Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 100 of 295
Found at i:29627652 original size:39 final size:39
Alignment explanation
Indices: 29627566--29627727 Score: 193
Period size: 39 Copynumber: 4.1 Consensus size: 39
29627556 CAAATCCAAT
* * *
29627566 CACCACCAC-AAAGCATGCGGGACTTTAAGCCTGGATATAA
1 CACCAGCACGAAAGCCTGCGGGAC-TT-AGCCCGGATATAA
*
29627606 TACCAGCAC-AAAGCCTGCGGGACTTTAGCCCGGATATAA
1 CACCAGCACGAAAGCCTGCGGGAC-TTAGCCCGGATATAA
* *
29627645 CACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAAAGCCTGCGGGACTTAGCCCGGATATAA
* * * *
29627684 CACCAACACGAATGCCTTCAGGACTTAGCCCGGATATAA
1 CACCAGCACGAAAGCCTGCGGGACTTAGCCCGGATATAA
29627723 CACCA
1 CACCA
29627728 TTATAAAGTC
Statistics
Matches: 112, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
39 77 0.69
40 35 0.31
ACGTcount: A:0.32, C:0.30, G:0.20, T:0.17
Consensus pattern (39 bp):
CACCAGCACGAAAGCCTGCGGGACTTAGCCCGGATATAA
Found at i:29627833 original size:28 final size:28
Alignment explanation
Indices: 29627800--29627881 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
29627790 AGTTAATCAT
* *
29627800 TCAATATTTTGCACACTAAGTGTCATTC
1 TCAATATTTCGCACACTAAGTGCCATTC
* *
29627828 TCAATATCTCGCACATTAAGTGCCATTC
1 TCAATATTTCGCACACTAAGTGCCATTC
* * *
29627856 TCAATATTTCGTACACTGAGTACCAT
1 TCAATATTTCGCACACTAAGTGCCAT
29627882 ATTTGATTGC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.35
Consensus pattern (28 bp):
TCAATATTTCGCACACTAAGTGCCATTC
Found at i:29629755 original size:18 final size:20
Alignment explanation
Indices: 29629728--29629767 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
29629718 AATTATACCC
29629728 CTATTATCATTTATCT-TTT
1 CTATTATCATTTATCTATTT
29629747 CTATT-TCATTTATCTATTT
1 CTATTATCATTTATCTATTT
29629766 CT
1 CT
29629768 CCAGTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.62
Consensus pattern (20 bp):
CTATTATCATTTATCTATTT
Found at i:29632033 original size:5 final size:5
Alignment explanation
Indices: 29632023--29632070 Score: 96
Period size: 5 Copynumber: 9.6 Consensus size: 5
29632013 ACCTATGTGA
29632023 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
29632071 GAACACACAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:29636500 original size:5 final size:5
Alignment explanation
Indices: 29636490--29636521 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
29636480 CAATTTGTGA
29636490 AAAAT AAAAT AAAAT -AAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
29636522 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:29636510 original size:14 final size:14
Alignment explanation
Indices: 29636491--29636521 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
29636481 AATTTGTGAA
29636491 AAATAAAATAAAAT
1 AAATAAAATAAAAT
29636505 AAATAAAATAAAAT
1 AAATAAAATAAAAT
29636519 AAA
1 AAA
29636522 GAACACACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:29641009 original size:13 final size:14
Alignment explanation
Indices: 29640978--29641008 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29640968 TTGAAATAAC
*
29640978 AAAATGATAAAAAG
1 AAAATAATAAAAAG
29640992 AAAATAATAAAAAG
1 AAAATAATAAAAAG
29641006 AAA
1 AAA
29641009 TTAAAACCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (14 bp):
AAAATAATAAAAAG
Found at i:29642548 original size:88 final size:88
Alignment explanation
Indices: 29642337--29642606 Score: 346
Period size: 88 Copynumber: 3.1 Consensus size: 88
29642327 TTCAGGGAGA
** * ** *
29642337 TAAGGCTCACTGTCTTCGATCTGCTCTGCTACTGTTTAGGGAGATAAGATCTGTAATTTCCAACC
1 TAAGGCTCACTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAGCC
* *
29642402 TATTACACC-ACTACTTA-GGGGT
66 TGTTAC-CCTACTGCTTAGGGGGT
* * * *
29642424 TAAGACTCACTGTTTTCAATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTTTAGCC
1 TAAGGCTCACTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAGCC
29642489 TGTTACCCTACTGCTTAGGGGGT
66 TGTTACCCTACTGCTTAGGGGGT
* ** * *
29642512 TAAGGCTCACCGTCTTCGATCCACTCCACTACTGCTTAGGGAGATAAAATCTATAATTTTTAGCC
1 TAAGGCTCACTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAGCC
* *
29642577 TGTTTCCCTACTGCTTAGGAGGT
66 TGTTACCCTACTGCTTAGGGGGT
29642600 TAAGGCT
1 TAAGGCT
29642607 TACATCTTCG
Statistics
Matches: 158, Mismatches: 23, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
86 2 0.01
87 67 0.42
88 89 0.56
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (88 bp):
TAAGGCTCACTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAGCC
TGTTACCCTACTGCTTAGGGGGT
Found at i:29642685 original size:70 final size:70
Alignment explanation
Indices: 29642548--29642687 Score: 201
Period size: 70 Copynumber: 2.0 Consensus size: 70
29642538 CACTACTGCT
* * * *
29642548 TAGGGAGATAAAATCTATAATTTTTAGCCTGTTTCCCTACTGCTTAGGAGGTTAAGGCTTACATC
1 TAGGGAGATAAAATCTATAATTTTCAGCCTGTTACCCTACTGCTTAGGAGGTTAAGACTCACATC
29642613 TTCGA
66 TTCGA
* * *
29642618 TAGGGAGATAAGATCTATAATTTTCA-CCTGTTACCCTACTGCTTAGGGGGTTAAGACTCACCGT
1 TAGGGAGATAAAATCTATAATTTTCAGCCTGTTACCCTACTGCTTAGGAGGTTAAGACTCA-CAT
29642682 CTTCGA
65 CTTCGA
29642688 GCTGCTTCGC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
69 30 0.48
70 32 0.52
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (70 bp):
TAGGGAGATAAAATCTATAATTTTCAGCCTGTTACCCTACTGCTTAGGAGGTTAAGACTCACATC
TTCGA
Found at i:29642706 original size:44 final size:44
Alignment explanation
Indices: 29642651--29642885 Score: 157
Period size: 44 Copynumber: 5.3 Consensus size: 44
29642641 TCACCTGTTA
29642651 CCCTACTGCTTAGGGGGTTAAGACTCACCGTCTTCGAGCTGCTT
1 CCCTACTGCTTAGGGGGTTAAGACTCACCGTCTTCGAGCTGCTT
* * * * * *
29642695 CGCTACTGCTTAGGGAGATAAGA-T--CTGTAATTTCCAGCCTG-TT
1 CCCTACTGCTTAGGGGGTTAAGACTCACCGT--CTTCGAG-CTGCTT
* *
29642738 ACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTT
1 -CCCTACTGCTTAGGGGGTTAAGACTCACCGTCTTCGAGCTGCTT
* * * * *
29642783 CACTACTGCTTAGGGAGATT-AGA-T--CTGTAATTTCTAGCCTG-TT
1 CCCTACTGCTTAGGG-GGTTAAGACTCACCGT--CTTCGAG-CTGCTT
* * *
29642826 ACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTTGATCTGC-T
1 -CCCTACTGCTTAGGGGGTTAAGACTCACCGTCTTCGAGCTGCTT
*
29642870 CCGCTACTGTTTAGGG
1 CC-CTACTGCTTAGGG
29642886 AGATAAGATC
Statistics
Matches: 142, Mismatches: 30, Indels: 38
0.68 0.14 0.18
Matches are distributed among these distances:
41 6 0.04
43 20 0.14
44 96 0.68
45 14 0.10
47 6 0.04
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.32
Consensus pattern (44 bp):
CCCTACTGCTTAGGGGGTTAAGACTCACCGTCTTCGAGCTGCTT
Found at i:29642766 original size:88 final size:88
Alignment explanation
Indices: 29642618--29643196 Score: 789
Period size: 88 Copynumber: 6.7 Consensus size: 88
29642608 ACATCTTCGA
* * *
29642618 TAGGGAGATAAGATCTATAATTTTCA-CCTGTTACCCTACTGCTTAGGGGGTTAAGACTCACCGT
1 TAGGGAGATAAGATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
* * *
29642682 CTTCGAGCTGCTTCGCTACTGCT
66 CTTCGATCTGCTCCACTACTGCT
29642705 TAGGGAGATAAGATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
1 TAGGGAGATAAGATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
*
29642770 CTTCGATCTGCTTCACTACTGCT
66 CTTCGATCTGCTCCACTACTGCT
* *
29642793 TAGGGAGATTAGATCTGTAATTTCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
1 TAGGGAGATAAGATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
* * *
29642858 CTTTGATCTGCTCCGCTACTGTT
66 CTTCGATCTGCTCCACTACTGCT
* * *
29642881 TAGGGAGATAAGATCTGTAATTTCCAGCCTATTACCCTACTGCTTATGGGGTTAAGGCGCACCGT
1 TAGGGAGATAAGATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
** * *
29642946 CTTTTATCTGCTCCGCTACTACT
66 CTTCGATCTGCTCCACTACTGCT
* * * **
29642969 TAGGGAGATTAGATCTGTAATTTTCAGCCTGTTACCCTAGTGCTTAGGGGGTTAAGGCTCATTGT
1 TAGGGAGATAAGATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
**
29643034 CTTCGATCTGCTCCACTACTATT
66 CTTCGATCTGCTCCACTACTGCT
* * * *
29643057 TA-GGAG---AGATCTGTATTTTCGAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTGT
1 TAGGGAGATAAGATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
*
29643118 CTTCGATCTGCTCCACTACTGTT
66 CTTCGATCTGCTCCACTACTGCT
* * *
29643141 TA-GG-G--AAGATCTGTATTTTCTAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTC
1 TAGGGAGATAAGATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTC
29643197 GTGGATTCAC
Statistics
Matches: 449, Mismatches: 41, Indels: 7
0.90 0.08 0.01
Matches are distributed among these distances:
83 1 0.00
84 122 0.27
87 28 0.06
88 298 0.66
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (88 bp):
TAGGGAGATAAGATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
CTTCGATCTGCTCCACTACTGCT
Found at i:29642823 original size:245 final size:244
Alignment explanation
Indices: 29642373--29643124 Score: 929
Period size: 245 Copynumber: 3.0 Consensus size: 244
29642363 TGCTACTGTT
* *
29642373 TAGGGAGATAAGATCTGTAATTTCCAACCTATTACACC-ACTACTTAGGGGTTAAGACTCACTGT
1 TAGGGAGATAAGATCTGTAATTTCC-ACCTATTAC-CCTACTGCTTAGGGGTTAAGACTCACCGT
* * * *
29642437 TTTCAATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTTTAGCCTGTTACCCTACTG
64 CTTCAATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTG
** * *
29642502 CTTAGGGGGTTAAGGCTCACCGTCTTCGATCCACTCCACTACTGCTTAGGGAGATAAAATCTATA
129 CTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGAT-AGATCTGTA
* * *
29642567 ATTTTTAGCCTGTTTCCCTACTGCTTAGGAGGTTAAGGCTTAC-ATCTTCGA
193 ATTTCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTATCTTCGA
* * *
29642618 TAGGGAGATAAGATCTATAATTTTCACCTGTTACCCTACTGCTTAGGGGGTTAAGACTCACCGTC
1 TAGGGAGATAAGATCTGTAATTTCCACCTATTACCCTACTGCTTA-GGGGTTAAGACTCACCGTC
* * * *
29642683 TTCGAGCTGCTTCGCTACTGCTTAGGGAGATAAGATCTGTAATTTCCAGCCTGTTACCCTACTGC
65 TTCAATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGC
*
29642748 TTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTTCACTACTGCTTAGGGAGATTAGATCTGTAA
130 TTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA-TAGATCTGTAA
*
29642813 TTTCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCGCTA
194 TTTCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTA----C--T-ATCT--T-CG--A
* *
29642876 CTGTTTAGGGAGATAAGATCTGTAATTTCCAGCCTATTACCCTACTGCTTATGGGGTTAAGGCGC
1 -----TAGGGAGATAAGATCTGTAATTTCCA-CCTATTACCCTACTGCTTA-GGGGTTAAGACTC
** * *
29642941 ACCGTCTTTTATCTGCTCCGCTACTACTTAGGGAGATTAGATCTGTAATTTTCAGCCTGTTACCC
59 ACCGTCTTCAATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCC
* ** **
29643006 TAGTGCTTAGGGGGTTAAGGCTCATTGTCTTCGATCTGCTCCACTACTATTTA-GGAG--AGATC
124 TACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGATC
* * *
29643068 TGTATTTTCGAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTGTCTTCGA
189 TGTAATTTCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTATCTTCGA
29643124 T
1 T
29643125 CTGCTCCACT
Statistics
Matches: 440, Mismatches: 45, Indels: 46
0.83 0.08 0.09
Matches are distributed among these distances:
243 3 0.01
244 15 0.03
245 193 0.44
246 1 0.00
248 1 0.00
249 1 0.00
250 2 0.00
251 1 0.00
253 7 0.02
254 1 0.00
255 1 0.00
256 3 0.01
258 1 0.00
260 48 0.11
263 28 0.06
264 134 0.30
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (244 bp):
TAGGGAGATAAGATCTGTAATTTCCACCTATTACCCTACTGCTTAGGGGTTAAGACTCACCGTCT
TCAATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCT
TAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGATCTGTAATT
TCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTATCTTCGA
Found at i:29643688 original size:126 final size:127
Alignment explanation
Indices: 29643550--29643801 Score: 407
Period size: 126 Copynumber: 2.0 Consensus size: 127
29643540 AAGTGTGTGC
* * * * * *
29643550 ACAACTCGAGTTGGATTTTAGGATTCACTCGTTCCAAAGGAATAAAATACTACATCCATCATGTT
1 ACAACTCAAGTTGGATCTTAAGATTCACTCGTTCCAAAGGAATAAAATACCACATCCAGCACGTT
*
29643615 AGGATACGATATTTTAAGCCT-AAAAAACTGAGATCACCTCATGATTTCCAAAACATGCGAA
66 AGGACACGATATTTTAAGCCTCAAAAAACTGAGATCACCTCATGATTTCCAAAACATGCGAA
*
29643676 ACAACTCAAGTTGGATCTTAAGATTCACTCGTTCTAAAGGAATAAAATACCACATCCAGCACGTT
1 ACAACTCAAGTTGGATCTTAAGATTCACTCGTTCCAAAGGAATAAAATACCACATCCAGCACGTT
* *
29643741 AGGACACGATATTTTAAGCCTCCAAAAATTGAGATCACCTCATGATTTCCAAAACATGCGA
66 AGGACACGATATTTTAAGCCTCAAAAAACTGAGATCACCTCATGATTTCCAAAACATGCGA
29643802 CGAAAATTTT
Statistics
Matches: 115, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
126 78 0.68
127 37 0.32
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (127 bp):
ACAACTCAAGTTGGATCTTAAGATTCACTCGTTCCAAAGGAATAAAATACCACATCCAGCACGTT
AGGACACGATATTTTAAGCCTCAAAAAACTGAGATCACCTCATGATTTCCAAAACATGCGAA
Found at i:29646376 original size:177 final size:177
Alignment explanation
Indices: 29646000--29646805 Score: 1254
Period size: 177 Copynumber: 4.5 Consensus size: 177
29645990 AGACAAAGTA
* ** * *
29646000 GGTGGCTAAAATTTGCTCCATAATCGATACATGGAGATAAGACTCGCCATCTTCGACCTGCTCCA
1 GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCA
* *
29646065 TAGCCGATACATGGCGATAAGATCTGTAATTTTTAGTCTGCTTCCTTGCTACCTCAGGAAGATAA
66 TAGCCGATACATGGAGATAAGATCTGTAA-TTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAA
*
29646130 GACTTGTACCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT
130 GACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT
* * *
29646178 GGTGGCTAAAATCTGCTCCATAGTCGATACATAGAGATAAGATTCGCCATCTTCAATCTGCTCCA
1 GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCA
* *
29646243 TAGCCTATACATGGAGATAAGATCTGTAATTTCAGTCTGCTTCATTGCTACCTCAGGAAGATAAG
66 TAGCCGATACATGGAGATAAGATCTGTAATTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAG
* * *
29646308 ACTTGTATCTTTAACCTTCTC-CTTTGCTACCTTAGAGAGATAAGGCT
131 ACTTGTATCTTCAACCTGCTCTC-TTGCTACCTCAGAGAGATAAGGCT
* * * *
29646355 GGTGGCTAAAATCTACTCCATAGCCAATACATGAAGATAAGATTCGCCATCTTCAATCTGCTCCA
1 GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCA
* ** * *
29646420 TAGCCGATACATGGAGATAAGATCTGTAATTTCAATCTGCTTCCTTATTACCTTAGGAAGGTAAG
66 TAGCCGATACATGGAGATAAGATCTGTAATTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAG
* *
29646485 ACTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAAGCT
131 ACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT
* * *
29646532 GGTGGCTAAAATCTACTTCATAGCCGATACATGGATATAAGATTCGCCATCTTCGATCTGCTCCA
1 GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCA
* *
29646597 TTGCCGATACATGGAGATAAGATCTGTAATTTCAGTCTGCTTCCTTGCTACCTTAGGAAGATAAG
66 TAGCCGATACATGGAGATAAGATCTGTAATTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAG
* *
29646662 ACTTGTATCTCCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGACT
131 ACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT
* * *
29646709 AGTGGCTAAAATCTGCTCCATAGCCGATATATGGAGATAAGATTCACCATCTTCGATCTGCTCCA
1 GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCA
29646774 TAGCCGATACATGGAGATAAGATCTGTAATTT
66 TAGCCGATACATGGAGATAAGATCTGTAATTT
29646806 TATCGACATC
Statistics
Matches: 574, Mismatches: 52, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
176 1 0.00
177 486 0.85
178 87 0.15
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30
Consensus pattern (177 bp):
GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCA
TAGCCGATACATGGAGATAAGATCTGTAATTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAG
ACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT
Found at i:29651434 original size:21 final size:21
Alignment explanation
Indices: 29651409--29651452 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
29651399 GAAATGCAAG
*
29651409 AAAAGAAGATTTGCTCAAGAT
1 AAAAGAAGATTTGCTCAAAAT
*
29651430 AAAAGAATATTTGCTCAAAAT
1 AAAAGAAGATTTGCTCAAAAT
29651451 AA
1 AA
29651453 GACATAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.25
Consensus pattern (21 bp):
AAAAGAAGATTTGCTCAAAAT
Found at i:29659658 original size:17 final size:18
Alignment explanation
Indices: 29659636--29659673 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
29659626 TCCACAATCT
*
29659636 TTTTTTTGTC-GTTTTTG
1 TTTTTTTGTCACTTTTTG
*
29659653 TTTTTTTTTCACTTTTTG
1 TTTTTTTGTCACTTTTTG
29659671 TTT
1 TTT
29659674 CTTTCTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.03, C:0.08, G:0.11, T:0.79
Consensus pattern (18 bp):
TTTTTTTGTCACTTTTTG
Found at i:29664361 original size:12 final size:12
Alignment explanation
Indices: 29664344--29664368 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29664334 CAATGGCAAC
29664344 ACATCATATACT
1 ACATCATATACT
29664356 ACATCATATACT
1 ACATCATATACT
29664368 A
1 A
29664369 TGTAAATGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (12 bp):
ACATCATATACT
Found at i:29664753 original size:14 final size:14
Alignment explanation
Indices: 29664728--29664758 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29664718 TTGAAATAAT
29664728 AAAATGATAAAAAG
1 AAAATGATAAAAAG
*
29664742 AAAATTATAAAAAG
1 AAAATGATAAAAAG
29664756 AAA
1 AAA
29664759 CTAAAACCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (14 bp):
AAAATGATAAAAAG
Found at i:29681206 original size:17 final size:18
Alignment explanation
Indices: 29681184--29681217 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
29681174 AGTCATATTG
29681184 AAATTGCG-AAATTAAAT
1 AAATTGCGAAAATTAAAT
29681201 AAATTGCGAAAATTAAA
1 AAATTGCGAAAATTAAA
29681218 ATGGAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (18 bp):
AAATTGCGAAAATTAAAT
Found at i:29681965 original size:20 final size:20
Alignment explanation
Indices: 29681936--29681987 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
29681926 AATTAAATTC
29681936 TAAAAGATAAATACAA-ATAAA
1 TAAAA-ATAAATA-AATATAAA
*
29681957 TAAAAATAATTAAATATAAA
1 TAAAAATAAATAAATATAAA
*
29681977 TAAAATTAAAT
1 TAAAAATAAAT
29681988 CCTAAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 20 0.74
21 5 0.19
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (20 bp):
TAAAAATAAATAAATATAAA
Found at i:29681975 original size:16 final size:16
Alignment explanation
Indices: 29681942--29681987 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
29681932 ATTCTAAAAG
29681942 ATAAATACAAA-TAAAT
1 ATAAATA-AAATTAAAT
*
29681958 A-AAA-ATAATTAAAT
1 ATAAATAAAATTAAAT
29681972 ATAAATAAAATTAAAT
1 ATAAATAAAATTAAAT
29681988 CCTAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 2 0.08
14 7 0.28
15 6 0.24
16 10 0.40
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (16 bp):
ATAAATAAAATTAAAT
Found at i:29683719 original size:21 final size:21
Alignment explanation
Indices: 29683693--29683741 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
29683683 AATAATTAAC
* *
29683693 TAATAAATCATTAAGATAAAA
1 TAATAAATAATTAAAATAAAA
29683714 TAATAAATAATTAAAATAAAA
1 TAATAAATAATTAAAATAAAA
29683735 TAATAAA
1 TAATAAA
29683742 GAAAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (21 bp):
TAATAAATAATTAAAATAAAA
Found at i:29687339 original size:14 final size:14
Alignment explanation
Indices: 29687320--29687351 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
29687310 GAAAATATGG
*
29687320 AGAGTATAAAAGAC
1 AGAGTACAAAAGAC
29687334 AGAGTACAAAAGAC
1 AGAGTACAAAAGAC
29687348 AGAG
1 AGAG
29687352 CTTTTGGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.09, G:0.25, T:0.09
Consensus pattern (14 bp):
AGAGTACAAAAGAC
Found at i:29690953 original size:15 final size:16
Alignment explanation
Indices: 29690911--29690963 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
29690901 AAAAGTGACT
*
29690911 AAAATAGAAACAATCA
1 AAAATAGAAATAATCA
*
29690927 AAAATATG-AATAA-CC
1 AAAATA-GAAATAATCA
*
29690942 AAAATAGAAATAATCT
1 AAAATAGAAATAATCA
29690958 AAAATA
1 AAAATA
29690964 TTAGTAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 1 0.03
15 12 0.39
16 17 0.55
17 1 0.03
ACGTcount: A:0.66, C:0.09, G:0.06, T:0.19
Consensus pattern (16 bp):
AAAATAGAAATAATCA
Found at i:29698502 original size:22 final size:22
Alignment explanation
Indices: 29698467--29698509 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29698457 TATTAGTTAC
*
29698467 ATTTTAATTTTTAAT-AATTAT
1 ATTTTAAGTTTTAATGAATTAT
29698488 ATTTTACAGTTTTAATGAATTA
1 ATTTTA-AGTTTTAATGAATTA
29698510 GTTGAACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 8 0.42
23 5 0.26
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (22 bp):
ATTTTAAGTTTTAATGAATTAT
Found at i:29721995 original size:12 final size:12
Alignment explanation
Indices: 29721978--29722014 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
29721968 GTGTCAAGCG
*
29721978 AAGGGGAAGGGC
1 AAGGGGAAGGGA
29721990 AAGGGGAAGGGA
1 AAGGGGAAGGGA
*
29722002 AAGGGAAAGGGA
1 AAGGGGAAGGGA
29722014 A
1 A
29722015 GATCGGTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.43, C:0.03, G:0.54, T:0.00
Consensus pattern (12 bp):
AAGGGGAAGGGA
Found at i:29721998 original size:18 final size:18
Alignment explanation
Indices: 29721977--29722012 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29721967 GGTGTCAAGC
* *
29721977 GAAGGGGAAGGGCAAGGG
1 GAAGGGAAAGGGAAAGGG
29721995 GAAGGGAAAGGGAAAGGG
1 GAAGGGAAAGGGAAAGGG
29722013 AAGATCGGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.58, T:0.00
Consensus pattern (18 bp):
GAAGGGAAAGGGAAAGGG
Found at i:29722533 original size:12 final size:13
Alignment explanation
Indices: 29722511--29722543 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
29722501 TTATTACAAA
*
29722511 TATTTTAATTAAT
1 TATTATAATTAAT
29722524 TA-TATAATTAAT
1 TATTATAATTAAT
29722536 TATTATAA
1 TATTATAA
29722544 AAATCCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTATAATTAAT
Found at i:29731177 original size:25 final size:25
Alignment explanation
Indices: 29731143--29731193 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
29731133 TTCCTTATAA
* **
29731143 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAAGAATTAGATTAGG
29731168 ACTTTAAATTAAGAATTAGATTAGG
1 ACTTTAAATTAAGAATTAGATTAGG
29731193 A
1 A
29731194 TTTTCCTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAAGAATTAGATTAGG
Found at i:29735495 original size:25 final size:25
Alignment explanation
Indices: 29735461--29735511 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
29735451 TTCCTAATAA
**
29735461 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
29735486 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
29735511 A
1 A
29735512 TTTTCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:29735510 original size:12 final size:12
Alignment explanation
Indices: 29735464--29735511 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
29735454 CTAATAAACT
29735464 TTAAATTAGGAA
1 TTAAATTAGGAA
** *
29735476 TTCTATTAGGACT
1 TTAAATTAGGA-A
29735489 TTAAATTAGGAA
1 TTAAATTAGGAA
*
29735501 TTAGATTAGGA
1 TTAAATTAGGA
29735512 TTTTCCTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (12 bp):
TTAAATTAGGAA
Found at i:29739329 original size:18 final size:18
Alignment explanation
Indices: 29739306--29739369 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
29739296 ACTCATTTCC
29739306 TTAAAAAAATAAAAGAAA
1 TTAAAAAAATAAAAGAAA
*
29739324 TTAAAAATATAAAATG-AA
1 TTAAAAAAATAAAA-GAAA
**
29739342 TGGAAAAAATAAAA-AAA
1 TTAAAAAAATAAAAGAAA
29739359 CTTAAAAAAAT
1 -TTAAAAAAAT
29739370 TAGTTAATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 2 0.05
18 34 0.92
19 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (18 bp):
TTAAAAAAATAAAAGAAA
Found at i:29742646 original size:18 final size:18
Alignment explanation
Indices: 29742625--29742684 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
29742615 GCAGTCATGA
* *
29742625 GTGAGCTTGCAGTTTTGG
1 GTGAGCTCGCAGCTTTGG
29742643 GTGAGCTCGCAGCTTT--
1 GTGAGCTCGCAGCTTTGG
* *
29742659 GTAGAGCTCG-AACTTTTG
1 GT-GAGCTCGCAGCTTTGG
29742677 GTGAGCTC
1 GTGAGCTC
29742685 ATAGTCTTGC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
16 7 0.19
17 13 0.36
18 16 0.44
ACGTcount: A:0.15, C:0.18, G:0.33, T:0.33
Consensus pattern (18 bp):
GTGAGCTCGCAGCTTTGG
Found at i:29745549 original size:35 final size:35
Alignment explanation
Indices: 29745500--29745571 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
29745490 GTTTTAGACA
*
29745500 TTACAAATTGGTAAGTCAAAATTTGAACTGTTTTT
1 TTACAAATTGGTAAGTCAAAATTTGAACTATTTTT
* *
29745535 TTACGAATTTGTAAGTCAAAATTTGAACTATTTTT
1 TTACAAATTGGTAAGTCAAAATTTGAACTATTTTT
29745570 TT
1 TT
29745572 CTCTGATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.46
Consensus pattern (35 bp):
TTACAAATTGGTAAGTCAAAATTTGAACTATTTTT
Found at i:29751749 original size:15 final size:15
Alignment explanation
Indices: 29751729--29751806 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
29751719 TTTATGGAAA
29751729 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
29751744 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
29751758 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
29751774 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
29751788 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
29751804 ATC
1 ATC
29751807 GAGATATTGA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.19
15 29 0.62
16 9 0.19
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:29751758 original size:30 final size:30
Alignment explanation
Indices: 29751722--29751806 Score: 152
Period size: 30 Copynumber: 2.8 Consensus size: 30
29751712 ATCCATATTT
*
29751722 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
29751752 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
29751782 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
29751807 GAGATATTGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:29756411 original size:15 final size:15
Alignment explanation
Indices: 29756391--29756498 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
29756381 TTTATGGAAA
29756391 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
29756406 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
29756420 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
29756436 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
29756450 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
29756466 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
29756480 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
29756496 ATC
1 ATC
29756499 GAGATATTGG
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.62
16 13 0.19
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:29756420 original size:30 final size:30
Alignment explanation
Indices: 29756384--29756498 Score: 203
Period size: 30 Copynumber: 3.8 Consensus size: 30
29756374 ATCCATATTT
*
29756384 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
29756414 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
29756444 TTGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
29756474 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
29756499 GAGATATTGG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:29758404 original size:25 final size:25
Alignment explanation
Indices: 29758376--29758424 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
29758366 GTTTACTACA
29758376 AAAAAAAAAATACCGAAATAGGTTT
1 AAAAAAAAAATACCGAAATAGGTTT
*
29758401 AAAAAAAAAATACCGAAATGGGTT
1 AAAAAAAAAATACCGAAATAGGTT
29758425 ATTTGCTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.59, C:0.08, G:0.14, T:0.18
Consensus pattern (25 bp):
AAAAAAAAAATACCGAAATAGGTTT
Found at i:29761855 original size:22 final size:22
Alignment explanation
Indices: 29761827--29761902 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
29761817 AGGTGTGTAT
29761827 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
* *** ***
29761849 ATGTGATGAATGTGAAAGTGTGTAT
1 ATGTGAT-AAGGCCTAA-TG-GCCG
29761874 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
29761896 ATGTGAT
1 ATGTGAT
29761903 GAATGTGAAA
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
22 15 0.41
23 7 0.19
24 7 0.19
25 8 0.22
ACGTcount: A:0.29, C:0.11, G:0.32, T:0.29
Consensus pattern (22 bp):
ATGTGATAAGGCCTAATGGCCG
Found at i:29761888 original size:47 final size:47
Alignment explanation
Indices: 29761819--29762212 Score: 617
Period size: 47 Copynumber: 8.4 Consensus size: 47
29761809 GGTGTACAAG
* *
29761819 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* *
29761866 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* *
29761913 GTGTGTATATGTGATATGGCCTAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
*
29761960 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
*
29762007 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* ** *
29762054 GTGTGTATATGTGATAAGGCCTAATGGCTGATGTGATGGATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* * * *
29762101 GTGTATATATGAGATAAGACCTAATGGCCAATGTGATGGATGTGAAG
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* *
29762148 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
*
29762195 GTGTATAAATGTGATAAG
1 GTGTATATATGTGATAAG
29762213 TCCCGAAGGG
Statistics
Matches: 326, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 326 1.00
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (47 bp):
GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
Found at i:29761996 original size:22 final size:22
Alignment explanation
Indices: 29761968--29762043 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
29761958 AAGTGTATAT
29761968 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * ***
29761990 ATGTGATGAATG-TGAAAGTGTATA
1 ATGTGAT-AAGGCCG-AA-TGGCCA
29762014 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
29762037 ATGTGAT
1 ATGTGAT
29762044 GAATGTGAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 15 0.38
23 8 0.21
24 8 0.21
25 8 0.21
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:29763818 original size:26 final size:26
Alignment explanation
Indices: 29763788--29763857 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 26
29763778 ATATTCAGTA
*
29763788 CATGTTATTAATTGTGTTACTACCTT
1 CATGTTATTAATTGTGTTACTACCTC
* *
29763814 CATGTTATTTTAATCGTGTTACTATCTC
1 CATGTTA--TTAATTGTGTTACTACCTC
*
29763842 CATGGTATTAATTGTG
1 CATGTTATTAATTGTG
29763858 CAGTTCATCT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 15 0.41
28 22 0.59
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.49
Consensus pattern (26 bp):
CATGTTATTAATTGTGTTACTACCTC
Found at i:29765118 original size:40 final size:41
Alignment explanation
Indices: 29765074--29765175 Score: 120
Period size: 40 Copynumber: 2.5 Consensus size: 41
29765064 GCCTGGAGCA
* *
29765074 ATTTTGACTTGTTTGAAAATTATTTTGA-TGTG-TTAAAATG
1 ATTTTAACTTGTTTGAAAATTATTTTGACT-TGATTAAAATC
*
29765114 ATTTTAACTTGGTTG-AAATTATTTTGACTTGATTAAAATC
1 ATTTTAACTTGTTTGAAAATTATTTTGACTTGATTAAAATC
* *
29765154 ATTTTTACTTGATTTTAAAATT
1 ATTTTAACTTG-TTTGAAAATT
29765176 GTTTCAAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
39 14 0.27
40 31 0.60
41 2 0.04
42 5 0.10
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51
Consensus pattern (41 bp):
ATTTTAACTTGTTTGAAAATTATTTTGACTTGATTAAAATC
Found at i:29765137 original size:20 final size:20
Alignment explanation
Indices: 29765074--29765164 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
29765064 GCCTGGAGCA
*
29765074 ATTTTGACTTGTTTGAAAATT
1 ATTTTGACTTGGTT-AAAATT
*
29765095 ATTTTGA--TGTGTTAAAATG
1 ATTTTGACTTG-GTTAAAATT
* *
29765114 ATTTTAACTTGGTTGAAATT
1 ATTTTGACTTGGTTAAAATT
* *
29765134 ATTTTGACTTGATTAAAATC
1 ATTTTGACTTGGTTAAAATT
*
29765154 ATTTTTACTTG
1 ATTTTGACTTG
29765165 ATTTTAAAAT
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
19 13 0.23
20 35 0.61
21 9 0.16
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (20 bp):
ATTTTGACTTGGTTAAAATT
Found at i:29767574 original size:5 final size:5
Alignment explanation
Indices: 29767564--29767629 Score: 59
Period size: 5 Copynumber: 13.4 Consensus size: 5
29767554 CAAGCTAATT
*
29767564 AATAA AAT-A AA-AA AATAA AAAAA AAT-A AAT-A AATATA AATAAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATA-A AAT-AA AATAA
*
29767612 AAGTAA AAGAA AATAA AA
1 AA-TAA AATAA AATAA AA
29767630 ATACTAAACA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
4 14 0.27
5 23 0.45
6 13 0.25
7 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (5 bp):
AATAA
Found at i:29767596 original size:22 final size:24
Alignment explanation
Indices: 29767568--29767632 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 24
29767558 CTAATTAATA
29767568 AAATAAAAAAATAAAAA-AAAA-T
1 AAATAAAAAAATAAAAATAAAAGT
29767590 AAATAAATATAAATAAAAATAAAAGT
1 AAATAAA-A-AAATAAAAATAAAAGT
*
29767616 -AA-AAGAAAATAAAAATA
1 AAATAAAAAAATAAAAATA
29767633 CTAAACAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
22 18 0.47
23 2 0.05
24 11 0.29
25 6 0.16
26 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (24 bp):
AAATAAAAAAATAAAAATAAAAGT
Found at i:29769366 original size:51 final size:51
Alignment explanation
Indices: 29769290--29769409 Score: 170
Period size: 51 Copynumber: 2.4 Consensus size: 51
29769280 TCCCAAACTT
* * * *
29769290 ACTTCATACTTCATCCGGAATTATTACTTTGTTGTTCTGGCTTCAACAAGA
1 ACTTCATATTTCATCCGGAATTATTACTTTATTGCTCTAGCTTCAACAAGA
*
29769341 ACTTCATATTTCATCCGG-ATATATTACTTTATTGCTCTAGTTTCAACAAGA
1 ACTTCATATTTCATCCGGAAT-TATTACTTTATTGCTCTAGCTTCAACAAGA
*
29769392 GCTTCATATTTCATCCGG
1 ACTTCATATTTCATCCGG
29769410 TTAACTTAGT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
50 2 0.03
51 60 0.97
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (51 bp):
ACTTCATATTTCATCCGGAATTATTACTTTATTGCTCTAGCTTCAACAAGA
Found at i:29770338 original size:16 final size:16
Alignment explanation
Indices: 29770300--29770349 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
29770290 TCTATAATTC
*
29770300 ATATTATAATTTAAATA
1 ATATAATAA-TTAAATA
* *
29770317 AAATAATAATTATATA
1 ATATAATAATTAAATA
*
29770333 ATATAATAATTTAATA
1 ATATAATAATTAAATA
29770349 A
1 A
29770350 AGTAAGAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 20 0.74
17 7 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAATAATTAAATA
Found at i:29777022 original size:51 final size:51
Alignment explanation
Indices: 29776946--29777065 Score: 161
Period size: 51 Copynumber: 2.4 Consensus size: 51
29776936 TCTCAAACTT
* * * *
29776946 ACTTCATACTTCATCCGGAATTATTACTTTGTTGTTCTGGCTTCAACAAGA
1 ACTTCATATTTCATCCGGAATTATTACTTTATTGCTCTAGCTTCAACAAGA
* *
29776997 ACTTTATATTTCATCCGG-ATATATTACTTTATTGCTCTAGTTTCAACAAGA
1 ACTTCATATTTCATCCGGAAT-TATTACTTTATTGCTCTAGCTTCAACAAGA
*
29777048 GCTTCATATTTCATCCGG
1 ACTTCATATTTCATCCGG
29777066 TTAACTTAGT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 2 0.03
51 58 0.97
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (51 bp):
ACTTCATATTTCATCCGGAATTATTACTTTATTGCTCTAGCTTCAACAAGA
Found at i:29779965 original size:46 final size:46
Alignment explanation
Indices: 29779913--29780226 Score: 405
Period size: 46 Copynumber: 6.8 Consensus size: 46
29779903 AGTGTGCTCT
* * *
29779913 CTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
29779959 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
29780005 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
29780051 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
29780097 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** * * *
29780143 ATGACGGGAAAATGAATAAGACTATGGTTGAAAGATACCATGACAAC
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * ** * *
29780190 ATGACA-GAAAACAAGTAAAACCATAGTTGAAAGATAC
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATAC
29780227 TATGACATCA
Statistics
Matches: 246, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
46 206 0.84
47 40 0.16
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:29781490 original size:16 final size:16
Alignment explanation
Indices: 29781445--29781495 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
29781435 TTATTTATCT
*
29781445 ATAATT-TATATTATA
1 ATAATTATATAATATA
* *
29781460 AT--TTAAATAAAATA
1 ATAATTATATAATATA
29781474 ATAATTATATAATATA
1 ATAATTATATAATATA
29781490 ATAATT
1 ATAATT
29781496 TAATAAAGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
13 2 0.07
14 8 0.29
15 2 0.07
16 16 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAATTATATAATATA
Found at i:29781501 original size:16 final size:16
Alignment explanation
Indices: 29781452--29781501 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
29781442 TCTATAATTT
*
29781452 ATATTATAATTTAAATA
1 ATATAATAATTT-AATA
*
29781469 AAATAATAA-TTATATA
1 ATATAATAATTTA-ATA
29781485 ATATAATAATTTAATA
1 ATATAATAATTTAATA
29781501 A
1 A
29781502 AGTAAGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 1 0.04
16 17 0.61
17 10 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAATAATTTAATA
Found at i:29781795 original size:3 final size:3
Alignment explanation
Indices: 29781787--29781907 Score: 86
Period size: 3 Copynumber: 40.3 Consensus size: 3
29781777 GGGTCATTAC
* * *
29781787 AAT AAT AAT AAAT AA- AAT AAT AGT AAC AAT AAT GAT AAT AAAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
* * * ** *
29781833 AAT AGT AA- AAA AAT AAT AGT AAT AAT AAT AGG AAT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
29781880 AAAT AA- AAT ATT GAT AAT AAA AAT AAT A
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT A
29781908 CAAATAAGTA
Statistics
Matches: 89, Mismatches: 23, Indels: 12
0.72 0.19 0.10
Matches are distributed among these distances:
2 6 0.07
3 74 0.83
4 9 0.10
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:29781872 original size:54 final size:56
Alignment explanation
Indices: 29781787--29781907 Score: 155
Period size: 54 Copynumber: 2.2 Consensus size: 56
29781777 GGGTCATTAC
* *
29781787 AATAATAATAA-A-TAA-AATAATAGTAACAATAATGATAATAAATAATAATA-G-T
1 AATAAAAATAATAGTAATAATAATAGGAACAATAATGATAATAAATAA-AATATGAT
*
29781839 AA-AAAAATAATAGTAATAATAATAGGAATAATAATGATAATAAATAAAATATTGAT
1 AATAAAAATAATAGTAATAATAATAGGAACAATAATGATAATAAATAAAATA-TGAT
29781895 AATAAAAATAATA
1 AATAAAAATAATA
29781908 CAAATAAGTA
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
51 7 0.12
52 3 0.05
53 7 0.12
54 28 0.47
55 1 0.02
56 3 0.05
57 10 0.17
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (56 bp):
AATAAAAATAATAGTAATAATAATAGGAACAATAATGATAATAAATAAAATATGAT
Found at i:29782290 original size:17 final size:15
Alignment explanation
Indices: 29782228--29782303 Score: 52
Period size: 17 Copynumber: 4.9 Consensus size: 15
29782218 TTAATACATA
29782228 AATATATATAGAGATAT
1 AATATATATA-A-ATAT
29782245 AATATATA-AAATAT
1 AATATATATAAATAT
* *
29782259 AATATTAACAGAAATAT
1 AATA-T-ATATAAATAT
29782276 AAATATATAATAAATA-
1 -AATATAT-ATAAATAT
29782292 AATA-A-ATAAATA
1 AATATATATAAATA
29782304 AAAATTAGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
12 7 0.14
14 9 0.18
15 6 0.12
16 4 0.08
17 21 0.41
18 4 0.08
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (15 bp):
AATATATATAAATAT
Found at i:29782293 original size:4 final size:4
Alignment explanation
Indices: 29782274--29782319 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
29782264 TAACAGAAAT
* * *
29782274 ATAA ATAT AT-A ATAA ATAA ATAA ATAA ATAA A-AA TTAG ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
29782320 GAAGAAAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
3 4 0.12
4 30 0.88
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (4 bp):
ATAA
Found at i:29782298 original size:19 final size:19
Alignment explanation
Indices: 29782274--29782319 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
29782264 TAACAGAAAT
*
29782274 ATAAATATATAATAAA-TAA
1 ATAAATAAATAA-AAATTAA
*
29782293 ATAAATAAATAAAAATTAG
1 ATAAATAAATAAAAATTAA
29782312 ATAAATAA
1 ATAAATAA
29782320 GAAGAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 3 0.12
19 21 0.88
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (19 bp):
ATAAATAAATAAAAATTAA
Found at i:29782298 original size:25 final size:25
Alignment explanation
Indices: 29782225--29782299 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
29782215 ATATTAATAC
* * *
29782225 ATAAATATAT-ATAGAGATATAATAT
1 ATAAATATATAATAAATAAATAA-AT
* *
29782250 ATAAA-ATATAAT-ATTAACAGAAAT
1 ATAAATATATAATAAATAA-ATAAAT
29782274 ATAAATATATAATAAATAAATAAAT
1 ATAAATATATAATAAATAAATAAAT
29782299 A
1 A
29782300 AATAAAAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
24 12 0.31
25 23 0.59
26 4 0.10
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (25 bp):
ATAAATATATAATAAATAAATAAAT
Found at i:29782353 original size:3 final size:3
Alignment explanation
Indices: 29782345--29782553 Score: 55
Period size: 3 Copynumber: 72.0 Consensus size: 3
29782335 AGATGAAAAT
* * * *
29782345 ATA ATA ATA GTA ATA AT- ACA ATA GTA ATA ATA ATA ATA ACA CA-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* * * * * * * * *
29782389 AAA AGTA ATG ATA ATA AT- ATG TTAA ATA AAA AAA ATA ACA GTA ACA
1 ATA A-TA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA
* * * *
29782435 ATA AT- TTA A-A AAA GATA ATA ATA A-A AAA ATA A-G ATA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
29782477 AGA ATA AGA ATA A-A AAA ATA A-A AAA ATA A-A AAA ATA AAA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
29782522 A-A AGGA ATA ATA ATA ATA GTA A-A ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29782554 GTATATTAAA
Statistics
Matches: 150, Mismatches: 39, Indels: 34
0.67 0.17 0.15
Matches are distributed among these distances:
2 20 0.13
3 122 0.81
4 8 0.05
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.23
Consensus pattern (3 bp):
ATA
Found at i:29782367 original size:14 final size:14
Alignment explanation
Indices: 29782350--29782376 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29782340 AAAATATAAT
29782350 AATAGTAATAATAC
1 AATAGTAATAATAC
29782364 AATAGTAATAATA
1 AATAGTAATAATA
29782377 ATAATAACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (14 bp):
AATAGTAATAATAC
Found at i:29782372 original size:23 final size:22
Alignment explanation
Indices: 29782342--29782405 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
29782332 TATAGATGAA
* *
29782342 AATATAATAATAGTAATAATAC
1 AATATAATAATAATAATAACAC
29782364 AATAGTAATAATAATAATAACAC
1 AATA-TAATAATAATAATAACAC
* *
29782387 AA-AAAAGTAATGATAATAA
1 AATATAA-TAATAATAATAA
29782406 TATGTTAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.06
22 16 0.44
23 18 0.50
ACGTcount: A:0.62, C:0.05, G:0.06, T:0.27
Consensus pattern (22 bp):
AATATAATAATAATAATAACAC
Found at i:29782473 original size:8 final size:8
Alignment explanation
Indices: 29782451--29782551 Score: 69
Period size: 8 Copynumber: 12.0 Consensus size: 8
29782441 TAAAAAAGAT
29782451 AATAATAA
1 AATAATAA
*
29782459 AAAAATAA
1 AATAATAA
*
29782467 GATAATAA
1 AATAATAA
*
29782475 TAAGAATAA
1 -AATAATAA
*
29782484 GAATAAAAA
1 -AATAATAA
*
29782493 AATAAAAA
1 AATAATAA
*
29782501 AATAAAAA
1 AATAATAA
*
29782509 AATAAAAAA
1 AAT-AATAA
29782518 AATAA-AA
1 AATAATAA
29782525 GGAATAATAA
1 --AATAATAA
*
29782535 TAATAGTAA
1 -AATAATAA
29782544 AATAATAA
1 AATAATAA
29782552 TAGTATATTA
Statistics
Matches: 77, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
7 2 0.03
8 41 0.53
9 32 0.42
10 2 0.03
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (8 bp):
AATAATAA
Found at i:29782505 original size:31 final size:30
Alignment explanation
Indices: 29782441--29782513 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 30
29782431 AACAATAATT
* * *
29782441 TAAAAAAGATAATAATAAAAAAATAAGATAA
1 TAAAAAA-ATAAGAATAAAAAAATAAAAAAA
*
29782472 TAATAAGAATAAGAATAAAAAAATAAAAAAA
1 TAA-AAAAATAAGAATAAAAAAATAAAAAAA
29782503 TAAAAAAATAA
1 TAAAAAAATAA
29782514 AAAAAATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 7 0.19
31 26 0.72
32 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (30 bp):
TAAAAAAATAAGAATAAAAAAATAAAAAAA
Found at i:29782510 original size:17 final size:17
Alignment explanation
Indices: 29782457--29782524 Score: 75
Period size: 17 Copynumber: 3.7 Consensus size: 17
29782447 AGATAATAAT
29782457 AAAAAAATAAGATAATAATA
1 AAAAAAATAA-A-AA-AATA
29782477 AGAATAAGAATAAAAAAAT-
1 A-AA-AA-AATAAAAAAATA
29782496 AAAAAAATAAAAAAATA
1 AAAAAAATAAAAAAATA
29782513 AAAAAAATAAAA
1 AAAAAAATAAAA
29782525 GGAATAATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
16 11 0.25
17 14 0.32
18 2 0.05
19 1 0.02
20 4 0.09
21 4 0.09
22 3 0.07
23 5 0.11
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (17 bp):
AAAAAAATAAAAAAATA
Found at i:29782549 original size:14 final size:14
Alignment explanation
Indices: 29782530--29782556 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29782520 TAAAAGGAAT
29782530 AATAATAATAGTAA
1 AATAATAATAGTAA
29782544 AATAATAATAGTA
1 AATAATAATAGTA
29782557 TATTAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (14 bp):
AATAATAATAGTAA
Found at i:29783268 original size:13 final size:14
Alignment explanation
Indices: 29783244--29783273 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
29783234 TAGATTTGAA
29783244 AAAATAAAATAAAG
1 AAAATAAAATAAAG
29783258 AAAAT-AAATAAAG
1 AAAATAAAATAAAG
29783271 AAA
1 AAA
29783274 GAAAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (14 bp):
AAAATAAAATAAAG
Found at i:29783730 original size:26 final size:26
Alignment explanation
Indices: 29783707--29783758 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
29783697 GGTTGTTTGG
*
29783707 GTTT-GTTTGGGGTTTAGTTGGTTTA
1 GTTTGGTTTGGGGTGTAGTTGGTTTA
*
29783732 GTTTGGTTTTGGGTGTAGTTGGGTTTA
1 GTTTGGTTTGGGGTGTAGTT-GGTTTA
29783759 TTTTATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 13 0.57
27 6 0.26
ACGTcount: A:0.08, C:0.00, G:0.38, T:0.54
Consensus pattern (26 bp):
GTTTGGTTTGGGGTGTAGTTGGTTTA
Found at i:29784872 original size:26 final size:26
Alignment explanation
Indices: 29784836--29784945 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
29784826 TGGTACAAAT
29784836 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
29784862 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
29784888 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
29784914 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
29784940 TGATAA
1 TGATAA
29784946 GAATTTCATG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 78 0.98
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:29786429 original size:28 final size:26
Alignment explanation
Indices: 29786387--29786457 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
29786377 GAAAGTAGCT
* *
29786387 AAATTACTATAATACCCCTATGTATGAA
1 AAATTACTGTTATACCCCTA-G-ATGAA
* *
29786415 AAATTACTGTTATACCCCTAGGTGCA
1 AAATTACTGTTATACCCCTAGATGAA
*
29786441 AAATTACCGTTATACCC
1 AAATTACTGTTATACCC
29786458 GTAGGGTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
26 19 0.50
27 1 0.03
28 18 0.47
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.31
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGATGAA
Found at i:29786667 original size:27 final size:26
Alignment explanation
Indices: 29786563--29786677 Score: 140
Period size: 27 Copynumber: 4.3 Consensus size: 26
29786553 TGGAGGAAGC
* *
29786563 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
**
29786590 AATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTCTGCCACAT-TATCT
29786617 GTTCTGGTGGCTCTGCCACGATTATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
* *
29786644 GTATCTGGTGACTCTGTCACATTATCT
1 GT-TCTGGTGGCTCTGCCACATTATCT
29786671 GTTCTGG
1 GTTCTGG
29786678 CAGCTATGCT
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
26 6 0.08
27 54 0.70
28 17 0.22
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACATTATCT
Found at i:29786670 original size:54 final size:54
Alignment explanation
Indices: 29786563--29786686 Score: 160
Period size: 54 Copynumber: 2.3 Consensus size: 54
29786553 TGGAGGAAGC
*
29786563 GTTCTGGTGGCTATGCCACAAATATCTAATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTAATCTGGTGACTCTGCCACATATATCT
* * * * *
29786617 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCT-AATCTGGTGACTCTGCCACATATATCT
**
29786671 GTTCTGGCAGCTATGC
1 GTTCTGGTGGCTATGC
29786687 TGCAAATTCT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
54 42 0.70
55 18 0.30
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTAATCTGGTGACTCTGCCACATATATCT
Found at i:29786763 original size:19 final size:22
Alignment explanation
Indices: 29786739--29786778 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
29786729 CTCCCCACAC
29786739 GGTGTA-A-GGTTGG-TATGGG
1 GGTGTATACGGTTGGATATGGG
29786758 GGTGTATACGGTTGGATATGG
1 GGTGTATACGGTTGGATATGG
29786779 TTGGGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.17, C:0.03, G:0.47, T:0.33
Consensus pattern (22 bp):
GGTGTATACGGTTGGATATGGG
Found at i:29794065 original size:13 final size:13
Alignment explanation
Indices: 29794046--29794083 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
29794036 CCCAAAATGT
29794046 CACACGGCCGTGG
1 CACACGGCCGTGG
*
29794059 TACACGGCCGTGG
1 CACACGGCCGTGG
*
29794072 CACACGCCCGTG
1 CACACGGCCGTG
29794084 TACTAGGCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.16, C:0.39, G:0.34, T:0.11
Consensus pattern (13 bp):
CACACGGCCGTGG
Found at i:29795026 original size:46 final size:48
Alignment explanation
Indices: 29794940--29795106 Score: 197
Period size: 46 Copynumber: 3.6 Consensus size: 48
29794930 GATAGGGTGT
*
29794940 CGATGCCATGTCCCAGACATGGTCTTACACTGAC--ACATCTCGCA-GC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATCTCG-AGGC
29794986 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGAGGC
* * * * *
29795032 CTATG-CATGTCCCAGACAT-GTCTTACACTAGCTCT-CGTCTCAATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TACATCTCGAGGC
*
29795078 CAATGCCATGTCCCAGACATGGTCTTACA
1 CGATGCCATGTCCCAGACATGGTCTTACA
29795107 GTAGCTCACA
Statistics
Matches: 108, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
44 12 0.11
45 15 0.14
46 58 0.54
47 15 0.14
48 8 0.07
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGAGGC
Found at i:29797097 original size:75 final size:76
Alignment explanation
Indices: 29796975--29797139 Score: 210
Period size: 75 Copynumber: 2.2 Consensus size: 76
29796965 CACAACCGTT
* * * *
29796975 GGTTGACCCGACTAGCACTGGGTTCAATTTACCGTTGGTATATCCAACTAGAGCTAGGCTCACAA
1 GGTTAACCTGACTAGCACTGGGTGCAATATACCGTTGGTATATCCAACTAGAGCTAGGCTCAC-A
29797040 TT-ATTA-TCGTC
65 TTCATTACT-GTC
** * *
29797051 GGTTAACCTGACTAGCACTGGGTGCAA-ATATTGTTGGTTTATCCAACTAGAGCTGGGCTCACAT
1 GGTTAACCTGACTAGCACTGGGTGCAATATACCGTTGGTATATCCAACTAGAGCTAGGCTCACAT
29797115 TCATTACTGTC
66 TCATTACTGTC
*
29797126 GGTTAATCTGACTA
1 GGTTAACCTGACTA
29797140 ACGCTGGGCG
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
74 3 0.04
75 50 0.64
76 25 0.32
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.32
Consensus pattern (76 bp):
GGTTAACCTGACTAGCACTGGGTGCAATATACCGTTGGTATATCCAACTAGAGCTAGGCTCACAT
TCATTACTGTC
Found at i:29799104 original size:21 final size:22
Alignment explanation
Indices: 29799080--29799123 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
29799070 ATTTAACATC
* *
29799080 AATTTAATCCATTTCATA-CTT
1 AATTCAATCCAATTCATATCTT
29799101 AATTCAATCCAATTCATATCTT
1 AATTCAATCCAATTCATATCTT
29799123 A
1 A
29799124 GGCAAAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTCAATCCAATTCATATCTT
Found at i:29806552 original size:22 final size:21
Alignment explanation
Indices: 29806515--29806559 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
29806505 AACCCAGAAT
* *
29806515 AATAATAATAATAATCATAGA
1 AATAATAAAAATAATCAGAGA
29806536 AATAAGTAAAAATAATCAGAGA
1 AATAA-TAAAAATAATCAGAGA
29806558 AA
1 AA
29806560 AAAAAAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.22
Consensus pattern (21 bp):
AATAATAAAAATAATCAGAGA
Found at i:29811545 original size:42 final size:42
Alignment explanation
Indices: 29811486--29811570 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
29811476 TACCACAATG
*
29811486 TTTGAGATTTACCTCGCTCGTAGGATTTACTCGTCTTAACTA
1 TTTGAGATTTACCTCGCTCGTAGGATTTACTCGTCCTAACTA
29811528 TTTGAGATTTACCTCGCTCGTAGGATTTACTCGTCCTAACTA
1 TTTGAGATTTACCTCGCTCGTAGGATTTACTCGTCCTAACTA
29811570 T
1 T
29811571 CCAGTTTGCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.40
Consensus pattern (42 bp):
TTTGAGATTTACCTCGCTCGTAGGATTTACTCGTCCTAACTA
Found at i:29818886 original size:45 final size:45
Alignment explanation
Indices: 29818824--29818911 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
29818814 TTAGTTTAAT
* *
29818824 AGATTTCTAGATCTTTTAGCTGAATTAAGTTTTAAGTTTAAATTA
1 AGATTTCTACATCTTTTAGCTCAATTAAGTTTTAAGTTTAAATTA
29818869 AGATTT-TACATCTTTTTAGCTCAATTAAGTTTTAAGTTTAAAT
1 AGATTTCTACATC-TTTTAGCTCAATTAAGTTTTAAGTTTAAAT
29818912 CTTTAATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 5 0.12
45 35 0.88
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.48
Consensus pattern (45 bp):
AGATTTCTACATCTTTTAGCTCAATTAAGTTTTAAGTTTAAATTA
Found at i:29821862 original size:18 final size:17
Alignment explanation
Indices: 29821839--29821885 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
29821829 ATTGTAAGGG
*
29821839 TTAATTTTTTAATATTAT
1 TTAATTTTTTAAT-TTAA
29821857 TTAATTTTTATAATTTAA
1 TTAATTTTT-TAATTTAA
29821875 TTAATATTTTT
1 TTAAT-TTTTT
29821886 TATGATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTAATTTTTTAATTTAA
Found at i:29823956 original size:59 final size:57
Alignment explanation
Indices: 29823816--29824003 Score: 220
Period size: 59 Copynumber: 3.2 Consensus size: 57
29823806 ATTGATTTAT
* *
29823816 TTTTGAATATTTTTGTACAAATTGTTTTTATATTGTTCCATTTAATAAAAT---AGTTC
1 TTTTGAATATTTTTGTAC-AATTATTTTTATATTCTT-CATTTAATAAAATAGAAGTTC
*
29823872 TTTTGAATATTTTTGTACAAGTTATTTTAATATTACTTCATTTAATAAAATAGAAGTTC
1 TTTTGAATATTTTTGTACAA-TTATTTTTATATT-CTTCATTTAATAAAATAGAAGTTC
** * **
29823931 TTTTGAATATTTTCATACATATTATTTTTATATTGTTTCATTTAATAAAATAGAAACTC
1 TTTTGAATATTTTTGTACA-ATTATTTTTATATT-CTTCATTTAATAAAATAGAAGTTC
*
29823990 TTTGGAATATTTTT
1 TTTTGAATATTTTT
29824004 TAACAAATAT
Statistics
Matches: 114, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
55 2 0.02
56 42 0.37
57 2 0.02
59 67 0.59
60 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.08, T:0.52
Consensus pattern (57 bp):
TTTTGAATATTTTTGTACAATTATTTTTATATTCTTCATTTAATAAAATAGAAGTTC
Found at i:29824310 original size:67 final size:64
Alignment explanation
Indices: 29824187--29824314 Score: 177
Period size: 67 Copynumber: 2.0 Consensus size: 64
29824177 ATTAAACTGT
29824187 AAAACCTTAAACAATTAAAAACTAATACCCTATTTTGTTTTTCTCTAAACCCTAATCAAACCCA
1 AAAACCTTAAACAATTAAAAACTAATACCCTATTTTGTTTTTCTCTAAACCCTAATCAAACCCA
* * * *
29824251 AAAATCTTAAACAATTAAAAACTTGATACCCTAATTTAAT-TTTTTTTCTAAATCCTAATCAAAC
1 AAAACCTTAAACAATTAAAAAC-TAATACCCT-ATTT--TGTTTTTCTCTAAACCCTAATCAAAC
29824315 ATCAAAGCCC
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
64 21 0.38
65 8 0.14
66 4 0.07
67 22 0.39
68 1 0.02
ACGTcount: A:0.43, C:0.21, G:0.02, T:0.34
Consensus pattern (64 bp):
AAAACCTTAAACAATTAAAAACTAATACCCTATTTTGTTTTTCTCTAAACCCTAATCAAACCCA
Found at i:29825969 original size:27 final size:27
Alignment explanation
Indices: 29825916--29825976 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
29825906 GAAGGCATCT
* * *
29825916 CATAGGCGGCACCGATTGTTGGACTGC
1 CATAGGCGGCACCAATGGTAGGACTGC
*
29825943 CATAGGCGGCACCAATGGTAGGGCTGC
1 CATAGGCGGCACCAATGGTAGGACTGC
*
29825970 CAGAGGC
1 CATAGGC
29825977 AACACCCTGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.26, G:0.36, T:0.16
Consensus pattern (27 bp):
CATAGGCGGCACCAATGGTAGGACTGC
Found at i:29826115 original size:3 final size:3
Alignment explanation
Indices: 29826102--29826174 Score: 130
Period size: 3 Copynumber: 24.7 Consensus size: 3
29826092 AAGGGAAAGG
29826102 AGA AG- AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
29826149 AGA ATA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
29826175 GAGGAGGAGG
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (3 bp):
AGA
Found at i:29826179 original size:3 final size:3
Alignment explanation
Indices: 29826173--29826223 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
29826163 AAGAAGAAGA
* * *
29826173 AGG AGG AGG AGG AGG AGG AGG AAG AGG ATG AGG AAG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
29826221 AGG
1 AGG
29826224 CGGCATTGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.37, C:0.00, G:0.61, T:0.02
Consensus pattern (3 bp):
AGG
Found at i:29826773 original size:16 final size:15
Alignment explanation
Indices: 29826754--29826796 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
29826744 ATATCTTAAT
*
29826754 GAAAAAATAAAATAC
1 GAAAAAATAAAACAC
29826769 GGAAAGAAATAAAACAC
1 -GAAA-AAATAAAACAC
29826786 GAAAATAATAA
1 GAAAA-AATAA
29826797 CTTTTTTGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 1 0.04
16 13 0.54
17 10 0.42
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.12
Consensus pattern (15 bp):
GAAAAAATAAAACAC
Found at i:29826856 original size:13 final size:13
Alignment explanation
Indices: 29826838--29826862 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29826828 TTACTAAAAT
29826838 AATATAAAAATAA
1 AATATAAAAATAA
29826851 AATATAAAAATA
1 AATATAAAAATA
29826863 GTTTATTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AATATAAAAATAA
Found at i:29827010 original size:25 final size:25
Alignment explanation
Indices: 29826982--29827057 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 25
29826972 ATTATGTACT
29826982 AAAATAATATAAAAAATAAAATACG
1 AAAATAATATAAAAAATAAAATACG
*
29827007 AAAATAGTATATTTTAAAAAATAAAATCCG
1 AAAATA--ATA---TAAAAAATAAAATACG
* *
29827037 AAAATAAAATAAATAATAAAA
1 AAAATAATATAAAAAATAAAA
29827058 ACAAAGGGCC
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
25 17 0.40
27 3 0.07
28 2 0.05
30 21 0.49
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.24
Consensus pattern (25 bp):
AAAATAATATAAAAAATAAAATACG
Found at i:29827165 original size:12 final size:12
Alignment explanation
Indices: 29827138--29827211 Score: 51
Period size: 12 Copynumber: 5.8 Consensus size: 12
29827128 ATTATGTACT
*
29827138 AAAATAATAT-A
1 AAAATAAAATAA
29827149 AAAATAAAATAA
1 AAAATAAAATAA
29827161 AAAATAACATATTTTAA
1 AAAATAA-A-A---TAA
* *
29827178 AAATTAAAATCTA
1 AAAATAAAAT-AA
29827191 AAAATAAAATAA
1 AAAATAAAATAA
*
29827203 ATAATAAAA
1 AAAATAAAA
29827212 ACAAAGGGCC
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
11 9 0.18
12 18 0.36
13 11 0.22
14 1 0.02
15 1 0.02
16 1 0.02
17 9 0.18
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:29827173 original size:154 final size:156
Alignment explanation
Indices: 29826829--29827459 Score: 923
Period size: 154 Copynumber: 4.1 Consensus size: 156
29826819 GGCGGTTTTT
* ***
29826829 TACTAAAATAATATAAAAATAAAATATAAAAATAGTTTATTTTAAAAAATAAAATATGAAAAT--
1 TACTAAAATAATATAAAAATAAAATATAAAAATAGTATATTTTAAAAAATAAAATCCAAAAATAA
* * *
29826892 AA-AAA-AATAAAAACAAATGGCCAAAACCAGAG-TTTTTTACTAAATTAATAT-AAAAAATACT
66 AATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTTACTAAATTAATATAAAAAAACACT
*
29826953 AAAATAATACATTT-AAAACATTATG
131 AAAATAATACATTTGAAACCATTATG
** *
29826978 TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATA
1 TACTAAAATAATAT-AAAAATAAAATATAAAAATAGTATATTTTAAAAAATAAAATCCAAAAATA
* *
29827043 AAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTTAC-AAATTTATATAAAAAAATAC
65 AAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTTACTAAATTAATATAAAAAAACAC
29827107 TAAAATAATACATTTGAAACCATTATG
130 TAAAATAATACATTTGAAACCATTATG
** * *
29827134 TACTAAAATAATATAAAAATAAAATA-AAAAATAACATATTTTAAAAATTAAAATCTAAAAATAA
1 TACTAAAATAATATAAAAATAAAATATAAAAATAGTATATTTTAAAAAATAAAATCCAAAAATAA
29827198 AATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTTTACTAAATTAATATAAAAAAACAC
66 AATAAATAATAAAAACAAAGGGCCAAAATCAGAG-TTTTTTTACTAAATTAATATAAAAAAACAC
*
29827263 TAAAATAATACATTCG-AACCATTATG
130 TAAAATAATACATTTGAAACCATTATG
* *
29827289 TACTAAAATAATATAAAAAATAAAATATGAAGATAGTATATTTTAAAAAATAAAATCCAAAAATA
1 TACTAAAATAATAT-AAAAATAAAATATAAAAATAGTATATTTTAAAAAATAAAATCCAAAAATA
* *
29827354 AAATAAATAATAAAAACAAAGGGCCAAAATCAGA-ATCTTTTACTAAATTAATAT--AAAAACAC
65 AAATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTTACTAAATTAATATAAAAAAACAC
29827416 TAAAATAATACATTTGAAA--ATTATG
130 TAAAATAATACATTTGAAACCATTATG
*
29827441 TATTAAAATAATATAAAAA
1 TACTAAAATAATATAAAAA
29827460 AGTATATTTT
Statistics
Matches: 441, Mismatches: 28, Indels: 24
0.89 0.06 0.05
Matches are distributed among these distances:
149 14 0.03
150 44 0.10
151 5 0.01
152 21 0.05
153 26 0.06
154 102 0.23
155 95 0.22
156 69 0.16
157 65 0.15
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.28
Consensus pattern (156 bp):
TACTAAAATAATATAAAAATAAAATATAAAAATAGTATATTTTAAAAAATAAAATCCAAAAATAA
AATAAATAATAAAAACAAAGGGCCAAAATCAGAGTTTTTTTACTAAATTAATATAAAAAAACACT
AAAATAATACATTTGAAACCATTATG
Found at i:29827460 original size:25 final size:23
Alignment explanation
Indices: 29827432--29827485 Score: 54
Period size: 25 Copynumber: 2.2 Consensus size: 23
29827422 AATACATTTG
*
29827432 AAAATTATGTATTAAAATAATATAA
1 AAAATTATATATTAAAA-AATA-AA
* *
29827457 AAAAGTATATTTTAAAAAATAAA
1 AAAATTATATATTAAAAAATAAA
29827480 ATAAAT
1 A-AAAT
29827486 ACCAAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 3 0.12
24 7 0.29
25 14 0.58
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (23 bp):
AAAATTATATATTAAAAAATAAA
Found at i:29837605 original size:45 final size:45
Alignment explanation
Indices: 29837495--29837605 Score: 145
Period size: 45 Copynumber: 2.5 Consensus size: 45
29837485 GAAATTTGAG
*
29837495 CTCGTTGAG-TGGTCCGAGTTCGTGATATATGTGAGAAATCTGAA
1 CTCGTTGAGTTGGTCCGAGTTCGTGATATATGTGAGAAATCCGAA
** * *
29837539 CTTATTGAGTTGGTCCAAGTTCGTGATATATGTGA-AGCATCCGAA
1 CTCGTTGAGTTGGTCCGAGTTCGTGATATATGTGAGA-AATCCGAA
*
29837584 CTCGTTGAGTTGGTCTGAGTTC
1 CTCGTTGAGTTGGTCCGAGTTC
29837606 ATTATGGATG
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
44 8 0.14
45 48 0.86
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (45 bp):
CTCGTTGAGTTGGTCCGAGTTCGTGATATATGTGAGAAATCCGAA
Found at i:29839003 original size:28 final size:29
Alignment explanation
Indices: 29838963--29839017 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
29838953 CACGGGCGAT
29838963 GACACGGGCGTGT-CTAGGCAGTGTGAGG
1 GACACGGGCGTGTGCTAGGCAGTGTGAGG
* *
29838991 GACACGGGCGTGTGCTCGGCCGTGTGA
1 GACACGGGCGTGTGCTAGGCAGTGTGA
29839018 AAACCTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.15, C:0.22, G:0.45, T:0.18
Consensus pattern (29 bp):
GACACGGGCGTGTGCTAGGCAGTGTGAGG
Found at i:29848127 original size:16 final size:17
Alignment explanation
Indices: 29848108--29848387 Score: 124
Period size: 16 Copynumber: 17.4 Consensus size: 17
29848098 CGTCACTCTA
29848108 CTAGCAGAGTGAG-GAG
1 CTAGCAGAGTGAGCGAG
29848124 CTAG-AGAGTG-GCGAG
1 CTAGCAGAGTGAGCGAG
*
29848139 TTAGC-GAG-GAGGCGAG
1 CTAGCAGAGTGA-GCGAG
*
29848155 CTAGCAGAGTG-GCAAG
1 CTAGCAGAGTGAGCGAG
*
29848171 CTAG-AAAGTG-GTC-AG
1 CTAGCAGAGTGAG-CGAG
* * *
29848186 CTAACAGGGT-CGCGAG
1 CTAGCAGAGTGAGCGAG
* * *
29848202 CTAGCAGACAATTA-TGAG
1 CTAGCAG--AGTGAGCGAG
*
29848220 CTAGCAGAGTG-GTGAG
1 CTAGCAGAGTGAGCGAG
29848236 CTAGCAGACAGTGA-CGAG
1 CTAGCAG--AGTGAGCGAG
* *
29848254 CTAGTAGAGTG-GTGAG
1 CTAGCAGAGTGAGCGAG
*
29848270 CTAGC-GA-TGAGGTGAG
1 CTAGCAGAGTGA-GCGAG
*
29848286 CTAGTAGAGTG-GCGAG
1 CTAGCAGAGTGAGCGAG
*
29848302 CTAGC-GAG-GAGGTGAG
1 CTAGCAGAGTGA-GCGAG
*
29848318 CTAGCAGAGTG-GTGAG
1 CTAGCAGAGTGAGCGAG
*
29848334 CTAG-TGAG-GAGGCGAG
1 CTAGCAGAGTGA-GCGAG
*
29848350 CTAGCA-A-TGAGGTGAG
1 CTAGCAGAGTGA-GCGAG
*
29848366 CTAGCAGGGT-AGCGAG
1 CTAGCAGAGTGAGCGAG
29848382 CTAGCA
1 CTAGCA
29848388 AAGCGTCGCA
Statistics
Matches: 204, Mismatches: 28, Indels: 64
0.69 0.09 0.22
Matches are distributed among these distances:
14 6 0.03
15 35 0.17
16 125 0.61
17 9 0.04
18 29 0.14
ACGTcount: A:0.28, C:0.15, G:0.41, T:0.16
Consensus pattern (17 bp):
CTAGCAGAGTGAGCGAG
Found at i:29848254 original size:18 final size:18
Alignment explanation
Indices: 29848198--29848257 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
29848188 AACAGGGTCG
* *
29848198 CGAGCTAGCAGACAATTA
1 CGAGCTAGCAGACAGTGA
* *
29848216 TGAGCTAGCAG--AGTGG
1 CGAGCTAGCAGACAGTGA
*
29848232 TGAGCTAGCAGACAGTGA
1 CGAGCTAGCAGACAGTGA
29848250 CGAGCTAG
1 CGAGCTAG
29848258 TAGAGTGGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 13 0.38
18 21 0.62
ACGTcount: A:0.32, C:0.18, G:0.33, T:0.17
Consensus pattern (18 bp):
CGAGCTAGCAGACAGTGA
Found at i:29848321 original size:48 final size:48
Alignment explanation
Indices: 29848216--29848372 Score: 176
Period size: 48 Copynumber: 3.2 Consensus size: 48
29848206 CAGACAATTA
* * * *
29848216 TGAGCTAGCAGAGTGGTGAGCTAGCAGACAGTGACGAGCTAG-TAGAGTGG
1 TGAGCTAGCAGAGTGGTGAGCTAGTAG--AGTGGCGAGCTAGCAAG-GAGG
* *
29848266 TGAGCTAGC-GATGAGGTGAGCTAGTAGAGTGGCGAGCTAGCGAGGAGG
1 TGAGCTAGCAGA-GTGGTGAGCTAGTAGAGTGGCGAGCTAGCAAGGAGG
* *
29848314 TGAGCTAGCAGAGTGGTGAGCTAGT-GAGGAGGCGAGCTAGCAATGAGG
1 TGAGCTAGCAGAGTGGTGAGCTAGTAGA-GTGGCGAGCTAGCAAGGAGG
29848362 TGAGCTAGCAG
1 TGAGCTAGCAG
29848373 GGTAGCGAGC
Statistics
Matches: 94, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
47 2 0.02
48 64 0.68
49 6 0.06
50 22 0.23
ACGTcount: A:0.27, C:0.13, G:0.43, T:0.17
Consensus pattern (48 bp):
TGAGCTAGCAGAGTGGTGAGCTAGTAGAGTGGCGAGCTAGCAAGGAGG
Found at i:29848364 original size:32 final size:32
Alignment explanation
Indices: 29848121--29848370 Score: 184
Period size: 32 Copynumber: 7.8 Consensus size: 32
29848111 GCAGAGTGAG
* * *
29848121 GAGCTAG-AGAGTGGCGAGTTAGCGAGGAGGC
1 GAGCTAGCAGAGTGGTGAGCTAGCGAGGAGGT
** * * *
29848152 GAGCTAGCAGAGTGGCAAGCTAG-AAAGTGGT
1 GAGCTAGCAGAGTGGTGAGCTAGCGAGGAGGT
* * * * * ** **
29848183 CAGCTAACAGGGTCGCGAGCTAGCAGACAATTAT
1 GAGCTAGCAGAGTGGTGAGCTAGC-GAGGA-GGT
* *
29848217 GAGCTAGCAGAGTGGTGAGCTAGC-AGACAGTGAC
1 GAGCTAGCAGAGTGGTGAGCTAGCGAG-GAG-G-T
* *
29848251 GAGCTAGTAGAGTGGTGAGCTAGCGATGAGGT
1 GAGCTAGCAGAGTGGTGAGCTAGCGAGGAGGT
* *
29848283 GAGCTAGTAGAGTGGCGAGCTAGCGAGGAGGT
1 GAGCTAGCAGAGTGGTGAGCTAGCGAGGAGGT
* *
29848315 GAGCTAGCAGAGTGGTGAGCTAGTGAGGAGGC
1 GAGCTAGCAGAGTGGTGAGCTAGCGAGGAGGT
*
29848347 GAGCTAGCA-ATGAGGTGAGCTAGC
1 GAGCTAGCAGA-GTGGTGAGCTAGC
29848371 AGGGTAGCGA
Statistics
Matches: 171, Mismatches: 39, Indels: 17
0.75 0.17 0.07
Matches are distributed among these distances:
31 30 0.18
32 92 0.54
33 3 0.02
34 45 0.26
35 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.41, T:0.16
Consensus pattern (32 bp):
GAGCTAGCAGAGTGGTGAGCTAGCGAGGAGGT
Found at i:29849791 original size:16 final size:16
Alignment explanation
Indices: 29849746--29849801 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
29849736 AAAGGTTAAG
*
29849746 AAAA-AAATATTTAGAA
1 AAAATAAATATTT-GTA
*
29849762 AAATATAAAAATTTGTA
1 AAA-ATAAATATTTGTA
29849779 AAAATAAATATTT-TA
1 AAAATAAATATTTGTA
29849794 AATAATAA
1 AA-AATAA
29849802 TTAAATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 4 0.12
16 17 0.50
17 6 0.18
18 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (16 bp):
AAAATAAATATTTGTA
Found at i:29849820 original size:20 final size:20
Alignment explanation
Indices: 29849783--29849820 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29849773 TTTGTAAAAA
*
29849783 TAAATATTTTAAATAATAAT
1 TAAATATTTTAAAGAATAAT
*
29849803 TAAATATTTTTAAGAATA
1 TAAATATTTTAAAGAATA
29849821 TTTTAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
TAAATATTTTAAAGAATAAT
Found at i:29849895 original size:51 final size:51
Alignment explanation
Indices: 29849791--29849901 Score: 120
Period size: 51 Copynumber: 2.2 Consensus size: 51
29849781 AATAAATATT
* * *
29849791 TTAAATAATAATTAAATATTTTTAAGAATATTTTAAAATTGTAAAAAAGTTA
1 TTAAA-AATAATAAAATATTTTTAAGAATATTTTAAAACTGCAAAAAAGTTA
* *
29849843 TTGAAAATAATAAAATATTTTTTAA-AAT-TTATTAAAAACTGCAAATAA-TTA
1 TTAAAAATAATAAAATA-TTTTTAAGAATATT-TT-AAAACTGCAAAAAAGTTA
29849894 TTAAAAAT
1 TTAAAAAT
29849902 TGTAAATAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
50 2 0.04
51 26 0.52
52 22 0.44
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (51 bp):
TTAAAAATAATAAAATATTTTTAAGAATATTTTAAAACTGCAAAAAAGTTA
Found at i:29849896 original size:20 final size:20
Alignment explanation
Indices: 29849871--29849913 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
29849861 TTTTTAAAAT
29849871 TTATTAAAAACTGCAAATAA
1 TTATTAAAAACTGCAAATAA
* *
29849891 TTATTAAAAATTGTAAATAA
1 TTATTAAAAACTGCAAATAA
29849911 TTA
1 TTA
29849914 ACTAATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (20 bp):
TTATTAAAAACTGCAAATAA
Found at i:29850144 original size:10 final size:10
Alignment explanation
Indices: 29850129--29850337 Score: 70
Period size: 10 Copynumber: 21.5 Consensus size: 10
29850119 TACCAATTCA
*
29850129 AATTTTAAAT
1 AATTTTTAAT
29850139 AATTTTTTAAT
1 AA-TTTTTAAT
*
29850150 AATTATTT-AC
1 AATT-TTTAAT
29850160 AATTTTTAAT
1 AATTTTTAAT
**
29850170 AATTTTCCCA-
1 AATTTT-TAAT
29850180 AA-TTTTAAT
1 AATTTTTAAT
**
29850189 AATTTTCCCA-
1 AATTTT-TAAT
29850199 AA-TTTTAAT
1 AATTTTTAAT
29850208 AATTTTTACA-
1 AATTTTTA-AT
* *
29850218 AATTTTAAAA
1 AATTTTTAAT
*
29850228 AATGTTTT-GT
1 AAT-TTTTAAT
29850238 AATTTTTAAT
1 AATTTTTAAT
29850248 AATTTTT--T
1 AATTTTTAAT
*
29850256 AAGATTTTAAGT
1 AA-TTTTTAA-T
* * *
29850268 TATTTTCAAA
1 AATTTTTAAT
*
29850278 AATATTTAAT
1 AATTTTTAAT
*
29850288 AATTATTTGA-
1 AATT-TTTAAT
*
29850298 AA-TATT--T
1 AATTTTTAAT
29850305 AATTTTT-AT
1 AATTTTTAAT
*
29850314 AATTTTTTAT
1 AATTTTTAAT
*
29850324 -TTTTTTAAT
1 AATTTTTAAT
29850333 AATTT
1 AATTT
29850338 AAACATTTTT
Statistics
Matches: 144, Mismatches: 32, Indels: 46
0.65 0.14 0.21
Matches are distributed among these distances:
7 2 0.01
8 10 0.07
9 38 0.26
10 65 0.45
11 27 0.19
12 2 0.01
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:29850167 original size:20 final size:19
Alignment explanation
Indices: 29850142--29850254 Score: 109
Period size: 19 Copynumber: 5.8 Consensus size: 19
29850132 TTTAAATAAT
29850142 TTTTTAATAATTATTTACAA
1 TTTTTAATAATT-TTTACAA
**
29850162 TTTTTAATAATTTTCCCAA
1 TTTTTAATAATTTTTACAA
* **
29850181 ATTTTAATAATTTTCCCAA
1 TTTTTAATAATTTTTACAA
*
29850200 ATTTTAATAATTTTTACAAA
1 TTTTTAATAATTTTTAC-AA
* * **
29850220 TTTTAAAAAATGTTTTGTAA
1 TTTTTAATAAT-TTTTACAA
29850240 TTTTTAATAATTTTT
1 TTTTTAATAATTTTT
29850255 TAAGATTTTA
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
19 42 0.53
20 33 0.42
21 4 0.05
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (19 bp):
TTTTTAATAATTTTTACAA
Found at i:29850187 original size:19 final size:19
Alignment explanation
Indices: 29850143--29850225 Score: 112
Period size: 19 Copynumber: 4.3 Consensus size: 19
29850133 TTAAATAATT
* *
29850143 TTTTAATAATTATTTACAAT
1 TTTTAATAATT-TTCACAAA
*
29850163 TTTTAATAATTTTCCCAAA
1 TTTTAATAATTTTCACAAA
*
29850182 TTTTAATAATTTTCCCAAA
1 TTTTAATAATTTTCACAAA
*
29850201 TTTTAATAATTTTTACAAA
1 TTTTAATAATTTTCACAAA
29850220 TTTTAA
1 TTTTAA
29850226 AAAATGTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
19 47 0.81
20 11 0.19
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTTAATAATTTTCACAAA
Found at i:29850255 original size:20 final size:20
Alignment explanation
Indices: 29850142--29850255 Score: 97
Period size: 20 Copynumber: 5.8 Consensus size: 20
29850132 TTTAAATAAT
* *
29850142 TTTTTAATAATTATTTACAA
1 TTTTTAATAATTTTTTCCAA
*
29850162 TTTTTAATAA-TTTTCCCAA
1 TTTTTAATAATTTTTTCCAA
* *
29850181 ATTTTAATAA-TTTTCCCAA
1 TTTTTAATAATTTTTTCCAA
* * *
29850200 ATTTTAATAATTTTTACAAA
1 TTTTTAATAATTTTTTCCAA
* * * **
29850220 TTTTAAAAAATGTTTTGTAA
1 TTTTTAATAATTTTTTCCAA
29850240 TTTTTAATAATTTTTT
1 TTTTTAATAATTTTTT
29850256 AAGATTTTAA
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
19 34 0.44
20 43 0.56
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTTTAATAATTTTTTCCAA
Found at i:29850263 original size:19 final size:18
Alignment explanation
Indices: 29850143--29850307 Score: 96
Period size: 19 Copynumber: 8.4 Consensus size: 18
29850133 TTAAATAATT
*
29850143 TTTTAATAATTATTTACAA
1 TTTTAATAATTTTTTA-AA
**
29850162 TTTTTAATAATTTTCCCAAA
1 -TTTTAATAATTTT-TTAAA
**
29850182 TTTTAATAATTTTCCCAAA
1 TTTTAATAATTTT-TTAAA
*
29850201 TTTTAATAATTTTTACAAA
1 TTTTAATAATTTTT-TAAA
* *
29850220 TTTTAAAAAATGTTTTGTAAT
1 TTTT-AATAAT-TTTT-TAAA
29850241 TTTTAATAATTTTTTAAGA
1 TTTTAATAATTTTTTAA-A
* **
29850260 TTTTAAGTTATTTTCAAAAA
1 TTTTAA-TAATTTT-TTAAA
*
29850280 TATTTAATAATTATTTGAAA
1 T-TTTAATAATT-TTTTAAA
29850300 TATTTAAT
1 T-TTTAAT
29850308 TTTTATAATT
Statistics
Matches: 120, Mismatches: 16, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
18 3 0.03
19 50 0.42
20 47 0.39
21 20 0.17
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.52
Consensus pattern (18 bp):
TTTTAATAATTTTTTAAA
Found at i:29854669 original size:16 final size:16
Alignment explanation
Indices: 29854645--29854675 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29854635 TTGGAGAATG
*
29854645 GAATGGAGTTGTAATA
1 GAATAGAGTTGTAATA
29854661 GAATAGAGTTGTAAT
1 GAATAGAGTTGTAAT
29854676 TAGTAATTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (16 bp):
GAATAGAGTTGTAATA
Found at i:29854768 original size:51 final size:51
Alignment explanation
Indices: 29854661--29854757 Score: 128
Period size: 49 Copynumber: 1.9 Consensus size: 51
29854651 AGTTGTAATA
*
29854661 GAATAGAGTTGTAATTAGTAATTCAGTCGTTTGGTTGAAAGGAATGGAATG
1 GAATAGAGTTGTAATTAGTAATTCAGTCGTTTGGTTGAAAGGAATAGAATG
* **
29854712 GAATAGAGTTGTAA-TAGT-ATTCTTGT-GTTTGGTTGATTGGAATAGA
1 GAATAGAGTTGTAATTAGTAATTC-AGTCGTTTGGTTGAAAGGAATAGA
29854758 CATTGTAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 21 0.51
50 6 0.15
51 14 0.34
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.37
Consensus pattern (51 bp):
GAATAGAGTTGTAATTAGTAATTCAGTCGTTTGGTTGAAAGGAATAGAATG
Found at i:29854919 original size:62 final size:58
Alignment explanation
Indices: 29854853--29855012 Score: 175
Period size: 57 Copynumber: 2.7 Consensus size: 58
29854843 TTTTAATAAG
* * *
29854853 ATTATTATTAAATATAATTTAATAATAAATAATAATAAATAATTTAATCATATTTTAACAT
1 ATTATTATTAAATATAATTTAATAA-AAATAATAAT-AATAATTTAATAACATTCTAA-AT
* *
29854914 AATTATTATTAAATACAATTTAAT-AAAATAAT-AT-ATAATTTAATAACATTCTCAAT
1 -ATTATTATTAAATATAATTTAATAAAAATAATAATAATAATTTAATAACATTCTAAAT
*
29854970 ATTATTATTAAAATATGAA-TTAATAAAAATCATAATATATAAT
1 ATTATTATT-AAATAT-AATTTAATAAAAATAATAATA-ATAAT
29855013 ATTATAAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
55 9 0.11
56 12 0.14
57 25 0.29
58 2 0.02
59 2 0.02
60 12 0.14
61 1 0.01
62 22 0.26
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (58 bp):
ATTATTATTAAATATAATTTAATAAAAATAATAATAATAATTTAATAACATTCTAAAT
Found at i:29855009 original size:24 final size:23
Alignment explanation
Indices: 29854982--29855031 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
29854972 TATTATTAAA
*
29854982 ATATGAAT-TAATAAAAATCATAAT
1 ATAT-AATATAATAAAAATAAT-AT
*
29855006 ATATAATATTATAAAAATAATAT
1 ATATAATATAATAAAAATAATAT
29855029 ATA
1 ATA
29855032 ACTACTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
ATATAATATAATAAAAATAATAT
Found at i:29856072 original size:43 final size:43
Alignment explanation
Indices: 29856021--29856196 Score: 262
Period size: 43 Copynumber: 4.1 Consensus size: 43
29856011 AAAAATTCCG
* * *
29856021 CTAAAAGTCAAGGCTTTTAGTGGCGTTTGTGGGAAAAGTGCCA
1 CTAAAAGTCATGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCA
* *
29856064 CTAAAAGTCATGGCTTTTAGTGGCGTTTGTGGGAAAAGTGCCA
1 CTAAAAGTCATGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCA
* *
29856107 CTAAAAGTCATGGCTTTTAGCGGCGTTTGTGGTAAAAGCGCCG
1 CTAAAAGTCATGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCA
* * *
29856150 CTAAAAATCACGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCG
1 CTAAAAGTCATGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCA
29856193 CTAA
1 CTAA
29856197 TTTTGGCAGA
Statistics
Matches: 125, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 125 1.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (43 bp):
CTAAAAGTCATGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCA
Found at i:29856325 original size:32 final size:31
Alignment explanation
Indices: 29856248--29856327 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
29856238 CTTCCTGCAT
* * * *
29856248 TAAAATCCAACCAAATATAACAAATATAGTA
1 TAAAATACAACCAAAAACAACAAATATAGCA
* * *
29856279 TAAAATACAGCCAAAAACAGCAAATTTAGCA
1 TAAAATACAACCAAAAACAACAAATATAGCA
29856310 TAAAAATACAACCAAAAA
1 T-AAAATACAACCAAAAA
29856328 ATTAATTCTA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 25 0.62
32 15 0.38
ACGTcount: A:0.60, C:0.17, G:0.05, T:0.17
Consensus pattern (31 bp):
TAAAATACAACCAAAAACAACAAATATAGCA
Found at i:29857073 original size:46 final size:46
Alignment explanation
Indices: 29857030--29857124 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
29857020 TGATGAATTG
29857030 AATTAAACAATTATAATTAAAGATTATAAATATTTAGAATGAATCA
1 AATTAAACAATTATAATTAAAGATTATAAATATTTAGAATGAATCA
* *
29857076 AATTAAACAATTATCATTAAAGATTATAAATATTTAGAATAAATCA
1 AATTAAACAATTATAATTAAAGATTATAAATATTTAGAATGAATCA
29857122 AAT
1 AAT
29857125 ATTATTAAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (46 bp):
AATTAAACAATTATAATTAAAGATTATAAATATTTAGAATGAATCA
Found at i:29862267 original size:9 final size:9
Alignment explanation
Indices: 29862255--29862313 Score: 82
Period size: 9 Copynumber: 6.6 Consensus size: 9
29862245 TCCGTAAGTT
*
29862255 GTTATGTAC
1 GTTATGTAA
*
29862264 GTTATGTGA
1 GTTATGTAA
29862273 GTTATGTAA
1 GTTATGTAA
*
29862282 ATTATGTAA
1 GTTATGTAA
*
29862291 GTTATGTGA
1 GTTATGTAA
29862300 GTTATGTAA
1 GTTATGTAA
29862309 GTTAT
1 GTTAT
29862314 TTTTTAAGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.46
Consensus pattern (9 bp):
GTTATGTAA
Found at i:29862287 original size:27 final size:27
Alignment explanation
Indices: 29862256--29862313 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
29862246 CCGTAAGTTG
*
29862256 TTATGTACGTTATGTGAGTTATGTAAA
1 TTATGTAAGTTATGTGAGTTATGTAAA
*
29862283 TTATGTAAGTTATGTGAGTTATGTAAG
1 TTATGTAAGTTATGTGAGTTATGTAAA
29862310 TTAT
1 TTAT
29862314 TTTTTAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.22, T:0.47
Consensus pattern (27 bp):
TTATGTAAGTTATGTGAGTTATGTAAA
Found at i:29862818 original size:33 final size:33
Alignment explanation
Indices: 29862774--29862837 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
29862764 CATACTTAAG
*
29862774 AACATAAGCATTGGAACCT-GTAGCAATGAGAAA
1 AACATAAGCATTGGAA-CTAGTAGCAAAGAGAAA
*
29862807 AACATACGCATTGGAACTAGTAGCAAAGAGA
1 AACATAAGCATTGGAACTAGTAGCAAAGAGA
29862838 TCCAAAGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.17
Consensus pattern (33 bp):
AACATAAGCATTGGAACTAGTAGCAAAGAGAAA
Found at i:29866071 original size:40 final size:40
Alignment explanation
Indices: 29865988--29866071 Score: 132
Period size: 40 Copynumber: 2.1 Consensus size: 40
29865978 TAAATTACTT
* *
29865988 TTTTGCGGCGTTTTTATCATAAACGCCGCTATTGCTTGCC
1 TTTTGCGGCGTTTTTATCATAAACGCCGCTAATGCTTGAC
* *
29866028 TTTTGCGGCGTTTTTATCATAAACTCCGCTAATGTTTGAC
1 TTTTGCGGCGTTTTTATCATAAACGCCGCTAATGCTTGAC
29866068 TTTT
1 TTTT
29866072 TTATAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (40 bp):
TTTTGCGGCGTTTTTATCATAAACGCCGCTAATGCTTGAC
Found at i:29866097 original size:22 final size:20
Alignment explanation
Indices: 29866070--29866126 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 20
29866060 TGTTTGACTT
29866070 TTTTATAATTTTTATATTGAA
1 TTTTATAATTTTTATATT-AA
29866091 TTATTAT-ATCTTTTATATTAA
1 TT-TTATAAT-TTTTATATTAA
29866112 TTTTAAATAATTTTT
1 TTTT--ATAATTTTT
29866127 TAAAAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
20 2 0.06
21 8 0.26
22 19 0.61
23 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTATAATTTTTATATTAA
Found at i:29866138 original size:22 final size:21
Alignment explanation
Indices: 29866113--29866157 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
29866103 TTATATTAAT
*
29866113 TTTAAATAATTTTTTAAAAAAA
1 TTTAAATAA-TATTTAAAAAAA
* *
29866135 TTTAAGTAATATTTAAAATAA
1 TTTAAATAATATTTAAAAAAA
29866156 TT
1 TT
29866158 AGATTAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TTTAAATAATATTTAAAAAAA
Done.