Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001619.1 Hibiscus syriacus cultivar Beakdansim tig00003217_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: 141596
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4932 original size:20 final size:20
Alignment explanation
Indices: 4907--4952 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
4897 TATATAATCA
* *
4907 CAACGCGATTTTGATTATCG
1 CAACGCGATTCTGACTATCG
*
4927 CAACGCGATTCTGACTGTCG
1 CAACGCGATTCTGACTATCG
4947 CAACGC
1 CAACGC
4953 TGAATTTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (20 bp):
CAACGCGATTCTGACTATCG
Found at i:5789 original size:24 final size:23
Alignment explanation
Indices: 5756--5809 Score: 90
Period size: 24 Copynumber: 2.3 Consensus size: 23
5746 GGTATTCAAA
5756 ATTTGATCTTGGTCAATACCCGG
1 ATTTGATCTTGGTCAATACCCGG
*
5779 ACTTTGATCTTGGTCAATACTCGG
1 A-TTTGATCTTGGTCAATACCCGG
5803 ATTTGAT
1 ATTTGAT
5810 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 7 0.24
24 22 0.76
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (23 bp):
ATTTGATCTTGGTCAATACCCGG
Found at i:6028 original size:14 final size:14
Alignment explanation
Indices: 5999--6035 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5989 AGAAAAAGAA
5999 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
6014 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
6028 GAAGAAAA
1 GAAGAAAA
6036 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:8347 original size:135 final size:138
Alignment explanation
Indices: 8139--8416 Score: 490
Period size: 135 Copynumber: 2.0 Consensus size: 138
8129 GCAAACGTTG
8139 TATTATCTGTATTTTATGTGTAAACTATTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATCTGTATTTTATGTGTAAACTATTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
8204 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTG-A-A-CAACGCG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATACCAACGCG
8266 AATTTGAC
131 AATTTGAC
* *
8274 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATCTGTATTTTATGTGTAAACTATTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
8339 TTGAACATTGCTATGATCTGTTCAGTTGTTATCATTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATA-C-CAACG
8404 CGAATTTGAC
129 CGAATTTGAC
8414 TAT
1 TAT
8417 CGCAACACGA
Statistics
Matches: 135, Mismatches: 3, Indels: 5
0.94 0.02 0.03
Matches are distributed among these distances:
135 115 0.85
136 1 0.01
137 1 0.01
140 18 0.13
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (138 bp):
TATTATCTGTATTTTATGTGTAAACTATTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATACCAACGCG
AATTTGAC
Found at i:8412 original size:20 final size:20
Alignment explanation
Indices: 8387--8532 Score: 162
Period size: 20 Copynumber: 7.7 Consensus size: 20
8377 TTACACATTC
*
8387 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
8407 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
8427 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
8447 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
8467 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
8487 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
8501 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
8521 A-TTGACTTTCGC
1 ATTTGACTATCGC
8533 GTTGCGATTT
Statistics
Matches: 106, Mismatches: 14, Indels: 13
0.80 0.11 0.10
Matches are distributed among these distances:
14 10 0.09
16 1 0.01
18 1 0.01
19 9 0.08
20 85 0.80
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:8551 original size:20 final size:20
Alignment explanation
Indices: 8522--8582 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
8512 GCAACGCGAA
*
8522 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
* *
8542 TTGGCTTTCGCATTACGATT
1 TTGACTTTCGCATTGCGATT
8562 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
8582 T
1 T
8583 GAGTTTAGCG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:8755 original size:63 final size:65
Alignment explanation
Indices: 8672--8807 Score: 240
Period size: 63 Copynumber: 2.1 Consensus size: 65
8662 TTTATATTTC
*
8672 AATCAATTAAATAAGCACAAATAAGAATTATTTACACAT-AA-ATTAAACAAAGCAACTTTTACA
1 AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATATTAAACAAAGCAACTTTTACA
*
8735 AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATATTAAACAAATCAACTTTTACA
1 AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATATTAAACAAAGCAACTTTTACA
8800 AATCAATT
1 AATCAATT
8808 TTTACAAATC
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
63 38 0.55
64 2 0.03
65 29 0.42
ACGTcount: A:0.53, C:0.15, G:0.04, T:0.28
Consensus pattern (65 bp):
AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATATTAAACAAAGCAACTTTTACA
Found at i:8799 original size:29 final size:28
Alignment explanation
Indices: 8765--8819 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
8755 ATAAGAATTA
*
8765 TTTACACATCAATATTAAACAAATCAACT
1 TTTACAAATCAAT-TTAAACAAATCAACT
**
8794 TTTACAAATCAATTTTTACAAATCAA
1 TTTACAAATCAATTTAAACAAATCAA
8820 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (28 bp):
TTTACAAATCAATTTAAACAAATCAACT
Found at i:8820 original size:14 final size:14
Alignment explanation
Indices: 8760--8821 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
8750 CACAAATAAG
*
8760 AATTATTTACACATC
1 AATT-TTTACAAATC
**
8775 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
8790 AACTTTTACAAATC
1 AATTTTTACAAATC
8804 AATTTTTACAAATC
1 AATTTTTACAAATC
8818 AATT
1 AATT
8822 AAACAAGCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 26 0.67
15 12 0.31
16 1 0.03
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:10226 original size:21 final size:21
Alignment explanation
Indices: 10202--10275 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
10192 GGGAGGGACA
*
10202 TCTTCAACGATGATAGGGGCC
1 TCTTGAACGATGATAGGGGCC
* ** *
10223 TCTTGAACAATGGGAGGGGAC
1 TCTTGAACGATGATAGGGGCC
**
10244 TCTTGAGGGATGATAGGGGCC
1 TCTTGAACGATGATAGGGGCC
10265 TCTTGAACGAT
1 TCTTGAACGAT
10276 AGGAGATGCC
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.24
Consensus pattern (21 bp):
TCTTGAACGATGATAGGGGCC
Found at i:10228 original size:42 final size:42
Alignment explanation
Indices: 10191--10272 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
10181 TCTTGAATGG
10191 TGGGA-GGGACATCTTCAACGATGATAGGGGCCTCTTGAACAA
1 TGGGAGGGGAC-TCTTCAACGATGATAGGGGCCTCTTGAACAA
* **
10233 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAAC
1 TGGGAGGGGACTCTTCAACGATGATAGGGGCCTCTTGAAC
10273 GATAGGAGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 31 0.86
43 5 0.14
ACGTcount: A:0.24, C:0.17, G:0.37, T:0.22
Consensus pattern (42 bp):
TGGGAGGGGACTCTTCAACGATGATAGGGGCCTCTTGAACAA
Found at i:10298 original size:42 final size:42
Alignment explanation
Indices: 10193--10298 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
10183 TTGAATGGTG
* *
10193 GGAG-GGACATCTTCAACGATGATAGGGGCCTCTTGAACAATG
1 GGAGAGGAC-TCTTAAACGATGATAGGGGCCTCTTGAACAATA
* * ** *
10235 GGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATA
1 GGAGAGGACTCTTAAACGATGATAGGGGCCTCTTGAACAATA
* *
10277 GGAGATGCCTCTTAAACGATGA
1 GGAGAGGACTCTTAAACGATGA
10299 CAGGTGAGTC
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 48 0.92
43 4 0.08
ACGTcount: A:0.27, C:0.17, G:0.34, T:0.22
Consensus pattern (42 bp):
GGAGAGGACTCTTAAACGATGATAGGGGCCTCTTGAACAATA
Found at i:10809 original size:19 final size:20
Alignment explanation
Indices: 10773--10815 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
10763 AATAGTTTCT
*
10773 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCACAACAC
*
10793 GAAACTT-AAATCACAACGC
1 GAAACTTAAAATCACAACAC
10812 GAAA
1 GAAA
10816 ATGACTATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.51, C:0.23, G:0.12, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCACAACAC
Found at i:10831 original size:20 final size:20
Alignment explanation
Indices: 10806--10870 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
10796 ACTTAAATCA
10806 CAACGCGAAAATGACTATCG
1 CAACGCGAAAATGACTATCG
*
10826 CAACGCGGAAATGACTATCG
1 CAACGCGAAAATGACTATCG
**
10846 CAACGCGAATTTGACTATCG
1 CAACGCGAAAATGACTATCG
10866 CAACG
1 CAACG
10871 GGATAATCGC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (20 bp):
CAACGCGAAAATGACTATCG
Found at i:10974 original size:33 final size:34
Alignment explanation
Indices: 10918--11016 Score: 128
Period size: 33 Copynumber: 2.9 Consensus size: 34
10908 AATAAATTCG
10918 CGTTGCGATAGTCATTTTCGCATTGCGATTTTCA
1 CGTTGCGATAGTCATTTTCGCATTGCGATTTTCA
** * * * *
10952 CGTTGCGATTTTTA-TTTCGCATTGCAATTATCC
1 CGTTGCGATAGTCATTTTCGCATTGCGATTTTCA
*
10985 CGTTGCGATAGTCATTTTCGCGTTGCGATTTT
1 CGTTGCGATAGTCATTTTCGCATTGCGATTTT
11017 TAAGTTTCGT
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
33 27 0.52
34 25 0.48
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.43
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTTCGCATTGCGATTTTCA
Found at i:12999 original size:20 final size:20
Alignment explanation
Indices: 12907--12999 Score: 71
Period size: 20 Copynumber: 4.7 Consensus size: 20
12897 CTGAAACTTT
12907 TATCGCAACACGAAAATGAA
1 TATCGCAACACGAAAATGAA
* * * *
12927 AATTGCAACACAAAAATGAC
1 TATCGCAACACGAAAATGAA
** *
12947 TATCGCAATGCG-AATTGAA
1 TATCGCAACACGAAAATGAA
* * * *
12966 AATCGTAATACGAAAATGAC
1 TATCGCAACACGAAAATGAA
*
12986 TATCGCAACGCGAA
1 TATCGCAACACGAA
13000 TTAAACTATC
Statistics
Matches: 52, Mismatches: 20, Indels: 2
0.70 0.27 0.03
Matches are distributed among these distances:
19 14 0.27
20 38 0.73
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.18
Consensus pattern (20 bp):
TATCGCAACACGAAAATGAA
Found at i:13346 original size:22 final size:22
Alignment explanation
Indices: 13318--13374 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
13308 GATGGATATA
13318 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
13340 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
13362 GACGGATGTCGCC
1 GACGGATTTCGCC
13375 TTAGAGAGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.18, C:0.19, G:0.44, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:15346 original size:8 final size:8
Alignment explanation
Indices: 15333--15357 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
15323 AATCAGTTAT
15333 ATTATTAA
1 ATTATTAA
15341 ATTATTAA
1 ATTATTAA
15349 ATTATTAA
1 ATTATTAA
15357 A
1 A
15358 CCATTAATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTATTAA
Found at i:16677 original size:271 final size:271
Alignment explanation
Indices: 16194--16738 Score: 914
Period size: 271 Copynumber: 2.0 Consensus size: 271
16184 ACATAAAATC
16194 ATGTGTCCGTCCTGTAAACCTTACATATGGAAAAATAAAATAATAATAATAAAAACATAATTTTT
1 ATGTGTCCGTCCTGTAAACCTTACATATGGAAAAATAAAATAATAATAATAAAAACATAATTTTT
*
16259 TTTGTTAATATGGGGTAAATACAAGATAATATTTGTTCATAGATAACTCTCTATCATTTGACATT
66 TTTGTTAATATGGGGTAAATACAAGATAATATTTGTTCATAGATAACTCTCCATCATTTGACATT
* * *
16324 GAACGTTTACGCCTCTAATATTTCTGGTACTTAAACTCAGAATCTTAAAGAATAACAATAATTCT
131 GAACGTTTACGCCTCTAATATTTATGGTACTCAAACTCAGAATCTCAAAGAATAACAATAATTCT
* * * *
16389 TTTATTACTGAGCTCGTATAAAGGGATTGAAGAAGAGGAAGAGGGCAGGTGGGATTTTCAAACGG
196 TTTATTACCGAGCTCGTATAAAGGGATTAAAGAAGAGGAAGAGAGCAGGTGGGACTTTCAAACGG
16454 TTTAAGCCGTT
261 TTTAAGCCGTT
*
16465 ATGTGTCCGTCCTGTAAACCTTACATATGGAAAAATAAAATAATAA-AA-AAAAATATAATTTTT
1 ATGTGTCCGTCCTGTAAACCTTACATATGGAAAAATAAAATAATAATAATAAAAACATAA--TTT
* * * **
16528 TTTTTGTTAATATGGGGTAAATATAAGATAATATTTGTTTATAGATAATTCTCCATCATTTGTTA
64 TTTTTGTTAATATGGGGTAAATACAAGATAATATTTGTTCATAGATAACTCTCCATCATTTGACA
*
16593 TTGAACGTTTACGCCTCTAATATTTATGGTACTCGAACTCAGAATCTCAAAGAATAACAATAATT
129 TTGAACGTTTACGCCTCTAATATTTATGGTACTCAAACTCAGAATCTCAAAGAATAACAATAATT
*
16658 TTTTTATTACCGAGCTCGTATAAAGGGATTAAAGAAGAGGAAGAGAGCAGGTGGGACTTTCAAAC
194 CTTTTATTACCGAGCTCGTATAAAGGGATTAAAGAAGAGGAAGAGAGCAGGTGGGACTTTCAAAC
16723 GGTTTAAGCCGTT
259 GGTTTAAGCCGTT
16736 ATG
1 ATG
16739 GGTTAGGAGC
Statistics
Matches: 256, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
269 9 0.04
270 2 0.01
271 245 0.96
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (271 bp):
ATGTGTCCGTCCTGTAAACCTTACATATGGAAAAATAAAATAATAATAATAAAAACATAATTTTT
TTTGTTAATATGGGGTAAATACAAGATAATATTTGTTCATAGATAACTCTCCATCATTTGACATT
GAACGTTTACGCCTCTAATATTTATGGTACTCAAACTCAGAATCTCAAAGAATAACAATAATTCT
TTTATTACCGAGCTCGTATAAAGGGATTAAAGAAGAGGAAGAGAGCAGGTGGGACTTTCAAACGG
TTTAAGCCGTT
Found at i:25000 original size:29 final size:29
Alignment explanation
Indices: 24958--25030 Score: 130
Period size: 29 Copynumber: 2.6 Consensus size: 29
24948 AGGAGAATAC
24958 GAGTTTGTTTGTCTCGTGGAATATATTTT
1 GAGTTTGTTTGTCTCGTGGAATATATTTT
24987 GAGTTTGTTTGTCTCGTGGAATATATTTT
1 GAGTTTGTTTGTCTCGTGGAATATATTTT
*
25016 GAATTTGTTT-TCTCG
1 GAGTTTGTTTGTCTCG
25031 GAAAGTTTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 5 0.12
29 38 0.88
ACGTcount: A:0.16, C:0.08, G:0.23, T:0.52
Consensus pattern (29 bp):
GAGTTTGTTTGTCTCGTGGAATATATTTT
Found at i:25276 original size:17 final size:17
Alignment explanation
Indices: 25254--25316 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
25244 CTAAGTTAAG
25254 TTTAGTTTTTGTTTCAT
1 TTTAGTTTTTGTTTCAT
**
25271 TTTAGTATTTCGTCGTTAAAAAT
1 TTTAGT-TTT--T-GTT--TCAT
25294 TTTAGTTTTTGTTTCAT
1 TTTAGTTTTTGTTTCAT
25311 TTTAGT
1 TTTAGT
25317 ACGCTCATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
17 14 0.39
18 3 0.08
19 3 0.08
20 2 0.06
21 3 0.08
22 3 0.08
23 8 0.22
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.62
Consensus pattern (17 bp):
TTTAGTTTTTGTTTCAT
Found at i:25399 original size:31 final size:31
Alignment explanation
Indices: 25355--25439 Score: 136
Period size: 31 Copynumber: 2.8 Consensus size: 31
25345 TTGAAGAAAA
* *
25355 AAAATGAAT-GTTTAGGTATTAAATCAGACC
1 AAAATTAATAGTTTAAGTATTAAATCAGACC
*
25385 AAAATTAATAGTTTATGTATTAAATCAGACC
1 AAAATTAATAGTTTAAGTATTAAATCAGACC
25416 AAAATTAATAGTTTAAGTATTAAA
1 AAAATTAATAGTTTAAGTATTAAA
25440 CGTGTTATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 8 0.16
31 43 0.84
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (31 bp):
AAAATTAATAGTTTAAGTATTAAATCAGACC
Found at i:31034 original size:35 final size:35
Alignment explanation
Indices: 30988--31057 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
30978 GGGCACATTA
30988 CATAGCTAGTCATCCATGTGTAACTTGTATTCCGT
1 CATAGCTAGTCATCCATGTGTAACTTGTATTCCGT
31023 CATAGCTAGTCATCCATGTGTAACTTGTATTCCGT
1 CATAGCTAGTCATCCATGTGTAACTTGTATTCCGT
31058 TTTTCCTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (35 bp):
CATAGCTAGTCATCCATGTGTAACTTGTATTCCGT
Found at i:34553 original size:19 final size:19
Alignment explanation
Indices: 34529--34566 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
34519 CATATACTCA
34529 CCATGCAGACGAGCCATAC
1 CCATGCAGACGAGCCATAC
34548 CCATGCAGACGAGCCATAC
1 CCATGCAGACGAGCCATAC
34567 AAGCCATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.37, G:0.21, T:0.11
Consensus pattern (19 bp):
CCATGCAGACGAGCCATAC
Found at i:34625 original size:32 final size:32
Alignment explanation
Indices: 34581--34651 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
34571 CATATACTCA
* *
34581 CCATGCAGACGAGCCAGCCAACGGAGAGGTCG
1 CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
*
34613 CCATGCAAACGAGCCAGCCAATAGAGAGGTCG
1 CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
34645 CCATGCA
1 CCATGCA
34652 GTCTGGGCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.31, C:0.31, G:0.30, T:0.08
Consensus pattern (32 bp):
CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
Found at i:34742 original size:29 final size:29
Alignment explanation
Indices: 34639--34733 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
34629 GCCAATAGAG
* **
34639 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
34668 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
34697 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
34726 AGGTCGCC
1 AGGTCGCC
34734 CCGGCGTCCG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:34812 original size:50 final size:50
Alignment explanation
Indices: 34758--34875 Score: 170
Period size: 50 Copynumber: 2.4 Consensus size: 50
34748 CTCCCGAGAC
34758 CATGCATGCACATGCA-GCCAA-ATAACTTCACGTGCTCCTGCTCCCCGCTG
1 CATGCATG--CATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCCGCTG
*
34808 CATGCCTGCATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCCGCTG
1 CATGCATGCATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCCGCTG
* *
34858 CATGCCTACA-GCATGCCA
1 CATGCATGCATGCATGCCA
34876 TGTGATCCTA
Statistics
Matches: 64, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
48 6 0.09
49 13 0.20
50 45 0.70
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.22
Consensus pattern (50 bp):
CATGCATGCATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCCGCTG
Found at i:35111 original size:16 final size:18
Alignment explanation
Indices: 35090--35128 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
35080 GGAGATAAGG
*
35090 TAAATTTGTTTA-TATT-
1 TAAATTAGTTTATTATTA
35106 TAAATTAGTTTATTATTA
1 TAAATTAGTTTATTATTA
35124 TAAAT
1 TAAAT
35129 GTTAATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TAAATTAGTTTATTATTA
Found at i:35275 original size:47 final size:47
Alignment explanation
Indices: 35232--35322 Score: 127
Period size: 45 Copynumber: 2.0 Consensus size: 47
35222 TTATATAGTT
35232 AAAAAA-TAATTAATTAGTTTGTT-TT-GTT-AATAGTTAGTTATATA
1 AAAAAATTAATTAATTAGTTT-TTGTTAGTTAAATAGTTAGTTATATA
*
35276 AAAAAATTATTTAATTAGTTTTTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAATTAATTAATTAGTTTTTGTTAGTTAAATAGTT-AGTTATAT
35323 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
44 8 0.20
45 15 0.37
46 3 0.07
47 7 0.17
48 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (47 bp):
AAAAAATTAATTAATTAGTTTTTGTTAGTTAAATAGTTAGTTATATA
Found at i:35396 original size:32 final size:33
Alignment explanation
Indices: 35360--35436 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 33
35350 TTAGTTAGTA
*
35360 AGTTTATTAGTAG-TATA-TTATAATGAAAAAAT
1 AGTTTATTAGTAGTTATAGTTAT-ATAAAAAAAT
*
35392 AGTTTATTAGTTAGTTTTAGTTATATAAAAAAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAAAAT
*
35426 ATTTTATTAGT
1 AGTTTATTAGT
35437 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
32 10 0.26
33 4 0.10
34 21 0.54
35 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (33 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAAAAT
Found at i:35514 original size:16 final size:16
Alignment explanation
Indices: 35482--35528 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
35472 TTTAAAAAGT
*
35482 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
35498 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
35514 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
35529 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:35523 original size:15 final size:14
Alignment explanation
Indices: 35503--35533 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
35493 GTTTATTAGT
35503 TTATTATATTATAAG
1 TTATTATATTA-AAG
35518 TTATTATATTAAAG
1 TTATTATATTAAAG
35532 TT
1 TT
35534 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:37704 original size:17 final size:17
Alignment explanation
Indices: 37682--37714 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
37672 CAATGATGTT
37682 TAGTATCAAATAATTAC
1 TAGTATCAAATAATTAC
37699 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
37715 GTATTAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:37718 original size:14 final size:14
Alignment explanation
Indices: 37681--37731 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
37671 ACAATGATGT
37681 TTAGTATCAAATAA
1 TTAGTATCAAATAA
37695 TTACTAGTATCAAATAA
1 -T--TAGTATCAAATAA
* *
37712 TTAGTATTAAATCA
1 TTAGTATCAAATAA
37726 TTAGTA
1 TTAGTA
37732 ATAATTAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 17 0.53
15 1 0.03
16 1 0.03
17 13 0.41
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (14 bp):
TTAGTATCAAATAA
Found at i:37733 original size:21 final size:21
Alignment explanation
Indices: 37709--37752 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
37699 TAGTATCAAA
* *
37709 TAATTAGTATTAAATCATTAG
1 TAATAAGTAGTAAATCATTAG
*
37730 TAATAATTAGTAAATCATTAG
1 TAATAAGTAGTAAATCATTAG
37751 TA
1 TA
37753 TCAAATCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (21 bp):
TAATAAGTAGTAAATCATTAG
Found at i:37750 original size:35 final size:32
Alignment explanation
Indices: 37706--37795 Score: 108
Period size: 32 Copynumber: 2.7 Consensus size: 32
37696 TACTAGTATC
* * *
37706 AAATAATTAGTATTAAATCATTAGTAATAATTAGT
1 AAATCATTAGTATCAAATCATTA--AATAATTA-A
*
37741 AAATCATTAGTATCAAATCATTAAATATTTAA
1 AAATCATTAGTATCAAATCATTAAATAATTAA
*
37773 AAATCATTATTATCAAATCATTA
1 AAATCATTAGTATCAAATCATTA
37796 CTATAATGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
32 22 0.44
33 7 0.14
35 21 0.42
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (32 bp):
AAATCATTAGTATCAAATCATTAAATAATTAA
Found at i:37751 original size:11 final size:11
Alignment explanation
Indices: 37719--37752 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
37709 TAATTAGTAT
37719 TAAATCATTAG
1 TAAATCATTAG
*
37730 T-AATAATTAG
1 TAAATCATTAG
37740 TAAATCATTAG
1 TAAATCATTAG
37751 TA
1 TA
37753 TCAAATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (11 bp):
TAAATCATTAG
Found at i:37760 original size:14 final size:14
Alignment explanation
Indices: 37699--37821 Score: 66
Period size: 14 Copynumber: 9.1 Consensus size: 14
37689 AAATAATTAC
*
37699 TAGTATCAAATAAT
1 TAGTATCAAATCAT
*
37713 TAGTATTAAATCAT
1 TAGTATCAAATCAT
*
37727 TAG--T--AATAAT
1 TAGTATCAAATCAT
37737 TAG--T-AAATCAT
1 TAGTATCAAATCAT
37748 TAGTATCAAATCAT
1 TAGTATCAAATCAT
* *
37762 TAAATATTTAAAAATCAT
1 T-AGTA--T-CAAATCAT
*
37780 TATTATCAAATCAT
1 TAGTATCAAATCAT
* *
37794 TACTAT--AATGAT
1 TAGTATCAAATCAT
*
37806 TATTATCAAATCAT
1 TAGTATCAAATCAT
37820 TA
1 TA
37822 CTAAATCATC
Statistics
Matches: 87, Mismatches: 12, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
10 9 0.10
11 8 0.09
12 11 0.13
13 1 0.01
14 42 0.48
15 4 0.05
17 4 0.05
18 8 0.09
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (14 bp):
TAGTATCAAATCAT
Found at i:37866 original size:72 final size:76
Alignment explanation
Indices: 37752--37896 Score: 219
Period size: 72 Copynumber: 1.9 Consensus size: 76
37742 AATCATTAGT
37752 ATCAAATCATTAAATATTTAAAAATCATTATTATCAAATCATTACTATAATGATTATTA-TCAAA
1 ATCAAATCATTAAATATTT-AAAATCATTATTATCAAATCATTACTATAATGATTATTACT-AAA
37816 TCATTACTAAATC
64 TCATTACTAAATC
**
37829 ATCAAATCATTAAATATTT-AAATCATTA-T-T-AAATCATTTTTATAATGATTATTACTAAATC
1 ATCAAATCATTAAATATTTAAAATCATTATTATCAAATCATTACTATAATGATTATTACTAAATC
37890 ATTACTA
66 ATTACTA
37897 TAATGATTAT
Statistics
Matches: 65, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
72 34 0.52
73 2 0.03
74 1 0.02
75 9 0.14
77 19 0.29
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.41
Consensus pattern (76 bp):
ATCAAATCATTAAATATTTAAAATCATTATTATCAAATCATTACTATAATGATTATTACTAAATC
ATTACTAAATC
Found at i:37880 original size:98 final size:98
Alignment explanation
Indices: 37778--38020 Score: 461
Period size: 98 Copynumber: 2.5 Consensus size: 98
37768 TTTAAAAATC
37778 ATTATTA-TCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAA
1 ATTATTACT-AAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAA
37842 ATATTTAAATCATTATTAAATCATTTTTATAATG
65 ATATTTAAATCATTATTAAATCATTTTTATAATG
37876 ATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
1 ATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
37941 TATTTAAATCATTATTAAATCATTTTTATAATG
66 TATTTAAATCATTATTAAATCATTTTTATAATG
*
37974 ATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTA
1 ATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTACTA
38021 TAATGATTAT
Statistics
Matches: 143, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
98 142 0.99
99 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (98 bp):
ATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
TATTTAAATCATTATTAAATCATTTTTATAATG
Found at i:37906 original size:124 final size:121
Alignment explanation
Indices: 37778--38392 Score: 503
Period size: 124 Copynumber: 5.0 Consensus size: 121
37768 TTTAAAAATC
* * *
37778 ATTATTATCAAATCATTACTATAATGAT-TATTATCAAATCATTACTAAATCATCAAATCATTAA
1 ATTATTATCAAATCATTACTA-AATCATAAATCATCAAAT-ATT--TAAATCAT----T-ATTAA
*
37842 AT-A-TTTA-AATCATTA-T-TAAATCATTTTTATAATGATTATTA-CTAAATCATTACTATAAT
57 ATCATTTTATAATCATTATTATAAATCATTATTATAATGATTATTATC-AAATCATTACTATAAT
37901 G
121 G
*
37902 ATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTT
1 ATTATTATCAAATCATTACTAAATCAT-AAATCATCAAATATTTAAATCATTATTAAATCA-TTT
*
37967 TATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATG
64 TATAATCATTATTA-TAAATCATTATTATAATGATTATTATCAAATCATTACTATAATG
*
38026 ATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTT
1 ATTATTATCAAATCATTACTAAATCAT-AAATCATCAAATATTTAAATCATTATTAAATCA-TTT
* * *
38091 TATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCATTACTA-AATC
64 TATAATCATTATTA-TAAATCATTATTATAATGATTATTATCAAATCATTACTATAATG
* * * * * * * *
38149 ATCAAATCATTAAAT-ATT--TAAATCATTATTAAATC--ATTTTTATAATGATTATTACTAAAT
1 AT--TATTATCAAATCATTACTAAATCATAAAT-CATCAAATATTTA-AATCATTA-T--TAAAT
* * *
38209 CATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTA-AATC
59 CATT-TTATAATCATTATTAT-AAATCATTATTATAATGATTATTATCAAATCATTACTATAATG
* * * * * * * * *
38273 ATCAAATCATTAAAT-ATT--TAAATAATTATTAAATC--ATTTTTATAATGATTATTACTAAAT
1 AT--TATTATCAAATCATTACTAAATCATAAAT-CATCAAATATTTA-AATCATTA-T--TAAAT
* *
38333 CATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTA
59 CATT-TTATAATCATTATTAT-AAATCATTATTATAATGATTATTATCAAATCATTACTA
38393 AATCATCAAA
Statistics
Matches: 454, Mismatches: 18, Indels: 38
0.89 0.04 0.07
Matches are distributed among these distances:
117 7 0.02
118 2 0.00
120 10 0.02
121 16 0.04
122 20 0.04
123 13 0.03
124 369 0.81
125 17 0.04
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (121 bp):
ATTATTATCAAATCATTACTAAATCATAAATCATCAAATATTTAAATCATTATTAAATCATTTTA
TAATCATTATTATAAATCATTATTATAATGATTATTATCAAATCATTACTATAATG
Found at i:37992 original size:23 final size:24
Alignment explanation
Indices: 37951--38388 Score: 236
Period size: 26 Copynumber: 17.6 Consensus size: 24
37941 TATTTAAATC
*
37951 ATTATTAAATCATTTTTATAATGATT
1 ATTATCAAATCA--TTTATAATGATT
37977 ATTA-CTAAATCATTATTATAATGATT
1 ATTATC-AAATCA-T-TTATAATGATT
38003 ATTATCAAATCATTACTATAATGATT
1 ATTATCAAATCATT--TATAATGATT
* *
38029 ATTATCAAATCA-TTACTAAATCATCAA
1 ATTATCAAATCATTTA-T-AATGAT--T
* * *
38056 ATCATTAAAT-ATTTA-AATCATT
1 ATTATCAAATCATTTATAATGATT
38078 A-T-T-AAATCATTTTTATAATGATT
1 ATTATCAAATCA--TTTATAATGATT
38101 ATTA-CTAAATCATTACTATAATGATT
1 ATTATC-AAATCATT--TATAATGATT
* *
38127 ATTATCAAATCA-TTACTAAATCATCAA
1 ATTATCAAATCATTTA-T-AATGAT--T
* * *
38154 ATCATTAAAT-ATTTA-AATCATT
1 ATTATCAAATCATTTATAATGATT
38176 A-T-T-AAATCATTTTTATAATGATT
1 ATTATCAAATCA--TTTATAATGATT
38199 ATTA-CTAAATCATTATTATAATGATT
1 ATTATC-AAATCA-T-TTATAATGATT
38225 ATTATCAAATCATTACTATAATGATT
1 ATTATCAAATCATT--TATAATGATT
* *
38251 ATTATCAAATCA-TTACTAAATCATCAA
1 ATTATCAAATCATTTA-T-AATGAT--T
* *
38278 ATCATTAAAT-ATTTA-AAT-A--
1 ATTATCAAATCATTTATAATGATT
*
38297 ATTATTAAATCATTTTTATAATGATT
1 ATTATCAAATCA--TTTATAATGATT
38323 ATTA-CTAAATCATTATTATAATGATT
1 ATTATC-AAATCA-T-TTATAATGATT
38349 ATTATCAAATCATTACTATAATGATT
1 ATTATCAAATCATT--TATAATGATT
38375 ATTATCAAATCATT
1 ATTATCAAATCATT
38389 ACTAAATCAT
Statistics
Matches: 336, Mismatches: 21, Indels: 110
0.72 0.04 0.24
Matches are distributed among these distances:
19 17 0.05
20 5 0.01
22 14 0.04
23 24 0.07
24 26 0.08
25 27 0.08
26 186 0.55
27 37 0.11
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (24 bp):
ATTATCAAATCATTTATAATGATT
Found at i:38071 original size:222 final size:222
Alignment explanation
Indices: 37778--38366 Score: 1160
Period size: 222 Copynumber: 2.7 Consensus size: 222
37768 TTTAAAAATC
37778 ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
1 ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
37843 TATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATT
66 TATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATT
37908 ATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAAT
131 ATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAAT
37973 GATTATTACTAAATCATTATTATAATG
196 GATTATTACTAAATCATTATTATAATG
38000 ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
1 ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
38065 TATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATT
66 TATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATT
38130 ATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAAT
131 ATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAAT
38195 GATTATTACTAAATCATTATTATAATG
196 GATTATTACTAAATCATTATTATAATG
38222 ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
1 ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
* *
38287 TATTTAAATAATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATT
66 TATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATT
38352 ATCAAATCATTACTA
131 ATCAAATCATTACTA
38367 TAATGATTAT
Statistics
Matches: 365, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
222 365 1.00
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (222 bp):
ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
TATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATT
ATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAAT
GATTATTACTAAATCATTATTATAATG
Found at i:38084 original size:98 final size:98
Alignment explanation
Indices: 37977--38242 Score: 489
Period size: 98 Copynumber: 2.7 Consensus size: 98
37967 TATAATGATT
* *
37977 ATTACTAAATCATTATTATAATGATTATTA-TCAAATCATTACTATAATGATTATTATCAAATCA
1 ATTATTAAATCATTTTTATAATGATTATTACT-AAATCATTACTATAATGATTATTATCAAATCA
38041 TTACTAAATCATCAAATCATTAAATATTTAAATC
65 TTACTAAATCATCAAATCATTAAATATTTAAATC
38075 ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCAT
1 ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCAT
38140 TACTAAATCATCAAATCATTAAATATTTAAATC
66 TACTAAATCATCAAATCATTAAATATTTAAATC
*
38173 ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCAT
1 ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCAT
38238 TACTA
66 TACTA
38243 TAATGATTAT
Statistics
Matches: 164, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
98 163 0.99
99 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (98 bp):
ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCAT
TACTAAATCATCAAATCATTAAATATTTAAATC
Found at i:38317 original size:20 final size:19
Alignment explanation
Indices: 38281--38323 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
38271 TCATCAAATC
*
38281 ATTAAATATTTAAATAATT
1 ATTAAATATTTAAATAATG
**
38300 ATTAAATCATTTTTATAATG
1 ATTAAAT-ATTTAAATAATG
38320 ATTA
1 ATTA
38324 TTACTAAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTAAATATTTAAATAATG
Found at i:38393 original size:124 final size:124
Alignment explanation
Indices: 37951--38447 Score: 715
Period size: 124 Copynumber: 4.0 Consensus size: 124
37941 TATTTAAATC
* * *
37951 ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCAT
1 ATTACTAAATCATTATTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCAT
* * * * * * *
38016 TACTATAATGAT--TATTATCAAATCA-TT-ACTAAATCATCAAATCATTAAATATT-TAA--AT
66 TACTA-AATCATCAAATCATTAAAT-ATTTAAAT-AATTATTAAATCATT---T-TTATAATGAT
*
38074 C
124 T
* *
38075 ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCAT
1 ATTACTAAATCATTATTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCAT
*
38140 TACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATT
66 TACTAAATCATCAAATCATTAAATATTTAAATAATTATTAAATCATTTTTATAATGATT
38199 ATTACTAAATCATTATTATAATGATTATTA-TCAAATCATTACTATAATGATTATTATCAAATCA
1 ATTACTAAATCATTATTATAATGATTATTACT-AAATCATTACTATAATGATTATTATCAAATCA
38263 TTACTAAATCATCAAATCATTAAATATTTAAATAATTATTAAATCATTTTTATAATGATT
65 TTACTAAATCATCAAATCATTAAATATTTAAATAATTATTAAATCATTTTTATAATGATT
38323 ATTACTAAATCATTATTATAATGATTATTA-TCAAATCATTACTATAATGATTATTATCAAATCA
1 ATTACTAAATCATTATTATAATGATTATTACT-AAATCATTACTATAATGATTATTATCAAATCA
*
38387 TTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATT
65 TTACTAAATCATCAAATCATTAAATATTTAAATAATTATTAAATCATTTTTATAATGATT
38447 A
1 A
38448 ATAAATACAT
Statistics
Matches: 351, Mismatches: 14, Indels: 16
0.92 0.04 0.04
Matches are distributed among these distances:
121 2 0.01
122 4 0.01
123 6 0.02
124 315 0.90
125 22 0.06
126 2 0.01
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (124 bp):
ATTACTAAATCATTATTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCAT
TACTAAATCATCAAATCATTAAATATTTAAATAATTATTAAATCATTTTTATAATGATT
Found at i:41344 original size:26 final size:24
Alignment explanation
Indices: 41284--41344 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 24
41274 TACTAATATT
*
41284 ATTAATAATGATTTAATAATTATT
1 ATTAATAATGATTTAATAATTATG
* *
41308 ATTAATCTAATGATTTGATATTTAATG
1 ATTAA--TAATGATTTAATAATT-ATG
41335 ATTTAATAAT
1 A-TTAATAAT
41345 AATATGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 5 0.17
26 18 0.60
27 3 0.10
28 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (24 bp):
ATTAATAATGATTTAATAATTATG
Found at i:41602 original size:18 final size:18
Alignment explanation
Indices: 41579--41647 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
41569 AATATAAATA
*
41579 AAACAAAATATTTTTTTT
1 AAACAAAATATTATTTTT
* *
41597 AAACAACACTAAATATTTTT
1 AAACAA-AAT-ATTATTTTT
* *
41617 AAACACAATATAATTTTT
1 AAACAAAATATTATTTTT
41635 AAACAAAA-ATTAT
1 AAACAAAATATTAT
41648 CTCGCACAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
17 4 0.10
18 20 0.50
19 4 0.10
20 12 0.30
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (18 bp):
AAACAAAATATTATTTTT
Found at i:41726 original size:14 final size:14
Alignment explanation
Indices: 41707--41733 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41697 CACATGCACA
41707 ACAACAAAAAATAG
1 ACAACAAAAAATAG
41721 ACAACAAAAAATA
1 ACAACAAAAAATA
41734 ATAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (14 bp):
ACAACAAAAAATAG
Found at i:41726 original size:17 final size:17
Alignment explanation
Indices: 41704--41736 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41694 CTTCACATGC
41704 ACAACAACAAAA-AATAG
1 ACAACAA-AAAATAATAG
41721 ACAACAAAAAATAATA
1 ACAACAAAAAATAATA
41737 AATTACTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.73, C:0.15, G:0.03, T:0.09
Consensus pattern (17 bp):
ACAACAAAAAATAATAG
Found at i:42168 original size:21 final size:21
Alignment explanation
Indices: 42135--42183 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
42125 AATATAATAT
*
42135 ATAACTTAAACTAACCAACTA
1 ATAACTTAAACTAACAAACTA
* *
42156 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
42177 ATTAACT
1 A-TAACT
42184 AGATTTTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:42654 original size:34 final size:34
Alignment explanation
Indices: 42616--42681 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
42606 GGATGCAACG
*
42616 CATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
1 CATGCATGAGTGATACAGTTAAAGCTGGGTCGTT
*
42650 CATGCATGAGTGCTACAGTTAAAGCTGGGTCG
1 CATGCATGAGTGATACAGTTAAAGCTGGGTCG
42682 CGATGCAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (34 bp):
CATGCATGAGTGATACAGTTAAAGCTGGGTCGTT
Found at i:42735 original size:12 final size:12
Alignment explanation
Indices: 42718--42742 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42708 TCCATGGCGA
42718 CCTACCACCTAC
1 CCTACCACCTAC
42730 CCTACCACCTAC
1 CCTACCACCTAC
42742 C
1 C
42743 ATGTCGTCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.60, G:0.00, T:0.16
Consensus pattern (12 bp):
CCTACCACCTAC
Found at i:43025 original size:13 final size:13
Alignment explanation
Indices: 43007--43063 Score: 78
Period size: 13 Copynumber: 4.1 Consensus size: 13
42997 GATGGACGAG
43007 CAACAGCGGCCAC
1 CAACAGCGGCCAC
43020 CAACAGCGGCCACCC
1 CAACAGCGGCCA--C
43035 CAAAGCAGCGGCCAC
1 C-AA-CAGCGGCCAC
43050 CAACAGCGGCCAC
1 CAACAGCGGCCAC
43063 C
1 C
43064 CCAAGCAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
13 23 0.57
14 2 0.05
15 4 0.10
16 2 0.05
17 9 0.22
ACGTcount: A:0.30, C:0.47, G:0.23, T:0.00
Consensus pattern (13 bp):
CAACAGCGGCCAC
Found at i:43046 original size:30 final size:30
Alignment explanation
Indices: 43010--43067 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
43000 GGACGAGCAA
43010 CAGCGGCCACCAACAGCGGCCACCCCAAAG
1 CAGCGGCCACCAACAGCGGCCACCCCAAAG
43040 CAGCGGCCACCAACAGCGGCCACCCCAA
1 CAGCGGCCACCAACAGCGGCCACCCCAA
43068 GCAAATAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.48, G:0.22, T:0.00
Consensus pattern (30 bp):
CAGCGGCCACCAACAGCGGCCACCCCAAAG
Found at i:43118 original size:29 final size:29
Alignment explanation
Indices: 43081--43224 Score: 263
Period size: 29 Copynumber: 5.0 Consensus size: 29
43071 AATAACTTAT
*
43081 AGGACGCCGGGCGTGCATGGCGTCCT-TA
1 AGGACGCCGGGCGTGCATGGCGACCTATA
43109 TAGGACGCCGGGCGTGCATGGCGACCTATA
1 -AGGACGCCGGGCGTGCATGGCGACCTATA
43139 AGGACGCCGGGCGTGCATGGCGACCTATA
1 AGGACGCCGGGCGTGCATGGCGACCTATA
43168 AGGACGCCGGGCGTGCATGGCGACCTATA
1 AGGACGCCGGGCGTGCATGGCGACCTATA
43197 AGGACGCCGGGCGTGCATGGCGACCTAT
1 AGGACGCCGGGCGTGCATGGCGACCTAT
43225 GTTGCCACTG
Statistics
Matches: 113, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
29 111 0.98
30 2 0.02
ACGTcount: A:0.19, C:0.28, G:0.38, T:0.15
Consensus pattern (29 bp):
AGGACGCCGGGCGTGCATGGCGACCTATA
Found at i:43843 original size:14 final size:14
Alignment explanation
Indices: 43809--43843 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
43799 TGATCGATAA
*
43809 TATGTTCGTTCATT
1 TATGTTTGTTCATT
43823 TATGTTTGTTCATT
1 TATGTTTGTTCATT
43837 TATGTTT
1 TATGTTT
43844 AACTCAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.14, C:0.09, G:0.14, T:0.63
Consensus pattern (14 bp):
TATGTTTGTTCATT
Found at i:44075 original size:14 final size:14
Alignment explanation
Indices: 44056--44101 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
44046 GTTAATTTAT
44056 GTTCGTTTACGTTC
1 GTTCGTTTACGTTC
* *
44070 GTTCGTTTACATCC
1 GTTCGTTTACGTTC
* *
44084 GTTCGTTCATGTTC
1 GTTCGTTTACGTTC
44098 GTTC
1 GTTC
44102 ATTTGTATTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.09, C:0.24, G:0.20, T:0.48
Consensus pattern (14 bp):
GTTCGTTTACGTTC
Found at i:46807 original size:28 final size:27
Alignment explanation
Indices: 46766--46823 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
46756 ATATTCATAC
*
46766 AAAATTTTATATATAA-TAAATACAAAT
1 AAAATTTTAAATATAATTAAATA-AAAT
*
46793 AAAATTTTAAAATATAATTAATTAAAAT
1 AAAATTTT-AAATATAATTAAATAAAAT
46821 AAA
1 AAA
46824 TCTAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 8 0.30
28 14 0.52
29 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (27 bp):
AAAATTTTAAATATAATTAAATAAAAT
Found at i:57522 original size:21 final size:21
Alignment explanation
Indices: 57496--57540 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
57486 AAATTACACA
*
57496 TTTAGTATCTAAATTATTAGT
1 TTTAGTATCTAAATTATTAAT
* *
57517 TTTAGTGTCTAAATTTTTAAT
1 TTTAGTATCTAAATTATTAAT
57538 TTT
1 TTT
57541 TTTAAAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.04, G:0.09, T:0.58
Consensus pattern (21 bp):
TTTAGTATCTAAATTATTAAT
Found at i:61648 original size:31 final size:33
Alignment explanation
Indices: 61583--61662 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
61573 TTAATAATTC
* *
61583 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATATTA-TTTAA
*
61617 TAAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAAATAATAATTACATAAATATTATTTAA
*
61648 TATAAAATATAATAA
1 TA-AAAAAATAATAA
61663 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 6 0.15
32 10 0.25
33 2 0.05
34 22 0.55
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
TAAAAAAATAATAATTACATAAATATTATTTAA
Found at i:61688 original size:35 final size:34
Alignment explanation
Indices: 61616--61693 Score: 88
Period size: 35 Copynumber: 2.3 Consensus size: 34
61606 TATTATTTTA
* * * *
61616 ATAAAAA-AATAATATTTACATAAATATATTAAT
1 ATAAAAATAATAATATTTACAAAAAAATACTAAC
61649 ATAAAATATAATAACTATTTA-AAAAAAATACTAAC
1 ATAAAA-ATAATAA-TATTTACAAAAAAATACTAAC
61684 ATAAAAATAA
1 ATAAAAATAA
61694 ATTTCTTACC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
33 6 0.16
34 5 0.13
35 21 0.55
36 6 0.16
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (34 bp):
ATAAAAATAATAATATTTACAAAAAAATACTAAC
Found at i:64998 original size:63 final size:65
Alignment explanation
Indices: 64865--65000 Score: 179
Period size: 63 Copynumber: 2.1 Consensus size: 65
64855 AGTATAGGTA
* ** *
64865 CAAAAATAGACTAAAACTGATAATTTAAGTATTAAATGATAAATACGTAGTTTACAGTTATA-CC
1 CAAAAATAGACTAAAACTGATAATTTAAATATTAAATGATAAATACGTAGTTTACAAATACACCC
* * *
64929 TAAAAA-AAACTAAAACTGATAATTTAAAT-TCTAAATGATAAATGCGTAGTTTACAAATACACC
1 CAAAAATAGACTAAAACTGATAATTTAAATAT-TAAATGATAAATACGTAGTTTACAAATACACC
64992 C
65 C
64993 CAAAAATA
1 CAAAAATA
65001 CATATATATA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
62 1 0.02
63 47 0.77
64 12 0.20
65 1 0.02
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (65 bp):
CAAAAATAGACTAAAACTGATAATTTAAATATTAAATGATAAATACGTAGTTTACAAATACACCC
Found at i:69600 original size:120 final size:119
Alignment explanation
Indices: 69387--69607 Score: 266
Period size: 120 Copynumber: 1.8 Consensus size: 119
69377 TGGCTAAACT
* * * * *
69387 ACGCATTTAATATCTAAACTATCAGTTTTTATCTATTTAGTATTTAAATTTTTAATTTTTTAAAA
1 ACGCATTTAATACCTAAACTATCAGATTTTATCAATTTAGTATCTAAATTTTTAATTTTTAAAAA
* * *
69452 TCACACCTAATATTTAATTTTTGTTTCATTTTAGTACCCACCGTTAAAAACTTA
66 TCACACCTAAGATTTAATTTTTGCTTCATTTCAGTACCCACCGTTAAAAACTTA
* * *
69506 ACGCATTTAGTACCTAAACTATGA-ATTTTAGTCAATTTTAGTATCTAAA-TTTTCATTTCTTAA
1 ACGCATTTAATACCTAAACTATCAGATTTTA-TCAA-TTTAGTATCTAAATTTTTAATTT-TTAA
* * * *
69569 AAATTATACCTAAGGTTTAGTTTTTGCTTCATTTCAGTA
63 AAATCACACCTAAGATTTAATTTTTGCTTCATTTCAGTA
69608 ATTTGTCGTT
Statistics
Matches: 84, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
118 5 0.06
119 32 0.38
120 47 0.56
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46
Consensus pattern (119 bp):
ACGCATTTAATACCTAAACTATCAGATTTTATCAATTTAGTATCTAAATTTTTAATTTTTAAAAA
TCACACCTAAGATTTAATTTTTGCTTCATTTCAGTACCCACCGTTAAAAACTTA
Found at i:72770 original size:2 final size:2
Alignment explanation
Indices: 72763--72792 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
72753 TCCGGTAAAC
*
72763 AG AG AG AG AG AG AG AG AG AG AG AC AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
72793 TTTGATTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:74435 original size:22 final size:21
Alignment explanation
Indices: 74410--74458 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
74400 ATTATAAATC
*
74410 ATATACATATATAGATATATTA
1 ATATACATATATA-ATACATTA
**
74432 ATATTATTTATATAATACATTA
1 ATA-TACATATATAATACATTA
74454 ATATA
1 ATATA
74459 TAAATAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.09
22 13 0.57
23 8 0.35
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (21 bp):
ATATACATATATAATACATTA
Found at i:74505 original size:18 final size:20
Alignment explanation
Indices: 74464--74506 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
74454 ATATATAAAT
* *
74464 AATATTTTTTACTATATATT
1 AATATTGTTTACTATATATA
74484 AATATTGTTTA-TA-ATATA
1 AATATTGTTTACTATATATA
74502 AATAT
1 AATAT
74507 ATAATAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 2 0.10
20 10 0.48
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
AATATTGTTTACTATATATA
Found at i:74509 original size:51 final size:54
Alignment explanation
Indices: 74424--74523 Score: 145
Period size: 53 Copynumber: 1.9 Consensus size: 54
74414 ACATATATAG
*
74424 ATATATTAATATTATTTATATAATACATTAATAT-ATAAATAATATTTTTTACT
1 ATATATTAATATTATTTATATAATACAATAATATAATAAATAATATTTTTTACT
*
74477 ATATATTAATATTGTTTATA-ATATA-AAT-ATATAATAAATAATATTTT
1 ATATATTAATATTATTTATATA-ATACAATAATATAATAAATAATATTTT
74524 CATTTTAGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
51 4 0.09
52 17 0.40
53 22 0.51
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (54 bp):
ATATATTAATATTATTTATATAATACAATAATATAATAAATAATATTTTTTACT
Found at i:89565 original size:2 final size:2
Alignment explanation
Indices: 89558--89582 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
89548 ACTTTAATTA
89558 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
89583 ATGGAAGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:100250 original size:20 final size:20
Alignment explanation
Indices: 100225--100271 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
100215 CCTTGATGTT
100225 GGCAGAACAGAAGAACTCTC
1 GGCAGAACAGAAGAACTCTC
***
100245 GGCAGATTTGAAGAACTCTC
1 GGCAGAACAGAAGAACTCTC
100265 GGC-GAAC
1 GGCAGAAC
100272 CTGGAAGTTC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.34, C:0.23, G:0.28, T:0.15
Consensus pattern (20 bp):
GGCAGAACAGAAGAACTCTC
Found at i:102282 original size:80 final size:80
Alignment explanation
Indices: 102149--102354 Score: 308
Period size: 80 Copynumber: 2.5 Consensus size: 80
102139 GCCATGGACT
* *
102149 ATGTCATGCCAAACCTTGCTGACATGTATGAATCAGT-A-CAAGCTACTGATTTCAAGATAATCT
1 ATGTCATGCCAAACCTTGCTAACATG--TGAATCAGTAAGCAAGCTACTGATTTCAAGATAATCC
102212 AATTAGTATGGTAGACC
64 AATTAGTATGGTAGACC
*
102229 ATGTCAAGCCAAACCTTGCTAACATGTGAATCAGTAAGCAAGCTACTGATTTCAAGATAATCCAA
1 ATGTCATGCCAAACCTTGCTAACATGTGAATCAGTAAGCAAGCTACTGATTTCAAGATAATCCAA
102294 TTAGTATGGTAGACC
66 TTAGTATGGTAGACC
** *
102309 ATGTCATGCCAAACCTACCTAACATGTAGTAATCAGCAAGCAAGCT
1 ATGTCATGCCAAACCTTGCTAACATGT-G-AATCAGTAAGCAAGCT
102355 GTACACCATA
Statistics
Matches: 115, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
78 9 0.08
79 1 0.01
80 89 0.77
81 1 0.01
82 15 0.13
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (80 bp):
ATGTCATGCCAAACCTTGCTAACATGTGAATCAGTAAGCAAGCTACTGATTTCAAGATAATCCAA
TTAGTATGGTAGACC
Found at i:106507 original size:29 final size:28
Alignment explanation
Indices: 106429--106508 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
106419 ATTTTTTATT
* *
106429 TAAGTATTTAAAATATTTTTTAATCAAA
1 TAAGTATCTAAAATATTTTTTTATCAAA
* * *
106457 TAAATA-CATAAAGTTATCTTTTTATCAATA
1 TAAGTATC-TAAA-ATATTTTTTTATCAA-A
106487 TAAGTATCTAAAATATTTTTTT
1 TAAGTATCTAAAATATTTTTTT
106509 GGCCAAAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
28 9 0.22
29 20 0.50
30 10 0.25
31 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (28 bp):
TAAGTATCTAAAATATTTTTTTATCAAA
Found at i:106917 original size:165 final size:165
Alignment explanation
Indices: 106725--107057 Score: 577
Period size: 165 Copynumber: 2.0 Consensus size: 165
106715 AAAAAAATAC
106725 TTTAAATACTTATTTGCATATGAGTTTTTTTCTCACCGAACTG-AAATGGAAAATTATGATGTGA
1 TTTAAATACTTATTTGCATATGAG-TTTTTTCTCACCGAACTGAAAATGGAAAATTATGATGTGA
106789 TTTAGAAGTCAATGGAAGTGATATTTTATGCTTAATGATTAATAATTAAAGCTTGGAAGATGTGA
65 TTTAGAAGTCAATGGAAGTGATATTTTATGCTTAATG---AATAATTAAAGCTTGGAAGATGTGA
106854 ACG-TGTGGGGCG-GTACAC-TACAATAAATATTCTCTCT
127 A-GATGTGGGGCGTGTACACATACAATAAATATTCTCTCT
106891 TTTAAATACTTA-TTGCATATGAGTTTTTTCTCACCGAACTGAAAATGGAAAATTATGATGTGAT
1 TTTAAATACTTATTTGCATATGAGTTTTTTCTCACCGAACTGAAAATGGAAAATTATGATGTGAT
106955 TTAGAAGTCAATGGAAGTGATATTTTATGCTTAATGAATAATTAAAGCTTGGAAGATGTGAAGAC
66 TTAGAAGTCAATGGAAGTGATATTTTATGCTTAATGAATAATTAAAGCTTGGAAGATGTGAAGA-
107020 TGTGGGGCGTGTACACATACAATAAATATTCTCTCT
130 TGTGGGGCGTGTACACATACAATAAATATTCTCTCT
107056 TT
1 TT
107058 CTGAAAAAAA
Statistics
Matches: 162, Mismatches: 0, Indels: 11
0.94 0.00 0.06
Matches are distributed among these distances:
161 1 0.01
162 26 0.16
163 9 0.06
164 24 0.15
165 90 0.56
166 12 0.07
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (165 bp):
TTTAAATACTTATTTGCATATGAGTTTTTTCTCACCGAACTGAAAATGGAAAATTATGATGTGAT
TTAGAAGTCAATGGAAGTGATATTTTATGCTTAATGAATAATTAAAGCTTGGAAGATGTGAAGAT
GTGGGGCGTGTACACATACAATAAATATTCTCTCT
Found at i:116423 original size:21 final size:21
Alignment explanation
Indices: 116380--116423 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
116370 TATTATAAAC
* *
116380 CATCGTGGACTGTCACGTCAG
1 CATCGTGAACTGTCACATCAG
*
116401 CATCGTGAACTGTCACATTAG
1 CATCGTGAACTGTCACATCAG
116422 CA
1 CA
116424 CTATAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (21 bp):
CATCGTGAACTGTCACATCAG
Found at i:116732 original size:11 final size:11
Alignment explanation
Indices: 116716--116745 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
116706 AACTATCTGT
116716 TAATTTAATCC
1 TAATTTAATCC
*
116727 TAATTTAGTCC
1 TAATTTAATCC
116738 TAATTTAA
1 TAATTTAA
116746 ATCATAAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.47
Consensus pattern (11 bp):
TAATTTAATCC
Found at i:116987 original size:25 final size:25
Alignment explanation
Indices: 116953--117002 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
116943 TGGTGACATG
116953 GTTAAAGGAAAAAACAACACACAAC
1 GTTAAAGGAAAAAACAACACACAAC
116978 GTTAAAGGAAAAAACAACACACAAC
1 GTTAAAGGAAAAAACAACACACAAC
117003 AATTTGAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.12, T:0.08
Consensus pattern (25 bp):
GTTAAAGGAAAAAACAACACACAAC
Found at i:129255 original size:14 final size:15
Alignment explanation
Indices: 129236--129272 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
129226 TAACATAATT
*
129236 AATATTTTA-TTTTA
1 AATATTTTACCTTTA
129250 AATATTTTACCTTTA
1 AATATTTTACCTTTA
129265 AAT-TTTTA
1 AATATTTTA
129273 ACTAATTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (15 bp):
AATATTTTACCTTTA
Found at i:140954 original size:43 final size:43
Alignment explanation
Indices: 140906--140992 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
140896 TTAAAGTTCA
140906 ACTCTTCCTAAACGTTTTAATCTCAGCTTCGTGAGTTTCCTGG
1 ACTCTTCCTAAACGTTTTAATCTCAGCTTCGTGAGTTTCCTGG
140949 ACTCTTCCTAAACGTTTTAATCTCAGCTTCGTGAGTTTCCTGG
1 ACTCTTCCTAAACGTTTTAATCTCAGCTTCGTGAGTTTCCTGG
140992 A
1 A
140993 AGAAAATGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (43 bp):
ACTCTTCCTAAACGTTTTAATCTCAGCTTCGTGAGTTTCCTGG
Done.