Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008010.1 Hibiscus syriacus cultivar Beakdansim tig00110472_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3152856
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 14
Found at i:284816 original size:7 final size:7
Alignment explanation
Indices: 284769--284799 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
284759 GTCAAAGAAA
284769 GTCAACG
1 GTCAACG
284776 GTCAACG
1 GTCAACG
284783 GTCAACG
1 GTCAACG
284790 GTCAACG
1 GTCAACG
284797 GTC
1 GTC
284800 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:284824 original size:22 final size:22
Alignment explanation
Indices: 284782--284848 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
284772 AACGGTCAAC
*
284782 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
284806 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
284828 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
284849 AGACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 31 0.74
24 11 0.26
ACGTcount: A:0.12, C:0.24, G:0.46, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:284863 original size:9 final size:9
Alignment explanation
Indices: 284845--284943 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
284835 GGTCGGGTCG
*
284845 GGTCAGACC
1 GGTCAAACC
284854 GGTCAAACC
1 GGTCAAACC
* *
284863 GATTCAGACC
1 G-GTCAAACC
284873 GGTCAAACC
1 GGTCAAACC
*
284882 GGTTCGAACC
1 GG-TCAAACC
*
284892 GGTTGAAACC
1 GG-TCAAACC
284902 GGTCAAACC
1 GGTCAAACC
284911 GGTCAGAACC
1 GGTCA-AACC
*
284921 GGTTGAAAACC
1 GG-T-CAAACC
284932 GGTCAAACC
1 GGTCAAACC
284941 GGT
1 GGT
284944 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:284869 original size:19 final size:19
Alignment explanation
Indices: 284847--284944 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
284837 TCGGGTCGGG
*
284847 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGGT
284866 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
284885 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
284904 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* *
284924 TGAAAACCGGTCAAACCGGT
1 T-CAGACCGGTCAAACCGGT
284944 T
1 T
284945 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.04
19 38 0.56
20 17 0.25
21 10 0.15
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:284902 original size:29 final size:31
Alignment explanation
Indices: 284870--284944 Score: 129
Period size: 29 Copynumber: 2.5 Consensus size: 31
284860 ACCGATTCAG
284870 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
284899 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
284929 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
284945 TCCAGCAGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.56
30 16 0.37
31 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:286430 original size:20 final size:21
Alignment explanation
Indices: 286400--286438 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
286390 ATTACAGGTA
286400 CAAATATGACAAAACCGGTCT
1 CAAATATGACAAAACCGGTCT
286421 CAAA-ATGACAAAACCGGT
1 CAAATATGACAAAACCGGT
286439 AAAACGCTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (21 bp):
CAAATATGACAAAACCGGTCT
Found at i:286804 original size:199 final size:198
Alignment explanation
Indices: 286489--287311 Score: 1166
Period size: 199 Copynumber: 4.1 Consensus size: 198
286479 ATAAGTATCG
* * *
286489 AAAATATCGAAAAATATAATTATAACGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATAC
1 AAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATAC
*
286554 CGGTTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATCTAACAAGTGTCGATACTTTTT
66 CGGTTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTTT
* * *
286619 CTCTAGATTGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATATATAACAAGTGTCGAT
131 CTCCAGAATGTATTTCAAAACCAAGTGCAC-AAAAAGTGTCGATACATTTATAACAAGTGTCGAT
286684 CCCA
195 CCCA
* * * * *
286688 AAAACATTGAAAACCATAATTATAATGTAATAGGTAAATTA-GCAATATAATCGGTCTAAATATA
1 AAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTC-ATGTAAACGGTCTAAATATA
* * *
286752 CCGGTTTTTGAGAAAACAGGTGTACAAACAGTATCGACACAAATAGAACAAGTGTCGATACTTTT
65 CCGGTTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTT
** * * * *
286817 GGTCCATAATGTATTTCAGAACCAAGTGCACATAAAAGTGTCGATACATTTAAAACAAGTATCGA
130 TCTCCAGAATGTATTTCAAAACCAAGTGCACA-AAAAGTGTCGATACATTTATAACAAGTGTCGA
286882 TCCCA
194 TCCCA
*
286887 AAAACATCGAAAAACATAATTATAATGCAATAGGTAAATTATTCATGTAAACGGTCTAAATATAC
1 AAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATAC
* *
286952 CGGTTTTTGAGAAAACAAGTGTACAAAAAGTATCGACACAAATATAACAAGTGCCGATACTTTTT
66 CGGTTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTTT
287017 CTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATTTATAACAAGTGTCGAT
131 CTCCAGAATGTATTTCAAAACCAAGTGCAC-AAAAAGTGTCGATACATTTATAACAAGTGTCGAT
287082 CCCA
195 CCCA
* * *
287086 AAAACATCG-AAAACTATAATTATAATGTAATAGGTAAATTA-ACAATGTAACCGGTCTAAATGT
1 AAAACATCGAAAAAC-ATAATTATAATGTAATAGGTAAATTATTC-ATGTAAACGGTCTAAATAT
* * * ** * * *
287149 ACCGATTTATGAGAAAACATGTATACATGAAGTATCGACACAAATACATCAAGTTTCGATACATT
64 ACCGGTTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATATAACAAGTGTCGATAC-TT
* * * * * *
287214 TTTGTCCAGACTATATTTTAAAAACCAAGTGCACAACAAAGTTTCGATACATTTATAACAATTGT
128 TTTCTCCAGAATGTA-TTTCAAAACCAAGTGCACAA-AAAGTGTCGATACATTTATAACAAGTGT
287279 CGATCCCA
191 CGATCCCA
*
287287 AAAATATCGAAAAACATAATTATAA
1 AAAACATCGAAAAACATAATTATAA
287312 CCAAATGTCT
Statistics
Matches: 556, Mismatches: 58, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
198 8 0.01
199 456 0.82
200 18 0.03
201 69 0.12
202 5 0.01
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (198 bp):
AAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATAC
CGGTTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATATAACAAGTGTCGATACTTTTT
CTCCAGAATGTATTTCAAAACCAAGTGCACAAAAAGTGTCGATACATTTATAACAAGTGTCGATC
CCA
Found at i:287192 original size:398 final size:400
Alignment explanation
Indices: 286489--287312 Score: 1296
Period size: 398 Copynumber: 2.1 Consensus size: 400
286479 ATAAGTATCG
* *
286489 AAAATATCGAAAAATATAATTATAACGTAATAGGTAAATTATTCATGTAAACGGTCTAAATATAC
1 AAAATATCGAAAAACATAATTATAACGCAATAGGTAAATTATTCATGTAAACGGTCTAAATATAC
* * *
286554 CGGTTTTTGAGAAAACATGTGTACAAAAAGTATCGACACAAATCTAACAAGTGTCGATACTTTTT
66 CGGTTTTTGAGAAAACAAGTGTACAAAAAGTATCGACACAAATATAACAAGTGCCGATACTTTTT
* *
286619 CTCTAGATTGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATATATAACAAGTGTCGAT
131 CTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATATATAACAAGTGTCGAT
* * *
286684 CCCAAAAACATTGAAAACCATAATTATAATGTAATAGGTAAATTAGCAATATAATCGGTCTAAAT
196 CCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAACAATATAACCGGTCTAAAT
* * * *
286749 ATACCGGTTTTTGAGAAAACAGGTGTACAAACAGTATCGACACAAATAGAACAAGTGTCGATAC-
261 ATACCGATTTATGAGAAAACAGGTATACAAACAGTATCGACACAAATACAACAAGTGTCGATACA
* * * *
286813 TTTTGGTCCATAATGTA-TTTCAGAACCAAGTGCACATA-AAAGTGTCGATACATTTAAAACAAG
326 TTTTGGTCCAGAATATATTTTAAAAACCAAGTGCACA-ACAAAGTGTCGATACATTTAAAACAAG
286876 TATCGATCCCA
390 TATCGATCCCA
* *
286887 AAAACATCGAAAAACATAATTATAATGCAATAGGTAAATTATTCATGTAAACGGTCTAAATATAC
1 AAAATATCGAAAAACATAATTATAACGCAATAGGTAAATTATTCATGTAAACGGTCTAAATATAC
286952 CGGTTTTTGAGAAAACAAGTGTACAAAAAGTATCGACACAAATATAACAAGTGCCGATACTTTTT
66 CGGTTTTTGAGAAAACAAGTGTACAAAAAGTATCGACACAAATATAACAAGTGCCGATACTTTTT
*
287017 CTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATTTATAACAAGTGTCGAT
131 CTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATATATAACAAGTGTCGAT
* *
287082 CCCAAAAACATCGAAAACTATAATTATAATGTAATAGGTAAATTAACAATGTAACCGGTCTAAAT
196 CCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAACAATATAACCGGTCTAAAT
* * * * *
287147 GTACCGATTTATGAGAAAACATGTATACATGA-AGTATCGACACAAATACATCAAGTTTCGATAC
261 ATACCGATTTATGAGAAAACAGGTATACA-AACAGTATCGACACAAATACAACAAGTGTCGATAC
* * * * *
287211 ATTTTTGTCCAGACTATATTTTAAAAACCAAGTGCACAACAAAGTTTCGATACATTTATAACAAT
325 ATTTTGGTCCAGAATATATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAACAAG
*
287276 TGTCGATCCCA
390 TATCGATCCCA
287287 AAAATATCGAAAAACATAATTATAAC
1 AAAATATCGAAAAACATAATTATAAC
287313 CAAATGTCTC
Statistics
Matches: 386, Mismatches: 36, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
398 298 0.77
399 15 0.04
400 73 0.19
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (400 bp):
AAAATATCGAAAAACATAATTATAACGCAATAGGTAAATTATTCATGTAAACGGTCTAAATATAC
CGGTTTTTGAGAAAACAAGTGTACAAAAAGTATCGACACAAATATAACAAGTGCCGATACTTTTT
CTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATATATAACAAGTGTCGAT
CCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAACAATATAACCGGTCTAAAT
ATACCGATTTATGAGAAAACAGGTATACAAACAGTATCGACACAAATACAACAAGTGTCGATACA
TTTTGGTCCAGAATATATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTAAAACAAGT
ATCGATCCCA
Found at i:288015 original size:31 final size:32
Alignment explanation
Indices: 287968--288155 Score: 158
Period size: 31 Copynumber: 6.0 Consensus size: 32
287958 GATCCTCGGT
* * *
287968 AACTGTCTATAGGTTCCGAT-GAACCTAGGTA
1 AACTGTCCATATGTTCCGATAGAACATAGGTA
* *
287999 AACTATCCATATGTTCC-TTAGAACATAGGTA
1 AACTGTCCATATGTTCCGATAGAACATAGGTA
* *
288030 TACTGTCCATATG-TCTCGA-AAAACATAGGTA
1 AACTGTCCATATGTTC-CGATAGAACATAGGTA
*
288061 ATTCTGTCCATATGTTCCG-TAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGATAGAACATAGGTA
* * *
288093 TACTGTCCATATG-TCTC-AAAAAACATAGGTA
1 AACTGTCCATATGTTC-CGATAGAACATAGGTA
** *
288124 ATTTTGTCCATATATTCCG-TAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGATAGAACATAGGTA
288156 TACCCTCGAC
Statistics
Matches: 124, Mismatches: 22, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
30 5 0.04
31 70 0.56
32 45 0.36
33 4 0.03
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (32 bp):
AACTGTCCATATGTTCCGATAGAACATAGGTA
Found at i:288073 original size:32 final size:31
Alignment explanation
Indices: 288020--288158 Score: 147
Period size: 32 Copynumber: 4.4 Consensus size: 31
288010 TGTTCCTTAG
288020 AACATAGGTATACTGTCCATATGTCTCGAAA
1 AACATAGGTATACTGTCCATATGTCTCGAAA
* * *
288051 AACATAGGTAATTCTGTCCATATGT-TCCGTAG
1 AACATAGGT-ATACTGTCCATATGTCT-CGAAA
*
288083 AACATAGGTATACTGTCCATATGTCTCAAAA
1 AACATAGGTATACTGTCCATATGTCTCGAAA
** * * *
288114 AACATAGGTAATTTTGTCCATATAT-TCCGTAG
1 AACATAGGT-ATACTGTCCATATGTCT-CGAAA
288146 AACATAGGTATAC
1 AACATAGGTATAC
288159 CCTCGACTCT
Statistics
Matches: 88, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
31 38 0.43
32 50 0.57
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (31 bp):
AACATAGGTATACTGTCCATATGTCTCGAAA
Found at i:288084 original size:63 final size:63
Alignment explanation
Indices: 288004--288158 Score: 274
Period size: 63 Copynumber: 2.5 Consensus size: 63
287994 AGGTAAACTA
* *
288004 TCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAAACATAGGTAATTCTG
1 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAAACATAGGTAATTCTG
*
288067 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAAACATAGGTAATTTTG
1 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAAACATAGGTAATTCTG
*
288130 TCCATATATTCCGTAGAACATAGGTATAC
1 TCCATATGTTCCGTAGAACATAGGTATAC
288159 CCTCGACTCT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 88 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (63 bp):
TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAAACATAGGTAATTCTG
Found at i:289293 original size:64 final size:64
Alignment explanation
Indices: 289139--289295 Score: 151
Period size: 64 Copynumber: 2.5 Consensus size: 64
289129 CAATGAAAGT
* * ** *
289139 ATGCATCGATGCACTA-CTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATCACTGGG
1 ATGCATCGATGCACTACCTG-TGCATCGATGCATAAAATGCATTCGATGTTGTATTATAAAAGAG
* * * * * *
289203 ATGCATCGATGCA-TGCCTTATACATCGATGCACT-AATTGCATTCGATGTTTTTATTTTAAAAG
1 ATGCATCGATGCACTACC-TGTGCATCGATGCA-TAAAATGCATTCGATG-TTGTATTATAAAAG
289266 AG
63 AG
289268 -TGCATCGATGCACTACCTGTGCATCGAT
1 ATGCATCGATGCACTACCTGTGCATCGAT
289296 ACACCTTCAA
Statistics
Matches: 74, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
63 1 0.01
64 58 0.78
65 15 0.20
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATGCATTCGATGTTGTATTATAAAAGAG
Found at i:292841 original size:32 final size:31
Alignment explanation
Indices: 292788--292969 Score: 224
Period size: 32 Copynumber: 5.8 Consensus size: 31
292778 TGTTCCTTAG
292788 AACATAGGTATACTGTCCATATGTCTCGAAA
1 AACATAGGTATACTGTCCATATGTCTCGAAA
* * *
292819 AACATAGGTAATTCTGTCCATATGT-TCCGTAG
1 AACATAGGT-ATACTGTCCATATGTCT-CGAAA
292851 AACATAGGTATACTGTCCATATGTCTCGAAA
1 AACATAGGTATACTGTCCATATGTCTCGAAA
* * *
292882 AACATAGGTAATTCTGTCCATATGT-TCCGTAG
1 AACATAGGT-ATACTGTCCATATGTCT-CGAAA
*
292914 AACATAGGTATACTGTCCATATGTCTCAAAA
1 AACATAGGTATACTGTCCATATGTCTCGAAA
**
292945 AACATAGGTAATTTTGTCCATATGT
1 AACATAGGT-ATACTGTCCATATGT
292970 TCCGTAGAAC
Statistics
Matches: 129, Mismatches: 15, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
31 62 0.48
32 67 0.52
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Consensus pattern (31 bp):
AACATAGGTATACTGTCCATATGTCTCGAAA
Found at i:292852 original size:63 final size:63
Alignment explanation
Indices: 292772--292989 Score: 400
Period size: 63 Copynumber: 3.5 Consensus size: 63
292762 AGGTAAACTA
*
292772 TCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAAACATAGGTAATTCTG
1 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAAACATAGGTAATTCTG
292835 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAAACATAGGTAATTCTG
1 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAAACATAGGTAATTCTG
* *
292898 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCAAAAAACATAGGTAATTTTG
1 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAAACATAGGTAATTCTG
*
292961 TCCATATGTTCCGTAGAACATATGTATAC
1 TCCATATGTTCCGTAGAACATAGGTATAC
292990 CATCGACTCT
Statistics
Matches: 151, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 151 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (63 bp):
TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAAACATAGGTAATTCTG
Found at i:292981 original size:32 final size:31
Alignment explanation
Indices: 292733--292989 Score: 254
Period size: 31 Copynumber: 8.2 Consensus size: 31
292723 AAAGATCCTC
* * *
292733 GGTA-ACTGTCTATAGGTTCCG-ATGAACCTA
1 GGTATACTGTCCATATGTTCCGTA-GAACATA
* * *
292763 GGTAAACTATCCATATGTTCCTTAGAACATA
1 GGTATACTGTCCATATGTTCCGTAGAACATA
* *
292794 GGTATACTGTCCATATG-TCTCGAAAAACATA
1 GGTATACTGTCCATATGTTC-CGTAGAACATA
*
292825 GGTAATTCTGTCCATATGTTCCGTAGAACATA
1 GGT-ATACTGTCCATATGTTCCGTAGAACATA
* *
292857 GGTATACTGTCCATATG-TCTCGAAAAACATA
1 GGTATACTGTCCATATGTTC-CGTAGAACATA
*
292888 GGTAATTCTGTCCATATGTTCCGTAGAACATA
1 GGT-ATACTGTCCATATGTTCCGTAGAACATA
** *
292920 GGTATACTGTCCATATG-TCTCAAAAAACATA
1 GGTATACTGTCCATATGTTC-CGTAGAACATA
**
292951 GGTAATTTTGTCCATATGTTCCGTAGAACATA
1 GGT-ATACTGTCCATATGTTCCGTAGAACATA
*
292983 TGTATAC
1 GGTATAC
292990 CATCGACTCT
Statistics
Matches: 185, Mismatches: 31, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
30 10 0.05
31 96 0.52
32 73 0.39
33 6 0.03
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (31 bp):
GGTATACTGTCCATATGTTCCGTAGAACATA
Found at i:295732 original size:30 final size:30
Alignment explanation
Indices: 295696--295888 Score: 341
Period size: 30 Copynumber: 6.4 Consensus size: 30
295686 TCCGAAGGAC
*
295696 CTATCCAGAGGTCATAAAGATCTTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
295726 CTATCCAGAGGTCATAAAGATCATCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
295756 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
295786 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
295816 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
295846 CTATCTAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
295876 CTGTCCATAGGTC
1 CTATCCAGAGGTC
295889 CCGAAGAACC
Statistics
Matches: 157, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 157 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:295905 original size:30 final size:30
Alignment explanation
Indices: 295862--295955 Score: 89
Period size: 31 Copynumber: 3.1 Consensus size: 30
295852 AGAGGTCATA
* * *
295862 AAGATCCTCGGTAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAACTGTCCATATGTCCCG
* * *
295892 AAGAACCTAGGTAAACTATCCATATGTTCCT
1 AAGAACCTAGGT-AACTGTCCATATGTCCCG
* * *
295923 TAGAACATAGGTATACTGTCCATATGTCTCG
1 AAGAACCTAGGTA-ACTGTCCATATGTCCCG
295954 AA
1 AA
295956 AGACATAGGT
Statistics
Matches: 49, Mismatches: 13, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
30 11 0.22
31 38 0.78
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (30 bp):
AAGAACCTAGGTAACTGTCCATATGTCCCG
Found at i:295905 original size:90 final size:90
Alignment explanation
Indices: 295696--295913 Score: 310
Period size: 90 Copynumber: 2.4 Consensus size: 90
295686 TCCGAAGGAC
* * * *
295696 CTATCCAGAGGTCATAAAGATCTTCGGTAACTATCCAGAGGTCATAAAGATCATCGGTAACTATC
1 CTATCCAGAGGTCACAAAGAACCTAGGTAACTATCCAGAGGTCATAAAGATCATCGGTAACTATC
295761 CAGAGGTCATAAAGATCCTCGGTAA
66 CAGAGGTCATAAAGATCCTCGGTAA
* * * *
295786 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCACAAAGAACCTAGGTAACTATCCAGAGGTCATAAAGATCATCGGTAACTATC
*
295851 TAGAGGTCATAAAGATCCTCGGTAA
66 CAGAGGTCATAAAGATCCTCGGTAA
* * * *
295876 CTGTCCATAGGTCCCGAAGAACCTAGGTAAACTATCCA
1 CTATCCAGAGGTCACAAAGAACCTAGGT-AACTATCCA
295914 TATGTTCCTT
Statistics
Matches: 117, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 108 0.92
91 9 0.08
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (90 bp):
CTATCCAGAGGTCACAAAGAACCTAGGTAACTATCCAGAGGTCATAAAGATCATCGGTAACTATC
CAGAGGTCATAAAGATCCTCGGTAA
Found at i:295962 original size:31 final size:30
Alignment explanation
Indices: 295871--295966 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
295861 AAAGATCCTC
* * *
295871 GGTAACTGTCCATAGGTCCCGAAGAACCTA
1 GGTAACTGTCCATATGTCTCGAAGAACATA
* **
295901 GGTAAACTATCCATATGT-TCCTTAGAACATA
1 GGT-AACTGTCCATATGTCT-CGAAGAACATA
295932 GGTATACTGTCCATATGTCTCGAA-AGACATA
1 GGTA-ACTGTCCATATGTCTCGAAGA-ACATA
295963 GGTA
1 GGTA
295967 GTTCTTTGAC
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
30 5 0.10
31 46 0.88
32 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (30 bp):
GGTAACTGTCCATATGTCTCGAAGAACATA
Found at i:297056 original size:40 final size:41
Alignment explanation
Indices: 297001--297097 Score: 108
Period size: 43 Copynumber: 2.3 Consensus size: 41
296991 TTTCTCTTGA
* *
297001 AGTGCATCAATGCATTC-AACA-GTGCATCGATGCATTCAAC
1 AGTGCATCGATGCATTCTAACATGTGCATCGATGCAGT-AAC
* *
297041 AGTGCATCGATGCATTCTTTAGCATGTGCATCGATGCAGTACC
1 AGTGCATCGATGCATTC--TAACATGTGCATCGATGCAGTAAC
*
297084 CGTGCATCGATGCA
1 AGTGCATCGATGCA
297098 CAAATCACCT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
40 16 0.33
43 18 0.38
44 14 0.29
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (41 bp):
AGTGCATCGATGCATTCTAACATGTGCATCGATGCAGTAAC
Found at i:297074 original size:24 final size:20
Alignment explanation
Indices: 297001--297097 Score: 106
Period size: 20 Copynumber: 4.7 Consensus size: 20
296991 TTTCTCTTGA
*
297001 AGTGCATCAATGCATTCAAC
1 AGTGCATCGATGCATTCAAC
297021 AGTGCATCGATGCATTCAAC
1 AGTGCATCGATGCATTCAAC
*
297041 AGTGCATCGATGCATTCTTTAGC
1 AGTGCATCGATGCATTC---AAC
* *
297064 ATGTGCATCGATGCAGT-ACC
1 A-GTGCATCGATGCATTCAAC
*
297084 CGTGCATCGATGCA
1 AGTGCATCGATGCA
297098 CAAATCACCT
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
19 13 0.19
20 38 0.56
23 3 0.04
24 14 0.21
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (20 bp):
AGTGCATCGATGCATTCAAC
Found at i:299464 original size:199 final size:197
Alignment explanation
Indices: 299049--299729 Score: 716
Period size: 198 Copynumber: 3.4 Consensus size: 197
299039 TTTTCAAAAA
* ** ** *
299049 GTATCGA-CCTCAAAAATATCGAAACAAATAATTATAATGTAATATTTAAATTAACAATGTAACC
1 GTATCGATCC-CAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACC
* * * *
299113 AGTATACATATACCAGTTAATTAT-A-AAACAT-G-TC-AACATAAAGTATCGACACTTTTTAAG
65 GGTATAAATATATCAGTT--TTATGAGAAA-ATAGATCTAA-ATAAAGTATCGACACTTTATAA-
* * * * * * *
299173 TTTGTGTCGATACTTTTTTCCA-AAAGAAAGCACAAACATGTTCACGCATAAAGTGTCGATACAT
125 TTTGTGTCGATACTTTTTTCCATAATGAATGCCCAAAGAGGTGCAAGCATAAAGTGTCGATACAT
299237 TTAAAATT
190 TTAAAATT
* * * *
299245 GTATCGATCACAAAAACATCGAAACCGATAATTATAATGTAATATGTCAATTTATAATGTAACCG
1 GTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * * * *
299310 GTTTAAATTTATCGGTTTTATGAGAAAATAGGTC-AGAATAAAGTATTGACACTTGTATAATTTG
66 GTATAAATATATCAGTTTTATGAGAAAATAGATCTA-AATAAAGTATCGACACTT-TATAATTTG
* * *
299374 TGTCGATACATTTTGTCCATAATGAATGCCCAATGAGGTGCAAGAATAAAGTGTCGATACATTTA
129 TGTCGATAC-TTTTTTCCATAATGAATGCCCAAAGAGGTGCAAGCATAAAGTGTCGATACATTTA
299439 AAATT
193 AAATT
* * * * * * *
299444 GTATCAATCCCAAGAACATCGAAA-TGAAAATTACAATGTTATAGGTAAATTTACAATGTACCCG
1 GTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * *
299508 GTATAAATATATCAGTTTTATGAGAAAATAGATCTAAATAATGTATCCACACCTTTATAGTTTGT
66 GTATAAATATATCAGTTTTATGAGAAAATAGATCTAAATAAAGTATCGACA-CTTTATAATTTGT
*
299573 GTCGATACTTTTTTCCAGAGTGAATTAGGAATGCCCAACGAGGTGCAAGCATAAAGTGTCGATAC
130 GTCGATACTTTTTTCC--A-T-AA-T--GAATGCCCAAAGAGGTGCAAGCATAAAGTGTCGATAC
299638 ATTTAAAATT
188 ATTTAAAATT
* * * **
299648 GTATCGATCCAAAAAACAACGAAACCAATAATTATAATACAATAGGTAAATTTACAATGCT-ACC
1 GTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATG-TAACC
*
299712 GGTATAAATATACCAGTT
65 GGTATAAATATATCAGTT
299730 AAATGCCTAT
Statistics
Matches: 404, Mismatches: 61, Indels: 31
0.81 0.12 0.06
Matches are distributed among these distances:
194 4 0.01
195 3 0.01
196 70 0.17
197 40 0.10
198 104 0.26
199 67 0.17
200 1 0.00
201 2 0.00
202 1 0.00
204 65 0.16
205 46 0.11
206 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (197 bp):
GTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
GTATAAATATATCAGTTTTATGAGAAAATAGATCTAAATAAAGTATCGACACTTTATAATTTGTG
TCGATACTTTTTTCCATAATGAATGCCCAAAGAGGTGCAAGCATAAAGTGTCGATACATTTAAAA
TT
Found at i:299793 original size:23 final size:23
Alignment explanation
Indices: 299743--299787 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
299733 TGCCTATTTT
*
299743 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
299766 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
299788 TGTTATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:301423 original size:131 final size:131
Alignment explanation
Indices: 301142--301629 Score: 608
Period size: 131 Copynumber: 3.7 Consensus size: 131
301132 CAATGTTATC
301142 AACATATTACCGTGTACATTGTTAATTTACATATTACTTTAAAGTAATATGTTTCGAAAA-TATA
1 AACAT-TTACCGTGTACATTGTTAATTTACATATTACTTTAAAGTAATATGTTTC-AAAATTATA
* * * * * *
301206 AGTATCGATAC-TTATATGA-CATTATCAATACTTGTATATTTACGCCTATTTTCATTATACCGA
64 AGTATCGATACTTTATAT-ATGAGTATCGATACTTGGACATTTACGACTATTTTCATTATACCGA
301269 TAGA
128 TAGA
** * *
301273 AATGTTTACCGTGTACATTGTTAATTTACATATTACTTTAAAATAATATATTTCAAAATTATAAG
1 AACATTTACCGTGTACATTGTTAATTTACATATTACTTTAAAGTAATATGTTTCAAAATTATAAG
* * * *
301338 TATCGATATTTTATAAATGAGTATCGATACTTGGACATTTAAGTCTATTTTCATTATACCGATAG
66 TATCGATACTTTATATATGAGTATCGATACTTGGACATTTACGACTATTTTCATTATACCGATAG
301403 A
131 A
* * ** *
301404 AACATTTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTTGAAATTAAAAG
1 AACATTTACCGTGTACATTGTTAATTTACATATTACTTTAAAGTAATATGTTTCAAAATTATAAG
* * *
301469 TATC-AGTACTTTGTATATGAGTATCGATACTTGGACATTTGCGACTATTTTCATTATA-CAAGT
66 TATCGA-TACTTTATATATGAGTATCGATACTTGGACATTTACGACTATTTTCATTATACCGA-T
*
301532 AAA
129 AGA
* * * * * **
301535 AACGTTTATCATGCACATTGTTAATTTACCTATTACTTTAAAGTAATATGTTTCAAAATTATTGG
1 AACATTTACCGTGTACATTGTTAATTTACATATTACTTTAAAGTAATATGTTTCAAAATTATAAG
* *
301600 TACCGATACTTTATATATGTGTATCGATAC
66 TATCGATACTTTATATATGAGTATCGATAC
301630 ATTTTGCATG
Statistics
Matches: 308, Mismatches: 43, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
129 4 0.01
130 65 0.21
131 238 0.77
132 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.41
Consensus pattern (131 bp):
AACATTTACCGTGTACATTGTTAATTTACATATTACTTTAAAGTAATATGTTTCAAAATTATAAG
TATCGATACTTTATATATGAGTATCGATACTTGGACATTTACGACTATTTTCATTATACCGATAG
A
Found at i:302155 original size:198 final size:198
Alignment explanation
Indices: 301549--302204 Score: 996
Period size: 199 Copynumber: 3.3 Consensus size: 198
301539 TTTATCATGC
* ** *
301549 ACATTGTTAATTTACCTATTACTTTAAAGTAATATGTTTCAAAATTAT-TGGTACCGATACTTTA
1 ACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATT-TCAAGTATCGATACTTTA
* *
301613 TATATGTGTATCGATACATTTTGCATGCAAATTGTTTGAGAAACATACTGAAATAAAAGTATCGA
65 TATA-GTGTATCGATACATTTTGCGTGCAAATTGTTTGAGAAACATACTGAAATAAAAGTATCCA
*
301678 TACCTATATAAAAGTATCGATACTTGGTATTTACACCTATTATCATTATATTGGTGGACTTTTAC
129 TACCTATATAAAAGTATCGATACTTGGTATTTACGCCTATTATCATTATATTGGTGGACTTTTAC
*
301743 CATTT
194 CGTTT
** *
301748 ACATTGTTAATTTATATATTACTTTAAAGTAATAGGTTTCGAAA-TTCAAAGTATCGATACTTTA
1 ACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTTC-AAGTATCGATACTTTA
* * ** *
301812 TATATGTGTATAGATACATTTTGCGTGTAAATTGTTTGAGAAGTATACTGAAATAAAAGTATTCA
65 TATA-GTGTATCGATACATTTTGCGTGCAAATTGTTTGAGAAACATACTGAAATAAAAGTATCCA
301877 TACCTATATAAAAGTATCGATACTTGGTATTTACGCCTATTATCATTATATTGGTGGACTTTTAC
129 TACCTATATAAAAGTATCGATACTTGGTATTTACGCCTATTATCATTATATTGGTGGACTTTTAC
301942 CGTTT
194 CGTTT
*
301947 ATATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTTCAAGTATCGATACTTTAT
1 ACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTTCAAGTATCGATACTTTAT
* *
302012 ACA-TGTATCGATACATTTTGCGTGCAAATTGTTTGAGAAACATACTGGAATAAAAGTATCCATA
66 ATAGTGTATCGATACATTTTGCGTGCAAATTGTTTGAGAAACATACTGAAATAAAAGTATCCATA
* ** *
302076 CCTATATAAAGAGTATCGATACTTGGTATTTACGCCTATTATCATTATACTGGTACACTTTTATC
131 CCTATATAAA-AGTATCGATACTTGGTATTTACGCCTATTATCATTATATTGGTGGACTTTTACC
302141 GTTT
195 GTTT
* * *
302145 ACATTGTTAATTTACTTATTACTTTAAAGTAATAGG-TTCTGAAATTCCAAGTATCGATAC
1 ACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTC-AAAATTTCAAGTATCGATAC
302205 ATTTTGCGTG
Statistics
Matches: 417, Mismatches: 35, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
197 69 0.17
198 107 0.26
199 238 0.57
200 3 0.01
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (198 bp):
ACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTTCAAGTATCGATACTTTAT
ATAGTGTATCGATACATTTTGCGTGCAAATTGTTTGAGAAACATACTGAAATAAAAGTATCCATA
CCTATATAAAAGTATCGATACTTGGTATTTACGCCTATTATCATTATATTGGTGGACTTTTACCG
TTT
Found at i:305594 original size:35 final size:35
Alignment explanation
Indices: 305529--305596 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
305519 CATTCAAAAA
*
305529 GTATCGATACCTAGGAGGGTGGTATCGATACCATGG
1 GTATCGATACCTA-GAGGGAGGTATCGATACCATGG
305565 GTATCGATACCCTA-AGGGAGGTATCGATACCA
1 GTATCGATA-CCTAGAGGGAGGTATCGATACCA
305597 GAAAATATCG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
35 17 0.57
36 9 0.30
37 4 0.13
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (35 bp):
GTATCGATACCTAGAGGGAGGTATCGATACCATGG
Found at i:306898 original size:68 final size:68
Alignment explanation
Indices: 306787--306922 Score: 263
Period size: 68 Copynumber: 2.0 Consensus size: 68
306777 TGATGATGTG
306787 GGTATTGTTTGGTTAAATGAGTCGTATGTTGATTAAAAGGTTAGGTACAAGAGGATAAAATTAAA
1 GGTATTGTTTGGTTAAATGAGTCGTATGTTGATTAAAAGGTTAGGTACAAGAGGATAAAATTAAA
306852 GAT
66 GAT
*
306855 GGTATTGTTTGGTTAAATGAGTCGTATGTTGATTAAAATGTTAGGTACAAGAGGATAAAATTAAA
1 GGTATTGTTTGGTTAAATGAGTCGTATGTTGATTAAAAGGTTAGGTACAAGAGGATAAAATTAAA
306920 GAT
66 GAT
306923 ATAAATGATA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.35
Consensus pattern (68 bp):
GGTATTGTTTGGTTAAATGAGTCGTATGTTGATTAAAAGGTTAGGTACAAGAGGATAAAATTAAA
GAT
Found at i:307731 original size:20 final size:20
Alignment explanation
Indices: 307706--307799 Score: 77
Period size: 20 Copynumber: 4.7 Consensus size: 20
307696 TCTTTATTAG
*
307706 TTTTGTCAAATTTAAATTGA
1 TTTTGTCAAATTTAAATCGA
* * *
307726 TTTTGTCAATTTTCAATCGG
1 TTTTGTCAAATTTAAATCGA
*
307746 TTTTGTCAAATTCGTTACAT-G-
1 TTTTGTCAAA-T--TTAAATCGA
*
307767 TTTTGTCAAATTGAAATCAGA
1 TTTTGTCAAATTTAAATC-GA
307788 -TTTGTCAAATTT
1 TTTTGTCAAATTT
307800 TATCTTGTTA
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
18 4 0.07
20 38 0.66
21 11 0.19
22 1 0.02
23 4 0.07
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.48
Consensus pattern (20 bp):
TTTTGTCAAATTTAAATCGA
Found at i:320617 original size:16 final size:16
Alignment explanation
Indices: 320577--320624 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
320567 GGATAAATTA
*
320577 AATTTGAGTTGCTTTC
1 AATTTGAGTTACTTTC
* *
320593 AAATCGAGTTACTTTC
1 AATTTGAGTTACTTTC
* *
320609 ATTTTGAGTTATTTTC
1 AATTTGAGTTACTTTC
320625 GGTTCAAGTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (16 bp):
AATTTGAGTTACTTTC
Found at i:325779 original size:24 final size:25
Alignment explanation
Indices: 325729--325780 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
325719 TTTATTTTCT
*
325729 TAAAATTTTAAAAATCTATCTCTCC
1 TAAAATTTTAAAAATCTATATCTCC
325754 TAAAATTTTAAAAAAT-TATATC-CC
1 TAAAATTTT-AAAAATCTATATCTCC
325778 TAA
1 TAA
325781 CATTATTACG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 5 0.20
25 14 0.56
26 6 0.24
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (25 bp):
TAAAATTTTAAAAATCTATATCTCC
Found at i:329802 original size:22 final size:22
Alignment explanation
Indices: 329774--329833 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
329764 GGTCTACTTA
*
329774 GTCCTTCGGGACATATACAGAG
1 GTCCTTCGGGACAAATACAGAG
* *
329796 GTCCTTCGGGGCAAATACATAG
1 GTCCTTCGGGACAAATACAGAG
*
329818 GT-CTTCCGAGACAAAT
1 GTCCTT-CGGGACAAAT
329834 TTCACATACC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 3 0.09
22 29 0.91
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.23
Consensus pattern (22 bp):
GTCCTTCGGGACAAATACAGAG
Found at i:329910 original size:16 final size:17
Alignment explanation
Indices: 329891--329924 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
329881 GTGCACAACC
329891 TCTATAG-ACTCACATA
1 TCTATAGTACTCACATA
*
329907 TCTATAGTTCTCACATA
1 TCTATAGTACTCACATA
329924 T
1 T
329925 GTACATGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (17 bp):
TCTATAGTACTCACATA
Found at i:361579 original size:24 final size:25
Alignment explanation
Indices: 361552--361607 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
361542 AAATATTTTA
*
361552 TCTGATTTC-TGACTTGAATTATGT
1 TCTGATTTCATGACCTGAATTATGT
* *
361576 TCTGA-TACATGACCTGAATTCTGT
1 TCTGATTTCATGACCTGAATTATGT
361600 TCTGATTT
1 TCTGATTT
361608 GGATTCCGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 2 0.08
24 23 0.88
25 1 0.04
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.46
Consensus pattern (25 bp):
TCTGATTTCATGACCTGAATTATGT
Found at i:373924 original size:9 final size:9
Alignment explanation
Indices: 373907--373999 Score: 123
Period size: 9 Copynumber: 10.0 Consensus size: 9
373897 ACCTGCTCAG
373907 GACGATGAC
1 GACGATGAC
*
373916 GATGATGAC
1 GACGATGAC
*
373925 GACGACGAC
1 GACGATGAC
*
373934 GACGATGAT
1 GACGATGAC
373943 GACGATGAC
1 GACGATGAC
373952 GACGATGAC
1 GACGATGAC
373961 GACGATGAC
1 GACGATGAC
373970 GACGATGAC
1 GACGATGAC
*
373979 AATGACGACGAC
1 ---GACGATGAC
373991 GACGATGAC
1 GACGATGAC
374000 AGCGAGGAGT
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
9 65 0.89
12 8 0.11
ACGTcount: A:0.34, C:0.22, G:0.32, T:0.12
Consensus pattern (9 bp):
GACGATGAC
Found at i:373993 original size:6 final size:6
Alignment explanation
Indices: 373907--373995 Score: 79
Period size: 6 Copynumber: 14.8 Consensus size: 6
373897 ACCTGCTCAG
* * * * * *
373907 GACGAT GACGAT GATGAC GACGAC GACGAC GATGAT GACGAT GACGAC
1 GACGAC GACGAC GACGAC GACGAC GACGAC GACGAC GACGAC GACGAC
* * * * *
373955 GATGAC GACGAT GACGAC GATGAC AATGAC GACGAC GACGA
1 GACGAC GACGAC GACGAC GACGAC GACGAC GACGAC GACGA
373996 TGACAGCGAG
Statistics
Matches: 68, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.35, C:0.21, G:0.33, T:0.11
Consensus pattern (6 bp):
GACGAC
Found at i:374183 original size:26 final size:24
Alignment explanation
Indices: 374112--374183 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
374102 TTATATTTGT
374112 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
374137 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
374159 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
374184 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:374251 original size:35 final size:35
Alignment explanation
Indices: 374211--374290 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 35
374201 GTATTACAGT
374211 TAATTTTGTT-T-A-TTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATCATTTACCATTTAAT-TC--TTATTG
374246 TAA-TTTGATTATCATTTACCATTTAATTCTTATTG
1 TAATTTTG-TTATCATTTACCATTTAATTCTTATTG
374281 TAATTTTGTT
1 TAATTTTGTT
374291 GTTTTTAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
34 4 0.10
35 16 0.40
36 5 0.12
37 3 0.08
38 12 0.30
ACGTcount: A:0.28, C:0.09, G:0.07, T:0.56
Consensus pattern (35 bp):
TAATTTTGTTATCATTTACCATTTAATTCTTATTG
Found at i:377600 original size:14 final size:13
Alignment explanation
Indices: 377566--377602 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
377556 AATAAGTATA
377566 ATAA-AAAAATTT
1 ATAACAAAAATTT
377578 ATAAC-AAAATTT
1 ATAACAAAAATTT
377590 ATAACGAAAAATT
1 ATAAC-AAAAATT
377603 GCACAAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 16 0.73
14 6 0.27
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (13 bp):
ATAACAAAAATTT
Found at i:377969 original size:51 final size:51
Alignment explanation
Indices: 377863--377974 Score: 127
Period size: 51 Copynumber: 2.2 Consensus size: 51
377853 CTACGTGGCG
* ** * *
377863 TATAACGCGGAACAGAGGGCGCGCTATACCCACGTGTAAGCCATGTCAGCG
1 TATAGCGCGGAACAGAGGGCGCGCTATACCCACGTGTAAGCCAAATCAACA
* * * *
377914 TATAGCGCGGTACAGGGGGTGCGCTATACCCCACGTG-ACGCCAAATCAACA
1 TATAGCGCGGAACAGAGGGCGCGCTATA-CCCACGTGTAAGCCAAATCAACA
377965 TATAGCGCGG
1 TATAGCGCGG
377975 GGTAGGGAGC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
51 43 0.84
52 8 0.16
ACGTcount: A:0.27, C:0.28, G:0.29, T:0.16
Consensus pattern (51 bp):
TATAGCGCGGAACAGAGGGCGCGCTATACCCACGTGTAAGCCAAATCAACA
Found at i:377989 original size:51 final size:51
Alignment explanation
Indices: 377863--377989 Score: 114
Period size: 51 Copynumber: 2.5 Consensus size: 51
377853 CTACGTGGCG
* * ** * *
377863 TATAACGCGGAACAGAGG-GCGCGCTATACCCACGTGTAAGCCATGTCAGCG
1 TATAGCGCGGGACAG-GGAGCGCGCTATACCCACGTGTAAGCCAAATCAACA
* * * *
377914 TATAGCGCGGTACAGGGGGTGCGCTATACCCCACGTG-ACGCCAAATCAACA
1 TATAGCGCGGGACAGGGAGCGCGCTATA-CCCACGTGTAAGCCAAATCAACA
**
377965 TATAGCGCGGGGTAGGGAGCGCGCT
1 TATAGCGCGGGACAGGGAGCGCGCT
377990 TTACTGCTAC
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
50 2 0.03
51 51 0.84
52 8 0.13
ACGTcount: A:0.25, C:0.27, G:0.32, T:0.16
Consensus pattern (51 bp):
TATAGCGCGGGACAGGGAGCGCGCTATACCCACGTGTAAGCCAAATCAACA
Found at i:378472 original size:14 final size:14
Alignment explanation
Indices: 378453--378479 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
378443 TAACTTCTGA
378453 AATTTTTATTATGT
1 AATTTTTATTATGT
378467 AATTTTTATTATG
1 AATTTTTATTATG
378480 GAGAAAGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (14 bp):
AATTTTTATTATGT
Found at i:390515 original size:23 final size:23
Alignment explanation
Indices: 390472--390516 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
390462 CTCCCGATTT
*
390472 TCTTCATTGTTCATTTATGTTCA
1 TCTTCATTGTTCATTCATGTTCA
*
390495 TCTTC-TTGTTCGTTCATTGTTC
1 TCTTCATTGTTCATTCA-TGTTC
390517 TTCATTGCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.11, C:0.20, G:0.11, T:0.58
Consensus pattern (23 bp):
TCTTCATTGTTCATTCATGTTCA
Found at i:391815 original size:18 final size:17
Alignment explanation
Indices: 391761--391809 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
391751 TTGGATCCTT
* *
391761 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
391779 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
391797 AGTGCATTCGATG
1 AGTGCA-TCGATG
391810 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:400338 original size:18 final size:17
Alignment explanation
Indices: 400284--400332 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
400274 TTGGATCCTT
* *
400284 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
400302 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
400320 AGTGCATTCGATG
1 AGTGCA-TCGATG
400333 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:400437 original size:65 final size:64
Alignment explanation
Indices: 400278--400463 Score: 216
Period size: 65 Copynumber: 2.9 Consensus size: 64
400268 TAACCGTTGG
* * *
400278 ATCCTTAGTGCATCGGTGCACTAAG-AGTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAA
1 ATCCTCAGTGCATCGGTGCA-T-GGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAA
400341 T
64 T
* ** * * *
400342 AGCCAGAGTGCATCGATACATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA
1 ATCCTCAGTGCATCGGTGCATGG-TAGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAA
400407 -
64 T
*
400407 ATCCTCAGTGCATCGGTGCATGGTATGTGCATCGATGCATGAAATGCATTCGATGTT
1 ATCCTCAGTGCATCGGTGCATGGTA-GTGCATCGATGCATCAAATGCATTCGATGTT
400464 CAATTTAATT
Statistics
Matches: 102, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 44 0.43
65 53 0.52
66 3 0.03
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (64 bp):
ATCCTCAGTGCATCGGTGCATGGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAT
Found at i:400482 original size:129 final size:130
Alignment explanation
Indices: 400278--400513 Score: 293
Period size: 129 Copynumber: 1.8 Consensus size: 130
400268 TAACCGTTGG
* *
400278 ATCCTTAGTGCATCGGTGCACTAAGAGTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATA
1 ATCCTCAGTGCATCGGTGCACTAAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATA
*
400343 GCCAGAGTGCATCGATACATGG-CTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA
66 GCCAGAGTGCATCGATACATGGACTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA
* * **
400407 ATCCTCAGTGCATCGGTGCA-T-GGTATGTGCATCGATGCATGAAATGCATTCGATG-TTCAATT
1 ATCCTCAGTGCATCGGTGCACTAAG-A-GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAA
** * * *
400469 TAATTCATG-GTGCATCGATGCATGGATTAGTGCATCGGTGCATCA
64 T-AGCCA-GAGTGCATCGATACATGGACTAGTGCATCGATGCATCA
400514 CTCTGAAAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
127 1 0.01
128 8 0.09
129 64 0.71
130 17 0.19
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (130 bp):
ATCCTCAGTGCATCGGTGCACTAAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATA
GCCAGAGTGCATCGATACATGGACTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA
Found at i:400502 original size:65 final size:63
Alignment explanation
Indices: 400303--400513 Score: 214
Period size: 65 Copynumber: 3.3 Consensus size: 63
400293 GTGCACTAAG
* * ** *
400303 AGTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATACATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGG-T
* * *
400367 GGTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGGTGCATGG
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGG
400430 T
63 T
* *
400431 ATGTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGA
1 A-GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCATGG-
400495 TT
63 -T
*
400497 AGTGCATCGGTGCATCA
1 AGTGCATCGATGCATCA
400514 CTCTGAAAAA
Statistics
Matches: 122, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 51 0.42
65 61 0.50
66 2 0.02
67 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (63 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGT
Found at i:406114 original size:125 final size:125
Alignment explanation
Indices: 405891--406227 Score: 620
Period size: 125 Copynumber: 2.7 Consensus size: 125
405881 ACAGCCCATC
* *
405891 GGTGCCATATAACCACTGCATGAACGTCGTCAGGTAAAGAAAAAAAATTATTAGGGATTATGGAT
1 GGTGCCATATAACCACTGCATGAACGTCGTCAGATAAAGAAAAAAAA-TATTAGGGATTATGGAA
405956 CCAATAGTATGACAAATGGCAATCTGATTTTACTGAAAACAGCCCATCGGTGGCATATTCT
65 CCAATAGTATGACAAATGGCAATCTGATTTTACTGAAAACAGCCCATCGGTGGCATATTCT
*
406017 GGTGCCATATAACCACTGCATGAACGTCGTCAGATAAATAAAAAAAATATTAGGGATTATGGAAC
1 GGTGCCATATAACCACTGCATGAACGTCGTCAGATAAAGAAAAAAAATATTAGGGATTATGGAAC
406082 CAATAGTATGACAAATGGCAATCTGATTTTACTGAAAACAGCCCATCGGTGGCATATTCT
66 CAATAGTATGACAAATGGCAATCTGATTTTACTGAAAACAGCCCATCGGTGGCATATTCT
*
406142 GGTGCCATATAACCACTGCATGAACGTCGTCAGATAAAGAAAAAAATTTATTAGGGATTATGGAA
1 GGTGCCATATAACCACTGCATGAACGTCGTCAGATAAAGAAAAAAA-ATATTAGGGATTATGGAA
406207 CCAATAGTATGACAAATGGCA
65 CCAATAGTATGACAAATGGCA
406228 TAAAACAACA
Statistics
Matches: 205, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
125 122 0.60
126 83 0.40
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (125 bp):
GGTGCCATATAACCACTGCATGAACGTCGTCAGATAAAGAAAAAAAATATTAGGGATTATGGAAC
CAATAGTATGACAAATGGCAATCTGATTTTACTGAAAACAGCCCATCGGTGGCATATTCT
Found at i:411928 original size:23 final size:23
Alignment explanation
Indices: 411902--411968 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
411892 CCACAGCTCA
411902 TATAATTGCACCAAAGTGCCACG
1 TATAATTGCACCAAAGTGCCACG
** **
411925 TATAATTGCACCGGAGTGCCGTG
1 TATAATTGCACCAAAGTGCCACG
* *
411948 TAGAATTGCACCATAGTGCCA
1 TATAATTGCACCAAAGTGCCA
411969 TATAATAATG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
TATAATTGCACCAAAGTGCCACG
Found at i:412155 original size:103 final size:103
Alignment explanation
Indices: 411984--412201 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
411974 TAATGTCCAT
* *
411984 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
412049 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
412087 AAGGACCACATATCATTCCTTAAGAATGATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
412152 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
412190 AAGGACCACATA
1 AAGGACCACATA
412202 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:421224 original size:13 final size:13
Alignment explanation
Indices: 421208--421233 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
421198 TTTGTCAATA
421208 ATACCTATTAATT
1 ATACCTATTAATT
421221 ATACCTATTAATT
1 ATACCTATTAATT
421234 GATTCATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (13 bp):
ATACCTATTAATT
Found at i:421588 original size:21 final size:21
Alignment explanation
Indices: 421547--421610 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
421537 ATTCAAAAAG
* *
421547 GGGAATCGATTCCCCTACTACA
1 GGGAATCGA-TACCCTGCTACA
421569 GGGAATCGATACCCTGCTACA
1 GGGAATCGATACCCTGCTACA
*
421590 GGGAATCGATATCCTGCTACA
1 GGGAATCGATACCCTGCTACA
421611 ATACTGCTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
21 30 0.77
22 9 0.23
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (21 bp):
GGGAATCGATACCCTGCTACA
Found at i:422384 original size:24 final size:24
Alignment explanation
Indices: 422357--422422 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
422347 AGCTCGTATA
422357 AATTTGCAGT-GTAGTGCCACGTAG
1 AATTTGCA-TCGTAGTGCCACGTAG
* *
422381 AATTTGCATCGAAGTGCCGCGTAG
1 AATTTGCATCGTAGTGCCACGTAG
*
422405 AA-ATGCATCGTAGTGCCA
1 AATTTGCATCGTAGTGCCA
422423 TATAAGATTC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 14 0.39
24 22 0.61
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (24 bp):
AATTTGCATCGTAGTGCCACGTAG
Found at i:423501 original size:22 final size:21
Alignment explanation
Indices: 423460--423499 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
423450 TTTTTTCTTT
423460 AGGGGGGAATCGATACCCCTC
1 AGGGGGGAATCGATACCCCTC
423481 AGGGGGGAATCTG-TACCCC
1 AGGGGGGAATC-GATACCCC
423500 CTGCACAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.23, C:0.28, G:0.35, T:0.15
Consensus pattern (21 bp):
AGGGGGGAATCGATACCCCTC
Found at i:424274 original size:26 final size:28
Alignment explanation
Indices: 424226--424277 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
424216 ATTGTTTTAG
*
424226 ATATTAATTTATTATTATGATATTTCTC
1 ATATTAATTTATTATTATAATATTTCTC
*
424254 ATATT-ATTT-TTATTTTAATATTTC
1 ATATTAATTTATTATTATAATATTTC
424278 CACAGCTCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 13 0.59
27 4 0.18
28 5 0.23
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (28 bp):
ATATTAATTTATTATTATAATATTTCTC
Found at i:425266 original size:19 final size:20
Alignment explanation
Indices: 425238--425285 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
425228 AGCTTTGATG
* *
425238 AAATTAATTTTCAAAAT-TT
1 AAATTTATTTTAAAAATATT
425257 AAATTTATTTTAAAAATATT
1 AAATTTATTTTAAAAATATT
425277 AAATTTATT
1 AAATTTATT
425286 ATTATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATTTATTTTAAAAATATT
Found at i:425667 original size:9 final size:9
Alignment explanation
Indices: 425653--425688 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
425643 TAGCTTACAG
425653 AATAAAATA
1 AATAAAATA
425662 AATAAAATA
1 AATAAAATA
* *
425671 ATTAAAATT
1 AATAAAATA
425680 AATAAAATA
1 AATAAAATA
425689 TACTTCAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
AATAAAATA
Found at i:442371 original size:2 final size:2
Alignment explanation
Indices: 442366--442400 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
442356 ACAAAAAATC
442366 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
442401 TTTAATGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:442821 original size:2 final size:2
Alignment explanation
Indices: 442814--442859 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
442804 AAAAATATTT
* * *
442814 TA TA TA TA T- TA TA TA AA AA TA TA -A AA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
442854 TA TA TA
1 TA TA TA
442860 ATCGGGGCGG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:443315 original size:3 final size:3
Alignment explanation
Indices: 443307--443389 Score: 130
Period size: 3 Copynumber: 27.7 Consensus size: 3
443297 TTTAATAAAT
* *
443307 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
443355 TAA TAA TAA GGA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
443390 TGGATAAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:443771 original size:113 final size:113
Alignment explanation
Indices: 443632--444180 Score: 805
Period size: 113 Copynumber: 4.9 Consensus size: 113
443622 GCTCTTGATG
443632 ATTCTTCTCATTATGAACTT-TCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-
1 ATTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CT
* *
443695 CTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAA
64 CTGGAAAAGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAA
443745 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
1 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
* * * * * *
443810 GGAAAAGATGATTCACCAAATGATGGATTCAGGTAAAAGGTTGAACAA
66 GGAAAAGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAA
* *
443858 ATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCT
1 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
* * * * *
443923 GGCAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAA
66 GGAAAAGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAA
* *
443971 GTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
1 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
* * * *
444036 GGAAAAGCTGATCCATCAAATGACGGATTCAAGTAAAAGGTTGAACAA
66 GGAAAAGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAA
* * * *
444084 ATTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACCTTCTTT
1 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
* * * *
444149 GGAAAAGCTGTTCTATCAAATGATGGATTCAA
66 GGAAAAGTTGATCCATCAAATGATGAATTCAA
444181 ATCTTTGCTA
Statistics
Matches: 391, Mismatches: 43, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
112 1 0.00
113 389 0.99
114 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (113 bp):
ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
GGAAAAGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAA
Found at i:444955 original size:50 final size:50
Alignment explanation
Indices: 444901--445194 Score: 588
Period size: 50 Copynumber: 5.9 Consensus size: 50
444891 GGTTCTGCCA
444901 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
444951 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
445001 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
445051 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
445101 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
445151 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
445195 AGTCTCTTTC
Statistics
Matches: 244, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 244 1.00
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.23
Consensus pattern (50 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCT
Found at i:446380 original size:20 final size:18
Alignment explanation
Indices: 446333--446387 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
446323 TTGACCCCCC
*
446333 TTTCT-TTTTCTTCTCTTT
1 TTTCTATTTTCTT-TTTTT
446351 TTTCTATTTTCTATTTTTT
1 TTTCTATTTTCT-TTTTTT
*
446370 TTTCTTCTTTTCTTTTTT
1 TTTC-TATTTTCTTTTTT
446388 CTTCAAGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 5 0.16
19 19 0.59
20 8 0.25
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTCTATTTTCTTTTTTT
Found at i:456841 original size:18 final size:18
Alignment explanation
Indices: 456820--456854 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
456810 TGCAAATAAA
456820 ATGAAACAT-ATAAATATT
1 ATGAAA-ATAATAAATATT
456838 ATGAAAATAATAAATAT
1 ATGAAAATAATAAATAT
456855 ATATAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (18 bp):
ATGAAAATAATAAATATT
Found at i:459055 original size:3 final size:3
Alignment explanation
Indices: 459047--459129 Score: 139
Period size: 3 Copynumber: 27.7 Consensus size: 3
459037 TAATATAAAT
459047 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** *
459095 TAA TAA GGA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
459130 TGGATAAAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:467525 original size:19 final size:19
Alignment explanation
Indices: 467501--467537 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
467491 TCGAATGCAT
467501 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
467520 TCCATGCATCGATGCACT
1 TCCATGCACCGATGCACT
467538 TTGATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:467563 original size:64 final size:65
Alignment explanation
Indices: 467436--467582 Score: 174
Period size: 64 Copynumber: 2.2 Consensus size: 65
467426 TTTTCAAAGG
*
467436 CATGCACCGATGCATCAATACAATGCATCGATGCATTAATGAATAAATTGAAACATCGAATGCAT
1 CATGCACCGATGCATC-ATACAATGCATCGATGCATT-ATGAATAAATTAAAACATCGAATGCAT
467501 TC
64 TC
* * *
467503 CATGCACCGATGCACTC-T-CCATGCATCGATGCACTT-TGATTTAATTAAAACATCGAATGCAT
1 CATGCACCGATGCA-TCATACAATGCATCGATGCA-TTATGAATAAATTAAAACATCGAATGCAT
*
467565 TT
64 TC
* *
467567 GATGCATCGATGCATC
1 CATGCACCGATGCATC
467583 GATGCACAAG
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
63 2 0.03
64 36 0.51
65 14 0.20
66 3 0.04
67 14 0.20
68 2 0.03
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (65 bp):
CATGCACCGATGCATCATACAATGCATCGATGCATTATGAATAAATTAAAACATCGAATGCATTC
Found at i:473482 original size:24 final size:22
Alignment explanation
Indices: 473454--473533 Score: 92
Period size: 24 Copynumber: 3.5 Consensus size: 22
473444 CACTTAACAA
473454 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCAT-CC-TTGAATG
*
473478 TGCATCGATGCATCC--GCATG
1 TGCATCGATGCATCCTTGAATG
*
473498 ATGCACCGATGCATGCCTTGAATG
1 -TGCATCGATGCAT-CCTTGAATG
473522 TGCATCGATGCA
1 TGCATCGATGCA
473534 CAAGACCATG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
20 4 0.08
21 12 0.25
22 2 0.04
23 13 0.27
24 17 0.35
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:475746 original size:26 final size:26
Alignment explanation
Indices: 475710--475762 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
475700 AGGGGGAGAA
475710 GATTAAGATGTGTGTCATAGTAAGGG
1 GATTAAGATGTGTGTCATAGTAAGGG
475736 GATTAAGATGTGTGTCATAGTAAGGG
1 GATTAAGATGTGTGTCATAGTAAGGG
475762 G
1 G
475763 GAGTAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.30
Consensus pattern (26 bp):
GATTAAGATGTGTGTCATAGTAAGGG
Found at i:479707 original size:21 final size:20
Alignment explanation
Indices: 479682--479762 Score: 81
Period size: 20 Copynumber: 3.9 Consensus size: 20
479672 CAGAACCCCA
* *
479682 GGGGGTATCGATTCCCCTAT
1 GGGGGAATCGATTCCCTTAT
*
479702 GGGGGGAATCGATTCTCCTTCAAA
1 -GGGGGAATCGATTC-CCTT--AT
*
479726 GGGGGAATCGGTTCCCTTAT
1 GGGGGAATCGATTCCCTTAT
*
479746 GGGGGTATCGATTCCCT
1 GGGGGAATCGATTCCCT
479763 CTGCACCAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 16 0.32
21 13 0.26
22 7 0.14
23 13 0.26
24 1 0.02
ACGTcount: A:0.17, C:0.22, G:0.32, T:0.28
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTTAT
Found at i:489235 original size:23 final size:23
Alignment explanation
Indices: 489186--489249 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 23
489176 AAATATTGTA
* * * *
489186 TTTTAATTAAATTATATTTAGAT
1 TTTTAACTAATTTATAATTAGAG
*
489209 TTTTAACTAATTTATAATTATAG
1 TTTTAACTAATTTATAATTAGAG
* *
489232 TTTT-AGTACTTTATAATT
1 TTTTAACTAATTTATAATT
489250 TAACGTTTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 12 0.35
23 22 0.65
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (23 bp):
TTTTAACTAATTTATAATTAGAG
Found at i:490263 original size:4 final size:4
Alignment explanation
Indices: 490211--490247 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
490201 ATATATGCAG
490211 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
490248 AAACTATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:491389 original size:2 final size:2
Alignment explanation
Indices: 491382--491422 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
491372 TCAACCGACA
491382 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
491423 CATGTGTGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:495212 original size:21 final size:21
Alignment explanation
Indices: 495186--495322 Score: 100
Period size: 21 Copynumber: 6.6 Consensus size: 21
495176 GTTTCCAGAT
*
495186 TCGCAATGCGATTTTAGACTA
1 TCGCAATGCGATCTTAGACTA
* * *
495207 TCGCAATGCGAACCTGGACTA
1 TCGCAATGCGATCTTAGACTA
* *
495228 TCGTAATGCGAATATGTA-A--A
1 TCGCAATGCG-ATCT-TAGACTA
** *
495248 TCGCAATGCGATAGTCGACTA
1 TCGCAATGCGATCTTAGACTA
* *
495269 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGATCTTAGACTA
* * *
495290 ACGCAATGCGAACTTCGACTA
1 TCGCAATGCGATCTTAGACTA
*
495311 TCGCATTGCGAT
1 TCGCAATGCGAT
495323 TTACATATTC
Statistics
Matches: 90, Mismatches: 21, Indels: 10
0.74 0.17 0.08
Matches are distributed among these distances:
18 1 0.01
19 4 0.04
20 10 0.11
21 72 0.80
22 2 0.02
23 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.26
Consensus pattern (21 bp):
TCGCAATGCGATCTTAGACTA
Found at i:495384 original size:21 final size:19
Alignment explanation
Indices: 495311--495385 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 19
495301 ACTTCGACTA
*
495311 TCGCATTGCGAT-TTACATAT
1 TCGCATTGCGATAGT-CA-AT
495331 TCGCATTGCGATAGTCAA-
1 TCGCATTGCGATAGTCAAT
* * *
495349 TCGCAATGTGGTAGTCGAAGT
1 TCGCATTGCGATAGTC-AA-T
495370 TCGCATTGCGATAGTC
1 TCGCATTGCGATAGTC
495386 CAAAATCGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
18 13 0.30
19 3 0.07
20 14 0.32
21 14 0.32
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (19 bp):
TCGCATTGCGATAGTCAAT
Found at i:495394 original size:21 final size:21
Alignment explanation
Indices: 495331--495395 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
495321 ATTTACATAT
495331 TCGCATTGCGATAGT-C--AA
1 TCGCATTGCGATAGTCCAAAA
* * * * **
495349 TCGCAATGTGGTAGTCGAAGT
1 TCGCATTGCGATAGTCCAAAA
495370 TCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAA
495391 TCGCA
1 TCGCA
495396 ACGACTGGTG
Statistics
Matches: 32, Mismatches: 12, Indels: 3
0.68 0.26 0.06
Matches are distributed among these distances:
18 12 0.38
21 20 0.62
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.26
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAA
Found at i:496120 original size:21 final size:21
Alignment explanation
Indices: 496094--496182 Score: 115
Period size: 21 Copynumber: 4.2 Consensus size: 21
496084 CACCAGTCGT
496094 TGCGATTTTGGACTATCGCAA
1 TGCGATTTTGGACTATCGCAA
** * *
496115 TGCGATAGTCGATTATCGCAA
1 TGCGATTTTGGACTATCGCAA
496136 TGCGATTTTGGACTATCGCAA
1 TGCGATTTTGGACTATCGCAA
** *
496157 TGCGAACTTGAACTATCGCAA
1 TGCGATTTTGGACTATCGCAA
496178 TGCGA
1 TGCGA
496183 ATATGTAAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (21 bp):
TGCGATTTTGGACTATCGCAA
Found at i:496141 original size:42 final size:42
Alignment explanation
Indices: 496094--496266 Score: 138
Period size: 42 Copynumber: 4.1 Consensus size: 42
496084 CACCAGTCGT
*
496094 TGCGATTTTGGACTATCGCAATGCGATAGTCGATTATCGCAA
1 TGCGATTTTGGACTATCGCAATGCGATAGTCGACTATCGCAA
* *
496136 TGCGATTTTGGACTATCGCAATGCGA-ACTTGAACTATCGCAA
1 TGCGATTTTGGACTATCGCAATGCGATAGTCG-ACTATCGCAA
* * * * * * *
496178 TGCGAATATGTA-AATCGCAATACGATAGTCGAAGT-TCGCAT
1 TGCGATTTTGGACTATCGCAATGCGATAGTCG-ACTATCGCAA
* *** * * *
496219 TGCGATAGTCAAAGT-TCGCATTGCGATAGTCGACTATCGCAT
1 TGCGAT-TTTGGACTATCGCAATGCGATAGTCGACTATCGCAA
496261 TGCGAT
1 TGCGAT
496267 AGTCCAAAAT
Statistics
Matches: 104, Mismatches: 22, Indels: 10
0.76 0.16 0.07
Matches are distributed among these distances:
41 26 0.25
42 78 0.75
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (42 bp):
TGCGATTTTGGACTATCGCAATGCGATAGTCGACTATCGCAA
Found at i:496224 original size:21 final size:21
Alignment explanation
Indices: 496200--496270 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
496190 AATCGCAATA
496200 CGATAGTCGAAGTTCGCATTG
1 CGATAGTCGAAGTTCGCATTG
*
496221 CGATAGTCAAAGTTCGCATTG
1 CGATAGTCGAAGTTCGCATTG
*
496242 CGATAGTCG-ACTATCGCATTG
1 CGATAGTCGAAGT-TCGCATTG
496263 CGATAGTC
1 CGATAGTC
496271 CAAAATCGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 2 0.04
21 44 0.96
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.28
Consensus pattern (21 bp):
CGATAGTCGAAGTTCGCATTG
Found at i:496278 original size:21 final size:21
Alignment explanation
Indices: 496189--496282 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
496179 GCGAATATGT
* * *
496189 AAATCGCAATACGATAGTCGA
1 AAATCGCATTGCGATAGTCCA
**
496210 AGTTCGCATTGCGATAGT-CA
1 AAATCGCATTGCGATAGTCCA
* *
496230 AAGTTCGCATTGCGATAGTCGA
1 AA-ATCGCATTGCGATAGTCCA
**
496252 CTATCGCATTGCGATAGTCCA
1 AAATCGCATTGCGATAGTCCA
496273 AAATCGCATT
1 AAATCGCATT
496283 ACGAATCTGG
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
20 2 0.03
21 55 0.95
22 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (21 bp):
AAATCGCATTGCGATAGTCCA
Found at i:496280 original size:42 final size:41
Alignment explanation
Indices: 496189--496286 Score: 126
Period size: 42 Copynumber: 2.3 Consensus size: 41
496179 GCGAATATGT
* *
496189 AAATCGCAATACGATAGTCGAAGTTCGCATTGCGATAGTCA
1 AAATCGCATTACGATAGTCGAACTTCGCATTGCGATAGTCA
* *
496230 AAGTTCGCATTGCGATAGTCG-ACTATCGCATTGCGATAGTCCA
1 AA-ATCGCATTACGATAGTCGAACT-TCGCATTGCGATAGT-CA
496273 AAATCGCATTACGA
1 AAATCGCATTACGA
496287 ATCTGGAAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
41 4 0.08
42 40 0.83
43 4 0.08
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (41 bp):
AAATCGCATTACGATAGTCGAACTTCGCATTGCGATAGTCA
Found at i:501554 original size:7 final size:7
Alignment explanation
Indices: 501542--501567 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
501532 AGAATGGAAT
501542 GCAGAAA
1 GCAGAAA
501549 GCAGAAA
1 GCAGAAA
501556 GCAGAAA
1 GCAGAAA
501563 GCAGA
1 GCAGA
501568 TGGATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.15, G:0.31, T:0.00
Consensus pattern (7 bp):
GCAGAAA
Found at i:504479 original size:20 final size:20
Alignment explanation
Indices: 504454--504499 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
504444 TTGACATTAT
*
504454 ATATGTGTATTATTCTTT-TA
1 ATATGTATATT-TTCTTTCTA
*
504474 ATATGTATATTTTGTTTCTA
1 ATATGTATATTTTCTTTCTA
504494 ATATGT
1 ATATGT
504500 CATGTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.26, C:0.04, G:0.11, T:0.59
Consensus pattern (20 bp):
ATATGTATATTTTCTTTCTA
Found at i:509772 original size:36 final size:36
Alignment explanation
Indices: 509726--509819 Score: 152
Period size: 36 Copynumber: 2.6 Consensus size: 36
509716 GGAAAGTGAC
*
509726 GATGAAGATGAACGGCCAGATGATGCCTTTATCGAT
1 GATGAAGATGAAGGGCCAGATGATGCCTTTATCGAT
* * *
509762 GATGTAGATGAAGGGCCAGATGATGTCTTTATCGTT
1 GATGAAGATGAAGGGCCAGATGATGCCTTTATCGAT
509798 GATGAAGATGAAGGGCCAGATG
1 GATGAAGATGAAGGGCCAGATG
509820 CTGTCACTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.30, C:0.13, G:0.32, T:0.26
Consensus pattern (36 bp):
GATGAAGATGAAGGGCCAGATGATGCCTTTATCGAT
Found at i:514657 original size:20 final size:19
Alignment explanation
Indices: 514617--514691 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 19
514607 AATGTATTTT
* *
514617 GTGCACCGATGCACAAGTAA
1 GTGCATCGATGCAC-CGTAA
514637 GTGCATCGATGCACCGTTAA
1 GTGCATCGATGCACCG-TAA
* *
514657 GGATGCATCGATACACTGTATA
1 -G-TGCATCGATGCACCGTA-A
*
514679 GTGCATCGCTGCA
1 GTGCATCGATGCA
514692 TACATTCATT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.02
20 26 0.58
21 4 0.09
22 14 0.31
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (19 bp):
GTGCATCGATGCACCGTAA
Found at i:515423 original size:22 final size:22
Alignment explanation
Indices: 515398--515494 Score: 130
Period size: 22 Copynumber: 4.6 Consensus size: 22
515388 GGGTATATTA
515398 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
*
515420 GTCCTTCAGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
* *
515442 GTTCTTCGGGACGTATCTAGTG
1 GTCCTTCGGGACGTATCCAGTG
*
515464 GTCCTTCAGGAC--AT--AGTG
1 GTCCTTCGGGACGTATCCAGTG
515482 GTCCTTCGGGACG
1 GTCCTTCGGGACG
515495 AATACTGAAC
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
18 15 0.22
20 2 0.03
22 50 0.75
ACGTcount: A:0.15, C:0.25, G:0.31, T:0.29
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:515482 original size:18 final size:18
Alignment explanation
Indices: 515459--515493 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
515449 GGGACGTATC
515459 TAGTGGTCCTTCAGGACA
1 TAGTGGTCCTTCAGGACA
*
515477 TAGTGGTCCTTCGGGAC
1 TAGTGGTCCTTCAGGAC
515494 GAATACTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (18 bp):
TAGTGGTCCTTCAGGACA
Found at i:524181 original size:20 final size:20
Alignment explanation
Indices: 524156--524194 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
524146 AACCATTCAG
524156 GGGGGAATCGGTACCCCCTT
1 GGGGGAATCGGTACCCCCTT
* *
524176 GGGGGAATTGGTTCCCCCT
1 GGGGGAATCGGTACCCCCT
524195 GAGCATTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.28, G:0.36, T:0.23
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTT
Found at i:526461 original size:23 final size:23
Alignment explanation
Indices: 526433--526479 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
526423 ATTCCCCTAA
526433 GGGGAATCGGTTCCCATTCAAAG
1 GGGGAATCGGTTCCCATTCAAAG
*
526456 GGGGAATCGGTTCCCCTTCAAAG
1 GGGGAATCGGTTCCCATTCAAAG
526479 G
1 G
526480 TATCGATTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.23, C:0.23, G:0.32, T:0.21
Consensus pattern (23 bp):
GGGGAATCGGTTCCCATTCAAAG
Found at i:531397 original size:20 final size:20
Alignment explanation
Indices: 531372--531409 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
531362 CGTTTAACAG
531372 TGGGGGGAATTGGTTCCCCC
1 TGGGGGGAATTGGTTCCCCC
531392 TGGGGGGAATTGGTTCCC
1 TGGGGGGAATTGGTTCCC
531410 TCCGAGCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.21, G:0.42, T:0.26
Consensus pattern (20 bp):
TGGGGGGAATTGGTTCCCCC
Found at i:534189 original size:21 final size:21
Alignment explanation
Indices: 534165--534211 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
534155 GAGAAAAAGT
*
534165 AAAAGTTAAGAATGAAAGAGA
1 AAAAGTTAAGAATAAAAGAGA
* *
534186 AAAAATTAATAATAAAAGAGA
1 AAAAGTTAAGAATAAAAGAGA
534207 AAAAG
1 AAAAG
534212 AAAAAGTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (21 bp):
AAAAGTTAAGAATAAAAGAGA
Found at i:535861 original size:647 final size:649
Alignment explanation
Indices: 534627--535925 Score: 2541
Period size: 646 Copynumber: 2.0 Consensus size: 649
534617 TGTAGATGCA
534627 AAACTGCGTTATTGTGTGGTGGTGGAACTCCATTATAGGCTTTCAGATGCTGGCCATTGACTTTG
1 AAACTGCGTTATTGTGTGGTGGTGGAACTCCATTATAGGCTTTCAGATGCTGGCCATTGACTTTG
534692 AAGATCGTGCCATCTATATTCTTGATGTCAACAACTCTATAGGGATAGACATAATGCACCTCAAA
66 AAGATCGTGCCATCTATATTCTTGATGTCAACAACTCTATAGGGATAGACATAATGCACCTCAAA
*
534757 TGGTTCTGACCATCGAGATTTGAGCTTCCCAGGAAAAATGTTTGAGTCTGGAGTTATAAAGTAAT
131 TGGTTCTGACCATCAAGATTTGAGCTTCCCAGGAAAAATGTTTGAGTCTGGAGTTATAAAGTAAT
534822 ACTTGTCGGCCCATATGAAAATGTCGTGGCATCAGTTTTTGGTTATGCCACTTCTTGGTTTTCTA
196 ACTTGTCGGCCCATATGAAAATGTCGTGGCATCAGTTTTTGGTTATGCCACTTCTTGGTTTTCTA
534887 CTTGTATATCCTAGTATTCTCATATGCTTGTGCTCTAAACTCTTCCATTTCATTAAGTTCTAGTA
261 CTTGTATATCCTAGTATTCTCATATGCTTGTGCTCTAAACTCTTCCATTTCATTAAGTTCTAGTA
534952 ATCTCTGTTCCCCAGCTAGTTGAGCATCAAAATTTAATTGCTTGATGGCCCAGTACGCCTTATGT
326 ATCTCTGTTCCCCAGCTAGTTGAGCATCAAAATTTAATTGCTTGATGGCCCAGTACGCCTTATGT
535017 TCAAGTTCAACCAGGAGATGACAAGTTTTCGCATACACTAGCTTGAATGATGACATCCCCAAAAG
391 TCAAGTTCAACCAGGAGATGACAAGTTTTCGCATACACTAGCTTGAATGATGACATCCCCAAAAG
535082 AGTTTTGAACAATATTTTGTATGCCCAAAGTGATCCATCTAACTTTGGCGACCAATCCTTACGCC
456 AGTTTTGAACAATATTTTGTATGCCCAAAGTGATCCATCTAACTTTGGCGACCAATCCTTACGCC
535147 TTGGGTTCACCACTTTCTCTAAAATCTGTTTGACTCTTGATTGAATATTGTTGCTTGGTCATTCG
521 TTGGGTTCACCACTTTCTCTAAAATCTGTTTGACTCTTGATTGAATATTGTTGCTTGGTCATTCG
535212 TCTGC-GATG-ATATCGTGGCAATCTTGTGTCGAACTCCATATCTCCTAAATGTCTTGGCAGTC
586 TCTGCGGATGAATATCGTGGCAATCTTGTGTCGAACTCCATATCTCCTAAATGTCTTGGCAGTC
535274 AAACTGCGTTATTGTGTGGTGGTGGAACTCCATTATAGGCTTTCAGATGCTGGCCATTGACTTTG
1 AAACTGCGTTATTGTGTGGTGGTGGAACTCCATTATAGGCTTTCAGATGCTGGCCATTGACTTTG
535339 AAGATCGTGCCATCTATATTCTTGATGTCAACAACTCTATAGGGATAGACATAATGCACCTCAAA
66 AAGATCGTGCCATCTATATTCTTGATGTCAACAACTCTATAGGGATAGACATAATGCACCTCAAA
535404 TGGTTCTGACCATCAAGATTTGAGCTTCCCAGGAAAAATGTTTGAGTCTGGAGTTATAAAGTAAT
131 TGGTTCTGACCATCAAGATTTGAGCTTCCCAGGAAAAATGTTTGAGTCTGGAGTTATAAAGTAAT
535469 ACTTGTCGGCCCATATGAAAATGTCGTGGCATCA-TTTTTGGTTATGCCACTTCTTGGTTTTCTA
196 ACTTGTCGGCCCATATGAAAATGTCGTGGCATCAGTTTTTGGTTATGCCACTTCTTGGTTTTCTA
535533 CTTGTATATCCTAGTATTCTCATATGCTTGTGCTCTAAACTCTTCCATTTCATTAAGTTCTAGTA
261 CTTGTATATCCTAGTATTCTCATATGCTTGTGCTCTAAACTCTTCCATTTCATTAAGTTCTAGTA
535598 ATCTCTGTTCCCCAGCTAGTTGAGCATCAAAATTTAATTGCTTGATGGCCCAGTACGCCTTATGT
326 ATCTCTGTTCCCCAGCTAGTTGAGCATCAAAATTTAATTGCTTGATGGCCCAGTACGCCTTATGT
535663 TCAAGTTCAACCAGGAGATGACAAGTTTTCGCATACACTAGCTTGAATGATGACATCCCCAAAAG
391 TCAAGTTCAACCAGGAGATGACAAGTTTTCGCATACACTAGCTTGAATGATGACATCCCCAAAAG
*
535728 AGTTTTGAACAATATTTTGTATGCCCAAAGTGATCCATCTAACTTTGGCGACCAATTCTTACGCC
456 AGTTTTGAACAATATTTTGTATGCCCAAAGTGATCCATCTAACTTTGGCGACCAATCCTTACGCC
535793 TTGGGTTCACCACTTTCTCTAAAATCTGTTTGATCTCTTGATTGAATATTGTTGCTTGGTCATTC
521 TTGGGTTCACCACTTTCTCTAAAATCTGTTTGA-CTCTTGATTGAATATTGTTGCTTGGTCATTC
535858 GTCTGCGGATGATATATCGTGGCAATCTTGTGTCGAACTCCATATCTCCTAAATGTCTTGGCAGT
585 GTCTGCGGATGA-ATATCGTGGCAATCTTGTGTCGAACTCCATATCTCCTAAATGTCTTGGCAGT
535923 C
649 C
535924 AA
1 AA
535926 CTTGTTATCA
Statistics
Matches: 646, Mismatches: 2, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
646 322 0.50
647 265 0.41
648 4 0.01
650 55 0.09
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (649 bp):
AAACTGCGTTATTGTGTGGTGGTGGAACTCCATTATAGGCTTTCAGATGCTGGCCATTGACTTTG
AAGATCGTGCCATCTATATTCTTGATGTCAACAACTCTATAGGGATAGACATAATGCACCTCAAA
TGGTTCTGACCATCAAGATTTGAGCTTCCCAGGAAAAATGTTTGAGTCTGGAGTTATAAAGTAAT
ACTTGTCGGCCCATATGAAAATGTCGTGGCATCAGTTTTTGGTTATGCCACTTCTTGGTTTTCTA
CTTGTATATCCTAGTATTCTCATATGCTTGTGCTCTAAACTCTTCCATTTCATTAAGTTCTAGTA
ATCTCTGTTCCCCAGCTAGTTGAGCATCAAAATTTAATTGCTTGATGGCCCAGTACGCCTTATGT
TCAAGTTCAACCAGGAGATGACAAGTTTTCGCATACACTAGCTTGAATGATGACATCCCCAAAAG
AGTTTTGAACAATATTTTGTATGCCCAAAGTGATCCATCTAACTTTGGCGACCAATCCTTACGCC
TTGGGTTCACCACTTTCTCTAAAATCTGTTTGACTCTTGATTGAATATTGTTGCTTGGTCATTCG
TCTGCGGATGAATATCGTGGCAATCTTGTGTCGAACTCCATATCTCCTAAATGTCTTGGCAGTC
Found at i:537387 original size:20 final size:22
Alignment explanation
Indices: 537340--537393 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
537330 TGCAAGTAAC
537340 TGCATCGATGCACTGTTAAGGA
1 TGCATCGATGCACTGTTAAGGA
*
537362 TGCATCGATTCACTG-TATA-G-
1 TGCATCGATGCACTGTTA-AGGA
537382 TGCATCGATGCA
1 TGCATCGATGCA
537394 TACCTTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 11 0.38
21 3 0.10
22 15 0.52
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGGA
Found at i:543533 original size:21 final size:22
Alignment explanation
Indices: 543507--543553 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
543497 CGATTCCCCT
543507 AGGGGGAATCGGTT-CCCATCA
1 AGGGGGAATCGGTTCCCCATCA
* *
543528 AGGGGGAATCGTTTCCCCTTCA
1 AGGGGGAATCGGTTCCCCATCA
543550 AGGG
1 AGGG
543554 TATCGATTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.21, C:0.23, G:0.34, T:0.21
Consensus pattern (22 bp):
AGGGGGAATCGGTTCCCCATCA
Found at i:544216 original size:113 final size:113
Alignment explanation
Indices: 544013--544234 Score: 417
Period size: 113 Copynumber: 2.0 Consensus size: 113
544003 TCTAGAGTGT
544013 TGGATGGGATTTTTAGTGAGACAAATAGCACTAGTATTGTCACACTTGATAGGAATGGTACCTAC
1 TGGATGGGATTTTTAGTGAGACAAATAGCACTAGTATTGTCACACTTGATAGGAATGGTACCTAC
*
544078 TTCAATTCCATAATCAAAAAATTGTTGTTTCATCTATAAAACTTGTGC
66 TTCAATTCCATAATCAAAAAATTGTTGTTTCATCCATAAAACTTGTGC
*
544126 TGGATGGGATTTTTAGTGAGAGAAATAGCACTAGTATTGTCACACTTGATAGGAATGGTACCTAC
1 TGGATGGGATTTTTAGTGAGACAAATAGCACTAGTATTGTCACACTTGATAGGAATGGTACCTAC
*
544191 TTCAATTCCATAATCAAAAAGTTGTTGTTTCATCCATAAAACTT
66 TTCAATTCCATAATCAAAAAATTGTTGTTTCATCCATAAAACTT
544235 ATGCACAACA
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 106 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (113 bp):
TGGATGGGATTTTTAGTGAGACAAATAGCACTAGTATTGTCACACTTGATAGGAATGGTACCTAC
TTCAATTCCATAATCAAAAAATTGTTGTTTCATCCATAAAACTTGTGC
Found at i:559519 original size:16 final size:16
Alignment explanation
Indices: 559497--559542 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
559487 AACTTTTAGA
559497 AAATTTTAACAAAT-TT
1 AAATTTTAA-AAATATT
*
559513 TAATTTTAAAAATATT
1 AAATTTTAAAAATATT
559529 AAATTTTTAAAAAT
1 AAA-TTTTAAAAAT
559543 TAGAAGTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 4 0.15
16 12 0.46
17 10 0.38
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATTTTAAAAATATT
Found at i:570790 original size:64 final size:64
Alignment explanation
Indices: 570712--570844 Score: 239
Period size: 64 Copynumber: 2.1 Consensus size: 64
570702 CATTGGGGTT
*
570712 TTCCCCATAGCTCTGCCTATGGTTTTGCAGTTTCTTTTATTGTCCACCACCTCACTATCTTTCA
1 TTCCCCATAGCTCTGCCTATAGTTTTGCAGTTTCTTTTATTGTCCACCACCTCACTATCTTTCA
**
570776 TTCCCCATAGCTCTGCCTATAGTTTTGCAGTTTCTTTTATTGTCCACCGGCTCACTATCTTTCA
1 TTCCCCATAGCTCTGCCTATAGTTTTGCAGTTTCTTTTATTGTCCACCACCTCACTATCTTTCA
570840 TTCCC
1 TTCCC
570845 TCACTATACA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.15, C:0.32, G:0.11, T:0.42
Consensus pattern (64 bp):
TTCCCCATAGCTCTGCCTATAGTTTTGCAGTTTCTTTTATTGTCCACCACCTCACTATCTTTCA
Found at i:580377 original size:60 final size:60
Alignment explanation
Indices: 580250--580379 Score: 136
Period size: 60 Copynumber: 2.2 Consensus size: 60
580240 ACATTATGTT
** * * * * * *
580250 CTTAAACTATAATTCTCATTCTGAATTAGCCCCTGAACTTTAAAGCATTCTATAGGCATC
1 CTTAAACTATAACCCTCATTCTAAATTAGACCATAAAATTTAAAACATTCTATAGGCATC
** * *
580310 CCAAAACTATAACCCTCATTCTAAATTGGACCATAAAATTTAAAACATTCTATA-TCAATC
1 CTTAAACTATAACCCTCATTCTAAATTAGACCATAAAATTTAAAACATTCTATAGGC-ATC
580370 CTTAAACTAT
1 CTTAAACTAT
580380 TAGTATTAGT
Statistics
Matches: 55, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
59 1 0.02
60 54 0.98
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (60 bp):
CTTAAACTATAACCCTCATTCTAAATTAGACCATAAAATTTAAAACATTCTATAGGCATC
Found at i:607412 original size:21 final size:21
Alignment explanation
Indices: 607386--607448 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
607376 TTAAAGACTT
607386 AAAGATGAGCAAGATCAACAG
1 AAAGATGAGCAAGATCAACAG
607407 AAAGATGAGCAAGATCAACAG
1 AAAGATGAGCAAGATCAACAG
*
607428 AAAGATGTGCAAGATCAACAG
1 AAAGATGAGCAAGATCAACAG
607449 CACGATAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.51, C:0.14, G:0.24, T:0.11
Consensus pattern (21 bp):
AAAGATGAGCAAGATCAACAG
Found at i:616950 original size:21 final size:21
Alignment explanation
Indices: 616924--616965 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
616914 TTAAAGACTT
*
616924 AAAGATGAGCAAGATCAACAG
1 AAAGATAAGCAAGATCAACAG
*
616945 AAAGATAAGCTAGATCAACAG
1 AAAGATAAGCAAGATCAACAG
616966 CATGATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.14, G:0.21, T:0.12
Consensus pattern (21 bp):
AAAGATAAGCAAGATCAACAG
Found at i:624259 original size:13 final size:13
Alignment explanation
Indices: 624238--624311 Score: 67
Period size: 13 Copynumber: 5.4 Consensus size: 13
624228 TGTTCAGGTT
*
624238 ATCTAATTTTTTA
1 ATCTTATTTTTTA
624251 ATCTTATTTTTTA
1 ATCTTATTTTTTA
** *
624264 ATCTTCATAATTGA
1 ATCTT-ATTTTTTA
*
624278 TGTCTCTAATTTTTTA
1 -ATCT-T-ATTTTTTA
624294 ATCTTATTTTTTA
1 ATCTTATTTTTTA
624307 ATCTT
1 ATCTT
624312 TATAATTGAT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
13 30 0.62
14 6 0.12
15 6 0.12
16 6 0.12
ACGTcount: A:0.26, C:0.11, G:0.03, T:0.61
Consensus pattern (13 bp):
ATCTTATTTTTTA
Found at i:624462 original size:42 final size:43
Alignment explanation
Indices: 624240--624685 Score: 263
Period size: 43 Copynumber: 10.3 Consensus size: 43
624230 TTCAGGTTAT
* * * * * *
624240 CTAATTTTTT-AATCTTATTTTTTAATCTTCATAATTGATGTCT
1 CTAATTTTTTCAATCTTACTTTTT-ACCTTTATAATTAAGGTCC
* * * * *
624283 CTAATTTTTT-AATCTTATTTTTTAATCTTTATAATTGATGTCT
1 CTAATTTTTTCAATCTTACTTTTT-ACCTTTATAATTAAGGTCC
* * * *
624326 CTAATTTTTTTAAAT-TT-CATTTTCTATCTTTATAAGTGAA--ACC
1 CTAA-TTTTTTCAATCTTAC-TTTT-TACCTTTATAA-TTAAGGTCC
* * * *
624369 CTTAATTTTTGT-AATCTCAC-ATTTATCTTTATAATT--GGACCC
1 C-TAATTTTT-TCAATCTTACTTTTTACCTTTATAATTAAGG-TCC
* * *
624411 CTACTTTTTTCAATCTTACATTTTACCTTTATAATTAAGGTCT
1 CTAATTTTTTCAATCTTACTTTTTACCTTTATAATTAAGGTCC
* * ** *
624454 CTCATTTTTTTCAATCTCACTTTTTACCTTTATAATTAATATCT
1 CT-AATTTTTTCAATCTTACTTTTTACCTTTATAATTAAGGTCC
* * *
624498 CTAATTCTTTTTAAT-TTCACTTTCTACCTTTATAATAAAGG-CC
1 CTAATT-TTTTCAATCTT-ACTTTTTACCTTTATAATTAAGGTCC
* * * * *
624541 CTAGTTTTTTTAATCTCACTTTTTACCTTTATAACTAAGGCCC
1 CTAATTTTTTCAATCTTACTTTTTACCTTTATAATTAAGGTCC
** *
624584 CTAATTTTTTCAATAGTACTTTTTACTTTTATAATTAAGG-CAC
1 CTAATTTTTTCAATCTTACTTTTTACCTTTATAATTAAGGTC-C
* * * * *
624627 CTATTTTTTTCAATCTTATTTTTTTTACTTTTATAATTGA-GACC
1 CTAATTTTTTCAATCTTA--CTTTTTACCTTTATAATTAAGGTCC
624671 TCTAATTTTTTCAAT
1 -CTAATTTTTTCAAT
624686 TACAATTTTT
Statistics
Matches: 330, Mismatches: 47, Indels: 50
0.77 0.11 0.12
Matches are distributed among these distances:
40 1 0.00
41 15 0.05
42 57 0.17
43 123 0.37
44 95 0.29
45 39 0.12
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (43 bp):
CTAATTTTTTCAATCTTACTTTTTACCTTTATAATTAAGGTCC
Found at i:624573 original size:172 final size:172
Alignment explanation
Indices: 624240--624686 Score: 473
Period size: 172 Copynumber: 2.6 Consensus size: 172
624230 TTCAGGTTAT
* * * * * *
624240 CTAATTTTTT-AATCTTATTTTTTAATCTTCATAATTGATGTCTCT-AATTTTTT-AATCTTATT
1 CTAATTTTTTCAATCTTACTTTTT-ACCTTTATAATTAAGGTCTCTCATTTTTTTCAATCTTATT
* * * *
624302 TTTTAATCTTTATAATTGATGTCTCTAATTTTTTTAAATTTCATTTTCTATCTTTATAAGTGAAA
65 TTTT-ACCTTTATAATTGATATCTCTAATTTTTTT-AATTTCACTTTCTACCTTTATAAGTGAAA
* *
624367 CCCTTAATTTTTGTAATCTCACATTTATCTTTATAA-T-TGGACCC
128 CCCTTAATTTTTGTAATCTCACATTTACCTTTATAACTAAGG-CCC
* * * *
624411 CTACTTTTTTCAATCTTACATTTTACCTTTATAATTAAGGTCTCTCATTTTTTTCAATCTCACTT
1 CTAATTTTTTCAATCTTACTTTTTACCTTTATAATTAAGGTCTCTCATTTTTTTCAATCTTATTT
*
624476 TTTACCTTTATAATTAATATCTCTAATTCTTTTTAATTTCACTTTCTACCTTTATAA-T-AAAGG
66 TTTACCTTTATAATTGATATCTCTAATT-TTTTTAATTTCACTTTCTACCTTTATAAGTGAAA--
* * *
624539 CCC-TAGTTTTTTTAATCTCACTTTTTACCTTTATAACTAAGGCCC
128 CCCTTAATTTTTGTAATCTCAC-ATTTACCTTTATAACTAAGGCCC
** * *
624584 CTAATTTTTTCAATAGTACTTTTTACTTTTATAATTAAGG-CAC-CTATTTTTTTCAATCTTATT
1 CTAATTTTTTCAATCTTACTTTTTACCTTTATAATTAAGGTCTCTC-ATTTTTTTCAATCTTA--
* * * *
624647 TTTTTTACTTTTATAATTGAGACCTCTAATTTTTTCAATT
63 TTTTTTACCTTTATAATTGATATCTCTAATTTTTTTAATT
624687 ACAATTTTTT
Statistics
Matches: 231, Mismatches: 33, Indels: 22
0.81 0.12 0.08
Matches are distributed among these distances:
170 3 0.01
171 44 0.19
172 93 0.40
173 63 0.27
174 28 0.12
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (172 bp):
CTAATTTTTTCAATCTTACTTTTTACCTTTATAATTAAGGTCTCTCATTTTTTTCAATCTTATTT
TTTACCTTTATAATTGATATCTCTAATTTTTTTAATTTCACTTTCTACCTTTATAAGTGAAACCC
TTAATTTTTGTAATCTCACATTTACCTTTATAACTAAGGCCC
Found at i:624605 original size:43 final size:43
Alignment explanation
Indices: 624283--624731 Score: 247
Period size: 44 Copynumber: 10.3 Consensus size: 43
624273 ATTGATGTCT
* * * * * *
624283 CTAATTTTTT-AATCTT-ATTTTTTAATCTTTATAATTGATGTCT
1 CTAATTTTTTCAAT-TTCACTTTTT-ACCTTTATAATTAAGGCCC
* * * *
624326 CTAATTTTTTTAAATTTCA-TTTTCTATCTTTATAAGTGAA-ACCC
1 CTAA-TTTTTTCAATTTCACTTTT-TACCTTTATAA-TTAAGGCCC
* * * *
624370 TTAATTTTTGT-AATCTCAC-ATTTATCTTTATAATT--GGACCC
1 CTAATTTTT-TCAATTTCACTTTTTACCTTTATAATTAAGG-CCC
* * * *
624411 CTACTTTTTTCAATCTT-ACATTTTACCTTTATAATTAAGGTCT
1 CTAATTTTTTCAAT-TTCACTTTTTACCTTTATAATTAAGGCCC
* * *** *
624454 CTCATTTTTTTCAATCTCACTTTTTACCTTTATAATTAATATCT
1 CT-AATTTTTTCAATTTCACTTTTTACCTTTATAATTAAGGCCC
* * *
624498 CTAATTCTTTTTAATTTCACTTTCTACCTTTATAATAAAGG-CC
1 CTAATT-TTTTCAATTTCACTTTTTACCTTTATAATTAAGGCCC
* * * *
624541 CTAGTTTTTTTAATCTCACTTTTTACCTTTATAACTAAGGCCC
1 CTAATTTTTTCAATTTCACTTTTTACCTTTATAATTAAGGCCC
* * *
624584 CTAATTTTTTCAATAGT-ACTTTTTACTTTTATAATTAAGGCAC
1 CTAATTTTTTCAAT-TTCACTTTTTACCTTTATAATTAAGGCCC
* * * * * *
624627 CTATTTTTTTCAATCTT-ATTTTTTTTACTTTTATAATTGAGACCT
1 CTAATTTTTTCAAT-TTCA--CTTTTTACCTTTATAATTAAGGCCC
* * * * * *
624672 CTAATTTTTTCAATTACAATTTTTTATCATTACAATTAATGCCC
1 CTAATTTTTTCAATTTC-ACTTTTTACCTTTATAATTAAGGCCC
*
624716 CAAATTTTTTTCAATT
1 CTAA-TTTTTTCAATT
624732 CCATAAAATT
Statistics
Matches: 322, Mismatches: 60, Indels: 46
0.75 0.14 0.11
Matches are distributed among these distances:
40 1 0.00
41 16 0.05
42 56 0.17
43 82 0.25
44 115 0.36
45 51 0.16
46 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.04, T:0.52
Consensus pattern (43 bp):
CTAATTTTTTCAATTTCACTTTTTACCTTTATAATTAAGGCCC
Found at i:628949 original size:14 final size:14
Alignment explanation
Indices: 628930--628962 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
628920 CATCTAGTAA
628930 CTGAGAAGCAAATG
1 CTGAGAAGCAAATG
628944 CTGAGAAGCAAATG
1 CTGAGAAGCAAATG
628958 CTGAG
1 CTGAG
628963 CACCTATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.39, C:0.15, G:0.30, T:0.15
Consensus pattern (14 bp):
CTGAGAAGCAAATG
Found at i:635853 original size:68 final size:68
Alignment explanation
Indices: 635717--635868 Score: 186
Period size: 68 Copynumber: 2.2 Consensus size: 68
635707 ACCCATTCAA
* *
635717 GGGAACCGATA-CCCCTCAATGAAATGAATTTCCAGAATGCTAGAGGGGAATCGGTACCCCCA-G
1 GGGAACCGATACCCCCTCAATGAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAGG
635780 GGG
66 GGG
* * *
635783 GGGAACCGATACCCCCTC-ATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATA-CCCCA
1 GGGAACCGATACCCCCTCAAT-G-AAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
635846 GGGGGGG
64 --GGGGG
*
635853 GGGAACCGATTCCCCC
1 GGGAACCGATACCCCC
635869 ATGGAAAAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
66 13 0.18
67 12 0.16
68 30 0.41
70 19 0.26
ACGTcount: A:0.27, C:0.26, G:0.29, T:0.18
Consensus pattern (68 bp):
GGGAACCGATACCCCCTCAATGAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAGG
GGG
Found at i:649602 original size:15 final size:14
Alignment explanation
Indices: 649565--649603 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
649555 AATGGGAAGT
*
649565 AATCCCTGCAAATA
1 AATCCCTGCAAAAA
649579 AATCCCTGCGAAAAA
1 AATCCCTGC-AAAAA
*
649594 AATCTCTGCA
1 AATCCCTGCA
649604 TATAGACAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.41, C:0.28, G:0.10, T:0.21
Consensus pattern (14 bp):
AATCCCTGCAAAAA
Found at i:651447 original size:12 final size:12
Alignment explanation
Indices: 651430--651510 Score: 103
Period size: 12 Copynumber: 6.9 Consensus size: 12
651420 TCGATTGAAA
*
651430 CTCGATTTTGAG
1 CTCGATTTTAAG
*
651442 CTCGATTTTAAA
1 CTCGATTTTAAG
*
651454 CTCGA-TTCAAG
1 CTCGATTTTAAG
*
651465 CTCGATTTTGAG
1 CTCGATTTTAAG
651477 CTCGA-TTTAAG
1 CTCGATTTTAAG
*
651488 CTCGATTTTGAG
1 CTCGATTTTAAG
651500 CTCGATTTTAA
1 CTCGATTTTAA
651511 ACTCAATTCA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
11 19 0.33
12 39 0.67
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (12 bp):
CTCGATTTTAAG
Found at i:651469 original size:35 final size:34
Alignment explanation
Indices: 651420--651508 Score: 115
Period size: 35 Copynumber: 2.6 Consensus size: 34
651410 AGACTCGAAA
* *
651420 TCGATTGAAACTCGATTTTGAGCTCGATTTTAAAC
1 TCGATTCAAGCTCGATTTTGAGCTCGA-TTTAAAC
*
651455 TCGATTCAAGCTCGATTTTGAGCTCGATTTAAGC
1 TCGATTCAAGCTCGATTTTGAGCTCGATTTAAAC
**
651489 TCGATTTTGAGCTCGATTTT
1 TCGA-TTCAAGCTCGATTTT
651509 AAACTCAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 10 0.21
35 38 0.79
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (34 bp):
TCGATTCAAGCTCGATTTTGAGCTCGATTTAAAC
Found at i:651470 original size:11 final size:11
Alignment explanation
Indices: 651420--651507 Score: 77
Period size: 12 Copynumber: 7.6 Consensus size: 11
651410 AGACTCGAAA
* *
651420 TCGATTGAAAC
1 TCGATTTAAGC
*
651431 TCGATTTTGAGC
1 TCGA-TTTAAGC
*
651443 TCGATTTTAAAC
1 TCGA-TTTAAGC
*
651455 TCGATTCAAGC
1 TCGATTTAAGC
*
651466 TCGATTTTGAGC
1 TCGA-TTTAAGC
651478 TCGATTTAAGC
1 TCGATTTAAGC
*
651489 TCGATTTTGAGC
1 TCGA-TTTAAGC
651501 TCGATTT
1 TCGATTT
651508 TAAACTCAAT
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
11 26 0.41
12 37 0.59
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (11 bp):
TCGATTTAAGC
Found at i:651507 original size:23 final size:23
Alignment explanation
Indices: 651430--651507 Score: 111
Period size: 23 Copynumber: 3.3 Consensus size: 23
651420 TCGATTGAAA
* * *
651430 CTCGATTTTGAGCTCGATTTTAAA
1 CTCGA-TTTAAGCTCGATTTTGAG
*
651454 CTCGATTCAAGCTCGATTTTGAG
1 CTCGATTTAAGCTCGATTTTGAG
651477 CTCGATTTAAGCTCGATTTTGAG
1 CTCGATTTAAGCTCGATTTTGAG
651500 CTCGATTT
1 CTCGATTT
651508 TAAACTCAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 44 0.90
24 5 0.10
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (23 bp):
CTCGATTTAAGCTCGATTTTGAG
Found at i:657085 original size:50 final size:50
Alignment explanation
Indices: 656959--657091 Score: 144
Period size: 51 Copynumber: 2.6 Consensus size: 50
656949 CACCCTTAGC
* * **
656959 AGTAAAGCGCGCCTCCTGCACCGCGTTATACGATGATTTGACGCCACGAGTG
1 AGTATAGCGCGCC-CCTGCACCGCGCTATACGATGAGCTGACGCCAC-AGTG
* * *
657011 A-TATAGCGCGCCCTCTGAACCGCGCTATACGGTGAGCTGGCGCCAC-GTG
1 AGTATAGCGCGCCC-CTGCACCGCGCTATACGATGAGCTGACGCCACAGTG
*
657060 AGTATAGCGCGGCCCCTGCAGCGCGCTATACG
1 AGTATAGCGC-GCCCCTGCACCGCGCTATACG
657092 CCACGTAGGG
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
49 4 0.06
50 24 0.35
51 40 0.58
52 1 0.01
ACGTcount: A:0.20, C:0.32, G:0.29, T:0.19
Consensus pattern (50 bp):
AGTATAGCGCGCCCCTGCACCGCGCTATACGATGAGCTGACGCCACAGTG
Found at i:657223 original size:50 final size:51
Alignment explanation
Indices: 657103--657226 Score: 171
Period size: 50 Copynumber: 2.5 Consensus size: 51
657093 CACGTAGGGG
*
657103 TATAGCGCGGATCAGGAACCGCGCTATACCTTTACTCCCGACATAATTTTA
1 TATAGCGCGGATCAGGTACCGCGCTATACCTTTACTCCCGACATAATTTTA
* ** * *
657154 TATAACGCGGGGCATGTACCGCGAC-ATACCTTTACT-CTGACATAATTTTA
1 TATAGCGCGGATCAGGTACCGCG-CTATACCTTTACTCCCGACATAATTTTA
657204 TATAGCGCGGATCAGGTACCGCG
1 TATAGCGCGGATCAGGTACCGCG
657227 TTTTGTATAA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
50 32 0.52
51 29 0.47
52 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (51 bp):
TATAGCGCGGATCAGGTACCGCGCTATACCTTTACTCCCGACATAATTTTA
Found at i:663103 original size:20 final size:19
Alignment explanation
Indices: 663075--663113 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
663065 CCTTAAAAAG
*
663075 AGAGTATTTGAGAGAAATTT
1 AGAGAATTTGAGA-AAATTT
663095 AGAGAATTTGAGAAAATTT
1 AGAGAATTTGAGAAAATTT
663114 GGTGTGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (19 bp):
AGAGAATTTGAGAAAATTT
Found at i:663249 original size:50 final size:50
Alignment explanation
Indices: 663195--663345 Score: 146
Period size: 50 Copynumber: 3.0 Consensus size: 50
663185 GCCCCCTGCA
* * *
663195 CCGCGCTATACCCCACGT-G-TCAGATATACATGTATAGCGCGCTGCAGGGG
1 CCGCGCTATACCCCACGTGGCGCAGAT-CAC-CGTATAGCGCGCTGCAGGGG
* *
663245 CCGCGCTATA-CCCACGTGGCGCCAGCTCACCGTATAGCGCGGTGCAGGGG
1 CCGCGCTATACCCCACGTGGCG-CAGATCACCGTATAGCGCGCTGCAGGGG
* * * * * *
663295 GCGCGCTATACCCCACGTGGCACCAAATCATCGTATAGCGCGGTGTAGGGG
1 CCGCGCTATACCCCACGTGGC-GCAGATCACCGTATAGCGCGCTGCAGGGG
663346 GCGCACTACT
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
49 7 0.08
50 38 0.45
51 36 0.42
52 4 0.05
ACGTcount: A:0.20, C:0.32, G:0.31, T:0.17
Consensus pattern (50 bp):
CCGCGCTATACCCCACGTGGCGCAGATCACCGTATAGCGCGCTGCAGGGG
Found at i:663330 original size:51 final size:51
Alignment explanation
Indices: 663196--663349 Score: 188
Period size: 51 Copynumber: 3.1 Consensus size: 51
663186 CCCCCTGCAC
* * * * *
663196 CGCGCTATACCCCACGTGTCA-GATATACAT-GTATAGCGCGCTGCAGGGGC
1 CGCGCTATACCCCACGTGGCACCAAAT-CATCGTATAGCGCGGTGCAGGGGG
* ** *
663246 CGCGCTATA-CCCACGTGGCGCCAGCTCACCGTATAGCGCGGTGCAGGGGG
1 CGCGCTATACCCCACGTGGCACCAAATCATCGTATAGCGCGGTGCAGGGGG
*
663296 CGCGCTATACCCCACGTGGCACCAAATCATCGTATAGCGCGGTGTAGGGGG
1 CGCGCTATACCCCACGTGGCACCAAATCATCGTATAGCGCGGTGCAGGGGG
663347 CGC
1 CGC
663350 ACTACTAAGG
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
49 11 0.12
50 38 0.43
51 39 0.44
ACGTcount: A:0.19, C:0.32, G:0.32, T:0.17
Consensus pattern (51 bp):
CGCGCTATACCCCACGTGGCACCAAATCATCGTATAGCGCGGTGCAGGGGG
Found at i:664027 original size:23 final size:22
Alignment explanation
Indices: 663972--664027 Score: 53
Period size: 24 Copynumber: 2.4 Consensus size: 22
663962 TCATTATTTT
663972 TTATTTTT-TATAAAATAAATCA
1 TTATTTTTATATAAAATAAA-CA
663994 TTAATTTTTTATATAATAATAAA-A
1 TT-A-TTTTTATATAA-AATAAACA
664018 TTATTCTTTA
1 TTATT-TTTA
664028 ACGTTTACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
22 4 0.14
23 6 0.21
24 8 0.28
25 5 0.17
26 6 0.21
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
TTATTTTTATATAAAATAAACA
Found at i:666482 original size:2 final size:2
Alignment explanation
Indices: 666475--666499 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
666465 TGAAACCAAC
666475 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
666500 GTTTAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:667276 original size:16 final size:17
Alignment explanation
Indices: 667255--667288 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
667245 TTCTTTTTCA
667255 ACTAAT-TATTTATTTT
1 ACTAATATATTTATTTT
667271 ACTAATGATATTTATTTT
1 ACTAAT-ATATTTATTTT
667289 TAAAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (17 bp):
ACTAATATATTTATTTT
Found at i:669378 original size:126 final size:127
Alignment explanation
Indices: 669151--669439 Score: 375
Period size: 126 Copynumber: 2.3 Consensus size: 127
669141 GCTACGTCTT
* * * **
669151 GGAAAACAAAACAGGAACACGTTTGATACTTATAAGCGCACACACAGTGTTTAATGTAAATATTG
1 GGAAAACAAAACAGGAACACATTTGATACTTACAA-CGCACACACAGTGTTTAATGTAAACATCA
** *
669216 GAATAGCATATACATGAACAATCGGACGATAAGGCTCT-GGCAATTTCAGCACGGCCACATCTC
65 GAATAGCATATACATGAACAATAAGACGACAAGGCTCTAGG-AATTTCAGCACGGCCACATCTC
*
669279 GGAAAACAAAACAGGAACACATTTGATACTTACAA-GCATACACAGTGTTTAATGTAAACATCAG
1 GGAAAACAAAACAGGAACACATTTGATACTTACAACGCACACACAGTGTTTAATGTAAACATCAG
* ** *
669343 AATAGTATATACATGAACTGTAAGACGACAAGGCTCTAGGAATTTCAGCACGGCCGCATCTC
66 AATAGCATATACATGAACAATAAGACGACAAGGCTCTAGGAATTTCAGCACGGCCACATCTC
* * * ** *
669405 CGAACATAAAACAGGAACGTATTTGATTCTTACAA
1 GGAAAACAAAACAGGAACACATTTGATACTTACAA
669440 TCACGCGCCA
Statistics
Matches: 141, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
126 106 0.75
127 2 0.01
128 33 0.23
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (127 bp):
GGAAAACAAAACAGGAACACATTTGATACTTACAACGCACACACAGTGTTTAATGTAAACATCAG
AATAGCATATACATGAACAATAAGACGACAAGGCTCTAGGAATTTCAGCACGGCCACATCTC
Done.