
Indices: 45838--45871 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
45828 CACGTGAGGA
45838 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
45854 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
45871 T
1 T
45872 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:52270 original size:19 final size:20
Alignment explanation
Indices: 52229--52270 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
52219 TTCTTTTATA
*
52229 TTTCATTATTAATTTTTCTC
1 TTTCATTATTAATTTTACTC
52249 TTTCATT-TTAACTTTTAC-C
1 TTTCATTATTAA-TTTTACTC
52268 TTT
1 TTT
52271 TCTCTTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.19, C:0.17, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCATTATTAATTTTACTC
Found at i:69474 original size:53 final size:53
Alignment explanation
Indices: 69404--69718 Score: 361
Period size: 53 Copynumber: 5.9 Consensus size: 53
69394 CCAAAATGGA
* * * * *
69404 AATTAACAAACTTATTATGAATTCCATGGATTTCACACATAGTGCCGATACGG
1 AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATACGG
* * *
69457 CATTCACAAACTCATTATGAATTTCGTGGGTTGCACACATAGTGCCAATACGG
1 AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATACGG
* * *
69510 TAATTCACAAACTCATTATGAA-TCTCGTGGGTTGCACATATAGTGTCGATACAGT
1 -AATTCACAAACTCATTATGAATTC-CGTGGGTTGCACACATAGTGCCGATAC-GG
* * *
69565 AATTCAC-AACTCATTATGAATTCTGTGGGTTGCACAC--AGTGTCGATACTGC
1 AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATAC-GG
* * *
69616 AATTTACAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGCTGATACGG
1 AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATACGG
* * * *
69669 TAATTCA-AAACTAATTATGAATTTCGTGGATTGCACACATAGTGTCGATA
1 -AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATA
69719 GTACATAATA
Statistics
Matches: 225, Mismatches: 29, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
51 18 0.08
52 30 0.13
53 109 0.48
54 67 0.30
55 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (53 bp):
AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATACGG
Found at i:69672 original size:105 final size:106
Alignment explanation
Indices: 69404--69718 Score: 379
Period size: 105 Copynumber: 3.0 Consensus size: 106
69394 CCAAAATGGA
* ** * * * *
69404 AATTAACAAACTTATTATGAATTCCATGGATTTCACACATAGTGCCGATACGG-CATTCACAAAC
1 AATTAACAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGCTGATACGGTAATTCAC-AAC
* * *
69468 TCATTATGAATTTCGTGGGTTGCACACATAGTGCCAATACGGT
65 TCATTATGAATTTCGTGGGTTGCACACA-AGTGTCGATACGGC
* * *
69511 AATTCACAAACTCATTATGAA-TCTCGTGGGTTGCACATATAGTG-TCGATACAGTAATTCACAA
1 AATTAACAAACTCATTATGAATTCT-GTGGGTTGCACACATAGTGCT-GATACGGTAATTCACAA
*
69574 CTCATTATGAA-TTCTGTGGGTTGCACAC-AGTGTCGATACTGC
64 CTCATTATGAATTTC-GTGGGTTGCACACAAGTGTCGATACGGC
* *
69616 AATTTACAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGCTGATACGGTAATTCAAAACT
1 AATTAACAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGCTGATACGGTAATTCACAACT
* *
69681 AATTATGAATTTCGTGGATTGCACACATAGTGTCGATA
66 CATTATGAATTTCGTGGGTTGCACACA-AGTGTCGATA
69719 GTACATAATA
Statistics
Matches: 179, Mismatches: 20, Indels: 18
0.82 0.09 0.08
Matches are distributed among these distances:
105 85 0.47
106 12 0.07
107 76 0.42
108 6 0.03
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (106 bp):
AATTAACAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGCTGATACGGTAATTCACAACT
CATTATGAATTTCGTGGGTTGCACACAAGTGTCGATACGGC
Done.