Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 112 of 216
Found at i:35642814 original size:44 final size:44
Alignment explanation
Indices: 35642680--35642852 Score: 197
Period size: 44 Copynumber: 3.9 Consensus size: 44
35642670 TACTGGTGGC
* *
35642680 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCAT
1 GAAGTAGATCGAAGAAAGCAGATATTGTCTTCATGTATTGGCGT
* *** * *
35642724 GAAGTAGATCGAAG-ATGCAGATATTGTCTTCCCATACTGGTGGT
1 GAAGTAGATCGAAGAAAGCAGATATTGTCTTCATGTATTGG-CGT
* *
35642768 GAAGTAGATCGAAGAAAGAAGATATTGTCTTCATGTATTAGCGT
1 GAAGTAGATCGAAGAAAGCAGATATTGTCTTCATGTATTGGCGT
* * *
35642812 GAAGTAGATCGAAGATAGCAGAT-TATGTCTTCTTATATTGG
1 GAAGTAGATCGAAGAAAGCAGATAT-TGTCTTCATGTATTGG
35642853 TAGTGAGGCA
Statistics
Matches: 105, Mismatches: 21, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
43 21 0.20
44 65 0.62
45 19 0.18
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (44 bp):
GAAGTAGATCGAAGAAAGCAGATATTGTCTTCATGTATTGGCGT
Found at i:35643021 original size:44 final size:43
Alignment explanation
Indices: 35642919--35643037 Score: 107
Period size: 44 Copynumber: 2.7 Consensus size: 43
35642909 TCGCATCTAG
* *
35642919 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAA
1 TCTTAT-TTCCTGAAGTAGCAGTGGAGCAGATTAAAACCGATAA
* * ** *
35642963 TAC-TATCTCCCTGAAGTAGCAGTGGAGCGGATTAAAACCTTTGA
1 T-CTTAT-TTCCTGAAGTAGCAGTGGAGCAGATTAAAACCGATAA
* *
35643007 TCTTATTTCTCTGAAGTCGCAG-AGAGCAGAT
1 TCTTATTTC-CTGAAGTAGCAGTGGAGCAGAT
35643038 CGTATCAAGC
Statistics
Matches: 61, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
43 10 0.16
44 50 0.82
45 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (43 bp):
TCTTATTTCCTGAAGTAGCAGTGGAGCAGATTAAAACCGATAA
Found at i:35645187 original size:17 final size:18
Alignment explanation
Indices: 35645148--35645192 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
35645138 TGTCATGGAC
35645148 TTTATTT-TTTCCTTATA
1 TTTATTTGTTTCCTTATA
* *
35645165 TATATTTGTTTCGTT-TA
1 TTTATTTGTTTCCTTATA
35645182 TTTATTTGTTT
1 TTTATTTGTTT
35645193 ATATTATTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.71
Consensus pattern (18 bp):
TTTATTTGTTTCCTTATA
Found at i:35645233 original size:15 final size:15
Alignment explanation
Indices: 35645213--35645243 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35645203 TATGCCATTA
35645213 TTGTATTTATTATTG
1 TTGTATTTATTATTG
*
35645228 TTGTATTTGTTATTG
1 TTGTATTTATTATTG
35645243 T
1 T
35645244 GACATTCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (15 bp):
TTGTATTTATTATTG
Found at i:35651376 original size:18 final size:20
Alignment explanation
Indices: 35651307--35651367 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 20
35651297 AAATATAAAT
35651307 TTATAAAAATATA-AAAATAA
1 TTATAAAAATATATAAAA-AA
* *
35651327 ATACAATTAATATATATAAAAAA
1 TTATAA--AA-ATATATAAAAAA
35651350 TTATAAAAATATATAAAA
1 TTATAAAAATATATAAAA
35651368 TTTAAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
20 14 0.42
21 2 0.06
22 2 0.06
23 11 0.33
24 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
TTATAAAAATATATAAAAAA
Found at i:35651513 original size:19 final size:20
Alignment explanation
Indices: 35651491--35651528 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35651481 ATTTTAATAA
35651491 TTTATATA-TTTTAAATTTT
1 TTTATATATTTTTAAATTTT
*
35651510 TTTATGTATTTTTAAATTT
1 TTTATATATTTTTAAATTT
35651529 CAAAATAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTATATATTTTTAAATTTT
Found at i:35651906 original size:40 final size:40
Alignment explanation
Indices: 35651829--35652001 Score: 256
Period size: 40 Copynumber: 4.3 Consensus size: 40
35651819 AGCGGCACTT
* * * *
35651829 TTAGCGGCGTTTGGAGCAAAAACGCTGCTAAAGAGTGAGCA
1 TTAGCGGCGTTT-AAGGAAAAGCGCCGCTAAAGAGTGAGCA
35651870 TTAGCGGCGTTTAAGGAAAAGCGCCGCTAAAGAGTGAGCA
1 TTAGCGGCGTTTAAGGAAAAGCGCCGCTAAAGAGTGAGCA
* *
35651910 TTAGTGGCGTTTAAGGAAAAGTGCCGCTAAAGAGTGAGCA
1 TTAGCGGCGTTTAAGGAAAAGCGCCGCTAAAGAGTGAGCA
* *
35651950 TTAGTGGCGTTTAAGGAAAAGCGCCGCTAAAGAGTGAACA
1 TTAGCGGCGTTTAAGGAAAAGCGCCGCTAAAGAGTGAGCA
*
35651990 TTAGCAGCGTTT
1 TTAGCGGCGTTT
35652002 GTAAAAAACG
Statistics
Matches: 122, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
40 110 0.90
41 12 0.10
ACGTcount: A:0.32, C:0.16, G:0.31, T:0.21
Consensus pattern (40 bp):
TTAGCGGCGTTTAAGGAAAAGCGCCGCTAAAGAGTGAGCA
Found at i:35652235 original size:112 final size:112
Alignment explanation
Indices: 35651949--35652429 Score: 827
Period size: 112 Copynumber: 4.3 Consensus size: 112
35651939 AAGAGTGAGC
*** * *
35651949 ATTAGTGGCGTTTAAGGAAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTGTAAAAAACGCC
1 ATTAGTGGCGTTTTTTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
35652014 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGGGA
66 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTT--GGGGGGGA
* * *
35652063 ATTAGTGGCGTTTTTTGTAAAGCGCCGGTAAAGAGTGAACATTAGTAGCGTTTGTAAAAAACGCC
1 ATTAGTGGCGTTTTTTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
*
35652128 GCAAATAATACACCCAGACGATGCCGTTTTGTGGCCTTTGGGGGGGA
66 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
* *
35652175 ATTAGTGGCGTTTTTTGTAAAGCGCCACTAAAGCGTGAACATTAGCAGCGTTTATAAAAAACGCC
1 ATTAGTGGCGTTTTTTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
35652240 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
66 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
35652287 ATTAGTGGCGTTTTTTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
1 ATTAGTGGCGTTTTTTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
* *
35652352 ACAAATAATACACCCAGACGGTGCCGTTTTGTGTCCTTTGGGGGGGA
66 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
35652399 ATTAGTGGCGTTTTTTGTAAAGCGCCGCTAA
1 ATTAGTGGCGTTTTTTGTAAAGCGCCGCTAA
35652430 TCTAGGTGTT
Statistics
Matches: 350, Mismatches: 17, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
112 253 0.72
114 97 0.28
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (112 bp):
ATTAGTGGCGTTTTTTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
Found at i:35654517 original size:84 final size:87
Alignment explanation
Indices: 35654346--35654539 Score: 313
Period size: 84 Copynumber: 2.2 Consensus size: 87
35654336 GAAGCAGTCC
*
35654346 TGGCGTTTTTAGGAAAACGCCACAAATAATGCAATTATTCCAGACCACGCAAAACGGTGTCGTTT
1 TGGCGTTTTTAGGAAAACGCCACAAATAATGCAA-TATTCCAGACCACGCAAAACGGTGTCATTT
35654411 CTGTTCACAACTGTAATATTTAG
65 CTGTTCACAACTGTAATATTTAG
*
35654434 TGGCGTTTTTAGGAAAACGCCACAAATAATGC-A-ATTCCAGACCATG-AAAACGGTGTCATTTC
1 TGGCGTTTTTAGGAAAACGCCACAAATAATGCAATATTCCAGACCACGCAAAACGGTGTCATTTC
*
35654496 TGTTCACAGCTGTAATATTTAG
66 TGTTCACAACTGTAATATTTAG
*
35654518 TGGTGTTTTTTAGGAAAACGCC
1 TGGCG-TTTTTAGGAAAACGCC
35654540 GGAAATGTGG
Statistics
Matches: 101, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
84 40 0.40
85 28 0.28
87 1 0.01
88 32 0.32
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (87 bp):
TGGCGTTTTTAGGAAAACGCCACAAATAATGCAATATTCCAGACCACGCAAAACGGTGTCATTTC
TGTTCACAACTGTAATATTTAG
Found at i:35656661 original size:40 final size:40
Alignment explanation
Indices: 35656605--35657018 Score: 432
Period size: 40 Copynumber: 9.5 Consensus size: 40
35656595 AATACATTAC
*
35656605 TTACTAAAATAAATTACTTACTAAAATTTGTTTAAATTTA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
35656645 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
*
35656685 TTACTAAAATACATTACTTACTAAAATAAATTACTTACTACAATTTGATTAAATTTA
1 TTACTAAAATACATTACTTACTAAAAT---TT-GTT--TA-AA--T--TT------A
*
35656742 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTG
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
* *
35656782 TTACTAAAATAAATTACTTATTAAAATTTGTTTAAATTTA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
35656822 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
*
35656862 TTACTAAAATACATTACTTACTAAAATAAATTACTTACTACAATTTGATTAAATTTA
1 TTACTAAAATACATTACTTACTAAAAT---TT-GTT--TA-AA--T--TT------A
*
35656919 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTG
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
35656959 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
* **
35656999 TTACTTAAATATGTTACTTA
1 TTACTAAAATACATTACTTA
35657019 AATACATTAC
Statistics
Matches: 324, Mismatches: 16, Indels: 68
0.79 0.04 0.17
Matches are distributed among these distances:
40 224 0.69
43 4 0.01
44 4 0.01
46 8 0.02
47 4 0.01
48 2 0.01
49 2 0.01
50 4 0.01
51 8 0.02
53 4 0.01
54 4 0.01
57 56 0.17
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (40 bp):
TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
Found at i:35656706 original size:57 final size:57
Alignment explanation
Indices: 35656645--35656945 Score: 346
Period size: 57 Copynumber: 5.2 Consensus size: 57
35656635 TTTAAATTTA
* *
35656645 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTAC
1 TTACTAAAATAAATTACTTACTAAAATTTGATTAAATTTATTACTAAAATACATTAC
*
35656702 TTACTAAAATAAATTACTTACTACAATTTGATTAAATTTATTACTAAAATACATTAC
1 TTACTAAAATAAATTACTTACTAAAATTTGATTAAATTTATTACTAAAATACATTAC
** * *
35656759 TTACTAAAATTTGTTTAAATTTGTTACTAAAATAAATTACTTATTAAAATTTGTT--T-AAAT--
1 TTACTAAAA------TAAATTACTTACT---A-AAATT--TGATT-AAATTTATTACTAAAATAC
35656819 -TTA-
53 ATTAC
* *
35656822 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTAC
1 TTACTAAAATAAATTACTTACTAAAATTTGATTAAATTTATTACTAAAATACATTAC
*
35656879 TTACTAAAATAAATTACTTACTACAATTTGATTAAATTTATTACTAAAATACATTAC
1 TTACTAAAATAAATTACTTACTAAAATTTGATTAAATTTATTACTAAAATACATTAC
35656936 TTACTAAAAT
1 TTACTAAAAT
35656946 TTGTTTAAAT
Statistics
Matches: 207, Mismatches: 17, Indels: 40
0.78 0.06 0.15
Matches are distributed among these distances:
50 8 0.04
51 3 0.01
52 1 0.00
53 9 0.04
54 1 0.00
56 3 0.01
57 137 0.66
63 20 0.10
64 3 0.01
66 1 0.00
67 8 0.04
68 1 0.00
69 4 0.02
70 8 0.04
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (57 bp):
TTACTAAAATAAATTACTTACTAAAATTTGATTAAATTTATTACTAAAATACATTAC
Found at i:35656706 original size:97 final size:97
Alignment explanation
Indices: 35656579--35656808 Score: 406
Period size: 97 Copynumber: 2.4 Consensus size: 97
35656569 CGATTGAATG
* *
35656579 TTAATTTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGTTTAAATTT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGATTAAATTT
35656644 ATTACTAAAATACATTACTTACTAAAATTTGT
66 ATTACTAAAATACATTACTTACTAAAATTTGT
*
35656676 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTACAATTTGATTAAATTT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGATTAAATTT
35656741 ATTACTAAAATACATTACTTACTAAAATTTGT
66 ATTACTAAAATACATTACTTACTAAAATTTGT
* * *
35656773 TTAAATTTGTTACTAAAATAAATTACTTATTAAAAT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAAT
35656809 TTGTTTAAAT
Statistics
Matches: 127, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
97 127 1.00
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.43
Consensus pattern (97 bp):
TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGATTAAATTT
ATTACTAAAATACATTACTTACTAAAATTTGT
Found at i:35656828 original size:177 final size:177
Alignment explanation
Indices: 35656605--35657018 Score: 783
Period size: 177 Copynumber: 2.3 Consensus size: 177
35656595 AATACATTAC
35656605 TTACTAAAATAAATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAA
1 TTACTAAAATAAATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAA
35656670 ATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTACAATTTGATT
66 ATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTACAATTTGATT
35656735 AAATTTATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTG
131 AAATTTATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTG
*
35656782 TTACTAAAATAAATTACTTATTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAA
1 TTACTAAAATAAATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAA
35656847 ATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTACAATTTGATT
66 ATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTACAATTTGATT
35656912 AAATTTATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTG
131 AAATTTATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTG
* * **
35656959 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTTAAATATGTTACTTA
1 TTACTAAAATAAATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTA
35657019 AATACATTAC
Statistics
Matches: 231, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
177 231 1.00
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (177 bp):
TTACTAAAATAAATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAA
ATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTACAATTTGATT
AAATTTATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTG
Found at i:35656843 original size:97 final size:96
Alignment explanation
Indices: 35656645--35656945 Score: 288
Period size: 97 Copynumber: 3.1 Consensus size: 96
35656635 TTTAAATTTA
*
35656645 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATAAATTACTTACTAAA
*
35656710 A-----TAAA-TTACTTACTACAATTTGATTAAATTTA-
66 ATTTGTTAAATTTA-TTACTA-AA----A-TACA-TTAC
* *
35656742 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTGTTACTAAAATAAATTACTTATTAAA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATAAATTACTTACTAAA
35656807 ATTTGTTTAAATTTATTACTAAAATACATTAC
66 ATTTG-TTAAATTTATTACTAAAATACATTAC
* *
35656839 TTACTAAAAT---TT-GTT--T-AAATTTATTACTAAAATACATTACTTACTAAAATAAATTACT
1 TTACTAAAATACATTACTTACTAAAATTTGTT--T-AAAT---TTA-TTACTAAAATAAATTACT
*
35656897 TACTACAATTTGATTAAATTTATTACTAAAATACATTAC
59 TACTAAAATTTG-TTAAATTTATTACTAAAATACATTAC
35656936 TTACTAAAAT
1 TTACTAAAAT
35656946 TTGTTTAAAT
Statistics
Matches: 179, Mismatches: 10, Indels: 30
0.82 0.05 0.14
Matches are distributed among these distances:
90 8 0.04
91 1 0.01
92 1 0.01
93 6 0.03
94 2 0.01
96 5 0.03
97 140 0.78
98 1 0.01
102 2 0.01
103 10 0.06
104 3 0.02
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (96 bp):
TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATAAATTACTTACTAAA
ATTTGTTAAATTTATTACTAAAATACATTAC
Found at i:35656948 original size:97 final size:97
Alignment explanation
Indices: 35656782--35656985 Score: 372
Period size: 97 Copynumber: 2.1 Consensus size: 97
35656772 TTTAAATTTG
* *
35656782 TTACTAAAATAAATTACTTATTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAA
1 TTACTAAAATAAATTACTTACTAAAATTTGATTAAATTTATTACTAAAATACATTACTTACTAAA
35656847 ATTTGTTTAAATTTATTACTAAAATACATTAC
66 ATTTGTTTAAATTTATTACTAAAATACATTAC
*
35656879 TTACTAAAATAAATTACTTACTACAATTTGATTAAATTTATTACTAAAATACATTACTTACTAAA
1 TTACTAAAATAAATTACTTACTAAAATTTGATTAAATTTATTACTAAAATACATTACTTACTAAA
*
35656944 ATTTGTTTAAATTTGTTACTAAAATACATTAC
66 ATTTGTTTAAATTTATTACTAAAATACATTAC
35656976 TTACTAAAAT
1 TTACTAAAAT
35656986 TTGTTTAAAT
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
97 103 1.00
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.43
Consensus pattern (97 bp):
TTACTAAAATAAATTACTTACTAAAATTTGATTAAATTTATTACTAAAATACATTACTTACTAAA
ATTTGTTTAAATTTATTACTAAAATACATTAC
Found at i:35657008 original size:13 final size:13
Alignment explanation
Indices: 35656990--35657031 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
35656980 TAAAATTTGT
*
35656990 TTAAATTTATTAC
1 TTAAATATATTAC
*
35657003 TTAAATATGTTAC
1 TTAAATATATTAC
*
35657016 TTAAATACATTAC
1 TTAAATATATTAC
35657029 TTA
1 TTA
35657032 CTAAAATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (13 bp):
TTAAATATATTAC
Found at i:35657033 original size:137 final size:136
Alignment explanation
Indices: 35656579--35657033 Score: 552
Period size: 137 Copynumber: 3.3 Consensus size: 136
35656569 CGATTGAATG
* * * * *
35656579 TTAATTTTATTACTAAAATACATTACTTACTAA-A-ATAAATTACTTACTAAAATTTGTTTAAAT
1 TTAAATTTATTACTTAAATATATTACTTA--AATACATTACTTACTTACT-AAATTTGTTTAAAT
35656642 TTATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACT
63 TTATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACT
*
35656707 AAAATAAATTACT
128 AAAAT---TT-GT
* * *
35656720 TACTACAA-TT-TGA-TTAAATTTATTACTAAAATACATTACTTAC-TA--AAATTTGTTTAAAT
1 T--TA-AATTTATTACTTAAATATATTACTTAAATACATTACTTACTTACTAAATTTGTTTAAAT
* * *
35656779 TTGTTACTAAAATAAATTACTTATTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACT
63 TTATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACT
35656844 AAAATTTGT
128 AAAATTTGT
* * * * *
35656853 TTAAATTTATTACTAAAATACATTACTTACTAA-A-ATAAATTACTTACTACAATTTGATTAAAT
1 TTAAATTTATTACTTAAATATATTACTTA--AATACATTACTTACTTACTA-AATTTGTTTAAAT
*
35656916 TTATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTGTTACTAAAATACATTACTTACT
63 TTATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACT
35656981 AAAATTTGT
128 AAAATTTGT
*
35656990 TTAAATTTATTACTTAAATATGTTACTTAAATACATTACTTACT
1 TTAAATTTATTACTTAAATATATTACTTAAATACATTACTTACT
35657034 AAAATTTAAG
Statistics
Matches: 269, Mismatches: 29, Indels: 36
0.81 0.09 0.11
Matches are distributed among these distances:
130 2 0.01
131 4 0.01
132 2 0.01
133 21 0.08
134 5 0.02
135 4 0.01
136 2 0.01
137 197 0.73
139 2 0.01
140 3 0.01
141 20 0.07
142 2 0.01
143 4 0.01
144 1 0.00
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (136 bp):
TTAAATTTATTACTTAAATATATTACTTAAATACATTACTTACTTACTAAATTTGTTTAAATTTA
TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAA
ATTTGT
Found at i:35657503 original size:9 final size:9
Alignment explanation
Indices: 35657463--35657846 Score: 83
Period size: 7 Copynumber: 45.0 Consensus size: 9
35657453 TTTAATAACA
*
35657463 ATAACCTAC
1 ATAACTTAC
*
35657472 ATAACCTAC
1 ATAACTTAC
35657481 ATAA--TAC
1 ATAACTTAC
*
35657488 ATTTAACTTAT
1 A--TAACTTAC
35657499 ATAACTTAC
1 ATAACTTAC
35657508 ATAA--TAC
1 ATAACTTAC
35657515 ATTTAACTTAC
1 A--TAACTTAC
35657526 --AACTTAC
1 ATAACTTAC
*
35657533 ATAATACATA-
1 AT-A-ACTTAC
35657543 ATAACTTAC
1 ATAACTTAC
35657552 --AACTTAC
1 ATAACTTAC
*
35657559 ACAA--TAC
1 ATAACTTAC
35657566 ATTGAACTTAC
1 A-T-AACTTAC
35657577 --AACTTAC
1 ATAACTTAC
*
35657584 ATAATACATA-
1 AT-A-ACTTAC
35657594 ATAACTTAC
1 ATAACTTAC
35657603 --AACTTAC
1 ATAACTTAC
35657610 ATAA--TAC
1 ATAACTTAC
35657617 ATTTAACTTAC
1 A--TAACTTAC
35657628 --AACTTAC
1 ATAACTTAC
35657635 --AACTTAC
1 ATAACTTAC
35657642 ATAA--TAC
1 ATAACTTAC
35657649 ATTTAACTTAC
1 A--TAACTTAC
35657660 --AACTTAC
1 ATAACTTAC
*
35657667 ATAATACATA-
1 AT-A-ACTTAC
35657677 ATAACTTAC
1 ATAACTTAC
35657686 --AACTTAC
1 ATAACTTAC
*
35657693 ACAA--TAC
1 ATAACTTAC
35657700 ATTTAACTTAC
1 A--TAACTTAC
35657711 --AACTTAC
1 ATAACTTAC
*
35657718 ATAATACATA-
1 AT-A-ACTTAC
35657728 ATAACTTAC
1 ATAACTTAC
35657737 --AACTTAC
1 ATAACTTAC
35657744 ATAA--TAC
1 ATAACTTAC
35657751 ATTTAACTTAC
1 A--TAACTTAC
35657762 --AACTTAC
1 ATAACTTAC
*
35657769 ATAATACATA-
1 AT-A-ACTTAC
35657779 ATAACTTAC
1 ATAACTTAC
35657788 --AACTTAC
1 ATAACTTAC
35657795 ATAA--TAC
1 ATAACTTAC
35657802 ATTTAACTTAC
1 A--TAACTTAC
35657813 --AACTTAC
1 ATAACTTAC
35657820 ATAA--TAC
1 ATAACTTAC
35657827 ATTTAACTTAC
1 A--TAACTTAC
35657838 ATAACTTAC
1 ATAACTTAC
35657847 CATTGTAATT
Statistics
Matches: 286, Mismatches: 14, Indels: 150
0.64 0.03 0.33
Matches are distributed among these distances:
7 127 0.44
8 20 0.07
9 76 0.27
10 15 0.05
11 48 0.17
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (9 bp):
ATAACTTAC
Found at i:35657565 original size:51 final size:50
Alignment explanation
Indices: 35657478--35657838 Score: 515
Period size: 51 Copynumber: 6.9 Consensus size: 50
35657468 CTACATAACC
*
35657478 TACATAATACATTTAACTTATATAACTTACATAATACATTTAACTTACAACT
1 TACATAATACATTTAAC-T-TACAACTTACATAATACATTTAACTTACAACT
* * *
35657530 TACATAATACATAATAACTTACAACTTACACAATACATTGAACTTACAACT
1 TACATAATACAT-TTAACTTACAACTTACATAATACATTTAACTTACAACT
*
35657581 TACATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTACAACT
1 TACATAATACAT-TTAACTTACAACTTACATAATACA--T---TT--AACTTACAACT
*
35657639 TACATAATACATTTAACTTACAACTTACATAATACATAATAACTTACAACT
1 TACATAATACATTTAACTTACAACTTACATAATACAT-TTAACTTACAACT
* *
35657690 TACACAATACATTTAACTTACAACTTACATAATACATAATAACTTACAACT
1 TACATAATACATTTAACTTACAACTTACATAATACAT-TTAACTTACAACT
*
35657741 TACATAATACATTTAACTTACAACTTACATAATACATAATAACTTACAACT
1 TACATAATACATTTAACTTACAACTTACATAATACAT-TTAACTTACAACT
35657792 TACATAATACATTTAACTTACAACTTACATAATACATTTAACTTACA
1 TACATAATACATTTAACTTACAACTTACATAATACATTTAACTTACA
35657839 TAACTTACCA
Statistics
Matches: 289, Mismatches: 12, Indels: 18
0.91 0.04 0.06
Matches are distributed among these distances:
50 9 0.03
51 213 0.74
52 13 0.04
53 6 0.02
55 1 0.00
56 1 0.00
57 23 0.08
58 23 0.08
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (50 bp):
TACATAATACATTTAACTTACAACTTACATAATACATTTAACTTACAACT
Found at i:35657637 original size:32 final size:32
Alignment explanation
Indices: 35657570--35657667 Score: 154
Period size: 32 Copynumber: 3.2 Consensus size: 32
35657560 CAATACATTG
35657570 AACTTACAACTTACATAATACA--TAA--T--
1 AACTTACAACTTACATAATACATTTAACTTAC
35657596 AACTTACAACTTACATAATACATTTAACTTAC
1 AACTTACAACTTACATAATACATTTAACTTAC
35657628 AACTTACAACTTACATAATACATTTAACTTAC
1 AACTTACAACTTACATAATACATTTAACTTAC
35657660 AACTTACA
1 AACTTACA
35657668 TAATACATAA
Statistics
Matches: 66, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
26 22 0.33
28 3 0.05
30 1 0.02
32 40 0.61
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (32 bp):
AACTTACAACTTACATAATACATTTAACTTAC
Found at i:35657713 original size:134 final size:134
Alignment explanation
Indices: 35657478--35657838 Score: 586
Period size: 134 Copynumber: 2.8 Consensus size: 134
35657468 CTACATAACC
*
35657478 TACATAATACATTTAACTT---A--TATAACTTACATAATACATTTAACTTACAACTTACATAAT
1 TACATAATACATTTAACTTACAACTTACAACTTACATAATACATTTAACTTACAACTTACATAAT
*
35657538 ACATAATAACTTACAACTTACACAATACATTGAACTTACAACTTACATAATACATAATAACTTAC
66 ACATAATAACTTACAACTTACACAATACATTTAACTTACAACTTACATAATACATAATAACTTAC
35657603 AACT
131 AACT
35657607 TACATAATACATTTAACTTACAACTTACAACTTACATAATACATTTAACTTACAACTTACATAAT
1 TACATAATACATTTAACTTACAACTTACAACTTACATAATACATTTAACTTACAACTTACATAAT
35657672 ACATAATAACTTACAACTTACACAATACATTTAACTTACAACTTACATAATACATAATAACTTAC
66 ACATAATAACTTACAACTTACACAATACATTTAACTTACAACTTACATAATACATAATAACTTAC
35657737 AACT
131 AACT
35657741 TACATAATACATTTAACTTACAACTTAC-A--TA-ATACATA-A--TAACTTACAACTTACATAA
1 TACATAATACATTTAACTTACAACTTACAACTTACATA-ATACATTTAACTTACAACTTACATAA
* *
35657799 TACAT-TTAACTTACAACTTACATAATACATTTAACTTACA
65 TACATAATAACTTACAACTTACACAATACATTTAACTTACA
35657839 TAACTTACCA
Statistics
Matches: 222, Mismatches: 4, Indels: 14
0.93 0.02 0.06
Matches are distributed among these distances:
127 33 0.15
128 24 0.11
129 19 0.09
130 4 0.02
131 5 0.02
132 1 0.00
133 1 0.00
134 135 0.61
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (134 bp):
TACATAATACATTTAACTTACAACTTACAACTTACATAATACATTTAACTTACAACTTACATAAT
ACATAATAACTTACAACTTACACAATACATTTAACTTACAACTTACATAATACATAATAACTTAC
AACT
Found at i:35660423 original size:18 final size:17
Alignment explanation
Indices: 35660397--35660432 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
35660387 TTTGGTTATA
35660397 TTTAATTTTCGATATGTT
1 TTTAATTTT-GATATGTT
*
35660415 TTTATTTTTGATATGTT
1 TTTAATTTTGATATGTT
35660432 T
1 T
35660433 CATTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTAATTTTGATATGTT
Found at i:35660988 original size:11 final size:11
Alignment explanation
Indices: 35660972--35660997 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35660962 CATTCTTTTC
35660972 TTTTATTTCTT
1 TTTTATTTCTT
35660983 TTTTATTTCTT
1 TTTTATTTCTT
35660994 TTTT
1 TTTT
35660998 GGGTGATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTATTTCTT
Found at i:35662228 original size:18 final size:18
Alignment explanation
Indices: 35662205--35662244 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
35662195 AATCTTTAAG
35662205 ATTATACTTTTTTGGGAA
1 ATTATACTTTTTTGGGAA
35662223 ATTATACTTTTTTGGGAA
1 ATTATACTTTTTTGGGAA
35662241 ATTA
1 ATTA
35662245 ACCATGTCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (18 bp):
ATTATACTTTTTTGGGAA
Found at i:35664445 original size:25 final size:24
Alignment explanation
Indices: 35664398--35664447 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
35664388 TTTGTTTAAG
*
35664398 TGCAAAATTCTCTTTGAGTTTTTC
1 TGCAAAATTCTCTTTGAGGTTTTC
35664422 TGCAAGAATTCTCTCTTG-GGTTTTC
1 TGCAA-AATTCTCT-TTGAGGTTTTC
35664447 T
1 T
35664448 TTAGAAGCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 5 0.22
25 15 0.65
26 3 0.13
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (24 bp):
TGCAAAATTCTCTTTGAGGTTTTC
Found at i:35672101 original size:58 final size:57
Alignment explanation
Indices: 35672033--35672196 Score: 176
Period size: 58 Copynumber: 2.8 Consensus size: 57
35672023 TTTATAGTAT
* *
35672033 ATTATATATTACGATTTT-TT-AATTCATA-TAATAATAATTATATTAAGAATTTTATTAA
1 ATTATATATTA--ATTTTATTAAATT-ATATTAATAATAATTATATTAA-AATATGATTAA
*
35672091 ATTATATATT-ATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGATTAA
1 ATTATATATTAATTTTATTAAATTATA-TTAATAATAATTATATTAAAATATGATTAA
* * *
35672148 ATTATTTATTATTTTTATTAAATTATTTTTAATAATAATCT-TATTAAAA
1 ATTATATATTAATTTTATTAAATTA-TATTAATAATAAT-TATATTAAAA
35672197 ATTAATAACA
Statistics
Matches: 92, Mismatches: 7, Indels: 14
0.81 0.06 0.12
Matches are distributed among these distances:
55 5 0.05
56 5 0.05
57 22 0.24
58 58 0.63
59 2 0.02
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (57 bp):
ATTATATATTAATTTTATTAAATTATATTAATAATAATTATATTAAAATATGATTAA
Found at i:35685845 original size:15 final size:15
Alignment explanation
Indices: 35685825--35685859 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
35685815 TAATGGTTAT
35685825 TAATTATCCAATTTA
1 TAATTATCCAATTTA
35685840 TAATTATCCAATTTA
1 TAATTATCCAATTTA
35685855 TAATT
1 TAATT
35685860 GCTAGGATTA
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:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (15 bp):
TAATTATCCAATTTA
Found at i:35691756 original size:54 final size:54
Alignment explanation
Indices: 35691643--35691758 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
35691633 TTGTGTGTAT
* * * * *
35691643 CAAGTCAGAGAGTTACACGGTTTAGTACACGGCCTATGTCACGACCGTGTGACA
1 CAAGTTAGAGAGTTACACGGTCTAGCACACGGCCTACGACACGACCGTGTGACA
* * *
35691697 CAAGTTAGAGAGTTACACTGTCTAGCACACGGCCTACGACACGGCCGTGTGACC
1 CAAGTTAGAGAGTTACACGGTCTAGCACACGGCCTACGACACGACCGTGTGACA
35691751 CAAGTTAG
1 CAAGTTAG
35691759 TAAGTTGCAC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.21
Consensus pattern (54 bp):
CAAGTTAGAGAGTTACACGGTCTAGCACACGGCCTACGACACGACCGTGTGACA
Found at i:35691792 original size:54 final size:54
Alignment explanation
Indices: 35691614--35691801 Score: 157
Period size: 54 Copynumber: 3.5 Consensus size: 54
35691604 GTGTGAGTAT
* ** * * * *
35691614 CACATGGCCTAAGACACGGTTGTGTGTA-TCAAGTCAGAGAGTTACACGGTTTAG
1 CACACGGCCTAAGACACGGCCGTGTG-ACACAAGTTAGAGAGTTACACAGTCTAG
* * * * *
35691668 TACACGGCCTATGTCACGACCGTGTGACACAAGTTAGAGAGTTACACTGTCTAG
1 CACACGGCCTAAGACACGGCCGTGTGACACAAGTTAGAGAGTTACACAGTCTAG
* * * *
35691722 CACACGGCCTACGACACGGCCGTGTGACCCAAGTTAGTA-AGTTGCACAGTTTAAG
1 CACACGGCCTAAGACACGGCCGTGTGACACAAGTTAG-AGAGTTACACAGTCT-AG
* * *
35691777 -ATACGGGCTAAGACACGGCTGTGTG
1 CACACGGCCTAAGACACGGCCGTGTG
35691802 TCTAATTGTT
Statistics
Matches: 108, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
53 1 0.01
54 104 0.96
55 3 0.03
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (54 bp):
CACACGGCCTAAGACACGGCCGTGTGACACAAGTTAGAGAGTTACACAGTCTAG
Found at i:35696824 original size:43 final size:43
Alignment explanation
Indices: 35696763--35696921 Score: 162
Period size: 43 Copynumber: 3.7 Consensus size: 43
35696753 TAAGTGTTTT
* * *
35696763 CGTGTAAGACCACGTCTGGAACGATGGCATCGAGTTGTATTTC
1 CGTGTAAGACCACGTCTGGGACGATGGCATCGACTTGTATTTA
* * *
35696806 CGTGTAAGACCACGTCTGGGATGATGACATCGACTTGTATTTT
1 CGTGTAAGACCACGTCTGGGACGATGGCATCGACTTGTATTTA
* * *
35696849 TGGGTAAGACC-CTGTCTGGGAC-AGTGGCATCGATTTGTGA-TTA
1 CGTGTAAGACCAC-GTCTGGGACGA-TGGCATCGACTTGT-ATTTA
* * *
35696892 CATGTAGGACCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGATGGCAT
35696922 TGTACGAATC
Statistics
Matches: 95, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
42 2 0.02
43 91 0.96
44 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGATGGCATCGACTTGTATTTA
Found at i:35703493 original size:21 final size:22
Alignment explanation
Indices: 35703469--35703513 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
35703459 TATTTAACCC
*
35703469 AAAATAAATTGGATTA-AAATT
1 AAAATAAATTAGATTATAAATT
* *
35703490 AAAATTAATTATATTATAAATT
1 AAAATAAATTAGATTATAAATT
35703512 AA
1 AA
35703514 TATTCATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
AAAATAAATTAGATTATAAATT
Found at i:35704271 original size:21 final size:21
Alignment explanation
Indices: 35704247--35704288 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
35704237 TAGGAACACA
*
35704247 AGGTGAATAGCCTCGTTGTGG
1 AGGTGAACAGCCTCGTTGTGG
*
35704268 AGGTGAACAGTCTCGTTGTGG
1 AGGTGAACAGCCTCGTTGTGG
35704289 CTGCCTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.14, G:0.38, T:0.29
Consensus pattern (21 bp):
AGGTGAACAGCCTCGTTGTGG
Found at i:35705554 original size:101 final size:101
Alignment explanation
Indices: 35705438--35705620 Score: 289
Period size: 101 Copynumber: 1.8 Consensus size: 101
35705428 TGATGGTCAC
* * *
35705438 GTGTGTAGTATTATGTGCAGGCTACTACGTGTACCGGAAT-G-ATAGGTCGCATGTGTAGTACTA
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG-ATCGAATA-GTCACATCTGTAGTACTA
35705501 TGTGCAGGCTACTATGTGTACCAGATAGTTTCGTTCAT
64 TGTGCAGGCTACTATGTGTACCAGATAGTTTCGTTCAT
*
35705539 GTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATCGTAATAGTCACATCTGTAGTACTAT
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATCG-AATAGTCACATCTGTAGTACTAT
35705604 GTGCAGGCTACTATGTG
65 GTGCAGGCTACTATGTG
35705621 AACCGAACAT
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
100 2 0.03
101 36 0.48
102 34 0.45
103 3 0.04
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.33
Consensus pattern (101 bp):
GTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATCGAATAGTCACATCTGTAGTACTATG
TGCAGGCTACTATGTGTACCAGATAGTTTCGTTCAT
Found at i:35705562 original size:51 final size:49
Alignment explanation
Indices: 35705433--35705616 Score: 176
Period size: 51 Copynumber: 3.6 Consensus size: 49
35705423 AAAAGTGATG
* *
35705433 GTCACGTGTGTAGTATTATGTGCAGGCTACTACGTGTACCGGAATGATAG-GTC
1 GTCA-GTGTGTAGTACTATGTGCAGGCTACTACGTGTACC---A-GATAGTATC
* *
35705486 G-CA-TGTGTAGTACTATGTGCAGGCTACTATGTGTACCAGATAGTTTC
1 GTCAGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTATC
* * * *
35705533 GTTCATGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATCGTAATA
1 G-TCA-GTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGT-ATC
* *
35705585 GTCACATCTGTAGTACTATGTGCAGGCTACTA
1 GTCA-GTGTGTAGTACTATGTGCAGGCTACTA
35705617 TGTGAACCGA
Statistics
Matches: 113, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
46 5 0.04
47 4 0.04
49 2 0.02
50 32 0.28
51 65 0.58
52 4 0.04
53 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (49 bp):
GTCAGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTATC
Found at i:35705678 original size:45 final size:45
Alignment explanation
Indices: 35705622--35705714 Score: 141
Period size: 45 Copynumber: 2.1 Consensus size: 45
35705612 TACTATGTGA
* *
35705622 ACCGAACATCATTGATTAGTAAAGTGCTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAAGTGCTTGCTATGTGCTGAATCC
* * *
35705667 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAAGTGCTTGCTATGTGCTGAATCC
35705712 ACC
1 ACC
35705715 AAGTATCTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAAGTGCTTGCTATGTGCTGAATCC
Found at i:35707384 original size:47 final size:47
Alignment explanation
Indices: 35707316--35707409 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
35707306 AATTGCATGA
*
35707316 GTATGTATTGGGTCTTAGAAGCCCTATTTGTTACAAATATAGTATTT
1 GTATGTATTGGATCTTAGAAGCCCTATTTGTTACAAATATAGTATTT
35707363 GTATGTATTGGATCTTAGAAGCCCTATTTGTTACAAATATAGTATTT
1 GTATGTATTGGATCTTAGAAGCCCTATTTGTTACAAATATAGTATTT
35707410 TGAAGCTATA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.43
Consensus pattern (47 bp):
GTATGTATTGGATCTTAGAAGCCCTATTTGTTACAAATATAGTATTT
Found at i:35719556 original size:40 final size:40
Alignment explanation
Indices: 35719372--35719556 Score: 205
Period size: 40 Copynumber: 4.7 Consensus size: 40
35719362 GCTACTCGTT
* **
35719372 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAATAGTAACTCGCA
* * **
35719412 CAAATGCCTTCGGGACTTAACCAGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAATAGTAACTCGCA
* *
35719452 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAATAGTAACTCGCA
* * * * *
35719491 CAAATGCCTTC-GGATCGTAGTCCGGAAATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAATAGTAAC-TCGCA
35719532 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
35719557 CATCATTCGA
Statistics
Matches: 123, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 78 0.63
41 11 0.09
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAAATAGTAACTCGCA
Found at i:35723838 original size:16 final size:16
Alignment explanation
Indices: 35723809--35723852 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
35723799 ATTTATTATT
35723809 TTAATTTT--AATTAA
1 TTAATTTTCCAATTAA
35723823 TTAATTTTCCAATTAA
1 TTAATTTTCCAATTAA
*
35723839 ATAATTTTCTCAAT
1 TTAATTTTC-CAAT
35723853 ACAATTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 8 0.31
16 14 0.54
17 4 0.15
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAATTTTCCAATTAA
Found at i:35724384 original size:38 final size:39
Alignment explanation
Indices: 35724327--35724400 Score: 123
Period size: 38 Copynumber: 1.9 Consensus size: 39
35724317 ATTATAGTTT
35724327 GAGTCTTTAATTATGTCATAATTTGAACAACATTAAAAA
1 GAGTCTTTAATTATGTCATAATTTGAACAACATTAAAAA
* *
35724366 GAGT-TTTAATTATTTCATAATTTGAACATCATTAA
1 GAGTCTTTAATTATGTCATAATTTGAACAACATTAA
35724401 TATGTACCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
38 29 0.88
39 4 0.12
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (39 bp):
GAGTCTTTAATTATGTCATAATTTGAACAACATTAAAAA
Found at i:35732483 original size:38 final size:39
Alignment explanation
Indices: 35732429--35732519 Score: 130
Period size: 38 Copynumber: 2.4 Consensus size: 39
35732419 TATTATAGTT
*
35732429 TGAGTCTTTAATTATGTCATAATTTGAACAACATTAATA
1 TGAGTCTTTAATTATGTCATAATCTGAACAACATTAATA
* *
35732468 TGAGT-TTTATTTATGTCATAATCTGAACATCATTAATA
1 TGAGTCTTTAATTATGTCATAATCTGAACAACATTAATA
* *
35732506 TGTGTCTTTTATTA
1 TGAGTCTTTAATTA
35732520 AGTTTTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 34 0.76
39 11 0.24
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (39 bp):
TGAGTCTTTAATTATGTCATAATCTGAACAACATTAATA
Found at i:35738855 original size:6 final size:6
Alignment explanation
Indices: 35738801--35738840 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
35738791 TCAAAAGAAA
35738801 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTT
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTT
35738841 CTTCTTTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.70
Consensus pattern (6 bp):
TTTTGC
Found at i:35740506 original size:25 final size:25
Alignment explanation
Indices: 35740460--35740508 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
35740450 ACTAAATATC
** *
35740460 AAACCCTTTTACTTTCCTTCCCCCT
1 AAACCCTTTTACTCCCCCTCCCCCT
35740485 AAACCCTTTTACTCCCCCTCCCCC
1 AAACCCTTTTACTCCCCCTCCCCC
35740509 CCTCAAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.16, C:0.51, G:0.00, T:0.33
Consensus pattern (25 bp):
AAACCCTTTTACTCCCCCTCCCCCT
Found at i:35740590 original size:18 final size:19
Alignment explanation
Indices: 35740563--35740608 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
35740553 CCTTTTTTCC
* *
35740563 CCCCTCAAAACTTTTACTT
1 CCCCTAAAAAATTTTACTT
35740582 CCCCTAAAAAATTTTACTT
1 CCCCTAAAAAATTTTACTT
35740601 CCCCTAAA
1 CCCCTAAA
35740609 CTTCCAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (19 bp):
CCCCTAAAAAATTTTACTT
Found at i:35740654 original size:28 final size:26
Alignment explanation
Indices: 35740626--35740679 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
35740616 AAAAAAATTT
35740626 CTTTTACTTTTCCCCCAAAAACTTTTTTC
1 CTTTT-CTTTT-CCCC-AAAACTTTTTTC
*
35740655 CTTTTGTTTTCCCCAAAACTTTTTT
1 CTTTTCTTTTCCCCAAAACTTTTTT
35740680 TTCACATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 11 0.46
27 4 0.17
28 4 0.17
29 5 0.21
ACGTcount: A:0.19, C:0.28, G:0.02, T:0.52
Consensus pattern (26 bp):
CTTTTCTTTTCCCCAAAACTTTTTTC
Found at i:35740745 original size:36 final size:38
Alignment explanation
Indices: 35740679--35740750 Score: 103
Period size: 36 Copynumber: 1.9 Consensus size: 38
35740669 AAAACTTTTT
*
35740679 TTTCACATTTATGTCTACTATTTATATTATTGAATTAAA
1 TTTCACATTTATG-CTAATATTTATATTATTGAATTAAA
*
35740718 TTTCACATTT-TG-TAATATTTATTTTATTGAATT
1 TTTCACATTTATGCTAATATTTATATTATTGAATT
35740751 GTTTAATCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 19 0.61
38 2 0.06
39 10 0.32
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.56
Consensus pattern (38 bp):
TTTCACATTTATGCTAATATTTATATTATTGAATTAAA
Found at i:35750152 original size:19 final size:17
Alignment explanation
Indices: 35750118--35750152 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
35750108 CTAAAATGGT
35750118 AACAAAATTAACAATAA
1 AACAAAATTAACAATAA
35750135 AACAAGAATTATACAATA
1 AACAA-AATTA-ACAATA
35750153 TTTAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (17 bp):
AACAAAATTAACAATAA
Found at i:35750632 original size:32 final size:33
Alignment explanation
Indices: 35750595--35750670 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 33
35750585 ACCAAAAATT
* **
35750595 TATTTTAAAAATTAAAAAA-AGTATTTTAAAAA-
1 TATTTTAAAAATTAAAAAATAATA-AATAAAAAG
35750627 TATTTT-AAAATTAAAAAATAATAAATAAAAAG
1 TATTTTAAAAATTAAAAAATAATAAATAAAAAG
35750659 TATTTTAAAAAT
1 TATTTTAAAAAT
35750671 ATTTTAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
31 18 0.47
32 15 0.39
33 5 0.13
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (33 bp):
TATTTTAAAAATTAAAAAATAATAAATAAAAAG
Found at i:35750656 original size:31 final size:32
Alignment explanation
Indices: 35750595--35750668 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
35750585 ACCAAAAATT
* **
35750595 TATTTTAAAAATTAAAAAAAGTATTTTAAAAA-
1 TATTTT-AAAATTAAAAAAAATATAATAAAAAG
35750627 TATTTTAAAATTAAAAAATAATA-AATAAAAAG
1 TATTTTAAAATTAAAAAA-AATATAATAAAAAG
35750659 TATTTTAAAA
1 TATTTTAAAA
35750669 ATATTTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 18 0.49
32 19 0.51
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (32 bp):
TATTTTAAAATTAAAAAAAATATAATAAAAAG
Found at i:35750708 original size:17 final size:16
Alignment explanation
Indices: 35750666--35750708 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
35750656 AAGTATTTTA
* *
35750666 AAAATATTTTAAAATT
1 AAAATATTTAAAAAAT
*
35750682 AAAAAATTTAAAAAAT
1 AAAATATTTAAAAAAT
35750698 AAATATATTTA
1 AAA-ATATTTA
35750709 TTATATCGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATATTTAAAAAAT
Found at i:35751629 original size:31 final size:31
Alignment explanation
Indices: 35751592--35751681 Score: 87
Period size: 31 Copynumber: 3.0 Consensus size: 31
35751582 ACAATTAAAT
35751592 GAGAAAATCAAAGTTTCATGTATAGAATTGA
1 GAGAAAATCAAAGTTTCATGTATAGAATTGA
* * * *
35751623 -ATGAAAATTAAAGTTTTATATATATAATT-A
1 GA-GAAAATCAAAGTTTCATGTATAGAATTGA
* * *
35751653 GAGCAAATCAAA-ATTCATGTATTGAATTG
1 GAGAAAATCAAAGTTTCATGTATAGAATTG
35751682 CACATTTGAT
Statistics
Matches: 45, Mismatches: 11, Indels: 7
0.71 0.17 0.11
Matches are distributed among these distances:
29 11 0.24
30 10 0.22
31 24 0.53
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (31 bp):
GAGAAAATCAAAGTTTCATGTATAGAATTGA
Found at i:35752198 original size:30 final size:29
Alignment explanation
Indices: 35752163--35752219 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
35752153 GCCACAGGGG
35752163 ACACACGGCCGTGTCACCTGACCGTGTGTC
1 ACACACGGCCGTGTC-CCTGACCGTGTGTC
* *
35752193 ACACACGTCCGTGTCTCTGACCGTGTG
1 ACACACGGCCGTGTCCCTGACCGTGTG
35752220 GATGAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.16, C:0.35, G:0.26, T:0.23
Consensus pattern (29 bp):
ACACACGGCCGTGTCCCTGACCGTGTGTC
Found at i:35755401 original size:13 final size:13
Alignment explanation
Indices: 35755385--35755410 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35755375 TTTTTATTTA
35755385 TATTTATATTTTT
1 TATTTATATTTTT
35755398 TATTTATATTTTT
1 TATTTATATTTTT
35755411 ATCAAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TATTTATATTTTT
Found at i:35755539 original size:22 final size:21
Alignment explanation
Indices: 35755514--35755579 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 21
35755504 TTTAAATATT
35755514 TAAAATTTAAAAAATTATTAAA
1 TAAAATTT-AAAAATTATTAAA
* *
35755536 TAAAATTTTAACATTATT--A
1 TAAAATTTAAAAATTATTAAA
35755555 -AAAATTATAAAAATTA-TAAA
1 TAAAATT-TAAAAATTATTAAA
35755575 -AAAAT
1 TAAAAT
35755580 ATACTTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 7 0.19
19 8 0.22
20 6 0.16
21 8 0.22
22 8 0.22
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAAATTTAAAAATTATTAAA
Found at i:35755545 original size:38 final size:40
Alignment explanation
Indices: 35755492--35755579 Score: 105
Period size: 38 Copynumber: 2.3 Consensus size: 40
35755482 CACGTCAATA
** *
35755492 ATTAAATAATTTTTTAA-A-TATTTAAAATT-TAAAAAATT
1 ATTAAATAAAATTTTAACATTATTAAAAATTAT-AAAAATT
35755530 ATTAAATAAAATTTTAACATTATTAAAAATTATAAAAATT
1 ATTAAATAAAATTTTAACATTATTAAAAATTATAAAAATT
35755570 A-TAAA-AAAAT
1 ATTAAATAAAAT
35755580 ATACTTTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
38 20 0.45
39 5 0.11
40 18 0.41
41 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (40 bp):
ATTAAATAAAATTTTAACATTATTAAAAATTATAAAAATT
Found at i:35763847 original size:18 final size:18
Alignment explanation
Indices: 35763824--35763858 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35763814 TGTGGGCCAC
*
35763824 ACGGGCGTGTAGGCCCAT
1 ACGGGCATGTAGGCCCAT
*
35763842 ACGGGCATGTGGGCCCA
1 ACGGGCATGTAGGCCCA
35763859 AGATTCTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.29, G:0.40, T:0.14
Consensus pattern (18 bp):
ACGGGCATGTAGGCCCAT
Found at i:35766876 original size:110 final size:110
Alignment explanation
Indices: 35766680--35766999 Score: 394
Period size: 110 Copynumber: 2.9 Consensus size: 110
35766670 ACTTTGACCA
* * * * *
35766680 GCTCATGATGCTACTCACACAAGCTATAGAGAATCCGCAATACATGTAGGATCTCAAGCCATTGT
1 GCTCATGATGCTGCTCACACAAGCTATAGAGAATCCGCAACATATGCAGGATCTCAAGCCATCGT
* * *
35766745 TACGGTCTGTATCACCAGTACATAGTACCTACTAATTAATCCCTC-
66 TACGGTCTGTATCATCGGTACATAGTACCTACTAATTAA-CCCCCG
* * ** * * *
35766790 GCTCATGATACTGCTCACACAAGTTGCAGAGAAGCCACAACATATGCAGGATCTCAAGCCAACGT
1 GCTCATGATGCTGCTCACACAAGCTATAGAGAATCCGCAACATATGCAGGATCTCAAGCCATCGT
*
35766855 TACGGCCTGTATCATCGGTACATAGTACCTACTAATTAACCCCCG
66 TACGGTCTGTATCATCGGTACATAGTACCTACTAATTAACCCCCG
* * * *
35766900 GCTCACGATGCTGCTCACATAAGCTATAAAGAATCTGCAACATATGCAGGATCTCAAGCCATCGT
1 GCTCATGATGCTGCTCACACAAGCTATAGAGAATCCGCAACATATGCAGGATCTCAAGCCATCGT
* *
35766965 TA-GTGTCTGTATCAAT-GGTACATAGCACGTACTAA
66 TACG-GTCTGTATC-ATCGGTACATAGTACCTACTAA
35767000 ATGATCACCG
Statistics
Matches: 177, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
109 5 0.03
110 170 0.96
111 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25
Consensus pattern (110 bp):
GCTCATGATGCTGCTCACACAAGCTATAGAGAATCCGCAACATATGCAGGATCTCAAGCCATCGT
TACGGTCTGTATCATCGGTACATAGTACCTACTAATTAACCCCCG
Found at i:35767090 original size:40 final size:40
Alignment explanation
Indices: 35767046--35767122 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
35767036 ACAAGGCCTT
*
35767046 CTAGGCACAAAGCTCGATAAACACACCGA-CACAAAGCTTG
1 CTAGGCACAAAGCTAGATAAACACACC-ATCACAAAGCTTG
*
35767086 CTAGGCACAAAGCTAGATAAATACACCATCACAAAGC
1 CTAGGCACAAAGCTAGATAAACACACCATCACAAAGC
35767123 CCGATAGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 1 0.03
40 33 0.97
ACGTcount: A:0.43, C:0.29, G:0.16, T:0.13
Consensus pattern (40 bp):
CTAGGCACAAAGCTAGATAAACACACCATCACAAAGCTTG
Found at i:35767128 original size:24 final size:24
Alignment explanation
Indices: 35767090--35767162 Score: 74
Period size: 25 Copynumber: 3.0 Consensus size: 24
35767080 AGCTTGCTAG
**
35767090 GCACAAAGCTAGATAAATACACCA
1 GCACAAAGCCCGATAAATACACCA
* * *
35767114 TCACAAAGCCCGATAGATAACACCG
1 GCACAAAGCCCGATAAAT-ACACCA
*
35767139 GCATAAAGCCCGATAAATAGCACC
1 GCACAAAGCCCGATAAATA-CACC
35767163 GATATAAAGC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
24 15 0.38
25 24 0.62
ACGTcount: A:0.44, C:0.29, G:0.15, T:0.12
Consensus pattern (24 bp):
GCACAAAGCCCGATAAATACACCA
Found at i:35767146 original size:25 final size:25
Alignment explanation
Indices: 35767101--35767178 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 25
35767091 CACAAAGCTA
*
35767101 GATAAAT-ACACC-ATCACAAAGCCC
1 GATAAATAACACCGA-CATAAAGCCC
* *
35767125 GATAGATAACACCGGCATAAAGCCC
1 GATAAATAACACCGACATAAAGCCC
* * *
35767150 GATAAATAGCACCGATATAAAGCCT
1 GATAAATAACACCGACATAAAGCCC
35767175 GATA
1 GATA
35767179 TTCAGGTACA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
24 6 0.14
25 38 0.86
ACGTcount: A:0.44, C:0.26, G:0.15, T:0.15
Consensus pattern (25 bp):
GATAAATAACACCGACATAAAGCCC
Found at i:35773918 original size:38 final size:39
Alignment explanation
Indices: 35773826--35773925 Score: 121
Period size: 38 Copynumber: 2.6 Consensus size: 39
35773816 CGAATGTAAT
* * * * *
35773826 AATTATAATTACCATATTTATAATAATGTTTGAATGAAA
1 AATTATAATTACAATAATTATAATAATGATTCAATCAAA
* *
35773865 AATTACAATTACAATAATTATAATAAT-ATTCAATCATA
1 AATTATAATTACAATAATTATAATAATGATTCAATCAAA
*
35773903 AATTATAATTTCAATAATTATAA
1 AATTATAATTACAATAATTATAA
35773926 CAAAGATTTC
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
38 28 0.54
39 24 0.46
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (39 bp):
AATTATAATTACAATAATTATAATAATGATTCAATCAAA
Found at i:35777200 original size:31 final size:31
Alignment explanation
Indices: 35777162--35777222 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
35777152 CAATCGAAAG
35777162 AAGTTACTAAGTCAATTCTAAAGACTTAAAA
1 AAGTTACTAAGTCAATTCTAAAGACTTAAAA
35777193 AAGTTACTAAGTCAATTCTAAAGACTTAAA
1 AAGTTACTAAGTCAATTCTAAAGACTTAAA
35777223 CCTTCATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.30
Consensus pattern (31 bp):
AAGTTACTAAGTCAATTCTAAAGACTTAAAA
Found at i:35777465 original size:24 final size:24
Alignment explanation
Indices: 35777436--35777481 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
35777426 ACATACTTTA
35777436 AAAATTCATGCAAAATACCTTATT
1 AAAATTCATGCAAAATACCTTATT
* *
35777460 AAAATTGATGCAAAATGCCTTA
1 AAAATTCATGCAAAATACCTTA
35777482 CCCCTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (24 bp):
AAAATTCATGCAAAATACCTTATT
Found at i:35792081 original size:28 final size:29
Alignment explanation
Indices: 35792022--35792083 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
35792012 AAAATCCATT
*
35792022 TTTTTTAAAAATTTATCGAAATGGGCCAA
1 TTTTTTAAAAATTTACCGAAATGGGCCAA
** *
35792051 TTTTTTAATTATTTACCGGAATGGGCC-A
1 TTTTTTAAAAATTTACCGAAATGGGCCAA
35792079 TTTTT
1 TTTTT
35792084 CGGGAAATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (29 bp):
TTTTTTAAAAATTTACCGAAATGGGCCAA
Found at i:35792581 original size:123 final size:123
Alignment explanation
Indices: 35792362--35792586 Score: 387
Period size: 123 Copynumber: 1.8 Consensus size: 123
35792352 TTATTTCGAG
** **
35792362 TTGACGTTTCTGGTCAAATAGTATAAAATCGCTTCTACCAGGATGTTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGACCAAATAGTATAAAATCGCTTCTACCAGGATACTATTTGAGAAGAAATTGTG
*
35792427 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTT
66 AAATCGCACCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTT
*
35792485 TTGACGTTTCTGACCAAATAGTATAAAATCGCTTCTACCAGGATACTATTTGAGAATAAATTGTG
1 TTGACGTTTCTGACCAAATAGTATAAAATCGCTTCTACCAGGATACTATTTGAGAAGAAATTGTG
*
35792550 AAATTGCACCCTCGTGGACGCGATTTTGCTACAGTAG
66 AAATCGCACCCTCGTGGACGCGATTTTGCTACAGTAG
35792587 CAAGTTTGGG
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
123 95 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (123 bp):
TTGACGTTTCTGACCAAATAGTATAAAATCGCTTCTACCAGGATACTATTTGAGAAGAAATTGTG
AAATCGCACCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTT
Found at i:35795724 original size:10 final size:10
Alignment explanation
Indices: 35795695--35795737 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
35795685 CAAATCTAAC
35795695 ATTATGTAAA
1 ATTATGTAAA
*
35795705 ATTA--TCAA
1 ATTATGTAAA
35795713 ATTATGTAAA
1 ATTATGTAAA
35795723 ATTATGTAAA
1 ATTATGTAAA
35795733 ATTAT
1 ATTAT
35795738 TAAGCCAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 7 0.24
10 22 0.76
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:35795782 original size:18 final size:18
Alignment explanation
Indices: 35795759--35795793 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35795749 TTTTTTAATT
35795759 AAATTAGGTAAAATTATC
1 AAATTAGGTAAAATTATC
*
35795777 AAATTATGTAAAATTAT
1 AAATTAGGTAAAATTAT
35795794 TAAGTCCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (18 bp):
AAATTAGGTAAAATTATC
Found at i:35795879 original size:29 final size:29
Alignment explanation
Indices: 35795845--35796220 Score: 276
Period size: 29 Copynumber: 14.2 Consensus size: 29
35795835 TTATATAAAA
35795845 TTAGGTTAGGGTTAGGGTTTTTAATTAAG
1 TTAGGTTAGGGTTAGGGTTTTTAATTAAG
35795874 TTAGGTTAGGGTTAGGGTTTTTAATTAAG
1 TTAGGTTAGGGTTAGGGTTTTTAATTAAG
* * *
35795903 TTAGGGTT----TTA----ATTAAATTAGG
1 TTA-GGTTAGGGTTAGGGTTTTTAATTAAG
35795925 TTAGGGTTA--G----GGTTTTTAATTAAG
1 TTA-GGTTAGGGTTAGGGTTTTTAATTAAG
* * *
35795949 TTAGGGCTT----TTA----ATTGAATTAGG
1 TTA-GG-TTAGGGTTAGGGTTTTTAATTAAG
* *
35795972 TTAGGGTTAGGGTTAGTGTTTTTAATTAAA
1 TTA-GGTTAGGGTTAGGGTTTTTAATTAAG
*
35796002 TTAGGTTAGAGTTAGGGTTTTTAATTAAG
1 TTAGGTTAGGGTTAGGGTTTTTAATTAAG
35796031 TTAGGTTAGGGTTAGGGTTTTTAATTAAG
1 TTAGGTTAGGGTTAGGGTTTTTAATTAAG
35796060 TTAGGTTAGGGTTA-GGTTTTTAATT-A-
1 TTAGGTTAGGGTTAGGGTTTTTAATTAAG
35796086 --A-GTTA-GGTTAGGGTTTTTAATTAAG
1 TTAGGTTAGGGTTAGGGTTTTTAATTAAG
* * * *
35796111 TTAGGGTT---TTTA----ATTAAATTAGG
1 TTA-GGTTAGGGTTAGGGTTTTTAATTAAG
*
35796134 TTAGG-----GTTAGGGTTTTTAATTAAA
1 TTAGGTTAGGGTTAGGGTTTTTAATTAAG
*
35796158 TTAGGTTAGAGTTAGGGTTTTTAATTAAG
1 TTAGGTTAGGGTTAGGGTTTTTAATTAAG
35796187 TTAGGTTAGGGTTAGGGTTTTTAATTAAG
1 TTAGGTTAGGGTTAGGGTTTTTAATTAAG
35796216 TTAGG
1 TTAGG
35796221 GCTTTTAATT
Statistics
Matches: 285, Mismatches: 28, Indels: 68
0.75 0.07 0.18
Matches are distributed among these distances:
20 3 0.01
22 25 0.09
23 40 0.14
24 28 0.10
25 2 0.01
26 6 0.02
27 5 0.02
28 11 0.04
29 151 0.53
30 14 0.05
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.45
Consensus pattern (29 bp):
TTAGGTTAGGGTTAGGGTTTTTAATTAAG
Found at i:35795907 original size:18 final size:17
Alignment explanation
Indices: 35795884--35795924 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
35795874 TTAGGTTAGG
35795884 GTTAGGGTTTTTAATTAA
1 GTTAGGG-TTTTAATTAA
35795902 GTTAGGGTTTTAATTAA
1 GTTAGGGTTTTAATTAA
*
35795919 ATTAGG
1 GTTAGG
35795925 TTAGGGTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.46
Consensus pattern (17 bp):
GTTAGGGTTTTAATTAA
Found at i:35795914 original size:17 final size:18
Alignment explanation
Indices: 35795884--35795963 Score: 68
Period size: 18 Copynumber: 4.9 Consensus size: 18
35795874 TTAGGTTAGG
35795884 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
35795902 GTTAGGG-TTTTAATTAA
1 GTTAGGGTTTTTAATTAA
* **
35795919 ATTA-GG---TT-A--GG
1 GTTAGGGTTTTTAATTAA
35795930 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
*
35795948 GTTAGGGCTTTTAATT
1 GTTAGGGTTTTTAATT
35795964 GAATTAGGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
11 3 0.06
12 2 0.04
13 1 0.02
14 2 0.04
15 2 0.04
16 3 0.06
17 13 0.27
18 22 0.46
ACGTcount: A:0.26, C:0.01, G:0.25, T:0.47
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:35795978 original size:47 final size:47
Alignment explanation
Indices: 35795855--35796349 Score: 453
Period size: 47 Copynumber: 10.1 Consensus size: 47
35795845 TTAGGTTAGG
*
35795855 GTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
35795902 GTTAGGG-TTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
* *
35795948 GTTAGGGCTTTTAATTGAATTAGGTTAGGGTTAGGGTTAGTGTTTTTAATTAAATTAGGTTAGA
1 GTTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGTTAG-G-GTTT--TT-AATTA------A
*
35796012 GTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
* * * *
35796059 GTTA-GGTTAGGGTTAGGTTTTTAATTAAGTTA-GGTTAGGGTTTTTAATTAA
1 GTTAGGGTT---TTTA---ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
35796110 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGG--TTT--TT--A--A--TTA-A
*
35796168 GTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
*
35796215 GTTAGGGCTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
* *
35796262 ATTA-GG-------TT--A--GGGTTAGGGTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
*
35796297 GTTAGGGTTTTTAATTAAATTATGTTAGGGTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
*
35796344 ATTAGG
1 GTTAGG
35796350 TTAGGGTTAG
Statistics
Matches: 376, Mismatches: 23, Indels: 98
0.76 0.05 0.20
Matches are distributed among these distances:
35 28 0.07
36 2 0.01
37 1 0.00
39 2 0.01
43 2 0.01
45 1 0.00
46 62 0.16
47 106 0.28
48 5 0.01
49 9 0.02
50 2 0.01
51 25 0.07
52 18 0.05
53 18 0.05
54 5 0.01
55 4 0.01
56 6 0.02
57 6 0.02
58 53 0.14
59 3 0.01
63 2 0.01
64 16 0.04
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (47 bp):
GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
Found at i:35795987 original size:35 final size:34
Alignment explanation
Indices: 35795948--35796302 Score: 214
Period size: 29 Copynumber: 10.7 Consensus size: 34
35795938 TTTTAATTAA
*
35795948 GTTAGGGCTTTTAATTGAATTAGGTTAGGGTTAGG
1 GTTAGGGTTTTTAATT-AATTAGGTTAGGGTTAGG
* *
35795983 GTTAGTGTTTTTAATTAA--A--TTA-GGTTAGA
1 GTTAGGGTTTTTAATTAATTAGGTTAGGGTTAGG
35796012 GTTAGGGTTTTTAATT-A--A-GTTA-GGTTAGG
1 GTTAGGGTTTTTAATTAATTAGGTTAGGGTTAGG
35796041 GTTAGGGTTTTTAATT-A--A-GTTA-GGTTAGG
1 GTTAGGGTTTTTAATTAATTAGGTTAGGGTTAGG
**
35796070 GTTA-GGTTTTTAATTAAGTTAGGTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA-TTAGGTTAGGG---TT-A--GG
35796110 GTTAGGGTTTTTAATTAA--A--TTA-GGTTAGG
1 GTTAGGGTTTTTAATTAATTAGGTTAGGGTTAGG
*
35796139 GTTAGGGTTTTTAATTAA--A--TTA-GGTTAGA
1 GTTAGGGTTTTTAATTAATTAGGTTAGGGTTAGG
35796168 GTTAGGGTTTTTAATT-A--A-GTTA-GGTTAGG
1 GTTAGGGTTTTTAATTAATTAGGTTAGGGTTAGG
**
35796197 GTTAGGGTTTTTAATTAAGTTAGGGCTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAA-TTA-GG-------TT--A-GGG-TTAGG
35796244 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGG
1 GTTAGGGTTTTTAATT-AATTAGGTTAGGGTTAGG
35796279 GTTAGGGTTTTTAATTAAGTTAGG
1 GTTAGGGTTTTTAATTAA-TTAGG
35796303 GTTTTTAATT
Statistics
Matches: 271, Mismatches: 14, Indels: 70
0.76 0.04 0.20
Matches are distributed among these distances:
28 15 0.06
29 133 0.49
30 4 0.01
31 1 0.00
32 4 0.01
33 5 0.02
34 6 0.02
35 43 0.16
36 4 0.01
37 3 0.01
38 2 0.01
39 2 0.01
40 4 0.01
41 13 0.05
42 2 0.01
44 1 0.00
46 3 0.01
47 24 0.09
48 2 0.01
ACGTcount: A:0.26, C:0.01, G:0.28, T:0.45
Consensus pattern (34 bp):
GTTAGGGTTTTTAATTAATTAGGTTAGGGTTAGG
Found at i:35796010 original size:58 final size:54
Alignment explanation
Indices: 35795854--35796378 Score: 333
Period size: 58 Copynumber: 10.0 Consensus size: 54
35795844 ATTAGGTTAG
35795854 GGTTAGGG-TTT--TTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATT--A--A
1 GGTTAGGGTTTTAATTAATT-AGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
35795902 -GTTAGGGTTTTAATTAA--A-TTAGGTTAGGGTTAGGGTTTTTAATT--A--A
1 GGTTAGGGTTTTAATTAATTAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
*
35795948 -GTTAGGGCTTTTAATTGAATTAGGTTAGGGTTAGGGTTAGTGTTTTTAATTAAATTA
1 GGTTAGGG-TTTTAATT-AATTA-GTTA-GGTTAGGGTTAGGGTTTTTAATTAAATTA
* * *
35796005 GGTTAGAGTTAGGGTT-TTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTA
1 GGTTAGGGTT----TTAATTAATT-AGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
* * * *
35796063 GGTTAGGG--TTAGGTT-TTTAATTAAGTTA-GGTTAGGGTTTTTAATT--A--A
1 GGTTAGGGTTTTA-ATTAATTAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
35796110 -GTTAGGGTTTTTAATTAA--A-TTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGG-TTTTAATTAATTAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
* *
35796161 GGTTAGAGTTAGGGTT-TTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATT--A--A
1 GGTTAGGGTT----TTAATTAATT-AGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
35796215 -GTTAGGGCTTTTAATTAA--A-TTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGG-TTTTAATTAATTAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
**** * * * *
35796266 GGTTAGGGTTAGGGTTAGGGTT-TTTA-ATTA-AGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTAATTA--ATTAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
* * * *
35796319 TGTTAGGGTTAGGGTT-TTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTA
1 GGTTAGGGTT----TTAATTAATT-AGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
35796377 GG
1 GG
35796379 GTTTTTAATC
Statistics
Matches: 382, Mismatches: 35, Indels: 110
0.72 0.07 0.21
Matches are distributed among these distances:
46 49 0.13
47 61 0.16
48 8 0.02
49 5 0.01
50 7 0.02
51 30 0.08
52 26 0.07
53 61 0.16
54 14 0.04
55 6 0.02
56 7 0.02
57 7 0.02
58 88 0.23
59 8 0.02
60 3 0.01
61 2 0.01
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (54 bp):
GGTTAGGGTTTTAATTAATTAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
Found at i:35796115 original size:18 final size:18
Alignment explanation
Indices: 35796092--35796133 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
35796082 ATTAAGTTAG
35796092 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
35796110 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
*
35796128 ATTAGG
1 GTTAGG
35796134 TTAGGGTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.48
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:35796220 original size:18 final size:18
Alignment explanation
Indices: 35796197--35796314 Score: 74
Period size: 18 Copynumber: 7.0 Consensus size: 18
35796187 TTAGGTTAGG
35796197 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
*
35796215 GTTAGGGCTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
* **
35796233 ATTA-GG---TT-A--GG
1 GTTAGGGTTTTTAATTAA
35796244 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
* **** *
35796262 ATTA-GG-TTAGGGTTAGG
1 GTTAGGGTTTTTAATTA-A
35796279 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
35796297 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
35796315 ATTATGTTAG
Statistics
Matches: 71, Mismatches: 19, Indels: 20
0.65 0.17 0.18
Matches are distributed among these distances:
11 3 0.04
12 2 0.03
13 1 0.01
14 2 0.03
15 2 0.03
16 6 0.08
17 7 0.10
18 43 0.61
19 5 0.07
ACGTcount: A:0.27, C:0.01, G:0.26, T:0.46
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:35796247 original size:29 final size:29
Alignment explanation
Indices: 35796215--35796378 Score: 154
Period size: 29 Copynumber: 5.8 Consensus size: 29
35796205 TTTTAATTAA
*
35796215 GTTAGGGCTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
35796244 GTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
*
35796273 GTTAGGGTTAGGGTTT--TT-AATTAAGTTAGG
1 GTTAGGGTT----TTTAATTAAATTAGGTTAGG
35796303 GTT----TTTAATTAAATT--A-T--GTTAGG
1 GTTAGGGTTT--TT-AATTAAATTAGGTTAGG
35796326 GTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
*
35796355 GTTAGGGTTTTTAATTAAGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGG
35796379 GTTTTTAATC
Statistics
Matches: 114, Mismatches: 3, Indels: 36
0.75 0.02 0.24
Matches are distributed among these distances:
22 1 0.01
23 9 0.08
24 6 0.05
25 3 0.03
26 4 0.04
27 6 0.05
29 66 0.58
30 14 0.12
31 2 0.02
33 3 0.03
ACGTcount: A:0.27, C:0.01, G:0.27, T:0.45
Consensus pattern (29 bp):
GTTAGGGTTTTTAATTAAATTAGGTTAGG
Found at i:35796378 original size:18 final size:18
Alignment explanation
Indices: 35796355--35796403 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
35796345 TTAGGTTAGG
*
35796355 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATCAA
35796373 GTTAGGGTTTTTAATCAA
1 GTTAGGGTTTTTAATCAA
*
35796391 ATTAGGGTTTTTA
1 GTTAGGGTTTTTA
35796404 TTACATCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (18 bp):
GTTAGGGTTTTTAATCAA
Found at i:35796451 original size:25 final size:26
Alignment explanation
Indices: 35796399--35796462 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
35796389 AAATTAGGGT
35796399 TTTTATTACATCAAATAGAACTTCTA
1 TTTTATTACATCAAATAGAACTTCTA
* * *
35796425 TTTTATTATATTAAATA-AACTTTTA
1 TTTTATTACATCAAATAGAACTTCTA
35796450 TTTTATTACATCA
1 TTTTATTACATCA
35796463 GATAATAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 18 0.55
26 15 0.45
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (26 bp):
TTTTATTACATCAAATAGAACTTCTA
Found at i:35797566 original size:7 final size:7
Alignment explanation
Indices: 35797556--35797580 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
35797546 TTATATACAT
35797556 AATACTA
1 AATACTA
35797563 AATACTA
1 AATACTA
35797570 AATACTA
1 AATACTA
35797577 AATA
1 AATA
35797581 TCAATCGACT
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:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:35798691 original size:11 final size:11
Alignment explanation
Indices: 35798667--35798705 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
35798657 GATGAAAATA
35798667 TAAAAAAA-TT
1 TAAAAAAATTT
**
35798677 TAAAATTATTT
1 TAAAAAAATTT
35798688 TAAAAAAATTT
1 TAAAAAAATTT
35798699 TAAAAAA
1 TAAAAAA
35798706 TGAAATTGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 6 0.25
11 18 0.75
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TAAAAAAATTT
Found at i:35798765 original size:22 final size:22
Alignment explanation
Indices: 35798740--35798790 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
35798730 AAATATGGGT
35798740 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
35798762 TTGA-ATGAATTTTGGAAGGAAA
1 TTGAGA-GAATTTTGGAAGGAAA
35798784 TTGAGAG
1 TTGAGAG
35798791 GATTAGAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 1 0.04
22 25 0.93
23 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.29
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:35800915 original size:17 final size:17
Alignment explanation
Indices: 35800893--35800930 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
35800883 TAAAAAACAA
35800893 CATAACTCTTGACCTTT
1 CATAACTCTTGACCTTT
35800910 CATAACTCTTGACCTTT
1 CATAACTCTTGACCTTT
35800927 CATA
1 CATA
35800931 TAACATAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.29, G:0.05, T:0.39
Consensus pattern (17 bp):
CATAACTCTTGACCTTT
Found at i:35809315 original size:17 final size:17
Alignment explanation
Indices: 35809295--35809327 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35809285 GTTATGTTAT
35809295 ATGAAAGGTCAAGAGTC
1 ATGAAAGGTCAAGAGTC
*
35809312 ATGAAATGTCAAGAGT
1 ATGAAAGGTCAAGAGT
35809328 TATGTTGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.09, G:0.27, T:0.21
Consensus pattern (17 bp):
ATGAAAGGTCAAGAGTC
Found at i:35813482 original size:11 final size:11
Alignment explanation
Indices: 35813468--35813498 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
35813458 GTTCTCGATG
35813468 TTTTCTTTTAC
1 TTTTCTTTTAC
*
35813479 TTTTTTTTTAC
1 TTTTCTTTTAC
35813490 TTTTCTTTT
1 TTTTCTTTT
35813499 TTTTACCTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTCTTTTAC
Found at i:35813497 original size:16 final size:16
Alignment explanation
Indices: 35813468--35813502 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
35813458 GTTCTCGATG
35813468 TTTTCTTTTACTTTTT
1 TTTTCTTTTACTTTTT
35813484 TTTTACTTTT-CTTTTT
1 TTTT-CTTTTACTTTTT
35813500 TTT
1 TTT
35813503 ACCTGTTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTCTTTTACTTTTT
Found at i:35824001 original size:20 final size:20
Alignment explanation
Indices: 35823967--35824008 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
35823957 AACTTTTTAA
** *
35823967 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
35823987 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
35824007 AT
1 AT
35824009 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:35829067 original size:15 final size:15
Alignment explanation
Indices: 35829043--35829073 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35829033 ATTAAGCAAA
*
35829043 ATGCTTAGTAAGTTT
1 ATGCTCAGTAAGTTT
35829058 ATGCTCAGTAAGTTT
1 ATGCTCAGTAAGTTT
35829073 A
1 A
35829074 CAAGTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (15 bp):
ATGCTCAGTAAGTTT
Found at i:35829532 original size:50 final size:50
Alignment explanation
Indices: 35829390--35829679 Score: 314
Period size: 50 Copynumber: 5.7 Consensus size: 50
35829380 ACATGCTAAA
** * *
35829390 GCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC--TGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGGTGCCAAT
* * * * ** * *
35829439 TCCATATCCCAGATATGGCCTTACATGGGAGTTCTCATATCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
* ** *
35829489 GCCATGTCCCAGACATGGTCTAACGGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
* *
35829539 GCCATGTCCCAGACATGGTCTTACATGAGACCTCTCGTCTCGGTGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
* *
35829589 GCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATGATCTCAAGGATGTCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG-TGCCAAT
*
35829645 GCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
35829680 TTACCCAAAT
Statistics
Matches: 200, Mismatches: 33, Indels: 9
0.83 0.14 0.04
Matches are distributed among these distances:
48 1 0.00
49 32 0.16
50 122 0.61
53 4 0.02
55 2 0.01
56 39 0.19
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
Found at i:35833119 original size:15 final size:15
Alignment explanation
Indices: 35833099--35833129 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35833089 AGTAAGAAAA
35833099 ATGCTTAGTAAGTTT
1 ATGCTTAGTAAGTTT
35833114 ATGCTTAGTAAGTTT
1 ATGCTTAGTAAGTTT
35833129 A
1 A
35833130 CAAGTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.45
Consensus pattern (15 bp):
ATGCTTAGTAAGTTT
Found at i:35833563 original size:50 final size:50
Alignment explanation
Indices: 35833446--35833735 Score: 287
Period size: 50 Copynumber: 5.7 Consensus size: 50
35833436 ACATGCTAAA
** * *
35833446 GCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC--TGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGGTGCCAAT
* * * ** *
35833495 GCCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAT
** * * *
35833545 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAT
* * * *
35833595 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTACCAGT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAT
** * *
35833645 GTGATGTCCTAGACATGGTCTTACATGAGACCTCTCATGATCTCAAGGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC--GG-TGCCAAT
*
35833701 GCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
35833736 TTACCCAAAT
Statistics
Matches: 194, Mismatches: 39, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
48 1 0.01
49 33 0.17
50 121 0.62
53 2 0.01
55 2 0.01
56 35 0.18
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAT
Found at i:35838611 original size:19 final size:19
Alignment explanation
Indices: 35838583--35838621 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
35838573 CGTAAAATAA
35838583 TTTCTAAAAAATAATTTAC
1 TTTCTAAAAAATAATTTAC
*
35838602 TTTCTGAAAAATAATTTAC
1 TTTCTAAAAAATAATTTAC
35838621 T
1 T
35838622 GAAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (19 bp):
TTTCTAAAAAATAATTTAC
Found at i:35843346 original size:47 final size:47
Alignment explanation
Indices: 35843275--35844091 Score: 1402
Period size: 47 Copynumber: 17.3 Consensus size: 47
35843265 CCCTTCGGGA
* * * * * * *
35843275 CTTATCACATTTATACACTTTCACATCCATCACGTTGGTCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
35843322 CCTATCACATATATACACTTTCACATTTATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35843369 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35843416 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35843463 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35843510 CTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35843557 CTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
35843604 CTTATCACATATATACACATTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35843651 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35843698 CTTATCACATATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35843747 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35843794 CTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35843841 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35843888 CTTATCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35843934 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35843981 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35844028 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35844079 CTTATCACATATA
1 CTTATCACATATA
35844092 CTATCATGTA
Statistics
Matches: 738, Mismatches: 25, Indels: 14
0.95 0.03 0.02
Matches are distributed among these distances:
46 46 0.06
47 599 0.81
49 46 0.06
51 47 0.06
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:35847992 original size:40 final size:40
Alignment explanation
Indices: 35847960--35848311 Score: 544
Period size: 40 Copynumber: 8.8 Consensus size: 40
35847950 CCAGCATGAT
* * * * *
35847960 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
* ** * *
35848000 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
35848040 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
*
35848080 TGCTCTTTGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
35848120 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
* * *
35848160 TGCTCTTCGAAACTTAGTCCAGATACATCACTAGCACGAA
1 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
*
35848200 TGCTCTTCG-GAACTTAGCTCGGATACATCACTAGCACGAA
1 TGCTCTTCGAG-ACTTAGCCCGGATACATCACTAGCACGAA
35848240 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
*
35848280 TGCTCTTCGGGACTTAGCCCGGATACATCACT
1 TGCTCTTCGAGACTTAGCCCGGATACATCACT
35848312 CTCAATTCTC
Statistics
Matches: 288, Mismatches: 22, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
40 287 1.00
41 1 0.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:35849784 original size:47 final size:47
Alignment explanation
Indices: 35849713--35850533 Score: 1329
Period size: 47 Copynumber: 17.3 Consensus size: 47
35849703 CCCTTCGGGA
* * * * * *
35849713 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
35849760 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35849807 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35849854 CTTATCACATATATATACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35849901 CTTATCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
35849947 CTTGTCACATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
35849994 CTTATCACATATATACACATTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35850041 CTTATCACATATAGACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35850088 CTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35850135 CTTATCACATATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35850184 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35850231 CTTATCACATATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35850280 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
35850327 CTTATCACATATATATACACATTCACATTCACCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
35850376 CTTATCACATATATACACTTTCACATTCATCACATCAGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35850423 CTTATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35850470 CTTATCACATATATATATACACTTTCAAATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35850521 CTTATCACATATA
1 CTTATCACATATA
35850534 CTATCATGTA
Statistics
Matches: 730, Mismatches: 33, Indels: 22
0.93 0.04 0.03
Matches are distributed among these distances:
46 45 0.06
47 501 0.69
49 138 0.19
51 46 0.06
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:35849791 original size:25 final size:25
Alignment explanation
Indices: 35849763--35849841 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
35849753 ACTCGGCCCT
35849763 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
35849788 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
35849810 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
35849835 ATCACAT
1 ATCACAT
35849842 CGGCCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:35849874 original size:94 final size:94
Alignment explanation
Indices: 35849713--35850533 Score: 1329
Period size: 96 Copynumber: 8.6 Consensus size: 94
35849703 CCCTTCGGGA
* * * * * * *
35849713 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* * *
35849778 TTTCACATTCATCACATTGGCCATTCGGC
66 TTTCACATTCACCACATCGGCCATTAGGC
*
35849807 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
35849872 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCACCACATCGGCCATTAGGC
*
35849901 CTTATCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGCCTTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
35849965 TTTCACATTCACCACATCGGCCATTAGGC
66 TTTCACATTCACCACATCGGCCATTAGGC
* * *
35849994 CTTATCACATATATACACATTCACATTCATCACATCGGCTATTAGGCCTTATCACATATAGACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
35850059 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCACCACATCGGCCATTAGGC
*
35850088 CTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
35850153 ACTTTCACATTCACCACATCGGCCATTAGGC
64 ACTTTCACATTCACCACATCGGCCATTAGGC
35850184 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
35850249 ACTTTCACATTCACCACATCGGCCATTAGGC
64 ACTTTCACATTCACCACATCGGCCATTAGGC
35850280 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
*
35850345 ACATTCACATTCACCACATCGGCCATTAGGC
64 ACTTTCACATTCACCACATCGGCCATTAGGC
* *
35850376 CTTATCACATATATACACTTTCACATTCATCACATCAGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* *
35850441 TTTCATATTCATCACATCGGCCATTAGGC
66 TTTCACATTCACCACATCGGCCATTAGGC
*
35850470 CTTATCACATATATATATACACTTTCAAATTCATCACATCGGCCATTAGGCCTTATCACATATA
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
35850534 CTATCATGTA
Statistics
Matches: 687, Mismatches: 33, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
93 89 0.13
94 269 0.39
96 280 0.41
98 49 0.07
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCACCACATCGGCCATTAGGC
Found at i:35853716 original size:52 final size:52
Alignment explanation
Indices: 35853654--35853757 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
35853644 AAGCTTAAAG
*
35853654 ACTTGAATGGGAATTGGGTGACTGACAATAAAGACATTTGCAATGTGGCTAA
1 ACTTGAATGGGAATTGGGTGACTGACAATAAAGACATTTGCAATATGGCTAA
35853706 ACTTGAATGGGAATTGGGTGACTGACAATAAAGACATTTGCAATATGGCTAA
1 ACTTGAATGGGAATTGGGTGACTGACAATAAAGACATTTGCAATATGGCTAA
35853758 TTAAAGACTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.27
Consensus pattern (52 bp):
ACTTGAATGGGAATTGGGTGACTGACAATAAAGACATTTGCAATATGGCTAA
Found at i:35856566 original size:61 final size:61
Alignment explanation
Indices: 35856469--35856589 Score: 188
Period size: 61 Copynumber: 2.0 Consensus size: 61
35856459 CGGGAAATCG
** *
35856469 CGTCCACGTCAGCGTGATGTCAGGGTACGTGGCAGGACATCGCGTCCATGTCAGCAGGTCA
1 CGTCCACGTCAGCGTGATGTCAGGGTACGTAACAGGACATCGCGTCCACGTCAGCAGGTCA
* * *
35856530 CGTCCACGTCAGCGTGATGTTAGGGTATGTAACAGGACATCGCGTCCACGTCAGTAGGTC
1 CGTCCACGTCAGCGTGATGTCAGGGTACGTAACAGGACATCGCGTCCACGTCAGCAGGTC
35856590 GCGCTGACGT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.21, C:0.26, G:0.31, T:0.21
Consensus pattern (61 bp):
CGTCCACGTCAGCGTGATGTCAGGGTACGTAACAGGACATCGCGTCCACGTCAGCAGGTCA
Found at i:35857070 original size:122 final size:123
Alignment explanation
Indices: 35856751--35857079 Score: 552
Period size: 123 Copynumber: 2.7 Consensus size: 123
35856741 TGTTTCTGGT
* *
35856751 CAAATAGTATAAAATCGCTTCTACCAAGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
1 CAAATAGTATAAAATCGCTTATACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
*
35856816 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTGACGTTTCTAAG
66 TGGACGCGATTTTGCTACAATAGGTCATGTAAGAAATAATTTTTTTGACGTTTCTAAG
*
35856874 CAAATAGTATAAAATCGCCTATACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
1 CAAATAGTATAAAATCGCTTATACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
* * *
35856939 TGTACGCGATTTTGCTACAATAGGTCATGTAAGAAATAA-TTTTTTGACGTTTTTGAG
66 TGGACGCGATTTTGCTACAATAGGTCATGTAAGAAATAATTTTTTTGACGTTTCTAAG
* * *
35856996 CAAATAGTAAAAAATCACTTATACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGTGCCCTCG
1 CAAATAGTATAAAATCGCTTATACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
*
35857061 TGGATGCGATTTTGCTACA
66 TGGACGCGATTTTGCTACA
35857080 GTAGCAAGTT
Statistics
Matches: 193, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
122 94 0.49
123 99 0.51
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (123 bp):
CAAATAGTATAAAATCGCTTATACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
TGGACGCGATTTTGCTACAATAGGTCATGTAAGAAATAATTTTTTTGACGTTTCTAAG
Found at i:35860206 original size:10 final size:10
Alignment explanation
Indices: 35860193--35860217 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
35860183 CAAATCTAAC
35860193 ATTATGTAAA
1 ATTATGTAAA
35860203 ATTATGTAAA
1 ATTATGTAAA
35860213 ATTAT
1 ATTAT
35860218 TAAGTCCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:35860302 original size:18 final size:18
Alignment explanation
Indices: 35860279--35860320 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
35860269 TTAGGTTTGG
35860279 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
35860297 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
*
35860315 ATTAGG
1 GTTAGG
35860321 TTAGAGTGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.48
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:35860333 original size:29 final size:29
Alignment explanation
Indices: 35860297--35860803 Score: 456
Period size: 29 Copynumber: 16.8 Consensus size: 29
35860287 TTTTAATTAA
*
35860297 GTTAGGGTTTTTAATTAAATTAGGTTAGA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
*
35860326 GTGAGGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
*
35860355 GTTAGGGTTTTTAATTAAATTAGGTTAGA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
* ***
35860384 GTTAGGGTTTTTAATTAAGTTAAGGTTTTTA
1 GTTAGGGTTTTTAATTAAATT-AGG-TTAGG
* * * * *
35860415 ATTA-AGTTAGGTTAAGGTTTTTAATTAAGTTAGG
1 GTTAGGGTT--TTTAA----TTAAATTAGGTTAGG
*
35860449 GTTTTAGGG-TTTTAGGGTT---TTAGGGTTTAGG
1 G--TTAGGGTTTTTA--ATTAAATTA-GG-TTAGG
* * **
35860480 GTTTAAGGTTTTTAATTAAGTTAGAGTTTTTAATTAA
1 G-TTAGGGTTTTTAATTAAATTAG-G---TT-A--GG
35860517 GTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
* *
35860546 GTTAGGGTTTTAAATTAAATTAGGTTAGA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
35860575 GTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
* * * * *
35860604 GTTAGGGTTAGGGTTAGGGTT--TTTA-ATTA-A
1 GTTAGGGTT---TTTA--ATTAAATTAGGTTAGG
*
35860634 GTTAGGGTTTTTAATTAAATTATGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
*
35860663 GTTAGGGTTTTTTAATTAAATTAGGTTAGA
1 GTTAGGG-TTTTTAATTAAATTAGGTTAGG
35860693 GTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
35860722 GTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
35860751 GTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
*
35860780 GTTAGGGTTTTTAATTAAGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGG
35860804 GTTTTTAATT
Statistics
Matches: 396, Mismatches: 47, Indels: 70
0.77 0.09 0.14
Matches are distributed among these distances:
25 2 0.01
27 6 0.02
28 3 0.01
29 251 0.63
30 49 0.12
31 22 0.06
32 18 0.05
34 10 0.03
35 4 0.01
36 29 0.07
37 2 0.01
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (29 bp):
GTTAGGGTTTTTAATTAAATTAGGTTAGG
Found at i:35860335 original size:47 final size:47
Alignment explanation
Indices: 35860266--35860868 Score: 389
Period size: 47 Copynumber: 12.2 Consensus size: 47
35860256 AAATTATGTA
*
35860266 AAATTAGGTTTGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATT
* *
35860313 AAATTAGGTTAGAGTGAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGG--TTT--TT-AATTA----A--GTTAGGGTTTTTAATT
* *
35860371 AAATTAGGTTAGAGTTAGGGTTTTTAATTAAGTTAAGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATT
* *
35860418 --A--A-GTTA-GGTTAAGGTTTTTAATTAAGTTAGGG-TTTTAGGGTTTT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTA----ATT
** * *
35860462 AGGGTTTTAGGGTTTAGGGTTTAAGGTTTTTAATTAAGTTAGAGTTTTTAATT
1 A---AATTA-GG-TTAGGG-TTAGGGTTTTTAATTAAGTTAGGGTTTTTAATT
* * * * * * *
35860515 AAGTTAGGGTT---TTTA--ATTAAATTAGGTTAGGGTTAGGGTTTTAAATT
1 AAATTA-GGTTAGGGTTAGGGTT--TTTA-ATTA-AGTTAGGGTTTTTAATT
* *
35860562 AAATTAGGTTAGAGTTAGGGTTTTTAATTAAATTA-GG---TT-A--
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATT
***
35860602 GGGTTAGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATT
1 AAATTA-GGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATT
*
35860650 AAATTATGTTAGGGTTAGGGTTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGG---TTT--TT--A--A--TTA-AGTTAGGGTTTTTAATT
35860709 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGG--TTT--TT-AATTA----A--GTTAGGGTTTTTAATT
35860767 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATT
* *
35860814 AAGTTAGGTTAGAGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATT
35860861 AAATTAGG
1 AAATTAGG
35860869 GTTTTTAATT
Statistics
Matches: 451, Mismatches: 43, Indels: 124
0.73 0.07 0.20
Matches are distributed among these distances:
40 8 0.02
41 50 0.11
42 7 0.02
43 4 0.01
44 2 0.00
45 9 0.02
46 10 0.02
47 135 0.30
48 6 0.01
49 13 0.03
50 9 0.02
51 5 0.01
52 7 0.02
53 17 0.04
54 8 0.02
55 3 0.01
56 32 0.07
57 7 0.02
58 83 0.18
59 36 0.08
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (47 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATT
Found at i:35860439 original size:41 final size:42
Alignment explanation
Indices: 35860372--35860453 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 42
35860362 TTTTTAATTA
* *
35860372 AATTAGGTTAGAGTTAGGGTTTTTAATTAAGTTAAGGTTTTT
1 AATTAAGTTAGAGTTAAGGTTTTTAATTAAGTTAAGGTTTTT
*
35860414 AATTAAGTTAG-GTTAAGGTTTTTAATTAAGTTAGGGTTTT
1 AATTAAGTTAGAGTTAAGGTTTTTAATTAAGTTAAGGTTTT
35860454 AGGGTTTTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 27 0.73
42 10 0.27
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (42 bp):
AATTAAGTTAGAGTTAAGGTTTTTAATTAAGTTAAGGTTTTT
Found at i:35860479 original size:7 final size:8
Alignment explanation
Indices: 35860444--35860493 Score: 75
Period size: 8 Copynumber: 6.4 Consensus size: 8
35860434 TTTAATTAAG
35860444 TTAGGGTT
1 TTAGGGTT
35860452 TTAGGGTT
1 TTAGGGTT
35860460 TTAGGGTT
1 TTAGGGTT
35860468 TTAGGG-T
1 TTAGGGTT
35860475 TTAGGGTT
1 TTAGGGTT
* *
35860483 TAAGGTTT
1 TTAGGGTT
35860491 TTA
1 TTA
35860494 ATTAAGTTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
7 7 0.18
8 31 0.82
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (8 bp):
TTAGGGTT
Found at i:35860539 original size:18 final size:18
Alignment explanation
Indices: 35860383--35860540 Score: 110
Period size: 18 Copynumber: 8.4 Consensus size: 18
35860373 ATTAGGTTAG
35860383 AGTTAGGGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
*
35860401 AGTTAAGGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
35860419 AGTTAGGTTAAGGTTTTTAATTA
1 AGTTA-G----GGTTTTTAATTA
*
35860442 AGTTAGGG-TTTTAGGGTT-
1 AGTTAGGGTTTTTA--ATTA
*
35860460 --TTAGGG-TTTTAGGGTTTA
1 AGTTAGGGTTTTTA---ATTA
* *
35860478 GGGTTTAAGGTTTTTAATTA
1 -AG-TTAGGGTTTTTAATTA
*
35860498 AGTTAGAGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
35860516 AGTTAGGGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
*
35860534 AATTAGG
1 AGTTAGG
35860541 TTAGGGTTAG
Statistics
Matches: 115, Mismatches: 11, Indels: 28
0.75 0.07 0.18
Matches are distributed among these distances:
16 11 0.10
17 9 0.08
18 61 0.53
19 3 0.03
20 3 0.03
22 6 0.05
23 22 0.19
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (18 bp):
AGTTAGGGTTTTTAATTA
Found at i:35860608 original size:6 final size:6
Alignment explanation
Indices: 35860597--35860624 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
35860587 AATTAAATTA
35860597 GGTTAG GGTTAG GGTTAG GGTTAG GGTT
1 GGTTAG GGTTAG GGTTAG GGTTAG GGTT
35860625 TTTAATTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.50, T:0.36
Consensus pattern (6 bp):
GGTTAG
Found at i:35860621 original size:41 final size:41
Alignment explanation
Indices: 35860568--35860701 Score: 135
Period size: 41 Copynumber: 3.1 Consensus size: 41
35860558 AATTAAATTA
* *
35860568 GGTTAGAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
1 GGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAG
* * *
35860609 GGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAAATTA-
1 GGTTAGGGTTAGGGTTTTTAATTAAATTA-GG---TT-A--GAGTTAG
*
35860656 TGTTAGGGTTAGGGTTTTTTAATTAAATTAGGTTAGAGTTAG
1 GGTTAGGGTTAGGG-TTTTTAATTAAATTAGGTTAGAGTTAG
35860698 GGTT
1 GGTT
35860702 TTTAATTAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
41 31 0.42
42 5 0.07
43 1 0.01
44 2 0.03
45 2 0.03
46 1 0.01
47 15 0.20
48 17 0.23
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (41 bp):
GGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAG
Found at i:35860637 original size:18 final size:18
Alignment explanation
Indices: 35860616--35860651 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
35860606 TAGGGTTAGG
35860616 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
35860634 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
35860652 ATTATGTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:35860803 original size:18 final size:18
Alignment explanation
Indices: 35860780--35860893 Score: 161
Period size: 18 Copynumber: 6.7 Consensus size: 18
35860770 TTAGGTTAGG
35860780 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
35860798 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
*
35860816 GTTA-GG---TT-A--GA
1 GTTAGGGTTTTTAATTAA
35860827 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
35860845 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
*
35860863 ATTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
35860881 GTTAGGGTTTTTA
1 GTTAGGGTTTTTA
35860894 TTACATCAAA
Statistics
Matches: 85, Mismatches: 4, Indels: 14
0.83 0.04 0.14
Matches are distributed among these distances:
11 5 0.06
12 2 0.02
13 1 0.01
14 2 0.02
15 2 0.02
16 1 0.01
17 2 0.02
18 70 0.82
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:35860832 original size:87 final size:85
Alignment explanation
Indices: 35860516--35860850 Score: 279
Period size: 87 Copynumber: 4.0 Consensus size: 85
35860506 TTTTTAATTA
* *
35860516 AGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTT-TTAAATTAAATTAGGTTAGAGTTAG
1 AGTTAGGGTTTTTAATTAAATTAGGTT--GGTTA-GATTGTT-AATTAAATTAGGTTAGGGTTAG
35860580 GG-TTTTTAATTAAATTAGGTTAG
62 GGTTTTTTAATTAAATTAGGTTAG
* * * * * * *
35860603 GGTTAGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGG---G-TTTTTAATTAAATTATGTTAGGG
1 AGTTAGGGTT---TTTA----ATTAAATTAGGTT-GGTTAGATTGTTAATTAAATTAGGTTAGGG
35860664 TTAGGGTTTTTTAATTAAATTAGGTTAG
58 TTAGGGTTTTTTAATTAAATTAGGTTAG
* *
35860692 AGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGG
1 AGTTAGGGTTTTTAATTAAATTAGGTT--GGTTA-GATTGTTAATTAAATTAGGTTAGGGTTAGG
35860757 G-TTTTTAATTAAATTAGGTTAG
63 GTTTTTTAATTAAATTAGGTTAG
* * * *
35860779 GGTTAGGGTTTTTAATTAAGTTA-G--GG-T---TT-TTAATTAAGTTAGGTTAGAGTTAGGG-T
1 AGTTAGGGTTTTTAATTAAATTAGGTTGGTTAGATTGTTAATTAAATTAGGTTAGGGTTAGGGTT
*
35860835 TTTTAATTAAGTTAGG
66 TTTTAATTAAATTAGG
35860851 GTTTTTAATT
Statistics
Matches: 213, Mismatches: 20, Indels: 41
0.78 0.07 0.15
Matches are distributed among these distances:
76 40 0.19
77 2 0.01
81 1 0.00
82 12 0.06
83 2 0.01
86 4 0.02
87 52 0.24
88 52 0.24
89 33 0.15
90 3 0.01
93 2 0.01
94 10 0.05
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (85 bp):
AGTTAGGGTTTTTAATTAAATTAGGTTGGTTAGATTGTTAATTAAATTAGGTTAGGGTTAGGGTT
TTTTAATTAAATTAGGTTAG
Found at i:35860941 original size:25 final size:26
Alignment explanation
Indices: 35860889--35860952 Score: 103
Period size: 25 Copynumber: 2.5 Consensus size: 26
35860879 AAGTTAGGGT
35860889 TTTTATTACATCAAATAGAACTTCTA
1 TTTTATTACATCAAATAGAACTTCTA
* *
35860915 TTTTATTATATTAAATA-AACTTCTA
1 TTTTATTACATCAAATAGAACTTCTA
35860940 TTTTATTACATCA
1 TTTTATTACATCA
35860953 GATAATAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 19 0.56
26 15 0.44
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (26 bp):
TTTTATTACATCAAATAGAACTTCTA
Found at i:35861388 original size:18 final size:18
Alignment explanation
Indices: 35861361--35861395 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35861351 CAGAAAATGA
* *
35861361 TACATGTAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
35861379 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
35861396 AAACACACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:35863190 original size:28 final size:30
Alignment explanation
Indices: 35863150--35863212 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
35863140 GCCATTGATG
*
35863150 AAAATATAAAAAAATTTAAAATTATTTT-A
1 AAAATATAAAAAAAATTAAAATTATTTTCA
35863179 AAAATAT-AAAAAAATTAAAATTATTTTCA
1 AAAATATAAAAAAAATTAAAATTATTTTCA
35863208 AAAAT
1 AAAAT
35863213 GAAATTGAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 13 0.41
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (30 bp):
AAAATATAAAAAAAATTAAAATTATTTTCA
Found at i:35863191 original size:29 final size:29
Alignment explanation
Indices: 35863150--35863212 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
35863140 GCCATTGATG
35863150 AAAATATAAAAAAATTTAAAATTATTTT-A
1 AAAATATAAAAAAA-TTAAAATTATTTTCA
35863179 AAAATATAAAAAAATTAAAATTATTTTCA
1 AAAATATAAAAAAATTAAAATTATTTTCA
35863208 AAAAT
1 AAAAT
35863213 GAAATTGAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 13 0.39
29 20 0.61
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (29 bp):
AAAATATAAAAAAATTAAAATTATTTTCA
Found at i:35863275 original size:40 final size:40
Alignment explanation
Indices: 35863223--35863313 Score: 164
Period size: 40 Copynumber: 2.3 Consensus size: 40
35863213 GAAATTGAGG
*
35863223 GGAAATTCAAATTAAATATGGATTTGAGAGAATTTTGGAA
1 GGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAA
*
35863263 GGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAA
1 GGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAA
35863303 GGAAATTGAAA
1 GGAAATTGAAA
35863314 GGATTAGAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.43, C:0.01, G:0.25, T:0.31
Consensus pattern (40 bp):
GGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAA
Found at i:35863927 original size:22 final size:21
Alignment explanation
Indices: 35863897--35863948 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
35863887 AAAAGAGCGT
*
35863897 GATTATGAAAAATTTTCTCCAA
1 GATTTTGAAAAA-TTTCTCCAA
**
35863919 GATTTTGAAGCATTTCTCCAA
1 GATTTTGAAAAATTTCTCCAA
35863940 GATTTTGAA
1 GATTTTGAA
35863949 GCATTCTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (21 bp):
GATTTTGAAAAATTTCTCCAA
Found at i:35863936 original size:21 final size:21
Alignment explanation
Indices: 35863910--35863953 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
35863900 TATGAAAAAT
35863910 TTTCTCCAAGATTTTGAAGCA
1 TTTCTCCAAGATTTTGAAGCA
35863931 TTTCTCCAAGATTTTGAAGCA
1 TTTCTCCAAGATTTTGAAGCA
35863952 TT
1 TT
35863954 CTATTCTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (21 bp):
TTTCTCCAAGATTTTGAAGCA
Found at i:35864026 original size:6 final size:6
Alignment explanation
Indices: 35864015--35864051 Score: 65
Period size: 6 Copynumber: 6.0 Consensus size: 6
35864005 ATAATTGGAC
35864015 GGTTGT GGTTGT GGTTGT GGTTGT GGTTGT GGGTTGT
1 GGTTGT GGTTGT GGTTGT GGTTGT GGTTGT -GGTTGT
35864052 CCCTACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (6 bp):
GGTTGT
Found at i:35865984 original size:17 final size:17
Alignment explanation
Indices: 35865962--35865995 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
35865952 AGTTATGTTA
35865962 CATGAAAGGTCAAGAGT
1 CATGAAAGGTCAAGAGT
35865979 CATGAAAGGTCAAGAGT
1 CATGAAAGGTCAAGAGT
35865996 TATGTTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.29, T:0.18
Consensus pattern (17 bp):
CATGAAAGGTCAAGAGT
Found at i:35870262 original size:17 final size:17
Alignment explanation
Indices: 35870242--35870274 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
35870232 GTTATGTTAT
35870242 ATGAAAGGTCAAGAGTC
1 ATGAAAGGTCAAGAGTC
35870259 ATGAAAGGTCAAGAGT
1 ATGAAAGGTCAAGAGT
35870275 TATGTTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.30, T:0.18
Consensus pattern (17 bp):
ATGAAAGGTCAAGAGTC
Done.