Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 162 of 352
Found at i:53035832 original size:26 final size:26
Alignment explanation
Indices: 53035803--53035900 Score: 90
Period size: 27 Copynumber: 3.7 Consensus size: 26
53035793 TTAATTTACC
**
53035803 AAATTACTGAAATACCCCCAGTTGTA
1 AAATTACCCAAATACCCCCAGTTGTA
*
53035829 AAATTA-CCAAAGTACCCCCAGTTTATA
1 AAATTACCCAAA-TACCCCCAG-TTGTA
* * *
53035856 AAATTACCCAAATATCCTCGATTTGTA
1 AAATTACCCAAATA-CCCCCAGTTGTA
* *
53035883 AAATTACCGAAAAACCCC
1 AAATTACCCAAATACCCC
53035901 TGTAAGGTAG
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
25 3 0.05
26 18 0.31
27 28 0.48
28 9 0.16
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (26 bp):
AAATTACCCAAATACCCCCAGTTGTA
Found at i:53035914 original size:27 final size:27
Alignment explanation
Indices: 53035884--53036402 Score: 607
Period size: 27 Copynumber: 19.3 Consensus size: 27
53035874 CGATTTGTAA
* *
53035884 AATTACCGAAAAACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
53035911 AATTACTGAAATACCTCTGTAAGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
53035938 AATTATCGAAATACCCTTGT-GGTGTAG
1 AATTACCGAAATACCCCTGTAGG-GTAG
* * *
53035965 AATTACTGAAATACCCTTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
53035992 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
53036019 AA-TACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
53036045 AATTACTGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
53036072 AATTACTAAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
53036099 AATTACTGAAATACCCCTATATGGCAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
53036126 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * * *
53036153 AATTATCAAAATATCCTTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
53036180 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
53036207 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
53036234 AATTACCGAAATACCCCTATAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
53036261 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
53036288 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
53036315 AATTATAGAAATACTCTTGTAGGGTAGG
1 AATTACCGAAATACCCCTGTAGGGTA-G
*
53036343 AA-TACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
53036369 AATTACCGATAA-A-CCCTCGTGGGGTAA
1 AATTACCGA-AATACCCCT-GTAGGGTAG
53036396 AATTACC
1 AATTACC
53036403 ATTTTACCCC
Statistics
Matches: 428, Mismatches: 57, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
26 33 0.08
27 389 0.91
28 6 0.01
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:53036847 original size:25 final size:25
Alignment explanation
Indices: 53036819--53036914 Score: 102
Period size: 25 Copynumber: 3.6 Consensus size: 25
53036809 CATTCACATT
*
53036819 CTGATTTTGATTCTGTTACCTGATA
1 CTGATTCTGATTCTGTTACCTGATA
53036844 CTGATTCTGAATTTGATTCTGTTACCTGATA
1 CTGATTC------TGATTCTGTTACCTGATA
* *
53036875 CTGATTCTGATTCTGTTACCTAATT
1 CTGATTCTGATTCTGTTACCTGATA
*
53036900 CTGATTCTAATTCTG
1 CTGATTCTGATTCTG
53036915 ATTCTAGTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
25 36 0.59
31 25 0.41
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.47
Consensus pattern (25 bp):
CTGATTCTGATTCTGTTACCTGATA
Found at i:53036848 original size:19 final size:19
Alignment explanation
Indices: 53036826--53036883 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
53036816 ATTCTGATTT
53036826 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACCTGATAC
*
53036845 TGATTCTG--A----AT-T
1 TGATTCTGTTACCTGATAC
53036857 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACCTGATAC
53036876 TGATTCTG
1 TGATTCTG
53036884 ATTCTGTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
12 8 0.27
13 2 0.07
14 1 0.03
17 1 0.03
18 2 0.07
19 16 0.53
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (19 bp):
TGATTCTGTTACCTGATAC
Found at i:53036851 original size:31 final size:31
Alignment explanation
Indices: 53036816--53036886 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
53036806 TTGCATTCAC
53036816 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
53036847 ATTCTGAATTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53036878 ATTCTGATT
1 ATTCTGATT
53036887 CTGTTACCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.48
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:53036886 original size:6 final size:6
Alignment explanation
Indices: 53036816--53036928 Score: 74
Period size: 6 Copynumber: 18.3 Consensus size: 6
53036806 TTGCATTCAC
* *
53036816 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG AATT-TG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG -ATTCTG ATTCTG
* * *
53036865 -TTACCTG ATACTG ATTCTG ATTCTG -TTACCTA ATTCTG ATTCTA ATTCTG
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG
53036915 ATTCT- AGTTCTG AT
1 ATTCTG A-TTCTG AT
53036929 AATGTTTCTT
Statistics
Matches: 84, Mismatches: 10, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
5 10 0.12
6 58 0.69
7 12 0.14
8 4 0.05
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:53036904 original size:31 final size:29
Alignment explanation
Indices: 53036816--53036919 Score: 101
Period size: 31 Copynumber: 3.6 Consensus size: 29
53036806 TTGCATTCAC
*
53036816 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTTACCT-AT-CTG
53036847 ATTCTGAATT-TGATTCTGTTA-C---CTG
1 ATTCTG-ATTCTGATTCTGTTACCTATCTG
*
53036872 ATACTGATTCTGATTCTGTTACCTAATTCTG
1 ATTCTGATTCTGATTCTGTTACCT-A-TCTG
*
53036903 ATTCTAATTCTGATTCT
1 ATTCTGATTCTGATTCT
53036920 AGTTCTGATA
Statistics
Matches: 62, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
24 3 0.05
25 19 0.31
26 1 0.02
30 1 0.02
31 35 0.56
32 3 0.05
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.48
Consensus pattern (29 bp):
ATTCTGATTCTGATTCTGTTACCTATCTG
Found at i:53040731 original size:27 final size:27
Alignment explanation
Indices: 53040691--53040802 Score: 138
Period size: 27 Copynumber: 4.1 Consensus size: 27
53040681 AGGAAGCGTC
*
53040691 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
53040718 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
*
53040745 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
53040773 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
53040799 CTGG
1 CTGG
53040803 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.11
27 49 0.65
28 18 0.24
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:53040797 original size:54 final size:54
Alignment explanation
Indices: 53040691--53040802 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
53040681 AGGAAGCGTC
* *
53040691 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
53040745 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
53040799 CTGG
1 CTGG
53040803 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:53041827 original size:26 final size:26
Alignment explanation
Indices: 53041798--53041895 Score: 106
Period size: 27 Copynumber: 3.7 Consensus size: 26
53041788 TTAGTTTACC
*
53041798 AAATTACTAAAATACCCCCAGTTGTA
1 AAATTACCAAAATACCCCCAGTTGTA
* *
53041824 AAATTACCAAAGTACCCCCAGTTTATA
1 AAATTACCAAAATACCCCCAG-TTGTA
* * * *
53041851 AAATTACCCAAATATCCTCGATTTGTA
1 AAATTACCAAAATA-CCCCCAGTTGTA
*
53041878 AAATTACCGAAATACCCC
1 AAATTACCAAAATACCCC
53041896 TATAAGGTAG
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
26 22 0.37
27 33 0.56
28 4 0.07
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.27
Consensus pattern (26 bp):
AAATTACCAAAATACCCCCAGTTGTA
Found at i:53042351 original size:27 final size:27
Alignment explanation
Indices: 53041879--53042369 Score: 560
Period size: 27 Copynumber: 18.3 Consensus size: 27
53041869 CGATTTGTAA
* *
53041879 AATTACCGAAATACCCCTATAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * * * *
53041906 AATTACTAAAATAGCCATGTAAGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
53041933 AATTACCGGAATACCCCTGTAGTGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
53041960 AATTACTGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
53041987 AATTATCGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
53042014 AATTACTGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
53042041 AATTACCGAAATACCCCTGTATGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
53042068 AATTACCGAAATAGCCCTGTATGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
53042095 AATTACTGAAA-ACCTCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
53042121 AATTATCGAAATACCCTTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
53042148 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
53042175 AATTACTGAAATACCCCTGTATGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
53042202 AATTACCGAAATAGCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
53042229 AATTATCGAAATATCCCTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
53042256 AATTGCTGAAATACCCTTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
53042283 AATTACCGAAATACCCTTGTAGGGTAGG
1 AATTACCGAAATACCCCTGTAGGGTA-G
* *
53042311 AA-TA-CTAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
53042336 AATTACCGAGAA-A-CCCTCGTGGGGTAA
1 AATTACCGA-AATACCCCT-GTAGGGTAG
53042363 AATTACC
1 AATTACC
53042370 ATTTTACCCC
Statistics
Matches: 393, Mismatches: 65, Indels: 12
0.84 0.14 0.03
Matches are distributed among these distances:
25 3 0.01
26 44 0.11
27 341 0.87
28 5 0.01
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:53042815 original size:6 final size:6
Alignment explanation
Indices: 53042784--53042905 Score: 79
Period size: 6 Copynumber: 19.8 Consensus size: 6
53042774 TTGCATTCAC
* * * * *
53042784 ATTCTG ATTTTG ATTTTG -TTACCTG ATACTG ATTTTG ATTTTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
53042833 -TTACCTG ATACTG ATTCTG ATTCTG ATTCTG -TCACCTA ATTCTG ATTCTA
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
*
53042883 ATTTTG ATTCTG ATTCTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATTCT
53042906 AGTTCTGAAA
Statistics
Matches: 91, Mismatches: 16, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
5 5 0.05
6 76 0.84
7 7 0.08
8 3 0.03
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.51
Consensus pattern (6 bp):
ATTCTG
Found at i:53042826 original size:31 final size:31
Alignment explanation
Indices: 53042784--53042894 Score: 159
Period size: 31 Copynumber: 3.6 Consensus size: 31
53042774 TTGCATTCAC
*
53042784 ATTCTGATTTTGATTTTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
53042815 ATTTTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* * * *
53042846 ATTCTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
53042877 ATTCTAATTTTGATTCTG
1 ATTCTGATTTTGATTCTG
53042895 ATTCTGATTC
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 71 1.00
ACGTcount: A:0.20, C:0.15, G:0.14, T:0.50
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:53042840 original size:25 final size:24
Alignment explanation
Indices: 53042787--53042859 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 24
53042777 CATTCACATT
53042787 CTGATTTTGATTTTG-TTACCTGATA
1 CTGATTTTGATTTTGATT--CTGATA
*
53042812 CTGATTTTGATTTTGATTCTGTTA
1 CTGATTTTGATTTTGATTCTGATA
** *
53042836 CCTGATACTGATTCTGATTCTGAT
1 -CTGATTTTGATTTTGATTCTGAT
53042860 TCTGTCACCT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 5 0.12
25 34 0.83
26 2 0.05
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (24 bp):
CTGATTTTGATTTTGATTCTGATA
Found at i:53042911 original size:12 final size:12
Alignment explanation
Indices: 53042872--53042913 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
53042862 TGTCACCTAA
*
53042872 TTCTGATTCTAA
1 TTCTGATTCTAG
*
53042884 TTTTGATTCT-G
1 TTCTGATTCTAG
53042895 ATTCTGATTCTAG
1 -TTCTGATTCTAG
53042908 TTCTGA
1 TTCTGA
53042914 AAATGTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
12 24 0.96
13 1 0.04
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.52
Consensus pattern (12 bp):
TTCTGATTCTAG
Found at i:53046332 original size:53 final size:53
Alignment explanation
Indices: 53046263--53046365 Score: 181
Period size: 53 Copynumber: 1.9 Consensus size: 53
53046253 TATATCAGGA
*
53046263 TTACCCATTCGAGCTAAATCCTTTCTATAATGAGGTCAATAGGAATACTCATC
1 TTACCCATTCGAGCTAAATCCTTTCTATAATAAGGTCAATAGGAATACTCATC
53046316 TTACCCATTC-AGGCTAAATCCTTTCTATAATAAGGTCAATAGGAATACTC
1 TTACCCATTCGA-GCTAAATCCTTTCTATAATAAGGTCAATAGGAATACTC
53046366 GTCCGAGCTA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 1 0.02
53 47 0.98
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (53 bp):
TTACCCATTCGAGCTAAATCCTTTCTATAATAAGGTCAATAGGAATACTCATC
Found at i:53049617 original size:23 final size:23
Alignment explanation
Indices: 53049587--53049631 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
53049577 TCAATATATA
*
53049587 TATGTGATATA-TATTTAAATGAG
1 TATGTGAT-TACTATGTAAATGAG
53049610 TATGTGATTACTATGTAAATGA
1 TATGTGATTACTATGTAAATGA
53049632 ATCAATGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.38, C:0.02, G:0.18, T:0.42
Consensus pattern (23 bp):
TATGTGATTACTATGTAAATGAG
Found at i:53063554 original size:46 final size:46
Alignment explanation
Indices: 53063468--53063693 Score: 157
Period size: 46 Copynumber: 4.9 Consensus size: 46
53063458 GGGGTAAGTT
* *
53063468 GCCGATGCCATATCCCAGACATGGTCTTACACTGAC--ACATTTCATA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATTT-ATAG
53063514 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATTT-TGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATTTAT-AG
* * * * *
53063560 GCCAATGCATG-CCCTAGACATGTCTTACATTAGCGC-T-CGTCTCA-AT
1 GCCGATGCATGTCCC-AGACATGTCTTACACT-G-GCTTACAT-TTATAG
* * *
53063606 GCCAATACCATGTCCCAGACATGGTCTTACACTGGCTCT-CA-TAATATG
1 GCCGAT-GCATGTCCCAGACAT-GTCTTACACTGGCT-TACATTTATA-G
* * *
53063654 GCTGATGCATGTCCCAGACATGTCTTACACTAGCTCACAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACAT
53063694 AAGTGACTCA
Statistics
Matches: 145, Mismatches: 17, Indels: 35
0.74 0.09 0.18
Matches are distributed among these distances:
44 13 0.09
45 17 0.12
46 66 0.46
47 29 0.20
48 20 0.14
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATTTATAG
Found at i:53066177 original size:21 final size:17
Alignment explanation
Indices: 53066136--53066171 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
53066126 ATGTCCTTAA
53066136 TCTCTTTGGGATAATAT
1 TCTCTTTGGGATAATAT
53066153 TCTCTTTGGGATAATAT
1 TCTCTTTGGGATAATAT
53066170 TC
1 TC
53066172 ATTCTCCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (17 bp):
TCTCTTTGGGATAATAT
Found at i:53067142 original size:19 final size:19
Alignment explanation
Indices: 53067106--53067144 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
53067096 GTTTCATCAT
* *
53067106 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
53067125 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
53067144 A
1 A
53067145 AAATAATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:53067667 original size:27 final size:27
Alignment explanation
Indices: 53067599--53067699 Score: 112
Period size: 28 Copynumber: 3.6 Consensus size: 27
53067589 ATACAGAAAA
* *
53067599 TGTGACAGAGTCACCAGATACAGATATTT
1 TGTGGCAGAGCCACCAGA-ACAGATA-TT
* * *
53067628 TGTGGCTGTGCCACCAGAACAGATATA
1 TGTGGCAGAGCCACCAGAACAGATATT
*
53067655 TGTGGCAGGGCCACCAGAACAGATAATT
1 TGTGGCAGAGCCACCAGAACAGAT-ATT
*
53067683 TGTGGCATAGCCACCAG
1 TGTGGCAGAGCCACCAG
53067700 GACGCTTCCT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
27 23 0.38
28 24 0.39
29 14 0.23
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.22
Consensus pattern (27 bp):
TGTGGCAGAGCCACCAGAACAGATATT
Found at i:53067852 original size:28 final size:29
Alignment explanation
Indices: 53067805--53067870 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
53067795 AAATTAACCC
*
53067805 TAGGGGTATAAAGGTCA-TTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTTGCATACA
*
53067833 TAGGGGTATAATGGTAATTTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTTGCATACA
*
53067862 TCGGGGTAT
1 TAGGGGTAT
53067871 TCTATTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 15 0.44
29 19 0.56
ACGTcount: A:0.29, C:0.09, G:0.27, T:0.35
Consensus pattern (29 bp):
TAGGGGTATAAAGGTAATTTTTGCATACA
Found at i:53070777 original size:40 final size:40
Alignment explanation
Indices: 53070703--53070914 Score: 214
Period size: 40 Copynumber: 5.3 Consensus size: 40
53070693 TCTTTGGGAT
** * *
53070703 TTAG-CCGGATATAACCACTCGCAC-AAGGCCTTCGGGTC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTC
* * * *
53070741 TTAGCCCGGATATGGTCGCTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTC
* *
53070781 TTAGCCCGGATATAGTCGCTAGCACAAATGCCTTCGGGTT
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTC
* * * *
53070821 TTGGCCCGGATATAGTAACTCGCACAAATGCCTTCGGATC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTC
* * * *
53070861 TTAGTCCTGATATAATCACTTAGCACAAAAT-CCTTCGGGAC
1 TTAGCCCGGATATAGTCAC-TAGCAC-AAATGCCTTCGGGTC
*
53070902 TTAGCCCGAATAT
1 TTAGCCCGGATAT
53070915 CATTCGAATA
Statistics
Matches: 141, Mismatches: 29, Indels: 5
0.81 0.17 0.03
Matches are distributed among these distances:
38 4 0.03
39 14 0.10
40 96 0.68
41 23 0.16
42 4 0.03
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTC
Found at i:53073643 original size:19 final size:19
Alignment explanation
Indices: 53073619--53073657 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
53073609 TTATTGAGTT
53073619 AGTACCCACATACTCTAAA
1 AGTACCCACATACTCTAAA
** *
53073638 AGTACCTGCATACTGTAAA
1 AGTACCCACATACTCTAAA
53073657 A
1 A
53073658 TGAATCGTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.23
Consensus pattern (19 bp):
AGTACCCACATACTCTAAA
Found at i:53074327 original size:118 final size:118
Alignment explanation
Indices: 53074119--53074358 Score: 471
Period size: 118 Copynumber: 2.0 Consensus size: 118
53074109 TACAACAAAA
*
53074119 ATAGACACGACCGTGTGGAGCAATCGTGTATGTTACACAGTCGTGTGACGCCCTGTGTCTTAGGT
1 ATAGACACGACCGTGTGGAGCAATCGTGTATGTTACACAGTCGTGTGACACCCTGTGTCTTAGGT
53074184 CGTGTGATCCAAATTAAGCCCCCAAAACAAGCCATTTCAAGACCTATGCATGC
66 CGTGTGATCCAAATTAAGCCCCCAAAACAAGCCATTTCAAGACCTATGCATGC
53074237 ATAGACACGACCGTGTGGAGCAATCGTGTATGTTACACAGTCGTGTGACACCCTGTGTCTTAGGT
1 ATAGACACGACCGTGTGGAGCAATCGTGTATGTTACACAGTCGTGTGACACCCTGTGTCTTAGGT
53074302 CGTGTGATCCAAATTAAGCCCCCAAAACAAGCCATTTCAAGACCTATGCATGC
66 CGTGTGATCCAAATTAAGCCCCCAAAACAAGCCATTTCAAGACCTATGCATGC
53074355 ATAG
1 ATAG
53074359 CAAGATACAT
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
118 121 1.00
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (118 bp):
ATAGACACGACCGTGTGGAGCAATCGTGTATGTTACACAGTCGTGTGACACCCTGTGTCTTAGGT
CGTGTGATCCAAATTAAGCCCCCAAAACAAGCCATTTCAAGACCTATGCATGC
Found at i:53075704 original size:40 final size:41
Alignment explanation
Indices: 53075611--53075711 Score: 132
Period size: 41 Copynumber: 2.5 Consensus size: 41
53075601 ATTATACACC
* *
53075611 GGCACCAATCCTGATTATATACACCGGCACAAAGCCTACTA
1 GGCACAAAGCCTGATTATATACACCGGCACAAAGCCTACTA
* ** *
53075652 GGCATAAAGCCTGATTATATACATTGGCACAAAG-CTGCTA
1 GGCACAAAGCCTGATTATATACACCGGCACAAAGCCTACTA
*
53075692 GGCACAAAGCCTGATAATAT
1 GGCACAAAGCCTGATTATAT
53075712 CTCCAATAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 23 0.44
41 29 0.56
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.22
Consensus pattern (41 bp):
GGCACAAAGCCTGATTATATACACCGGCACAAAGCCTACTA
Found at i:53078743 original size:27 final size:27
Alignment explanation
Indices: 53078713--53078804 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
53078703 ATTATCAAAG
* * *
53078713 TACCCTCGATTTATAGAATTATCATTT
1 TACCCTCGATTTACAAAATTACCATTT
53078740 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACCATTT
**
53078767 TACCCTC-AGTTTACAAAATTACTGTTT
1 TACCCTCGA-TTTACAAAATTACCATTT
*
53078794 CACCCTCGATT
1 TACCCTCGATT
53078805 ATGAAATTAC
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.02
27 55 0.96
28 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCATTT
Found at i:53078959 original size:27 final size:27
Alignment explanation
Indices: 53078836--53078948 Score: 147
Period size: 27 Copynumber: 4.2 Consensus size: 27
53078826 TGTAGGATAG
*
53078836 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAATTTGTAA
* *
53078863 AATTACCAAAATACCACTAATTTGTGA
1 AATTACCAAAATACCCCTAATTTGTAA
**
53078890 AATTACTGAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-AATTTGTAA
**
53078917 AATTACCAAAATACCCCTAATTTACAA
1 AATTACCAAAATACCCCTAATTTGTAA
53078944 AATTA
1 AATTA
53078949 TTGAAATACC
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
26 3 0.04
27 66 0.90
28 4 0.05
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAATTTGTAA
Found at i:53078968 original size:54 final size:54
Alignment explanation
Indices: 53078844--53078986 Score: 178
Period size: 54 Copynumber: 2.6 Consensus size: 54
53078834 AGAATTACCA
* * ***
53078844 AAATACCCCTAGTTTGTAAAATTACCAAAATACCACTAATTTGTGAAATTACTG
1 AAATACCCTTAGTTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTACTG
* * *
53078898 AAATACCCTCAATTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTATTG
1 AAATACCCTTAGTTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTACTG
* * * *
53078952 AAATACCCTTGGTTTGTAGATTTACCAAAACACCC
1 AAATACCCTTAGTTTGTAAAATTACCAAAATACCC
53078987 TTGTAGGATG
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 75 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (54 bp):
AAATACCCTTAGTTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTACTG
Found at i:53079941 original size:24 final size:25
Alignment explanation
Indices: 53079865--53079934 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
53079855 AGGAAGTGCT
* * * *
53079865 AAAATGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
53079890 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
53079915 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
53079935 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:53079947 original size:24 final size:25
Alignment explanation
Indices: 53079870--53079947 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 25
53079860 GTGCTAAAAT
* *
53079870 GGCTATGCCCCAGTTTACCGAAAAG-
1 GGCTTTGCCCCAGTTTATC-AAAAGA
53079895 GGCTTTGCCCCAGTTTATCAAAA-A
1 GGCTTTGCCCCAGTTTATCAAAAGA
*
53079919 GGGCTTTGCCCCAG-TTATTAAAAGA
1 -GGCTTTGCCCCAGTTTATCAAAAGA
53079944 GGCT
1 GGCT
53079948 AGGCCTCCAG
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
24 16 0.34
25 31 0.66
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (25 bp):
GGCTTTGCCCCAGTTTATCAAAAGA
Found at i:53080203 original size:31 final size:31
Alignment explanation
Indices: 53080154--53080236 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
53080144 CGCTTACAGT
53080154 AAAGGCTTCGG-CCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
53080184 AAAGGATTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
53080215 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
53080237 TCGAGACTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
30 15 0.30
31 35 0.70
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:53085826 original size:7 final size:7
Alignment explanation
Indices: 53085814--53085838 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53085804 ACCACTAATT
53085814 TTTTCTC
1 TTTTCTC
53085821 TTTTCTC
1 TTTTCTC
53085828 TTTTCTC
1 TTTTCTC
53085835 TTTT
1 TTTT
53085839 TCTCCTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTCTC
Found at i:53085980 original size:28 final size:28
Alignment explanation
Indices: 53085925--53085988 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
53085915 CTCAATTTCT
* * **
53085925 AGACCACCGCTGAGCTACCGTTGTCGTC
1 AGACAACCGCTGAGCTACCATTACCGTC
*
53085953 -GAACAACCGCTGAGCTACTATTACCGTC
1 AG-ACAACCGCTGAGCTACCATTACCGTC
53085981 AGACAACC
1 AGACAACC
53085989 ACTGCCAGTC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 1 0.03
28 27 0.93
29 1 0.03
ACGTcount: A:0.27, C:0.34, G:0.20, T:0.19
Consensus pattern (28 bp):
AGACAACCGCTGAGCTACCATTACCGTC
Found at i:53103714 original size:20 final size:20
Alignment explanation
Indices: 53103691--53103740 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
53103681 TATGGACTCA
53103691 CACGCCCGTGTATCTTGGGG
1 CACGCCCGTGTATCTTGGGG
53103711 CACGCCCGTGTATCTTGGGG
1 CACGCCCGTGTATCTTGGGG
53103731 CACGCCCGTG
1 CACGCCCGTG
53103741 CCCTTCAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.10, C:0.34, G:0.34, T:0.22
Consensus pattern (20 bp):
CACGCCCGTGTATCTTGGGG
Found at i:53107863 original size:21 final size:21
Alignment explanation
Indices: 53107824--53107866 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
53107814 ATCATAGAAC
53107824 TTCAAAAACCTATCAAACTCA
1 TTCAAAAACCTATCAAACTCA
53107845 TTCAAAAACCTATCAAACTCA
1 TTCAAAAACCTATCAAACTCA
53107866 T
1 T
53107867 ACATGGCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.26
Consensus pattern (21 bp):
TTCAAAAACCTATCAAACTCA
Found at i:53116426 original size:26 final size:27
Alignment explanation
Indices: 53116397--53116463 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 27
53116387 TTAGTTTACC
* *
53116397 AAATTACTAAAATACCCCCAG-TTGTA
1 AAATTACCAAAATACCCCCAGTTTATA
* *
53116423 AAATTACCAAAGTACCCCCGGTTTATA
1 AAATTACCAAAATACCCCCAGTTTATA
*
53116450 AAATTACCCAAATA
1 AAATTACCAAAATA
53116464 TCCTCGATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 18 0.53
27 16 0.47
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.25
Consensus pattern (27 bp):
AAATTACCAAAATACCCCCAGTTTATA
Found at i:53116478 original size:27 final size:27
Alignment explanation
Indices: 53116397--53116482 Score: 86
Period size: 27 Copynumber: 3.2 Consensus size: 27
53116387 TTAGTTTACC
* * *
53116397 AAATTACTAAAATACCCCC-AGTTGTA
1 AAATTACCAAAGTACCCCCGATTTGTA
* *
53116423 AAATTACCAAAGTACCCCCGGTTTATA
1 AAATTACCAAAGTACCCCCGATTTGTA
* *
53116450 AAATTACCCAAA-TATCCTCGATTTGTA
1 AAATTA-CCAAAGTACCCCCGATTTGTA
53116477 AAATTA
1 AAATTA
53116483 ACGAAATACC
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
26 17 0.35
27 27 0.55
28 5 0.10
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (27 bp):
AAATTACCAAAGTACCCCCGATTTGTA
Found at i:53116591 original size:54 final size:53
Alignment explanation
Indices: 53116474--53116591 Score: 123
Period size: 54 Copynumber: 2.2 Consensus size: 53
53116464 TCCTCGATTT
*
53116474 GTAAAATTAACGAAATACCCTTATAGGGTAGAAATACCTAAATACCCCTGTAGG
1 GTAAAATT-ACGAAATACCCTTATAGGGTAGAAATACCGAAATACCCCTGTAGG
** * * * *
53116528 GTAGGATTACTGAAATACTCCTGTA-A-GGTAGAATTACCGAGATACCCTTGTGGG
1 GTAAAATTAC-GAAATAC-CCT-TATAGGGTAGAAATACCGAAATACCCCTGTAGG
53116582 GTAAAATTAC
1 GTAAAATTAC
53116592 CATTTTACCC
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
53 2 0.04
54 44 0.85
55 4 0.08
56 2 0.04
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.26
Consensus pattern (53 bp):
GTAAAATTACGAAATACCCTTATAGGGTAGAAATACCGAAATACCCCTGTAGG
Found at i:53116592 original size:27 final size:27
Alignment explanation
Indices: 53116474--53116592 Score: 107
Period size: 27 Copynumber: 4.4 Consensus size: 27
53116464 TCCTCGATTT
* *
53116474 GTAAAATTAACGAAATACCCTTATAGG
1 GTAAAATTACCGAAATACCCTTGTAGG
* *
53116501 GTAGAAA-TACCTAAATACCCCTGTAGG
1 GTA-AAATTACCGAAATACCCTTGTAGG
** * *
53116528 GTAGGATTACTGAAATACTCC-TGTAAG
1 GTAAAATTACCGAAATAC-CCTTGTAGG
* * *
53116555 GTAGAATTACCGAGATACCCTTGTGGG
1 GTAAAATTACCGAAATACCCTTGTAGG
53116582 GTAAAATTACC
1 GTAAAATTACC
53116593 ATTTTACCCC
Statistics
Matches: 73, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
26 3 0.04
27 65 0.89
28 5 0.07
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (27 bp):
GTAAAATTACCGAAATACCCTTGTAGG
Found at i:53116875 original size:27 final size:26
Alignment explanation
Indices: 53116837--53116888 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
53116827 CTCGCTGCAA
*
53116837 TCTGGTGGCTTCGCCACATATATCTGT
1 TCTGGTGACTTCGCCACA-ATATCTGT
*
53116864 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACTTCGCCACAATATCTG
53116889 GCAGCCTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (26 bp):
TCTGGTGACTTCGCCACAATATCTGT
Found at i:53116926 original size:67 final size:67
Alignment explanation
Indices: 53116818--53116971 Score: 281
Period size: 67 Copynumber: 2.3 Consensus size: 67
53116808 GAGGAAGCGT
53116818 TCTGGCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
53116883 TA
66 TA
* *
53116885 TCTGGCAGCCTCGCTGCAATGTGGTGGCTTCGTCACATATATCTGTTCTGGTGACTTCGTCACAA
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
53116950 TA
66 TA
*
53116952 TCTGGCAGCCTCGCTACAAT
1 TCTGGCAGCCTCGCTGCAAT
53116972 TTCTGTGGTA
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 84 1.00
ACGTcount: A:0.18, C:0.28, G:0.23, T:0.31
Consensus pattern (67 bp):
TCTGGCAGCCTCGCTGCAATCTGGTGGCTTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
TA
Found at i:53117104 original size:6 final size:6
Alignment explanation
Indices: 53117073--53117178 Score: 83
Period size: 6 Copynumber: 17.3 Consensus size: 6
53117063 TTGCATTCAC
* * * *
53117073 ATTCTG ATTTTG ATTTTG -TTACCTG ATACTG ATTCTG GTTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
53117122 -TCACCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTC ATTTTG ATTCT-
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG
53117170 AGTTCTG AT
1 A-TTCTG AT
53117179 AATGTTTCTT
Statistics
Matches: 80, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
5 4 0.05
6 68 0.85
7 6 0.08
8 2 0.03
ACGTcount: A:0.17, C:0.17, G:0.16, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:53117108 original size:31 final size:31
Alignment explanation
Indices: 53117073--53117152 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
53117063 TTGCATTCAC
* * *
53117073 ATTCTGATTTTGATTTTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTCACCTGATACTG
* *
53117104 ATTCTGGTTCTGATTCTGTCACCTGATTCTG
1 ATTCTGATTCTGATTCTGTCACCTGATACTG
53117135 ATTCTGATTCTGATTCTG
1 ATTCTGATTCTGATTCTG
53117153 ATTCTCATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.16, C:0.17, G:0.17, T:0.49
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTCACCTGATACTG
Found at i:53130334 original size:23 final size:23
Alignment explanation
Indices: 53130299--53130358 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
53130289 TGTCCCTAAG
* *
53130299 CACACGGGTGTGTGCTTTGCCTC
1 CACACGGGCGTGTGCTTTCCCTC
*
53130322 CACATGGGCGTGTGCTTTCCCTC
1 CACACGGGCGTGTGCTTTCCCTC
* *
53130345 TACACGGGCATGTG
1 CACACGGGCGTGTG
53130359 AGGCATAACT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.12, C:0.30, G:0.30, T:0.28
Consensus pattern (23 bp):
CACACGGGCGTGTGCTTTCCCTC
Found at i:53132944 original size:13 final size:13
Alignment explanation
Indices: 53132922--53132998 Score: 91
Period size: 13 Copynumber: 5.9 Consensus size: 13
53132912 AGTTCTTCAT
*
53132922 TGCTTCTGAAAAG
1 TGCTTTTGAAAAG
53132935 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
53132948 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
53132961 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
53132974 TACTTTTGAGAAG
1 TGCTTTTGAAAAG
*
53132987 TGCTTTGGAAAA
1 TGCTTTTGAAAA
53132999 ATTTAAGTGT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 54 1.00
ACGTcount: A:0.30, C:0.09, G:0.27, T:0.34
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:53132980 original size:39 final size:39
Alignment explanation
Indices: 53132922--53132998 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
53132912 AGTTCTTCAT
*
53132922 TGCTTCTGAAAAGTGCTTTTGAAAAGTGCTGTGGAAAAG
1 TGCTTCTGAAAAGTACTTTTGAAAAGTGCTGTGGAAAAG
* * * *
53132961 TGCTTTTGAGAAGTACTTTTGAGAAGTGCTTTGGAAAA
1 TGCTTCTGAAAAGTACTTTTGAAAAGTGCTGTGGAAAA
53132999 ATTTAAGTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.30, C:0.09, G:0.27, T:0.34
Consensus pattern (39 bp):
TGCTTCTGAAAAGTACTTTTGAAAAGTGCTGTGGAAAAG
Found at i:53135027 original size:37 final size:37
Alignment explanation
Indices: 53134968--53135041 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
53134958 AGCTCAGACG
* *
53134968 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGAAGTCATCGGGCCTTACCCGGACA
*
53135005 AAATCTCCACACGTAGTCATCGGGCCTTACCCGGACA
1 AAATCTCCACACGAAGTCATCGGGCCTTACCCGGACA
53135042 TAGTACGAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.20
Consensus pattern (37 bp):
AAATCTCCACACGAAGTCATCGGGCCTTACCCGGACA
Found at i:53135216 original size:47 final size:47
Alignment explanation
Indices: 53135147--53135743 Score: 969
Period size: 47 Copynumber: 12.6 Consensus size: 47
53135137 CCCTTCGGGA
*
53135147 CTTATCACATTTATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53135194 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53135241 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53135288 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53135337 CTTATCACATATATACACTTTCACATTCATCATATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
53135384 CTTATCACATATATATACACTTTCACATTCATCACATTGGTCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53135433 CTTATCACATATACACACTTTCACATTCATAACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53135480 CTTATCACATATATATACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
53135527 CTTATAACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53135574 CTTATCACATATATACACTTTCACATTCATCATATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53135621 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53135670 CTTATCACATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53135717 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
53135744 TATTCAAATA
Statistics
Matches: 507, Mismatches: 37, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
47 375 0.74
49 132 0.26
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:53135362 original size:96 final size:94
Alignment explanation
Indices: 53135147--53135743 Score: 969
Period size: 96 Copynumber: 6.3 Consensus size: 94
53135137 CCCTTCGGGA
*
53135147 CTTATCACATTTATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
53135212 TTTCACATTCATCACATCGGCTATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
53135241 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
* *
53135306 ACTTTCACATTCATCACATTGGCCATTCGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
*
53135337 CTTATCACATATATACACTTTCACATTCATCATATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
* * *
53135402 ACTTTCACATTCATCACATTGGTCATTCGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
* * *
53135433 CTTATCACATATACACACTTTCACATTCATAACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
53135498 TTTCACATTCATCACATCGGCTATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
* * *
53135527 CTTATAACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
53135592 TTTCACATTCATCATATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
* * *
53135621 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
53135686 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
53135717 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
53135744 TATTCAAATA
Statistics
Matches: 474, Mismatches: 25, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
94 200 0.42
96 274 0.58
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:53135445 original size:143 final size:141
Alignment explanation
Indices: 53135147--53135743 Score: 969
Period size: 143 Copynumber: 4.2 Consensus size: 141
53135137 CCCTTCGGGA
*
53135147 CTTATCACATTTATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
53135212 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
53135277 GGCCATTAGGC
131 GGCCATTAGGC
* *
53135288 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
53135353 ACTTTCACATTCATCATATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCA
* * *
53135418 CATTGGTCATTCGGC
127 CATCGGCCATTAGGC
* * *
53135433 CTTATCACATATACACACTTTCACATTCATAACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* * *
53135498 TTTCACATTCATCACATCGGCTATTAGGCCTTATAACATATATACACTTTCACATTCATCACATT
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
*
53135563 GGCCATTCGGC
131 GGCCATTAGGC
*
53135574 CTTATCACATATATACACTTTCACATTCATCATATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
* * *
53135639 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
53135704 TCGGCCATTAGGC
129 TCGGCCATTAGGC
53135717 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
53135744 TATTCAAATA
Statistics
Matches: 422, Mismatches: 28, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
141 98 0.23
143 280 0.66
145 44 0.10
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:53139325 original size:20 final size:21
Alignment explanation
Indices: 53139275--53139331 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
53139265 GATAAAAATA
*
53139275 AAAAGGAAAAAAAA-AGACAG
1 AAAAGTAAAAAAAATAGACAG
* * *
53139295 AAAATTCAAAAAAATCGA-AG
1 AAAAGTAAAAAAAATAGACAG
53139315 AAAAGTAAAAATAAATA
1 AAAAGTAAAAA-AAATA
53139332 AATAAAAAGA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.72, C:0.05, G:0.12, T:0.11
Consensus pattern (21 bp):
AAAAGTAAAAAAAATAGACAG
Found at i:53140269 original size:15 final size:15
Alignment explanation
Indices: 53140239--53140286 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
53140229 TGAAAAATGA
53140239 ATTTTTAAATAATTTTT
1 ATTTTT-AA-AATTTTT
53140256 ATTTTTAAAATTTTT
1 ATTTTTAAAATTTTT
* **
53140271 GTTTTTTGAATTTTT
1 ATTTTTAAAATTTTT
53140286 A
1 A
53140287 AGATTAAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 19 0.70
16 2 0.07
17 6 0.22
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (15 bp):
ATTTTTAAAATTTTT
Found at i:53142357 original size:50 final size:50
Alignment explanation
Indices: 53142282--53142382 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
53142272 TTGCTAACCT
* *
53142282 ACACAAGTTAGAAGGTAGAAGCACCACCATAAATAACACTTTCTTCACCC
1 ACACAAGTTAGAAGGTAGAAGCACCACCAAAAACAACACTTTCTTCACCC
53142332 ACACAAGTTAGAAGGTAGAAGCACCACCAAAAACAACACTTTCTTCACCC
1 ACACAAGTTAGAAGGTAGAAGCACCACCAAAAACAACACTTTCTTCACCC
53142382 A
1 A
53142383 ATTAATTAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.42, C:0.29, G:0.12, T:0.18
Consensus pattern (50 bp):
ACACAAGTTAGAAGGTAGAAGCACCACCAAAAACAACACTTTCTTCACCC
Found at i:53145124 original size:30 final size:30
Alignment explanation
Indices: 53145088--53145145 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
53145078 ATACGAGAAA
*
53145088 AGACACGGGCGTGTGTCTTAGCCATGTGCG
1 AGACACGGGCGTGTGGCTTAGCCATGTGCG
53145118 AGACACGGGCGTGTGGCTTAGCCATGTG
1 AGACACGGGCGTGTGGCTTAGCCATGTG
53145146 TCCCCTGGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.17, C:0.22, G:0.38, T:0.22
Consensus pattern (30 bp):
AGACACGGGCGTGTGGCTTAGCCATGTGCG
Found at i:53153490 original size:8 final size:8
Alignment explanation
Indices: 53153477--53153507 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
53153467 TAAGTGTAGC
53153477 GTTGGAGT
1 GTTGGAGT
53153485 GTTGGAGT
1 GTTGGAGT
53153493 GTTGGAGT
1 GTTGGAGT
53153501 GTTGGAG
1 GTTGGAG
53153508 GTCTTGTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.52, T:0.35
Consensus pattern (8 bp):
GTTGGAGT
Found at i:53171184 original size:14 final size:14
Alignment explanation
Indices: 53171167--53171195 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
53171157 AGAGTTTTAC
53171167 ATTGATTCTTTTGG
1 ATTGATTCTTTTGG
53171181 ATTGATTCTTTTGG
1 ATTGATTCTTTTGG
53171195 A
1 A
53171196 CCTTCGACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.07, G:0.21, T:0.55
Consensus pattern (14 bp):
ATTGATTCTTTTGG
Found at i:53174258 original size:13 final size:13
Alignment explanation
Indices: 53174235--53174263 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
53174225 TTTAATTTAA
53174235 TTAGTTAATTAGT
1 TTAGTTAATTAGT
53174248 TTAGTTAATTAGT
1 TTAGTTAATTAGT
53174261 TTA
1 TTA
53174264 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:53182197 original size:60 final size:60
Alignment explanation
Indices: 53182119--53182255 Score: 172
Period size: 60 Copynumber: 2.3 Consensus size: 60
53182109 CAGTGTTAAC
* *
53182119 TGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCC-CTTAC-AGTATC-AGAGTATAT
1 TGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAG--TCGAGA-TATAT
* *
53182180 TGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACAAGTCGAGATATAT
1 TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGTCGAGATATAT
*
53182240 TGGGCCTTGCCCATAT
1 TGGGCCTAGCCCATAT
53182256 TAACATAGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
60 53 0.78
61 13 0.19
62 2 0.03
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (60 bp):
TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGTCGAGATATAT
Found at i:53182219 original size:28 final size:27
Alignment explanation
Indices: 53182118--53182219 Score: 80
Period size: 28 Copynumber: 3.5 Consensus size: 27
53182108 TCAGTGTTAA
* *
53182118 CTGGGCCTTAGCCCATATCAATATTAAT
1 CTGGGCC-TAGCCCATATCAGTATCAAT
*
53182146 CTGGGCCATAGCCCCT-TACAGTATCAGAGTAT
1 CTGGGCC-TAGCCCATAT-CAGTATC--A--AT
*
53182178 ATTGGGCCTAGCCCATATCAGTATCAAT
1 -CTGGGCCTAGCCCATATCAGTATCAAT
53182206 CTGGGCCGTAGCCC
1 CTGGGCC-TAGCCC
53182220 TATTACAAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
27 7 0.12
28 27 0.46
30 2 0.03
32 16 0.27
33 7 0.12
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (27 bp):
CTGGGCCTAGCCCATATCAGTATCAAT
Found at i:53189272 original size:27 final size:27
Alignment explanation
Indices: 53189240--53189294 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
53189230 CGTTGCAAAA
* *
53189240 GTCCTCCCTATCGGGAATGATCACTGG
1 GTCCTCCCTACCGAGAATGATCACTGG
53189267 GTCCTCCCTACCGAGAATGATCACTGG
1 GTCCTCCCTACCGAGAATGATCACTGG
53189294 G
1 G
53189295 CCCATAACAA
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:0.20, C:0.31, G:0.25, T:0.24
Consensus pattern (27 bp):
GTCCTCCCTACCGAGAATGATCACTGG
Found at i:53189597 original size:9 final size:9
Alignment explanation
Indices: 53189583--53189609 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
53189573 AAAAAAATAA
53189583 ATTTAAAAT
1 ATTTAAAAT
53189592 ATTTAAAAT
1 ATTTAAAAT
53189601 ATTTAAAAT
1 ATTTAAAAT
53189610 TAAGTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
ATTTAAAAT
Found at i:53191467 original size:22 final size:23
Alignment explanation
Indices: 53191437--53191480 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
53191427 ATTAATAAAC
*
53191437 ACAATTTTTCTTTT-AAAATTTA
1 ACAACTTTTCTTTTGAAAATTTA
*
53191459 ACAACTTTTTTTTTGAAAATTT
1 ACAACTTTTCTTTTGAAAATTT
53191481 TAACTAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (23 bp):
ACAACTTTTCTTTTGAAAATTTA
Found at i:53191484 original size:24 final size:22
Alignment explanation
Indices: 53191437--53191480 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
53191427 ATTAATAAAC
53191437 ACAATTTTTCTTTTAAAATTTA
1 ACAATTTTTCTTTTAAAATTTA
53191459 ACAACTTTTT-TTTTGAAAATTT
1 ACAA-TTTTTCTTTT-AAAATTT
53191481 TAACTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (22 bp):
ACAATTTTTCTTTTAAAATTTA
Found at i:53198207 original size:27 final size:27
Alignment explanation
Indices: 53198159--53198318 Score: 168
Period size: 27 Copynumber: 5.9 Consensus size: 27
53198149 GCGAGGCTGC
* *
53198159 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
*
53198186 CAGATATTATGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
53198212 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
53198239 CAGATAATTGTGGCATAGCCACCAG-GA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
53198266 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
53198293 TAGATAAATTGTGGCATAGCCACCAG
1 CAGAT--ATTGTGGCAGAGCCACCAG
53198319 GACGCTTCCT
Statistics
Matches: 114, Mismatches: 10, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
26 10 0.09
27 83 0.73
28 19 0.17
29 2 0.02
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:53198253 original size:54 final size:54
Alignment explanation
Indices: 53198177--53198318 Score: 223
Period size: 54 Copynumber: 2.6 Consensus size: 54
53198167 GTGACGAAGT
* *
53198177 CACCAGATACAGAT-ATTATGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
*
53198231 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
*
53198285 CACCAGATTAGATAAATTGTGGCATAGCCACCAG
1 CACCAGATCAGAT-AATTGTGGCATAGCCACCAG
53198319 GACGCTTCCT
Statistics
Matches: 82, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
53 5 0.06
54 57 0.70
55 20 0.24
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:53201538 original size:15 final size:17
Alignment explanation
Indices: 53201507--53201538 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
53201497 AAATAAATCA
53201507 AATAGTTTAAAATGGAT
1 AATAGTTTAAAATGGAT
53201524 AATA-TTTAAAA-GGAT
1 AATAGTTTAAAATGGAT
53201539 TTAAGATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 7 0.47
17 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (17 bp):
AATAGTTTAAAATGGAT
Found at i:53201707 original size:31 final size:31
Alignment explanation
Indices: 53201659--53201724 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
53201649 GTATTAAAAT
53201659 AAATAAATAGAGTTTAAAAGATATATATATATA
1 AAATAAATA-AGTTTAAAAGATATA-ATATATA
*
53201692 AAATAAAT-AGTTTAAAATATATAATATATA
1 AAATAAATAAGTTTAAAAGATATAATATATA
53201722 AAA
1 AAA
53201725 GGAAATCTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 10 0.31
31 14 0.44
33 8 0.25
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (31 bp):
AAATAAATAAGTTTAAAAGATATAATATATA
Found at i:53216148 original size:26 final size:26
Alignment explanation
Indices: 53216109--53216175 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
53216099 ACCCTCTCTT
53216109 GCACATAACCCTAATATATAA-TTTG
1 GCACATAACCCTAATATATAACTTTG
* *
53216134 GGATCATAACCCTAATATATAACTTTT
1 GCA-CATAACCCTAATATATAACTTTG
53216161 GCACATAACCCTAAT
1 GCACATAACCCTAAT
53216176 TTCATCATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 2 0.05
26 30 0.81
27 5 0.14
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.31
Consensus pattern (26 bp):
GCACATAACCCTAATATATAACTTTG
Found at i:53217636 original size:101 final size:101
Alignment explanation
Indices: 53217456--53217671 Score: 315
Period size: 101 Copynumber: 2.1 Consensus size: 101
53217446 GTGTGATGGA
* * *
53217456 ACACAGGCGTGTGATCAACGAGCCAGGCCGTCCACGCATGACACTGCCGTGTGATGGCCAGGTAG
1 ACACAGGCGTGTGATCAACGAGCCAGGCCGTCCACGCATGACACGGCCGTGTGATAGCCAGATAG
* * *
53217521 GCCGTGTGCTAGACACGGGCTACACTGAGTGAGACT
66 GCCGTGTGCGAGACACAGGCTACACTGAGTAAGACT
* * * * * * *
53217557 ACACGGGCGTGTGATCGACGAGCCAGGCTGTGCACGCATGACACGGCTGTGTGGTAGCCATATAG
1 ACACAGGCGTGTGATCAACGAGCCAGGCCGTCCACGCATGACACGGCCGTGTGATAGCCAGATAG
53217622 GCCGTGTGCGAGACACAGGCTACACTGAGTAAGACT
66 GCCGTGTGCGAGACACAGGCTACACTGAGTAAGACT
53217658 ACACAGGCGTGTGA
1 ACACAGGCGTGTGA
53217672 GATTCTGGGT
Statistics
Matches: 101, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.24, C:0.26, G:0.33, T:0.17
Consensus pattern (101 bp):
ACACAGGCGTGTGATCAACGAGCCAGGCCGTCCACGCATGACACGGCCGTGTGATAGCCAGATAG
GCCGTGTGCGAGACACAGGCTACACTGAGTAAGACT
Found at i:53218636 original size:21 final size:22
Alignment explanation
Indices: 53218582--53218637 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
53218572 AAAACCCGGG
*
53218582 TTTTCTCTAAAAAAAAACTATGGT
1 TTTTC-CTAAAATAAAAC-ATGGT
*
53218606 TTTT-GT-AAATAAAA-ATGGT
1 TTTTCCTAAAATAAAACATGGT
53218625 TTTTCCTAAAATA
1 TTTTCCTAAAATA
53218638 GTAGGTTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
19 9 0.33
20 1 0.04
21 12 0.44
22 1 0.04
24 4 0.15
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (22 bp):
TTTTCCTAAAATAAAACATGGT
Found at i:53219688 original size:30 final size:30
Alignment explanation
Indices: 53219642--53219698 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
53219632 TAGACACTTC
*
53219642 CACACGGGTAATCCACAAACCCGTGTGAGA
1 CACACGGGTAAGCCACAAACCCGTGTGAGA
* **
53219672 CACACGGGTAGGCCACATGCCCGTGTG
1 CACACGGGTAAGCCACAAACCCGTGTG
53219699 TCATGACCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (30 bp):
CACACGGGTAAGCCACAAACCCGTGTGAGA
Found at i:53225022 original size:18 final size:19
Alignment explanation
Indices: 53224999--53225039 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
53224989 TAATTAAAAA
53224999 AATTGTTCAATCATAAG-T
1 AATTGTTCAATCATAAGCT
*
53225017 AATTGTTCAATTATAAGCT
1 AATTGTTCAATCATAAGCT
53225036 AATT
1 AATT
53225040 AATTATTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (19 bp):
AATTGTTCAATCATAAGCT
Found at i:53228712 original size:25 final size:24
Alignment explanation
Indices: 53228683--53228730 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
53228673 CATGTAAAAA
53228683 ATAAAGAAAATAAAAAACAAAATAT
1 ATAAAGAAAATAAAAAA-AAAATAT
* *
53228708 ATAAATAAAATAAAATAAAAATA
1 ATAAAGAAAATAAAAAAAAAATA
53228731 AAATTGTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (24 bp):
ATAAAGAAAATAAAAAAAAAATAT
Found at i:53228729 original size:16 final size:16
Alignment explanation
Indices: 53228679--53228734 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
53228669 TTAACATGTA
*
53228679 AAAAAT-AAAGAAAAT
1 AAAAATAAAATAAAAT
* *
53228694 AAAAA-ACAA-AATAT
1 AAAAATAAAATAAAAT
*
53228708 ATAAATAAAATAAAAT
1 AAAAATAAAATAAAAT
53228724 AAAAATAAAAT
1 AAAAATAAAAT
53228735 TGTGTTGCCT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
14 8 0.25
15 10 0.31
16 14 0.44
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (16 bp):
AAAAATAAAATAAAAT
Found at i:53233256 original size:50 final size:50
Alignment explanation
Indices: 53233181--53233282 Score: 177
Period size: 50 Copynumber: 2.0 Consensus size: 50
53233171 CGTACAGGCC
* *
53233181 TTGCTTTTACTGTAAAAAGAGAATTCACAATATTAGTAAGTTTATCAACT
1 TTGCTTTTACTATAAAAAGAGAATTCACAATATTAGTAAGTCTATCAACT
*
53233231 TTGCTTTTACTATAAAAAGAGAATTCATAATATTAGTAAGTCTATCAACT
1 TTGCTTTTACTATAAAAAGAGAATTCACAATATTAGTAAGTCTATCAACT
53233281 TT
1 TT
53233283 ATCTTCTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (50 bp):
TTGCTTTTACTATAAAAAGAGAATTCACAATATTAGTAAGTCTATCAACT
Found at i:53242064 original size:12 final size:12
Alignment explanation
Indices: 53242047--53242079 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
53242037 CGGCCCACCC
53242047 ATATTAATTTTT
1 ATATTAATTTTT
53242059 ATATT-ATTTTT
1 ATATTAATTTTT
53242070 ATA-TAATTTT
1 ATATTAATTTT
53242080 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:53242237 original size:30 final size:29
Alignment explanation
Indices: 53242201--53242260 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 29
53242191 CAATTTAACA
53242201 AGCAAAT-TCTTCTAAAATAATAACAAAATT
1 AGCAAATGTCTT-TAAAATAATAA-AAAATT
53242231 AGCAAATGTCTTTAAAATAATAAAAAATT
1 AGCAAATGTCTTTAAAATAATAAAAAATT
53242260 A
1 A
53242261 ACAATAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 7 0.24
30 18 0.62
31 4 0.14
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.30
Consensus pattern (29 bp):
AGCAAATGTCTTTAAAATAATAAAAAATT
Found at i:53242319 original size:22 final size:22
Alignment explanation
Indices: 53242294--53242336 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
53242284 TATTCAAATA
53242294 ATAACAACAAAATAGTAGCAAT
1 ATAACAACAAAATAGTAGCAAT
* **
53242316 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
53242337 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAT
Found at i:53242340 original size:11 final size:11
Alignment explanation
Indices: 53242301--53242341 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
53242291 ATAATAACAA
53242301 CAAAATAGTAG
1 CAAAATAGTAG
* *
53242312 CAATATAATAG
1 CAAAATAGTAG
*
53242323 TAAAATAGTAG
1 CAAAATAGTAG
53242334 CAAAATAG
1 CAAAATAG
53242342 GGAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:53246486 original size:18 final size:18
Alignment explanation
Indices: 53246463--53246499 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
53246453 AAAATCAAAG
53246463 TAAAAGCACGGTGGCCCA
1 TAAAAGCACGGTGGCCCA
*
53246481 TAAAAGCACGGTGGGCCA
1 TAAAAGCACGGTGGCCCA
53246499 T
1 T
53246500 GGGTGACGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.30, T:0.14
Consensus pattern (18 bp):
TAAAAGCACGGTGGCCCA
Found at i:53248028 original size:28 final size:28
Alignment explanation
Indices: 53247996--53248051 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
53247986 TTGCAAGTAA
53247996 GTGATCTTGATGACTTTTCTTAAATATT
1 GTGATCTTGATGACTTTTCTTAAATATT
*
53248024 GTGATTTTGATGACTTTTCTTAAATATT
1 GTGATCTTGATGACTTTTCTTAAATATT
53248052 TTTGTACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.09, G:0.14, T:0.52
Consensus pattern (28 bp):
GTGATCTTGATGACTTTTCTTAAATATT
Found at i:53250132 original size:13 final size:13
Alignment explanation
Indices: 53250116--53250150 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
53250106 ACGAGCATGG
53250116 GACACGGGCCATA
1 GACACGGGCCATA
*
53250129 GACAAGGGCCATA
1 GACACGGGCCATA
53250142 GACACGGGC
1 GACACGGGC
53250151 GTGTGTCAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.31, C:0.29, G:0.34, T:0.06
Consensus pattern (13 bp):
GACACGGGCCATA
Found at i:53250168 original size:99 final size:99
Alignment explanation
Indices: 53250036--53250223 Score: 295
Period size: 99 Copynumber: 1.9 Consensus size: 99
53250026 GAGGGACACA
*
53250036 GGCCATAGACACGAGCGTGTGTTAGGCCGTGTGAAAACCCCTGTAGGTTCGAATTTAGAATTTAA
1 GGCCATAGACACGAGCGTGTGTCAGGCCGTGTGAAAACCCCTGTAGGTTCGAATTTAGAATTTAA
53250101 TTCACACGAGCATGGGACACGGGCCATAGACAAG
66 TTCACACGAGCATGGGACACGGGCCATAGACAAG
* ** * *
53250135 GGCCATAGACACGGGCGTGTGTCAGGCTTTGTGAAAACCTCTGTAGGTTTGAATTTAGAATTTAA
1 GGCCATAGACACGAGCGTGTGTCAGGCCGTGTGAAAACCCCTGTAGGTTCGAATTTAGAATTTAA
* * *
53250200 TTTACACGGGCATGGGTCACGGGC
66 TTCACACGAGCATGGGACACGGGC
53250224 GTGTCCCTTA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 80 1.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (99 bp):
GGCCATAGACACGAGCGTGTGTCAGGCCGTGTGAAAACCCCTGTAGGTTCGAATTTAGAATTTAA
TTCACACGAGCATGGGACACGGGCCATAGACAAG
Found at i:53273067 original size:46 final size:46
Alignment explanation
Indices: 53272961--53273089 Score: 168
Period size: 46 Copynumber: 2.8 Consensus size: 46
53272951 TATGAGGCAT
* * * *
53272961 CCGAACTCGTTGAGTTGCATTCCGAGTTCACCTATGGATGCAAACAT
1 CCGAACTCGTTGAGTTGCGTTTCGAGTTCA-TTATGGATGCAAACAC
* * *
53273008 CCGAACTCATTGAGTTGTGTTTCGAGTTCATTATGGATGCGAACAC
1 CCGAACTCGTTGAGTTGCGTTTCGAGTTCATTATGGATGCAAACAC
* *
53273054 CCGAGCTCGTTGAGTTGCGTTTCGAGTTTATTATGG
1 CCGAACTCGTTGAGTTGCGTTTCGAGTTCATTATGG
53273090 GTGAGATTAT
Statistics
Matches: 71, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
46 45 0.63
47 26 0.37
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.33
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGCGTTTCGAGTTCATTATGGATGCAAACAC
Found at i:53290049 original size:92 final size:92
Alignment explanation
Indices: 53289938--53290107 Score: 313
Period size: 92 Copynumber: 1.8 Consensus size: 92
53289928 CGCCCTAAGT
* *
53289938 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
53290003 CGAGTTCGGATGCCTAGTTACATTCAC
66 CGAGTTCGGATGCCTAGTTACATTCAC
*
53290030 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
53290095 CGAGTTCGGATGC
66 CGAGTTCGGATGC
53290108 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTCAC
Found at i:53290104 original size:46 final size:46
Alignment explanation
Indices: 53289933--53290104 Score: 217
Period size: 46 Copynumber: 3.7 Consensus size: 46
53289923 TAACCCGCCC
* * *
53289933 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
53289979 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CTAGTTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A--TCCA
* *
53290025 TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 -TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
53290071 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
53290105 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 95 0.88
47 2 0.02
48 4 0.04
49 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:53290123 original size:46 final size:46
Alignment explanation
Indices: 53289935--53290123 Score: 151
Period size: 46 Copynumber: 4.1 Consensus size: 46
53289925 ACCCGCCCTA
* ** * *
53289935 AGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC--GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCC-T
*
53289980 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATTC-
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCCT
* * * * *
53290028 A-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATCCT
53290073 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
53290119 AGTGA
1 AGTGA
53290124 CATGTCACTT
Statistics
Matches: 116, Mismatches: 13, Indels: 28
0.74 0.08 0.18
Matches are distributed among these distances:
44 9 0.08
45 2 0.02
46 95 0.82
47 1 0.01
48 4 0.03
49 1 0.01
50 4 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
Found at i:53290559 original size:30 final size:30
Alignment explanation
Indices: 53290525--53290584 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
53290515 ATTTAATACG
53290525 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
53290555 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
53290585 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:53297595 original size:93 final size:92
Alignment explanation
Indices: 53297484--53297653 Score: 304
Period size: 93 Copynumber: 1.8 Consensus size: 92
53297474 GCCCCTAAGT
* *
53297484 GAACTCGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
53297549 GAGTTCGGATGCCTAGTTACATTTCAC
66 GAGTTCGGATGCCTAGTTACATTTCAC
*
53297576 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTC-GACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
53297641 CGAGTTCGGATGC
65 CGAGTTCGGATGC
53297654 TCAACCATCC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 6 0.08
93 68 0.92
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (92 bp):
GAACTCGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATTTCAC
Found at i:53297650 original size:46 final size:46
Alignment explanation
Indices: 53297479--53297650 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
53297469 AACCCGCCCC
* * *
53297479 TAAGTGAACTC-GACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
53297524 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
53297572 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
53297617 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
53297651 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 11, Indels: 19
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 13 0.12
46 49 0.46
47 29 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:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:53298108 original size:30 final size:30
Alignment explanation
Indices: 53298074--53298133 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
53298064 ATTTAATACG
53298074 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
53298104 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
53298134 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:53302427 original size:93 final size:93
Alignment explanation
Indices: 53302315--53302486 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
53302305 CGCCCATAAG
*
53302315 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
53302379 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
53302408 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
53302473 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
53302487 TCAATCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:53302481 original size:46 final size:46
Alignment explanation
Indices: 53302308--53302483 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
53302298 TGTAACCCGC
* *
53302308 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
53302354 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
53302404 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
53302447 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
53302484 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:53309361 original size:48 final size:48
Alignment explanation
Indices: 53309300--53309527 Score: 216
Period size: 48 Copynumber: 4.8 Consensus size: 48
53309290 CAACCACATT
53309300 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAG
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAG
* * * *
53309348 ACGAGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAG
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAG
* * *
53309394 ATGTA-AGCCAATGTAAGACCATGTCTGGGACGTGGCATCAGCACGTAT-AG
1 ATG-AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA--T-TGAG
* * * * ** *
53309444 A-G-GTGACGGTGTAAGACCATGTCTGGGACATGGCATTGGCACGGAT
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAG
* *
53309490 ATGTGAGAGCTAGAGTAAGACCATGTCTGGGACATGGC
1 A--TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGC
53309528 GTTGGCCTTG
Statistics
Matches: 142, Mismatches: 26, Indels: 22
0.75 0.14 0.12
Matches are distributed among these distances:
46 27 0.19
47 28 0.20
48 54 0.38
49 2 0.01
50 31 0.22
ACGTcount: A:0.27, C:0.19, G:0.33, T:0.21
Consensus pattern (48 bp):
ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAG
Found at i:53309422 original size:94 final size:94
Alignment explanation
Indices: 53309260--53309527 Score: 262
Period size: 94 Copynumber: 2.8 Consensus size: 94
53309250 TTAATTGTGT
* * ** *
53309260 ACTAGTGTAAGACATGTTTAGGACATGCATCAACCAC-ATTATG-AGAGCCAGTGTAAGACCATG
1 ACTAGTGTAAGACATGTCTGGGACATGCATCGGCC-CGA-TATGTAGAGCCAATGTAAGACCATG
*
53309323 TCTGGGACATGGCATCGGCA-T-TGAGACGAG
64 TCTGGGACATGGCATCAGCACTAT-AGACGAG
*
53309353 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTA-AGCCAATGTAAGACCATG
1 A-CTAGTGTAAGACATGTCTGGGACATGCATCGGCC-CGATATGTAGAGCCAATGTAAGACCATG
* * *
53309417 TCTGGGACGTGGCATCAGCACGTATAGAGGTG
64 TCTGGGACATGGCATCAGCAC-TATAGACGAG
* * * *
53309449 AC-GGTGTAAGACCATGTCTGGGACATGGCATTGGCACGGATATGTGAGAGCTAGA-GTAAGACC
1 ACTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CCGATATGT-AGAGCCA-ATGTAAGACC
53309512 ATGTCTGGGACATGGC
61 ATGTCTGGGACATGGC
53309528 GTTGGCCTTG
Statistics
Matches: 146, Mismatches: 17, Indels: 19
0.80 0.09 0.10
Matches are distributed among these distances:
93 1 0.01
94 77 0.53
95 17 0.12
96 20 0.14
97 3 0.02
98 27 0.18
99 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.22
Consensus pattern (94 bp):
ACTAGTGTAAGACATGTCTGGGACATGCATCGGCCCGATATGTAGAGCCAATGTAAGACCATGTC
TGGGACATGGCATCAGCACTATAGACGAG
Found at i:53312596 original size:20 final size:20
Alignment explanation
Indices: 53312571--53312615 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
53312561 AGGGACAAAA
* *
53312571 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
53312591 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
53312611 ATGAA
1 ATGAA
53312616 TACATGTGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:53315469 original size:40 final size:40
Alignment explanation
Indices: 53315406--53315531 Score: 171
Period size: 40 Copynumber: 3.1 Consensus size: 40
53315396 CTTAATTTGG
* *
53315406 ACCTGATAATATCTCGATCGAAGGTCATTTTTTGAAAACA
1 ACCTTATAATATCCCGATCGAAGGTCATTTTTTGAAAACA
* * *
53315446 ACCTTATAATATCCCGATTGAAGGTTAGTTTTTGAAAACA
1 ACCTTATAATATCCCGATCGAAGGTCATTTTTTGAAAACA
* * * *
53315486 ACTTTATAATATCCTGGTCAAAGGTCATTTTTTGAAAACA
1 ACCTTATAATATCCCGATCGAAGGTCATTTTTTGAAAACA
53315526 ACCTTA
1 ACCTTA
53315532 CTCTCTTGAG
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 73 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (40 bp):
ACCTTATAATATCCCGATCGAAGGTCATTTTTTGAAAACA
Found at i:53319473 original size:41 final size:41
Alignment explanation
Indices: 53319412--53319494 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
53319402 AAGAGTTAGT
*
53319412 TTAGAGACTCAACTGTTAAAGATGTTTAATAGCTCCGGCAC
1 TTAGAGACTCAACTGATAAAGATGTTTAATAGCTCCGGCAC
** *
53319453 TTAGAGACTCAA-TAGATAAAGATGTTTTGTAGCTCGGGCAC
1 TTAGAGACTCAACT-GATAAAGATGTTTAATAGCTCCGGCAC
53319494 T
1 T
53319495 AGGCCTAAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 1 0.03
41 36 0.97
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (41 bp):
TTAGAGACTCAACTGATAAAGATGTTTAATAGCTCCGGCAC
Found at i:53327728 original size:15 final size:15
Alignment explanation
Indices: 53327708--53327764 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
53327698 CGATGAATTT
*
53327708 ATTGAATTTATATTA
1 ATTGAATTTATATTG
* *
53327723 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
53327738 ATTGAATTTATATTG
1 ATTGAATTTATATTG
53327753 ATTGAA-TTATAT
1 ATTGAATTTATAT
53327765 AATATATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
14 6 0.16
15 31 0.84
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:53328197 original size:21 final size:23
Alignment explanation
Indices: 53328136--53328200 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
53328126 GGTTTACTGA
53328136 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
* ** *
53328159 TCAGGCACCTCGTTTGTCGT-TT
1 TCAGGCACTTTATGTGTCGTATT
53328181 T-AGGCACTTTATGTGTCGTA
1 TCAGGCACTTTATGTGTCGTA
53328201 CTCTGATCAG
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
21 14 0.42
22 3 0.09
23 16 0.48
ACGTcount: A:0.15, C:0.20, G:0.23, T:0.42
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:53330273 original size:45 final size:45
Alignment explanation
Indices: 53330209--53330299 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
53330199 CACGCTTGTC
*
53330209 TACTAGGTGTCTTCACTTGTGTCAGCAGAAATACATTCGTGATCT
1 TACTAGATGTCTTCACTTGTGTCAGCAGAAATACATTCGTGATCT
53330254 TACTAGATGTCTTCACTTGTGTCAGCAGAAATACATTCGTGATCT
1 TACTAGATGTCTTCACTTGTGTCAGCAGAAATACATTCGTGATCT
53330299 T
1 T
53330300 CTTGCTCGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (45 bp):
TACTAGATGTCTTCACTTGTGTCAGCAGAAATACATTCGTGATCT
Found at i:53332101 original size:46 final size:46
Alignment explanation
Indices: 53332051--53332222 Score: 179
Period size: 46 Copynumber: 3.7 Consensus size: 46
53332041 TGAGCATCCA
* *
53332051 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACGTCCG
* * *
53332097 AACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAA--A--CGTCCG
* * * *
53332144 AACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGTGAACGGCTG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACGTCCG
* * *
53332190 AGCTGGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53332223 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 57 0.55
47 29 0.28
48 3 0.03
50 6 0.06
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACGTCCG
Found at i:53332203 original size:93 final size:93
Alignment explanation
Indices: 53332044--53332215 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
53332034 GGATGGTTGA
* * *
53332044 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGGCCGAACTCGTTGAGT
53332109 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* ** * * *
53332137 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGTGAACGGCTGAGCTGGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGGCCGAACTCGTTGAGT
53332202 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
53332216 CTTATGGGCG
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGGCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:53335198 original size:14 final size:15
Alignment explanation
Indices: 53335149--53335198 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
53335139 GTATCTTGGG
*
53335149 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
53335164 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
53335179 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
53335193 TTTCTT
1 TTTCTT
53335199 GTTATCTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 8 0.26
15 23 0.74
ACGTcount: A:0.10, C:0.18, G:0.12, T:0.60
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:53337627 original size:45 final size:45
Alignment explanation
Indices: 53337578--53337751 Score: 212
Period size: 45 Copynumber: 3.8 Consensus size: 45
53337568 TGGTTGAGCA
53337578 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATG
* * *
53337623 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA-T--G
*
53337668 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AATG
* *
53337715 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53337752 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 9, Indels: 19
0.80 0.07 0.14
Matches are distributed among these distances:
42 6 0.05
43 1 0.01
44 2 0.02
45 59 0.54
46 5 0.05
47 31 0.28
49 4 0.04
50 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATG
Found at i:53337732 original size:92 final size:92
Alignment explanation
Indices: 53337575--53337743 Score: 295
Period size: 92 Copynumber: 1.8 Consensus size: 92
53337565 GGATGGTTGA
* *
53337575 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATGTCCGAACTCGTTGAGTT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGCCCGAACTCGTTGAGTT
53337640 GAGTCCGAGTTCGTGAGATGTAACTAG
66 GAGTCCGAGTTCGTGAGATGTAACTAG
*
53337667 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AACGCCCGAACTCGTTGAGT
53337731 TGAGTCCGAGTTC
65 TGAGTCCGAGTTC
53337744 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
91 9 0.12
92 64 0.88
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGCCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:53340417 original size:59 final size:59
Alignment explanation
Indices: 53340325--53340442 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
53340315 TTGCCTCAAA
*
53340325 TTATCATTCATCACATCTTCTAAAATGATACCAAATCTATCTCCAATATAATATCAATT
1 TTATCAGTCATCACATCTTCTAAAATGATACCAAATCTATCTCCAATATAATATCAATT
53340384 TTATCAGTCATCACATCTTCTAAAATGATACCAAATCTATCTCCAATATAATATCAATT
1 TTATCAGTCATCACATCTTCTAAAATGATACCAAATCTATCTCCAATATAATATCAATT
53340443 CAAATTACTT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (59 bp):
TTATCAGTCATCACATCTTCTAAAATGATACCAAATCTATCTCCAATATAATATCAATT
Found at i:53345668 original size:18 final size:20
Alignment explanation
Indices: 53345642--53345680 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
53345632 GAAAATAATT
53345642 TTTAAAAAAA-T-CAAAATA
1 TTTAAAAAAATTCCAAAATA
*
53345660 TTTATAAAAATTCCAAAATA
1 TTTAAAAAAATTCCAAAATA
53345680 T
1 T
53345681 ATGTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 1 0.06
20 8 0.44
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
TTTAAAAAAATTCCAAAATA
Found at i:53346475 original size:16 final size:17
Alignment explanation
Indices: 53346448--53346479 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
53346438 AGATCAAGAC
53346448 AAAAATATTAAAAATTT
1 AAAAATATTAAAAATTT
53346465 AAAAATA-TAAAAATT
1 AAAAATATTAAAAATT
53346480 AAATTAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAATATTAAAAATTT
Found at i:53347248 original size:24 final size:25
Alignment explanation
Indices: 53347209--53347255 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
53347199 TAAATAAACT
* *
53347209 AATTTTTAAGAGTAAAAATTAATAA
1 AATTTTTAACAGTAAAAACTAATAA
53347234 AATTTTTAACA-TAAAAACTAAT
1 AATTTTTAACAGTAAAAACTAAT
53347256 TTATTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.36
Consensus pattern (25 bp):
AATTTTTAACAGTAAAAACTAATAA
Found at i:53347596 original size:9 final size:9
Alignment explanation
Indices: 53347581--53347614 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
53347571 TCTTAAAGGG
53347581 CAAAAAAAA
1 CAAAAAAAA
53347590 -AAAAAAAA
1 CAAAAAAAA
53347598 CAAAAAAAA
1 CAAAAAAAA
53347607 CAAAAAAA
1 CAAAAAAA
53347615 GTAATGACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:53347603 original size:17 final size:18
Alignment explanation
Indices: 53347581--53347614 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
53347571 TCTTAAAGGG
53347581 CAAAAAAAA-AAAAAAAA
1 CAAAAAAAACAAAAAAAA
53347598 CAAAAAAAACAAAAAAA
1 CAAAAAAAACAAAAAAA
53347615 GTAATGACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (18 bp):
CAAAAAAAACAAAAAAAA
Found at i:53348368 original size:21 final size:22
Alignment explanation
Indices: 53348328--53348369 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
53348318 ATTAGAAAAA
*
53348328 CTTATAAAAAAATTCATAAATG
1 CTTATAAAAAAATCCATAAATG
*
53348350 CTTATAAATAAA-CCATAAAT
1 CTTATAAAAAAATCCATAAAT
53348370 AATATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (22 bp):
CTTATAAAAAAATCCATAAATG
Found at i:53348408 original size:10 final size:10
Alignment explanation
Indices: 53348395--53348437 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
53348385 ATGAACGTAT
53348395 AAAACTTATA
1 AAAACTTATA
53348405 AAAACTTATA
1 AAAACTTATA
* * *
53348415 AAAAATCACA
1 AAAACTTATA
*
53348425 AAAACCTATA
1 AAAACTTATA
53348435 AAA
1 AAA
53348438 TGTAAAAAAC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.65, C:0.14, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAACTTATA
Found at i:53349209 original size:12 final size:10
Alignment explanation
Indices: 53349143--53349227 Score: 77
Period size: 10 Copynumber: 8.3 Consensus size: 10
53349133 TATATTACAA
53349143 TTTTATAATT
1 TTTTATAATT
53349153 TTTTATAATT
1 TTTTATAATT
*
53349163 TTATAATATAAGT
1 TT-T--TATAATT
53349176 TTTTAT-ATT
1 TTTTATAATT
53349185 TTTTATAAGTT
1 TTTTATAA-TT
*
53349196 TTTAATGAATT
1 TTTTAT-AATT
53349207 TTTT-T-ATT
1 TTTTATAATT
*
53349215 TTTTATGATT
1 TTTTATAATT
53349225 TTT
1 TTT
53349228 ATAGTTTTAT
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
8 7 0.11
9 9 0.14
10 23 0.37
11 13 0.21
12 3 0.05
13 8 0.13
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (10 bp):
TTTTATAATT
Found at i:53349209 original size:23 final size:21
Alignment explanation
Indices: 53349143--53349213 Score: 74
Period size: 23 Copynumber: 3.3 Consensus size: 21
53349133 TATATTACAA
*
53349143 TTTTATAATTTTTTATAATTT
1 TTTTATAAGTTTTTATAATTT
*
53349164 TATAATATAAGTTTTTAT-A-TT
1 T-T-TTATAAGTTTTTATAATTT
53349185 TTTTATAAGTTTTTAATGAATTT
1 TTTTATAAGTTTTT-AT-AATTT
53349208 TTTTAT
1 TTTTAT
53349214 TTTTTATGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
19 11 0.27
20 3 0.07
21 4 0.10
22 3 0.07
23 20 0.49
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (21 bp):
TTTTATAAGTTTTTATAATTT
Found at i:53349211 original size:32 final size:32
Alignment explanation
Indices: 53349143--53349226 Score: 102
Period size: 30 Copynumber: 2.7 Consensus size: 32
53349133 TATATTACAA
53349143 TTTTATAATTTTTTATAATTTTATAATATAAGT
1 TTTTAT-ATTTTTTATAATTTTATAATATAAGT
*
53349176 TTTTATATTTTTTATAAGTTTT-TAAT-GAA-T
1 TTTTATATTTTTTATAA-TTTTATAATATAAGT
* *
53349206 TTTTTTATTTTTTATGATTTT
1 TTTTATATTTTTTATAATTTT
53349227 TATAGTTTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
29 4 0.09
30 16 0.34
31 2 0.04
32 15 0.32
33 10 0.21
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (32 bp):
TTTTATATTTTTTATAATTTTATAATATAAGT
Found at i:53349216 original size:19 final size:18
Alignment explanation
Indices: 53349175--53349247 Score: 60
Period size: 18 Copynumber: 3.9 Consensus size: 18
53349165 ATAATATAAG
*
53349175 TTTTTAT-ATTTTTTATAA
1 TTTTTATGAATTTTTAT-A
*
53349193 GTTTTTAATGAATTTTTTTA
1 -TTTTT-ATGAATTTTTATA
53349213 TTTTTTATG-ATTTTTATA
1 -TTTTTATGAATTTTTATA
* *
53349231 GTTTTATGAATATTTAT
1 TTTTTATGAATTTTTAT
53349248 GAGGAAAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
17 7 0.16
18 15 0.33
19 8 0.18
20 8 0.18
21 7 0.16
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (18 bp):
TTTTTATGAATTTTTATA
Found at i:53361462 original size:49 final size:49
Alignment explanation
Indices: 53361407--53361644 Score: 262
Period size: 49 Copynumber: 4.8 Consensus size: 49
53361397 TAGCCAAAGC
* *
53361407 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* * *
53361456 TATCTGGTACATGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAAC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACC-AAT
* * * * * * * *
53361506 CAACTGATACACGTAGCAGCCTGTACTTAGTACTACACACGTGATCGAAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-T
* * * * *
53361557 TATCAGGTACGCATAGTAGCTTGCACTTAGTACTACACATGCGACTAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
*
53361606 AAT-TCGGTACACGTAGTAGCCTGCACTTAGTACTACACA
1 TATCT-GGTACACGTAGTAGCCTGCACTTAGTACTACACA
53361645 CGTGACCTAA
Statistics
Matches: 154, Mismatches: 31, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
49 76 0.49
50 44 0.29
51 34 0.22
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (49 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
Done.