Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 91 of 185
Found at i:28946790 original size:34 final size:34
Alignment explanation
Indices: 28946652--28946790 Score: 94
Period size: 34 Copynumber: 4.1 Consensus size: 34
28946642 AAAAGTATGC
* *
28946652 TATGTAAGTTATGTAAGTCGTATAAGTTATGT-AAG
1 TATGTAAGTTATGTAAGT--TGTAAGTTATGTAAAA
* *
28946687 T-TGTAAGTTATGTAAGTTATTTA-TTATG-AAAA
1 TATGTAAGTTATGTAAGTT-GTAAGTTATGTAAAA
* * *
28946719 TTAAGTAAGTTATGTAA-TT-TACGAATAAT-TAAAAA
1 -TATGTAAGTTATGTAAGTTGTA--AGTTATGT-AAAA
*
28946754 TATGTAAGTTATGTAAGTTGTAAGTTATGTATAA
1 TATGTAAGTTATGTAAGTTGTAAGTTATGTAAAA
28946788 TAT
1 TAT
28946791 TAAATAACTA
Statistics
Matches: 82, Mismatches: 10, Indels: 25
0.70 0.09 0.21
Matches are distributed among these distances:
31 1 0.01
32 8 0.10
33 6 0.07
34 57 0.70
35 8 0.10
36 2 0.02
ACGTcount: A:0.39, C:0.01, G:0.17, T:0.42
Consensus pattern (34 bp):
TATGTAAGTTATGTAAGTTGTAAGTTATGTAAAA
Found at i:28946810 original size:34 final size:31
Alignment explanation
Indices: 28946772--28946851 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
28946762 TTATGTAAGT
*
28946772 TGTAAGTTATGTATAATATTAAATAACTAAGTTA
1 TGTAATTTATGTATAATATT-AAT--CTAAGTTA
* *
28946806 TGTAATTTATGTATAATATTAATGTATGTTA
1 TGTAATTTATGTATAATATTAATCTAAGTTA
28946837 TGTAATTTATGTATA
1 TGTAATTTATGTATA
28946852 TTAACTAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
31 21 0.49
33 3 0.07
34 19 0.44
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.47
Consensus pattern (31 bp):
TGTAATTTATGTATAATATTAATCTAAGTTA
Found at i:28946864 original size:156 final size:156
Alignment explanation
Indices: 28946704--28946996 Score: 577
Period size: 156 Copynumber: 1.9 Consensus size: 156
28946694 TTATGTAAGT
28946704 TATTTATTATGAAAATTAAGTAAGTTATGTAATTTACGAATAATTAAAAATATGTAAGTTATGTA
1 TATTTATTATGAAAATTAAGTAAGTTATGTAATTTACGAATAATTAAAAATATGTAAGTTATGTA
*
28946769 AGTTGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAATGTATG
66 AGTTGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAATGTAAG
28946834 TTATGTAATTTATGTATATTAACTAA
131 TTATGTAATTTATGTATATTAACTAA
28946860 TATTTATTATGAAAATTAAGTAAGTTATGTAATTTACGAATAATTAAAAATATGTAAGTTATGTA
1 TATTTATTATGAAAATTAAGTAAGTTATGTAATTTACGAATAATTAAAAATATGTAAGTTATGTA
28946925 AGTTGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAATGTAAG
66 AGTTGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAATGTAAG
28946990 TTATGTA
131 TTATGTA
28946997 TAATATTAAA
Statistics
Matches: 136, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 136 1.00
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.44
Consensus pattern (156 bp):
TATTTATTATGAAAATTAAGTAAGTTATGTAATTTACGAATAATTAAAAATATGTAAGTTATGTA
AGTTGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAATGTAAG
TTATGTAATTTATGTATATTAACTAA
Found at i:28946946 original size:34 final size:34
Alignment explanation
Indices: 28946928--28947095 Score: 123
Period size: 34 Copynumber: 5.6 Consensus size: 34
28946918 TTATGTAAGT
28946928 TGTAAGTTATGTATAATATTAAATAACTAAGTTA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTA
* *
28946962 TGTAATTTATGTATAATATT-AAT--GTAAGTTA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTA
28946993 --T--G---T--ATAATATTAAATAACTAAGTTA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTA
* *
28947018 TGTAATTTATGTATAATATT-AAT--GTAAGTTA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTA
28947049 --T--G---T--ATAATATTAAATAACTAAGTTA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTA
*
28947074 TGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAA
28947096 TGTAAGTTAT
Statistics
Matches: 101, Mismatches: 9, Indels: 48
0.64 0.06 0.30
Matches are distributed among these distances:
22 16 0.16
23 6 0.06
24 2 0.02
25 14 0.14
27 2 0.02
29 2 0.02
31 14 0.14
32 2 0.02
33 6 0.06
34 37 0.37
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.45
Consensus pattern (34 bp):
TGTAAGTTATGTATAATATTAAATAACTAAGTTA
Found at i:28946993 original size:22 final size:22
Alignment explanation
Indices: 28946961--28947005 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
28946951 TAACTAAGTT
*
28946961 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
28946983 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
28947005 A
1 A
28947006 ATAACTAAGT
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:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:28946995 original size:56 final size:56
Alignment explanation
Indices: 28946928--28947130 Score: 397
Period size: 56 Copynumber: 3.6 Consensus size: 56
28946918 TTATGTAAGT
28946928 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
28946984 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
28947040 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
*
28947096 TGTAAGTTATGTATAATATTAAATAACTAATTTAT
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTAT
28947131 ATTTTAATTT
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 146 1.00
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (56 bp):
TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
Found at i:28947049 original size:22 final size:22
Alignment explanation
Indices: 28947017--28947061 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
28947007 TAACTAAGTT
*
28947017 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
28947039 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
28947061 A
1 A
28947062 ATAACTAAGT
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:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:28947105 original size:22 final size:22
Alignment explanation
Indices: 28947073--28947117 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
28947063 TAACTAAGTT
*
28947073 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
28947095 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
28947117 A
1 A
28947118 ATAACTAATT
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:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:28950908 original size:16 final size:17
Alignment explanation
Indices: 28950882--28950913 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28950872 CTAACCCCTA
28950882 AATTAACCTTAAATCTC
1 AATTAACCTTAAATCTC
28950899 AATT-ACCTTAAATCT
1 AATTAACCTTAAATCT
28950914 ATACTCCGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTAACCTTAAATCTC
Found at i:28951506 original size:41 final size:41
Alignment explanation
Indices: 28951468--28951679 Score: 219
Period size: 41 Copynumber: 5.2 Consensus size: 41
28951458 TAGAAACGTT
28951468 GCTAAAGACCCGAGCATTAGCGGCGCATAGACAAAAACGCC
1 GCTAAAGACCCGAGCATTAGCGGCGCATAGACAAAAACGCC
*
28951509 GCTAAAGACCCCAGCATTAGCGGCGCATAGACAAAAACGCC
1 GCTAAAGACCCGAGCATTAGCGGCGCATAGACAAAAACGCC
* * * * *
28951550 GCTAAAGATCCGAGCATTAGCGGAGCTTAGACGAAATCGCC
1 GCTAAAGACCCGAGCATTAGCGGCGCATAGACAAAAACGCC
* *** * ** * ** *
28951591 GTTAAAGATTGGGGCATTAGCGGCGTTTTTGTGAAAGA-GCC
1 GCTAAAGACCCGAGCATTAGCGGCG-CATAGACAAAAACGCC
* * * *
28951632 GCTAAAGATCGGAGCATTAGCGGCGCTTACACAAAAACGCC
1 GCTAAAGACCCGAGCATTAGCGGCGCATAGACAAAAACGCC
28951673 GCTAAAG
1 GCTAAAG
28951680 GTTTAAAAAA
Statistics
Matches: 141, Mismatches: 28, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
40 6 0.04
41 130 0.92
42 5 0.04
ACGTcount: A:0.33, C:0.25, G:0.26, T:0.16
Consensus pattern (41 bp):
GCTAAAGACCCGAGCATTAGCGGCGCATAGACAAAAACGCC
Found at i:28951528 original size:82 final size:82
Alignment explanation
Indices: 28951401--28951679 Score: 193
Period size: 82 Copynumber: 3.4 Consensus size: 82
28951391 AGGTAAATAT
* * * * * * ** *
28951401 ATTAGCGGCGCTTAGATACAAACGCTGCTGAAGACAAGAGAATTAGTGGCAC-TCAGTTAGAAAC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACAACAGAATTAGCGGCACAT-AGACAAAAAC
**
28951465 GTTGCTAAAGACCCGAGC
65 GCCGCTAAAGACCCGAGC
* ** * *
28951483 ATTAGCGGCGCATAGACAAAAACGCCGCTAAAGACCCCAGCATTAGCGGCGCATAGACAAAAACG
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACAACAGAATTAGCGGCACATAGACAAAAACG
*
28951548 CCGCTAAAGATCCGAGC
66 CCGCTAAAGACCCGAGC
* * * * ***** * *** * ** *
28951565 ATTAGCGGAGCTTAGACGAAATCGCCGTTAAAGATTGGGGCATTAGCGGCGTTTTTGTGAAAGA-
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACAACAGAATTAGCGGC-ACATAGACAAAAAC
* *
28951629 GCCGCTAAAGATCGGAGC
65 GCCGCTAAAGACCCGAGC
*
28951647 ATTAGCGGCGCTTACACAAAAACGCCGCTAAAG
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAG
28951680 GTTTAAAAAA
Statistics
Matches: 155, Mismatches: 40, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
82 148 0.95
83 7 0.05
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (82 bp):
ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACAACAGAATTAGCGGCACATAGACAAAAACG
CCGCTAAAGACCCGAGC
Found at i:28951822 original size:40 final size:40
Alignment explanation
Indices: 28951759--28951834 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
28951749 AATTCCTATT
* *
28951759 TTTAGCGGCGCTTCCGGATAATCGCTGCTGATGCTCTACC
1 TTTAGCGGCGCTTCCGGATAATCGCCGCTAATGCTCTACC
* *
28951799 TTTAGCGGCGCTT-TGGCTAAATCGCCGCTAATGCTC
1 TTTAGCGGCGCTTCCGGAT-AATCGCCGCTAATGCTC
28951835 GATTTTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 3 0.10
40 28 0.90
ACGTcount: A:0.16, C:0.29, G:0.25, T:0.30
Consensus pattern (40 bp):
TTTAGCGGCGCTTCCGGATAATCGCCGCTAATGCTCTACC
Found at i:28959015 original size:14 final size:14
Alignment explanation
Indices: 28958996--28959022 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28958986 ATTCTTATCA
28958996 ATTTTTTAATAGGC
1 ATTTTTTAATAGGC
28959010 ATTTTTTAATAGG
1 ATTTTTTAATAGG
28959023 AGAATGACAA
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:0.30, C:0.04, G:0.15, T:0.52
Consensus pattern (14 bp):
ATTTTTTAATAGGC
Found at i:28965184 original size:41 final size:39
Alignment explanation
Indices: 28965139--28965262 Score: 119
Period size: 37 Copynumber: 3.2 Consensus size: 39
28965129 ACTTCGAGTT
* *
28965139 GATGAGACACTGGGTGTCAATTTACTATTTCGGATTAATTC
1 GATGAGACACTAGGTGTCAATTTACTA-TTCGGATT-ACTC
* * * *
28965180 GATGAGGCACTAGGTGCCAATTTAC--TTCAGTTTAGC-C
1 GATGAGACACTAGGTGTCAATTTACTATTCGGATTA-CTC
* *
28965217 GATGAGACACTAGGTGTCAATTTATTACTTCGAATTACTC
1 GATGAGACACTAGGTGTCAATTTACTA-TTCGGATTACTC
28965257 GATGAG
1 GATGAG
28965263 GTACTGGGTG
Statistics
Matches: 66, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
37 24 0.36
38 6 0.09
39 1 0.02
40 13 0.20
41 22 0.33
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (39 bp):
GATGAGACACTAGGTGTCAATTTACTATTCGGATTACTC
Found at i:28968297 original size:38 final size:37
Alignment explanation
Indices: 28968253--28968330 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 37
28968243 TTTTATTTGT
* **
28968253 TTTGTTTCGTTTTCAGTTTATTAGTTCAATTTTTTTTC
1 TTTGTTTCATTTTCAGTTTATTAGTT-AAAATTTTTTC
28968291 TTTGTTTCATTTTCAGTTTATTAGTTAAAATTTTTTC
1 TTTGTTTCATTTTCAGTTTATTAGTTAAAATTTTTTC
28968328 TTT
1 TTT
28968331 TGTGTTTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
37 12 0.32
38 25 0.68
ACGTcount: A:0.17, C:0.09, G:0.09, T:0.65
Consensus pattern (37 bp):
TTTGTTTCATTTTCAGTTTATTAGTTAAAATTTTTTC
Found at i:28970055 original size:18 final size:18
Alignment explanation
Indices: 28970032--28970069 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
28970022 TCCCGAAGGG
28970032 ATTAATTGGTTTTAAATC
1 ATTAATTGGTTTTAAATC
28970050 ATTAATTGGTTTTAAATC
1 ATTAATTGGTTTTAAATC
28970068 AT
1 AT
28970070 GTATGCTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (18 bp):
ATTAATTGGTTTTAAATC
Found at i:28972277 original size:28 final size:29
Alignment explanation
Indices: 28972246--28972316 Score: 92
Period size: 27 Copynumber: 2.5 Consensus size: 29
28972236 TTTTATAAAA
* * *
28972246 TTTATAAATTTTTTATGATTTTTTAT-TT
1 TTTATAAATTTTATATAATTTTTAATATT
*
28972274 TTTAT-AAGTTTATATAATTTTTAATATT
1 TTTATAAATTTTATATAATTTTTAATATT
28972302 TTTATAAATTTTATA
1 TTTATAAATTTTATA
28972317 AGAAAATATA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 16 0.44
28 12 0.33
29 8 0.22
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (29 bp):
TTTATAAATTTTATATAATTTTTAATATT
Found at i:28972293 original size:37 final size:36
Alignment explanation
Indices: 28972170--28972318 Score: 108
Period size: 37 Copynumber: 4.0 Consensus size: 36
28972160 AACGATTTCT
* *
28972170 TTTAT-AATTTCTAAT-TTTTTATAAATTTTAAATATAT
1 TTTATAAATTTTTAATATTTTTATAAATTTT--ATA-AG
** * *
28972207 TTTATAAATTAATAGA-ACTTATTATAAAATTTTATAAAA
1 TTTATAAATTTTTA-ATA-TTTTTAT-AAATTTTAT-AAG
* **
28972246 TTTATAAATTTTTTATGATTTTT-TATTTTTTATAAG
1 TTTATAAATTTTTAAT-ATTTTTATAAATTTTATAAG
28972282 TTTATATAATTTTTAATATTTTTATAAATTTTATAAG
1 TTTATA-AATTTTTAATATTTTTATAAATTTTATAAG
28972319 AAAATATAAG
Statistics
Matches: 88, Mismatches: 14, Indels: 20
0.72 0.11 0.16
Matches are distributed among these distances:
36 14 0.16
37 32 0.36
38 8 0.09
39 19 0.22
40 8 0.09
41 7 0.08
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (36 bp):
TTTATAAATTTTTAATATTTTTATAAATTTTATAAG
Found at i:28972304 original size:10 final size:10
Alignment explanation
Indices: 28972185--28972317 Score: 68
Period size: 10 Copynumber: 13.9 Consensus size: 10
28972175 AATTTCTAAT
28972185 TTTTTATAAA
1 TTTTTATAAA
28972195 -TTTTA-AATA
1 TTTTTATAA-A
28972204 TATTTTATAAA
1 T-TTTTATAAA
** * *
28972215 TTAATAGAAC
1 TTTTTATAAA
*
28972225 TTATTATAAA
1 TTTTTATAAA
*
28972235 ATTTTATAAA
1 TTTTTATAAA
*
28972245 -ATTTATAAA
1 TTTTTATAAA
*
28972254 TTTTT-TATGA
1 TTTTTATA-AA
*
28972264 TTTTT-T-AT
1 TTTTTATAAA
*
28972272 TTTTTATAAG
1 TTTTTATAAA
*
28972282 TTTATAT-AA
1 TTTTTATAAA
*
28972291 TTTTTA-ATA
1 TTTTTATAAA
28972300 TTTTTATAAA
1 TTTTTATAAA
28972310 -TTTTATAA
1 TTTTTATAA
28972318 GAAAATATAA
Statistics
Matches: 93, Mismatches: 20, Indels: 21
0.69 0.15 0.16
Matches are distributed among these distances:
8 7 0.08
9 38 0.41
10 39 0.42
11 7 0.08
12 2 0.02
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (10 bp):
TTTTTATAAA
Found at i:28972313 original size:9 final size:9
Alignment explanation
Indices: 28972186--28972317 Score: 72
Period size: 9 Copynumber: 13.9 Consensus size: 9
28972176 ATTTCTAATT
28972186 TTTTATAAA
1 TTTTATAAA
*
28972195 TTTTAAATATA
1 TTTT--ATAAA
28972206 TTTTATAAA
1 TTTTATAAA
*
28972215 -TTAATAGAA
1 TTTTATA-AA
28972224 CTTATTATAAAA
1 -TT-TTAT-AAA
28972236 TTTTATAAA
1 TTTTATAAA
*
28972245 ATTTATAAA
1 TTTTATAAA
* *
28972254 TTTTTTATGA
1 TTTTATA-AA
* **
28972264 TTTTTTATT
1 TTTTATAAA
28972273 TTTTAT-AA
1 TTTTATAAA
*
28972281 GTTTATATAA
1 TTTTATA-AA
28972291 TTTT-TAATA
1 TTTTATAA-A
28972300 TTTTTATAAA
1 -TTTTATAAA
28972310 TTTTATAA
1 TTTTATAA
28972318 GAAAATATAA
Statistics
Matches: 95, Mismatches: 15, Indels: 26
0.70 0.11 0.19
Matches are distributed among these distances:
8 11 0.12
9 42 0.44
10 22 0.23
11 14 0.15
12 5 0.05
13 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (9 bp):
TTTTATAAA
Found at i:28972314 original size:18 final size:18
Alignment explanation
Indices: 28972169--28972314 Score: 61
Period size: 20 Copynumber: 7.8 Consensus size: 18
28972159 AAACGATTTC
28972169 TTTTAT-AATTTCTAAT-T
1 TTTTATAAATTT-TAATAT
28972186 TTTTATAAATTTTAAATAT
1 TTTTATAAATTTT-AATAT
*
28972205 ATTTTATAAATTAATAGA-ACT
1 -TTTTATAAATT-TTA-ATA-T
* *
28972226 TATTATAAAATTTT-ATAAA
1 TTTTAT-AAATTTTAAT-AT
* *
28972245 ATTTATAAATTTTTTATGAT
1 TTTTATAAA-TTTTAAT-AT
* *
28972265 TTTT-T-ATTTTTTATAAGT
1 TTTTATAAATTTTAAT-A-T
* *
28972283 TTATATAATTTTTAATAT
1 TTTTATAAATTTTAATAT
28972301 TTTTATAAATTTTA
1 TTTTATAAATTTTA
28972315 TAAGAAAATA
Statistics
Matches: 99, Mismatches: 15, Indels: 29
0.69 0.10 0.20
Matches are distributed among these distances:
17 15 0.15
18 30 0.30
19 12 0.12
20 34 0.34
21 8 0.08
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTTATAAATTTTAATAT
Found at i:28977999 original size:2 final size:2
Alignment explanation
Indices: 28977992--28978028 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
28977982 TCCTTCATTT
28977992 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
28978029 TTTCATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:28986343 original size:21 final size:21
Alignment explanation
Indices: 28986317--28986356 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28986307 ATCCAACATG
28986317 GCTAGTTAACTAGCCACGTTA
1 GCTAGTTAACTAGCCACGTTA
*
28986338 GCTAGTTAACTGGCCACGT
1 GCTAGTTAACTAGCCACGT
28986357 CACCTGTCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (21 bp):
GCTAGTTAACTAGCCACGTTA
Found at i:28986883 original size:95 final size:95
Alignment explanation
Indices: 28986680--28986853 Score: 258
Period size: 95 Copynumber: 1.8 Consensus size: 95
28986670 GATTACCTTG
* *
28986680 ACTAAGAGAAATCAGAATTTATAAAATTAATAAATAATTTATATAAATTTACCTAATATTAAAAT
1 ACTAAGAAAAATAAGAATTTATAAAATTAATAAATAATTTATATAAATTTACCTAATATTAAAAT
** * *
28986745 TCAATATTTTGATTACCCTATACTAAAATA
66 TCAATATCATGATTACACTATACGAAAATA
* *
28986775 ACTAAGAGAAATAAGAATTTCTAAAATTAATAAATAATTTATATAAATTTTACCTAATATTAAAA
1 ACTAAGAAAAATAAGAATTTATAAAATTAATAAATAATTTATATAAA-TTTACCTAATATTAAAA
*
28986840 TTCCATATCATGAT
65 TTCAATATCATGAT
28986854 CACATGAGAA
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
95 45 0.62
96 28 0.38
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (95 bp):
ACTAAGAAAAATAAGAATTTATAAAATTAATAAATAATTTATATAAATTTACCTAATATTAAAAT
TCAATATCATGATTACACTATACGAAAATA
Found at i:28988664 original size:17 final size:17
Alignment explanation
Indices: 28988642--28988689 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 17
28988632 AACTGAATTA
*
28988642 GGGCGTATGGGCCACAC
1 GGGCGTGTGGGCCACAC
*
28988659 GGGCGTGTAGGCCCACAC
1 GGGCGTGT-GGGCCACAC
28988677 GGGCGTGTGGGCC
1 GGGCGTGTGGGCC
28988690 CATATGGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.12, C:0.29, G:0.46, T:0.12
Consensus pattern (17 bp):
GGGCGTGTGGGCCACAC
Found at i:28997438 original size:26 final size:26
Alignment explanation
Indices: 28997409--28997464 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
28997399 CACCATAGAG
* * *
28997409 GCTTCCATTTTAGATACTCCACAAAA
1 GCTTCCATTTCAAATACGCCACAAAA
*
28997435 GCTTCCATTTCAAATACGCCACAAAG
1 GCTTCCATTTCAAATACGCCACAAAA
28997461 GCTT
1 GCTT
28997465 TTATTTTTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.32, C:0.29, G:0.11, T:0.29
Consensus pattern (26 bp):
GCTTCCATTTCAAATACGCCACAAAA
Found at i:29012706 original size:22 final size:23
Alignment explanation
Indices: 29012664--29012712 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
29012654 TAGAGATACT
29012664 TGTAATCTTAGAAGATATGATTC
1 TGTAATCTTAGAAGATATGATTC
* *
29012687 TGTAATCTTAG-AGATTTGATTT
1 TGTAATCTTAGAAGATATGATTC
29012709 TGTA
1 TGTA
29012713 GATAGCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.31, C:0.06, G:0.18, T:0.45
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATGATTC
Found at i:29017502 original size:26 final size:26
Alignment explanation
Indices: 29017466--29017531 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
29017456 CCTGACCCAT
* *
29017466 AGCTCATGTGAGCAGGCTCATTTCAC
1 AGCTCGTGTGAGCAGACTCATTTCAC
29017492 AGCTCGTGTGAGCAGACTCATTTCAC
1 AGCTCGTGTGAGCAGACTCATTTCAC
*
29017518 ATCTCGTGTGAGCA
1 AGCTCGTGTGAGCA
29017532 TATACAGTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (26 bp):
AGCTCGTGTGAGCAGACTCATTTCAC
Found at i:29020013 original size:30 final size:31
Alignment explanation
Indices: 29019958--29020015 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
29019948 ACAACTCCCA
29019958 TTCCCAGCCACAAAGCCTAATTGAGCAAATG
1 TTCCCAGCCACAAAGCCTAATTGAGCAAATG
* * *
29019989 TTCCTAGCCACGAAG-CTAGTTGAGCAA
1 TTCCCAGCCACAAAGCCTAATTGAGCAA
29020016 GAATTCTCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.21
Consensus pattern (31 bp):
TTCCCAGCCACAAAGCCTAATTGAGCAAATG
Found at i:29022249 original size:109 final size:109
Alignment explanation
Indices: 29022080--29023071 Score: 1767
Period size: 109 Copynumber: 9.1 Consensus size: 109
29022070 AATTTGGTTA
*
29022080 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACACAAAACATT
1 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATT
* * ** * * * *
29022145 GTCTTGTTTTAAAATTTTTAAAAGGATATTAAGCCA-TTTGGTTG
66 GCCTTATTTTGGAATTTTTAGAAGGATATTTAGCTAGTCT-GTTG
29022189 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATT
1 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATT
29022254 GCCTTATTTTGGAATTTTTAGAAGGATATTTAGCTAGTCTGTTG
66 GCCTTATTTTGGAATTTTTAGAAGGATATTTAGCTAGTCTGTTG
29022298 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATT
1 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATT
29022363 GCCTTATTTTGGAATTTTTAGAAGGATATTTAGCTAGTCTGTTG
66 GCCTTATTTTGGAATTTTTAGAAGGATATTTAGCTAGTCTGTTG
29022407 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATT
1 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATT
29022472 GCCTTATTTTGGAATTTTTAGAAGGATATTTAGCTAGTCTGTTG
66 GCCTTATTTTGGAATTTTTAGAAGGATATTTAGCTAGTCTGTTG
29022516 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATT
1 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATT
29022581 GCCTTATTTTGGAATTTTTAGAAGGATATTTAGCTAGTCTGTTG
66 GCCTTATTTTGGAATTTTTAGAAGGATATTTAGCTAGTCTGTTG
29022625 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATT
1 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATT
29022690 GCCTTATTTTGGAATTTTTAGAAGGATATTTAGCTAGTCTGTTG
66 GCCTTATTTTGGAATTTTTAGAAGGATATTTAGCTAGTCTGTTG
29022734 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATT
1 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATT
29022799 GCCTTATTTTGGAATTTTTAGAAGGATATTTAGCTAGTCTGTTG
66 GCCTTATTTTGGAATTTTTAGAAGGATATTTAGCTAGTCTGTTG
29022843 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATT
1 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATT
*
29022908 GCCTTATTTTGGAATTTTTAGAAGGATATTTAGCTA-TTTGGTTG
66 GCCTTATTTTGGAATTTTTAGAAGGATATTTAGCTAGTCT-GTTG
*
29022952 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCT-AGAATTTCCAAATGCAAAACAT
1 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCA-AATTTCCAAACGCAAAACAT
** * * * *
29023016 TGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCCA-TTTGGTTG
65 TGCCTTATTTTGGAATTTTTAGAAGGATATTTAGCTAGTCT-GTTG
29023061 AACGAGAAAAA
1 AACGAGAAAAA
29023072 AAACTCGAAT
Statistics
Matches: 864, Mismatches: 16, Indels: 6
0.98 0.02 0.01
Matches are distributed among these distances:
108 3 0.00
109 859 0.99
110 2 0.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (109 bp):
AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATT
GCCTTATTTTGGAATTTTTAGAAGGATATTTAGCTAGTCTGTTG
Found at i:29023230 original size:172 final size:172
Alignment explanation
Indices: 29022930--29023243 Score: 524
Period size: 172 Copynumber: 1.8 Consensus size: 172
29022920 AATTTTTAGA
* *
29022930 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTA
1 AGGATATTTAGCAATTTGGTTAAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTA
*
29022995 GAATTTCCAAATGCAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCCATTTGGTT
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCCATTTGGTT
29023060 GAACGAGAAAAAAAACTCGAATGGTATGGATTAAAATTCAAG
131 GAACGAGAAAAAAAACTCGAATGGTATGGATTAAAATTCAAG
29023102 AGGATATTT-GACAATTTGGTTAAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCT
1 AGGATATTTAG-CAATTTGGTTAAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCT
* * * *
29023166 CGAATTTCCAAACGCAAAACATTGCCTTATTTTAGAATTTTTAGAAA-GATATTTAGCTATTTGG
65 AGAATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTA-AAAGGATATTAAGCCATTTGG
*
29023230 TTGAACGAGGAAAA
129 TTGAACGAGAAAAA
29023244 TCGACACCCA
Statistics
Matches: 132, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
171 1 0.01
172 128 0.97
173 3 0.02
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.31
Consensus pattern (172 bp):
AGGATATTTAGCAATTTGGTTAAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTA
GAATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCCATTTGGTT
GAACGAGAAAAAAAACTCGAATGGTATGGATTAAAATTCAAG
Found at i:29023295 original size:109 final size:109
Alignment explanation
Indices: 29023115--29023396 Score: 476
Period size: 109 Copynumber: 2.6 Consensus size: 109
29023105 ATATTTGACA
* *
29023115 ATTTGGTTAAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACA
* * *
29023180 CAAAACATTGCCTTATTTTAGAATTTTTAGAAA-GATATTTAGCT
66 CAAAACATTGCCTTATTTTAAAATTTTTA-AAAGGATATTAAGCC
*
29023224 ATTTGGTTGAACGAGGAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACA
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACA
* *
29023289 CAAAACATTGTCTTGTTTTAAAATTTTTAAAAGGATATTAAGCC
66 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
29023333 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAAC
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAAC
29023397 NNNNNNNNNN
Statistics
Matches: 163, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
108 3 0.02
109 160 0.98
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (109 bp):
ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACA
CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
Found at i:29023324 original size:281 final size:281
Alignment explanation
Indices: 29022843--29023352 Score: 939
Period size: 281 Copynumber: 1.8 Consensus size: 281
29022833 TAGTCTGTTG
29022843 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATT
1 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATT
* *
29022908 GCCTTATTTTGGAATTTTTAGAAGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCA
66 GCCTTATTTTAGAATTTTTAGAAAGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCA
**
29022973 GCACCTTAGGGCATGTTTTCTAGAATTTCCAAATGCAAAACATTGCCTTATTTTAAAATTTTTAA
131 GCACCTTAGGGCATGTTTTCTAGAATTTCCAAACACAAAACATTGCCTTATTTTAAAATTTTTAA
29023038 AAGGATATTAAGCCATTTGGTTGAACGAGAAAAAAAACTCGAATGGTATGGATTAAAATTCAAGA
196 AAGGATATTAAGCCATTTGGTTGAACGAGAAAAAAAACTCGAATGGTATGGATTAAAATTCAAGA
29023103 GGATATTTGACAATTTGGTTA
261 GGATATTTGACAATTTGGTTA
*
29023124 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATT
1 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATT
*
29023189 GCCTTATTTTAGAATTTTTAGAAAGATATTTAGCTATTTGGTTGAACGAGGAAAATCGACACCCA
66 GCCTTATTTTAGAATTTTTAGAAAGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCA
* * *
29023254 GCACCTTAGGGCATGTTTTCTCGAATTTCCAAACACAAAACATTGTCTTGTTTTAAAATTTTTAA
131 GCACCTTAGGGCATGTTTTCTAGAATTTCCAAACACAAAACATTGCCTTATTTTAAAATTTTTAA
29023319 AAGGATATTAAGCCATTTGGTTGAACGAGAAAAA
196 AAGGATATTAAGCCATTTGGTTGAACGAGAAAAA
29023353 TCGACACCCA
Statistics
Matches: 220, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
281 220 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (281 bp):
AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCAAATTTCCAAACGCAAAACATT
GCCTTATTTTAGAATTTTTAGAAAGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCA
GCACCTTAGGGCATGTTTTCTAGAATTTCCAAACACAAAACATTGCCTTATTTTAAAATTTTTAA
AAGGATATTAAGCCATTTGGTTGAACGAGAAAAAAAACTCGAATGGTATGGATTAAAATTCAAGA
GGATATTTGACAATTTGGTTA
Found at i:29035361 original size:19 final size:19
Alignment explanation
Indices: 29035339--29035376 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
29035329 TAAATACTAA
*
29035339 AGAAACTGAAAAATAAAAG
1 AGAAACAGAAAAATAAAAG
*
29035358 AGAAACAGAGAAATAAAAG
1 AGAAACAGAAAAATAAAAG
29035377 TTGAAATCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.05, G:0.18, T:0.08
Consensus pattern (19 bp):
AGAAACAGAAAAATAAAAG
Found at i:29035584 original size:21 final size:20
Alignment explanation
Indices: 29035560--29035599 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
29035550 TGCAAGTGGG
29035560 GGTGGCCGACGTGACGTTGGT
1 GGTGG-CGACGTGACGTTGGT
*
29035581 GGTGGCGGCGTGACGTTGG
1 GGTGGCGACGTGACGTTGG
29035600 CGGCAGTGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.07, C:0.17, G:0.53, T:0.23
Consensus pattern (20 bp):
GGTGGCGACGTGACGTTGGT
Found at i:29036563 original size:40 final size:40
Alignment explanation
Indices: 29036472--29036677 Score: 180
Period size: 40 Copynumber: 5.3 Consensus size: 40
29036462 CGTTTTTCTT
* * * * *
29036472 AAAAACGCCGCAAAAGATCAAGCACTAGCGACGTCTATGAG
1 AAAAACGCCACAAAAGGTCAAGCATTAGCGGCG-CTAGGAG
* *
29036513 AAATACGCCACAAAAGGTCAAACATTAGCGGCGCTAGGAG
1 AAAAACGCCACAAAAGGTCAAGCATTAGCGGCGCTAGGAG
* *
29036553 AAAAATGCCACAAAAGGTC--G----A-C--AGCTAGGAG
1 AAAAACGCCACAAAAGGTCAAGCATTAGCGGCGCTAGGAG
** * *
29036584 AAAATTGCCGCAAAAGGTCAAGCATTAGCGGCGCTAGAAG
1 AAAAACGCCACAAAAGGTCAAGCATTAGCGGCGCTAGGAG
* *
29036624 AAAAACG-CAGCAAAAGGTCGAGCATTAGCCGCGCTAGGAG
1 AAAAACGCCA-CAAAAGGTCAAGCATTAGCGGCGCTAGGAG
*
29036664 AAAAACGCCGCAAA
1 AAAAACGCCACAAA
29036678 GTAGAATTTT
Statistics
Matches: 132, Mismatches: 22, Indels: 23
0.75 0.12 0.13
Matches are distributed among these distances:
31 25 0.19
33 2 0.02
34 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 73 0.55
41 28 0.21
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.11
Consensus pattern (40 bp):
AAAAACGCCACAAAAGGTCAAGCATTAGCGGCGCTAGGAG
Found at i:29037084 original size:18 final size:18
Alignment explanation
Indices: 29037061--29037097 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
29037051 CATCCATTGT
29037061 TCGAATTTGATTTTAGCA
1 TCGAATTTGATTTTAGCA
*
29037079 TCGAATTTGATTTTGGCA
1 TCGAATTTGATTTTAGCA
29037097 T
1 T
29037098 GCATCAGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (18 bp):
TCGAATTTGATTTTAGCA
Found at i:29038926 original size:41 final size:41
Alignment explanation
Indices: 29038881--29038960 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
29038871 CTCGGAGAAG
*
29038881 GGAAAAATAGTTAATAGTTGCTGCAGTTTGCTTTGTTCGCA
1 GGAAAAATAGTTAATAGTTGCTGCAGTTTACTTTGTTCGCA
29038922 GGAAAAATAGTTAATAGTTGCTGCAGTTTACTTTGTTCG
1 GGAAAAATAGTTAATAGTTGCTGCAGTTTACTTTGTTCG
29038961 TAGCATTCTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.38
Consensus pattern (41 bp):
GGAAAAATAGTTAATAGTTGCTGCAGTTTACTTTGTTCGCA
Found at i:29050796 original size:24 final size:24
Alignment explanation
Indices: 29050699--29050816 Score: 80
Period size: 24 Copynumber: 4.9 Consensus size: 24
29050689 TCACAACCAA
*
29050699 ATCGGGATGCTCATAAGAGC-AATT
1 ATCGGGATGCTCATGAGAGCTAA-T
* * * *
29050723 AACGGGAGGCTCGTGAGAGCCATAT
1 ATCGGGATGCTCATGAGAGCTA-AT
*
29050748 ATCGGG-TAGCTCAAGAGAG-TCAAT
1 ATCGGGAT-GCTCATGAGAGCT-AAT
*
29050772 ATCGAGATGCTCATGAGAGCTAAT
1 ATCGGGATGCTCATGAGAGCTAAT
* * * *
29050796 AACGGGACGCTCTTGCGAGCT
1 ATCGGGATGCTCATGAGAGCT
29050817 GTGATGTGTC
Statistics
Matches: 72, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
24 52 0.72
25 19 0.26
26 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.21
Consensus pattern (24 bp):
ATCGGGATGCTCATGAGAGCTAAT
Found at i:29053542 original size:49 final size:48
Alignment explanation
Indices: 29053482--29053663 Score: 156
Period size: 49 Copynumber: 3.7 Consensus size: 48
29053472 GATAAAAACA
* * *
29053482 TGCCAAAGCCATGTCCTAGACATGGTCTTACATGAGATGTTTTCTGTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGA-GTTCTCTGTAC
* * * *
29053531 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTC-ATATC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGAGTTCTCTGTA-C
* * * * *
29053579 GGTGCCCATGCCATGTCCCAAACATGGTCTTAC-GGAGGACCTCTCACTCG-A-
1 --TGCCAATGCCATGTCCCAGACATGGTCTTACATGA-GA-GT-TCTCT-GTAC
29053630 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
29053664 GGACCTCTTA
Statistics
Matches: 105, Mismatches: 19, Indels: 17
0.74 0.13 0.12
Matches are distributed among these distances:
47 2 0.02
48 6 0.06
49 62 0.59
50 30 0.29
51 1 0.01
52 3 0.03
53 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (48 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGAGTTCTCTGTAC
Found at i:29053606 original size:50 final size:50
Alignment explanation
Indices: 29053531--29053721 Score: 242
Period size: 50 Copynumber: 3.8 Consensus size: 50
29053521 TTTTCTGTAC
* * ** *
29053531 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
29053581 TGCCCATGCCATGTCCCAAACATGGTCTTAC-GGAGGACCTCTCA-CTCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG-GGACCTCTCATCTCGG
*
29053630 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
29053680 TACCAACGCCATGTCCCAGAAATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
29053722 TTACCCAAAT
Statistics
Matches: 121, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
49 42 0.35
50 79 0.65
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:29053668 original size:49 final size:50
Alignment explanation
Indices: 29053481--29053721 Score: 240
Period size: 50 Copynumber: 4.9 Consensus size: 50
29053471 TGATAAAAAC
* * * * **
29053481 ATGCCAAAGCCATGTCCTAGACATGGTCTTACATGAGA--TGTTTTCT-G
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * ** *
29053528 TACTGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCG
1 -A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * * *
29053580 GTGCCCATGCCATGTCCCAAACATGGTCTTAC-GGAGGACCTCTCA-CTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATG-GGACCTCTCATCTCG
*
29053629 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * * *
29053679 GTACCAACGCCATGTCCCAGAAATGGTCTTACATGGGACCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
29053722 TTACCCAAAT
Statistics
Matches: 159, Mismatches: 27, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
48 1 0.01
49 74 0.47
50 79 0.50
51 4 0.03
52 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
Found at i:29053721 original size:99 final size:99
Alignment explanation
Indices: 29053531--29053710 Score: 263
Period size: 99 Copynumber: 1.8 Consensus size: 99
29053521 TTTTCTGTAC
* ** * * *
29053531 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTC
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTACCAACGCCATGTC
29053596 CCAAACATGGTCTTACGGAGGACCTCTCACTCGA
66 CCAAACATGGTCTTACGGAGGACCTCTCACTCGA
* * *
29053630 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTACCAACGCCATGTC
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTACCAACGCCATGTC
29053695 CCAGAA-ATGGTCTTAC
66 CCA-AACATGGTCTTAC
29053711 ATGGGACCTC
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 69 0.97
100 2 0.03
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (99 bp):
TGCCAATGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTACCAACGCCATGTC
CCAAACATGGTCTTACGGAGGACCTCTCACTCGA
Found at i:29063113 original size:16 final size:16
Alignment explanation
Indices: 29063092--29063128 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
29063082 GTAATAGTTC
*
29063092 GTTTCGAACTGATATT
1 GTTTCGAACTAATATT
29063108 GTTTCGAACTAATATT
1 GTTTCGAACTAATATT
29063124 GTTTC
1 GTTTC
29063129 ATGTATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (16 bp):
GTTTCGAACTAATATT
Found at i:29063490 original size:24 final size:24
Alignment explanation
Indices: 29063406--29063497 Score: 71
Period size: 24 Copynumber: 3.8 Consensus size: 24
29063396 TCACAATGAA
* *
29063406 ATCGGGATGCTCATA-AGAGCTATT
1 ATCGGGATGCTCA-AGAGAGCCAAT
* * **
29063430 AACGGGAGGCTCGTGAGAGCCATAT
1 ATCGGGATGCTCAAGAGAGCCA-AT
*
29063455 ATTGGG-TAGCTCAAGAGAGCCAAT
1 ATCGGGAT-GCTCAAGAGAGCCAAT
*
29063479 ATCGGGATGCTCATGAGAG
1 ATCGGGATGCTCAAGAGAG
29063498 ATAATAACGG
Statistics
Matches: 51, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
24 33 0.65
25 18 0.35
ACGTcount: A:0.29, C:0.17, G:0.32, T:0.22
Consensus pattern (24 bp):
ATCGGGATGCTCAAGAGAGCCAAT
Found at i:29063503 original size:24 final size:24
Alignment explanation
Indices: 29063406--29063514 Score: 69
Period size: 24 Copynumber: 4.5 Consensus size: 24
29063396 TCACAATGAA
* * *
29063406 ATCGGGATGCTCATAAGAGCTATT
1 ATCGGGATGCTCATGAGAGATAAT
* * *
29063430 AACGGGAGGCTCGTGAGAGCCAT-AT
1 ATCGGGATGCTCATGAGAG--ATAAT
* * **
29063455 ATTGGG-TAGCTCAAGAGAGCCAAT
1 ATCGGGAT-GCTCATGAGAGATAAT
29063479 ATCGGGATGCTCATGAGAGATAAT
1 ATCGGGATGCTCATGAGAGATAAT
* *
29063503 AACGGGACGCTC
1 ATCGGGATGCTC
29063515 TTGTGAGTTA
Statistics
Matches: 61, Mismatches: 19, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
24 45 0.74
25 15 0.25
26 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.21
Consensus pattern (24 bp):
ATCGGGATGCTCATGAGAGATAAT
Found at i:29066121 original size:16 final size:18
Alignment explanation
Indices: 29066102--29066134 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29066092 TGAACCTTGT
29066102 ATCAT-TCA-AAATTATA
1 ATCATATCATAAATTATA
29066118 ATCATATCATAAATTAT
1 ATCATATCATAAATTAT
29066135 TCATGGACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 3 0.20
18 7 0.47
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (18 bp):
ATCATATCATAAATTATA
Found at i:29073930 original size:17 final size:17
Alignment explanation
Indices: 29073886--29073931 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
29073876 AAGTTGGAAC
*
29073886 AATT-AATAATCAATTA
1 AATTCAATAATTAATTA
*
29073902 CATTCAATAATTAATTA
1 AATTCAATAATTAATTA
*
29073919 AATTCCATAATTA
1 AATTCAATAATTA
29073932 CAAGTAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 3 0.12
17 22 0.88
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTCAATAATTAATTA
Found at i:29075048 original size:78 final size:77
Alignment explanation
Indices: 29074958--29075203 Score: 291
Period size: 78 Copynumber: 3.2 Consensus size: 77
29074948 CTGGAATAGT
* * *
29074958 ATTCAGTATATTTTCAGTAAGTTTTGCTCGATTGAGCAGTATTCAGTATATTCGGTAAGTTTGCT
1 ATTCAGTATA-TTTCAGTAAGTTTTGCTCGATTGAGCAATATTCAATATATTCAGTAAGTTTGCT
* *
29075023 TGTTTGAGCAAC-
65 CGATTGAGCAACA
* * * *
29075035 ATTGCAGTATATTT-AGTAAGCTTTGCTCGATTGAGCAACAATTCATTATATTCAGTAAGTTTTC
1 ATT-CAGTATATTTCAGTAAGTTTTGCTCGATTGAGCAA-TATTCAATATATTCAGTAAG-TTTG
29075099 CTCGATTGAGCAACA
63 CTCGATTGAGCAACA
* * *
29075114 ATTCAGTATA-TTCAGTAAGTCTTGCTTGATTGAGCAATAATTCAATATATTTAGTAAGTCTTGC
1 ATTCAGTATATTTCAGTAAGTTTTGCTCGATTGAGCAAT-ATTCAATATATTCAGTAAGT-TTGC
* *
29075178 TCAATTGAGCAATA
64 TCGATTGAGCAACA
29075192 ATTCAGTATATT
1 ATTCAGTATATT
29075204 CGGTATTCCA
Statistics
Matches: 144, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
76 22 0.15
77 26 0.18
78 92 0.64
79 4 0.03
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (77 bp):
ATTCAGTATATTTCAGTAAGTTTTGCTCGATTGAGCAATATTCAATATATTCAGTAAGTTTGCTC
GATTGAGCAACA
Found at i:29075071 original size:39 final size:37
Alignment explanation
Indices: 29074958--29075204 Score: 260
Period size: 39 Copynumber: 6.4 Consensus size: 37
29074948 CTGGAATAGT
**
29074958 ATTCAGTATATTTTCAGTAAGTTTTGCTCGATTGAGCAGT
1 ATTCAGTATA--TTCAGTAAG-TTTGCTCGATTGAGCAAC
* * *
29074998 ATTCAGTATATTCGGTAAGTTTGCTTGTTTGAGCAAC
1 ATTCAGTATATTCAGTAAGTTTGCTCGATTGAGCAAC
*
29075035 ATTGCAGTATATTTAGTAAGCTTTGCTCGATTGAGCAAC
1 ATT-CAGTATATTCAGTAAG-TTTGCTCGATTGAGCAAC
* *
29075074 AATTCATTATATTCAGTAAGTTTTCCTCGATTGAGCAAC
1 -ATTCAGTATATTCAGTAAG-TTTGCTCGATTGAGCAAC
* *
29075113 AATTCAGTATATTCAGTAAGTCTTGCTTGATTGAGCAATA
1 -ATTCAGTATATTCAGTAAGT-TTGCTCGATTGAGCAA-C
* * * *
29075153 ATTCAATATATTTAGTAAGTCTTGCTCAATTGAGCAATA
1 ATTCAGTATATTCAGTAAGT-TTGCTCGATTGAGCAA-C
29075192 ATTCAGTATATTC
1 ATTCAGTATATTC
29075205 GGTATTCCAT
Statistics
Matches: 179, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
37 17 0.09
38 23 0.13
39 126 0.70
40 13 0.07
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (37 bp):
ATTCAGTATATTCAGTAAGTTTGCTCGATTGAGCAAC
Found at i:29075141 original size:117 final size:115
Alignment explanation
Indices: 29074958--29075204 Score: 336
Period size: 117 Copynumber: 2.1 Consensus size: 115
29074948 CTGGAATAGT
* ** *
29074958 ATTCAGTATATTTTCAGTAAGTTTTGCTCGATTGAGCAGTATTCAGTATATTCGGTAAGTTTGCT
1 ATTCAGTATA--TTCAGTAAGTTTTCCTCGATTGAGCACAATTCAGTATATTCAGTAAGTTTGCT
* * * *
29075023 TGTTTGAGCAA-CATTGCAGTATATTTAGTAAG-CTTTGCTCGATTGAGCAACA
64 TGATTGAGCAATAATT-CAATATATTTAGTAAGTC-TTGCTCAATTGAGCAACA
*
29075075 ATTCATTATATTCAGTAAGTTTTCCTCGATTGAGCAACAATTCAGTATATTCAGTAAGTCTTGCT
1 ATTCAGTATATTCAGTAAGTTTTCCTCGATTGAGC-ACAATTCAGTATATTCAGTAAGT-TTGCT
*
29075140 TGATTGAGCAATAATTCAATATATTTAGTAAGTCTTGCTCAATTGAGCAATA
64 TGATTGAGCAATAATTCAATATATTTAGTAAGTCTTGCTCAATTGAGCAACA
29075192 ATTCAGTATATTC
1 ATTCAGTATATTC
29075205 GGTATTCCAT
Statistics
Matches: 115, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
115 24 0.21
116 20 0.17
117 67 0.58
118 4 0.03
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (115 bp):
ATTCAGTATATTCAGTAAGTTTTCCTCGATTGAGCACAATTCAGTATATTCAGTAAGTTTGCTTG
ATTGAGCAATAATTCAATATATTTAGTAAGTCTTGCTCAATTGAGCAACA
Found at i:29076088 original size:26 final size:26
Alignment explanation
Indices: 29076059--29076110 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
29076049 AACATTAACT
*
29076059 AAACCATCCACCTATACATAGCACCA
1 AAACCATCCACCTATACATAACACCA
29076085 AAACCATCCACCTATACATAACACCA
1 AAACCATCCACCTATACATAACACCA
29076111 TCTCATTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.38, G:0.02, T:0.15
Consensus pattern (26 bp):
AAACCATCCACCTATACATAACACCA
Found at i:29080435 original size:21 final size:21
Alignment explanation
Indices: 29080388--29080444 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
29080378 ATAAGTCAAT
*
29080388 AGAAGCTC--AAAACCTGAAC
1 AGAAGCTCGTAAAAGCTGAAC
* *
29080407 AGAAGCTCGTAAGAGCTGAAT
1 AGAAGCTCGTAAAAGCTGAAC
*
29080428 AGACGCTCGTAAAAGCT
1 AGAAGCTCGTAAAAGCT
29080445 AATTCACCCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 8 0.26
21 23 0.74
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.16
Consensus pattern (21 bp):
AGAAGCTCGTAAAAGCTGAAC
Found at i:29087958 original size:19 final size:20
Alignment explanation
Indices: 29087931--29087982 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
29087921 CGAATAATTC
* *
29087931 AACAAAAGCTC-AAAAGTTG
1 AACAGAAGCTCGAAAAGCTG
*
29087950 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCG-AAAAGCTG
29087971 AACAGAAGCTCG
1 AACAGAAGCTCG
29087983 TAAGAGCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
21 18 0.64
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.13
Consensus pattern (20 bp):
AACAGAAGCTCGAAAAGCTG
Found at i:29087974 original size:21 final size:21
Alignment explanation
Indices: 29087948--29087990 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
29087938 GCTCAAAAGT
29087948 TGAACAGAAGCTCGTAAGAGC
1 TGAACAGAAGCTCGTAAGAGC
29087969 TGAACAGAAGCTCGTAAGAGC
1 TGAACAGAAGCTCGTAAGAGC
29087990 T
1 T
29087991 AATTCACCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.19, G:0.28, T:0.16
Consensus pattern (21 bp):
TGAACAGAAGCTCGTAAGAGC
Found at i:29091826 original size:16 final size:17
Alignment explanation
Indices: 29091780--29091833 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
29091770 AGACTCTATT
29091780 TTAATT-ATA-TTAGGA
1 TTAATTAATATTTAGGA
*
29091795 -TAATTAATATTAAGGA
1 TTAATTAATATTTAGGA
*
29091811 TTATTTAAT-TTTAGGA
1 TTAATTAATATTTAGGA
29091827 TTTAATT
1 -TTAATT
29091834 TTATTTATCT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 5 0.16
15 3 0.10
16 11 0.35
17 12 0.39
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (17 bp):
TTAATTAATATTTAGGA
Found at i:29095437 original size:12 final size:12
Alignment explanation
Indices: 29095420--29095466 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
29095410 CTTTGTTTCT
29095420 TTACTTTATTTA
1 TTACTTTATTTA
29095432 TTACTTTATTTTA
1 TTACTTTA-TTTA
*
29095445 TT-TTATTATTTA
1 TTACT-TTATTTA
29095457 TTAC-TTATTT
1 TTACTTTATTT
29095467 GGATATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
11 6 0.20
12 15 0.50
13 9 0.30
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (12 bp):
TTACTTTATTTA
Found at i:29095444 original size:17 final size:18
Alignment explanation
Indices: 29095418--29095458 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
29095408 TTCTTTGTTT
*
29095418 CTTTACTTTA-TTTATTA
1 CTTTATTTTATTTTATTA
29095435 CTTTATTTTATTTTATTA
1 CTTTATTTTATTTTATTA
29095453 -TTTATT
1 CTTTATT
29095459 ACTTATTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (18 bp):
CTTTATTTTATTTTATTA
Found at i:29099040 original size:47 final size:45
Alignment explanation
Indices: 29098989--29099156 Score: 132
Period size: 47 Copynumber: 3.6 Consensus size: 45
29098979 TATTTAATAT
*
29098989 TAATTATTTTAAATTGTATAAATTCATATAAGAAAAATTATTATCAA
1 TAATTATTTTAAATT-TATAAATTCATATAAGAAAATTTATTAT-AA
* * **
29099036 TAATT-TTATGAAA-TTATATATT-AT-T-ATTAAATTATATGTAATAA
1 TAATTATT-TTAAATTTATAAATTCATATAAGAAAATT-TAT-T-ATAA
* * *
29099080 TAATTATTTTAAATTATACAAATTCATATAAGATAATTTATTAGTTA
1 TAATTATTTTAAATT-TATAAATTCATATAAGAAAATTTATTA-TAA
29099127 TAATTATTTTAAATTTTATTAAA-TCATATA
1 TAATTATTTTAAA-TTTA-TAAATTCATATA
29099157 TTTTAATTAA
Statistics
Matches: 95, Mismatches: 13, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
42 5 0.05
43 4 0.04
44 14 0.15
45 12 0.13
46 10 0.11
47 36 0.38
48 9 0.09
49 5 0.05
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.48
Consensus pattern (45 bp):
TAATTATTTTAAATTTATAAATTCATATAAGAAAATTTATTATAA
Found at i:29099062 original size:91 final size:91
Alignment explanation
Indices: 29098915--29099122 Score: 317
Period size: 91 Copynumber: 2.3 Consensus size: 91
29098905 TTGATTTTAG
* *
29098915 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
29098980 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
* * *
29099007 TAAATTCATATAAGAAAAATTATTATCAATAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
29099072 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
29099098 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
29099123 GTTATAATTA
Statistics
Matches: 105, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
91 89 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:29099083 original size:44 final size:43
Alignment explanation
Indices: 29098936--29099097 Score: 116
Period size: 44 Copynumber: 3.6 Consensus size: 43
29098926 AAGAACATTT
* * *
29098936 TATTATTAAGAATT-TTATGAAATTATATATCATTATTAAATTA
1 TATTAATAATAATTATT-TGAAATTATATATAATTATTAAATTA
* * * *
29098979 TATTTAATATTAATTATTTTAAATTGTATA-AATTCATATAAGA-AA
1 TA-TTAATAATAATTATTTGAAATTATATATAATT-AT-TAA-ATTA
* *
29099024 AATTATTATCAATAATT-TTATGAAATTATATATTATTATTAAATTA
1 TATTA--AT-AATAATTATT-TGAAATTATATATAATTATTAAATTA
*
29099070 TATGTAATAATAATTATTTTAAATTATA
1 TAT-TAATAATAATTATTTGAAATTATA
29099098 CAAATTCATA
Statistics
Matches: 91, Mismatches: 15, Indels: 25
0.69 0.11 0.19
Matches are distributed among these distances:
43 5 0.05
44 40 0.44
45 12 0.13
46 11 0.12
47 20 0.22
48 3 0.03
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.49
Consensus pattern (43 bp):
TATTAATAATAATTATTTGAAATTATATATAATTATTAAATTA
Found at i:29099097 original size:26 final size:28
Alignment explanation
Indices: 29098935--29099011 Score: 52
Period size: 28 Copynumber: 2.8 Consensus size: 28
29098925 TAAGAACATT
* *
29098935 TTATTATTAAGAATTTTATGAAATTATATA
1 TTATTATT-A-AATTATATGAAATAATATA
* ** *
29098965 TCATTATTAAATTATATTTAATATTA-A
1 TTATTATTAAATTATATGAAATAATATA
*
29098992 TTATT-TTAAATTGTAT-AAAT
1 TTATTATTAAATTATATGAAAT
29099012 TCATATAAGA
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
25 3 0.08
26 10 0.26
27 5 0.13
28 12 0.32
29 1 0.03
30 7 0.18
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (28 bp):
TTATTATTAAATTATATGAAATAATATA
Found at i:29099304 original size:25 final size:26
Alignment explanation
Indices: 29099272--29099326 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
29099262 TTATTAAATT
*
29099272 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
29099297 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
29099322 A-ATAT
1 ATATAT
29099327 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:29099550 original size:45 final size:44
Alignment explanation
Indices: 29099449--29099558 Score: 122
Period size: 45 Copynumber: 2.6 Consensus size: 44
29099439 TTTTCCATTA
29099449 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* ** ***
29099488 TACTATTATGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
29099533 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
29099559 CCTCTAATTC
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
39 15 0.27
40 1 0.02
44 16 0.29
45 24 0.43
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:29099558 original size:16 final size:16
Alignment explanation
Indices: 29099539--29099590 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
29099529 GATTTGCTAT
*
29099539 TACACCTCTATTCCAT
1 TACACCTCTATTCCAA
29099555 TACACCTCTAATT-CAA
1 TACACCTCT-ATTCCAA
*
29099571 TACACCTCTAATCCAA
1 TACACCTCTATTCCAA
29099587 TACA
1 TACA
29099591 GTGAACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 2 0.06
16 27 0.84
17 3 0.09
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (16 bp):
TACACCTCTATTCCAA
Found at i:29100300 original size:21 final size:20
Alignment explanation
Indices: 29100276--29100331 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
29100266 TTTCTAAAGC
*
29100276 ATAAAAAAATATAAATAATAA
1 ATAAAAAAATATAAA-AAGAA
29100297 ATAAAAAGAA-ATAAAAAGAA
1 ATAAAAA-AATATAAAAAGAA
*
29100317 AAAGAAAAAATATAA
1 ATA-AAAAAATATAA
29100332 TTTGGAGACT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 8 0.27
21 20 0.67
22 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (20 bp):
ATAAAAAAATATAAAAAGAA
Found at i:29100308 original size:10 final size:10
Alignment explanation
Indices: 29100276--29100317 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
29100266 TTTCTAAAGC
29100276 ATAAAAA-AA
1 ATAAAAAGAA
*
29100285 TATAAATAATAA
1 -ATAAA-AAGAA
29100297 ATAAAAAGAA
1 ATAAAAAGAA
29100307 ATAAAAAGAA
1 ATAAAAAGAA
29100317 A
1 A
29100318 AAGAAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 20 0.69
11 7 0.24
12 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (10 bp):
ATAAAAAGAA
Found at i:29100320 original size:16 final size:17
Alignment explanation
Indices: 29100288--29100328 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
29100278 AAAAAAATAT
*
29100288 AAATAATAAATAAAAAG
1 AAATAATAAAGAAAAAG
29100305 AAATAA-AAAGAAAAAG
1 AAATAATAAAGAAAAAG
*
29100321 AAAAAATA
1 AAATAATA
29100329 TAATTTGGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12
Consensus pattern (17 bp):
AAATAATAAAGAAAAAG
Found at i:29104425 original size:70 final size:70
Alignment explanation
Indices: 29104312--29104451 Score: 235
Period size: 70 Copynumber: 2.0 Consensus size: 70
29104302 TGGGGGAGAT
* * * *
29104312 TTTGATGAGAGTGGTGATTATAAATGGTATTTAAATAAATCTAGCACTAAGATTGAAAATTCGCA
1 TTTGATGAGAGTGATGATTATAAATGGTATTTAAATAAATCTAGCACTAAGAGTAAAAATTCACA
29104377 GTTGG
66 GTTGG
*
29104382 TTTGATGAGAGTGATGATTATAAATGGTATTTAAATGAATCTAGCACTAAGAGTAAAAATTCACA
1 TTTGATGAGAGTGATGATTATAAATGGTATTTAAATAAATCTAGCACTAAGAGTAAAAATTCACA
29104447 GTTGG
66 GTTGG
29104452 ACATTTATTT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (70 bp):
TTTGATGAGAGTGATGATTATAAATGGTATTTAAATAAATCTAGCACTAAGAGTAAAAATTCACA
GTTGG
Found at i:29105032 original size:23 final size:23
Alignment explanation
Indices: 29104980--29105053 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
29104970 TTTTGCAGGT
* *
29104980 TTTTGGTGTTG-TTTTGGTGTTG
1 TTTTGGTGTTGTTTTTTGTGCTG
**
29105002 CTAGTGGTGTTGTTTTTTGTGCTG
1 -TTTTGGTGTTGTTTTTTGTGCTG
*
29105026 TTTTGGTGTTGTTTTTTGTGCTA
1 TTTTGGTGTTGTTTTTTGTGCTG
29105049 TTTTG
1 TTTTG
29105054 ATACCATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 34 0.79
24 9 0.21
ACGTcount: A:0.03, C:0.04, G:0.31, T:0.62
Consensus pattern (23 bp):
TTTTGGTGTTGTTTTTTGTGCTG
Found at i:29106373 original size:41 final size:41
Alignment explanation
Indices: 29106315--29106423 Score: 182
Period size: 41 Copynumber: 2.6 Consensus size: 41
29106305 TTTAATTTAA
*
29106315 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
29106357 CAGATCACCGACACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
29106398 CAGATCACCGGCACTTAGCCTGCTAG
1 CAGATCACCGGCACTTAGCCTGCTAG
29106424 ACGTATAGTC
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
41 59 0.94
42 4 0.06
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
Found at i:29110988 original size:20 final size:19
Alignment explanation
Indices: 29110950--29111015 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
29110940 ACCTCTTGCA
*
29110950 CCAGGATGCACTTCATGTG
1 CCAGGATGCACTTCGTGTG
*
29110969 CCAGGTATGCACTTGGTGTG
1 CCAGG-ATGCACTTCGTGTG
* * *
29110989 CTAAGATGCACTTTGTGTG
1 CCAGGATGCACTTCGTGTG
*
29111008 CTAGGATG
1 CCAGGATG
29111016 TGCTTTGTGC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
19 25 0.62
20 15 0.38
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (19 bp):
CCAGGATGCACTTCGTGTG
Found at i:29119716 original size:37 final size:37
Alignment explanation
Indices: 29119672--29119747 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
29119662 CGCCTCAAAT
29119672 TTATTTATTTTTCACTCATATTCTATTCTCTCAATTC
1 TTATTTATTTTTCACTCATATTCTATTCTCTCAATTC
29119709 TTATTTATTTTTCACTCATATTCTATTCTCTCAATTC
1 TTATTTATTTTTCACTCATATTCTATTCTCTCAATTC
29119746 TT
1 TT
29119748 TCTAATTTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (37 bp):
TTATTTATTTTTCACTCATATTCTATTCTCTCAATTC
Found at i:29119774 original size:18 final size:18
Alignment explanation
Indices: 29119737--29119787 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
29119727 TATTCTATTC
*
29119737 TCTCAATTCTTTCTAA-TT
1 TCTCAATTCTCTC-AACTT
29119755 TC-CTAATTCTCTCAACTT
1 TCTC-AATTCTCTCAACTT
*
29119773 TCTCAATTTTCTCAA
1 TCTCAATTCTCTCAA
29119788 GTTCTTGTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 3 0.11
18 24 0.86
19 1 0.04
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCTCAATTCTCTCAACTT
Found at i:29119815 original size:23 final size:23
Alignment explanation
Indices: 29119772--29119823 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
29119762 TCTCTCAACT
* * *
29119772 TTCTCAATTTTCTCAAGTTCTTG
1 TTCTAAATTTTCTCAAATTCTCG
29119795 TTCTAAATTTT-TCAATATTCTCG
1 TTCTAAATTTTCTCAA-ATTCTCG
29119818 TT-TAAA
1 TTCTAAA
29119824 AATATTAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.52
Consensus pattern (23 bp):
TTCTAAATTTTCTCAAATTCTCG
Found at i:29122634 original size:19 final size:19
Alignment explanation
Indices: 29122610--29122650 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
29122600 AAATTAATTT
29122610 AATTAA-CTAAATGCAAATG
1 AATTAACCTAAATGC-AATG
29122629 AATTAACCTAAATGCAATG
1 AATTAACCTAAATGCAATG
29122648 AAT
1 AAT
29122651 GAAATGCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (19 bp):
AATTAACCTAAATGCAATG
Found at i:29124353 original size:15 final size:15
Alignment explanation
Indices: 29124333--29124369 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
29124323 TAGTTTTTGT
29124333 CAAAAATCCTAAACC
1 CAAAAATCCTAAACC
*
29124348 CAAAAACCCTAAACC
1 CAAAAATCCTAAACC
*
29124363 TAAAAAT
1 CAAAAAT
29124370 ATTAAAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (15 bp):
CAAAAATCCTAAACC
Found at i:29124378 original size:24 final size:24
Alignment explanation
Indices: 29124349--29124402 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
29124339 TCCTAAACCC
29124349 AAAAACCCTAAACCTAAAAATATT
1 AAAAACCCTAAACCTAAAAATATT
**
29124373 AAAAACTTTAAACCTAAAAATATT
1 AAAAACCCTAAACCTAAAAATATT
29124397 AAAAAC
1 AAAAAC
29124403 TTAACCTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.61, C:0.17, G:0.00, T:0.22
Consensus pattern (24 bp):
AAAAACCCTAAACCTAAAAATATT
Found at i:29124403 original size:24 final size:24
Alignment explanation
Indices: 29124357--29124404 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
29124347 CCAAAAACCC
29124357 TAAACCTAAAAATATTAAAAACTT
1 TAAACCTAAAAATATTAAAAACTT
29124381 TAAACCTAAAAATATTAAAAACTT
1 TAAACCTAAAAATATTAAAAACTT
29124405 AACCTTAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.29
Consensus pattern (24 bp):
TAAACCTAAAAATATTAAAAACTT
Found at i:29124557 original size:20 final size:19
Alignment explanation
Indices: 29124528--29124571 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
29124518 CGGAAAATAA
*
29124528 TTTTTGGAAAATGATTTAC
1 TTTTTGGAAAATAATTTAC
29124547 TTTTCTGGAAAATAATTTAC
1 TTTT-TGGAAAATAATTTAC
29124567 TTTTT
1 TTTTT
29124572 TGGTGTTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52
Consensus pattern (19 bp):
TTTTTGGAAAATAATTTAC
Found at i:29124682 original size:20 final size:20
Alignment explanation
Indices: 29124657--29124694 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
29124647 GTTTTTACAT
29124657 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
29124677 ATATTAATAAATTTATAT
1 ATATTAATAAATTTATAT
29124695 TTTAAATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:29125988 original size:32 final size:32
Alignment explanation
Indices: 29125947--29126091 Score: 160
Period size: 32 Copynumber: 4.7 Consensus size: 32
29125937 TGTCAATCAT
*
29125947 TTCAATATCCAACAAACTTAAAACATAATAAA
1 TTCAATATCTAACAAACTTAAAACATAATAAA
* *
29125979 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCTAACAAACTTAAAACATAATAAA
*
29126011 TTCAATATCTAACAAGCTT-AAA-AT-AT-AA
1 TTCAATATCTAACAAACTTAAAACATAATAAA
* *
29126039 -TCAATATCTAACAAA-TTCAAGACATAATAAT
1 TTCAATATCTAACAAACTT-AAAACATAATAAA
* *
29126070 TTCAAAATCTAATAAAC-TAAAA
1 TTCAATATCTAACAAACTTAAAA
29126092 TGGAACCTAT
Statistics
Matches: 98, Mismatches: 8, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
26 2 0.02
27 14 0.14
28 4 0.04
29 4 0.04
30 4 0.04
31 7 0.07
32 63 0.64
ACGTcount: A:0.54, C:0.17, G:0.02, T:0.28
Consensus pattern (32 bp):
TTCAATATCTAACAAACTTAAAACATAATAAA
Found at i:29126065 original size:27 final size:27
Alignment explanation
Indices: 29125980--29126066 Score: 68
Period size: 27 Copynumber: 3.0 Consensus size: 27
29125970 CATAATAAAT
* *
29125980 TCAATATCCAACAAGCTTAAAACATAATAAA
1 TCAATATCTAACAAGATTAAAAC---AT-AA
* *
29126011 TTCAATATCTAACAAGCTTAAAATATAA
1 -TCAATATCTAACAAGATTAAAACATAA
*
29126039 TCAATATCTAACAA-ATTCAAGACATAA
1 TCAATATCTAACAAGATT-AAAACATAA
29126066 T
1 T
29126067 AATTTCAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
26 2 0.04
27 22 0.45
28 2 0.04
29 2 0.04
32 21 0.43
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (27 bp):
TCAATATCTAACAAGATTAAAACATAA
Found at i:29126074 original size:59 final size:64
Alignment explanation
Indices: 29125945--29126091 Score: 164
Period size: 59 Copynumber: 2.4 Consensus size: 64
29125935 ATTGTCAATC
* *
29125945 ATTTCAATATCCAACAAACTTAAAACATAATAAATTCAATATCCAACAAGCTTAAAACATAATA
1 ATTTCAATATCTAACAAACTTAAAACATAATAAATTCAATATCCAACAAGATTAAAACATAATA
* * * *
29126009 AATTCAATATCTAACAAGCTT-AAA-AT-AT-AA-TCAATATCTAACAA-ATTCAAGACATAATA
1 ATTTCAATATCTAACAAACTTAAAACATAATAAATTCAATATCCAACAAGATT-AAAACATAATA
* *
29126068 ATTTCAAAATCTAATAAAC-TAAAA
1 ATTTCAATATCTAACAAACTTAAAA
29126092 TGGAACCTAT
Statistics
Matches: 71, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
58 3 0.04
59 41 0.58
60 2 0.03
61 2 0.03
62 2 0.03
63 3 0.04
64 18 0.25
ACGTcount: A:0.54, C:0.16, G:0.02, T:0.28
Consensus pattern (64 bp):
ATTTCAATATCTAACAAACTTAAAACATAATAAATTCAATATCCAACAAGATTAAAACATAATA
Found at i:29129867 original size:76 final size:76
Alignment explanation
Indices: 29129741--29129936 Score: 383
Period size: 76 Copynumber: 2.6 Consensus size: 76
29129731 TGAAAGGACT
29129741 TAACCACATGCAAGCTACCAGAAGGGGAAGACAAAAGGGGATACCAGAAACAACAATAAAAATTC
1 TAACCACATGCAAGCTACCAGAAGGGGAAGACAAAAGGGGATACCAGAAACAACAATAAAAATTC
29129806 CCAATTCGACA
66 CCAATTCGACA
29129817 TAACCACATGCAAGCTACCAGAAGGGGAAGACAAAAGGGGATACCAGAAACAACAATAAAAATTC
1 TAACCACATGCAAGCTACCAGAAGGGGAAGACAAAAGGGGATACCAGAAACAACAATAAAAATTC
29129882 CCAATTCGACA
66 CCAATTCGACA
*
29129893 TAACCACATGCAAGCTACCAGAAGGGGAAGACAGAAGGGGATAC
1 TAACCACATGCAAGCTACCAGAAGGGGAAGACAAAAGGGGATAC
29129937 TTACAATATT
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 119 1.00
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (76 bp):
TAACCACATGCAAGCTACCAGAAGGGGAAGACAAAAGGGGATACCAGAAACAACAATAAAAATTC
CCAATTCGACA
Found at i:29132097 original size:21 final size:21
Alignment explanation
Indices: 29132071--29132116 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
29132061 ATATTGACCC
29132071 AAAAATTCCTAGATCCCTTTG
1 AAAAATTCCTAGATCCCTTTG
* *
29132092 AAAAATTCCTAGATTCCTTTT
1 AAAAATTCCTAGATCCCTTTG
29132113 AAAA
1 AAAA
29132117 GTGCACCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.35
Consensus pattern (21 bp):
AAAAATTCCTAGATCCCTTTG
Found at i:29132796 original size:42 final size:42
Alignment explanation
Indices: 29132744--29132827 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
29132734 TTAGAATTAC
29132744 CAAAAAACTTGAGTTGAAGTCTCGTTATAAGTAATTTTAACT
1 CAAAAAACTTGAGTTGAAGTCTCGTTATAAGTAATTTTAACT
*
29132786 CAAAGAACTTGAGTTGAAGTCTCGTTATAAGTAATTTTAACT
1 CAAAAAACTTGAGTTGAAGTCTCGTTATAAGTAATTTTAACT
29132828 TTCTTTTCGG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (42 bp):
CAAAAAACTTGAGTTGAAGTCTCGTTATAAGTAATTTTAACT
Found at i:29133215 original size:91 final size:91
Alignment explanation
Indices: 29133076--29133260 Score: 334
Period size: 91 Copynumber: 2.0 Consensus size: 91
29133066 TATAAGGAAT
*
29133076 ATAAATAATATAAACTCTACTCCTAATAAATAGTAGAATTCTAATGAATATTAAACTTAATGATA
1 ATAAATAATATAAACTCTACTCCTAATAAATAGTAGAATTCTAATGAATATCAAACTTAATGATA
29133141 AAATTGTATTTGAATTCAAGTTTTGA
66 AAATTGTATTTGAATTCAAGTTTTGA
* *
29133167 ATAAATAATATAAACTCTACTCCTAATAAATATTAGAATTCTATTGAATATCAAACTTAATGATA
1 ATAAATAATATAAACTCTACTCCTAATAAATAGTAGAATTCTAATGAATATCAAACTTAATGATA
*
29133232 AAGTTGTATTTGAATTCAAGTTTTGA
66 AAATTGTATTTGAATTCAAGTTTTGA
29133258 ATA
1 ATA
29133261 TCAAACTTAA
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 90 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (91 bp):
ATAAATAATATAAACTCTACTCCTAATAAATAGTAGAATTCTAATGAATATCAAACTTAATGATA
AAATTGTATTTGAATTCAAGTTTTGA
Found at i:29136115 original size:43 final size:43
Alignment explanation
Indices: 29136017--29136181 Score: 158
Period size: 43 Copynumber: 3.9 Consensus size: 43
29136007 TTCGGGTTAC
* * *
29136017 TGAGATTACGTGTAAGACCATATCTGGGATA-TGGCATCAACA
1 TGAGATTACGTGTAAGACCATGTCTGGGACATTGGCATCAATA
* * *
29136059 TGAGAATT-TGTGTAAGACCATGTTTGGGACATTGGCATCGATA
1 TGAG-ATTACGTGTAAGACCATGTCTGGGACATTGGCATCAATA
* * *
29136102 TGTGATTTCGTGTAAGACCATGGCTGGG-CTATTGGCATCAATA
1 TGAGATTACGTGTAAGACCATGTCTGGGAC-ATTGGCATCAATA
* * * * *
29136145 CGAGATTACATGTAAGACCGTATCTGGGATA-TGGCAT
1 TGAGATTACGTGTAAGACCATGTCTGGGACATTGGCAT
29136182 TGTTACGGTA
Statistics
Matches: 99, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
42 33 0.33
43 66 0.67
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (43 bp):
TGAGATTACGTGTAAGACCATGTCTGGGACATTGGCATCAATA
Found at i:29136180 original size:85 final size:85
Alignment explanation
Indices: 29136020--29136181 Score: 184
Period size: 85 Copynumber: 1.9 Consensus size: 85
29136010 GGGTTACTGA
* * ** * *
29136020 GATTACGTGTAAGACCATATCTGGGATATGGCATCAACATGAGAATTTGTGTAAGACCATGTTTG
1 GATTACGTGTAAGACCATAGCTGGGATATGGCATCAACACGAGAATTCATGTAAGACCATATCTG
29136085 GGACATTGGCATCGATATGT
66 GGACATTGGCATCGATATGT
* * * * *
29136105 GATTTCGTGTAAGACCATGGCTGGGCTATTGGCATCAATACGAG-ATTACATGTAAGACCGTATC
1 GATTACGTGTAAGACCATAGCTGGGATA-TGGCATCAACACGAGAATT-CATGTAAGACCATATC
*
29136169 TGGGATA-TGGCAT
64 TGGGACATTGGCAT
29136182 TGTTACGGTA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
85 33 0.52
86 30 0.48
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (85 bp):
GATTACGTGTAAGACCATAGCTGGGATATGGCATCAACACGAGAATTCATGTAAGACCATATCTG
GGACATTGGCATCGATATGT
Found at i:29138426 original size:21 final size:21
Alignment explanation
Indices: 29138381--29138420 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29138371 GGGTGTTACA
29138381 AAAAATGCCTAGATCCCTTCC
1 AAAAATGCCTAGATCCCTTCC
* *
29138402 AAAAATTCCTAGATTCCTT
1 AAAAATGCCTAGATCCCTT
29138421 TTAAAAGTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (21 bp):
AAAAATGCCTAGATCCCTTCC
Found at i:29146122 original size:54 final size:54
Alignment explanation
Indices: 29146040--29146146 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
29146030 GGGAAGGAAA
*
29146040 GGAAAGATAGAGATCTTCTTCTGCAAACTTTGGGGTTTTGGTT-GGATTGGTCNG
1 GGAAAGAGAGAGATCTTCTTCTGCAAACTTTGGGGTTTTGGTTGGGATTGGTC-G
29146094 GGAAAGAGAGAGATCTTCTTCTGCAAACTTTGGGGTTTTGGTTGGGATTGGTC
1 GGAAAGAGAGAGATCTTCTTCTGCAAACTTTGGGGTTTTGGTTGGGATTGGTC
29146147 AGGTCAGGTC
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
54 42 0.82
55 9 0.18
ACGTcount: A:0.21, C:0.11, G:0.33, T:0.35
Consensus pattern (54 bp):
GGAAAGAGAGAGATCTTCTTCTGCAAACTTTGGGGTTTTGGTTGGGATTGGTCG
Found at i:29153864 original size:16 final size:19
Alignment explanation
Indices: 29153843--29153883 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 19
29153833 TTATTAGATA
29153843 ATTTTAAA-A-AAAATA-T
1 ATTTTAAACATAAAATATT
29153859 ATTTTAAACATAAAATATT
1 ATTTTAAACATAAAATATT
29153878 ATTTTA
1 ATTTTA
29153884 CTTACGACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.36
17 1 0.05
18 6 0.27
19 7 0.32
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTTTAAACATAAAATATT
Found at i:29161900 original size:24 final size:23
Alignment explanation
Indices: 29161864--29161909 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
29161854 TCAAATTTTG
* *
29161864 TTGTATATGTACATACTTACATT
1 TTGTATATATACATACGTACATT
29161887 TTGTCATATATACATACGTACAT
1 TTGT-ATATATACATACGTACAT
29161910 ATTTTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (23 bp):
TTGTATATATACATACGTACATT
Found at i:29161952 original size:18 final size:19
Alignment explanation
Indices: 29161931--29161975 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
29161921 TTTATTTGTA
29161931 TATATATATTT-TCATA-CT
1 TATATATATTTAT-ATACCT
29161949 TATATATTATTTATATACCT
1 TATATA-TATTTATATACCT
29161969 TATATAT
1 TATATAT
29161976 GTACACATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 6 0.25
19 9 0.38
20 9 0.38
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATATATTTATATACCT
Found at i:29161954 original size:20 final size:20
Alignment explanation
Indices: 29161929--29161975 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
29161919 AATTTATTTG
29161929 TATATATATATTT-TCATA-CT
1 TATATAT-TATTTAT-ATACCT
29161949 TATATATTATTTATATACCT
1 TATATATTATTTATATACCT
29161969 TATATAT
1 TATATAT
29161976 GTACACATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATATTATTTATATACCT
Found at i:29168528 original size:44 final size:44
Alignment explanation
Indices: 29168461--29169535 Score: 694
Period size: 44 Copynumber: 24.6 Consensus size: 44
29168451 ATCATATTAG
* *
29168461 ATCCTATCTCCCTAAGCAGTAGTGGACCAGATTGAAGACGACGA
1 ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
* * * * * ** * *
29168505 ATCTTATCTTCCTAAGTAGTAGTGAAGCAAATTTAAG-CCACCA
1 ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
* * *
29168548 GTCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATG--GTA
1 ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACG-A
* * *
29168591 GATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATG--GTA
1 -ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACG-A
*
29168635 GATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGA
1 -ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
* * * * ** * *
29168680 AT-CTCATCTTCTTAAGTAGTAGTGAAGCAGATTTAAG-CCACCA
1 ATCCT-ATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
* * * * *
29168723 GTCCTATCTCCTTAAGCAGTAGTGGAGCAGGTCAAAGATG--GTA
1 ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACG-A
*
29168766 GATCATATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
1 -ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
* * * ** * *
29168811 ATCTTATCTTCCTAAGCAGTAGTGAAGCAGATTTAAG-CCACCA
1 ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
* * * * ***
29168854 GTCCTATCTCCCTAAGTAGTAGTGGAGCAGGTCGAAGATGGTAA
1 ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
* * * * ***
29168898 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAA
1 ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
* * * * ***
29168942 ATCATATCTCCCTAAGCAGTAGTGGAGCAGGTCGGAGATGGTAA
1 ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
* * * * *
29168986 ATCATATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATG--GTA
1 ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACG-A
*
29169029 GATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGA
1 -ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
* * * * ** * *
29169074 AT-CTCATCTTCTTAAGTAGTAGTGAAGCAGATTTAAG-CCACCA
1 ATCCT-ATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
* * * *
29169117 GTCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATG--GTA
1 ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACG-A
* *
29169160 GATCCTATCTCCTTAAGCAGTAGTGGAGCAGATC---G-C-ACCA
1 -ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
* * * ***
29169200 AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAGGAGATGGTAA
1 A-TCCTATCTCCCTAAGCAGTAGTGGAGCAGATC-GAAGACGACGA
* * * * *
29169245 ATCATATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATG--GTA
1 ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACG-A
* * * ***
29169288 GATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGGAGATGGTAA
1 -ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
* * * * *
29169333 ATCATATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATG--GTA
1 ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACG-A
* * * ***
29169376 GATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGGAGATGGTAA
1 -ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
* * * * *
29169421 ATCATATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATG--GTA
1 ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACG-A
* * * ***
29169464 GATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGGAGATGGTAA
1 -ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
*
29169509 ATCATATCTCCCTAAGCAGTAGTGGAG
1 ATCCTATCTCCCTAAGCAGTAGTGGAG
29169536 TAGGTCAAAG
Statistics
Matches: 837, Mismatches: 150, Indels: 88
0.78 0.14 0.08
Matches are distributed among these distances:
39 2 0.00
40 29 0.03
41 1 0.00
43 136 0.16
44 657 0.78
45 9 0.01
46 3 0.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (44 bp):
ATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGA
Found at i:29168660 original size:88 final size:88
Alignment explanation
Indices: 29168552--29169551 Score: 1151
Period size: 88 Copynumber: 11.4 Consensus size: 88
29168542 CCACCAGTCC
*
29168552 TATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTGG
* * *
29168617 AGCAGGTCAAAGATGGTAGATCC
66 AGCAGGTCGAAGATGGTAAATCA
* * * * * * *
29168640 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGG-CGAAT-CTCATCTTCTTAAGTAGTAGT
1 TATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAG-ATCCT-ATCTCCCTAAGCAGTAGT
* * ** ***** * *
29168703 GAAGCAGATTTAAG-CCACCAGTCC
64 GGAGCAGGTCGAAGATGGTAAATCA
* *
29168727 TATCTCCTTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCATATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTGG
* * *** *
29168792 AGCAGATCGAAGACGACGAATCT
66 AGCAGGTCGAAGATGGTAAATCA
* * * ** ***** *
29168815 TATCTTCCTAAGCAGTAGTGAAGCAGATTTAAGCCACCAG-TCCTATCTCCCTAAGTAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTGG
*
29168879 AGCAGGTCGAAGATGGTAAATCT
66 AGCAGGTCGAAGATGGTAAATCA
* *
29168902 TATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAAATCATATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTGG
*
29168967 AGCAGGTCGGAGATGGTAAATCA
66 AGCAGGTCGAAGATGGTAAATCA
*
29168990 TATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTGG
* * **
29169055 AGCAGATCGAAGACGGCGAATC-
66 AGCAGGTCGAAGATGGTAAATCA
* * * * * ** *****
29169077 TCATCTTCTTAAGTAGTAGTGAAGCAGATTTAAGCCACCAG-TCCTATCTCCCTAAGCAGTAGTG
1 T-ATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTG
* * *
29169141 GAGCAGGTCAAAGATGGTAGATCC
65 GAGCAGGTCGAAGATGGTAAATCA
* * *** *
29169165 TATCTCCTTAAGCAGTAGTGGAGCAGATC---GCA-CCAAG-TCTTATCTCCCTAAGCAGTAGTG
1 TATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAG-ATGGTAGATCCTATCTCCCTAAGCAGTAGTG
* *
29169225 GAGCA-GACAGGAGATGGTAAATCA
65 GAGCAGGTC-GAAGATGGTAAATCA
*
29169249 TATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTGG
*
29169314 AGCAGGTCGGAGATGGTAAATCA
66 AGCAGGTCGAAGATGGTAAATCA
*
29169337 TATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTGG
*
29169402 AGCAGGTCGGAGATGGTAAATCA
66 AGCAGGTCGAAGATGGTAAATCA
*
29169425 TATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTGG
*
29169490 AGCAGGTCGGAGATGGTAAATCA
66 AGCAGGTCGAAGATGGTAAATCA
*
29169513 TATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATGGTA
1 TATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTA
29169552 TCTGAAGTCA
Statistics
Matches: 782, Mismatches: 114, Indels: 32
0.84 0.12 0.03
Matches are distributed among these distances:
83 2 0.00
84 68 0.09
86 1 0.00
87 204 0.26
88 505 0.65
89 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (88 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTGG
AGCAGGTCGAAGATGGTAAATCA
Found at i:29168728 original size:131 final size:130
Alignment explanation
Indices: 29168593--29169551 Score: 1015
Period size: 131 Copynumber: 7.3 Consensus size: 130
29168583 AGATGGTAGA
29168593 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
* * *
29168658 TGGAGCAGATCGAAGACGGCGAATCTCATCTTCTTAAGTAGTAGTGAAGCAGATTTAAGCCACCA
66 TGGAGCAGATCGAAGACGGCGAATCT-ATCTCCCTAAGCAGTAGTGAAGCAGATTTAAGCCACCA
29168723 G
130 G
* *
29168724 TCCTATCTCCTTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCATATCTCCCTAAGCAGTAG
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
* *
29168789 TGGAGCAGATCGAAGACGACGAATCTTATCTTCCTAAGCAGTAGTGAAGCAGATTTAAGCCACCA
66 TGGAGCAGATCGAAGACGGCGAATC-TATCTCCCTAAGCAGTAGTGAAGCAGATTTAAGCCACCA
29168854 G
130 G
* * * *
29168855 TCCTATCTCCCTAAGTAGTAGTGGAGCAGGTCGAAGATGGTAAATCTTATCTCCCTAAGCAGTAG
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
* * * ** * * ** **
29168920 TGGAGCAGGTCAAAGATGGTAAATCATATCTCCCTAAGCAGTAGTGGAGCAGGTCGGAGATGGTA
66 TGGAGCAGATCGAAGACGGCGAATC-TATCTCCCTAAGCAGTAGTGAAGCAGAT-TTA-A-GCCA
*
29168985 --AA
127 CCAG
* *
29168987 TCATATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
* * *
29169052 TGGAGCAGATCGAAGACGGCGAATCTCATCTTCTTAAGTAGTAGTGAAGCAGATTTAAGCCACCA
66 TGGAGCAGATCGAAGACGGCGAATCT-ATCTCCCTAAGCAGTAGTGAAGCAGATTTAAGCCACCA
29169117 G
130 G
*
29169118 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCTTAAGCAGTAG
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
* * *** **
29169183 TGGAGCAGATCG--CAC--C-AAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGGAGATGGT
66 TGGAGCAGATCGAAGACGGCGAA-TC-TATCTCCCTAAGCAGTAGTGAAGCAGA-TTTA-A-GCC
*
29169243 A--AA
126 ACCAG
* *
29169246 TCATATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
* * * ** * * * ** *****
29169311 TGGAGCAGGTCGGAGATGGTAAATCATATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATGGTA
66 TGGAGCAGATCGAAGACGGCGAATC-TATCTCCCTAAGCAGTAGTGAAGCAGATTTAAGCCACCA
29169376 G
130 G
** * *
29169377 ATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGGAGATGGTAAATCATATCTCCCTAAGCAGTA
1 -TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTA
* * * * * * * ** *
29169442 GTGGAGTAGGTCAAAGATGG-TAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGGAGATGG
65 GTGGAGCAGATCGAAGACGGCGA-AT-CTATCTCCCTAAGCAGTAGTGAAGCAGAT-TTA-A-GC
* *
29169506 TA--AA
125 CACCAG
* *
29169510 TCATATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATGGTA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTA
29169552 TCTGAAGTCA
Statistics
Matches: 707, Mismatches: 96, Indels: 49
0.83 0.11 0.06
Matches are distributed among these distances:
126 2 0.00
127 25 0.04
128 76 0.11
129 7 0.01
130 5 0.01
131 308 0.44
132 273 0.39
133 6 0.01
134 3 0.00
135 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (130 bp):
TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAG
TGGAGCAGATCGAAGACGGCGAATCTATCTCCCTAAGCAGTAGTGAAGCAGATTTAAGCCACCAG
Found at i:29168749 original size:175 final size:174
Alignment explanation
Indices: 29168458--29169535 Score: 1074
Period size: 175 Copynumber: 6.2 Consensus size: 174
29168448 GTCATCATAT
* * * * * * *
29168458 TAGATCCTATCTCCCTAAGCAGTAGTGGACCAGATTGAAGACGACGAATCTTATCTTCCTAAGTA
1 TAGATCATATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCCTATCTCCCTAAGCA
* * ** * *
29168523 GTAGTGAAGCAAATTTAAGCCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATG
66 GTAGTGGAGCAGATCGAAGCCA-CAATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATG
*
29168588 GTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGG
130 GTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGG
* * * *
29168633 TAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAAT-CTCATCTTCTTAAGT
1 TAGATCATATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCCT-ATCTCCCTAAGC
* ** * *
29168697 AGTAGTGAAGCAGATTTAAGCCACCAGTCCTATCTCCTTAAGCAGTAGTGGAGCAGGTCAAAGAT
65 AGTAGTGGAGCAGATCGAAGCCA-CAATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGAT
* * *
29168762 GGTAGATCATATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-CG
129 GGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGG
* * * ** ** * *
29168807 -ACGAATCTTATCTTCCTAAGCAGTAGTGAAGCAGATTTAAG-CCACCAGTCCTATCTCCCTAAG
1 TA-G-ATCATATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCCTATCTCCCTAAG
* * ** *
29168870 TAGTAGTGGAGCAGGTCGAAGATGGTA-AATCTTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAA
64 CAGTAGTGGAGCAGATCG-A-A-GCCACAATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAA
* * *
29168934 GATGGTAAATCATATCTCCCTAAGCAGTAGTGGAGCAGGTCGGAGATGG
126 GATGGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGG
* * * * * *
29168983 TAAATCATATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATGG-TAGATCCTATCTCCCTAAGC
1 TAGATCATATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGA-ATCCTATCTCCCTAAGC
** * * * * * **
29169047 AGTAGTGGAGCAGATCGAAGACGGCGAAT-CTCATCTTCTTAAGTAGTAGTGAAGCAGATTTAAG
65 AGTAGTGGAGCAGATCGAAG-CCAC-AATCCT-ATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAG
***** *
29169111 CCACCAG-TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGG
127 ATGGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGG
* * * *
29169158 TAGATCCTATCTCCTTAAGCAGTAGTGGAGCAGATCG--CAC--C-AAGTCTTATCTCCCTAAGC
1 TAGATCATATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAA-TCCTATCTCCCTAAGC
** * *
29169218 AGTAGTGGAGCAGA-CAGGAGATGGTA-AATCATATCTCCCTAAGCAGTAGTGGAGTAGGTCAAA
65 AGTAGTGGAGCAGATC--GA-A-GCCACAATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAA
*
29169281 GATGGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGGAGATGG
126 GATGGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGG
* * * * * *
29169330 TAAATCATATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATGG-TAGATCCTATCTCCCTAAGC
1 TAGATCATATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGA-ATCCTATCTCCCTAAGC
* ** * *
29169394 AGTAGTGGAGCAGGTCGGAGATGGTA-AATCATATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAG
65 AGTAGTGGAGCAGATC-GA-A-GCCACAATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAG
*
29169458 ATGGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGGAGATGG
127 ATGGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGG
*
29169506 TAAATCATATCTCCCTAAGCAGTAGTGGAG
1 TAGATCATATCTCCCTAAGCAGTAGTGGAG
29169536 TAGGTCAAAG
Statistics
Matches: 764, Mismatches: 109, Indels: 59
0.82 0.12 0.06
Matches are distributed among these distances:
170 2 0.00
171 59 0.08
172 72 0.09
173 4 0.01
174 33 0.04
175 372 0.49
176 217 0.28
177 5 0.01
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (174 bp):
TAGATCATATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCCTATCTCCCTAAGCA
GTAGTGGAGCAGATCGAAGCCACAATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGG
TAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGG
Found at i:29171475 original size:12 final size:12
Alignment explanation
Indices: 29171460--29171502 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
29171450 TTATGGTTAA
*
29171460 TATTTTCACTAT
1 TATTTTCAATAT
* *
29171472 TATTTTTATTAT
1 TATTTTCAATAT
29171484 TATTTTCAATAT
1 TATTTTCAATAT
29171496 ATATTTT
1 -TATTTT
29171503 TTTCTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 20 0.77
13 6 0.23
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (12 bp):
TATTTTCAATAT
Found at i:29177597 original size:28 final size:30
Alignment explanation
Indices: 29177566--29177622 Score: 82
Period size: 28 Copynumber: 1.9 Consensus size: 30
29177556 TTCCTAAAAC
*
29177566 TTTTAATTATAATAT-TTTTTG-TTTTAAT
1 TTTTAATTAGAATATATTTTTGATTTTAAT
29177594 TTTTAATTAGAATATAGTTTTTGATTTTA
1 TTTTAATTAGAATATA-TTTTTGATTTTA
29177623 TAAAAAAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 14 0.56
30 6 0.24
31 5 0.20
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (30 bp):
TTTTAATTAGAATATATTTTTGATTTTAAT
Found at i:29180663 original size:29 final size:29
Alignment explanation
Indices: 29180630--29180729 Score: 159
Period size: 29 Copynumber: 3.5 Consensus size: 29
29180620 AAAAATAAAA
*
29180630 ATTTACCAAAACATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
29180659 ATTTACCAAAATATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
*
29180688 ATTTACTAAAATATATA-AAC-TTTTTTTT
1 ATTTACCAAAATAT-TACAACTTTTTTTTT
29180716 ATTTACCAAAATAT
1 ATTTACCAAAATAT
29180730 ATCAAAAAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
28 21 0.31
29 44 0.66
30 2 0.03
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTTACCAAAATATTACAACTTTTTTTTT
Found at i:29180801 original size:27 final size:27
Alignment explanation
Indices: 29180763--29180846 Score: 134
Period size: 27 Copynumber: 3.1 Consensus size: 27
29180753 CCTGATCACC
29180763 CCAATGCCATTGGCGGCACCAAAGGTG
1 CCAATGCCATTGGCGGCACCAAAGGTG
* *
29180790 CCAATGCCATTGGCAGCACCAATGGTG
1 CCAATGCCATTGGCGGCACCAAAGGTG
*
29180817 CCAATGCCATTGGCGGCACC-AATGTG
1 CCAATGCCATTGGCGGCACCAAAGGTG
29180843 CCAA
1 CCAA
29180847 AGGACTAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
26 8 0.15
27 44 0.85
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.17
Consensus pattern (27 bp):
CCAATGCCATTGGCGGCACCAAAGGTG
Found at i:29181388 original size:18 final size:19
Alignment explanation
Indices: 29181337--29181397 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
29181327 CTGATATTTC
*
29181337 TATTAATTTAAAATA-TAGT
1 TATTAAATTAAAATAGTA-T
* *
29181356 TATTAAATGAGAATAGT-T
1 TATTAAATTAAAATAGTAT
*
29181374 TATTAAATTAAAATAGAAT
1 TATTAAATTAAAATAGTAT
29181393 TATTA
1 TATTA
29181398 CTTAATTAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 15 0.44
19 18 0.53
20 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (19 bp):
TATTAAATTAAAATAGTAT
Found at i:29182090 original size:27 final size:28
Alignment explanation
Indices: 29182032--29182128 Score: 162
Period size: 28 Copynumber: 3.5 Consensus size: 28
29182022 TTTTTTTGAT
29182032 ATATTTTGGTAAATAAAAAAAAGTT-TA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
29182059 TATATTTTGGTAAATAAAAAAAA-TTGTA
1 -ATATTTTGGTAAATAAAAAAAAGTTGTA
29182087 ATATTTTGGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
*
29182115 ATGTTTTGGTAAAT
1 ATATTTTGGTAAAT
29182129 TTTTATTTTT
Statistics
Matches: 66, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
27 24 0.36
28 42 0.64
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTGTA
Found at i:29184175 original size:33 final size:31
Alignment explanation
Indices: 29184138--29184212 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
29184128 AGGTAATAAG
*
29184138 TTTAGAAATAAAGTTTAAAAAATTA-TTTTTTAT
1 TTTAGAAATAAAGTTT--AAAA-TAGTTTTTAAT
* * *
29184171 TTTAGGAATAGAGTTTTAAATAGTTTTTAAT
1 TTTAGAAATAAAGTTTAAAATAGTTTTTAAT
29184202 TTTAGAAATAA
1 TTTAGAAATAA
29184213 TATATATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
30 2 0.06
31 19 0.54
33 14 0.40
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.47
Consensus pattern (31 bp):
TTTAGAAATAAAGTTTAAAATAGTTTTTAAT
Found at i:29184261 original size:30 final size:33
Alignment explanation
Indices: 29184189--29184262 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
29184179 TAGAGTTTTA
*
29184189 AATAGTTTTT-AATTTTAGAAATAATATATATTT
1 AATA-TTTTTAAATATTAGAAATAATATATATTT
*
29184222 AATACTTTTAAATATTAGAAATAA-AT-T-TTT
1 AATATTTTTAAATATTAGAAATAATATATATTT
*
29184252 AATTTTTTTAA
1 AATATTTTTAA
29184263 TTTTTTAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 12 0.33
31 1 0.03
32 6 0.17
33 17 0.47
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (33 bp):
AATATTTTTAAATATTAGAAATAATATATATTT
Found at i:29185436 original size:19 final size:19
Alignment explanation
Indices: 29185407--29185455 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
29185397 TTTTAGGAGC
*
29185407 CACACGGGCTGTGCCATTT
1 CACAAGGGCTGTGCCATTT
*
29185426 CGCAAGGGCTGTGCCATTT
1 CACAAGGGCTGTGCCATTT
*
29185445 CACACGGGCTG
1 CACAAGGGCTG
29185456 GAAACACGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.16, C:0.31, G:0.31, T:0.22
Consensus pattern (19 bp):
CACAAGGGCTGTGCCATTT
Found at i:29199828 original size:41 final size:41
Alignment explanation
Indices: 29199766--29199961 Score: 268
Period size: 41 Copynumber: 4.8 Consensus size: 41
29199756 TTTTGACCTT
* * *
29199766 TCGGGGCTTTAGCGGCATTTTTGAGAAGGCGCCGCTAAGGC
1 TCGGGGCTTTAGCGGCGTTTTTGAAAAGGCGCCGCTAATGC
*
29199807 TCGGGGCTTTAGCGGCGTTTTTAAAAAGGCGCCGCTAATGC
1 TCGGGGCTTTAGCGGCGTTTTTGAAAAGGCGCCGCTAATGC
* *
29199848 TCGGGGCTTTAGCGGCGTTTTTGAAAAGGCACCACTAATGC
1 TCGGGGCTTTAGCGGCGTTTTTGAAAAGGCGCCGCTAATGC
* *
29199889 TCGGGGCTTTAGCGACGTTTTTGGAAAA-GCGCCTCTAATGC
1 TCGGGGCTTTAGCGGCGTTTTT-GAAAAGGCGCCGCTAATGC
* * * *
29199930 TTGGAGCTTTAGCGGCGTTTCTGAAAAAGCGC
1 TCGGGGCTTTAGCGGCGTTTTTGAAAAGGCGC
29199962 TGTAAAAACA
Statistics
Matches: 139, Mismatches: 14, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
40 5 0.04
41 129 0.93
42 5 0.04
ACGTcount: A:0.20, C:0.21, G:0.32, T:0.27
Consensus pattern (41 bp):
TCGGGGCTTTAGCGGCGTTTTTGAAAAGGCGCCGCTAATGC
Found at i:29200002 original size:20 final size:18
Alignment explanation
Indices: 29199979--29200016 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
29199969 ACATTTTATC
29199979 TGTTTATTTACTATTTAATT
1 TGTTTATTTA-TA-TTAATT
29199999 TGTTTATTTATATTAATT
1 TGTTTATTTATATTAATT
29200017 AAAATTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 2 0.11
20 10 0.56
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (18 bp):
TGTTTATTTATATTAATT
Found at i:29200365 original size:15 final size:15
Alignment explanation
Indices: 29200347--29200378 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
29200337 TAGTGTAAGG
29200347 TTTAGGGAGTATGGA
1 TTTAGGGAGTATGGA
*
29200362 TTTAGGGATTATGGA
1 TTTAGGGAGTATGGA
29200377 TT
1 TT
29200379 AGGAATTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.34, T:0.41
Consensus pattern (15 bp):
TTTAGGGAGTATGGA
Found at i:29200386 original size:14 final size:15
Alignment explanation
Indices: 29200356--29200393 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
29200346 GTTTAGGGAG
*
29200356 TATGGATTTAGGGAT
1 TATGGATTTAGGAAT
29200371 TATGGA-TTAGGAAT
1 TATGGATTTAGGAAT
29200385 TAT-GATTTA
1 TATGGATTTA
29200394 AGGGTTGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 13 0.62
15 6 0.29
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (15 bp):
TATGGATTTAGGAAT
Found at i:29200851 original size:19 final size:19
Alignment explanation
Indices: 29200822--29200871 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
29200812 GGACCAAATT
*
29200822 ATAAGAAATAAAAATA-AA
1 ATAAAAAATAAAAATAGAA
29200840 ATACAAAAAT-AAAATAGAA
1 ATA-AAAAATAAAAATAGAA
29200859 ATAAAAAACTAAA
1 ATAAAAAA-TAAA
29200872 TTTTATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.52
19 11 0.41
20 2 0.07
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (19 bp):
ATAAAAAATAAAAATAGAA
Found at i:29200866 original size:13 final size:13
Alignment explanation
Indices: 29200831--29200855 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29200821 TATAAGAAAT
29200831 AAAAATAAAATAC
1 AAAAATAAAATAC
29200844 AAAAATAAAATA
1 AAAAATAAAATA
29200856 GAAATAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAATAAAATAC
Found at i:29200872 original size:18 final size:18
Alignment explanation
Indices: 29200827--29200871 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
29200817 AAATTATAAG
29200827 AAATAAAAATAAAATACAA
1 AAAT-AAAATAAAATACAA
29200846 AAATAAAATAGAAATA-AA
1 AAATAAAATA-AAATACAA
29200864 AAACTAAA
1 AAA-TAAA
29200872 TTTTATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (18 bp):
AAATAAAATAAAATACAA
Found at i:29200920 original size:22 final size:22
Alignment explanation
Indices: 29200895--29200938 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
29200885 TCTAATTCTT
29200895 ATAAATA-TTACTTAAAAATTTA
1 ATAAATATTTA-TTAAAAATTTA
* *
29200917 ATAATTATTTATTTAAAATTTA
1 ATAAATATTTATTAAAAATTTA
29200939 TATGAAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATATTTATTAAAAATTTA
Found at i:29204917 original size:43 final size:43
Alignment explanation
Indices: 29204864--29204992 Score: 131
Period size: 43 Copynumber: 3.0 Consensus size: 43
29204854 ATAGGATTTC
*
29204864 CGATATGTGTTATCGTGTAAGACCATGTCGGGGACGTTGGCAT
1 CGATATGTGTTATCGTGTAAGACCATGTCTGGGACGTTGGCAT
* * *
29204907 CGAGT-TGTGTTCAT-GTGTAAGACCCTGTCTAGGATAG-TGGCAT
1 CGA-TATGTGTT-ATCGTGTAAGACCATGTCTGGGA-CGTTGGCAT
* * *
29204950 CGATATGTGATT-GCATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATGTG-TTATCGTGTAAGACCATGTCTGGGACGTTGGCAT
29204993 TGTATGAGTT
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
42 2 0.03
43 61 0.88
44 6 0.09
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (43 bp):
CGATATGTGTTATCGTGTAAGACCATGTCTGGGACGTTGGCAT
Found at i:29215333 original size:19 final size:20
Alignment explanation
Indices: 29215309--29215356 Score: 53
Period size: 23 Copynumber: 2.3 Consensus size: 20
29215299 GATCAGTTGG
29215309 ACCTTT-GATTAATTAACAT
1 ACCTTTGGATTAATTAACAT
*
29215328 ACCTTTTTTGGATTAATTAACTT
1 ACC---TTTGGATTAATTAACAT
29215351 ACCTTT
1 ACCTTT
29215357 TTTTGACTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
19 3 0.12
20 3 0.12
22 3 0.12
23 15 0.62
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.48
Consensus pattern (20 bp):
ACCTTTGGATTAATTAACAT
Found at i:29215341 original size:23 final size:23
Alignment explanation
Indices: 29215315--29215359 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
29215305 TTGGACCTTT
29215315 GATTAATTAACATACCTTTTTTG
1 GATTAATTAACATACCTTTTTTG
*
29215338 GATTAATTAACTTACCTTTTTT
1 GATTAATTAACATACCTTTTTT
29215360 TGACTGACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.13, G:0.07, T:0.51
Consensus pattern (23 bp):
GATTAATTAACATACCTTTTTTG
Done.