Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold412
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: 4645160
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 13 of 32
Found at i:1773247 original size:2 final size:2
Alignment explanation
Indices: 1773242--1773269 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1773232 CAAAAAGGCG
1773242 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
1773270 GTACAGAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1775440 original size:14 final size:14
Alignment explanation
Indices: 1775405--1775433 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1775395 AAAAATATTA
1775405 TAAATTTTAAAATT
1 TAAATTTTAAAATT
1775419 TAAATTTTAAAATT
1 TAAATTTTAAAATT
1775433 T
1 T
1775434 CTATTTTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAAATTTTAAAATT
Found at i:1778956 original size:10 final size:10
Alignment explanation
Indices: 1778938--1779007 Score: 56
Period size: 10 Copynumber: 7.2 Consensus size: 10
1778928 TCGTTTTATT
*
1778938 TTTTTATATA
1 TTTTAATATA
1778948 TTTTAATATA
1 TTTTAATATA
* *
1778958 TTATAATTTA
1 TTTTAATATA
*
1778968 TGTTTAAAATA
1 T-TTTAATATA
1778979 TTTT-ATAT-
1 TTTTAATATA
* *
1778987 TTATATTA-A
1 TTTTAATATA
1778996 TTTTAATATA
1 TTTTAATATA
1779006 TT
1 TT
1779008 AATAATTTAT
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
8 3 0.07
9 11 0.24
10 24 0.53
11 7 0.16
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (10 bp):
TTTTAATATA
Found at i:1778974 original size:21 final size:22
Alignment explanation
Indices: 1778949--1778990 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1778939 TTTTATATAT
*
1778949 TTTAATATATTATA-ATTTATG
1 TTTAAAATATTATATATTTATG
*
1778970 TTTAAAATATTTTATATTTAT
1 TTTAAAATATTATATATTTAT
1778991 ATTAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTAAAATATTATATATTTATG
Found at i:1778995 original size:21 final size:23
Alignment explanation
Indices: 1778952--1779021 Score: 56
Period size: 27 Copynumber: 3.0 Consensus size: 23
1778942 TATATATTTT
*
1778952 AATATATTATAATTTATGTTTAA
1 AATATATTATAATTTATGATTAA
*
1778975 AATATTTTAT-ATTTAT-ATTAA
1 AATATATTATAATTTATGATTAA
1778996 TTTTAATATATTAATAATTTAT-ATTA
1 ----AATATATT-ATAATTTATGATTA
1779022 TAAAATTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
21 4 0.11
22 6 0.16
23 9 0.24
25 7 0.18
26 2 0.05
27 10 0.26
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (23 bp):
AATATATTATAATTTATGATTAA
Found at i:1779019 original size:33 final size:30
Alignment explanation
Indices: 1778975--1779054 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 30
1778965 TTATGTTTAA
*
1778975 AATATTTTATATTTATATTAATTTTAATATATT
1 AATAATTTATATTTATATTAATTTTAA-A-A-T
*
1779008 AATAATTTATA-TTATA-AAATTTTAAAAT
1 AATAATTTATATTTATATTAATTTTAAAAT
1779036 ACAT-ATTTATATTT-TATTA
1 A-ATAATTTATATTTATATTA
1779055 TATCATATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
28 11 0.27
29 6 0.15
30 1 0.02
31 8 0.20
32 5 0.12
33 10 0.24
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (30 bp):
AATAATTTATATTTATATTAATTTTAAAAT
Found at i:1779042 original size:49 final size:50
Alignment explanation
Indices: 1778944--1779070 Score: 138
Period size: 49 Copynumber: 2.6 Consensus size: 50
1778934 TATTTTTTTA
* * * **
1778944 TATATTTTAATATATTATAATTTATGTTTAAAATATTTTATATTTATA-T
1 TATATTTTAATATATTATAATTTATATTTAAAATATTTAAAATACATATT
1778993 TA-ATTTTAATATATTAATAATTTATATTATAAAAT-TTTAAAATACATATT
1 TATATTTTAATATATT-ATAATTTATATT-TAAAATATTTAAAATACATATT
* *
1779043 TATATTTTATTATATCAT-ATTT-TATTTA
1 TATATTTTAATATATTATAATTTATATTTA
1779071 TATAATTATA
Statistics
Matches: 67, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
47 2 0.03
48 17 0.25
49 26 0.39
50 11 0.16
51 11 0.16
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.57
Consensus pattern (50 bp):
TATATTTTAATATATTATAATTTATATTTAAAATATTTAAAATACATATT
Found at i:1779051 original size:20 final size:20
Alignment explanation
Indices: 1779026--1779069 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1779016 ATATTATAAA
1779026 ATTTTAAAATA-CATATTTAT
1 ATTTTAAAATATCATATTT-T
**
1779046 ATTTTATTATATCATATTTT
1 ATTTTAAAATATCATATTTT
1779066 ATTT
1 ATTT
1779070 ATATAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTAAAATATCATATTTT
Found at i:1779064 original size:15 final size:16
Alignment explanation
Indices: 1779044--1779073 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1779034 ATACATATTT
1779044 ATATTTTA-TTATATC
1 ATATTTTATTTATATC
1779059 ATATTTTATTTATAT
1 ATATTTTATTTATAT
1779074 AATTATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
ATATTTTATTTATATC
Found at i:1781034 original size:2 final size:2
Alignment explanation
Indices: 1781027--1781053 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1781017 TTTCTTTATG
1781027 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1781054 TGCATTTTGG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1782368 original size:13 final size:13
Alignment explanation
Indices: 1782350--1782382 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1782340 CTTTAAAAAA
1782350 AATTATTAAAT-T
1 AATTATTAAATCT
1782362 AAGTTATTAAATCT
1 AA-TTATTAAATCT
1782376 AATTATT
1 AATTATT
1782383 GATAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 14 0.74
14 3 0.16
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (13 bp):
AATTATTAAATCT
Found at i:1789907 original size:2 final size:2
Alignment explanation
Indices: 1789894--1789930 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1789884 TTACTTCCTT
*
1789894 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1789931 CTTTAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1790644 original size:19 final size:21
Alignment explanation
Indices: 1790620--1790663 Score: 65
Period size: 19 Copynumber: 2.1 Consensus size: 21
1790610 CTACCATTTT
1790620 AAATATAAAT-AT-GATATAA
1 AAATATAAATAATAGATATAA
1790639 AAATATAAATAAATAGATATAA
1 AAATATAAAT-AATAGATATAA
1790661 AAA
1 AAA
1790664 AATTACACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.45
21 2 0.09
22 10 0.45
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (21 bp):
AAATATAAATAATAGATATAA
Found at i:1791065 original size:2 final size:2
Alignment explanation
Indices: 1791058--1791103 Score: 74
Period size: 2 Copynumber: 22.5 Consensus size: 2
1791048 CCTCTTTTCC
*
1791058 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT ACT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
1791101 AT A
1 AT A
1791104 ACATATAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1791940 original size:2 final size:2
Alignment explanation
Indices: 1791933--1791962 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1791923 GGGATGTAAA
1791933 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
1791963 CATCAAATTA
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:1792664 original size:167 final size:167
Alignment explanation
Indices: 1792383--1792715 Score: 567
Period size: 167 Copynumber: 2.0 Consensus size: 167
1792373 TACCCAATAT
*
1792383 GATTTAGTCAAGACTAAACTTGATTAAGTTTTGTTTAATTACTCTTAATCAGCAAACATCAATAT
1 GATTTAGTCAAGACTAAACTTGATTAAGTTTTGTTTAATTACTCTTAATCACCAAACATCAATAT
*
1792448 AATTTCACCTTAATCCTCCACTTAGCATGTGCTTAAAGCTTTCGCATCGACCATTGTAGTCTACC
66 AATTTCACCTTAAACCTCCACTTAGCATGTGCTTAAAGCTTTCGCATCGACCATTGTAGTCTACC
**
1792513 AAATTTGTTGCTCATATTTGGCTTCTTTTAACAGCAC
131 AAATTTGTTGCTCATATTTGGCTTCTCCTAACAGCAC
* * * *
1792550 GATTTAGTCAAGATTAAACTTGATTAAGTTTTGTTTAATTATTCTTAATCACCAGACATTAATAT
1 GATTTAGTCAAGACTAAACTTGATTAAGTTTTGTTTAATTACTCTTAATCACCAAACATCAATAT
* * *
1792615 AATTTCACCTTAAACCTTCACTTAGCATGTGGTTAAAGCTTTTGCATCGACCATTGTAGTCTACC
66 AATTTCACCTTAAACCTCCACTTAGCATGTGCTTAAAGCTTTCGCATCGACCATTGTAGTCTACC
1792680 AAATTTGTTGCTCATATTTGGCTTCTCCTAACAGCA
131 AAATTTGTTGCTCATATTTGGCTTCTCCTAACAGCA
1792716 TGAAAGATAC
Statistics
Matches: 155, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
167 155 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.38
Consensus pattern (167 bp):
GATTTAGTCAAGACTAAACTTGATTAAGTTTTGTTTAATTACTCTTAATCACCAAACATCAATAT
AATTTCACCTTAAACCTCCACTTAGCATGTGCTTAAAGCTTTCGCATCGACCATTGTAGTCTACC
AAATTTGTTGCTCATATTTGGCTTCTCCTAACAGCAC
Found at i:1797545 original size:32 final size:31
Alignment explanation
Indices: 1797457--1797546 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 31
1797447 AATTTAAAAT
* * * *
1797457 AATTTATTATTTAGAT-TAAAATTAATATAAA
1 AATTTA-TATTTAAATAAAAAAATAATATTAA
*
1797488 AATTTAT-TTT-AATAATTAAAA-AATATTAA
1 AATTTATATTTAAATAA-AAAAATAATATTAA
1797517 AATTTATAATTTAAATAAAAAAATAATATT
1 AATTTAT-ATTTAAATAAAAAAATAATATT
1797547 TTATTATTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
28 2 0.04
29 17 0.36
30 4 0.09
31 13 0.28
32 11 0.23
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (31 bp):
AATTTATATTTAAATAAAAAAATAATATTAA
Found at i:1797789 original size:45 final size:45
Alignment explanation
Indices: 1797740--1797825 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
1797730 AAAATAAAAA
* * * *
1797740 AATTTATATATTTATATTTAATTTT-TTTTAAAAATTATATTATAT
1 AATTTA-ATAATTAAATTAAATTTTAATTTAAAAATTATATTATAT
*
1797785 AATTTAATAATTAAATTAAATTTTAATTTAAAAATTTTATT
1 AATTTAATAATTAAATTAAATTTTAATTTAAAAATTATATT
1797826 TTATTATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 15 0.43
45 20 0.57
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (45 bp):
AATTTAATAATTAAATTAAATTTTAATTTAAAAATTATATTATAT
Found at i:1801220 original size:22 final size:20
Alignment explanation
Indices: 1801181--1801223 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
1801171 ATAATTCGTA
*
1801181 TATTTTTATAAAATTTATAT
1 TATTTTTATAAAAGTTATAT
1801201 TATTTTTATATAATAGTTATAT
1 TATTTTTATA-AA-AGTTATAT
1801223 T
1 T
1801224 TAATGTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 2 0.10
22 8 0.40
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TATTTTTATAAAAGTTATAT
Found at i:1807890 original size:51 final size:51
Alignment explanation
Indices: 1807849--1807962 Score: 192
Period size: 51 Copynumber: 2.2 Consensus size: 51
1807839 TCCGCCACCC
*
1807849 CCACCTCCACCTCCACCACCATTGCCTCCTGGTCACAGAGCTTCTCCTCCA
1 CCACCTCCACCACCACCACCATTGCCTCCTGGTCACAGAGCTTCTCCTCCA
** *
1807900 CCACCTCCACCACCACCACCATTGCCTCCTGGTCATGGAGCTTCTCCTCCT
1 CCACCTCCACCACCACCACCATTGCCTCCTGGTCACAGAGCTTCTCCTCCA
1807951 CCACCTCCACCA
1 CCACCTCCACCA
1807963 TTACCTCTTG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.18, C:0.52, G:0.10, T:0.21
Consensus pattern (51 bp):
CCACCTCCACCACCACCACCATTGCCTCCTGGTCACAGAGCTTCTCCTCCA
Found at i:1807898 original size:42 final size:42
Alignment explanation
Indices: 1807852--1808007 Score: 123
Period size: 51 Copynumber: 3.4 Consensus size: 42
1807842 GCCACCCCCA
*
1807852 CCTCCACCTCCACCACCATTGCCTCCTGGTCACAGAGCTTCT
1 CCTCCACCTCCACCACCATTGCCTCCTGGTCACGGAGCTTCT
*
1807894 CCTCCACCACCTCCACCACCACCACCATTGCCTCCTGGTCATGGAGCTTCT
1 CCT---CCACCT------CCACCACCATTGCCTCCTGGTCACGGAGCTTCT
* * * * * * *
1807945 CCTCCTCCACCTCCACCATTACCTCTTGGCCGCGGAGCTTCTCCT
1 CCTCCACCTCCACCACCATTGCCTCCTGGTCACGGAGC-T-T-CT
1807990 CCTCCACCTCCACCACCA
1 CCTCCACCTCCACCACCA
1808008 CCTCTTTTAC
Statistics
Matches: 89, Mismatches: 13, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
42 26 0.29
43 1 0.01
44 1 0.01
45 23 0.26
48 4 0.04
51 34 0.38
ACGTcount: A:0.16, C:0.51, G:0.11, T:0.22
Consensus pattern (42 bp):
CCTCCACCTCCACCACCATTGCCTCCTGGTCACGGAGCTTCT
Found at i:1808218 original size:39 final size:39
Alignment explanation
Indices: 1808148--1808250 Score: 158
Period size: 39 Copynumber: 2.7 Consensus size: 39
1808138 CTCCCCGACA
*
1808148 TGGAGCACCA-C-CC-CCACCACCTCCTCCACCTGTTCG
1 TGGAGCACCAGCACCACCCCCACCTCCTCCACCTGTTCG
**
1808184 TGGAGTGCCAGCACCACCCCCACCTCCTCCACCTGTTCG
1 TGGAGCACCAGCACCACCCCCACCTCCTCCACCTGTTCG
1808223 TGGAGCACCAGCACCACCCCCACCTCCT
1 TGGAGCACCAGCACCACCCCCACCTCCT
1808251 ATGTGTGGAG
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
36 8 0.14
37 1 0.02
38 2 0.03
39 48 0.81
ACGTcount: A:0.17, C:0.51, G:0.16, T:0.16
Consensus pattern (39 bp):
TGGAGCACCAGCACCACCCCCACCTCCTCCACCTGTTCG
Found at i:1810360 original size:25 final size:25
Alignment explanation
Indices: 1810307--1810360 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
1810297 GATAGATGAT
* * * *
1810307 TGCATTGCCATTGGCCTGTCATAAT
1 TGCATTGCCACTGGCCTGCCACAAA
*
1810332 TGCATTGCCACTGGCGTGCCACAAA
1 TGCATTGCCACTGGCCTGCCACAAA
1810357 TGCA
1 TGCA
1810361 CTTTCCTGCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (25 bp):
TGCATTGCCACTGGCCTGCCACAAA
Found at i:1815913 original size:2 final size:2
Alignment explanation
Indices: 1815902--1815942 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
1815892 TCAAAATTAT
*
1815902 TA TA -A TA TA TA TA TA TA TA TA TA TA T- TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1815942 T
1 T
1815943 TCAAGTGGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1815926 original size:21 final size:21
Alignment explanation
Indices: 1815902--1815942 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1815892 TCAAAATTAT
1815902 TATAATATATATATATATATA
1 TATAATATATATATATATATA
* *
1815923 TATATTATATATTTATATAT
1 TATAATATATATATATATAT
1815943 TCAAGTGGGT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATAATATATATATATATATA
Found at i:1816819 original size:15 final size:15
Alignment explanation
Indices: 1816799--1816835 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1816789 AGGCTGACTT
*
1816799 GGAGAAGAGGAAAGC
1 GGAGAAGAAGAAAGC
1816814 GGAGAAGAAGAAAGC
1 GGAGAAGAAGAAAGC
*
1816829 AGAGAAG
1 GGAGAAG
1816836 GAGGCTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.43, T:0.00
Consensus pattern (15 bp):
GGAGAAGAAGAAAGC
Found at i:1818621 original size:19 final size:20
Alignment explanation
Indices: 1818574--1818635 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 20
1818564 AAAAAATTAA
*
1818574 AAATAATACAAAACATGATA-
1 AAATAATA-TAAACATGATAT
*
1818594 AAATAATATCAACATGATAT
1 AAATAATATAAACATGATAT
*
1818614 AAAT-ATATAAATAT-ATAT
1 AAATAATATAAACATGATAT
1818632 AAAT
1 AAAT
1818636 TTATATAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 8 0.22
19 17 0.46
20 12 0.32
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.29
Consensus pattern (20 bp):
AAATAATATAAACATGATAT
Found at i:1818659 original size:18 final size:17
Alignment explanation
Indices: 1818610--1818659 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
1818600 TATCAACATG
*
1818610 ATATAAATATATAAATAT
1 ATATAAAT-TATTAATAT
1818628 ATATAAA-T-TT-ATAT
1 ATATAAATTATTAATAT
1818642 AGTATAAATTATTAATAT
1 A-TATAAATTATTAATAT
1818660 GTCAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
14 5 0.19
15 7 0.26
16 2 0.07
17 2 0.07
18 11 0.41
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
ATATAAATTATTAATAT
Found at i:1821786 original size:14 final size:14
Alignment explanation
Indices: 1821767--1821812 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 14
1821757 GGATAAGAAT
1821767 TTTATAAACTAAGA
1 TTTATAAACTAAGA
*
1821781 TTTATAACCTAAGA
1 TTTATAAACTAAGA
1821795 TCTTTATAAACTAAGA
1 --TTTATAAACTAAGA
1821811 TT
1 TT
1821813 ACTATGATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 15 0.54
16 13 0.46
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (14 bp):
TTTATAAACTAAGA
Found at i:1821802 original size:16 final size:15
Alignment explanation
Indices: 1821760--1821812 Score: 72
Period size: 16 Copynumber: 3.5 Consensus size: 15
1821750 GATATTTGGA
1821760 TAAGAATTTTATAAAC
1 TAAG-ATTTTATAAAC
*
1821776 TAAGA-TTTATAACC
1 TAAGATTTTATAAAC
1821790 TAAGATCTTTATAAAC
1 TAAGAT-TTTATAAAC
1821806 TAAGATT
1 TAAGATT
1821813 ACTATGATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
14 13 0.39
15 2 0.06
16 18 0.55
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (15 bp):
TAAGATTTTATAAAC
Found at i:1822021 original size:22 final size:20
Alignment explanation
Indices: 1821996--1822035 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1821986 ATTAGACAAA
1821996 TATAATCAATAATAAAAATATT
1 TATAAT-AA-AATAAAAATATT
1822018 TATAATAAAATAAAAATA
1 TATAATAAAATAAAAATA
1822036 ATAATTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
TATAATAAAATAAAAATATT
Found at i:1822958 original size:3 final size:3
Alignment explanation
Indices: 1822950--1822978 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1822940 CCATCCACAC
1822950 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1822979 TATTATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1822983 original size:3 final size:3
Alignment explanation
Indices: 1822977--1823014 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1822967 AATAATAATA
1822977 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1823015 GATAATGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1823599 original size:13 final size:14
Alignment explanation
Indices: 1823579--1823638 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 14
1823569 ATAATAATAA
1823579 ATAA-TAATATTTT
1 ATAATTAATATTTT
1823592 AT-ATTAATA-TTT
1 ATAATTAATATTTT
*
1823604 ATAATTAA-ATTTAA
1 ATAATTAATATTT-T
*
1823618 ATAA-AAATATTTT
1 ATAATTAATATTTT
1823631 -TAATTAAT
1 ATAATTAAT
1823639 TAAATGATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
12 10 0.27
13 19 0.51
14 8 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAATTAATATTTT
Found at i:1823946 original size:2 final size:2
Alignment explanation
Indices: 1823939--1823969 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1823929 AATAATAAAG
1823939 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1823970 TGCCTTCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1824052 original size:3 final size:3
Alignment explanation
Indices: 1824044--1824095 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
1824034 GTTACTGAAA
*
1824044 TAT TAT TAT TGT ATAT T-T TA- TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1824088 TAT TAT TA
1 TAT TAT TA
1824096 ATGGGATAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 4 0.09
3 38 0.86
4 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1824470 original size:2 final size:2
Alignment explanation
Indices: 1824458--1824492 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1824448 TTATAATCTC
*
1824458 AT AT AT CT 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 A
1824493 ATAAAGCAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1827945 original size:205 final size:203
Alignment explanation
Indices: 1827568--1827975 Score: 631
Period size: 205 Copynumber: 2.0 Consensus size: 203
1827558 ATTAGGAAAT
** * * *
1827568 TGCCTTTGAATAGCAGTGAAACTTGTGATGTGAGGAGTAAAATAAGGTCCAGTACTTGAACTAGC
1 TGCCTTTGAATAGCAGTGAAACTTGTGACATGAGCAGTAAAATAAGGTCCAGTACTTGAACCAAC
* *
1827633 AATAATGAATGCTTTGCTTAACTCAATTAACATAAGCAATCATACTGCAAAAGCCACACCTATTA
66 AATAACGAATGCTTTGCTTAACTCAATTAACATAAGCAATCAAACTGCAAAAGCCACACCTATTA
* * * *
1827698 GTGAATCAGAAAGTGAATCTGATGAAGATAAGTTTGGCATACATCTTACAGCCAGAAAATTCTTT
131 GTAAATCAGAAAGTGAACCTGACGAAGATAAATTTGGCATACATCTTACAGCCAGAAAATTCTTT
1827763 CTTAGCAA
196 CTTAGCAA
*
1827771 TGCCTTTGAATAGCAGTAGTAAACTTGTGACAT-ATGCAGTAAAATAAGGTCCAGTAGTTGAACC
1 TGCCTTTGAATAGCAGT-G-AAACTTGTGACATGA-GCAGTAAAATAAGGTCCAGTACTTGAACC
*
1827835 AACAATAACGAATGCTTTGCTTAACTCAATTAACATAAGCAATCAAACTGCAAAAGCCACGCCTA
63 AACAATAACGAATGCTTTGCTTAACTCAATTAACATAAGCAATCAAACTGCAAAAGCCACACCTA
*
1827900 TTAGTAAATCGGAAAGTGAACCTGACGAAGATAAATTCT-GCATACATCTTACAGCCAGAAAATT
128 TTAGTAAATCAGAAAGTGAACCTGACGAAGATAAATT-TGGCATACATCTTACAGCCAGAAAATT
*
1827964 CTTTCTTGGCAA
192 CTTTCTTAGCAA
1827976 CGCACGGTGC
Statistics
Matches: 186, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
203 17 0.09
204 2 0.01
205 166 0.89
206 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (203 bp):
TGCCTTTGAATAGCAGTGAAACTTGTGACATGAGCAGTAAAATAAGGTCCAGTACTTGAACCAAC
AATAACGAATGCTTTGCTTAACTCAATTAACATAAGCAATCAAACTGCAAAAGCCACACCTATTA
GTAAATCAGAAAGTGAACCTGACGAAGATAAATTTGGCATACATCTTACAGCCAGAAAATTCTTT
CTTAGCAA
Found at i:1830127 original size:12 final size:12
Alignment explanation
Indices: 1830087--1830121 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1830077 GTCCCACTTG
*
1830087 CACCAGCACCAA
1 CACCAACACCAA
1830099 CACCAACACCAA
1 CACCAACACCAA
1830111 CACCAACACCA
1 CACCAACACCA
1830122 GGACCAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.46, C:0.51, G:0.03, T:0.00
Consensus pattern (12 bp):
CACCAACACCAA
Found at i:1830127 original size:18 final size:18
Alignment explanation
Indices: 1830087--1830121 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1830077 GTCCCACTTG
*
1830087 CACCAGCACCAACACCAA
1 CACCAACACCAACACCAA
1830105 CACCAACACCAACACCA
1 CACCAACACCAACACCA
1830122 GGACCAGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.51, G:0.03, T:0.00
Consensus pattern (18 bp):
CACCAACACCAACACCAA
Found at i:1831525 original size:15 final size:15
Alignment explanation
Indices: 1831505--1831535 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1831495 TTGAATTTTA
*
1831505 TTTTTTAAATATAAT
1 TTTTTTAAAAATAAT
1831520 TTTTTTAAAAATAAT
1 TTTTTTAAAAATAAT
1831535 T
1 T
1831536 ATATAAATCA
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTTTAAAAATAAT
Found at i:1832649 original size:16 final size:17
Alignment explanation
Indices: 1832618--1832650 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1832608 GTAATTATAT
*
1832618 AAAAATTAATTTTTTAA
1 AAAAATTAATTATTTAA
1832635 AAAAATT-ATTATTTAA
1 AAAAATTAATTATTTAA
1832651 TATAGATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAAATTAATTATTTAA
Found at i:1833254 original size:2 final size:2
Alignment explanation
Indices: 1833247--1833272 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1833237 GACTTACCTT
1833247 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
1833273 AATAAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1835793 original size:2 final size:2
Alignment explanation
Indices: 1835788--1835817 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1835778 TTTAATTGTT
1835788 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
1835818 ACCAATCTAA
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):
TA
Found at i:1837387 original size:18 final size:18
Alignment explanation
Indices: 1837358--1837409 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
1837348 TTAATATATA
*
1837358 TATATATATATATTATTT
1 TATATATTTATATTATTT
*
1837376 TTTATATTTATA-TATTT
1 TATATATTTATATTATTT
1837393 TATATAATTTATATTAT
1 TATAT-ATTTATATTAT
1837410 ATGTAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 9 0.31
18 17 0.59
19 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATATATTTATATTATTT
Found at i:1837765 original size:2 final size:2
Alignment explanation
Indices: 1837758--1837810 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1837748 GAGAAAGATT
1837758 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1837800 TA TA TA TA TA T
1 TA TA TA TA TA T
1837811 CTCAAATCTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1837980 original size:20 final size:19
Alignment explanation
Indices: 1837952--1838039 Score: 63
Period size: 20 Copynumber: 4.4 Consensus size: 19
1837942 GTATTATGTT
*
1837952 ATATTTTATAATTATATTTA
1 ATATATTATAATT-TATTTA
1837972 ATATATTATATATTTATTTAA
1 ATATATTATA-ATTTATTT-A
* * *
1837993 ATTTTTTATAATTTAATTA
1 ATATATTATAATTTATTTA
*
1838012 TTTATATTAT-ATTATATTTTA
1 -ATATATTATAATT-TA-TTTA
1838033 AT-TATTA
1 ATATATTA
1838040 ATTTTATATT
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
19 9 0.17
20 30 0.56
21 15 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATATTATAATTTATTTA
Found at i:1838021 original size:5 final size:5
Alignment explanation
Indices: 1837943--1838053 Score: 53
Period size: 5 Copynumber: 23.6 Consensus size: 5
1837933 ATAATATTTG
* * *
1837943 TATTA TGTTA TATTT TA-TA -ATTA TATT- TAATA TATTA TA-TA T-TTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
* * *
1837988 T-TTA AATT- TTTTA TAATT- TAATTA T-TTA TATTA TATTA TATTT TAATTA
1 TATTA TATTA TATTA T-ATTA T-ATTA TATTA TATTA TATTA TATTA T-ATTA
* *
1838037 T-TAA TTTTA TATTA TAT
1 TATTA TATTA TATTA TAT
1838054 AGTAAATTTG
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
3 1 0.01
4 24 0.30
5 48 0.60
6 7 0.09
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (5 bp):
TATTA
Found at i:1838033 original size:41 final size:41
Alignment explanation
Indices: 1837955--1838035 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
1837945 TTATGTTATA
* *
1837955 TTTTATAATTATATTTAATATATTATATATTTATTTAAATT
1 TTTTATAATTATAATTAATATATTATATATATATTTAAATT
* *
1837996 TTTTATAATT-TAATTATTTATATTATAT-TATATTTTAATT
1 TTTTATAATTATAATTA-ATATATTATATATATATTTAAATT
1838036 ATTAATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 15 0.43
41 20 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (41 bp):
TTTTATAATTATAATTAATATATTATATATATATTTAAATT
Found at i:1839541 original size:19 final size:19
Alignment explanation
Indices: 1839470--1839574 Score: 65
Period size: 19 Copynumber: 5.5 Consensus size: 19
1839460 TTAAAAAAAT
*
1839470 ATATATAATATTAATATATA
1 ATATATAATATTAATTTA-A
* *
1839490 A-ATATAATATAAATTATTA
1 ATATATAATATTAATT-TAA
* *
1839509 ATATATTAAAATTTATTTAA
1 ATATA-TAATATTAATTTAA
*
1839529 ATATATAATATTTAA--AAA
1 ATATATAATA-TTAATTTAA
* *
1839547 ATATAATAACA-TAATATAA
1 ATAT-ATAATATTAATTTAA
1839566 ATATATAAT
1 ATATATAAT
1839575 TAAAATATAA
Statistics
Matches: 65, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
17 3 0.05
18 10 0.15
19 29 0.45
20 15 0.23
21 8 0.12
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATATAATATTAATTTAA
Found at i:1839591 original size:13 final size:13
Alignment explanation
Indices: 1839450--1839592 Score: 76
Period size: 13 Copynumber: 11.2 Consensus size: 13
1839440 GATCTAATAT
1839450 AAATATAATATTA
1 AAATATAATATTA
1839463 AAA-A-AATATATA
1 AAATATAATAT-TA
*
1839475 TAATATTAATA-TA
1 AAATA-TAATATTA
1839488 TAAATATAATA-TA
1 -AAATATAATATTA
*
1839501 AATTATTAATATATTA
1 AAATA-T-A-ATATTA
*
1839517 AAAT-TTAT-TTA
1 AAATATAATATTA
*
1839528 AATATATAATATTT
1 AA-ATATAATATTA
1839542 AAA-A-AATA-TA
1 AAATATAATATTA
*
1839552 ATAACATAATA-T-
1 A-AATATAATATTA
1839564 AAATAT-ATAATTA
1 AAATATAAT-ATTA
1839577 AAATATAATATTA
1 AAATATAATATTA
1839590 AAA
1 AAA
1839593 ACTTATAGTT
Statistics
Matches: 102, Mismatches: 9, Indels: 38
0.68 0.06 0.26
Matches are distributed among these distances:
10 4 0.04
11 21 0.21
12 17 0.17
13 36 0.35
14 12 0.12
15 7 0.07
16 5 0.05
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (13 bp):
AAATATAATATTA
Found at i:1840208 original size:20 final size:22
Alignment explanation
Indices: 1840183--1840222 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1840173 GTTTTTTGTC
1840183 GATTTAAA-TAA-ATTTAATTT
1 GATTTAAATTAATATTTAATTT
1840203 GATTTAAATTAATATTTAAT
1 GATTTAAATTAATATTTAAT
1840223 AATTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 3 0.17
22 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
GATTTAAATTAATATTTAATTT
Found at i:1840220 original size:32 final size:31
Alignment explanation
Indices: 1840184--1840244 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
1840174 TTTTTTGTCG
1840184 ATTTAAATAAATTT-AATTTGATTTAAATTAAT
1 ATTT-AAT-AATTTAAATTTGATTTAAATTAAT
*
1840216 ATTTAATAATTTAAAATTTTATTTAAATT
1 ATTTAATAATTT-AAATTTGATTTAAATT
1840245 TAATTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 5 0.19
31 3 0.12
32 18 0.69
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (31 bp):
ATTTAATAATTTAAATTTGATTTAAATTAAT
Found at i:1840288 original size:47 final size:48
Alignment explanation
Indices: 1840191--1840288 Score: 112
Period size: 47 Copynumber: 2.1 Consensus size: 48
1840181 TCGATTTAAA
* * * *
1840191 TAAATTTAATTTGATTTAAATTAATATTTAATAATTTAAAATTTTATT
1 TAAATTTAATTTGATATAAAATAATAATTAATAATATAAAATTTTATT
*
1840239 TAAATTTAA-TT-ATATAAAATATATAATTATTAATATAAAATTATT-TT
1 TAAATTTAATTTGATATAAAATA-ATAATTAATAATATAAAATT-TTATT
1840286 TAA
1 TAA
1840289 TTTTTAATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
46 8 0.19
47 24 0.56
48 11 0.26
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (48 bp):
TAAATTTAATTTGATATAAAATAATAATTAATAATATAAAATTTTATT
Found at i:1840311 original size:13 final size:13
Alignment explanation
Indices: 1840293--1840323 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1840283 TTTTAATTTT
*
1840293 TAATAATTATAAA
1 TAATAAATATAAA
1840306 TAATAAATATAAA
1 TAATAAATATAAA
1840319 TAATA
1 TAATA
1840324 TAAATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TAATAAATATAAA
Found at i:1840334 original size:14 final size:15
Alignment explanation
Indices: 1840295--1840335 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
1840285 TTAATTTTTA
*
1840295 ATAATTATAAAT-A-
1 ATAAATATAAATAAT
1840308 ATAAATATAAATAAT
1 ATAAATATAAATAAT
1840323 ATAAAT-TAAATAA
1 ATAAATATAAATAA
1840336 ACAAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 11 0.44
14 8 0.32
15 6 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAAATATAAATAAT
Found at i:1847588 original size:46 final size:46
Alignment explanation
Indices: 1847521--1847615 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
1847511 GATATAAGTA
1847521 GAAGGATATGACCCTCCAAAAACATAGAAAAACTTAAAAAAAATTT
1 GAAGGATATGACCCTCCAAAAACATAGAAAAACTTAAAAAAAATTT
*
1847567 GAAGGATATGACCCTCCAAAAACATAGAAGAACTTAAAAAAAATTT
1 GAAGGATATGACCCTCCAAAAACATAGAAAAACTTAAAAAAAATTT
1847613 GAA
1 GAA
1847616 CATATTCGTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.54, C:0.15, G:0.13, T:0.19
Consensus pattern (46 bp):
GAAGGATATGACCCTCCAAAAACATAGAAAAACTTAAAAAAAATTT
Found at i:1849228 original size:14 final size:14
Alignment explanation
Indices: 1849209--1849250 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
1849199 TAATTTGTTA
*
1849209 AATTAATTAAATTT
1 AATTAATTTAATTT
*
1849223 AATTAATTTTATTT
1 AATTAATTTAATTT
*
1849237 AATTTATTTAATTT
1 AATTAATTTAATTT
1849251 TAAAATAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
AATTAATTTAATTT
Found at i:1849758 original size:19 final size:19
Alignment explanation
Indices: 1849731--1849776 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1849721 TAAAATTTTT
1849731 ATAAAATAT-TTATATAATA
1 ATAAAATATATTATA-AATA
* *
1849750 ATTAAATATATTTTAAATA
1 ATAAAATATATTATAAATA
1849769 ATAAAATA
1 ATAAAATA
1849777 AATTTTTGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAAAATATATTATAAATA
Found at i:1849769 original size:22 final size:20
Alignment explanation
Indices: 1849732--1849772 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
1849722 AAAATTTTTA
*
1849732 TAAAATATTTATATAATAAT
1 TAAAATATTTAAATAATAAT
1849752 TAAATATATTTTAAATAATAA
1 TAAA-ATA-TTTAAATAATAA
1849773 AATAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 3 0.17
22 11 0.61
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAAATATTTAAATAATAAT
Found at i:1849781 original size:19 final size:19
Alignment explanation
Indices: 1849746--1849782 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1849736 ATATTTATAT
* *
1849746 AATAATTAAATATATTTTA
1 AATAATAAAATAAATTTTA
1849765 AATAATAAAATAAATTTT
1 AATAATAAAATAAATTTT
1849783 TGGGTCGAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATAATAAAATAAATTTTA
Found at i:1850443 original size:18 final size:18
Alignment explanation
Indices: 1850401--1850452 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
1850391 ATATCACGAT
1850401 AAAAT-TAAATAAA-TATA
1 AAAATATAAA-AAATTATA
*
1850418 AATCATATAAAAAATTATA
1 AA-AATATAAAAAATTATA
*
1850437 AAAATATATAAAATTA
1 AAAATATAAAAAATTA
1850453 ATTAATTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 2 0.07
18 17 0.59
19 10 0.34
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATATAAAAAATTATA
Found at i:1850594 original size:19 final size:18
Alignment explanation
Indices: 1850570--1850607 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
1850560 AGATTTGATA
1850570 ATTTATATATTTATATTAT
1 ATTTATATATTT-TATTAT
1850589 ATTTATATATTTTATTAT
1 ATTTATATATTTTATTAT
1850607 A
1 A
1850608 AAATAATCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTATATATTTTATTAT
Found at i:1854067 original size:2 final size:2
Alignment explanation
Indices: 1854055--1854127 Score: 83
Period size: 2 Copynumber: 36.5 Consensus size: 2
1854045 TGTTTGCCTT
* * * * *
1854055 TA TA TA CA TA TA TA TA TA TA TT TA TA TT TA TA TA TG TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1854097 TA TA TA TA TA TA TA TA TA TT TA TA GA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1854128 TAATATTTGT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1854195 original size:21 final size:20
Alignment explanation
Indices: 1854169--1854210 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1854159 TATTTTATTT
1854169 TATTTTAAAAATATAATTAAA
1 TATTTTAAAAATA-AATTAAA
* *
1854190 TATTTTATAAATAATTTAAA
1 TATTTTAAAAATAAATTAAA
1854210 T
1 T
1854211 TAATAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATTTTAAAAATAAATTAAA
Found at i:1854788 original size:14 final size:14
Alignment explanation
Indices: 1854769--1854807 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
1854759 CTTTAAAATT
1854769 TTTTAAAAATATAA
1 TTTTAAAAATATAA
1854783 TTTTAAAAA-ATAA
1 TTTTAAAAATATAA
1854796 TTATTAAAAATA
1 TT-TTAAAAATA
1854808 ATTTTTCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 16 0.70
15 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTTAAAAATATAA
Found at i:1854795 original size:13 final size:13
Alignment explanation
Indices: 1854769--1854812 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
1854759 CTTTAAAATT
1854769 TTTTAAAAATATAA
1 TTTTAAAAA-ATAA
1854783 TTTTAAAAAATAA
1 TTTTAAAAAATAA
1854796 TTATT-AAAAATAA
1 TT-TTAAAAAATAA
1854809 TTTT
1 TTTT
1854813 TCATCATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.07
13 16 0.55
14 11 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TTTTAAAAAATAA
Found at i:1855179 original size:23 final size:24
Alignment explanation
Indices: 1855133--1855187 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
1855123 TGACTCAAAT
1855133 TATTATTTAATAATTAATAAAAAA
1 TATTATTTAATAATTAATAAAAAA
* *
1855157 -ATTATTTAA-ATTTAATTATAAAA
1 TATTATTTAATAATTAA-TAAAAAA
1855180 TATT-TTTA
1 TATTATTTA
1855188 TTTTTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.19
23 19 0.70
24 3 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TATTATTTAATAATTAATAAAAAA
Found at i:1855234 original size:19 final size:20
Alignment explanation
Indices: 1855202--1855241 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1855192 TTATTATTTA
*
1855202 TAAATAATAAATTTTAAATT
1 TAAATAATAAATTTAAAATT
1855222 TAAATAA-AAATTTAAAATT
1 TAAATAATAAATTTAAAATT
1855241 T
1 T
1855242 TTTAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAATAATAAATTTAAAATT
Found at i:1855319 original size:13 final size:14
Alignment explanation
Indices: 1855291--1855321 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1855281 CCTTCATGGA
1855291 TCTTTGGGGCAGAG
1 TCTTTGGGGCAGAG
1855305 TCTTTGGGG-AGAG
1 TCTTTGGGGCAGAG
1855318 TCTT
1 TCTT
1855322 ATTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.39, T:0.35
Consensus pattern (14 bp):
TCTTTGGGGCAGAG
Found at i:1855515 original size:17 final size:16
Alignment explanation
Indices: 1855480--1855546 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 16
1855470 TTTATTATAA
*
1855480 TTATATT-TAAAATATT
1 TTATATTATATAA-ATT
1855496 TTATATTAATATAAATT
1 TTATATT-ATATAAATT
*
1855513 TTA-A-TATATTAATAAT
1 TTATATTATA-TAA-ATT
1855529 TTATATTATATAAATT
1 TTATATTATATAAATT
1855545 TT
1 TT
1855547 TAAAAATTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 3 0.07
15 4 0.10
16 17 0.40
17 10 0.24
18 8 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATATTATATAAATT
Found at i:1855567 original size:22 final size:24
Alignment explanation
Indices: 1855521--1855571 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
1855511 TTTTAATATA
*
1855521 TTAATAATTTATATTATATAAATTT
1 TTAAAAATTTATATTATAT-AATTT
*
1855546 TTAAAAATTTAT-TTATATATTTT
1 TTAAAAATTTATATTATATAATTT
1855569 TTA
1 TTA
1855572 TTATATTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.29
24 6 0.25
25 11 0.46
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTAAAAATTTATATTATATAATTT
Found at i:1859261 original size:17 final size:17
Alignment explanation
Indices: 1859235--1859282 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1859225 ATTCAAATTC
1859235 ATTT-AATTTATTAAAA
1 ATTTAAATTTATTAAAA
* **
1859251 ATTTAAATTTATTTATT
1 ATTTAAATTTATTAAAA
1859268 ATTTAAATATTATTA
1 ATTTAAAT-TTATTA
1859283 TTTAAATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 4 0.15
17 17 0.65
18 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTAAATTTATTAAAA
Found at i:1859282 original size:14 final size:14
Alignment explanation
Indices: 1859263--1859304 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1859253 TTAAATTTAT
1859263 TTATTATTTAAATA
1 TTATTATTTAAATA
*
1859277 TTATTATTTAAATT
1 TTATTATTTAAATA
1859291 TATATTCATTTAAA
1 T-TATT-ATTTAAA
1859305 AAATAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 14 0.56
15 4 0.16
16 7 0.28
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATTATTTAAATA
Found at i:1859283 original size:17 final size:17
Alignment explanation
Indices: 1859251--1859293 Score: 65
Period size: 14 Copynumber: 2.7 Consensus size: 17
1859241 TTTATTAAAA
1859251 ATTTAAATTTATTTATT
1 ATTTAAATTTATTTATT
1859268 ATTTAAA--TA-TTATT
1 ATTTAAATTTATTTATT
1859282 ATTTAAATTTAT
1 ATTTAAATTTAT
1859294 ATTCATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 12 0.52
15 2 0.09
16 2 0.09
17 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTAAATTTATTTATT
Found at i:1859548 original size:20 final size:20
Alignment explanation
Indices: 1859499--1859548 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1859489 AAAATTTATA
* *
1859499 TTTAACTATATTATTTAAAT
1 TTTAAATATACTATTTAAAT
**
1859519 AATAAATATACTATTTAAAT
1 TTTAAATATACTATTTAAAT
*
1859539 TTTAATTATA
1 TTTAAATATA
1859549 TTAAAAAATA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAAATATACTATTTAAAT
Found at i:1863354 original size:22 final size:22
Alignment explanation
Indices: 1863324--1863366 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1863314 AAAAATATTT
*
1863324 ATATTTAAAT-TTAATTATAAAA
1 ATATATAAATATTAA-TATAAAA
1863346 ATATATAAATATTAATATAAA
1 ATATATAAATATTAATATAAA
1863367 TTTTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATATATAAATATTAATATAAAA
Found at i:1864435 original size:53 final size:54
Alignment explanation
Indices: 1864342--1864451 Score: 125
Period size: 53 Copynumber: 2.1 Consensus size: 54
1864332 AAATAACTTA
* *
1864342 AACCCGATTTAACCCAAATGTTAAAACCAATTTACTCGAATCCAAAATGATCCG
1 AACCCGATTTAACCCAAATGTTAAAACCAATTGACTCGAATCCAAAATGACCCG
* * * * * *
1864396 AACCCGA-TTAACCCGAGTGTTAAACCCGATTGA-TCCGAATTCGAAATGACCCG
1 AACCCGATTTAACCCAAATGTTAAAACCAATTGACT-CGAATCCAAAATGACCCG
1864449 AAC
1 AAC
1864452 TCGAAATGAC
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
52 1 0.02
53 39 0.83
54 7 0.15
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.22
Consensus pattern (54 bp):
AACCCGATTTAACCCAAATGTTAAAACCAATTGACTCGAATCCAAAATGACCCG
Found at i:1864455 original size:16 final size:16
Alignment explanation
Indices: 1864430--1864505 Score: 127
Period size: 16 Copynumber: 4.8 Consensus size: 16
1864420 CCCGATTGAT
*
1864430 CCGAATTCGAAATGAC
1 CCGAACTCGAAATGAC
1864446 CCGAACTCGAAATGAC
1 CCGAACTCGAAATGAC
1864462 CCGAACTCGAAATGAC
1 CCGAACTCGAAATGAC
1864478 CCGAAC-CTGAAATGAC
1 CCGAACTC-GAAATGAC
1864494 CCGAACTCGAAA
1 CCGAACTCGAAA
1864506 ATTTTAAAAC
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
15 1 0.02
16 55 0.96
17 1 0.02
ACGTcount: A:0.38, C:0.30, G:0.18, T:0.13
Consensus pattern (16 bp):
CCGAACTCGAAATGAC
Found at i:1864571 original size:16 final size:16
Alignment explanation
Indices: 1864550--1864580 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1864540 ACTCAACCCG
1864550 AAACTAACCCAATCCA
1 AAACTAACCCAATCCA
1864566 AAACTAACCCAATCC
1 AAACTAACCCAATCC
1864581 GCCCAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.39, G:0.00, T:0.13
Consensus pattern (16 bp):
AAACTAACCCAATCCA
Found at i:1864805 original size:34 final size:36
Alignment explanation
Indices: 1864739--1864811 Score: 105
Period size: 34 Copynumber: 2.1 Consensus size: 36
1864729 AGCAAGGAAT
*
1864739 CTAGCTTTGATTACCAAGTTACAGAAAACTCGAAAC
1 CTAGATTTGATTACCAAGTTACAGAAAACTCGAAAC
* *
1864775 CTAGATTTGA-TATCAAGTTACA-AAAACTCGAACC
1 CTAGATTTGATTACCAAGTTACAGAAAACTCGAAAC
1864809 CTA
1 CTA
1864812 CCTCAAAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 14 0.41
35 11 0.32
36 9 0.26
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (36 bp):
CTAGATTTGATTACCAAGTTACAGAAAACTCGAAAC
Found at i:1868493 original size:15 final size:15
Alignment explanation
Indices: 1868469--1868499 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1868459 CAAGAGCAGC
1868469 TAAAAAAAGCTAACA
1 TAAAAAAAGCTAACA
*
1868484 TAAAAGAAGCTAACA
1 TAAAAAAAGCTAACA
1868499 T
1 T
1868500 GTTTGCTATC
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:0.61, C:0.13, G:0.10, T:0.16
Consensus pattern (15 bp):
TAAAAAAAGCTAACA
Found at i:1870803 original size:21 final size:20
Alignment explanation
Indices: 1870779--1870821 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1870769 ACTCGAATTT
*
1870779 TTAAAAAAATTTTATTTAAAA
1 TTAAAAAAA-TTTAATTAAAA
**
1870800 TTAATGAAATTTAATTAAAA
1 TTAAAAAAATTTAATTAAAA
1870820 TT
1 TT
1870822 TTATATTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TTAAAAAAATTTAATTAAAA
Found at i:1870875 original size:21 final size:21
Alignment explanation
Indices: 1870851--1870890 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1870841 ATTAATAAAT
1870851 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
1870872 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
1870891 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:1871414 original size:17 final size:16
Alignment explanation
Indices: 1871392--1871423 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1871382 TAAAAACTAT
1871392 TTTTTAAATTTATTTTC
1 TTTTTAAATTT-TTTTC
1871409 TTTTTAAATTTTTTT
1 TTTTTAAATTTTTTT
1871424 AAAAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTAAATTTTTTTC
Found at i:1871702 original size:16 final size:16
Alignment explanation
Indices: 1871657--1871702 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
1871647 ACATACATCA
*
1871657 TTAAATTATTTATTTC
1 TTAAATTATTAATTTC
*
1871673 AT-AA-TATATAATTTC
1 TTAAATTAT-TAATTTC
1871688 TTAAATTATTAATTT
1 TTAAATTATTAATTT
1871703 TTTCACTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
14 3 0.12
15 9 0.38
16 9 0.38
17 3 0.12
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAAATTATTAATTTC
Found at i:1871782 original size:34 final size:34
Alignment explanation
Indices: 1871712--1871930 Score: 289
Period size: 34 Copynumber: 6.5 Consensus size: 34
1871702 TTTTCACTCA
* * *
1871712 CATTGTTGATTAAAT-GGTGATTTAGTAGTTTAC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
* * * *
1871745 CATTGTTGATTAAATGGGTGATTTGGTGGTTTGC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
*
1871779 CATTGTTGACTAAAT-GGAGATTTGGTAGCTTAC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
* *
1871812 CATTGTTGATTAAATGAGAAATTTGGTAGCTTAC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
* *
1871846 CATTGTTGATTAAATGGGTGATTTGGTGGCTTAC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
* * *
1871880 CATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
1871914 CATTGTTGATTAAATGG
1 CATTGTTGATTAAATGG
1871931 TGGTTTTTTA
Statistics
Matches: 163, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
33 43 0.26
34 120 0.74
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
Found at i:1871783 original size:67 final size:66
Alignment explanation
Indices: 1871712--1871932 Score: 307
Period size: 67 Copynumber: 3.3 Consensus size: 66
1871702 TTTTCACTCA
* * *
1871712 CATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTT
1 CATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTGG-TT
1871777 GC
65 GC
* * * * *
1871779 CATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGAGAAATTTGGTAGCTT
1 CATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGT-GGTT
*
1871844 AC
65 GC
* *
1871846 CATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGT
1 CATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGT-GGT
1871911 TGC
64 TGC
1871914 CATTGTTGATTAAATGGTG
1 CATTGTTGATTAAATGGTG
1871933 GTTTTTTACC
Statistics
Matches: 135, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
67 74 0.55
68 61 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (66 bp):
CATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTGGTTG
C
Found at i:1871863 original size:101 final size:101
Alignment explanation
Indices: 1871712--1871930 Score: 350
Period size: 101 Copynumber: 2.2 Consensus size: 101
1871702 TTTTCACTCA
** * *
1871712 CATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTT
1 CATTGTTGATTAAATGGAAATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
*
1871777 GCCATTGTTGACTAAAT-GGAGATTTGGTAGCTTAC
66 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTAC
*
1871812 CATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCT
1 CATTGTTGATTAAATG-GAAATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCT
* *
1871877 TACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
65 TACCATTGTTGACTAAATGGGAGATTTGGTAGCTTAC
1871914 CATTGTTGATTAAATGG
1 CATTGTTGATTAAATGG
1871931 TGGTTTTTTA
Statistics
Matches: 109, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
100 16 0.15
101 61 0.56
102 32 0.29
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.40
Consensus pattern (101 bp):
CATTGTTGATTAAATGGAAATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTAC
Found at i:1872293 original size:19 final size:19
Alignment explanation
Indices: 1872237--1872299 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1872227 TGGTTGTCGA
**
1872237 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
1872256 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
1872275 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
1872294 GTTACT
1 GGTACT
1872300 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:1876434 original size:34 final size:34
Alignment explanation
Indices: 1876365--1876582 Score: 296
Period size: 34 Copynumber: 6.5 Consensus size: 34
1876355 AAGTGGGAGA
* * *
1876365 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
1876398 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
1876432 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
1876465 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
1876499 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1876533 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1876567 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1876583 TGGTTTTTTA
Statistics
Matches: 164, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 42 0.26
34 122 0.74
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1876548 original size:68 final size:67
Alignment explanation
Indices: 1876365--1876584 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
1876355 AAGTGGGAGA
* * * * *
1876365 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
1876430 CC
66 CC
* * * *
1876432 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
1876497 CC
66 CC
* * *
1876499 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
1876564 GCC
65 GCC
1876567 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
1876585 GTTTTTTACC
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:1877001 original size:18 final size:18
Alignment explanation
Indices: 1876978--1877013 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1876968 TTAAAAAATC
**
1876978 ATATTAAATTTATTATAT
1 ATATTAAAAATATTATAT
1876996 ATATTAAAAATATTATAT
1 ATATTAAAAATATTATAT
1877014 TGATGTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATTAAAAATATTATAT
Found at i:1877811 original size:18 final size:18
Alignment explanation
Indices: 1877756--1877826 Score: 58
Period size: 18 Copynumber: 4.1 Consensus size: 18
1877746 ATTATAAATA
* *
1877756 AATTTATCATTATATTTT
1 AATTTATTATTAAATTTT
* **
1877774 ATTTTATT-TT-AATTAA
1 AATTTATTATTAAATTTT
1877790 AATTTATTATTAAATTTT
1 AATTTATTATTAAATTTT
*
1877808 AATTT-TTAATTAAAATTT
1 AATTTATT-ATTAAATTTT
1877826 A
1 A
1877827 TTACTAAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
16 10 0.24
17 6 0.15
18 25 0.61
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (18 bp):
AATTTATTATTAAATTTT
Found at i:1877815 original size:31 final size:31
Alignment explanation
Indices: 1877780--1877839 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1877770 TTTTATTTTA
* *
1877780 TTTTAATTAAAATTTATTATTAAATTTTAAT
1 TTTTAATTAAAATTTATTACTAAAATTTAAT
1877811 TTTTAATTAAAATTTATTACTAAAATTTA
1 TTTTAATTAAAATTTATTACTAAAATTTA
1877840 CTCTTAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (31 bp):
TTTTAATTAAAATTTATTACTAAAATTTAAT
Found at i:1878016 original size:22 final size:22
Alignment explanation
Indices: 1877991--1878033 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1877981 ATTATTAAAA
1877991 ATATTTTTATAA-TAATATTTAT
1 ATATTTTTATAATTAA-ATTTAT
1878013 ATATTTTTATAATTAAATTTA
1 ATATTTTTATAATTAAATTTA
1878034 ATTAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATTTTTATAATTAAATTTAT
Found at i:1878375 original size:22 final size:22
Alignment explanation
Indices: 1878314--1878380 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
1878304 TTTTGAATCG
* *
1878314 ATTTAATATTTTTTTCATATTA
1 ATTTAATTTTTTTTTAATATTA
*
1878336 ATTAAATATTATTTTTTAATA-TA
1 ATTTAAT-TT-TTTTTTAATATTA
*
1878359 TATTTAATTTTTTTTTAGTATT
1 -ATTTAATTTTTTTTTAATATT
1878381 TGATGATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
22 15 0.42
23 6 0.17
24 15 0.42
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (22 bp):
ATTTAATTTTTTTTTAATATTA
Found at i:1878609 original size:20 final size:22
Alignment explanation
Indices: 1878584--1878640 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 22
1878574 AAATATGATG
1878584 ATTAGATTAAATAAAT-AT-AA
1 ATTAGATTAAATAAATCATAAA
1878604 ATTAGA-TAAA-AAATCATAAA
1 ATTAGATTAAATAAATCATAAA
*
1878624 ATTATATTAAATTAAAT
1 ATTAGATTAAA-TAAAT
1878641 TAATTTATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 4 0.13
19 6 0.19
20 13 0.42
21 4 0.13
23 4 0.13
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (22 bp):
ATTAGATTAAATAAATCATAAA
Found at i:1878794 original size:12 final size:13
Alignment explanation
Indices: 1878779--1878808 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1878769 AACAAAAGAC
1878779 TAAAAAAAAAA-T
1 TAAAAAAAAAATT
1878791 TAAAAAAAAAATT
1 TAAAAAAAAAATT
1878804 TAAAA
1 TAAAA
1878809 TAAGGTGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAAAAAAAAATT
Found at i:1879143 original size:22 final size:22
Alignment explanation
Indices: 1879118--1879174 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
1879108 TAGACTTGAG
**
1879118 TTTAAATTTATATGAGTTTTTA
1 TTTAAATTTATATGAGTTTAAA
* *
1879140 TTTAGATTTAAATGAGTTTAAA
1 TTTAAATTTATATGAGTTTAAA
1879162 TTTAAATTTATAT
1 TTTAAATTTATAT
1879175 TTTATTAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (22 bp):
TTTAAATTTATATGAGTTTAAA
Found at i:1879457 original size:2 final size:2
Alignment explanation
Indices: 1879452--1879491 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1879442 TACATTAATA
1879452 AT AT AT 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 AT AT AT
1879492 TTAATGTAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1879718 original size:11 final size:11
Alignment explanation
Indices: 1879688--1879726 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 11
1879678 AATGACTTTT
1879688 TTTTTAATTTA
1 TTTTTAATTTA
1879699 TAATTTTAATTTA
1 T--TTTTAATTTA
1879712 TTTTTAATTT-
1 TTTTTAATTTA
1879722 TTTTT
1 TTTTT
1879727 CAAATTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 5 0.19
11 10 0.38
13 11 0.42
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTAATTTA
Found at i:1880249 original size:21 final size:23
Alignment explanation
Indices: 1880219--1880267 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
1880209 TTTAATTTTT
1880219 ATTTATTAATTTTTAAAAATT-A
1 ATTTATTAATTTTTAAAAATTAA
* *
1880241 ATTTA-TAATTTTTTATAATTAA
1 ATTTATTAATTTTTAAAAATTAA
1880263 ATTTA
1 ATTTA
1880268 AAATAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATTTATTAATTTTTAAAAATTAA
Found at i:1880343 original size:7 final size:7
Alignment explanation
Indices: 1880309--1880352 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
1880299 TTATGTTTAA
1880309 AAATTTT
1 AAATTTT
*
1880316 AAATATT
1 AAATTTT
1880323 AAATATTT
1 AAAT-TTT
1880331 ATAATTTT
1 A-AATTTT
1880339 AAATTTT
1 AAATTTT
*
1880346 ATATTTT
1 AAATTTT
1880353 CATATAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
7 22 0.69
8 7 0.22
9 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AAATTTT
Found at i:1880819 original size:15 final size:16
Alignment explanation
Indices: 1880797--1880857 Score: 67
Period size: 15 Copynumber: 3.9 Consensus size: 16
1880787 AAAATAAAAA
1880797 TTATAAATATTAATAT
1 TTATAAATATTAATAT
1880813 TTA-AAAT-TTAA-AT
1 TTATAAATATTAATAT
1880826 TTATTAAATATTAATTAT
1 TTA-TAAATATTAA-TAT
1880844 TTATATAA-ATTAAT
1 TTATA-AATATTAAT
1880858 TAAATTAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 5 0.13
14 4 0.10
15 8 0.21
16 8 0.21
17 7 0.18
18 7 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATAAATATTAATAT
Found at i:1884379 original size:16 final size:16
Alignment explanation
Indices: 1884358--1884388 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1884348 AATTAGAGAA
1884358 AAAAATTCACAATTAT
1 AAAAATTCACAATTAT
*
1884374 AAAAATTCACTATTA
1 AAAAATTCACAATTA
1884389 GATATTTCAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAATTCACAATTAT
Found at i:1884732 original size:2 final size:2
Alignment explanation
Indices: 1884725--1884758 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1884715 TGATTTGATA
1884725 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
1884759 GATCAGATGA
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:1885284 original size:34 final size:35
Alignment explanation
Indices: 1885246--1885314 Score: 81
Period size: 34 Copynumber: 2.0 Consensus size: 35
1885236 TAAATCTATC
*
1885246 TTATTCAAATTATT-ATT-TAACAATA-ATAAATATT
1 TTATT-AAATT-TTAATTATAAAAATATATAAATATT
*
1885280 TTATTTAATTTTAATTATAAAAATATATAAATATT
1 TTATTAAATTTTAATTATAAAAATATATAAATATT
1885315 AATATAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
32 2 0.07
33 7 0.23
34 12 0.40
35 9 0.30
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (35 bp):
TTATTAAATTTTAATTATAAAAATATATAAATATT
Found at i:1889016 original size:3 final size:3
Alignment explanation
Indices: 1889008--1889038 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1888998 CAAAACTAAA
1889008 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1889039 TTTCAGATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:1889706 original size:19 final size:19
Alignment explanation
Indices: 1889677--1889726 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
1889667 AATTTTAAAA
1889677 AATTTA-ATATATTTA-AT
1 AATTTATATATATTTATAT
1889694 AATTTATATTATATTTATAT
1 AATTTATA-TATATTTATAT
*
1889714 GATTTATATATAT
1 AATTTATATATAT
1889727 CAAGGTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 6 0.21
18 1 0.03
19 13 0.45
20 9 0.31
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
AATTTATATATATTTATAT
Found at i:1891056 original size:14 final size:14
Alignment explanation
Indices: 1891034--1891075 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1891024 TAAAGATTAA
1891034 ATTTT-AAAAATAT
1 ATTTTAAAAAATAT
*
1891047 ATTTTAAAAAATAA
1 ATTTTAAAAAATAT
*
1891061 ATTATAAAAAA-AT
1 ATTTTAAAAAATAT
1891074 AT
1 AT
1891076 AGTAGAGGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATTTTAAAAAATAT
Found at i:1891898 original size:2 final size:2
Alignment explanation
Indices: 1891891--1891921 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1891881 ATTTTGCTCC
1891891 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1891922 GCTTGTTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1892580 original size:2 final size:2
Alignment explanation
Indices: 1892575--1892619 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1892565 AGGAGAGAAA
1892575 AT AT AT AT 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 AT AT AT AT
1892617 AT A
1 AT A
1892620 AGCATTTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1893183 original size:2 final size:2
Alignment explanation
Indices: 1893176--1893200 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1893166 CATCTGTTGC
1893176 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1893201 GTATGTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1894095 original size:21 final size:21
Alignment explanation
Indices: 1894070--1894111 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1894060 TTATCATTTA
*
1894070 ATAAATAAAAATAAATATAAT
1 ATAAACAAAAATAAATATAAT
* *
1894091 ATAAACATATATAAATATAAT
1 ATAAACAAAAATAAATATAAT
1894112 TAATGTAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAAACAAAAATAAATATAAT
Found at i:1894144 original size:6 final size:6
Alignment explanation
Indices: 1894120--1894202 Score: 60
Period size: 6 Copynumber: 13.0 Consensus size: 6
1894110 ATTAATGTAA
* * * *
1894120 TATATT TAATATAT TATATT TATATT TAAAAT TATA-A TAAATT TAATTATT
1 TATATT T-ATAT-T TATATT TATATT TATATT TATATT TATATT T-A-TATT
*
1894171 TATATT AATAATAT TATATT TATATT TATATT
1 TATATT TAT-AT-T TATATT TATATT TATATT
1894203 ATTAATTTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 14
0.73 0.11 0.17
Matches are distributed among these distances:
5 3 0.05
6 35 0.57
7 14 0.23
8 9 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (6 bp):
TATATT
Found at i:1894212 original size:20 final size:20
Alignment explanation
Indices: 1894167--1894210 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1894157 TAAATTTAAT
1894167 TATTTATATTAATAATATTA
1 TATTTATATTAATAATATTA
* *
1894187 TATTTATATTTATATTATTA
1 TATTTATATTAATAATATTA
1894207 -ATTT
1 TATTT
1894211 TAAAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTTATATTAATAATATTA
Found at i:1896366 original size:26 final size:25
Alignment explanation
Indices: 1896337--1896386 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
1896327 CATTAATGGA
1896337 TTAAATAAAATTAAAA-TATGATAATT
1 TTAAATAAAA-TAAAATTAT-ATAATT
*
1896363 TTAAATATAATAAAATTATATAAT
1 TTAAATAAAATAAAATTATATAAT
1896387 ATAATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
TTAAATAAAATAAAATTATATAATT
Found at i:1896389 original size:18 final size:18
Alignment explanation
Indices: 1896366--1896456 Score: 69
Period size: 18 Copynumber: 4.7 Consensus size: 18
1896356 GATAATTTTA
1896366 AATATAATAAAATTATAT
1 AATATAATAAAATTATAT
* *
1896384 AATATAATAAAAATAATAAA
1 AATATAAT-AAAATTAT-AT
*
1896404 AATATTATATAAAATATAAATT
1 AATA-TA-ATAAAAT-TATA-T
1896426 AATAT-A-AAAATTAATAT
1 AATATAATAAAATT-ATAT
1896443 AAATATAATAAAAT
1 -AATATAATAAAAT
1896457 AAATTAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
17 2 0.04
18 20 0.35
19 9 0.16
20 10 0.18
21 9 0.16
22 7 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AATATAATAAAATTATAT
Found at i:1896411 original size:30 final size:29
Alignment explanation
Indices: 1896365--1896469 Score: 99
Period size: 30 Copynumber: 3.5 Consensus size: 29
1896355 TGATAATTTT
1896365 AAATATAATAAA-ATTATATAATATAATAA
1 AAATATAA-AAATATTATATAATATAATAA
*
1896394 AAATAATAAAAATATTATATAAAAT-ATAA
1 AAAT-ATAAAAATATTATATAATATAATAA
*
1896423 ATTAATATAAAAAT-TAATATAAATATAATAA
1 A--AATATAAAAATATTATAT-AATATAATAA
*
1896454 AATAAATTAAAAATAT
1 AA-ATA-TAAAAATAT
1896470 AAAATTTTAT
Statistics
Matches: 63, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
29 18 0.29
30 29 0.46
31 15 0.24
32 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (29 bp):
AAATATAAAAATATTATATAATATAATAA
Done.