Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000260.1 Hibiscus syriacus cultivar Beakdansim tig00000477_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: 5583615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 26
Found at i:4903138 original size:44 final size:44
Alignment explanation
Indices: 4903007--4903145 Score: 115
Period size: 44 Copynumber: 3.2 Consensus size: 44
4902997 TTATGACGCG
* *
4903007 CATTGCGTGTCATTGAAGCCCCCGTCATAAATGAAGATGACACA
1 CATTGCGTGTCATTGAAGCCCTCGTCATAAATGAAGATGACATA
* * **** * ** * *
4903051 CATTTGTGTGTCA-TAAATTTAT-GACATGCATG--TATGACTTA
1 CA-TTGCGTGTCATTGAAGCCCTCGTCATAAATGAAGATGACATA
4903092 CATTGCGTGTCATTGAAGCCCTCGTCATAAATGAAGATGACATA
1 CATTGCGTGTCATTGAAGCCCTCGTCATAAATGAAGATGACATA
*
4903136 CATTGTGTGT
1 CATTGCGTGT
4903146 TCGAGAGTAT
Statistics
Matches: 65, Mismatches: 25, Indels: 10
0.65 0.25 0.10
Matches are distributed among these distances:
40 9 0.14
41 12 0.18
42 7 0.11
43 7 0.11
44 21 0.32
45 9 0.14
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (44 bp):
CATTGCGTGTCATTGAAGCCCTCGTCATAAATGAAGATGACATA
Found at i:4903859 original size:14 final size:14
Alignment explanation
Indices: 4903826--4903867 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
4903816 AACCTTAAAA
4903826 AAATATA-AGAACAC
1 AAATATAGA-AACAC
4903840 ACAATATAGAAACAC
1 A-AATATAGAAACAC
4903855 AAATATAGAAACA
1 AAATATAGAAACA
4903868 ATCACAGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 13 0.50
15 12 0.46
16 1 0.04
ACGTcount: A:0.64, C:0.14, G:0.07, T:0.14
Consensus pattern (14 bp):
AAATATAGAAACAC
Found at i:4906941 original size:24 final size:24
Alignment explanation
Indices: 4906914--4906965 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
4906904 TCATCTTCAT
4906914 CTTCGCCATCGTCTTCAGTTCCAC
1 CTTCGCCATCGTCTTCAGTTCCAC
4906938 CTTCGCCATCGTCTTCAGTTCCAC
1 CTTCGCCATCGTCTTCAGTTCCAC
4906962 CTTC
1 CTTC
4906966 AGTCTTAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.12, C:0.42, G:0.12, T:0.35
Consensus pattern (24 bp):
CTTCGCCATCGTCTTCAGTTCCAC
Found at i:4911117 original size:34 final size:30
Alignment explanation
Indices: 4911079--4911147 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
4911069 TCGATATAAC
*
4911079 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTATTTGGACTT-AATTG
4911113 AATTT-ACAAAATGTATTTGGACTTAATTG
1 AATTTAACAAAATGTATTTGGACTTAATTG
4911142 AATTTA
1 AATTTA
4911148 TTTAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.41
Consensus pattern (30 bp):
AATTTAACAAAATGTATTTGGACTTAATTG
Found at i:4911155 original size:31 final size:31
Alignment explanation
Indices: 4911088--4911147 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
4911078 CAATTTAAGG
*
4911088 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
4911119 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
4911148 TTTAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:4911245 original size:21 final size:21
Alignment explanation
Indices: 4911219--4911260 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4911209 TTATGAATAT
* *
4911219 TATGAAGGGGTATCGATTCCC
1 TATGAAGCGGTACCGATTCCC
4911240 TATGAAGCGGTACCGATTCCC
1 TATGAAGCGGTACCGATTCCC
4911261 CCCATTATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (21 bp):
TATGAAGCGGTACCGATTCCC
Found at i:4911322 original size:21 final size:21
Alignment explanation
Indices: 4911289--4911328 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
4911279 TTTTTGCAGA
*
4911289 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
4911311 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
4911329 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:4913548 original size:16 final size:16
Alignment explanation
Indices: 4913524--4913567 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
4913514 TAAAGATACA
4913524 AAAGAAAAGAAAAATC
1 AAAGAAAAGAAAAATC
*
4913540 AAAGGAAAGAAAAAT-
1 AAAGAAAAGAAAAATC
*
4913555 AAA-AAACGAAAAA
1 AAAGAAAAGAAAAA
4913568 AATAATAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 8 0.32
15 3 0.12
16 14 0.56
ACGTcount: A:0.77, C:0.05, G:0.14, T:0.05
Consensus pattern (16 bp):
AAAGAAAAGAAAAATC
Found at i:4919546 original size:24 final size:24
Alignment explanation
Indices: 4919511--4919575 Score: 112
Period size: 24 Copynumber: 2.7 Consensus size: 24
4919501 TGTCCTTAGT
*
4919511 TTCTCTCAAACACTAAAGATGAGC
1 TTCTCTCGAACACTAAAGATGAGC
4919535 TTCTCTCGAACACTAAAGATGAGC
1 TTCTCTCGAACACTAAAGATGAGC
*
4919559 TTTTCTCGAACACTAAA
1 TTCTCTCGAACACTAAA
4919576 TATTTTCCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (24 bp):
TTCTCTCGAACACTAAAGATGAGC
Found at i:4924064 original size:42 final size:42
Alignment explanation
Indices: 4923996--4924088 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
4923986 TTTTTAGTTT
*
4923996 TGAGCTCCTCAATCTTAGCTTTCAACCCTTACACTTCAAAAG
1 TGAGCTCCTCAATCTTAGCTTGCAACCCTTACACTTCAAAAG
* * *
4924038 TGATCTCCTCAATCTTAGCTTGCAACCCTTGCACTTTAAAAG
1 TGAGCTCCTCAATCTTAGCTTGCAACCCTTACACTTCAAAAG
4924080 TGAGCTCCT
1 TGAGCTCCT
4924089 TATCTTACTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (42 bp):
TGAGCTCCTCAATCTTAGCTTGCAACCCTTACACTTCAAAAG
Found at i:4934348 original size:164 final size:164
Alignment explanation
Indices: 4934077--4934405 Score: 658
Period size: 164 Copynumber: 2.0 Consensus size: 164
4934067 TGACAATGTT
4934077 TGAGGTCTTCTAAACATAGGCTCACCTCAACGCTCCAGAAATAATTAGTGCAAAAACTTTTATAC
1 TGAGGTCTTCTAAACATAGGCTCACCTCAACGCTCCAGAAATAATTAGTGCAAAAACTTTTATAC
4934142 TAATAATGGTTGGAAGAATTTGAACTTTATTTCTTGATTTTCGAGTGATTCAATATGATGAATAT
66 TAATAATGGTTGGAAGAATTTGAACTTTATTTCTTGATTTTCGAGTGATTCAATATGATGAATAT
4934207 GGAAAACATAAGATTTCTTGGTATTACTTTGAGC
131 GGAAAACATAAGATTTCTTGGTATTACTTTGAGC
4934241 TGAGGTCTTCTAAACATAGGCTCACCTCAACGCTCCAGAAATAATTAGTGCAAAAACTTTTATAC
1 TGAGGTCTTCTAAACATAGGCTCACCTCAACGCTCCAGAAATAATTAGTGCAAAAACTTTTATAC
4934306 TAATAATGGTTGGAAGAATTTGAACTTTATTTCTTGATTTTCGAGTGATTCAATATGATGAATAT
66 TAATAATGGTTGGAAGAATTTGAACTTTATTTCTTGATTTTCGAGTGATTCAATATGATGAATAT
4934371 GGAAAACATAAGATTTCTTGGTATTACTTTGAGC
131 GGAAAACATAAGATTTCTTGGTATTACTTTGAGC
4934405 T
1 T
4934406 AATCTTTGAA
Statistics
Matches: 165, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
164 165 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (164 bp):
TGAGGTCTTCTAAACATAGGCTCACCTCAACGCTCCAGAAATAATTAGTGCAAAAACTTTTATAC
TAATAATGGTTGGAAGAATTTGAACTTTATTTCTTGATTTTCGAGTGATTCAATATGATGAATAT
GGAAAACATAAGATTTCTTGGTATTACTTTGAGC
Found at i:4939272 original size:145 final size:145
Alignment explanation
Indices: 4939104--4939393 Score: 580
Period size: 145 Copynumber: 2.0 Consensus size: 145
4939094 GGAATAAAAG
4939104 GAGCATTAAATAAATAAATATTTGAATTTTTTAATTTTTCAATATAGGGATAAAATAATAATTGA
1 GAGCATTAAATAAATAAATATTTGAATTTTTTAATTTTTCAATATAGGGATAAAATAATAATTGA
4939169 AGGCACTAATTTTGGGTGTTGTTGGGGTGGTAATCCATCCCCAAGCGTAATCGACTCCCGAACCC
66 AGGCACTAATTTTGGGTGTTGTTGGGGTGGTAATCCATCCCCAAGCGTAATCGACTCCCGAACCC
4939234 GAAATCTCTAACACA
131 GAAATCTCTAACACA
4939249 GAGCATTAAATAAATAAATATTTGAATTTTTTAATTTTTCAATATAGGGATAAAATAATAATTGA
1 GAGCATTAAATAAATAAATATTTGAATTTTTTAATTTTTCAATATAGGGATAAAATAATAATTGA
4939314 AGGCACTAATTTTGGGTGTTGTTGGGGTGGTAATCCATCCCCAAGCGTAATCGACTCCCGAACCC
66 AGGCACTAATTTTGGGTGTTGTTGGGGTGGTAATCCATCCCCAAGCGTAATCGACTCCCGAACCC
4939379 GAAATCTCTAACACA
131 GAAATCTCTAACACA
4939394 CATACTAAAT
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 145 1.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (145 bp):
GAGCATTAAATAAATAAATATTTGAATTTTTTAATTTTTCAATATAGGGATAAAATAATAATTGA
AGGCACTAATTTTGGGTGTTGTTGGGGTGGTAATCCATCCCCAAGCGTAATCGACTCCCGAACCC
GAAATCTCTAACACA
Found at i:4940903 original size:24 final size:24
Alignment explanation
Indices: 4940868--4940932 Score: 112
Period size: 24 Copynumber: 2.7 Consensus size: 24
4940858 CGTCCTTAGT
4940868 TTCTCTCGAACACTAAAGATGAGC
1 TTCTCTCGAACACTAAAGATGAGC
*
4940892 TTCTCTCAAACACTAAAGATGAGC
1 TTCTCTCGAACACTAAAGATGAGC
*
4940916 TTTTCTCGAACACTAAA
1 TTCTCTCGAACACTAAA
4940933 TATTTCCCTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (24 bp):
TTCTCTCGAACACTAAAGATGAGC
Found at i:4945400 original size:38 final size:40
Alignment explanation
Indices: 4945345--4945434 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 40
4945335 TTTTTAGTTT
4945345 TGAGCTCCTCAATCTTAGCTTGC-A-TTGCACTTCAAAAG
1 TGAGCTCCTCAATCTTAGCTTGCAACTTGCACTTCAAAAG
* *
4945383 TGATCTCCTCAATCTTAGCTTGCAACCCTTGCACTTTAAAAG
1 TGAGCTCCTCAATCTTAGCTTGCAA--CTTGCACTTCAAAAG
4945425 TGAGCTCCTC
1 TGAGCTCCTC
4945435 TTCTTACTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
38 22 0.49
39 1 0.02
42 22 0.49
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.32
Consensus pattern (40 bp):
TGAGCTCCTCAATCTTAGCTTGCAACTTGCACTTCAAAAG
Found at i:4950123 original size:91 final size:92
Alignment explanation
Indices: 4949991--4950206 Score: 267
Period size: 95 Copynumber: 2.3 Consensus size: 92
4949981 GATGATATAT
** * *
4949991 TAGGGTT-TGA-GAAACCCTAAATACTGCCTTGATCCGGATCGTTGGAAGGGGTCCAAATCCGAC
1 TAGGGTTGTGAGGAAACCCT-AATTTTGCTTTGATCCGAATCGTTGGAAGGGGTCCAAATCCGAC
*
4950054 GGTC-GTCAGTGACGCCTGGCATCATAC
65 GGTCTGTCAGCGACGCCTGGCATCATAC
* * *
4950081 TAGGGTTGTGAGGAAACCCTAATTTTGCTTTGATCTGAATCGTTGGAAGGGGTCCAGATTCGACG
1 TAGGGTTGTGAGGAAACCCTAATTTTGCTTTGATCCGAATCGTTGGAAGGGGTCCAAATCCGACG
*
4950146 GTCTATGGTGAGCGACGCCTGGCATCATAC
66 GTC--T-GTCAGCGACGCCTGGCATCATAC
* * *
4950176 TAGGGTTGCGAGAAAACCCTAATTTTTCTTT
1 TAGGGTTGTGAGGAAACCCTAATTTTGCTTT
4950207 ACTCTAGACC
Statistics
Matches: 108, Mismatches: 12, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
90 7 0.06
91 44 0.41
92 8 0.07
95 49 0.45
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (92 bp):
TAGGGTTGTGAGGAAACCCTAATTTTGCTTTGATCCGAATCGTTGGAAGGGGTCCAAATCCGACG
GTCTGTCAGCGACGCCTGGCATCATAC
Found at i:4955830 original size:105 final size:105
Alignment explanation
Indices: 4955631--4956115 Score: 654
Period size: 105 Copynumber: 4.6 Consensus size: 105
4955621 GTTCTTTGGA
* * *
4955631 CAAGTTCTTCTCATTATGAACTCTTCTGGCAAT-TTCGATCCACCT-CTTCTGCGAAGGATTTGA
1 CAAGTTCTTCTCATTATGAACTCTTATGGAAATGTTC-ATCCACCTCCTTCTGCGATGGATTTGA
* *
4955694 AAGGAACAAGTTATTCTCATTATGAAATTTCTCCTTTAGAG
65 AAGGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGAG
* * * *
4955735 CAAGTTCTTCTCATTATGAACTCTTCTAGAAATGTTCATCCACCTCATTCTACGATGGATTTGAA
1 CAAGTTCTTCTCATTATGAACTCTTATGGAAATGTTCATCCACCTCCTTCTGCGATGGATTTGAA
* *
4955800 AGGAAAAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGG
66 AGGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGAG
* * * * *
4955840 CGAGTTCTTCTCATTATGAACTCTTTTGAAAATGTTAATCCACCTCCTTCTGTGATGGATTTGAA
1 CAAGTTCTTCTCATTATGAACTCTTATGGAAATGTTCATCCACCTCCTTCTGCGATGGATTTGAA
*
4955905 ATGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAG-G
66 AGGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGAG
*
4955944 GAGAGTTCTTCTCATTATGAACTCTTATGGAAATG-TCGATCCACCTCCTTCTGCGATGGATTTG
1 CA-AGTTCTTCTCATTATGAACTCTTATGGAAATGTTC-ATCCACCTCCTTCTGCGATGGATTTG
* * *
4956008 AAAGGAACAATTTCTTCTCATTCTGAACTTTCTCCTTTAGGG
64 AAAGGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGAG
** * * * * **
4956050 TGAGCTCTTCTCATTATGAAATCTTATGGAAATGTTGATCCACCTCCTGCTATGATGGATTTGAA
1 CAAGTTCTTCTCATTATGAACTCTTATGGAAATGTTCATCCACCTCCTTCTGCGATGGATTTGAA
4956115 A
66 A
4956116 AAAGTGTTGA
Statistics
Matches: 339, Mismatches: 36, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
104 41 0.12
105 296 0.87
106 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (105 bp):
CAAGTTCTTCTCATTATGAACTCTTATGGAAATGTTCATCCACCTCCTTCTGCGATGGATTTGAA
AGGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGAG
Found at i:4958687 original size:18 final size:17
Alignment explanation
Indices: 4958661--4958703 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
4958651 TTCAGTTTTC
*
4958661 TTTTT-TTTTTCTCTCT
1 TTTTTATTTTTCTCTAT
4958677 TTTTTGATTTTTCTCTAT
1 TTTTT-ATTTTTCTCTAT
4958695 TTTTTATTT
1 TTTTTATTT
4958704 ATTTTTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 5 0.21
17 4 0.17
18 15 0.62
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTTTATTTTTCTCTAT
Found at i:4958718 original size:20 final size:19
Alignment explanation
Indices: 4958683--4958762 Score: 80
Period size: 20 Copynumber: 4.3 Consensus size: 19
4958673 CTCTTTTTTG
4958683 ATTTTTCTCTATTTTTTATTT
1 ATTTTTCT-TA-TTTTTATTT
4958704 ATTTTTCATTATTTTTATTT
1 ATTTTTC-TTATTTTTATTT
*
4958724 CTTTTTC----TTTTATTT
1 ATTTTTCTTATTTTTATTT
4958739 ATTTTCTCTTATTTTTATTT
1 ATTTT-TCTTATTTTTATTT
4958759 -TTTT
1 ATTTT
4958763 ATTTTCTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
15 12 0.24
16 2 0.04
19 4 0.08
20 23 0.45
21 9 0.18
22 1 0.02
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.78
Consensus pattern (19 bp):
ATTTTTCTTATTTTTATTT
Found at i:4958735 original size:35 final size:34
Alignment explanation
Indices: 4958656--4958762 Score: 114
Period size: 35 Copynumber: 3.1 Consensus size: 34
4958646 CTCCTTTCAG
*
4958656 TTTTCTTTT-TTT-TTTCTCTCTT-TTTTGATTTT
1 TTTTCTTTTATTTATTT-TCTCTTATTTTTATTTT
*
4958688 TCTCTATTTTTTATTTATTTT-TCATTATTTTTATTTCT
1 T-T-T-TCTTTTATTTATTTTCTC-TTATTTTTATTT-T
4958726 TTTTCTTTTATTTATTTTCTCTTATTTTTATTTT
1 TTTTCTTTTATTTATTTTCTCTTATTTTTATTTT
4958760 TTT
1 TTT
4958763 ATTTTCTTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
32 1 0.02
33 1 0.02
34 5 0.08
35 33 0.52
36 9 0.14
37 12 0.19
38 2 0.03
ACGTcount: A:0.10, C:0.10, G:0.01, T:0.79
Consensus pattern (34 bp):
TTTTCTTTTATTTATTTTCTCTTATTTTTATTTT
Found at i:4958743 original size:14 final size:14
Alignment explanation
Indices: 4958716--4958786 Score: 60
Period size: 14 Copynumber: 5.3 Consensus size: 14
4958706 TTTTCATTAT
*
4958716 TTTTATTTCTTTTTC
1 TTTTATTT-ATTTTC
4958731 TTTTATTTATTTTC
1 TTTTATTTATTTTC
* *
4958745 TCTTA--T-TTTTA
1 TTTTATTTATTTTC
4958756 TTTT-TTTATTTTC
1 TTTTATTTATTTTC
* *
4958769 TTTTATCTCTTTTC
1 TTTTATTTATTTTC
4958783 TTTT
1 TTTT
4958787 CTTCAGGTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
11 7 0.16
12 2 0.04
13 8 0.18
14 20 0.44
15 8 0.18
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTATTTATTTTC
Found at i:4958786 original size:24 final size:24
Alignment explanation
Indices: 4958736--4958786 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
4958726 TTTTCTTTTA
* *
4958736 TTTATTTTCTCTTATTTTTATTTT
1 TTTATTTTCTCTTATTCTTATTCT
*
4958760 TTTATTTTCTTTTATCTCTT-TTCT
1 TTTATTTTCTCTTAT-TCTTATTCT
4958784 TTT
1 TTT
4958787 CTTCAGGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTATTTTCTCTTATTCTTATTCT
Found at i:4961300 original size:2 final size:2
Alignment explanation
Indices: 4961293--4961332 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4961283 CATTCTTCAA
4961293 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
4961333 TAAACACGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4961985 original size:54 final size:54
Alignment explanation
Indices: 4961889--4962025 Score: 186
Period size: 54 Copynumber: 2.6 Consensus size: 54
4961879 GGAAATTCGC
* * * * *
4961889 AAACTTATTATG-ATTCCATGGATTGCACACATAGTGCAGATACGATCATTCAT
1 AAACTCATTATGAATTACGTGGGTTGCACACAAAGTGCAGATACGATCATTCAT
** *
4961942 AAACTCATTATGAATTACGTGGGTTGCACACAAAGTGTTGATACGGTCATTCAT
1 AAACTCATTATGAATTACGTGGGTTGCACACAAAGTGCAGATACGATCATTCAT
*
4961996 AAACTCATTATGAATTTCGTGGGTTGCACA
1 AAACTCATTATGAATTACGTGGGTTGCACA
4962026 TATAGTGATG
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
53 11 0.15
54 63 0.85
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (54 bp):
AAACTCATTATGAATTACGTGGGTTGCACACAAAGTGCAGATACGATCATTCAT
Found at i:4981249 original size:21 final size:21
Alignment explanation
Indices: 4981225--4981283 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
4981215 AGGAAGAATG
4981225 GATGAAAAAATGAAAAAGAAA
1 GATGAAAAAATGAAAAAGAAA
4981246 GATGAAAAAA-GAAAAAAGAAA
1 GATGAAAAAATG-AAAAAGAAA
*
4981267 -AAGAAAAATGATGAAAA
1 GATGAAAAA--ATGAAAA
4981284 GATGAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 8 0.24
21 19 0.58
22 5 0.15
23 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (21 bp):
GATGAAAAAATGAAAAAGAAA
Found at i:4981252 original size:13 final size:13
Alignment explanation
Indices: 4981234--4981297 Score: 53
Period size: 13 Copynumber: 5.1 Consensus size: 13
4981224 GGATGAAAAA
4981234 ATGAAAAAGAAAG
1 ATGAAAAAGAAAG
*
4981247 ATGAAAAAAGAAAA
1 ATG-AAAAAGAAAG
* *
4981261 AAGAAAAAGAAAA
1 ATGAAAAAGAAAG
**
4981274 ATG-ATGA-AAAG
1 ATGAAAAAGAAAG
4981285 ATGAAAAA-AAAG
1 ATGAAAAAGAAAG
4981297 A
1 A
4981298 AATAAAATGA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
11 6 0.15
12 9 0.22
13 15 0.37
14 11 0.27
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (13 bp):
ATGAAAAAGAAAG
Found at i:4981259 original size:7 final size:7
Alignment explanation
Indices: 4981228--4981274 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
4981218 AAGAATGGAT
4981228 GAAAAAA
1 GAAAAAA
4981235 TG-AAAAA
1 -GAAAAAA
* *
4981242 GAAAGAT
1 GAAAAAA
4981249 GAAAAAA
1 GAAAAAA
4981256 GAAAAAA
1 GAAAAAA
4981263 G-AAAAA
1 GAAAAAA
4981269 GAAAAA
1 GAAAAA
4981275 TGATGAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
6 7 0.21
7 25 0.76
8 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (7 bp):
GAAAAAA
Found at i:4981294 original size:27 final size:28
Alignment explanation
Indices: 4981252--4981316 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
4981242 GAAAGATGAA
4981252 AAAAGAAAAAAGAAAAAGAAAAATGATG
1 AAAAGAAAAAAGAAAAAGAAAAATGATG
** *
4981280 AAAAGATGAAA-AAAAAGAAATAA-AATG
1 AAAAGAAAAAAGAAAAAGAAA-AATGATG
4981307 AAAAGAAAAA
1 AAAAGAAAAA
4981317 GTAGGGTTCG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 20 0.65
28 11 0.35
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (28 bp):
AAAAGAAAAAAGAAAAAGAAAAATGATG
Found at i:4982387 original size:105 final size:105
Alignment explanation
Indices: 4982253--4982661 Score: 615
Period size: 105 Copynumber: 3.9 Consensus size: 105
4982243 AACAACTATG
* * *
4982253 ATCCACCGCAGAAGGAGGTGAACCAACATTTCTAGAAGAGTTCATAATGAGAAGAACTCTTCCTA
1 ATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCTTCTTA
** * **
4982318 AAGGAGAAAGTTTGTAATGAGAAGAACATGTTCCTTTTGA
66 AAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
* * *
4982358 ATCCACCACAGAAGGAGGTAAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTA
1 ATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCTTCTTA
4982423 AAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
66 AAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
* * *
4982463 ATTCACCACAGAATGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACT-TATCTT
1 ATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCT-TCTT
4982527 AAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
65 AAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
* * * * *
4982568 ATCCACCGCATAAAGAGGTGAACCAACATTTCTAGAAGAGTTCATAATGAGAAGAACTC-ACTGT
1 ATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCTTCT-T
4982632 AAAGGAGAAAGTTCATAATGAGAAGAACTT
65 AAAGGAGAAAGTTCATAATGAGAAGAACTT
4982662 ACTCAACTTT
Statistics
Matches: 279, Mismatches: 22, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
104 2 0.01
105 277 0.99
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (105 bp):
ATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCTTCTTA
AAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
Found at i:4985142 original size:2 final size:2
Alignment explanation
Indices: 4985135--4985175 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4985125 CGGTTACGAC
4985135 AT AT AT AT AT 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 AT AT AT AT AT A
4985176 ACAAGTCTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4985784 original size:54 final size:53
Alignment explanation
Indices: 4985720--4985925 Score: 277
Period size: 54 Copynumber: 3.8 Consensus size: 53
4985710 CGAAATAGAA
* * * *
4985720 ATTCACAAACTTATTATGAATTCCATGGATTGCACACATAGTGTCGATACAGTC
1 ATTCATAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGTCGATAC-GTC
* *
4985774 ATTCATAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGTCGATATGGTC
1 ATTCATAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGTCGATA-CGTC
** *
4985828 ATTCATAAACTCATTATGAATTTTTGTAGGTTGCACACATAGTGTCGATACGATC
1 ATTCATAAACTCATTATGAA-TTCCGTGGGTTGCACACATAGTGTCGATACG-TC
* *
4985883 ATTCATAAACTCATTATAAATTACGTGGGTTGCACACATAGTG
1 ATTCATAAACTCATTATGAATTCCGTGGGTTGCACACATAGTG
4985926 CCGAAAGTAC
Statistics
Matches: 136, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
54 88 0.65
55 48 0.35
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (53 bp):
ATTCATAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGTCGATACGTC
Found at i:4992601 original size:21 final size:21
Alignment explanation
Indices: 4992575--4992616 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
4992565 GATTTTGACT
4992575 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGTATCCGTAAA
*
4992596 ATCGCAACGCGTATCCGTAAA
1 ATCGCAACGAGTATCCGTAAA
4992617 TTGTAATGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (21 bp):
ATCGCAACGAGTATCCGTAAA
Found at i:4992918 original size:27 final size:27
Alignment explanation
Indices: 4992846--4992912 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
4992836 CATCTCCGGC
4992846 GAAATCCCTCACAGCCATTCACGGTCA
1 GAAATCCCTCACAGCCATTCACGGTCA
*
4992873 GAAATCCCTCACAGCCATTTACGGTCA
1 GAAATCCCTCACAGCCATTCACGGTCA
4992900 GAAATCCCTCACA
1 GAAATCCCTCACA
4992913 ATCATTCAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.31, C:0.36, G:0.13, T:0.19
Consensus pattern (27 bp):
GAAATCCCTCACAGCCATTCACGGTCA
Found at i:4993295 original size:19 final size:20
Alignment explanation
Indices: 4993216--4993307 Score: 114
Period size: 20 Copynumber: 4.6 Consensus size: 20
4993206 TTCTAAACTT
**
4993216 AAAATCGCAACATGAAAATG
1 AAAATCGCAACGCGAAAATG
*
4993236 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
** *
4993256 ACTATTGCAACGCGAGAAATG
1 AAAATCGCAACGCGA-AAATG
4993277 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
4993296 AAAATCGCAACG
1 AAAATCGCAACG
4993308 AGATAATCGC
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
19 17 0.27
20 30 0.48
21 16 0.25
ACGTcount: A:0.49, C:0.20, G:0.18, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:4993397 original size:20 final size:20
Alignment explanation
Indices: 4993333--4993410 Score: 115
Period size: 19 Copynumber: 4.0 Consensus size: 20
4993323 GAAACCAAAA
* *
4993333 TCGCATTGCGATTTT-AATT
1 TCGCGTTGCGATTTTCATTT
4993352 TCGCGTTGCGATTTTCA-TT
1 TCGCGTTGCGATTTTCATTT
4993371 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCATTT
*
4993391 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCATTT
4993411 CAACCAAAAG
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
19 33 0.60
20 22 0.40
ACGTcount: A:0.13, C:0.19, G:0.18, T:0.50
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATTT
Found at i:4993403 original size:39 final size:38
Alignment explanation
Indices: 4993333--4993411 Score: 122
Period size: 39 Copynumber: 2.1 Consensus size: 38
4993323 GAAACCAAAA
4993333 TCGCATTGCGATTTTAATTTCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCGTTGCGATTTTCATT
* * *
4993371 TCGCGTTGCGATTTTCATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTT-AATTTCGCGTTGCGATTTTCATT
4993410 TC
1 TC
4993412 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
38 14 0.38
39 23 0.62
ACGTcount: A:0.13, C:0.20, G:0.18, T:0.49
Consensus pattern (38 bp):
TCGCATTGCGATTTTAATTTCGCGTTGCGATTTTCATT
Found at i:4995408 original size:21 final size:21
Alignment explanation
Indices: 4995384--4995450 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
4995374 TCATTCCTCG
4995384 AGAGTCCCCTCCCACCATTCA
1 AGAGTCCCCTCCCACCATTCA
* * ** * * *
4995405 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCATTCA
4995426 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCATTCA
4995447 AGAG
1 AGAG
4995451 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 14, Indels: 3
0.65 0.29 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCATTCA
Found at i:4995408 original size:42 final size:42
Alignment explanation
Indices: 4995362--4995450 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
4995352 CCTATCGTTG
*
4995362 AAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTC
1 AAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCACCATTC
* * *
4995404 AAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
4995446 AAGAG
1 AAGAG
4995451 CCCGATTCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 4 0.10
42 35 0.85
43 2 0.05
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.20
Consensus pattern (42 bp):
AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
Found at i:4996809 original size:14 final size:14
Alignment explanation
Indices: 4996790--4996823 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4996780 ATTGTTTAAT
4996790 TGATTTCTAAAAGA
1 TGATTTCTAAAAGA
* *
4996804 TGATTTGTAAAAGT
1 TGATTTCTAAAAGA
4996818 TGATTT
1 TGATTT
4996824 ATTTAATAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.18, T:0.44
Consensus pattern (14 bp):
TGATTTCTAAAAGA
Found at i:4996954 original size:19 final size:19
Alignment explanation
Indices: 4996932--4996997 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
4996922 AAAAATGACT
4996932 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4996951 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
* *
4996965 ATCGTAATGCGAAATTAAA
1 ATCGCAATGCGAAATGAAA
*
4996984 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
4996998 CTAAATCGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
14 9 0.25
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 21 0.58
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4997005 original size:18 final size:19
Alignment explanation
Indices: 4996982--4997025 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
4996972 TGCGAAATTA
*
4996982 AAATCGCAACGCG-AAACT
1 AAATCGCAACACGAAAACT
4997000 AAATCGCAACACGAAAACT
1 AAATCGCAACACGAAAACT
4997019 AAATCGC
1 AAATCGC
4997026 GTTGCGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.48, C:0.27, G:0.14, T:0.11
Consensus pattern (19 bp):
AAATCGCAACACGAAAACT
Found at i:4997067 original size:33 final size:33
Alignment explanation
Indices: 4997025--4997118 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
4997015 AACTAAATCG
4997025 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
* *
4997058 CGTTGCGATTTTCATTTCGTATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
4997091 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
4997119 AGTCATTTCC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:4997180 original size:119 final size:119
Alignment explanation
Indices: 4997025--4997262 Score: 449
Period size: 119 Copynumber: 2.0 Consensus size: 119
4997015 AACTAAATCG
* *
4997025 CGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGTATTGCGATTCTC
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCATCGTTGCGATTTTCATTTCGCATTGCGATTCTC
4997090 TCGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCGCGGTGCGATTTTCA
66 TCGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCGCGGTGCGATTTTCA
4997144 CGTTGCGATTTTCATTTCGCATTGCGATTCCATCGTTGCGATTTTCATTTCGCATTGCGATTCTC
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCATCGTTGCGATTTTCATTTCGCATTGCGATTCTC
*
4997209 TCGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCGCGTTGCGATTTTCA
66 TCGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCGCGGTGCGATTTTCA
4997263 TTTCGCATTG
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
119 116 1.00
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.43
Consensus pattern (119 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCATCGTTGCGATTTTCATTTCGCATTGCGATTCTC
TCGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCGCGGTGCGATTTTCA
Found at i:4997255 original size:86 final size:83
Alignment explanation
Indices: 4997058--4997258 Score: 212
Period size: 86 Copynumber: 2.3 Consensus size: 83
4997048 GCGATTCCCT
** *
4997058 CGTTGCGATTTTCATTTCGTATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATAGTC
1 CGTTGCGATAGTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATA-TC
4997123 ATTTCCGCGGTGCGATTTTCA
65 --TTCCGCGGTGCGATTTTCA
**
4997144 CGTTGCGATTTTCATTTCGCATTGCGATTC-CATCGTTGCGATTTTCATTTCGCATTGCGAT-TC
1 CGTTGCGATAGTCATTTCGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCATTGCGATATC
* *
4997207 -T-CTCGTTGCGATTTTCA
65 TTCCGCGGTGCGATTTTCA
*
4997224 TTTCGCATTGCGATAGTCATTTCCGCGTTGCGATT
1 ---CG--TTGCGATAGTCATTT-CGCATTGCGATT
4997259 TTCATTTCGC
Statistics
Matches: 102, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
80 14 0.14
81 1 0.01
83 2 0.02
84 2 0.02
85 14 0.14
86 69 0.68
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (83 bp):
CGTTGCGATAGTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATATCT
TCCGCGGTGCGATTTTCA
Found at i:4997256 original size:20 final size:19
Alignment explanation
Indices: 4997210--4997317 Score: 82
Period size: 20 Copynumber: 5.8 Consensus size: 19
4997200 GCGATTCTCT
**
4997210 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
4997229 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
**
4997249 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
4997268 CATTGCGAT--T-A--TCT
1 CGTTGCGATAGTCATTTCG
*
4997282 CGTTGCGATAGTAATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
4997302 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
4997318 AAGAGTCCCA
Statistics
Matches: 70, Mismatches: 12, Indels: 13
0.74 0.13 0.14
Matches are distributed among these distances:
14 10 0.14
16 2 0.03
17 2 0.03
19 25 0.36
20 31 0.44
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:4997276 original size:72 final size:73
Alignment explanation
Indices: 4997177--4997317 Score: 221
Period size: 72 Copynumber: 1.9 Consensus size: 73
4997167 GCGATTCCAT
* ** * *
4997177 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATAGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATAGTAATTTCCGCATTGCGATAGA
4997241 CATTTCCG
66 CATTTCCG
*
4997249 CGTTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATAGTAATTTCCGCGTTGCGATAGA
1 CGTTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATAGTAATTTCCGCATTGCGATAGA
4997314 CATT
66 CATT
4997318 AAGAGTCCCA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
72 46 0.74
73 16 0.26
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.41
Consensus pattern (73 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATAGTAATTTCCGCATTGCGATAGA
CATTTCCG
Found at i:4997299 original size:33 final size:33
Alignment explanation
Indices: 4997133--4997290 Score: 201
Period size: 33 Copynumber: 4.6 Consensus size: 33
4997123 ATTTCCGCGG
* *
4997133 TGCGATTTTCACGTTGCGATTTTCATTTCGCAT
1 TGCGATTATCTCGTTGCGATTTTCATTTCGCAT
*
4997166 TGCGATT-CCATCGTTGCGATTTTCATTTCGCAT
1 TGCGATTATC-TCGTTGCGATTTTCATTTCGCAT
*
4997199 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTATCTCGTTGCGATTTTCATTTCGCAT
*
4997232 TGCGATAGTCATTTCCGCGTTGCGATTTTCATTTCGCAT
1 TGCGAT--T-A--T-CTCGTTGCGATTTTCATTTCGCAT
4997271 TGCGATTATCTCGTTGCGAT
1 TGCGATTATCTCGTTGCGAT
4997291 AGTAATTTCC
Statistics
Matches: 111, Mismatches: 6, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
32 1 0.01
33 75 0.68
34 2 0.02
35 1 0.01
36 1 0.01
37 1 0.01
38 1 0.01
39 29 0.26
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (33 bp):
TGCGATTATCTCGTTGCGATTTTCATTTCGCAT
Found at i:4999698 original size:69 final size:69
Alignment explanation
Indices: 4999622--4999792 Score: 315
Period size: 69 Copynumber: 2.5 Consensus size: 69
4999612 CGGCTGTTTC
* * *
4999622 ATCATCAAAATTCGGGTATTGACCAATATCAAAATCATTACACGCAGGGTCTGTTTCTTCTTCTG
1 ATCATCAAAATCCGAGTATTGACCAAGATCAAAATCATTACACGCAGGGTCTGTTTCTTCTTCTG
4999687 AAAA
66 AAAA
4999691 ATCATCAAAATCCGAGTATTGACCAAGATCAAAATCATTACACGCAGGGTCTGTTTCTTCTTCTG
1 ATCATCAAAATCCGAGTATTGACCAAGATCAAAATCATTACACGCAGGGTCTGTTTCTTCTTCTG
4999756 AAAA
66 AAAA
4999760 ATCATCAAAATCCGAGTATTGACCAAGATCAAA
1 ATCATCAAAATCCGAGTATTGACCAAGATCAAA
4999793 GTCCGGGTAT
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 99 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (69 bp):
ATCATCAAAATCCGAGTATTGACCAAGATCAAAATCATTACACGCAGGGTCTGTTTCTTCTTCTG
AAAA
Found at i:4999797 original size:24 final size:24
Alignment explanation
Indices: 4999763--4999816 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
4999753 CTGAAAAATC
4999763 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
4999787 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
4999811 ATCAAA
1 ATCAAA
4999817 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:5000695 original size:20 final size:20
Alignment explanation
Indices: 5000670--5000921 Score: 188
Period size: 20 Copynumber: 12.5 Consensus size: 20
5000660 GTCAGAATCT
5000670 CGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
* *
5000690 CATTGCGATTTATGTATTCG
1 CGTTGCGATTTACGTATTCG
* * *
5000710 CATTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCG
*
5000730 CATTGCGATTTACGTATT-G
1 CGTTGCGATTTACGTATTCG
** *
5000749 TCGTTGCGATTTACAAATACG
1 -CGTTGCGATTTACGTATTCG
* * *
5000770 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGTATTCG
*
5000790 CGTTGCGATTTTACGTATTCT
1 CGTTGCGA-TTTACGTATTCG
* *
5000811 CGTTGCGATTTATGGATAT-G
1 CGTTGCGATTTACGTAT-TCG
* * *
5000831 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACGTATTCG
* *
5000852 CGTTGCGATAGT-CAG-AATCG
1 CGTTGCGAT-TTAC-GTATTCG
** * *
5000872 CGTTGCGATTTATATGTTCA
1 CGTTGCGATTTACGTATTCG
* *
5000892 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGTATTCG
5000912 CGTTGCGATT
1 CGTTGCGATT
5000922 ATGGAAAATC
Statistics
Matches: 185, Mismatches: 37, Indels: 20
0.76 0.15 0.08
Matches are distributed among these distances:
19 2 0.01
20 146 0.79
21 37 0.20
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTACGTATTCG
Found at i:5000736 original size:60 final size:60
Alignment explanation
Indices: 5000670--5000902 Score: 233
Period size: 60 Copynumber: 3.9 Consensus size: 60
5000660 GTCAGAATCT
* * * *
5000670 CGTTGCGATTTACGTATTCGCATTGCGATTTATGTATTCGCATTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCGCGTTGCGATTTATGAATTCGCGTTGCGATTTACGGATACA
* ** *
5000730 CATTGCGATTTACGTATT-GTCGTTGCGATTTACAAATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGTATTCG-CGTTGCGATTTATGAATTCGCGTTGCGATTTACGGATACA
* * *
5000790 CGTTGCGATTTTACGTATTCTCGTTGCGATTTATGGATAT-GCGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACGTATTCGCGTTGCGATTTATGAAT-TCGCGTTGCGA-TTTACGGATACA
* * * *
5000852 CGTTGCGATAGT-CAG-AATCGCGTTGCGATTTAT-ATGTTCACGTTGCGATTT
1 CGTTGCGAT-TTAC-GTATTCGCGTTGCGATTTATGA-ATTCGCGTTGCGATTT
5000903 TCATATTCGC
Statistics
Matches: 143, Mismatches: 21, Indels: 18
0.79 0.12 0.10
Matches are distributed among these distances:
59 1 0.01
60 61 0.43
61 60 0.42
62 21 0.15
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.38
Consensus pattern (60 bp):
CGTTGCGATTTACGTATTCGCGTTGCGATTTATGAATTCGCGTTGCGATTTACGGATACA
Found at i:5000875 original size:41 final size:40
Alignment explanation
Indices: 5000712--5000882 Score: 122
Period size: 41 Copynumber: 4.2 Consensus size: 40
5000702 TGTATTCGCA
* *
5000712 TTGCGA-TTTACGGATACGCATTGCGATT-TACG-TATTGTCG
1 TTGCGATTTTACGGATACTCGTTGCGATTATA-GATA-TG-CG
** * **
5000752 TTGCGA-TTTACAAATACGCGTTGCGATT-TACGGATACACG
1 TTGCGATTTTACGGATACTCGTTGCGATTATA--GATATGCG
* * *
5000792 TTGCGATTTTACGTATTCTCGTTGCGATTTATGGATATGCG
1 TTGCGATTTTACGGATACTCGTTGCGA-TTATAGATATGCG
5000833 TTGCGATTTTACGGATACTCGTTGCGA-TAGTCAGA-ATCGCG
1 TTGCGATTTTACGGATACTCGTTGCGATTA-T-AGATAT-GCG
5000874 TTGCGATTT
1 TTGCGATTT
5000883 ATATGTTCAC
Statistics
Matches: 107, Mismatches: 16, Indels: 15
0.78 0.12 0.11
Matches are distributed among these distances:
39 2 0.02
40 38 0.36
41 62 0.58
42 4 0.04
43 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.37
Consensus pattern (40 bp):
TTGCGATTTTACGGATACTCGTTGCGATTATAGATATGCG
Found at i:5001020 original size:20 final size:19
Alignment explanation
Indices: 5000971--5001024 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
5000961 ATTCTTCATA
5000971 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
5000990 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
5001011 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
5001025 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:5003497 original size:178 final size:178
Alignment explanation
Indices: 5003198--5003529 Score: 664
Period size: 178 Copynumber: 1.9 Consensus size: 178
5003188 GAACAAGTTC
5003198 ACTGCAATCGGGTGCGACACCTATGCTCGTGTGGAAGGTTTCCTCGGACAACGTTATGCAACCGG
1 ACTGCAATCGGGTGCGACACCTATGCTCGTGTGGAAGGTTTCCTCGGACAACGTTATGCAACCGG
5003263 CTGCTTGTCGTTGTGTAATAACATCACCGATGTTTCAAGCGGGTCTTGCTCTGGGATCGGCTGCT
66 CTGCTTGTCGTTGTGTAATAACATCACCGATGTTTCAAGCGGGTCTTGCTCTGGGATCGGCTGCT
5003328 GTCAGACGAGTATCCCAAAGGATGATGATTGTTACAACACATCGGGTG
131 GTCAGACGAGTATCCCAAAGGATGATGATTGTTACAACACATCGGGTG
5003376 ACTGCAATCGGGTGCGACACCTATGCTCGTGTGGAAGGTTTCCTCGGACAACGTTATGCAACCGG
1 ACTGCAATCGGGTGCGACACCTATGCTCGTGTGGAAGGTTTCCTCGGACAACGTTATGCAACCGG
5003441 CTGCTTGTCGTTGTGTAATAACATCACCGATGTTTCAAGCGGGTCTTGCTCTGGGATCGGCTGCT
66 CTGCTTGTCGTTGTGTAATAACATCACCGATGTTTCAAGCGGGTCTTGCTCTGGGATCGGCTGCT
5003506 GTCAGACGAGTATCCCAAAGGATG
131 GTCAGACGAGTATCCCAAAGGATG
5003530 TGAGGAGCTA
Statistics
Matches: 154, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
178 154 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.27
Consensus pattern (178 bp):
ACTGCAATCGGGTGCGACACCTATGCTCGTGTGGAAGGTTTCCTCGGACAACGTTATGCAACCGG
CTGCTTGTCGTTGTGTAATAACATCACCGATGTTTCAAGCGGGTCTTGCTCTGGGATCGGCTGCT
GTCAGACGAGTATCCCAAAGGATGATGATTGTTACAACACATCGGGTG
Found at i:5009740 original size:19 final size:19
Alignment explanation
Indices: 5009716--5009753 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5009706 GGTGTCTTAA
5009716 GACAGCTCTTTTCTTCGAT
1 GACAGCTCTTTTCTTCGAT
5009735 GACAGCTCTTTTCTTCGAT
1 GACAGCTCTTTTCTTCGAT
5009754 ATAAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.16, T:0.42
Consensus pattern (19 bp):
GACAGCTCTTTTCTTCGAT
Found at i:5010189 original size:23 final size:23
Alignment explanation
Indices: 5010141--5010189 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
5010131 CAAATAAATA
* *
5010141 AAATTAAATCAACTACTAATAAT
1 AAATGAAATCAACAACTAATAAT
*
5010164 AAATGAAATCAA-AACTATATAGT
1 AAATGAAATCAACAACTA-ATAAT
5010187 AAA
1 AAA
5010190 AAGCTAATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.59, C:0.10, G:0.04, T:0.27
Consensus pattern (23 bp):
AAATGAAATCAACAACTAATAAT
Found at i:5011412 original size:3 final size:3
Alignment explanation
Indices: 5011404--5011465 Score: 90
Period size: 3 Copynumber: 20.7 Consensus size: 3
5011394 GGCCTGTTTG
**
5011404 TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TAA TAA TAAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
5011449 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
5011466 TCAATAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5011949 original size:113 final size:113
Alignment explanation
Indices: 5011812--5012133 Score: 446
Period size: 113 Copynumber: 2.8 Consensus size: 113
5011802 TAGAGTCATG
* * *
5011812 CAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
5011877 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAA
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTCAAA
* *
5011925 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** * ** * * * * * *
5011990 TTATGAACTCTAACTGGCACTGCTGATTCACCGAGTGATGAATTCGAG
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTCAAA
* *
5012038 CAAAATGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
5012103 TTATTAACTTTCTTTGGAAAAGTTGATCCAT
66 TTATGAACTTTCTCTGGAAAAGTTGATCCAT
5012134 TGTGATGGAT
Statistics
Matches: 176, Mismatches: 33, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
113 176 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (113 bp):
CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTCAAA
Found at i:5014040 original size:76 final size:76
Alignment explanation
Indices: 5013881--5014055 Score: 217
Period size: 76 Copynumber: 2.3 Consensus size: 76
5013871 AGGATGATAT
* * * *
5013881 GGGTCTTCAGCATGCCCCAACA-TTGGCTAATACAAGTGTTCAAAATGCATCAACAGTCCTGATT
1 GGGTTTTCAGCATGCCCCAACATTTGGCTAATACAAATATTCAAAATACATCAACAGTCCTGATT
5013945 CTGATTGAAAG
66 CTGATTGAAAG
* * * * * * * * *
5013956 GGGCTTTCAGCATGCCCCAACATTTTGCTGATATAAATATTCAGAATACTTCAATATTCCTTATT
1 GGGTTTTCAGCATGCCCCAACATTTGGCTAATACAAATATTCAAAATACATCAACAGTCCTGATT
5014021 CTGATTGAAAG
66 CTGATTGAAAG
*
5014032 GGGTTTTCAGCATGCCACAACATT
1 GGGTTTTCAGCATGCCCCAACATT
5014056 CGATTCTTGT
Statistics
Matches: 84, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
75 20 0.24
76 64 0.76
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (76 bp):
GGGTTTTCAGCATGCCCCAACATTTGGCTAATACAAATATTCAAAATACATCAACAGTCCTGATT
CTGATTGAAAG
Found at i:5015403 original size:114 final size:114
Alignment explanation
Indices: 5015203--5015428 Score: 346
Period size: 114 Copynumber: 2.0 Consensus size: 114
5015193 GGTCATGCAG
* * **
5015203 TTCATCTTTCAATTCCAATGATTAGTTCTGGGGTTCCTACTGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
5015268 ACACTTCCAAGAGATGCTATTGGGTCTCCTTATTTTTACTATGAGAAAA
66 ACACTTCCAAGAGATGCTATTGGGTCTCCTTATTTCTACTACGAGAAAA
* * *
5015317 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
5015382 ACACTTTC-AGAAGATGCTATTGGGTCTCCTTATTTCTACTACGAGAA
66 ACACTTCCAAG-AGATGCTATTGGGTCTCCTTATTTCTACTACGAGAA
5015429 CGTGGCACTT
Statistics
Matches: 101, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
113 2 0.02
114 99 0.98
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAAGAGATGCTATTGGGTCTCCTTATTTCTACTACGAGAAAA
Found at i:5017591 original size:17 final size:18
Alignment explanation
Indices: 5017570--5017673 Score: 117
Period size: 17 Copynumber: 5.9 Consensus size: 18
5017560 CTCCCCTTTT
5017570 TCTTTTTTCCTTTTTTTCC
1 TCTTTTTTCC-TTTTTTCC
*
5017589 TTTTTTTTCCTTTTTT-C
1 TCTTTTTTCCTTTTTTCC
* *
5017606 TCATTTTTCC-TTTTTCA
1 TCTTTTTTCCTTTTTTCC
5017623 TCTTTTTTCC-TTTTTCC
1 TCTTTTTTCCTTTTTTCC
* *
5017640 TCATTTTT-CTTTTTTCA
1 TCTTTTTTCCTTTTTTCC
*
5017657 TCTTTTTTCTTTTTTTC
1 TCTTTTTTCCTTTTTTC
5017674 TTTCTTTGCT
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
16 6 0.08
17 44 0.61
18 13 0.18
19 9 0.12
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (18 bp):
TCTTTTTTCCTTTTTTCC
Found at i:5017593 original size:10 final size:10
Alignment explanation
Indices: 5017572--5017604 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
5017562 CCCCTTTTTC
5017572 TTTTTTCC-T
1 TTTTTTCCTT
5017581 TTTTTTCCTT
1 TTTTTTCCTT
5017591 TTTTTTCCTT
1 TTTTTTCCTT
5017601 TTTT
1 TTTT
5017605 CTCATTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTCCTT
Found at i:5017612 original size:10 final size:9
Alignment explanation
Indices: 5017566--5017674 Score: 83
Period size: 8 Copynumber: 12.7 Consensus size: 9
5017556 ATTTCTCCCC
5017566 TTTT-TCTT
1 TTTTCTCTT
5017574 TTTTC-CTT
1 TTTTCTCTT
5017582 TTTT-TCCTT
1 TTTTCT-CTT
*
5017591 TTTTTTCCTT
1 TTTTCT-CTT
*
5017601 TTTTCTCAT
1 TTTTCTCTT
5017610 TTTTC-C-T
1 TTTTCTCTT
5017617 TTTTCATCTT
1 TTTTC-TCTT
5017627 TTTTC-CTT
1 TTTTCTCTT
* *
5017635 TTTCCTC-A
1 TTTTCTCTT
5017643 TTTT-TCTT
1 TTTTCTCTT
5017651 TTTTCATCTT
1 TTTTC-TCTT
5017661 TTTTCT-TT
1 TTTTCTCTT
5017669 TTTTCT
1 TTTTCT
5017675 TTCTTTGCTG
Statistics
Matches: 84, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
7 8 0.10
8 34 0.40
9 17 0.20
10 25 0.30
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTCTCTT
Found at i:5017690 original size:27 final size:26
Alignment explanation
Indices: 5017660--5017713 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 26
5017650 TTTTTCATCT
5017660 TTTTTCTTTTTTTCTTTCTTTGCTGGA
1 TTTTTC-TTTTTTCTTTCTTTGCTGGA
5017687 TTTTTCTTTTTTCTTTCTTTGCTGGA
1 TTTTTCTTTTTTCTTTCTTTGCTGGA
5017713 T
1 T
5017714 GAGTATAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.04, C:0.15, G:0.11, T:0.70
Consensus pattern (26 bp):
TTTTTCTTTTTTCTTTCTTTGCTGGA
Found at i:5020451 original size:6 final size:6
Alignment explanation
Indices: 5020428--5020473 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
5020418 CAAACGTAAA
* * *
5020428 AAATGC AAAGGT AAATGC AAATGC AAATGC AAATGC AAATGT AAAT
1 AAATGC AAATGC AAATGC AAATGC AAATGC AAATGC AAATGC AAAT
5020474 ATGTGAATGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.52, C:0.11, G:0.17, T:0.20
Consensus pattern (6 bp):
AAATGC
Found at i:5022090 original size:26 final size:26
Alignment explanation
Indices: 5022055--5022113 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
5022045 TTAATACTTG
5022055 AATAAAATAA-ATAAATAAAAAATAA-T
1 AATAAAATAATAT-AA-AAAAAATAAGT
*
5022081 AATAAAATAATATAAAAATAATAAGT
1 AATAAAATAATATAAAAAAAATAAGT
5022107 AATAAAA
1 AATAAAA
5022114 AATTTGAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 8 0.27
26 20 0.67
27 2 0.07
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (26 bp):
AATAAAATAATATAAAAAAAATAAGT
Found at i:5022097 original size:22 final size:21
Alignment explanation
Indices: 5022055--5022112 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
5022045 TTAATACTTG
5022055 AATAA-AATAAATAAATAAAA
1 AATAATAATAAATAAATAAAA
5022075 AATAATAATAAA-ATAATATAAA
1 AATAATAATAAATA-AATA-AAA
5022097 AATAATAAGT-AATAAA
1 AATAATAA-TAAATAAA
5022113 AAATTTGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 6 0.18
21 10 0.30
22 15 0.45
23 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (21 bp):
AATAATAATAAATAAATAAAA
Found at i:5022099 original size:11 final size:11
Alignment explanation
Indices: 5022063--5022103 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
5022053 TGAATAAAAT
5022063 AAATAA-ATAAA
1 AAATAATAT-AA
5022074 AAATAATA-ATA
1 AAATAATATA-A
5022085 AAATAATATAA
1 AAATAATATAA
5022096 AAATAATA
1 AAATAATA
5022104 AGTAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 1 0.04
11 24 0.89
12 2 0.07
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATAATATAA
Found at i:5022100 original size:16 final size:18
Alignment explanation
Indices: 5022078--5022116 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5022068 AATAAAAAAT
*
5022078 AATAATAAAATAATATAAA
1 AATAAT-AAGTAATATAAA
5022097 AATAATAAGTAATA-AAA
1 AATAATAAGTAATATAAA
5022114 AAT
1 AAT
5022117 TTGAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 7 0.37
19 6 0.32
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
AATAATAAGTAATATAAA
Found at i:5024334 original size:39 final size:40
Alignment explanation
Indices: 5024291--5024382 Score: 100
Period size: 42 Copynumber: 2.3 Consensus size: 40
5024281 CTATATTTTC
* *
5024291 TGTTATGCTCACATAACT-GAAT-TTTCTTATTCTCAAATT
1 TGTTATGCTCACATAACTAAAATCTTT-TTATTCTCAAACT
*
5024330 TGTTATGAC-CACATAACTAAAATCCCTTTTTCTTCTCAAACT
1 TGTTATG-CTCACATAACTAAAAT--CTTTTTATTCTCAAACT
5024372 TGTTATGCTCA
1 TGTTATGCTCA
5024383 GGGAATAGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
39 16 0.36
40 4 0.09
41 1 0.02
42 20 0.45
43 3 0.07
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (40 bp):
TGTTATGCTCACATAACTAAAATCTTTTTATTCTCAAACT
Found at i:5030702 original size:22 final size:21
Alignment explanation
Indices: 5030650--5030708 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
5030640 TTCAATTAAT
*
5030650 ATGATCCAAAGCTGCCGCTTC
1 ATGAACCAAAGCTGCCGCTTC
* *
5030671 ATGATA-CAAAGCTGCCGTTTTG
1 ATGA-ACCAAAGCTGCCG-CTTC
5030693 ATGAACCAAAGCTGCC
1 ATGAACCAAAGCTGCC
5030709 TGATTAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (21 bp):
ATGAACCAAAGCTGCCGCTTC
Found at i:5035377 original size:41 final size:38
Alignment explanation
Indices: 5035332--5035447 Score: 108
Period size: 41 Copynumber: 2.9 Consensus size: 38
5035322 CAAATGTCGG
5035332 AATAGAGTTGTTTATAGTGGCGTTTTTTCAACAAACGCTGT
1 AATAGAGTTGTTTATAGTGGCGTTTTTTCAA-AAAC-C-GT
* * * *
5035373 AATAGAGTAGTAATT-TAGCGGCGTTGTTGTACAAATACCGT
1 AATAGAGTTGT--TTATAGTGGCGTT-TT-TTCAAAAACCGT
* *
5035414 AATAGGGTTGTTTATAGTGGCGTTTGTTCAAAAA
1 AATAGAGTTGTTTATAGTGGCGTTTTTTCAAAAA
5035448 AGATGCTATA
Statistics
Matches: 60, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
38 6 0.10
39 3 0.05
40 9 0.15
41 21 0.35
42 10 0.17
43 7 0.12
44 4 0.07
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.36
Consensus pattern (38 bp):
AATAGAGTTGTTTATAGTGGCGTTTTTTCAAAAACCGT
Found at i:5035434 original size:82 final size:83
Alignment explanation
Indices: 5035271--5035444 Score: 214
Period size: 82 Copynumber: 2.1 Consensus size: 83
5035261 TTTAGCGACA
* **
5035271 TTTTTTCAACAAACGTCGTAATAGAGCGGTAATTTTACGGCGTTTATAGCTCAAATGTCGGAATA
1 TTTTTTCAACAAACGTCGTAATAGAGCAGTAATTTTACGGCGTTTATAGCTCAAATACCGGAATA
5035336 GAGTTGTTTATAGTGGCG
66 GAGTTGTTTATAGTGGCG
* *
5035354 TTTTTTCAACAAACG-CTGTAATAGAGTAGTAA-TTTAGCGGCGTTGT-T-G-TACAAATACCGT
1 TTTTTTCAACAAACGTC-GTAATAGAGCAGTAATTTTA-CGGCGTT-TATAGCT-CAAATACCGG
*
5035414 AATAGGGTTGTTTATAGTGGCG
62 AATAGAGTTGTTTATAGTGGCG
*
5035436 TTTGTTCAA
1 TTTTTTCAA
5035445 AAAAGATGCT
Statistics
Matches: 80, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
81 1 0.01
82 42 0.52
83 36 0.45
84 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.36
Consensus pattern (83 bp):
TTTTTTCAACAAACGTCGTAATAGAGCAGTAATTTTACGGCGTTTATAGCTCAAATACCGGAATA
GAGTTGTTTATAGTGGCG
Found at i:5037213 original size:83 final size:82
Alignment explanation
Indices: 5037096--5037287 Score: 208
Period size: 82 Copynumber: 2.3 Consensus size: 82
5037086 CAAACGCCAT
* * ** *
5037096 AATAGGTATAATCTATAGTGGCGTTTGGATAACAAACATCGTA-AAATATTTATATTTTAGCGGC
1 AATAGGTATAATCTATAGTGGCGTTTGGATAACAAAC-GC-CACAAATATTTATACATTAACGGC
5037160 ATTTTAGCACAAATCCCGC
64 ATTTTAGCACAAATCCCGC
* ** * *
5037179 AATAGGTCTAATCTATAGTGGCGTTT-TTTCAACAAACGCCACAAATATTTTTACATTAACGGCG
1 AATAGGTATAATCTATAGTGGCGTTTGGAT-AACAAACGCCACAAATATTTATACATTAACGGCA
* * *
5037243 TTTTTGTACAAATGCCGC
65 TTTTAGCACAAATCCCGC
* *
5037261 AATAGGTGTAATCTATAGTGGTGTTTG
1 AATAGGTATAATCTATAGTGGCGTTTG
5037288 TTAAGTAAAC
Statistics
Matches: 91, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
81 1 0.01
82 58 0.64
83 32 0.35
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (82 bp):
AATAGGTATAATCTATAGTGGCGTTTGGATAACAAACGCCACAAATATTTATACATTAACGGCAT
TTTAGCACAAATCCCGC
Found at i:5037273 original size:82 final size:82
Alignment explanation
Indices: 5037008--5037286 Score: 249
Period size: 83 Copynumber: 3.4 Consensus size: 82
5036998 ATCAATAAAC
* * * * * *
5037008 GCCGCAATAGGTTTACTATATAGTGGTGTTTTATCAAGAAACGTCGCAAAATA-TTAGTACTTTT
1 GCCGCAATAGGTATAATCTATAGTGGCGTTTTATCAACAAACG-CGCAAAATATTTA-TACTTTA
* * * *
5037072 CCTGCGTTTTTATACAAAC
64 ACGGCGTTTTTGTACAAAT
** * * * *
5037091 GCCATAATAGGTATAATCTATAGTGGCGTTTGGAT-AACAAACATCGTAAAATATTTATATTTTA
1 GCCGCAATAGGTATAATCTATAGTGGCGTTT-TATCAACAAAC-GCGCAAAATATTTATACTTTA
* * * *
5037155 GCGGCATTTTAGCACAAAT
64 ACGGCGTTTTTGTACAAAT
* * * * *
5037174 CCCGCAATAGGTCTAATCTATAGTGGCGTTTTTTCAACAAACGC-CACAAATATTTTTACATTAA
1 GCCGCAATAGGTATAATCTATAGTGGCGTTTTATCAACAAACGCGCA-AAATATTTATACTTTAA
5037238 CGGCGTTTTTGTACAAAT
65 CGGCGTTTTTGTACAAAT
* *
5037256 GCCGCAATAGGTGTAATCTATAGTGGTGTTT
1 GCCGCAATAGGTATAATCTATAGTGGCGTTT
5037287 GTTAAGTAAA
Statistics
Matches: 154, Mismatches: 37, Indels: 11
0.76 0.18 0.05
Matches are distributed among these distances:
81 1 0.01
82 58 0.38
83 90 0.58
84 5 0.03
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (82 bp):
GCCGCAATAGGTATAATCTATAGTGGCGTTTTATCAACAAACGCGCAAAATATTTATACTTTAAC
GGCGTTTTTGTACAAAT
Found at i:5037371 original size:41 final size:41
Alignment explanation
Indices: 5037294--5037384 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 41
5037284 TTTGTTAAGT
* * *
5037294 AAACGTCGCAATAGAGTTGCACTATAGAGGCATTTTTGTAC
1 AAACGCCGCAATAGAGTTGAACTAAAGAGGCATTTTTGTAC
* *
5037335 AAACGCCGCAATAGAGTTTAAC-AAAGTGGCATTTTT-TACC
1 AAACGCCGCAATAGAGTTGAACTAAAGAGGCATTTTTGTA-C
5037375 TAAACGCCGC
1 -AAACGCCGC
5037385 GATATATCTG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
39 2 0.05
40 13 0.30
41 28 0.65
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (41 bp):
AAACGCCGCAATAGAGTTGAACTAAAGAGGCATTTTTGTAC
Found at i:5046278 original size:19 final size:19
Alignment explanation
Indices: 5046250--5046286 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5046240 TATATTTGAA
*
5046250 AAATACATGTTATATGATG
1 AAATACATGTTACATGATG
*
5046269 AAATATATGTTACATGAT
1 AAATACATGTTACATGAT
5046287 ATGACATGCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (19 bp):
AAATACATGTTACATGATG
Found at i:5046435 original size:21 final size:23
Alignment explanation
Indices: 5046411--5046452 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
5046401 ATACATGCGG
*
5046411 TATGTGA-CAGAAGA-AAATGTA
1 TATGTGATCACAAGAGAAATGTA
5046432 TATGTGATCACAAGAGAAATG
1 TATGTGATCACAAGAGAAATG
5046453 ACATGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.24
Consensus pattern (23 bp):
TATGTGATCACAAGAGAAATGTA
Found at i:5049252 original size:43 final size:43
Alignment explanation
Indices: 5049173--5049396 Score: 218
Period size: 43 Copynumber: 5.2 Consensus size: 43
5049163 AAACATCACG
* * * * ** * **
5049173 AAATCTCAACACCTATTGCGGTGTCTGTCATCAAAATGACATT
1 AAATCTCAACACTTATTGCGGCGTTTGTGAGAAAAATGCCGCT
* *
5049216 AAATCTCAACACTTATTGTGGCGTTTATGAGAAAAATGCCGCT
1 AAATCTCAACACTTATTGCGGCGTTTGTGAGAAAAATGCCGCT
* * *
5049259 AAATCTCAACACTTATTGCGGTGTTTGTCAGAAAAACGCCGCT
1 AAATCTCAACACTTATTGCGGCGTTTGTGAGAAAAATGCCGCT
* * *
5049302 -AATCTCAACACCTATTGCGGCGTTTGTGATAAAAACGCCGCT
1 AAATCTCAACACTTATTGCGGCGTTTGTGAGAAAAATGCCGCT
* * * * *
5049344 AAA-CATAAAAACCTATTGCGGCGTTTGTAAGACAAATGCCGCT
1 AAATC-TCAACACTTATTGCGGCGTTTGTGAGAAAAATGCCGCT
*
5049387 AAATATCAAC
1 AAATCTCAAC
5049397 CAACAAACGC
Statistics
Matches: 149, Mismatches: 29, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
42 39 0.26
43 110 0.74
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.27
Consensus pattern (43 bp):
AAATCTCAACACTTATTGCGGCGTTTGTGAGAAAAATGCCGCT
Found at i:5049342 original size:85 final size:85
Alignment explanation
Indices: 5049173--5049388 Score: 245
Period size: 85 Copynumber: 2.5 Consensus size: 85
5049163 AAACATCACG
* ** * ** * *
5049173 AAATCTCAACACCTATTGCGGTGTCTGTCATCAAAATGACATTAAATCTCAACACTTATTGTGGC
1 AAATCTCAACACCTATTGCGGTGTTTGTCAGAAAAATGCCGCT-AATCTCAACACCTATTGCGGC
*
5049238 GTTTATGAGAAAAATGCCGCT
65 GTTTATGAGAAAAACGCCGCT
* *
5049259 AAATCTCAACACTTATTGCGGTGTTTGTCAGAAAAACGCCGCTAATCTCAACACCTATTGCGGCG
1 AAATCTCAACACCTATTGCGGTGTTTGTCAGAAAAATGCCGCTAATCTCAACACCTATTGCGGCG
* *
5049324 TTTGTGATAAAAACGCCGCT
66 TTTATGAGAAAAACGCCGCT
* * * * *
5049344 AAA-CATAAAAACCTATTGCGGCGTTTGTAAGACAAATGCCGCTAA
1 AAATC-TCAACACCTATTGCGGTGTTTGTCAGAAAAATGCCGCTAA
5049389 ATATCAACCA
Statistics
Matches: 109, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
84 1 0.01
85 73 0.67
86 35 0.32
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (85 bp):
AAATCTCAACACCTATTGCGGTGTTTGTCAGAAAAATGCCGCTAATCTCAACACCTATTGCGGCG
TTTATGAGAAAAACGCCGCT
Found at i:5050061 original size:41 final size:41
Alignment explanation
Indices: 5050002--5050095 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
5049992 ACTGGAATCG
* *
5050002 AAGGGATCGATCCATTAGTCAAAT-GAATCGATCCTTTTACT
1 AAGGGATCGATCCATTAGTCAAATAG-ATCAATCATTTTACT
* *
5050043 AAGGGATCGATCCTTTAGTCAACTAGATCAATCATTTTACT
1 AAGGGATCGATCCATTAGTCAAATAGATCAATCATTTTACT
*
5050084 AATGGATCGATC
1 AAGGGATCGATC
5050096 TTTTGACACA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 46 0.98
42 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (41 bp):
AAGGGATCGATCCATTAGTCAAATAGATCAATCATTTTACT
Found at i:5055795 original size:25 final size:25
Alignment explanation
Indices: 5055761--5055820 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
5055751 TCCCCCTTAC
*
5055761 TTTAACACTTCTCCCATTTAAAATA
1 TTTAACACTTCTCCCATTTAAAACA
5055786 TTTAACACTTCTCCCATTTAAAACA
1 TTTAACACTTCTCCCATTTAAAACA
*
5055811 CTTAACACTT
1 TTTAACACTT
5055821 AAAACACTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.35, C:0.27, G:0.00, T:0.38
Consensus pattern (25 bp):
TTTAACACTTCTCCCATTTAAAACA
Found at i:5055822 original size:16 final size:16
Alignment explanation
Indices: 5055803--5055836 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5055793 CTTCTCCCAT
5055803 TTAAAACACTTAACAC
1 TTAAAACACTTAACAC
5055819 TTAAAACACTTAACAC
1 TTAAAACACTTAACAC
5055835 TT
1 TT
5055837 CTCCCCCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (16 bp):
TTAAAACACTTAACAC
Found at i:5064333 original size:47 final size:49
Alignment explanation
Indices: 5064209--5064339 Score: 137
Period size: 47 Copynumber: 2.7 Consensus size: 49
5064199 ATATAAATTT
* *
5064209 CTTACC-TTTTATCCCATAAGCTCATAAGCTTA--TTTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
* ** *
5064255 CTTACCATTTAAAATTCCATAAGCTCGTAAGCTTATTTTTTTTTCAATATA
1 CTTACCATTT--AATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
* *
5064306 CTTGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTT
5064340 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
46 6 0.08
47 26 0.37
49 20 0.28
50 2 0.03
51 17 0.24
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.42
Consensus pattern (49 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
Found at i:5067634 original size:25 final size:25
Alignment explanation
Indices: 5067600--5067659 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
5067590 TCCCCCTTAC
*
5067600 TTTAACACTTCTCCCATTTAAAATA
1 TTTAACACTTCTCCCATTTAAAACA
5067625 TTTAACACTTCTCCCATTTAAAACA
1 TTTAACACTTCTCCCATTTAAAACA
*
5067650 CTTAACACTT
1 TTTAACACTT
5067660 AAAACACTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.35, C:0.27, G:0.00, T:0.38
Consensus pattern (25 bp):
TTTAACACTTCTCCCATTTAAAACA
Found at i:5067661 original size:16 final size:16
Alignment explanation
Indices: 5067642--5067675 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5067632 CTTCTCCCAT
5067642 TTAAAACACTTAACAC
1 TTAAAACACTTAACAC
5067658 TTAAAACACTTAACAC
1 TTAAAACACTTAACAC
5067674 TT
1 TT
5067676 CTCCCCCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (16 bp):
TTAAAACACTTAACAC
Found at i:5068209 original size:20 final size:20
Alignment explanation
Indices: 5068184--5068234 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
5068174 TCTATAGAAG
5068184 TGGGGGGAATCGGTACCCCC
1 TGGGGGGAATCGGTACCCCC
5068204 TGGGGGGAATCGGTACCCCC
1 TGGGGGGAATCGGTACCCCC
5068224 TGGGGGGAATC
1 TGGGGGGAATC
5068235 AGTTCCCTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.16, C:0.25, G:0.43, T:0.16
Consensus pattern (20 bp):
TGGGGGGAATCGGTACCCCC
Found at i:5068903 original size:39 final size:39
Alignment explanation
Indices: 5068833--5068907 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
5068823 AGTATTAGAA
** *
5068833 TATTTTATTAAAAATAAATAGTTTTATAATAATTTTATG
1 TATTTTATTAAAAATAAATAAATTTAAAATAATTTTATG
*
5068872 TATTTTA-TAAAAATATATAAAATTTAAAATAATTTT
1 TATTTTATTAAAAATAAAT-AAATTTAAAATAATTTT
5068908 TATATAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 10 0.32
39 21 0.68
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (39 bp):
TATTTTATTAAAAATAAATAAATTTAAAATAATTTTATG
Found at i:5071933 original size:21 final size:21
Alignment explanation
Indices: 5071883--5071944 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
5071873 TTTTAATATC
*
5071883 ATTTTAATAAAAATATTAATT
1 ATTTTAATAAAAATATTAATG
** **
5071904 ATTAAAATAAATTTATTAATG
1 ATTTTAATAAAAATATTAATG
5071925 ATTTTAATAATATAATATTA
1 ATTTTAATAA-A-AATATTA
5071945 TTTTTTAAGT
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 24 0.80
22 1 0.03
23 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTTTAATAAAAATATTAATG
Found at i:5072103 original size:22 final size:23
Alignment explanation
Indices: 5072069--5072112 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5072059 TATAATTAAA
5072069 TTATTAAGTA-TTTAAAATATAT
1 TTATTAAGTATTTTAAAATATAT
*
5072091 TTATTAA-TAATTTTAGAATATA
1 TTATTAAGT-ATTTTAAAATATA
5072113 ATATAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 1 0.05
22 8 0.42
23 10 0.53
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (23 bp):
TTATTAAGTATTTTAAAATATAT
Found at i:5072137 original size:14 final size:14
Alignment explanation
Indices: 5072118--5072144 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5072108 ATATAATATA
5072118 ATATTATAATTTTC
1 ATATTATAATTTTC
5072132 ATATTATAATTTT
1 ATATTATAATTTT
5072145 TTATTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
ATATTATAATTTTC
Found at i:5072270 original size:15 final size:13
Alignment explanation
Indices: 5072234--5072277 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
5072224 AAATTGTAGA
*
5072234 AATAATATTTTAAT
1 AATAATA-TTAAAT
5072248 AATAATATTAACAT
1 AATAATATTAA-AT
5072262 AATTAATATTAAAT
1 AA-TAATATTAAAT
5072276 AA
1 AA
5072278 ATTATTCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 3 0.11
14 15 0.56
15 9 0.33
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (13 bp):
AATAATATTAAAT
Found at i:5072281 original size:15 final size:15
Alignment explanation
Indices: 5072246--5072277 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5072236 TAATATTTTA
5072246 ATAA-TAATATTAAC
1 ATAATTAATATTAAC
5072260 ATAATTAATATTAA-
1 ATAATTAATATTAAC
5072274 ATAA
1 ATAA
5072278 ATTATTCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAATTAATATTAAC
Found at i:5075254 original size:21 final size:21
Alignment explanation
Indices: 5075228--5075268 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
5075218 ACTTGGAGGG
5075228 GAATTGATGAGAGAAGAGAGA
1 GAATTGATGAGAGAAGAGAGA
5075249 GAATTGATGAGAGAAGAGAG
1 GAATTGATGAGAGAAGAGAG
5075269 CATCATCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.39, T:0.15
Consensus pattern (21 bp):
GAATTGATGAGAGAAGAGAGA
Found at i:5075262 original size:12 final size:12
Alignment explanation
Indices: 5075228--5075263 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5075218 ACTTGGAGGG
5075228 GAATTGATGAGA
1 GAATTGATGAGA
5075240 GAA--GA-GAGA
1 GAATTGATGAGA
5075249 GAATTGATGAGA
1 GAATTGATGAGA
5075261 GAA
1 GAA
5075264 GAGAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
9 7 0.33
10 2 0.10
11 2 0.10
12 10 0.48
ACGTcount: A:0.47, C:0.00, G:0.36, T:0.17
Consensus pattern (12 bp):
GAATTGATGAGA
Found at i:5076728 original size:35 final size:35
Alignment explanation
Indices: 5076682--5076761 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
5076672 AACATAATCA
5076682 TCAATTACATTCTAAACC-CTAAATTCCAAAATACT
1 TCAATTACATTCTAAACCTC-AAATTCCAAAATACT
* *
5076717 TCAATTACATTCTAAACCTCAAATTCTAGAATACT
1 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
*
5076752 TTAATTACAT
1 TCAATTACAT
5076762 GCCTAACCCC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 40 0.98
36 1 0.02
ACGTcount: A:0.41, C:0.23, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTACATTCTAAACCTCAAATTCCAAAATACT
Found at i:5076775 original size:35 final size:35
Alignment explanation
Indices: 5076682--5076782 Score: 114
Period size: 35 Copynumber: 2.9 Consensus size: 35
5076672 AACATAATCA
* *
5076682 TCAATTACATTCTAAACCCTAAATTCCAAAATACT
1 TCAATTACATCCTAAACCCCAAATTCCAAAATACT
* * * *
5076717 TCAATTACATTCTAAACCTCAAATTCTAGAATACT
1 TCAATTACATCCTAAACCCCAAATTCCAAAATACT
*
5076752 TTAATTACATGCCT-AACCCCAAATTCACAAA
1 TCAATTACAT-CCTAAACCCCAAATTC-CAAA
5076783 CCATTCTCAA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
35 51 0.93
36 4 0.07
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.31
Consensus pattern (35 bp):
TCAATTACATCCTAAACCCCAAATTCCAAAATACT
Found at i:5077194 original size:148 final size:148
Alignment explanation
Indices: 5076936--5077222 Score: 468
Period size: 148 Copynumber: 1.9 Consensus size: 148
5076926 ACTCAATTTA
* *
5076936 GTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGTGTTTATAAAATTTAAATCAAGTCGAAT
1 GTTTATAAAATAATTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAAT
* * * * * * *
5077001 TTAATCGGATTTTCGAGTTTCTGTTTAGATTTAAATATAAATATTTATCATATTATAATATTATT
66 TGAATCGAATTTTCGAGTTTCTATTTAAATTTAAATACAAATATTTATAATACTATAATATTATT
5077066 TGATTCTAACTCAGTTCT
131 TGATTCTAACTCAGTTCT
5077084 GTTTATAAAATAATTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAAT
1 GTTTATAAAATAATTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAAT
*
5077149 TGAAGT-GAATTTTCGAGTTTCTATTTAAATTTAATTACAAATATTTATAATACTATAATATTAT
66 TGAA-TCGAATTTTCGAGTTTCTATTTAAATTTAAATACAAATATTTATAATACTATAATATTAT
5077213 TTGATTCTAA
130 TTGATTCTAA
5077223 TTTAAATAGT
Statistics
Matches: 128, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
148 127 0.99
149 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.46
Consensus pattern (148 bp):
GTTTATAAAATAATTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAAT
TGAATCGAATTTTCGAGTTTCTATTTAAATTTAAATACAAATATTTATAATACTATAATATTATT
TGATTCTAACTCAGTTCT
Found at i:5077736 original size:35 final size:35
Alignment explanation
Indices: 5077697--5077776 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
5077687 GGGGTTGGTC
*
5077697 ATGTAATTGAAGTATTTTAGAATTT-GAGGTTTAAA
1 ATGTAATTGAAATATTTTAGAATTTAG-GGTTTAAA
* *
5077732 ATGTAATTGAAATATTTTGGAATTTAGGGTTTAGA
1 ATGTAATTGAAATATTTTAGAATTTAGGGTTTAAA
*
5077767 ATATAATTGA
1 ATGTAATTGA
5077777 TGACTGTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 39 0.98
36 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.20, T:0.42
Consensus pattern (35 bp):
ATGTAATTGAAATATTTTAGAATTTAGGGTTTAAA
Found at i:5081244 original size:20 final size:21
Alignment explanation
Indices: 5081205--5081250 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
5081195 ATGTTTACAG
5081205 AGAAAACATCCTCAAACGGCT
1 AGAAAACATCCTCAAACGGCT
* *
5081226 AGAAATCATCC-CCAACGGCT
1 AGAAAACATCCTCAAACGGCT
5081246 AGAAA
1 AGAAA
5081251 CGACCACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.43, C:0.28, G:0.15, T:0.13
Consensus pattern (21 bp):
AGAAAACATCCTCAAACGGCT
Found at i:5083010 original size:20 final size:20
Alignment explanation
Indices: 5082980--5083027 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
5082970 AATGATTCTC
*
5082980 TTTTG-AAAGCAAAATTG-GA
1 TTTTGAAAAGCAAAA-TGAAA
5082999 TTTTGAAAAGCAAAATGAAA
1 TTTTGAAAAGCAAAATGAAA
5083019 TTTTGAAAA
1 TTTTGAAAA
5083028 ATGATTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.31
Consensus pattern (20 bp):
TTTTGAAAAGCAAAATGAAA
Found at i:5084714 original size:20 final size:20
Alignment explanation
Indices: 5084685--5084729 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5084675 ATTTTTGCAC
*
5084685 AGAAAACATCCCAAATGGCT
1 AGAAAACATCCCAAACGGCT
* *
5084705 AGAAATCATCCCCAACGGCT
1 AGAAAACATCCCAAACGGCT
5084725 AGAAA
1 AGAAA
5084730 CAACCACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.44, C:0.27, G:0.16, T:0.13
Consensus pattern (20 bp):
AGAAAACATCCCAAACGGCT
Found at i:5086694 original size:10 final size:10
Alignment explanation
Indices: 5086616--5086709 Score: 71
Period size: 10 Copynumber: 8.6 Consensus size: 10
5086606 TTTTCACATC
5086616 TCAACATATT
1 TCAACATATT
*
5086626 TTAACATAATAGT
1 TCAACAT-AT--T
* *
5086639 TCAACACATC
1 TCAACATATT
5086649 TCAACATATT
1 TCAACATATT
5086659 TCATAGCATATT
1 TCA-A-CATATT
* *
5086671 TCAGCATATC
1 TCAACATATT
5086681 TCAACATATT
1 TCAACATATT
5086691 TCAATAGCATATT
1 TC-A-A-CATATT
5086704 TCAACA
1 TCAACA
5086710 GAAATTTAAC
Statistics
Matches: 66, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
10 34 0.52
11 5 0.08
12 13 0.20
13 14 0.21
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.35
Consensus pattern (10 bp):
TCAACATATT
Found at i:5086703 original size:33 final size:33
Alignment explanation
Indices: 5086610--5086709 Score: 130
Period size: 33 Copynumber: 3.1 Consensus size: 33
5086600 TAATGGTTTT
* * ** *
5086610 CACATCTCAACATATTTTAACATAATAGTTCAA
1 CACATCTCAACATATTTCAATAGCATATTTCAA
*
5086643 CACATCTCAACATATTTC-ATAGCATATTTCAG
1 CACATCTCAACATATTTCAATAGCATATTTCAA
*
5086675 CATATCTCAACATATTTCAATAGCATATTTCAA
1 CACATCTCAACATATTTCAATAGCATATTTCAA
5086708 CA
1 CA
5086710 GAAATTTAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
32 26 0.45
33 32 0.55
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (33 bp):
CACATCTCAACATATTTCAATAGCATATTTCAA
Found at i:5086707 original size:23 final size:20
Alignment explanation
Indices: 5086638--5086709 Score: 63
Period size: 22 Copynumber: 3.4 Consensus size: 20
5086628 AACATAATAG
* * *
5086638 TTCAACACATCTCAACATAT
1 TTCAACATATTTCAGCATAT
5086658 TTCATAGCATATTTCAGCATAT
1 TTCA-A-CATATTTCAGCATAT
*
5086680 CTCAACATATTTCAATAGCATAT
1 TTCAACATATTTC---AGCATAT
5086703 TTCAACA
1 TTCAACA
5086710 GAAATTTAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
20 12 0.29
21 2 0.05
22 15 0.36
23 13 0.31
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.35
Consensus pattern (20 bp):
TTCAACATATTTCAGCATAT
Found at i:5089193 original size:19 final size:19
Alignment explanation
Indices: 5089169--5089244 Score: 59
Period size: 19 Copynumber: 4.2 Consensus size: 19
5089159 GAATTTGAAT
*
5089169 AATGTTAATGAGTTACTGG
1 AATGTTAATGAGTTACTAG
* * *
5089188 AATGTTAAAGTGTT--TAA
1 AATGTTAATGAGTTACTAG
* *
5089205 AAT-TTAATGATTTAATAG
1 AATGTTAATGAGTTACTAG
* *
5089223 AATATTAATGAGTTACTGG
1 AATGTTAATGAGTTACTAG
5089242 AAT
1 AAT
5089245 TTGAATATAC
Statistics
Matches: 43, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
16 7 0.16
17 4 0.09
18 5 0.12
19 27 0.63
ACGTcount: A:0.39, C:0.03, G:0.18, T:0.39
Consensus pattern (19 bp):
AATGTTAATGAGTTACTAG
Found at i:5094463 original size:35 final size:35
Alignment explanation
Indices: 5094417--5094488 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
5094407 CACATGCAAA
*
5094417 CTATAAGCTAATTCACAAATGTTTTCCTCAAATTT
1 CTATAAGCTAATTCACAAATGTTTACCTCAAATTT
* *
5094452 CTATAAGCTAATTCACGAATGTTTACCTCACATTT
1 CTATAAGCTAATTCACAAATGTTTACCTCAAATTT
5094487 CT
1 CT
5094489 CCTCTTCGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (35 bp):
CTATAAGCTAATTCACAAATGTTTACCTCAAATTT
Found at i:5098573 original size:142 final size:142
Alignment explanation
Indices: 5098417--5098682 Score: 396
Period size: 142 Copynumber: 1.9 Consensus size: 142
5098407 GTATTGATAG
* * *
5098417 TTGTCGTGAAATAAATATTCAGCCGCAATTT-TTATTTTAGATTGCAAT-GAAAAATGTTACCAA
1 TTGTCGTGAAATAAATATTCAACCAC-ATTTAATATTTTAGATTGCAATCG-AAAATGTTACCAA
* * * *
5098480 ATG-TATAATATTTTAGGTTGGATT-AGATAATATTTTAGGTTGTAACTAAGTATCGATGCTTAG
64 A-GATATAACATTTTAGGTTGGATTGA-ATAAAAATTTAGGTTGTAACTAAATATCGATGCTTAG
5098543 TTGTAAGTATCAATAC
127 TTGTAAGTATCAATAC
*
5098559 TTGTCGTGAAATAAATATTGAACCACATTTAATATTTTAGATTGCAATCGAAAATGTTACCAAAG
1 TTGTCGTGAAATAAATATTCAACCACATTTAATATTTTAGATTGCAATCGAAAATGTTACCAAAG
5098624 ATATAACATTTTAGGTTGGATTGAATAAAAATTTAGGTTGTAACTAAATATCGATGCTT
66 ATATAACATTTTAGGTTGGATTGAATAAAAATTTAGGTTGTAACTAAATATCGATGCTT
5098683 GTCGTGAAAT
Statistics
Matches: 112, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
141 5 0.04
142 105 0.94
143 2 0.02
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.38
Consensus pattern (142 bp):
TTGTCGTGAAATAAATATTCAACCACATTTAATATTTTAGATTGCAATCGAAAATGTTACCAAAG
ATATAACATTTTAGGTTGGATTGAATAAAAATTTAGGTTGTAACTAAATATCGATGCTTAGTTGT
AAGTATCAATAC
Found at i:5099045 original size:74 final size:73
Alignment explanation
Indices: 5098967--5099138 Score: 170
Period size: 74 Copynumber: 2.3 Consensus size: 73
5098957 ATATATGTCC
* *
5098967 ATATTTTATATTTTGAACTTATTTTCAG-AATTTTTTTTAA-AGTCAAAGTATCAAACCACATAG
1 ATATTTTATATTTTGAACTTATTTTCAGAAATATTTTTTAACA---AAAGTATCAAACCACAAAG
* **
5099030 CATAGGTCTTG
63 CATAGGTATCA
* * * * *
5099041 ATATTTCAAATTTAGAAC-TATTTTTCAGCAAATATTTTTTAACAAAAGTATCGAACCTCAAAGC
1 ATATTTTATATTTTGAACTTA-TTTTCAG-AAATATTTTTTAACAAAAGTATCAAACCACAAAGC
*
5099105 ATATGTATCA
64 ATAGGTATCA
*
5099115 ATATTTTTTATTTTGAACTTATTT
1 ATATTTTATATTTTGAACTTATTT
5099139 AAAAAAAATA
Statistics
Matches: 78, Mismatches: 15, Indels: 10
0.76 0.15 0.10
Matches are distributed among these distances:
73 2 0.03
74 62 0.79
75 2 0.03
76 11 0.14
77 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (73 bp):
ATATTTTATATTTTGAACTTATTTTCAGAAATATTTTTTAACAAAAGTATCAAACCACAAAGCAT
AGGTATCA
Found at i:5100359 original size:186 final size:187
Alignment explanation
Indices: 5099474--5100311 Score: 822
Period size: 187 Copynumber: 4.5 Consensus size: 187
5099464 ATTTTTTATC
* * * * * * * * * *
5099474 CAACTTAATTTCTTAGCAATCAATAAGATTCTTGGGCGCAGCTGGATTAGTTAACACAATTGATC
1 CAACCTAATTTCTTAGCGACCAATAACATTCTTGGACGCAACCGAATTTGTTAACACAATTGATA
* * * * ** *
5099539 ATATTTTCGACTTTCAACTT-TTTATATTATCGTGGTTATTTTCTTTGACCCATTTGCTAAACTC
66 ACATTTTCAACTTTCAACTTATTT-TGTTACCGTGACTATTTTCTTTGACTCATTTGCTAAACTC
* * * *
5099603 T-ATTAACATTTTACGTCCAAACCGGATTTATTAAAGAAGCTTATAACATTCAAGGTCT
130 TGA-TAACATTTTAGGTCCAAACCGGATTTGTTAAAGAAACTTATAACATTCAAGATCT
* ** * * * * *
5099661 CAACCTAATTTCTTAAC-AATAGGTAACATTCTTGGGA-GCAGCCGGATTTGCTAACACGATT-A
1 CAACCTAATTTCTTAGCGACCA-ATAACATTCTT-GGACGCAACCGAATTTGTTAACACAATTGA
* ** *
5099723 GTAATATTTTTTACTTTCAACTTA----GTTATCGTGACTATTTTCTTTGACTCATTTGCTAAAC
64 -TAACATTTTCAACTTTCAACTTATTTTGTTACCGTGACTATTTTCTTTGACTCATTTGCTAAAC
* ** * * *
5099784 TCTGATAATATTTTAGGTCCAAATTGAATTTGTTAAAGGAACTTATAACATTCCAGATCT
128 TCTGATAACATTTTAGGTCCAAACCGGATTTGTTAAAGAAACTTATAACATTCAAGATCT
* * * * ** * * *
5099844 CAATCTAATTTCTTAGTGGCCGATAACATTCTTGGGGGCAAACGAATTCGTTAACGCAATTGATA
1 CAACCTAATTTCTTAGCGACCAATAACATTCTTGGACGCAACCGAATTTGTTAACACAATTGATA
* *
5099909 ACATCTTT-AGCTTTCAACTTATTTTGTTACCGTGACTATTTTCTTTGACTCATTTGCTAAATTC
66 ACAT-TTTCAACTTTCAACTTATTTTGTTACCGTGACTATTTTCTTTGACTCATTTGCTAAACTC
* * * ** * **
5099973 CGACAACATTTTAGGTACAAACAAGAATTGTTATTGAAACTTATAACATTCAAGATCT
130 TGATAACATTTTAGGTCCAAACCGGATTTGTTAAAGAAACTTATAACATTCAAGATCT
* * * *
5100031 CAACCTAATTTCTTAGCGACCAATAACATTCTTGGGCGCAATC-AGATTTGTGAACGCAATTGAT
1 CAACCTAATTTCTTAGCGACCAATAACATTCTTGGACGCAACCGA-ATTTGTTAACACAATTGAT
* * * * * *
5100095 AACATTTTCAGCATTCAACTTATTTTGTTA-CGTGATTATTTTCTCTGACTCATTTGCTAAATTT
65 AACATTTTCAACTTTCAACTTATTTTGTTACCGTGACTATTTTCTTTGACTCATTTGCTAAACTC
* * *
5100159 TGGTAGCATTTTAGGTCCAGACCGGATTTGTTAAAGAAACTTATAACATTCCAA-ATCT
130 TGATAACATTTTAGGTCCAAACCGGATTTGTTAAAGAAACTTATAACATT-CAAGATCT
* * * *
5100217 TAACCTAATTTCTTAGCGACCAATAATATTCTTGGACACAACCGAATTT-TTAACACGATTGATA
1 CAACCTAATTTCTTAGCGACCAATAACATTCTTGGACGCAACCGAATTTGTTAACACAATTGATA
*
5100281 ATATTTTCAACTTTCAACTTATTTTGTTACC
66 ACATTTTCAACTTTCAACTTATTTTGTTACC
5100312 ATGGGCTAAA
Statistics
Matches: 537, Mismatches: 96, Indels: 37
0.80 0.14 0.06
Matches are distributed among these distances:
182 2 0.00
183 138 0.26
184 5 0.01
185 38 0.07
186 124 0.23
187 228 0.42
188 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (187 bp):
CAACCTAATTTCTTAGCGACCAATAACATTCTTGGACGCAACCGAATTTGTTAACACAATTGATA
ACATTTTCAACTTTCAACTTATTTTGTTACCGTGACTATTTTCTTTGACTCATTTGCTAAACTCT
GATAACATTTTAGGTCCAAACCGGATTTGTTAAAGAAACTTATAACATTCAAGATCT
Found at i:5101411 original size:143 final size:143
Alignment explanation
Indices: 5101149--5101436 Score: 540
Period size: 143 Copynumber: 2.0 Consensus size: 143
5101139 TAAATGTACA
5101149 CTAATCAAATTATTGAAAACAATATATATACACATGTGTTGCCACTGTAGTCCAACCCAACTTTT
1 CTAATCAAATTATTGAAAACAATATATATACACATGTGTTGCCACTGTAGTCCAACCCAACTTTT
* *
5101214 GTACTTGCAATTACGTGTCTTCAACACTTCTAACAAGCATTTTTTTTCTTTTTGAATAAAAATCG
66 GTACTTGCAATTACGGGTCTTCAACACTTCTAACAAGCATTTTTTTTCTCTTTGAATAAAAATCG
5101279 TACATTTTTTACT
131 TACATTTTTTACT
*
5101292 CTAATCAAATTATTGAAAACAATATATATACACGTGTGTTGCCACTGTAGTCCAACCCAACTTTT
1 CTAATCAAATTATTGAAAACAATATATATACACATGTGTTGCCACTGTAGTCCAACCCAACTTTT
*
5101357 GTCCTTGCAATTACGGGTCTTCAACACTTCTAACAAGCATTTTTTTTCTCTTTGAATAAAAATCG
66 GTACTTGCAATTACGGGTCTTCAACACTTCTAACAAGCATTTTTTTTCTCTTTGAATAAAAATCG
5101422 TACATTTTTTACT
131 TACATTTTTTACT
5101435 CT
1 CT
5101437 TTTACCATTT
Statistics
Matches: 141, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
143 141 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (143 bp):
CTAATCAAATTATTGAAAACAATATATATACACATGTGTTGCCACTGTAGTCCAACCCAACTTTT
GTACTTGCAATTACGGGTCTTCAACACTTCTAACAAGCATTTTTTTTCTCTTTGAATAAAAATCG
TACATTTTTTACT
Found at i:5101825 original size:2 final size:2
Alignment explanation
Indices: 5101818--5101847 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5101808 GAAGATTGAA
5101818 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
5101848 TATTTTAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5104489 original size:82 final size:82
Alignment explanation
Indices: 5104275--5104582 Score: 438
Period size: 82 Copynumber: 3.7 Consensus size: 82
5104265 GTATAAAAAA
* *
5104275 CTAAAATATTTCAGTTTATCTAAGTTGATGTGATATTTCAATGAAAAGCAAAGGACGTGAATAGT
1 CTAAAATATTTCAGTTTATCTGAGTTGATGTGAAATTTCAATGAAAAGCAAAGGACGTGAATAGT
*
5104340 GTAGATTCTCTGATT-T
66 GTAGATTCCCTGATTCT
* * * *
5104356 CAATGGAAATTATTTCAGTTTATCTGAGTTGATGTGAAATATCAATGAAAAGCGAAGGACGTAAA
1 C--T--AAAATATTTCAGTTTATCTGAGTTGATGTGAAATTTCAATGAAAAGCAAAGGACGTGAA
5104421 TAGTGTAGATTCCCTGATTCT
62 TAGTGTAGATTCCCTGATTCT
* *
5104442 CTAAAATATTTCAGTTTATATGAGTTGATGTGAAATGTCAATGAAAAGCAAAGGACGTGAATAGT
1 CTAAAATATTTCAGTTTATCTGAGTTGATGTGAAATTTCAATGAAAAGCAAAGGACGTGAATAGT
* *
5104507 ATAGATTCCCTTATTCT
66 GTAGATTCCCTGATTCT
* * * *
5104524 CTAAAAAATTTTAGTTTATCTGAGTTGATGTGATATTTCAATGAAAAGCAAAGAACGTG
1 CTAAAATATTTCAGTTTATCTGAGTTGATGTGAAATTTCAATGAAAAGCAAAGGACGTG
5104583 CGTATTGTAT
Statistics
Matches: 202, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
81 1 0.00
82 126 0.62
83 1 0.00
84 1 0.00
85 71 0.35
86 2 0.01
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.34
Consensus pattern (82 bp):
CTAAAATATTTCAGTTTATCTGAGTTGATGTGAAATTTCAATGAAAAGCAAAGGACGTGAATAGT
GTAGATTCCCTGATTCT
Found at i:5104627 original size:167 final size:164
Alignment explanation
Indices: 5104276--5104581 Score: 409
Period size: 167 Copynumber: 1.8 Consensus size: 164
5104266 TATAAAAAAC
* * * *
5104276 TAAAATATTTCAGTTTATCTAAGTTGATGTGATATTTCAATGAAAAGCAAAGGACGTGAATAGTG
1 TAAAATATTTCAGTTTATATAAGTTGATGTGAAATGTCAATGAAAAGCAAAGGACGTGAATAGTA
*
5104341 TAGATTCTCTGATTTCAATGGAAATTATTTCAGTTTATCTGAGTTGATGTGAAATATCAATGAAA
66 TAGATTCCCTGATTTCAA--GAAA-TATTTCAGTTTATCTGAGTTGATGTGAAATATCAATGAAA
* * * * * *
5104406 AGCGAAGGACGTAAATAGTGTAGATTCCCTGATTCTC
128 AGCAAAGAACGTAAATAGTGTAGATTACATAATTCTA
*
5104443 TAAAATATTTCAGTTTATATGAGTTGATGTGAAATGTCAATGAAAAGCAAAGGACGTGAATAGTA
1 TAAAATATTTCAGTTTATATAAGTTGATGTGAAATGTCAATGAAAAGCAAAGGACGTGAATAGTA
* * * *
5104508 TAGATTCCCTTATTCTCTAA-AAA-ATTTTAGTTTATCTGAGTTGATGTGATATTTCAATGAAAA
66 TAGATTCCCTGATT-TC-AAGAAATATTTCAGTTTATCTGAGTTGATGTGAAATATCAATGAAAA
5104571 GCAAAGAACGT
129 GCAAAGAACGT
5104582 GCGTATTGTA
Statistics
Matches: 125, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
164 46 0.37
166 3 0.02
167 72 0.58
168 2 0.02
169 2 0.02
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (164 bp):
TAAAATATTTCAGTTTATATAAGTTGATGTGAAATGTCAATGAAAAGCAAAGGACGTGAATAGTA
TAGATTCCCTGATTTCAAGAAATATTTCAGTTTATCTGAGTTGATGTGAAATATCAATGAAAAGC
AAAGAACGTAAATAGTGTAGATTACATAATTCTA
Found at i:5119655 original size:27 final size:27
Alignment explanation
Indices: 5119625--5119679 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
5119615 CCTAGAGTTA
5119625 AATAATTTACCGATCTTAAATATGCTT
1 AATAATTTACCGATCTTAAATATGCTT
5119652 AATAATTTACCGATCTTAAATATGCTT
1 AATAATTTACCGATCTTAAATATGCTT
5119679 A
1 A
5119680 CTTGGGTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (27 bp):
AATAATTTACCGATCTTAAATATGCTT
Found at i:5125916 original size:22 final size:21
Alignment explanation
Indices: 5125891--5125932 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5125881 TGAGTTCACT
5125891 ATGGATGCTTAAGTTTTCTTTA
1 ATGGATGCTT-AGTTTTCTTTA
* *
5125913 ATGGATGGTTGGTTTTCTTT
1 ATGGATGCTTAGTTTTCTTT
5125933 TTATACTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.17, C:0.07, G:0.24, T:0.52
Consensus pattern (21 bp):
ATGGATGCTTAGTTTTCTTTA
Found at i:5129330 original size:24 final size:24
Alignment explanation
Indices: 5129303--5129352 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
5129293 ATAAAGAACC
5129303 AAAATAAACTT-AAACATACCATTA
1 AAAATAAACTTGAAACAT-CCATTA
*
5129327 AAAATAAAGTTGAAACATCCATTA
1 AAAATAAACTTGAAACATCCATTA
5129351 AA
1 AA
5129353 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.58, C:0.14, G:0.04, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTGAAACATCCATTA
Found at i:5131586 original size:15 final size:15
Alignment explanation
Indices: 5131553--5131595 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
5131543 AAAATAATAT
* *
5131553 TAAAATTAAAACTAA
1 TAAAAATAAAACAAA
5131568 -AAAAATAAAACAAA
1 TAAAAATAAAACAAA
5131582 TAAAAAT-AAACAAA
1 TAAAAATAAAACAAA
5131596 CAAATACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (15 bp):
TAAAAATAAAACAAA
Found at i:5134756 original size:24 final size:24
Alignment explanation
Indices: 5134729--5134778 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
5134719 ATAAAGAACC
5134729 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
5134753 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
5134777 AA
1 AA
5134779 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:5136303 original size:15 final size:15
Alignment explanation
Indices: 5136283--5136314 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5136273 ATACAAAAAT
*
5136283 AAAAATAGAAGATAA
1 AAAAATAAAAGATAA
5136298 AAAAATAAAAGATAA
1 AAAAATAAAAGATAA
5136313 AA
1 AA
5136315 TGAAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (15 bp):
AAAAATAAAAGATAA
Found at i:5136338 original size:16 final size:17
Alignment explanation
Indices: 5136317--5136382 Score: 72
Period size: 16 Copynumber: 4.1 Consensus size: 17
5136307 AGATAAAATG
5136317 AAATATATA-AAATAAT
1 AAATATATATAAATAAT
5136333 AAATATATATAACAT-AT
1 AAATATATATAA-ATAAT
5136350 -AAT-TATAGT-AATAA-
1 AAATATATA-TAAATAAT
5136364 AAATATATATAAATAAT
1 AAATATATATAAATAAT
5136381 AA
1 AA
5136383 TGATATATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
14 2 0.05
15 10 0.24
16 22 0.52
17 6 0.14
18 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
AAATATATATAAATAAT
Done.