Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 60 of 276
Found at i:18637273 original size:45 final size:45
Alignment explanation
Indices: 18637209--18637294 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
18637199 TGAAATCTGT
* *
18637209 ACTCATTGAGTTGTGGTCTGAGTTCATGATATATGTGACATTTGA
1 ACTCATTGACTTGTGGTCTGAGTTCATGATATATGCGACATTTGA
*
18637254 ACTCATTGACTTGTGGTCTGAGTTCATGATGTATGCGACAT
1 ACTCATTGACTTGTGGTCTGAGTTCATGATATATGCGACAT
18637295 ATGTTTTGGC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.38
Consensus pattern (45 bp):
ACTCATTGACTTGTGGTCTGAGTTCATGATATATGCGACATTTGA
Found at i:18643801 original size:4 final size:4
Alignment explanation
Indices: 18643792--18643844 Score: 106
Period size: 4 Copynumber: 13.2 Consensus size: 4
18643782 AAAAGACTAA
18643792 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
18643840 TATG T
1 TATG T
18643845 TTTTCATAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:18648590 original size:138 final size:138
Alignment explanation
Indices: 18648342--18648616 Score: 523
Period size: 138 Copynumber: 2.0 Consensus size: 138
18648332 GGCTAAGTTT
*
18648342 GGGCTATTTTGGGTATTCCAAAGTCTATTTAAACACACGAGGAGAGGATCTAAGGGGTAGACAGA
1 GGGCTATTTTGGGCATTCCAAAGTCTATTTAAACACACGAGGAGAGGATCTAAGGGGTAGACAGA
18648407 GGAGAAGGCAGAAAATACTCGAAGACAGCCATTGGAATCAACTCGGAAGCAAGATTTACTTCAAG
66 GGAGAAGGCAGAAAATACTCGAAGACAGCCATTGGAATCAACTCGGAAGCAAGATTTACTTCAAG
18648472 GTTGAAGC
131 GTTGAAGC
18648480 GGGCTATTTTGGGCATTCCAAAGTCTATTTAAACACACGAGGAGAGGATCTAAGGGGTAGACAGA
1 GGGCTATTTTGGGCATTCCAAAGTCTATTTAAACACACGAGGAGAGGATCTAAGGGGTAGACAGA
* *
18648545 GGAGAAGGCAGAAAATACTCGAAGACAGCCATTGGAATCAACTCGGAAGTAGGATTTACTTCAAG
66 GGAGAAGGCAGAAAATACTCGAAGACAGCCATTGGAATCAACTCGGAAGCAAGATTTACTTCAAG
18648610 GTTGAAG
131 GTTGAAG
18648617 ATCTCCATTC
Statistics
Matches: 134, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
138 134 1.00
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.21
Consensus pattern (138 bp):
GGGCTATTTTGGGCATTCCAAAGTCTATTTAAACACACGAGGAGAGGATCTAAGGGGTAGACAGA
GGAGAAGGCAGAAAATACTCGAAGACAGCCATTGGAATCAACTCGGAAGCAAGATTTACTTCAAG
GTTGAAGC
Found at i:18652331 original size:21 final size:23
Alignment explanation
Indices: 18652290--18652350 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
18652280 TACTTTAGCC
*
18652290 ATTTTTATTTTTATTGCAATT-TA
1 ATTTTTA-TTTTATTTCAATTATA
* *
18652313 A-TTTTGTTTTATTTTAATTACTA
1 ATTTTTATTTTATTTCAATTA-TA
18652336 ATTTTTATTTTATTT
1 ATTTTTATTTTATTT
18652351 ACTTTTGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 11 0.35
22 4 0.13
23 4 0.13
24 12 0.39
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (23 bp):
ATTTTTATTTTATTTCAATTATA
Found at i:18661876 original size:29 final size:29
Alignment explanation
Indices: 18661809--18661877 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
18661799 GAATATCCAA
*
18661809 CCCAAACACACCCAGAATAATATAAATCCT
1 CCCAAACACACCCAGAATAATAT-AAGCCT
*
18661839 -CCATAACACA-CCAGTATAATAT-AGCCT
1 CCCA-AACACACCCAGAATAATATAAGCCT
18661866 CCCAAACACACC
1 CCCAAACACACC
18661878 AATAAGGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
27 10 0.29
28 4 0.12
29 14 0.41
30 6 0.18
ACGTcount: A:0.43, C:0.36, G:0.04, T:0.16
Consensus pattern (29 bp):
CCCAAACACACCCAGAATAATATAAGCCT
Found at i:18662331 original size:15 final size:15
Alignment explanation
Indices: 18662306--18662363 Score: 82
Period size: 15 Copynumber: 3.8 Consensus size: 15
18662296 AATCATATAT
18662306 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
18662322 TATAAATTCAATCAA
1 TATAAATTCAATCAA
*
18662337 AAT-AATTGCAATCAA
1 TATAAATT-CAATCAA
18662352 TATAAATTCAAT
1 TATAAATTCAAT
18662364 AAATTCATCG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
14 4 0.11
15 26 0.68
16 8 0.21
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.34
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:18662645 original size:97 final size:99
Alignment explanation
Indices: 18662473--18662668 Score: 315
Period size: 97 Copynumber: 2.0 Consensus size: 99
18662463 TAAGTTCGGA
* * *
18662473 TTATAGAAATACAAACCGTATTTTCTCGAGCTAACTCCCCTCGTCTTTGCCATTTTTCTTTGCTT
1 TTATAGAAATACAAACCGTAGTTTCTCAAGCTAACTCCCCTCGTCTTTGCCA-TTGTCTTTGCTT
18662538 AGCTGAGATTTCCCGAGACAACATTAGCTACGGGT
65 AGCTGAGATTTCCCGAGACAACATTAGCTACGGGT
* * *
18662573 TTATAGAAATACAAACCGTAGTTTC-CAAGCTAACTCCCGTTGTCTTTGTC-TTGTCTTTGCTTA
1 TTATAGAAATACAAACCGTAGTTTCTCAAGCTAACTCCCCTCGTCTTTGCCATTGTCTTTGCTTA
18662636 GCTGAGATTTCCCGAGACAACATTAGCTACGGG
66 GCTGAGATTTCCCGAGACAACATTAGCTACGGG
18662669 AATTAAAACA
Statistics
Matches: 90, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
97 45 0.50
99 21 0.23
100 24 0.27
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.34
Consensus pattern (99 bp):
TTATAGAAATACAAACCGTAGTTTCTCAAGCTAACTCCCCTCGTCTTTGCCATTGTCTTTGCTTA
GCTGAGATTTCCCGAGACAACATTAGCTACGGGT
Found at i:18663253 original size:2 final size:2
Alignment explanation
Indices: 18663246--18663280 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
18663236 TGTTCTGTTT
18663246 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18663281 ATAAGTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18663434 original size:31 final size:32
Alignment explanation
Indices: 18663376--18663439 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
18663366 CATACATTTG
*
18663376 TCATAATTTAATATATTTATTACATAAAAATC
1 TCATAATATAATATATTTATTACATAAAAATC
*
18663408 TCATAATATAAT-TATTTAATTA-ATAAATATC
1 TCATAATATAATATATTT-ATTACATAAAAATC
18663439 T
1 T
18663440 TATTTAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 14 0.48
32 15 0.52
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (32 bp):
TCATAATATAATATATTTATTACATAAAAATC
Found at i:18663697 original size:3 final size:3
Alignment explanation
Indices: 18663689--18663745 Score: 53
Period size: 3 Copynumber: 17.7 Consensus size: 3
18663679 TCAATTTATT
18663689 TAA TAA TAA TAA TAA TAA TTAA TAA CTAA TATA TAA -ACCA TAA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA -TAA TA-A TAA TA--A TAA TAA
*
18663735 TAA TTA TAA TA
1 TAA TAA TAA TA
18663746 TATTTATATA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
2 1 0.02
3 34 0.74
4 10 0.22
5 1 0.02
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:18665848 original size:19 final size:19
Alignment explanation
Indices: 18665824--18665862 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
18665814 ATCCAAACAC
18665824 CAGAAAAGTAAATCATTTT
1 CAGAAAAGTAAATCATTTT
*
18665843 CAGAAAAGTAAATTATTTT
1 CAGAAAAGTAAATCATTTT
18665862 C
1 C
18665863 CGGAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (19 bp):
CAGAAAAGTAAATCATTTT
Found at i:18665884 original size:15 final size:14
Alignment explanation
Indices: 18665852--18665889 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
18665842 TCAGAAAAGT
18665852 AAATTATTTTCCGG
1 AAATTATTTTCCGG
*
18665866 AAATTATTTTTCGG
1 AAATTATTTTCCGG
*
18665880 AAAATATTTT
1 AAATTATTTT
18665890 ACTGGCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (14 bp):
AAATTATTTTCCGG
Found at i:18667520 original size:17 final size:17
Alignment explanation
Indices: 18667479--18667520 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
18667469 TTTGAGTCCA
18667479 TTTATTTTCACTTTGTT
1 TTTATTTTCACTTTGTT
*
18667496 TTGT-TTTTCATTTTGTT
1 TT-TATTTTCACTTTGTT
18667513 TTTATTTT
1 TTTATTTT
18667521 TTTTCATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 20 0.91
18 1 0.05
ACGTcount: A:0.10, C:0.07, G:0.07, T:0.76
Consensus pattern (17 bp):
TTTATTTTCACTTTGTT
Found at i:18670063 original size:22 final size:22
Alignment explanation
Indices: 18670035--18670079 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
18670025 TACTTGTTCT
18670035 TATTCTTAATTATGAGTTTTAA
1 TATTCTTAATTATGAGTTTTAA
18670057 TATTCTTAATTATGAGTTTTAA
1 TATTCTTAATTATGAGTTTTAA
18670079 T
1 T
18670080 CTTTGTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.04, G:0.09, T:0.56
Consensus pattern (22 bp):
TATTCTTAATTATGAGTTTTAA
Found at i:18670867 original size:41 final size:41
Alignment explanation
Indices: 18670811--18670989 Score: 270
Period size: 41 Copynumber: 4.4 Consensus size: 41
18670801 CGTTTTAGTA
** *
18670811 AAAAACGCCGC-AAAAAATAGAGCATTAGCGGCGCTTCTGG
1 AAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
* * *
18670851 CAAAACGCTGCTAAAAACCAGAGCATTAGCGGTGCTTTTGG
1 AAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
*
18670892 AAAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGG
1 AAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
*
18670933 AAAAACGCCGCTAAAAACCAGAGGATTAGCGGCGCTTTTGG
1 AAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
*
18670974 AAAAATGCCGCTAAAA
1 AAAAACGCCGCTAAAA
18670990 GTCATATAAC
Statistics
Matches: 125, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
40 9 0.07
41 116 0.93
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.18
Consensus pattern (41 bp):
AAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
Found at i:18671160 original size:7 final size:7
Alignment explanation
Indices: 18671145--18671197 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
18671135 TTAATTATCA
*
18671145 TTATAGT
1 TTATGGT
18671152 TTATGGT
1 TTATGGT
18671159 TTATGGT
1 TTATGGT
* *
18671166 TTAAGAT
1 TTATGGT
*
18671173 ATATGGT
1 TTATGGT
*
18671180 TTAGGGT
1 TTATGGT
*
18671187 TTAAGGT
1 TTATGGT
18671194 TTAT
1 TTAT
18671198 AAGTTAACTA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (7 bp):
TTATGGT
Found at i:18671177 original size:21 final size:21
Alignment explanation
Indices: 18671153--18671237 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
18671143 CATTATAGTT
*
18671153 TATGGTTTATGGTTTAAGATA
1 TATGGTTTAGGGTTTAAGATA
* *
18671174 TATGGTTTAGGGTTTAAGGTT
1 TATGGTTTAGGGTTTAAGATA
* **
18671195 TATAAGTTAACTATAGTTTAAGATA
1 TAT-GGTT---TAGGGTTTAAGATA
18671220 TATGGTTTAGGGTTTAAG
1 TATGGTTTAGGGTTTAAG
18671238 GTTTAGGAGT
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
21 30 0.61
22 3 0.06
24 3 0.06
25 13 0.27
ACGTcount: A:0.29, C:0.01, G:0.25, T:0.45
Consensus pattern (21 bp):
TATGGTTTAGGGTTTAAGATA
Found at i:18671216 original size:46 final size:46
Alignment explanation
Indices: 18671164--18671253 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 46
18671154 ATGGTTTATG
*
18671164 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTATAAGTTAACTATA
1 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGAAGTTAACTATA
*
18671210 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAACTA
1 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGAAGTTAACTA
18671254 GTATTTGAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.31, C:0.02, G:0.24, T:0.42
Consensus pattern (46 bp):
GTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGAAGTTAACTATA
Found at i:18671309 original size:7 final size:7
Alignment explanation
Indices: 18671280--18671399 Score: 91
Period size: 7 Copynumber: 17.1 Consensus size: 7
18671270 GATGAATTAT
18671280 GGGTTTA
1 GGGTTTA
*
18671287 GGGATTA
1 GGGTTTA
* *
18671294 TGATTTA
1 GGGTTTA
18671301 GGGTTTA
1 GGGTTTA
*
18671308 GGGGTTA
1 GGGTTTA
18671315 GGG-TT-
1 GGGTTTA
18671320 GGAGTTTA
1 GG-GTTTA
* *
18671328 AGGTGTAA
1 GGGT-TTA
**
18671336 GTATTTA
1 GGGTTTA
*
18671343 GGGTTAA
1 GGGTTTA
* *
18671350 AGGTTAA
1 GGGTTTA
18671357 GGGTTTA
1 GGGTTTA
*
18671364 GAGTTTA
1 GGGTTTA
*
18671371 GTGTTTA
1 GGGTTTA
18671378 GGGTTTA
1 GGGTTTA
18671385 GGGTTTA
1 GGGTTTA
18671392 GGGTTTA
1 GGGTTTA
18671399 G
1 G
18671400 TGGTGTTTTT
Statistics
Matches: 87, Mismatches: 22, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
5 2 0.02
6 3 0.03
7 78 0.90
8 4 0.05
ACGTcount: A:0.22, C:0.00, G:0.38, T:0.40
Consensus pattern (7 bp):
GGGTTTA
Found at i:18671695 original size:14 final size:14
Alignment explanation
Indices: 18671672--18671716 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
18671662 TTAATTATCA
18671672 TTATAGTTTAGGGT
1 TTATAGTTTAGGGT
18671686 TTAT-GATTTAGGGT
1 TTATAG-TTTAGGGT
*
18671700 ATATAGTTTAGGGT
1 TTATAGTTTAGGGT
18671714 TTA
1 TTA
18671717 AGGTGTAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (14 bp):
TTATAGTTTAGGGT
Found at i:18673049 original size:157 final size:155
Alignment explanation
Indices: 18672694--18673066 Score: 375
Period size: 157 Copynumber: 2.4 Consensus size: 155
18672684 AGAGAGTAGT
* *
18672694 GGCGTTTTTTAAAAAAACGCCGC-AAAAACAGTATAGTTGAAAGAAAACGGCGTCGTTTTAGATT
1 GGCGTTTTTT-AAAAAACGCCGCAAAAAACA-T-TAGTTTAACGAAAACGGCGTCGTTTTAGATT
* * *
18672758 GATAGAGTACTAGTGGCGTTTTTAAAAACACCGCAACAGAAGTAAAGTGTACTGGAAGCGTCGTC
63 GATAGAGTACTAGTGGCGCTTTCAAAAACACCGCAAAAGAAGTAAAGTGTACTGGAAGCGTCGTC
*
18672823 GTTTTAGTTCAATATATAGGGGATTTGC
128 GTTTTAGTTCAATATATAGGGGATTAGC
* * * *
18672851 -GCGTTTTTATAGAAAACGCCACAAAATACAGATTAGTTTAACGAAAACGGCGCCGTTTTAG-TA
1 GGCGTTTTT-TAAAAAACGCCGCAAAA-A-ACATTAGTTTAACGAAAACGGCGTCGTTTTAGAT-
* * * * * * * *
18672914 T-ATACGGGTATTAGTGGCGCTTTCAAAAACGCCGCAAAATAATTCAAGTTTA-TAGTACA-CGT
62 TGATA-GAGTACTAGTGGCGCTTTCAAAAACACCGCAAAAGAAGTAAAGTGTACT-GGA-AGCGT
* *
18672976 CGTCGTTTTAGTTGAGTATATA-GGGATTAGC
124 CGTCGTTTTAGTTCAATATATAGGGGATTAGC
*
18673007 GGCGTTTTTTAAATAAACGCCGCAAAAAACATTAGTGCTTAAC-AGGAACGGCGTCGTTTT
1 GGCGTTTTTTAAA-AAACGCCGCAAAAAACATTAGT--TTAACGA-AAACGGCGTCGTTTT
18673067 CTTCAAAGAT
Statistics
Matches: 178, Mismatches: 25, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
155 7 0.04
156 36 0.20
157 130 0.73
158 3 0.02
159 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.29
Consensus pattern (155 bp):
GGCGTTTTTTAAAAAACGCCGCAAAAAACATTAGTTTAACGAAAACGGCGTCGTTTTAGATTGAT
AGAGTACTAGTGGCGCTTTCAAAAACACCGCAAAAGAAGTAAAGTGTACTGGAAGCGTCGTCGTT
TTAGTTCAATATATAGGGGATTAGC
Found at i:18673356 original size:25 final size:25
Alignment explanation
Indices: 18673318--18673376 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
18673308 CTCATCGTTG
*
18673318 TTCGCCGTCGTCTCTTCTGCGTCCC
1 TTCGCCGTCATCTCTTCTGCGTCCC
*
18673343 TTTGCCGTCATCTCTTCTGCGTCCC
1 TTCGCCGTCATCTCTTCTGCGTCCC
18673368 TTCGCCGTC
1 TTCGCCGTC
18673377 GCTCTCCGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.02, C:0.42, G:0.19, T:0.37
Consensus pattern (25 bp):
TTCGCCGTCATCTCTTCTGCGTCCC
Found at i:18681736 original size:43 final size:43
Alignment explanation
Indices: 18681685--18681891 Score: 369
Period size: 43 Copynumber: 4.8 Consensus size: 43
18681675 TAAAAAAAAG
18681685 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAA
* *
18681728 CGCCGCTAAAAGCTTTGACCTTTAGCGGTGCTTTTCCCACAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAA
18681771 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAA
* *
18681814 CGCCGCTAAAAGCTTTGACCTTTAGCGGTGCTTTTCCCACAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAA
*
18681857 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGTTTTT
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTT
18681892 TTCCCAATAA
Statistics
Matches: 155, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 155 1.00
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.27
Consensus pattern (43 bp):
CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAA
Found at i:18691602 original size:3 final size:3
Alignment explanation
Indices: 18691588--18691850 Score: 175
Period size: 3 Copynumber: 89.3 Consensus size: 3
18691578 TTAGTCCTTT
* * ** *
18691588 TTA TTA TT- TTA TTA TTA CTA TTA TTA TTC TTA TTA TTA CCA TTA TGA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
18691635 TTA TCA TCA TCA TTA TTA TTA TT- TT- TTA CTA TTA TCA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
18691681 TTA TTA TTA TTT TTA TTA CTA TTG CTA TTA CTA TTA TCTT TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
* *
18691727 TTA TTA TTA TTA CTA TTA TT- TT- TTA TTA TT- TATA TTA TTG TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
* * ** *
18691769 GTA TTT TTA TTA TCC TTCA TTA TTA TTA TTA TT- TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
18691814 TT- TTA CTA TTA TTA TTTA TTA TCA ATA TTA TTA TTA T
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA T
18691851 CATAAAAGAA
Statistics
Matches: 198, Mismatches: 51, Indels: 22
0.73 0.19 0.08
Matches are distributed among these distances:
2 16 0.08
3 174 0.88
4 8 0.04
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:18691672 original size:31 final size:32
Alignment explanation
Indices: 18691634--18691693 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
18691624 TACCATTATG
18691634 ATTATCATCATCATTATTATTATT-TTTTACT
1 ATTATCATCATCATTATTATTATTATTTTACT
*
18691665 ATTATCATTATCATTATTATTATTATTTT
1 ATTATCATCATCATTATTATTATTATTTT
18691694 TATTACTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (32 bp):
ATTATCATCATCATTATTATTATTATTTTACT
Found at i:18691811 original size:14 final size:14
Alignment explanation
Indices: 18691792--18691830 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
18691782 CCTTCATTAT
18691792 TATTATTATTTTAC
1 TATTATTATTTTAC
18691806 TATTATTATTTTAC
1 TATTATTATTTTAC
18691820 TATTATTATTT
1 TATTATTATTT
18691831 ATTATCAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTATTATTTTAC
Found at i:18697227 original size:57 final size:57
Alignment explanation
Indices: 18697129--18697239 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 57
18697119 GAGAATGGCA
* * *
18697129 TTTCGGAGCAAGTTCGCTATAAGTTTGACAAGATAAAGCAAATGCGTCCAGACATCT
1 TTTCAGAGCAAGTTCGCCATAAGTTTGACAAGATAAAGCAAAGGCGTCCAGACATCT
* * * * * *
18697186 TTTCAGAGCAGGTTCGCCATGAGTTTGAGAGGATAAGGCAAAGGCGTTCAGACA
1 TTTCAGAGCAAGTTCGCCATAAGTTTGACAAGATAAAGCAAAGGCGTCCAGACA
18697240 GATGAGAGAA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (57 bp):
TTTCAGAGCAAGTTCGCCATAAGTTTGACAAGATAAAGCAAAGGCGTCCAGACATCT
Found at i:18697600 original size:3 final size:3
Alignment explanation
Indices: 18697594--18697717 Score: 71
Period size: 3 Copynumber: 43.3 Consensus size: 3
18697584 TCAAAAAAAA
** * * *
18697594 TAT TAT TAT TAT TAT T-T GCT AAT T-T TTT TA- TAT T-T TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
18697638 TAT CAT TAT TAT TAT T-T TAC CAT TAT TAC TAT CAT TA- TAG TAT GAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
18697684 TAT TAT TAC TAT TAT TTT TAT TAT CAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
18697718 TTTAAACCAT
Statistics
Matches: 89, Mismatches: 26, Indels: 12
0.70 0.20 0.09
Matches are distributed among these distances:
2 11 0.12
3 78 0.88
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:18697856 original size:24 final size:23
Alignment explanation
Indices: 18697813--18697857 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
18697803 TTTGTTTTTC
*
18697813 ATTTATTATTCCTTTATTATTGT
1 ATTTATTATTCATTTATTATTGT
18697836 ATTTATTTATTTCATTT-TTATT
1 ATTTA-TTA-TTCATTTATTATT
18697858 CTGTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 8 0.42
25 6 0.32
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (23 bp):
ATTTATTATTCATTTATTATTGT
Found at i:18701329 original size:44 final size:44
Alignment explanation
Indices: 18701266--18701353 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
18701256 TTCATTCTGG
18701266 AGTAGTGAGTGCCAATTGCCTGAACGGTGTGGGGAATTAGGGCT
1 AGTAGTGAGTGCCAATTGCCTGAACGGTGTGGGGAATTAGGGCT
18701310 AGTAGTGAGTGCCAATTGCCTGAACGGTGTGGGGAATTAGGGCT
1 AGTAGTGAGTGCCAATTGCCTGAACGGTGTGGGGAATTAGGGCT
18701354 TTGTGAGGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.23, C:0.14, G:0.39, T:0.25
Consensus pattern (44 bp):
AGTAGTGAGTGCCAATTGCCTGAACGGTGTGGGGAATTAGGGCT
Found at i:18705808 original size:3 final size:3
Alignment explanation
Indices: 18705797--18705826 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
18705787 ATAGATAGTG
*
18705797 GAT GGT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
18705827 AATGGCCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:18707481 original size:83 final size:84
Alignment explanation
Indices: 18707341--18707503 Score: 292
Period size: 83 Copynumber: 2.0 Consensus size: 84
18707331 ACACACCCAT
18707341 CTGGTAGTTATAGACCAATTATGAAGATAACTTCGTGATTTATGAGATTAGGCTATTGAAACCGA
1 CTGGTAGTTATAGACCAATTATGAAGATAACTTCGTGATTTATGAGATTAGGCTATTGAAACCGA
*
18707406 GGAATGTTGCTTTGTCCAA
66 GGAATATTGCTTTGTCCAA
* *
18707425 CTGGTAGTTGTAGACCAATTATGAAGAT-ACTTCGTGATTTATGAGATTAGGGTATTGAAACCGA
1 CTGGTAGTTATAGACCAATTATGAAGATAACTTCGTGATTTATGAGATTAGGCTATTGAAACCGA
18707489 GGAATATTGCTTTGT
66 GGAATATTGCTTTGT
18707504 TCATGTAACA
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
83 49 0.64
84 27 0.36
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (84 bp):
CTGGTAGTTATAGACCAATTATGAAGATAACTTCGTGATTTATGAGATTAGGCTATTGAAACCGA
GGAATATTGCTTTGTCCAA
Found at i:18708004 original size:8 final size:8
Alignment explanation
Indices: 18707993--18708024 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
18707983 TATGTTTTTA
18707993 TATTATAT
1 TATTATAT
18708001 TATTATAT
1 TATTATAT
18708009 TATTATAT
1 TATTATAT
18708017 TATTATAT
1 TATTATAT
18708025 ATATGACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTATAT
Found at i:18708094 original size:40 final size:40
Alignment explanation
Indices: 18708037--18708132 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
18708027 ATGACAAAGA
18708037 AAGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
1 AAGAAAG-AAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
* *
18708078 GAGAAAGAAAGAAACAGAGAGCAAAACGAAACAGAGAAGG
1 AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
*
18708118 AAGGAAGGAAAGAAA
1 AA-GAAAGAAAGAAA
18708133 GAAAGAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 33 0.66
41 17 0.34
ACGTcount: A:0.64, C:0.08, G:0.28, T:0.00
Consensus pattern (40 bp):
AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
Found at i:18708874 original size:30 final size:30
Alignment explanation
Indices: 18708840--18708897 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
18708830 TCCGGGCCTT
*
18708840 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
** *
18708870 GGGGCAAATTTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
18708898 AGAATCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:18709325 original size:44 final size:45
Alignment explanation
Indices: 18709230--18709363 Score: 162
Period size: 44 Copynumber: 3.0 Consensus size: 45
18709220 ACAGGACAGA
* *
18709230 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
18709276 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * *
18709320 ACAGGAATAATTCATGTAAGTCCATGTTAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
18709364 CAGGATATTG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
44 37 0.49
45 1 0.01
46 37 0.49
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:18713229 original size:42 final size:43
Alignment explanation
Indices: 18713139--18713289 Score: 137
Period size: 42 Copynumber: 3.5 Consensus size: 43
18713129 CAATGCCGAC
* * * *
18713139 GTCCCGGACATGGTCTTACATGTAATTCAGTATCGATGCCTCT
1 GTCCCAGACATGGTCTTACACGTAAATCAGTATCGATGCCTAT
* *
18713182 GTCCCAGACAGGGTCTTACACG-AAATCAG-ATACGATGCTTAT
1 GTCCCAGACATGGTCTTACACGTAAATCAGTAT-CGATGCCTAT
* * * * * *
18713224 GTCCCATACATGGTCTTACATGTAAATATCA-AATCGAGGACTGT
1 GTCCCAGACATGGTCTTACACGT-AA-ATCAGTATCGATGCCTAT
*
18713268 GTCCCAGACACGGTCTTACACG
1 GTCCCAGACATGGTCTTACACG
18713290 ATATCTCAGA
Statistics
Matches: 87, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
41 2 0.02
42 33 0.38
43 19 0.22
44 27 0.31
45 6 0.07
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACGTAAATCAGTATCGATGCCTAT
Found at i:18714042 original size:23 final size:23
Alignment explanation
Indices: 18714012--18714058 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
18714002 TCAAAAATCG
18714012 AGCAAAACAAACTTACCTAATTA
1 AGCAAAACAAACTTACCTAATTA
18714035 AGCAAAACAAACTTACCTAATTA
1 AGCAAAACAAACTTACCTAATTA
18714058 A
1 A
18714059 TCATGTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.53, C:0.21, G:0.04, T:0.21
Consensus pattern (23 bp):
AGCAAAACAAACTTACCTAATTA
Found at i:18725354 original size:46 final size:46
Alignment explanation
Indices: 18725287--18725641 Score: 505
Period size: 46 Copynumber: 7.7 Consensus size: 46
18725277 TGGCAACCTG
18725287 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
*
18725333 TGTGTAAGACTATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
* *
18725379 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
* ** * *
18725425 AGAATAAGATCATGGTTGAAAGATACCATGACAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
*
18725471 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAGA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
* * *
18725517 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATCAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
* ** * *
18725563 AGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG-AAA
* * * *
18725609 TGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCA
18725642 TCACGTTAAA
Statistics
Matches: 277, Mismatches: 31, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
46 277 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
Found at i:18725478 original size:138 final size:138
Alignment explanation
Indices: 18725238--18725641 Score: 619
Period size: 138 Copynumber: 3.0 Consensus size: 138
18725228 AGTGTGCTCT
* *
18725238 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG---TG---TG--TAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAG
*
18725295 ACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACTATGGTTGAAAGATACC
66 ACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACC
18725360 ATGGCAAC
131 ATGGCAAC
18725368 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAG
* *
18725433 ATCATGGTTGAAAGATACCATGACAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACC
66 ACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACC
18725498 ATGGCAAC
131 ATGGCAAC
* *
18725506 CTGATATGAGATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATCAAAAGAATAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAG
* * * * *
18725571 ACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACAC
66 ACCATGGTTGAAAGATACCATGGCAACCTGATATG-AAATGTGTAAGACCATGGTTGAAAGATAC
*
18725635 TATGGCA
130 CATGGCA
18725642 TCACGTTAAA
Statistics
Matches: 250, Mismatches: 15, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
130 48 0.19
133 2 0.01
136 1 0.00
137 1 0.00
138 198 0.79
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (138 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAG
ACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACC
ATGGCAAC
Found at i:18725947 original size:23 final size:25
Alignment explanation
Indices: 18725902--18725948 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
18725892 AATAAATATA
*
18725902 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
18725927 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
18725949 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:18726320 original size:14 final size:14
Alignment explanation
Indices: 18726301--18726328 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18726291 CGGATACGGG
18726301 TTAGGGGTGTTACA
1 TTAGGGGTGTTACA
18726315 TTAGGGGTGTTACA
1 TTAGGGGTGTTACA
18726329 CGCACACCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.36, T:0.36
Consensus pattern (14 bp):
TTAGGGGTGTTACA
Found at i:18734418 original size:3 final size:3
Alignment explanation
Indices: 18734410--18734440 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
18734400 TGGCGAGTTT
18734410 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
18734441 GGCAAGTTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:18741819 original size:20 final size:20
Alignment explanation
Indices: 18741794--18741867 Score: 139
Period size: 20 Copynumber: 3.7 Consensus size: 20
18741784 AAGGGCACAC
*
18741794 GCCCGTGTGGCCTGGGACAT
1 GCCCGTGTGGCCTGGAACAT
18741814 GCCCGTGTGGCCTGGAACAT
1 GCCCGTGTGGCCTGGAACAT
18741834 GCCCGTGTGGCCTGGAACAT
1 GCCCGTGTGGCCTGGAACAT
18741854 GCCCGTGTGGCCTG
1 GCCCGTGTGGCCTG
18741868 CCCGTGGGCA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.11, C:0.31, G:0.38, T:0.20
Consensus pattern (20 bp):
GCCCGTGTGGCCTGGAACAT
Found at i:18743989 original size:3 final size:3
Alignment explanation
Indices: 18743975--18744008 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
18743965 TTATCTCAAT
18743975 TAA TAGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
18744009 AAGTAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:18744404 original size:46 final size:46
Alignment explanation
Indices: 18744351--18744442 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
18744341 GAAATATGGG
18744351 TTGTTACAGTCCTAATCGTCCCATCGTGCATCTTAATTTTAACAGT
1 TTGTTACAGTCCTAATCGTCCCATCGTGCATCTTAATTTTAACAGT
*
18744397 TTGTTACAGTCCTAATCGTCTCATCGTGCATCTTAATTTTAACAGT
1 TTGTTACAGTCCTAATCGTCCCATCGTGCATCTTAATTTTAACAGT
18744443 ACCAATACCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (46 bp):
TTGTTACAGTCCTAATCGTCCCATCGTGCATCTTAATTTTAACAGT
Found at i:18746812 original size:85 final size:85
Alignment explanation
Indices: 18746666--18746836 Score: 261
Period size: 85 Copynumber: 2.0 Consensus size: 85
18746656 TAGCTTAAGA
* * * * *
18746666 GTCTATTGAGAAAGGATTTAAAAGGAAGTTAGACCCAAAAGTTATTTGGGCTGGACGGCAAGAGT
1 GTCTAATGAGAAAGGATTTAAAAGGAAATTAGACCCAAAAGTTATTTGGACTGGACAGCAAGAGC
18746731 ATGAAATCAGCAGAAAAATT
66 ATGAAATCAGCAGAAAAATT
* *
18746751 GTCTAATGAGAAAGGATTTAAAAGGAAATTAGACCCAAAATTTATTTGGATTGGACAGCAAGAGC
1 GTCTAATGAGAAAGGATTTAAAAGGAAATTAGACCCAAAAGTTATTTGGACTGGACAGCAAGAGC
* *
18746816 ATGAAATCTGCAGGAAAATT
66 ATGAAATCAGCAGAAAAATT
18746836 G
1 G
18746837 ATGATTTAAG
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
85 77 1.00
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.24
Consensus pattern (85 bp):
GTCTAATGAGAAAGGATTTAAAAGGAAATTAGACCCAAAAGTTATTTGGACTGGACAGCAAGAGC
ATGAAATCAGCAGAAAAATT
Found at i:18749119 original size:14 final size:14
Alignment explanation
Indices: 18749100--18749129 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18749090 TATCTTATAA
18749100 ATATGCGTGAATCT
1 ATATGCGTGAATCT
*
18749114 ATATGCGTTAATCT
1 ATATGCGTGAATCT
18749128 AT
1 AT
18749130 CTTGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (14 bp):
ATATGCGTGAATCT
Found at i:18764224 original size:39 final size:39
Alignment explanation
Indices: 18764181--18764357 Score: 221
Period size: 39 Copynumber: 4.5 Consensus size: 39
18764171 AACATGTTTT
*
18764181 TGAGTATTGTGACATATGCTTGAATGTTATGTAATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTAATTATA
** *
18764220 TGAGTATTACGATGTATGCTTGAATGTTATGTAATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTAATTATA
* * * **
18764259 TGAGTATCGCGATATGTGCTTGAACATTATGTAATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTAATTATA
*
18764298 TGAGTATTGTGATATATGCTT-AAGTGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAA-TGTTATGTAATTATA
* * *
18764337 TGTGTAATGTAATATATGCTT
1 TGAGTATTGTGATATATGCTT
18764358 AAAAGTGAAT
Statistics
Matches: 118, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
38 2 0.02
39 116 0.98
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.44
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTGAATGTTATGTAATTATA
Found at i:18765718 original size:20 final size:21
Alignment explanation
Indices: 18765695--18765735 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
18765685 GAATATGTTG
* *
18765695 TAAATTAAAAGTTTA-TGATA
1 TAAAATAAAAGGTTATTGATA
18765715 TAAAATAAAAGGTTATTGATA
1 TAAAATAAAAGGTTATTGATA
18765736 GAGAAATCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (21 bp):
TAAAATAAAAGGTTATTGATA
Found at i:18766560 original size:29 final size:29
Alignment explanation
Indices: 18766527--18766595 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
18766517 TGTGTGTACC
*
18766527 ATGTGAAAAGGGATAGCTTCGGCTATCGA
1 ATGTGAAAAGGGATAGCTTCGGCTATCAA
*
18766556 ATGTGAAAAGGGATAGCTTTGGCTATCAA
1 ATGTGAAAAGGGATAGCTTCGGCTATCAA
18766585 ATGTGAAAAGG
1 ATGTGAAAAGG
18766596 AAAGGTATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25
Consensus pattern (29 bp):
ATGTGAAAAGGGATAGCTTCGGCTATCAA
Found at i:18766625 original size:33 final size:33
Alignment explanation
Indices: 18766588--18766722 Score: 124
Period size: 33 Copynumber: 4.3 Consensus size: 33
18766578 CTATCAAATG
* *
18766588 TGAAAAGGAAAGGTATACTTTGTGTATACCACA
1 TGAAAAGGAAAGGTATACTTTGTGTGTACCACT
** *
18766621 TGAAAAGGCTATGTATACTTTGTGTGTA-CACT
1 TGAAAAGGAAAGGTATACTTTGTGTGTACCACT
* * *
18766653 TG---A--AACGGCATAC-TT-TGTGTACCATT
1 TGAAAAGGAAAGGTATACTTTGTGTGTACCACT
* *
18766679 TGAAAAGGAAAGGTATACTTTGCGTGTACCATT
1 TGAAAAGGAAAGGTATACTTTGTGTGTACCACT
18766712 TGAAAAGGAAA
1 TGAAAAGGAAA
18766723 TGTGCACAAA
Statistics
Matches: 80, Mismatches: 14, Indels: 16
0.73 0.13 0.15
Matches are distributed among these distances:
25 6 0.08
26 7 0.09
27 5 0.06
29 2 0.03
31 8 0.10
32 7 0.09
33 45 0.56
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (33 bp):
TGAAAAGGAAAGGTATACTTTGTGTGTACCACT
Found at i:18766685 original size:58 final size:60
Alignment explanation
Indices: 18766602--18766716 Score: 144
Period size: 58 Copynumber: 1.9 Consensus size: 60
18766592 AAGGAAAGGT
** * *
18766602 ATACTTTGTGTATACCACATGAAAAGGCTATGTATACTTTGTGTGTA-CACTTGAAACGGC
1 ATACTTTGTG-ATACCACATGAAAAGGAAAGGTATACTTTGCGTGTACCACTTGAAACGGC
** *
18766662 ATACTTTGTG-TACCATTTGAAAAGGAAAGGTATACTTTGCGTGTACCATTTGAAA
1 ATACTTTGTGATACCACATGAAAAGGAAAGGTATACTTTGCGTGTACCACTTGAAA
18766717 AGGAAATGTG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
58 29 0.62
59 8 0.17
60 10 0.21
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (60 bp):
ATACTTTGTGATACCACATGAAAAGGAAAGGTATACTTTGCGTGTACCACTTGAAACGGC
Found at i:18769503 original size:25 final size:25
Alignment explanation
Indices: 18769475--18769525 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
18769465 TTATTGTGTG
18769475 TATAACATGAGAAGGTGGTGTAGCA
1 TATAACATGAGAAGGTGGTGTAGCA
*
18769500 TATAACATGAGAAGGTGGTGTGGCA
1 TATAACATGAGAAGGTGGTGTAGCA
18769525 T
1 T
18769526 CTTGATATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.33, T:0.25
Consensus pattern (25 bp):
TATAACATGAGAAGGTGGTGTAGCA
Found at i:18777808 original size:16 final size:15
Alignment explanation
Indices: 18777787--18777816 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
18777777 ATTACACATG
18777787 AAAAGAATAGAATAAC
1 AAAAGAATA-AATAAC
18777803 AAAAGAATAAATAA
1 AAAAGAATAAATAA
18777817 TGAAATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.03, G:0.10, T:0.13
Consensus pattern (15 bp):
AAAAGAATAAATAAC
Found at i:18780819 original size:24 final size:24
Alignment explanation
Indices: 18780788--18780840 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
18780778 TAACAAAATT
*
18780788 TTTCTCACTTTTGCAATTTAATCA
1 TTTCTCACTTTTACAATTTAATCA
*
18780812 TTTCTCACTTTTACAATTTAATCC
1 TTTCTCACTTTTACAATTTAATCA
18780836 TTTCT
1 TTTCT
18780841 TCAATTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.23, C:0.23, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTCTCACTTTTACAATTTAATCA
Found at i:18794243 original size:76 final size:76
Alignment explanation
Indices: 18794118--18794259 Score: 198
Period size: 76 Copynumber: 1.9 Consensus size: 76
18794108 GAAACCGGTA
18794118 TAGCTGAAGGAGCAGAATTCGAAAGAGGTTTTACATCTGCACAACATCAACGC-TTTTAACTTCA
1 TAGCTGAAGGAGCAGAATTCGAAAGAGGTTTTACATCTGCACAACATCAACGCTTTTTAACTTCA
18794182 ACACGCTATGG
66 ACACGCTATGG
* * * * * *
18794193 TAGCTGAAGGAGCAGATTTTGGTAA-AGGTCTTTACATTTGCACAACATCAATGCTTTTTAATTT
1 TAGCTGAAGGAGCAGA-ATTCGAAAGAGGT-TTTACATCTGCACAACATCAACGCTTTTTAACTT
18794257 CAA
64 CAA
18794260 AAATCATGCA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
75 20 0.34
76 27 0.47
77 11 0.19
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (76 bp):
TAGCTGAAGGAGCAGAATTCGAAAGAGGTTTTACATCTGCACAACATCAACGCTTTTTAACTTCA
ACACGCTATGG
Found at i:18795915 original size:17 final size:18
Alignment explanation
Indices: 18795878--18795919 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
18795868 ATTGAACCAG
*
18795878 TTTTATAAATTTTATATAT
1 TTTTA-AAATTTTATAGAT
18795897 TTTTAAAATTTTAT-GAT
1 TTTTAAAATTTTATAGAT
18795914 TTTTAA
1 TTTTAA
18795920 TTGTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
18 9 0.41
19 5 0.23
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTAAAATTTTATAGAT
Found at i:18796122 original size:91 final size:90
Alignment explanation
Indices: 18795988--18796157 Score: 198
Period size: 91 Copynumber: 1.9 Consensus size: 90
18795978 TAGGGGTTGA
* * * ** *
18795988 AACTTTTTTTTATCCAAGTTAATCCCTAAACTTGATAATTGTTCTTATATTAA-AGCTTGAACTT
1 AACTTTTTTTTATCCAAATTAACCCCTAAACTTGACAATTGTTCCCAAATTAAGA-CTTGAACTT
*
18796052 GGTAATTGTTCTCACATTGGAGTTTG
65 GATAATTGTTCTCACATTGGAGTTTG
* * * * *
18796078 AACTTTTTTTTGGTTCAAATTAACCCCTGAATTTGACAATTGTTCCCAAATTGAGACTTGAACTT
1 AACTTTTTTTT-ATCCAAATTAACCCCTAAACTTGACAATTGTTCCCAAATTAAGACTTGAACTT
*
18796143 GATAGTTGTTCTCAC
65 GATAATTGTTCTCAC
18796158 TTTGAGGCCT
Statistics
Matches: 65, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
90 11 0.17
91 53 0.82
92 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (90 bp):
AACTTTTTTTTATCCAAATTAACCCCTAAACTTGACAATTGTTCCCAAATTAAGACTTGAACTTG
ATAATTGTTCTCACATTGGAGTTTG
Found at i:18796391 original size:59 final size:56
Alignment explanation
Indices: 18796199--18796391 Score: 126
Period size: 58 Copynumber: 3.3 Consensus size: 56
18796189 AATATCAAGA
* * * *
18796199 ATTAATTTG-AAAAAAAAATTTAAACCCCAATATGAGATTAATCGACAAGTTCAAAA
1 ATTAATTGGAAAAAAAAAATTTAAACCCCTATATGAGACTAAT-GACAAGTTCAAAG
* * * *
18796255 ATTAATTTGGACAAAAAAAATTCAAA-TCCTATGA-AAGAAC-AATTG-CGAAGTTCAAAG
1 ATTAA-TTGGAAAAAAAAAATTTAAACCCCTAT-ATGAG-ACTAA-TGAC-AAGTTCAAAG
* * * * **
18796312 ATCAACTTAGACCAAGAAAAATTTAAACCCCTATATGAGACTAACTGTTAAGTTCAAAG
1 ATTAA-TTGGA-AAAAAAAAATTTAAACCCCTATATGAGACTAA-TGACAAGTTCAAAG
18796371 ATTAATTCGGATAAAAAAAAA
1 ATTAATT-GGA-AAAAAAAAA
18796392 GTGTGAATGT
Statistics
Matches: 103, Mismatches: 22, Indels: 21
0.71 0.15 0.14
Matches are distributed among these distances:
56 6 0.06
57 29 0.28
58 34 0.33
59 34 0.33
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.25
Consensus pattern (56 bp):
ATTAATTGGAAAAAAAAAATTTAAACCCCTATATGAGACTAATGACAAGTTCAAAG
Found at i:18804058 original size:11 final size:11
Alignment explanation
Indices: 18804037--18804073 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
18804027 AGCCTGGCCC
18804037 ATATTAAATAT
1 ATATTAAATAT
**
18804048 ATATTTTATAT
1 ATATTAAATAT
18804059 ATATTAAATAT
1 ATATTAAATAT
18804070 ATAT
1 ATAT
18804074 ATTTGATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATATTAAATAT
Found at i:18804076 original size:24 final size:23
Alignment explanation
Indices: 18804037--18804109 Score: 76
Period size: 24 Copynumber: 3.1 Consensus size: 23
18804027 AGCCTGGCCC
*
18804037 ATATT-AAATATATATTTTATAT
1 ATATTAAAATATATATTTAATAT
* *
18804059 ATATTAAATATATATATTTGATTAA
1 ATATTAAA-ATATATATTT-AATAT
* *
18804084 AAATAAAAATATATATTTAATAT
1 ATATTAAAATATATATTTAATAT
18804107 ATA
1 ATA
18804110 ATTTCGGCTA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
22 5 0.12
23 7 0.17
24 20 0.50
25 8 0.20
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (23 bp):
ATATTAAAATATATATTTAATAT
Found at i:18806118 original size:6 final size:6
Alignment explanation
Indices: 18806107--18806134 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
18806097 TTTTCCTTGT
18806107 CATTGC CATTGC CATTGC CATTGC CATT
1 CATTGC CATTGC CATTGC CATTGC CATT
18806135 TCCAGCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.14, T:0.36
Consensus pattern (6 bp):
CATTGC
Found at i:18814387 original size:22 final size:22
Alignment explanation
Indices: 18814362--18814453 Score: 132
Period size: 22 Copynumber: 4.2 Consensus size: 22
18814352 AAATTCAATA
*
18814362 TCAATTTCCTTCAAAAATTCGC
1 TCAATTTCCTTCAAAAATTCTC
18814384 TCAA-TTCCTTTCAAAAATTCTC
1 TCAATTTCC-TTCAAAAATTCTC
* *
18814406 TCAATTCCCTTCAAAATTTCTC
1 TCAATTTCCTTCAAAAATTCTC
*
18814428 TCAATTTCCTTCTAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
18814450 TCAA
1 TCAA
18814454 ACTCTCAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
21 4 0.06
22 55 0.89
23 3 0.05
ACGTcount: A:0.30, C:0.28, G:0.01, T:0.40
Consensus pattern (22 bp):
TCAATTTCCTTCAAAAATTCTC
Found at i:18814461 original size:30 final size:30
Alignment explanation
Indices: 18814425--18814483 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
18814415 TTCAAAATTT
* * *
18814425 CTCTCAATTTCCTTCTAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
18814455 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
18814484 TTTCCTTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.36
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:18814469 original size:52 final size:51
Alignment explanation
Indices: 18814403--18814505 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 51
18814393 TTCAAAAATT
* * *
18814403 CTCTCAATTCCCTT-CAAAATTTCTCTCAATTTCCTTCTAAAATTCTCTCAAA
1 CTCTCAATTCCCTTCCAAAA-TCCTCTCAATTTCCTTCAAAAAATCTC-CAAA
18814455 CTCTCAAATT-CCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
18814506 TCCATATTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
51 4 0.09
52 33 0.72
53 9 0.20
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (51 bp):
CTCTCAATTCCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
Found at i:18814494 original size:21 final size:22
Alignment explanation
Indices: 18814455--18814496 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
18814445 TTCTCTCAAA
18814455 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
18814477 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
18814497 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:18814602 original size:31 final size:32
Alignment explanation
Indices: 18814539--18814603 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 32
18814529 TTAAATTTCA
** **
18814539 TTTTTTAAGAAAATTTTAATTTTTTTTTTATT
1 TTTTTTAAGAAAATTTTAAAATTTTTAATATT
*
18814571 TTTTTTAA-ATAATTTTAAAATTTTTAATATT
1 TTTTTTAAGAAAATTTTAAAATTTTTAATATT
18814602 TT
1 TT
18814604 CAACAATGGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (32 bp):
TTTTTTAAGAAAATTTTAAAATTTTTAATATT
Found at i:18814691 original size:49 final size:49
Alignment explanation
Indices: 18814614--18814711 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
18814604 CAACAATGGC
18814614 CGGATCATTGATTCGTCTCGATAAGAATCACATATCGGTGGAGCAAATG
1 CGGATCATTGATTCGTCTCGATAAGAATCACATATCGGTGGAGCAAATG
* *
18814663 CGGATCATTGATTCGTCTTGATAGGAATCACATATCGGTGGAGCAAATG
1 CGGATCATTGATTCGTCTCGATAAGAATCACATATCGGTGGAGCAAATG
18814712 AACATGGTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.28
Consensus pattern (49 bp):
CGGATCATTGATTCGTCTCGATAAGAATCACATATCGGTGGAGCAAATG
Found at i:18814771 original size:14 final size:15
Alignment explanation
Indices: 18814742--18814775 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
18814732 TAAATTTAAA
18814742 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
18814757 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
18814771 TTTTA
1 TTTTA
18814776 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:18816975 original size:29 final size:29
Alignment explanation
Indices: 18816920--18817795 Score: 316
Period size: 23 Copynumber: 34.2 Consensus size: 29
18816910 TTTGATTAAA
*
18816920 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
18816949 AA--C---CCT-ACTTAATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
*
18816972 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
18817001 AA--C--A--TAACTTAATTATAAAA-CCT
1 AACCCTAACCTAACTTAATTA-AAAACCCT
*
18817024 AA-CCTAACTTAA-TTAAATTAAAAACCCT
1 AACCCTAACCTAACTT-AATTAAAAACCCT
18817052 AA--C--A--TAACTTAATTATAAAA-CCT
1 AACCCTAACCTAACTTAATTA-AAAACCCT
*
18817075 AA-CCTAACTTAA-TTAAATTAAAAACCCT
1 AACCCTAACCTAACTT-AATTAAAAACCCT
18817103 AA--C--A--TAACTTAATTATAAAA-CCT
1 AACCCTAACCTAACTTAATTA-AAAACCCT
*
18817126 AA-CCTAACTTAA-TTAAATTAAAAACCCT
1 AACCCTAACCTAACTT-AATTAAAAACCCT
18817154 AA--C--A--TAACTTAATTATAAAA-CCT
1 AACCCTAACCTAACTTAATTA-AAAACCCT
*
18817177 AA-CCTAACTTAA-TTAAATTAAAAACCCT
1 AACCCTAACCTAACTT-AATTAAAAACCCT
18817205 AA--C--A--TAACTTAATTATAAAA-CCT
1 AACCCTAACCTAACTTAATTA-AAAACCCT
*
18817228 AA-CCTAACTTAA-TTAAATTAAAAACCCT
1 AACCCTAACCTAACTT-AATTAAAAACCCT
18817256 AA--C--A--TAACTTAATTATAAAA-CCT
1 AACCCTAACCTAACTTAATTA-AAAACCCT
*
18817279 AA-CCTAACTTAA-TTAAATTAAAAACCCT
1 AACCCTAACCTAACTT-AATTAAAAACCCT
18817307 AA--C--A--TAACTTAATTATAAAA-CCT
1 AACCCTAACCTAACTTAATTA-AAAACCCT
*
18817330 AA-CCTAACTTAA-TTAAATTAAAAACCCT
1 AACCCTAACCTAACTT-AATTAAAAACCCT
18817358 AA--C--A--TAACTTAATTATAAAA-CCT
1 AACCCTAACCTAACTTAATTA-AAAACCCT
*
18817381 AA-CCTAACTTAA-TTAAATTAAAAACCCT
1 AACCCTAACCTAACTT-AATTAAAAACCCT
18817409 AA--C--A--TAACTTAATTATAAAA-CCT
1 AACCCTAACCTAACTTAATTA-AAAACCCT
*
18817432 AA-CCTAACTTAA-TTAAATTAAAAACCCT
1 AACCCTAACCTAACTT-AATTAAAAACCCT
18817460 AA--C--A--TAACTTAATTATAAAA-CCT
1 AACCCTAACCTAACTTAATTA-AAAACCCT
*
18817483 AA-CCTAACTTAA-TTAAATTAAAAACCCT
1 AACCCTAACCTAACTT-AATTAAAAACCCT
18817511 AA--C--A--TAACTTAATTATAAAA-CCT
1 AACCCTAACCTAACTTAATTA-AAAACCCT
*
18817534 AA-CCTAACTTAA-TTAAATTAAAAACCCT
1 AACCCTAACCTAACTT-AATTAAAAACCCT
18817562 AA--C--A--TAACTTAATTATAAAA-CCT
1 AACCCTAACCTAACTTAATTA-AAAACCCT
*
18817585 AA-CCTAACTTAA-TTAAATTAAAAACCCT
1 AACCCTAACCTAACTT-AATTAAAAACCCT
18817613 AA--C--A--TAACTTAATTATAAAA-CCT
1 AACCCTAACCTAACTTAATTA-AAAACCCT
*
18817636 AA-CCTAACTTAA-TTAAATTAAAAACCCT
1 AACCCTAACCTAACTT-AATTAAAAACCCT
18817664 AA--C--A--TAACTTAATTATAAAA-CCT
1 AACCCTAACCTAACTTAATTA-AAAACCCT
*
18817687 -ACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
18817715 AA--C--A--TAACTTAATTATAAAA-CCT
1 AACCCTAACCTAACTTAATTA-AAAACCCT
*
18817738 AA-CCTAACTTAA-TTAAATTAAAAACCCT
1 AACCCTAACCTAACTT-AATTAAAAACCCT
18817766 AA--C--A--TAACTTAATTAAAAACCCT
1 AACCCTAACCTAACTTAATTAAAAACCCT
18817789 AACCCTA
1 AACCCTA
18817796 CTTAATTAAA
Statistics
Matches: 697, Mismatches: 5, Indels: 292
0.70 0.01 0.29
Matches are distributed among these distances:
22 1 0.00
23 233 0.33
24 106 0.15
25 18 0.03
26 15 0.02
27 105 0.15
28 198 0.28
29 21 0.03
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (29 bp):
AACCCTAACCTAACTTAATTAAAAACCCT
Found at i:18817051 original size:51 final size:51
Alignment explanation
Indices: 18816923--18817841 Score: 1622
Period size: 51 Copynumber: 18.1 Consensus size: 51
18816913 GATTAAAAAC
* * *
18816923 CCTAACCTAATTTAATTAAAAACCCTAACCCT-ACTTAATTA-AAAACCCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAA-CATAACTTAATTATAAAA-CCTAA
* *
18816974 CCCTAACCTAATTTAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
1 -CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
18817026 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
18817077 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
18817128 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
18817179 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
18817230 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
18817281 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
18817332 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
18817383 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
18817434 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
18817485 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
18817536 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
18817587 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
*
18817638 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAC
1 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
* *
18817689 CCTAACCTAATTTAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
18817740 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTA-AAAACCCTAA
1 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAA-CCTAA
* * * *
18817791 CC---C-TACTT-AATTAAAAACCTTAACCTAATTTAATTA-AAAACCTTAA
1 CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACC-TAA
18817837 CCTAA
1 CCTAA
18817842 TCGAAGCAAC
Statistics
Matches: 847, Mismatches: 13, Indels: 17
0.97 0.01 0.02
Matches are distributed among these distances:
45 2 0.00
46 34 0.04
47 4 0.00
48 1 0.00
50 4 0.00
51 756 0.89
52 42 0.05
53 4 0.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (51 bp):
CCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTATAAAACCTAA
Found at i:18820117 original size:125 final size:126
Alignment explanation
Indices: 18819878--18820145 Score: 387
Period size: 125 Copynumber: 2.1 Consensus size: 126
18819868 CCACGAGGGT
18819878 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAAAATTATTTCCTACATGACCAACTGTAG
1 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAAAATTATTTCCTACATGACCAACTGTAG
* * * * **
18819943 CGAAATCGCGTCCACGAGGGCGCAATTTCAGAATTTCTTCTCATATAGCATCCTGGTATCA
66 CGAAATCGCGTCCACGAGGCCACAATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
* * *
18820004 GCGATTTTATACTATTTGCTCAGAAAACGTC-AAAAAAAAATTATTTCTTACATGACC-ACTGTA
1 GCGATTTGACACTATTTGCTCAG-AAACGTCAAAAAAAAAATTATTTCCTACATGACCAACTGTA
* * *
18820067 GCGAAATCGCGTCTACGAGGCCACTATTTCACAATTTCTTCTTAAATAGCATCCTGGTAGAA
65 GCGAAATCGCGTCCACGAGGCCACAATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
**
18820129 GCGATTTCCCACTATTT
1 GCGATTTGACACTATTT
18820146 AACCAGATAC
Statistics
Matches: 126, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
125 73 0.58
126 46 0.37
127 7 0.06
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.30
Consensus pattern (126 bp):
GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAAAATTATTTCCTACATGACCAACTGTAG
CGAAATCGCGTCCACGAGGCCACAATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
Found at i:18821557 original size:52 final size:52
Alignment explanation
Indices: 18821479--18821636 Score: 307
Period size: 52 Copynumber: 3.0 Consensus size: 52
18821469 AGGGACTTCG
18821479 GATGAAAGGTATAAAACTGCCTATGCTTTAGATAGCATTTAGGTTCTTTATT
1 GATGAAAGGTATAAAACTGCCTATGCTTTAGATAGCATTTAGGTTCTTTATT
18821531 GATGAAAGGTATAAAACTGCCTATGCTTTAGATAGCATTTAGGTTCTTTATT
1 GATGAAAGGTATAAAACTGCCTATGCTTTAGATAGCATTTAGGTTCTTTATT
*
18821583 GATGAAAGGTATAAAACTGCCTATGCTTTTGATAGCATTTAGGTTCTTTATT
1 GATGAAAGGTATAAAACTGCCTATGCTTTAGATAGCATTTAGGTTCTTTATT
18821635 GA
1 GA
18821637 AAATATTTAC
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 105 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (52 bp):
GATGAAAGGTATAAAACTGCCTATGCTTTAGATAGCATTTAGGTTCTTTATT
Found at i:18821771 original size:21 final size:22
Alignment explanation
Indices: 18821745--18821789 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
18821735 TTTAAAATTT
18821745 AAAATTAATTAAAAA-CTATAA
1 AAAATTAATTAAAAAGCTATAA
* *
18821766 AAAATTTATTAAAAAGTTATAA
1 AAAATTAATTAAAAAGCTATAA
18821788 AA
1 AA
18821790 TTTTTATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAATTAATTAAAAAGCTATAA
Found at i:18821807 original size:20 final size:20
Alignment explanation
Indices: 18821744--18821807 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
18821734 TTTTAAAATT
*
18821744 TAAAATTAATTAAAAACTATAA
1 TAAAATTTATTAAAAA--ATAA
* *
18821766 -AAAATTTATTAAAAAGTTA
1 TAAAATTTATTAAAAAATAA
18821785 TAAAATTT-TTATAAAAATAA
1 TAAAATTTATTA-AAAAATAA
18821805 TAA
1 TAA
18821808 TATCAACCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 5 0.14
20 16 0.46
21 14 0.40
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
TAAAATTTATTAAAAAATAA
Found at i:18822487 original size:20 final size:19
Alignment explanation
Indices: 18822434--18822487 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 19
18822424 GGTTGAACCG
18822434 ATTTTCTTTATTTTTTAAAT
1 ATTTT-TTTATTTTTTAAAT
18822454 A-TTTTTTA--TTTTAAAT
1 ATTTTTTTATTTTTTAAAT
18822470 ATTTTTTTAATTTTTTAA
1 ATTTTTTT-ATTTTTTAA
18822488 TAATTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
16 9 0.30
17 6 0.20
18 5 0.17
19 3 0.10
20 7 0.23
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTTTTTTATTTTTTAAAT
Found at i:18822493 original size:20 final size:19
Alignment explanation
Indices: 18822434--18822498 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
18822424 GGTTGAACCG
18822434 ATTTTCTTTATTTTTT-A-A
1 ATTTT-TTTATTTTTTAATA
*
18822452 ATATTTTTTA-TTTTAAAT-
1 AT-TTTTTTATTTTTTAATA
18822470 ATTTTTTTAATTTTTTAATA
1 ATTTTTTT-ATTTTTTAATA
*
18822490 ATTTATTTA
1 ATTTTTTTA
18822499 ATTTATTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
17 10 0.26
18 10 0.26
19 11 0.29
20 7 0.18
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTTTTTTATTTTTTAATA
Found at i:18822499 original size:20 final size:19
Alignment explanation
Indices: 18822443--18822502 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 19
18822433 GATTTTCTTT
18822443 ATTTTTTAA-ATATTTTTT-
1 ATTTTTTAATA-ATTTTTTA
* *
18822461 A-TTTTAAATATTTTTTTA
1 ATTTTTTAATAATTTTTTA
18822479 ATTTTTTAATAATTTATTTA
1 ATTTTTTAATAATTT-TTTA
18822499 ATTT
1 ATTT
18822503 ATTTTAATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 12 0.35
18 3 0.09
19 11 0.32
20 8 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTTTTAATAATTTTTTA
Found at i:18822722 original size:25 final size:26
Alignment explanation
Indices: 18822679--18822727 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
18822669 TCGACTGAAA
18822679 TATTATTTTTATAATAATTTTATTCT
1 TATTATTTTTATAATAATTTTATTCT
18822705 TATTA-TTTTATCAA-AATTTTATT
1 TATTATTTTTAT-AATAATTTTATT
18822728 ATAATTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (26 bp):
TATTATTTTTATAATAATTTTATTCT
Found at i:18830571 original size:23 final size:23
Alignment explanation
Indices: 18830528--18830572 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
18830518 TGCTTTTGTA
*
18830528 CCCTAAAACCCGAAGCTATTAAT
1 CCCTAAAACCCGAAACTATTAAT
*
18830551 CCCTATAACCCGTAAAC-ATTAA
1 CCCTAAAACCCG-AAACTATTAA
18830573 AATTAAAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.22
Consensus pattern (23 bp):
CCCTAAAACCCGAAACTATTAAT
Found at i:18830675 original size:78 final size:78
Alignment explanation
Indices: 18830565--18830737 Score: 296
Period size: 78 Copynumber: 2.2 Consensus size: 78
18830555 ATAACCCGTA
* *
18830565 AACATTAAAATTAA-AA-GCTAAACCCTAGCTAACTCATATTCTTCATGCAAATCCGAACACAAA
1 AACATTCAAATCAATAAGGCTAAACCCTAGCTAACTCATATTCTTCATGCAAATCCGAACACAAA
18830628 AACCAAGCATTGT
66 AACCAAGCATTGT
* *
18830641 AACATTCAAATCAATAAGGCTAAACCCTAGCTAACTCGTATTCTTCATGCAAATCCGAACGCAAA
1 AACATTCAAATCAATAAGGCTAAACCCTAGCTAACTCATATTCTTCATGCAAATCCGAACACAAA
18830706 AACCAAGCATTGT
66 AACCAAGCATTGT
18830719 AACATTCAAATCAATAAGG
1 AACATTCAAATCAATAAGG
18830738 GTGAACCATA
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
76 12 0.13
77 2 0.02
78 77 0.85
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.23
Consensus pattern (78 bp):
AACATTCAAATCAATAAGGCTAAACCCTAGCTAACTCATATTCTTCATGCAAATCCGAACACAAA
AACCAAGCATTGT
Found at i:18831463 original size:23 final size:23
Alignment explanation
Indices: 18831420--18831464 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
18831410 TGCTTTTGTA
*
18831420 CCCTAAAACCCGAAGCTATTAAT
1 CCCTAAAACCCGAAACTATTAAT
*
18831443 CCCTATAACCCGTAAAC-ATTAA
1 CCCTAAAACCCG-AAACTATTAA
18831465 AATTAAAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.22
Consensus pattern (23 bp):
CCCTAAAACCCGAAACTATTAAT
Found at i:18835506 original size:39 final size:39
Alignment explanation
Indices: 18835463--18835545 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 39
18835453 TTAAATCGTA
* *
18835463 AAAATCGTAAAAGTTAATCGCTATCAAATTCTACTAACT
1 AAAATCGTAAAAATTAATCACTATCAAATTCTACTAACT
* **
18835502 AAAATCGTAAAAATTAATCATTATTGAATTCTACTAACT
1 AAAATCGTAAAAATTAATCACTATCAAATTCTACTAACT
18835541 AAAAT
1 AAAAT
18835546 GCTTATTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (39 bp):
AAAATCGTAAAAATTAATCACTATCAAATTCTACTAACT
Found at i:18843721 original size:19 final size:19
Alignment explanation
Indices: 18843694--18843730 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18843684 AGATTGTATT
*
18843694 TTATTTTTATCTTATTTTA
1 TTATCTTTATCTTATTTTA
*
18843713 TTATCTTTATTTTATTTT
1 TTATCTTTATCTTATTTT
18843731 GAAATTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (19 bp):
TTATCTTTATCTTATTTTA
Found at i:18850051 original size:75 final size:78
Alignment explanation
Indices: 18849850--18850048 Score: 262
Period size: 75 Copynumber: 2.6 Consensus size: 78
18849840 AATTAAAGGT
* * * *
18849850 AAATAAAATCTATTTCGGGATTGATTCCCGACGTTTAACGATTTTATTCTAAATTTTGTTTTATT
1 AAATAAAATCTGTTTCGAGATTGATTCCCGCCGTTCAACGATTTTATTCTAAA-TTTGTTTTATT
18849915 TCCAAAAACGAGTA
65 TCCAAAAACGAGTA
* * *
18849929 AAATAAAATCCGTTTC-AGGTTTGATTCCCGCCGTTCAACGATTTTATTC-CAA-TT-TTTTATT
1 AAATAAAATCTGTTTCGA-GATTGATTCCCGCCGTTCAACGATTTTATTCTAAATTTGTTTTATT
18849990 TCCAAAAACGAGTA
65 TCCAAAAACGAGTA
* *
18850004 AAATAAAATATGTTTCGAGATTCATTCCCGCCGTTCAACGGATTT
1 AAATAAAATCTGTTTCGAGATTGATTCCCGCCGTTCAAC-GATTT
18850049 ATTACATTTT
Statistics
Matches: 106, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
75 54 0.51
76 8 0.08
78 2 0.02
79 42 0.40
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.38
Consensus pattern (78 bp):
AAATAAAATCTGTTTCGAGATTGATTCCCGCCGTTCAACGATTTTATTCTAAATTTGTTTTATTT
CCAAAAACGAGTA
Found at i:18850168 original size:87 final size:87
Alignment explanation
Indices: 18850004--18850408 Score: 339
Period size: 87 Copynumber: 4.7 Consensus size: 87
18849994 AAAACGAGTA
* * * * ** ** *
18850004 AAATAAAATATGTTTCGAGATTCATTCCCGCCGTTCAA-CGGA-TTTATTACATTTTAATTTTGT
1 AAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTTAATAAGATTTTATTTGA-TTTGATTTTGT
*
18850067 TGCCAAAAATGAGAAATTAAATT
65 TGCCACAAATGAGAAATTAAATT
* * * ** * *
18850090 AAATAAAATCTATTTTGGGATTTATTCCCAACGTTTAATAAAAATTTATTTGATTTGATTTTGTT
1 AAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTTAATAAGATTTTATTTGATTTGATTTTGTT
*
18850155 GCCACAAACGAGAAATTAAATT
66 GCCACAAATGAGAAATTAAATT
* * * *
18850177 AAATAAAATTTGTTTCGAGATTTATTCTCGCCATTTAATAAGATTTTATTTGATTTTATTTTGTT
1 AAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTTAATAAGATTTTATTTGATTTGATTTTGTT
* * ** *
18850242 -TC-CTAATTTG-AATTGAATT
66 GCCACAAATGAGAAATTAAATT
*
18850261 AAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTTAACAAGATTTTATTTGATGTTG-TTTTGT
1 AAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTTAATAAGATTTTATTTGAT-TTGATTTTGT
* * ** *
18850325 TTCCA-AACA-AAG-ACGT-AATC
65 TGCCACAA-ATGAGAAATTAAATT
* * * * * *
18850345 AAAT--AATTCTGTTTCAGAATTTATTCCTGCCATTTAACAAGATTTTATTTGATTTTATTTTGT
1 AAATAAAATT-TGTTTCGGGATTTATTCCCGCCGTTTAATAAGATTTTATTTGATTTGATTTTGT
18850408 T
65 T
18850409 TCCTAATTTG
Statistics
Matches: 261, Mismatches: 50, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
82 6 0.02
83 47 0.18
84 72 0.28
85 11 0.04
86 32 0.12
87 86 0.33
88 7 0.03
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (87 bp):
AAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTTAATAAGATTTTATTTGATTTGATTTTGTT
GCCACAAATGAGAAATTAAATT
Found at i:18850298 original size:84 final size:84
Alignment explanation
Indices: 18850004--18850441 Score: 364
Period size: 84 Copynumber: 5.2 Consensus size: 84
18849994 AAAACGAGTA
* * * * * * **
18850004 AAATAAAATATGTTTCGAGATTCATTCCCGCCGTTCAAC-GGA-TTTATTACATTTTAATTTTGT
1 AAATAAAATTTGTTTCGGGATTTATTCCCGCCATTTAACAAGATTTTATTTGATTTT-ATTTTGT
* *
18850067 TGCCAAAAATGAGAAATTAAATT
65 TTCC--AAATTAG-AATTAAATT
* * * ** * * * * *
18850090 AAATAAAATCTATTTTGGGATTTATTCCCAACGTTTAATAAAAATTTATTTGATTTGATTTTGTT
1 AAATAAAATTTGTTTCGGGATTTATTCCCGCCATTTAACAAGATTTTATTTGATTTTATTTTGTT
* **
18850155 GCCACAAACGAGAAATTAAATT
66 -TC-CAAATTAG-AATTAAATT
* * *
18850177 AAATAAAATTTGTTTCGAGATTTATTCTCGCCATTTAATAAGATTTTATTTGATTTTATTTTGTT
1 AAATAAAATTTGTTTCGGGATTTATTCCCGCCATTTAACAAGATTTTATTTGATTTTATTTTGTT
* * *
18850242 TCCTAATTTGAATTGAATT
66 TCCAAATTAGAATTAAATT
* * *
18850261 AAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTTAACAAGATTTTATTTGATGTTGTTTTGTT
1 AAATAAAATTTGTTTCGGGATTTATTCCCGCCATTTAACAAGATTTTATTTGATTTTATTTTGTT
** ** *
18850326 TCCAAACAAAGACGT-AATC
66 TCCAAA-TTAGAATTAAATT
* * *
18850345 AAAT--AATTCTGTTTCAGAATTTATTCCTGCCATTTAACAAGATTTTATTTGATTTTATTTTGT
1 AAATAAAATT-TGTTTCGGGATTTATTCCCGCCATTTAACAAGATTTTATTTGATTTTATTTTGT
* * *
18850408 TTCCTAATTTGAATTGAATT
65 TTCCAAATTAGAATTAAATT
18850428 AAATAAAATCTTGT
1 AAATAAAAT-TTGT
18850442 AACAACCCAA
Statistics
Matches: 283, Mismatches: 59, Indels: 21
0.78 0.16 0.06
Matches are distributed among these distances:
82 7 0.02
83 61 0.22
84 79 0.28
85 13 0.05
86 32 0.11
87 79 0.28
88 11 0.04
89 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (84 bp):
AAATAAAATTTGTTTCGGGATTTATTCCCGCCATTTAACAAGATTTTATTTGATTTTATTTTGTT
TCCAAATTAGAATTAAATT
Found at i:18850415 original size:167 final size:170
Alignment explanation
Indices: 18850081--18850441 Score: 470
Period size: 167 Copynumber: 2.1 Consensus size: 170
18850071 AAAAATGAGA
* * * * *
18850081 AATTAAATTAAATAAAATCTATTTTGGGATTTATTCCCAACGTTTAATAAAAATTTATTTGATTT
1 AATTGAATTAAATAAAATTTGTTTCGGGATTTATTCCCAACGTTTAACAAAAATTTATTTGATTT
* *
18850146 GATTTTGTTGCCACAAACGAGAAATTAAATTAAATAAAATTTGTTTCGAGATTTATTCTCGCCAT
66 GATTTTGTTGCCACAAACGAGAAAGTAAATCAAAT-AAATTTGTTTCGAGATTTATTCTCGCCAT
*
18850211 TTAATAAGATTTTATTTGATTTTATTTTGTTTCCTAATTTG
130 TTAACAAGATTTTATTTGATTTTATTTTGTTTCCTAATTTG
** * *
18850252 AATTGAATTAAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTTAACAAGATTTTATTTGATGT
1 AATTGAATTAAATAAAATTTGTTTCGGGATTTATTCCCAACGTTTAACAAAAATTTATTTGAT-T
*
18850317 TG-TTTTGTT-TC-CAAAC-A-AAGACGT-AATCAAAT-AATTCTGTTTC-AGAATTTATTC-CT
65 TGATTTTGTTGCCACAAACGAGAA-A-GTAAATCAAATAAATT-TGTTTCGAG-ATTTATTCTC-
18850373 GCCATTTAACAAGATTTTATTTGATTTTATTTTGTTTCCTAATTTG
125 GCCATTTAACAAGATTTTATTTGATTTTATTTTGTTTCCTAATTTG
18850419 AATTGAATTAAATAAAATCTTGT
1 AATTGAATTAAATAAAAT-TTGT
18850442 AACAACCCAA
Statistics
Matches: 170, Mismatches: 13, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
166 7 0.04
167 79 0.46
168 13 0.08
169 6 0.04
170 1 0.01
171 61 0.36
172 3 0.02
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (170 bp):
AATTGAATTAAATAAAATTTGTTTCGGGATTTATTCCCAACGTTTAACAAAAATTTATTTGATTT
GATTTTGTTGCCACAAACGAGAAAGTAAATCAAATAAATTTGTTTCGAGATTTATTCTCGCCATT
TAACAAGATTTTATTTGATTTTATTTTGTTTCCTAATTTG
Found at i:18856460 original size:42 final size:41
Alignment explanation
Indices: 18856401--18856529 Score: 150
Period size: 42 Copynumber: 3.0 Consensus size: 41
18856391 TAATTTTTTG
*
18856401 TTTAACCCTTATGGGTTTCCGTTCAGCTCTTTTGAGCTTCAT
1 TTTAACCCTTAT-GGTTTCCGTTCAGCTCTTATGAGCTTCAT
* * * *
18856443 TTTAACCCTTATAGGTTTTCGTTCAACTCTTACGAGCTTCAG
1 TTTAACCCTTAT-GGTTTCCGTTCAGCTCTTATGAGCTTCAT
* * *
18856485 TTCAACCCTTATGGATTTCCGTTTAGCTCTCATGAGCTTCTAT
1 TTTAACCCTTATGG-TTTCCGTTCAGCTCTTATGAGCTTC-AT
18856528 TT
1 TT
18856530 AGCCTTCAGG
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
41 2 0.03
42 67 0.93
43 3 0.04
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.43
Consensus pattern (41 bp):
TTTAACCCTTATGGTTTCCGTTCAGCTCTTATGAGCTTCAT
Found at i:18856676 original size:8 final size:8
Alignment explanation
Indices: 18856663--18856690 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
18856653 TGAAATGTAT
18856663 ATATATTA
1 ATATATTA
18856671 ATATATTA
1 ATATATTA
18856679 ATATATTA
1 ATATATTA
18856687 ATAT
1 ATAT
18856691 GTGATACATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATATATTA
Found at i:18863173 original size:3 final size:3
Alignment explanation
Indices: 18863160--18863348 Score: 369
Period size: 3 Copynumber: 63.0 Consensus size: 3
18863150 AATTTTCACA
*
18863160 TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18863208 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18863256 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18863304 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18863349 ACTCCTCAAT
Statistics
Matches: 184, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
3 184 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:18866761 original size:33 final size:33
Alignment explanation
Indices: 18866719--18866785 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
18866709 TCTACTAGGC
*
18866719 ATTCGTACGCCATGGTGCAATCAGGGAGGAGAT
1 ATTCGTACGCCATGGTGCAATCAAGGAGGAGAT
* *
18866752 ATTCGTACGCCATGGTGCGATTAAGGAGGAGAT
1 ATTCGTACGCCATGGTGCAATCAAGGAGGAGAT
18866785 A
1 A
18866786 ACAAATTAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.16, G:0.33, T:0.22
Consensus pattern (33 bp):
ATTCGTACGCCATGGTGCAATCAAGGAGGAGAT
Found at i:18868770 original size:21 final size:20
Alignment explanation
Indices: 18868744--18868798 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
18868734 ATTTATATTT
18868744 TATAAAAAAATTCTAAAAATA
1 TATAAAAAAATTCTAAAAA-A
* *
18868765 TATAAAGAAAGT-TAAAAAA
1 TATAAAAAAATTCTAAAAAA
*
18868784 TAAAAAAAAATTCTA
1 TATAAAAAAATTCTA
18868799 GAATAATAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 10 0.36
20 8 0.29
21 10 0.36
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (20 bp):
TATAAAAAAATTCTAAAAAA
Found at i:18869421 original size:3 final size:3
Alignment explanation
Indices: 18869413--18869446 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
18869403 TGCATTTGAC
18869413 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
18869447 GTTTTTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:18873728 original size:3 final size:3
Alignment explanation
Indices: 18873720--18873753 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
18873710 TGCATTTGAC
18873720 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
18873754 GTTTTTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:18878837 original size:17 final size:17
Alignment explanation
Indices: 18878811--18878846 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
18878801 GAGCATTACT
* *
18878811 AGGGATGTAGATAGAGA
1 AGGGAAGTAGAGAGAGA
18878828 AGGGAAGTAGAGAGAGA
1 AGGGAAGTAGAGAGAGA
18878845 AG
1 AG
18878847 ATAAAAAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.11
Consensus pattern (17 bp):
AGGGAAGTAGAGAGAGA
Found at i:18879317 original size:5 final size:5
Alignment explanation
Indices: 18879309--18879334 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
18879299 ACAAAAGATA
18879309 AAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG A
18879335 CCAAGATTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:18893785 original size:15 final size:15
Alignment explanation
Indices: 18893765--18893797 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
18893755 AATTATCAGT
18893765 ATTAACTAATTATAA
1 ATTAACTAATTATAA
18893780 ATTAACTAATTATAA
1 ATTAACTAATTATAA
18893795 ATT
1 ATT
18893798 TCATATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTAACTAATTATAA
Found at i:18894235 original size:20 final size:21
Alignment explanation
Indices: 18894198--18894245 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
18894188 TACACATTTG
* *
18894198 AAATTTTTATATATTTTTTAA
1 AAATTTTAATATACTTTTTAA
*
18894219 AAATTTTAATA-ACTTTTTAT
1 AAATTTTAATATACTTTTTAA
18894239 AAATTTT
1 AAATTTT
18894246 GAAGTTCCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
AAATTTTAATATACTTTTTAA
Found at i:18894361 original size:23 final size:24
Alignment explanation
Indices: 18894322--18894372 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
18894312 TATATGCACA
18894322 TTTTAATTATTT-AAAAAAATATT
1 TTTTAATTATTTAAAAAAAATATT
*
18894345 TTTTTATT-TTTATAAAAAAATATT
1 TTTTAATTATTTA-AAAAAAATATT
18894369 TTTT
1 TTTT
18894373 GAAAAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 3 0.12
23 7 0.28
24 15 0.60
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTTAATTATTTAAAAAAAATATT
Found at i:18894368 original size:16 final size:16
Alignment explanation
Indices: 18894349--18894381 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18894339 AATATTTTTT
18894349 TATTTTTAT-AAAAAAA
1 TATTTTT-TGAAAAAAA
18894365 TATTTTTTGAAAAAAA
1 TATTTTTTGAAAAAAA
18894381 T
1 T
18894382 TGAAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 15 0.94
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TATTTTTTGAAAAAAA
Found at i:18906557 original size:26 final size:26
Alignment explanation
Indices: 18906502--18906603 Score: 118
Period size: 26 Copynumber: 3.9 Consensus size: 26
18906492 TCTCATCCAA
* *
18906502 ATTTCACCCTTAATAAAATTTTGACA-
1 ATTTTACCCTTAGTAAAATTTTGA-AG
18906528 ATTTTACCCTTAGTAAAATTTTGAAG
1 ATTTTACCCTTAGTAAAATTTTGAAG
*
18906554 ATTTTA-CCTATGGTAAAATTTTGAAG
1 ATTTTACCCT-TAGTAAAATTTTGAAG
* * *
18906580 ATTTTACCCATGGTAAATTTTTGA
1 ATTTTACCCTTAGTAAAATTTTGA
18906604 GAAAATTTGT
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
25 4 0.06
26 62 0.91
27 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (26 bp):
ATTTTACCCTTAGTAAAATTTTGAAG
Found at i:18906788 original size:42 final size:42
Alignment explanation
Indices: 18906697--18906788 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
18906687 CAAAAAGCTA
18906697 GCTTGAGCCTATAAGGACTGACTAGAGGGTCATCAAGAACTT
1 GCTTGAGCCTATAAGGACTGACTAGAGGGTCATCAAGAACTT
* * * *
18906739 GCCTGAGCCTATGGAGG-CTGACTAGAGGGTCA-CTAGGGACTT
1 GCTTGAGCCTAT-AAGGACTGACTAGAGGGTCATC-AAGAACTT
18906781 GCTTGAGC
1 GCTTGAGC
18906789 ACATTGGGAC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
41 1 0.02
42 39 0.91
43 3 0.07
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.23
Consensus pattern (42 bp):
GCTTGAGCCTATAAGGACTGACTAGAGGGTCATCAAGAACTT
Found at i:18912932 original size:17 final size:17
Alignment explanation
Indices: 18912912--18912970 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
18912902 TCAATATGAT
18912912 TAAATAATTCAATAATA
1 TAAATAATTCAATAATA
* *
18912929 TAAATAGTACAAT-ATA
1 TAAATAATTCAATAATA
*
18912945 TGAAATTTAATTTAATAATA
1 T-AAA--TAATTCAATAATA
18912965 TAAATA
1 TAAATA
18912971 GTAGATATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 4 0.12
17 16 0.48
19 9 0.27
20 4 0.12
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.37
Consensus pattern (17 bp):
TAAATAATTCAATAATA
Found at i:18913321 original size:9 final size:9
Alignment explanation
Indices: 18913307--18913354 Score: 69
Period size: 9 Copynumber: 5.3 Consensus size: 9
18913297 ATTCAAGTTG
18913307 ACTCGAATA
1 ACTCGAATA
*
18913316 ACTCGATTA
1 ACTCGAATA
18913325 ACTCGAATA
1 ACTCGAATA
**
18913334 ACTCGTTTA
1 ACTCGAATA
18913343 ACTCGAATA
1 ACTCGAATA
18913352 ACT
1 ACT
18913355 TGATTCGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (9 bp):
ACTCGAATA
Found at i:18913330 original size:18 final size:18
Alignment explanation
Indices: 18913307--18913359 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
18913297 ATTCAAGTTG
18913307 ACTCGAATAACTCGATTA
1 ACTCGAATAACTCGATTA
*
18913325 ACTCGAATAACTCGTTTA
1 ACTCGAATAACTCGATTA
*
18913343 ACTCGAATAACTTGATT
1 ACTCGAATAACTCGATT
18913360 CGTTTAACTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (18 bp):
ACTCGAATAACTCGATTA
Found at i:18914599 original size:38 final size:39
Alignment explanation
Indices: 18914555--18914634 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 39
18914545 TTTTTGAGGC
* *
18914555 AGATAAGTTTA-TATCTAAGGGAGGAATTTTTGTAGGGA
1 AGATAAGTTTATTATATAAGGGAGGAATTTTGGTAGGGA
*
18914593 AGATAAGTTTATTTTGTATAAGGGAGGAATTTTGGTAGGGA
1 AGATAAGTTTA--TTATATAAGGGAGGAATTTTGGTAGGGA
18914634 A
1 A
18914635 AGGGTATATG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
38 11 0.31
41 25 0.69
ACGTcount: A:0.34, C:0.01, G:0.30, T:0.35
Consensus pattern (39 bp):
AGATAAGTTTATTATATAAGGGAGGAATTTTGGTAGGGA
Found at i:18916253 original size:16 final size:15
Alignment explanation
Indices: 18916227--18916256 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
18916217 CCTTTGTTTG
18916227 CTTTTTTTTCTTTTT
1 CTTTTTTTTCTTTTT
18916242 CTTTTTTCTTCTTTT
1 CTTTTTT-TTCTTTT
18916257 GGGAAGCAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
CTTTTTTTTCTTTTT
Found at i:18920722 original size:26 final size:26
Alignment explanation
Indices: 18920687--18920767 Score: 108
Period size: 26 Copynumber: 3.1 Consensus size: 26
18920677 TATTTTCTTG
*
18920687 AAAATTTACCAGGGGCAAAATCATCA
1 AAAATTTACCAGGGGCAAAATCGTCA
* *
18920713 AAAATTTACCAGGGGCAATATTGTCA
1 AAAATTTACCAGGGGCAAAATCGTCA
* * *
18920739 AAATTTTACCAGAGGTAAAATCGTCA
1 AAAATTTACCAGGGGCAAAATCGTCA
18920765 AAA
1 AAA
18920768 TATTGCTAGG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.23
Consensus pattern (26 bp):
AAAATTTACCAGGGGCAAAATCGTCA
Found at i:18932174 original size:45 final size:44
Alignment explanation
Indices: 18932125--18932316 Score: 185
Period size: 45 Copynumber: 4.2 Consensus size: 44
18932115 TTAGCTACGA
*
18932125 TCTTATCGATTTCTGACAT-GATGCTATAGTGTCTTTCAACTATGG
1 TCTTATC-ATTTCTGACATAG-TGCCATAGTGTCTTTCAACTATGG
* * *
18932170 TCTTATTTATTTCAT-TCAT-GTTGCCATAGTTTCTTTCAACTATGG
1 TCTTA-TCATTTC-TGACATAG-TGCCATAGTGTCTTTCAACTATGG
* * *
18932215 TCTTATTCATTTC-CAGTATAGTGCCATAGAGTCTTTCAACTATGG
1 TCTTA-TCATTTCTGA-CATAGTGCCATAGTGTCTTTCAACTATGG
** *
18932260 TCTTATTCATTTCTGTTATAGTGCCATAGTGTCTTTCACCTATGG
1 TCTTA-TCATTTCTGACATAGTGCCATAGTGTCTTTCAACTATGG
18932305 TCTTATTCATTT
1 TCTTA-TCATTT
18932317 TTCAAGCCAA
Statistics
Matches: 127, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
45 124 0.98
46 3 0.02
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.46
Consensus pattern (44 bp):
TCTTATCATTTCTGACATAGTGCCATAGTGTCTTTCAACTATGG
Found at i:18932182 original size:21 final size:21
Alignment explanation
Indices: 18932158--18932227 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
18932148 CTATAGTGTC
18932158 TTTCAACTATGGTCTTATTTA
1 TTTCAACTATGGTCTTATTTA
* * * *
18932179 TTTC-ATTCATGTTGCCATAGTTTC
1 TTTCAACT-ATG--GTCTTA-TTTA
*
18932203 TTTCAACTATGGTCTTATTCA
1 TTTCAACTATGGTCTTATTTA
18932224 TTTC
1 TTTC
18932228 CAGTATAGTG
Statistics
Matches: 35, Mismatches: 9, Indels: 10
0.65 0.17 0.19
Matches are distributed among these distances:
20 2 0.06
21 13 0.37
22 4 0.11
23 4 0.11
24 10 0.29
25 2 0.06
ACGTcount: A:0.20, C:0.19, G:0.10, T:0.51
Consensus pattern (21 bp):
TTTCAACTATGGTCTTATTTA
Found at i:18932254 original size:90 final size:90
Alignment explanation
Indices: 18932150--18932316 Score: 257
Period size: 90 Copynumber: 1.9 Consensus size: 90
18932140 ACATGATGCT
* * *
18932150 ATAGTGTCTTTCAACTATGGTCTTATTTATTTCAT-TCAT-GTTGCCATAGTTTCTTTCAACTAT
1 ATAGAGTCTTTCAACTATGGTCTTATTCATTTC-TGTCATAG-TGCCATAGTGTCTTTCAACTAT
18932213 GGTCTTATTCATTTCCAGTATAGTGCC
64 GGTCTTATTCATTTCCAGTATAGTGCC
* *
18932240 ATAGAGTCTTTCAACTATGGTCTTATTCATTTCTGTTATAGTGCCATAGTGTCTTTCACCTATGG
1 ATAGAGTCTTTCAACTATGGTCTTATTCATTTCTGTCATAGTGCCATAGTGTCTTTCAACTATGG
18932305 TCTTATTCATTT
66 TCTTATTCATTT
18932317 TTCAAGCCAA
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
89 1 0.01
90 68 0.97
91 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.47
Consensus pattern (90 bp):
ATAGAGTCTTTCAACTATGGTCTTATTCATTTCTGTCATAGTGCCATAGTGTCTTTCAACTATGG
TCTTATTCATTTCCAGTATAGTGCC
Found at i:18932272 original size:21 final size:21
Alignment explanation
Indices: 18932203--18932272 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
18932193 CCATAGTTTC
18932203 TTTCAACTATGGTCTTATTCA
1 TTTCAACTATGGTCTTATTCA
* * * * *
18932224 TTTCCAGTATAGTGCCATAGAGTC-
1 TTTCAACTAT-G-GTC-T-TATTCA
18932248 TTTCAACTATGGTCTTATTCA
1 TTTCAACTATGGTCTTATTCA
18932269 TTTC
1 TTTC
18932273 TGTTATAGTG
Statistics
Matches: 34, Mismatches: 10, Indels: 10
0.63 0.19 0.19
Matches are distributed among these distances:
20 3 0.09
21 13 0.38
22 3 0.09
23 3 0.09
24 9 0.26
25 3 0.09
ACGTcount: A:0.23, C:0.20, G:0.13, T:0.44
Consensus pattern (21 bp):
TTTCAACTATGGTCTTATTCA
Found at i:18935144 original size:26 final size:25
Alignment explanation
Indices: 18935114--18935215 Score: 114
Period size: 26 Copynumber: 3.9 Consensus size: 25
18935104 ACAAATTTTC
* *
18935114 TCAAAATTTTACCAGGGGAGAAATCA
1 TCAAAATTTTACAAGGGGA-AAATCG
* *
18935140 TCAAAATTTTACTAGGGGCAAAATTG
1 TCAAAATTTTACAAGGGG-AAAATCG
*
18935166 TCAAAATTTTACTAAGGGCAAAATCG
1 TCAAAATTTTAC-AAGGGGAAAATCG
*
18935192 TCAAAATTTTATAAGGGGTAAAAT
1 TCAAAATTTTACAAGGGG-AAAAT
18935216 AGGGATGATA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
25 5 0.08
26 55 0.85
27 5 0.08
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (25 bp):
TCAAAATTTTACAAGGGGAAAATCG
Found at i:18935190 original size:52 final size:52
Alignment explanation
Indices: 18935114--18935215 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 52
18935104 ACAAATTTTC
* *
18935114 TCAAAATTTTACCAGGGGAGAAATCATCAAAATTTTACT-AGGGGCAAAATTG
1 TCAAAATTTTACAAGGGCAGAAATCATCAAAATTTTA-TAAGGGGCAAAATTG
* *
18935166 TCAAAATTTTACTAAGGGCA-AAATCGTCAAAATTTTATAAGGGGTAAAAT
1 TCAAAATTTTAC-AAGGGCAGAAATCATCAAAATTTTATAAGGGGCAAAAT
18935216 AGGGATGATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
51 1 0.02
52 38 0.86
53 5 0.11
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (52 bp):
TCAAAATTTTACAAGGGCAGAAATCATCAAAATTTTATAAGGGGCAAAATTG
Found at i:18937073 original size:32 final size:32
Alignment explanation
Indices: 18937002--18937073 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
18936992 ATTGACAAAG
* * *
18937002 AATTATGATTATTCAAAAAATATTATTTGAAT
1 AATTATGTTTAATCAAAAAATATTAGTTGAAT
* * *
18937034 AGTTATGTTTAATCAAGAGATATTAGTTGAAT
1 AATTATGTTTAATCAAAAAATATTAGTTGAAT
18937066 AATTATGT
1 AATTATGT
18937074 ATCTTTTAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.43
Consensus pattern (32 bp):
AATTATGTTTAATCAAAAAATATTAGTTGAAT
Found at i:18938261 original size:13 final size:12
Alignment explanation
Indices: 18938232--18938273 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
18938222 GGTAATTAGC
18938232 ATTTTAA-GGATT
1 ATTTTAATGGA-T
18938244 ATTTTAATGAGAT
1 ATTTTAATG-GAT
18938257 ATTTTAATGGA-
1 ATTTTAATGGAT
18938268 ATTTTA
1 ATTTTA
18938274 TAGAAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.21
12 9 0.32
13 11 0.39
14 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (12 bp):
ATTTTAATGGAT
Found at i:18961987 original size:30 final size:28
Alignment explanation
Indices: 18961948--18962004 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 28
18961938 ATGGATTTAA
18961948 ATTACTTATTATTTAAGTAAATAGATATTT
1 ATTACTTATTA-TTAAGTAAA-AGATATTT
*
18961978 ATTATTTATTATTAAGTAAAAGATATT
1 ATTACTTATTATTAAGTAAAAGATATT
18962005 ATAAGATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 7 0.27
29 9 0.35
30 10 0.38
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (28 bp):
ATTACTTATTATTAAGTAAAAGATATTT
Found at i:18962017 original size:28 final size:29
Alignment explanation
Indices: 18961953--18962017 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
18961943 TTTAAATTAC
**
18961953 TTATTATTTAAGTAAATAGATATTTATTAT
1 TTATTA-TTAAGTAAATAGATATTTAAGAT
18961983 TTATTATTAAGTAAA-AGATATTATAAGAT
1 TTATTATTAAGTAAATAGATATT-TAAGAT
18962012 TT-TTAT
1 TTATTAT
18962018 GTGATAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 11 0.34
29 15 0.47
30 6 0.19
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (29 bp):
TTATTATTAAGTAAATAGATATTTAAGAT
Done.