Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008128.1 Hibiscus syriacus cultivar Beakdansim tig00110683_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: 4987688
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 20
Found at i:2125801 original size:77 final size:78
Alignment explanation
Indices: 2125605--2125811 Score: 229
Period size: 78 Copynumber: 2.7 Consensus size: 78
2125595 TCTATAACTT
* * * * * * **
2125605 GTAAGTCCTTGCCATAAGCTCCTCGATTTTATGCTCATGGTAAGTCTTTACCGTAGGCTCCTCGG
1 GTAAGTCCTTACCACAAGCTCCTAGACTTTATGCTCAGGGTAAGTCCTTACCACAGGCTCCTCGG
2125670 CTTTGTGCTCAGG
66 CTTTGTGCTCAGG
* * * **
2125683 GTAAGTCCTTATCGCAAGCTCCTAGACTTTGTGCTTTGGGTAAGTCCTTACCACAGGCTCCTCGG
1 GTAAGTCCTTACCACAAGCTCCTAGACTTTATGCTCAGGGTAAGTCCTTACCACAGGCTCCTCGG
*
2125748 C-TTGTGCTTAGG
66 CTTTGTGCTCAGG
* * * *
2125760 GTAATTCCTTACCACATGCTCCTCTG-CTTTATGCACAGGGTAAGTCCTTACC
1 GTAAGTCCTTACCACAAGCTCCT-AGACTTTATGCTCAGGGTAAGTCCTTACC
2125812 GCATGTCCTT
Statistics
Matches: 105, Mismatches: 23, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
77 51 0.49
78 54 0.51
ACGTcount: A:0.18, C:0.27, G:0.22, T:0.33
Consensus pattern (78 bp):
GTAAGTCCTTACCACAAGCTCCTAGACTTTATGCTCAGGGTAAGTCCTTACCACAGGCTCCTCGG
CTTTGTGCTCAGG
Found at i:2130198 original size:39 final size:39
Alignment explanation
Indices: 2130155--2130380 Score: 213
Period size: 39 Copynumber: 5.8 Consensus size: 39
2130145 AAGCTCATCG
2130155 ACTTTGTGCTCAAGGTAAGTCCTTACCGCAGGCTCCTCT
1 ACTTTGTGCTCAAGGTAAGTCCTTACCGCAGGCTCCTCT
* * * * * * *
2130194 ACTTTGTGCAT-AGGGTAAGTTCTTACTGCATGTTTCTCA
1 ACTTTGTGC-TCAAGGTAAGTCCTTACCGCAGGCTCCTCT
* * * *
2130233 ATTTTGTGCTCAGGGTAAGTCCTTACCGCATGCTTCT-T
1 ACTTTGTGCTCAAGGTAAGTCCTTACCGCAGGCTCCTCT
** * * *
2130271 AGCTTTGTGCTCAAGGTAAGTCCTTATTGTAGGCACCTCG
1 A-CTTTGTGCTCAAGGTAAGTCCTTACCGCAGGCTCCTCT
* * *
2130311 GCTTTGTACTTAAGGTAAGTCCTTACCGCAGGCTCCTCT
1 ACTTTGTGCTCAAGGTAAGTCCTTACCGCAGGCTCCTCT
* * *
2130350 GCTTTGTGCACATGGTAAGTCCCTTACCGCA
1 ACTTTGTGCTCAAGGTAAGT-CCTTACCGCA
2130381 AGTCATTATG
Statistics
Matches: 149, Mismatches: 33, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
38 2 0.01
39 136 0.91
40 11 0.07
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.35
Consensus pattern (39 bp):
ACTTTGTGCTCAAGGTAAGTCCTTACCGCAGGCTCCTCT
Found at i:2130356 original size:117 final size:118
Alignment explanation
Indices: 2130156--2130380 Score: 272
Period size: 117 Copynumber: 1.9 Consensus size: 118
2130146 AGCTCATCGA
* * * * * *
2130156 CTTTGTGCTCAAGGTAAGTCCTTACCGCAGGCTCCTCTACTTTGTGCATAGGGTAAGTTCTTACT
1 CTTTGTGCTCAAGGTAAGTCCTTACCGCAGGCACCTCGACTTTGTACATAAGGTAAGTCCTTACC
* * * * *
2130221 GCATGTTTCTCAATTTTGTGCTCAGGGTAAGT-CCTTACCGCATGCTTCTTAG
66 GCAGGCTCCTCAACTTTGTGCACAGGGTAAGTCCCTTACCGCATGCTTCTTAG
** * * *
2130273 CTTTGTGCTCAAGGTAAGTCCTTATTGTAGGCACCTCGGCTTTGTACTTAAGGTAAGTCCTTACC
1 CTTTGTGCTCAAGGTAAGTCCTTACCGCAGGCACCTCGACTTTGTACATAAGGTAAGTCCTTACC
** *
2130338 GCAGGCTCCTCTGCTTTGTGCACATGGTAAGTCCCTTACCGCA
66 GCAGGCTCCTCAACTTTGTGCACAGGGTAAGTCCCTTACCGCA
2130381 AGTCATTATG
Statistics
Matches: 88, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
117 78 0.89
118 10 0.11
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (118 bp):
CTTTGTGCTCAAGGTAAGTCCTTACCGCAGGCACCTCGACTTTGTACATAAGGTAAGTCCTTACC
GCAGGCTCCTCAACTTTGTGCACAGGGTAAGTCCCTTACCGCATGCTTCTTAG
Found at i:2130609 original size:107 final size:105
Alignment explanation
Indices: 2130423--2130629 Score: 326
Period size: 107 Copynumber: 2.0 Consensus size: 105
2130413 GAGTGTACAT
* *
2130423 GTGGGTGTATGGTTCTAGGGAACCTATACATTATAGTGATCGGATGGGGTTAGTGTTCATATTTT
1 GTGGGTGTATGGTTCTAGGGAACCTACACATTATAGTGATCGGATGGGGTTAATGTTCATATTTT
2130488 TAAAACATGTTTGATAAACTGATTTTTTACTGAAGTATTCAG
66 TAAAACATGTTTGATAAACTGA--TTTTACTGAAGTATTCAG
* * * *
2130530 GTGGGTGTGTGGTTCTAGGGAACCTACACATTCTGGTGATCGGATGAGGG-TAATGTTCTTATTT
1 GTGGGTGTATGGTTCTAGGGAACCTACACATTATAGTGATCGGATG-GGGTTAATGTTCATATTT
2130594 TTAAAACATGTTTGATAAACTGATTTTACTGAAGTA
65 TTAAAACATGTTTGATAAACTGATTTTACTGAAGTA
2130630 CTTAATATGT
Statistics
Matches: 93, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
105 13 0.14
107 77 0.83
108 3 0.03
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (105 bp):
GTGGGTGTATGGTTCTAGGGAACCTACACATTATAGTGATCGGATGGGGTTAATGTTCATATTTT
TAAAACATGTTTGATAAACTGATTTTACTGAAGTATTCAG
Found at i:2131551 original size:54 final size:54
Alignment explanation
Indices: 2131469--2131577 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
2131459 TAACTTTAAC
2131469 AGATGTTGTTGTTGAAGATAAGTTGTCTTTTGATTGTTTCGATCTAGGAAGGCA
1 AGATGTTGTTGTTGAAGATAAGTTGTCTTTTGATTGTTTCGATCTAGGAAGGCA
2131523 AGATGTTGTTGTTGAAGATAAGTTGTCTTTTGATTGTTTCGATCTAGGAAGGCA
1 AGATGTTGTTGTTGAAGATAAGTTGTCTTTTGATTGTTTCGATCTAGGAAGGCA
2131577 A
1 A
2131578 CGAGGATCAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.25, C:0.07, G:0.28, T:0.40
Consensus pattern (54 bp):
AGATGTTGTTGTTGAAGATAAGTTGTCTTTTGATTGTTTCGATCTAGGAAGGCA
Found at i:2137566 original size:2 final size:2
Alignment explanation
Indices: 2137559--2137590 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2137549 AATAACGTGA
2137559 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
2137591 GAAAAGTGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2138823 original size:87 final size:87
Alignment explanation
Indices: 2138677--2138858 Score: 364
Period size: 87 Copynumber: 2.1 Consensus size: 87
2138667 GGAAACTACA
2138677 TGTTCATAAACAAATATTATATTTGTTCTTAATAAAATTTTAATTTTAAACTTTTTTATTAATTT
1 TGTTCATAAACAAATATTATATTTGTTCTTAATAAAATTTTAATTTTAAACTTTTTTATTAATTT
2138742 AGAGTGATTACAAAATAATATT
66 AGAGTGATTACAAAATAATATT
2138764 TGTTCATAAACAAATATTATATTTGTTCTTAATAAAATTTTAATTTTAAACTTTTTTATTAATTT
1 TGTTCATAAACAAATATTATATTTGTTCTTAATAAAATTTTAATTTTAAACTTTTTTATTAATTT
2138829 AGAGTGATTACAAAATAATATT
66 AGAGTGATTACAAAATAATATT
2138851 TGTTCATA
1 TGTTCATA
2138859 TCTTTTTTGA
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 95 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (87 bp):
TGTTCATAAACAAATATTATATTTGTTCTTAATAAAATTTTAATTTTAAACTTTTTTATTAATTT
AGAGTGATTACAAAATAATATT
Found at i:2139230 original size:23 final size:24
Alignment explanation
Indices: 2139190--2139240 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
2139180 AACGTGTCCG
** *
2139190 TTTATATGTTCATGAACATGTTCA
1 TTTATATGTTCACAAACAAGTTCA
2139214 TTTA-ATGTTCACAAACAAGTTCA
1 TTTATATGTTCACAAACAAGTTCA
2139237 TTTA
1 TTTA
2139241 GCGTTCATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (24 bp):
TTTATATGTTCACAAACAAGTTCA
Found at i:2139246 original size:23 final size:23
Alignment explanation
Indices: 2139204--2139247 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2139194 TATGTTCATG
* *
2139204 AACATGTTCATTTAATGTTCACA
1 AACAAGTTCATTTAACGTTCACA
*
2139227 AACAAGTTCATTTAGCGTTCA
1 AACAAGTTCATTTAACGTTCA
2139248 TTTATATGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (23 bp):
AACAAGTTCATTTAACGTTCACA
Found at i:2139482 original size:12 final size:12
Alignment explanation
Indices: 2139467--2139526 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 12
2139457 GGACGAGTTA
2139467 ATAAACGAGCTC
1 ATAAACGAGCTC
** *
2139479 ATAATGGAGCTT
1 ATAAACGAGCTC
*
2139491 ATAACCGAGCTC
1 ATAAACGAGCTC
* *
2139503 ATAAATGAGCCC
1 ATAAACGAGCTC
*
2139515 ATAAACAAGCTC
1 ATAAACGAGCTC
2139527 GTTCTAAATA
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (12 bp):
ATAAACGAGCTC
Found at i:2139518 original size:24 final size:24
Alignment explanation
Indices: 2139467--2139526 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
2139457 GGACGAGTTA
**
2139467 ATAAACGAGCTCATAATGGAGCTT
1 ATAAACGAGCTCATAATGGAGCCC
*
2139491 ATAACCGAGCTCATAAAT-GAGCCC
1 ATAAACGAGCTCAT-AATGGAGCCC
*
2139515 ATAAACAAGCTC
1 ATAAACGAGCTC
2139527 GTTCTAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 27 0.90
25 3 0.10
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (24 bp):
ATAAACGAGCTCATAATGGAGCCC
Found at i:2140852 original size:24 final size:23
Alignment explanation
Indices: 2140796--2140853 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
2140786 TGAATAAGAA
2140796 TCTCTA-TACTTGTGACATGTTTT
1 TCTCTACT-CTTGTGACATGTTTT
* *
2140819 TCTTTGCTCTTGTGGAGCATG-TTT
1 TCTCTACTCTTGT-GA-CATGTTTT
2140843 TCTCTACTCTT
1 TCTCTACTCTT
2140854 TTGGCACGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
23 9 0.32
24 15 0.54
25 4 0.14
ACGTcount: A:0.12, C:0.21, G:0.16, T:0.52
Consensus pattern (23 bp):
TCTCTACTCTTGTGACATGTTTT
Found at i:2142211 original size:19 final size:19
Alignment explanation
Indices: 2142185--2142225 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2142175 ACATACATGT
*
2142185 ATTTTTTATTCTAAATGAAA
1 ATTTTTAATTCTAAAT-AAA
*
2142205 ATTTTTAATTTTAAATAAA
1 ATTTTTAATTCTAAATAAA
2142224 AT
1 AT
2142226 AAGCAACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
ATTTTTAATTCTAAATAAA
Found at i:2151674 original size:24 final size:23
Alignment explanation
Indices: 2151647--2151695 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
2151637 TACGGCCTCC
2151647 AAATAAATCATA-AAACAAATTTAA
1 AAATAAATCATATAAA-AAA-TTAA
* *
2151671 AAATGAATTATATAAAAAATTAA
1 AAATAAATCATATAAAAAATTAA
2151694 AA
1 AA
2151696 TTTAAGGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 6 0.27
24 13 0.59
25 3 0.14
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (23 bp):
AAATAAATCATATAAAAAATTAA
Found at i:2153136 original size:14 final size:14
Alignment explanation
Indices: 2153119--2153154 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
2153109 TTCTTCTTTC
2153119 TTTCTTTCGAAATA
1 TTTCTTTCGAAATA
2153133 TTTCTTTCGAAATA
1 TTTCTTTCGAAATA
2153147 TTTCTTTC
1 TTTCTTTC
2153155 CTTCTTTCTT
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:0.22, C:0.17, G:0.06, T:0.56
Consensus pattern (14 bp):
TTTCTTTCGAAATA
Found at i:2154907 original size:14 final size:14
Alignment explanation
Indices: 2154890--2154916 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2154880 AATAATGCAT
2154890 TGAAAATAAAAAAG
1 TGAAAATAAAAAAG
2154904 TGAAAATAAAAAA
1 TGAAAATAAAAAA
2154917 TTCACCAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (14 bp):
TGAAAATAAAAAAG
Found at i:2156750 original size:16 final size:16
Alignment explanation
Indices: 2156729--2156760 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2156719 ATTATTAATA
2156729 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
*
2156745 ATCATTATTAAATCAT
1 ATCATTACTAAATCAT
2156761 TAAATATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.41
Consensus pattern (16 bp):
ATCATTACTAAATCAT
Found at i:2156848 original size:36 final size:33
Alignment explanation
Indices: 2156779--2156848 Score: 86
Period size: 36 Copynumber: 2.0 Consensus size: 33
2156769 AACTCATTAG
* **
2156779 ATTAATAATAATTATTAAATCATTATTGGTAAT
1 ATTAATAATAATTATTAAATAATTATTAATAAT
2156812 ATTAATAATCAATCATATTAAATAATTATTAATAAT
1 ATTAATAAT-AAT--TATTAAATAATTATTAATAAT
2156848 A
1 A
2156849 ATTCTCTCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 9 0.29
34 3 0.10
36 19 0.61
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (33 bp):
ATTAATAATAATTATTAAATAATTATTAATAAT
Found at i:2156961 original size:16 final size:18
Alignment explanation
Indices: 2156939--2156981 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
2156929 TTCGACTATT
*
2156939 TATAAATAAT-AATAAGA
1 TATAAATAATAAATAAAA
2156956 TA-AAAT-ATAAATAAAA
1 TATAAATAATAAATAAAA
2156972 TATAAATAAT
1 TATAAATAAT
2156982 TCAATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 2 0.09
16 12 0.55
17 6 0.27
18 2 0.09
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
TATAAATAATAAATAAAA
Found at i:2156969 original size:11 final size:11
Alignment explanation
Indices: 2156939--2156980 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
2156929 TTCGACTATT
2156939 TATAAATAATAA
1 TATAAATAA-AA
*
2156951 TA-AGATAAAA
1 TATAAATAAAA
2156961 TATAAATAAAA
1 TATAAATAAAA
2156972 TATAAATAA
1 TATAAATAA
2156981 TTCAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 4 0.15
11 21 0.78
12 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (11 bp):
TATAAATAAAA
Found at i:2161442 original size:16 final size:16
Alignment explanation
Indices: 2161423--2161455 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2161413 TTTATTTGTG
2161423 ATTTGGTTTACAAATA
1 ATTTGGTTTACAAATA
2161439 ATTTGGTTTACAAATA
1 ATTTGGTTTACAAATA
2161455 A
1 A
2161456 ATAGTTGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.42
Consensus pattern (16 bp):
ATTTGGTTTACAAATA
Found at i:2171035 original size:55 final size:55
Alignment explanation
Indices: 2170961--2171767 Score: 1210
Period size: 55 Copynumber: 14.7 Consensus size: 55
2170951 CAGGTTCCCT
* * * *
2170961 ACGATCGTTGAAGACTGTTCAAGTCTCATACTCTCTGAAGAAATAGGGGGCGGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
* *
2171016 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAGGAAATAGGGGGCGGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
* *
2171071 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
*
2171126 ACAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGC-GAAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAG-AC
* * *
2171181 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGAGGGCAGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
* * *
2171236 GCGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAGGAAATAGGGGGCGGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
* *
2171291 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
*
2171346 GCGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGC-GAAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAG-AC
* * *
2171401 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGAGGGCAGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
* * *
2171456 GCGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAGGAAATAGGGGGCGGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
* * *
2171511 ATGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
*
2171566 GCGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
* * * * *
2171621 GCGATTGATGAAGATTG-T-GGGTTTTATACTCTCTGAAGAAATA-GGGGCAGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
* * *
2171673 GCGATCGTTGAAGATTTTTTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
* * *
2171728 GCGATTGTTAAAGATTGTTCGAGTCTTATACTCTCTGAAG
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAG
2171768 GACTATGGAG
Statistics
Matches: 683, Mismatches: 62, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
52 23 0.03
53 24 0.04
54 26 0.04
55 608 0.89
56 2 0.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (55 bp):
ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
Found at i:2171154 original size:110 final size:110
Alignment explanation
Indices: 2170961--2171767 Score: 1350
Period size: 110 Copynumber: 7.4 Consensus size: 110
2170951 CAGGTTCCCT
* * ** * * *
2170961 ACGATCGTTGAAGACTGTTCAAGTCTCATACTCTCTGAAGAAATAGGGGGCGGACACGATCGTTG
1 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTG
*
2171026 AAGATTGTTCGAGTCTTATACTCTCTGAGGAAATAGGGGGCGGAC
66 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
* *
2171071 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATCGTTG
1 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTG
*
2171136 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGAAC
66 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
*
2171181 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGAGGGCAGACGCGATCGTTG
1 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTG
*
2171246 AAGATTGTTCGAGTCTTATACTCTCTGAGGAAATAGGGGGCGGAC
66 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
2171291 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTG
1 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTG
*
2171356 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGAAC
66 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
*
2171401 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGAGGGCAGACGCGATCGTTG
1 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTG
*
2171466 AAGATTGTTCGAGTCTTATACTCTCTGAGGAAATAGGGGGCGGAC
66 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
*
2171511 ATGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTG
1 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTG
*
2171576 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
66 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
* * *
2171621 GCGATTGATGAAGATTG-T-GGGTTTTATACTCTCTGAAGAAATA-GGGGCAGACGCGATCGTTG
1 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTG
* * *
2171683 AAGATTTTTTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
66 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
* * *
2171728 GCGATTGTTAAAGATTGTTCGAGTCTTATACTCTCTGAAG
1 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAG
2171768 GACTATGGAG
Statistics
Matches: 661, Mismatches: 34, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
107 77 0.12
108 25 0.04
109 19 0.03
110 540 0.82
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (110 bp):
ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTG
AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
Found at i:2179042 original size:37 final size:36
Alignment explanation
Indices: 2178952--2179053 Score: 161
Period size: 36 Copynumber: 2.8 Consensus size: 36
2178942 TAATCTTCAC
*
2178952 TAAG-AAAACACCCAAATTTCTTATGAAACATTTAA
1 TAAGAAAAACACTCAAATTTCTTATGAAACATTTAA
2178987 TAAGAAAAACACTCAAATTTCTTATGAAACATTTAA
1 TAAGAAAAACACTCAAATTTCTTATGAAACATTTAA
* *
2179023 TAAGAAAAAATACTTAAATTTCTTATGAAAC
1 TAAG-AAAAACACTCAAATTTCTTATGAAAC
2179054 CTAAATTGGT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 4 0.06
36 34 0.55
37 24 0.39
ACGTcount: A:0.50, C:0.14, G:0.06, T:0.30
Consensus pattern (36 bp):
TAAGAAAAACACTCAAATTTCTTATGAAACATTTAA
Found at i:2179419 original size:20 final size:19
Alignment explanation
Indices: 2179392--2179431 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
2179382 TTTTTTTTCT
2179392 TTTAAGAGAAAAAAAAGTC
1 TTTAAGAGAAAAAAAAGTC
*
2179411 TTTAGAGAGAAAAAAATGTC
1 TTTA-AGAGAAAAAAAAGTC
2179431 T
1 T
2179432 GCCACATGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.53, C:0.05, G:0.17, T:0.25
Consensus pattern (19 bp):
TTTAAGAGAAAAAAAAGTC
Found at i:2180661 original size:30 final size:30
Alignment explanation
Indices: 2180610--2180702 Score: 136
Period size: 30 Copynumber: 3.1 Consensus size: 30
2180600 AAATGATATG
*
2180610 CTCTCAACCTGTAAA-ATCACACAGCAATC
1 CTCTCAACCTGTAAACATCACACAACAATC
* *
2180639 CTCTCAACCCGAAAACATCACACAACAATC
1 CTCTCAACCTGTAAACATCACACAACAATC
2180669 CTCTCAACCTGTAAACATCA-ACCAACAATC
1 CTCTCAACCTGTAAACATCACA-CAACAATC
2180699 CTCT
1 CTCT
2180703 TATCTTTGAT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
29 14 0.25
30 43 0.75
ACGTcount: A:0.39, C:0.38, G:0.04, T:0.19
Consensus pattern (30 bp):
CTCTCAACCTGTAAACATCACACAACAATC
Found at i:2180776 original size:18 final size:16
Alignment explanation
Indices: 2180744--2180776 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2180734 CGTTGTAAGG
2180744 TAATTTTTTTAATATA
1 TAATTTTTTTAATATA
2180760 TAATATTTTTT-ATATA
1 TAAT-TTTTTTAATATA
2180776 T
1 T
2180777 GATTATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TAATTTTTTTAATATA
Found at i:2183497 original size:185 final size:185
Alignment explanation
Indices: 2183121--2183481 Score: 618
Period size: 185 Copynumber: 1.9 Consensus size: 185
2183111 ATAAAATTTT
*
2183121 AAATTTTAAATATATTATATATAACATATGGGCTCACCCTAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCACCCTAAACCATTTAAAACCCAATTAATAA
* *
2183186 TTTAATATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAACAATTTATATAAATTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAATTTT
* *
2183251 TTTTATATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTCTGAATTAAA
131 TTTTATACAATTATATATTATTTAAATTAATTATAAACTGTTTTTCTGAATTAAA
*
2183306 AAATATTATATATATTATATATAACATATGGGCTCAGCCC-AAACCATTTAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCTCA-CCCTAAACCATTTAAAACCCAATTAATA
*
2183370 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATATAAAATT
65 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATAT-AAATT
2183435 TTTATTT-TACAATTATATATTATTTAAATTAATTATAAACTGTTTTT
129 TTT-TTTATACAATTATATATTATTTAAATTAATTATAAACTGTTTTT
2183482 TTTATTATAA
Statistics
Matches: 166, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
185 114 0.69
186 49 0.30
187 3 0.02
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (185 bp):
AAATATTAAATATATTATATATAACATATGGGCTCACCCTAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAATTTT
TTTTATACAATTATATATTATTTAAATTAATTATAAACTGTTTTTCTGAATTAAA
Found at i:2183522 original size:20 final size:21
Alignment explanation
Indices: 2183480--2183524 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
2183470 TAAACTGTTT
**
2183480 TTTTTATTATAAAATATTTAA
1 TTTTTATTATAAAATATAAAA
*
2183501 TTTTTA-TATAAATTATAAAA
1 TTTTTATTATAAAATATAAAA
2183521 TTTT
1 TTTT
2183525 AAAACTTTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTTTATTATAAAATATAAAA
Found at i:2187476 original size:28 final size:27
Alignment explanation
Indices: 2187412--2187481 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 27
2187402 TGTTCTCCTA
* * *
2187412 AAATTATTAATAATTACAAAAAATAAT
1 AAATTATTACTAATAATAAAAAATAAT
* *
2187439 ATA-TA-AACTAATAATAAAAAATAAAT
1 AAATTATTACTAATAATAAAAAAT-AAT
2187465 AAATTATTACTAATAAT
1 AAATTATTACTAATAAT
2187482 TTAAATTAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
25 13 0.39
26 7 0.21
27 4 0.12
28 9 0.27
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (27 bp):
AAATTATTACTAATAATAAAAAATAAT
Found at i:2192503 original size:3 final size:3
Alignment explanation
Indices: 2192495--2192553 Score: 55
Period size: 3 Copynumber: 19.7 Consensus size: 3
2192485 GTTGTCACCA
* * * * * *
2192495 TCG TCG TCG TCG TCG TCG TCG TCA TCA TTG TCG TCG TCG TTG TTG TTG
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG
*
2192543 TCG TTG TCG TC
1 TCG TCG TCG TC
2192554 CTGAGTAGGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.03, C:0.25, G:0.29, T:0.42
Consensus pattern (3 bp):
TCG
Found at i:2192510 original size:12 final size:12
Alignment explanation
Indices: 2192495--2192553 Score: 64
Period size: 12 Copynumber: 4.9 Consensus size: 12
2192485 GTTGTCACCA
*
2192495 TCGTCGTCGTCG
1 TCGTTGTCGTCG
* *
2192507 TCGTCGTCGTCA
1 TCGTTGTCGTCG
*
2192519 TCATTGTCGTCG
1 TCGTTGTCGTCG
* *
2192531 TCGTTGTTGTTG
1 TCGTTGTCGTCG
2192543 TCGTTGTCGTC
1 TCGTTGTCGTC
2192554 CTGAGTAGGT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.03, C:0.25, G:0.29, T:0.42
Consensus pattern (12 bp):
TCGTTGTCGTCG
Found at i:2192904 original size:27 final size:27
Alignment explanation
Indices: 2192864--2192926 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
2192854 TGGTAGCGAC
* *
2192864 GGCGGCATCGGGTAAGGGAATGGAGGT
1 GGCGACATCGGGTAAGGGAAAGGAGGT
* * *
2192891 GGCGACATCTGGTAATGGAAAGGCGGT
1 GGCGACATCGGGTAAGGGAAAGGAGGT
*
2192918 GACGACATC
1 GGCGACATC
2192927 ATATATGGCT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.25, C:0.16, G:0.43, T:0.16
Consensus pattern (27 bp):
GGCGACATCGGGTAAGGGAAAGGAGGT
Found at i:2198949 original size:8 final size:8
Alignment explanation
Indices: 2198936--2198976 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
2198926 ACCATTTTCA
2198936 GAGAATTT
1 GAGAATTT
2198944 GAGAATTT
1 GAGAATTT
*
2198952 -AGAGTTT
1 GAGAATTT
*
2198959 GGGAATTT
1 GAGAATTT
2198967 GAGAATTT
1 GAGAATTT
2198975 GA
1 GA
2198977 AAGATGTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:2199216 original size:125 final size:128
Alignment explanation
Indices: 2199048--2199902 Score: 1239
Period size: 128 Copynumber: 6.9 Consensus size: 128
2199038 ATCGGAGTAT
2199048 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
* *
2199113 TTTCCCTATTATATCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
* *
2199176 TATTCAC-TGAAGGCGC-TTCCC-GGGACGCGCCTTCCATTATTTCATCAGAG-A-A--TTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
2199234 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA-CTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
2199296 TATTCACATGAAGGCGCGTTCCCGGGGGCGCG----CC-----TTC--C-----ATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
* * *
2199345 TTGCCCTATTATGTCACTCATGT-CCTCGGGGACACTCGATATATCAGTACCTATTTTTTCTC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*** * * *
2199407 -AGGGGACATGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCATAGAATAT-TTATC
1 TA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
**
2199470 A-TGCCCTATTATGTCA-TCATGTCCCTCGGGGACACCCGATATATCAGTACCTATTATTTCAC
65 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
2199532 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
*
2199597 TTGCCCTATTATGTCACTCATGGCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
* *
2199660 TATTCACATGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
* *
2199725 TTGCCCTATTATGTGACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*** * * * *
2199788 -AGGGGACATGAAGGCGCGTTCCTGAGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATC
1 TA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
2199852 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
65 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
2199903 AATCAGGTAA
Statistics
Matches: 657, Mismatches: 40, Indels: 60
0.87 0.05 0.08
Matches are distributed among these distances:
108 1 0.00
109 1 0.00
110 26 0.04
111 65 0.10
112 1 0.00
114 3 0.00
115 2 0.00
119 2 0.00
120 21 0.03
121 63 0.10
122 6 0.01
123 8 0.01
124 7 0.01
125 128 0.19
126 18 0.03
127 29 0.04
128 276 0.42
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
Found at i:2199547 original size:236 final size:237
Alignment explanation
Indices: 2199102--2199827 Score: 968
Period size: 253 Copynumber: 3.0 Consensus size: 237
2199092 TCGTCAGAGA
* *
2199102 ATATGTTATCATTTCCCTATTATATCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTA
1 ATATGTTATCATTGCCCTATTATGTCACTCATGT-CCTCGGGGACACTAGATATATCAGTACCTA
*
2199167 TTATTTCACTATTCAC-TGAAGGCGC-TTCCCGGGACGCGCCTTCCATTATTTCATCAGAG-A-A
65 TTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCATCAGAGAATA
2199228 -TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA-CTATTAT
130 TTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
2199291 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCC
195 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCC
*
2199334 ATATGTTATCATTGCCCTATTATGTCACTCATGTCCTCGGGGACACTCGATATATCAGTACCTAT
1 ATATGTTATCATTGCCCTATTATGTCACTCATGTCCTCGGGGACACTAGATATATCAGTACCTAT
* * *** ** *
2199399 TTTTTCTC-AGGGGACATGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCATAGAAT
66 TATTTCACTA-TTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCATCAGAGAAT
**
2199463 ATTTATCA-TGCCCTATTATGTCA-TCATGTCCCTCGGGGACACCCGATATATCAGTACCTATTA
129 ATTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTA
2199526 TTTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTC
194 TTTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCG----CC-----TTC--C
*
2199581 AGAGAATATGTTATCATTGCCCTATTATGTCACTCATGGCCCTCGGGGACACTAGATATATCAGT
1 -----ATATGTTATCATTGCCCTATTATGTCACTCAT-GTCCTCGGGGACACTAGATATATCAGT
*
2199646 ACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTCATCAG
60 ACCTATTATTTCACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCATCAG
*
2199711 AGAATATGTTATCATTGCCCTATTATGTGACTCATGTCCCTCGGGGACACTAGATATATCAGTAC
124 AGAATAT-TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTAC
* *** * *
2199776 CTATTATTTCTC-AGGGGACATGAAGGCGCGTTCCTGAGGGCGCGCCTTCC
188 CTATTATTTCACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCC
2199826 AT
1 AT
2199828 TATTTTGTCA
Statistics
Matches: 429, Mismatches: 35, Indels: 52
0.83 0.07 0.10
Matches are distributed among these distances:
230 1 0.00
231 38 0.09
232 41 0.10
233 5 0.01
234 25 0.06
235 32 0.07
236 60 0.14
237 6 0.01
240 4 0.01
245 4 0.01
247 4 0.01
252 34 0.08
253 85 0.20
254 7 0.02
255 15 0.03
256 68 0.16
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.32
Consensus pattern (237 bp):
ATATGTTATCATTGCCCTATTATGTCACTCATGTCCTCGGGGACACTAGATATATCAGTACCTAT
TATTTCACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCATCAGAGAATAT
TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATT
TCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCC
Found at i:2200364 original size:34 final size:33
Alignment explanation
Indices: 2200292--2200396 Score: 129
Period size: 34 Copynumber: 3.1 Consensus size: 33
2200282 TAAGTTGAAA
*
2200292 TTTAATGTTAAATTTCGAATACTATAATTTATTATT
1 TTTAAT-TTAAATTT-GAATAATATAATTT-TTATT
* *
2200328 TTAAATTTAAATTTGAATAATATTATTTTTATT
1 TTTAATTTAAATTTGAATAATATAATTTTTATT
* *
2200361 TTTATTTTAAATTTTGAATAATATAATTTGTATT
1 TTTAATTTAAA-TTTGAATAATATAATTTTTATT
2200395 TT
1 TT
2200397 AAAAACATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
33 14 0.23
34 34 0.56
35 8 0.13
36 5 0.08
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (33 bp):
TTTAATTTAAATTTGAATAATATAATTTTTATT
Found at i:2200980 original size:20 final size:21
Alignment explanation
Indices: 2200915--2201002 Score: 121
Period size: 21 Copynumber: 4.3 Consensus size: 21
2200905 TATGGTATAA
*
2200915 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
2200936 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
2200957 AACCCTGCGGGCTCGGAA-GT
1 AACCCTGCGGGCTAGGAATGT
2200977 AACCCTGCGGGC--GGAATGT
1 AACCCTGCGGGCTAGGAATGT
2200996 AACCCTG
1 AACCCTG
2201003 AGAGATGGCA
Statistics
Matches: 62, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
18 4 0.06
19 9 0.15
20 17 0.27
21 29 0.47
22 3 0.05
ACGTcount: A:0.22, C:0.27, G:0.34, T:0.17
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:2201034 original size:21 final size:21
Alignment explanation
Indices: 2201008--2201055 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2200998 CCCTGAGAGA
*
2201008 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
2201029 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
2201050 GGGCAT
1 TGGCAT
2201056 GTACCCCATG
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:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:2202798 original size:19 final size:21
Alignment explanation
Indices: 2202776--2202817 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
2202766 TATATAAAAT
2202776 TATTTTA-ATAAAAATA-TAA
1 TATTTTACATAAAAATATTAA
*
2202795 TA-TTTACATAAATATATTAA
1 TATTTTACATAAAAATATTAA
2202815 TAT
1 TAT
2202818 AAAAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
18 4 0.21
19 10 0.53
20 5 0.26
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TATTTTACATAAAAATATTAA
Found at i:2202806 original size:33 final size:31
Alignment explanation
Indices: 2202756--2202828 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
2202746 AATTCTAAAT
* *
2202756 AAATAATAATTATATAAAATTATTTTAATA-AA
1 AAATAATAATTACAT-AAA-TATATTAATATAA
*
2202788 AATATAATATTTACATAAATATATTAATATAA
1 AA-ATAATAATTACATAAATATATTAATATAA
2202820 AAATAATAA
1 AAATAATAA
2202829 CTATTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
31 15 0.43
32 9 0.26
33 11 0.31
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (31 bp):
AAATAATAATTACATAAATATATTAATATAA
Found at i:2202856 original size:32 final size:34
Alignment explanation
Indices: 2202783--2202857 Score: 95
Period size: 32 Copynumber: 2.3 Consensus size: 34
2202773 AATTATTTTA
* *
2202783 ATAAAAAT-ATAATATTTACATAAATATATTAAT
1 ATAAAAATAATAATATTTACATAAATATACTAAC
2202816 ATAAAAATAATAACTATTTA-A-AAA-ATACTAAC
1 ATAAAAATAATAA-TATTTACATAAATATACTAAC
2202848 ATAAAAATAA
1 ATAAAAATAA
2202858 ATTTCTTACC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
32 16 0.42
33 11 0.29
34 5 0.13
35 6 0.16
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (34 bp):
ATAAAAATAATAATATTTACATAAATATACTAAC
Found at i:2204814 original size:23 final size:24
Alignment explanation
Indices: 2204788--2204836 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
2204778 ATTATTGATT
2204788 TTTTGTTAATTTTT-AAATTT-TTA
1 TTTT-TTAATTTTTAAAATTTATTA
**
2204811 TTTTTTTCTTTTTAAAATTTATTA
1 TTTTTTAATTTTTAAAATTTATTA
2204835 TT
1 TT
2204837 GATAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 7 0.32
23 10 0.45
24 5 0.23
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (24 bp):
TTTTTTAATTTTTAAAATTTATTA
Found at i:2205118 original size:64 final size:64
Alignment explanation
Indices: 2205034--2205167 Score: 250
Period size: 64 Copynumber: 2.1 Consensus size: 64
2205024 TTCAATACAT
*
2205034 AAACTTTTAAAATTTTTAAAATTTAATATGAAATTTTGAACTGAACAGAGTATTAAATTAAACAA
1 AAAC-TTTAAAAATTTTAAAATTTAATATGAAATTTTGAACTGAACAGAGTATTAAATTAAACAA
2205099 AAACTTTAAAAATTTTAAAATTTAATATGAAATTTTGAACTGAACAGAGTATTAAATTAAACAA
1 AAACTTTAAAAATTTTAAAATTTAATATGAAATTTTGAACTGAACAGAGTATTAAATTAAACAA
2205163 AAACT
1 AAACT
2205168 AAAGTTTTTA
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
64 64 0.94
65 4 0.06
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (64 bp):
AAACTTTAAAAATTTTAAAATTTAATATGAAATTTTGAACTGAACAGAGTATTAAATTAAACAA
Found at i:2205620 original size:26 final size:26
Alignment explanation
Indices: 2205590--2205672 Score: 82
Period size: 26 Copynumber: 3.1 Consensus size: 26
2205580 ATATTCAATT
* *
2205590 AAACATATACATT-AAACATTATATGA
1 AAACATA-ACATTAAAACATAATATAA
2205616 AAACATAACATTAAAACATAATATAA
1 AAACATAACATTAAAACATAATATAA
2205642 AAACATTAAACA-TAATATACA-AATATAA
1 AAACA-T-AACATTAA-A-ACATAATATAA
2205670 AAA
1 AAA
2205673 TTAAATAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
25 5 0.10
26 23 0.46
27 4 0.08
28 15 0.30
29 3 0.06
ACGTcount: A:0.63, C:0.11, G:0.01, T:0.25
Consensus pattern (26 bp):
AAACATAACATTAAAACATAATATAA
Found at i:2205636 original size:13 final size:13
Alignment explanation
Indices: 2205590--2205647 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
2205580 ATATTCAATT
2205590 AAACATATACATT-
1 AAACATA-ACATTA
* * *
2205603 AAACATTATATGA
1 AAACATAACATTA
2205616 AAACATAACATTA
1 AAACATAACATTA
* *
2205629 AAACATAATATAA
1 AAACATAACATTA
2205642 AAACAT
1 AAACAT
2205648 TAAACATAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
12 3 0.08
13 33 0.92
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (13 bp):
AAACATAACATTA
Found at i:2205654 original size:20 final size:21
Alignment explanation
Indices: 2205622--2205660 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2205612 ATGAAAACAT
2205622 AACATTAAAACATAATATAAA
1 AACATTAAAACATAATATAAA
2205643 AACATT-AAACATAATATA
1 AACATTAAAACATAATATA
2205661 CAAATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (21 bp):
AACATTAAAACATAATATAAA
Found at i:2207526 original size:54 final size:54
Alignment explanation
Indices: 2207432--2208119 Score: 906
Period size: 54 Copynumber: 12.7 Consensus size: 54
2207422 GTGTCGGCAA
* * *
2207432 TAAGTGTGCAACCCACAAAATTTTATAATAAGTTTATGAACGGCCGTATCGACAC
1 TAAGTGTGCAACCCACGAAA-TTCATAATAAGTTTATGAACGACCGTATCGACAC
* *
2207487 TAAGTGTGCAACACACGAAATTCATAATAAGTTTATGAACTACCGTATCGACAC
1 TAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGACAC
* * *
2207541 TAATTGTGCAACCCATGAAATTCATAATGAGTTTATGAACGACCGTATCGACAC
1 TAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGACAC
*
2207595 TAAGTGTGCAACCCATGAAATTCATAATAAGTTTATGAACGACCGTATC-AGCAC
1 TAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGA-CAC
** * *
2207649 TAAGTGTGCAACCCACGAAATTCATAACGAGTTTATGAACGACCGTATTGGCAC
1 TAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGACAC
* *
2207703 TAAGTGTGCAACCCATGAAATTCATAATAAGTTTATGAAAGACCGTATC-AGCAC
1 TAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGA-CAC
* ** * * ***
2207757 TAAGTGTGCATCCCACGAAATTCATAATGGGTTTATAAAAGACCGTATCGGTGC
1 TAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGACAC
* * **
2207811 TAAGTGCGC-ACCACAC-ATAATTCATAATGAGTTTATGAACGGTCGTATCTG-CAC
1 TAAGTGTGCAACC-CACGA-AATTCATAATAAGTTTATGAACGACCGTATC-GACAC
2207865 TAAGTGTGCAACCCACGAAATTCATAATGAA-TTTATGAACGACCGTATCGACAC
1 TAAGTGTGCAACCCACGAAATTCATAAT-AAGTTTATGAACGACCGTATCGACAC
*
2207919 TAAGTGTGCAACCCAC-AGAATTCATAATAAGTTTATGAACGACCGTATCGATAC
1 TAAGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGACCGTATCGACAC
* * *
2207973 TAAGTGTGCAACCCACGAAATTCATAATGAGTTTATGAACGATCGTATTGACAC
1 TAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGACAC
* *
2208027 TAAGTGTGCAACCCAC-ATAATTCATAATAGGTTTATGAACCACCGTATCGACAC
1 TAAGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGACCGTATCGACAC
* * * *
2208081 TAAGTGTGTAACCCACGGAATTCATAATGAGTTTGTGAA
1 TAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAA
2208120 TTTCCATATT
Statistics
Matches: 558, Mismatches: 59, Indels: 33
0.86 0.09 0.05
Matches are distributed among these distances:
53 9 0.02
54 524 0.94
55 25 0.04
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (54 bp):
TAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGACAC
Found at i:2213294 original size:27 final size:27
Alignment explanation
Indices: 2213210--2213295 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
2213200 GTATCTGCAC
* *
2213210 TAAGTGTGCAACCCACAAAATTCATAA
1 TAAGTGTACAACCCACATAATTCATAA
* * * * * *
2213237 TAAGTTTATGAA-CGACCAT-ATTGACAC
1 TAAGTGTA-CAACCCA-CATAATTCATAA
2213264 TAAGTGTACAACCCACATAATTCATAA
1 TAAGTGTACAACCCACATAATTCATAA
2213291 TAAGT
1 TAAGT
2213296 TTATGAACCA
Statistics
Matches: 41, Mismatches: 14, Indels: 8
0.65 0.22 0.13
Matches are distributed among these distances:
26 5 0.12
27 32 0.78
28 4 0.10
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.27
Consensus pattern (27 bp):
TAAGTGTACAACCCACATAATTCATAA
Found at i:2213306 original size:27 final size:27
Alignment explanation
Indices: 2213222--2213357 Score: 75
Period size: 27 Copynumber: 5.0 Consensus size: 27
2213212 AGTGTGCAAC
*
2213222 CCACAAAATTCATAATAAGTTTATGAA
1 CCACATAATTCATAATAAGTTTATGAA
* * * * * *
2213249 CGACCAT-ATTGACACTAAGTGTA-CAA
1 CCA-CATAATTCATAATAAGTTTATGAA
2213275 CCCACATAATTCATAATAAGTTTATGAA
1 -CCACATAATTCATAATAAGTTTATGAA
* * *
2213303 CCACCAT-A-TCGGTACTAAGTTTA-CAA
1 CCA-CATAATTC-ATAATAAGTTTATGAA
* * *
2213329 CCCACAGAATTTATAATGAGTTTATGAA
1 -CCACATAATTCATAATAAGTTTATGAA
2213357 C
1 C
2213358 GACCGTATCG
Statistics
Matches: 77, Mismatches: 22, Indels: 20
0.65 0.18 0.17
Matches are distributed among these distances:
26 11 0.14
27 56 0.73
28 10 0.13
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (27 bp):
CCACATAATTCATAATAAGTTTATGAA
Found at i:2213449 original size:161 final size:160
Alignment explanation
Indices: 2213154--2213727 Score: 731
Period size: 161 Copynumber: 3.5 Consensus size: 160
2213144 TAGTATCGAA
* * * ** *
2213154 ACTAAGTGTGCAACCCACATAATTCATAATAAGTTTACGAACGGTCGTATCTGCACTAAGTGTGC
1 ACTAAGTGTGCAACCCACAGAATTCATAATGAGTTTATGAACGACCGTATCGGCACTAAGTGTGC
* * * *
2213219 AACCCACAAAATTCATAATAAGTTTATGAACGACCATATTGACACTAAGTGTACAACCCACATAA
66 AA-CCAC-GAATTCATAATGAGTTTATGAACGACCATATCGACACTAAGTGTGCAACCCACATAA
* *
2213284 TTCATAATAAGTTTATGAACCACCATATCGGT
129 TTCATAATAAGTTTATGAACGACCGTATCGGT
* * * *
2213316 ACTAAGTTTACAACCCACAGAATTTATAATGAGTTTATGAACGACCGTATCGTCACTAAGTGTGC
1 ACTAAGTGTGCAACCCACAGAATTCATAATGAGTTTATGAACGACCGTATCGGCACTAAGTGTGC
* * * * *
2213381 AACCAACGAATTCATAATGAGTTTATGAACAACCGTATCGACTCTAAGTGTGCATCCCACAAAAT
66 AACC-ACGAATTCATAATGAGTTTATGAACGACCATATCGACACTAAGTGTGCAACCCACATAAT
**
2213446 TCATAATAAGTTTATGAACGACCGTATCGAC
130 TCATAATAAGTTTATGAACGACCGTATCGGT
* *
2213477 ACTAAGTTTGCAACCCACAGAATTCATAATGAGTTTATGAACGACCGTATTGGCACTAAGTGTGC
1 ACTAAGTGTGCAACCCACAGAATTCATAATGAGTTTATGAACGACCGTATCGGCACTAAGTGTGC
* **
2213542 AACTCACGACATTCATAATGAGTTTATGAACGACCATATCG-CCCTAAGTGTGCAACCCATGTAA
66 AAC-CACGA-ATTCATAATGAGTTTATGAACGACCATATCGACACTAAGTGTGCAACCCACATAA
2213606 TTCATAATAAGTTTATGAACGACCGTATCGGCT
129 TTCATAATAAGTTTATGAACGACCGTATCGG-T
*** * * *
2213639 -CTAAGTGTGCAACCCAC-GAAATTCATAATGAGTTTATGAATTTCCTTATTGGCACTATGTGTG
1 ACTAAGTGTGCAACCCACAG-AATTCATAATGAGTTTATGAACGACCGTATCGGCACTAAGTGTG
*
2213702 CAACCTACGAAATTCACAATGAGTTT
65 CAACC-ACG-AATTCATAATGAGTTT
2213728 GGAACGTATC
Statistics
Matches: 362, Mismatches: 43, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
160 2 0.01
161 270 0.75
162 90 0.25
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (160 bp):
ACTAAGTGTGCAACCCACAGAATTCATAATGAGTTTATGAACGACCGTATCGGCACTAAGTGTGC
AACCACGAATTCATAATGAGTTTATGAACGACCATATCGACACTAAGTGTGCAACCCACATAATT
CATAATAAGTTTATGAACGACCGTATCGGT
Found at i:2213701 original size:54 final size:54
Alignment explanation
Indices: 2213154--2213727 Score: 665
Period size: 54 Copynumber: 10.7 Consensus size: 54
2213144 TAGTATCGAA
* * ** *
2213154 ACTAAGTGTGCAACCCAC-ATAATTCATAATAAGTTTACGAACGGTCGTATCTGC
1 ACTAAGTGTGCAACCCACGA-AATTCATAATGAGTTTATGAACGACCGTATCGGC
* * * * *
2213208 ACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCATATTGAC
1 ACTAAGTGTGCAACCCACGAAATTCATAATGAGTTTATGAACGACCGTATCGGC
* * * * *
2213262 ACTAAGTGTACAACCCAC-ATAATTCATAATAAGTTTATGAACCACCATATCGGT
1 ACTAAGTGTGCAACCCACGA-AATTCATAATGAGTTTATGAACGACCGTATCGGC
* * * *
2213316 ACTAAGTTTACAACCCAC-AGAATTTATAATGAGTTTATGAACGACCGTATCGTC
1 ACTAAGTGTGCAACCCACGA-AATTCATAATGAGTTTATGAACGACCGTATCGGC
* * *
2213370 ACTAAGTGTGCAACCAACG-AATTCATAATGAGTTTATGAACAACCGTATCGAC
1 ACTAAGTGTGCAACCCACGAAATTCATAATGAGTTTATGAACGACCGTATCGGC
* * * * *
2213423 TCTAAGTGTGCATCCCACAAAATTCATAATAAGTTTATGAACGACCGTATCGAC
1 ACTAAGTGTGCAACCCACGAAATTCATAATGAGTTTATGAACGACCGTATCGGC
* *
2213477 ACTAAGTTTGCAACCCAC-AGAATTCATAATGAGTTTATGAACGACCGTATTGGC
1 ACTAAGTGTGCAACCCACGA-AATTCATAATGAGTTTATGAACGACCGTATCGGC
* * *
2213531 ACTAAGTGTGCAACTCACGACATTCATAATGAGTTTATGAACGACCATATC-GC
1 ACTAAGTGTGCAACCCACGAAATTCATAATGAGTTTATGAACGACCGTATCGGC
* * * *
2213584 CCTAAGTGTGCAACCCATGTAATTCATAATAAGTTTATGAACGACCGTATCGGC
1 ACTAAGTGTGCAACCCACGAAATTCATAATGAGTTTATGAACGACCGTATCGGC
* *** * *
2213638 TCTAAGTGTGCAACCCACGAAATTCATAATGAGTTTATGAATTTCCTTATTGGC
1 ACTAAGTGTGCAACCCACGAAATTCATAATGAGTTTATGAACGACCGTATCGGC
* * *
2213692 ACTATGTGTGCAACCTACGAAATTCACAATGAGTTT
1 ACTAAGTGTGCAACCCACGAAATTCATAATGAGTTT
2213728 GGAACGTATC
Statistics
Matches: 450, Mismatches: 63, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
53 94 0.21
54 354 0.79
55 2 0.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (54 bp):
ACTAAGTGTGCAACCCACGAAATTCATAATGAGTTTATGAACGACCGTATCGGC
Found at i:2213706 original size:215 final size:216
Alignment explanation
Indices: 2213154--2213727 Score: 760
Period size: 215 Copynumber: 2.7 Consensus size: 216
2213144 TAGTATCGAA
* * ** * *
2213154 ACTAAGTGTGCAACCCACATAATTCATAATAAGTTTACGAACGGTCGTATCTGCACTAAGTGTGC
1 ACTAAGTGTGCAACCCACGTAATTCATAATAAGTTTATGAACGACCGTATCGGCTCTAAGTGTGC
* *
2213219 AACCCACAAAATTCATAATAAGTTTATGAACGACCATATTGACACTAAGTGTACAACCCACATAA
66 AACCCACAAAATTCATAATAAGTTTATGAACGACCATATTGACACTAAGTGTGCAACCCACAGAA
* * * *
2213284 TTCATAATAAGTTTATGAACCACCATATCGGTACTAAGTTTACAACCCACAGAATTTATAATGAG
131 TTCATAATGAGTTTATGAACCACCATATCGGCACTAAGTGTACAACCCACAGAATTCATAATGAG
*
2213349 TTTATGAACGACCGTATCGTC
196 TTTATGAACGACCATATCGTC
* * * *
2213370 ACTAAGTGTGCAACCAACG-AATTCATAATGAGTTTATGAACAACCGTATCGACTCTAAGTGTGC
1 ACTAAGTGTGCAACCCACGTAATTCATAATAAGTTTATGAACGACCGTATCGGCTCTAAGTGTGC
* * * *
2213434 ATCCCACAAAATTCATAATAAGTTTATGAACGACCGTATCGACACTAAGTTTGCAACCCACAGAA
66 AACCCACAAAATTCATAATAAGTTTATGAACGACCATATTGACACTAAGTGTGCAACCCACAGAA
* * * * *
2213499 TTCATAATGAGTTTATGAACGACCGTATTGGCACTAAGTGTGCAACTCAC-GACATTCATAATGA
131 TTCATAATGAGTTTATGAACCACCATATCGGCACTAAGTGTACAACCCACAGA-ATTCATAATGA
2213563 GTTTATGAACGACCATATCG-C
195 GTTTATGAACGACCATATCGTC
* *
2213584 CCTAAGTGTGCAACCCATGTAATTCATAATAAGTTTATGAACGACCGTATCGGCTCTAAGTGTGC
1 ACTAAGTGTGCAACCCACGTAATTCATAATAAGTTTATGAACGACCGTATCGGCTCTAAGTGTGC
* * *** * * * *
2213649 AACCCACGAAATTCATAATGAGTTTATGAATTTCCTTATTGGCACTATGTGTGCAACCTAC-GAA
66 AACCCACAAAATTCATAATAAGTTTATGAACGACCATATTGACACTAAGTGTGCAACCCACAG-A
*
2213713 ATTCACAATGAGTTT
130 ATTCATAATGAGTTT
2213728 GGAACGTATC
Statistics
Matches: 310, Mismatches: 45, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
214 20 0.06
215 273 0.88
216 17 0.05
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (216 bp):
ACTAAGTGTGCAACCCACGTAATTCATAATAAGTTTATGAACGACCGTATCGGCTCTAAGTGTGC
AACCCACAAAATTCATAATAAGTTTATGAACGACCATATTGACACTAAGTGTGCAACCCACAGAA
TTCATAATGAGTTTATGAACCACCATATCGGCACTAAGTGTACAACCCACAGAATTCATAATGAG
TTTATGAACGACCATATCGTC
Found at i:2216513 original size:253 final size:255
Alignment explanation
Indices: 2216092--2216594 Score: 983
Period size: 253 Copynumber: 2.0 Consensus size: 255
2216082 CCCTCCTCAA
2216092 TTGGTTCAAATTCAAAGACACCCATTTAAGCACCTATTGGGGTCATCTAAGGCCCAAGTAAATTT
1 TTGGTTCAAATTCAAAGACACCCATTTAAGCACCTATTGGGGTCATCTAAGGCCCAAGTAAATTT
2216157 CCATTTGGGTTAAAAGCTTAATATACTAGGAGAAAGTTATTCTAAAGTCCATCCGAATAGCTCGA
66 CCATTTGGGTTAAAAGCTTAATATACTAGGAGAAAGTTATTCTAAAGTCCATCCGAATAGCTCGA
*
2216222 AACTCCTAACTCATATTTTGGGGCGTTAAATTAAAACATAATAGTCAATT-AAAAAGATTATATT
131 AACTCCTAACTCATATTTTGGGGCGTTAAATTAAAACATAATAGTCAATTAAAAAAGATTACATT
2216286 AAACAT-AAACCTAAATATAAAAGGTATAATATTTAATTAAAAAACATAAAAAAATCCAT
196 AAACATAAAACCTAAATATAAAAGGTATAATATTTAATTAAAAAACATAAAAAAATCCAT
2216345 TTGGTTCAAATTCAAAGACACCCATTTAAGCACCTATTGGGGTCATCTAAGGCCCAAGTAAATTT
1 TTGGTTCAAATTCAAAGACACCCATTTAAGCACCTATTGGGGTCATCTAAGGCCCAAGTAAATTT
2216410 CCATTTGGGTTAAAAGCTTAATATACTAGGAGAAAGTTATTCTAAAGTCCATCCGAATAGCTCGA
66 CCATTTGGGTTAAAAGCTTAATATACTAGGAGAAAGTTATTCTAAAGTCCATCCGAATAGCTCGA
2216475 AACTCCTAACTCATATTTTGGGGCGTTAAATTAAAACATAATAGTCAATTAAAAAAGATTACATT
131 AACTCCTAACTCATATTTTGGGGCGTTAAATTAAAACATAATAGTCAATTAAAAAAGATTACATT
2216540 AAACATAAAACCTAAATATAAAAGGTATAATATTTAATTAAAAAACATAAAAAAA
196 AAACATAAAACCTAAATATAAAAGGTATAATATTTAATTAAAAAACATAAAAAAA
2216595 ACATAATATA
Statistics
Matches: 247, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
253 180 0.73
254 19 0.08
255 48 0.19
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (255 bp):
TTGGTTCAAATTCAAAGACACCCATTTAAGCACCTATTGGGGTCATCTAAGGCCCAAGTAAATTT
CCATTTGGGTTAAAAGCTTAATATACTAGGAGAAAGTTATTCTAAAGTCCATCCGAATAGCTCGA
AACTCCTAACTCATATTTTGGGGCGTTAAATTAAAACATAATAGTCAATTAAAAAAGATTACATT
AAACATAAAACCTAAATATAAAAGGTATAATATTTAATTAAAAAACATAAAAAAATCCAT
Found at i:2219061 original size:9 final size:9
Alignment explanation
Indices: 2219047--2219085 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
2219037 GTGCATCCTA
2219047 ACAAGTTTG
1 ACAAGTTTG
*
2219056 ACAAGTTTA
1 ACAAGTTTG
2219065 ACCAA-TTTG
1 A-CAAGTTTG
2219074 ACAAGTTTG
1 ACAAGTTTG
2219083 ACA
1 ACA
2219086 TGTAAGTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
8 3 0.12
9 20 0.77
10 3 0.12
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (9 bp):
ACAAGTTTG
Found at i:2220462 original size:30 final size:30
Alignment explanation
Indices: 2220421--2220526 Score: 142
Period size: 30 Copynumber: 3.5 Consensus size: 30
2220411 TAGAAAATGC
2220421 AATTCATTTTACATAAAACAAATTTT-AAAT
1 AATTCATTTTACATAAAAC-AATTTTCAAAT
* * * *
2220451 AGTTTATTTTACGTAAAACACTTTTCAAAT
1 AATTCATTTTACATAAAACAATTTTCAAAT
*
2220481 AATTCATTTTACGTAAAACAATTTTCAAAT
1 AATTCATTTTACATAAAACAATTTTCAAAT
*
2220511 AATTCATATTACATAA
1 AATTCATTTTACATAA
2220527 CTTGTATTTC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
29 5 0.08
30 61 0.92
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (30 bp):
AATTCATTTTACATAAAACAATTTTCAAAT
Found at i:2221122 original size:15 final size:14
Alignment explanation
Indices: 2221102--2221131 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2221092 ATATTTTAAT
2221102 AATAATATTAACATA
1 AATAATATTAA-ATA
2221117 AATAATATTAAATA
1 AATAATATTAAATA
2221131 A
1 A
2221132 GTTATTCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAATATTAAATA
Found at i:2228164 original size:20 final size:17
Alignment explanation
Indices: 2228123--2228165 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
2228113 TGGTTACTCG
2228123 AATATTCATTTATTTTA
1 AATATTCATTTATTTTA
*
2228140 AATATGTCATTTTTTGTTGA
1 AATAT-TCATTTATT-TT-A
2228160 AATATT
1 AATATT
2228166 GATTGTCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.23
18 8 0.36
19 3 0.14
20 6 0.27
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.56
Consensus pattern (17 bp):
AATATTCATTTATTTTA
Found at i:2228837 original size:20 final size:19
Alignment explanation
Indices: 2228790--2228837 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
2228780 GAAAAGAGTT
*
2228790 CTCTTTC-TTCCTTACCTC
1 CTCTTTCTTTCCTTACCAC
*
2228808 TTCTTCTCTTTCCTTACCAC
1 CTCTT-TCTTTCCTTACCAC
2228828 CTCATTTCTT
1 CTC-TTTCTT
2228838 ATTCACTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 4 0.17
19 2 0.08
20 16 0.67
21 2 0.08
ACGTcount: A:0.08, C:0.40, G:0.00, T:0.52
Consensus pattern (19 bp):
CTCTTTCTTTCCTTACCAC
Found at i:2235075 original size:20 final size:20
Alignment explanation
Indices: 2235031--2235088 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
2235021 CTAGATAATC
*
2235031 TGGTATCCATACCGAAGATT
1 TGGTATCCATACCAAAGATT
*
2235051 GGGTATCCATACCAAAG-TCT
1 TGGTATCCATACCAAAGAT-T
*
2235071 TGGTATCAATACCAAAGA
1 TGGTATCCATACCAAAGA
2235089 GGTTGAGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (20 bp):
TGGTATCCATACCAAAGATT
Found at i:2236938 original size:38 final size:38
Alignment explanation
Indices: 2236886--2237006 Score: 161
Period size: 38 Copynumber: 3.2 Consensus size: 38
2236876 TATGCACTGT
2236886 AGTGCTTACACATAAGGTTGTGCCCACCATATCCACCGA
1 AGTGC-TACACATAAGGTTGTGCCCACCATATCCACCGA
** * * *
2236925 AGTGCTACACATAATATCGTGCCCACCATATGCACCAA
1 AGTGCTACACATAAGGTTGTGCCCACCATATCCACCGA
* * *
2236963 AGTGCTACACATAAGGTTGTTCCCACCATATTCATCGA
1 AGTGCTACACATAAGGTTGTGCCCACCATATCCACCGA
2237001 AGTGCT
1 AGTGCT
2237007 TAATTGATAT
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
38 65 0.93
39 5 0.07
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.25
Consensus pattern (38 bp):
AGTGCTACACATAAGGTTGTGCCCACCATATCCACCGA
Found at i:2237021 original size:23 final size:23
Alignment explanation
Indices: 2236990--2237044 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
2236980 TGTTCCCACC
*
2236990 ATATTCATCGAAGTGCTTAATTG
1 ATATGCATCGAAGTGCTTAATTG
2237013 ATATGCATCGAAGTGCTTAATTG
1 ATATGCATCGAAGTGCTTAATTG
2237036 ATATGCATC
1 ATATGCATC
2237045 TGCTAGACTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (23 bp):
ATATGCATCGAAGTGCTTAATTG
Found at i:2237488 original size:19 final size:19
Alignment explanation
Indices: 2237464--2237505 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
2237454 ATTTACAAGC
2237464 TTCACATTCTAATATCAAT
1 TTCACATTCTAATATCAAT
2237483 TTCACATTCTAATATCAAT
1 TTCACATTCTAATATCAAT
2237502 TTCA
1 TTCA
2237506 ACTCTCAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (19 bp):
TTCACATTCTAATATCAAT
Found at i:2241471 original size:30 final size:31
Alignment explanation
Indices: 2241411--2241471 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
2241401 ACACAACATG
* * *
2241411 TATAACTTTTCCAAAATTATCGATTAGGTCC
1 TATAACTTTTCAAAAATTATAGAATAGGTCC
2241442 TATAACTTTTCAAAAATTATAGAAT-GGTCC
1 TATAACTTTTCAAAAATTATAGAATAGGTCC
2241472 CCAAATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 5 0.19
31 22 0.81
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (31 bp):
TATAACTTTTCAAAAATTATAGAATAGGTCC
Found at i:2245986 original size:38 final size:38
Alignment explanation
Indices: 2245941--2246093 Score: 254
Period size: 38 Copynumber: 4.0 Consensus size: 38
2245931 CCGTAGCGCT
*
2245941 TACACATAAAGTCGTGCCCACCATATGCA-CTGAAGTGC
1 TACACATAAGGTCGTGCCCACCATATGCATC-GAAGTGC
*
2245979 TACACATAAGGTCATGCCCACCATATGCATCGAAGTGC
1 TACACATAAGGTCGTGCCCACCATATGCATCGAAGTGC
*
2246017 TACATATAAGGTCGTGCCCACCATATGCATCGAAGTGC
1 TACACATAAGGTCGTGCCCACCATATGCATCGAAGTGC
*
2246055 TACACATAAGGTCGTGCCCACCATATGCACCGAAGTGC
1 TACACATAAGGTCGTGCCCACCATATGCATCGAAGTGC
2246093 T
1 T
2246094 TAATTGATAT
Statistics
Matches: 108, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
38 107 0.99
39 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (38 bp):
TACACATAAGGTCGTGCCCACCATATGCATCGAAGTGC
Found at i:2247642 original size:30 final size:31
Alignment explanation
Indices: 2247585--2247642 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
2247575 CAACATCCAC
* * *
2247585 AACTTTTCCAAAATTATCGATTAGGTCCTCT
1 AACTTTTCAAAAATTATAGAATAGGTCCTCT
2247616 AACTTTTCAAAAATTATAGAAT-GGTCC
1 AACTTTTCAAAAATTATAGAATAGGTCC
2247643 CCAAATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.36
Consensus pattern (31 bp):
AACTTTTCAAAAATTATAGAATAGGTCCTCT
Found at i:2248479 original size:22 final size:21
Alignment explanation
Indices: 2248454--2248511 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 21
2248444 TATATATTTT
2248454 AAATATTCATTTTTAAAAATAA
1 AAATATT-ATTTTTAAAAATAA
2248476 AAATATTATTTTATTTAAAAATAA
1 AAATATTA--TT-TTTAAAAATAA
2248500 AAATATTATTTT
1 AAATATTATTTT
2248512 AACTTTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
21 3 0.09
22 9 0.27
23 2 0.06
24 19 0.58
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATATTATTTTTAAAAATAA
Found at i:2248528 original size:26 final size:24
Alignment explanation
Indices: 2248465--2248512 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2248455 AATATTCATT
2248465 TTTAAAAATAAAAATATTATTTTA
1 TTTAAAAATAAAAATATTATTTTA
2248489 TTTAAAAATAAAAATATTATTTTA
1 TTTAAAAATAAAAATATTATTTTA
2248513 ACTTTATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTAAAAATAAAAATATTATTTTA
Found at i:2248639 original size:3 final size:3
Alignment explanation
Indices: 2248633--2248734 Score: 204
Period size: 3 Copynumber: 34.0 Consensus size: 3
2248623 GTTAATCTGA
2248633 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
2248681 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
2248729 GAT GAT
1 GAT GAT
2248735 AATAATAATA
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 99 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:2249117 original size:13 final size:13
Alignment explanation
Indices: 2249099--2249129 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2249089 TTGTGAATTA
*
2249099 TGTCTCAAAGTTT
1 TGTCTCAAAGTTG
2249112 TGTCTCAAAGTTG
1 TGTCTCAAAGTTG
2249125 TGTCT
1 TGTCT
2249130 ATGATTGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.45
Consensus pattern (13 bp):
TGTCTCAAAGTTG
Found at i:2249326 original size:35 final size:35
Alignment explanation
Indices: 2249278--2249349 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
2249268 TAAACTAACA
*
2249278 AATAAGTTCATTCACCAATTGACATGACTTATTAT
1 AATAAGTTCATTCACCAAGTGACATGACTTATTAT
2249313 AATAAGTGT-ATTCACCAAGTGACATGACTTATTAT
1 AATAAGT-TCATTCACCAAGTGACATGACTTATTAT
2249348 AA
1 AA
2249350 ATAGCATCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 34 0.97
36 1 0.03
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (35 bp):
AATAAGTTCATTCACCAAGTGACATGACTTATTAT
Found at i:2252503 original size:13 final size:13
Alignment explanation
Indices: 2252478--2252513 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2252468 ACTTTGTGAA
2252478 TTGTGTCTAAAAG
1 TTGTGTCTAAAAG
* *
2252491 TTTTGTCTCAAAG
1 TTGTGTCTAAAAG
2252504 TTGTGTCTAA
1 TTGTGTCTAA
2252514 GATTGTGCCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.44
Consensus pattern (13 bp):
TTGTGTCTAAAAG
Found at i:2257997 original size:128 final size:128
Alignment explanation
Indices: 2257769--2258218 Score: 623
Period size: 128 Copynumber: 3.5 Consensus size: 128
2257759 CTTAGAGAAT
*
2257769 ATTCGATCTGGCCCTCGCCTTAATGCCCGAGGGTCCATTACGACTATTCGATTCAATAATTGGTT
1 ATTCGATCTGACCCTCGCCTTAATGCCCGAGGGTCCATTACGACTATTCGATTCAATAATTGGTT
*
2257834 AGGACTAATATTAGAGCCTCCATTTTAGGGTTAATTTCACTTTAGTCCTTTAATTAGGAAATA
66 AGGACTAATATTAGAGCCTCCATTTTAGGCTTAATTTCACTTTAGTCCTTTAATTAGGAAATA
2257897 ATTCGATCTGACCCTCGCCTTAATGCCCGAGGGTCCATTACGACTATTCGATTCAATAATTGGTT
1 ATTCGATCTGACCCTCGCCTTAATGCCCGAGGGTCCATTACGACTATTCGATTCAATAATTGGTT
*
2257962 AGGACTAATATTAGAGCCTCCATTTTAGGCTTAATTTCACTTTAGTCCTTTAATTAGGGAATA
66 AGGACTAATATTAGAGCCTCCATTTTAGGCTTAATTTCACTTTAGTCCTTTAATTAGGAAATA
* * * * * ** * **
2258025 ATTTGATTTAACCCTCACCTTAATGCCTGAGGGTCCATTTTGATTA-TCTGATTCAATAATTAAT
1 ATTCGATCTGACCCTCGCCTTAATGCCCGAGGGTCCATTACGACTATTC-GATTCAATAATTGGT
** * * * *
2258089 TAGGGTTATTATTAGAGCCTCAACTTTAGGCTTAATTTCACTTTAGTCCTTTAGTTTAGGAAATA
65 TAGGACTAATATTAGAGCCTCCATTTTAGGCTTAATTTCACTTTAGTCCTTTA-ATTAGGAAATA
* * * * * ** * *
2258154 ATTCGATCTGGCCTTCGCCTGAATGCCCGAGAGTCAATTTTGATTATTTGATTCAATAATTGGTT
1 ATTCGATCTGACCCTCGCCTTAATGCCCGAGGGTCCATTACGACTATTCGATTCAATAATTGGTT
2258219 CAAATCAATT
Statistics
Matches: 286, Mismatches: 33, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
127 2 0.01
128 224 0.78
129 59 0.21
130 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.37
Consensus pattern (128 bp):
ATTCGATCTGACCCTCGCCTTAATGCCCGAGGGTCCATTACGACTATTCGATTCAATAATTGGTT
AGGACTAATATTAGAGCCTCCATTTTAGGCTTAATTTCACTTTAGTCCTTTAATTAGGAAATA
Found at i:2259336 original size:38 final size:38
Alignment explanation
Indices: 2259287--2259362 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
2259277 ACTAAAAATC
*
2259287 AATTAAGAATATAATTTAGCCACTTATTTTTACATTAA
1 AATTAAGAATATAATTTAGACACTTATTTTTACATTAA
* * *
2259325 AATTCAGAATATAATTTAGATACTTATTTTTATATTAA
1 AATTAAGAATATAATTTAGACACTTATTTTTACATTAA
2259363 GTCGTAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (38 bp):
AATTAAGAATATAATTTAGACACTTATTTTTACATTAA
Found at i:2261420 original size:39 final size:39
Alignment explanation
Indices: 2261273--2261401 Score: 195
Period size: 39 Copynumber: 3.3 Consensus size: 39
2261263 TCTATGACTT
*
2261273 GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGG
1 GTAAGTCCTTACCGTAGGCTCCTCGGCTTTGTGCTCAGG
* * * * *
2261312 ATAAGTCCTTACCGTAGGTTTCTCGGCTTTGTGCTTAAG
1 GTAAGTCCTTACCGTAGGCTCCTCGGCTTTGTGCTCAGG
*
2261351 GTAAGTCCTTACCGTATGCTCCTCGGCTTTGTGCTCAGG
1 GTAAGTCCTTACCGTAGGCTCCTCGGCTTTGTGCTCAGG
2261390 GTAAGTCCTTAC
1 GTAAGTCCTTAC
2261402 TGAGGGCTCC
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.16, C:0.26, G:0.25, T:0.33
Consensus pattern (39 bp):
GTAAGTCCTTACCGTAGGCTCCTCGGCTTTGTGCTCAGG
Found at i:2261432 original size:78 final size:78
Alignment explanation
Indices: 2261273--2261445 Score: 197
Period size: 78 Copynumber: 2.2 Consensus size: 78
2261263 TCTATGACTT
* *
2261273 GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGGATAAGTCCTTACCGTAGGTTTCTCGG
1 GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGGATAAGTCCTTACCGTAGGCTCCTCGG
* ***
2261338 CTTTGTGCTTAAG
66 CTTTGAGAACAAG
* * * * **
2261351 GTAAGTCCTTACCGTATGCTCCTCGGCTTTGTGCTCAGGGTAAGTCCTTACTG-AGGGCTCCTTT
1 GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGGATAAGTCCTTACCGTA-GGCTCCTCG
*
2261415 GCTTTGAGAACAGG
65 GCTTTGAGAACAAG
*
2261429 GTAAG-CCTTACTGCAGG
1 GTAAGTCCTTACCGCAGG
2261446 TACTTATGCT
Statistics
Matches: 78, Mismatches: 16, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
77 10 0.13
78 68 0.87
ACGTcount: A:0.17, C:0.25, G:0.27, T:0.32
Consensus pattern (78 bp):
GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGGATAAGTCCTTACCGTAGGCTCCTCGG
CTTTGAGAACAAG
Found at i:2265787 original size:2 final size:2
Alignment explanation
Indices: 2265780--2265830 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2265770 ATACATATGT
2265780 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2265822 TA TA TA TA T
1 TA TA TA TA T
2265831 CAATTTATAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2266507 original size:21 final size:21
Alignment explanation
Indices: 2266468--2266507 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2266458 AAACAAGTTT
*
2266468 TTGTCTTTAAAATATTTTTAA
1 TTGTCTTTAAAAGATTTTTAA
2266489 TTGT-TTTAAAAGATGTTTT
1 TTGTCTTTAAAAGAT-TTTT
2266508 TAGGTATTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (21 bp):
TTGTCTTTAAAAGATTTTTAA
Found at i:2270560 original size:25 final size:24
Alignment explanation
Indices: 2270520--2270581 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 24
2270510 GGGAAATATG
2270520 TTTTTCAAAATTTTTT-ATTAAAC
1 TTTTTCAAAATTTTTTAATTAAAC
* *
2270543 ATTTTTCAAAATTCTTTTAATTGATC
1 -TTTTTCAAAATT-TTTTAATTAAAC
2270569 TTTTTCAAAATTT
1 TTTTTCAAAATTT
2270582 GAAAATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 13 0.38
25 16 0.47
26 5 0.15
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTTTCAAAATTTTTTAATTAAAC
Found at i:2272684 original size:2 final size:2
Alignment explanation
Indices: 2272679--2272706 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2272669 CAAGTGTGTG
2272679 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2272707 ATAACTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2275796 original size:102 final size:102
Alignment explanation
Indices: 2275690--2275884 Score: 277
Period size: 102 Copynumber: 1.9 Consensus size: 102
2275680 AAATAAGCCT
* *
2275690 TTGAGATTGTTTAT-CTCA-AAACAAATTTCGTCTCGCTTGAAACAGTTTTCCCTCGAAACACAA
1 TTGAGATTGTTT-TCCT-AGAAACAAATTTCGTCTCACATGAAACAGTTTTCCCTCGAAACACAA
* *
2275753 ATTTTGAAATTGTTTCATTTGAAACAAAATGGATCTCAC
64 ATTTTGAAATTGTTTCACTCGAAACAAAATGGATCTCAC
* * * *
2275792 TTGAGATTGTTTTCCTAGAAACAAATTTCGTCTCACATGAGATAGTTTTCCTTTGAAACACAAAT
1 TTGAGATTGTTTTCCTAGAAACAAATTTCGTCTCACATGAAACAGTTTTCCCTCGAAACACAAAT
*
2275857 TTTGAAATTGTTTCCCTCGAAACAAAAT
66 TTTGAAATTGTTTCACTCGAAACAAAAT
2275885 TTTATCTTAC
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
101 2 0.02
102 80 0.98
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (102 bp):
TTGAGATTGTTTTCCTAGAAACAAATTTCGTCTCACATGAAACAGTTTTCCCTCGAAACACAAAT
TTTGAAATTGTTTCACTCGAAACAAAATGGATCTCAC
Found at i:2275813 original size:36 final size:36
Alignment explanation
Indices: 2275773--2275843 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
2275763 TGTTTCATTT
* * *
2275773 GAAACAAA-ATGGATCTCACTTGAGATTGTTTTCCTA
1 GAAACAAATATCG-TCTCACATGAGATAGTTTTCCTA
*
2275809 GAAACAAATTTCGTCTCACATGAGATAGTTTTCCT
1 GAAACAAATATCGTCTCACATGAGATAGTTTTCCT
2275844 TTGAAACACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 28 0.93
37 2 0.07
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (36 bp):
GAAACAAATATCGTCTCACATGAGATAGTTTTCCTA
Found at i:2276516 original size:137 final size:137
Alignment explanation
Indices: 2276288--2276535 Score: 345
Period size: 137 Copynumber: 1.8 Consensus size: 137
2276278 AGTATGACTA
* * * *
2276288 GACGTCCTCAACACGAAGAAACAATTTTGTCCATCGACCAGATCTCCTCAACGCGGAAGAGTAAT
1 GACGTCCTCAACACGAAGAAACAATATTGTCCATCAACCAGATCTCCTCAACGCGAAAGAGCAAT
*
2276353 GTCATCCTCAGATAATCAGACATCCTCAACGTGAAAGAACCGTGTTGTCTCCAAATTATCCAAAT
66 GTCATCCTCAGACAATCAGACATCCTCAACGTGAAAGAACCGTGTTGTCTCCAAATTATCCAAAT
2276418 ACGTCTC
131 ACGTCTC
** * * *
2276425 GACGTCCTCAATGCGAAGAAACAATATTGTCCATCAACCAGATCTCGTCAATGC-AAAGGAGCAG
1 GACGTCCTCAACACGAAGAAACAATATTGTCCATCAACCAGATCTCCTCAACGCGAAA-GAGCAA
* * ** *
2276489 TGTCATTCTCAGACAATTAGATTTCCTCAACGTGAAATAACCGTGTT
65 TGTCATCCTCAGACAATCAGACATCCTCAACGTGAAAGAACCGTGTT
2276536 ACCTTTAAAT
Statistics
Matches: 95, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
136 2 0.02
137 93 0.98
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (137 bp):
GACGTCCTCAACACGAAGAAACAATATTGTCCATCAACCAGATCTCCTCAACGCGAAAGAGCAAT
GTCATCCTCAGACAATCAGACATCCTCAACGTGAAAGAACCGTGTTGTCTCCAAATTATCCAAAT
ACGTCTC
Found at i:2276767 original size:97 final size:97
Alignment explanation
Indices: 2276638--2276835 Score: 272
Period size: 97 Copynumber: 2.0 Consensus size: 97
2276628 TGTCGTTTTT
* * *
2276638 AACACCAAATTATCTCCATATTGACTCGACTTCCTCAACGAGAAGGAACAACATCATTTTCAACA
1 AACACCAAATTATCTCCATATTGACCCAACTTCCTAAACGAGAAGGAACAACATCATTTTCAACA
*
2276703 AATAATTTACCTAAAAGCGGCTAAAACTCTTC
66 AATAATTTACCTAAAAGCGGCCAAAACTCTTC
* * *
2276735 AACACCAAATTATCT-CTTGATTGACCCAACTTCCTAAACGAGAAGGAACATCATCATTTTCAGC
1 AACACCAAATTATCTCCAT-ATTGACCCAACTTCCTAAACGAGAAGGAACAACATCATTTTCAAC
* * * * *
2276799 AAATATTTTACTTGAAAGTGGCCAGAACTCTTC
65 AAATAATTTACCTAAAAGCGGCCAAAACTCTTC
2276832 AACA
1 AACA
2276836 TGGATGAGCA
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
96 2 0.02
97 86 0.98
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.27
Consensus pattern (97 bp):
AACACCAAATTATCTCCATATTGACCCAACTTCCTAAACGAGAAGGAACAACATCATTTTCAACA
AATAATTTACCTAAAAGCGGCCAAAACTCTTC
Found at i:2276949 original size:122 final size:120
Alignment explanation
Indices: 2276730--2276984 Score: 316
Period size: 122 Copynumber: 2.1 Consensus size: 120
2276720 CGGCTAAAAC
* *
2276730 TCTTCAACACCAAATTATCTCTTGATTGACCCAACTTCCTAAACGAGAAGGAACATCATCATTTT
1 TCTTCAACACCAAATTATCTCTAGATTGACCCAACTTCCTAAACGAGAAGGAACATCA-CAATTT
* * * * ** *
2276795 CAGCAAATATTTTACTTGAAAGTGGCCAGAACTCTTCAACATGGATGAGCAATATTGT
65 CAACAAATAATTTACCTAAAAGCAGCCAGAACTCTTCAACA-AGATGAGCAATATT-T
* **
2276853 T-TTCAACACCAAATTATCTCTAGATTGACCCGACTTCCTCTACGAGAAGGAACAATGC-CAATT
1 TCTTCAACACCAAATTATCTCTAGATTGACCCAACTTCCTAAACGAGAAGGAAC-AT-CACAATT
* * *
2276916 TCAACAAATAATTTACCTAAAAGCAGCCAGAACTCTTTAACAAGATGAGTAGTATTT
64 TCAACAAATAATTTACCTAAAAGCAGCCAGAACTCTTCAACAAGATGAGCAATATTT
2276973 TCTTCAACACCA
1 TCTTCAACACCA
2276985 TATAATCGAT
Statistics
Matches: 114, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
120 2 0.02
121 21 0.18
122 87 0.76
123 3 0.03
124 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.29
Consensus pattern (120 bp):
TCTTCAACACCAAATTATCTCTAGATTGACCCAACTTCCTAAACGAGAAGGAACATCACAATTTC
AACAAATAATTTACCTAAAAGCAGCCAGAACTCTTCAACAAGATGAGCAATATTT
Found at i:2277226 original size:3 final size:3
Alignment explanation
Indices: 2277218--2277258 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
2277208 GAGTTTTAAT
* *
2277218 TTA TTA TTA CTA TTA TTA TTA TTA CTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2277259 ATAATATTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:2277238 original size:15 final size:15
Alignment explanation
Indices: 2277218--2277252 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
2277208 GAGTTTTAAT
2277218 TTATTATTACTATTA
1 TTATTATTACTATTA
2277233 TTATTATTACTATTA
1 TTATTATTACTATTA
2277248 TTATT
1 TTATT
2277253 TTATTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATTATTACTATTA
Found at i:2277656 original size:21 final size:22
Alignment explanation
Indices: 2277632--2277678 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
2277622 GTCACTGTCA
2277632 TCAACAAAA-CACACC-AATCAG
1 TCAACAAAACCA-ACCAAATCAG
* *
2277653 TCAATAAATCCAACCAAATCAG
1 TCAACAAAACCAACCAAATCAG
2277675 TCAA
1 TCAA
2277679 AAATGTACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.51, C:0.30, G:0.04, T:0.15
Consensus pattern (22 bp):
TCAACAAAACCAACCAAATCAG
Found at i:2280159 original size:16 final size:16
Alignment explanation
Indices: 2280138--2280187 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
2280128 TGTTTATATT
2280138 TTAAAATGATGTTTTC
1 TTAAAATGATGTTTTC
* *
2280154 TTAAAA--A-ATCTT-
1 TTAAAATGATGTTTTC
2280166 TTAAAATGATGTTTTC
1 TTAAAATGATGTTTTC
2280182 TTAAAA
1 TTAAAA
2280188 AATCTTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
12 6 0.23
13 3 0.12
14 2 0.08
15 3 0.12
16 12 0.46
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (16 bp):
TTAAAATGATGTTTTC
Found at i:2280168 original size:28 final size:28
Alignment explanation
Indices: 2280136--2280199 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
2280126 TTTGTTTATA
2280136 TTTTAAAATGATGTTTTCTTAAAAAATC
1 TTTTAAAATGATGTTTTCTTAAAAAATC
2280164 TTTTAAAATGATGTTTTCTTAAAAAATC
1 TTTTAAAATGATGTTTTCTTAAAAAATC
2280192 TTTTAAAA
1 TTTTAAAA
2280200 GACAACTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (28 bp):
TTTTAAAATGATGTTTTCTTAAAAAATC
Found at i:2280209 original size:29 final size:28
Alignment explanation
Indices: 2280136--2280216 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 28
2280126 TTTGTTTATA
**
2280136 TTTTAAAATGATGTTTTCTTAAAAAATC
1 TTTTAAAATGAACTTTTCTTAAAAAATC
**
2280164 TTTTAAAATGATGTTTTCTTAAAAAATC
1 TTTTAAAATGAACTTTTCTTAAAAAATC
*
2280192 TTTTAAAA-GACAACTTTTATTAAAA
1 TTTTAAAATG--AACTTTTCTTAAAA
2280217 TACAATTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
27 1 0.02
28 36 0.75
29 11 0.23
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.44
Consensus pattern (28 bp):
TTTTAAAATGAACTTTTCTTAAAAAATC
Found at i:2280216 original size:17 final size:17
Alignment explanation
Indices: 2280194--2280227 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2280184 AAAAAATCTT
2280194 TTAAAAGACAACTTTTA
1 TTAAAAGACAACTTTTA
* *
2280211 TTAAAATACAATTTTTA
1 TTAAAAGACAACTTTTA
2280228 CGTATTCGAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (17 bp):
TTAAAAGACAACTTTTA
Found at i:2283201 original size:21 final size:21
Alignment explanation
Indices: 2283177--2283218 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2283167 AGTTTATTTT
2283177 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
2283198 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
2283219 AACTTGGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:2283289 original size:33 final size:31
Alignment explanation
Indices: 2283207--2283282 Score: 100
Period size: 33 Copynumber: 2.4 Consensus size: 31
2283197 GTAAACTTTG
2283207 TTTCAATTATCGAACTTGGAAGTTTTTAAGTA
1 TTTCAATTATCGAACTTGGAAGTTTTT-AGTA
* *
2283239 TTTGAATTTACCGAACTTGGAAGTATTTT-GTA
1 TTTCAA-TTATCGAACTTGGAAGT-TTTTAGTA
2283271 TTTCAATTATCG
1 TTTCAATTATCG
2283283 TAAACTTTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
31 5 0.13
32 13 0.34
33 16 0.42
34 4 0.11
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.45
Consensus pattern (31 bp):
TTTCAATTATCGAACTTGGAAGTTTTTAGTA
Found at i:2310533 original size:18 final size:18
Alignment explanation
Indices: 2310512--2310554 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
2310502 GTTGTTTTTA
2310512 AAATAAAAGATAAA-AATT
1 AAATAAAAGA-AAATAATT
2310530 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAATAATT
2310548 AAATAAA
1 AAATAAA
2310555 TATTCTAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:2319198 original size:18 final size:18
Alignment explanation
Indices: 2319171--2319221 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
2319161 CTGGAACTGG
2319171 TGCT-GGCTAGGAGCTGC
1 TGCTGGGCTAGGAGCTGC
*
2319188 TTCTGGGCTAGGAGCTGC
1 TGCTGGGCTAGGAGCTGC
2319206 TGCTGGGCTAGGAGCT
1 TGCTGGGCTAGGAGCT
2319222 TGATGGACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 3 0.10
18 28 0.90
ACGTcount: A:0.12, C:0.22, G:0.41, T:0.25
Consensus pattern (18 bp):
TGCTGGGCTAGGAGCTGC
Found at i:2325274 original size:21 final size:20
Alignment explanation
Indices: 2325230--2325270 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2325220 TGCATTAAGG
*
2325230 TCTTTGTGGAGGCCATGAAA
1 TCTTTGTCGAGGCCATGAAA
2325250 TCTTTCGTCGAGGCCAT-AAA
1 TCTTT-GTCGAGGCCATGAAA
2325270 T
1 T
2325271 TCTTGCAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (20 bp):
TCTTTGTCGAGGCCATGAAA
Found at i:2329411 original size:11 final size:11
Alignment explanation
Indices: 2329395--2329419 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2329385 AAACAAGATT
2329395 ATATTTTAAGC
1 ATATTTTAAGC
2329406 ATATTTTAAGC
1 ATATTTTAAGC
2329417 ATA
1 ATA
2329420 CTAGTTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
ATATTTTAAGC
Found at i:2332489 original size:7 final size:7
Alignment explanation
Indices: 2332463--2332520 Score: 50
Period size: 7 Copynumber: 8.1 Consensus size: 7
2332453 AAAAAGGAAA
2332463 AAATAAT
1 AAATAAT
2332470 AAAATAAGT
1 -AAATAA-T
2332479 -AATAAT
1 AAATAAT
2332485 AAATAA-
1 AAATAAT
*
2332491 AAGAGAA-
1 AA-ATAAT
2332498 AAATAAT
1 AAATAAT
2332505 AAAATAAT
1 -AAATAAT
2332513 AAATAAT
1 AAATAAT
2332520 A
1 A
2332521 GTAGTAAAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
6 6 0.14
7 23 0.53
8 13 0.30
9 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.22
Consensus pattern (7 bp):
AAATAAT
Found at i:2332500 original size:35 final size:36
Alignment explanation
Indices: 2332430--2332520 Score: 107
Period size: 35 Copynumber: 2.5 Consensus size: 36
2332420 TTTGAAATAA
* *
2332430 AATAAAATAAATAATTATAATTTAAAAAGGAAAAAAT
1 AATAAAAT-AATAATAATAATATAAAAAGGAAAAAAT
2332467 AATAAAATAAGTAATAATAA-AT-AAAA-GAGAAAAAT
1 AATAAAATAA-TAATAATAATATAAAAAGGA-AAAAAT
2332502 AATAAAATAATAAATAATA
1 AATAAAATAAT-AATAATA
2332521 GTAGTAAAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
34 3 0.06
35 27 0.55
36 3 0.06
37 16 0.33
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (36 bp):
AATAAAATAATAATAATAATATAAAAAGGAAAAAAT
Found at i:2332585 original size:18 final size:18
Alignment explanation
Indices: 2332558--2332603 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
2332548 AAAGTTACTT
*
2332558 TTAAATTAAAAGATAACAA
1 TTAAA-TAAAAGAAAACAA
*
2332577 TTAAATAAAAGAAAATAA
1 TTAAATAAAAGAAAACAA
2332595 TTAAATAAA
1 TTAAATAAA
2332604 TAACCTAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (18 bp):
TTAAATAAAAGAAAACAA
Found at i:2337471 original size:16 final size:16
Alignment explanation
Indices: 2337438--2337486 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
2337428 ACTATGCTTG
* *
2337438 AAAA-AATGATGAATA
1 AAAAGAATGAAGAAAA
2337453 AAAAGAATGAAGAAAA
1 AAAAGAATGAAGAAAA
*
2337469 AAAAGAA-AAAGAAAA
1 AAAAGAATGAAGAAAA
2337484 AAA
1 AAA
2337487 TAAAGGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
15 14 0.47
16 16 0.53
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (16 bp):
AAAAGAATGAAGAAAA
Found at i:2337479 original size:6 final size:6
Alignment explanation
Indices: 2337468--2337543 Score: 55
Period size: 6 Copynumber: 11.8 Consensus size: 6
2337458 AATGAAGAAA
* * *
2337468 AAAAAG AAAAAG AAAAA- AATAAAGG AAAAGG AAAAAGG AAAATG AAAATGAA
1 AAAAAG AAAAAG AAAAAG AA-AAA-G AAAAAG AAAAA-G AAAAAG AAAA--AG
*
2337520 AAAAAG AAAAAAG AAGAAG AAAAA
1 AAAAAG -AAAAAG AAAAAG AAAAA
2337544 AGAGGGTTCG
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
5 2 0.04
6 34 0.62
7 13 0.24
8 6 0.11
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:2337483 original size:13 final size:13
Alignment explanation
Indices: 2337468--2337546 Score: 65
Period size: 13 Copynumber: 6.1 Consensus size: 13
2337458 AATGAAGAAA
2337468 AAAAAG-AAAAAG
1 AAAAAGAAAAAAG
*
2337480 AAAAA-AATAAAGG
1 AAAAAGAA-AAAAG
* *
2337493 AAAAGGAAAAAGG
1 AAAAAGAAAAAAG
*
2337506 AAAATGAAAATGAA-
1 AAAAAGAAAA--AAG
2337520 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
*
2337533 AAGAAGAAAAAAG
1 AAAAAGAAAAAAG
2337546 A
1 A
2337547 GGGTTCGAGA
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
12 8 0.15
13 35 0.64
14 11 0.20
15 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:2337501 original size:19 final size:17
Alignment explanation
Indices: 2337465--2337544 Score: 63
Period size: 19 Copynumber: 4.4 Consensus size: 17
2337455 AAGAATGAAG
2337465 AAAAAAAAGAAAAAGAA
1 AAAAAAAAGAAAAAGAA
*
2337482 AAAAATAAAGGAAAAGGAA
1 AAAAA-AAA-GAAAAAGAA
* *
2337501 AAAGGAAAATGAAAATGAA
1 AAA--AAAAAGAAAAAGAA
2337520 AAAAAGAAA-AAAGAAGAA
1 AAAAA-AAAGAAA-AAGAA
2337538 GAAAAAA
1 -AAAAAA
2337545 GAGGGTTCGA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
17 10 0.20
18 10 0.20
19 27 0.53
20 2 0.04
21 2 0.04
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (17 bp):
AAAAAAAAGAAAAAGAA
Found at i:2337525 original size:21 final size:21
Alignment explanation
Indices: 2337462--2337544 Score: 61
Period size: 21 Copynumber: 4.0 Consensus size: 21
2337452 AAAAAGAATG
2337462 AAGAAAAAA-AAGAA-AAAGAA
1 AAGAAAAAAGAAGAAGAAA-AA
*
2337482 AA-AAATAAAGGAA-AAG-GAAA
1 AAGAAA-AAA-GAAGAAGAAAAA
* *
2337502 AAGGAAAATGAA-AATGAAAAA
1 AAGAAAAAAGAAGAA-GAAAAA
2337523 AAGAAAAAAGAAGAAGAAAAA
1 AAGAAAAAAGAAGAAGAAAAA
2337544 A
1 A
2337545 GAGGGTTCGA
Statistics
Matches: 49, Mismatches: 6, Indels: 15
0.70 0.09 0.21
Matches are distributed among these distances:
19 8 0.16
20 12 0.24
21 25 0.51
22 4 0.08
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (21 bp):
AAGAAAAAAGAAGAAGAAAAA
Found at i:2338704 original size:105 final size:104
Alignment explanation
Indices: 2338474--2338770 Score: 339
Period size: 105 Copynumber: 2.8 Consensus size: 104
2338464 AATGACTATG
* * * * * *
2338474 ATCCATCACAG-AAGAAGGTGTACCAAAATTT-CATAACATTTCATAATGAGAAGAACTC-ACCA
1 ATCCATCCCAGAAAG-AGGTGGACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGA-CA
* **
2338536 TAAAGAAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
64 -AAAGGAGAAAGTTCATAATGAGAAGAAAATGTTCCTTTCAA
* * * * * *
2338578 ATCTATCCCATAAGGATGTGGACCAACCTTTCCAGAAGAGTTCATAATGAGAATAACTCGGACAA
1 ATCCATCCCAGAAAGAGGTGGACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTC-GACAA
2338643 AAGGAGAAAGTTCATAATGAGAAGAAAATGTTCCTTTCAA
65 AAGGAGAAAGTTCATAATGAGAAGAAAATGTTCCTTTCAA
* * * * *
2338683 ATCCATCGCAGAAAGAGGTGGATCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCCCA
1 ATCCATCCCAGAAAGAGGTGGACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCG-ACAA
*
2338748 AAGGATAAAGTTCATAATGAGAA
65 AAGGAGAAAGTTCATAATGAGAA
2338771 TAACTCACCC
Statistics
Matches: 161, Mismatches: 27, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
104 21 0.13
105 137 0.85
106 2 0.01
107 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.23
Consensus pattern (104 bp):
ATCCATCCCAGAAAGAGGTGGACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGACAAA
AGGAGAAAGTTCATAATGAGAAGAAAATGTTCCTTTCAA
Found at i:2338767 original size:35 final size:35
Alignment explanation
Indices: 2338716--2338811 Score: 129
Period size: 35 Copynumber: 2.7 Consensus size: 35
2338706 CAATATTTCC
* *
2338716 AGAAGAGTTCATAATGAGAAGAACTCGCCCCAAAGG
1 AGAA-AGTTCATAATGAGAAGAACTCACCCCAAAGA
* * *
2338752 ATAAAGTTCATAATGAGAATAACTCACCCCAAATA
1 AGAAAGTTCATAATGAGAAGAACTCACCCCAAAGA
*
2338787 AGAAATTTCATAATGAGAAGAACTC
1 AGAAAGTTCATAATGAGAAGAACTC
2338812 TTTCCTTTCA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
35 49 0.94
36 3 0.06
ACGTcount: A:0.46, C:0.18, G:0.17, T:0.20
Consensus pattern (35 bp):
AGAAAGTTCATAATGAGAAGAACTCACCCCAAAGA
Found at i:2338868 original size:101 final size:103
Alignment explanation
Indices: 2338756--2339023 Score: 335
Period size: 101 Copynumber: 2.6 Consensus size: 103
2338746 CAAAGGATAA
* * *
2338756 AGTTCATAATGAGAATAACTCACCCCAAATAAGAAATTTCATAATGAGAAGAACTCTTTCCTTTC
1 AGTTCATAATGAGAAGAACTCACCCCAAATAAGAAAGTTCATAATGAGAAGAACTCGTTCCTTTC
* * *
2338821 AAATCCAT-C-AAGGAGGTGGACCAACATTTCTAGAGG
66 AAATCCATACAAAGGAGATGAACCAACATTTCCAGAGG
* ** *
2338857 AGTTCATAATGAGCAGAACTCACCCCAAAGGAGAAAGTTCATAATGAGAAGAACTGGTTCCTTTC
1 AGTTCATAATGAGAAGAACTCACCCCAAATAAGAAAGTTCATAATGAGAAGAACTCGTTCCTTTC
2338922 AAATCCATCACAGAAGGAGATGAACCAACATTTCCAGAGG
66 AAATCCAT-ACA-AAGGAGATGAACCAACATTTCCAGAGG
* * * * *
2338962 AATTCATAATGAGAAGAACTC-GCCCAGATGAAGAAGAAGTTCATAAGGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCACCCCAAAT-AAG-A-AAGTTCATAATGAGAAGAACTCGTTC
2339024 AACCTTGTGC
Statistics
Matches: 142, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
101 66 0.46
103 1 0.01
104 5 0.04
105 45 0.32
106 1 0.01
107 24 0.17
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (103 bp):
AGTTCATAATGAGAAGAACTCACCCCAAATAAGAAAGTTCATAATGAGAAGAACTCGTTCCTTTC
AAATCCATACAAAGGAGATGAACCAACATTTCCAGAGG
Found at i:2338904 original size:136 final size:138
Alignment explanation
Indices: 2338611--2338911 Score: 383
Period size: 136 Copynumber: 2.2 Consensus size: 138
2338601 CAACCTTTCC
** *
2338611 AGAAGAGTTCATAATGAGAATAACTCGGACAAAAGGAGAAAGTTCATAATGAGAAGAAAATGTTC
1 AGAA-AGTTCATAATGAGAATAACTCACACAAAAGAAGAAAGTTCATAATGAGAAGAAAATGTTC
* *
2338676 CTTTCAAATCCATCGCAGAAAGAGGTGGATCAATATTTCCAGAAGAGTTCATAATGAGAAGAACT
65 CTTTCAAATCCATC-CA-AAAGAGGTGGACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACT
*
2338741 CGCCCCAAAGG
128 CACCCCAAAGG
* * * * * * *
2338752 ATAAAGTTCATAATGAGAATAACTCACCCCAAATAAGAAATTTCATAATGAGAAG-AACTCTTTC
1 AGAAAGTTCATAATGAGAATAACTCACACAAAAGAAGAAAGTTCATAATGAGAAGAAAAT-GTTC
* * * *
2338816 CTTTCAAATCCAT-C-AAGGAGGTGGACCAACATTTCTAGAGGAGTTCATAATGAGCAGAACTCA
65 CTTTCAAATCCATCCAAAAGAGGTGGACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCA
2338879 CCCCAAAGG
130 CCCCAAAGG
*
2338888 AGAAAGTTCATAATGAGAAGAACT
1 AGAAAGTTCATAATGAGAATAACT
2338912 GGTTCCTTTC
Statistics
Matches: 140, Mismatches: 19, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
136 73 0.52
138 1 0.01
139 3 0.02
140 60 0.43
141 3 0.02
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (138 bp):
AGAAAGTTCATAATGAGAATAACTCACACAAAAGAAGAAAGTTCATAATGAGAAGAAAATGTTCC
TTTCAAATCCATCCAAAAGAGGTGGACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCAC
CCCAAAGG
Found at i:2338957 original size:241 final size:243
Alignment explanation
Indices: 2338513--2338986 Score: 659
Period size: 241 Copynumber: 2.0 Consensus size: 243
2338503 TTCATAACAT
*
2338513 TTCATAATGAGAAGAACTCACCATAAAGAAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
1 TTCATAATGAGAAGAACTCACCACAAAGAAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
* * * * **
2338578 ATCTATCCCATAAGGATGTGGACCAACCTTTCCAGAAGAGTTCATAATGAGAATAACTCGGACAA
66 ATCCAT-CCA-AAGGAGGTGGACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCACACAA
* * * *
2338643 AAGGAGAAAGTTCATAATGAGAAGAAAATGTTCCTTTCAAATCCATCGCAGAAAGAGGTGGATCA
129 AAGGAGAAAGTTCATAATGAGAAGAAAATGTTCCTTTCAAATCCATCACAGAAAGAGATGAACCA
* *
2338708 ATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCCCAAAGGATAAAG
194 ACATTTCCAGAAGAATTCATAATGAGAAGAACTCGCCCCAAAGGATAAAG
* * * *
2338758 TTCATAATGAGAATAACTCACCCCAAATAAGAAATTTCATAATGAGAAGAACTCT-TTCCTTTCA
1 TTCATAATGAGAAGAACTCACCACAAAGAAGAAAGTTCATAATGAGAAGAACT-TGTTCCTTTCA
* * * * *
2338822 AATCCAT-C-AAGGAGGTGGACCAACATTTCTAGAGGAGTTCATAATGAGCAGAACTCACCCCAA
65 AATCCATCCAAAGGAGGTGGACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCACACAAA
* *
2338885 AGGAGAAAGTTCATAATGAGAAG-AACTGGTTCCTTTCAAATCCATCACAGAAGGAGATGAACCA
130 AGGAGAAAGTTCATAATGAGAAGAAAAT-GTTCCTTTCAAATCCATCACAGAAAGAGATGAACCA
*
2338949 ACATTTCCAGAGGAATTCATAATGAGAAGAACTCGCCC
194 ACATTTCCAGAAGAATTCATAATGAGAAGAACTCGCCC
2338987 AGATGAAGAA
Statistics
Matches: 202, Mismatches: 25, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
240 3 0.01
241 134 0.66
243 1 0.00
245 63 0.31
246 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (243 bp):
TTCATAATGAGAAGAACTCACCACAAAGAAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
ATCCATCCAAAGGAGGTGGACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCACACAAAA
GGAGAAAGTTCATAATGAGAAGAAAATGTTCCTTTCAAATCCATCACAGAAAGAGATGAACCAAC
ATTTCCAGAAGAATTCATAATGAGAAGAACTCGCCCCAAAGGATAAAG
Found at i:2340352 original size:29 final size:29
Alignment explanation
Indices: 2340317--2340386 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
2340307 TAGTATTCGT
*
2340317 ATTTCAACATCTTTACTCTATTTATTTAC
1 ATTTCAACACCTTTACTCTATTTATTTAC
*
2340346 ATTTCAACACCTTTACTTTATTTATTTAC
1 ATTTCAACACCTTTACTCTATTTATTTAC
2340375 ATTTCAACACCT
1 ATTTCAACACCT
2340387 CTTTATTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTTCAACACCTTTACTCTATTTATTTAC
Found at i:2341233 original size:41 final size:41
Alignment explanation
Indices: 2341176--2341258 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
2341166 AAAAATCGAG
2341176 TATGCTTAAAATTAATCAAGATTAAAAGGAAAAGGAAATGT
1 TATGCTTAAAATTAATCAAGATTAAAAGGAAAAGGAAATGT
2341217 TATGCTTAAAATTAATCAAGATTAAAAGGAAAAGGAAATGT
1 TATGCTTAAAATTAATCAAGATTAAAAGGAAAAGGAAATGT
2341258 T
1 T
2341259 CTTTTACTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.28
Consensus pattern (41 bp):
TATGCTTAAAATTAATCAAGATTAAAAGGAAAAGGAAATGT
Found at i:2346351 original size:83 final size:83
Alignment explanation
Indices: 2346247--2346402 Score: 199
Period size: 83 Copynumber: 1.9 Consensus size: 83
2346237 TCAGATAGTC
** * * * *
2346247 AGTATCGATATTGAGAGATTTTTAAAAACATCGAAGCTGATTTTAGTATTGATACTCATGG-GAG
1 AGTATCGATATCAAGAGATTTTTAAAAACATCGAAGATAAATTTAGTATCGATACTCA-GGTGAG
*
2346311 TATCGATACTCCCTATCGG
65 TATCAATACTCCCTATCGG
* *
2346330 AGTATCGATATCAAG-GCATTTTTCAAAACATTGAAGATAAATTTAGTATCGATACTCAGGTGAG
1 AGTATCGATATCAAGAG-ATTTTTAAAAACATCGAAGATAAATTTAGTATCGATACTCAGGTGAG
2346394 TATCAATAC
65 TATCAATAC
2346403 CCTAGGTGGT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
82 3 0.05
83 59 0.95
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (83 bp):
AGTATCGATATCAAGAGATTTTTAAAAACATCGAAGATAAATTTAGTATCGATACTCAGGTGAGT
ATCAATACTCCCTATCGG
Found at i:2346397 original size:18 final size:20
Alignment explanation
Indices: 2346374--2346425 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 20
2346364 AGATAAATTT
2346374 AGTATCGATACTC-A-GGTG
1 AGTATCGATACTCTAGGGTG
* *
2346392 AGTATCAATACCCTAGGTGGTG
1 AGTATCGATACTCTA-G-GGTG
2346414 AGTATCGATACT
1 AGTATCGATACT
2346426 GGTGGCACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 11 0.42
19 1 0.04
22 14 0.54
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (20 bp):
AGTATCGATACTCTAGGGTG
Found at i:2346575 original size:3 final size:3
Alignment explanation
Indices: 2346567--2346642 Score: 71
Period size: 3 Copynumber: 24.0 Consensus size: 3
2346557 CAGTTTACTT
** * *
2346567 TTA TTA TTA TTA AAA TTA TTA TTA TTAA ATA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
*
2346613 TCA TATA TTA TATA TATA TTA TTA TTA TTA
1 TTA T-TA TTA T-TA T-TA TTA TTA TTA TTA
2346643 AATAAAATAC
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
3 49 0.82
4 11 0.18
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:2348333 original size:12 final size:11
Alignment explanation
Indices: 2348316--2348349 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
2348306 ATATGTTTAA
2348316 ATTATTATTTT
1 ATTATTATTTT
2348327 CATTATTATTTT
1 -ATTATTATTTT
2348339 ATTATTATTTT
1 ATTATTATTTT
2348350 TATCTTAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:2348350 original size:12 final size:12
Alignment explanation
Indices: 2348316--2348352 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
2348306 ATATGTTTAA
*
2348316 ATTATTATTTTC
1 ATTATTATTTTT
2348328 ATTATTA-TTTT
1 ATTATTATTTTT
2348339 ATTATTATTTTT
1 ATTATTATTTTT
2348351 AT
1 AT
2348353 CTTAGTCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTATTATTTTT
Found at i:2348559 original size:2 final size:2
Alignment explanation
Indices: 2348552--2348584 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2348542 CCATATTTTA
2348552 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2348585 TAAGAAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2348804 original size:2 final size:2
Alignment explanation
Indices: 2348797--2348843 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2348787 ATAAATATCT
2348797 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2348839 TA TA T
1 TA TA T
2348844 TTTCTTAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.