Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003144.1 Hibiscus syriacus cultivar Beakdansim tig00006615_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: 57632
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:1447 original size:20 final size:19
Alignment explanation
Indices: 1424--1462 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1414 CATAAAATTT
1424 TTTTTTATTAAATATTTTTA
1 TTTTTTATTAAAT-TTTTTA
*
1444 TTTTTTATTTAATTTTTTA
1 TTTTTTATTAAATTTTTTA
1463 AATAATTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTTATTAAATTTTTTA
Found at i:1738 original size:21 final size:22
Alignment explanation
Indices: 1714--1766 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 22
1704 ATTCGCATCG
*
1714 TCCACGCCGACCGGGCA-TTCC
1 TCCAAGCCGACCGGGCATTTCC
1735 TCCAAGCCGACCGGGCATTTCC
1 TCCAAGCCGACCGGGCATTTCC
1757 TCCAAGCCGA
1 TCCAAGCCGA
1767 AGGCAATGCG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 16 0.53
22 14 0.47
ACGTcount: A:0.19, C:0.43, G:0.23, T:0.15
Consensus pattern (22 bp):
TCCAAGCCGACCGGGCATTTCC
Found at i:4090 original size:20 final size:20
Alignment explanation
Indices: 4067--4122 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
4057 TGCGATTTTC
4067 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* * **
4087 CAAATTTGCAAC-TGAATTT
1 CAAATTCGCAACGCGAAAGT
4106 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
4123 TTTAATTTCG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:4125 original size:20 final size:20
Alignment explanation
Indices: 4026--4125 Score: 89
Period size: 20 Copynumber: 5.0 Consensus size: 20
4016 ACATGACCAA
4026 CAAATTCGCAACGCGAATATGT
1 CAAATTCGCAACGCGAAT-T-T
** *
4048 -AAA-TCGCATTGCGATTTT
1 CAAATTCGCAACGCGAATTT
**
4066 CCAAATTCGCAACGCGAAAGT
1 -CAAATTCGCAACGCGAATTT
* *
4087 CAAATTTGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
4106 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
4126 AATTTCGTAA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
18 1 0.02
19 16 0.27
20 30 0.50
21 13 0.22
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:4903 original size:12 final size:12
Alignment explanation
Indices: 4882--4915 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4872 ACCAAATTTC
*
4882 CAATACCAAACA
1 CAATATCAAACA
4894 CAATATCAAACA
1 CAATATCAAACA
*
4906 CAATCTCAAA
1 CAATATCAAA
4916 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:5073 original size:24 final size:24
Alignment explanation
Indices: 5041--5094 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
5031 GTATTCGAAA
5041 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
5065 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
5089 TTTGAT
1 TTTGAT
5095 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:7717 original size:20 final size:20
Alignment explanation
Indices: 7692--7729 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
7682 CGCAAAATAA
7692 GCGTTGCGAATTTACCTTTC
1 GCGTTGCGAATTTACCTTTC
7712 GCGTTGCGAATTTACCTT
1 GCGTTGCGAATTTACCTT
7730 CAACATGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.16, C:0.24, G:0.21, T:0.39
Consensus pattern (20 bp):
GCGTTGCGAATTTACCTTTC
Found at i:7828 original size:25 final size:25
Alignment explanation
Indices: 7790--7839 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
7780 AAATCAATTA
* *
7790 AACATTGTTGTGGGTACATTATTTG
1 AACATTGATATGGGTACATTATTTG
7815 AACATTGATATGGGTACATTATTTG
1 AACATTGATATGGGTACATTATTTG
7840 GAAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (25 bp):
AACATTGATATGGGTACATTATTTG
Found at i:7953 original size:23 final size:23
Alignment explanation
Indices: 7921--7979 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
7911 ATATTTGAAC
7921 ATTGTTATGTATAAATTTG-TTAT
1 ATTG-TATGTATAAATTTGATTAT
* * **
7944 GTATGTATGTTTTGATTTGATTAT
1 AT-TGTATGTATAAATTTGATTAT
7968 ATTGTATGTATA
1 ATTGTATGTATA
7980 TTTTCATTCA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (23 bp):
ATTGTATGTATAAATTTGATTAT
Found at i:8234 original size:24 final size:25
Alignment explanation
Indices: 8207--8258 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
8197 TTTCAAATTC
*
8207 ATTTTATATGT-AATTGGAGTTTGA
1 ATTTTAAATGTCAATTGGAGTTTGA
* *
8231 A-TTTAAATTTCAATTTGAGTTTGA
1 ATTTTAAATGTCAATTGGAGTTTGA
8255 ATTT
1 ATTT
8259 CAATATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
23 7 0.30
24 14 0.61
25 2 0.09
ACGTcount: A:0.31, C:0.02, G:0.15, T:0.52
Consensus pattern (25 bp):
ATTTTAAATGTCAATTGGAGTTTGA
Found at i:8247 original size:18 final size:18
Alignment explanation
Indices: 8226--8262 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
8216 GTAATTGGAG
8226 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
8244 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
8262 T
1 T
8263 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:8269 original size:24 final size:24
Alignment explanation
Indices: 8218--8270 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
8208 TTTTATATGT
* * *
8218 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
8242 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
8266 AATTT
1 AATTT
8271 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:11043 original size:21 final size:21
Alignment explanation
Indices: 11015--11064 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
11005 ACCATTATCT
*
11015 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
*
11036 TGACGTAAAGCACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
11057 TCACGTAA
1 TCACGTAA
11065 TTCCCCTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:12765 original size:19 final size:20
Alignment explanation
Indices: 12743--12785 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
12733 AATTCGCAAC
12743 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
*
12762 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
12782 GCGA
1 GCGA
12786 ATTTGGTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.12, C:0.19, G:0.26, T:0.44
Consensus pattern (20 bp):
GCGATTTTCAGTTTCGCGTT
Found at i:13274 original size:20 final size:19
Alignment explanation
Indices: 13219--13322 Score: 91
Period size: 20 Copynumber: 5.3 Consensus size: 19
13209 GCGTAAAAAC
*
13219 ATTTGACTTCGCGTTGCAA
1 ATTTGACTTCGCGTTGCGA
13238 ATTTGACTATCGCGTTGCGA
1 ATTTGACT-TCGCGTTGCGA
*
13258 ATTTGACTTCTGTGTTGCGA
1 ATTTGACTTC-GCGTTGCGA
* * *
13278 TTTATAAATTCGCGTTGCGAA
1 ATT-TGACTTCGCGTTGCG-A
* * **
13299 ATTGGAATTTACGTTGCGA
1 ATTTGACTTCGCGTTGCGA
13318 ATTTG
1 ATTTG
13323 TTGGTCATTT
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
19 15 0.22
20 46 0.67
21 8 0.12
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.39
Consensus pattern (19 bp):
ATTTGACTTCGCGTTGCGA
Found at i:15307 original size:19 final size:19
Alignment explanation
Indices: 15261--15308 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
15251 ACTGGAAAAT
15261 CGGTTTGACCGGTTCGAAC
1 CGGTTTGACCGGTTCGAAC
*
15280 CGATTTGACCGG-TCTGAAC
1 CGGTTTGACCGGTTC-GAAC
*
15299 CGGTCTGACC
1 CGGTTTGACC
15309 CGACCCGACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 2 0.08
19 23 0.92
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.25
Consensus pattern (19 bp):
CGGTTTGACCGGTTCGAAC
Found at i:15407 original size:30 final size:30
Alignment explanation
Indices: 15371--15464 Score: 118
Period size: 30 Copynumber: 3.2 Consensus size: 30
15361 GAAATAATGC
* *
15371 TATTTTGGGAATTAATTCAAAAAGGGGTGT
1 TATTTTGGTAATTAATTTAAAAAGGGGTGT
* *
15401 TATTTTGGTAATTAATTTGAAAA-GGGTGC
1 TATTTTGGTAATTAATTTAAAAAGGGGTGT
* * *
15430 TATTTTGGTTATTATTTTAAAGAGGGGTGT
1 TATTTTGGTAATTAATTTAAAAAGGGGTGT
15460 TATTT
1 TATTT
15465 ATGTAAAATG
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 24 0.44
30 30 0.56
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.45
Consensus pattern (30 bp):
TATTTTGGTAATTAATTTAAAAAGGGGTGT
Found at i:16188 original size:31 final size:31
Alignment explanation
Indices: 16152--16245 Score: 95
Period size: 31 Copynumber: 3.0 Consensus size: 31
16142 CCCGAAGGAC
* *
16152 CAGTCCATAGATTCCGAAGAACCTAGGTAAT
1 CAGTCCATAGATTCCGAAGAACATAGGTAAA
*
16183 CAGTCCAT--ATCTCTCGAAGAACATAGGCAAA
1 CAGTCCATAGAT-TC-CGAAGAACATAGGTAAA
* *
16214 CGGTCCATATG-TCCCGAAGAACATAGGTAAA
1 CAGTCCATA-GATTCCGAAGAACATAGGTAAA
16245 C
1 C
16246 CCTCGACCCT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
29 2 0.04
30 2 0.04
31 46 0.88
32 1 0.02
33 1 0.02
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATAGATTCCGAAGAACATAGGTAAA
Found at i:19337 original size:2 final size:2
Alignment explanation
Indices: 19316--19368 Score: 63
Period size: 2 Copynumber: 26.0 Consensus size: 2
19306 ATATGTTCAC
* *
19316 AT AT CAT AT AT CAT AT -T AT AT AA AC 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 AT AT
19359 AT AT AT AT AT
1 AT AT AT AT AT
19369 CTCATAACTC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
1 1 0.02
2 40 0.89
3 4 0.09
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:20202 original size:31 final size:31
Alignment explanation
Indices: 20164--20257 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
20154 TCCGAAGGAC
* * *
20164 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
20195 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
20226 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
20257 C
1 C
20258 CCTCGACCAT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:24239 original size:31 final size:31
Alignment explanation
Indices: 24173--24266 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 31
24163 CCCGAAGGAC
* * * * *
24173 CAGTCCATAGATTCC-GATGAACCTAGGTAAT
1 CAGTCCATATA-TCCAGAAGAACATAGGCAAA
*
24204 CAGTCCATATATCCAGCAGAACATAGGCAAA
1 CAGTCCATATATCCAGAAGAACATAGGCAAA
* * *
24235 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATATCCAGAAGAACATAGGCAAA
24266 C
1 C
24267 CCTCGACCTT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
30 3 0.06
31 49 0.94
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATATCCAGAAGAACATAGGCAAA
Found at i:25827 original size:24 final size:24
Alignment explanation
Indices: 25800--25860 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
25790 TACCTGATTG
25800 TTGACCTGGATTCAAATATGATAC
1 TTGACCTGGATTCAAATATGATAC
* ***
25824 TTGACCTGAATTTTTATATGATAC
1 TTGACCTGGATTCAAATATGATAC
*
25848 TTGACATGGATTC
1 TTGACCTGGATTC
25861 TGATTTGTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (24 bp):
TTGACCTGGATTCAAATATGATAC
Found at i:26902 original size:34 final size:34
Alignment explanation
Indices: 26843--26909 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
26833 TTTTTTAGAG
*
26843 TTGTTTTCTCCTTTTTATCAAGAGAGAA-TTGTTA
1 TTGTTTTCTCCTTTTGATC-AGAGAGAAGTTGTTA
26877 TTGTTTTCTCCTTGTTAGATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTT-TT-GATCAGAGAGAAGTTGT
26910 AATTCCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 6 0.21
36 3 0.10
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTGATCAGAGAGAAGTTGTTA
Found at i:30298 original size:14 final size:14
Alignment explanation
Indices: 30258--30299 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
30248 TAGGTAATTG
**
30258 TTTGTTTATATTCG
1 TTTGTTTATATTTA
30272 TTTGTTTATATTTA
1 TTTGTTTATATTTA
30286 TTTGTTTATATTTA
1 TTTGTTTATATTTA
30300 GTCCAATGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.19, C:0.02, G:0.10, T:0.69
Consensus pattern (14 bp):
TTTGTTTATATTTA
Found at i:32893 original size:21 final size:21
Alignment explanation
Indices: 32837--32894 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
32827 AAATGACCAA
*
32837 CAAATTCGCAACGCGAATATG
1 CAAATTCGCAACGCGAATATC
* ** * *
32858 TAAA-TCGCATTGCGATTTTC
1 CAAATTCGCAACGCGAATATC
32878 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
32895 AGTCAAATTT
Statistics
Matches: 26, Mismatches: 10, Indels: 2
0.68 0.26 0.05
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (21 bp):
CAAATTCGCAACGCGAATATC
Found at i:46457 original size:11 final size:11
Alignment explanation
Indices: 46441--46465 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
46431 TAATATATAG
46441 TTTTGAAAACA
1 TTTTGAAAACA
46452 TTTTGAAAACA
1 TTTTGAAAACA
46463 TTT
1 TTT
46466 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:46512 original size:73 final size:73
Alignment explanation
Indices: 46352--46534 Score: 208
Period size: 73 Copynumber: 2.5 Consensus size: 73
46342 TTTTGACAAA
* * *
46352 ATATAATATATAATTTTTAAAAAACGATTTTCG-AAAATTTATATATTATATAGTTTTTTAAAAT
1 ATATAATATATAA-TTTT-GAAAAC-ATTTT-GAAAAATTTATATATTATATAGATTTTTAAAAC
*
46416 ATTTTAAAAAAG
62 ATTTGAAAAAAG
*
46428 ATATAATATATAGTTTTGAAAACATTTTGAAAACATTTATATATTATATA-ATTTTTAAAACATT
1 ATATAATATATAATTTTGAAAACATTTTGAAAA-ATTTATATATTATATAGATTTTTAAAACATT
***
46492 TGAAAACTT
65 TGAAAAAAG
* *
46501 ATATAGTATATAATTTTTAAAACATTTTTGAAAA
1 ATATAATATATAATTTTGAAAACA-TTTTGAAAA
46535 TTATAATGTA
Statistics
Matches: 93, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
72 1 0.01
73 46 0.49
74 30 0.32
75 4 0.04
76 12 0.13
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.44
Consensus pattern (73 bp):
ATATAATATATAATTTTGAAAACATTTTGAAAAATTTATATATTATATAGATTTTTAAAACATTT
GAAAAAAG
Found at i:46567 original size:32 final size:32
Alignment explanation
Indices: 46524--46683 Score: 109
Period size: 32 Copynumber: 5.0 Consensus size: 32
46514 TTTTTAAAAC
*
46524 ATTTTTG-AAAATTATAATGTATAGTTTAAAT
1 ATTTTTGAAAAATTATAATATATAGTTTAAAT
46555 ATTTTTGAAAAA-TATATATATATAGTTTTAAA-
1 ATTTTTGAAAAATTATA-ATATATAG-TTTAAAT
* * *
46587 AATTTTGAAAACTTAT-ATA-ATAATTTTAAACAT
1 ATTTTTGAAAAATTATAATATAT-AGTTT-AA-AT
* * * *
46620 TTTTTTGAAAACTATAAAATATATAGTTTTAAAA
1 ATTTTTGAAAAAT-TATAATATATAG-TTTAAAT
* *
46654 ACTTTTTTAAAAA-TA-AATGTATAGTTTAAA
1 A-TTTTTGAAAAATTATAATATATAGTTTAAA
46684 CAAATATTTT
Statistics
Matches: 103, Mismatches: 13, Indels: 26
0.73 0.09 0.18
Matches are distributed among these distances:
30 5 0.05
31 23 0.22
32 30 0.29
33 22 0.21
34 3 0.03
35 15 0.15
36 5 0.05
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (32 bp):
ATTTTTGAAAAATTATAATATATAGTTTAAAT
Found at i:46737 original size:14 final size:15
Alignment explanation
Indices: 46718--46751 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
46708 ATAATTATAA
46718 TATTTT-TATTTATT
1 TATTTTCTATTTATT
46732 TATTTTCTATTTATT
1 TATTTTCTATTTATT
*
46747 AATTT
1 TATTT
46752 ATTTTTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTTTCTATTTATT
Found at i:50583 original size:54 final size:55
Alignment explanation
Indices: 50525--50642 Score: 125
Period size: 58 Copynumber: 2.1 Consensus size: 55
50515 CTTTATTTAT
* * * *
50525 TATATGGATATT-TTA-TCATTT-ATTTTATTATTCATGTTTATTATTATATGTATA
1 TATATAGATATTATTATTCATTTGATTTT-TTACT-ATATTTATTATTATATATATA
*
50579 TATATATATATTAAATTATTTCATTTGATTTTTTACTATATTTATTATTATATATATA
1 TATATAGATATT--ATTA-TTCATTTGATTTTTTACTATATTTATTATTATATATATA
50637 TATATA
1 TATATA
50643 TTTCTTTAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
54 10 0.19
57 3 0.06
58 25 0.47
59 10 0.19
60 5 0.09
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.58
Consensus pattern (55 bp):
TATATAGATATTATTATTCATTTGATTTTTTACTATATTTATTATTATATATATA
Found at i:52199 original size:16 final size:16
Alignment explanation
Indices: 52178--52221 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
52168 GAATAATAAG
52178 CATGTGGGGTAGATAT
1 CATGTGGGGTAGATAT
52194 CATGTGGGGTAGATAT
1 CATGTGGGGTAGATAT
52210 CATGTGGGGTAG
1 CATGTGGGGTAG
52222 GACTTTCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.23, C:0.07, G:0.41, T:0.30
Consensus pattern (16 bp):
CATGTGGGGTAGATAT
Found at i:54920 original size:15 final size:14
Alignment explanation
Indices: 54902--54949 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 14
54892 GGGCAAAAAG
54902 AAAAAAAAAAAGCAA
1 AAAAAAAAAAAG-AA
54917 AAAAAAGCAAAAAGAA
1 AAAAAA--AAAAAGAA
*
54933 CAAAAGAAAAAAGAA
1 -AAAAAAAAAAAGAA
54948 AA
1 AA
54950 GGGACAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 2 0.07
15 14 0.48
16 2 0.07
17 11 0.38
ACGTcount: A:0.83, C:0.06, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGAA
Found at i:54920 original size:29 final size:29
Alignment explanation
Indices: 54887--54959 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
54877 TAATCAGAAT
54887 AAAAAGGGCAAAAAGAA-AAAA-AAAAAGCA
1 AAAAAGGGCAAAAAGAACAAAAGAAAAA--A
**
54916 AAAAAAAGCAAAAAGAACAAAAGAAAAAA
1 AAAAAGGGCAAAAAGAACAAAAGAAAAAA
*
54945 GAAAAGGGACAAAAA
1 AAAAAGGG-CAAAAA
54960 ACACATGCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
29 21 0.58
30 10 0.28
31 5 0.14
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.00
Consensus pattern (29 bp):
AAAAAGGGCAAAAAGAACAAAAGAAAAAA
Found at i:54928 original size:7 final size:7
Alignment explanation
Indices: 54896--54949 Score: 56
Period size: 7 Copynumber: 7.4 Consensus size: 7
54886 TAAAAAGGGC
54896 AAAAAGA
1 AAAAAGA
54903 AAAAA-A
1 AAAAAGA
*
54909 AAAAGCAAA
1 AAAA--AGA
*
54918 AAAAAGC
1 AAAAAGA
54925 AAAAAGA
1 AAAAAGA
54932 ACAAAAGA
1 A-AAAAGA
54940 AAAAAGA
1 AAAAAGA
54947 AAA
1 AAA
54950 GGGACAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 5 0.12
7 22 0.55
8 8 0.20
9 5 0.12
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:55565 original size:22 final size:22
Alignment explanation
Indices: 55537--55580 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
55527 AGCTACCCCA
55537 TCAAACC-TTTGAGCATCAAATG
1 TCAAACCATTT-AGCATCAAATG
55559 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTTAGCATCAAATG
55581 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCATTTAGCATCAAATG
Found at i:56645 original size:35 final size:36
Alignment explanation
Indices: 56530--56660 Score: 151
Period size: 35 Copynumber: 3.7 Consensus size: 36
56520 AACATAAACA
* * *
56530 TTGAAACA-TTTCCCTTGAAATAAATTTCGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAATTTTCGTCTCTC
* *
56565 TTGAGATAGTTTCCCTTGGAACTAAGTTTT-GTCTCTC
1 TTGAGACAGTTTCCCTTGAAAC-AA-TTTTCGTCTCTC
* * *
56602 TTAAGACAGTTTCTC-TGAAACAATTTTCGTCTATC
1 TTGAGACAGTTTCCCTTGAAACAATTTTCGTCTCTC
56637 TTGAGACAGTTTCCCTTGAAACAA
1 TTGAGACAGTTTCCCTTGAAACAA
56661 AACCTTTGAA
Statistics
Matches: 79, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
34 4 0.05
35 27 0.34
36 24 0.30
37 21 0.27
38 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (36 bp):
TTGAGACAGTTTCCCTTGAAACAATTTTCGTCTCTC
Found at i:57602 original size:104 final size:105
Alignment explanation
Indices: 57422--57632 Score: 327
Period size: 104 Copynumber: 2.0 Consensus size: 105
57412 GCACTCGAGG
**
57422 CAACACAAGTTCAACTTCACAACGAAGGGACAAACTGGTTGTCAACAACAACTTCTCAATTTCAG
1 CAACACAAGTTCAACTTCACAACGAAGGGACAAACTGCCTGTCAACAACAACTTCTCAATTTCAG
57487 AGCCAATTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 AGCCAATTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * **
57527 CAACGCAAGTTCAACTTCACGACGAAGGGAC-CGCTGCCTGTCAACAACAACTTCTC-ATTTCAG
1 CAACACAAGTTCAACTTCACAACGAAGGGACAAACTGCCTGTCAACAACAACTTCTCAATTTCAG
* *
57590 AGCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 AGCCAA-TTCAACTTCACAACGAAGGATATTGGACTCCAGA
57631 CA
1 CA
Statistics
Matches: 97, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
103 13 0.13
104 55 0.57
105 29 0.30
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.22
Consensus pattern (105 bp):
CAACACAAGTTCAACTTCACAACGAAGGGACAAACTGCCTGTCAACAACAACTTCTCAATTTCAG
AGCCAATTCAACTTCACAACGAAGGATATTGGACTCCAGA
Done.