Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 108 of 226
Found at i:33685307 original size:71 final size:71
Alignment explanation
Indices: 33685133--33685660 Score: 810
Period size: 71 Copynumber: 7.5 Consensus size: 71
33685123 CTGTAACAAT
* *
33685133 TTGGGCAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAT
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAC
33685198 C-AAAA
66 CAAAAA
* * * *
33685203 TTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACAC
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAC
33685268 CAAAAA
66 CAAAAA
* *
33685274 TTGGACAACATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAT
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAC
33685339 C-AAAA
66 CAAAAA
* * * *
33685344 TTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACAC
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAC
33685409 CAAAAA
66 CAAAAA
* *
33685415 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGTAGCATTTTTACAT
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAC
33685480 C-AAAA
66 CAAAAA
* * * *
33685485 TTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACAC
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAC
33685550 CAAAAA
66 CAAAAA
* * **
33685556 TCGGAGAGCATATATACAACAAATTGGATAGCATATATATACCAAATTGAGCAGCATTTTTACAC
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAC
*
33685621 CAAAAT
66 CAAAAA
* *
33685627 TTGGACAGCATATATATAACAATTTGGGCAGCAT
1 TTGGACAGCATATATACAACAAATTGGGCAGCAT
33685661 TTAAGCATCT
Statistics
Matches: 410, Mismatches: 45, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
70 188 0.46
71 222 0.54
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (71 bp):
TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAC
CAAAAA
Found at i:33685395 original size:141 final size:141
Alignment explanation
Indices: 33685133--33685660 Score: 966
Period size: 141 Copynumber: 3.7 Consensus size: 141
33685123 CTGTAACAAT
*
33685133 TTGGGCAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAT
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAT
33685198 CAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTT
66 CAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTT
33685263 TACACCAAAAA
131 TACACCAAAAA
*
33685274 TTGGACAACATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAT
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAT
33685339 CAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTT
66 CAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTT
33685404 TACACCAAAAA
131 TACACCAAAAA
*
33685415 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGTAGCATTTTTACAT
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAT
33685480 CAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTT
66 CAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTT
33685545 TACACCAAAAA
131 TACACCAAAAA
* * ** *
33685556 TCGGAGAGCATATATACAACAAATTGGATAGCATATATATACCAAATTGAGCAGCATTTTTACAC
1 TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAT
*
33685621 CAAAATTTGGACAGCATATATATAACAATTTGGGCAGCAT
66 CAAAA-TTGGACAGCATATATACAACAATTTGGGCAGCAT
33685661 TTAAGCATCT
Statistics
Matches: 375, Mismatches: 11, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
141 342 0.91
142 33 0.09
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (141 bp):
TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACAT
CAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTT
TACACCAAAAA
Found at i:33686729 original size:24 final size:24
Alignment explanation
Indices: 33686702--33686782 Score: 72
Period size: 28 Copynumber: 3.0 Consensus size: 24
33686692 TCGAAAATAT
*
33686702 TTAATAAGTTCGCACACTTAGTGC
1 TTAATAAATTCGCACACTTAGTGC
33686726 TTAATAATCAATCTCGCACACTTAGTGC
1 TTAAT-A--AAT-TCGCACACTTAGTGC
*
33686754 TTTACAATTAAACTCGCACACTTAGTGC
1 -TT--AA-TAAATTCGCACACTTAGTGC
33686782 T
1 T
33686783 AATCTCATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
24 5 0.11
25 1 0.02
27 3 0.06
28 30 0.64
29 4 0.09
31 3 0.06
32 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.33
Consensus pattern (24 bp):
TTAATAAATTCGCACACTTAGTGC
Found at i:33686743 original size:28 final size:28
Alignment explanation
Indices: 33686711--33686782 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
33686701 TTTAATAAGT
* *
33686711 TCGCACACTTAGTGCTTAATAATCAATC
1 TCGCACACTTAGTGCTTAACAATCAAAC
* *
33686739 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTAACAATCAAAC
33686767 TCGCACACTTAGTGCT
1 TCGCACACTTAGTGCT
33686783 AATCTCATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTAACAATCAAAC
Found at i:33690898 original size:70 final size:67
Alignment explanation
Indices: 33690813--33690941 Score: 195
Period size: 70 Copynumber: 1.9 Consensus size: 67
33690803 AATAAGGAAA
** *
33690813 GGCAAAACTAAGTCGTTTTGATAAATGTTTACCTTTTCTAAAGTTAAAAGTCAAAACCATTAAGT
1 GGCAAAACTAAGTCGTTTTGATAAATGTTTA-CTCAT-T-AAGTTAAAAGGCAAAACCATTAAGT
33690878 TAAAG
63 TAAAG
*
33690883 GGCAAAACTATGTCGTTTTGATAAATGTTTACTCATTAAGTTAAAAGGCAAAACCATTA
1 GGCAAAACTAAGTCGTTTTGATAAATGTTTACTCATTAAGTTAAAAGGCAAAACCATTA
33690942 TATTGTTTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
67 21 0.38
68 1 0.02
69 3 0.05
70 30 0.55
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (67 bp):
GGCAAAACTAAGTCGTTTTGATAAATGTTTACTCATTAAGTTAAAAGGCAAAACCATTAAGTTAA
AG
Found at i:33702937 original size:33 final size:31
Alignment explanation
Indices: 33702897--33702985 Score: 108
Period size: 33 Copynumber: 2.7 Consensus size: 31
33702887 GCATCCACAG
*
33702897 AGATAGTCTGCTGGGACAGTAAACATAGAACAT
1 AGATAGTCTACTGGGACAGTAAACATA-AA-AT
33702930 AGATAGTCTACTGGGACAGTAAACATAAAAT
1 AGATAGTCTACTGGGACAGTAAACATAAAAT
*
33702961 AGAGATAATCTA-TCGGGACAGTAAA
1 --AGATAGTCTACT-GGGACAGTAAA
33702986 TATGAGTAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
31 2 0.04
32 3 0.06
33 46 0.90
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.21
Consensus pattern (31 bp):
AGATAGTCTACTGGGACAGTAAACATAAAAT
Found at i:33703061 original size:28 final size:28
Alignment explanation
Indices: 33702991--33703061 Score: 65
Period size: 28 Copynumber: 2.5 Consensus size: 28
33702981 GTAAATATGA
* * *
33702991 GTAAGTCCACTGAGATAATAAACATGAG
1 GTAAGTCTACTGGGATAATAAACACGAG
* *
33703019 GTAAGTTTA-TCGGGATAGTAAACACG-G
1 GTAAGTCTACT-GGGATAATAAACACGAG
33703046 CGTAAGTCTACTGGGA
1 -GTAAGTCTACTGGGA
33703062 CATGAGAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
27 2 0.06
28 31 0.91
29 1 0.03
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (28 bp):
GTAAGTCTACTGGGATAATAAACACGAG
Found at i:33706509 original size:39 final size:39
Alignment explanation
Indices: 33706421--33706513 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 39
33706411 AAATAGAACC
** * *
33706421 TTGGCTTTGCAAAGGAATGTATAGGTTTTACTTTTGAAG
1 TTGGCTTTGCGGAGGAATGTATAGGCTTTACTTTTAAAG
*
33706460 TTGGCTTTGCGGAGGAATGTATATGCTTTA-TTTTCAAAG
1 TTGGCTTTGCGGAGGAATGTATAGGCTTTACTTTT-AAAG
*
33706499 TTGGTTTTGCGGAGG
1 TTGGCTTTGCGGAGG
33706514 GAAGTTGTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 4 0.09
39 43 0.91
ACGTcount: A:0.22, C:0.09, G:0.29, T:0.41
Consensus pattern (39 bp):
TTGGCTTTGCGGAGGAATGTATAGGCTTTACTTTTAAAG
Found at i:33706620 original size:26 final size:26
Alignment explanation
Indices: 33706582--33707199 Score: 485
Period size: 26 Copynumber: 23.7 Consensus size: 26
33706572 GTAGAGAGGG
*
33706582 ATGTGTGCTAGCTGTTATTACCATGC
1 ATGTGTGCGAGCTGTTATTACCATGC
*
33706608 ATGTGTGCCAGCTAG-TATTACCATGCC
1 ATGTGTGCGAGCT-GTTATTACCATG-C
*
33706635 ATGCATGTATGCGAGCTGTTATTAACATGC
1 ATG--TG--TGCGAGCTGTTATTACCATGC
* **
33706665 ATGTTTGCGATTTGTTATTACCATGC
1 ATGTGTGCGAGCTGTTATTACCATGC
33706691 ATGTGTGCGAGCTGTTATTACC-TAGC
1 ATGTGTGCGAGCTGTTATTACCAT-GC
* *
33706717 ATGTATGTGAGCTGTTATTACCATGC
1 ATGTGTGCGAGCTGTTATTACCATGC
* * * *
33706743 ATGCGTGCG-GACTATTGTTACCTTGC
1 ATGTGTGCGAG-CTGTTATTACCATGC
* * * *
33706769 ATGTATGCGAGCTATTATTAACTTGC
1 ATGTGTGCGAGCTGTTATTACCATGC
* *
33706795 ATGTATGTGAGCTGTTATTACCATGC
1 ATGTGTGCGAGCTGTTATTACCATGC
* *
33706821 ATGTGT-CTGAGTTGTTATTACCTTGC
1 ATGTGTGC-GAGCTGTTATTACCATGC
* * * *
33706847 ATGTGTGCAAGCTATCATTACCTTGC
1 ATGTGTGCGAGCTGTTATTACCATGC
** * *
33706873 ATGAATG-TATGCTATTATTACCATGC
1 ATGTGTGCGA-GCTGTTATTACCATGC
* *
33706899 ATGT-CGCGAGCTGTTATTACCTTGC
1 ATGTGTGCGAGCTGTTATTACCATGC
* * * * *
33706924 ATGTATACGAGTTTTTATTACCTTGC
1 ATGTGTGCGAGCTGTTATTACCATGC
** * * *
33706950 ATGAATGTGAGCTATTATTCCCATGC
1 ATGTGTGCGAGCTGTTATTACCATGC
* *
33706976 ATGTGTGCGAGCTGTTATTACCTTGT
1 ATGTGTGCGAGCTGTTATTACCATGC
** *
33707002 ATGTGTATGAGCTGTTA-TACCATAC
1 ATGTGTGCGAGCTGTTATTACCATGC
* * *
33707027 ATGTGTGTGAGCTATTATTGCCATGC
1 ATGTGTGCGAGCTGTTATTACCATGC
* ** * *
33707053 ATGTGTGCAAATTTTTATTACCTTGC
1 ATGTGTGCGAGCTGTTATTACCATGC
* ** * *
33707079 ATGTATATGAGATTTTATTACCATGC
1 ATGTGTGCGAGCTGTTATTACCATGC
* * * *
33707105 ATGTGTGCAAGTTGTTATTACCTTAC
1 ATGTGTGCGAGCTGTTATTACCATGC
* *
33707131 ATGTATGCGAGCTGTTATTACCTTGC
1 ATGTGTGCGAGCTGTTATTACCATGC
* * * *
33707157 ATGTATGTGAGTTGTTATTACAATGC
1 ATGTGTGCGAGCTGTTATTACCATGC
33707183 ATGTGTGCGAGCTGTTA
1 ATGTGTGCGAGCTGTTA
33707200 ATTGAAAGTA
Statistics
Matches: 471, Mismatches: 104, Indels: 34
0.77 0.17 0.06
Matches are distributed among these distances:
25 42 0.09
26 397 0.84
27 8 0.02
28 1 0.00
29 2 0.00
30 5 0.01
31 16 0.03
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (26 bp):
ATGTGTGCGAGCTGTTATTACCATGC
Found at i:33706637 original size:31 final size:31
Alignment explanation
Indices: 33706602--33706664 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
33706592 GCTGTTATTA
* *
33706602 CCATGCATGTGTGCCAGCTAG-TATTACCATG
1 CCATGCATGTATGCCAGCT-GTTATTAACATG
*
33706633 CCATGCATGTATGCGAGCTGTTATTAACATG
1 CCATGCATGTATGCCAGCTGTTATTAACATG
33706664 C
1 C
33706665 ATGTTTGCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (31 bp):
CCATGCATGTATGCCAGCTGTTATTAACATG
Found at i:33706977 original size:129 final size:129
Alignment explanation
Indices: 33706633--33707193 Score: 443
Period size: 129 Copynumber: 4.3 Consensus size: 129
33706623 TATTACCATG
* * * * * *
33706633 CCATGCATGTATGCGAGCTGTTATTAACATGCATGTTTGCGA-TTTGTTATTACCATGCATGTGT
1 CCATGCATGTATGCGAGCTATTATTACCTTGCATGTATGCGAGTTT-TTATTACCTTGCATGTAT
** * * * ** * * ** *
33706697 GCGAGCTGTTATTACC-TAGCATGTATGTGAGCTGTTATTACCATGCATG-CGTGCGGACTATTG
65 ATGAGATATTATTACCAT-GCATGTGTGCAAGCTGTTATTACCTTGCATGATGT-ATG-CTATTA
33706760 TTA
127 TTA
* * * * * * * *
33706763 CCTTGCATGTATGCGAGCTATTATTAACTTGCATGTATGTGAGCTGTTATTACCATGCATGTGTC
1 CCATGCATGTATGCGAGCTATTATTACCTTGCATGTATGCGAGTTTTTATTACCTTGCATGTATA
* * * * *
33706828 TGAGTTGTTATTACCTTGCATGTGTGCAAGCTATCATTACCTTGCATGAATGTATGCTATTATTA
66 TGAGATATTATTACCATGCATGTGTGCAAGCTGTTATTACCTTGCATG-ATGTATGCTATTATTA
* * * * *
33706893 CCATGCATGT-CGCGAGCTGTTATTACCTTGCATGTATACGAGTTTTTATTACCTTGCATGAATG
1 CCATGCATGTATGCGAGCTATTATTACCTTGCATGTATGCGAGTTTTTATTACCTTGCATGTATA
* * * * *
33706957 TGAGCTATTATTCCCATGCATGTGTGCGAGCTGTTATTACCTTGTATG-TGTATGAGCTGTTA-T
66 TGAGATATTATTACCATGCATGTGTGCAAGCTGTTATTACCTTGCATGATGTAT--GCTATTATT
33707020 A
129 A
* * * * * * * *
33707021 CCATACATGTGTGTGAGCTATTATTGCCATGCATGTGTGCAAATTTTTATTACCTTGCATGTATA
1 CCATGCATGTATGCGAGCTATTATTACCTTGCATGTATGCGAGTTTTTATTACCTTGCATGTATA
* * * * *
33707086 TGAGATTTTATTACCATGCATGTGTGCAAGTTGTTATTACCTTACATGTATGCGA-GCTGTTATT
66 TGAGATATTATTACCATGCATGTGTGCAAGCTGTTATTACCTTGCATG-ATG-TATGCTATTATT
33707150 A
129 A
* * * * ** *
33707151 CCTTGCATGTATGTGAGTTGTTATTACAATGCATGTGTGCGAG
1 CCATGCATGTATGCGAGCTATTATTACCTTGCATGTATGCGAG
33707194 CTGTTAATTG
Statistics
Matches: 350, Mismatches: 70, Indels: 22
0.79 0.16 0.05
Matches are distributed among these distances:
127 5 0.01
128 11 0.03
129 180 0.51
130 146 0.42
131 5 0.01
132 3 0.01
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (129 bp):
CCATGCATGTATGCGAGCTATTATTACCTTGCATGTATGCGAGTTTTTATTACCTTGCATGTATA
TGAGATATTATTACCATGCATGTGTGCAAGCTGTTATTACCTTGCATGATGTATGCTATTATTA
Found at i:33731422 original size:27 final size:27
Alignment explanation
Indices: 33731384--33731671 Score: 312
Period size: 27 Copynumber: 10.6 Consensus size: 27
33731374 TGGACCGAAG
* *
33731384 ATTACCGAAATACCCTCGAGGGGTAAA
1 ATTATCGAAATACCCTCGAAGGGTAAA
* ** *
33731411 ATTA-CTAAAATACCCTCGAATAGTACA
1 ATTATC-GAAATACCCTCGAAGGGTAAA
*
33731438 ATTA-CTGAAATACCCTCAAAGGGTAAA
1 ATTATC-GAAATACCCTCGAAGGGTAAA
*
33731465 ATTATCGAAATAACCCT-AAAGGGTAAA
1 ATTATCGAAAT-ACCCTCGAAGGGTAAA
*
33731492 ATTATCAAAATACCCTCGAAGGGTAAA
1 ATTATCGAAATACCCTCGAAGGGTAAA
33731519 ATTATCGAAATACCCTCGAAGGGTAAA
1 ATTATCGAAATACCCTCGAAGGGTAAA
* * *
33731546 ATTACCGAAATACTCTTGAAGGGTAAA
1 ATTATCGAAATACCCTCGAAGGGTAAA
* * * *
33731573 ATTACCAAAATACCCTTGAATGGTAAA
1 ATTATCGAAATACCCTCGAAGGGTAAA
* *
33731600 ATGATCGAAATACCCTTGAAGGGGTAAA
1 ATTATCGAAATACCCTCGAA-GGGTAAA
*
33731628 ATGATCGAAATACCCTCGAAAGGGTAAA
1 ATTATCGAAATACCCTCG-AAGGGTAAA
* **
33731656 ATGATCGTTATACCCT
1 ATTATCGAAATACCCT
33731672 AGGAGATGAA
Statistics
Matches: 229, Mismatches: 26, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
26 6 0.03
27 171 0.75
28 50 0.22
29 2 0.01
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (27 bp):
ATTATCGAAATACCCTCGAAGGGTAAA
Found at i:33731884 original size:26 final size:26
Alignment explanation
Indices: 33731853--33731923 Score: 106
Period size: 26 Copynumber: 2.7 Consensus size: 26
33731843 CCACATATAA
* *
33731853 TGTTACTGGCAGCTTTGTTGCGTTAC
1 TGTTACTGGCAGCTTTGCTACGTTAC
*
33731879 TGTTACTGGCAGCTTTGCTACGTTAT
1 TGTTACTGGCAGCTTTGCTACGTTAC
*
33731905 TATTACTGGCAGCTTTGCT
1 TGTTACTGGCAGCTTTGCT
33731924 TCGATATTGG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.42
Consensus pattern (26 bp):
TGTTACTGGCAGCTTTGCTACGTTAC
Found at i:33731931 original size:26 final size:26
Alignment explanation
Indices: 33731855--33731931 Score: 102
Period size: 26 Copynumber: 3.0 Consensus size: 26
33731845 ACATATAATG
* *
33731855 TTACTGGCAGCTTTG-TTGCGTTACTG
1 TTACTGGCAGCTTTGCTT-CGTTATTA
*
33731881 TTACTGGCAGCTTTGCTACGTTATTA
1 TTACTGGCAGCTTTGCTTCGTTATTA
*
33731907 TTACTGGCAGCTTTGCTTCGATATT
1 TTACTGGCAGCTTTGCTTCGTTATT
33731932 GGTGTGTTGG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
26 44 0.98
27 1 0.02
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTTCGTTATTA
Found at i:33732056 original size:28 final size:28
Alignment explanation
Indices: 33732016--33732100 Score: 116
Period size: 28 Copynumber: 3.0 Consensus size: 28
33732006 ATTGTACCGA
* * * *
33732016 TTACTGTTTTGGGCTAATGCCCATATTG
1 TTACTGTATTGGGCTAAGGCCCACACTG
*
33732044 TTACTGTATTGGGCTAAGGCTCACACTG
1 TTACTGTATTGGGCTAAGGCCCACACTG
*
33732072 TTACTGTAATGGGCTAAGGCCCACACTG
1 TTACTGTATTGGGCTAAGGCCCACACTG
33732100 T
1 T
33732101 ACTTATACTG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (28 bp):
TTACTGTATTGGGCTAAGGCCCACACTG
Found at i:33732119 original size:33 final size:28
Alignment explanation
Indices: 33732016--33732127 Score: 91
Period size: 28 Copynumber: 3.8 Consensus size: 28
33732006 ATTGTACCGA
* * * * *
33732016 TTACTGTTTTGGGCTAATGCCCATATTG
1 TTACTGTATAGGGCTAAGGCCCACACTG
* *
33732044 TTACTGTATTGGGCTAAGGCTCACACTG
1 TTACTGTATAGGGCTAAGGCCCACACTG
33732072 TTACTGTA-ATGGGCTAAGGCCCACACTG
1 TTACTGTATA-GGGCTAAGGCCCACACTG
*
33732100 TACTTATACTGTATAGGGCTCAGGCCCA
1 ----T-TACTGTATAGGGCTAAGGCCCA
33732128 GATTGATTCT
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
28 48 0.70
32 1 0.01
33 19 0.28
34 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.32
Consensus pattern (28 bp):
TTACTGTATAGGGCTAAGGCCCACACTG
Found at i:33732695 original size:12 final size:12
Alignment explanation
Indices: 33732678--33732704 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
33732668 GTGTTACACA
33732678 TTTCATTTCCAT
1 TTTCATTTCCAT
33732690 TTTCATTTCCAT
1 TTTCATTTCCAT
33732702 TTT
1 TTT
33732705 TGGAAACCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTCATTTCCAT
Found at i:33734030 original size:10 final size:10
Alignment explanation
Indices: 33733998--33734037 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
33733988 TAAAAGAATG
33733998 AATTTTAATT
1 AATTTTAATT
33734008 AATTCTATAATT
1 AATT-T-TAATT
*
33734020 AATTTTGATT
1 AATTTTAATT
33734030 AATTTTAA
1 AATTTTAA
33734038 CTATTTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 15 0.58
11 2 0.08
12 9 0.35
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (10 bp):
AATTTTAATT
Found at i:33734583 original size:7 final size:7
Alignment explanation
Indices: 33734571--33734610 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
33734561 ATCAAACACA
33734571 CCTCATC
1 CCTCATC
33734578 CCTCATC
1 CCTCATC
33734585 CCTCATC
1 CCTCATC
33734592 CCTCATC
1 CCTCATC
33734599 CCTCATC
1 CCTCATC
33734606 CCTCA
1 CCTCA
33734611 CACTCTCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.15, C:0.57, G:0.00, T:0.28
Consensus pattern (7 bp):
CCTCATC
Found at i:33738599 original size:29 final size:29
Alignment explanation
Indices: 33738538--33738599 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
33738528 TGATTATATT
* *
33738538 TTATCAAGTACTATGTACCGGTGACTATA
1 TTATCAAGTACTATGTACCGATGACCATA
* * * *
33738567 TTATCAGGTACTTTGTACCGATGTCCATG
1 TTATCAAGTACTATGTACCGATGACCATA
33738596 TTAT
1 TTAT
33738600 ACTAGGCATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.39
Consensus pattern (29 bp):
TTATCAAGTACTATGTACCGATGACCATA
Found at i:33741632 original size:17 final size:18
Alignment explanation
Indices: 33741607--33741644 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
33741597 TTATATATTT
*
33741607 TTTAGAAATT-TTTAAAA
1 TTTAAAAATTATTTAAAA
*
33741624 TTTAAAAATTATTTTAAA
1 TTTAAAAATTATTTAAAA
33741642 TTT
1 TTT
33741645 TTTTGTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTAAAAATTATTTAAAA
Found at i:33748328 original size:16 final size:16
Alignment explanation
Indices: 33748291--33748330 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
33748281 TTAATAAAAT
* *
33748291 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
33748307 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
33748323 TAAAATTA
1 TAAAATTA
33748331 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:33748409 original size:59 final size:59
Alignment explanation
Indices: 33748341--33748519 Score: 259
Period size: 68 Copynumber: 2.9 Consensus size: 59
33748331 TCAAATTATT
*
33748341 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
33748400 AATTATTAATTGTATTAATTGTATTAATTTTTGTAATAAAATCTAACATTTGATTAGTAAATTTA
1 AATTATTAATTGTATTAATTG---------TTGTAATAAAATCTAACATTTGATTAGTAAATTTA
33748465 TCA
57 TCA
*
33748468 AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
33748520 ATAAACTTGA
Statistics
Matches: 109, Mismatches: 2, Indels: 18
0.84 0.02 0.14
Matches are distributed among these distances:
59 50 0.46
68 59 0.54
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:33748415 original size:9 final size:9
Alignment explanation
Indices: 33748403--33748428 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
33748393 TTTATCAAAT
33748403 TATTAATTG
1 TATTAATTG
33748412 TATTAATTG
1 TATTAATTG
33748421 TATTAATT
1 TATTAATT
33748429 TTTGTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (9 bp):
TATTAATTG
Found at i:33748441 original size:68 final size:68
Alignment explanation
Indices: 33748319--33748489 Score: 310
Period size: 68 Copynumber: 2.5 Consensus size: 68
33748309 AAATTAATTG
*
33748319 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
33748382 TGA
66 TGA
*
33748385 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTTTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
33748450 TGA
66 TGA
33748453 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
33748490 TGTAACAAAA
Statistics
Matches: 101, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
66 26 0.26
68 75 0.74
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:33748555 original size:59 final size:58
Alignment explanation
Indices: 33748412--33748525 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 58
33748402 TTATTAATTG
* * * *
33748412 TATTAATTGTATTAATTTTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAAT
1 TATTAATTGTATTAA-TTTTGTAACAAAATCTAACATTTGATTAGTAAAATAAACAAAT
33748471 TATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAATAAAC
1 TATTAATTGTATTAATT-TTGTAACAAAATCTAACATTTGATTAGTAAAATAAAC
33748526 TTGATGTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 2 0.04
59 48 0.96
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (58 bp):
TATTAATTGTATTAATTTTGTAACAAAATCTAACATTTGATTAGTAAAATAAACAAAT
Found at i:33748626 original size:22 final size:24
Alignment explanation
Indices: 33748586--33748629 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
33748576 AAATAAACTT
33748586 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
33748610 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
33748630 AATAATTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:33750184 original size:8 final size:7
Alignment explanation
Indices: 33750158--33750182 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
33750148 AAAAATAAAA
33750158 AAAATTC
1 AAAATTC
33750165 AAAATTC
1 AAAATTC
33750172 AAAATTC
1 AAAATTC
33750179 AAAA
1 AAAA
33750183 ATAAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTC
Found at i:33750339 original size:4 final size:4
Alignment explanation
Indices: 33750330--33750356 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
33750320 GGGCCAAATT
33750330 TAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAA
33750357 TAATAACCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:33753656 original size:19 final size:19
Alignment explanation
Indices: 33753632--33753672 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
33753622 TTGAACTTGA
*
33753632 AAATTGGACCTGAGATCCT
1 AAATTGGACCTGAGAGCCT
* *
33753651 AAATTGGGCTTGAGAGCCT
1 AAATTGGACCTGAGAGCCT
33753670 AAA
1 AAA
33753673 ATCGAGACCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.24
Consensus pattern (19 bp):
AAATTGGACCTGAGAGCCT
Found at i:33754205 original size:25 final size:25
Alignment explanation
Indices: 33754170--33754217 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
33754160 TTGTAAAGAG
33754170 AAAATTCTCTAAAGAGATTATTCCAA
1 AAAATTCTCTAAAGAGATT-TTCCAA
*
33754196 AAAATT-TCTAAAGATATTTTCC
1 AAAATTCTCTAAAGAGATTTTCC
33754218 TGATTTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 11 0.52
26 6 0.29
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (25 bp):
AAAATTCTCTAAAGAGATTTTCCAA
Found at i:33758108 original size:44 final size:44
Alignment explanation
Indices: 33758045--33758132 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
33758035 AGGATGAAAA
*
33758045 GAAGTTGAATGCATGGACAAAATTGTGCATGTTTGTAAGATATC
1 GAAGTTGAATGCATGGACAAAATTGTGCATATTTGTAAGATATC
33758089 GAAGTTGAATGCATGGACAAAATTGTGCATATTTGTAAGATATC
1 GAAGTTGAATGCATGGACAAAATTGTGCATATTTGTAAGATATC
33758133 TAAAAGGAAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (44 bp):
GAAGTTGAATGCATGGACAAAATTGTGCATATTTGTAAGATATC
Found at i:33758149 original size:44 final size:44
Alignment explanation
Indices: 33758057--33758149 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
33758047 AGTTGAATGC
* *** ***
33758057 ATGGACAAAATTGTGCATGTTTGTAAGATATCGAAGTTGAATGC
1 ATGGACAAAATTGTGCATATTTGTAAGATATCGAAAAGGAACAA
*
33758101 ATGGACAAAATTGTGCATATTTGTAAGATATCTAAAAGGAACAA
1 ATGGACAAAATTGTGCATATTTGTAAGATATCGAAAAGGAACAA
33758145 ATGGA
1 ATGGA
33758150 GGATTATTCT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.29
Consensus pattern (44 bp):
ATGGACAAAATTGTGCATATTTGTAAGATATCGAAAAGGAACAA
Found at i:33761914 original size:36 final size:31
Alignment explanation
Indices: 33761836--33761898 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
33761826 TTAAAATGAT
33761836 TATCTTAATATTAAATTAAATTTAGTGTTTA
1 TATCTTAATATTAAATTAAATTTAGTGTTTA
33761867 TATCTTAATATTAAATTAAATTTAGTGTTTA
1 TATCTTAATATTAAATTAAATTTAGTGTTTA
33761898 T
1 T
33761899 CTTGTAGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.52
Consensus pattern (31 bp):
TATCTTAATATTAAATTAAATTTAGTGTTTA
Found at i:33761937 original size:62 final size:59
Alignment explanation
Indices: 33761871--33761986 Score: 151
Period size: 62 Copynumber: 1.9 Consensus size: 59
33761861 TGTTTATATC
* * * * *
33761871 TTAATATTAAATTAAATTTAGTGTTTATCTTGTAGATAAATATTCTATTATTTTAATGAGAT
1 TTAATATTAAATTAAATATAATATTTATC-T-T-GATAAATATTATATTAATTTAATGAGAT
*
33761933 TTAATATTAAATTTAATATAATATTTATCTTGATAAATATTATATTAATTTAAT
1 TTAATATTAAATTAAATATAATATTTATCTTGATAAATATTATATTAATTTAAT
33761987 ATTATAGTGA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 21 0.44
60 1 0.02
61 1 0.02
62 25 0.52
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.51
Consensus pattern (59 bp):
TTAATATTAAATTAAATATAATATTTATCTTGATAAATATTATATTAATTTAATGAGAT
Found at i:33763773 original size:48 final size:48
Alignment explanation
Indices: 33763701--33763796 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
33763691 TTTTTTTGCT
* **
33763701 TAAAAACGCCTAAGTCAGCCTAACTTGCAGTGATAAAGGATTCAACAG
1 TAAAAACGCCTAAGTCAGCCTAACTCGCAACGATAAAGGATTCAACAG
*
33763749 TAAAAACGCCTAAGTCAGCTTAACTCGCAACGATAAAGGATTCAACAG
1 TAAAAACGCCTAAGTCAGCCTAACTCGCAACGATAAAGGATTCAACAG
33763797 AATTCCCTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.20
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTCGCAACGATAAAGGATTCAACAG
Found at i:33764072 original size:35 final size:36
Alignment explanation
Indices: 33764021--33764090 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 36
33764011 TACAATTAAA
* *
33764021 AGCTGTATACAATTAGAACTCTAAGCTT-CATAATC
1 AGCTATATACAATTAGAACTCTAAGATTCCATAATC
33764056 AGCTATATACAATTAGAACTCTAAGATTCCATAAT
1 AGCTATATACAATTAGAACTCTAAGATTCCATAAT
33764091 TATATCTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 26 0.81
36 6 0.19
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (36 bp):
AGCTATATACAATTAGAACTCTAAGATTCCATAATC
Found at i:33767858 original size:64 final size:66
Alignment explanation
Indices: 33767778--33767910 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 66
33767768 CTCTTGTCCC
33767778 AAGGCTTCTTACCATTCCCGTT-CT-TGGGCCTTTCTTTATCTCCCCCACTATTACCCTTTTGAT
1 AAGGCTTCTTACCATTCCCGTTCCTATGGGCCTTTCTTTATCTCCCCCACTATTACCCTTTTGAT
33767841 T
66 T
33767842 AAGGCTTCTTACCATTCCCGTTCCTAGTGGGCCTTTCTTTATCTCCCCCACTATTACCCTTTTGA
1 AAGGCTTCTTACCATTCCCGTTCCTA-TGGGCCTTTCTTTATCTCCCCCACTATTACCCTTTTGA
33767907 TT
65 TT
33767909 AA
1 AA
33767911 ATCTGGGCTT
Statistics
Matches: 66, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
64 22 0.33
65 2 0.03
67 42 0.64
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (66 bp):
AAGGCTTCTTACCATTCCCGTTCCTATGGGCCTTTCTTTATCTCCCCCACTATTACCCTTTTGAT
T
Found at i:33768971 original size:48 final size:48
Alignment explanation
Indices: 33768899--33768994 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
33768889 TTTCTTTGCT
* * * **
33768899 TAAAAACGCCTAAGTGAGCCTAACTTGTAGTGATAAAGGATTCAACAG
1 TAAAAACGCCTAAGTCAGCCTAACTCGCAACGATAAAGGATTCAACAG
*
33768947 TAAAAACGCCTAAGTCAGCTTAACTCGCAACGATAAAGGATTCAACAG
1 TAAAAACGCCTAAGTCAGCCTAACTCGCAACGATAAAGGATTCAACAG
33768995 AATTCCCTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.21
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTCGCAACGATAAAGGATTCAACAG
Found at i:33769270 original size:36 final size:36
Alignment explanation
Indices: 33769219--33769289 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
33769209 TACAATTAAA
* * *
33769219 AGCTGTATATAATTAGAACTCTAAGCTTACATAATC
1 AGCTATATACAATTAGAACTCTAAGATTACATAATC
*
33769255 AGCTATATACAATTAGAACTCTAAGATTCCATAAT
1 AGCTATATACAATTAGAACTCTAAGATTACATAAT
33769290 TATATCTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (36 bp):
AGCTATATACAATTAGAACTCTAAGATTACATAATC
Found at i:33770495 original size:192 final size:193
Alignment explanation
Indices: 33770165--33770514 Score: 460
Period size: 192 Copynumber: 1.8 Consensus size: 193
33770155 TGGAATTTCC
* * * * * * * *
33770165 ATATTTCAACAATAAAATCTGGAAATAATTTGATTTTTTTTTACTTTGTTTTGAAGTTTTTTGGA
1 ATATTTCAACAATAAAATCAGAAAATAATTTGATATTTTGTAACGTTGTTTTGAAGCTTTTGGGA
* *
33770230 ATTGAGTTTTTAAGAATGAATCAATATTTGATGCAATAACACTTAATAATTTTACTTATCATCAT
66 ATTGAGTTTTCAAGAATCAATCAATATTTGATGCAATAACACTTAATAATTTTAC-TATCATCAT
33770295 TGAAGCAAATGATGATATATCATAAAAAAATTAAAAAAAATGTTTTTTCCAATGTGAAAATTCT
130 TGAAGCAAATGATGATATATCATAAAAAAATTAAAAAAAATGTTTTTTCCAATGTGAAAATTCT
*
33770359 ATATTTCAATAATAAAATCAGAAAATAATTTGA-ATTTTGTAACGTTG-TTTGAAGCTTTTGGGA
1 ATATTTCAACAATAAAATCAGAAAATAATTTGATATTTTGTAACGTTGTTTTGAAGCTTTTGGGA
* * * * *
33770422 ATTGAGTTTTCACA-AATCAATTAATATTTGATGCACTTACA-TTGTATAATTTTA-T-TCTTCA
66 ATTGAGTTTTCA-AGAATCAATCAATATTTGATGCAATAACACTT-AATAATTTTACTATCATCA
33770483 TTGCTAAAGCAAATGATGATATATCATAAAAA
129 TTG---AAGCAAATGATGATATATCATAAAAA
33770515 GATTTTAAAA
Statistics
Matches: 135, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
189 8 0.06
190 1 0.01
191 2 0.01
192 83 0.61
193 11 0.08
194 30 0.22
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (193 bp):
ATATTTCAACAATAAAATCAGAAAATAATTTGATATTTTGTAACGTTGTTTTGAAGCTTTTGGGA
ATTGAGTTTTCAAGAATCAATCAATATTTGATGCAATAACACTTAATAATTTTACTATCATCATT
GAAGCAAATGATGATATATCATAAAAAAATTAAAAAAAATGTTTTTTCCAATGTGAAAATTCT
Found at i:33772458 original size:35 final size:35
Alignment explanation
Indices: 33772419--33772490 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
33772409 TGTGTTATTA
*
33772419 TACCAGTTAGAAAAAAGCCATGCCATTATTTTCAT
1 TACCAGTTAGAAAAAAGCCACGCCATTATTTTCAT
33772454 TACCAGTTAGAAAAAAGCCACGCCATTATTTTCAT
1 TACCAGTTAGAAAAAAGCCACGCCATTATTTTCAT
33772489 TA
1 TA
33772491 TCATTTTAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.31
Consensus pattern (35 bp):
TACCAGTTAGAAAAAAGCCACGCCATTATTTTCAT
Found at i:33772699 original size:16 final size:16
Alignment explanation
Indices: 33772675--33772726 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
33772665 TGGTTCACTG
* *
33772675 TAATTGAATAGGGCTA
1 TAATGGAATAGAGCTA
* *
33772691 TAATGGAATAGAGTTG
1 TAATGGAATAGAGCTA
33772707 TAATGGAATAGAGCTA
1 TAATGGAATAGAGCTA
33772723 TAAT
1 TAAT
33772727 AGCATTCTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (16 bp):
TAATGGAATAGAGCTA
Found at i:33772921 original size:59 final size:57
Alignment explanation
Indices: 33772848--33772983 Score: 173
Period size: 59 Copynumber: 2.3 Consensus size: 57
33772838 TTGTTATTAA
* * * * *
33772848 ATTTTAATAAAATTATTATTAAATATATTTTATTAAAAAATAATAAATAATTTAATCAT
1 ATTTTAATATAATTATTATTAAATAAAATTTA--AAAAAATAATAAATAATTTAATAAC
* * *
33772907 ATTTTAACATAATTATTATTAAATAAAATTTAATAAAATAATATATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATAAAATTTAAAAAAATAATAAATAATTTAATAAC
33772964 ATTCTTAATATAATTATTAT
1 ATT-TTAATATAATTATTAT
33772984 ATGAATTAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 24 0.36
58 15 0.22
59 28 0.42
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (57 bp):
ATTTTAATATAATTATTATTAAATAAAATTTAAAAAAATAATAAATAATTTAATAAC
Found at i:33773019 original size:23 final size:21
Alignment explanation
Indices: 33772988--33773030 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
33772978 TATTATATGA
33772988 ATTAAAAAATCATAATATATAAT
1 ATTAAAAAA--ATAATATATAAT
*
33773011 ATTATAAAAATAATATATAA
1 ATTAAAAAAATAATATATAA
33773031 CCTACTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTAAAAAAATAATATATAAT
Found at i:33777386 original size:22 final size:20
Alignment explanation
Indices: 33777361--33777403 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
33777351 ATTCGATTTG
33777361 TTTTGTATTATATATTATTATA
1 TTTTGTATTATA-ATT-TTATA
* *
33777383 TTTTTTTTTATAATTTTATA
1 TTTTGTATTATAATTTTATA
33777403 T
1 T
33777404 CTTTTTCAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 3 0.16
22 10 0.53
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTGTATTATAATTTTATA
Found at i:33777401 original size:20 final size:23
Alignment explanation
Indices: 33777368--33777409 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
33777358 TTGTTTTGTA
33777368 TTATATATTATTATAT-TTTTTT
1 TTATATATTATTATATCTTTTTT
33777390 TTATA-ATT-TTATATCTTTTT
1 TTATATATTATTATATCTTTTT
33777410 CAGTTCTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 8 0.42
22 5 0.26
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (23 bp):
TTATATATTATTATATCTTTTTT
Found at i:33778802 original size:27 final size:27
Alignment explanation
Indices: 33778764--33778903 Score: 185
Period size: 27 Copynumber: 5.2 Consensus size: 27
33778754 CATAACAGTT
33778764 ATTTTACCCTATGGGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
33778791 ATTTTACCCTATAGGGGGGTATTTCGGTC
1 ATTTTACCCTAT--GGGGGTATTTCGGTC
*
33778820 ATTCTACCCTAT--GGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * *
33778845 ATTTTACCTTATGGAGGTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * *
33778872 ATTTTTCCCTATGAGGGTATTTCGGTT
1 ATTTTACCCTATGGGGGTATTTCGGTC
33778899 ATTTT
1 ATTTT
33778904 TCCTTATTTT
Statistics
Matches: 98, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
25 23 0.23
27 49 0.50
29 26 0.27
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.44
Consensus pattern (27 bp):
ATTTTACCCTATGGGGGTATTTCGGTC
Found at i:33786725 original size:28 final size:27
Alignment explanation
Indices: 33786632--33786767 Score: 130
Period size: 28 Copynumber: 4.9 Consensus size: 27
33786622 AATTTTGGGT
* * *
33786632 CAAAACTGTAAAATGTGCAAAATAGGGG
1 CAAAACTATAAAATCT-AAAAATAGGGG
* *
33786660 -AAAACTGTAAAATCTGAAAATAGGGG
1 CAAAACTATAAAATCTAAAAATAGGGG
*
33786686 CAAAACTGTAAAATCTAAAAATCAGGGG
1 CAAAACTATAAAATCTAAAAAT-AGGGG
* * * *
33786714 AAAAATTATAAAATCTAAAAAACAGTGG
1 CAAAACTATAAAATCT-AAAAATAGGGG
*
33786742 CAAAACTATAAAATTTGAAAAATAGG
1 CAAAACTATAAAATCT-AAAAATAGG
33786768 AGACACACGA
Statistics
Matches: 91, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
26 10 0.11
27 34 0.37
28 42 0.46
29 5 0.05
ACGTcount: A:0.53, C:0.10, G:0.18, T:0.20
Consensus pattern (27 bp):
CAAAACTATAAAATCTAAAAATAGGGG
Found at i:33788430 original size:15 final size:15
Alignment explanation
Indices: 33788410--33788445 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
33788400 GACAACCAAC
33788410 TGAATGGGCATGATT
1 TGAATGGGCATGATT
33788425 TGAATGGGCATGATT
1 TGAATGGGCATGATT
33788440 TGAATG
1 TGAATG
33788446 TAGGTACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.06, G:0.33, T:0.33
Consensus pattern (15 bp):
TGAATGGGCATGATT
Found at i:33791663 original size:23 final size:23
Alignment explanation
Indices: 33791633--33791686 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
33791623 AATTAAAACT
33791633 AGTTCAATTTAAACATACATCAA
1 AGTTCAATTTAAACATACATCAA
33791656 AGTTCAATTTAAACATACATCAA
1 AGTTCAATTTAAACATACATCAA
*
33791679 AGCTCAAT
1 AGTTCAAT
33791687 CGAACATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.30
Consensus pattern (23 bp):
AGTTCAATTTAAACATACATCAA
Found at i:33793395 original size:16 final size:17
Alignment explanation
Indices: 33793374--33793405 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
33793364 AAATATGCAA
33793374 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
33793390 TCACATAACTTCATAT
1 TCACATAACTTCATAT
33793406 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:33793631 original size:42 final size:41
Alignment explanation
Indices: 33793608--33793720 Score: 122
Period size: 41 Copynumber: 2.7 Consensus size: 41
33793598 ATCACATATC
*
33793608 ATGCCACTGTCCCAAACAGGGTCTTACACAAATCAAATACG
1 ATGCCAATGTCCCAAACAGGGTCTTACACAAATCAAATACG
* **
33793649 ATGCCAATGTCCCAAACATGGTCTTACACGTATACACAAGT-CG
1 ATGCCAATGTCCCAAACAGGGTCTTACACAAAT-CA-AA-TACG
* *
33793692 ATGCCAACGTCCCAGAC-GTGGTCTTACAC
1 ATGCCAATGTCCCAAACAG-GGTCTTACAC
33793721 GAAAATGCAT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
41 29 0.48
42 2 0.03
43 29 0.48
44 1 0.02
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (41 bp):
ATGCCAATGTCCCAAACAGGGTCTTACACAAATCAAATACG
Found at i:33798764 original size:22 final size:23
Alignment explanation
Indices: 33798734--33798776 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
33798724 GCACCAAAAC
* *
33798734 AGGCTTTTAGTGGC-CTTTTTTT
1 AGGCCTTTAGCGGCTCTTTTTTT
33798756 AGGCCTTTAGCGGCTCTTTTT
1 AGGCCTTTAGCGGCTCTTTTT
33798777 AACGCCGCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.09, C:0.19, G:0.23, T:0.49
Consensus pattern (23 bp):
AGGCCTTTAGCGGCTCTTTTTTT
Found at i:33798905 original size:43 final size:43
Alignment explanation
Indices: 33798844--33798925 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
33798834 GACAACGCCA
* * *
33798844 CTAAAGAACAAGACCTTTAGCGGCGCTTCTATCACAAACTCCG
1 CTAAAGAACAAGACCTTTAGCGACGCTTATACCACAAACTCCG
* *
33798887 CTAAAGATCATGACCTTTAGCGACGCTTATACCACAAAC
1 CTAAAGAACAAGACCTTTAGCGACGCTTATACCACAAAC
33798926 GCCACTATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (43 bp):
CTAAAGAACAAGACCTTTAGCGACGCTTATACCACAAACTCCG
Found at i:33803470 original size:22 final size:22
Alignment explanation
Indices: 33803416--33803473 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
33803406 GTATGTTTGT
*
33803416 AAAGTTGGGGGTTTCAAGGGGG
1 AAAGTTGGGGATTTCAAGGGGG
* *
33803438 AAA-TTAGGGATTT-TAGGGGAG
1 AAAGTTGGGGATTTCAAGGGG-G
33803459 AAAGTTGGGGATTTC
1 AAAGTTGGGGATTTC
33803474 GGGGGAGGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
20 5 0.17
21 12 0.41
22 12 0.41
ACGTcount: A:0.28, C:0.03, G:0.41, T:0.28
Consensus pattern (22 bp):
AAAGTTGGGGATTTCAAGGGGG
Found at i:33803478 original size:22 final size:22
Alignment explanation
Indices: 33803416--33803480 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
33803406 GTATGTTTGT
*
33803416 AAAGTTGGGGGTTTCAAGGGG-G
1 AAAGTTGGGGATTTC-AGGGGAG
* *
33803438 AAA-TTAGGGATTTTAGGGGAG
1 AAAGTTGGGGATTTCAGGGGAG
*
33803459 AAAGTTGGGGATTTCGGGGGAG
1 AAAGTTGGGGATTTCAGGGGAG
33803481 GAGATTTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 5 0.14
21 12 0.34
22 18 0.51
ACGTcount: A:0.26, C:0.03, G:0.46, T:0.25
Consensus pattern (22 bp):
AAAGTTGGGGATTTCAGGGGAG
Found at i:33803622 original size:105 final size:106
Alignment explanation
Indices: 33803488--33803699 Score: 329
Period size: 107 Copynumber: 2.0 Consensus size: 106
33803478 GAGGAGATTT
* *
33803488 TATAAAATGGGCTATTTTTTTAAAGTAAAA-TA-TTTTTGTGGCTTTTTTTATAAAAACGCCGCA
1 TATAAAATGGGCTATTTTTTAAAAGTAAAATTATTTTTTGTGGCGTTTTTTATAAAAACGCCGCA
*
33803551 AAAAATTATTTCATTTGGAATAAAACAACACTGTTTTGCTA
66 AAAAATTATTTCATTTGAAATAAAACAACACTGTTTTGCTA
**
33803592 TATAAAATGGTGCTATTTTTTAAAAGTAAAATTATTTTTTGTGGCGTTTTTTATAAAAACGTTGC
1 TATAAAATGG-GCTATTTTTTAAAAGTAAAATTATTTTTTGTGGCGTTTTTTATAAAAACGCCGC
** *
33803657 AAAAAATTATTTCATTTGAAATAAAATGACATTGTTTTGCTA
65 AAAAAATTATTTCATTTGAAATAAAACAACACTGTTTTGCTA
33803699 T
1 T
33803700 GCTAAAAATA
Statistics
Matches: 97, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
104 10 0.10
105 19 0.20
106 2 0.02
107 66 0.68
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.42
Consensus pattern (106 bp):
TATAAAATGGGCTATTTTTTAAAAGTAAAATTATTTTTTGTGGCGTTTTTTATAAAAACGCCGCA
AAAAATTATTTCATTTGAAATAAAACAACACTGTTTTGCTA
Found at i:33803718 original size:24 final size:22
Alignment explanation
Indices: 33803691--33803736 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
33803681 AATGACATTG
33803691 TTTTGCTATGCTAAAAATATTTTA
1 TTTTG-TATGCTAAAAAT-TTTTA
* *
33803715 TTTTGTCTGTTAAAAATTTTTA
1 TTTTGTATGCTAAAAATTTTTA
33803737 GTTAAGTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 10 0.50
24 5 0.25
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.54
Consensus pattern (22 bp):
TTTTGTATGCTAAAAATTTTTA
Found at i:33804512 original size:21 final size:22
Alignment explanation
Indices: 33804488--33804544 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
33804478 GATCCTAAAT
33804488 CTCTAAACCCTAAATCACTAA-
1 CTCTAAACCCTAAATCACTAAC
* * *
33804509 CTCTTAACCCCAAATCCCTAAC
1 CTCTAAACCCTAAATCACTAAC
* *
33804531 CACTAACCCCTAAA
1 CTCTAAACCCTAAA
33804545 CTTTATTTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.39, C:0.40, G:0.00, T:0.21
Consensus pattern (22 bp):
CTCTAAACCCTAAATCACTAAC
Found at i:33804781 original size:14 final size:15
Alignment explanation
Indices: 33804762--33804794 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
33804752 CTTAAATTAG
33804762 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
33804776 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
33804791 AATC
1 AATC
33804795 TACAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:33805318 original size:82 final size:83
Alignment explanation
Indices: 33805179--33805402 Score: 249
Period size: 82 Copynumber: 2.7 Consensus size: 83
33805169 ATGTTTTTGT
** * * **
33805179 GGCGCTTTTTCAAAAACGCCGCTAAAGCCCCAAGCATTAGTGGCG-CTTCTTGGAAAACGGCT-C
1 GGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGCCTT-TTCAAAAACGGCTGC
*
33805242 TAAAG-CCTCGAGCATTAGC
65 TAAAGATCT-GAGCATTAGC
* * *
33805261 GGCGCTTCTTGAAAAACGCCGCTAAAGCCCTGAGTATTAGCGACGCCTTTTCAAAAAC-GCTGCT
1 GGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGCCTTTTCAAAAACGGCTGCT
33805325 AAAGATCTGAGCATTAGC
66 AAAGATCTGAGCATTAGC
* * ** * *
33805343 AGCGCTTTTTCAAAAACGCCGTTAAAGATCTGAGCATTAGCGACGCTTTTTTTAAAAACG
1 GGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGC-CTTTTCAAAAACG
33805403 CCGTTAAAGC
Statistics
Matches: 118, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
81 3 0.03
82 100 0.85
83 15 0.13
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (83 bp):
GGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGCCTTTTCAAAAACGGCTGCT
AAAGATCTGAGCATTAGC
Found at i:33805407 original size:42 final size:41
Alignment explanation
Indices: 33805181--33805411 Score: 214
Period size: 41 Copynumber: 5.6 Consensus size: 41
33805171 GTTTTTGTGG
** ** * *
33805181 CGCTTTTTCAAAAACGCCGCTAAAGCCCCAAGCATTAGTGG
1 CGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGA
* ** * * * *
33805222 CGCTTCTTGGAAAACGGCTCTAAAG-CCTCGAGCATTAGCGG
1 CGCTTTTTCAAAAACGCCGCTAAAGATCT-GAGCATTAGCGA
* * ** *
33805263 CGCTTCTTGAAAAACGCCGCTAAAGCCCTGAGTATTAGCGA
1 CGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGA
* *
33805304 CGCCTTTTCAAAAACGCTGCTAAAGATCTGAGCATTAGC-A
1 CGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGA
*
33805344 GCGCTTTTTCAAAAACGCCGTTAAAGATCTGAGCATTAGCGA
1 -CGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGA
* *
33805386 CGCTTTTTTTAAAAACGCCGTTAAAG
1 CGC-TTTTTCAAAAACGCCGCTAAAG
33805412 CCCCAAAAGG
Statistics
Matches: 161, Mismatches: 24, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
40 3 0.02
41 133 0.83
42 25 0.16
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (41 bp):
CGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGA
Found at i:33820345 original size:17 final size:17
Alignment explanation
Indices: 33820325--33820363 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
33820315 TCAAAAATAA
*
33820325 TAATATTTTAA-TAGATT
1 TAATA-TTTAATTAAATT
33820342 TAATATTTAATTAAATT
1 TAATATTTAATTAAATT
33820359 TAATA
1 TAATA
33820364 CTTATCTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TAATATTTAATTAAATT
Found at i:33825672 original size:16 final size:16
Alignment explanation
Indices: 33825651--33825690 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
33825641 TAAAAGAGGA
33825651 TTCGCCAATGCTAGTG
1 TTCGCCAATGCTAGTG
33825667 TTCGCCAATGCTAGTG
1 TTCGCCAATGCTAGTG
33825683 TTCGCCAA
1 TTCGCCAA
33825691 AACATAGGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.30
Consensus pattern (16 bp):
TTCGCCAATGCTAGTG
Found at i:33828459 original size:29 final size:29
Alignment explanation
Indices: 33828427--33828501 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
33828417 TGGCAGTCGG
*
33828427 AGCCACACGAGTGTGTGTTTGGCCGTGTA
1 AGCCACACGAGTGTGTGTCTGGCCGTGTA
* * * * * *
33828456 AGCCACAAGGGCGTTTGTCTGGCTGTGTG
1 AGCCACACGAGTGTGTGTCTGGCCGTGTA
33828485 AGCCACACGAGTGTGTG
1 AGCCACACGAGTGTGTG
33828502 CTTAGTCGTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.17, C:0.21, G:0.36, T:0.25
Consensus pattern (29 bp):
AGCCACACGAGTGTGTGTCTGGCCGTGTA
Found at i:33839553 original size:19 final size:19
Alignment explanation
Indices: 33839513--33839556 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
33839503 ATTTTCTAAC
*
33839513 TTTTATATTTTATTAGAAT
1 TTTTATATTATATTAGAAT
*
33839532 TTTTATATTAT-TTATAAGT
1 TTTTATATTATATTAGAA-T
33839551 TTTTAT
1 TTTTAT
33839557 GAATTTTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTTATATTATATTAGAAT
Found at i:33840524 original size:16 final size:17
Alignment explanation
Indices: 33840502--33840539 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
33840492 TAACTTGAAA
33840502 ATTTTATATAAAAATAT
1 ATTTTATATAAAAATAT
33840519 -TTTTATATAAAAATAT
1 ATTTTATATAAAAATAT
33840535 ATTTT
1 ATTTT
33840540 TTTTTCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTATATAAAAATAT
Found at i:33843129 original size:16 final size:14
Alignment explanation
Indices: 33843104--33843145 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
33843094 CCTTATCTTT
*
33843104 ATTTTATTTATATTC
1 ATTTTTTTTAT-TTC
33843119 AATTTTTTTTATTTC
1 -ATTTTTTTTATTTC
33843134 -TTTTTTTTATTT
1 ATTTTTTTTATTT
33843146 ATCCATCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 12 0.48
15 3 0.12
16 10 0.40
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (14 bp):
ATTTTTTTTATTTC
Found at i:33844492 original size:32 final size:32
Alignment explanation
Indices: 33844456--33844517 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
33844446 AGCTCTTGGT
*
33844456 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
1 TTTTTCATGTTGTCAAAAAGTTGAACAATGGA
* *
33844488 TTTTTCGTGTTGTTAAAAAGTTGAACAATG
1 TTTTTCATGTTGTCAAAAAGTTGAACAATG
33844518 AAAATAGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (32 bp):
TTTTTCATGTTGTCAAAAAGTTGAACAATGGA
Found at i:33845570 original size:19 final size:19
Alignment explanation
Indices: 33845546--33845585 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
33845536 TATAATTTTG
33845546 ATCAAATAAAATT-AAATTA
1 ATCAAAT-AAATTAAAATTA
*
33845565 ATCAAATTAATTAAAATTA
1 ATCAAATAAATTAAAATTA
33845584 AT
1 AT
33845586 ATAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Found at i:33846786 original size:35 final size:35
Alignment explanation
Indices: 33846695--33846936 Score: 289
Period size: 35 Copynumber: 7.1 Consensus size: 35
33846685 GTCCAAAAAG
* * * *
33846695 AAATAATACATGAACAGGAGAGATTCCCTGTAA-G
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
* *
33846729 AAATTAT--GTGAATAGGAGAGATTCCCTGCAACA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
*
33846762 AAATAATGCGTGAACAGGAAAGATTCCCTGCAACA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
*
33846797 AAATAATGTGTGAACAGGAGAGATTCCCTGCAACA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
* *
33846832 AAATAATGCGTGAACAGGAGGGATTCCCTGCAA-G
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
* * *
33846866 AAATGAT--GTGAACAGGAAAGATTCCCTGTAACA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
* * * *
33846899 GAATAATGCGTGAACAGGAAATATTCCCTGCAAGA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
33846934 AAA
1 AAA
33846937 GACAAGTGAA
Statistics
Matches: 178, Mismatches: 24, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
32 42 0.24
33 11 0.06
34 12 0.07
35 113 0.63
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (35 bp):
AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
Found at i:33846913 original size:67 final size:67
Alignment explanation
Indices: 33846695--33846935 Score: 329
Period size: 67 Copynumber: 3.6 Consensus size: 67
33846685 GTCCAAAAAG
* * * * * *
33846695 AAATAATACATGAACAGGAGAGATTCCCTGTAAGAAATTATGTGAATAGGAGAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAAAGATTCCCTGCAAGAAATAATGTGAACAGGAGAGATTCCCTGCAA
33846760 CA
66 CA
*
33846762 AAATAATGCGTGAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTG
1 AAATAATGCGTGAACAGGAAAGATTCCCTGCAA-GAAATAA--TGTGAACAGGAGAGATTCCCTG
33846827 CAACA
63 CAACA
** * * *
33846832 AAATAATGCGTGAACAGGAGGGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGTAA
1 AAATAATGCGTGAACAGGAAAGATTCCCTGCAAGAAATAATGTGAACAGGAGAGATTCCCTGCAA
33846897 CA
66 CA
* *
33846899 GAATAATGCGTGAACAGGAAATATTCCCTGCAAGAAA
1 AAATAATGCGTGAACAGGAAAGATTCCCTGCAAGAAA
33846936 AGACAAGTGA
Statistics
Matches: 154, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
67 87 0.56
68 5 0.03
69 5 0.03
70 57 0.37
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (67 bp):
AAATAATGCGTGAACAGGAAAGATTCCCTGCAAGAAATAATGTGAACAGGAGAGATTCCCTGCAA
CA
Found at i:33851569 original size:20 final size:22
Alignment explanation
Indices: 33851539--33851582 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
33851529 AGAAAAAGAG
33851539 AAATACAAAAA-AGAATAG-ATC
1 AAATACAAAAAGA-AATAGAATC
33851560 AAAT-CAAAAAGAAATAGAATC
1 AAATACAAAAAGAAATAGAATC
33851581 AA
1 AA
33851583 CAATTTGCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.68, C:0.09, G:0.09, T:0.14
Consensus pattern (22 bp):
AAATACAAAAAGAAATAGAATC
Found at i:33854428 original size:32 final size:33
Alignment explanation
Indices: 33854377--33854618 Score: 319
Period size: 32 Copynumber: 7.2 Consensus size: 33
33854367 CAGGTCCAAA
*
33854377 AAGAAATAATACATGAACAGGAGAGATTCCCTGC
1 AAGAAATAAT-CGTGAACAGGAGAGATTCCCTGC
*
33854411 AAGAAATTAT-GTGAACAGGAGAGATTCCCTGC
1 AAGAAATAATCGTGAACAGGAGAGATTCCCTGC
*
33854443 AACAAAATAATGCGTGAACAGGAGAGATTCCCTGC
1 AA-GAAATAAT-CGTGAACAGGAGAGATTCCCTGC
*
33854478 AAGAAATGAT-GTGAACAGGAGAGATTCCCTGC
1 AAGAAATAATCGTGAACAGGAGAGATTCCCTGC
*
33854510 AACAAAATAATGCGTGAACAGGAGAGATTCCCTGC
1 AA-GAAATAAT-CGTGAACAGGAGAGATTCCCTGC
* *
33854545 AAGAAATGAT-GTGAACAGGAAAGATTCCCTGC
1 AAGAAATAATCGTGAACAGGAGAGATTCCCTGC
* *
33854577 AACAAAATAATGCGTGAACAGGAGAGATTCCCTAC
1 AA-GAAATAAT-CGTGAACAGGAGAGATTCCCTGC
33854612 AAGAAAT
1 AAGAAAT
33854619 GAACAGAACA
Statistics
Matches: 183, Mismatches: 16, Indels: 18
0.84 0.07 0.08
Matches are distributed among these distances:
32 70 0.38
33 18 0.10
34 25 0.14
35 70 0.38
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.18
Consensus pattern (33 bp):
AAGAAATAATCGTGAACAGGAGAGATTCCCTGC
Found at i:33854490 original size:67 final size:67
Alignment explanation
Indices: 33854380--33854620 Score: 437
Period size: 67 Copynumber: 3.6 Consensus size: 67
33854370 GTCCAAAAAG
* * *
33854380 AAATAATACATGAACAGGAGAGATTCCCTGCAAGAAATTATGTGAACAGGAGAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
33854445 CA
66 CA
33854447 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
33854512 CA
66 CA
*
33854514 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
33854579 CA
66 CA
*
33854581 AAATAATGCGTGAACAGGAGAGATTCCCTACAAGAAATGA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGA
33854621 ACAGAACAGG
Statistics
Matches: 169, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 169 1.00
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.18
Consensus pattern (67 bp):
AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
CA
Found at i:33858570 original size:20 final size:22
Alignment explanation
Indices: 33858540--33858583 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
33858530 AGAAAAAGAG
33858540 AAATACAAAAA-AGAATAG-ATC
1 AAATACAAAAAGA-AATAGAATC
33858561 AAAT-CAAAAAGAAATAGAATC
1 AAATACAAAAAGAAATAGAATC
33858582 AA
1 AA
33858584 CAATTTGCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.68, C:0.09, G:0.09, T:0.14
Consensus pattern (22 bp):
AAATACAAAAAGAAATAGAATC
Found at i:33861471 original size:35 final size:35
Alignment explanation
Indices: 33861383--33861608 Score: 263
Period size: 35 Copynumber: 6.7 Consensus size: 35
33861373 GTCCAAAAAG
* * *
33861383 AAATAATACATGAACAGGAGAGATTCCCTGCAA-G
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
*
33861417 AAATGAT--GTGAACAGGAGAGATTCCCTGCAACA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
* * *
33861450 AAATAATGCGTGAACATGAGAGATTCCCTACAA-G
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
* *
33861484 AAATGAT--GTGAACAGGAAAGATTCCCTGCAACA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
* *
33861517 AAATAATGTGTGAACAGGAGAGATTCCCTGTAACA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
*
33861552 AAATAATGCGTGAACAGGAGAGATTCCCTGCAA-G
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
* *
33861586 AAATGAT--GTGAACAGGAAAGATT
1 AAATAATGCGTGAACAGGAGAGATT
33861609 ATTTTGGTGG
Statistics
Matches: 166, Mismatches: 20, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
32 59 0.36
33 12 0.07
34 18 0.11
35 77 0.46
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (35 bp):
AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
Found at i:33861491 original size:67 final size:67
Alignment explanation
Indices: 33861383--33861608 Score: 289
Period size: 67 Copynumber: 3.4 Consensus size: 67
33861373 GTCCAAAAAG
* * *
33861383 AAATAATACATGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTACAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
33861448 CA
66 CA
* *
33861450 AAATAATGCGTGAACATGAGAGATTCCCTACAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTACAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
33861515 CA
66 CA
* * *
33861517 AAATAATGTGTGAACAGGAGAGATTCCCTGTAACAAAATAATG-CGTGAACAGGAGAGATTCCCT
1 AAATAATGCGTGAACAGGAGAGATTCCC--T-ACAAGA-AATGATGTGAACAGGAGAGATTCCCT
*
33861581 GCAA-G
62 GCAACA
* *
33861586 AAATGAT--GTGAACAGGAAAGATT
1 AAATAATGCGTGAACAGGAGAGATT
33861609 ATTTTGGTGG
Statistics
Matches: 142, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
67 103 0.73
69 7 0.05
70 28 0.20
71 4 0.03
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (67 bp):
AAATAATGCGTGAACAGGAGAGATTCCCTACAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
CA
Found at i:33861566 original size:102 final size:99
Alignment explanation
Indices: 33861393--33861608 Score: 351
Period size: 102 Copynumber: 2.2 Consensus size: 99
33861383 AAATAATACA
* * *
33861393 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAACAAAATAATG
1 TGAACAGGAAAGATTCCCTGCAAAAAATAATGTGAACAGGAGAGATTCCCTGCAACAAAATAATG
*
33861458 CGTGAACATGAGAGATTCCCTACAAGAAATGATG
66 CGTGAACAGGAGAGATTCCCTACAAGAAATGATG
*
33861492 TGAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTGTAACAAAATA
1 TGAACAGGAAAGATTCCCTGCAA-AAAATAA--TGTGAACAGGAGAGATTCCCTGCAACAAAATA
*
33861557 ATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATG
63 ATGCGTGAACAGGAGAGATTCCCTACAAGAAATGATG
33861594 TGAACAGGAAAGATT
1 TGAACAGGAAAGATT
33861609 ATTTTGGTGG
Statistics
Matches: 108, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
99 22 0.20
100 5 0.05
102 81 0.75
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.19
Consensus pattern (99 bp):
TGAACAGGAAAGATTCCCTGCAAAAAATAATGTGAACAGGAGAGATTCCCTGCAACAAAATAATG
CGTGAACAGGAGAGATTCCCTACAAGAAATGATG
Found at i:33862313 original size:48 final size:48
Alignment explanation
Indices: 33862237--33862334 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
33862227 GGATCTGAGG
33862237 ACCGAATTGGTAATGATATATTTGTAATTTGAAAGCTTAAGTTTGAAA
1 ACCGAATTGGTAATGATATATTTGTAATTTGAAAGCTTAAGTTTGAAA
*
33862285 ACCGGATTGGTAATGATATATTTGTAATTTGAAAGCTTAAGTTTGAAA
1 ACCGAATTGGTAATGATATATTTGTAATTTGAAAGCTTAAGTTTGAAA
33862333 AC
1 AC
33862335 TTAATTTGAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (48 bp):
ACCGAATTGGTAATGATATATTTGTAATTTGAAAGCTTAAGTTTGAAA
Found at i:33862344 original size:13 final size:13
Alignment explanation
Indices: 33862309--33862346 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
33862299 GATATATTTG
*
33862309 TAATTTGAAAGCT
1 TAATTTGAAAACT
33862322 TAAGTTTGAAAACT
1 TAA-TTTGAAAACT
33862336 TAATTTGAAAA
1 TAATTTGAAAA
33862347 TTTGGAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (13 bp):
TAATTTGAAAACT
Found at i:33864061 original size:20 final size:23
Alignment explanation
Indices: 33864026--33864070 Score: 69
Period size: 20 Copynumber: 2.1 Consensus size: 23
33864016 GAGCAAATCG
33864026 TTGATTCTATTTCTTTTTTG-AT
1 TTGATTCTATTTCTTTTTTGTAT
33864048 TTGA-TCTA-TTCTTTTTTGTAT
1 TTGATTCTATTTCTTTTTTGTAT
33864069 TT
1 TT
33864071 CTCTTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 8 0.36
22 4 0.18
ACGTcount: A:0.13, C:0.09, G:0.09, T:0.69
Consensus pattern (23 bp):
TTGATTCTATTTCTTTTTTGTAT
Found at i:33871797 original size:23 final size:22
Alignment explanation
Indices: 33871752--33871807 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
33871742 GAGAGAATGC
**
33871752 AAAAAAAAAGAGCATGAGGGAA
1 AAAAAAAAAGAGCATGAAAGAA
33871774 AAGAAAAAAAGAGCGAT-AAAGAA
1 AA-AAAAAAAGAGC-ATGAAAGAA
*
33871797 AAAATAAAAGA
1 AAAAAAAAAGA
33871808 AAAACAAGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 10 0.34
23 17 0.59
24 2 0.07
ACGTcount: A:0.70, C:0.04, G:0.21, T:0.05
Consensus pattern (22 bp):
AAAAAAAAAGAGCATGAAAGAA
Found at i:33874950 original size:55 final size:55
Alignment explanation
Indices: 33874875--33874979 Score: 158
Period size: 55 Copynumber: 1.9 Consensus size: 55
33874865 TAAAGTTGTG
* **
33874875 TTTATGTTTCATTGAATGTTTTGTTGTATTCATAAATAAAGTTGTGTTTTCTTTA
1 TTTATGTTTCATTGAATGTTTTGTTGCATTCATAAATAAAGCGGTGTTTTCTTTA
*
33874930 TTTATGTTTTATT-AATTGTTTTGTTGCATTCATAAATAAAGCGGTGTTTT
1 TTTATGTTTCATTGAA-TGTTTTGTTGCATTCATAAATAAAGCGGTGTTTT
33874980 TAATTATGCT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 2 0.04
55 43 0.96
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.55
Consensus pattern (55 bp):
TTTATGTTTCATTGAATGTTTTGTTGCATTCATAAATAAAGCGGTGTTTTCTTTA
Found at i:33874997 original size:55 final size:52
Alignment explanation
Indices: 33874891--33875012 Score: 124
Period size: 55 Copynumber: 2.3 Consensus size: 52
33874881 TTTCATTGAA
* * * *
33874891 TGTTTTGTTGTATTCATAAATAAAGTTGTGTTTTCTTTATTTATGTTTTATTAAT
1 TGTTTTGTTGCATTCATAAATAAAGTCGTGTGTTCTTTAATTATGTTTTA-T--T
33874946 TGTTTTGTTGCATTCATAAATAAAG-CG-GTGTT-TTTAATTATGCTTCATTATT
1 TGTTTTGTTGCATTCATAAATAAAGTCGTGTGTTCTTTAATTATG-TT--TTATT
33874998 TGTTTTTGTTGCATT
1 TG-TTTTGTTGCATT
33875013 TATTTTTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
52 12 0.20
53 18 0.31
54 2 0.03
55 27 0.46
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.57
Consensus pattern (52 bp):
TGTTTTGTTGCATTCATAAATAAAGTCGTGTGTTCTTTAATTATGTTTTATT
Found at i:33884447 original size:2 final size:2
Alignment explanation
Indices: 33884440--33884469 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
33884430 AAATATACCA
33884440 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
33884470 TAATTGTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33886860 original size:10 final size:11
Alignment explanation
Indices: 33886834--33886866 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
33886824 AGTTAAGATT
33886834 AAAACTTCTGGA
1 AAAACTTCT-GA
33886846 AAAACTTCT-A
1 AAAACTTCTGA
33886856 AAAACTTCTGA
1 AAAACTTCTGA
33886867 TAAATACTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 1 0.05
12 9 0.45
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.27
Consensus pattern (11 bp):
AAAACTTCTGA
Found at i:33892536 original size:17 final size:18
Alignment explanation
Indices: 33892514--33892547 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
33892504 CATTTTTGGC
33892514 GTGTGGGT-CACACGGGT
1 GTGTGGGTCCACACGGGT
33892531 GTGTGGGTCCACACGGG
1 GTGTGGGTCCACACGGG
33892548 CATGTGGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.12, C:0.21, G:0.47, T:0.21
Consensus pattern (18 bp):
GTGTGGGTCCACACGGGT
Found at i:33892553 original size:18 final size:17
Alignment explanation
Indices: 33892515--33892554 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
33892505 ATTTTTGGCG
**
33892515 TGTGGGTCACACGGGTG
1 TGTGGGTCACACGGGCA
33892532 TGTGGGTCCACACGGGCA
1 TGTGGGT-CACACGGGCA
33892550 TGTGG
1 TGTGG
33892555 TTATGGGCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.12, C:0.20, G:0.45, T:0.23
Consensus pattern (17 bp):
TGTGGGTCACACGGGCA
Found at i:33896459 original size:21 final size:22
Alignment explanation
Indices: 33896418--33896461 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
33896408 CTTATTTTGT
*
33896418 GGAGAAATAAGAGGTGAGAGAA
1 GGAGAAATAAGAGGGGAGAGAA
33896440 GGAGAAATAA-AGGGGAGAGAA
1 GGAGAAATAAGAGGGGAGAGAA
33896461 G
1 G
33896462 TATGTTCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.50, C:0.00, G:0.43, T:0.07
Consensus pattern (22 bp):
GGAGAAATAAGAGGGGAGAGAA
Found at i:33899572 original size:22 final size:21
Alignment explanation
Indices: 33899547--33899611 Score: 57
Period size: 22 Copynumber: 3.2 Consensus size: 21
33899537 TTATATAGTG
33899547 ACAAAACATTTAAGCATCTATC
1 ACAAAACATTTAAGCAT-TATC
* * *
33899569 ACAATAC--TT-A-TATAATC
1 ACAAAACATTTAAGCATTATC
33899586 ACAAAACATTTAAGCATATATC
1 ACAAAACATTTAAGCAT-TATC
33899608 ACAA
1 ACAA
33899612 TACTCATATA
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
17 9 0.28
18 2 0.06
19 3 0.09
20 3 0.09
21 2 0.06
22 13 0.41
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.28
Consensus pattern (21 bp):
ACAAAACATTTAAGCATTATC
Found at i:33899577 original size:39 final size:39
Alignment explanation
Indices: 33899516--33899654 Score: 188
Period size: 39 Copynumber: 3.6 Consensus size: 39
33899506 CATATTCACT
* * * * *
33899516 TTTAAGTATATATCGCATTACTTATATAGTGACAAAACA
1 TTTAAGCATATATCACAATACTTATATAATCACAAAACA
*
33899555 TTTAAGCATCTATCACAATACTTATATAATCACAAAACA
1 TTTAAGCATATATCACAATACTTATATAATCACAAAACA
* * *
33899594 TTTAAGCATATATCACAATACTCATATAATCACAGAATA
1 TTTAAGCATATATCACAATACTTATATAATCACAAAACA
*
33899633 TTTAAGCATATATCGCAATACT
1 TTTAAGCATATATCACAATACT
33899655 CAAAAACATG
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 89 1.00
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.33
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTTATATAATCACAAAACA
Found at i:33899588 original size:17 final size:17
Alignment explanation
Indices: 33899566--33899627 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
33899556 TTAAGCATCT
33899566 ATCACAATACTTATATA
1 ATCACAATACTTATATA
* *
33899583 ATCACAAAACATTTAAGCATA
1 ATCACAATAC--TT-A-TATA
*
33899604 TATCACAATACTCATATA
1 -ATCACAATACTTATATA
33899622 ATCACA
1 ATCACA
33899628 GAATATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
17 15 0.43
18 3 0.09
19 3 0.09
20 2 0.06
21 3 0.09
22 9 0.26
ACGTcount: A:0.48, C:0.21, G:0.02, T:0.29
Consensus pattern (17 bp):
ATCACAATACTTATATA
Found at i:33901265 original size:32 final size:32
Alignment explanation
Indices: 33901229--33901320 Score: 184
Period size: 32 Copynumber: 2.9 Consensus size: 32
33901219 TTTCTAAAAA
33901229 ACCATAATCGAAAACATTACCAATAAACCATG
1 ACCATAATCGAAAACATTACCAATAAACCATG
33901261 ACCATAATCGAAAACATTACCAATAAACCATG
1 ACCATAATCGAAAACATTACCAATAAACCATG
33901293 ACCATAATCGAAAACATTACCAATAAAC
1 ACCATAATCGAAAACATTACCAATAAAC
33901321 TATGTCACAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.51, C:0.25, G:0.05, T:0.18
Consensus pattern (32 bp):
ACCATAATCGAAAACATTACCAATAAACCATG
Found at i:33901318 original size:19 final size:18
Alignment explanation
Indices: 33901229--33901314 Score: 80
Period size: 18 Copynumber: 5.2 Consensus size: 18
33901219 TTTCTAAAAA
33901229 ACCATAATCGAAAACATT
1 ACCATAATCGAAAACATT
* *
33901247 ACC--AAT--AAACCATG
1 ACCATAATCGAAAACATT
33901261 ACCATAATCGAAAACATT
1 ACCATAATCGAAAACATT
* *
33901279 ACC--AAT--AAACCATG
1 ACCATAATCGAAAACATT
33901293 ACCATAATCGAAAACATT
1 ACCATAATCGAAAACATT
33901311 ACCA
1 ACCA
33901315 ATAAACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
14 18 0.35
16 12 0.23
18 22 0.42
ACGTcount: A:0.50, C:0.26, G:0.06, T:0.19
Consensus pattern (18 bp):
ACCATAATCGAAAACATT
Found at i:33913001 original size:125 final size:125
Alignment explanation
Indices: 33912779--33913067 Score: 463
Period size: 125 Copynumber: 2.3 Consensus size: 125
33912769 TTTTTTTAAG
* ** *
33912779 GAAATCACTCCCATGTGGACACGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTTGAGTAGAC
1 GAAATCACTCCCATGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCAAGTAGAA
*
33912844 GTTTCTGAGCAAATAATGTCAAAAATGCTTTAAACAGGATGCATTGTCAGCAAAAGTACT
66 GTTTCTGAGCAAATAATGTCAAAAACGCTTTAAACAGGATGCATTGTCAGCAAAAGTACT
* *
33912904 GAAATCGA-TCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCAAGTAGA
1 GAAATC-ACTCCCATGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCAAGTAGA
* * *
33912968 AGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACT
65 AGTTTCTGAGCAAATAATGTCAAAAACGCTTTAAACAGGATGCATTGTCAGCAAAAGTACT
*
33913029 GAAATCACTTCCATGTGGACGCGCTTTTGCTACAGTAGC
1 GAAATCACTCCCATGTGGACGCGCTTTTGCTACAGTAGC
33913068 GCATGTTTGG
Statistics
Matches: 150, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
124 1 0.01
125 148 0.99
126 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (125 bp):
GAAATCACTCCCATGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCAAGTAGAA
GTTTCTGAGCAAATAATGTCAAAAACGCTTTAAACAGGATGCATTGTCAGCAAAAGTACT
Found at i:33913625 original size:24 final size:24
Alignment explanation
Indices: 33913598--33913643 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
33913588 GTAGCGATAT
* *
33913598 GGAATACACATCCTTGACGAAGTA
1 GGAAAACACATCCTTGAAGAAGTA
* *
33913622 GGAAAACGCTTCCTTGAAGAAG
1 GGAAAACACATCCTTGAAGAAG
33913644 CGTTTTGTCC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (24 bp):
GGAAAACACATCCTTGAAGAAGTA
Found at i:33913797 original size:14 final size:14
Alignment explanation
Indices: 33913743--33913799 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
33913733 CTACCGTTAG
33913743 GGTTTAGGG-TTTA
1 GGTTTAGGGTTTTA
* **
33913756 GGGTTAGGGTTAAA
1 GGTTTAGGGTTTTA
* *
33913770 GTTTTGGGGTTTTTA
1 GGTTTAGGG-TTTTA
33913785 GGTTTAGGGTTTTA
1 GGTTTAGGGTTTTA
33913799 G
1 G
33913800 AGATAAAATT
Statistics
Matches: 32, Mismatches: 10, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
13 8 0.25
14 14 0.44
15 10 0.31
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.46
Consensus pattern (14 bp):
GGTTTAGGGTTTTA
Found at i:33914185 original size:123 final size:124
Alignment explanation
Indices: 33913972--33914250 Score: 470
Period size: 123 Copynumber: 2.2 Consensus size: 124
33913962 AGGAAATCGC
* * *
33913972 TCCCACGTAGACGCGTTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGACGTTTCTGA
1 TCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCT-AAAAAATAATTTCGAGTAGACGTTTCTGA
33914037 GCAAATAGTGTCAAAAACACTTTAAACAGGATGCATTGTCAGCAAAAGTACTGAAATCAA
65 GCAAATAGTGTCAAAAACACTTTAAACAGGATGCATTGTCAGCAAAAGTACTGAAATCAA
33914097 TCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCT-AAAAATAATTTCGAGTAGACGTTTCTGAG
1 TCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAATAATTTCGAGTAGACGTTTCTGAG
** * * *
33914161 CAAATAGTGTCAAAAATGCTTTAAACAGGATGCATTGTTAGCAAAAGTATTGAAATCGA
66 CAAATAGTGTCAAAAACACTTTAAACAGGATGCATTGTCAGCAAAAGTACTGAAATCAA
33914220 TCCCACGTGGACGCGCTTTTGCTACAGTAGC
1 TCCCACGTGGACGCGCTTTTGCTACAGTAGC
33914251 GCATGTTTGG
Statistics
Matches: 146, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
123 114 0.78
125 32 0.22
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (124 bp):
TCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAATAATTTCGAGTAGACGTTTCTGAG
CAAATAGTGTCAAAAACACTTTAAACAGGATGCATTGTCAGCAAAAGTACTGAAATCAA
Found at i:33914857 original size:7 final size:7
Alignment explanation
Indices: 33914845--33914901 Score: 73
Period size: 7 Copynumber: 8.3 Consensus size: 7
33914835 TGCCCTGCCG
33914845 TTAGGGT
1 TTAGGGT
33914852 TTAGGGT
1 TTAGGGT
33914859 TTAGGG-
1 TTAGGGT
33914865 TTAGGGT
1 TTAGGGT
* *
33914872 TAAGGTT
1 TTAGGGT
33914879 TTAGGGTT
1 TTAGGG-T
33914887 TTA-GGT
1 TTAGGGT
33914893 TTAGGGT
1 TTAGGGT
33914900 TT
1 TT
33914902 TAGAGAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
6 10 0.23
7 29 0.67
8 4 0.09
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.46
Consensus pattern (7 bp):
TTAGGGT
Found at i:33914904 original size:14 final size:13
Alignment explanation
Indices: 33914849--33914901 Score: 70
Period size: 13 Copynumber: 3.9 Consensus size: 13
33914839 CTGCCGTTAG
33914849 GGTTTAGGGTTTA
1 GGTTTAGGGTTTA
* *
33914862 GGGTTAGGGTTAA
1 GGTTTAGGGTTTA
33914875 GGTTTTAGGGTTTTA
1 GG-TTTAGGG-TTTA
33914890 GGTTTAGGGTTT
1 GGTTTAGGGTTT
33914902 TAGAGAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
13 16 0.47
14 13 0.38
15 5 0.15
ACGTcount: A:0.15, C:0.00, G:0.40, T:0.45
Consensus pattern (13 bp):
GGTTTAGGGTTTA
Found at i:33915296 original size:123 final size:125
Alignment explanation
Indices: 33915077--33915361 Score: 389
Period size: 123 Copynumber: 2.3 Consensus size: 125
33915067 AAGGAAATCG
* *
33915077 CTCCCACA-TGGACGCGCTTTTTCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACATTTAT
1 CTCCCA-AGTGGACGCGCTTTTGCTACAGTAGCTCATGAAAAAATAATTTCGAGTAGACATTTAT
*
33915141 AAGCAAATAGTGTCAAAAACGCTTTAAACAGGATGCATTATCAGCAAAAGTACTGAAATCAA
65 AAGCAAATAGTGTAAAAAACGCTTTAAACAGGATGCATTATCAGCAAAAGTACTGAAAT-AA
* * * *
33915203 -TCCCAAGTGGACGCGCTTTTGCTACTGTAGCTCATG-AAAAA-AATTTCGAGTAGACGTTTCTG
1 CTCCCAAGTGGACGCGCTTTTGCTACAGTAGCTCATGAAAAAATAATTTCGAGTAGACATTTATA
* * * * *
33915265 AGCAAATAGTGTAAAAAATGCTTTAAGCAGGATGCTTTGTTAGCAAAAGTACTGAAATAA
66 AGCAAATAGTGTAAAAAACGCTTTAAACAGGATGCATTATCAGCAAAAGTACTGAAATAA
* * *
33915325 CTCCCACGTGGACGCACTTTTGCTACAGTAGCGCATG
1 CTCCCAAGTGGACGCGCTTTTGCTACAGTAGCTCATG
33915362 TTTGGCCTGA
Statistics
Matches: 141, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
122 2 0.01
123 102 0.72
124 6 0.04
125 31 0.22
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (125 bp):
CTCCCAAGTGGACGCGCTTTTGCTACAGTAGCTCATGAAAAAATAATTTCGAGTAGACATTTATA
AGCAAATAGTGTAAAAAACGCTTTAAACAGGATGCATTATCAGCAAAAGTACTGAAATAA
Found at i:33918449 original size:55 final size:56
Alignment explanation
Indices: 33918369--33918530 Score: 159
Period size: 61 Copynumber: 2.8 Consensus size: 56
33918359 AGAATATTGA
* **
33918369 CTTATTTAAAATAAAATCTATTTTATTAAAAATATAAAAGTAAATT-ACA-ATTAC
1 CTTATTTAAAACAATTTCTATTTTATTAAAAATATAAAAGTAAATTAACATATTAC
* * *
33918423 TTTATTTAAAACAATGTTCTATTTTATTAAATGAA-ATAATATAGAAATATTCAACATATTGC
1 CTTATTTAAAACAAT-TTCTATTTTATTAAA--AATATAA-A-AGTAA-ATT-AACATATTAC
* * *
33918485 CTTATTTAAAAGAATTTCTATTATATTAAAAATGTAAAAGTAAATT
1 CTTATTTAAAACAATTTCTATTTTATTAAAAATATAAAAGTAAATT
33918531 TCTATTTTAG
Statistics
Matches: 87, Mismatches: 11, Indels: 17
0.76 0.10 0.15
Matches are distributed among these distances:
54 12 0.14
55 14 0.16
56 4 0.05
57 6 0.07
58 8 0.09
59 6 0.07
60 3 0.03
61 17 0.20
62 17 0.20
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (56 bp):
CTTATTTAAAACAATTTCTATTTTATTAAAAATATAAAAGTAAATTAACATATTAC
Found at i:33919711 original size:14 final size:15
Alignment explanation
Indices: 33919694--33919726 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
33919684 TTATATACAT
33919694 AATACAT-AATACTA
1 AATACATAAATACTA
33919708 AATA-ATAAATACTA
1 AATACATAAATACTA
33919722 AATAC
1 AATAC
33919727 CAATCGACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.12
14 15 0.88
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (15 bp):
AATACATAAATACTA
Found at i:33920925 original size:22 final size:23
Alignment explanation
Indices: 33920900--33920957 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 23
33920890 TTTTTTAAAT
33920900 AGGAAATTGAGAG-GAA-ATTGAG
1 AGGAAATTGAGAGAGAATATT-AG
33920922 AGG-AATTG-GAGAGAATATTAG
1 AGGAAATTGAGAGAGAATATTAG
*
33920943 AGATAAATTGAGAGA
1 AG-GAAATTGAGAGA
33920958 AAGGATTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
20 3 0.10
21 12 0.40
22 6 0.20
23 5 0.17
24 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.33, T:0.21
Consensus pattern (23 bp):
AGGAAATTGAGAGAGAATATTAG
Found at i:33920955 original size:10 final size:10
Alignment explanation
Indices: 33920902--33920959 Score: 62
Period size: 11 Copynumber: 5.4 Consensus size: 10
33920892 TTTTAAATAG
33920902 GAAATTGAGA
1 GAAATTGAGA
33920912 GGAAATTGAGA
1 -GAAATTGAGA
*
33920923 GGAATTGGAGA
1 GAAATT-GAGA
33920934 GAATATTAGAGA
1 GAA-ATT-GAGA
*
33920946 TAAATTGAGA
1 GAAATTGAGA
33920956 GAAA
1 GAAA
33920960 GGATTAAGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
10 12 0.30
11 19 0.47
12 9 0.22
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (10 bp):
GAAATTGAGA
Found at i:33931148 original size:25 final size:24
Alignment explanation
Indices: 33931111--33931157 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
33931101 TTACAACATC
*
33931111 AAATAAATGATATTTAATAAATTTT
1 AAATAAATAATA-TTAATAAATTTT
* *
33931136 AAATATATAATATTCATAAATT
1 AAATAAATAATATTAATAAATT
33931158 ATATAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 9 0.47
25 10 0.53
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
AAATAAATAATATTAATAAATTTT
Found at i:33931339 original size:14 final size:15
Alignment explanation
Indices: 33931312--33931346 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
33931302 TTGGGTGAGT
*
33931312 TTTTTATTTATTATA
1 TTTTAATTTATTATA
33931327 TTTTAATTT-TTATA
1 TTTTAATTTATTATA
33931341 TTTTAA
1 TTTTAA
33931347 ATGTGAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTAATTTATTATA
Found at i:33932151 original size:19 final size:20
Alignment explanation
Indices: 33932127--33932174 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
33932117 TTATAATTTA
*
33932127 AAAATTAAGTAAATT-AATT
1 AAAATTAAGTAAATTAAAGT
*
33932146 AAAATTAA-TTAATTAAAGT
1 AAAATTAAGTAAATTAAAGT
33932165 AAAATTAAGT
1 AAAATTAAGT
33932175 TAGAGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.20
19 19 0.76
20 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (20 bp):
AAAATTAAGTAAATTAAAGT
Found at i:33933936 original size:38 final size:38
Alignment explanation
Indices: 33933845--33933928 Score: 123
Period size: 38 Copynumber: 2.2 Consensus size: 38
33933835 AGAACATGAA
** *
33933845 TACATATTAAACATGTTTACTTTTAATGATGAATTGCG
1 TACATATTAAACATGTTTACGATTAATGATGAATTGAG
* *
33933883 TACATGTTAAACATGTTTACGATTAGTGATGAATTGAG
1 TACATATTAAACATGTTTACGATTAATGATGAATTGAG
33933921 TACATATT
1 TACATATT
33933929 GTACATGTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (38 bp):
TACATATTAAACATGTTTACGATTAATGATGAATTGAG
Found at i:33933948 original size:38 final size:38
Alignment explanation
Indices: 33933845--33933948 Score: 93
Period size: 38 Copynumber: 2.7 Consensus size: 38
33933835 AGAACATGAA
* *** * *
33933845 TACATATTAAACATGTTTACTTTTAATGATGAATTGCG
1 TACATATTAAACATGTCTACGACTAGTGATGAATTGAG
* * *
33933883 TACATGTTAAACATGTTTACGATTAGTGATGAATTGAG
1 TACATATTAAACATGTCTACGACTAGTGATGAATTGAG
**
33933921 TACATATTGTACATGTCTACTG-CTAGTG
1 TACATATTAAACATGTCTAC-GACTAGTG
33933949 TTGAGTTGTT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 54 0.98
39 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (38 bp):
TACATATTAAACATGTCTACGACTAGTGATGAATTGAG
Found at i:33934164 original size:43 final size:43
Alignment explanation
Indices: 33934075--33934208 Score: 126
Period size: 43 Copynumber: 3.1 Consensus size: 43
33934065 GTATTTTTCC
* * * **
33934075 TTTAACTGCAAGTATGTTGTGCATCCAGAACCTAGTGGCAGCT
1 TTTAACTGCAATTATGTTGTGCATCCACAGCCTAGTGGCAAAT
* * *
33934118 TTTACCTGCAATTATGTAGTGCATCCACAGTCTAGTGGCAAAT
1 TTTAACTGCAATTATGTTGTGCATCCACAGCCTAGTGGCAAAT
** * * *
33934161 TTTATTTGCGAACTT-TGTTGTGTACCCATAGCCTAGTGGCAAAT
1 TTTAACTGC-AA-TTATGTTGTGCATCCACAGCCTAGTGGCAAAT
33934205 TTTA
1 TTTA
33934209 TTTGCGAATT
Statistics
Matches: 74, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
43 42 0.57
44 30 0.41
45 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.35
Consensus pattern (43 bp):
TTTAACTGCAATTATGTTGTGCATCCACAGCCTAGTGGCAAAT
Found at i:33935315 original size:91 final size:89
Alignment explanation
Indices: 33935212--33935383 Score: 240
Period size: 91 Copynumber: 1.9 Consensus size: 89
33935202 TGTTTTTTTT
* * *
33935212 TTTTTTTTGCACTCATTTGGGTACTTGAACTTTCAAAATGCAT-CAGAAAGGCCCTT-AAACCTT
1 TTTTTTTTGCACTCAATTCGGTACTTGAACTTTCAAAATGCATCCA-AAA-GACCTTCAAACCTT
33935275 TTCTAAAAAAAAGCAATTAATCCCTTAC
64 TTC-AAAAAAAA-CAATTAATCCCTTAC
* *
33935303 TTTTTTTTGCACTCAATTCGGTACTTGAACTTTCAAAATGTATCCAAAAGACCTTCAAACTTTTT
1 TTTTTTTTGCACTCAATTCGGTACTTGAACTTTCAAAATGCATCCAAAAGACCTTCAAACCTTTT
*
33935368 CAGAAAAAACAATTAA
66 CAAAAAAAACAATTAA
33935384 GCCATTGCTT
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
89 7 0.10
90 12 0.16
91 52 0.71
92 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (89 bp):
TTTTTTTTGCACTCAATTCGGTACTTGAACTTTCAAAATGCATCCAAAAGACCTTCAAACCTTTT
CAAAAAAAACAATTAATCCCTTAC
Found at i:33935600 original size:10 final size:10
Alignment explanation
Indices: 33935480--33935606 Score: 54
Period size: 10 Copynumber: 13.1 Consensus size: 10
33935470 ATTCAAATAT
*
33935480 TAAAAATTTA
1 TAAAAAATTA
*
33935490 TTAAAAATTA
1 TAAAAAATTA
* *
33935500 GAAAAAAATA
1 TAAAAAATTA
33935510 TATAAAAATCT-
1 TA-AAAAAT-TA
33935521 TAAAAAA-TA
1 TAAAAAATTA
*
33935530 T--AAAATTT
1 TAAAAAATTA
* * *
33935538 TATAAAGTTG
1 TAAAAAATTA
33935548 TAAGAAAATTA
1 TAA-AAAATTA
*
33935559 TACAAAA-TA
1 TAAAAAATTA
33935568 TAAAGAAA-TA
1 TAAA-AAATTA
** *
33935578 T-AAATTTTG
1 TAAAAAATTA
33935587 TAAAAAATTA
1 TAAAAAATTA
33935597 T-AAAAATTA
1 TAAAAAATTA
33935606 T
1 T
33935607 CGTACCAAAA
Statistics
Matches: 86, Mismatches: 21, Indels: 21
0.67 0.16 0.16
Matches are distributed among these distances:
7 4 0.05
8 4 0.05
9 19 0.22
10 44 0.51
11 14 0.16
12 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:33935761 original size:30 final size:29
Alignment explanation
Indices: 33935703--33935759 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
33935693 CCAGGGGTCG
*
33935703 TTATTTTTTTATGATTTTTATAAAAAAAT
1 TTATTTATTTATGATTTTTATAAAAAAAT
33935732 TTATTTATTTATGATTTTTATAAAAAAA
1 TTATTTATTTATGATTTTTATAAAAAAA
33935760 ATGTAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (29 bp):
TTATTTATTTATGATTTTTATAAAAAAAT
Found at i:33935771 original size:29 final size:28
Alignment explanation
Indices: 33935708--33935771 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 28
33935698 GGTCGTTATT
* *
33935708 TTTTTATGATTTTTATAAAAAAATTTAT
1 TTTTTATGATTTTTATAAAAAAATGTAA
33935736 TTATTTATGATTTTTATAAAAAAAATGTAA
1 TT-TTTATGATTTTTAT-AAAAAAATGTAA
33935766 TTTTTA
1 TTTTTA
33935772 ATAAATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 2 0.06
29 18 0.56
30 12 0.38
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (28 bp):
TTTTTATGATTTTTATAAAAAAATGTAA
Found at i:33956060 original size:4 final size:4
Alignment explanation
Indices: 33956051--33956076 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
33956041 AGTATACATA
33956051 AGTT AGTT AGTT AGTT AGTT AGTT AG
1 AGTT AGTT AGTT AGTT AGTT AGTT AG
33956077 CAAATAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (4 bp):
AGTT
Found at i:33957555 original size:7 final size:7
Alignment explanation
Indices: 33957539--33957573 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
33957529 ATTACGATTT
*
33957539 ATTTTGA
1 ATTTTAA
33957546 ATTTTAA
1 ATTTTAA
33957553 ATTTTAA
1 ATTTTAA
33957560 ATTTTAA
1 ATTTTAA
33957567 ATTTTAA
1 ATTTTAA
33957574 TTGAATTGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (7 bp):
ATTTTAA
Found at i:33957910 original size:8 final size:8
Alignment explanation
Indices: 33957897--33957960 Score: 58
Period size: 8 Copynumber: 7.6 Consensus size: 8
33957887 TAAATATATT
33957897 TAAAAATA
1 TAAAAATA
33957905 TAAAAAT-
1 TAAAAATA
*
33957912 CAAAAATA
1 TAAAAATA
33957920 TAAAAATTA
1 TAAAAA-TA
33957929 TAAAAATAAA
1 TAAAAAT--A
*
33957939 TAAAAGTGA
1 TAAAAAT-A
*
33957948 AAAAAATA
1 TAAAAATA
33957956 TAAAA
1 TAAAA
33957961 CAAATATATA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
7 6 0.13
8 18 0.40
9 14 0.31
10 7 0.16
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.22
Consensus pattern (8 bp):
TAAAAATA
Done.