Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 147 of 208
Found at i:44883871 original size:22 final size:22
Alignment explanation
Indices: 44883846--44883890 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
44883836 AAAATAAATC
* *
44883846 AAAATTTATGAAAAATTATTAT
1 AAAATTAATGAAAAATTAATAT
*
44883868 AAAATTAATGAAAATTTAATAT
1 AAAATTAATGAAAAATTAATAT
44883890 A
1 A
44883891 TTAATAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
AAAATTAATGAAAAATTAATAT
Found at i:44890882 original size:17 final size:18
Alignment explanation
Indices: 44890857--44890893 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
44890847 TATAAAATAT
*
44890857 AATATAAAGAA-AATAAA
1 AATAAAAAGAAGAATAAA
44890874 AATAAAAAGAAGAATAAA
1 AATAAAAAGAAGAATAAA
44890892 AA
1 AA
44890894 AGAAGTGCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (18 bp):
AATAAAAAGAAGAATAAA
Found at i:44891614 original size:41 final size:42
Alignment explanation
Indices: 44891526--44891614 Score: 112
Period size: 42 Copynumber: 2.1 Consensus size: 42
44891516 TTGTCCTCAC
* *
44891526 CCGTGTAACTTACTGAGTAGCCTCATATGCCCGTGTGTCAGG
1 CCGTGTAACTCACTGAGTAGCCTCACATGCCCGTGTGTCAGG
*
44891568 CCGTGTAACTCACTGAGTAGCAC-CACATG-TCGTGTG-CTAGG
1 CCGTGTAACTCACTGAGTAGC-CTCACATGCCCGTGTGTC-AGG
44891609 CCGTGT
1 CCGTGT
44891615 GCTAGGCTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
40 1 0.02
41 15 0.36
42 25 0.60
43 1 0.02
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (42 bp):
CCGTGTAACTCACTGAGTAGCCTCACATGCCCGTGTGTCAGG
Found at i:44892971 original size:17 final size:18
Alignment explanation
Indices: 44892949--44892990 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
44892939 TCCCTCATCT
44892949 TTTCTTTTCT-TTTCTTC
1 TTTCTTTTCTATTTCTTC
*
44892966 TTTCTTTTCTATTTTTTC
1 TTTCTTTTCTATTTCTTC
44892984 TTCTCTT
1 TT-TCTT
44892991 GTTGCTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.45
18 8 0.36
19 4 0.18
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTCTTTTCTATTTCTTC
Found at i:44893944 original size:27 final size:27
Alignment explanation
Indices: 44893906--44894208 Score: 357
Period size: 27 Copynumber: 11.3 Consensus size: 27
44893896 TGCGTATCGT
44893906 GGGTAAAATTATCAAAATACCCTCGAA
1 GGGTAAAATTATCAAAATACCCTCGAA
44893933 GGGTAAAATTAT-AAAATACCCTCGAA
1 GGGTAAAATTATCAAAATACCCTCGAA
44893959 GGGTAAAATTAT-AAAATACCCTCGAA
1 GGGTAAAATTATCAAAATACCCTCGAA
**
44893985 GGGTAAAATTATTGAAATACCCTCGAA
1 GGGTAAAATTATCAAAATACCCTCGAA
* ** * * *
44894012 AGGTAAAATTATTGAATTAACCTCAAA
1 GGGTAAAATTATCAAAATACCCTCGAA
* *
44894039 GGGTAAAATTATCGAAATACCCTCAAA
1 GGGTAAAATTATCAAAATACCCTCGAA
* * *
44894066 GTGTAAAATTA-CTGAAATACCC-CTAA
1 GGGTAAAATTATC-AAAATACCCTCGAA
** *
44894092 AAGTTAAATTATCAAAATACCCTCGAA
1 GGGTAAAATTATCAAAATACCCTCGAA
* *
44894119 GGGTAAAATTA-CATAAATACCCCCAAA
1 GGGTAAAATTATCA-AAATACCCTCGAA
*
44894146 GGGTAAAATTATCGAAATACCCTCGAA
1 GGGTAAAATTATCAAAATACCCTCGAA
*
44894173 GGGTAAAATTA-CTAAAATACCCCCGAA
1 GGGTAAAATTATC-AAAATACCCTCGAA
44894200 GGGTAAAAT
1 GGGTAAAAT
44894209 GACCGTTATA
Statistics
Matches: 243, Mismatches: 26, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
26 75 0.31
27 167 0.69
28 1 0.00
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (27 bp):
GGGTAAAATTATCAAAATACCCTCGAA
Found at i:44894102 original size:107 final size:106
Alignment explanation
Indices: 44893907--44894195 Score: 375
Period size: 107 Copynumber: 2.7 Consensus size: 106
44893897 GCGTATCGTG
* * *
44893907 GGTAAAATTATCAAAATACCCTCGAAGGGTAAAATTAT-AAAATACCCTCGAAGGGTAAAATTA-
1 GGTAAAATTAT-TAAATACCCTCAAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTAC
** **
44893970 TAAAATACCCTCGAAGGGTAAAATTATTGAAATACCCTCGAAA
65 TAAAATACCC-CGAAAAGTAAAATTATCAAAATACCCTCGAAA
* * * *
44894013 GGTAAAATTATTGAATTAACCTCAAAGGGTAAAATTATCGAAATACCCTCAAAGTGTAAAATTAC
1 GGTAAAATTATT-AAATACCCTCAAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTAC
* * * *
44894078 TGAAATACCCCTAAAAGTTAAATTATCAAAATACCCTCGAAG
65 TAAAATACCCCGAAAAGTAAAATTATCAAAATACCCTCGAAA
* *
44894120 GGTAAAATTACATAAATACCCCCAAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTAC
1 GGTAAAATTA-TTAAATACCCTCAAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTAC
44894185 TAAAATACCCC
65 TAAAATACCCC
44894196 CGAAGGGTAA
Statistics
Matches: 157, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
106 33 0.21
107 114 0.73
108 10 0.06
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (106 bp):
GGTAAAATTATTAAATACCCTCAAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACT
AAAATACCCCGAAAAGTAAAATTATCAAAATACCCTCGAAA
Found at i:44895335 original size:40 final size:39
Alignment explanation
Indices: 44895284--44895660 Score: 371
Period size: 40 Copynumber: 9.4 Consensus size: 39
44895274 AGTATAAATA
44895284 GGGCACGTATGTG-AGTTCAGGGGTGTCGAAGTACAAACAG
1 GGGCACGTATGTGCA-TTCAGGGGT-TCGAAGTACAAACAG
* * * *
44895324 GGGCACGTATGTGCATTCAGGGGTACCAAACTACAAATAG
1 GGGCACGTATGTGCATTCAGGGGT-TCGAAGTACAAACAG
* * * * * *
44895364 GGGAACATATGTGCATTCAGTGGTACCGAAGTACAAATAA
1 GGGCACGTATGTGCATTCAGGGGT-TCGAAGTACAAACAG
* * *
44895404 GGTCACGTATGTGCATTCAAGGGTACTGAAGTACAAACAG
1 GGGCACGTATGTGCATTCAGGGGTTC-GAAGTACAAACAG
* * *
44895444 GGGTACGTATGTGTATTCA-GGGTTACTGAATTACAAACAG
1 GGGCACGTATGTGCATTCAGGGGTT-C-GAAGTACAAACAG
* * * *
44895484 GGGCACGTATGTGTATTCAGAGGTACTGAAGTACAAATAG
1 GGGCACGTATGTGCATTCAGGGGTTC-GAAGTACAAACAG
* * * *
44895524 GGGCACATATGTGCATTCAGGGGTACTAAAGTACAAACAA
1 GGGCACGTATGTGCATTCAGGGGTTC-GAAGTACAAACAG
* *
44895564 GGGCACGTATGTGCATTCAGGGGTATCAAAGTACAAATAG
1 GGGCACGTATGTGCATTCAGGGGT-TCGAAGTACAAACAG
* *
44895604 GGGCACGTATGTGTATTCAGGGGTATCGAAGTACAAACAT
1 GGGCACGTATGTGCATTCAGGGGT-TCGAAGTACAAACAG
* *
44895644 GGGCATGTTTGTGCATT
1 GGGCACGTATGTGCATT
44895661 TAGCAATAAT
Statistics
Matches: 286, Mismatches: 46, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
39 5 0.02
40 276 0.97
41 5 0.02
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (39 bp):
GGGCACGTATGTGCATTCAGGGGTTCGAAGTACAAACAG
Found at i:44895394 original size:80 final size:80
Alignment explanation
Indices: 44895259--44895660 Score: 457
Period size: 80 Copynumber: 5.0 Consensus size: 80
44895249 GTACTATTTG
* * * * **
44895259 ATTCAGGGTTACAAAAGTATAAATA-GGGCACGTATGTG-AGTTCAGGGGTGTCGAAGTACAAAC
1 ATTCAGGGGTACCAAAGTACAAATAGGGGCACATATGTGCA-TTCAGGGGTACCGAAGTACAAAC
*
44895322 AGGGGCACGTATGTGC
65 AAGGGCACGTATGTGC
* * * *
44895338 ATTCAGGGGTACCAAACTACAAATAGGGGAACATATGTGCATTCAGTGGTACCGAAGTACAAATA
1 ATTCAGGGGTACCAAAGTACAAATAGGGGCACATATGTGCATTCAGGGGTACCGAAGTACAAACA
*
44895403 AGGTCACGTATGTGC
66 AGGGCACGTATGTGC
* ** * * * * * * *
44895418 ATTCAAGGGTACTGAAGTACAAACAGGGGTACGTATGTGTATTCAGGGTTACTGAATTACAAACA
1 ATTCAGGGGTACCAAAGTACAAATAGGGGCACATATGTGCATTCAGGGGTACCGAAGTACAAACA
* *
44895483 GGGGCACGTATGTGT
66 AGGGCACGTATGTGC
* ** **
44895498 ATTCAGAGGTACTGAAGTACAAATAGGGGCACATATGTGCATTCAGGGGTACTAAAGTACAAACA
1 ATTCAGGGGTACCAAAGTACAAATAGGGGCACATATGTGCATTCAGGGGTACCGAAGTACAAACA
44895563 AGGGCACGTATGTGC
66 AGGGCACGTATGTGC
* * * *
44895578 ATTCAGGGGTATCAAAGTACAAATAGGGGCACGTATGTGTATTCAGGGGTATCGAAGTACAAACA
1 ATTCAGGGGTACCAAAGTACAAATAGGGGCACATATGTGCATTCAGGGGTACCGAAGTACAAACA
* * *
44895643 TGGGCATGTTTGTGC
66 AGGGCACGTATGTGC
44895658 ATT
1 ATT
44895661 TAGCAATAAT
Statistics
Matches: 270, Mismatches: 51, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
79 21 0.08
80 248 0.92
81 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (80 bp):
ATTCAGGGGTACCAAAGTACAAATAGGGGCACATATGTGCATTCAGGGGTACCGAAGTACAAACA
AGGGCACGTATGTGC
Found at i:44895479 original size:120 final size:120
Alignment explanation
Indices: 44895273--44895660 Score: 478
Period size: 120 Copynumber: 3.2 Consensus size: 120
44895263 AGGGTTACAA
* *
44895273 AAGTATAAAT-AGGGCACGTATGTG-AGTTCAGGGGT-GTCGAAGTACAAACAGGGGCACGTATG
1 AAGTACAAATAAGGGCACGTATGTGCA-TTCAGGGGTACT-GAAGTACAAACAGGGGCACGTATG
* * * * *
44895335 TGCATTCAGGGGTACCAAACTACAAATAGGGGAACATATGTGCATTCAGTGGTACCG
64 TGCATTCAGGGGTACTAAACTACAAATAGGGGCACGTATGTGTATTCAGAGGTACCG
* * *
44895392 AAGTACAAATAAGGTCACGTATGTGCATTCAAGGGTACTGAAGTACAAACAGGGGTACGTATGTG
1 AAGTACAAATAAGGGCACGTATGTGCATTCAGGGGTACTGAAGTACAAACAGGGGCACGTATGTG
* * * * * *
44895457 TATTCAGGGTTACTGAATTACAAACAGGGGCACGTATGTGTATTCAGAGGTACTG
66 CATTCAGGGGTACTAAACTACAAATAGGGGCACGTATGTGTATTCAGAGGTACCG
* * * *
44895512 AAGTACAAATAGGGGCACATATGTGCATTCAGGGGTACTAAAGTACAAACAAGGGCACGTATGTG
1 AAGTACAAATAAGGGCACGTATGTGCATTCAGGGGTACTGAAGTACAAACAGGGGCACGTATGTG
* * *
44895577 CATTCAGGGGTA-TCAAAGTACAAATAGGGGCACGTATGTGTATTCAGGGGTATCG
66 CATTCAGGGGTACT-AAACTACAAATAGGGGCACGTATGTGTATTCAGAGGTACCG
* * * *
44895632 AAGTACAAACATGGGCATGTTTGTGCATT
1 AAGTACAAATAAGGGCACGTATGTGCATT
44895661 TAGCAATAAT
Statistics
Matches: 229, Mismatches: 36, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
119 10 0.04
120 217 0.95
121 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (120 bp):
AAGTACAAATAAGGGCACGTATGTGCATTCAGGGGTACTGAAGTACAAACAGGGGCACGTATGTG
CATTCAGGGGTACTAAACTACAAATAGGGGCACGTATGTGTATTCAGAGGTACCG
Found at i:44896451 original size:28 final size:28
Alignment explanation
Indices: 44896392--44896452 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
44896382 TACATTACTG
* *
44896392 TGTGGGCCTTAGCCTAATACAGAATCAG
1 TGTGGGCCTTAGCCCAATACAGAATCAA
44896420 TGTGGGCCTTAGCCCAATACAGTAA-CAA
1 TGTGGGCCTTAGCCCAATACAG-AATCAA
44896448 TGTGG
1 TGTGG
44896453 CAAATGGGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 28 0.93
29 2 0.07
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (28 bp):
TGTGGGCCTTAGCCCAATACAGAATCAA
Found at i:44896848 original size:32 final size:32
Alignment explanation
Indices: 44896812--44896919 Score: 128
Period size: 32 Copynumber: 3.4 Consensus size: 32
44896802 CCACCAATAG
* *
44896812 TAGTAATATGATCGACACACATCGATCAGTAA
1 TAGTAATATGATCGACACACAGCCATCAGTAA
* * *
44896844 TAGTAGTATGATC-AGCACAAAGCCATCAGTAG
1 TAGTAATATGATCGA-CACACAGCCATCAGTAA
* *
44896876 TAGTAATATGATCGGCACACAGCCATCGGTAA
1 TAGTAATATGATCGACACACAGCCATCAGTAA
*
44896908 TGGTAATATGAT
1 TAGTAATATGAT
44896920 AGGTAAAAAG
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
31 1 0.02
32 62 0.98
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (32 bp):
TAGTAATATGATCGACACACAGCCATCAGTAA
Found at i:44896930 original size:64 final size:64
Alignment explanation
Indices: 44896781--44896939 Score: 194
Period size: 64 Copynumber: 2.5 Consensus size: 64
44896771 CCATAAGTAC
* * * * *
44896781 AGTAATATGATTGGCAGAAAGCCACCAATAGTAGTAATATGATCGACACACATCGATCAGTAAT
1 AGTAATATGATAGGCAAAAAGCCATCAATAGTAGTAATATGATCGACACACAGCCATCAGTAAT
* * * * *
44896845 AGTAGTATGATCA-GCACAAAGCCATCAGTAGTAGTAATATGATCGGCACACAGCCATCGGTAAT
1 AGTAATATGAT-AGGCAAAAAGCCATCAATAGTAGTAATATGATCGACACACAGCCATCAGTAAT
* *
44896909 GGTAATATGATAGGTAAAAAGCCATCAATAG
1 AGTAATATGATAGGCAAAAAGCCATCAATAG
44896940 CATCACTGCA
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
63 1 0.01
64 78 0.99
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (64 bp):
AGTAATATGATAGGCAAAAAGCCATCAATAGTAGTAATATGATCGACACACAGCCATCAGTAAT
Found at i:44896932 original size:32 final size:32
Alignment explanation
Indices: 44896768--44896935 Score: 115
Period size: 32 Copynumber: 5.3 Consensus size: 32
44896758 GAATGACTAC
* * * *
44896768 AAGCCATAAGT-ACAGTAATATGATTGGCAGA
1 AAGCCATCAGTAATAGTAATATGATAGGCAAA
* * * * * *
44896799 AAGCCACCAATAGTAGTAATATGATCGACACA
1 AAGCCATCAGTAATAGTAATATGATAGGCAAA
* * * * *
44896831 CATCGATCAGTAATAGTAGTATGATCA-GCACA
1 AAGCCATCAGTAATAGTAATATGAT-AGGCAAA
* * *
44896863 AAGCCATCAGTAGTAGTAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATAGGCAAA
* * * *
44896895 CAGCCATCGGTAATGGTAATATGATAGGTAAA
1 AAGCCATCAGTAATAGTAATATGATAGGCAAA
44896927 AAGCCATCA
1 AAGCCATCA
44896936 ATAGCATCAC
Statistics
Matches: 102, Mismatches: 32, Indels: 5
0.73 0.23 0.04
Matches are distributed among these distances:
31 8 0.08
32 94 0.92
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (32 bp):
AAGCCATCAGTAATAGTAATATGATAGGCAAA
Found at i:44896991 original size:27 final size:27
Alignment explanation
Indices: 44896956--44897016 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
44896946 TGCAAAACTG
*
44896956 CCAGCAACAGT-ATATGTGGCCA-AGCCA
1 CCAGAAACAGTGAT-TGTGG-CAGAGCCA
44896983 CCAGAAACAGTGATTGTGGCAGAGCCA
1 CCAGAAACAGTGATTGTGGCAGAGCCA
44897010 CCAGAAA
1 CCAGAAA
44897017 ACTACTTCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 2 0.06
27 27 0.87
28 2 0.06
ACGTcount: A:0.36, C:0.26, G:0.25, T:0.13
Consensus pattern (27 bp):
CCAGAAACAGTGATTGTGGCAGAGCCA
Found at i:44897123 original size:24 final size:24
Alignment explanation
Indices: 44897096--44897217 Score: 163
Period size: 24 Copynumber: 5.1 Consensus size: 24
44897086 TCAGTCATAC
*
44897096 AAATCACAGACAAATCAACCATTT
1 AAATCACAGACAAATCAATCATTT
* * *
44897120 AAATTACAGGCAAATCAGTCATTT
1 AAATCACAGACAAATCAATCATTT
*
44897144 AAATCATAGACAAATCAATCATTT
1 AAATCACAGACAAATCAATCATTT
* * *
44897168 ACATCTCGGACAAATCAATCATTT
1 AAATCACAGACAAATCAATCATTT
*
44897192 ACATCACAGACAAATCAATCATTT
1 AAATCACAGACAAATCAATCATTT
44897216 AA
1 AA
44897218 CCCTGATGGG
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 83 1.00
ACGTcount: A:0.46, C:0.21, G:0.07, T:0.26
Consensus pattern (24 bp):
AAATCACAGACAAATCAATCATTT
Found at i:44897268 original size:27 final size:27
Alignment explanation
Indices: 44897238--44897368 Score: 163
Period size: 27 Copynumber: 4.9 Consensus size: 27
44897228 TAAAATAGTT
*
44897238 ATTTTACCCTACAGGGGCATTACGGTC
1 ATTTTACCCTACAGGAGCATTACGGTC
* ** *
44897265 ATTTTACCCTACAGAAGCATTATAGTT
1 ATTTTACCCTACAGGAGCATTACGGTC
* *
44897292 ATTTTATCCTACACGAGCATTACGGTC
1 ATTTTACCCTACAGGAGCATTACGGTC
* *
44897319 ATTTTATCCTACAGGGGCATTACGGTC
1 ATTTTACCCTACAGGAGCATTACGGTC
* *
44897346 ATTTTACCCTACAAGAGCCTTAC
1 ATTTTACCCTACAGGAGCATTAC
44897369 AATCTTTTCG
Statistics
Matches: 87, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 87 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (27 bp):
ATTTTACCCTACAGGAGCATTACGGTC
Found at i:44900693 original size:16 final size:16
Alignment explanation
Indices: 44900674--44900707 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
44900664 ATAATAAAAT
*
44900674 AACAAAAATAATGAGA
1 AACAAAAATAAAGAGA
*
44900690 AACAATAATAAAGAGA
1 AACAAAAATAAAGAGA
44900706 AA
1 AA
44900708 TTAATAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.06, G:0.12, T:0.12
Consensus pattern (16 bp):
AACAAAAATAAAGAGA
Found at i:44904363 original size:50 final size:50
Alignment explanation
Indices: 44904276--44904426 Score: 115
Period size: 50 Copynumber: 3.0 Consensus size: 50
44904266 TCATCCATCC
* * * * * *
44904276 ATAACACCATTTGTGGACAAGCCACTATTGATTTGCAGATAAACTGTCGCTG
1 ATAACA-C-TTTGTGGACAAACCACCACTGATATGCAGATAAACTGCCACTG
* * **
44904328 ATAACACTTTGTGGACAAACCTCCACTGATATGCAGTTATGCTGCCACTG
1 ATAACACTTTGTGGACAAACCACCACTGATATGCAGATAAACTGCCACTG
* * * * * * *
44904378 ATAACATTTTATGGACAAGCTACGA-TAGATATGTAGATATACTGCCACT
1 ATAACACTTTGTGGACAAACCACCACT-GATATGCAGATAAACTGCCACT
44904427 TACTTCCACT
Statistics
Matches: 79, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
49 1 0.01
50 71 0.90
51 1 0.01
52 6 0.08
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (50 bp):
ATAACACTTTGTGGACAAACCACCACTGATATGCAGATAAACTGCCACTG
Found at i:44905200 original size:29 final size:29
Alignment explanation
Indices: 44905167--44905224 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
44905157 AACATAATTC
44905167 TTTTGGTCCCTATGACATTCGGTCAAGGG
1 TTTTGGTCCCTATGACATTCGGTCAAGGG
44905196 TTTTGGTCCCTATGACATTCGGTCAAGGG
1 TTTTGGTCCCTATGACATTCGGTCAAGGG
44905225 AGAAAAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.17, C:0.21, G:0.28, T:0.34
Consensus pattern (29 bp):
TTTTGGTCCCTATGACATTCGGTCAAGGG
Found at i:44910331 original size:21 final size:20
Alignment explanation
Indices: 44910307--44910345 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
44910297 ACTGTGGGAA
*
44910307 GAGAACATAAAAGGTGGATGT
1 GAGAACA-AAAAGGGGGATGT
*
44910328 GAGAAGAAAAAGGGGGAT
1 GAGAACAAAAAGGGGGAT
44910346 TTTTTCTGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.46, C:0.03, G:0.38, T:0.13
Consensus pattern (20 bp):
GAGAACAAAAAGGGGGATGT
Found at i:44911548 original size:17 final size:17
Alignment explanation
Indices: 44911526--44911578 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
44911516 TTAAAAAAAT
44911526 CATATCTTCAAAGATTA
1 CATATCTTCAAAGATTA
**
44911543 CATATCATATCAAAGATCG
1 CATATC-T-TCAAAGATTA
*
44911562 CATATCCTCAAAGATTA
1 CATATCTTCAAAGATTA
44911579 TGTTTCCATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 14 0.48
18 1 0.03
19 14 0.48
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.30
Consensus pattern (17 bp):
CATATCTTCAAAGATTA
Found at i:44924300 original size:72 final size:72
Alignment explanation
Indices: 44924183--44924328 Score: 229
Period size: 72 Copynumber: 2.0 Consensus size: 72
44924173 TGTTGTTGTA
* * *
44924183 TGTTGTTAACTTCCGGTAATGCTCCGTAGCCATAATCTAGAGACGGGTACAGGCTAGAGGTGTTA
1 TGTTGTTAACTTCCGGTAATGCTCCATAGCCATAATCTAGAGACGGATACAGGATAGAGGTGTTA
44924248 CATTTAG
66 CATTTAG
* * *
44924255 TGTTGTTAACTTCTGGTAATGCTCCATAGTCATAATTTAGAGACGGATACAGGATAGAGGTGTTA
1 TGTTGTTAACTTCCGGTAATGCTCCATAGCCATAATCTAGAGACGGATACAGGATAGAGGTGTTA
*
44924320 GATTTAG
66 CATTTAG
44924327 TG
1 TG
44924329 GTATTAGAGC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (72 bp):
TGTTGTTAACTTCCGGTAATGCTCCATAGCCATAATCTAGAGACGGATACAGGATAGAGGTGTTA
CATTTAG
Found at i:44929815 original size:25 final size:25
Alignment explanation
Indices: 44929787--44929840 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
44929777 TGTAGTGGAA
44929787 AGGTGGCAACACAGGTGTGGCAAGG
1 AGGTGGCAACACAGGTGTGGCAAGG
** *
44929812 AGGTGGCGTCACAGGTGTGGTAAGG
1 AGGTGGCAACACAGGTGTGGCAAGG
44929837 AGGT
1 AGGT
44929841 CAGAGGTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.13, G:0.46, T:0.17
Consensus pattern (25 bp):
AGGTGGCAACACAGGTGTGGCAAGG
Found at i:44929995 original size:24 final size:21
Alignment explanation
Indices: 44929956--44930002 Score: 51
Period size: 24 Copynumber: 2.1 Consensus size: 21
44929946 TCAAATGAGT
44929956 GATTTAAGGAATGGATCATGGAG
1 GATTTAAGGAATGGAT--TGGAG
44929979 GATTTCAAGGAGA-GGATTGGAG
1 GATTT-AAGGA-ATGGATTGGAG
44930001 GA
1 GA
44930003 GTGATTTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
22 7 0.32
23 5 0.23
24 9 0.41
25 1 0.05
ACGTcount: A:0.34, C:0.04, G:0.38, T:0.23
Consensus pattern (21 bp):
GATTTAAGGAATGGATTGGAG
Found at i:44931334 original size:27 final size:27
Alignment explanation
Indices: 44931304--44931407 Score: 138
Period size: 27 Copynumber: 3.9 Consensus size: 27
44931294 TTAAATGACC
* *
44931304 GAATTACCTTTGGAGGGTAAAATGATT
1 GAATTACCCTTGAAGGGTAAAATGATT
* *
44931331 GAATTACCCGTGAAGGGTAAAATGATC
1 GAATTACCCTTGAAGGGTAAAATGATT
44931358 GAATTACTCC-TGAAGGGTAAAATGATT
1 GAATTAC-CCTTGAAGGGTAAAATGATT
* *
44931385 GAAATACCCTCGAAGGGTAAAAT
1 GAATTACCCTTGAAGGGTAAAAT
44931408 TATCAAAATA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 2 0.03
27 64 0.94
28 2 0.03
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (27 bp):
GAATTACCCTTGAAGGGTAAAATGATT
Found at i:44931416 original size:27 final size:27
Alignment explanation
Indices: 44931317--44931449 Score: 108
Period size: 27 Copynumber: 4.9 Consensus size: 27
44931307 TTACCTTTGG
** *
44931317 AGGGTAAAATGATTGAATTACCCGT-GA
1 AGGGTAAAATGATCAAAATACCC-TCGA
* *
44931344 AGGGTAAAATGATCGAATTACTCCT-GA
1 AGGGTAAAATGATCAAAATAC-CCTCGA
**
44931371 AGGGTAAAATGATTGAAATACCCTCGA
1 AGGGTAAAATGATCAAAATACCCTCGA
* * *
44931398 AGGGTAAAATTATCAAAATAGCCTCAA
1 AGGGTAAAATGATCAAAATACCCTCGA
* * *
44931425 ATGGTAAAATAACCAAAATAACCCT
1 AGGGTAAAATGATCAAAAT-ACCCT
44931450 ATAGGATAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
26 3 0.03
27 82 0.90
28 6 0.07
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (27 bp):
AGGGTAAAATGATCAAAATACCCTCGA
Found at i:44931431 original size:54 final size:54
Alignment explanation
Indices: 44931317--44931434 Score: 141
Period size: 54 Copynumber: 2.2 Consensus size: 54
44931307 TTACCTTTGG
* * * * *
44931317 AGGGTAAAATGATTGAATTACCCGTGAAGGGTAAAATGATCGAATTACTCCTGA
1 AGGGTAAAATGATTGAAATACCCGTGAAGGGTAAAATGATCAAAATACGCCTAA
*
44931371 AGGGTAAAATGATTGAAATACCC-TCGAAGGGTAAAATTATCAAAATA-GCCTCAA
1 AGGGTAAAATGATTGAAATACCCGT-GAAGGGTAAAATGATCAAAATACGCCT-AA
*
44931425 ATGGTAAAAT
1 AGGGTAAAAT
44931435 AACCAAAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
53 4 0.07
54 51 0.93
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.25
Consensus pattern (54 bp):
AGGGTAAAATGATTGAAATACCCGTGAAGGGTAAAATGATCAAAATACGCCTAA
Found at i:44938205 original size:23 final size:23
Alignment explanation
Indices: 44938175--44938228 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
44938165 TAAAAACATA
***
44938175 TCCTAGTTATGGGTGGTACGAGT
1 TCCTAGTTATGGGCACTACGAGT
44938198 TCCTAGTTATGGGCACTACGAGT
1 TCCTAGTTATGGGCACTACGAGT
*
44938221 TCTTAGTT
1 TCCTAGTT
44938229 CTGCTAAGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.37
Consensus pattern (23 bp):
TCCTAGTTATGGGCACTACGAGT
Found at i:44974613 original size:50 final size:50
Alignment explanation
Indices: 44974538--44974729 Score: 294
Period size: 50 Copynumber: 3.8 Consensus size: 50
44974528 GATAATAACA
* * *
44974538 TGCCAAAGCCATGTCCCAGACATGGTTTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * **
44974588 TGCCAATGCCATGTCCCAAACATGGTTTTATGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
*
44974638 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
44974688 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
44974730 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 133 1.00
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:44977556 original size:18 final size:19
Alignment explanation
Indices: 44977533--44977568 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
44977523 CTATAGAATA
44977533 AAATTG-CATATAAAAAAT
1 AAATTGTCATATAAAAAAT
44977551 AAATTGTCATATAAAAAA
1 AAATTGTCATATAAAAAA
44977569 AGGGTACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (19 bp):
AAATTGTCATATAAAAAAT
Found at i:44977588 original size:3 final size:3
Alignment explanation
Indices: 44977582--44977622 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
44977572 GTACTTACGC
* *
44977582 TAA TAA TAA TAG TAA TAG TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
44977623 TATTTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:44979192 original size:44 final size:44
Alignment explanation
Indices: 44979141--44979252 Score: 145
Period size: 44 Copynumber: 2.5 Consensus size: 44
44979131 TTTGATCCGC
* **
44979141 TCCACTGCAACTTTAGGGAGATAGGATTGATTTCTTCTGTCT-T
1 TCCACTGCAACTTCAGGGAGATAACATTGATTTCTTCTGTCTGT
* * *
44979184 CTCTACTGCAACTTCAGGGAGATAACATTGGTTTCTTTTGTCTGT
1 -TCCACTGCAACTTCAGGGAGATAACATTGATTTCTTCTGTCTGT
*
44979229 TCCATTGCAACTTCAGGGAGATAA
1 TCCACTGCAACTTCAGGGAGATAA
44979253 GACTGCTATC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
44 58 0.98
45 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.37
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGAGATAACATTGATTTCTTCTGTCTGT
Found at i:44979328 original size:45 final size:45
Alignment explanation
Indices: 44979266--44979813 Score: 706
Period size: 45 Copynumber: 12.1 Consensus size: 45
44979256 TGCTATCCTT
* *
44979266 GATCTACTTCGCTACCAATACAGGAAGACATGATCTGTTATCTTT
1 GATCTACTTCGCTACCAATACAGGAAGACAAGATCTGTTATCTTC
* * * *
44979311 GATCTACTTCACTACCAATACAAGAAGACAAGAT-TTTCTATCTTT
1 GATCTACTTCGCTACCAATACAGGAAGACAAGATCTGT-TATCTTC
* *
44979356 GATCTACTTC-CTTGCCCATACAGGAAGACAAGATCTGTTATCTTC
1 GATCTACTTCGC-TACCAATACAGGAAGACAAGATCTGTTATCTTC
* *
44979401 GATCTACTTCGCTGCCAATACAAGAAGACAAGATCTGTTATCTTC
1 GATCTACTTCGCTACCAATACAGGAAGACAAGATCTGTTATCTTC
* *
44979446 GATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCTTC
1 GATCTACTTCGCTACCAATACAGGAAGACAAGATCTGTTATCTTC
* * * *
44979491 GATATACTTCGTTGCCAATACAGGAAGACAAGATCTATTATCTTC
1 GATCTACTTCGCTACCAATACAGGAAGACAAGATCTGTTATCTTC
* * * *
44979536 GATATACTTCGTTGCCAATATAGGAAGACAAGATCTGTTATCTTC
1 GATCTACTTCGCTACCAATACAGGAAGACAAGATCTGTTATCTTC
*
44979581 GATCTACTTCGCTACCAATATAGGAAGGGAAGACAAGATCTGTTATCTTC
1 GATCTACTTCGCTACC-A-ATA--CA-GGAAGACAAGATCTGTTATCTTC
* *
44979631 GATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCATT-
1 GATCTACTTCGCTACCAATACAGGAAGACAAGATCTGTTATC-TTC
* *
44979676 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCCGTTATCTTC
1 GATCTACTTCGCTACCAATACAGGAAGACAAGATCTGTTATCTTC
* * ** *
44979721 GATCTACTTCGCTACCAATATAGGAAAACAAGATCTACTATCTTT
1 GATCTACTTCGCTACCAATACAGGAAGACAAGATCTGTTATCTTC
* * *
44979766 GATCTACTTCGCTGCCAAGATAGGAAGACAAGATCTGTTATCTTC
1 GATCTACTTCGCTACCAATACAGGAAGACAAGATCTGTTATCTTC
44979811 GAT
1 GAT
44979814 ATGTTCTCTG
Statistics
Matches: 446, Mismatches: 46, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
44 5 0.01
45 387 0.87
46 7 0.02
47 3 0.01
48 3 0.01
49 2 0.00
50 39 0.09
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30
Consensus pattern (45 bp):
GATCTACTTCGCTACCAATACAGGAAGACAAGATCTGTTATCTTC
Found at i:44980937 original size:42 final size:42
Alignment explanation
Indices: 44980875--44980955 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 42
44980865 AGTATAGCAA
44980875 GACCACTGCATGCCCCATTCTGATCAATATTTGAACTGCCCT
1 GACCACTGCATGCCCCATTCTGATCAATATTTGAACTGCCCT
* *
44980917 GACCATCT-CATGCCCTATTCTGATCAATATTTGAGCTGC
1 GACCA-CTGCATGCCCCATTCTGATCAATATTTGAACTGC
44980956 TCTTTTTGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 34 0.94
43 2 0.06
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (42 bp):
GACCACTGCATGCCCCATTCTGATCAATATTTGAACTGCCCT
Found at i:44984933 original size:22 final size:22
Alignment explanation
Indices: 44984854--44984920 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
44984844 ATCCAATAAT
* **
44984854 GAGCTTAGTACGTGAAACATGA
1 GAGCTTAGTACGTTAGCCATGA
44984876 GAGCTTAGTACGTTAGCCATGA
1 GAGCTTAGTACGTTAGCCATGA
44984898 GAGCTTAGTACGTTAGCCATGA
1 GAGCTTAGTACGTTAGCCATGA
44984920 G
1 G
44984921 GGTTTAGTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.25
Consensus pattern (22 bp):
GAGCTTAGTACGTTAGCCATGA
Found at i:44992491 original size:19 final size:19
Alignment explanation
Indices: 44992471--44992506 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
44992461 CTATAGAATA
44992471 AAATT-ACATATAAAAAAT
1 AAATTGACATATAAAAAAT
*
44992489 AAATTGTCATATAAAAAA
1 AAATTGACATATAAAAAA
44992507 AGGGTACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.28
Consensus pattern (19 bp):
AAATTGACATATAAAAAAT
Found at i:44994683 original size:14 final size:15
Alignment explanation
Indices: 44994653--44994692 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
44994643 AGAGCTCGGA
44994653 AAAAC-ATAGCTTAT
1 AAAACTATAGCTTAT
*
44994667 AAAACTATA-CTTTT
1 AAAACTATAGCTTAT
44994681 AAAA-TATAGCTT
1 AAAACTATAGCTT
44994693 GAAAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 4 0.17
14 16 0.70
15 3 0.13
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.35
Consensus pattern (15 bp):
AAAACTATAGCTTAT
Found at i:44997562 original size:3 final size:3
Alignment explanation
Indices: 44997542--44997649 Score: 137
Period size: 3 Copynumber: 36.3 Consensus size: 3
44997532 AAATATATAT
* * * * *
44997542 TTA TTA TTG TTA TT- TTA TTA TTA TTA CTA TTA CTA TTA CTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
44997589 TTA CTG TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44997637 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
44997650 AAAGCAAGGT
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
2 2 0.02
3 88 0.98
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:44999629 original size:15 final size:15
Alignment explanation
Indices: 44999611--44999640 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44999601 GATGAATAAG
44999611 TGAGAGATGATTGAA
1 TGAGAGATGATTGAA
*
44999626 TGAGGGATGATTGAA
1 TGAGAGATGATTGAA
44999641 AAGTGAGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.27
Consensus pattern (15 bp):
TGAGAGATGATTGAA
Found at i:45002609 original size:40 final size:40
Alignment explanation
Indices: 45002550--45002635 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
45002540 TATCGAAGTA
* * * * *
45002550 CAAACAGGGGTACCGAAGTAAAAATAGCGGCACGTGTGTG
1 CAAACAGGAGTACCAAAGTAAAAACAGCGACACGTATGTG
*
45002590 CAAACAGGAGTACCAAAGTACAAACAGCGACACGTATGTG
1 CAAACAGGAGTACCAAAGTAAAAACAGCGACACGTATGTG
45002630 CAAACA
1 CAAACA
45002636 TTCAATAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.41, C:0.21, G:0.26, T:0.13
Consensus pattern (40 bp):
CAAACAGGAGTACCAAAGTAAAAACAGCGACACGTATGTG
Found at i:45019672 original size:25 final size:24
Alignment explanation
Indices: 45019616--45019703 Score: 72
Period size: 25 Copynumber: 3.6 Consensus size: 24
45019606 TTACCGATTC
*
45019616 CAGCTCTTATGAGCTTACTTATACT
1 CAGCTCGTATGAGCTTACTTATA-T
*
45019641 CAACTCGTATGAGCTTACCATTAT-T
1 CAGCTCGTATGAGCTTA-C-TTATAT
* * * *
45019666 CAGCTCGAAGGAGCCTACTGTTTAT
1 CAGCTCGTATGAGCTTACT-TATAT
45019691 CA-CTCGTATGAGC
1 CAGCTCGTATGAGC
45019704 ATGCATGTAC
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
23 1 0.02
24 12 0.24
25 32 0.64
26 1 0.02
27 4 0.08
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (24 bp):
CAGCTCGTATGAGCTTACTTATAT
Found at i:45022190 original size:16 final size:16
Alignment explanation
Indices: 45022164--45022217 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
45022154 TTTGGTTCGC
*
45022164 TGTATTGGAATAGAGG
1 TGTAATGGAATAGAGG
*
45022180 CGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
45022196 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
45022212 TGTAAT
1 TGTAAT
45022218 AGCATAATGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.35, C:0.02, G:0.35, T:0.28
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:45022409 original size:51 final size:51
Alignment explanation
Indices: 45022354--45022533 Score: 117
Period size: 51 Copynumber: 3.2 Consensus size: 51
45022344 TATTTAAACA
45022354 TAATAATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCT
1 TAATAATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCT
** * **
45022405 TAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
1 TAATAAT---TATT-AAATAT--A-TTA-T--AAT-TTAA-ATAT-ATA--ATTTAATA-AAATT
*
45022470 AACA
50 --CT
* * *
45022474 TAATTATTATTAAATATATTATAATTAAAATATATAATTTACTAAAATTCT
1 TAATAATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCT
45022525 TAATAATTA
1 TAATAATTA
45022534 ATATTCTTAT
Statistics
Matches: 95, Mismatches: 16, Indels: 36
0.65 0.11 0.24
Matches are distributed among these distances:
51 16 0.17
53 5 0.05
54 9 0.09
55 4 0.04
56 3 0.03
57 5 0.05
58 5 0.05
59 4 0.04
61 4 0.04
62 6 0.06
63 5 0.05
64 3 0.03
65 4 0.04
66 10 0.11
67 5 0.05
69 7 0.07
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (51 bp):
TAATAATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCT
Found at i:45022493 original size:120 final size:120
Alignment explanation
Indices: 45022350--45022762 Score: 693
Period size: 120 Copynumber: 3.4 Consensus size: 120
45022340 ATCATATTTA
* * *
45022350 AACATAATAATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
45022415 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
*
45022470 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTACTAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* * *
45022535 TATTCTTATACGAATCTGCTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
*
45022590 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTCATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
45022655 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
* * * *
45022710 GAA-ATAATTAATATTAAATATATTTTATTTAAAATATATGATTTAATAAAATT
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
45022763 TAAAATAATT
Statistics
Matches: 274, Mismatches: 18, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
120 272 0.99
121 2 0.01
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:45022494 original size:15 final size:15
Alignment explanation
Indices: 45022466--45022512 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
45022456 ATAAAATATA
45022466 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
45022481 TATTAAATATATTAT
1 AATTAAATATATTAT
45022496 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
45022509 AATT
1 AATT
45022513 TACTAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 7 0.24
14 6 0.21
15 16 0.55
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:45022614 original size:15 final size:15
Alignment explanation
Indices: 45022586--45022632 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
45022576 ATAAAATATA
45022586 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
45022601 TATTAAATATATTAT
1 AATTAAATATATTAT
45022616 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
45022629 AATT
1 AATT
45022633 TCATAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 7 0.24
14 6 0.21
15 16 0.55
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:45022700 original size:61 final size:61
Alignment explanation
Indices: 45022395--45022702 Score: 230
Period size: 61 Copynumber: 5.1 Consensus size: 61
45022385 ATATAATTTA
* *
45022395 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTCTTAATAATTAATATTCTTATATGAATATACTCAAATCATAATATATGATACT
* * * * * * * *
45022456 ATAAAA-T-AT-A-AATTAACATAATTATTAT-TAAATATA-TTATAATTAAAATATATAAT-TT
1 ATAAAATTCTTAATAATT-A-AT-ATTCTTATATGAATATACTCA-AATCATAATATATGATACT
* * *
45022514 ACTAAAATTCTTAATAATTAATATTCTTATACGAATCTGCTCAAATCATAATATATGATACT
1 A-TAAAATTCTTAATAATTAATATTCTTATATGAATATACTCAAATCATAATATATGATACT
* * * * * * * *
45022576 ATAAAA-T-AT-A-AATTAACATAATTATTAT-TAAATATA-TTATAATTAAAATATATAAT-TT
1 ATAAAATTCTTAATAATT-A-AT-ATTCTTATATGAATATACTCA-AATCATAATATATGATACT
*
45022634 CATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATTAATATTCTTATATGAATATACTCAAATCATAATATATGATACT
45022696 ATAAAAT
1 ATAAAAT
45022703 ATAATTTGAA
Statistics
Matches: 182, Mismatches: 41, Indels: 48
0.67 0.15 0.18
Matches are distributed among these distances:
57 7 0.04
58 11 0.06
59 53 0.29
60 32 0.18
61 60 0.33
62 11 0.06
63 8 0.04
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.41
Consensus pattern (61 bp):
ATAAAATTCTTAATAATTAATATTCTTATATGAATATACTCAAATCATAATATATGATACT
Found at i:45022864 original size:91 final size:91
Alignment explanation
Indices: 45022769--45022985 Score: 267
Period size: 91 Copynumber: 2.4 Consensus size: 91
45022759 AATTTAAAAT
* * * * *
45022769 AATTA-TAACTAATAAATTATCTTATATGAATTTTTATAATTTAAAATAATTATTATTACATATA
1 AATTATTAA-TAATAAATTATCTTATATGAATTTATACAATTTAAAATAAATAATATTAAATATA
*
45022833 ATTTAATAATAATATACGATTTCATAA
65 ATTTAATAATAATATACAATTTCATAA
* *
45022860 AATTATTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAAATAATATTAAATATAA
1 AATTATTAATAATAAATTATCTTATATGAATTTATACAATTTAAAATAAATAATATTAAATATAA
* *
45022925 TTTAATAATGATATATAATTTCATAA
66 TTTAATAATAATATACAATTTCATAA
* * * *
45022951 ATTTCTTAATAAAAAAATGT-TATTATATGAATTTA
1 AATTATTAAT-AATAAAT-TATCTTATATGAATTTA
45022986 CTAAAATCAA
Statistics
Matches: 108, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
91 85 0.79
92 22 0.20
93 1 0.01
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (91 bp):
AATTATTAATAATAAATTATCTTATATGAATTTATACAATTTAAAATAAATAATATTAAATATAA
TTTAATAATAATATACAATTTCATAA
Found at i:45025043 original size:8 final size:8
Alignment explanation
Indices: 45025030--45025069 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
45025020 GTAAAGAGCA
45025030 ATACAAAC
1 ATACAAAC
45025038 ATACAAAC
1 ATACAAAC
*
45025046 A-A-AACC
1 ATACAAAC
45025052 ATACAAAC
1 ATACAAAC
45025060 ATACAAAC
1 ATACAAAC
45025068 AT
1 AT
45025070 GCAATCGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 4 0.14
7 2 0.07
8 22 0.79
ACGTcount: A:0.62, C:0.25, G:0.00, T:0.12
Consensus pattern (8 bp):
ATACAAAC
Found at i:45031019 original size:8 final size:8
Alignment explanation
Indices: 45030997--45031030 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
45030987 ATTTTTAAAG
45030997 TTAGGT-A
1 TTAGGTAA
45031004 TT-GGTAA
1 TTAGGTAA
45031011 TTAGGTAA
1 TTAGGTAA
45031019 TTAGGTAA
1 TTAGGTAA
45031027 TTAG
1 TTAG
45031031 CCAATTAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 3 0.12
7 5 0.20
8 17 0.68
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.41
Consensus pattern (8 bp):
TTAGGTAA
Found at i:45039907 original size:56 final size:50
Alignment explanation
Indices: 45039834--45040029 Score: 193
Period size: 49 Copynumber: 3.8 Consensus size: 50
45039824 ATTTGGGTAA
45039834 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC----GAT-ATG
* * *
45039890 AGAGGTCCCAGGTAAGACCATGTCTGGGACATTGCA-TGGCACCGATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATG
* * * * *
45039939 AGA-ACTCCCATGTAAGACCATATCTGGGATATGGCTTTGGTA--GTACATG
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-ATATG
* * *
45039988 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
45040030 TATTATTATC
Statistics
Matches: 121, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
48 1 0.01
49 72 0.60
50 8 0.07
54 2 0.02
55 5 0.04
56 33 0.27
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATG
Found at i:45061105 original size:7 final size:7
Alignment explanation
Indices: 45061081--45061129 Score: 57
Period size: 7 Copynumber: 7.3 Consensus size: 7
45061071 TGTCTCTGCG
45061081 TTAGGG-
1 TTAGGGT
*
45061087 TTAGGAT
1 TTAGGGT
*
45061094 TTTGGGT
1 TTAGGGT
*
45061101 TTTGGGT
1 TTAGGGT
45061108 TTAGGGT
1 TTAGGGT
45061115 TTAGGG-
1 TTAGGGT
45061121 TTAGGGT
1 TTAGGGT
45061128 TT
1 TT
45061130 TAAAGAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
6 11 0.30
7 26 0.70
ACGTcount: A:0.12, C:0.00, G:0.41, T:0.47
Consensus pattern (7 bp):
TTAGGGT
Found at i:45061116 original size:14 final size:13
Alignment explanation
Indices: 45061097--45061130 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
45061087 TTAGGATTTT
45061097 GGGTTTTGGGTTTA
1 GGGTTTTGGG-TTA
*
45061111 GGGTTTAGGGTTA
1 GGGTTTTGGGTTA
45061124 GGGTTTT
1 GGGTTTT
45061131 AAAGAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.09, C:0.00, G:0.44, T:0.47
Consensus pattern (13 bp):
GGGTTTTGGGTTA
Found at i:45061263 original size:96 final size:95
Alignment explanation
Indices: 45061108--45061459 Score: 404
Period size: 96 Copynumber: 3.6 Consensus size: 95
45061098 GGTTTTGGGT
* * * *
45061108 TTAGGGTTTAGGGTTAGGGTTTTAAAGAAAAATTAAAT-AAATAAGGGATTAGGGTTTAGGGTTT
1 TTAGGGTTTAGTGTTAGGGTTTTTAAG-GAAA--AAATCAAATAA---ATTAGGGTTTAGGGTTA
* * * * *
45061172 TTTAATTAAATTAATTATAAAATTTTCAAAATTAGA
60 CTTGAGTAAATTAATTATAAATTTTTAAAAATTAGA
* * * *
45061208 TTAAGGTTCT-GTGCTTATGGTTTTTAAGGAAAAAATCAATTAATTTAGGGTTTAGGGTTACTTG
1 TTAGGGTT-TAGTG-TTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTG
* **
45061272 AGTAAATTAATTATTAATTTTTTTAAATTAGA
64 AGTAAATTAATTATAAATTTTTAAAAATTAGA
45061304 TTAGGGTTTAGTGTTAAGGGTTTTTAAGG-AAAAATCAAATAAATTAGGGTTTAGGGTTACTTGA
1 TTAGGGTTTAGTGTT-AGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGA
*
45061368 GTAAATTAATTATAAATTTTTAAAAAAAATAGA
65 GTAAATTAATTATAAATTTTT--AAAAATTAGA
* *
45061401 TTAGGGTTTAGTGTTTAGGGTTTTTAAGGAAAAACTCAAATAAATTAGGGTTTGGGGTT
1 TTAGGGTTTAGTG-TTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTAGGGTT
45061460 TAGGGTTATT
Statistics
Matches: 218, Mismatches: 25, Indels: 20
0.83 0.10 0.08
Matches are distributed among these distances:
95 56 0.26
96 66 0.30
97 33 0.15
98 33 0.15
99 5 0.02
100 12 0.06
101 13 0.06
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.40
Consensus pattern (95 bp):
TTAGGGTTTAGTGTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAG
TAAATTAATTATAAATTTTTAAAAATTAGA
Found at i:45061715 original size:125 final size:125
Alignment explanation
Indices: 45061492--45061783 Score: 460
Period size: 125 Copynumber: 2.3 Consensus size: 125
45061482 TTGTTTATTT
* * * **
45061492 AAAAAAGCTCCCACGTGGACGCTTTTTTTCTATAGTAGTTACTGAAAATATAATTTTGAGAAGAC
1 AAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTT-CTGAAAATATAATTTCAAGAAGAC
*
45061557 GTTTCTGAGCAAATAGTGGCAAAAACGCTTTAAGCAGGATGCATTGTCAGCAAAAGTACTG
65 CTTTCTGAGCAAATAGTGGCAAAAACGCTTTAAGCAGGATGCATTGTCAGCAAAAGTACTG
*
45061618 AAAAAAGCTCCCTCGTGGACGCTCTTTTGCTACAGTAGTTCTTGAAAA-ATAATTTCAAGAAGAC
1 AAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTC-TGAAAATATAATTTCAAGAAGAC
* * *
45061682 CTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGTTGCTTTGTCAGCAAAAGTACTG
65 CTTTCTGAGCAAATAGTGGCAAAAACGCTTTAAGCAGGATGCATTGTCAGCAAAAGTACTG
*
45061743 AAAGAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTC
1 AAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTC
45061784 CTATTTGGCC
Statistics
Matches: 153, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
125 111 0.73
126 42 0.27
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (125 bp):
AAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCTGAAAATATAATTTCAAGAAGACC
TTTCTGAGCAAATAGTGGCAAAAACGCTTTAAGCAGGATGCATTGTCAGCAAAAGTACTG
Found at i:45065502 original size:18 final size:18
Alignment explanation
Indices: 45065476--45065517 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
45065466 GACTAGAAAA
* * *
45065476 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
45065494 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
45065512 AGGATA
1 AGGATA
45065518 AGCACTTGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.07, G:0.29, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:45067365 original size:23 final size:21
Alignment explanation
Indices: 45067323--45067386 Score: 94
Period size: 23 Copynumber: 3.0 Consensus size: 21
45067313 AAGAGGAATT
45067323 TGTGAG-GAATTTGAGAGAAA
1 TGTGAGAGAATTTGAGAGAAA
45067343 TGTGAGAGAATATTGGAGAGAAA
1 TGTGAGAGAAT-TT-GAGAGAAA
*
45067366 TATGAGAGAATTTGAGAGAAA
1 TGTGAGAGAATTTGAGAGAAA
45067387 GGATTTAAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
20 6 0.15
21 12 0.30
22 4 0.10
23 18 0.45
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.23
Consensus pattern (21 bp):
TGTGAGAGAATTTGAGAGAAA
Found at i:45072708 original size:18 final size:18
Alignment explanation
Indices: 45072682--45072718 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
45072672 TCTCTCCATG
45072682 TCTTCCTCATCATCATCA
1 TCTTCCTCATCATCATCA
* *
45072700 TCTTTCTCATCCTCATCA
1 TCTTCCTCATCATCATCA
45072718 T
1 T
45072719 TTTATTCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.38, G:0.00, T:0.43
Consensus pattern (18 bp):
TCTTCCTCATCATCATCA
Found at i:45084847 original size:40 final size:40
Alignment explanation
Indices: 45084764--45084848 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
45084754 ATAATATATG
* * * *
45084764 ATTCAGAGTTACCGAAGTATAAATAGGGGCACATAAGTTC
1 ATTCAGAGGTACCAAAGTACAAATAGGGGCACATAAGTGC
* *
45084804 ATTCAGAGGTACCAAAGTACAAATAGGGGCACGTATGTGC
1 ATTCAGAGGTACCAAAGTACAAATAGGGGCACATAAGTGC
45084844 ATTCA
1 ATTCA
45084849 TTCAATACTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (40 bp):
ATTCAGAGGTACCAAAGTACAAATAGGGGCACATAAGTGC
Found at i:45094646 original size:27 final size:27
Alignment explanation
Indices: 45094606--45094671 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
45094596 CTATTAGAGA
* * *
45094606 ACACCATCTCGCTAGTCTTGCTGGCGT
1 ACACCATCTCGCTAGACTTACTGACGT
*
45094633 ACACCATCTTGCTAGACTTACTGACGT
1 ACACCATCTCGCTAGACTTACTGACGT
* *
45094660 ATACCAGCTCGC
1 ACACCATCTCGC
45094672 CAAGCCTTCT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.21, C:0.33, G:0.18, T:0.27
Consensus pattern (27 bp):
ACACCATCTCGCTAGACTTACTGACGT
Found at i:45096416 original size:16 final size:15
Alignment explanation
Indices: 45096395--45096424 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
45096385 ATATCAAGGT
45096395 TAATTAAGTGAATTAG
1 TAATTAAGT-AATTAG
45096411 TAATTAAGTAATTA
1 TAATTAAGTAATTA
45096425 AAATAGGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (15 bp):
TAATTAAGTAATTAG
Found at i:45097246 original size:29 final size:29
Alignment explanation
Indices: 45097213--45097282 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
45097203 ATCGACAAAT
* *
45097213 GAAAAGCGATGGCTTCGGCTATCGAATAC
1 GAAAAGCGATAGCTTCGACTATCGAATAC
* * *
45097242 GAAAAGGGATAGCTTCGACTATCGATTAT
1 GAAAAGCGATAGCTTCGACTATCGAATAC
*
45097271 GAAAAGAGATAG
1 GAAAAGCGATAG
45097283 TGATGACCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.21
Consensus pattern (29 bp):
GAAAAGCGATAGCTTCGACTATCGAATAC
Found at i:45097391 original size:60 final size:61
Alignment explanation
Indices: 45097327--45097521 Score: 170
Period size: 60 Copynumber: 3.2 Consensus size: 61
45097317 ACCATCGAAC
45097327 TATGAAAAAGGATGGCTTCAG-CTATCGATA-TATGAAAAGGGATAGCTTCAGCTATCAAAT
1 TATGAAAAAGGATGGCTTCAGACTATCGA-ACTATGAAAAGGGATAGCTTCAGCTATCAAAT
* * * * * * * * *
45097387 TATGAAAAGGGATGG--TGACGACCATCAAACAATGAAAAGGGGT-G-GTGACGACCATCAAAT
1 TATGAAAAAGGATGGCTTCA-GACTATCGAACTATGAAAAGGGATAGCTTCA-G-CTATCAAAT
* * * ** *
45097447 TATGAAAAGGGATAGCTTC-GACTATCGAACTATGAAAAGGGATAACTTTGGTTATCAAAT
1 TATGAAAAAGGATGGCTTCAGACTATCGAACTATGAAAAGGGATAGCTTCAGCTATCAAAT
45097507 TATGAAAAAGGATGG
1 TATGAAAAAGGATGG
45097522 GTCAACCATT
Statistics
Matches: 103, Mismatches: 23, Indels: 18
0.72 0.16 0.12
Matches are distributed among these distances:
58 4 0.04
59 4 0.04
60 92 0.89
61 1 0.01
62 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24
Consensus pattern (61 bp):
TATGAAAAAGGATGGCTTCAGACTATCGAACTATGAAAAGGGATAGCTTCAGCTATCAAAT
Found at i:45097410 original size:90 final size:90
Alignment explanation
Indices: 45097293--45097489 Score: 231
Period size: 90 Copynumber: 2.2 Consensus size: 90
45097283 TGATGACCAT
* * * * *
45097293 AAACAATGAAAAGGGATGGTGAAGACCATCGAACTATGAAAAAGGATGGCTTCA-G-CTATC-GA
1 AAACTATGAAAAGGGATGGTGAAGACCATCAAACAATGAAAAAGGATGG--TCACGACCATCAAA
45097355 TATATGAAAAGGGATAGCTTC-AGCTATC
64 T-TATGAAAAGGGATAGCTTCGA-CTATC
* * * * *
45097383 AAATTATGAAAAGGGATGGTGACGACCATCAAACAATGAAAAGGGGTGGTGACGACCATCAAATT
1 AAACTATGAAAAGGGATGGTGAAGACCATCAAACAATGAAAAAGGATGGTCACGACCATCAAATT
45097448 ATGAAAAGGGATAGCTTCGACTATC
66 ATGAAAAGGGATAGCTTCGACTATC
*
45097473 GAACTATGAAAAGGGAT
1 AAACTATGAAAAGGGAT
45097490 AACTTTGGTT
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
88 2 0.02
89 1 0.01
90 85 0.93
91 3 0.03
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (90 bp):
AAACTATGAAAAGGGATGGTGAAGACCATCAAACAATGAAAAAGGATGGTCACGACCATCAAATT
ATGAAAAGGGATAGCTTCGACTATC
Found at i:45097481 original size:30 final size:30
Alignment explanation
Indices: 45097211--45097490 Score: 159
Period size: 30 Copynumber: 9.4 Consensus size: 30
45097201 TCATCGACAA
* * *
45097211 ATGAAAAGCGATGGCTTCGGCTATCGAA-T
1 ATGAAAAGGGATAGCTTCGACTATCGAACT
* *
45097240 ACGAAAAGGGATAGCTTCGACTATCG-ATT
1 ATGAAAAGGGATAGCTTCGACTATCGAACT
* * * *
45097269 ATGAAAAGAGATAG-TGAT-GACCAT-AAACA
1 ATGAAAAGGGATAGCT--TCGACTATCGAACT
* ** *
45097298 ATGAAAAGGGAT-GGTGAAGACCATCGAACT
1 ATGAAAAGGGATAGCT-TCGACTATCGAACT
* *
45097328 ATGAAAAAGGATGGCTTC-AGCTATCGATA-T
1 ATGAAAAGGGATAGCTTCGA-CTATCGA-ACT
* *
45097358 ATGAAAAGGGATAGCTTC-AGCTATCAAATT
1 ATGAAAAGGGATAGCTTCGA-CTATCGAACT
* * * * *
45097388 ATGAAAAGGGAT-GGTGACGACCATCAAACA
1 ATGAAAAGGGATAGCT-TCGACTATCGAACT
* * * * * *
45097418 ATGAAAAGGGGT-GGTGACGACCATCAAATT
1 ATGAAAAGGGATAGCT-TCGACTATCGAACT
45097448 ATGAAAAGGGATAGCTTCGACTATCGAACT
1 ATGAAAAGGGATAGCTTCGACTATCGAACT
45097478 ATGAAAAGGGATA
1 ATGAAAAGGGATA
45097491 ACTTTGGTTA
Statistics
Matches: 200, Mismatches: 37, Indels: 27
0.76 0.14 0.10
Matches are distributed among these distances:
28 3 0.01
29 63 0.31
30 128 0.64
31 6 0.03
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.21
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTTCGACTATCGAACT
Found at i:45097511 original size:30 final size:30
Alignment explanation
Indices: 45097357--45097519 Score: 107
Period size: 30 Copynumber: 5.4 Consensus size: 30
45097347 GCTATCGATA
*
45097357 TATGAAAAGGGATAGCTTC-AGCTATCAAAT
1 TATGAAAAGGGATAACTTCGA-CTATCAAAT
** * * *
45097387 TATGAAAAGGGAT-GGTGACGACCATCAAAC
1 TATGAAAAGGGATAACT-TCGACTATCAAAT
* * ** * *
45097417 AATGAAAAGGGGT-GGTGACGACCATCAAAT
1 TATGAAAAGGGATAACT-TCGACTATCAAAT
* * *
45097447 TATGAAAAGGGATAGCTTCGACTATCGAAC
1 TATGAAAAGGGATAACTTCGACTATCAAAT
* **
45097477 TATGAAAAGGGATAACTTTGGTTATCAAAT
1 TATGAAAAGGGATAACTTCGACTATCAAAT
*
45097507 TATGAAAAAGGAT
1 TATGAAAAGGGAT
45097520 GGGTCAACCA
Statistics
Matches: 109, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
29 2 0.02
30 104 0.95
31 3 0.03
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.23
Consensus pattern (30 bp):
TATGAAAAGGGATAACTTCGACTATCAAAT
Found at i:45114912 original size:22 final size:23
Alignment explanation
Indices: 45114881--45114933 Score: 83
Period size: 22 Copynumber: 2.4 Consensus size: 23
45114871 GGTAAGCAAC
*
45114881 ACTTCCTAATTACATCATATGTA
1 ACTTCCTAATTACAGCATATGTA
45114904 ACTT-CTAATTACAGCATATGTA
1 ACTTCCTAATTACAGCATATGTA
45114926 A-TTCCTAA
1 ACTTCCTAA
45114934 AGTTTGGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 2 0.07
22 22 0.79
23 4 0.14
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.38
Consensus pattern (23 bp):
ACTTCCTAATTACAGCATATGTA
Found at i:45115359 original size:12 final size:13
Alignment explanation
Indices: 45115342--45115370 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
45115332 CTCATACATG
45115342 AATAAATAAA-GC
1 AATAAATAAATGC
45115354 AATAAATAAATGC
1 AATAAATAAATGC
45115367 AATA
1 AATA
45115371 GTTATAGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:45115877 original size:34 final size:33
Alignment explanation
Indices: 45115825--45115896 Score: 99
Period size: 34 Copynumber: 2.2 Consensus size: 33
45115815 GGAACTACCA
45115825 CGGTAGGAACAGGGGTGCGAGGCGGAGCCCCCG
1 CGGTAGGAACAGGGGTGCGAGGCGGAGCCCCCG
* * * *
45115858 TGGTATGGACCAGGGGTGCGCGGCGGAGCGCCCG
1 CGGTA-GGAACAGGGGTGCGAGGCGGAGCCCCCG
45115892 CGGTA
1 CGGTA
45115897 CAAACCGCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
33 4 0.12
34 29 0.88
ACGTcount: A:0.15, C:0.26, G:0.49, T:0.10
Consensus pattern (33 bp):
CGGTAGGAACAGGGGTGCGAGGCGGAGCCCCCG
Found at i:45119642 original size:134 final size:134
Alignment explanation
Indices: 45119412--45119678 Score: 358
Period size: 134 Copynumber: 2.0 Consensus size: 134
45119402 TATTAATTCA
* *
45119412 AATTAAACTACTCATTTAAAATAAATATCTATAACCAATCAAGACTTCAAAAGCTATACTCAAAT
1 AATTAAAATACTCATATAAAATAAATATCTATAACCAATCAAGACTTCAAAAGCTATACTCAAAT
*
45119477 TTTAATTCTAATTATTGGATTTAAATAATCATTAAAAATAGTTTAAATATCTAATAATATATATA
66 CTTAA-T-TAATTATTGGATTTAAATAATCATTAAAAATAGTTTAAATATCTAATAATATATATA
45119542 TGTTCG
129 TGTTCG
* * * ** * * *
45119548 AATTAAAATATTCATATAAAATAAATATCTGATGACGAATCTTGACTTCAAAAAGTTATATTCAG
1 AATTAAAATACTCATATAAAATAAATATCT-ATAACCAATCAAGACTTC-AAAAGCTATACTCAA
* * *
45119613 ATCTTAA-T-ATTATTGGATTTGAATAATCATTAAAAATAGTTTGAGTATCTAATAATATATATA
64 ATCTTAATTAATTATTGGATTTAAATAATCATTAAAAATAGTTTAAATATCTAATAATATATATA
45119676 TGT
129 TGT
45119679 CCAAAATATG
Statistics
Matches: 115, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
134 55 0.48
135 1 0.01
136 27 0.23
137 14 0.12
138 18 0.16
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (134 bp):
AATTAAAATACTCATATAAAATAAATATCTATAACCAATCAAGACTTCAAAAGCTATACTCAAAT
CTTAATTAATTATTGGATTTAAATAATCATTAAAAATAGTTTAAATATCTAATAATATATATATG
TTCG
Found at i:45121339 original size:12 final size:12
Alignment explanation
Indices: 45121322--45121346 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45121312 CAAAGGCTAT
45121322 TAACAATATTTA
1 TAACAATATTTA
45121334 TAACAATATTTA
1 TAACAATATTTA
45121346 T
1 T
45121347 GTTATAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAACAATATTTA
Found at i:45123218 original size:75 final size:75
Alignment explanation
Indices: 45122953--45123437 Score: 434
Period size: 76 Copynumber: 6.6 Consensus size: 75
45122943 ATATAACAGT
* ** * * * *
45122953 TGTGAACGTAGGTCAACGAGCTATTAGAAAATTGAGGGTCTCGATCTTAATTCAGCGGACTATAA
1 TGTGAACGTAGGTCAGCGAGCTATTAGAAAACCGAGGGTCGCGATCTTAAATCAACGGACCATAA
45123018 AAAATATCAAC
66 AAAA-ATCAAC
* * * * *
45123029 TGTGAACGTAGGTCAACGAGTTATTAGAAAACCGAGGGTCGTGATATTAAATCAATGGACCATAA
1 TGTGAACGTAGGTCAGCGAGCTATTAGAAAACCGAGGGTCGCGATCTTAAATCAACGGACCATAA
*
45123094 AAAATAACAAC
66 AAAA-ATCAAC
* * * *
45123105 TGTGAACGTAGGTCAGCAAGCTATTAGAAAACCAAGGGTCGCGATCTTAAATCAACGAACCGTAA
1 TGTGAACGTAGGTCAGCGAGCTATTAGAAAACCGAGGGTCGCGATCTTAAATCAACGGACCATAA
*
45123170 AAAAATCAAT
66 AAAAATCAAC
* * * * * *
45123180 TGTGAACGTAGGTCAACAAGTTTTTAGAAAACCGAGGGTCACAATCTTAAAT-AAGCGGACCAT-
1 TGTGAACGTAGGTCAGCGAGCTATTAGAAAACCGAGGGTCGCGATCTTAAATCAA-CGGACCATA
45123243 -AAAAA--AA-
65 AAAAAATCAAC
* * * * * * *
45123250 --T---CGTAGGTCAGCAAGCTACTAGAAAATCGAGGGTCGCGACCATAAATCAGCGGACCGTAA
1 TGTGAACGTAGGTCAGCGAGCTATTAGAAAACCGAGGGTCGCGATCTTAAATCAACGGACCATAA
*
45123310 AAAAATCAGC
66 AAAAATCAAC
* * * * * * **
45123320 TGTGAACATAAGTTAGCGAGCTGTTAGAAAACTGAGGGTCACGATCTTAAATCAACAAACCATAA
1 TGTGAACGTAGGTCAGCGAGCTATTAGAAAACCGAGGGTCGCGATCTTAAATCAACGGACCAT-A
45123385 AAAAAATCAAC
65 AAAAAATCAAC
* * * * * **
45123396 TATGAACATAGATCAGCGAGTTGTTAGAAAATAGAGGGTCGC
1 TGTGAACGTAGGTCAGCGAGCTATTAGAAAACCGAGGGTCGC
45123438 AATCCAAGGA
Statistics
Matches: 330, Mismatches: 66, Indels: 26
0.78 0.16 0.06
Matches are distributed among these distances:
65 44 0.13
66 1 0.00
67 5 0.02
68 1 0.00
69 1 0.00
71 2 0.01
72 1 0.00
73 5 0.02
74 2 0.01
75 98 0.30
76 170 0.52
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (75 bp):
TGTGAACGTAGGTCAGCGAGCTATTAGAAAACCGAGGGTCGCGATCTTAAATCAACGGACCATAA
AAAAATCAAC
Found at i:45123296 original size:65 final size:65
Alignment explanation
Indices: 45123186--45123316 Score: 163
Period size: 65 Copynumber: 2.0 Consensus size: 65
45123176 CAATTGTGAA
* ** * *
45123186 CGTAGGTCAACAAGTTTTTAGAAAACCGAGGGTCACAATCTTAAATAAGCGGACCATAAAAAAAT
1 CGTAGGTCAACAAGCTACTAGAAAACCGAGGGTCACAACCATAAATAAGCGGACCATAAAAAAAT
* * * * * *
45123251 CGTAGGTCAGCAAGCTACTAGAAAATCGAGGGTCGCGACCATAAATCAGCGGACCGTAAAAAAAT
1 CGTAGGTCAACAAGCTACTAGAAAACCGAGGGTCACAACCATAAATAAGCGGACCATAAAAAAAT
45123316 C
1 C
45123317 AGCTGTGAAC
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
65 55 1.00
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.18
Consensus pattern (65 bp):
CGTAGGTCAACAAGCTACTAGAAAACCGAGGGTCACAACCATAAATAAGCGGACCATAAAAAAAT
Found at i:45123367 original size:140 final size:140
Alignment explanation
Indices: 45123111--45123389 Score: 362
Period size: 140 Copynumber: 2.0 Consensus size: 140
45123101 CAACTGTGAA
* * *
45123111 CGTAGGTCAGCAAGCTATTAGAAAACCAAGGGTCGCGATCTTAAATCAACGAACCGTAAAAAAAT
1 CGTAGGTCAGCAAGCTACTAGAAAACCAAGGGTCGCGACCATAAATCAACGAACCGTAAAAAAAT
* * * * * **
45123176 CAATTGTGAACGTAGGTCAACAAGTTTTTAGAAAACCGAGGGTCACAATCTTAAAT-AAGCGGAC
66 CAACTGTGAACATAAGTCAACAAGCTGTTAGAAAACCGAGGGTCACAATCTTAAATCAA-CAAAC
45123240 CATAAAAAAAT
130 CATAAAAAAAT
* * * *
45123251 CGTAGGTCAGCAAGCTACTAGAAAATCGAGGGTCGCGACCATAAATCAGCGGACCGTAAAAAAAT
1 CGTAGGTCAGCAAGCTACTAGAAAACCAAGGGTCGCGACCATAAATCAACGAACCGTAAAAAAAT
* * * * * *
45123316 CAGCTGTGAACATAAGTTAGCGAGCTGTTAGAAAACTGAGGGTCACGATCTTAAATCAACAAACC
66 CAACTGTGAACATAAGTCAACAAGCTGTTAGAAAACCGAGGGTCACAATCTTAAATCAACAAACC
45123381 ATAAAAAAA
131 ATAAAAAAA
45123390 ATCAACTATG
Statistics
Matches: 118, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
140 116 0.98
141 2 0.02
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.19
Consensus pattern (140 bp):
CGTAGGTCAGCAAGCTACTAGAAAACCAAGGGTCGCGACCATAAATCAACGAACCGTAAAAAAAT
CAACTGTGAACATAAGTCAACAAGCTGTTAGAAAACCGAGGGTCACAATCTTAAATCAACAAACC
ATAAAAAAAT
Found at i:45123539 original size:18 final size:18
Alignment explanation
Indices: 45123516--45123563 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
45123506 CATAACAGAT
45123516 GCTATTGCGGTCATTGTA
1 GCTATTGCGGTCATTGTA
45123534 GCTATTGCGGTCATTGTA
1 GCTATTGCGGTCATTGTA
* *
45123552 GGTATCGCGGTC
1 GCTATTGCGGTC
45123564 GTGAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.19, G:0.31, T:0.35
Consensus pattern (18 bp):
GCTATTGCGGTCATTGTA
Found at i:45127916 original size:17 final size:18
Alignment explanation
Indices: 45127876--45127916 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
45127866 TTGAAATATT
45127876 ATATATATTGAATATGAA
1 ATATATATTGAATATGAA
45127894 A-ATATATT-ATATAT-AA
1 ATATATATTGA-ATATGAA
45127910 ATATATA
1 ATATATA
45127917 AGTGTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.19
17 16 0.76
18 1 0.05
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
ATATATATTGAATATGAA
Found at i:45128308 original size:53 final size:52
Alignment explanation
Indices: 45128227--45128340 Score: 165
Period size: 53 Copynumber: 2.2 Consensus size: 52
45128217 AAATAATGAA
* *
45128227 AAAATATGAAAACTTGATGTGATCAATTGTGTTATTATAAAAGTTAAAGATATT
1 AAAA-ATGAAAACTTAATGTGATCAATTGTATTATTATAAAAGTTAAA-ATATT
* * *
45128281 AAAAATGAAAAGTTAATGTGATTAATTGTATTATTATAAAAGTTAGAATATT
1 AAAAATGAAAACTTAATGTGATCAATTGTATTATTATAAAAGTTAAAATATT
45128333 AAAAATGA
1 AAAAATGA
45128341 CCGTTATTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
52 13 0.24
53 38 0.69
54 4 0.07
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (52 bp):
AAAAATGAAAACTTAATGTGATCAATTGTATTATTATAAAAGTTAAAATATT
Found at i:45137333 original size:23 final size:23
Alignment explanation
Indices: 45137289--45137333 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
45137279 TAAGGTTTAA
*
45137289 TATTTGTTTTTTAATTTTGTATC
1 TATTTGTTTTTTAATTTGGTATC
*
45137312 TATTTTTTTATTTAA-TTGGTAT
1 TATTTGTTT-TTTAATTTGGTAT
45137334 ATGAATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.20, C:0.02, G:0.09, T:0.69
Consensus pattern (23 bp):
TATTTGTTTTTTAATTTGGTATC
Found at i:45139358 original size:23 final size:23
Alignment explanation
Indices: 45139332--45139377 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
45139322 TTTTCACGTA
*
45139332 ACATACTGAGAGGTTGTCACATG
1 ACATACTGAGAGATTGTCACATG
45139355 ACATACTGAGAGATTGTCACATG
1 ACATACTGAGAGATTGTCACATG
45139378 TTACCACTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (23 bp):
ACATACTGAGAGATTGTCACATG
Found at i:45140372 original size:39 final size:39
Alignment explanation
Indices: 45140303--45140377 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
45140293 GGCATTTGGA
*
45140303 TAAAAAAACGCCGCTAAAAATCAAGCATTAGTGGCGCTT
1 TAAAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTT
* * *
45140342 TAAAAACACGCCGCTAAAGATCCAA-TATTAGCGGCG
1 TAAAAAAACGCCGCTAAAAAT-CAAGCATTAGCGGCG
45140378 TTTTCCAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 28 0.90
40 3 0.10
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (39 bp):
TAAAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTT
Found at i:45140508 original size:20 final size:19
Alignment explanation
Indices: 45140480--45140527 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
45140470 TGCTCGGGGC
*
45140480 TTTAGTATTTTATCTGTCTA
1 TTTA-TATTTAATCTGTCTA
* *
45140500 TTTACTATTTAATTTGTTTA
1 TTTA-TATTTAATCTGTCTA
45140520 TTTATATT
1 TTTATATT
45140528 AATTAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (19 bp):
TTTATATTTAATCTGTCTA
Found at i:45140624 original size:26 final size:26
Alignment explanation
Indices: 45140576--45140626 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
45140566 AAAATGGATA
** * *
45140576 AATTTGAAATAATGACACGTAGAAAT
1 AATTTGAAATAAAAAAACATAGAAAT
45140602 AATTTGAAATAAAAAAACATAGAAA
1 AATTTGAAATAAAAAAACATAGAAA
45140627 AATATTTGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (26 bp):
AATTTGAAATAAAAAAACATAGAAAT
Found at i:45140930 original size:14 final size:14
Alignment explanation
Indices: 45140913--45140942 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
45140903 TATGGATTAG
45140913 GGGTTCTGATTTAA
1 GGGTTCTGATTTAA
*
45140927 GGGTTGTGATTTAA
1 GGGTTCTGATTTAA
45140941 GG
1 GG
45140943 TTTATGGGTT
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:0.20, C:0.03, G:0.37, T:0.40
Consensus pattern (14 bp):
GGGTTCTGATTTAA
Found at i:45141178 original size:88 final size:88
Alignment explanation
Indices: 45141017--45141178 Score: 238
Period size: 88 Copynumber: 1.8 Consensus size: 88
45141007 GTTAGGTAAA
* *
45141017 GGTTTAGGGTTTAGATTAATTAGTGTATTTTAATTTATATATTAAATAATGTTTAAGGGTTAGGG
1 GGTTTAGGATTTAGATTAATTAGTGTATTTTAATTTATATATTAAATAATGCTTAAGGGTTAGGG
*
45141082 ATTCGGGGTCGGGATAGGGTTAG
66 ATTAGGGGTCGGGATAGGGTTAG
* * *
45141105 GGTTTAGGATTTATATTAATTAGTGTTTTTTAATTTATATATTAAATAA-GCTTATTGGGTTAGT
1 GGTTTAGGATTTAGATTAATTAGTGTATTTTAATTTATATATTAAATAATGCTTA-AGGGTTAG-
45141169 GG-TTAGGGGT
64 GGATTAGGGGT
45141179 TTGGAGTTTG
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
87 4 0.06
88 60 0.91
89 2 0.03
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.44
Consensus pattern (88 bp):
GGTTTAGGATTTAGATTAATTAGTGTATTTTAATTTATATATTAAATAATGCTTAAGGGTTAGGG
ATTAGGGGTCGGGATAGGGTTAG
Found at i:45141213 original size:21 final size:21
Alignment explanation
Indices: 45141164--45141214 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
45141154 GCTTATTGGG
*
45141164 TTAGTGGTTAGGGGTTTGGAGT
1 TTAG-GGTTAGGGGTTAGGAGT
*
45141186 TTGGGGTTAGGGGTTAGTGA-T
1 TTAGGGTTAGGGGTTAG-GAGT
45141207 TTAGGGTT
1 TTAGGGTT
45141215 TAGAGATTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.14, C:0.00, G:0.45, T:0.41
Consensus pattern (21 bp):
TTAGGGTTAGGGGTTAGGAGT
Found at i:45142554 original size:21 final size:21
Alignment explanation
Indices: 45142528--45142572 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
45142518 ATCCCTTCCC
45142528 CCCCCCGAAA-TCCCCAACTTT
1 CCCCCCGAAATTCCCCAA-TTT
* *
45142549 CCCCCCTAAATTCCCTAATTT
1 CCCCCCGAAATTCCCCAATTT
45142570 CCC
1 CCC
45142573 ACATCCAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.22, C:0.51, G:0.02, T:0.24
Consensus pattern (21 bp):
CCCCCCGAAATTCCCCAATTT
Found at i:45143900 original size:5 final size:5
Alignment explanation
Indices: 45143890--45143921 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
45143880 GATTCTTGTT
45143890 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
45143922 GGCAAGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:45144938 original size:2 final size:2
Alignment explanation
Indices: 45144933--45144957 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45144923 CCTTAATGGC
45144933 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
45144958 TATTTTAACT
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:45145739 original size:44 final size:44
Alignment explanation
Indices: 45145534--45145814 Score: 337
Period size: 43 Copynumber: 6.5 Consensus size: 44
45145524 AAGTTATGTT
* * * * *
45145534 TTTAGCGACGTTTGT--GAAAAAGCGTCACTAAAAGTCAT--TT
1 TTTAGCGGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCATGGTC
* * *
45145574 TTATAGTGGCGTTTGT-GGTAGAAGCGCCGCTAAAGGT-ACTGGTC
1 TT-TAGCGGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCA-TGGTC
* *
45145618 TTTAACGGCGTTTGTGGG-AAAAGCGCCGCTAAAGGTCATGATC
1 TTTAGCGGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCATGGTC
* *
45145661 TTTAGCAGCGTTTAT-GGAAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCATGGTC
*
45145704 TTTAGCTGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCATGGTC
*
45145748 TTTAGCGGCGTTTGTGGG-AAAAGCGCCGCTAAAGGTCATGGTA
1 TTTAGCGGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCATGGTC
*
45145791 TATAGCCGGCGTTTGTGGGAAAAA
1 TTTAG-CGGCGTTTGTGGGAAAAA
45145815 CACCGTTAAA
Statistics
Matches: 209, Mismatches: 21, Indels: 17
0.85 0.09 0.07
Matches are distributed among these distances:
40 2 0.01
41 12 0.06
42 18 0.09
43 109 0.52
44 64 0.31
45 4 0.02
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (44 bp):
TTTAGCGGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:45145770 original size:87 final size:87
Alignment explanation
Indices: 45145534--45145814 Score: 349
Period size: 87 Copynumber: 3.3 Consensus size: 87
45145524 AAGTTATGTT
* * * * * * * *
45145534 TTTAGCGACGTTTGT--GAAAAAGCGTCACTAAAAGTCAT--TTTTATAGTGGCGTTTGTGGTAG
1 TTTAGCGGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCATGATCTT-TAGCGGCGTTTGTGGAAA
45145595 AAGCGCCGCTAAAGGT-ACTGGTC
65 AAGCGCCGCTAAAGGTCA-TGGTC
* * *
45145618 TTTAACGGCGTTTGTGGG-AAAAGCGCCGCTAAAGGTCATGATCTTTAGCAGCGTTTATGGAAAA
1 TTTAGCGGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGGAAAA
45145682 AGCGCCGCTAAAGGTCATGGTC
66 AGCGCCGCTAAAGGTCATGGTC
* * *
45145704 TTTAGCTGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAA
1 TTTAGCGGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGGAAAA
*
45145769 AGCGCCGCTAAAGGTCATGGTA
66 AGCGCCGCTAAAGGTCATGGTC
*
45145791 TATAGCCGGCGTTTGTGGGAAAAA
1 TTTAG-CGGCGTTTGTGGGAAAAA
45145815 CACCGTTAAA
Statistics
Matches: 170, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
84 13 0.08
85 18 0.11
86 51 0.30
87 71 0.42
88 17 0.10
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (87 bp):
TTTAGCGGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGGAAAA
AGCGCCGCTAAAGGTCATGGTC
Found at i:45151593 original size:23 final size:23
Alignment explanation
Indices: 45151567--45151618 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
45151557 TGATTTTTAA
* *
45151567 ATTTTGAATTATTTTGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
*
45151590 ATTTAGAATTCTTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
45151613 ATTTAG
1 ATTTAG
45151619 GAAAAATCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (23 bp):
ATTTAGAATTATTTAGTGATAAT
Found at i:45158679 original size:4 final size:4
Alignment explanation
Indices: 45158670--45158694 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
45158660 AATACTCGTT
45158670 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
45158695 TGCTTGGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:45170287 original size:16 final size:15
Alignment explanation
Indices: 45170260--45170289 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
45170250 TAAATCTGAA
45170260 AAATAAAATAAAAAC
1 AAATAAAATAAAAAC
45170275 AAATAACAATAAAAA
1 AAATAA-AATAAAAA
45170290 TAAAGATAGT
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:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (15 bp):
AAATAAAATAAAAAC
Found at i:45170288 original size:27 final size:27
Alignment explanation
Indices: 45170231--45170293 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
45170221 AAGTGCATAA
* *
45170231 AAAAATAAAATAAAACATATAAATCTG
1 AAAAATAAAATAAAACAAATAAATATG
45170258 AAAAATAAAATAAAAACAAATAACA-AT-
1 AAAAATAAAAT-AAAACAAATAA-ATATG
45170285 AAAAATAAA
1 AAAAATAAA
45170294 GATAGTTCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 20 0.62
28 11 0.34
29 1 0.03
ACGTcount: A:0.75, C:0.06, G:0.02, T:0.17
Consensus pattern (27 bp):
AAAAATAAAATAAAACAAATAAATATG
Found at i:45174833 original size:25 final size:22
Alignment explanation
Indices: 45174790--45174840 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
45174780 AAACGCCATC
*
45174790 CAACAACTACCATATCACCACA
1 CAACAACAACCATATCACCACA
*
45174812 CAACAACAACCATATAACCAC-
1 CAACAACAACCATATCACCACA
45174833 CATACAAC
1 CA-ACAAC
45174841 CACCTAATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.49, C:0.39, G:0.00, T:0.12
Consensus pattern (22 bp):
CAACAACAACCATATCACCACA
Found at i:45201290 original size:21 final size:21
Alignment explanation
Indices: 45201250--45201329 Score: 101
Period size: 21 Copynumber: 3.9 Consensus size: 21
45201240 ATACACCAAG
*
45201250 AGAAGCTCG-AA-AGATGAAC
1 AGAAGCTCGTAAGAGCTGAAC
* *
45201269 AAAAGCTCATAAGAGCTGAAC
1 AGAAGCTCGTAAGAGCTGAAC
*
45201290 AGAAGCTCGTAAGAGCTAAAC
1 AGAAGCTCGTAAGAGCTGAAC
*
45201311 AGAAGCCCGTAAGAGCTGA
1 AGAAGCTCGTAAGAGCTGA
45201330 TCCACCCAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
19 7 0.14
20 2 0.04
21 42 0.82
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (21 bp):
AGAAGCTCGTAAGAGCTGAAC
Found at i:45206867 original size:20 final size:20
Alignment explanation
Indices: 45206839--45206882 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
45206829 ATTGAACAAG
45206839 AGTGCAATAGTTTCAATATT
1 AGTGCAATAGTTTCAATATT
* *
45206859 AGTGTAATAGTTTTAATATT
1 AGTGCAATAGTTTCAATATT
45206879 AGTG
1 AGTG
45206883 AGCTTCATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (20 bp):
AGTGCAATAGTTTCAATATT
Found at i:45221115 original size:27 final size:27
Alignment explanation
Indices: 45221079--45221148 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
45221069 CCAAATTTGG
* *
45221079 GGCGAATTGGGGGTTCACCAAGATTCA
1 GGCGAGTTGGGTGTTCACCAAGATTCA
* *
45221106 GGTGAGTTGGGTGTTCACCAAGATTTA
1 GGCGAGTTGGGTGTTCACCAAGATTCA
*
45221133 GGCGAGCTGGGTGTTC
1 GGCGAGTTGGGTGTTC
45221149 GCGAAAGAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.20, C:0.16, G:0.37, T:0.27
Consensus pattern (27 bp):
GGCGAGTTGGGTGTTCACCAAGATTCA
Found at i:45221267 original size:52 final size:53
Alignment explanation
Indices: 45221210--45221325 Score: 162
Period size: 52 Copynumber: 2.2 Consensus size: 53
45221200 AAGTGGTAAG
* * * *
45221210 GGGGTTCGCCAGTTTCACTGTGAGGTAGCTTTGCTAATGTGT-TGGCAAGTTA
1 GGGGTTCGCCAGTTTCACTGTGAGGCAGCTTCGCTAATCTGTCTGGCAAGCTA
* * *
45221262 GGGGTTCACAAGTTTCACTGTGAGGCAGCTTCGCTAATCTGTCTGGCAAGCTG
1 GGGGTTCGCCAGTTTCACTGTGAGGCAGCTTCGCTAATCTGTCTGGCAAGCTA
45221315 GGGGTTCGCCA
1 GGGGTTCGCCA
45221326 TTCTATTTGG
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
52 37 0.69
53 17 0.31
ACGTcount: A:0.17, C:0.20, G:0.33, T:0.30
Consensus pattern (53 bp):
GGGGTTCGCCAGTTTCACTGTGAGGCAGCTTCGCTAATCTGTCTGGCAAGCTA
Found at i:45222328 original size:95 final size:95
Alignment explanation
Indices: 45222209--45222587 Score: 474
Period size: 95 Copynumber: 4.0 Consensus size: 95
45222199 CAATCTTAAT
* *
45222209 TCTCACTCTGTGGGCTCCTTTCAGAGCATGAGCAATTGTGAGCCTCACTGTACGTGCTCCTTAAG
1 TCTCACTCTGTGTGCTCCTTTCAGAGCATGAGCAATTGTGAGCCTCACTCTACGTGCTCCTTAAG
45222274 AGCATGGGCTTTTGTGATTTTTGTGATAAG
66 AGCATGGGCTTTTGTGATTTTTGTGATAAG
* * *
45222304 TCTCACTCTGTGTGCTCCTTTCAGAGCATGAACAATTGTGAGCCTCACTGTACGTGCTCTTTAAG
1 TCTCACTCTGTGTGCTCCTTTCAGAGCATGAGCAATTGTGAGCCTCACTCTACGTGCTCCTTAAG
45222369 AGCATGGGCTTTTGTGATTTTTGTGATAAG
66 AGCATGGGCTTTTGTGATTTTTGTGATAAG
* ** * ** *
45222399 TCTCACTCTGTGTGCTCCTTTAAGAGCATGAGCTTTTATGAGCCTCACTCTGTGTGCTCCTTTAG
1 TCTCACTCTGTGTGCTCCTTTCAGAGCATGAGCAATTGTGAGCCTCACTCTACGTGCTCCTTAAG
*
45222464 AGCATGGGCTTTTGTGAGTTTTT-TTATAAG
66 AGCATGGGCTTTTGTGA-TTTTTGTGATAAG
* ** * * ** * ** *
45222494 TCCCACTCTACGTTCTCCTTTGAGAGCATGAGCTTTTGTAAGCATCTCACTCTGTGTGCTCCTTG
1 TCTCACTCTGTGTGCTCCTTTCAGAGCATGAGCAATTGTGAGC--CTCACTCTACGTGCTCCTTA
* **
45222559 AGAGCAT-AGCTTTTGTGAGATTTGTGATA
64 AGAGCATGGGCTTTTGTGATTTTTGTGATA
45222588 TCTCAAACTA
Statistics
Matches: 254, Mismatches: 26, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
95 209 0.82
96 19 0.07
97 26 0.10
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (95 bp):
TCTCACTCTGTGTGCTCCTTTCAGAGCATGAGCAATTGTGAGCCTCACTCTACGTGCTCCTTAAG
AGCATGGGCTTTTGTGATTTTTGTGATAAG
Found at i:45222425 original size:54 final size:53
Alignment explanation
Indices: 45222357--45222532 Score: 162
Period size: 54 Copynumber: 3.5 Consensus size: 53
45222347 CTCACTGTAC
*
45222357 GTGCT-CTTTAAGAGCATGGGCTTTTGTGATTTTTGTGATAAGTCTCACTCTGT
1 GTGCTCCTTTAAGAGCATGAGCTTTTGTGATTTTT-TGATAAGTCTCACTCTGT
*
45222410 GTGCTCCTTTAAGAGCATGAGC-TTT-T-A-----TG---AGCCTCACTCTGT
1 GTGCTCCTTTAAGAGCATGAGCTTTTGTGATTTTTTGATAAGTCTCACTCTGT
* * * **
45222452 GTGCTCCTTT-AGAGCATGGGCTTTTGTGAGTTTTTTTATAAGTCCCACTCTAC
1 GTGCTCCTTTAAGAGCATGAGCTTTTGTGA-TTTTTTGATAAGTCTCACTCTGT
* *
45222505 GTTCTCCTTTGAGAGCATGAGCTTTTGT
1 GTGCTCCTTTAAGAGCATGAGCTTTTGT
45222533 AAGCATCTCA
Statistics
Matches: 99, Mismatches: 10, Indels: 27
0.73 0.07 0.20
Matches are distributed among these distances:
41 10 0.10
42 25 0.25
43 1 0.01
44 1 0.01
45 2 0.02
50 1 0.01
51 1 0.01
52 1 0.01
53 26 0.26
54 31 0.31
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (53 bp):
GTGCTCCTTTAAGAGCATGAGCTTTTGTGATTTTTTGATAAGTCTCACTCTGT
Found at i:45222459 original size:42 final size:41
Alignment explanation
Indices: 45222400--45222481 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 41
45222390 TGTGATAAGT
45222400 CTCACTCTGTGTGCTCCTTTAAGAGCATGAGCTTTTATGAGC
1 CTCACTCTGTGTGCTCCTTT-AGAGCATGAGCTTTTATGAGC
* *
45222442 CTCACTCTGTGTGCTCCTTTAGAGCATGGGCTTTTGTGAG
1 CTCACTCTGTGTGCTCCTTTAGAGCATGAGCTTTTATGAG
45222482 TTTTTTTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 18 0.47
42 20 0.53
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (41 bp):
CTCACTCTGTGTGCTCCTTTAGAGCATGAGCTTTTATGAGC
Found at i:45223967 original size:40 final size:40
Alignment explanation
Indices: 45223902--45224058 Score: 208
Period size: 40 Copynumber: 3.9 Consensus size: 40
45223892 TTGCACCTTG
* * * *
45223902 GTGCCCCTGA-AAACACTTTGATGTCCCTGTTTTCACAACT
1 GTGCCCCT-ATAAACACTTCGGTGTCCCTATTTGCACAACT
* * * *
45223942 ATGCCCCTGTAAACAATTCGGTGTCCCTGTTTGCACAACT
1 GTGCCCCTATAAACACTTCGGTGTCCCTATTTGCACAACT
*
45223982 GTGCCCCTATGAACACTTCGGTGTCCCTATTTGCACAACT
1 GTGCCCCTATAAACACTTCGGTGTCCCTATTTGCACAACT
*
45224022 GTGCCCCTATGAACACTTCGGTGTCCCTATTTGCACA
1 GTGCCCCTATAAACACTTCGGTGTCCCTATTTGCACA
45224059 TCCGTGCTCC
Statistics
Matches: 105, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 105 1.00
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.31
Consensus pattern (40 bp):
GTGCCCCTATAAACACTTCGGTGTCCCTATTTGCACAACT
Found at i:45224011 original size:20 final size:20
Alignment explanation
Indices: 45223986--45224051 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
45223976 ACAACTGTGC
45223986 CCCTATGAACACTTCGGTGT
1 CCCTATGAACACTTCGGTGT
*** ** * *
45224006 CCCTATTTGCACAACTGTGC
1 CCCTATGAACACTTCGGTGT
45224026 CCCTATGAACACTTCGGTGT
1 CCCTATGAACACTTCGGTGT
45224046 CCCTAT
1 CCCTAT
45224052 TTGCACATCC
Statistics
Matches: 32, Mismatches: 14, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.20, C:0.33, G:0.17, T:0.30
Consensus pattern (20 bp):
CCCTATGAACACTTCGGTGT
Found at i:45224151 original size:40 final size:39
Alignment explanation
Indices: 45224052--45224151 Score: 96
Period size: 40 Copynumber: 2.5 Consensus size: 39
45224042 GTGTCCCTAT
*
45224052 TTGCACATCCGTGCTCCTGAATGCACTCTGGTGCCTCTGA
1 TTGCACAT-CGTGTTCCTGAATGCACTCTGGTGCCTCTGA
* * * *
45224092 TAGTACAT-TTGTTCCCCTGACTGCACTCTGGTGCC-CGTGA
1 TTGCACATCGTGTT--CCTGAATGCACTCTGGTGCCTC-TGA
45224132 TTGCACACTCGTGTTCCTGA
1 TTGCACA-TCGTGTTCCTGA
45224152 TTGAGCTTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
38 3 0.06
39 1 0.02
40 38 0.81
41 1 0.02
42 4 0.09
ACGTcount: A:0.15, C:0.31, G:0.22, T:0.32
Consensus pattern (39 bp):
TTGCACATCGTGTTCCTGAATGCACTCTGGTGCCTCTGA
Found at i:45227779 original size:13 final size:12
Alignment explanation
Indices: 45227747--45227771 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45227737 TAATTTTTAT
45227747 AACTTTTTCCTA
1 AACTTTTTCCTA
45227759 AACTTTTTCCTA
1 AACTTTTTCCTA
45227771 A
1 A
45227772 GCTATTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (12 bp):
AACTTTTTCCTA
Found at i:45228376 original size:42 final size:41
Alignment explanation
Indices: 45228282--45228379 Score: 99
Period size: 42 Copynumber: 2.3 Consensus size: 41
45228272 ACAAGCTTGC
* * *
45228282 GACACGGCTGTGTGAGCCAAGTCAGAGAGTTACACGGGTTG
1 GACACGGCCGTGTGAGCCAAGTAAGAGAGTTACACGAGTTG
* * * *
45228323 GCACACAGCCGTGTGAGCCAAGTAAGTGAGTTATAC-AGTCTAT
1 G-ACACGGCCGTGTGAGCCAAGTAAGAGAGTTACACGAGT-T-G
45228366 GACACGGCCGTGTG
1 GACACGGCCGTGTG
45228380 CTCCCACTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
41 3 0.07
42 42 0.91
43 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.33, T:0.20
Consensus pattern (41 bp):
GACACGGCCGTGTGAGCCAAGTAAGAGAGTTACACGAGTTG
Found at i:45239268 original size:24 final size:25
Alignment explanation
Indices: 45239214--45239269 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
45239204 AAGGTAGTAC
45239214 AACAGAACAAAGTAAAATAAAACAG
1 AACAGAACAAAGTAAAATAAAACAG
* * * *
45239239 AGCAGAACAACGT-AATTCAAACAG
1 AACAGAACAAAGTAAAATAAAACAG
45239263 AACAGAA
1 AACAGAA
45239270 TAGAATAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.61, C:0.16, G:0.14, T:0.09
Consensus pattern (25 bp):
AACAGAACAAAGTAAAATAAAACAG
Found at i:45239279 original size:10 final size:10
Alignment explanation
Indices: 45239258--45239302 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
45239248 ACGTAATTCA
*
45239258 AACAGAACAG
1 AACAGAATAG
*
45239268 AATAGAATAG
1 AACAGAATAG
45239278 AACAGAATAG
1 AACAGAATAG
* *
45239288 AACAAAATGG
1 AACAGAATAG
45239298 AACAG
1 AACAG
45239303 TGCAGAACAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.60, C:0.11, G:0.20, T:0.09
Consensus pattern (10 bp):
AACAGAATAG
Found at i:45239281 original size:15 final size:15
Alignment explanation
Indices: 45239261--45239289 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
45239251 TAATTCAAAC
45239261 AGAACAGAATAGAAT
1 AGAACAGAATAGAAT
45239276 AGAACAGAATAGAA
1 AGAACAGAATAGAA
45239290 CAAAATGGAA
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:0.62, C:0.07, G:0.21, T:0.10
Consensus pattern (15 bp):
AGAACAGAATAGAAT
Found at i:45250963 original size:16 final size:16
Alignment explanation
Indices: 45250942--45250973 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
45250932 GTTTTGTTGC
*
45250942 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
45250958 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
45250974 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:45251255 original size:51 final size:52
Alignment explanation
Indices: 45251191--45251391 Score: 225
Period size: 51 Copynumber: 4.0 Consensus size: 52
45251181 ATTAATGATA
* * *
45251191 CCGGTTCACATAGTAGCCTACACATAGTACTACATATGTGA-CCATCACTAT
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGAGCCATCACTAT
* ** * *
45251242 CCGATACACATAGTAGCCTGCACATAGTACTACACACATGATCGA--AGCTAT
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGAGCCATCA-CTAT
* * *
45251293 CCGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGAGCTATCA-T-T
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGAGCCATCACTAT
** *
45251343 TTGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCATCACT
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGAGCCATCACT
45251392 TTCACTTTCA
Statistics
Matches: 125, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
49 5 0.04
50 39 0.31
51 78 0.62
52 2 0.02
53 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (52 bp):
CCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGAGCCATCACTAT
Found at i:45251407 original size:101 final size:102
Alignment explanation
Indices: 45251191--45251378 Score: 254
Period size: 102 Copynumber: 1.9 Consensus size: 102
45251181 ATTAATGATA
* *
45251191 CCGGTTCACATAGTAGCCTACACATAGTACTACATATGTGACCATCACTATCCGATACACATAGT
1 CCGGTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATCACTATCCGATACACATAGT
*
45251256 AGCCTGCACATAGTACTACACACATGATCGAAGCTAT
66 AGCCTGCACATAGTACTACACACATGATCCAAGCTAT
* * * * ** * *
45251293 CCGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGAGCTATCA-T-TTTGGTACACGTAG
1 CCGGTTCACATAGTAGCCTACACATAGTACTACACATGCGA-CCATCACTATCCGATACACATAG
45251356 TAGCCTGCACATAGTACTACACA
65 TAGCCTGCACATAGTACTACACA
45251379 TGTGACCATC
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
101 33 0.44
102 37 0.49
103 5 0.07
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (102 bp):
CCGGTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATCACTATCCGATACACATAGT
AGCCTGCACATAGTACTACACACATGATCCAAGCTAT
Found at i:45256918 original size:16 final size:16
Alignment explanation
Indices: 45256897--45256928 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
45256887 GTTTTGTTGC
*
45256897 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
45256913 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
45256929 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:45257210 original size:51 final size:50
Alignment explanation
Indices: 45257152--45257296 Score: 211
Period size: 50 Copynumber: 2.9 Consensus size: 50
45257142 GATACCGGTT
45257152 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACT-TCCGATA
* * * *
45257203 CACATAGTAGCCTGCACATAGTACTACACATGCGAGCTATCA-TTCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGA-CCATCACTTCCGATA
* *
45257253 CACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTT
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTT
45257297 TCACTTTCAC
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
49 5 0.06
50 39 0.46
51 35 0.42
52 5 0.06
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTTCCGATA
Found at i:45260544 original size:17 final size:17
Alignment explanation
Indices: 45260522--45260556 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
45260512 AATATGAGAA
45260522 GTAATCTAAGAAGATTT
1 GTAATCTAAGAAGATTT
*
45260539 GTAATCTTAGAAGATTT
1 GTAATCTAAGAAGATTT
45260556 G
1 G
45260557 ATTTGTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (17 bp):
GTAATCTAAGAAGATTT
Found at i:45263568 original size:153 final size:154
Alignment explanation
Indices: 45263262--45263573 Score: 486
Period size: 153 Copynumber: 2.0 Consensus size: 154
45263252 ATTATACAAG
* * *
45263262 TTGTATTGCAATTTTTTGATGGACATAGAGATATTGGTTCTAATTGCAATCTGTTTTATTCCCCT
1 TTGTATTGCAAATTTTTGATAGACATA-AGATATTGGTTCTAATTGCAATCTGTTTAATTCCCCT
* * *
45263327 AAATGGAATTTGATCCGATACTTGGCTTTATTAGCCTACAATATATGGAAAAATCAAAATAGGCC
65 AAATGGAATTTGATCCGATACATAGCTTTATTAGCCAACAATATATGGAAAAATCAAAATAGGCC
*
45263392 TTGAAGCTGACAATACAATATTTTA
130 TTGAAGCTAACAATACAATATTTTA
*
45263417 TTGTTTTGCAAATTTTTGATAGACAT-AGATATTGGTTCTAATTGCAATCTG-TTAATTCCCCCT
1 TTGTATTGCAAATTTTTGATAGACATAAGATATTGGTTCTAATTGCAATCTGTTTAATT-CCCCT
*
45263480 AAATGGAACTTT-ATCTGATACATAGCTTTATTAGCCAACAATATATGGAAAAATCAAAATAGGC
65 AAATGGAA-TTTGATCCGATACATAGCTTTATTAGCCAACAATATATGGAAAAATCAAAATAGGC
*
45263544 CTTGAAGCTAACTATACAATATTTTA
129 CTTGAAGCTAACAATACAATATTTTA
45263570 TTGT
1 TTGT
45263574 GCATATAACC
Statistics
Matches: 145, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
152 5 0.03
153 114 0.79
154 3 0.02
155 23 0.16
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (154 bp):
TTGTATTGCAAATTTTTGATAGACATAAGATATTGGTTCTAATTGCAATCTGTTTAATTCCCCTA
AATGGAATTTGATCCGATACATAGCTTTATTAGCCAACAATATATGGAAAAATCAAAATAGGCCT
TGAAGCTAACAATACAATATTTTA
Found at i:45270563 original size:46 final size:46
Alignment explanation
Indices: 45270491--45270587 Score: 185
Period size: 46 Copynumber: 2.1 Consensus size: 46
45270481 TAAGGGTTTC
*
45270491 TTAAAGTTTATGTGAAGTAATAGGGATGAATTAGGTTTAAAACAAT
1 TTAATGTTTATGTGAAGTAATAGGGATGAATTAGGTTTAAAACAAT
45270537 TTAATGTTTATGTGAAGTAATAGGGATGAATTAGGTTTAAAACAAT
1 TTAATGTTTATGTGAAGTAATAGGGATGAATTAGGTTTAAAACAAT
45270583 TTAAT
1 TTAAT
45270588 CACACAAATT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.37
Consensus pattern (46 bp):
TTAATGTTTATGTGAAGTAATAGGGATGAATTAGGTTTAAAACAAT
Found at i:45280924 original size:4 final size:4
Alignment explanation
Indices: 45280915--45280966 Score: 54
Period size: 4 Copynumber: 12.8 Consensus size: 4
45280905 AAGTCACAAA
*
45280915 AAAT AAAT -AAT AAAT AATAT AAGAT AAAT AAAT AAA- AATAA AAAT AAAT
1 AAAT AAAT AAAT AAAT AA-AT AA-AT AAAT AAAT AAAT AA-AT AAAT AAAT
45280964 AAA
1 AAA
45280967 CCAAATTGCA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
3 5 0.12
4 27 0.64
5 10 0.24
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:45280928 original size:7 final size:7
Alignment explanation
Indices: 45280916--45280965 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
45280906 AGTCACAAAA
45280916 AATAAAT
1 AATAAAT
45280923 AATAAAT
1 AATAAAT
45280930 AATATAA-
1 AATA-AAT
*
45280937 GATAAAT
1 AATAAAT
45280944 AAATAAA-
1 -AATAAAT
45280951 AATAAA-
1 AATAAAT
45280957 AATAAAT
1 AATAAAT
45280964 AA
1 AA
45280966 ACCAAATTGC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 14 0.38
7 16 0.43
8 7 0.19
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (7 bp):
AATAAAT
Done.