Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004684.1 Hibiscus syriacus cultivar Beakdansim tig00010502_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: 52730
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:4778 original size:16 final size:18
Alignment explanation
Indices: 4747--4779 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
4737 CTTGTATTAG
4747 ATTTTATATATTTTTAAA
1 ATTTTATATATTTTTAAA
4765 ATTTTAT-T-TTTTTAA
1 ATTTTATATATTTTTAA
4780 TTTTTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTATATATTTTTAAA
Found at i:5358 original size:173 final size:171
Alignment explanation
Indices: 5073--5382 Score: 460
Period size: 173 Copynumber: 1.8 Consensus size: 171
5063 TTTTTGTGAA
** *
5073 AAACGCCGCAATAAGTATTGATATTTAGCGGCGTTTGTGTTAAAAACGTCGCAATAGGTGTTGAT
1 AAACGCCGCAATAAGTATTGATATTTAGCGGCGTTTGTGTTAAAAACACCGCAAAAGGTGTTGAT
* * * *
5138 ATTTAGTGGCGTTTGTTATAAAAACGCCGCAATAGATGTTGATATTTAGC-GTCGTTTGTCATAA
66 ATTTAGTGGCGTTTGTCATAAAAACGCCGCAATAGATGTTAATATTTAGCAG-CGTTTCTCAGAA
5202 AAACGCCGCTATAGGTGTTGATATTTAGCAGCGTTTTTCAAC
130 AAACGCCGCTATAGGTGTTGATATTTAGCAGCGTTTTTCAAC
* * * * *
5244 AAACGCCGCAATAGGTGTTGATATTTAGTGGCGTTTTTTTTATAAAAACACCGCAAAAGGTGTTG
1 AAACGCCGCAATAAGTATTGATATTTAGCGGCG-TTTGTGT-TAAAAACACCGCAAAAGGTGTTG
*
5309 ATATTTAGTGGCGTTTGTCATAAAAACGCCGCAATAGGTGTTAATATTTAGCAGCGTTTCTCAGA
64 ATATTTAGTGGCGTTTGTCATAAAAACGCCGCAATAGATGTTAATATTTAGCAGCGTTTCTCAGA
*
5374 CAAACGCCG
129 AAAACGCCG
5383 TAATATGTTA
Statistics
Matches: 122, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
171 30 0.25
172 5 0.04
173 86 0.70
174 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (171 bp):
AAACGCCGCAATAAGTATTGATATTTAGCGGCGTTTGTGTTAAAAACACCGCAAAAGGTGTTGAT
ATTTAGTGGCGTTTGTCATAAAAACGCCGCAATAGATGTTAATATTTAGCAGCGTTTCTCAGAAA
AACGCCGCTATAGGTGTTGATATTTAGCAGCGTTTTTCAAC
Found at i:5379 original size:43 final size:43
Alignment explanation
Indices: 5071--5410 Score: 387
Period size: 43 Copynumber: 7.9 Consensus size: 43
5061 GTTTTTTGTG
* * **
5071 AAAAACGCCGCAATAAGTATTGATATTTAGCGGCGTTTGTGTT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAT
* * *
5114 AAAAACGTCGCAATAGGTGTTGATATTTAGTGGCGTTTGTTAT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAT
* *
5157 AAAAACGCCGCAATAGATGTTGATATTTAGCGTCGTTTGTCAT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAT
* * *
5200 AAAAACGCCGCTATAGGTGTTGATATTTAGCAGCGTTTTTCA-
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAT
* * * *
5242 ACAAACGCCGCAATAGGTGTTGATATTTAGTGGCGTTTTTTTTAT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCG--TTTGTCAT
* * *
5287 AAAAACACCGCAAAAGGTGTTGATATTTAGTGGCGTTTGTCAT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAT
* * * *
5330 AAAAACGCCGCAATAGGTGTTAATATTTAGCAGCGTTTCTCAG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAT
* * * * *
5373 ACAAACGCCGTAATATGT-TATGATGTTTAGCGGTGTTT
1 AAAAACGCCGCAATAGGTGT-TGATATTTAGCGGCGTTT
5411 TTTGTTAAAA
Statistics
Matches: 253, Mismatches: 40, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
42 32 0.13
43 183 0.72
44 6 0.02
45 32 0.13
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (43 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAT
Found at i:5420 original size:130 final size:130
Alignment explanation
Indices: 5071--5420 Score: 422
Period size: 130 Copynumber: 2.7 Consensus size: 130
5061 GTTTTTTGTG
* * * * * * *
5071 AAAAACGCCGCAATAAGTATTGATATTTAGCGGCGTTTGTGTTAA-AAACGTCGCAATAGGTGTT
1 AAAAACGCCGCAATAGGTGTTAATATTTAGCAGCG-TT-TCTCAACAAACGCCGCAATAGGTGTT
* * * * *
5135 GATATTTAGTGGCG-TTTGT-TATAAAAACGCCGCAATAGATGTTGATATTTAGCGTCGTTTGTC
64 GATATTTAGCGGCGTTTTTTGTATAAAAACACCGCAAAAGATGTTGATATTTAGCGGCGTTTGTC
5198 AT
129 AT
* * *
5200 AAAAACGCCGCTATAGGTGTTGATATTTAGCAGCGTTTTTCAACAAACGCCGCAATAGGTGTTGA
1 AAAAACGCCGCAATAGGTGTTAATATTTAGCAGCGTTTCTCAACAAACGCCGCAATAGGTGTTGA
* * * *
5265 TATTTAGTGGCGTTTTTTTTATAAAAACACCGCAAAAGGTGTTGATATTTAGTGGCGTTTGTCAT
66 TATTTAGCGGCGTTTTTTGTATAAAAACACCGCAAAAGATGTTGATATTTAGCGGCGTTTGTCAT
* *
5330 AAAAACGCCGCAATAGGTGTTAATATTTAGCAGCGTTTCTCAGACAAACGCCGTAATATGT-TAT
1 AAAAACGCCGCAATAGGTGTTAATATTTAGCAGCGTTTCTCA-ACAAACGCCGCAATAGGTGT-T
* *
5394 GATGTTTAGCGGTGTTTTTTGT-TAAAA
64 GATATTTAGCGGCGTTTTTTGTATAAAA
5421 CAAAATTTCT
Statistics
Matches: 194, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
127 4 0.02
128 34 0.18
129 35 0.18
130 86 0.44
131 35 0.18
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.34
Consensus pattern (130 bp):
AAAAACGCCGCAATAGGTGTTAATATTTAGCAGCGTTTCTCAACAAACGCCGCAATAGGTGTTGA
TATTTAGCGGCGTTTTTTGTATAAAAACACCGCAAAAGATGTTGATATTTAGCGGCGTTTGTCAT
Found at i:5897 original size:17 final size:17
Alignment explanation
Indices: 5875--5908 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5865 AAATACGTTG
5875 AAAAGACTTATATGGAA
1 AAAAGACTTATATGGAA
5892 AAAAGACTTATATGGAA
1 AAAAGACTTATATGGAA
5909 GTTTTGAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.24
Consensus pattern (17 bp):
AAAAGACTTATATGGAA
Found at i:9591 original size:18 final size:18
Alignment explanation
Indices: 9554--9592 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
9544 AACTCTGGTC
* * *
9554 AAAGTCAACGGGTTGGGT
1 AAAGTCAACAGGTCGAGT
9572 AAAGTCAACAGGTCGAGT
1 AAAGTCAACAGGTCGAGT
9590 AAA
1 AAA
9593 AGTTAAAGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.13, G:0.31, T:0.18
Consensus pattern (18 bp):
AAAGTCAACAGGTCGAGT
Found at i:9648 original size:20 final size:20
Alignment explanation
Indices: 9623--9660 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9613 TTGGGTTGAC
9623 TCGGTTC-AGGTTGACTCGAT
1 TCGGTTCGA-GTTGACTCGAT
9643 TCGGTTCGAGTTGACTCG
1 TCGGTTCGAGTTGACTCG
9661 GACCGGTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.13, C:0.21, G:0.32, T:0.34
Consensus pattern (20 bp):
TCGGTTCGAGTTGACTCGAT
Found at i:11042 original size:20 final size:20
Alignment explanation
Indices: 11014--11051 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11004 TATCATAGAA
11014 GAGAAGTATCGATACTATAG
1 GAGAAGTATCGATACTATAG
*
11034 GAGAGGTATCGATACTAT
1 GAGAAGTATCGATACTAT
11052 TCAGTCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (20 bp):
GAGAAGTATCGATACTATAG
Found at i:11622 original size:23 final size:23
Alignment explanation
Indices: 11595--11670 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 23
11585 TTATCTATTG
11595 ATTTTGTTTAATGCATAAGTTGC
1 ATTTTGTTTAATGCATAAGTTGC
* * ** * * *
11618 ATTTTCGTATGATGGTTATCGATCC
1 ATTTT-GTTTAATGCATA-AGTTGC
*
11643 ATTTTGTTTAATGCATATGTTGC
1 ATTTTGTTTAATGCATAAGTTGC
11666 ATTTT
1 ATTTT
11671 CGTATCTATA
Statistics
Matches: 37, Mismatches: 14, Indels: 4
0.67 0.25 0.07
Matches are distributed among these distances:
23 13 0.35
24 16 0.43
25 8 0.22
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (23 bp):
ATTTTGTTTAATGCATAAGTTGC
Found at i:11633 original size:48 final size:48
Alignment explanation
Indices: 11576--11675 Score: 164
Period size: 48 Copynumber: 2.1 Consensus size: 48
11566 CATACTTTGT
* **
11576 GTATGATGGTTATCTATTGATTTTGTTTAATGCATAAGTTGCATTTTC
1 GTATGATGGTTATCGATCCATTTTGTTTAATGCATAAGTTGCATTTTC
*
11624 GTATGATGGTTATCGATCCATTTTGTTTAATGCATATGTTGCATTTTC
1 GTATGATGGTTATCGATCCATTTTGTTTAATGCATAAGTTGCATTTTC
11672 GTAT
1 GTAT
11676 CTATACTATG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.22, C:0.10, G:0.19, T:0.49
Consensus pattern (48 bp):
GTATGATGGTTATCGATCCATTTTGTTTAATGCATAAGTTGCATTTTC
Found at i:11775 original size:53 final size:53
Alignment explanation
Indices: 11691--11814 Score: 160
Period size: 53 Copynumber: 2.4 Consensus size: 53
11681 CTATGTGTAC
* *
11691 TTTCGACACTATGTGTGCACCCATGGTATTCATAATGAGTTTATGAATGACCA
1 TTTCGACACTATATGTGCACCCATGGAATTCATAATGAGTTTATGAATGACCA
* * * * *
11744 TTTCGACATTATATGTGCATCCATGGAATTCATAATGAGTTTGTGGATTACCA
1 TTTCGACACTATATGTGCACCCATGGAATTCATAATGAGTTTATGAATGACCA
* *
11797 TTTTGACACT-TAGGTGCA
1 TTTCGACACTATATGTGCA
11815 ACTCATGTAC
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
52 7 0.11
53 54 0.89
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (53 bp):
TTTCGACACTATATGTGCACCCATGGAATTCATAATGAGTTTATGAATGACCA
Found at i:12961 original size:68 final size:68
Alignment explanation
Indices: 12852--13127 Score: 462
Period size: 68 Copynumber: 4.0 Consensus size: 68
12842 TTAGGGATTT
* *
12852 TTTAGGGTAAACTACCTATTTGGTTACTTATATATTATCTAATTTATGTTTTGGTCACTCAATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
12917 TTA
66 TTA
* * *
12920 TTTAGGGTAAACTACCTATTTGGTCTCTTATATATTATCTAATTTATGGTTTGATCACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
12985 TTA
66 TTA
* *
12988 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATATTTTGGTCACTCTATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
13053 TTA
66 TTA
*
13056 TTTTAGGGTAAACTACCTATTTGGTCACTTATATATTATATAATTTATGTTTTGGTCACTCGATT
1 -TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATT
*
13121 AATA
65 ATTA
13125 TTT
1 TTT
13128 TTTTCAAAAT
Statistics
Matches: 193, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
68 129 0.67
69 64 0.33
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (68 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
TTA
Found at i:13041 original size:31 final size:31
Alignment explanation
Indices: 13006--13115 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 31
12996 AAACTACCTA
*
13006 TTTGGTCACTTATATATTATCTAATTTATAT
1 TTTGGTCACTTATATATTATATAATTTATAT
* **
13037 TTTGGTCACTCTATTATTATTTTAGGGTAAACTACCTA-
1 TTTGGTCACT-TA-TA-TATTATA---TAATTTA--TAT
*
13075 TTTGGTCACTTATATATTATATAATTTATGT
1 TTTGGTCACTTATATATTATATAATTTATAT
13106 TTTGGTCACT
1 TTTGGTCACT
13116 CGATTAATAT
Statistics
Matches: 62, Mismatches: 8, Indels: 18
0.70 0.09 0.20
Matches are distributed among these distances:
30 1 0.02
31 20 0.32
32 7 0.11
33 2 0.03
34 5 0.08
35 6 0.10
36 2 0.03
37 7 0.11
38 10 0.16
39 2 0.03
ACGTcount: A:0.26, C:0.12, G:0.11, T:0.51
Consensus pattern (31 bp):
TTTGGTCACTTATATATTATATAATTTATAT
Found at i:13273 original size:32 final size:32
Alignment explanation
Indices: 13210--13273 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
13200 TGCTAACATG
** *
13210 ACATTTTTTAATTATGTTTGGATGTTGGACTA
1 ACATTTTTTAATTATGTTTGGATACTAGACTA
13242 ACATTTTTTAATTATGTTTGGATACTAGACTA
1 ACATTTTTTAATTATGTTTGGATACTAGACTA
13274 TGTAATTCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (32 bp):
ACATTTTTTAATTATGTTTGGATACTAGACTA
Found at i:13754 original size:6 final size:6
Alignment explanation
Indices: 13743--13771 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
13733 CATGATTTTT
13743 TTTGAG TTTGAG TTTGAG TTTGAG TTTGA
1 TTTGAG TTTGAG TTTGAG TTTGAG TTTGA
13772 TTCTTGGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (6 bp):
TTTGAG
Found at i:14787 original size:14 final size:15
Alignment explanation
Indices: 14768--14798 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
14758 TTTGATTCAA
14768 AAATAATAT-TAATT
1 AAATAATATGTAATT
14782 AAATAATATGTAATT
1 AAATAATATGTAATT
14797 AA
1 AA
14799 GGTTTGGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
AAATAATATGTAATT
Found at i:17377 original size:21 final size:21
Alignment explanation
Indices: 17353--17394 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
17343 ATTATCCAAT
17353 AAACATGACATT-CATAACAAC
1 AAACATGA-ATTCCATAACAAC
* *
17374 AAACTTTAATTCCATAACAAC
1 AAACATGAATTCCATAACAAC
17395 CAACTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.50, C:0.24, G:0.02, T:0.24
Consensus pattern (21 bp):
AAACATGAATTCCATAACAAC
Found at i:17399 original size:21 final size:21
Alignment explanation
Indices: 17365--17409 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
17355 ACATGACATT
*
17365 CATAACAACAAACTTTAATTC
1 CATAACAACAAACTTTAAATC
*
17386 CATAACAACCAACTTTAAATC
1 CATAACAACAAACTTTAAATC
17407 CAT
1 CAT
17410 TATAATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (21 bp):
CATAACAACAAACTTTAAATC
Found at i:24297 original size:83 final size:83
Alignment explanation
Indices: 24200--24666 Score: 499
Period size: 83 Copynumber: 5.6 Consensus size: 83
24190 TATAATAAAC
** * * ** *
24200 GCCACTATAGATGAACCCTATTATGGTATTTGTATAAAAACATTGCTAATGTACTACTCTGTTGC
1 GCCACTATAGATGAACCCTATTACAGCATTTATATAAAAACACCGCTAAAGTACTACTCTGTTGC
*
24265 GGCATTTGTTGAAAAAAT
66 GGCGTTTGTTGAAAAAAT
* * * * *
24283 GACACTATATATGAACCCTATTGCAGCATTTATATAAAAACACCGCTAGCA-TATTACTCTGTTG
1 GCCACTATAGATGAACCCTATTACAGCATTTATATAAAAACACCGCTA-AAGTACTACTCTGTTG
24347 CGGCGTTTGTTGAAAAAAT
65 CGGCGTTTGTTGAAAAAAT
* * ** * * *
24366 GCCACTATAGATAAACCCTATTGCAATATTTTTGTAAAAACACTGCTAAAGTACTACTCCT-TTG
1 GCCACTATAGATGAACCCTATTACAGCATTTATATAAAAACACCGCTAAAGTACTACT-CTGTTG
*
24430 CGGCGTTTGTTGAGAAAAT
65 CGGCGTTTGTTGAAAAAAT
* * * ** *
24449 ACCACTATAGATGAACCCTATTACAACATTTGTATAAAAATGCCAC-AAATGTACTACTCTGTTG
1 GCCACTATAGATGAACCCTATTACAGCATTTATATAAAAACACCGCTAAA-GTACTACTCTGTTG
24513 CGGCGTTTGTTGAAAAAAT
65 CGGCGTTTGTTGAAAAAAT
* * ** * * * * * * *
24532 GCCACTATAAATTAACCCTATTATGGCATTTTTGTAAAGACACCGATAAAGTACTACTCTATAGA
1 GCCACTATAGATGAACCCTATTACAGCATTTATATAAAAACACCGCTAAAGTACTACTCTGTTGC
24597 GGCGTTTGTTGAAAAAAT
66 GGCGTTTGTTGAAAAAAT
* * ** *
24615 GCCACTATAGATGAACCATATTATATTATTTATATAAAAACACCACTAAAGT
1 GCCACTATAGATGAACCCTATTACAGCATTTATATAAAAACACCGCTAAAGT
24667 TACCATATTG
Statistics
Matches: 316, Mismatches: 62, Indels: 12
0.81 0.16 0.03
Matches are distributed among these distances:
82 6 0.02
83 305 0.97
84 5 0.02
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (83 bp):
GCCACTATAGATGAACCCTATTACAGCATTTATATAAAAACACCGCTAAAGTACTACTCTGTTGC
GGCGTTTGTTGAAAAAAT
Found at i:24487 original size:166 final size:166
Alignment explanation
Indices: 24200--24660 Score: 557
Period size: 166 Copynumber: 2.8 Consensus size: 166
24190 TATAATAAAC
* * * * * *
24200 GCCACTATAGATGAACCCTATTATGGTATTTGTATAAAAACATTGCTAATGTACTACTCTGTTGC
1 GCCACTATAGATAAACCCTATTATGGTATTTTTGTAAAAACACTGCTAAAGTACTACTCTATTGC
* * * * *
24265 GGCATTTGTTGAAAAAATGA-CACTATATATGAACCCTATTGCAGCATTTATATAAAAACACCGC
66 GGCGTTTGTTGAAAAAAT-ACCACTATAGATGAACCCTATTACAACATTTATATAAAAACACCAC
* * *
24329 TAGCATATTACTCTGTTGCGGCGTTTGTTGAAAAAAT
130 AAACATACTACTCTGTTGCGGCGTTTGTTGAAAAAAT
****
24366 GCCACTATAGATAAACCCTATTGCAATATTTTTGTAAAAACACTGCTAAAGTACTACTCCT-TTG
1 GCCACTATAGATAAACCCTATTATGGTATTTTTGTAAAAACACTGCTAAAGTACTACT-CTATTG
* * **
24430 CGGCGTTTGTTGAGAAAATACCACTATAGATGAACCCTATTACAACATTTGTATAAAAATGCCAC
65 CGGCGTTTGTTGAAAAAATACCACTATAGATGAACCCTATTACAACATTTATATAAAAACACCAC
**
24495 AAATGTACTACTCTGTTGCGGCGTTTGTTGAAAAAAT
130 AAACATACTACTCTGTTGCGGCGTTTGTTGAAAAAAT
* * * * * * * *
24532 GCCACTATAAATTAACCCTATTATGGCATTTTTGTAAAGACACCGATAAAGTACTACTCTATAGA
1 GCCACTATAGATAAACCCTATTATGGTATTTTTGTAAAAACACTGCTAAAGTACTACTCTATTGC
* * * **
24597 GGCGTTTGTTGAAAAAATGCCACTATAGATGAACCATATTATATTATTTATATAAAAACACCAC
66 GGCGTTTGTTGAAAAAATACCACTATAGATGAACCCTATTACAACATTTATATAAAAACACCAC
24661 TAAAGTTACC
Statistics
Matches: 248, Mismatches: 44, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
165 3 0.01
166 243 0.98
167 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (166 bp):
GCCACTATAGATAAACCCTATTATGGTATTTTTGTAAAAACACTGCTAAAGTACTACTCTATTGC
GGCGTTTGTTGAAAAAATACCACTATAGATGAACCCTATTACAACATTTATATAAAAACACCACA
AACATACTACTCTGTTGCGGCGTTTGTTGAAAAAAT
Found at i:24655 original size:249 final size:249
Alignment explanation
Indices: 24201--24666 Score: 601
Period size: 249 Copynumber: 1.9 Consensus size: 249
24191 ATAATAAACG
**** *** *
24201 CCACTATAGATGAACCCTATTATGGTATTTGTATAAAAACATTGCTAATGTACTACTCTGTTGCG
1 CCACTATAGATGAACCCTATTACAACATTTGTATAAAAACACCACAAATGTACTACTCTGTTGCG
* * *
24266 GCATTTGTTGAAAAAATGACACTATATATGAACCCTATTGCAGCATTTATATAAAAACACCGCTA
66 GCATTTGTTGAAAAAATGACACTATAAATGAACCCTATTACAGCATTTATATAAAAACACCGATA
* * * * * * *
24331 GCATATTACTCTGTTGCGGCGTTTGTTGAAAAAATGCCACTATAGATAAACCCTATTGCAATATT
131 GAATACTACTCTATAGAGGCGTTTGTTGAAAAAATGCCACTATAGATAAACCATATTACAATATT
* * **
24396 TTTGTAAAAACACTGCTAAAGTACTACTCCTTTGCGGCGTTTGTTGAGAAAATA
196 TATATAAAAACACCACTAAAGTACTACTCCTTTGCGGCGTTTGTTGAGAAAATA
**
24450 CCACTATAGATGAACCCTATTACAACATTTGTATAAAAATGCCACAAATGTACTACTCTGTTGCG
1 CCACTATAGATGAACCCTATTACAACATTTGTATAAAAACACCACAAATGTACTACTCTGTTGCG
* * * ** * * *
24515 GCGTTTGTTGAAAAAATGCCACTATAAATTAACCCTATTATGGCATTTTTGTAAAGACACCGATA
66 GCATTTGTTGAAAAAATGACACTATAAATGAACCCTATTACAGCATTTATATAAAAACACCGATA
* * *
24580 -AAGTACTACTCTATAGAGGCGTTTGTTGAAAAAATGCCACTATAGATGAACCATATTATATTAT
131 GAA-TACTACTCTATAGAGGCGTTTGTTGAAAAAATGCCACTATAGATAAACCATATTACAATAT
24644 TTATATAAAAACACCACTAAAGT
195 TTATATAAAAACACCACTAAAGT
24667 TACCATATTG
Statistics
Matches: 181, Mismatches: 35, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
248 1 0.01
249 180 0.99
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (249 bp):
CCACTATAGATGAACCCTATTACAACATTTGTATAAAAACACCACAAATGTACTACTCTGTTGCG
GCATTTGTTGAAAAAATGACACTATAAATGAACCCTATTACAGCATTTATATAAAAACACCGATA
GAATACTACTCTATAGAGGCGTTTGTTGAAAAAATGCCACTATAGATAAACCATATTACAATATT
TATATAAAAACACCACTAAAGTACTACTCCTTTGCGGCGTTTGTTGAGAAAATA
Found at i:27525 original size:29 final size:29
Alignment explanation
Indices: 27483--27539 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
27473 TGAACTTTGG
27483 AGGCATGATTAAATCTGGGACCAAGCTTC
1 AGGCATGATTAAATCTGGGACCAAGCTTC
27512 AGGCATGATTAAATCTGGGACCAAGCTT
1 AGGCATGATTAAATCTGGGACCAAGCTT
27540 AACTCTTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (29 bp):
AGGCATGATTAAATCTGGGACCAAGCTTC
Found at i:28545 original size:13 final size:13
Alignment explanation
Indices: 28527--28551 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28517 ACAATCTTAG
28527 AGACAACTTTGAT
1 AGACAACTTTGAT
28540 AGACAACTTTGA
1 AGACAACTTTGA
28552 GACACAATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
AGACAACTTTGAT
Found at i:28909 original size:3 final size:3
Alignment explanation
Indices: 28903--28933 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
28893 ATAATAATAT
*
28903 TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28934 CTCGGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:33036 original size:2 final size:2
Alignment explanation
Indices: 33020--33118 Score: 56
Period size: 2 Copynumber: 53.5 Consensus size: 2
33010 CTTTAAATGG
*
33020 TA TA TA GTA TA -A TA TA TA GTC TA TA TA TA T- TA T- TA -A TA TA
1 TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
33060 TA TA -A TA TC TA TA TT TT TA T- TA TG TA CA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33099 TA -A TA T- TA TA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
33119 TACTTTATTT
Statistics
Matches: 76, Mismatches: 9, Indels: 24
0.70 0.08 0.22
Matches are distributed among these distances:
1 10 0.13
2 63 0.83
3 3 0.04
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33059 original size:15 final size:16
Alignment explanation
Indices: 33041--33115 Score: 61
Period size: 15 Copynumber: 4.9 Consensus size: 16
33031 ATATATAGTC
33041 TATATATATTAT-TAA
1 TATATATATTATATAA
* *
33056 TATATATAATATCT-A
1 TATATATATTATATAA
* * *
33071 TATTTTTATTATGTACA
1 TATATATATTATATA-A
33088 -ATATATA-TATATAA
1 TATATATATTATATAA
33102 TAT-TATATTATATA
1 TATATATATTATATA
33116 TATTACTTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
14 5 0.11
15 35 0.74
16 6 0.13
17 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (16 bp):
TATATATATTATATAA
Found at i:33126 original size:19 final size:19
Alignment explanation
Indices: 33089--33138 Score: 50
Period size: 21 Copynumber: 2.6 Consensus size: 19
33079 TTATGTACAA
33089 TATATATATATAATATTATAT
1 TATATATAT-TAATATTAT-T
*
33110 TATATATATTACT-TTATT
1 TATATATATTAATATTATT
33128 TAGTATA-ATTA
1 TA-TATATATTA
33139 TACATATAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 7 0.26
19 8 0.30
20 3 0.11
21 9 0.33
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
TATATATATTAATATTATT
Found at i:33260 original size:52 final size:50
Alignment explanation
Indices: 33168--33268 Score: 116
Period size: 52 Copynumber: 2.0 Consensus size: 50
33158 ATCATAGCAT
* *
33168 TTATAGTATATAAATATTATTAGTGTATTTATATTATATTATATTATTATTA
1 TTATACTATATAAATATTATTAGTGTATTTATATGATATTAT-TT-TTATTA
* *
33220 TTATACTATATAAGTATATATTA-T-TATTTATGATGCTATTATTTTTATT
1 TTATACTATATAAATAT-TATTAGTGTATTTAT-ATGATATTATTTTTATT
33269 TTTAGGTCTG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
50 5 0.12
51 9 0.21
52 24 0.56
53 5 0.12
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (50 bp):
TTATACTATATAAATATTATTAGTGTATTTATATGATATTATTTTTATTA
Found at i:34243 original size:19 final size:19
Alignment explanation
Indices: 34219--34267 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
34209 ATTTTCAATT
34219 ATTTGTAATTTGATCACTG
1 ATTTGTAATTTGATCACTG
34238 ATTTGTAATTTGATCACTG
1 ATTTGTAATTTGATCACTG
34257 ATTTGTAATTT
1 ATTTGTAATTT
34268 AATTTAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.51
Consensus pattern (19 bp):
ATTTGTAATTTGATCACTG
Found at i:36432 original size:31 final size:31
Alignment explanation
Indices: 36394--36480 Score: 149
Period size: 31 Copynumber: 2.8 Consensus size: 31
36384 AGAATGATAA
36394 CATCTTGATACCCAATATTGAGGATCAATAT
1 CATCTTGATACCCAATATTGAGGATCAATAT
36425 CATCTTGATACCCAATATTGAGGATCAATAT
1 CATCTTGATACCCAATATTGAGGATCAATAT
*
36456 CATCTCGATACCCAAT-TGTGAGGAT
1 CATCTTGATACCCAATAT-TGAGGAT
36481 ACATAGTCCA
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
30 1 0.02
31 53 0.98
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (31 bp):
CATCTTGATACCCAATATTGAGGATCAATAT
Found at i:37978 original size:2 final size:2
Alignment explanation
Indices: 37971--38105 Score: 73
Period size: 2 Copynumber: 72.0 Consensus size: 2
37961 AGTCTTAGAC
* * *
37971 TA TA TA TA TA TA CTA TA CCA TGC TA TA CTA TA TA -A AA TA T- TA
1 TA TA TA TA TA TA -TA TA -TA T-A TA TA -TA TA TA TA TA TA TA TA
*
38013 TA TA -A TA TA TA T- TA TA TA -A TA TA AA TA T- TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
38050 TA TA -A TA TA -A TA TCA TA TA -A TA TA -A TA TA TA T- TA AA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
*
38088 TA TA CA -A TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA
38106 AACTCTACAT
Statistics
Matches: 104, Mismatches: 10, Indels: 38
0.68 0.07 0.25
Matches are distributed among these distances:
1 14 0.13
2 82 0.79
3 8 0.08
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (2 bp):
TA
Found at i:38015 original size:5 final size:5
Alignment explanation
Indices: 38006--38106 Score: 92
Period size: 5 Copynumber: 21.4 Consensus size: 5
37996 TACTATATAA
* * *
38006 AATAT TATAT AATAT -ATAT TATAT AATAT AA-AT ATTAT -ATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
*
38053 AATAT AATAT CATAT AATAT AATAT -ATATT AA-AT -ATAT ACA-AT -ATAT
1 AATAT AATAT AATAT AATAT AATAT AATA-T AATAT AATAT A-ATAT AATAT
38100 AATAT AA
1 AATAT AA
38107 ACTCTACATG
Statistics
Matches: 79, Mismatches: 7, Indels: 20
0.75 0.07 0.19
Matches are distributed among these distances:
3 2 0.03
4 18 0.23
5 57 0.72
6 2 0.03
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (5 bp):
AATAT
Found at i:38068 original size:52 final size:52
Alignment explanation
Indices: 38006--38106 Score: 134
Period size: 52 Copynumber: 1.9 Consensus size: 52
37996 TACTATATAA
* **
38006 AATATTATATAATAT-ATAT-TATATAATATAAATATTATATATAATATAATAT
1 AATATCATATAATATAATATATAT-TAA-ATAAATACAATATATAATATAATAT
*
38058 AATATCATATAATATAATATATATTAAATATATACAATATATAATATAA
1 AATATCATATAATATAATATATATTAAATAAATACAATATATAATATAA
38107 ACTCTACATG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
52 33 0.77
53 7 0.16
54 3 0.07
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (52 bp):
AATATCATATAATATAATATATATTAAATAAATACAATATATAATATAATAT
Found at i:38170 original size:21 final size:22
Alignment explanation
Indices: 38135--38175 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
38125 ATACTATAGG
38135 TTAATAATATATACTATATATT
1 TTAATAATATATACTATATATT
*
38157 TTAAT-ATGTATACTATATA
1 TTAATAATATATACTATATA
38176 CTATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAATAATATATACTATATATT
Done.