Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004862.1 Hibiscus syriacus cultivar Beakdansim tig00010968_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: 2846896
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 13
Found at i:2092732 original size:88 final size:90
Alignment explanation
Indices: 2092624--2092788 Score: 205
Period size: 88 Copynumber: 1.9 Consensus size: 90
2092614 ATGTATAAAC
* *
2092624 TATAAAAAGTATATAGGTATAAATTATAATATAATATATAG-ATATATTAT-ATATGATA-T-AT
1 TATAAAAACTATATAGGTATAAACTATAA-A-AATATATAGTATATATTATAAT-TGATATTAAT
2092685 ATA-TATATATATGTGTGTGTGTGTGTG
63 ATAGTATATATATGTGTGTGTGTGTGTG
* * * * *
2092712 TATATAAACTATATATGTATAAACTATAAAAGTATATAGTTTATATTATAATTTATATTAATATA
1 TATAAAAACTATATAGGTATAAACTATAAAAATATATAGTATATATTATAATTGATATTAATATA
2092777 GTATATATATGT
66 GTATATATATGT
2092789 ATGTATAACT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
86 8 0.12
87 13 0.20
88 28 0.43
89 5 0.08
90 11 0.17
ACGTcount: A:0.44, C:0.01, G:0.11, T:0.44
Consensus pattern (90 bp):
TATAAAAACTATATAGGTATAAACTATAAAAATATATAGTATATATTATAATTGATATTAATATA
GTATATATATGTGTGTGTGTGTGTG
Found at i:2092746 original size:15 final size:15
Alignment explanation
Indices: 2092714--2092747 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2092704 TGTGTGTGTA
* *
2092714 TATAAACTATATATG
1 TATAAACTATAAAAG
2092729 TATAAACTATAAAAG
1 TATAAACTATAAAAG
2092744 TATA
1 TATA
2092748 TAGTTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (15 bp):
TATAAACTATAAAAG
Found at i:2093027 original size:22 final size:22
Alignment explanation
Indices: 2093002--2093045 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2092992 ATTAACCTAT
2093002 AGTATATAAACAATAGTTAATA
1 AGTATATAAACAATAGTTAATA
2093024 AGTATATAAACAATAGTTAATA
1 AGTATATAAACAATAGTTAATA
2093046 TATGTAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.32
Consensus pattern (22 bp):
AGTATATAAACAATAGTTAATA
Found at i:2093113 original size:35 final size:36
Alignment explanation
Indices: 2093043--2093117 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 36
2093033 ACAATAGTTA
* *
2093043 ATATATGTAACTTATAGTATATATATACATGTAAACT
1 ATATATGTAACTTATAGTACATATATA-ATATAAACT
* *
2093080 ATATATGTAACTTATAGTACATGTAT-GTATAAACT
1 ATATATGTAACTTATAGTACATATATAATATAAACT
2093115 ATA
1 ATA
2093118 GTATATATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 10 0.29
37 24 0.71
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (36 bp):
ATATATGTAACTTATAGTACATATATAATATAAACT
Found at i:2093121 original size:16 final size:16
Alignment explanation
Indices: 2093102--2093159 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
2093092 TATAGTACAT
*
2093102 GTATGTATAAACTATA
1 GTATATATAAACTATA
2093118 GTATATATAAACTATA
1 GTATATATAAACTATA
*
2093134 TATATATATATAACTATA
1 -GTATATATA-AACTATA
2093152 -TATATATA
1 GTATATATA
2093160 TATAAAACTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
16 23 0.61
17 8 0.21
18 7 0.18
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.41
Consensus pattern (16 bp):
GTATATATAAACTATA
Found at i:2093126 original size:2 final size:2
Alignment explanation
Indices: 2093114--2093163 Score: 57
Period size: 2 Copynumber: 24.0 Consensus size: 2
2093104 ATGTATAAAC
*
2093114 TA TA GTA TA TA TA AA CTA TA TA TA TA TA TA TA -A CTA TA TA TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA
2093156 TA TA TA TA
1 TA TA TA TA
2093164 AAACTTATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
1 1 0.02
2 37 0.88
3 4 0.10
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2093164 original size:18 final size:17
Alignment explanation
Indices: 2093107--2093161 Score: 85
Period size: 18 Copynumber: 3.2 Consensus size: 17
2093097 TACATGTATG
*
2093107 TATAAACTATA-GTATA
1 TATAAACTATATATATA
2093123 TATAAACTATATATATA
1 TATAAACTATATATATA
2093140 TATATAACTATATATATA
1 TATA-AACTATATATATA
2093158 TATA
1 TATA
2093162 TAAAACTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
16 11 0.31
17 8 0.22
18 17 0.47
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (17 bp):
TATAAACTATATATATA
Found at i:2093439 original size:20 final size:21
Alignment explanation
Indices: 2093395--2093522 Score: 120
Period size: 22 Copynumber: 6.1 Consensus size: 21
2093385 ATGTAAACTA
* * *
2093395 TATATGTAAATTATAGTACATG
1 TATATATAAACTAT-GTATATG
*
2093417 TATGTATAAACTATGTATA-G
1 TATATATAAACTATGTATATG
* *
2093437 TATATATAAACTATATATATA
1 TATATATAAACTATGTATATG
*
2093458 TATATATAACCTATAGTATATG
1 TATATATAAACTAT-GTATATG
*
2093480 TATATATACAATCTATTTATATG
1 TATATATA-AA-CTATGTATATG
2093503 T-TATATAAACTA--TATATG
1 TATATATAAACTATGTATATG
2093521 TA
1 TA
2093523 ACCTATAGTT
Statistics
Matches: 89, Mismatches: 12, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.08
20 21 0.24
21 19 0.21
22 30 0.34
23 8 0.09
24 4 0.04
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (21 bp):
TATATATAAACTATGTATATG
Found at i:2093600 original size:21 final size:21
Alignment explanation
Indices: 2093560--2093607 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2093550 ATTAGTGTAC
* *
2093560 TATATAGTTTATAACCTATAG
1 TATATAATTTATAAACTATAG
*
2093581 TATATAATTTATAAATTATAG
1 TATATAATTTATAAACTATAG
*
2093602 TTTATA
1 TATATA
2093608 TTAATTTACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (21 bp):
TATATAATTTATAAACTATAG
Found at i:2094686 original size:23 final size:24
Alignment explanation
Indices: 2094655--2094705 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
2094645 ATTATTTTTC
*
2094655 TTTACATAAATTAAACTATA-TAA
1 TTTAAATAAATTAAACTATATTAA
2094678 TTTAAATAAATTAAACTATATTAA
1 TTTAAATAAATTAAACTATATTAA
2094702 TTTA
1 TTTA
2094706 CATTTAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTAAATAAATTAAACTATATTAA
Found at i:2096787 original size:239 final size:240
Alignment explanation
Indices: 2096368--2096844 Score: 938
Period size: 239 Copynumber: 2.0 Consensus size: 240
2096358 AGCCCATCAC
2096368 CCCAAGGCATAACCAACCAAACCCGCCCGGTTTCGACCCAAGACTGGAACCCAATAGAAGACTCG
1 CCCAAGGCATAACCAACCAAACCCGCCCGGTTTCGACCCAAGACTGGAACCCAATAGAAGACTCG
2096433 ACTAGAGCCCAGTTGCAGGACCCTAGAGGATCTGACCCGACCCAATAGCAACACCCTAGGGTTTC
66 ACTAGAGCCCAGTTGCAGGACCCTAGAGGATCTGACCCGACCCAATAGCAACACCCTAGGGTTTC
2096498 TGAAACCCTAACCCTATAGAGTTATCACCTGTTGCTGCTATCGCCGTCGATTGCTCTCGCCGAAG
131 TGAAACCCTAACCCTATAGAGTTATCACCTGTTGCTGCTATCGCCGTCGATTGCTCTCGCCGAAG
2096563 TCAGCAGTCTGGCCAAACAGTGACAGAACCTG-ACCATTAGTCCA
196 TCAGCAGTCTGGCCAAACAGTGACAGAACCTGCACCATTAGTCCA
2096607 CCCAAGGCATAACCAACCAAACCCGCCCGGTTTCGACCCAAGACTGGAACCCAATAGAAGACTCG
1 CCCAAGGCATAACCAACCAAACCCGCCCGGTTTCGACCCAAGACTGGAACCCAATAGAAGACTCG
*
2096672 ACTAGAGCCCAGTTGCAGGACCCTAGAGGATCTGACCCGACCCAATAGCAACACCCTAGGGTTTT
66 ACTAGAGCCCAGTTGCAGGACCCTAGAGGATCTGACCCGACCCAATAGCAACACCCTAGGGTTTC
2096737 TGAAACCCTAACCCTATAGAGTTATCACCTGTTGCTGCTATCGCCGTCGATTGCTCTCGCCGAAG
131 TGAAACCCTAACCCTATAGAGTTATCACCTGTTGCTGCTATCGCCGTCGATTGCTCTCGCCGAAG
2096802 TCAGCAGTCTGGCCAAACAGTGACAGAACCTGCACCATTAGTC
196 TCAGCAGTCTGGCCAAACAGTGACAGAACCTGCACCATTAGTC
2096845 AAAATAAATC
Statistics
Matches: 236, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
239 226 0.96
240 10 0.04
ACGTcount: A:0.28, C:0.32, G:0.21, T:0.19
Consensus pattern (240 bp):
CCCAAGGCATAACCAACCAAACCCGCCCGGTTTCGACCCAAGACTGGAACCCAATAGAAGACTCG
ACTAGAGCCCAGTTGCAGGACCCTAGAGGATCTGACCCGACCCAATAGCAACACCCTAGGGTTTC
TGAAACCCTAACCCTATAGAGTTATCACCTGTTGCTGCTATCGCCGTCGATTGCTCTCGCCGAAG
TCAGCAGTCTGGCCAAACAGTGACAGAACCTGCACCATTAGTCCA
Found at i:2097049 original size:2 final size:2
Alignment explanation
Indices: 2097042--2097078 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2097032 ACTTTTGAGA
2097042 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2097079 TTCAAACGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2101465 original size:2 final size:2
Alignment explanation
Indices: 2101458--2101505 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
2101448 AATAAAGGCA
*
2101458 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2101500 AT AT AT
1 AT AT AT
2101506 GTACAATAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2104314 original size:66 final size:66
Alignment explanation
Indices: 2104239--2104677 Score: 644
Period size: 66 Copynumber: 6.6 Consensus size: 66
2104229 ATTGTTCTCC
* * * *
2104239 AAACAAATTTTGTCTTGCTTGAGACAATTTCTCTTGATACATAAACCTTTGAGATTATTTCTCTT
1 AAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTT
2104304 G
66 G
* * * *
2104305 AAACGAATTTTGTCTCGCTTGAGAAAATTTCTCTTGAAACATAAACATTTGAGATTGTTTCTCTT
1 AAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTT
2104370 G
66 G
*
2104371 AAACGAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTT
1 AAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTT
2104436 G
66 G
* * *
2104437 AAACAAGTTTTGTCTCGCTTGAGACCGTTTCTCTTGAAACATAAACCTTTGAGATAGTTTCTCTT
1 AAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTT
2104502 G
66 G
* ** * * * *
2104503 AAATAGGTTTTGTCTCACTTAAGACAGTTTCTCTTGAAACATAAACATTTGAGGTTGTTTCTCTT
1 AAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTT
2104568 G
66 G
*
2104569 AAACAAAGTTTTGTCTCGCTTAAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCT
1 AAACAAA-TTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCT
2104634 TG
65 TG
* * * *
2104636 AAATAAAGTTTCGTATCGCCTGAGACAGTTTCTCTTGAAACA
1 AAACAAA-TTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACA
2104678 AATTTAATCT
Statistics
Matches: 340, Mismatches: 32, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
66 247 0.73
67 93 0.27
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (66 bp):
AAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTT
G
Found at i:2104401 original size:36 final size:35
Alignment explanation
Indices: 2104296--2104610 Score: 134
Period size: 30 Copynumber: 9.4 Consensus size: 35
2104286 TTTGAGATTA
* *
2104296 TTTCTCTTGAAACGAATTTTGTCTCGCTTGAGAAAA
1 TTTCTCTTGAAAC-AATTTTGTCTCGCTTGAGACAG
*** **
2104332 TTTCTCTTGAAAC-A--TAAACAT---TTGAGATTG
1 TTTCTCTTGAAACAATTTTGTC-TCGCTTGAGACAG
2104362 TTTCTCTTGAAACGAATTTTGTCTCGCTTGAGACAG
1 TTTCTCTTGAAAC-AATTTTGTCTCGCTTGAGACAG
*** * **
2104398 TTTCTCTTGAAAC-A--TAAAC-C-TTTGAGATTG
1 TTTCTCTTGAAACAATTTTGTCTCGCTTGAGACAG
*
2104428 TTTCTCTTGAAACAAGTTTTGTCTCGCTTGAGACCG
1 TTTCTCTTGAAACAA-TTTTGTCTCGCTTGAGACAG
*** * *
2104464 TTTCTCTTGAAAC-A--TAAAC-C-TTTGAGATAG
1 TTTCTCTTGAAACAATTTTGTCTCGCTTGAGACAG
* * * *
2104494 TTTCTCTTGAAATAGGTTTTGTCTCACTTAAGACAG
1 TTTCTCTTGAAACA-ATTTTGTCTCGCTTGAGACAG
*** ***
2104530 TTTCTCTTGAAAC-A--TAAACAT---TTGAGGTTG
1 TTTCTCTTGAAACAATTTTGTC-TCGCTTGAGACAG
*
2104560 TTTCTCTTGAAACAAAGTTTTGTCTCGCTTAAGACAG
1 TTTCTCTTGAAAC-AA-TTTTGTCTCGCTTGAGACAG
2104597 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
2104611 TAAACCTTTG
Statistics
Matches: 197, Mismatches: 53, Indels: 58
0.64 0.17 0.19
Matches are distributed among these distances:
30 76 0.39
31 3 0.02
32 10 0.05
33 3 0.02
34 9 0.05
35 5 0.03
36 73 0.37
37 18 0.09
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.39
Consensus pattern (35 bp):
TTTCTCTTGAAACAATTTTGTCTCGCTTGAGACAG
Found at i:2104998 original size:139 final size:139
Alignment explanation
Indices: 2104703--2105237 Score: 698
Period size: 139 Copynumber: 3.9 Consensus size: 139
2104693 GAGATCGTTA
* *
2104703 TCTCTAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTACG-AACAATGTTGTCCACCGA
1 TCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTA-GAAACAATGTCGTCCACCGA
* * * * * *
2104767 CTAGATCTCCTCAACGCGTAGGAGCATC-TTATCCTCAGACAATCAGAATTCCTCATCACGTAGG
65 CCAAATCTCCTCAACACGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCACGTAGG
2104831 AACCGTGTTG
130 AACCGTGTTG
* * * *
2104841 TCTCCAAATTATCCCTAAAGACGGCTAGACATCCTCATCATGTAGAAACAGTGTCGTCCACCGAC
1 TCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGAAACAATGTCGTCCACCGAC
* *
2104906 CAAATCTCCTCAACACGTATGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCACGTAGAA
66 CAAATCTCCTCAACACGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCACGTAGGA
2104971 ACCGTGTTG
131 ACCGTGTTG
* * * * *
2104980 TCTCTAAATTATACCTAAAGATGGGTAGACGTCCTCATCACATA-AGAACAATGTCGTCCACAGA
1 TCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGA-AACAATGTCGTCCACCGA
** * * * * * *
2105044 CCAAATCTCCTCAATGCTTAGGAGCAACGTTATCCTCAGATAACCAGACTTCTTCATCACGTAGG
65 CCAAATCTCCTCAACACGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCACGTAGG
2105109 AACCGTGTTG
130 AACCGTGTTG
* * *
2105119 TCTCCAAATTACCCCTAAAGATGGCTAGACGTCGTCATCACGTAGGAACAATGTCGTCCACCGAC
1 TCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGAAACAATGTCGTCCACCGAC
* * * ** * *
2105184 CAGATCTCTTAAACACAAAGGAGCAGTGTCATCCTTAGACAATCAGACTTCCTC
66 CAAATCTCCTCAACACGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTC
2105238 GATGAGCGTG
Statistics
Matches: 338, Mismatches: 55, Indels: 7
0.85 0.14 0.02
Matches are distributed among these distances:
137 1 0.00
138 80 0.24
139 257 0.76
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (139 bp):
TCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGAAACAATGTCGTCCACCGAC
CAAATCTCCTCAACACGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCACGTAGGA
ACCGTGTTG
Found at i:2105217 original size:278 final size:277
Alignment explanation
Indices: 2104703--2105237 Score: 791
Period size: 278 Copynumber: 1.9 Consensus size: 277
2104693 GAGATCGTTA
* * * * *
2104703 TCTCTAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTACGAACAATGTTGTCCACCGAC
1 TCTCTAAATTATACCTAAAGATGGCTAGACGTCCTCATCACATAAGAACAATGTCGTCCACAGAC
* * * *
2104768 TAGATCTCCTCAACGCGTAGGAGCATCTTATCCTCAGACAATCAGAATTCCTCATCACGTAGGAA
66 CAAATCTCCTCAACGCGTAGGAGCAACTTATCCTCAGACAACCAGAATTCCTCATCACGTAGGAA
* * *
2104833 CCGTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACATCCTCATCATGTAGAAACAGTGTCGT
131 CCGTGTTGTCTCCAAATTACCCCTAAAGACGGCTAGACATCCTCATCACGTAGAAACAATGTCGT
* ** *
2104898 CCACCGACCAAATCTCCTCAACACGTATGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATC
196 CCACCGACCAAATCTCCTAAACACAAAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATC
2104963 ACGTAGAAACCGTGTTG
261 ACGTAGAAACCGTGTTG
*
2104980 TCTCTAAATTATACCTAAAGATGGGTAGACGTCCTCATCACATAAGAACAATGTCGTCCACAGAC
1 TCTCTAAATTATACCTAAAGATGGCTAGACGTCCTCATCACATAAGAACAATGTCGTCCACAGAC
* * * * *
2105045 CAAATCTCCTCAATGCTTAGGAGCAACGTTATCCTCAGATAACCAGACTTCTTCATCACGTAGGA
66 CAAATCTCCTCAACGCGTAGGAGCAAC-TTATCCTCAGACAACCAGAATTCCTCATCACGTAGGA
* * * *
2105110 ACCGTGTTGTCTCCAAATTACCCCTAAAGATGGCTAGACGTCGTCATCACGTAGGAACAATGTCG
130 ACCGTGTTGTCTCCAAATTACCCCTAAAGACGGCTAGACATCCTCATCACGTAGAAACAATGTCG
* * * *
2105175 TCCACCGACCAGATCTCTTAAACACAAAGGAGCAGTGTCATCCTTAGACAATCAGACTTCCTC
195 TCCACCGACCAAATCTCCTAAACACAAAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTC
2105238 GATGAGCGTG
Statistics
Matches: 227, Mismatches: 30, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
277 81 0.36
278 146 0.64
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (277 bp):
TCTCTAAATTATACCTAAAGATGGCTAGACGTCCTCATCACATAAGAACAATGTCGTCCACAGAC
CAAATCTCCTCAACGCGTAGGAGCAACTTATCCTCAGACAACCAGAATTCCTCATCACGTAGGAA
CCGTGTTGTCTCCAAATTACCCCTAAAGACGGCTAGACATCCTCATCACGTAGAAACAATGTCGT
CCACCGACCAAATCTCCTAAACACAAAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATC
ACGTAGAAACCGTGTTG
Found at i:2105627 original size:3 final size:3
Alignment explanation
Indices: 2105610--2105672 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
2105600 GGGTTTTAAT
*
2105610 TTA TCA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
2105657 TATA ATA TTA TAA TTA
1 T-TA TTA TTA TTA TTA
2105673 CATTTTTGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 2 0.04
3 48 0.92
4 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:2106561 original size:2 final size:2
Alignment explanation
Indices: 2106554--2106584 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2106544 GCTTTTGAGA
*
2106554 TC TC TC TC TC TC TC TC TC TC GC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2106585 TTCAAACAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.03, T:0.48
Consensus pattern (2 bp):
TC
Found at i:2116683 original size:24 final size:24
Alignment explanation
Indices: 2116656--2116704 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2116646 GAGTTTTCCA
2116656 AGATCGAGTCAATGGAGTCAACTC
1 AGATCGAGTCAATGGAGTCAACTC
* * *
2116680 AGATCGAGTCAGTTGATTCAACTC
1 AGATCGAGTCAATGGAGTCAACTC
2116704 A
1 A
2116705 AAGAGTCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (24 bp):
AGATCGAGTCAATGGAGTCAACTC
Found at i:2116753 original size:13 final size:13
Alignment explanation
Indices: 2116735--2116781 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
2116725 TCGAGTTAAC
2116735 CCGTTGACCTAGA
1 CCGTTGACCTAGA
2116748 CCGTTGACC-AGA
1 CCGTTGACCTAGA
* *
2116760 CCCGTTGACTTTGA
1 -CCGTTGACCTAGA
2116774 CC-TTGACC
1 CCGTTGACC
2116782 AGGATTGACG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 8 0.28
13 19 0.66
14 2 0.07
ACGTcount: A:0.19, C:0.34, G:0.21, T:0.26
Consensus pattern (13 bp):
CCGTTGACCTAGA
Found at i:2116762 original size:26 final size:25
Alignment explanation
Indices: 2116733--2116783 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
2116723 AATCGAGTTA
2116733 ACCCGTTGACCTAGACCGTTGACCAG
1 ACCCGTTGACCTAGACC-TTGACCAG
* *
2116759 ACCCGTTGACTTTGACCTTGACCAG
1 ACCCGTTGACCTAGACCTTGACCAG
2116784 GATTGACGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.24
Consensus pattern (25 bp):
ACCCGTTGACCTAGACCTTGACCAG
Found at i:2130858 original size:17 final size:17
Alignment explanation
Indices: 2130818--2130869 Score: 77
Period size: 17 Copynumber: 3.0 Consensus size: 17
2130808 ACCGGTCATA
* *
2130818 ACCCGACCCGTTAACCCA
1 ACCCGACCCGTTGA-CCG
2130836 ACCCGACCCGTTGACCG
1 ACCCGACCCGTTGACCG
2130853 ACCCGACCCGTTGACCG
1 ACCCGACCCGTTGACCG
2130870 TTGACCGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 19 0.59
18 13 0.41
ACGTcount: A:0.21, C:0.48, G:0.19, T:0.12
Consensus pattern (17 bp):
ACCCGACCCGTTGACCG
Found at i:2133167 original size:24 final size:25
Alignment explanation
Indices: 2133140--2133192 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
2133130 AAAATTATTC
*
2133140 TTTTTGATGCAA-TTTTATTTATGAT
1 TTTTTGA-GCAATTTTTATTTATAAT
*
2133165 TTTTTGAGGAATTTTTATTTATAAT
1 TTTTTGAGCAATTTTTATTTATAAT
2133190 TTT
1 TTT
2133193 AAATGTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.25, C:0.02, G:0.11, T:0.62
Consensus pattern (25 bp):
TTTTTGAGCAATTTTTATTTATAAT
Found at i:2133845 original size:2 final size:2
Alignment explanation
Indices: 2133838--2133873 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2133828 TTACAAATAC
2133838 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2133874 TCCTCAACCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2134195 original size:3 final size:3
Alignment explanation
Indices: 2134189--2134221 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2134179 CTGAGTTTTA
*
2134189 ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2134222 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2135350 original size:31 final size:31
Alignment explanation
Indices: 2135252--2135342 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
2135242 CAATTTAAGG
2135252 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
2135283 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
2135314 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
2135343 TTCAAAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 12 0.20
31 37 0.62
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:2135568 original size:21 final size:21
Alignment explanation
Indices: 2135542--2135583 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2135532 ATTTGAATAT
*
2135542 TATGAAGAGGTATCGATTCCC
1 TATGAAGAGGTACCGATTCCC
*
2135563 TATGAAGGGGTACCGATTCCC
1 TATGAAGAGGTACCGATTCCC
2135584 CCTATTCTGG
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:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
TATGAAGAGGTACCGATTCCC
Found at i:2135645 original size:21 final size:21
Alignment explanation
Indices: 2135612--2135651 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2135602 TTTGAGTAGA
*
2135612 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
2135634 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
2135652 AGATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:2135905 original size:34 final size:34
Alignment explanation
Indices: 2135866--2135968 Score: 158
Period size: 33 Copynumber: 3.1 Consensus size: 34
2135856 TTTTGTAAAG
*
2135866 GGGAAATGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
2135900 GGGAAAGGTTCTAGCTTAG-CCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
* *
2135933 GGGAAAGGTTCTAGTTTAGCCCG-G-AAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
2135965 GGGA
1 GGGA
2135969 GTTGTAAGGT
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
32 11 0.17
33 33 0.51
34 21 0.32
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (34 bp):
GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
Found at i:2137965 original size:26 final size:26
Alignment explanation
Indices: 2137932--2137982 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
2137922 GTTTAGTTTG
2137932 AAAAATTCAATTTCTTAATAAAAAAA
1 AAAAATTCAATTTCTTAATAAAAAAA
*
2137958 AAAAATTCAATTTCTTAATGAAAAA
1 AAAAATTCAATTTCTTAATAAAAAA
2137983 GGGGGAGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (26 bp):
AAAAATTCAATTTCTTAATAAAAAAA
Found at i:2138226 original size:29 final size:31
Alignment explanation
Indices: 2138142--2138232 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
2138132 CAATTTAAGG
2138142 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
2138173 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
*
2138204 CAATAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
2138233 TTCAAAATTT
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 11 0.19
30 12 0.20
31 36 0.61
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.44
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:2138457 original size:21 final size:21
Alignment explanation
Indices: 2138431--2138472 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2138421 ATTTGAATAT
*
2138431 TATGAAGAGGTATCGATTCCC
1 TATGAAGAGGTACCGATTCCC
*
2138452 TATGAAGGGGTACCGATTCCC
1 TATGAAGAGGTACCGATTCCC
2138473 CCCATTCTGG
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:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
TATGAAGAGGTACCGATTCCC
Found at i:2138794 original size:34 final size:34
Alignment explanation
Indices: 2138755--2138858 Score: 176
Period size: 34 Copynumber: 3.1 Consensus size: 34
2138745 TTTTGTAAAG
2138755 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
2138789 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
* *
2138823 GGGAAAGGTTCTAGTTTAGCCCG-G-AAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
2138855 GGGA
1 GGGA
2138859 GTTGTAAGGT
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 11 0.16
33 1 0.01
34 56 0.82
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.22
Consensus pattern (34 bp):
GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
Found at i:2148137 original size:127 final size:127
Alignment explanation
Indices: 2147948--2148210 Score: 296
Period size: 127 Copynumber: 2.1 Consensus size: 127
2147938 CTCCAAATTA
* * * ** *
2147948 TCTCCAAATACAGCTAAACGTCCTCAACAGAAAGAACAATGTCGTCCACCGATGAGATCTCCTCA
1 TCTCCAAATACAGCTAAACATCCTCAACAGAAAGAACAATGACATCCACCGACCAGAACTCCTCA
** * * * * * * * *
2148013 ACTTGAATGAGCAGTGTCATCCTCAAACAATCAGACTTCTTCAACGTGAATGAATTATGTTG
66 ACGCGAAGGAGCAATGTCATCCTCAAACAACCAAACTTCCTCAACATGAAGGAACTATGTTG
* *
2148075 TCTCCAAATAC-GACTAGACATCCTCAACACGAAGGAACAATGACATCCACCGACCA-AACTCCT
1 TCTCCAAATACAG-CTAAACATCCTCAACA-GAAAGAACAATGACATCCACCGACCAGAACTCCT
* ** *
2148138 CAACGCGAAGGAGCAATGTCATCCTCATATTACCAAACTTCCTCAACATGAAGGAACTGTGTTG
64 CAACGCGAAGGAGCAATGTCATCCTCAAACAACCAAACTTCCTCAACATGAAGGAACTATGTTG
2148202 TCTCCAAAT
1 TCTCCAAAT
2148211 TATCCAAACA
Statistics
Matches: 112, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
126 1 0.01
127 90 0.80
128 21 0.19
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.23
Consensus pattern (127 bp):
TCTCCAAATACAGCTAAACATCCTCAACAGAAAGAACAATGACATCCACCGACCAGAACTCCTCA
ACGCGAAGGAGCAATGTCATCCTCAAACAACCAAACTTCCTCAACATGAAGGAACTATGTTG
Found at i:2148605 original size:3 final size:3
Alignment explanation
Indices: 2148597--2148626 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2148587 TCGGGTTTTA
2148597 ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2148627 ATAATATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:2151028 original size:33 final size:33
Alignment explanation
Indices: 2150989--2151056 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
2150979 ATTGGGCTGA
2150989 GAATGTGTCCTCGCTACAACTACGATAGCCAAT
1 GAATGTGTCCTCGCTACAACTACGATAGCCAAT
2151022 GAATGTGTCCTCGCTACAACTACGATAGCCAAT
1 GAATGTGTCCTCGCTACAACTACGATAGCCAAT
2151055 GA
1 GA
2151057 CCTCAGATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (33 bp):
GAATGTGTCCTCGCTACAACTACGATAGCCAAT
Found at i:2160229 original size:2 final size:2
Alignment explanation
Indices: 2160222--2160258 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2160212 TTATTATTAT
2160222 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2160259 TCAAATATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2164697 original size:23 final size:23
Alignment explanation
Indices: 2164625--2164687 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
2164615 TCCCAAAGGA
*
2164625 CCACATA-GTTTGCATCGAAGTG
1 CCACATAGGGTTGCATCGAAGTG
*
2164647 CCATATAGGGTTGCATCGAAGTG
1 CCACATAGGGTTGCATCGAAGTG
2164670 CCACATAGGGTTGCATCG
1 CCACATAGGGTTGCATCG
2164688 GAGGACCACA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
22 6 0.16
23 31 0.84
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (23 bp):
CCACATAGGGTTGCATCGAAGTG
Found at i:2164740 original size:21 final size:21
Alignment explanation
Indices: 2164686--2164741 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
2164676 AGGGTTGCAT
* *
2164686 CGGAGGACCACACAATTGTCC
1 CGGAGGACCACATAATTATCC
*
2164707 CGAAGGACCACATAATTATCC
1 CGGAGGACCACATAATTATCC
2164728 CGGAGGACCACATA
1 CGGAGGACCACATA
2164742 GACCCTCGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.34, C:0.30, G:0.21, T:0.14
Consensus pattern (21 bp):
CGGAGGACCACATAATTATCC
Found at i:2165304 original size:22 final size:20
Alignment explanation
Indices: 2165254--2165305 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
2165244 ATGCTTGGAA
* *
2165254 GTATCGGTACTACCCTAATG
1 GTATCGATACTACCCTAAGG
2165274 GTA-CTGATACTAGCCCTCAAGG
1 GTATC-GATACTA-CCCT-AAGG
2165296 GTATCGATAC
1 GTATCGATAC
2165306 CTCCACATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 1 0.04
20 9 0.35
21 4 0.15
22 11 0.42
23 1 0.04
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (20 bp):
GTATCGATACTACCCTAAGG
Found at i:2165353 original size:53 final size:53
Alignment explanation
Indices: 2165290--2165412 Score: 160
Period size: 53 Copynumber: 2.3 Consensus size: 53
2165280 ATACTAGCCC
*
2165290 TCAAGGGTATCGATACCTCCACATGGTACCGATACCGAAA-TAG-ATTCGATGTT
1 TCAAGGGTATCGATACCTCCACAAGGTACCGATA-C-AAATTAGCATTCGATGTT
* *
2165343 TCAAGGGTATCGATACCTCCTCAAGGTACCGATACAAATTTGGCATTCGATGTT
1 TCAAGGGTATCGATACCTCCACAAGGTACCGATACAAA-TTAGCATTCGATGTT
**
2165397 TTGAGGGTATCGATAC
1 TCAAGGGTATCGATAC
2165413 ATCCTACAGG
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 3 0.05
52 1 0.02
53 34 0.55
54 24 0.39
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (53 bp):
TCAAGGGTATCGATACCTCCACAAGGTACCGATACAAATTAGCATTCGATGTT
Found at i:2165424 original size:54 final size:53
Alignment explanation
Indices: 2165290--2165424 Score: 161
Period size: 54 Copynumber: 2.5 Consensus size: 53
2165280 ATACTAGCCC
2165290 TCAAGGGTATCGATACCTCC-ACATGGTACCGATACCGAAATAGATTCGATGTT
1 TCAAGGGTATCGATACCTCCTACA-GGTACCGATACCGAAATAGATTCGATGTT
*
2165343 TCAAGGGTATCGATACCTCCT-CAAGGTACCGATA-C-AAATTTGGCATTCGATGTT
1 TCAAGGGTATCGATACCTCCTAC-AGGTACCGATACCGAAA--TAG-ATTCGATGTT
** *
2165397 TTGAGGGTATCGATACATCCTACAGGTA
1 TCAAGGGTATCGATACCTCCTACAGGTA
2165425 TCAATACTAC
Statistics
Matches: 72, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
51 3 0.04
52 1 0.01
53 33 0.46
54 34 0.47
55 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (53 bp):
TCAAGGGTATCGATACCTCCTACAGGTACCGATACCGAAATAGATTCGATGTT
Found at i:2172239 original size:54 final size:54
Alignment explanation
Indices: 2172133--2172277 Score: 145
Period size: 54 Copynumber: 2.7 Consensus size: 54
2172123 GATACTACCC
* * *
2172133 TTCAA-GGTATTGATATCTCCTCATGGTACCGATACTGAAATAAGATTCGATGT
1 TTCAAGGGTATTGATACCTCCTCAAGGTACCGATACTCAAATAAGATTCGATGT
*
2172186 TTCAAGGGTATTGATACCTCCTCAAGGTACCGATAC-C-AATATAGCATTTGATGT
1 TTCAAGGGTATTGATACCTCCTCAAGGTACCGATACTCAAATA-AG-ATTCGATGT
** ** *
2172240 TTTGAGGGTATCAATACCATCCT-ATAGGTATCGATACT
1 TTCAAGGGTATTGATACC-TCCTCA-AGGTACCGATACT
2172278 ACCCTTAGAG
Statistics
Matches: 77, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
52 4 0.05
53 7 0.09
54 51 0.66
55 15 0.19
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (54 bp):
TTCAAGGGTATTGATACCTCCTCAAGGTACCGATACTCAAATAAGATTCGATGT
Found at i:2172271 original size:20 final size:19
Alignment explanation
Indices: 2172246--2172299 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
2172236 ATGTTTTGAG
* *
2172246 GGTATCAATACCATCCTATA
1 GGTATCGATACCACCCT-TA
*
2172266 GGTATCGATACTACCCTTA
1 GGTATCGATACCACCCTTA
2172285 GAGTATCGATACCAC
1 G-GTATCGATACCAC
2172300 TATCAATAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (19 bp):
GGTATCGATACCACCCTTA
Found at i:2177806 original size:48 final size:48
Alignment explanation
Indices: 2177726--2177849 Score: 131
Period size: 48 Copynumber: 2.5 Consensus size: 48
2177716 TATGTATTTT
* * * *
2177726 TATTTGTGGCATCCTTTCATACCAATTATGCACTGTTATACATCTAACATG
1 TATTAGTGGCA-CCTTTC-TGCCAA-AATGCACTGTTAGACATCTAACATG
* *
2177777 TATTAGTGGCACCTTTCTGCCAAAATGCACTGTTAGGCATCTAACTTG
1 TATTAGTGGCACCTTTCTGCCAAAATGCACTGTTAGACATCTAACATG
* * * *
2177825 CATTAATGACACCTTTCTGTCAAAA
1 TATTAGTGGCACCTTTCTGCCAAAA
2177850 ACCTCAGTTA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
48 42 0.67
49 5 0.08
50 6 0.10
51 10 0.16
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (48 bp):
TATTAGTGGCACCTTTCTGCCAAAATGCACTGTTAGACATCTAACATG
Found at i:2177860 original size:48 final size:48
Alignment explanation
Indices: 2177766--2177861 Score: 111
Period size: 48 Copynumber: 2.0 Consensus size: 48
2177756 CACTGTTATA
* * * ** *
2177766 CATCTAACATGTATTAGTGGCACCTTTCTGCCAAAATGCACTGTTAGG
1 CATCTAACATGCATTAATGACACCTTTCTGCCAAAAACCACAGTTAGG
* * *
2177814 CATCTAACTTGCATTAATGACACCTTTCTGTCAAAAACCTCAGTTAGG
1 CATCTAACATGCATTAATGACACCTTTCTGCCAAAAACCACAGTTAGG
2177862 TATTTAGTCT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (48 bp):
CATCTAACATGCATTAATGACACCTTTCTGCCAAAAACCACAGTTAGG
Found at i:2178180 original size:56 final size:56
Alignment explanation
Indices: 2178032--2178381 Score: 486
Period size: 56 Copynumber: 6.3 Consensus size: 56
2178022 AACTCTATAG
** * *
2178032 TTTGCACACGTAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAG-T
1 TTTGCACACAAAGTGCCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTT
* * *
2178087 TTTGCACACACAGTGTCCATACGAAAATTCATAAACTTATTACGAATTTCTTAGTT
1 TTTGCACACAAAGTGCCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTT
* * * *
2178143 TTCGCACACAAAGTGCCCATACAAAAATTCATTAACTTATTATGAATTTCATAGTT
1 TTTGCACACAAAGTGCCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTT
* * *
2178199 TTCGCACACACAGTGCCCATACGAAAATTCATAAACTTATTACGAATTTCTTAGTT
1 TTTGCACACAAAGTGCCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTT
* * * *
2178255 TTTGCACACAAAGTGCCCATACGGAAATTCATTAACTCATTATGAATATCTTAGTT
1 TTTGCACACAAAGTGCCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTT
** * * *
2178311 TTTGCACGGACAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAGTT
1 TTTGCACACAAAGTGCCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTT
2178367 TTTGCACACAAAGTG
1 TTTGCACACAAAGTG
2178382 TCATTTGTTA
Statistics
Matches: 261, Mismatches: 33, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
55 48 0.18
56 213 0.82
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.34
Consensus pattern (56 bp):
TTTGCACACAAAGTGCCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTT
Found at i:2181771 original size:2 final size:2
Alignment explanation
Indices: 2181764--2181792 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2181754 CCAGAAAAGC
2181764 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2181793 CTGACATCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2184129 original size:56 final size:56
Alignment explanation
Indices: 2184011--2184492 Score: 605
Period size: 56 Copynumber: 8.8 Consensus size: 56
2184001 CTACCAATAA
* **
2184011 GGAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACATACAACGCCCATAC
1 GGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACAAACAGTGCCCATAC
* * *
2184066 GAAAATTCATAAACTTATTGTGAATTTCTTAGTTTTTGCACAAACAATGCCCATAC
1 GGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACAAACAGTGCCCATAC
* *
2184122 GGAAATTCATAAACTTATTATGAGTTTCTTAGTTTTTGCACACAA-A-TATCCCATAC
1 GGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACA-AACAGT-GCCCATAC
* *
2184178 GGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCA-AACGCAGTGCCCATAT
1 GGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACAA-ACAGTGCCCATAC
* * *
2184234 GGAAATTCATAAACATATTA-CAATTTTCTTAGTTTTT-CACACAA-AGTGCTCATAC
1 GGAAATTCATAAACTTATTATGAA-TTTCTTAGTTTTTGCACA-AACAGTGCCCATAC
* * *
2184289 GGAAATTC----A--TATTATGAATTTTTTAGTTTTTGCACACATAGTGCCCATAC
1 GGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACAAACAGTGCCCATAC
*
2184339 GGAAATTCATAAACTTATTACGAATTTCTTAGTTTTTGCACATAA-AGTGCCCATAC
1 GGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACA-AACAGTGCCCATAC
* * **
2184395 GAAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACGCACAGTGCCCATAC
1 GGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACAAACAGTGCCCATAC
* *
2184451 GGAAATTCATAAACTCATTATGAATTTCTTAATTTTTGCACA
1 GGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACA
2184493 CAAAGTGTCA
Statistics
Matches: 375, Mismatches: 32, Indels: 39
0.84 0.07 0.09
Matches are distributed among these distances:
49 18 0.05
50 24 0.06
51 1 0.00
54 2 0.01
55 54 0.14
56 271 0.72
57 5 0.01
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.37
Consensus pattern (56 bp):
GGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACAAACAGTGCCCATAC
Found at i:2184343 original size:217 final size:217
Alignment explanation
Indices: 2184081--2184503 Score: 629
Period size: 217 Copynumber: 1.9 Consensus size: 217
2184071 TTCATAAACT
* * *
2184081 TATTGTGAATTTCTTAGTTTTTGCACAAACAATGCCCATACGGAAATTCATAAACTTATTATGAG
1 TATTATGAATTTCTTAGTTTTTGCACAAACAATGCCCATACGGAAATTCATAAACTTATTACGAA
* * *
2184146 TTTCTTAGTTTTTGCACACAAA-TATCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAG
66 TTTCTTAGTTTTTGCACACAAAGT-GCCCATACGAAAATTCATAAACTCATTATGAATTTCTTAG
* * *
2184210 TTTTTGCAAACGCAGTGCCCATATGGAAATTCATAAACAT-ATTA-CAATTTTCTTAGTTTTT-C
130 TTTTTGCAAACACAGTGCCCATACGGAAATTCATAAAC-TCATTATCAA-TTTCTTAATTTTTGC
2184272 ACACAAAGTGCTCATACGGAAATTCA
193 ACACAAAGTG-TCATACGGAAATTCA
* * * *
2184298 TATTATGAATTTTTTAGTTTTTGCACACATAGTGCCCATACGGAAATTCATAAACTTATTACGAA
1 TATTATGAATTTCTTAGTTTTTGCACAAACAATGCCCATACGGAAATTCATAAACTTATTACGAA
*
2184363 TTTCTTAGTTTTTGCACATAAAGTGCCCATACGAAAATTCATAAACTCATTATGAATTTCTTAGT
66 TTTCTTAGTTTTTGCACACAAAGTGCCCATACGAAAATTCATAAACTCATTATGAATTTCTTAGT
** *
2184428 TTTTGCACGCACAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAATTTTTGCACA
131 TTTTGCAAACACAGTGCCCATACGGAAATTCATAAACTCATTATCAATTTCTTAATTTTTGCACA
2184493 CAAAGTGTCAT
196 CAAAGTGTCAT
2184504 TTGGTAATCA
Statistics
Matches: 185, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
216 1 0.01
217 170 0.92
218 14 0.08
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (217 bp):
TATTATGAATTTCTTAGTTTTTGCACAAACAATGCCCATACGGAAATTCATAAACTTATTACGAA
TTTCTTAGTTTTTGCACACAAAGTGCCCATACGAAAATTCATAAACTCATTATGAATTTCTTAGT
TTTTGCAAACACAGTGCCCATACGGAAATTCATAAACTCATTATCAATTTCTTAATTTTTGCACA
CAAAGTGTCATACGGAAATTCA
Found at i:2187807 original size:48 final size:48
Alignment explanation
Indices: 2187713--2187808 Score: 111
Period size: 48 Copynumber: 2.0 Consensus size: 48
2187703 CATTGTTATA
* * * * *
2187713 CATCTAACATGTATTAGTGGCACCTTTCTGCCAAAATGCACCGTTAGG
1 CATCTAACATGCATTAATGACACCTTTCTGCCAAAAAGCACAGTTAGG
* * * *
2187761 CATCTAACTTGCATTAATGACACCTTTTTGTCAAAAAGCTCAGTTAGG
1 CATCTAACATGCATTAATGACACCTTTCTGCCAAAAAGCACAGTTAGG
2187809 TATTTAGTCT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (48 bp):
CATCTAACATGCATTAATGACACCTTTCTGCCAAAAAGCACAGTTAGG
Found at i:2188167 original size:56 final size:56
Alignment explanation
Indices: 2188054--2188555 Score: 709
Period size: 56 Copynumber: 9.0 Consensus size: 56
2188044 CCCACTACCA
* *
2188054 ATACAGAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACACAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* * * * *
2188109 ATACGAAAATTCATAAACTTTTTACGAATTTCCTAGATTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* *
2188165 ATACGGAAATTCATAAACTTATTATGAGTTTCTTAGTTTTTGCACACAAAGTTCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* *
2188221 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTAGCACACACAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* ** *
2188277 ATACGGAAATTCATAAACATATTACAAATTTCTTAGCTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* * *
2188333 ATACGGAAATTCATAAACTCATTATGAATTTTTTAGTTTTTGCACACATAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* * * * *
2188389 ATACAGAAATTCATAAACTTATTACGAGTTTCTTAGTTTTTGCACATAAAGTGCCT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* * * * *
2188445 AAACGAAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACGCACAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* * * *
2188501 ATACGGAAATTCATAAACTCACTATGAATTTCTTAATTTTTTCACACAAAGTGCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCC
2188556 ATTTGGTAAT
Statistics
Matches: 391, Mismatches: 55, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
55 31 0.08
56 360 0.92
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (56 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
Found at i:2193270 original size:17 final size:18
Alignment explanation
Indices: 2193242--2193282 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
2193232 GTAGGAGAAT
2193242 AAAATCATTTTTATGAAA
1 AAAATCATTTTTATGAAA
2193260 AAAATCATTTTTATGAAA
1 AAAATCATTTTTATGAAA
2193278 AAAAT
1 AAAAT
2193283 AAAACATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (18 bp):
AAAATCATTTTTATGAAA
Found at i:2193302 original size:22 final size:23
Alignment explanation
Indices: 2193239--2193295 Score: 72
Period size: 18 Copynumber: 2.7 Consensus size: 23
2193229 AAGGTAGGAG
2193239 AATAAAATCATTTTTATG----A
1 AATAAAATCATTTTTATGAAAAA
2193258 AA-AAAATCATTTTTATGAAAAA
1 AATAAAATCATTTTTATGAAAAA
2193280 AATAAAA-CATTTTTAT
1 AATAAAATCATTTTTAT
2193296 TCAAAAAGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
18 15 0.45
19 2 0.06
22 12 0.36
23 4 0.12
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.39
Consensus pattern (23 bp):
AATAAAATCATTTTTATGAAAAA
Found at i:2194575 original size:12 final size:12
Alignment explanation
Indices: 2194542--2194576 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2194532 TTCTCTCGAT
2194542 TTTCTTGTTTTC
1 TTTCTTGTTTTC
*
2194554 TTTTTTGTTTTC
1 TTTCTTGTTTTC
*
2194566 TTTCTAGTTTT
1 TTTCTTGTTTT
2194577 AGTGTTGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.03, C:0.11, G:0.09, T:0.77
Consensus pattern (12 bp):
TTTCTTGTTTTC
Found at i:2195319 original size:17 final size:16
Alignment explanation
Indices: 2195297--2195342 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
2195287 ATTTTGGTTG
2195297 TAATTTATTTAAGTATT
1 TAATTTATTTAA-TATT
*
2195314 TAATTTTTTTAATATT
1 TAATTTATTTAATATT
*
2195330 TTATTTATTTAAT
1 TAATTTATTTAAT
2195343 TTTTTTGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 15 0.58
17 11 0.42
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
TAATTTATTTAATATT
Found at i:2202469 original size:226 final size:224
Alignment explanation
Indices: 2202076--2202685 Score: 810
Period size: 226 Copynumber: 2.7 Consensus size: 224
2202066 TAGCATACTC
* * * * *
2202076 GGTTAATTACTGGAAACATTATCAACCAAAATAACAT-ATAGGTAGCGCTTATGTAACGTAATAG
1 GGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATAG
* * * * *
2202140 CTAGCACCTTTTTAAAGCTGTTGGAACCTTAGAAATTTGATGATAACAAAATAGGTTAATTACTT
66 GTAGCGCCTATTTAAAGCTATTGG--CCTTAGAAATATGATGATAACAAAATAGGTTAATTACTT
* *
2202205 GATTTGTTATCATTATTATCCACATATTAGGTAGCGCCTAAAATCTTACCAAAGTTTAAGCTGAT
129 GATTTGTTATCAGTATTATCAACATATTAGGTAGCGCCTAAAATCTTACCAAAGTTTAAGCTGAT
* * *
2202270 GGAGCCTTAG-AATTTCGACGATAACAAAATA
194 GAAGCCTTAGAAATCT-AACGATAACAAAATA
* * **
2202301 GGTTAATTACTGTAAACATTACCAACCATAATAACATAACAAGTAGAACTTATTTAATGTAATAG
1 GGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATAG
* * * **
2202366 GTAGCGTCTGTTTAAAGTTAATTGCGCCTTAGAAATCCGATGATAACAAAATAGGTTAATTACTT
66 GTAGCGCCTATTTAAAGCT-ATTG-GCCTTAGAAATATGATGATAACAAAATAGGTTAATTACTT
* *
2202431 GATTTGTTATCAGTATTATCAACATATTAGGTAGCGCCTAAAATGTTACCAAATTTTAAGCTGAT
129 GATTTGTTATCAGTATTATCAACATATTAGGTAGCGCCTAAAATCTTACCAAAGTTTAAGCTGAT
*
2202496 GAAGCCTTATAAATCTAACGATAACAAAATA
194 GAAGCCTTAGAAATCTAACGATAACAAAATA
* * * *
2202527 AGTTAATTACTGGACACAATATCAACCATAATAACATAACATGTAGCGCTTATTTAATGTAATAG
1 GGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATAG
* * * *
2202592 GTAGCGCCTATTTAAAGCTGATGGGGCCTTAAAAATATGACGATAGCAAAATAGGTTAATTACTT
66 GTAGCGCCTATTTAAAGCT-AT-TGGCCTTAGAAATATGATGATAACAAAATAGGTTAATTACTT
* *
2202657 GATTCGTTATCTGTATTATCAACATATTA
129 GATTTGTTATCAGTATTATCAACATATTA
2202686 TCGTGTACAT
Statistics
Matches: 335, Mismatches: 45, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
225 34 0.10
226 292 0.87
227 8 0.02
228 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (224 bp):
GGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATAG
GTAGCGCCTATTTAAAGCTATTGGCCTTAGAAATATGATGATAACAAAATAGGTTAATTACTTGA
TTTGTTATCAGTATTATCAACATATTAGGTAGCGCCTAAAATCTTACCAAAGTTTAAGCTGATGA
AGCCTTAGAAATCTAACGATAACAAAATA
Found at i:2210896 original size:2 final size:2
Alignment explanation
Indices: 2210889--2210923 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2210879 GATGAATGTG
2210889 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 A
2210924 AATGAATGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2210978 original size:31 final size:31
Alignment explanation
Indices: 2210936--2211019 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 31
2210926 TGAATGTTTG
*
2210936 TAAACCCTATTTATATTTGAATAAATATTTA
1 TAAACCATATTTATATTTGAATAAATATTTA
* * *
2210967 TAAA-TATTATTTCTATTTGAATAAATGTTTA
1 TAAACCA-TATTTATATTTGAATAAATATTTA
*
2210998 TAAACCATATTTGTATTTGAAT
1 TAAACCATATTTATATTTGAAT
2211020 TATCATTCTA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 44 0.98
32 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (31 bp):
TAAACCATATTTATATTTGAATAAATATTTA
Found at i:2218983 original size:24 final size:24
Alignment explanation
Indices: 2218956--2219019 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
2218946 ACTTGAATGT
*
2218956 TGTTATGATTTCTGATCTGGATTC
1 TGTTATGATTTCTGATCTGAATTC
2218980 TGTTATGATATT-TGATCTGAATTC
1 TGTTATGAT-TTCTGATCTGAATTC
*
2219004 TGTTTTGATTTCTGAT
1 TGTTATGATTTCTGAT
2219020 ATCTCCGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
23 2 0.06
24 32 0.89
25 2 0.06
ACGTcount: A:0.19, C:0.09, G:0.19, T:0.53
Consensus pattern (24 bp):
TGTTATGATTTCTGATCTGAATTC
Found at i:2222397 original size:20 final size:21
Alignment explanation
Indices: 2222356--2222408 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
2222346 AATGCTTGAT
*
2222356 GGTATCGATACCTAAGTAGGG
1 GGTATCGATACCTAACTAGGG
2222377 GGTATCGATACCT-ACTAGGG
1 GGTATCGATACCTAACTAGGG
*
2222397 GGTATCGGTACC
1 GGTATCGATACC
2222409 ATCCGAGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (21 bp):
GGTATCGATACCTAACTAGGG
Found at i:2222471 original size:95 final size:95
Alignment explanation
Indices: 2222372--2222585 Score: 349
Period size: 95 Copynumber: 2.2 Consensus size: 95
2222362 GATACCTAAG
2222372 TAGGGGGTATCGATACCTACTAGGGGGTATCGGTACCATCCGAGCATTCTATTATTTCTCGAAAC
1 TAGGGGGTATCGATACCTACTAGGGGGTATCGGTACCATCCGAGCATTCTATTATTTCTCGAAAC
2222437 CAAAATGTTCATAGGGGTATCGGTACCCTA
66 CAAAATGTTCATAGGGGTATCGGTACCCTA
* * * *
2222467 TAGGGGGTATCGGTACCCTA-TAGGGGGTATCGGTACCATCTGAGCATTCTGTTATTTCTCGGAA
1 TAGGGGGTATCGATA-CCTACTAGGGGGTATCGGTACCATCCGAGCATTCTATTATTTCTCGAAA
*
2222531 CTAAAATGTTCATAGGGGTATCGGTACCCTA
65 CCAAAATGTTCATAGGGGTATCGGTACCCTA
2222562 TATGGGGGTATCGATACCATACTA
1 TA-GGGGGTATCGATACC-TACTA
2222586 AATAAAATTT
Statistics
Matches: 109, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
95 89 0.82
96 18 0.17
97 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (95 bp):
TAGGGGGTATCGATACCTACTAGGGGGTATCGGTACCATCCGAGCATTCTATTATTTCTCGAAAC
CAAAATGTTCATAGGGGTATCGGTACCCTA
Found at i:2222475 original size:20 final size:20
Alignment explanation
Indices: 2222450--2222503 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
2222440 AATGTTCATA
2222450 GGGGTATCGGTACCCTATAG
1 GGGGTATCGGTACCCTATAG
2222470 GGGGTATCGGTACCCTATAG
1 GGGGTATCGGTACCCTATAG
2222490 GGGGTATCGGTACC
1 GGGGTATCGGTACC
2222504 ATCTGAGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.19, C:0.20, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGTATCGGTACCCTATAG
Found at i:2223404 original size:30 final size:32
Alignment explanation
Indices: 2223353--2223413 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
2223343 AAAATAAAAA
* *
2223353 TAATCTAAATTAATCTGAAC-A-AAAATAATT
1 TAATATAAATTAATCTAAACAACAAAATAATT
*
2223383 TAATATAAATTAATTTAAACAACAAAATAAT
1 TAATATAAATTAATCTAAACAACAAAATAAT
2223414 CTAAACAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 17 0.65
31 1 0.04
32 8 0.31
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (32 bp):
TAATATAAATTAATCTAAACAACAAAATAATT
Found at i:2223418 original size:17 final size:17
Alignment explanation
Indices: 2223393--2223427 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2223383 TAATATAAAT
* *
2223393 TAATTTAAACAACAAAA
1 TAATCTAAACAAAAAAA
2223410 TAATCTAAACAAAAAAA
1 TAATCTAAACAAAAAAA
2223427 T
1 T
2223428 TTAACTTGTT
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:0.11, G:0.00, T:0.23
Consensus pattern (17 bp):
TAATCTAAACAAAAAAA
Found at i:2226285 original size:17 final size:17
Alignment explanation
Indices: 2226263--2226324 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 17
2226253 AAACCCGACC
2226263 CGTTGACCTTTGACCGA
1 CGTTGACCTTTGACCGA
2226280 CGTTGACCAAAACTTTGACC--
1 CGTTGA-C----CTTTGACCGA
2226300 CGTTGACCTTTGACCGA
1 CGTTGACCTTTGACCGA
2226317 CGTTGACC
1 CGTTGACC
2226325 AAAACTTTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
15 8 0.21
17 14 0.37
18 1 0.03
19 1 0.03
20 6 0.16
22 8 0.21
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.27
Consensus pattern (17 bp):
CGTTGACCTTTGACCGA
Found at i:2226298 original size:22 final size:22
Alignment explanation
Indices: 2226270--2226335 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
2226260 ACCCGTTGAC
2226270 CTTTGACCGACGTTGACCAAAA
1 CTTTGACCGACGTTGACCAAAA
2226292 CTTTGACC--CGTTGA-C----
1 CTTTGACCGACGTTGACCAAAA
2226307 CTTTGACCGACGTTGACCAAAA
1 CTTTGACCGACGTTGACCAAAA
2226329 CTTTGAC
1 CTTTGAC
2226336 TGGCTTTGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
15 8 0.22
17 6 0.16
18 1 0.03
19 1 0.03
20 6 0.16
22 15 0.41
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (22 bp):
CTTTGACCGACGTTGACCAAAA
Found at i:2226300 original size:37 final size:37
Alignment explanation
Indices: 2226259--2226335 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
2226249 GACCAAACCC
2226259 GACCCGTTGACCTTTGACCGACGTTGACCAAAACTTT
1 GACCCGTTGACCTTTGACCGACGTTGACCAAAACTTT
2226296 GACCCGTTGACCTTTGACCGACGTTGACCAAAACTTT
1 GACCCGTTGACCTTTGACCGACGTTGACCAAAACTTT
2226333 GAC
1 GAC
2226336 TGGCTTTGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (37 bp):
GACCCGTTGACCTTTGACCGACGTTGACCAAAACTTT
Found at i:2228847 original size:12 final size:12
Alignment explanation
Indices: 2228811--2228854 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
2228801 ATTTAAATTA
* *
2228811 TGTTTTGATATC
1 TGTTCTGATATT
* *
2228823 TGATCTGAAATT
1 TGTTCTGATATT
2228835 TGTTCTGATATT
1 TGTTCTGATATT
2228847 TGTTCTGA
1 TGTTCTGA
2228855 ATTCTGTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.52
Consensus pattern (12 bp):
TGTTCTGATATT
Found at i:2228862 original size:24 final size:24
Alignment explanation
Indices: 2228790--2228855 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
2228780 TAATATTTTA
* *
2228790 TCTGATTTCTGAT-TTAAATTATGT
1 TCTGATATCTGATCTGAAATT-TGT
*
2228814 TTTGATATCTGATCTGAAATTTGT
1 TCTGATATCTGATCTGAAATTTGT
* *
2228838 TCTGATATTTGTTCTGAA
1 TCTGATATCTGATCTGAA
2228856 TTCTGTTTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 29 0.83
25 6 0.17
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.52
Consensus pattern (24 bp):
TCTGATATCTGATCTGAAATTTGT
Found at i:2232741 original size:12 final size:12
Alignment explanation
Indices: 2232720--2232796 Score: 59
Period size: 12 Copynumber: 6.4 Consensus size: 12
2232710 TTTATCTGAT
*
2232720 TTCTGATTTGAA
1 TTCTGTTTTGAA
2232732 TTCTGTTTTGACA
1 TTCTGTTTTGA-A
* *
2232745 -TCTGATCTGAA
1 TTCTGTTTTGAA
* *
2232756 ATCTGTTATGATA
1 TTCTGTTTTGA-A
*
2232769 TT-TGTTCTGAA
1 TTCTGTTTTGAA
*
2232780 TTCTGTTTTGAT
1 TTCTGTTTTGAA
2232792 TTCTG
1 TTCTG
2232797 ATATCTCCGT
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
11 4 0.08
12 45 0.87
13 3 0.06
ACGTcount: A:0.19, C:0.12, G:0.17, T:0.52
Consensus pattern (12 bp):
TTCTGTTTTGAA
Found at i:2232791 original size:24 final size:24
Alignment explanation
Indices: 2232716--2232798 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 24
2232706 ATATTTTATC
* *
2232716 TGATTTCTGATTTGAATTCTGTTT
1 TGATATCTGATCTGAATTCTGTTT
* * *
2232740 TGACATCTGATCTGAAATCTGTTA
1 TGATATCTGATCTGAATTCTGTTT
* *
2232764 TGATATTTGTTCTGAATTCTGTTT
1 TGATATCTGATCTGAATTCTGTTT
*
2232788 TGATTTCTGAT
1 TGATATCTGAT
2232799 ATCTCCGTTT
Statistics
Matches: 46, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.52
Consensus pattern (24 bp):
TGATATCTGATCTGAATTCTGTTT
Found at i:2239862 original size:21 final size:21
Alignment explanation
Indices: 2239838--2239878 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2239828 AAACATGGTA
2239838 TCTATAACAACAAACTTTAAT
1 TCTATAACAACAAACTTTAAT
*
2239859 TCTATAACAACCAACTTTAA
1 TCTATAACAACAAACTTTAA
2239879 ATCATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (21 bp):
TCTATAACAACAAACTTTAAT
Found at i:2243935 original size:6 final size:6
Alignment explanation
Indices: 2243924--2243950 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2243914 GTAAATACAT
2243924 AATATA AATATA AATATA AATATA AAT
1 AATATA AATATA AATATA AATATA AAT
2243951 CTACTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AATATA
Found at i:2252464 original size:24 final size:24
Alignment explanation
Indices: 2252428--2252536 Score: 59
Period size: 24 Copynumber: 4.6 Consensus size: 24
2252418 AAATCCTAAT
* *
2252428 TAAAACACTTAAAACTATTTAAAC
1 TAAAATACCTAAAACTATTTAAAC
* *
2252452 TAAAATACCTAAAAATAATATTTAAAA
1 TAAAATACCT--AAA-ACTATTTAAAC
* * * *
2252479 TAATAT-TCT-AAA-T-TCT-AAT
1 TAAAATACCTAAAACTATTTAAAC
2252498 TAAAATA-CTAAAACATATTTAAAC
1 TAAAATACCTAAAAC-TATTTAAAC
*
2252522 TAAAATATCTAAAAC
1 TAAAATACCTAAAAC
2252537 AAAGATAAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 19
0.68 0.12 0.20
Matches are distributed among these distances:
19 9 0.14
20 5 0.08
21 1 0.02
22 2 0.03
23 4 0.06
24 17 0.27
25 7 0.11
26 5 0.08
27 14 0.22
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (24 bp):
TAAAATACCTAAAACTATTTAAAC
Found at i:2252523 original size:70 final size:74
Alignment explanation
Indices: 2252410--2252604 Score: 217
Period size: 76 Copynumber: 2.7 Consensus size: 74
2252400 AACAAGCTAA
* * * *
2252410 AATATCTTAAATCCTAATTAAAACACTTAAAAC-TATTTAAACTAAAATACCT-A-AAA-ATAAT
1 AATATCATAAATTCTAATTAAAATAC-TAAAACATATTTAAACTAAAATACCTAACAAAGATAAA
*
2252471 AT-TTAAAAT
65 ATATAAAAAT
*
2252480 AATATTC-TAAATTCTAATTAAAATACTAAAACATATTTAAACTAAAATATCTAAAACAAAGATA
1 AATA-TCATAAATTCTAATTAAAATACTAAAACATATTTAAACTAAAATACCT--AACAAAGATA
2252544 AAATATAAAAAT
63 AAATATAAAAAT
*
2252556 AATATCATACAACT-TAATTAAAATACTAAAA-ACTATTTAAACTAAAATA
1 AATATCATA-AATTCTAATTAAAATACTAAAACA-TATTTAAACTAAAATA
2252605 AAAAGATAAA
Statistics
Matches: 108, Mismatches: 6, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
69 6 0.06
70 39 0.36
71 2 0.02
73 1 0.01
74 3 0.03
75 9 0.08
76 45 0.42
77 3 0.03
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.31
Consensus pattern (74 bp):
AATATCATAAATTCTAATTAAAATACTAAAACATATTTAAACTAAAATACCTAACAAAGATAAAA
TATAAAAAT
Found at i:2252545 original size:25 final size:24
Alignment explanation
Indices: 2252498--2252545 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
2252488 AAATTCTAAT
* **
2252498 TAAAATACTAAAACATATTTAAAC
1 TAAAATACTAAAACAAAGATAAAC
2252522 TAAAATATCTAAAACAAAGATAAA
1 TAAAATA-CTAAAACAAAGATAAA
2252546 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.25
Consensus pattern (24 bp):
TAAAATACTAAAACAAAGATAAAC
Found at i:2252629 original size:76 final size:75
Alignment explanation
Indices: 2252423--2252629 Score: 202
Period size: 76 Copynumber: 2.8 Consensus size: 75
2252413 ATCTTAAATC
* *
2252423 CTAATTAAAACACTTAAAACTATTTAAACTAAAAT----ACCTAAAA-ATAATATTT-AAAATAA
1 CTAATTAAAATAC-TAAAACTATTTAAACTAAAATAAAAACATAAAATATAATATTTAAAAATAA
*
2252482 TATTCTAAATT
65 TATTCTAAACT
* *
2252493 CTAATTAAAATACTAAAACATATTTAAACTAAAATATCTAAAACA-AAGATA-AA-ATATAAAAA
1 CTAATTAAAATACTAAAAC-TATTTAAACTAAAATA---AAAACATAAAATATAATATTTAAAAA
2252555 TAATA-TCATACAACT
62 TAATATTC-TA-AACT
* *
2252570 -TAATTAAAATACTAAAAACTATTTAAACTAAAATAAAAAGATAAAATATAATGTTTAAAA
1 CTAATTAAAATACT-AAAACTATTTAAACTAAAATAAAAACATAAAATATAATATTTAAAA
2252630 TATTATCCTA
Statistics
Matches: 112, Mismatches: 9, Indels: 26
0.76 0.06 0.18
Matches are distributed among these distances:
69 6 0.05
70 27 0.24
73 5 0.04
74 5 0.04
75 7 0.06
76 51 0.46
77 11 0.10
ACGTcount: A:0.58, C:0.10, G:0.01, T:0.30
Consensus pattern (75 bp):
CTAATTAAAATACTAAAACTATTTAAACTAAAATAAAAACATAAAATATAATATTTAAAAATAAT
ATTCTAAACT
Found at i:2253177 original size:58 final size:58
Alignment explanation
Indices: 2253107--2253385 Score: 389
Period size: 58 Copynumber: 4.8 Consensus size: 58
2253097 ATATTTCCCG
*
2253107 TACGGAAATTCATACACTTAGTATGAATCTCTTAACTTTTTGCACACAAAGTGCCCAA
1 TACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAA
* ** * * *
2253165 TACGAAAATTCATTGACTAAGTATGAATTTCTTATCTTTTTGCACACAAACTGCCCAA
1 TACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAA
* * *
2253223 TATAGG-AATTTATACACTTAATATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAA
1 TA-CGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAA
* * * *
2253281 TATGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAATTACTCAA
1 TACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAA
* * *
2253339 TATGGAAATTGATACACTTAGTATGAATTTCTTAACTTTTTCCACAC
1 TACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACAC
2253386 TTAGTGTCAT
Statistics
Matches: 195, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
57 2 0.01
58 192 0.98
59 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (58 bp):
TACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAA
Found at i:2253840 original size:18 final size:18
Alignment explanation
Indices: 2253813--2253847 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2253803 TTAATACCTT
*
2253813 CCCTTTGGTATCGATACC
1 CCCTTCGGTATCGATACC
2253831 CCCTTCGGTATCGATAC
1 CCCTTCGGTATCGATAC
2253848 TGATTCAATC
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:0.34, G:0.17, T:0.31
Consensus pattern (18 bp):
CCCTTCGGTATCGATACC
Found at i:2260243 original size:58 final size:58
Alignment explanation
Indices: 2259783--2260236 Score: 676
Period size: 58 Copynumber: 7.8 Consensus size: 58
2259773 CATATTTCCC
*
2259783 ATACGGAAATTCATACACTTAGTATGAATCTCTTAACTTTTTGCACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
* * *
2259841 ATAAGGAAATTCATACACTTAGTATGAATTT-TATATCTTTTTGCTCACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCT-TAACTTTTTGCACACAAAGTGCCCA
* * *
2259899 ATACGGAAATTCATACACTTAGTATGGATTTCTTAACTTTTTGTACACAAAGTGCACA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
* *
2259957 ATACGGAAATTCATACACATAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCTA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
* *
2260015 ATACGGAAATTCATACACTTAGTATGAATTTCATAACTTTTTGCACACAAAGTGTCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
* * * *
2260073 ATATGGAAATTCATACACTTAGTAAGAATTTATTAAGTTTTTGCACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
* * * * * * *
2260131 ATACGAAAATTCATTCACTTTGTATGAATTCCTTACCTTTTTGAACACAAAGTGCCAA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
* *
2260189 ATACGGAAATTCATAAACTTAGTATGAATTTCTTAACTTTTTACACAC
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACAC
2260237 TTAGTGCTAT
Statistics
Matches: 350, Mismatches: 44, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
57 1 0.00
58 348 0.99
59 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.34
Consensus pattern (58 bp):
ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
Found at i:2260617 original size:22 final size:19
Alignment explanation
Indices: 2260567--2260635 Score: 77
Period size: 19 Copynumber: 3.4 Consensus size: 19
2260557 TGGCTCCACA
*
2260567 GTATCGATACCCCTACCATG
1 GTATCGATA-CCCTACTATG
2260587 GTATCGATACTACCATACTATG
1 GTATCGATAC--CC-TACTATG
2260609 GTA-CTGATACCCTACTATG
1 GTATC-GATACCCTACTATG
2260628 GTATCGAT
1 GTATCGAT
2260636 GCCATTTTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
19 14 0.33
20 12 0.28
21 3 0.07
22 14 0.33
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (19 bp):
GTATCGATACCCTACTATG
Found at i:2263942 original size:84 final size:84
Alignment explanation
Indices: 2263823--2264681 Score: 613
Period size: 84 Copynumber: 10.4 Consensus size: 84
2263813 AAATTTGGTT
* * * * * *
2263823 TGCCTTTGAGTTGAGTGTAATCGAAA-TCGAAGGTCTTCGGTTGGCAGATAACCCTTCTTGACTT
1 TGCCTTGGAGCTGAGCGTAGTC-AAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTT
2263887 AAGCTATGCTGCAAATGATG
65 AAGCTATGCTGCAAATGATG
* * ** * * *
2263907 TGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTTGG-TGATATATAACCCTTATAGCCTT
1 TGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGACTT
* * * *
2263971 GAGTTATGCTGTAATTGATG
65 AAGCTATGCTGCAAATGATG
* * * * ** * *
2263991 TGCCCTTGAAGCTAAGTGTAATCAAACTCGAAGGTCTTCAGTTGGCA-AGTAGCCCTTCTCGACT
1 TG-CCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGA-TAACCCTTCTAGACT
**
2264055 TAAGCTATATTGCAAATGATG
64 TAAGCTATGCTGCAAATGATG
* * * ** *
2264076 TGCCTTGGAGCTGAGTGTAGTCGAAA-TCGAAGGTCTTTAG-CGATAGATAACCCTTCTAGCCTT
1 TGCCTTGGAGCTGAGCGTAGTC-AAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTT
* * * *
2264139 GAGTTATGTTGTAAATGATG
65 AAGCTATGCTGCAAATGATG
* * * * * * *
2264159 TGCCATCGAAGCTGAGTGTAATCGAACTCG-AGTGTC--T--TTGGCAGATAGCCCTTCTCGACT
1 TGCC-TTGGAGCTGAGCGTAGTCAAACTCGAAG-GTCTTTGGTTGGCAGATAACCCTTCTAGACT
* *
2264219 TAAGCTATGTTGCAAATAATG
64 TAAGCTATGCTGCAAATGATG
* * * *
2264240 TGCCTTGGAGCTGAGCATAGTTAAACTCGAAGGTCTTTGGTTGGCAGATAACCATTCTTGACTTA
1 TGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTA
* ** * *
2264305 AGTTATATTGTAAATGATA
66 AGCTATGCTGCAAATGATG
* * *** * *
2264324 TGCCATAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGG-TCATAGATAACCCTTATAGCCTT
1 TGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGACTT
* * *
2264388 GAGTTATGCTGTAAAATGATG
65 AAGCTATGCTG-CAAATGATG
* * * * * * * *
2264409 TGCCCTCGAAGATGAGCATAGTCAAACTCGAGGGTC-----TTAGCAGATAGCCCTTCTTGACTT
1 TG-CCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTT
* *
2264469 AAGCTATGTTGCAAATAATG
65 AAGCTATGCTGCAAATGATG
* * * * * * *
2264489 AGCCTTGGAGCTGAGCGTAATCGAACTTGAAGGTATTTAGTTGGCAGATAACCCTTCTCGACTTA
1 TGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTA
* *
2264554 AGTTATGCTGCAAATGATA
66 AGCTATGCTGCAAATGATG
* * * *
2264573 CGCCTT--A---GAGC----T-AAACTCGATGGTC-TTGG-TGGCAGATAACCCTTCTAGCCTTG
1 TGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTA
* **
2264626 AGCTATGCTGCAGATGACA
66 AGCTATGCTGCAAATGATG
2264645 TGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTT
1 TGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTT
2264682 GGCTAACAGA
Statistics
Matches: 593, Mismatches: 146, Indels: 73
0.73 0.18 0.09
Matches are distributed among these distances:
72 42 0.07
73 3 0.01
74 10 0.02
75 1 0.00
77 4 0.01
79 28 0.05
80 29 0.05
81 64 0.11
82 15 0.03
83 42 0.07
84 250 0.42
85 79 0.13
86 26 0.04
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (84 bp):
TGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTA
AGCTATGCTGCAAATGATG
Found at i:2264254 original size:164 final size:164
Alignment explanation
Indices: 2263834--2264571 Score: 625
Period size: 165 Copynumber: 4.4 Consensus size: 164
2263824 GCCTTTGAGT
* * *
2263834 TGAGTGTAATCGAAA-TCGAAGGTCTTCGGTTGGCAGATAACCCTTCTTGACTTAAGCTATGCTG
1 TGAGTGTAATC-AAACTCGAAGGTC-T---TTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTG
* *
2263898 CAAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTTGGTGATATATAACCCTT
61 CAAATGATGTGCCTTGGAGCTGAGCATAGTCGAAATCGAAGGTC-TTTGGTGATAGATAACCCTT
* * * * *
2263963 ATAGCCTTGAGTTATGCTGTAATTGATGTGCCCTTGAAGC
125 CTAGCCTTGAGTTATGTTGTAAATGATGTGCCATAGAAGC
* *
2264003 TAAGTGTAATCAAACTCGAAGGTCTTCAGTTGGCA-AGTAGCCCTTCTCGACTTAAGCTATATTG
1 TGAGTGTAATCAAACTCGAAGGTC-T---TTGGCAGA-TAGCCCTTCTCGACTTAAGCTATGTTG
** * *
2264067 CAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAAATCGAAGGTCTTTAGCGATAGATAACCCTTC
61 CAAATGATGTGCCTTGGAGCTGAGCATAGTCGAAATCGAAGGTCTTTGGTGATAGATAACCCTTC
*
2264132 TAGCCTTGAGTTATGTTGTAAATGATGTGCCATCGAAGC
126 TAGCCTTGAGTTATGTTGTAAATGATGTGCCATAGAAGC
*
2264171 TGAGTGTAATCGAACTCG-AGTGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAA
1 TGAGTGTAATCAAACTCGAAG-GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAA
* * ** * *
2264235 TAATGTGCCTTGGAGCTGAGCATAGT-TAAACTCGAAGGTCTTTGGTTGGCAGATAACCATTCTT
65 TGATGTGCCTTGGAGCTGAGCATAGTCGAAA-TCGAAGGTCTTTGG-TGATAGATAACCCTTCTA
* * * *
2264299 GACTTAAGTTATATTGTAAATGATATGCCATAG-AGC
128 GCCTTGAGTTATGTTGTAAATGATGTGCCATAGAAGC
* * * * * * * * *
2264335 TGAGCGTAGTCAAACTCGAAGGTCTTTTGGTCATAGATAACCCTTATAGCCTTGAGTTATGCTGT
1 TGAGTGTAATCAAACTCGAAGGTC-TTTGG-C--AGATAGCCCTTCTCGACTTAAGCTATGTTG-
* * * * * * * *
2264400 AAAATGATGTGCCCTCGAAGATGAGCATAGTC-AAACTCGAGGGTC-TT--AG-CAGATAGCCCT
61 CAAATGATGTG-CCTTGGAGCTGAGCATAGTCGAAA-TCGAAGGTCTTTGGTGATAGATAACCCT
* * * * * * * * *
2264460 TCTTGACTTAAGCTATGTTGCAAATAATGAGCC-TTGGAGC
124 TCTAGCCTTGAGTTATGTTGTAAATGATGTGCCATAGAAGC
* * * * * * *
2264500 TGAGCGTAATCGAACTTGAAGGTATTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
1 TGAGTGTAATCAAACTCGAAGG--TCT--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGC
2264565 AAATGAT
62 AAATGAT
2264572 ACGCCTTAGA
Statistics
Matches: 480, Mismatches: 70, Indels: 43
0.81 0.12 0.07
Matches are distributed among these distances:
163 3 0.01
164 102 0.21
165 133 0.28
166 3 0.01
167 5 0.01
168 102 0.21
169 104 0.22
170 28 0.06
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (164 bp):
TGAGTGTAATCAAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAAT
GATGTGCCTTGGAGCTGAGCATAGTCGAAATCGAAGGTCTTTGGTGATAGATAACCCTTCTAGCC
TTGAGTTATGTTGTAAATGATGTGCCATAGAAGC
Found at i:2264477 original size:249 final size:248
Alignment explanation
Indices: 2264009--2264584 Score: 782
Period size: 249 Copynumber: 2.3 Consensus size: 248
2263999 AAGCTAAGTG
* * *
2264009 TAATCAAACTCGAAGGTCTTCAGTTGGCA-AGTAGCCCTTCTCGACTTAAGCTATATTGCAAATG
1 TAATCAAACTCGAAGGTCTTTAGTTGGCAGA-TAACCCTTCTCGACTTAAGTTATATTGCAAATG
* * * *
2264073 ATGTGCCTTGGAGCTGAGTGTAGTCGAAATCGAAGGTCTTTAGCGATAGATAACCCTTCTAGCCT
65 ATATGCCTTAGAGCTGAGCGTAGTCGAAATCGAAGGTCTTTAGCGATAGATAACCCTTATAGCCT
* * ** * * *
2264138 TGAGTTATGTTGTAAATGATGTGCCATCGAAGCTGAGTGTAATCGAACTCGAGTGTCTTTGGCAG
130 TGAGTTATGCTGTAAATGATGTGCCATCGAAGATGAGCATAATCAAACTCGAGGGTCTTTAGCAG
*
2264203 ATAGCCCTTCTCGACTTAAGCTATGTTGCAAATAATGTGCCTTGGAGCTGAGCA
195 ATAGCCCTTCTCGACTTAAGCTATGTTGCAAATAATGAGCCTTGGAGCTGAGCA
* * * * * *
2264257 TAGTTAAACTCGAAGGTCTTTGGTTGGCAGATAACCATTCTTGACTTAAGTTATATTGTAAATGA
1 TAATCAAACTCGAAGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATATTGCAAATGA
* *
2264322 TATGCCATAGAGCTGAGCGTAGTC-AAACTCGAAGGTCTTTTG-GTCATAGATAACCCTTATAGC
66 TATGCCTTAGAGCTGAGCGTAGTCGAAA-TCGAAGGTCTTTAGCG--ATAGATAACCCTTATAGC
* *
2264385 CTTGAGTTATGCTGTAAAATGATGTGCCCTCGAAGATGAGCATAGTCAAACTCGAGGGTC-TTAG
128 CTTGAGTTATGCTGT-AAATGATGTGCCATCGAAGATGAGCATAATCAAACTCGAGGGTCTTTAG
* *
2264449 CAGATAGCCCTTCTTGACTTAAGCTATGTTGCAAATAATGAGCCTTGGAGCTGAGCG
192 CAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATAATGAGCCTTGGAGCTGAGCA
* * * **
2264506 TAATCGAACTTGAAGGTATTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
1 TAATCAAACTCGAAGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATATTGCAAATGA
*
2264571 TACGCCTTAGAGCT
66 TATGCCTTAGAGCT
2264585 AAACTCGATG
Statistics
Matches: 283, Mismatches: 40, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
247 4 0.01
248 87 0.31
249 155 0.55
250 37 0.13
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (248 bp):
TAATCAAACTCGAAGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATATTGCAAATGA
TATGCCTTAGAGCTGAGCGTAGTCGAAATCGAAGGTCTTTAGCGATAGATAACCCTTATAGCCTT
GAGTTATGCTGTAAATGATGTGCCATCGAAGATGAGCATAATCAAACTCGAGGGTCTTTAGCAGA
TAGCCCTTCTCGACTTAAGCTATGTTGCAAATAATGAGCCTTGGAGCTGAGCA
Found at i:2264535 original size:333 final size:331
Alignment explanation
Indices: 2263824--2264568 Score: 779
Period size: 333 Copynumber: 2.2 Consensus size: 331
2263814 AATTTGGTTT
* * * * * *
2263824 GCCTTTGAGTTGAGTGTAATCGAAATCGAAGGTCTTCGGTTGGCAGATAACCCTTCTTGACTTAA
1 GCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTATT-TGTTGGCAGATAACCCTTCTCGACTTAA
* * * *
2263889 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTTGGTGATAT
65 GCTATGCTGCAAATAATGTGCCTTGGAGCTGAGCATAGTCAAACTCGAAGGTCTTTTGGTGACAG
* * * * * * * * *
2263954 ATAACCCTTATAGCCTTGAGTTATGCTGTAATTGATGTGCCCTTGAAGCTAAGTGTAATCAAACT
130 ATAACCATTATAGACTTAAGTTATACTGTAAATGATATGCCATAGAAGCTAAGCGTAATCAAACT
* * * * * * *
2264019 CGAAGGTCTTCAGTTGGCAAGTAGCCCTTCTCGACTTAAGCTATATTGCAAATGATGTGCCTTGG
195 CGAAGGTCTT-A-TTGGCAAGTAACCCTTATAGACTTAAGCTATACTGAAAATGATGTGCCTCGA
* ** * * *
2264084 AGCTGAGTGTAGTCGAAATCGAAGGTCTTTAGCGATAGATAACCCTTCTAGCCTTGAGTTATGTT
258 AGATGAGCATAGTCGAAATCGAAGGTCTTTAGC-A-AGATAACCCTTCTAGACTTAAGCTATGTT
* * *
2264149 GTAAATGATGT
321 GCAAATAATGA
* * * * *
2264160 GCCATCGAAGCTGAGTGTAATCGAACTCG-A-GTGTCT-TTGGCAGATAGCCCTTCTCGACTTAA
1 GCC-TTGGAGCTGAGTGTAATCGAACTCGAAGGTATTTGTTGGCAGATAACCCTTCTCGACTTAA
* * *
2264222 GCTATGTTGCAAATAATGTGCCTTGGAGCTGAGCATAGTTAAACTCGAAGGTC-TTTGGTTGGCA
65 GCTATGCTGCAAATAATGTGCCTTGGAGCTGAGCATAGTCAAACTCGAAGGTCTTTTGG-TGACA
* * * * *
2264286 GATAACCATTCTTGACTTAAGTTATATTGTAAATGATATGCCATAG-AGCTGAGCGTAGTCAAAC
129 GATAACCATTATAGACTTAAGTTATACTGTAAATGATATGCCATAGAAGCTAAGCGTAATCAAAC
* * * *
2264350 TCGAAGGTCTT-TTGGTCATAGATAACCCTTATAGCCTTGAGTTATGCTGTAAAATGATGTGCCC
194 TCGAAGGTCTTATTGG-CA-AG-TAACCCTTATAGACTTAAGCTATACTG-AAAATGATGTG-CC
* * *
2264414 TCGAAGATGAGCATAGTC-AAACTCGAGGGTC-TTAGC-AGATAGCCCTTCTTGACTTAAGCTAT
254 TCGAAGATGAGCATAGTCGAAA-TCGAAGGTCTTTAGCAAGATAACCCTTCTAGACTTAAGCTAT
2264476 GTTGCAAATAATGA
318 GTTGCAAATAATGA
* *
2264490 GCCTTGGAGCTGAGCGTAATCGAACTTGAAGGTATTTAGTTGGCAGATAACCCTTCTCGACTTAA
1 GCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTATTT-GTTGGCAGATAACCCTTCTCGACTTAA
*
2264555 GTTATGCTGCAAAT
65 GCTATGCTGCAAAT
2264569 GATACGCCTT
Statistics
Matches: 334, Mismatches: 63, Indels: 27
0.79 0.15 0.06
Matches are distributed among these distances:
329 25 0.07
330 38 0.11
331 6 0.02
332 50 0.15
333 165 0.49
334 23 0.07
335 3 0.01
336 4 0.01
337 20 0.06
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (331 bp):
GCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTATTTGTTGGCAGATAACCCTTCTCGACTTAAG
CTATGCTGCAAATAATGTGCCTTGGAGCTGAGCATAGTCAAACTCGAAGGTCTTTTGGTGACAGA
TAACCATTATAGACTTAAGTTATACTGTAAATGATATGCCATAGAAGCTAAGCGTAATCAAACTC
GAAGGTCTTATTGGCAAGTAACCCTTATAGACTTAAGCTATACTGAAAATGATGTGCCTCGAAGA
TGAGCATAGTCGAAATCGAAGGTCTTTAGCAAGATAACCCTTCTAGACTTAAGCTATGTTGCAAA
TAATGA
Found at i:2269908 original size:26 final size:26
Alignment explanation
Indices: 2269878--2269927 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
2269868 AACAATGCTA
*
2269878 AAATAATAAAATAGAA-AGAAATATAG
1 AAATAA-AAAATAGAATAAAAATATAG
2269904 AAATAAAAAATAGAATAAAAATAT
1 AAATAAAAAATAGAATAAAAATAT
2269928 CAACATAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (26 bp):
AAATAAAAAATAGAATAAAAATATAG
Found at i:2269935 original size:26 final size:26
Alignment explanation
Indices: 2269878--2269940 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
2269868 AACAATGCTA
* *
2269878 AAATAATAAAATAGAAAGAAATATAG
1 AAATAACAAAATAGAAAAAAATATAG
2269904 AAATAA-AAAATAGAATAAAAATATCA-
1 AAATAACAAAATAGAA-AAAAATAT-AG
*
2269930 ACATAACAAAA
1 AAATAACAAAA
2269941 AAAACAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 9 0.28
26 18 0.56
27 5 0.16
ACGTcount: A:0.71, C:0.05, G:0.06, T:0.17
Consensus pattern (26 bp):
AAATAACAAAATAGAAAAAAATATAG
Found at i:2269953 original size:4 final size:4
Alignment explanation
Indices: 2269946--2270002 Score: 50
Period size: 4 Copynumber: 14.5 Consensus size: 4
2269936 CAAAAAAAAC
*
2269946 AAAT AAAT AAAT AAAT -AAT AAA- ATAAT AAAT AAA- AGGAA- ACAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT A--AAT AAAT AAAT
2269993 AAAT AAAT AA
1 AAAT AAAT AA
2270003 GAGGATGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
3 6 0.13
4 35 0.78
5 4 0.09
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:2269963 original size:12 final size:11
Alignment explanation
Indices: 2269904--2270002 Score: 62
Period size: 12 Copynumber: 8.5 Consensus size: 11
2269894 AGAAATATAG
2269904 AAATAAAAAAT
1 AAATAAAAAAT
2269915 AGAATAAAAATAT
1 A-AATAAAAA-AT
*
2269928 CAACATAACAAA-
1 -AA-ATAAAAAAT
*
2269940 AAA-AACAAAT
1 AAATAAAAAAT
2269950 AAATAAATAAAT
1 AAATAAA-AAAT
2269962 -AATAAAATAAT
1 AAATAAAA-AAT
2269973 AAATAAAAGGAA-
1 AAATAAAA--AAT
*
2269985 ACATAAATAAAT
1 AAATAAA-AAAT
2269997 AAATAA
1 AAATAA
2270003 GAGGATGAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
9 6 0.08
10 5 0.07
11 16 0.23
12 30 0.42
13 7 0.10
14 7 0.10
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:2271363 original size:2 final size:2
Alignment explanation
Indices: 2271356--2271408 Score: 74
Period size: 2 Copynumber: 27.0 Consensus size: 2
2271346 AATAAATAAA
*
2271356 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AA ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
2271398 AT A- AT AT AT AT
1 AT AT AT AT AT AT
2271409 GTTTTTTTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
1 2 0.04
2 44 0.94
3 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2271434 original size:40 final size:39
Alignment explanation
Indices: 2271390--2271802 Score: 287
Period size: 38 Copynumber: 10.4 Consensus size: 39
2271380 ATATATATAT
* *
2271390 AAAACTATATAATATATATGTTTTTTTTAAAA-TAATTTTG
1 AAAACTATATAATATATA--TTTTTTTAAAAACTAATTTTC
* ** * *
2271430 AAAACCATATAATATATAAGATTTTAAAAAAATAATTTTC
1 AAAACTATATAATATAT-ATTTTTTTAAAAACTAATTTTC
* *
2271470 AAATCTATATAATATATA-ATTTTTAAAAACTAATTTTC
1 AAAACTATATAATATATATTTTTTTAAAAACTAATTTTC
* **
2271508 AAAACTATATAATATATATATATTTTAAAAACTAGCTTTC
1 AAAACTATATAATATATAT-TTTTTTAAAAACTAATTTTC
* *
2271548 AAAATTATATAATATATA-TATTTTAAAAACTAATTTTC
1 AAAACTATATAATATATATTTTTTTAAAAACTAATTTTC
*
2271586 AAAACTATATAATATATATATATTATATATATATTTAAAAACT-AATTT-
1 AAAAC----T-ATATA-ATATA-TAT-T-T-T-TTTAAAAACTAATTTTC
** *
2271634 TCAA-GACTATATAATATATATTTTTTT--AAACTAATTTTC
1 AAAACTA-TAT--AATATATATTTTTTTAAAAACTAATTTTC
* *
2271673 AAAACTATATAATATATATATTTTTAAAAACTAGTTTTC
1 AAAACTATATAATATATATTTTTTTAAAAACTAATTTTC
* * **
2271712 AAAACTATATAATATATA-TATTTCAAAAA-TTGTTTT-
1 AAAACTATATAATATATATTTTTTTAAAAACTAATTTTC
* * * **
2271748 AAAGACTATA-AATTTATATGTTTTCAAAAA-TTGTTTT-
1 AAA-ACTATATAATATATATTTTTTTAAAAACTAATTTTC
2271785 AAAATCTATATAATATAT
1 AAAA-CTATATAATATAT
2271803 GTTCTCATAA
Statistics
Matches: 307, Mismatches: 38, Indels: 58
0.76 0.09 0.14
Matches are distributed among these distances:
36 11 0.04
37 55 0.18
38 75 0.24
39 46 0.15
40 73 0.24
41 2 0.01
42 3 0.01
43 11 0.04
44 10 0.03
45 3 0.01
47 1 0.00
48 2 0.01
49 5 0.02
50 10 0.03
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (39 bp):
AAAACTATATAATATATATTTTTTTAAAAACTAATTTTC
Found at i:2271485 original size:78 final size:79
Alignment explanation
Indices: 2271394--2271802 Score: 387
Period size: 78 Copynumber: 5.2 Consensus size: 79
2271384 ATATATAAAA
* * * *
2271394 CTATATAATATATATGTTTTTTTTAAAA-TAATTTTGAAAACCATATAATATATA-AGATTTTAA
1 CTATATAATATATA---TTTTTTAAAAACTAATTTTCAAAACTATATAATATATATATATTTTAA
2271457 AAAAATAATTTTCAAAT
63 AAAAATAATTTTCAAAT
*
2271474 CTATATAATATATAATTTTTAAAAACTAATTTTCAAAACTATATAATATATATATATTTT-AAAA
1 CTATATAATATATATTTTTTAAAAACTAATTTTCAAAACTATATAATATATATATATTTTAAAAA
* **
2271538 ACTAGCTTTCAAAAT
66 AATAATTTTC-AAAT
*
2271553 -TATATAATATATATATTTTAAAAACTAATTTTCAAAACTATATAATATATATATATTATATATA
1 CTATATAATATATATTTTTTAAAAACTAATTTTCAAAACTATATAATATATATATA-T-T-T-TA
2271617 TATTTAAAAACTAATTTTCAAGA-
62 -A---AAAAA-TAATTTTCAA-AT
*
2271640 CTATATAATATATATTTTTT-TAAACTAATTTTCAAAACTATATAATATATATAT-TTTT-AAAA
1 CTATATAATATATATTTTTTAAAAACTAATTTTCAAAACTATATAATATATATATATTTTAAAAA
* * *
2271702 ACTAGTTTTCAAAA
66 AATAATTTTCAAAT
* * ** * *
2271716 CTATATAATATATATATTTCAAAAA-TTGTTTT-AAAGACTATA-AAT-T-TATATGTTTT-CAA
1 CTATATAATATATATTTTTTAAAAACTAATTTTCAAA-ACTATATAATATATATATATTTTAAAA
** *
2271775 AAATTGTTTTAAAAT
65 AAATAATTTTCAAAT
2271790 CTATATAATATAT
1 CTATATAATATAT
2271803 GTTCTCATAA
Statistics
Matches: 283, Mismatches: 27, Indels: 44
0.80 0.08 0.12
Matches are distributed among these distances:
73 5 0.02
74 31 0.11
75 7 0.02
76 38 0.13
77 16 0.06
78 88 0.31
79 11 0.04
80 16 0.06
81 1 0.00
82 2 0.01
83 1 0.00
84 2 0.01
85 1 0.00
87 39 0.14
88 25 0.09
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (79 bp):
CTATATAATATATATTTTTTAAAAACTAATTTTCAAAACTATATAATATATATATATTTTAAAAA
AATAATTTTCAAAT
Found at i:2271498 original size:38 final size:39
Alignment explanation
Indices: 2271390--2271802 Score: 319
Period size: 40 Copynumber: 10.4 Consensus size: 39
2271380 ATATATATAT
* ** *
2271390 AAAACTATATAATATATATGTTTTTTTTAAAATAATTTTG
1 AAAACTATATAATATATAT-ATTTTTAAAAAATAATTTTC
* * *
2271430 AAAACCATATAATATATAAGATTTTAAAAAAATAATTTTC
1 AAAACTATATAATATAT-ATATTTTTAAAAAATAATTTTC
* *
2271470 AAATCTATATAATATATA-ATTTTTAAAAACTAATTTTC
1 AAAACTATATAATATATATATTTTTAAAAAATAATTTTC
* **
2271508 AAAACTATATAATATATATATATTTTAAAAACTAGCTTTC
1 AAAACTATATAATATATATAT-TTTTAAAAAATAATTTTC
* *
2271548 AAAATTATATAATATATATA-TTTTAAAAACTAATTTTC
1 AAAACTATATAATATATATATTTTTAAAAAATAATTTTC
* * * *
2271586 AAAACTATATAATATATATA-TATT-ATATAT-ATATTTA
1 AAAACTATATAATATATATATTTTTAAAAAATAAT-TTTC
** *
2271623 AAAACTAATTTTCAAGACTATATAATATATATTTTTTTAAACTAATTTTC
1 AAAACT-A---T----A-TA-AT-ATATATATTTTTAAAAAATAATTTTC
* *
2271673 AAAACTATATAATATATATATTTTTAAAAACTAGTTTTC
1 AAAACTATATAATATATATATTTTTAAAAAATAATTTTC
* **
2271712 AAAACTATATAATATATATA--TTTCAAAAATTGTTTT-
1 AAAACTATATAATATATATATTTTTAAAAAATAATTTTC
* **
2271748 AAAGACTATA-AAT-T-TATATGTTTTCAAAAATTGTTTT-
1 AAA-ACTATATAATATATATAT-TTTTAAAAAATAATTTTC
2271785 AAAATCTATATAATATAT
1 AAAA-CTATATAATATAT
2271803 GTTCTCATAA
Statistics
Matches: 312, Mismatches: 35, Indels: 52
0.78 0.09 0.13
Matches are distributed among these distances:
34 4 0.01
35 1 0.00
36 9 0.03
37 55 0.18
38 77 0.25
39 47 0.15
40 84 0.27
41 4 0.01
42 1 0.00
45 1 0.00
46 3 0.01
47 2 0.01
48 7 0.02
49 4 0.01
50 11 0.04
51 2 0.01
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (39 bp):
AAAACTATATAATATATATATTTTTAAAAAATAATTTTC
Found at i:2271613 original size:87 final size:86
Alignment explanation
Indices: 2271513--2271693 Score: 276
Period size: 87 Copynumber: 2.1 Consensus size: 86
2271503 TTTTCAAAAC
* *
2271513 TATATA-ATATATATATAT-TTTAAAAACTAGCTTTCAAAATTATATAATATATATATTTTAAAA
1 TATATATATATATATATATATTTAAAAACTAACTTTCAAAACTATATAATATATAT-TTTTAAAA
2271576 ACTAATTTTCAAAACTATATAA
65 ACTAATTTTCAAAACTATATAA
* * **
2271598 TATATATATATTATATATATATTTAAAAACTAATTTTCAAGACTATATAATATATATTTTTTTAA
1 TATATATATA-TATATATATATTTAAAAACTAACTTTCAAAACTATATAATATATATTTTTAAAA
2271663 ACTAATTTTCAAAACTATATAA
65 ACTAATTTTCAAAACTATATAA
2271685 TATATATAT
1 TATATATAT
2271694 TTTTAAAAAC
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
85 6 0.07
86 3 0.03
87 46 0.53
88 32 0.37
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.45
Consensus pattern (86 bp):
TATATATATATATATATATATTTAAAAACTAACTTTCAAAACTATATAATATATATTTTTAAAAA
CTAATTTTCAAAACTATATAA
Found at i:2271619 original size:11 final size:11
Alignment explanation
Indices: 2271591--2271620 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2271581 TTTTCAAAAC
*
2271591 TATATAATATA
1 TATATATTATA
2271602 TATATATTATA
1 TATATATTATA
2271613 TATATATT
1 TATATATT
2271621 TAAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TATATATTATA
Found at i:2271643 original size:50 final size:49
Alignment explanation
Indices: 2271553--2271654 Score: 177
Period size: 50 Copynumber: 2.1 Consensus size: 49
2271543 CTTTCAAAAT
2271553 TATATAATATATATATTTTAAAAACTAATTTTCAAAACTATATAATATA
1 TATATAATATATATATTTTAAAAACTAATTTTCAAAACTATATAATATA
* *
2271602 TATATATTATATATATATTTAAAAACTAATTTTCAAGACTATATAATATA
1 TATATAATATATATAT-TTTAAAAACTAATTTTCAAAACTATATAATATA
2271652 TAT
1 TAT
2271655 TTTTTTAAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 15 0.30
50 35 0.70
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (49 bp):
TATATAATATATATATTTTAAAAACTAATTTTCAAAACTATATAATATA
Found at i:2271662 original size:39 final size:39
Alignment explanation
Indices: 2271602--2271802 Score: 220
Period size: 37 Copynumber: 5.3 Consensus size: 39
2271592 ATATAATATA
* * * *
2271602 TATATATTATATATATATTTAAAAACTAATTTTCAAGAC
1 TATATAATATATATATTTTTAAAAACTAGTTTTCAAAAC
* *
2271641 TATATAATATATAT-TTTTT-TAAACTAATTTTCAAAAC
1 TATATAATATATATATTTTTAAAAACTAGTTTTCAAAAC
2271678 TATATAATATATATATTTTTAAAAACTAGTTTTCAAAAC
1 TATATAATATATATATTTTTAAAAACTAGTTTTCAAAAC
* *
2271717 TATATAATATATATA-TTTCAAAAA-TTGTTTT-AAAGAC
1 TATATAATATATATATTTTTAAAAACTAGTTTTCAAA-AC
* * * *
2271754 TATA-AATTTATATGTTTTCAAAAA-TTGTTTT-AAAATC
1 TATATAATATATATATTTTTAAAAACTAGTTTTCAAAA-C
2271791 TATATAATATAT
1 TATATAATATAT
2271803 GTTCTCATAA
Statistics
Matches: 145, Mismatches: 11, Indels: 13
0.86 0.07 0.08
Matches are distributed among these distances:
36 12 0.08
37 66 0.46
38 23 0.16
39 44 0.30
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (39 bp):
TATATAATATATATATTTTTAAAAACTAGTTTTCAAAAC
Found at i:2271747 original size:37 final size:37
Alignment explanation
Indices: 2271604--2271884 Score: 207
Period size: 37 Copynumber: 7.4 Consensus size: 37
2271594 ATAATATATA
* * *
2271604 TATATTATATATATATTT-AAAAACTAATTTTCAAGAC
1 TATATAATATATATATTTCAAAAA-TAGTTTTCAAAAC
* ** * *
2271641 TATATAATATATATTTTTTTAAACTAATTTTCAAAAC
1 TATATAATATATATATTTCAAAAATAGTTTTCAAAAC
*
2271678 TATATAATATATATATTTTTAAAAACTAGTTTTCAAAAC
1 TATATAATATATATA-TTTCAAAAA-TAGTTTTCAAAAC
*
2271717 TATATAATATATATATTTCAAAAATTGTTTT-AAAGAC
1 TATATAATATATATATTTCAAAAATAGTTTTCAAA-AC
* * *
2271754 TATA-AATTTATATGTTTTCAAAAATTGTTTT-AAAATC
1 TATATAATATATAT-ATTTCAAAAATAGTTTTCAAAA-C
* * * *
2271791 TATATAATATATGT-TCTCATAAAT-GTTTTATAAAGAC
1 TATATAATATATATATTTCAAAAATAGTTTT-CAAA-AC
* ** *
2271828 TATATATTATATACGTATTTTCAAAAACCGTTTGC-AAAC
1 TATATAATATATA--TA-TTTCAAAAATAGTTTTCAAAAC
2271867 TATAATATATATATATAT
1 TAT-ATA-ATATATATAT
2271885 ATATACAAAA
Statistics
Matches: 202, Mismatches: 25, Indels: 33
0.78 0.10 0.13
Matches are distributed among these distances:
35 5 0.02
36 20 0.10
37 93 0.46
38 27 0.13
39 35 0.17
40 5 0.02
41 13 0.06
42 4 0.02
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.44
Consensus pattern (37 bp):
TATATAATATATATATTTCAAAAATAGTTTTCAAAAC
Found at i:2271756 original size:76 final size:76
Alignment explanation
Indices: 2271602--2271884 Score: 251
Period size: 76 Copynumber: 3.7 Consensus size: 76
2271592 ATATAATATA
* * * * ** *
2271602 TATATATTATATATATATTT-AAAAACTAATTTTCAAGACTATATAATATATATTTTTTTAAACT
1 TATATAATATATATAT-TTTCAAAAACTAGTTTTCAAAACTATATAATATATATATTTCAAAAAT
**
2271666 AATTTTCAAA-AC
65 TGTTTT-AAAGAC
*
2271678 TATATAATATATATATTTTTAAAAACTAGTTTTCAAAACTATATAATATATATATTTCAAAAATT
1 TATATAATATATATATTTTCAAAAACTAGTTTTCAAAACTATATAATATATATATTTCAAAAATT
2271743 GTTTTAAAGAC
66 GTTTTAAAGAC
* * * * * *
2271754 TATA-AATTTATATGTTTTCAAAAA-TTGTTTT-AAAATCTATATAATATATGT-TCTCATAAA-
1 TATATAATATATATATTTTCAAAAACTAGTTTTCAAAA-CTATATAATATATATATTTCAAAAAT
2271814 TGTTTTATAAAGAC
65 TG-TTT-TAAAGAC
* * *
2271828 TATATATTATATACGTATTTTCAAAAAC-CGTTTGC-AAACTATAATATATATATATAT
1 TATATAATATATA--TATTTTCAAAAACTAGTTTTCAAAACTAT-ATA-ATATATATAT
2271885 ATATACAAAA
Statistics
Matches: 172, Mismatches: 22, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
72 2 0.01
73 14 0.08
74 31 0.18
75 29 0.17
76 67 0.39
77 21 0.12
78 7 0.04
79 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (76 bp):
TATATAATATATATATTTTCAAAAACTAGTTTTCAAAACTATATAATATATATATTTCAAAAATT
GTTTTAAAGAC
Found at i:2273836 original size:14 final size:15
Alignment explanation
Indices: 2273817--2273845 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2273807 GAAATATTGG
2273817 ATGAAA-GAGAAGAA
1 ATGAAATGAGAAGAA
2273831 ATGAAATGAGAAGAA
1 ATGAAATGAGAAGAA
2273846 GAAGAAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.10
Consensus pattern (15 bp):
ATGAAATGAGAAGAA
Found at i:2274093 original size:13 final size:13
Alignment explanation
Indices: 2274075--2274099 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2274065 TACGTTAGGT
2274075 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
2274088 TTTTTTTCTTTT
1 TTTTTTTCTTTT
2274100 TATGTTTTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:2274786 original size:28 final size:28
Alignment explanation
Indices: 2274727--2274825 Score: 101
Period size: 28 Copynumber: 3.4 Consensus size: 28
2274717 TAAATTCATA
*
2274727 ATATTTTATATATATTAACTTTAAAAAAAT
1 ATATTTTAT-TATATTAACTTT-TAAAAAT
*
2274757 ATATTTT-TTATATTAACTTATTAAATAT
1 ATATTTTATTATATTAACTT-TTAAAAAT
* * * *
2274785 ATTTTGTTCTTATCTAAACTTTTAAAAAT
1 ATATT-TTATTATATTAACTTTTAAAAAT
2274814 ATATTTTATTAT
1 ATATTTTATTAT
2274826 TATTTTTAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
28 26 0.45
29 15 0.26
30 17 0.29
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.54
Consensus pattern (28 bp):
ATATTTTATTATATTAACTTTTAAAAAT
Found at i:2274988 original size:23 final size:23
Alignment explanation
Indices: 2274936--2274988 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
2274926 TTTAACATAA
2274936 AATATATATTTTTAAATTAAAATT
1 AATA-ATATTTTTAAATTAAAATT
*
2274960 AA-AATACTTTTTAAATT-AAGTT
1 AATAATA-TTTTTAAATTAAAATT
2274982 AATAATA
1 AATAATA
2274989 AAATATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 9 0.35
23 15 0.58
24 2 0.08
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
AATAATATTTTTAAATTAAAATT
Found at i:2275000 original size:17 final size:19
Alignment explanation
Indices: 2274980--2275015 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
2274970 TTAAATTAAG
2274980 TTAATAA-TAAA-ATATAT
1 TTAATAAGTAAATATATAT
2274997 TTAATAAGTAAATATATAT
1 TTAATAAGTAAATATATAT
2275016 AAAATATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 4 0.24
19 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TTAATAAGTAAATATATAT
Found at i:2278423 original size:22 final size:21
Alignment explanation
Indices: 2278389--2278429 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2278379 ATAATTATTT
2278389 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
2278410 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
2278430 ATTTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:2279903 original size:32 final size:32
Alignment explanation
Indices: 2279867--2279932 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
2279857 TTTAAATATA
2279867 AAAATTAGGAGGCACAAATATCTTATTTGATT
1 AAAATTAGGAGGCACAAATATCTTATTTGATT
2279899 AAAATTAGGAGGCACAAATATCTTATTTGATT
1 AAAATTAGGAGGCACAAATATCTTATTTGATT
2279931 AA
1 AA
2279933 TATTTAAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.33
Consensus pattern (32 bp):
AAAATTAGGAGGCACAAATATCTTATTTGATT
Found at i:2282997 original size:3 final size:3
Alignment explanation
Indices: 2282991--2283026 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
2282981 CAGCAGCAGC
2282991 AGG AGG AGG A-G AGG AGG AGG AGG A-G AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
2283027 ACACGTGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:2283007 original size:11 final size:11
Alignment explanation
Indices: 2282993--2283027 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
2282983 GCAGCAGCAG
2282993 GAGGAGGA-GA
1 GAGGAGGAGGA
2283003 GGAGGAGGAGGA
1 -GAGGAGGAGGA
2283015 GAGGAGGAGGA
1 GAGGAGGAGGA
2283026 GA
1 GA
2283028 CACGTGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 21 0.91
12 2 0.09
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (11 bp):
GAGGAGGAGGA
Found at i:2283010 original size:14 final size:14
Alignment explanation
Indices: 2282991--2283026 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
2282981 CAGCAGCAGC
2282991 AGGAGGAGGAGAGG
1 AGGAGGAGGAGAGG
2283005 AGGAGGAGGAGAGG
1 AGGAGGAGGAGAGG
2283019 AGGAGGAG
1 AGGAGGAG
2283027 ACACGTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (14 bp):
AGGAGGAGGAGAGG
Found at i:2293305 original size:18 final size:19
Alignment explanation
Indices: 2293263--2293308 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
2293253 CAATTGGGAA
* *
2293263 TATCGATACTCTACCCTGGG
1 TATCGATACTC-ACCATGAG
2293283 TATCGATACTC-CCATGAG
1 TATCGATACTCACCATGAG
2293301 TATCGATA
1 TATCGATA
2293309 TGAAAAATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 13 0.54
20 11 0.46
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (19 bp):
TATCGATACTCACCATGAG
Found at i:2306752 original size:19 final size:19
Alignment explanation
Indices: 2306728--2306769 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
2306718 TCATCAACTT
*
2306728 ATTCCCACAAGCTATCCTA
1 ATTCCCACAAGCAATCCTA
2306747 ATTCCCACAAGCAATCCTA
1 ATTCCCACAAGCAATCCTA
2306766 ATTC
1 ATTC
2306770 TTACTAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.33, C:0.36, G:0.05, T:0.26
Consensus pattern (19 bp):
ATTCCCACAAGCAATCCTA
Found at i:2311878 original size:2 final size:2
Alignment explanation
Indices: 2311873--2311898 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2311863 TATATATATA
2311873 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
2311899 CATTTGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2319768 original size:21 final size:20
Alignment explanation
Indices: 2319742--2319796 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 20
2319732 AAAATGCCTT
2319742 GGTATCGATACTCCTA-TTG
1 GGTATCGATACTCCTACTTG
2319761 GGAATATCGATACT-CTACCTTG
1 GG--TATCGATACTCCTA-CTTG
2319783 GGTATCGATACTCC
1 GGTATCGATACTCC
2319797 CATGAGTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
19 2 0.06
20 13 0.42
21 11 0.35
22 5 0.16
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (20 bp):
GGTATCGATACTCCTACTTG
Found at i:2319807 original size:18 final size:19
Alignment explanation
Indices: 2319765--2319810 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
2319755 CTATTGGGAA
* *
2319765 TATCGATACTCTACCTTGGG
1 TATCGATACTC-ACCATGAG
2319785 TATCGATACTC-CCATGAG
1 TATCGATACTCACCATGAG
2319803 TATCGATA
1 TATCGATA
2319811 TAAAAAATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 13 0.54
20 11 0.46
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (19 bp):
TATCGATACTCACCATGAG
Found at i:2322016 original size:45 final size:45
Alignment explanation
Indices: 2321942--2322047 Score: 142
Period size: 45 Copynumber: 2.4 Consensus size: 45
2321932 AGTTGGACTT
* * *
2321942 CCAACTTATTT-CTCACACTATGTTGGAGCTATTACCAGAACTAA
1 CCAACTTATTTCCTAAAAATATGTTGGAGCTATTACCAGAACTAA
* * * *
2321986 CCAACTTATTTCCTAAAAATATGTTGGAGCTATTACTAGCATTAC
1 CCAACTTATTTCCTAAAAATATGTTGGAGCTATTACCAGAACTAA
2322031 CCAACTTATTTCCTAAA
1 CCAACTTATTTCCTAAA
2322048 TCTCTCTTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 11 0.20
45 43 0.80
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (45 bp):
CCAACTTATTTCCTAAAAATATGTTGGAGCTATTACCAGAACTAA
Found at i:2327281 original size:2 final size:2
Alignment explanation
Indices: 2327274--2327351 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
2327264 GTTATCATGA
2327274 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2327316 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2327352 GATGTTTATT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2355422 original size:61 final size:60
Alignment explanation
Indices: 2355284--2355435 Score: 171
Period size: 61 Copynumber: 2.5 Consensus size: 60
2355274 GGCTATGGAT
* ** * * *
2355284 CATAAGGTCGTGCCCATAACCTGCACTAAGTTTACATTTAGTGCTAATCTAGATATGACA
1 CATAAGGTCGTTCCCACCACCTGCACTAAGTTTACATCTAATGCTAATATAGATATGACA
* * * * *
2355344 -ATTAAGGTCATTGCCACCACCTGCACTAAGTTTACAGTCTAATGTTGATATGGATATGACA
1 CA-TAAGGTCGTTCCCACCACCTGCACTAAGTTTACA-TCTAATGCTAATATAGATATGACA
*
2355405 CATAAGGTTGTTCCCACCACCTGCACTAAGT
1 CATAAGGTCGTTCCCACCACCTGCACTAAGT
2355436 GTCCTTACAC
Statistics
Matches: 75, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
59 1 0.01
60 29 0.39
61 44 0.59
62 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (60 bp):
CATAAGGTCGTTCCCACCACCTGCACTAAGTTTACATCTAATGCTAATATAGATATGACA
Found at i:2363285 original size:55 final size:55
Alignment explanation
Indices: 2363224--2363594 Score: 424
Period size: 55 Copynumber: 6.7 Consensus size: 55
2363214 TTATGCGTGA
* ** *
2363224 AAAACTAAGAAATTCATAATAAGTTTATGATTTTTTGTATGGGTACTTTGTATGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTATGC
* * *
2363279 AAAACTATGAAATTCATAATAAGTTTATGAATTTCCATATGGGCACTTTGTGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTATGC
* * * *
2363334 AAAGCTAAGAAATTCATAATAAGTTTATAAATTTCCATATGGGCACTTTGTGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTATGC
* * * * *
2363389 AAAGCTAAGAATTTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTGTGTGT
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTATGC
* * * ***
2363444 ACAA--AA-AAATTCATATTAAGTTTATGAATTTCCTTACAAGCACTTTATGTATGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAC-TT-TGTA--TGC
* * * *
2363500 AAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGAGCAGTTTGTATAC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTATGC
* * *
2363555 AAAACTAATAAATTCATAATAAATTTATGAATTTCAGTAT
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
2363595 TGTTAATGGG
Statistics
Matches: 271, Mismatches: 38, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
52 30 0.11
53 4 0.01
54 3 0.01
55 190 0.70
56 5 0.02
57 4 0.01
58 4 0.01
59 31 0.11
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.38
Consensus pattern (55 bp):
AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTATGC
Done.