Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold160
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: 1852349
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.32
Warning! 51288 characters in sequence are not A, C, G, or T
File 6 of 6
Found at i:1558228 original size:18 final size:18
Alignment explanation
Indices: 1558201--1558240 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1558191 CAGGTGCGTT
* *
1558201 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
1558219 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
1558237 TCCT
1 TCCT
1558241 TTTCCAAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:1558791 original size:21 final size:22
Alignment explanation
Indices: 1558767--1558809 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1558757 GACAAACCCT
1558767 AAACCCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
1558788 AAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
1558810 TTTAAAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (22 bp):
AAACCCTAAACCCTTAACTTAA
Found at i:1558792 original size:28 final size:28
Alignment explanation
Indices: 1558760--1558891 Score: 148
Period size: 28 Copynumber: 4.8 Consensus size: 28
1558750 TATAATTGAC
1558760 AAACCCTAAACCCTAACCCTTAACTTAA
1 AAACCCTAAACCCTAACCCTTAACTTAA
*
1558788 AAACCCTAAACCCTTAA--CTTAATTTAA
1 AAACCCTAAACCC-TAACCCTTAACTTAA
* **
1558815 AAATCCTCT-AACCTTAAACCCTTAA-TTGT
1 AAA-CC-CTAAACCCT-AACCCTTAACTTAA
*
1558844 AAACCCTAAACCTTAACCCTTAACTTAA
1 AAACCCTAAACCCTAACCCTTAACTTAA
1558872 AAACCCT-AACCCTAACCCTT
1 AAACCCTAAACCCTAACCCTT
1558892 GACTGGTACT
Statistics
Matches: 89, Mismatches: 7, Indels: 17
0.79 0.06 0.15
Matches are distributed among these distances:
27 36 0.40
28 38 0.43
29 10 0.11
30 5 0.06
ACGTcount: A:0.40, C:0.33, G:0.01, T:0.27
Consensus pattern (28 bp):
AAACCCTAAACCCTAACCCTTAACTTAA
Found at i:1559333 original size:54 final size:54
Alignment explanation
Indices: 1559267--1559375 Score: 182
Period size: 54 Copynumber: 2.0 Consensus size: 54
1559257 TACACTTCGT
*
1559267 CCACATAGCTCATCAGATCCAGACAGAGATTCTGACAAGTTGCAATAACATGAG
1 CCACATAACTCATCAGATCCAGACAGAGATTCTGACAAGTTGCAATAACATGAG
* * *
1559321 CCACATAACTCATCGGATCCAGACAGAGATTCTGAGAAGTTGTAATAACATGAG
1 CCACATAACTCATCAGATCCAGACAGAGATTCTGACAAGTTGCAATAACATGAG
1559375 C
1 C
1559376 GCATAGATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (54 bp):
CCACATAACTCATCAGATCCAGACAGAGATTCTGACAAGTTGCAATAACATGAG
Found at i:1562296 original size:127 final size:126
Alignment explanation
Indices: 1562032--1562729 Score: 1031
Period size: 127 Copynumber: 5.5 Consensus size: 126
1562022 TCCAAACATG
* * ** *
1562032 CTACTGTAGCAAAAGTGCGTCCACGTGGGCATGATTTCACAAATTCTTCTCATAAAGTATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* *
1562097 TTGAAACG-TTTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTTCCAGGAC
66 TTGAAACGTTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTCTTCCAGGAC
** *
1562157 CTACTGTAGCAAAAGCGCGTCCATAAGGGTGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * *
1562222 TTGAAAAGTTTTTTAAAACTATTTGCTCAGAAACGTTAAGTTGAAATTATTTCTTCCAGGAC
66 TTGAAACGTTTTTT-AAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTCTTCCAGGAC
1562284 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * *
1562349 TTGAAAAGTTTTTTAAAACTATTTGCTCAGAAACGTTAAGTTGAAATTATTTCTTCCAGGAC
66 TTGAAACGTTTTTT-AAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTCTTCCAGGAC
*
1562411 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGTATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * *
1562476 TTGAAGCGTTTTTTTAAATTATTTACTCAGAAACGTCAAGTCGAAATTATTTCTTCCAGGAA
66 TTGAAACG-TTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTCTTCCAGGAC
* * ** * *
1562538 CTATTGTAGCAAAAACATGTCTACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCTTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * *
1562603 TTGAAGCG-TTTTTATACTATTTGCTCAGAAACGTCAAGTCAAAATTATTTCTTCCAGGAC
66 TTGAAACGTTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTCTTCCAGGAC
* * * * * *
1562663 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCAACTTCAGAAATTCTTCTAATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1562728 TT
66 TT
1562730 TGATTTTTAT
Statistics
Matches: 522, Mismatches: 48, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
125 166 0.32
126 5 0.01
127 345 0.66
128 6 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAACGTTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTCTTCCAGGAC
Found at i:1562899 original size:21 final size:22
Alignment explanation
Indices: 1562859--1562901 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1562849 TCCTAAAAAT
* *
1562859 CCTAAAAACCCTAAACCCTAAC
1 CCTAAAAACCCAAAAACCTAAC
1562881 CCTAAAAA-CCAAAAACCTAAC
1 CCTAAAAACCCAAAAACCTAAC
1562902 GTGGGATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.12
Consensus pattern (22 bp):
CCTAAAAACCCAAAAACCTAAC
Found at i:1563067 original size:40 final size:39
Alignment explanation
Indices: 1562970--1563068 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 39
1562960 TCCATGTCAG
* * * * *
1562970 AGCGCTTTGTTGACATGGCAACAAATCGCGCTTACGTGA
1 AGCGATTTGTTGACACGTCAACAAAGCGCGCTGACGTGA
* *
1563009 ACGCGATTTGTTGCCACGTCAACAAAGCGCTCTGACGTGGA
1 A-GCGATTTGTTGACACGTCAACAAAGCGCGCTGACGT-GA
*
1563050 AGCGATTTGCTGACACGTC
1 AGCGATTTGTTGACACGTC
1563069 CTCTGACTTC
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.02
40 45 0.92
41 3 0.06
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.24
Consensus pattern (39 bp):
AGCGATTTGTTGACACGTCAACAAAGCGCGCTGACGTGA
Found at i:1566771 original size:17 final size:17
Alignment explanation
Indices: 1566751--1566784 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1566741 TGTACAACTC
1566751 TTGTT-TTATTGTTAATT
1 TTGTTATTATT-TTAATT
1566768 TTGTTATTATTTTAATT
1 TTGTTATTATTTTAATT
1566785 GCAACTATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.71
Consensus pattern (17 bp):
TTGTTATTATTTTAATT
Found at i:1570289 original size:4 final size:4
Alignment explanation
Indices: 1570282--1570336 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
1570272 GAAACAAACA
1570282 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1570330 TATG TAT
1 TATG TAT
1570337 ATAAATGGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:1574286 original size:72 final size:73
Alignment explanation
Indices: 1574136--1574285 Score: 191
Period size: 72 Copynumber: 2.1 Consensus size: 73
1574126 TTTCACATAT
* *
1574136 AAAAATAATGATATTTTTTAAATAATTATTTGATTTTATGATATTAGAATCTACCATACCCACAA
1 AAAAATAATGATA-TTTTGAAATAATTATTTGATTTTATAATATTAGAATCTACCATACCCACAA
* *
1574201 TGTAGGTGA
65 TATAGGTAA
*
1574210 AAAAATAATGATA-TTTGAAATGATTATTTGATTTT-TCAATATTAGAAGTC-ACCATACCCA-A
1 AAAAATAATGATATTTTGAAATAATTATTTGATTTTAT-AATATTAGAA-TCTACCATACCCACA
*
1574271 ATATATGTAA
64 ATATAGGTAA
1574281 AAAAA
1 AAAAA
1574286 ACATTTGACA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
71 14 0.21
72 39 0.57
73 2 0.03
74 13 0.19
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (73 bp):
AAAAATAATGATATTTTGAAATAATTATTTGATTTTATAATATTAGAATCTACCATACCCACAAT
ATAGGTAA
Found at i:1579594 original size:15 final size:15
Alignment explanation
Indices: 1579574--1579610 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
1579564 TCGGGCCAAC
1579574 CAGGCTTCAATCTGA
1 CAGGCTTCAATCTGA
1579589 CAGGCTTCAATCTGA
1 CAGGCTTCAATCTGA
1579604 CAGGCTT
1 CAGGCTT
1579611 ATCAAGTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (15 bp):
CAGGCTTCAATCTGA
Found at i:1579903 original size:32 final size:32
Alignment explanation
Indices: 1579862--1579928 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
1579852 TTACGTCGCT
1579862 TCTTCACTCGAACCGTCCTACTCGTTTGTACA
1 TCTTCACTCGAACCGTCCTACTCGTTTGTACA
1579894 TCTTCACTCGAACCGTCCTACTCGTTTGTACA
1 TCTTCACTCGAACCGTCCTACTCGTTTGTACA
1579926 TCT
1 TCT
1579929 CGATGACAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.18, C:0.34, G:0.12, T:0.36
Consensus pattern (32 bp):
TCTTCACTCGAACCGTCCTACTCGTTTGTACA
Found at i:1583012 original size:116 final size:117
Alignment explanation
Indices: 1582808--1583042 Score: 445
Period size: 116 Copynumber: 2.0 Consensus size: 117
1582798 GTTTTTTTTC
*
1582808 TTTTGGTTGTTTCTAAGCCTACTGTTTTTAGGCAAATTATGTGTGCACTTTGGTATATTTGGCAT
1 TTTTGGTTGTCTCTAAGCCTACTGTTTTTAGGCAAATTATGTGTGCACTTTGGTATATTTGGCAT
1582873 GCTCGAAATCAGCATGTACATCC-AATGCTATTGTTCAAGTGCAGGATATTG
66 GCTCGAAATCAGCATGTACATCCAAATGCTATTGTTCAAGTGCAGGATATTG
*
1582924 TTTTGGTTGTCTCTAAGCCTACTGTTTTTAGGCAAATTGTGTGTGCACTTTGGTATATTTGGCAT
1 TTTTGGTTGTCTCTAAGCCTACTGTTTTTAGGCAAATTATGTGTGCACTTTGGTATATTTGGCAT
1582989 GCTCGAAATCAGCATGTACATCCAAATGCTATTGTTCAAGTGCAGGATATTG
66 GCTCGAAATCAGCATGTACATCCAAATGCTATTGTTCAAGTGCAGGATATTG
1583041 TT
1 TT
1583043 CGCAAGGTCA
Statistics
Matches: 116, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
116 86 0.74
117 30 0.26
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.40
Consensus pattern (117 bp):
TTTTGGTTGTCTCTAAGCCTACTGTTTTTAGGCAAATTATGTGTGCACTTTGGTATATTTGGCAT
GCTCGAAATCAGCATGTACATCCAAATGCTATTGTTCAAGTGCAGGATATTG
Found at i:1584751 original size:37 final size:37
Alignment explanation
Indices: 1584701--1584771 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
1584691 CATAGTACAT
*
1584701 AACTAGTAATTAAACTTAACCAAATCGATTTAACACA
1 AACTAGTAATTAAACTGAACCAAATCGATTTAACACA
1584738 AACTAGTAATTAAACTGAACCAAATCGATTTAAC
1 AACTAGTAATTAAACTGAACCAAATCGATTTAAC
1584772 TATATGTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.48, C:0.18, G:0.07, T:0.27
Consensus pattern (37 bp):
AACTAGTAATTAAACTGAACCAAATCGATTTAACACA
Found at i:1584825 original size:31 final size:33
Alignment explanation
Indices: 1584790--1584873 Score: 86
Period size: 33 Copynumber: 2.5 Consensus size: 33
1584780 TTGGATCAGG
1584790 ACTAAAATT-TCAAAATTTTAAAAATAT-A-AAA
1 ACTAAAATTATCAAAATTTTAAAAA-ATCACAAA
**
1584821 ACTAAAATTGATCAATTTTTTAAAAAATCACAAA
1 ACTAAAATT-ATCAAAATTTTAAAAAATCACAAA
1584855 AGCTAAAATTGAT-AAAATT
1 A-CTAAAATT-ATCAAAATT
1584874 AAAGAACAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
31 9 0.20
32 2 0.05
33 14 0.32
34 8 0.18
35 11 0.25
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (33 bp):
ACTAAAATTATCAAAATTTTAAAAAATCACAAA
Found at i:1588923 original size:40 final size:40
Alignment explanation
Indices: 1588879--1588986 Score: 110
Period size: 40 Copynumber: 2.7 Consensus size: 40
1588869 GTTTGGACAA
* * * *
1588879 AAAACGCAGCTAAAAATCGAGCATTAGCGGCGCTTTATGG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGATTTATAG
* * * * *
1588919 AAAACACCGCTAAAGATCTAGCATTTGCGGCGATTTTTAG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGATTTATAG
* *
1588959 AACACGCCGCTGAAAAT-AAGCATTAGCG
1 AAAACGCCGCTAAAAATCAAGCATTAGCG
1588987 CCGTTTTTCT
Statistics
Matches: 54, Mismatches: 14, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
39 9 0.17
40 45 0.83
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.21
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATCAAGCATTAGCGGCGATTTATAG
Found at i:1589116 original size:41 final size:41
Alignment explanation
Indices: 1589039--1589116 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
1589029 GTTACCTTTT
* * *
1589039 GGGGCTTTAGCAGCGTTTTTAGAAAAGCGCCTCTAATACTC
1 GGGGATTTAGCAGCGTTTTTAGAAAAGCACCGCTAATACTC
*
1589080 GGGGATTTAGCGGCGTTTTT-GAAAAGCCACCGCTAAT
1 GGGGATTTAGCAGCGTTTTTAGAAAAG-CACCGCTAAT
1589117 GCTTTAGCGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 6 0.19
41 26 0.81
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (41 bp):
GGGGATTTAGCAGCGTTTTTAGAAAAGCACCGCTAATACTC
Found at i:1591192 original size:86 final size:86
Alignment explanation
Indices: 1591092--1591370 Score: 353
Period size: 86 Copynumber: 3.2 Consensus size: 86
1591082 TCCTTCTACT
* * * * * ** *
1591092 TTATAAAATTTGAAAATTTGGTCTGGCTGTTAGTGAATGCATGAACTTGAACTGTTGATTTTTTC
1 TTATAAAAATTGAAAATTTAGTCTGGTTATTAGTAAATGCATGAACTTGAACCATTGATTTTTGC
*
1591157 TAATTTGTTGCACATAAGTTG
66 TAATTTGTTGCATATAAGTTG
* *
1591178 TTATAAAAATTGAAAATTTAGTCTGGTTATTGGTAAATGCATGAACTTGAACCATTTATTTTTGC
1 TTATAAAAATTGAAAATTTAGTCTGGTTATTAGTAAATGCATGAACTTGAACCATTGATTTTTGC
1591243 TAATTTGTTGCATATAAGTTG
66 TAATTTGTTGCATATAAGTTG
* * * * *
1591264 TTATAAATATTGAAAAATTAGTCTGATTTTTCA-TAAATACATGAACTTGAACCATTGATTTTTG
1 TTATAAAAATTGAAAATTTAGTCTGGTTATT-AGTAAATGCATGAACTTGAACCATTGATTTTTG
* **
1591328 CTAATTTGTTGCATATAAATCA
65 CTAATTTGTTGCATATAAGTTG
* *
1591350 TTATAGAAATTGAAGATTTAG
1 TTATAAAAATTGAAAATTTAG
1591371 CCCTATTGCC
Statistics
Matches: 167, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
86 167 1.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (86 bp):
TTATAAAAATTGAAAATTTAGTCTGGTTATTAGTAAATGCATGAACTTGAACCATTGATTTTTGC
TAATTTGTTGCATATAAGTTG
Found at i:1591387 original size:86 final size:85
Alignment explanation
Indices: 1591131--1591448 Score: 318
Period size: 86 Copynumber: 3.7 Consensus size: 85
1591121 TTAGTGAATG
** * *
1591131 CATGAACTTGAACTGTTGATTTTTTCTAATTTGTTGCACATAAGTTGTTATAAAAATTGAAAATT
1 CATGAACTTGAACCATTGATTTTTGCTAATTTGTTGCACATAAATTGTTAT-AAAATTGAAAATT
* * *
1591196 TAGTCTGGTTATTGGTAAATG
65 TAGTCTGATTATCGGTAAATA
* * * *
1591217 CATGAACTTGAACCATTTATTTTTGCTAATTTGTTGCATATAAGTTGTTATAAATATTGAAAAAT
1 CATGAACTTGAACCATTGATTTTTGCTAATTTGTTGCACATAAATTGTTATAAA-ATTGAAAATT
* *
1591282 TAGTCTGATTTTTC-ATAAATA
65 TAGTCTGA-TTATCGGTAAATA
* ** *
1591303 CATGAACTTGAACCATTGATTTTTGCTAATTTGTTGCATATAAATCATTATAGAAATTGAAGATT
1 CATGAACTTGAACCATTGATTTTTGCTAATTTGTTGCACATAAATTGTTATA-AAATTGAAAATT
* **
1591368 TAGCCCT-ATTGCCGGTAAATA
65 TAG-TCTGATTATCGGTAAATA
* * * * * *
1591389 TATGAACTATGAA-TAGTTGATTTTTGCTAATTTGTTTCACATAAACTGTTGTAAGATTGA
1 CATGAACT-TGAACCA-TTGATTTTTGCTAATTTGTTGCACATAAATTGTTATAAAATTGA
1591449 TTTTTGTTAA
Statistics
Matches: 195, Mismatches: 30, Indels: 14
0.82 0.13 0.06
Matches are distributed among these distances:
85 6 0.03
86 147 0.75
87 42 0.22
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (85 bp):
CATGAACTTGAACCATTGATTTTTGCTAATTTGTTGCACATAAATTGTTATAAAATTGAAAATTT
AGTCTGATTATCGGTAAATA
Found at i:1591473 original size:40 final size:40
Alignment explanation
Indices: 1591388--1591529 Score: 121
Period size: 40 Copynumber: 3.6 Consensus size: 40
1591378 GCCGGTAAAT
* * * *
1591388 ATATGAACTA-TG-AATAGTTGATTTTTGCTAATTTGTTTC
1 ATATAAACTATTGAAAT-GTTGATTTTTGATAATTTCTTAC
* * * * *
1591427 ACATAAACTGTTGTAA-GATTGATTTTTGTTAATTTCTTGC
1 ATATAAACTATTGAAATG-TTGATTTTTGATAATTTCTTAC
* *
1591467 ATATAAATTATTGAAATGTTGATTTTTGATAATTCCTTAC
1 ATATAAACTATTGAAATGTTGATTTTTGATAATTTCTTAC
*
1591507 ATATTAAA-TATTGAAGTGTTGAT
1 ATA-TAAACTATTGAAATGTTGAT
1591530 ATTCAAGCTA
Statistics
Matches: 84, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
39 8 0.10
40 69 0.82
41 7 0.08
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (40 bp):
ATATAAACTATTGAAATGTTGATTTTTGATAATTTCTTAC
Found at i:1592199 original size:172 final size:172
Alignment explanation
Indices: 1591913--1592257 Score: 690
Period size: 172 Copynumber: 2.0 Consensus size: 172
1591903 GTTCCTATCG
1591913 TATTAAAAAGAATCAAAATATGGCCAAATTGGAAAATGGACTATTTGATTCTTTTTATAGGATAG
1 TATTAAAAAGAATCAAAATATGGCCAAATTGGAAAATGGACTATTTGATTCTTTTTATAGGATAG
1591978 GGACTGAATTGATCTATTTAATTGGATGCATCATTGCTTTCACATGGTGGACCAATAATATCCAA
66 GGACTGAATTGATCTATTTAATTGGATGCATCATTGCTTTCACATGGTGGACCAATAATATCCAA
1592043 ATCTCATGATTTGCCTGGCCATTGTGAAACATTAGCGTGTGT
131 ATCTCATGATTTGCCTGGCCATTGTGAAACATTAGCGTGTGT
1592085 TATTAAAAAGAATCAAAATATGGCCAAATTGGAAAATGGACTATTTGATTCTTTTTATAGGATAG
1 TATTAAAAAGAATCAAAATATGGCCAAATTGGAAAATGGACTATTTGATTCTTTTTATAGGATAG
1592150 GGACTGAATTGATCTATTTAATTGGATGCATCATTGCTTTCACATGGTGGACCAATAATATCCAA
66 GGACTGAATTGATCTATTTAATTGGATGCATCATTGCTTTCACATGGTGGACCAATAATATCCAA
1592215 ATCTCATGATTTGCCTGGCCATTGTGAAACATTAGCGTGTGT
131 ATCTCATGATTTGCCTGGCCATTGTGAAACATTAGCGTGTGT
1592257 T
1 T
1592258 CCGCAGACGC
Statistics
Matches: 173, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 173 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.34
Consensus pattern (172 bp):
TATTAAAAAGAATCAAAATATGGCCAAATTGGAAAATGGACTATTTGATTCTTTTTATAGGATAG
GGACTGAATTGATCTATTTAATTGGATGCATCATTGCTTTCACATGGTGGACCAATAATATCCAA
ATCTCATGATTTGCCTGGCCATTGTGAAACATTAGCGTGTGT
Found at i:1599096 original size:20 final size:18
Alignment explanation
Indices: 1599073--1599121 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 18
1599063 TTAAAAAATA
*
1599073 TTTTATTTTCTTAAATTTAT
1 TTTTATTTTC--AAATATAT
1599093 TTTTGCATTTTCAAATATAT
1 TTTT--ATTTTCAAATATAT
1599113 TTTTATTTT
1 TTTTATTTT
1599122 ATTTTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 5 0.19
20 15 0.58
22 6 0.23
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTATTTTCAAATATAT
Found at i:1602584 original size:11 final size:11
Alignment explanation
Indices: 1602568--1602597 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1602558 TTATAGACAT
1602568 AAGAAGTATAA
1 AAGAAGTATAA
1602579 AAGAAGTATAA
1 AAGAAGTATAA
1602590 AAGAAGTA
1 AAGAAGTA
1602598 GAAATCTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (11 bp):
AAGAAGTATAA
Found at i:1611041 original size:23 final size:24
Alignment explanation
Indices: 1611010--1611071 Score: 83
Period size: 23 Copynumber: 2.6 Consensus size: 24
1611000 AAGAAATTTA
1611010 TTTATTTATTTGATATGTTGA-GAT
1 TTTA-TTATTTGATATGTTGACGAT
* *
1611034 TTTATTATTTGAT-TTTTGACGCT
1 TTTATTATTTGATATGTTGACGAT
1611057 TTTATTATTTGATAT
1 TTTATTATTTGATAT
1611072 TTAATATTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 5 0.15
23 24 0.71
24 5 0.15
ACGTcount: A:0.23, C:0.03, G:0.13, T:0.61
Consensus pattern (24 bp):
TTTATTATTTGATATGTTGACGAT
Found at i:1611873 original size:102 final size:103
Alignment explanation
Indices: 1611746--1611939 Score: 327
Period size: 102 Copynumber: 1.9 Consensus size: 103
1611736 ACTCAAAAAT
*
1611746 ATATTTTAAATGTATTTTAATTTATCTAAATATTTTTGAGCCAATCCAAAATGATTTT-GGTGTT
1 ATATTTTAAATGTATTTTAATTTATCTAAATATTTTTGAGCCAATCCAAAATGATTTTAAGTGTT
1611810 TTAAACTCATTTTATACAAGTATGGGAAGTTATATAAC
66 TTAAACTCATTTTATACAAGTATGGGAAGTTATATAAC
* * *
1611848 ATATTTTAAATGTATTTTAATTTATCTAAATATTTTTGAGTCAATCTAAAATGTTTTTAAGTGTT
1 ATATTTTAAATGTATTTTAATTTATCTAAATATTTTTGAGCCAATCCAAAATGATTTTAAGTGTT
* *
1611913 TTAAACTCGTTTTATACAAGTTTGGGA
66 TTAAACTCATTTTATACAAGTATGGGA
1611940 TGTTGTATCG
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
102 55 0.65
103 30 0.35
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.46
Consensus pattern (103 bp):
ATATTTTAAATGTATTTTAATTTATCTAAATATTTTTGAGCCAATCCAAAATGATTTTAAGTGTT
TTAAACTCATTTTATACAAGTATGGGAAGTTATATAAC
Found at i:1630112 original size:12 final size:10
Alignment explanation
Indices: 1630085--1630213 Score: 60
Period size: 10 Copynumber: 11.6 Consensus size: 10
1630075 TAACATGTTG
1630085 AATTTTAATT
1 AATTTTAATT
1630095 AATTTTATATT
1 AATTTTA-ATT
*
1630106 AAATTTTGATT
1 -AATTTTAATT
*
1630117 AATTTTGATT
1 AATTTTAATT
* *
1630127 TATTAAATAATT
1 AATT--TTAATT
**
1630139 AATTAAAATT
1 AATTTTAATT
1630149 AAAATTTTAACATGTT
1 --AATTTT-A-A--TT
1630165 GAATTTTAATT
1 -AATTTTAATT
1630176 AATTTTATATT
1 AATTTTA-ATT
*
1630187 AAATTTTGATT
1 -AATTTTAATT
*
1630198 AATTTTGATT
1 AATTTTAATT
*
1630208 TATTTT
1 AATTTT
1630214 CGACAGATTC
Statistics
Matches: 96, Mismatches: 11, Indels: 24
0.73 0.08 0.18
Matches are distributed among these distances:
10 47 0.49
11 14 0.15
12 23 0.24
13 2 0.02
14 2 0.02
15 6 0.06
16 2 0.02
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.56
Consensus pattern (10 bp):
AATTTTAATT
Found at i:1630153 original size:81 final size:82
Alignment explanation
Indices: 1630044--1630211 Score: 320
Period size: 81 Copynumber: 2.1 Consensus size: 82
1630034 TATATAATAA
*
1630044 TTATAAAATAATTAAATTAAAATTAAAATTTTAACATGTTGAATTTTAATTAATTTTATATTAAA
1 TTATTAAATAATTAAATTAAAATTAAAATTTTAACATGTTGAATTTTAATTAATTTTATATTAAA
1630109 TTTTGATTAATTTTGAT
66 TTTTGATTAATTTTGAT
1630126 TTATTAAATAATT-AATTAAAATTAAAATTTTAACATGTTGAATTTTAATTAATTTTATATTAAA
1 TTATTAAATAATTAAATTAAAATTAAAATTTTAACATGTTGAATTTTAATTAATTTTATATTAAA
1630190 TTTTGATTAATTTTGAT
66 TTTTGATTAATTTTGAT
1630207 TTATT
1 TTATT
1630212 TTCGACAGAT
Statistics
Matches: 85, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
81 73 0.86
82 12 0.14
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (82 bp):
TTATTAAATAATTAAATTAAAATTAAAATTTTAACATGTTGAATTTTAATTAATTTTATATTAAA
TTTTGATTAATTTTGAT
Found at i:1651820 original size:18 final size:19
Alignment explanation
Indices: 1651785--1651827 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
1651775 ATGCAATTAC
1651785 TTTGG-TTTGGAATATGAA
1 TTTGGTTTTGGAATATGAA
*
1651803 TTTGGTTTTGTAAT-TGAA
1 TTTGGTTTTGGAATATGAA
1651821 TTGTGGT
1 TT-TGGT
1651828 GTCAATGAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (19 bp):
TTTGGTTTTGGAATATGAA
Found at i:1655567 original size:19 final size:17
Alignment explanation
Indices: 1655545--1655579 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
1655535 TCAATCATCC
1655545 CTCATCTCATCATCTCTCA
1 CTCAT-TCATCAT-TCTCA
1655564 CTCATTCATCATTCTC
1 CTCATTCATCATTCTC
1655580 TTAACACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 7 0.44
19 5 0.31
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (17 bp):
CTCATTCATCATTCTCA
Found at i:1663993 original size:19 final size:19
Alignment explanation
Indices: 1663971--1664008 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1663961 TCAATCATCC
1663971 CTCATCCCATCATT-TCTCA
1 CTCAT-CCATCATTCTCTCA
*
1663990 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
1664009 ACACTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.21, C:0.39, G:0.00, T:0.39
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:1665877 original size:14 final size:14
Alignment explanation
Indices: 1665858--1665885 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1665848 GACTTGAGTT
1665858 CATCATTTTCCCAA
1 CATCATTTTCCCAA
1665872 CATCATTTTCCCAA
1 CATCATTTTCCCAA
1665886 AATTCAGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.00, T:0.36
Consensus pattern (14 bp):
CATCATTTTCCCAA
Found at i:1668446 original size:54 final size:54
Alignment explanation
Indices: 1668348--1668454 Score: 142
Period size: 54 Copynumber: 2.0 Consensus size: 54
1668338 GAAAACCTTA
* * * ** *
1668348 TTCCAAAAAACATCATTGTCCAAGAGGATGCTACTATTTGGGGGGAGGCTATTG
1 TTCCAAAAAACACCATTGTCCAAGAGGAAGCTACTACTCAGGGGGAGACTATTG
* *
1668402 TTCCAAAAAACACCATTGTTCAAGAGGAAGCTACTGCTCAGGGGGAGACTATT
1 TTCCAAAAAACACCATTGTCCAAGAGGAAGCTACTACTCAGGGGGAGACTATT
1668455 ATTTAGAAGG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (54 bp):
TTCCAAAAAACACCATTGTCCAAGAGGAAGCTACTACTCAGGGGGAGACTATTG
Found at i:1680492 original size:31 final size:31
Alignment explanation
Indices: 1680439--1680500 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
1680429 GTGTATTGAA
* *
1680439 AGAATGAAACTATACTGGGTATTAAAAGAAT
1 AGAATGAAAATATACTGAGTATTAAAAGAAT
* * *
1680470 AGAATGAAAATGTATTGAGTATTGAAAGAAT
1 AGAATGAAAATATACTGAGTATTAAAAGAAT
1680501 TCTTTGTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.48, C:0.03, G:0.21, T:0.27
Consensus pattern (31 bp):
AGAATGAAAATATACTGAGTATTAAAAGAAT
Found at i:1680500 original size:26 final size:26
Alignment explanation
Indices: 1680421--1680500 Score: 70
Period size: 31 Copynumber: 2.9 Consensus size: 26
1680411 TTAGTGAGTT
*
1680421 AATGTATTGTGTATTGAAAGAATGAA
1 AATGTATTGAGTATTGAAAGAATGAA
* * * *
1680447 ACTATACTGGGTATTAAAAGAATAGAATGAA
1 AATGTATTGAGTATT----GAA-AGAATGAA
1680478 AATGTATTGAGTATTGAAAGAAT
1 AATGTATTGAGTATTGAAAGAAT
1680501 TCTTTGTATT
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
26 16 0.39
27 3 0.07
30 3 0.07
31 19 0.46
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.31
Consensus pattern (26 bp):
AATGTATTGAGTATTGAAAGAATGAA
Found at i:1685520 original size:26 final size:26
Alignment explanation
Indices: 1685481--1685557 Score: 73
Period size: 31 Copynumber: 2.8 Consensus size: 26
1685471 GTGATTTGTT
* *
1685481 AATGTATTGTGTATTGAAAGAATGAA
1 AATGTACTGAGTATTGAAAGAATGAA
*
1685507 ATTGTACTGAGTATTGAAGGAATAGAATGAA
1 AATGTACTGAGTATT----GAA-AGAATGAA
*
1685538 AATGTATTGAGTATTGAAAG
1 AATGTACTGAGTATTGAAAG
1685558 TATTCTTTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
26 14 0.34
27 3 0.07
30 3 0.07
31 21 0.51
ACGTcount: A:0.42, C:0.01, G:0.25, T:0.32
Consensus pattern (26 bp):
AATGTACTGAGTATTGAAAGAATGAA
Found at i:1686657 original size:10 final size:9
Alignment explanation
Indices: 1686622--1686744 Score: 61
Period size: 9 Copynumber: 12.9 Consensus size: 9
1686612 AGAAAAATTT
1686622 AATTTTTTA
1 AATTTTTTA
*
1686631 ATTTTTTTA
1 AATTTTTTA
*
1686640 TATGTTTTTA
1 AAT-TTTTTA
1686650 GAATTTTTTTGA
1 -AA-TTTTTT-A
1686662 AATTTTTATA
1 AATTTTT-TA
*
1686672 ATTTTTTTA
1 AATTTTTTA
* * *
1686681 AAATATATA
1 AATTTTTTA
*
1686690 AATTTTGGT-
1 AATTTT-TTA
1686699 -ATTTTTATA
1 AATTTTT-TA
*
1686708 AATATTTTA
1 AATTTTTTA
*
1686717 AATTTTTAA
1 AATTTTTTA
1686726 AATTTATTTTA
1 AA-TT-TTTTA
*
1686737 GATTTTTT
1 AATTTTTT
1686745 GCAATTTTTG
Statistics
Matches: 85, Mismatches: 18, Indels: 22
0.68 0.14 0.18
Matches are distributed among these distances:
8 6 0.07
9 35 0.41
10 28 0.33
11 14 0.16
12 2 0.02
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (9 bp):
AATTTTTTA
Found at i:1686684 original size:20 final size:20
Alignment explanation
Indices: 1686622--1686684 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
1686612 AGAAAAATTT
1686622 AATTTTT-TAATTTTTTTATA
1 AATTTTTATAATTTTTTTA-A
** * *
1686642 TGTTTTTAGAATTTTTTTGA
1 AATTTTTATAATTTTTTTAA
1686662 AATTTTTATAATTTTTTTAA
1 AATTTTTATAATTTTTTTAA
1686682 AAT
1 AAT
1686685 ATATAAATTT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 25 0.74
21 9 0.26
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (20 bp):
AATTTTTATAATTTTTTTAA
Found at i:1686723 original size:20 final size:19
Alignment explanation
Indices: 1686699--1686743 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
1686689 AAATTTTGGT
1686699 ATTTTTATAAA-TATTTTAA
1 ATTTTTA-AAATTATTTTAA
*
1686718 ATTTTTAAAATTTATTTTAG
1 ATTTTTAAAA-TTATTTTAA
1686738 ATTTTT
1 ATTTTT
1686744 TGCAATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 3 0.13
19 7 0.30
20 13 0.57
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
ATTTTTAAAATTATTTTAA
Found at i:1694281 original size:6 final size:6
Alignment explanation
Indices: 1694266--1694295 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1694256 TACGTGTTCC
1694266 TTTC-T TTTCTT TTTCTT TTTCTT TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
1694296 ATTATCATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTCTT
Found at i:1695064 original size:63 final size:63
Alignment explanation
Indices: 1694941--1695065 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
1694931 GCCTATTTCT
* * * * *
1694941 AGGCCGTGTAACTCGCTATTTTGGAATTATAAGAACATGGGCTAGAGAAATGGACTTGTGTCC
1 AGGCCGTGTAACTCACTATTTTGGAATTATAAGAACATGGGCCAAAGAAACGGACGTGTGTCC
* * * * *
1695004 AGGCCGTGTAACTCATTGTTTTGGAATTA-GAGACACATGGGCCAAAGACACGGGCGTGTGTC
1 AGGCCGTGTAACTCACTATTTTGGAATTATAAGA-ACATGGGCCAAAGAAACGGACGTGTGTC
1695066 TAGGTCATAT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
62 3 0.06
63 48 0.94
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (63 bp):
AGGCCGTGTAACTCACTATTTTGGAATTATAAGAACATGGGCCAAAGAAACGGACGTGTGTCC
Found at i:1697453 original size:76 final size:75
Alignment explanation
Indices: 1697362--1697626 Score: 228
Period size: 76 Copynumber: 3.5 Consensus size: 75
1697352 TATAGAGGTT
* * * * *
1697362 GTGCCCAGCACTAGTCAGATAAACTGATGAAGATTTGTGCCTAG-TGCTAGTTGGAGAAACTGAA
1 GTGCCCAGCACTAGTCAGGTAAACTGACGAAGATTTGTGCCCAGCT-CTAGTCGGAGAAAC-CAA
1697426 -AATTATAATGAC
64 GAA-TATAATGAC
* * * * *
1697438 GTGCCTAGTACTAGTCAGGTACACTAACGAAGATTTGTGCCCAGCTCTAGTCGGATAAACCAATG
1 GTGCCCAGCACTAGTCAGGTAAACTGACGAAGATTTGTGCCCAGCTCTAGTCGGAGAAACCAA-G
*
1697503 AATATAATGAT
65 AATATAATGAC
* ** * * * ** * * *
1697514 GTGCCCAGCACTAGTTAGGTAAACTGACGAAGATTTGCACTCAACGCTAGTTAGATAAATCGACG
1 GTGCCCAGCACTAGTCAGGTAAACTGACGAAGATTTGTGCCCAGCTCTAGTCGGAGAAA-CCAAG
* *
1697579 AATATATTGAT
65 AATATAATGAC
* * *
1697590 GTGCCCAACACTAGTAAGGTAAACTAACGAAGATTTG
1 GTGCCCAGCACTAGTCAGGTAAACTGACGAAGATTTG
1697627 CTAACCACAA
Statistics
Matches: 156, Mismatches: 29, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
75 2 0.01
76 149 0.96
77 5 0.03
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (75 bp):
GTGCCCAGCACTAGTCAGGTAAACTGACGAAGATTTGTGCCCAGCTCTAGTCGGAGAAACCAAGA
ATATAATGAC
Found at i:1704467 original size:36 final size:36
Alignment explanation
Indices: 1704416--1704552 Score: 103
Period size: 36 Copynumber: 3.7 Consensus size: 36
1704406 GTTATAGAGG
**
1704416 TTGTGCCTAAAACTAGTCAGATAAACTGATGAAGAT
1 TTGTGCCTAGCACTAGTCAGATAAACTGATGAAGAT
* * * *
1704452 TTGTGCCTAGCACTAGTCGGAGAAACTGTTGAATAT
1 TTGTGCCTAGCACTAGTCAGATAAACTGATGAAGAT
* ** * *
1704488 AATGATGTGCCTAGTACTAGTCAGGCAAGCTGACGAAGAT
1 --T--TGTGCCTAGCACTAGTCAGATAAACTGATGAAGAT
** * *
1704528 TTACGCCCAGCACTAGTCGGATAAA
1 TTGTGCCTAGCACTAGTCAGATAAA
1704553 TCGACGAATA
Statistics
Matches: 75, Mismatches: 22, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
36 46 0.61
38 2 0.03
40 27 0.36
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (36 bp):
TTGTGCCTAGCACTAGTCAGATAAACTGATGAAGAT
Found at i:1704511 original size:76 final size:76
Alignment explanation
Indices: 1704417--1704584 Score: 203
Period size: 76 Copynumber: 2.2 Consensus size: 76
1704407 TTATAGAGGT
* * * ** * *
1704417 TGTGCCTAAAACTAGTCAGATAAACTGATGAAGATTTGTGCCTAGCACTAGTCGGAGAAA-CTGT
1 TGTGCCTAGAACTAGTCAGACAAACTGACGAAGATTTACGCCCAGCACTAGTCGGAGAAATC-GA
*
1704481 TGAATATAATGA
65 CGAATATAATGA
* * * *
1704493 TGTGCCTAGTACTAGTCAGGCAAGCTGACGAAGATTTACGCCCAGCACTAGTCGGATAAATCGAC
1 TGTGCCTAGAACTAGTCAGACAAACTGACGAAGATTTACGCCCAGCACTAGTCGGAGAAATCGAC
1704558 GAATATAATGA
66 GAATATAATGA
*
1704569 TGTGCCTAGCACTAGT
1 TGTGCCTAGAACTAGT
1704585 AGGGTAAACT
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
76 77 0.99
77 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (76 bp):
TGTGCCTAGAACTAGTCAGACAAACTGACGAAGATTTACGCCCAGCACTAGTCGGAGAAATCGAC
GAATATAATGA
Found at i:1704581 original size:40 final size:39
Alignment explanation
Indices: 1704453--1704584 Score: 112
Period size: 40 Copynumber: 3.4 Consensus size: 39
1704443 GATGAAGATT
**
1704453 TGTGCCTAGCACTAGTCGGAGAAACTGTTGAATATAATGA
1 TGTGCCTAGCACTAGTCGGA-AAACTGACGAATATAATGA
* * * *
1704493 TGTGCCTAGTACTAGTCAGGCAAGCTGACGAAGAT--T--
1 TGTGCCTAGCACTAGTC-GGAAAACTGACGAATATAATGA
** *
1704529 TACGCCCAGCACTAGTCGGATAAA-TCGACGAATATAATGA
1 TGTGCCTAGCACTAGTCGGA-AAACT-GACGAATATAATGA
1704569 TGTGCCTAGCACTAGT
1 TGTGCCTAGCACTAGT
1704585 AGGGTAAACT
Statistics
Matches: 69, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
35 3 0.04
36 23 0.33
38 2 0.03
40 39 0.57
41 2 0.03
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (39 bp):
TGTGCCTAGCACTAGTCGGAAAACTGACGAATATAATGA
Found at i:1704603 original size:76 final size:76
Alignment explanation
Indices: 1704460--1704605 Score: 188
Period size: 76 Copynumber: 1.9 Consensus size: 76
1704450 ATTTGTGCCT
** * * * *
1704460 AGCACTAGTCGGAGAAACTGTTGAATATAATGATGTGCCTAGTACTAGTCAGGCAAGCTGACGAA
1 AGCACTAGTCGGAGAAACTGACGAATATAATGATGTGCCTAGCACTAGTCAGGCAAACTAACAAA
1704525 GATTTACGCCC
66 GATTTACGCCC
* *
1704536 AGCACTAGTCGGATAAA-TCGACGAATATAATGATGTGCCTAGCACTAGT-AGGGTAAACTAACA
1 AGCACTAGTCGGAGAAACT-GACGAATATAATGATGTGCCTAGCACTAGTCA-GGCAAACTAACA
1704599 AAGATTT
64 AAGATTT
1704606 GCTCACCAAG
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
75 2 0.03
76 58 0.97
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (76 bp):
AGCACTAGTCGGAGAAACTGACGAATATAATGATGTGCCTAGCACTAGTCAGGCAAACTAACAAA
GATTTACGCCC
Found at i:1715744 original size:80 final size:80
Alignment explanation
Indices: 1715611--1715773 Score: 326
Period size: 80 Copynumber: 2.0 Consensus size: 80
1715601 ACCATATTTT
1715611 AGATAACTCCATCTTTTTCAATGTTAAGATAATCTCGATACAAAATTCATCAACTCTCTATTTCT
1 AGATAACTCCATCTTTTTCAATGTTAAGATAATCTCGATACAAAATTCATCAACTCTCTATTTCT
1715676 ATAATCAACAAAGTC
66 ATAATCAACAAAGTC
1715691 AGATAACTCCATCTTTTTCAATGTTAAGATAATCTCGATACAAAATTCATCAACTCTCTATTTCT
1 AGATAACTCCATCTTTTTCAATGTTAAGATAATCTCGATACAAAATTCATCAACTCTCTATTTCT
1715756 ATAATCAACAAAGTC
66 ATAATCAACAAAGTC
1715771 AGA
1 AGA
1715774 AATATCACAT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 83 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (80 bp):
AGATAACTCCATCTTTTTCAATGTTAAGATAATCTCGATACAAAATTCATCAACTCTCTATTTCT
ATAATCAACAAAGTC
Found at i:1720761 original size:43 final size:42
Alignment explanation
Indices: 1720695--1720827 Score: 123
Period size: 41 Copynumber: 3.1 Consensus size: 42
1720685 GGCTCATACA
1720695 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGTAATCACATATTG
1 ATGCC-ACTGTCCCAGACAG-GGTCTTACA-GTAATCACATATTG
** * *
1720738 ATGCCACTGTCCCAGACAGGGTCTTACACAAATCAAATA-CG
1 ATGCCACTGTCCCAGACAGGGTCTTACAGTAATCACATATTG
* *
1720779 ATGCCAATGTCCCAGACATGGTCTTACACGT-ATACACA-ATTCG
1 ATGCCACTGTCCCAGACAGGGTCTTACA-GTAAT-CACATATT-G
1720822 ATGCCA
1 ATGCCA
1720828 ACATCCCAGA
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
41 30 0.41
42 13 0.18
43 30 0.41
44 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (42 bp):
ATGCCACTGTCCCAGACAGGGTCTTACAGTAATCACATATTG
Found at i:1720794 original size:41 final size:41
Alignment explanation
Indices: 1720690--1720807 Score: 130
Period size: 41 Copynumber: 2.8 Consensus size: 41
1720680 CGGAAGGCTC
* * ** *
1720690 ATACAATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCAC
1 ATACGATGCCAATGTCCCAGACAG-GGTCTTACA-CAAATCAA
* *
1720732 ATATTGATGCCACTGTCCCAGACAGGGTCTTACACAAATCAA
1 ATA-CGATGCCAATGTCCCAGACAGGGTCTTACACAAATCAA
*
1720774 ATACGATGCCAATGTCCCAGACATGGTCTTACAC
1 ATACGATGCCAATGTCCCAGACAGGGTCTTACAC
1720808 GTATACACAA
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
41 28 0.44
42 11 0.17
43 24 0.38
44 1 0.02
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (41 bp):
ATACGATGCCAATGTCCCAGACAGGGTCTTACACAAATCAA
Found at i:1720837 original size:43 final size:43
Alignment explanation
Indices: 1720695--1720851 Score: 162
Period size: 43 Copynumber: 3.7 Consensus size: 43
1720685 GGCTCATACA
* *
1720695 ATGCCAACGTCCCAGACGTGGTCTTACATGTA-ATCACATATT-G
1 ATGCCAACGTCCCAGACATGGTCTTACACGTATA-CACA-ATTCG
* ** *
1720738 ATGCC-ACTGTCCCAGACAGGGTCTTACACAAAT-CA-AATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGTATACACAATTCG
*
1720779 ATGCCAATGTCCCAGACATGGTCTTACACGTATACACAATTCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTATACACAATTCG
* * *
1720822 ATGCCAACATCCCAGACGTGTTCTTACACG
1 ATGCCAACGTCCCAGACATGGTCTTACACG
1720852 AAAATACATA
Statistics
Matches: 93, Mismatches: 15, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
40 2 0.02
41 29 0.31
42 7 0.08
43 55 0.59
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTATACACAATTCG
Found at i:1723514 original size:22 final size:20
Alignment explanation
Indices: 1723463--1723514 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
1723453 AATTGATCCT
1723463 AATTTTAAAAAAATTAAAGA
1 AATTTTAAAAAAATTAAAGA
*
1723483 AATATATAAAAATACA-TAAAGAA
1 AAT-TTTAAAAA-A-ATTAAAG-A
1723506 AATTTTAAA
1 AATTTTAAA
1723515 TTTTATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 3 0.12
21 7 0.27
22 11 0.42
23 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (20 bp):
AATTTTAAAAAAATTAAAGA
Found at i:1723546 original size:19 final size:20
Alignment explanation
Indices: 1723505--1723546 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
1723495 TACATAAAGA
*
1723505 AAAT-TTTAAATTTTATATT
1 AAATATTTAAATTTCATATT
1723524 -AATATTTAAA-TTCATATT
1 AAATATTTAAATTTCATATT
1723542 AAATA
1 AAATA
1723547 AATATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATATTTAAATTTCATATT
Found at i:1729797 original size:20 final size:21
Alignment explanation
Indices: 1729756--1729796 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1729746 TTTGTCCGGG
* *
1729756 CTCAAAATTAAATAAATAAAA
1 CTCAAAATAAAAAAAATAAAA
1729777 CTCAAAATAAAAAAAATAAA
1 CTCAAAATAAAAAAAATAAA
1729797 CAGTCCATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.20
Consensus pattern (21 bp):
CTCAAAATAAAAAAAATAAAA
Found at i:1731266 original size:147 final size:146
Alignment explanation
Indices: 1731018--1731310 Score: 516
Period size: 147 Copynumber: 2.0 Consensus size: 146
1731008 TTTTAATCTC
1731018 AATTTAATCTTTTATTCGCTTAATTTCAAGCTTTCATTTATTTATTTATTCTTTTTTTTTCTGTT
1 AATTTAATCTTTTATTCGCTTAATTTCAAGCTTTCATTTATTTATTTATTCTTTTTTTTTCTGTT
* *
1731083 TTATTTATTTGTACATTCATTCATTTATCTATTTCTTTACTTTTCTTGTACTTAGAATTTATATT
66 TTATTTATTTATACATTCATTCATTTATCTATTTCTTTACTTTTATTGTACTTAGAATTTATATT
*
1731148 GTTATTTATTCATTTA
131 ATTATTTATTCATTTA
1731164 AATTTAATC-TTTATTCGCTTAATTTCAAGCTTTCATTTATTTATTTATTCTTTTTTTTGTTCTG
1 AATTTAATCTTTTATTCGCTTAATTTCAAGCTTTCATTTATTTATTTATTC-TTTTTTT-TTCTG
*
1731228 TTTTATTTATTTATACATTCATTCATTTATCTATTTCTTTACTTTTATTGTATTTAGAATTTATA
64 TTTTATTTATTTATACATTCATTCATTTATCTATTTCTTTACTTTTATTGTACTTAGAATTTATA
*
1731293 TTATTATTTATTCCTTTA
129 TTATTATTTATTCATTTA
1731311 TTTATACATT
Statistics
Matches: 140, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
145 41 0.29
146 16 0.11
147 83 0.59
ACGTcount: A:0.23, C:0.11, G:0.04, T:0.62
Consensus pattern (146 bp):
AATTTAATCTTTTATTCGCTTAATTTCAAGCTTTCATTTATTTATTTATTCTTTTTTTTTCTGTT
TTATTTATTTATACATTCATTCATTTATCTATTTCTTTACTTTTATTGTACTTAGAATTTATATT
ATTATTTATTCATTTA
Found at i:1731330 original size:15 final size:15
Alignment explanation
Indices: 1731312--1731345 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1731302 ATTCCTTTAT
1731312 TTATACATT-TCATTA
1 TTAT-CATTATCATTA
1731327 TTATCATTATCATTA
1 TTATCATTATCATTA
1731342 TTAT
1 TTAT
1731346 TAGTGTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATCATTATCATTA
Found at i:1738240 original size:13 final size:13
Alignment explanation
Indices: 1738220--1738255 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1738210 TCAAAGTTAT
1738220 CCTAGCCCAAATA
1 CCTAGCCCAAATA
*
1738233 CTTAGCCCAAATA
1 CCTAGCCCAAATA
1738246 CCTAGCCCAA
1 CCTAGCCCAA
1738256 TTGCTAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.39, G:0.08, T:0.17
Consensus pattern (13 bp):
CCTAGCCCAAATA
Found at i:1738656 original size:23 final size:22
Alignment explanation
Indices: 1738626--1738668 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
1738616 AATTTTACGA
1738626 TTTCTTTT-TTTCTTCTTCTTTGT
1 TTTCTTTTGTTT-TTC-TCTTTGT
1738649 TTTCTTTTGTTTTTCTCTTT
1 TTTCTTTTGTTTTTCTCTTT
1738669 CCAAATCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 11 0.58
24 3 0.16
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (22 bp):
TTTCTTTTGTTTTTCTCTTTGT
Found at i:1739512 original size:45 final size:46
Alignment explanation
Indices: 1739417--1739543 Score: 123
Period size: 45 Copynumber: 2.7 Consensus size: 46
1739407 ACATTGTTTT
* * * * * * *
1739417 AAATTTATCATTAGTATTATTTTAATATATAATATACTATTATTTT
1 AAATTTATCATTAATATTATTTAAATTTATCATACACTATAATTTG
1739463 AAA-TTATCATTAATATTATTTAAATTTATCATACA-TCATAATTTG
1 AAATTTATCATTAATATTATTTAAATTTATCATACACT-ATAATTTG
* * *
1739508 AAATTTATCATGTACTATAATTTTAAACTTATCATA
1 AAATTTATCAT-TAATATTA-TTTAAATTTATCATA
1739544 TCATTATTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
44 1 0.01
45 36 0.54
46 10 0.15
47 6 0.09
48 14 0.21
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (46 bp):
AAATTTATCATTAATATTATTTAAATTTATCATACACTATAATTTG
Found at i:1739514 original size:24 final size:21
Alignment explanation
Indices: 1739414--1739543 Score: 75
Period size: 24 Copynumber: 5.7 Consensus size: 21
1739404 TTAACATTGT
* *
1739414 TTTAAATTTATCATTAGTATTAT
1 TTTAAATTTATCA-TACTA-TAA
* *
1739437 TTTAATATATAAT-ATACTATTAT
1 TTTAA-AT-TTATCATACTA-TAA
* *
1739460 TTTAAA-TTATCATTAATATTA
1 TTTAAATTTATCA-TACTATAA
1739481 TTTAAATTTATCATACATCATAA
1 TTTAAATTTATCATAC-T-ATAA
1739504 TTTGAAATTTATCATGTACTATAA
1 TTT-AAATTTATCA--TACTATAA
*
1739528 TTTTAAACTTATCATA
1 -TTTAAATTTATCATA
1739544 TCATTATTTA
Statistics
Matches: 87, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
20 3 0.03
21 10 0.11
22 14 0.16
23 24 0.28
24 26 0.30
25 7 0.08
26 3 0.03
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (21 bp):
TTTAAATTTATCATACTATAA
Found at i:1744260 original size:9 final size:9
Alignment explanation
Indices: 1744243--1744273 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1744233 TCGAGTTGAT
1744243 TCGAATAAC
1 TCGAATAAC
*
1744252 TCGATTAAC
1 TCGAATAAC
1744261 TCGAATAAC
1 TCGAATAAC
1744270 TCGA
1 TCGA
1744274 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:1747327 original size:89 final size:91
Alignment explanation
Indices: 1747203--1747550 Score: 239
Period size: 89 Copynumber: 3.8 Consensus size: 91
1747193 CATCATGGTA
* *
1747203 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGC-CATT-AG-TCTTATCTCTCTGAAG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAA-CAAATTCAGATCTTATCTCTCTGAAG
*
1747265 TTGCAGTGGAGCAGACTGAAGATAGCG
65 TTGCAGTAGAGCAGACTGAAGATAGCG
* * *
1747292 AATCTTATTTCCTTGAAGTTGCAGTGGAATGGATTAAACTATAAATTGCAGATCTTATCTCTCTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAAC---AAATT-CAGATCTTATCTCTCTG
* * *
1747357 AAGTTGCAGTAGAGCAGA-TCATG--A-CA
62 AAGTTGCAGTAGAGCAGACTGAAGATAGCG
* * ** * * *** *
1747383 AACCTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTGAAGTTA-CCA-AGTCTTATCTC-CTTGAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAACAAATTCAGA-TCTTATCTCTC-TGAA
* * * *
1747445 GTCGCAGTAGAGAAGACTGAAGATCATATCA
64 GTTGCAGTAGAGCAGACTGAAG---ATAGCG
* * * * *
1747476 AATCTTATTTCCCTGAAGTTGCAGTGGAACATATTGAAGCTATAAATTGTAGATCTTATCTCTCT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAATAGATT-AA---ACAAATT-CAGATCTTATCTCTCT
1747541 GAAGTTGCAG
61 GAAGTTGCAG
1747551 CAGATCATAG
Statistics
Matches: 196, Mismatches: 39, Indels: 38
0.72 0.14 0.14
Matches are distributed among these distances:
85 2 0.01
86 29 0.15
87 3 0.02
88 2 0.01
89 34 0.17
91 30 0.15
92 5 0.03
93 31 0.16
94 6 0.03
95 30 0.15
97 2 0.01
99 20 0.10
100 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (91 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTAAACAAATTCAGATCTTATCTCTCTGAAGT
TGCAGTAGAGCAGACTGAAGATAGCG
Found at i:1747514 original size:48 final size:47
Alignment explanation
Indices: 1747372--1747514 Score: 123
Period size: 48 Copynumber: 3.0 Consensus size: 47
1747362 GCAGTAGAGC
* * * *
1747372 AGATCATGACAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTGA
1 AGATCAT-ACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGA
* * * * *
1747420 AG-T--TACCAAGTCTTATCTCCTTGAAGTCGCAGTAGAGA-AGACTGA
1 AGATCATA-CAAATCTTATCTCCCTGAAGTTGCAGTGGA-ACAGATTGA
* *
1747465 AGATCATATCAAATCTTATTTCCCTGAAGTTGCAGTGGAACATATTGA
1 AGATCATA-CAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGA
1747513 AG
1 AG
1747515 CTATAAATTG
Statistics
Matches: 72, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
44 1 0.01
45 32 0.44
46 1 0.01
47 2 0.03
48 36 0.50
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (47 bp):
AGATCATACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGA
Found at i:1747558 original size:180 final size:175
Alignment explanation
Indices: 1747206--1747594 Score: 462
Period size: 180 Copynumber: 2.2 Consensus size: 175
1747196 CATGGTAAAT
* *
1747206 CTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCATTAGTCTTATCTCTCTGAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-TAGTCTTATCTCTCTGAAGTCGCAG
* * * * **
1747271 TGGAGCAGACTGAAGATAGCGAATCTTATTTCCTTGAAGTTGCAGTGGAATGGATTAAACTATAA
65 TAGAGAAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAACTATAA
1747336 ATTGCAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCAT-GACAAAC
130 ATTGCAGATCTTATCTCTCTGAAGTTGC---A-AGCAGATCATAG-CAAAC
* * *
1747386 CTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTGAAGTTACCA-AGTCTTATCTC-CTTGAAGTCG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG---CCATAGTCTTATCTCTC-TGAAGTCG
* *
1747449 CAGTAGAGAAGACTGAAGATCATATCAAATCTTATTTCCCTGAAGTTGCAGTGGAACATATTGAA
62 CAGTAGAGAAGACTGAAG---ATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATT-AA
* *
1747514 GCTATAAATTGTAGATCTTATCTCTCTGAAGTTGC-AGCAGATCATAGCAAAC
123 ACTATAAATTGCAGATCTTATCTCTCTGAAGTTGCAAGCAGATCATAGCAAAC
* * *
1747566 ATTATCGCCCTGAAGTTACAGTGGAGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAG
1747595 TTGTAGTAGA
Statistics
Matches: 181, Mismatches: 19, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
180 73 0.40
181 35 0.19
183 3 0.02
184 35 0.19
185 35 0.19
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (175 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCATAGTCTTATCTCTCTGAAGTCGCAGT
AGAGAAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAACTATAAA
TTGCAGATCTTATCTCTCTGAAGTTGCAAGCAGATCATAGCAAAC
Found at i:1747829 original size:21 final size:19
Alignment explanation
Indices: 1747803--1747841 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 19
1747793 TTTTCCCAGG
1747803 CCCAAAACTAAATAAATAAAA
1 CCCAAAA-TAAA-AAATAAAA
1747824 CCCAAAATAAAAAATAAA
1 CCCAAAATAAAAAATAAA
1747842 CAATCCATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.69, C:0.18, G:0.00, T:0.13
Consensus pattern (19 bp):
CCCAAAATAAAAAATAAAA
Found at i:1750916 original size:31 final size:31
Alignment explanation
Indices: 1750881--1750940 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1750871 TTTTTAGTTA
* * *
1750881 AATTTAACTCTCAATATTTCAAAATGAGTCC
1 AATTTAACTATCAACATTTCAAAAAGAGTCC
* *
1750912 AATTTAGCTATCACCATTTCAAAAAGAGT
1 AATTTAACTATCAACATTTCAAAAAGAGT
1750941 TGACTTGTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.33
Consensus pattern (31 bp):
AATTTAACTATCAACATTTCAAAAAGAGTCC
Found at i:1755952 original size:11 final size:10
Alignment explanation
Indices: 1755927--1755968 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
1755917 TTTTTACAAG
1755927 TATATAAAAA
1 TATATAAAAA
1755937 T-TATAAAATA
1 TATATAAAA-A
1755947 TATATAAAAA
1 TATATAAAAA
*
1755957 CATGATAAAAA
1 TAT-ATAAAAA
1755968 T
1 T
1755969 CCTAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 7 0.26
10 6 0.22
11 14 0.52
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (10 bp):
TATATAAAAA
Found at i:1756381 original size:20 final size:21
Alignment explanation
Indices: 1756338--1756383 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
1756328 CCTTTTTTTT
*
1756338 TTTTTTTTAAAGAATTTTGAA
1 TTTTTTTTAAAGAATTATGAA
1756359 TTTTTTTTAAA-AATTAT-ATA
1 TTTTTTTTAAAGAATTATGA-A
1756379 TTTTT
1 TTTTT
1756384 AAAATTGTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 11 0.48
21 11 0.48
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (21 bp):
TTTTTTTTAAAGAATTATGAA
Found at i:1759880 original size:40 final size:40
Alignment explanation
Indices: 1759807--1759926 Score: 95
Period size: 40 Copynumber: 3.0 Consensus size: 40
1759797 AAACTGTTCA
* *
1759807 TCCACGTCAGCAAATCGCGTCCT--CGTAGG-CGCGATTTGTG
1 TCCACGTAAGCAAATCGCG--CTGACGT-GGACGCGATTTCTG
1759847 TCCACGTAAGCAAATCGCGCTGACGTGGACGCGATGTTCTG
1 TCCACGTAAGCAAATCGCGCTGACGTGGACGCGAT-TTCTG
* ** * *
1759888 -ACACGTACCCTGACATCGCGCTGACGTGGACGTGATTTC
1 TCCACGTAAGC--AAATCGCGCTGACGTGGACGCGATTTC
1759927 GCGGAAAATA
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 34 0.51
41 7 0.10
42 22 0.33
ACGTcount: A:0.20, C:0.29, G:0.28, T:0.23
Consensus pattern (40 bp):
TCCACGTAAGCAAATCGCGCTGACGTGGACGCGATTTCTG
Found at i:1764553 original size:17 final size:18
Alignment explanation
Indices: 1764521--1764555 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1764511 TAGGGCCAAA
1764521 ACCCGCATGTGTGACCCG
1 ACCCGCATGTGTGACCCG
*
1764539 ACCCGCTTG-GTGACCCG
1 ACCCGCATGTGTGACCCG
1764556 CGTGTTTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.14, C:0.40, G:0.29, T:0.17
Consensus pattern (18 bp):
ACCCGCATGTGTGACCCG
Found at i:1766182 original size:10 final size:10
Alignment explanation
Indices: 1766153--1766183 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1766143 AGTATGAATG
*
1766153 GTGAGAATTG
1 GTGAGAATTA
1766163 GTGAGAATTA
1 GTGAGAATTA
1766173 GTGAGAATTA
1 GTGAGAATTA
1766183 G
1 G
1766184 ACTAAATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (10 bp):
GTGAGAATTA
Found at i:1766588 original size:51 final size:51
Alignment explanation
Indices: 1766511--1766611 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
1766501 AGATACTTGA
** * *
1766511 GTATCCGAGTTCGTTTAATAACGTTCATCGGGTGAAATAAATTACATGAAG
1 GTATCCGAGCCCGTTTAATAACGTTCATCGGGCGAAACAAATTACATGAAG
* *
1766562 GTATCCGAGCCCGTTTACTAAGGTTCATCGGGCGAAACAAATTACATGAA
1 GTATCCGAGCCCGTTTAATAACGTTCATCGGGCGAAACAAATTACATGAA
1766612 TTGAGAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28
Consensus pattern (51 bp):
GTATCCGAGCCCGTTTAATAACGTTCATCGGGCGAAACAAATTACATGAAG
Found at i:1767457 original size:31 final size:31
Alignment explanation
Indices: 1767419--1767478 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 31
1767409 GATTTAAATA
1767419 TTTTTTAA-TTTTAAAATATTTTTAAAATACT
1 TTTTTTAATTTTTAAAA-ATTTTTAAAATACT
1767450 TTTTTTAATTTTTAAAAATTTTTAAAATA
1 TTTTTTAATTTTTAAAAATTTTTAAAATA
1767479 AAAATGGGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (31 bp):
TTTTTTAATTTTTAAAAATTTTTAAAATACT
Found at i:1767469 original size:10 final size:11
Alignment explanation
Indices: 1767427--1767478 Score: 56
Period size: 10 Copynumber: 4.9 Consensus size: 11
1767417 TATTTTTTAA
1767427 TTTTAAAATAT
1 TTTTAAAATAT
1767438 TTTTAAAATACT
1 TTTTAAAATA-T
**
1767450 TTTT-TTA-AT
1 TTTTAAAATAT
1767459 TTTTAAAA-AT
1 TTTTAAAATAT
1767469 TTTTAAAATA
1 TTTTAAAATA
1767479 AAAATGGGCC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 5 0.15
10 12 0.35
11 12 0.35
12 5 0.15
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:1771047 original size:8 final size:8
Alignment explanation
Indices: 1771030--1771091 Score: 115
Period size: 8 Copynumber: 7.8 Consensus size: 8
1771020 TACTTGGGAA
1771030 AAATGATT
1 AAATGATT
*
1771038 AAATGGTT
1 AAATGATT
1771046 AAATGATT
1 AAATGATT
1771054 AAATGATT
1 AAATGATT
1771062 AAATGATT
1 AAATGATT
1771070 AAATGATT
1 AAATGATT
1771078 AAATGATT
1 AAATGATT
1771086 AAATGA
1 AAATGA
1771092 ACTTGAACAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (8 bp):
AAATGATT
Found at i:1774876 original size:17 final size:17
Alignment explanation
Indices: 1774849--1774882 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1774839 CCATTTTTAA
1774849 TTTTAATTTTAATATATT
1 TTTTAATTTTAAT-TATT
1774867 TTTTAA-TTTAATTATT
1 TTTTAATTTTAATTATT
1774883 ACGTTTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 6 0.38
18 6 0.38
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTAATTTTAATTATT
Found at i:1780469 original size:20 final size:20
Alignment explanation
Indices: 1780444--1780483 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1780434 AATGGTAAGT
*
1780444 AAAATGGTAAATATGCATGA
1 AAAATGGTAAATATACATGA
1780464 AAAATGGTAAATATACATGA
1 AAAATGGTAAATATACATGA
1780484 TTTTTGCTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.17, T:0.25
Consensus pattern (20 bp):
AAAATGGTAAATATACATGA
Found at i:1782385 original size:12 final size:12
Alignment explanation
Indices: 1782368--1782397 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1782358 ACAAAGTCCG
1782368 AATTTAATTTCC
1 AATTTAATTTCC
*
1782380 AATTTAATTTCT
1 AATTTAATTTCC
1782392 AATTTA
1 AATTTA
1782398 TTTATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTAATTTCC
Found at i:1782402 original size:4 final size:4
Alignment explanation
Indices: 1782393--1782418 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1782383 TTAATTTCTA
1782393 ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT
1782419 GCTATTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:1787913 original size:3 final size:3
Alignment explanation
Indices: 1787905--1787945 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
1787895 GTTATTAGGC
* * *
1787905 TTA TTA TTA TTA TGA TTA TTA TTA TTA TTA TCA TTA ATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1787946 TTCGTATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1788104 original size:9 final size:9
Alignment explanation
Indices: 1788081--1788130 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
1788071 ACATAGATTT
*
1788081 TTATTTTTA
1 TTATTTTCA
*
1788090 TAATTTT-A
1 TTATTTTCA
1788098 TTTATTTTCA
1 -TTATTTTCA
1788108 TTATTTTCA
1 TTATTTTCA
*
1788117 TTATTGTC-
1 TTATTTTCA
1788125 TTATTT
1 TTATTT
1788131 GATATTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 6 0.17
9 28 0.80
10 1 0.03
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.70
Consensus pattern (9 bp):
TTATTTTCA
Found at i:1788113 original size:18 final size:18
Alignment explanation
Indices: 1788080--1788141 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
1788070 TACATAGATT
* *
1788080 TTTATTTTTATAATTTTA
1 TTTATTTTCATTATTTTA
1788098 TTTATTTTCATTATTTTCA
1 TTTATTTTCATTATTTT-A
*
1788117 -TTATTGTC-TTATTTGATA
1 TTTATTTTCATTATTT--TA
1788135 TTTATTT
1 TTTATTT
1788142 ATGTGTTCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
17 6 0.17
18 23 0.64
19 7 0.19
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTATTTTCATTATTTTA
Found at i:1789354 original size:11 final size:11
Alignment explanation
Indices: 1789334--1789371 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
1789324 TAAAAATTAA
1789334 AAAAAGTATTTT
1 AAAAA-TATTTT
1789346 AAAAATATTTT
1 AAAAATATTTT
*
1789357 TAAAATATTTT
1 AAAAATATTTT
1789368 AAAA
1 AAAA
1789372 TTAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 19 0.79
12 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:1789390 original size:40 final size:40
Alignment explanation
Indices: 1789319--1789499 Score: 206
Period size: 40 Copynumber: 4.5 Consensus size: 40
1789309 ACCAAAAATT
** *
1789319 TATTTTAAAAATTAAAAAAAGTATTTTAAAAATATTTTTAAAA
1 TATTTT-AAAATTAAAAAAA--ATTAAAAAAATATTTTAAAAA
1789362 TATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTT-AAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAA-TATTTTAAAAA
***
1789402 T-TAAAAAAATT-AAAAAAATTAAAAAAAATATTTTAAAAA
1 TATTTTAAAATTAAAAAAAATT-AAAAAAATATTTTAAAAA
* * * *
1789441 TATTTTAAAATTTAAAAAAATTAAAAAAGTATGTAAAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAATATTTTAAAAA
1789481 TATTTTAAAATTAAAAAAA
1 TATTTTAAAATTAAAAAAA
1789500 TAAATATATT
Statistics
Matches: 121, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
38 15 0.12
39 19 0.16
40 53 0.44
41 15 0.12
42 13 0.11
43 6 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAAATTAAAAAAATATTTTAAAAA
Found at i:1789396 original size:30 final size:28
Alignment explanation
Indices: 1789358--1789468 Score: 119
Period size: 29 Copynumber: 4.1 Consensus size: 28
1789348 AAATATTTTT
1789358 AAAATATTTTAAAATTAAAAAAAATTAAA
1 AAAATATTTTAAAATT-AAAAAAATTAAA
1789387 AAAAGTATTTTAAAATTAAAAAAATT-AA
1 AAAA-TATTTTAAAATTAAAAAAATTAAA
* **
1789415 AAAA-A--TT-AAA--AAAAATATTTTA
1 AAAATATTTTAAAATTAAAAAAATTAAA
1789437 AAAATATTTTAAAATTTAAAAAAATTAAA
1 AAAATATTTTAAAA-TTAAAAAAATTAAA
1789466 AAA
1 AAA
1789469 GTATGTAAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
21 8 0.12
22 5 0.07
23 4 0.06
24 2 0.03
25 2 0.03
26 4 0.06
28 6 0.09
29 25 0.37
30 12 0.18
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.32
Consensus pattern (28 bp):
AAAATATTTTAAAATTAAAAAAATTAAA
Found at i:1789460 original size:10 final size:10
Alignment explanation
Indices: 1789368--1789468 Score: 54
Period size: 9 Copynumber: 10.3 Consensus size: 10
1789358 AAAATATTTT
1789368 AAAA-TTAAA
1 AAAATTTAAA
*
1789377 AAAAATTAAA
1 AAAATTTAAA
**
1789387 AAAAGTATT-TT
1 AAAA-T-TTAAA
1789398 AAAA-TTAAA
1 AAAATTTAAA
1789407 AAAA-TTAAA
1 AAAATTTAAA
*
1789416 AAAATTAAAAA
1 AAAATT-TAAA
1789427 AAATATTTTAAA
1 AAA-A-TTTAAA
* *
1789439 AATATTT--T
1 AAAATTTAAA
1789447 AAAATTTAAA
1 AAAATTTAAA
1789457 AAAA-TTAAA
1 AAAATTTAAA
1789466 AAA
1 AAA
1789469 GTATGTAAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 20
0.70 0.11 0.20
Matches are distributed among these distances:
8 8 0.11
9 25 0.35
10 17 0.24
11 11 0.15
12 8 0.11
13 2 0.03
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:1789467 original size:89 final size:90
Alignment explanation
Indices: 1789325--1789500 Score: 261
Period size: 89 Copynumber: 2.0 Consensus size: 90
1789315 AATTTATTTT
* **
1789325 AAAAATTAAAAAAAGTATTTTAAAAATATTTTTAAAATATTTTAAAATTAAAAAA-AAT-TAAAA
1 AAAAATTAAAAAAAATATTTTAAAAATATTTTTAAAATATTAAAAAATTAAAAAAGAATGT-AAA
1789388 AAAGTATTTTAAAATTAAAAAAATTAA
65 AAA-TATTTTAAAATTAAAAAAATTAA
*
1789415 AAAAATTAAAAAAAATATTTTAAAAATA-TTTTAAAAT-TTAAAAAAATTAAAAAAGTATGTAAA
1 AAAAATTAAAAAAAATATTTTAAAAATATTTTTAAAATATT-AAAAAATTAAAAAAGAATGTAAA
1789478 AAATATTTTAAAATTAAAAAAAT
65 AAATATTTTAAAATTAAAAAAAT
1789501 AAATATATTT
Statistics
Matches: 79, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
88 2 0.03
89 41 0.52
90 35 0.44
91 1 0.01
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (90 bp):
AAAAATTAAAAAAAATATTTTAAAAATATTTTTAAAATATTAAAAAATTAAAAAAGAATGTAAAA
AATATTTTAAAATTAAAAAAATTAA
Found at i:1789481 original size:79 final size:80
Alignment explanation
Indices: 1789346--1789500 Score: 224
Period size: 79 Copynumber: 1.9 Consensus size: 80
1789336 AAAGTATTTT
* **
1789346 AAAAATATTTTTAAAATATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAT-TAAAAAA
1 AAAAATATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAAGTATTAAAAAATATAAAAAA
1789410 ATTAAAAAAATTAAA
66 ATTAAAAAAATTAAA
* ***
1789425 AAAAATATTTTAAAAATATTTTAAAATTTAAAAAAATT-AAAAAAGTATGTAAAAAATATTTTAA
1 AAAAATATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAAGTAT-TAAAAAATATAAAAA
1789489 AATTAAAAAAAT
65 AATTAAAAAAAT
1789501 AAATATATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
78 10 0.15
79 42 0.63
80 15 0.22
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (80 bp):
AAAAATATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAAGTATTAAAAAATATAAAAAA
ATTAAAAAAATTAAA
Found at i:1789491 original size:10 final size:11
Alignment explanation
Indices: 1789425--1789450 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1789415 AAAAATTAAA
1789425 AAAAATATTTT
1 AAAAATATTTT
1789436 AAAAATATTTT
1 AAAAATATTTT
1789447 AAAA
1 AAAA
1789451 TTTAAAAAAA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:1789491 original size:50 final size:49
Alignment explanation
Indices: 1789368--1789490 Score: 160
Period size: 50 Copynumber: 2.5 Consensus size: 49
1789358 AAAATATTTT
**
1789368 AAAATT-AAAAAAA-ATTAAAAAAAGTATTTTAAAATTAAAAAAATTAAA
1 AAAATTAAAAAAAATATTTTAAAAA-TATTTTAAAATTAAAAAAATTAAA
1789416 AAAATTAAAAAAAATATTTTAAAAATATTTTAAAATTTAAAAAAATTAAA
1 AAAATTAAAAAAAATATTTTAAAAATATTTTAAAA-TTAAAAAAATTAAA
* **
1789466 AAAGTATGTAAAAAATATTTTAAAA
1 AAAAT-TAAAAAAAATATTTTAAAA
1789491 TTAAAAAAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
48 6 0.09
49 17 0.26
50 26 0.39
51 17 0.26
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (49 bp):
AAAATTAAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAAATTAAA
Found at i:1791051 original size:3 final size:3
Alignment explanation
Indices: 1791045--1791079 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1791035 CTCCTCCTCC
1791045 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1791080 TACTTTAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1796587 original size:2 final size:2
Alignment explanation
Indices: 1796580--1796606 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1796570 GCTCAATTAA
1796580 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1796607 GCAAAAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1796634 original size:22 final size:21
Alignment explanation
Indices: 1796604--1796647 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1796594 ATATATATAT
* *
1796604 ATAGCAAAAGTAAAAAGTAAAA
1 ATAGAAAAAG-AAAAAGAAAAA
1796626 ATAGAAAAAGAAAAAGAAAAA
1 ATAGAAAAAGAAAAAGAAAAA
1796647 A
1 A
1796648 GTAAGTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.75, C:0.02, G:0.14, T:0.09
Consensus pattern (21 bp):
ATAGAAAAAGAAAAAGAAAAA
Found at i:1798404 original size:3 final size:3
Alignment explanation
Indices: 1798396--1798491 Score: 63
Period size: 3 Copynumber: 30.3 Consensus size: 3
1798386 ATATGTAAGT
*
1798396 ATA ATA ATAA ATA AT- ATA ATA ATA ATTA TTA AT- ATGA ATA ATA ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA A-TA ATA ATA AT-A ATA ATA ATA
* * *
1798442 ATA ATAA ATA ATGCA ATA ATA ATG ATGCA ATA ACA ATA TTA ATA A-A
1 ATA AT-A ATA AT--A ATA ATA ATA AT--A ATA ATA ATA ATA ATA ATA
1798488 ATA A
1 ATA A
1798492 ACTAAAAAAG
Statistics
Matches: 74, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
2 6 0.08
3 53 0.72
4 10 0.14
5 5 0.07
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1798415 original size:15 final size:15
Alignment explanation
Indices: 1798395--1798463 Score: 72
Period size: 15 Copynumber: 4.7 Consensus size: 15
1798385 TATATGTAAG
1798395 TATAATAATAAATAA
1 TATAATAATAAATAA
*
1798410 TATAATAAT-AATTA
1 TATAATAATAAATAA
*
1798424 T-TAAT-ATGAATAA
1 TATAATAATAAATAA
1798437 TAATAATAATAAATAA
1 T-ATAATAATAAATAA
**
1798453 TGCAATAATAA
1 TATAATAATAA
1798464 TGATGCAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
12 2 0.04
13 9 0.20
14 5 0.11
15 21 0.47
16 8 0.18
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (15 bp):
TATAATAATAAATAA
Found at i:1798439 original size:22 final size:24
Alignment explanation
Indices: 1798396--1798464 Score: 85
Period size: 22 Copynumber: 3.1 Consensus size: 24
1798386 ATATGTAAGT
1798396 ATAATAATAAATAAT---ATAATA
1 ATAATAATAAATAATGCAATAATA
* *
1798417 ATAATTATTAAT-ATG-AATAATA
1 ATAATAATAAATAATGCAATAATA
1798439 ATAATAATAAATAATGCAATAATA
1 ATAATAATAAATAATGCAATAATA
1798463 AT
1 AT
1798465 GATGCAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 2 0.05
21 10 0.25
22 16 0.40
23 3 0.08
24 9 0.22
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (24 bp):
ATAATAATAAATAATGCAATAATA
Found at i:1798471 original size:14 final size:15
Alignment explanation
Indices: 1798441--1798474 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1798431 GAATAATAAT
1798441 AATAATAAATAATGC
1 AATAATAAATAATGC
*
1798456 AATAAT-AATGATGC
1 AATAATAAATAATGC
1798470 AATAA
1 AATAA
1798475 CAATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.26
Consensus pattern (15 bp):
AATAATAAATAATGC
Found at i:1798491 original size:43 final size:43
Alignment explanation
Indices: 1798396--1798492 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 43
1798386 ATATGTAAGT
* * * **
1798396 ATAATAATAAATAATATAATAATAATTATTAATATGAATAATA
1 ATAATAATAAATAATACAATAATAATGATCAATAACAATAATA
* *
1798439 ATAATAATAAATAATGCAATAATAATGATGCAATAACAATATTA
1 ATAATAATAAATAATACAATAATAATGAT-CAATAACAATAATA
1798483 ATAA-AATAAA
1 ATAATAATAAA
1798493 CTAAAAAAGC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
43 32 0.70
44 14 0.30
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (43 bp):
ATAATAATAAATAATACAATAATAATGATCAATAACAATAATA
Found at i:1799860 original size:50 final size:50
Alignment explanation
Indices: 1799806--1800316 Score: 239
Period size: 50 Copynumber: 10.2 Consensus size: 50
1799796 ACCGTCGTGA
* * * * *
1799806 CTTCAATCTATTTCACTACACCGCTAGGGAAGTAAGATCTGCCGTTGTGG
1 CTTCAATCTGTTTCACTGCACCGCTAGGGAAATAAGATCCGCCGTTGTAG
* * * * ** *
1799856 CTTCAATCTTTTTAATTGTAATG-TCGGGGAAACT-AGATCCGCCGTTGTAG
1 CTTCAATCTGTTTCACTGCACCGCT-AGGGAAA-TAAGATCCGCCGTTGTAG
* * * * * * * *
1799906 CTTCAATTTGCTCCACTGCACCGCCAGAGAAGTAAGATCTGCCGTTGTGG
1 CTTCAATCTGTTTCACTGCACCGCTAGGGAAATAAGATCCGCCGTTGTAG
* * * ** * ** * * *
1799956 CTTCAATCT-TTTAATTACAATG-TCGAGGAAACCAGATCCACCATCGTAG
1 CTTCAATCTGTTTCACTGCACCGCTAG-GGAAATAAGATCCGCCGTTGTAG
* * * *
1800005 CTTCAATCT-TCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGT-TTCACTGCACCGCTAGGGAAATAAGATCCGCCGTTGTAG
* * ** * ** * *
1800055 CTTCAATCAT-TTTAATTGCAATG-TCGGGGAAACCAGATCTGCCGTCGTAG
1 CTTCAATC-TGTTTCACTGCACCGCT-AGGGAAATAAGATCCGCCGTTGTAG
* * * *
1800105 CTTCAATCTGTTCCACTACACCGCAAGGGAAATAAGATCCGCCATTGTAG
1 CTTCAATCTGTTTCACTGCACCGCTAGGGAAATAAGATCCGCCGTTGTAG
* * * * ** * * *
1800155 CTTCAATCTTTTTAATTGTAATG-TCGGGGAAACAAGATCCGCCGTCGTAG
1 CTTCAATCTGTTTCACTGCACCGCT-AGGGAAATAAGATCCGCCGTTGTAG
* * * * *
1800205 CTTCAATCTGTTCCACTGCACCGCCAGAGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTTCACTGCACCGCTAGGGAAATAAGATCCGCCGTTGTAG
* * * ** * * * *
1800255 CTTCAATCTTTTTAATTGCAATGTTGGGGAAATCAGATCCGCCGTCGT-G
1 CTTCAATCTGTTTCACTGCACCGCTAGGGAAATAAGATCCGCCGTTGTAG
*
1800304 ATTTCAATCTGTT
1 -CTTCAATCTGTT
1800317 CCTCTACACC
Statistics
Matches: 319, Mismatches: 128, Indels: 28
0.67 0.27 0.06
Matches are distributed among these distances:
48 1 0.00
49 34 0.11
50 280 0.88
51 4 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (50 bp):
CTTCAATCTGTTTCACTGCACCGCTAGGGAAATAAGATCCGCCGTTGTAG
Found at i:1799938 original size:100 final size:100
Alignment explanation
Indices: 1799772--1800360 Score: 736
Period size: 100 Copynumber: 5.9 Consensus size: 100
1799762 TCTGCTCAAC
* * * * ** * * *
1799772 TGCAATGTCGGGAAAACAAGATTCACCGTCGT-GACTTCAATCTATTTCACTACACCGCTAGGGA
1 TGCAATGTCGGGGAAACCAGATCCGCCGTCGTAG-CTTCAATCTGCTCCACTGCACCGCCAGGGA
*
1799836 AGTAAGATCTGCCGTTGTGGCTTCAATCTTTTTAAT
65 AGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* * * * *
1799872 TGTAATGTCGGGGAAACTAGATCCGCCGTTGTAGCTTCAATTTGCTCCACTGCACCGCCAGAGAA
1 TGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAA
*
1799937 GTAAGATCTGCCGTTGTGGCTTCAATC-TTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* * * * *
1799971 TACAATGTCGAGGAAACCAGATCCACCATCGTAGCTTCAATCTTCTCCACTGCACCGCCAGGGAA
1 TGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAA
*
1800036 GTAAGATCCGCCGTTGTGGCTTCAATCATTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* * * *
1800071 TGCAATGTCGGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCAAGGGAA
1 TGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAA
* * *
1800136 ATAAGATCCGCCATTGTAGCTTCAATCTTTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* * * *
1800171 TGTAATGTCGGGGAAACAAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAGAGAA
1 TGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAA
1800236 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* * * * * * *
1800271 TGCAATGTTGGGGAAATCAGATCCGCCGTCGT-GATTTCAATCTGTTCCTCTACACCACC-GGGA
1 TGCAATGTCGGGGAAACCAGATCCGCCGTCGTAG-CTTCAATCTGCTCCACTGCACCGCCAGGGA
* * **
1800334 AGTAAGATTCACCGTTGTCACTTCAAT
65 AGTAAGATCCGCCGTTGTGGCTTCAAT
1800361 AATTTCCACT
Statistics
Matches: 427, Mismatches: 59, Indels: 7
0.87 0.12 0.01
Matches are distributed among these distances:
99 115 0.27
100 311 0.73
101 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (100 bp):
TGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAA
GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
Found at i:1800336 original size:299 final size:299
Alignment explanation
Indices: 1799772--1800365 Score: 838
Period size: 299 Copynumber: 2.0 Consensus size: 299
1799762 TCTGCTCAAC
* *
1799772 TGCAATGTCGGGAAAACAAGATTCACCGTCGTGACTTCAATCTATTTCACTACACCGCTAGGGAA
1 TGCAATGTCGGGAAAACAAGATTCACCGTCGTGACTTCAATCTATTCCACTACACCGCAAGGGAA
* * * * * *
1799837 GTAAGATCTGCCGTTGTGGCTTCAATCTTTTTAATTGTAATGTCGGGGAAACTAGATCCGCCGTT
66 ATAAGATCCGCCATTGTAGCTTCAATCTTTTTAATTGTAATGTCGGGGAAACAAGATCCGCCGTC
* *
1799902 GTAGCTTCAATTTGCTCCACTGCACCGCCAGAGAAGTAAGATCTGCCGTTGTGGCTTCAATCTTT
131 GTAGCTTCAATCTGCTCCACTGCACCGCCAGAGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTT
* *
1799967 TAATTACAATGTCGAGGAAACCAGATCCACCATCGTAGCTTCAATCTTCTCCACTGCACCGCCAG
196 TAATTACAATGTCGAGGAAACCAGATCCACCATCGTAGCTTCAATCTTCTCCACTACACCACCAG
* ** *
1800032 GGAAGTAAGATCCGCCGTTGTGGCTTCAATCATTTTAAT
261 GGAAGTAAGATCCACCGTTGTCACTTCAATAATTTTAAT
* * * *
1800071 TGCAATGTCGGGGAAACCAGA-TCTGCCGTCGT-AGCTTCAATCTGTTCCACTACACCGCAAGGG
1 TGCAATGTCGGGAAAACAAGATTC-ACCGTCGTGA-CTTCAATCTATTCCACTACACCGCAAGGG
1800134 AAATAAGATCCGCCATTGTAGCTTCAATCTTTTTAATTGTAATGTCGGGGAAACAAGATCCGCCG
64 AAATAAGATCCGCCATTGTAGCTTCAATCTTTTTAATTGTAATGTCGGGGAAACAAGATCCGCCG
*
1800199 TCGTAGCTTCAATCTGTTCCACTGCACCGCCAGAGAAGTAAGATCCGCCGTTGTGGCTTCAATCT
129 TCGTAGCTTCAATCTGCTCCACTGCACCGCCAGAGAAGTAAGATCCGCCGTTGTGGCTTCAATC-
* * * * * * * *
1800264 TTTTAATTGCAATGTTGGGGAAATCAGATCCGCCGTCGT-GATTTCAATCTGT-TCCTCTACACC
193 TTTTAATTACAATGTCGAGGAAACCAGATCCACCATCGTAG-CTTCAATCT-TCTCCACTACACC
*
1800327 ACC-GGGAAGTAAGATTCACCGTTGTCACTTCAATAATTT
256 ACCAGGGAAGTAAGATCCACCGTTGTCACTTCAATAATTT
1800366 CCACTGTAAT
Statistics
Matches: 260, Mismatches: 30, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
298 3 0.01
299 204 0.78
300 52 0.20
301 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.29
Consensus pattern (299 bp):
TGCAATGTCGGGAAAACAAGATTCACCGTCGTGACTTCAATCTATTCCACTACACCGCAAGGGAA
ATAAGATCCGCCATTGTAGCTTCAATCTTTTTAATTGTAATGTCGGGGAAACAAGATCCGCCGTC
GTAGCTTCAATCTGCTCCACTGCACCGCCAGAGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTT
TAATTACAATGTCGAGGAAACCAGATCCACCATCGTAGCTTCAATCTTCTCCACTACACCACCAG
GGAAGTAAGATCCACCGTTGTCACTTCAATAATTTTAAT
Found at i:1800409 original size:200 final size:200
Alignment explanation
Indices: 1799806--1800421 Score: 569
Period size: 199 Copynumber: 3.1 Consensus size: 200
1799796 ACCGTCGTGA
* * * * * *
1799806 CTTCAATCTAT-TTCACTACACCGCTAGGGAAGTAAGATCTGCCGTTGTGGCTTCAATCTTTTTA
1 CTTCAATCT-TCTCCACTGCACCGCCAGAGAAGTAAGATCCGCCGTTGTGGCTTCAATCATTTTA
* * * * * * * * *
1799870 ATTGTAATGTCGGGGAAACTAGATCCGCCGTTGTAGCTTCAATTTGCTCCACTGCACCGCCAGAG
65 ATTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACACCACAAGGG
* ** * * * * * ** * * * * * *
1799935 AAGTAAGATCTGCCGTTGTGGCTTCAAT-CTTTTAATTACAATGTCGAGGAAACCAGATCCACCA
130 AAATAAGATCCACCATTGTAGCTTCAATAATTTCAACTGTAATGCCAAAGAAACAAGATCCGCCG
**
1799999 TCGTAG
195 TCACAG
*
1800005 CTTCAATCTTCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCATTTTAA
1 CTTCAATCTTCTCCACTGCACCGCCAGAGAAGTAAGATCCGCCGTTGTGGCTTCAATCATTTTAA
* *
1800070 TTGCAATGTCGGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCAAGGGA
66 TTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACACCACAAGGGA
* ** * * * ***
1800135 AATAAGATCCGCCATTGTAGCTTCAATCTTTTTAATTGTAATGTCGGGGAAACAAGATCCGCCGT
131 AATAAGATCCACCATTGTAGCTTCAATAATTTCAACTGTAATGCCAAAGAAACAAGATCCGCCGT
**
1800200 CGTAG
196 CACAG
*
1800205 CTTCAATCTGT-TCCACTGCACCGCCAGAGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTA
1 CTTCAATCT-TCTCCACTGCACCGCCAGAGAAGTAAGATCCGCCGTTGTGGCTTCAATCATTTTA
* * * * *
1800269 ATTGCAATGTTGGGGAAATCAGATCCGCCGTCGT-GATTTCAATCTGTTCCTCTACACCAC-CGG
65 ATTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAG-CTTCAATCTGTTCCACTACACCACAAGG
* * * * *** * *
1800332 GAAGTAAGATTCACCGTTGTCA-CTTCAATAATTTCCACTGTAATGCCAAAGAGGTAGGATTCGC
129 GAAATAAGATCCACCATTGT-AGCTTCAATAATTTCAACTGTAATGCCAAAGAAACAAGATCCGC
1800396 CGTTCACAG
193 CG-TCACAG
**
1800405 CTTCAATCCACTCCACT
1 CTTCAATCTTCTCCACT
1800422 TCAGCTAATC
Statistics
Matches: 354, Mismatches: 56, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
198 1 0.00
199 186 0.53
200 166 0.47
201 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (200 bp):
CTTCAATCTTCTCCACTGCACCGCCAGAGAAGTAAGATCCGCCGTTGTGGCTTCAATCATTTTAA
TTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACACCACAAGGGA
AATAAGATCCACCATTGTAGCTTCAATAATTTCAACTGTAATGCCAAAGAAACAAGATCCGCCGT
CACAG
Found at i:1801341 original size:23 final size:23
Alignment explanation
Indices: 1801311--1801354 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1801301 TCCAAAGAGA
1801311 AAGTCTTAATTTAGACTCTTTTT
1 AAGTCTTAATTTAGACTCTTTTT
*
1801334 AAGTCTTAATTTATACTCTTT
1 AAGTCTTAATTTAGACTCTTT
1801355 CTTATCAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.52
Consensus pattern (23 bp):
AAGTCTTAATTTAGACTCTTTTT
Found at i:1802013 original size:15 final size:15
Alignment explanation
Indices: 1801995--1802052 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
1801985 TTTTTTCATC
1801995 ATTTTTATTTTTTCG
1 ATTTTTATTTTTTCG
* *
1802010 ATTTTAATTTTTT-T
1 ATTTTTATTTTTTCG
*
1802024 ATTTTGA-TTTTTCTG
1 ATTTTTATTTTTTC-G
1802039 ATTTTTGATTTTTT
1 ATTTTT-ATTTTTT
1802053 TTATTTTGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 5 0.15
14 6 0.18
15 17 0.50
16 1 0.03
17 5 0.15
ACGTcount: A:0.16, C:0.03, G:0.07, T:0.74
Consensus pattern (15 bp):
ATTTTTATTTTTTCG
Found at i:1802020 original size:20 final size:20
Alignment explanation
Indices: 1801995--1802034 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1801985 TTTTTTCATC
*
1801995 ATTTTTATTTTTTCGATTTTA
1 ATTTTT-TTATTTCGATTTTA
*
1802016 ATTTTTTTATTTTGATTTT
1 ATTTTTTTATTTCGATTTT
1802035 TCTGATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (20 bp):
ATTTTTTTATTTCGATTTTA
Found at i:1802059 original size:15 final size:15
Alignment explanation
Indices: 1801995--1802068 Score: 71
Period size: 14 Copynumber: 5.0 Consensus size: 15
1801985 TTTTTTCATC
* **
1801995 ATTTTTATTTTTTCG
1 ATTTTGATTTTTTTT
*
1802010 ATTTT-AATTTTTTT
1 ATTTTGATTTTTTTT
* *
1802024 ATTTTGATTTTTCTG
1 ATTTTGATTTTTTTT
1802039 ATTTTTGATTTTTTTT
1 A-TTTTGATTTTTTTT
1802055 ATTTTG-TTTTTTTT
1 ATTTTGATTTTTTTT
1802069 TTCAGATTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
14 19 0.39
15 17 0.35
16 13 0.27
ACGTcount: A:0.14, C:0.03, G:0.07, T:0.77
Consensus pattern (15 bp):
ATTTTGATTTTTTTT
Found at i:1802070 original size:16 final size:16
Alignment explanation
Indices: 1802017--1802069 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
1802007 TCGATTTTAA
1802017 TTTTTTTATTTTG-AT
1 TTTTTTTATTTTGTAT
* *
1802032 TTTTCTGATTTT-TGAT
1 TTTTTTTATTTTGT-AT
1802048 TTTTTTTATTTTGT-T
1 TTTTTTTATTTTGTAT
1802063 TTTTTTT
1 TTTTTTT
1802070 TCAGATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 18 0.58
16 12 0.39
17 1 0.03
ACGTcount: A:0.09, C:0.02, G:0.08, T:0.81
Consensus pattern (16 bp):
TTTTTTTATTTTGTAT
Found at i:1802912 original size:25 final size:25
Alignment explanation
Indices: 1802859--1802918 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
1802849 TAGAAAATCC
* *
1802859 AAAAGAATGAAAGAATAATTATTCG
1 AAAAGAATGAAAGAATAATTACTCA
*
1802884 AAAAGAATGAAAGAAT-ATTGGCTCA
1 AAAAGAATGAAAGAATAATT-ACTCA
1802909 AAAA-AATGAA
1 AAAAGAATGAA
1802919 TGCAAAGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.29
25 22 0.71
ACGTcount: A:0.58, C:0.05, G:0.17, T:0.20
Consensus pattern (25 bp):
AAAAGAATGAAAGAATAATTACTCA
Found at i:1808958 original size:22 final size:24
Alignment explanation
Indices: 1808933--1808979 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
1808923 TATCTAAATT
1808933 ACAAAATTGAAT-GAAATTT-AGA
1 ACAAAATTGAATGGAAATTTGAGA
* *
1808955 ACAATATTGAGTGGAAATTTGAGA
1 ACAAAATTGAATGGAAATTTGAGA
1808979 A
1 A
1808980 AAATAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 7 0.33
24 4 0.19
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (24 bp):
ACAAAATTGAATGGAAATTTGAGA
Found at i:1811081 original size:18 final size:18
Alignment explanation
Indices: 1811058--1811093 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1811048 TTAGAATGCT
1811058 ATTTTGGTATCAATATTA
1 ATTTTGGTATCAATATTA
*
1811076 ATTTTGGTATCGATATTA
1 ATTTTGGTATCAATATTA
1811094 GATGTAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.50
Consensus pattern (18 bp):
ATTTTGGTATCAATATTA
Found at i:1815795 original size:15 final size:16
Alignment explanation
Indices: 1815775--1815808 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1815765 TCTTCACCTG
1815775 CAAGGAAACAAA-AAA
1 CAAGGAAACAAATAAA
*
1815790 CAAGGAAAGAAATAAA
1 CAAGGAAACAAATAAA
1815806 CAA
1 CAA
1815809 CAAATGAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.71, C:0.12, G:0.15, T:0.03
Consensus pattern (16 bp):
CAAGGAAACAAATAAA
Found at i:1829831 original size:98 final size:98
Alignment explanation
Indices: 1829710--1829906 Score: 358
Period size: 98 Copynumber: 2.0 Consensus size: 98
1829700 AAAAAAAAAA
* *
1829710 TAAAGGAAATATTTTGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCTGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
1829775 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTAGGATAAGTGGATGTTCTTTTAAAG
*
1829808 TAAAGGAAATATTCTGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCTGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1829873 TTAAATCTAGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTAGGATAAGTGGATGTTCTTTTAAAG
1829906 T
1 T
1829907 TTTATTACTC
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 95 1.00
ACGTcount: A:0.28, C:0.08, G:0.25, T:0.39
Consensus pattern (98 bp):
TAAAGGAAATATTCTGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTAGGATAAGTGGATGTTCTTTTAAAG
Found at i:1832514 original size:204 final size:204
Alignment explanation
Indices: 1832159--1832566 Score: 690
Period size: 204 Copynumber: 2.0 Consensus size: 204
1832149 TACATGCTGG
* * * *
1832159 ATCCTGATATAACCTGTAATAATCTTTGTACAATCACATATCTCATATAAGCGCACATATAACCT
1 ATCCCGATATAACATGTAATAATCTTCGTACAATCACATATCTCATATAAGCGCACATATAACCC
* * *
1832224 TATTAGCATGTCAATTGTATTCTAACCTTTTACGAAGTTCATATAGGCATAAATATTCATATTTT
66 TATTAGCATGTCAATCGTATCCTAACATTTTACGAAGTTCATATAGGCATAAATATTCATATTTT
*
1832289 CTTTATCATACTTGTAACTACTCTTGTTCGCATATCCATATCCTATAATCATTTACATTTATTTG
131 CTTTATCATACTTATAACTACTCTTGTTCGCATATCCATATCCTATAATCATTTACATTTATTTG
1832354 TCATACCCT
196 TCATACCCT
* *
1832363 ATCCCGATATAACATGTAATAATCTTCGTGCAATCACATATCTCATATAAGCGGACATATAACCC
1 ATCCCGATATAACATGTAATAATCTTCGTACAATCACATATCTCATATAAGCGCACATATAACCC
* * *
1832428 TATTAGCATGTCAATCGTATCCTAGCATTTTACTAAGTTCATATGGGCATAAATATTCATATTTT
66 TATTAGCATGTCAATCGTATCCTAACATTTTACGAAGTTCATATAGGCATAAATATTCATATTTT
*
1832493 CTTTATCATACTTATAACTACTCTTGTTCGCATATCCATGTCCTATAATCATTTACATTTATTTG
131 CTTTATCATACTTATAACTACTCTTGTTCGCATATCCATATCCTATAATCATTTACATTTATTTG
1832558 TCATACCCT
196 TCATACCCT
1832567 GTGTTCGGTC
Statistics
Matches: 190, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
204 190 1.00
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (204 bp):
ATCCCGATATAACATGTAATAATCTTCGTACAATCACATATCTCATATAAGCGCACATATAACCC
TATTAGCATGTCAATCGTATCCTAACATTTTACGAAGTTCATATAGGCATAAATATTCATATTTT
CTTTATCATACTTATAACTACTCTTGTTCGCATATCCATATCCTATAATCATTTACATTTATTTG
TCATACCCT
Found at i:1833302 original size:22 final size:21
Alignment explanation
Indices: 1833268--1833317 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
1833258 TTAGTCCTTT
* *
1833268 TCAAAATCTAAGCTTAATATCTA
1 TCAAATTCTAAGCCTAAT-TC-A
1833291 TCAAATTC-AAGCCTAATTCA
1 TCAAATTCTAAGCCTAATTCA
1833311 TCAAATT
1 TCAAATT
1833318 ATCGATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.32
21 2 0.08
22 8 0.32
23 7 0.28
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.34
Consensus pattern (21 bp):
TCAAATTCTAAGCCTAATTCA
Found at i:1839625 original size:3 final size:3
Alignment explanation
Indices: 1839617--1839652 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1839607 AATAGGTTTA
1839617 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1839653 TAAACACATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1839910 original size:158 final size:158
Alignment explanation
Indices: 1839653--1839961 Score: 618
Period size: 158 Copynumber: 2.0 Consensus size: 158
1839643 TAATAATAAT
1839653 TAAACACATTCCAACAACCATGATCTAAGGTACGAATACCAAAGTCTAGGGGTAAGATGATTTGC
1 TAAACACATTCCAACAACCATGATCTAAGGTACGAATACCAAAGTCTAGGGGTAAGATGATTTGC
1839718 TCAAGTATAAGAAAAAAATAGGATATCAAAATTACAAGTGTGACAAACGGTGAACGTAAATTTAA
66 TCAAGTATAAGAAAAAAATAGGATATCAAAATTACAAGTGTGACAAACGGTGAACGTAAATTTAA
1839783 TAGCGTTTGAGGAATATGAATCGCTGGA
131 TAGCGTTTGAGGAATATGAATCGCTGGA
1839811 TAAACACATTCCAACAACCATGATCTAAGGTACGAATACCAAAGTCTAGGGGTAAGATGATTTGC
1 TAAACACATTCCAACAACCATGATCTAAGGTACGAATACCAAAGTCTAGGGGTAAGATGATTTGC
1839876 TCAAGTATAAGAAAAAAATAGGATATCAAAATTACAAGTGTGACAAACGGTGAACGTAAATTTAA
66 TCAAGTATAAGAAAAAAATAGGATATCAAAATTACAAGTGTGACAAACGGTGAACGTAAATTTAA
1839941 TAGCGTTTGAGGAATATGAAT
131 TAGCGTTTGAGGAATATGAAT
1839962 AGTATGTATG
Statistics
Matches: 151, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
158 151 1.00
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (158 bp):
TAAACACATTCCAACAACCATGATCTAAGGTACGAATACCAAAGTCTAGGGGTAAGATGATTTGC
TCAAGTATAAGAAAAAAATAGGATATCAAAATTACAAGTGTGACAAACGGTGAACGTAAATTTAA
TAGCGTTTGAGGAATATGAATCGCTGGA
Found at i:1840534 original size:9 final size:9
Alignment explanation
Indices: 1840498--1840551 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
1840488 TTTAATTATT
1840498 TTTTAA-AA
1 TTTTAATAA
1840506 -TTT-ATAA
1 TTTTAATAA
1840513 TTTT-ATAA
1 TTTTAATAA
1840521 CTTTTAATAA
1 -TTTTAATAA
*
1840531 TTTTAATGA
1 TTTTAATAA
1840540 TTTTAA-AA
1 TTTTAATAA
1840548 TTTT
1 TTTT
1840552 TAAAATAGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 1 0.03
7 5 0.12
8 12 0.30
9 18 0.45
10 4 0.10
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (9 bp):
TTTTAATAA
Found at i:1846618 original size:2 final size:2
Alignment explanation
Indices: 1846611--1846644 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1846601 TACCCTTTTA
1846611 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1846645 GAAAAGATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1847775 original size:19 final size:18
Alignment explanation
Indices: 1847725--1847775 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
1847715 GTATATTTTA
1847725 ATATTTCAAATTTTAAAT
1 ATATTTCAAATTTTAAAT
* *
1847743 ATGGTTGC-AATTTTAAAT
1 AT-ATTTCAAATTTTAAAT
1847761 ATATATTCAAATTTT
1 ATAT-TTCAAATTTT
1847776 TAACAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
17 1 0.04
18 16 0.62
19 9 0.35
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (18 bp):
ATATTTCAAATTTTAAAT
Found at i:1848409 original size:17 final size:16
Alignment explanation
Indices: 1848373--1848412 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
1848363 TATTTTTATG
1848373 TTATTAAATTACATTA
1 TTATTAAATTACATTA
1848389 TTATTAATATATACA-TA
1 TTATTAA-AT-TACATTA
1848406 TTATTAA
1 TTATTAA
1848413 CCTGAAGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 11 0.50
18 4 0.18
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATTAAATTACATTA
Done.