Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold192
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: 2196177
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 12544 characters in sequence are not A, C, G, or T
File 12 of 14
Found at i:1786877 original size:113 final size:113
Alignment explanation
Indices: 1786679--1786904 Score: 407
Period size: 113 Copynumber: 2.0 Consensus size: 113
1786669 TATTATATAT
*
1786679 TATGTAAAATTATTTGATATAAACATAAATATTGATATTTTTTATTAATATAAAAATCTATAGTT
1 TATGTAAAATTATTTGATATAAACATAAATATTGATATTTTTCATTAATATAAAAATCTATAGTT
*
1786744 TAATAAAGCTTTCTTATTATTTCAAAAAAGATATCATACACAACGCAA
66 TAATAAAGCTTTCTTATTATTTCAAAAAAGAAATCATACACAACGCAA
*
1786792 TATGTAAAATTATTTGATATAAACATAAATATTGATATTTTTCATTAATATAAAAATCTATATTT
1 TATGTAAAATTATTTGATATAAACATAAATATTGATATTTTTCATTAATATAAAAATCTATAGTT
* *
1786857 TAATAAAGCTTTCTTGTTATTTCACAAAAGAAATCATACACAACGCAA
66 TAATAAAGCTTTCTTATTATTTCAAAAAAGAAATCATACACAACGCAA
1786905 ACCAATTTTA
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 108 1.00
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (113 bp):
TATGTAAAATTATTTGATATAAACATAAATATTGATATTTTTCATTAATATAAAAATCTATAGTT
TAATAAAGCTTTCTTATTATTTCAAAAAAGAAATCATACACAACGCAA
Found at i:1792509 original size:21 final size:21
Alignment explanation
Indices: 1792483--1792525 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1792473 CCTTTACAAA
1792483 CGCTGGTTTTGCCCACCCAAC
1 CGCTGGTTTTGCCCACCCAAC
*
1792504 CGCTGGTTTTGCCTACCCAAC
1 CGCTGGTTTTGCCCACCCAAC
1792525 C
1 C
1792526 TAACCAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.42, G:0.19, T:0.26
Consensus pattern (21 bp):
CGCTGGTTTTGCCCACCCAAC
Found at i:1796747 original size:26 final size:26
Alignment explanation
Indices: 1796718--1796771 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1796708 CCAGCAGAAC
1796718 AAGTCTCACCATGCACTAATAATAAT
1 AAGTCTCACCATGCACTAATAATAAT
1796744 AAGTCTCACCATGCACTAATAATAAT
1 AAGTCTCACCATGCACTAATAATAAT
1796770 AA
1 AA
1796772 TAATAATAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.26
Consensus pattern (26 bp):
AAGTCTCACCATGCACTAATAATAAT
Found at i:1802115 original size:87 final size:87
Alignment explanation
Indices: 1802015--1802191 Score: 311
Period size: 87 Copynumber: 2.0 Consensus size: 87
1802005 CTTTCCAAAC
*
1802015 TTTATTATTTTTTTGATTACATGTTATTTGGAAT-CTCAAATCTAGCAACCAAAATCAATAATGC
1 TTTATTATTTTTTTGATTACATGCTATTTGGAATCCT-AAATCTAGCAACCAAAATCAATAATGC
*
1802079 ATTATTTTTTATCCACCAAAAGA
65 ACTATTTTTTATCCACCAAAAGA
*
1802102 TTTATTATTTTTTTGATTACATGCTATTTGGAATCCTAAATCTAGCAACCAAGATCAATAATGCA
1 TTTATTATTTTTTTGATTACATGCTATTTGGAATCCTAAATCTAGCAACCAAAATCAATAATGCA
1802167 CTATTTTTTATCCACCAAAAGA
66 CTATTTTTTATCCACCAAAAGA
1802189 TTT
1 TTT
1802192 TTTTGAATTT
Statistics
Matches: 86, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
87 84 0.98
88 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.41
Consensus pattern (87 bp):
TTTATTATTTTTTTGATTACATGCTATTTGGAATCCTAAATCTAGCAACCAAAATCAATAATGCA
CTATTTTTTATCCACCAAAAGA
Found at i:1808576 original size:13 final size:13
Alignment explanation
Indices: 1808558--1808582 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1808548 AAAAAAAATA
1808558 TGTATCGATACAT
1 TGTATCGATACAT
1808571 TGTATCGATACA
1 TGTATCGATACA
1808583 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1811458 original size:30 final size:30
Alignment explanation
Indices: 1811415--1811513 Score: 93
Period size: 30 Copynumber: 3.5 Consensus size: 30
1811405 GCTAGAAGTT
* *
1811415 GCTGCCGGTCGTGGGATGCACGAGCTGCAA
1 GCTGCTGGACGTGGGATGCACGAGCTGCAA
* * * *
1811445 GCTGCTGGACGTGGGCTGGA--AGTTGC-T
1 GCTGCTGGACGTGGGATGCACGAGCTGCAA
*
1811472 G-T-C-GGTCGTGGGATGCACGAGCTGCAA
1 GCTGCTGGACGTGGGATGCACGAGCTGCAA
1811499 GCTGCTGGACGTGGG
1 GCTGCTGGACGTGGG
1811514 CTGGAAGTTG
Statistics
Matches: 51, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
24 11 0.22
25 1 0.02
26 6 0.12
27 2 0.04
28 6 0.12
29 1 0.02
30 24 0.47
ACGTcount: A:0.14, C:0.22, G:0.43, T:0.20
Consensus pattern (30 bp):
GCTGCTGGACGTGGGATGCACGAGCTGCAA
Found at i:1811478 original size:54 final size:54
Alignment explanation
Indices: 1811404--1811538 Score: 252
Period size: 54 Copynumber: 2.5 Consensus size: 54
1811394 CAGTGTTCGT
* *
1811404 GGCTAGAAGTTGCTGCCGGTCGTGGGATGCACGAGCTGCAAGCTGCTGGACGTG
1 GGCTGGAAGTTGCTGTCGGTCGTGGGATGCACGAGCTGCAAGCTGCTGGACGTG
1811458 GGCTGGAAGTTGCTGTCGGTCGTGGGATGCACGAGCTGCAAGCTGCTGGACGTG
1 GGCTGGAAGTTGCTGTCGGTCGTGGGATGCACGAGCTGCAAGCTGCTGGACGTG
1811512 GGCTGGAAGTTGCTGTCGGTCGTGGGA
1 GGCTGGAAGTTGCTGTCGGTCGTGGGA
1811539 CGGATGCGGG
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 79 1.00
ACGTcount: A:0.15, C:0.20, G:0.43, T:0.22
Consensus pattern (54 bp):
GGCTGGAAGTTGCTGTCGGTCGTGGGATGCACGAGCTGCAAGCTGCTGGACGTG
Found at i:1811481 original size:24 final size:24
Alignment explanation
Indices: 1811454--1811537 Score: 69
Period size: 24 Copynumber: 3.2 Consensus size: 24
1811444 AGCTGCTGGA
1811454 CGTGGGCTGGAAGTTGCTGTCGGT
1 CGTGGGCTGGAAGTTGCTGTCGGT
* * * * *
1811478 CGTGGGATGCACGAGCTGCAAGCTGCTGGA
1 CGTGGGCTGGA--AGTTGC-TG-T-C-GGT
1811508 CGTGGGCTGGAAGTTGCTGTCGGT
1 CGTGGGCTGGAAGTTGCTGTCGGT
1811532 CGTGGG
1 CGTGGG
1811538 ACGGATGCGG
Statistics
Matches: 44, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
24 17 0.39
25 1 0.02
26 6 0.14
27 2 0.05
28 6 0.14
29 1 0.02
30 11 0.25
ACGTcount: A:0.12, C:0.19, G:0.45, T:0.24
Consensus pattern (24 bp):
CGTGGGCTGGAAGTTGCTGTCGGT
Found at i:1812038 original size:5 final size:5
Alignment explanation
Indices: 1812025--1812123 Score: 117
Period size: 5 Copynumber: 19.8 Consensus size: 5
1812015 GCATGAAAGC
* * * *
1812025 AATGT AATGA AATGC AATGC AATGA AATGA AATGA AATGA AATGA AATGC
1 AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA
* * * * *
1812075 AATGC AATGA AATGC AATGA AATGA AATGA AGTGC AATGC AATGA AATG
1 AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATG
1812124 TTTTTGAAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 83 1.00
ACGTcount: A:0.51, C:0.07, G:0.21, T:0.21
Consensus pattern (5 bp):
AATGA
Found at i:1812120 original size:15 final size:15
Alignment explanation
Indices: 1812013--1812103 Score: 123
Period size: 15 Copynumber: 6.2 Consensus size: 15
1812003 CGGCCATTTC
*
1812013 ATGC-ATGAAA-GCA
1 ATGCAATGAAATGAA
* *
1812026 ATGTAATGAAATGCA
1 ATGCAATGAAATGAA
1812041 ATGCAATGAAATGAA
1 ATGCAATGAAATGAA
*
1812056 ATGAAATGAAATGAA
1 ATGCAATGAAATGAA
*
1812071 ATGCAATGCAATGAA
1 ATGCAATGAAATGAA
1812086 ATGCAATGAAATGAA
1 ATGCAATGAAATGAA
1812101 ATG
1 ATG
1812104 AAGTGCAATG
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
13 3 0.04
14 6 0.09
15 60 0.87
ACGTcount: A:0.51, C:0.08, G:0.21, T:0.21
Consensus pattern (15 bp):
ATGCAATGAAATGAA
Found at i:1812140 original size:35 final size:35
Alignment explanation
Indices: 1812017--1812123 Score: 171
Period size: 35 Copynumber: 3.1 Consensus size: 35
1812007 CATTTCATGC
* *
1812017 ATGAAA-GCAATGTAATGAAATGCAATGCAATGAA
1 ATGAAATGAAATGAAATGAAATGCAATGCAATGAA
1812051 ATGAAATGAAATGAAATGAAATGCAATGCAATGAA
1 ATGAAATGAAATGAAATGAAATGCAATGCAATGAA
* *
1812086 ATGCAATGAAATGAAATGAAGTGCAATGCAATGAA
1 ATGAAATGAAATGAAATGAAATGCAATGCAATGAA
1812121 ATG
1 ATG
1812124 TTTTTGAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
34 6 0.09
35 62 0.91
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.21
Consensus pattern (35 bp):
ATGAAATGAAATGAAATGAAATGCAATGCAATGAA
Found at i:1812160 original size:22 final size:22
Alignment explanation
Indices: 1812132--1812251 Score: 85
Period size: 22 Copynumber: 5.5 Consensus size: 22
1812122 TGTTTTTGAA
1812132 ATGCATGAAATGAAAATTATGC
1 ATGCATGAAATGAAAATTATGC
*
1812154 ATGCATGAAATG----TTACGTGAA
1 ATGCATGAAATGAAAATTA--TG-C
*
1812175 AAGCATGAAATGAAAATTATGC
1 ATGCATGAAATGAAAATTATGC
*
1812197 ATGCATGAAATG----TTACGTGAA
1 ATGCATGAAATGAAAATTA--TG-C
**
1812218 AAACATGAAATGAAAATTATGC
1 ATGCATGAAATGAAAATTATGC
1812240 ATGCATGAAATG
1 ATGCATGAAATG
1812252 TTACGTGAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 28
0.66 0.09 0.25
Matches are distributed among these distances:
18 6 0.08
20 4 0.05
21 21 0.28
22 33 0.45
23 4 0.05
25 6 0.08
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.26
Consensus pattern (22 bp):
ATGCATGAAATGAAAATTATGC
Found at i:1812181 original size:43 final size:43
Alignment explanation
Indices: 1812135--1812277 Score: 277
Period size: 43 Copynumber: 3.3 Consensus size: 43
1812125 TTTTGAAATG
*
1812135 CATGAAATGAAAATTATGCATGCATGAAATGTTACGTGAAAAG
1 CATGAAATGAAAATTATGCATGCATGAAATGTTACGTGAAAAA
1812178 CATGAAATGAAAATTATGCATGCATGAAATGTTACGTGAAAAA
1 CATGAAATGAAAATTATGCATGCATGAAATGTTACGTGAAAAA
1812221 CATGAAATGAAAATTATGCATGCATGAAATGTTACGTGAAAAA
1 CATGAAATGAAAATTATGCATGCATGAAATGTTACGTGAAAAA
1812264 CATGAAATGAAAAT
1 CATGAAATGAAAAT
1812278 GCATGCAATG
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 99 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (43 bp):
CATGAAATGAAAATTATGCATGCATGAAATGTTACGTGAAAAA
Found at i:1812182 original size:21 final size:21
Alignment explanation
Indices: 1812156--1812272 Score: 66
Period size: 21 Copynumber: 5.5 Consensus size: 21
1812146 AATTATGCAT
1812156 GCATGAAATGTTACGTGAAAA
1 GCATGAAATGTTACGTGAAAA
* *
1812177 GCATGAAATGAAAATTA--TG-CAT
1 GCATGAAATG----TTACGTGAAAA
1812199 GCATGAAATGTTACGTGAAAA
1 GCATGAAATGTTACGTGAAAA
* * *
1812220 ACATGAAATGAAAATTA--TG-CAT
1 GCATGAAATG----TTACGTGAAAA
1812242 GCATGAAATGTTACGTGAAAA
1 GCATGAAATGTTACGTGAAAA
*
1812263 ACATGAAATG
1 GCATGAAATG
1812273 AAAATGCATG
Statistics
Matches: 71, Mismatches: 11, Indels: 28
0.65 0.10 0.25
Matches are distributed among these distances:
18 6 0.08
20 4 0.06
21 30 0.42
22 21 0.30
23 4 0.06
25 6 0.08
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.25
Consensus pattern (21 bp):
GCATGAAATGTTACGTGAAAA
Found at i:1818044 original size:18 final size:19
Alignment explanation
Indices: 1818021--1818059 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1818011 TATGATGATA
1818021 AAATAAAAAATATTAA-AT
1 AAATAAAAAATATTAATAT
* *
1818039 AAATAATAAATTTTAATAT
1 AAATAAAAAATATTAATAT
1818058 AA
1 AA
1818060 TTTTTATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATAAAAAATATTAATAT
Found at i:1825111 original size:23 final size:21
Alignment explanation
Indices: 1825085--1825136 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 21
1825075 GGGTAGAGCA
1825085 TATAAT-CTGTATAATCTATCATC
1 TATAATACTGTAT--TCT-TCATC
1825108 TATAACATACTGTATTCTTCATC
1 TAT-A-ATACTGTATTCTTCATC
1825131 TATAAT
1 TATAAT
1825137 TTAACAGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
21 2 0.08
22 1 0.04
23 11 0.42
24 4 0.15
25 2 0.08
26 6 0.23
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.44
Consensus pattern (21 bp):
TATAATACTGTATTCTTCATC
Found at i:1825347 original size:20 final size:21
Alignment explanation
Indices: 1825318--1825356 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1825308 TATAATTAAA
1825318 TTTAAATAAAAA-ATTATTAT
1 TTTAAATAAAAATATTATTAT
*
1825338 TTTAATTAAAAATATTATT
1 TTTAAATAAAAATATTATT
1825357 TTGGGCTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTAAATAAAAATATTATTAT
Found at i:1825575 original size:29 final size:29
Alignment explanation
Indices: 1825541--1825614 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
1825531 CTATTGGTAG
* *
1825541 TTTAT-TTATTATA-TAAGTATTTTAATT
1 TTTATATTATTAAATTAAGTATTTTAATA
* *
1825568 TTTATATTATTAAATTTATTATTTTAATA
1 TTTATATTATTAAATTAAGTATTTTAATA
*
1825597 TTTATAATTTTTAAATTA
1 TTTAT-ATTATTAAATTA
1825615 TAGCAAATGA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 5 0.13
28 7 0.18
29 16 0.42
30 10 0.26
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (29 bp):
TTTATATTATTAAATTAAGTATTTTAATA
Found at i:1825580 original size:15 final size:14
Alignment explanation
Indices: 1825558--1825607 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
1825548 ATTATATAAG
*
1825558 TATTTTAATTTTTA
1 TATTTTAATATTTA
1825572 TATTATTAA-ATTTA
1 TATT-TTAATATTTA
1825586 TTATTTTAATATTTA
1 -TATTTTAATATTTA
1825601 TAATTTT
1 T-ATTTT
1825608 TAAATTATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 13 0.42
15 18 0.58
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTTTAATATTTA
Found at i:1826253 original size:15 final size:16
Alignment explanation
Indices: 1826227--1826256 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1826217 ATATTTTTAA
1826227 TTTATATAATATAAAT
1 TTTATATAATATAAAT
1826243 TTTATAT-ATATAAA
1 TTTATATAATATAAA
1826257 AAATTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTATATAATATAAAT
Found at i:1826841 original size:23 final size:23
Alignment explanation
Indices: 1826806--1826850 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1826796 AACTGTCAAC
*
1826806 TATGACAACATGTAAATTCTTTTA
1 TATGACAAAATGTAAATT-TTTTA
1826830 TATG-CAAAATGTAAATTTTTT
1 TATGACAAAATGTAAATTTTTT
1826851 CTTTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (23 bp):
TATGACAAAATGTAAATTTTTTA
Found at i:1828867 original size:35 final size:36
Alignment explanation
Indices: 1828812--1828882 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
1828802 CTTCAATTAA
*
1828812 AATTATTATTTATATAATAAAA-ATTAATTTAATTT
1 AATTATTATTTATATAATAAAATAATAATTTAATTT
*
1828847 AATTATTAATATTA-AT-ATAAAATAATATTTTAATTT
1 AATTATT-AT-TTATATAATAAAATAATAATTTAATTT
1828883 TTAATATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 13 0.42
36 15 0.48
37 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (36 bp):
AATTATTATTTATATAATAAAATAATAATTTAATTT
Found at i:1828948 original size:48 final size:50
Alignment explanation
Indices: 1828864--1828962 Score: 184
Period size: 49 Copynumber: 2.0 Consensus size: 50
1828854 AATATTAATA
1828864 TAAAATAATATTTTAATTTTTAATATTATTTTTAATAATG-AACAAGCTT
1 TAAAATAATATTTTAATTTTTAATATTATTTTTAATAATGAAACAAGCTT
1828913 TAAAATAATATTTTAA-TTTTAATATTATTTTTAATAATGAAACAAGCTT
1 TAAAATAATATTTTAATTTTTAATATTATTTTTAATAATGAAACAAGCTT
1828962 T
1 T
1828963 CAAGGTAAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 23 0.47
49 26 0.53
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (50 bp):
TAAAATAATATTTTAATTTTTAATATTATTTTTAATAATGAAACAAGCTT
Found at i:1830854 original size:17 final size:17
Alignment explanation
Indices: 1830832--1830865 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1830822 GTATTTGATT
1830832 AGATGAAAATTCAGATG
1 AGATGAAAATTCAGATG
*
1830849 AGATGAAAATTTAGATG
1 AGATGAAAATTCAGATG
1830866 CTAAATTGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.24, T:0.26
Consensus pattern (17 bp):
AGATGAAAATTCAGATG
Found at i:1832298 original size:11 final size:11
Alignment explanation
Indices: 1832272--1832314 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
1832262 CTTGCTTCCA
*
1832272 TTTTTCCTAGC
1 TTTTTCCTTGC
1832283 TTTTTTCCTTGC
1 -TTTTTCCTTGC
*
1832295 TTTTTCTTTGC
1 TTTTTCCTTGC
1832306 TTTTTCCTT
1 TTTTTCCTT
1832315 TTTTTTCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.02, C:0.23, G:0.07, T:0.67
Consensus pattern (11 bp):
TTTTTCCTTGC
Found at i:1832319 original size:21 final size:22
Alignment explanation
Indices: 1832284--1832324 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1832274 TTTCCTAGCT
1832284 TTTTTCCTTGCTTTTTCTTTGC
1 TTTTTCCTTGCTTTTTCTTTGC
*
1832306 TTTTTCCTT-TTTTTTCTTT
1 TTTTTCCTTGCTTTTTCTTT
1832325 CTTGAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.00, C:0.20, G:0.05, T:0.76
Consensus pattern (22 bp):
TTTTTCCTTGCTTTTTCTTTGC
Found at i:1832948 original size:21 final size:21
Alignment explanation
Indices: 1832919--1832985 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
1832909 TATCACCGAA
*
1832919 GTATTAATACATTTAAGTAAT
1 GTATCAATACATTTAAGTAAT
****
1832940 GTATCAATACATTGGCCTAAT
1 GTATCAATACATTTAAGTAAT
*
1832961 GTATCAATACA-TTAGGTAAT
1 GTATCAATACATTTAAGTAAT
1832981 GTATC
1 GTATC
1832986 GACAACTTAG
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
20 10 0.27
21 27 0.73
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.37
Consensus pattern (21 bp):
GTATCAATACATTTAAGTAAT
Found at i:1836707 original size:79 final size:79
Alignment explanation
Indices: 1836598--1836975 Score: 351
Period size: 79 Copynumber: 4.8 Consensus size: 79
1836588 GAATTTTTCA
** **
1836598 TCTAAGGGGATACT-CAACCCCGCTTTTATTTCCAAAATATTAAAATTTTCATCTTAGGGATACT
1 TCTAAGGGGATACTCCAACCCTACTTTTATTTCCAAAATATTAAAATTTTCATCTCGGGGATACT
*
1836662 CTAACCCCATCAAT
66 CCAACCCCATCAAT
* ** * *
1836676 TCTAAGGGGATACTCCAACCCTACTTTTATTTCTAAAATGCTAAATTTTTCATCTTGGGGATACT
1 TCTAAGGGGATACTCCAACCCTACTTTTATTTCCAAAATATTAAAATTTTCATCTCGGGGATACT
1836741 CCAACCCCATCAAT
66 CCAACCCCATCAAT
* * *
1836755 TCTGAGGGGATAC-CCTAACCCTACTTTTATTTTCAAAATATT-AAATTTT--TTTCGAGGG-TA
1 TCTAAGGGGATACTCC-AACCCTACTTTTATTTCCAAAATATTAAAATTTTCATCTCG-GGGATA
* * * *
1836815 CTCCAACCTCGTTATTT
64 CTCCAACCCCATCA-AT
* * * * * *
1836832 TCGAA-GGGATACTCCACCCCCATTTTTATTTCCAAAAATATT-GATTTTTCATCTCGGGGATAC
1 TCTAAGGGGATACTCCAACCCTACTTTTATTTCC-AAAATATTAAAATTTTCATCTCGGGGATAC
* * *
1836895 TCCAACCCTATTATT
65 TCCAACCCCATCAAT
* * * ** * *
1836910 TTTGAA-GGGATACTTCAACCTTGTTTTTATTTCAAAAATATTAAAATTTTCATCTCGGGGGTAC
1 TCT-AAGGGGATACTCCAACCCTACTTTTATTTCCAAAATATTAAAATTTTCATCTCGGGGATAC
1836974 TC
65 TC
1836976 TAACTCCGCA
Statistics
Matches: 246, Mismatches: 43, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
76 37 0.15
77 22 0.09
78 36 0.15
79 151 0.61
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (79 bp):
TCTAAGGGGATACTCCAACCCTACTTTTATTTCCAAAATATTAAAATTTTCATCTCGGGGATACT
CCAACCCCATCAAT
Found at i:1841736 original size:20 final size:20
Alignment explanation
Indices: 1841711--1841769 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
1841701 GATGTATCAT
*
1841711 ACAATTGTATTGATACATGC
1 ACAATTGTATCGATACATGC
*
1841731 ACAATTGTATCAATACATGC
1 ACAATTGTATCGATACATGC
1841751 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
1841770 AAACTGGCAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (20 bp):
ACAATTGTATCGATACATGC
Found at i:1841823 original size:20 final size:19
Alignment explanation
Indices: 1841798--1841851 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
1841788 CTACTAGTGT
1841798 TTGTATCGATACATG-GCACA
1 TTGTATCGATACATGAG-A-A
*
1841818 TTGTATCGATGCATGATGAA
1 TTGTATCGATACATGA-GAA
1841838 TTGTATCGATACAT
1 TTGTATCGATACAT
1841852 TACTTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 28 0.93
21 1 0.03
22 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATGAGAA
Found at i:1850506 original size:20 final size:20
Alignment explanation
Indices: 1850481--1850531 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1850471 CCACTGTTTT
1850481 TATCGATACATGA-CACATTG
1 TATCGATACATGATCA-ATTG
* *
1850501 TATCGATACATGATGAATTT
1 TATCGATACATGATCAATTG
1850521 TATCGATACAT
1 TATCGATACAT
1850532 TGCTTCAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (20 bp):
TATCGATACATGATCAATTG
Found at i:1853240 original size:26 final size:26
Alignment explanation
Indices: 1853204--1853257 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
1853194 TTAAAAGCTA
1853204 AAGGTGCTAATGCAAGCAAGAGAAAT
1 AAGGTGCTAATGCAAGCAAGAGAAAT
*
1853230 AAGGTGCTAATGCAGGCAAGAGAAAT
1 AAGGTGCTAATGCAAGCAAGAGAAAT
1853256 AA
1 AA
1853258 TCATGTATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.46, C:0.11, G:0.28, T:0.15
Consensus pattern (26 bp):
AAGGTGCTAATGCAAGCAAGAGAAAT
Found at i:1860798 original size:23 final size:22
Alignment explanation
Indices: 1860770--1860819 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
1860760 CATAACTATA
*
1860770 TAATTTAAATATAAAAATAAAAC
1 TAATTTAAAAATAAAAA-AAAAC
* *
1860793 TAATTTAAAAATAACAAAAAAT
1 TAATTTAAAAATAAAAAAAAAC
1860815 TAATT
1 TAATT
1860820 AATTTTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (22 bp):
TAATTTAAAAATAAAAAAAAAC
Found at i:1865015 original size:20 final size:21
Alignment explanation
Indices: 1864968--1865022 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
1864958 TTTTTACAAT
*
1864968 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACATACAGTAA
1864989 TTGTATCGATACATA-AGTGAA
1 TTGTATCGATACATACAGT-AA
*
1865010 -TGTATCAATACAT
1 TTGTATCGATACAT
1865023 GCCTAAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (21 bp):
TTGTATCGATACATACAGTAA
Found at i:1874045 original size:17 final size:17
Alignment explanation
Indices: 1874023--1874061 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1874013 TCAAAAACTG
1874023 ATGAATAAAGACCAAAT
1 ATGAATAAAGACCAAAT
*
1874040 ATGAATGAAGACCAAAT
1 ATGAATAAAGACCAAAT
1874057 A-GAAT
1 ATGAAT
1874062 TCTACCATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.18
Consensus pattern (17 bp):
ATGAATAAAGACCAAAT
Found at i:1880693 original size:52 final size:51
Alignment explanation
Indices: 1880588--1880706 Score: 123
Period size: 52 Copynumber: 2.3 Consensus size: 51
1880578 CTTGCCAAAA
* * * **
1880588 TTTGTCATCTTTCAATCCAATGTTGCTGACCTTGGATCAGCACATTGGCACC
1 TTTGTCATCTTT-AAACCAATGTTGCTGACCTCGAATCAAAACATTGGCACC
* *
1880640 TTTGTCATCTTTAAGACCAATGTTGCT-AGCCTCGAATCAAAACGTTGGTACC
1 TTTGTCATCTTTAA-ACCAATGTTGCTGA-CCTCGAATCAAAACATTGGCACC
**
1880692 TTCATCATCTTTAAA
1 TTTGTCATCTTTAAA
1880707 TTCAATTCGC
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
51 4 0.07
52 52 0.93
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.35
Consensus pattern (51 bp):
TTTGTCATCTTTAAACCAATGTTGCTGACCTCGAATCAAAACATTGGCACC
Found at i:1881013 original size:32 final size:33
Alignment explanation
Indices: 1880948--1881085 Score: 138
Period size: 32 Copynumber: 4.2 Consensus size: 33
1880938 TCATCCTTTT
* * * *
1880948 AAGCCCAAATAAGTTGGTGGTAACCCCTTCTCA
1 AAGCCCAAACAAGTCGATGGCAACCCCTTCTCA
* * *
1880981 AAGCCCATATAATTCGATGGCAA-CCCTTCTCA
1 AAGCCCAAACAAGTCGATGGCAACCCCTTCTCA
*
1881013 AAGCTCAAACAAGTCGATGGCAACCCCTTCT-A
1 AAGCCCAAACAAGTCGATGGCAACCCCTTCTCA
* *
1881045 AAGCCCACACAAGTC-AGTGGTAACCCCCTTCCTCA
1 AAGCCCAAACAAGTCGA-TGGCAA-CCCCTT-CTCA
1881080 AAGCCC
1 AAGCCC
1881086 TTGCAAGTTG
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
31 1 0.01
32 47 0.53
33 31 0.35
34 2 0.02
35 7 0.08
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.20
Consensus pattern (33 bp):
AAGCCCAAACAAGTCGATGGCAACCCCTTCTCA
Found at i:1881574 original size:61 final size:60
Alignment explanation
Indices: 1881507--1881708 Score: 194
Period size: 61 Copynumber: 3.3 Consensus size: 60
1881497 CACATTGGTG
* * *
1881507 TTCTTCTCATCTTCAAGCCCAATATCATTAGCCTTGAATCAACATATTGGCACATTTATCA
1 TTCTTCTCATCTTCAAGTCCAATATCACT-GCCTTGAATCAGCATATTGGCACATTTATCA
** * * * * *
1881568 TTCTTCTCATCTTCAAGTCTGATATCGCTGGTCGTGAATCAGCATCTTGGCACCTTTATCA
1 TTCTTCTCATCTTCAAGTCCAATATCACT-GCCTTGAATCAGCATATTGGCACATTTATCA
* * * *
1881629 TTCTT-TGCATCCTT-AAGTCCAACATCACTGACCTTGAATCAGCACATTGGCACTTTTCTCA
1 TTCTTCT-CAT-CTTCAAGTCCAATATCACTG-CCTTGAATCAGCATATTGGCACATTTATCA
*
1881690 -TCATTATCATCTTCAAGTC
1 TTC-TTCTCATCTTCAAGTC
1881709 TAGAGTCGCA
Statistics
Matches: 114, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
60 7 0.06
61 103 0.90
62 4 0.04
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.37
Consensus pattern (60 bp):
TTCTTCTCATCTTCAAGTCCAATATCACTGCCTTGAATCAGCATATTGGCACATTTATCA
Found at i:1882341 original size:21 final size:21
Alignment explanation
Indices: 1882311--1882385 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 21
1882301 TTCTACAATT
*
1882311 TGTATTGATACAAACAGTAAA
1 TGTATCGATACAAACAGTAAA
* *
1882332 TGTATCGATAC--ATAGTGAA
1 TGTATCGATACAAACAGTAAA
* ** *
1882351 TGTATCAATACATGC-TTGAAA
1 TGTATCGATACAAACAGT-AAA
1882372 TGTATCGATACAAA
1 TGTATCGATACAAA
1882386 ACCATCTTGC
Statistics
Matches: 40, Mismatches: 11, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 16 0.40
20 1 0.03
21 23 0.57
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (21 bp):
TGTATCGATACAAACAGTAAA
Found at i:1882354 original size:19 final size:20
Alignment explanation
Indices: 1882329--1882383 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
1882319 TACAAACAGT
1882329 AAATGTATCGATACATAG-TG
1 AAATGTATCGATACAT-GCTG
*
1882349 -AATGTATCAATACATGCTTG
1 AAATGTATCGATACATGC-TG
1882369 AAATGTATCGATACA
1 AAATGTATCGATACA
1882384 AAACCATCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 1 0.03
19 14 0.47
20 2 0.07
21 13 0.43
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (20 bp):
AAATGTATCGATACATGCTG
Found at i:1886488 original size:22 final size:22
Alignment explanation
Indices: 1886463--1886512 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 22
1886453 GGGTATTTTT
1886463 ATTAAAA-ATGAATTTTAAA-AAA
1 ATTAAAATAT-AA-TTTAAATAAA
1886485 ATTAAAATTATAATTTAAATAAA
1 ATTAAAA-TATAATTTAAATAAA
1886508 ATTAA
1 ATTAA
1886513 TTAAAGATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 10 0.40
24 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
ATTAAAATATAATTTAAATAAA
Found at i:1888339 original size:12 final size:12
Alignment explanation
Indices: 1888322--1888347 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1888312 ATAGTGCTAC
1888322 ATTATCAAGAAT
1 ATTATCAAGAAT
1888334 ATTATCAAGAAT
1 ATTATCAAGAAT
1888346 AT
1 AT
1888348 ATTTTAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.35
Consensus pattern (12 bp):
ATTATCAAGAAT
Found at i:1888664 original size:112 final size:114
Alignment explanation
Indices: 1888522--1888736 Score: 276
Period size: 114 Copynumber: 1.9 Consensus size: 114
1888512 CTCAATATAC
* * *
1888522 TTAAATAAAATATGCCTTAAATAAATTAATTAAATATGCA-CATGAGCCTTATTTTATCT-A-AT
1 TTAAATAAAATATGCC-TAAATAAAATAATTAAATATGCACCATGAACC-TATTCTATCTAATAT
* *
1888584 ATATTTTTTCTAAGACTCGATCTTAAATTAAATAATTTATAACCTAATAAA
64 ATATTTTTTATAAGACTCGACCTTAAATTAAATAATTTATAACCTAATAAA
* * *
1888635 TTAAATAAAATATGTCC-AAATAAAATAATTAAATGTGCACCTTGAACCTATTCTATTTAATATA
1 TTAAATAAAATATG-CCTAAATAAAATAATTAAATATGCACCATGAACCTATTCTATCTAATATA
* * *
1888699 TATTTTTTATAATATTTGACCTTAAATTAAATAATTTA
65 TATTTTTTATAAGACTCGACCTTAAATTAAATAATTTA
1888737 CGACTTTATC
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
112 28 0.32
113 21 0.24
114 38 0.44
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (114 bp):
TTAAATAAAATATGCCTAAATAAAATAATTAAATATGCACCATGAACCTATTCTATCTAATATAT
ATTTTTTATAAGACTCGACCTTAAATTAAATAATTTATAACCTAATAAA
Found at i:1889520 original size:51 final size:51
Alignment explanation
Indices: 1889444--1889546 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
1889434 TGAAGACCAG
* *
1889444 AAACGCTAGGTACTTTGGCAATGAAGGAAAGCTTCACCGCTGAAACAACCC
1 AAACGCTAGGTACTTTGGAAATGAAGGAAAGCTTCACCGCTAAAACAACCC
1889495 AAACGCTAGGTACTTTGGAAATGAAGGAAAGCTTCACCGCTAAAACAACCC
1 AAACGCTAGGTACTTTGGAAATGAAGGAAAGCTTCACCGCTAAAACAACCC
1889546 A
1 A
1889547 TTGTTGGTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.17
Consensus pattern (51 bp):
AAACGCTAGGTACTTTGGAAATGAAGGAAAGCTTCACCGCTAAAACAACCC
Found at i:1894995 original size:10 final size:12
Alignment explanation
Indices: 1894982--1895013 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1894972 TAAATTTAAT
1894982 TATA-AAATT-A
1 TATACAAATTCA
1894992 TATACAAATTCA
1 TATACAAATTCA
1895004 TATACAAATT
1 TATACAAATT
1895014 TTTTTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 4 0.20
11 5 0.25
12 11 0.55
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (12 bp):
TATACAAATTCA
Found at i:1897972 original size:21 final size:21
Alignment explanation
Indices: 1897942--1897981 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1897932 ATAAGTTCTA
1897942 ATAGACAAGTTACTTATGTTG
1 ATAGACAAGTTACTTATGTTG
*
1897963 ATAGATAAGTTACTTATGT
1 ATAGACAAGTTACTTATGT
1897982 CAATAATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.40
Consensus pattern (21 bp):
ATAGACAAGTTACTTATGTTG
Found at i:1904074 original size:52 final size:51
Alignment explanation
Indices: 1903933--1904081 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
1903923 CGAAATATGA
1903933 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* * *
1903985 AAATTTGCCTGCATGTATCGATATATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
1904037 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
1904082 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:1904088 original size:13 final size:13
Alignment explanation
Indices: 1904070--1904094 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1904060 CAAAGATCAG
1904070 TGTATCGATACAA
1 TGTATCGATACAA
1904083 TGTATCGATACA
1 TGTATCGATACA
1904095 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1904172 original size:33 final size:33
Alignment explanation
Indices: 1904135--1904201 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1904125 AGTAGCTTAA
1904135 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1904168 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1904201 A
1 A
1904202 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1904175 original size:13 final size:13
Alignment explanation
Indices: 1904157--1904181 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1904147 CAAAAAAATA
1904157 TGTATCGATACAT
1 TGTATCGATACAT
1904170 TGTATCGATACA
1 TGTATCGATACA
1904182 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1907251 original size:21 final size:19
Alignment explanation
Indices: 1907233--1907292 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
1907223 TCCAAATTTC
1907233 AATATATATTTATATAATT
1 AATATATATTTATATAATT
1907252 AATATATATTTATAT-ATT
1 AATATATATTTATATAATT
* **
1907270 AA-A-ATAATTATATTTTT
1 AATATATATTTATATAATT
1907287 AATATA
1 AATATA
1907293 AAATTAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
16 9 0.25
17 5 0.14
18 6 0.17
19 16 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AATATATATTTATATAATT
Found at i:1909184 original size:19 final size:19
Alignment explanation
Indices: 1909160--1909197 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1909150 TTTTTAAAAA
1909160 AAATTTATTTAAATTAAAT
1 AAATTTATTTAAATTAAAT
* *
1909179 AAATTTTTTTAATTTAAAT
1 AAATTTATTTAAATTAAAT
1909198 CGATCTAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATTTATTTAAATTAAAT
Found at i:1909255 original size:28 final size:29
Alignment explanation
Indices: 1909219--1909276 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
1909209 GAATTAATAG
* * *
1909219 TTATTAAATAATATTAATATT-ATTTTAA
1 TTATAAAATAATATAAAAATTAATTTTAA
1909247 TTATAAAATAATATAAAAATTAATTTTAA
1 TTATAAAATAATATAAAAATTAATTTTAA
1909276 T
1 T
1909277 ACTTTTAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TTATAAAATAATATAAAAATTAATTTTAA
Found at i:1911594 original size:5 final size:5
Alignment explanation
Indices: 1911584--1911619 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
1911574 TTGCCTACCT
1911584 TTTTC TTTTC TTTTC TTTT- TTTTC TTTT- TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1911620 GGGTGCTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 12 0.40
5 18 0.60
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (5 bp):
TTTTC
Found at i:1911599 original size:10 final size:9
Alignment explanation
Indices: 1911583--1911619 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
1911573 ATTGCCTACC
1911583 TTTTTCTTT
1 TTTTTCTTT
1911592 TCTTTTCTTT
1 T-TTTTCTTT
1911602 TTTTTCTTT
1 TTTTTCTTT
1911611 TTTTT-TTT
1 TTTTTCTTT
1911619 T
1 T
1911620 GGGTGCTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 4 0.15
9 14 0.52
10 9 0.33
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:1911607 original size:19 final size:17
Alignment explanation
Indices: 1911583--1911619 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
1911573 ATTGCCTACC
1911583 TTTTTCTTTTCTTTTCTTT
1 TTTTTCTTTT-TTTT-TTT
1911602 TTTTTCTTTTTTTTTTT
1 TTTTTCTTTTTTTTTTT
1911619 T
1 T
1911620 GGGTGCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 4 0.22
19 10 0.56
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (17 bp):
TTTTTCTTTTTTTTTTT
Found at i:1911608 original size:14 final size:13
Alignment explanation
Indices: 1911583--1911619 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
1911573 ATTGCCTACC
*
1911583 TTTTTCTTTTCTT
1 TTTTTTTTTTCTT
1911596 TTCTTTTTTTTCTT
1 TT-TTTTTTTTCTT
1911610 TTTTTTTTTT
1 TTTTTTTTTT
1911620 GGGTGCTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTTCTT
Found at i:1912883 original size:14 final size:14
Alignment explanation
Indices: 1912866--1912917 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
1912856 ATTATATATT
1912866 TATATAAATTTTAA
1 TATATAAATTTTAA
*
1912880 TATATAAAATAATTAA
1 TATAT-AAAT-TTTAA
1912896 TATTTTATAAATTTTAA
1 TA---TATAAATTTTAA
1912913 TATAT
1 TATAT
1912918 TTATATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 8 0.26
15 4 0.13
16 6 0.19
17 6 0.19
18 4 0.13
19 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:1912932 original size:33 final size:33
Alignment explanation
Indices: 1912851--1912932 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 33
1912841 CATGAAATTG
1912851 TTAT-TATTATATATTTATATAAATTTTAATATA
1 TTATATATT-TATATTTATATAAATTTTAATATA
* * *
1912884 TAAAATAATTAATATTT-TATAAATTTTAATATA
1 TTATAT-ATTTATATTTATATAAATTTTAATATA
1912917 TTTATATATTTATATT
1 -TTATATATTTATATT
1912933 ATTTTTTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
33 26 0.65
34 11 0.28
35 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
TTATATATTTATATTTATATAAATTTTAATATA
Found at i:1912944 original size:14 final size:14
Alignment explanation
Indices: 1912927--1912969 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1912917 TTTATATATT
1912927 TATATTATTTTTTA
1 TATATTATTTTTTA
* *
1912941 TATAATATTTTTAA
1 TATATTATTTTTTA
*
1912955 TATATT-TTATTTA
1 TATATTATTTTTTA
1912968 TA
1 TA
1912970 ATATCATGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TATATTATTTTTTA
Found at i:1916992 original size:14 final size:16
Alignment explanation
Indices: 1916964--1917036 Score: 66
Period size: 15 Copynumber: 4.8 Consensus size: 16
1916954 TGTATATTTT
*
1916964 TTTTATTATAGTTAT-A
1 TTTTAATATA-TTATAA
1916980 TTTTAA-ATATTATAA
1 TTTTAATATATTATAA
1916995 TTTTAATATATTAATAA
1 TTTTAATATATT-ATAA
* *
1917012 TTTT--TATAATGT-A
1 TTTTAATATATTATAA
1917025 TTTTAATATATT
1 TTTTAATATATT
1917037 TACATATTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
13 5 0.10
14 5 0.10
15 20 0.42
16 10 0.21
17 8 0.17
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTTAATATATTATAA
Found at i:1917576 original size:23 final size:23
Alignment explanation
Indices: 1917535--1917606 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
1917525 TGATATATTA
**
1917535 ATATTTTTTATTAAATATATTTT
1 ATATTTTTTATTATTTATATTTT
*
1917558 ATATTTTTTAATATTTATA--TT
1 ATATTTTTTATTATTTATATTTT
*
1917579 ATATTTATATTATTTTTTATATTTT
1 ATATTT-T-TTATTATTTATATTTT
1917604 ATA
1 ATA
1917607 ATATATTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 8 0.20
22 1 0.03
23 26 0.65
25 5 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
ATATTTTTTATTATTTATATTTT
Found at i:1917578 original size:39 final size:39
Alignment explanation
Indices: 1917507--1917610 Score: 97
Period size: 39 Copynumber: 2.6 Consensus size: 39
1917497 TTAAAGTATC
1917507 ATATATTTATATAAATTTTGAT-ATATTAATATT-T-TTTATTAA
1 ATATATTT-TAT--ATTTT-ATAATATTAATATTATATTTA-T-A
* *
1917549 ATATATTTTATATTTTTTAATATTTATATTATATTTATA
1 ATATATTTTATATTTTATAATATTAATATTATATTTATA
* *
1917588 TTATTTTTTATATTTTATAATAT
1 ATATATTTTATATTTTATAATAT
1917611 ATTTTAATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
38 1 0.02
39 36 0.67
40 2 0.04
41 7 0.13
42 8 0.15
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (39 bp):
ATATATTTTATATTTTATAATATTAATATTATATTTATA
Found at i:1917593 original size:30 final size:30
Alignment explanation
Indices: 1917548--1917627 Score: 112
Period size: 30 Copynumber: 2.7 Consensus size: 30
1917538 TTTTTTATTA
1917548 AATATATTTTA-TATTTTTTAATA-TTTAT
1 AATATATTTTATTATTTTTTAATATTTTAT
*
1917576 ATTATATTTATATTATTTTTT-ATATTTTAT
1 AATATATTT-TATTATTTTTTAATATTTTAT
1917606 AATATATTTTAATTATTTTTTA
1 AATATATTTT-ATTATTTTTTA
1917628 TTTGTATAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
28 8 0.18
29 6 0.13
30 31 0.69
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (30 bp):
AATATATTTTATTATTTTTTAATATTTTAT
Found at i:1917621 original size:23 final size:22
Alignment explanation
Indices: 1917548--1917628 Score: 79
Period size: 19 Copynumber: 4.0 Consensus size: 22
1917538 TTTTTTATTA
1917548 AATATATTTTA-TAT-TTTT-T
1 AATATATTTTATTATATTTTAT
*
1917567 AATAT-TTATATTATA-TTTAT
1 AATATATTTTATTATATTTTAT
1917587 -AT-TATTTT-TTATATTTTAT
1 AATATATTTTATTATATTTTAT
*
1917606 AATATATTTTAATTATTTTTTAT
1 AATATATTTT-ATTATATTTTAT
1917629 TTGTATAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
18 10 0.20
19 21 0.42
20 3 0.06
21 6 0.12
23 10 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
AATATATTTTATTATATTTTAT
Found at i:1917628 original size:30 final size:30
Alignment explanation
Indices: 1917548--1917636 Score: 107
Period size: 30 Copynumber: 3.1 Consensus size: 30
1917538 TTTTTTATTA
1917548 AATATATTTT-A-TATTTTTTA-ATATTTAT
1 AATATATTTTAATTATTTTTTATAT-TTTAT
*
1917576 ATTATA-TTTATATTATTTTTTATATTTTAT
1 AATATATTTTA-ATTATTTTTTATATTTTAT
*
1917606 AATATATTTTAATTATTTTTTAT-TTGTAT
1 AATATATTTTAATTATTTTTTATATTTTAT
1917635 AA
1 AA
1917637 ATTTTGAGAT
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
27 3 0.06
28 5 0.09
29 8 0.15
30 31 0.58
31 6 0.11
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (30 bp):
AATATATTTTAATTATTTTTTATATTTTAT
Found at i:1917629 original size:37 final size:39
Alignment explanation
Indices: 1917554--1917630 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
1917544 ATTAAATATA
* *
1917554 TTTTATATTTTTTAATATTTATATTATATTTATATTATT
1 TTTTATATTTTATAATATTTATAATATATTTATATTATT
*
1917593 TTTTATATTTTATAATATATTTTAAT-TATTT-T-TTATT
1 TTTTATATTTTATAATAT-TTATAATATATTTATATTATT
1917630 T
1 T
1917631 GTATAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 6 0.18
38 1 0.03
39 22 0.65
40 5 0.15
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (39 bp):
TTTTATATTTTATAATATTTATAATATATTTATATTATT
Found at i:1921168 original size:16 final size:17
Alignment explanation
Indices: 1921147--1921179 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1921137 AGATCTCATC
1921147 TTTTA-TCATAGTTTTT
1 TTTTATTCATAGTTTTT
*
1921163 TTTTATTCATTGTTTTT
1 TTTTATTCATAGTTTTT
1921180 ATCTAAATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.73
Consensus pattern (17 bp):
TTTTATTCATAGTTTTT
Found at i:1921947 original size:15 final size:15
Alignment explanation
Indices: 1921927--1921957 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1921917 ATTCTGAACA
1921927 AGAGAAAAGAAATAT
1 AGAGAAAAGAAATAT
*
1921942 AGAGAAAAGATATAT
1 AGAGAAAAGAAATAT
1921957 A
1 A
1921958 TATATATATA
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:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (15 bp):
AGAGAAAAGAAATAT
Found at i:1921958 original size:2 final size:2
Alignment explanation
Indices: 1921951--1921989 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1921941 TAGAGAAAAG
1921951 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1921990 GTTTCTCTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1922748 original size:48 final size:48
Alignment explanation
Indices: 1922695--1922790 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
1922685 ATTTTCTAGG
*
1922695 GAGAAAGAAACTTCATTTACACATGTTTGCACCAATGGTAATGACTGA
1 GAGAAAGAAACTTCATTTACACATGTTTGCACCAACGGTAATGACTGA
* *
1922743 GAGAAAGAAACTTCATTTACACATTTTTGCCCCAACGGTAATGACTGA
1 GAGAAAGAAACTTCATTTACACATGTTTGCACCAACGGTAATGACTGA
1922791 TTATTTAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (48 bp):
GAGAAAGAAACTTCATTTACACATGTTTGCACCAACGGTAATGACTGA
Found at i:1923532 original size:6 final size:6
Alignment explanation
Indices: 1923521--1923549 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1923511 CTCTTCTTTT
1923521 CCTTCC CCTTCC CCTTCC CCTTCC CCTTC
1 CCTTCC CCTTCC CCTTCC CCTTCC CCTTC
1923550 TTTTGTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CCTTCC
Found at i:1924888 original size:2 final size:2
Alignment explanation
Indices: 1924883--1924912 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1924873 ATATACCTAA
1924883 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
1924913 CTTTATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1925573 original size:21 final size:22
Alignment explanation
Indices: 1925549--1925601 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
1925539 TATTAATATA
*
1925549 TTAAAATTTATA-TAAAATACT
1 TTAAAATATATATTAAAATACT
1925570 TT-AAATATA-ATTAAAATACT
1 TTAAAATATATATTAAAATACT
*
1925590 ATAAAATATATA
1 TTAAAATATATA
1925602 AATATCATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 1 0.04
20 16 0.59
21 9 0.33
22 1 0.04
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAAATATATATTAAAATACT
Found at i:1925593 original size:30 final size:28
Alignment explanation
Indices: 1925504--1925606 Score: 77
Period size: 30 Copynumber: 3.5 Consensus size: 28
1925494 ACATGATATG
*
1925504 AATATATAAAT-TTTTAAAATTTTTATGATATA
1 AATATATAAATATATTAAAA---TTAT-ATA-A
*
1925536 AAT-TATTAATATATTAAAATTTATATAA
1 AATATATAAATATATTAAAA-TTATATAA
*
1925564 AATACTTTAAATATAATTAAAA-TACTATAA
1 AATA-TATAAATAT-ATTAAAATTA-TATAA
1925594 AATATATAAATAT
1 AATATATAAATAT
1925607 CATAACAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
28 4 0.07
29 13 0.21
30 21 0.34
31 13 0.21
32 10 0.16
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (28 bp):
AATATATAAATATATTAAAATTATATAA
Found at i:1926759 original size:25 final size:24
Alignment explanation
Indices: 1926731--1926785 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1926721 GTTTATGAAC
*
1926731 AATTTAATTAA-TAAAATTAATTAAA
1 AATTTAATAAATTAAAATT-A-TAAA
*
1926756 AATTAAAATAAATTAAAATTATAAA
1 AATT-TAATAAATTAAAATTATAAA
1926781 AATTT
1 AATTT
1926786 TGATTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
25 12 0.48
26 6 0.24
27 7 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AATTTAATAAATTAAAATTATAAA
Found at i:1929071 original size:22 final size:23
Alignment explanation
Indices: 1929045--1929094 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1929035 ATCTTTTAAA
*
1929045 TTTTA-CTAAATAACTAATC-ATT
1 TTTTATCTAAA-AAATAATCTATT
*
1929067 TTTTATCTAAAAAATTATCTATT
1 TTTTATCTAAAAAATAATCTATT
1929090 TTTTA
1 TTTTA
1929095 AAAAACTACC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTATCTAAAAAATAATCTATT
Found at i:1929098 original size:19 final size:20
Alignment explanation
Indices: 1929074--1929127 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
1929064 ATTTTTTATC
*
1929074 TAAAAAATTATCT-ATTTTT
1 TAAAAAATTACCTAATTTTT
*
1929093 TAAAAAACTACCTAAATTTTT
1 TAAAAAATTACCT-AATTTTT
*
1929114 TTAAAAATTACCTA
1 TAAAAAATTACCTA
1929128 CTCAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 11 0.38
20 1 0.03
21 17 0.59
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAAAAATTACCTAATTTTT
Found at i:1930585 original size:20 final size:19
Alignment explanation
Indices: 1930558--1930596 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1930548 ATTAATAAAA
* *
1930558 ATATATAAATATTATTTTT
1 ATATATAAAAAATATTTTT
1930577 ATATAATAAAAAATATTTTT
1 ATAT-ATAAAAAATATTTTT
1930597 TTAAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATATAAAAAATATTTTT
Found at i:1931088 original size:57 final size:57
Alignment explanation
Indices: 1931000--1931108 Score: 191
Period size: 57 Copynumber: 1.9 Consensus size: 57
1930990 CTAGGGTTGT
* * *
1931000 TGTTTTTGTTCTTCTTGGTTAACCGGTAAGTGTCTTTTTCAATTTCCTTTTTTTCTC
1 TGTTTCTGTTCTTCTCGGTTAACCGGTAAGTGTCTTTTTAAATTTCCTTTTTTTCTC
1931057 TGTTTCTGTTCTTCTCGGTTAACCGGTAAGTGTCTTTTTAAATTTCCTTTTT
1 TGTTTCTGTTCTTCTCGGTTAACCGGTAAGTGTCTTTTTAAATTTCCTTTTT
1931109 CTTTTCTCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.12, C:0.17, G:0.15, T:0.56
Consensus pattern (57 bp):
TGTTTCTGTTCTTCTCGGTTAACCGGTAAGTGTCTTTTTAAATTTCCTTTTTTTCTC
Found at i:1938133 original size:13 final size:13
Alignment explanation
Indices: 1938115--1938139 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1938105 CAAATAGATT
1938115 AAAGATGATAATC
1 AAAGATGATAATC
1938128 AAAGATGATAAT
1 AAAGATGATAAT
1938140 AACCCAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.16, T:0.24
Consensus pattern (13 bp):
AAAGATGATAATC
Found at i:1939017 original size:4 final size:4
Alignment explanation
Indices: 1939010--1939034 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1939000 AGAGAGAGAA
1939010 ACAG ACAG ACAG ACAG ACAG ACAG A
1 ACAG ACAG ACAG ACAG ACAG ACAG A
1939035 AGGAAAGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.24, T:0.00
Consensus pattern (4 bp):
ACAG
Found at i:1940515 original size:2 final size:2
Alignment explanation
Indices: 1940508--1940541 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1940498 AGATTTCTCT
1940508 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1940542 AACTCATAAT
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):
TA
Found at i:1942666 original size:42 final size:42
Alignment explanation
Indices: 1942549--1942671 Score: 105
Period size: 42 Copynumber: 3.0 Consensus size: 42
1942539 AGATTTATAC
* *
1942549 ATTTATATAATAT-AGT-ATT-ATAT-TAAAAA-TAATTAAA
1 ATTTATATAATATAAATAATTAATATATAAAAATTTATTAAA
* * * **
1942586 ATTTTATATGATATAAAAAATATAA-ATATATATTTTTATTAAA
1 A-TTTATATAATATAAATAAT-TAATATATAAAAATTTATTAAA
*
1942629 ATTTATATAATATAAATAATTAATTTATAAAAATTTATATAAA
1 ATTTATATAATATAAATAATTAATATATAAAAATTTAT-TAAA
1942672 TATATAATAT
Statistics
Matches: 64, Mismatches: 13, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
37 1 0.02
38 11 0.17
39 1 0.02
40 2 0.03
41 6 0.09
42 31 0.48
43 12 0.19
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (42 bp):
ATTTATATAATATAAATAATTAATATATAAAAATTTATTAAA
Found at i:1942992 original size:41 final size:43
Alignment explanation
Indices: 1942889--1942992 Score: 99
Period size: 44 Copynumber: 2.4 Consensus size: 43
1942879 ATTATATTTT
* * *
1942889 ATAAAATAATATTAAA-AATTTTTATATTAATATTAATATTTAA
1 ATAAAATAAT-TTAAATTATTTTAATAATAATATTAATATTTAA
* **
1942932 ATAAAAATATTTTTTATTATTTTAATAATAAT-TTAA-A-TTAA
1 AT-AAAATAATTTAAATTATTTTAATAATAATATTAATATTTAA
1942973 ATAAAATTAATTTAAATTAT
1 ATAAAA-TAATTTAAATTAT
1942993 AAAATATGTT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
40 4 0.08
41 16 0.33
42 1 0.02
43 9 0.18
44 19 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (43 bp):
ATAAAATAATTTAAATTATTTTAATAATAATATTAATATTTAA
Found at i:1943270 original size:16 final size:16
Alignment explanation
Indices: 1943249--1943286 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1943239 GCCAACATTA
1943249 AAAAAAAAAAAAAAGG
1 AAAAAAAAAAAAAAGG
**
1943265 AAAAAAAAGGAAAAGG
1 AAAAAAAAAAAAAAGG
1943281 AAAAAA
1 AAAAAA
1943287 TGCTTACTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAGG
Found at i:1944575 original size:15 final size:15
Alignment explanation
Indices: 1944555--1944601 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
1944545 TAATTTTTTA
1944555 TATATTTTTAAATAT
1 TATATTTTTAAATAT
1944570 TATATTTTT--ATAT
1 TATATTTTTAAATAT
*
1944583 TA-ATATTTAAATA-
1 TATATTTTTAAATAT
1944596 TATATT
1 TATATT
1944602 AAATAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
12 5 0.19
13 8 0.30
14 5 0.19
15 9 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATATTTTTAAATAT
Found at i:1944591 original size:27 final size:24
Alignment explanation
Indices: 1944549--1944601 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 24
1944539 TACAGTTAAT
*
1944549 TTTTTATATATTTTTAAATATTATA
1 TTTTTATATATATTTAAATA-TATA
1944574 TTTTTATATTAATATTTAAATATATA
1 TTTTTATA-T-ATATTTAAATATATA
1944600 TT
1 TT
1944602 AAATAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 8 0.32
26 7 0.28
27 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTTATATATATTTAAATATATA
Found at i:1944622 original size:15 final size:14
Alignment explanation
Indices: 1944602--1944637 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
1944592 AATATATATT
1944602 AAATAAAAATTTTA
1 AAATAAAAATTTTA
*
1944616 AATATAAAATTTTTA
1 AA-ATAAAAATTTTA
1944631 AAATAAA
1 AAATAAA
1944638 CTAAATGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATAAAAATTTTA
Found at i:1944626 original size:14 final size:15
Alignment explanation
Indices: 1944600--1944637 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
1944590 TAAATATATA
1944600 TTAAATA-AAAA-TT
1 TTAAATATAAAATTT
1944613 TTAAATATAAAATTT
1 TTAAATATAAAATTT
1944628 TTAAA-ATAAA
1 TTAAATATAAA
1944638 CTAAATGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.30
14 9 0.39
15 7 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TTAAATATAAAATTT
Found at i:1945639 original size:31 final size:32
Alignment explanation
Indices: 1945599--1945680 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 32
1945589 TCAAAAATTT
* *
1945599 AAATGTAAAAAAATTTGGA-TTCAAAAAACCC
1 AAATCTAAAAAAATTTGAATTTCAAAAAACCC
* * * *
1945630 GAATCTAAAAAAATTTGAATTTGAAAAAGCCT
1 AAATCTAAAAAAATTTGAATTTCAAAAAACCC
*
1945662 AAATCTAAAAAAGTTTGAA
1 AAATCTAAAAAAATTTGAA
1945681 ACCCATAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 16 0.38
32 26 0.62
ACGTcount: A:0.54, C:0.10, G:0.11, T:0.26
Consensus pattern (32 bp):
AAATCTAAAAAAATTTGAATTTCAAAAAACCC
Found at i:1945898 original size:23 final size:23
Alignment explanation
Indices: 1945872--1945915 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1945862 TATGAAAAGG
*
1945872 TATTTATAAT-TATTATGCAATTA
1 TATTAATAATATATTAT-CAATTA
1945895 TATTAATAATATATTATCAAT
1 TATTAATAATATATTATCAAT
1945916 CAAAATAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (23 bp):
TATTAATAATATATTATCAATTA
Found at i:1948325 original size:79 final size:79
Alignment explanation
Indices: 1948187--1948395 Score: 244
Period size: 79 Copynumber: 2.6 Consensus size: 79
1948177 GAGATAATAA
* * * *
1948187 CGGGGTTGGAGTATCCCCT-TGAAAATAACGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATG
1 CGGGGTTGGAGTATCCCCTCAG-AAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAAT-
*
1948251 A-TTAGAAAATAGAA-T
64 ATTTAGAAAATA-AAGC
* * * *
1948266 CGGGATTGGAGTATCCTCTCAGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATAT
* *
1948331 TTTGGAAATAAAGC
66 TTAGAAAATAAAGC
* **
1948345 CGGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATTA
1 CGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTA
1948396 AATAACGAGG
Statistics
Matches: 110, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
78 3 0.03
79 106 0.96
80 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATAT
TTAGAAAATAAAGC
Found at i:1948535 original size:51 final size:51
Alignment explanation
Indices: 1948404--1949050 Score: 369
Period size: 51 Copynumber: 12.4 Consensus size: 51
1948394 TAAATAACGA
* * *
1948404 GGTTGGAGTATCCTCC-ATTGTGAAAAATTAGTATTTTTTG-AAATAAAATCGG
1 GGTTGGAGTATCC-CCGATTGTGGAAAATT-G-GTGTTTTGAAAATAAAATCGG
* ** *
1948456 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-GTGGAAAATTGGTGTTTTGAAAATAAAATCGG
1948508 GGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTT-AGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGA-AAATAAAATCGG
* *** * *
1948559 GGTTGGAGTATCCCCGATTAT-GAGAAATCAATATTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGGA-AAATTGGTGTTTTGAAAATAAAATCGG
* * * * * ***** **
1948610 GGTTGGAGTATCCCC--TCGGAGGTAACGGGATTGGAGTATCCCCGATAAAATAACAA
1 GGTTGGAGTATCCCCGAT-TGTGG-AA---AATTGGTGTTTTGAAAATAAAAT--CGG
* * * *
1948666 GGTTGGAGAATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGGAAAATTGGTG-TTTTGAAAATAAAATCGG
* ** *
1948718 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-GTGGAAAATTGGTGTTTTGAAAATAAAATCGG
* * *
1948770 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTT-AGAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGA-AAATAAAATCGG
* * *** * ** ** *
1948821 GGTTGGAGTATCCCCGATTAT-AAGAAATCAATATTTTGGGAATAAAGCCAG
1 GGTTGGAGTATCCCCGATTGTGGA-AAATTGGTGTTTTGAAAATAAAATCGG
* * * ** * * ***** *
1948872 GGTTTGAGTATCCCC--TCGGAGGTAACGGGGTTGGAGTATCCCCGATAAAATAACGA
1 GGTTGGAGTATCCCCGAT-TGTGG-AA---AATTGGTGTTTTGAAAATAAAAT--CGG
* * * *
1948928 GATTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGGAAAATTGGTG-TTTTGAAAATAAAATCGG
* ** * *
1948980 AGTTGGAGTATCCCCGATTAAAGGAGACTTGGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATT-GTGGAAAATTGGTGTTTTGAAAATAAAATCGG
1949032 GGTTGGAGTATCCCCGATT
1 GGTTGGAGTATCCCCGATT
1949051 ATGAACAATT
Statistics
Matches: 444, Mismatches: 118, Indels: 66
0.71 0.19 0.11
Matches are distributed among these distances:
49 2 0.00
50 6 0.01
51 173 0.39
52 151 0.34
53 38 0.09
54 37 0.08
56 31 0.07
57 4 0.01
58 2 0.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGAAAATAAAATCGG
Found at i:1948759 original size:262 final size:262
Alignment explanation
Indices: 1948294--1949060 Score: 1318
Period size: 262 Copynumber: 2.9 Consensus size: 262
1948284 TCAGAAATAA
*
1948294 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
* *
1948359 CCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATTAAATAACGAGGTTGGAGTATCCTCCATTG
66 CCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATAAAATAACGAGGTTGGAGTATCCTCGATTG
* * *
1948424 TGAAAAATTAGTATTTTTTGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
131 TGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
* *
1948489 GTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAATAAA
196 GTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAA
*
1948554 AT
261 AC
**
1948556 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAATCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
* * *
1948621 CCCCTCGGAGGTAACGGGATTGGAGTATCCCCGATAAAATAACAAGGTTGGAGAATCCTCGATTG
66 CCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATAAAATAACGAGGTTGGAGTATCCTCGATTG
1948686 TGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
131 TGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
1948751 GTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAA
196 GTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAA
1948816 AC
261 AC
* * * *
1948818 CGGGGTTGGAGTATCCCCGATTATAAGAAATCAATATTTTGGGAATAAAGCCAGGGTTTGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
*
1948883 CCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATAAAATAACGAGATTGGAGTATCCTCGATTG
66 CCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATAAAATAACGAGGTTGGAGTATCCTCGATTG
* *
1948948 TGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAGACTTGGT
131 TGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
* * *
1949013 GTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTATGAACAATT
196 GTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGAAAAATT
1949061 GAGAAACTTA
Statistics
Matches: 476, Mismatches: 29, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
262 476 1.00
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (262 bp):
CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
CCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATAAAATAACGAGGTTGGAGTATCCTCGATTG
TGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
GTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAA
AC
Found at i:1951446 original size:13 final size:13
Alignment explanation
Indices: 1951428--1951453 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1951418 ACAAAGATCG
1951428 ATGTATCGATACA
1 ATGTATCGATACA
1951441 ATGTATCGATACA
1 ATGTATCGATACA
1951454 TTTCCTTAAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1951530 original size:19 final size:18
Alignment explanation
Indices: 1951506--1951568 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
1951496 AGTGATACAT
1951506 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1951525 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1951538 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1951557 TGTATCGATACA
1 TGTATCGATACA
1951569 TTTACGGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1951540 original size:32 final size:32
Alignment explanation
Indices: 1951499--1951570 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
1951489 GCTTCGTAGT
1951499 GATACATTGTATCGATACAAAACTTATGTATC
1 GATACATTGTATCGATACAAAACTTATGTATC
*
1951531 GATACATTGTATCGATACAACACTTATGTATC
1 GATACATTGTATCGATACAAAACTTATGTATC
1951563 GATACATT
1 GATACATT
1951571 TACGGTTTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (32 bp):
GATACATTGTATCGATACAAAACTTATGTATC
Found at i:1951543 original size:13 final size:13
Alignment explanation
Indices: 1951525--1951549 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1951515 ACAAAACTTA
1951525 TGTATCGATACAT
1 TGTATCGATACAT
1951538 TGTATCGATACA
1 TGTATCGATACA
1951550 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1953342 original size:13 final size:13
Alignment explanation
Indices: 1953324--1953362 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1953314 GTCCATTTCA
1953324 TTTTTTTTCTTTTT
1 TTTTTTTTC-TTTT
1953338 TTTTTTTTCTTTT
1 TTTTTTTTCTTTT
* *
1953351 TCTTTTTCCTTT
1 TTTTTTTTCTTT
1953363 CTTCCTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTTTTCTTTT
Found at i:1953343 original size:14 final size:15
Alignment explanation
Indices: 1953319--1953357 Score: 62
Period size: 14 Copynumber: 2.6 Consensus size: 15
1953309 TGCTAGTCCA
1953319 TTTCATTTTTTTTCTT
1 TTTC-TTTTTTTTCTT
1953335 TTT-TTTTTTTTCTT
1 TTTCTTTTTTTTCTT
1953349 TTTCTTTTT
1 TTTCTTTTT
1953358 CCTTTCTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 14 0.64
15 5 0.23
16 3 0.14
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTCTTTTTTTTCTT
Found at i:1954875 original size:32 final size:33
Alignment explanation
Indices: 1954744--1954972 Score: 229
Period size: 32 Copynumber: 7.1 Consensus size: 33
1954734 TGGTGTTTTC
*
1954744 AAAAAGGGTTGCCA-CTGACTTGTGTGGGCCTTT-
1 AAAAAGAGTTGCCATC-GACTTGTGTGGG-CTTTG
* * *
1954777 AAAAAGAGGTGCCATCGACATGTGTGGGCCTTG
1 AAAAAGAGTTGCCATCGACTTGTGTGGGCTTTG
* * * *
1954810 AAAAAAAGGTGCCACCGACTTATGTGGGC-TTG
1 AAAAAGAGTTGCCATCGACTTGTGTGGGCTTTG
* *
1954842 AAAAAG-GTTACCATCGACTTGTGTGGACTTTG
1 AAAAAGAGTTGCCATCGACTTGTGTGGGCTTTG
*
1954874 -AAAAGGGTTGCCATCGACTTGTGTGGGCTTT-
1 AAAAAGAGTTGCCATCGACTTGTGTGGGCTTTG
* * * * *
1954905 TAAAAGAGTTGCCACCAACTTGTATAGGCTTTG
1 AAAAAGAGTTGCCATCGACTTGTGTGGGCTTTG
* *
1954938 -AAAAGAGTTGCCATCGACTTATGTAGGCTTTG
1 AAAAAGAGTTGCCATCGACTTGTGTGGGCTTTG
1954970 AAA
1 AAA
1954973 GGTGCCACTG
Statistics
Matches: 164, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
31 22 0.13
32 91 0.55
33 50 0.30
34 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (33 bp):
AAAAAGAGTTGCCATCGACTTGTGTGGGCTTTG
Found at i:1955075 original size:30 final size:29
Alignment explanation
Indices: 1954745--1955773 Score: 622
Period size: 29 Copynumber: 35.1 Consensus size: 29
1954735 GGTGTTTTCA
*
1954745 AAAAGGGTTGCCACTGACTTGTGTGGGCCTTTA
1 AAAAGGG-TGCCACTGAC-T-TGTGGG-CTTTG
*
1954778 AAAAGAGGTGCCA-TCGACATGTGTGGGCCTTG
1 AAAAG-GGTGCCACT-GAC-T-TGTGGGCTTTG
* *
1954810 AAAAAAAGGTGCCACCGACTTATGTGGGC-TTG
1 --AAAAGGGTGCCACTGAC-T-TGTGGGCTTTG
* *
1954842 AAAAAGGTTACCA-TCGACTTGTGTGGACTTTG
1 -AAAAGGGTGCCACT-GACTTGTG-GG-CTTTG
*
1954874 AAAAGGGTTGCCA-TCGACTTGTGTGGGCTTTT
1 AAAAGGG-TGCCACT-GAC-T-TGTGGGCTTTG
* ** *
1954906 AAAAGAGTTGCCACCAACTTGTATAGGCTTTG
1 AAAAG-GGTGCCACTGACTTG--TGGGCTTTG
* *
1954938 AAAAGAGTTGCCA-TCGACTTATGTAGGCTTTG
1 AAAAG-GGTGCCACT-GAC-T-TGTGGGCTTTG
***
1954970 -AAA-GGTGCCACTGACTTGTAAACTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* * *
1954997 -AAA-GGTGGCACTGACTTGCGGGATTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1955024 AAAAGGGTGCCACTGATTTGTGGGCTATG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1955053 AAAATGGGTGTCATTGACTTGTGGGCTTTG
1 AAAA-GGGTGCCACTGACTTGTGGGCTTTG
**
1955083 AAAAGGGGTGCCACTGACTTGTTTGCTTTG
1 AAAA-GGGTGCCACTGACTTGTGGGCTTTG
* * *
1955113 AAAAGTGTGGCACTGATTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* * * *
1955142 AAAA--GTACTATTGACTTGT-AGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* * *
1955168 AAAGGGGGTGCCACTAACTTGTGGTCTTTG
1 AAA-AGGGTGCCACTGACTTGTGGGCTTTG
* * *
1955198 AAAA--GTGCTACTGACCTGTGGCCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
**
1955225 -AAA-GGTGCCACTGACTTGTAAGC-TTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
** *
1955251 AAAAAAGTGCCACTGACTTGTGAGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
1955280 AAAAGGGTGCCACTAACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
1955309 AAAAGGGTGCCACTGACTTGTAGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
1955338 AAAAGGTTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* * *
1955367 AAAAGGTTGCTACCGACTTGTGTGGACTTTG
1 AAAAGGGTGCCACTGACTTGTG-GG-CTTTG
* **
1955398 AAAAGAGTTGCCACCAACTTGTGTGGGCTTTG
1 AAAAG-GGTGCCACTGAC-T-TGTGGGCTTTG
* *
1955430 -AAAGAGTGCCACTGACTTGTAGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* * *
1955458 AAAAAGGTGCTACTGACTTCTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* * * *
1955487 AAAAAGGTGCCACCGACTTATGGGTTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
** **
1955516 AAAAGATTGCCACCAACTTGTGTGGGCTTTG
1 AAAAGGGTGCCACTGAC-T-TGTGGGCTTTG
* * * * *
1955547 AAAAGGATGCCACAGAGTTGTGGAC-TTA
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* * *
1955575 AAAAGGGTGCCACGGAGTTGTGGACTTT-
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* * * *
1955603 AAAAAGGTGCCATTGAATTGTGGAC-TT-
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* * *
1955630 AAATAGGGTGCCACAGAGTTGTGGACTTT-
1 AAA-AGGGTGCCACTGACTTGTGGGCTTTG
* * * *
1955659 AAAA-GGTGCCACAGAGTTGTAGAC-TT-
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* * * *
1955685 AAAAGGGTGTCACAGAGTTGTGGAC-TT-
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* * * * *
1955712 AAATAGAGTGCCACGGAGTTGT-GGATTTT
1 AAA-AGGGTGCCACTGACTTGTGGGCTTTG
* * *
1955741 AAAAGGGAGTGCCACTGAATCGTGGACTTTG
1 AAAA-GG-GTGCCACTGACTTGTGGGCTTTG
1955772 AA
1 AA
1955774 GAGGTTACAT
Statistics
Matches: 809, Mismatches: 138, Indels: 100
0.77 0.13 0.10
Matches are distributed among these distances:
26 21 0.03
27 124 0.15
28 115 0.14
29 252 0.31
30 88 0.11
31 65 0.08
32 81 0.10
33 47 0.06
34 16 0.02
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (29 bp):
AAAAGGGTGCCACTGACTTGTGGGCTTTG
Found at i:1955473 original size:149 final size:144
Alignment explanation
Indices: 1954753--1955670 Score: 613
Period size: 149 Copynumber: 6.2 Consensus size: 144
1954743 CAAAAAGGGT
* * * * * *
1954753 TGCCACTGACTTGTGTGGGCCTTTAAAAAGAGGTGCCATCGACATGTGTGGGCCTTGAAAAAAAG
1 TGCCACTGAC-T-TGTGGG-CTTTGAAAAG-GTTGCCACCGAC-T-TGTTGGCTTTG-AAAAGA-
* * * *
1954818 GTGCCACCGACTTATGTGGGC-TTGAAAAAGGTTACCA-TCGACTTGTGTGGACTTTGAAAAGGG
58 GTGCCACTGACTT-TGTGGGCTTTGAAAGA-G-TGCCACT-GACTTGT-AGG-CTTTGAAAAGGG
*
1954881 TTGCCA-TCGACTTGTGTGGGCTTTTAAAAGAG
117 -TGCCACT-GAC-T-TGTGGGCTTTGAAAAG-G
** * * *
1954913 TTGCCACCAACTTGTATAGGCTTTGAAAAGAGTTGCCATCGACTTATGTAGGCTTTG-AAAG-GT
1 -TGCCACTGACTTG--TGGGCTTTGAAAAG-GTTGCCACCGAC-T-TGTTGGCTTTGAAAAGAGT
*** * ** *
1954976 GCCACTGAC-TTGTAAACTTTGAAAG-GTGGCACTGACTTGCGGGATTTGAAAAGGGTGCCACTG
60 GCCACTGACTTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTAGGCTTTGAAAAGGGTGCCACTG
* *
1955039 ATTTGTGGGCTATGAAAATGGG
125 ACTTGTGGGCTTTGAAAA--GG
* * * * * * *
1955061 TGTCATTGACTTGTGGGCTTTGAAAAGGGGTGCCACTGACTTGTTTGCTTTGAAAAGTGTGGCAC
1 TGCCACTGACTTGTGGGCTTTGAAAA-GGTTGCCACCGACTTGTTGGCTTTGAAAAGAGTGCCAC
* * * * *
1955126 TGA-TTTGTGGGCTTTGAAA-AGTACTATTGACTTGTA-GCTTTGAAAGGGGGTGCCACTAACTT
65 TGACTTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTAGGCTTTGAAA-AGGGTGCCACTGACTT
*
1955188 GTGGTCTTTGAAAA-G
129 GTGGGCTTTGAAAAGG
* * * * ** *
1955203 TGCTACTGACCTGTGGCCTTTG-AAAGG-TGCCACTGACTTGTAAGC-TTGAAAAAAGTGCCACT
1 TGCCACTGACTTGTGGGCTTTGAAAAGGTTGCCACCGACTTGTTGGCTTTGAAAAGAGTGCCACT
* * * *
1955265 GAC-TTGTGAGCTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTG
66 GACTTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTAGGCTTTGAAAAGGGTGCCACTGACTTG
*
1955329 TAGGCTTTGAAAAGG
130 TGGGCTTTGAAAAGG
*
1955344 TTGCCACTGACTTGTGGGCTTTGAAAAGGTTGCTACCGACTTGTGTGGACTTTGAAAAGAGTTGC
1 -TGCCACTGACTTGTGGGCTTTGAAAAGGTTGCCACCGACTTGT-TGG-CTTTGAAAAGAG-TGC
** * *
1955409 CACCAACTTGTGTGGGCTTTGAAAGAGTGCCACTGACTTGTAGGCTTTGAAAAAGGTGCTACTGA
62 CACTGACTT-TGTGGGCTTTGAAAGAGTGCCACTGACTTGTAGGCTTTGAAAAGGGTGCCACTGA
*
1955474 CTTCTGGGCTTTGAAAAAGG
126 CTTGTGGGCTTTG-AAAAGG
* * * * *
1955494 TGCCACCGACTTATGGGTTTTGAAAAGATTGCCACCAACTTGTGTGGGCTTTGAAAAG-GATGCC
1 TGCCACTGACTTGTGGGCTTTGAAAAGGTTGCCACCGACTTGT-T-GGCTTTGAAAAGAG-TGCC
* * * ** * * * * * *
1955558 ACAGA-GTTGTGGACTTAAAAAGGGTGCCACGGAGTTGT-GGACTTT-AAAAAGGTGCCATTGAA
63 ACTGACTTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTAGG-CTTTGAAAAGGGTGCCACTGAC
*
1955620 TTGTGGAC-TT-AAATAGGG
127 TTGTGGGCTTTGAAA-A-GG
* * *
1955638 TGCCACAGAGTTGTGGACTTT-AAAAGG-TGCCAC
1 TGCCACTGACTTGTGGGCTTTGAAAAGGTTGCCAC
1955671 AGAGTTGTAG
Statistics
Matches: 610, Mismatches: 115, Indels: 83
0.75 0.14 0.10
Matches are distributed among these distances:
138 27 0.04
139 19 0.03
140 39 0.06
141 13 0.02
142 46 0.08
143 20 0.03
144 45 0.07
145 100 0.16
146 31 0.05
147 32 0.05
148 18 0.03
149 108 0.18
150 30 0.05
151 2 0.00
152 9 0.01
153 2 0.00
154 4 0.01
155 7 0.01
156 10 0.02
158 3 0.00
159 2 0.00
160 32 0.05
161 11 0.02
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (144 bp):
TGCCACTGACTTGTGGGCTTTGAAAAGGTTGCCACCGACTTGTTGGCTTTGAAAAGAGTGCCACT
GACTTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTAGGCTTTGAAAAGGGTGCCACTGACTTGT
GGGCTTTGAAAAGG
Found at i:1955586 original size:28 final size:28
Alignment explanation
Indices: 1955547--1955747 Score: 246
Period size: 28 Copynumber: 7.2 Consensus size: 28
1955537 GTGGGCTTTG
*
1955547 AAAAGGATGCCACAGAGTTGTGGACTTA
1 AAAAGGGTGCCACAGAGTTGTGGACTTA
*
1955575 AAAAGGGTGCCACGGAGTTGTGGACTTTA
1 AAAAGGGTGCCACAGAGTTGTGGAC-TTA
** *
1955604 AAAA-GGTGCCATTGAATTGTGGACTTA
1 AAAAGGGTGCCACAGAGTTGTGGACTTA
* *
1955631 AATAGGGTGCCACAGAGTTGTGGACTTT
1 AAAAGGGTGCCACAGAGTTGTGGACTTA
*
1955659 AAAA-GGTGCCACAGAGTTGTAGACTT-
1 AAAAGGGTGCCACAGAGTTGTGGACTTA
*
1955685 AAAAGGGTGTCACAGAGTTGTGGACTTA
1 AAAAGGGTGCCACAGAGTTGTGGACTTA
* * * * *
1955713 AATAGAGTGCCACGGAGTTGTGGATTTT
1 AAAAGGGTGCCACAGAGTTGTGGACTTA
1955741 AAAAGGG
1 AAAAGGG
1955748 AGTGCCACTG
Statistics
Matches: 147, Mismatches: 22, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
26 4 0.03
27 47 0.32
28 89 0.61
29 7 0.05
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.25
Consensus pattern (28 bp):
AAAAGGGTGCCACAGAGTTGTGGACTTA
Found at i:1955630 original size:56 final size:56
Alignment explanation
Indices: 1955536--1955770 Score: 269
Period size: 56 Copynumber: 4.2 Consensus size: 56
1955526 CACCAACTTG
* * *
1955536 TGTGGGCTTTGAAAAGGATGCCACAGAGTTGTGGACTTAAAAAGGGTGCCACGGAGT
1 TGTGGACTTTAAAAAGG-TGCCACAGAGTTGTGGACTTAAAAAGGGTGCCACAGAGT
** * *
1955593 TGTGGACTTTAAAAAGGTGCCATTGAATTGTGGACTTAAATAGGGTGCCACAGAGT
1 TGTGGACTTTAAAAAGGTGCCACAGAGTTGTGGACTTAAAAAGGGTGCCACAGAGT
* *
1955649 TGTGGACTTT-AAAAGGTGCCACAGAGTTGTAGACTT-AAAAGGGTGTCACAGAGT
1 TGTGGACTTTAAAAAGGTGCCACAGAGTTGTGGACTTAAAAAGGGTGCCACAGAGT
* * * * * *
1955703 TGTGGAC-TTAAATAGAGTGCCACGGAGTTGTGGATTTTAAAAGGGAGTGCCACTGAAT
1 TGTGGACTTTAAAAAG-GTGCCACAGAGTTGTGGA-CTTAAAAAGG-GTGCCACAGAGT
*
1955761 CGTGGACTTT
1 TGTGGACTTT
1955771 GAAGAGGTTA
Statistics
Matches: 150, Mismatches: 22, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
53 2 0.01
54 27 0.18
55 38 0.25
56 46 0.31
57 20 0.13
58 15 0.10
59 2 0.01
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (56 bp):
TGTGGACTTTAAAAAGGTGCCACAGAGTTGTGGACTTAAAAAGGGTGCCACAGAGT
Found at i:1955723 original size:82 final size:83
Alignment explanation
Indices: 1955554--1955746 Score: 271
Period size: 82 Copynumber: 2.3 Consensus size: 83
1955544 TTGAAAAGGA
* * * **
1955554 TGCCACAGAGTTGTGGACTTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAAGGTGCCATTGA
1 TGCCACAGAGTTGTGGACTTTAAAA-GGTGCCACAGAGTTGTAGACTTTAAAAAGGTGCCACAGA
*
1955619 ATTGTGGACTTAAATAGGG
65 ATTGTGGACTTAAATAGAG
* * *
1955638 TGCCACAGAGTTGTGGACTTTAAAAGGTGCCACAGAGTTGTAGAC-TTAAAAGGGTGTCACAGAG
1 TGCCACAGAGTTGTGGACTTTAAAAGGTGCCACAGAGTTGTAGACTTTAAAAAGGTGCCACAGAA
1955702 TTGTGGACTTAAATAGAG
66 TTGTGGACTTAAATAGAG
* *
1955720 TGCCACGGAGTTGTGGATTTTAAAAGG
1 TGCCACAGAGTTGTGGACTTTAAAAGG
1955747 GAGTGCCACT
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
82 56 0.57
83 18 0.18
84 24 0.24
ACGTcount: A:0.30, C:0.13, G:0.31, T:0.26
Consensus pattern (83 bp):
TGCCACAGAGTTGTGGACTTTAAAAGGTGCCACAGAGTTGTAGACTTTAAAAAGGTGCCACAGAA
TTGTGGACTTAAATAGAG
Found at i:1956003 original size:13 final size:12
Alignment explanation
Indices: 1955987--1956016 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
1955977 ACATGTGGTG
1955987 ATGATACGAATA
1 ATGATACGAATA
1955999 CATGATACGAATA
1 -ATGATACGAATA
1956012 ATGAT
1 ATGAT
1956017 GTTATTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.27
Consensus pattern (12 bp):
ATGATACGAATA
Found at i:1957430 original size:2 final size:2
Alignment explanation
Indices: 1957423--1957463 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1957413 GATTTTCAAG
*
1957423 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1957464 AATAAAACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1957864 original size:20 final size:21
Alignment explanation
Indices: 1957839--1957881 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1957829 TTTCATTTCA
1957839 TTTTTTTCTT-TCTCTT-CTTC
1 TTTTTTTCTTCT-TCTTCCTTC
1957859 TTTTTTTCTTCTTCTTCCTTC
1 TTTTTTTCTTCTTCTTCCTTC
1957880 TT
1 TT
1957882 CCTTGCCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTTTCTTCTTCTTCCTTC
Found at i:1957871 original size:17 final size:17
Alignment explanation
Indices: 1957842--1957875 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1957832 CATTTCATTT
1957842 TTTTCTTTCTCTTCTTC
1 TTTTCTTTCTCTTCTTC
1957859 TTTT-TTTCTTCTTCTTC
1 TTTTCTTTC-TCTTCTTC
1957876 CTTCTTCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTCTTTCTCTTCTTC
Found at i:1965124 original size:52 final size:52
Alignment explanation
Indices: 1964976--1965104 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1964966 CGAAATATGA
1964976 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
1965028 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
1965080 AAATTTGCCTACATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1965105 AAGATGAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1965131 original size:13 final size:13
Alignment explanation
Indices: 1965113--1965137 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1965103 CAAAGATGAG
1965113 TGTATCGATACAA
1 TGTATCGATACAA
1965126 TGTATCGATACA
1 TGTATCGATACA
1965138 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1966768 original size:29 final size:29
Alignment explanation
Indices: 1966687--1966768 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
1966677 ATATAGGTTC
* *
1966687 TTTTACATAATCTATGTTCACTTTAGCATT
1 TTTTACATAATCTAGGGTCA-TTTAGCATT
* * *
1966717 TTTTATATATTTTAGGG-CTATTTAG-ATT
1 TTTTACATAATCTAGGGTC-ATTTAGCATT
1966745 ATTTTACATAATCTAGGGTCATTT
1 -TTTTACATAATCTAGGGTCATTT
1966769 TAGAGATTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
28 3 0.07
29 24 0.59
30 14 0.34
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (29 bp):
TTTTACATAATCTAGGGTCATTTAGCATT
Found at i:1966771 original size:59 final size:59
Alignment explanation
Indices: 1966489--1966771 Score: 300
Period size: 59 Copynumber: 4.8 Consensus size: 59
1966479 AAATACTATA
* * * * *
1966489 TATTTTAGGGTCATTTAGGTTAATTTATAT-ATCAAGGGATCA-TTTAGCAATTTTCATG
1 TATTTTAGGGCCATTTAGGTTATTTTACATAATCTAGGG-TCACTTTAGCATTTTTCATG
* * * * * *
1966547 TATTTAAAGGCCATTTAGGTTATTTTATATAGTCTAAGGTTACTTTAGCATTTTTCATG
1 TATTTTAGGGCCATTTAGGTTATTTTACATAATCTAGGGTCACTTTAGCATTTTTCATG
* * * * *
1966606 CATTTTAGGGCCATTAAGATTATTTTACATAATCTATGTTCACTTTAGCATTTTTCATG
1 TATTTTAGGGCCATTTAGGTTATTTTACATAATCTAGGGTCACTTTAGCATTTTTCATG
** * * * * * *
1966665 CGTTTTAGGGCCATATAGGTTCTTTTACATAATCTATGTTCACTTTAGCATTTTTTATA
1 TATTTTAGGGCCATTTAGGTTATTTTACATAATCTAGGGTCACTTTAGCATTTTTCATG
* * *
1966724 TATTTTAGGGCTATTTAGATTATTTTACATAATCTAGGGTCATTTTAG
1 TATTTTAGGGCCATTTAGGTTATTTTACATAATCTAGGGTCACTTTAG
1966772 AGATTTTCAT
Statistics
Matches: 188, Mismatches: 35, Indels: 3
0.83 0.15 0.01
Matches are distributed among these distances:
58 28 0.15
59 160 0.85
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.47
Consensus pattern (59 bp):
TATTTTAGGGCCATTTAGGTTATTTTACATAATCTAGGGTCACTTTAGCATTTTTCATG
Found at i:1967234 original size:78 final size:77
Alignment explanation
Indices: 1966968--1967264 Score: 220
Period size: 78 Copynumber: 3.9 Consensus size: 77
1966958 TACATGTTTG
* * ** * * *
1966968 TTAGTGTCATTTAGGTAATAATATCTTAAAACCAAGTCTCTAAGGTCATGTGAGAATTATCATAT
1 TTAGGGTCATTTAGGTAAAAATGCCTTAAAATCAAGTCTCTAGGGTCATGTGAGAATTTTCATAT
* *
1967033 CGATGTATGTTCA
66 CGAT-TATATTTA
** * * *
1967046 TTAAGGGT-ATTTAGG--AATTTGTTCCTTAAAAATTAAGTCTCT-GAGGTCATGTAAAAATTTT
1 TT-AGGGTCATTTAGGTAAAAATG--CCTT-AAAATCAAGTCTCTAG-GGTCATGTGAGAATTTT
*
1967107 --TAT--ATTA-ATCTA
61 CATATCGATTATATTTA
* * * * * *
1967119 TTAAGGTTATTTAGATAAAATTGCATTAATAAT-GAGTCTCTAGGGTCATGTG-GAAATTTTCAT
1 TTAGGGTCATTTAGGTAAAAATGCCTTAA-AATCAAGTCTCTAGGGTCATGTGAG-AATTTTCAT
1967182 ATCGATATATATTTA
64 ATCGAT-TATATTTA
* * *
1967197 TTAGGGTCATTTAGGTAAAAATGCCTTAAAATCGAGTCTCTAGGGTCATATGAGAACTTTCATAT
1 TTAGGGTCATTTAGGTAAAAATGCCTTAAAATCAAGTCTCTAGGGTCATGTGAGAATTTTCATAT
1967262 CGA
66 CGA
1967265 AACATGTCCA
Statistics
Matches: 170, Mismatches: 30, Indels: 38
0.71 0.13 0.16
Matches are distributed among these distances:
72 27 0.16
73 17 0.10
74 5 0.03
75 7 0.04
76 4 0.02
77 8 0.05
78 71 0.42
79 31 0.18
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (77 bp):
TTAGGGTCATTTAGGTAAAAATGCCTTAAAATCAAGTCTCTAGGGTCATGTGAGAATTTTCATAT
CGATTATATTTA
Found at i:1968747 original size:23 final size:21
Alignment explanation
Indices: 1968692--1968747 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 21
1968682 TTAAATTTAG
1968692 TTATTTAAAATATTTTTGAAA
1 TTATTTAAAATATTTTTGAAA
* * * *
1968713 TGATATATAATATTTTTTTAATA
1 TTATTTAAAATA-TTTTTGAA-A
1968736 TTATTTAAAATA
1 TTATTTAAAATA
1968748 ATAAAATAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
21 9 0.35
22 7 0.27
23 10 0.38
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (21 bp):
TTATTTAAAATATTTTTGAAA
Found at i:1969353 original size:23 final size:21
Alignment explanation
Indices: 1969323--1969372 Score: 82
Period size: 23 Copynumber: 2.3 Consensus size: 21
1969313 ATGTATGAAT
1969323 TTATATATAATCAATAAATTAAA
1 TTATATATAATCAAT-AATT-AA
1969346 TTATATATAATCAATAATTAA
1 TTATATATAATCAATAATTAA
1969367 TTATAT
1 TTATAT
1969373 CATGTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 8 0.30
22 4 0.15
23 15 0.56
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
TTATATATAATCAATAATTAA
Found at i:1974384 original size:9 final size:9
Alignment explanation
Indices: 1974370--1974402 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1974360 AAATATAAAT
1974370 TAATTAATA
1 TAATTAATA
1974379 TAATTAATA
1 TAATTAATA
*
1974388 AAATT-ATA
1 TAATTAATA
1974396 TAATTAA
1 TAATTAA
1974403 ATTTAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TAATTAATA
Found at i:1974425 original size:35 final size:35
Alignment explanation
Indices: 1974357--1974426 Score: 83
Period size: 35 Copynumber: 2.0 Consensus size: 35
1974347 TAATCAATGG
1974357 TATAAATATAAATTAATTAATATAATTAATAAAAT
1 TATAAATATAAATTAATTAATATAATTAATAAAAT
*
1974392 TATATAAT-TAAATTTAA-TAAT-TAATTTATTAAAAT
1 TATA-AATATAAA-TTAATTAATATAA-TTAATAAAAT
1974427 ATTAATAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
34 3 0.10
35 21 0.68
36 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (35 bp):
TATAAATATAAATTAATTAATATAATTAATAAAAT
Done.