Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397284.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_115.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1289616
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.30
Warning! 135248 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:836213 original size:160 final size:159
Alignment explanation
Indices: 835841--836196 Score: 475
Period size: 160 Copynumber: 2.2 Consensus size: 159
835831 GTAATAGAAT
* **
835841 TGGAATTGCGTTACTAGTAAATATGGAATCACACGAGTATTTGATATGGAATCAAGCATCCTTAG
1 TGGAATTGCGTGACTAGTAAATATGGAATCACGTGAGTATTTGATATGGAATCAAGCATCCTTAG
* *
835906 ATATGGAATCACGTGAGTACTAAATTTTGATTCACATGACTAGTTAATATGCAATCGCGTGAGTA
66 ATATGGAATCACGTGAGTACAAAATTTTGAGTCACATGACTAGTTAATATGCAATCGCGTGAGTA
835971 ATAGAATTGGAATTGCCTAACTAGTAAATA
131 ATAGAATTGGAATTG-CTAACTAGTAAATA
* * * * * * * *
836001 TGGAATCGTGCGACAAGTATATATGGAATCACGTGAGTATTTGATATGGAATCACGCGTCCTTAT
1 TGGAATTGCGTGACTAGTAAATATGGAATCACGTGAGTATTTGATATGGAATCAAGCATCCTTAG
* *
836066 ATATGGAATCACGCGTG-GT-CAAAATTTTGAGTCACGTGATTAGTTAATATGCAATCGCGTGAG
66 ATATGGAATCA--CGTGAGTACAAAATTTTGAGTCACATGACTAGTTAATATGCAATCGCGTGAG
* *
836129 TAATAGAATTGGAATCCTG-TTACTCGTAAATA
129 TAATAGAATTGGAAT--TGCTAACTAGTAAATA
* *
836161 TGGAATTGCGTGACTAGTAAATAGGGAATCGCGTGA
1 TGGAATTGCGTGACTAGTAAATATGGAATCACGTGA
836197 CTAGTAAATA
Statistics
Matches: 168, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
160 160 0.95
161 2 0.01
162 6 0.04
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (159 bp):
TGGAATTGCGTGACTAGTAAATATGGAATCACGTGAGTATTTGATATGGAATCAAGCATCCTTAG
ATATGGAATCACGTGAGTACAAAATTTTGAGTCACATGACTAGTTAATATGCAATCGCGTGAGTA
ATAGAATTGGAATTGCTAACTAGTAAATA
Found at i:836214 original size:23 final size:23
Alignment explanation
Indices: 835906--836216 Score: 127
Period size: 23 Copynumber: 13.6 Consensus size: 23
835896 GCATCCTTAG
* * *
835906 ATATGGAATCACGTGAGTACTAA
1 ATATGGAATCGCGTGACTAGTAA
* * * * * *
835929 ATTTTGATTCACATGACTAGTTA
1 ATATGGAATCGCGTGACTAGTAA
* * *
835952 ATATGCAATCGCGTGAGTAATAGA
1 ATATGGAATCGCGTGACTAGTA-A
* * *
835976 AT-TGGAATTGCCTAACTAGTAA
1 ATATGGAATCGCGTGACTAGTAA
* * * *
835998 ATATGGAATCGTGCGACAAGTAT
1 ATATGGAATCGCGTGACTAGTAA
* * * **
836021 ATATGGAATCACGTGAGTATTTG
1 ATATGGAATCGCGTGACTAGTAA
* *
836044 ATATGGAATCACGCGT-CCT--TAT
1 ATATGGAAT--CGCGTGACTAGTAA
*
836066 ATATGGAATCACGCGTG-GTCA--AA
1 ATATGGAAT--CGCGTGACT-AGTAA
* * * * * *
836089 ATTTTGAGTCACGTGATTAGTTA
1 ATATGGAATCGCGTGACTAGTAA
* * *
836112 ATATGCAATCGCGTGAGTAATAGA
1 ATATGGAATCGCGTGACTAGTA-A
* *
836136 AT-TGGAATC-CTGTTACTCGTAA
1 ATATGGAATCGC-GTGACTAGTAA
*
836158 ATATGGAATTGCGTGACTAGTAA
1 ATATGGAATCGCGTGACTAGTAA
*
836181 ATAGGGAATCGCGTGACTAGTAA
1 ATATGGAATCGCGTGACTAGTAA
836204 ATATGGAATCGCG
1 ATATGGAATCGCG
836217 CCAGTATTTG
Statistics
Matches: 205, Mismatches: 69, Indels: 28
0.68 0.23 0.09
Matches are distributed among these distances:
21 6 0.03
22 26 0.13
23 161 0.79
24 8 0.04
25 4 0.02
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (23 bp):
ATATGGAATCGCGTGACTAGTAA
Found at i:840866 original size:202 final size:202
Alignment explanation
Indices: 840520--841210 Score: 945
Period size: 202 Copynumber: 3.4 Consensus size: 202
840510 TGTAGACTCT
* * *
840520 AAAACTAGTGAACAAAAGCCTCAAAACAAGAGATGAATTGCATAAGCCACGCACTGTCAGTCTCG
1 AAAACTAGTGAACAAAAGCCTCAAAACAAGTGATGAATTGCACAAGTCACGCACTGTCAGTCTCG
* * *
840585 CAATACCTAATAATAAGTCACTTAATGCGTAATATCTATTGACATTATGCCAACATAACTAGTCA
66 CAATACCTAATAATAAGTCACTTAATGCGTAATATCTACTCACATTATGCCAACATAACCAGTCA
* * *
840650 TGTAACGGCCCAATGTCATGCAAAACATAACAACAGGTTATGTAATACATAAAAACAGTCATGCA
131 CGTAACGGCCCAATGTCACGCAAAACATAACAACAGGTTACGTAATACATAAAAACAGTCATGCA
840715 TCGTCTA
196 TCGTCTA
* *
840722 AAAACTAGTTAACAAAAGCCTCAAAACAAGTGATGAATTTCACAAGTCACGCACTGTCAGTCTCG
1 AAAACTAGTGAACAAAAGCCTCAAAACAAGTGATGAATTGCACAAGTCACGCACTGTCAGTCTCG
* *
840787 CAATACCTAATAATAAGTCACTCAATGCGTAATATGTACTCACATTATGCCAACATAACCAGTCA
66 CAATACCTAATAATAAGTCACTTAATGCGTAATATCTACTCACATTATGCCAACATAACCAGTCA
* *
840852 CGTAATGGCCCAATGTAACGCAAAACATAACAACAGGTTACGTAATACATAAAAACAGTCATGCA
131 CGTAACGGCCCAATGTCACGCAAAACATAACAACAGGTTACGTAATACATAAAAACAGTCATGCA
840917 TCGTCTA
196 TCGTCTA
* * * **
840924 AAAACTAGTTAACAAAAGCCTTAAAACAAGTGATGAATTCCACAAGTCACGCACTACCAGTCTCG
1 AAAACTAGTGAACAAAAGCCTCAAAACAAGTGATGAATTGCACAAGTCACGCACTGTCAGTCTCG
* * *
840989 CAATACCTAATAATAAGTCACTTAATGTGTAACATCCACTCGCACATTATGCCAACATAACCAGT
66 CAATACCTAATAATAAGTCACTTAATGCGTAATATCTACT--CACATTATGCCAACATAACCAGT
** * * ** * * *
841054 TGCGTAACGGCCCAATGTCACACAAAACATAACAACAGGTCACACAATATATAAAAAAAAGTCAC
129 CACGTAACGGCCCAATGTCACGCAAAACATAACAACAGGTTACGTAATACAT-AAAAACAGTCAT
*
841119 ACAGT-GTCTA
193 GCA-TCGTCTA
* * * * * * *
841129 CAAAACGACTGAAAAAAAGCCTTAAAACAAGGGATGAATTGCACAAGTCACGCAC-CTCGACTCT
1 -AAAACTAGTGAACAAAAGCCTCAAAACAAGTGATGAATTGCACAAGTCACGCACTGTC-AGTCT
*
841193 TGCAATACCTAATAATAA
64 CGCAATACCTAATAATAA
841211 TAACTCACTC
Statistics
Matches: 437, Mismatches: 46, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
202 283 0.65
204 66 0.15
205 18 0.04
206 70 0.16
ACGTcount: A:0.41, C:0.23, G:0.13, T:0.22
Consensus pattern (202 bp):
AAAACTAGTGAACAAAAGCCTCAAAACAAGTGATGAATTGCACAAGTCACGCACTGTCAGTCTCG
CAATACCTAATAATAAGTCACTTAATGCGTAATATCTACTCACATTATGCCAACATAACCAGTCA
CGTAACGGCCCAATGTCACGCAAAACATAACAACAGGTTACGTAATACATAAAAACAGTCATGCA
TCGTCTA
Found at i:841107 original size:22 final size:22
Alignment explanation
Indices: 841070--841121 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
841060 ACGGCCCAAT
* * *
841070 GTCACACAAAACATAACAACAG
1 GTCACACAAAACATAAAAAAAA
* *
841092 GTCACACAATATATAAAAAAAA
1 GTCACACAAAACATAAAAAAAA
841114 GTCACACA
1 GTCACACA
841122 GTGTCTACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.56, C:0.23, G:0.08, T:0.13
Consensus pattern (22 bp):
GTCACACAAAACATAAAAAAAA
Found at i:842351 original size:28 final size:28
Alignment explanation
Indices: 842286--842456 Score: 234
Period size: 28 Copynumber: 6.0 Consensus size: 28
842276 AATGTTGATA
842286 TAAATGCAATTAAGGGGGCTGAAAATTGGT
1 TAAATGCAATTAAGGGGGCT--AAATTGGT
*
842316 TAAGTGCAATTAAGGGGGCTAAATTGGT
1 TAAATGCAATTAAGGGGGCTAAATTGGT
* *
842344 TAAATGCAATTAAGGGGGTTGAATTGGT
1 TAAATGCAATTAAGGGGGCTAAATTGGT
* * *
842372 TCAGTGCAATTAATGGGGCTAAATTGGT
1 TAAATGCAATTAAGGGGGCTAAATTGGT
*
842400 TAAATGCAATTAAGGGGGCTGAATTGGT
1 TAAATGCAATTAAGGGGGCTAAATTGGT
* * *
842428 TCAGTGCAATTAAGGGGGCTGAATTGGT
1 TAAATGCAATTAAGGGGGCTAAATTGGT
842456 T
1 T
842457 GAATTAGTAG
Statistics
Matches: 126, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
28 107 0.85
30 19 0.15
ACGTcount: A:0.31, C:0.08, G:0.32, T:0.30
Consensus pattern (28 bp):
TAAATGCAATTAAGGGGGCTAAATTGGT
Found at i:842383 original size:56 final size:56
Alignment explanation
Indices: 842286--842456 Score: 288
Period size: 56 Copynumber: 3.0 Consensus size: 56
842276 AATGTTGATA
*
842286 TAAATGCAATTAAGGGGGCTGAAAATTGGTTAAGTGCAATTAAGGGGGCTAAATTGGT
1 TAAATGCAATTAAGGGGGCTG--AATTGGTTCAGTGCAATTAAGGGGGCTAAATTGGT
* *
842344 TAAATGCAATTAAGGGGGTTGAATTGGTTCAGTGCAATTAATGGGGCTAAATTGGT
1 TAAATGCAATTAAGGGGGCTGAATTGGTTCAGTGCAATTAAGGGGGCTAAATTGGT
*
842400 TAAATGCAATTAAGGGGGCTGAATTGGTTCAGTGCAATTAAGGGGGCTGAATTGGT
1 TAAATGCAATTAAGGGGGCTGAATTGGTTCAGTGCAATTAAGGGGGCTAAATTGGT
842456 T
1 T
842457 GAATTAGTAG
Statistics
Matches: 107, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
56 87 0.81
58 20 0.19
ACGTcount: A:0.31, C:0.08, G:0.32, T:0.30
Consensus pattern (56 bp):
TAAATGCAATTAAGGGGGCTGAATTGGTTCAGTGCAATTAAGGGGGCTAAATTGGT
Found at i:842408 original size:84 final size:85
Alignment explanation
Indices: 842290--842456 Score: 264
Period size: 84 Copynumber: 2.0 Consensus size: 85
842280 TTGATATAAA
*
842290 TGCAATTAAGGGGGCTGAAAATTGGTTAAGTGCAATTAAGGGGGCTAAATTGGTTAAATGCAATT
1 TGCAATTAAGGGGGCT-AAAATTGGTTAAATGCAATTAAGGGGGCTAAATTGGTTAAATGCAATT
*
842355 AAGGGGGTTGAATTGGTTCAG
65 AAGGGGGCTGAATTGGTTCAG
* * * *
842376 TGCAATTAATGGGGCT-AAATTGGTTAAATGCAATTAAGGGGGCTGAATTGGTTCAGTGCAATTA
1 TGCAATTAAGGGGGCTAAAATTGGTTAAATGCAATTAAGGGGGCTAAATTGGTTAAATGCAATTA
842440 AGGGGGCTGAATTGGTT
66 AGGGGGCTGAATTGGTT
842457 GAATTAGTAG
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
84 60 0.80
86 15 0.20
ACGTcount: A:0.30, C:0.08, G:0.32, T:0.30
Consensus pattern (85 bp):
TGCAATTAAGGGGGCTAAAATTGGTTAAATGCAATTAAGGGGGCTAAATTGGTTAAATGCAATTA
AGGGGGCTGAATTGGTTCAG
Found at i:847235 original size:38 final size:38
Alignment explanation
Indices: 847184--847310 Score: 227
Period size: 38 Copynumber: 3.3 Consensus size: 38
847174 TATTTACTTG
*
847184 TGATGGAGGGGTAAAAATCACACAAGGCGACATGGTCT
1 TGATGAAGGGGTAAAAATCACACAAGGCGACATGGTCT
*
847222 TGATGAAGGGGTAAAAATCACACAAGGCGAGATGGTCT
1 TGATGAAGGGGTAAAAATCACACAAGGCGACATGGTCT
*
847260 TGATGAAGGGGTAAAAATCACACAAGGTGACATGGTCT
1 TGATGAAGGGGTAAAAATCACACAAGGCGACATGGTCT
847298 TGATGAAGGGGTA
1 TGATGAAGGGGTA
847311 TTTGCTTAAT
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 85 1.00
ACGTcount: A:0.35, C:0.13, G:0.32, T:0.20
Consensus pattern (38 bp):
TGATGAAGGGGTAAAAATCACACAAGGCGACATGGTCT
Found at i:854687 original size:16 final size:15
Alignment explanation
Indices: 854666--854715 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
854656 TTGAAACTTT
854666 ATTTATGTTTAGTGTA
1 ATTTATGTTT-GTGTA
*
854682 ATTTAT-TTTCT-T-
1 ATTTATGTTTGTGTA
854694 ATTTATGTTTGATGTA
1 ATTTATGTTTG-TGTA
854710 ATTTAT
1 ATTTAT
854716 TTGTTTTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 6 0.21
13 4 0.14
14 2 0.07
15 4 0.14
16 12 0.43
ACGTcount: A:0.24, C:0.02, G:0.12, T:0.62
Consensus pattern (15 bp):
ATTTATGTTTGTGTA
Found at i:854696 original size:28 final size:28
Alignment explanation
Indices: 854664--854717 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
854654 AATTGAAACT
854664 TTATTTATGTTT-AGTGTAATTTATTTTC
1 TTATTTATGTTTGA-TGTAATTTATTTTC
854692 TTATTTATGTTTGATGTAATTTATTT
1 TTATTTATGTTTGATGTAATTTATTT
854718 GTTTTAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.22, C:0.02, G:0.11, T:0.65
Consensus pattern (28 bp):
TTATTTATGTTTGATGTAATTTATTTTC
Found at i:860647 original size:5 final size:5
Alignment explanation
Indices: 860636--860681 Score: 65
Period size: 5 Copynumber: 8.8 Consensus size: 5
860626 GGAAATGGCA
*
860636 TCATT TCCTT TCATT TCATT TCATT TCAATT TACATT TCATT TCAT
1 TCATT TCATT TCATT TCATT TCATT TC-ATT T-CATT TCATT TCAT
860682 CTTATTTAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
5 28 0.76
6 8 0.22
7 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.57
Consensus pattern (5 bp):
TCATT
Found at i:875426 original size:29 final size:29
Alignment explanation
Indices: 875384--875452 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
875374 TAACATTGTT
* *
875384 TTGTTTCATGTAC-ATATTATTATTCTTTG
1 TTGTATCATTTACAATATTATTA-TCTTTG
* *
875413 TTGTATCATTTACAATATTTTTATCTTTT
1 TTGTATCATTTACAATATTATTATCTTTG
*
875442 TTGTACCATTT
1 TTGTATCATTT
875453 TATAACAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 26 0.76
30 8 0.24
ACGTcount: A:0.22, C:0.12, G:0.07, T:0.59
Consensus pattern (29 bp):
TTGTATCATTTACAATATTATTATCTTTG
Found at i:875791 original size:23 final size:23
Alignment explanation
Indices: 875765--876128 Score: 128
Period size: 23 Copynumber: 15.9 Consensus size: 23
875755 TGATTCCCAC
* *
875765 GAGTATTTGATATGGAATCACGT
1 GAGTACTTAATATGGAATCACGT
* *
875788 GAGTACTAAATTTGGAATCACGT
1 GAGTACTTAATATGGAATCACGT
* * *
875811 GAGTATTTGATATGGAATCACGC
1 GAGTACTTAATATGGAATCACGT
** * *
875834 GAGTACAAAATTTTGAATCACGT
1 GAGTACTTAATATGGAATCACGT
* * *
875857 GAGTAGTTAATATGCAATCGCGT
1 GAGTACTTAATATGGAATCACGT
* * * *
875880 GAGTAATAGAAT-TGGGATCATGT
1 GAGTACT-TAATATGGAATCACGT
* * * * **
875903 TACTAGTAAATATGGAATCACAC
1 GAGTACTTAATATGGAATCACGT
* * *
875926 AAGTATTTGATATGGAATCA-G-
1 GAGTACTTAATATGGAATCACGT
* * * *
875947 GTGTCCTTACATATGGAATCATGC
1 GAGTACTTA-ATATGGAATCACGT
* * * *
875971 GAGTACTAAATTTTGAATCACAT
1 GAGTACTTAATATGGAATCACGT
* * * * *
875994 GACTAGTTAATATGCATTCGCGT
1 GAGTACTTAATATGGAATCACGT
* * * * *
876017 GAGAAATAGAAT-TGGAATCGCCT
1 GAGTACT-TAATATGGAATCACGT
* * * *
876040 GACTAGTAAATATGGAATCGCGT
1 GAGTACTTAATATGGAATCACGT
* * * *
876063 GACTAGTAAATATGGAATCACGC
1 GAGTACTTAATATGGAATCACGT
* * *
876086 AAGTATTTGATATGGAATCAC--
1 GAGTACTTAATATGGAATCACGT
* *
876107 GCGTCCTTAGATATGGAATCAC
1 GAGTACTTA-ATATGGAATCAC
876129 CCGGGGACAA
Statistics
Matches: 244, Mismatches: 89, Indels: 17
0.70 0.25 0.05
Matches are distributed among these distances:
21 8 0.03
22 29 0.12
23 195 0.80
24 12 0.05
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.30
Consensus pattern (23 bp):
GAGTACTTAATATGGAATCACGT
Found at i:875815 original size:46 final size:46
Alignment explanation
Indices: 875765--876107 Score: 208
Period size: 46 Copynumber: 7.5 Consensus size: 46
875755 TGATTCCCAC
* *
875765 GAGTATTTGATATGGAATCACGTGAGTACTAAATTTGGAATCACGT
1 GAGTAGTTAATATGGAATCACGTGAGTACTAAATTTGGAATCACGT
* * * * *
875811 GAGTATTTGATATGGAATCACGCGAGTACAAAATTTTGAATCACGT
1 GAGTAGTTAATATGGAATCACGTGAGTACTAAATTTGGAATCACGT
* * * * *
875857 GAGTAGTTAATATGCAATCGCGTGAGTAATAGAA-TTGGGATCATGT
1 GAGTAGTTAATATGGAATCACGTGAGTACTA-AATTTGGAATCACGT
* * * *** * ** *
875903 TACTAGTAAATATGGAATCACACAAGTATTTGATATGGAATCA-G-
1 GAGTAGTTAATATGGAATCACGTGAGTACTAAATTTGGAATCACGT
* ** * * * *
875947 GTGTCCTTACATATGGAATCATGCGAGTACTAAATTTTGAATCACAT
1 GAGTAGTTA-ATATGGAATCACGTGAGTACTAAATTTGGAATCACGT
* * * * * * * *
875994 GACTAGTTAATATGCATTCGCGTGAGAAATAGAA-TTGGAATCGCCT
1 GAGTAGTTAATATGGAATCACGTGAGTACTA-AATTTGGAATCACGT
* * * * * * *
876040 GACTAGTAAATATGGAATCGCGTGACTAGTAAATATGGAATCACGC
1 GAGTAGTTAATATGGAATCACGTGAGTACTAAATTTGGAATCACGT
* * *
876086 AAGTATTTGATATGGAATCACG
1 GAGTAGTTAATATGGAATCACG
876108 CGTCCTTAGA
Statistics
Matches: 219, Mismatches: 71, Indels: 14
0.72 0.23 0.05
Matches are distributed among these distances:
44 3 0.01
45 30 0.14
46 177 0.81
47 9 0.04
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (46 bp):
GAGTAGTTAATATGGAATCACGTGAGTACTAAATTTGGAATCACGT
Found at i:876072 original size:160 final size:160
Alignment explanation
Indices: 875904--876241 Score: 498
Period size: 160 Copynumber: 2.1 Consensus size: 160
875894 GGATCATGTT
* * *
875904 ACTAGTAAATATGGAATCACACAAGTATTTGATATGGAATCAGGTGTCCTTACATATGGAATCAT
1 ACTAGTAAATATGGAATCACACAAGTATTTGATATGGAATCACGCGTCCTTACATATGGAATCAC
* * * * *
875969 GCGAGTACTAAATTTTGAATCACATGACTAGTTAATATGC-ATTCGCGTGAGAAATAGAATTGGA
66 CCGAGGACAAAATTTTGAATCACATGACTAGTTAATATGCAATT-ACGTGAGAAATAGAATTAGA
876033 ATCGCCTGACTAGTAAATATGGAATCGCGTG
130 ATCGCCTGACTAGTAAATATGGAATCGCGTG
* *
876064 ACTAGTAAATATGGAATCACGCAAGTATTTGATATGGAATCACGCGTCCTTAGATATGGAATCAC
1 ACTAGTAAATATGGAATCACACAAGTATTTGATATGGAATCACGCGTCCTTACATATGGAATCAC
* * *
876129 CCGGGGACAAAATTTTGAGTCACATGACTAGTTAATATGCAATTACGTGAGTAATAGAATTAGAA
66 CCGAGGACAAAATTTTGAATCACATGACTAGTTAATATGCAATTACGTGAGAAATAGAATTAGAA
* * * *
876194 TCGCGTTACTCGTAAATATGGAATTGCGTG
131 TCGCCTGACTAGTAAATATGGAATCGCGTG
*
876224 ACTAGTAAATAGGGAATC
1 ACTAGTAAATATGGAATC
876242 GTGTGACTAG
Statistics
Matches: 159, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
160 156 0.98
161 3 0.02
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (160 bp):
ACTAGTAAATATGGAATCACACAAGTATTTGATATGGAATCACGCGTCCTTACATATGGAATCAC
CCGAGGACAAAATTTTGAATCACATGACTAGTTAATATGCAATTACGTGAGAAATAGAATTAGAA
TCGCCTGACTAGTAAATATGGAATCGCGTG
Found at i:876076 original size:137 final size:137
Alignment explanation
Indices: 875820--876082 Score: 355
Period size: 137 Copynumber: 1.9 Consensus size: 137
875810 TGAGTATTTG
* * *
875820 ATATGGAATCACGCGAGTACAAAATTTTGAATCACGTGAGTAGTTAATATGCAATCGCGTGAGTA
1 ATATGGAATCACGCGAGTACAAAATTTTGAATCACATGACTAGTTAATATGCAATCGCGTGAGAA
* ** * * * **
875885 ATAGAATTGGGATCATGTTACTAGTAAATATGGAATCACACAAGTATTTGATATGGAATCAGGTG
66 ATAGAATTGGAATCACCTGACTAGTAAATATGGAATCACACAACTAGTAAATATGGAATCAGGTG
875950 TCCTTAC
131 TCCTTAC
* * *
875957 ATATGGAATCATGCGAGTACTAAATTTTGAATCACATGACTAGTTAATATGCATTCGCGTGAGAA
1 ATATGGAATCACGCGAGTACAAAATTTTGAATCACATGACTAGTTAATATGCAATCGCGTGAGAA
* * ***
876022 ATAGAATTGGAATCGCCTGACTAGTAAATATGGAATCGCGTGACTAGTAAATATGGAATCA
66 ATAGAATTGGAATCACCTGACTAGTAAATATGGAATCACACAACTAGTAAATATGGAATCA
876083 CGCAAGTATT
Statistics
Matches: 107, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
137 107 1.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (137 bp):
ATATGGAATCACGCGAGTACAAAATTTTGAATCACATGACTAGTTAATATGCAATCGCGTGAGAA
ATAGAATTGGAATCACCTGACTAGTAAATATGGAATCACACAACTAGTAAATATGGAATCAGGTG
TCCTTAC
Found at i:876122 original size:22 final size:22
Alignment explanation
Indices: 876072--876128 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
876062 TGACTAGTAA
*
876072 ATATGGAATCACGCAAGTATTTG
1 ATATGGAATCACGC-AGTATTAG
*
876095 ATATGGAATCACGC-GTCCTTAG
1 ATATGGAATCACGCAGT-ATTAG
876117 ATATGGAATCAC
1 ATATGGAATCAC
876129 CCGGGGACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 2 0.06
22 15 0.48
23 14 0.45
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (22 bp):
ATATGGAATCACGCAGTATTAG
Found at i:876217 original size:23 final size:23
Alignment explanation
Indices: 876191--876263 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
876181 AATAGAATTA
* *
876191 GAATCGCGTTACTCGTAAATATG
1 GAATCGCGTGACTAGTAAATATG
* *
876214 GAATTGCGTGACTAGTAAATAGG
1 GAATCGCGTGACTAGTAAATATG
* *
876237 GAATCGTGTGACTAGTTAATATG
1 GAATCGCGTGACTAGTAAATATG
876260 GAAT
1 GAAT
876264 TGCGCCAGTA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (23 bp):
GAATCGCGTGACTAGTAAATATG
Found at i:883733 original size:29 final size:29
Alignment explanation
Indices: 883698--883766 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
883688 AAATTATAAT
883698 GAAGGTCATTTTTGAAGTGACCTTATGAG
1 GAAGGTCATTTTTGAAGTGACCTTATGAG
883727 GAAGGTCATTTTTGAAGTGACCTTATGAG
1 GAAGGTCATTTTTGAAGTGACCTTATGAG
883756 GAAGGTCATTT
1 GAAGGTCATTT
883767 CTCACAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.35
Consensus pattern (29 bp):
GAAGGTCATTTTTGAAGTGACCTTATGAG
Found at i:889647 original size:42 final size:42
Alignment explanation
Indices: 889568--889647 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
889558 TCCGAGCAAT
* *
889568 CATAAAAGGTATAGTTGCAAATTCTAGTTATTATTTAGTAAC
1 CATAAAAGGTATAATTGCAAATTCTAGTTAGTATTTAGTAAC
*
889610 CATAAAAGGTATAATTGCAAATTCTAGTTAGTGTTTAG
1 CATAAAAGGTATAATTGCAAATTCTAGTTAGTATTTAG
889648 ATTTTGCTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (42 bp):
CATAAAAGGTATAATTGCAAATTCTAGTTAGTATTTAGTAAC
Found at i:900362 original size:16 final size:15
Alignment explanation
Indices: 900341--900390 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
900331 TTGAAACTTT
900341 ATTTATGTTTAGTGTA
1 ATTTATGTTT-GTGTA
*
900357 ATTTAT-TTTCT-T-
1 ATTTATGTTTGTGTA
900369 ATTTATGTTTGGTGTA
1 ATTTATGTTT-GTGTA
900385 ATTTAT
1 ATTTAT
900391 TTGTTTTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 6 0.21
13 4 0.14
14 2 0.07
15 4 0.14
16 12 0.43
ACGTcount: A:0.22, C:0.02, G:0.14, T:0.62
Consensus pattern (15 bp):
ATTTATGTTTGTGTA
Found at i:900371 original size:28 final size:28
Alignment explanation
Indices: 900339--900392 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
900329 GATTGAAACT
900339 TTATTTATGTTTAGTGTAATTTATTTTC
1 TTATTTATGTTTAGTGTAATTTATTTTC
*
900367 TTATTTATGTTTGGTGTAATTTATTT
1 TTATTTATGTTTAGTGTAATTTATTT
900393 GTTTTAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.20, C:0.02, G:0.13, T:0.65
Consensus pattern (28 bp):
TTATTTATGTTTAGTGTAATTTATTTTC
Found at i:900404 original size:28 final size:28
Alignment explanation
Indices: 900345--900406 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
900335 AACTTTATTT
**
900345 ATGTTTAGTGTAATTTATTTTCTTATTT
1 ATGTTTAGTGTAATTTATTTTCTTATAC
* *
900373 ATGTTTGGTGTAATTTATTTGTTTTA-AC
1 ATGTTTAGTGTAATTTATTT-TCTTATAC
900401 ATGTTT
1 ATGTTT
900407 TTATTATTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.21, C:0.03, G:0.15, T:0.61
Consensus pattern (28 bp):
ATGTTTAGTGTAATTTATTTTCTTATAC
Found at i:921498 original size:229 final size:230
Alignment explanation
Indices: 921026--921704 Score: 918
Period size: 229 Copynumber: 3.0 Consensus size: 230
921016 CCTTTGCCCA
* * * *
921026 TAGAATGTATAAATTCTCAAAGGGCAGCAAAGATATTTCTTCTCCCA-AATGCACAGCAAAGTCC
1 TAGAATGTATAAATTCTTAAAGGGCAGCAAAGATATTTCTTC-ACCAGAATGCACACCAAGGTCC
* * * *
921090 GGTTGTTGCAAACCATAACTGTCCAAATGTCCGACCTCTAATGTAGTCCACACAATCACTGTGAA
65 GATTGTTGCAAACCA-AAATGTCCAAATGTCCGACCTCTAACGTAGTCCACACAATCACTATGAA
* * * * *
921155 CTTGAACCTTT-TTCAAGAGGTTGGGGTTGTTTTGATCAAACCTTGTGCTAGTAAGGAAGTTTTA
129 C-TCAAACTTTCTTTAAGAGGTTGGGGTTGTTTTGACCAAACCTTGTGCTAGCAAGGAAGTTTTA
*
921219 CAAAGCTCAAGTGTTTTTCTTACTCTTACCTTAACCCT
193 CAAAGTTCAAGTGTTTTTCTTACTCTTACCTTAACCCT
* * * *
921257 TAGAATGTATAAATTTTTAAAGGGTAGCAAAGATATTTCTTCACCTGAATGCACACCAAGGTCTG
1 TAGAATGTATAAATTCTTAAAGGGCAGCAAAGATATTTCTTCACCAGAATGCACACCAAGGTCCG
* * * * ** **
921322 ATTGTTGCAAACCAAAATATCTAACTATTTGACCTCTAACAAAGTCCACACAATCACTATGAACT
66 ATTGTTGCAAACCAAAATGTCCAAATGTCCGACCTCTAACGTAGTCCACACAATCACTATGAACT
* ** * *
921387 CAAATTTTCTTTAAGATATTGGGG-TGTTTTAACCAAACCTTGTGCTAGCAAGGAAGTTTTATAA
131 CAAACTTTCTTTAAGAGGTTGGGGTTGTTTTGACCAAACCTTGTGCTAGCAAGGAAGTTTTACAA
* * * *
921451 AGTTCTAGTGTTTTTCGTACTCTTACCTTAATCTT
196 AGTTCAAGTGTTTTTCTTACTCTTACCTTAACCCT
* * *
921486 TAGAACGTATAAATTCTTAAAAGGCAGCAAAGATATTTCTTCACCAGAATGCACACCGAGGTCCG
1 TAGAATGTATAAATTCTTAAAGGGCAGCAAAGATATTTCTTCACCAGAATGCACACCAAGGTCCG
921551 ATTGTTGCAAA-CAAAACTGTCCAAATGTCCGACCTCTAACGTAGTCCACACAATCACTATGAAC
66 ATTGTTGCAAACCAAAA-TGTCCAAATGTCCGACCTCTAACGTAGTCCACACAATCACTATGAAC
* *
921615 TCAAACCTTCTTTAAGAGGTTGGGGTTCTTTTGACCAAACCTTGTGCTAGCAAGGAAGTTTTACA
130 TCAAACTTTCTTTAAGAGGTTGGGGTTGTTTTGACCAAACCTTGTGCTAGCAAGGAAGTTTTACA
921680 AA-TCTCAAGTGTTTTTCTTACTCTT
195 AAGT-TCAAGTGTTTTTCTTACTCTT
921705 TNNNNNNNNN
Statistics
Matches: 384, Mismatches: 59, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
228 5 0.01
229 202 0.53
230 110 0.29
231 67 0.17
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (230 bp):
TAGAATGTATAAATTCTTAAAGGGCAGCAAAGATATTTCTTCACCAGAATGCACACCAAGGTCCG
ATTGTTGCAAACCAAAATGTCCAAATGTCCGACCTCTAACGTAGTCCACACAATCACTATGAACT
CAAACTTTCTTTAAGAGGTTGGGGTTGTTTTGACCAAACCTTGTGCTAGCAAGGAAGTTTTACAA
AGTTCAAGTGTTTTTCTTACTCTTACCTTAACCCT
Found at i:923550 original size:25 final size:25
Alignment explanation
Indices: 923517--923571 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
923507 CACAACCAAC
* *
923517 TATATCAACCCATGGCCTAGCCACA
1 TATAACAACCAATGGCCTAGCCACA
* *
923542 TATAACAACCAATGGCCTTGCCACG
1 TATAACAACCAATGGCCTAGCCACA
923567 TATAA
1 TATAA
923572 TCACAAACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.31, G:0.13, T:0.22
Consensus pattern (25 bp):
TATAACAACCAATGGCCTAGCCACA
Found at i:928145 original size:21 final size:21
Alignment explanation
Indices: 928096--928164 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
928086 TTAATAAATT
*
928096 AAGTTCAAAAACACACTT-AAAC
1 AAGTTCAAAAA-TCA-TTCAAAC
* *
928118 AATTTCAAAAATCATTCAAAT
1 AAGTTCAAAAATCATTCAAAC
**
928139 AAGTTCAATGATCATTCAAAC
1 AAGTTCAAAAATCATTCAAAC
928160 AAGTT
1 AAGTT
928165 TAAATATAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
20 2 0.05
21 27 0.69
22 10 0.26
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (21 bp):
AAGTTCAAAAATCATTCAAAC
Found at i:939128 original size:228 final size:229
Alignment explanation
Indices: 938626--939310 Score: 866
Period size: 228 Copynumber: 3.0 Consensus size: 229
938616 AAAAAGGTTG
* *
938626 TACCTTAGCCCATAGAATGTATAAATTCTTAAAGGGCAGCAAAGATATTTCTTCACCCAAATGCA
1 TACCTTAACCCTTAGAATGTATAAATTCTTAAAGGGCAGCAAAGATATTTCTTCACCCAAATGCA
* * * * * *
938691 CACCAAAGTCCTG-TTGTTGCAAACCATAACTGTCCAAATGTCTGACCTCTAACGTATTGCACAC
66 CACCAAAGTCC-GATTGTTGCAAACCA-AAATATCCAAATTTC-CACCTCTAACGTAGTCCACAC
* *
938755 AATCACTATGAACTTGAACCTT-TTTCAAGAGGTTGGGGTTGTTTTGACCAAACCTTATGCTAGT
128 AATCACTATGAACTCGAACCTTCTTT-AAGAGGTTGGGGTTGTTTTGACCAAACCTTATGCTAGC
* * * * *
938819 AAAGAAGTTTGACAAAGCTCAAGTGTTTTGCTTGCTTT
192 AAGGAAGTTTTACAAAGTTCAAGTGTTTTTCTTACTTT
* *
938857 TACCTTAGCCCTTAGAATGTATAAATTTTTAAAGGGCAGCAAAGATATTTCTTCACCCAAATGCA
1 TACCTTAACCCTTAGAATGTATAAATTCTTAAAGGGCAGCAAAGATATTTCTTCACCCAAATGCA
* *
938922 CA-CAAAGTCCGATTGTTGCAAACCAAAATATCTAAATATTCCACCTCTAATGTAGTCCACACAA
66 CACCAAAGTCCGATTGTTGCAAACCAAAATATCCAAAT-TTCCACCTCTAACGTAGTCCACACAA
* ** *
938986 TCACTATGAACTCAAACCTTCTTTAAGATATTGGGGTTGTTTTAACCAAACCTT-TGCTAGCAAG
130 TCACTATGAACTCGAACCTTCTTTAAGAGGTTGGGGTTGTTTTGACCAAACCTTATGCTAGCAAG
* *
939050 GAAGTTTTATAAAGTTCTAGTGTTTTTCTTACTTT
195 GAAGTTTTACAAAGTTCAAGTGTTTTTCTTACTTT
* * * * * *
939085 TACCTTAATCCTTAGAACGTATAAATTCTTAGAA-GGTAGCAAAGATATTTTTTAACCCGAATGC
1 TACCTTAACCCTTAGAATGTATAAATTCTTA-AAGGGCAGCAAAGATATTTCTTCACCCAAATGC
* *
939149 ACAGCAAGGTCCGATTGTTGCAAA-CAAAACTATCCAAATTTCCGACCTCTAACGTAGTCCACAC
65 ACACCAAAGTCCGATTGTTGCAAACCAAAA-TATCCAAATTTCC-ACCTCTAACGTAGTCCACAC
* ** * ** *
939213 AATCACTATGAACTCGAACCTTC-TTAACAGGTTACGGCTCATTTGACC-AACCTTGTGCTAGCA
128 AATCACTATGAACTCGAACCTTCTTTAAGAGGTTGGGGTTGTTTTGACCAAACCTTATGCTAGCA
939276 AGGAAGTTTTACAAA-TCTCAAGTGTTTTTCTTACT
193 AGGAAGTTTTACAAAGT-TCAAGTGTTTTTCTTACT
939311 CTTTCTCTTG
Statistics
Matches: 399, Mismatches: 46, Indels: 21
0.86 0.10 0.05
Matches are distributed among these distances:
227 7 0.02
228 157 0.39
229 144 0.36
230 26 0.07
231 65 0.16
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (229 bp):
TACCTTAACCCTTAGAATGTATAAATTCTTAAAGGGCAGCAAAGATATTTCTTCACCCAAATGCA
CACCAAAGTCCGATTGTTGCAAACCAAAATATCCAAATTTCCACCTCTAACGTAGTCCACACAAT
CACTATGAACTCGAACCTTCTTTAAGAGGTTGGGGTTGTTTTGACCAAACCTTATGCTAGCAAGG
AAGTTTTACAAAGTTCAAGTGTTTTTCTTACTTT
Found at i:945737 original size:21 final size:20
Alignment explanation
Indices: 945713--945760 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
945703 TTAAACGTAT
*
945713 TTCAAAACTCATTCAAATAAG
1 TTCAAAA-TCATTCAAACAAG
*
945734 TTCAATTATCATTCAAACAAG
1 TTCAA-AATCATTCAAACAAG
945755 TTCAAA
1 TTCAAA
945761 TATAATTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.46, C:0.19, G:0.04, T:0.31
Consensus pattern (20 bp):
TTCAAAATCATTCAAACAAG
Found at i:947538 original size:16 final size:16
Alignment explanation
Indices: 947517--947550 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
947507 AAAATGCAAG
*
947517 CATGATTATAATTTTT
1 CATGATTACAATTTTT
947533 CATGATTACAATTTTT
1 CATGATTACAATTTTT
947549 CA
1 CA
947551 ATCTTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.12, G:0.06, T:0.50
Consensus pattern (16 bp):
CATGATTACAATTTTT
Found at i:953726 original size:114 final size:114
Alignment explanation
Indices: 953526--953742 Score: 310
Period size: 114 Copynumber: 1.9 Consensus size: 114
953516 GAATGGGAAT
* * ** * *
953526 CATAGGCACTTATACACCTAAATCATATAACCTTGTCGATATAGTTCAATAACTTTAAAAGTGAA
1 CATAGGCACTCATACACCTAAATCATATAACCTTATAAATATAGTTCAATAACTTCAAAAGTCAA
*
953591 GCTTATAACTATGCAAGAACAAATGTATGGGAGTTAAACCATTGATTCC
66 GCTTATAACTATGCAAGAACAAACGTATGGGAGTTAAACCATTGATTCC
** * *
953640 CATAGGCACTCATATGCCTAAGTCATATAAGCTTATAAATATAGTTCAATAACTTCAAACA-TCA
1 CATAGGCACTCATACACCTAAATCATATAACCTTATAAATATAGTTCAATAACTTCAAA-AGTCA
*
953704 AGCTTATAACTATGTAAGAACAAACGTATGGGAGTTAAA
65 AGCTTATAACTATGCAAGAACAAACGTATGGGAGTTAAA
953743 TAATTTCAAC
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
114 89 0.99
115 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (114 bp):
CATAGGCACTCATACACCTAAATCATATAACCTTATAAATATAGTTCAATAACTTCAAAAGTCAA
GCTTATAACTATGCAAGAACAAACGTATGGGAGTTAAACCATTGATTCC
Found at i:963190 original size:28 final size:25
Alignment explanation
Indices: 963153--963234 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 25
963143 GCTATTAGAC
* *
963153 GTGGCTAGGCCACGATTAATGATTATAT
1 GTGGCTAGGCCACCAGT--TGA-TATAT
*
963181 GTGGCAAGGCCACCAGTTGATATAT
1 GTGGCTAGGCCACCAGTTGATATAT
* *
963206 GTGGCTAGGCCACAAGTTGATATAC
1 GTGGCTAGGCCACCAGTTGATATAT
963231 GTGG
1 GTGG
963235 TTGTGACCAC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
25 31 0.65
26 3 0.06
28 14 0.29
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (25 bp):
GTGGCTAGGCCACCAGTTGATATAT
Found at i:969517 original size:21 final size:21
Alignment explanation
Indices: 969491--969570 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
969481 AAATTGCTTC
969491 AATGATTTTTGAACTTGTTTG
1 AATGATTTTTGAACTTGTTTG
** *
969512 AATGATGCTTGAACTTATTTG
1 AATGATTTTTGAACTTGTTTG
*
969533 AATGATTTTTGAAGTTGTTTG
1 AATGATTTTTGAACTTGTTTG
*
969554 AATGTGTTTTTGAACTT
1 AATG-ATTTTTGAACTT
969571 AATTTAATAA
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 39 0.80
22 10 0.20
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50
Consensus pattern (21 bp):
AATGATTTTTGAACTTGTTTG
Found at i:970588 original size:21 final size:21
Alignment explanation
Indices: 970563--970612 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
970553 GACTCAATCG
970563 ACCAAGAAAGCTTGACGATCA
1 ACCAAGAAAGCTTGACGATCA
*
970584 ACCAAGAAAGCTTGTCGATCA
1 ACCAAGAAAGCTTGACGATCA
970605 ACCAAGAA
1 ACCAAGAA
970613 GATACTACCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.14
Consensus pattern (21 bp):
ACCAAGAAAGCTTGACGATCA
Found at i:974842 original size:23 final size:23
Alignment explanation
Indices: 974816--974869 Score: 56
Period size: 25 Copynumber: 2.3 Consensus size: 23
974806 ACAACCACGT
**
974816 ATATAAACTTGTGGCC-TAGCCAC
1 ATATAAACCCGTGGCCAT-GCCAC
974839 ATATATCAACCCGTGGCCATGCCAC
1 ATATA--AACCCGTGGCCATGCCAC
974864 ATATAA
1 ATATAA
974870 TCATTGATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
23 6 0.23
25 19 0.73
26 1 0.04
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (23 bp):
ATATAAACCCGTGGCCATGCCAC
Found at i:982286 original size:21 final size:21
Alignment explanation
Indices: 982245--982324 Score: 97
Period size: 21 Copynumber: 3.8 Consensus size: 21
982235 TTATTAAATT
*
982245 AAGTTCAAAAACACATTCAAAC
1 AAGTTCAAAAA-TCATTCAAAC
* * *
982267 AACTTCAAAAATCATACAAAT
1 AAGTTCAAAAATCATTCAAAC
**
982288 AAGTTCAAGCATCATTCAAAC
1 AAGTTCAAAAATCATTCAAAC
982309 AAGTTCAAAAATCATT
1 AAGTTCAAAAATCATT
982325 GAAGCAATTT
Statistics
Matches: 47, Mismatches: 11, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
21 37 0.79
22 10 0.21
ACGTcount: A:0.51, C:0.20, G:0.05, T:0.24
Consensus pattern (21 bp):
AAGTTCAAAAATCATTCAAAC
Found at i:1000820 original size:29 final size:28
Alignment explanation
Indices: 1000772--1000851 Score: 97
Period size: 29 Copynumber: 2.8 Consensus size: 28
1000762 AATATTTTTT
*
1000772 TTGTCTGAAATTAAGGCAAACATATTTGC
1 TTGTCT-AAATTAAGCCAAACATATTTGC
* * *
1000801 TTGTCTAAGTTAAGACCAAACATGTTTTC
1 TTGTCTAAATTAAG-CCAAACATATTTGC
*
1000830 TTGTCTAAATTAAGTCAAACAT
1 TTGTCTAAATTAAGCCAAACAT
1000852 GTTAAAGCTG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 14 0.32
29 30 0.68
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (28 bp):
TTGTCTAAATTAAGCCAAACATATTTGC
Found at i:1000851 original size:57 final size:59
Alignment explanation
Indices: 1000741--1000851 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
1000731 AATACGTTTT
* *
1000741 CTTGTCTAGATTAAGACAAAAAATATTTTTTTTGTCTGAAATTAAGGCAAACATATTTG
1 CTTGTCTAGATTAAGACAAAAAATAGTTTTCTTGTCTGAAATTAAGGCAAACATATTTG
* * *
1000800 CTTGTCTA-AGTTAAGACCAAACAT-GTTTTCTTGTCT-AAATTAAGTCAAACAT
1 CTTGTCTAGA-TTAAGACAAAAAATAGTTTTCTTGTCTGAAATTAAGGCAAACAT
1000852 GTTAAAGCTG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
57 15 0.33
58 11 0.24
59 20 0.43
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (59 bp):
CTTGTCTAGATTAAGACAAAAAATAGTTTTCTTGTCTGAAATTAAGGCAAACATATTTG
Found at i:1008086 original size:48 final size:49
Alignment explanation
Indices: 1007990--1008086 Score: 126
Period size: 48 Copynumber: 2.0 Consensus size: 49
1007980 GATTCAAAAT
* *
1007990 TAGTATCAAAACCTTTGTAGCAACAACAATATATAATACATAATAGTCC
1 TAGTATCAAAACCTTTGTAGCAACAACAACATATAATACACAATAGTCC
* * *
1008039 TAGTATCAAAGCCTTTGTA-CAACAAGAACATATGATA-AGCAATAGTCC
1 TAGTATCAAAACCTTTGTAGCAACAACAACATATAATACA-CAATAGTCC
1008087 ATGTACTTCT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
47 1 0.02
48 23 0.55
49 18 0.43
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.27
Consensus pattern (49 bp):
TAGTATCAAAACCTTTGTAGCAACAACAACATATAATACACAATAGTCC
Found at i:1018883 original size:18 final size:19
Alignment explanation
Indices: 1018860--1018902 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1018850 AGGTAGAAAG
1018860 AATATTTT-TAAATAAAAT
1 AATATTTTATAAATAAAAT
*
1018878 AATATTTTATGAATAAAAT
1 AATATTTTATAAATAAAAT
*
1018897 ATTATT
1 AATATT
1018903 AAAATATNNN
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
AATATTTTATAAATAAAAT
Found at i:1023160 original size:4 final size:4
Alignment explanation
Indices: 1023128--1023258 Score: 128
Period size: 4 Copynumber: 33.2 Consensus size: 4
1023118 GAACCTTGTC
* * *
1023128 TCTT T-TT TCTT CCTT T-TT TCTT CCTT TCTT TCTT TGCTT CCTT TC-T
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T-CTT TCTT TCTT
* * *
1023174 TCTT TCTT TCTT CCTT T-TT TCTT CCTT TCTT TCTT TGCTT CCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T-CTT TCTT TCTT
* *
1023222 TCTT TGCTT CCTT TC-T TCTT TCTT TCTT TCTT CCTT T
1 TCTT T-CTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
1023259 GCTTCCTAGC
Statistics
Matches: 103, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
3 15 0.15
4 79 0.77
5 9 0.09
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (4 bp):
TCTT
Found at i:1023717 original size:24 final size:23
Alignment explanation
Indices: 1023672--1023719 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
1023662 TTCATTTTCA
* *
1023672 TTTCCTTTCACATGATTATACCT
1 TTTCCTTTCAAATCATTATACCT
*
1023695 TTTCCTTTTCAAATCATTGTACCT
1 TTTCC-TTTCAAATCATTATACCT
1023719 T
1 T
1023720 CCTTATGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.21, C:0.25, G:0.04, T:0.50
Consensus pattern (23 bp):
TTTCCTTTCAAATCATTATACCT
Found at i:1027567 original size:14 final size:14
Alignment explanation
Indices: 1027548--1027586 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
1027538 CATTGCACAA
1027548 GCCAAAAGGCATCT
1 GCCAAAAGGCATCT
1027562 GCCAAAAGGCATCT
1 GCCAAAAGGCATCT
1027576 GCCAAAAGGCA
1 GCCAAAAGGCA
1027587 AAAGAGCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.38, C:0.28, G:0.23, T:0.10
Consensus pattern (14 bp):
GCCAAAAGGCATCT
Found at i:1029612 original size:26 final size:25
Alignment explanation
Indices: 1029563--1029613 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
1029553 GTTTTAAAAC
*
1029563 TTTGCTTTTCTATTTCTTGCTTTTA
1 TTTGCTTTTATATTTCTTGCTTTTA
1029588 TTTGCTTGTTATAGTTTC-TGCTTTTA
1 TTTGCTT-TTATA-TTTCTTGCTTTTA
1029614 AACTTCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.30
26 12 0.52
27 4 0.17
ACGTcount: A:0.10, C:0.14, G:0.12, T:0.65
Consensus pattern (25 bp):
TTTGCTTTTATATTTCTTGCTTTTA
Found at i:1034905 original size:74 final size:74
Alignment explanation
Indices: 1034719--1034916 Score: 215
Period size: 74 Copynumber: 2.7 Consensus size: 74
1034709 TTTAGACAGT
* * * *
1034719 GCTCTTAGTTGACTAACGATACTTTTTATTCAATTAA-TTCTTCTTTGTCTTGTAATTGAATTCT
1 GCTCTTAGTTGACTAAC-ATACTTCTTAGTCGATTAAGTTCTTCTCTGTCTTGTAATTGAATTCT
* *
1034783 TTATCAATGA
65 CTAACAATGA
* * * * *
1034793 GCTCTTAATTTACTAACCATACTTCTCAGTTGATTAAGTTTTTC-CTGTCTTGTAATTGAAGTT-
1 GCTCTTAGTTGACTAA-CATACTTCTTAGTCGATTAAGTTCTTCTCTGTCTTGTAATTGAA-TTC
*
1034856 TCTAACAGTGA
64 TCTAACAATGA
*
1034867 GCTCTTAGTTGACTAATCATACTTCTTAGTCGACTAAG-TCTTCTCTGTCT
1 GCTCTTAGTTGACTAA-CATACTTCTTAGTCGATTAAGTTCTTCTCTGTCT
1034917 CATAATCTGC
Statistics
Matches: 101, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
73 4 0.04
74 89 0.88
75 8 0.08
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.45
Consensus pattern (74 bp):
GCTCTTAGTTGACTAACATACTTCTTAGTCGATTAAGTTCTTCTCTGTCTTGTAATTGAATTCTC
TAACAATGA
Found at i:1040424 original size:18 final size:18
Alignment explanation
Indices: 1040398--1040433 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1040388 TTTCGTTGCG
1040398 TTATATTTTAATGTATTGA
1 TTATATTTTAATGT-TTGA
1040417 TTAT-TTTTAATGTTTGA
1 TTATATTTTAATGTTTGA
1040434 ACCTGAGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 9 0.53
19 4 0.24
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (18 bp):
TTATATTTTAATGTTTGA
Found at i:1041648 original size:17 final size:18
Alignment explanation
Indices: 1041626--1041659 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1041616 TACTTTCCCT
*
1041626 TTCACTT-TGTCTGTGGA
1 TTCACTTCTGCCTGTGGA
1041643 TTCACTTCTGCCTGTGG
1 TTCACTTCTGCCTGTGG
1041660 TGTGAACTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.09, C:0.24, G:0.24, T:0.44
Consensus pattern (18 bp):
TTCACTTCTGCCTGTGGA
Found at i:1045715 original size:36 final size:36
Alignment explanation
Indices: 1045624--1045811 Score: 162
Period size: 38 Copynumber: 5.1 Consensus size: 36
1045614 GGTATTTTTG
* * *
1045624 CCCCCACAATGGGCTTTATGTATGTGGTGTTCTTAAC
1 CCCCCACAATGGGCTTTATTTAGGTGGTATTCTT-AC
** *
1045661 CCCCCATGATGGGCCTTTATTTGGGTGGTATTCTTAC
1 CCCCCACAATGGG-CTTTATTTAGGTGGTATTCTTAC
* * *
1045698 CCCCCTCAATGGGCTTTATTCAGGTGGTATTCGAATAC
1 CCCCCACAATGGGCTTTATTTAGGTGGTATTC--TTAC
* * ** * *
1045736 TCCCCACAATGGGCTTTATTCAAATGGTGTTCCTAC
1 CCCCCACAATGGGCTTTATTTAGGTGGTATTCTTAC
* * *
1045772 CCCCCACAGTGGG-TTTTTTTCATGTGGTATTCTTAC
1 CCCCCACAATGGGCTTTATTT-AGGTGGTATTCTTAC
1045808 CCCC
1 CCCC
1045812 ATGATACGCT
Statistics
Matches: 121, Mismatches: 26, Indels: 9
0.78 0.17 0.06
Matches are distributed among these distances:
35 5 0.04
36 46 0.38
37 23 0.19
38 47 0.39
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (36 bp):
CCCCCACAATGGGCTTTATTTAGGTGGTATTCTTAC
Found at i:1045753 original size:38 final size:36
Alignment explanation
Indices: 1045624--1045811 Score: 153
Period size: 36 Copynumber: 5.1 Consensus size: 36
1045614 GGTATTTTTG
* * *
1045624 CCCCCACAATGGGCTTTATGT-ATGTGGTGTTCTTAAC
1 CCCCCACAATGGGCTTTAT-TCAGGTGGTATTCAT-AC
** ** *
1045661 CCCCCATGATGGGCCTTTATTTGGGTGGTATTCTTAC
1 CCCCCACAATGGG-CTTTATTCAGGTGGTATTCATAC
*
1045698 CCCCCTCAATGGGCTTTATTCAGGTGGTATTCGAATAC
1 CCCCCACAATGGGCTTTATTCAGGTGGTATTC--ATAC
* ** * *
1045736 TCCCCACAATGGGCTTTATTCAAATGGTGTTCCTAC
1 CCCCCACAATGGGCTTTATTCAGGTGGTATTCATAC
* * * * *
1045772 CCCCCACAGTGGGTTTTTTTCATGTGGTATTCTTAC
1 CCCCCACAATGGGCTTTATTCAGGTGGTATTCATAC
1045808 CCCC
1 CCCC
1045812 ATGATACGCT
Statistics
Matches: 122, Mismatches: 25, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
36 52 0.43
37 24 0.20
38 46 0.38
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (36 bp):
CCCCCACAATGGGCTTTATTCAGGTGGTATTCATAC
Found at i:1045829 original size:35 final size:35
Alignment explanation
Indices: 1045790--1045884 Score: 120
Period size: 34 Copynumber: 2.7 Consensus size: 35
1045780 GTGGGTTTTT
1045790 TTCATGTGGTATTCTTACCCCCATGATACGCTTAG
1 TTCATGTGGTATTCTTACCCCCATGATACGCTTAG
* * ** *
1045825 TTCATGAGGTATTTTTA-CCCCATGATGGGCTTTG
1 TTCATGTGGTATTCTTACCCCCATGATACGCTTAG
* *
1045859 TTCATATGATATTCTTACCCCCATGA
1 TTCATGTGGTATTCTTACCCCCATGA
1045885 AGAGATTAAG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
34 27 0.54
35 23 0.46
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (35 bp):
TTCATGTGGTATTCTTACCCCCATGATACGCTTAG
Found at i:1057003 original size:57 final size:58
Alignment explanation
Indices: 1056893--1057004 Score: 163
Period size: 57 Copynumber: 1.9 Consensus size: 58
1056883 CATTTTTGCA
* * *
1056893 TGCATAGCATTTATTAAATCACATAAAATAAATCTACCACATACATACTACTTTGTAT
1 TGCATAGCATTTACTAAATCACATAAAATAAATCTACCAAATACAAACTACTTTGTAT
** *
1056951 TGCATAGCATTTACTAAATTGCAT-AAATAAATCTATCAAATACAAACTACTTTG
1 TGCATAGCATTTACTAAATCACATAAAATAAATCTACCAAATACAAACTACTTTG
1057005 GATGATTATG
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 27 0.56
58 21 0.44
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.34
Consensus pattern (58 bp):
TGCATAGCATTTACTAAATCACATAAAATAAATCTACCAAATACAAACTACTTTGTAT
Found at i:1060911 original size:14 final size:14
Alignment explanation
Indices: 1060892--1060954 Score: 81
Period size: 14 Copynumber: 4.5 Consensus size: 14
1060882 TTCCATCACA
1060892 AATGTTAAATGATG
1 AATGTTAAATGATG
* *
1060906 AATGTTAGATGATA
1 AATGTTAAATGATG
*
1060920 AATGTTAACTGATG
1 AATGTTAAATGATG
* *
1060934 AATGCTAATTGATG
1 AATGTTAAATGATG
1060948 AATGTTA
1 AATGTTA
1060955 CTTAATGTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.37
Consensus pattern (14 bp):
AATGTTAAATGATG
Found at i:1064969 original size:2 final size:2
Alignment explanation
Indices: 1064962--1064993 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1064952 TTGCATACTT
1064962 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1064994 AAGCTCAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1069456 original size:18 final size:18
Alignment explanation
Indices: 1069433--1069471 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1069423 CTAACATTAC
1069433 TAAATAAAATAATATATA
1 TAAATAAAATAATATATA
** *
1069451 TAAATAGCATGATATATA
1 TAAATAAAATAATATATA
1069469 TAA
1 TAA
1069472 TTTAATTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (18 bp):
TAAATAAAATAATATATA
Found at i:1070498 original size:51 final size:51
Alignment explanation
Indices: 1070403--1070507 Score: 156
Period size: 51 Copynumber: 2.1 Consensus size: 51
1070393 TGTCGGCCTA
* **
1070403 GCTCGCCCAGGGGCCTGTGCTGTGCGCCCCTGTTGGCATTCTGTCGAGCTG
1 GCTCGCCCAGGGGCCTGTGCTGTGCGCCCCTGCTGGCACCCTGTCGAGCTG
* * *
1070454 GCTCGCCCAGGGGCCTGTGTTGTGCGCCCCTGCTGGTACCCTGTCGGGCTG
1 GCTCGCCCAGGGGCCTGTGCTGTGCGCCCCTGCTGGCACCCTGTCGAGCTG
1070505 GCT
1 GCT
1070508 TGGGAACACC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.05, C:0.34, G:0.36, T:0.25
Consensus pattern (51 bp):
GCTCGCCCAGGGGCCTGTGCTGTGCGCCCCTGCTGGCACCCTGTCGAGCTG
Found at i:1076601 original size:17 final size:17
Alignment explanation
Indices: 1076579--1076612 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1076569 ATAATAATAA
1076579 AATAAG-AGTTATTATTT
1 AATAAGTAGTT-TTATTT
1076596 AATAAGTAGTTTTATTT
1 AATAAGTAGTTTTATTT
1076613 TATCAAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (17 bp):
AATAAGTAGTTTTATTT
Found at i:1085675 original size:24 final size:22
Alignment explanation
Indices: 1085630--1085675 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
1085620 TCTTCAATGC
* *
1085630 CCTTTTTTTATAAACTTTAAAA
1 CCTTTTTTTATAAAATTCAAAA
1085652 CCTTATTTTTATTAAAATTCAAAA
1 CCTT-TTTTTA-TAAAATTCAAAA
1085676 AATTGATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 6 0.30
24 10 0.50
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (22 bp):
CCTTTTTTTATAAAATTCAAAA
Found at i:1089015 original size:31 final size:31
Alignment explanation
Indices: 1088977--1089081 Score: 97
Period size: 30 Copynumber: 3.4 Consensus size: 31
1088967 ATAAAAATTT
1088977 ATTTAATTTAAAATAAAAATAAAAATA-AAAA
1 ATTTAATTT-AAATAAAAATAAAAATATAAAA
* * *
1089008 ATTTAATTTAATTTAAAATAAAAATATTAAA
1 ATTTAATTTAAATAAAAATAAAAATATAAAA
** ***
1089039 ATTTAACCTAAA-CGTAATAAAAATATAAAA
1 ATTTAATTTAAATAAAAATAAAAATATAAAA
* *
1089069 TTTTATTTTAAAT
1 ATTTAATTTAAAT
1089082 TTTTAAATAA
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
30 37 0.64
31 21 0.36
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (31 bp):
ATTTAATTTAAATAAAAATAAAAATATAAAA
Found at i:1092403 original size:13 final size:13
Alignment explanation
Indices: 1092380--1092412 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1092370 TTTTTTTAAA
1092380 AAAATTATTTTTTT
1 AAAATT-TTTTTTT
1092394 -AAATTTTTTTTT
1 AAAATTTTTTTTT
1092406 AAAATTT
1 AAAATTT
1092413 ATATTTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
AAAATTTTTTTTT
Found at i:1092746 original size:12 final size:12
Alignment explanation
Indices: 1092731--1092758 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1092721 AATTATTTAA
1092731 AAATTTTAAATT
1 AAATTTTAAATT
1092743 AAATTTTAAATT
1 AAATTTTAAATT
1092755 AAAT
1 AAAT
1092759 AAATTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AAATTTTAAATT
Found at i:1092766 original size:17 final size:18
Alignment explanation
Indices: 1092736--1092774 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
1092726 TTTAAAAATT
1092736 TTAAATTAAATTTTA-AA
1 TTAAATTAAATTTTATAA
1092753 TTAAA-TAAATTTTTATAA
1 TTAAATTAAA-TTTTATAA
1092771 TTAA
1 TTAA
1092775 TAATTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
17 10 0.50
18 6 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAAATTAAATTTTATAA
Found at i:1093060 original size:30 final size:30
Alignment explanation
Indices: 1093004--1093070 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
1092994 TATCAATTAT
* *
1093004 AAAAATTTATTTAATTTAAAATAAAAATAA
1 AAAAATTAATTTAATATAAAATAAAAATAA
*
1093034 AAAAACTTAATTTAATATAATA-AAAAATAA
1 AAAAA-TTAATTTAATATAAAATAAAAATAA
1093064 AAAAATT
1 AAAAATT
1093071 TTAAAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 2 0.06
30 18 0.55
31 13 0.39
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (30 bp):
AAAAATTAATTTAATATAAAATAAAAATAA
Found at i:1093081 original size:31 final size:30
Alignment explanation
Indices: 1093026--1093084 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1093016 AATTTAAAAT
**
1093026 AAAAATAAAAAAACTTAATTTAATATAATA
1 AAAAATAAAAAAACTTAAAATAATATAATA
*
1093056 AAAAATAAAAAAATTTTAAAATAATATAA
1 AAAAATAAAAAAA-CTTAAAATAATATAA
1093085 AAATTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (30 bp):
AAAAATAAAAAAACTTAAAATAATATAATA
Found at i:1093086 original size:19 final size:18
Alignment explanation
Indices: 1093054--1093090 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1093044 TTTAATATAA
1093054 TAAAAAATAAAAAAATTT
1 TAAAAAATAAAAAAATTT
*
1093072 TAAAATAATATAAAAATTT
1 TAAAA-AATAAAAAAATTT
1093091 ATTTGAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAAATAAAAAAATTT
Found at i:1098121 original size:17 final size:17
Alignment explanation
Indices: 1098087--1098121 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1098077 AAAATAACCC
* *
1098087 TTAAAAATAAGATGTTT
1 TTAAAAATAACATCTTT
1098104 TTAAAAATAACATCTTT
1 TTAAAAATAACATCTTT
1098121 T
1 T
1098122 ANNNNNNNNN
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (17 bp):
TTAAAAATAACATCTTT
Found at i:1098267 original size:45 final size:45
Alignment explanation
Indices: 1098187--1098414 Score: 217
Period size: 45 Copynumber: 5.1 Consensus size: 45
1098177 CGCCAGGATA
* * * * * * *
1098187 TTACACACCATATACAGAAACATGTTACACGCCATGGTTAGGTTG
1 TTACACGCCATGTACAAAAACATATGACATGACATGGTTAGGTTG
* * * *
1098232 TTACACGCCATGTAAAAAAACGTGTGACATGCCATGGTTAGGTTG
1 TTACACGCCATGTACAAAAACATATGACATGACATGGTTAGGTTG
* * *
1098277 TTACACGTCATGTACAAAAACATATTACATGACATGATTAGGTTG
1 TTACACGCCATGTACAAAAACATATGACATGACATGGTTAGGTTG
** * * * **
1098322 TTACACGCCATGTACAAAAATGTATGACACGTCATGGTTAAGTAA
1 TTACACGCCATGTACAAAAACATATGACATGACATGGTTAGGTTG
* * * *
1098367 TTACACGTCATGTAC--AAACATGTTACATGACATGGTTAAGTTG
1 TTACACGCCATGTACAAAAACATATGACATGACATGGTTAGGTTG
1098410 TTACA
1 TTACA
1098415 TACGATGTTA
Statistics
Matches: 150, Mismatches: 33, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
43 25 0.17
45 125 0.83
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (45 bp):
TTACACGCCATGTACAAAAACATATGACATGACATGGTTAGGTTG
Found at i:1098432 original size:90 final size:89
Alignment explanation
Indices: 1098199--1098414 Score: 290
Period size: 90 Copynumber: 2.4 Consensus size: 89
1098189 ACACACCATA
* * * * *
1098199 TACAGAAACATGTTACACGCCATGGTTAGGTTGTTACACGCCATGTAAAAAAACGTGTGACATGC
1 TACA-AAACATGTTACATGACATGGTTAGGTTGTTACACGCCATGTAAAAAAATGTATGACACGC
* **
1098264 CATGGTTAGGTTGTTACACGTCATG
65 CATGGTTAAGTAATTACACGTCATG
* * * *
1098289 TACAAAAACATATTACATGACATGATTAGGTTGTTACACGCCATGTACAAAAATGTATGACACGT
1 TAC-AAAACATGTTACATGACATGGTTAGGTTGTTACACGCCATGTAAAAAAATGTATGACACGC
1098354 CATGGTTAAGTAATTACACGTCATG
65 CATGGTTAAGTAATTACACGTCATG
*
1098379 TAC-AAACATGTTACATGACATGGTTAAGTTGTTACA
1 TACAAAACATGTTACATGACATGGTTAGGTTGTTACA
1098415 TACGATGTTA
Statistics
Matches: 110, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
88 30 0.27
90 79 0.72
91 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (89 bp):
TACAAAACATGTTACATGACATGGTTAGGTTGTTACACGCCATGTAAAAAAATGTATGACACGCC
ATGGTTAAGTAATTACACGTCATG
Found at i:1101846 original size:4 final size:4
Alignment explanation
Indices: 1101837--1101906 Score: 59
Period size: 4 Copynumber: 17.0 Consensus size: 4
1101827 TAAACAAAAT
* * * * * *
1101837 CATA CATA CATA CATA TATA TATA CACA CATG CATA CATA TATA TATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1101885 CACA CACGTA CATA CATA CATA
1 CATA CA--TA CATA CATA CATA
1101907 TATATATAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
4 51 0.94
6 3 0.06
ACGTcount: A:0.47, C:0.23, G:0.03, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:1101872 original size:24 final size:24
Alignment explanation
Indices: 1101840--1101910 Score: 106
Period size: 24 Copynumber: 2.9 Consensus size: 24
1101830 ACAAAATCAT
1101840 ACATACATACATATATATATACAC
1 ACATACATACATATATATATACAC
*
1101864 ACATGCATACATATATATATACAC
1 ACATACATACATATATATATACAC
*
1101888 ACACGTACATACATACATATATA
1 ACA--TACATACATATATATATA
1101911 TATAATATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
24 26 0.62
26 16 0.38
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.28
Consensus pattern (24 bp):
ACATACATACATATATATATACAC
Found at i:1101889 original size:26 final size:25
Alignment explanation
Indices: 1101840--1101910 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 25
1101830 ACAAAATCAT
1101840 ACATACATACATATATATAT-ACAC
1 ACATACATACATATATATATAACAC
*
1101864 ACATGCATACATATATATATACACAC
1 ACATACATACATATATATATA-ACAC
* *
1101890 ACGTACATACATACATATATA
1 ACATACATACATATATATATA
1101911 TATAATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 19 0.46
26 22 0.54
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.28
Consensus pattern (25 bp):
ACATACATACATATATATATAACAC
Found at i:1102180 original size:185 final size:183
Alignment explanation
Indices: 1101874--1102242 Score: 675
Period size: 185 Copynumber: 2.0 Consensus size: 183
1101864 ACATGCATAC
* *
1101874 ATATATATATACACACACGTACATACATACATATATATATAATATAACACATAATAAATATTGCA
1 ATATATATACACACACACATACATACATACATATATATATAATATAACACATAATAAATATTGCA
*
1101939 CTCTGGATGCAACCACATAATCCAACAAACATCTTTAGACATAGGCCATATCATTATCCCTAAAA
66 CTATGGATGCAACCACATAATCCAACAAACATCTTTAGACATAGGCCATATCATTATCCCTAAAA
* *
1102004 TCTCTAATGTGAAGGCCTACCATCATTCTTAATGTCTCTAAAGATTATCACAT
131 TCTCTAATGTGAAGGCATACCATCATTCTCAATGTCTCTAAAGATTATCACAT
1102057 ATATATATACACACACATACATACATACATACATATATATATAATATAACACATAATAAATATTG
1 ATATATATACACACAC--ACATACATACATACATATATATATAATATAACACATAATAAATATTG
1102122 CACTATGGATGCAACCACATAATCCAACAAACATCTTTAGACATAGGCCATATCATTATCCCTAA
64 CACTATGGATGCAACCACATAATCCAACAAACATCTTTAGACATAGGCCATATCATTATCCCTAA
1102187 AATCTCTAATGTGAAGGCATACCATCATTCTCAATGTCTCTAAAGATTATCACAT
129 AATCTCTAATGTGAAGGCATACCATCATTCTCAATGTCTCTAAAGATTATCACAT
1102242 A
1 A
1102243 CATCATTAGG
Statistics
Matches: 179, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
183 15 0.08
185 164 0.92
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (183 bp):
ATATATATACACACACACATACATACATACATATATATATAATATAACACATAATAAATATTGCA
CTATGGATGCAACCACATAATCCAACAAACATCTTTAGACATAGGCCATATCATTATCCCTAAAA
TCTCTAATGTGAAGGCATACCATCATTCTCAATGTCTCTAAAGATTATCACAT
Found at i:1103104 original size:10 final size:10
Alignment explanation
Indices: 1103074--1103107 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
1103064 TCTAGGCAAT
1103074 CATATATATA
1 CATATATATA
*
1103084 TATATATATA
1 CATATATATA
1103094 CATATATATA
1 CATATATATA
1103104 CATA
1 CATA
1103108 CACACATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (10 bp):
CATATATATA
Found at i:1110844 original size:9 final size:9
Alignment explanation
Indices: 1110830--1110860 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1110820 TTAAGTTTAA
1110830 GTGTATCAT
1 GTGTATCAT
1110839 GTGTATCAT
1 GTGTATCAT
*
1110848 ATGTATCAT
1 GTGTATCAT
1110857 GTGT
1 GTGT
1110861 TACGCGCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.45
Consensus pattern (9 bp):
GTGTATCAT
Found at i:1114642 original size:32 final size:32
Alignment explanation
Indices: 1114605--1114669 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
1114595 CAAGGTTTTG
1114605 AAGAATTTTGATACAAGAGAGGGGAGAAAAGA
1 AAGAATTTTGATACAAGAGAGGGGAGAAAAGA
1114637 AAGAATTTTGATACAAGAGAGGGGAGAAAAGA
1 AAGAATTTTGATACAAGAGAGGGGAGAAAAGA
1114669 A
1 A
1114670 TCTAAACAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.31, T:0.15
Consensus pattern (32 bp):
AAGAATTTTGATACAAGAGAGGGGAGAAAAGA
Found at i:1141280 original size:21 final size:20
Alignment explanation
Indices: 1141245--1141297 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
1141235 ACTCTTAAAG
*
1141245 TAAATTTAAAATAAAATAACT
1 TAAATTT-AACTAAAATAACT
1141266 TAAAATTTAACTAAAATAACT
1 T-AAATTTAACTAAAATAACT
1141287 TAAA-TTAACTA
1 TAAATTTAACTA
1141298 CTTAACAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 7 0.23
20 3 0.10
21 14 0.47
22 6 0.20
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAATTTAACTAAAATAACT
Found at i:1150806 original size:40 final size:41
Alignment explanation
Indices: 1150729--1150814 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 41
1150719 GATGACTTAT
* *
1150729 TCTTGATCATGAGCTAGAACTTGAGATTTTCGATTCAACG-G
1 TCTTGATCATGAACTAGAACTTGAGATCTTCGATTCAA-GAG
*
1150770 TCTTGATCATGAACTAG-ACTTGGGATCTTC-ACTTCAAGAG
1 TCTTGATCATGAACTAGAACTTGAGATCTTCGA-TTCAAGAG
1150810 TCTTG
1 TCTTG
1150815 GTGACTTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
39 2 0.05
40 22 0.55
41 16 0.40
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (41 bp):
TCTTGATCATGAACTAGAACTTGAGATCTTCGATTCAAGAG
Found at i:1150852 original size:54 final size:54
Alignment explanation
Indices: 1150770--1150900 Score: 165
Period size: 54 Copynumber: 2.4 Consensus size: 54
1150760 GATTCAACGG
** *
1150770 TCTTGATCATGAACTAGACTTGGGATCTTCACTTCAAGAGTCTTGGTGACTTAA
1 TCTTGATCACAAACTAGACTTGAGATCTTCACTTCAAGAGTCTTGGTGACTTAA
* * **
1150824 TCTTGATCACAAACTCA-ACTTGAGATCTTCATTTCAAGGGTCTTGGTGACTTGC
1 TCTTGATCACAAACT-AGACTTGAGATCTTCACTTCAAGAGTCTTGGTGACTTAA
* *
1150878 TCTTCATCACAAACAAGACTTGA
1 TCTTGATCACAAACTAGACTTGA
1150901 AAACTTCATT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
53 1 0.02
54 64 0.97
55 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (54 bp):
TCTTGATCACAAACTAGACTTGAGATCTTCACTTCAAGAGTCTTGGTGACTTAA
Found at i:1151563 original size:55 final size:55
Alignment explanation
Indices: 1151479--1151585 Score: 178
Period size: 55 Copynumber: 1.9 Consensus size: 55
1151469 NNNNNNNNTG
*
1151479 TGTCTTTGAAATAATCCAACCAATAAATTAATTATTTTATAATTAATTATATTGT
1 TGTCTTTAAAATAATCCAACCAATAAATTAATTATTTTATAATTAATTATATTGT
* * *
1151534 TGTCTTTAAAATGATCCAATCAATAAATTAATTATTTTCTAATTAATTATAT
1 TGTCTTTAAAATAATCCAACCAATAAATTAATTATTTTATAATTAATTATAT
1151586 GTTTATCTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (55 bp):
TGTCTTTAAAATAATCCAACCAATAAATTAATTATTTTATAATTAATTATATTGT
Found at i:1151595 original size:55 final size:55
Alignment explanation
Indices: 1151481--1151597 Score: 173
Period size: 55 Copynumber: 2.1 Consensus size: 55
1151471 NNNNNNTGTG
* *
1151481 TCTTTGAAATAATCCAACCAATAAATTAATTATTTTATAATTAATTATATTGTTG
1 TCTTTAAAATAATCCAACCAATAAATTAATTATTTTATAATTAATTATATTGTTA
* * *
1151536 TCTTTAAAATGATCCAATCAATAAATTAATTATTTTCTAATTAATTATA-TGTTTA
1 TCTTTAAAATAATCCAACCAATAAATTAATTATTTTATAATTAATTATATTG-TTA
1151591 TCTTTAA
1 TCTTTAA
1151598 TGATATCATC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 2 0.04
55 54 0.96
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.47
Consensus pattern (55 bp):
TCTTTAAAATAATCCAACCAATAAATTAATTATTTTATAATTAATTATATTGTTA
Found at i:1154881 original size:28 final size:29
Alignment explanation
Indices: 1154820--1154882 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
1154810 NNNNNNNNTA
* *
1154820 AAATGATGTGGTGCATATGTTTGGCACAT
1 AAATGATATAGTGCATATGTTTGGCACAT
* *
1154849 GAATGATATAGTGCAT-TGTTTGGCACTT
1 AAATGATATAGTGCATATGTTTGGCACAT
1154877 AAATGA
1 AAATGA
1154883 GTATGACATG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 16 0.55
29 13 0.45
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (29 bp):
AAATGATATAGTGCATATGTTTGGCACAT
Found at i:1155863 original size:229 final size:229
Alignment explanation
Indices: 1155455--1155874 Score: 549
Period size: 229 Copynumber: 1.8 Consensus size: 229
1155445 ACCCACGGAC
* * *
1155455 CACCATGGTGATATTTTAACATAAAGAATGACACATAAAATCATAAAATCAAAAGCTAACCTTGG
1 CACCATAGTGATATTTTAACACAAAGAATGACACATAAAATCATAAAATCAAAAGCTAACCTAGG
* * *
1155520 CAACATTATTTTGCTTAAACTAACAACCTCCTCAATGCAACTTGCGAACACCACAAGAAACAGGA
66 CAACATTATTCTGCTTAAACTAACAACCTCCTCAATGCAACTCGCGAACACCACAAGAAACAAGA
* *
1155585 ACCCTAGCCAATCAAGCTCTTGGTCTCCAATAGTAGTACATATGATTTCACCTCAACCTTTTAGC
131 ACCCTAGCCAATCAAGCTCTTGGTCTCCAATAGTACTACATACGATTTCACCTCAACCTTTTAGC
1155650 AAAGGAGGGAGAAAACATACCTTCAACCACAAAT
196 AAAGGAGGGAGAAAACATACCTTCAACCACAAAT
* * *
1155684 CACCATAGTGATATTTTAACACATAA-AATGGCATATAAAATCATAAAATCAGAAGCTAACCTAG
1 CACCATAGTGATATTTTAACACA-AAGAATGACACATAAAATCATAAAATCAAAAGCTAACCTAG
** * * * * * * * *
1155748 GCAATGTTCTTCTGCTTGGAA-TAATAATCTCTTCAATGCAACTCGTGTACACCACAAGAAGCAA
65 GCAACATTATTCTGCTT-AAACTAACAACCTCCTCAATGCAACTCGCGAACACCACAAGAAACAA
* ** * * *
1155812 GAACCGTAGCCAATCAAGCTCTTGG-CTTTTAATGGTACTACATACGATTTCACTTGAACCTTT
129 GAACCCTAGCCAATCAAGCTCTTGGTC-TCCAATAGTACTACATACGATTTCACCTCAACCTTT
1155875 CAATAAAGGA
Statistics
Matches: 161, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
228 1 0.01
229 156 0.97
230 4 0.02
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (229 bp):
CACCATAGTGATATTTTAACACAAAGAATGACACATAAAATCATAAAATCAAAAGCTAACCTAGG
CAACATTATTCTGCTTAAACTAACAACCTCCTCAATGCAACTCGCGAACACCACAAGAAACAAGA
ACCCTAGCCAATCAAGCTCTTGGTCTCCAATAGTACTACATACGATTTCACCTCAACCTTTTAGC
AAAGGAGGGAGAAAACATACCTTCAACCACAAAT
Found at i:1156630 original size:21 final size:22
Alignment explanation
Indices: 1156575--1156632 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 22
1156565 CCTGCGAAAG
*
1156575 CATAAAACTAAATTAATATTAA
1 CATAAAACTAAAATAATATTAA
1156597 C-T-AAACTAAAAATAAT-TTAA
1 CATAAAACT-AAAATAATATTAA
1156617 CATAAAACTAAAATAA
1 CATAAAACTAAAATAA
1156633 AACAGATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 10 0.31
21 16 0.50
22 6 0.19
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (22 bp):
CATAAAACTAAAATAATATTAA
Found at i:1166495 original size:16 final size:16
Alignment explanation
Indices: 1166476--1166508 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1166466 TCATATATAT
*
1166476 ATATATATATATACAC
1 ATATATATACATACAC
1166492 ATATATATACATACAC
1 ATATATATACATACAC
1166508 A
1 A
1166509 CATTCTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATATATACATACAC
Found at i:1166497 original size:18 final size:18
Alignment explanation
Indices: 1166474--1166511 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1166464 AATCATATAT
* *
1166474 ATATATATATATATACAC
1 ATATATATACATACACAC
1166492 ATATATATACATACACAC
1 ATATATATACATACACAC
1166510 AT
1 AT
1166512 TCTTATATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATATATACATACACAC
Found at i:1166501 original size:12 final size:12
Alignment explanation
Indices: 1166467--1166502 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1166457 TCTAGGCAAT
*
1166467 CATATATATATA
1 CATATATATACA
*
1166479 TATATATATACA
1 CATATATATACA
1166491 CATATATATACA
1 CATATATATACA
1166503 TACACACATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (12 bp):
CATATATATACA
Found at i:1185739 original size:18 final size:19
Alignment explanation
Indices: 1185699--1185741 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1185689 TTAATATTGT
*
1185699 AATATTATTTTATTTATAA
1 AATATTATTTTATTCATAA
1185718 AATATTATTTTATTCA-AA
1 AATATTATTTTATTCATAA
1185736 AATATT
1 AATATT
1185742 CTTTCTAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
AATATTATTTTATTCATAA
Found at i:1188085 original size:21 final size:21
Alignment explanation
Indices: 1188061--1188100 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1188051 CTAGAAAAAC
1188061 ACCTAAAATGCT-AAAATTTGA
1 ACCTAAAAT-CTCAAAATTTGA
1188082 ACCTAAAATCTCAAAATTT
1 ACCTAAAATCTCAAAATTT
1188101 TAGCTACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.30
Consensus pattern (21 bp):
ACCTAAAATCTCAAAATTTGA
Found at i:1199655 original size:35 final size:35
Alignment explanation
Indices: 1199608--1199796 Score: 200
Period size: 35 Copynumber: 5.3 Consensus size: 35
1199598 TCTCAAGTAC
*
1199608 TTGATTAAAATTGTTTAATTAAGTTGTTGGGCTTAA
1 TTGATT-AAATTGTTTAATTAAGTTATTGGGCTTAA
* * * * *
1199644 TTAATTAAATTGTTGAATTAAGTCATTAGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCTTAA
* * *
1199679 TTGATTAAAATTGCTTAATTAAGTCATTGGACATT-A
1 TTGATT-AAATTGTTTAATTAAGTTATTGGGC-TTAA
* * ***
1199715 TTGATTAAAATTGTTTAATTATGTTGTTCATCTTAA
1 TTGATT-AAATTGTTTAATTAAGTTATTGGGCTTAA
*
1199751 TTAATTAAATTGTTTAATTAAGTTATTGGGCTTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCTTAA
1199786 TTGATTAAATT
1 TTGATTAAATT
1199797 AAATGATTAA
Statistics
Matches: 124, Mismatches: 26, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
35 65 0.52
36 58 0.47
37 1 0.01
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (35 bp):
TTGATTAAATTGTTTAATTAAGTTATTGGGCTTAA
Found at i:1199683 original size:71 final size:71
Alignment explanation
Indices: 1199608--1199796 Score: 222
Period size: 71 Copynumber: 2.7 Consensus size: 71
1199598 TCTCAAGTAC
* *
1199608 TTGATTAAAATTGTTTAATTAAGTTGTTGGGCTTAATTAATTAAATTGTTGAATTAAGTCATT-A
1 TTGATTAAAATTGTTTAATTAAGTTATTGGGCTTAATTGATTAAATTGTTGAATTAAGTCATTCA
1199672 GGCCTAA
66 -GCCTAA
* * * * * **
1199679 TTGATTAAAATTGCTTAATTAAGTCATTGGACATT-ATTGATTAAAATTGTTTAATTATGTTGTT
1 TTGATTAAAATTGTTTAATTAAGTTATTGGGC-TTAATTGATT-AAATTGTTGAATTAAGTCATT
* *
1199743 CATCTTAA
64 CAGCCTAA
*
1199751 TTAATT-AAATTGTTTAATTAAGTTATTGGGCTTAATTGATTAAATT
1 TTGATTAAAATTGTTTAATTAAGTTATTGGGCTTAATTGATTAAATT
1199797 AAATGATTAA
Statistics
Matches: 99, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
70 7 0.07
71 63 0.64
72 28 0.28
73 1 0.01
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (71 bp):
TTGATTAAAATTGTTTAATTAAGTTATTGGGCTTAATTGATTAAATTGTTGAATTAAGTCATTCA
GCCTAA
Found at i:1204090 original size:15 final size:15
Alignment explanation
Indices: 1204070--1204099 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1204060 TACTCAGTAA
1204070 TTTTTAAAAATTACT
1 TTTTTAAAAATTACT
*
1204085 TTTTTAATAATTACT
1 TTTTTAAAAATTACT
1204100 AAATCTTTTC
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:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTTTAAAAATTACT
Found at i:1208403 original size:36 final size:36
Alignment explanation
Indices: 1208359--1208545 Score: 200
Period size: 36 Copynumber: 5.2 Consensus size: 36
1208349 TCTCAAGTAC
* ** *
1208359 TTGATTAAAATTGTTTAATTAATTTGTTGGGCTTAA
1 TTGATTAAAATTGTTTAATTAAGTCATTGGGCCTAA
* *
1208395 TT-ATTTAAATTGTTTAATTAAGTCATTAGGCCTAA
1 TTGATTAAAATTGTTTAATTAAGTCATTGGGCCTAA
1208430 TTGATTAAAATTGTTTAATTAAGTCATTGGGCCTAA
1 TTGATTAAAATTGTTTAATTAAGTCATTGGGCCTAA
* * ** * *
1208466 TTGATCAAAATTGTTCAATTAAGTTGTTCGGCTTAA
1 TTGATTAAAATTGTTTAATTAAGTCATTGGGCCTAA
* * * *
1208502 TTAATT-AAATTGTTTAATTGAGTTATTAGG-CTGAA
1 TTGATTAAAATTGTTTAATTAAGTCATTGGGCCT-AA
1208537 TTGATTAAA
1 TTGATTAAA
1208546 TTAAACAATT
Statistics
Matches: 126, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
34 1 0.01
35 56 0.44
36 69 0.55
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (36 bp):
TTGATTAAAATTGTTTAATTAAGTCATTGGGCCTAA
Found at i:1208434 original size:71 final size:72
Alignment explanation
Indices: 1208359--1208520 Score: 202
Period size: 71 Copynumber: 2.3 Consensus size: 72
1208349 TCTCAAGTAC
* ** * ** *
1208359 TTGATTAAAATTGTTTAATTAATTTGTTGGGCTTAATT-ATTTAAATTGTTTAATTAAGTCATTA
1 TTGATTAAAATTGTTTAATTAAGTCATTGGGCCTAATTGATCAAAATTGTTCAATTAAGTCATTA
1208423 GGCCTAA
66 GGCCTAA
** *
1208430 TTGATTAAAATTGTTTAATTAAGTCATTGGGCCTAATTGATCAAAATTGTTCAATTAAGTTGTTC
1 TTGATTAAAATTGTTTAATTAAGTCATTGGGCCTAATTGATCAAAATTGTTCAATTAAGTCATTA
*
1208495 GGCTTAA
66 GGCCTAA
*
1208502 TTAATT-AAATTGTTTAATT
1 TTGATTAAAATTGTTTAATT
1208521 GAGTTATTAG
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
71 47 0.60
72 31 0.40
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.46
Consensus pattern (72 bp):
TTGATTAAAATTGTTTAATTAAGTCATTGGGCCTAATTGATCAAAATTGTTCAATTAAGTCATTA
GGCCTAA
Found at i:1208561 original size:35 final size:35
Alignment explanation
Indices: 1208481--1208561 Score: 81
Period size: 35 Copynumber: 2.3 Consensus size: 35
1208471 CAAAATTGTT
* * * ***
1208481 CAATTAAGTTGTTCGGCTTAATTAATTAAATTGTT
1 CAATTAAGTTATTAGGCTGAATTAATTAAATTAAA
* * *
1208516 TAATTGAGTTATTAGGCTGAATTGATTAAATTAAA
1 CAATTAAGTTATTAGGCTGAATTAATTAAATTAAA
1208551 CAATTAAGTTA
1 CAATTAAGTTA
1208562 ACTAGGCTTC
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (35 bp):
CAATTAAGTTATTAGGCTGAATTAATTAAATTAAA
Found at i:1211657 original size:37 final size:36
Alignment explanation
Indices: 1211610--1211837 Score: 181
Period size: 37 Copynumber: 6.1 Consensus size: 36
1211600 GGTGATTCTA
* *
1211610 AATTATGCTATTATAAAGAGCACCTTCCAAGGATAAC
1 AATTGTGCTATTATAAAGAGCACCTT-CAAAGATAAC
* * *
1211647 AATTGTGCTATTATAAAGAACACATTCAAAGATTAGC
1 AATTGTGCTATTATAAAGAGCACCTTCAAAGA-TAAC
* * * *
1211684 AATTGTTGTGCAATTATAAAGTGCATCTTTCAAGGATAAC
1 AA---TTGTGCTATTATAAAGAGCA-CCTTCAAAGATAAC
* * *
1211724 AATTGTGCTATTATAAAGAGCACCCTCCAAAGTTAGC
1 AATTGTGCTATTATAAAGAGCA-CCTTCAAAGATAAC
* *
1211761 AATTGTGCTATTACAAAGAGCAGCCTTCAAAGATCGAC
1 AATTGTGCTATTATAAAGAGCA-CCTTCAAAGAT-AAC
* * * *
1211799 AA--GTGATATTATAAAAAACACCTTTCAAGGATCAAC
1 AATTGTGCTATTATAAAGAGCACC-TTCAAAGAT-AAC
1211835 AAT
1 AAT
1211838 AATTGTACAC
Statistics
Matches: 152, Mismatches: 31, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
35 2 0.01
36 32 0.21
37 85 0.56
38 3 0.02
40 22 0.14
41 8 0.05
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (36 bp):
AATTGTGCTATTATAAAGAGCACCTTCAAAGATAAC
Found at i:1211760 original size:77 final size:77
Alignment explanation
Indices: 1211619--1211766 Score: 226
Period size: 77 Copynumber: 1.9 Consensus size: 77
1211609 AAATTATGCT
*
1211619 ATTATAAAGAGCACCTTCCAAGGATAACAATTGTGCTATTATAAAGAACACATTCAAAGATTAGC
1 ATTATAAAGAGCACCTTCCAAGGATAACAATTGTGCTATTATAAAGAACACATCCAAAGATTAGC
1211684 AATTGTTGTGCA
66 AATTGTTGTGCA
* * * * *
1211696 ATTATAAAGTGCATCTTTCAAGGATAACAATTGTGCTATTATAAAGAGCACCCTCCAAAG-TTAG
1 ATTATAAAGAGCACCTTCCAAGGATAACAATTGTGCTATTATAAAGAACA-CATCCAAAGATTAG
1211760 CAATTGT
65 CAATTGT
1211767 GCTATTACAA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
77 57 0.89
78 7 0.11
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (77 bp):
ATTATAAAGAGCACCTTCCAAGGATAACAATTGTGCTATTATAAAGAACACATCCAAAGATTAGC
AATTGTTGTGCA
Found at i:1214554 original size:21 final size:21
Alignment explanation
Indices: 1214528--1214570 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1214518 CTCTTAAAAT
1214528 AATTTAAATAAAATAACTTAA
1 AATTTAAATAAAATAACTTAA
*
1214549 AATTTAACTAAAATAACTTAA
1 AATTTAAATAAAATAACTTAA
1214570 A
1 A
1214571 TTAATCACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTTAAATAAAATAACTTAA
Found at i:1215198 original size:32 final size:30
Alignment explanation
Indices: 1215151--1215209 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
1215141 TATTTGCTTA
1215151 AGTGGTTATAATTTAACCAATAGAAAAGGTAG
1 AGTGGTTATAATTTAACC-ATA-AAAAGGTAG
**
1215183 AGTGGTTATGCTTTAACCATAAAAAGG
1 AGTGGTTATAATTTAACCATAAAAAGG
1215210 CATTGTATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.24
31 3 0.12
32 16 0.64
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (30 bp):
AGTGGTTATAATTTAACCATAAAAAGGTAG
Found at i:1216061 original size:55 final size:55
Alignment explanation
Indices: 1215970--1216086 Score: 173
Period size: 55 Copynumber: 2.1 Consensus size: 55
1215960 TGACATTATT
* * *
1215970 AAAGATAATCATATAATTAATTATAAAGTAAATAATTTATTGGTTGGA-TCATTTC
1 AAAGACAACCATATAATTAATTATAAAATAAATAATTTATTGGTTGGACT-ATTTC
* *
1216025 AAAGACAACCATATAATTAATTATAAAATAATTAATTTATTGGTTGTACTATTTC
1 AAAGACAACCATATAATTAATTATAAAATAAATAATTTATTGGTTGGACTATTTC
1216080 AAAGACA
1 AAAGACA
1216087 TATAGTTGGA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
55 55 0.98
56 1 0.02
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (55 bp):
AAAGACAACCATATAATTAATTATAAAATAAATAATTTATTGGTTGGACTATTTC
Found at i:1216312 original size:55 final size:57
Alignment explanation
Indices: 1216249--1216354 Score: 162
Period size: 57 Copynumber: 1.9 Consensus size: 57
1216239 ATTGGCCATC
* *
1216249 TAATTTATCTCT-AA-AAATTATGATAATTTGGAGATAAAAATCAAATTTGATTATT
1 TAATTTATCTCTAAATAAATTAAGATAATTTAGAGATAAAAATCAAATTTGATTATT
* *
1216304 TAATTTATCTCTAAATAAATTAAGATAATTTAGAGATAAAACTTAAATTTG
1 TAATTTATCTCTAAATAAATTAAGATAATTTAGAGATAAAAATCAAATTTG
1216355 GCCAATCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
55 12 0.27
56 2 0.04
57 31 0.69
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (57 bp):
TAATTTATCTCTAAATAAATTAAGATAATTTAGAGATAAAAATCAAATTTGATTATT
Found at i:1216713 original size:54 final size:54
Alignment explanation
Indices: 1216569--1216713 Score: 175
Period size: 54 Copynumber: 2.7 Consensus size: 54
1216559 AGAAGACTTC
* ** *
1216569 TGAAGTAAAGT-TTTCAAGTCTAGTTTGTGATCAAGACTAAGTAGCCAAGACCAT
1 TGAAGTAAA-TATTTCAAGTCGAGTTCATGATCAAGATTAAGTAGCCAAGACCAT
* * * * * *
1216623 TGAAATAAAGATTTGAAGTTGAGTTCATGATCAAGATTAAGTTGCCAAGACCCT
1 TGAAGTAAATATTTCAAGTCGAGTTCATGATCAAGATTAAGTAGCCAAGACCAT
*
1216677 TGAAGTAAATATCTCAAGTCGAGTTCATGATCAAGAT
1 TGAAGTAAATATTTCAAGTCGAGTTCATGATCAAGAT
1216714 GAAGACACCA
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
54 75 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.30
Consensus pattern (54 bp):
TGAAGTAAATATTTCAAGTCGAGTTCATGATCAAGATTAAGTAGCCAAGACCAT
Found at i:1216725 original size:54 final size:54
Alignment explanation
Indices: 1216613--1216728 Score: 142
Period size: 54 Copynumber: 2.1 Consensus size: 54
1216603 GACTAAGTAG
* * * * ***
1216613 CCAAGACCATTGAAATAAAGATTTGAAGTTGAGTTCATGATCAAGATTAAGTTG
1 CCAAGACCATTGAAATAAAGATCTCAAGTCGAGTTCATGATCAAGATGAAGACA
* * *
1216667 CCAAGACCCTTGAAGTAAATATCTCAAGTCGAGTTCATGATCAAGATGAAGACA
1 CCAAGACCATTGAAATAAAGATCTCAAGTCGAGTTCATGATCAAGATGAAGACA
1216721 CCAAGACC
1 CCAAGACC
1216729 TTTTCTCATG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (54 bp):
CCAAGACCATTGAAATAAAGATCTCAAGTCGAGTTCATGATCAAGATGAAGACA
Found at i:1217608 original size:24 final size:25
Alignment explanation
Indices: 1217568--1217617 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
1217558 TAATCAAGAG
*
1217568 CCAATTAAATCCAAAATAATTGTTT
1 CCAATAAAATCCAAAATAATTGTTT
*
1217593 CCAATAAAATCC-AAATATTTGTTT
1 CCAATAAAATCCAAAATAATTGTTT
1217617 C
1 C
1217618 TTCACCTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (25 bp):
CCAATAAAATCCAAAATAATTGTTT
Found at i:1226090 original size:8 final size:8
Alignment explanation
Indices: 1226068--1226134 Score: 61
Period size: 8 Copynumber: 8.8 Consensus size: 8
1226058 ATAAAAAGTT
1226068 GAGAAAGA
1 GAGAAAGA
1226076 -AGAAAAGA
1 GAG-AAAGA
1226084 GAGAAAGA
1 GAGAAAGA
*
1226092 AAGAAAGA
1 GAGAAAGA
*
1226100 AAGAAAGA
1 GAGAAAGA
*
1226108 AAGAAAG-
1 GAGAAAGA
*
1226115 GAGGAAGA
1 GAGAAAGA
1226123 -AGAAA-A
1 GAGAAAGA
1226129 GAGAAA
1 GAGAAA
1226135 AGAAGGTCCG
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
6 1 0.02
7 16 0.31
8 32 0.63
9 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (8 bp):
GAGAAAGA
Found at i:1226092 original size:4 final size:4
Alignment explanation
Indices: 1226069--1226114 Score: 67
Period size: 4 Copynumber: 11.5 Consensus size: 4
1226059 TAAAAAGTTG
*
1226069 AGAA AG-A AGAAA AGAG AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
1 AGAA AGAA AG-AA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
1226115 GAGGAAGAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 3 0.08
4 32 0.84
5 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:1228701 original size:17 final size:18
Alignment explanation
Indices: 1228676--1228723 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
1228666 ACGATGGGCG
*
1228676 AAAAGAATATTTTA-AAT
1 AAAATAATATTTTAGAAT
1228693 AAAATAATATTTTTATGAAT
1 AAAATAATA-TTTTA-GAAT
1228713 AAAATAATATT
1 AAAATAATATT
1228724 AAAATATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 8 0.30
18 5 0.19
19 2 0.07
20 12 0.44
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
AAAATAATATTTTAGAAT
Found at i:1244942 original size:53 final size:53
Alignment explanation
Indices: 1244879--1244982 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 53
1244869 CCAGAGAAAG
1244879 AATAAAATTTTGT-GTTCTATATATTATAAAAGCAAACTTTGACTGAAGCCCTA
1 AATAAAATTTT-TCGTTCTATATATTATAAAAGCAAACTTTGACTGAAGCCCTA
*
1244932 AATAAAATTTTTCGTTCTATATATTATGAAAGCAAACTTTGACTGAAGCCC
1 AATAAAATTTTTCGTTCTATATATTATAAAAGCAAACTTTGACTGAAGCCC
1244983 AGATGCATTA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 1 0.02
53 48 0.98
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (53 bp):
AATAAAATTTTTCGTTCTATATATTATAAAAGCAAACTTTGACTGAAGCCCTA
Found at i:1261550 original size:11 final size:11
Alignment explanation
Indices: 1261534--1261559 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1261524 TTTTTTATGC
1261534 AATAAAATAAT
1 AATAAAATAAT
1261545 AATAAAATAAT
1 AATAAAATAAT
1261556 AATA
1 AATA
1261560 TCTTATTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:1269281 original size:80 final size:79
Alignment explanation
Indices: 1269143--1269439 Score: 326
Period size: 80 Copynumber: 3.7 Consensus size: 79
1269133 AGATTGTAAC
* * *
1269143 ATGTATGCCATGAAATGTATGTGATGATATAGTCATATATACTATGGGCTAAGTATGTAAGTGAT
1 ATGTATGCCATGAGATGTATGTGAT-AAATAGTCATATACACTATGGGCTAAGTATGTAAGTGAT
*
1269208 TTATAAGCTTATGAA
65 TTATAAGGTTATGAA
* * * * ** *
1269223 ATGTATGCCATGAGATGTATGTGTTAAGCATA-TCATTTACACTACGGGCAAAACATGTAAGTGG
1 ATGTATGCCATGAGATGTATGTGATAA--ATAGTCATATACACTATGGGCTAAGTATGTAAGTGA
*
1269287 TTTACAAGGTTATGAA
64 TTTATAAGGTTATGAA
* * * *
1269303 ATGTATGCTATGAGATGTATATGATGAGATAGTCATATACACTATGGGCTAAGTATGTAGGTGAT
1 ATGTATGCCATGAGATGTATGTGAT-AAATAGTCATATACACTATGGGCTAAGTATGTAAGTGAT
* * *
1269368 TTTTGAGGTTATAAA
65 TTATAAGGTTATGAA
* * * * *
1269383 ATATATGCAATGAGATGTATGTGTTAAAATAATCATATACACTATAGGCTAAGTATG
1 ATGTATGCCATGAGATGTATGTGAT-AAATAGTCATATACACTATGGGCTAAGTATG
1269440 ATGATAGTTT
Statistics
Matches: 178, Mismatches: 35, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
79 4 0.02
80 170 0.96
81 4 0.02
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.34
Consensus pattern (79 bp):
ATGTATGCCATGAGATGTATGTGATAAATAGTCATATACACTATGGGCTAAGTATGTAAGTGATT
TATAAGGTTATGAA
Done.