Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015366.1 Kokia drynarioides strain JFW-HI SEQ_130413, 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: 628308
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 91 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:434694 original size:164 final size:163
Alignment explanation
Indices: 434406--434907 Score: 501
Period size: 164 Copynumber: 3.0 Consensus size: 163
434396 TATCGTATAA
* * * *
434406 CATAATCAATCAAATATTATTTACCATATCATGCATATCGTATAGCATAATCAATCAAATAATAT
1 CATAATCAATCAAATAGTATTTACCACATCATGAATATCGTATAGCATAATCAATCAAATAATAG
* ** * * **
434471 TTACCATATCATGCATATTGTATAGCATAATCAATCAAATAATATTTATCATATCATGCATATTG
66 TTACCATATCATACATAACGTATAACATAATCAATCAAATAATATTCATCATATCATGCATATCA
* * * *
434536 TATAACATACTTAATCAATTAATATTTACCATAT
131 TATAACATAATCAATCAA-AAATATTTAACATAT
* *
434570 CATAATTAATCAAATAGTATTTACCACATCATGAATATCGTATAGCATGATCAATCAAATAATAG
1 CATAATCAATCAAATAGTATTTACCACATCATGAATATCGTATAGCATAATCAATCAAATAATAG
*
434635 TTACCATATCATACATAACGTATAACATAATCAATCAAATAATATTCATCATGTCATGCATATCA
66 TTACCATATCATACATAACGTATAACATAATCAATCAAATAATATTCATCATATCATGCATATCA
*
434700 TATAGCATAATCAATCAAAAATATTTAACATAT
131 TATAACATAATCAATCAAAAATATTTAACATAT
*** * * * *
434733 CAT-A-CATATTGTATAGCA-TAATCA-ATCAAAT-AATATTTACCATGTCATGCATACATAATC
1 CATAATCA-ATCAAATAGTATTTACCACATC--ATGAATA--T--C--GT-AT--A-GCATAATC
* ** * * *
434793 AATCAAATAATATTTACCATATCATACATGTCGTACAACATAATCAATCAAATAATATTTACCAT
53 AATCAAATAATAGTTACCATATCATACATAACGTATAACATAATCAATCAAATAATATTCATCAT
* * * * *
434858 ATCATGCATATCGTATAGCATAATCAATCTAATAATATTTACCATGT
118 ATCATGCATATCATATAACATAATCAATC-AAAAATATTTAACATAT
434905 CAT
1 CAT
434908 GCATATCATA
Statistics
Matches: 285, Mismatches: 39, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
160 3 0.01
161 9 0.03
162 10 0.04
163 17 0.06
164 131 0.46
165 1 0.00
167 2 0.01
168 2 0.01
170 1 0.00
171 92 0.32
172 17 0.06
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (163 bp):
CATAATCAATCAAATAGTATTTACCACATCATGAATATCGTATAGCATAATCAATCAAATAATAG
TTACCATATCATACATAACGTATAACATAATCAATCAAATAATATTCATCATATCATGCATATCA
TATAACATAATCAATCAAAAATATTTAACATAT
Found at i:434793 original size:33 final size:34
Alignment explanation
Indices: 434748--434817 Score: 97
Period size: 37 Copynumber: 2.0 Consensus size: 34
434738 ATATTGTATA
*
434748 GCAT-AATCAATCAAATAATATTTACCATGTCAT
1 GCATAAATCAATCAAATAATATTTACCATATCAT
434781 GCATACATAATCAATCAAATAATATTTACCATATCAT
1 GCAT--A-AATCAATCAAATAATATTTACCATATCAT
434818 ACATGTCGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 4 0.12
37 28 0.88
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (34 bp):
GCATAAATCAATCAAATAATATTTACCATATCAT
Found at i:434821 original size:171 final size:172
Alignment explanation
Indices: 434619--434957 Score: 509
Period size: 171 Copynumber: 2.0 Consensus size: 172
434609 GTATAGCATG
* *
434619 ATCAATCAAATAATAGTTACCATATCATACATAACGTATAACATAATCAATCAAATAATATTCAT
1 ATCAATCAAATAATAGTTACCATATCATACATAACGTACAACATAATCAATCAAATAATATTCAC
* **
434684 CATGTCATGCATATCATATAGCATAATCAATC-AAAAATATTTAACATATCATACATATTGTATA
66 CATATCATGCATATCATATAGCATAATCAATCTAAAAATATTTAACATATCATACATATCATATA
* * *
434748 GCATAATCAATCAAATAATATTTACCATGTCATGCATACATA
131 GCACAATCAATCAAATAATATTTACCATATCATACATACATA
* ** *
434790 ATCAATCAAATAATATTTACCATATCATACATGTCGTACAACATAATCAATCAAATAATATTTAC
1 ATCAATCAAATAATAGTTACCATATCATACATAACGTACAACATAATCAATCAAATAATATTCAC
* * * * *
434855 CATATCATGCATATCGTATAGCATAATCAATCTAATAATATTTACCATGTCATGCATATCATATA
66 CATATCATGCATATCATATAGCATAATCAATCTAAAAATATTTAACATATCATACATATCATATA
*
434920 GCACAATCAATCAAATAATATTTATCATATCATACATA
131 GCACAATCAATCAAATAATATTTACCATATCATACATA
434958 TCGTATAGCA
Statistics
Matches: 149, Mismatches: 18, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
171 89 0.60
172 60 0.40
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.33
Consensus pattern (172 bp):
ATCAATCAAATAATAGTTACCATATCATACATAACGTACAACATAATCAATCAAATAATATTCAC
CATATCATGCATATCATATAGCATAATCAATCTAAAAATATTTAACATATCATACATATCATATA
GCACAATCAATCAAATAATATTTACCATATCATACATACATA
Found at i:435013 original size:172 final size:170
Alignment explanation
Indices: 434659--435310 Score: 566
Period size: 172 Copynumber: 3.9 Consensus size: 170
434649 ATAACGTATA
* * *
434659 ACATAATCAATCAAATAATATTCATCATGTCATGCATATCATATAGCATAATCAATCAAA-AATA
1 ACATAATCAATCAAATAATATTTACCATGTCATGCATATCGTATAGCATAATCAATCAAATAATA
* * ** *
434723 TTTAACATATCATACATATTGTATAGCATAATCAATCAAATAATATTTACCATGTCATGCATA-C
66 TTTACCATATCATGCATATCATATAGCATAATCAATCAAATAATATTTACCATATCATGCATATC
* *
434787 --ATA--ATCAATCAAAT-AATATTTACCATATCATACA-TGTCGTACA-
131 GTATAGCAT-AAT-AAATCAA-A--TA--ATAT-TTA-AGTGTC-TGCAT
* *
434830 ACATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAGCATAATCAATCTAATAATA
1 ACATAATCAATCAAATAATATTTACCATGTCATGCATATCGTATAGCATAATCAATCAAATAATA
* * * *
434895 TTTACCATGTCATGCATATCATATAGCACAATCAATCAAATAATATTTATCATATCATACATATC
66 TTTACCATATCATGCATATCATATAGCATAATCAATCAAATAATATTTACCATATCATGCATATC
434960 GTATAGCATAATAAATCAAATAATATTTAAGGTGTCATGCAT
131 GTATAGCATAATAAATCAAATAATATTTAA-GTGTC-TGCAT
* * * * *
435002 ACATAATCAATCAAATAATATTTACCATGTCATGCATATTGTATAGAACACTTAATCAAATAATA
1 ACATAATCAATCAAATAATATTTACCATGTCATGCATATCGTATAGCATAATCAATCAAATAATA
* * * **
435067 TTTACCACATCGTGCATACCATATAGCATTGTCAATCAAATAATA-TT----TATCATG----TC
66 TTTACCATATCATGCATATCATATAGCATAATCAATCAAATAATATTTACCATATCATGCATATC
** * * * *
435123 GTATAGCATAAGCAATCAAATAACATTTATCGTAT-TGTAT
131 GTATAGCATAATAAATCAAATAATATTTA-AGTGTCTGCAT
* *
435163 AGCATAATTAATCAAATAATATTTACCAT-T--T-C--AT-GCATA-CATAATCAATCAAATAAT
1 A-CATAATCAATCAAATAATATTTACCATGTCATGCATATCGTATAGCATAATCAATCAAATAAT
* * ** * * * ** *
435220 ATTTACAATGTCATGCATATTGTATAGAATACTTAATCGGATAATATTTACCATATCATGCATAC
65 ATTTACCATATCATGCATATCATATAGCATAATCAATCAAATAATATTTACCATATCATGCATAT
* * *
435285 CGTATAACATAGTCAATCAAATAATA
130 CGTATAGCATAATAAATCAAATAATA
435311 CTTACCATAT
Statistics
Matches: 398, Mismatches: 62, Indels: 50
0.78 0.12 0.10
Matches are distributed among these distances:
154 47 0.12
155 6 0.02
156 2 0.01
158 1 0.00
159 8 0.02
161 6 0.02
162 26 0.07
163 53 0.13
167 6 0.02
169 1 0.00
170 2 0.01
171 68 0.17
172 154 0.39
173 3 0.01
175 8 0.02
176 5 0.01
177 2 0.01
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.34
Consensus pattern (170 bp):
ACATAATCAATCAAATAATATTTACCATGTCATGCATATCGTATAGCATAATCAATCAAATAATA
TTTACCATATCATGCATATCATATAGCATAATCAATCAAATAATATTTACCATATCATGCATATC
GTATAGCATAATAAATCAAATAATATTTAAGTGTCTGCAT
Found at i:435139 original size:36 final size:36
Alignment explanation
Indices: 435088--435224 Score: 150
Period size: 36 Copynumber: 3.8 Consensus size: 36
435078 GTGCATACCA
** *
435088 TATAGCATTGTCAATCAAATAATATTTATCATGTCG
1 TATAGCATAATCAATCAAATAATATTTATCATATCG
* * * *
435124 TATAGCATAAGCAATCAAATAACATTTATCGTATTG
1 TATAGCATAATCAATCAAATAATATTTATCATATCG
* * *
435160 TATAGCATAATTAATCAAATAATATTTACCATTTCATG
1 TATAGCATAATCAATCAAATAATATTTATCATATC--G
*
435198 CATA-CATAATCAATCAAATAATATTTA
1 TATAGCATAATCAATCAAATAATATTTA
435225 CAATGTCATG
Statistics
Matches: 83, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
36 57 0.69
37 22 0.27
38 4 0.05
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.36
Consensus pattern (36 bp):
TATAGCATAATCAATCAAATAATATTTATCATATCG
Found at i:435266 original size:199 final size:199
Alignment explanation
Indices: 434362--435449 Score: 847
Period size: 199 Copynumber: 5.3 Consensus size: 199
434352 GTCGTAAAGT
* * * * * *
434362 ATAATCAATCAAATAATATTTACCATATCACGCATATCGTATA-ACATAATCAATCAAATATTAT
1 ATAATCAATCAAATAATATTTACCATGTCATGCATATTGTATAGA-ATACTTAATCAAATAATAT
* * *
434426 TTACCATATCATGCATATCGTATAGCATAATCAATCAAATAATATTTACCATATCATGCATATTG
65 TTACCATATCATGCATACCGTATAGCATAGTCAATCAAATAATA-TT----TATCATG----TCG
* * * *
434491 TATAGCATAATCAATCAAATAATATTTATCATATCATGCATATTGTATAACATACTTAATCAATT
121 TATAGCATAATCAATCAAATAACATTTATCATAT--TG--TATAGCAT-A-ATA---AATCAAAT
434556 AATATTTACCA--T-AT-CATA-
177 AATATTTACCATGTCATGCATAC
* ** * * * * *
434574 AT--T-AATCAAATAGTATTTACCACATCATGAATATCGTATAGCATGA-TCAATCAAATAATAG
1 ATAATCAATCAAATAATATTTACCATGTCATGCATATTGTATAGAAT-ACTTAATCAAATAATAT
* * * * *
434635 TTACCATATCATACATAACGTATAACATAATCAATCAAATAATATTCATCATGTCATGCATATCA
65 TTACCATATCATGCATACCGTATAGCATAGTCAATCAAATAATATT--T-A--TCATG----TCG
* *
434700 TATAGCATAATCAATCAAAAATATTTAACATATCATACATATTGTATAGCATAATCAATCAAATA
121 TATAGCATAATCAATC---AA-A--TAACAT-TTAT-CATATTGTATAGCATAATAAATCAAATA
434765 ATATTTACCATGTCATGCATAC
178 ATATTTACCATGTCATGCATAC
* * * * * * *
434787 ATAATCAATCAAATAATATTTACCATATCATACATGTCGTACA-ACATAATCAATCAAATAATAT
1 ATAATCAATCAAATAATATTTACCATGTCATGCATATTGTATAGA-ATACTTAATCAAATAATAT
* * * *
434851 TTACCATATCATGCATATCGTATAGCATAATCAATCTAATAATATTTACCATGTCATGCATATCA
65 TTACCATATCATGCATACCGTATAGCATAGTCAATCAAATAATATTT---A--TCATG----TCG
* *
434916 TATAGCACAATCAATCAAATAATATTTATCATATCATACATATCGTATAGCATAATAAATCAAAT
121 TATAGCATAATCAATCAAATAACA--T-T--TATCAT--AT-T-GTATAGCATAATAAATCAAAT
***
434981 AATATTTAAGGTGTCATGCATAC
177 AATATTTACCATGTCATGCATAC
*
435004 ATAATCAATCAAATAATATTTACCATGTCATGCATATTGTATAGAACACTTAATCAAATAATATT
1 ATAATCAATCAAATAATATTTACCATGTCATGCATATTGTATAGAATACTTAATCAAATAATATT
* * * *
435069 TACCACATCGTGCATACCATATAGCATTGTCAATCAAATAATATTTATCATGTCGTATAGCATAA
66 TACCATATCATGCATACCGTATAGCATAGTCAATCAAATAATATTTATCATGTCGTATAGCATAA
* * * *
435134 GCAATCAAATAACATTTATCGTATTGTATAGCATAATTAATCAAATAATATTTACCATTTCATGC
131 TCAATCAAATAACATTTATCATATTGTATAGCATAATAAATCAAATAATATTTACCATGTCATGC
435199 ATAC
196 ATAC
* **
435203 ATAATCAATCAAATAATATTTACAATGTCATGCATATTGTATAGAATACTTAATCGGATAATATT
1 ATAATCAATCAAATAATATTTACCATGTCATGCATATTGTATAGAATACTTAATCAAATAATATT
* * * * *
435268 TACCATATCATGCATACCGTATAACATAGTCAATCAAATAATACTTACCATATCGTGTAGCATAA
66 TACCATATCATGCATACCGTATAGCATAGTCAATCAAATAATATTTATCATGTCGTATAGCATAA
* * * *
435333 TCAATCAAAT---A---A-C--ATT-T-TAGCATAATTAATCAAATAATAATTACCATATC--GT
131 TCAATCAAATAACATTTATCATATTGTATAGCATAATAAATCAAATAATATTTACCATGTCATGC
435385 ATAGC
196 ATA-C
* * * ** * *
435390 ACAATCAATCAAATAACATTTACCATATCATGCATATCATATAGCATAATTAATCAAATA
1 ATAATCAATCAAATAATATTTACCATGTCATGCATATTGTATAGAATACTTAATCAAATA
435450 CTAACTAACT
Statistics
Matches: 752, Mismatches: 89, Indels: 95
0.80 0.10 0.10
Matches are distributed among these distances:
186 4 0.01
187 51 0.07
188 31 0.04
189 1 0.00
190 3 0.00
192 1 0.00
193 1 0.00
196 1 0.00
199 165 0.22
200 1 0.00
201 2 0.00
203 5 0.01
205 1 0.00
206 4 0.01
207 1 0.00
208 43 0.06
209 115 0.15
210 7 0.01
211 4 0.01
212 18 0.02
213 14 0.02
214 4 0.01
215 11 0.01
216 124 0.16
217 139 0.18
218 1 0.00
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.34
Consensus pattern (199 bp):
ATAATCAATCAAATAATATTTACCATGTCATGCATATTGTATAGAATACTTAATCAAATAATATT
TACCATATCATGCATACCGTATAGCATAGTCAATCAAATAATATTTATCATGTCGTATAGCATAA
TCAATCAAATAACATTTATCATATTGTATAGCATAATAAATCAAATAATATTTACCATGTCATGC
ATAC
Found at i:435342 original size:36 final size:34
Alignment explanation
Indices: 435292--435418 Score: 110
Period size: 36 Copynumber: 3.9 Consensus size: 34
435282 TACCGTATAA
*
435292 CATAGTCAATCAAATAATACTTACCATATCGTGTAG
1 CATAATCAATCAAATAATA-TTACCATATCGT-TAG
435328 CATAATCAATC--A-AATA--A-CAT-T--TTAG
1 CATAATCAATCAAATAATATTACCATATCGTTAG
*
435353 CATAATTAATCAAATAATAATTACCATATCGTATAG
1 CATAATCAATCAAATAAT-ATTACCATATCGT-TAG
* *
435389 CACAATCAATCAAATAACATTTACCATATC
1 CATAATCAATCAAATAATA-TTACCATATC
435419 ATGCATATCA
Statistics
Matches: 74, Mismatches: 5, Indels: 24
0.72 0.05 0.23
Matches are distributed among these distances:
25 13 0.18
26 1 0.01
27 1 0.01
28 4 0.05
29 4 0.05
30 1 0.01
31 1 0.01
32 3 0.04
33 5 0.07
34 1 0.01
35 2 0.03
36 38 0.51
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.31
Consensus pattern (34 bp):
CATAATCAATCAAATAATATTACCATATCGTTAG
Found at i:435831 original size:57 final size:57
Alignment explanation
Indices: 435685--435859 Score: 228
Period size: 57 Copynumber: 3.1 Consensus size: 57
435675 TAATTTTTTT
* * * *
435685 GAAAAATTGTGGCAAAACTATAAAATCTGGAAAATTAGTAGTAAAACTAT-AAATCT-
1 GAAAAATAGTGGCAAAACTGTAAAATCTGGAAAA-TAGTGGCAAAACTATAAAATCTG
* * *
435741 GCAAAACAGTGGCAAAACTGTAAAATCTGGAAAATAATGGCAAAACTATAAAATCTG
1 GAAAAATAGTGGCAAAACTGTAAAATCTGGAAAATAGTGGCAAAACTATAAAATCTG
* * * *
435798 GAAAAATAGTGGCAAAATTGTAAAATCTAGAAAATAGTGGCAAAACTGTAAAATATG
1 GAAAAATAGTGGCAAAACTGTAAAATCTGGAAAATAGTGGCAAAACTATAAAATCTG
435855 GAAAA
1 GAAAA
435860 CCAATAGCAA
Statistics
Matches: 103, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
55 12 0.12
56 36 0.35
57 55 0.53
ACGTcount: A:0.51, C:0.10, G:0.17, T:0.22
Consensus pattern (57 bp):
GAAAAATAGTGGCAAAACTGTAAAATCTGGAAAATAGTGGCAAAACTATAAAATCTG
Found at i:435870 original size:57 final size:57
Alignment explanation
Indices: 435696--435880 Score: 176
Period size: 57 Copynumber: 3.3 Consensus size: 57
435686 AAAAATTGTG
* * * * * * * * *
435696 GCAAAACTATAAAATCTGGAAAATTAGTAGTAAAACTAT-AAATCT-GCAAAACAGTG
1 GCAAAACTGTAAAATCTAGAAAA-TAATGGCAAAACTATAAAATATGGAAAAACAATA
* * * * *
435752 GCAAAACTGTAAAATCTGGAAAATAATGGCAAAACTATAAAATCTGGAAAAATAGTG
1 GCAAAACTGTAAAATCTAGAAAATAATGGCAAAACTATAAAATATGGAAAAACAATA
* * * *
435809 GCAAAATTGTAAAATCTAGAAAATAGTGGCAAAACTGTAAAATATGGAAAACCAATA
1 GCAAAACTGTAAAATCTAGAAAATAATGGCAAAACTATAAAATATGGAAAAACAATA
*
435866 GCAAAACTATAAAAT
1 GCAAAACTGTAAAAT
435881 AGTGGCAATT
Statistics
Matches: 110, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
55 12 0.11
56 28 0.25
57 70 0.64
ACGTcount: A:0.52, C:0.11, G:0.15, T:0.22
Consensus pattern (57 bp):
GCAAAACTGTAAAATCTAGAAAATAATGGCAAAACTATAAAATATGGAAAAACAATA
Found at i:435881 original size:29 final size:28
Alignment explanation
Indices: 435687--435880 Score: 219
Period size: 28 Copynumber: 6.9 Consensus size: 28
435677 ATTTTTTTGA
*
435687 AAAATTGTGGCAAAACTATAAAATCTGG
1 AAAATAGTGGCAAAACTATAAAATCTGG
* * *
435715 AAAATTAGTAGTAAAACTAT-AAATCTGC
1 AAAA-TAGTGGCAAAACTATAAAATCTGG
* *
435743 AAAACAGTGGCAAAACTGTAAAATCTGG
1 AAAATAGTGGCAAAACTATAAAATCTGG
*
435771 AAAATAATGGCAAAACTATAAAATCTGG
1 AAAATAGTGGCAAAACTATAAAATCTGG
* * *
435799 AAAAATAGTGGCAAAATTGTAAAATCTAG
1 -AAAATAGTGGCAAAACTATAAAATCTGG
* *
435828 AAAATAGTGGCAAAACTGTAAAATATGG
1 AAAATAGTGGCAAAACTATAAAATCTGG
* * *
435856 AAAACCAATAGCAAAACTATAAAAT
1 AAAA-TAGTGGCAAAACTATAAAAT
435881 AGTGGCAATT
Statistics
Matches: 139, Mismatches: 23, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
27 11 0.08
28 76 0.55
29 52 0.37
ACGTcount: A:0.52, C:0.11, G:0.15, T:0.22
Consensus pattern (28 bp):
AAAATAGTGGCAAAACTATAAAATCTGG
Found at i:446690 original size:14 final size:14
Alignment explanation
Indices: 446673--446703 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
446663 CGAAAATAGT
446673 TTTCAAAAAAATGA
1 TTTCAAAAAAATGA
*
446687 TTTCTAAAAAATGA
1 TTTCAAAAAAATGA
446701 TTT
1 TTT
446704 ATTGGGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (14 bp):
TTTCAAAAAAATGA
Found at i:446980 original size:30 final size:30
Alignment explanation
Indices: 446929--446988 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
446919 AAATAAATAC
446929 ATTAAATTAAATATATAATAG-TACTAAATT
1 ATTAAATTAAATATATAATAGTTA-TAAATT
* *
446959 ATTAAGTTAGAATAT-TTATAGTTATAAATT
1 ATTAAATTA-AATATATAATAGTTATAAATT
446989 GAAAACAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (30 bp):
ATTAAATTAAATATATAATAGTTATAAATT
Found at i:453566 original size:37 final size:37
Alignment explanation
Indices: 453504--453594 Score: 119
Period size: 37 Copynumber: 2.5 Consensus size: 37
453494 TTGGATCACA
* * * *
453504 GACACAAAGCCTACTAGGCAGATAGCTCGAAGACACC
1 GACACGAAGCCTACTAGACACATAGCCCGAAGACACC
* * *
453541 GGCACGAAGCCTGCTAGACACATAGCCCGAATACACC
1 GACACGAAGCCTACTAGACACATAGCCCGAAGACACC
453578 GACACGAAGCCTACTAG
1 GACACGAAGCCTACTAG
453595 GCATACAACC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.35, C:0.32, G:0.22, T:0.11
Consensus pattern (37 bp):
GACACGAAGCCTACTAGACACATAGCCCGAAGACACC
Found at i:453610 original size:37 final size:36
Alignment explanation
Indices: 453504--453635 Score: 111
Period size: 37 Copynumber: 3.6 Consensus size: 36
453494 TTGGATCACA
* * * * *
453504 GACACAAAGCCTACTAGGCAGATAGCTCGAAGACACC
1 GACACGAAGCCTACTAGGCACAAACCT-GAATACACC
* * * * *
453541 GGCACGAAGCCTGCTAGACACATAGCCCGAATACACC
1 GACACGAAGCCTACTAGGCACA-AACCTGAATACACC
* *
453578 GACACGAAGCCTACTAGGCATACAACCTGAATACATC
1 GACACGAAGCCTACTAGGCACA-AACCTGAATACACC
* *
453615 GGCACGAAGCCTATTAGGCAC
1 GACACGAAGCCTACTAGGCAC
453636 GAAGCCTATT
Statistics
Matches: 73, Mismatches: 21, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
37 72 0.99
38 1 0.01
ACGTcount: A:0.35, C:0.31, G:0.21, T:0.13
Consensus pattern (36 bp):
GACACGAAGCCTACTAGGCACAAACCTGAATACACC
Found at i:453658 original size:16 final size:16
Alignment explanation
Indices: 453615--453651 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
453605 TGAATACATC
453615 GGCACGAAGCCTATTA
1 GGCACGAAGCCTATTA
453631 GGCACGAAGCCTATTA
1 GGCACGAAGCCTATTA
453647 GGCAC
1 GGCAC
453652 ATAGCCTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (16 bp):
GGCACGAAGCCTATTA
Found at i:453686 original size:37 final size:37
Alignment explanation
Indices: 453631--453810 Score: 216
Period size: 37 Copynumber: 4.9 Consensus size: 37
453621 AAGCCTATTA
** *
453631 GGCACGAAGCCTATTAGGCACATAGCCTGAATACACC
1 GGCACGAAGCCTGCTAGGCACACAGCCTGAATACACC
* * * *
453668 GGTACGAAGCTTGCTAGGCACACAGTCTGAATACATC
1 GGCACGAAGCCTGCTAGGCACACAGCCTGAATACACC
* *
453705 GGCACGAAGTCTGCTAGGCACACAGCCTGAATGCACC
1 GGCACGAAGCCTGCTAGGCACACAGCCTGAATACACC
* * * *
453742 GGCAGGAAGCCTGCTAGGCACGCAGCATGAATATACC
1 GGCACGAAGCCTGCTAGGCACACAGCCTGAATACACC
* * *
453779 AGCACGAAGCCTACTAGGCACACAACCTGAAT
1 GGCACGAAGCCTGCTAGGCACACAGCCTGAAT
453811 TTGTAGATGT
Statistics
Matches: 118, Mismatches: 25, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 118 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (37 bp):
GGCACGAAGCCTGCTAGGCACACAGCCTGAATACACC
Found at i:453686 original size:53 final size:53
Alignment explanation
Indices: 453580--453688 Score: 137
Period size: 53 Copynumber: 2.1 Consensus size: 53
453570 AATACACCGA
* * *
453580 CACGAAGCCTACTAGGCATACAACCTGAATACATCGGCACGAAGCCTATTAGG
1 CACGAAGCCTACTAGGCACACAACCTGAATACACCGGCACGAAGCCTACTAGG
* * * * * *
453633 CACGAAGCCTATTAGGCACATAGCCTGAATACACCGGTACGAAGCTTGCTAGG
1 CACGAAGCCTACTAGGCACACAACCTGAATACACCGGCACGAAGCCTACTAGG
453686 CAC
1 CAC
453689 ACAGTCTGAA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.17
Consensus pattern (53 bp):
CACGAAGCCTACTAGGCACACAACCTGAATACACCGGCACGAAGCCTACTAGG
Found at i:453698 original size:90 final size:90
Alignment explanation
Indices: 453541--453713 Score: 247
Period size: 90 Copynumber: 1.9 Consensus size: 90
453531 CGAAGACACC
* *
453541 GGCACGAAGCCTGCTAGACACATAGCCCGAATACACCGACACGAAGCCTACTAGGCATACAACCT
1 GGCACGAAGCCTACTAGACACATAGCCCGAATACACCGACACGAAGCCTACTAGGCACACAACCT
453606 GAATACATCGGCACGAAGCCTATTA
66 GAATACATCGGCACGAAGCCTATTA
* * * ** * * **
453631 GGCACGAAGCCTATTAGGCACATAGCCTGAATACACCGGTACGAAGCTTGCTAGGCACACAGTCT
1 GGCACGAAGCCTACTAGACACATAGCCCGAATACACCGACACGAAGCCTACTAGGCACACAACCT
453696 GAATACATCGGCACGAAG
66 GAATACATCGGCACGAAG
453714 TCTGCTAGGC
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
90 72 1.00
ACGTcount: A:0.33, C:0.29, G:0.23, T:0.16
Consensus pattern (90 bp):
GGCACGAAGCCTACTAGACACATAGCCCGAATACACCGACACGAAGCCTACTAGGCACACAACCT
GAATACATCGGCACGAAGCCTATTA
Found at i:453736 original size:127 final size:127
Alignment explanation
Indices: 453510--453763 Score: 312
Period size: 127 Copynumber: 2.0 Consensus size: 127
453500 CACAGACACA
* *
453510 AAGCCTACTAGGCAGATAGCTCGAAGACACCGGCACGAAGCCTGCTAGACACATAGCCCGAATAC
1 AAGCCTACTAGGCACATAGCTCGAAGACACCGGCACGAAGCCTGCTAGACACACAGCCCGAATAC
* * *
453575 ACCGACACGAAGCCTACTAGGCATACAACCTGAATACATCGGCACGAAGCCTATTAGGCACG
66 ACCGACACGAAGCCTACTAGGCACACAACCTGAATACACCGGCACGAAGCCTACTAGGCACG
* * * * * * *
453637 AAGCCTATTAGGCACATAGC-CTGAATACACCGGTACGAAGCTTGCTAGGCACACAGTCTGAATA
1 AAGCCTACTAGGCACATAGCTC-GAAGACACCGGCACGAAGCCTGCTAGACACACAGCCCGAATA
* * * * * * * *
453701 CATCGGCACGAAGTCTGCTAGGCACACAGCCTGAATGCACCGGCAGGAAGCCTGCTAGGCACG
65 CACCGACACGAAGCCTACTAGGCACACAACCTGAATACACCGGCACGAAGCCTACTAGGCACG
453764 CAGCATGAAT
Statistics
Matches: 106, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
126 1 0.01
127 105 0.99
ACGTcount: A:0.31, C:0.30, G:0.24, T:0.15
Consensus pattern (127 bp):
AAGCCTACTAGGCACATAGCTCGAAGACACCGGCACGAAGCCTGCTAGACACACAGCCCGAATAC
ACCGACACGAAGCCTACTAGGCACACAACCTGAATACACCGGCACGAAGCCTACTAGGCACG
Found at i:455902 original size:41 final size:41
Alignment explanation
Indices: 455780--455902 Score: 133
Period size: 41 Copynumber: 3.0 Consensus size: 41
455770 GTCACACAGT
* * * *
455780 CGTGTGGTAGGACGTGTGGCAGACCGTTTGGGTCACACGA-C
1 CGTGTGGTAGGTCGTGTGGCA-AACGTGTGGGTCACACGATA
* *
455821 CGTGTGGTAGGTTGTGTGGCAAACTGTGTTGGTCACACGATA
1 CGTGTGGTAGGTCGTGTGGCAAAC-GTGTGGGTCACACGATA
* *
455863 GGT-TGGTAGGTCATGTGGCAAATCGTGTGGGTCACACGAT
1 CGTGTGGTAGGTCGTGTGGCAAA-CGTGTGGGTCACACGAT
455903 CGTATGATAG
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
40 2 0.03
41 64 0.93
42 3 0.04
ACGTcount: A:0.19, C:0.17, G:0.37, T:0.27
Consensus pattern (41 bp):
CGTGTGGTAGGTCGTGTGGCAAACGTGTGGGTCACACGATA
Found at i:455919 original size:41 final size:39
Alignment explanation
Indices: 455770--455920 Score: 124
Period size: 41 Copynumber: 3.7 Consensus size: 39
455760 AGCAGAATGC
* * * *
455770 GTCACAC-AGTCGTGTGGTAGGACGTGTGGCAGACCGTTTGG
1 GTCACACGA-TCGT-TGGTAGGTCATGTGGCA-AACGTGTGG
* ** *
455811 GTCACACGACCGTGTGGTAGGTTGTGTGGCAAACTGTGTTG
1 GTCACACGATCGT-TGGTAGGTCATGTGGCAAAC-GTGTGG
*
455852 GTCACACGATAGGTTGGTAGGTCATGTGGCAAATCGTGTGG
1 GTCACACGAT-CGTTGGTAGGTCATGTGGCAAA-CGTGTGG
* *
455893 GTCACACGATCGTATGATAGGCCATGTG
1 GTCACACGATCGT-TGGTAGGTCATGTG
455921 AGCCACACGA
Statistics
Matches: 91, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
40 4 0.04
41 83 0.91
42 4 0.04
ACGTcount: A:0.20, C:0.18, G:0.36, T:0.26
Consensus pattern (39 bp):
GTCACACGATCGTTGGTAGGTCATGTGGCAAACGTGTGG
Found at i:457065 original size:54 final size:54
Alignment explanation
Indices: 457015--457117 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 54
457005 TTGTGCCCAC
* * * *
457015 CCATGTGACTCACTGACATGGATCACACGATTGTGTCATAGACCGTGTGCCAGA
1 CCATGTAACTCACAGACATGGAACACACGATCGTGTCATAGACCGTGTGCCAGA
* *
457069 CCATGTAACTCACAGACATGGAACACAGGGTCGTGTCATAGACCGTGTG
1 CCATGTAACTCACAGACATGGAACACACGATCGTGTCATAGACCGTGTG
457118 TAGCACACGA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.22
Consensus pattern (54 bp):
CCATGTAACTCACAGACATGGAACACACGATCGTGTCATAGACCGTGTGCCAGA
Found at i:459062 original size:27 final size:26
Alignment explanation
Indices: 459016--459067 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
459006 AAAAAGATGA
*
459016 AACTAATGAGGTAAACAACAATGTTCC
1 AACTAATGAGGCAAACAAC-ATGTTCC
*
459043 AACTAATGAGGCAAAGAACATGTTC
1 AACTAATGAGGCAAACAACATGTTC
459068 TTCGGTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.21
Consensus pattern (26 bp):
AACTAATGAGGCAAACAACATGTTCC
Found at i:470718 original size:2 final size:2
Alignment explanation
Indices: 470711--470738 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
470701 AAAAAGGGTA
470711 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
470739 TCTGCCAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:493178 original size:36 final size:36
Alignment explanation
Indices: 493137--493236 Score: 137
Period size: 36 Copynumber: 2.8 Consensus size: 36
493127 GGTAATAAGC
493137 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
1 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
* * *
493173 ATGACCTTTGGGTCAACAAGAAGTAAAATGAGCATC
1 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
* * * *
493209 ATGACATTTAGGTCAACAGTGACTAAAA
1 ATGACCTTTGGGTCAACAGGGAGTAAAA
493237 CGAATAACGA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (36 bp):
ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
Found at i:493933 original size:21 final size:21
Alignment explanation
Indices: 493907--493958 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
493897 TTTTTAGTAC
*
493907 CGGTAGAAGTAAG-ACTTGTTT
1 CGGTAGAAGT-AGCACTTGTAT
493928 CGGTAGAA-TAGTCACTTGTAT
1 CGGTAGAAGTAG-CACTTGTAT
493949 CGGTAGAAGT
1 CGGTAGAAGT
493959 TTGCACCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 1 0.04
21 23 0.85
22 1 0.04
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.31
Consensus pattern (21 bp):
CGGTAGAAGTAGCACTTGTAT
Found at i:509236 original size:19 final size:20
Alignment explanation
Indices: 509211--509260 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
509201 AGTTAAGTAA
*
509211 AAAATATCATTTTTATAGGT
1 AAAATATCATTTTTATAGAT
*
509231 AAATATATTATTTTTATAGAT
1 AAA-ATATCATTTTTATAGAT
509252 -AAATATCAT
1 AAAATATCAT
509261 GAACACGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 6 0.23
20 5 0.19
21 15 0.58
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (20 bp):
AAAATATCATTTTTATAGAT
Found at i:509243 original size:21 final size:21
Alignment explanation
Indices: 509214--509257 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
509204 TAAGTAAAAA
*
509214 ATATCATTTTTATAGGTAAAT
1 ATATCATTTTTATAGATAAAT
*
509235 ATATTATTTTTATAGATAAAT
1 ATATCATTTTTATAGATAAAT
509256 AT
1 AT
509258 CATGAACACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (21 bp):
ATATCATTTTTATAGATAAAT
Found at i:510951 original size:19 final size:19
Alignment explanation
Indices: 510929--510994 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
510919 GGTTACAAAC
510929 TTTATCTGATTTTTACATG
1 TTTATCTGATTTTTACATG
*
510948 TTTATCTGAAAAATTTT-C-T-
1 TTTATCTG---ATTTTTACATG
*
510967 TTTATCTGTTTTTTACATG
1 TTTATCTGATTTTTACATG
510986 TTTATCTGA
1 TTTATCTGA
510995 CGAATTTTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
16 4 0.11
17 1 0.03
18 1 0.03
19 24 0.65
20 1 0.03
21 1 0.03
22 5 0.14
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.58
Consensus pattern (19 bp):
TTTATCTGATTTTTACATG
Found at i:510971 original size:38 final size:38
Alignment explanation
Indices: 510929--511010 Score: 137
Period size: 38 Copynumber: 2.2 Consensus size: 38
510919 GGTTACAAAC
510929 TTTATCTGATTTTTACATGTTTATCTGAAAAATTTTCT
1 TTTATCTGATTTTTACATGTTTATCTGAAAAATTTTCT
* **
510967 TTTATCTGTTTTTTACATGTTTATCTGACGAATTTTCT
1 TTTATCTGATTTTTACATGTTTATCTGAAAAATTTTCT
511005 TTTATC
1 TTTATC
511011 AAATTTTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.22, C:0.12, G:0.09, T:0.57
Consensus pattern (38 bp):
TTTATCTGATTTTTACATGTTTATCTGAAAAATTTTCT
Found at i:513745 original size:32 final size:31
Alignment explanation
Indices: 513709--513771 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
513699 TAAGTCCGTC
* *
513709 TATATTATTTCTAATTTTTCA-AATATTTATAT
1 TATATTATTT-TAATATTTAATAAT-TTTATAT
513741 TATATTATTTTAATATTTAATAATTTTATAT
1 TATATTATTTTAATATTTAATAATTTTATAT
513772 ATTTTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 15 0.54
32 13 0.46
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (31 bp):
TATATTATTTTAATATTTAATAATTTTATAT
Found at i:513785 original size:28 final size:28
Alignment explanation
Indices: 513741--513810 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
513731 ATATTTATAT
*
513741 TATATTATTTTAATATTTAATAATTTTA
1 TATATTATTTTAATATTGAATAATTTTA
* **
513769 TATATT-TTTTATTTATTGAATTTTTTTA
1 TATATTATTTTA-ATATTGAATAATTTTA
*
513797 TATAATCATTTTAA
1 TAT-ATTATTTTAA
513811 CATTATTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
27 5 0.15
28 21 0.64
29 2 0.06
30 5 0.15
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (28 bp):
TATATTATTTTAATATTGAATAATTTTA
Found at i:514423 original size:18 final size:18
Alignment explanation
Indices: 514400--514438 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
514390 AGGCTCAAAT
514400 ACCAGCAACATCCCCAAC
1 ACCAGCAACATCCCCAAC
*
514418 ACCAGCATCATCCCCAAC
1 ACCAGCAACATCCCCAAC
514436 ACC
1 ACC
514439 GGAGACTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.51, G:0.05, T:0.08
Consensus pattern (18 bp):
ACCAGCAACATCCCCAAC
Found at i:519834 original size:50 final size:50
Alignment explanation
Indices: 519629--519843 Score: 175
Period size: 50 Copynumber: 4.3 Consensus size: 50
519619 TTCATCTTGC
* * *
519629 TCCACTGCAACTTCAAGGAGATA-AAGATTTTCTTTCATAACTTTAATCCAA
1 TCCACTGCAACTTC-AGG-GATATAAGATTTGCTTTCGTAACTTCAATCCAA
* * * * * *
519680 -CCTACTGCAACTTCAGGGGTATAGGATTTGGTTTTGTAGCTTC-ATCCTAC
1 TCC-ACTGCAACTTCAGGGATATAAGATTTGCTTTCGTAACTTCAATCC-AA
* * * * * * * **
519730 TCTATTGCAACTTCAGAGAAATAAGTATTCGCCTTCGTAGCTTCAATCTGA
1 TCCACTGCAACTTCAGGGATATAAG-ATTTGCTTTCGTAACTTCAATCCAA
* *
519781 TCCACTGCAACTTCAGGGATATAAGATTTGGTTTCGTAACTTCACTCCAA
1 TCCACTGCAACTTCAGGGATATAAGATTTGCTTTCGTAACTTCAATCCAA
*
519831 TCCACTACAACTT
1 TCCACTGCAACTT
519844 TGTGGAGATC
Statistics
Matches: 124, Mismatches: 34, Indels: 13
0.73 0.20 0.08
Matches are distributed among these distances:
49 7 0.06
50 67 0.54
51 47 0.38
52 3 0.02
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.33
Consensus pattern (50 bp):
TCCACTGCAACTTCAGGGATATAAGATTTGCTTTCGTAACTTCAATCCAA
Found at i:519944 original size:152 final size:148
Alignment explanation
Indices: 519788--520124 Score: 381
Period size: 149 Copynumber: 2.2 Consensus size: 148
519778 TGATCCACTG
* * **
519788 CAACTTCAGGGATATAAGATTTG-GTTTCGTAACTTCACTCCAATCCACTACAACTTTGTGGAGA
1 CAACTTCAGGG-TATAAGATTCGAGGTT-GTAACTTCACTCCAATCCACTACAACTTCATGGAGA
* * * *
519852 TCGAGGTCTGCTACTGTGAGTTTTAATCTGCCCTTTTACAACTTTAAGGGTGTAGGATTTGCTAT
64 TCAAGGTCTGCTA-T-T-AGTTTTAATCTGCCCCTCTACAACTTTAAGGGTATAGGATTTGCTAT
*
519917 TGTAGTTTCAATCTGCCCCTCTA
126 TGTAGTTTCAACCTGCCCCTCTA
* * * * * *
519940 CAACTTTAGATGTATAAGATTCGAGGTTGTAACTTCGCTTCATTCCACTGCAACTTCATGGAGAT
1 CAACTTCAG-GGTATAAGATTCGAGGTTGTAACTTCACTCCAATCCACTACAACTTCATGGAGAT
* * * * * *
520005 TAAGGTTTGTTATTTGTTTTAATTTGCCCCTCTACAACTTTAAGGGTATAGGATTTGCTTTTGTA
65 CAAGGTCTGCTATTAGTTTTAATCTGCCCCTCTACAACTTTAAGGGTATAGGATTTGCTATTGTA
*
520070 GTTTCAACCTGCCCCTTTA
130 GTTTCAACCTGCCCCTCTA
*
520089 CAGC-TCTAGGGGTATAAGATTCGAGGTTGTAACTTC
1 CAACTTC-A-GGGTATAAGATTCGAGGTTGTAACTTC
520125 GCTACATTCT
Statistics
Matches: 156, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
148 1 0.01
149 91 0.58
150 2 0.01
151 1 0.01
152 57 0.37
153 4 0.03
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (148 bp):
CAACTTCAGGGTATAAGATTCGAGGTTGTAACTTCACTCCAATCCACTACAACTTCATGGAGATC
AAGGTCTGCTATTAGTTTTAATCTGCCCCTCTACAACTTTAAGGGTATAGGATTTGCTATTGTAG
TTTCAACCTGCCCCTCTA
Found at i:520189 original size:149 final size:149
Alignment explanation
Indices: 519888--520207 Score: 374
Period size: 149 Copynumber: 2.1 Consensus size: 149
519878 TCTGCCCTTT
* * * *
519888 TACAACTTTAAGGGTGTAGGATTTGCTATTGTAGTTTCAATCTGCCCCTCTACAACTTTAGATGT
1 TACAACTTTAAGGGTATAGGATTTGCTATTGTAGTTTCAACCTGCCCCTCTACAACTCTAGAGGT
* * * * * * *
519953 ATAAGATTCGAGGTTGTAACTTCGCTTCATTCCACTGCAACTTCATGGAGATTAAGGTTTGTTAT
66 ATAAGATTCGAGGTTGTAACTTCGCTACATTCCACTACAACTTCAGGGACATTAAGATTCGTTAC
** * * *
520018 TTGTTTTAATTTGCCCCTC
131 TCATTTTAATCTGACCCAC
* * * *
520037 TACAACTTTAAGGGTATAGGATTTGCTTTTGTAGTTTCAACCTGCCCCTTTACAGCTCTAGGGGT
1 TACAACTTTAAGGGTATAGGATTTGCTATTGTAGTTTCAACCTGCCCCTCTACAACTCTAGAGGT
* * *
520102 ATAAGATTCGAGGTTGTAACTTCGCTACATTCTACTATAACCTT-AGGGACATTGAGATTCGTTA
66 ATAAGATTCGAGGTTGTAACTTCGCTACATTCCACTACAA-CTTCAGGGACATTAAGATTCGTTA
* *
520166 CTCATTTTGATCTGATCCAC
130 CTCATTTTAATCTGACCCAC
*
520186 TACAAC-TTCAGGGATATAGGAT
1 TACAACTTTAAGGG-TATAGGAT
520208 CTGGTGCTTC
Statistics
Matches: 143, Mismatches: 26, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
148 6 0.04
149 134 0.94
150 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (149 bp):
TACAACTTTAAGGGTATAGGATTTGCTATTGTAGTTTCAACCTGCCCCTCTACAACTCTAGAGGT
ATAAGATTCGAGGTTGTAACTTCGCTACATTCCACTACAACTTCAGGGACATTAAGATTCGTTAC
TCATTTTAATCTGACCCAC
Found at i:520527 original size:49 final size:49
Alignment explanation
Indices: 520474--520681 Score: 204
Period size: 49 Copynumber: 4.2 Consensus size: 49
520464 TCATCTTCAA
** * *
520474 GGTATAAGATTCATCATTGTAGCTTCAATATTTCCCTTCATATCTCTAG
1 GGTATAAGATTCGCCATTATAGCTTCAATCTTTCCCTTCATATCTCTAG
* ** * *
520523 GGTATAAGGTTCGCCATTACGGCTTCAATCTTTCCCTTCATGTCTTTAG
1 GGTATAAGATTCGCCATTATAGCTTCAATCTTTCCCTTCATATCTCTAG
* * * * *
520572 GGTATAA-AGTTTGTCATTATGGCTTAAACCTTTCCC-TCGATATCTCTAG
1 GGTATAAGA-TTCGCCATTATAGCTTCAATCTTTCCCTTC-ATATCTCTAG
* * * * *
520621 GGTACAAGATTCGCCATTGTAGCTTCAATCTTTCCCTTCACATATCTAA
1 GGTATAAGATTCGCCATTATAGCTTCAATCTTTCCCTTCATATCTCTAG
*
520670 GGTATATGATTC
1 GGTATAAGATTC
520682 AACGTTTCCT
Statistics
Matches: 126, Mismatches: 29, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
48 2 0.02
49 121 0.96
50 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.38
Consensus pattern (49 bp):
GGTATAAGATTCGCCATTATAGCTTCAATCTTTCCCTTCATATCTCTAG
Found at i:521182 original size:112 final size:112
Alignment explanation
Indices: 521032--521253 Score: 345
Period size: 112 Copynumber: 2.0 Consensus size: 112
521022 CTTATATCGT
521032 TTAGACCACCAACCGTCATTCCAATGCAAAAATGCTTGAACAGAGTTGTAAAGTGGATAAAATTG
1 TTAGACCACCAACCGTCATTCCAATGCAAAAATGCTTGAACAGAGTTGTAAAGTGGATAAAATTG
***
521097 AATTTTATTGGAGGCAAAGCTCTTGTGAATGAAAAGATTAAAAATCA
66 AATTTTATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAATCA
* * * * * * * *
521144 TTAGTCCACTAACCGTTATTTCAATGCAAACATGCTTGAATAGGGTTGTAAGGTGGATAAAATTG
1 TTAGACCACCAACCGTCATTCCAATGCAAAAATGCTTGAACAGAGTTGTAAAGTGGATAAAATTG
521209 AATTTTATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAAT
66 AATTTTATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAAT
521254 GACAAACATT
Statistics
Matches: 99, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
112 99 1.00
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (112 bp):
TTAGACCACCAACCGTCATTCCAATGCAAAAATGCTTGAACAGAGTTGTAAAGTGGATAAAATTG
AATTTTATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAATCA
Found at i:521599 original size:12 final size:12
Alignment explanation
Indices: 521579--521621 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
521569 CTTTTTTCCC
*
521579 TTCTATTTCATTT
1 TTCT-TTTCTTTT
521592 TTCTTTTCTTTT
1 TTCTTTTCTTTT
521604 TTCTTTT-TTTT
1 TTCTTTTCTTTT
521615 TTCTTTT
1 TTCTTTT
521622 TTTCCTTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 11 0.38
12 14 0.48
13 4 0.14
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (12 bp):
TTCTTTTCTTTT
Found at i:521614 original size:9 final size:9
Alignment explanation
Indices: 521590--521664 Score: 53
Period size: 9 Copynumber: 7.9 Consensus size: 9
521580 TCTATTTCAT
521590 TTTTCTTTTC
1 TTTT-TTTTC
521600 TTTTTTCTT-
1 TTTTTT-TTC
521609 TTTTTTTTC
1 TTTTTTTTC
*
521618 TTTTTTTCC
1 TTTTTTTTC
* *
521627 TTTCTTTCC
1 TTTTTTTTC
*
521636 TTTCCTTTTC
1 TTT-TTTTTC
*
521646 TTCCTTTTCTC
1 TT--TTTTTTC
521657 TTTTTTTT
1 TTTTTTTT
521665 TGGGTGAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
8 2 0.04
9 32 0.59
10 13 0.24
11 6 0.11
12 1 0.02
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:521615 original size:23 final size:23
Alignment explanation
Indices: 521589--521665 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 23
521579 TTCTATTTCA
521589 TTTTTCTTTTCTTTTTTCTTTTT
1 TTTTTCTTTTCTTTTTTCTTTTT
*
521612 TTTTTCTTTT-TTTCCTTTC-TTTC
1 TTTTTCTTTTCTTT--TTTCTTTTT
* *
521635 CTTTCCTTTTCTTCCTTTTCTCTTTT
1 TTTTTCTTTTCTT--TTTTCT-TTTT
521661 TTTTT
1 TTTTT
521666 GGGTGAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
22 3 0.07
23 21 0.51
24 10 0.24
26 7 0.17
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTTCTTTTCTTTTTTCTTTTT
Found at i:521621 original size:48 final size:48
Alignment explanation
Indices: 521564--521665 Score: 127
Period size: 48 Copynumber: 2.1 Consensus size: 48
521554 CGACCTCTCC
* *
521564 TTTTTCTTTTTTCCCTTCTATTTCATTTTTCTTTTCTT-TTTTCT-TTTT
1 TTTTTCTTTTTTCCCTT-TATTTC-CTTTCCTTTTCTTCTTTTCTCTTTT
* *
521612 TTTTTCTTTTTTTCCTTTCTTTCCTTTCCTTTTCTTCCTTTTCTCTTTT
1 TTTTTCTTTTTTCCCTTTATTTCCTTTCCTTTTCTT-CTTTTCTCTTTT
521661 TTTTT
1 TTTTT
521666 GGGTGAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
46 11 0.23
47 5 0.11
48 22 0.47
49 9 0.19
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (48 bp):
TTTTTCTTTTTTCCCTTTATTTCCTTTCCTTTTCTTCTTTTCTCTTTT
Found at i:521623 original size:30 final size:31
Alignment explanation
Indices: 521565--521633 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 31
521555 GACCTCTCCT
521565 TTTTCTTTTTTCCCTTCTATTTC-ATTTTTC
1 TTTTCTTTTTTCCCTTCTATTTCTATTTTTC
** * * *
521595 TTTTCTTTTTTCTTTTTTTTTTCTTTTTTTC
1 TTTTCTTTTTTCCCTTCTATTTCTATTTTTC
*
521626 CTTTCTTT
1 TTTTCTTT
521634 CCTTTCCTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 19 0.59
31 13 0.41
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (31 bp):
TTTTCTTTTTTCCCTTCTATTTCTATTTTTC
Found at i:526117 original size:17 final size:17
Alignment explanation
Indices: 526085--526116 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
526075 AATGATCCAA
526085 ATTTAAAAAATTAAAAG
1 ATTTAAAAAATTAAAAG
526102 ATTT-AAAAATTAAAA
1 ATTTAAAAAATTAAAA
526117 AAAAAACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
ATTTAAAAAATTAAAAG
Found at i:527066 original size:12 final size:13
Alignment explanation
Indices: 527049--527087 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
527039 TTTGGGTGTT
527049 TATTTTATTT-TA
1 TATTTTATTTATA
*
527061 TATTTTATTTATT
1 TATTTTATTTATA
527074 TATTTATATTTATA
1 TATTT-TATTTATA
527088 AAATAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 10 0.43
13 6 0.26
14 7 0.30
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTTTATTTATA
Found at i:527699 original size:29 final size:29
Alignment explanation
Indices: 527648--527705 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
527638 TATATAATTG
*
527648 TTGTGTGATATTACTCATTGATGTGTTAT
1 TTGTGTGATATTACTCATAGATGTGTTAT
*
527677 TTGTGTGATATTA-TTATGAGATGTGTTAT
1 TTGTGTGATATTACTCAT-AGATGTGTTAT
527706 CAGTATGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 23 0.88
ACGTcount: A:0.22, C:0.03, G:0.22, T:0.52
Consensus pattern (29 bp):
TTGTGTGATATTACTCATAGATGTGTTAT
Found at i:530560 original size:126 final size:126
Alignment explanation
Indices: 530335--530587 Score: 497
Period size: 126 Copynumber: 2.0 Consensus size: 126
530325 AAACTTCTCG
*
530335 ATCCAGCTGTGTGCGTGAATTTTTGTTTTTGCCTACTTATAGTTCCAACATGCTCACGATCCTAC
1 ATCCAGCTGTGTGCGTGAATTTTTGTTTTTACCTACTTATAGTTCCAACATGCTCACGATCCTAC
530400 ATGAAATTATTATTACGTATATAATAAATACTATAAACCGAAATAATTAAAAGAGTTTGGT
66 ATGAAATTATTATTACGTATATAATAAATACTATAAACCGAAATAATTAAAAGAGTTTGGT
530461 ATCCAGCTGTGTGCGTGAATTTTTGTTTTTACCTACTTATAGTTCCAACATGCTCACGATCCTAC
1 ATCCAGCTGTGTGCGTGAATTTTTGTTTTTACCTACTTATAGTTCCAACATGCTCACGATCCTAC
530526 ATGAAATTATTATTACGTATATAATAAATACTATAAACCGAAATAATTAAAAGAGTTTGGT
66 ATGAAATTATTATTACGTATATAATAAATACTATAAACCGAAATAATTAAAAGAGTTTGGT
530587 A
1 A
530588 GTACATAATA
Statistics
Matches: 126, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 126 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (126 bp):
ATCCAGCTGTGTGCGTGAATTTTTGTTTTTACCTACTTATAGTTCCAACATGCTCACGATCCTAC
ATGAAATTATTATTACGTATATAATAAATACTATAAACCGAAATAATTAAAAGAGTTTGGT
Found at i:531949 original size:15 final size:15
Alignment explanation
Indices: 531929--531958 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
531919 TTTTCCACAA
*
531929 CAAGATTACTGTCCT
1 CAAGATTACTATCCT
531944 CAAGATTACTATCCT
1 CAAGATTACTATCCT
531959 TAGCAGTAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (15 bp):
CAAGATTACTATCCT
Found at i:535474 original size:8 final size:8
Alignment explanation
Indices: 535461--535489 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
535451 ACATAGGTGC
535461 AAATAATT
1 AAATAATT
535469 AAATAATT
1 AAATAATT
535477 AAATAATT
1 AAATAATT
535485 AAATA
1 AAATA
535490 TTTGAGTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAATAATT
Found at i:535570 original size:70 final size:72
Alignment explanation
Indices: 535481--535664 Score: 266
Period size: 74 Copynumber: 2.6 Consensus size: 72
535471 ATAATTAAAT
* *
535481 AATTAAATATTTGAGTTGTTTTTAATAATTAAATAT-TTAATTAA-ATATAATTAAACAATTAAA
1 AATTAAATATTTGGGTTGTTTTTAATAATTAAATATATTAATTAATAAATAATTAAACAATTAAA
535544 TATTTTG
66 TATTTTG
* *
535551 AATTAAATATTTGGGTTGTTTTTAATAATTAAATATAATTATTTAATTAAATAATTAAATAATTA
1 AATTAAATATTTGGGTTGTTTTTAATAATTAAATAT-ATTAATTAA-TAAATAATTAAACAATTA
535616 AATATTTTG
64 AATATTTTG
* * *
535625 AATTAAATATTTGGATTGCTTTTAATAATTAACTA-ATTAA
1 AATTAAATATTTGGGTTGTTTTTAATAATTAAATATATTAA
535665 ATATTTGGGT
Statistics
Matches: 102, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
70 35 0.34
72 11 0.11
74 56 0.55
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.47
Consensus pattern (72 bp):
AATTAAATATTTGGGTTGTTTTTAATAATTAAATATATTAATTAATAAATAATTAAACAATTAAA
TATTTTG
Found at i:535605 original size:8 final size:8
Alignment explanation
Indices: 535574--535619 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
535564 GGTTGTTTTT
535574 AATAATTAA
1 AATAATT-A
535583 ATATAATTA
1 A-ATAATTA
**
535592 TTTAATTA
1 AATAATTA
535600 AATAATTA
1 AATAATTA
535608 AATAATTA
1 AATAATTA
535616 AATA
1 AATA
535620 TTTTGAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
8 24 0.75
9 2 0.06
10 6 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
AATAATTA
Found at i:535606 original size:16 final size:16
Alignment explanation
Indices: 535585--535633 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
535575 ATAATTAAAT
535585 ATAATTATTTAATTAA
1 ATAATTATTTAATTAA
**
535601 ATAATTAAATAATTAA
1 ATAATTATTTAATTAA
*
535617 AT-ATT-TTGAATTAA
1 ATAATTATTTAATTAA
535631 ATA
1 ATA
535634 TTTGGATTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 8 0.30
15 3 0.11
16 16 0.59
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
ATAATTATTTAATTAA
Found at i:535652 original size:40 final size:38
Alignment explanation
Indices: 535608--535695 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 38
535598 TAAATAATTA
535608 AATAATTAAATATTTTGAATTAAATATTTGGATTGCTTTT
1 AATAATTAAATATTTT-AATTAAATATTTGGATTG-TTTT
* *
535648 AATAATT--A-A--CTAATTAAATATTTGGGTTGTTTT
1 AATAATTAAATATTTTAATTAAATATTTGGATTGTTTT
*
535681 AATAATTAATTATTT
1 AATAATTAAATATTT
535696 AAATAATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
33 11 0.28
34 17 0.44
35 1 0.03
36 1 0.03
37 1 0.03
38 1 0.03
40 7 0.18
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (38 bp):
AATAATTAAATATTTTAATTAAATATTTGGATTGTTTT
Found at i:535686 original size:33 final size:34
Alignment explanation
Indices: 535625--535756 Score: 119
Period size: 33 Copynumber: 3.9 Consensus size: 34
535615 AAATATTTTG
535625 AATTAAATATTTGGATTGCTTTTAATAATTAACT
1 AATTAAATATTTGGATTGCTTTTAATAATTAACT
* *
535659 AATTAAATATTTGGGTTG-TTTTAATAATTAATT
1 AATTAAATATTTGGATTGCTTTTAATAATTAACT
* * ** * * *
535692 ATTTAAATAATTAAATT--TGTTAAT-TTTAATTT
1 AATTAAATATTTGGATTGCTTTTAATAATTAA-CT
* *
535724 CAATCAAATATTTGGATTGTTTTTAATAATTAA
1 -AATTAAATATTTGGATTGCTTTTAATAATTAA
535757 ATATTTTGAT
Statistics
Matches: 77, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
31 4 0.05
32 8 0.10
33 38 0.49
34 17 0.22
35 6 0.08
36 4 0.05
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (34 bp):
AATTAAATATTTGGATTGCTTTTAATAATTAACT
Found at i:537639 original size:6 final size:6
Alignment explanation
Indices: 537628--537661 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
537618 TGAATGAGAA
*
537628 AAAACG AAAACG AAAACG AAAACA AAAAC- AAAAC
1 AAAACG AAAACG AAAACG AAAACG AAAACG AAAAC
537662 TAGTTCTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.74, C:0.18, G:0.09, T:0.00
Consensus pattern (6 bp):
AAAACG
Found at i:539464 original size:20 final size:21
Alignment explanation
Indices: 539397--539465 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 21
539387 TTTCACGCTA
*
539397 ATTTTTAAATTTTTTATGAATT
1 ATTTTTAAATTTTTTAT-ATTT
*
539419 -TTTTTAAATCTTGATTTATTTTT
1 ATTTTTAAAT-TT--TTTATATTT
539442 ATTTTTAAATTTTTTA-ATTT
1 ATTTTTAAATTTTTTATATTT
539462 ATTT
1 ATTT
539466 ATTGACATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
20 7 0.17
21 13 0.32
22 2 0.05
23 4 0.10
24 14 0.35
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (21 bp):
ATTTTTAAATTTTTTATATTT
Found at i:540348 original size:24 final size:23
Alignment explanation
Indices: 540319--540365 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
540309 TTAATTTTCA
540319 ACTTTTTACGATTGAAAAAATTC
1 ACTTTTTACGATTGAAAAAATTC
*
540342 ACTTTTTACGATTGGAAAAATTC
1 ACTTTTTACGATTGAAAAAATTC
540365 A
1 A
540366 AATTCAATTA
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:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (23 bp):
ACTTTTTACGATTGAAAAAATTC
Found at i:540724 original size:41 final size:40
Alignment explanation
Indices: 540667--540819 Score: 173
Period size: 41 Copynumber: 3.8 Consensus size: 40
540657 GTTTATGGGA
* * * *
540667 AAACGCCGCTATTGCT-TAACCTTTAGCGATGTTTTTCCCAT
1 AAACGCCGCTAATGCTCTTACCTTTTGCGA-G-TTTTCTCAT
* * *
540708 AAACGCCGCTAATGCTTTTACCTTTTGTGACGTTTTCTTAT
1 AAACGCCGCTAATGCTCTTACCTTTTGCGA-GTTTTCTCAT
* *
540749 AAACGTCGCTAATGCTCTTACCTTTTGCGACATTTTCTCAT
1 AAACGCCGCTAATGCTCTTACCTTTTGCGA-GTTTTCTCAT
*
540790 AAATGCCGCTAATGCTCTTACCTTTTGCGA
1 AAACGCCGCTAATGCTCTTACCTTTTGCGA
540820 AAACGCCGCT
Statistics
Matches: 97, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
41 86 0.89
42 11 0.11
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (40 bp):
AAACGCCGCTAATGCTCTTACCTTTTGCGAGTTTTCTCAT
Found at i:540872 original size:40 final size:40
Alignment explanation
Indices: 540819--540925 Score: 117
Period size: 40 Copynumber: 2.7 Consensus size: 40
540809 ACCTTTTGCG
* * * *
540819 AAAACGCCGCTATTGCTTTACGTTTT-ACGGCGTTTATGGA
1 AAAACGTCGCTATTGCTTTACCTTTTGA-GGCATTTATGAA
* *
540859 AAAATGTCGCTATTGTTTTACCTTTTGAGGCATTTATGAA
1 AAAACGTCGCTATTGCTTTACCTTTTGAGGCATTTATGAA
* * *
540899 AAAACGTCACTATTACTTTACTTTTTG
1 AAAACGTCGCTATTGCTTTACCTTTTG
540926 CAACGTTTTC
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
40 54 0.98
41 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (40 bp):
AAAACGTCGCTATTGCTTTACCTTTTGAGGCATTTATGAA
Found at i:541210 original size:47 final size:47
Alignment explanation
Indices: 541123--541231 Score: 123
Period size: 47 Copynumber: 2.3 Consensus size: 47
541113 AAGGTGGAAG
* * *
541123 AAGTTGTAGTTTATTTGCAAAAGTGGTGGTTTGTCTACAATATTACA
1 AAGTGGTAGTTTATTTGCAAAAGTGATGGTTTGTCCACAATATTACA
* **
541170 AAGTGGTAGTTT-TCTTGCAAAAGTGAT-GTCTTTTCCACAATATTATT
1 AAGTGGTAGTTTAT-TTGCAAAAGTGATGGT-TTGTCCACAATATTACA
*
541217 AAGTGGCAGTTTATT
1 AAGTGGTAGTTTATT
541232 CACGTTACTG
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
46 3 0.06
47 48 0.92
48 1 0.02
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.41
Consensus pattern (47 bp):
AAGTGGTAGTTTATTTGCAAAAGTGATGGTTTGTCCACAATATTACA
Found at i:551054 original size:20 final size:18
Alignment explanation
Indices: 551014--551061 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 18
551004 AATATATATG
*
551014 ATTATACAAAAAATAAAA
1 ATTATAAAAAAAATAAAA
551032 ATTATAAAAAAATATAGAAA
1 ATTATAAAAAAA-ATA-AAA
551052 ATTATAAAAA
1 ATTATAAAAA
551062 TATTATGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 11 0.41
19 3 0.11
20 13 0.48
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (18 bp):
ATTATAAAAAAAATAAAA
Found at i:551062 original size:18 final size:17
Alignment explanation
Indices: 551014--551098 Score: 64
Period size: 18 Copynumber: 4.7 Consensus size: 17
551004 AATATATATG
*
551014 ATTATACAAAAAATAAAA
1 ATTATA-AAAATATAAAA
551032 ATTATAAAAAAATATAGAAA
1 ATTAT--AAAAATATA-AAA
**
551052 ATTATAAAAATATTATGA
1 ATTATAAAAATA-TAAAA
* *
551070 ATGAAAAAAATAT-AAA
1 ATTATAAAAATATAAAA
551086 ATTATTAAAAATA
1 ATTA-TAAAAATA
551099 GCCCAAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
16 4 0.08
17 8 0.15
18 23 0.43
19 9 0.17
20 9 0.17
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (17 bp):
ATTATAAAAATATAAAA
Found at i:551190 original size:42 final size:40
Alignment explanation
Indices: 551123--551201 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 40
551113 AAAAAAGGGT
*
551123 TTAAAAATTATATAAATAATGAAAATATTTTAAAAATACTTA
1 TTAAAAATTATATAAATAA-GAAAATA-TCTAAAAATACTTA
551165 TTAAAAATTATATAAAATTAA-AAAATATCTAAAAATA
1 TTAAAAATTATAT-AAA-TAAGAAAATATCTAAAAATA
551202 ATAGAAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
41 9 0.26
42 19 0.56
43 3 0.09
44 3 0.09
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (40 bp):
TTAAAAATTATATAAATAAGAAAATATCTAAAAATACTTA
Found at i:551200 original size:18 final size:17
Alignment explanation
Indices: 551164--551198 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
551154 AAAAATACTT
*
551164 ATTAAAAATTATATAAA
1 ATTAAAAAATATATAAA
*
551181 ATTAAAAAATATCTAAA
1 ATTAAAAAATATATAAA
551198 A
1 A
551199 ATAATAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
ATTAAAAAATATATAAA
Found at i:551240 original size:10 final size:10
Alignment explanation
Indices: 551168--551241 Score: 50
Period size: 10 Copynumber: 7.6 Consensus size: 10
551158 ATACTTATTA
551168 AAAATTATAT
1 AAAATTATAT
551178 AAAATTA-A-
1 AAAATTATAT
*
551186 AAAA-TATCT
1 AAAATTATAT
* *
551195 AAAAATAATAG
1 -AAAATTATAT
551206 AAAATTA-A-
1 AAAATTATAT
*
551214 AAAATGATTATT
1 AAAATTA-TA-T
551226 AAAATTATAT
1 AAAATTATAT
551236 AAAATT
1 AAAATT
551242 TCAAAAATAT
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
7 2 0.04
8 10 0.20
9 2 0.04
10 25 0.51
11 4 0.08
12 6 0.12
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (10 bp):
AAAATTATAT
Found at i:551688 original size:19 final size:19
Alignment explanation
Indices: 551643--551697 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
551633 CAAATATTTA
* * *
551643 ATTTTTTTGTAATTTATAT
1 ATTTTTTTATATTTTAAAT
*
551662 AGTTTTTTATATTTTAAAT
1 ATTTTTTTATATTTTAAAT
551681 ATTTTTTTAT-TTTTAAA
1 ATTTTTTTATATTTTAAA
551698 GTTAATGATT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
18 7 0.23
19 24 0.77
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
ATTTTTTTATATTTTAAAT
Found at i:551728 original size:18 final size:17
Alignment explanation
Indices: 551705--551771 Score: 57
Period size: 18 Copynumber: 3.9 Consensus size: 17
551695 AAAGTTAATG
*
551705 ATTTTTAATATTTTTGCA
1 ATTTATAATATTTTT-CA
* *
551723 ATTTTTATTAATTTTAT-A
1 ATTTATAAT-ATTTT-TCA
*
551741 ATTTATAAT-TTTTTCC
1 ATTTATAATATTTTTCA
551757 ATTTATAATATTTTT
1 ATTTATAATATTTTT
551772 TTATAATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
15 1 0.02
16 13 0.32
17 5 0.12
18 16 0.39
19 5 0.12
20 1 0.02
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (17 bp):
ATTTATAATATTTTTCA
Found at i:551753 original size:16 final size:14
Alignment explanation
Indices: 551726--551787 Score: 54
Period size: 16 Copynumber: 4.2 Consensus size: 14
551716 TTTTGCAATT
*
551726 TTTATTAATTTTATAA
1 TTTA-TAATTTT-TTA
551742 TTTATAATTTTTTCCA
1 TTTATAATTTTTT--A
*
551758 TTTATAATATTTT-
1 TTTATAATTTTTTA
*
551771 TTTATAATTTTCTA
1 TTTATAATTTTTTA
551785 TTT
1 TTT
551788 TTATACTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 11 0.28
14 4 0.10
15 7 0.18
16 17 0.44
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTATAATTTTTTA
Found at i:551786 original size:18 final size:17
Alignment explanation
Indices: 551769--551825 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 17
551759 TTATAATATT
551769 TTTTTATA-ATTTTCTA
1 TTTTTATATATTTTCTA
551785 TTTTTATACTATTTTC-A
1 TTTTTATA-TATTTTCTA
*
551802 CTTTTTCTATATTTTCTGA
1 -TTTTTATATATTTTCT-A
551821 TTTTT
1 TTTTT
551826 GTAATTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
16 8 0.23
17 8 0.23
18 18 0.51
19 1 0.03
ACGTcount: A:0.19, C:0.11, G:0.02, T:0.68
Consensus pattern (17 bp):
TTTTTATATATTTTCTA
Found at i:556254 original size:27 final size:26
Alignment explanation
Indices: 556224--556276 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
556214 TTTTTTAGAA
556224 TTTTAT-ATATTTTATAAATTTTGAAAT
1 TTTTATAATATTTTA-AAA-TTTGAAAT
556251 TTTTATAAATATTTTAAAATTTGAAA
1 TTTTAT-AATATTTTAAAATTTGAAA
556277 ATTATTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 13 0.54
28 3 0.12
29 8 0.33
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (26 bp):
TTTTATAATATTTTAAAATTTGAAAT
Found at i:556270 original size:20 final size:18
Alignment explanation
Indices: 556205--556272 Score: 59
Period size: 18 Copynumber: 3.6 Consensus size: 18
556195 TTTTTTAATT
556205 TTTTAAGAATTTTT-TAGAA
1 TTTTAA-AATTTTTATA-AA
*
556224 TTTT-ATATATTTTATAAA
1 TTTTAAAAT-TTTTATAAA
*
556242 TTTTGAAATTTTTATAAATA
1 TTTTAAAATTTTTAT-AA-A
556262 TTTTAAAATTT
1 TTTTAAAATTT
556273 GAAAATTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
17 2 0.05
18 17 0.41
19 11 0.27
20 11 0.27
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (18 bp):
TTTTAAAATTTTTATAAA
Found at i:556293 original size:28 final size:27
Alignment explanation
Indices: 556224--556293 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
556214 TTTTTTAGAA
* * *
556224 TTTTATATATTTTATAAATTTTGAAAT
1 TTTTATAAATTTTTTAAAATTTGAAAT
*
556251 TTTTATAAATATTTTAAAATTTGAAAAT
1 TTTTATAAATTTTTTAAAATTTG-AAAT
*
556279 TATTT-TGAATTTTTT
1 T-TTTATAAATTTTTT
556294 TTTTTTGTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
27 19 0.54
28 13 0.37
29 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (27 bp):
TTTTATAAATTTTTTAAAATTTGAAAT
Found at i:559487 original size:21 final size:22
Alignment explanation
Indices: 559459--559509 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
559449 GTTTTTTAGT
559459 TATTTTAAAGAAAAATTTT-AAA
1 TATTTTAAA-AAAAATTTTGAAA
*
559481 T-TTTTAAACAAAATTTTGAAA
1 TATTTTAAAAAAAATTTTGAAA
559502 TATTTTAA
1 TATTTTAA
559510 CTATTTCGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.31
21 11 0.42
22 7 0.27
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (22 bp):
TATTTTAAAAAAAATTTTGAAA
Found at i:559535 original size:149 final size:149
Alignment explanation
Indices: 559353--559688 Score: 512
Period size: 149 Copynumber: 2.3 Consensus size: 149
559343 TTTGTTTTTT
* * *
559353 TATTTAAACAATTTCAAAATAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTTCTTAAAAAAAG
1 TATTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTTCTTAAAAAAAG
*
559418 ACAAAGTTTATATTTTTAAAAATAAAAATATG-TTTTTTAGTTATTTTAAAGAAAAATTTTAAAT
66 ACAAAGTTTATA-TTTTAAAAATAAAAATATGTTTTTTTAGTTATTTTAAAGAAAAAATTTAAAT
*
559482 TTTTAAACAAAATTTTGAAA
130 TTTTAAACAAAATTTCGAAA
** * *
559502 TATTTTAACTATTTCGAAATAAAAGTTCGGATTTTTAAGTAAAATAGTTATTTTCTTTAAAAAAG
1 TATTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTTCTTAAAAAAAG
*
559567 ATAAAGTTTATATTTTAAAAATAAAAATATGTTTTTTTAGTTATTTTAAAGAAAAAATTTAAATT
66 ACAAAGTTTATATTTTAAAAATAAAAATATGTTTTTTTAGTTATTTTAAAGAAAAAATTTAAATT
* * **
559632 TTTAAATAAAGTTTCGATT
131 TTTAAACAAAATTTCGAAA
* *
559651 TTTTTTAACTATTTCGAAATAAAAATTTAGATTTTTAA
1 TATTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAA
559689 AAAATAAAAA
Statistics
Matches: 168, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
148 19 0.11
149 149 0.89
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.44
Consensus pattern (149 bp):
TATTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTTCTTAAAAAAAG
ACAAAGTTTATATTTTAAAAATAAAAATATGTTTTTTTAGTTATTTTAAAGAAAAAATTTAAATT
TTTAAACAAAATTTCGAAA
Found at i:559636 original size:52 final size:52
Alignment explanation
Indices: 559579--559741 Score: 147
Period size: 52 Copynumber: 3.1 Consensus size: 52
559569 AAAGTTTATA
559579 TTTTAAAAATAAAAATATGTTTTTTTAGTTATTTTAAAGAAAAAATTTAAAT
1 TTTTAAAAATAAAAATATGTTTTTTTAGTTATTTTAAAGAAAAAATTTAAAT
* * ** * * *
559631 TTTT--AAAT-AAAGTTTCGATTTTTTTTAACTATTTCGAAA-TAAAAATTTAGAT
1 TTTTAAAAATAAAAATAT-G--TTTTTTTAGTTATTT-TAAAGAAAAAATTTAAAT
* * * *
559683 TTTTAAAAAATAAAAAAAT-ATTTTTTAGTGATTTTAAAGAAAAAGTTTAAAT
1 TTTT-AAAAATAAAAATATGTTTTTTTAGTTATTTTAAAGAAAAAATTTAAAT
559735 TTTTAAA
1 TTTTAAA
559742 CAACGTTTTT
Statistics
Matches: 84, Mismatches: 18, Indels: 19
0.69 0.15 0.16
Matches are distributed among these distances:
49 5 0.06
50 5 0.06
51 6 0.07
52 57 0.68
53 3 0.04
55 4 0.05
56 4 0.05
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (52 bp):
TTTTAAAAATAAAAATATGTTTTTTTAGTTATTTTAAAGAAAAAATTTAAAT
Found at i:559711 original size:104 final size:105
Alignment explanation
Indices: 559579--559779 Score: 289
Period size: 104 Copynumber: 1.9 Consensus size: 105
559569 AAAGTTTATA
* * * *
559579 TTTTAAAAATAAAAATATGTTTTTTTAGTTATTTTAAAGAAAAAATTTAAATTTTTAAATAAAGT
1 TTTTAAAAATAAAAAAATGATTTTTTAGTGATTTTAAAGAAAAAATTTAAATTTTTAAACAAAGT
*
559644 TTCGA-TTTTTTTTAACTATTTCGAAATAAAAATTTAGAT
66 TTCGATTTTTTTTTAACTATTTCAAAATAAAAATTTAGAT
* *
559683 TTTTAAAAAATAAAAAAAT-ATTTTTTAGTGATTTTAAAGAAAAAGTTTAAATTTTTAAACAACG
1 TTTT-AAAAATAAAAAAATGATTTTTTAGTGATTTTAAAGAAAAAATTTAAATTTTTAAACAAAG
** *
559747 TTTTTATTTTTTTTTAACTATTTTAAAATAAAA
65 TTTCGATTTTTTTTTAACTATTTCAAAATAAAA
559780 GTTTTAATTT
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
104 48 0.56
105 37 0.44
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (105 bp):
TTTTAAAAATAAAAAAATGATTTTTTAGTGATTTTAAAGAAAAAATTTAAATTTTTAAACAAAGT
TTCGATTTTTTTTTAACTATTTCAAAATAAAAATTTAGAT
Found at i:559759 original size:52 final size:52
Alignment explanation
Indices: 559598--559799 Score: 142
Period size: 52 Copynumber: 3.8 Consensus size: 52
559588 TAAAAATATG
** * * **
559598 TTTTTTTAGTTATTTTAAAGAAAAAATTTAAATTTTTAAATAAAGTTTCGAT
1 TTTTTTTAACTATTTTAAAGAAAAAGTTTAAATTTTTAAAAAAAGTTTAAAT
* * * ***
559650 TTTTTTTAACTATTTCGAAATAAAAA-TTTAGATTTTTAAAAAATA-AAAAAAT
1 TTTTTTTAACTATTT-TAAAGAAAAAGTTTAAATTTTTAAAAAA-AGTTTAAAT
* * * * * *
559702 ATTTTTT-AGTGATTTTAAAGAAAAAGTTTAAATTTTTAAACAACGTTTTTATT
1 TTTTTTTAACT-ATTTTAAAGAAAAAGTTTAAATTTTTAAAAAAAG-TTTAAAT
* *
559755 TTTTTTTAACTATTTTAAA-ATAAAAGTTTTAATTTTGAAATAAAA
1 TTTTTTTAACTATTTTAAAGA-AAAAGTTTAAATTTTTAAA-AAAA
559800 CAGTTATTTT
Statistics
Matches: 112, Mismatches: 29, Indels: 16
0.71 0.18 0.10
Matches are distributed among these distances:
51 10 0.09
52 56 0.50
53 42 0.38
54 4 0.04
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (52 bp):
TTTTTTTAACTATTTTAAAGAAAAAGTTTAAATTTTTAAAAAAAGTTTAAAT
Found at i:562144 original size:25 final size:25
Alignment explanation
Indices: 562110--562163 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
562100 CCTCATGAGC
562110 ATTTATTCGT-ATGTTTTATG-TTTGA
1 ATTTATTCGTAAT-TTTTATGATTT-A
*
562135 ATTTGTTCGTAATTTTTATGATTTA
1 ATTTATTCGTAATTTTTATGATTTA
562160 ATTT
1 ATTT
562164 CATTTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.22, C:0.04, G:0.13, T:0.61
Consensus pattern (25 bp):
ATTTATTCGTAATTTTTATGATTTA
Found at i:585144 original size:20 final size:20
Alignment explanation
Indices: 585108--585188 Score: 93
Period size: 20 Copynumber: 4.2 Consensus size: 20
585098 GAATTTCACC
585108 AAAAA-AAA-AAG-AAAAAG
1 AAAAAGAAAGAAGAAAAAAG
585125 AAAAAGAAAGAAGAAAAAAG
1 AAAAAGAAAGAAGAAAAAAG
585145 AAAAAG-AAG-AGCAAAAAAG
1 AAAAAGAAAGAAG-AAAAAAG
585164 AAATAAGAAAGAA-AAAAAAGG
1 AAA-AAGAAAGAAGAAAAAA-G
585185 AAAA
1 AAAA
585189 TAAAAAAGAG
Statistics
Matches: 56, Mismatches: 0, Indels: 13
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.09
18 5 0.09
19 16 0.29
20 22 0.39
21 7 0.12
22 1 0.02
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAGAAGAAAAAAG
Found at i:585148 original size:26 final size:25
Alignment explanation
Indices: 585108--585197 Score: 85
Period size: 26 Copynumber: 3.5 Consensus size: 25
585098 GAATTTCACC
585108 AAAA-AAAAAAGAAAAAGAAAAAGA
1 AAAAGAAAAAAGAAAAAGAAAAAGA
*
585132 AAGAAGAAAAAAGAAAAAG-AAGAGCAA
1 AA-AAGAAAAAAGAAAAAGAAAAAG--A
* * *
585159 AAAAGAAATAAGAAAGAAAAAAAAGG
1 AAAAGAAAAAAGAAA-AAGAAAAAGA
*
585185 AAAATAAAAAAGA
1 AAAAGAAAAAAGA
585198 GTGGTCGAGG
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
24 2 0.04
25 6 0.11
26 36 0.68
27 5 0.09
28 4 0.08
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.02
Consensus pattern (25 bp):
AAAAGAAAAAAGAAAAAGAAAAAGA
Found at i:585194 original size:33 final size:30
Alignment explanation
Indices: 585108--585197 Score: 99
Period size: 33 Copynumber: 2.8 Consensus size: 30
585098 GAATTTCACC
585108 AAAAAAAAAAGAAAAAGAAAAAGAAAGAAGA
1 AAAAAAAAAAGAAAAA-AAAAAGAAAGAAGA
* *
585139 AAAAAGAAAAAGAAGAGCAAAAAAGAAATAAGA
1 AAAAA-AAAAAGAA-A-AAAAAAAGAAAGAAGA
585172 AAGAAAAAAAAGGAAAATAAAAAAGA
1 AA-AAAAAAAA-GAAAA-AAAAAAGA
585198 GTGGTCGAGG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
31 5 0.10
32 8 0.16
33 30 0.60
34 7 0.14
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.02
Consensus pattern (30 bp):
AAAAAAAAAAGAAAAAAAAAAGAAAGAAGA
Found at i:586345 original size:147 final size:147
Alignment explanation
Indices: 586078--586351 Score: 347
Period size: 147 Copynumber: 1.9 Consensus size: 147
586068 ATGACAAATC
* ** * * * *
586078 TACCCTAGAGATGTGGAGGGAAAGATTGAAGACGCAATGATGAATCTTATACCTTAGAGAAGTGA
1 TACCCTAGAGATATGGAGGGAAAGATTGAAGACGCAACAACGAACCTTATACCCTAAAGAAGTGA
* *
586143 AGGGAAAGATTGAAGCCTCAACGACAAATCTTATACCTTAAAGATATAGAGGGAAAGATTGATGT
66 AGGGAAAGATTGAAGCCTCAACGACAAACCTTATACCCTAAAGATATAGAGGGAAAGATTGATGT
586208 CATAATGGCGAATCTTG
131 CATAATGGCGAATCTTG
* * * *
586225 TACCCTAGAGATATGGAGGGAAAGGTTGAAGCCGCAACAACGAACCTTATACCCTAAAGATGTGG
1 TACCCTAGAGATATGGAGGGAAAGATTGAAGACGCAACAACGAACCTTATACCCTAAAGAAGTGA
* * * *
586290 AGGGAAATG-TTGAAGCCGT-AATGACTAACCTTATACCCTAGAGATGT-GAAGGGAAAGATTGA
66 AGGGAAA-GATTGAAGCC-TCAACGACAAACCTTATACCCTAAAGATATAG-AGGGAAAGATTGA
586352 AACCACAACG
Statistics
Matches: 107, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
146 1 0.01
147 104 0.97
148 2 0.02
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (147 bp):
TACCCTAGAGATATGGAGGGAAAGATTGAAGACGCAACAACGAACCTTATACCCTAAAGAAGTGA
AGGGAAAGATTGAAGCCTCAACGACAAACCTTATACCCTAAAGATATAGAGGGAAAGATTGATGT
CATAATGGCGAATCTTG
Found at i:586367 original size:147 final size:147
Alignment explanation
Indices: 586078--586383 Score: 339
Period size: 147 Copynumber: 2.1 Consensus size: 147
586068 ATGACAAATC
* ** * * * *
586078 TACCCTAGAGATGTGGAGGGAAAGATTGAAGACGCAATGATGAATCTTATACCTTAGAGAAGTGA
1 TACCCTAGAGATATGGAGGGAAAGATTGAAGACGCAACAACGAACCTTATACCCTAAAGAAGTGA
* * ***
586143 AGGGAAAGATTGAAGCCTCAACGACAAATCTTATACCTTAAAGATATAGAGGGAAAGATTGATGT
66 AGGGAAAGATTGAAGCCTCAACGACAAACCTTATACCCTAAAGATATAGAGGGAAAGATTGAAAC
* * * *
586208 CATAATGGCGAATCTTG
131 CACAACGACGAATCTTA
* * * *
586225 TACCCTAGAGATATGGAGGGAAAGGTTGAAGCCGCAACAACGAACCTTATACCCTAAAGATGTGG
1 TACCCTAGAGATATGGAGGGAAAGATTGAAGACGCAACAACGAACCTTATACCCTAAAGAAGTGA
* * * *
586290 AGGGAAATG-TTGAAGCCGT-AATGACTAACCTTATACCCTAGAGATGT-GAAGGGAAAGATTGA
66 AGGGAAA-GATTGAAGCC-TCAACGACAAACCTTATACCCTAAAGATATAG-AGGGAAAGATTGA
586352 AACCACAACGACGAATCTTA
128 AACCACAACGACGAATCTTA
*
586372 TACCCTAAAGAT
1 TACCCTAGAGAT
586384 GAGGAGAAGC
Statistics
Matches: 131, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
146 1 0.01
147 128 0.98
148 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (147 bp):
TACCCTAGAGATATGGAGGGAAAGATTGAAGACGCAACAACGAACCTTATACCCTAAAGAAGTGA
AGGGAAAGATTGAAGCCTCAACGACAAACCTTATACCCTAAAGATATAGAGGGAAAGATTGAAAC
CACAACGACGAATCTTA
Found at i:586384 original size:49 final size:49
Alignment explanation
Indices: 586047--586384 Score: 299
Period size: 49 Copynumber: 7.0 Consensus size: 49
586037 AGAAGACATT
* * * *
586047 AAGGGAAAGATTAAAGTCGCAATGACAAATC---TACCCTAGAGATGTG
1 AAGGGAAAGATTGAAGCCGCAACGACGAATCTTATACCCTAGAGATGTG
* * * * * *
586093 GAGGGAAAGATTGAAGACGCAATGATGAATCTTATACCTTAGAGAAGTG
1 AAGGGAAAGATTGAAGCCGCAACGACGAATCTTATACCCTAGAGATGTG
* * * * *
586142 AAGGGAAAGATTGAAGCCTCAACGACAAATCTTATACCTTAAAGATAT-
1 AAGGGAAAGATTGAAGCCGCAACGACGAATCTTATACCCTAGAGATGTG
* * ** * * * *
586190 AGAGGGAAAGATTGATGTCATAATGGCGAATCTTGTACCCTAGAGATATG
1 A-AGGGAAAGATTGAAGCCGCAACGACGAATCTTATACCCTAGAGATGTG
* * * * *
586240 GAGGGAAAGGTTGAAGCCGCAACAACGAACCTTATACCCTAAAGATGTG
1 AAGGGAAAGATTGAAGCCGCAACGACGAATCTTATACCCTAGAGATGTG
* * * * *
586289 GAGGGAAATG-TTGAAGCCGTAATGACTAACCTTATACCCTAGAGATGTG
1 AAGGGAAA-GATTGAAGCCGCAACGACGAATCTTATACCCTAGAGATGTG
* * *
586338 AAGGGAAAGATTGAAACCACAACGACGAATCTTATACCCTAAAGATG
1 AAGGGAAAGATTGAAGCCGCAACGACGAATCTTATACCCTAGAGATG
586385 AGGAGAAGCA
Statistics
Matches: 233, Mismatches: 52, Indels: 11
0.79 0.18 0.04
Matches are distributed among these distances:
46 26 0.11
48 2 0.01
49 204 0.88
50 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (49 bp):
AAGGGAAAGATTGAAGCCGCAACGACGAATCTTATACCCTAGAGATGTG
Found at i:586384 original size:98 final size:98
Alignment explanation
Indices: 586078--586389 Score: 367
Period size: 98 Copynumber: 3.2 Consensus size: 98
586068 ATGACAAATC
* * * *
586078 TACCCTAGAGATGTGGAGGGAAAGATTGAAGACGCAATGA-TGAATCTTATACCTTAGAGAAGTG
1 TACCCTAAAGATGTGGAGGGAAAGATTGAAGACGTAATGACT-AATCTTATACCCTAGAGATGTG
* *
586142 AAGGGAAAGATTGAAGCCTCAACGACAAATCTTA
65 AAGGGAAAGATTGAAGCCACAACGACGAATCTTA
* * * * * * * * * * *
586176 TACCTTAAAGATATAGAGGGAAAGATTGATGTCATAATGGCGAATCTTGTACCCTAGAGATATGG
1 TACCCTAAAGATGTGGAGGGAAAGATTGAAGACGTAATGACTAATCTTATACCCTAGAGATGTGA
* * * *
586241 AGGGAAAGGTTGAAGCCGCAACAACGAACCTTA
66 AGGGAAAGATTGAAGCCACAACGACGAATCTTA
* *
586274 TACCCTAAAGATGTGGAGGGAAATG-TTGAAGCCGTAATGACTAACCTTATACCCTAGAGATGTG
1 TACCCTAAAGATGTGGAGGGAAA-GATTGAAGACGTAATGACTAATCTTATACCCTAGAGATGTG
*
586338 AAGGGAAAGATTGAAACCACAACGACGAATCTTA
65 AAGGGAAAGATTGAAGCCACAACGACGAATCTTA
*
586372 TACCCTAAAGATGAGGAG
1 TACCCTAAAGATGTGGAG
586390 AAGCAAATTG
Statistics
Matches: 174, Mismatches: 38, Indels: 4
0.81 0.18 0.02
Matches are distributed among these distances:
98 173 0.99
99 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (98 bp):
TACCCTAAAGATGTGGAGGGAAAGATTGAAGACGTAATGACTAATCTTATACCCTAGAGATGTGA
AGGGAAAGATTGAAGCCACAACGACGAATCTTA
Found at i:587173 original size:190 final size:192
Alignment explanation
Indices: 586535--587350 Score: 923
Period size: 190 Copynumber: 4.3 Consensus size: 192
586525 ACAGTGAAAG
* * *
586535 CAGATTAAAACAAC-AAAGCATATCACAATGTCCCTGAGGTTATAGTGGAATGAAGTGAAGCACC
1 CAGATTAAAACAACGAAA-CAGATCTCAATGTCCCTGAGGTTACAGTGGAATGAAGTGAAGCACC
* * * * * *
586599 AGATCTTATATCCCTAAAGTTACAGTGGATCAGATCAAAATGAGCAACGGATCTCAAAGTCCTTG
65 AGATCCTATATCCCTGAAGTTACAGTGGATCAGATCAAAATGAGTAACGAATCTCAATGTCCTTA
*
586664 AGGTTACAGTGGAATGAAGAGAAGTTACAACATCAAATCCCATACCCCTGAGTTGCAGTAGGT
130 AGGTTACAGTGGAATGAAGAGAAGTTACAACATCAAATCCCATACCCTTGAGTTGCAGTAGGT
* * *
586727 CGGATTAAAACAACAAAACAGATCTTAATGTCCCTGA--TTACAGTGGAATGAAGTGAAGCACCA
1 CAGATTAAAACAACGAAACAGATCTCAATGTCCCTGAGGTTACAGTGGAATGAAGTGAAGCACCA
** ** * *
586790 GATCCTATATCCCTGAAGTTGTAGTGGATTGGATC--AA--A--AACGAATTTCAATGTCCCTGA
66 GATCCTATATCCCTGAAGTTACAGTGGATCAGATCAAAATGAGTAACGAATCTCAATGT-CCTTA
* *
586849 A-TTTACAGTGGAATGAAGAGAAGTTACAACATCAAATCCCATACCCTTGAGTTGCA-TTGAGT
130 AGGTTACAGTGGAATGAAGAGAAGTTACAACATCAAATCCCATACCCTTGAGTTGCAGTAG-GT
* ** * * * * *
586911 CAGATTAAAGCAACGAAGTAGATCTTAATGTCCTTAAGGTTACAGTAGAATGGAGTGAAGCACCA
1 CAGATTAAAACAACGAAACAGATCTCAATGTCCCTGAGGTTACAGTGGAATGAAGTGAAGCACCA
* ** * *
586976 GATCCTATATCCCTGAAGTTACAATGGATTGGATCAAAATGAGTAATGAATTTCAATGTCC-TAA
66 GATCCTATATCCCTGAAGTTACAGTGGATCAGATCAAAATGAGTAACGAATCTCAATGTCCTTAA
* *
587040 GGTTATAGTGGAATTG-AGAGAAGTTAAAACATCAAATCCCATACCCTTGAGTTGCAGT-GGT
131 GGTTACAGTGGAA-TGAAGAGAAGTTACAACATCAAATCCCATACCCTTGAGTTGCAGTAGGT
* * ***
587101 CAGATTAAAACAATGAAACAGATCTCAATGTCCCTGAGGTTACAGTGGAATGGACAAAAGCACCA
1 CAGATTAAAACAACGAAACAGATCTCAATGTCCCTGAGGTTACAGTGGAATGAAGTGAAGCACCA
* ** * *
587166 AATCCTATATCCCTGAAGTTGTAGTGGATCAGATCAAAATGAGTAAC-AGGTCTCAATGTCCTTG
66 GATCCTATATCCCTGAAGTTACAGTGGATCAGATCAAAATGAGTAACGA-ATCTCAATGTCCTTA
* * * *
587230 AGGTTATAGT-GAATTG-AGAGAAGTTACAACGTCAAATCCCATACCCATGAGTTGCAGTGGGT
130 AGGTTACAGTGGAA-TGAAGAGAAGTTACAACATCAAATCCCATACCCTTGAGTTGCAGTAGGT
* * * * * *
587292 -TGAATTAAAACAATGAAGCAGATCTCAATGTCCTTGAGGTTATAGTAGAAT-AGAGTGAA
1 CAG-ATTAAAACAACGAAACAGATCTCAATGTCCCTGAGGTTACAGTGGAATGA-AGTGAA
587351 ACTTGAAAAC
Statistics
Matches: 536, Mismatches: 69, Indels: 39
0.83 0.11 0.06
Matches are distributed among these distances:
183 2 0.00
184 97 0.18
185 4 0.01
186 57 0.11
188 4 0.01
189 1 0.00
190 209 0.39
191 113 0.21
192 46 0.09
193 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.25
Consensus pattern (192 bp):
CAGATTAAAACAACGAAACAGATCTCAATGTCCCTGAGGTTACAGTGGAATGAAGTGAAGCACCA
GATCCTATATCCCTGAAGTTACAGTGGATCAGATCAAAATGAGTAACGAATCTCAATGTCCTTAA
GGTTACAGTGGAATGAAGAGAAGTTACAACATCAAATCCCATACCCTTGAGTTGCAGTAGGT
Found at i:587214 original size:93 final size:92
Alignment explanation
Indices: 586560--587342 Score: 357
Period size: 93 Copynumber: 8.3 Consensus size: 92
586550 AAGCATATCA
* * ** * * * *
586560 CAATGTCCCTGAGGTTATAGTGGAATGAAGTGAAGCACCAGATCTTATATCCCTAAAGTTACAGT
1 CAATGTCCCTGAGGTTACAGTGGAATGGAGAAAAGCACCAAATCCTATATCCCTGAAGTTGCAGT
** *
586625 GGATCAGATCAAAATGAGCAACGGATCT
66 GGATCAGATCAAAACAAG-AACAGATCT
* * * * * *
586653 CAAAGTCCTTGAGGTTACAGTGGAATGAAGAGAAGTTACAACATCAAATCCCATACCCCTG-AGT
1 CAATGTCCCTGAGGTTACAGTGGAATG--GAGAA---A-AGCACCAAATCCTATATCCCTGAAGT
* * *
586717 TGCAGTAGG-TCGGATTAAAACAACAAAACAGATCT
60 TGCAGT-GGATCAGATCAAAAC-A-AGAACAGATCT
* * ** * *
586752 TAATGTCCCTGA--TTACAGTGGAATGAAGTGAAGCACCAGATCCTATATCCCTGAAGTTGTAGT
1 CAATGTCCCTGAGGTTACAGTGGAATGGAGAAAAGCACCAAATCCTATATCCCTGAAGTTGCAGT
** * *
586815 GGATTGGATCAAAA-ACG---A-ATTT
66 GGATCAGATCAAAACAAGAACAGATCT
** * * *
586837 CAATGTCCCTGAATTTACAGTGGAATGAAGAGAAGTTACAACATCAAATCCCATA-CCCTTG-AG
1 CAATGTCCCTGAGGTTACAGTGGAATG--GAGAA---A-AGCACCAAATCCTATATCCC-TGAAG
* * * *
586900 TTGCA-TTGAGTCAGATTAAAGCAACGAAGTAGATCT
59 TTGCAGTGGA-TCAGATCAAAACAA-GAA-CAGATCT
* * * * ** * * *
586936 TAATGTCCTTAAGGTTACAGTAGAATGGAGTGAAGCACCAGATCCTATATCCCTGAAGTTACAAT
1 CAATGTCCCTGAGGTTACAGTGGAATGGAGAAAAGCACCAAATCCTATATCCCTGAAGTTGCAGT
** ** * *
587001 GGATTGGATCAAAATGAGTAA-TGAATTT
66 GGATCAGATCAAAACAAG-AACAG-ATCT
* * * * *
587029 CAATGT-CCTAAGGTTATAGTGGAATTGAGAGAAGTTAAAACATCAAATCCCATA-CCCTTG-AG
1 CAATGTCCCTGAGGTTACAGTGGAA-TG-GAG-A---AAAGCACCAAATCCTATATCCC-TGAAG
*
587091 TTGCAGTGG-TCAGATTAAAACAATGAAACAGATCT
59 TTGCAGTGGATCAGATCAAAACAA-G-AACAGATCT
* *
587126 CAATGTCCCTGAGGTTACAGTGGAATGGACAAAAGCACCAAATCCTATATCCCTGAAGTTGTAGT
1 CAATGTCCCTGAGGTTACAGTGGAATGGAGAAAAGCACCAAATCCTATATCCCTGAAGTTGCAGT
** *
587191 GGATCAGATCAAAATGAGTAACAGGTCT
66 GGATCAGATCAAAACAAG-AACAGATCT
* * * * *
587219 CAATGTCCTTGAGGTTATAGT-GAATTGAGAGAAGTTACAACGTCAAATCCCATA-CCCATG-AG
1 CAATGTCCCTGAGGTTACAGTGGAATGGAGAAAAG---C-AC--CAAATCCTATATCCC-TGAAG
* * *
587281 TTGCAGTGGGT-TGAATTAAAACAATGAAGCAGATCT
59 TTGCAGTGGATCAG-ATCAAAACAA-GAA-CAGATCT
* * *
587317 CAATGTCCTTGAGGTTATAGTAGAAT
1 CAATGTCCCTGAGGTTACAGTGGAAT
587343 AGAGTGAAAC
Statistics
Matches: 513, Mismatches: 120, Indels: 108
0.69 0.16 0.15
Matches are distributed among these distances:
85 14 0.03
86 1 0.00
87 13 0.03
89 2 0.00
90 1 0.00
91 22 0.04
92 78 0.15
93 105 0.20
94 35 0.07
95 9 0.02
96 14 0.03
97 65 0.13
98 91 0.18
99 62 0.12
100 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (92 bp):
CAATGTCCCTGAGGTTACAGTGGAATGGAGAAAAGCACCAAATCCTATATCCCTGAAGTTGCAGT
GGATCAGATCAAAACAAGAACAGATCT
Found at i:587321 original size:98 final size:95
Alignment explanation
Indices: 586648--587342 Score: 374
Period size: 93 Copynumber: 7.3 Consensus size: 95
586638 ATGAGCAACG
* *
586648 GATCTCAAAGTCCTTGAGGTTACAGTGGAA-TGAAGAGAAGTTACAACATCAAATCCCATACCCC
1 GATCTCAATGTCCTTGAGGTTATAGTGGAATTG-AGAGAAGTTACAAC-TCAAATCCCATA-CCC
* **
586712 TGAGTTGCAGTAGGTCGGATTAAAACAACAAAACA
63 TGAGTTGCAGT-GGTCAGATTAAAACAA-TGAACA
* * * * * *
586747 GATCTTAATGTCCCTGA--TTACAGTGGAA-TGAAGTGAAG---C-AC-CAGATCCTATATCCCT
1 GATCTCAATGTCCTTGAGGTTATAGTGGAATTG-AGAGAAGTTACAACTCAAATCCCATA-CCCT
* ** * *
586804 GAAGTTGTAGT-G---GATTGGATCAA-AAAC-
64 G-AGTTGCAGTGGTCAGATTAAAACAATGAACA
* * ** *
586831 GAATTTCAATGTCCCTGAATTTACAGTGGAA-TGAAGAGAAGTTACAACATCAAATCCCATACCC
1 G-ATCTCAATGTCCTTGAGGTTATAGTGGAATTG-AGAGAAGTTACAAC-TCAAATCCCATACCC
* * * *
586895 TTGAGTTGCATTGAGTCAGATTAAAGCAACGAAGTA
63 -TGAGTTGCAGTG-GTCAGATTAAAACAATGAA-CA
* * * * * * * *
586931 GATCTTAATGTCCTTAAGGTTACAGTAGAATGGAGTGAAG---C-AC-CAGATCCTATATCCCTG
1 GATCTCAATGTCCTTGAGGTTATAGTGGAATTGAGAGAAGTTACAACTCAAATCCCATA-CCCTG
* * ** * ** *
586991 AAGTTACAATGGATTGGATCAAAATGA-GTAA-T
65 -AGTTGCAGTGG-TCAGATTAAAACAATG-AACA
* * *
587023 GAATTTCAATGTCC-TAAGGTTATAGTGGAATTGAGAGAAGTTAAAACATCAAATCCCATACCCT
1 G-ATCTCAATGTCCTTGAGGTTATAGTGGAATTGAGAGAAGTTACAAC-TCAAATCCCATACCC-
587087 TGAGTTGCAGTGGTCAGATTAAAACAATGAAACA
63 TGAGTTGCAGTGGTCAGATTAAAACAATG-AACA
* * * * * *
587121 GATCTCAATGTCCCTGAGGTTACAGTGGAATGGACAAAAG---C-AC-CAAATCCTATATCCCTG
1 GATCTCAATGTCCTTGAGGTTATAGTGGAATTGAGAGAAGTTACAACTCAAATCCCATA-CCCTG
* * **
587181 AAGTTGTAGTGGATCAGATCAAAATGA-GTAACA
65 -AGTTGCAGTGG-TCAGATTAAAACAATG-AACA
*
587214 GGTCTCAATGTCCTTGAGGTTATAGT-GAATTGAGAGAAGTTACAACGTCAAATCCCATACCCAT
1 GATCTCAATGTCCTTGAGGTTATAGTGGAATTGAGAGAAGTTACAAC-TCAAATCCCATACCC-T
*
587278 GAGTTGCAGTGGGT-TGAATTAAAACAATGAAGCA
64 GAGTTGCAGT-GGTCAG-ATTAAAACAATGAA-CA
*
587312 GATCTCAATGTCCTTGAGGTTATAGTAGAAT
1 GATCTCAATGTCCTTGAGGTTATAGTGGAAT
587343 AGAGTGAAAC
Statistics
Matches: 459, Mismatches: 87, Indels: 100
0.71 0.13 0.15
Matches are distributed among these distances:
84 1 0.00
85 18 0.04
87 28 0.06
90 2 0.00
91 16 0.03
92 63 0.14
93 77 0.17
94 36 0.08
95 3 0.01
96 15 0.03
97 75 0.16
98 77 0.17
99 46 0.10
100 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (95 bp):
GATCTCAATGTCCTTGAGGTTATAGTGGAATTGAGAGAAGTTACAACTCAAATCCCATACCCTGA
GTTGCAGTGGTCAGATTAAAACAATGAACA
Found at i:587413 original size:93 final size:93
Alignment explanation
Indices: 587295--587477 Score: 303
Period size: 93 Copynumber: 2.0 Consensus size: 93
587285 AGTGGGTTGA
* * * *
587295 ATTAAAACAATGAAGCAGATCTCAATGTCCTTGAGGTTATAGTAGAATAGAGTGAAACTTGAAAA
1 ATTAAAACAATAAAGCAGATATCAATGTCCTTGAGGTTATAGTAGAATAGACTGAAACTTCAAAA
*
587360 CCTATCTTCCTGAGGTTACAGTAAATTG
66 CCTATCTTCCTGAGGCTACAGTAAATTG
*
587388 ATTAAAACAATAAAGCAGATATCAATGTCCTTGAGGTTATAGTGGAATAGACTGAAACTTCAAAA
1 ATTAAAACAATAAAGCAGATATCAATGTCCTTGAGGTTATAGTAGAATAGACTGAAACTTCAAAA
*
587453 CCTATCTTCTTGAGGCTACAGTAAA
66 CCTATCTTCCTGAGGCTACAGTAAA
587478 GTGGATCAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 83 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (93 bp):
ATTAAAACAATAAAGCAGATATCAATGTCCTTGAGGTTATAGTAGAATAGACTGAAACTTCAAAA
CCTATCTTCCTGAGGCTACAGTAAATTG
Found at i:587415 original size:381 final size:377
Alignment explanation
Indices: 586535--587435 Score: 933
Period size: 376 Copynumber: 2.4 Consensus size: 377
586525 ACAGTGAAAG
* * * * * * * *
586535 CAGATTAAAACAACAAAGCATATCACAATGTCCCTGAGGTTATAGTGGAAT-GAAGTGAAGCACC
1 CAGATTAAAACAACGAAGCAGATCTCAATGTCCTTAAGGTTACAGTAGAATAG-AGTGAAACACC
* * * * * ** ** * ** * * * * *
586599 AGATCTTATATCCCTAAAGTTACAGTGGATCAGATCAAAATGAGCAACGGATCTCAAAGTCCTTG
65 AAAACCTATATCCCTGAAGTTACAATAAATTGGATCAAAATCAATAAAGAATATCAATGTCCTTA
* *
586664 AGGTTACAGTGGAA-TGAAGAGAAGTTACAACATCAAATCCCATACCCCTGAGTTGCAGTAGGTC
130 AGGTTATAGTGGAATTGAAGAGAAGTTAAAACATCAAATCCCATACCCCTGAGTTGCAGTAGGTC
* * *** *
586728 GGATTAAAACAACAAAACAGATCTTAATGTCCCTGATTACAGTGGAATGAAGTGAAGCACCAGAT
195 AGATTAAAACAACAAAACAGATCTCAATGTCCCTGATTACAGTGGAATGAACAAAAGCACCAAAT
** * *
586793 CCTATATCCCTGAAGTTGTAGTGGATTGGATCAAAAACGAATTTCAATGTCCCTGAATTTACAGT
260 CCTATATCCCTGAAGTTGTAGTGGATCAGATCAAAAACGAATCTCAATGTCCCTGAAGTTACAGT
* *
586858 GGAATGAAGAGAAGTTACAACATCAAATCCCATACCCTTGAGTTGCATTGAGT
325 GGAATGAAGAGAAGTTACAACATCAAATCCCATACCCATGAGTTGCAGTGAGT
* * * * *
586911 CAGATTAAAGCAACGAAGTAGATCTTAATGTCCTTAAGGTTACAGTAGAATGGAGTGAAGCACCA
1 CAGATTAAAACAACGAAGCAGATCTCAATGTCCTTAAGGTTACAGTAGAATAGAGTGAAACACCA
* * ** * * * *
586976 GATCCTATATCCCTGAAGTTACAATGGATTGGATCAAAATGAGTAATGAATTTCAATGTCC-TAA
66 AAACCTATATCCCTGAAGTTACAATAAATTGGATCAAAATCAATAAAGAATATCAATGTCCTTAA
*
587040 GGTTATAGTGGAATTG-AGAGAAGTTAAAACATCAAATCCCATACCCTTGAGTTGCAGT-GGTCA
131 GGTTATAGTGGAATTGAAGAGAAGTTAAAACATCAAATCCCATACCCCTGAGTTGCAGTAGGTCA
** *
587103 GATTAAAACAATGAAACAGATCTCAATGTCCCTGAGGTTACAGTGGAATGGACAAAAGCACCAAA
196 GATTAAAACAACAAAACAGATCTCAATGTCCCTGA--TTACAGTGGAATGAACAAAAGCACCAAA
* *
587168 TCCTATATCCCTGAAGTTGTAGTGGATCAGATCAAAATGA-GTAACAGGTCTCAATGTCCTTGAG
259 TCCTATATCCCTGAAGTTGTAGTGGATCAGATCAAAA--ACG--A-A--TCTCAATGTCCCTGAA
* * *
587232 GTTATAGT-GAATTG-AGAGAAGTTACAACGTCAAATCCCATACCCATGAGTTGCAGTGGGT
317 GTTACAGTGGAA-TGAAGAGAAGTTACAACATCAAATCCCATACCCATGAGTTGCAGTGAGT
* * * * ***
587292 -TGAATTAAAACAATGAAGCAGATCTCAATGTCCTTGAGGTTATAGTAGAATAGAGTGAAACTTG
1 CAG-ATTAAAACAACGAAGCAGATCTCAATGTCCTTAAGGTTACAGTAGAATAGAGTGAAACACC
* * * * *
587356 AAAACCTATCTTCCTGAGGTTACAGTAAATT-GATTAAAA-CAATAAAGCAGATATCAATGTCCT
65 AAAACCTATATCCCTGAAGTTACAATAAATTGGATCAAAATCAATAAAG-A-ATATCAATGTCCT
*
587419 TGAGGTTATAGTGGAAT
128 TAAGGTTATAGTGGAAT
587436 AGACTGAAAC
Statistics
Matches: 439, Mismatches: 70, Indels: 26
0.82 0.13 0.05
Matches are distributed among these distances:
374 36 0.08
375 54 0.12
376 164 0.37
377 2 0.00
378 1 0.00
379 6 0.01
380 10 0.02
381 129 0.29
382 37 0.08
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (377 bp):
CAGATTAAAACAACGAAGCAGATCTCAATGTCCTTAAGGTTACAGTAGAATAGAGTGAAACACCA
AAACCTATATCCCTGAAGTTACAATAAATTGGATCAAAATCAATAAAGAATATCAATGTCCTTAA
GGTTATAGTGGAATTGAAGAGAAGTTAAAACATCAAATCCCATACCCCTGAGTTGCAGTAGGTCA
GATTAAAACAACAAAACAGATCTCAATGTCCCTGATTACAGTGGAATGAACAAAAGCACCAAATC
CTATATCCCTGAAGTTGTAGTGGATCAGATCAAAAACGAATCTCAATGTCCCTGAAGTTACAGTG
GAATGAAGAGAAGTTACAACATCAAATCCCATACCCATGAGTTGCAGTGAGT
Found at i:587508 original size:93 final size:93
Alignment explanation
Indices: 587298--587528 Score: 295
Period size: 93 Copynumber: 2.5 Consensus size: 93
587288 GGGTTGAATT
* * * *
587298 AAAACAATGAAGCAGATCTCAATGTCCTTGAGGTTATAGTAGAATAGAGTGAAACTTGAAAACCT
1 AAAACAATAAAGCAGATCTCAATGTCCTTGAGGTTATAGTGGAATAGACTGAAACTTCAAAACCT
* * *
587363 ATCTTCCTGAGGTTACAGTAAATTGATT
66 ATCTTCCTGAGGCTACAGTAAATGGATC
*
587391 AAAACAATAAAGCAGATATCAATGTCCTTGAGGTTATAGTGGAATAGACTGAAACTTCAAAACCT
1 AAAACAATAAAGCAGATCTCAATGTCCTTGAGGTTATAGTGGAATAGACTGAAACTTCAAAACCT
*
587456 ATCTTCTTGAGGCTACAGTAAAGTGGATC
66 ATCTTCCTGAGGCTACAGTAAA-TGGATC
* * * * * *
587485 AAAATAGGT-AA-TAGATCTTAATGTCCCTGAGGTTATAATGGAAT
1 AAAACA-ATAAAGCAGATCTCAATGTCCTTGAGGTTATAGTGGAAT
587529 GGGGTGAAGT
Statistics
Matches: 120, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
93 108 0.90
94 11 0.09
95 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (93 bp):
AAAACAATAAAGCAGATCTCAATGTCCTTGAGGTTATAGTGGAATAGACTGAAACTTCAAAACCT
ATCTTCCTGAGGCTACAGTAAATGGATC
Found at i:593653 original size:2 final size:2
Alignment explanation
Indices: 593648--593672 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
593638 TATATATATA
593648 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
593673 ATATAACAAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:601576 original size:20 final size:21
Alignment explanation
Indices: 601551--601589 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
601541 TCAAGGAATT
601551 TGAAAC-AACAAAAGTAAAAG
1 TGAAACGAACAAAAGTAAAAG
*
601571 TGAAACGAATAAAAGTAAA
1 TGAAACGAACAAAAGTAAA
601590 TAAAAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.64, C:0.08, G:0.15, T:0.13
Consensus pattern (21 bp):
TGAAACGAACAAAAGTAAAAG
Found at i:607427 original size:13 final size:14
Alignment explanation
Indices: 607409--607439 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
607399 TGTTAACGCA
607409 GTCAGA-GTTAAAT
1 GTCAGAGGTTAAAT
607422 GTCAGAGGTTAAAT
1 GTCAGAGGTTAAAT
607436 GTCA
1 GTCA
607440 ATGTATTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (14 bp):
GTCAGAGGTTAAAT
Found at i:609731 original size:14 final size:14
Alignment explanation
Indices: 609681--609730 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
609671 TCATATATAA
609681 AAAAAAGAGAGAAAAG
1 AAAAAA-AG-GAAAAG
*
609697 AGAAAAAGGAAAAG
1 AAAAAAAGGAAAAG
*
609711 AAGAAAAGG-AAAG
1 AAAAAAAGGAAAAG
609724 AAAAAAA
1 AAAAAAA
609731 ATATATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 10 0.33
14 13 0.43
15 2 0.07
16 5 0.17
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AAAAAAAGGAAAAG
Found at i:610244 original size:60 final size:60
Alignment explanation
Indices: 610151--610273 Score: 219
Period size: 60 Copynumber: 2.0 Consensus size: 60
610141 TGCCTTTGAA
*
610151 TTTATGATATTTTTACTACTGATGTCGCTGCATTAGTCTGCTTAGCATTGCGCCCAAAAT
1 TTTATGATATTTTTACTACTGATGTCACTGCATTAGTCTGCTTAGCATTGCGCCCAAAAT
* *
610211 TTTATGATATTTTTACTACTGATGTCACTGCATTAGTTTGCTTAGCATTGCGCCCAAGAT
1 TTTATGATATTTTTACTACTGATGTCACTGCATTAGTCTGCTTAGCATTGCGCCCAAAAT
610271 TTT
1 TTT
610274 CACTGTAGAA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (60 bp):
TTTATGATATTTTTACTACTGATGTCACTGCATTAGTCTGCTTAGCATTGCGCCCAAAAT
Found at i:620777 original size:20 final size:20
Alignment explanation
Indices: 620754--620798 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
620744 TTTTATTGAT
620754 GTTTGCCATTTTTTACCAAC
1 GTTTGCCATTTTTTACCAAC
* *
620774 GTTTGCTATTTTTTACCAAT
1 GTTTGCCATTTTTTACCAAC
620794 GTTTG
1 GTTTG
620799 TAATCTTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.51
Consensus pattern (20 bp):
GTTTGCCATTTTTTACCAAC
Found at i:623050 original size:30 final size:30
Alignment explanation
Indices: 623028--623095 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
623018 TAAATTGGAA
* *
623028 ATTTTA-TGAAATTTAAAGACTAATTTGTG
1 ATTTTAGTGAAACTTAAAGACTAAATTGTG
** *
623057 ATTTTAGTGAAACTTAGGGACTAAATTGTA
1 ATTTTAGTGAAACTTAAAGACTAAATTGTG
*
623087 ATTCTAGTG
1 ATTTTAGTG
623096 GAATTAGGGG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 6 0.19
30 26 0.81
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (30 bp):
ATTTTAGTGAAACTTAAAGACTAAATTGTG
Found at i:623107 original size:30 final size:30
Alignment explanation
Indices: 623045--623110 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
623035 GAAATTTAAA
* * *
623045 GACTAATTTGTGATTTTAGTGAAACTTAGG
1 GACTAAATTGTAATTCTAGTGAAACTTAGG
*
623075 GACTAAATTGTAATTCTAGTGGAA-TTAGGG
1 GACTAAATTGTAATTCTAGTGAAACTTA-GG
623105 GACTAA
1 GACTAA
623111 TTTGAACTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 3 0.10
30 28 0.90
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (30 bp):
GACTAAATTGTAATTCTAGTGAAACTTAGG
Found at i:625125 original size:13 final size:15
Alignment explanation
Indices: 625109--625141 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
625099 TTTGATTCAG
625109 TTATTTT-ATTAA-A
1 TTATTTTAATTAACA
625122 TTATTTTAATTAACA
1 TTATTTTAATTAACA
625137 TTATT
1 TTATT
625142 ACGTCCGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 5 0.28
15 6 0.33
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATTTTAATTAACA
Found at i:625825 original size:30 final size:31
Alignment explanation
Indices: 625789--625881 Score: 102
Period size: 30 Copynumber: 3.1 Consensus size: 31
625779 CCAAAAATTG
625789 ATTTAAGGACTAAATTAGAAATTTT-GTGAA
1 ATTTAAGGACTAAATTAGAAATTTTAGTGAA
**
625819 ATTTAAGGACTAAATT-GTGATTTTAGTGAA
1 ATTTAAGGACTAAATTAGAAATTTTAGTGAA
* * * * *
625849 ACTTAGGGACTACATTA-TAATTTTAGTGGA
1 ATTTAAGGACTAAATTAGAAATTTTAGTGAA
625879 ATT
1 ATT
625882 AGGGAACTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 6 0.11
30 47 0.89
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.39
Consensus pattern (31 bp):
ATTTAAGGACTAAATTAGAAATTTTAGTGAA
Found at i:625902 original size:29 final size:30
Alignment explanation
Indices: 625795--625902 Score: 69
Period size: 30 Copynumber: 3.6 Consensus size: 30
625785 ATTGATTTAA
* * * * * *
625795 GGACTAAATTAGAAATTTTGTGAAATTTAA
1 GGACTACATTATAACTTTAGTGAAACTTAG
* * * *
625825 GGACTAAATTGTGATTTTAGTGAAACTTAG
1 GGACTACATTATAACTTTAGTGAAACTTAG
* *
625855 GGACTACATTATAATTTTAGTGGAA-TTAG
1 GGACTACATTATAACTTTAGTGAAACTTAG
625884 GGAACTA-ATT-TGAACTTTA
1 GG-ACTACATTAT-AACTTTA
625903 AATAAAATTC
Statistics
Matches: 64, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
28 1 0.02
29 15 0.23
30 48 0.75
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.37
Consensus pattern (30 bp):
GGACTACATTATAACTTTAGTGAAACTTAG
Done.