Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 52 of 97
Found at i:21009590 original size:37 final size:37
Alignment explanation
Indices: 21009435--21009582 Score: 217
Period size: 37 Copynumber: 4.0 Consensus size: 37
21009425 AATGCAATGT
*
21009435 CATCATCATGTGTGCACTCTCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
*
21009472 CATCATCATGTGTGAACTCCCTACTCGCACAC-TCTAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTC-AA
* * *
21009509 CATCATCATGTATGCACTCCCTATTCGCATACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
* *
21009546 CATCATCATATGTGCACTTCCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
21009583 TGTCATCACA
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
36 2 0.02
37 94 0.96
38 2 0.02
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.30
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
Found at i:21010832 original size:20 final size:20
Alignment explanation
Indices: 21010807--21010853 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
21010797 GAAGAACAAG
21010807 AAGCTGCTGGACAAATGAGA
1 AAGCTGCTGGACAAATGAGA
21010827 AAGCTGCTGGACAAATGAGA
1 AAGCTGCTGGACAAATGAGA
21010847 AAGCTGC
1 AAGCTGC
21010854 AAGAGAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.17, G:0.30, T:0.15
Consensus pattern (20 bp):
AAGCTGCTGGACAAATGAGA
Found at i:21010862 original size:20 final size:20
Alignment explanation
Indices: 21010816--21010866 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
21010806 GAAGCTGCTG
**
21010816 GACAAATGAGAAAGCTGCTG
1 GACAAATGAGAAAGCTGCAA
21010836 GACAAATGAGAAAGCTGCAA
1 GACAAATGAGAAAGCTGCAA
*
21010856 GAGAAATGAGA
1 GACAAATGAGA
21010867 TATTTATAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.47, C:0.12, G:0.29, T:0.12
Consensus pattern (20 bp):
GACAAATGAGAAAGCTGCAA
Found at i:21011016 original size:23 final size:25
Alignment explanation
Indices: 21010982--21011029 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
21010972 TCATTATTTC
*
21010982 TATTTTCTTCA-TCATTT-TGTCTT
1 TATTTTCATCATTCATTTATGTCTT
21011005 TATTTTCATCATTCATTTATGTCTT
1 TATTTTCATCATTCATTTATGTCTT
21011030 AGGCCTACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.45
24 6 0.27
25 6 0.27
ACGTcount: A:0.17, C:0.17, G:0.04, T:0.62
Consensus pattern (25 bp):
TATTTTCATCATTCATTTATGTCTT
Found at i:21017743 original size:80 final size:79
Alignment explanation
Indices: 21017631--21017856 Score: 353
Period size: 80 Copynumber: 2.8 Consensus size: 79
21017621 TGTAACATGT
* *
21017631 ATGCCATGAGATGTATGTGTTGAGATAGTCATATACACTATGGACTAAGCATGTGAGTGATTTAT
1 ATGCCATGAGATGTATGTGTTGAGTTAGTCATATACACTATGGGCTAAGCATGTGA-TGATTTAT
21017696 GAGGTTATGAAATGC
65 GAGGTTATGAAATGC
*
21017711 ATGCCATGAGATGTATGTGTTGAGTTAGTCATATACACTATGGGCTAAGCATATGAATGATTTAT
1 ATGCCATGAGATGTATGTGTTGAGTTAGTCATATACACTATGGGCTAAGCATGTG-ATGATTTAT
* *
21017776 GAGGTTGTGCAATGC
65 GAGGTTATGAAATGC
* * *
21017791 ATGCCATGAGATGTATCTGTTGAGTTAGTTATATATACTATGGGCTAAGCATGATGATGATTTAT
1 ATGCCATGAGATGTATGTGTTGAGTTAGTCATATACACTATGGGCTAAGCATG-TGATGATTTAT
21017856 G
65 G
21017857 GAAATGTTAT
Statistics
Matches: 135, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
80 132 0.98
81 3 0.02
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.35
Consensus pattern (79 bp):
ATGCCATGAGATGTATGTGTTGAGTTAGTCATATACACTATGGGCTAAGCATGTGATGATTTATG
AGGTTATGAAATGC
Found at i:21022277 original size:19 final size:19
Alignment explanation
Indices: 21022253--21022294 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
21022243 GAAGAAAAAT
*
21022253 AAAATATTAATTCTATAAA
1 AAAATATTAATTATATAAA
* *
21022272 AAAATATTATTTATTTAAA
1 AAAATATTAATTATATAAA
21022291 AAAA
1 AAAA
21022295 GAGATAGCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATATTAATTATATAAA
Found at i:21023308 original size:24 final size:25
Alignment explanation
Indices: 21023262--21023309 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
21023252 AGAATGGGAG
21023262 AGAGGAAGAGAGGTACGACAAAGTTA
1 AGAGGAAGAGAGG-ACGACAAAGTTA
21023288 AGAGGAAGAGGAGG-CGA-AAAGT
1 AGAGGAAGA-GAGGACGACAAAGT
21023310 GACAGATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 9 0.43
27 4 0.19
ACGTcount: A:0.46, C:0.06, G:0.40, T:0.08
Consensus pattern (25 bp):
AGAGGAAGAGAGGACGACAAAGTTA
Found at i:21023766 original size:28 final size:28
Alignment explanation
Indices: 21023722--21023917 Score: 241
Period size: 28 Copynumber: 6.8 Consensus size: 28
21023712 TCCGGTCTTT
* *
21023722 AATTAAGACAAATCATGTTATCTTGTTTA
1 AATTAAGACAAA-CATGTTTTCTTGTCTA
*
21023751 AATTGAGACAAACATGTTTTCTTGTCTA
1 AATTAAGACAAACATGTTTTCTTGTCTA
* * *
21023779 GATTAAGACAAAGCATATTTTTCTTGTTTA
1 AATTAAGACAAA-CAT-GTTTTCTTGTCTA
*
21023809 AATGAAGACAAACATGTTTT-TTAGTCTA
1 AATTAAGACAAACATGTTTTCTT-GTCTA
*
21023837 AATTAAGACAAAACATGTTTTCTTGTCCA
1 AATTAAGAC-AAACATGTTTTCTTGTCTA
* *
21023866 AATTAAGACAAACATGTTTTGTTGTCCA
1 AATTAAGACAAACATGTTTTCTTGTCTA
21023894 AATTAAGACAAAACATGTTTTCTT
1 AATTAAGAC-AAACATGTTTTCTT
21023918 TGTTGATTGT
Statistics
Matches: 146, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
27 2 0.01
28 67 0.46
29 54 0.37
30 23 0.16
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (28 bp):
AATTAAGACAAACATGTTTTCTTGTCTA
Found at i:21023885 original size:57 final size:57
Alignment explanation
Indices: 21023722--21023917 Score: 268
Period size: 57 Copynumber: 3.4 Consensus size: 57
21023712 TCCGGTCTTT
* * *
21023722 AATTAAGACAAATCATGTTATCTTGTTTAAATTGAGACAAACATGTTTTCTTGTCTA
1 AATTAAGACAAAACATGTTTTCTTGTTTAAATTAAGACAAACATGTTTTCTTGTCTA
* * * *
21023779 GATTAAGACAAAGCATATTTTTCTTGTTTAAATGAAGACAAACATGTTTT-TTAGTCTA
1 AATTAAGACAAAACAT-GTTTTCTTGTTTAAATTAAGACAAACATGTTTTCTT-GTCTA
** * *
21023837 AATTAAGACAAAACATGTTTTCTTGTCCAAATTAAGACAAACATGTTTTGTTGTCCA
1 AATTAAGACAAAACATGTTTTCTTGTTTAAATTAAGACAAACATGTTTTCTTGTCTA
21023894 AATTAAGACAAAACATGTTTTCTT
1 AATTAAGACAAAACATGTTTTCTT
21023918 TGTTGATTGT
Statistics
Matches: 123, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
57 73 0.59
58 50 0.41
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (57 bp):
AATTAAGACAAAACATGTTTTCTTGTTTAAATTAAGACAAACATGTTTTCTTGTCTA
Found at i:21031100 original size:37 final size:38
Alignment explanation
Indices: 21031017--21031111 Score: 115
Period size: 39 Copynumber: 2.5 Consensus size: 38
21031007 CTCACCCAGC
* *
21031017 TCATGTGCAACCCCCACATTGTGCACATAGCTAAAGTCA
1 TCATGTGCATCCCCCACATTGTGCACA-AGCTAAAGCCA
*
21031056 TCATGTGCATCCCCCATATTGTGCAC-AGCTAATA-CCA
1 TCATGTGCATCCCCCACATTGTGCACAAGCTAA-AGCCA
21031093 -CAGTGTGCATCCCCCACAT
1 TCA-TGTGCATCCCCCACAT
21031112 CGCACACAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
36 2 0.04
37 23 0.46
38 1 0.02
39 24 0.48
ACGTcount: A:0.27, C:0.34, G:0.15, T:0.24
Consensus pattern (38 bp):
TCATGTGCATCCCCCACATTGTGCACAAGCTAAAGCCA
Found at i:21037652 original size:23 final size:23
Alignment explanation
Indices: 21037619--21037672 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
21037609 TACATATACT
*
21037619 CATCATTATCATGCACACCATCC
1 CATCATCATCATGCACACCATCC
* *
21037642 CATCATCATCATGCACACCGTCT
1 CATCATCATCATGCACACCATCC
21037665 CATCATCA
1 CATCATCA
21037673 CCAGTTCATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.30, C:0.39, G:0.06, T:0.26
Consensus pattern (23 bp):
CATCATCATCATGCACACCATCC
Found at i:21039283 original size:18 final size:18
Alignment explanation
Indices: 21039260--21039302 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
21039250 TTATTTTGCT
21039260 TTTACGCTACAATAATTA
1 TTTACGCTACAATAATTA
21039278 TTTACGCTACAATAATTA
1 TTTACGCTACAATAATTA
21039296 TTTACGC
1 TTTACGC
21039303 AAAGTTCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.40
Consensus pattern (18 bp):
TTTACGCTACAATAATTA
Found at i:21053603 original size:17 final size:17
Alignment explanation
Indices: 21053583--21053615 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21053573 CTCTTGATAA
21053583 AATAA-AACTCCTTATTG
1 AATAATAACT-CTTATTG
21053600 AATAATAACTCTTATT
1 AATAATAACTCTTATT
21053616 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAATAACTCTTATTG
Found at i:21053818 original size:28 final size:28
Alignment explanation
Indices: 21053756--21054081 Score: 393
Period size: 28 Copynumber: 11.8 Consensus size: 28
21053746 TTTAAGACAA
* *
21053756 TTCTTGTCTTTAATTAAAACAAAACATGTT
1 TTCTTGTC-TAAATTAAGAC-AAACATGTT
* * *
21053786 ATCTTGTCTAAATTGAGACAGACATGTT
1 TTCTTGTCTAAATTAAGACAAACATGTT
* *
21053814 TTCTTGTCTAAATTAAGAGAAA-AGTATT
1 TTCTTGTCTAAATTAAGACAAACA-TGTT
21053842 TTCTTGTCTAAATTAAG----AC----T
1 TTCTTGTCTAAATTAAGACAAACATGTT
21053862 TTCTTGTCTAAATTAAGACAAAACATGTT
1 TTCTTGTCTAAATTAAGAC-AAACATGTT
*
21053891 TTCTTATCTAAATTAAGACAAACATGTT
1 TTCTTGTCTAAATTAAGACAAACATGTT
21053919 TTCTTGTCTAAATTAAGACAAACATGTT
1 TTCTTGTCTAAATTAAGACAAACATGTT
* *
21053947 TTCTTGTCTAAATGAAGACAAAGATGTT
1 TTCTTGTCTAAATTAAGACAAACATGTT
* * * *
21053975 GTCTTATCTAGATTAAGAGAAAACATGTT
1 TTCTTGTCTAAATTAAGA-CAAACATGTT
21054004 TT-TTGTCTAAATTAAGACAAACATGTT
1 TTCTTGTCTAAATTAAGACAAACATGTT
* *
21054031 TTCTTGTCTAAATTAAGACAACCATATT
1 TTCTTGTCTAAATTAAGACAAACATGTT
21054059 TTCTTGTCTAAATTAAGACAAAC
1 TTCTTGTCTAAATTAAGACAAAC
21054082 TGATTTTTTG
Statistics
Matches: 256, Mismatches: 27, Indels: 28
0.82 0.09 0.09
Matches are distributed among these distances:
20 18 0.07
24 1 0.00
25 2 0.01
27 12 0.05
28 180 0.70
29 36 0.14
30 7 0.03
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.39
Consensus pattern (28 bp):
TTCTTGTCTAAATTAAGACAAACATGTT
Found at i:21053866 original size:20 final size:20
Alignment explanation
Indices: 21053841--21053880 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
21053831 AGAAAAGTAT
21053841 TTTCTTGTCTAAATTAAGAC
1 TTTCTTGTCTAAATTAAGAC
21053861 TTTCTTGTCTAAATTAAGAC
1 TTTCTTGTCTAAATTAAGAC
21053881 AAAACATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (20 bp):
TTTCTTGTCTAAATTAAGAC
Found at i:21054205 original size:114 final size:116
Alignment explanation
Indices: 21054074--21054299 Score: 366
Period size: 116 Copynumber: 2.0 Consensus size: 116
21054064 GTCTAAATTA
* * *
21054074 AGACAAACTGATTTTTTGTGTAGATTAA-A-AAAAATGTACAAGCTGTCATTTTTGTGCACATAT
1 AGACAAACTGATTTTTTGTCTAGATTAAGACAAAAATGTACAAGCTGTCACTTTTGTGCACAAAT
* * *
21054137 TTAATTAATTAAATAAAACATGCATTCGAACTTGAACAAGTTGAATTATTG
66 TTAATTAATTAAACAAAACATGCATTCCAACTTAAACAAGTTGAATTATTG
* *
21054188 AGACAAACTGTTTTTTTGTCTAGATTAAGACAAAAATGTACAAGCTGTCACTTTTGTGCATAAAT
1 AGACAAACTGATTTTTTGTCTAGATTAAGACAAAAATGTACAAGCTGTCACTTTTGTGCACAAAT
21054253 TTAATTAATTAAACAAAACATGCATTCCAACTTAAACAAGTTGAATT
66 TTAATTAATTAAACAAAACATGCATTCCAACTTAAACAAGTTGAATT
21054300 CTACAAAGCT
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
114 26 0.25
115 1 0.01
116 75 0.74
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (116 bp):
AGACAAACTGATTTTTTGTCTAGATTAAGACAAAAATGTACAAGCTGTCACTTTTGTGCACAAAT
TTAATTAATTAAACAAAACATGCATTCCAACTTAAACAAGTTGAATTATTG
Found at i:21061711 original size:15 final size:15
Alignment explanation
Indices: 21061683--21061720 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
21061673 ATTTTTCCAT
21061683 TTTCTTTT-CTTTCC
1 TTTCTTTTCCTTTCC
21061697 TTTCTTTTCCTTTCC
1 TTTCTTTTCCTTTCC
21061712 TTTCTTTTC
1 TTTCTTTTC
21061721 TTACTTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTCTTTTCCTTTCC
Found at i:21062719 original size:39 final size:39
Alignment explanation
Indices: 21062626--21062741 Score: 162
Period size: 39 Copynumber: 3.0 Consensus size: 39
21062616 AGCACACGTC
** **
21062626 GATGATATATGCCATACGCGGTGTGGGAGAGCACATGAT
1 GATGATATATGCCATGTGCGGTGTTAGAGAGCACATGAT
21062665 GATGATATATGCCATGTGCGGTGTTAGAGAGCACATGAT
1 GATGATATATGCCATGTGCGGTGTTAGAGAGCACATGAT
* *
21062704 GATGATATATGCCATGTGCAGTG-TAGAAGTGCACATGA
1 GATGATATATGCCATGTGCGGTGTTAG-AGAGCACATGA
21062742 GGATATTAGT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
38 3 0.04
39 67 0.96
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.26
Consensus pattern (39 bp):
GATGATATATGCCATGTGCGGTGTTAGAGAGCACATGAT
Found at i:21069664 original size:30 final size:28
Alignment explanation
Indices: 21069618--21069676 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 28
21069608 TGGTTCTAGG
*
21069618 TGTTCTCAACTTCAAATGTATCGATACA
1 TGTTCTCAACTTCAAATCTATCGATACA
*
21069646 TGTTCATCAATTTCCAAATCTATCGATACA
1 TGTTC-TCAACTT-CAAATCTATCGATACA
21069676 T
1 T
21069677 CCTTAAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 5 0.19
29 6 0.22
30 16 0.59
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.37
Consensus pattern (28 bp):
TGTTCTCAACTTCAAATCTATCGATACA
Found at i:21071971 original size:25 final size:25
Alignment explanation
Indices: 21071943--21072002 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
21071933 GTGGTCGCAA
* *
21071943 CCACGTATATCAACTTATGACCTTG
1 CCACGTATAACAACCTATGACCTTG
* *
21071968 CCACGTATAACAACCTGTGGCCTTG
1 CCACGTATAACAACCTATGACCTTG
*
21071993 CCATGTATAA
1 CCACGTATAA
21072003 TCACAGACCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (25 bp):
CCACGTATAACAACCTATGACCTTG
Found at i:21073369 original size:19 final size:20
Alignment explanation
Indices: 21073345--21073394 Score: 84
Period size: 19 Copynumber: 2.5 Consensus size: 20
21073335 AGGAAGGAGA
21073345 AAGAAGAAAAGAGAAAGGT-
1 AAGAAGAAAAGAGAAAGGTG
21073364 AAGAAGAAAAGAGAAAGGTGG
1 AAGAAGAAAAGAGAAAGGT-G
21073385 AAGAAGAAAA
1 AAGAAGAAAA
21073395 AAGCTTGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 19 0.66
21 10 0.34
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.04
Consensus pattern (20 bp):
AAGAAGAAAAGAGAAAGGTG
Found at i:21078925 original size:20 final size:19
Alignment explanation
Indices: 21078893--21078934 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
21078883 TCATTTCTAC
*
21078893 AATAAAAAGTAGAGAGAGA
1 AATAAAAACTAGAGAGAGA
*
21078912 AATAGAAAACTAGAGTGAGA
1 AATA-AAAACTAGAGAGAGA
21078932 AAT
1 AAT
21078935 GAGTTACTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.60, C:0.02, G:0.24, T:0.14
Consensus pattern (19 bp):
AATAAAAACTAGAGAGAGA
Found at i:21085819 original size:43 final size:43
Alignment explanation
Indices: 21085770--21085880 Score: 161
Period size: 43 Copynumber: 2.6 Consensus size: 43
21085760 ATTGACTCGA
*
21085770 CTATGTGCGAGTAGGGAGTGCGCATAAGCCAAG-GATGACCCTG
1 CTATGTGCGAGTAGGGAGTGCGCATAA-CCAAGTGATGACCCAG
* **
21085813 TTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAG
1 CTATGTGCGAGTAGGGAGTGCGCATAACCAAGTGATGACCCAG
*
21085856 CCATGTGCGAGTAGGGAGTGCGCAT
1 CTATGTGCGAGTAGGGAGTGCGCAT
21085881 GAGCTGGTGA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 3 0.05
43 58 0.95
ACGTcount: A:0.23, C:0.21, G:0.36, T:0.20
Consensus pattern (43 bp):
CTATGTGCGAGTAGGGAGTGCGCATAACCAAGTGATGACCCAG
Found at i:21085890 original size:43 final size:43
Alignment explanation
Indices: 21085772--21085893 Score: 156
Period size: 43 Copynumber: 2.8 Consensus size: 43
21085762 TGACTCGACT
* * **
21085772 ATGTGCGAGTAGGGAGTGCGCATAAGCCAAG-GATGACCCTGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAG-CAGGTGATGACCCAGCC
* *
21085815 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCAGGTGATGACCCAGCC
* *
21085858 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCAGGTGATGA
21085894 TGATGATGGG
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 2 0.03
43 67 0.97
ACGTcount: A:0.24, C:0.19, G:0.38, T:0.20
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCAGGTGATGACCCAGCC
Found at i:21087367 original size:23 final size:23
Alignment explanation
Indices: 21087337--21087396 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
21087327 TATACGTATA
* *
21087337 CCCATCATCATGATGCACACCAT
1 CCCATCATCATCATACACACCAT
*
21087360 CCCATCATCATCATATACACCAT
1 CCCATCATCATCATACACACCAT
*
21087383 CACATCATCATCAT
1 CCCATCATCATCAT
21087397 CACCAGCTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.33, C:0.38, G:0.03, T:0.25
Consensus pattern (23 bp):
CCCATCATCATCATACACACCAT
Found at i:21087481 original size:43 final size:43
Alignment explanation
Indices: 21087406--21087505 Score: 121
Period size: 43 Copynumber: 2.3 Consensus size: 43
21087396 TCACCAGCTC
** * *
21087406 ATGCGCACTCCCTACTCGCACATGGCTAGGTCATTATCGAG-TT
1 ATGCGCACTCCCTACTCGCACATAACCAGGTCATCATCG-GCTT
* *
21087449 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCAGGTCATCATCGGCTT
*
21087492 TTGCGCACTCCCTA
1 ATGCGCACTCCCTA
21087506 TTAACACATG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 1 0.02
43 48 0.98
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.26
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCAGGTCATCATCGGCTT
Found at i:21089591 original size:12 final size:12
Alignment explanation
Indices: 21089574--21089609 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
21089564 TTTTTGGAGA
21089574 ACATGTATCGAT
1 ACATGTATCGAT
21089586 ACATGT-TC-AT
1 ACATGTATCGAT
21089596 A-ATGTATCGAT
1 ACATGTATCGAT
21089607 ACA
1 ACA
21089610 ATTTTTCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
9 4 0.19
10 5 0.24
11 5 0.24
12 7 0.33
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (12 bp):
ACATGTATCGAT
Found at i:21090794 original size:68 final size:68
Alignment explanation
Indices: 21090636--21090803 Score: 203
Period size: 68 Copynumber: 2.5 Consensus size: 68
21090626 AGTTACTATG
* * *
21090636 TTATGTACATGACGTATATACCATATGCTACATGAGATGATTGAGAAAGCATGATGAATACCATG
1 TTATGTACATGACGTATATTCCATATACTACATGAAATGATTGAGAAAGCATGATGAATACCATG
21090701 AAA
66 AAA
* * * * * * *
21090704 TTAAGTATATGATGTACATTCCATATACTACTTGAAATGATTGAGAAGGCATGATGAAT-GCATG
1 TTATGTACATGACGTATATTCCATATACTACATGAAATGATTGAGAAAGCATGATGAATACCATG
*
21090768 AGA
66 AAA
* *
21090771 TTATGTACATGACGTATTTTTCCATATATTACA
1 TTATGTACATGACGTA-TATTCCATATACTACA
21090804 AAAGATGGGT
Statistics
Matches: 81, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
67 19 0.23
68 62 0.77
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (68 bp):
TTATGTACATGACGTATATTCCATATACTACATGAAATGATTGAGAAAGCATGATGAATACCATG
AAA
Found at i:21096105 original size:35 final size:35
Alignment explanation
Indices: 21096067--21096321 Score: 216
Period size: 35 Copynumber: 7.3 Consensus size: 35
21096057 CTAATTGTTT
*
21096067 AATTTAATCAATTAGACCCAATAACTTAATTAAAT
1 AATTTAATCAATTAGACCCAATAACTTAATTAAAC
* *
21096102 AATTTAAAT-AATTA-AGCCCAACAATTTAATTAAAC
1 AATTT-AATCAATTAGA-CCCAATAACTTAATTAAAC
* *
21096137 AATTTAATCAATTATG-CCCAATGACATAATTAAAC
1 AATTTAATCAATTA-GACCCAATAACTTAATTAAAC
* ****
21096172 AAATTTAATCAATTAGGCCCAATAACTTAATTGTTT
1 -AATTTAATCAATTAGACCCAATAACTTAATTAAAC
* * * *
21096208 AATTTAATTAGTTAGGCCCAATGACTTAATTAAAC
1 AATTTAATCAATTAGACCCAATAACTTAATTAAAC
* * * * *
21096243 AATTTAATTAATTAGGCCTAATGATTTAATTAAAC
1 AATTTAATCAATTAGACCCAATAACTTAATTAAAC
* * * *
21096278 GATTTAGTTAATTAGA--C-ACAACTTAATTAAAC
1 AATTTAATCAATTAGACCCAATAACTTAATTAAAC
21096310 AATTTTAATCAA
1 AA-TTTAATCAA
21096322 GTGCTTGAGA
Statistics
Matches: 179, Mismatches: 33, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
32 13 0.07
33 7 0.04
34 4 0.02
35 125 0.70
36 30 0.17
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.35
Consensus pattern (35 bp):
AATTTAATCAATTAGACCCAATAACTTAATTAAAC
Found at i:21096266 original size:106 final size:106
Alignment explanation
Indices: 21096067--21096314 Score: 288
Period size: 106 Copynumber: 2.4 Consensus size: 106
21096057 CTAATTGTTT
*
21096067 AATTTAATCAATTAGACCCAATAACTTAATTAAATAATTTAAATAATTAAGCCCAACAATTTAAT
1 AATTTAATCAATTAGACCCAATAACTTAATTAAATAATTTAAATAATTAAGCCCAACAACTTAAT
*
21096132 TAAACAATTTAATCAATTATGCCCAATGACATAATTAAACA
66 TAAACAATTTAATCAATTAGGCCCAATGACATAATTAAACA
* *** * * * **
21096173 AATTTAATCAATTAGGCCCAATAACTTAATTGTTTAATTTAATTAGTTAGGCCCAATGACTTAAT
1 AATTTAATCAATTAGACCCAATAACTTAATTAAATAATTTAAATAATTAAGCCCAACAACTTAAT
* * **
21096238 TAAACAATTTAATTAATTAGGCCTAATGATTTAATTAAAC-
66 TAAACAATTTAATCAATTAGGCCCAATGACATAATTAAACA
* * * * *
21096278 GATTTAGTTAATTAGA--C-ACAACTTAATTAAACAATTT
1 AATTTAATCAATTAGACCCAATAACTTAATTAAATAATTT
21096315 TAATCAAGTG
Statistics
Matches: 118, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
102 15 0.13
103 1 0.01
105 12 0.10
106 90 0.76
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.35
Consensus pattern (106 bp):
AATTTAATCAATTAGACCCAATAACTTAATTAAATAATTTAAATAATTAAGCCCAACAACTTAAT
TAAACAATTTAATCAATTAGGCCCAATGACATAATTAAACA
Found at i:21111744 original size:18 final size:18
Alignment explanation
Indices: 21111721--21111779 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
21111711 TAATTTAATC
21111721 AATTAAGCCCAATAACTT
1 AATTAAGCCCAATAACTT
*
21111739 AATTAA--ACAATTTAAC-T
1 AATTAAGCCCAA--TAACTT
* *
21111756 AATTAAGCCCAACAATTT
1 AATTAAGCCCAATAACTT
21111774 AATTAA
1 AATTAA
21111780 ATAATTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
16 3 0.09
17 9 0.28
18 17 0.53
19 3 0.09
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.31
Consensus pattern (18 bp):
AATTAAGCCCAATAACTT
Found at i:21111751 original size:35 final size:35
Alignment explanation
Indices: 21111712--21111896 Score: 210
Period size: 35 Copynumber: 5.2 Consensus size: 35
21111702 GTAATTGTTT
21111712 AATTTAATCAATTAAGCCCAATAACTTAATTAAAC
1 AATTTAATCAATTAAGCCCAATAACTTAATTAAAC
* * *
21111747 AATTTAA-CTAATTAAGCCCAACAATTTAATTAAAT
1 AATTTAATC-AATTAAGCCCAATAACTTAATTAAAC
* * *
21111782 AATTTTAATCAATTAGGCCTAATGACTTAATTAAAC
1 AA-TTTAATCAATTAAGCCCAATAACTTAATTAAAC
* ****
21111818 AAATTTAATCAATTAAGCCTAATAACTTAATTTTTT
1 -AATTTAATCAATTAAGCCCAATAACTTAATTAAAC
* * *
21111854 AATTTAATTAATTAGGCCCAAAAACTTAATTAAAC
1 AATTTAATCAATTAAGCCCAATAACTTAATTAAAC
21111889 AATTTAAT
1 AATTTAAT
21111897 TAGGCTCAAT
Statistics
Matches: 123, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
34 1 0.01
35 67 0.54
36 52 0.42
37 3 0.02
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.36
Consensus pattern (35 bp):
AATTTAATCAATTAAGCCCAATAACTTAATTAAAC
Found at i:21111789 original size:71 final size:70
Alignment explanation
Indices: 21111711--21111896 Score: 239
Period size: 71 Copynumber: 2.6 Consensus size: 70
21111701 CGTAATTGTT
* *
21111711 TAATTTAATCAATTAAGCCCAATAACTTAATTAAACAATTTAA-CTAATTAAGCCCAACAATTTA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATC-AATTAAGCCCAACAACTTA
21111775 ATTAAA
65 ATTAAA
* * * *
21111781 TAATTTTAATCAATTAGGCCTAATGACTTAATTAAACAAATTTAATCAATTAAGCCTAATAACTT
1 TAA-TTTAATCAATTAGGCCCAATAACTTAATTAAAC-AATTTAATCAATTAAGCCCAACAACTT
***
21111846 AATTTTT
64 AATTAAA
* *
21111853 TAATTTAATTAATTAGGCCCAAAAACTTAATTAAACAATTTAAT
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAAT
21111897 TAGGCTCAAT
Statistics
Matches: 100, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
70 11 0.11
71 59 0.59
72 29 0.29
73 1 0.01
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (70 bp):
TAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATCAATTAAGCCCAACAACTTAA
TTAAA
Found at i:21111897 original size:35 final size:35
Alignment explanation
Indices: 21111712--21111956 Score: 207
Period size: 35 Copynumber: 7.1 Consensus size: 35
21111702 GTAATTGTTT
* *
21111712 AATTTAATCAATTAAGCCCAATAACTTAATTAAAC
1 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
* * * * *
21111747 AATTTAACTAATTAAGCCCAACAATTTAATTAAAT
1 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
* * *
21111782 AATTTTAATCAATTAGGCCTAATGACTTAATTAAAC
1 AA-TTTAATTAATTAGGCCCAATAACTTAATTAAAC
* * * ****
21111818 AAATTTAATCAATTAAGCCTAATAACTTAATTTTTT
1 -AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
*
21111854 AATTTAATTAATTAGGCCCAAAAACTTAATTAAAC
1 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
* * * *
21111889 AA--T--TTAATTAGGCTCAATGATTTAGTTAAAC
1 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
* *
21111920 AATTTAGTTAATTAGG--C-ACAACTTAATTAAAC
1 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
21111952 AATTT
1 AATTT
21111957 TAATCGAGTG
Statistics
Matches: 168, Mismatches: 36, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
31 25 0.15
32 16 0.10
33 3 0.02
35 70 0.42
36 52 0.31
37 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.36
Consensus pattern (35 bp):
AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
Found at i:21111899 original size:31 final size:31
Alignment explanation
Indices: 21111861--21111925 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
21111851 TTTAATTTAA
21111861 TTAATTAGGCCCAAAAACTTAATTAAACAAT
1 TTAATTAGGCCCAAAAACTTAATTAAACAAT
* ** * *
21111892 TTAATTAGGCTCAATGATTTAGTTAAACAAT
1 TTAATTAGGCCCAAAAACTTAATTAAACAAT
21111923 TTA
1 TTA
21111926 GTTAATTAGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.35
Consensus pattern (31 bp):
TTAATTAGGCCCAAAAACTTAATTAAACAAT
Found at i:21116904 original size:3 final size:3
Alignment explanation
Indices: 21116896--21116920 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
21116886 CCAACAGCTT
21116896 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
21116921 CTTTCATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:21117750 original size:42 final size:42
Alignment explanation
Indices: 21117684--21117807 Score: 122
Period size: 42 Copynumber: 3.0 Consensus size: 42
21117674 AATGATATTA
* * ** ** *
21117684 ACCCAGCTATGTGCGAGTAAGAGTGCACACAAGCTGTTGTTG
1 ACCCGGCTATGTGTGAGTGGGAGTGCACACAAGCCATTGCTG
** *
21117726 ACTTGGCTATGTGTGAGTGGGAGTGCACATAAGCCATTGCTG
1 ACCCGGCTATGTGTGAGTGGGAGTGCACACAAGCCATTGCTG
* ** *
21117768 ACCCGGTTATGTGTGAGTGGGAGTGTGCATAAGCCATTGC
1 ACCCGGCTATGTGTGAGTGGGAGTGCACACAAGCCATTGC
21117808 ATATGAGATG
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.27
Consensus pattern (42 bp):
ACCCGGCTATGTGTGAGTGGGAGTGCACACAAGCCATTGCTG
Found at i:21117855 original size:2 final size:2
Alignment explanation
Indices: 21117848--21117919 Score: 108
Period size: 2 Copynumber: 36.0 Consensus size: 2
21117838 ATGATGATTG
* **
21117848 AT AT AT AT AT AT AT AT AT AT AT AN NN 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
*
21117890 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21117920 GGTATATGGT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:21119598 original size:29 final size:28
Alignment explanation
Indices: 21119556--21119700 Score: 173
Period size: 29 Copynumber: 5.0 Consensus size: 28
21119546 TGACAGCTTT
21119556 AACATGTTTGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
21119584 AACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATGTTT-GTCTTAATTTAGACAAGAA
*
21119613 AATATGTTTGTCTTAATTTAAGACAAGAAA
1 AACATGTTTGTCTTAATTT-AGACAAG-AA
* * *
21119643 AATATTTTTTTGTCTTAATCTAGACAAGAA
1 AACA--TGTTTGTCTTAATTTAGACAAGAA
* * *
21119673 TACATATTTGTCTCAAATTTAGACAAGA
1 AACATGTTTGTCT-TAATTTAGACAAGA
21119701 TAAAATATTT
Statistics
Matches: 103, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
28 27 0.26
29 46 0.45
30 10 0.10
31 7 0.07
32 13 0.13
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.37
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:21119671 original size:60 final size:58
Alignment explanation
Indices: 21119556--21119722 Score: 219
Period size: 60 Copynumber: 2.8 Consensus size: 58
21119546 TGACAGCTTT
* * * *
21119556 AACATGTTTGTCTTAATTTAGACAAG-AAAACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATCTAGACAAGAA
*
21119613 AATATGTTTGTCTTAATTTAAGACAAGAAAAATATTTTTTTGTCTTAATCTAGACAAGAA
1 AACATGTTTGTCTTAATTT-AGACAAGAAAAATA-TTTTTTGTCTTAATCTAGACAAGAA
* * *
21119673 TACATATTTGTCTCAAATTTAGACAAGATAAAATATTTTTTGTCTTAATC
1 AACATGTTTGTCT-TAATTTAGACAAGA-AAAATATTTTTTGTCTTAATC
21119723 ACGGACAAGA
Statistics
Matches: 96, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
57 18 0.19
58 7 0.07
59 5 0.05
60 55 0.57
61 11 0.11
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (58 bp):
AACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATCTAGACAAGAA
Found at i:21125264 original size:42 final size:42
Alignment explanation
Indices: 21125205--21125490 Score: 394
Period size: 42 Copynumber: 6.8 Consensus size: 42
21125195 GTGGACCCAG
* * *
21125205 CTATGTGTGAGTAGGAGTGCACATAAGTCGTTGCTGACCTGA
1 CTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGACCCGA
* *
21125247 CTATGTGCGAGTTGGAGTGCACATAAGCCGTTGCTGACCCAA
1 CTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGACCCGA
*
21125289 CTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGACCCGG
1 CTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGACCCGA
* * *
21125331 CTATGTGCGAGTATGAGTGCACATAAGCCGTTGCTGAACCGG
1 CTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGACCCGA
* * *
21125373 CTATGTGCAAGTAAGAGTGCACATAAGCCGTTGCTGACCCGG
1 CTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGACCCGA
* *
21125415 CTATGTGTGAGTGGGAGTGCACATAAGCCGTTGCTGACCC-A
1 CTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGACCCGA
* * * *
21125456 GCTATATGCGAGTGGGAGTACGCATAAGCCGTTGC
1 -CTATGTGCGAGTAGGAGTGCACATAAGCCGTTGC
21125491 ATATGAGATG
Statistics
Matches: 221, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
42 221 1.00
ACGTcount: A:0.23, C:0.22, G:0.31, T:0.24
Consensus pattern (42 bp):
CTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGACCCGA
Found at i:21125339 original size:84 final size:84
Alignment explanation
Indices: 21125198--21125490 Score: 435
Period size: 84 Copynumber: 3.5 Consensus size: 84
21125188 TGTTGATGTG
* * * *
21125198 GACCCAGCTATGTGTGAGTAGGAGTGCACATAAGTCGTTGCTGACCTGACTATGTGCGAGTTGGA
1 GACCCAGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGACCCGGCTATGTGCGAGTTGGA
21125263 GTGCACATAAGCCGTTGCT
66 GTGCACATAAGCCGTTGCT
*
21125282 GACCCAACTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGACCCGGCTATGTGCGAGTAT-G
1 GACCCAGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGACCCGGCTATGTGCGAGT-TGG
21125346 AGTGCACATAAGCCGTTGCT
65 AGTGCACATAAGCCGTTGCT
* * * * * *
21125366 GAACCGGCTATGTGCAAGTAAGAGTGCACATAAGCCGTTGCTGACCCGGCTATGTGTGAGTGGGA
1 GACCCAGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGACCCGGCTATGTGCGAGTTGGA
21125431 GTGCACATAAGCCGTTGCT
66 GTGCACATAAGCCGTTGCT
* * * *
21125450 GACCCAGCTATATGCGAGTGGGAGTACGCATAAGCCGTTGC
1 GACCCAGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGC
21125491 ATATGAGATG
Statistics
Matches: 187, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
84 186 0.99
85 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (84 bp):
GACCCAGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGACCCGGCTATGTGCGAGTTGGA
GTGCACATAAGCCGTTGCT
Found at i:21128214 original size:80 final size:80
Alignment explanation
Indices: 21128079--21128406 Score: 433
Period size: 80 Copynumber: 4.1 Consensus size: 80
21128069 TATCTCAACA
* * ** * *
21128079 CATACATTTCATAATCTCATAAAATCATTTACATGCTTAGCGTATAGTGTCTATGACTATTTCAA
1 CATACATTTCATAACCTCAT-AAATCACTTACATGCTTAGCCCATAGTGTATATGACTATCTCAA
21128144 CACATACATCTCATGG
65 CACATACATCTCATGG
** * * * *
21128160 CATACATTTCATAGTCTCATAAATCAATTACATGCTTAGCCTATAGTGAATATGACTATCTCAAA
1 CATACATTTCATAACCTCATAAATCACTTACATGCTTAGCCCATAGTGTATATGACTATCTCAAC
*
21128225 ATATACATCTCATGG
66 ACATACATCTCATGG
* * *
21128240 CATACATTTCATAGCCTTAAAAATCACTTACATGCTTAGCCCATAGTGTATATGACTATCTCAAC
1 CATACATTTCATAACCTCATAAATCACTTACATGCTTAGCCCATAGTGTATATGACTATCTCAAC
*
21128305 ATATACATCTCATGG
66 ACATACATCTCATGG
* * * *
21128320 CATAGATTTCATAACCTCATAAATCACTTACATGCTTAGCCCATAGTGTACATG-GTATGCTTAA
1 CATACATTTCATAACCTCATAAATCACTTACATGCTTAGCCCATAGTGTATATGACTAT-CTCAA
*
21128384 CACATACATTTCATGG
65 CACATACATCTCATGG
21128400 CATACAT
1 CATACAT
21128407 GTTACAATCT
Statistics
Matches: 221, Mismatches: 25, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
79 3 0.01
80 199 0.90
81 19 0.09
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (80 bp):
CATACATTTCATAACCTCATAAATCACTTACATGCTTAGCCCATAGTGTATATGACTATCTCAAC
ACATACATCTCATGG
Found at i:21130422 original size:2 final size:2
Alignment explanation
Indices: 21130415--21130455 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
21130405 ACCCTAACTT
* *
21130415 TC TC TC TC TC TC TC TC TC TC TC TC TC GC TC TC TC TT TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
21130456 AACCCATCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.46, G:0.02, T:0.51
Consensus pattern (2 bp):
TC
Found at i:21134231 original size:30 final size:31
Alignment explanation
Indices: 21134195--21134253 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
21134185 GCACATAAGT
* *
21134195 CCTCAAA-CTTTTCCTTATTTATAATTTGAC
1 CCTCAAATCTTTTCATTATTTACAATTTGAC
*
21134225 CCTCAAATCTTTTCATTCTTTACAATTTG
1 CCTCAAATCTTTTCATTATTTACAATTTG
21134254 GTCCTTCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.25, C:0.24, G:0.03, T:0.47
Consensus pattern (31 bp):
CCTCAAATCTTTTCATTATTTACAATTTGAC
Found at i:21137240 original size:3 final size:3
Alignment explanation
Indices: 21137232--21137295 Score: 64
Period size: 3 Copynumber: 22.7 Consensus size: 3
21137222 CATGAGCTGG
* * * *
21137232 TGA TGA TGA TGA TG- GGA TGG TG- TGA TGA TGA TGA TGA TG- GGA TGG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
21137277 TG- TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TG
21137296 GGTATATGCG
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 6 0.12
3 45 0.88
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:21137258 original size:8 final size:8
Alignment explanation
Indices: 21137232--21137295 Score: 65
Period size: 8 Copynumber: 7.6 Consensus size: 8
21137222 CATGAGCTGG
21137232 TGATGATGA
1 TGATG-TGA
*
21137241 TGATGGGA
1 TGATGTGA
*
21137249 TGGTGTGA
1 TGATGTGA
21137257 TGATGATGA
1 TGATG-TGA
*
21137266 TGATGGGA
1 TGATGTGA
*
21137274 TGGTGTGA
1 TGATGTGA
21137282 TGATGATGA
1 TGATG-TGA
21137291 TGATG
1 TGATG
21137296 GGTATATGCG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
8 24 0.53
9 21 0.47
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.33
Consensus pattern (8 bp):
TGATGTGA
Found at i:21137266 original size:25 final size:25
Alignment explanation
Indices: 21137232--21137297 Score: 132
Period size: 25 Copynumber: 2.6 Consensus size: 25
21137222 CATGAGCTGG
21137232 TGATGATGATGATGGGATGGTGTGA
1 TGATGATGATGATGGGATGGTGTGA
21137257 TGATGATGATGATGGGATGGTGTGA
1 TGATGATGATGATGGGATGGTGTGA
21137282 TGATGATGATGATGGG
1 TGATGATGATGATGGG
21137298 TATATGCGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (25 bp):
TGATGATGATGATGGGATGGTGTGA
Found at i:21137712 original size:60 final size:59
Alignment explanation
Indices: 21137619--21137766 Score: 152
Period size: 60 Copynumber: 2.5 Consensus size: 59
21137609 CAAAATACAT
* * * * * **
21137619 TCTCGTTGCAGTGAGAAACTTTCTATTTCTGGGTTGCAATTTCGCTACAGTGAGATTGAA
1 TCTCGCTGCAGCGAGAAACTTT-TGTTTCTGGGTTACAATTTCACTACAACGAGATTGAA
* * *
21137679 TTTCGCTGCAGCGAGAAACATTTTGTTTGTGGGTTACAATTTCACTGCAACGAGATTGAA
1 TCTCGCTGCAGCGAGAAAC-TTTTGTTTCTGGGTTACAATTTCACTACAACGAGATTGAA
* * *
21137739 TCTCGCTGTAGCGAAAAACCTTCTGTTT
1 TCTCGCTGCAGCGAGAAA-CTTTTGTTT
21137767 TGGTCTCCTA
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
60 68 0.94
61 4 0.06
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (59 bp):
TCTCGCTGCAGCGAGAAACTTTTGTTTCTGGGTTACAATTTCACTACAACGAGATTGAA
Found at i:21141448 original size:42 final size:42
Alignment explanation
Indices: 21141382--21141501 Score: 177
Period size: 42 Copynumber: 2.9 Consensus size: 42
21141372 ATGTGAACTT
* * * *
21141382 GGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGACTA
1 GGCTATGTGCAAGTGGGAGTGCACATAAGCCGTTGCTAACCA
* *
21141424 GGCTATGTGCAAGTGGGAGAGCACATAAGCCGTTGCTAACCG
1 GGCTATGTGCAAGTGGGAGTGCACATAAGCCGTTGCTAACCA
*
21141466 GGCTATGTGCAAGTGGGAGTGCACATAAGCTGTTGC
1 GGCTATGTGCAAGTGGGAGTGCACATAAGCCGTTGC
21141502 ATATGAGATG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.23
Consensus pattern (42 bp):
GGCTATGTGCAAGTGGGAGTGCACATAAGCCGTTGCTAACCA
Found at i:21151949 original size:21 final size:21
Alignment explanation
Indices: 21151923--21151964 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
21151913 TTCGCCACTT
* *
21151923 GAATCTCGCTGCAGTGAGAAA
1 GAATCTCACTGCAGCGAGAAA
21151944 GAATCTCACTGCAGCGAGAAA
1 GAATCTCACTGCAGCGAGAAA
21151965 CTTTCTGTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (21 bp):
GAATCTCACTGCAGCGAGAAA
Found at i:21159136 original size:43 final size:43
Alignment explanation
Indices: 21159056--21159137 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
21159046 TATATTGACT
*
21159056 CGGTTATGTGCGAGTAGGAAGTGCACATAGGCCGATGATAAAC
1 CGGTTATGTGCGAGTAGGAAGTGCACATAGACCGATGATAAAC
* *
21159099 CGGTTATGTGCGAGTAGGGAGTGCATATA-ACCAGATGAT
1 CGGTTATGTGCGAGTAGGAAGTGCACATAGACC-GATGAT
21159138 GACCCAACCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 2 0.06
43 33 0.94
ACGTcount: A:0.29, C:0.15, G:0.33, T:0.23
Consensus pattern (43 bp):
CGGTTATGTGCGAGTAGGAAGTGCACATAGACCGATGATAAAC
Found at i:21159207 original size:23 final size:23
Alignment explanation
Indices: 21159177--21159232 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
21159167 CATGAGCTGG
21159177 TGATGATGAGACGGTGTGCATGA
1 TGATGATGAGACGGTGTGCATGA
* *
21159200 TGATGATGGGATGGTGTGCATGA
1 TGATGATGAGACGGTGTGCATGA
21159223 TGATGATGAG
1 TGATGATGAG
21159233 TATATGTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.25, C:0.05, G:0.41, T:0.29
Consensus pattern (23 bp):
TGATGATGAGACGGTGTGCATGA
Found at i:21169636 original size:42 final size:42
Alignment explanation
Indices: 21169558--21169638 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
21169548 CACACTTCGT
*
21169558 TCATGTGCACTCCCTACTCGCACATAGCTGGGTCATCATCAGC
1 TCATGTGCACTCCCTAC-CGCACATAGCTGGATCATCATCAGC
* *
21169601 TCATGTGCACTCCCATA-CGCACATAGTTGTATCATCAT
1 TCATGTGCACTCCC-TACCGCACATAGCTGGATCATCAT
21169639 TATCACACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
42 18 0.53
43 14 0.41
44 2 0.06
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.28
Consensus pattern (42 bp):
TCATGTGCACTCCCTACCGCACATAGCTGGATCATCATCAGC
Found at i:21172748 original size:19 final size:17
Alignment explanation
Indices: 21172702--21172749 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
21172692 ATGAATACAA
*
21172702 TCAT-ATTTTTGAACTT
1 TCATCATTTTTCAACTT
21172718 TCATCATTTTTCAACTT
1 TCATCATTTTTCAACTT
*
21172735 TACTATCCTTTTTCA
1 T-C-ATCATTTTTCA
21172750 CCATTTAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 4 0.15
17 12 0.44
18 1 0.04
19 10 0.37
ACGTcount: A:0.23, C:0.21, G:0.02, T:0.54
Consensus pattern (17 bp):
TCATCATTTTTCAACTT
Found at i:21175234 original size:47 final size:46
Alignment explanation
Indices: 21175182--21175309 Score: 111
Period size: 44 Copynumber: 2.8 Consensus size: 46
21175172 AATAAAAATT
*
21175182 ATATATATGTAGTACATCAAATTTATCATTATATATAATT-TATATAC
1 ATATATAT-TAGTACATCAAATTTATCATTATATATAATTAAATAT-C
* * * * * * *
21175229 ATATATA-TAAT-GAT-AACTTTTATTATTGTAAATAATTAAATATT
1 ATATATATTAGTACATCAA-ATTTATCATTATATATAATTAAATATC
*
21175273 ATACATATATAGTACATCAAATTTATCATTATATATA
1 ATATATAT-TAGTACATCAAATTTATCATTATATATA
21175310 TTATATTTAA
Statistics
Matches: 60, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
43 2 0.03
44 24 0.40
45 7 0.12
46 3 0.05
47 22 0.37
48 2 0.03
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (46 bp):
ATATATATTAGTACATCAAATTTATCATTATATATAATTAAATATC
Found at i:21175483 original size:174 final size:166
Alignment explanation
Indices: 21175151--21175490 Score: 437
Period size: 174 Copynumber: 2.0 Consensus size: 166
21175141 ATATAGTATC
* * *
21175151 TAATTTTTGTTATTGTAAATCAATAAAAATTATATATATGTAGTACATCAAATTTATCATTATAT
1 TAATTTTGGTTATTGTAAATCAATAAAAATTATACATATATAGTACATCAAATTTATCATTATAT
* * *
21175216 ATAATTTATATACATATATATAATGATAACTTTTATTATTGTAAATAATTAAATATTATACATAT
66 AAAATTTAAATACATATATATAATGATAACTTTTATTATTGTAAATAATTAAAAATTATACATAT
*
21175281 ATAGTACATCAAATTTATCATTATATATATTATATT
131 ATAGTACATCAAATTTATCATTATATATAATATATT
* *
21175317 TAATTTTGGTTATTGTAAATTATTAAAAATTATACATATATAGTACATCAAATTTATCATTATTT
1 TAATTTTGGTTATTGTAAATCAATAAAAATTATACATATATAGTACATCAAATTTATCATTA---
* ** * * * *
21175382 CTTTTGAAAAGTTTCAAATTTATCTATATAATGATAATTTTTGTTATTGTAAATCATTAAAAATT
63 --TAT-AAAA-TTT-AAATACATATATATAATGATAACTTTTATTATTGTAAATAATTAAAAATT
* * *
21175447 ATGCATGTATAGTATATCAAATTTATCATTATATATAATATATT
123 ATACATATATAGTACATCAAATTTATCATTATATATAATATATT
21175491 ATATACATTT
Statistics
Matches: 147, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
166 57 0.39
171 2 0.01
172 3 0.02
173 3 0.02
174 82 0.56
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (166 bp):
TAATTTTGGTTATTGTAAATCAATAAAAATTATACATATATAGTACATCAAATTTATCATTATAT
AAAATTTAAATACATATATATAATGATAACTTTTATTATTGTAAATAATTAAAAATTATACATAT
ATAGTACATCAAATTTATCATTATATATAATATATT
Found at i:21176478 original size:16 final size:16
Alignment explanation
Indices: 21176457--21176507 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
21176447 AACATAGGAA
21176457 AGGGTTTGCATGAGAG
1 AGGGTTTGCATGAGAG
* **
21176473 AGGGTTGGCACAAGAG
1 AGGGTTTGCATGAGAG
* *
21176489 AGGCTTTGCTTGAGAG
1 AGGGTTTGCATGAGAG
21176505 AGG
1 AGG
21176508 TGGAGCAAAG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.25, C:0.10, G:0.43, T:0.22
Consensus pattern (16 bp):
AGGGTTTGCATGAGAG
Found at i:21183944 original size:47 final size:47
Alignment explanation
Indices: 21183890--21183983 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
21183880 AGGGAAAGAA
21183890 AAAGTCACTGCAGCATCACAAGCAAAGACAAAACCACCTACTAAAGG
1 AAAGTCACTGCAGCATCACAAGCAAAGACAAAACCACCTACTAAAGG
21183937 AAAGTCACTGCAGCATCACAAGCAAAGACAAAACCACCTACTAAAGG
1 AAAGTCACTGCAGCATCACAAGCAAAGACAAAACCACCTACTAAAGG
21183984 GAAGAAAACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.47, C:0.28, G:0.15, T:0.11
Consensus pattern (47 bp):
AAAGTCACTGCAGCATCACAAGCAAAGACAAAACCACCTACTAAAGG
Found at i:21186311 original size:51 final size:52
Alignment explanation
Indices: 21186246--21186349 Score: 183
Period size: 51 Copynumber: 2.0 Consensus size: 52
21186236 TTTAGGTTCG
* *
21186246 AATTGTAGCATTTTAGGTGTTTTTCTAGTTTAAG-TTGGTTACATGTTGAGT
1 AATTATAGCATTTTAGGTGTTTTTCTAGTTTAAGTTTGATTACATGTTGAGT
21186297 AATTATAGCATTTTAGGTGTTTTTCTAGTTTAAGTTTGATTACATGTTGAGT
1 AATTATAGCATTTTAGGTGTTTTTCTAGTTTAAGTTTGATTACATGTTGAGT
21186349 A
1 A
21186350 GTTAATTTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 33 0.66
52 17 0.34
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.49
Consensus pattern (52 bp):
AATTATAGCATTTTAGGTGTTTTTCTAGTTTAAGTTTGATTACATGTTGAGT
Found at i:21191247 original size:28 final size:28
Alignment explanation
Indices: 21191213--21191286 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 28
21191203 TTTATTGTTT
21191213 TAAATTAAGACAAACATATTTTCCTT-CC
1 TAAATTAAGACAAACATATTTT-CTTACC
* * *
21191241 TAAATTAAGACCAAAAATGTTTTCTTATC
1 TAAATTAAGA-CAAACATATTTTCTTACC
21191270 TAAATTAAGACAAACAT
1 TAAATTAAGACAAACAT
21191287 GTTAAAGTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
28 19 0.47
29 21 0.52
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (28 bp):
TAAATTAAGACAAACATATTTTCTTACC
Found at i:21191272 original size:29 final size:28
Alignment explanation
Indices: 21191213--21191289 Score: 102
Period size: 28 Copynumber: 2.7 Consensus size: 28
21191203 TTTATTGTTT
*
21191213 TAAATTAAGACAAACATATTTTCCTTCC
1 TAAATTAAGACAAACATGTTTTCCTTCC
* *
21191241 TAAATTAAGACCAAAAATGTTTT-CTTATC
1 TAAATTAAGA-CAAACATGTTTTCCTT-CC
21191270 TAAATTAAGACAAACATGTT
1 TAAATTAAGACAAACATGTT
21191290 AAAGTTGCCA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 22 0.51
29 21 0.49
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (28 bp):
TAAATTAAGACAAACATGTTTTCCTTCC
Found at i:21196459 original size:5 final size:5
Alignment explanation
Indices: 21196445--21196487 Score: 70
Period size: 5 Copynumber: 8.6 Consensus size: 5
21196435 CTGGACGGTG
21196445 AAAG- AAAGA AAAGA AAAGA AAAGA AAAGA AAAGAA AAAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAG-A AAAGA AAA
21196488 AAAGAAAGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
4 4 0.11
5 28 0.76
6 5 0.14
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:21201391 original size:17 final size:18
Alignment explanation
Indices: 21201369--21201404 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
21201359 TCCCCTTTTT
21201369 TTTTAATA-AAAAAAATA
1 TTTTAATAGAAAAAAATA
*
21201386 TTTTAATAGAAGAAAATA
1 TTTTAATAGAAAAAAATA
21201404 T
1 T
21201405 ATATTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (18 bp):
TTTTAATAGAAAAAAATA
Found at i:21202527 original size:17 final size:17
Alignment explanation
Indices: 21202497--21202529 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21202487 TTCTTGATTA
21202497 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
21202514 AATAATAACT-CTTATT
1 AATAA-AACTCCTTATT
21202530 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:21202706 original size:31 final size:29
Alignment explanation
Indices: 21202671--21202807 Score: 111
Period size: 31 Copynumber: 4.6 Consensus size: 29
21202661 TTAAGACAAC
21202671 TCTTGTCTGTAATTAAGACAAAAAAATTTGA
1 TCTTGTCT-TAATTAAGACAAAAAAATTT-A
* * * *
21202702 TCTTGTCTAAATTTGAGAC--AAATATCTA
1 TCTTGTCTTAA-TTAAGACAAAAAAATTTA
*
21202730 TTCTTGTC-TAGATTAAGACAAAAAATATTTT
1 -TCTTGTCTTA-ATTAAGACAAAAAA-ATTTA
* *
21202761 TCTTGTCTTAAATTAAGACAAACATATTT-
1 TCTTGTCTT-AATTAAGACAAAAAAATTTA
*
21202790 TCTTGTCTAAATTAAGAC
1 TCTTGTCTTAATTAAGAC
21202808 CAAACATGTT
Statistics
Matches: 86, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
28 17 0.20
29 22 0.26
30 16 0.19
31 30 0.35
32 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
TCTTGTCTTAATTAAGACAAAAAAATTTA
Found at i:21202748 original size:59 final size:59
Alignment explanation
Indices: 21202671--21202842 Score: 181
Period size: 59 Copynumber: 2.9 Consensus size: 59
21202661 TTAAGACAAC
* * * *
21202671 TCTTGTCTGTAATTAAGACAAAAAA-ATTTGATCTTGTC-TAAATTTGAGACAAATATCTAT
1 TCTTGTCT-AAATTAAGACAAAAAATATTT-ATCTTGTCTTAAA-TTAAGACAAACATATAT
* * *
21202731 TCTTGTCTAGATTAAGACAAAAAATATTTTTCTTGTCTTAAATTAAGACAAACATATTT
1 TCTTGTCTAAATTAAGACAAAAAATATTTATCTTGTCTTAAATTAAGACAAACATATAT
* * * * *
21202790 TCTTGTCTAAATTAAGACCAAACATGTTT-TCTTATC-CAAATTAAGACAAACAT
1 TCTTGTCTAAATTAAGACAAAAAATATTTATCTTGTCTTAAATTAAGACAAACAT
21202843 TTTAGAGCTG
Statistics
Matches: 97, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
57 16 0.16
58 6 0.06
59 59 0.61
60 16 0.16
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (59 bp):
TCTTGTCTAAATTAAGACAAAAAATATTTATCTTGTCTTAAATTAAGACAAACATATAT
Found at i:21202811 original size:29 final size:28
Alignment explanation
Indices: 21202671--21202842 Score: 164
Period size: 29 Copynumber: 5.9 Consensus size: 28
21202661 TTAAGACAAC
* * *
21202671 TCTTGTCTGTAATTAAGACAAAAAAATTT
1 TCTTGTCT-AAATTAAGACAAACATATTT
* * * *
21202700 GATCTTGTCTAAATTTGAGACAAATATCTAT
1 --TCTTGTCTAAA-TTAAGACAAACATATTT
* *
21202731 TCTTGTCTAGATTAAGACAAAAAATATTTT
1 TCTTGTCTAAATTAAGAC-AAACATA-TTT
21202761 TCTTGTCTTAAATTAAGACAAACATATTT
1 TCTTGTC-TAAATTAAGACAAACATATTT
*
21202790 TCTTGTCTAAATTAAGACCAAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATATTT
* *
21202819 TCTTATCCAAATTAAGACAAACAT
1 TCTTGTCTAAATTAAGACAAACAT
21202843 TTTAGAGCTG
Statistics
Matches: 120, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
28 23 0.19
29 50 0.42
30 17 0.14
31 30 0.25
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATATTT
Found at i:21202833 original size:88 final size:89
Alignment explanation
Indices: 21202671--21202839 Score: 209
Period size: 88 Copynumber: 1.9 Consensus size: 89
21202661 TTAAGACAAC
* * *
21202671 TCTTGTCTGTAATTAAGACAAAAAAATTTGATCTTGTCTAAATTTGAGACAAATATCTATTCTTG
1 TCTTGTCTGTAATTAAGACAAAAAAATTT-ATCTTGTCTAAATTTAAGACAAACATCTATTCTTA
* *
21202736 TCTAGATTAAGACAAAAAATATTTT
65 TCCAAATTAAGACAAAAAATATTTT
* * * *
21202761 TCTTGTCT-TAAATTAAGACAAACATATTT-TCTTGTCTAAA-TTAAGACCAAACATGTTTTCTT
1 TCTTGTCTGT-AATTAAGACAAAAAAATTTATCTTGTCTAAATTTAAGA-CAAACATCTATTCTT
21202823 ATCCAAATTAAGACAAA
64 ATCCAAATTAAGACAAA
21202840 CATTTTAGAG
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
87 5 0.07
88 37 0.54
89 1 0.01
90 25 0.37
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (89 bp):
TCTTGTCTGTAATTAAGACAAAAAAATTTATCTTGTCTAAATTTAAGACAAACATCTATTCTTAT
CCAAATTAAGACAAAAAATATTTT
Found at i:21205835 original size:23 final size:23
Alignment explanation
Indices: 21205784--21205857 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
21205774 TTTTAGAGTT
* *
21205784 TGTGAAACGAAATGGTGGGAATG
1 TGTGACACGACATGGTGGGAATG
21205807 TGTGACACGACATGGTGGGAATG
1 TGTGACACGACATGGTGGGAATG
* *
21205830 TGTGACAC-ATCATGGTGAGAATA
1 TGTGACACGA-CATGGTGGGAATG
21205853 TGTGA
1 TGTGA
21205858 GACGGGTGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 1 0.02
23 45 0.98
ACGTcount: A:0.31, C:0.09, G:0.35, T:0.24
Consensus pattern (23 bp):
TGTGACACGACATGGTGGGAATG
Found at i:21206043 original size:23 final size:23
Alignment explanation
Indices: 21206012--21206064 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
21206002 ACGTTTAGAG
*
21206012 TGTGGGACACACCAGGGTCAGAA
1 TGTGTGACACACCAGGGTCAGAA
** *
21206035 TGTGTGACACGGCAGGGTCATAA
1 TGTGTGACACACCAGGGTCAGAA
21206058 TGTGTGA
1 TGTGTGA
21206065 AACGGCATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.36, T:0.21
Consensus pattern (23 bp):
TGTGTGACACACCAGGGTCAGAA
Found at i:21206069 original size:23 final size:23
Alignment explanation
Indices: 21206024--21206071 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
21206014 TGGGACACAC
*
21206024 CAGGGTCAGAATGTGTGACACGG
1 CAGGGTCAGAATGTGTGAAACGG
*
21206047 CAGGGTCATAATGTGTGAAACGG
1 CAGGGTCAGAATGTGTGAAACGG
21206070 CA
1 CA
21206072 TAATGATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.29, C:0.17, G:0.35, T:0.19
Consensus pattern (23 bp):
CAGGGTCAGAATGTGTGAAACGG
Found at i:21206162 original size:23 final size:23
Alignment explanation
Indices: 21206119--21206162 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
21206109 TTTAGAATGT
*
21206119 GTGACACGCCATGGAGGGAATCC
1 GTGACACGCCATGGAGAGAATCC
* *
21206142 GTGACACGGCATGGTGAGAAT
1 GTGACACGCCATGGAGAGAAT
21206163 ATGTGGGACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.20, G:0.36, T:0.16
Consensus pattern (23 bp):
GTGACACGCCATGGAGAGAATCC
Found at i:21206317 original size:185 final size:185
Alignment explanation
Indices: 21206003--21206414 Score: 522
Period size: 185 Copynumber: 2.2 Consensus size: 185
21205993 GACACGACAA
* * * *
21206003 CGTTTAGAGTGTGGGACACACCAGGGTCAGAATGTGTGACACGGCAGGGTCATAATGTGTGAAAC
1 CGTTTAGAGTGTGGGACACGCCATGGTCAGAACGTGTGACACGCCAGGGTCATAATGTGTGAAAC
* *
21206068 GGCATAATGATAATGTTTGACACAAGTGTGACACGACAAGGTTTAGAATGTGTGACACGCCATGG
66 GGCACAATGATAATGTTGGACACAAGTGTGACACGACAAGGTTTAGAATGTGTGACACGCCATGG
* * *
21206133 AGGGAATCCGTGACACGGCATGGTGAGAATATGTGGGACTG-GTGTAACACGGTAG
131 AGGGAATCCGTGACACGGCACGATGAGAATATGTGGGAC-GAGTATAACACGGTAG
* * * *
21206188 CGTTTAGAGTGTGCGACATGCTATGGTCAGAACGTGTGACACGCCAGGGTCATACTGTGTGAAAC
1 CGTTTAGAGTGTGGGACACGCCATGGTCAGAACGTGTGACACGCCAGGGTCATAATGTGTGAAAC
* *** ** * *
21206253 GGCACAGTGATAATGTTGGACAGGGGTGTGACACG-GTAGGCTTTAGAGTGTGTGACATGCCATG
66 GGCACAATGATAATGTTGGACACAAGTGTGACACGACAAGG-TTTAGAATGTGTGACACGCCATG
* * * * *
21206317 GAGTGAATCTGTGACATGGCACGATGAGAATATGTTGGACGAGTATGACACGGTAG
130 GAGGGAATCCGTGACACGGCACGATGAGAATATGTGGGACGAGTATAACACGGTAG
* * * *
21206373 CATTTAAAGTGTGGGACACGCCATGGTCAAAACATGTGACAC
1 CGTTTAGAGTGTGGGACACGCCATGGTCAGAACGTGTGACAC
21206415 ACCATGGAGG
Statistics
Matches: 192, Mismatches: 33, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
184 4 0.02
185 188 0.98
ACGTcount: A:0.28, C:0.16, G:0.33, T:0.23
Consensus pattern (185 bp):
CGTTTAGAGTGTGGGACACGCCATGGTCAGAACGTGTGACACGCCAGGGTCATAATGTGTGAAAC
GGCACAATGATAATGTTGGACACAAGTGTGACACGACAAGGTTTAGAATGTGTGACACGCCATGG
AGGGAATCCGTGACACGGCACGATGAGAATATGTGGGACGAGTATAACACGGTAG
Found at i:21206467 original size:185 final size:184
Alignment explanation
Indices: 21206093--21206502 Score: 445
Period size: 185 Copynumber: 2.2 Consensus size: 184
21206083 TTTGACACAA
* * * * *
21206093 GTGTGACACGACAAG-GTTTAGAATGTGTGACACGCCATGGAGGGAATCCGTGACACGGCATGGT
1 GTGTGACACGGC-AGCGTTTAGAGTGTGTGACATGCCATGGAGGGAATCCGTGACACGGCACGAT
* * * * * * *
21206157 GAGAATATGTGGGACTGGTGTAACACGGTAGCGTTTAGAGTGTGCGACATGCTATGGTCAGAACG
65 GAGAATATGTGGGACTGGTATAACACGGTAGCATTTAAAGTGTGCGACACGCCATGGTCAAAACA
* * * * * * *
21206222 TGTGACACGCCAGGGTCATACTGTGTGAAACGGCACAGTGATAATGTTGGACAGGG
130 TGTGACACACCAGGGGCATACTCTGTGAAACGACACAATGAAAATGTGGGACA-GG
* * * *
21206278 GTGTGACACGGTAG-GCTTTAGAGTGTGTGACATGCCATGGAGTGAATCTGTGACATGGCACGAT
1 GTGTGACACGGCAGCG-TTTAGAGTGTGTGACATGCCATGGAGGGAATCCGTGACACGGCACGAT
* * *
21206342 GAGAATATGTTGGAC-GAGTATGACACGGTAGCATTTAAAGTGTGGGACACGCCATGGTCAAAAC
65 GAGAATATGTGGGACTG-GTATAACACGGTAGCATTTAAAGTGTGCGACACGCCATGGTCAAAAC
* *
21206406 ATGTGACACACCATGGAGGGA-A-TCTGTGACACGACACAATGAGAATATGTGGGAC-GG
129 ATGTGACACACCA-GG-GGCATACTCTGTGAAACGACACAATGA-AA-ATGTGGGACAGG
*
21206463 GTGTGACACGGCAGCGTTTAGAGTGTGGGACATGCCATGG
1 GTGTGACACGGCAGCGTTTAGAGTGTGTGACATGCCATGG
21206503 TCAGAACGTG
Statistics
Matches: 188, Mismatches: 30, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
184 4 0.02
185 169 0.90
186 5 0.03
187 10 0.05
ACGTcount: A:0.27, C:0.17, G:0.34, T:0.22
Consensus pattern (184 bp):
GTGTGACACGGCAGCGTTTAGAGTGTGTGACATGCCATGGAGGGAATCCGTGACACGGCACGATG
AGAATATGTGGGACTGGTATAACACGGTAGCATTTAAAGTGTGCGACACGCCATGGTCAAAACAT
GTGACACACCAGGGGCATACTCTGTGAAACGACACAATGAAAATGTGGGACAGG
Found at i:21206538 original size:104 final size:104
Alignment explanation
Indices: 21206302--21206542 Score: 313
Period size: 104 Copynumber: 2.3 Consensus size: 104
21206292 GCTTTAGAGT
* * * * *
21206302 GTGTGACATGCCATGGAGTGAATCTGTGACATGGCACGATGAGAATATGTTGGACGAGTATGACA
1 GTGTGACACGCCATGGAGTGAATCTGTGACACGACACAATGAGAATATGTGGGACGAGTATGACA
*
21206367 CGGTAGCATTTAAAGTGTGGGACACGCCATGGTCAAAAC
66 CGGCAGCATTTAAAGTGTGGGACACGCCATGGTCAAAAC
* * * * *
21206406 ATGTGACACACCATGGAGGGAATCTGTGACACGACACAATGAGAATATGTGGGACGGGTGTGACA
1 GTGTGACACGCCATGGAGTGAATCTGTGACACGACACAATGAGAATATGTGGGACGAGTATGACA
* * * *
21206471 CGGCAGCGTTTAGAGTGTGGGACATGCCATGGTCAGAAC
66 CGGCAGCATTTAAAGTGTGGGACACGCCATGGTCAAAAC
* *
21206510 GTGTGACACGCCATGG-GTTTAATATGTGACACG
1 GTGTGACACGCCATGGAG-TGAATCTGTGACACG
21206543 CCATGGTGTG
Statistics
Matches: 116, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
103 1 0.01
104 115 0.99
ACGTcount: A:0.29, C:0.17, G:0.32, T:0.22
Consensus pattern (104 bp):
GTGTGACACGCCATGGAGTGAATCTGTGACACGACACAATGAGAATATGTGGGACGAGTATGACA
CGGCAGCATTTAAAGTGTGGGACACGCCATGGTCAAAAC
Found at i:21207188 original size:54 final size:55
Alignment explanation
Indices: 21206978--21207194 Score: 240
Period size: 55 Copynumber: 4.0 Consensus size: 55
21206968 CGTTTGCGTA
* * * * * * *
21206978 TGGCGCGTTGTGGCTTAATTGGTTTTTTTGGTTTTTAGCGTGTCACAGCTATTCC
1 TGGCGTGTTGTGGGTTAACTAGTTTTTTGGGTTTTTAGCGTGTCACGGCTGTTCC
* * *
21207033 TGACATGTTGTGGGTTAACTAGTTTTTTGGGTTTTTAACGTGTCACGGCTGTTCC
1 TGGCGTGTTGTGGGTTAACTAGTTTTTTGGGTTTTTAGCGTGTCACGGCTGTTCC
* ** * * *
21207088 TGGAGTGTCATGGGTTAACTAGATTTATGGGTTTTT-GACGTATCACGGCTGTT-C
1 TGGCGTGTTGTGGGTTAACTAGTTTTTTGGGTTTTTAG-CGTGTCACGGCTGTTCC
* * *
21207142 TGGCGTGTTGTGGGTAAACTGGTTTTTTGGGTTTTTAGCGTGTCACGACTGTT
1 TGGCGTGTTGTGGGTTAACTAGTTTTTTGGGTTTTTAGCGTGTCACGGCTGTT
21207195 GGTGTAACGA
Statistics
Matches: 132, Mismatches: 28, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
54 43 0.33
55 89 0.67
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (55 bp):
TGGCGTGTTGTGGGTTAACTAGTTTTTTGGGTTTTTAGCGTGTCACGGCTGTTCC
Found at i:21207253 original size:23 final size:23
Alignment explanation
Indices: 21207227--21207283 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
21207217 GGTGATTGGT
21207227 GTGTCACGACAATGATGCATGGC
1 GTGTCACGACAATGATGCATGGC
* *
21207250 GTGTCACGACACTGATGCATGGG
1 GTGTCACGACAATGATGCATGGC
21207273 GTGTCACGACA
1 GTGTCACGACA
21207284 TTTGAGTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.25, C:0.23, G:0.32, T:0.21
Consensus pattern (23 bp):
GTGTCACGACAATGATGCATGGC
Found at i:21217905 original size:147 final size:146
Alignment explanation
Indices: 21217638--21217931 Score: 561
Period size: 147 Copynumber: 2.0 Consensus size: 146
21217628 TTTTCCATTG
21217638 TTGAATCACAAGATATCATGAAGGATAGTGTGCTGATCAAACCCTAAGAGAGAGAAATTGATGAT
1 TTGAATCACAAGATATCATGAAGGATAGTGTGCTGATCAAACCCTAAGAGAGAGAAATTGATGAT
21217703 GATTTAGATAGATTTTTAAGATATATGGATGTTTTTAGTTGTTTATGGTGTTAAGTGTAAGAATT
66 GATTTAGATAGATTTTTAAGATATATGGATGTTTTTAGTTGTTTATGGTGTTAAGTGTAAGAATT
21217768 AAGCTTGAAATTCACA
131 AAGCTTGAAATTCACA
* *
21217784 NTTGAATCACAAGATATCATGAAGGATAGTGTGCTGATCAAACCCTAGGAGAGAGAATTTGATGA
1 -TTGAATCACAAGATATCATGAAGGATAGTGTGCTGATCAAACCCTAAGAGAGAGAAATTGATGA
21217849 TGATTTAGATAGATTTTTAAGATATATGGATGTTTTTAGTTGTTTATGGTGTTAAGTGTAAGAAT
65 TGATTTAGATAGATTTTTAAGATATATGGATGTTTTTAGTTGTTTATGGTGTTAAGTGTAAGAAT
21217914 TAAGCTTGAAATTCACA
130 TAAGCTTGAAATTCACA
21217931 T
1 T
21217932 ATTCCTCATG
Statistics
Matches: 145, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
146 1 0.01
147 144 0.99
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.35
Consensus pattern (146 bp):
TTGAATCACAAGATATCATGAAGGATAGTGTGCTGATCAAACCCTAAGAGAGAGAAATTGATGAT
GATTTAGATAGATTTTTAAGATATATGGATGTTTTTAGTTGTTTATGGTGTTAAGTGTAAGAATT
AAGCTTGAAATTCACA
Found at i:21220017 original size:20 final size:21
Alignment explanation
Indices: 21219992--21220032 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
21219982 GAGTGGTATC
21219992 AGAGCTTTT-GATTTAAAGTT
1 AGAGCTTTTGGATTTAAAGTT
*
21220012 AGAGCTTTTGGGTTTAAAGTT
1 AGAGCTTTTGGATTTAAAGTT
21220033 GTTTTAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.27, C:0.05, G:0.24, T:0.44
Consensus pattern (21 bp):
AGAGCTTTTGGATTTAAAGTT
Found at i:21220040 original size:11 final size:11
Alignment explanation
Indices: 21220024--21220051 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
21220014 AGCTTTTGGG
21220024 TTTAAAGTTGT
1 TTTAAAGTTGT
21220035 TTTAAAGTTGT
1 TTTAAAGTTGT
21220046 TTTAAA
1 TTTAAA
21220052 AACTACAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (11 bp):
TTTAAAGTTGT
Found at i:21220348 original size:26 final size:26
Alignment explanation
Indices: 21220312--21220365 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
21220302 GAGCCAGTGT
21220312 TAGAGAGATCTTAAAACAAATGCTCC
1 TAGAGAGATCTTAAAACAAATGCTCC
*
21220338 TAGAGAGATCTTAAAACGAATGCTCC
1 TAGAGAGATCTTAAAACAAATGCTCC
21220364 TA
1 TA
21220366 ATGAAAGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (26 bp):
TAGAGAGATCTTAAAACAAATGCTCC
Found at i:21231088 original size:23 final size:23
Alignment explanation
Indices: 21231062--21231172 Score: 100
Period size: 23 Copynumber: 4.8 Consensus size: 23
21231052 TCAAGTAAAA
* *
21231062 TGTCGTGACACACCATACAATGG
1 TGTCATGACACACCATGCAATGG
* *
21231085 TGTCATGACACACCATGCATTAG
1 TGTCATGACACACCATGCAATGG
* *
21231108 TGTCATGACGCGCCATGC-ATCGG
1 TGTCATGACACACCATGCAAT-GG
* **
21231131 TGTCGTGACATGCCATGC-ATCGG
1 TGTCATGACACACCATGCAAT-GG
*
21231154 TGTCATGACACGCCATGCA
1 TGTCATGACACACCATGCA
21231173 TCAGTGTCAT
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
22 1 0.01
23 72 0.99
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.23
Consensus pattern (23 bp):
TGTCATGACACACCATGCAATGG
Found at i:21231173 original size:23 final size:23
Alignment explanation
Indices: 21231083--21231182 Score: 137
Period size: 23 Copynumber: 4.3 Consensus size: 23
21231073 ACCATACAAT
* *
21231083 GGTGTCATGACACACCATGCATT
1 GGTGTCATGACACGCCATGCATC
* *
21231106 AGTGTCATGACGCGCCATGCATC
1 GGTGTCATGACACGCCATGCATC
* *
21231129 GGTGTCGTGACATGCCATGCATC
1 GGTGTCATGACACGCCATGCATC
21231152 GGTGTCATGACACGCCATGCATC
1 GGTGTCATGACACGCCATGCATC
*
21231175 AGTGTCAT
1 GGTGTCAT
21231183 ATAAAAAATC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 66 1.00
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.25
Consensus pattern (23 bp):
GGTGTCATGACACGCCATGCATC
Found at i:21231258 original size:31 final size:30
Alignment explanation
Indices: 21231215--21231642 Score: 561
Period size: 31 Copynumber: 13.8 Consensus size: 30
21231205 ATTTTTTCAT
*
21231215 ATGTGGTAACACGCCATGCATAAAACGTAAA
1 ATGT-GTAACACGCCATGCATATAACGTAAA
*
21231246 ATGCTGTAACACGCCATGCATATAATGTAAA
1 ATG-TGTAACACGCCATGCATATAACGTAAA
* *
21231277 ATATTATAACACGCCATGCATATAACGTAAA
1 AT-GTGTAACACGCCATGCATATAACGTAAA
21231308 ATGTTGTAACACGCCATGCATATAACGTAAA
1 ATG-TGTAACACGCCATGCATATAACGTAAA
*
21231339 ATGTGGTAACACGCCATGCATATAACATAAA
1 ATGT-GTAACACGCCATGCATATAACGTAAA
* *
21231370 ATGTTGTAACACACCATGCATATAGCGTAAA
1 ATG-TGTAACACGCCATGCATATAACGTAAA
* *
21231401 ATGTGATAACACGCCATGCATATAACATACA
1 ATGTG-TAACACGCCATGCATATAACGTAAA
*
21231432 ATGTTGTAACACGCCATGCATATAGCGTAAA
1 ATG-TGTAACACGCCATGCATATAACGTAAA
*
21231463 ATGTGGTAACACGCCATGCATATAACATAAA
1 ATGT-GTAACACGCCATGCATATAACGTAAA
* *
21231494 ATGTCGTAACACTCCATGCATATAACATAAA
1 ATGT-GTAACACGCCATGCATATAACGTAAA
* *
21231525 ATGTAATAACACGCCATGCATATAACGAAAA
1 ATGT-GTAACACGCCATGCATATAACGTAAA
* *
21231556 ATGTGGTAACATGCCATGCATATAACATAAA
1 ATGT-GTAACACGCCATGCATATAACGTAAA
*
21231587 ATGTGGTAACACGCCATGCATATAACGTTAAT
1 ATGT-GTAACACGCCATGCATATAACG-TAAA
21231619 AT-TGTAACACGCCATGCATATAAC
1 ATGTGTAACACGCCATGCATATAAC
21231643 CAATGTCGTG
Statistics
Matches: 353, Mismatches: 35, Indels: 19
0.87 0.09 0.05
Matches are distributed among these distances:
30 25 0.07
31 319 0.90
32 9 0.03
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (30 bp):
ATGTGTAACACGCCATGCATATAACGTAAA
Found at i:21238409 original size:20 final size:21
Alignment explanation
Indices: 21238384--21238423 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
21238374 TCCTATCAAG
21238384 AATGTATCGATACAT-TTGCT
1 AATGTATCGATACATCTTGCT
21238404 AATGTATCGATACATCTTGC
1 AATGTATCGATACATCTTGC
21238424 CCAGATTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
AATGTATCGATACATCTTGCT
Found at i:21238890 original size:28 final size:28
Alignment explanation
Indices: 21238797--21238880 Score: 150
Period size: 28 Copynumber: 3.0 Consensus size: 28
21238787 ATTCATCTAA
21238797 GTGCCAAACAATGCACTATACCATTCAT
1 GTGCCAAACAATGCACTATACCATTCAT
21238825 GTGCCAAACAATGCACTATACCATTCAT
1 GTGCCAAACAATGCACTATACCATTCAT
* *
21238853 GTGCCAAACAATGCATTATGCCATTCAT
1 GTGCCAAACAATGCACTATACCATTCAT
21238881 ATGCACAACA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.26
Consensus pattern (28 bp):
GTGCCAAACAATGCACTATACCATTCAT
Found at i:21239490 original size:14 final size:14
Alignment explanation
Indices: 21239473--21239499 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21239463 CAAAATTAAT
21239473 TAATTAACTAAAAA
1 TAATTAACTAAAAA
21239487 TAATTAACTAAAA
1 TAATTAACTAAAA
21239500 TTAAAACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATTAACTAAAAA
Found at i:21240667 original size:16 final size:15
Alignment explanation
Indices: 21240623--21240667 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
21240613 TAACATAAAA
21240623 TTAAAA-TAACTAAC
1 TTAAAAGTAACTAAC
*
21240637 TTAAAAGTAACCTAAT
1 TTAAAAGTAA-CTAAC
21240653 TATAAAAGTAACTAA
1 T-TAAAAGTAACTAA
21240668 AAATAAGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 6 0.22
15 3 0.11
16 9 0.33
17 9 0.33
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (15 bp):
TTAAAAGTAACTAAC
Found at i:21246908 original size:54 final size:55
Alignment explanation
Indices: 21246745--21246922 Score: 250
Period size: 55 Copynumber: 3.3 Consensus size: 55
21246735 GTTAGAGTTA
* * *
21246745 TTTTAGCGTGTCACGGCTGTTCCTGGCATGTTGTGGGTTAACTAGTTTTTTGGGT
1 TTTTAGCGTGTCACGGCTGTTCCTGGCGTGTCGTGGGTTAACTGGTTTTTTGGGT
* ** *
21246800 TGTTAGCGTGTCACGGCTGTTCCTGGCGTGTCGTGGGTTAACTGAATTTATGGGT
1 TTTTAGCGTGTCACGGCTGTTCCTGGCGTGTCGTGGGTTAACTGGTTTTTTGGGT
* * *
21246855 TTTTGGTGTGTCACGGTTGTTCC-GGCGTGTCGTGGGTTAACTGGTTTTTTGGGT
1 TTTTAGCGTGTCACGGCTGTTCCTGGCGTGTCGTGGGTTAACTGGTTTTTTGGGT
*
21246909 TTTTAACGTGTCAC
1 TTTTAGCGTGTCAC
21246923 AACTGTTGGT
Statistics
Matches: 106, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
54 39 0.37
55 67 0.63
ACGTcount: A:0.11, C:0.15, G:0.33, T:0.42
Consensus pattern (55 bp):
TTTTAGCGTGTCACGGCTGTTCCTGGCGTGTCGTGGGTTAACTGGTTTTTTGGGT
Found at i:21246975 original size:20 final size:21
Alignment explanation
Indices: 21246950--21247018 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 21
21246940 GTCAGTAATT
21246950 ACAGTGAT-TGGCGTGACACG
1 ACAGTGATATGGCGTGACACG
*
21246970 ACAGTGATGCATGGCGTGTCACG
1 ACAGTGAT--ATGGCGTGACACG
* *
21246993 ATAGTGATGCATGGCGTGTCACG
1 ACAGTGAT--ATGGCGTGACACG
21247016 ACA
1 ACA
21247019 TTTGACTTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
20 8 0.19
23 35 0.81
ACGTcount: A:0.25, C:0.20, G:0.33, T:0.22
Consensus pattern (21 bp):
ACAGTGATATGGCGTGACACG
Found at i:21246992 original size:23 final size:23
Alignment explanation
Indices: 21246958--21247018 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
21246948 TTACAGTGAT
*
21246958 TGGCGTGACACGACAGTGATGCA
1 TGGCGTGTCACGACAGTGATGCA
*
21246981 TGGCGTGTCACGATAGTGATGCA
1 TGGCGTGTCACGACAGTGATGCA
21247004 TGGCGTGTCACGACA
1 TGGCGTGTCACGACA
21247019 TTTGACTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.23, C:0.21, G:0.34, T:0.21
Consensus pattern (23 bp):
TGGCGTGTCACGACAGTGATGCA
Found at i:21247034 original size:31 final size:31
Alignment explanation
Indices: 21246999--21247080 Score: 119
Period size: 31 Copynumber: 2.6 Consensus size: 31
21246989 CACGATAGTG
*
21246999 ATGCATGGCGTGTCACGACATTTGACTTGAT
1 ATGCATGGCGTGTCACAACATTTGACTTGAT
* * *
21247030 ATGCATGGCGTGTTACAACATTTTACTTTAT
1 ATGCATGGCGTGTCACAACATTTGACTTGAT
*
21247061 ATGCATGGCGTGTAACAACA
1 ATGCATGGCGTGTCACAACA
21247081 CGACTGACAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (31 bp):
ATGCATGGCGTGTCACAACATTTGACTTGAT
Found at i:21251585 original size:31 final size:31
Alignment explanation
Indices: 21251549--21251882 Score: 355
Period size: 31 Copynumber: 10.8 Consensus size: 31
21251539 ACAAATGTGA
* *
21251549 GACACGCCATGCAAAACAAGTAAAATGTTGT
1 GACACGCCATGCATAACAAGTAAAATGTTCT
* * * *
21251580 GACACGTCGTGCATATCAAGTAAAATATTCT
1 GACACGCCATGCATAACAAGTAAAATGTTCT
* *
21251611 GACATGCCATGCATAACAAGTAAATTGTTCT
1 GACACGCCATGCATAACAAGTAAAATGTTCT
* * * * *
21251642 GACATGCCATGCATAACAAGTTAGACGTTGT
1 GACACGCCATGCATAACAAGTAAAATGTTCT
* * *
21251673 GACACGCCATGTATAACAATTAAATTGTTCT
1 GACACGCCATGCATAACAAGTAAAATGTTCT
* * *
21251704 GACCCGCCATGAATAACAAGTAAATTGTTCT
1 GACACGCCATGCATAACAAGTAAAATGTTCT
* * *
21251735 GACACGCCATGCATAACAAGTTAAACGTTGT
1 GACACGCCATGCATAACAAGTAAAATGTTCT
* * *
21251766 AACACGCCATGCATAACAATTAAATTGTTCT
1 GACACGCCATGCATAACAAGTAAAATGTTCT
*
21251797 GAC-CTGCCATGCATAACAAGTAAATTGTTCT
1 GACAC-GCCATGCATAACAAGTAAAATGTTCT
* * * * *
21251828 AACACACCATGCATAACAAGTTAAACGTTGT
1 GACACGCCATGCATAACAAGTAAAATGTTCT
* *
21251859 GACATGCCATGCATAACAATTAAA
1 GACACGCCATGCATAACAAGTAAA
21251883 TTTATAGGTC
Statistics
Matches: 248, Mismatches: 53, Indels: 4
0.81 0.17 0.01
Matches are distributed among these distances:
30 1 0.00
31 246 0.99
32 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (31 bp):
GACACGCCATGCATAACAAGTAAAATGTTCT
Found at i:21251713 original size:93 final size:93
Alignment explanation
Indices: 21251549--21251884 Score: 501
Period size: 93 Copynumber: 3.6 Consensus size: 93
21251539 ACAAATGTGA
* * * * * * * * *
21251549 GACACGCCATGCAAAACAAGTAAAATGTTGTGACACGTCGTGCATATCAAGTAAAATATTCTGAC
1 GACACGCCATGCATAACAAGTTAAACGTTGTGACACGCCATGCATAACAATTAAATTGTTCTGAC
*
21251614 ATGCCATGCATAACAAGTAAATTGTTCT
66 CTGCCATGCATAACAAGTAAATTGTTCT
* * *
21251642 GACATGCCATGCATAACAAGTTAGACGTTGTGACACGCCATGTATAACAATTAAATTGTTCTGAC
1 GACACGCCATGCATAACAAGTTAAACGTTGTGACACGCCATGCATAACAATTAAATTGTTCTGAC
* *
21251707 CCGCCATGAATAACAAGTAAATTGTTCT
66 CTGCCATGCATAACAAGTAAATTGTTCT
*
21251735 GACACGCCATGCATAACAAGTTAAACGTTGTAACACGCCATGCATAACAATTAAATTGTTCTGAC
1 GACACGCCATGCATAACAAGTTAAACGTTGTGACACGCCATGCATAACAATTAAATTGTTCTGAC
21251800 CTGCCATGCATAACAAGTAAATTGTTCT
66 CTGCCATGCATAACAAGTAAATTGTTCT
* * *
21251828 AACACACCATGCATAACAAGTTAAACGTTGTGACATGCCATGCATAACAATTAAATT
1 GACACGCCATGCATAACAAGTTAAACGTTGTGACACGCCATGCATAACAATTAAATT
21251885 TATAGGTCTT
Statistics
Matches: 218, Mismatches: 25, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 218 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (93 bp):
GACACGCCATGCATAACAAGTTAAACGTTGTGACACGCCATGCATAACAATTAAATTGTTCTGAC
CTGCCATGCATAACAAGTAAATTGTTCT
Found at i:21252020 original size:31 final size:31
Alignment explanation
Indices: 21251932--21252008 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
21251922 CCCAATTGTT
*
21251932 CTGACACGCTGAGTGGAAGCAGATTTATGGG
1 CTGACACGCTGAGTGGAAGCAGATTTATGGA
* * *
21251963 CTGACACGCTAAGTGGAAGCAAATTTATTGA
1 CTGACACGCTGAGTGGAAGCAGATTTATGGA
21251994 CTGACACGCTGAGTG
1 CTGACACGCTGAGTG
21252009 ATAGTGGATT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (31 bp):
CTGACACGCTGAGTGGAAGCAGATTTATGGA
Found at i:21252236 original size:19 final size:20
Alignment explanation
Indices: 21252195--21252241 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 20
21252185 TCTTGGTATC
21252195 AAATTAATTGTGTATAGGCAAAA
1 AAATTAATTGTGTAT--G-AAAA
21252218 AAATTAATTGTGTAT-AAAA
1 AAATTAATTGTGTATGAAAA
*
21252237 TAATT
1 AAATT
21252242 GTATAAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 8 0.35
23 15 0.65
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
AAATTAATTGTGTATGAAAA
Found at i:21252262 original size:52 final size:50
Alignment explanation
Indices: 21252190--21252370 Score: 201
Period size: 52 Copynumber: 3.6 Consensus size: 50
21252180 AATATTCTTG
* *
21252190 GTATCAAATTAATTGTGTATAGGCAAAAAAATTAATTGTGTATAAAATAATT
1 GTATAAAATAAATTGTGTATA--CAAAAAAATTAATTGTGTATAAAATAATT
* * * * * *
21252242 GTATAAAGTATATTGTGTATACCAAAAGAATTAATTATGTTTACAATGAATT
1 GTATAAAATAAATTGTGTATA-CAAAAAAATTAATTGTGTATAAAAT-AATT
21252294 GTATAAAATAAATTGTGTATAC-AAAAAA-T--TTGTGTATAAAATTAATT
1 GTATAAAATAAATTGTGTATACAAAAAAATTAATTGTGTATAAAA-TAATT
*
21252341 GTATAAAA-AAATTCTGTATACAAAAAAATT
1 GTATAAAATAAATTGTGTATACAAAAAAATT
21252371 GTACAGACAA
Statistics
Matches: 109, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
46 12 0.11
47 27 0.25
48 2 0.02
49 1 0.01
50 5 0.05
51 22 0.20
52 40 0.37
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.36
Consensus pattern (50 bp):
GTATAAAATAAATTGTGTATACAAAAAAATTAATTGTGTATAAAATAATT
Found at i:21252328 original size:17 final size:15
Alignment explanation
Indices: 21252293--21252372 Score: 74
Period size: 17 Copynumber: 5.1 Consensus size: 15
21252283 TACAATGAAT
21252293 TGTATAAAATAAATTG
1 TGTATAAAA-AAATTG
21252309 TGTATACAAAAAATTTG
1 TGTATA-AAAAAA-TTG
*
21252326 TGTATAAAATTAA-T-
1 TGTATAAAA-AAATTG
*
21252340 TGTATAAAAAAATTC
1 TGTATAAAAAAATTG
21252355 TGTATACAAAAAAATTG
1 TGTAT--AAAAAAATTG
21252372 T
1 T
21252373 ACAGACAAGG
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
13 2 0.04
14 10 0.19
15 6 0.11
16 12 0.22
17 24 0.44
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.36
Consensus pattern (15 bp):
TGTATAAAAAAATTG
Found at i:21253940 original size:31 final size:31
Alignment explanation
Indices: 21253905--21254234 Score: 374
Period size: 31 Copynumber: 10.6 Consensus size: 31
21253895 AACCATAAAC
*
21253905 AGTAAAATGTTGTGACACGCCATGCATATCA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* *
21253936 AGTAAAATGTTGTCACACGCCATGCAAAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
**
21253967 AGTAAAATGTTGTGACACATCATGCATAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* *
21253998 AGATAAACT-TTGTGACATGCCATGCATAACA
1 AG-TAAAATGTTGTGACACGCCATGCATAACA
21254029 AGTAAAATGTTGTGACACGCCATGCATAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* * * * *
21254060 AGTTAAACGTTATGACACACCATCCATAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* * * * * *
21254091 AGCAAATTGTTATGACACACCAAGGATAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* * * *
21254122 AGCAAAATGTTCTGACACACCATGCATATCA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* * * *
21254153 AATCAAACGTTGTGACACGCCATGAATAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* *
21254184 AGTAAAATGTTGTGACATGCCATGCATATCA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* *
21254215 AGTCAAATGTTGTCACACGC
1 AGTAAAATGTTGTGACACGC
21254235 TAAGGCTGAC
Statistics
Matches: 250, Mismatches: 47, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
30 5 0.02
31 240 0.96
32 5 0.02
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.23
Consensus pattern (31 bp):
AGTAAAATGTTGTGACACGCCATGCATAACA
Found at i:21254915 original size:156 final size:155
Alignment explanation
Indices: 21254589--21255066 Score: 629
Period size: 156 Copynumber: 3.1 Consensus size: 155
21254579 CTACTGGGTC
* * * * *
21254589 AACTGCAATAACATATACAACTGTGTTATTCAATAATCATATATGAAATTGTTGAACATTAACCG
1 AACTGCAATTACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACCT
* * * *
21254654 TTACAACTTTAATATCCTAACTGGT-GCTCGATA-ATAGTCTACGGTGGAGCCGGACCGATCGAT
66 TTACAACTTTAATATCCTTACT-GTCGCTCGTTAGCTA-TCTACGGTTGAGCCGGACCGATCGAT
*
21254717 GCATGAGGACCTATCGTCGCTTTCGCA
129 GCTTGAGGACCTATCGTCGCTTTCGCA
* * *
21254744 AACTGCAATTACATATATAATTGTGTTATTTAATAATCATGTATGGAACTGTTGAACATTAACCT
1 AACTGCAATTACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACCT
* ** *
21254809 TTACAACTTTAATATTCTTACTGTCGACTCGTTAGCTATCTGTGGTTGAGCCGGACAGATCGATG
66 TTACAACTTTAATATCCTTACTGTCG-CTCGTTAGCTATCTACGGTTGAGCCGGACCGATCGATG
* *
21254874 CTTAAGGACCTATCGTCGCTTCCGCA
130 CTTGAGGACCTATCGTCGCTTTCGCA
21254900 AACTGCAATTACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAA-CT
1 AACTGCAATTACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACCT
* * * * * * * *
21254964 ATTACAACTTTAATATCCTTACCGCCGGCTTGTTAGCTGTCTACGATTGAGCCGAACCGATTGGT
66 -TTACAACTTTAATATCCTTACTGTC-GCTCGTTAGCTATCTACGGTTGAGCCGGACCGATCGAT
* *
21255029 GCTTGAGGACCTGTCGTCGCTTTCGTA
129 GCTTGAGGACCTATCGTCGCTTTCGCA
21255056 AACTGCAATTA
1 AACTGCAATTA
21255067 TAAAAATTAC
Statistics
Matches: 280, Mismatches: 38, Indels: 9
0.86 0.12 0.03
Matches are distributed among these distances:
154 2 0.01
155 80 0.29
156 195 0.70
157 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (155 bp):
AACTGCAATTACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACCT
TTACAACTTTAATATCCTTACTGTCGCTCGTTAGCTATCTACGGTTGAGCCGGACCGATCGATGC
TTGAGGACCTATCGTCGCTTTCGCA
Found at i:21256770 original size:31 final size:31
Alignment explanation
Indices: 21256732--21256994 Score: 298
Period size: 31 Copynumber: 8.5 Consensus size: 31
21256722 AATAAGGAAT
*
21256732 AAATGTTGTGACACGCCAAGCATTACAAGTA
1 AAATGTTGTGACACGCCATGCATTACAAGTA
* *
21256763 AAATGTTGTGACACGCCAAGCATTACAAGCA
1 AAATGTTGTGACACGCCATGCATTACAAGTA
**
21256794 AAATGTTGTGACACGCCATGCACAACAAGTA
1 AAATGTTGTGACACGCCATGCATTACAAGTA
* *
21256825 AAATGTTGTGACACGCCATGCATAACAAGTT
1 AAATGTTGTGACACGCCATGCATTACAAGTA
* * *
21256856 AAACGTTGTGACATGCTATGCA-TATCAAGTA
1 AAATGTTGTGACACGCCATGCATTA-CAAGTA
* * * *
21256887 AAATGCTGTCACATGCCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATTACAAGTA
* *
21256918 AAATGCTGTCACACGCCATGCA-TATCAAGTA
1 AAATGTTGTGACACGCCATGCATTA-CAAGTA
* *
21256949 AAATGCTGTCACACGCCATGCA-TATCAAGTA
1 AAATGTTGTGACACGCCATGCATTA-CAAGTA
* *
21256980 AAATGCTGTCACACG
1 AAATGTTGTGACACG
21256995 TCAATAACTA
Statistics
Matches: 210, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
30 2 0.01
31 207 0.99
32 1 0.00
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATTACAAGTA
Found at i:21256829 original size:62 final size:62
Alignment explanation
Indices: 21256732--21256994 Score: 328
Period size: 62 Copynumber: 4.2 Consensus size: 62
21256722 AATAAGGAAT
* * * * * * *
21256732 AAATGTTGTGACACGCCAAGCATTACAAGTAAAATGTTGTGACACGCCAAGCATTACAAGCA
1 AAATGTTGTGACACGCCATGCATAACAAGTAAAATGCTGTCACACGCCATGCATAACAAGTA
* * * *
21256794 AAATGTTGTGACACGCCATGCACAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGTT
1 AAATGTTGTGACACGCCATGCATAACAAGTAAAATGCTGTCACACGCCATGCATAACAAGTA
* * * * *
21256856 AAACGTTGTGACATGCTATGCATATCAAGTAAAATGCTGTCACATGCCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTAAAATGCTGTCACACGCCATGCATAACAAGTA
* * * *
21256918 AAATGCTGTCACACGCCATGCATATCAAGTAAAATGCTGTCACACGCCATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTAAAATGCTGTCACACGCCATGCATAACAAGTA
* *
21256980 AAATGCTGTCACACG
1 AAATGTTGTGACACG
21256995 TCAATAACTA
Statistics
Matches: 178, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 178 1.00
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (62 bp):
AAATGTTGTGACACGCCATGCATAACAAGTAAAATGCTGTCACACGCCATGCATAACAAGTA
Found at i:21256891 original size:93 final size:93
Alignment explanation
Indices: 21256732--21256994 Score: 357
Period size: 93 Copynumber: 2.8 Consensus size: 93
21256722 AATAAGGAAT
* * * *
21256732 AAATGTTGTGACACGCCAAGCATTACAAGTAAAATGTTGTGACACGCCAAGCAT-TACAAGCAAA
1 AAATGTTGTGACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATAT-CAAGTAAA
* *
21256796 ATGTTGTGACACGCCATGCACAACAAGTA
65 ATGCTGTCACACGCCATGCACAACAAGTA
* * * *
21256825 AAATGTTGTGACACGCCATGCATAACAAGTTAAACGTTGTGACATGCTATGCATATCAAGTAAAA
1 AAATGTTGTGACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATATCAAGTAAAA
* *
21256890 TGCTGTCACATGCCATGCATAACAAGTA
66 TGCTGTCACACGCCATGCACAACAAGTA
* * * * *
21256918 AAATGCTGTCACACGCCATGCATATCAAGTAAAATGCTGTCACACGCCATGCATATCAAGTAAAA
1 AAATGTTGTGACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATATCAAGTAAAA
21256983 TGCTGTCACACG
66 TGCTGTCACACG
21256995 TCAATAACTA
Statistics
Matches: 147, Mismatches: 22, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
93 146 0.99
94 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (93 bp):
AAATGTTGTGACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATATCAAGTAAAA
TGCTGTCACACGCCATGCACAACAAGTA
Found at i:21257542 original size:53 final size:53
Alignment explanation
Indices: 21257466--21257586 Score: 172
Period size: 53 Copynumber: 2.3 Consensus size: 53
21257456 TCTATTTAAA
*
21257466 ACCATGACGTGTCACCTACTCAAGCACA-ATCGTGTCACACACTCTAAACCATG
1 ACCATGGCGTGTCACCTACTCAAGCA-ATATCGTGTCACACACTCTAAACCATG
* ** * *
21257519 ACCATGGCGTGTCAGCTTTTCAAGCAATGTCGTGTCACACACTCTAAATCATG
1 ACCATGGCGTGTCACCTACTCAAGCAATATCGTGTCACACACTCTAAACCATG
21257572 ACCATGGCGTGTCAC
1 ACCATGGCGTGTCAC
21257587 TAACTCTGAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
52 1 0.02
53 59 0.98
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (53 bp):
ACCATGGCGTGTCACCTACTCAAGCAATATCGTGTCACACACTCTAAACCATG
Found at i:21257647 original size:47 final size:47
Alignment explanation
Indices: 21257573--21257875 Score: 288
Period size: 47 Copynumber: 6.4 Consensus size: 47
21257563 TAAATCATGA
* * *
21257573 CCATGGCGTGTCACTAACTCTGAACTCTGGAGTGTCACAGCTTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGAGTGTCACAGATTCCCT
* * * * *
21257620 CCATGGCATGTCACTAACTCTTCACTCT-AACGTGTCACAGATTCCTT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGA-GTGTCACAGATTCCCT
* * * *
21257667 CCATGGCGTCTCACGAACTCTAAACGT-TGGCGTGTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAAC-TCTGGAGTGTCACAGATTCCCT
* *
21257714 CCATGTCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGAGTGTCACAGATTCCCT
* * * ** *
21257761 CCATGGCGTCTCACCAACTCTGAACGCTACCA-TGTCACAGATTCCCA
1 CCATGGCGTGTCACCAACTCTTAACTCT-GGAGTGTCACAGATTCCCT
* * * * * * * *
21257808 CCATGGCTTGCCACTAATTCTTAACTCTAGCGTTTCACAAATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGAGTGTCACAGATTCCCT
* *
21257855 CCATGGTGTCTCACCAACTCT
1 CCATGGCGTGTCACCAACTCT
21257876 GAGCAGTGTC
Statistics
Matches: 205, Mismatches: 45, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
46 2 0.01
47 202 0.99
48 1 0.00
ACGTcount: A:0.22, C:0.34, G:0.16, T:0.28
Consensus pattern (47 bp):
CCATGGCGTGTCACCAACTCTTAACTCTGGAGTGTCACAGATTCCCT
Found at i:21257846 original size:141 final size:141
Alignment explanation
Indices: 21257573--21257877 Score: 355
Period size: 141 Copynumber: 2.2 Consensus size: 141
21257563 TAAATCATGA
* * * * *
21257573 CCATGGCGTGTCACTAACTCTGAACTCTGGAGTGTCACAGCTTCCCTCCATGGCATGTCACTAAC
1 CCATGTCGTGTCACCAACTCTGAACTCTGGAGTGTCACAGATTCCCTCCATGGCATCTCACCAAC
** * * ** *
21257638 TCTTCACTCTAACGTGTCACAGATTCCTTCCATGGCGTCTCACGAACTCTAAACGTTGGCGTGTC
66 TCTGAACGCTAACATGTCACAGATTCCCACCATGGCGTCTCACGAACTCTAAACGTTAGCGTGTC
*
21257703 ACAGATTCCCT
131 ACAAATTCCCT
* * *
21257714 CCATGTCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCTCCATGGCGTCTCACCAAC
1 CCATGTCGTGTCACCAACTCTGAACTCTGGAGTGTCACAGATTCCCTCCATGGCATCTCACCAAC
* * * * * *
21257779 TCTGAACGCTACCATGTCACAGATTCCCACCATGGCTTGC-CACTAATTCTTAAC-TCTAGCGTT
66 TCTGAACGCTAACATGTCACAGATTCCCACCATGGCGT-CTCACGAACTCTAAACGT-TAGCGTG
21257842 TCACAAATTCCCT
129 TCACAAATTCCCT
*
21257855 CCATGGT-GTCTCACCAACTCTGA
1 CCAT-GTCGTGTCACCAACTCTGA
21257878 GCAGTGTCGT
Statistics
Matches: 137, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
140 1 0.01
141 133 0.97
142 3 0.02
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.28
Consensus pattern (141 bp):
CCATGTCGTGTCACCAACTCTGAACTCTGGAGTGTCACAGATTCCCTCCATGGCATCTCACCAAC
TCTGAACGCTAACATGTCACAGATTCCCACCATGGCGTCTCACGAACTCTAAACGTTAGCGTGTC
ACAAATTCCCT
Found at i:21257891 original size:94 final size:94
Alignment explanation
Indices: 21257573--21257906 Score: 373
Period size: 94 Copynumber: 3.6 Consensus size: 94
21257563 TAAATCATGA
* * * ** * *
21257573 CCATGGCGTGTCACTAACTCTGAACTCTGGAGTGTCACAGCTTCCCTCCATGGCATGTCACTAAC
1 CCATGGCGTCTCACCAACTCTGAACGCTGCCGTGTCACAGATTCCCACCATGGCATGTCACTAAC
* * *
21257638 TCTTCACTCTAACGTGTCACAGATTCCTT
66 TCTTAACTCTAGCGTGTCACAGATTCCCT
* * * * * * * *
21257667 CCATGGCGTCTCACGAACTCTAAACGTTGGCGTGTCACAGATTCCCTCCATGTCGTGTCACCAAC
1 CCATGGCGTCTCACCAACTCTGAACGCTGCCGTGTCACAGATTCCCACCATGGCATGTCACTAAC
*
21257732 TCTTAACTCTGGCGTGTCACAGATTCCCT
66 TCTTAACTCTAGCGTGTCACAGATTCCCT
* * * * *
21257761 CCATGGCGTCTCACCAACTCTGAACGCTACCATGTCACAGATTCCCACCATGGCTTGCCACTAAT
1 CCATGGCGTCTCACCAACTCTGAACGCTGCCGTGTCACAGATTCCCACCATGGCATGTCACTAAC
* *
21257826 TCTTAACTCTAGCGTTTCACAAATTCCCT
66 TCTTAACTCTAGCGTGTCACAGATTCCCT
* * * * *
21257855 CCATGGTGTCTCACCAACTCTGAGCAG-TGTCGTGTCACACATTCCCAACATG
1 CCATGGCGTCTCACCAACTCTGAAC-GCTGCCGTGTCACAGATTCCCACCATG
21257907 ACGTTTCACA
Statistics
Matches: 203, Mismatches: 36, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
94 202 1.00
95 1 0.00
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.28
Consensus pattern (94 bp):
CCATGGCGTCTCACCAACTCTGAACGCTGCCGTGTCACAGATTCCCACCATGGCATGTCACTAAC
TCTTAACTCTAGCGTGTCACAGATTCCCT
Found at i:21263754 original size:2 final size:2
Alignment explanation
Indices: 21263747--21263786 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
21263737 NNNNNNNNNN
* *
21263747 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT -T AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21263787 AACACCAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:21267632 original size:2 final size:2
Alignment explanation
Indices: 21267625--21267656 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21267615 AAAACAAATG
21267625 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
21267657 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21267696 original size:14 final size:17
Alignment explanation
Indices: 21267662--21267698 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
21267652 TATATGTGTG
21267662 TGTGTGTGTGTGAATTA
1 TGTGTGTGTGTGAATTA
21267679 TGTGTGT-TGTG-A-TA
1 TGTGTGTGTGTGAATTA
21267693 TGTGTG
1 TGTGTG
21267699 CCTTGAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 4 0.20
17 7 0.35
ACGTcount: A:0.14, C:0.00, G:0.38, T:0.49
Consensus pattern (17 bp):
TGTGTGTGTGTGAATTA
Found at i:21268753 original size:15 final size:15
Alignment explanation
Indices: 21268733--21268770 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
21268723 TATATATATA
21268733 TTATAATTAATAA-TT
1 TTATAATT-ATAATTT
21268748 TTATAAGTTATAATTT
1 TTATAA-TTATAATTT
21268764 TTATAAT
1 TTATAAT
21268771 GTTAATACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTATAATTATAATTT
Found at i:21269495 original size:362 final size:344
Alignment explanation
Indices: 21268725--21269693 Score: 1064
Period size: 342 Copynumber: 2.8 Consensus size: 344
21268715 CATGTTTATA
* ** * *
21268725 TATATATATTATAATTAATAATTTTATAAGTTATAAT-TTTTATAATGTTAATACAAAATAAAAA
1 TATATATATTATAATTAATAATTTTACAAGTTATAATATTTT-TAACATTAACACAAAATAGAAA
* *
21268789 GTAAATATATTTATATTTGAA--GTATATATAT------ATTAAAAGTATTTTAGTGCATATATA
65 GTAAATATATTTATATTTAAAGTGTATATATATACCAAAACTAAAAGTATTTTA-T--ATAT-TA
* ** *
21268846 TAATAGTAATTATATTCCTTATAAATGAACTTAATATATATATA-TAAAGCATAGATATTAAAAG
126 TAATAGTAATTATATTCTTTATAAATGAACCCAATATATATAAAGT-AA--AT--ATATTAAAAG
* *
21268910 ACATTACAAGTTAATTAATAATCATAGTTTCATTAATTAA-TTAATTAATTATATGGGTTTGTCC
186 ACATTACAAGTTAATTAATAATCATAGTTTAATGAATTAATTTAATTAATTATATGGGTTTGTCC
* * *
21268974 TTAATTACATGAAATT-AAAAAAAATAGCTAAGTTTCAAAACTATTCTAGTCTCACAACTTCTTT
251 TTAATTACATGAAATTAAAAAAAAATAACTAAGTCTCAAAACTATTCTAATCTCACAACTTCTTT
21269038 TTAGATAATTAAGTTTATATAAACAAAGG
316 TTAGATAATTAAGTTTATATAAACAAAGG
* * *
21269067 TATATATATTATAATTAATAATTTTATAAGTTATAATATTTTTAATATTAACACAAAATTGAAAG
1 TATATATATTATAATTAATAATTTTACAAGTTATAATATTTTTAACATTAACACAAAATAGAAAG
*
21269132 TAAATATGTTTATATTTAAAGTGTATATATCTATATATATACACACACACACTAAAAGTATTTTA
66 TAAATATATTTATATTTAAAGTG--------TATATATATAC-CA-A-A-ACTAAAAGTATTTTA
21269197 CTATATGTATAATAGTAATTATATTCTTTATAAATGAACCCAATATATATAAAGTAAATATATTA
119 -TATAT-TATAATAGTAATTATATTCTTTATAAATGAACCCAATATATATAAAGTAAATATATTA
* * *
21269262 AAAGACATTACAAGGTAATTAATAATCATAGTTTTATGAATTAATTTAATTAATTATATGAGTTT
182 AAAGACATTACAAGTTAATTAATAATCATAGTTTAATGAATTAATTTAATTAATTATATGGGTTT
* * **
21269327 GTCCTTAATTGCATGAAATTAAAAAAAAATAACTAGGTCTCAAAACTATTCTAATCTCACTTC-T
247 GTCCTTAATTACATGAAATTAAAAAAAAATAACTAAGTCTCAAAACTATTCTAATCTCACAACTT
* *
21269391 CTTAAGGTTT-GTATATTATAAGTTTATATAAACAAATG
312 CTT----TTTAG-ATAAT-TAAGTTTATATAAACAAAGG
* * * *
21269429 TGTATATATTATAATTAATAATTTTACAAGTTATAAT-TTTTGTAACGTTAATATAAAATAGAAA
1 TATATATATTATAATTAATAATTTTACAAGTTATAATATTTT-TAACATTAACACAAAATAGAAA
* * * ** * *
21269493 GTAAATATATTTATATTTCAAGTGTATATATATACTAAAAGTATTAGGA---TATATATAAT-AT
65 GTAAATATATTTATATTTAAAGTGTATATATATACCAAAACTAAAAGTATTTTATATATTATAAT
* * *
21269554 AGTAATTATATT-TCTTATAAATGAACCCAATATATATAATGT--ATATATTAAAAAACATTCCA
130 AGTAATTATATTCT-TTATAAATGAACCCAATATATATAAAGTAAATATATTAAAAGACATTACA
* * * *
21269616 AGTTAATTAATAATCATACTTTAATGAATTAATTTAATTAACTATATGGGTTTATCTTTAATTAC
194 AGTTAATTAATAATCATAGTTTAATGAATTAATTTAATTAATTATATGGGTTTGTCCTTAATTAC
*
21269681 AGGAAATTAAAAA
259 ATGAAATTAAAAA
21269694 TAATTAGATT
Statistics
Matches: 542, Mismatches: 53, Indels: 64
0.82 0.08 0.10
Matches are distributed among these distances:
342 161 0.30
343 5 0.01
344 42 0.08
345 2 0.00
346 5 0.01
347 2 0.00
350 6 0.01
351 1 0.00
352 10 0.02
353 1 0.00
354 11 0.02
356 47 0.09
357 42 0.08
358 38 0.07
360 49 0.09
361 12 0.02
362 108 0.20
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (344 bp):
TATATATATTATAATTAATAATTTTACAAGTTATAATATTTTTAACATTAACACAAAATAGAAAG
TAAATATATTTATATTTAAAGTGTATATATATACCAAAACTAAAAGTATTTTATATATTATAATA
GTAATTATATTCTTTATAAATGAACCCAATATATATAAAGTAAATATATTAAAAGACATTACAAG
TTAATTAATAATCATAGTTTAATGAATTAATTTAATTAATTATATGGGTTTGTCCTTAATTACAT
GAAATTAAAAAAAAATAACTAAGTCTCAAAACTATTCTAATCTCACAACTTCTTTTTAGATAATT
AAGTTTATATAAACAAAGG
Found at i:21272789 original size:19 final size:19
Alignment explanation
Indices: 21272765--21272802 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
21272755 ACTTGTCGAC
*
21272765 CTCAAATCATACTCCAATA
1 CTCAAATCACACTCCAATA
21272784 CTCAAATCACACTCCAATA
1 CTCAAATCACACTCCAATA
21272803 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.34, G:0.00, T:0.24
Consensus pattern (19 bp):
CTCAAATCACACTCCAATA
Found at i:21276295 original size:17 final size:17
Alignment explanation
Indices: 21276265--21276297 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21276255 TTCTTGATAA
21276265 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
21276282 AATAATAACT-CTTATT
1 AATAA-AACTCCTTATT
21276298 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:21276494 original size:28 final size:28
Alignment explanation
Indices: 21276462--21276526 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
21276452 TAAGACAAAA
*
21276462 AAATAT-TTTATCCTGTCTAAATTGAGAC
1 AAATATGTTT-TCCTGTCTAAATTAAGAC
* *
21276490 AAATATGTTTTCTTGTGTAAATTAAGAC
1 AAATATGTTTTCCTGTCTAAATTAAGAC
*
21276518 AAAAATGTT
1 AAATATGTT
21276527 AAAGCTGTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 29 0.91
29 3 0.09
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.40
Consensus pattern (28 bp):
AAATATGTTTTCCTGTCTAAATTAAGAC
Found at i:21286692 original size:28 final size:27
Alignment explanation
Indices: 21286645--21286697 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
21286635 AATGCTCTGA
*
21286645 GGGTGCAAAATTACCGTTTTGCCCCCG
1 GGGTGCAAAATTACAGTTTTGCCCCCG
* *
21286672 GGGTGGCAAAATTACATTTTTTCCCC
1 GGGT-GCAAAATTACAGTTTTGCCCC
21286698 AAAAACTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (27 bp):
GGGTGCAAAATTACAGTTTTGCCCCCG
Found at i:21286899 original size:19 final size:19
Alignment explanation
Indices: 21286877--21286914 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
21286867 ACTGCCAAAC
*
21286877 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
21286896 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
21286915 AGTTAAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:21307385 original size:35 final size:37
Alignment explanation
Indices: 21307340--21307428 Score: 137
Period size: 39 Copynumber: 2.4 Consensus size: 37
21307330 TGATGTGGCA
21307340 TGGGAGTGCACATGATGA-TATT-GCCATGTGCGGTG
1 TGGGAGTGCACATGATGAGTATTAGCCATGTGCGGTG
*
21307375 TGGGAGTGCACATGATGACGGTATTAGCTATGTGCGGTG
1 TGGGAGTGCACATGATGA--GTATTAGCCATGTGCGGTG
21307414 TGGGAGTGCACATGA
1 TGGGAGTGCACATGA
21307429 ACTGGGTTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
35 18 0.37
38 4 0.08
39 27 0.55
ACGTcount: A:0.21, C:0.13, G:0.38, T:0.27
Consensus pattern (37 bp):
TGGGAGTGCACATGATGAGTATTAGCCATGTGCGGTG
Found at i:21307789 original size:62 final size:62
Alignment explanation
Indices: 21307692--21307899 Score: 222
Period size: 62 Copynumber: 3.3 Consensus size: 62
21307682 AATTTTTGTT
* * ** *
21307692 GCAGCAAAATTGATTTTCGACGGGGCAAGAAACTTTCTGCCTTAGGAGTTACTATTCTTGCC
1 GCAGCCAAATTGATTTTCGCCATGACAAGAAACTTTCTGCCTTAGGAGTTACTATTCTTGCC
* * * * * *
21307754 GCAGCCAAATTGATTTTCGCTATGACGAGAAACTTTTTGCCTTAAGAGTTACTATTCTCGCT
1 GCAGCCAAATTGATTTTCGCCATGACAAGAAACTTTCTGCCTTAGGAGTTACTATTCTTGCC
* ** * *
21307816 GCAACCAAATTGATTTTTACCATGGCAAGAAACTTTCTGCCTT-GAGAGTCACTGA-TCTTGCC
1 GCAGCCAAATTGATTTTCGCCATGACAAGAAACTTTCTGCCTTAG-GAGTTACT-ATTCTTGCC
*
21307878 GCAGCCAAATTTGATTCTCGCC
1 GCAGCCAAA-TTGATTTTCGCC
21307900 GCAGCGAGAA
Statistics
Matches: 117, Mismatches: 26, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
62 107 0.91
63 10 0.09
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (62 bp):
GCAGCCAAATTGATTTTCGCCATGACAAGAAACTTTCTGCCTTAGGAGTTACTATTCTTGCC
Done.