Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 5 of 187
Found at i:1832624 original size:7 final size:7
Alignment explanation
Indices: 1832607--1832641 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
1832597 ATAATTATAT
1832607 ATTTTT-
1 ATTTTTA
1832613 ATTTTTA
1 ATTTTTA
*
1832620 TTTTTTA
1 ATTTTTA
1832627 ATTTTTA
1 ATTTTTA
1832634 ATTTTTA
1 ATTTTTA
1832641 A
1 A
1832642 ATACTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
ATTTTTA
Found at i:1832697 original size:26 final size:27
Alignment explanation
Indices: 1832646--1832699 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1832636 TTTTAAATAC
* *
1832646 TTTTAAAATATTCTTTTATTTTTTTAT
1 TTTTAAAATATTCTTTTATATGTTTAT
1832673 TTTTAAAATAATT-TTTTA-ATGTTTAT
1 TTTTAAAAT-ATTCTTTTATATGTTTAT
1832699 T
1 T
1832700 AAAAATGGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.29
27 14 0.58
28 3 0.12
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (27 bp):
TTTTAAAATATTCTTTTATATGTTTAT
Found at i:1839421 original size:194 final size:193
Alignment explanation
Indices: 1839087--1839474 Score: 740
Period size: 194 Copynumber: 2.0 Consensus size: 193
1839077 AACTCACAAG
1839087 TTGGTAAGACTAATACAGTTGATTAGTGACATCAAATCTCCGGATAAATTATTGTTTTCTATTCT
1 TTGGTAAGACTAATACAGTTGATTAGTGACATCAAATCTCCGGATAAATTATTGTTTTCTATTCT
1839152 CCTGCATTATATAGAACCAGCAGCTTATAAACAAGAGCAAATATTCTATTCTAAGTCAAGACCAT
66 CCTGCATTATATAGAACCAGCAGCTTATAAACAAGAGCAAATATTCTATTCTAAGTCAAGACCAT
*
1839217 ATAAGATATTTAGGTACATGAGATGTTTTGCTAGAGCGTTAAGGTTTTGCGAAGGCCATAAAA
131 ATAAGATATTTAGGCACATGAGATGTTTTGCTAGAGCGTTAAGGTTTTGCGAAGGCCATAAAA
*
1839280 TTGGTAAAGACTAATACAGTTGATTAGTGACATCAAATCTCCGGATGAATTATTGTTTTCTATTC
1 TTGGT-AAGACTAATACAGTTGATTAGTGACATCAAATCTCCGGATAAATTATTGTTTTCTATTC
1839345 TCCTGCATTATATAGAACCAGCAGCTTATAAACAAGAGCAAATATTCTATTCTAAGTCAAGACCA
65 TCCTGCATTATATAGAACCAGCAGCTTATAAACAAGAGCAAATATTCTATTCTAAGTCAAGACCA
*
1839410 TATAAGATATTTAGGCACATGAGGTGTTTTGCTAGAGCGTTAAGGTTTTGCGAAGGCCATAAAA
130 TATAAGATATTTAGGCACATGAGATGTTTTGCTAGAGCGTTAAGGTTTTGCGAAGGCCATAAAA
1839474 T
1 T
1839475 GCCACCATTT
Statistics
Matches: 191, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
193 5 0.03
194 186 0.97
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (193 bp):
TTGGTAAGACTAATACAGTTGATTAGTGACATCAAATCTCCGGATAAATTATTGTTTTCTATTCT
CCTGCATTATATAGAACCAGCAGCTTATAAACAAGAGCAAATATTCTATTCTAAGTCAAGACCAT
ATAAGATATTTAGGCACATGAGATGTTTTGCTAGAGCGTTAAGGTTTTGCGAAGGCCATAAAA
Found at i:1870099 original size:19 final size:21
Alignment explanation
Indices: 1870077--1870115 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
1870067 ACATGTAACA
1870077 AAAATTT-TAAA-AAAAATTC
1 AAAATTTATAAACAAAAATTC
1870096 AAAATTTATAAACAAAAATT
1 AAAATTTATAAACAAAAATT
1870116 ACATGTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAATTTATAAACAAAAATTC
Found at i:1872213 original size:22 final size:24
Alignment explanation
Indices: 1872188--1872369 Score: 69
Period size: 24 Copynumber: 7.9 Consensus size: 24
1872178 TATATTATAC
1872188 AAAAACTAT-AA-AAAATAAAAAT
1 AAAAACTATAAATAAAATAAAAAT
*
1872210 AAAAATTATAAATAAAAT-AAAAT
1 AAAAACTATAAATAAAATAAAAAT
* ** *** * * * *
1872233 AATATTTATTTTTATATTATACA-
1 AAAAACTATAAATAAAATAAAAAT
1872256 -AAAACTATAAA-AAAAGTAAAAAT
1 AAAAACTATAAATAAAA-TAAAAAT
*
1872279 AAAAATTATAAATAAAAT-AAAAT
1 AAAAACTATAAATAAAATAAAAAT
* ** ** * * * * *
1872302 AATATTTAT-TTTTATAT-TATAC
1 AAAAACTATAAATAAAATAAAAAT
1872324 AAAAACTATAAA-AAAAGTAAAAAT
1 AAAAACTATAAATAAAA-TAAAAAT
*
1872348 AAAAATTATAAATAAAATAAAA
1 AAAAACTATAAATAAAATAAAA
1872370 TAATATTTAT
Statistics
Matches: 108, Mismatches: 41, Indels: 20
0.64 0.24 0.12
Matches are distributed among these distances:
21 2 0.02
22 31 0.29
23 31 0.29
24 36 0.33
25 8 0.07
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (24 bp):
AAAAACTATAAATAAAATAAAAAT
Found at i:1872303 original size:69 final size:69
Alignment explanation
Indices: 1872166--1872395 Score: 439
Period size: 69 Copynumber: 3.4 Consensus size: 69
1872156 TTACGTATAA
1872166 AATATTTATTTTTATATTATACAAAAACTAT-AAAAAA-TAAAAATAAAAATTATAAATAAAATA
1 AATATTTATTTTTATATTATACAAAAACTATAAAAAAAGTAAAAATAAAAATTATAAATAAAATA
1872229 AAAT
66 AAAT
1872233 AATATTTATTTTTATATTATACAAAAACTATAAAAAAAGTAAAAATAAAAATTATAAATAAAATA
1 AATATTTATTTTTATATTATACAAAAACTATAAAAAAAGTAAAAATAAAAATTATAAATAAAATA
1872298 AAAT
66 AAAT
1872302 AATATTTATTTTTATATTATACAAAAACTATAAAAAAAGTAAAAATAAAAATTATAAATAAAATA
1 AATATTTATTTTTATATTATACAAAAACTATAAAAAAAGTAAAAATAAAAATTATAAATAAAATA
1872367 AAAT
66 AAAT
1872371 AATATTTATTTTTATATTATA-AAAA
1 AATATTTATTTTTATATTATACAAAA
1872396 TCAAATTTAA
Statistics
Matches: 161, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
67 31 0.19
68 10 0.06
69 120 0.75
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.36
Consensus pattern (69 bp):
AATATTTATTTTTATATTATACAAAAACTATAAAAAAAGTAAAAATAAAAATTATAAATAAAATA
AAAT
Found at i:1876883 original size:5 final size:6
Alignment explanation
Indices: 1876868--1876892 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1876858 CGAAGCTTGA
1876868 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
1876893 GACCGGCGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:1878652 original size:26 final size:27
Alignment explanation
Indices: 1878622--1878676 Score: 67
Period size: 30 Copynumber: 2.0 Consensus size: 27
1878612 TTTTTTAGGC
*
1878622 AAAT-AAACTTTTAATTTGTATTAATT
1 AAATAAAACTTATAATTTGTATTAATT
1878648 AAATAACCAAACTTATAATTTGTATTAAT
1 AAAT-A--AAACTTATAATTTGTATTAAT
1878677 CCCAACATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 4 0.17
30 20 0.83
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (27 bp):
AAATAAAACTTATAATTTGTATTAATT
Found at i:1879863 original size:2 final size:2
Alignment explanation
Indices: 1879856--1879890 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1879846 GCAACCTATG
1879856 TA TA 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 T
1879891 GTAATATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1881919 original size:22 final size:22
Alignment explanation
Indices: 1881886--1881946 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
1881876 GCCCGGCCCG
* *
1881886 TTTTTAATTAAAATTAAAATTAT
1 TTTTTAA-TAAAATTAAAACTAA
1881909 TTTTTAATAAAATTAAAACTAA
1 TTTTTAATAAAATTAAAACTAA
* *
1881931 TTGTTATTAAAATTAA
1 TTTTTAATAAAATTAA
1881947 TTGTTAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 27 0.79
23 7 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTAATAAAATTAAAACTAA
Found at i:1881959 original size:16 final size:16
Alignment explanation
Indices: 1881922--1881961 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1881912 TTAATAAAAT
* *
1881922 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
1881938 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
1881954 TAAAATTA
1 TAAAATTA
1881962 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:1882067 original size:9 final size:9
Alignment explanation
Indices: 1882034--1882061 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1882024 TTTATCAAAT
1882034 TATTAATTG
1 TATTAATTG
1882043 TATTAATTG
1 TATTAATTG
1882052 TATTAATTG
1 TATTAATTG
1882061 T
1 T
1882062 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:1882071 original size:68 final size:68
Alignment explanation
Indices: 1881950--1882159 Score: 388
Period size: 68 Copynumber: 3.1 Consensus size: 68
1881940 AAATTAATTG
*
1881950 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1882013 TGA
66 TGA
1882016 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1882081 TGA
66 TGA
*
1882084 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1882149 TGA
66 TGA
1882152 TTAGTAAA
1 TTAGTAAA
1882160 ACGAACTTTA
Statistics
Matches: 140, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
66 26 0.19
68 114 0.81
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:1882114 original size:9 final size:9
Alignment explanation
Indices: 1882102--1882129 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1882092 TTTATCAAAT
1882102 TATTAATTG
1 TATTAATTG
1882111 TATTAATTG
1 TATTAATTG
1882120 TATTAATTG
1 TATTAATTG
1882129 T
1 T
1882130 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:1882255 original size:24 final size:23
Alignment explanation
Indices: 1882226--1882270 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
1882216 AAATAAACTT
1882226 AAAATAA-AAAACTATTATATTTTA
1 AAAATAATAAAA-TA-TATATTTTA
1882250 AAAATAATAAAATATATATTT
1 AAAATAATAAAATATATATTT
1882271 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 9 0.45
25 4 0.20
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAATAATAAAATATATATTTTA
Found at i:1897246 original size:2 final size:2
Alignment explanation
Indices: 1897239--1897272 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1897229 AACAGATAGA
1897239 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1897273 CACTGGAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1899151 original size:24 final size:23
Alignment explanation
Indices: 1899100--1899148 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
1899090 ATTTTTAAAA
1899100 TTTAAAAAATTCAAAAAATTATT
1 TTTAAAAAATTCAAAAAATTATT
1899123 TTTAAGAAAATT-ATAAAAA-TATT
1 TTTAA-AAAATTCA-AAAAATTATT
1899146 TTT
1 TTT
1899149 TAATTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTAAAAAATTCAAAAAATTATT
Found at i:1899965 original size:24 final size:24
Alignment explanation
Indices: 1899900--1899953 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1899890 TCTTTCTAGA
* * *
1899900 ATATTTAGTATTTATGAGTATAAT
1 ATATTTAGCATTTATTAGCATAAT
1899924 ATATTTAGCATTTATTAGCATAAT
1 ATATTTAGCATTTATTAGCATAAT
1899948 ATATTT
1 ATATTT
1899954 GACTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (24 bp):
ATATTTAGCATTTATTAGCATAAT
Found at i:1902086 original size:29 final size:29
Alignment explanation
Indices: 1902032--1902089 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1902022 ATGGGGTTTG
*
1902032 AAAAAATAAATTAAGGTTTAAGGTTTTTT
1 AAAAAATAAATTAAGGTCTAAGGTTTTTT
* **
1902061 AAAAAATAAATTAGGGTCTATTGTTTTTT
1 AAAAAATAAATTAAGGTCTAAGGTTTTTT
1902090 TTCAAAAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.43
Consensus pattern (29 bp):
AAAAAATAAATTAAGGTCTAAGGTTTTTT
Found at i:1902970 original size:9 final size:9
Alignment explanation
Indices: 1902958--1902996 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
1902948 ATAAATAACA
1902958 AAAATATTT
1 AAAATATTT
**
1902967 AAAATAAAT
1 AAAATATTT
1902976 AAAATATTT
1 AAAATATTT
*
1902985 AAAGTATTT
1 AAAATATTT
1902994 AAA
1 AAA
1902997 TTAAAAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (9 bp):
AAAATATTT
Found at i:1903014 original size:27 final size:27
Alignment explanation
Indices: 1902947--1903021 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
1902937 GCCCGATTTT
*
1902947 AATAAATAACAAAAATATTTAAAATAAA
1 AATAAATAA-TAAAATATTTAAAATAAA
* * * *
1902975 TA-AAATATTTAAAGTATTTAAATTAAA
1 AATAAATA-ATAAAATATTTAAAATAAA
1903002 AATAAATAATAAAATATTTA
1 AATAAATAATAAAATATTTA
1903022 TTATATTCGG
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
27 31 0.84
28 6 0.16
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (27 bp):
AATAAATAATAAAATATTTAAAATAAA
Found at i:1904587 original size:26 final size:29
Alignment explanation
Indices: 1904549--1904609 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 29
1904539 TTAATTTTTT
*
1904549 AAAATT-TTAAAAA-TGTCAAAAAA-ATA
1 AAAATTATTAAAAATTATCAAAAAATATA
*
1904575 AAAATTATT-AAAATTATTAAAAAATATA
1 AAAATTATTAAAAATTATCAAAAAATATA
1904603 AAAATTA
1 AAAATTA
1904610 AAAAAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 10 0.33
27 10 0.33
28 10 0.33
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (29 bp):
AAAATTATTAAAAATTATCAAAAAATATA
Found at i:1904597 original size:19 final size:19
Alignment explanation
Indices: 1904573--1904618 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1904563 GTCAAAAAAA
* *
1904573 TAAAAATTATTAAAATTAT
1 TAAAAAATATAAAAATTAT
1904592 TAAAAAATATAAAAATTA-
1 TAAAAAATATAAAAATTAT
1904610 -AAAAAATAT
1 TAAAAAATAT
1904619 TTTATTAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAAAATATAAAAATTAT
Found at i:1905081 original size:17 final size:17
Alignment explanation
Indices: 1905051--1905095 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1905041 TTTTTTAATT
*
1905051 TAAAAATATCAAAA-AA
1 TAAAAATATTAAAAGAA
*
1905067 TAAAAATTATTAAAAGTA
1 TAAAAA-TATTAAAAGAA
1905085 TAAAAATATTA
1 TAAAAATATTA
1905096 TTTGCTAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.24
17 12 0.48
18 7 0.28
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (17 bp):
TAAAAATATTAAAAGAA
Found at i:1906164 original size:17 final size:18
Alignment explanation
Indices: 1906129--1906172 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
1906119 ATCATTATTT
**
1906129 AAATAAAATACAATGGTA
1 AAATAAAATACAAAAGTA
1906147 AAATAAAATA-AAAAGTA
1 AAATAAAATACAAAAGTA
*
1906164 AAGTAAAAT
1 AAATAAAAT
1906173 CCATATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.68, C:0.02, G:0.09, T:0.20
Consensus pattern (18 bp):
AAATAAAATACAAAAGTA
Found at i:1906920 original size:18 final size:17
Alignment explanation
Indices: 1906875--1906922 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
1906865 TTTAAAACAC
** *
1906875 TAAAAATTGTAAATTTT
1 TAAAAATTAAAAATTGT
1906892 TAAAAATTAAAAATTGT
1 TAAAAATTAAAAATTGT
1906909 TAAAATATTAAAAA
1 TAAAA-ATTAAAAA
1906923 AGTGTTCTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (17 bp):
TAAAAATTAAAAATTGT
Found at i:1907103 original size:16 final size:17
Alignment explanation
Indices: 1907082--1907114 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1907072 AACTTTTTAA
*
1907082 ATATATT-TTTAATTAT
1 ATATATTCTTAAATTAT
1907098 ATATATTCTTAAATTAT
1 ATATATTCTTAAATTAT
1907115 TTAAAAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATATTCTTAAATTAT
Found at i:1907172 original size:20 final size:20
Alignment explanation
Indices: 1907138--1907194 Score: 57
Period size: 18 Copynumber: 3.0 Consensus size: 20
1907128 TGAAAAAGTA
1907138 TAAAAA-TGTAAAAATATATT
1 TAAAAATTGT-AAAATATATT
1907158 TAAAAATTGTAAAAT-TA-T
1 TAAAAATTGTAAAATATATT
* * *
1907176 TAAAAGTTATAAAAAATAT
1 TAAAAATTGTAAAATATAT
1907195 ATAATTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 13 0.42
19 4 0.13
20 11 0.35
21 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (20 bp):
TAAAAATTGTAAAATATATT
Found at i:1907314 original size:30 final size:29
Alignment explanation
Indices: 1907280--1907336 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
1907270 TTGAAAATAC
* * *
1907280 TTTTTAATCATTTTTACAATTTTTAAAATT
1 TTTTTAATAACTTTTAC-ATTTTAAAAATT
1907310 TTTTTAATAACTTTTACATTTTAAAAA
1 TTTTTAATAACTTTTACATTTTAAAAA
1907337 AAATCATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTTTAATAACTTTTACATTTTAAAAATT
Found at i:1907358 original size:11 final size:11
Alignment explanation
Indices: 1907342--1907378 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
1907332 AAAAAAAATC
*
1907342 ATTTTTAGTAA
1 ATTTTTAATAA
1907353 ATTTTTAATAA
1 ATTTTTAATAA
1907364 A-TTTTAAT-A
1 ATTTTTAATAA
1907373 ATTTTT
1 ATTTTT
1907379 CCAACTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
9 2 0.08
10 11 0.46
11 11 0.46
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (11 bp):
ATTTTTAATAA
Found at i:1907536 original size:19 final size:18
Alignment explanation
Indices: 1907510--1907574 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 18
1907500 AAATTTTCTT
1907510 TTTTG-TATCTATTAAAAA
1 TTTTGATAT-TATTAAAAA
* *
1907528 TTTTGGTATTACTTAGAAA
1 TTTTGATATTA-TTAAAAA
* *
1907547 TATTGATATTCATTATAAA
1 TTTTGATATT-ATTAAAAA
1907566 TTTTGATAT
1 TTTTGATAT
1907575 CATATGAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 7 0.18
19 31 0.79
20 1 0.03
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (18 bp):
TTTTGATATTATTAAAAA
Found at i:1912530 original size:21 final size:21
Alignment explanation
Indices: 1912468--1912555 Score: 79
Period size: 21 Copynumber: 4.1 Consensus size: 21
1912458 CCTAATCTGT
*
1912468 ATACAACACATAAA-TGCCTG
1 ATACGACACATAAAGTGCCTG
* ** * *
1912488 AAACGACACACGAGGTGGCTG
1 ATACGACACATAAAGTGCCTG
*
1912509 ATATGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCT--G
*
1912532 ATACGACACATAAAGTGACTG
1 ATACGACACATAAAGTGCCTG
1912553 ATA
1 ATA
1912556 GGCAAAGCCG
Statistics
Matches: 51, Mismatches: 14, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
20 9 0.18
21 23 0.45
23 19 0.37
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.18
Consensus pattern (21 bp):
ATACGACACATAAAGTGCCTG
Found at i:1912539 original size:23 final size:23
Alignment explanation
Indices: 1912468--1912553 Score: 74
Period size: 23 Copynumber: 4.0 Consensus size: 23
1912458 CCTAATCTGT
*
1912468 ATACAACACATAAA-TGCCTGA-
1 ATACGACACATAAAGTGCCTGAG
** * *
1912489 A-ACGACACACGAGGTGGCT--G
1 ATACGACACATAAAGTGCCTGAG
*
1912509 ATATGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
*
1912532 ATACGACACATAAAGTGACTGA
1 ATACGACACATAAAGTGCCTGA
1912554 TAGGCAAAGC
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
20 9 0.19
21 18 0.38
23 21 0.44
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:1912554 original size:44 final size:41
Alignment explanation
Indices: 1912473--1912555 Score: 103
Period size: 44 Copynumber: 2.0 Consensus size: 41
1912463 TCTGTATACA
* * *
1912473 ACACATAAATGCCTGAAACGACACACGAGGTGGCTGATATG
1 ACACATAAATGCCTGAAACGACACACAAAGTGACTGATATG
*
1912514 ACACATAAAGTGCCTGAGATACGACACATAAAGTGACTGATA
1 ACACATAAA-TGCCTGA-A-ACGACACACAAAGTGACTGATA
1912556 GGCAAAGCCG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 9 0.26
42 7 0.20
43 1 0.03
44 18 0.51
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (41 bp):
ACACATAAATGCCTGAAACGACACACAAAGTGACTGATATG
Found at i:1913177 original size:3 final size:3
Alignment explanation
Indices: 1913169--1913201 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1913159 ACATTAATTT
1913169 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1913202 GAATTTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1913679 original size:22 final size:21
Alignment explanation
Indices: 1913654--1913703 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
1913644 CTTCCCCTGT
1913654 TTTCGTCTCTT-TCTCTGTTTC
1 TTTCGTCTCTTCTCT-TGTTTC
1913675 GTTTCTGT-TCTTCTCTTGTTTC
1 -TTTC-GTCTCTTCTCTTGTTTC
1913697 TTT-GTCT
1 TTTCGTCT
1913704 TTTTATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
19 2 0.08
20 1 0.04
21 3 0.12
22 14 0.56
23 5 0.20
ACGTcount: A:0.00, C:0.24, G:0.12, T:0.64
Consensus pattern (21 bp):
TTTCGTCTCTTCTCTTGTTTC
Found at i:1913891 original size:5 final size:5
Alignment explanation
Indices: 1913883--1913910 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1913873 TTATTTTATT
1913883 TAATA TAATA TAATA TAATA TAATA TAA
1 TAATA TAATA TAATA TAATA TAATA TAA
1913911 AAATCTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
TAATA
Found at i:1915543 original size:12 final size:12
Alignment explanation
Indices: 1915528--1915554 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1915518 TTTTAAATGG
1915528 GGACTTGCATGA
1 GGACTTGCATGA
1915540 GGACTTGCATGA
1 GGACTTGCATGA
1915552 GGA
1 GGA
1915555 AATTTACATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.15, G:0.37, T:0.22
Consensus pattern (12 bp):
GGACTTGCATGA
Found at i:1918150 original size:28 final size:28
Alignment explanation
Indices: 1918118--1918175 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
1918108 GGTAAATTTG
*
1918118 TTTACCTATTTTAGGTTCAGGGACTAAA
1 TTTACCTATTTTAGGTTCAGGGACCAAA
* *
1918146 TTTACCTGTTTTAGGTTTAGGGACCAAA
1 TTTACCTATTTTAGGTTCAGGGACCAAA
1918174 TT
1 TT
1918176 GCATGAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (28 bp):
TTTACCTATTTTAGGTTCAGGGACCAAA
Found at i:1920401 original size:26 final size:27
Alignment explanation
Indices: 1920351--1920411 Score: 106
Period size: 26 Copynumber: 2.3 Consensus size: 27
1920341 AATAAAAAAC
1920351 CAAAATATTATAACTTTTTTTATTTAT
1 CAAAATATTATAACTTTTTTTATTTAT
1920378 CAAAATATTATAA-TTTTTTTATTTAT
1 CAAAATATTATAACTTTTTTTATTTAT
*
1920404 TAAAATAT
1 CAAAATAT
1920412 ACCAAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 20 0.61
27 13 0.39
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (27 bp):
CAAAATATTATAACTTTTTTTATTTAT
Found at i:1921082 original size:23 final size:23
Alignment explanation
Indices: 1921056--1921127 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 23
1921046 ACTCTATTTT
1921056 AATTTAATAAACTATTCTCATCA
1 AATTTAATAAACTATTCTCATCA
*
1921079 AATTACTTAATAACTCTATT-T--T--
1 AA-T--TTAATAA-ACTATTCTCATCA
1921101 AATTTAATAAACTATTCTCATCA
1 AATTTAATAAACTATTCTCATCA
1921124 AATT
1 AATT
1921128 ACCAAAATAG
Statistics
Matches: 38, Mismatches: 2, Indels: 18
0.66 0.03 0.31
Matches are distributed among these distances:
18 5 0.13
19 8 0.21
21 2 0.05
22 2 0.05
23 6 0.16
24 2 0.05
26 8 0.21
27 5 0.13
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.43
Consensus pattern (23 bp):
AATTTAATAAACTATTCTCATCA
Found at i:1921090 original size:45 final size:45
Alignment explanation
Indices: 1921041--1921129 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
1921031 TCTAATTAAG
1921041 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
1921086 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTAC
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTAC
1921130 CAAAATAGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (45 bp):
TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
Found at i:1921155 original size:15 final size:15
Alignment explanation
Indices: 1921135--1921184 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
1921125 ATTACCAAAA
1921135 TAGAGTTTATTAAAT
1 TAGAGTTTATTAAAT
1921150 TAGAGTTTATTAAAT
1 TAGAGTTTATTAAAT
*
1921165 GAGAATAGTTTATTAAAT
1 TAG---AGTTTATTAAAT
1921183 TA
1 TA
1921185 AAATAGAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 17 0.57
18 13 0.43
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (15 bp):
TAGAGTTTATTAAAT
Found at i:1921189 original size:18 final size:18
Alignment explanation
Indices: 1921153--1921190 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1921143 ATTAAATTAG
*
1921153 AGTTTATTAAATGAGAAT
1 AGTTTATTAAATGAAAAT
*
1921171 AGTTTATTAAATTAAAAT
1 AGTTTATTAAATGAAAAT
1921189 AG
1 AG
1921191 AGTTATTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (18 bp):
AGTTTATTAAATGAAAAT
Found at i:1921475 original size:16 final size:17
Alignment explanation
Indices: 1921454--1921485 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1921444 GCTGCAGCCA
1921454 CAGGTTTTT-TTTTTTG
1 CAGGTTTTTATTTTTTG
1921470 CAGGTTTTTATTTTTT
1 CAGGTTTTTATTTTTT
1921486 TGGTATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.09, C:0.06, G:0.16, T:0.69
Consensus pattern (17 bp):
CAGGTTTTTATTTTTTG
Found at i:1923168 original size:2 final size:2
Alignment explanation
Indices: 1923161--1923186 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1923151 GGAGAGCTGG
1923161 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
1923187 AAACCCCAAA
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:1926543 original size:31 final size:31
Alignment explanation
Indices: 1926507--1926568 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1926497 AGATAATTTT
1926507 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1926538 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1926569 TAATTTGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:1927104 original size:11 final size:11
Alignment explanation
Indices: 1927090--1927138 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
1927080 TTATTCTTTA
1927090 AAAAAAAGCGC
1 AAAAAAAGCGC
**
1927101 AAAAAAAAAGC
1 AAAAAAAGCGC
1927112 --AAAAAGCGC
1 AAAAAAAGCGC
*
1927121 AAAAAAACCGC
1 AAAAAAAGCGC
1927132 AAAAAAA
1 AAAAAAA
1927139 AATGTTGCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
9 7 0.23
11 24 0.77
ACGTcount: A:0.71, C:0.16, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAAGCGC
Found at i:1933460 original size:3 final size:3
Alignment explanation
Indices: 1933452--1933480 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1933442 TTTATGTATC
1933452 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1933481 TACTTAATTC
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1933608 original size:31 final size:31
Alignment explanation
Indices: 1933572--1933633 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1933562 AGATAATTTT
1933572 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1933603 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1933634 TAATTTGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:1934832 original size:6 final size:7
Alignment explanation
Indices: 1934812--1934844 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
1934802 TCCTCATTTC
1934812 ATTAAAA
1 ATTAAAA
1934819 ATTAAAA
1 ATTAAAA
1934826 ATTAAAA
1 ATTAAAA
1934833 ATTAAAA
1 ATTAAAA
1934840 TATTA
1 -ATTA
1934845 TGTTTAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.84
8 4 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
ATTAAAA
Found at i:1939210 original size:3 final size:3
Alignment explanation
Indices: 1939202--1939245 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1939192 TATTAACATG
1939202 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1939246 AGAATAATGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1939320 original size:15 final size:15
Alignment explanation
Indices: 1939300--1939328 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1939290 AGACAAGGGC
1939300 AAAGAAATAATAATT
1 AAAGAAATAATAATT
1939315 AAAGAAATAATAAT
1 AAAGAAATAATAAT
1939329 AATAATGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (15 bp):
AAAGAAATAATAATT
Found at i:1939474 original size:76 final size:76
Alignment explanation
Indices: 1939308--1939449 Score: 202
Period size: 76 Copynumber: 1.9 Consensus size: 76
1939298 GCAAAGAAAT
* ** *
1939308 AATAATTAAAGAAATAATAATAATAATGAAAAATTGGAATTAAAATAAAATTAAGGGCATAAATT
1 AATAATTAAATAAATAATAATAATAATGAAAAATTCAAATTAAAATAAAATTAAAGGCATAAATT
*
1939373 GTAAAAAAAAC
66 GGAAAAAAAAC
1939384 AATAATTAAATAAATAATAATAATAATGAAAAATTCAAATT-AAAT-AAA-TAAAGG-ATAAAAT
1 AATAATTAAATAAATAATAATAATAATGAAAAATTCAAATTAAAATAAAATTAAAGGCAT-AAAT
1939445 TGGAA
65 TGGAA
1939450 TTAAAATAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
72 2 0.03
73 13 0.22
74 3 0.05
75 4 0.07
76 38 0.63
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (76 bp):
AATAATTAAATAAATAATAATAATAATGAAAAATTCAAATTAAAATAAAATTAAAGGCATAAATT
GGAAAAAAAAC
Found at i:1939563 original size:112 final size:103
Alignment explanation
Indices: 1939337--1939544 Score: 265
Period size: 103 Copynumber: 1.9 Consensus size: 103
1939327 ATAATAATGA
*
1939337 AAAATTGGAATTAAAATAAAATTAAGGGCATAAATTGTAAAAAAAACAATAATTAAATAAATAAT
1 AAAATTGGAATTAAAATAAAATTAAGGGCATAAATTGTAAAAAAAACAATAATTAAATAAAAAAT
* *
1939402 AATAATAATGAAAAATTCAAATTAAATAAATAAAGGAT
66 AAAAATAATGAAAAATTCAAATTAAATAAACAAAGGAT
*
1939440 AAAATTGGAATTAAAATAAAATTAAGGGCATAAATTGTAAAAATTAAATAGATAAATAAGTAAAT
1 AAAATTGGAATTAAAATAAAATTAAGGGCATAAATTGTAAAAA--AAACA-AT-AAT---TAAAT
* *
1939505 AACGAAAATAAAAATTAT-AAAAGATTTAAATTAAATAAAC
59 AA--AAAATAAAAATAATGAAAA-ATTCAAATTAAATAAAC
1939545 CGAGGAATAA
Statistics
Matches: 89, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
103 43 0.48
105 4 0.04
106 2 0.02
107 3 0.03
110 7 0.08
111 4 0.04
112 26 0.29
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.26
Consensus pattern (103 bp):
AAAATTGGAATTAAAATAAAATTAAGGGCATAAATTGTAAAAAAAACAATAATTAAATAAAAAAT
AAAAATAATGAAAAATTCAAATTAAATAAACAAAGGAT
Found at i:1939638 original size:21 final size:20
Alignment explanation
Indices: 1939591--1939643 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
1939581 AATAAATTTA
1939591 AATAAAATAAGTAAATAAAAT
1 AATAAAATAAG-AAATAAAAT
*
1939612 ACTAAAATAA-AAATAAAAAT
1 AATAAAATAAGAAAT-AAAAT
1939632 ATATAAAA-AAGA
1 A-ATAAAATAAGA
1939644 CAGTAAATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 4 0.15
20 8 0.30
21 15 0.56
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (20 bp):
AATAAAATAAGAAATAAAAT
Found at i:1940056 original size:24 final size:23
Alignment explanation
Indices: 1940001--1940079 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 23
1939991 TTGATTTTAT
1940001 TTTTTTGATTGCTTCTTTCTTTTATC
1 TTTTTTGATTGCTT-TTT-TTTT-TC
1940027 TGTTTTTCGATTGCTTTTTTTTTTC
1 T-TTTTT-GATTGCTTTTTTTTTTC
*
1940052 TTTTTTGTATT-ATTTTTTTCTTTC
1 TTTTTTG-ATTGCTTTTTTT-TTTC
1940076 TTTT
1 TTTT
1940080 CGAAAAAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
23 8 0.17
24 16 0.33
25 3 0.06
26 5 0.10
27 8 0.17
28 8 0.17
ACGTcount: A:0.06, C:0.11, G:0.08, T:0.75
Consensus pattern (23 bp):
TTTTTTGATTGCTTTTTTTTTTC
Found at i:1940427 original size:31 final size:33
Alignment explanation
Indices: 1940391--1940452 Score: 92
Period size: 31 Copynumber: 1.9 Consensus size: 33
1940381 TGGACGGTTG
*
1940391 TTTATTATTT-TTTATTTT-TATTTTGGTTTTA
1 TTTATTATTTATTTATTTTGTATTTGGGTTTTA
*
1940422 TTTATTATTTATTTTTTTTGTATTTGGGTTT
1 TTTATTATTTATTTATTTTGTATTTGGGTTT
1940453 CTGTTTGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 10 0.37
32 7 0.26
33 10 0.37
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.76
Consensus pattern (33 bp):
TTTATTATTTATTTATTTTGTATTTGGGTTTTA
Found at i:1940781 original size:88 final size:91
Alignment explanation
Indices: 1940660--1940833 Score: 237
Period size: 88 Copynumber: 1.9 Consensus size: 91
1940650 CTTTGTTTTG
* * * *
1940660 TTTTTTTGTACTCATTTGAGTACTTGAACTTTCAAAATGCATAAAAAAG-CCTTTAA-ACTTTTT
1 TTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATAAAAAAGACCCTCAATACTTTTT
1940723 C-AAAAAAGCAATTAAGCCCTACTTT
66 CAAAAAAAGCAATTAAGCCCTACTTT
* ** * **
1940748 TTTTTTTGCACTCAATTGGGTACTTGAGTTTTCAAAATGCATCAAAAAGACCCTCAATTTTTTTT
1 TTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATAAAAAAGACCCTCAATACTTTTT
1940813 CAAAAAAAGCAATTAAGCCCT
66 CAAAAAAAGCAATTAAGCCCT
1940834 TTTATTAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
88 43 0.59
89 5 0.07
90 6 0.08
91 19 0.26
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.37
Consensus pattern (91 bp):
TTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATAAAAAAGACCCTCAATACTTTTT
CAAAAAAAGCAATTAAGCCCTACTTT
Found at i:1940863 original size:10 final size:10
Alignment explanation
Indices: 1940835--1940966 Score: 50
Period size: 10 Copynumber: 14.1 Consensus size: 10
1940825 TTAAGCCCTT
1940835 TTATTAAAAA
1 TTATTAAAAA
**
1940845 TTAGAAAAAA
1 TTATTAAAAA
1940855 TTATTAAAAA
1 TTATTAAAAA
1940865 -T-TT-AAAA
1 TTATTAAAAA
* * *
1940872 TAAATAAAAT
1 TTATTAAAAA
*
1940882 TTA-TAAATA
1 TTATTAAAAA
**
1940891 TTATTAAATT
1 TTATTAAAAA
*
1940901 TTAATAAAAA
1 TTATTAAAAA
*
1940911 --ATT-CAAA
1 TTATTAAAAA
*
1940918 -TATTAAAATT
1 TTATTAAAA-A
1940928 TTATTAAAAA
1 TTATTAAAAA
*
1940938 TTA-AAAAAA
1 TTATTAAAAA
*
1940947 TT-GTAAAAA
1 TTATTAAAAA
* *
1940956 ATATAAAAAA
1 TTATTAAAAA
1940966 T
1 T
1940967 GTAAAATTTT
Statistics
Matches: 87, Mismatches: 25, Indels: 20
0.66 0.19 0.15
Matches are distributed among these distances:
7 7 0.08
8 7 0.08
9 24 0.28
10 41 0.47
11 8 0.09
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (10 bp):
TTATTAAAAA
Found at i:1940871 original size:17 final size:18
Alignment explanation
Indices: 1940835--1941002 Score: 67
Period size: 18 Copynumber: 9.1 Consensus size: 18
1940825 TTAAGCCCTT
*
1940835 TTATTAAAAATTAGAAAAAA
1 TTATTAAAAATT--ATAAAA
1940855 TTATTAAAAATT-TAAAA
1 TTATTAAAAATTATAAAA
* * *
1940872 TAAATAAAATTTATAAATA
1 TTATTAAAAATTATAAA-A
**
1940891 TTATTAAATTTTAATAAAA
1 TTATTAAAAATT-ATAAAA
* * *
1940910 -AATTCAAATATTA-AAATT
1 TTATT-AAAAATTATAAA-A
*
1940928 TTATTAAAAATTAAAAAAA
1 TTATTAAAAATT-ATAAAA
* *
1940947 TT-GTAAAAAATATAAAA
1 TTATTAAAAATTATAAAA
* *
1940964 -AATGTAAAATTTTATAAAAA
1 TTAT-TAAAA-ATTAT-AAAA
* *
1940984 TTGTAAAAAATTATAAAA
1 TTATTAAAAATTATAAAA
1941002 T
1 T
1941003 ATATAGAAAT
Statistics
Matches: 111, Mismatches: 24, Indels: 28
0.68 0.15 0.17
Matches are distributed among these distances:
17 21 0.19
18 31 0.28
19 30 0.27
20 28 0.25
21 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (18 bp):
TTATTAAAAATTATAAAA
Found at i:1940956 original size:46 final size:45
Alignment explanation
Indices: 1940833--1941001 Score: 137
Period size: 46 Copynumber: 3.6 Consensus size: 45
1940823 AATTAAGCCC
* * *
1940833 TTTTATTAAAAATTAGAAAAAATTATTAAAAATTTAAAATAAATAAAA
1 TTTTA-TAAAAATTA-AAAAAATTATAAAAAAATTAAAAT-ATTAAAA
* ** * *
1940881 -TTTATAAATATT-ATTAAATTTTAATAAAAAATTCAAATATTAAAA
1 TTTTATAAAAATTAAAAAAATTAT-A-AAAAAATTAAAATATTAAAA
* *
1940926 TTTTATTAAAAATTAAAAAAATTGT-AAAAAATATAAAAAATGTAAAA
1 TTTTA-TAAAAATTAAAAAAATTATAAAAAAAT-TAAAATAT-TAAAA
*
1940973 TTTTATAAAAATTGTAAAAAATTATAAAA
1 TTTTATAAAAATT-AAAAAAATTATAAAA
1941002 TATATAGAAA
Statistics
Matches: 96, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
44 7 0.07
45 13 0.14
46 36 0.38
47 30 0.31
48 10 0.10
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (45 bp):
TTTTATAAAAATTAAAAAAATTATAAAAAAATTAAAATATTAAAA
Found at i:1940966 original size:9 final size:9
Alignment explanation
Indices: 1940932--1941020 Score: 56
Period size: 9 Copynumber: 9.8 Consensus size: 9
1940922 AAAATTTTAT
*
1940932 TAAAAATTA
1 TAAAAAATA
*
1940941 -AAAAAATTG
1 TAAAAAA-TA
1940950 TAAAAAATA
1 TAAAAAATA
*
1940959 TAAAAAATG
1 TAAAAAATA
**
1940968 TAAAATTTTA
1 TAAAA-AATA
* *
1940978 TAAAAATTG
1 TAAAAAATA
1940987 TAAAAAAT-
1 TAAAAAATA
*
1940995 TATAAAATA
1 TAAAAAATA
*
1941004 TATAGAAATA
1 TA-AAAAATA
1941014 TAAAAAA
1 TAAAAAA
1941021 ATTATGAAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
8 12 0.20
9 30 0.49
10 19 0.31
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.29
Consensus pattern (9 bp):
TAAAAAATA
Found at i:1940981 original size:28 final size:28
Alignment explanation
Indices: 1940933--1941030 Score: 76
Period size: 28 Copynumber: 3.5 Consensus size: 28
1940923 AAATTTTATT
* *
1940933 AAAAATTA-AAAAAATTGTAAAAAATATA
1 AAAAATTATAAAATA-TATAAAAAATATA
* * * *
1940961 AAAAATGTA-AAATTTTATAAAAATTGTA
1 AAAAAT-TATAAAATATATAAAAAATATA
*
1940989 AAAAATTATAAAATATAT-AGAAATATAA
1 AAAAATTATAAAATATATAAAAAATAT-A
*
1941017 AAAAATTATGAAAT
1 AAAAATTATAAAAT
1941031 TTTAGAAAGC
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
27 7 0.13
28 43 0.78
29 5 0.09
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (28 bp):
AAAAATTATAAAATATATAAAAAATATA
Found at i:1940992 original size:10 final size:10
Alignment explanation
Indices: 1940941--1941001 Score: 58
Period size: 10 Copynumber: 6.4 Consensus size: 10
1940931 TTAAAAATTA
1940941 AAAAAATTGT
1 AAAAAATTGT
*
1940951 AAAAAA-TAT
1 AAAAAATTGT
1940960 AAAAAA-TGT
1 AAAAAATTGT
*
1940969 --AAAATTTT
1 AAAAAATTGT
1940977 ATAAAAATTGT
1 A-AAAAATTGT
*
1940988 AAAAAATTAT
1 AAAAAATTGT
1940998 AAAA
1 AAAA
1941002 TATATAGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
7 4 0.10
8 2 0.05
9 10 0.24
10 18 0.43
11 8 0.19
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (10 bp):
AAAAAATTGT
Found at i:1943378 original size:22 final size:22
Alignment explanation
Indices: 1943353--1943395 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1943343 TATCCAAAAA
1943353 ATAACAAAAAAATAGTAGCAAT
1 ATAACAAAAAAATAGTAGCAAT
* **
1943375 ATAATAGTAAAATAGTAGCAA
1 ATAACAAAAAAATAGTAGCAA
1943396 AACAACAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.12, T:0.21
Consensus pattern (22 bp):
ATAACAAAAAAATAGTAGCAAT
Found at i:1943415 original size:14 final size:11
Alignment explanation
Indices: 1943393--1943435 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
1943383 AAAATAGTAG
1943393 CAAAACAACAA
1 CAAAACAACAA
* *
1943404 CATACCAACAA
1 CAAAACAACAA
1943415 CAAAACAACAA
1 CAAAACAACAA
1943426 C-AAACAACAA
1 CAAAACAACAA
1943436 TAGGGAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.67, C:0.30, G:0.00, T:0.02
Consensus pattern (11 bp):
CAAAACAACAA
Found at i:1943421 original size:22 final size:21
Alignment explanation
Indices: 1943393--1943435 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
1943383 AAAATAGTAG
*
1943393 CAAAACAACAACATACCAACAA
1 CAAAACAACAACA-AACAACAA
1943415 CAAAACAACAACAAACAACAA
1 CAAAACAACAACAAACAACAA
1943436 TAGGGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.67, C:0.30, G:0.00, T:0.02
Consensus pattern (21 bp):
CAAAACAACAACAAACAACAA
Found at i:1944115 original size:34 final size:34
Alignment explanation
Indices: 1944072--1944140 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
1944062 TAAAATAAAA
1944072 TAAAAAGAAGTGTAGTTCTATATGGATTTTACTT
1 TAAAAAGAAGTGTAGTTCTATATGGATTTTACTT
1944106 TAAAAAGAAGTGTAGTTCTATATGGATTTTACTT
1 TAAAAAGAAGTGTAGTTCTATATGGATTTTACTT
1944140 T
1 T
1944141 TATTTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (34 bp):
TAAAAAGAAGTGTAGTTCTATATGGATTTTACTT
Found at i:1949519 original size:5 final size:5
Alignment explanation
Indices: 1949509--1949533 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1949499 AACCATATTC
1949509 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
1949534 GAAGTGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:1951503 original size:8 final size:8
Alignment explanation
Indices: 1951490--1951533 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
1951480 TAGCAAATCA
1951490 TATATTTT
1 TATATTTT
1951498 TATATTTT
1 TATATTTT
1951506 TAATAATTTT
1 T-AT-ATTTT
1951516 TAT-TTTT
1 TATATTTT
1951523 TGATATTTT
1 T-ATATTTT
1951532 TA
1 TA
1951534 AATTAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
7 5 0.16
8 12 0.38
9 9 0.28
10 6 0.19
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (8 bp):
TATATTTT
Found at i:1951982 original size:450 final size:449
Alignment explanation
Indices: 1951082--1951969 Score: 950
Period size: 450 Copynumber: 2.0 Consensus size: 449
1951072 AGAGATCAAC
* * * *
1951082 TTAAATAAAAAAAATTCAAATCTTAATATAAAGAAAGCTATCAAGTTCAAATATTAATTTAAAAA
1 TTAAATAAAAAAAATTCAAATCTCAATATAAAAAAAACTACCAAGTTCAAATATTAATTTAAAAA
* * * * * * *
1951147 AAATTCAAGGCTAATATGAAAATAATTATTAAGTTTAAAGATTAATTCTAAAGAAAACAAGAGTT
66 AAATTCAAGCCTAATATAAAAACAACTACTAAATTTAAAGATTAATTCTAAAGAAAAAAAGAGTT
* * * ** * ** *
1951212 CTATCCACGTAATTATGAGGATAGACCATATAGCGAAAGGTTGTTAGCAATGGCAATGGGATGGA
131 CTATCCACGTAATCATGAGGATAGACCACATAGCAAAAGGTTACTAGAAATGGCAACAGGATAGA
* * ** * * * *
1951277 TTGGTATTACTCGGTTTTATTCAAAAGGTATAATAATTGGCCCTCCAACTTTATAAAAAAAGAAA
196 GTGGTATCACTCCATTTTAATCAAAAGGCATAATAATTGACCCTCCAACTTTACAAAAAAAGAAA
* * * * * *
1951342 AAGTCATTTTAACCTTCTAATTAATTTTCACCTCTTTTAGCCTTTAAATTTGTATTATTTGTTAA
261 AAGTAATTTGAACCCTCCAATTAATTTTCACCTATTTTAACCTTTAAATTTGTATTATTTGTTAA
* * * *
1951407 ATCATCTTAAAATAGATGGAAAAATGAATGGTTGTTAAATTTACAAACGCGACAGTCCACGTGTT
326 ATCACCATAAAATAGATGGAAAAATGAATGGTTGTTAAATTTACAAACGCGACAGTCCACCTGTC
* * * *** * **** * *
1951472 TGTCACGTTAGCAAATCATATATTTTTATATTTTTAATAATTTTTATTTTTTGATATTT
391 TATCACGCTAACAAATCATATATTAAAAAAAAACTAATAAATATTATTTTTTGATATTT
*
1951531 TTAAATTAAAAAAAA-TCAAATCTCAATATAAAAAAAACTACCAAGTTCAAATGTTAACTTATAA
1 TTAAA-TAAAAAAAATTCAAATCTCAATATAAAAAAAACTACCAAGTTCAAATATTAA-TT-TAA
** *
1951595 AAAGGATTTAAGCCTAATATAAAAACAACTACTAAATTTAGAA-ATTAATT-TAAA-ATAAAAAA
63 AAAAAATTCAAGCCTAATATAAAAACAACTACTAAATTTA-AAGATTAATTCTAAAGA-AAAAAA
* * * * *
1951657 GAGTTTTGTCCACGTAATCATGAGGATAGACGACATTGCAAAAGGTTACTAGAAATGGCAACATG
126 GAGTTCTATCCACGTAATCATGAGGATAGACCACATAGCAAAAGGTTACTAGAAATGGCAACAGG
1951722 ATAGAGTGGTATCACTCCATTTTAATCAAAAGGCATAATAATTGACCCTCCAACTTTACAAAAAA
191 ATAGAGTGGTATCACTCCATTTTAATCAAAAGGCATAATAATTGACCCTCCAACTTTACAAAAAA
* * * *
1951787 A-AAACA-TAATTTGAACCCTCCAATTAATTTTCATCTATTTTAACTTTTGAATTTGTATTATTT
256 AGAAAAAGTAATTTGAACCCTCCAATTAATTTTCACCTATTTTAACCTTTAAATTTGTATTATTT
* * * * ** * * **
1951850 TTTAAATCACCATAAAATGGATGGAAAAATTAAT-GTCTGTTAACTTTATTAATGTGGTAGTCCA
321 GTTAAATCACCATAAAATAGATGGAAAAATGAATGGT-TGTTAAATTTACAAACGCGACAGTCCA
*
1951914 CCTGTCTATCACGCTAACAAAT-A-A-ATTCAAAAAAAAAACTAATAAAATATTCTTTT
385 CCTGTCTATCACGCTAACAAATCATATATT--AAAAAAAAACTAAT-AAATATTATTTT
1951970 ATATTCTATT
Statistics
Matches: 355, Mismatches: 75, Indels: 19
0.79 0.17 0.04
Matches are distributed among these distances:
445 3 0.01
446 1 0.00
447 9 0.03
448 123 0.35
449 47 0.13
450 129 0.36
451 41 0.12
452 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (449 bp):
TTAAATAAAAAAAATTCAAATCTCAATATAAAAAAAACTACCAAGTTCAAATATTAATTTAAAAA
AAATTCAAGCCTAATATAAAAACAACTACTAAATTTAAAGATTAATTCTAAAGAAAAAAAGAGTT
CTATCCACGTAATCATGAGGATAGACCACATAGCAAAAGGTTACTAGAAATGGCAACAGGATAGA
GTGGTATCACTCCATTTTAATCAAAAGGCATAATAATTGACCCTCCAACTTTACAAAAAAAGAAA
AAGTAATTTGAACCCTCCAATTAATTTTCACCTATTTTAACCTTTAAATTTGTATTATTTGTTAA
ATCACCATAAAATAGATGGAAAAATGAATGGTTGTTAAATTTACAAACGCGACAGTCCACCTGTC
TATCACGCTAACAAATCATATATTAAAAAAAAACTAATAAATATTATTTTTTGATATTT
Found at i:1954282 original size:28 final size:29
Alignment explanation
Indices: 1954217--1954291 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
1954207 GGTTTTTGAA
*
1954217 AAAATAAACAATAAACCCTAATTTATTTTT
1 AAAA-AAACCATAAACCCTAATTTATTTTT
*
1954247 AAAAAAACCATAAACCCTAATTTTTTTTT
1 AAAAAAACCATAAACCCTAATTTATTTTT
** *
1954276 CTAAAACCCATAAACC
1 AAAAAAACCATAAACC
1954292 ATAAAACCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 36 0.90
30 4 0.10
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (29 bp):
AAAAAAACCATAAACCCTAATTTATTTTT
Found at i:1954298 original size:16 final size:15
Alignment explanation
Indices: 1954277--1954306 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1954267 TTTTTTTTTC
1954277 TAAAACCCATAAACCA
1 TAAAACCC-TAAACCA
1954293 TAAAACCCTAAACC
1 TAAAACCCTAAACC
1954307 CTAACATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.13
Consensus pattern (15 bp):
TAAAACCCTAAACCA
Found at i:1956191 original size:20 final size:20
Alignment explanation
Indices: 1956166--1956207 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1956156 GAATGTGATT
1956166 TTTTTAAAAATAATAAAATA
1 TTTTTAAAAATAATAAAATA
*
1956186 TTTTTAAAAATTATAAAATA
1 TTTTTAAAAATAATAAAATA
1956206 TT
1 TT
1956208 AAAAACTCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTTTAAAAATAATAAAATA
Found at i:1964929 original size:26 final size:23
Alignment explanation
Indices: 1964887--1964950 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 23
1964877 AACAATAAGT
1964887 TAAAAAAAACTAAAATTATTAAAATTA
1 TAAAAAAAA-TAAAATTA-T--AATTA
*
1964914 TAAAAAAAATATAATTATAATTA
1 TAAAAAAAATAAAATTATAATTA
*
1964937 TATAAAAAATAAAA
1 TAAAAAAAATAAAA
1964951 ATCATGTGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 17 0.50
25 1 0.03
26 7 0.21
27 9 0.26
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAAAAAAATAAAATTATAATTA
Found at i:1971648 original size:2 final size:2
Alignment explanation
Indices: 1971641--1971667 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1971631 TTATTACCTC
1971641 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1971668 GTTGAAGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1973119 original size:18 final size:18
Alignment explanation
Indices: 1973096--1973131 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1973086 ATATTGATGC
*
1973096 TAAATATAGATACCAAAT
1 TAAATATAGAAACCAAAT
*
1973114 TAAATATTGAAACCAAAT
1 TAAATATAGAAACCAAAT
1973132 AGATAATAAA
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:0.56, C:0.11, G:0.06, T:0.28
Consensus pattern (18 bp):
TAAATATAGAAACCAAAT
Found at i:1978990 original size:44 final size:44
Alignment explanation
Indices: 1978937--1979025 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 44
1978927 ATAATTTTAA
**
1978937 ATTAAATTATAATTATTTTTAAATGTGTAATTATCAC-AACTTCT
1 ATTAAATTATAATTATTTTTAAATGTACAATTATCACGAA-TTCT
1978981 ATTAAATTATAATTATTTTTAAATGTACAATTATCACGAATTCT
1 ATTAAATTATAATTATTTTTAAATGTACAATTATCACGAATTCT
1979025 A
1 A
1979026 CTTTGCCTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 40 0.95
45 2 0.05
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.46
Consensus pattern (44 bp):
ATTAAATTATAATTATTTTTAAATGTACAATTATCACGAATTCT
Found at i:1985362 original size:23 final size:24
Alignment explanation
Indices: 1985329--1985377 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
1985319 TAGAATTATA
1985329 TATTTTATAATTTTTATAAAAAAT
1 TATTTTATAATTTTTATAAAAAAT
* *
1985353 TATTTT-TAATTTTTTTTAAAAAT
1 TATTTTATAATTTTTATAAAAAAT
1985376 TA
1 TA
1985378 CAATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTTTATAATTTTTATAAAAAAT
Found at i:1985547 original size:26 final size:26
Alignment explanation
Indices: 1985460--1985550 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 26
1985450 GTAAATTTTA
1985460 TTTGTATAATTTTT-TATAATTTATATTT
1 TTTGTATAATTTTTATAT-A-TT-TATTT
* * *
1985488 TTTTTCTAGA-TTTTATATATATA-TT
1 TTTGTATA-ATTTTTATATATTTATTT
*
1985513 TCTG---AATTTTTATATATTTATTT
1 TTTGTATAATTTTTATATATTTATTT
1985536 TTTGTATAATTTTTA
1 TTTGTATAATTTTTA
1985551 ATGTGTATAT
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
21 1 0.02
22 13 0.27
23 5 0.10
25 4 0.08
26 10 0.20
27 1 0.02
28 11 0.22
29 4 0.08
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.66
Consensus pattern (26 bp):
TTTGTATAATTTTTATATATTTATTT
Found at i:1994147 original size:19 final size:19
Alignment explanation
Indices: 1994123--1994161 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1994113 AAGGTTATTG
*
1994123 AAATTTCGATTATCAATTA
1 AAATTTCAATTATCAATTA
* *
1994142 AAATTTTAATTATTAATTA
1 AAATTTCAATTATCAATTA
1994161 A
1 A
1994162 TTCGGTTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (19 bp):
AAATTTCAATTATCAATTA
Found at i:2001195 original size:3 final size:3
Alignment explanation
Indices: 2001187--2001213 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2001177 TCACTACCTG
2001187 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
2001214 AATGACTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:2002223 original size:5 final size:5
Alignment explanation
Indices: 2002201--2002240 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
2002191 ACTCTAAACA
2002201 TGTTT T-TTT CTGTTT T-TTT T-TTT TGTTT TGTTT TGTTT TG
1 TGTTT TGTTT -TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT TG
2002241 GTTCTGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 11 0.34
5 18 0.56
6 3 0.09
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (5 bp):
TGTTT
Found at i:2012142 original size:30 final size:30
Alignment explanation
Indices: 2012108--2012168 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
2012098 TATCATTTTG
2012108 TATGAGTCATAAAAGTAAATTTGTTTGTTA
1 TATGAGTCATAAAAGTAAATTTGTTTGTTA
*
2012138 TATGAGTCATAAAAGTAAGTTTGTTTGTTA
1 TATGAGTCATAAAAGTAAATTTGTTTGTTA
2012168 T
1 T
2012169 GTAAAAGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.44
Consensus pattern (30 bp):
TATGAGTCATAAAAGTAAATTTGTTTGTTA
Found at i:2012560 original size:10 final size:10
Alignment explanation
Indices: 2012545--2012582 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
2012535 AATGTTGATT
2012545 TTATTAAAAA
1 TTATTAAAAA
**
2012555 TTATT-AATT
1 TTATTAAAAA
2012564 TTATTAAAAA
1 TTATTAAAAA
2012574 TTATTAAAA
1 TTATTAAAA
2012583 TATCTTATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TTATTAAAAA
Found at i:2012566 original size:19 final size:19
Alignment explanation
Indices: 2012542--2012580 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2012532 TTAAATGTTG
2012542 ATTTTATTAAAAATTATTA
1 ATTTTATTAAAAATTATTA
2012561 ATTTTATTAAAAATTATTA
1 ATTTTATTAAAAATTATTA
2012580 A
1 A
2012581 AATATCTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTTATTAAAAATTATTA
Found at i:2017074 original size:22 final size:23
Alignment explanation
Indices: 2017016--2017076 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
2017006 GAAATTTTAA
*
2017016 AAATATTAATTCTATAAAATAGT
1 AAATGTTAATTCTATAAAATAGT
* *
2017039 AAATGATATTTTCTA-AAAATAGT
1 AAATGTTA-ATTCTATAAAATAGT
*
2017062 AAGTGTTAATTCTAT
1 AAATGTTAATTCTAT
2017077 TTCAATTTGG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
22 5 0.17
23 20 0.67
24 5 0.17
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (23 bp):
AAATGTTAATTCTATAAAATAGT
Found at i:2020257 original size:51 final size:51
Alignment explanation
Indices: 2020193--2020293 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
2020183 ACGGATACCC
*
2020193 AGTGGCCTACACATGGTACCACCCTTGTAGCCAAAGCTACCTTCTTCACAA
1 AGTGGCCTACACATAGTACCACCCTTGTAGCCAAAGCTACCTTCTTCACAA
*
2020244 AGTGGCCTGCACATAGTACCACCCTTGTAGCCAAAGCTACCTTCTTCACA
1 AGTGGCCTACACATAGTACCACCCTTGTAGCCAAAGCTACCTTCTTCACA
2020294 TAGTACCACA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.27, C:0.34, G:0.16, T:0.24
Consensus pattern (51 bp):
AGTGGCCTACACATAGTACCACCCTTGTAGCCAAAGCTACCTTCTTCACAA
Found at i:2020294 original size:37 final size:38
Alignment explanation
Indices: 2020253--2020331 Score: 117
Period size: 37 Copynumber: 2.1 Consensus size: 38
2020243 AAGTGGCCTG
*
2020253 CACATAGTACCACCCTTGT-AGCCAAAGCTA-CCTTCTT
1 CACATAGTACCACACTTGTGA-CCAAAGCTATCCTTCTT
*
2020290 CACATAGTACCACACTTGTGACCAAAGCTATCTTTCTT
1 CACATAGTACCACACTTGTGACCAAAGCTATCCTTCTT
2020328 CACA
1 CACA
2020332 AAGTGGCCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
37 27 0.71
38 11 0.29
ACGTcount: A:0.29, C:0.33, G:0.10, T:0.28
Consensus pattern (38 bp):
CACATAGTACCACACTTGTGACCAAAGCTATCCTTCTT
Found at i:2031337 original size:12 final size:11
Alignment explanation
Indices: 2031317--2031348 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
2031307 TTATCACAAA
2031317 AAAAAAAAAAG
1 AAAAAAAAAAG
2031328 AAAAAGAAAAAG
1 AAAAA-AAAAAG
2031340 AAAAAAAAA
1 AAAAAAAAA
2031349 GGAATATCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:2034425 original size:14 final size:14
Alignment explanation
Indices: 2034406--2034435 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2034396 TTTCATGCTT
2034406 AAATCTAACTGTTA
1 AAATCTAACTGTTA
*
2034420 AAATCTAATTGTTA
1 AAATCTAACTGTTA
2034434 AA
1 AA
2034436 TTTATTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (14 bp):
AAATCTAACTGTTA
Found at i:2034436 original size:13 final size:13
Alignment explanation
Indices: 2034404--2034448 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
2034394 CTTTTCATGC
*
2034404 TTAAATCTAACTG
1 TTAAATCTAATTG
2034417 TTAAAATCTAATTG
1 TT-AAATCTAATTG
* *
2034431 TTAAATTTATTTG
1 TTAAATCTAATTG
2034444 TTAAA
1 TTAAA
2034449 ATTTAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (13 bp):
TTAAATCTAATTG
Found at i:2034450 original size:14 final size:14
Alignment explanation
Indices: 2034415--2034454 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
2034405 TAAATCTAAC
*
2034415 TGTTAAAATCTAAT
1 TGTTAAAATTTAAT
*
2034429 TGTT-AAATTTATT
1 TGTTAAAATTTAAT
2034442 TGTTAAAATTTAA
1 TGTTAAAATTTAA
2034455 AAATTTTAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (14 bp):
TGTTAAAATTTAAT
Found at i:2041473 original size:22 final size:23
Alignment explanation
Indices: 2041419--2041474 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
2041409 ACTCTTTTTG
2041419 AAATATTAATAATCAAATTTAACAA
1 AAATA-TAA-AATCAAATTTAACAA
* **
2041444 AAAAATAAAATCAAA-TTAATTA
1 AAATATAAAATCAAATTTAACAA
2041466 AAATATAAA
1 AAATATAAA
2041475 CATTAAGAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 13 0.48
23 7 0.26
24 3 0.11
25 4 0.15
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (23 bp):
AAATATAAAATCAAATTTAACAA
Found at i:2047072 original size:42 final size:42
Alignment explanation
Indices: 2047012--2047134 Score: 151
Period size: 42 Copynumber: 2.9 Consensus size: 42
2047002 CGCTTTACTT
*
2047012 AGTTTAA-TTTTTGAATTCGAAGTAAGGTTAATAGTATGTTTC
1 AGTTTAATTTTTTG-ATTCGAAGTAAGATTAATAGTATGTTTC
* **
2047054 AGTTTACTTTTTTGATTCGAAGTAAGATTCTTAGTATGTTTC
1 AGTTTAATTTTTTGATTCGAAGTAAGATTAATAGTATGTTTC
** *
2047096 AGTTTAATTTTCGGATT-GCAAGTAAGATTAATAATATGT
1 AGTTTAATTTTTTGATTCG-AAGTAAGATTAATAGTATGT
2047135 GTGATTAAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.01
42 62 0.90
43 6 0.09
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.46
Consensus pattern (42 bp):
AGTTTAATTTTTTGATTCGAAGTAAGATTAATAGTATGTTTC
Found at i:2047341 original size:42 final size:42
Alignment explanation
Indices: 2047282--2047364 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
2047272 CTTAGTTCTA
*
2047282 TTTTTGGATTCGAAGTAAGATTAATAGTATGTTTCAGTTTAC
1 TTTTTGGATTCGAAGTAAGATTAAGAGTATGTTTCAGTTTAC
* *
2047324 TTTTTGGATTCGAAGTAAGATTTAGAGTATGTTTCGGTTTA
1 TTTTTGGATTCGAAGTAAGATTAAGAGTATGTTTCAGTTTA
2047365 TATTTGATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.46
Consensus pattern (42 bp):
TTTTTGGATTCGAAGTAAGATTAAGAGTATGTTTCAGTTTAC
Found at i:2047522 original size:97 final size:98
Alignment explanation
Indices: 2047421--2047607 Score: 279
Period size: 97 Copynumber: 1.9 Consensus size: 98
2047411 TTTAGTTTAA
* * *
2047421 TTTTTGGATTTGAAGTAAGATTCATGATATGTTCTTTTGTTTGATTAAGTTATCTCGTAGCT-TT
1 TTTTTGGATTTGAAGTAAGATTCATGATATGTTCTTTTGTTTGATTAAATTACCTCATAGCTCTT
*
2047485 ACATTTCTACATTTCCTC-TTTACTTAATTTATT
66 -CATTTCCACATTTCCTCTTTTACTTAATTTATT
* *
2047518 TTTTTTGATTTGATGTAAGATTCATGATATGTTCTTTTGTTTGATTAAATTACCTCATAGCTCTT
1 TTTTTGGATTTGAAGTAAGATTCATGATATGTTCTTTTGTTTGATTAAATTACCTCATAGCTCTT
* *
2047583 CGTTTCCATATTTCCTCTTTTACTT
66 CATTTCCACATTTCCTCTTTTACTT
2047608 TGGTGTTCTT
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
97 71 0.89
98 9 0.11
ACGTcount: A:0.21, C:0.14, G:0.12, T:0.53
Consensus pattern (98 bp):
TTTTTGGATTTGAAGTAAGATTCATGATATGTTCTTTTGTTTGATTAAATTACCTCATAGCTCTT
CATTTCCACATTTCCTCTTTTACTTAATTTATT
Found at i:2054967 original size:18 final size:17
Alignment explanation
Indices: 2054941--2054975 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2054931 ACTTCACATG
2054941 TTGTATAATTATATTTTA
1 TTGTATAATTAT-TTTTA
*
2054959 TTGTTTAATTATTTTTA
1 TTGTATAATTATTTTTA
2054976 GTTGAAGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (17 bp):
TTGTATAATTATTTTTA
Found at i:2057469 original size:16 final size:16
Alignment explanation
Indices: 2057434--2057468 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2057424 CAATTCCTTA
*
2057434 TTTTAATTTTTATGAT
1 TTTTAATATTTATGAT
2057450 TTTTAATATTTAT-AT
1 TTTTAATATTTATGAT
2057465 TTTT
1 TTTT
2057469 TTATTAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTAATATTTATGAT
Found at i:2060896 original size:22 final size:22
Alignment explanation
Indices: 2060871--2060913 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2060861 AATATAAGTC
2060871 AAAAAAATAAAAATAGAAAATA
1 AAAAAAATAAAAATAGAAAATA
** *
2060893 AAAATGATAAAAATATAAAAT
1 AAAAAAATAAAAATAGAAAAT
2060914 TTATTTAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.19
Consensus pattern (22 bp):
AAAAAAATAAAAATAGAAAATA
Found at i:2067722 original size:23 final size:23
Alignment explanation
Indices: 2067678--2067724 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2067668 ATGAACAAAT
* * **
2067678 TTAATAAAATAATTTTTGCAGTA
1 TTAACAAAAGAATTTTAACAGTA
2067701 TTAACAAAAGAATTTTAACAGTA
1 TTAACAAAAGAATTTTAACAGTA
2067724 T
1 T
2067725 GAACTAGAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (23 bp):
TTAACAAAAGAATTTTAACAGTA
Found at i:2075944 original size:24 final size:25
Alignment explanation
Indices: 2075915--2075969 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
2075905 TCTTCCATTC
* *
2075915 CTCTCCTCAAAT-TCA-CTCTTCTGT
1 CTCTCCACAAATCTCATCTCTT-TGA
2075939 CTCTCCACAAATCTCATCTCTTTGA
1 CTCTCCACAAATCTCATCTCTTTGA
2075964 CTCTCC
1 CTCTCC
2075970 CATTTCTCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 11 0.41
25 11 0.41
26 5 0.19
ACGTcount: A:0.18, C:0.40, G:0.04, T:0.38
Consensus pattern (25 bp):
CTCTCCACAAATCTCATCTCTTTGA
Found at i:2089789 original size:9 final size:9
Alignment explanation
Indices: 2089775--2089805 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2089765 GTTAAACGAA
2089775 TCGAGTTAT
1 TCGAGTTAT
*
2089784 TCGAGTTAA
1 TCGAGTTAT
2089793 TCGAGTTAT
1 TCGAGTTAT
2089802 TCGA
1 TCGA
2089806 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:2089876 original size:9 final size:9
Alignment explanation
Indices: 2089859--2089895 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
2089849 TGAGTTTTCG
2089859 AATTCGAAT
1 AATTCGAAT
*
2089868 AACTCGAAT
1 AATTCGAAT
*
2089877 AATTCAAAT
1 AATTCGAAT
2089886 AATTCGAAT
1 AATTCGAAT
2089895 A
1 A
2089896 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:2099665 original size:11 final size:11
Alignment explanation
Indices: 2099651--2099696 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
2099641 TGTAGAAAAA
2099651 TAAATGATTTT
1 TAAATGATTTT
*
2099662 TAAATAATTTT
1 TAAATGATTTT
2099673 T--ATG-TTTT
1 TAAATGATTTT
*
2099681 TTAATGATTTT
1 TAAATGATTTT
2099692 TAAAT
1 TAAAT
2099697 TTAAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
8 5 0.17
9 2 0.07
10 3 0.10
11 19 0.66
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.59
Consensus pattern (11 bp):
TAAATGATTTT
Found at i:2099693 original size:10 final size:10
Alignment explanation
Indices: 2099653--2099694 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
2099643 TAGAAAAATA
2099653 AATGATTTTT
1 AATGATTTTT
*
2099663 AAATAATTTTT
1 -AATGATTTTT
*
2099674 -ATGTTTTTT
1 AATGATTTTT
2099683 AATGATTTTT
1 AATGATTTTT
2099693 AA
1 AA
2099695 ATTTAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
9 7 0.27
10 10 0.38
11 9 0.35
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (10 bp):
AATGATTTTT
Found at i:2102497 original size:27 final size:27
Alignment explanation
Indices: 2102467--2102549 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 27
2102457 TGTTGAACCC
2102467 TATTTTA-ACATTTTGT-AATTTTTATTT
1 TATTTTATA-ATTTT-TAAATTTTTATTT
2102494 TATTTTATAATTTTTACAATTTTTATTTTT
1 TATTTTATAATTTTTA-AATTTTTA--TTT
*
2102524 GTAATTTATATATTTTT-AATTTTTAT
1 -TATTTTATA-ATTTTTAAATTTTTAT
2102550 AAAATTTAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
26 1 0.02
27 12 0.25
28 10 0.21
30 11 0.23
31 8 0.17
32 6 0.12
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (27 bp):
TATTTTATAATTTTTAAATTTTTATTT
Found at i:2102508 original size:9 final size:9
Alignment explanation
Indices: 2102477--2102670 Score: 61
Period size: 9 Copynumber: 21.4 Consensus size: 9
2102467 TATTTTAACA
*
2102477 TTTTGTAAT
1 TTTTATAAT
**
2102486 TTTTATTTT
1 TTTTATAAT
2102495 ATTTTATAAT
1 -TTTTATAAT
*
2102505 TTTTACAA-
1 TTTTATAAT
2102513 TTTT-T-AT
1 TTTTATAAT
*
2102520 TTTTGTAAT
1 TTTTATAAT
*
2102529 TTATAT-A-
1 TTTTATAAT
2102536 TTTT-TAAT
1 TTTTATAAT
*
2102544 TTTTATAAA
1 TTTTATAAT
*
2102553 ATTTA-AACT
1 TTTTATAA-T
*
2102562 TTTCGAT-AT
1 TTT-TATAAT
2102571 TTTTATAATAT
1 TTTTAT-A-AT
*
2102582 TTTTAAATATT
1 TTTT--ATAAT
2102593 TTTTCATAAT
1 TTTT-ATAAT
2102603 TTTTAT-A-
1 TTTTATAAT
* *
2102610 TTTTGTACT
1 TTTTATAAT
*
2102619 TTTAATAAT
1 TTTTATAAT
2102628 TTTTA-AAT
1 TTTTATAAT
2102636 GCTTTT-TGAAT
1 --TTTTAT-AAT
2102647 TTTTAATAAT
1 TTTT-ATAAT
*
2102657 TTATATAACT
1 TTTTATAA-T
2102667 TTTT
1 TTTT
2102671 GTCATCTATA
Statistics
Matches: 134, Mismatches: 27, Indels: 47
0.64 0.13 0.23
Matches are distributed among these distances:
6 2 0.01
7 13 0.10
8 18 0.13
9 52 0.39
10 31 0.23
11 15 0.11
12 1 0.01
13 2 0.01
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:2102523 original size:15 final size:13
Alignment explanation
Indices: 2102476--2102549 Score: 53
Period size: 15 Copynumber: 5.2 Consensus size: 13
2102466 CTATTTTAAC
2102476 ATTTTGTAATTTTT
1 ATTTT-TAATTTTT
2102490 A-TTTT-ATTTTAT
1 ATTTTTAATTTT-T
2102502 AATTTTTACAATTTTT
1 -ATTTTT--AATTTTT
2102518 ATTTTTGTAATTTATAT
1 A-TTTT-TAATTT-T-T
2102535 ATTTTTAATTTTT
1 ATTTTTAATTTTT
2102548 AT
1 AT
2102550 AAAATTTAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 21
0.70 0.00 0.30
Matches are distributed among these distances:
11 5 0.10
12 2 0.04
13 7 0.14
14 6 0.12
15 12 0.24
16 10 0.20
17 8 0.16
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (13 bp):
ATTTTTAATTTTT
Found at i:2102550 original size:15 final size:15
Alignment explanation
Indices: 2102496--2102550 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
2102486 TTTTATTTTA
2102496 TTTTATAATTTTTACAAT
1 TTTTAT-ATTTTT--AAT
2102514 TTTTAT-TTTTGTAAT
1 TTTTATATTTT-TAAT
*
2102529 TTATATATTTTTAAT
1 TTTTATATTTTTAAT
2102544 TTTTATA
1 TTTTATA
2102551 AAATTTAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
15 18 0.55
16 8 0.24
17 1 0.03
18 6 0.18
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTTATATTTTTAAT
Found at i:2102583 original size:11 final size:11
Alignment explanation
Indices: 2102567--2102609 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
2102557 AAACTTTTCG
2102567 ATATTTTTATA
1 ATATTTTTATA
2102578 ATATTTTTA-A
1 ATATTTTTATA
*
2102588 ATATTTTT-TC
1 ATATTTTTATA
2102598 ATAATTTTTATA
1 AT-ATTTTTATA
2102610 TTTTGTACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 11 0.41
11 15 0.56
12 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATTTTTATA
Found at i:2102670 original size:29 final size:30
Alignment explanation
Indices: 2102637--2102700 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
2102627 TTTTTAAATG
* *
2102637 CTTTTTG-AATTTTTAATAATT-TATATAA
1 CTTTTTGTAATCTATAATAATTGTATATAA
* *
2102665 CTTTTTGTCATCTATAATAATTGTGTATAA
1 CTTTTTGTAATCTATAATAATTGTATATAA
2102695 CTTTTT
1 CTTTTT
2102701 TGTACTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 7 0.23
29 11 0.37
30 12 0.40
ACGTcount: A:0.30, C:0.08, G:0.06, T:0.56
Consensus pattern (30 bp):
CTTTTTGTAATCTATAATAATTGTATATAA
Found at i:2117613 original size:20 final size:19
Alignment explanation
Indices: 2117590--2117630 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
2117580 CAAGTTTTTT
2117590 TTTAAT-ATTCAAAGTTCTAA
1 TTTAATAATT-AAAGTTC-AA
2117610 TTTAATAATTAAAGTTCAA
1 TTTAATAATTAAAGTTCAA
2117629 TT
1 TT
2117631 CATAAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 13 0.65
21 3 0.15
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (19 bp):
TTTAATAATTAAAGTTCAA
Found at i:2118275 original size:21 final size:22
Alignment explanation
Indices: 2118233--2118276 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2118223 GGATTATGTC
* *
2118233 AATTAATTCATTTTATTATTAA
1 AATTAATTAATTTAATTATTAA
*
2118255 AATT-ATTAATTTAATTGTTAA
1 AATTAATTAATTTAATTATTAA
2118276 A
1 A
2118277 TAATATATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
AATTAATTAATTTAATTATTAA
Found at i:2120429 original size:42 final size:42
Alignment explanation
Indices: 2120362--2120496 Score: 135
Period size: 42 Copynumber: 3.2 Consensus size: 42
2120352 GGCTAAACAA
* * * * * *
2120362 AAGCACATAAGTGCTAAACAGAAACCTATAAGGGTTGAATGG
1 AAGCTCATAAGAGCTGAACGGAAACCCATAAGGGTTGAACGG
* ** *
2120404 AAGCTTATAAGAGCTGAACGGAAACCCATAAGGGTCAAACAG
1 AAGCTCATAAGAGCTGAACGGAAACCCATAAGGGTTGAACGG
* * * *
2120446 AAGCTCAAAAGAGCAGAACGAAAACCCATATGGGTTGAACGG
1 AAGCTCATAAGAGCTGAACGGAAACCCATAAGGGTTGAACGG
*
2120488 AAACTCATA
1 AAGCTCATA
2120497 TGAGTTAAAC
Statistics
Matches: 73, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.16
Consensus pattern (42 bp):
AAGCTCATAAGAGCTGAACGGAAACCCATAAGGGTTGAACGG
Found at i:2126062 original size:24 final size:24
Alignment explanation
Indices: 2126037--2126082 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
2126027 AAAATATTTA
2126037 AAAAATA-ATAATTTTTTAAAAAT
1 AAAAATACATAATTTTTTAAAAAT
2126060 AAAAATACTATAATTTTTTAAAA
1 AAAAATAC-ATAATTTTTTAAAA
2126083 GAAATTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 7 0.33
25 14 0.67
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
AAAAATACATAATTTTTTAAAAAT
Found at i:2128856 original size:31 final size:31
Alignment explanation
Indices: 2128818--2128879 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
2128808 ACAGAATTCA
2128818 GATGATGTTCTCGTTTGTTTCTTTTGAAAAT
1 GATGATGTTCTCGTTTGTTTCTTTTGAAAAT
2128849 GATGATGTTCTCGTTTGTTTCTTTTGAAAAT
1 GATGATGTTCTCGTTTGTTTCTTTTGAAAAT
2128880 AGACTCATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (31 bp):
GATGATGTTCTCGTTTGTTTCTTTTGAAAAT
Found at i:2135462 original size:16 final size:16
Alignment explanation
Indices: 2135441--2135481 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2135431 CATATAATCT
2135441 TTATATAATAATTTTA
1 TTATATAATAATTTTA
**
2135457 TTATATTTTAATTTTA
1 TTATATAATAATTTTA
2135473 TTATA-AATA
1 TTATATAATA
2135482 TATATTTCCT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATATAATAATTTTA
Found at i:2140727 original size:11 final size:11
Alignment explanation
Indices: 2140711--2140735 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2140701 TGATAGAGGG
2140711 ACATTCCCTAT
1 ACATTCCCTAT
2140722 ACATTCCCTAT
1 ACATTCCCTAT
2140733 ACA
1 ACA
2140736 GTTCATGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (11 bp):
ACATTCCCTAT
Done.