Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008736.1 Hibiscus syriacus cultivar Beakdansim tig00111810_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: 2478687
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 13
Found at i:358404 original size:46 final size:46
Alignment explanation
Indices: 358306--358404 Score: 128
Period size: 46 Copynumber: 2.2 Consensus size: 46
358296 TGAAGTGTCA
*
358306 CGTAGAAATGTCCCGAAGGACCACATAGATATGTCCCGAAGGACCG
1 CGTAGAAATGTCACGAAGGACCACATAGATATGTCCCGAAGGACCG
* * ***
358352 CATAGAAATGTCACGAAGGACCACGTAGA-ATTGTCCTTTAGGACCG
1 CGTAGAAATGTCACGAAGGACCACATAGATA-TGTCCCGAAGGACCG
358398 CGTAGAA
1 CGTAGAA
358405 CCCTCGACTC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 1 0.02
46 44 0.98
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.18
Consensus pattern (46 bp):
CGTAGAAATGTCACGAAGGACCACATAGATATGTCCCGAAGGACCG
Found at i:359026 original size:20 final size:20
Alignment explanation
Indices: 358998--359047 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
358988 CCTAAAAATG
358998 GTATCGATACTTGTACATTA
1 GTATCGATACTTGTACATTA
*
359018 GTATTGATACTTGTACATTA
1 GTATCGATACTTGTACATTA
359038 GTATCGATAC
1 GTATCGATAC
359048 CCTTGGTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (20 bp):
GTATCGATACTTGTACATTA
Found at i:361060 original size:43 final size:43
Alignment explanation
Indices: 361007--361388 Score: 556
Period size: 43 Copynumber: 8.9 Consensus size: 43
360997 ACGCTGCCAT
* *
361007 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGTAAA
1 AGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
*
361050 AGGACGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
1 AGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* *
361093 AGGTCGAGATCTATAGCGGCATTTTTAGAACAAACGCCGCAAA
1 AGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* * *
361136 ACGTC-AGATCTATAGCGGCGTTTGTTGGAACCAATGCCGCAAA
1 AGGTCGAGATCTATAGCGGCGTTT-TTGGAACAAACGCCGCAAA
* *
361179 AGGT-TAGATCTATAGCGGCGTTTTTTGAACAAACGCCGCAAA
1 AGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
*
361221 AGGTCGAGACCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
1 AGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
*
361264 AGGTC-AGATCTATAGCGGCGTTTATTGGAACAAACGCCGTAAA
1 AGGTCGAGATCTATAGCGGCGTTT-TTGGAACAAACGCCGCAAA
* * *
361307 AGGT-TAGATCTATAGCGGCGTTTTTTGAACAAACGCCACAAA
1 AGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
** *
361349 ATTTCGAGATCTATAGCAGCGTTTTTGGAACAAACGCCGC
1 AGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGC
361389 TAATTACATT
Statistics
Matches: 304, Mismatches: 29, Indels: 12
0.88 0.08 0.03
Matches are distributed among these distances:
42 72 0.24
43 232 0.76
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (43 bp):
AGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
Found at i:361215 original size:171 final size:170
Alignment explanation
Indices: 361013--361388 Score: 567
Period size: 171 Copynumber: 2.2 Consensus size: 170
361003 CCATAGGTCA
* *
361013 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGTAAAAGGACGAGATCTATAGCGGCGTTTTTGG
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGACGAGACCTATAGCGGCGTTTTTGG
361078 AACAAACGCCGCAAAAGGTCGAGATCTATAGCGGCATTT-TTAGAACAAACGCCGCAAAACGTCA
66 AACAAACGCCGCAAAAGGTC-AGATCTATAGCGGCATTTATTAGAACAAACGCCGCAAAACGTCA
* * *
361142 GATCTATAGCGGCGTTTGTTGGAACCAATGCCGCAAAAGGTT-
130 GATCTATAGCGGCGTTT-TTGGAACAAACGCCACAAAA-GTTC
* *
361184 AGATCTATAGCGGCGTTTTTTGAACAAACGCCGCAAAAGGTCGAGACCTATAGCGGCGTTTTTGG
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGACGAGACCTATAGCGGCGTTTTTGG
* * * * *
361249 AACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTATTGGAACAAACGCCGTAAAAGGTTAG
66 AACAAACGCCGCAAAAGGTCAGATCTATAGCGGCATTTATTAGAACAAACGCCGCAAAACGTCAG
* *
361314 ATCTATAGCGGCGTTTTTTGAACAAACGCCACAAAATTTC
131 ATCTATAGCGGCGTTTTTGGAACAAACGCCACAAAAGTTC
*
361354 GAGATCTATAGCAGCGTTTTTGGAACAAACGCCGC
1 -AGATCTATAGCGGCGTTTTTGGAACAAACGCCGC
361389 TAATTACATT
Statistics
Matches: 186, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
169 2 0.01
170 33 0.18
171 151 0.81
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (170 bp):
AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGACGAGACCTATAGCGGCGTTTTTGG
AACAAACGCCGCAAAAGGTCAGATCTATAGCGGCATTTATTAGAACAAACGCCGCAAAACGTCAG
ATCTATAGCGGCGTTTTTGGAACAAACGCCACAAAAGTTC
Found at i:361224 original size:128 final size:127
Alignment explanation
Indices: 361013--361388 Score: 599
Period size: 128 Copynumber: 2.9 Consensus size: 127
361003 CCATAGGTCA
** *
361013 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGTAAAAGGACGAGATCTATAGCGGCGTTTTTGG
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGTAAAAGG-TTAGATCTATAGCGGCGTTTTTTG
* *
361078 AACAAACGCCGCAAAAGGTCGAGATCTATAGCGGCATTTTTAGAACAAACGCCGCAAAACGTC
65 AACAAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAACGTC
* * *
361141 AGATCTATAGCGGCGTTTGTTGGAACCAATGCCGCAAAAGGTTAGATCTATAGCGGCGTTTTTTG
1 AGATCTATAGCGGCGTTT-TTGGAACAAACGCCGTAAAAGGTTAGATCTATAGCGGCGTTTTTTG
* *
361206 AACAAACGCCGCAAAAGGTCGAGACCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
65 AACAAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAACGTC
361269 AGATCTATAGCGGCGTTTATTGGAACAAACGCCGTAAAAGGTTAGATCTATAGCGGCGTTTTTTG
1 AGATCTATAGCGGCGTTT-TTGGAACAAACGCCGTAAAAGGTTAGATCTATAGCGGCGTTTTTTG
* ** *
361334 AACAAACGCCACAAAATTTCGAGATCTATAGCAGCGTTTTTGGAACAAACGCCGC
65 AACAAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGC
361389 TAATTACATT
Statistics
Matches: 228, Mismatches: 19, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
128 209 0.92
129 19 0.08
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (127 bp):
AGATCTATAGCGGCGTTTTTGGAACAAACGCCGTAAAAGGTTAGATCTATAGCGGCGTTTTTTGA
ACAAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAACGTC
Found at i:365044 original size:42 final size:42
Alignment explanation
Indices: 364995--365196 Score: 214
Period size: 41 Copynumber: 4.9 Consensus size: 42
364985 TTGTAAATAC
*
364995 AAACGCCACTAAAGTACGAGTCAT-TAGCGGCGTTTGTATTCA
1 AAACGCCACTAAAGTACGAGT-ATATAGCGGCGTTTGCATTCA
* * **
365037 AAACGCCACTAAAGTACGAGTCTTTAGCGATGTTTGCATTC-
1 AAACGCCACTAAAGTACGAGTATATAGCGGCGTTTGCATTCA
* *
365078 AAACGCCACTAAAGTACGAGTTTATAGCGGTGTTTGCATTCA
1 AAACGCCACTAAAGTACGAGTATATAGCGGCGTTTGCATTCA
* * * *
365120 AAATGCCACTAAAGTATGAGTATATAGTGGCGTTTGTA-T-A
1 AAACGCCACTAAAGTACGAGTATATAGCGGCGTTTGCATTCA
*** * *
365160 GAAATATCACTAAAGTACTAGTATATAGTGGCGTTTG
1 -AAACGCCACTAAAGTACGAGTATATAGCGGCGTTTG
365197 TATAAAAATT
Statistics
Matches: 140, Mismatches: 17, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
40 1 0.01
41 72 0.51
42 67 0.48
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (42 bp):
AAACGCCACTAAAGTACGAGTATATAGCGGCGTTTGCATTCA
Found at i:365094 original size:41 final size:42
Alignment explanation
Indices: 364995--365140 Score: 215
Period size: 42 Copynumber: 3.5 Consensus size: 42
364985 TTGTAAATAC
* * *
364995 AAACGCCACTAAAGTACGAGTCATTAGCGGCGTTTGTATTCA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGTGTTTGCATTCA
*
365037 AAACGCCACTAAAGTACGAGTCTTTAGCGATGTTTGCATTC-
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGTGTTTGCATTCA
365078 AAACGCCACTAAAGTACGAGT-TTATAGCGGTGTTTGCATTCA
1 AAACGCCACTAAAGTACGAGTCTT-TAGCGGTGTTTGCATTCA
* *
365120 AAATGCCACTAAAGTATGAGT
1 AAACGCCACTAAAGTACGAGT
365141 ATATAGTGGC
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
40 2 0.02
41 37 0.39
42 56 0.59
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (42 bp):
AAACGCCACTAAAGTACGAGTCTTTAGCGGTGTTTGCATTCA
Found at i:365155 original size:83 final size:83
Alignment explanation
Indices: 364994--365155 Score: 218
Period size: 83 Copynumber: 2.0 Consensus size: 83
364984 TTTGTAAATA
* *
364994 CAAACGCCACTAAAGTACGAGTCATTAGCGGCGTTTGTATTCAAAACGCCACTAAAGTACGAGTC
1 CAAACGCCACTAAAGTACGAGTCATTAGCGGCGTTTGCATTCAAAACGCCACTAAAGTACGAGTA
* *
365059 TTTAGCGATGTTTGCATT
66 TATAGCGACGTTTGCATT
* * * *
365077 CAAACGCCACTAAAGTACGAGT-TTATAGCGGTGTTTGCATTCAAAATGCCACTAAAGTATGAGT
1 CAAACGCCACTAAAGTACGAGTCAT-TAGCGGCGTTTGCATTCAAAACGCCACTAAAGTACGAGT
* *
365141 ATATAGTGGCGTTTG
65 ATATAGCGACGTTTG
365156 TATAGAAATA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
82 1 0.01
83 67 0.99
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (83 bp):
CAAACGCCACTAAAGTACGAGTCATTAGCGGCGTTTGCATTCAAAACGCCACTAAAGTACGAGTA
TATAGCGACGTTTGCATT
Found at i:365171 original size:83 final size:83
Alignment explanation
Indices: 364991--365196 Score: 216
Period size: 83 Copynumber: 2.5 Consensus size: 83
364981 ACGTTTGTAA
* * *
364991 ATACAAACGCCACTAAAGTACGAG-TCATTAGCGGCGTTTGTATTCAAAACGCCACTAAAGTACG
1 ATACAAACACCACTAAAGTACGAGTTTA-TAGCGGCGTTTGCATTCAAAACGCCACTAAAGTACG
* * *
365055 AGTCTTTAGCGATGTTTGC
65 AGTATATAGCGACGTTTGC
* * * * *
365074 ATTCAAACGCCACTAAAGTACGAGTTTATAGCGGTGTTTGCATTCAAAATGCCACTAAAGTATGA
1 ATACAAACACCACTAAAGTACGAGTTTATAGCGGCGTTTGCATTCAAAACGCCACTAAAGTACGA
* * *
365139 GTATATAGTGGCGTTTGT
66 GTATATAGCGACGTTTGC
* * * * * *
365157 ATAGAAATATCACTAAAGTACTAGTATATAGTGGCGTTTG
1 ATACAAACACCACTAAAGTACGAGTTTATAGCGGCGTTTG
365197 TATAAAAATT
Statistics
Matches: 101, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
83 99 0.98
84 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Consensus pattern (83 bp):
ATACAAACACCACTAAAGTACGAGTTTATAGCGGCGTTTGCATTCAAAACGCCACTAAAGTACGA
GTATATAGCGACGTTTGC
Found at i:366683 original size:42 final size:40
Alignment explanation
Indices: 366652--366831 Score: 182
Period size: 41 Copynumber: 4.4 Consensus size: 40
366642 CGTTTATACA
* *
366652 AAAAAATGCCACTATTGATT-ACACTATTGTGGCGTTTGTTT
1 AAAAAATGCCACTATTGATTAACACTATTGCGGCG-TT-TTC
* * * *
366693 AAAAAACGCCACTATTGATTAAAACTATTGAGGCATTTTTC
1 AAAAAATGCCACTATTGATTAACACTATTGCGGC-GTTTTC
* *
366734 TAAAAATGCCACTATTGATTAACACTATTGCGGCATTTGTC
1 AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTT-TC
* * * * *
366775 TAAAAACGCCACTATTTATTATCACTATTGCGGCGTTTTA
1 AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTTC
366815 AGAATAAATGCCACTAT
1 A-AA-AAATGCCACTAT
366832 ATGTGTAATC
Statistics
Matches: 117, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
40 4 0.03
41 89 0.76
42 24 0.21
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (40 bp):
AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTTC
Found at i:366709 original size:41 final size:41
Alignment explanation
Indices: 366653--366808 Score: 199
Period size: 41 Copynumber: 3.8 Consensus size: 41
366643 GTTTATACAA
* * *
366653 AAAAATGCCACTATTGATT-ACACTATTGTGGCGTTTGTTT
1 AAAAACGCCACTATTGATTAACACTATTGCGGCATTTGTTT
* *
366693 AAAAAACGCCACTATTGATTAAAACTATTGAGGCATTT-TTCT
1 -AAAAACGCCACTATTGATTAACACTATTGCGGCATTTGTT-T
* *
366735 AAAAATGCCACTATTGATTAACACTATTGCGGCATTTGTCT
1 AAAAACGCCACTATTGATTAACACTATTGCGGCATTTGTTT
* *
366776 AAAAACGCCACTATTTATTATCACTATTGCGGC
1 AAAAACGCCACTATTGATTAACACTATTGCGGC
366809 GTTTTAAGAA
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
41 85 0.84
42 16 0.16
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (41 bp):
AAAAACGCCACTATTGATTAACACTATTGCGGCATTTGTTT
Found at i:366773 original size:83 final size:82
Alignment explanation
Indices: 366653--366856 Score: 234
Period size: 82 Copynumber: 2.5 Consensus size: 82
366643 GTTTATACAA
* * *
366653 AAAAATGCCACTATTGATT-ACACTATTGTGGCGTTTGTTTAAAAAACGCCACTATTGATTAAAA
1 AAAAATGCCACTATTGATTAACACTATTGCGGCATTTGTCT-AAAAACGCCACTATTGATTAAAA
***
366717 CTATTGAGGCATTTTTCT
65 CTATTGAGGCATTTTAAG
* **
366735 AAAAATGCCACTATTGATTAACACTATTGCGGCATTTGTCTAAAAACGCCACTATTTATTATCAC
1 AAAAATGCCACTATTGATTAACACTATTGCGGCATTTGTCTAAAAACGCCACTATTGATTAAAAC
* *
366800 TATTGCGGCGTTTTAAG
66 TATTGAGGCATTTTAAG
* *
366817 AATAAATGCCACTATATG-TGTAA-TCTATTGCGACATTTGT
1 AA-AAATGCCACTAT-TGAT-TAACACTATTGCGGCATTTGT
366857 GGTATAAAAG
Statistics
Matches: 105, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
82 54 0.51
83 46 0.44
84 5 0.05
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (82 bp):
AAAAATGCCACTATTGATTAACACTATTGCGGCATTTGTCTAAAAACGCCACTATTGATTAAAAC
TATTGAGGCATTTTAAG
Found at i:366864 original size:42 final size:41
Alignment explanation
Indices: 366737--366980 Score: 139
Period size: 42 Copynumber: 5.9 Consensus size: 41
366727 ATTTTTCTAA
* * * *
366737 AAATGCCACTAT-TGATTAACACTATTGCGGCATTTGT-CTAA
1 AAATGCCACTATATG-TTAA-TCTATTGCGGCGTTTGTGGTAT
* * * * *
366778 AAACGCCACTATTTATT-ATCACTATTGCGGCGTTT-TAAGAAT
1 AAATGCCACTATATGTTAAT--CTATTGCGGCGTTTGT-GGTAT
* *
366820 AAATGCCACTATATGTGTAATCTATTGCGACATTTGTGGTAT
1 AAATGCCACTATATGT-TAATCTATTGCGGCGTTTGTGGTAT
* * *
366862 AAAAGCCGCTA-AT-TTACCGATCTATTGTGGCGTTT-TGGCTA-
1 AAATGCCACTATATGTTA---ATCTATTGCGGCGTTTGTGG-TAT
* *
366903 AAACGCCACTATATGTTAATCTATTGCGGTGTTTGTGGTAT
1 AAATGCCACTATATGTTAATCTATTGCGGCGTTTGTGGTAT
* *
366944 AAATGCCGCTA-AT-TTACCACTCTATTACGGCGTTTGT
1 AAATGCCACTATATGTTA--A-TCTATTGCGGCGTTTGT
366981 TAAAAAATGC
Statistics
Matches: 157, Mismatches: 27, Indels: 37
0.71 0.12 0.17
Matches are distributed among these distances:
39 5 0.03
40 21 0.13
41 53 0.34
42 71 0.45
43 5 0.03
44 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (41 bp):
AAATGCCACTATATGTTAATCTATTGCGGCGTTTGTGGTAT
Found at i:366939 original size:82 final size:83
Alignment explanation
Indices: 366824--366978 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 83
366814 AAGAATAAAT
366824 GCCACTATATGTGTAATCTATTGCGACATTTGTGGTATAAAAGCCGCTAATTTACCGA-TCTATT
1 GCCACTATATGTGTAATCTATTGCGACATTTGTGGTATAAAAGCCGCTAATTTACC-ACTCTATT
**
366888 GTGGCGTTTTGGCTAAAAC
65 ACGGCGTTTTGGCTAAAAC
*** *
366907 GCCACTATATGT-TAATCTATTGCGGTGTTTGTGGTATAAATGCCGCTAATTTACCACTCTATTA
1 GCCACTATATGTGTAATCTATTGCGACATTTGTGGTATAAAAGCCGCTAATTTACCACTCTATTA
366971 CGGCGTTT
66 CGGCGTTT
366979 GTTAAAAAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 1 0.02
82 52 0.80
83 12 0.18
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.37
Consensus pattern (83 bp):
GCCACTATATGTGTAATCTATTGCGACATTTGTGGTATAAAAGCCGCTAATTTACCACTCTATTA
CGGCGTTTTGGCTAAAAC
Found at i:371154 original size:22 final size:22
Alignment explanation
Indices: 371126--371174 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
371116 TTATTGTAAA
*
371126 AAAAATCGCATAAAATCTTTGT
1 AAAAATCACATAAAATCTTTGT
371148 AAAAATCACATAAAATCTTTGT
1 AAAAATCACATAAAATCTTTGT
371170 AAAAA
1 AAAAA
371175 ATGGGTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (22 bp):
AAAAATCACATAAAATCTTTGT
Found at i:371264 original size:16 final size:17
Alignment explanation
Indices: 371233--371271 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
371223 CCCTTATTTT
371233 CAAAAAACAATAGAAAG
1 CAAAAAACAATAGAAAG
*
371250 CAAAAAA-AATTGAAAG
1 CAAAAAACAATAGAAAG
*
371266 TAAAAA
1 CAAAAA
371272 GCTTTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.72, C:0.08, G:0.10, T:0.10
Consensus pattern (17 bp):
CAAAAAACAATAGAAAG
Found at i:378013 original size:16 final size:16
Alignment explanation
Indices: 377992--378022 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
377982 GGCACGCCCC
377992 TATAAGTTAACTCCCG
1 TATAAGTTAACTCCCG
*
378008 TATAAGTTAATTCCC
1 TATAAGTTAACTCCC
378023 CTCCAGCCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (16 bp):
TATAAGTTAACTCCCG
Found at i:380338 original size:14 final size:14
Alignment explanation
Indices: 380294--380338 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
380284 TCTTCGCATT
*
380294 TTTGCACCGTATTC
1 TTTGCACCATATTC
* **
380308 TATGCACCATAGCC
1 TTTGCACCATATTC
380322 TTTGCACCATATTC
1 TTTGCACCATATTC
380336 TTT
1 TTT
380339 ATTCCATATT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.20, C:0.29, G:0.11, T:0.40
Consensus pattern (14 bp):
TTTGCACCATATTC
Found at i:386426 original size:27 final size:27
Alignment explanation
Indices: 386395--386456 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
386385 GACTTGTCAA
386395 AGAAGTGAATAAGAGATTTAGAGACTT
1 AGAAGTGAATAAGAGATTTAGAGACTT
* *
386422 AGAAGTGAATATGAGATTTAGAGCCTT
1 AGAAGTGAATAAGAGATTTAGAGACTT
386449 AGAAGTGA
1 AGAAGTGA
386457 TTAAAAACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.42, C:0.05, G:0.27, T:0.26
Consensus pattern (27 bp):
AGAAGTGAATAAGAGATTTAGAGACTT
Found at i:387316 original size:55 final size:55
Alignment explanation
Indices: 387215--387559 Score: 453
Period size: 55 Copynumber: 6.3 Consensus size: 55
387205 TTACCGAAGG
* * * *
387215 GGCACTATGTGTGCAACCT-AAGAAAATCATAATAAGTTTATGAATTTCTGTGTT
1 GGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCTGTATT
* **
387269 GGCACTATGTGTGCAACCTCACGAAATTCATAACGAGTTTATGAATTTCCATATT
1 GGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCTGTATT
* *
387324 GGTACTATGTGTGCAACCTCTCGAAATTCATAATGAGTTTATGAATTT-TCGTATT
1 GGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCT-GTATT
* * *
387379 GGTACTATGTGTGCAACCTCACAAAATTCATAATGAGTTTATGAATTT-TCGTACT
1 GGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCT-GTATT
* * *
387434 GGCACTATGTGTGCAACCCCATGAAATTCATAATGAGTTTATGAATTTCAGTATT
1 GGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCTGTATT
* * * * * * *
387489 GGCACTATCTGTGCAACCCCACGTAATTCATAATGAGTTTGTGAATTACCGTATC
1 GGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCTGTATT
387544 GGCACTATGTGTGCAA
1 GGCACTATGTGTGCAA
387560 AACCATATAA
Statistics
Matches: 259, Mismatches: 29, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
54 19 0.07
55 240 0.93
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (55 bp):
GGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCTGTATT
Found at i:387938 original size:22 final size:22
Alignment explanation
Indices: 387895--387941 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
387885 ATTGTTTACA
*
387895 TATTATAAGTTAAAGAACGTTT
1 TATTATAAATTAAAGAACGTTT
*
387917 TATTATTAAATTAAA-AATGTTT
1 TATTA-TAAATTAAAGAACGTTT
387939 TAT
1 TAT
387942 GTTTAGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.47
Consensus pattern (22 bp):
TATTATAAATTAAAGAACGTTT
Found at i:388117 original size:10 final size:10
Alignment explanation
Indices: 388102--388132 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
388092 TATTACGCTT
388102 AAAAAATGAA
1 AAAAAATGAA
388112 AAAAAATGAAA
1 AAAAAATG-AA
388123 AAAAAATGAA
1 AAAAAATGAA
388133 CGAACGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAAAATGAA
Found at i:388124 original size:11 final size:11
Alignment explanation
Indices: 388102--388132 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
388092 TATTACGCTT
388102 AAAAAATG-AA
1 AAAAAATGAAA
388112 AAAAAATGAAA
1 AAAAAATGAAA
388123 AAAAAATGAA
1 AAAAAATGAA
388133 CGAACGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (11 bp):
AAAAAATGAAA
Found at i:390937 original size:18 final size:18
Alignment explanation
Indices: 390914--391003 Score: 117
Period size: 18 Copynumber: 4.8 Consensus size: 18
390904 TGTATATTTA
390914 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
390932 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
*
390950 TCCCGAAAGACCACTGATTTG
1 TCCCGAAGGACCACT-A--TG
*
390971 TCCCAAAGGACCACTATG
1 TCCCGAAGGACCACTATG
* *
390989 TCTCGAATGACCACT
1 TCCCGAAGGACCACT
391004 CCTTAAGAAC
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
18 46 0.73
19 1 0.02
20 1 0.02
21 15 0.24
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.20
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:390983 original size:39 final size:36
Alignment explanation
Indices: 390914--391003 Score: 117
Period size: 39 Copynumber: 2.4 Consensus size: 36
390904 TGTATATTTA
* *
390914 TCCCGAAGGACCACTATGTCCCGAAGGACCACTATG
1 TCCCGAAAGACCACTATGTCCCAAAGGACCACTATG
390950 TCCCGAAAGACCACTGATTTGTCCCAAAGGACCACTATG
1 TCCCGAAAGACCACT-A--TGTCCCAAAGGACCACTATG
* *
390989 TCTCGAATGACCACT
1 TCCCGAAAGACCACT
391004 CCTTAAGAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
36 14 0.30
37 1 0.02
39 32 0.68
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.20
Consensus pattern (36 bp):
TCCCGAAAGACCACTATGTCCCAAAGGACCACTATG
Found at i:396250 original size:18 final size:18
Alignment explanation
Indices: 396224--396331 Score: 144
Period size: 18 Copynumber: 5.8 Consensus size: 18
396214 TATATATTTA
*
396224 TCCCAAAGGACCACTATG
1 TCCCGAAGGACCACTATG
396242 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
396260 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
*
396278 TCCCGAAAGACCACTGATTTG
1 TCCCGAAGGACCACT-A--TG
*
396299 TCCCAAAGGACCACTATG
1 TCCCGAAGGACCACTATG
* *
396317 TCTCGAATGACCACT
1 TCCCGAAGGACCACT
396332 CCTTAAGAAC
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
18 63 0.79
19 1 0.01
20 1 0.01
21 15 0.19
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:401600 original size:18 final size:18
Alignment explanation
Indices: 401574--401680 Score: 135
Period size: 18 Copynumber: 5.8 Consensus size: 18
401564 TGTATATTTA
*
401574 TCCCAAAGGACCACTATG
1 TCCCGAAGGACCACTATG
401592 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
401610 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
*
401628 TCCCGAAAGACCACTGATTTG
1 TCCCGAAGGACCACT-A--TG
*
401649 TCCCAAAGGACCA-TATG
1 TCCCGAAGGACCACTATG
* *
401666 TCTCGAATGACCACT
1 TCCCGAAGGACCACT
401681 CCTTAAGAAC
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
17 12 0.15
18 50 0.64
19 2 0.03
20 1 0.01
21 13 0.17
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.20
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:406931 original size:19 final size:18
Alignment explanation
Indices: 406867--406938 Score: 108
Period size: 18 Copynumber: 3.9 Consensus size: 18
406857 ACTGTATATT
406867 TGTCCCGAAAGACCACTA
1 TGTCCCGAAAGACCACTA
406885 TGTCCCGAAAGACCACTA
1 TGTCCCGAAAGACCACTA
* *
406903 TGTTCCGAAGGACCACTA
1 TGTCCCGAAAGACCACTA
*
406921 TGTCCCCGAAGGACCACT
1 TGT-CCCGAAAGACCACT
406939 CCTTAAGAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
18 37 0.74
19 13 0.26
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAAGACCACTA
Found at i:407799 original size:19 final size:19
Alignment explanation
Indices: 407775--407826 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
407765 TTTAAGGGTG
407775 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
407794 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
407813 TGCATCGATGCACT
1 TGCATCGATGCACT
407827 AATTGAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.31
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:409767 original size:10 final size:10
Alignment explanation
Indices: 409752--409802 Score: 102
Period size: 10 Copynumber: 5.1 Consensus size: 10
409742 TTTATGTTTA
409752 ATTTCAATTT
1 ATTTCAATTT
409762 ATTTCAATTT
1 ATTTCAATTT
409772 ATTTCAATTT
1 ATTTCAATTT
409782 ATTTCAATTT
1 ATTTCAATTT
409792 ATTTCAATTT
1 ATTTCAATTT
409802 A
1 A
409803 GTCACTGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 41 1.00
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59
Consensus pattern (10 bp):
ATTTCAATTT
Found at i:411622 original size:21 final size:21
Alignment explanation
Indices: 411580--411647 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
411570 GAAATAATAT
* *
411580 ATATAATATATATTTTCCAAAAA
1 ATATAATACAT-TTTT-TAAAAA
* *
411603 ATCTAATACATTTTTTAAAAT
1 ATATAATACATTTTTTAAAAA
* *
411624 ATATTATATATTTTTTAAAAA
1 ATATAATACATTTTTTAAAAA
411645 ATA
1 ATA
411648 CAAATTATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
21 24 0.65
22 4 0.11
23 9 0.24
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATAATACATTTTTTAAAAA
Found at i:411717 original size:84 final size:86
Alignment explanation
Indices: 411622--411804 Score: 198
Period size: 84 Copynumber: 2.2 Consensus size: 86
411612 ATTTTTTAAA
* * **
411622 ATATAT-TATATATTTTTTAAAAAA-TACAAAT-TATATATTTTTCGAAAACTATATA-ATACTA
1 ATATATATATATATTATTCAAAAAATTA-AAATATATATATTTTTAAAAAACTATATATATA-TA
*
411683 TATATTAAAAAAACTATAT-TAT
64 TATATTAAAAAAACAATATATAT
* * *
411705 ATGTATATATATA-TATTCAAAAAATTATATTATATATATTTTTAAAAAACTATATATTATATAT
1 ATATATATATATATTATTCAAAAAATTAAAATATATATATTTTTAAAAAACTATATA-TATATAT
* **
411769 ATGTTTCAAAAACAATATATAT
65 ATATTAAAAAAACAATATATAT
411791 ATATATATATATAT
1 ATATATATATATAT
411805 ATATATATAA
Statistics
Matches: 81, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
83 16 0.20
84 30 0.37
85 17 0.21
86 18 0.22
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (86 bp):
ATATATATATATATTATTCAAAAAATTAAAATATATATATTTTTAAAAAACTATATATATATATA
TATTAAAAAAACAATATATAT
Found at i:411738 original size:27 final size:27
Alignment explanation
Indices: 411700--411800 Score: 116
Period size: 28 Copynumber: 3.7 Consensus size: 27
411690 AAAAAACTAT
*
411700 ATTATATGTATATATATATATTCAAAAA
1 ATTATATATATATATATAT-TTCAAAAA
*
411728 ATTATAT-TATATATAT-TTTTAAAAA
1 ATTATATATATATATATATTTCAAAAA
* *
411753 ACTATATATTATATATATGTTTCAAAAA
1 ATTATATA-TATATATATATTTCAAAAA
*
411781 CAATATATATATATATATAT
1 -ATTATATATATATATATAT
411801 ATATATATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
25 13 0.20
26 1 0.02
27 18 0.28
28 25 0.39
29 7 0.11
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (27 bp):
ATTATATATATATATATATTTCAAAAA
Found at i:411741 original size:25 final size:25
Alignment explanation
Indices: 411710--411800 Score: 101
Period size: 27 Copynumber: 3.4 Consensus size: 25
411700 ATTATATGTA
411710 TATATATATATTCAAAAAATTATAT
1 TATATATATATTCAAAAAATTATAT
* *
411735 TATATATATTTTTAAAAAACTATATAT
1 TATATATATATTCAAAAAA-T-TATAT
* *
411762 TATATATATGTTTCAAAAACAATATAT
1 TATATATAT-ATTCAAAAA-ATTATAT
411789 ATATATATATAT
1 -TATATATATAT
411801 ATATATATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
25 17 0.30
26 1 0.02
27 20 0.36
28 17 0.30
29 1 0.02
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (25 bp):
TATATATATATTCAAAAAATTATAT
Found at i:411788 original size:2 final size:2
Alignment explanation
Indices: 411783--411828 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
411773 TTCAAAAACA
411783 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
411822 AT -T AT AT
1 AT AT AT AT
411829 TTTCTAAGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 4 0.10
2 36 0.90
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:413484 original size:74 final size:75
Alignment explanation
Indices: 413360--413501 Score: 250
Period size: 74 Copynumber: 1.9 Consensus size: 75
413350 TTTTCGAAAA
* *
413360 TTTATATATTATATAGTTTTTGAAAATATTTTGAAAATATATATAATATATAGTTTTAAAAACAT
1 TTTATATATTATATAGTTTTTGAAAACATTTTGAAAACATATATAATATATAGTTTTAAAAACAT
413425 TTTGAAACCG
66 TTTGAAACCG
*
413435 TTTATATATTATATAGTTTTT-AAAACATTTTGAAAACATATATAGTATATAGTTTTAAAAACAT
1 TTTATATATTATATAGTTTTTGAAAACATTTTGAAAACATATATAATATATAGTTTTAAAAACAT
413499 TTT
66 TTT
413502 TTGTGAAATT
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
74 43 0.67
75 21 0.33
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.46
Consensus pattern (75 bp):
TTTATATATTATATAGTTTTTGAAAACATTTTGAAAACATATATAATATATAGTTTTAAAAACAT
TTTGAAACCG
Found at i:413504 original size:38 final size:37
Alignment explanation
Indices: 413295--413668 Score: 194
Period size: 38 Copynumber: 10.2 Consensus size: 37
413285 GTTTTTTTAT
* *
413295 TATAGTTTGTAAAAATA-TTTTTGACAAA-ATATAATA
1 TATAGTTT-TAAAAACATTTTTTGAAAAATATATAATA
* * * * *
413331 TATAATTTTTAGAAA-ATGATTTTCGAAAATTTATATATTA
1 TAT-AGTTTTAAAAACAT--TTTTTGAAAA-ATATATAATA
** *
413371 TATAGTTTTTGAAA-ATATTTTGAAAATATATATAATA
1 TATAGTTTTAAAAACATTTTTTGAAAA-ATATATAATA
** *
413408 TATAGTTTTAAAAACA--TTTTGAAACCGTTTATATATTA
1 TATAGTTTTAAAAACATTTTTTGAAA---AATATATAATA
* *
413446 TATAGTTTTTAAAACA--TTTTGAAAACATATATAGTA
1 TATAGTTTTAAAAACATTTTTTGAAAA-ATATATAATA
* *
413482 TATAGTTTTAAAAACATTTTTTGTGAAATTATATAATA
1 TATAGTTTTAAAAACATTTTTTG-AAAAATATATAATA
* *
413520 TATAGTTTTAAAAATATTTTTTTTTGAAAACT-TAT-ATA
1 TATAGTTTTAAAAACA---TTTTTTGAAAAATATATAATA
* * * *
413558 -ATA-TTTTTAAAAC--GTTTTGAAAACTATGTAATA
1 TATAGTTTTAAAAACATTTTTTGAAAAATATATAATA
** * *
413591 TATAGTTTT-GGAA-ATTTTTT---TAA-GTATAATA
1 TATAGTTTTAAAAACATTTTTTGAAAAATATATAATA
* * *
413622 TATAGTTTTCTAAAACATATTTTTGAAATATATATATTA
1 TATAGTTTT-AAAAACAT-TTTTTGAAAAATATATAATA
413661 TATAGTTT
1 TATAGTTT
413669 ATATCATATT
Statistics
Matches: 262, Mismatches: 45, Indels: 59
0.72 0.12 0.16
Matches are distributed among these distances:
31 26 0.10
32 3 0.01
33 5 0.02
34 7 0.03
35 14 0.05
36 47 0.18
37 36 0.14
38 72 0.27
39 31 0.12
40 14 0.05
41 7 0.03
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (37 bp):
TATAGTTTTAAAAACATTTTTTGAAAAATATATAATA
Found at i:413514 original size:74 final size:71
Alignment explanation
Indices: 413295--413539 Score: 244
Period size: 74 Copynumber: 3.3 Consensus size: 71
413285 GTTTTTTTAT
* * * *
413295 TATAGTTTGTAAAAATATTTTTGACAA-A-ATATAATATATAATTTTTAGAAAATGATTTTCGAA
1 TATAGTTT-TTAAAATA-TTTTGAAAACATATATAATATAT-AGTTTTA-AAAA-CATTTT-G-A
*
413358 AATTTATATATTA
59 AACTTATATATTA
*
413371 TATAGTTTTTGAAAATATTTTGAAAATATATATAATATATAGTTTTAAAAACATTTTGAAACCGT
1 TATAGTTTTT-AAAATATTTTGAAAACATATATAATATATAGTTTTAAAAACATTTTGAAA-C--
413436 TTATATATTA
62 TTATATATTA
* *
413446 TATAGTTTTTAAAACATTTTGAAAACATATATAGTATATAGTTTTAAAAACATTTTTTGTGAAA-
1 TATAGTTTTTAAAATATTTTGAAAACATATATAATATATAGTTTTAAAAACA---TTT-TGAAAC
*
413510 TTATATAATA
62 TTATATATTA
*
413520 TATAGTTTTAAAAATATTTT
1 TATAGTTTTTAAAATATTTT
413540 TTTTTGAAAA
Statistics
Matches: 148, Mismatches: 11, Indels: 22
0.82 0.06 0.12
Matches are distributed among these distances:
72 3 0.02
73 1 0.01
74 71 0.48
75 33 0.22
76 21 0.14
77 14 0.09
78 5 0.03
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (71 bp):
TATAGTTTTTAAAATATTTTGAAAACATATATAATATATAGTTTTAAAAACATTTTGAAACTTAT
ATATTA
Found at i:413688 original size:5 final size:5
Alignment explanation
Indices: 413680--413705 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
413670 TATCATATTA
413680 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
413706 AATTTAATTT
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:418960 original size:106 final size:106
Alignment explanation
Indices: 418772--419740 Score: 1573
Period size: 106 Copynumber: 9.2 Consensus size: 106
418762 AACCATGAGC
* *
418772 ACGAAGAAAATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
*
418837 ATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
66 ATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
* *
418878 GCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
418943 ATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
66 ATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
* *
418984 ACGAATGATATTGGACTCCAGGCAACGCAAGTTCAACTTCACGACGAAGGGACCGC-GGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
*
419048 ATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
66 ATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
** ** * * *
419089 ACGAAGGATATTGGACTTTAGACAACTTAAGTTCAACTTCATGACGAAGGGACCGTTGGTTGTCG
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
419154 ATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
66 ATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
*
419195 ACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC-GGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* * *
419259 ATAACCAACTTCTCAATTTCAGAGTCAATTTCAACTTCACG
66 ATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
** *
419300 ACGAAGGATATTGGACTTTAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
419365 ATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
66 ATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
*
419406 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* *
419471 ATAACCAACTTCTCAGTTTCAGAGCCAATTTCAACTTCACA
66 ATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
* * *
419512 ATGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* *
419577 ATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACA
66 ATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
*
419618 ACGAAGGATATTGGACTCCAGACAACGCGAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* * * * *
419683 ACAAACAATTTCCCAATTCCAGAGCCAATTTCAACTTCACG
66 ATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
** *
419724 GTGGAGGATATTGGACT
1 ACGAAGGATATTGGACT
419741 TGGAACAATA
Statistics
Matches: 799, Mismatches: 62, Indels: 4
0.92 0.07 0.00
Matches are distributed among these distances:
105 193 0.24
106 606 0.76
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (106 bp):
ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
ATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
Found at i:419151 original size:211 final size:212
Alignment explanation
Indices: 418772--419741 Score: 1602
Period size: 211 Copynumber: 4.6 Consensus size: 212
418762 AACCATGAGC
* *
418772 ACGAAGAAAATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* * * *
418837 ATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACA
66 ATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACA
* *
418902 ACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
131 ACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
418967 CCAATTTCAACTTCACA
196 CCAATTTCAACTTCACA
* *
418984 ACGAATGATATTGGACTCCAGGCAACGCAAGTTCAACTTCACGACGAAGGGACCGC-GGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
*
419048 ATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTTAGACA
66 ATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACA
* * * *
419113 ACTTAAGTTCAACTTCATGACGAAGGGACCGTTGGTTGTCGATAAACAACTTCTCAATTTCAGAG
131 ACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
419178 CCAATTTCAACTTCACA
196 CCAATTTCAACTTCACA
*
419195 ACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC-GGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* * *
419259 ATAACCAACTTCTCAATTTCAGAGTCAATTTCAACTTCACGACGAAGGATATTGGACTTTAGACA
66 ATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACA
419324 ACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
131 ACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
419389 CCAATTTCAACTTCACA
196 CCAATTTCAACTTCACA
*
419406 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* * *
419471 ATAACCAACTTCTCAGTTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACA
66 ATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACA
* * *
419536 ACGTAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAG
131 ACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
419601 CCAATTTCAACTTCACA
196 CCAATTTCAACTTCACA
*
419618 ACGAAGGATATTGGACTCCAGACAACGCGAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* * * * * *** *
419683 ACAAACAATTTCCCAATTCCAGAGCCAATTTCAACTTCACGGTGGAGGATATTGGACTT
66 ATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTT
419742 GGAACAATAC
Statistics
Matches: 710, Mismatches: 47, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
211 400 0.56
212 310 0.44
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (212 bp):
ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
ATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACA
ACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
CCAATTTCAACTTCACA
Found at i:419363 original size:317 final size:318
Alignment explanation
Indices: 418772--419740 Score: 1573
Period size: 317 Copynumber: 3.1 Consensus size: 318
418762 AACCATGAGC
* *
418772 ACGAAGAAAATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* *
418837 ATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACA
66 ATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
*
418902 ACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
131 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
* *
418967 CCAATTTCAACTTCACAACGAATGATATTGGACTCCAGGCAACGCAAGTTCAACTTCACGACGAA
196 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
419032 GGGACCGC-GGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
261 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
** ** * * *
419089 ACGAAGGATATTGGACTTTAGACAACTTAAGTTCAACTTCATGACGAAGGGACCGTTGGTTGTCG
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
*
419154 ATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCCAGACA
66 ATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
*
419219 ACGCAAGTTCAACTTCACGACGAAGGGACCGC-GGTTGTCAATAACCAACTTCTCAATTTCAGAG
131 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
* * ** *
419283 TCAATTTCAACTTCACGACGAAGGATATTGGACTTTAGACAACGTAAGTTCAACTTCACGACGAA
196 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
419348 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
261 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
*
419406 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* * *
419471 ATAACCAACTTCTCAGTTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACA
66 ATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
* * * *
419536 ACGTAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAG
131 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
*
419601 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCGAGTTCAACTTCACGACGAA
196 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * * * *
419666 GGGACCGCTGGTTGTCAACAAACAATTTCCCAATTCCAGAGCCAATTTCAACTTCACG
261 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
** *
419724 GTGGAGGATATTGGACT
1 ACGAAGGATATTGGACT
419741 TGGAACAATA
Statistics
Matches: 597, Mismatches: 53, Indels: 3
0.91 0.08 0.00
Matches are distributed among these distances:
316 97 0.16
317 345 0.58
318 155 0.26
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (318 bp):
ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
ATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAG
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
Found at i:420068 original size:81 final size:81
Alignment explanation
Indices: 419974--420260 Score: 378
Period size: 81 Copynumber: 3.5 Consensus size: 81
419964 TCATCTCAAT
* **
419974 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGAT
1 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTTGAGTTCGAT
*
420039 TACACTCAGCTTCGAG
66 TACACTCAACTTCGAG
* * *
420055 GGCACATCATTTGCAGCACAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTT
1 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG----CCAAAGACCCTTGAGTT
** * * *
420120 CGACAACGCTCAAC-TCAAC
62 CGATTACACTCAACTTCGAG
*
420139 GGTACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTTGAGTTCGAT
1 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTTGAGTTCGAT
*
420204 TGCACTCAACTTCGAG
66 TACACTCAACTTCGAG
* * *
420220 GGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTAT
1 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTAT
420261 ATGTCAATAA
Statistics
Matches: 175, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
80 26 0.15
81 81 0.46
84 44 0.25
85 24 0.14
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (81 bp):
GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTTGAGTTCGAT
TACACTCAACTTCGAG
Found at i:420170 original size:84 final size:81
Alignment explanation
Indices: 419940--420260 Score: 367
Period size: 81 Copynumber: 3.9 Consensus size: 81
419930 TCTGCCAACA
* * ** * *
419940 AAAGACCTTTGAGTTTGACTATGCTCATC-TCAATGGCACATCATTTGCAGCATAGCTTAAGTCG
1 AAAGACCCTTGAGTTCGACTACACTCAACTTCAAGGGCACATCATTTGCAGCATAGCTTAAGTCG
*
420004 AGAAGGGCTATCTGCC
66 AGAAGGGTTATCTGCC
** * * * * *
420020 AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCACAACTTAAGTCG
1 AAAGACCCTTGAGTTCGACTACACTCAACTTCAAGGGCACATCATTTGCAGCATAGCTTAAGTCG
420085 AGAAGGGTTATCTGCCAACC
66 AGAAGGGTTATCTG----CC
* * * * *
420105 AAAGACCTTTGAGTTCGACAACGCTCAAC-TCAACGGTACATCATTTGCAGCATAGCTTAAGTCG
1 AAAGACCCTTGAGTTCGACTACACTCAACTTCAAGGGCACATCATTTGCAGCATAGCTTAAGTCG
420169 AGAAGGGTTATCTGCC
66 AGAAGGGTTATCTGCC
* * * * * *
420185 AAAGACCCTTGAGTTCGATTGCACTCAACTTCGAGGGCACATCATTTGCAGCATAGCTCAAGGCA
1 AAAGACCCTTGAGTTCGACTACACTCAACTTCAAGGGCACATCATTTGCAGCATAGCTTAAGTCG
420250 AGAAGGGTTAT
66 AGAAGGGTTAT
420261 ATGTCAATAA
Statistics
Matches: 199, Mismatches: 36, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
80 47 0.24
81 84 0.42
84 44 0.22
85 24 0.12
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (81 bp):
AAAGACCCTTGAGTTCGACTACACTCAACTTCAAGGGCACATCATTTGCAGCATAGCTTAAGTCG
AGAAGGGTTATCTGCC
Found at i:420202 original size:165 final size:165
Alignment explanation
Indices: 419930--420260 Score: 509
Period size: 165 Copynumber: 2.0 Consensus size: 165
419920 AGAAGGAGTG
* * * * *
419930 TCTGCCAACAAAAGACCTTTGAGTTTGACTATGCTCATCTCAATGGCACATCATTTGCAGCATAG
1 TCTGCCAACAAAAGACCTTTGAGTTCGACAACGCTCAACTCAACGGCACATCATTTGCAGCATAG
*
419995 CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
66 CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAACTTCGAGGGCAC
* * *
420060 ATCATTTGCAGCACAACTTAAGTCGAGAAGGGTTA
131 ATCATTTGCAGCACAACTCAAGGCAAGAAGGGTTA
* *
420095 TCTGCCAACCAAAGACCTTTGAGTTCGACAACGCTCAACTCAACGGTACATCATTTGCAGCATAG
1 TCTGCCAACAAAAGACCTTTGAGTTCGACAACGCTCAACTCAACGGCACATCATTTGCAGCATAG
* ** *
420160 CTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTTGAGTTCGATTGCACTCAACTTCGAGGGCAC
66 CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAACTTCGAGGGCAC
* *
420225 ATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTA
131 ATCATTTGCAGCACAACTCAAGGCAAGAAGGGTTA
420260 T
1 T
420261 ATGTCAATAA
Statistics
Matches: 149, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
165 149 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (165 bp):
TCTGCCAACAAAAGACCTTTGAGTTCGACAACGCTCAACTCAACGGCACATCATTTGCAGCATAG
CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAACTTCGAGGGCAC
ATCATTTGCAGCACAACTCAAGGCAAGAAGGGTTA
Found at i:420916 original size:37 final size:36
Alignment explanation
Indices: 420875--421046 Score: 153
Period size: 34 Copynumber: 4.8 Consensus size: 36
420865 TCAGAAAATG
*
420875 ATTTTCGAAAATTTATATATATATAGTTTTTGAAAAT
1 ATTTT-GAAAATTTATATATATATAGTTTTTGAAAAC
*
420912 ATTTTGAAAATATATATA-ATATAG-TTTTGAAAAC
1 ATTTTGAAAATTTATATATATATAGTTTTTGAAAAC
**
420946 ATTTTGAAACCGTTATATATTATATAGTTTTT-AAAAC
1 ATTTTGAAA-ATTTATATA-TATATAGTTTTTGAAAAC
* * *
420983 ATTTTGAAAA--CATATA-GTATAG-TTTTAAAAAC
1 ATTTTGAAAATTTATATATATATAGTTTTTGAAAAC
*
421015 ATTTTTTGTGAAA-TTATATAATATATAGTTTT
1 A--TTTTG-AAAATTTATAT-ATATATAGTTTT
421047 AAACATTTTT
Statistics
Matches: 112, Mismatches: 11, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
31 4 0.04
32 11 0.10
34 28 0.25
35 15 0.13
36 16 0.14
37 26 0.23
38 9 0.08
39 3 0.03
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (36 bp):
ATTTTGAAAATTTATATATATATAGTTTTTGAAAAC
Found at i:420918 original size:11 final size:11
Alignment explanation
Indices: 420902--420954 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
420892 TATATATAGT
420902 TTTTGAAAATA
1 TTTTGAAAATA
420913 TTTTGAAAATA
1 TTTTGAAAATA
* *
420924 TATAT-AATATA
1 T-TTTGAAAATA
*
420935 GTTTTGAAAACA
1 -TTTTGAAAATA
420947 TTTTGAAA
1 TTTTGAAA
420955 CCGTTATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
11 27 0.79
12 7 0.21
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (11 bp):
TTTTGAAAATA
Found at i:421014 original size:32 final size:33
Alignment explanation
Indices: 420851--421019 Score: 133
Period size: 37 Copynumber: 4.8 Consensus size: 33
420841 TTTTGACAAA
* * *
420851 ATATAATATAATTTTCAGAAAATGATTTTCGAAAATTT
1 ATATAATATAGTTTT-A-AAAA-CATTTT-GAAAA-CT
* * *
420889 ATATATATATAGTTTTTGAAAATATTTTGAAAATAT
1 ATATA-ATATAG-TTTTAAAAACATTTTGAAAA-CT
* *
420925 ATATAATATAGTTTTGAAAACATTTTGAAACCGTT
1 ATATAATATAGTTTTAAAAACATTTTGAAAAC--T
*
420960 ATATATTATATAGTTTTTAAAACATTTTGAAAAC-
1 ATATA--ATATAGTTTTAAAAACATTTTGAAAACT
*
420994 ATATAGTATAGTTTTAAAAACATTTT
1 ATATAATATAGTTTTAAAAACATTTT
421020 TTGTGAAATT
Statistics
Matches: 114, Mismatches: 11, Indels: 18
0.80 0.08 0.13
Matches are distributed among these distances:
32 19 0.17
34 23 0.20
35 12 0.11
36 12 0.11
37 30 0.26
38 9 0.08
39 5 0.04
40 4 0.04
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (33 bp):
ATATAATATAGTTTTAAAAACATTTTGAAAACT
Found at i:421014 original size:69 final size:71
Alignment explanation
Indices: 420887--421019 Score: 200
Period size: 69 Copynumber: 1.9 Consensus size: 71
420877 TTTCGAAAAT
* * *
420887 TTATATATATATAGTTTTTGAAAATATTTTGAAAATATATATAATATAGTTTTGAAAACATTTTG
1 TTATATATATATAGTTTTTGAAAACATTTTGAAAATACATATAATATAGTTTTAAAAACATTTTG
420952 AAACCG
66 AAACCG
*
420958 TTATATATTATATAGTTTTT-AAAACATTTTG-AAA-ACATATAGTATAGTTTTAAAAACATTTT
1 TTATATA-TATATAGTTTTTGAAAACATTTTGAAAATACATATAATATAGTTTTAAAAACATTTT
421020 TTGTGAAATT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
69 25 0.44
70 3 0.05
71 17 0.30
72 12 0.21
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (71 bp):
TTATATATATATAGTTTTTGAAAACATTTTGAAAATACATATAATATAGTTTTAAAAACATTTTG
AAACCG
Found at i:421034 original size:36 final size:37
Alignment explanation
Indices: 420881--421073 Score: 107
Period size: 37 Copynumber: 5.4 Consensus size: 37
420871 AATGATTTTC
* *
420881 GAAAATTTATATATATATAGTTTTTGAAA-A-TATTT-T
1 GAAAACTTATATATATATAG-TTTT-AAACATTTTTTGT
420917 GAAAA--TATATATAATATAGTTTTGAAAACA---TTT-T
1 GAAAACTTATATAT-ATATAGTTTT--AAACATTTTTTGT
*
420951 GAAACCGTTATATATTATATAGTTTTTAAAACA---TTT-T
1 GAAAAC-TTATATA-TATATAG-TTTT-AAACATTTTTTGT
*
420988 GAAAAC--ATATA-GTATAGTTTTAAAAACATTTTTTGT
1 GAAAACTTATATATATATAGTTTT--AAACATTTTTTGT
*
421024 G-AAA-TTATATAATATATAGTTTTAAACATTTTTTTT
1 GAAAACTTATAT-ATATATAGTTTTAAACATTTTTTGT
421060 GAAAACTTATATAT
1 GAAAACTTATATAT
421074 TTAAAACGTT
Statistics
Matches: 132, Mismatches: 6, Indels: 37
0.75 0.03 0.21
Matches are distributed among these distances:
31 4 0.03
32 11 0.08
34 24 0.18
35 15 0.11
36 25 0.19
37 33 0.25
38 20 0.15
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (37 bp):
GAAAACTTATATATATATAGTTTTAAACATTTTTTGT
Found at i:421047 original size:38 final size:38
Alignment explanation
Indices: 421000--421072 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
420990 AAACATATAG
421000 TATAGTTTTAAAAACATTTTTTGTG-AAA-TTATATAATA
1 TATAGTTTT--AAACATTTTTTGTGAAAACTTATATAATA
*
421038 TATAGTTTTAAACATTTTTTTTGAAAACTTATATA
1 TATAGTTTTAAACATTTTTTGTGAAAACTTATATA
421073 TTTAAAACGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 13 0.41
37 3 0.09
38 16 0.50
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (38 bp):
TATAGTTTTAAACATTTTTTGTGAAAACTTATATAATA
Found at i:421047 original size:69 final size:69
Alignment explanation
Indices: 420851--421055 Score: 188
Period size: 69 Copynumber: 2.9 Consensus size: 69
420841 TTTTGACAAA
* * * *
420851 ATATAATATAATTTTCAGAAAATGATTTTCGAAAATT-TATATATATATAGTTTTTGAAAATATT
1 ATATAATATAGTTTT-A-AAAA-CATTTT-GAAACTTATATA-ATATATAGTTTTT-AAAACATT
*
420915 TTGAAAATAT
60 TTGAAAATAC
* *
420925 ATATAATATAGTTTTGAAAACATTTTGAAACCGTTATATATTATATAGTTTTTAAAACATTTTG-
1 ATATAATATAGTTTTAAAAACATTTTGAAA-C-TTATATAATATATAGTTTTTAAAACATTTTGA
420989 AAA-AC
64 AAATAC
*
420994 ATATAGTATAGTTTTAAAAACATTTTTTGTGAAA-TTATATAATATATAG-TTTT-AAACATTTT
1 ATATAATATAGTTTTAAAAACA---TTT-TGAAACTTATATAATATATAGTTTTTAAAACATTTT
421056 TTTTGAAAAC
Statistics
Matches: 114, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
68 9 0.08
69 25 0.22
70 21 0.18
71 15 0.13
72 21 0.18
73 9 0.08
74 14 0.12
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.45
Consensus pattern (69 bp):
ATATAATATAGTTTTAAAAACATTTTGAAACTTATATAATATATAGTTTTTAAAACATTTTGAAA
ATAC
Found at i:423352 original size:48 final size:48
Alignment explanation
Indices: 423299--423395 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
423289 ATATAATTTC
423299 TTTGTTGTTTAGGTTGATATTTAAGGTTCGGCTCTTGCTTTCATCTTA
1 TTTGTTGTTTAGGTTGATATTTAAGGTTCGGCTCTTGCTTTCATCTTA
423347 TTTGTTGTTTAGGTTGATATTTAAGGTTCGGCTCTTGCTTTCATCTTA
1 TTTGTTGTTTAGGTTGATATTTAAGGTTCGGCTCTTGCTTTCATCTTA
423395 T
1 T
423396 AAGTCTAGTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.14, C:0.12, G:0.21, T:0.53
Consensus pattern (48 bp):
TTTGTTGTTTAGGTTGATATTTAAGGTTCGGCTCTTGCTTTCATCTTA
Found at i:425982 original size:27 final size:27
Alignment explanation
Indices: 425898--425985 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
425888 ATATTTAGGA
**
425898 TTTATAATTTAGGGTTAAGGTTTTAATA-
1 TTTATAATTTAGGGTTAA-AATTTAA-AG
* * * * *
425926 TTTA-ATTTTTAGGGTTCAAGTTCAAGG
1 TTTATA-ATTTAGGGTTAAAATTTAAAG
425953 TTTATAATTTAGGGTTAAAATTTAAAG
1 TTTATAATTTAGGGTTAAAATTTAAAG
425980 TTTATA
1 TTTATA
425986 GTTTGATATC
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
27 31 0.67
28 15 0.33
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (27 bp):
TTTATAATTTAGGGTTAAAATTTAAAG
Found at i:434230 original size:174 final size:175
Alignment explanation
Indices: 433940--434289 Score: 661
Period size: 174 Copynumber: 2.0 Consensus size: 175
433930 GGGCAGGTAG
433940 TAAAAATCCAAGATCAAACTGCACATAGAGTGGATTGCAGAGTGGCGCAGTTTACTAAGGGTTGA
1 TAAAAATCCAAGATCAAACTGCACATAGAGTGGATTGCAGAGTGGCGCAGTTTACTAAGGGTTGA
434005 GAGTCCATATGACATTCCAGAACAGATCATCATCACTACGTATGGGAGAAAATTCATGATC-AAA
66 GAGTCCATATGACATTCCAGAACAGATCATCATCACTACGTATGGGAGAAAATTCATGATCAAAA
434069 TTAAAGTTGATGGTGCTGAGGATTTTTTTCCAGAATTAACAGATA
131 TTAAAGTTGATGGTGCTGAGGATTTTTTTCCAGAATTAACAGATA
434114 TAAAAATCCAAGATCAAACTGCACATAGAGTGGATTGCAGAGTGGCGCAGTTGTTACTAA-GGTT
1 TAAAAATCCAAGATCAAACTGCACATAGAGTGGATTGCAGAGTGGCGCAG-T-TTACTAAGGGTT
434178 GAGAGTCCATATGACA-TCCAGAACAGATCATCATCACTACGTATGGGAGAAAATTCATGATCAA
64 GAGAGTCCATATGACATTCCAGAACAGATCATCATCACTACGTATGGGAGAAAATTCATGATCAA
434242 AATTAAAGTTGATGGTGCTGAGGATTTTTTTCCAGAATTAACAGATA
129 AATTAAAGTTGATGGTGCTGAGGATTTTTTTCCAGAATTAACAGATA
434289 T
1 T
434290 GGAGGTAGAA
Statistics
Matches: 173, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
174 96 0.55
175 70 0.40
176 7 0.04
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (175 bp):
TAAAAATCCAAGATCAAACTGCACATAGAGTGGATTGCAGAGTGGCGCAGTTTACTAAGGGTTGA
GAGTCCATATGACATTCCAGAACAGATCATCATCACTACGTATGGGAGAAAATTCATGATCAAAA
TTAAAGTTGATGGTGCTGAGGATTTTTTTCCAGAATTAACAGATA
Found at i:440184 original size:22 final size:22
Alignment explanation
Indices: 440151--440193 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
440141 AAACCAAAAG
440151 CACAGCTCCTAA-CAATATCCTC
1 CACAGCTCCTAACCAAT-TCCTC
440173 CACAG-TCACTAACCAATTCCT
1 CACAGCTC-CTAACCAATTCCT
440194 GACTTAGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.11
22 13 0.68
23 4 0.21
ACGTcount: A:0.33, C:0.40, G:0.05, T:0.23
Consensus pattern (22 bp):
CACAGCTCCTAACCAATTCCTC
Found at i:443524 original size:18 final size:17
Alignment explanation
Indices: 443501--443543 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
443491 AAACAAAAAT
*
443501 CGAGGAAGTGGTGGAACA
1 CGAGGAAGTGCTGGAA-A
443519 CGAGGAAGTGCTGGAAA
1 CGAGGAAGTGCTGGAAA
443536 CGATGGAA
1 CGA-GGAA
443544 CACGAGGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.35, C:0.12, G:0.42, T:0.12
Consensus pattern (17 bp):
CGAGGAAGTGCTGGAAA
Found at i:453433 original size:24 final size:24
Alignment explanation
Indices: 453382--453442 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
453372 ACAATTTTCT
* * *
453382 ATAATAATAGGGATTGTTTTTAGT
1 ATAATATTAGGGATTGTTTATAGA
453406 ATAATATTAGGGATTGTTTCAT-GA
1 ATAATATTAGGGATTGTTT-ATAGA
* *
453430 ATAAGATAAGGGA
1 ATAATATTAGGGA
453443 GTGAAGTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 30 0.97
25 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.38
Consensus pattern (24 bp):
ATAATATTAGGGATTGTTTATAGA
Found at i:459684 original size:12 final size:12
Alignment explanation
Indices: 459664--459700 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
459654 ATAACCTTTG
459664 ACACTCTCTCTC
1 ACACTCTCTCTC
* *
459676 ACTCTCTCTCTG
1 ACACTCTCTCTC
459688 ACACTCTCTCTC
1 ACACTCTCTCTC
459700 A
1 A
459701 TGTTTTTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.16, C:0.46, G:0.03, T:0.35
Consensus pattern (12 bp):
ACACTCTCTCTC
Found at i:459833 original size:23 final size:23
Alignment explanation
Indices: 459799--459849 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
459789 TTTCTTTTAT
*
459799 CATGTACTTTGCCCCGTCATAAA
1 CATGTACGTTGCCCCGTCATAAA
*
459822 CATGTACGTTGCCCTGTCATAAA
1 CATGTACGTTGCCCCGTCATAAA
459845 CATGT
1 CATGT
459850 TTAAGGTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (23 bp):
CATGTACGTTGCCCCGTCATAAA
Found at i:460529 original size:37 final size:37
Alignment explanation
Indices: 460479--460555 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
460469 TTTGTTGTTC
460479 CATCACCTGTTTTCTCATGAATAATCTGAATGAACTT
1 CATCACCTGTTTTCTCATGAATAATCTGAATGAACTT
460516 CATCACCTGTTTTCTCATGAATAATCTGAATGAACTT
1 CATCACCTGTTTTCTCATGAATAATCTGAATGAACTT
460553 CAT
1 CAT
460556 TCCATCATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (37 bp):
CATCACCTGTTTTCTCATGAATAATCTGAATGAACTT
Found at i:466433 original size:16 final size:16
Alignment explanation
Indices: 466401--466439 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
466391 AAAGAGAAAA
466401 TAGTTGTAATATTAAT
1 TAGTTGTAATATTAAT
466417 TAGTT-TAATATTAAAT
1 TAGTTGTAATATT-AAT
466433 TA-TTGTA
1 TAGTTGTA
466440 CACAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (16 bp):
TAGTTGTAATATTAAT
Found at i:484194 original size:20 final size:20
Alignment explanation
Indices: 484169--484208 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
484159 AGCAACAGAA
*
484169 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
484189 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
484209 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:484251 original size:20 final size:21
Alignment explanation
Indices: 484222--484261 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
484212 TAATAGAATA
*
484222 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
484243 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
484262 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:484303 original size:20 final size:20
Alignment explanation
Indices: 484275--484313 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
484265 TAATAGAATA
* *
484275 AAAATTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
484295 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
484314 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:484304 original size:52 final size:51
Alignment explanation
Indices: 484165--484314 Score: 264
Period size: 53 Copynumber: 2.9 Consensus size: 51
484155 AATTAGCAAC
484165 AGAATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
484216 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
*
484269 AGAATAAAAATTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATA
484315 TTTAATTTAG
Statistics
Matches: 95, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
51 5 0.05
52 44 0.46
53 46 0.48
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (51 bp):
AGAATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:488706 original size:20 final size:20
Alignment explanation
Indices: 488681--488720 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
488671 AGCAACAGAA
488681 TAAAAATAATTCTATCTAAT
1 TAAAAATAATTCTATCTAAT
*
488701 TAAAAATGATTCTATCTAAT
1 TAAAAATAATTCTATCTAAT
488721 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (20 bp):
TAAAAATAATTCTATCTAAT
Found at i:488763 original size:20 final size:21
Alignment explanation
Indices: 488734--488773 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
488724 TAATAGAATA
*
488734 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
488755 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
488774 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:488812 original size:20 final size:20
Alignment explanation
Indices: 488787--488825 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
488777 TAATAGAATA
* *
488787 AAAACTGATTCTATCTAATT
1 AAAACTAATCCTATCTAATT
488807 AAAACTAATCCTATCTAAT
1 AAAACTAATCCTATCTAAT
488826 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.36
Consensus pattern (20 bp):
AAAACTAATCCTATCTAATT
Found at i:488818 original size:52 final size:52
Alignment explanation
Indices: 488677--488826 Score: 248
Period size: 52 Copynumber: 2.9 Consensus size: 52
488667 AATTAGCAAC
* *
488677 AGAATAAAAA-TAATTCTATCTAATTAAAAATGATTCTATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
488728 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
* *
488781 AGAATAAAAACTGATTCTATCTAATTAAAACTAATCCTATCTAATA
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
488827 TTTAATTTAG
Statistics
Matches: 93, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
51 5 0.05
52 44 0.47
53 44 0.47
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:491437 original size:137 final size:137
Alignment explanation
Indices: 491191--491465 Score: 523
Period size: 137 Copynumber: 2.0 Consensus size: 137
491181 TGTGGGAGTA
491191 AAGCATTCACCAAACAGAAATAACCTGTGATCATTTTATGCAAGTGGCCAACTGCATTACAGTTG
1 AAGCATTCACCAAACAGAAATAACCTGTGATCATTTTATGCAAGTGGCCAACTGCATTACAGTTG
491256 CTTGACTTTTGAGAATATGTTTCCTTGCTAAATTTCCATCTCTTTACCATCATCCTTGCCCTTTG
66 CTTGACTTTTGAGAATATGTTTCCTTGCTAAATTTCCATCTCTTTACCATCATCCTTGCCCTTTG
491321 ATGTAGC
131 ATGTAGC
* *
491328 AAGCATTCACCAAACAGAAATAACCTGTGATCATTTTATGCTAGTGGCCAACTGCATTACTGTTG
1 AAGCATTCACCAAACAGAAATAACCTGTGATCATTTTATGCAAGTGGCCAACTGCATTACAGTTG
*
491393 CTTGACTTTTGAGAATATGTTTCCTTGCTAAATTTCCATCTCTTTACCATCATGCTTGCCCTTTG
66 CTTGACTTTTGAGAATATGTTTCCTTGCTAAATTTCCATCTCTTTACCATCATCCTTGCCCTTTG
491458 ATGTAGC
131 ATGTAGC
491465 A
1 A
491466 TTTAGCTATC
Statistics
Matches: 135, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
137 135 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.36
Consensus pattern (137 bp):
AAGCATTCACCAAACAGAAATAACCTGTGATCATTTTATGCAAGTGGCCAACTGCATTACAGTTG
CTTGACTTTTGAGAATATGTTTCCTTGCTAAATTTCCATCTCTTTACCATCATCCTTGCCCTTTG
ATGTAGC
Found at i:504861 original size:27 final size:27
Alignment explanation
Indices: 504823--504877 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
504813 AAATTTTAAT
* *
504823 ACTCTATTCTAAAATATTTTGGTATGC
1 ACTCTATTCTAAAAAATTTAGGTATGC
504850 ACTCTATTCTAAAAAATTTAGGTATGC
1 ACTCTATTCTAAAAAATTTAGGTATGC
504877 A
1 A
504878 ACTTTTCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (27 bp):
ACTCTATTCTAAAAAATTTAGGTATGC
Found at i:509288 original size:59 final size:59
Alignment explanation
Indices: 509188--509315 Score: 166
Period size: 59 Copynumber: 2.2 Consensus size: 59
509178 GTAGTGCTAA
* * * * * **
509188 CCCGAGTATGACACATAAGGTCGTGTCTACCATCTGTACTAGGTATCCTTAAGTATAGT
1 CCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTATAGT
* * *
509247 CCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTTAGTGTATT
1 CCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTATAGT
509306 CCCGAATATG
1 CCCGAATATG
509316 CAGCCTGCTG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (59 bp):
CCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTATAGT
Found at i:510149 original size:14 final size:14
Alignment explanation
Indices: 510126--510169 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
510116 CCTCTCTTTT
510126 TTAT-TTATTTATA
1 TTATATTATTTATA
*
510139 TTATATTATTTTTA
1 TTATATTATTTATA
510153 TTATATATATCTTATA
1 TTATAT-TAT-TTATA
510169 T
1 T
510170 CATTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 4 0.15
14 14 0.54
15 3 0.12
16 5 0.19
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (14 bp):
TTATATTATTTATA
Found at i:510150 original size:25 final size:25
Alignment explanation
Indices: 510123--510189 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
510113 ATTCCTCTCT
*
510123 TTTTTATT-TATTTATATTATATTA
1 TTTTTATTATATATATATTATATTA
* *
510147 TTTTTATTATATATATCTTATATCA
1 TTTTTATTATATATATATTATATTA
*
510172 -TTATATATATATATATAT
1 TTTTTAT-TATATATATAT
510190 GTATGTATAG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 13 0.36
25 23 0.64
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTTTATTATATATATATTATATTA
Found at i:513706 original size:36 final size:35
Alignment explanation
Indices: 513663--513733 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
513653 CAATCAGAAT
*
513663 AAAAAGAGAAAAAAGAGA-AAAAAAGCAAAGAGAAAA
1 AAAAAGAGAAAAAAAAGAGAAAAAA-CAAAG-GAAAA
513699 AAAAAGAGAAAAAAAAGAGAAAAAACAAAGGAAAA
1 AAAAAGAGAAAAAAAAGAGAAAAAACAAAGGAAAA
513734 TTGAAGAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 5 0.15
36 22 0.67
37 6 0.18
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (35 bp):
AAAAAGAGAAAAAAAAGAGAAAAAACAAAGGAAAA
Found at i:513732 original size:12 final size:12
Alignment explanation
Indices: 513663--513733 Score: 78
Period size: 11 Copynumber: 6.0 Consensus size: 12
513653 CAATCAGAAT
513663 AAAAAGAG-AAA
1 AAAAAGAGAAAA
*
513674 AAAGAGA-AAAA
1 AAAAAGAGAAAA
513685 AAGCAAAGAGAAAA
1 AA--AAAGAGAAAA
513699 AAAAAGAG-AAA
1 AAAAAGAGAAAA
513710 AAAAAGAGAAAA
1 AAAAAGAGAAAA
513722 AACAAAG-GAAAA
1 AA-AAAGAGAAAA
513734 TTGAAGAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
11 22 0.42
12 16 0.31
13 8 0.15
14 6 0.12
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAAAA
Found at i:513749 original size:10 final size:10
Alignment explanation
Indices: 513663--513750 Score: 51
Period size: 9 Copynumber: 9.0 Consensus size: 10
513653 CAATCAGAAT
513663 AAAAAG-AGA
1 AAAAAGAAGA
513672 AAAAAG-AG-
1 AAAAAGAAGA
*
513680 AAAAA-AAGC
1 AAAAAGAAGA
* *
513689 AAAGAGAAAA
1 AAAAAGAAGA
513699 AAAAAG-AGA
1 AAAAAGAAGA
*
513708 AAAAAAAGAGA
1 AAAAAGA-AGA
*
513719 AAAAACAAAGGA
1 AAAAA-GAA-GA
**
513731 AAATTGAAGA
1 AAAAAGAAGA
513741 AAAAAGAAGA
1 AAAAAGAAGA
513751 CAATATGCAT
Statistics
Matches: 61, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
8 7 0.11
9 19 0.31
10 17 0.28
11 11 0.18
12 7 0.11
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.02
Consensus pattern (10 bp):
AAAAAGAAGA
Found at i:515441 original size:37 final size:37
Alignment explanation
Indices: 515389--515460 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
515379 AAAAAAGAAG
* *
515389 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAA
*
515426 ATTTTATCTCCCTTGAGACAGTTTCTCTTGAAACA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACA
515461 TAAACATTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (37 bp):
ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:515523 original size:36 final size:36
Alignment explanation
Indices: 515476--515699 Score: 198
Period size: 36 Copynumber: 6.4 Consensus size: 36
515466 ATTGAAAACA
* *
515476 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCCTTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
515512 TTTCCTTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCTTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * *
515548 TTTCCCTTGAAACAAA-----T-TAT-TTGA-ATATG
1 TTTCCTTTGAAACAAATTTCGTCTCTCTTGAGACA-G
** * * *
515577 TTTTATTTGAAAAAAATTTCATCTCCCTTGAGACAG
1 TTTCCTTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * * * *
515613 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAAACAG
1 TTTCCTTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
515650 TTT-CTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCCT-TTGAAACAAATTTCGTCTCTCTTGAGACAG
515686 TTT-CTCTTGAAACA
1 TTTCCT-TTGAAACA
515700 CAAAATCTTC
Statistics
Matches: 150, Mismatches: 27, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
28 2 0.01
29 17 0.11
30 2 0.01
31 1 0.01
34 1 0.01
35 1 0.01
36 97 0.65
37 29 0.19
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCCTTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:515587 original size:101 final size:101
Alignment explanation
Indices: 515389--515667 Score: 326
Period size: 101 Copynumber: 2.8 Consensus size: 101
515379 AAAAAAGAAG
* * * * * *
515389 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCTCT
1 ATTTCATCTCCCTTGAGACAGTTTCCTTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCT
** * *
515454 TGAAACATAAACATTGAAAACATTTCCCTTGAAATAA
66 TGAAACA-AATTATTGAAAACATTTCACTTGAAAAAA
* * *
515491 ATTTCGTCTCTCTTGAGACAGTTTCCTTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCT
1 ATTTCATCTCCCTTGAGACAGTTTCCTTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCT
* ** * *
515555 TGAAACAAATTATTTGAATATGTTTTATTTGAAAAAA
66 TGAAACAAATTA-TTGAAAACATTTCACTTGAAAAAA
* * * * *
515592 ATTTCATCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAAACAGTTTCTCT
1 ATTTCATCTCCCTTGAGACAGTTTCCTTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCT
515657 TGAAACAAATT
66 TGAAACAAATT
515668 TCGTCTCTCT
Statistics
Matches: 151, Mismatches: 24, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
100 3 0.02
101 81 0.54
102 67 0.44
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (101 bp):
ATTTCATCTCCCTTGAGACAGTTTCCTTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCT
TGAAACAAATTATTGAAAACATTTCACTTGAAAAAA
Found at i:516426 original size:22 final size:23
Alignment explanation
Indices: 516363--516428 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 23
516353 ACGAAGGAGC
*
516363 CATCCGCGATTTCAACTCCACGA
1 CATCCACGATTTCAACTCCACGA
* * *
516386 CA--GACGATATCGTAC-CCAC-A
1 CATCCACGATTTC-AACTCCACGA
516406 CATCCACGATTTCAACTCCACGA
1 CATCCACGATTTCAACTCCACGA
516429 TGGAGGATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 10
0.65 0.15 0.21
Matches are distributed among these distances:
20 3 0.10
21 12 0.39
22 13 0.42
23 3 0.10
ACGTcount: A:0.30, C:0.38, G:0.12, T:0.20
Consensus pattern (23 bp):
CATCCACGATTTCAACTCCACGA
Found at i:516685 original size:111 final size:111
Alignment explanation
Indices: 516491--516690 Score: 321
Period size: 111 Copynumber: 1.8 Consensus size: 111
516481 GTTTCAGAGC
* *
516491 CAATTTCAACTTCACATCGAGGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAG
*
516556 GGGCGACTGGTTGTCAACAAACAACTTTTTCAGTTTCATTCAAAGT
66 GGGCGACTGGCTGTCAACAAACAACTTTTTCAGTTTCATTCAAAGT
** *
516602 CAATTTCAACTTCACAGCGAAGGATATT-GAACTTGAGACAACACAAGCTCAACTTCACAGCGAA
1 CAATTTCAACTTCACAGCGAAGGATATTAG-ACTCAAGACAACACAAGCTCAACTTCACAACGAA
*
516666 GGGGCGGCTGGCTGTCAACAAACAA
65 GGGGCGACTGGCTGTCAACAAACAA
516691 TTTACCAGTT
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
110 1 0.01
111 80 0.99
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (111 bp):
CAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAG
GGGCGACTGGCTGTCAACAAACAACTTTTTCAGTTTCATTCAAAGT
Found at i:518126 original size:25 final size:25
Alignment explanation
Indices: 518098--518168 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 25
518088 TATATTCCTC
* *
518098 TTTTTTTTATATTTATATTATATTA
1 TTTTTATTATATATATATTATATTA
* *
518123 TTTTTATTATATATATCTTATATCA
1 TTTTTATTATATATATATTATATTA
*
518148 -TTATA-TATATATATATGTATA
1 TTTTTATTATATATATAT-TATA
518169 GATGTATTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
23 10 0.26
24 8 0.21
25 21 0.54
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (25 bp):
TTTTTATTATATATATATTATATTA
Found at i:518130 original size:14 final size:14
Alignment explanation
Indices: 518107--518145 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
518097 CTTTTTTTTA
518107 TATTTATATTATAT
1 TATTTATATTATAT
*
518121 TATTTTTATTATAT
1 TATTTATATTATAT
518135 ATATCTTATAT
1 -TAT-TTATAT
518146 CATTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 13 0.62
15 3 0.14
16 5 0.24
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTTATATTATAT
Found at i:518242 original size:38 final size:36
Alignment explanation
Indices: 518200--518313 Score: 115
Period size: 38 Copynumber: 3.0 Consensus size: 36
518190 TTGCTATGTA
*
518200 TATATATTTTTTCTTAATATTATATTTTATACGTTT-TT
1 TATATATATTTTCTTAATATTATATTTT-TA--TTTATT
*
518238 TATATATATTTTCTTAATATTTTATTTTTATTTATT
1 TATATATATTTTCTTAATATTATATTTTTATTTATT
* *
518274 TATATATATATAT-ATATATATATATATTTTTACTTTATT
1 TATATATAT-TTTCTTA-ATAT-TATATTTTTA-TTTATT
518313 T
1 T
518314 TATTTTTTCT
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
35 3 0.05
36 13 0.20
37 8 0.12
38 35 0.53
39 7 0.11
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.65
Consensus pattern (36 bp):
TATATATATTTTCTTAATATTATATTTTTATTTATT
Found at i:518281 original size:2 final size:2
Alignment explanation
Indices: 518274--518300 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
518264 TTTATTTATT
518274 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
518301 TTTTACTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:533354 original size:21 final size:21
Alignment explanation
Indices: 533328--533367 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
533318 TAAAATGTGT
*
533328 ATCGATGCACTGCTACAGTGC
1 ATCGATGCACTACTACAGTGC
533349 ATCGATGCACTACTACAGT
1 ATCGATGCACTACTACAGT
533368 AATTTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (21 bp):
ATCGATGCACTACTACAGTGC
Found at i:534033 original size:59 final size:59
Alignment explanation
Indices: 533907--534034 Score: 148
Period size: 59 Copynumber: 2.2 Consensus size: 59
533897 GTAGTGCTAA
* * * * ** *
533907 CCCGAGTATGACACATAAGGTCGTGTCTACCATCTGTACTAGGTATCCTTAAGTACAAT
1 CCCGAATATGACACATAAGGTCGTGCCCACCATATACAATAGGTATCCTTAAGTACAAT
* * ** *
533966 CCCAAATATGACACATAAGGTCGTGCCCACCATATACAATAGGTATCCTTTAGTGTATT
1 CCCGAATATGACACATAAGGTCGTGCCCACCATATACAATAGGTATCCTTAAGTACAAT
534025 CCCGAATATG
1 CCCGAATATG
534035 CAGCCTGCTG
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (59 bp):
CCCGAATATGACACATAAGGTCGTGCCCACCATATACAATAGGTATCCTTAAGTACAAT
Found at i:536745 original size:15 final size:14
Alignment explanation
Indices: 536674--536749 Score: 57
Period size: 14 Copynumber: 5.2 Consensus size: 14
536664 CTTCTTGTCT
*
536674 TTTTTATTTCTTT-C
1 TTTTT-TTTATTTGC
*
536688 TTTTCTTTTCTTTG-
1 TTTT-TTTTATTTGC
*
536702 TTTTTTTCTCTTTGC
1 TTTTTTT-TATTTGC
*
536717 TTCTTTTTTCTTTGC
1 TT-TTTTTTATTTGC
536732 TTTTTCTTTATTTGC
1 TTTTT-TTTATTTGC
536747 TTT
1 TTT
536750 GATTTGATCT
Statistics
Matches: 55, Mismatches: 1, Indels: 11
0.82 0.01 0.16
Matches are distributed among these distances:
13 3 0.05
14 24 0.44
15 23 0.42
16 5 0.09
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (14 bp):
TTTTTTTTATTTGC
Found at i:549486 original size:76 final size:76
Alignment explanation
Indices: 549360--549513 Score: 308
Period size: 76 Copynumber: 2.0 Consensus size: 76
549350 CATGCATGCA
549360 TGCACGCATACGTAAATAGCATTTTCTTGAAACTTGAAAGAAATTTGGCAAGTATAGTGAAATAA
1 TGCACGCATACGTAAATAGCATTTTCTTGAAACTTGAAAGAAATTTGGCAAGTATAGTGAAATAA
549425 ATCACCGAAGC
66 ATCACCGAAGC
549436 TGCACGCATACGTAAATAGCATTTTCTTGAAACTTGAAAGAAATTTGGCAAGTATAGTGAAATAA
1 TGCACGCATACGTAAATAGCATTTTCTTGAAACTTGAAAGAAATTTGGCAAGTATAGTGAAATAA
549501 ATCACCGAAGC
66 ATCACCGAAGC
549512 TG
1 TG
549514 TGATCGCCAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.27
Consensus pattern (76 bp):
TGCACGCATACGTAAATAGCATTTTCTTGAAACTTGAAAGAAATTTGGCAAGTATAGTGAAATAA
ATCACCGAAGC
Found at i:550176 original size:84 final size:84
Alignment explanation
Indices: 550075--550243 Score: 329
Period size: 84 Copynumber: 2.0 Consensus size: 84
550065 CGCATGGAAA
*
550075 TGCACAAACCCTAGCAACTAAAACCATTCAAAACATGAAATTAGTATCAATTACATATATTGATA
1 TGCACAAACCCTAGCAACTAAAACCATTCAAAACATGAAATTAGTATCAACTACATATATTGATA
550140 CCTCTGCAAACAATAAGGC
66 CCTCTGCAAACAATAAGGC
550159 TGCACAAACCCTAGCAACTAAAACCATTCAAAACATGAAATTAGTATCAACTACATATATTGATA
1 TGCACAAACCCTAGCAACTAAAACCATTCAAAACATGAAATTAGTATCAACTACATATATTGATA
550224 CCTCTGCAAACAATAAGGC
66 CCTCTGCAAACAATAAGGC
550243 T
1 T
550244 ACATTGCGGC
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.44, C:0.23, G:0.09, T:0.24
Consensus pattern (84 bp):
TGCACAAACCCTAGCAACTAAAACCATTCAAAACATGAAATTAGTATCAACTACATATATTGATA
CCTCTGCAAACAATAAGGC
Found at i:550369 original size:43 final size:41
Alignment explanation
Indices: 550322--550403 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 41
550312 AAGAACAACT
550322 CTATTACGACGTTTGTTGAAAAAAAC-ACCACTATAGATGAACC
1 CTATTACGACGTTTGTT--AAAAAACGA-CACTATAGATGAACC
* ** *
550365 CTATTGCGGTGTTTGTTAAAAAACGATACTATAGATGAA
1 CTATTACGACGTTTGTTAAAAAACGACACTATAGATGAA
550404 TTCTATTGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
41 19 0.56
42 1 0.03
43 14 0.41
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (41 bp):
CTATTACGACGTTTGTTAAAAAACGACACTATAGATGAACC
Found at i:571559 original size:16 final size:16
Alignment explanation
Indices: 571540--571574 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
571530 CAAAAAAAAC
571540 AAAATAAATAAAGAATA
1 AAAAT-AATAAAGAATA
*
571557 AAAATAATAAATAATA
1 AAAATAATAAAGAATA
571573 AA
1 AA
571575 GAAATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (16 bp):
AAAATAATAAAGAATA
Found at i:571569 original size:13 final size:13
Alignment explanation
Indices: 571542--571590 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
571532 AAAAAAACAA
571542 AATAAATAAAGAAT
1 AATAAATAAA-AAT
571556 AA-AAATAATAAAT
1 AATAAATAA-AAAT
* *
571569 AATAAAGAAATAT
1 AATAAATAAAAAT
571582 AATAAATAA
1 AATAAATAA
571591 TATACTATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 22 0.73
14 8 0.27
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (13 bp):
AATAAATAAAAAT
Found at i:571572 original size:23 final size:20
Alignment explanation
Indices: 571542--571592 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
571532 AAAAAAACAA
*
571542 AATAAATAA-AGAATAAAAAT
1 AATAAATAATA-AAGAAAAAT
*
571562 AATAAATAATAAAGAAATAT
1 AATAAATAATAAAGAAAAAT
571582 AATAAATAATA
1 AATAAATAATA
571593 TACTATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (20 bp):
AATAAATAATAAAGAAAAAT
Found at i:571591 original size:7 final size:7
Alignment explanation
Indices: 571542--571592 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
571532 AAAAAAACAA
571542 AATAAAT
1 AATAAAT
571549 AA-AGAAT
1 AATA-AAT
571556 AA-AAAT
1 AATAAAT
571562 AATAAAT
1 AATAAAT
*
571569 AATAAAG
1 AATAAAT
*
571576 AA-ATAT
1 AATAAAT
571582 AATAAAT
1 AATAAAT
571589 AATA
1 AATA
571593 TACTATAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
6 10 0.27
7 27 0.73
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (7 bp):
AATAAAT
Found at i:571600 original size:10 final size:10
Alignment explanation
Indices: 571587--571622 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
571577 AATATAATAA
571587 ATAATATACT
1 ATAATATACT
571597 ATAATATA--
1 ATAATATACT
571605 ATAATATACT
1 ATAATATACT
571615 ATAATATA
1 ATAATATA
571623 TAATATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.33
10 16 0.67
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (10 bp):
ATAATATACT
Found at i:571609 original size:18 final size:18
Alignment explanation
Indices: 571579--571629 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
571569 AATAAAGAAA
571579 TATAATA-AATAATATAC
1 TATAATATAATAATATAC
571596 TATAATATAATAATATAC
1 TATAATATAATAATATAC
571614 TATAATAT-ATAATATA
1 TATAATATAATAATATA
571630 AATATTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 15 0.45
18 18 0.55
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (18 bp):
TATAATATAATAATATAC
Found at i:571633 original size:13 final size:13
Alignment explanation
Indices: 571563--571634 Score: 55
Period size: 13 Copynumber: 5.6 Consensus size: 13
571553 AATAAAAATA
571563 ATAAATA-ATAA-
1 ATAAATATATAAT
*
571574 AGAAATATAATAA-
1 ATAAATAT-ATAAT
571587 ATAATATACTATAAT
1 ATAA-ATA-TATAAT
*
571602 AT-AATAATATACT
1 ATAAAT-ATATAAT
571615 AT-AATATATAAT
1 ATAAATATATAAT
571627 ATAAATAT
1 ATAAATAT
571635 TTTTATATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
11 6 0.12
12 8 0.16
13 24 0.48
14 9 0.18
15 3 0.06
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (13 bp):
ATAAATATATAAT
Found at i:571906 original size:11 final size:11
Alignment explanation
Indices: 571892--571929 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
571882 TTTCAAAAAC
571892 TATATATTATA
1 TATATATTATA
* *
571903 TATATGTTTTA
1 TATATATTATA
571914 TATATATTATA
1 TATATATTATA
571925 TATAT
1 TATAT
571930 TAAATAGAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
TATATATTATA
Found at i:571912 original size:39 final size:37
Alignment explanation
Indices: 571638--571907 Score: 407
Period size: 39 Copynumber: 7.1 Consensus size: 37
571628 TAAATATTTT
571638 TATATTTTCAAAATGTTTTCAAAAACTATATATTAT-
1 TATATTTTCAAAATGTTTTCAAAAACTATATATTATA
*
571674 TATATTTTCAAAATGTTTCCAAAAACTATATATTATA
1 TATATTTTCAAAATGTTTTCAAAAACTATATATTATA
*
571711 TATATTTTCAAAAATATTTTCAAAAACTATATATTATA
1 TATATTTTC-AAAATGTTTTCAAAAACTATATATTATA
* *
571749 TATATTTTCAAAATATTTTTAAAAACTATATATTATA
1 TATATTTTCAAAATGTTTTCAAAAACTATATATTATA
571786 TATAGGTTTTCAAAATGTTTTCAAAAACTATATATTATA
1 TATA--TTTTCAAAATGTTTTCAAAAACTATATATTATA
* *
571825 TATATTTTTTCAAAATATTTTTAAAAACTATATATTATA
1 TATA--TTTTCAAAATGTTTTCAAAAACTATATATTATA
*
571864 TATATGTTTTCAAAACGTTTTCAAAAACTATATATTATA
1 TATA--TTTTCAAAATGTTTTCAAAAACTATATATTATA
571903 TATAT
1 TATAT
571908 GTTTTATATA
Statistics
Matches: 216, Mismatches: 14, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
36 35 0.16
37 41 0.19
38 35 0.16
39 105 0.49
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (37 bp):
TATATTTTCAAAATGTTTTCAAAAACTATATATTATA
Found at i:573472 original size:13 final size:15
Alignment explanation
Indices: 573454--573486 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
573444 ACCCACCTTA
573454 TTTTTCTTTT-TCT-
1 TTTTTCTTTTCTCTC
573467 TTTTTCTTTTCTCTC
1 TTTTTCTTTTCTCTC
573482 TTTTT
1 TTTTT
573487 TTCCAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 3 0.17
15 5 0.28
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTCTTTTCTCTC
Found at i:584133 original size:5 final size:5
Alignment explanation
Indices: 584112--584152 Score: 57
Period size: 5 Copynumber: 8.0 Consensus size: 5
584102 AAATATTTAC
584112 TAAAA TTAAAA TAAAAA TAAAA T-AAA TAAAA TAAAA TAAAA
1 TAAAA -TAAAA T-AAAA TAAAA TAAAA TAAAA TAAAA TAAAA
584153 AATATAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.12
5 19 0.58
6 10 0.30
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:584140 original size:9 final size:10
Alignment explanation
Indices: 584112--584152 Score: 57
Period size: 9 Copynumber: 4.0 Consensus size: 10
584102 AAATATTTAC
584112 TAAAATTAAAA
1 TAAAA-TAAAA
584123 TAAAAATAAAA
1 T-AAAATAAAA
584134 T-AAATAAAA
1 TAAAATAAAA
584143 TAAAATAAAA
1 TAAAATAAAA
584153 AATATAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 9 0.32
10 8 0.29
11 7 0.25
12 4 0.14
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (10 bp):
TAAAATAAAA
Found at i:584144 original size:14 final size:15
Alignment explanation
Indices: 584120--584151 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
584110 ACTAAAATTA
584120 AAATAAAAATAAAAT
1 AAATAAAAATAAAAT
584135 AAAT-AAAATAAAAT
1 AAATAAAAATAAAAT
584149 AAA
1 AAA
584152 AAATATAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AAATAAAAATAAAAT
Found at i:584159 original size:14 final size:13
Alignment explanation
Indices: 584124--584159 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
584114 AAATTAAAAT
584124 AAAAATAAAATAA
1 AAAAATAAAATAA
584137 ATAAAATAAAATAA
1 A-AAAATAAAATAA
584151 AAAATATAA
1 AAAA-ATAA
584160 GAACCCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAAATAAAATAA
Found at i:584202 original size:9 final size:9
Alignment explanation
Indices: 584190--584227 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
584180 TTAAAAAAGG
584190 AAAAA-AAA
1 AAAAATAAA
*
584198 TAAAATAAA
1 AAAAATAAA
584207 AAAGAATAAA
1 AAA-AATAAA
584217 AAAAATAAA
1 AAAAATAAA
584226 AA
1 AA
584228 TGATCATGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 4 0.15
9 13 0.50
10 9 0.35
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.11
Consensus pattern (9 bp):
AAAAATAAA
Found at i:584206 original size:22 final size:23
Alignment explanation
Indices: 584176--584226 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
584166 AAAAAGTAGC
*
584176 TAAATTAAAAAAG-GAAAAAAAA
1 TAAAATAAAAAAGAGAAAAAAAA
*
584198 TAAAATAAAAAAGAATAAAAAAAA
1 TAAAATAAAAAAG-AGAAAAAAAA
584222 TAAAA
1 TAAAA
584227 ATGATCATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 12 0.48
24 13 0.52
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (23 bp):
TAAAATAAAAAAGAGAAAAAAAA
Found at i:585247 original size:16 final size:17
Alignment explanation
Indices: 585221--585256 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
585211 AAAAAGAAAG
585221 AAAAATAAATAAAGAAT
1 AAAAATAAATAAAGAAT
*
585238 AAAAAT-AATAAATAAT
1 AAAAATAAATAAAGAAT
585254 AAA
1 AAA
585257 CCAATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (17 bp):
AAAAATAAATAAAGAAT
Found at i:585253 original size:7 final size:7
Alignment explanation
Indices: 585224--585288 Score: 50
Period size: 7 Copynumber: 9.6 Consensus size: 7
585214 AAGAAAGAAA
585224 AATAAAT
1 AATAAAT
585231 AA-AGAAT
1 AATA-AAT
585238 AA-AAAT
1 AATAAAT
585244 AATAAAT
1 AATAAAT
*
585251 AATAAACC
1 AATAAA-T
585259 AAT--AT
1 AATAAAT
585264 AATAAAT
1 AATAAAT
*
585271 AATATAT
1 AATAAAT
585278 -ATAATAT
1 AATAA-AT
585285 AATA
1 AATA
585289 TTATACTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
5 3 0.06
6 10 0.21
7 28 0.60
8 6 0.13
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.28
Consensus pattern (7 bp):
AATAAAT
Found at i:585298 original size:18 final size:17
Alignment explanation
Indices: 585260--585310 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
585250 TAATAAACCA
585260 ATATAATA-AATAATAT
1 ATATAATATAATAATAT
*
585276 ATATAATATAATATTAT
1 ATATAATATAATAATAT
585293 ACTATAATAT-ATAATAT
1 A-TATAATATAATAATAT
585310 A
1 A
585311 ACTATTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 8 0.26
17 15 0.48
18 8 0.26
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATATAATAATAT
Found at i:585307 original size:7 final size:7
Alignment explanation
Indices: 585260--585310 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
585250 TAATAAACCA
585260 ATATAAT
1 ATATAAT
*
585267 AAATAAT
1 ATATAAT
585274 ATAT-AT
1 ATATAAT
585280 AATATAAT
1 -ATATAAT
585288 AT-T-AT
1 ATATAAT
585293 ACTATAAT
1 A-TATAAT
585301 ATATAAT
1 ATATAAT
585308 ATA
1 ATA
585311 ACTATTTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
5 3 0.08
6 4 0.11
7 25 0.68
8 5 0.14
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (7 bp):
ATATAAT
Found at i:585334 original size:24 final size:24
Alignment explanation
Indices: 585302--585347 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
585292 TACTATAATA
585302 TATAATATA-ACTATTTTCAAAAAC
1 TATAATATATA-TATTTTCAAAAAC
585326 TATAATATATATATTTTCAAAA
1 TATAATATATATATTTTCAAAA
585348 TGTTTTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (24 bp):
TATAATATATATATTTTCAAAAAC
Found at i:585647 original size:39 final size:37
Alignment explanation
Indices: 585315--585642 Score: 480
Period size: 37 Copynumber: 8.7 Consensus size: 37
585305 AATATAACTA
585315 TTTTCAAAAACTATA-A-TATATATATTTTCAAAATG
1 TTTTCAAAAACTATATATTATATATATTTTCAAAATG
*
585350 TTTTCAAAAACTATATATTATATATATTTACAAAATG
1 TTTTCAAAAACTATATATTATATATATTTTCAAAATG
* *
585387 TTTCCAAAAACTATATATTATATATATTTTTCAAAAGG
1 TTTTCAAAAACTATATATTATATATA-TTTTCAAAATG
* *
585425 TTTCCAAAAACTATATATTATATATATTTTCAAAAGG
1 TTTTCAAAAACTATATATTATATATATTTTCAAAATG
*
585462 TTTTCAAAAACTATATATTATATATATTTTCAAAATA
1 TTTTCAAAAACTATATATTATATATATTTTCAAAATG
* * *
585499 TTTTCGAAAACTATATATTATATATAGGTTTACTAAATG
1 TTTTCAAAAACTATATATTATATATA--TTTTCAAAATG
*
585538 TTTTCAAAAACTATATATTATATACATGTTTTCAAAATG
1 TTTTCAAAAACTATATATTATAT--ATATTTTCAAAATG
*
585577 TTTTCAAAAACTATATATTATATATATGTTTTCAAAACG
1 TTTTCAAAAACTATATATTATATATA--TTTTCAAAATG
585616 TTTTCAAAAACTATATATTATATATAT
1 TTTTCAAAAACTATATATTATATATAT
585643 GTTTTATATA
Statistics
Matches: 267, Mismatches: 17, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
35 15 0.06
36 1 0.00
37 116 0.43
38 35 0.13
39 98 0.37
41 2 0.01
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (37 bp):
TTTTCAAAAACTATATATTATATATATTTTCAAAATG
Found at i:589804 original size:13 final size:13
Alignment explanation
Indices: 589786--589812 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
589776 CCTTTATAGC
589786 TTTTTGGCTCACG
1 TTTTTGGCTCACG
589799 TTTTTGGCTCACG
1 TTTTTGGCTCACG
589812 T
1 T
589813 GCTCGATGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.22, G:0.22, T:0.48
Consensus pattern (13 bp):
TTTTTGGCTCACG
Found at i:591779 original size:16 final size:16
Alignment explanation
Indices: 591754--591838 Score: 55
Period size: 16 Copynumber: 4.9 Consensus size: 16
591744 TACTATAATA
591754 AAAAT-AAAAATAAAT
1 AAAATAAAAAATAAAT
591769 AAAATAAAAAATATAAT
1 AAAATAAAAAATA-AAT
*** *
591786 AACCCAAAAAGTAGTTAATT
1 AAAATAAAAA--A--TAAAT
*
591806 AAAAAAAGAAAAATAAAT
1 -AAAATA-AAAAATAAAT
591824 AAAATAAAAAATAAA
1 AAAATAAAAAATAAA
591839 AACGATTATG
Statistics
Matches: 53, Mismatches: 9, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
15 5 0.09
16 16 0.30
17 15 0.28
18 4 0.08
19 1 0.02
20 3 0.06
21 5 0.09
22 4 0.08
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.19
Consensus pattern (16 bp):
AAAATAAAAAATAAAT
Found at i:593164 original size:16 final size:17
Alignment explanation
Indices: 593139--593173 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
593129 AAAAAGAAAG
593139 AAAATAAATAAAGAATA
1 AAAATAAATAAAGAATA
*
593156 AAAAT-AATAAATAATA
1 AAAATAAATAAAGAATA
593172 AA
1 AA
593174 CCAATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (17 bp):
AAAATAAATAAAGAATA
Found at i:593599 original size:39 final size:37
Alignment explanation
Indices: 593232--593594 Score: 502
Period size: 37 Copynumber: 9.7 Consensus size: 37
593222 AATATAACTA
593232 TTTTCAAAAACTATA-A-TATATAT-TTTT--AAATG
1 TTTTCAAAAACTATATATTATATATATTTTCAAAATG
*
593264 TTTTCAAAAACTATATATTATATATATTTTCAAAAGG
1 TTTTCAAAAACTATATATTATATATATTTTCAAAATG
*
593301 TTTTCAAAAACTATATATTATATATATTTTCAAAAGG
1 TTTTCAAAAACTATATATTATATATATTTTCAAAATG
*
593338 TTTTCAAAAACTATATATTATATATATTTTCAAAAGG
1 TTTTCAAAAACTATATATTATATATATTTTCAAAATG
* *
593375 TTTTCAAAAACTACATATTATATATATTTTCAAAATA
1 TTTTCAAAAACTATATATTATATATATTTTCAAAATG
* *
593412 TTTTCAAAACCTATATATTATATATAGGTATTCAAAATG
1 TTTTCAAAAACTATATATTATATATA--TTTTCAAAATG
* *
593451 TTTTCAAAAACTATATATTATATATAGGTTTACTAAATG
1 TTTTCAAAAACTATATATTATATATA--TTTTCAAAATG
593490 TTTTCAAAAACTATATATTATATATATGTTTTCAAAATG
1 TTTTCAAAAACTATATATTATATATA--TTTTCAAAATG
* * * *
593529 TTTTCAAAAATTATATATTATACATCTGTTTTCAAAACG
1 TTTTCAAAAACTATATATTAT--ATATATTTTCAAAATG
593568 TTTTCAAAAACTATATATTATATATAT
1 TTTTCAAAAACTATATATTATATATAT
593595 GTTTTATATA
Statistics
Matches: 300, Mismatches: 22, Indels: 13
0.90 0.07 0.04
Matches are distributed among these distances:
32 15 0.05
33 1 0.00
34 7 0.02
35 4 0.01
37 140 0.47
39 130 0.43
41 3 0.01
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (37 bp):
TTTTCAAAAACTATATATTATATATATTTTCAAAATG
Found at i:594055 original size:19 final size:19
Alignment explanation
Indices: 594032--594072 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
594022 AATTTAATGT
*
594032 ATTTTTAAAAAATA-ATAA
1 ATTTTTTAAAAATATATAA
594050 ATTTTTTAAAAATATATAA
1 ATTTTTTAAAAATATATAA
594069 ATTT
1 ATTT
594073 GAAATATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTTTTAAAAATATATAA
Done.