Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 10 of 235
Found at i:2692150 original size:93 final size:93
Alignment explanation
Indices: 2691991--2692163 Score: 283
Period size: 93 Copynumber: 1.9 Consensus size: 93
2691981 CGCCCATAAG
* * *
2691991 CGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
2692056 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* * * *
2692084 CGAACTCGGACTCAACTCAATGAGTTCGGACATTCTCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
2692149 ACGAGTTCGGATGCC
66 ACGAGTTCGGATGCC
2692164 CAAACATCCT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:2692178 original size:46 final size:45
Alignment explanation
Indices: 2692035--2692178 Score: 148
Period size: 46 Copynumber: 3.1 Consensus size: 45
2692025 CGCATCCATG
*
2692035 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA--TACATCT
* * * * * *
2692082 CA-CGAACTCGGACTCAACTCAATGAGTTCGGACATTCTCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCATACATCT
*
2692128 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAACATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACAT-CT
2692174 AGTGA
1 AGTGA
2692179 CATGTCACTT
Statistics
Matches: 77, Mismatches: 14, Indels: 12
0.75 0.14 0.12
Matches are distributed among these distances:
44 8 0.10
45 1 0.01
46 32 0.42
47 31 0.40
48 1 0.01
49 4 0.05
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCT
Found at i:2695203 original size:48 final size:48
Alignment explanation
Indices: 2695136--2695227 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
2695126 TCAAATTAAC
*
2695136 ATGTATAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAAT
1 ATGTATAACCGTGGCATATCCACTTAGCACCACGTTACACGTATCAAT
* * * *
2695184 ATGTGTAATCGTGGTATATCCACTTAGTACCACGTTACACGTAT
1 ATGTATAACCGTGGCATATCCACTTAGCACCACGTTACACGTAT
2695228 AACCATGGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (48 bp):
ATGTATAACCGTGGCATATCCACTTAGCACCACGTTACACGTATCAAT
Found at i:2696866 original size:10 final size:10
Alignment explanation
Indices: 2696844--2696873 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
2696834 TTGATCGTCT
2696844 ATTAAACAATA
1 ATTAAA-AATA
2696855 ATTAAAAATA
1 ATTAAAAATA
2696865 ATTAAAAAT
1 ATTAAAAAT
2696874 TATGCAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.68
11 6 0.32
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (10 bp):
ATTAAAAATA
Found at i:2701607 original size:49 final size:49
Alignment explanation
Indices: 2701548--2701643 Score: 156
Period size: 49 Copynumber: 2.0 Consensus size: 49
2701538 CATAGGGAAT
*
2701548 ATGACAAGAAAATTGGGCGGTCCATTAATTTCAAAAAAAATATTCGTAG
1 ATGACAAGAAAATCGGGCGGTCCATTAATTTCAAAAAAAATATTCGTAG
***
2701597 ATGACAAGAAAATCGGGCGGTCCATTAATTTTTTAAAAAATATTCGT
1 ATGACAAGAAAATCGGGCGGTCCATTAATTTCAAAAAAAATATTCGT
2701644 GGGGAAAGCT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (49 bp):
ATGACAAGAAAATCGGGCGGTCCATTAATTTCAAAAAAAATATTCGTAG
Found at i:2708182 original size:27 final size:27
Alignment explanation
Indices: 2708125--2708182 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
2708115 TAGAAAAGGT
* * * *
2708125 CTCTTATTGAGTATTCCCTGATAACTT
1 CTCTTATCGAGTATTCCATGAGAACTA
* *
2708152 CTCTTATCGAGTATTCTATGAGAGCTA
1 CTCTTATCGAGTATTCCATGAGAACTA
2708179 CTCT
1 CTCT
2708183 CTGTTGAAAG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.41
Consensus pattern (27 bp):
CTCTTATCGAGTATTCCATGAGAACTA
Found at i:2715391 original size:48 final size:50
Alignment explanation
Indices: 2715254--2715393 Score: 180
Period size: 48 Copynumber: 2.9 Consensus size: 50
2715244 AACGTAGTAG
* * * *
2715254 GATGCCGATGCCATATCCCAGATATGGTCTTACAAGGGAT--TACATATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCGTACATATC
* *
2715302 GATGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGATCGTAGAT-T-
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCGTACATATC
* *
2715350 GATGCCAATTCCATGTCCCAAACATGGTCTTACATGGGATCGTA
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCGTA
2715394 TATAACTCTA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
48 76 0.94
49 1 0.01
50 4 0.05
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (50 bp):
GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCGTACATATC
Found at i:2720250 original size:44 final size:44
Alignment explanation
Indices: 2720184--2720499 Score: 195
Period size: 44 Copynumber: 6.9 Consensus size: 44
2720174 AAGTAAAGCC
* *
2720184 ACAAATTTTATCTCTCTGAAGTTGCAG-GGTAATAGATTGAAGAT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGG-AATAGATTGAAGAT
* * * *
2720228 ACAAATCTCATCTCCCTAAAGTTGAAGTGGAGTAGATTGAAGAT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTGAAGAT
* * * * * * *
2720272 GCGAATCTTATTTTCCTGAAGTTGCAGTAGAACATATTGAAGCTACAAGTT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTGAAG-----A--T
** *
2720323 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCATATTGAAGAT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTGAAGAT
* * * * *
2720367 ACGAATCTTATTTCCCTGAAGTTGTAGTGGAATATATTAAAGCTACGAGTT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATT---G--A--AGAT
* * ** *
2720418 ACGAATCTTATCT-CTTGGAAGTTGCAGTGGAGCAGATTGAAGTT
1 ACAAATCTTATCTCCCT-GAAGTTGCAGTGGAATAGATTGAAGAT
* * * * *
2720462 ACTAATCTTATCTCCCTAAAGTTACAGTAGAGTAGATT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATT
2720500 AAAGCGACAA
Statistics
Matches: 214, Mismatches: 41, Indels: 34
0.74 0.14 0.12
Matches are distributed among these distances:
44 133 0.62
45 4 0.02
46 2 0.01
47 1 0.00
48 1 0.00
49 2 0.01
50 2 0.01
51 69 0.32
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (44 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTGAAGAT
Found at i:2720359 original size:51 final size:50
Alignment explanation
Indices: 2720273--2720459 Score: 190
Period size: 51 Copynumber: 3.8 Consensus size: 50
2720263 ATTGAAGATG
* * *
2720273 CGAATCTTATTTTCCTGAAGTTGCAGTAGAACATATTGAAGCTACAAGTTA
1 CGAATCTTATCTCCCTGAAGTTGCAGTGGAACATATTGAAGCTAC-AGTTA
* *
2720324 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCATATTGAAG----A--TA
1 CGAATCTTATCTCCCTGAAGTTGCAGTGGAACATATTGAAGCTACAGTTA
* * * *
2720368 CGAATCTTATTTCCCTGAAGTTGTAGTGGAATATATTAAAGCTACGAGTTA
1 CGAATCTTATCTCCCTGAAGTTGCAGTGGAACATATTGAAGCTAC-AGTTA
* * *
2720419 CGAATCTTATCT-CTTGGAAGTTGCAGTGGAGCAGATTGAAG
1 CGAATCTTATCTCCCT-GAAGTTGCAGTGGAACATATTGAAG
2720460 TTACTAATCT
Statistics
Matches: 110, Mismatches: 18, Indels: 16
0.76 0.12 0.11
Matches are distributed among these distances:
44 37 0.34
46 1 0.01
49 1 0.01
50 2 0.02
51 69 0.63
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (50 bp):
CGAATCTTATCTCCCTGAAGTTGCAGTGGAACATATTGAAGCTACAGTTA
Found at i:2720501 original size:95 final size:95
Alignment explanation
Indices: 2720227--2720509 Score: 352
Period size: 95 Copynumber: 3.0 Consensus size: 95
2720217 AGATTGAAGA
* * * * * *
2720227 TACAAATCTCATCTCCCTAAAGTTGAAGTGGAGTAGATTGAAGATGCGAATCTTATTTTCCTGAA
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACGAATCTTATTTCCCTGAA
* *
2720292 GTTGCAGTAGAACATATTGAAGCTACAAGT
66 GTTGCAGTAGAATATATTAAAGCTACAAGT
*
2720322 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCATATTGAAGATACGAATCTTATTTCCCTGAA
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACGAATCTTATTTCCCTGAA
* * *
2720387 GTTGTAGTGGAATATATTAAAGCTACGAGT
66 GTTGCAGTAGAATATATTAAAGCTACAAGT
* * * * * *
2720417 TACGAATCTTATCT-CTTGGAAGTTGCAGTGGAGCAGATTGAAGTTACTAATCTTATCTCCCTAA
1 TACAAATCTTATCTCCCT-GAAGTTGCAGTGGAGCAGATTGAAGATACGAATCTTATTTCCCTGA
* * * *
2720481 AGTTACAGTAGAGTAGATTAAAGCGACAA
65 AGTTGCAGTAGAATATATTAAAGCTACAA
2720510 ACCCTGTACC
Statistics
Matches: 161, Mismatches: 26, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
94 2 0.01
95 159 0.99
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (95 bp):
TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACGAATCTTATTTCCCTGAA
GTTGCAGTAGAATATATTAAAGCTACAAGT
Found at i:2723549 original size:22 final size:23
Alignment explanation
Indices: 2723524--2723568 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2723514 TAGTTTTGGA
* *
2723524 TTTGATTTA-TTTATTTATATGT
1 TTTGAGTTACTTTATTAATATGT
2723546 TTTGAGTTACTTTATTAATATGT
1 TTTGAGTTACTTTATTAATATGT
2723569 AAATATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.24, C:0.02, G:0.11, T:0.62
Consensus pattern (23 bp):
TTTGAGTTACTTTATTAATATGT
Found at i:2724393 original size:22 final size:22
Alignment explanation
Indices: 2724352--2724393 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2724342 ATTTACTGTA
*
2724352 TTTCATATTATCTTTATGTTTT
1 TTTCATATTATATTTATGTTTT
2724374 TTTCATATATATATTT-TGTT
1 TTTCATAT-TATATTTATGTT
2724394 ACTTATACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (22 bp):
TTTCATATTATATTTATGTTTT
Found at i:2735617 original size:31 final size:31
Alignment explanation
Indices: 2735582--2735641 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
2735572 TATATAACTC
*
2735582 AATAGC-CTAATGACTTAGATAAAAACTTTTG
1 AATAGCTC-AATGACTTAAATAAAAACTTTTG
* *
2735613 AATAGTTCAATGACTTAAATGAAAACTTT
1 AATAGCTCAATGACTTAAATAAAAACTTT
2735642 CAAATAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (31 bp):
AATAGCTCAATGACTTAAATAAAAACTTTTG
Found at i:2735656 original size:31 final size:31
Alignment explanation
Indices: 2735589--2735656 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
2735579 CTCAATAGCC
* ** *
2735589 TAATGACTTAGATAAAAACTTTTGAATAGTT
1 TAATGACTTAAATAAAAACTTTCAAATAATT
* *
2735620 CAATGACTTAAATGAAAACTTTCAAATAATT
1 TAATGACTTAAATAAAAACTTTCAAATAATT
2735651 TAATGA
1 TAATGA
2735657 TCATTTTGCA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.35
Consensus pattern (31 bp):
TAATGACTTAAATAAAAACTTTCAAATAATT
Found at i:2746195 original size:62 final size:61
Alignment explanation
Indices: 2746097--2746219 Score: 194
Period size: 62 Copynumber: 2.0 Consensus size: 61
2746087 ATATAAGCAT
*
2746097 AAGATTAAAAGAGAGGGAGAGAATAGAAACTACCCTGAATTTGGATGTAATCCTTGGAAGA
1 AAGATTAAAAGAGAGGGAGAGAATAGAAACTACCCTGAATTTGGATGTAATCCTTCGAAGA
* *
2746158 NAAGATTAGAAA-AGAGGGAGAGAATAGAAATTGCCCTGAATTTGGATGTAATCCTTCGAAGA
1 -AAGATTA-AAAGAGAGGGAGAGAATAGAAACTACCCTGAATTTGGATGTAATCCTTCGAAGA
2746220 GCGGAAACAG
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 54 0.95
63 3 0.05
ACGTcount: A:0.41, C:0.10, G:0.26, T:0.22
Consensus pattern (61 bp):
AAGATTAAAAGAGAGGGAGAGAATAGAAACTACCCTGAATTTGGATGTAATCCTTCGAAGA
Found at i:2748194 original size:19 final size:19
Alignment explanation
Indices: 2748172--2748246 Score: 64
Period size: 19 Copynumber: 3.8 Consensus size: 19
2748162 AGAATAAAAT
*
2748172 AATAAGAATGAAATAGTAA
1 AATAAGAATGAAATAATAA
*
2748191 AATAATAAAT-AAATAAATAA
1 AATAA-GAATGAAAT-AATAA
* *
2748211 GAATAATAA-GAAATAATACT
1 -AATAAGAATGAAATAATA-A
2748231 AATAAGAATGAAATAA
1 AATAAGAATGAAATAA
2748247 ATAAGTAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
19 20 0.44
20 20 0.44
21 5 0.11
ACGTcount: A:0.67, C:0.01, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAGAATGAAATAATAA
Found at i:2748224 original size:16 final size:16
Alignment explanation
Indices: 2748205--2748238 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2748195 ATAAATAAAT
2748205 AAATAAGAATAATAAG
1 AAATAAGAATAATAAG
* *
2748221 AAATAATACTAATAAG
1 AAATAAGAATAATAAG
2748237 AA
1 AA
2748239 TGAAATAAAT
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:0.68, C:0.03, G:0.09, T:0.21
Consensus pattern (16 bp):
AAATAAGAATAATAAG
Found at i:2758123 original size:43 final size:43
Alignment explanation
Indices: 2758062--2758144 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
2758052 AATAATAGGC
*
2758062 AATTCTTGCAAACTTTATCAACCAAGACACTTTTGCCTAAAGT
1 AATTCTTGCAAACTTTATCAACCAAAACACTTTTGCCTAAAGT
*
2758105 AATTCTTGCAGACTTTATCAACCAAAACACTTTTGCCTAA
1 AATTCTTGCAAACTTTATCAACCAAAACACTTTTGCCTAA
2758145 GGGGTTCGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (43 bp):
AATTCTTGCAAACTTTATCAACCAAAACACTTTTGCCTAAAGT
Found at i:2763528 original size:22 final size:23
Alignment explanation
Indices: 2763503--2763548 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2763493 CAACCAAACC
2763503 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
2763525 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
2763548 A
1 A
2763549 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:2763554 original size:23 final size:23
Alignment explanation
Indices: 2763510--2763554 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2763500 ACCAATTCAA
*
2763510 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
2763533 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
2763555 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:2771150 original size:22 final size:23
Alignment explanation
Indices: 2771125--2771170 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2771115 CAACCAAACC
2771125 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
2771147 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
2771170 A
1 A
2771171 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:2771176 original size:23 final size:23
Alignment explanation
Indices: 2771132--2771176 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2771122 ACCAATTCAA
*
2771132 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
2771155 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
2771177 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:2773589 original size:88 final size:87
Alignment explanation
Indices: 2773440--2773614 Score: 278
Period size: 88 Copynumber: 2.0 Consensus size: 87
2773430 TAGTCCTAGC
* * *
2773440 TTTATTTAGTTAATTTTACAATATTCCAATTTTGCCCTTAATTTATCAATTTTCCTGCTGATTTC
1 TTTATTTAGTTAATTATACAATATTCCAATTTTGCCCTTAAATAATCAATTTTCCTGCTGATTTC
2773505 ATGCCCTTGCCGTCCAGCCCAA
66 ATGCCCTTGCCGTCCAGCCCAA
* * *
2773527 NTTTATTTAGTTAATTATGCAATATTCCAATTTTGCCCTTAAATAATCCATTTTCTTGCTGATTT
1 -TTTATTTAGTTAATTATACAATATTCCAATTTTGCCCTTAAATAATCAATTTTCCTGCTGATTT
*
2773592 CATGCCCTTGCTGTCCAGCCCAA
65 CATGCCCTTGCCGTCCAGCCCAA
2773615 ATAAATTTTA
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 80 1.00
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.43
Consensus pattern (87 bp):
TTTATTTAGTTAATTATACAATATTCCAATTTTGCCCTTAAATAATCAATTTTCCTGCTGATTTC
ATGCCCTTGCCGTCCAGCCCAA
Found at i:2787120 original size:18 final size:18
Alignment explanation
Indices: 2787097--2787135 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
2787087 AAGTCTCTCC
2787097 TTTAGAAAGTTTTGTTAT
1 TTTAGAAAGTTTTGTTAT
2787115 TTTAGAAAGTTTTGTTAT
1 TTTAGAAAGTTTTGTTAT
2787133 TTT
1 TTT
2787136 GTTCTAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (18 bp):
TTTAGAAAGTTTTGTTAT
Found at i:2787343 original size:14 final size:12
Alignment explanation
Indices: 2787323--2787401 Score: 56
Period size: 11 Copynumber: 6.2 Consensus size: 12
2787313 TTTCTTCATC
2787323 TTTTTTC-TTC-
1 TTTTTTCTTTCT
*
2787333 TTTGTTCTTTCTT
1 TTTTTTCTTTC-T
2787346 TTCTTTTCTTTCT
1 TT-TTTTCTTTCT
2787359 TTTCTTTCTTTTACT
1 TTT-TTTC-TTT-CT
*
2787374 TCCTTGTTCTTT-T
1 T--TTTTTCTTTCT
2787387 TTTTTTCTTTCT
1 TTTTTTCTTTCT
2787399 TTT
1 TTT
2787402 ACTTTTTTGT
Statistics
Matches: 55, Mismatches: 4, Indels: 18
0.71 0.05 0.23
Matches are distributed among these distances:
10 6 0.11
11 11 0.20
12 5 0.09
13 11 0.20
14 11 0.20
15 6 0.11
16 3 0.05
17 2 0.04
ACGTcount: A:0.01, C:0.19, G:0.03, T:0.77
Consensus pattern (12 bp):
TTTTTTCTTTCT
Found at i:2787351 original size:9 final size:9
Alignment explanation
Indices: 2787340--2787400 Score: 65
Period size: 9 Copynumber: 6.8 Consensus size: 9
2787330 TTCTTTGTTC
2787340 TTTCTTTTCT
1 TTTC-TTTCT
2787350 TTTCTTTCT
1 TTTCTTTCT
2787359 TTTCTTTCT
1 TTTCTTTCT
*
2787368 TTTACTTCCT
1 TTT-CTTTCT
2787378 TGTTCTTT-T
1 T-TTCTTTCT
2787387 TTT-TTTC-
1 TTTCTTTCT
2787394 TTTCTTT
1 TTTCTTT
2787401 TACTTTTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
7 6 0.13
8 5 0.11
9 19 0.42
10 13 0.29
11 2 0.04
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.77
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:2787356 original size:31 final size:31
Alignment explanation
Indices: 2787323--2787422 Score: 123
Period size: 31 Copynumber: 3.2 Consensus size: 31
2787313 TTTCTTCATC
*
2787323 TTTTTTC-TTCTTTGTTCTTTCTT-TTCTTTTCT
1 TTTTTTCTTTCTTT-TACTTTCTTGTTC-TTT-T
*
2787355 TTCTTTTCTTTCTTTTACTTCCTTGTTCTTTT
1 TT-TTTTCTTTCTTTTACTTTCTTGTTCTTTT
*
2787387 TTTTTTCTTTCTTTTACTTTTTTGTTCTTTT
1 TTTTTTCTTTCTTTTACTTTCTTGTTCTTTT
2787418 TTTTT
1 TTTTT
2787423 CTTGTTTTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
31 32 0.52
32 5 0.08
33 15 0.25
34 9 0.15
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (31 bp):
TTTTTTCTTTCTTTTACTTTCTTGTTCTTTT
Found at i:2787430 original size:10 final size:9
Alignment explanation
Indices: 2787309--2787431 Score: 77
Period size: 10 Copynumber: 13.0 Consensus size: 9
2787299 ACGTTAGTTC
*
2787309 TCTTTTTCT
1 TCTTTTTTT
*
2787318 TCATCTTTTT
1 TC-TTTTTTT
*
2787328 TCTTCTTTGT
1 TCTT-TTTTT
*
2787338 TCTTTCTTT
1 TCTTTTTTT
*
2787347 TCTTTTCTT
1 TCTTTTTTT
*
2787356 TCTTTTCTT
1 TCTTTTTTT
*
2787365 TCTTTTACTT
1 TCTTTT-TTT
* * *
2787375 CCTTGTTCT
1 TCTTTTTTT
2787384 T-TTTTTTT
1 TCTTTTTTT
2787392 TCTTTCTTTT
1 TCTTT-TTTT
*
2787402 ACTTTTTTGT
1 TCTTTTTT-T
2787412 TCTTTTTTTT
1 TC-TTTTTTT
2787422 TCTTGTTTTT
1 TCTT-TTTTT
2787432 GTATAGATAC
Statistics
Matches: 89, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
8 6 0.07
9 37 0.42
10 40 0.45
11 6 0.07
ACGTcount: A:0.02, C:0.18, G:0.03, T:0.76
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:2787430 original size:13 final size:13
Alignment explanation
Indices: 2787311--2787431 Score: 54
Period size: 13 Copynumber: 9.1 Consensus size: 13
2787301 GTTAGTTCTC
* *
2787311 TTTTTCTTCATCT
1 TTTTTCTTCTTTT
2787324 TTTTTCTTCTTTGT
1 TTTTTCTTCTTT-T
*
2787338 TCTTTCTT-TTCTT
1 TTTTTCTTCTT-TT
2787351 TTCTTTCTT-TTCTT
1 TT-TTTCTTCTT-TT
*
2787365 TCTTTTACTTCCTTGT
1 T-TTTT-CTT-CTTTT
*
2787381 TCTTT-TT-TTTT
1 TTTTTCTTCTTTT
* *
2787392 TCTTTCTT-TTACT
1 TTTTTCTTCTT-TT
*
2787405 TTTTTGTTCTTTT
1 TTTTTCTTCTTTT
*
2787418 TTTTTCTTGTTTT
1 TTTTTCTTCTTTT
2787431 T
1 T
2787432 GTATAGATAC
Statistics
Matches: 85, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
11 8 0.09
12 4 0.05
13 36 0.42
14 26 0.31
15 7 0.08
16 2 0.02
17 2 0.02
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTTTCTTCTTTT
Found at i:2787431 original size:9 final size:8
Alignment explanation
Indices: 2787309--2787420 Score: 64
Period size: 9 Copynumber: 12.1 Consensus size: 8
2787299 ACGTTAGTTC
2787309 TCTTTTTCT
1 TCTTTTT-T
2787318 TCATCTTTTT
1 TC-T-TTTTT
2787328 TCTTCTTTGT
1 TCTT-TTT-T
2787338 TCTTTCTTT
1 TCTTT-TTT
2787347 TCTTTTCTT
1 TCTTTT-TT
2787356 TCTTTTCTT
1 TCTTTT-TT
2787365 TCTTTTACTT
1 TCTTTT--TT
*
2787375 CCTTGTTCTT
1 TCTT-TT-TT
2787385 T-TTTTTT
1 TCTTTTTT
2787392 TCTTTCTTT
1 TCTTT-TTT
2787401 TACTTTTTTGT
1 T-C-TTTTT-T
2787412 TCTTTTTT
1 TCTTTTTT
2787420 T
1 T
2787421 TTCTTGTTTT
Statistics
Matches: 88, Mismatches: 2, Indels: 27
0.75 0.02 0.23
Matches are distributed among these distances:
7 3 0.03
8 9 0.10
9 41 0.47
10 24 0.27
11 11 0.12
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.76
Consensus pattern (8 bp):
TCTTTTTT
Found at i:2789545 original size:41 final size:40
Alignment explanation
Indices: 2789430--2789548 Score: 107
Period size: 41 Copynumber: 3.0 Consensus size: 40
2789420 CCTTATTCGA
* * * **
2789430 GCTTTGTGTCTAGCAGGCTTTGTGCTG-GTGATAT-TTGG
1 GCTTTGTGCCTAGCAGGCTTTGTGCAGTGTGTTATATCAG
* * ** * *
2789468 GCTCTATGCCTAGCAGGCTTCATGCCGGTGTATTATATCAG
1 GCTTTGTGCCTAGCAGGCTTTGTG-CAGTGTGTTATATCAG
2789509 GCTTTGTGCCTAGCAGGCTTTGTGTCAGTGTGTTATATCA
1 GCTTTGTGCCTAGCAGGCTTTGTG-CAGTGTGTTATATCA
2789549 ACCTTTGAGC
Statistics
Matches: 61, Mismatches: 17, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
38 19 0.31
39 2 0.03
40 5 0.08
41 35 0.57
ACGTcount: A:0.15, C:0.18, G:0.29, T:0.38
Consensus pattern (40 bp):
GCTTTGTGCCTAGCAGGCTTTGTGCAGTGTGTTATATCAG
Found at i:2789555 original size:41 final size:41
Alignment explanation
Indices: 2789474--2789570 Score: 104
Period size: 41 Copynumber: 2.4 Consensus size: 41
2789464 TTGGGCTCTA
* **
2789474 TGCCTAGCAGGCTTCATGCCGGTGTATTATATCAGGCTTTG
1 TGCCTAGCAGGCTTCATGCCAGTGTATTATATCAACCTTTG
** * *
2789515 TGCCTAGCAGGCTTTGTGTCAGTGTGTTATATCAACCTTTG
1 TGCCTAGCAGGCTTCATGCCAGTGTATTATATCAACCTTTG
* * *
2789556 AGCCTGGCAGTCTTC
1 TGCCTAGCAGGCTTC
2789571 GTACCAATAT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.35
Consensus pattern (41 bp):
TGCCTAGCAGGCTTCATGCCAGTGTATTATATCAACCTTTG
Found at i:2792432 original size:30 final size:31
Alignment explanation
Indices: 2792367--2792434 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
2792357 ATACATTAAC
* * *
2792367 TTAAACAAAAAATTTCGAATAATTTAATGAT
1 TTAAACAAAAAATTTCAAATAATTCAACGAT
* *
2792398 TTAAATAAAAAATTTTAAATAATTCAACGAT
1 TTAAACAAAAAATTTCAAATAATTCAACGAT
*
2792429 TAAAAC
1 TTAAAC
2792435 GTAAACTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.34
Consensus pattern (31 bp):
TTAAACAAAAAATTTCAAATAATTCAACGAT
Found at i:2794891 original size:16 final size:18
Alignment explanation
Indices: 2794857--2794896 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
2794847 CGTATAATAA
*
2794857 TAAATTTAATTTTTCGTT
1 TAAATTTAATTTTTAGTT
2794875 TAAATTT-A-TTTTAGTT
1 TAAATTTAATTTTTAGTT
2794891 TAAATT
1 TAAATT
2794897 AAAATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.62
17 1 0.05
18 7 0.33
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (18 bp):
TAAATTTAATTTTTAGTT
Found at i:2797430 original size:30 final size:30
Alignment explanation
Indices: 2797396--2797458 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
2797386 ACTTAACAAG
2797396 CAAATG-CTTCTAAAATAATAAAAAAATTAA
1 CAAATGCCTT-TAAAATAATAAAAAAATTAA
*
2797426 CAAATGCCTTTAAAATAATAAGAAAATTAA
1 CAAATGCCTTTAAAATAATAAAAAAATTAA
2797456 CAA
1 CAA
2797459 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.25
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAAAAAAATTAA
Found at i:2799430 original size:37 final size:37
Alignment explanation
Indices: 2799377--2799479 Score: 188
Period size: 37 Copynumber: 2.8 Consensus size: 37
2799367 CGAATAGTCC
*
2799377 CCACACGTAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
2799414 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
2799451 CCACACGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
2799480 ATATATTTCC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.23
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:2799678 original size:48 final size:48
Alignment explanation
Indices: 2799620--2800003 Score: 351
Period size: 48 Copynumber: 8.0 Consensus size: 48
2799610 ATATACACAC
*
2799620 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
2799668 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * * * * * ***
2799716 ATATGGCTTTACCACATAT-ACA-TATCTCATACATATTT--CACAT-TAGCCAT
1 ATCT--C-ATA-CATATTTCACACTAGC-CATTCGGCTTTACCACATATA--CAT
* * * * *
2799766 -TCGGCTTTACCACATAT-ACA-TA--TA-T-GGCTTTACCACATATACAT
1 ATC-TC-ATA-CATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
2799810 ATCTCATACATATTTCACACTAGCCATTCAGCTTTACCACATAAACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * * * *
2799858 ATCTCATATATATTTCACATTAGCCATTCAGCTTTACTATATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
2799906 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * *
2799954 ATCTCATACATATTTCACACTAGTCATTCGGCTTTACCACACATATAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
2800002 AT
1 AT
2800004 ATTTATCTTG
Statistics
Matches: 280, Mismatches: 38, Indels: 36
0.79 0.11 0.10
Matches are distributed among these distances:
42 5 0.02
43 8 0.03
44 6 0.02
45 8 0.03
46 3 0.01
47 1 0.00
48 219 0.78
49 6 0.02
50 7 0.03
51 12 0.04
52 5 0.02
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.35
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:2799724 original size:23 final size:23
Alignment explanation
Indices: 2799697--2799811 Score: 105
Period size: 23 Copynumber: 4.9 Consensus size: 23
2799687 TTAGCCATTC
2799697 GGCTTTACCACATATACATATAT
1 GGCTTTACCACATATACATATAT
2799720 GGCTTTACCACATATACATATCTCAT
1 GGCTTTACCACATATACATA--T-AT
* * *
2799746 -ACATATT-TCACAT-TAGCCAT-T-C
1 GGC-T-TTACCACATATA--CATATAT
2799768 GGCTTTACCACATATACATATAT
1 GGCTTTACCACATATACATATAT
2799791 GGCTTTACCACATATACATAT
1 GGCTTTACCACATATACATAT
2799812 CTCATACATA
Statistics
Matches: 74, Mismatches: 6, Indels: 24
0.71 0.06 0.23
Matches are distributed among these distances:
21 5 0.07
22 7 0.09
23 44 0.59
24 1 0.01
25 4 0.05
26 8 0.11
27 5 0.07
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.35
Consensus pattern (23 bp):
GGCTTTACCACATATACATATAT
Found at i:2799733 original size:71 final size:71
Alignment explanation
Indices: 2799649--2799859 Score: 395
Period size: 71 Copynumber: 3.0 Consensus size: 71
2799639 CTAGCCATTC
2799649 GGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATAC
1 GGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATAC
2799714 ATATAT
66 ATATAT
2799720 GGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATAC
1 GGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATAC
2799785 ATATAT
66 ATATAT
* * *
2799791 GGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCATTCAGCTTTACCACATAAAC
1 GGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATAC
2799856 ATAT
66 ATAT
2799860 CTCATATATA
Statistics
Matches: 137, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 137 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.34
Consensus pattern (71 bp):
GGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATAC
ATATAT
Found at i:2799755 original size:119 final size:118
Alignment explanation
Indices: 2799620--2799956 Score: 398
Period size: 119 Copynumber: 2.8 Consensus size: 118
2799610 ATATACACAC
* *
2799620 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
*
2799685 CATTAGCCATTCGGCTTTACCACATATACATAT-ATGGCTTTACCACATATACAT
66 CATTAGCCATTCGGCTTTACCACATATACATATCA--GCTTTACCACATAAACAT
* * *
2799739 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATATGGCTTTACCACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCT--C-ATA-CATAT
* * * *** **
2799804 AT-ACA-TATCTCATACATATTT--CACACTAGCCAT-TCAGCTTTACCACATAAACAT
62 TTCACATTAGC-CATTCGGCTTTACCACA-TATACATATCAGCTTTACCACATAAACAT
* * * *
2799858 ATCTCATATATATTTCACATTAGCCATTCAGCTTTACTATATATACATATCTCATACATATTTCA
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
2799923 CATTAGCCATTCGGCTTTACCACATATACATATC
66 CATTAGCCATTCGGCTTTACCACATATACATATC
2799957 TCATACATAT
Statistics
Matches: 177, Mismatches: 29, Indels: 25
0.77 0.13 0.11
Matches are distributed among these distances:
115 5 0.03
116 12 0.07
117 9 0.05
118 6 0.03
119 113 0.64
120 5 0.03
121 10 0.06
122 12 0.07
123 5 0.03
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.35
Consensus pattern (118 bp):
ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
CATTAGCCATTCGGCTTTACCACATATACATATCAGCTTTACCACATAAACAT
Found at i:2800872 original size:14 final size:14
Alignment explanation
Indices: 2800853--2800880 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2800843 TCTTTAAAAA
2800853 GAATTAACTTATTT
1 GAATTAACTTATTT
2800867 GAATTAACTTATTT
1 GAATTAACTTATTT
2800881 TTAAAGGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (14 bp):
GAATTAACTTATTT
Found at i:2805237 original size:25 final size:25
Alignment explanation
Indices: 2805210--2805304 Score: 75
Period size: 26 Copynumber: 3.4 Consensus size: 25
2805200 AAAATATTTG
2805210 AAATATTTTAATATAATTTAATATGA
1 AAATATTTTAATATAATTTAATAT-A
*
2805236 AATATTTAATTTCAAAATATAATTTTAA-ATA
1 AA-A--T-ATTT--TAATATAA-TTTAATATA
*
2805267 AAATATTTTAATAAAATTTAATATAA
1 AAATATTTTAATATAATTTAATAT-A
2805293 AAATATTATTAA
1 AAATATT-TTAA
2805305 ATTATATATT
Statistics
Matches: 56, Mismatches: 3, Indels: 19
0.72 0.04 0.24
Matches are distributed among these distances:
24 5 0.09
25 8 0.14
26 10 0.18
27 9 0.16
28 1 0.02
29 1 0.02
30 5 0.09
31 3 0.05
32 9 0.16
33 5 0.09
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (25 bp):
AAATATTTTAATATAATTTAATATA
Found at i:2805305 original size:24 final size:24
Alignment explanation
Indices: 2805259--2805305 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2805249 AAAATATAAT
*
2805259 TTTAAATAAAATATTTTAATAAAA
1 TTTAAATAAAATATATTAATAAAA
*
2805283 TTTAATATAAAA-ATATTATTAAA
1 TTTAA-ATAAAATATATTAATAAA
2805306 TTATATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTAAATAAAATATATTAATAAAA
Found at i:2805379 original size:26 final size:26
Alignment explanation
Indices: 2805318--2805376 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
2805308 ATATATTTTT
*
2805318 ATTTTATTAAAATATATTTAATAATA
1 ATTTTATTAAAATATAATTAATAATA
*
2805344 ATTATATTAAAATATAATTAA-AATA
1 ATTTTATTAAAATATAATTAATAATA
*
2805369 TTTTTATT
1 ATTTTATT
2805377 TAATTATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 10 0.34
26 19 0.66
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATTTTATTAAAATATAATTAATAATA
Found at i:2810595 original size:68 final size:70
Alignment explanation
Indices: 2810504--2810642 Score: 174
Period size: 72 Copynumber: 2.0 Consensus size: 70
2810494 TTTTAATAGA
* * * * *
2810504 TTTAATATTGAATTAAAATTAATATTTA-TGT-TAATAGTATTTTATTAATTTAATATTAAAGTA
1 TTTAATATTAAATTAAAATTAATATTTATTGTAGAAAAATATTCTATTAATTTAATATTAAAGTA
2810567 ATTAT
66 ATTAT
* *
2810572 TTTAATATTAAATTTAATTTAATATTTATCTTGTAGAAAAATATTCTATTAATTTAATATTAAAG
1 TTTAATATTAAATTAAAATTAATATTTA--TTGTAGAAAAATATTCTATTAATTTAATATTAAAG
*
2810637 TGATTA
64 TAATTA
2810643 CGTTTAATTA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
68 25 0.42
71 3 0.05
72 31 0.53
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.50
Consensus pattern (70 bp):
TTTAATATTAAATTAAAATTAATATTTATTGTAGAAAAATATTCTATTAATTTAATATTAAAGTA
ATTAT
Found at i:2811488 original size:25 final size:25
Alignment explanation
Indices: 2811460--2811511 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
2811450 TTTGGCTTGA
**
2811460 CATTTACTAAGCAATATCGGATATT
1 CATTTACTAAGCAATATCAAATATT
* *
2811485 CATTTATTAGGCAATATCAAATATT
1 CATTTACTAAGCAATATCAAATATT
2811510 CA
1 CA
2811512 AATTATTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (25 bp):
CATTTACTAAGCAATATCAAATATT
Found at i:2813509 original size:22 final size:22
Alignment explanation
Indices: 2813484--2813528 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
2813474 CGACTGATTT
*
2813484 TCAAAGTATGCGACCTTTATTC
1 TCAAAGTATGCGACCTTCATTC
2813506 TCAAAGTATGCGACCTTCATTC
1 TCAAAGTATGCGACCTTCATTC
2813528 T
1 T
2813529 TGCCATGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (22 bp):
TCAAAGTATGCGACCTTCATTC
Found at i:2815862 original size:23 final size:23
Alignment explanation
Indices: 2815836--2815882 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
2815826 TAAATTTTGA
*
2815836 ATTATTTAATGATAATATTTAGG
1 ATTATTCAATGATAATATTTAGG
*
2815859 ATTATTCAGTGATAATATTTAGG
1 ATTATTCAATGATAATATTTAGG
2815882 A
1 A
2815883 AAAATCTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.15, T:0.45
Consensus pattern (23 bp):
ATTATTCAATGATAATATTTAGG
Found at i:2825802 original size:23 final size:23
Alignment explanation
Indices: 2825775--2825822 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2825765 ATCTTTCTAC
2825775 ATTCTTATATTAAATCAATAAAA
1 ATTCTTATATTAAATCAATAAAA
2825798 ATTCTTATATTAAATCAATAAAA
1 ATTCTTATATTAAATCAATAAAA
2825821 AT
1 AT
2825823 CCATATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (23 bp):
ATTCTTATATTAAATCAATAAAA
Found at i:2825829 original size:23 final size:23
Alignment explanation
Indices: 2825780--2825830 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
2825770 TCTACATTCT
* *
2825780 TATATTAAATCAATAAAAATTCT
1 TATATTAAATCAATAAAAATCCA
2825803 TATATTAAATCAATAAAAATCCA
1 TATATTAAATCAATAAAAATCCA
2825826 TATAT
1 TATAT
2825831 AATAAAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (23 bp):
TATATTAAATCAATAAAAATCCA
Found at i:2832209 original size:14 final size:15
Alignment explanation
Indices: 2832181--2832210 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2832171 ACATAGAAAG
2832181 ATATAAAACAAATAA
1 ATATAAAACAAATAA
2832196 ATATAAAA-AAATAA
1 ATATAAAACAAATAA
2832210 A
1 A
2832211 AAAACTTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (15 bp):
ATATAAAACAAATAA
Found at i:2832813 original size:13 final size:15
Alignment explanation
Indices: 2832783--2832819 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2832773 TTTTAATTTC
2832783 AATATTATTTATATT
1 AATATTATTTATATT
2832798 AATA-TATTTA-ATT
1 AATATTATTTATATT
*
2832811 AATGTTATT
1 AATATTATT
2832820 ATTATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 6 0.30
14 10 0.50
15 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
AATATTATTTATATT
Found at i:2845386 original size:36 final size:36
Alignment explanation
Indices: 2845336--2845407 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
2845326 ATTTGTAGCC
* *
2845336 GTTGAATGCGATCCCTTTCCTCTTTATGATACCTTT
1 GTTGAATGCAATCCCCTTCCTCTTTATGATACCTTT
2845372 GTTGAATGCAATCCCCTTCCTCTTTATGATACCTTT
1 GTTGAATGCAATCCCCTTCCTCTTTATGATACCTTT
2845408 TACTGTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.18, C:0.26, G:0.12, T:0.43
Consensus pattern (36 bp):
GTTGAATGCAATCCCCTTCCTCTTTATGATACCTTT
Found at i:2846039 original size:14 final size:14
Alignment explanation
Indices: 2846020--2846050 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2846010 GCTGAGGTAA
*
2846020 TTTCAATTTCTATT
1 TTTCAATTTATATT
2846034 TTTCAATTTATATT
1 TTTCAATTTATATT
2846048 TTT
1 TTT
2846051 TAAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTCAATTTATATT
Found at i:2846089 original size:87 final size:87
Alignment explanation
Indices: 2845957--2846469 Score: 439
Period size: 87 Copynumber: 5.9 Consensus size: 87
2845947 TTGATGTTTT
* **
2845957 TATTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGATACGCTGAGGTAATT
1 TATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGCTGAGGTAATT
*
2846022 TCAATTTCTATTTTTCAATTTA
66 TCAATTTCTATTTTTCAATTTC
* * *
2846044 TATTTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGTACGCTGATG-AATT
1 TATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGCTGAGGTAA-T
* ** *
2846108 TTC-ATTTTTGCTTTTCAATCTC
65 TTCAATTTCTATTTTTCAATTTC
* *
2846130 TA-TTTTCAAAAATCAACTCATATTGC--GAGGTGAGTTGAGCCT-TGGCTCACATGCTGAGG--
1 TATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAT-AC--GCTGAGGTA
* *
2846189 ----CATTTTC-AGTTTTT--ATTTA
63 ATTTCAATTTCTA-TTTTTCAATTTC
* * * * * * * *
2846208 TACTTTTCAAAAATCAACTCATATTGTGAGAGATGAGTTGAACCTCGGGCCACATGCCGAGGT-A
1 TATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ATACGCTGAGGTAA
* **
2846272 TTCTCAAAATTCCGTTTTTCAATTTC
64 TT-TC-AATTTCTATTTTTCAATTTC
* *
2846298 TGTTTCTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCATAAGCTGAGGT
1 TATTT-TT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ATACGCTGAGGT
*
2846363 AATTTCAATTTCTGTTTTTCAATTTC
62 AATTTCAATTTCTATTTTTCAATTTC
** * * * *
2846389 TGCTTTTCAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACGTGCTGAGCTA
1 TATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAT-AC--GCTGAGGTA
*
2846453 CTTTCAATTTCTATTTT
63 ATTTCAATTTCTATTTT
2846470 CAAAAATCAA
Statistics
Matches: 345, Mismatches: 53, Indels: 54
0.76 0.12 0.12
Matches are distributed among these distances:
78 5 0.01
79 24 0.07
80 7 0.02
81 20 0.06
82 5 0.01
83 19 0.06
85 29 0.08
86 19 0.06
87 60 0.17
88 11 0.03
89 60 0.17
90 9 0.03
91 24 0.07
92 50 0.14
93 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (87 bp):
TATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGCTGAGGTAATT
TCAATTTCTATTTTTCAATTTC
Found at i:2846384 original size:14 final size:14
Alignment explanation
Indices: 2846365--2846398 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2846355 GCTGAGGTAA
*
2846365 TTTCAATTTCTGTT
1 TTTCAATTTCTGCT
2846379 TTTCAATTTCTGCT
1 TTTCAATTTCTGCT
2846393 TTTCAA
1 TTTCAA
2846399 AAATCAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.59
Consensus pattern (14 bp):
TTTCAATTTCTGCT
Found at i:2846448 original size:89 final size:90
Alignment explanation
Indices: 2845960--2846469 Score: 492
Period size: 89 Copynumber: 5.9 Consensus size: 90
2845950 ATGTTTTTAT
* ** *
2845960 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGAT-AC--GCTGAGGTAATT
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCTCACATGCTGAGGTAATT
* * *
2846022 TCAATTTCTATTTTTCAATTTATAT
66 TCAATTTCTGTTTTTCAATTTCTAC
* * *
2846047 TTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGT-AC--GCTGATG-AATT
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCTCACATGCTGAGGTAA-T
* * *
2846108 TTC-ATTTTTGCTTTTCAATCTCTA-
65 TTCAATTTCTGTTTTTCAATTTCTAC
*
2846132 TTTTCAAAAATCAACTCATATTGC--GAGGTGAGTTGAGCCT-TGGCTCACATGCTGAGG-----
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCTCACATGCTGAGGTAATT
* * *
2846189 -CATTTTCAGTTTTT--ATTTATAC
66 TCAATTTCTGTTTTTCAATTTCTAC
* * * * *
2846211 TTTTCAAAAATCAACTCATATTGTGAGAGATGAGTTGAACCTCGGGC-CACATGCCGAGGT-ATT
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCTCACATGCTGAGGTAATT
* * **
2846274 CTCAAAATTCCGTTTTTCAATTTCTGT
66 -TC-AATTTCTGTTTTTCAATTTCTAC
* *
2846301 TTCTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCATAAGCTGAGGTAA
1 TT-TT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCTCACATGCTGAGGTAA
*
2846365 TTTCAATTTCTGTTTTTCAATTTCTGC
64 TTTCAATTTCTGTTTTTCAATTTCTAC
* * * * *
2846392 TTTTCAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACGTGCTGAGCTACTT
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCTCACATGCTGAGGTAATT
*
2846456 TCAATTTCTATTTT
66 TCAATTTCTGTTTT
2846470 CAAAAATCAA
Statistics
Matches: 350, Mismatches: 50, Indels: 44
0.79 0.11 0.10
Matches are distributed among these distances:
78 5 0.01
79 24 0.07
80 8 0.02
81 25 0.07
82 6 0.02
83 18 0.05
85 29 0.08
86 18 0.05
87 56 0.16
88 12 0.03
89 63 0.18
90 9 0.03
91 24 0.07
92 50 0.14
93 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (90 bp):
TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCTCACATGCTGAGGTAATT
TCAATTTCTGTTTTTCAATTTCTAC
Found at i:2846492 original size:163 final size:162
Alignment explanation
Indices: 2846288--2846757 Score: 764
Period size: 163 Copynumber: 2.9 Consensus size: 162
2846278 AAATTCCGTT
*
2846288 TTTCAATTTCTGTTTCTTCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCAT
1 TTTCAATTTCT-ATT-TT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCAT
*
2846353 AAGCTGAGGTAATTTCAATTTCTGTTTTTCAATTTCTGCTTTTCAAAAATCAACTCACATTGCGA
63 AAGTTGAGGTAATTTCAATTTCTGTTTTTCAATTTCT-CTTTTCAAAAATCAACTCACATTGCGA
2846418 GAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTAC
127 GAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTAC
*
2846454 TTTCAATTTCTATTTTCAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCAGGTCATAAG
1 TTTCAATTTCTATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCATAAG
* *
2846519 TTGGGGTAATTTCAATTTTTGTTTTTCAATTTCTACTTTTCAAAAATCAACTCACATTGCGAGAG
66 TTGAGGTAATTTCAATTTCTGTTTTTCAATTTCT-CTTTTCAAAAATCAACTCACATTGCGAGAG
2846584 GTGAGTTGAGCCTTGGCTCACGTGCTGAGCTAC
130 GTGAGTTGAGCCTTGGCTCACGTGCTGAGCTAC
* *
2846617 TTTCAATTTCTATTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACAT--G
1 TTTCAATTTCTATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCATAAG
* * * * *
2846680 TTGAGGTATTTTCAATTTCTATTTTTCAATTTATATCTTTCAAAAATCAACTCATATTGCGAGAG
66 TTGAGGTAATTTCAATTTCTGTTTTTCAATTTCTCT-TTTCAAAAATCAACTCACATTGCGAGAG
2846745 GTGAGTTGAGCCT
130 GTGAGTTGAGCCT
2846758 CAGGGCACGC
Statistics
Matches: 287, Mismatches: 16, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
160 1 0.00
161 70 0.24
163 201 0.70
164 2 0.01
165 2 0.01
166 11 0.04
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.37
Consensus pattern (162 bp):
TTTCAATTTCTATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCATAAG
TTGAGGTAATTTCAATTTCTGTTTTTCAATTTCTCTTTTCAAAAATCAACTCACATTGCGAGAGG
TGAGTTGAGCCTTGGCTCACGTGCTGAGCTAC
Found at i:2846532 original size:74 final size:75
Alignment explanation
Indices: 2846379--2846547 Score: 198
Period size: 74 Copynumber: 2.3 Consensus size: 75
2846369 AATTTCTGTT
* * **
2846379 TTTCAATTTCTGCTTTTCAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGT
1 TTTCAATTTCTGATTTTCAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTAGGCTCACAA
*
2846444 GCTGAGCTAC
66 GCTGAGCTAA
* * *
2846454 TTTCAATTTCT-ATTTTCAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCAGG-TCATA
1 TTTCAATTTCTGATTTTCAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCT-AGGCTCACA
* * *
2846517 AGTTGGGGTAA
65 AGCTGAGCTAA
* *
2846528 TTTCAATTTTTGTTTTTCAA
1 TTTCAATTTCTGATTTTCAA
2846548 TTTCTACTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
74 59 0.75
75 20 0.25
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (75 bp):
TTTCAATTTCTGATTTTCAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTAGGCTCACAA
GCTGAGCTAA
Found at i:2846621 original size:89 final size:88
Alignment explanation
Indices: 2846454--2846625 Score: 229
Period size: 89 Copynumber: 1.9 Consensus size: 88
2846444 GCTGAGCTAC
* * *
2846454 TTTCAATTTCTATTTTCAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCAGGTCATAAG
1 TTTCAATTTCTATTTTCAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCAGGTCACAAG
* * *
2846519 TTGGGGTAATTTCAATTTTTGTT
66 CTGAGCTAATTTCAATTTTTGTT
* *
2846542 TTTCAATTTCTACTTTTCAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACG
1 TTTCAATTTCTA-TTTTCAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCAGG-TCACA
* *
2846606 TGCTGAGCTACTTTCAATTT
64 AGCTGAGCTAATTTCAATTT
2846626 CTATTTTCAA
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
88 14 0.19
89 58 0.81
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.38
Consensus pattern (88 bp):
TTTCAATTTCTATTTTCAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCAGGTCACAAG
CTGAGCTAATTTCAATTTTTGTT
Found at i:2846707 original size:14 final size:14
Alignment explanation
Indices: 2846688--2846722 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2846678 TGTTGAGGTA
*
2846688 TTTTCAATTTCTAT
1 TTTTCAATTTATAT
2846702 TTTTCAATTTATAT
1 TTTTCAATTTATAT
*
2846716 CTTTCAA
1 TTTTCAA
2846723 AAATCAACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTATAT
Found at i:2846776 original size:87 final size:86
Alignment explanation
Indices: 2846613--2846842 Score: 295
Period size: 87 Copynumber: 2.7 Consensus size: 86
2846603 ACGTGCTGAG
* *
2846613 CTAC-TTTCAATTTCTATTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
1 CTACTTTTCAATTTATATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
* * **
2846677 ATGTTGAGGTATTTTCAATTT
66 ACGCTGAGGTATTTTCAAAAT
* *
2846698 CTATTTTTCAATTTATATCTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGG
1 CTACTTTTCAATTTATAT-TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
2846763 CACGCTGCA-GTATTTTCAAAAT
65 CACGCTG-AGGTATTTTCAAAAT
* * * * * *
2846785 CTGCTTTCCAAATTA-AGTTTCAAAAACCAACTCACATTGCGAGAGGTGAGTTGAGCCT
1 CTACTTTTCAATTTATATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
2846843 TGGCTCACGT
Statistics
Matches: 127, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
85 42 0.33
86 13 0.10
87 71 0.56
88 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (86 bp):
CTACTTTTCAATTTATATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
ACGCTGAGGTATTTTCAAAAT
Found at i:2847958 original size:14 final size:15
Alignment explanation
Indices: 2847930--2847959 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2847920 ACATAGAAAG
2847930 ATATAAAACAAATAA
1 ATATAAAACAAATAA
2847945 ATATAAAA-AAATAA
1 ATATAAAACAAATAA
2847959 A
1 A
2847960 AAAACTTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (15 bp):
ATATAAAACAAATAA
Found at i:2860440 original size:46 final size:46
Alignment explanation
Indices: 2860388--2860799 Score: 727
Period size: 46 Copynumber: 9.0 Consensus size: 46
2860378 AGTGTGCTCT
2860388 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
2860434 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
2860480 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
2860526 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
2860572 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
2860618 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
2860664 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
2860710 ATGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
2860756 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
2860800 TCATGTCAAA
Statistics
Matches: 357, Mismatches: 8, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
45 1 0.00
46 356 1.00
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:2867542 original size:22 final size:22
Alignment explanation
Indices: 2867512--2867559 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
2867502 ATTGATACTA
*
2867512 AATTTATTC-TTTATTATTTTTG
1 AATTGATTCGTTT-TTATTTTTG
* *
2867534 AATTGATTCGTTTTTCTTTTTT
1 AATTGATTCGTTTTTATTTTTG
2867556 AATT
1 AATT
2867560 TTATGTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (22 bp):
AATTGATTCGTTTTTATTTTTG
Found at i:2869995 original size:67 final size:67
Alignment explanation
Indices: 2869923--2870122 Score: 348
Period size: 67 Copynumber: 3.0 Consensus size: 67
2869913 TCCTTTTCAA
* * * *
2869923 AGAGCACACTCTCACGAACCTCATTTCTTACAGCAGGATTA-TCAATCCAGGCTAAATCCCCTGT
1 AGAGCACACTCCCGCGAACCTCATTTCTTACAGCAAGATTACT-AGTCCAGGCTAAATCCCCTGT
2869987 AAG
65 AAG
2869990 AGAGCACACTCCCGCGAACCTCATTTCTTACAGCAAGATTACTAGTCCAGGCTAAATCCCCTGTA
1 AGAGCACACTCCCGCGAACCTCATTTCTTACAGCAAGATTACTAGTCCAGGCTAAATCCCCTGTA
2870055 AG
66 AG
2870057 AGAGCACACTCCCGCGAACCTCATTTCTTACAGCAAGATTACTAGTCCAGGCTAAATCCCCTGTA
1 AGAGCACACTCCCGCGAACCTCATTTCTTACAGCAAGATTACTAGTCCAGGCTAAATCCCCTGTA
2870122 A
66 A
2870123 CATATGCTCA
Statistics
Matches: 128, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
67 127 0.99
68 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.15, T:0.23
Consensus pattern (67 bp):
AGAGCACACTCCCGCGAACCTCATTTCTTACAGCAAGATTACTAGTCCAGGCTAAATCCCCTGTA
AG
Found at i:2876188 original size:23 final size:23
Alignment explanation
Indices: 2876156--2876199 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2876146 ACTATCATTT
2876156 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
2876179 TCTAATTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
2876200 ACAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:2876589 original size:3 final size:3
Alignment explanation
Indices: 2876575--2876606 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2876565 CTTCTTAATT
*
2876575 ATC ATT ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
2876607 TATTATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.28, G:0.00, T:0.38
Consensus pattern (3 bp):
ATC
Found at i:2881497 original size:26 final size:25
Alignment explanation
Indices: 2881468--2881517 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2881458 AACAATAATT
* *
2881468 ATATAAATTATTTAAAATTTATAAAA
1 ATATAAA-TATTGAAAAATTATAAAA
*
2881494 ATATATATATTGAAAAATTATAAA
1 ATATAAATATTGAAAAATTATAAA
2881518 TCAACTCAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
ATATAAATATTGAAAAATTATAAAA
Found at i:2889427 original size:5 final size:5
Alignment explanation
Indices: 2889414--2889491 Score: 52
Period size: 5 Copynumber: 14.8 Consensus size: 5
2889404 CCTGACACCT
* * * *
2889414 TTTTG TTTTC TTTTTC TTTTA TTTTC ATATTTT TTTTG TTTT- TTTTC
1 TTTTC TTTTC -TTTTC TTTTC TTTTC -T-TTTC TTTTC TTTTC TTTTC
2889461 TTTTC TTTTC ATATTTC TTTT- TTTTAC TTTT
1 TTTTC TTTTC -T-TTTC TTTTC TTTT-C TTTT
2889492 TTATTTTGTT
Statistics
Matches: 60, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
4 8 0.13
5 32 0.53
6 13 0.22
7 7 0.12
ACGTcount: A:0.08, C:0.10, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:2889459 original size:31 final size:31
Alignment explanation
Indices: 2889413--2889498 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 31
2889403 GCCTGACACC
2889413 TTTTTGTTTTCTTTTTCTTTTATTTTCATATTT
1 TTTTTG-TTT-TTTTTCTTTTATTTTCATATTT
*
2889446 TTTTTGTTTTTTTTCTTTTCTTTTCATATTT
1 TTTTTGTTTTTTTTCTTTTATTTTCATATTT
* **
2889477 CTTTT-TTTTACTT-TTTTATTTT
1 TTTTTGTTTTTTTTCTTTTATTTT
2889499 GTTCCTTAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 8 0.17
30 6 0.12
31 25 0.52
32 3 0.06
33 6 0.12
ACGTcount: A:0.08, C:0.09, G:0.02, T:0.80
Consensus pattern (31 bp):
TTTTTGTTTTTTTTCTTTTATTTTCATATTT
Found at i:2889585 original size:17 final size:16
Alignment explanation
Indices: 2889517--2889585 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 16
2889507 ATAAATTGTC
2889517 TTTTTT-TTTTTTTTA
1 TTTTTTATTTTTTTTA
*
2889532 CTTTTTTGATTTTTTTTC
1 -TTTTTT-ATTTTTTTTA
* *
2889550 TTATTTCATTTTGTTTA
1 TT-TTTTATTTTTTTTA
2889567 TTTTGTT-TTATTTTTTA
1 TTTT-TTATT-TTTTTTA
2889584 TT
1 TT
2889586 ATTAACTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
16 10 0.24
17 21 0.50
18 11 0.26
ACGTcount: A:0.10, C:0.04, G:0.04, T:0.81
Consensus pattern (16 bp):
TTTTTTATTTTTTTTA
Found at i:2889767 original size:14 final size:14
Alignment explanation
Indices: 2889750--2889776 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2889740 TTTTTTAAAA
2889750 TTTTAAATATTAAT
1 TTTTAAATATTAAT
2889764 TTTTAAATATTAA
1 TTTTAAATATTAA
2889777 CCATATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTAAATATTAAT
Found at i:2889776 original size:37 final size:35
Alignment explanation
Indices: 2889634--2889776 Score: 137
Period size: 37 Copynumber: 4.0 Consensus size: 35
2889624 TTTATAATAC
* *
2889634 TTTTTTAAAATTTTAATTATTATTTTTAAAAAT-A
1 TTTTTTAAAATTTTAAATATTATTTTTAAAATTAA
* * * * *
2889668 TTTTTT-TAACTTTAGATATATATTTGTGAAATTAA
1 TTTTTTAAAATTTTAAATAT-TATTTTTAAAATTAA
* * *
2889703 TTTTTTATATATTTTAAAAATGTATTTTTCAAATTAA
1 TTTTTTA-AAATTTTAAATAT-TATTTTTAAAATTAA
2889740 TTTTTTAAAATTTTAAATATTAATTTTTAAATATTAA
1 TTTTTTAAAATTTTAAATATT-ATTTTTAAA-ATTAA
2889777 CCATATTTTT
Statistics
Matches: 85, Mismatches: 18, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
33 9 0.11
34 16 0.19
35 8 0.09
36 19 0.22
37 33 0.39
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (35 bp):
TTTTTTAAAATTTTAAATATTATTTTTAAAATTAA
Found at i:2889783 original size:23 final size:23
Alignment explanation
Indices: 2889735--2889776 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
2889725 TATTTTTCAA
*
2889735 ATTAATTTTTTAAAATTTTAAAT
1 ATTAATTTTTTAAAATATTAAAT
2889758 ATTAA-TTTTT-AAATATTAA
1 ATTAATTTTTTAAAATATTAA
2889777 CCATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 5 0.28
23 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTAATTTTTTAAAATATTAAAT
Found at i:2889866 original size:20 final size:19
Alignment explanation
Indices: 2889828--2889874 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
2889818 TTGTAAATAC
2889828 AATTTCTTTAATTTCTTTTT
1 AATTT-TTTAATTTCTTTTT
2889848 AAATTTTTTAACTTT-TTTTT
1 -AATTTTTTAA-TTTCTTTTT
2889868 AATTTTT
1 AATTTTT
2889875 GAAAAGTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.28
20 10 0.40
21 8 0.32
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (19 bp):
AATTTTTTAATTTCTTTTT
Found at i:2891666 original size:21 final size:21
Alignment explanation
Indices: 2891638--2891681 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2891628 TTAAAAAAAG
2891638 AATTT-AAAAATAATATT-TAA
1 AATTTAAAAAAT-ATATTATAA
2891658 AATTGTAAAAAATATATTATAA
1 AATT-TAAAAAATATATTATAA
2891680 AA
1 AA
2891682 CATTTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.19
21 6 0.29
22 11 0.52
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AATTTAAAAAATATATTATAA
Found at i:2891773 original size:26 final size:27
Alignment explanation
Indices: 2891740--2891798 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
2891730 TAAACAAAAT
*
2891740 AAAATTATGATTTCTTATAT-TATTAA
1 AAAATTATGATTTCTTAAATGTATTAA
* *
2891766 AAAATTATGATTTTTTAAATGTATTTA
1 AAAATTATGATTTCTTAAATGTATTAA
2891793 AAAATT
1 AAAATT
2891799 GTATTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 18 0.62
27 11 0.38
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (27 bp):
AAAATTATGATTTCTTAAATGTATTAA
Found at i:2891927 original size:16 final size:16
Alignment explanation
Indices: 2891904--2891942 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2891894 AATAATAATT
2891904 AAAC-ATAAAAAAACA
1 AAACAATAAAAAAACA
*
2891919 AAACAATAAAAAAAGA
1 AAACAATAAAAAAACA
*
2891935 AAAAAATA
1 AAACAATA
2891943 TTTAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.82, C:0.08, G:0.03, T:0.08
Consensus pattern (16 bp):
AAACAATAAAAAAACA
Found at i:2892125 original size:12 final size:13
Alignment explanation
Indices: 2892094--2892127 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
2892084 ATATCTAATG
2892094 TTAAAAAAAGAAT
1 TTAAAAAAAGAAT
2892107 TTAAAAATAA-AAT
1 TTAAAAA-AAGAAT
2892120 TTAAAAAA
1 TTAAAAAA
2892128 TTGTATGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 1 0.05
13 17 0.85
14 2 0.10
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (13 bp):
TTAAAAAAAGAAT
Found at i:2892194 original size:25 final size:24
Alignment explanation
Indices: 2892161--2892245 Score: 72
Period size: 24 Copynumber: 3.5 Consensus size: 24
2892151 TTAAACATAC
2892161 ATTTC-AAATATTATAAAACTAATA
1 ATTTCAAAATATTATAAAA-TAATA
2892185 ATTTCAAAATTAATT-TAAAA-ATATA
1 ATTTCAAAA-T-ATTATAAAATA-ATA
*
2892210 TATTT-AAAAT-TTATAAAAAAATA
1 -ATTTCAAAATATTATAAAATAATA
2892233 ATTTCACAAATAT
1 ATTTCA-AAATAT
2892246 ATATCTAAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 19
0.73 0.00 0.27
Matches are distributed among these distances:
22 6 0.12
23 9 0.18
24 12 0.24
25 11 0.22
26 10 0.20
27 3 0.06
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (24 bp):
ATTTCAAAATATTATAAAATAATA
Found at i:2892277 original size:33 final size:33
Alignment explanation
Indices: 2892184--2892308 Score: 114
Period size: 33 Copynumber: 3.7 Consensus size: 33
2892174 TAAAACTAAT
* *
2892184 AATTTCAAAATTAA-TTTAAAAATATATATTTAA
1 AATTTAAAAAATAATTTTAAAAATATATA-TTAA
* *
2892217 AATTTATAAAAAAATAATTTCACAAATATATATCT-A
1 AA-TT-T-AAAAAATAATTTTAAAAATATATAT-TAA
*
2892253 AAGTTAAAAAATAATTTTAAAAATA-ATAATTAA
1 AATTTAAAAAATAATTTTAAAAATATAT-ATTAA
*
2892286 AATTTAAAAAA-AATTGTAAAAAT
1 AATTTAAAAAATAATTTTAAAAAT
2892309 TAATAATATA
Statistics
Matches: 76, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
32 14 0.18
33 33 0.43
34 3 0.04
35 2 0.03
36 11 0.14
37 13 0.17
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (33 bp):
AATTTAAAAAATAATTTTAAAAATATATATTAA
Found at i:2892322 original size:33 final size:32
Alignment explanation
Indices: 2892184--2892322 Score: 97
Period size: 33 Copynumber: 4.1 Consensus size: 32
2892174 TAAAACTAAT
* * *
2892184 AATTTCAAAATTAATT-TAAAAATATATATTTAA
1 AATTTAAAAAATAATTGTAAAAATA-ATAATT-A
*
2892217 AATTTATAAAAAAATAATT-TCACAAAT-ATATATCTA
1 AA-TT-T-AAAAAATAATTGT-AAAAATAATA-AT-TA
* *
2892253 AAGTTAAAAAATAATTTTAAAAATAATAATTAA
1 AATTTAAAAAATAATTGTAAAAATAATAATT-A
2892286 AATTTAAAAAA-AATTGTAAAAATTAATAATATA
1 AATTTAAAAAATAATTGTAAAAA-TAATAAT-TA
2892319 AATT
1 AATT
2892323 ACAATTTTTT
Statistics
Matches: 87, Mismatches: 8, Indels: 22
0.74 0.07 0.19
Matches are distributed among these distances:
32 11 0.13
33 43 0.49
34 8 0.09
35 5 0.06
36 14 0.16
37 6 0.07
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (32 bp):
AATTTAAAAAATAATTGTAAAAATAATAATTA
Found at i:2892360 original size:18 final size:17
Alignment explanation
Indices: 2892339--2892413 Score: 69
Period size: 18 Copynumber: 4.1 Consensus size: 17
2892329 TTTTAAAATT
*
2892339 AATAATATAAATTAAATA
1 AATAAAATAAATTAAA-A
*
2892357 AATAAAATAAAATAAGAA
1 AATAAAATAAATTAA-AA
*
2892375 AATAATATAAAACTTAAAA
1 AATAAAAT-AAA-TTAAAA
*
2892394 AAGAAAATAAATTAAGAA
1 AATAAAATAAATTAA-AA
2892412 AA
1 AA
2892414 AGACAAAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
17 4 0.09
18 28 0.60
19 12 0.26
20 3 0.06
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (17 bp):
AATAAAATAAATTAAAA
Found at i:2892559 original size:21 final size:22
Alignment explanation
Indices: 2892533--2892575 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2892523 TTTTCAAAAA
2892533 TTAAAAA-AAAGTTAAA-AAATT
1 TTAAAAAGAAA-TTAAAGAAATT
2892554 TTAAAAAGAAATTAAAGAAATT
1 TTAAAAAGAAATTAAAGAAATT
2892576 GTATTTACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (22 bp):
TTAAAAAGAAATTAAAGAAATT
Found at i:2892646 original size:14 final size:14
Alignment explanation
Indices: 2892627--2892653 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2892617 AAAAATATGG
2892627 TTAATATTTAAAAA
1 TTAATATTTAAAAA
2892641 TTAATATTTAAAA
1 TTAATATTTAAAA
2892654 TTTTAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTAATATTTAAAAA
Found at i:2892668 original size:37 final size:36
Alignment explanation
Indices: 2892627--2892768 Score: 141
Period size: 37 Copynumber: 4.0 Consensus size: 36
2892617 AAAAATATGG
2892627 TTAATATTTAAAAAT-TAATATTTAAAATTTTAAAAAA
1 TTAAT-TTTAAAAATAT-ATATTTAAAATTTTAAAAAA
* * *
2892664 TTAATTTGAAAAATATATTTTTAAAATATATAAAAAA
1 TTAATTTTAAAAATATATATTTAAAAT-TTTAAAAAA
* * * *
2892701 TTAATTTCACAAATATATATCT-AAA-GTTAAAAAA
1 TTAATTTTAAAAATATATATTTAAAATTTTAAAAAA
* *
2892735 -TATTTTTAAAAATA-ATAATTAAAATTTTAAAAAA
1 TTAATTTTAAAAATATATATTTAAAATTTTAAAAAA
2892769 GTATTATAAA
Statistics
Matches: 86, Mismatches: 15, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
32 4 0.05
33 14 0.16
34 15 0.17
36 21 0.24
37 32 0.37
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (36 bp):
TTAATTTTAAAAATATATATTTAAAATTTTAAAAAA
Found at i:2892868 original size:24 final size:24
Alignment explanation
Indices: 2892823--2892883 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 24
2892813 TAATAATAAA
*
2892823 AAATAAAACAAAATAAACAAAATG
1 AAATAAAAAAAAATAAACAAAATG
2892847 AAATAAGAAAAAAAT---CAAAA--
1 AAATAA-AAAAAAATAAACAAAATG
*
2892867 AAGTAAAAAAAAATAAA
1 AAATAAAAAAAAATAAA
2892884 AAGATAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
19 8 0.26
20 5 0.16
22 5 0.16
24 6 0.19
25 7 0.23
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.11
Consensus pattern (24 bp):
AAATAAAAAAAAATAAACAAAATG
Found at i:2892877 original size:11 final size:10
Alignment explanation
Indices: 2892814--2892885 Score: 56
Period size: 10 Copynumber: 6.8 Consensus size: 10
2892804 TTTTAAAGTT
*
2892814 AATAATAAAA
1 AATAAAAAAA
*
2892824 AATAAAACAA
1 AATAAAAAAA
2892834 AATAAACAAAATGA
1 AAT-AA-AAAA--A
2892848 AATAAGAAAAA
1 AATAA-AAAAA
*
2892859 AAT-CAAAAA
1 AATAAAAAAA
*
2892868 AGTAAAAAAA
1 AATAAAAAAA
2892878 AATAAAAA
1 AATAAAAA
2892886 GATAAAATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
9 7 0.14
10 23 0.47
11 6 0.12
12 3 0.06
13 6 0.12
14 4 0.08
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.12
Consensus pattern (10 bp):
AATAAAAAAA
Found at i:2892891 original size:18 final size:18
Alignment explanation
Indices: 2892847--2892892 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
2892837 AAACAAAATG
2892847 AAATAAGAAAAAAATCAAA
1 AAATAA-AAAAAAATCAAA
2892866 AAAGTAAAAAAAAAT-AAA
1 AAA-TAAAAAAAAATCAAA
2892884 AAGATAAAA
1 AA-ATAAAA
2892893 TTTATTAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.40
19 12 0.48
20 3 0.12
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.11
Consensus pattern (18 bp):
AAATAAAAAAAAATCAAA
Found at i:2892943 original size:17 final size:17
Alignment explanation
Indices: 2892919--2892978 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 17
2892909 ATAAAAAAGT
2892919 AAAA-AAAAGAAATATG
1 AAAATAAAAGAAATATG
2892935 AAAATAAAAGAAA-A--
1 AAAATAAAAGAAATATG
*
2892949 AAAACAAAAGAAATATG
1 AAAATAAAAGAAATATG
*
2892966 AAAATAAGAGAAA
1 AAAATAAAAGAAA
2892979 AAAATAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
14 12 0.32
15 1 0.03
16 5 0.14
17 19 0.51
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.10
Consensus pattern (17 bp):
AAAATAAAAGAAATATG
Found at i:2892982 original size:30 final size:30
Alignment explanation
Indices: 2892906--2892990 Score: 118
Period size: 31 Copynumber: 2.8 Consensus size: 30
2892896 ATTAAGGAAC
**
2892906 AAAATAAAA-AAGTAAAAAAAAGAAATATG
1 AAAATAAAAGAAAAAAAAAAAAGAAATATG
2892935 AAAATAAAAGAAAAAAAACAAAAGAAATATG
1 AAAATAAAAGAAAAAAAA-AAAAGAAATATG
*
2892966 AAAATAAGAGAAAAAAATAAAAAGA
1 AAAATAAAAGAAAAAAA-AAAAAGA
2892991 TGTCAGAAGG
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
29 9 0.18
30 6 0.12
31 34 0.68
32 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.11, T:0.11
Consensus pattern (30 bp):
AAAATAAAAGAAAAAAAAAAAAGAAATATG
Found at i:2896691 original size:22 final size:24
Alignment explanation
Indices: 2896663--2896778 Score: 81
Period size: 22 Copynumber: 5.2 Consensus size: 24
2896653 TCATGGTCGA
2896663 TAAGCTCCT-TCGAGCTG-AACAG
1 TAAGCTCCTATCGAGCTGAAACAG
* *
2896685 TAAGCT-CTATTGAGCTGAAACGG
1 TAAGCTCCTATCGAGCTGAAACAG
*
2896708 TAAGCT-CTAAT-GAGCT-AAACGG
1 TAAGCTCCT-ATCGAGCTGAAACAG
* *
2896730 TAAG-TTCTA-CTAAGCTG-AACAG
1 TAAGCTCCTATC-GAGCTGAAACAG
**
2896752 TAAGCTCAAAT-GAGCTGAAACAG
1 TAAGCTCCTATCGAGCTGAAACAG
2896775 TAAG
1 TAAG
2896779 TTCTTACGAG
Statistics
Matches: 76, Mismatches: 8, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
21 4 0.05
22 42 0.55
23 28 0.37
24 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.23
Consensus pattern (24 bp):
TAAGCTCCTATCGAGCTGAAACAG
Found at i:2896779 original size:45 final size:46
Alignment explanation
Indices: 2896674--2896782 Score: 143
Period size: 45 Copynumber: 2.4 Consensus size: 46
2896664 AAGCTCCTTC
* * * * *
2896674 GAGCTG-AACAGTAAGCTCTATTGAGCTGAAACGGTAAGCTCTAAT
1 GAGCTGAAACAGTAAGTTCTACTAAGCTGAAACAGTAAGCTCAAAT
*
2896719 GAGCT-AAACGGTAAGTTCTACTAAGCTG-AACAGTAAGCTCAAAT
1 GAGCTGAAACAGTAAGTTCTACTAAGCTGAAACAGTAAGCTCAAAT
2896763 GAGCTGAAACAGTAAGTTCT
1 GAGCTGAAACAGTAAGTTCT
2896783 TACGAGCTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 19 0.35
45 36 0.65
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (46 bp):
GAGCTGAAACAGTAAGTTCTACTAAGCTGAAACAGTAAGCTCAAAT
Found at i:2903238 original size:242 final size:241
Alignment explanation
Indices: 2902813--2903292 Score: 825
Period size: 242 Copynumber: 2.0 Consensus size: 241
2902803 TGATACCAAT
* * *
2902813 AAATGTAACACCCTTAACCCGTAACTATCACCGGAATAGGTCAAGAGGCATTACCAGACCTATAA
1 AAATGTAACACCCCTAACCCGTAACTATCACCAGAATAGGTCAAGAGGCATTACAAGACCTATAA
2902878 CACAATTCAAAACATTCATTTAACAAATTCCATCTCATTTCAGTAACCATCAATCATTCACATTC
66 CACAATTCAAAACATTCATTTAACAAATTCCATCTCATTTCAGTAACCATCAATCATTCACATTC
* *
2902943 AAAATGTACTTAAATTAATCATACAAAGTCTTAATCATGCATTTGGTACTAAATTGATAATATAT
131 AAAATGTACTTAAATTAATCATACAAAATCTTAATCATGCATTTGGTACTAAATTGATAACATAT
*
2903008 AAAAATTTCAAAAACTTAGAAAGTTTTCAATTTTTCAAGTGACAAAC
196 AAAAATTTCAAAAACTTAGAAA-TTTTCAACTTTTCAAGTGACAAAC
* * * * *
2903055 AAATGTAACACCCCTAACCTGTAACTGTCGCCAGAATAGGTTAAGAGGCATTACAAGACCTGTAA
1 AAATGTAACACCCCTAACCCGTAACTATCACCAGAATAGGTCAAGAGGCATTACAAGACCTATAA
*
2903120 CTCAATTCAAAACATTCATTTAACAAATTCCATCTCATTTCAGTAACCATCAATCATTCACATTC
66 CACAATTCAAAACATTCATTTAACAAATTCCATCTCATTTCAGTAACCATCAATCATTCACATTC
*
2903185 AAAATGTACTTAAATTACTCATACAAAATCTTAATCATGCATTTGGTACTAAATTGATAACATAT
131 AAAATGTACTTAAATTAATCATACAAAATCTTAATCATGCATTTGGTACTAAATTGATAACATAT
*
2903250 AAAAATTTCAGAAACTTAGAAATTTTCAACTTTTCAAGTGACA
196 AAAAATTTCAAAAACTTAGAAATTTTCAACTTTTCAAGTGACA
2903293 CAAGCCCGTG
Statistics
Matches: 224, Mismatches: 14, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
241 20 0.09
242 204 0.91
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (241 bp):
AAATGTAACACCCCTAACCCGTAACTATCACCAGAATAGGTCAAGAGGCATTACAAGACCTATAA
CACAATTCAAAACATTCATTTAACAAATTCCATCTCATTTCAGTAACCATCAATCATTCACATTC
AAAATGTACTTAAATTAATCATACAAAATCTTAATCATGCATTTGGTACTAAATTGATAACATAT
AAAAATTTCAAAAACTTAGAAATTTTCAACTTTTCAAGTGACAAAC
Found at i:2904506 original size:22 final size:22
Alignment explanation
Indices: 2904477--2904605 Score: 109
Period size: 22 Copynumber: 5.8 Consensus size: 22
2904467 AAGCTCCTTC
*
2904477 GAGCTGAACAGTAAGCTCTATT
1 GAGCTGAACAGTAAGCTCTAAT
* *
2904499 GAGTTGAA-ATGGTAAGCTTTAAT
1 GAGCTGAACA--GTAAGCTCTAAT
* * *
2904522 GAGCTGAACGGTAAGATCTATT
1 GAGCTGAACAGTAAGCTCTAAT
* *
2904544 GAG-TAGAACGGTAAGCTCTACT
1 GAGCT-GAACAGTAAGCTCTAAT
* * *
2904566 GAGATGAACGGTAAGCTCCAAT
1 GAGCTGAACAGTAAGCTCTAAT
2904588 GAGCTGAAACAGTAAGCT
1 GAGCTG-AACAGTAAGCT
2904606 ATTACGAGCT
Statistics
Matches: 87, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
21 2 0.02
22 57 0.66
23 28 0.32
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (22 bp):
GAGCTGAACAGTAAGCTCTAAT
Found at i:2904514 original size:45 final size:43
Alignment explanation
Indices: 2904465--2904583 Score: 123
Period size: 45 Copynumber: 2.7 Consensus size: 43
2904455 GTCATGGTCT
* * *
2904465 GTAAGCTCCTTCGAGCTGAACAGTAAGCTCTATTGAGTTGAAATG
1 GTAAGCT-CTTCGAGCTGAACGGTAAGCTCTATTGAGTAG-AACG
* *
2904510 GTAAGCT-TTAATGAGCTGAACGGTAAGATCTATTGAGTAGAACG
1 GTAAGCTCTT--CGAGCTGAACGGTAAGCTCTATTGAGTAGAACG
* *
2904554 GTAAGCTCTACTGAGATGAACGGTAAGCTC
1 GTAAGCTCTTC-GAGCTGAACGGTAAGCTC
2904584 CAATGAGCTG
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
43 2 0.03
44 26 0.43
45 33 0.54
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (43 bp):
GTAAGCTCTTCGAGCTGAACGGTAAGCTCTATTGAGTAGAACG
Found at i:2904574 original size:44 final size:45
Alignment explanation
Indices: 2904481--2904580 Score: 130
Period size: 44 Copynumber: 2.2 Consensus size: 45
2904471 TCCTTCGAGC
* * * * * *
2904481 TGAACAGTAAGCTCTATTGAGTTGAAATGGTAAGCTTTAATGAGC
1 TGAACGGTAAGATCTATTGAGTAGAAACGGTAAGCTCTAATGAGA
*
2904526 TGAACGGTAAGATCTATTGAGTAG-AACGGTAAGCTCTACTGAGA
1 TGAACGGTAAGATCTATTGAGTAGAAACGGTAAGCTCTAATGAGA
2904570 TGAACGGTAAG
1 TGAACGGTAAG
2904581 CTCCAATGAG
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 27 0.56
45 21 0.44
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (45 bp):
TGAACGGTAAGATCTATTGAGTAGAAACGGTAAGCTCTAATGAGA
Found at i:2906114 original size:40 final size:38
Alignment explanation
Indices: 2906051--2906180 Score: 113
Period size: 40 Copynumber: 3.3 Consensus size: 38
2906041 GTTTGGTACT
* *
2906051 CAGTGCCTCATCGGATAATTCGAAGTAATAATTTGACACC
1 CAGTGCCTCATCAG-TAAATCGAAGTAATAA-TTGACACC
* *
2906091 CAGTGTCTCATCAGCTAAATCGAAGT-A-AATTGGCACC
1 CAGTGCCTCATCAG-TAAATCGAAGTAATAATTGACACC
* *
2906128 CTA-TGCCTCATCGAGTTAATCCGAAGTAGTGAATTGACACC
1 C-AGTGCCTCATC-AGTAAAT-CGAAGTAAT-AATTGACACC
*
2906169 CAGTGTCTCATC
1 CAGTGCCTCATC
2906181 GACTCGAAGT
Statistics
Matches: 73, Mismatches: 10, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
37 20 0.27
38 11 0.15
39 1 0.01
40 23 0.32
41 18 0.25
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (38 bp):
CAGTGCCTCATCAGTAAATCGAAGTAATAATTGACACC
Found at i:2906169 original size:41 final size:38
Alignment explanation
Indices: 2906051--2906182 Score: 119
Period size: 41 Copynumber: 3.4 Consensus size: 38
2906041 GTTTGGTACT
*
2906051 CAGTGCCTCATCG-GATAATTCGAAGTAATAATTTGACACC
1 CAGTGCCTCATCGAGTTAA-TCGAAGT-ATAA-TTGACACC
* * *
2906091 CAGTGTCTCATC-AGCTAAATCGAAGTA-AATTGGCACC
1 CAGTGCCTCATCGAG-TTAATCGAAGTATAATTGACACC
2906128 CTA-TGCCTCATCGAGTTAATCCGAAGTAGTGAATTGACACC
1 C-AGTGCCTCATCGAGTTAAT-CGAAGTA-T-AATTGACACC
*
2906169 CAGTGTCTCATCGA
1 CAGTGCCTCATCGA
2906183 CTCGAAGTCG
Statistics
Matches: 75, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
37 20 0.27
38 12 0.16
39 1 0.01
40 20 0.27
41 22 0.29
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (38 bp):
CAGTGCCTCATCGAGTTAATCGAAGTATAATTGACACC
Found at i:2908810 original size:17 final size:16
Alignment explanation
Indices: 2908783--2908815 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
2908773 ATAGATTAAC
2908783 ATGATTTGTATATGAA
1 ATGATTTGTATATGAA
2908799 ATGATATTGTATATGAA
1 ATGAT-TTGTATATGAA
2908816 TCGGTTGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (16 bp):
ATGATTTGTATATGAA
Found at i:2912311 original size:46 final size:46
Alignment explanation
Indices: 2912261--2912436 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
2912251 TGGTTGAGCA
2912261 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
2912307 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
2912352 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
2912400 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2912437 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 65 0.58
47 28 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:2912417 original size:93 final size:93
Alignment explanation
Indices: 2912258--2912428 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
2912248 GGATGGTTGA
* *
2912258 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
2912323 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
2912351 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
2912416 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
2912429 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:2922965 original size:23 final size:23
Alignment explanation
Indices: 2922939--2922984 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2922929 TATCATTCCA
2922939 GTCAGTCACATCTATGTCTCTAT
1 GTCAGTCACATCTATGTCTCTAT
2922962 GTCAGTCACATCTATGTCTCTAT
1 GTCAGTCACATCTATGTCTCTAT
2922985 CTTCTAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.39
Consensus pattern (23 bp):
GTCAGTCACATCTATGTCTCTAT
Found at i:2927105 original size:18 final size:19
Alignment explanation
Indices: 2927084--2927120 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2927074 TAAAATTGAT
*
2927084 GTGTTTCTTA-AATTTTAA
1 GTGTTTATTATAATTTTAA
2927102 GTGTTTATTATAATTTTAA
1 GTGTTTATTATAATTTTAA
2927121 AAACAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.57
Consensus pattern (19 bp):
GTGTTTATTATAATTTTAA
Found at i:2933006 original size:27 final size:27
Alignment explanation
Indices: 2932976--2933032 Score: 62
Period size: 29 Copynumber: 2.1 Consensus size: 27
2932966 TTGACAGGGC
2932976 AAAA-CTTTAGGAACCAAACTGAGAAAA
1 AAAATCTTTAGGAACCAAACTGA-AAAA
** *
2933003 AAAATTCTTTAGGTGCCAAATTGAAAAA
1 AAAA-TCTTTAGGAACCAAACTGAAAAA
2933031 AA
1 AA
2933033 CAGCTATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 4 0.16
28 6 0.24
29 15 0.60
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.21
Consensus pattern (27 bp):
AAAATCTTTAGGAACCAAACTGAAAAA
Found at i:2935263 original size:15 final size:15
Alignment explanation
Indices: 2935243--2935272 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2935233 GAAAATATGG
*
2935243 AAATGTGGTGAGGAA
1 AAATGTGGTAAGGAA
2935258 AAATGTGGTAAGGAA
1 AAATGTGGTAAGGAA
2935273 GTTACAGTTC
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:0.43, C:0.00, G:0.37, T:0.20
Consensus pattern (15 bp):
AAATGTGGTAAGGAA
Found at i:2937864 original size:20 final size:19
Alignment explanation
Indices: 2937839--2937887 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
2937829 GCCCAACAGT
*
2937839 AAAAAAAAACTCTGAAAACG
1 AAAAAAAAA-GCTGAAAACG
*
2937859 AAAAAAAAAGCTGAAAATG
1 AAAAAAAAAGCTGAAAACG
2937878 AAAAAAAAAG
1 AAAAAAAAAG
2937888 GGACATGTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.71, C:0.08, G:0.12, T:0.08
Consensus pattern (19 bp):
AAAAAAAAAGCTGAAAACG
Found at i:2938454 original size:151 final size:149
Alignment explanation
Indices: 2938161--2938487 Score: 406
Period size: 151 Copynumber: 2.2 Consensus size: 149
2938151 AGTATAACAT
* *
2938161 TTTCGTATATTATTTTTTAAAATATATTATTTACGTATTTTATTTTTTATATTATTTTAGCAAAA
1 TTTCGGATATTATTTTTTAAAATATATTATTTACATATTTTATTTTTTATATTATTTTAGCAAAA
* ***
2938226 AGTGTTTCAAATGTATTACTTAAGTGTTTTTTATATTAATTTAATAAATAACTCTGACTTTGGTA
66 AGTGTTTCAAATGTATTACTTAAGTGTTTTTTATATTAATTTAATAAATAACCCTGACTTTACCA
* *
2938291 CCTTGTTCGTATTTTTTAAT
131 CCTTATTCGTATTTTTT-AC
* * * *
2938311 TTTTGGATTTTATTTTTTAAAATATATTATTTTCATATTTTATTTCTTTATATTATTTTAGTACA
1 TTTCGGATATTATTTTTTAAAATATATTATTTACATATTTTATTT-TTTATATTATTTTAGCA-A
** * * * *
2938376 TTA-TGTTTCAAATGTATTATTTAAGTGTTTTTTTGTATT-TTTTAATAAATAACCCTGATTTTA
64 AAAGTGTTTCAAATGTATTACTTAAGTG-TTTTTTATATTAATTTAATAAATAACCCTGACTTTA
* *
2938439 CCACTTTATTTGTATTTTTTAC
128 CCACCTTATTCGTATTTTTTAC
* *
2938461 TTTCGTATATTATTTTTTTAAATATAT
1 TTTCGGATATTATTTTTTAAAATATAT
2938488 ATAATACATT
Statistics
Matches: 150, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
150 64 0.43
151 74 0.49
152 12 0.08
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.57
Consensus pattern (149 bp):
TTTCGGATATTATTTTTTAAAATATATTATTTACATATTTTATTTTTTATATTATTTTAGCAAAA
AGTGTTTCAAATGTATTACTTAAGTGTTTTTTATATTAATTTAATAAATAACCCTGACTTTACCA
CCTTATTCGTATTTTTTAC
Found at i:2939017 original size:20 final size:21
Alignment explanation
Indices: 2938992--2939042 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
2938982 CCACATGTCC
2938992 CTTTTTTTTTTCATTTTCAG-
1 CTTTTTTTTTTCATTTTCAGA
*
2939012 CTTTTTTTTTTCGTTTTCAGA
1 CTTTTTTTTTTCATTTTCAGA
*
2939033 GTTTTTTTTT
1 CTTTTTTTTT
2939043 ACTGTTGGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.08, C:0.12, G:0.08, T:0.73
Consensus pattern (21 bp):
CTTTTTTTTTTCATTTTCAGA
Found at i:2943263 original size:13 final size:13
Alignment explanation
Indices: 2943245--2943275 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2943235 TTCATGTGAA
2943245 TATAAAAAATTAT
1 TATAAAAAATTAT
2943258 TATAAAAAATTAT
1 TATAAAAAATTAT
2943271 T-TAAA
1 TATAAA
2943276 TATCATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TATAAAAAATTAT
Found at i:2946306 original size:18 final size:18
Alignment explanation
Indices: 2946265--2946359 Score: 92
Period size: 18 Copynumber: 5.4 Consensus size: 18
2946255 AGAACCAGAG
2946265 AAGAAAG-AGG-G-ACCA
1 AAGAAAGAAGGTGAACCA
2946280 AAGAAAGAAGGTGAAGCCA
1 AAGAAAGAAGGTGAA-CCA
* *
2946299 AA-AAAGAAGATGAACAA
1 AAGAAAGAAGGTGAACCA
*
2946316 AAGAAAGAAGGTGAACCC
1 AAGAAAGAAGGTGAACCA
* *
2946334 AAGAAGGAAGATGAA-CA
1 AAGAAAGAAGGTGAACCA
2946351 AACGAAAGA
1 AA-GAAAGA
2946360 TGAAGCCAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
15 7 0.11
16 3 0.05
17 8 0.12
18 42 0.65
19 5 0.08
ACGTcount: A:0.58, C:0.11, G:0.27, T:0.04
Consensus pattern (18 bp):
AAGAAAGAAGGTGAACCA
Found at i:2946320 original size:36 final size:36
Alignment explanation
Indices: 2946279--2946377 Score: 141
Period size: 36 Copynumber: 2.8 Consensus size: 36
2946269 AAGAGGGACC
*
2946279 AAAGAAAGAAGGTGAAGCCAAAAAAGAAGATGAACA
1 AAAGAAAGAAGGTGAAGCCAAAAAGGAAGATGAACA
* *
2946315 AAAGAAAGAAGGTGAACCCAAGAAGGAAGATGAACA
1 AAAGAAAGAAGGTGAAGCCAAAAAGGAAGATGAACA
*
2946351 AACGAAAG-A--TGAAGCCAAAAAGGAAGA
1 AAAGAAAGAAGGTGAAGCCAAAAAGGAAGA
2946378 AGGTAAGAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
33 16 0.28
35 1 0.02
36 40 0.70
ACGTcount: A:0.59, C:0.10, G:0.26, T:0.05
Consensus pattern (36 bp):
AAAGAAAGAAGGTGAAGCCAAAAAGGAAGATGAACA
Found at i:2946393 original size:33 final size:32
Alignment explanation
Indices: 2946280--2946406 Score: 85
Period size: 33 Copynumber: 3.8 Consensus size: 32
2946270 AGAGGGACCA
* * *
2946280 AAGAAAGAAGGTGAAGCCAAAAAAGAAGATGAACAA
1 AAGAAAGAAGATGAAGCC-AAAAAG--GAAGAAC-G
* * * *
2946316 AAGAAAGAAGGTGAACCCAAGAAGGAAG-ATG
1 AAGAAAGAAGATGAAGCCAAAAAGGAAGAACG
* *
2946347 AACAAACGAAAGATGAAGCCAAAAAGGAAGAAGG
1 AAGAAA-G-AAGATGAAGCCAAAAAGGAAGAACG
*
2946381 TAAGAAAGAAGATGAAACCAAGAAAG
1 -AAGAAAGAAGATGAAGCCAA-AAAG
2946407 ATGGTGAGAA
Statistics
Matches: 74, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
31 5 0.07
32 2 0.03
33 33 0.45
34 7 0.09
35 10 0.14
36 17 0.23
ACGTcount: A:0.58, C:0.09, G:0.27, T:0.06
Consensus pattern (32 bp):
AAGAAAGAAGATGAAGCCAAAAAGGAAGAACG
Found at i:2946405 original size:18 final size:18
Alignment explanation
Indices: 2946280--2946407 Score: 65
Period size: 18 Copynumber: 7.4 Consensus size: 18
2946270 AGAGGGACCA
* *
2946280 AAGAAAGAAGGTGAAGCC
1 AAGAAAGAAGATGAAACC
* *
2946298 AAAAAAGAAGATG-AACAA
1 AAGAAAGAAGATGAAAC-C
* *
2946316 AAGAAAGAAGGTGAACCC
1 AAGAAAGAAGATGAAACC
*
2946334 AAGAAGGAAGATG-AA-C
1 AAGAAAGAAGATGAAACC
* *
2946350 -A-AACGAAAGATGAAGCC
1 AAGAAAG-AAGATGAAACC
* ***
2946367 AA-AAAG--GAAGAAGGT
1 AAGAAAGAAGATGAAACC
2946382 AAGAAAGAAGATGAAACC
1 AAGAAAGAAGATGAAACC
2946400 AAGAAAGA
1 AAGAAAGA
2946408 TGGTGAGAAG
Statistics
Matches: 80, Mismatches: 21, Indels: 18
0.67 0.18 0.15
Matches are distributed among these distances:
14 3 0.04
15 15 0.19
16 6 0.08
17 4 0.05
18 50 0.62
19 2 0.03
ACGTcount: A:0.59, C:0.09, G:0.27, T:0.05
Consensus pattern (18 bp):
AAGAAAGAAGATGAAACC
Found at i:2948565 original size:21 final size:22
Alignment explanation
Indices: 2948527--2948582 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
2948517 AAACCAAAAT
* * *
2948527 TTAACAATGTTAGTGTTTATTGC
1 TTAACAAAGTTA-CGTTTATTAC
*
2948550 TTAA-AAAGTTACGTTTATTAT
1 TTAACAAAGTTACGTTTATTAC
2948571 TTAACAAAGTTA
1 TTAACAAAGTTA
2948583 ATATTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 11 0.39
22 13 0.46
23 4 0.14
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (22 bp):
TTAACAAAGTTACGTTTATTAC
Found at i:2952969 original size:29 final size:28
Alignment explanation
Indices: 2952937--2953057 Score: 93
Period size: 29 Copynumber: 4.2 Consensus size: 28
2952927 TTCGATTTAT
2952937 GTTTAGGGCTTTTGAATTTGGGGATTTTG
1 GTTTAGGG-TTTTGAATTTGGGGATTTTG
* *
2952966 GTTTA-AGTTATTGAATTTGAGGATTTTAG
1 GTTTAGGGTT-TTGAATTTGGGGATTTT-G
* * *
2952995 G-TTAGGGGTTCTGATTTTGGGGATTTTT
1 GTTTA-GGGTTTTGAATTTGGGGATTTTG
** * *
2953023 GTTTAAAGTATTTCGATTTTGGGGATTTTA
1 GTTTAGGGT-TTT-GAATTTGGGGATTTTG
2953053 GTTTA
1 GTTTA
2953058 TTATTTTTTA
Statistics
Matches: 74, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
27 2 0.03
28 23 0.31
29 26 0.35
30 23 0.31
ACGTcount: A:0.19, C:0.02, G:0.29, T:0.50
Consensus pattern (28 bp):
GTTTAGGGTTTTGAATTTGGGGATTTTG
Found at i:2953998 original size:24 final size:23
Alignment explanation
Indices: 2953971--2954033 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 23
2953961 TAAAGGTGGT
2953971 AAGGGTGTTGAAGGTTTAAATGGG
1 AAGGGTGTTGAAGGTTTAAAT-GG
*
2953995 AAGGGTGTTAAAGGTTTAAATGG
1 AAGGGTGTTGAAGGTTTAAATGG
2954018 AGAGGGTGTTG-AGGTT
1 A-AGGGTGTTGAAGGTT
2954034 GCTAGCAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
23 8 0.22
24 28 0.78
ACGTcount: A:0.29, C:0.00, G:0.41, T:0.30
Consensus pattern (23 bp):
AAGGGTGTTGAAGGTTTAAATGG
Found at i:2954049 original size:24 final size:23
Alignment explanation
Indices: 2954022--2954103 Score: 67
Period size: 24 Copynumber: 3.4 Consensus size: 23
2954012 AAATGGAGAG
*
2954022 GGTGTTGAGGTTGCTAGCAGTGAA
1 GGTGGTGAGGTTG-TAGCAGTGAA
** *
2954046 GGTGGTGAAGGTT-TAGGTGGGAAA
1 GGTGGTG-AGGTTGTAGCAGTG-AA
* *
2954070 GGTGTTGAGGTTGTTAGCAGTAAA
1 GGTGGTGAGGTTG-TAGCAGTGAA
2954094 GGTGGTGAGG
1 GGTGGTGAGG
2954104 GTGGTGAGGT
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
23 10 0.23
24 25 0.57
25 9 0.20
ACGTcount: A:0.22, C:0.04, G:0.46, T:0.28
Consensus pattern (23 bp):
GGTGGTGAGGTTGTAGCAGTGAA
Found at i:2954057 original size:48 final size:48
Alignment explanation
Indices: 2954005--2954101 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 48
2953995 AAGGGTGTTA
* *
2954005 AAGGTTTAAAT-GGAGAGGGTGTTGAGGTTGCTAGCAGTGAAGGTGGTG
1 AAGGTTTAAATGGGA-AAGGTGTTGAGGTTGCTAGCAGTAAAGGTGGTG
** *
2954053 AAGGTTTAGGTGGGAAAGGTGTTGAGGTTGTTAGCAGTAAAGGTGGTG
1 AAGGTTTAAATGGGAAAGGTGTTGAGGTTGCTAGCAGTAAAGGTGGTG
2954101 A
1 A
2954102 GGGTGGTGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
48 40 0.93
49 3 0.07
ACGTcount: A:0.26, C:0.03, G:0.43, T:0.28
Consensus pattern (48 bp):
AAGGTTTAAATGGGAAAGGTGTTGAGGTTGCTAGCAGTAAAGGTGGTG
Done.