Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 270 of 310
Found at i:89191302 original size:27 final size:27
Alignment explanation
Indices: 89191090--89191295 Score: 270
Period size: 27 Copynumber: 7.6 Consensus size: 27
89191080 TGTAAATCAA
* *
89191090 GGGTATTTTGGTAGTTTTACAAA-TTG
1 GGGTATTTTGGTAATTTTACAAACTAG
* * *
89191116 AGGGTATTTCGGTAATTTCACAAACCAG
1 -GGGTATTTTGGTAATTTTACAAACTAG
* *
89191144 TGGTATTTTGATAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
89191171 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
*
89191198 GGGCATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
* * *
89191225 GGGTATTTTGGTAATTTTATAAACAAA
1 GGGTATTTTGGTAATTTTACAAACTAG
* * *
89191252 TGGTATTTTAGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACTAG
89191279 GGGTATTTTGGTAATTT
1 GGGTATTTTGGTAATTT
89191296 GGTAAACAAA
Statistics
Matches: 154, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
27 153 0.99
28 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACTAG
Found at i:89198233 original size:48 final size:48
Alignment explanation
Indices: 89198128--89198260 Score: 144
Period size: 48 Copynumber: 2.8 Consensus size: 48
89198118 CTCAATCGAT
* * * *
89198128 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATTCCCG
1 AAGTACCTATACCATGGCCCGAAGCCAAATCAAGGCAACTTATCCCCA
* *
89198176 GAGTACCTATACCATGGCCCAAAGCCAAATCAAGGCAA-TT-TGCCTCCA
1 AAGTACCTATACCATGGCCCGAAGCCAAATCAAGGCAACTTAT-CC-CCA
* * * *
89198224 AAGTGCCTATAACATGGCTCGAAGCCAAACCAAGGCA
1 AAGTACCTATACCATGGCCCGAAGCCAAATCAAGGCA
89198261 TAACTCGCAG
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
46 1 0.01
47 3 0.04
48 67 0.94
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.19
Consensus pattern (48 bp):
AAGTACCTATACCATGGCCCGAAGCCAAATCAAGGCAACTTATCCCCA
Found at i:89201939 original size:40 final size:40
Alignment explanation
Indices: 89201902--89202126 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
89201892 GCTACTCGTT
* *
89201902 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
89201942 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
89201982 CAAATGCCTTCGGGCCTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
89202022 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
89202061 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
89202102 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
89202127 CATCATTCAA
Statistics
Matches: 166, Mismatches: 14, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
38 2 0.01
39 33 0.20
40 118 0.71
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:89202086 original size:119 final size:120
Alignment explanation
Indices: 89201902--89202126 Score: 296
Period size: 119 Copynumber: 1.9 Consensus size: 120
89201892 GCTACTCGTT
*
89201902 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* * *
89201967 ATTTAGTAAC-TCGCACAAATGCCTTCGGGCCTTAACCCGGATTTAGTAACTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * **
89202022 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* * *
89202084 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
89202127 CATCATTCAA
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
118 4 0.04
119 65 0.71
120 22 0.24
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:89215353 original size:29 final size:28
Alignment explanation
Indices: 89215293--89215382 Score: 105
Period size: 28 Copynumber: 3.3 Consensus size: 28
89215283 AGCATGGCCG
* * *
89215293 CCAG-AACAGAT-ATTATGATAGAGTCA
1 CCAGAAACAGATAATTGTGGTAGAGCCA
*
89215319 CCAGAAAACAGATAATTGTGGTAGGGCCA
1 CCAG-AAACAGATAATTGTGGTAGAGCCA
*
89215348 CCAGAAACAGATATTTGTGGTAGAGCCA
1 CCAGAAACAGATAATTGTGGTAGAGCCA
89215376 CCA-AAAC
1 CCAGAAAC
89215383 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
26 4 0.07
27 4 0.07
28 32 0.58
29 15 0.27
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (28 bp):
CCAGAAACAGATAATTGTGGTAGAGCCA
Found at i:89216664 original size:18 final size:18
Alignment explanation
Indices: 89216608--89216664 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
89216598 GACTATAGAG
89216608 GAAAAGAAGAAGAAGAGAA
1 GAAAAGAAGAAG-AGAGAA
* * *
89216627 -AATAGATGAAGAGAGGA
1 GAAAAGAAGAAGAGAGAA
*
89216644 GAAAAGAAGAAGAGAAAA
1 GAAAAGAAGAAGAGAGAA
89216662 GAA
1 GAA
89216665 TTGTCAGAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
17 5 0.17
18 25 0.83
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.04
Consensus pattern (18 bp):
GAAAAGAAGAAGAGAGAA
Found at i:89221226 original size:40 final size:41
Alignment explanation
Indices: 89221167--89221287 Score: 158
Period size: 40 Copynumber: 3.0 Consensus size: 41
89221157 TGTTCGGATG
89221167 ATAACCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTA
1 ATAACCGGGCTAAGTCCCGAAG-GCATTTGAGCTAGTGGCTA
* * * **
89221208 AT-TCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT-
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTA
*
89221247 ATAACCGAGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTA
89221288 TATCCGACTA
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
39 2 0.03
40 60 0.91
41 4 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (41 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTA
Found at i:89231947 original size:27 final size:26
Alignment explanation
Indices: 89231881--89231962 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 26
89231871 ATAGAGTCAC
* *
89231881 CAGATACAGATAATTGTGGCAGGGCCA
1 CAGAT-CAGATATTTGTGGCAGAGCCA
*
89231908 CAGAAAT-AAATATTTGTGGCAGAGCCA
1 CAG--ATCAGATATTTGTGGCAGAGCCA
*
89231935 CTAGATCAGATATTTATGGCAGAGCCA
1 C-AGATCAGATATTTGTGGCAGAGCCA
89231962 C
1 C
89231963 CAGAATGCTT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
26 2 0.04
27 40 0.87
28 2 0.04
29 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.22
Consensus pattern (26 bp):
CAGATCAGATATTTGTGGCAGAGCCA
Found at i:89233242 original size:18 final size:18
Alignment explanation
Indices: 89233193--89233244 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
89233183 GGCTATAGAG
89233193 GAAAAGAAG-AG-GAAGA
1 GAAAAGAAGAAGAGAAGA
* *
89233209 GAAAATAGATGAAGAGAGGA
1 G-AAA-AGAAGAAGAGAAGA
89233229 GAAAAGAAGAAGAGAA
1 GAAAAGAAGAAGAGAA
89233245 AAAATTGTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
16 1 0.04
17 3 0.11
18 14 0.50
19 5 0.18
20 5 0.18
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.04
Consensus pattern (18 bp):
GAAAAGAAGAAGAGAAGA
Found at i:89237413 original size:42 final size:42
Alignment explanation
Indices: 89237305--89237447 Score: 146
Period size: 42 Copynumber: 3.4 Consensus size: 42
89237295 GCCATATCCT
* * *
89237305 AGATATGGTCTTACA-TAAGATCTCATATCGATGCTAATAGCCC
1 AGATATGGTCTTACACGAA-ATCTCATATCGATG-TCATACCCC
* * *
89237348 AGCTATGGTCTTATACGAGATCTCATATCGATGTCATACCCC
1 AGATATGGTCTTACACGAAATCTCATATCGATGTCATACCCC
* ** * *
89237390 AGATATGGTCATACACGAAATCTCATAAT-GATACCATATCTC
1 AGATATGGTCTTACACGAAATCTCAT-ATCGATGTCATACCCC
89237432 AGATATGGTCTTACAC
1 AGATATGGTCTTACAC
89237448 ATAGCCTCGG
Statistics
Matches: 83, Mismatches: 15, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
42 53 0.64
43 29 0.35
44 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.30
Consensus pattern (42 bp):
AGATATGGTCTTACACGAAATCTCATATCGATGTCATACCCC
Found at i:89246840 original size:27 final size:27
Alignment explanation
Indices: 89246141--89246842 Score: 225
Period size: 27 Copynumber: 25.9 Consensus size: 27
89246131 TACCGTCGAC
* ***
89246141 TTGTAAAATTACCAAAGTACCCCCAAT
1 TTGTAAAATTACCAAAATACCCTTGAT
* * * *
89246168 TTATAAAATTACCCAAATATCCTCGAT
1 TTGTAAAATTACCAAAATACCCTTGAT
* * *
89246195 TTGCAAAATTACCGAAATACCC-TCAGT
1 TTGTAAAATTACCAAAATACCCTTGA-T
* * *
89246222 TTGCAAAATTACTAAAATACCCTCGATT
1 TTGTAAAATTACCAAAATACCCTTGA-T
*
89246250 TTGTAAAATTACTAAAATACTCC-TG-T
1 TTGTAAAATTACCAAAATAC-CCTTGAT
** * *** *
89246276 AAGATAGAATTACCATTTTACCCTCGAT
1 TTG-TAAAATTACCAAAATACCCTTGAT
* * *** *
89246304 TTATAGAATTACCATTTTACCCTCGAT
1 TTGTAAAATTACCAAAATACCCTTGAT
** ***** *
89246331 TTACAAAATTACTGTCTTACCCTCGAT
1 TTGTAAAATTACCAAAATACCCTTGAT
* * *** * *
89246358 TTATAGAATTACCATTTTACCCTCGGT
1 TTGTAAAATTACCAAAATACCCTTGAT
** ** *
89246385 TTACAAAATTACTGAAATACCCTTGGT
1 TTGTAAAATTACCAAAATACCCTTGAT
** *
89246412 TTACAAAATTACCAAAATACCCTCGAT
1 TTGTAAAATTACCAAAATACCCTTGAT
*** * *
89246439 CAATAAAATTACCAAAATACCCCTGGT
1 TTGTAAAATTACCAAAATACCCTTGAT
* * *
89246466 TTGTAAAATTACTAAAATGCCCCT-AGT
1 TTGTAAAATTACCAAAATACCCTTGA-T
* *
89246493 TTGTAAAATTACTAAAATACCACCTGAT
1 TTGTAAAATTACCAAAATACC-CTTGAT
*** * *
89246521 TTGTAAAATTATTGAAATACCCTCGAC
1 TTGTAAAATTACCAAAATACCCTTGAT
* *
89246548 TTGTAAAAATTACCAAAGTACCCTCGAT
1 TTGT-AAAATTACCAAAATACCCTTGAT
* * *****
89246576 TTATAGAATTACTGTTTTACCCTTGAT
1 TTGTAAAATTACCAAAATACCCTTGAT
** * *****
89246603 TTACAGAATTACTGTTTTACCCTTGAT
1 TTGTAAAATTACCAAAATACCCTTGAT
** ***** *
89246630 TTACAAAATTACTGTTTTACCCTCGA-
1 TTGTAAAATTACCAAAATACCCTTGAT
* * *
89246656 TTGTGAAATTACTAAAATACCCCTG-T
1 TTGTAAAATTACCAAAATACCCTTGAT
** * * *
89246682 AGGGTAGAATTACCAAAACACCCCT-AGT
1 -TTGTAAAATTACCAAAATACCCTTGA-T
* *
89246710 TTGTAAAATTACCAAAAGACCACTAG-T
1 TTGTAAAATTACCAAAATACC-CTTGAT
* ** **
89246737 TTGTTAAATTACTGAAATACCCTCAAT
1 TTGTAAAATTACCAAAATACCCTTGAT
* * *
89246764 TTATAAAATTACCAAAATACCCCTAAT
1 TTGTAAAATTACCAAAATACCCTTGAT
**
89246791 TTACAAAATTA-CAGAAATACCCTTGAT
1 TTGTAAAATTACCA-AAATACCCTTGAT
* *
89246818 TTGTAAATTTACCAAAACACCCTTG
1 TTGTAAAATTACCAAAATACCCTTG
89246843 TAGGATGAAA
Statistics
Matches: 529, Mismatches: 127, Indels: 38
0.76 0.18 0.05
Matches are distributed among these distances:
26 25 0.05
27 430 0.81
28 71 0.13
29 3 0.01
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (27 bp):
TTGTAAAATTACCAAAATACCCTTGAT
Found at i:89246903 original size:27 final size:27
Alignment explanation
Indices: 89246860--89246933 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
89246850 AAAAGACTAA
*
89246860 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
89246887 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
* *
89246914 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
89246934 TGATGAATAC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:89247671 original size:20 final size:20
Alignment explanation
Indices: 89247646--89247709 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
89247636 GATATGATAT
*
89247646 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGAAATGC
*
89247666 ACATGATATGTATAAAATGC
1 ACATGATATGTATGAAATGC
89247686 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
89247706 ACAT
1 ACAT
89247710 AATGTATTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 38 0.95
21 2 0.05
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGAAATGC
Found at i:89247792 original size:26 final size:26
Alignment explanation
Indices: 89247762--89247949 Score: 231
Period size: 26 Copynumber: 7.3 Consensus size: 26
89247752 GAGGAAGTGC
* *
89247762 AAAAGGGCTTATACCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
89247788 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
89247814 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* * **
89247840 AAAAGGGCTTATACCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
89247866 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* * **
89247892 AAAAGGGCTT-CGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* *
89247917 AAATGGG-TTTTGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
89247940 AAAAGAGGCT
1 AAAAG-GGCT
89247950 AGGCCTCCAG
Statistics
Matches: 139, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
23 4 0.03
24 7 0.05
25 24 0.17
26 104 0.75
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:89247840 original size:52 final size:52
Alignment explanation
Indices: 89247762--89247949 Score: 258
Period size: 52 Copynumber: 3.7 Consensus size: 52
89247752 GAGGAAGTGC
* * * **
89247762 AAAAGGGCTTATACCCTAGTTTATTGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCTAGTTTACCG
*
89247814 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATACCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCTAGTTTACCG
*
89247866 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTT-CGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCTAGTTTACCG
* *
89247917 AAATGGG-TTTTGCCCCAG-TTATT-AAAAGAGGCT
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAG-GGCT
89247950 AGGCCTCCAG
Statistics
Matches: 125, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
48 5 0.04
49 9 0.07
50 10 0.08
51 19 0.15
52 82 0.66
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCTAGTTTACCG
Found at i:89248147 original size:42 final size:42
Alignment explanation
Indices: 89248082--89248173 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
89248072 TAGTCTCCCC
* * ** *
89248082 AAATAGGCTTGCATACATTCATTGGTATTTCATAAGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATAAGATATTG
**
89248124 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATAAGATATTG
89248166 AAATGGGC
1 AAATGGGC
89248174 CTATGGGCCA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.34
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATAAGATATTG
Found at i:89250790 original size:25 final size:25
Alignment explanation
Indices: 89250761--89250808 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
89250751 TTATAACATG
* * *
89250761 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
89250786 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
89250809 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:89250892 original size:11 final size:11
Alignment explanation
Indices: 89250856--89250911 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
89250846 CATGGTATGT
89250856 ATGATATGCAC
1 ATGATATGCAC
* *
89250867 ATGACATG--T
1 ATGATATGCAC
89250876 ATGATATGCAC
1 ATGATATGCAC
*
89250887 ATGATATG--T
1 ATGATATGCAC
89250896 ATGATATGCAC
1 ATGATATGCAC
89250907 ATGAT
1 ATGAT
89250912 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:89250911 original size:20 final size:20
Alignment explanation
Indices: 89250845--89250911 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
89250835 ATTTTGATAA
*
89250845 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
89250865 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
89250885 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
89250905 ACATGAT
1 ACATGAT
89250912 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:89251047 original size:24 final size:23
Alignment explanation
Indices: 89250962--89251059 Score: 135
Period size: 23 Copynumber: 4.2 Consensus size: 23
89250952 AGGAAGTGTA
*
89250962 AAAGGGCTTACGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
89250985 AAAGGGCTTATGCCCCAGCTATT
1 AAAGGGCTTATGCCCCAGTTATT
89251008 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
89251031 AAAAGGGCGTT-TTCCCCAGTTATT
1 -AAAGGGC-TTATGCCCCAGTTATT
89251055 GAAAG
1 -AAAG
89251060 AGGATAGGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
23 43 0.63
24 23 0.34
25 2 0.03
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:89251307 original size:31 final size:31
Alignment explanation
Indices: 89251272--89251335 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
89251262 CATTTACAGT
89251272 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
89251303 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
89251334 AA
1 AA
89251336 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:89273191 original size:27 final size:27
Alignment explanation
Indices: 89273160--89273337 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
89273150 TAAATTGTAC
89273160 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
89273187 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
89273213 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
89273241 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
89273269 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
89273296 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
89273323 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
89273338 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:89273274 original size:82 final size:81
Alignment explanation
Indices: 89273161--89273316 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
89273151 AAATTGTACA
* *
89273161 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
89273225 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
89273242 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
89273307 TGCGAGTTGA
65 TGCGAATTGA
89273317 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:89273328 original size:82 final size:81
Alignment explanation
Indices: 89273157--89273337 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
89273147 GATTAAATTG
* *
89273157 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
89273222 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
89273238 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
89273302 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
89273320 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
89273338 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:89278382 original size:26 final size:26
Alignment explanation
Indices: 89278352--89278462 Score: 150
Period size: 27 Copynumber: 4.2 Consensus size: 26
89278342 AGCATGGCTG
* *
89278352 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
89278378 CCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
*
89278405 CCAGAACAGATATATGGGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
89278432 CCAGATCAGATAATGGTGGCATAGCCA
1 CCAGAACAGATAAT-GTGGCAGAGCCA
89278459 CCAG
1 CCAG
89278463 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
26 15 0.20
27 60 0.79
28 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:89279884 original size:24 final size:24
Alignment explanation
Indices: 89279849--89279949 Score: 157
Period size: 24 Copynumber: 4.2 Consensus size: 24
89279839 CCAACACTGT
* *
89279849 TCTCCCTAATCAGCTCCTAAATCC
1 TCTCCCTTATCAACTCCTAAATCC
89279873 TCTCCCTTATCAACTCCTAAATCC
1 TCTCCCTTATCAACTCCTAAATCC
*
89279897 TATCCCTTATCAACTCCTAAATCC
1 TCTCCCTTATCAACTCCTAAATCC
* *
89279921 TATCCCTTATTAACTCCTAAATCC
1 TCTCCCTTATCAACTCCTAAATCC
89279945 TCTCC
1 TCTCC
89279950 TGACAGACTT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.26, C:0.40, G:0.01, T:0.34
Consensus pattern (24 bp):
TCTCCCTTATCAACTCCTAAATCC
Found at i:89286221 original size:27 final size:27
Alignment explanation
Indices: 89286167--89286277 Score: 127
Period size: 27 Copynumber: 4.1 Consensus size: 27
89286157 AGCATGGCTG
** *
89286167 CCAGAACAGATAA-TGTGATAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
89286193 CCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
*
89286220 CCAGAACAGAT-ATATGGGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
** * *
89286247 TAAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
89286274 CCAG
1 CCAG
89286278 GACGCTTCCT
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
26 15 0.21
27 54 0.76
28 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:89286707 original size:8 final size:8
Alignment explanation
Indices: 89286690--89286722 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
89286680 TCTTAAAATG
89286690 TCGGCTTT
1 TCGGCTTT
*
89286698 TCGGCATT
1 TCGGCTTT
89286706 TCGGCTTT
1 TCGGCTTT
89286714 TCGGCTTT
1 TCGGCTTT
89286722 T
1 T
89286723 GCCGATCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.03, C:0.24, G:0.24, T:0.48
Consensus pattern (8 bp):
TCGGCTTT
Found at i:89287717 original size:24 final size:24
Alignment explanation
Indices: 89287684--89288522 Score: 1642
Period size: 24 Copynumber: 35.0 Consensus size: 24
89287674 AACACTGTTC
* * *
89287684 TCCCTAATCAGCTCCTAAATCCTC
1 TCCCTTATCAACTCCTAAATCCTA
*
89287708 TCCCTTATCAGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89287732 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89287756 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89287780 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89287804 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89287828 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89287852 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89287876 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89287900 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89287924 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89287948 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89287972 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89287996 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288020 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288044 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288068 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288092 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288116 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288140 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288164 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288188 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288212 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288236 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288260 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288284 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288308 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288332 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288356 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288380 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288404 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288428 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288452 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288476 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
89288500 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
89288523 CTCCTGACAG
Statistics
Matches: 812, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 812 1.00
ACGTcount: A:0.29, C:0.38, G:0.00, T:0.33
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:89290345 original size:17 final size:17
Alignment explanation
Indices: 89290299--89290350 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
89290289 ATATCTATCA
*
89290299 AATTATAATATA-ACAT
1 AATTATAATATATAAAT
*
89290315 AATTA-AGTATTATAAAT
1 AATTATAATA-TATAAAT
*
89290332 AATTATAATATATATAT
1 AATTATAATATATAAAT
89290349 AA
1 AA
89290351 GGAGATGAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 3 0.10
16 7 0.24
17 16 0.55
18 3 0.10
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
AATTATAATATATAAAT
Found at i:89290576 original size:21 final size:22
Alignment explanation
Indices: 89290551--89290598 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
89290541 TCCGGCTCAC
**
89290551 AAAAATTCTATGAATTTTTAAA
1 AAAAATTCTATGAATTTAAAAA
89290573 AAAAATTCTATGAATTTAAAAA
1 AAAAATTCTATGAATTTAAAAA
89290595 AAAA
1 AAAA
89290599 TTCCTACGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (22 bp):
AAAAATTCTATGAATTTAAAAA
Found at i:89290599 original size:21 final size:22
Alignment explanation
Indices: 89290551--89290601 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 22
89290541 TCCGGCTCAC
*
89290551 AAAAATTCTATGAATTTTTAAA
1 AAAAATTCTATGAATTTTAAAA
89290573 AAAAATTCTATGAA-TTTAAAA
1 AAAAATTCTATGAATTTTAAAA
89290594 AAAAATTC
1 AAAAATTC
89290602 CTACGTGGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (22 bp):
AAAAATTCTATGAATTTTAAAA
Found at i:89292426 original size:49 final size:47
Alignment explanation
Indices: 89292354--89292615 Score: 175
Period size: 47 Copynumber: 5.5 Consensus size: 47
89292344 ATAAGTTGCC
89292354 GATGCCATGTCCCA-AGCATGGTCTTACACTGGCTATCATCATCGAGGCT
1 GATG-CATGTCCCAGA-CATGGTCTTACACTGGCTATCATC-TCGAGGCT
* * * *
89292403 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTATATACG-TGCT
1 GATG-CATGTCCCAGACATGGTCTTACACTGGCTATC--ATCT-CGAGGCT
* * * *
89292453 GATGCATGTCCCAGACAT-GTCTTACACT-ACCA-CAACTCTTA-GCT
1 GATGCATGTCCCAGACATGGTCTTACACTGGCTATCATCTC-GAGGCT
* * * * *
89292497 GATGCGTGTCTCAGACA-CGTCTTACACAGGCTATCATCGTCGAGGCC
1 GATGCATGTCCCAGACATGGTCTTACACTGGCTATCATC-TCGAGGCT
* * * *
89292544 GATGCATGTCCCAGTCAT-GTTTTACACTGGC-ACTCATCTCTG-TGCC
1 GATGCATGTCCCAGACATGGTCTTACACTGGCTA-TCATCTC-GAGGCT
* *
89292590 GATGCCATGTCCTAAACATGGTCTTA
1 GATG-CATGTCCCAGACATGGTCTTA
89292616 TACATGTCTT
Statistics
Matches: 169, Mismatches: 28, Indels: 33
0.73 0.12 0.14
Matches are distributed among these distances:
43 1 0.01
44 29 0.17
45 2 0.01
46 15 0.09
47 47 0.28
48 15 0.09
49 47 0.28
50 9 0.05
51 4 0.02
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (47 bp):
GATGCATGTCCCAGACATGGTCTTACACTGGCTATCATCTCGAGGCT
Found at i:89293014 original size:30 final size:30
Alignment explanation
Indices: 89292973--89293030 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
89292963 AAATTCACAT
* *
89292973 CTTTGGAAAAATGACCATTTTGCCCCTAAA
1 CTTTGGAAAAATAACCATTTTACCCCTAAA
*
89293003 CTTTGGCAAAATAACCATTTTACCCCTA
1 CTTTGGAAAAATAACCATTTTACCCCTA
89293031 TGCTCAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (30 bp):
CTTTGGAAAAATAACCATTTTACCCCTAAA
Found at i:89300059 original size:47 final size:48
Alignment explanation
Indices: 89299796--89300062 Score: 230
Period size: 49 Copynumber: 5.6 Consensus size: 48
89299786 ACAAAATGTC
* * *
89299796 GATGCCATGTCCCAAACATGGTCTTACACTAGCTATCATCATCAAGGCC
1 GATG-CATGTCCCAGACATGGTCTTACACTAGCTATCATCATCGAGGCT
* *
89299845 GATACCATGTCCCAGACATGGTCTTACACTGGCTATCATCATCGAGG-T
1 GAT-GCATGTCCCAGACATGGTCTTACACTAGCTATCATCATCGAGGCT
* * ** *
89299893 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGT-ATATATGTACT
1 -GATG-CATGTCCCAGACATGGTCTTACACTAGCTATCATCATCGA-G-GCT
* * *
89299944 GATGCATGTCCCAG-CGT-GTCTTACACTAGC-A-CAAC-TCTTA-GCT
1 GATGCATGTCCCAGACATGGTCTTACACTAGCTATCATCATC-GAGGCT
* * * * *
89299987 GATGCGTGTCCCAGACA-CGTGTTACACTGGCTATCATCGTCGAGGCT
1 GATGCATGTCCCAGACATGGTCTTACACTAGCTATCATCATCGAGGCT
*
89300034 GATGCATGTCCCAGACAT-TTCTTACACTA
1 GATGCATGTCCCAGACATGGTCTTACACTA
89300063 ATACTCGTCT
Statistics
Matches: 175, Mismatches: 28, Indels: 32
0.74 0.12 0.14
Matches are distributed among these distances:
43 15 0.09
44 12 0.07
45 3 0.02
46 6 0.03
47 42 0.24
48 5 0.03
49 87 0.50
50 4 0.02
51 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (48 bp):
GATGCATGTCCCAGACATGGTCTTACACTAGCTATCATCATCGAGGCT
Found at i:89300710 original size:15 final size:15
Alignment explanation
Indices: 89300690--89300719 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
89300680 AAAATAGTCC
89300690 CTTTAGCTGTTTTCA
1 CTTTAGCTGTTTTCA
*
89300705 CTTTAGGTGTTTTCA
1 CTTTAGCTGTTTTCA
89300720 TGCTAGCACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.17, G:0.17, T:0.53
Consensus pattern (15 bp):
CTTTAGCTGTTTTCA
Found at i:89303306 original size:46 final size:45
Alignment explanation
Indices: 89303162--89303378 Score: 181
Period size: 46 Copynumber: 4.7 Consensus size: 45
89303152 TGTGTGAGCT
* * *
89303162 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GACGA-AGCC
* * * *
89303208 AGTGTAATACCATGTCTGGGACATGGCATCGGCATTGAGAC-AATTGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGACGAA--GCC
*
89303256 AGTGTAAGACATGTCTGGGACATGCTTCGGCCTCGAGACGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACG-AAGCC
* * *** *
89303302 AGTGTAAGACATGTCTGGGACATGTATCAG-CTACGAGA-TTTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGACGAAGCC
*
89303346 AGTGTAAGACCATGTCTAGGACATGGCATCGGC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
89303379 ACAGATATGC
Statistics
Matches: 138, Mismatches: 22, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
44 11 0.08
45 15 0.11
46 61 0.44
47 29 0.21
48 21 0.15
49 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGAAGCC
Found at i:89306086 original size:12 final size:12
Alignment explanation
Indices: 89306069--89306099 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
89306059 CCAATAGGGT
89306069 TTGTACGAGCAC
1 TTGTACGAGCAC
*
89306081 TTGTACGAGCGC
1 TTGTACGAGCAC
89306093 TTGTACG
1 TTGTACG
89306100 GGATTGCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (12 bp):
TTGTACGAGCAC
Found at i:89306661 original size:5 final size:5
Alignment explanation
Indices: 89306651--89306684 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
89306641 ATCTGTGTTC
89306651 TTTAT TTTAT TTTAGT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT TTT
89306685 CACAAATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:89306672 original size:16 final size:15
Alignment explanation
Indices: 89306651--89306684 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
89306641 ATCTGTGTTC
89306651 TTTATTTTATTTTAGT
1 TTTATTTTATTTTA-T
89306667 TTTATTTTATTTTAT
1 TTTATTTTATTTTAT
89306682 TTT
1 TTT
89306685 CACAAATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTATTTTATTTTAT
Found at i:89312745 original size:43 final size:43
Alignment explanation
Indices: 89312684--89312881 Score: 315
Period size: 43 Copynumber: 4.6 Consensus size: 43
89312674 GCTGGTATTA
* *
89312684 TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTACCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* *
89312727 TATTCGGGCTTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* *
89312770 TATTCGGGCCTTCATGCCTAGTAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* * *
89312813 TATTCGGGCCTTCGTGCCTAGCAAGCTTCGTGCCGGTTATGTA
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
89312856 TATTCGGGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
89312882 GTAATGCCGG
Statistics
Matches: 142, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 142 1.00
ACGTcount: A:0.12, C:0.24, G:0.32, T:0.32
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:89318046 original size:46 final size:46
Alignment explanation
Indices: 89317965--89318081 Score: 139
Period size: 46 Copynumber: 2.5 Consensus size: 46
89317955 GACAGGACAG
* * *
89317965 GACAGAAATGAGCCATGTAAGTCCACATCAAATATATGGCTTTGGA
1 GACAGGAATGAGCCATGTAAGTCCAAATCAAATATATGGCATTGGA
*
89318011 GACAGGAATGAGCCATGTAAG-CCTATAAT-ATATATATGGCATTGGA
1 GACAGGAATGAGCCATGTAAGTCC-A-AATCAAATATATGGCATTGGA
* **
89318057 GACAGGAATAATTCATGTAAGTCCA
1 GACAGGAATGAGCCATGTAAGTCCA
89318082 TGTCGAAGAC
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
45 2 0.03
46 55 0.90
47 4 0.07
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (46 bp):
GACAGGAATGAGCCATGTAAGTCCAAATCAAATATATGGCATTGGA
Found at i:89322578 original size:37 final size:37
Alignment explanation
Indices: 89322528--89322599 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 37
89322518 GGAAATATAT
89322528 TCCGGGTAAGACCCGA-AGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATA-ACTACGTGTGGAGATTTTG
*
89322565 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATTT
89322600 CATCTGAGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
37 32 0.97
38 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATAACTACGTGTGGAGATTTTG
Found at i:89323873 original size:20 final size:20
Alignment explanation
Indices: 89323848--89323964 Score: 101
Period size: 20 Copynumber: 5.9 Consensus size: 20
89323838 AGAAGCTAAT
*
89323848 AGAGGCACCAGAGTGCAAAC
1 AGAGGCACCAAAGTGCAAAC
* ** **
89323868 AGAGGCACGATTGTGCAATT
1 AGAGGCACCAAAGTGCAAAC
** *
89323888 AGAGGCACTGAATTGCAAAC
1 AGAGGCACCAAAGTGCAAAC
* * *
89323908 AGAGACACCAAAGTG-TAAT
1 AGAGGCACCAAAGTGCAAAC
89323927 AGAGGCACCAAAGTGCAAAC
1 AGAGGCACCAAAGTGCAAAC
* *
89323947 AGAGGCATCGAAGTGCAA
1 AGAGGCACCAAAGTGCAA
89323965 TCTCATACAA
Statistics
Matches: 73, Mismatches: 23, Indels: 2
0.74 0.23 0.02
Matches are distributed among these distances:
19 16 0.22
20 57 0.78
ACGTcount: A:0.40, C:0.20, G:0.27, T:0.13
Consensus pattern (20 bp):
AGAGGCACCAAAGTGCAAAC
Found at i:89323961 original size:39 final size:38
Alignment explanation
Indices: 89323844--89323961 Score: 128
Period size: 39 Copynumber: 3.0 Consensus size: 38
89323834 TCATAGAAGC
* *
89323844 TAATAGAGGCACCAGAGTGCAAACAGAGGCACGATTGTG
1 TAATAGAGGCACCAAAGTGCAAACAGAGGCACGA-AGTG
* ** * * *
89323883 CAATTAGAGGCACTGAATTGCAAACAGAGACACCAAAGTG
1 TAA-TAGAGGCACCAAAGTGCAAACAGAGGCA-CGAAGTG
89323923 TAATAGAGGCACCAAAGTGCAAACAGAGGCATCGAAGTG
1 TAATAGAGGCACCAAAGTGCAAACAGAGGCA-CGAAGTG
89323962 CAATCTCATA
Statistics
Matches: 62, Mismatches: 15, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
39 32 0.52
40 28 0.45
41 2 0.03
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.14
Consensus pattern (38 bp):
TAATAGAGGCACCAAAGTGCAAACAGAGGCACGAAGTG
Found at i:89329855 original size:46 final size:46
Alignment explanation
Indices: 89329783--89329883 Score: 141
Period size: 46 Copynumber: 2.2 Consensus size: 46
89329773 GACAGGAAAG
* * *
89329783 GACAGAAATGAGCCATGTAAGTCCAT-ATCAAATATACGGCTTTGGA
1 GACAGGAATGAGCCATGTAAGCCCATAAT-AAATATACGGCATTGGA
* *
89329829 GACAGGAATGAGCCATGTAAGCCCATAATATATATATGGCATTGGA
1 GACAGGAATGAGCCATGTAAGCCCATAATAAATATACGGCATTGGA
89329875 GACAGGAAT
1 GACAGGAAT
89329884 AATTCATGTA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
46 47 0.96
47 2 0.04
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.23
Consensus pattern (46 bp):
GACAGGAATGAGCCATGTAAGCCCATAATAAATATACGGCATTGGA
Found at i:89329892 original size:46 final size:46
Alignment explanation
Indices: 89329783--89329895 Score: 129
Period size: 46 Copynumber: 2.5 Consensus size: 46
89329773 GACAGGAAAG
* * * *
89329783 GACAGAAATGAGCCATGTAAGTCCATATCAAATATACGGCTTTGGA
1 GACAGGAATAAGCCATGTAAGCCCATATCAAATATACGGCATTGGA
* * *
89329829 GACAGGAATGAGCCATGTAAGCCCATAAT-ATATATATGGCATTGGA
1 GACAGGAATAAGCCATGTAAGCCCAT-ATCAAATATACGGCATTGGA
**
89329875 GACAGGAATAATTCATGTAAG
1 GACAGGAATAAGCCATGTAAG
89329896 TTCATGTCGA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 56 0.97
47 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (46 bp):
GACAGGAATAAGCCATGTAAGCCCATATCAAATATACGGCATTGGA
Found at i:89332362 original size:20 final size:20
Alignment explanation
Indices: 89332337--89332453 Score: 83
Period size: 20 Copynumber: 5.9 Consensus size: 20
89332327 AGATGCTAAT
*
89332337 AGAGGCACCAGAGTGCAAAC
1 AGAGGCACCAAAGTGCAAAC
* ** **
89332357 AGAGGCACGATTGTGCAATT
1 AGAGGCACCAAAGTGCAAAC
* ** *
89332377 AGAGGTACTGAATTGCAAAC
1 AGAGGCACCAAAGTGCAAAC
* * * *
89332397 AAAGACACCAAAGTG-TAAT
1 AGAGGCACCAAAGTGCAAAC
89332416 AGAGGCACCAAAGTGCAAAC
1 AGAGGCACCAAAGTGCAAAC
* *
89332436 AGAGGCATCGAAGTGCAA
1 AGAGGCACCAAAGTGCAA
89332454 TCTCATACAA
Statistics
Matches: 69, Mismatches: 27, Indels: 2
0.70 0.28 0.02
Matches are distributed among these distances:
19 15 0.22
20 54 0.78
ACGTcount: A:0.41, C:0.19, G:0.26, T:0.14
Consensus pattern (20 bp):
AGAGGCACCAAAGTGCAAAC
Found at i:89332450 original size:39 final size:38
Alignment explanation
Indices: 89332333--89332450 Score: 110
Period size: 39 Copynumber: 3.0 Consensus size: 38
89332323 TCATAGATGC
* *
89332333 TAATAGAGGCACCAGAGTGCAAACAGAGGCACGATTGTG
1 TAATAGAGGCACCAAAGTGCAAACAGAGGCACGA-AGTG
* * ** * * * *
89332372 CAATTAGAGGTACTGAATTGCAAACAAAGACACCAAAGTG
1 TAA-TAGAGGCACCAAAGTGCAAACAGAGGCA-CGAAGTG
89332412 TAATAGAGGCACCAAAGTGCAAACAGAGGCATCGAAGTG
1 TAATAGAGGCACCAAAGTGCAAACAGAGGCA-CGAAGTG
89332451 CAATCTCATA
Statistics
Matches: 58, Mismatches: 19, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
39 30 0.52
40 26 0.45
41 2 0.03
ACGTcount: A:0.41, C:0.18, G:0.26, T:0.15
Consensus pattern (38 bp):
TAATAGAGGCACCAAAGTGCAAACAGAGGCACGAAGTG
Found at i:89334114 original size:58 final size:60
Alignment explanation
Indices: 89334052--89334164 Score: 194
Period size: 61 Copynumber: 1.9 Consensus size: 60
89334042 TCACTTTAAT
*
89334052 ATTAAATTAATATAATACTTA-T-CAAGATAAATATTAAATTAAATTTAATATTCAATCA
1 ATTAAATTAATAGAATACTTACTACAAGATAAATATTAAATTAAATTTAATATTCAATCA
89334110 ATTAAATTAATAGAATACTTATCTACAAGATAAATATTAAATTAAATTTAATATT
1 ATTAAATTAATAGAATACTTA-CTACAAGATAAATATTAAATTAAATTTAATATT
89334165 AAGATAATCG
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
58 20 0.39
60 1 0.02
61 30 0.59
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (60 bp):
ATTAAATTAATAGAATACTTACTACAAGATAAATATTAAATTAAATTTAATATTCAATCA
Found at i:89337016 original size:46 final size:45
Alignment explanation
Indices: 89336873--89337016 Score: 129
Period size: 46 Copynumber: 3.1 Consensus size: 45
89336863 CCCGCCCATA
*
89336873 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTA-CATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATC-CT
* *
89336922 --CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCA-AC-CATCC-T
89336965 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCATCCT
89337012 AGTGA
1 AGTGA
89337017 CATGTCACTT
Statistics
Matches: 80, Mismatches: 5, Indels: 23
0.74 0.05 0.21
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 6 0.08
44 1 0.01
46 34 0.43
47 29 0.36
48 5 0.06
49 1 0.01
50 2 0.03
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCCT
Found at i:89348702 original size:362 final size:362
Alignment explanation
Indices: 89348037--89349125 Score: 2169
Period size: 362 Copynumber: 3.0 Consensus size: 362
89348027 ACGAGGCCCA
89348037 AAACATGTGTTTGGAGTGGTTTGGGACTAAACCGAGAACTTTGAAAACTTTTGGGGAAACTTAGA
1 AAACATGTGTTTGGAGTGGTTTGGGACTAAACCGAGAACTTTGAAAACTTTTGGGGAAACTTAGA
89348102 AAATTTTCATCATGAAACAGATCCACACGCCCGTGTGGGTGAAGGGACACGCCCATGTGGCATAT
66 AAATTTTCATCATGAAACAGATCCACACGCCCGTGTGGGTGAAGGGACACGCCCATGTGGCATAT
89348167 CACACGCCCATGCTTCAAGTCGTGTCCATCTTAGGGTGCATTATGTTTATGACATCATCATAAAA
131 CACACGCCCATGCTTCAAGTCGTGTCCATCTTAGGGTGCATTATGTTTATGACATCATCATAAAA
89348232 ATGAGGTTACATGGCCAAATCACATGCCCGTGTGTTTAGGCCGTGTCCTCCACACGGCTAAGACA
196 ATGAGGTTACATGGCCAAATCACATGCCCGTGTGTTTAGGCCGTGTCCTCCACACGGCTAAGACA
89348297 CACGCCCGTGTCTCTACCTGTGTGTTGAATCCTGGACATTCTATTTTTTTTTTCAAAATCAAGGT
261 CACGCCCGTGTCTCTACCTGTGTGTTGAATCCTGGACATTCTATTTTTTTTTTCAAAATCAAGGT
89348362 GCATGGGACACATGGCTGGAGCATATGCCCATGGGGC
326 GCATGGGACACATGGCTGGAGCATATGCCCATGGGGC
89348399 AAACATGTGTTTGGAGTGGTTTGGGACTAAACCGAGAACTTTGAAAACTTTTGGGGAAACTTAGA
1 AAACATGTGTTTGGAGTGGTTTGGGACTAAACCGAGAACTTTGAAAACTTTTGGGGAAACTTAGA
89348464 AAATTTTCATCATGAAACAGATCCACACGCCCGTGTGGGTGAAGGGACACGCCCATGTGGCATAT
66 AAATTTTCATCATGAAACAGATCCACACGCCCGTGTGGGTGAAGGGACACGCCCATGTGGCATAT
89348529 CACACGCCCATGCTTCAAGTCGTGTCCATCTTAGGGTGCATTATGTTTATGACATCATCATAAAA
131 CACACGCCCATGCTTCAAGTCGTGTCCATCTTAGGGTGCATTATGTTTATGACATCATCATAAAA
89348594 ATGAGGTTACATGGCCAAATCACATGCCCGTGTGTTTAGGCCGTGTCCTCCACACGGCTAAGACA
196 ATGAGGTTACATGGCCAAATCACATGCCCGTGTGTTTAGGCCGTGTCCTCCACACGGCTAAGACA
89348659 CACGCCCGTGTCTCTACCTGTGTGTTGAATCCTGGACATTCTATTTTTTTTTTCAAAATCAAGGT
261 CACGCCCGTGTCTCTACCTGTGTGTTGAATCCTGGACATTCTATTTTTTTTTTCAAAATCAAGGT
89348724 GCATGGGACACATGGCTGGAGCATATGCCCATGGGGC
326 GCATGGGACACATGGCTGGAGCATATGCCCATGGGGC
89348761 AAACATGTGTTTGGAGTGGTTTGGGACTAAACCGAGAACTTTGAAAACTTTTGGGGAAACTTAGA
1 AAACATGTGTTTGGAGTGGTTTGGGACTAAACCGAGAACTTTGAAAACTTTTGGGGAAACTTAGA
89348826 AAATTTTCATCATGAAACAGATCCACACGCCCGTGTGGGTGAAGGGACACGCCCATGTGGCATAT
66 AAATTTTCATCATGAAACAGATCCACACGCCCGTGTGGGTGAAGGGACACGCCCATGTGGCATAT
89348891 CACACGCCCATGCTTCAAGTCGTGTCCATCTTAGGGTGCATTATGTTTATGACATCATCATAAAA
131 CACACGCCCATGCTTCAAGTCGTGTCCATCTTAGGGTGCATTATGTTTATGACATCATCATAAAA
89348956 ATGAGGTTACATGGCCAAATCACATGCCCGTGTGTTTAGGCCGTGTCCTCCACACGGCTAAGACA
196 ATGAGGTTACATGGCCAAATCACATGCCCGTGTGTTTAGGCCGTGTCCTCCACACGGCTAAGACA
89349021 CACGCCCGTGTCTCTACCTGTGTGTTGAATCCTGGACATTCTATTTTTTTTTTCAAAATCAAGGT
261 CACGCCCGTGTCTCTACCTGTGTGTTGAATCCTGGACATTCTATTTTTTTTTTCAAAATCAAGGT
*
89349086 GCATGGGACACATGGCCGGAGCATATGCCCATGGGGC
326 GCATGGGACACATGGCTGGAGCATATGCCCATGGGGC
89349123 AAA
1 AAA
89349126 TTGTGTGTCA
Statistics
Matches: 726, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
362 726 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.27
Consensus pattern (362 bp):
AAACATGTGTTTGGAGTGGTTTGGGACTAAACCGAGAACTTTGAAAACTTTTGGGGAAACTTAGA
AAATTTTCATCATGAAACAGATCCACACGCCCGTGTGGGTGAAGGGACACGCCCATGTGGCATAT
CACACGCCCATGCTTCAAGTCGTGTCCATCTTAGGGTGCATTATGTTTATGACATCATCATAAAA
ATGAGGTTACATGGCCAAATCACATGCCCGTGTGTTTAGGCCGTGTCCTCCACACGGCTAAGACA
CACGCCCGTGTCTCTACCTGTGTGTTGAATCCTGGACATTCTATTTTTTTTTTCAAAATCAAGGT
GCATGGGACACATGGCTGGAGCATATGCCCATGGGGC
Found at i:89352308 original size:50 final size:50
Alignment explanation
Indices: 89352233--89352348 Score: 189
Period size: 50 Copynumber: 2.3 Consensus size: 50
89352223 TGCTCCAGCA
* *
89352233 CTTACATGGGATCACATATATCGATGCGAATGCCAT-GTCCCAGACATGGT
1 CTTACATGGGATCACATATATCGATGCCAATGCCATACT-CCAGACATGGT
*
89352283 CTTACATGGGATCACATATATCGATGCCAATGTCATACTCCAGACATGGT
1 CTTACATGGGATCACATATATCGATGCCAATGCCATACTCCAGACATGGT
89352333 CTTACATGGGATCACA
1 CTTACATGGGATCACA
89352349 AATAACCCTA
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
50 61 0.98
51 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (50 bp):
CTTACATGGGATCACATATATCGATGCCAATGCCATACTCCAGACATGGT
Found at i:89358603 original size:16 final size:17
Alignment explanation
Indices: 89358572--89358605 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
89358562 TTAAAGTCAC
*
89358572 ATTCATAGTGATCATGA
1 ATTCATAATGATCATGA
89358589 ATTCATAAT-ATCATGA
1 ATTCATAATGATCATGA
89358605 A
1 A
89358606 GCCAATGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
ATTCATAATGATCATGA
Found at i:89358883 original size:42 final size:42
Alignment explanation
Indices: 89358810--89358890 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
89358800 AATCCGACAA
* * ** *
89358810 CCCAGCTATGGTCTTAGACAATGTCTCATATCGATGCCATGT
1 CCCAGATATGGTCTTACACAAAATCTCATATCAATGCCATGT
89358852 CCCAGATATGGTCTTACACAAAATCAT-ATATCAATGCCA
1 CCCAGATATGGTCTTACACAAAATC-TCATATCAATGCCA
89358891 ATGCCATATC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 32 0.97
43 1 0.03
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (42 bp):
CCCAGATATGGTCTTACACAAAATCTCATATCAATGCCATGT
Found at i:89358945 original size:50 final size:49
Alignment explanation
Indices: 89358876--89359027 Score: 223
Period size: 50 Copynumber: 3.0 Consensus size: 49
89358866 TACACAAAAT
* * *
89358876 CATATATCAATGCCAATGCCATATCCCAAATATGGTCGTACATGGGATCA
1 CATATATCGATGCCAATGCCATGTCCCAAA-ATGGTCTTACATGGGATCA
89358926 CATATATCGATGCCAATGCCATGTCCCGAAAATGGTCTTACATGGGATCA
1 CATATATCGATGCCAATGCCATGTCCC-AAAATGGTCTTACATGGGATCA
* * *
89358976 CATATATTGATGCCAATGCCATGTCCCAGACATGGTCTTACATTGGATCA
1 CATATATCGATGCCAATGCCATGTCCCA-AAATGGTCTTACATGGGATCA
89359026 CA
1 CA
89359028 AATAACCCTA
Statistics
Matches: 94, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
49 1 0.01
50 90 0.96
51 3 0.03
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (49 bp):
CATATATCGATGCCAATGCCATGTCCCAAAATGGTCTTACATGGGATCA
Found at i:89366322 original size:46 final size:48
Alignment explanation
Indices: 89366142--89366408 Score: 221
Period size: 47 Copynumber: 5.7 Consensus size: 48
89366132 GGTAAAGTGT
* * * ***
89366142 CGATGCCATGTCCCAGACATGGTCTTACATTGGCTCACATCTC-AATT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCGAGGC
* * * *
89366189 CAATGCCATGTCCCAGACATGGTCTTATACTAACTATCATCTCGTA-GC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCG-AGGC
* * *
89366237 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACGTCTCGAGGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT-CATCTCGAGGC
* * ** *
89366283 CGATG-CATGTCCCAGACAT-GTCTTACACTAGTTCTCGTCTTAATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCGAGGC
* * * *
89366329 CAATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATAAT-GTGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-CTCGAGGC
* *
89366377 CGATG-CATGTCCCAAACAT-GTCTTGCACTAGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGC
89366409 CAACAATAAC
Statistics
Matches: 179, Mismatches: 33, Indels: 17
0.78 0.14 0.07
Matches are distributed among these distances:
45 2 0.01
46 72 0.40
47 76 0.42
48 27 0.15
49 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCGAGGC
Found at i:89366400 original size:140 final size:141
Alignment explanation
Indices: 89366140--89366405 Score: 358
Period size: 140 Copynumber: 1.9 Consensus size: 141
89366130 TGGGTAAAGT
* * *
89366140 GTCGATGCCATGTCCCAGACATGGTCTTACATTGGCTCACATCTCAATTCAATGCCATGTCCCAG
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATCTCAATCCAATGCCATGTCCCAG
* * *
89366205 ACATGGTCTTATACTAACTATCATCTCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGCT
66 ACATGGTCTTACACTAACTATCATATCGTAGCCGATGCATGTCCCAAACATGTCTTACACTGGCT
89366270 TACGTCTCGAG
131 TACGTCTCGAG
* * * * *
89366281 GTCGATG-CATGTCCCAGACAT-GTCTTACACTAGTTCTCGTCTTAATGCCAATGCCATGTCCTA
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATCTCAAT-CCAATGCCATGTCCCA
* * * *
89366344 GACATGGTCTTACACTAGCTCTCATAAT-GTGGCCGATGCATGTCCCAAACATGTCTTGCACT
65 GACATGGTCTTACACTAACTATCAT-ATCGTAGCCGATGCATGTCCCAAACATGTCTTACACT
89366406 AGCCAACAAT
Statistics
Matches: 108, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
139 19 0.18
140 81 0.75
141 8 0.07
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.30
Consensus pattern (141 bp):
GTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATCTCAATCCAATGCCATGTCCCAG
ACATGGTCTTACACTAACTATCATATCGTAGCCGATGCATGTCCCAAACATGTCTTACACTGGCT
TACGTCTCGAG
Found at i:89373846 original size:46 final size:47
Alignment explanation
Indices: 89373803--89373973 Score: 170
Period size: 46 Copynumber: 3.7 Consensus size: 47
89373793 TCATCTCGTA
*
89373803 GCCGATGCATGTCGTAGACATGTCTTACACTGGCTTAT-GTCTCGAG
1 GCCGATGCATGTCCTAGACATGTCTTACACTGGCTTATCGTCTCGAG
* * * * *
89373849 GCCGATGCATGTCCCAGACATGTCTTACACTAG-TTCTCGTCTCAAT
1 GCCGATGCATGTCCTAGACATGTCTTACACTGGCTTATCGTCTCGAG
* ** * * *
89373895 GCCGATGCCATGTCCTAGACATGGTCTTACGCTGGC-TCCCATAAT-GTG
1 GCCGATG-CATGTCCTAGACAT-GTCTTACACTGGCTTATCGT-CTCGAG
*
89373943 GCCGATGCATGTCCCAGACATGTCTTACACT
1 GCCGATGCATGTCCTAGACATGTCTTACACT
89373974 AGCCAACAAT
Statistics
Matches: 103, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
45 3 0.03
46 52 0.50
47 26 0.25
48 21 0.20
49 1 0.01
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (47 bp):
GCCGATGCATGTCCTAGACATGTCTTACACTGGCTTATCGTCTCGAG
Found at i:89377508 original size:27 final size:27
Alignment explanation
Indices: 89377476--89377653 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
89377466 TAAATTGTAC
89377476 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
** ** *
89377503 TTCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
89377529 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
89377557 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
89377585 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
89377612 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
89377639 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
89377654 GACTCAATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:89377591 original size:82 final size:81
Alignment explanation
Indices: 89377477--89377632 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
89377467 AAATTGTACA
** *
89377477 GCACTAAGTGTGCGATTTGACTATGTTTCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
89377541 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
89377558 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
89377623 TGCGAGTTGA
65 TGCGAATTGA
89377633 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:89377644 original size:82 final size:81
Alignment explanation
Indices: 89377473--89377653 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
89377463 GATTAAATTG
** *
89377473 TACAGCACTAAGTGTGCGATTTGACTATGTTTCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
89377538 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
89377554 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
89377618 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
89377636 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
89377654 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:89379159 original size:50 final size:49
Alignment explanation
Indices: 89379059--89379270 Score: 219
Period size: 50 Copynumber: 4.2 Consensus size: 49
89379049 ATCACTCATT
* * * *
89379059 TGGTCGATTATAGAAAATCAAATATAATATCACATATGTGCATACCTATA
1 TGGTCGAATATA-CAAATCAAATATAACATCACATATGTACATACCTATA
* * * * * *
89379109 TGGCCGAATATGCAAGATCAAATTTAACATCAAATATGTACTTACTTATA
1 TGGTCGAATATACAA-ATCAAATATAACATCACATATGTACATACCTATA
* * * *
89379159 TAGTCGAATATACAAATTCAAATATAATATCACATTTGTGCATACCT-TCA
1 TGGTCGAATATACAAA-TCAAATATAACATCACATATGTACATACCTAT-A
* * *
89379209 TGGTCGAATATTCAAAATCCAATATAACATCACATATGTACATACCTATG
1 TGGTCGAATATAC-AAATCAAATATAACATCACATATGTACATACCTATA
89379259 TGGTCGAATATA
1 TGGTCGAATATA
89379271 TACAAGGTCA
Statistics
Matches: 129, Mismatches: 28, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
49 4 0.03
50 121 0.94
51 4 0.03
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (49 bp):
TGGTCGAATATACAAATCAAATATAACATCACATATGTACATACCTATA
Found at i:89379183 original size:100 final size:100
Alignment explanation
Indices: 89379061--89379270 Score: 278
Period size: 100 Copynumber: 2.1 Consensus size: 100
89379051 CACTCATTTG
* * *
89379061 GTCGATTATAGAAAATCAAATATAATATCACATATGTGCATACCTAT-ATGGCCGAATATGCAAG
1 GTCGAATATACAAAATCAAATATAATATCACATATGTGCATACCT-TCATGGCCGAATATGCAAA
* * *
89379125 ATCAAATTTAACATCAAATATGTACTTACTTATATA
65 ATCAAATATAACATCAAATATGTACATACCTATATA
* * * *
89379161 GTCGAATATACAAATTCAAATATAATATCACATTTGTGCATACCTTCATGGTCGAATATTCAAAA
1 GTCGAATATACAAAATCAAATATAATATCACATATGTGCATACCTTCATGGCCGAATATGCAAAA
* * * *
89379226 TCCAATATAACATCACATATGTACATACCTATGTG
66 TCAAATATAACATCAAATATGTACATACCTATATA
89379261 GTCGAATATA
1 GTCGAATATA
89379271 TACAAGGTCA
Statistics
Matches: 95, Mismatches: 14, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
99 1 0.01
100 94 0.99
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (100 bp):
GTCGAATATACAAAATCAAATATAATATCACATATGTGCATACCTTCATGGCCGAATATGCAAAA
TCAAATATAACATCAAATATGTACATACCTATATA
Found at i:89383109 original size:12 final size:12
Alignment explanation
Indices: 89383094--89383118 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
89383084 TTTCAATATT
89383094 ATTTTCAACTCA
1 ATTTTCAACTCA
89383106 ATTTTCAACTCA
1 ATTTTCAACTCA
89383118 A
1 A
89383119 ACTCATACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTTTCAACTCA
Found at i:89391651 original size:42 final size:42
Alignment explanation
Indices: 89391588--89391698 Score: 143
Period size: 42 Copynumber: 2.6 Consensus size: 42
89391578 CGAGGCTATG
* *
89391588 TGTAAGACCAGATCTGGGATATGGCAT-CATTATAAGATTTCA
1 TGTAAGACCATATCTGGGATATGGCATGCA-TATAACATTTCA
* * * * *
89391630 TGTAAAACCATATCTAGGATATGGCATGGATATGACATTTCG
1 TGTAAGACCATATCTGGGATATGGCATGCATATAACATTTCA
89391672 TGTAAGACCATATCTGGGATATGGCAT
1 TGTAAGACCATATCTGGGATATGGCAT
89391699 TGGTATGGTA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 58 0.98
43 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATGCATATAACATTTCA
Found at i:89399831 original size:3 final size:3
Alignment explanation
Indices: 89399811--89399844 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
89399801 TAATAGAATC
* *
89399811 AGA AAA AGA AGT AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
89399845 AATGTCAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:89401538 original size:49 final size:49
Alignment explanation
Indices: 89401473--89401577 Score: 165
Period size: 49 Copynumber: 2.1 Consensus size: 49
89401463 TATCAAACAT
* * *
89401473 AAGTGTGGGTGAGAACATGTTTTAAGTTCCTTACCCATTCTGATAAGAC
1 AAGTGTGGGCGAGAACATGTTTTAAGTTCCTCAACCATTCTGATAAGAC
* *
89401522 AAGTGTGGGCGAGAACATGTTTTATGTTCCTCAACCATTCTGATAGGAC
1 AAGTGTGGGCGAGAACATGTTTTAAGTTCCTCAACCATTCTGATAAGAC
89401571 AAGTGTG
1 AAGTGTG
89401578 TGAACATGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (49 bp):
AAGTGTGGGCGAGAACATGTTTTAAGTTCCTCAACCATTCTGATAAGAC
Found at i:89420939 original size:27 final size:27
Alignment explanation
Indices: 89420909--89421084 Score: 174
Period size: 27 Copynumber: 6.5 Consensus size: 27
89420899 ATATTGAGTC
* *
89420909 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
89420936 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
89420963 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
89420991 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
89421018 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
** * *
89421045 CGCACACTTAGTGAAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
89421072 CGCACACTTAGTG
1 CGCACACTTAGTG
89421085 TTGTACAATT
Statistics
Matches: 127, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:89421048 original size:82 final size:81
Alignment explanation
Indices: 89420930--89421084 Score: 222
Period size: 82 Copynumber: 1.9 Consensus size: 81
89420920 TGCTATATAA
* **
89420930 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGAAACATAGTCAAA-TCGCA
89420995 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
89421012 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGAAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGAAACATAGTCAAATCGCA
89421076 CACTTAGTG
65 CACTTAGTG
89421085 TTGTACAATT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.77
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGAAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:89421069 original size:54 final size:54
Alignment explanation
Indices: 89420909--89421084 Score: 194
Period size: 54 Copynumber: 3.2 Consensus size: 54
89420899 ATATTGAGTC
* * * *
89420909 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
89420963 CGCACACTTAGTGC-TACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* ** *
89421018 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGAAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
89421072 CGCACACTTAGTG
1 CGCACACTTAGTG
89421085 TTGTACAATT
Statistics
Matches: 102, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
52 1 0.01
54 55 0.54
55 45 0.44
56 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:89423226 original size:40 final size:40
Alignment explanation
Indices: 89423166--89423244 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
89423156 TCAGATTAGT
*
89423166 CAAACAGTGAAACATGGGAAACTTTGAGAAAAATCTGGTA
1 CAAACAGTGAAACATGGGAAACTTTGAGAAAAATATGGTA
*
89423206 CAAATAGTGAAACATGGGAAACTTTGAGAAAAATATGGT
1 CAAACAGTGAAACATGGGAAACTTTGAGAAAAATATGGT
89423245 TTTGATTGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.22
Consensus pattern (40 bp):
CAAACAGTGAAACATGGGAAACTTTGAGAAAAATATGGTA
Found at i:89424133 original size:54 final size:54
Alignment explanation
Indices: 89424051--89424182 Score: 219
Period size: 54 Copynumber: 2.4 Consensus size: 54
89424041 AGGAAGCGTC
* * * *
89424051 CTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACGATTATCTGATCTGGTGGCTCTACCACATATATCTGTT
*
89424105 CTGGTGGCTCTGTCACGATTATCTGATCTGGTGGCTCTACCACATATATCTGTT
1 CTGGTGGCTCTGCCACGATTATCTGATCTGGTGGCTCTACCACATATATCTGTT
89424159 CTGGTGGCTCTGCCACGATTATCT
1 CTGGTGGCTCTGCCACGATTATCT
89424183 ATTCTGACAG
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 72 1.00
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (54 bp):
CTGGTGGCTCTGCCACGATTATCTGATCTGGTGGCTCTACCACATATATCTGTT
Found at i:89424181 original size:27 final size:26
Alignment explanation
Indices: 89424051--89424188 Score: 168
Period size: 27 Copynumber: 5.1 Consensus size: 26
89424041 AGGAAGCGTC
* * *
89424051 CTGGTGGCTATGCCACAAATATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
89424078 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
* *
89424105 CTGGTGGCTCTGTCACGATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
*
89424132 CTGGTGGCTCTACCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
*
89424159 CTGGTGGCTCTGCCACGATTATCTATT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
89424186 CTG
1 CTG
89424189 ACAGCCATGC
Statistics
Matches: 97, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
26 3 0.03
27 90 0.93
28 4 0.04
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.36
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:89427245 original size:36 final size:36
Alignment explanation
Indices: 89427198--89427266 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
89427188 GGTTAGGACT
*
89427198 GTAAAAGAGTTCCAAGATGTTTTT-TCGGAAGAGACC
1 GTAAAAGAGTTCCAAGATATTTTTCT-GGAAGAGACC
*
89427234 GTAAAGGAGTTCCAAGATATTTTTCTGGAAGAG
1 GTAAAAGAGTTCCAAGATATTTTTCTGGAAGAG
89427267 CTTCCAGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 29 0.97
37 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (36 bp):
GTAAAAGAGTTCCAAGATATTTTTCTGGAAGAGACC
Found at i:89430410 original size:26 final size:26
Alignment explanation
Indices: 89430381--89430488 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
89430371 TGGTACAAAT
89430381 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
89430407 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
89430433 TGATAATGGGTTAGGTCAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
89430459 TGATAATGGTTTAAGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
89430485 TGAT
1 TGAT
89430489 GGGCATTTCA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:89432199 original size:27 final size:28
Alignment explanation
Indices: 89432071--89432209 Score: 164
Period size: 27 Copynumber: 5.1 Consensus size: 28
89432061 AGGAAGCGTC
* * *
89432071 CTGGTGGCTATGCCACAAATATCTG-AT
1 CTGGTGGCTCTGCCACGATTATCTGTAT
89432098 CTGGTGGCTCTGCCAC-ATATATCTGTA-
1 CTGGTGGCTCTGCCACGAT-TATCTGTAT
*
89432125 CTGGTGGCTCTGCCACGAGTATCTG-AT
1 CTGGTGGCTCTGCCACGATTATCTGTAT
89432152 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACGATTATCTGTAT
* * *
89432180 CTGGTGACTTTGTCAC-ATTATCTGT-T
1 CTGGTGGCTCTGCCACGATTATCTGTAT
89432206 CTGG
1 CTGG
89432210 CAGCCATGCT
Statistics
Matches: 100, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
26 7 0.07
27 76 0.76
28 17 0.17
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (28 bp):
CTGGTGGCTCTGCCACGATTATCTGTAT
Found at i:89440449 original size:29 final size:29
Alignment explanation
Indices: 89440410--89440488 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
89440400 CTTAATAATC
*
89440410 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
89440440 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
89440469 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
89440489 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:89448571 original size:29 final size:29
Alignment explanation
Indices: 89448532--89448610 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
89448522 CTTAATAATC
*
89448532 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
89448562 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
89448591 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
89448611 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:89453503 original size:20 final size:20
Alignment explanation
Indices: 89453480--89453526 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
89453470 GGGTTAAGAT
*
89453480 TGAGCTGAATTAAGCTTGAG
1 TGAGCTGAATTAAGCTCGAG
* * *
89453500 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTAAGCTCGAG
89453520 TGAGCTG
1 TGAGCTG
89453527 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTAAGCTCGAG
Found at i:89455248 original size:48 final size:48
Alignment explanation
Indices: 89455196--89455301 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
89455186 TTGTCTTTTC
*
89455196 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
89455244 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
89455292 TTTCTTTTTC
1 TTTCTTTTTC
89455302 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:89458719 original size:28 final size:28
Alignment explanation
Indices: 89458688--89458750 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 28
89458678 GCGGTACGGA
*
89458688 CACCAGAAACAGATATTTGTAGCAGAGC
1 CACCAGAAACAAATATTTGTAGCAGAGC
* *
89458716 CACCAG-ATCAAATATTTGTTGCAGAGC
1 CACCAGAAACAAATATTTGTAGCAGAGC
89458743 CACCAGAA
1 CACCAGAA
89458751 CGCTTCCTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 24 0.77
28 7 0.23
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (28 bp):
CACCAGAAACAAATATTTGTAGCAGAGC
Found at i:89460038 original size:18 final size:18
Alignment explanation
Indices: 89459982--89460038 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
89459972 AACTATAGAG
89459982 GAAAAGAAGAAGA-AGAGA
1 GAAAAGAAGAAGAGA-AGA
* * *
89460000 GAATAGATGAAGAGAGGA
1 GAAAAGAAGAAGAGAAGA
*
89460018 GAAAAGAAGAAGAGAAAA
1 GAAAAGAAGAAGAGAAGA
89460036 GAA
1 GAA
89460039 TTGTCAGAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
18 30 0.97
19 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.04
Consensus pattern (18 bp):
GAAAAGAAGAAGAGAAGA
Found at i:89462031 original size:33 final size:33
Alignment explanation
Indices: 89461985--89462052 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
89461975 AGGTAAAATT
89461985 TTAAGGTCAAAATTTTCTTTAAGGGGGGAAGAG
1 TTAAGGTCAAAATTTTCTTTAAGGGGGGAAGAG
*
89462018 TTAAGGTCGAAATTTTCTTTAAGGGGGGAAGAG
1 TTAAGGTCAAAATTTTCTTTAAGGGGGGAAGAG
89462051 TT
1 TT
89462053 GTTGTGACAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.32
Consensus pattern (33 bp):
TTAAGGTCAAAATTTTCTTTAAGGGGGGAAGAG
Found at i:89464677 original size:47 final size:47
Alignment explanation
Indices: 89464619--89465253 Score: 946
Period size: 47 Copynumber: 13.5 Consensus size: 47
89464609 GTGAATGTGT
* ** *
89464619 ATATATGTGATAAGGCCAAATGGGTAATGTGATGAATGTGAGCATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
* * *
89464666 ATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAACATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
*
89464713 ATATATGTGATAAGGCCGAATGGCCTATGTGATGAATGTGAACATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
* * *
89464760 ATATATGTGATGAGGCCGAATGGCCAATGTGGTGAATATGAACATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
* * *
89464807 ATATATGTGATGAGGCCGAATGGCCAATGTGATGAACGTGAGCATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
* *
89464854 ATATATTTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
* * *
89464901 ATATGTGTGATAAGGCCGAATGGCCAATGTGGTGAATGTGAACATGT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
** *
89464948 ATATATGTGATAAGGCCGAATCACCAATGTGATGAATGTGAGCATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
* *
89464995 ATATATGTGATAAGGCCGAATGGACAATGTGGTGAATGTGAACATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
* *
89465042 ATATATGTGATGAGGCCGAATGGCCAATGTGGTGAATGTGAACATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
* *
89465089 ATATATGTGATGAGGCCGAATGGCCAATGTGATGAATGTGAGCATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
*
89465136 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
* * * *
89465183 ATATGTGTGATAAGGCTGAATGGCCAATGTGGTGAATATGAACATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
* * *
89465230 ATACATGTGGTAAAGCCGAATGGC
1 ATATATGTGATAAGGCCGAATGGC
89465254 TAGTGTGAAA
Statistics
Matches: 535, Mismatches: 53, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 535 1.00
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (47 bp):
ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
Found at i:89464935 original size:25 final size:25
Alignment explanation
Indices: 89464861--89464935 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 25
89464851 TGCATATATT
*
89464861 TGATAAGGCCGAATGGCCAATGTGA
1 TGATAAGGCCGAATGGCCAATGTGG
* * *
89464886 TGA-ATGTG-AGCAT-G-CATATGT-G
1 TGATAAG-GCCGAATGGCCA-ATGTGG
89464908 TGATAAGGCCGAATGGCCAATGTGG
1 TGATAAGGCCGAATGGCCAATGTGG
89464933 TGA
1 TGA
89464936 ATGTGAACAT
Statistics
Matches: 36, Mismatches: 7, Indels: 14
0.63 0.12 0.25
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.24
Consensus pattern (25 bp):
TGATAAGGCCGAATGGCCAATGTGG
Found at i:89465049 original size:25 final size:25
Alignment explanation
Indices: 89465021--89465097 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
89465011 CGAATGGACA
89465021 ATGTGGTGAATGTGAACATGCATAT
1 ATGTGGTGAATGTGAACATGCATAT
* * * *
89465046 ATGTGATG-AGGCCG-A-ATGGC-CA-
1 ATGTGGTGAATG-TGAACAT-GCATAT
89465068 ATGTGGTGAATGTGAACATGCATAT
1 ATGTGGTGAATGTGAACATGCATAT
89465093 ATGTG
1 ATGTG
89465098 ATGAGGCCGA
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
22 8 0.22
23 8 0.22
24 8 0.22
25 13 0.35
ACGTcount: A:0.30, C:0.10, G:0.31, T:0.29
Consensus pattern (25 bp):
ATGTGGTGAATGTGAACATGCATAT
Found at i:89465530 original size:37 final size:37
Alignment explanation
Indices: 89465416--89465530 Score: 185
Period size: 37 Copynumber: 3.1 Consensus size: 37
89465406 GGAAATATAT
*
89465416 TCCGGGTGAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
89465453 TCCAGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * *
89465490 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTTCG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
89465527 TCCG
1 TCCG
89465531 AGCTAAAGGT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:89469184 original size:64 final size:64
Alignment explanation
Indices: 89469083--89469210 Score: 247
Period size: 64 Copynumber: 2.0 Consensus size: 64
89469073 TCATCTTCTT
*
89469083 TCCCTCCCAAAAATCAGCCATTAAAGGGGGTTTGAAAGCTTAAAAATTTCAACAACTTGAAGCA
1 TCCCTACCAAAAATCAGCCATTAAAGGGGGTTTGAAAGCTTAAAAATTTCAACAACTTGAAGCA
89469147 TCCCTACCAAAAATCAGCCATTAAAGGGGGTTTGAAAGCTTAAAAATTTCAACAACTTGAAGCA
1 TCCCTACCAAAAATCAGCCATTAAAGGGGGTTTGAAAGCTTAAAAATTTCAACAACTTGAAGCA
89469211 CTTACAAGTA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (64 bp):
TCCCTACCAAAAATCAGCCATTAAAGGGGGTTTGAAAGCTTAAAAATTTCAACAACTTGAAGCA
Found at i:89477667 original size:47 final size:43
Alignment explanation
Indices: 89477592--89477721 Score: 134
Period size: 47 Copynumber: 2.8 Consensus size: 43
89477582 GAGTCATTCG
* * *
89477592 TGTGTGAGCTAGTTTAAGACATATCTGGGACATGCATTGGCCACAT
1 TGTGAGAGCTAGTGTAAGACATGTCTGGGACATGCATTGG---CAT
*
89477638 TGTGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCAT
1 TGTGAGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATTGGCAT
* *
89477683 TGAGACGAGGGCTAGTGTAAGACATGTCTAGGACATGCA
1 TGTGA-GA--GCTAGTGTAAGACATGTCTGGGACATGCA
89477722 ACGCCTCGAG
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
45 7 0.10
46 21 0.29
47 26 0.36
48 18 0.25
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (43 bp):
TGTGAGAGCTAGTGTAAGACATGTCTGGGACATGCATTGGCAT
Found at i:89486922 original size:22 final size:22
Alignment explanation
Indices: 89486889--89486938 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
89486879 TAACATGTCT
*
89486889 CACATATATCATGAGCTCATAC
1 CACATATATCATGAGCTCAGAC
*
89486911 CACATA-ACTCATGAGCTCAGAT
1 CACATATA-TCATGAGCTCAGAC
89486933 CACATA
1 CACATA
89486939 GTCCCTAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.24
Consensus pattern (22 bp):
CACATATATCATGAGCTCAGAC
Found at i:89493177 original size:48 final size:48
Alignment explanation
Indices: 89493101--89493308 Score: 186
Period size: 48 Copynumber: 4.3 Consensus size: 48
89493091 ATTTATACGA
* * ** **
89493101 GAGCTAGTGTAAGACCATGTCTAAGACATGGAATTGGCCTCGATATGT
1 GAGCTAGTGTAAGACCATATTTGGGACATGGAATCAGCCTCGATATGT
* * * *
89493149 GAGCTAGTGTAAGACCATATTTGGGACATGGCATCCGCGTCAATATGT
1 GAGCTAGTGTAAGACCATATTTGGGACATGGAATCAGCCTCGATATGT
* * * * ** *
89493197 GAGCCAGAGTAAGACCATATTT-GGAGCAT-GACATCAACATTTATATGA
1 GAGCTAGTGTAAGACCATATTTGGGA-CATGGA-ATCAGCCTCGATATGT
* * * *
89493245 GACCTAGTGTAAGACCATGTTTGGGACATGGTACCAGCCTCGATATGT
1 GAGCTAGTGTAAGACCATATTTGGGACATGGAATCAGCCTCGATATGT
*
89493293 GGGCTAGTGTAAGACC
1 GAGCTAGTGTAAGACC
89493309 GTGTTTGGCC
Statistics
Matches: 125, Mismatches: 31, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
47 4 0.03
48 117 0.94
49 4 0.03
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (48 bp):
GAGCTAGTGTAAGACCATATTTGGGACATGGAATCAGCCTCGATATGT
Found at i:89493316 original size:144 final size:144
Alignment explanation
Indices: 89493047--89493308 Score: 371
Period size: 144 Copynumber: 1.8 Consensus size: 144
89493037 GATACTAGCG
* * * * * *
89493047 ATATGTGAGCCAGTGTAAGACCATGTTCAGAGCATGGCGTCAGCATTTATACGAGAGCTAGTGTA
1 ATATGTGAGCCAGAGTAAGACCATATTCAGAGCATGACATCAACATTTATACGAGACCTAGTGTA
***
89493112 AGACCATGTCTAAGACATGGAATTGGCCTCGATATGTGAGCTAGTGTAAGACCATATTTGGGACA
66 AGACCATGTCTAAGACATGGAACCAGCCTCGATATGTGAGCTAGTGTAAGACCATATTTGGGACA
89493177 TGGCATCCGCGTCA
131 TGGCATCCGCGTCA
** *
89493191 ATATGTGAGCCAGAGTAAGACCATATTTGGAGCATGACATCAACATTTATATGAGACCTAGTGTA
1 ATATGTGAGCCAGAGTAAGACCATATTCAGAGCATGACATCAACATTTATACGAGACCTAGTGTA
* ** * *
89493256 AGACCATGTTTGGGACATGGTACCAGCCTCGATATGTGGGCTAGTGTAAGACC
66 AGACCATGTCTAAGACATGGAACCAGCCTCGATATGTGAGCTAGTGTAAGACC
89493309 GTGTTTGGCC
Statistics
Matches: 101, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
144 101 1.00
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (144 bp):
ATATGTGAGCCAGAGTAAGACCATATTCAGAGCATGACATCAACATTTATACGAGACCTAGTGTA
AGACCATGTCTAAGACATGGAACCAGCCTCGATATGTGAGCTAGTGTAAGACCATATTTGGGACA
TGGCATCCGCGTCA
Found at i:89500816 original size:48 final size:48
Alignment explanation
Indices: 89500754--89501029 Score: 301
Period size: 48 Copynumber: 5.7 Consensus size: 48
89500744 ATTTATACGA
*
89500754 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCTCGATATGT
1 GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGACCTCGATATGT
* * *
89500802 GCA-CTAATGTAAGACCATGTTTGGGACATGGCATCGGCCTCAATATGT
1 G-AGCTAGTGTAAGACCATGTTTGGGACATGGCATCGACCTCGATATGT
* * ** * *
89500850 GAGCTAGTGTAAGACCATGTTT-GGAGCATGG-ATCGGCATTTATAGGA
1 GAGCTAGTGTAAGACCATGTTTGGGA-CATGGCATCGACCTCGATATGT
* *
89500897 GAGCTAGTGTAAGACCATGTCTGAGACATGGCATC-AGCCTCGATATGT
1 GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGA-CCTCGATATGT
* * * * *
89500945 GGGCTAGTGTAAGACCATGTTTGGAACTTGGCATCAACAC-CGATATATGA
1 GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGAC-CTCG--ATATGT
*
89500995 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATC
1 GAGCTAGTGTAAGACCATGTTTGGGACATGGCATC
89501030 AGCATCTTAC
Statistics
Matches: 190, Mismatches: 28, Indels: 18
0.81 0.12 0.08
Matches are distributed among these distances:
47 41 0.22
48 110 0.58
49 3 0.02
50 36 0.19
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (48 bp):
GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGACCTCGATATGT
Found at i:89500937 original size:95 final size:97
Alignment explanation
Indices: 89500754--89501032 Score: 316
Period size: 95 Copynumber: 2.9 Consensus size: 97
89500744 ATTTATACGA
* * * * * * *
89500754 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCTCGATAT-GTG-CA-CTAATGTAAGA
1 GAGCTAGTGTAAGACCATGTTTGGAACATGGCATC-AACACGATATAG-GAGAGCCAGTGTAAGA
*
89500816 CCATGTTTGGGACATGGCATCGGCCTCAATATGT
64 CCATGTTTGGGACATGGCATCAGCCTCAATATGT
* ** ** *
89500850 GAGCTAGTGTAAGACCATGTTTGGAGCATGG-ATCGGCA-TTTATAGGAGAGCTAGTGTAAGACC
1 GAGCTAGTGTAAGACCATGTTTGGAACATGGCATCAACACGATATAGGAGAGCCAGTGTAAGACC
* * *
89500913 ATGTCTGAGACATGGCATCAGCCTCGATATGT
66 ATGTTTGGGACATGGCATCAGCCTCAATATGT
* * *
89500945 GGGCTAGTGTAAGACCATGTTTGGAACTTGGCATCAACACCGATATATGAGAGCCAGTGTAAGAC
1 GAGCTAGTGTAAGACCATGTTTGGAACATGGCATCAACA-CGATATAGGAGAGCCAGTGTAAGAC
89501010 CATGTTTGGGACATGGCATCAGC
65 CATGTTTGGGACATGGCATCAGC
89501033 ATCTTACCCT
Statistics
Matches: 152, Mismatches: 25, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
93 4 0.03
94 3 0.02
95 71 0.47
96 33 0.22
98 41 0.27
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (97 bp):
GAGCTAGTGTAAGACCATGTTTGGAACATGGCATCAACACGATATAGGAGAGCCAGTGTAAGACC
ATGTTTGGGACATGGCATCAGCCTCAATATGT
Found at i:89505538 original size:22 final size:22
Alignment explanation
Indices: 89505510--89505561 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
89505500 GAAAATCAAA
89505510 GGGATTTTGAGATTTCGATTTG
1 GGGATTTTGAGATTTCGATTTG
* *
89505532 GGGATTTTGGGATTTTGATTTG
1 GGGATTTTGAGATTTCGATTTG
*
89505554 GGGTTTTT
1 GGGATTTT
89505562 AATTTTGGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.13, C:0.02, G:0.35, T:0.50
Consensus pattern (22 bp):
GGGATTTTGAGATTTCGATTTG
Found at i:89505551 original size:14 final size:14
Alignment explanation
Indices: 89505534--89505573 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
89505524 TCGATTTGGG
89505534 GATTTTGGGATTTT
1 GATTTTGGGATTTT
* *
89505548 GATTTGGGGTTTTT
1 GATTTTGGGATTTT
*
89505562 AATTTTGGGATT
1 GATTTTGGGATT
89505574 CCAATTTTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.55
Consensus pattern (14 bp):
GATTTTGGGATTTT
Found at i:89506120 original size:18 final size:17
Alignment explanation
Indices: 89506097--89506135 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
89506087 TTATCTCTTA
89506097 AATAATTTAAACTATAAT
1 AATAATTTAAA-TATAAT
* *
89506115 AATAATTTTAATATATT
1 AATAATTTAAATATAAT
89506132 AATA
1 AATA
89506136 TTATATTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AATAATTTAAATATAAT
Found at i:89515942 original size:28 final size:28
Alignment explanation
Indices: 89515902--89516018 Score: 137
Period size: 28 Copynumber: 4.2 Consensus size: 28
89515892 AATACTGTTG
* *
89515902 CATATTCAACATCTCGCACTCTAAGTGC
1 CATACTCAACATCTCGCACACTAAGTGC
*
89515930 CATACTCAACATCTCGCACAATAAGTGC
1 CATACTCAACATCTCGCACACTAAGTGC
* * * *
89515958 CATTCTTAATGAT-TCGCACACTAAGTTC
1 CATACTCAA-CATCTCGCACACTAAGTGC
* *
89515986 CATACTCAATATCTAGCACACTAAGTGC
1 CATACTCAACATCTCGCACACTAAGTGC
89516014 CATAC
1 CATAC
89516019 ATAGCTGAAG
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
27 2 0.03
28 70 0.95
29 2 0.03
ACGTcount: A:0.32, C:0.30, G:0.10, T:0.27
Consensus pattern (28 bp):
CATACTCAACATCTCGCACACTAAGTGC
Found at i:89516087 original size:40 final size:40
Alignment explanation
Indices: 89516002--89516095 Score: 125
Period size: 40 Copynumber: 2.4 Consensus size: 40
89515992 CAATATCTAG
*
89516002 CACACTAAGTGCCATACATAGCTGAAGCTATCTCAAATCA
1 CACACTAAGTGCCATACATAGCTGAAGCTATCTCAAACCA
* * * *
89516042 CACACTAAGTGTCGTACATAGCTGAAGCTATCTCGAACCG
1 CACACTAAGTGCCATACATAGCTGAAGCTATCTCAAACCA
* *
89516082 TACACTAAATGCCA
1 CACACTAAGTGCCA
89516096 CATTTAGTTG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (40 bp):
CACACTAAGTGCCATACATAGCTGAAGCTATCTCAAACCA
Found at i:89519674 original size:64 final size:64
Alignment explanation
Indices: 89519490--89519723 Score: 256
Period size: 64 Copynumber: 3.6 Consensus size: 64
89519480 TCTCTTGTAC
* * * * * * * *
89519490 ACATGGTGAATACTTAGTACCACCCATGTGACCTAGC--CAGTTTATCTCGTAGCTCTCTTGTCT
1 ACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACA-TATATCCCGTAGCTCTCTTCTCT
* * * * * * * *
89519553 ACATGGTGTCCTTCACTTGGAACCACGCATGCAACCTAGCTACATATATCCCGTAGCTCTCTTGT
1 ACATGGTG---TACACATAGTATCACCCATGCGACCTAGCTACATATATCCCGTAGCTCTCTTCT
89519618 CT
63 CT
* *
89519620 ACATGGTGTACACATAGTATTACCCATTCGACCTAGCTACATATATCCCGTAGCTCTCTTCTCT
1 ACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACATATATCCCGTAGCTCTCTTCTCT
89519684 ACATGGTGTACACATAGTATCACCCATGCGACCTAGCTAC
1 ACATGGTGTACACATAGTATCACCCATGCGACCTAGCTAC
89519724 GTCATAATGT
Statistics
Matches: 144, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
63 8 0.06
64 84 0.58
66 21 0.15
67 29 0.20
68 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.30
Consensus pattern (64 bp):
ACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACATATATCCCGTAGCTCTCTTCTCT
Found at i:89523821 original size:25 final size:25
Alignment explanation
Indices: 89523787--89523848 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
89523777 CCCACAGCTT
89523787 GTGAGAGCATACC-GATTTATAACTC
1 GTGAGAGCATACCAG-TTTATAACTC
* *
89523812 GTGAGAGCATATCAGTTTATAGCTC
1 GTGAGAGCATACCAGTTTATAACTC
*
89523837 GTGCGAGCATAC
1 GTGAGAGCATAC
89523849 ATGTACAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 31 0.97
26 1 0.03
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.27
Consensus pattern (25 bp):
GTGAGAGCATACCAGTTTATAACTC
Found at i:89525004 original size:25 final size:27
Alignment explanation
Indices: 89524966--89525015 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
89524956 GGAGGGATAA
*
89524966 GGGGAGAGATTTTAG-GGATTTGAGAG
1 GGGGAGAGATTTTAGCCGATTTGAGAG
*
89524992 GGGGATAGA-TTTAGCCGATTTGAG
1 GGGGAGAGATTTTAGCCGATTTGAG
89525016 GGGATTTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.26, C:0.04, G:0.42, T:0.28
Consensus pattern (27 bp):
GGGGAGAGATTTTAGCCGATTTGAGAG
Found at i:89526364 original size:20 final size:20
Alignment explanation
Indices: 89526339--89526385 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
89526329 ATTCTGATAT
89526339 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
89526359 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
89526379 ACATGAT
1 ACATGAT
89526386 GTACTCATAA
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:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:89526518 original size:25 final size:26
Alignment explanation
Indices: 89526431--89526497 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 26
89526421 GGAGGAAGTG
* *
89526431 CAAAAAGGGCTTTTGCCCTAGTTTAC
1 CAAAAAGGGCTTTTGCCCCAGTTTAT
*
89526457 CGAAAAGGGCTTTTGCCCCAGTTTAT
1 CAAAAAGGGCTTTTGCCCCAGTTTAT
89526483 CAAAAAGGGCTTTTG
1 CAAAAAGGGCTTTTG
89526498 TCTCAGTTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (26 bp):
CAAAAAGGGCTTTTGCCCCAGTTTAT
Found at i:89529079 original size:50 final size:49
Alignment explanation
Indices: 89528957--89529189 Score: 208
Period size: 50 Copynumber: 4.8 Consensus size: 49
89528947 TGATGCTACG
* * * * **
89528957 GATATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGGATCAGCTT
1 GATAGATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCC
*** *
89529006 GAT--AT--GTTTCAGTGTAAGACCATGTCTGGAACATGGCATCGGCACC
1 GATAGATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CC
89529052 GATAGATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC
1 GATAGATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCC-C
* * ** * * **
89529102 GATATACGAGAGTTAGTGTAAGACCATGTTTGGGACATGGCATCGACTTT
1 GATAGATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CC
* * *
89529152 GTTGGGT-A-AGCCAGTGTAAGACCATGTCTGGGACATGG
1 GATAGATGAGAGCCAGTGTAAGACCATGTCTGGGACATGG
89529190 TGTCTGCACC
Statistics
Matches: 148, Mismatches: 29, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
45 31 0.21
46 3 0.02
47 2 0.01
48 29 0.20
49 5 0.03
50 78 0.53
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (49 bp):
GATAGATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCC
Found at i:89538011 original size:24 final size:24
Alignment explanation
Indices: 89537983--89538031 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
89537973 CCTCCGGTTG
*
89537983 ATAAGATTCGAAAGTAAGGGGCTA
1 ATAAGATTCGAAAGCAAGGGGCTA
89538007 ATAAGATTCGAAAGCAAGGGGCTA
1 ATAAGATTCGAAAGCAAGGGGCTA
89538031 A
1 A
89538032 GAAATTCAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.10, G:0.29, T:0.18
Consensus pattern (24 bp):
ATAAGATTCGAAAGCAAGGGGCTA
Found at i:89544002 original size:9 final size:9
Alignment explanation
Indices: 89543988--89544012 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
89543978 TTATAGCTTA
89543988 CTTTCCTTC
1 CTTTCCTTC
89543997 CTTTCCTTC
1 CTTTCCTTC
89544006 CTTTCCT
1 CTTTCCT
89544013 GTATCTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (9 bp):
CTTTCCTTC
Found at i:89547438 original size:40 final size:40
Alignment explanation
Indices: 89547334--89548157 Score: 1231
Period size: 40 Copynumber: 20.6 Consensus size: 40
89547324 CGGATGATAA
*
89547334 CCGGGCTAAGCCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATA-T
*
89547374 CCGGGCTAAG-CCCGAAGGCATTTGTG-TGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGTGACTATAT
* *
89547413 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
*
89547453 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
* **
89547493 CTGGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
*
89547533 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
* **
89547573 CTGGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
*
89547613 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
* **
89547653 CTGGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
*
89547693 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
* **
89547733 CTGGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
*
89547773 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
* **
89547813 CTGGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
*
89547853 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
* **
89547893 CTGGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
*
89547933 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
* **
89547973 CTGGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
*
89548013 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
* * * *
89548053 CTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
* * *
89548093 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
* *
89548133 CTGGGCTAAGTCCCAAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
89548158 AGCAAGTAGC
Statistics
Matches: 711, Mismatches: 69, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
38 1 0.00
39 34 0.05
40 676 0.95
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
Found at i:89548171 original size:80 final size:80
Alignment explanation
Indices: 89547336--89548157 Score: 1425
Period size: 80 Copynumber: 10.3 Consensus size: 80
89547326 GATGATAACC
* ** *
89547336 GGGCTAAGCCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAG-CCCGAAGGCATTTGT
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATA-TCCGGGCTAAGTCCCGAAGGCATTTAT
* *
89547399 G-TGAGTTACTATATCC
65 GCT-AGTGACTATATCT
* ***
89547415 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTATG
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATATCCGGGCTAAGTCCCGAAGGCATTTATG
89547480 CTAGTGACTATATCT
66 CTAGTGACTATATCT
89547495 GGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATATCCGGGCTAAGTCCCGAAGGCATTTATG
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATATCCGGGCTAAGTCCCGAAGGCATTTATG
89547560 CTAGTGACTATATCT
66 CTAGTGACTATATCT
89547575 GGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATATCCGGGCTAAGTCCCGAAGGCATTTATG
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATATCCGGGCTAAGTCCCGAAGGCATTTATG
89547640 CTAGTGACTATATCT
66 CTAGTGACTATATCT
89547655 GGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATATCCGGGCTAAGTCCCGAAGGCATTTATG
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATATCCGGGCTAAGTCCCGAAGGCATTTATG
89547720 CTAGTGACTATATCT
66 CTAGTGACTATATCT
89547735 GGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATATCCGGGCTAAGTCCCGAAGGCATTTATG
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATATCCGGGCTAAGTCCCGAAGGCATTTATG
89547800 CTAGTGACTATATCT
66 CTAGTGACTATATCT
89547815 GGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATATCCGGGCTAAGTCCCGAAGGCATTTATG
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATATCCGGGCTAAGTCCCGAAGGCATTTATG
89547880 CTAGTGACTATATCT
66 CTAGTGACTATATCT
89547895 GGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATATCCGGGCTAAGTCCCGAAGGCATTTATG
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATATCCGGGCTAAGTCCCGAAGGCATTTATG
89547960 CTAGTGACTATATCT
66 CTAGTGACTATATCT
89547975 GGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATATCCGGGCTAAGTCCCGAAGGCATTTATG
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATATCCGGGCTAAGTCCCGAAGGCATTTATG
89548040 CTAGTGACTATATCT
66 CTAGTGACTATATCT
* *** * *
89548055 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGTG
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATATCCGGGCTAAGTCCCGAAGGCATTTATG
* * *
89548120 CGAGTTACTATAACT
66 CTAGTGACTATATCT
*
89548135 GGGCTAAGTCCCAAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
89548158 AGCAAGTAGC
Statistics
Matches: 720, Mismatches: 20, Indels: 5
0.97 0.03 0.01
Matches are distributed among these distances:
79 43 0.06
80 676 0.94
81 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (80 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCTAACGACTATATCCGGGCTAAGTCCCGAAGGCATTTATG
CTAGTGACTATATCT
Found at i:89560435 original size:21 final size:21
Alignment explanation
Indices: 89560376--89560436 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
89560366 CTCTTGAAAT
*
89560376 AGGGC-ACACGCCCGTGCGGA
1 AGGGCAACACGCCCGTGTGGA
*
89560396 AGGGCAACACGCCCATGTGGA
1 AGGGCAACACGCCCGTGTGGA
*
89560417 AGGGCAACATGCCCGTGTGG
1 AGGGCAACACGCCCGTGTGG
89560437 TCCTTATAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 5 0.14
21 31 0.86
ACGTcount: A:0.23, C:0.30, G:0.38, T:0.10
Consensus pattern (21 bp):
AGGGCAACACGCCCGTGTGGA
Found at i:89561756 original size:49 final size:48
Alignment explanation
Indices: 89561610--89561786 Score: 132
Period size: 49 Copynumber: 3.6 Consensus size: 48
89561600 AAGCTGACGT
* * * **
89561610 CATGTTCCAGACATGGTCTTACACTTA-CTTTCAT-ATAGTGAGGCCGACGC
1 CATGTCCCAGACA-GGTCTTACAC-TAGCTCTCATCAT--CGAGGCCGATAC
* *
89561660 CATATCCCAGACAGGTCTTACACTAGCTCTCATCTATC-AGTGTCGATAC
1 CATGTCCCAGACAGGTCTTACACTAGCTCTCATC-ATCGAG-GCCGATAC
* *
89561709 CATGTCCCAGATAGGTCTTACACTAGCTTGTCTATC-TCGAGGCCGATA-
1 CATGTCCCAGACAGGTCTTACACTAGC-TCTC-ATCATCGAGGCCGATAC
* *
89561757 CATGT-CCTGAACATGTCTTACACTAGCTCT
1 CATGTCCCAG-ACAGGTCTTACACTAGCTCT
89561787 TGTCTCAATG
Statistics
Matches: 104, Mismatches: 15, Indels: 19
0.75 0.11 0.14
Matches are distributed among these distances:
47 5 0.05
48 24 0.23
49 54 0.52
50 16 0.15
51 5 0.05
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (48 bp):
CATGTCCCAGACAGGTCTTACACTAGCTCTCATCATCGAGGCCGATAC
Found at i:89561824 original size:46 final size:47
Alignment explanation
Indices: 89561664--89561824 Score: 148
Period size: 49 Copynumber: 3.4 Consensus size: 47
89561654 CGACGCCATA
*
89561664 TCCCAGACAGGTCTTACACTAGCTCTC-ATCTATCAGTGTCGATACCATG
1 TCCCAGACAGGTCTTACACTAGCTCTCTATC--TCAATGTCGATA-CATG
* * * * *
89561713 TCCCAGATAGGTCTTACACTAGCTTGTCTATCTCGAGGCCGATACATG
1 TCCCAGACAGGTCTTACACTAGC-TCTCTATCTCAATGTCGATACATG
* * * *
89561761 T-CCTGAACATGTCTTACACTAGCTCT-TGTCTCAATGTCGATGCATG
1 TCCCAG-ACAGGTCTTACACTAGCTCTCTATCTCAATGTCGATACATG
**
89561807 TCCCAGACATTTCTTACA
1 TCCCAGACAGGTCTTACA
89561825 TATCTCCCAA
Statistics
Matches: 91, Mismatches: 17, Indels: 11
0.76 0.14 0.09
Matches are distributed among these distances:
46 27 0.30
47 8 0.09
48 20 0.22
49 30 0.33
50 3 0.03
51 3 0.03
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.31
Consensus pattern (47 bp):
TCCCAGACAGGTCTTACACTAGCTCTCTATCTCAATGTCGATACATG
Found at i:89564643 original size:29 final size:28
Alignment explanation
Indices: 89564607--89564684 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
89564597 TCATGAGATT
89564607 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
89564637 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
89564664 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
89564685 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:89564960 original size:173 final size:174
Alignment explanation
Indices: 89564637--89564963 Score: 557
Period size: 173 Copynumber: 1.9 Consensus size: 174
89564627 AAATTGTACA
* *
89564637 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
* *
89564702 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
89564767 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * * *
89564811 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
* *
89564876 TGTGC-AACCCAGTATATATTTTCTATAAATTATTTACGTGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
89564940 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
89564964 ACCTTGAGTT
Statistics
Matches: 143, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
173 79 0.55
174 64 0.45
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:89566781 original size:17 final size:17
Alignment explanation
Indices: 89566759--89566794 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
89566749 ATTAACTTTG
89566759 TTACATTAGGGAACAAA
1 TTACATTAGGGAACAAA
89566776 TTACATTAGGGAACAAA
1 TTACATTAGGGAACAAA
89566793 TT
1 TT
89566795 GAATACATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (17 bp):
TTACATTAGGGAACAAA
Found at i:89568961 original size:28 final size:28
Alignment explanation
Indices: 89568921--89568985 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
89568911 CCTAATTCAT
*
89568921 GCTCATGTTAGCAAAAGAGCTTTCGTAG
1 GCTCGTGTTAGCAAAAGAGCTTTCGTAG
*
89568949 GCTCGTGTTAGCAAAAGAGCTTTTGTAG
1 GCTCGTGTTAGCAAAAGAGCTTTCGTAG
* *
89568977 ACTTGTGTT
1 GCTCGTGTT
89568986 GGACCCATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (28 bp):
GCTCGTGTTAGCAAAAGAGCTTTCGTAG
Found at i:89572813 original size:47 final size:47
Alignment explanation
Indices: 89572744--89572838 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
89572734 AGACATTAAC
89572744 ACTGCCACATGCTATTTATTTCAATCCTTAGGTAACTACAATATCCA
1 ACTGCCACATGCTATTTATTTCAATCCTTAGGTAACTACAATATCCA
* *
89572791 ACTGCCACATGCTTTTTATTTCAATCCTTAGGTAACTATAATATCCA
1 ACTGCCACATGCTATTTATTTCAATCCTTAGGTAACTACAATATCCA
89572838 A
1 A
89572839 GTATTTTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (47 bp):
ACTGCCACATGCTATTTATTTCAATCCTTAGGTAACTACAATATCCA
Found at i:89574567 original size:13 final size:13
Alignment explanation
Indices: 89574527--89574569 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
89574517 CTTGCTTAAT
89574527 TGTTCAAGAATT-
1 TGTTCAAGAATTA
* **
89574539 TGTTCAAAAAAGA
1 TGTTCAAGAATTA
89574552 TGTTCAAGAATTA
1 TGTTCAAGAATTA
89574565 TGTTC
1 TGTTC
89574570 GCCAGCTCTA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTTCAAGAATTA
Found at i:89577999 original size:101 final size:101
Alignment explanation
Indices: 89577815--89578041 Score: 283
Period size: 101 Copynumber: 2.2 Consensus size: 101
89577805 CAATTATTCA
* * * * * ***
89577815 AACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGTTCATAGTTGGGTTATGGCATT
1 AACGAAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGATAATAGCTGAACTATGGCATT
* * * *
89577880 CTTATGATAAGGCCATAATTGGGTTATGACACTATG
66 CTGATAATAAGACCATAATTGGGTTATGACACTACG
*
89577916 GACGAAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGATAATAGCTGAACTATGGCATT
1 AACGAAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGATAATAGCTGAACTATGGCATT
* *
89577981 CTGATAATAAGACTATAATTGGGTTATGGCACTACG
66 CTGATAATAAGACCATAATTGGGTTATGACACTACG
* * * *
89578017 AATGTAAGACCATGGTAGGGCCATG
1 AACGAAAGACCATGGTTGGACCATG
89578042 GCAATGCATA
Statistics
Matches: 106, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
101 106 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.30
Consensus pattern (101 bp):
AACGAAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGATAATAGCTGAACTATGGCATT
CTGATAATAAGACCATAATTGGGTTATGACACTACG
Done.