Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 162 of 250
Found at i:52088526 original size:12 final size:13
Alignment explanation
Indices: 52088490--52088527 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
52088480 AAATATTTGA
52088490 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
52088503 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
52088517 CTTG-TCTTAAT
1 CTTGTTCTTAAT
52088528 ATTTCAGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:52093527 original size:20 final size:20
Alignment explanation
Indices: 52093502--52093568 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
52093492 GATATAATAT
52093502 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGATATGC
52093522 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
52093542 ACATGATATGTATGAAATGC
1 ACATGATATGTATGATATGC
52093562 ACATGAT
1 ACATGAT
52093569 GAATTTATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:52093529 original size:11 final size:11
Alignment explanation
Indices: 52093513--52093568 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
52093503 CATGATTGAT
52093513 ATGATATGCAC
1 ATGATATGCAC
*
52093524 ATGATATG--T
1 ATGATATGCAC
52093533 ATGATATGCAC
1 ATGATATGCAC
*
52093544 ATGATATG--T
1 ATGATATGCAC
*
52093553 ATGAAATGCAC
1 ATGATATGCAC
52093564 ATGAT
1 ATGAT
52093569 GAATTTATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:52093647 original size:26 final size:26
Alignment explanation
Indices: 52093618--52093712 Score: 156
Period size: 26 Copynumber: 3.7 Consensus size: 26
52093608 GAGGAAGTGC
52093618 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
52093644 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
52093670 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
52093696 AAAAGGG-TTTTGCCCCA
1 AAAAGGGCTTATGCCCCA
52093713 ATTATTAAAG
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
25 9 0.14
26 57 0.86
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:52097840 original size:46 final size:46
Alignment explanation
Indices: 52097680--52097849 Score: 168
Period size: 46 Copynumber: 3.7 Consensus size: 46
52097670 AACCCGCCCC
* * *
52097680 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* * * *
52097726 TAAGTGAACTCGGACTCAACTTAACAAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* * *
52097774 TCA-CGAACTCGGACTCAACTCAACGAGTTCCGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
52097819 TAAGTGAACTCGGACTCAACTCAACGTGTTC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC
52097850 AGATGCTCAA
Statistics
Matches: 98, Mismatches: 17, Indels: 18
0.74 0.13 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 55 0.56
47 26 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:52097855 original size:93 final size:93
Alignment explanation
Indices: 52097685--52097855 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
52097675 GCCCCTAAGT
* * * *
52097685 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTTAA
1 GAACTCGGACTCAACTCAACGAGCTCCGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
52097750 CAAGTTCGGATGCCTAGTTACATTTCAC
66 CAAGTTCAGATGCCTAGTTACATTTCAC
*
52097778 GAACTCGGACTCAACTCAACGAGTTCCGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCCGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
**
52097843 CGTGTTCAGATGC
66 CAAGTTCAGATGC
52097856 TCAACCATCC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCCGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CAAGTTCAGATGCCTAGTTACATTTCAC
Found at i:52100269 original size:15 final size:15
Alignment explanation
Indices: 52100245--52100292 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
52100235 AGGAAACCGA
52100245 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
*
52100260 ATAGAGAAATCC-AG
1 ATAAAGAAATCCAAG
*
52100274 AATAAAGAAACCCAAG
1 -ATAAAGAAATCCAAG
52100290 ATA
1 ATA
52100293 CGATACTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 2 0.07
15 24 0.86
16 2 0.07
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:52103850 original size:40 final size:40
Alignment explanation
Indices: 52103753--52103968 Score: 325
Period size: 39 Copynumber: 5.5 Consensus size: 40
52103743 CGGATGATAA
* *
52103753 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
52103793 CC-GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
52103832 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
52103872 CCGGGCTAGGT-CCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
52103911 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
52103951 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
52103969 TACTTGGTTT
Statistics
Matches: 164, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
39 89 0.54
40 75 0.46
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:52103887 original size:79 final size:80
Alignment explanation
Indices: 52103749--52103968 Score: 333
Period size: 79 Copynumber: 2.8 Consensus size: 80
52103739 TATCCGGATG
* *
52103749 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCC-GGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGC
52103812 ATTTGTGCGAGTTACT
65 ATTTGTGCGAGTTACT
* *
52103828 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAGGT-CCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
52103892 TTTGTGCGAGTTACT
66 TTTGTGCGAGTTACT
* *
52103907 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCC-GGCTAAATCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCCCGAAGG
52103969 TACTTGGTTT
Statistics
Matches: 129, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
78 8 0.06
79 113 0.88
80 8 0.06
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
TTTGTGCGAGTTACT
Found at i:52176766 original size:31 final size:31
Alignment explanation
Indices: 52176728--52176791 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
52176718 CCTTTTCATA
52176728 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
52176759 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
52176790 TT
1 TT
52176792 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:52177036 original size:23 final size:23
Alignment explanation
Indices: 52177006--52177077 Score: 144
Period size: 23 Copynumber: 3.1 Consensus size: 23
52176996 CCTAGCCTCT
52177006 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
52177029 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
52177052 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
52177075 TTT
1 TTT
52177078 TCACTTCCTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:52177150 original size:20 final size:20
Alignment explanation
Indices: 52177127--52177193 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
52177117 TTTATGATAC
52177127 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
52177147 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
52177167 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
52177187 ACCATGT
1 ATCATGT
52177194 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:52177158 original size:11 final size:11
Alignment explanation
Indices: 52177127--52177182 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
52177117 TTTATGATAC
52177127 ATCATGTGCAT
1 ATCATGTGCAT
*
52177138 ATCA--TACAT
1 ATCATGTGCAT
52177147 ATCATGTGCAT
1 ATCATGTGCAT
*
52177158 ATCA--TACAT
1 ATCATGTGCAT
*
52177167 GTCATGTGCAT
1 ATCATGTGCAT
52177178 ATCAT
1 ATCAT
52177183 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:52177262 original size:25 final size:25
Alignment explanation
Indices: 52177230--52177277 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
52177220 ATACATAAAC
* * *
52177230 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
52177255 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
52177278 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:52184691 original size:25 final size:24
Alignment explanation
Indices: 52184649--52184720 Score: 94
Period size: 23 Copynumber: 3.0 Consensus size: 24
52184639 GATTTATCAT
*
52184649 ATAATTGGAGGCCT-AGCCTCTTTTA
1 ATAATTGG-GGCATAAGCC-CTTTTA
52184674 ATAATTGGGGCATAAGCCC-TTTA
1 ATAATTGGGGCATAAGCCCTTTTA
*
52184697 ATAACTGGGGCATAAGCCCTTTTA
1 ATAATTGGGGCATAAGCCCTTTTA
52184721 CACTTCCTAC
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
23 22 0.51
24 9 0.21
25 12 0.28
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (24 bp):
ATAATTGGGGCATAAGCCCTTTTA
Found at i:52184795 original size:20 final size:20
Alignment explanation
Indices: 52184770--52184828 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
52184760 TATGATTACA
52184770 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
*
52184790 TCATGTGCATATCATAAATG
1 TCATGTGCATATCATACATG
52184810 TCATGTGCATATCATACAT
1 TCATGTGCATATCATACAT
52184829 ACCCTGTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
TCATGTGCATATCATACATG
Found at i:52187553 original size:30 final size:31
Alignment explanation
Indices: 52187474--52187556 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
52187464 TTAGTCTCGA
*
52187474 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTAGGCCGAAGCCTTTTCATAAAT
52187504 CATATCACTAGGCCGAAGCCTTTTCATAAAT
1 CATATCACTAGGCCGAAGCCTTTTCATAAAT
*
52187535 CATATCACT-GGTCGAAGCCTTT
1 CATATCACTAGGCCGAAGCCTTT
52187557 ACTGTATGCA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
30 17 0.34
31 33 0.66
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (31 bp):
CATATCACTAGGCCGAAGCCTTTTCATAAAT
Found at i:52187804 original size:25 final size:25
Alignment explanation
Indices: 52187776--52187845 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
52187766 CTCTTTTAAT
*
52187776 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
52187801 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
52187826 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
52187846 AGCACTTCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:52188709 original size:26 final size:26
Alignment explanation
Indices: 52188660--52188709 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
52188650 ATTCGTCATT
*
52188660 TTACCATATAGGGGTATTATGGTCAC
1 TTACCATATAGGGGTATTACGGTCAC
*
52188686 TTACCCTATAGGGGCT-TTACGGTC
1 TTACCATATAGGGG-TATTACGGTC
52188710 TTTTTACCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (26 bp):
TTACCATATAGGGGTATTACGGTCAC
Found at i:52188801 original size:27 final size:27
Alignment explanation
Indices: 52188771--52188856 Score: 95
Period size: 27 Copynumber: 3.1 Consensus size: 27
52188761 GTAAATCTAC
52188771 AAACCAAGGGTATTTC-AGTAATTTTGT
1 AAACCAAGGGTATTTCTA-TAATTTTGT
*
52188798 AAACCAATGGTATTTCTATAATTTT-T
1 AAACCAAGGGTATTTCTATAATTTTGT
* *
52188824 AGAAAGTCAAGGGTATTCCTATAATTTTGT
1 --AAA-CCAAGGGTATTTCTATAATTTTGT
52188854 AAA
1 AAA
52188857 TTAGGGGTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
26 1 0.02
27 22 0.44
28 7 0.14
29 19 0.38
30 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (27 bp):
AAACCAAGGGTATTTCTATAATTTTGT
Found at i:52188965 original size:27 final size:27
Alignment explanation
Indices: 52188935--52188999 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
52188925 GTAATTTCAC
* * *
52188935 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACAGTAATTCTATA
* * *
52188962 AATCGATGGTAAAATAGTGATTCTATA
1 AATCGAGGGTAAAACAGTAATTCTATA
52188989 AATCGAGGGTA
1 AATCGAGGGTA
52189000 CTTTGGTAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAACAGTAATTCTATA
Found at i:52190091 original size:56 final size:57
Alignment explanation
Indices: 52189965--52190113 Score: 219
Period size: 56 Copynumber: 2.6 Consensus size: 57
52189955 CATACAGGGC
* *
52189965 CTTACTCGTACACATATATCGGAATCACATATCGATGATGCCAACGTATTAAATGTGGT
1 CTTACTCGCACACATATATCGGAATCACATATC-A-GATGCCAACGTATTAAACGTGGT
* * *
52190024 CTTACTCGCACACATATATCAGAATCACATATC-GATGCCAATGTTTTAAACGTGGT
1 CTTACTCGCACACATATATCGGAATCACATATCAGATGCCAACGTATTAAACGTGGT
*
52190080 CTTACTTGCACACATATATCGGAATCACATATCA
1 CTTACTCGCACACATATATCGGAATCACATATCA
52190114 CAAGTCGAAG
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
56 51 0.62
59 31 0.38
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (57 bp):
CTTACTCGCACACATATATCGGAATCACATATCAGATGCCAACGTATTAAACGTGGT
Found at i:52210434 original size:40 final size:40
Alignment explanation
Indices: 52210360--52210580 Score: 288
Period size: 40 Copynumber: 5.6 Consensus size: 40
52210350 AACCCAAGTA
* *
52210360 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
52210399 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
52210439 CCTTCGGGACTTAGCCCGGATATAG-CAACTCGCACAAACG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* * * * *
52210479 CCTTCGGGACTTAGCCTGGGTATAGTCAATAGCACAACTA
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
52210519 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAC-CATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
52210558 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
52210581 CATCCGAATA
Statistics
Matches: 158, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 119 0.75
41 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:52210492 original size:80 final size:80
Alignment explanation
Indices: 52210359--52210580 Score: 317
Period size: 80 Copynumber: 2.8 Consensus size: 80
52210349 AAACCCAAGT
* *
52210359 ACCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATA
1 ACCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATA
*
52210423 GTCACTAGCACAA-A
66 GTCAATAGCACAACA
* * *
52210437 AGCCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAACGCCTTCGGGACTTAGCCTGGGTAT
1 A-CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
*
52210502 AGTCAATAGCACAACT
65 AGTCAATAGCACAACA
* *
52210518 ACCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCAC-CATGCCTTCGGGACTTAGCCCGGATAT
1 ACCTTCGGGACTTAGCCCGGATATAG-CAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
52210581 CATCCGAATA
Statistics
Matches: 128, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
78 1 0.01
79 36 0.28
80 89 0.70
81 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (80 bp):
ACCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATA
GTCAATAGCACAACA
Found at i:52214562 original size:53 final size:54
Alignment explanation
Indices: 52214499--52214606 Score: 200
Period size: 53 Copynumber: 2.0 Consensus size: 54
52214489 ATTTATAATG
52214499 TTAGGGTTGGCCATAGTCCTTATCCCTAGTTTGGCTGAC-GTTTTACATTAAAA
1 TTAGGGTTGGCCATAGTCCTTATCCCTAGTTTGGCTGACAGTTTTACATTAAAA
*
52214552 TTAGGGTTGGCCATAGTCCTTATCCCTAGTTTGGCTGACATTTTTACATTAAAA
1 TTAGGGTTGGCCATAGTCCTTATCCCTAGTTTGGCTGACAGTTTTACATTAAAA
52214606 T
1 T
52214607 ACATTGTGCA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 39 0.74
54 14 0.26
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (54 bp):
TTAGGGTTGGCCATAGTCCTTATCCCTAGTTTGGCTGACAGTTTTACATTAAAA
Found at i:52219015 original size:46 final size:45
Alignment explanation
Indices: 52218939--52219067 Score: 152
Period size: 46 Copynumber: 2.8 Consensus size: 45
52218929 CATTAGGTGG
* *
52218939 TATGTGAGCCAGTGTAAGACATGTTTGGGACATGCATCGACCACTT-
1 TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCG-CCA-TTA
* *
52218985 TATGAGAGCCAGTGTAAGACATGTCCGGGACATGCATCGGCATTGA
1 TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGCCATT-A
* * * *
52219031 GACGAGAGCTAGTGTAAGACATGTCTTGGACATGCAT
1 TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCAT
52219068 TAGCCTCGGG
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
44 2 0.03
45 2 0.03
46 68 0.94
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.25
Consensus pattern (45 bp):
TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGCCATTA
Found at i:52219220 original size:49 final size:49
Alignment explanation
Indices: 52219136--52219252 Score: 128
Period size: 49 Copynumber: 2.4 Consensus size: 49
52219126 GTTTGTCAGC
* *
52219136 GTAAGACCTGTCTAGGACATGGCATCGACACCGATAGATGAGAGCTAGT
1 GTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAAAGCTAGT
* * * * *
52219185 GTAAGACCTGTCTGGGACGTGGCATTGGC-CTCGATATATGAAAGTTAGT
1 GTAAGACCTGTCTGGGACATGGCATCGACAC-CGATAGATGAAAGCTAGT
* * *
52219234 GTAACACCTATATGGGACA
1 GTAAGACCTGTCTGGGACA
52219253 CAACATCGAC
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
48 1 0.02
49 55 0.98
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (49 bp):
GTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAAAGCTAGT
Found at i:52220507 original size:20 final size:21
Alignment explanation
Indices: 52220468--52220507 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
52220458 GTCAACAGGG
* *
52220468 CCACACGGGTGTGTTGCCCTT
1 CCACACGGGCGTGATGCCCTT
52220489 CCACACGGGCGT-ATGCCCT
1 CCACACGGGCGTGATGCCCT
52220508 GTTTTAAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.12, C:0.38, G:0.28, T:0.23
Consensus pattern (21 bp):
CCACACGGGCGTGATGCCCTT
Found at i:52221521 original size:15 final size:16
Alignment explanation
Indices: 52221479--52221526 Score: 62
Period size: 15 Copynumber: 2.9 Consensus size: 16
52221469 TAAAATCTTT
52221479 TTTGAATCCCTAACAATC
1 TTTGAATCCCT-A-AATC
*
52221497 TTTAAATCCCTAAATC
1 TTTGAATCCCTAAATC
52221513 -TTGAATCCCTAAAT
1 TTTGAATCCCTAAAT
52221527 AGTTAGCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 13 0.46
16 4 0.14
17 1 0.04
18 10 0.36
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (16 bp):
TTTGAATCCCTAAATC
Found at i:52221639 original size:23 final size:24
Alignment explanation
Indices: 52221598--52221643 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
52221588 CCTATAAAAA
*
52221598 TTAGAAACAAAATCGTGAAATCCC
1 TTAGAAACAAAATCATGAAATCCC
*
52221622 TTAG-AACCAAATCATGAAATCC
1 TTAGAAACAAAATCATGAAATCC
52221644 TTATTCCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.46, C:0.22, G:0.11, T:0.22
Consensus pattern (24 bp):
TTAGAAACAAAATCATGAAATCCC
Found at i:52222635 original size:22 final size:22
Alignment explanation
Indices: 52222605--52222646 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
52222595 TAAGCATATG
*
52222605 ATTTGGATAAATGTAATTTAAA
1 ATTTCGATAAATGTAATTTAAA
*
52222627 ATTTCGATAAATGTACTTTA
1 ATTTCGATAAATGTAATTTA
52222647 CAAAAGCATA
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:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (22 bp):
ATTTCGATAAATGTAATTTAAA
Found at i:52232693 original size:48 final size:45
Alignment explanation
Indices: 52232580--52232750 Score: 168
Period size: 48 Copynumber: 3.6 Consensus size: 45
52232570 AGGTGCCTAT
* *
52232580 GCCATGTCCCAGACATGGTCTTTCACAAGTTCTAGCATATCT-GTGCCGAA
1 GCCATGTCCCAGACATGGTC-TT-AC-A---CTGGCACATCTCGTGCCGAA
* *
52232630 GCCATGTCCCAGACATGGTCTTACGCTGGCACATCTATACGTGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTGGCACATC--T-CGTGCCGAA
* * *
52232678 GCCATATCCCAGACATGGTCTTACACTGACACATCTCGTAGCCGAC
1 GCCATGTCCCAGACATGGTCTTACACTGGCACATCTCGT-GCCGAA
52232724 G-CATGTCCCAGACAT-GTCTTACACTGG
1 GCCATGTCCCAGACATGGTCTTACACTGG
52232751 ATTACATCAC
Statistics
Matches: 106, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
44 19 0.18
45 16 0.15
46 8 0.08
48 41 0.39
49 2 0.02
50 20 0.19
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.25
Consensus pattern (45 bp):
GCCATGTCCCAGACATGGTCTTACACTGGCACATCTCGTGCCGAA
Found at i:52232834 original size:47 final size:47
Alignment explanation
Indices: 52232724--52232846 Score: 151
Period size: 46 Copynumber: 2.6 Consensus size: 47
52232714 CGTAGCCGAC
* *
52232724 GCATGTCCCAGACATGTCTTACACTGGAT-TACATCACAAGGCCAAT
1 GCATGTCCCAGACATGTCTTACACTAGCTCTACATCACAAGGCCAAT
* * * * * *
52232770 GCATGTCCTAGACATGTCTTACACTAGCTCT-CGTCTCAATGTCGAT
1 GCATGTCCCAGACATGTCTTACACTAGCTCTACATCACAAGGCCAAT
52232816 GCCATGTCCCAGACATGTCTTACACTAGCTC
1 G-CATGTCCCAGACATGTCTTACACTAGCTC
52232847 ACAACAAGTG
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
46 37 0.56
47 29 0.44
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (47 bp):
GCATGTCCCAGACATGTCTTACACTAGCTCTACATCACAAGGCCAAT
Found at i:52240393 original size:48 final size:44
Alignment explanation
Indices: 52240326--52240491 Score: 174
Period size: 48 Copynumber: 3.6 Consensus size: 44
52240316 TATCTGTGCT
*
52240326 GATGCCATGTCCCAAACATGGTCTTACATTGACACATCTATACGTTCC
1 GATG-CATGTCCCAGACAT-GTCTTACATTGACACATCTATACG--CC
* *
52240374 GATGCCATGTCCCAGACATGGTCTTACACTGACACATCTGGTA-GCC
1 GATG-CATGTCCCAGACAT-GTCTTACATTGACACATCT-ATACGCC
* *
52240420 GACGCATGTCCCAGACATGTCTTACATTGGCTTACATC-ATAACGCC
1 GATGCATGTCCCAGACATGTCTTACATTGAC--ACATCTAT-ACGCC
*
52240466 GATGCATGTCCTAGACATGTCTTACA
1 GATGCATGTCCCAGACATGTCTTACA
52240492 CTAGCTCTCG
Statistics
Matches: 104, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
44 12 0.12
45 15 0.14
46 37 0.36
48 38 0.37
49 2 0.02
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (44 bp):
GATGCATGTCCCAGACATGTCTTACATTGACACATCTATACGCC
Found at i:52240473 original size:46 final size:47
Alignment explanation
Indices: 52240326--52240587 Score: 176
Period size: 46 Copynumber: 5.6 Consensus size: 47
52240316 TATCTGTGCT
* * *
52240326 GATGCCATGTCCCAAACATGGTCTTACATTGAC--ACATCTATACGTTCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATCTA-ACG--CC
* *
52240374 GATGCCATGTCCCAGACATGGTCTTACACTGAC--ACATCTGGTA-GCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATCT--AACGCC
* *
52240420 GACG-CATGTCCCAGACAT-GTCTTACATTGGCTTACATCATAACGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATC-TAACGCC
* * * *
52240466 GATG-CATGTCCTAGACAT-GTCTTACACTAGCTCT-CGTCTCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCT-TACATCT-AACGCC
* * * *
52240512 GATGTCATGTCCTAGACATGGTCTTACACTAG-TT-C-TCATAATGTGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATC-TAA---CGCC
52240560 GATG-CATGTCCCAGACAT-GTCTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
52240588 AGCTCACAAC
Statistics
Matches: 185, Mismatches: 15, Indels: 30
0.80 0.07 0.13
Matches are distributed among these distances:
44 11 0.06
45 20 0.11
46 66 0.36
47 30 0.16
48 57 0.31
49 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (47 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATCTAACGCC
Found at i:52245100 original size:80 final size:80
Alignment explanation
Indices: 52244967--52245224 Score: 430
Period size: 80 Copynumber: 3.2 Consensus size: 80
52244957 CGAATGATAA
52244967 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
52245032 TGCGAGTTACTATAT
66 TGCGAGTTACTATAT
*
52245047 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
52245112 TGCGAGTTACTATAT
66 TGCGAGTTACTATAT
* * *
52245127 TCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAATCCCGAAGGCATTTG
1 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
*
52245192 AGCGAG-TAGCTATAT
66 TGCGAGTTA-CTATAT
* *
52245207 -CTGGCTAATTCCTGAAGG
1 CCGGGCTAAGTCCTGAAGG
52245225 TACTTGGTTT
Statistics
Matches: 168, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
79 17 0.10
80 151 0.90
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTTACTATAT
Found at i:52245185 original size:120 final size:120
Alignment explanation
Indices: 52244967--52245224 Score: 412
Period size: 120 Copynumber: 2.2 Consensus size: 120
52244957 CGAATGATAA
52244967 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
* * * *
52245032 TGCGAGTTACTATATCCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTA-CTATAT
66 TGCGAGTTACTATAACCGGGCTAAATCCCGAAGGCATTTGAGCGAG-TAGCTATAT
* **
52245087 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATTCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
52245152 TGCGAGTTACTATAACCGGGCTAAATCCCGAAGGCATTTGAGCGAGTAGCTATAT
66 TGCGAGTTACTATAACCGGGCTAAATCCCGAAGGCATTTGAGCGAGTAGCTATAT
* *
52245207 -CTGGCTAATTCCTGAAGG
1 CCGGGCTAAGTCCTGAAGG
52245225 TACTTGGTTT
Statistics
Matches: 127, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
119 17 0.13
120 110 0.87
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (120 bp):
CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTTACTATAACCGGGCTAAATCCCGAAGGCATTTGAGCGAGTAGCTATAT
Found at i:52245205 original size:40 final size:40
Alignment explanation
Indices: 52244963--52245198 Score: 400
Period size: 40 Copynumber: 5.9 Consensus size: 40
52244953 TATTCGAATG
*
52244963 ATAACCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
52245003 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
52245043 ATATCCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
52245083 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
**
52245123 ATATTCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
52245163 ATAACCGGGCTAAATCCCGAAGGCATTTGAGCGAGT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
52245199 AGCTATATCT
Statistics
Matches: 187, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 187 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:52253217 original size:40 final size:40
Alignment explanation
Indices: 52253162--52253498 Score: 579
Period size: 40 Copynumber: 8.4 Consensus size: 40
52253152 GGATGATAAT
*
52253162 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
52253202 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
52253242 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
** *
52253282 ATGGATAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
52253322 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
52253362 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
*
52253402 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
* *
52253442 CGGGCTAAATCCCGAAGGCATTTGAGCGAG-TAGCTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATC
*
52253482 C-GGCTAATTCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
52253499 TACTTGGTTT
Statistics
Matches: 284, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
39 17 0.06
40 267 0.94
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:52257457 original size:28 final size:29
Alignment explanation
Indices: 52257419--52257516 Score: 110
Period size: 29 Copynumber: 3.4 Consensus size: 29
52257409 ACCCCTACAT
* *
52257419 ACATGCATATGGCCCA-CTTGGCCCAA-TC
1 ACATTCATATGGCCCATC-AGGCCCAATTC
* *
52257447 TCATTTATATGGCCCATCAGGCCCAATTC
1 ACATTCATATGGCCCATCAGGCCCAATTC
*
52257476 ACATTCATATGGCCCATCAGGCCCAAATC
1 ACATTCATATGGCCCATCAGGCCCAATTC
* *
52257505 ACCTTTATATGG
1 ACATTCATATGG
52257517 ACCGTTAGGC
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
28 20 0.34
29 39 0.66
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.27
Consensus pattern (29 bp):
ACATTCATATGGCCCATCAGGCCCAATTC
Found at i:52257526 original size:29 final size:29
Alignment explanation
Indices: 52257482--52257542 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
52257472 ATTCACATTC
52257482 ATATGGCCCATCAGGCCCAAATCACCTTT
1 ATATGGCCCATCAGGCCCAAATCACCTTT
* * * * *
52257511 ATATGGACCGTTAGGCCGAAATAACC-TT
1 ATATGGCCCATCAGGCCCAAATCACCTTT
52257539 ATAT
1 ATAT
52257543 TCATGCTCAC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (29 bp):
ATATGGCCCATCAGGCCCAAATCACCTTT
Found at i:52257793 original size:16 final size:16
Alignment explanation
Indices: 52257758--52257794 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
52257748 AAACTTTCAG
* *
52257758 CTTTTCGGTATTTTGG
1 CTTTTCGGTATTTCGA
52257774 CTTTTCGGTATTTCGA
1 CTTTTCGGTATTTCGA
52257790 CTTTT
1 CTTTT
52257795 GCCGATCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.08, C:0.16, G:0.19, T:0.57
Consensus pattern (16 bp):
CTTTTCGGTATTTCGA
Found at i:52264385 original size:29 final size:29
Alignment explanation
Indices: 52264319--52264388 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
52264309 GGCCAAATCT
* * * *
52264319 CATTTATATTGTCCATCAGGCACAATTCA
1 CATTTATATGGCCCATCAGGCACAAATAA
* *
52264348 CATTCATATGGCCCATCAGGCCCAAATAA
1 CATTTATATGGCCCATCAGGCACAAATAA
*
52264377 CCTTTATATGGC
1 CATTTATATGGC
52264389 TCGTTAGGCT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (29 bp):
CATTTATATGGCCCATCAGGCACAAATAA
Found at i:52264646 original size:16 final size:16
Alignment explanation
Indices: 52264625--52264667 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
52264615 GCCGCCAAAC
52264625 TTTCGACTTTTCGGCA
1 TTTCGACTTTTCGGCA
*
52264641 TTTCGACTTTTTGGCA
1 TTTCGACTTTTCGGCA
52264657 TTTCGACTTTT
1 TTTCGACTTTT
52264668 GCCGATCTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.12, C:0.21, G:0.16, T:0.51
Consensus pattern (16 bp):
TTTCGACTTTTCGGCA
Found at i:52265927 original size:16 final size:16
Alignment explanation
Indices: 52265906--52265937 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
52265896 AAATTCAAGA
52265906 TTTCAAGATTTTTGGG
1 TTTCAAGATTTTTGGG
52265922 TTTCAAGATTTTTGGG
1 TTTCAAGATTTTTGGG
52265938 GCGCTACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (16 bp):
TTTCAAGATTTTTGGG
Found at i:52271007 original size:34 final size:34
Alignment explanation
Indices: 52270968--52271033 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
52270958 AGCTCGAGCC
* *
52270968 CAGTGGGCCTAAGCCCTATTCAG-ATAACAGTACA
1 CAGTGGACCGAAGCCCTATTCAGAAT-ACAGTACA
* *
52271002 CAGTGGACCGAAGCCTTTTTCAGAATACAGTA
1 CAGTGGACCGAAGCCCTATTCAGAATACAGTA
52271034 GCAAGGCCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 25 0.93
35 2 0.07
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (34 bp):
CAGTGGACCGAAGCCCTATTCAGAATACAGTACA
Found at i:52274419 original size:11 final size:12
Alignment explanation
Indices: 52274392--52274418 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
52274382 GAAAATAGGG
52274392 TTTTAGCGGCAT
1 TTTTAGCGGCAT
52274404 TTTTAGCGGCAT
1 TTTTAGCGGCAT
52274416 TTT
1 TTT
52274419 ATCAAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (12 bp):
TTTTAGCGGCAT
Found at i:52275440 original size:8 final size:8
Alignment explanation
Indices: 52275427--52275535 Score: 120
Period size: 8 Copynumber: 14.0 Consensus size: 8
52275417 CTCAAAAAAT
52275427 AAAATTTA
1 AAAATTTA
52275435 AAAATTT-
1 AAAATTTA
52275442 AAAATTTA
1 AAAATTTA
52275450 AAAATTTA
1 AAAATTTA
52275458 AAAATTTA
1 AAAATTTA
52275466 AAAATTT-
1 AAAATTTA
52275473 AAAATTTA
1 AAAATTTA
*
52275481 AAAA-TAA
1 AAAATTTA
52275488 AAAATTTAAA
1 AAAATTT--A
*
52275498 AAAAATTA
1 AAAATTTA
52275506 AAAATTT-
1 AAAATTTA
*
52275513 AATATTT-
1 AAAATTTA
*
52275520 AATATTTA
1 AAAATTTA
*
52275528 ATAATTTA
1 AAAATTTA
52275536 GTCCATATTT
Statistics
Matches: 88, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
7 33 0.38
8 48 0.55
10 7 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AAAATTTA
Found at i:52275503 original size:18 final size:18
Alignment explanation
Indices: 52275480--52275514 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
52275470 TTTAAAATTT
52275480 AAAAATAAAAAATTTAAA
1 AAAAATAAAAAATTTAAA
*
52275498 AAAAATTAAAAATTTAA
1 AAAAATAAAAAATTTAA
52275515 TATTTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATAAAAAATTTAAA
Found at i:52275508 original size:6 final size:7
Alignment explanation
Indices: 52275426--52275535 Score: 100
Period size: 7 Copynumber: 15.3 Consensus size: 7
52275416 ACTCAAAAAA
52275426 TAAAATT
1 TAAAATT
52275433 TAAAAATT
1 T-AAAATT
52275441 TAAAATT
1 TAAAATT
52275448 TAAAAATT
1 T-AAAATT
52275456 TAAAAATT
1 T-AAAATT
52275464 TAAAAATT
1 T-AAAATT
52275472 TAAAATT
1 TAAAATT
*
52275479 TAAAAATA
1 T-AAAATT
*
52275487 AAAAATT
1 TAAAATT
52275494 TAAAA--
1 TAAAATT
52275499 -AAAATT
1 TAAAATT
*
52275505 AAAAATT
1 TAAAATT
*
52275512 TAATATT
1 TAAAATT
*
52275519 TAATATT
1 TAAAATT
52275526 TAATAATT
1 TAA-AATT
52275534 TA
1 TA
52275536 GTCCATATTT
Statistics
Matches: 89, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
4 4 0.04
7 45 0.51
8 40 0.45
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
TAAAATT
Found at i:52275534 original size:15 final size:15
Alignment explanation
Indices: 52275426--52275535 Score: 124
Period size: 15 Copynumber: 7.6 Consensus size: 15
52275416 ACTCAAAAAA
52275426 TAAAATTTAAAAATT
1 TAAAATTTAAAAATT
52275441 TAAAATTTAAAAATT
1 TAAAATTTAAAAATT
52275456 TAAAAATTTAAAAATT
1 T-AAAATTTAAAAATT
*
52275472 TAAAATTTAAAAATA
1 TAAAATTTAAAAATT
*
52275487 AAAAATTT-AAAA--
1 TAAAATTTAAAAATT
52275499 -AAAA-TTAAAAATT
1 TAAAATTTAAAAATT
* *
52275512 TAATATTT-AATATT
1 TAAAATTTAAAAATT
52275526 TAATAATTTA
1 TAA-AATTTA
52275536 GTCCATATTT
Statistics
Matches: 82, Mismatches: 5, Indels: 15
0.80 0.05 0.15
Matches are distributed among these distances:
10 2 0.02
11 8 0.10
14 15 0.18
15 42 0.51
16 15 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAAATTTAAAAATT
Found at i:52275605 original size:17 final size:18
Alignment explanation
Indices: 52275585--52275623 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
52275575 AATAAATTTC
52275585 AAAAA-GAGAAAAATAAA
1 AAAAATGAGAAAAATAAA
**
52275602 AAAAATGTTAAAAATAAA
1 AAAAATGAGAAAAATAAA
52275620 AAAA
1 AAAA
52275624 TTTAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (18 bp):
AAAAATGAGAAAAATAAA
Found at i:52275622 original size:26 final size:26
Alignment explanation
Indices: 52275567--52275624 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
52275557 TTTAATATTC
* * *
52275567 AAAATTAAAATAAATTTCAAAAAGAG
1 AAAAATAAAAAAAATTTCAAAAAGAA
*
52275593 AAAAATAAAAAAAATGTT-AAAAATAA
1 AAAAATAAAAAAAAT-TTCAAAAAGAA
52275619 AAAAAT
1 AAAAAT
52275625 TTAAAATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 25 0.93
27 2 0.07
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (26 bp):
AAAAATAAAAAAAATTTCAAAAAGAA
Found at i:52281208 original size:19 final size:19
Alignment explanation
Indices: 52281186--52281226 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
52281176 TTTATTGATA
52281186 TTTTTA-TATTTAATCTAG
1 TTTTTATTATTTAATCTAG
* *
52281204 TTTTTATTATTTATTTTAG
1 TTTTTATTATTTAATCTAG
52281223 TTTT
1 TTTT
52281227 GATTCTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTATTATTTAATCTAG
Found at i:52281497 original size:21 final size:21
Alignment explanation
Indices: 52281471--52281514 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
52281461 TGAATTTCAT
52281471 GACCTTTAGCGGCGTTTGTGG
1 GACCTTTAGCGGCGTTTGTGG
*
52281492 GACCTTTAGCGGCGTTTTTGG
1 GACCTTTAGCGGCGTTTGTGG
52281513 GA
1 GA
52281515 TAAGCGCCGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.36, T:0.34
Consensus pattern (21 bp):
GACCTTTAGCGGCGTTTGTGG
Found at i:52282161 original size:16 final size:16
Alignment explanation
Indices: 52282140--52282185 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
52282130 AAATGTTAAC
52282140 GATTTAGGGATTTCAA
1 GATTTAGGGATTTCAA
* *
52282156 GATTTAAGGATTTGAA
1 GATTTAGGGATTTCAA
52282172 GATTGTTAGGGATT
1 GA-T-TTAGGGATT
52282186 CAATGAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 16 0.64
17 1 0.04
18 8 0.32
ACGTcount: A:0.30, C:0.02, G:0.28, T:0.39
Consensus pattern (16 bp):
GATTTAGGGATTTCAA
Found at i:52290044 original size:18 final size:20
Alignment explanation
Indices: 52290021--52290057 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52290011 AATTATATTC
52290021 ATTTA-TTG-ATTTTTATAT
1 ATTTATTTGTATTTTTATAT
52290039 ATTTATTTGTATTTTTATA
1 ATTTATTTGTATTTTTATA
52290058 AAAATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (20 bp):
ATTTATTTGTATTTTTATAT
Found at i:52296691 original size:53 final size:53
Alignment explanation
Indices: 52296634--52296740 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
52296624 TGATCTTAAA
52296634 CGTACTTTATCTTATTATTGAAATATGCTGTAATGATCTCTTTCCATCTTGTC
1 CGTACTTTATCTTATTATTGAAATATGCTGTAATGATCTCTTTCCATCTTGTC
52296687 CGTACTTTATCTTATTATTGAAATATGCTGTAATGATCTCTTTCCATCTTGTC
1 CGTACTTTATCTTATTATTGAAATATGCTGTAATGATCTCTTTCCATCTTGTC
52296740 C
1 C
52296741 TATCTTTTAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.47
Consensus pattern (53 bp):
CGTACTTTATCTTATTATTGAAATATGCTGTAATGATCTCTTTCCATCTTGTC
Found at i:52303251 original size:18 final size:18
Alignment explanation
Indices: 52303228--52303275 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
52303218 TGCCAGGTGC
*
52303228 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
52303246 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
52303264 GTATCCTAACCC
1 GTATCCTAACCC
52303276 GATTACTCCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.25, C:0.31, G:0.08, T:0.35
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:52307316 original size:20 final size:20
Alignment explanation
Indices: 52307291--52307363 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
52307281 TCTTGTATGT
52307291 ATCAATTAACCTTAAATTTA
1 ATCAATTAACCTTAAATTTA
* * *
52307311 ATCAATTAACCCTAAACCCTAA
1 ATCAATTAACCTTAAA--TTTA
*
52307333 ATCAA-T--CCAT-AATTTA
1 ATCAATTAACCTTAAATTTA
52307349 ATCAATTAACCTTAA
1 ATCAATTAACCTTAA
52307364 TACTCTAAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
16 7 0.17
17 1 0.03
18 2 0.05
19 6 0.15
20 16 0.40
21 1 0.03
22 7 0.17
ACGTcount: A:0.45, C:0.22, G:0.00, T:0.33
Consensus pattern (20 bp):
ATCAATTAACCTTAAATTTA
Found at i:52308312 original size:121 final size:120
Alignment explanation
Indices: 52308120--52308350 Score: 286
Period size: 121 Copynumber: 1.9 Consensus size: 120
52308110 ATAATTTTTT
* * *
52308120 AAAAATTATTTATAACAAATTTTAAAATAATTATCCTTTAAATTAGACAATTTATCTATTAATCA
1 AAAAATCATTTATAACAAATTTTAAAAGAATTATCCTTTAAATTAAACAATTTATCTATTAATCA
* * *
52308185 AATTTTAATA-TCATTTTTAAATAACTTCACAATAACTATTATATATTTTTTCAAA
66 AATTTTAACACTAATTTCT-AATAACTTCACAATAACTATTATATATTTTTTCAAA
* * ** *
52308240 AAAAATCATTTATTAC-AGTTTTCAAAAGAATTATTTTTTAAAATTAAATAATTTATCTATTAAT
1 AAAAATCATTTATAACAAATTTT-AAAAGAATTATCCTTT-AAATTAAACAATTTATCTATTAAT
* * * *
52308304 TAAATTTTAACACTAATTTCTAATCACTTCATAATAATTATTATATA
64 CAAATTTTAACACTAATTTCTAATAACTTCACAATAACTATTATATA
52308351 CTTAAATAAT
Statistics
Matches: 93, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
119 5 0.05
120 27 0.29
121 55 0.59
122 6 0.06
ACGTcount: A:0.45, C:0.10, G:0.01, T:0.45
Consensus pattern (120 bp):
AAAAATCATTTATAACAAATTTTAAAAGAATTATCCTTTAAATTAAACAATTTATCTATTAATCA
AATTTTAACACTAATTTCTAATAACTTCACAATAACTATTATATATTTTTTCAAA
Found at i:52311068 original size:44 final size:45
Alignment explanation
Indices: 52310978--52311106 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
52310968 ACAGAATAGA
*
52310978 AATAAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATAAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* * *
52311024 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
** * * *
52311068 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATAAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
52311107 TAGGATATTG
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
44 36 0.52
45 1 0.01
46 32 0.46
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (45 bp):
AATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:52315696 original size:13 final size:14
Alignment explanation
Indices: 52315668--52315697 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
52315658 ACATCTTAAA
52315668 AATCGAGTTAGTAG
1 AATCGAGTTAGTAG
52315682 AATCGAGTT-GTAG
1 AATCGAGTTAGTAG
52315695 AAT
1 AAT
52315698 TGGGTTGGCA
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:0.37, C:0.07, G:0.27, T:0.30
Consensus pattern (14 bp):
AATCGAGTTAGTAG
Found at i:52317073 original size:18 final size:18
Alignment explanation
Indices: 52317047--52317081 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52317037 CTTAAGGGAT
* *
52317047 TTACCAAATTCTCTAAGA
1 TTACAAAATACTCTAAGA
52317065 TTACAAAATACTCTAAG
1 TTACAAAATACTCTAAG
52317082 GTTATAGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (18 bp):
TTACAAAATACTCTAAGA
Found at i:52318797 original size:17 final size:17
Alignment explanation
Indices: 52318768--52318800 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
52318758 ACTCATTTAA
52318768 ACACAGTTCCAAATCAT
1 ACACAGTTCCAAATCAT
52318785 ACACATGTT-CAAATCA
1 ACACA-GTTCCAAATCA
52318801 ATTTACGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.42, C:0.27, G:0.06, T:0.24
Consensus pattern (17 bp):
ACACAGTTCCAAATCAT
Found at i:52323019 original size:15 final size:14
Alignment explanation
Indices: 52323001--52323038 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
52322991 CCTATCTTAT
52323001 TTCCTTCTTTCTTTC
1 TTCCTTCTTTC-TTC
52323016 TTCCTTCCTTTCTTC
1 TTCCTT-CTTTCTTC
52323031 TT-CTTCTT
1 TTCCTTCTT
52323039 GCTATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.14
14 3 0.14
15 11 0.50
16 5 0.23
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (14 bp):
TTCCTTCTTTCTTC
Found at i:52336254 original size:34 final size:34
Alignment explanation
Indices: 52336211--52336278 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
52336201 TGTACTAATG
52336211 TACTTGAAGATTTGAACTATGGAACGGGTTATCA
1 TACTTGAAGATTTGAACTATGGAACGGGTTATCA
52336245 TACTTGAAGATTTGAACTATGGAACGGGTTATCA
1 TACTTGAAGATTTGAACTATGGAACGGGTTATCA
52336279 ATCATTCTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (34 bp):
TACTTGAAGATTTGAACTATGGAACGGGTTATCA
Found at i:52337140 original size:232 final size:234
Alignment explanation
Indices: 52336795--52337242 Score: 584
Period size: 232 Copynumber: 1.9 Consensus size: 234
52336785 TAACCGTCAA
* * *
52336795 TAAACCTCACAGCAGCTAGGAAGCTCACTCGAATTAAGTAATTCAATTGAACTTCAAAACAAAAG
1 TAAACCTCACAG-AGCTAGGAAGCTCACTCAAATGAAGTAATTCAATTGAACTTCAAAAAAAAAG
* * * * * *
52336860 ACTAAAACCTGCATAGTTTCTTGTACAGATACCTTAATTCAACCAAATTTC-TAGAACCTCACAT
65 ACGAAAACCTACAAAGTTTCTTGTACACATACCCTAATTCAACCAAATTTCAT-GAAACTCACAT
* * *
52336924 CTAATTACGAACTAACTTCCTCTAAGAAAGC-GATTTCAT-G-AAAGAGGTTTATGACGCCCTAT
129 CTAATTACGAACTAACTTCCTCTAAGAAAGCAAATTT-ATAGAAAAGAGGTTCATGACACCCTAT
*
52336986 TAAAACCCAAAATCCTAAGGAAAGAAAAGGCTTAAGTGCAAG
193 TAAAACCCAAAATACTAAGGAAAGAAAAGGCTTAAGTGCAAG
*
52337028 TAAACCTCACAG-GCTAGGAAGCTCGCTCAAATGAAGTAATTCAATTGAACTTTCAAAAAACAAA
1 TAAACCTCACAGAGCTAGGAAGCTCACTCAAATGAAGTAATTCAATTGAAC-TTCAAAAAA-AAA
* * * *
52337092 TACGGAAACTTACAAAG-TTCTTGTACACATACCCTAATTCAACCAAATTTCATGAAACTCGCAT
64 GACGAAAACCTACAAAGTTTCTTGTACACATACCCTAATTCAACCAAATTTCATGAAACTCACAT
* * ** * *
52337156 CTAATTAGGAACTAGCTTCCTCTGGGAAAGCAAATTTATAGAAAAGAGGTTCATGATACCCTTTT
129 CTAATTACGAACTAACTTCCTCTAAGAAAGCAAATTTATAGAAAAGAGGTTCATGACACCCTATT
*
52337221 AAAACCTAAAATACTAAGGAAA
194 AAAACCCAAAATACTAAGGAAA
52337243 CACAGAAAAA
Statistics
Matches: 184, Mismatches: 25, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
231 35 0.19
232 78 0.42
233 32 0.17
234 39 0.21
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (234 bp):
TAAACCTCACAGAGCTAGGAAGCTCACTCAAATGAAGTAATTCAATTGAACTTCAAAAAAAAAGA
CGAAAACCTACAAAGTTTCTTGTACACATACCCTAATTCAACCAAATTTCATGAAACTCACATCT
AATTACGAACTAACTTCCTCTAAGAAAGCAAATTTATAGAAAAGAGGTTCATGACACCCTATTAA
AACCCAAAATACTAAGGAAAGAAAAGGCTTAAGTGCAAG
Found at i:52338522 original size:168 final size:168
Alignment explanation
Indices: 52338235--52338539 Score: 533
Period size: 168 Copynumber: 1.8 Consensus size: 168
52338225 ACTTAATGAA
*
52338235 TTAACAATTACCGTTTCGTAAGGATCAAAATTTTAAAATTTGAAAAGTACAGGGACTAAATATAA
1 TTAAAAATTACCGTTTCGTAAGGATCAAAATTTTAAAATTTGAAAAGTACAGGGACTAAATATAA
52338300 CCAAATTAAAGTAGAGAAATAAAATCAATAACTTTTGCAAAGTATAGAGACTGTGGTAGAGTTTA
66 CCAAATTAAAGTAGAGAAATAAAATCAATAACTTTTGCAAAGTATAGAGACTGTGGTAGAGTTTA
52338365 ACCTTTTACATATTATAATATGCTTGACGTATCAAATT
131 ACCTTTTACATATTATAATATGCTTGACGTATCAAATT
52338403 TTAAAAATTACCGTTT-GATAAGGATCAAAATTTT-AAATTCTGAAAAGTACAGGGACTAAATAT
1 TTAAAAATTACCGTTTCG-TAAGGATCAAAATTTTAAAATT-TGAAAAGTACAGGGACTAAATAT
* * * *
52338466 AACCAAATTGAAGTAGAGAGATTAAATCAATAACTTTTGCAAAGTATAGGGACTGTGGTAGAGTT
64 AACCAAATTAAAGTAGAGAAATAAAATCAATAACTTTTGCAAAGTATAGAGACTGTGGTAGAGTT
52338531 TAACCTTTT
129 TAACCTTTT
52338540 CTTTTATATT
Statistics
Matches: 130, Mismatches: 5, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
167 6 0.05
168 124 0.95
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (168 bp):
TTAAAAATTACCGTTTCGTAAGGATCAAAATTTTAAAATTTGAAAAGTACAGGGACTAAATATAA
CCAAATTAAAGTAGAGAAATAAAATCAATAACTTTTGCAAAGTATAGAGACTGTGGTAGAGTTTA
ACCTTTTACATATTATAATATGCTTGACGTATCAAATT
Found at i:52340010 original size:28 final size:26
Alignment explanation
Indices: 52339979--52340040 Score: 83
Period size: 24 Copynumber: 2.4 Consensus size: 26
52339969 TAAAATTTTG
52339979 ATTAAATATTTATTGGTAGAAAAAACTA
1 ATTAAATATTT-TTGGTAG-AAAAACTA
52340007 ATTAAATA--TTTGGTAGAAAAACTA
1 ATTAAATATTTTTGGTAGAAAAACTA
*
52340031 ATTAACTATT
1 ATTAAATATT
52340041 AAATGCGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 15 0.48
25 7 0.23
26 1 0.03
28 8 0.26
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.37
Consensus pattern (26 bp):
ATTAAATATTTTTGGTAGAAAAACTA
Found at i:52340026 original size:24 final size:25
Alignment explanation
Indices: 52339991--52340040 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
52339981 TAAATATTTA
52339991 TTGGTAGAAAAAACTAATTAAATAT
1 TTGGTAGAAAAAACTAATTAAATAT
*
52340016 TTGGTAG-AAAAACTAATTAACTAT
1 TTGGTAGAAAAAACTAATTAAATAT
52340040 T
1 T
52340041 AAATGCGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.34
Consensus pattern (25 bp):
TTGGTAGAAAAAACTAATTAAATAT
Found at i:52342434 original size:47 final size:48
Alignment explanation
Indices: 52342361--52342625 Score: 246
Period size: 47 Copynumber: 5.7 Consensus size: 48
52342351 AAGGTGACCA
* *
52342361 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-ATCTCAAGTCG
1 ATGCCATGTCCTAGACATGGTCTTACACTGGCTCATCATCTCAAGCCG
* * *
52342408 ATGCCATGTCCTAGACATGGTTTTACACTGACT-ATCATCTCGTAGCCG
1 ATGCCATGTCCTAGACATGGTCTTACACTGGCTCATCATCTC-AAGCCG
* * * * *
52342456 ATG-CATGTCCCAGACAT-GTCTTACACTGGCTTA-CGTCTCGAGGCAG
1 ATGCCATGTCCTAGACATGGTCTTACACTGGCTCATCATCTC-AAGCCG
* * *
52342502 ATG-CATGTCCTAGACAT-GTCTTACACTAGCAC-TCGTCTCAATGCCG
1 ATGCCATGTCCTAGACATGGTCTTACACTGGCTCATCATCTCAA-GCCG
* * * ***
52342548 ATACCATGTCCTAGACATGGTCTTACACTAGCTC-TCATAATGTGGCCG
1 ATGCCATGTCCTAGACATGGTCTTACACTGGCTCATCAT-CTCAAGCCG
52342596 ATG-CATGTCCTAGACAT-GTCTTACACTGGC
1 ATGCCATGTCCTAGACATGGTCTTACACTGGC
52342626 AAAAAATAAC
Statistics
Matches: 183, Mismatches: 27, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
45 1 0.01
46 74 0.40
47 77 0.42
48 30 0.16
49 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (48 bp):
ATGCCATGTCCTAGACATGGTCTTACACTGGCTCATCATCTCAAGCCG
Found at i:52342617 original size:140 final size:140
Alignment explanation
Indices: 52342365--52342625 Score: 359
Period size: 140 Copynumber: 1.9 Consensus size: 140
52342355 TGACCAATGC
* * * * *
52342365 CATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAAGTCGATGCCATGTCCTAGACATGGTT
1 CATGTCCCAGACATGGTCTTACACTAGCACATATCTCAAGCCGATACCATGTCCTAGACATGGTC
*
52342430 TTACACTGACTATCATCTCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTC
66 TTACACTGACTATCATATCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTC
52342495 GAGGCAGATG
131 GAGGCAGATG
* *
52342505 CATGTCCTAGACAT-GTCTTACACTAGCAC-TCGTCTCAATGCCGATACCATGTCCTAGACATGG
1 CATGTCCCAGACATGGTCTTACACTAGCACAT-ATCTCAA-GCCGATACCATGTCCTAGACATGG
* * *
52342568 TCTTACACT-AGCTCTCATAAT-GTGGCCGATGCATGTCCTAGACATGTCTTACACTGGC
64 TCTTACACTGA-CTATCAT-ATCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGC
52342626 AAAAAATAAC
Statistics
Matches: 106, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
138 1 0.01
139 20 0.19
140 84 0.79
141 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (140 bp):
CATGTCCCAGACATGGTCTTACACTAGCACATATCTCAAGCCGATACCATGTCCTAGACATGGTC
TTACACTGACTATCATATCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTC
GAGGCAGATG
Found at i:52352769 original size:21 final size:20
Alignment explanation
Indices: 52352702--52352770 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
52352692 TATAATGATT
*
52352702 ATTATAATGGTTTTATATTAA
1 ATTATTATGGTTTTATATT-A
**
52352723 ATTATTATAATTATTA-ATTA
1 ATTATTATGGTT-TTATATTA
*
52352743 A-CATTATGGTTTTATATTA
1 ATTATTATGGTTTTATATTA
52352762 GATTATTAT
1 -ATTATTAT
52352771 TATTAGCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 11 0.30
20 3 0.08
21 17 0.46
22 3 0.08
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.54
Consensus pattern (20 bp):
ATTATTATGGTTTTATATTA
Found at i:52352783 original size:15 final size:14
Alignment explanation
Indices: 52352757--52352787 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
52352747 TATGGTTTTA
52352757 TATTAGATTATTAT
1 TATTAGATTATTAT
52352771 TATTAGCATTATTAT
1 TATTAG-ATTATTAT
52352786 TA
1 TA
52352788 AATAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTAGATTATTAT
Found at i:52360393 original size:26 final size:26
Alignment explanation
Indices: 52360303--52360401 Score: 128
Period size: 26 Copynumber: 3.8 Consensus size: 26
52360293 TCCCCATTTT
52360303 AGATAGTCCTGACGGACTTCCACAAA
1 AGATAGTCCTGACGGACTTCCACAAA
* * * * *
52360329 GGATAGTCCTCAC-AAGCTTCTACCAA
1 AGATAGTCCTGACGGA-CTTCCACAAA
52360355 AGATAGTCCTGACGGACTTCCACAAA
1 AGATAGTCCTGACGGACTTCCACAAA
*
52360381 AGATAGTCTTGACGGACTTCC
1 AGATAGTCCTGACGGACTTCC
52360402 CACATTATAG
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
25 1 0.02
26 58 0.97
27 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.22
Consensus pattern (26 bp):
AGATAGTCCTGACGGACTTCCACAAA
Found at i:52361324 original size:23 final size:23
Alignment explanation
Indices: 52361272--52361317 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
52361262 ACAAGATTTC
52361272 CAATTTCTAAGACTTAGATCTTA
1 CAATTTCTAAGACTTAGATCTTA
52361295 CAATTTCTAAGACTTAGATCTTA
1 CAATTTCTAAGACTTAGATCTTA
52361318 GTCTTTCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (23 bp):
CAATTTCTAAGACTTAGATCTTA
Found at i:52364192 original size:46 final size:46
Alignment explanation
Indices: 52364132--52364397 Score: 307
Period size: 46 Copynumber: 6.0 Consensus size: 46
52364122 TTTGACGTGA
* * * * * *
52364132 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * **
52364178 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACCT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
52364224 TGCCATTGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
52364270 TTCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
52364316 TGCCATGATATCTTTCAACCATGGTCTTACACA---C--AT---GT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
52364354 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
52364398 AGAGCACACT
Statistics
Matches: 191, Mismatches: 20, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
38 34 0.18
41 3 0.02
43 3 0.02
45 4 0.02
46 147 0.77
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:52364366 original size:38 final size:38
Alignment explanation
Indices: 52364314--52364386 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
52364304 CTCATATCAG
52364314 GTTGCCATGATATCTTTCAACCATGGTCTTACACACAT
1 GTTGCCATGATATCTTTCAACCATGGTCTTACACACAT
*
52364352 GTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 GTTGCCATGATATCTTTCAACCATGGTCTTACACA
52364387 TTTCATATCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (38 bp):
GTTGCCATGATATCTTTCAACCATGGTCTTACACACAT
Found at i:52368034 original size:28 final size:28
Alignment explanation
Indices: 52368002--52368063 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
52367992 ATTTACTAGA
*
52368002 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
52368030 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
52368058 ATACCC
1 ATACCC
52368064 TTAGGGTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:52368231 original size:27 final size:27
Alignment explanation
Indices: 52368172--52368261 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 27
52368162 ACGAAGCGTC
52368172 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* * *
52368200 TTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
52368227 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
52368256 CTGGTG
1 CTGGTG
52368262 ACTCTGTCAC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 22 0.42
28 24 0.45
29 7 0.13
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:52368272 original size:29 final size:28
Alignment explanation
Indices: 52368182--52368272 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 28
52368172 CTGGTGGCTA
* * * *
52368182 TGCCACAAATTATCTGTTTTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
* *
52368210 TGCCAC-ATATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
52368237 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
52368266 TGTCACA
1 TGCCACA
52368273 TTTTCTGTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
27 23 0.43
28 15 0.28
29 15 0.28
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:52368280 original size:55 final size:56
Alignment explanation
Indices: 52368172--52368286 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
52368162 ACGAAGCGTC
* * *
52368172 CTGGTGGCTATGCCACAAATTATCTGTTTTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
52368227 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
52368283 CTGG
1 CTGG
52368287 ATGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.59
56 20 0.39
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:52375860 original size:28 final size:28
Alignment explanation
Indices: 52375829--52375890 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
52375819 GATTACTAGA
*
52375829 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
52375857 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
52375885 ATACCC
1 ATACCC
52375891 TAGGGTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:52376056 original size:27 final size:27
Alignment explanation
Indices: 52375998--52376087 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 27
52375988 AGGAAGCGTC
52375998 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
52376026 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
52376053 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
52376082 CTGGTG
1 CTGGTG
52376088 ACTCTGTCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.42
28 25 0.45
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:52376106 original size:55 final size:56
Alignment explanation
Indices: 52375998--52376112 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 56
52375988 AGGAAGCGTC
* *
52375998 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
52376053 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
52376109 CTGG
1 CTGG
52376113 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.58
56 21 0.40
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:52381641 original size:342 final size:342
Alignment explanation
Indices: 52381016--52381701 Score: 1363
Period size: 342 Copynumber: 2.0 Consensus size: 342
52381006 TTTAGCAACT
52381016 ACTAGTACTATAATTGATGTTGGTACAGGTGAACTCACACTTCGTGTGGGTGAGGAAACAATCAC
1 ACTAGTACTATAATTGATGTTGGTACAGGTGAACTCACACTTCGTGTGGGTGAGGAAACAATCAC
52381081 TCTTCAAGCTTGAAATTTTACTAATGTTGATCATGTGGTGCAACCTTCCTTGCAGGAAATACGTT
66 TCTTCAAGCTTGAAATTTTACTAATGTTGATCATGTGGTGCAACCTTCCTTGCAGGAAATACGTT
52381146 CGAAAAGCATACATAAGTCTTGTTCAAATGACAATAAAGAACCCATCTATGAAGAACGAAGGCTA
131 CGAAAAGCATACATAAGTCTTGTTCAAATGACAATAAAGAACCCATCTATGAAGAACGAAGGCTA
52381211 CAAGTCGAGGAACTAGATGAATGGCGGACACAGAAACTGAGAGCACACGATAGACCAAAACCACC
196 CAAGTCGAGGAACTAGATGAATGGCGGACACAGAAACTGAGAGCACACGATAGACCAAAACCACC
52381276 CCATGACGAGCTCAATATTTCACCAAAACAACTTAAGGTTGGAGACAAAGTACTATTAGATGCAG
261 CCATGACGAGCTCAATATTTCACCAAAACAACTTAAGGTTGGAGACAAAGTACTATTAGATGCAG
52381341 CAGACCCTCGGATTGCC
326 CAGACCCTCGGATTGCC
52381358 ACTAGTACTATAATTGATGTTGGTACAGGTGAACTCACACTTCGTGTGGGTGAGGAAACAATCAC
1 ACTAGTACTATAATTGATGTTGGTACAGGTGAACTCACACTTCGTGTGGGTGAGGAAACAATCAC
52381423 TCTTCAAGCTTGAAATTTTACTAATGTTGATCATGTGGTGCAACCTTCCTTGCAGGAAATACGTT
66 TCTTCAAGCTTGAAATTTTACTAATGTTGATCATGTGGTGCAACCTTCCTTGCAGGAAATACGTT
52381488 CGAAAAGCATACATAAGTCTTGTTCAAATGACAATAAAGAACCCATCTATGAAGAACGAAGGCTA
131 CGAAAAGCATACATAAGTCTTGTTCAAATGACAATAAAGAACCCATCTATGAAGAACGAAGGCTA
*
52381553 CAAGTCGAGGAACTAGATGAATGGCGGACACAGAAACTGAGAGCACACGATAGCCCAAAACCACC
196 CAAGTCGAGGAACTAGATGAATGGCGGACACAGAAACTGAGAGCACACGATAGACCAAAACCACC
52381618 CCATGACGAGCTCAATATTTCACCAAAACAACTTAAGGTTGGAGACAAAGTACTATTAGATGCAG
261 CCATGACGAGCTCAATATTTCACCAAAACAACTTAAGGTTGGAGACAAAGTACTATTAGATGCAG
52381683 CAGACCCTCGGATTGCC
326 CAGACCCTCGGATTGCC
52381700 AC
1 AC
52381702 CTCTGAACCT
Statistics
Matches: 343, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
342 343 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (342 bp):
ACTAGTACTATAATTGATGTTGGTACAGGTGAACTCACACTTCGTGTGGGTGAGGAAACAATCAC
TCTTCAAGCTTGAAATTTTACTAATGTTGATCATGTGGTGCAACCTTCCTTGCAGGAAATACGTT
CGAAAAGCATACATAAGTCTTGTTCAAATGACAATAAAGAACCCATCTATGAAGAACGAAGGCTA
CAAGTCGAGGAACTAGATGAATGGCGGACACAGAAACTGAGAGCACACGATAGACCAAAACCACC
CCATGACGAGCTCAATATTTCACCAAAACAACTTAAGGTTGGAGACAAAGTACTATTAGATGCAG
CAGACCCTCGGATTGCC
Found at i:52384294 original size:25 final size:26
Alignment explanation
Indices: 52384259--52384316 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
52384249 CACTTTTATC
52384259 TTTA-TTTATCTTC-TTTAAGTACT-T
1 TTTATTTTATCTTCATTTAA-TACTAT
52384283 TTTATTTTATCTTCATTTAATACTAT
1 TTTATTTTATCTTCATTTAATACTAT
*
52384309 TTCATTTT
1 TTTATTTT
52384317 TAGGTTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 4 0.13
25 13 0.43
26 13 0.43
ACGTcount: A:0.22, C:0.12, G:0.02, T:0.64
Consensus pattern (26 bp):
TTTATTTTATCTTCATTTAATACTAT
Found at i:52386402 original size:13 final size:13
Alignment explanation
Indices: 52386384--52386410 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52386374 GAAGAAATCG
52386384 CATACGGGCATGT
1 CATACGGGCATGT
52386397 CATACGGGCATGT
1 CATACGGGCATGT
52386410 C
1 C
52386411 CTTGTTGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (13 bp):
CATACGGGCATGT
Found at i:52393905 original size:47 final size:47
Alignment explanation
Indices: 52393850--52393980 Score: 172
Period size: 47 Copynumber: 2.8 Consensus size: 47
52393840 CTCAACTGAA
*
52393850 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCCG
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCG
* * * * *
52393897 GAGTACCTATACCATGGCTCGTAGCCAAATCAAGGTAACTCCTCTCT
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCG
* * **
52393944 AAATACCTATACCATGACCCGTATTCAAATCAAGGTA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
52393981 TTATTTGCAC
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (47 bp):
AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCG
Found at i:52400326 original size:21 final size:22
Alignment explanation
Indices: 52400300--52400340 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
52400290 ATCTGATGTC
52400300 GCAATA-AGATT-TGAATTTGAG
1 GCAATACAGATTATG-ATTTGAG
52400321 GCAATACAGATTATGATTTG
1 GCAATACAGATTATGATTTG
52400341 GTTATCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 10 0.56
23 2 0.11
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (22 bp):
GCAATACAGATTATGATTTGAG
Found at i:52408466 original size:23 final size:23
Alignment explanation
Indices: 52408440--52408486 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
52408430 CATTCTATTG
*
52408440 TCATACCCATGCCATTACTATGC
1 TCATACCCATGCCATTACCATGC
* * *
52408463 TCATTCTCATGCTATTACCATGC
1 TCATACCCATGCCATTACCATGC
52408486 T
1 T
52408487 AATGTCACGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.32, G:0.09, T:0.36
Consensus pattern (23 bp):
TCATACCCATGCCATTACCATGC
Found at i:52409865 original size:23 final size:23
Alignment explanation
Indices: 52409814--52409866 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
52409804 ATGATGATGT
*
52409814 TTAA-TTTTATTTTATCTTTATT
1 TTAATTTTTATTTTATCTTTATA
* * *
52409836 TTTATTTTTATTTTATGTTTGTA
1 TTAATTTTTATTTTATCTTTATA
52409859 TTAATTTT
1 TTAATTTT
52409867 ACCTTTAACT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.74
Consensus pattern (23 bp):
TTAATTTTTATTTTATCTTTATA
Found at i:52416511 original size:48 final size:49
Alignment explanation
Indices: 52416421--52416548 Score: 134
Period size: 48 Copynumber: 2.6 Consensus size: 49
52416411 ATTAAAGTCG
* * * *
52416421 ATGCCGTGTCCCAGACGGGTCTTACATTGACTTTCATATATCGAG-GCCA
1 ATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCG-GTGCCA
* * ***
52416470 ATGCCATGT-CCAGACAGGTCTTACACTGGCTCTCATCTATCGGTGTTG
1 ATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCGGTGCCA
* *
52416518 ATGCCATGTCCCAGATAGGTCTTAAACTGAC
1 ATGCCATGTCCCAGACAGGTCTTACACTGAC
52416549 ACACAACAAG
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
47 1 0.02
48 38 0.58
49 26 0.40
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.29
Consensus pattern (49 bp):
ATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCGGTGCCA
Found at i:52416638 original size:48 final size:49
Alignment explanation
Indices: 52416567--52416730 Score: 160
Period size: 49 Copynumber: 3.4 Consensus size: 49
52416557 AGCTGACACT
* * *
52416567 ATGTCCCA-AGCAGGTCTTACACTAGCT-TGTAT-ATCCCGAGGCCGATGC
1 ATGTCCCAGA-CATGTCTTACACTAGCTCT-CATCATCCCAAGGCCGATGC
* * * *
52416615 ATGTCTCAGACATGTCTTACACTAGCTCTCATCGTCTCAATGCCGATGC
1 ATGTCCCAGACATGTCTTACACTAGCTCTCATCATCCCAAGGCCGATGC
* * ** *
52416664 ATGTCCCAGACATGTCTTACACTGGCTCTCATAAT---GTGGCTGATGC
1 ATGTCCCAGACATGTCTTACACTAGCTCTCATCATCCCAAGGCCGATGC
52416710 ATGTCCCAGACATGTCTTACA
1 ATGTCCCAGACATGTCTTACA
52416731 TTGGCTCACA
Statistics
Matches: 98, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
46 28 0.29
48 25 0.26
49 45 0.46
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (49 bp):
ATGTCCCAGACATGTCTTACACTAGCTCTCATCATCCCAAGGCCGATGC
Found at i:52416726 original size:46 final size:47
Alignment explanation
Indices: 52416605--52416742 Score: 170
Period size: 49 Copynumber: 2.9 Consensus size: 47
52416595 GTATATCCCG
* * **
52416605 AGGCCGATGCATGTCTCAGACATGTCTTACACTAGCTCTCATCGTCT
1 AGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAATCT
* *
52416652 CAATGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAATGT
1 --AGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAATCT
* * *
52416701 -GGCTGATGCATGTCCCAGACATGTCTTACATTGGCTCACATA
1 AGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATA
52416743 CCACCCAATG
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
46 38 0.48
49 41 0.52
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (47 bp):
AGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAATCT
Found at i:52419150 original size:17 final size:16
Alignment explanation
Indices: 52419123--52419157 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
52419113 TTACAATCAA
52419123 ACAAAACGTATATTCC
1 ACAAAACGTATATTCC
52419139 ACAAATACGTATATTCC
1 ACAAA-ACGTATATTCC
52419156 AC
1 AC
52419158 TTATTCTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.43, C:0.26, G:0.06, T:0.26
Consensus pattern (16 bp):
ACAAAACGTATATTCC
Found at i:52423203 original size:15 final size:14
Alignment explanation
Indices: 52423175--52423218 Score: 65
Period size: 13 Copynumber: 3.2 Consensus size: 14
52423165 ATTAATATTA
52423175 TTACAAAG-AAAGT
1 TTACAAAGAAAAGT
52423188 TTACAAATGAAAAGT
1 TTACAAA-GAAAAGT
52423203 TTAC-AAGAAAAGT
1 TTACAAAGAAAAGT
52423216 TTA
1 TTA
52423219 AAAAAAGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 17 0.59
14 3 0.10
15 9 0.31
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.27
Consensus pattern (14 bp):
TTACAAAGAAAAGT
Found at i:52424093 original size:22 final size:21
Alignment explanation
Indices: 52424065--52424109 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
52424055 TAATATAGTA
* *
52424065 TTAATAATTGCAGGAAAATCTT
1 TTAATAATTGAAAGAAAAT-TT
52424087 TTAATAATTGAAAGAAAATTT
1 TTAATAATTGAAAGAAAATTT
52424108 TT
1 TT
52424110 GAACTACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.40
Consensus pattern (21 bp):
TTAATAATTGAAAGAAAATTT
Found at i:52427195 original size:23 final size:23
Alignment explanation
Indices: 52427169--52427733 Score: 243
Period size: 23 Copynumber: 24.5 Consensus size: 23
52427159 TTTCAGCAAC
*
52427169 TAAACAATTCAATTTACAACATT
1 TAAACACTTCAATTTACAACATT
*
52427192 TAAACACTTCAATTTACAGCATT
1 TAAACACTTCAATTTACAACATT
* * * *
52427215 TTAACGCTTCAATTCACATCATT
1 TAAACACTTCAATTTACAACATT
* *
52427238 TAAACGCTTCAATTTGCAACACTT
1 TAAACACTTCAATTTACAACA-TT
* *
52427262 T-AGCACTTCAATTTACAGCATT
1 TAAACACTTCAATTTACAACATT
* *
52427284 T-AACACTTCAATTTGCAGCACTT
1 TAAACACTTCAATTTACAACA-TT
*
52427307 T-AACA-TCTCAATTAACAACATT
1 TAAACACT-TCAATTTACAACATT
* * * *
52427329 TATACACCTCAA-TTATAGCGA-T
1 TAAACACTTCAATTTACAAC-ATT
* * * **
52427351 AAAACA-TCTCAATTTCCAGCAAC
1 TAAACACT-TCAATTTACAACATT
* * *
52427374 TAAACAATTCAACTTGCAGTAC-TT
1 TAAACACTTCAATTTACA--ACATT
* *
52427398 AAAACACTTCAATTTATAACATT
1 TAAACACTTCAATTTACAACATT
* *
52427421 TAAACACTTCAATTTGCAGCACTT
1 TAAACACTTCAATTTACAACA-TT
*
52427445 T-AACACTTCAATTCACAACATT
1 TAAACACTTCAATTTACAACATT
* * *
52427467 TAAACAGTACTTCAATGTGCAATACTT
1 TAAAC---ACTTCAATTTACAACA-TT
* *
52427494 T-AACACTTCAAATTAAAACATT
1 TAAACACTTCAATTTACAACATT
** *
52427516 TAAACACTTCAATTTGTAGCACTT
1 TAAACACTTCAATTTACAACA-TT
52427540 T-AACATCTT-AA-TTAGCAACATT
1 TAAACA-CTTCAATTTA-CAACATT
* * * * *
52427562 TATACACCTGAA-TTACAGCAAT
1 TAAACACTTCAATTTACAACATT
* * **
52427584 AAAACA-TCTCAATTT-CTAGCAAC
1 TAAACACT-TCAATTTAC-AACATT
* *
52427607 TAAGCACTTCAATTTACAACATG
1 TAAACACTTCAATTTACAACATT
** * *
52427630 TGTACACTTCAATTTGCAGCACTT
1 TAAACACTTCAATTTACAACA-TT
* *
52427654 T-AACA-TCTCAATTAACAACGTT
1 TAAACACT-TCAATTTACAACATT
* * *
52427676 TATACACCTCAATTTACAGA-AAT
1 TAAACACTTCAATTTACA-ACATT
* * **
52427699 AAAACATTTCAATTT-CAAGCAAC
1 TAAACACTTCAATTTACAA-CATT
52427722 TAAACACTTCAA
1 TAAACACTTCAA
52427734 ATTGCAGTAC
Statistics
Matches: 404, Mismatches: 101, Indels: 74
0.70 0.17 0.13
Matches are distributed among these distances:
21 1 0.00
22 72 0.18
23 281 0.70
24 31 0.08
25 1 0.00
26 15 0.04
27 3 0.01
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.32
Consensus pattern (23 bp):
TAAACACTTCAATTTACAACATT
Found at i:52427212 original size:46 final size:46
Alignment explanation
Indices: 52427154--52427568 Score: 362
Period size: 46 Copynumber: 9.0 Consensus size: 46
52427144 CATATACATC
* * *
52427154 TCAATTTTCAGCAAC-TAAACAATTCAATTTACAACATTTAAACACT
1 TCAATTTGCAGC-ACTTTAACACTTCAATTTACAACATTTAAACACT
* * * * * *
52427200 TCAATTTACAGCATTTTAACGCTTCAATTCACATCATTTAAACGCT
1 TCAATTTGCAGCACTTTAACACTTCAATTTACAACATTTAAACACT
* * *
52427246 TCAATTTGCAACACTTTAGCACTTCAATTTACAGCATTT-AACACT
1 TCAATTTGCAGCACTTTAACACTTCAATTTACAACATTTAAACACT
* * *
52427291 TCAATTTGCAGCACTTTAACA-TCTCAATTAACAACATTTATACACC
1 TCAATTTGCAGCACTTTAACACT-TCAATTTACAACATTTAAACACT
** * * ** *
52427337 TCAATTAT--AGCGA-TAAAACA-TCTCAATTTCCAGCAACTAAACAAT
1 TCAATT-TGCAGC-ACTTTAACACT-TCAATTTACAACATTTAAACACT
* * * *
52427382 TCAACTTGCAGTACTTAAAACACTTCAATTTATAACATTTAAACACT
1 TCAATTTGCAGCACTT-TAACACTTCAATTTACAACATTTAAACACT
*
52427429 TCAATTTGCAGCACTTTAACACTTCAATTCACAACATTTAAACAGTACT
1 TCAATTTGCAGCACTTTAACACTTCAATTTACAACATTTAAAC---ACT
* ** * *
52427478 TCAATGTGCAATACTTTAACACTTCAAATTAAAACATTTAAACACT
1 TCAATTTGCAGCACTTTAACACTTCAATTTACAACATTTAAACACT
* *
52427524 TCAATTTGTAGCACTTTAACATCTT-AA-TTAGCAACATTTATACAC
1 TCAATTTGCAGCACTTTAACA-CTTCAATTTA-CAACATTTAAACAC
52427569 CTGAATTACA
Statistics
Matches: 296, Mismatches: 58, Indels: 30
0.77 0.15 0.08
Matches are distributed among these distances:
44 2 0.01
45 73 0.25
46 140 0.47
47 40 0.14
48 1 0.00
49 40 0.14
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (46 bp):
TCAATTTGCAGCACTTTAACACTTCAATTTACAACATTTAAACACT
Found at i:52427588 original size:233 final size:229
Alignment explanation
Indices: 52427170--52427618 Score: 673
Period size: 233 Copynumber: 1.9 Consensus size: 229
52427160 TTCAGCAACT
* * *
52427170 AAACAATTCAATTTACAACATTTAAACACTTCAATTTACAGCATTTTAACGCTTCAATTCACATC
1 AAACAATTCAATTTACAACATTTAAACACTTCAATTTACAGCACTTTAACACTTCAATTCACAAC
* * * * *
52427235 ATTTAAACGCTTCAATTTGCAACACTTTAGCACTTCAATTTACAGCATTTAACACTTCAATTTGC
66 ATTTAAACGCTTCAATGTGCAACACTTTAACACTTCAAATTAAAACATTTAACACTTCAATTTGC
* *
52427300 AGCACTTTAACATCTCAATTAACAACATTTATACACCTCAATTATAGCGATAAAACATCTCAATT
131 AGCACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCAATAAAACATCTCAATT
52427365 TCCAGCAACTAAACAATTCAACTTGCAGTACTTA
196 TCCAGCAACTAAACAATTCAACTTGCAGTACTTA
* * *
52427399 AAACACTTCAATTTATAACATTTAAACACTTCAATTTGCAGCACTTTAACACTTCAATTCACAAC
1 AAACAATTCAATTTACAACATTTAAACACTTCAATTTACAGCACTTTAACACTTCAATTCACAAC
*
52427464 ATTTAAACAGTACTTCAATGTGCAATACTTTAACACTTCAAATTAAAACATTTAAACACTTCAAT
66 ATTTAAAC-G--CTTCAATGTGCAACACTTTAACACTTCAAATTAAAACATTT-AACACTTCAAT
* * * *
52427529 TTGTAGCACTTTAACATCTTAATTAGCAACATTTATACACCTGAATTACAGCAATAAAACATCTC
127 TTGCAGCACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCAATAAAACATCTC
* * *
52427594 AATTTCTAGCAACTAAGCACTTCAA
192 AATTTCCAGCAACTAAACAATTCAA
52427619 TTTACAACAT
Statistics
Matches: 195, Mismatches: 21, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
229 67 0.34
230 1 0.01
232 35 0.18
233 92 0.47
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.33
Consensus pattern (229 bp):
AAACAATTCAATTTACAACATTTAAACACTTCAATTTACAGCACTTTAACACTTCAATTCACAAC
ATTTAAACGCTTCAATGTGCAACACTTTAACACTTCAAATTAAAACATTTAACACTTCAATTTGC
AGCACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCAATAAAACATCTCAATT
TCCAGCAACTAAACAATTCAACTTGCAGTACTTA
Found at i:52428260 original size:15 final size:15
Alignment explanation
Indices: 52428236--52428266 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
52428226 GTTTTAAGAA
52428236 AACATAAATACTTAC
1 AACATAAATACTTAC
*
52428251 AACATGAATACTTAC
1 AACATAAATACTTAC
52428266 A
1 A
52428267 TTTTAATCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.03, T:0.26
Consensus pattern (15 bp):
AACATAAATACTTAC
Found at i:52429965 original size:74 final size:75
Alignment explanation
Indices: 52429782--52429967 Score: 166
Period size: 74 Copynumber: 2.5 Consensus size: 75
52429772 ACCTTAGCTC
* *
52429782 TTATGAACATCCCGATTATAGGCTCTTCATGAGCTTCATGTTAAATTGGCTCTTGGTGAGCTTCC
1 TTATGAACTTCCCGATTAT-GGCTCTT-ACGAGCTTCATGTTAAATTGGCTCTTGGTGAGCTTCC
52429847 CGATAGCTCTCG
64 CGATAGCTCTCG
* ** * * * * *
52429859 CT-TGAACTTCTTGATATATGACT-ATCCGGAGCTTCCTGTTACATT-GCTCTCT-GTGAGCTTC
1 TTATGAACTTCCCGAT-TATGGCTCTTAC-GAGCTTCATGTTAAATTGGCTCT-TGGTGAGCTTC
* * *
52429920 CTGATATGGT-TCT
63 CCGATA-GCTCTCG
52429933 TTATGAACTTCCCGATTATGGCTCTTACGAGCTTC
1 TTATGAACTTCCCGATTATGGCTCTTACGAGCTTC
52429968 TCGATATGGC
Statistics
Matches: 84, Mismatches: 19, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
74 35 0.42
75 32 0.38
76 13 0.15
77 4 0.05
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (75 bp):
TTATGAACTTCCCGATTATGGCTCTTACGAGCTTCATGTTAAATTGGCTCTTGGTGAGCTTCCCG
ATAGCTCTCG
Found at i:52429967 original size:24 final size:24
Alignment explanation
Indices: 52429913--52429978 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
52429903 TGCTCTCTGT
* * *
52429913 GAGCTTCCTGATATGGTTCTTTAT
1 GAGCTTCCCGATATGGCTCTTTAC
*
52429937 GAACTTCCCGATTATGGCTC-TTAC
1 GAGCTTCCCGA-TATGGCTCTTTAC
*
52429961 GAGCTTCTCGATATGGCT
1 GAGCTTCCCGATATGGCT
52429979 ATGTCTGAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
23 7 0.20
24 21 0.60
25 7 0.20
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (24 bp):
GAGCTTCCCGATATGGCTCTTTAC
Found at i:52433923 original size:40 final size:40
Alignment explanation
Indices: 52433861--52434044 Score: 230
Period size: 40 Copynumber: 4.6 Consensus size: 40
52433851 TATTCGAATG
*
52433861 ATATCCGGGCTAAG-TCCTGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGATCC-GAAGGCATTTATGCTAGTGACT
* * *
52433901 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* * * *
52433941 ATATCTGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
*
52433981 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
*
52434021 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
52434045 CTTGTGCGAG
Statistics
Matches: 124, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
39 1 0.01
40 118 0.95
41 5 0.04
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:52444055 original size:23 final size:23
Alignment explanation
Indices: 52444028--52444084 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
52444018 ACGTTTACCG
52444028 CTATTAGCAGCATCGCTACGTTA
1 CTATTAGCAGCATCGCTACGTTA
* * **
52444051 CTATTAGCAGCTTTGCTGTGTTA
1 CTATTAGCAGCATCGCTACGTTA
*
52444074 CTACTAGCAGC
1 CTATTAGCAGC
52444085 TTTACTGTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (23 bp):
CTATTAGCAGCATCGCTACGTTA
Found at i:52444085 original size:23 final size:23
Alignment explanation
Indices: 52444047--52444106 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
52444037 GCATCGCTAC
*
52444047 GTTACTATTAGCAGCTTTGCTGT
1 GTTACTATTAGCAGCTTTACTGT
*
52444070 GTTACTACTAGCAGCTTTACTGT
1 GTTACTATTAGCAGCTTTACTGT
52444093 GTTACTATTAGCAG
1 GTTACTATTAGCAG
52444107 TTACGCTGCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (23 bp):
GTTACTATTAGCAGCTTTACTGT
Found at i:52444298 original size:33 final size:33
Alignment explanation
Indices: 52444250--52444312 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
52444240 ATAGGCCCAC
* *
52444250 ACTGTTACTGTATAGGGCTTAGGCCCAGACTGT
1 ACTGTTACTGAATAGGGCTCAGGCCCAGACTGT
* *
52444283 ACTGTTATTGAATAGGGCTCAGGCCTAGAC
1 ACTGTTACTGAATAGGGCTCAGGCCCAGAC
52444313 CGTTATTGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.29
Consensus pattern (33 bp):
ACTGTTACTGAATAGGGCTCAGGCCCAGACTGT
Found at i:52450505 original size:2 final size:2
Alignment explanation
Indices: 52450500--52450541 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
52450490 AAGATATATA
52450500 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
52450542 ATGCTAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:52450756 original size:44 final size:44
Alignment explanation
Indices: 52450706--52450863 Score: 164
Period size: 43 Copynumber: 3.7 Consensus size: 44
52450696 TATGTGTTTT
52450706 CGTGTAAGACCACGTCTAGGACATTGGCATCGATTTATGATTTA
1 CGTGTAAGACCACGTCTAGGACATTGGCATCGATTTATGATTTA
* *
52450750 CGTGTAAGACCATGTCTAGGACATTGGCATCG-TATATGATTT-
1 CGTGTAAGACCACGTCTAGGACATTGGCATCGATTTATGATTTA
* * * * * *
52450792 CGTGTAAGACC-CTGCCTGGGGCAGTGTCATCAATATT-TGA-TTA
1 CGTGTAAGACCAC-GTCTAGGACATTGGCATCGAT-TTATGATTTA
* * *
52450835 CATGTAAGACCACGTCTGGGACGTTGGCA
1 CGTGTAAGACCACGTCTAGGACATTGGCA
52450864 CTGTACGAGC
Statistics
Matches: 93, Mismatches: 16, Indels: 11
0.77 0.13 0.09
Matches are distributed among these distances:
42 26 0.28
43 34 0.37
44 33 0.35
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (44 bp):
CGTGTAAGACCACGTCTAGGACATTGGCATCGATTTATGATTTA
Found at i:52457443 original size:44 final size:43
Alignment explanation
Indices: 52457395--52457546 Score: 179
Period size: 44 Copynumber: 3.5 Consensus size: 43
52457385 TGTGTTTTCG
52457395 TGTAAGACCATGTCTGGGACGTTGGCATCGATTTGTGATTTACA
1 TGTAAGACCATGTCTGGGACGTTGGCATCGATTT-TGATTTACA
* * *
52457439 TGTAAGACCATGTCTGGGACATTGGCATCG-TATATGATTT-CG
1 TGTAAGACCATGTCTGGGACGTTGGCATCGAT-TTTGATTTACA
**
52457481 TGTAAGA-CACTGTCTGGGAC-TGTGTTATCGATATTTGA-TTACA
1 TGTAAGACCA-TGTCTGGGACGT-TGGCATCGAT-TTTGATTTACA
52457524 TGTAAGACCATGTCTGGGACGTT
1 TGTAAGACCATGTCTGGGACGTT
52457547 CACATTGTAC
Statistics
Matches: 94, Mismatches: 7, Indels: 15
0.81 0.06 0.13
Matches are distributed among these distances:
41 3 0.03
42 26 0.28
43 32 0.34
44 33 0.35
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACGTTGGCATCGATTTTGATTTACA
Found at i:52457520 original size:43 final size:43
Alignment explanation
Indices: 52457379--52457543 Score: 178
Period size: 43 Copynumber: 3.8 Consensus size: 43
52457369 GAAATAGGAT
* * *
52457379 TCGATATGTGTTTTCGTGTAAGACCATGTCTGGGAC-GTTGGCA
1 TCGATATTTGATTTCATGTAAGACCATGTCTGGGACTG-TGGCA
52457422 TCGAT-TTGTGATTTACATGTAAGACCATGTCTGGGACAT-TGGCA
1 TCGATATT-TGATTT-CATGTAAGACCATGTCTGGGAC-TGTGGCA
* * **
52457466 TCG-TATATGATTTCGTGTAAGA-CACTGTCTGGGACTGTGTTA
1 TCGATATTTGATTTCATGTAAGACCA-TGTCTGGGACTGTGGCA
*
52457508 TCGATATTTGATTACATGTAAGACCATGTCTGGGAC
1 TCGATATTTGATTTCATGTAAGACCATGTCTGGGAC
52457544 GTTCACATTG
Statistics
Matches: 103, Mismatches: 10, Indels: 18
0.79 0.08 0.14
Matches are distributed among these distances:
41 3 0.03
42 25 0.24
43 43 0.42
44 32 0.31
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (43 bp):
TCGATATTTGATTTCATGTAAGACCATGTCTGGGACTGTGGCA
Found at i:52458847 original size:23 final size:23
Alignment explanation
Indices: 52458820--52458865 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
52458810 ATTGAAATTG
*
52458820 GCTGAAATTATAGTGCAATTGTA
1 GCTGAAATTACAGTGCAATTGTA
52458843 GCTGAAATTACAGTGCAATTGTA
1 GCTGAAATTACAGTGCAATTGTA
52458866 CTTGGTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.33
Consensus pattern (23 bp):
GCTGAAATTACAGTGCAATTGTA
Found at i:52467649 original size:46 final size:46
Alignment explanation
Indices: 52467466--52467771 Score: 141
Period size: 46 Copynumber: 6.6 Consensus size: 46
52467456 TGATATGTGT
* * ** * **
52467466 GCCAGTGTAAGACATGTCTGGAACGTGCATTGGCTGCATTATG-AGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCTACACGATGTA-A
* * *
52467512 GCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGACGA-GT--
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGC--T-ACACGATGTAA
* * * * * *
52467560 GCTACTATAAGACATGTCTGGGACATGCATTGACCT-CAGGATGTAA
1 GCCAGTGTAAGACATGTCTGGGACATGCA-TCAGCTACACGATGTAA
52467606 GCCAGTGTAAGACATGTCTGGGACATGCATC-GACTACGA-GATGT--
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAG-CTAC-ACGATGTAA
* * * * * **
52467650 GTCAGTGTAAGACCATGTTTGGAACATGGCGTCAGC-ACGGA-TATGTGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCTAC--ACGATGTAA
* * * *
52467698 GCTAGTGTAAGACATGTCTAGGACATGCATCAGCCACATCG-TGAAA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCTACA-CGATGTAA
*
52467744 GCTAGTGTAAGACCATGTCTGGGACATG
1 GCCAGTGTAAGA-CATGTCTGGGACATG
52467772 GCTTGATATG
Statistics
Matches: 199, Mismatches: 38, Indels: 45
0.71 0.13 0.16
Matches are distributed among these distances:
43 3 0.02
44 13 0.07
45 19 0.10
46 79 0.40
47 55 0.28
48 26 0.13
50 2 0.01
51 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (46 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCAGCTACACGATGTAA
Found at i:52467716 original size:138 final size:139
Alignment explanation
Indices: 52467514--52467771 Score: 333
Period size: 138 Copynumber: 1.9 Consensus size: 139
52467504 TTATGAGAGC
* * **
52467514 CAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGACGAGTGCTACTATAAGACATGTCT
1 CAGTGTAAGACCATGTTTGGAACATGGCATCAGCACGGAGACGAGTGCTACTATAAGACATGTCT
* * * * *
52467579 GGGACATGCAT-TGACCTCA-GGATGTAAGCCAGTGTAAGA-CATGTCTGGGACATGCATCGACT
66 AGGACATGCATCAG-CCACATCG-TGAAAGCCAGTGTAAGACCATGTCTGGGACATGCATCGACT
52467641 ACGAGATGTGT
129 ACGAGATGTGT
* * * * * *
52467652 CAGTGTAAGACCATGTTTGGAACATGGCGTCAGCACGGATATGTGTGCTAGTGTAAGACATGTCT
1 CAGTGTAAGACCATGTTTGGAACATGGCATCAGCACGGAGACGAGTGCTACTATAAGACATGTCT
*
52467717 AGGACATGCATCAGCCACATCGTGAAAGCTAGTGTAAGACCATGTCTGGGACATG
66 AGGACATGCATCAGCCACATCGTGAAAGCCAGTGTAAGACCATGTCTGGGACATG
52467772 GCTTGATATG
Statistics
Matches: 101, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
138 84 0.83
139 17 0.17
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (139 bp):
CAGTGTAAGACCATGTTTGGAACATGGCATCAGCACGGAGACGAGTGCTACTATAAGACATGTCT
AGGACATGCATCAGCCACATCGTGAAAGCCAGTGTAAGACCATGTCTGGGACATGCATCGACTAC
GAGATGTGT
Found at i:52474221 original size:9 final size:9
Alignment explanation
Indices: 52474207--52474231 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
52474197 TAAGGTTGCA
52474207 CAAGTCGCC
1 CAAGTCGCC
52474216 CAAGTCGCC
1 CAAGTCGCC
52474225 CAAGTCG
1 CAAGTCG
52474232 ACTGTGGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.40, G:0.24, T:0.12
Consensus pattern (9 bp):
CAAGTCGCC
Found at i:52475761 original size:32 final size:31
Alignment explanation
Indices: 52475690--52475761 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 31
52475680 TTTATTTAAA
52475690 AATATAAAGTTAAAATATATTATAATATTATT
1 AATA-AAAGTTAAAATATATTATAATATTATT
* *
52475722 ACTTAAAAGTT-AAGTATATTATATATATTATAT
1 A-ATAAAAGTTAAAATATATTATA-ATATTAT-T
52475755 AATAAAA
1 AATAAAA
52475762 ACAAACAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
31 11 0.32
32 19 0.56
33 4 0.12
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (31 bp):
AATAAAAGTTAAAATATATTATAATATTATT
Found at i:52476737 original size:25 final size:25
Alignment explanation
Indices: 52476704--52476837 Score: 131
Period size: 25 Copynumber: 5.6 Consensus size: 25
52476694 CTTTAGCGCA
*
52476704 CTCTCTGATTATTAGCACGTTAGCG
1 CTCTCTGATTATTAGCACGTTAGTG
* *
52476729 CTCTATGATTATTAGCACGCTAGTG
1 CTCTCTGATTATTAGCACGTTAGTG
* *
52476754 TTCTCCGATTATTAGCACGTTAGTG
1 CTCTCTGATTATTAGCACGTTAGTG
* *
52476779 CTCTCT-A-T-TTAGCACATTCGTG
1 CTCTCTGATTATTAGCACGTTAGTG
52476801 CTCTCTG--TA-TAGCAC-TTCAGTG
1 CTCTCTGATTATTAGCACGTT-AGTG
52476823 CTCTCT-ATTCATTAG
1 CTCTCTGATT-ATTAG
52476838 TGCATAATAA
Statistics
Matches: 90, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
21 2 0.02
22 34 0.38
23 2 0.02
24 2 0.02
25 50 0.56
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (25 bp):
CTCTCTGATTATTAGCACGTTAGTG
Found at i:52476793 original size:22 final size:22
Alignment explanation
Indices: 52476715--52476831 Score: 83
Period size: 22 Copynumber: 5.0 Consensus size: 22
52476705 TCTCTGATTA
* *
52476715 TTAGCACGTTAGCGCTCTATGATT
1 TTAGCACGTTAGTGCTCTCT-A-T
* * *
52476739 ATTAGCACGCTAGTGTTCTCCGATT
1 -TTAGCACGTTAGTGCTCT-CTA-T
52476764 ATTAGCACGTTAGTGCTCTCTAT
1 -TTAGCACGTTAGTGCTCTCTAT
* * *
52476787 TTAGCACATTCGTGCTCTCTGT
1 TTAGCACGTTAGTGCTCTCTAT
*
52476809 ATAGCAC-TTCAGTGCTCTCTAT
1 TTAGCACGTT-AGTGCTCTCTAT
52476831 T
1 T
52476832 CATTAGTGCA
Statistics
Matches: 75, Mismatches: 15, Indels: 7
0.77 0.15 0.07
Matches are distributed among these distances:
21 2 0.03
22 35 0.47
23 1 0.01
24 2 0.03
25 35 0.47
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (22 bp):
TTAGCACGTTAGTGCTCTCTAT
Done.