Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 159 of 163
Found at i:53404044 original size:24 final size:22
Alignment explanation
Indices: 53403999--53404070 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
53403989 TAATTTATTT
**
53403999 TTTTAAAAATTATAAAGCTATAGA
1 TTTT-AAAATTATAAAATTATA-A
*
53404023 TTATTAAAATTATAAAATTATAC
1 TT-TTAAAATTATAAAATTATAA
**
53404046 TTTTACTATTATAAAATTATAA
1 TTTTAAAATTATAAAATTATAA
53404068 TTT
1 TTT
53404071 AATTTCCGCC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 20 0.49
23 2 0.05
24 17 0.41
25 2 0.05
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (22 bp):
TTTTAAAATTATAAAATTATAA
Found at i:53413211 original size:23 final size:23
Alignment explanation
Indices: 53413179--53413222 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
53413169 GCTACCATTT
53413179 TCTAAATAAAATAATAATAAACA
1 TCTAAATAAAATAATAATAAACA
* *
53413202 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
53413223 ATAATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAACA
Found at i:53421576 original size:213 final size:212
Alignment explanation
Indices: 53421209--53421604 Score: 749
Period size: 213 Copynumber: 1.9 Consensus size: 212
53421199 TTAGCAGAAG
53421209 AATAGAATGTAAAGTCTTGTTAGTAATTTTATTATTTGAAAGCTATTTTGTTAGGTTATTAATTT
1 AATAGAATGTAAAGTCTTGTTAGTAATTTTATTATTTGAAAGCTATTTTGTTAGGTTATTAATTT
53421274 TGTTAGCTTCTGAATGAAAAATGTTACATTAAAAATTTTATGTAATTTTTTTTGCATTTCGAAAC
66 TGTTAGCTTCTGAATGAAAAATGTTACATTAAAAATTTTATGTAATTTTTTTTGCATTTCGAAAC
*
53421339 TGTTTTAAGAATTTTGAAATTTTTTTAACAAATCTAGTATTGAAGATGAAGAATGATAATGTATT
131 TGTTTTAAGAATTTTGAAA-TTTTTTAACAAATATAGTATTGAAGATGAAGAATGATAATGTATT
53421404 TTGGTTTATTTCTTTTTA
195 TTGGTTTATTTCTTTTTA
*
53421422 AATAGAATGTAGAGTCTTGTTAGTAATTTTATTATTTGAAAGCTATTTTGTTAGGTTATTAATTT
1 AATAGAATGTAAAGTCTTGTTAGTAATTTTATTATTTGAAAGCTATTTTGTTAGGTTATTAATTT
53421487 TGTTAGCTTCTGAATGAAAAATGTTACATTAAAAATTTTATGTAA-TTTTTTTGCATTTCGAAAC
66 TGTTAGCTTCTGAATGAAAAATGTTACATTAAAAATTTTATGTAATTTTTTTTGCATTTCGAAAC
53421551 TGTTTTAAGAATTTTGAAAATTTTTTAACAAATATAGTATTGAAGATGAAGAAT
131 TGTTTTAAGAATTTTG-AAATTTTTTAACAAATATAGTATTGAAGATGAAGAAT
53421605 CAGTTTTTTT
Statistics
Matches: 180, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
212 68 0.38
213 112 0.62
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.46
Consensus pattern (212 bp):
AATAGAATGTAAAGTCTTGTTAGTAATTTTATTATTTGAAAGCTATTTTGTTAGGTTATTAATTT
TGTTAGCTTCTGAATGAAAAATGTTACATTAAAAATTTTATGTAATTTTTTTTGCATTTCGAAAC
TGTTTTAAGAATTTTGAAATTTTTTAACAAATATAGTATTGAAGATGAAGAATGATAATGTATTT
TGGTTTATTTCTTTTTA
Found at i:53423226 original size:25 final size:25
Alignment explanation
Indices: 53423162--53423226 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 25
53423152 ATATATTTAA
* *
53423162 ATAT-TTTTAATAAAAATAAAAAAT
1 ATATATTTTAATATAAACAAAAAAT
*
53423186 -TAATATTTT-ATTTAAACAAAAAAT
1 AT-ATATTTTAATATAAACAAAAAAT
53423210 ATATATTTTAATATAAA
1 ATATATTTTAATATAAA
53423227 AAATTGATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
23 1 0.03
24 21 0.64
25 11 0.33
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
ATATATTTTAATATAAACAAAAAAT
Found at i:53423850 original size:13 final size:13
Alignment explanation
Indices: 53423824--53423862 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
53423814 TAATAAACTT
53423824 AAATTTAATAAAA
1 AAATTTAATAAAA
53423837 AAATTATAATAAAA
1 AAATT-TAATAAAA
*
53423851 GAAACTTAATAA
1 -AAATTTAATAA
53423863 TGTTAACAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 5 0.22
14 14 0.61
15 4 0.17
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (13 bp):
AAATTTAATAAAA
Found at i:53424416 original size:23 final size:24
Alignment explanation
Indices: 53424371--53424417 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
53424361 CTTAATTTTC
*
53424371 CTTTAAAAAAACAATCCATATATT
1 CTTTAAAAAAACAATCCACATATT
* *
53424395 CTTTCAAAAAA-AATCCGCATATT
1 CTTTAAAAAAACAATCCACATATT
53424418 ATATAATGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (24 bp):
CTTTAAAAAAACAATCCACATATT
Found at i:53426542 original size:2 final size:2
Alignment explanation
Indices: 53426535--53426559 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53426525 TCCATGTAAG
53426535 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
53426560 GAATGTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53427764 original size:2 final size:2
Alignment explanation
Indices: 53427757--53427789 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
53427747 TTTAAAATTA
53427757 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53427790 ACACTCAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53428692 original size:123 final size:124
Alignment explanation
Indices: 53428521--53428781 Score: 488
Period size: 123 Copynumber: 2.1 Consensus size: 124
53428511 TTTATATAAA
* *
53428521 ATCAATAAAAAGAGAGTTGAACTAGAGATAATAATATTTACATCAACAAAACTTGTGTTTAGTTT
1 ATCAAAAAAAAAAGAGTTGAACTA-AGATAATAATATTTACATCAACAAAACTTGTGTTTAGTTT
53428586 ATAAAGTTGTTTTTAAAGAAAATATTTAATTTGGGGTATTTTAAAATCTACTCAAAGAAT
65 ATAAAGTTGTTTTTAAAGAAAATATTTAATTTGGGGTATTTTAAAATCTACTCAAAGAAT
53428646 ATCAAAAAAAAAAGAGTTGAACT-AGATAATAATATTTACATCAACAAAACTTGTGTTTAGTTTA
1 ATCAAAAAAAAAAGAGTTGAACTAAGATAATAATATTTACATCAACAAAACTTGTGTTTAGTTTA
53428710 TAAAGTTGTTTTTAAAGAAAATATTTAATTTGGGGTATTTTAAAATCTACTCAAAGAAT
66 TAAAGTTGTTTTTAAAGAAAATATTTAATTTGGGGTATTTTAAAATCTACTCAAAGAAT
53428769 ATCAAAAAAAAAA
1 ATCAAAAAAAAAA
53428782 AAAAACAACT
Statistics
Matches: 134, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
123 113 0.84
125 21 0.16
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.34
Consensus pattern (124 bp):
ATCAAAAAAAAAAGAGTTGAACTAAGATAATAATATTTACATCAACAAAACTTGTGTTTAGTTTA
TAAAGTTGTTTTTAAAGAAAATATTTAATTTGGGGTATTTTAAAATCTACTCAAAGAAT
Found at i:53430444 original size:5 final size:5
Alignment explanation
Indices: 53430434--53430462 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
53430424 TATATATATA
53430434 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
53430463 TCTATGTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:53444688 original size:44 final size:46
Alignment explanation
Indices: 53444598--53444689 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 46
53444588 TTTGGTTCGC
*
53444598 TGTAATGGAATAAAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAA
1 TGTAATGGAATAAAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAA
* *
53444644 TGTAATGGAATAGAGGCGTAAT-GG-CATTCTTGTGTTTGGTTGAA
1 TGTAATGGAATAAAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAA
53444688 TG
1 TG
53444690 GAATAGAGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 20 0.47
45 2 0.05
46 21 0.49
ACGTcount: A:0.27, C:0.05, G:0.29, T:0.38
Consensus pattern (46 bp):
TGTAATGGAATAAAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAA
Found at i:53444690 original size:39 final size:42
Alignment explanation
Indices: 53444598--53444709 Score: 122
Period size: 39 Copynumber: 2.6 Consensus size: 42
53444588 TTTGGTTCGC
* * *
53444598 TGTAATGGAATAAAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAAT-GG-CATTCTTGTGTTTGGTT--A
53444644 TGTAATGGAATAGAGGCGTAATGGCATTCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGCGTAATGGCATTCTTGTGTTTGGTTA
* *
53444684 TG-AATGGAATAGAGGTGTAATAGCAT
1 TGTAATGGAATAGAGGCGTAATGGCAT
53444710 AAGGAAAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
39 22 0.36
40 2 0.03
43 1 0.02
44 13 0.21
45 2 0.03
46 21 0.34
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.36
Consensus pattern (42 bp):
TGTAATGGAATAGAGGCGTAATGGCATTCTTGTGTTTGGTTA
Found at i:53444868 original size:15 final size:15
Alignment explanation
Indices: 53444848--53444886 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 15
53444838 CATAATTGTT
53444848 ATAAAATATAATTTA
1 ATAAAATATAATTTA
53444863 ATAAAATATATAATTTA
1 AT-AAA-ATATAATTTA
53444880 ATAAAAT
1 ATAAAAT
53444887 TGTTAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.18
16 6 0.27
17 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAAATATAATTTA
Found at i:53444893 original size:17 final size:17
Alignment explanation
Indices: 53444853--53444886 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
53444843 TTGTTATAAA
53444853 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
53444870 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
53444887 TGTTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:53444958 original size:20 final size:21
Alignment explanation
Indices: 53444919--53444958 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
53444909 AATTTACTAA
*
53444919 TAAAATCATAATATATAATAC
1 TAAAATCATAATATAAAATAC
*
53444940 TAAAAT-ATAATTTAAAATA
1 TAAAATCATAATATAAAATA
53444959 ATTATTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATCATAATATAAAATAC
Found at i:53449296 original size:16 final size:16
Alignment explanation
Indices: 53449259--53449300 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
53449249 NNNNNNNNNN
*
53449259 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
53449275 TT-AAATATATTATAA
1 TTAAAATATATTATAA
53449290 TTAAAATATAT
1 TTAAAATATAT
53449301 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:53449307 original size:14 final size:15
Alignment explanation
Indices: 53449268--53449309 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
53449258 NTTAAACATA
*
53449268 ATTATTATTAAATAT
1 ATTATAATTAAATAT
53449283 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
53449297 A-TATAATTTAATA
1 ATTATAATTAAATA
53449310 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:53456333 original size:11 final size:11
Alignment explanation
Indices: 53456317--53456341 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53456307 TCTCATGATC
53456317 TAAATTATATA
1 TAAATTATATA
53456328 TAAATTATATA
1 TAAATTATATA
53456339 TAA
1 TAA
53456342 TCAGTGTTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TAAATTATATA
Found at i:53459705 original size:5 final size:5
Alignment explanation
Indices: 53459695--53459719 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
53459685 ACTTATTCAT
53459695 GGGTC GGGTC GGGTC GGGTC GGGTC
1 GGGTC GGGTC GGGTC GGGTC GGGTC
53459720 ATGTGCCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.60, T:0.20
Consensus pattern (5 bp):
GGGTC
Found at i:53464118 original size:112 final size:111
Alignment explanation
Indices: 53463922--53464122 Score: 253
Period size: 112 Copynumber: 1.8 Consensus size: 111
53463912 TTTGAAACAG
* * *
53463922 AAAATGGTATATGAACATGTTTCTTAAGAATACATAAAATATATGTTTCCCAAACACACCTTTTT
1 AAAATAGTATATGAACATATTTCTTAAGAATACATAAAATATATGTTTCCCAAACACACCTTTGT
* * *
53463987 GGGTCTTGGTTGCATAAAACAAATGTTATCACAAGGAATAAGACTC
66 CGGTCATGGTTGCAGAAAACAAATGTTATCACAAGGAATAAGACTC
* * *** *
53464033 AAAATAGTATATGGACATATTTCTTAAAGAATACTTAAAATAT-TCGCTTTCCCCCGCATACC-T
1 AAAATAGTATATGAACATATTTCTT-AAGAATACATAAAATATAT-G-TTTCCCAAACACACCTT
53464096 TGTCGGTCATGGTTGCAGAAAACAAAT
63 TGTCGGTCATGGTTGCAGAAAACAAAT
53464123 ATGGGTACCA
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
111 23 0.31
112 41 0.55
113 11 0.15
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.31
Consensus pattern (111 bp):
AAAATAGTATATGAACATATTTCTTAAGAATACATAAAATATATGTTTCCCAAACACACCTTTGT
CGGTCATGGTTGCAGAAAACAAATGTTATCACAAGGAATAAGACTC
Found at i:53472374 original size:24 final size:24
Alignment explanation
Indices: 53472321--53472367 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
53472311 CAAGTTTTCA
*
53472321 TGTCTTGAAAGATTGGAAATTGTT
1 TGTCTTGAAAGATTGAAAATTGTT
53472345 TGTCTTGAAAGATTGAAAATTGT
1 TGTCTTGAAAGATTGAAAATTGT
53472368 CTTTCTTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.32, C:0.04, G:0.23, T:0.40
Consensus pattern (24 bp):
TGTCTTGAAAGATTGAAAATTGTT
Found at i:53475966 original size:26 final size:26
Alignment explanation
Indices: 53475937--53475989 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
53475927 ATACTATAAA
* *
53475937 AATTAGATTGAGAACCCTATGTATTG
1 AATTAGATTGAAAACCATATGTATTG
*
53475963 AATTAGATTGAAAATCATATGTATTG
1 AATTAGATTGAAAACCATATGTATTG
53475989 A
1 A
53475990 CTTAATGGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.36
Consensus pattern (26 bp):
AATTAGATTGAAAACCATATGTATTG
Found at i:53478707 original size:20 final size:20
Alignment explanation
Indices: 53478671--53478708 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53478661 TATGTTTGAA
*
53478671 ATGTTATGTTTTAGTTACTT
1 ATGTTATGTTCTAGTTACTT
53478691 ATGTTATCGTTCT-GTTAC
1 ATGTTAT-GTTCTAGTTAC
53478709 AAAGTGATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.18, C:0.11, G:0.16, T:0.55
Consensus pattern (20 bp):
ATGTTATGTTCTAGTTACTT
Found at i:53480578 original size:14 final size:14
Alignment explanation
Indices: 53480559--53480586 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53480549 GATGTGAAAA
53480559 AAAGAGAGAGAGAG
1 AAAGAGAGAGAGAG
53480573 AAAGAGAGAGAGAG
1 AAAGAGAGAGAGAG
53480587 GAAAAAGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (14 bp):
AAAGAGAGAGAGAG
Found at i:53511299 original size:18 final size:18
Alignment explanation
Indices: 53511278--53511314 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
53511268 TCGAAACCGG
53511278 TCGGTTAACCGAAAAAAT
1 TCGGTTAACCGAAAAAAT
53511296 TCGGTTAACCGAAAAAAT
1 TCGGTTAACCGAAAAAAT
53511314 T
1 T
53511315 AATAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.24
Consensus pattern (18 bp):
TCGGTTAACCGAAAAAAT
Found at i:53511402 original size:17 final size:18
Alignment explanation
Indices: 53511373--53511406 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
53511363 CAAGTATTTA
53511373 ACCCAACCCAACCCAATT
1 ACCCAACCCAACCCAATT
53511391 ACCCAA-CCAACCCAAT
1 ACCCAACCCAACCCAAT
53511407 CAATAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.41, C:0.50, G:0.00, T:0.09
Consensus pattern (18 bp):
ACCCAACCCAACCCAATT
Found at i:53511561 original size:18 final size:18
Alignment explanation
Indices: 53511514--53511562 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
53511504 GTAGTGATTC
53511514 AATTTGGTTAATTCGGTT
1 AATTTGGTTAATTCGGTT
* *
53511532 AATTCGGGTAATTCGGTT
1 AATTTGGTTAATTCGGTT
53511550 AATTTGGTTAATT
1 AATTTGGTTAATT
53511563 TTTAACCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.24, C:0.06, G:0.22, T:0.47
Consensus pattern (18 bp):
AATTTGGTTAATTCGGTT
Found at i:53511563 original size:9 final size:9
Alignment explanation
Indices: 53511514--53511562 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
53511504 GTAGTGATTC
*
53511514 AATTTGGTT
1 AATTCGGTT
53511523 AATTCGGTT
1 AATTCGGTT
*
53511532 AATTCGGGT
1 AATTCGGTT
53511541 AATTCGGTT
1 AATTCGGTT
*
53511550 AATTTGGTT
1 AATTCGGTT
53511559 AATT
1 AATT
53511563 TTTAACCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.24, C:0.06, G:0.22, T:0.47
Consensus pattern (9 bp):
AATTCGGTT
Found at i:53511741 original size:12 final size:12
Alignment explanation
Indices: 53511724--53511749 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53511714 TGTTATTTCG
53511724 GATCGGTTAACC
1 GATCGGTTAACC
53511736 GATCGGTTAACC
1 GATCGGTTAACC
53511748 GA
1 GA
53511750 ATGAACACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (12 bp):
GATCGGTTAACC
Found at i:53512213 original size:13 final size:12
Alignment explanation
Indices: 53512182--53512223 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 12
53512172 CTTTTCATTA
53512182 TATTTTCCAATC
1 TATTTTCCAATC
* *
53512194 AATTTTCCAGCTC
1 TATTTTCCA-ATC
53512207 TATTTTCCAAT-
1 TATTTTCCAATC
53512218 TATTTT
1 TATTTT
53512224 TCTGTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
11 6 0.24
12 9 0.36
13 10 0.40
ACGTcount: A:0.24, C:0.21, G:0.02, T:0.52
Consensus pattern (12 bp):
TATTTTCCAATC
Found at i:53512790 original size:27 final size:27
Alignment explanation
Indices: 53512752--53512806 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
53512742 GTTGAAGTTG
* *
53512752 ATTAGTGGGTCGATCAATAATATTATC
1 ATTAGTGGGTCGATAAATAATAATATC
53512779 ATTAGTGGGTCGATAAATAATAATATC
1 ATTAGTGGGTCGATAAATAATAATATC
53512806 A
1 A
53512807 CTTATCTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (27 bp):
ATTAGTGGGTCGATAAATAATAATATC
Found at i:53514143 original size:40 final size:39
Alignment explanation
Indices: 53514070--53514147 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 39
53514060 AAAAACGCTT
53514070 CCTCAAGGAAGCTCTTTGTCCACGTGGACACAAAGCGCGC
1 CCTCAAGGAAGCTCTTTGTCCACGTGGA-ACAAAGCGCGC
*
53514110 CCTCAAGGAAGCGTTTTCTGTCCACGTGG-ACAAAGCGC
1 CCTCAAGGAAGC-TCTT-TGTCCACGTGGAACAAAGCGC
53514148 TTCCTTCCCC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
40 21 0.60
41 3 0.09
42 11 0.31
ACGTcount: A:0.24, C:0.31, G:0.26, T:0.19
Consensus pattern (39 bp):
CCTCAAGGAAGCTCTTTGTCCACGTGGAACAAAGCGCGC
Found at i:53514358 original size:95 final size:95
Alignment explanation
Indices: 53514223--53514417 Score: 270
Period size: 95 Copynumber: 2.0 Consensus size: 95
53514213 GTTTTTAGAT
* *
53514223 TTTAGGGTTTTAAGGAAAAAATTAAATAAATAAGAGTTTAGGGTTTCTTAATTAAATTAATTATA
1 TTTAGGGTTTTAAGG-AAAAATTAAATAAATAAGAGTTTAGGGTTACTTAAGTAAATTAATTATA
* *
53514288 ACTTTTAAAAAA-T-TAGATTAGGGTTTAGTG
65 A-ATTAAAAAAATTATAGATTAGGGTTTAGTG
* * *
53514318 TTTATGGGTTTTAAGG-AAAATTCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
1 TTTA-GGGTTTTAAGGAAAAATT-AAATAAATAAGAGTTTAGGGTTACTTAAGTAAATTAATTAT
53514382 AAATTAAAAAAATTATAGATTAGGGTTTAGTG
64 AAATTAAAAAAATTATAGATTAGGGTTTAGTG
53514414 TTTA
1 TTTA
53514418 NNNNNNNNNN
Statistics
Matches: 89, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
94 14 0.16
95 43 0.48
96 32 0.36
ACGTcount: A:0.40, C:0.02, G:0.18, T:0.40
Consensus pattern (95 bp):
TTTAGGGTTTTAAGGAAAAATTAAATAAATAAGAGTTTAGGGTTACTTAAGTAAATTAATTATAA
ATTAAAAAAATTATAGATTAGGGTTTAGTG
Found at i:53514909 original size:11 final size:11
Alignment explanation
Indices: 53514893--53514943 Score: 67
Period size: 11 Copynumber: 5.1 Consensus size: 11
53514883 GTTAGACTTA
53514893 ATAATTAATTT
1 ATAATTAATTT
53514904 ATAATTAATTT
1 ATAATTAATTT
53514915 ATAATT--TTT
1 ATAATTAATTT
53514924 -TAA--AATTT
1 ATAATTAATTT
53514932 ATAATTAATTT
1 ATAATTAATTT
53514943 A
1 A
53514944 ATTAAGAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
8 6 0.17
9 6 0.17
11 23 0.66
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATAATTAATTT
Found at i:53515119 original size:110 final size:114
Alignment explanation
Indices: 53514920--53515137 Score: 313
Period size: 116 Copynumber: 1.9 Consensus size: 114
53514910 AATTTATAAT
*
53514920 TTTTTAAAATTTATAATTAATTTAATTAAGAAACCTAAACCCTAAACTCTTGTTTATTTATTTTT
1 TTTTTAAAATTTATAATTAATTTAATTAAGAAACCTAAACCCTAAACTCTTATTTA--TATTTTT
* *
53514985 TCCCTTTAAACCCTAAAATTTAAAAACT-AAAAACCTCCAAAACTCTAACCC
64 TCCCTTAAAACCCTAAAATCTAAAAACTCAAAAA-CTCCAAAACTCTAACCC
*
53515036 TTTTTAAAATTTATAATTAATTTAATTAAGAAATCCTAAACCCT-TA-T-TTATTTA-ATTTTTT
1 TTTTTAAAATTTATAATTAATTTAATTAAGAAA-CCTAAACCCTAAACTCTTATTTATATTTTTT
*
53515097 -CCTTAAAACCCTAAAATCTAAAAACTCCAAAACTCCAAAAC
65 CCCTTAAAACCCTAAAATCTAAAAACTCAAAAACTCCAAAAC
53515138 CTTAACTCTA
Statistics
Matches: 95, Mismatches: 5, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
110 33 0.35
111 11 0.12
114 6 0.06
115 1 0.01
116 34 0.36
117 10 0.11
ACGTcount: A:0.42, C:0.19, G:0.01, T:0.38
Consensus pattern (114 bp):
TTTTTAAAATTTATAATTAATTTAATTAAGAAACCTAAACCCTAAACTCTTATTTATATTTTTTC
CCTTAAAACCCTAAAATCTAAAAACTCAAAAACTCCAAAACTCTAACCC
Found at i:53515279 original size:40 final size:41
Alignment explanation
Indices: 53515206--53515287 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 41
53515196 GGAAACACTT
*
53515206 TGTCCACGTGGACACAAAGCGCGCCCTCAAGGAAGCTTTTTC
1 TGTCCACGTGGA-ACAAAGCGCGCCCTCAAGGAAGCGTTTTC
** **
53515248 TGTCCACGTGG-ACAAAGCGCTTCCTTGAGGAAGCGTTTTC
1 TGTCCACGTGGAACAAAGCGCGCCCTCAAGGAAGCGTTTTC
53515288 CTGCTTTATC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 24 0.69
42 11 0.31
ACGTcount: A:0.22, C:0.28, G:0.26, T:0.24
Consensus pattern (41 bp):
TGTCCACGTGGAACAAAGCGCGCCCTCAAGGAAGCGTTTTC
Found at i:53522382 original size:3 final size:3
Alignment explanation
Indices: 53522374--53522402 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
53522364 TCGAAAGCGA
53522374 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
53522403 TTTTTATTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:53544782 original size:3 final size:3
Alignment explanation
Indices: 53544774--53544811 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
53544764 CATCTAGTTT
53544774 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
53544812 GGGTTAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:53548752 original size:93 final size:92
Alignment explanation
Indices: 53548607--53548775 Score: 214
Period size: 93 Copynumber: 1.8 Consensus size: 92
53548597 TCACCTCTAC
* ** * *
53548607 TTCTAGACTAACAATTCAACCTAACATTTAAAACATAGGATGCCTAACATTTTCCAACCTAACAT
1 TTCTAGACTAACAATTCAACCTAACATTTAAAACACAGGACACATAAAATTTTCCAACCTAACAT
*
53548672 TTATAGCATAGAACTGTACTAGTTTAG
66 TTAAAGCATAGAACTGTACTAGTTTAG
* * ** *
53548699 TTCTAG-CTTAACAATTTCAACCTAACATTTAAAATACAGTACACATAAAATTTTCCAGTCTAAT
1 TTCTAGAC-TAACAA-TTCAACCTAACATTTAAAACACAGGACACATAAAATTTTCCAACCTAAC
53548763 ATTTAAAGCATAG
64 ATTTAAAGCATAG
53548776 TAGTTATTGG
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
91 1 0.02
92 12 0.19
93 51 0.80
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.33
Consensus pattern (92 bp):
TTCTAGACTAACAATTCAACCTAACATTTAAAACACAGGACACATAAAATTTTCCAACCTAACAT
TTAAAGCATAGAACTGTACTAGTTTAG
Found at i:53550935 original size:15 final size:15
Alignment explanation
Indices: 53550915--53550948 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
53550905 GTAATTGGGT
53550915 TTTGGGTTTAAGTGG
1 TTTGGGTTTAAGTGG
*
53550930 TTTGGGTTTAGGTGG
1 TTTGGGTTTAAGTGG
53550945 TTTG
1 TTTG
53550949 TTATTTTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.00, G:0.41, T:0.50
Consensus pattern (15 bp):
TTTGGGTTTAAGTGG
Found at i:53553462 original size:20 final size:20
Alignment explanation
Indices: 53553422--53553462 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
53553412 ATTTATATGC
*
53553422 ATAATGGAATAATAAACATG
1 ATAATGGAATAATAAAAATG
53553442 ATAATGTGAATAA-AAAAATG
1 ATAATG-GAATAATAAAAATG
53553462 A
1 A
53553463 ACAAAAAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.59, C:0.02, G:0.15, T:0.24
Consensus pattern (20 bp):
ATAATGGAATAATAAAAATG
Found at i:53553884 original size:17 final size:18
Alignment explanation
Indices: 53553845--53553890 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
53553835 ACATGTGTGT
53553845 ATAAAAATATGGAATATA
1 ATAAAAATATGGAATATA
**
53553863 A-AAAAATATTTAATA-A
1 ATAAAAATATGGAATATA
53553879 ATAAAAAGTATG
1 ATAAAAA-TATG
53553891 TACGTGTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 2 0.09
17 17 0.74
18 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (18 bp):
ATAAAAATATGGAATATA
Found at i:53554925 original size:33 final size:33
Alignment explanation
Indices: 53554883--53554949 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
53554873 TTATAGCCGA
53554883 TTTACATGAGATTTCTAGTCTATTTCCTATGCT
1 TTTACATGAGATTTCTAGTCTATTTCCTATGCT
53554916 TTTACATGAGATTTCTAGTCTATTTCCTATGCT
1 TTTACATGAGATTTCTAGTCTATTTCCTATGCT
53554949 T
1 T
53554950 GTCATGTCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.49
Consensus pattern (33 bp):
TTTACATGAGATTTCTAGTCTATTTCCTATGCT
Found at i:53555182 original size:21 final size:21
Alignment explanation
Indices: 53555156--53555200 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
53555146 GGTGGGTTTA
* *
53555156 GTTTGGGTATTTTGGTAATGG
1 GTTTGGGTATGTTGGAAATGG
*
53555177 GTTTGGGTCTGTTGGAAATGG
1 GTTTGGGTATGTTGGAAATGG
53555198 GTT
1 GTT
53555201 ATTTTGTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.02, G:0.40, T:0.44
Consensus pattern (21 bp):
GTTTGGGTATGTTGGAAATGG
Found at i:53582042 original size:4 final size:4
Alignment explanation
Indices: 53582035--53582891 Score: 1714
Period size: 4 Copynumber: 214.2 Consensus size: 4
53582025 ACATGCATGG
53582035 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
53582083 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
53582131 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
53582179 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
53582227 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
53582275 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
53582323 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
53582371 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
53582419 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
53582467 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
53582515 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
53582563 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
53582611 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
53582659 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
53582707 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
53582755 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
53582803 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
53582851 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
53582892 CAGCCACAGG
Statistics
Matches: 853, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 853 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:53591958 original size:17 final size:18
Alignment explanation
Indices: 53591932--53591966 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
53591922 CATATTTTTA
*
53591932 AATATTTTA-TAAAAATT
1 AATATATTATTAAAAATT
53591949 AATATATTATTAAAAATT
1 AATATATTATTAAAAATT
53591967 TAGATTACAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATATATTATTAAAAATT
Found at i:53599968 original size:23 final size:24
Alignment explanation
Indices: 53599915--53599968 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
53599905 ATAAACTCAT
* * *
53599915 ATTATATTTTTTAGTTTTTTAAAA
1 ATTATATTTTTTAGATATCTAAAA
*
53599939 ATATATATTTTTTA-ATATCTAATA
1 AT-TATATTTTTTAGATATCTAAAA
53599963 ATTATA
1 ATTATA
53599969 AATATGCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 4 0.16
24 10 0.40
25 11 0.44
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
ATTATATTTTTTAGATATCTAAAA
Found at i:53600147 original size:12 final size:12
Alignment explanation
Indices: 53600130--53600157 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
53600120 AGTTTAAACA
53600130 CATAGTTATTAG
1 CATAGTTATTAG
53600142 CATAGTTATTAG
1 CATAGTTATTAG
53600154 CATA
1 CATA
53600158 TTTACTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (12 bp):
CATAGTTATTAG
Found at i:53600203 original size:25 final size:23
Alignment explanation
Indices: 53600169--53600248 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 23
53600159 TTACTTTAAT
53600169 ATTTAAATATTAAAGTATATATG
1 ATTTAAATATTAAAGTATATATG
* ***
53600192 TATTTCTAATATTTACTTTAGTATCATG
1 -ATTT-AAATA-TTAAAGTA-TAT-ATG
53600220 ATTTAAATATTAAAGTATATATG
1 ATTTAAATATTAAAGTATATATG
53600243 AATTTA
1 -ATTTA
53600249 TAAATATAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
23 3 0.07
24 12 0.28
25 9 0.21
26 9 0.21
27 7 0.16
28 3 0.07
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.47
Consensus pattern (23 bp):
ATTTAAATATTAAAGTATATATG
Found at i:53600205 original size:45 final size:49
Alignment explanation
Indices: 53600155--53600247 Score: 131
Period size: 51 Copynumber: 1.9 Consensus size: 49
53600145 AGTTATTAGC
*
53600155 ATATTTAC-TT-TA-AT-ATTTAAATATTAAAGTATATATGTATTTCTA
1 ATATTTACTTTATACATGATTTAAATATTAAAGTATATATGAATTTCTA
53600200 ATATTTACTTTAGTATCATGATTTAAATATTAAAGTATATATGAATTT
1 ATATTTACTTTA-TA-CATGATTTAAATATTAAAGTATATATGAATTT
53600248 ATAAATATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
45 8 0.20
46 2 0.05
48 2 0.05
50 2 0.05
51 27 0.66
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.49
Consensus pattern (49 bp):
ATATTTACTTTATACATGATTTAAATATTAAAGTATATATGAATTTCTA
Found at i:53600252 original size:26 final size:24
Alignment explanation
Indices: 53600170--53600255 Score: 68
Period size: 26 Copynumber: 3.4 Consensus size: 24
53600160 TACTTTAATA
53600170 TTTAAATATTAAAGTATATATGTAT
1 TTTAAATATTAAAGTATATATG-AT
***
53600195 TTCT-AATATTTACTTTAGTATCATGA-
1 TT-TAAATA-TTAAAGTA-TAT-ATGAT
53600221 TTTAAATATTAAAGTATATATGAAT
1 TTTAAATATTAAAGTATATATG-AT
53600246 TTATAAATAT
1 TT-TAAATAT
53600256 AAATAACTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 15
0.69 0.09 0.22
Matches are distributed among these distances:
23 3 0.06
24 4 0.09
25 14 0.30
26 19 0.40
27 4 0.09
28 3 0.06
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (24 bp):
TTTAAATATTAAAGTATATATGAT
Found at i:53603724 original size:116 final size:116
Alignment explanation
Indices: 53603520--53603753 Score: 432
Period size: 116 Copynumber: 2.0 Consensus size: 116
53603510 GAAAAGAAAC
53603520 TGATACTTATATAAGACCGTGGGAAAGGCGGATTTTAAGTTTATATCAATTATACAATAATTAGA
1 TGATACTTATATAAGACCGTGGGAAAGGCGGATTTTAAGTTTATATCAATTATACAATAATTAGA
* *
53603585 TTTCAAATCCGTCTTTAATTAGGGATCATAATTATTACGTCACGGAAGTTT
66 TTTCAAATCCGCCTTTAATTAGGGATCATAATTATTACGTCACGGAAATTT
* *
53603636 TGATACTTATATAAGACCGTGGGAAAGGCGGATTTTAAGTTTCTATCAATTGTACAATAATTAGA
1 TGATACTTATATAAGACCGTGGGAAAGGCGGATTTTAAGTTTATATCAATTATACAATAATTAGA
53603701 TTTCAAATCCGCCTTTAATTAGGGATCATAATTATTACGTCACGGAAATTT
66 TTTCAAATCCGCCTTTAATTAGGGATCATAATTATTACGTCACGGAAATTT
53603752 TG
1 TG
53603754 TGGGTAATTA
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 114 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.36
Consensus pattern (116 bp):
TGATACTTATATAAGACCGTGGGAAAGGCGGATTTTAAGTTTATATCAATTATACAATAATTAGA
TTTCAAATCCGCCTTTAATTAGGGATCATAATTATTACGTCACGGAAATTT
Found at i:53620981 original size:186 final size:187
Alignment explanation
Indices: 53620591--53621152 Score: 941
Period size: 186 Copynumber: 3.0 Consensus size: 187
53620581 ATCAGGTACC
***
53620591 TTCATTTTTTGCTCGCACTTCTTTTCTAGATTTGACGATATGAAAACATGACATAAACACAACGC
1 TTCATTTTTTGCTCGGGTTTCTTTTCTAGATTTGACGATATGAAAACATGACATAAACACAACGC
*
53620656 ATTTTGGTACATTTATTGTACTCATATTTAGGATCATGACACATAATAATTTGTATTGAATTTAT
66 ATTTTGGTACATTTATTGTACTCATATTTAGGATCTTGACACA-AATAATTTGTATTGAATTTAT
*
53620721 ACTCTCACGGTTTACACGAAAAGAACATGAGCTAAGGGATGTATACAGGAATTAAACA
130 ACTCTCACGGTTTACACGAAAAGAACATGAGCTAAGGGATGTATACACGAATTAAACA
53620779 TTCATTTTTTGCTCGGGTTTCTTTTCTAGATTTGACGATATGAAAACATGACATAAACACAACGC
1 TTCATTTTTTGCTCGGGTTTCTTTTCTAGATTTGACGATATGAAAACATGACATAAACACAACGC
53620844 ATTTTGGTACATTTATTGTACTCATATTTAGGATCTTGACAC-AATAATTTGTATTGAATTTATA
66 ATTTTGGTACATTTATTGTACTCATATTTAGGATCTTGACACAAATAATTTGTATTGAATTTATA
*
53620908 CTCTCACGGTTTACACGAAAAGAACAGGAGCTAAGGGATGTATACACGAATTAAACA
131 CTCTCACGGTTTACACGAAAAGAACATGAGCTAAGGGATGTATACACGAATTAAACA
* *
53620965 TTCATTTTTTGCTCGGGTTTCTTTTCTAGATTTGACGATCTGAAAACATGACATAAACACAACAC
1 TTCATTTTTTGCTCGGGTTTCTTTTCTAGATTTGACGATATGAAAACATGACATAAACACAACGC
* * *
53621030 A-TTTAGTACATTTATTGTACTCGTATTTAGGATTTTGACACATAATAATTTGTATTGAATTTAT
66 ATTTTGGTACATTTATTGTACTCATATTTAGGATCTTGACACA-AATAATTTGTATTGAATTTAT
* * * *
53621094 A-TTTACACGGTTTACATGAAAAGGACATGAGCTAAGGCATGTATACACGAATTAAACA
130 ACTCT-CACGGTTTACACGAAAAGAACATGAGCTAAGGGATGTATACACGAATTAAACA
53621152 T
1 T
53621153 CTCTCTAATG
Statistics
Matches: 355, Mismatches: 16, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
185 37 0.10
186 143 0.40
187 72 0.20
188 103 0.29
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (187 bp):
TTCATTTTTTGCTCGGGTTTCTTTTCTAGATTTGACGATATGAAAACATGACATAAACACAACGC
ATTTTGGTACATTTATTGTACTCATATTTAGGATCTTGACACAAATAATTTGTATTGAATTTATA
CTCTCACGGTTTACACGAAAAGAACATGAGCTAAGGGATGTATACACGAATTAAACA
Found at i:53624222 original size:2 final size:2
Alignment explanation
Indices: 53624215--53624243 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53624205 GTGTCTTATG
53624215 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53624244 GTGTATGAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53629802 original size:24 final size:23
Alignment explanation
Indices: 53629755--53629803 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
53629745 CTATAAATTA
*
53629755 ATTTTTATATTAAAAATTTATTT
1 ATTTTTATATTAAAAATATATTT
* *
53629778 ATTTTTACTGTTAAAAATATCTTT
1 ATTTTTA-TATTAAAAATATATTT
53629802 AT
1 AT
53629804 ATATAGAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (23 bp):
ATTTTTATATTAAAAATATATTT
Found at i:53640264 original size:6 final size:6
Alignment explanation
Indices: 53640255--53640285 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
53640245 ATAGTGGTGG
*
53640255 TGCTGC TGCTGA TGCTGA TGCTGA TGCTGA T
1 TGCTGA TGCTGA TGCTGA TGCTGA TGCTGA T
53640286 CGTCACCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.13, C:0.19, G:0.32, T:0.35
Consensus pattern (6 bp):
TGCTGA
Found at i:53641709 original size:14 final size:14
Alignment explanation
Indices: 53641690--53641721 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
53641680 TAAGATGCCC
53641690 CTCCTTTCCCCTTT
1 CTCCTTTCCCCTTT
*
53641704 CTCCTTTCTCCTTT
1 CTCCTTTCCCCTTT
53641718 CTCC
1 CTCC
53641722 CTCCTTCCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (14 bp):
CTCCTTTCCCCTTT
Found at i:53642064 original size:19 final size:19
Alignment explanation
Indices: 53642040--53642076 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
53642030 GATTTGTTCG
53642040 AAAAATAAAAAATTTAAAT
1 AAAAATAAAAAATTTAAAT
* *
53642059 AAAAATATAAATTTTAAA
1 AAAAATAAAAAATTTAAA
53642077 AAAGGTTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAATAAAAAATTTAAAT
Found at i:53656578 original size:19 final size:16
Alignment explanation
Indices: 53656554--53656595 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 16
53656544 TAATCATTGT
53656554 ATTCAATATATATATACCA
1 ATTCAATATA-ATATA--A
53656573 ATTCAAT-TAATATAA
1 ATTCAATATAATATAA
53656588 ATTCAATA
1 ATTCAATA
53656596 AATTCATCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 8 0.36
17 5 0.23
18 2 0.09
19 7 0.32
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTCAATATAATATAA
Found at i:53661722 original size:20 final size:20
Alignment explanation
Indices: 53661699--53661738 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
53661689 TTTAATAGGA
53661699 GATATGATAATTTATAGTCT
1 GATATGATAATTTATAGTCT
53661719 GATATGATAATTTATAGTCT
1 GATATGATAATTTATAGTCT
53661739 TACATTGCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
GATATGATAATTTATAGTCT
Found at i:53661908 original size:18 final size:18
Alignment explanation
Indices: 53661885--53661932 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
53661875 TTGTGCTTAC
53661885 TCTTCTCCTTCTCGGGCT
1 TCTTCTCCTTCTCGGGCT
* *
53661903 TCTTCTTGC-TCTCGGTCT
1 TCTTC-TCCTTCTCGGGCT
*
53661921 TCTTTTCCTTCT
1 TCTTCTCCTTCT
53661933 TTTCCTTCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 2 0.08
18 20 0.83
19 2 0.08
ACGTcount: A:0.00, C:0.35, G:0.12, T:0.52
Consensus pattern (18 bp):
TCTTCTCCTTCTCGGGCT
Found at i:53661933 original size:9 final size:9
Alignment explanation
Indices: 53661919--53662006 Score: 83
Period size: 9 Copynumber: 9.8 Consensus size: 9
53661909 TGCTCTCGGT
53661919 CTTCTTTTC
1 CTTCTTTTC
53661928 CTTCTTTTC
1 CTTCTTTTC
53661937 CTTCTTTTC
1 CTTCTTTTC
*
53661946 TTTCTTTTC
1 CTTCTTTTC
*
53661955 CTTCTTGTC
1 CTTCTTTTC
53661964 CTTGTCTTTCTC
1 C-T-TCTTT-TC
*
53661976 CTTCTTGT-
1 CTTCTTTTC
**
53661984 CTT-TCAT-
1 CTTCTTTTC
53661991 CTTCTTTTC
1 CTTCTTTTC
53662000 CTTCTTT
1 CTTCTTT
53662007 CCATGGCAAG
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
7 5 0.08
8 5 0.08
9 42 0.65
10 5 0.08
11 5 0.08
12 3 0.05
ACGTcount: A:0.01, C:0.31, G:0.03, T:0.65
Consensus pattern (9 bp):
CTTCTTTTC
Found at i:53665735 original size:12 final size:12
Alignment explanation
Indices: 53665714--53665746 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
53665704 GAGGGATCCC
53665714 TTTCTTTCTTGG
1 TTTCTTTCTTGG
*
53665726 TTTTTTTCTTGG
1 TTTCTTTCTTGG
53665738 TTTCTTTCT
1 TTTCTTTCT
53665747 CACCTTCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.12, T:0.73
Consensus pattern (12 bp):
TTTCTTTCTTGG
Found at i:53666806 original size:43 final size:42
Alignment explanation
Indices: 53666758--53666845 Score: 149
Period size: 43 Copynumber: 2.1 Consensus size: 42
53666748 ACGGGGTGAG
*
53666758 GAACGGTCTGGTTTTTCAAAATTCAAAATATAAGATGAACGTT
1 GAACGGTCTGATTTTTCAAAATTC-AAATATAAGATGAACGTT
*
53666801 GAACGGTCTGATTTTTCAAAATTCAAATTTAAGATGAACGTT
1 GAACGGTCTGATTTTTCAAAATTCAAATATAAGATGAACGTT
53666843 GAA
1 GAA
53666846 TGGCTATTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
42 20 0.47
43 23 0.53
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (42 bp):
GAACGGTCTGATTTTTCAAAATTCAAATATAAGATGAACGTT
Found at i:53667777 original size:15 final size:16
Alignment explanation
Indices: 53667757--53667790 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
53667747 GAACAGTGTC
53667757 TTTTTTT-TTA-AATA
1 TTTTTTTCTTACAATA
53667771 TTTTTTTCTTACAATA
1 TTTTTTTCTTACAATA
53667787 TTTT
1 TTTT
53667791 GTCTAGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 3 0.17
16 8 0.44
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTTTCTTACAATA
Found at i:53671839 original size:318 final size:318
Alignment explanation
Indices: 53671262--53671898 Score: 1274
Period size: 318 Copynumber: 2.0 Consensus size: 318
53671252 CTCCCTGGAA
53671262 ATTTTTTAAATTAATGAGGAACTATTCAATGTCTATTACAACCAACCACAAATATGAATGGTGAA
1 ATTTTTTAAATTAATGAGGAACTATTCAATGTCTATTACAACCAACCACAAATATGAATGGTGAA
53671327 AAACATCCAAAAACTGAATGATTCTTTAGAATACACCATATGTCTATGGATGAGGGAGACAAGAT
66 AAACATCCAAAAACTGAATGATTCTTTAGAATACACCATATGTCTATGGATGAGGGAGACAAGAT
53671392 AAAAATCAAAATAACATTTGATGCATGCTATAAATGTAACAATAATTGACTACCTACTGACTACC
131 AAAAATCAAAATAACATTTGATGCATGCTATAAATGTAACAATAATTGACTACCTACTGACTACC
53671457 ATAAAACCACCACCATATAATCACAAGATAATACATTAACTCATGTCAAAGAGAAACAATGCAAA
196 ATAAAACCACCACCATATAATCACAAGATAATACATTAACTCATGTCAAAGAGAAACAATGCAAA
53671522 TGCTGAAATGTTTTCTTTCTATTTTAAACAACATCATTTCTCATGACATTTTAGATAT
261 TGCTGAAATGTTTTCTTTCTATTTTAAACAACATCATTTCTCATGACATTTTAGATAT
53671580 ATTTTTTAAATTAATGAGGAACTATTCAATGTCTATTACAACCAACCACAAATATGAATGGTGAA
1 ATTTTTTAAATTAATGAGGAACTATTCAATGTCTATTACAACCAACCACAAATATGAATGGTGAA
53671645 AAACATCCAAAAACTGAATGATTCTTTAGAATACACCATATGTCTATGGATGAGGGAGACAAGAT
66 AAACATCCAAAAACTGAATGATTCTTTAGAATACACCATATGTCTATGGATGAGGGAGACAAGAT
53671710 AAAAATCAAAATAACATTTGATGCATGCTATAAATGTAACAATAATTGACTACCTACTGACTACC
131 AAAAATCAAAATAACATTTGATGCATGCTATAAATGTAACAATAATTGACTACCTACTGACTACC
53671775 ATAAAACCACCACCATATAATCACAAGATAATACATTAACTCATGTCAAAGAGAAACAATGCAAA
196 ATAAAACCACCACCATATAATCACAAGATAATACATTAACTCATGTCAAAGAGAAACAATGCAAA
53671840 TGCTGAAATGTTTTCTTTCTATTTTAAACAACATCATTTCTCATGACATTTTAGATAT
261 TGCTGAAATGTTTTCTTTCTATTTTAAACAACATCATTTCTCATGACATTTTAGATAT
53671898 A
1 A
53671899 ATGAGCTGTC
Statistics
Matches: 319, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
318 319 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (318 bp):
ATTTTTTAAATTAATGAGGAACTATTCAATGTCTATTACAACCAACCACAAATATGAATGGTGAA
AAACATCCAAAAACTGAATGATTCTTTAGAATACACCATATGTCTATGGATGAGGGAGACAAGAT
AAAAATCAAAATAACATTTGATGCATGCTATAAATGTAACAATAATTGACTACCTACTGACTACC
ATAAAACCACCACCATATAATCACAAGATAATACATTAACTCATGTCAAAGAGAAACAATGCAAA
TGCTGAAATGTTTTCTTTCTATTTTAAACAACATCATTTCTCATGACATTTTAGATAT
Found at i:53676110 original size:21 final size:20
Alignment explanation
Indices: 53676055--53676116 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
53676045 TCATAAAATA
*
53676055 TAAATTATTTAAT-TATTTT
1 TAAATTAATTAATATATTTT
* *
53676074 TAAATAATATTTATATATTTT
1 TAAATTA-ATTAATATATTTT
*
53676095 TATAATTAATTAATATGTTTT
1 TA-AATTAATTAATATATTTT
53676116 T
1 T
53676117 TTATTATGAC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 6 0.18
20 4 0.12
21 20 0.59
22 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TAAATTAATTAATATATTTT
Found at i:53688225 original size:7 final size:7
Alignment explanation
Indices: 53688213--53688243 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
53688203 CCCTATGCTT
53688213 TTTGAAA
1 TTTGAAA
53688220 TTTGAAA
1 TTTGAAA
*
53688227 TTTGAGA
1 TTTGAAA
53688234 TTTGAAA
1 TTTGAAA
53688241 TTT
1 TTT
53688244 TAGTCCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.48
Consensus pattern (7 bp):
TTTGAAA
Found at i:53689620 original size:12 final size:12
Alignment explanation
Indices: 53689605--53689629 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53689595 TACTTTAAAT
53689605 TATAAAATGATA
1 TATAAAATGATA
53689617 TATAAAATGATA
1 TATAAAATGATA
53689629 T
1 T
53689630 TTTAATCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (12 bp):
TATAAAATGATA
Found at i:53689624 original size:20 final size:21
Alignment explanation
Indices: 53689578--53689624 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
53689568 TTATAAATTA
*
53689578 ATAAAATTATAAAATTATACT
1 ATAAAATTATAAAATGATACT
*
53689599 -TTAAATTATAAAATGATA-T
1 ATAAAATTATAAAATGATACT
53689618 ATAAAAT
1 ATAAAAT
53689625 GATATTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
ATAAAATTATAAAATGATACT
Found at i:53693978 original size:17 final size:18
Alignment explanation
Indices: 53693941--53693979 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
53693931 TATCATTAAC
* *
53693941 AAATAATTTAAAATTATA
1 AAATAATTTAAAAATAAA
53693959 AAAT-ATTTAAAAATAAA
1 AAATAATTTAAAAATAAA
53693976 AAAT
1 AAAT
53693980 CAAAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAATTTAAAAATAAA
Found at i:53710940 original size:31 final size:30
Alignment explanation
Indices: 53710866--53710941 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 30
53710856 TAACCAAGTC
* *
53710866 AGGACTAAAATTTTATAATTCAAAAAGCATA
1 AGGACTAAAA-TTGATAATTCAAAAAACATA
53710897 AGGACTAAAATTGACTAATTCAAAAAACATA
1 AGGACTAAAATTGA-TAATTCAAAAAACATA
*
53710928 GGGACTAAAATTGA
1 AGGACTAAAATTGA
53710942 GCAAATTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 3 0.07
31 38 0.93
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.25
Consensus pattern (30 bp):
AGGACTAAAATTGATAATTCAAAAAACATA
Found at i:53711286 original size:2 final size:2
Alignment explanation
Indices: 53711279--53711316 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
53711269 CGTTTGATTG
* *
53711279 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53711317 GATCTTTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:53711401 original size:37 final size:37
Alignment explanation
Indices: 53711351--53711428 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
53711341 AATTAAAATT
53711351 GTTTTTTAAAGTATGGGTCTGAACAGACTTTTTATGG
1 GTTTTTTAAAGTATGGGTCTGAACAGACTTTTTATGG
53711388 GTTTTTTAAAGTATGGGTCTGAACAGACTTTTTATGG
1 GTTTTTTAAAGTATGGGTCTGAACAGACTTTTTATGG
53711425 GTTT
1 GTTT
53711429 GATACAGATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.23, C:0.08, G:0.24, T:0.45
Consensus pattern (37 bp):
GTTTTTTAAAGTATGGGTCTGAACAGACTTTTTATGG
Found at i:53725478 original size:96 final size:96
Alignment explanation
Indices: 53725305--53725478 Score: 258
Period size: 96 Copynumber: 1.8 Consensus size: 96
53725295 AGTTGCGTAT
*** * * *
53725305 TTCAAATATTTCAAATTTACTTTTATTAATGACAACTCTTTGCTTTTCTAACACCGAGAACTACT
1 TTCAAATATTTCAAAACGACTTCTATTAATGAAAACTATTTGCTTTTCTAACACCGAGAACTACT
* *
53725370 TTTAAACTAAAATAAGTTGCCTGTTTCAAAA
66 CTTAAACAAAAATAAGTTGCCTGTTTCAAAA
*
53725401 TTCAAATATTTCAAAACGACTTCTATTAATGAAAACTATTTGCTTTTCTAACACTGAGAACTACT
1 TTCAAATATTTCAAAACGACTTCTATTAATGAAAACTATTTGCTTTTCTAACACCGAGAACTACT
*
53725466 CTTAAAGAAAAAT
66 CTTAAACAAAAAT
53725479 GGACATTTAA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
96 68 1.00
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.37
Consensus pattern (96 bp):
TTCAAATATTTCAAAACGACTTCTATTAATGAAAACTATTTGCTTTTCTAACACCGAGAACTACT
CTTAAACAAAAATAAGTTGCCTGTTTCAAAA
Found at i:53727767 original size:29 final size:30
Alignment explanation
Indices: 53727730--53727790 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 30
53727720 AAAATAAAAA
*
53727730 TATTTAATTTTA-AATGAAAATTAATTTAT
1 TATTTAATTTTACAATAAAAATTAATTTAT
53727759 TATTTAATTTTACGAATAAAAATTAATTTAT
1 TATTTAATTTTAC-AATAAAAATTAATTTAT
53727790 T
1 T
53727791 TACTTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 12 0.41
31 17 0.59
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (30 bp):
TATTTAATTTTACAATAAAAATTAATTTAT
Found at i:53733503 original size:88 final size:88
Alignment explanation
Indices: 53733365--53733776 Score: 542
Period size: 88 Copynumber: 4.7 Consensus size: 88
53733355 CCTGATTTGC
* * * * * *
53733365 AGTGGAGCAGGTTGAAAATAACATATCTTGCCTTCATGTA-CTGA-AGGCGAAACAGATCGAAAA
1 AGTGGAGCAGGTTGAAGATAGCATATCTTGCCTTCCTGCATC-GACA-GCGAAGCAGATCGAAGA
*
53733428 TACCAGCCTTGCATACCTGGGTTGT
64 TACCAGCCTTGCATCCCTGGGTTGT
* * * *
53733453 AGTGAAGCAGGTTGAAGATAGTAGATCTTGCCTTCCTGTATCGACAGCGAAGCAGATCGAAGATA
1 AGTGGAGCAGGTTGAAGATAGCATATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGATA
53733518 CCAGCCTTGCATCCCTGGGTTGT
66 CCAGCCTTGCATCCCTGGGTTGT
*
53733541 CGTGGAGCAGGTTGAAGATAGCATATCTAT-CCTTCCTGCATCGACAGCGAAGCAGATCGAAGAT
1 AGTGGAGCAGGTTGAAGATAGCATATCT-TGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGAT
* * * *
53733605 ACTAGCCTTGCCTCCTTGGGTTGC
65 ACCAGCCTTGCATCCCTGGGTTGT
* * *
53733629 AGTGGAGCAGGTTGAAGATAGCAGATTTTGCCTTCCTGCATCAACAGCGAAGCAGATCGAAGATA
1 AGTGGAGCAGGTTGAAGATAGCATATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGATA
* *
53733694 CCAGCCTTGCCTCCCTTGGTTGT
66 CCAGCCTTGCATCCCTGGGTTGT
* * * * *
53733717 AGTGGAGCAGGTTAAAAATAGCATACCTTGCCTTCCTGCACCGACAACGAAGCAGATCGA
1 AGTGGAGCAGGTTGAAGATAGCATATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGA
53733777 TGACCCCAAC
Statistics
Matches: 286, Mismatches: 34, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
87 1 0.00
88 282 0.99
89 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (88 bp):
AGTGGAGCAGGTTGAAGATAGCATATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGATA
CCAGCCTTGCATCCCTGGGTTGT
Found at i:53733515 original size:45 final size:45
Alignment explanation
Indices: 53733456--53733693 Score: 157
Period size: 45 Copynumber: 5.4 Consensus size: 45
53733446 GGGTTGTAGT
* * * *
53733456 GAAGCAGGTTGAAGATAGTAGATCTTGCCTTCCTGTATCGACAGC
1 GAAGCAGATCGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGC
* * * * ** * * *
53733501 GAAGCAGATCGAAGATACCAG-CCTTGCATCCCTGGGTTGTC-GT
1 GAAGCAGATCGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGC
* * * *
53733544 GGAGCAGGTTGAAGATAGCATATCTAT-CCTTCCTGCATCGACAGC
1 GAAGCAGATCGAAGATAGCAGATCT-TGCCTTCCTGCATCGACAGC
* ** * *
53733589 GAAGCAGATCGAAGATA-CTAG-CCTTGCC-TCCTTGGGTTG-CAGT
1 GAAGCAGATCGAAGATAGC-AGATCTTGCCTTCC-TGCATCGACAGC
* * * * *
53733632 GGAGCAGGTTGAAGATAGCAGATTTTGCCTTCCTGCATCAACAGC
1 GAAGCAGATCGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGC
53733677 GAAGCAGATCGAAGATA
1 GAAGCAGATCGAAGATA
53733694 CCAGCCTTGC
Statistics
Matches: 136, Mismatches: 47, Indels: 20
0.67 0.23 0.10
Matches are distributed among these distances:
43 40 0.29
44 42 0.31
45 54 0.40
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (45 bp):
GAAGCAGATCGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGC
Found at i:53733558 original size:43 final size:43
Alignment explanation
Indices: 53733427--53733560 Score: 115
Period size: 44 Copynumber: 3.1 Consensus size: 43
53733417 CAGATCGAAA
*
53733427 ATACCAGCCTTGCATACCTGGGTTGTAGTGAAGCAGGTTGAAG
1 ATACCAGCCTTGCATACCTGGGTTGTCGTGAAGCAGGTTGAAG
** * * * ** * * * * *
53733470 ATAGTAGATCTTGCCTTCCTGTATCGACAGCGAAGCAGATCGAAG
1 ATACCAG-CCTTGCATACCTGGGTTGTC-GTGAAGCAGGTTGAAG
* *
53733515 ATACCAGCCTTGCATCCCTGGGTTGTCGTGGAGCAGGTTGAAG
1 ATACCAGCCTTGCATACCTGGGTTGTCGTGAAGCAGGTTGAAG
53733558 ATA
1 ATA
53733561 GCATATCTAT
Statistics
Matches: 63, Mismatches: 26, Indels: 4
0.68 0.28 0.04
Matches are distributed among these distances:
43 20 0.32
44 25 0.40
45 18 0.29
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (43 bp):
ATACCAGCCTTGCATACCTGGGTTGTCGTGAAGCAGGTTGAAG
Found at i:53733809 original size:176 final size:176
Alignment explanation
Indices: 53733443--53733823 Score: 487
Period size: 176 Copynumber: 2.2 Consensus size: 176
53733433 GCCTTGCATA
* * * * * *
53733443 CCTGGGTTGTAGTGAAGCAGGTTGAAGATAGTAGATCTTGCCTTCCTGTATCGACAGCGAAGCAG
1 CCTGGGTAGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCAACAGCGAAGCAG
* * * *
53733508 ATCGAAGATACCAGCCTTGCATCCCTGGGTTGTCGTGGAGCAGGTTGAAGATAGCATATCTATCC
66 ATCGAAGATACCAGCCTTGCATCCCTGGGTTGTAGTGGAGCAGGTTAAAAATAGCATACCTATCC
* * * * * * *
53733573 TTCCTGCATCGACAGCGAAGCAGATCGAAGATACTAGCCTTGCCTC
131 TTCCTGCACCGACAACGAAGCAGATCGAAGACACCAACCCTACCTC
* * *
53733619 CTTGGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATTTTGCCTTCCTGCATCAACAGCGAAGCAG
1 CCTGGGTAGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCAACAGCGAAGCAG
* *
53733684 ATCGAAGATACCAGCCTTGCCTCCCTTGGTTGTAGTGGAGCAGGTTAAAAATAGCATACCT-TGC
66 ATCGAAGATACCAGCCTTGCATCCCTGGGTTGTAGTGGAGCAGGTTAAAAATAGCATACCTAT-C
* * *
53733748 CTTCCTGCACCGACAACGAAGCAGATCGATGACCCCAACCCTATCTC
130 CTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAACCCTACCTC
**
53733795 CCT-GGTCAGCAGTGGAATAGGTTGAAGAT
1 CCTGGGT-AGCAGTGGAGCAGGTTGAAGAT
53733824 TGTGAATCTT
Statistics
Matches: 176, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
175 4 0.02
176 172 0.98
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (176 bp):
CCTGGGTAGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCAACAGCGAAGCAG
ATCGAAGATACCAGCCTTGCATCCCTGGGTTGTAGTGGAGCAGGTTAAAAATAGCATACCTATCC
TTCCTGCACCGACAACGAAGCAGATCGAAGACACCAACCCTACCTC
Found at i:53733819 original size:264 final size:264
Alignment explanation
Indices: 53733344--53733823 Score: 585
Period size: 264 Copynumber: 1.8 Consensus size: 264
53733334 GAAATCACAA
* * * *
53733344 AGCCTTGCCTTCCTGATTTGCAGTGGAGCAGGTTGAAAATAACATATCTTGCCTTCATGTACTGA
1 AGCCTTGCCTTCCTGAGTTGCAGTGGAGCAGGTTGAAAATAACAGATCTTGCCTTCATGCACTCA
* * *
53733409 AGGCGAAACAGATCGAAAATACCAGCCTTGCATACCTGGGTTGTAGTGAAGCAGGTTGAAGATAG
66 AAGCGAAACAGATCGAAAATACCAGCCTTGCATACCTGGGTTGTAGTGAAGCAGGTTAAAAATAG
* * * * * * * *
53733474 TAGATCTTGCCTTCCTGTATCGACAGCGAAGCAGATCGAAGATACCAGCCTTGCATCCCTGGGTT
131 CAGACCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCACCCTTGCATCCCTGGGTA
*
53733539 GTCGTGGAGCAGGTTGAAGATAGCATATCTATCCTTCCTGCATCGACAGCGAAGCAGATCGAAGA
196 GTCGTGGAACAGGTTGAAGATAGCATATCTATCCTTCCTGCATCGACAGCGAAGCAGATCGAAGA
53733604 TACT
261 TACT
* * * * *
53733608 AGCCTTGCC-TCCTTGGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATTTTGCCTTCCTGCA-TC
1 AGCCTTGCCTTCC-TGAGTTGCAGTGGAGCAGGTTGAAAATAACAGATCTTGCCTTCATGCACTC
* * * * * *
53733671 AACAGCGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTTGGTTGTAGTGGAGCAGGTTAAAAAT
65 AA-AGCGAAACAGATCGAAAATACCAGCCTTGCATACCTGGGTTGTAGTGAAGCAGGTTAAAAAT
* * *
53733736 AGCATACCTTGCCTTCCTGCACCGACAACGAAGCAGATCGATGACCCCAACCCTAT-C-TCCCT-
129 AGCAGACCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACC-ACCCT-TGCATCCCTG
*
53733798 GGTCAG-CAGTGGAATAGGTTGAAGAT
192 GGT-AGTC-GTGGAACAGGTTGAAGAT
53733824 TGTGAATCTT
Statistics
Matches: 179, Mismatches: 31, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
263 10 0.06
264 163 0.91
265 5 0.03
266 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.25
Consensus pattern (264 bp):
AGCCTTGCCTTCCTGAGTTGCAGTGGAGCAGGTTGAAAATAACAGATCTTGCCTTCATGCACTCA
AAGCGAAACAGATCGAAAATACCAGCCTTGCATACCTGGGTTGTAGTGAAGCAGGTTAAAAATAG
CAGACCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCACCCTTGCATCCCTGGGTA
GTCGTGGAACAGGTTGAAGATAGCATATCTATCCTTCCTGCATCGACAGCGAAGCAGATCGAAGA
TACT
Found at i:53733877 original size:44 final size:44
Alignment explanation
Indices: 53733789--53733885 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
53733779 ACCCCAACCC
* * **
53733789 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCT
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTAAAAATTCAGAATCT
* *
53733833 TATCTCCTTGGTCAGCAGTGGAGTAGGTTAAAAATTACAG-ATCT
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTAAAAATT-CAGAATCT
53733877 TATCTCCCT
1 TATCTCCCT
53733886 AAGCAGTAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 44 0.98
45 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.33
Consensus pattern (44 bp):
TATCTCCCTGGTCAGCAGTGGAATAGGTTAAAAATTCAGAATCT
Found at i:53733897 original size:44 final size:44
Alignment explanation
Indices: 53733849--53733986 Score: 161
Period size: 44 Copynumber: 3.2 Consensus size: 44
53733839 CTTGGTCAGC
53733849 AGTGGAGTAGGTTAAAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGTAGGTTAAAAATTACAGATCTTATCTCCCTAAGCAGT
* * * *** * * *
53733893 AGTGGAGTAGATCAAAGACCCCAG-CCTTGTCTCCCTAAACAGT
1 AGTGGAGTAGGTTAAAAATTACAGATCTTATCTCCCTAAGCAGT
* *
53733936 AGTGGAGTAGGTTGAAAATTATAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGTAGGTTAAAAATTACAGATCTTATCTCCCTAAGCAGT
*
53733980 GGTGGAG
1 AGTGGAG
53733987 CAGATCGAAG
Statistics
Matches: 72, Mismatches: 21, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
43 32 0.44
44 40 0.56
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (44 bp):
AGTGGAGTAGGTTAAAAATTACAGATCTTATCTCCCTAAGCAGT
Found at i:53733945 original size:87 final size:87
Alignment explanation
Indices: 53733849--53734012 Score: 256
Period size: 87 Copynumber: 1.9 Consensus size: 87
53733839 CTTGGTCAGC
*
53733849 AGTGGAGTAGGTTAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGACCC
1 AGTGGAGTAGGTTAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACCC
* *
53733914 CAGCCTTGTCTCCCTAAACAGT
66 CAACCTTATCTCCCTAAACAGT
* * * * *
53733936 AGTGGAGTAGGTTGAAAATTATAGATCTTATCTCCCTAAGCAGTGGTGGAGCAGATCGAAGTCCC
1 AGTGGAGTAGGTTAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACCC
53734001 CAACCTTATCTC
66 CAACCTTATCTC
53734013 TCTGGTCAGC
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (87 bp):
AGTGGAGTAGGTTAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACCC
CAACCTTATCTCCCTAAACAGT
Found at i:53734034 original size:87 final size:87
Alignment explanation
Indices: 53733856--53734042 Score: 221
Period size: 87 Copynumber: 2.1 Consensus size: 87
53733846 AGCAGTGGAG
* * *
53733856 TAGGTTAAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGACCCCAGCCTT
1 TAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACCCCAACCTT
* * ** * *
53733921 GTCTCCCTAAACAGTAGTGGAG
66 ATCTCCCTAAACAGCAAAGAAA
* * * *
53733943 TAGGTTGAAAATTATAGATCTTATCTCCCTAAGCAGTGGTGGAGCAGATCGAAGTCCCCAACCTT
1 TAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACCCCAACCTT
* ***
53734008 ATCTCTCTGGTCAGCAAAGAAA
66 ATCTCCCTAAACAGCAAAGAAA
53734030 TAGGTTGAAAATT
1 TAGGTTGAAAATT
53734043 GTGAATCCCT
Statistics
Matches: 83, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
87 83 1.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (87 bp):
TAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACCCCAACCTT
ATCTCCCTAAACAGCAAAGAAA
Found at i:53741669 original size:13 final size:14
Alignment explanation
Indices: 53741651--53741680 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
53741641 GATCCGTCCG
53741651 TATTATT-TTTTTA
1 TATTATTATTTTTA
53741664 TATTATTATTTTTA
1 TATTATTATTTTTA
53741678 TAT
1 TAT
53741681 AAAAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTATTATTTTTA
Found at i:53741672 original size:16 final size:16
Alignment explanation
Indices: 53741651--53741681 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53741641 GATCCGTCCG
*
53741651 TATTATTTTTTTATAT
1 TATTATTTTTATATAT
53741667 TATTATTTTTATATA
1 TATTATTTTTATATA
53741682 AAAAATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTATTTTTATATAT
Found at i:53742695 original size:31 final size:31
Alignment explanation
Indices: 53742636--53742706 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
53742626 CTCATCAACC
*
53742636 CAATGACTTAAATAAAAACTATCAAATAACT
1 CAATAACTTAAATAAAAACTATCAAATAACT
* * *
53742667 CAATTACTTAAATAAAAACCT-TCGAATAATT
1 CAATAACTTAAATAAAAA-CTATCAAATAACT
53742698 CAATAACTT
1 CAATAACTT
53742707 TTTTGTAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 33 0.94
32 2 0.06
ACGTcount: A:0.51, C:0.17, G:0.03, T:0.30
Consensus pattern (31 bp):
CAATAACTTAAATAAAAACTATCAAATAACT
Found at i:53760703 original size:57 final size:56
Alignment explanation
Indices: 53760611--53760752 Score: 180
Period size: 57 Copynumber: 2.5 Consensus size: 56
53760601 AACCTATATT
* * *
53760611 TTTTTCTAATTTGGTA--TATAATTTTTTTTCTCAATTCGATACCTAAATTTGACAA
1 TTTTTCTAATTTGGTACCTA-AATTTTTTTCCCCAATTCGATACCTAAACTTGACAA
* * *
53760666 TTTTTCTTAATTTGGTACCTAAATTTTTTTCCCCAATTTGATACCTGAACTTGACAT
1 TTTTTC-TAATTTGGTACCTAAATTTTTTTCCCCAATTCGATACCTAAACTTGACAA
*
53760723 TTTTTCCTAATTTGGTACCTAAGTTTTTTT
1 TTTTT-CTAATTTGGTACCTAAATTTTTTT
53760753 TTTAGGTTTA
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
55 6 0.08
56 10 0.13
57 57 0.75
58 3 0.04
ACGTcount: A:0.25, C:0.15, G:0.08, T:0.51
Consensus pattern (56 bp):
TTTTTCTAATTTGGTACCTAAATTTTTTTCCCCAATTCGATACCTAAACTTGACAA
Found at i:53760975 original size:4 final size:4
Alignment explanation
Indices: 53760966--53760991 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
53760956 CATTATTGTC
53760966 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
53760992 CTAAAACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:53761642 original size:31 final size:31
Alignment explanation
Indices: 53761600--53761660 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
53761590 ACCCTCAAAC
* *
53761600 AGTTTAAGTACCAACTTAAGAAAATTTGTCT
1 AGTTTAAGTACCAAATTAAGAAAATGTGTCT
* *
53761631 AGTTTAGGTACCAAATTAGGAAAATGTGTC
1 AGTTTAAGTACCAAATTAAGAAAATGTGTC
53761661 AAATTCAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (31 bp):
AGTTTAAGTACCAAATTAAGAAAATGTGTCT
Found at i:53764663 original size:54 final size:54
Alignment explanation
Indices: 53764536--53764744 Score: 323
Period size: 55 Copynumber: 3.9 Consensus size: 54
53764526 TTCAAATTTT
* * * *
53764536 ATCTCATTGATTTCAAATTTATTTCATACATCTAACACCTATTTTTTTTCATTCA
1 ATCTCATTTATTTCAAATTTTTTTCCTACATCTAACACAT-TTTTTTTTCATTCA
53764591 ATCTCATTTATTTCAAATTTTTTTCCTACATCTAACACATTTTTTTTTCATTCA
1 ATCTCATTTATTTCAAATTTTTTTCCTACATCTAACACATTTTTTTTTCATTCA
* * *
53764645 ATCTAATTTATTTTAAATTTTTTTTTCTACATCTAACAC-TTTTTTTTTCATTCA
1 ATCTCATTTATTTCAAA-TTTTTTTCCTACATCTAACACATTTTTTTTTCATTCA
53764699 ATCTCA-TTATTTCAAATTTTTTTCCTACATCTAACACATTTTTTTT
1 ATCTCATTTATTTCAAATTTTTTTCCTACATCTAACACATTTTTTTT
53764745 ATTTTTTTCG
Statistics
Matches: 142, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
52 20 0.14
53 17 0.12
54 49 0.35
55 56 0.39
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (54 bp):
ATCTCATTTATTTCAAATTTTTTTCCTACATCTAACACATTTTTTTTTCATTCA
Found at i:53764854 original size:112 final size:112
Alignment explanation
Indices: 53764738--53765015 Score: 382
Period size: 112 Copynumber: 2.5 Consensus size: 112
53764728 TCTAACACAT
53764738 TTTTTTTATTTTTTTCGTATATTTATATCTGACTCTGACACAAAAAAAATAAATTTTTTTTTTTA
1 TTTTTTTATTTTTTTCGTATATTTATATCTGACTCTGACACAAAAAAAA-AAA--TTTTTTTTTA
*
53764803 AA-TTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCA-AA-AAAAA
63 AATTTTGTACTGGGTGCAGGCCATTGACAGGCCAGCACCCAGAATAAAAA
* * * * *
53764850 TTTTTTAAAATTTTTTTCGTAAATTTATATTTGACTCTGACACGAAAAAAAAGATTTTTTTTTAA
1 TTTTTT--TATTTTTTTCGTATATTTATATCTGACTCTGACACAAAAAAAAAAATTTTTTTTTAA
* ***
53764915 ATTTTGTACTGGGTGCAGGCCATTGACAGGCCAGCACCCAGAATTATTT
64 ATTTTGTACTGGGTGCAGGCCATTGACAGGCCAGCACCCAGAATAAAAA
* *
53764964 TTTTTTTATTTTTTTTGTATATTTATATCTGACTCTGACACGAAAAAAAAAA
1 TTTTTTTATTTTTTTCGTATATTTATATCTGACTCTGACACAAAAAAAAAAA
53765016 GAAAAAAAAT
Statistics
Matches: 146, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
111 12 0.08
112 84 0.58
113 4 0.03
114 46 0.32
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (112 bp):
TTTTTTTATTTTTTTCGTATATTTATATCTGACTCTGACACAAAAAAAAAAATTTTTTTTTAAAT
TTTGTACTGGGTGCAGGCCATTGACAGGCCAGCACCCAGAATAAAAA
Found at i:53769318 original size:29 final size:30
Alignment explanation
Indices: 53769267--53769325 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
53769257 GAACTGGATC
* *
53769267 AAATCAAAATTTTATGTATAAAATTACACA
1 AAATCAAAATTTTAAGTACAAAATTACACA
53769297 AAATCAAAA-TTTAAGTACAAAATTACACA
1 AAATCAAAATTTTAAGTACAAAATTACACA
53769326 TTAGGCCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.29
Consensus pattern (30 bp):
AAATCAAAATTTTAAGTACAAAATTACACA
Found at i:53776035 original size:18 final size:18
Alignment explanation
Indices: 53776014--53776056 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
53776004 TCTTGAACTC
53776014 CTTCTTCCTCTGGTTCCT
1 CTTCTTCCTCTGGTTCCT
*
53776032 CTTCTTCCTCTGGTTCTT
1 CTTCTTCCTCTGGTTCCT
53776050 CTTCTTC
1 CTTCTTC
53776057 TTCCTCCGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.00, C:0.37, G:0.09, T:0.53
Consensus pattern (18 bp):
CTTCTTCCTCTGGTTCCT
Found at i:53776506 original size:18 final size:17
Alignment explanation
Indices: 53776475--53776509 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
53776465 ATATAATCTC
*
53776475 AAAAAATAAGTTTAAAT
1 AAAAAATAAATTTAAAT
53776492 AAAAAATAATATTTAAAT
1 AAAAAATAA-ATTTAAAT
53776510 TTAAACGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
AAAAAATAAATTTAAAT
Found at i:53777572 original size:30 final size:30
Alignment explanation
Indices: 53777538--53777600 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
53777528 ACTTATTTTA
53777538 TTGTTAATTTTGTTAATATTTTAAAGGCAT
1 TTGTTAATTTTGTTAATATTTTAAAGGCAT
* *
53777568 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTAATATTTTAAAGGCAT
53777598 TTG
1 TTG
53777601 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.16, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTTAATATTTTAAAGGCAT
Found at i:53777930 original size:31 final size:31
Alignment explanation
Indices: 53777895--53777957 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
53777885 TATTTAAGTA
*
53777895 TAAATATTTATTTTAATGCATTTTCAATTTG
1 TAAATATTTATTTTAATACATTTTCAATTTG
53777926 TAAATATTTATTTTAATACATTTTCAATTTG
1 TAAATATTTATTTTAATACATTTTCAATTTG
53777957 T
1 T
53777958 TAGGAAACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.56
Consensus pattern (31 bp):
TAAATATTTATTTTAATACATTTTCAATTTG
Found at i:53777970 original size:35 final size:31
Alignment explanation
Indices: 53777895--53777978 Score: 105
Period size: 31 Copynumber: 2.6 Consensus size: 31
53777885 TATTTAAGTA
* *
53777895 TAAATATTTATTTTAATGCATTTTCAATTTG
1 TAAACATTTATTTTAATACATTTTCAATTTG
*
53777926 TAAATATTTATTTTAATACATTTTCAATTTG
1 TAAACATTTATTTTAATACATTTTCAATTTG
53777957 TTAGGAAACATTTATTTTAATA
1 -T---AAACATTTATTTTAATA
53777979 TTTTTAGTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
31 30 0.64
32 1 0.02
35 16 0.34
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (31 bp):
TAAACATTTATTTTAATACATTTTCAATTTG
Found at i:53782095 original size:22 final size:20
Alignment explanation
Indices: 53782040--53782103 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 20
53782030 AAAACGGTTG
53782040 TGTTTT-TACTATTTTTTAC
1 TGTTTTCTACTATTTTTTAC
* *
53782059 TGTTTTGCTATTATTTTCTTAT
1 TGTTTT-CTACTATTTT-TTAC
53782081 TGTTTTCTCACTATTTTTCTAC
1 TGTTTTCT-ACTATTTTT-TAC
53782103 T
1 T
53782104 ATTTCACTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
19 6 0.17
21 11 0.31
22 19 0.53
ACGTcount: A:0.14, C:0.14, G:0.06, T:0.66
Consensus pattern (20 bp):
TGTTTTCTACTATTTTTTAC
Found at i:53782825 original size:2 final size:2
Alignment explanation
Indices: 53782820--53782869 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
53782810 AATATATGTT
* *
53782820 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53782862 TA TA TA TA
1 TA TA TA TA
53782870 AAATTATAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53782826 original size:10 final size:10
Alignment explanation
Indices: 53782811--53782860 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
53782801 TATGGATGAA
53782811 ATATATGT-T
1 ATATATGTAT
*
53782820 -TATATATAT
1 ATATATGTAT
*
53782829 ATATATATAT
1 ATATATGTAT
53782839 ATATATGTAT
1 ATATATGTAT
*
53782849 ATATATATAT
1 ATATATGTAT
53782859 AT
1 AT
53782861 CTATATATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
8 6 0.17
9 1 0.03
10 29 0.81
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (10 bp):
ATATATGTAT
Found at i:53782828 original size:12 final size:12
Alignment explanation
Indices: 53782811--53782868 Score: 62
Period size: 12 Copynumber: 4.7 Consensus size: 12
53782801 TATGGATGAA
*
53782811 ATATATGTTTAT
1 ATATATATTTAT
53782823 ATATATATATATAT
1 ATATATAT-T-TAT
*
53782837 ATATATATGTAT
1 ATATATATTTAT
*
53782849 ATATATATATAT
1 ATATATATTTAT
*
53782861 CTATATAT
1 ATATATAT
53782869 AAAATTATAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
12 28 0.70
13 1 0.03
14 11 0.28
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (12 bp):
ATATATATTTAT
Found at i:53783086 original size:21 final size:21
Alignment explanation
Indices: 53783046--53783097 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
53783036 AAAAAAGATC
*
53783046 TTACTGTTTTTTCATATTTTG
1 TTACTGTTTTCTCATATTTTG
53783067 TTACTGTTTTCTCACT-TTTTG
1 TTACTGTTTTCTCA-TATTTTG
**
53783088 CCACTGTTTT
1 TTACTGTTTT
53783098 GCTATCATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.12, C:0.17, G:0.10, T:0.62
Consensus pattern (21 bp):
TTACTGTTTTCTCATATTTTG
Found at i:53783125 original size:22 final size:22
Alignment explanation
Indices: 53783100--53783141 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
53783090 ACTGTTTTGC
*
53783100 TATCATTTCATTATTATGTTAT
1 TATCATTTCACTATTATGTTAT
*
53783122 TATCATTTCACTATTTTGTT
1 TATCATTTCACTATTATGTT
53783142 GTTACGTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.05, T:0.60
Consensus pattern (22 bp):
TATCATTTCACTATTATGTTAT
Found at i:53784549 original size:2 final size:2
Alignment explanation
Indices: 53784542--53784572 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
53784532 GGTGACATCT
53784542 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53784573 TTCGAGATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53790059 original size:24 final size:24
Alignment explanation
Indices: 53790032--53790078 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
53790022 ATGTAATTTT
*
53790032 AAAAATTAAATTA-AATATTTATCA
1 AAAAATTAAAGTATAAT-TTTATCA
53790056 AAAAATTAAAGTATAATTTTATC
1 AAAAATTAAAGTATAATTTTATC
53790079 GTTATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (24 bp):
AAAAATTAAAGTATAATTTTATCA
Found at i:53796483 original size:14 final size:14
Alignment explanation
Indices: 53796464--53796491 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53796454 AAAAGCTAGC
53796464 AATTTCACTAAAAT
1 AATTTCACTAAAAT
53796478 AATTTCACTAAAAT
1 AATTTCACTAAAAT
53796492 TTAAAAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (14 bp):
AATTTCACTAAAAT
Found at i:53802252 original size:31 final size:30
Alignment explanation
Indices: 53802212--53802269 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 30
53802202 TATTCAGTTC
53802212 TTTTTATTTTAGTCACTCAACTATTAATTG
1 TTTTTATTTTAGTCACTCAACTATTAATTG
*
53802242 TTTTTCATTTTAGTTACTCAACTATTAA
1 TTTTT-ATTTTAGTCACTCAACTATTAA
53802270 ATATTAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.28, C:0.14, G:0.05, T:0.53
Consensus pattern (30 bp):
TTTTTATTTTAGTCACTCAACTATTAATTG
Found at i:53804647 original size:21 final size:20
Alignment explanation
Indices: 53804605--53804647 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
53804595 GAAATATTTA
* *
53804605 TTTCAATTTTTTAAATATAT
1 TTTCAATTTTTAAAAAATAT
53804625 TTTCAATTTGTTAAAAAATAT
1 TTTCAATTT-TTAAAAAATAT
53804646 TT
1 TT
53804648 ATTTTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTCAATTTTTAAAAAATAT
Found at i:53813024 original size:4 final size:4
Alignment explanation
Indices: 53813015--53813897 Score: 1766
Period size: 4 Copynumber: 220.8 Consensus size: 4
53813005 TGCGTGTCTG
53813015 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
53813063 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
53813111 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
53813159 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
53813207 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
53813255 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
53813303 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
53813351 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
53813399 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
53813447 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
53813495 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
53813543 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
53813591 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
53813639 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
53813687 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
53813735 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
53813783 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
53813831 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
53813879 TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGT
53813898 TAAAATTGAT
Statistics
Matches: 879, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 879 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:53822125 original size:14 final size:14
Alignment explanation
Indices: 53822106--53822133 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53822096 CCGAGTGGCC
53822106 GAGCACATAAACTA
1 GAGCACATAAACTA
53822120 GAGCACATAAACTA
1 GAGCACATAAACTA
53822134 TTGAATTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.14, T:0.14
Consensus pattern (14 bp):
GAGCACATAAACTA
Found at i:53825555 original size:14 final size:15
Alignment explanation
Indices: 53825535--53825575 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
53825525 TTTATTTTAG
53825535 ATTATATTTTAATAT
1 ATTATATTTTAATAT
*
53825550 -TTATATTTGAA-AT
1 ATTATATTTTAATAT
53825563 ATTATATTTTAAT
1 ATTATATTTTAAT
53825576 TACTTACGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 2 0.09
14 20 0.91
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
ATTATATTTTAATAT
Found at i:53825827 original size:21 final size:19
Alignment explanation
Indices: 53825761--53825828 Score: 50
Period size: 19 Copynumber: 3.5 Consensus size: 19
53825751 TGTTCTTTTA
* *
53825761 ATTTTTTT-CTTCATTTTTC
1 ATTTTTTTACTTC-TTCTCC
53825780 ATTTTTTT-CTTCTTCTCC
1 ATTTTTTTACTTCTTCTCC
* *
53825798 CTCTGTTTTACTGTCTTCTCC
1 AT-TTTTTTACT-TCTTCTCC
53825819 ATTTATTTTA
1 ATTT-TTTTA
53825829 ATGTAGTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 5 0.13
19 17 0.44
20 3 0.08
21 14 0.36
ACGTcount: A:0.10, C:0.22, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTTTTTTACTTCTTCTCC
Found at i:53829328 original size:1 final size:1
Alignment explanation
Indices: 53829322--53829357 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
53829312 AGCTCTTTGC
53829322 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
53829358 CTAGCTGTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:53830504 original size:284 final size:284
Alignment explanation
Indices: 53829990--53830541 Score: 883
Period size: 284 Copynumber: 1.9 Consensus size: 284
53829980 AGAACTCAGA
53829990 TATGTGTTGGCAATTAGTGTTGATTGGCCTAATTAAAAACCTAGATTATGTATCGTGTCAAGGTC
1 TATGTGTTGGCAATTAGTGTTGATTGGCCTAATTAAAAACCTAGATTATGTATCGTGTCAAGGTC
* *
53830055 TATAAGTGGTTACGGCAGTAGATCATGCATTTTTCTTATGATCAATCGATATGTGAGTAAGATGC
66 TATAAGTGGTTACGGCAGTAGATCATGCATTTTTCGTATGACCAATCGATATGTGAGTAAGATGC
* *
53830120 TTGTTGAAAATTTGATCAGTGGACTTATTTAATTGTCGGCCGTTACAACGGCTATAACTATCAGT
131 TTGTTGAAAATTTGATCAGTAGACTTATTTAATTGTCGGCCGTTACAACGGCTATAACTAGCAGT
* * *
53830185 TTAGATTCTTATTCTATGCTTATTCCAACATATCAGGCTTTGTTCGTCATATATT-TTGAGTAAA
196 TTAGATTCTTATTCTATGCTTATTCCAACATATCAGGCTTTGATCGCCATAT-TTGTTAAGTAAA
*
53830249 CAAGGCTAGAATAGGACTTATAGAT
260 CAAGACTAGAATAGGACTTATAGAT
* * ** *
53830274 TATGTGTTGGCAATTAGTGTTGATTGGCCTAATTAAGAACTTAGATTATGTATCGTGTTGAGGTT
1 TATGTGTTGGCAATTAGTGTTGATTGGCCTAATTAAAAACCTAGATTATGTATCGTGTCAAGGTC
* * *
53830339 TATAAGTGGTTATGGCAGTAGATCATGCA-TTTTCGGTATGACCGATTGATATGTGAGTAAGATG
66 TATAAGTGGTTACGGCAGTAGATCATGCATTTTTC-GTATGACCAATCGATATGTGAGTAAGATG
* * *
53830403 CTTGTTGAAAATTTGATCGGTAGACTTATTTAATTGTCGGTCGTTACAACGGCTATAACTAGCGG
130 CTTGTTGAAAATTTGATCAGTAGACTTATTTAATTGTCGGCCGTTACAACGGCTATAACTAGCAG
* *
53830468 TTTAGATTCTTATTCTATGCTTATTCCAATATATCAGGCTTTGATCGCCGTATTTGTTAAGTAAA
195 TTTAGATTCTTATTCTATGCTTATTCCAACATATCAGGCTTTGATCGCCATATTTGTTAAGTAAA
53830533 CAAGACTAG
260 CAAGACTAG
53830542 GATGGGAAAC
Statistics
Matches: 245, Mismatches: 21, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
283 7 0.03
284 238 0.97
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (284 bp):
TATGTGTTGGCAATTAGTGTTGATTGGCCTAATTAAAAACCTAGATTATGTATCGTGTCAAGGTC
TATAAGTGGTTACGGCAGTAGATCATGCATTTTTCGTATGACCAATCGATATGTGAGTAAGATGC
TTGTTGAAAATTTGATCAGTAGACTTATTTAATTGTCGGCCGTTACAACGGCTATAACTAGCAGT
TTAGATTCTTATTCTATGCTTATTCCAACATATCAGGCTTTGATCGCCATATTTGTTAAGTAAAC
AAGACTAGAATAGGACTTATAGAT
Found at i:53846550 original size:32 final size:32
Alignment explanation
Indices: 53846489--53846558 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
53846479 TATTTTAAAA
53846489 AAAATAAATGTATATAAAAAAATTACAAATAT
1 AAAATAAATGTATATAAAAAAATTACAAATAT
* * * *
53846521 CAAATGAATG-ATATTAAATAAATTTCAAATAT
1 AAAATAAATGTATA-TAAAAAAATTACAAATAT
53846553 AAAATA
1 AAAATA
53846559 TTCATATACC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
31 3 0.10
32 28 0.90
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.30
Consensus pattern (32 bp):
AAAATAAATGTATATAAAAAAATTACAAATAT
Found at i:53849343 original size:14 final size:14
Alignment explanation
Indices: 53849326--53849352 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53849316 CAACTAATCA
53849326 ATTTTGATTAATGT
1 ATTTTGATTAATGT
53849340 ATTTTGATTAATG
1 ATTTTGATTAATG
53849353 AATGATAATC
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:0.00, G:0.15, T:0.56
Consensus pattern (14 bp):
ATTTTGATTAATGT
Found at i:53849768 original size:24 final size:25
Alignment explanation
Indices: 53849731--53849777 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
53849721 CTTTTGTAGG
53849731 TTCAACAAAAATTAATACTGACACC
1 TTCAACAAAAATTAATACTGACACC
*
53849756 TTCAA-AAGAATTAATACTGACA
1 TTCAACAAAAATTAATACTGACA
53849778 TATTTAGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.49, C:0.19, G:0.06, T:0.26
Consensus pattern (25 bp):
TTCAACAAAAATTAATACTGACACC
Found at i:53850892 original size:2 final size:2
Alignment explanation
Indices: 53850885--53850910 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53850875 TTGAATTTTA
53850885 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
53850911 TTGAAGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.