Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 180 of 290
Found at i:58068799 original size:12 final size:12
Alignment explanation
Indices: 58068779--58068828 Score: 66
Period size: 12 Copynumber: 4.0 Consensus size: 12
58068769 AAACCGTATG
58068779 CAATTTTTTTTT
1 CAATTTTTTTTT
58068791 -AATTTTTTTTT
1 CAATTTTTTTTT
58068802 CAATTTTTTTTT
1 CAATTTTTTTTT
58068814 CGAACTCTTTTTTTT
1 C-AA-T-TTTTTTTT
58068829 TACGTACCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.32
12 12 0.35
13 2 0.06
14 1 0.03
15 8 0.24
ACGTcount: A:0.16, C:0.10, G:0.02, T:0.72
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:58069158 original size:22 final size:22
Alignment explanation
Indices: 58069128--58069171 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
58069118 TTTGGTATTT
58069128 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
58069150 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
58069172 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:58071513 original size:30 final size:30
Alignment explanation
Indices: 58071479--58071575 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
58071469 AGCTCACTCC
58071479 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
58071509 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
58071539 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
58071569 TAGCTCA
1 TAGCTCA
58071576 TTTTAGTTTT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:58072661 original size:20 final size:19
Alignment explanation
Indices: 58072638--58072702 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
58072628 AAGCTCAAAC
58072638 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
58072658 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
58072678 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
58072698 GAGCT
1 GAGCT
58072703 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:58076134 original size:20 final size:20
Alignment explanation
Indices: 58076111--58076157 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
58076101 TGGTTAAGAT
*
58076111 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
58076131 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
58076151 TGAGCTG
1 TGAGCTG
58076158 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:58079030 original size:22 final size:19
Alignment explanation
Indices: 58078985--58079034 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 19
58078975 CTTTTCACTT
*
58078985 TTTTTTGTTCTTTTTTTTAT
1 TTTTTT-TTCTTTTTTTTAC
58079005 TTTTTTTTCTTTTTTTGCTCAC
1 TTTTTTTTCTTTTTTT--T-AC
58079027 TTTTTTTT
1 TTTTTTTT
58079035 TGAATTTCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 10 0.38
20 6 0.23
21 1 0.04
22 9 0.35
ACGTcount: A:0.04, C:0.10, G:0.04, T:0.82
Consensus pattern (19 bp):
TTTTTTTTCTTTTTTTTAC
Found at i:58079758 original size:6 final size:6
Alignment explanation
Indices: 58079726--58079833 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
58079716 AAAGAGATTG
* * ** *
58079726 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
58079773 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
58079824 AAAGAA AAAG
1 AAAGAA AAAG
58079834 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 22, Indels: 11
0.69 0.20 0.10
Matches are distributed among these distances:
5 4 0.05
6 59 0.79
7 8 0.11
8 4 0.05
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:58079813 original size:14 final size:13
Alignment explanation
Indices: 58079794--58079831 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
58079784 AAAAGTGAGA
58079794 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
58079806 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
58079821 GAAAAAGAAAA
1 GAAAAAGAAAA
58079832 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:58079845 original size:21 final size:21
Alignment explanation
Indices: 58079795--58079845 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
58079785 AAAGTGAGAG
*
58079795 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
58079816 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
58079837 AAAAAGAAA
1 AAAAAGAAA
58079846 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:58079885 original size:33 final size:33
Alignment explanation
Indices: 58079848--58079910 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
58079838 AAAAGAAATT
58079848 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
58079881 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
58079911 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:58085212 original size:10 final size:10
Alignment explanation
Indices: 58085197--58085261 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
58085187 AGTTTTTCCC
58085197 AGCTCAATTT
1 AGCTCAATTT
*
58085207 AGCTCACA-TG
1 AGCTCA-ATTT
*
58085217 AGCTTAATTT
1 AGCTCAATTT
*
58085227 AGCTC-GTTT
1 AGCTCAATTT
58085236 GAGCTCAATTT
1 -AGCTCAATTT
* *
58085247 AGCTTACTTT
1 AGCTCAATTT
58085257 AGCTC
1 AGCTC
58085262 GTTTGAGCTT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
9 4 0.10
10 34 0.81
11 4 0.10
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (10 bp):
AGCTCAATTT
Found at i:58085220 original size:20 final size:20
Alignment explanation
Indices: 58085197--58085250 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
58085187 AGTTTTTCCC
58085197 AGCTCAATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
58085217 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
58085237 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
58085251 TACTTTAGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:58085231 original size:30 final size:30
Alignment explanation
Indices: 58085197--58085270 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
58085187 AGTTTTTCCC
58085197 AGCTCAATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTC-ATTTGAGCTCA-ATTGAGCTTAATTT
* * *
58085227 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCATTTGAGCTCAATTGAGCTTAATTT
*
58085257 AGCTCGTTTGAGCT
1 AGCTCATTTGAGCT
58085271 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 4 0.10
30 35 0.90
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (30 bp):
AGCTCATTTGAGCTCAATTGAGCTTAATTT
Found at i:58085260 original size:20 final size:20
Alignment explanation
Indices: 58085197--58085261 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
58085187 AGTTTTTCCC
* * *
58085197 AGCTCAATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
58085217 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
58085236 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
58085257 AGCTC
1 AGCTC
58085262 GTTTGAGCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 29 0.81
21 4 0.11
22 1 0.03
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:58088051 original size:17 final size:17
Alignment explanation
Indices: 58088015--58088047 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
58088005 GATTGAGAGT
*
58088015 GAAAAGGAATGTGAAAA
1 GAAAAGAAATGTGAAAA
58088032 GAAAAGAAAT-TGAAAA
1 GAAAAGAAATGTGAAAA
58088048 AGAAGTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.12
Consensus pattern (17 bp):
GAAAAGAAATGTGAAAA
Found at i:58088064 original size:13 final size:12
Alignment explanation
Indices: 58088033--58088087 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
58088023 ATGTGAAAAG
*
58088033 AAAAGAAATTGA
1 AAAAGAAGTTGA
58088045 AAAAGAAGTTGA
1 AAAAGAAGTTGA
*
58088057 AGAAAGAAG-AGA
1 A-AAAGAAGTTGA
*
58088069 AAATGAA-TTAGA
1 AAAAGAAGTT-GA
58088081 AAAAGAA
1 AAAAGAA
58088088 ACAAAAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
11 5 0.14
12 23 0.66
13 7 0.20
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.13
Consensus pattern (12 bp):
AAAAGAAGTTGA
Found at i:58091630 original size:20 final size:20
Alignment explanation
Indices: 58091583--58091630 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
58091573 AGTAAGCTCG
58091583 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
58091603 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
58091623 GTTGAGCT
1 GTTGAGCT
58091631 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:58093612 original size:18 final size:18
Alignment explanation
Indices: 58093591--58093672 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
58093581 ACCTCACTCC
*
58093591 CTTTTTGGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
58093609 CTTTTTCAATCTTTTCTTCTTT
1 CTTTTTCGA---TTTCTT-TTT
* * *
58093631 -TCTTTCGATTTCTCTTA
1 CTTTTTCGATTTCTTTTT
58093648 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
58093666 CTTTTTC
1 CTTTTTC
58093673 ATTACAATGT
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
17 2 0.04
18 33 0.66
21 12 0.24
22 3 0.06
ACGTcount: A:0.07, C:0.20, G:0.05, T:0.68
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:58095894 original size:20 final size:20
Alignment explanation
Indices: 58095847--58095894 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
58095837 AGTAAGCTCG
58095847 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
58095867 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
58095887 GTTGAGCT
1 GTTGAGCT
58095895 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:58103109 original size:6 final size:6
Alignment explanation
Indices: 58103100--58103133 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
58103090 CAATTTTTTC
* *
58103100 TCAATA TCAATA TCAATA TCAATC TCAATC TCAA
1 TCAATA TCAATA TCAATA TCAATA TCAATA TCAA
58103134 ATTCTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (6 bp):
TCAATA
Found at i:58103184 original size:20 final size:20
Alignment explanation
Indices: 58103141--58103184 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
58103131 CAAATTCTTT
*
58103141 TTTCTTTTTCTCACTCTCAT
1 TTTCTTTTTCTCACTCTCAA
*
58103161 TTTCTTTTT-TCTTCTCTCAA
1 TTTCTTTTTCTC-ACTCTCAA
58103181 TTTC
1 TTTC
58103185 ATTCAAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCTTTTTCTCACTCTCAA
Found at i:58103186 original size:26 final size:27
Alignment explanation
Indices: 58103122--58103187 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
58103112 TCAATATCAA
** *
58103122 TCTCAATCTCAAATTCTTTTTTCTTTT
1 TCTCAATCTCATTTTCTTTTTTCTTTC
*
58103149 TCTCACTCTCATTTTCTTTTTTC-TTC
1 TCTCAATCTCATTTTCTTTTTTCTTTC
*
58103175 TCTCAATTTCATT
1 TCTCAATCTCATT
58103188 CAAGATTCGT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 13 0.39
27 20 0.61
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (27 bp):
TCTCAATCTCATTTTCTTTTTTCTTTC
Found at i:58104201 original size:14 final size:14
Alignment explanation
Indices: 58104182--58104230 Score: 89
Period size: 14 Copynumber: 3.4 Consensus size: 14
58104172 GAATACAAAC
58104182 TTTTTTTTTTGAAT
1 TTTTTTTTTTGAAT
58104196 TTTTTTTTTTGAAT
1 TTTTTTTTTTGAAT
58104210 TTTTTTTTTTCGAAT
1 TTTTTTTTTT-GAAT
58104225 TTTTTT
1 TTTTTT
58104231 ATATTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 24 0.71
15 10 0.29
ACGTcount: A:0.12, C:0.02, G:0.06, T:0.80
Consensus pattern (14 bp):
TTTTTTTTTTGAAT
Found at i:58104202 original size:15 final size:15
Alignment explanation
Indices: 58104182--58104230 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
58104172 GAATACAAAC
58104182 TTTTTTTTTTGAA-T
1 TTTTTTTTTTGAATT
58104196 TTTTTTTTTTGAATT
1 TTTTTTTTTTGAATT
*
58104211 TTTTTTTTTCGAATT
1 TTTTTTTTTTGAATT
58104226 TTTTT
1 TTTTT
58104231 ATATTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 13 0.39
15 20 0.61
ACGTcount: A:0.12, C:0.02, G:0.06, T:0.80
Consensus pattern (15 bp):
TTTTTTTTTTGAATT
Found at i:58109231 original size:16 final size:17
Alignment explanation
Indices: 58109199--58109232 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
58109189 AAATCACTAA
*
58109199 AAATAGTAGAATGAATT
1 AAATAGTAGAATAAATT
58109216 AAATAGT-GAATAAATT
1 AAATAGTAGAATAAATT
58109232 A
1 A
58109233 TGTAATCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.29
Consensus pattern (17 bp):
AAATAGTAGAATAAATT
Found at i:58114331 original size:20 final size:19
Alignment explanation
Indices: 58114308--58114372 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
58114298 AAGCTCAAAC
58114308 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
58114328 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
58114348 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
58114368 GAGCT
1 GAGCT
58114373 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:58119020 original size:20 final size:19
Alignment explanation
Indices: 58118997--58119061 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
58118987 AAGCTCAAAC
58118997 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
58119017 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
58119037 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
58119057 GAGCT
1 GAGCT
58119062 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:58124211 original size:40 final size:40
Alignment explanation
Indices: 58124156--58124453 Score: 431
Period size: 40 Copynumber: 7.5 Consensus size: 40
58124146 TGGATGATAA
* * *
58124156 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
58124196 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
58124236 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
58124276 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
58124316 CCGGGCTAAGTCCCGAAGGCATTTGTTCGAGTTGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
58124356 CCGGGCTAAGTCCTGAAGTCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
58124396 TCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
58124436 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
58124454 TACTTGGCTT
Statistics
Matches: 236, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
39 16 0.07
40 220 0.93
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:58127504 original size:13 final size:13
Alignment explanation
Indices: 58127488--58127512 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58127478 AAAGAGTTCG
58127488 AAAAAAAAATTGA
1 AAAAAAAAATTGA
58127501 AAAAAAAAATTG
1 AAAAAAAAATTG
58127513 CATACGGTTT
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:0.08, T:0.16
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:58129743 original size:18 final size:18
Alignment explanation
Indices: 58129699--58129753 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 18
58129689 TCAAATGAGA
58129699 GAAAAAGAAAAGAGCGAAAAT
1 GAAAAAGAAAAGA---AAAAT
58129720 -ACAAAAGAAAAGAAAAAT
1 GA-AAAAGAAAAGAAAAAT
58129738 GAAAAAGAAAAGAAAA
1 GAAAAAGAAAAGAAAA
58129754 TTCAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 19 0.59
19 1 0.03
20 1 0.03
21 11 0.34
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.04
Consensus pattern (18 bp):
GAAAAAGAAAAGAAAAAT
Found at i:58129760 original size:18 final size:18
Alignment explanation
Indices: 58129700--58129761 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
58129690 CAAATGAGAG
58129700 AAAAAGAAAAGAGCGAAAAT-
1 AAAAAGAAAAGA---AAAATC
*
58129720 ACAAAAGAAAAGAAAAATG
1 A-AAAAGAAAAGAAAAATC
*
58129739 AAAAAGAAAAGAAAATTC
1 AAAAAGAAAAGAAAAATC
58129757 AAAAA
1 AAAAA
58129762 AAGAGAATGA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 25 0.66
19 1 0.03
20 1 0.03
21 11 0.29
ACGTcount: A:0.74, C:0.05, G:0.15, T:0.06
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAATC
Found at i:58139400 original size:17 final size:16
Alignment explanation
Indices: 58139375--58139412 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
58139365 CATTAAACAC
58139375 TTTTTTTTTC-AGATTT
1 TTTTTTTTTCGA-ATTT
58139391 TTTTTCTTTTCGAATTT
1 TTTTT-TTTTCGAATTT
58139408 TTTTT
1 TTTTT
58139413 GAATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 5 0.25
17 14 0.70
18 1 0.05
ACGTcount: A:0.11, C:0.08, G:0.05, T:0.76
Consensus pattern (16 bp):
TTTTTTTTTCGAATTT
Found at i:58139408 original size:16 final size:16
Alignment explanation
Indices: 58139375--58139412 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
58139365 CATTAAACAC
*
58139375 TTTTTTTTTCAGATTT
1 TTTTTTTTTCAGAATT
58139391 TTTTTCTTTTC-GAATT
1 TTTTT-TTTTCAGAATT
58139407 TTTTTT
1 TTTTTT
58139413 GAATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 14 0.70
17 5 0.25
ACGTcount: A:0.11, C:0.08, G:0.05, T:0.76
Consensus pattern (16 bp):
TTTTTTTTTCAGAATT
Found at i:58141177 original size:20 final size:20
Alignment explanation
Indices: 58141152--58141194 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
58141142 AAAAGAAAAG
58141152 AAAGAAGAGAGATTGAGAGA
1 AAAGAAGAGAGATTGAGAGA
** *
58141172 AAAGAATCGAGATTGTGAGA
1 AAAGAAGAGAGATTGAGAGA
58141192 AAA
1 AAA
58141195 ACAAGAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.30, T:0.14
Consensus pattern (20 bp):
AAAGAAGAGAGATTGAGAGA
Found at i:58146027 original size:20 final size:20
Alignment explanation
Indices: 58146002--58146044 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
58145992 AAAAGAAAAG
58146002 AAAGAAGAGAGATTGAGAGA
1 AAAGAAGAGAGATTGAGAGA
** *
58146022 AAAGAATCGAGATTGTGAGA
1 AAAGAAGAGAGATTGAGAGA
58146042 AAA
1 AAA
58146045 ACAAGAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.30, T:0.14
Consensus pattern (20 bp):
AAAGAAGAGAGATTGAGAGA
Found at i:58148827 original size:30 final size:30
Alignment explanation
Indices: 58148793--58148889 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
58148783 TAAACTAAAA
* *
58148793 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * * *
58148823 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* *
58148853 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGATTTAGCTCGTGAGCT-AAAGT
58148883 TGAGCTA
1 TGAGCTA
58148890 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 47 0.94
31 3 0.06
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:58151375 original size:11 final size:12
Alignment explanation
Indices: 58151359--58151413 Score: 60
Period size: 12 Copynumber: 4.8 Consensus size: 12
58151349 TTATAGATTC
*
58151359 AAAAAAACTCGA
1 AAAAAAAATCGA
58151371 AAAAAAAATCG-
1 AAAAAAAATCGA
*
58151382 AAAAAAAAT-TA
1 AAAAAAAATCGA
* *
58151393 AAAAAAATTTGA
1 AAAAAAAATCGA
58151405 AAAAAAAAT
1 AAAAAAAAT
58151414 TGCATACGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 17 0.47
12 19 0.53
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (12 bp):
AAAAAAAATCGA
Found at i:58151395 original size:22 final size:22
Alignment explanation
Indices: 58151370--58151411 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
58151360 AAAAAACTCG
58151370 AAAAAAAAATCGAAAAAAAATT
1 AAAAAAAAATCGAAAAAAAATT
* *
58151392 AAAAAAAATTTGAAAAAAAA
1 AAAAAAAAATCGAAAAAAAA
58151412 ATTGCATACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (22 bp):
AAAAAAAAATCGAAAAAAAATT
Found at i:58154777 original size:18 final size:18
Alignment explanation
Indices: 58154756--58154790 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
58154746 TTTTTCTTTT
58154756 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
58154774 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
58154791 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:58163991 original size:30 final size:30
Alignment explanation
Indices: 58163908--58163993 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
58163898 GCTCGTATCA
* *
58163908 AGCTAAGCTTTAGC-CCTTAAGCTAAAGTTG
1 AGCTAAGATTTAGCTCC-TAAGCTGAAGTTG
*
58163938 AGCTGAGATTATA-CTCCTAAGCTGAAGTTG
1 AGCTAAGATT-TAGCTCCTAAGCTGAAGTTG
* * *
58163968 AGCTAAGGTTTAGCTCGTGAGCTGAA
1 AGCTAAGATTTAGCTCCTAAGCTGAA
58163994 TATAAGCTAG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
29 2 0.04
30 40 0.87
31 4 0.09
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (30 bp):
AGCTAAGATTTAGCTCCTAAGCTGAAGTTG
Found at i:58176357 original size:13 final size:12
Alignment explanation
Indices: 58176339--58176382 Score: 56
Period size: 11 Copynumber: 3.7 Consensus size: 12
58176329 TTATACAAGT
58176339 AAAAAAAATTCGA
1 AAAAAAAATTC-A
58176352 AAAAAAAATTC-
1 AAAAAAAATTCA
58176363 AAAAAAAA-TCA
1 AAAAAAAATTCA
58176374 AAAAGAAAA
1 AAAA-AAAA
58176383 AAAAATCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 2 0.07
11 12 0.41
12 4 0.14
13 11 0.38
ACGTcount: A:0.77, C:0.07, G:0.05, T:0.11
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:58177336 original size:6 final size:5
Alignment explanation
Indices: 58177312--58177353 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
58177302 AAGAGAAAAT
58177312 AAAGA AAAGA AAAGA AAATGA AAATGA AATA-A AAAGA AAAGA
1 AAAGA AAAGA AAAGA AAA-GA AAA-GA AA-AGA AAAGA AAAGA
58177354 GAGGCAAGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 1 0.03
5 22 0.65
6 10 0.29
7 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (5 bp):
AAAGA
Found at i:58183412 original size:23 final size:22
Alignment explanation
Indices: 58183360--58183412 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
58183350 TCCACGTCTT
*
58183360 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
58183382 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
58183405 TTTCTTTT
1 TTTCTTTT
58183413 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:58188701 original size:559 final size:559
Alignment explanation
Indices: 58187644--58189882 Score: 4415
Period size: 559 Copynumber: 4.0 Consensus size: 559
58187634 AGCTTACCTC
58187644 ATTTTAGTTTAAACTCGGTTTTGTCTTTAATGCATTAAATAAAAATTTGCACATATTTATTTAAG
1 ATTTTAGTTTAAACTCGGTTTTGTCTTTAATGCATTAAATAAAAATTTGCACATATTTATTTAAG
58187709 CATTAAACTTGTCTTATATTAATATTTGTTATTAATATGCCATAGTCATTACATAAATTGATTAT
66 CATTAAACTTGTCTTATATTAATATTTGTTATTAATATGCCATAGTCATTACATAAATTGATTAT
58187774 GTTCACATAGCTGAATTAATGCATGACATTAATTGATACGAACCGCCTCGGGGAGAGTCGAGTCG
131 GTTCACATAGCTGAATTAATGCATGACATTAATTGATACGAACCGCCTCGGGGAGAGTCGAGTCG
58187839 TATGCGAGTTTGCCCGATCGTCTACGAGAAAGTATCGTTCGGTTTGTTAAAAAAAGATGTTTCTA
196 TATGCGAGTTTGCCCGATCGTCTACGAGAAAGTATCGTTCGGTTTGTTAAAAAAAGATGTTTCTA
58187904 AATAAATTATGCGGAAGCTATTCAAGGGGTTCAAATGAAGGGGTTAAAATATGAATATTAAGGTT
261 AATAAATTATGCGGAAGCTATTCAAGGGGTTCAAATGAAGGGGTTAAAATATGAATATTAAGGTT
58187969 CGGTTTAAAGTAAATGAAAGAATGGAAAGAAGGAACTCAAAAGCAAGCACGAACCAATATTAGAA
326 CGGTTTAAAGTAAATGAAAGAATGGAAAGAAGGAACTCAAAAGCAAGCACGAACCAATATTAGAA
58188034 AATATCGACCCAAATGCTTATAGGCTTTCAAGGCGAAAATGAAAATGATAGAACCTCAACCCACT
391 AATATCGACCCAAATGCTTATAGGCTTTCAAGGCGAAAATGAAAATGATAGAACCTCAACCCACT
58188099 ACTTAACAAAGTAGGAACCTAGGTATATGGGTGAACGAAATAGGGTTGACGCCACTACTAGGTAG
456 ACTTAACAAAGTAGGAACCTAGGTATATGGGTGAACGAAATAGGGTTGACGCCACTACTAGGTAG
58188164 ATAAGTCAACAAAGTCTCAAACAAAGTTTAGAGAAGAAA
521 ATAAGTCAACAAAGTCTCAAACAAAGTTTAGAGAAGAAA
58188203 ATTTTAGTTTAAACTCGGTTTTGTCTTTAATGCATTAAATAAAAATTTGCACATATTTATTTAAG
1 ATTTTAGTTTAAACTCGGTTTTGTCTTTAATGCATTAAATAAAAATTTGCACATATTTATTTAAG
58188268 CATTAAACTTGTCTTATATTAATATTTGTTATTAATATGCCATAGTCATTACATAAATTGATTAT
66 CATTAAACTTGTCTTATATTAATATTTGTTATTAATATGCCATAGTCATTACATAAATTGATTAT
*
58188333 GTTCACATAGCTGAATTAATGCATGACATTAATTGATACGAACCACCTCGGGGAGAGTCGAGTCG
131 GTTCACATAGCTGAATTAATGCATGACATTAATTGATACGAACCGCCTCGGGGAGAGTCGAGTCG
58188398 TATGCGAGTTTGCCCGATCGTCTACGAGAAAGTATCGTTCGGTTTGTTAAAAAAAGATGTTTCTA
196 TATGCGAGTTTGCCCGATCGTCTACGAGAAAGTATCGTTCGGTTTGTTAAAAAAAGATGTTTCTA
*
58188463 AATAAATTATGCAGAAGCTATTCAAGGGGTTCAAATGAAGGGGTTAAAATATGAATATTAAGGTT
261 AATAAATTATGCGGAAGCTATTCAAGGGGTTCAAATGAAGGGGTTAAAATATGAATATTAAGGTT
58188528 CGGTTTAAAGTAAATGAAAGAATGGAAAGAAGGAACTCAAAAGCAAGCACGAACCAATATTAGAA
326 CGGTTTAAAGTAAATGAAAGAATGGAAAGAAGGAACTCAAAAGCAAGCACGAACCAATATTAGAA
58188593 AATATCGACCCAAATGCTTATAGGCTTTCAAGGCGAAAATGAAAATGATAGAACCTCAACCCACT
391 AATATCGACCCAAATGCTTATAGGCTTTCAAGGCGAAAATGAAAATGATAGAACCTCAACCCACT
58188658 ACTTAACAAAGTAGGAACCTAGGTATATGGGTGAACGAAATAGGGTTGACGCCACTACTAGGTAG
456 ACTTAACAAAGTAGGAACCTAGGTATATGGGTGAACGAAATAGGGTTGACGCCACTACTAGGTAG
58188723 ATAAGTCAACAAAGTCTCAAACAAAGTTTAGAGAAGAAA
521 ATAAGTCAACAAAGTCTCAAACAAAGTTTAGAGAAGAAA
58188762 ATTTTAGTTTAAACTCGGTTTTGTCTTTAATGCATTAAATAAAAATTTGCACATATTTATTTAAG
1 ATTTTAGTTTAAACTCGGTTTTGTCTTTAATGCATTAAATAAAAATTTGCACATATTTATTTAAG
58188827 CATTAAACTTGTCTTATATTAATATTTGTTATTAATATGCCATAGTCATTACATAAATTGATTAT
66 CATTAAACTTGTCTTATATTAATATTTGTTATTAATATGCCATAGTCATTACATAAATTGATTAT
58188892 GTTCACATAGCTGAATTAATGCATGACATTAATTGATACGAACCGCCTCGGGGAGAGTCGAGTCG
131 GTTCACATAGCTGAATTAATGCATGACATTAATTGATACGAACCGCCTCGGGGAGAGTCGAGTCG
58188957 TATGCGAGTTTGCCCGATCGTCTACGAGAAAGTATCGTTCGGTTTGTTAAAAAAAGATGTTTCTA
196 TATGCGAGTTTGCCCGATCGTCTACGAGAAAGTATCGTTCGGTTTGTTAAAAAAAGATGTTTCTA
*
58189022 AATAAATTATGCGGAATCTATTCAAGGGGTTCAAATGAAGGGGTTAAAATATGAATATTAAGGTT
261 AATAAATTATGCGGAAGCTATTCAAGGGGTTCAAATGAAGGGGTTAAAATATGAATATTAAGGTT
58189087 CGGTTTAAAGTAAATGAAAGAATGGAAAGAAGGAACTCAAAAGCAAGCACGAACCAATATTAGAA
326 CGGTTTAAAGTAAATGAAAGAATGGAAAGAAGGAACTCAAAAGCAAGCACGAACCAATATTAGAA
58189152 AATATCGACCCAAATGCTTATAGGCTTTCAAGGCGAAAATGAAAATGATAGAACCTCAACCCACT
391 AATATCGACCCAAATGCTTATAGGCTTTCAAGGCGAAAATGAAAATGATAGAACCTCAACCCACT
58189217 ACTTAACAAAGTAGGAACCTAGGTATATGGGTGAACGAAATAGGGTTGACGCCACTACTAGGTAG
456 ACTTAACAAAGTAGGAACCTAGGTATATGGGTGAACGAAATAGGGTTGACGCCACTACTAGGTAG
58189282 ATAAGTCAACAAAGTCTCAAACAAAGTTTAGAGAAGAAA
521 ATAAGTCAACAAAGTCTCAAACAAAGTTTAGAGAAGAAA
58189321 ATTTTAGTTTAAACTCGGTTTTGTCTTTAATGCATTAAATAAAAATTTGCACATATTTATTTAAG
1 ATTTTAGTTTAAACTCGGTTTTGTCTTTAATGCATTAAATAAAAATTTGCACATATTTATTTAAG
58189386 CATTAAACTTGTCTTATATTAATATTTGTTATTAATATGCCATAGTCATTACATAAATTGATTAT
66 CATTAAACTTGTCTTATATTAATATTTGTTATTAATATGCCATAGTCATTACATAAATTGATTAT
58189451 GTTCACATAGCTGAATTAATGCATGACATTAATTGATACGAACCGCCTCGGGGAGAGTCGAGTCG
131 GTTCACATAGCTGAATTAATGCATGACATTAATTGATACGAACCGCCTCGGGGAGAGTCGAGTCG
*
58189516 TATGCGAGTTTGCCCGATCGTCTATGAGAAAGTATCGTTCGGTTTGTTAAAAAAAGATGTTTCTA
196 TATGCGAGTTTGCCCGATCGTCTACGAGAAAGTATCGTTCGGTTTGTTAAAAAAAGATGTTTCTA
*
58189581 AATAAATTATGCGGAAGCTATTCAAGGGGTTTAAATGAAGGGGTTAAAATATGAATATTAAGGTT
261 AATAAATTATGCGGAAGCTATTCAAGGGGTTCAAATGAAGGGGTTAAAATATGAATATTAAGGTT
*
58189646 TGGTTTAAAGTAAATGAAAGAATGGAAAGAAGGAACTCAAAAGCAAGCACGAACCAATATTAGAA
326 CGGTTTAAAGTAAATGAAAGAATGGAAAGAAGGAACTCAAAAGCAAGCACGAACCAATATTAGAA
*
58189711 AATATCGACCCAAATGCTTATAGGCTTTCAAGGCAAAAATGAAAATGATAGAACCTCAACCCACT
391 AATATCGACCCAAATGCTTATAGGCTTTCAAGGCGAAAATGAAAATGATAGAACCTCAACCCACT
58189776 ACTTAACAAAGTAGGAACCTAGGTATATGGGTGAACGAAATAGGGTTGACGCCACTACTAGGTAG
456 ACTTAACAAAGTAGGAACCTAGGTATATGGGTGAACGAAATAGGGTTGACGCCACTACTAGGTAG
58189841 ATAAGTCAACAAAGTCTCAAACAAAGTTTAGAGAAGAAA
521 ATAAGTCAACAAAGTCTCAAACAAAGTTTAGAGAAGAAA
58189880 ATT
1 ATT
58189883 CTCACAAGAT
Statistics
Matches: 1670, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
559 1670 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (559 bp):
ATTTTAGTTTAAACTCGGTTTTGTCTTTAATGCATTAAATAAAAATTTGCACATATTTATTTAAG
CATTAAACTTGTCTTATATTAATATTTGTTATTAATATGCCATAGTCATTACATAAATTGATTAT
GTTCACATAGCTGAATTAATGCATGACATTAATTGATACGAACCGCCTCGGGGAGAGTCGAGTCG
TATGCGAGTTTGCCCGATCGTCTACGAGAAAGTATCGTTCGGTTTGTTAAAAAAAGATGTTTCTA
AATAAATTATGCGGAAGCTATTCAAGGGGTTCAAATGAAGGGGTTAAAATATGAATATTAAGGTT
CGGTTTAAAGTAAATGAAAGAATGGAAAGAAGGAACTCAAAAGCAAGCACGAACCAATATTAGAA
AATATCGACCCAAATGCTTATAGGCTTTCAAGGCGAAAATGAAAATGATAGAACCTCAACCCACT
ACTTAACAAAGTAGGAACCTAGGTATATGGGTGAACGAAATAGGGTTGACGCCACTACTAGGTAG
ATAAGTCAACAAAGTCTCAAACAAAGTTTAGAGAAGAAA
Found at i:58191025 original size:5 final size:6
Alignment explanation
Indices: 58190996--58191039 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
58190986 TCTCTCAAAC
* * * *
58190996 TCTTTT TCATTC TCATTT TCTTTT TCTTTT TCTTTT TGTTTT TC
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TC
58191040 AAAGGATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (6 bp):
TCTTTT
Found at i:58191050 original size:13 final size:12
Alignment explanation
Indices: 58191034--58191065 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
58191024 TTTCTTTTTG
58191034 TTTTTCAAAGGA
1 TTTTTCAAAGGA
*
58191046 TTTTTCAAAGGC
1 TTTTTCAAAGGA
58191058 TTTTTCAA
1 TTTTTCAA
58191066 GTTCCCTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (12 bp):
TTTTTCAAAGGA
Found at i:58191123 original size:5 final size:5
Alignment explanation
Indices: 58191113--58191169 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
58191103 CTCTTGCCTC
*
58191113 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
58191160 TCTTT TCTTT
1 TCTTT TCTTT
58191170 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:58191153 original size:15 final size:14
Alignment explanation
Indices: 58191113--58191169 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
58191103 CTCTTGCCTC
*
58191113 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
58191128 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
58191143 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
58191160 TCTTTTCTTT
1 TCTTTTCTTT
58191170 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:58191170 original size:21 final size:21
Alignment explanation
Indices: 58191113--58191180 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
58191103 CTCTTGCCTC
* *
58191113 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
58191134 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
58191155 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
58191175 CTCTTT
1 -TCTTT
58191181 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:58193872 original size:30 final size:30
Alignment explanation
Indices: 58193787--58193883 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
58193777 TAAACTAAAA
* *
58193787 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
58193817 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
58193847 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
58193876 ATGAGCTA
1 -TGAGCTA
58193884 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:58197708 original size:20 final size:19
Alignment explanation
Indices: 58197685--58197749 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
58197675 AAGCTCAAAC
58197685 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
58197705 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
58197725 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
58197745 GAGCT
1 GAGCT
58197750 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:58199564 original size:33 final size:33
Alignment explanation
Indices: 58199526--58199588 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
58199516 GATTACTCAC
58199526 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
58199559 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
58199589 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:58199663 original size:12 final size:12
Alignment explanation
Indices: 58199648--58199711 Score: 62
Period size: 12 Copynumber: 5.6 Consensus size: 12
58199638 TTTTCTCTCA
58199648 CTTTTTCGATTT
1 CTTTTTCGATTT
**
58199660 CTTTTTCTTTTT
1 CTTTTTCGATTT
*
58199672 CTTTTTCGTTTT
1 CTTTTTCGATTT
58199684 CTTTTT-G-TTT
1 CTTTTTCGATTT
* *
58199694 -TCTTTCAATTT
1 CTTTTTCGATTT
58199705 CTTTTTC
1 CTTTTTC
58199712 AATCTCTTTC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 4 0.09
10 3 0.07
11 4 0.09
12 32 0.74
ACGTcount: A:0.05, C:0.17, G:0.05, T:0.73
Consensus pattern (12 bp):
CTTTTTCGATTT
Found at i:58199694 original size:24 final size:23
Alignment explanation
Indices: 58199618--58199711 Score: 81
Period size: 24 Copynumber: 4.2 Consensus size: 23
58199608 TCTTTTTCAA
*
58199618 TTTTCTTTTCTTTAT---TTTCT
1 TTTTCTTTTCTTTTTCGATTTCT
**
58199638 TTTTCTCTCACTTTTTCGATTTCT
1 TTTTCT-TTTCTTTTTCGATTTCT
*
58199662 TTTTCTTTTTCTTTTTCGTTTTCT
1 TTTTC-TTTTCTTTTTCGATTTCT
* *
58199686 TTTTGTTTTC--TTTCAATTTCT
1 TTTTCTTTTCTTTTTCGATTTCT
58199707 TTTTC
1 TTTTC
58199712 AATCTCTTTC
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
20 6 0.10
21 19 0.32
23 5 0.08
24 28 0.47
25 1 0.02
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.73
Consensus pattern (23 bp):
TTTTCTTTTCTTTTTCGATTTCT
Found at i:58199709 original size:57 final size:56
Alignment explanation
Indices: 58199583--58199730 Score: 128
Period size: 57 Copynumber: 2.6 Consensus size: 56
58199573 TTTCAAGCTC
*
58199583 TCTTTCAATTTCTTTTTTCG---CTTTTTCTTTTTCAATTTTCTTTTCTTTATTTTCT
1 TCTTTCAATTTC-TTTTTCGATTCTTTTTCTTTTTC-TTTTTCTTTTCTTTATTTTCT
** **
58199638 T-TTTCTCTCACTTTTTCGATTTCTTTTTCTTTTTCTTTTTCGTTTTCTTT-TTGTT-T
1 TCTTTCAATTTCTTTTTCGA-TTCTTTTTCTTTTTCTTTTTC-TTTTCTTTATT-TTCT
* * *
58199694 TCTTTCAATTTCTTTTTCAATCTCTTTCTCCTTTTCT
1 TCTTTCAATTTCTTTTTCGAT-TCTTTTTCTTTTTCT
58199731 CGCTCAATGG
Statistics
Matches: 73, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
53 7 0.10
54 6 0.08
55 1 0.01
56 10 0.14
57 49 0.67
ACGTcount: A:0.07, C:0.20, G:0.03, T:0.70
Consensus pattern (56 bp):
TCTTTCAATTTCTTTTTCGATTCTTTTTCTTTTTCTTTTTCTTTTCTTTATTTTCT
Found at i:58199711 original size:6 final size:6
Alignment explanation
Indices: 58199603--58199698 Score: 77
Period size: 6 Copynumber: 15.7 Consensus size: 6
58199593 TCTTTTTTCG
* * * **
58199603 CTTTTT CTTTTT CAATTTT CTTTTCT TTATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT CTTTT-T CT-TTTT CTTTTT CTTTTT CTTTTT
** * *
58199654 CGATTT CTTTTT CTTTTT CTTTTT CGTTTT CTTTTT -GTTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
58199699 CAATTTCTTT
Statistics
Matches: 68, Mismatches: 18, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
5 4 0.06
6 52 0.76
7 9 0.13
8 3 0.04
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (6 bp):
CTTTTT
Found at i:58199713 original size:12 final size:12
Alignment explanation
Indices: 58199606--58199720 Score: 56
Period size: 12 Copynumber: 9.6 Consensus size: 12
58199596 TTTTTCGCTT
58199606 TTTCTTTTTCAA
1 TTTCTTTTTCAA
* *
58199618 TTTTCTTTTCTTTAT
1 -TTTC-TTT-TTCAA
**
58199633 TTTCTTTTTCTC
1 TTTCTTTTTCAA
** *
58199645 TCACTTTTTCGA
1 TTTCTTTTTCAA
**
58199657 TTTCTTTTTCTT
1 TTTCTTTTTCAA
**
58199669 TTTCTTTTTCGT
1 TTTCTTTTTCAA
*
58199681 TTTCTTTTT--G
1 TTTCTTTTTCAA
*
58199691 TTT-TCTTTCAA
1 TTTCTTTTTCAA
58199702 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
58199714 TCTCTTT
1 TTTCTTT
58199721 CTCCTTTTCT
Statistics
Matches: 78, Mismatches: 19, Indels: 11
0.72 0.18 0.10
Matches are distributed among these distances:
9 4 0.05
10 3 0.04
11 3 0.04
12 51 0.65
13 7 0.09
14 7 0.09
15 3 0.04
ACGTcount: A:0.08, C:0.18, G:0.03, T:0.71
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:58200836 original size:12 final size:13
Alignment explanation
Indices: 58200792--58200840 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
58200782 TTTTTTTCAC
* *
58200792 TTTTTTTTGAATT
1 TTTTTTTTCAAAT
58200805 TTTTTTTCAATCAAAT
1 TTTTTTT---TCAAAT
58200821 TTTTTTTTCAAAT
1 TTTTTTTTCAAAT
58200834 TTTTTTT
1 TTTTTTT
58200841 ATTTTTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 20 0.65
16 11 0.35
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.71
Consensus pattern (13 bp):
TTTTTTTTCAAAT
Found at i:58203706 original size:30 final size:30
Alignment explanation
Indices: 58203611--58203707 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
58203601 AGCTCACTCC
** *
58203611 TAGCTCATTTTCAACTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAAGCT
* * **
58203641 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAAG-CT
* * *
58203671 CAGCTCAACTTTAGCTCACGAGCTAAAGTT
1 TAGCTCAACTTCAGCTCACGAGCTAAAGCT
58203701 TAGCTCA
1 TAGCTCA
58203708 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
29 3 0.06
30 44 0.88
31 3 0.06
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAAGCT
Found at i:58209084 original size:12 final size:12
Alignment explanation
Indices: 58209078--58209108 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
58209068 AAAAAAATAT
58209078 AAAAAAATTCAA
1 AAAAAAATTCAA
58209090 AAAAAAATTCAA
1 AAAAAAATTCAA
58209102 AAAAAAA
1 AAAAAAA
58209109 GTTTGTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:58209194 original size:27 final size:27
Alignment explanation
Indices: 58209156--58209219 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 27
58209146 ATTGAAGGAA
*
58209156 AAAAAAAGAAGAAAAAAAATTCGAAATT-
1 AAAAAAA-AAGAAAAAAAA-TCAAAATTG
58209184 AAAAAAAAAGAAAAAAAATCAAAATTG
1 AAAAAAAAAGAAAAAAAATCAAAATTG
58209211 AAAAAAAAA
1 AAAAAAAAA
58209220 AGAGTGATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 7 0.21
27 20 0.59
28 7 0.21
ACGTcount: A:0.78, C:0.03, G:0.08, T:0.11
Consensus pattern (27 bp):
AAAAAAAAAGAAAAAAAATCAAAATTG
Found at i:58209197 original size:26 final size:28
Alignment explanation
Indices: 58209156--58209219 Score: 87
Period size: 26 Copynumber: 2.3 Consensus size: 28
58209146 ATTGAAGGAA
* *
58209156 AAAAAAAGAAGAAAAAAAATTCGAAATT-
1 AAAAAAA-AAGAAAAAAAAATCAAAATTG
58209184 AAAAAAAAAG-AAAAAAAATCAAAATTG
1 AAAAAAAAAGAAAAAAAAATCAAAATTG
58209211 AAAAAAAAA
1 AAAAAAAAA
58209220 AGAGTGATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 14 0.42
27 12 0.36
28 7 0.21
ACGTcount: A:0.78, C:0.03, G:0.08, T:0.11
Consensus pattern (28 bp):
AAAAAAAAAGAAAAAAAAATCAAAATTG
Found at i:58210056 original size:21 final size:20
Alignment explanation
Indices: 58210027--58210072 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
58210017 AATCTTGAAT
*
58210027 GAAATTGAGAGAAGAAAAAAA
1 GAAAATGAGAG-AGAAAAAAA
* *
58210048 GAAAATGAGAGTGAGAAAAA
1 GAAAATGAGAGAGAAAAAAA
58210068 GAAAA
1 GAAAA
58210073 AAGAATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.09
Consensus pattern (20 bp):
GAAAATGAGAGAGAAAAAAA
Found at i:58210099 original size:12 final size:12
Alignment explanation
Indices: 58210079--58210114 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
58210069 AAAAAAGAAT
*
58210079 TTGAGATTGAGA
1 TTGATATTGAGA
*
58210091 TTGATATTGATA
1 TTGATATTGAGA
58210103 TTGATATTGAGA
1 TTGATATTGAGA
58210115 AAAAAATTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (12 bp):
TTGATATTGAGA
Found at i:58214152 original size:23 final size:22
Alignment explanation
Indices: 58214100--58214152 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
58214090 TCCACGTCTT
*
58214100 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
58214122 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
58214145 TTTCTTTT
1 TTTCTTTT
58214153 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:58218658 original size:30 final size:30
Alignment explanation
Indices: 58218624--58218720 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
58218614 AGCTCACTCC
58218624 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
58218654 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
58218684 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
58218714 TAGCTCA
1 TAGCTCA
58218721 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:58224749 original size:14 final size:14
Alignment explanation
Indices: 58224730--58224774 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
58224720 AACTCATCTT
*
58224730 AGTTTAATTAAATG
1 AGTTTAATTTAATG
58224744 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
58224757 AATTTAATTTAATG
1 AGTTTAATTTAATG
58224771 AGTT
1 AGTT
58224775 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:58233435 original size:30 final size:31
Alignment explanation
Indices: 58233356--58233437 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 31
58233346 CTTTTGTTTC
* *
58233356 AATTTCTTTTTCATCTT-TTTTTCACTCTCA
1 AATTTCTTTTTCATTTTCTTTTTCAATCTCA
* *
58233386 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTCATTTTCTTTTTCAATCTCA
* *
58233415 ATTTTCTTTTTCTTTTTCTTTTT
1 AATTTCTTTTTCATTTTCTTTTT
58233438 GCTTTCAAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 12 0.28
30 31 0.72
ACGTcount: A:0.12, C:0.21, G:0.01, T:0.66
Consensus pattern (31 bp):
AATTTCTTTTTCATTTTCTTTTTCAATCTCA
Found at i:58233529 original size:21 final size:19
Alignment explanation
Indices: 58233505--58233572 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 19
58233495 CTCTTGCCTC
58233505 TCTTTTCTATTTATTTCTTTT
1 TCTTTTCT-TTT-TTTCTTTT
*
58233526 TCTTTTTCTTCTTTTGCTTTT
1 TC-TTTTCTT-TTTTTCTTTT
*
58233547 TCTTTTCTTTTCTTTATTTT
1 TCTTTTCTTTT-TTTCTTTT
58233567 CTCTTT
1 -TCTTT
58233573 ACAAGAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 2 0.05
20 13 0.32
21 17 0.43
22 8 0.20
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.76
Consensus pattern (19 bp):
TCTTTTCTTTTTTTCTTTT
Found at i:58233537 original size:15 final size:15
Alignment explanation
Indices: 58233519--58233561 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
58233509 TTCTATTTAT
58233519 TTCTTTTTCTTTTTC
1 TTCTTTTTCTTTTTC
*
58233534 TTCTTTTGCTTTTTC
1 TTCTTTTTCTTTTTC
*
58233549 TTTTCTTTTCTTT
1 TTCT-TTTTCTTT
58233562 ATTTTCTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (15 bp):
TTCTTTTTCTTTTTC
Found at i:58239959 original size:13 final size:13
Alignment explanation
Indices: 58239941--58239997 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
58239931 CATTAAACAC
*
58239941 TTTTTTTTCAGAT
1 TTTTTTTTCAGAA
*
58239954 TTTTTTTTCAAAA
1 TTTTTTTTCAGAA
58239967 TTTTTTTT--GAA
1 TTTTTTTTCAGAA
*
58239978 TTTTTTTTTAGAA
1 TTTTTTTTCAGAA
58239991 TTTTTTT
1 TTTTTTT
58239998 ACTTGTATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
11 10 0.26
13 29 0.74
ACGTcount: A:0.19, C:0.04, G:0.05, T:0.72
Consensus pattern (13 bp):
TTTTTTTTCAGAA
Found at i:58240407 original size:15 final size:15
Alignment explanation
Indices: 58240387--58240415 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
58240377 AGGTTTCAAG
58240387 AAGGGTAAGTTTAGT
1 AAGGGTAAGTTTAGT
58240402 AAGGGTAAGTTTAG
1 AAGGGTAAGTTTAG
58240416 ACTTTATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (15 bp):
AAGGGTAAGTTTAGT
Found at i:58242199 original size:20 final size:20
Alignment explanation
Indices: 58242153--58242199 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
58242143 AGCTCGTTTC
*
58242153 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
58242173 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
58242193 CAGCTCA
1 CAGCTCA
58242200 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:58243541 original size:22 final size:22
Alignment explanation
Indices: 58243511--58243554 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
58243501 TTTGGTATTT
58243511 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
58243533 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
58243555 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:58246267 original size:48 final size:47
Alignment explanation
Indices: 58246188--58246293 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
58246178 GAGTGTCATG
*
58246188 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
58246236 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
58246284 GAAAAAGAAA
1 GAAAAAGAAA
58246294 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:58249543 original size:20 final size:20
Alignment explanation
Indices: 58249497--58249543 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
58249487 AGCTCGTTTC
*
58249497 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
58249517 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
58249537 CAGCTCA
1 CAGCTCA
58249544 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:58251038 original size:16 final size:16
Alignment explanation
Indices: 58251017--58251048 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
58251007 TAATGTGTTT
58251017 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
58251033 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
58251049 ATGCAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:58252664 original size:24 final size:23
Alignment explanation
Indices: 58252628--58252681 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
58252618 ATTAATACCT
*
58252628 AATTAACTAATTTAACTAACAGCA
1 AATTAAATAATTTAA-TAACAGCA
* * **
58252652 AATTAAATGATTTTATTCCAGCA
1 AATTAAATAATTTAATAACAGCA
58252675 AATTAAA
1 AATTAAA
58252682 CGTAAAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (23 bp):
AATTAAATAATTTAATAACAGCA
Found at i:58257411 original size:12 final size:12
Alignment explanation
Indices: 58257393--58257426 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
58257383 TCCCTCGTTT
58257393 CTTTTCACTCAC
1 CTTTTCACTCAC
* *
58257405 TTTTTCACACAC
1 CTTTTCACTCAC
58257417 CTTTTCACTC
1 CTTTTCACTC
58257427 TTTTCTTTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.18, C:0.38, G:0.00, T:0.44
Consensus pattern (12 bp):
CTTTTCACTCAC
Found at i:58260630 original size:77 final size:73
Alignment explanation
Indices: 58260477--58260649 Score: 170
Period size: 77 Copynumber: 2.3 Consensus size: 73
58260467 TTTTTTTTGA
* *
58260477 TTTTTTTATATACTTTTTTTTATAACTACTAAAATGATAATTACAACACAATACTCGAATCTCAC
1 TTTTTTTATATACTTTTTTTTATAACTACTAAAAAGATAAATACAACACAATACTCGAATCTCAC
* *
58260542 AAAGTAGT
66 AAAGCAAT
* * ** * * *
58260550 TTTTTTGTATATATTTTTTTGTTTATAAACTACTAAAAAGGTAAATACAGTATAATACTTGAATT
1 TTTTTT-TATATA-CTTTTT-TTTAT-AACTACTAAAAAGATAAATACAACACAATACTCGAATC
58260615 TCACGAAA-CAAT
62 TCAC-AAAGCAAT
*
58260627 TTTTTTTACACT-CTTTTTTTTAT
1 TTTTTTTATA-TACTTTTTTTTAT
58260650 CCTACCTCGG
Statistics
Matches: 81, Mismatches: 13, Indels: 11
0.77 0.12 0.10
Matches are distributed among these distances:
73 6 0.07
74 11 0.14
75 10 0.12
76 8 0.10
77 43 0.53
78 3 0.04
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.46
Consensus pattern (73 bp):
TTTTTTTATATACTTTTTTTTATAACTACTAAAAAGATAAATACAACACAATACTCGAATCTCAC
AAAGCAAT
Found at i:58261299 original size:20 final size:20
Alignment explanation
Indices: 58261253--58261299 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
58261243 AGCTTGTTTC
*
58261253 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
58261273 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
58261293 CAGCTCA
1 CAGCTCA
58261300 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:58262778 original size:19 final size:21
Alignment explanation
Indices: 58262742--58262791 Score: 68
Period size: 19 Copynumber: 2.4 Consensus size: 21
58262732 GAAATTCAAA
58262742 AAAAAAAAGTGAGCAAAAAAAG
1 AAAAAAAAGTGA-CAAAAAAAG
58262764 AAAAAAAAGT-A-AAAAAAAG
1 AAAAAAAAGTGACAAAAAAAG
58262783 AACAAAAAA
1 AA-AAAAAA
58262792 AAGTGAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.37
20 6 0.22
21 1 0.04
22 10 0.37
ACGTcount: A:0.80, C:0.04, G:0.12, T:0.04
Consensus pattern (21 bp):
AAAAAAAAGTGACAAAAAAAG
Found at i:58262800 original size:10 final size:9
Alignment explanation
Indices: 58262756--58262791 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
58262746 AAAAGTGAGC
58262756 AAAAAAAGA
1 AAAAAAAGA
58262765 AAAAAAAGTA
1 AAAAAAAG-A
58262775 AAAAAAAGA
1 AAAAAAAGA
58262784 ACAAAAAA
1 A-AAAAAA
58262792 AAGTGAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.86, C:0.03, G:0.08, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:58262800 original size:22 final size:21
Alignment explanation
Indices: 58262742--58262800 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
58262732 GAAATTCAAA
* *
58262742 AAAAAAAAGTGAGCAAAAAAAG
1 AAAAAAAAGTGA-AAAAAAAAC
*
58262764 AAAAAAAAGTAAAAAAAAGAAC
1 AAAAAAAAGTGAAAAAAA-AAC
58262786 AAAAAAAAGTGAAAA
1 AAAAAAAAGTGAAAA
58262801 GTCTTGTGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 5 0.16
22 27 0.84
ACGTcount: A:0.78, C:0.03, G:0.14, T:0.05
Consensus pattern (21 bp):
AAAAAAAAGTGAAAAAAAAAC
Found at i:58264718 original size:18 final size:18
Alignment explanation
Indices: 58264695--58264783 Score: 56
Period size: 18 Copynumber: 4.8 Consensus size: 18
58264685 AACAAGTGAG
58264695 GAAAAAGAAAAAGAGAAT
1 GAAAAAGAAAAAGAGAAT
*
58264713 GAAAAAGAGCAAAAAGAGATT
1 G-AAAA-AG-AAAAAGAGAAT
* **
58264734 GAGAGTGAAAAAGA-AATT
1 GAAAAAGAAAAAGAGAA-T
*
58264752 GAAGAAAG-AAAAGAAAAT
1 GAA-AAAGAAAAAGAGAAT
**
58264770 GAATTAGAAAAAGA
1 GAAAAAGAAAAAGA
58264784 AACAAAAGAA
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
17 3 0.06
18 27 0.50
19 9 0.17
20 4 0.07
21 11 0.20
ACGTcount: A:0.65, C:0.01, G:0.24, T:0.10
Consensus pattern (18 bp):
GAAAAAGAAAAAGAGAAT
Found at i:58269282 original size:20 final size:20
Alignment explanation
Indices: 58269236--58269282 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
58269226 AGCTCGTTTC
*
58269236 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
58269256 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
58269276 CAGCTCA
1 CAGCTCA
58269283 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:58271224 original size:18 final size:18
Alignment explanation
Indices: 58271179--58271225 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
58271169 TTGCACCTGC
* *
58271179 ACACACAAATTAATTTAG
1 ACACATAAATTTATTTAG
*
58271197 -CACATTAATTTATTTAG
1 ACACATAAATTTATTTAG
58271214 ACACATAAATTT
1 ACACATAAATTT
58271226 CGGGAGCTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (18 bp):
ACACATAAATTTATTTAG
Found at i:58272684 original size:12 final size:11
Alignment explanation
Indices: 58272638--58272688 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
58272628 TTATACAAGT
*
58272638 AAAAAAA-TCG
1 AAAAAAATTCA
58272648 AAAAAAATTCA
1 AAAAAAATTCA
58272659 AAAAAAATTCA
1 AAAAAAATTCA
*
58272670 AAAAAAATATGA
1 AAAAAAAT-TCA
58272682 AAAAAAA
1 AAAAAAA
58272689 GTGTTTAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
10 7 0.19
11 21 0.57
12 9 0.24
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:58276161 original size:23 final size:22
Alignment explanation
Indices: 58276110--58276161 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
58276100 CCTCGTCTTT
*
58276110 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
58276132 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
58276155 TTCTTTT
1 TTCTTTT
58276162 TCAATTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:58276170 original size:12 final size:12
Alignment explanation
Indices: 58276119--58276173 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
58276109 TTTCTTTTGT
58276119 TTCTTTTTCTAAC
1 TTCTTTTTC-AAC
* *
58276132 -TCATTTTC-TC
1 TTCTTTTTCAAC
58276142 TTCTTTCTTCAAC
1 TTCTTT-TTCAAC
*
58276155 TTCTTTTTCAAT
1 TTCTTTTTCAAC
58276167 TTCTTTT
1 TTCTTTT
58276174 CTGTTTCACA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 1 0.03
11 4 0.12
12 22 0.65
13 7 0.21
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:58276180 original size:17 final size:18
Alignment explanation
Indices: 58276155--58276192 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
58276145 TTTCTTCAAC
* *
58276155 TTCTTTTTCA-ATTTCTT
1 TTCTGTTTCACATTCCTT
58276172 TTCTGTTTCACATTCCTT
1 TTCTGTTTCACATTCCTT
58276190 TTC
1 TTC
58276193 ACTCTCAATC
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:0.11, C:0.24, G:0.03, T:0.63
Consensus pattern (18 bp):
TTCTGTTTCACATTCCTT
Found at i:58279369 original size:15 final size:14
Alignment explanation
Indices: 58279349--58279391 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
58279339 AATGAAAAGA
58279349 AAAAAGCAAAAGAAG
1 AAAAAG-AAAAGAAG
*
58279364 AAAAAGAAAACGAAAT
1 AAAAAGAAAA-G-AAG
58279380 AAAAAGAAAAGA
1 AAAAAGAAAAGA
58279392 GAGGCAAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 5 0.20
15 8 0.32
16 12 0.48
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.02
Consensus pattern (14 bp):
AAAAAGAAAAGAAG
Found at i:58279468 original size:12 final size:12
Alignment explanation
Indices: 58279460--58279484 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58279450 TTTGAAAAGC
58279460 AAAAAGAAAATG
1 AAAAAGAAAATG
58279472 AAAAAGAAAATG
1 AAAAAGAAAATG
58279484 A
1 A
58279485 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:58279481 original size:18 final size:19
Alignment explanation
Indices: 58279454--58279495 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
58279444 AAAGCCTTTG
58279454 AAAAGCAAAAAGAAAATGA
1 AAAAGCAAAAAGAAAATGA
* * *
58279473 AAAAG-AAAATGAGATTGA
1 AAAAGCAAAAAGAAAATGA
58279491 AAAAG
1 AAAAG
58279496 TGAACGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.69, C:0.02, G:0.19, T:0.10
Consensus pattern (19 bp):
AAAAGCAAAAAGAAAATGA
Found at i:58279494 original size:30 final size:31
Alignment explanation
Indices: 58279460--58279541 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
58279450 TTTGAAAAGC
*
58279460 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
** * *
58279490 AAAAAGTGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
58279520 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
58279542 TGAAACAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 8 0.20
30 24 0.59
31 9 0.22
ACGTcount: A:0.63, C:0.01, G:0.22, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:58281693 original size:30 final size:30
Alignment explanation
Indices: 58281659--58281746 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
58281649 CTAGCTTATA
*
58281659 TTCAGCTCACGAGCTAAACCTTAACTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* * * * * * *
58281689 TTCAGCTTAGGAGTTTAATCTCAGCTTAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* *
58281719 TTTAGCTCACGAGCTAAAGCTTAGCTCA
1 TTCAGCTCACGAGCTAAACCTTAGCTCA
58281747 TTTTAGTTTA
Statistics
Matches: 42, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAACCTTAGCTCAAC
Found at i:58282306 original size:30 final size:30
Alignment explanation
Indices: 58282272--58282369 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
58282262 AGCTCACTCC
58282272 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
58282302 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * * *
58282332 CAGCTCA-ACTTTAGCTCACAAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
58282362 TAGCTCAT
1 TAGCTCAT
58282370 TTTAGTTTAA
Statistics
Matches: 49, Mismatches: 17, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:58282835 original size:13 final size:13
Alignment explanation
Indices: 58282817--58282841 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58282807 GTATTGATCA
58282817 TGTGTTCACACCT
1 TGTGTTCACACCT
58282830 TGTGTTCACACC
1 TGTGTTCACACC
58282842 ATGATGACCA
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:58285172 original size:20 final size:20
Alignment explanation
Indices: 58285147--58285191 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
58285137 TCAAGTTGTA
58285147 TATGAGTTTGCCCGATCGTC
1 TATGAGTTTGCCCGATCGTC
58285167 TATGAGTTTGCCCGATCGTC
1 TATGAGTTTGCCCGATCGTC
58285187 TATGA
1 TATGA
58285192 AGAAGTAGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (20 bp):
TATGAGTTTGCCCGATCGTC
Found at i:58285291 original size:15 final size:15
Alignment explanation
Indices: 58285271--58285318 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
58285261 TCAAAGATGG
58285271 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
58285286 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
58285300 GTTTATGGATATAAA
1 GTTTATGGATATGAA
58285315 GTTT
1 GTTT
58285319 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:58285305 original size:14 final size:14
Alignment explanation
Indices: 58285265--58285308 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
58285255 AAGGATTCAA
58285265 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
58285279 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
58285294 AGATGGGTTTATGG
1 AGATGGGTTTATGG
58285308 A
1 A
58285309 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:58285334 original size:29 final size:29
Alignment explanation
Indices: 58285265--58285324 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
58285255 AAGGATTCAA
*
58285265 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
58285294 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
58285323 AG
1 AG
58285325 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:58286339 original size:14 final size:14
Alignment explanation
Indices: 58286297--58286341 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
58286287 TTAAAGAAGC
58286297 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
58286311 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
58286324 AACTCATTTAATTA
1 AACTCATTAAATTA
58286338 AACT
1 AACT
58286342 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:58291138 original size:30 final size:31
Alignment explanation
Indices: 58291104--58291200 Score: 94
Period size: 30 Copynumber: 3.2 Consensus size: 31
58291094 AGCTCACTCC
*
58291104 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * *
58291134 TAGCTCAAC-TTCAGCGT-AGGAGTTTAGCCT
1 TAGCTCAACTTTCAGC-TCACGAGCTAAACCT
* *
58291164 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
58291194 TAGCTCA
1 TAGCTCA
58291201 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
29 1 0.02
30 45 0.88
31 5 0.10
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:58292090 original size:22 final size:20
Alignment explanation
Indices: 58292058--58292106 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
58292048 GCCGAATTTA
58292058 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
58292081 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
58292101 TGAACA
1 TGAACA
58292107 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:58293755 original size:24 final size:24
Alignment explanation
Indices: 58293723--58293784 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
58293713 GTTAGGACAT
58293723 ATTAAATTCGTCCACCAGCAGCTC
1 ATTAAATTCGTCCACCAGCAGCTC
*
58293747 ATTAAATTCGTCAACCAGCAGCTC
1 ATTAAATTCGTCCACCAGCAGCTC
*
58293771 ATTAAATTTGTCCA
1 ATTAAATTCGTCCA
58293785 GGCATGCTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.29
Consensus pattern (24 bp):
ATTAAATTCGTCCACCAGCAGCTC
Found at i:58293871 original size:17 final size:18
Alignment explanation
Indices: 58293851--58293885 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
58293841 TGTACACACA
58293851 AATTAATTTAG-CACATT
1 AATTAATTTAGACACATT
58293868 AATTAATTTAGACACATT
1 AATTAATTTAGACACATT
58293886 TGAAAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (18 bp):
AATTAATTTAGACACATT
Found at i:58295321 original size:22 final size:22
Alignment explanation
Indices: 58295293--58295336 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
58295283 TTTTGAACCA
58295293 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
58295315 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
58295337 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:58304164 original size:10 final size:10
Alignment explanation
Indices: 58304148--58304205 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
58304138 CAACTCCGAC
58304148 CAGCTCAATT
1 CAGCTCAATT
* *
58304158 GAGCTCATTT
1 CAGCTCAATT
58304168 CAGCTCAA-T
1 CAGCTCAATT
58304177 CGAGCTCAATT
1 C-AGCTCAATT
*
58304188 TAGCTACAATT
1 CAGCT-CAATT
58304199 CAGCTCA
1 CAGCTCA
58304206 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:58304171 original size:20 final size:20
Alignment explanation
Indices: 58304148--58304208 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
58304138 CAACTCCGAC
58304148 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
58304168 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
58304189 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
58304209 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:58305466 original size:23 final size:22
Alignment explanation
Indices: 58305415--58305466 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
58305405 CCTCGTCTTT
*
58305415 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
58305437 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
58305460 TTCTTTT
1 TTCTTTT
58305467 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:58309273 original size:30 final size:30
Alignment explanation
Indices: 58309239--58309334 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
58309229 TAAACTAAAA
58309239 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
58309269 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
58309299 TGAGCT-AGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
58309328 TGAGCTA
1 TGAGCTA
58309335 GAAGTGAGCT
Statistics
Matches: 48, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
28 1 0.02
29 15 0.31
30 29 0.60
31 3 0.06
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:58310401 original size:57 final size:56
Alignment explanation
Indices: 58310297--58310404 Score: 139
Period size: 57 Copynumber: 1.9 Consensus size: 56
58310287 AGAATGAGAA
*
58310297 AAAGAAAAAGAAATTGATCAAGAAAAGAAAATTGAAAAAAGAGAGTGAGTATGAAG
1 AAAGAAAAAGAAATTGATCAAGAAAAGAAAATTGAAAAAAGAAAGTGAGTATGAAG
* * *
58310353 AAAGAAAGAA-AAA-TGATCAAGAAATGAATATTTTTAAAAAAGAAAGTGAGTA
1 AAAGAAA-AAGAAATTGATCAAGAAAAGAA-A-ATTGAAAAAAGAAAGTGAGTA
58310405 AAAAAAAAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
55 14 0.31
56 11 0.24
57 20 0.44
ACGTcount: A:0.60, C:0.02, G:0.20, T:0.18
Consensus pattern (56 bp):
AAAGAAAAAGAAATTGATCAAGAAAAGAAAATTGAAAAAAGAAAGTGAGTATGAAG
Found at i:58327447 original size:30 final size:30
Alignment explanation
Indices: 58327376--58327458 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
58327366 CTTTTGTTTC
* *
58327376 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
58327407 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
58327436 ATTTTCTTTTTCTTTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
58327459 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.12, C:0.22, G:0.01, T:0.65
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:58327553 original size:21 final size:20
Alignment explanation
Indices: 58327527--58327575 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
58327517 CTCTTGCCTC
* *
58327527 TCTTTTCTTTTTATTTCGTTT
1 TCTTTTCTTCTT-TTGCGTTT
*
58327548 TCTTTTTCTTCTTTTGCTTTT
1 TC-TTTTCTTCTTTTGCGTTT
58327569 TCTTTTC
1 TCTTTTC
58327576 ATTTCTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.21
21 10 0.42
22 9 0.38
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (20 bp):
TCTTTTCTTCTTTTGCGTTT
Found at i:58327567 original size:15 final size:14
Alignment explanation
Indices: 58327527--58327572 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
58327517 CTCTTGCCTC
*
58327527 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
58327542 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
58327557 TCTTTTGCTTTTTCT
1 TCTTTT-CTTTTTCT
58327572 T
1 T
58327573 TTCATTTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 4 0.14
15 14 0.50
16 10 0.36
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.76
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:58328521 original size:10 final size:10
Alignment explanation
Indices: 58328498--58328536 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
58328488 ATTAAACACT
*
58328498 TTTTTTTCATA
1 TTTTTTTGA-A
58328509 TTTTTTTGAA
1 TTTTTTTGAA
58328519 TTTTTTTTGAA
1 -TTTTTTTGAA
58328530 TTTTTTT
1 TTTTTTT
58328537 TTGACTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:58328540 original size:12 final size:11
Alignment explanation
Indices: 58328509--58328537 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
58328499 TTTTTTCATA
58328509 TTTTTTTGAAT
1 TTTTTTTGAAT
58328520 TTTTTTTGAAT
1 TTTTTTTGAAT
58328531 TTTTTTT
1 TTTTTTT
58328538 TGACTTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTTGAAT
Found at i:58330117 original size:17 final size:18
Alignment explanation
Indices: 58330072--58330118 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
58330062 TTAGCTCCCG
58330072 AAATTTATGTGTCTAAAT
1 AAATTTATGTGTCTAAAT
*
58330090 AAATTAATGTG-CTAAAT
1 AAATTTATGTGTCTAAAT
* *
58330107 TAATTTGTGTGT
1 AAATTTATGTGT
58330119 GCAGGTGCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (18 bp):
AAATTTATGTGTCTAAAT
Found at i:58332928 original size:12 final size:11
Alignment explanation
Indices: 58332905--58332942 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
58332895 GTTGTAAAGT
58332905 TTTA-TTTTTA
1 TTTATTTTTTA
58332915 TTTATTTATTTA
1 TTTATTT-TTTA
58332927 TTTATTTTTTA
1 TTTATTTTTTA
58332938 GTTTA
1 -TTTA
58332943 AATTTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.16
11 6 0.24
12 15 0.60
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (11 bp):
TTTATTTTTTA
Done.