Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_pilon, whole genome shotgun sequence
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: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 56 of 73
Found at i:13198149 original size:36 final size:37
Alignment explanation
Indices: 13198097--13198182 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 37
13198087 CCTATTATAT
* * * *
13198097 TTTTTATTTTTATAATTGTGTTCTTTCA-TTTT-TAA
1 TTTTAATTTTTATAATTGAGGTCTTTAATTTTTGTAA
13198132 TTTGTAATTTTTATAATTGAGGTCTTTAATTTTTGTAA
1 TTT-TAATTTTTATAATTGAGGTCTTTAATTTTTGTAA
*
13198170 TTTTACTTTTTAT
1 TTTTAATTTTTAT
13198183 CTTTATAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
35 3 0.07
36 21 0.49
37 13 0.30
38 6 0.14
ACGTcount: A:0.22, C:0.05, G:0.08, T:0.65
Consensus pattern (37 bp):
TTTTAATTTTTATAATTGAGGTCTTTAATTTTTGTAA
Found at i:13198164 original size:22 final size:22
Alignment explanation
Indices: 13198136--13198213 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 22
13198126 TTTTAATTTG
13198136 TAATTTTTATAATTGAGGTCTT
1 TAATTTTTATAATTGAGGTCTT
* * *
13198158 TAATTTTTGTAATTTTA-CT-TT
1 TAATTTTTATAA-TTGAGGTCTT
* * * *
13198179 TTATCTTTATAATTGAGGCCCT
1 TAATTTTTATAATTGAGGTCTT
13198201 TAATTTTT-TAATT
1 TAATTTTTATAATT
13198214 ATTTTTTTTA
Statistics
Matches: 41, Mismatches: 12, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
20 3 0.07
21 16 0.39
22 19 0.46
23 3 0.07
ACGTcount: A:0.26, C:0.08, G:0.09, T:0.58
Consensus pattern (22 bp):
TAATTTTTATAATTGAGGTCTT
Found at i:13198263 original size:85 final size:85
Alignment explanation
Indices: 13198174--13198511 Score: 278
Period size: 85 Copynumber: 4.0 Consensus size: 85
13198164 TTGTAATTTT
* * *
13198174 ACTTTTTATCTTTATAATTGAGGC-CCTTAATTTTTT-AATTATTTTTTTTACATTTATAATTGA
1 ACTTTTTACCTTTATAATTGAGGCTCC-TAATTTTTTCAATTATATTTTTTACCTTTATAATTGA
*
13198237 TGACTCCAATTTTTTCAATCCC
65 -GACTCCAATTTTTTCAATCTC
* * * * * *
13198259 ACTTTATACTTTTATAATTGA-GCTCCTAATTTTTTCAATT-TCACTTTCTACCTTCATTATTGA
1 ACTTTTTACCTTTATAATTGAGGCTCCTAATTTTTTCAATTAT-ATTTTTTACCTTTATAATTGA
* * *
13198322 GGTCCCCAATTTTTT-AATATC
65 -GACTCCAATTTTTTCAATCTC
** * * * *
13198343 ACTTTTTACCTTTATAATTGAGGCTCCTAATTTTTTCAATTCCATATTTTACTTTTATAATTTAA
1 ACTTTTTACCTTTATAATTGAGGCTCCTAATTTTTTCAATTATATTTTTTACCTTTATAATTGAG
* * *
13198408 ACTTCTATTTTTTTCAATCTT
66 AC-TCCAATTTTTTCAATCTC
* ** * * *
13198429 ACTTTTTACCTTTAAAATCAAGGC-CTCT-ATTTTTTTAATCTCA-CTTTTTTACCTTTGTAATT
1 ACTTTTTACCTTTATAATTGAGGCTC-CTAATTTTTTCAAT-T-ATATTTTTTACCTTTATAATT
*
13198491 GAGATCTCTAATTTTTTCAAT
63 GAGA-CTCCAATTTTTTCAAT
13198512 TATATTTTTT
Statistics
Matches: 199, Mismatches: 43, Indels: 21
0.76 0.16 0.08
Matches are distributed among these distances:
84 36 0.18
85 103 0.52
86 59 0.30
87 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.05, T:0.52
Consensus pattern (85 bp):
ACTTTTTACCTTTATAATTGAGGCTCCTAATTTTTTCAATTATATTTTTTACCTTTATAATTGAG
ACTCCAATTTTTTCAATCTC
Found at i:13198290 original size:42 final size:42
Alignment explanation
Indices: 13198141--13198511 Score: 251
Period size: 43 Copynumber: 8.7 Consensus size: 42
13198131 ATTTGTAATT
* * * * *
13198141 TTTATAATTGAGGTCTTTAATTTTTGT-AATTTTACTTTTTATC
1 TTTATAATTGAGCTC-CTAATTTTT-TCAATCTCACTTTTTACC
* *
13198184 TTTATAATTGAGGC-CCTTAATTTTTT-AAT-T-ATTTTTTTTACA
1 TTTATAATTGA-GCTCC-TAATTTTTTCAATCTCA--CTTTTTACC
* * *
13198226 TTTATAATTGATGACTCC-AATTTTTTCAATCCCACTTTATACT
1 TTTATAATTGA-G-CTCCTAATTTTTTCAATCTCACTTTTTACC
* *
13198269 TTTATAATTGAGCTCCTAATTTTTTCAATTTCACTTTCTACC
1 TTTATAATTGAGCTCCTAATTTTTTCAATCTCACTTTTTACC
* * * * *
13198311 TTCATTATTGAGGTCCCCAATTTTTT-AATATCACTTTTTACC
1 TTTATAATTGAGCT-CCTAATTTTTTCAATCTCACTTTTTACC
*
13198353 TTTATAATTGAGGCTCCTAATTTTTTCAAT-TC-CATATTTTACT
1 TTTATAATTGA-GCTCCTAATTTTTTCAATCTCAC-T-TTTTACC
* * * * *
13198396 TTTATAATTTAAACTTCTATTTTTTTCAATCTTACTTTTTACC
1 TTTATAA-TTGAGCTCCTAATTTTTTCAATCTCACTTTTTACC
* ** *
13198439 TTTAAAATCAAGGC-CTCT-ATTTTTTTAATCTCACTTTTTTACC
1 TTTATAATTGA-GCTC-CTAATTTTTTCAATCTCAC-TTTTTACC
* *
13198482 TTTGTAATTGAGATCTCTAATTTTTTCAAT
1 TTTATAATTGAGCTC-CTAATTTTTTCAAT
13198512 TATATTTTTT
Statistics
Matches: 261, Mismatches: 44, Indels: 45
0.75 0.13 0.13
Matches are distributed among these distances:
40 1 0.00
41 6 0.02
42 116 0.44
43 118 0.45
44 18 0.07
45 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.53
Consensus pattern (42 bp):
TTTATAATTGAGCTCCTAATTTTTTCAATCTCACTTTTTACC
Found at i:13199663 original size:192 final size:192
Alignment explanation
Indices: 13199336--13199709 Score: 488
Period size: 192 Copynumber: 1.9 Consensus size: 192
13199326 AAATAAATAA
* *
13199336 AAATTAGCTGACCCTTATTCACATATGTAATGGGGTAAGGGGAGCTAGGATAGTAGGCTGTCCCC
1 AAATTAGCTGACCCTTATTCACATATGTAATGCGATAAGGGGAGCTAGGATAGTAGGCTGTCCCC
* * * * * *
13199401 CAACGCCAGGTTTAGAGCAGCTTTCGTGGGAGACCTCCGAATTATGAAATGCCATCTGTGGGACT
66 CAACGCCAGGTTGAGAACAGCTTCCGTGGGAGACCTCCAAATTATGAAATGCCATCCGTAGGACT
* *
13199466 CGATCCCACGACC-CTAAAGTTAAAAACCTTGTGTTCTCCCAACTGAGCTGGACGGTCATTTC
131 CGATCCCACGACCTC-AAAGTTAAAAACCTTGTGCTCTACCAACTGAGCTGGACGGTCATTTC
* *
13199528 AAATTAG-TCGACCCTTATTCCCATATGTAATGCGATAAGGGGGATG-TAGTATAGTAGGCTG-C
1 AAATTAGCT-GACCCTTATTCACATATGTAATGCGATAA-GGGGA-GCTAGGATAGTAGGCTGTC
* * * *
13199590 CCCCAACGCCAGGTTGAGAACAGCTTCCGTTGGAGATCTCCAAATTATGAATTGTCCA-CCGTAT
63 CCCCAACGCCAGGTTGAGAACAGCTTCCGTGGGAGACCTCCAAATTATGAAATG-CCATCCGTAG
* * * *
13199654 GACTCGATCCCACGACCTCAAGGTTAAAAATCTTGTGCTCTACTAACTGAGTTGGA
127 GACTCGATCCCACGACCTCAAAGTTAAAAACCTTGTGCTCTACCAACTGAGCTGGA
13199710 TAAAATAATT
Statistics
Matches: 157, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
191 1 0.01
192 132 0.84
193 23 0.15
194 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (192 bp):
AAATTAGCTGACCCTTATTCACATATGTAATGCGATAAGGGGAGCTAGGATAGTAGGCTGTCCCC
CAACGCCAGGTTGAGAACAGCTTCCGTGGGAGACCTCCAAATTATGAAATGCCATCCGTAGGACT
CGATCCCACGACCTCAAAGTTAAAAACCTTGTGCTCTACCAACTGAGCTGGACGGTCATTTC
Found at i:13200438 original size:16 final size:16
Alignment explanation
Indices: 13200417--13200486 Score: 86
Period size: 16 Copynumber: 4.4 Consensus size: 16
13200407 AACCCGAGAT
13200417 TGACATGTTTTCAACC
1 TGACATGTTTTCAACC
13200433 TGACATGTTTTCAACC
1 TGACATGTTTTCAACC
* * *
13200449 CGACTTGTTTTTAACC
1 TGACATGTTTTCAACC
* *
13200465 TGACTTGTTTTTAACC
1 TGACATGTTTTCAACC
*
13200481 TAACAT
1 TGACAT
13200487 TTAAATGATC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.41
Consensus pattern (16 bp):
TGACATGTTTTCAACC
Found at i:13200793 original size:14 final size:14
Alignment explanation
Indices: 13200771--13200817 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
13200761 TGCAAAGGAA
*
13200771 AATTAATATAGTTT
1 AATTTATATAGTTT
13200785 AATTTATATA----
1 AATTTATATAGTTT
13200795 AA-TTATATAGTTT
1 AATTTATATAGTTT
13200808 AATTTATATA
1 AATTTATATA
13200818 AAGAAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:13200804 original size:23 final size:24
Alignment explanation
Indices: 13200770--13200819 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
13200760 ATGCAAAGGA
13200770 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
13200794 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
13200817 AAA
1 AAA
13200820 GAAAAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:13200998 original size:7 final size:7
Alignment explanation
Indices: 13200986--13201053 Score: 55
Period size: 7 Copynumber: 9.7 Consensus size: 7
13200976 TTTATATTAG
*
13200986 GGTTTAT
1 GGTTTAA
*
13200993 GGTTTAT
1 GGTTTAA
* *
13201000 TGTTTAG
1 GGTTTAA
13201007 GGTTTAA
1 GGTTTAA
* *
13201014 AGTTTAG
1 GGTTTAA
13201021 GGTTTAA
1 GGTTTAA
*
13201028 GGTTTAT
1 GGTTTAA
* *
13201035 GATTTAG
1 GGTTTAA
13201042 GGTTTAA
1 GGTTTAA
13201049 GGTTT
1 GGTTT
13201054 CTATAAATTA
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (7 bp):
GGTTTAA
Found at i:13201007 original size:21 final size:21
Alignment explanation
Indices: 13200982--13201053 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
13200972 TCCATTTATA
**
13200982 TTAGGGTTTATGGTTTATTGT
1 TTAGGGTTTATGGTTTAGGGT
**
13201003 TTAGGGTTTAAAGTTTAGGGT
1 TTAGGGTTTATGGTTTAGGGT
* *
13201024 TTAAGGTTTATGATTTAGGGT
1 TTAGGGTTTATGGTTTAGGGT
*
13201045 TTAAGGTTT
1 TTAGGGTTT
13201054 CTATAAATTA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (21 bp):
TTAGGGTTTATGGTTTAGGGT
Found at i:13201040 original size:14 final size:14
Alignment explanation
Indices: 13200986--13201053 Score: 64
Period size: 14 Copynumber: 4.9 Consensus size: 14
13200976 TTTATATTAG
* *
13200986 GGTTTATGGTTTAT
1 GGTTTAGGGTTTAA
*
13201000 TGTTTAGGGTTTAA
1 GGTTTAGGGTTTAA
*
13201014 AGTTTAGGGTTTAA
1 GGTTTAGGGTTTAA
* * *
13201028 GGTTTATGATTTAG
1 GGTTTAGGGTTTAA
*
13201042 GGTTTAAGGTTT
1 GGTTTAGGGTTT
13201054 CTATAAATTA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 44 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (14 bp):
GGTTTAGGGTTTAA
Found at i:13201686 original size:19 final size:19
Alignment explanation
Indices: 13201662--13201722 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
13201652 TAATTTACTT
13201662 TATATAGTTTATATATATA
1 TATATAGTTTATATATATA
13201681 TATATAGTTTATATATACTA
1 TATATAGTTTATATATA-TA
* * *
13201701 TACATGGTTTATACATATA
1 TATATAGTTTATATATATA
13201720 TAT
1 TAT
13201723 TATATAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 21 0.57
20 16 0.43
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (19 bp):
TATATAGTTTATATATATA
Found at i:13202034 original size:7 final size:7
Alignment explanation
Indices: 13202022--13202082 Score: 68
Period size: 7 Copynumber: 8.7 Consensus size: 7
13202012 TTTATATTAA
13202022 GGTTTAG
1 GGTTTAG
*
13202029 GGTTTAT
1 GGTTTAG
*
13202036 GGTTTAA
1 GGTTTAG
** *
13202043 AATTTAT
1 GGTTTAG
13202050 GGTTTAG
1 GGTTTAG
13202057 GGTTTAG
1 GGTTTAG
*
13202064 GGTGTAG
1 GGTTTAG
13202071 GGTTTAG
1 GGTTTAG
13202078 GGTTT
1 GGTTT
13202083 GTATAAACTA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.46
Consensus pattern (7 bp):
GGTTTAG
Found at i:13202171 original size:2 final size:2
Alignment explanation
Indices: 13202166--13202213 Score: 69
Period size: 2 Copynumber: 23.0 Consensus size: 2
13202156 TTATATAGTT
*
13202166 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
13202209 CTA TA
1 -TA TA
13202214 CATGGTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 39 0.93
3 3 0.07
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13202838 original size:14 final size:14
Alignment explanation
Indices: 13202819--13202847 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13202809 TCTGGTTCTT
13202819 TCTCGATATATAAA
1 TCTCGATATATAAA
13202833 TCTCGATATATAAA
1 TCTCGATATATAAA
13202847 T
1 T
13202848 TGCATTCACA
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:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (14 bp):
TCTCGATATATAAA
Found at i:13204032 original size:21 final size:20
Alignment explanation
Indices: 13203992--13204052 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
13203982 AACAGAATGT
13203992 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
13204012 CCAGGGGGTACCA-ATTCCCC
1 CCAGGGGGTA-CAGATTCCCC
* *
13204032 CCAGGGGGAATAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
13204052 C
1 C
13204053 TGTCTAACGA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.03
20 34 0.92
21 2 0.05
ACGTcount: A:0.21, C:0.36, G:0.28, T:0.15
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:13205346 original size:19 final size:20
Alignment explanation
Indices: 13205322--13205369 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
13205312 AATGATTTTC
*
13205322 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATAAAA
* *
13205341 TTTTGAAAGCCAAAATAAAA
1 TTTTGAAAACAAAAATAAAA
13205361 TTTTGAAAA
1 TTTTGAAAA
13205370 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.54, C:0.06, G:0.10, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATAAAA
Found at i:13207017 original size:29 final size:27
Alignment explanation
Indices: 13206977--13207041 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 27
13206967 CAAATAAACA
13206977 AAATA-ATA-ATAACAAAGTACGAATAA-T
1 AAATATATATATAACAAA-TA--AATAAGT
* *
13207004 ATATATATATATAATAAATAAATAAGT
1 AAATATATATATAACAAATAAATAAGT
13207031 AAATATATATA
1 AAATATATATA
13207042 AATTAATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 5 0.16
27 15 0.47
28 5 0.16
29 7 0.22
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (27 bp):
AAATATATATATAACAAATAAATAAGT
Found at i:13207109 original size:23 final size:23
Alignment explanation
Indices: 13207078--13207129 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
13207068 ACATATACAC
13207078 ATAAAATAATAAAAAAAATATAT
1 ATAAAATAATAAAAAAAATATAT
* * * *
13207101 ATAATATAATAATATATATATAT
1 ATAAAATAATAAAAAAAATATAT
13207124 ATAAAA
1 ATAAAA
13207130 AACAATACAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAAAATAATAAAAAAAATATAT
Found at i:13207301 original size:2 final size:2
Alignment explanation
Indices: 13207255--13207285 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13207245 CTTGTGTAGA
13207255 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13207286 GTAAAATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13207527 original size:12 final size:11
Alignment explanation
Indices: 13207499--13207539 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
13207489 TAATTAAATA
* *
13207499 AATAATATAAA
1 AATAATACAAG
13207510 AATAATACAAG
1 AATAATACAAG
13207521 TAATAATACAAG
1 -AATAATACAAG
13207533 AATAATA
1 AATAATA
13207540 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:13207644 original size:12 final size:12
Alignment explanation
Indices: 13207622--13207666 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
13207612 GAATAAAAGG
13207622 AAAATATAATAGT
1 AAAA-ATAATAGT
*
13207635 AAAAATAATAAT
1 AAAAATAATAGT
*
13207647 AAATATAATAGT
1 AAAAATAATAGT
*
13207659 AATAATAA
1 AAAAATAA
13207667 AAATGTAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:13209342 original size:106 final size:106
Alignment explanation
Indices: 13209017--13210497 Score: 2102
Period size: 106 Copynumber: 14.0 Consensus size: 106
13209007 GCATTGTTCT
* * ** * *
13209017 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* * *
13209081 ACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
13209123 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
** * * * * **
13209182 TTAGCCG-CCTCTTCGTCGTGAAGCTGAGCTTGTGTTACCTTG
66 CCAGCGGTCC-CTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * *
13209224 G-GTTCAAGATCCTTCGCTGAGAAGTTGAAATTGTCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
13209288 CTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
13209329 GAGTCCAATATCCTACGATGTAAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
13209394 CCAACGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * ** *
13209435 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTGGTTGAAAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
13209500 CCAGGGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
13209541 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
13209606 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
13209647 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
13209712 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
13209753 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTATTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
13209818 CCAGCGGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTGTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
13209859 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
13209924 CCAGTGGTCCCTTCGTTGTGAAGTTGAACTTGCTTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
13209965 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
13210030 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
13210071 GAGTCTAATATCCTTCGTTGCGAAGTTGAAATTGGCACTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
13210136 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTTTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
13210177 GAGTCCGATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
13210242 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
13210283 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGATATGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
13210348 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
13210389 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGAAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
** * * *
13210453 CCAGTTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
13210494 GAGT
1 GAGT
13210498 GGCACGATAT
Statistics
Matches: 1238, Mismatches: 125, Indels: 25
0.89 0.09 0.02
Matches are distributed among these distances:
99 3 0.00
100 72 0.06
101 5 0.00
102 4 0.00
104 3 0.00
105 54 0.04
106 1094 0.88
107 3 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:13211332 original size:22 final size:22
Alignment explanation
Indices: 13211306--13211382 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
13211296 TTATGTTTGG
*
13211306 TCAAAGGTTTAGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
13211328 TCAAAGGTTTGGCATGTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
13211350 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
13211372 TCAACGGTTTG
1 TCAAAGGTTTG
13211383 ATGGGGTAGC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:13212023 original size:15 final size:15
Alignment explanation
Indices: 13211986--13212036 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
13211976 TTTTTGTCCC
13211986 TTTTTCTTT-TTGATTT
1 TTTTTCTTTCTT--TTT
*
13212002 TTGTTCTTTCTTTTT
1 TTTTTCTTTCTTTTT
13212017 TTTTTC-TTCTTTTCT
1 TTTTTCTTTCTTTT-T
13212032 TTTTT
1 TTTTT
13212037 GTTTTTTCCC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 7 0.23
15 14 0.45
16 8 0.26
17 2 0.06
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.82
Consensus pattern (15 bp):
TTTTTCTTTCTTTTT
Found at i:13212041 original size:20 final size:20
Alignment explanation
Indices: 13211987--13212041 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
13211977 TTTTGTCCCT
*
13211987 TTTTC-TTTTTGATTTTTGTTC
1 TTTTCTTTTTTG--TTTTCTTC
13212008 -TTTCTTTTTT-TTTTCTTC
1 TTTTCTTTTTTGTTTTCTTC
13212026 TTTTCTTTTTTGTTTT
1 TTTTCTTTTTTGTTTT
13212042 TTCCCTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 7 0.23
19 10 0.33
20 8 0.27
21 5 0.17
ACGTcount: A:0.02, C:0.11, G:0.05, T:0.82
Consensus pattern (20 bp):
TTTTCTTTTTTGTTTTCTTC
Found at i:13216517 original size:31 final size:28
Alignment explanation
Indices: 13216481--13216616 Score: 100
Period size: 30 Copynumber: 4.7 Consensus size: 28
13216471 AAATGAAAAG
13216481 AAAAGAAAACAAATTAAGTAAAATAATAAA
1 AAAAGAAAACAAA-TAA-TAAAATAATAAA
* * * *
13216511 ATAAAGAAAGCAAA-GATAAAATAGTAAG
1 A-AAAGAAAACAAATAATAAAATAATAAA
13216539 AAAA-AAAACAAATAATAAAATATATATAA
1 AAAAGAAAACAAATAATAAAATA-ATA-AA
* *
13216568 AAAAGAAAA-AGAAAAAGAAAATAAATAAA
1 AAAAGAAAACA-AATAATAAAAT-AATAAA
*
13216597 ACAAA-TAAACAAAATAATAA
1 A-AAAGAAAAC-AAATAATAA
13216617 TAACAAAGTA
Statistics
Matches: 83, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
26 7 0.08
27 11 0.13
28 13 0.16
29 13 0.16
30 26 0.31
31 13 0.16
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (28 bp):
AAAAGAAAACAAATAATAAAATAATAAA
Found at i:13216559 original size:27 final size:27
Alignment explanation
Indices: 13216469--13216560 Score: 82
Period size: 28 Copynumber: 3.3 Consensus size: 27
13216459 TTAATTAAAT
13216469 TAAAATGAA-AAGAAAAGAAAACAAATTAA
1 TAAAAT-AATAAGAAAA-AAAACAAA-TAA
*
13216498 GTAAAATAATAA-AATAAAGAAAGCAAA-GA
1 -TAAAATAATAAGAA-AAA-AAA-CAAATAA
*
13216527 TAAAATAGTAAGAAAAAAAACAAATAA
1 TAAAATAATAAGAAAAAAAACAAATAA
13216554 TAAAATA
1 TAAAATA
13216561 TATATAAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
26 4 0.08
27 11 0.21
28 13 0.25
29 8 0.15
30 13 0.25
31 4 0.08
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (27 bp):
TAAAATAATAAGAAAAAAAACAAATAA
Found at i:13216569 original size:27 final size:27
Alignment explanation
Indices: 13216481--13216672 Score: 77
Period size: 27 Copynumber: 7.1 Consensus size: 27
13216471 AAATGAAAAG
*
13216481 AAAAGAAAACAAATTAAGTAAAATA-ATAA
1 AAAA-AAAACAAA-TAA-TAAAATATATAT
* *
13216510 AATAAAGAAAGCAAA-GATAAAATAGTA-AG
1 AA-AAA-AAA-CAAATAATAAAATA-TATAT
13216539 AAAAAAAACAAATAATAAAATATATAT
1 AAAAAAAACAAATAATAAAATATATAT
*
13216566 AAAAAAGAA-AAAGAA-AAAGA-A-A-AT
1 AAAAAA-AACAAATAATAAA-ATATATAT
* *
13216590 AAATAAAACAAATAAACAAAATA-ATAAT
1 AAAAAAAACAAAT-AATAAAATATAT-AT
** *
13216618 AACAAAGTACGAATAAT---ATATATAT
1 AA-AAAAAACAAATAATAAAATATATAT
* *
13216643 AAAATAAATAAATAAGT-AAATATATAT
1 AAAAAAAACAAATAA-TAAAATATATAT
13216670 AAA
1 AAA
13216673 TTAATAAATT
Statistics
Matches: 126, Mismatches: 17, Indels: 42
0.68 0.09 0.23
Matches are distributed among these distances:
23 2 0.02
24 18 0.14
25 12 0.10
26 17 0.13
27 35 0.28
28 18 0.14
29 14 0.11
30 6 0.05
31 4 0.03
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.19
Consensus pattern (27 bp):
AAAAAAAACAAATAATAAAATATATAT
Found at i:13216680 original size:18 final size:17
Alignment explanation
Indices: 13216641--13216686 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
13216631 TAATATATAT
13216641 ATAAA-ATAAATAAATA
1 ATAAATATAAATAAATA
*
13216657 AGTAAATATATATAAATTA
1 A-TAAATATAAATAAA-TA
13216676 ATAAAT-TAAAT
1 ATAAATATAAAT
13216687 GACGAAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 1 0.04
17 8 0.32
18 13 0.52
19 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
ATAAATATAAATAAATA
Found at i:13217027 original size:21 final size:21
Alignment explanation
Indices: 13216979--13217030 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
13216969 AAAAGAAAAT
13216979 AAATATAATAAAATGATAATAAA
1 AAATAT-ATAAAAT-ATAATAAA
*
13217002 AAATATATAAAAT-TAATAGGA
1 AAATATATAAAATATAATA-AA
13217023 AAATATAT
1 AAATATAT
13217031 GTATAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 5 0.19
21 9 0.33
22 7 0.26
23 6 0.22
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (21 bp):
AAATATATAAAATATAATAAA
Found at i:13217190 original size:12 final size:11
Alignment explanation
Indices: 13217162--13217202 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
13217152 TAACAAAATA
* *
13217162 AATAATATAAA
1 AATAATACAAG
13217173 AATAATACAAG
1 AATAATACAAG
13217184 TAATAATACAAG
1 -AATAATACAAG
13217196 AATAATA
1 AATAATA
13217203 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:13217248 original size:25 final size:26
Alignment explanation
Indices: 13217220--13217269 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
13217210 AGAGAAAGTA
13217220 AAAAAATATA-ATAATAATA-AAATAT
1 AAAAAATATACAT-ATAATATAAATAT
13217245 AAAAAATATACATATAATATAAATA
1 AAAAAATATACATATAATATAAATA
13217270 AGTAGAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (26 bp):
AAAAAATATACATATAATATAAATAT
Found at i:13217306 original size:12 final size:12
Alignment explanation
Indices: 13217284--13217328 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
13217274 GAATAAAAGG
13217284 AAAATATAATAGT
1 AAAA-ATAATAGT
*
13217297 AAAAATAATAAT
1 AAAAATAATAGT
*
13217309 AAATATAATAGT
1 AAAAATAATAGT
*
13217321 AATAATAA
1 AAAAATAA
13217329 AAATGCAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:13217323 original size:6 final size:5
Alignment explanation
Indices: 13217224--13217324 Score: 50
Period size: 5 Copynumber: 19.8 Consensus size: 5
13217214 AAAGTAAAAA
* * *
13217224 AATAT AATAAT AATAA AATAT AA-AA AATAT ACATAT AATAT AA-AT AAGTAG
1 AATAT AAT-AT AATAT AATAT AATAT AATAT A-ATAT AATAT AATAT AA-TAT
* * *
13217275 AATAA AAGGAA AATAT AATAGT AA-A- AATAAT AATA- AATAT AATAGT
1 AATAT AA-TAT AATAT AATA-T AATAT AAT-AT AATAT AATAT AATA-T
13217321 AATA
1 AATA
13217325 ATAAAAATGC
Statistics
Matches: 75, Mismatches: 9, Indels: 23
0.70 0.08 0.21
Matches are distributed among these distances:
3 2 0.03
4 11 0.15
5 34 0.45
6 28 0.37
ACGTcount: A:0.65, C:0.01, G:0.06, T:0.28
Consensus pattern (5 bp):
AATAT
Found at i:13217931 original size:37 final size:37
Alignment explanation
Indices: 13217890--13217986 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
13217880 CGATCTTATC
13217890 TTTAGGAGTTTAAATCATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTAAATCATAGTAGAACTCTATCCTATT
* * * *
13217927 TTTAGGAGTTTAAATCCTAGCAAAATTCTATCCTATT
1 TTTAGGAGTTTAAATCATAGTAGAACTCTATCCTATT
*
13217964 TTTAGGAGTTTGAATCATAGTAG
1 TTTAGGAGTTTAAATCATAGTAG
13217987 GACGAAAAGG
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.40
Consensus pattern (37 bp):
TTTAGGAGTTTAAATCATAGTAGAACTCTATCCTATT
Found at i:13218331 original size:19 final size:20
Alignment explanation
Indices: 13218292--13218332 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
13218282 ATCATATTGT
13218292 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
13218312 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
13218332 C
1 C
13218333 TGCAGGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.37, G:0.29, T:0.15
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:13218401 original size:20 final size:21
Alignment explanation
Indices: 13218367--13218406 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
13218357 CAGAATGTCT
13218367 AGGGGGTACAGATTC-CCCCC
1 AGGGGGTACAGATTCTCCCCC
13218387 AGGGGGTACCA-ATTCTCCCC
1 AGGGGGTA-CAGATTCTCCCC
13218407 TGTCTAACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.17
Consensus pattern (21 bp):
AGGGGGTACAGATTCTCCCCC
Found at i:13219705 original size:19 final size:20
Alignment explanation
Indices: 13219681--13219728 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
13219671 AATGATTTTC
*
13219681 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATAAAA
* *
13219700 TTTTGAAAGCCAAAATAAAA
1 TTTTGAAAACAAAAATAAAA
13219720 TTTTGAAAA
1 TTTTGAAAA
13219729 ATGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.54, C:0.06, G:0.10, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATAAAA
Found at i:13221298 original size:29 final size:27
Alignment explanation
Indices: 13221266--13221343 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 27
13221256 AATAGTAAGT
13221266 AAAAAAAAACAAATAATAAAATATATATA
1 AAAAAAAAACAAATAATAAAATA-A-ATA
* *
13221295 AAAAAGAAAAGAAA-AAGAAAATAAATA
1 AAAAA-AAAACAAATAATAAAATAAATA
13221322 AAACAAATAAACAAAATAATAA
1 AAA-AAA-AAAC-AAATAATAA
13221344 TAACAAAGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
27 7 0.17
28 6 0.15
29 16 0.40
30 11 0.28
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.14
Consensus pattern (27 bp):
AAAAAAAAACAAATAATAAAATAAATA
Found at i:13221716 original size:2 final size:2
Alignment explanation
Indices: 13221634--13221698 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
13221624 CTTGTGTAGA
13221634 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13221676 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
13221699 ATAGTAAAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13222066 original size:12 final size:12
Alignment explanation
Indices: 13222044--13222088 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
13222034 GAATAAAAGG
13222044 AAAATATAATAGT
1 AAAA-ATAATAGT
*
13222057 AAAAATAATAAT
1 AAAAATAATAGT
*
13222069 AAATATAATAGT
1 AAAAATAATAGT
*
13222081 AATAATAA
1 AAAAATAA
13222089 AAATGTAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:13222678 original size:37 final size:37
Alignment explanation
Indices: 13222637--13222741 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
13222627 GTGCTTGTGG
*
13222637 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCATAGTAGAACTCT
* * * *
13222674 ATCCTATTTTTAGGAGTTTAAATCCTAGAAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCATAGTAGAACTCT
* *
13222711 ATCTTATTTTTAGGAGTTTGAATCATAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCATAGTAG
13222742 GACGAAAAGG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCATAGTAGAACTCT
Found at i:13223086 original size:19 final size:20
Alignment explanation
Indices: 13223047--13223086 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
13223037 ATCATATTGT
13223047 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
13223067 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
13223087 ATGCAGGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.35, G:0.30, T:0.15
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:13223147 original size:21 final size:21
Alignment explanation
Indices: 13223122--13223192 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
13223112 CAGAATGTCT
13223122 AGGGGGTACAGATTTCCCCCC
1 AGGGGGTACAGATTTCCCCCC
*
13223143 AGGGGGTACCGA-TTCCCCCC
1 AGGGGGTACAGATTTCCCCCC
* *
13223163 AGGGGGAACAGATTCCCCCCC
1 AGGGGGTACAGATTTCCCCCC
13223184 AGGGGGTAC
1 AGGGGGTAC
13223193 CAATTCTCCC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
20 18 0.41
21 26 0.59
ACGTcount: A:0.20, C:0.34, G:0.32, T:0.14
Consensus pattern (21 bp):
AGGGGGTACAGATTTCCCCCC
Found at i:13225542 original size:4 final size:4
Alignment explanation
Indices: 13225535--13225623 Score: 63
Period size: 4 Copynumber: 21.2 Consensus size: 4
13225525 TATTTATTCA
* * * *
13225535 AAAT AAAT AAAT AAAT AATTT GAAAT TAAT AAAT AAAG AAAT TAAT AAAAT
1 AAAT AAAT AAAT AAAT AA-AT -AAAT AAAT AAAT AAAT AAAT AAAT -AAAT
* * *
13225586 AAAT TATT CAAAAT AAAT AAAT ATAT AAAT AAA- AAAT A
1 AAAT AAAT --AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
13225624 CCCCCTTAAT
Statistics
Matches: 65, Mismatches: 14, Indels: 12
0.71 0.15 0.13
Matches are distributed among these distances:
3 3 0.05
4 53 0.82
5 5 0.08
6 4 0.06
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:13225586 original size:39 final size:38
Alignment explanation
Indices: 13225535--13225623 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 38
13225525 TATTTATTCA
** *
13225535 AAATAAATAAATAAATAATTTGAAATTAATAAATAAAG
1 AAATAAATAAATAAATAATTCAAAATAAATAAATAAAG
* * * *
13225573 AAATTAATAAAATAAATTATTCAAAATAAATAAATATAT
1 AAATAAAT-AAATAAATAATTCAAAATAAATAAATAAAG
13225612 AAATAAA-AAATA
1 AAATAAATAAATA
13225624 CCCCCTTAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
37 5 0.12
38 7 0.17
39 30 0.71
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.29
Consensus pattern (38 bp):
AAATAAATAAATAAATAATTCAAAATAAATAAATAAAG
Found at i:13225618 original size:30 final size:30
Alignment explanation
Indices: 13225484--13225618 Score: 132
Period size: 30 Copynumber: 4.5 Consensus size: 30
13225474 AAATAAAGCG
* *
13225484 AATAAATTAA-AAATTATTCAAAATTAATAA
1 AATAAATAAATAAATTATTCAAAATAAAT-A
* *
13225514 AATAAATAAATTATTTATTCAAAATAAATA
1 AATAAATAAATAAATTATTCAAAATAAATA
* * *
13225544 AATAAATAATTTGAAATTAAT--AAATAAAGA
1 AATAAATAA-AT-AAATTATTCAAAATAAATA
*
13225574 AATTAATAAAATAAATTATTCAAAATAAATA
1 AATAAAT-AAATAAATTATTCAAAATAAATA
*
13225605 AATATATAAATAAA
1 AATAAATAAATAAA
13225619 AAATACCCCC
Statistics
Matches: 84, Mismatches: 15, Indels: 12
0.76 0.14 0.11
Matches are distributed among these distances:
29 7 0.08
30 41 0.49
31 31 0.37
32 5 0.06
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (30 bp):
AATAAATAAATAAATTATTCAAAATAAATA
Found at i:13226120 original size:4 final size:4
Alignment explanation
Indices: 13226111--13226169 Score: 55
Period size: 4 Copynumber: 13.8 Consensus size: 4
13226101 TAAATGTATA
* *
13226111 AAAT AAAT AAAT AAAT AAAT GATT CGAAAT AAAT AAAT AAAT CAAAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT --AAAT AAAT AAAT AAAT --AAAT
*
13226159 AAAA AAAT AAA
1 AAAT AAAT AAA
13226170 AAAAATAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
4 39 0.87
6 6 0.13
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:13226158 original size:14 final size:13
Alignment explanation
Indices: 13226108--13226178 Score: 53
Period size: 12 Copynumber: 5.8 Consensus size: 13
13226098 TAATAAATGT
13226108 ATAAAATAAATAA
1 ATAAAATAAATAA
*
13226121 AT-AAATAAATGA
1 ATAAAATAAATAA
* *
13226133 TTCGAAATAAATAA
1 AT-AAAATAAATAA
*
13226147 AT-AAAT-CA-AA
1 ATAAAATAAATAA
13226157 ATAAAA-AAATAA
1 ATAAAATAAATAA
*
13226169 AAAAAATAAA
1 ATAAAATAAA
13226179 AGTTATCTCC
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
10 4 0.09
11 5 0.11
12 21 0.47
13 5 0.11
14 10 0.22
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (13 bp):
ATAAAATAAATAA
Found at i:13226170 original size:8 final size:8
Alignment explanation
Indices: 13226137--13226179 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
13226127 AAATGATTCG
*
13226137 AAATAAAT
1 AAATAAAA
13226145 AAATAAATCA
1 AAATAAA--A
13226155 AAATAAAA
1 AAATAAAA
13226163 AAATAAAAA
1 AAAT-AAAA
13226172 AAATAAAA
1 AAATAAAA
13226180 GTTATCTCCG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
8 16 0.52
9 8 0.26
10 7 0.23
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.16
Consensus pattern (8 bp):
AAATAAAA
Found at i:13237306 original size:129 final size:129
Alignment explanation
Indices: 13237076--13237313 Score: 440
Period size: 129 Copynumber: 1.8 Consensus size: 129
13237066 CCTAAGTCCT
*
13237076 TGGATGGTCCCTGAACTTTAAAATGTATTTAACTTGGTCTAGAAACATGATTTTGGAATTAAAGT
1 TGGATGGTCCCTGAACTTTAAAATGTATTTAACTTGGTCTAGAAACATGATTTTGCAATTAAAGT
13237141 TTGGTTTCAACCCGGATTTTGTTGAAATTTATTCTATGACTCTATAATGATAATAATTTTATAA
66 TTGGTTTCAACCCGGATTTTGTTGAAATTTATTCTATGACTCTATAATGATAATAATTTTATAA
*
13237205 TGGATGGTTCCTGAACTTTAAAATGTATTTAACTTGGTCTAGAAACATGATTTTGCAATTAAAGT
1 TGGATGGTCCCTGAACTTTAAAATGTATTTAACTTGGTCTAGAAACATGATTTTGCAATTAAAGT
* *
13237270 TTGGTTTCAACTCGGATTTTGTTGAAATTTATTCTATGTCTCTA
66 TTGGTTTCAACCCGGATTTTGTTGAAATTTATTCTATGACTCTA
13237314 AATTGTTCAT
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
129 105 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (129 bp):
TGGATGGTCCCTGAACTTTAAAATGTATTTAACTTGGTCTAGAAACATGATTTTGCAATTAAAGT
TTGGTTTCAACCCGGATTTTGTTGAAATTTATTCTATGACTCTATAATGATAATAATTTTATAA
Found at i:13241210 original size:45 final size:45
Alignment explanation
Indices: 13241108--13241210 Score: 107
Period size: 45 Copynumber: 2.3 Consensus size: 45
13241098 TGGGTCAAAG
* * * * **
13241108 AGCATCAGTATCTCCCTATTACCTTAGGCTAGATCTGGGTCACAC
1 AGCATCAGCACCTCCCTAATACCTCAGGCTAGATCCAGGTCACAC
* * * * *
13241153 AACATAAACACCTCCCTAATACCTCAGGCTAGGTCCAGGTCACAT
1 AGCATCAGCACCTCCCTAATACCTCAGGCTAGATCCAGGTCACAC
13241198 AGCATCAGCACCT
1 AGCATCAGCACCT
13241211 TGCTAGGCTA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.23
Consensus pattern (45 bp):
AGCATCAGCACCTCCCTAATACCTCAGGCTAGATCCAGGTCACAC
Found at i:13242409 original size:14 final size:16
Alignment explanation
Indices: 13242379--13242410 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
13242369 TCTTCATTTC
13242379 TTCCTTTATCATCATT
1 TTCCTTTATCATCATT
13242395 TTCC-TTATC-TCATT
1 TTCCTTTATCATCATT
13242409 TT
1 TT
13242411 TCTCTTCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 5 0.31
16 4 0.25
ACGTcount: A:0.16, C:0.25, G:0.00, T:0.59
Consensus pattern (16 bp):
TTCCTTTATCATCATT
Found at i:13242411 original size:15 final size:17
Alignment explanation
Indices: 13242372--13242412 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
13242362 ATTCTTCTCT
13242372 TCATTTCTTCCTTTATCA
1 TCATTT-TTCCTTTATCA
13242390 TCA-TTTTCC-TTATC-
1 TCATTTTTCCTTTATCA
13242404 TCATTTTTC
1 TCATTTTTC
13242413 TCTTCAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.14
15 10 0.45
16 4 0.18
17 2 0.09
18 3 0.14
ACGTcount: A:0.15, C:0.27, G:0.00, T:0.59
Consensus pattern (17 bp):
TCATTTTTCCTTTATCA
Found at i:13243111 original size:9 final size:9
Alignment explanation
Indices: 13243097--13243124 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
13243087 AGAGGATTAC
13243097 AACCATAGT
1 AACCATAGT
13243106 AACCATAGT
1 AACCATAGT
13243115 AACCATAGT
1 AACCATAGT
13243124 A
1 A
13243125 GGCATAGTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.21
Consensus pattern (9 bp):
AACCATAGT
Found at i:13244352 original size:9 final size:9
Alignment explanation
Indices: 13244338--13244365 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
13244328 AGAGGATTAC
13244338 AACCATAGT
1 AACCATAGT
13244347 AACCATAGT
1 AACCATAGT
13244356 AACCATAGT
1 AACCATAGT
13244365 A
1 A
13244366 GGCATAGTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.21
Consensus pattern (9 bp):
AACCATAGT
Found at i:13245593 original size:9 final size:9
Alignment explanation
Indices: 13245579--13245606 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
13245569 AGAGGATTAC
13245579 AACCATAGT
1 AACCATAGT
13245588 AACCATAGT
1 AACCATAGT
13245597 AACCATAGT
1 AACCATAGT
13245606 A
1 A
13245607 GGCATAGTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.21
Consensus pattern (9 bp):
AACCATAGT
Found at i:13246834 original size:9 final size:9
Alignment explanation
Indices: 13246820--13246847 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
13246810 AGAGGATTAC
13246820 AACCATAGT
1 AACCATAGT
13246829 AACCATAGT
1 AACCATAGT
13246838 AACCATAGT
1 AACCATAGT
13246847 A
1 A
13246848 GGCATAGTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.21
Consensus pattern (9 bp):
AACCATAGT
Found at i:13256328 original size:15 final size:16
Alignment explanation
Indices: 13256297--13256329 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
13256287 TTTGGCAGGG
*
13256297 TCGTCTTCTTTTGCTT
1 TCGTCTTCTTTTCCTT
13256313 TCGTCTT-TTTTCCTT
1 TCGTCTTCTTTTCCTT
13256328 TC
1 TC
13256330 CTTTTTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.00, C:0.27, G:0.09, T:0.64
Consensus pattern (16 bp):
TCGTCTTCTTTTCCTT
Found at i:13258252 original size:32 final size:32
Alignment explanation
Indices: 13258216--13258280 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
13258206 GAGCCAATAT
* * * *
13258216 AAAGGAGTACTTTGGGGCCTTAGAGCCTACCC
1 AAAGGAGTACCTTAGGGCCTAAGAGACTACCC
13258248 AAAGGAGTACCTTAGGGCCTAAGAGACTACCC
1 AAAGGAGTACCTTAGGGCCTAAGAGACTACCC
13258280 A
1 A
13258281 TAACTGCATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (32 bp):
AAAGGAGTACCTTAGGGCCTAAGAGACTACCC
Found at i:13259446 original size:31 final size:31
Alignment explanation
Indices: 13259411--13259473 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
13259401 TTTGACTTAA
* *
13259411 GGAAGATGATAAGGTTGATGTGTTTTGGTTT
1 GGAAGATGATAAGGTTGAGGTGTCTTGGTTT
13259442 GGAAGATGATAAGGTTGAGGTGTCTTGGTTT
1 GGAAGATGATAAGGTTGAGGTGTCTTGGTTT
13259473 G
1 G
13259474 ATGGTAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.22, C:0.02, G:0.38, T:0.38
Consensus pattern (31 bp):
GGAAGATGATAAGGTTGAGGTGTCTTGGTTT
Found at i:13273404 original size:22 final size:23
Alignment explanation
Indices: 13273376--13273418 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
13273366 GTGGGTCCCC
*
13273376 TACAAAAC-AAATCAAAATAATA
1 TACAAAACTAAATAAAAATAATA
13273398 TACAAAACTAAATAAAAATAA
1 TACAAAACTAAATAAAAATAA
13273419 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.19
Consensus pattern (23 bp):
TACAAAACTAAATAAAAATAATA
Found at i:13273418 original size:6 final size:6
Alignment explanation
Indices: 13273407--13273444 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
13273397 ATACAAAACT
*
13273407 AAATAA AAATAA AAATAA AAATAA AGGA-AA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA A-AATAA AAATAA AA
13273445 TTATTATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 1 0.04
6 26 0.93
7 1 0.04
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (6 bp):
AAATAA
Found at i:13280959 original size:18 final size:17
Alignment explanation
Indices: 13280906--13280962 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 17
13280896 CAATTTAAAC
*
13280906 TATAATAAAAATATAA-
1 TATAATAAAATTATAAT
*
13280922 -A-AATATAATTATAAT
1 TATAATAAAATTATAAT
*
13280937 TATAATAAAATTATATTT
1 TATAATAAAATTATA-AT
13280955 TATAATAA
1 TATAATAA
13280963 CTCACCATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 11 0.33
15 1 0.03
16 1 0.03
17 11 0.33
18 9 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TATAATAAAATTATAAT
Found at i:13282319 original size:10 final size:10
Alignment explanation
Indices: 13282304--13282328 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
13282294 AGTGAAACGG
13282304 TTCGGTTCGA
1 TTCGGTTCGA
13282314 TTCGGTTCGA
1 TTCGGTTCGA
13282324 TTCGG
1 TTCGG
13282329 ATGACCTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.20, G:0.32, T:0.40
Consensus pattern (10 bp):
TTCGGTTCGA
Found at i:13283960 original size:20 final size:21
Alignment explanation
Indices: 13283915--13283960 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
13283905 AAAATAATAA
*
13283915 ATATAATCCTAAATGATAATG
1 ATATTATCCTAAATGATAATG
* *
13283936 A-ATTATCCTATATGA-AATT
1 ATATTATCCTAAATGATAATG
13283955 ATATTA
1 ATATTA
13283961 CAAGTAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.19
20 16 0.76
21 1 0.05
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.39
Consensus pattern (21 bp):
ATATTATCCTAAATGATAATG
Found at i:13287717 original size:26 final size:26
Alignment explanation
Indices: 13287667--13287718 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
13287657 TTTTTTCAAA
* *
13287667 TTTTTTCTTCTTTTTTTACCTTTTTC
1 TTTTTTCTTCTTATTTTACCCTTTTC
13287693 TTTTTTCTTCTTCATTTT-CCCTTTTC
1 TTTTTTCTTCTT-ATTTTACCCTTTTC
13287719 ATTTATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTTTTCTTCTTATTTTACCCTTTTC
Found at i:13294166 original size:5 final size:6
Alignment explanation
Indices: 13294151--13294194 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
13294141 ATTGGACCTA
13294151 AAAAAT AAAAAT AAAAAT AAAGAAAT AAAAAT --AAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT -AA-AAAT AAAAAT AAAAAT AAAAAT AA
13294195 GTATATTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 4 0.12
6 22 0.65
7 4 0.12
8 4 0.12
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:13294176 original size:14 final size:13
Alignment explanation
Indices: 13294151--13294185 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
13294141 ATTGGACCTA
13294151 AAAAAT-AAAAAT
1 AAAAATAAAAAAT
13294163 AAAAATAAAGAAAT
1 AAAAATAAA-AAAT
13294177 AAAAATAAA
1 AAAAATAAA
13294186 TAAAAATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.29
13 2 0.10
14 13 0.62
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:13294188 original size:10 final size:10
Alignment explanation
Indices: 13294153--13294194 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
13294143 TGGACCTAAA
13294153 AAATAAAAAT
1 AAATAAAAAT
*
13294163 AAA-AATAAAG
1 AAATAA-AAAT
13294173 AAATAAAAAT
1 AAATAAAAAT
13294183 AAATAAAAAT
1 AAATAAAAAT
13294193 AA
1 AA
13294195 GTATATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 2 0.07
10 24 0.86
11 2 0.07
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:13294254 original size:37 final size:36
Alignment explanation
Indices: 13294205--13294417 Score: 218
Period size: 37 Copynumber: 5.8 Consensus size: 36
13294195 GTATATTATA
* * *
13294205 ATATATTATATATATTTAAAAAAAACGTTTTCAAAACCC
1 ATATATTATATAT-TTT-TAAAAAATGTTTTCAAAA-CT
** * **
13294244 ATATATTATATATATTTTCCAACATGTTTTTTAAACT
1 ATATATTATATAT-TTTTAAAAAATGTTTTCAAAACT
*
13294281 ATATATTATATA-TTTTCAAAAATGTTTT-AAAACT
1 ATATATTATATATTTTTAAAAAATGTTTTCAAAACT
13294315 ATATATTATATATATTTTCAAAAAATGTTTTCAAAACT
1 ATATATTATATAT-TTTT-AAAAAATGTTTTCAAAACT
* *
13294353 ATATATTATATATATTTTCAAAAATGCTTTT-ATAACT
1 ATATATTATATAT-TTTTAAAAAATG-TTTTCAAAACT
*
13294390 ATATATTATATA-TTTTCAAAAATGTTTT
1 ATATATTATATATTTTTAAAAAATGTTTT
13294418 ATATTATATA
Statistics
Matches: 155, Mismatches: 14, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
34 21 0.14
35 26 0.17
36 4 0.03
37 48 0.31
38 39 0.25
39 17 0.11
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.46
Consensus pattern (36 bp):
ATATATTATATATTTTTAAAAAATGTTTTCAAAACT
Found at i:13294395 original size:109 final size:110
Alignment explanation
Indices: 13294205--13294418 Score: 342
Period size: 109 Copynumber: 2.0 Consensus size: 110
13294195 GTATATTATA
* *
13294205 ATATATTATATATATTTAAAAAAAACGTTTTCAAAACCCATATATTATATATATTTTCCAACATG
1 ATATATTATATATATTTAAAAAAAACGTTTTCAAAACCCATATATTATATATATTTTCAAAAATG
*
13294270 TTTTTTAAACTATATATTATATATTTTCAAAAATGTTTTAAAACT
66 TTTTATAAACTATATATTATATATTTTCAAAAATGTTTTAAAACT
** * *
13294315 ATATATTATATATATTTTCAAAAAATGTTTTCAAAA-CTATATATTATATATATTTTCAAAAATG
1 ATATATTATATATATTTAAAAAAAACGTTTTCAAAACCCATATATTATATATATTTTCAAAAATG
13294379 CTTTTAT-AACTATATATTATATATTTTCAAAAATGTTTTA
66 -TTTTATAAACTATATATTATATATTTTCAAAAATGTTTTA
13294419 TATTATATAT
Statistics
Matches: 96, Mismatches: 7, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
109 58 0.60
110 38 0.40
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (110 bp):
ATATATTATATATATTTAAAAAAAACGTTTTCAAAACCCATATATTATATATATTTTCAAAAATG
TTTTATAAACTATATATTATATATTTTCAAAAATGTTTTAAAACT
Found at i:13294427 original size:26 final size:27
Alignment explanation
Indices: 13294391--13294481 Score: 109
Period size: 28 Copynumber: 3.4 Consensus size: 27
13294381 TTTATAACTA
13294391 TATATTATATA-TTTTCAAAAATGT-TT
1 TATATTATATAGTTTTCAAAAAT-TATT
13294417 TATATTATATATGTTTTCAAAAATTATT
1 TATATTATATA-GTTTTCAAAAATTATT
*
13294445 TATATTATATAGTTTT-AAAACTATATAT
1 TATATTATATAGTTTTCAAAAAT-TAT-T
13294473 TATA-TATAT
1 TATATTATAT
13294482 TTTCGAGAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
26 16 0.27
27 14 0.24
28 29 0.49
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (27 bp):
TATATTATATAGTTTTCAAAAATTATT
Found at i:13299816 original size:22 final size:22
Alignment explanation
Indices: 13299729--13299816 Score: 63
Period size: 22 Copynumber: 4.0 Consensus size: 22
13299719 ATATCCTACA
* *
13299729 CAAAATGAAAGAAAATCAAATT
1 CAAAAGGAAAGAAAATGAAATT
* * *
13299751 CAAAAGGAAA-ATGAAACGAAGTA
1 CAAAAGGAAAGA--AAATGAAATT
* * *
13299774 CATAATGAAAGAAAATTAAATT
1 CAAAAGGAAAGAAAATGAAATT
13299796 CAAAAGGAAATGAAAA-GAAAT
1 CAAAAGGAAA-GAAAATGAAAT
13299817 GAAGTAAGAA
Statistics
Matches: 48, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
21 1 0.02
22 27 0.56
23 19 0.40
24 1 0.02
ACGTcount: A:0.62, C:0.07, G:0.15, T:0.16
Consensus pattern (22 bp):
CAAAAGGAAAGAAAATGAAATT
Found at i:13302768 original size:117 final size:117
Alignment explanation
Indices: 13302562--13302798 Score: 474
Period size: 117 Copynumber: 2.0 Consensus size: 117
13302552 TGGGAAGTTG
13302562 TTCCCATTGAACTCCTCAAACTCCAAGGATTTGAATTTCGGAAGAAGAACCAAATTTGGGACTAA
1 TTCCCATTGAACTCCTCAAACTCCAAGGATTTGAATTTCGGAAGAAGAACCAAATTTGGGACTAA
13302627 ACTTAGTTCATCAACATTTACTCCATAGTAGTCATGGTCTCCTTTAACCACC
66 ACTTAGTTCATCAACATTTACTCCATAGTAGTCATGGTCTCCTTTAACCACC
13302679 TTCCCATTGAACTCCTCAAACTCCAAGGATTTGAATTTCGGAAGAAGAACCAAATTTGGGACTAA
1 TTCCCATTGAACTCCTCAAACTCCAAGGATTTGAATTTCGGAAGAAGAACCAAATTTGGGACTAA
13302744 ACTTAGTTCATCAACATTTACTCCATAGTAGTCATGGTCTCCTTTAACCACC
66 ACTTAGTTCATCAACATTTACTCCATAGTAGTCATGGTCTCCTTTAACCACC
13302796 TTC
1 TTC
13302799 ATTTGGTATT
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 120 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (117 bp):
TTCCCATTGAACTCCTCAAACTCCAAGGATTTGAATTTCGGAAGAAGAACCAAATTTGGGACTAA
ACTTAGTTCATCAACATTTACTCCATAGTAGTCATGGTCTCCTTTAACCACC
Found at i:13302936 original size:48 final size:48
Alignment explanation
Indices: 13302865--13302960 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
13302855 ATCAAAATCT
13302865 GGTATATGGTAATCACCCGGATTATTCTCAGGGTTGGATACAGAAGTC
1 GGTATATGGTAATCACCCGGATTATTCTCAGGGTTGGATACAGAAGTC
13302913 GGTATATGGTAATCACCCGGATTATTCTCAGGGTTGGATACAGAAGTC
1 GGTATATGGTAATCACCCGGATTATTCTCAGGGTTGGATACAGAAGTC
13302961 TGTACTTTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (48 bp):
GGTATATGGTAATCACCCGGATTATTCTCAGGGTTGGATACAGAAGTC
Found at i:13306653 original size:6 final size:6
Alignment explanation
Indices: 13306642--13306668 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
13306632 TTAATTGCGA
13306642 AAATTT AAATTT AAATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAA
13306669 AGATTCGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
AAATTT
Found at i:13306842 original size:25 final size:25
Alignment explanation
Indices: 13306814--13306861 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
13306804 AAAACGTTTT
13306814 AAAAATATTAAAAAAAGAAAAAAGA
1 AAAAATATTAAAAAAAGAAAAAAGA
* * *
13306839 AAAAATTTTAAAGAGAGAAAAAA
1 AAAAATATTAAAAAAAGAAAAAA
13306862 ATATATACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (25 bp):
AAAAATATTAAAAAAAGAAAAAAGA
Found at i:13308043 original size:6 final size:6
Alignment explanation
Indices: 13308032--13308074 Score: 63
Period size: 6 Copynumber: 7.3 Consensus size: 6
13308022 ATTGGACCTA
13308032 AAAAAT AAAAAT AGAAAAT AAAAAT --AAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT A-AAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA
13308075 GTATACTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 4 0.12
6 24 0.71
7 6 0.18
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:13308067 original size:16 final size:17
Alignment explanation
Indices: 13308040--13308074 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
13308030 TAAAAAATAA
13308040 AAATAGAAAATAAAAAT
1 AAATAGAAAATAAAAAT
13308057 AAATA-AAAATAAAAAT
1 AAATAGAAAATAAAAAT
13308073 AA
1 AA
13308075 GTATACTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (17 bp):
AAATAGAAAATAAAAAT
Found at i:13308164 original size:35 final size:36
Alignment explanation
Indices: 13308085--13308328 Score: 250
Period size: 37 Copynumber: 6.7 Consensus size: 36
13308075 GTATACTATA
* *
13308085 ATATATTATATATA-TTTCAAAAAAACGTTTTCAAAATCC
1 ATATATTATATATATTTTC--AAAAATGTTTT-AAAA-CT
* * *
13308124 ATATATTATATATATTTTCCAACATGATTTCT-AAATT
1 ATATATTATATATATTTTCAAAAATG-TTT-TAAAACT
13308161 ATATA-T-TATATATTTTCAAAAATGTTTTAAAACT
1 ATATATTATATATATTTTCAAAAATGTTTTAAAACT
* *
13308195 ATATATTATATATATTTTTGAGAAATGTTTTCAAAACT
1 ATATATTATATATA-TTTTCAAAAATGTTTT-AAAACT
* *
13308233 ATATATTATATATTTTTTCAAAAATGTTTTTAAAACA
1 ATATATTATATATATTTTCAAAAATG-TTTTAAAACT
*
13308270 ATATA-T-TATATA-TTTCAAAAATGTTTTCAAAATT
1 ATATATTATATATATTTTCAAAAATGTTTT-AAAACT
*
13308304 ATATATTATATATGTTTTCAAAAAT
1 ATATATTATATATATTTTCAAAAAT
13308329 TTTATATATT
Statistics
Matches: 174, Mismatches: 18, Indels: 28
0.79 0.08 0.13
Matches are distributed among these distances:
33 5 0.03
34 32 0.18
35 23 0.13
36 13 0.07
37 49 0.28
38 30 0.17
39 17 0.10
40 5 0.03
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (36 bp):
ATATATTATATATATTTTCAAAAATGTTTTAAAACT
Found at i:13308278 original size:109 final size:110
Alignment explanation
Indices: 13308085--13308327 Score: 312
Period size: 109 Copynumber: 2.2 Consensus size: 110
13308075 GTATACTATA
* * *
13308085 ATATATTATATATATTTCAAAAAAACGTTTTCAAAATCCATATATTATATATATTTTCCAACATG
1 ATATATTATATATATTTTAAAAAAACGTTTTCAAAATCCATATATTATATATATTTTCAAAAATG
**
13308150 ATTTCTAAATTATATATTATATATTTTCAAAAATGTTTT-AAAACT
66 ATTTCTAAACAATATATTATATA-TTTCAAAAATGTTTTCAAAACT
** * * * *
13308195 ATATATTATATATATTTTTGAGAAATGTTTTCAAAA-CTATATATTATATATTTTTTCAAAAATG
1 ATATATTATATATATTTTAAAAAAACGTTTTCAAAATCCATATATTATATATATTTTCAAAAATG
* *
13308259 -TTTTTAAAACAATATATTATATATTTCAAAAATGTTTTCAAAATT
66 ATTTCT-AAACAATATATTATATATTTCAAAAATGTTTTCAAAACT
* *
13308304 ATATATTATATATGTTTTCAAAAA
1 ATATATTATATATATTTTAAAAAA
13308328 TTTTATATAT
Statistics
Matches: 114, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
108 19 0.17
109 64 0.56
110 31 0.27
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (110 bp):
ATATATTATATATATTTTAAAAAAACGTTTTCAAAATCCATATATTATATATATTTTCAAAAATG
ATTTCTAAACAATATATTATATATTTCAAAAATGTTTTCAAAACT
Found at i:13308309 original size:71 final size:71
Alignment explanation
Indices: 13308085--13308328 Score: 269
Period size: 71 Copynumber: 3.3 Consensus size: 71
13308075 GTATACTATA
* * * * * *
13308085 ATATATTATATATATTTCAAAAAAACGTTTTCAAAATCCATATATTATATATATTTTCCAACATG
1 ATATATTATATATTTTTC--AAAAATGTTTTTAAAA-CAATATA-TATATATA-TTTCAAAAATG
* *
13308150 ATTTCTAAATT
61 TTTTCAAAATT
* * *
13308161 ATATATTATATA-TTTTCAAAAATG-TTTTAAAACTATATATTATATATATTTTTGAGAAATGTT
1 ATATATTATATATTTTTCAAAAATGTTTTTAAAAC-A-ATA-TATATATATATTTCAAAAATGTT
*
13308224 TTCAAAACT
63 TTCAAAATT
13308233 ATATATTATATATTTTTTCAAAAATGTTTTTAAAACAATATAT-TATATATTTCAAAAATGTTTT
1 ATATATTATATA-TTTTTCAAAAATGTTTTTAAAACAATATATATATATATTTCAAAAATGTTTT
13308297 CAAAATT
65 CAAAATT
13308304 ATATATTATATATGTTTTCAAAAAT
1 ATATATTATATAT-TTTTCAAAAAT
13308329 TTTATATATT
Statistics
Matches: 145, Mismatches: 16, Indels: 19
0.81 0.09 0.11
Matches are distributed among these distances:
70 1 0.01
71 48 0.33
72 37 0.26
73 19 0.13
74 15 0.10
75 13 0.09
76 12 0.08
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (71 bp):
ATATATTATATATTTTTCAAAAATGTTTTTAAAACAATATATATATATATTTCAAAAATGTTTTC
AAAATT
Found at i:13308342 original size:28 final size:25
Alignment explanation
Indices: 13308290--13308372 Score: 89
Period size: 25 Copynumber: 3.3 Consensus size: 25
13308280 TATTTCAAAA
13308290 ATGTTTTCAAAATTATATATTATAT
1 ATGTTTTCAAAATTATATATTATAT
13308315 ATGTTTTCAAAAATTTTATATATTATAT
1 ATGTTTTC-AAAA--TTATATATTATAT
* * *
13308343 A-G-TTTGAAGACTATATATTATAT
1 ATGTTTTCAAAATTATATATTATAT
*
13308366 ATATTTT
1 ATGTTTT
13308373 TGGAAAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.27
25 14 0.29
26 7 0.14
27 1 0.02
28 14 0.29
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.52
Consensus pattern (25 bp):
ATGTTTTCAAAATTATATATTATAT
Found at i:13308816 original size:12 final size:12
Alignment explanation
Indices: 13308796--13308838 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
13308786 TATAATATGC
*
13308796 TATTTTATTTAT
1 TATTATATTTAT
*
13308808 TATTATATTTAC
1 TATTATATTTAT
13308820 TATTATATATTAT
1 TATTATAT-TTAT
13308833 TATTAT
1 TATTAT
13308839 TTTTTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 18 0.67
13 9 0.33
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (12 bp):
TATTATATTTAT
Found at i:13310281 original size:46 final size:47
Alignment explanation
Indices: 13310196--13310287 Score: 107
Period size: 46 Copynumber: 2.0 Consensus size: 47
13310186 TTAAATGCTT
** * * *
13310196 GTGAATTAGATATCATGTGGTTATGTTTATTTTTTTGAACA-AGCAC
1 GTGAATTAGATATCATGCAGTTAGGTTTATTATTATGAACATAGCAC
*
13310242 GTGAATTAGATATTATGCAGTTAGGATTT-TTATTATGAACATAGCA
1 GTGAATTAGATATCATGCAGTTAGG-TTTATTATTATGAACATAGCA
13310288 TGTGGGTAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
46 31 0.82
47 7 0.18
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.41
Consensus pattern (47 bp):
GTGAATTAGATATCATGCAGTTAGGTTTATTATTATGAACATAGCAC
Found at i:13317128 original size:22 final size:22
Alignment explanation
Indices: 13317100--13317174 Score: 123
Period size: 22 Copynumber: 3.4 Consensus size: 22
13317090 ATTCAAATAG
* *
13317100 CATCTCTTCTGAGCAAGCTAAA
1 CATCTCTTCTAATCAAGCTAAA
13317122 CATCTCTTCTAATCAAGCTAAA
1 CATCTCTTCTAATCAAGCTAAA
13317144 CATCTCTTCTAATCAAGCTAAA
1 CATCTCTTCTAATCAAGCTAAA
*
13317166 CACCTCTTC
1 CATCTCTTC
13317175 AAATAACATT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.32, C:0.31, G:0.07, T:0.31
Consensus pattern (22 bp):
CATCTCTTCTAATCAAGCTAAA
Found at i:13323454 original size:22 final size:22
Alignment explanation
Indices: 13323426--13323479 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
13323416 TGGCCTTAGA
13323426 GTATCGATACCCCTATATGAGG
1 GTATCGATACCCCTATATGAGG
13323448 GTATCGATACCCCTATATGAGG
1 GTATCGATACCCCTATATGAGG
13323470 GTATCGATAC
1 GTATCGATAC
13323480 TACCCGAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (22 bp):
GTATCGATACCCCTATATGAGG
Found at i:13326139 original size:19 final size:19
Alignment explanation
Indices: 13326115--13326165 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
13326105 ACCAGTTTTA
13326115 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
*
13326134 AACCGGTTTGATCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
13326153 AACCGGGTTGACC
1 AACCGGTTTGACC
13326166 CGACCCGACC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 27 0.96
20 1 0.04
ACGTcount: A:0.18, C:0.25, G:0.31, T:0.25
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:13326181 original size:17 final size:17
Alignment explanation
Indices: 13326159--13326222 Score: 110
Period size: 17 Copynumber: 3.7 Consensus size: 17
13326149 TCTGAACCGG
*
13326159 GTTGACCCGACCCGACC
1 GTTGACCTGACCCGACC
13326176 GTTGACCTGACCCGACC
1 GTTGACCTGACCCGACC
13326193 GTTGACCTGACCCGACC
1 GTTGACCTGACCCGACC
13326210 GTTGACCGTGACC
1 GTTGACC-TGACC
13326223 GTTGACTTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
17 40 0.89
18 5 0.11
ACGTcount: A:0.17, C:0.41, G:0.25, T:0.17
Consensus pattern (17 bp):
GTTGACCTGACCCGACC
Found at i:13333666 original size:17 final size:17
Alignment explanation
Indices: 13333643--13333700 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
13333633 TCTGAACCGG
13333643 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
*
13333660 ATTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
13333677 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
13333694 GTTGACC
1 GTTGACC
13333701 GTTGACTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.19, C:0.45, G:0.22, T:0.14
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:13340055 original size:13 final size:13
Alignment explanation
Indices: 13340037--13340079 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
13340027 AGTATCGTGG
13340037 TTTCCGACCTCGA
1 TTTCCGACCTCGA
13340050 TTTCCGACCTCGA
1 TTTCCGACCTCGA
*
13340063 TTTCCGACCTCTA
1 TTTCCGACCTCGA
13340076 TTTC
1 TTTC
13340080 GGCGCCGTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.14, C:0.37, G:0.12, T:0.37
Consensus pattern (13 bp):
TTTCCGACCTCGA
Found at i:13340612 original size:17 final size:17
Alignment explanation
Indices: 13340590--13340628 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
13340580 TCTGAACCGG
13340590 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
13340607 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
13340624 GTTGA
1 GTTGA
13340629 TCGTTGACCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.41, G:0.26, T:0.15
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:13340635 original size:7 final size:7
Alignment explanation
Indices: 13340620--13340656 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
13340610 GACCCGACCC
13340620 GACCGTT
1 GACCGTT
*
13340627 GATCGTT
1 GACCGTT
13340634 GACCG-T
1 GACCGTT
13340640 GACCGTT
1 GACCGTT
13340647 GACCGTT
1 GACCGTT
13340654 GAC
1 GAC
13340657 TTTCTTTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (7 bp):
GACCGTT
Found at i:13342597 original size:3 final size:3
Alignment explanation
Indices: 13342591--13342620 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
13342581 CCCATGTTAT
*
13342591 TTC TTC TTC TTC TTC TTC TCC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
13342621 CTCCTCCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:13344753 original size:32 final size:32
Alignment explanation
Indices: 13344695--13344786 Score: 96
Period size: 32 Copynumber: 2.9 Consensus size: 32
13344685 TATAAATTTT
* *
13344695 CATTAAA-TTTATTGAAATATTGCAAAATAAA
1 CATTAAATTTTATTAAAATATTACAAAATAAA
* * * **
13344726 CATTAAATTTTATTTAAATGTTACAAAACAGT
1 CATTAAATTTTATTAAAATATTACAAAATAAA
* *
13344758 CATTACATTTTATGAAAATATTACAAAAT
1 CATTAAATTTTATTAAAATATTACAAAAT
13344787 GCTCATTAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 7 0.14
32 42 0.86
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (32 bp):
CATTAAATTTTATTAAAATATTACAAAATAAA
Found at i:13344793 original size:32 final size:32
Alignment explanation
Indices: 13344694--13344798 Score: 90
Period size: 32 Copynumber: 3.3 Consensus size: 32
13344684 TTATAAATTT
* * *
13344694 TCATTAAA-TTTATTG-AAATATTGCAAAATAA
1 TCATTAAATTTTA-TGAAAATATTACAAAACAG
* ** *
13344725 ACATTAAATTTTATTTAAATGTTACAAAACAG
1 TCATTAAATTTTATGAAAATATTACAAAACAG
* *
13344757 TCATTACATTTTATGAAAATATTACAAAA-TG
1 TCATTAAATTTTATGAAAATATTACAAAACAG
13344788 CTCATTAAATT
1 -TCATTAAATT
13344799 ATCAATTTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
31 9 0.16
32 49 0.84
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.39
Consensus pattern (32 bp):
TCATTAAATTTTATGAAAATATTACAAAACAG
Found at i:13345313 original size:4 final size:4
Alignment explanation
Indices: 13345304--13345382 Score: 95
Period size: 4 Copynumber: 19.8 Consensus size: 4
13345294 TTTACCTTTT
* * * * * * *
13345304 ATAC ATAC ATAC ATGC ATAC ATAT ATAT ATAT ATAT ATAT ATAT ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
13345352 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
13345383 TATATATATA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 71 1.00
ACGTcount: A:0.49, C:0.16, G:0.01, T:0.33
Consensus pattern (4 bp):
ATAC
Found at i:13345387 original size:4 final size:4
Alignment explanation
Indices: 13345324--13345431 Score: 144
Period size: 4 Copynumber: 27.0 Consensus size: 4
13345314 ACATGCATAC
* * * * * *
13345324 ATAT ATAT ATAT ATAT ATAT ATAT ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* *
13345372 ATAC ATAC ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
13345420 ATAT ATAT ATAT
1 ATAT ATAT ATAT
13345432 GTAACATTCA
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 102 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (4 bp):
ATAT
Found at i:13346759 original size:23 final size:22
Alignment explanation
Indices: 13346725--13346777 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 22
13346715 TCGAGACTCG
13346725 AGCTCGAATTTGAGCTCGATTCA
1 AGCTC-AATTTGAGCTCGATTCA
*
13346748 AGCTCAATTTTGAGCTTGATTCA
1 AGCTCAA-TTTGAGCTCGATTCA
13346771 AGCTCAA
1 AGCTCAA
13346778 CAGATTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 2 0.07
23 26 0.93
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (22 bp):
AGCTCAATTTGAGCTCGATTCA
Found at i:13347797 original size:7 final size:7
Alignment explanation
Indices: 13347785--13347967 Score: 105
Period size: 7 Copynumber: 26.1 Consensus size: 7
13347775 TATAATCAGA
13347785 TTTAGGG
1 TTTAGGG
*
13347792 TTTAGGA
1 TTTAGGG
* *
13347799 CTTAGGA
1 TTTAGGG
*
13347806 CTTAGGG
1 TTTAGGG
13347813 TTTAGGG
1 TTTAGGG
*
13347820 GTTAGGG
1 TTTAGGG
**
13347827 TTTATAG
1 TTTAGGG
*
13347834 TTTAAGG
1 TTTAGGG
13347841 TTTAGGG
1 TTTAGGG
13347848 TTTAGGG
1 TTTAGGG
*
13347855 TTTAGGA
1 TTTAGGG
* **
13347862 CTTAGAA
1 TTTAGGG
*
13347869 CTTAGGG
1 TTTAGGG
13347876 TTTAGGG
1 TTTAGGG
*
13347883 TTTAAGG
1 TTTAGGG
* *
13347890 TTTATGA
1 TTTAGGG
13347897 TTTAGGG
1 TTTAGGG
*
13347904 CTTAGGG
1 TTTAGGG
* * *
13347911 CTTATGA
1 TTTAGGG
* *
13347918 CTTAGAG
1 TTTAGGG
13347925 TTTAGGG
1 TTTAGGG
* **
13347932 TTCAGCA
1 TTTAGGG
***
13347939 TTTATAT
1 TTTAGGG
*
13347946 TTTAGGA
1 TTTAGGG
13347953 TTTAGGG
1 TTTAGGG
13347960 TTTAGGG
1 TTTAGGG
13347967 T
1 T
13347968 GTAATCTAAC
Statistics
Matches: 135, Mismatches: 41, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 135 1.00
ACGTcount: A:0.22, C:0.05, G:0.32, T:0.41
Consensus pattern (7 bp):
TTTAGGG
Found at i:13347860 original size:56 final size:56
Alignment explanation
Indices: 13347785--13347966 Score: 199
Period size: 56 Copynumber: 3.2 Consensus size: 56
13347775 TATAATCAGA
* *
13347785 TTTAGGGTTTAGGACTTAGGACTTAGGGTTTAGGGGTTAGGGTTTATAGTTTAAGG
1 TTTAGGGTTTAGGGCTTAGGACTTAGAGTTTAGGGGTTAGGGTTTATAGTTTAAGG
* ** * * *
13347841 TTTAGGGTTTAGGGTTTAGGACTTAGAACTTAGGGTTTAGGGTTTA-AGGTTTATGA
1 TTTAGGGTTTAGGGCTTAGGACTTAGAGTTTAGGGGTTAGGGTTTATA-GTTTAAGG
* * ** *
13347897 TTTAGGGCTTAGGGCTTATGACTTAGAGTTTA-GGGTTCAGCATTTATA-TTTTAGG
1 TTTAGGGTTTAGGGCTTAGGACTTAGAGTTTAGGGGTT-AGGGTTTATAGTTTAAGG
13347952 ATTTAGGGTTTAGGG
1 -TTTAGGGTTTAGGG
13347967 TGTAATCTAA
Statistics
Matches: 102, Mismatches: 20, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
55 9 0.09
56 92 0.90
57 1 0.01
ACGTcount: A:0.22, C:0.05, G:0.32, T:0.41
Consensus pattern (56 bp):
TTTAGGGTTTAGGGCTTAGGACTTAGAGTTTAGGGGTTAGGGTTTATAGTTTAAGG
Found at i:13347928 original size:28 final size:28
Alignment explanation
Indices: 13347785--13347933 Score: 126
Period size: 28 Copynumber: 5.3 Consensus size: 28
13347775 TATAATCAGA
** *
13347785 TTTAGGGTTTAGGACTTAGGACTTAGGG
1 TTTAGGGTTTAGGGTTTAGGACTTAGAG
* * *
13347813 TTTAGGGGTTAGGGTTTA-TAGTTTA-AGG
1 TTTAGGGTTTAGGGTTTAGGA-CTTAGA-G
*
13347841 TTTAGGGTTTAGGGTTTAGGACTTAGAA
1 TTTAGGGTTTAGGGTTTAGGACTTAGAG
* *
13347869 CTTAGGGTTTAGGGTTTAAGG-TTTATGA-
1 TTTAGGGTTTAGGGTTT-AGGACTTA-GAG
* * *
13347897 TTTAGGGCTTAGGGCTTATGACTTAGAG
1 TTTAGGGTTTAGGGTTTAGGACTTAGAG
13347925 TTTAGGGTT
1 TTTAGGGTT
13347934 CAGCATTTAT
Statistics
Matches: 95, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
27 5 0.05
28 83 0.87
29 7 0.07
ACGTcount: A:0.21, C:0.05, G:0.34, T:0.40
Consensus pattern (28 bp):
TTTAGGGTTTAGGGTTTAGGACTTAGAG
Found at i:13357227 original size:29 final size:28
Alignment explanation
Indices: 13357194--13357266 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
13357184 TTAAATGTTA
13357194 TAATAAAATATTTATTATGAT-AATTAAAT
1 TAATAAAATATTTATTAT-ATAAATT-AAT
* * *
13357223 TAATAAATAGACTTATTATATAAATTATT
1 TAATAAA-ATATTTATTATATAAATTAAT
13357252 TAATAAAATTATTTA
1 TAATAAAA-TATTTA
13357267 AATGTAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
28 1 0.03
29 22 0.61
30 13 0.36
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (28 bp):
TAATAAAATATTTATTATATAAATTAAT
Found at i:13357363 original size:23 final size:24
Alignment explanation
Indices: 13357323--13357376 Score: 101
Period size: 23 Copynumber: 2.3 Consensus size: 24
13357313 CAATGATTAA
13357323 ATGTAAATTAATATAGTTTAATTT
1 ATGTAAATTAATATAGTTTAATTT
13357347 ATGTAAATT-ATATAGTTTAATTT
1 ATGTAAATTAATATAGTTTAATTT
13357370 ATGTAAA
1 ATGTAAA
13357377 GAAAAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 21 0.70
24 9 0.30
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (24 bp):
ATGTAAATTAATATAGTTTAATTT
Found at i:13357672 original size:23 final size:22
Alignment explanation
Indices: 13357632--13357680 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
13357622 TGATAATGTA
*
13357632 AATAACATTTGATCTAAAATTTG
1 AATAACATTTGATCT-AAAGTTG
13357655 AATAACATTTGAGT-TAAAGTTG
1 AATAACATTTGA-TCTAAAGTTG
13357677 AATA
1 AATA
13357681 CAGTAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 10 0.42
23 13 0.54
24 1 0.04
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (22 bp):
AATAACATTTGATCTAAAGTTG
Found at i:13360843 original size:7 final size:7
Alignment explanation
Indices: 13360831--13360864 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
13360821 GAACAAAATT
13360831 AAAATAA
1 AAAATAA
13360838 AAAATAA
1 AAAATAA
13360845 AAAATTAA
1 AAAA-TAA
*
13360853 ATAATAA
1 AAAATAA
13360860 AAAAT
1 AAAAT
13360865 TAAATATACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (7 bp):
AAAATAA
Found at i:13360850 original size:20 final size:22
Alignment explanation
Indices: 13360825--13360864 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
13360815 ATTAATGAAC
13360825 AAAATT-AA-AATAAAAAATAA
1 AAAATTAAATAATAAAAAATAA
13360845 AAAATTAAATAATAAAAAAT
1 AAAATTAAATAATAAAAAAT
13360865 TAAATATACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 2 0.11
22 10 0.56
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAATTAAATAATAAAAAATAA
Found at i:13360858 original size:15 final size:15
Alignment explanation
Indices: 13360831--13360870 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
13360821 GAACAAAATT
*
13360831 AAAA-TAAAAAATAA
1 AAAATTAAATAATAA
13360845 AAAATTAAATAATAA
1 AAAATTAAATAATAA
13360860 AAAATTAAATA
1 AAAATTAAATA
13360871 TACCTAGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAATTAAATAATAA
Found at i:13361098 original size:6 final size:6
Alignment explanation
Indices: 13361044--13361124 Score: 58
Period size: 6 Copynumber: 13.8 Consensus size: 6
13361034 TTTTAGGGTC
* * * * * *
13361044 GGGTTT GGATTT GGGTTC GGGTTC GGATTT -GGTTT GGATTT -GATTT
1 GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT
* * * *
13361090 GGGTTT GGGTTC AGGTTT GGGTTT AGGTTC GGGTT
1 GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTT
13361125 CAGGTTCAGG
Statistics
Matches: 58, Mismatches: 15, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
5 9 0.16
6 49 0.84
ACGTcount: A:0.07, C:0.05, G:0.42, T:0.46
Consensus pattern (6 bp):
GGGTTT
Found at i:13361108 original size:12 final size:12
Alignment explanation
Indices: 13361091--13361130 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
13361081 ATTTGATTTG
13361091 GGTTTGGGTTCA
1 GGTTTGGGTTCA
*
13361103 GGTTTGGGTTTA
1 GGTTTGGGTTCA
*
13361115 GGTTCGGGTTCA
1 GGTTTGGGTTCA
13361127 GGTT
1 GGTT
13361131 CAGGTTCGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.07, C:0.07, G:0.42, T:0.42
Consensus pattern (12 bp):
GGTTTGGGTTCA
Found at i:13361110 original size:18 final size:17
Alignment explanation
Indices: 13361053--13361121 Score: 68
Period size: 17 Copynumber: 4.0 Consensus size: 17
13361043 CGGGTTTGGA
*
13361053 TTTGGGTTCGGGTTCGG
1 TTTGGGTTTGGGTTCGG
* * *
13361070 ATTT-GGTTTGGATTTGA
1 -TTTGGGTTTGGGTTCGG
13361087 TTTGGGTTTGGGTTCAGG
1 TTTGGGTTTGGGTTC-GG
*
13361105 TTTGGGTTTAGGTTCGG
1 TTTGGGTTTGGGTTCGG
13361122 GTTCAGGTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
16 3 0.07
17 20 0.49
18 18 0.44
ACGTcount: A:0.07, C:0.06, G:0.41, T:0.46
Consensus pattern (17 bp):
TTTGGGTTTGGGTTCGG
Found at i:13361124 original size:18 final size:18
Alignment explanation
Indices: 13361091--13361148 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
13361081 ATTTGATTTG
* * *
13361091 GGTTTGGGTTCAGGTTTG
1 GGTTTAGGTTCGGGTTTA
*
13361109 GGTTTAGGTTCGGGTTCA
1 GGTTTAGGTTCGGGTTTA
*
13361127 GGTTCAGGTTCGGGTTTA
1 GGTTTAGGTTCGGGTTTA
13361145 GGTT
1 GGTT
13361149 ATAGAAGATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.09, C:0.09, G:0.41, T:0.41
Consensus pattern (18 bp):
GGTTTAGGTTCGGGTTTA
Found at i:13361148 original size:6 final size:6
Alignment explanation
Indices: 13361097--13361148 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
13361087 TTTGGGTTTG
** * * * *
13361097 GGTTCA GGTTTG GGTTTA GGTTCG GGTTCA GGTTCA GGTTCG GGTTTA
1 GGTTCA GGTTCA GGTTCA GGTTCA GGTTCA GGTTCA GGTTCA GGTTCA
13361145 GGTT
1 GGTT
13361149 ATAGAAGATG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.10, C:0.10, G:0.40, T:0.40
Consensus pattern (6 bp):
GGTTCA
Found at i:13361148 original size:12 final size:12
Alignment explanation
Indices: 13361091--13361142 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
13361081 ATTTGATTTG
*
13361091 GGTTTGGGTTCA
1 GGTTCGGGTTCA
* *
13361103 GGTTTGGGTTTA
1 GGTTCGGGTTCA
13361115 GGTTCGGGTTCA
1 GGTTCGGGTTCA
* *
13361127 GGTTCAGGTTCG
1 GGTTCGGGTTCA
13361139 GGTT
1 GGTT
13361143 TAGGTTATAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.08, C:0.10, G:0.42, T:0.40
Consensus pattern (12 bp):
GGTTCGGGTTCA
Found at i:13361961 original size:29 final size:29
Alignment explanation
Indices: 13361924--13362007 Score: 116
Period size: 29 Copynumber: 2.8 Consensus size: 29
13361914 ATTAATAGAG
13361924 TTAATATAAACTATCAT-TTATAATTAATA
1 TTAATATAAACTAT-ATATTATAATTAATA
13361953 TTAATATAAACTATATATTATAATTAATA
1 TTAATATAAACTATATATTATAATTAATA
* *
13361982 TTAATATTAACCTATATGAATATAAT
1 TTAATA-TAAACTATAT-ATTATAAT
13362008 GTAGTTTATA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
28 2 0.04
29 32 0.64
30 9 0.18
31 7 0.14
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (29 bp):
TTAATATAAACTATATATTATAATTAATA
Found at i:13362065 original size:31 final size:31
Alignment explanation
Indices: 13362024--13362136 Score: 120
Period size: 31 Copynumber: 3.5 Consensus size: 31
13362014 TATAATTTTT
*
13362024 AATTATTATTAATATAAAATATAGTTTATAA
1 AATTAATATTAATATAAAATATAGTTTATAA
* *
13362055 AATTAATATTAATATAAACTATATTTTAT-A
1 AATTAATATTAATATAAAATATAGTTTATAA
* * *
13362085 AATTATATAGTATAGTTTATAAAATATAGTTAATAT
1 AATTA-ATA-T-TA--ATATAAAATATAGTTTATAA
13362121 AATTAATATTAATATA
1 AATTAATATTAATATA
13362137 GTACATGTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
30 6 0.09
31 33 0.49
32 1 0.01
33 4 0.06
34 1 0.01
35 17 0.25
36 5 0.07
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (31 bp):
AATTAATATTAATATAAAATATAGTTTATAA
Found at i:13362183 original size:24 final size:25
Alignment explanation
Indices: 13362156--13362215 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
13362146 TTATAGACTA
*
13362156 ATTAATATTAATACTATA-TATTAT
1 ATTAATATTAATACTATAGTAATAT
13362180 ATTAAT-TTAA-ACTATAGTTAATAT
1 ATTAATATTAATACTATAG-TAATAT
*
13362204 GTTAATATTAAT
1 ATTAATATTAAT
13362216 GTAAACTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 6 0.20
23 4 0.13
24 16 0.53
25 4 0.13
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (25 bp):
ATTAATATTAATACTATAGTAATAT
Found at i:13362262 original size:36 final size:36
Alignment explanation
Indices: 13362222--13362300 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
13362212 TAATGTAAAC
*
13362222 TATAGTTTATAAACTATCTACTACATTAATACAAAT
1 TATAGTTTATAAACTATATACTACATTAATACAAAT
* *
13362258 TATAGTTTATAAACTATATACTATATTAATATAAAT
1 TATAGTTTATAAACTATATACTACATTAATACAAAT
13362294 TATAGTT
1 TATAGTT
13362301 AAGAAAATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (36 bp):
TATAGTTTATAAACTATATACTACATTAATACAAAT
Done.