Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 67 of 182
Found at i:21420936 original size:10 final size:10
Alignment explanation
Indices: 21420908--21420992 Score: 52
Period size: 10 Copynumber: 8.3 Consensus size: 10
21420898 TTTTTGTAGT
21420908 GAAGAAAATG
1 GAAGAAAATG
*
21420918 GAAAAAAAATG
1 G-AAGAAAATG
21420929 GAAGAAAATG
1 GAAGAAAATG
21420939 GAA-AATAACTTTG
1 GAAGAA-AA---TG
* * *
21420952 GCAG-CAGT-
1 GAAGAAAATG
21420960 GAAGAAAATG
1 GAAGAAAATG
21420970 AGAA-AAAATG
1 -GAAGAAAATG
21420980 GAAGAAAATG
1 GAAGAAAATG
21420990 GAA
1 GAA
21420993 AATAACTCTA
Statistics
Matches: 57, Mismatches: 8, Indels: 20
0.67 0.09 0.24
Matches are distributed among these distances:
8 3 0.05
9 8 0.14
10 29 0.51
11 12 0.21
12 1 0.02
13 4 0.07
ACGTcount: A:0.58, C:0.04, G:0.26, T:0.13
Consensus pattern (10 bp):
GAAGAAAATG
Found at i:21421457 original size:16 final size:16
Alignment explanation
Indices: 21421417--21421461 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
21421407 AGTTTAGGAT
*
21421417 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
21421434 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
21421448 TTAAAAATTTATTT
1 TTAAAAATTTATTT
21421462 CCATTCCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 10 0.40
17 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:21423487 original size:141 final size:141
Alignment explanation
Indices: 21423227--21423522 Score: 583
Period size: 141 Copynumber: 2.1 Consensus size: 141
21423217 TCAAGTAAGA
21423227 CTATTGTACTTTTCTTTATAAATAGAGACTGAAAGATTAGCAAATCACATACTTTATAGACATTG
1 CTATT-TACTTTTCTTTATAAATAGAGACTGAAAGATTAGCAAATCACATACTTTATAGACATTG
21423292 TGTGACACCCCAACGCCTGACCCGTTCCTTTAGATCCGGGTATGAAGTCTCACAGGTTGACCCGT
65 TGTGACACCCCAACGCCTGACCCGTTCCTTTAGATCCGGGTATGAAGTCTCACAGGTTGACCCGT
21423357 TCTAAGGTACGC
130 TCTAAGGTACGC
21423369 CTATTTACTTTTCTTTATAAATAGAGACTGAAAGATTAGCAAATCACATACTTTATAGACATTGT
1 CTATTTACTTTTCTTTATAAATAGAGACTGAAAGATTAGCAAATCACATACTTTATAGACATTGT
21423434 GTGACACCCCAACGCCTGACCCGTTCCTTTAGATCCGGGTATGAAGTCTCACAGGTTGACCCGTT
66 GTGACACCCCAACGCCTGACCCGTTCCTTTAGATCCGGGTATGAAGTCTCACAGGTTGACCCGTT
21423499 CTAAGGTACGC
131 CTAAGGTACGC
21423510 CTATTTACTTTTC
1 CTATTTACTTTTC
21423523 CTTACTAGAA
Statistics
Matches: 154, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
141 149 0.97
142 5 0.03
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (141 bp):
CTATTTACTTTTCTTTATAAATAGAGACTGAAAGATTAGCAAATCACATACTTTATAGACATTGT
GTGACACCCCAACGCCTGACCCGTTCCTTTAGATCCGGGTATGAAGTCTCACAGGTTGACCCGTT
CTAAGGTACGC
Found at i:21426944 original size:10 final size:10
Alignment explanation
Indices: 21426929--21426954 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
21426919 GCTATATTTG
21426929 ATTTATCCTC
1 ATTTATCCTC
21426939 ATTTATCCTC
1 ATTTATCCTC
21426949 ATTTAT
1 ATTTAT
21426955 TGTCCTGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (10 bp):
ATTTATCCTC
Found at i:21432839 original size:14 final size:15
Alignment explanation
Indices: 21432806--21432848 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
21432796 ATATTTTCTA
21432806 AAATT-ATATATAAT
1 AAATTAATATATAAT
21432820 -AATTAATA-ATAAT
1 AAATTAATATATAAT
21432833 AAATTAA-ATATAAT
1 AAATTAATATATAAT
21432847 AA
1 AA
21432849 TTTTTATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTAATATATAAT
Found at i:21435905 original size:27 final size:27
Alignment explanation
Indices: 21435849--21435929 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 27
21435839 CAACATCATT
** * *
21435849 TCGCAGCTTGCCACTTTGTCGAGACTTC
1 TCGCAGCTCACCAC-TTGTGGAGACATC
21435877 TCGCAGCTCACCACTTGTGGAGACATC
1 TCGCAGCTCACCACTTGTGGAGACATC
** *
21435904 TCATAGTTCACCACTTGTGGAGACAT
1 TCGCAGCTCACCACTTGTGGAGACAT
21435930 GTTGCACTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 34 0.74
28 12 0.26
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (27 bp):
TCGCAGCTCACCACTTGTGGAGACATC
Found at i:21435940 original size:27 final size:27
Alignment explanation
Indices: 21435884--21435943 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
21435874 TTCTCGCAGC
* *
21435884 TCACCACTTGTGGAGACATCTCATAGT
1 TCACCACTTGTGGAGACATCTCACACT
* **
21435911 TCACCACTTGTGGAGACATGTTGCACT
1 TCACCACTTGTGGAGACATCTCACACT
21435938 TCACCA
1 TCACCA
21435944 TGTGTTCAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.28
Consensus pattern (27 bp):
TCACCACTTGTGGAGACATCTCACACT
Found at i:21440978 original size:55 final size:55
Alignment explanation
Indices: 21440917--21441097 Score: 299
Period size: 55 Copynumber: 3.3 Consensus size: 55
21440907 TTATGATTTT
*
21440917 TTTATATGTTTAAATCGATTGTCATGTTGGAATATTACTTCTTTTGAATTGATTG
1 TTTATATGTTTAAATCGATTGTCATGTTGGAATATTGCTTCTTTTGAATTGATTG
* * * **
21440972 TTTATATGTTTAAATCGATTTTCATGTTTGAATATTGTTTCTTTTGAAACGATTG
1 TTTATATGTTTAAATCGATTGTCATGTTGGAATATTGCTTCTTTTGAATTGATTG
*
21441027 TTTATATGTTTAAATCGATTGTCATGTTGGAATACTGCTTCTTTTGAATTGATTG
1 TTTATATGTTTAAATCGATTGTCATGTTGGAATATTGCTTCTTTTGAATTGATTG
21441082 TTTATATGTTTAAATC
1 TTTATATGTTTAAATC
21441098 AAATGCTATA
Statistics
Matches: 114, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 114 1.00
ACGTcount: A:0.25, C:0.08, G:0.15, T:0.51
Consensus pattern (55 bp):
TTTATATGTTTAAATCGATTGTCATGTTGGAATATTGCTTCTTTTGAATTGATTG
Found at i:21442574 original size:82 final size:81
Alignment explanation
Indices: 21442474--21442665 Score: 226
Period size: 82 Copynumber: 2.4 Consensus size: 81
21442464 CCTGTATATG
* *
21442474 TTGCGGATTCTTGA-CAGCTTGTGTGAGCAGCATCGTGAGTGGATAGCATAGACCGTAG-CGATG
1 TTGCGGATTC-TCATCAGCTTGTGTGAGCAGCATCGTGAGTGGATAACATAGACCGT-GTCGATG
* **
21442537 GCTGAGTTTCTTGCATACA
64 ACTGAG-TTCCCGCATACA
* * * * * *
21442556 TTGCGGATTCTCATCAGCTTGTGTGAGCAGCATCGTGGGTGGGTAATATGGACGGTGTCGATGAT
1 TTGCGGATTCTCATCAGCTTGTGTGAGCAGCATCGTGAGTGGATAACATAGACCGTGTCGATGAC
*
21442621 TGAGTTCCCGTATACA
66 TGAGTTCCCGCATACA
*
21442637 TTACGGATTCTCATCAGCTTGTGTGAGCA
1 TTGCGGATTCTCATCAGCTTGTGTGAGCA
21442666 ATATCGTATA
Statistics
Matches: 95, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
81 40 0.42
82 55 0.58
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (81 bp):
TTGCGGATTCTCATCAGCTTGTGTGAGCAGCATCGTGAGTGGATAACATAGACCGTGTCGATGAC
TGAGTTCCCGCATACA
Found at i:21445133 original size:25 final size:24
Alignment explanation
Indices: 21445093--21445140 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
21445083 GTTTTGGGTA
21445093 CACACGGCTTGTGACACGGTCTGC
1 CACACGGCTTGTGACACGGTCTGC
*
21445117 CACACGGTTATGTGACACGGTCTG
1 CACACGGCT-TGTGACACGGTCTG
21445141 TAACACAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.19, C:0.29, G:0.29, T:0.23
Consensus pattern (24 bp):
CACACGGCTTGTGACACGGTCTGC
Found at i:21445146 original size:25 final size:24
Alignment explanation
Indices: 21445094--21445146 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
21445084 TTTTGGGTAC
*
21445094 ACACGGCTTGTGACACGGTCTGCC
1 ACACGGCTTGTGACACGGTCTGCA
* *
21445118 ACACGGTTATGTGACACGGTCTGTA
1 ACACGGCT-TGTGACACGGTCTGCA
21445143 ACAC
1 ACAC
21445147 AATCGTGTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.23
Consensus pattern (24 bp):
ACACGGCTTGTGACACGGTCTGCA
Found at i:21448060 original size:26 final size:26
Alignment explanation
Indices: 21447976--21448182 Score: 163
Period size: 26 Copynumber: 8.0 Consensus size: 26
21447966 TACGAGCCTA
* * *
21447976 TCAGAA-ATCGCTCATACGAGCTAAT
1 TCAGAATATCGCTCATTCGAGCCAGT
* *
21448001 TCAGAATATTGCTC-TTATGAGCCAGT
1 TCAGAATATCGCTCATT-CGAGCCAGT
*
21448027 T-AGAATATCGCTTATTCGAGCCAGT
1 TCAGAATATCGCTCATTCGAGCCAGT
* ** * *
21448052 TTAGAATATTTCTCATGCGAGCTAGT
1 TCAGAATATCGCTCATTCGAGCCAGT
* ** *
21448078 TCAGAATATCACTC-TTATAAGCCA-A
1 TCAGAATATCGCTCATT-CGAGCCAGT
*
21448103 TCAGAATATCGCTCATTCAAGCCAGT
1 TCAGAATATCGCTCATTCGAGCCAGT
* *
21448129 TCAAAATATCACTCATTACGAGCCAGT
1 TCAGAATATCGCTCATT-CGAGCCAGT
* *
21448156 TTAGAATATCGCTTATTTCGAGCCAGT
1 TCAGAATATCGCTCA-TTCGAGCCAGT
21448183 CTTCAAATGT
Statistics
Matches: 142, Mismatches: 31, Indels: 16
0.75 0.16 0.08
Matches are distributed among these distances:
25 46 0.32
26 66 0.46
27 28 0.20
28 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (26 bp):
TCAGAATATCGCTCATTCGAGCCAGT
Found at i:21448074 original size:77 final size:77
Alignment explanation
Indices: 21447986--21448165 Score: 207
Period size: 77 Copynumber: 2.3 Consensus size: 77
21447976 TCAGAAATCG
** * * * * *
21447986 CTCATACGAGCTAATTCAGAATATTGCTCTTATGAGCCAGTTAGAATATCGCTTATTCGAGCCAG
1 CTCATACGAGCTAATTCAGAATATCACTCTTATAAGCCAATCAGAATATCGCTCATTCAAGCCAG
21448051 TTTAGAATATTT
66 TTTAGAATATTT
* *
21448063 CTCATGCGAGCTAGTTCAGAATATCACTCTTATAAGCCAATCAGAATATCGCTCATTCAAGCCAG
1 CTCATACGAGCTAATTCAGAATATCACTCTTATAAGCCAATCAGAATATCGCTCATTCAAGCCAG
* * **
21448128 TTCAAAATATCA
66 TTTAGAATATTT
* * *
21448140 CTCATTACGAGCCAGTTTAGAATATC
1 CTCA-TACGAGCTAATTCAGAATATC
21448166 GCTTATTTCG
Statistics
Matches: 86, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
77 68 0.79
78 18 0.21
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (77 bp):
CTCATACGAGCTAATTCAGAATATCACTCTTATAAGCCAATCAGAATATCGCTCATTCAAGCCAG
TTTAGAATATTT
Found at i:21451508 original size:20 final size:20
Alignment explanation
Indices: 21451465--21451513 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
21451455 TTTCAGTTAG
*
21451465 AAATTAAATTAGTAAAATAT
1 AAATTAAATTAGTAAAATAA
*
21451485 AAATTAAATTAAGT-AATTAA
1 AAATTAAATT-AGTAAAATAA
21451505 AAATATAAA
1 AAAT-TAAA
21451514 AATGAAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (20 bp):
AAATTAAATTAGTAAAATAA
Found at i:21467890 original size:29 final size:29
Alignment explanation
Indices: 21467844--21467905 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
21467834 CTTATATTTT
*
21467844 TAAATTATAATGAAAAATATAAATAAAAA
1 TAAAATATAATGAAAAATATAAATAAAAA
* * *
21467873 TAAAATATAAT-AACAAATTTCAATGAAAA
1 TAAAATATAATGAA-AAATATAAATAAAAA
21467902 TAAA
1 TAAA
21467906 TTGAGTGCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (29 bp):
TAAAATATAATGAAAAATATAAATAAAAA
Found at i:21468162 original size:16 final size:16
Alignment explanation
Indices: 21468141--21468172 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21468131 AAGTTGAGAT
21468141 TTTTTTAATTTAGGCA
1 TTTTTTAATTTAGGCA
*
21468157 TTTTTTAGTTTAGGCA
1 TTTTTTAATTTAGGCA
21468173 CCTTCGGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.06, G:0.16, T:0.56
Consensus pattern (16 bp):
TTTTTTAATTTAGGCA
Found at i:21468940 original size:31 final size:31
Alignment explanation
Indices: 21468902--21468964 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
21468892 ATAAAAACTA
21468902 TTGTCATTCTTTGTAAGAAAAATACAATTTT
1 TTGTCATTCTTTGTAAGAAAAATACAATTTT
*
21468933 TTGTCATTCTTTGTAAGAAAAATTCAATTTT
1 TTGTCATTCTTTGTAAGAAAAATACAATTTT
21468964 T
1 T
21468965 CCAATCCTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (31 bp):
TTGTCATTCTTTGTAAGAAAAATACAATTTT
Found at i:21469442 original size:21 final size:21
Alignment explanation
Indices: 21469418--21469462 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
21469408 TATTGCTTGC
*
21469418 GAATTGTGATCTA-TATATTGT
1 GAATTGTGATC-AGCATATTGT
21469439 GAATTGTGATCAGCATATTGT
1 GAATTGTGATCAGCATATTGT
21469460 GAA
1 GAA
21469463 CTATGAACTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.40
Consensus pattern (21 bp):
GAATTGTGATCAGCATATTGT
Found at i:21473202 original size:15 final size:15
Alignment explanation
Indices: 21473184--21473223 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
21473174 ATATGTATCA
*
21473184 TGCTTTTATGTGAAT
1 TGCTTTTATGTGAAC
*
21473199 TGCTTTTATTTGAAC
1 TGCTTTTATGTGAAC
*
21473214 TGCTTATATG
1 TGCTTTTATG
21473224 CAAACTGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.17, T:0.53
Consensus pattern (15 bp):
TGCTTTTATGTGAAC
Found at i:21487300 original size:18 final size:18
Alignment explanation
Indices: 21487263--21487302 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
21487253 TATGGTTGTA
*
21487263 TGATTGCATCTGGTTCTG
1 TGATTGCATCTGGATCTG
21487281 TGATTGCATCT-GATCATG
1 TGATTGCATCTGGATC-TG
21487299 TGAT
1 TGAT
21487303 CGTATTTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.17, C:0.15, G:0.25, T:0.42
Consensus pattern (18 bp):
TGATTGCATCTGGATCTG
Found at i:21492485 original size:56 final size:55
Alignment explanation
Indices: 21492423--21492712 Score: 368
Period size: 56 Copynumber: 5.2 Consensus size: 55
21492413 GAGGATATTT
*
21492423 TGTAAAGGTTATATCCCTAAGAATATTATGAAAAGGGATGCTCGAAAGGATATCAA
1 TGTAAAGGTTATATCCCTAAGGATATTATGAAAAGGGATG-TCGAAAGGATATCAA
* **
21492479 TGTAAAGGTTATGTCTATAAGGATATTATGAAAAGGGATGTTCGAAAGGATATCAA
1 TGTAAAGGTTATATCCCTAAGGATATTATGAAAAGGGATG-TCGAAAGGATATCAA
* * *
21492535 TGTAAAGGTTAAATCCGTAAGGATATTA-CAGAAAGGGATGTCCGAAAGGATATCAA
1 TGTAAAGGTTATATCCCTAAGGATATTATGA-AAAGGGATGT-CGAAAGGATATCAA
* **
21492591 TATAAAGGTTATATCTGTAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
1 TGTAAAGGTTATATCCCTAAGGATATTATGAAAAGGGATGT-CGAAAGGATATCAA
* * * *
21492647 CGTAAAGGTTATA-CCCGTAAGGATAATATGAGAAGGGATGTCTAAAAGGATATCAA
1 TGTAAAGGTTATATCCC-TAAGGATATTATGAAAAGGGATGTC-GAAAGGATATCAA
*
21492703 TTTAAAGGTT
1 TGTAAAGGTT
21492713 TAAATATTTT
Statistics
Matches: 206, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
55 4 0.02
56 201 0.98
57 1 0.00
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (55 bp):
TGTAAAGGTTATATCCCTAAGGATATTATGAAAAGGGATGTCGAAAGGATATCAA
Found at i:21492527 original size:27 final size:27
Alignment explanation
Indices: 21492445--21492643 Score: 109
Period size: 28 Copynumber: 7.1 Consensus size: 27
21492435 ATCCCTAAGA
*
21492445 ATATTATGAAAAGGGATGCTCGAAAGG
1 ATATTATGAAAAGGGATGTTCGAAAGG
* * * *
21492472 ATATCAATGTAAAGGTTATG-TCTATAAGG
1 ATAT-TATGAAAAGG-GATGTTCGA-AAGG
21492501 ATATTATGAAAAGGGATGTTCGAAAGG
1 ATATTATGAAAAGGGATGTTCGAAAGG
* * * ** * *
21492528 ATATCAATGTAAAGGTTAAATCCGTAAGG
1 ATAT-TATGAAAAGG-GATGTTCGAAAGG
* *
21492557 ATATTA-CAGAAAGGGATGTCCGAAAGG
1 ATATTATGA-AAAGGGATGTTCGAAAGG
* * * *
21492584 ATATCAAT-ATAAAGGTTAT-ATCTGTAAGG
1 ATAT-TATGA-AAAGG-GATGTTC-GAAAGG
*
21492613 ATATTATGAAAAGGGATGTCCGAAAGG
1 ATATTATGAAAAGGGATGTTCGAAAGG
21492640 ATAT
1 ATAT
21492644 CAACGTAAAG
Statistics
Matches: 126, Mismatches: 33, Indels: 26
0.68 0.18 0.14
Matches are distributed among these distances:
27 39 0.31
28 52 0.41
29 35 0.28
ACGTcount: A:0.41, C:0.08, G:0.25, T:0.27
Consensus pattern (27 bp):
ATATTATGAAAAGGGATGTTCGAAAGG
Found at i:21492620 original size:112 final size:111
Alignment explanation
Indices: 21492423--21492712 Score: 411
Period size: 112 Copynumber: 2.6 Consensus size: 111
21492413 GAGGATATTT
* * *
21492423 TGTAAAGGTTATATCCCTAAGAATATTATGAAAAGGGATG-CTCGAAAGGATATCAATGTAAAGG
1 TGTAAAGGTTATATCCGTAAGGATATTATG-AAAGGGATGTC-CGAAAGGATATCAATATAAAGG
* *
21492487 TTATGTCTATAAGGATATTATGAAAAGGGATGTTCGAAAGGATATCAA
64 TTATATCTATAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
* *
21492535 TGTAAAGGTTAAATCCGTAAGGATATTACAGAAAGGGATGTCCGAAAGGATATCAATATAAAGGT
1 TGTAAAGGTTATATCCGTAAGGATATTA-TGAAAGGGATGTCCGAAAGGATATCAATATAAAGGT
*
21492600 TATATCTGTAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
65 TATATCTATAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
* * * ** *
21492647 CGTAAAGGTTATACCCGTAAGGATAATATGAGAAGGGATGTCTAAAAGGATATCAATTTAAAGGT
1 TGTAAAGGTTATATCCGTAAGGATATTATGA-AAGGGATGTCCGAAAGGATATCAATATAAAGGT
21492712 T
65 T
21492713 TAAATATTTT
Statistics
Matches: 159, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
111 2 0.01
112 155 0.97
113 2 0.01
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (111 bp):
TGTAAAGGTTATATCCGTAAGGATATTATGAAAGGGATGTCCGAAAGGATATCAATATAAAGGTT
ATATCTATAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
Found at i:21492670 original size:29 final size:29
Alignment explanation
Indices: 21492468--21492671 Score: 143
Period size: 29 Copynumber: 7.2 Consensus size: 29
21492458 GGATGCTCGA
* **
21492468 AAGGATATCAATGTAAAGGTTATGTCTAT
1 AAGGATATCAATGTAAAGGTTATATCCGT
* * * * * *
21492497 AAGGATAT-TATGAAAAGG-GATGTTCGA
1 AAGGATATCAATGTAAAGGTTATATCCGT
*
21492524 AAGGATATCAATGTAAAGGTTAAATCCGT
1 AAGGATATCAATGTAAAGGTTATATCCGT
* * * *
21492553 AAGGATATTACA-G-AAAGG-GATGTCCGA
1 AAGGATATCA-ATGTAAAGGTTATATCCGT
* *
21492580 AAGGATATCAATATAAAGGTTATATCTGT
1 AAGGATATCAATGTAAAGGTTATATCCGT
* * * * *
21492609 AAGGATAT-TATGAAAAGG-GATGTCCGA
1 AAGGATATCAATGTAAAGGTTATATCCGT
* *
21492636 AAGGATATCAACGTAAAGGTTATACCCGT
1 AAGGATATCAATGTAAAGGTTATATCCGT
21492665 AAGGATA
1 AAGGATA
21492672 ATATGAGAAG
Statistics
Matches: 128, Mismatches: 39, Indels: 16
0.70 0.21 0.09
Matches are distributed among these distances:
26 1 0.01
27 39 0.30
28 40 0.31
29 47 0.37
30 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (29 bp):
AAGGATATCAATGTAAAGGTTATATCCGT
Found at i:21499746 original size:56 final size:56
Alignment explanation
Indices: 21499675--21500140 Score: 356
Period size: 56 Copynumber: 8.2 Consensus size: 56
21499665 AAGAATACTT
*
21499675 TGTAAAGGTTATATCCATAAGGATATTATGAAAAGGGATGTCCGAAA-GATTATCAA
1 TGTAAAGGTTATATCCGTAAGGATATTATGAAAAGGGATGTCCGAAAGGA-TATCAA
*
21499731 TGTTAAGGTTATATCCGTAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
1 TGTAAAGGTTATATCCGTAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
* * * * *
21499787 TGTAAAGGTTATATACGTAAGGATATTATGAAAAGGGATGTTCGAAAGAACATTAA
1 TGTAAAGGTTATATCCGTAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
* * * **
21499843 CGTAAAGGTTATA-CCGGTAAGGATACTATGAGAAGGGATGTCTAAAAGGATATCAA
1 TGTAAAGGTTATATCC-GTAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
* ** * * * * ** * * * *
21499899 TGTAAAGGTTTAAATATTC-TAA-TTTCTTAAG-TATGAAAT-TCATGAATAAG-TTTCATT
1 TGTAAAGG-TT--ATATCCGTAAGGATATTATGAAAAGGGATGTC-CGAA-AGGATATCA-A
* * ** *
21499956 TTTCATACTCACGAACTTAT-TAAGCAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
1 TGT-A-A---A-G--GTTATATCCGTAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
* * * * *
21500019 TGTAAAGGTTATATACGTAAGGATATTATGAAAAGGGATGTTCGAAAGAACATTAA
1 TGTAAAGGTTATATCCGTAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
* * * **
21500075 CGTAAAGGTTATA-CCAGTAAGGATACTATGAGAAGGGATGTCTAAAAGGATATCAA
1 TGTAAAGGTTATATCC-GTAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
21500131 TGTAAAGGTT
1 TGTAAAGGTT
21500141 TAAATATTCT
Statistics
Matches: 317, Mismatches: 69, Indels: 48
0.73 0.16 0.11
Matches are distributed among these distances:
55 8 0.03
56 253 0.80
57 13 0.04
58 5 0.02
59 4 0.01
60 1 0.00
61 2 0.01
62 6 0.02
63 10 0.03
64 13 0.04
65 2 0.01
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (56 bp):
TGTAAAGGTTATATCCGTAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
Found at i:21499873 original size:112 final size:112
Alignment explanation
Indices: 21499675--21500140 Score: 444
Period size: 112 Copynumber: 4.1 Consensus size: 112
21499665 AAGAATACTT
* * * ** * * *
21499675 TGTAAAGGTTATATCCATAAGGATATTATGAAAAGGGATGTCCGAAAGATTATCAATGTTAAGGT
1 TGTAAAGGTTATATACGTAAGGATATTATGAAAAGGGATGTTCGAAAGAACATTAACGTAAAGGT
* *
21499740 TATATCC-GTAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
66 TATA-CCAGTAAGGATACTATGAAAAGGGATGTCCAAAAGGATATCAA
21499787 TGTAAAGGTTATATACGTAAGGATATTATGAAAAGGGATGTTCGAAAGAACATTAACGTAAAGGT
1 TGTAAAGGTTATATACGTAAGGATATTATGAAAAGGGATGTTCGAAAGAACATTAACGTAAAGGT
* * *
21499852 TATACCGGTAAGGATACTATGAGAAGGGATGTCTAAAAGGATATCAA
66 TATACCAGTAAGGATACTATGAAAAGGGATGTCCAAAAGGATATCAA
* *** * * * *****
21499899 TGTAAAGGTTTAAATATTC-TAATTTCTTAAGTATGAAATTCATGAATAAGTTTC-ATTTTTCAT
1 TGTAAAGG-TT--ATATACGTAA--GGAT-ATTATGAAA---AGGGAT--G-TTCGAAAGAACAT
* * * * *
21499962 ACTCACG--AA-CTTATTA--AGCAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
54 --TAACGTAAAGGTTA-TACCAGTAAGGATACTATGAAAAGGGATGTCCAAAAGGATATCAA
21500019 TGTAAAGGTTATATACGTAAGGATATTATGAAAAGGGATGTTCGAAAGAACATTAACGTAAAGGT
1 TGTAAAGGTTATATACGTAAGGATATTATGAAAAGGGATGTTCGAAAGAACATTAACGTAAAGGT
* *
21500084 TATACCAGTAAGGATACTATGAGAAGGGATGTCTAAAAGGATATCAA
66 TATACCAGTAAGGATACTATGAAAAGGGATGTCCAAAAGGATATCAA
21500131 TGTAAAGGTT
1 TGTAAAGGTT
21500141 TAAATATTCT
Statistics
Matches: 280, Mismatches: 51, Indels: 46
0.74 0.14 0.12
Matches are distributed among these distances:
108 4 0.01
109 3 0.01
110 9 0.03
111 5 0.02
112 155 0.55
113 2 0.01
114 3 0.01
115 13 0.05
116 2 0.01
117 13 0.05
118 3 0.01
119 2 0.01
120 47 0.17
121 3 0.01
122 9 0.03
123 3 0.01
124 4 0.01
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (112 bp):
TGTAAAGGTTATATACGTAAGGATATTATGAAAAGGGATGTTCGAAAGAACATTAACGTAAAGGT
TATACCAGTAAGGATACTATGAAAAGGGATGTCCAAAAGGATATCAA
Found at i:21500155 original size:232 final size:232
Alignment explanation
Indices: 21499749--21500213 Score: 921
Period size: 232 Copynumber: 2.0 Consensus size: 232
21499739 TTATATCCGT
21499749 AAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAATGTAAAGGTTATATACGTAAGGATATT
1 AAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAATGTAAAGGTTATATACGTAAGGATATT
*
21499814 ATGAAAAGGGATGTTCGAAAGAACATTAACGTAAAGGTTATACCGGTAAGGATACTATGAGAAGG
66 ATGAAAAGGGATGTTCGAAAGAACATTAACGTAAAGGTTATACCAGTAAGGATACTATGAGAAGG
21499879 GATGTCTAAAAGGATATCAATGTAAAGGTTTAAATATTCTAATTTCTTAAGTATGAAATTCATGA
131 GATGTCTAAAAGGATATCAATGTAAAGGTTTAAATATTCTAATTTCTTAAGTATGAAATTCATGA
21499944 ATAAGTTTCATTTTTCATACTCACGAACTTATTAAGC
196 ATAAGTTTCATTTTTCATACTCACGAACTTATTAAGC
21499981 AAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAATGTAAAGGTTATATACGTAAGGATATT
1 AAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAATGTAAAGGTTATATACGTAAGGATATT
21500046 ATGAAAAGGGATGTTCGAAAGAACATTAACGTAAAGGTTATACCAGTAAGGATACTATGAGAAGG
66 ATGAAAAGGGATGTTCGAAAGAACATTAACGTAAAGGTTATACCAGTAAGGATACTATGAGAAGG
21500111 GATGTCTAAAAGGATATCAATGTAAAGGTTTAAATATTCTAATTTCTTAAGTATGAAATTCATGA
131 GATGTCTAAAAGGATATCAATGTAAAGGTTTAAATATTCTAATTTCTTAAGTATGAAATTCATGA
21500176 ATAAGTTTCATTTTTCATACTCACGAACTTATTAAGC
196 ATAAGTTTCATTTTTCATACTCACGAACTTATTAAGC
21500213 A
1 A
21500214 TTAAGTGGTT
Statistics
Matches: 232, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
232 232 1.00
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (232 bp):
AAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAATGTAAAGGTTATATACGTAAGGATATT
ATGAAAAGGGATGTTCGAAAGAACATTAACGTAAAGGTTATACCAGTAAGGATACTATGAGAAGG
GATGTCTAAAAGGATATCAATGTAAAGGTTTAAATATTCTAATTTCTTAAGTATGAAATTCATGA
ATAAGTTTCATTTTTCATACTCACGAACTTATTAAGC
Found at i:21509043 original size:35 final size:36
Alignment explanation
Indices: 21508981--21509054 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
21508971 TAGTCATATT
* *
21508981 TTAATAATACTATTATTAAATATA-TTTTAATAAAA
1 TTAATAATACTATAATTAAATACATTTTTAATAAAA
* *
21509016 TTAATAATA-TATAATTTAATACCATTTTTAATATAA
1 TTAATAATACTATAATTAAATA-CATTTTTAATAAAA
21509052 TTA
1 TTA
21509055 TTTTTATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 10 0.30
35 10 0.30
36 13 0.39
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (36 bp):
TTAATAATACTATAATTAAATACATTTTTAATAAAA
Found at i:21509047 original size:24 final size:24
Alignment explanation
Indices: 21508985--21509050 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
21508975 CATATTTTAA
* *
21508985 TAATACTATTATTAA-ATATATTT
1 TAATACAATTATTAATATATAATT
* *
21509008 TAATAAAATTAATAATATATAATT
1 TAATACAATTATTAATATATAATT
* *
21509032 TAATACCATTTTTAATATA
1 TAATACAATTATTAATATA
21509051 ATTATTTTTA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 12 0.35
24 22 0.65
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (24 bp):
TAATACAATTATTAATATATAATT
Found at i:21509048 original size:59 final size:58
Alignment explanation
Indices: 21508934--21509056 Score: 126
Period size: 59 Copynumber: 2.1 Consensus size: 58
21508924 AATAGGATTT
* * *
21508934 TTATTAAATGTAATTTAATAATAAATAATAAATAATTTAGTCATATTTTAATAATACT-A
1 TTATTAAATATAATTTAATAATAAATAATAAATAATTTAATCACATTTT-ATAATA-TAA
* * *
21508993 TTATTAAATATATTTTAATAAAATTAATAATATATAATTTAAT-ACCATTTT-TAATATAA
1 TTATTAAATATAATTTAAT--AATAAATAATAAATAATTTAATCA-CATTTTATAATATAA
21509052 TTATT
1 TTATT
21509057 TTTATATTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
58 1 0.02
59 28 0.52
60 1 0.02
61 24 0.44
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (58 bp):
TTATTAAATATAATTTAATAATAAATAATAAATAATTTAATCACATTTTATAATATAA
Found at i:21514431 original size:17 final size:16
Alignment explanation
Indices: 21514411--21514502 Score: 116
Period size: 17 Copynumber: 5.7 Consensus size: 16
21514401 TAAGTTTAAA
*
21514411 TTAATTTTAAATTTTAT
1 TTAAATTTAAA-TTTAT
21514428 TTAAATTTAAATTTAT
1 TTAAATTTAAATTTAT
*
21514444 CTTAAATTTGAATTTAT
1 -TTAAATTTAAATTTAT
21514461 TT--ATTTAAATTTATT
1 TTAAATTTAAATTTA-T
*
21514476 TTAAATTTAAATTTAA
1 TTAAATTTAAATTTAT
21514492 TTAAATTTAAA
1 TTAAATTTAAA
21514503 AATGATATTA
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
14 10 0.15
15 3 0.04
16 18 0.27
17 36 0.54
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (16 bp):
TTAAATTTAAATTTAT
Found at i:21514442 original size:6 final size:6
Alignment explanation
Indices: 21514399--21514502 Score: 78
Period size: 6 Copynumber: 18.0 Consensus size: 6
21514389 ATTTTGATTT
* * *
21514399 TTTAAG TTTAAA -TTAAT TTTAAA TTT-TA TTTAAA TTTAAA TTT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
21514443 TCTTAAA TTTGAA TTTATTTA TTTAAA TTT-AT TTTAAA TTTAAA TTT-AA
1 T-TTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
21514492 -TTAAA TTTAAA
1 TTTAAA TTTAAA
21514503 AATGATATTA
Statistics
Matches: 77, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
4 4 0.05
5 18 0.23
6 48 0.62
7 2 0.03
8 5 0.06
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:21514448 original size:11 final size:10
Alignment explanation
Indices: 21514432--21514500 Score: 58
Period size: 10 Copynumber: 7.1 Consensus size: 10
21514422 TTTTATTTAA
21514432 ATTTAAATTT
1 ATTTAAATTT
21514442 ATCTTAAATTT
1 AT-TTAAATTT
21514453 GAATTT--ATTT
1 --ATTTAAATTT
21514463 ATTTAAATTT
1 ATTTAAATTT
*
21514473 ATTTTAA---
1 ATTTAAATTT
21514480 ATTTAAATTT
1 ATTTAAATTT
*
21514490 AATTAAATTT
1 ATTTAAATTT
21514500 A
1 A
21514501 AAAATGATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
7 6 0.12
8 4 0.08
10 26 0.54
11 8 0.17
12 2 0.04
13 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:21514470 original size:31 final size:32
Alignment explanation
Indices: 21514411--21514502 Score: 114
Period size: 31 Copynumber: 2.8 Consensus size: 32
21514401 TAAGTTTAAA
*
21514411 TTAATTTTAAATTTTATTTAAATTTAAATTTATC
1 TTAAATTTAAA-TTTATTT-AATTTAAATTTATC
* *
21514445 TTAAATTTGAATTTATTT-ATTTAAATTTATT
1 TTAAATTTAAATTTATTTAATTTAAATTTATC
*
21514476 TTAAATTTAAATTTAATTAAATTTAAA
1 TTAAATTTAAATTT-ATTTAATTTAAA
21514503 AATGATATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
31 25 0.49
32 3 0.06
33 14 0.27
34 9 0.18
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (32 bp):
TTAAATTTAAATTTATTTAATTTAAATTTATC
Found at i:21516436 original size:29 final size:28
Alignment explanation
Indices: 21516404--21516567 Score: 111
Period size: 30 Copynumber: 5.6 Consensus size: 28
21516394 AAATTTTAGG
21516404 AAATTACATTTTGACCCCAAAACTTCCAA
1 AAATTACATTTT-ACCCCAAAACTTCCAA
* *
21516433 AAATTACCATTTTACCCCTAAACCTT-CTA
1 AAATTA-CATTTTACCCC-AAAACTTCCAA
* * * *
21516462 AAATTCCATTTTTAGCCCC--GATTTCACCGA
1 AAATTACA-TTTTA-CCCCAAAACTT--CCAA
* *
21516492 AAATTACCATTTTACCCCTAAACTTTTC-A
1 AAATTA-CATTTTACCCCAAAAC-TTCCAA
*
21516521 AAATTCCATTTTTAACCCCAAAACTTCCAA
1 AAATTACA-TTTT-ACCCCAAAACTTCCAA
21516551 AAATTACTATTTTACCC
1 AAATTAC-ATTTTACCC
21516568 TCGAACCTTC
Statistics
Matches: 105, Mismatches: 15, Indels: 30
0.70 0.10 0.20
Matches are distributed among these distances:
27 2 0.02
28 4 0.04
29 44 0.42
30 49 0.47
31 4 0.04
32 2 0.02
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.34
Consensus pattern (28 bp):
AAATTACATTTTACCCCAAAACTTCCAA
Found at i:21516453 original size:59 final size:57
Alignment explanation
Indices: 21516381--21516708 Score: 256
Period size: 59 Copynumber: 5.6 Consensus size: 57
21516371 CCAGAAATTG
* * *
21516381 CATTTTGA-CCCTAAAATTTTAGGAAATTACATTTTGACCCCAAAACTTCCAAAAATTAC
1 CATTTT-ACCCCTAAACTTTTA--AAATTCCATTTTAACCCCAAAACTTCCAAAAATTAC
* * * * *
21516440 CATTTTACCCCTAAACCTTCTAAAATTCCATTTTTAGCCCC--GATTTCACCGAAAATTAC
1 CATTTTACCCCTAAA-CTTTTAAAATTCCA-TTTTAACCCCAAAACTT--CCAAAAATTAC
21516499 CATTTTACCCCTAAACTTTTCAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTAC
1 CATTTTACCCCTAAACTTTT-AAAATTCCA-TTTTAACCCCAAAACTTCCAAAAATTAC
* * * * ***
21516558 TATTTTACCCTCGAACCTTCTAAAATTCCATTTTTAACCCC--GGTTTCACCAAAAATTAC
1 CATTTTACCC-CTAAACTTTTAAAATTCCA-TTTTAACCCCAAAACTT--CCAAAAATTAC
* * ** *
21516617 CATTTTACCCC-AAACTCTCTAAAATTGCATTTTTAACCCC-AATTTTACCGAAAATTAC
1 CATTTTACCCCTAAACT-TTTAAAATTCCA-TTTTAACCCCAAAACTT-CCAAAAATTAC
* *
21516675 CATTTTACCCCCAAACTTTTCAAAATTTCATTTT
1 CATTTTACCCCTAAACTTTT-AAAATTCCATTTT
21516709 TACCTCGATT
Statistics
Matches: 226, Mismatches: 28, Indels: 31
0.79 0.10 0.11
Matches are distributed among these distances:
57 9 0.04
58 63 0.28
59 140 0.62
60 11 0.05
61 3 0.01
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (57 bp):
CATTTTACCCCTAAACTTTTAAAATTCCATTTTAACCCCAAAACTTCCAAAAATTAC
Found at i:21516592 original size:29 final size:28
Alignment explanation
Indices: 21516404--21516712 Score: 119
Period size: 29 Copynumber: 10.6 Consensus size: 28
21516394 AAATTTTAGG
* * *
21516404 AAATTACATTTTGACCCCAAAACTTCCAA
1 AAATTCCATTTTTACCCCAAAACTT-CTA
*
21516433 AAATTACCA-TTTTACCCCTAAACCTTCTA
1 AAATT-CCATTTTTACCCC-AAAACTTCTA
*** ** *
21516462 AAATTCCATTTTTAGCCCCGATTTCACCGA
1 AAATTCCATTTTTA-CCCC-AAAACTTCTA
* *
21516492 AAATTACCA-TTTTACCCCTAAACTTTTCA
1 AAATT-CCATTTTTACCCCAAAACTTCT-A
*
21516521 AAATTCCATTTTTAACCCCAAAACTTCCAA
1 AAATTCCATTTTT-ACCCCAAAACTT-CTA
* * *
21516551 AAATTAC-TATTTTACCCTCGAACCTTCTA
1 AAATTCCAT-TTTTACCC-CAAAACTTCTA
**** ** *
21516580 AAATTCCATTTTTAACCCCGGTTTCACCAA
1 AAATTCCATTTTT-ACCCC-AAAACTTCTA
21516610 AAATTACCA-TTTTACCCC-AAACTCTCTA
1 AAATT-CCATTTTTACCCCAAAACT-TCTA
* ** *
21516638 AAATTGCATTTTTAACCCC-AATTTTACCGA
1 AAATTCCATTTTT-ACCCCAAAACTT--CTA
* *
21516668 AAATTACCA-TTTTACCCCCAAACTTTTCA
1 AAATT-CCATTTTTACCCCAAAACTTCT-A
*
21516697 AAATTTCATTTTTACC
1 AAATTCCATTTTTACC
21516713 TCGATTTCAC
Statistics
Matches: 207, Mismatches: 49, Indels: 48
0.68 0.16 0.16
Matches are distributed among these distances:
27 3 0.01
28 21 0.10
29 88 0.43
30 87 0.42
31 8 0.04
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (28 bp):
AAATTCCATTTTTACCCCAAAACTTCTA
Found at i:21516777 original size:58 final size:58
Alignment explanation
Indices: 21516432--21516792 Score: 403
Period size: 59 Copynumber: 6.2 Consensus size: 58
21516422 AAAACTTCCA
*
21516432 AAAATTACCATTTTACCCCTAAACCTTCTAAAATTCCATTTTTAGCCCCGATTTCACCG
1 AAAATTACCATTTTACCCC-AAACCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
* * * *
21516491 AAAATTACCATTTTACCCCTAAA-CTTTTCAAAATTCCATTTTTAACCCCAAAACTT--CCA
1 AAAATTACCATTTTACCCC-AAACCTTCT-AAAATTCCATTTTTAACCCC--GATTTCACCG
* * * *
21516550 AAAATTACTATTTTACCCTCGAACCTTCTAAAATTCCATTTTTAACCCCGGTTTCACCA
1 AAAATTACCATTTTACCC-CAAACCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
* * *
21516609 AAAATTACCATTTTACCCCAAA-CTCTCTAAAATTGCATTTTTAACCCCAATTTTACCG
1 AAAATTACCATTTTACCCCAAACCT-TCTAAAATTCCATTTTTAACCCCGATTTCACCG
* * *
21516667 AAAATTACCATTTTACCCCCAAA-CTTTTCAAAATTTCATTTTT-ACCTCGATTTCACCG
1 AAAATTACCATTTTA-CCCCAAACCTTCT-AAAATTCCATTTTTAACCCCGATTTCACCG
* * * * **
21516725 AAAATTACCATTTTACCCCGAACCTTCAAAAATTTCATTTTTAACCCTGATTTTGCC-
1 AAAATTACCATTTTACCCCAAACCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
21516782 AAAATTACCAT
1 AAAATTACCAT
21516793 CTTGCCCCCG
Statistics
Matches: 260, Mismatches: 30, Indels: 26
0.82 0.09 0.08
Matches are distributed among these distances:
57 35 0.13
58 92 0.35
59 125 0.48
60 5 0.02
61 3 0.01
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCAAACCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
Found at i:21516834 original size:116 final size:116
Alignment explanation
Indices: 21516432--21516837 Score: 319
Period size: 116 Copynumber: 3.5 Consensus size: 116
21516422 AAAACTTCCA
* * * ** *
21516432 AAAATTACCATTTTACCCCTAAACCT-TCTAAAAT-TCCATTTTTAGCCCCGATTTCACCGAAAA
1 AAAATTACCATCTTACCCCCAAA-CTGTCCAAAATCT-CA-TTTTAAACCCGATTTCACCAAAAA
* * ** *
21516495 TTACCATTTTACCCCTAAACTTTTC-AAAATTCCATTTTTAACCCCAAAACTT-CCA
63 TTACCATTTTACCCC-AAAC-TCTCAAAAATTGCATTTTTAACCCC-AATTTTACCG
* * * * * * *
21516550 AAAATTACTATTTTACCCTCGAACCT-TCTAAAAT-TCCATTTTTAACCCCGGTTTCACCAAAAA
1 AAAATTACCATCTTACCC-CCAAACTGTCCAAAATCT-CA-TTTTAAACCCGATTTCACCAAAAA
*
21516613 TTACCATTTTACCCCAAACTCTCTAAAATTGCATTTTTAACCCCAATTTTACCG
63 TTACCATTTTACCCCAAACTCTCAAAAATTGCATTTTTAACCCCAATTTTACCG
* * * * * *
21516667 AAAATTACCATTTTACCCCCAAACTTTTCAAAATTTCATTTT-TACCTCGATTTCACCGAAAATT
1 AAAATTACCATCTTACCCCCAAACTGTCCAAAATCTCATTTTAAACC-CGATTTCACCAAAAATT
* * ** *
21516731 ACCATTTTACCCCGAAC-CTTCAAAAATTTCATTTTTAACCCTGATTTTGCC-
65 ACCATTTTACCCCAAACTC-TCAAAAATTGCATTTTTAACCCCAATTTTACCG
* ***
21516782 AAAATTACCATCTTGCCCCC-GGGTGTCCAAAAGTCTCATTTTCAAACCCGATTTCA
1 AAAATTACCATCTTACCCCCAAACTGTCCAAAA-TCTCATTTT-AAACCCGATTTCA
21516838 TTGTTTCTTC
Statistics
Matches: 243, Mismatches: 35, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
114 7 0.03
115 29 0.12
116 82 0.34
117 53 0.22
118 69 0.28
119 3 0.01
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (116 bp):
AAAATTACCATCTTACCCCCAAACTGTCCAAAATCTCATTTTAAACCCGATTTCACCAAAAATTA
CCATTTTACCCCAAACTCTCAAAAATTGCATTTTTAACCCCAATTTTACCG
Found at i:21518613 original size:19 final size:20
Alignment explanation
Indices: 21518598--21518671 Score: 67
Period size: 21 Copynumber: 3.6 Consensus size: 20
21518588 TCCAAATTTT
21518598 ATATTTTTAAAAAAATTATA
1 ATATTTTTAAAAAAATTATA
* *
21518618 ATTTTTTTAAAAAAATCTAAA
1 ATATTTTTAAAAAAAT-TATA
* * *
21518639 AAATATTTAAAGAAAGTTATA
1 ATATTTTTAAA-AAAATTATA
* *
21518660 AAATTTCTAAAA
1 ATATTTTTAAAA
21518672 TAATAATTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 16 0.37
21 23 0.53
22 4 0.09
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (20 bp):
ATATTTTTAAAAAAATTATA
Found at i:21522057 original size:56 final size:56
Alignment explanation
Indices: 21521989--21522109 Score: 188
Period size: 56 Copynumber: 2.2 Consensus size: 56
21521979 TTTTCTAAAT
* *
21521989 TATTTTTTATATATCATAAACAGTACTGATAGAATTAAAACAATGTACACATATCA
1 TATTTTTAATATATCATAAACAGTACTGATAGAATTAAAACAATATACACATATCA
** * *
21522045 TATTTTTAATATATTTTTAACTGTACTGATAGAATTAAAACAATATACACATATCA
1 TATTTTTAATATATCATAAACAGTACTGATAGAATTAAAACAATATACACATATCA
21522101 TATTTTTAA
1 TATTTTTAA
21522110 AGAAAAATCA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (56 bp):
TATTTTTAATATATCATAAACAGTACTGATAGAATTAAAACAATATACACATATCA
Found at i:21522239 original size:26 final size:26
Alignment explanation
Indices: 21522210--21522278 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
21522200 TCATTCTGGA
*
21522210 TTTAATTTTAAATATTT-TTTGATATT
1 TTTAATTTTAAAT-TTTATTTAATATT
* *
21522236 TTTATTTTTGAATTTTATTTAATATT
1 TTTAATTTTAAATTTTATTTAATATT
*
21522262 TTT-TTTTATAAATTTTA
1 TTTAATTT-TAAATTTTA
21522279 ATGATGCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 7 0.19
26 30 0.81
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (26 bp):
TTTAATTTTAAATTTTATTTAATATT
Found at i:21526500 original size:33 final size:33
Alignment explanation
Indices: 21526458--21526534 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 33
21526448 CTTTGGCGTT
*
21526458 CTCAGGTATATCCTCTTCTTAAGACTCTAAAGC
1 CTCAGGTATATCCTCTTCTCAAGACTCTAAAGC
21526491 CTCAGGTATATCCTCTTCTCAAGACTCTAAAGC
1 CTCAGGTATATCCTCTTCTCAAGACTCTAAAGC
21526524 CTCAGGTATAT
1 CTCAGGTATAT
21526535 TCACCAAGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.32
Consensus pattern (33 bp):
CTCAGGTATATCCTCTTCTCAAGACTCTAAAGC
Found at i:21533298 original size:10 final size:10
Alignment explanation
Indices: 21533280--21533318 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
21533270 TAAAGTAAAA
21533280 ATAATATATAT
1 ATAA-ATATAT
*
21533291 ATATATATAT
1 ATAAATATAT
*
21533301 ATAAATAAAT
1 ATAAATATAT
21533311 ATAAATAT
1 ATAAATAT
21533319 TTTATTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 21 0.88
11 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATAAATATAT
Found at i:21533628 original size:27 final size:28
Alignment explanation
Indices: 21533576--21533631 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
21533566 TTCATAATTT
*
21533576 AGAATTTAGTTTTTTATTTTTATTTTTA
1 AGAATTTAGTTTTTTATTATTATTTTTA
21533604 AGAATTTAG-TTTTTATATATT-TTTTTA
1 AGAATTTAGTTTTTTAT-TATTATTTTTA
21533631 A
1 A
21533632 ATTTCAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (28 bp):
AGAATTTAGTTTTTTATTATTATTTTTA
Found at i:21533629 original size:28 final size:28
Alignment explanation
Indices: 21533576--21533629 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
21533566 TTCATAATTT
*
21533576 AGAATTTAGTTTTTTATTTTTATTTTTA
1 AGAATTTAGTTTTTTATATTTATTTTTA
21533604 AGAATTTAGTTTTTATATATTT-TTTT
1 AGAATTTAGTTTTT-TATATTTATTTT
21533630 AAATTTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (28 bp):
AGAATTTAGTTTTTTATATTTATTTTTA
Found at i:21533992 original size:2 final size:2
Alignment explanation
Indices: 21533985--21534013 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21533975 TCGGCTACTT
21533985 TA 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 TA T
21534014 GCTAAAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21537019 original size:31 final size:31
Alignment explanation
Indices: 21536971--21537029 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
21536961 TTTGATTAAA
* *
21536971 GGACTAAATTTAAATTTTTGTGAAATTTTAG
1 GGACTAAATTTAAATTTTAGTAAAATTTTAG
**
21537002 GGACTAAATTTTGATTTTAGTAAAATTT
1 GGACTAAATTTAAATTTTAGTAAAATTT
21537030 AAGGTTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (31 bp):
GGACTAAATTTAAATTTTAGTAAAATTTTAG
Found at i:21537924 original size:13 final size:13
Alignment explanation
Indices: 21537882--21537933 Score: 61
Period size: 14 Copynumber: 3.9 Consensus size: 13
21537872 CGTTGACCTG
21537882 TTGACCTATTGACT
1 TTGACC-ATTGACT
* *
21537896 TTGA-CTTTGACC
1 TTGACCATTGACT
21537908 TTGACCATTGACT
1 TTGACCATTGACT
21537921 TTGACCCATTGAC
1 TTGA-CCATTGAC
21537934 CGTTGACCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 9 0.28
13 11 0.34
14 12 0.38
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGACCATTGACT
Found at i:21537933 original size:47 final size:49
Alignment explanation
Indices: 21537852--21538000 Score: 143
Period size: 47 Copynumber: 3.1 Consensus size: 49
21537842 CCCATTCACC
*
21537852 CATTGACC--GACCCATTGACTCGTTGACCTGTTGACCTATTGACTTTGA-
1 CATTGACCTTGACCCATTGACT-GTTGACC-CTTGACCTATTGACTTTGAT
* * *
21537900 CTTTGACCTTGA-CCATTGACT-TTGACCCATTGACC-GTTGACCTTGAT
1 CATTGACCTTGACCCATTGACTGTTGACCC-TTGACCTATTGACTTTGAT
* * *
21537947 CATTGACTTTGACCCGTTGATTGTTGA-CCTTGA-CTATTGACTTTGAT
1 CATTGACCTTGACCCATTGACTGTTGACCCTTGACCTATTGACTTTGAT
*
21537994 CGTTGAC
1 CATTGAC
21538001 TTTTTTTACC
Statistics
Matches: 83, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
46 10 0.12
47 42 0.51
48 16 0.19
49 13 0.16
50 2 0.02
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (49 bp):
CATTGACCTTGACCCATTGACTGTTGACCCTTGACCTATTGACTTTGAT
Found at i:21537940 original size:34 final size:34
Alignment explanation
Indices: 21537902--21537992 Score: 137
Period size: 34 Copynumber: 2.7 Consensus size: 34
21537892 GACTTTGACT
21537902 TTGACCTTGACCATTGACTTTGACCCATTGACCG
1 TTGACCTTGACCATTGACTTTGACCCATTGACCG
* * **
21537936 TTGACCTTGATCATTGACTTTGACCCGTTGATTG
1 TTGACCTTGACCATTGACTTTGACCCATTGACCG
*
21537970 TTGACCTTGACTATTGACTTTGA
1 TTGACCTTGACCATTGACTTTGA
21537993 TCGTTGACTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.38
Consensus pattern (34 bp):
TTGACCTTGACCATTGACTTTGACCCATTGACCG
Found at i:21537986 original size:13 final size:13
Alignment explanation
Indices: 21537882--21537992 Score: 66
Period size: 13 Copynumber: 8.3 Consensus size: 13
21537872 CGTTGACCTG
*
21537882 TTGACCTATTGACT
1 TTGA-CTATTGACC
21537896 TTGACT-TTGACC
1 TTGACTATTGACC
* *
21537908 TTGACCATTGACT
1 TTGACTATTGACC
*
21537921 TTGACCCATTGACC
1 TTGA-CTATTGACC
* *
21537935 GTTGAC-CTTGATCA
1 -TTGACTATTGA-CC
21537949 TTGACT-TTGACCC
1 TTGACTATTGA-CC
* *
21537962 GTTGATTGTTGACC
1 -TTGACTATTGACC
*
21537976 TTGACTATTGACT
1 TTGACTATTGACC
21537989 TTGA
1 TTGA
21537993 TCGTTGACTT
Statistics
Matches: 78, Mismatches: 12, Indels: 15
0.74 0.11 0.14
Matches are distributed among these distances:
12 10 0.13
13 39 0.50
14 21 0.27
15 8 0.10
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.40
Consensus pattern (13 bp):
TTGACTATTGACC
Found at i:21543189 original size:16 final size:16
Alignment explanation
Indices: 21543168--21543198 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21543158 CCCTGCACTA
21543168 TTAATGTCATTGCATT
1 TTAATGTCATTGCATT
*
21543184 TTAATGTCGTTGCAT
1 TTAATGTCATTGCAT
21543199 CTACATTATC
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:0.23, C:0.13, G:0.16, T:0.48
Consensus pattern (16 bp):
TTAATGTCATTGCATT
Found at i:21547496 original size:21 final size:21
Alignment explanation
Indices: 21547472--21547531 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
21547462 TAGTGCAGTT
* *
21547472 TTCTATCAATACAAGTGTCAA
1 TTCTACCAATACAAGTCTCAA
*
21547493 TTCTACCGAA-ACAAGTCTCAC
1 TTCTACC-AATACAAGTCTCAA
*
21547514 TTCTACCGATACAAGTCT
1 TTCTACCAATACAAGTCT
21547532 TACTTTTATC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 30 0.91
22 2 0.06
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.30
Consensus pattern (21 bp):
TTCTACCAATACAAGTCTCAA
Found at i:21547536 original size:21 final size:21
Alignment explanation
Indices: 21547482--21547536 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
21547472 TTCTATCAAT
* *
21547482 ACAAGTGTCAATTCTACCGAA
1 ACAAGTCTCACTTCTACCGAA
*
21547503 ACAAGTCTCACTTCTACCGAT
1 ACAAGTCTCACTTCTACCGAA
*
21547524 ACAAGTCTTACTT
1 ACAAGTCTCACTT
21547537 TTATCGACAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.29
Consensus pattern (21 bp):
ACAAGTCTCACTTCTACCGAA
Found at i:21548264 original size:36 final size:36
Alignment explanation
Indices: 21548211--21548311 Score: 130
Period size: 36 Copynumber: 2.8 Consensus size: 36
21548201 TTCGTTATTT
* * *
21548211 GTTTTACTCCTTGTTGACCCAAAGGTTATAATGCTC
1 GTTTTACTCCCTATTGACCCAAAGGTCATAATGCTC
* *
21548247 GTTTTACTCCCTATTGACCTAAAGGTCATGATGCTC
1 GTTTTACTCCCTATTGACCCAAAGGTCATAATGCTC
** *
21548283 GTTTTACTCCCTATAAACCCATAGGTCAT
1 GTTTTACTCCCTATTGACCCAAAGGTCAT
21548312 GCTTGTTACT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.37
Consensus pattern (36 bp):
GTTTTACTCCCTATTGACCCAAAGGTCATAATGCTC
Found at i:21552306 original size:23 final size:23
Alignment explanation
Indices: 21552280--21552337 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
21552270 CTATCACCAA
21552280 AAAACAGAAGTAGTATTTGAGAG
1 AAAACAGAAGTAGTATTTGAGAG
** * *
21552303 AAAACAAGAACAAGTTTTTGCGAG
1 AAAAC-AGAAGTAGTATTTGAGAG
*
21552327 AGAACAGAAGT
1 AAAACAGAAGT
21552338 TTTTTCTTCT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.48, C:0.09, G:0.24, T:0.19
Consensus pattern (23 bp):
AAAACAGAAGTAGTATTTGAGAG
Found at i:21557309 original size:6 final size:6
Alignment explanation
Indices: 21557298--21557332 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
21557288 AGATAAGGCT
21557298 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
21557333 TTTATCGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:21557782 original size:26 final size:26
Alignment explanation
Indices: 21557743--21557814 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 26
21557733 AATTATAAAA
*
21557743 AATAAAAATCAATAAAAATGATTAAATTTT
1 AATAAAAAT--ATAAAAA--ATTAAAGTTT
21557773 AATAAAAATATAAAAAATTAAAGTTT
1 AATAAAAATATAAAAAATTAAAGTTT
* *
21557799 -ATTAAAATAGAAAAAA
1 AATAAAAATATAAAAAA
21557815 ATTATAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
25 14 0.36
26 9 0.23
28 7 0.18
30 9 0.23
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (26 bp):
AATAAAAATATAAAAAATTAAAGTTT
Found at i:21558083 original size:90 final size:89
Alignment explanation
Indices: 21557915--21558168 Score: 318
Period size: 90 Copynumber: 2.8 Consensus size: 89
21557905 TTAGGGGTGA
* * *
21557915 TTCAAGTA-CTCAATTGAGTGCAAAAAAAAATCAGAGGCTTAATTG-TTTTTTTAAAAAGTTTGA
1 TTCAAGTATC-CAACTGAGTGCAAAATAAAAGCAGAGGCTTAATTGTTTTTTTTAAAAAGTTTGA
21557978 GGGTCTTTTTAATGCATTTTGAAAG
65 GGGTCTTTTTAATGCATTTTGAAAG
* * *
21558003 TTTAAGTATCTAACTGAGTGCAAAATAAAAGCA-AGGGCTTAATTGCTTTTTTTTTAAAAGTTTG
1 TTCAAGTATCCAACTGAGTGCAAAATAAAAGCAGA-GGCTTAATTG-TTTTTTTTAAAAAGTTTG
*
21558067 AGGGTCTTTTTGATGCATTTTGAAAG
64 AGGGTCTTTTTAATGCATTTTGAAAG
* * * ** *
21558093 TTCAAGTATCCAAGTGAGTGCAAAATAAAAGCAGTGACTTAATTGATTTTTCTAAAAAAAGTTTA
1 TTCAAGTATCCAACTGAGTGCAAAATAAAAGCAGAGGCTTAATTG-TTTTT-TTTAAAAAGTTTG
21558158 AGGG-CTTTTTA
64 AGGGTCTTTTTA
21558169 CACTCTTAAG
Statistics
Matches: 142, Mismatches: 18, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
87 1 0.01
88 36 0.25
89 1 0.01
90 91 0.64
91 13 0.09
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (89 bp):
TTCAAGTATCCAACTGAGTGCAAAATAAAAGCAGAGGCTTAATTGTTTTTTTTAAAAAGTTTGAG
GGTCTTTTTAATGCATTTTGAAAG
Found at i:21559302 original size:21 final size:22
Alignment explanation
Indices: 21559278--21559339 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 22
21559268 CGATATAAGC
21559278 ATACAAACTACCGATACAT-TA
1 ATACAAACTACCGATACATGTA
*
21559299 ATACTAAAACTACCGATACTTGTA
1 ATAC--AAACTACCGATACATGTA
*
21559323 ATTC-AACTACCGATACA
1 ATACAAACTACCGATACA
21559340 ACTCAAGTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
21 16 0.46
23 14 0.40
24 5 0.14
ACGTcount: A:0.44, C:0.24, G:0.06, T:0.26
Consensus pattern (22 bp):
ATACAAACTACCGATACATGTA
Found at i:21560967 original size:31 final size:31
Alignment explanation
Indices: 21560931--21560996 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
21560921 AAAGGCATAA
* * * *
21560931 AAAATAACATCCAAACAACCAAAATAGCAGT
1 AAAATAACAACAAAACAACAAAAATAGCAAT
21560962 AAAATAACAACAAAACAACAAAAATAGCAAT
1 AAAATAACAACAAAACAACAAAAATAGCAAT
21560993 AAAA
1 AAAA
21560997 ACAGCAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.67, C:0.18, G:0.05, T:0.11
Consensus pattern (31 bp):
AAAATAACAACAAAACAACAAAAATAGCAAT
Found at i:21560972 original size:23 final size:22
Alignment explanation
Indices: 21560944--21561020 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 22
21560934 ATAACATCCA
*
21560944 AACAACCAAAATAGCAGTAAAAT
1 AACAA-CAAAACAGCAGTAAAAT
*
21560967 AACAACAAAACAACA--AAAAT
1 AACAACAAAACAGCAGTAAAAT
* * *
21560987 AGCAATAAAAACAGCAATAAAAAT
1 AACAA-CAAAACAGCAGT-AAAAT
21561011 AACAACAAAA
1 AACAACAAAA
21561021 TAGTAGCAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
20 9 0.21
21 8 0.19
22 8 0.19
23 9 0.21
24 9 0.21
ACGTcount: A:0.69, C:0.17, G:0.05, T:0.09
Consensus pattern (22 bp):
AACAACAAAACAGCAGTAAAAT
Found at i:21561006 original size:38 final size:38
Alignment explanation
Indices: 21560964--21561040 Score: 97
Period size: 38 Copynumber: 2.0 Consensus size: 38
21560954 ATAGCAGTAA
21560964 AATAACAACAAAACAACAAAA-A-TAGCAATAAA-AACAGC
1 AATAA-AA-AAAACAACAAAATAGTAGCAA-AAATAACAGC
*
21561002 AATAAAAATAACAACAAAATAGTAGCAAAAATAACAGC
1 AATAAAAAAAACAACAAAATAGTAGCAAAAATAACAGC
21561040 A
1 A
21561041 TCAAAACAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
36 11 0.31
37 6 0.17
38 18 0.51
ACGTcount: A:0.68, C:0.16, G:0.06, T:0.10
Consensus pattern (38 bp):
AATAAAAAAAACAACAAAATAGTAGCAAAAATAACAGC
Found at i:21561045 original size:26 final size:22
Alignment explanation
Indices: 21560962--21561059 Score: 74
Period size: 23 Copynumber: 4.3 Consensus size: 22
21560952 AAATAGCAGT
*
21560962 AAAATAACAACAAAACA--ACA
1 AAAATAACAACAAAACAGTAAA
* * *
21560982 AAAATAGCAATAAAAACAGCAATA
1 AAAATAACAA-CAAAACAGTAA-A
* *
21561006 AAAATAACAACAAAATAGTAGCA
1 AAAATAACAACAAAACAGTA-AA
21561029 AAAATAACAGCATCAAAACAGTAAA
1 AAAATAACA--A-CAAAACAGTAAA
21561054 AAAATA
1 AAAATA
21561060 GCACTAAAAC
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
20 9 0.15
21 6 0.10
23 18 0.30
24 10 0.17
25 8 0.13
26 9 0.15
ACGTcount: A:0.68, C:0.14, G:0.06, T:0.11
Consensus pattern (22 bp):
AAAATAACAACAAAACAGTAAA
Found at i:21561116 original size:38 final size:39
Alignment explanation
Indices: 21561054--21561128 Score: 116
Period size: 38 Copynumber: 1.9 Consensus size: 39
21561044 AAACAGTAAA
21561054 AAAATAGCACTAAAACAACAACCAAAACAGTAAAAAAATC
1 AAAATAGCAC-AAAACAACAACCAAAACAGTAAAAAAATC
* *
21561094 AAAATAGCA-AAAACAGCAACCAAAACTGTAAAAAA
1 AAAATAGCACAAAACAACAACCAAAACAGTAAAAAA
21561129 GCACAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 24 0.73
40 9 0.27
ACGTcount: A:0.65, C:0.19, G:0.07, T:0.09
Consensus pattern (39 bp):
AAAATAGCACAAAACAACAACCAAAACAGTAAAAAAATC
Found at i:21567289 original size:21 final size:21
Alignment explanation
Indices: 21567265--21567317 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 21
21567255 TTGTGCTAGC
21567265 TCTACCGATACAAGT-ATG-A
1 TCTACCGATACAAGTCATGCA
21567284 TTTCTACCGATACAAGTCATGCA
1 --TCTACCGATACAAGTCATGCA
21567307 TCTACCGATAC
1 TCTACCGATAC
21567318 CAAAAACTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 26 0.87
22 3 0.10
23 1 0.03
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.28
Consensus pattern (21 bp):
TCTACCGATACAAGTCATGCA
Found at i:21569615 original size:31 final size:31
Alignment explanation
Indices: 21569577--21569647 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
21569567 AGAAAGTAAG
21569577 TACAATTTTATCATTATTAATTTATATTTTA
1 TACAATTTTATCATTATTAATTTATATTTTA
21569608 TACAATTTTATCATTATTAATTTATATTTTA
1 TACAATTTTATCATTATTAATTTATATTTTA
21569639 TAC-ATTTTA
1 TACAATTTTA
21569648 AAGAATAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 6 0.15
31 34 0.85
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (31 bp):
TACAATTTTATCATTATTAATTTATATTTTA
Found at i:21569624 original size:16 final size:16
Alignment explanation
Indices: 21569577--21569624 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
21569567 AGAAAGTAAG
21569577 TACAATTTTATCATTA
1 TACAATTTTATCATTA
* *
21569593 T-TAATTTATAT-TTTA
1 TACAATTT-TATCATTA
21569608 TACAATTTTATCATTA
1 TACAATTTTATCATTA
21569624 T
1 T
21569625 TAATTTATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.56
Consensus pattern (16 bp):
TACAATTTTATCATTA
Found at i:21569645 original size:15 final size:15
Alignment explanation
Indices: 21569596--21569645 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
21569586 ATCATTATTA
21569596 ATTTATATTTTATAC
1 ATTTATATTTTATAC
*
21569611 AATTT-TATCATTATTA-
1 -ATTTATAT-TTTA-TAC
21569627 ATTTATATTTTATAC
1 ATTTATATTTTATAC
21569642 ATTT
1 ATTT
21569646 TAAAGAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
14 2 0.07
15 14 0.50
16 10 0.36
17 2 0.07
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTATATTTTATAC
Found at i:21571661 original size:14 final size:14
Alignment explanation
Indices: 21571642--21571669 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21571632 ATTTTTGCAT
21571642 TTAAAATATAAAAA
1 TTAAAATATAAAAA
21571656 TTAAAATATAAAAA
1 TTAAAATATAAAAA
21571670 AACCACTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TTAAAATATAAAAA
Found at i:21571897 original size:2 final size:2
Alignment explanation
Indices: 21571890--21571945 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
21571880 TATTTATTTG
21571890 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21571932 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
21571946 TAAAATTGAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21572931 original size:38 final size:38
Alignment explanation
Indices: 21572884--21573347 Score: 466
Period size: 38 Copynumber: 12.4 Consensus size: 38
21572874 CAAGGTCGAT
* **
21572884 CTTTAAAAAAGGTTGGGATAGGTCTTGTCTAAGGCAAC
1 CTTTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAAC
* * *
21572922 CTTTTAAAAAAGGTTGGGATAAACC-CGTCTAAGACAAC
1 CTTTT-AAAAAGGTTGGGATAGACCTTGTCTAAGGCAAC
* *
21572960 C--TTAAAAAGGTTGGGATAGACCCTGTCTAAGTCAAC
1 CTTTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAAC
* * *
21572996 C--TTAAAAAAGTTGGGATATACTTTGTCTAAGGCAAC
1 CTTTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAAC
* * * *
21573032 CTTTAAAAAAGATTGGGATAGA-CATGTCTAAAGCAAC
1 CTTTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAAC
* *
21573069 C-TTT-AAAAGATTGGGATAGATCTTGTCTAAGGCAAC
1 CTTTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAAC
* * * *
21573105 CTTTTAGAAAAAGTTGGTATAAAACC--GTCTAAAGCAAC
1 CTTTTA-AAAAGGTTGGGAT-AGACCTTGTCTAAGGCAAC
* *
21573143 C--TTAAAAAGGTTGGGATAGACCTTGTTTAAAGCAAC
1 CTTTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAAC
* *
21573179 CTTTTAAATAGGTTGGGATAGATCTTGTCTAAGGCAAC
1 CTTTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAAC
* * * **
21573217 ATTTTAAAAAAGTTGGGATAGACCTTTTCTAAGATAAC
1 CTTTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAAC
* * * *
21573255 CTTTTAAAAAGGTTGGGATAAACCTTATCTAAAGCATC
1 CTTTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAAC
* * *
21573293 CTTTAAAAAAAGTTGGGATACACCTTGTCTAAGGCAAC
1 CTTTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAAC
*
21573331 CTTTAAGAAAAGGTTGG
1 CTTTTA-AAAAGGTTGG
21573348 TATAAACGCA
Statistics
Matches: 352, Mismatches: 60, Indels: 27
0.80 0.14 0.06
Matches are distributed among these distances:
34 4 0.01
35 45 0.13
36 76 0.22
37 16 0.05
38 173 0.49
39 35 0.10
40 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (38 bp):
CTTTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAAC
Found at i:21573362 original size:76 final size:73
Alignment explanation
Indices: 21572910--21573354 Score: 427
Period size: 74 Copynumber: 6.0 Consensus size: 73
21572900 GATAGGTCTT
* * * *
21572910 GTCTAAGGCAACCTTTTAAAAAAGGTTGGGATAAACC-CGTCTAAGACAACC--TTAAAAAGGTT
1 GTCTAAAGCAACC-TTTAAAAAA-GTTGGGATAGACCTTGTCTAAGGCAACCTTTTAAAAAGGTT
*
21572972 GGGATAGACCC
64 GGGATA-AACC
* * * *
21572983 TGTCT-AAGTCAACC-TTAAAAAAGTTGGGATATACTTTGTCTAAGGCAACCTTTAAAAAAGATT
1 -GTCTAAAG-CAACCTTTAAAAAAGTTGGGATAGACCTTGTCTAAGGCAACCTTTTAAAAAGGTT
* *
21573046 GGGATAGACAT
64 GGGATAAAC-C
* * *
21573057 GTCTAAAGCAACCTTTAAAAGA-TTGGGATAGATCTTGTCTAAGGCAACCTTTTAGAAAAAGTTG
1 GTCTAAAGCAACCTTTAAAAAAGTTGGGATAGACCTTGTCTAAGGCAACCTTTTA-AAAAGGTTG
*
21573121 GTATAAAACC
65 GGAT-AAACC
* * * *
21573131 GTCTAAAGCAACC-TTAAAAAGGTTGGGATAGACCTTGTTTAAAGCAACCTTTTAAATAGGTTGG
1 GTCTAAAGCAACCTTTAAAAAAGTTGGGATAGACCTTGTCTAAGGCAACCTTTTAAAAAGGTTGG
* *
21573195 GATAGATCTT
66 GATA-AAC-C
* * * **
21573205 GTCTAAGGCAACATTTTAAAAAAGTTGGGATAGACCTTTTCTAAGATAACCTTTTAAAAAGGTTG
1 GTCTAAAGCAAC-CTTTAAAAAAGTTGGGATAGACCTTGTCTAAGGCAACCTTTTAAAAAGGTTG
21573270 GGATAAACC
65 GGATAAACC
* * * *
21573279 TTATCTAAAGCATCCTTTAAAAAAAGTTGGGATACACCTTGTCTAAGGCAACCTTTAAGAAAAGG
1 --GTCTAAAGCAACCTTT-AAAAAAGTTGGGATAGACCTTGTCTAAGGCAACCTTTTA-AAAAGG
*
21573344 TTGGTATAAAC
62 TTGGGATAAAC
21573355 GCATCTAAGG
Statistics
Matches: 302, Mismatches: 51, Indels: 33
0.78 0.13 0.09
Matches are distributed among these distances:
71 11 0.04
72 21 0.07
73 58 0.19
74 97 0.32
75 8 0.03
76 91 0.30
77 16 0.05
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (73 bp):
GTCTAAAGCAACCTTTAAAAAAGTTGGGATAGACCTTGTCTAAGGCAACCTTTTAAAAAGGTTGG
GATAAACC
Found at i:21574326 original size:21 final size:20
Alignment explanation
Indices: 21574297--21574339 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
21574287 AATTCATGAA
* *
21574297 ATCACTAATTGCTAATTTAT
1 ATCACTAATGGCTAATATAT
21574317 ATCACCTAATGGCTAATATAT
1 ATCA-CTAATGGCTAATATAT
21574338 AT
1 AT
21574340 ATATATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (20 bp):
ATCACTAATGGCTAATATAT
Found at i:21580560 original size:17 final size:18
Alignment explanation
Indices: 21580524--21580561 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
21580514 TTGTTCTAGA
*
21580524 TAATAATTCCCATCAATT
1 TAATAATTCCAATCAATT
*
21580542 TAATCATTCCAAT-AATT
1 TAATAATTCCAATCAATT
21580559 TAA
1 TAA
21580562 AATATTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (18 bp):
TAATAATTCCAATCAATT
Found at i:21592202 original size:9 final size:9
Alignment explanation
Indices: 21592169--21592210 Score: 57
Period size: 9 Copynumber: 4.4 Consensus size: 9
21592159 CAGTAGAAGG
21592169 AGAAGGAAAA
1 AGAA-GAAAA
*
21592179 AGAAGAGAGA
1 AGAAGA-AAA
21592189 AGAAGAAAA
1 AGAAGAAAA
21592198 AGAAGAAAA
1 AGAAGAAAA
21592207 AGAA
1 AGAA
21592211 ATGAAGGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 17 0.59
10 12 0.41
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (9 bp):
AGAAGAAAA
Found at i:21597883 original size:18 final size:18
Alignment explanation
Indices: 21597860--21597894 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21597850 ATATGTAATT
21597860 TTAATTT-AGTTAATTCGG
1 TTAATTTGA-TTAATTCGG
21597878 TTAATTTGATTAATTCG
1 TTAATTTGATTAATTCG
21597895 ATCAAATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.29, C:0.06, G:0.14, T:0.51
Consensus pattern (18 bp):
TTAATTTGATTAATTCGG
Found at i:21649971 original size:24 final size:24
Alignment explanation
Indices: 21649926--21649971 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
21649916 TTTTGAAACA
* *
21649926 GATATACAAAAAATATATAAAAAT
1 GATATACAAAAAATAAAGAAAAAT
* *
21649950 GATATTCATAAAATAAAGAAAA
1 GATATACAAAAAATAAAGAAAA
21649972 TAATCATTAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.24
Consensus pattern (24 bp):
GATATACAAAAAATAAAGAAAAAT
Found at i:21653420 original size:25 final size:26
Alignment explanation
Indices: 21653383--21653432 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
21653373 TTAAAATATT
*
21653383 TTAATAAAATTATTATTTTTAAAAAA
1 TTAATAAAATTATTATTATTAAAAAA
21653409 TTAA-AAAATTATTATTATTAAAAA
1 TTAATAAAATTATTATTATTAAAAA
21653433 TACATTGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
TTAATAAAATTATTATTATTAAAAAA
Found at i:21653754 original size:18 final size:18
Alignment explanation
Indices: 21653731--21653765 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21653721 TTAATTCCAA
21653731 ATTTA-TTTACAAATTTAG
1 ATTTATTTTA-AAATTTAG
21653749 ATTTATTTTAAAATTTA
1 ATTTATTTTAAAATTTA
21653766 AATTGAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTTATTTTAAAATTTAG
Found at i:21653769 original size:24 final size:24
Alignment explanation
Indices: 21653741--21653794 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
21653731 ATTTATTTAC
* *
21653741 AAATTTAGATTTATTTTAAAATTT
1 AAATTTAAATTAATTTTAAAATTT
* *
21653765 AAATTGAAATTAATTTTTAAATTT
1 AAATTTAAATTAATTTTAAAATTT
21653789 AAATTT
1 AAATTT
21653795 GTGTTAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
AAATTTAAATTAATTTTAAAATTT
Found at i:21655008 original size:22 final size:23
Alignment explanation
Indices: 21654983--21655028 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
21654973 GCAAAATAAG
21654983 AAGAAAAAATAAAGA-ACAAAAA
1 AAGAAAAAATAAAGAGACAAAAA
* * *
21655005 AAGAGAAACTAAAGAGACCAAAA
1 AAGAAAAAATAAAGAGACAAAAA
21655028 A
1 A
21655029 TCGAAAGAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.74, C:0.09, G:0.13, T:0.04
Consensus pattern (23 bp):
AAGAAAAAATAAAGAGACAAAAA
Found at i:21655769 original size:29 final size:27
Alignment explanation
Indices: 21655737--21655955 Score: 158
Period size: 29 Copynumber: 7.5 Consensus size: 27
21655727 AAAATTTTAG
21655737 AAAATTCCATCTTTAACCCCGATTTCACC
1 AAAATTCCAT-TTTAACCCCGATTT-ACC
*
21655766 AAAAATTACCATTTT-ACCCCAAACTTT-CC
1 -AAAATT-CCATTTTAACCCC-GA-TTTACC
*
21655795 AAAATTCCATTTTTAACCCTGATTTTACC
1 AAAATTCCA-TTTTAACCCCGA-TTTACC
*
21655824 AAAAATTACCATTTTACCCCCGAACTTT-CC
1 -AAAATT-CCATTTTAACCCCG-A-TTTACC
21655854 AAAATTCCATTTTTAACCCCGATTTCACC
1 AAAATTCCA-TTTTAACCCCGATTT-ACC
* * *
21655883 AAAATTACCATTTT-ACCCCTAAATTTTCT
1 AAAATT-CCATTTTAACCCC--GATTTACC
*
21655912 AAAATTCCATTTTTGACCCCGATTTCACC
1 AAAATTCCA-TTTTAACCCCGATTT-ACC
21655941 AAAAATTACCATTTT
1 -AAAATT-CCATTTT
21655956 GCCCTCGAGT
Statistics
Matches: 155, Mismatches: 14, Indels: 40
0.74 0.07 0.19
Matches are distributed among these distances:
27 6 0.04
28 30 0.19
29 53 0.34
30 49 0.32
31 17 0.11
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (27 bp):
AAAATTCCATTTTAACCCCGATTTACC
Found at i:21655878 original size:59 final size:59
Alignment explanation
Indices: 21655737--21655955 Score: 352
Period size: 58 Copynumber: 3.7 Consensus size: 59
21655727 AAAATTTTAG
*
21655737 AAAATTCCATCTTTAACCCCGATTTCACCAAAAATTACCATTTTA-CCCCAAACTTTCC
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCC
* * *
21655795 AAAATTCCATTTTTAACCCTGATTTTACCAAAAATTACCATTTTACCCCCGAACTTTCC
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCC
* * *
21655854 AAAATTCCATTTTTAACCCCGATTTCACC-AAAATTACCATTTTACCCCTAAATTTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCC
*
21655912 AAAATTCCATTTTTGACCCCGATTTCACCAAAAATTACCATTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTT
21655956 GCCCTCGAGT
Statistics
Matches: 148, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
58 95 0.64
59 53 0.36
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (59 bp):
AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCC
Found at i:21655916 original size:117 final size:117
Alignment explanation
Indices: 21655737--21655955 Score: 368
Period size: 117 Copynumber: 1.9 Consensus size: 117
21655727 AAAATTTTAG
21655737 AAAATTCCATCTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCAAACTTTCCAAAATTC
1 AAAATTCCATCTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCAAACTTTCCAAAATTC
* *
21655802 CATTTTTAACCCTGATTTTACCAAAAATTACCATTTTACCCCCGAACTTTCC
66 CATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCC
* * *
21655854 AAAATTCCATTTTTAACCCCGATTTCACC-AAAATTACCATTTTACCCCTAAATTTTCTAAAATT
1 AAAATTCCATCTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCC-AAACTTTCCAAAATT
*
21655918 CCATTTTTGACCCCGATTTCACCAAAAATTACCATTTT
65 CCATTTTTAACCCCGATTTCACCAAAAATTACCATTTT
21655956 GCCCTCGAGT
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
116 19 0.20
117 76 0.80
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (117 bp):
AAAATTCCATCTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCAAACTTTCCAAAATTC
CATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCC
Found at i:21655997 original size:117 final size:117
Alignment explanation
Indices: 21655737--21655990 Score: 334
Period size: 117 Copynumber: 2.2 Consensus size: 117
21655727 AAAATTTTAG
*
21655737 AAAATTCCATCTTT-AACCCCGATTTCACCAAAAATTACCATTTTACCCCAAACTTTCCAAAATT
1 AAAATCCCAT-TTTCAACCCCGATTTCACCAAAAATTACCATTTTACCCCAAACTTTCCAAAATT
* * *
21655801 CCATTTTTAACCCTGATTTTACCAAAAATTACCATTTTACCCCCGAACTTTCC
65 CCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAACTATCC
* * * *
21655854 AAAATTCCATTTTTAACCCCGATTTCACC-AAAATTACCATTTTACCCCTAAATTTTCTAAAATT
1 AAAATCCCATTTTCAACCCCGATTTCACCAAAAATTACCATTTTACCCC-AAACTTTCCAAAATT
* * * * *
21655918 CCATTTTTGACCCCGATTTCACCAAAAATTACCATTTTGCCCTCG-AGTATCT
65 CCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAACTATCC
*
21655970 AAAAGTCCCGTTTTCAACCCC
1 AAAA-TCCCATTTTCAACCCC
21655991 TGTTTCATCG
Statistics
Matches: 121, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
116 30 0.25
117 91 0.75
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (117 bp):
AAAATCCCATTTTCAACCCCGATTTCACCAAAAATTACCATTTTACCCCAAACTTTCCAAAATTC
CATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAACTATCC
Found at i:21666720 original size:38 final size:38
Alignment explanation
Indices: 21666669--21667250 Score: 206
Period size: 38 Copynumber: 15.3 Consensus size: 38
21666659 TCTTTATCTC
21666669 TGAAATTGAAGTAAGAGCAAGATCGTTTCCCATCCTCT
1 TGAAATTGAAGTAAGAGCAAGATCGTTTCCCATCCTCT
* * * **
21666707 TGAAATTTAAGTAA-AGCTGGATATCACGTTT-TTAT-CTC-
1 TGAAATTGAAGTAAGAGC--AAGAT--CGTTTCCCATCCTCT
*
21666745 TAAAATTGAAGTAAGAGCAAGATCGTTTCCCATCCTCT
1 TGAAATTGAAGTAAGAGCAAGATCGTTTCCCATCCTCT
** * *
21666783 TGAAATTGAAGTAA-AGTTGGATATCACGTCTT--TAT-CTC-
1 TGAAATTGAAGTAAGAG--CAAGAT--CGT-TTCCCATCCTCT
21666821 TGAAATTGAAGTAAGAGCAAGATCGTTTCCCATCCTCT
1 TGAAATTGAAGTAAGAGCAAGATCGTTTCCCATCCTCT
* ** *
21666859 TGAAATTAAAGTAA-AGCTGGATGTCAAGTCTT--TAT-CTC-
1 TGAAATTGAAGTAAGAGCAAGA--TC--GT-TTCCCATCCTCT
** *
21666897 TGAAATTGAAGTAAGAGCAAGATCACTTCCTATCCTCT
1 TGAAATTGAAGTAAGAGCAAGATCGTTTCCCATCCTCT
* * * *
21666935 TGAAATCGAAGTAGAGATG-AATAACAAGTCTT-TC-T-CTC-
1 TGAAATTGAAGTA-AGA-GCAAGATC--GT-TTCCCATCCTCT
* * *
21666973 TGAAATTGAAGTAAGAGCAAGATCTTTTCCTATCCGCT
1 TGAAATTGAAGTAAGAGCAAGATCGTTTCCCATCCTCT
* * *
21667011 TGAAATTGAAGTAGAGTGGACAACA-CGTCTT--TAT-CTC-
1 TGAAATTGAAGTA-AG-AG-CAAGATCGT-TTCCCATCCTCT
* * *** *
21667048 TGAAATTGAAGTAAGAACAAGATCATTTTTTATCCGCT
1 TGAAATTGAAGTAAGAGCAAGATCGTTTCCCATCCTCT
*** *
21667086 TGAAATTGAAGT-AGAGTTGGATAACAAGTCTT--TAT-CTC-
1 TGAAATTGAAGTAAGAGCAAGAT--C--GT-TTCCCATCCTCT
* * *
21667124 TGAAATTGAAATAAGAGCAAGATCATTTCCTATCCTCT
1 TGAAATTGAAGTAAGAGCAAGATCGTTTCCCATCCTCT
*** *
21667162 TGAAATTGAAGT-AGAGTTGGATAACAAGTCTT--TAT-CTC-
1 TGAAATTGAAGTAAGAGCAAGAT--C--GT-TTCCCATCCTCT
* *
21667200 TGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCT
1 TGAAATTGAAGTAAGAGCAAGATCGTTTCCCATCCTCT
*
21667238 TGAAATCGAAGTA
1 TGAAATTGAAGTA
21667251 GAGACGGATA
Statistics
Matches: 404, Mismatches: 73, Indels: 134
0.66 0.12 0.22
Matches are distributed among these distances:
34 16 0.04
35 13 0.03
36 20 0.05
37 72 0.18
38 175 0.43
39 63 0.16
40 17 0.04
41 18 0.04
42 10 0.02
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (38 bp):
TGAAATTGAAGTAAGAGCAAGATCGTTTCCCATCCTCT
Found at i:21666754 original size:76 final size:76
Alignment explanation
Indices: 21666609--21667352 Score: 1051
Period size: 76 Copynumber: 9.8 Consensus size: 76
21666599 ATCAGACCGC
* *
21666609 AGCAAGATCATTTCCTATCCGCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
21666673 ATTGAAGTAAG
66 ATTGAAGTAAG
* * * * * * * * *
21666684 AGCAAGATCGTTTCCCATCCTCTTGAAATTTAAGTAAAGCTGGATATCACGTTTTTATCTCTAAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
21666749 ATTGAAGTAAG
66 ATTGAAGTAAG
* * * * *
21666760 AGCAAGATCGTTTCCCATCCTCTTGAAATTGAAGTAAAGTTGGATATCACGTCTTTATCTCTGAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
21666825 ATTGAAGTAAG
66 ATTGAAGTAAG
* * * * * **
21666836 AGCAAGATCGTTTCCCATCCTCTTGAAATTAAAGTAAAGCTGGATGTCAAGTCTTTATCTCTGAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
21666901 ATTGAAGTAAG
66 ATTGAAGTAAG
* * * * *
21666912 AGCAAGATCACTTCCTATCCTCTTGAAATCGAAGTAGAGATGAATAACAAGTCTTTCTCTCTGAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
21666977 ATTGAAGTAAG
66 ATTGAAGTAAG
* * * *
21666988 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAG-TGGACAACACGTCTTTATCTCTGAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
21667052 ATTGAAGTAAG
66 ATTGAAGTAAG
* ** *
21667063 AACAAGATCATTTTTTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
*
21667128 ATTGAAATAAG
66 ATTGAAGTAAG
21667139 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
21667204 ATTGAAGTAAG
66 ATTGAAGTAAG
* **
21667215 AGCAAGATCATTTCCTATCCTCTTGAAATCGAAGTAGAGACGGATAACAAGTCTTTATCTCTGAA
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
21667280 ATTGAAGTAAG
66 ATTGAAGTAAG
** * * * * *
21667291 AGCAAGATCGCTTCCTACCCTTTTGAAAGTGAAGTAAAGTTGGATAGCAAGTCTTTATCTCT
1 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCT
21667353 ATGAAGAGCA
Statistics
Matches: 607, Mismatches: 60, Indels: 3
0.91 0.09 0.00
Matches are distributed among these distances:
75 101 0.17
76 506 0.83
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (76 bp):
AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
ATTGAAGTAAG
Found at i:21667344 original size:379 final size:379
Alignment explanation
Indices: 21666609--21667352 Score: 1132
Period size: 379 Copynumber: 2.0 Consensus size: 379
21666599 ATCAGACCGC
*
21666609 AGCAAGATCATTTCCTATCCGCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAA
1 AGCAAGATCATTTCCTATCCGCTTGAAATTGAAGTAGAGTGGACAACACGTCTTTATCTCTGAAA
* * * * * * *
21666674 TTGAAGTAAGAGCAAGATCGTTTCCCATCCTCTTGAAATTTAAGTAAAGCTGGATATCACGTTTT
66 TTGAAGTAAGAACAAGATCATTTCCCATCCGCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTT
* *
21666739 TATCTCTAAAATTGAAGTAAGAGCAAGATCGTTTCCCATCCTCTTGAAATTGAAGTAAAGTTGGA
131 TATCTCTAAAATTGAAATAAGAGCAAGATCATTTCCCATCCTCTTGAAATTGAAGTAAAGTTGGA
* * * *
21666804 TATCACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCGTTTCCCATCCTCTTGAAATTAAA
196 TAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCCATCCTCTTGAAATCAAA
** *
21666869 GTAAAGCTGGATGTCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCACTTCCTATCCTC
261 GTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCACTTCCTACCCTC
* *
21666934 TTGAAATCGAAGTAGAGATGAATAACAAGTCTTTCTCTCTGAAATTGAAGTAAG
326 TTGAAATCGAAGTAAAGATGAATAACAAGTCTTTATCTCTGAAATTGAAGTAAG
*
21666988 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTGGACAACACGTCTTTATCTCTGAAA
1 AGCAAGATCATTTCCTATCCGCTTGAAATTGAAGTAGAGTGGACAACACGTCTTTATCTCTGAAA
*** * *
21667053 TTGAAGTAAGAACAAGATCATTTTTTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTT
66 TTGAAGTAAGAACAAGATCATTTCCCATCCGCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTT
* * *
21667118 TATCTCTGAAATTGAAATAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGA
131 TATCTCTAAAATTGAAATAAGAGCAAGATCATTTCCCATCCTCTTGAAATTGAAGTAAAGTTGGA
* *
21667183 TAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATCGAA
196 TAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCCATCCTCTTGAAATCAAA
* *
21667248 GTAGAGAC-GGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCGCTTCCTACCCT
261 GTAAAG-CTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCACTTCCTACCCT
* * * *
21667312 TTTGAAAGT-GAAGTAAAGTTGGATAGCAAGTCTTTATCTCT
325 CTTGAAA-TCGAAGTAAAGATGAATAACAAGTCTTTATCTCT
21667353 ATGAAGAGCA
Statistics
Matches: 327, Mismatches: 36, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
379 325 0.99
380 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (379 bp):
AGCAAGATCATTTCCTATCCGCTTGAAATTGAAGTAGAGTGGACAACACGTCTTTATCTCTGAAA
TTGAAGTAAGAACAAGATCATTTCCCATCCGCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTT
TATCTCTAAAATTGAAATAAGAGCAAGATCATTTCCCATCCTCTTGAAATTGAAGTAAAGTTGGA
TAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCCATCCTCTTGAAATCAAA
GTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCACTTCCTACCCTC
TTGAAATCGAAGTAAAGATGAATAACAAGTCTTTATCTCTGAAATTGAAGTAAG
Found at i:21667690 original size:18 final size:18
Alignment explanation
Indices: 21667665--21667707 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
21667655 AGTTAATTCC
21667665 AAATTTA-TTTACAAATTT
1 AAATTTATTTTA-AAATTT
*
21667683 AGATTTATTTTAAAATTT
1 AAATTTATTTTAAAATTT
21667701 AAATTTA
1 AAATTTA
21667708 AATTTGTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (18 bp):
AAATTTATTTTAAAATTT
Found at i:21667705 original size:24 final size:23
Alignment explanation
Indices: 21667677--21667729 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
21667667 ATTTATTTAC
* *
21667677 AAATTTAGATTTATTTTAAAATTT
1 AAATTTAAATTTATGTT-AAATTT
*
21667701 AAATTTAAATTTGTGTTAAATTT
1 AAATTTAAATTTATGTTAAATTT
21667724 AAATTT
1 AAATTT
21667730 GGTAAATTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (23 bp):
AAATTTAAATTTATGTTAAATTT
Found at i:21667721 original size:17 final size:16
Alignment explanation
Indices: 21667699--21667738 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
21667689 ATTTTAAAAT
21667699 TTAAATTTAAATTTGTG
1 TTAAATTTAAATTTG-G
21667716 TTAAATTTAAATTTGG
1 TTAAATTTAAATTTGG
21667732 -TAAATTT
1 TTAAATTT
21667739 GGAATAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 7 0.30
16 1 0.04
17 15 0.65
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (16 bp):
TTAAATTTAAATTTGG
Found at i:21669707 original size:30 final size:29
Alignment explanation
Indices: 21669673--21669892 Score: 143
Period size: 30 Copynumber: 7.4 Consensus size: 29
21669663 AAAATTTCAG
* *
21669673 AAAATTCTATCTTTAACCTCGATTTTACCA
1 AAAATTCCAT-TTTAACCCCGATTTTACCA
*
21669703 AAAATTACCATTTT-ACCACCGAACTTT-CC-
1 AAAATT-CCATTTTAACC-CCG-ATTTTACCA
*
21669732 AAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTCCA-TTTTAACCCCGATTTTACCA
* *
21669762 AAAATTACCATTTTACCCCCGAACTTT-CC-
1 AAAATT-CCATTTTAACCCCG-ATTTTACCA
** *
21669791 AAAATTCCATTTTTAACCCTAATTTCACC-
1 AAAATTCCA-TTTTAACCCCGATTTTACCA
* *
21669820 AAAATTACCATTTT-ACCCCTAAATTTT--CT
1 AAAATT-CCATTTTAACCCC--GATTTTACCA
* *
21669849 AAAATTCCATTTTCGACCCCGATTTCACCA
1 AAAATTCCATTTT-AACCCCGATTTTACCA
21669879 AAAATTACCATTTT
1 AAAATT-CCATTTT
21669893 GCTCTCGGGT
Statistics
Matches: 152, Mismatches: 18, Indels: 39
0.73 0.09 0.19
Matches are distributed among these distances:
28 28 0.18
29 50 0.33
30 54 0.36
31 20 0.13
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATTCCATTTTAACCCCGATTTTACCA
Found at i:21669745 original size:29 final size:27
Alignment explanation
Indices: 21669703--21669892 Score: 138
Period size: 29 Copynumber: 6.5 Consensus size: 27
21669693 GATTTTACCA
21669703 AAAATTACCATTTTACCACCGAACTTTCC
1 AAAATTACCATTTTACC-CCGAA-TTTCC
21669732 AAAATT-CCATTTTTAACCCCG-ATTTCACC
1 AAAATTACCA-TTTT-ACCCCGAATTT--CC
21669761 AAAAATTACCATTTTACCCCCGAACTTTCC
1 -AAAATTACCATTTTA-CCCCGAA-TTTCC
* *
21669791 AAAATT-CCATTTTTAACCCTAATTTCACC
1 AAAATTACCA-TTTTACCCCGAATTT--CC
* *
21669820 AAAATTACCATTTTACCCCTAAATTTTCT
1 AAAATTACCATTTTACCCC-GAA-TTTCC
21669849 AAAATT-CCATTTTCGACCCCG-ATTTCACC
1 AAAATTACCATTTT--ACCCCGAATTT--CC
21669878 AAAAATTACCATTTT
1 -AAAATTACCATTTT
21669893 GCTCTCGGGT
Statistics
Matches: 133, Mismatches: 7, Indels: 40
0.74 0.04 0.22
Matches are distributed among these distances:
27 9 0.07
28 20 0.15
29 51 0.38
30 36 0.27
31 14 0.11
32 3 0.02
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.35
Consensus pattern (27 bp):
AAAATTACCATTTTACCCCGAATTTCC
Found at i:21669853 original size:58 final size:58
Alignment explanation
Indices: 21669673--21669892 Score: 307
Period size: 59 Copynumber: 3.8 Consensus size: 58
21669663 AAAATTTCAG
* * * *
21669673 AAAATTCTATCTTTAACCTCGATTTTACCAAAAATTACCATTTTACCACCGAACTTTCC
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACC-CCGAACTTTCC
21669732 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCC
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTA-CCCCGAACTTTCC
** * * *
21669791 AAAATTCCATTTTTAACCCTAATTTCACC-AAAATTACCATTTTACCCCTAAATTTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCC-GAACTTTCC
**
21669849 AAAATTCCATTTTCGACCCCGATTTCACCAAAAATTACCATTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTT
21669893 GCTCTCGGGT
Statistics
Matches: 145, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
57 4 0.03
58 46 0.32
59 93 0.64
60 2 0.01
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (58 bp):
AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCGAACTTTCC
Found at i:21669926 original size:117 final size:118
Alignment explanation
Indices: 21669694--21669934 Score: 283
Period size: 117 Copynumber: 2.1 Consensus size: 118
21669684 TTTAACCTCG
* * *
21669694 ATTTTACCAAAAATTACCATTTTACCACCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 ATTTCACCAAAAATTACCATTTTACCACCAAACTTTCCAAAATTCCATTTTCAACCCCGATTTCA
* * * *
21669759 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAA-CCCT
66 CCAAAAATTACCATTTTACCCCCGAACTATCCAAAATCCCACTTTCAACCCCT
* * *
21669811 AATTTCACC-AAAATTACCATTTTACC-CCTAAATTTTCTAAAATTCCATTTTCGACCCCGATTT
1 -ATTTCACCAAAAATTACCATTTTACCACC-AAACTTTCCAAAATTCCATTTTCAACCCCGATTT
* * * ** *
21669874 CACCAAAAATTACCATTTTGCTCTCG-GGTATCCAAAAGTCCCGCTTTCAACCCCT
64 CACCAAAAATTACCATTTTACCCCCGAACTATCCAAAA-TCCCACTTTCAACCCCT
21669929 ATTTCA
1 ATTTCA
21669935 TCGTTTCTTC
Statistics
Matches: 104, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
116 10 0.10
117 83 0.80
118 11 0.11
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.34
Consensus pattern (118 bp):
ATTTCACCAAAAATTACCATTTTACCACCAAACTTTCCAAAATTCCATTTTCAACCCCGATTTCA
CCAAAAATTACCATTTTACCCCCGAACTATCCAAAATCCCACTTTCAACCCCT
Found at i:21671317 original size:20 final size:21
Alignment explanation
Indices: 21671292--21671330 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
21671282 TTAGAAAATT
21671292 AATCAAAAAAT-AAACATATC
1 AATCAAAAAATAAAACATATC
21671312 AATCAAAAAATAAAACATA
1 AATCAAAAAATAAAACATA
21671331 AACATACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.18
Consensus pattern (21 bp):
AATCAAAAAATAAAACATATC
Found at i:21671344 original size:27 final size:27
Alignment explanation
Indices: 21671296--21671349 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
21671286 AAAATTAATC
*
21671296 AAAAAATAAACATATCAATCAAAAAAT
1 AAAAAATAAACATACCAATCAAAAAAT
* **
21671323 AAAACATAAACATACCTTTCAAAAAAT
1 AAAAAATAAACATACCAATCAAAAAAT
21671350 CTTTTTTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.20
Consensus pattern (27 bp):
AAAAAATAAACATACCAATCAAAAAAT
Found at i:21671525 original size:7 final size:7
Alignment explanation
Indices: 21671513--21671545 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
21671503 ATTCCTTTTC
21671513 TCCTTTA
1 TCCTTTA
21671520 TCCTTTA
1 TCCTTTA
21671527 TCCTTTA
1 TCCTTTA
*
21671534 TCCTTTC
1 TCCTTTA
21671541 TCCTT
1 TCCTT
21671546 CCCTTCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.09, C:0.33, G:0.00, T:0.58
Consensus pattern (7 bp):
TCCTTTA
Found at i:21672258 original size:20 final size:20
Alignment explanation
Indices: 21672203--21672259 Score: 51
Period size: 26 Copynumber: 2.5 Consensus size: 20
21672193 ATGAGATTAA
*
21672203 CAATTTAATAATTTAAATAC
1 CAATTTAAAAATTTAAATAC
21672223 CAATTTTGACCAAAAAATTTAAATAC
1 CAA-TTT-----AAAAATTTAAATAC
21672249 CAATTTAAAAA
1 CAATTTAAAAA
21672260 ACTAATATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 12
0.70 0.02 0.28
Matches are distributed among these distances:
20 8 0.27
21 3 0.10
25 3 0.10
26 16 0.53
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (20 bp):
CAATTTAAAAATTTAAATAC
Found at i:21680664 original size:43 final size:43
Alignment explanation
Indices: 21680603--21680708 Score: 131
Period size: 43 Copynumber: 2.5 Consensus size: 43
21680593 GAGTGTTCTT
* * * *
21680603 AGTGCCAACTCAGTTGAAAGCTAATCTAGCTAGAAGCGTTTTC
1 AGTGCCAACTCAGTTGAAAGCGAATCCAACTAGAAGAGTTTTC
* * *
21680646 AGTGCCAACTCAGTTGAAAGCGCATCCAATTGGAAGAGTTTTC
1 AGTGCCAACTCAGTTGAAAGCGAATCCAACTAGAAGAGTTTTC
* *
21680689 AGTGCCAACTTAGCTGAAAG
1 AGTGCCAACTCAGTTGAAAG
21680709 AGCTTCCAGT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (43 bp):
AGTGCCAACTCAGTTGAAAGCGAATCCAACTAGAAGAGTTTTC
Found at i:21680722 original size:43 final size:43
Alignment explanation
Indices: 21680635--21680722 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
21680625 AATCTAGCTA
* * *
21680635 GAAGCGTTTTCAGTGCCAACTCAGTTGAAAGCGCATCCAATTG
1 GAAGAGTTTTCAGTGCCAACTCAGCTGAAAGAGCATCCAATTG
* * *
21680678 GAAGAGTTTTCAGTGCCAACTTAGCTGAAAGAGCTTCCAGTTG
1 GAAGAGTTTTCAGTGCCAACTCAGCTGAAAGAGCATCCAATTG
21680721 GA
1 GA
21680723 GACGCTTTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.26
Consensus pattern (43 bp):
GAAGAGTTTTCAGTGCCAACTCAGCTGAAAGAGCATCCAATTG
Found at i:21680732 original size:43 final size:43
Alignment explanation
Indices: 21680642--21680734 Score: 116
Period size: 43 Copynumber: 2.2 Consensus size: 43
21680632 CTAGAAGCGT
* * *
21680642 TTTCAGTGCCAACTCAGTTGAAAGCGCATCCAATTGGAAGAGT
1 TTTCAGTGCCAACTCAGCTGAAAGAGCATCCAATTGGAAGAGC
* * *
21680685 TTTCAGTGCCAACTTAGCTGAAAGAGCTTCCAGTTGG-AGACGC
1 TTTCAGTGCCAACTCAGCTGAAAGAGCATCCAATTGGAAGA-GC
21680728 TTTCAGT
1 TTTCAGT
21680735 ACTTTTGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 3 0.07
43 40 0.93
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.28
Consensus pattern (43 bp):
TTTCAGTGCCAACTCAGCTGAAAGAGCATCCAATTGGAAGAGC
Found at i:21681217 original size:17 final size:18
Alignment explanation
Indices: 21681178--21681225 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
21681168 AAACCACTAA
*
21681178 AAACCCTAAAACAATCTT
1 AAACCCTAAAACAATCAT
*
21681196 AAACCCTAAATCAA-CAT
1 AAACCCTAAAACAATCAT
21681213 AAACCACTAAAAC
1 AAACC-CTAAAAC
21681226 TGGAAGCGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.54, C:0.29, G:0.00, T:0.17
Consensus pattern (18 bp):
AAACCCTAAAACAATCAT
Found at i:21681488 original size:11 final size:10
Alignment explanation
Indices: 21681458--21681648 Score: 94
Period size: 10 Copynumber: 19.8 Consensus size: 10
21681448 TTATTAGAAT
21681458 TTTTTTAT-A
1 TTTTTTATAA
21681467 -TTTTTATAA
1 TTTTTTATAA
21681476 TTTTTTATGAA
1 TTTTTTAT-AA
* *
21681487 -TTCTTACAA
1 TTTTTTATAA
*
21681496 GTTTTTATAA
1 TTTTTTATAA
**
21681506 AATTTTA-AA
1 TTTTTTATAA
*
21681515 TGTTTTATAA
1 TTTTTTATAA
* *
21681525 TTTATTAGAA
1 TTTTTTATAA
* ** *
21681535 GTTAGTAGAA
1 TTTTTTATAA
21681545 TTTTTTATAA
1 TTTTTTATAA
*
21681555 GTTTTTTATAT
1 -TTTTTTATAA
21681566 TTTTTTATAA
1 TTTTTTATAA
*
21681576 -GTTTTATAA
1 TTTTTTATAA
**
21681585 -TTGGTATAA
1 TTTTTTATAA
* *
21681594 TTTTATATTA
1 TTTTTTATAA
* *
21681604 GTTTTAAT-A
1 TTTTTTATAA
*
21681613 TTTTTT-TTA
1 TTTTTTATAA
21681622 TTTTTTAT-A
1 TTTTTTATAA
* *
21681631 TTTTATATGA
1 TTTTTTATAA
21681641 TTTTTTAT
1 TTTTTTAT
21681649 GAGAAAAATA
Statistics
Matches: 139, Mismatches: 33, Indels: 19
0.73 0.17 0.10
Matches are distributed among these distances:
8 8 0.06
9 44 0.32
10 76 0.55
11 11 0.08
ACGTcount: A:0.30, C:0.01, G:0.07, T:0.62
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:21681537 original size:39 final size:40
Alignment explanation
Indices: 21681448--21681537 Score: 96
Period size: 39 Copynumber: 2.3 Consensus size: 40
21681438 CTTTGATATC
* * * *
21681448 TTATTAGAA-TTTTTTTATATTTTTATAATTTTTTATGAA
1 TTATTAGAAGTTTTTATAAAATTTTATAATGTTTTATGAA
* *
21681487 TTCTTACAAGTTTTTATAAAATTTTA-AATGTTTTAT-AA
1 TTATTAGAAGTTTTTATAAAATTTTATAATGTTTTATGAA
21681525 TTTATTAGAAGTT
1 -TTATTAGAAGTT
21681538 AGTAGAATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
38 2 0.05
39 26 0.63
40 13 0.32
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (40 bp):
TTATTAGAAGTTTTTATAAAATTTTATAATGTTTTATGAA
Found at i:21681624 original size:28 final size:28
Alignment explanation
Indices: 21681593--21681646 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
21681583 AATTGGTATA
21681593 ATTTTATATTAGTTTTA-AT-ATTTTTTTT
1 ATTTTATA-TA-TTTTATATGATTTTTTTT
*
21681621 ATTTTTTATATTTTATATGATTTTTT
1 ATTTTATATATTTTATATGATTTTTT
21681647 ATGAGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 5 0.22
27 4 0.17
28 14 0.61
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (28 bp):
ATTTTATATATTTTATATGATTTTTTTT
Found at i:21681643 original size:19 final size:19
Alignment explanation
Indices: 21681593--21681648 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
21681583 AATTGGTATA
* *
21681593 ATTTTATATTAGTTTTAAT
1 ATTTTATATTATTTTTTAT
*
21681612 ATTTT-TTTTATTTTTTAT
1 ATTTTATATTATTTTTTAT
*
21681630 ATTTTATATGATTTTTTAT
1 ATTTTATATTATTTTTTAT
21681649 GAGAAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (19 bp):
ATTTTATATTATTTTTTAT
Found at i:21682637 original size:31 final size:29
Alignment explanation
Indices: 21682596--21682723 Score: 100
Period size: 31 Copynumber: 4.3 Consensus size: 29
21682586 TTAATATAAC
*
21682596 ATTTGATACTTAAACTTTACAGTTTTTCTTA
1 ATTTGATACTTAAA-TTGACA-TTTTTCTTA
* * *
21682627 ATTTGGTACTTAAATT---TTTTTTGTCTA
1 ATTTGATACTTAAATTGACATTTTTCT-TA
*
21682654 ATTTGACACTTAAATTGACATTTTTTCTTA
1 ATTTGATACTTAAATTGACA-TTTTTCTTA
* * * *
21682684 ATTTGGTACCTAAACTTGACTCTTTTTCCTA
1 ATTTGATACTTAAA-TTGAC-ATTTTTCTTA
21682715 ATTTGATAC
1 ATTTGATAC
21682724 CTAATCTTTT
Statistics
Matches: 77, Mismatches: 13, Indels: 14
0.74 0.12 0.13
Matches are distributed among these distances:
26 6 0.08
27 16 0.21
30 15 0.19
31 40 0.52
ACGTcount: A:0.27, C:0.14, G:0.09, T:0.51
Consensus pattern (29 bp):
ATTTGATACTTAAATTGACATTTTTCTTA
Found at i:21682977 original size:59 final size:56
Alignment explanation
Indices: 21682879--21683053 Score: 161
Period size: 59 Copynumber: 3.0 Consensus size: 56
21682869 ATAAATTTAC
* * * *
21682879 GTACCAAATTAAATCTAAAAAAAGCTTAGATACCAAATTAGGAAAAAATGTCAAGTTCAA
1 GTACAAAATTAAA--TAAAAAAA--TTAAATACCAAATTAGGAAAAAATATCAAATTCAA
* * * * * *
21682939 GTATAAAATTGGATTCAAAAAAATTTAAATACCAAATTAAGAAAAATTATCAAATTTAA
1 GTACAAAATT-AAAT-AAAAAAA-TTAAATACCAAATTAGGAAAAAATATCAAATTCAA
* * *
21682998 GTACCAAATTAAATAAAAAAATTAAATACCAAATTAGAAAAAAAATATCAATTTCA
1 GTACAAAATTAAATAAAAAAATTAAATACCAAATTAG-GAAAAAATATCAAATTCA
21683054 GATACTAAAT
Statistics
Matches: 92, Mismatches: 20, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
56 15 0.16
57 21 0.23
58 2 0.02
59 38 0.41
60 15 0.16
61 1 0.01
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.26
Consensus pattern (56 bp):
GTACAAAATTAAATAAAAAAATTAAATACCAAATTAGGAAAAAATATCAAATTCAA
Found at i:21682997 original size:31 final size:27
Alignment explanation
Indices: 21682990--21683042 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 27
21682980 AAAAATTATC
* *
21682990 AAATTTAAGTACCAAATTAA-ATAAAA
1 AAATTTAAATACCAAATTAAGAAAAAA
21683016 AAA-TTAAATACCAAATT-AGAAAAAA
1 AAATTTAAATACCAAATTAAGAAAAAA
21683041 AA
1 AA
21683043 TATCAATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 1 0.04
25 20 0.83
26 3 0.12
ACGTcount: A:0.66, C:0.08, G:0.04, T:0.23
Consensus pattern (27 bp):
AAATTTAAATACCAAATTAAGAAAAAA
Found at i:21683028 original size:25 final size:25
Alignment explanation
Indices: 21682955--21683043 Score: 90
Period size: 31 Copynumber: 3.3 Consensus size: 25
21682945 AATTGGATTC
21682955 AAAAAAATTTAAATACCAAATTAAGAA
1 AAAAAAATTTAAATACCAAATT-A-AA
*
21682982 AAATTATCAAATTTAAGTACCAAATTAAA
1 AAA--A--AAATTTAAATACCAAATTAAA
*
21683011 TAAAAAAA-TTAAATACCAAATTAGA
1 -AAAAAAATTTAAATACCAAATTAAA
21683036 AAAAAAAT
1 AAAAAAAT
21683044 ATCAATTTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
24 7 0.13
25 15 0.28
26 3 0.06
27 3 0.06
28 1 0.02
29 3 0.06
30 4 0.08
31 17 0.32
ACGTcount: A:0.64, C:0.08, G:0.03, T:0.25
Consensus pattern (25 bp):
AAAAAAATTTAAATACCAAATTAAA
Found at i:21683556 original size:29 final size:30
Alignment explanation
Indices: 21683510--21683568 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
21683500 AAAATTAAAA
*
21683510 CTAAATTTTTTAAATTT-AAAATATAAGAG
1 CTAAATTTTTAAAATTTAAAAATATAAGAG
21683539 CTAAA-TTTTAAAATTTTAAAAAATATAAGA
1 CTAAATTTTTAAAA-TTT-AAAAATATAAGA
21683569 ACTTATGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 7 0.27
29 8 0.31
31 11 0.42
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (30 bp):
CTAAATTTTTAAAATTTAAAAATATAAGAG
Found at i:21689113 original size:26 final size:26
Alignment explanation
Indices: 21689081--21689131 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
21689071 AGCTGTTAAA
21689081 TTTTCTAAT-AAATGTTATTTATTTAT
1 TTTTCTAATAAAAT-TTATTTATTTAT
21689107 TTTTCTAATAAAAATTTATTTATTT
1 TTTTCTAAT-AAAATTTATTTATTT
21689132 TAGTTGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 9 0.39
27 10 0.43
28 4 0.17
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTTCTAATAAAATTTATTTATTTAT
Found at i:21692293 original size:2 final size:2
Alignment explanation
Indices: 21692286--21692316 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
21692276 AAAGATGATA
*
21692286 AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
21692317 AATAACATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21692602 original size:6 final size:6
Alignment explanation
Indices: 21692593--21692684 Score: 84
Period size: 6 Copynumber: 15.5 Consensus size: 6
21692583 GTTTGAATAG
* *
21692593 ATTTAA ATTT-A TTATTAA ATTTAA ATTT-A TTTTAA ATTTAA ATTTTTAA
1 ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA ATTTAA ATTTAA A--TTTAA
* * *
21692642 ATTTAA ATTT-G CTTTAA ATTTAA ATTT-A ATTAAA ATTTAA ATT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATT
21692685 AATATTAAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
5 13 0.19
6 48 0.70
7 2 0.03
8 6 0.09
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:21692629 original size:17 final size:17
Alignment explanation
Indices: 21692593--21692684 Score: 118
Period size: 17 Copynumber: 5.5 Consensus size: 17
21692583 GTTTGAATAG
21692593 ATTTAAATTTATTATTAA
1 ATTTAAATTTATT-TTAA
21692611 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
21692628 ATTTAAA--T-TTTTAA
1 ATTTAAATTTATTTTAA
**
21692642 ATTTAAATTTGCTTTAA
1 ATTTAAATTTATTTTAA
* *
21692659 ATTTAAATTTAATTAAA
1 ATTTAAATTTATTTTAA
21692676 ATTTAAATT
1 ATTTAAATT
21692685 AATATTAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.19
15 1 0.01
16 1 0.01
17 39 0.58
18 13 0.19
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:21692672 original size:11 final size:12
Alignment explanation
Indices: 21692593--21692684 Score: 84
Period size: 11 Copynumber: 7.8 Consensus size: 12
21692583 GTTTGAATAG
21692593 ATTTAAATTT-A
1 ATTTAAATTTAA
*
21692604 TTATTAAATTTAA
1 AT-TTAAATTTAA
*
21692617 ATTT-ATTTTAA
1 ATTTAAATTTAA
21692628 ATTTAAATTTTTAA
1 ATTTAAA--TTTAA
*
21692642 ATTTAAATTT-G
1 ATTTAAATTTAA
*
21692653 CTTTAAATTTAA
1 ATTTAAATTTAA
*
21692665 ATTT-AATTAAA
1 ATTTAAATTTAA
21692676 ATTTAAATT
1 ATTTAAATT
21692685 AATATTAAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
11 30 0.46
12 21 0.32
13 2 0.03
14 12 0.18
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (12 bp):
ATTTAAATTTAA
Found at i:21693467 original size:26 final size:25
Alignment explanation
Indices: 21693429--21693524 Score: 88
Period size: 26 Copynumber: 3.7 Consensus size: 25
21693419 TTAATTGCTG
*
21693429 TTTTATTAATAATAATAATAATAAC
1 TTTTATTATTAATAATAATAATAAC
*
21693454 TATTTATTATTAATAATAA-ATGTAAC
1 T-TTTATTATTAATAATAATA-ATAAC
* **
21693480 TTTAATATTATTAATGATAATTAATATT
1 TTT--TATTATTAATAATAA-TAATAAC
21693508 TTTTATTATTAA-AATAA
1 TTTTATTATTAATAATAA
21693525 AAAAAAGTGA
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
25 8 0.14
26 30 0.52
27 14 0.24
28 5 0.09
29 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (25 bp):
TTTTATTATTAATAATAATAATAAC
Done.