Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008755.1 Hibiscus syriacus cultivar Beakdansim tig00111847_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: 3030620
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 14
Found at i:20135 original size:77 final size:79
Alignment explanation
Indices: 20005--20151 Score: 194
Period size: 77 Copynumber: 1.9 Consensus size: 79
19995 ATATAGTAAG
*
20005 TAAACATTAAAAGAATGTAATTTTGATTACAACTCTTTTAATCGATATTTAATTCAGAA-TAATT
1 TAAACATTAAAAGAATGTAATTATGATTACAACTCTTTTAATCGATATTTAATT-AGAATTAATT
20069 AAATAAGAATTTAAA
65 AAATAAGAATTTAAA
* * * * *
20084 TAAACATT-AAAGATTGTAATTCAT-ATTATAAGTC-TTTAATGGATATTTAATTTGAATTAATT
1 TAAACATTAAAAGAATGTAATT-ATGATTACAACTCTTTTAATCGATATTTAATTAGAATTAATT
20146 AAATAA
65 AAATAA
20152 TTATTTTTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
76 3 0.05
77 28 0.47
78 20 0.33
79 9 0.15
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (79 bp):
TAAACATTAAAAGAATGTAATTATGATTACAACTCTTTTAATCGATATTTAATTAGAATTAATTA
AATAAGAATTTAAA
Found at i:21461 original size:43 final size:43
Alignment explanation
Indices: 21378--21480 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 43
21368 GACGCTGATT
*
21378 CAACTCCTTCTGTGAAGAACCAAGCGAAAGATTTTCACTAATC
1 CAACTCCTTCTATGAAGAACCAAGCGAAAGATTTTCACTAATC
** * * *
21421 CAACTCCTTCTATGAAGAATTAAGTGAAA-TTTTGTTACTAATC
1 CAACTCCTTCTATGAAGAACCAAGCGAAAGATTT-TCACTAATC
*
21464 CAACTCCTTCTCTGAAG
1 CAACTCCTTCTATGAAG
21481 GACCGAGTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
42 3 0.06
43 49 0.94
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (43 bp):
CAACTCCTTCTATGAAGAACCAAGCGAAAGATTTTCACTAATC
Found at i:21558 original size:43 final size:44
Alignment explanation
Indices: 21499--21586 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 44
21489 AATAGGAAAA
* * *
21499 ATGTTGATCAAACTCCTTTTGTGA-AGAATCAAGAAAAATGTTG
1 ATGTTGATCAAACTCCTTCTGCGATAGAATCAAGAAAAAGGTTG
* * * *
21542 ATGTTGATCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTG
1 ATGTTGATCAAACTCCTTCTGCGATAGAATCAAGAAAAAGGTTG
21586 A
1 A
21587 ACATGTTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 20 0.54
44 17 0.46
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (44 bp):
ATGTTGATCAAACTCCTTCTGCGATAGAATCAAGAAAAAGGTTG
Found at i:21753 original size:119 final size:119
Alignment explanation
Indices: 21554--21781 Score: 332
Period size: 119 Copynumber: 1.9 Consensus size: 119
21544 GTTGATCTAT
* * *
21554 CTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAACATGTTTTTCTCATTATGAACTTCTTCTCTC
1 CTCCTTCTGCGATAGAATCAAGCAAAAGGTCGAACATGTTCTTCTCATTATGAACTTCTTCTCTC
** *
21619 TTTTTGGACGAGTTCTTCTCATTATGAACACTTCCATTGGAAATGTTAATCCAA
66 TCCTCGGACGAGTTCTTCTCATTATGAACACTTCCATTGGAAATGTTAATCCAA
* ** *
21673 CTCCTTCTGTGATAGAATTTAGTAAAAGGTCGAACATGTTCTTCTCATTATGAACTTCTTCT-TC
1 CTCCTTCTGCGATAGAATCAAGCAAAAGGTCGAACATGTTCTTCTCATTATGAACTTCTTCTCT-
* *
21737 CTCCTCGGATGAGTTCTTCTCATTATGAACTCTTCCATTGGAAAT
65 CTCCTCGGACGAGTTCTTCTCATTATGAACACTTCCATTGGAAAT
21782 ATTGATCCCT
Statistics
Matches: 96, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
118 1 0.01
119 95 0.99
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (119 bp):
CTCCTTCTGCGATAGAATCAAGCAAAAGGTCGAACATGTTCTTCTCATTATGAACTTCTTCTCTC
TCCTCGGACGAGTTCTTCTCATTATGAACACTTCCATTGGAAATGTTAATCCAA
Found at i:21987 original size:139 final size:139
Alignment explanation
Indices: 21698--22059 Score: 510
Period size: 139 Copynumber: 2.6 Consensus size: 139
21688 AATTTAGTAA
* * * *
21698 AAGGTCGAACATGTTCTTCTCATTATGAACTTCTTCTTCC-TCCTCGGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTAATTATGAACTTCTTC-TCCTTCATCGGATGAGTTCTTCTCATTA
* **
21762 TGAACTCTTCCATTGGAAATATTGATCCCTCGAGTAAGATGTCGTTGATTCAACTCCATATGCGA
65 TGAACTC-TCCACTGGAAATATTGATCCCTCGAGTAAGATGTCACTGATTCAACTCCATATGCGA
* *
21827 TGAATTGAGTT
129 TGAATCGAGCT
* *
21838 AAGGTTGAACAAGTTCTTCTTATTATGAACATCTTCTCCTTCATCGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTAATTATGAACTTCTTCTCCTTCATCGGATGAGTTCTTCTCATTAT
* * * * * *
21903 GAATTCTCCACTGGAAATATTGATTCCTTGAGTAAGGTGTCACTGTTTCAACTCCATATGTGATG
66 GAACTCTCCACTGGAAATATTGATCCCTCGAGTAAGATGTCACTGATTCAACTCCATATGCGATG
21968 AATCGAGCT
131 AATCGAGCT
* * *
21977 AAGGTTGAACAAGTTCTTCTAACTATGAACTTTTTCTCATTCATCGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTAATTATGAACTTCTTCTCCTTCATCGGATGAGTTCTTCTCATTAT
*
22042 GAACTCTCCACTAGAAAT
66 GAACTCTCCACTGGAAAT
22060 GTTCATTGAT
Statistics
Matches: 198, Mismatches: 23, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
139 137 0.69
140 61 0.31
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.37
Consensus pattern (139 bp):
AAGGTTGAACAAGTTCTTCTAATTATGAACTTCTTCTCCTTCATCGGATGAGTTCTTCTCATTAT
GAACTCTCCACTGGAAATATTGATCCCTCGAGTAAGATGTCACTGATTCAACTCCATATGCGATG
AATCGAGCT
Found at i:23214 original size:13 final size:13
Alignment explanation
Indices: 23191--23225 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
23181 CTTGACCCCC
*
23191 TTTTTCATTTTCTT
1 TTTTTC-TTTTATT
23205 TTTTTCTTTTATT
1 TTTTTCTTTTATT
23218 TTTTTCTT
1 TTTTTCTT
23226 CAAGCATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTCTTTTATT
Found at i:31714 original size:54 final size:54
Alignment explanation
Indices: 31116--31697 Score: 790
Period size: 54 Copynumber: 10.8 Consensus size: 54
31106 TGCGGTTTGT
* * * * *
31116 ACACATAGTGCCGAAATGGTTATTCATCAACATATGATGAATTCCGTGAAAAGC
1 ACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGC
* *
31170 ACACTTAGTGCC-AAACGATTATTCATCCACCTAGGATGAATTCCGTGAAATGC
1 ACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGC
* * *
31223 ACACTTAGTGCC-AAACGGTTATTCATCCACCTAGGATGAATTCCGAGAAATGT
1 ACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGC
* * * *
31276 ACACTCAGTGCCGAAACCGTTATTCATCCATATAGGATGAATTCCGTGAAATGT
1 ACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGC
* * *
31330 ACACTTAGTGCCGAAATGATTATTCATCCACCTAGGATGAATTCCGTGAAATGC
1 ACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGC
*
31384 ACACTTAGTGCCAAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGC
1 ACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGC
* * * * *
31438 ACACTTAGTGCCAAAATGGTTATTCATCCACATATGATGAATTTCGGGAAATGC
1 ACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGC
* * * * * * *
31492 ACACATAGTGTCGAAACGATTATTCATTCACATAAGATGAATTCCTTGAAAAGC
1 ACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGC
* * * * *
31546 ACACTTAGTGCTGAAACCGTTATTCATCAACCTAGGATGAATTCCATGAAATGC
1 ACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGC
* * *
31600 ACACTTAGTGCCGAAACGGTTATTCATCCATATATGATGAATTCTGTGAAATGC
1 ACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGC
* *
31654 ACACTTAATGCCGAAACGATTATTCATCCACATAGGATGAATTC
1 ACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTC
31698 TGTGGTTTGT
Statistics
Matches: 463, Mismatches: 64, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
53 96 0.21
54 367 0.79
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (54 bp):
ACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGC
Found at i:37807 original size:48 final size:43
Alignment explanation
Indices: 37745--37859 Score: 131
Period size: 48 Copynumber: 2.6 Consensus size: 43
37735 TCCACTTTCT
* * *
37745 CTGAAGTGATTATCAAATCTTGGAACAGAAAGACCTGTTCTGCTTA
1 CTGAAGGGAATATCAGATCTTGGAACAGAAAGA-CTGTTC--CTTA
** *
37791 CGCTGAAGGGAATATCAGATCTTGGAGGAGAGAGACTGTTCCTTA
1 --CTGAAGGGAATATCAGATCTTGGAACAGAAAGACTGTTCCTTA
37836 CTGAAGGGAATATCAGATCTTGGA
1 CTGAAGGGAATATCAGATCTTGGA
37860 GGAGTTTGAT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
43 24 0.39
45 4 0.07
47 6 0.10
48 27 0.44
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (43 bp):
CTGAAGGGAATATCAGATCTTGGAACAGAAAGACTGTTCCTTA
Found at i:38024 original size:114 final size:115
Alignment explanation
Indices: 37787--38241 Score: 563
Period size: 115 Copynumber: 4.0 Consensus size: 115
37777 ACCTGTTCTG
* * * ** *
37787 CTTACGCTGAAGGGAATATCAGATCTTGGAGGAGAGAGAC-TGTT-C-CTTA--CTGAAGGGAAT
1 CTTACTCTAAAGGGAATATCAAATCTTGGAAAAGAGAGACTTGTTCCACTTACTCTGAAAGGAAT
* * *** *
37847 ATCAGATCTTGGAGGAGTTTGATCCATTGAATCAAAATAGACCTGTTCCA
66 ATCAGATCTTGAAGGAGTTTGATCCATTGAATCGAGGCAGACTTGTTCCA
* ** *
37897 CTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACTTGTTCTGCTTACTTTGAAAGGAAT
1 CTTACTCTAAAGGGAATATCAAATCTTGGAAAAGAGAGACTTGTTCCACTTACTCTGAAAGGAAT
* *
37962 ATCAGATC-TGAAGG-GTTTTAATCCATTGAATCGGGGCAGACTTGTTCCA
66 ATCAGATCTTGAAGGAG-TTTGATCCATTGAATCGAGGCAGACTTGTTCCA
*
38011 CTTACTCTAAAGGGAATATCAAATCTTGGGAAAGAGAGACCTT-TTCCACTTACTCT-AAAGGGA
1 CTTACTCTAAAGGGAATATCAAATCTTGGAAAAGAGAGA-CTTGTTCCACTTACTCTGAAA-GGA
* * * * *
38074 ATATCAGATCTTGGAGAAGTTTGATCCATTAAATCGGGGAAGACTTGTTCCA
64 ATATCAGATCTTGAAGGAGTTTGATCCATTGAATCGAGGCAGACTTGTTCCA
* *
38126 CTTACTCTAAAGGGAATATCAAATCTTGGGAAAGAGAGACATGTTCCACTTACTCTG-AAGGAAT
1 CTTACTCTAAAGGGAATATCAAATCTTGGAAAAGAGAGACTTGTTCCACTTACTCTGAAAGGAAT
*
38190 ATCAGATC-TGAAGGAGTTTGATCCATTGAATCGAGGCAAACTTGTTCCA
66 ATCAGATCTTGAAGGAGTTTGATCCATTGAATCGAGGCAGACTTGTTCCA
38239 CTT
1 CTT
38242 GTCTTTAATA
Statistics
Matches: 301, Mismatches: 32, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
110 36 0.12
111 4 0.01
113 46 0.15
114 106 0.35
115 108 0.36
116 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (115 bp):
CTTACTCTAAAGGGAATATCAAATCTTGGAAAAGAGAGACTTGTTCCACTTACTCTGAAAGGAAT
ATCAGATCTTGAAGGAGTTTGATCCATTGAATCGAGGCAGACTTGTTCCA
Found at i:38139 original size:115 final size:113
Alignment explanation
Indices: 37787--38241 Score: 532
Period size: 114 Copynumber: 4.0 Consensus size: 113
37777 ACCTGTTCTG
* * * * * * *
37787 CTTACGCTGAAGGGAATATCAGATCTT-GGAGGAGAGAGA-CTGTT-C-CTTACT-GAAGGGAAT
1 CTTACTCTAAAGGGAATATCAAATCTTGGGA-AAGAGAGACCTTTTCCACTTACTCTAAAGGAAT
* *** *
37847 ATCAGATCTTGGAGGAGTTTGATCCATTGAATC-AAAATAGACCTGTTCCA
65 ATCAGATC-TGAAGGAGTTTGATCCATTGAATCGGGGA-AGACTTGTTCCA
* * ** *
37897 CTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGA-CTTGTTCTGCTTACTTTGAAAGGAA
1 CTTACTCTAAAGGGAATATCAAATCTTGGGAAAGAGAGACCTT-TTCCACTTACTCT-AAAGGAA
* *
37961 TATCAGATCTGAAGG-GTTTTAATCCATTGAATCGGGGCAGACTTGTTCCA
64 TATCAGATCTGAAGGAG-TTTGATCCATTGAATCGGGGAAGACTTGTTCCA
38011 CTTACTCTAAAGGGAATATCAAATCTTGGGAAAGAGAGACCTTTTCCACTTACTCTAAAGGGAAT
1 CTTACTCTAAAGGGAATATCAAATCTTGGGAAAGAGAGACCTTTTCCACTTACTCTAAA-GGAAT
* * *
38076 ATCAGATCTTGGAGAAGTTTGATCCATTAAATCGGGGAAGACTTGTTCCA
65 ATCAGATC-TGAAGGAGTTTGATCCATTGAATCGGGGAAGACTTGTTCCA
* * *
38126 CTTACTCTAAAGGGAATATCAAATCTTGGGAAAGAGAGACATGTTCCACTTACTCTGAAGGAATA
1 CTTACTCTAAAGGGAATATCAAATCTTGGGAAAGAGAGACCTTTTCCACTTACTCTAAAGGAATA
*
38191 TCAGATCTGAAGGAGTTTGATCCATTGAATCGAGGCAA-ACTTGTTCCA
66 TCAGATCTGAAGGAGTTTGATCCATTGAATCG-GGGAAGACTTGTTCCA
38239 CTT
1 CTT
38242 GTCTTTAATA
Statistics
Matches: 300, Mismatches: 32, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
110 34 0.11
111 4 0.01
113 45 0.15
114 108 0.36
115 108 0.36
116 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (113 bp):
CTTACTCTAAAGGGAATATCAAATCTTGGGAAAGAGAGACCTTTTCCACTTACTCTAAAGGAATA
TCAGATCTGAAGGAGTTTGATCCATTGAATCGGGGAAGACTTGTTCCA
Found at i:39131 original size:12 final size:12
Alignment explanation
Indices: 39116--39184 Score: 65
Period size: 12 Copynumber: 5.9 Consensus size: 12
39106 TTTTTATGTA
39116 CTTTTTTTCTTT
1 CTTTTTTTCTTT
39128 C-TTTTTTCTTTT
1 CTTTTTTTC-TTT
*
39140 CTTCTTATTC-TT
1 CTT-TTTTTCTTT
39152 CTTTTTTT-TTT
1 CTTTTTTTCTTT
*
39163 -TTTTTTTTTTT
1 CTTTTTTTCTTT
*
39174 CTATTTTTCTT
1 CTTTTTTTCTT
39185 CAAGCAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
10 7 0.15
11 16 0.34
12 18 0.38
13 1 0.02
14 5 0.11
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (12 bp):
CTTTTTTTCTTT
Found at i:39180 original size:9 final size:8
Alignment explanation
Indices: 39120--39184 Score: 64
Period size: 8 Copynumber: 8.2 Consensus size: 8
39110 TATGTACTTT
39120 TTTTCTTTC
1 TTTT-TTTC
39129 -TTTTTTC
1 TTTTTTTC
*
39136 TTTTCTTC
1 TTTTTTTC
*
39144 TTATTCTTC
1 TT-TTTTTC
39153 TTTTTTT-
1 TTTTTTTC
39160 TTTTTTT-
1 TTTTTTTC
39167 TTTTTTTC
1 TTTTTTTC
*
39175 TATTTTTC
1 TTTTTTTC
39183 TT
1 TT
39185 CAAGCAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
7 18 0.37
8 23 0.47
9 8 0.16
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:54123 original size:54 final size:54
Alignment explanation
Indices: 54065--54727 Score: 614
Period size: 54 Copynumber: 12.4 Consensus size: 54
54055 GCCCATACGA
* * *** *
54065 TTATTCATAAACCTATTATGAATTCTGTGGTTTGCACACATAGTGCCGAAATGG
1 TTATTCATCAACCTATGATGAATTCTGTGAAATGCACACTTAGTGCCGAAATGG
* * *
54119 TTATTCATCAACGTATGATGAATTCTGTGGAATGCACACTTAGTGTCGAAATGG
1 TTATTCATCAACCTATGATGAATTCTGTGAAATGCACACTTAGTGCCGAAATGG
* * * * *
54173 TTATTCATCCACCTAGGATGAATTCCT-TGAAATGTACACTTAGTGCTGAAATAG
1 TTATTCATCAACCTATGATGAATT-CTGTGAAATGCACACTTAGTGCCGAAATGG
* * *
54227 TTATTCATCCACCTAAGATGAATT-TCGTGAAATGCACACTTAGTGTCGAAATGG
1 TTATTCATCAACCTATGATGAATTCT-GTGAAATGCACACTTAGTGCCGAAATGG
* * * * * *
54281 TTATTCATCCACATAGGAT-AATTCCGTGAAATGCACACTTAGTACCGAAACGG
1 TTATTCATCAACCTATGATGAATTCTGTGAAATGCACACTTAGTGCCGAAATGG
* * * * * *
54334 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAATGCCGAAACGG
1 TTATTCATCAACCTATGATGAATTCTGTGAAATGCACACTTAGTGCCGAAATGG
* * * ** * *
54388 TTATTCATCCA-C-AT-A-GGA---TG-AAAATGCACTTTTAGTGCCAAAATAG
1 TTATTCATCAACCTATGATGAATTCTGTGAAATGCACACTTAGTGCCGAAATGG
* * * *
54434 TTATTTATCCACCTATGATGAATTTTGTGAAATGCACACTTAGTGCCGAAACGG
1 TTATTCATCAACCTATGATGAATTCTGTGAAATGCACACTTAGTGCCGAAATGG
* *
54488 TTATTCATCCACCTA-GAATGAATTCTGTGAAATGCACACTTAGTGTCGAAATGG
1 TTATTCATCAACCTATG-ATGAATTCTGTGAAATGCACACTTAGTGCCGAAATGG
* * * * *
54542 TTATTCATCAACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGA
1 TTATTCATCAACCTATGATGAATTCTGTGAAATGCACACTTAGTGCCGAAATGG
* * * ** * * *
54596 TTATTCATCCACATAGGACAAATTCTATGAAAAGCACACTTAGTGCCGAAACGG
1 TTATTCATCAACCTATGATGAATTCTGTGAAATGCACACTTAGTGCCGAAATGG
* * * ** *
54650 TTATTTATCCACCTAGGATGAATT-TCGTGAAATGCACACTTAGTGTTGAAACGG
1 TTATTCATCAACCTATGATGAATTCT-GTGAAATGCACACTTAGTGCCGAAATGG
* * * *
54704 TTATTCCTCCACATAGGATGAATT
1 TTATTCATCAACCTATGATGAATT
54728 TCGTGGTTTT
Statistics
Matches: 518, Mismatches: 75, Indels: 32
0.83 0.12 0.05
Matches are distributed among these distances:
46 29 0.06
47 2 0.00
48 2 0.00
49 1 0.00
50 4 0.01
51 1 0.00
52 2 0.00
53 52 0.10
54 422 0.81
55 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (54 bp):
TTATTCATCAACCTATGATGAATTCTGTGAAATGCACACTTAGTGCCGAAATGG
Found at i:54247 original size:108 final size:107
Alignment explanation
Indices: 54097--54727 Score: 760
Period size: 108 Copynumber: 5.9 Consensus size: 107
54087 TTCTGTGGTT
* * * * *
54097 TGCACACATAGTGCCGAAATGGTTATTCATCAACGTATGATGAATTCTGTGGAATGCACACTTAG
1 TGCACACTTAGTGCCGAAATGGTTATTCATCCACCTAGGATGAATTCTGTGAAATGCACACTTAG
* * *
54162 TGTCGAAATGGTTATTCATCCACCTAGGATGAATTCCTTGAAA
66 TGCCGAAACGGTTATTCATCCACATAGGATGAATT-CTTGAAA
* * * *
54205 TGTACACTTAGTGCTGAAATAGTTATTCATCCACCTAAGATGAATT-TCGTGAAATGCACACTTA
1 TGCACACTTAGTGCCGAAATGGTTATTCATCCACCTAGGATGAATTCT-GTGAAATGCACACTTA
* * *
54269 GTGTCGAAATGGTTATTCATCCACATAGGAT-AATTCCGTGAAA
65 GTGCCGAAACGGTTATTCATCCACATAGGATGAATT-CTTGAAA
* * * * *
54312 TGCACACTTAGTACCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAA
1 TGCACACTTAGTGCCGAAATGGTTATTCATCCACCTAGGATGAATTCTGTGAAATGCACACTTAG
54377 TGCCGAAACGGTTATTCATCCACATAGGATG-A------AAA
66 TGCCGAAACGGTTATTCATCCACATAGGATGAATTCTTGAAA
** * * * * *
54412 TGCACTTTTAGTGCCAAAATAGTTATTTATCCACCTATGATGAATTTTGTGAAATGCACACTTAG
1 TGCACACTTAGTGCCGAAATGGTTATTCATCCACCTAGGATGAATTCTGTGAAATGCACACTTAG
* *
54477 TGCCGAAACGGTTATTCATCCACCTAGAATGAATTCTGTGAAA
66 TGCCGAAACGGTTATTCATCCACATAGGATGAATTCT-TGAAA
* * * *
54520 TGCACACTTAGTGTCGAAATGGTTATTCATCAACATAGGATGAATTCCGTGAAATGCACACTTAG
1 TGCACACTTAGTGCCGAAATGGTTATTCATCCACCTAGGATGAATTCTGTGAAATGCACACTTAG
* **
54585 TGCCGAAACGATTATTCATCCACATAGGACAAATTCTATGAAA
66 TGCCGAAACGGTTATTCATCCACATAGGATGAATTCT-TGAAA
* * *
54628 AGCACACTTAGTGCCGAAACGGTTATTTATCCACCTAGGATGAATT-TCGTGAAATGCACACTTA
1 TGCACACTTAGTGCCGAAATGGTTATTCATCCACCTAGGATGAATTCT-GTGAAATGCACACTTA
** *
54692 GTGTTGAAACGGTTATTCCTCCACATAGGATGAATT
65 GTGCCGAAACGGTTATTCATCCACATAGGATGAATT
54728 TCGTGGTTTT
Statistics
Matches: 446, Mismatches: 65, Indels: 24
0.83 0.12 0.04
Matches are distributed among these distances:
100 85 0.19
101 1 0.00
107 96 0.22
108 264 0.59
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (107 bp):
TGCACACTTAGTGCCGAAATGGTTATTCATCCACCTAGGATGAATTCTGTGAAATGCACACTTAG
TGCCGAAACGGTTATTCATCCACATAGGATGAATTCTTGAAA
Found at i:57349 original size:22 final size:23
Alignment explanation
Indices: 57300--57350 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
57290 TATGTATACG
*
57300 TGATATGTGATAGAAGAAAAAGA
1 TGATATGTGATACAAGAAAAAGA
* *
57323 T-ATATGTGATACATG-AAAATA
1 TGATATGTGATACAAGAAAAAGA
57344 TGATATG
1 TGATATG
57351 ATCCATATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 6 0.25
22 17 0.71
23 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.29
Consensus pattern (23 bp):
TGATATGTGATACAAGAAAAAGA
Found at i:66037 original size:28 final size:28
Alignment explanation
Indices: 65997--66053 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
65987 GCTCGAATAG
65997 ATCCACTACTGCAGCATCAATATATCCC
1 ATCCACTACTGCAGCATCAATATATCCC
66025 ATCCACTACTGCAGCATCAATATATCCC
1 ATCCACTACTGCAGCATCAATATATCCC
66053 A
1 A
66054 AGGCATTCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.35, G:0.07, T:0.25
Consensus pattern (28 bp):
ATCCACTACTGCAGCATCAATATATCCC
Found at i:70672 original size:24 final size:24
Alignment explanation
Indices: 70642--70745 Score: 88
Period size: 23 Copynumber: 4.4 Consensus size: 24
70632 CATTGAAGTG
70642 CCACGTAGAATTTATCCCAAAGGA
1 CCACGTAGAATTTATCCCAAAGGA
* *
70666 CCGCGTAGAATTTGTCCCGAAA-GA
1 CCACGTAGAATTTATCCC-AAAGGA
* **
70690 CCACATAGAA-TTATCCTTAAGGA
1 CCACGTAGAATTTATCCCAAAGGA
** * *
70713 CCATATAG-ATTTGTCCCGAAGGA
1 CCACGTAGAATTTATCCCAAAGGA
*
70736 CCGCGTAGAA
1 CCACGTAGAA
70746 CCCTCGACTC
Statistics
Matches: 62, Mismatches: 14, Indels: 8
0.74 0.17 0.10
Matches are distributed among these distances:
22 3 0.05
23 29 0.47
24 27 0.44
25 3 0.05
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (24 bp):
CCACGTAGAATTTATCCCAAAGGA
Found at i:70714 original size:47 final size:47
Alignment explanation
Indices: 70642--70737 Score: 113
Period size: 46 Copynumber: 2.0 Consensus size: 47
70632 CATTGAAGTG
* * *
70642 CCACGTAGAATTTATCCCAAAGGACCGCGTAGAATTTGTCCCGAAAGA
1 CCACATAGAATTTATCCCAAAGGACCACATAG-ATTTGTCCCGAAAGA
** * *
70690 CCACATAGAA-TTATCCTTAAGGACCATATAGATTTGTCCCGAAGGA
1 CCACATAGAATTTATCCCAAAGGACCACATAGATTTGTCCCGAAAGA
70736 CC
1 CC
70738 GCGTAGAACC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
46 16 0.39
47 16 0.39
48 9 0.22
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (47 bp):
CCACATAGAATTTATCCCAAAGGACCACATAGATTTGTCCCGAAAGA
Found at i:76519 original size:25 final size:25
Alignment explanation
Indices: 76485--76540 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
76475 TTTGATTGTA
76485 AGCTGTAATCGGGACGTGGAGGGAC
1 AGCTGTAATCGGGACGTGGAGGGAC
76510 AGCTGTAATCGGGACGTGGAGGGAC
1 AGCTGTAATCGGGACGTGGAGGGAC
76535 AGCTGT
1 AGCTGT
76541 TGGAGCGGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.23, C:0.16, G:0.43, T:0.18
Consensus pattern (25 bp):
AGCTGTAATCGGGACGTGGAGGGAC
Found at i:81447 original size:2 final size:2
Alignment explanation
Indices: 81440--81473 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
81430 AAATCCTTTC
81440 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
81474 TCATCAGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84977 original size:15 final size:16
Alignment explanation
Indices: 84959--84992 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
84949 TATGAACATC
84959 AAATAAAATAACAA-A
1 AAATAAAATAACAATA
*
84974 AAATAGAATAACAATA
1 AAATAAAATAACAATA
84990 AAA
1 AAA
84993 ATAATTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (16 bp):
AAATAAAATAACAATA
Found at i:87127 original size:3 final size:3
Alignment explanation
Indices: 87119--87160 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
87109 TAAAATTAAA
*
87119 AAT AAT AAT AAT AAT AAT AGTT AAT AAT AATT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AA-T AAT AAT AAT A
87161 TAAAAAAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 30 0.86
4 5 0.14
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:87158 original size:10 final size:10
Alignment explanation
Indices: 87121--87159 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
87111 AAATTAAAAA
87121 TAATAATAA-
1 TAATAATAAT
*
87130 TAATAATAGT
1 TAATAATAAT
87140 TAATAATAAT
1 TAATAATAAT
87150 TAATAATAAT
1 TAATAATAAT
87160 ATAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 8 0.30
10 19 0.70
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (10 bp):
TAATAATAAT
Found at i:87636 original size:130 final size:134
Alignment explanation
Indices: 87348--87656 Score: 382
Period size: 135 Copynumber: 2.3 Consensus size: 134
87338 GTTCGGGTCG
** * *
87348 TCTAAGGGTGACACGGTTCATACGTGATGAGGAAATCTGGTC-GAAGGATGACACGACTCATACG
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCAGAAGGATGACACGACTCATACG
* *
87412 TGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGC
66 TGATGAAGAGTTCTTGGCCATCTTTA-GAA-GGTGATAACTCAGTTCCTACGCAATGAGGACGGC
87477 TGGTTA
129 TGGTTA
* * *
87483 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTAGTCAG-GGGATGACACTG-CTCCTAC
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCAGAAGGATGACAC-GACTCATAC
* *
87546 GTGATGAAGAGTTCTTGGCCAT-TTTA-TA-GTGATAACAT-AGTTCCTACGTAATGAGGACGGC
65 GTGATGAAGAGTTCTTGGCCATCTTTAGAAGGTGATAAC-TCAGTTCCTACGCAATGAGGACGGC
87607 TGGTTA
129 TGGTTA
* * **
87613 TCTAATGTTGACGTTG-CTCCTACGTGATGAGGAGATCTGGTCAG
1 TCTAAGGGTGAC-ACGACTCCTACGTGATGAGGAGATCTGGTCAG
87657 CTGATGTTGA
Statistics
Matches: 154, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
130 71 0.46
131 2 0.01
132 1 0.01
134 4 0.03
135 74 0.48
136 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.27
Consensus pattern (134 bp):
TCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCAGAAGGATGACACGACTCATACG
TGATGAAGAGTTCTTGGCCATCTTTAGAAGGTGATAACTCAGTTCCTACGCAATGAGGACGGCTG
GTTA
Found at i:88625 original size:11 final size:11
Alignment explanation
Indices: 88595--88625 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
88585 TTTATTTAAT
88595 TTTTTTTTTGA
1 TTTTTTTTTGA
*
88606 TTTTCTTTTGA
1 TTTTTTTTTGA
88617 TTTTTTTTT
1 TTTTTTTTT
88626 AAGTGTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTGA
Found at i:100304 original size:15 final size:16
Alignment explanation
Indices: 100286--100319 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
100276 TATGAACATC
100286 AAATAAAATAACAA-A
1 AAATAAAATAACAATA
*
100301 AAATAGAATAACAATA
1 AAATAAAATAACAATA
100317 AAA
1 AAA
100320 ATAATTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (16 bp):
AAATAAAATAACAATA
Found at i:100500 original size:2 final size:2
Alignment explanation
Indices: 100493--100556 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
100483 AAAGAATACC
100493 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
100535 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
100557 TAATTAAAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:102496 original size:3 final size:3
Alignment explanation
Indices: 102488--102530 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
102478 TAAAATTAAA
*
102488 AAT AAT AAT AAT AAT AAT AGTT AAT AAT AATT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AA-T AAT AAT AAT AA
102531 AAAAACCCGG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 31 0.86
4 5 0.14
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:102527 original size:10 final size:10
Alignment explanation
Indices: 102490--102528 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
102480 AAATTAAAAA
102490 TAATAATAA-
1 TAATAATAAT
*
102499 TAATAATAGT
1 TAATAATAAT
102509 TAATAATAAT
1 TAATAATAAT
102519 TAATAATAAT
1 TAATAATAAT
102529 AAAAAAACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 8 0.30
10 19 0.70
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (10 bp):
TAATAATAAT
Found at i:102530 original size:13 final size:12
Alignment explanation
Indices: 102488--102530 Score: 59
Period size: 13 Copynumber: 3.4 Consensus size: 12
102478 TAAAATTAAA
102488 AATAATAATAAT
1 AATAATAATAAT
*
102500 AATAATAGTTAAT
1 AATAATA-ATAAT
102513 AATAATTAATAAT
1 AATAA-TAATAAT
102526 AATAA
1 AATAA
102531 AAAAACCCGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 7 0.26
13 18 0.67
14 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (12 bp):
AATAATAATAAT
Found at i:103219 original size:3 final size:3
Alignment explanation
Indices: 103201--103296 Score: 160
Period size: 3 Copynumber: 32.3 Consensus size: 3
103191 TTTCATTAAA
*
103201 ATT ATT CTT GATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
103246 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
103293 ATT A
1 ATT A
103297 CAAATACAAA
Statistics
Matches: 88, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
2 4 0.05
3 82 0.93
4 2 0.02
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:104935 original size:22 final size:22
Alignment explanation
Indices: 104873--104917 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
104863 TAAATAAATA
104873 TCTTATTTATATATTAATAGAT
1 TCTTATTTATATATTAATAGAT
104895 TCTTATTTATATATTAATAGAT
1 TCTTATTTATATATTAATAGAT
104917 T
1 T
104918 TTTTTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (22 bp):
TCTTATTTATATATTAATAGAT
Found at i:105452 original size:28 final size:27
Alignment explanation
Indices: 105410--105463 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
105400 TAATTCTTTC
*
105410 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATA-TTATTA
*
105438 TTTTCATAATATTTATATATATTATT
1 TTTTCAAAATATTTATATATATTATT
105464 TTATTAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATATTATTA
Found at i:105487 original size:15 final size:16
Alignment explanation
Indices: 105459--105488 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
105449 TTTATATATA
105459 TTATTTTATTAATGTT
1 TTATTTTATTAATGTT
105475 TTATTTT-TTAATGT
1 TTATTTTATTAATGT
105489 ATTAAATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (16 bp):
TTATTTTATTAATGTT
Found at i:109041 original size:13 final size:13
Alignment explanation
Indices: 109023--109047 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
109013 ACTTTAGAGG
109023 TATTTCAAACTTC
1 TATTTCAAACTTC
109036 TATTTCAAACTT
1 TATTTCAAACTT
109048 ATACCCTCAT
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:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (13 bp):
TATTTCAAACTTC
Found at i:114575 original size:22 final size:22
Alignment explanation
Indices: 114547--114604 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
114537 TATATCTACA
*
114547 CTCTTCAAAGATGATAGATTTT
1 CTCTTCAAAGATGATAGATTCT
114569 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
* *
114591 CTTTTCAAATATGA
1 CTCTTCAAAGATGA
114605 CCTCTTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:115343 original size:73 final size:73
Alignment explanation
Indices: 115265--115803 Score: 898
Period size: 73 Copynumber: 7.4 Consensus size: 73
115255 CTATTTCCAA
115265 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
115330 CTCAGGGT
66 CTCAGGGT
* *
115338 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
*
115403 CTAAGGGT
66 CTCAGGGT
*
115411 TATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
115476 CTCAGGGT
66 CTCAGGGT
*
115484 CATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
115549 CTCAGGGT
66 CTCAGGGT
* * * * *
115557 CATCTGTAAGACCAACAGTGGATGATGTTTTCCAAAAAGCCTTCGGTAGATTTTTGATTTTAAAG
1 CATCTGTAAGACCTACAGTGCATGATGTTTT-CAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAG
**
115622 CCTCAAAGT
65 CCTCAGGGT
115631 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
115696 CTCAGGGT
66 CTCAGGGT
* * *
115704 CATCTGTAAGACTTACACTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
**
115769 CTCACTGT
66 CTCAGGGT
* *
115777 CATCTATAAGACCTACAGTGCAAGATG
1 CATCTGTAAGACCTACAGTGCATGATG
115804 ATAGGACTTC
Statistics
Matches: 432, Mismatches: 33, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
73 366 0.85
74 66 0.15
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (73 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
CTCAGGGT
Found at i:115692 original size:220 final size:219
Alignment explanation
Indices: 115265--115803 Score: 920
Period size: 220 Copynumber: 2.5 Consensus size: 219
115255 CTATTTCCAA
115265 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
*
115330 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGAT
66 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGATTTTTGAT
* *
115395 TTTAAAGCCTAAGGGTTATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGC
131 TTTAAAGCCTAAGAGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGC
115460 TTTTTGATCTTAAAGCCTCAGGGT
196 TTTTTGATCTTAAAGCCTCAGGGT
*
115484 CATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
* *
115549 CTCAGGGTCATCTGTAAGACCAACAGTGGATGATGTTTTCCAAAAAGCCTTC-GGTAGATTTTTG
66 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTT-CAAAAAGCCTTCAGG-AGATTTTTG
115613 ATTTTAAAGCCTCAA-AGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGG
129 ATTTTAAAGCCT-AAGAGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGG
115677 AGCTTTTTGATCTTAAAGCCTCAGGGT
193 AGCTTTTTGATCTTAAAGCCTCAGGGT
* * *
115704 CATCTGTAAGACTTACACTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
** * *
115769 CTCACTGTCATCTATAAGACCTACAGTGCAAGATG
66 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATG
115804 ATAGGACTTC
Statistics
Matches: 301, Mismatches: 16, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
219 103 0.34
220 196 0.65
221 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (219 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGATTTTTGAT
TTTAAAGCCTAAGAGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGC
TTTTTGATCTTAAAGCCTCAGGGT
Found at i:115978 original size:3 final size:3
Alignment explanation
Indices: 115960--116025 Score: 82
Period size: 3 Copynumber: 22.3 Consensus size: 3
115950 TTTCATTAAA
* * *
115960 ATT ATT CTT GATT ATT ATT ATT ATT ATT ATT ATT A-A AAT ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
116005 ATT ATT ATT ATT ATT -TT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
116026 CAAATACAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
2 3 0.05
3 50 0.91
4 2 0.04
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:120940 original size:20 final size:21
Alignment explanation
Indices: 120915--120957 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
120905 TGGTCATTCC
120915 CTAGCC-ATTGGGGATGATTT
1 CTAGCCGATTGGGGATGATTT
* *
120935 CTAGCCGTTTGGGGATGTTTT
1 CTAGCCGATTGGGGATGATTT
120956 CT
1 CT
120958 CTACAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.14, C:0.16, G:0.30, T:0.40
Consensus pattern (21 bp):
CTAGCCGATTGGGGATGATTT
Found at i:121831 original size:21 final size:22
Alignment explanation
Indices: 121807--121858 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
121797 CACCAAAGTG
* *
121807 CCACATA-TTTGTCCAGAATGA
1 CCACATAGTTTATCCAGAAGGA
*
121828 CCACATAGTTTTATCCCGAAGGA
1 CCACATAG-TTTATCCAGAAGGA
121851 CCACATAG
1 CCACATAG
121859 AACCCTCGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 7 0.27
23 19 0.73
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (22 bp):
CCACATAGTTTATCCAGAAGGA
Found at i:134097 original size:21 final size:21
Alignment explanation
Indices: 134071--134116 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
134061 GCTTCCCAGA
134071 ACAGAGGGTATCAGTACTCCT
1 ACAGAGGGTATCAGTACTCCT
*
134092 ACAGAGGGTATCGGTACTCCT
1 ACAGAGGGTATCAGTACTCCT
134113 ACAG
1 ACAG
134117 GGAGTACGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (21 bp):
ACAGAGGGTATCAGTACTCCT
Found at i:136920 original size:29 final size:29
Alignment explanation
Indices: 136886--136944 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
136876 GTTAAATTAA
136886 TTTGATATCATTGCTTACATCAATTTAGT
1 TTTGATATCATTGCTTACATCAATTTAGT
*
136915 TTTGATATCATTGCTTAGATCAATTTAGT
1 TTTGATATCATTGCTTACATCAATTTAGT
136944 T
1 T
136945 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (29 bp):
TTTGATATCATTGCTTACATCAATTTAGT
Found at i:151877 original size:77 final size:79
Alignment explanation
Indices: 151726--151878 Score: 188
Period size: 77 Copynumber: 2.0 Consensus size: 79
151716 ATAGTAAGTA
*
151726 AACATTAAAAGAATGTAATTATGATTACAACTCTTTTAATGGATATTTAATTCGAAATAACTAAA
1 AACATTAAAAGAATGTAATTATGATTACAACTCTTTTAATGGATATATAATTCGAAATAACTAAA
151791 TAAAGGTTTAAATG
66 TAAAGGTTTAAATG
* * * * * * *
151805 AACATT-AAAGAGTGTAATTCA-GATTATAAGTC-TTTATTGGATATATAATTTGAATTAATTAA
1 AACATTAAAAGAATGTAATT-ATGATTACAACTCTTTTAATGGATATATAATTCGAAATAACTAA
151867 AT-AAGAGTTTAA
65 ATAAAG-GTTTAA
151879 TTAATTCGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
76 3 0.05
77 33 0.52
78 21 0.33
79 7 0.11
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.37
Consensus pattern (79 bp):
AACATTAAAAGAATGTAATTATGATTACAACTCTTTTAATGGATATATAATTCGAAATAACTAAA
TAAAGGTTTAAATG
Found at i:152812 original size:30 final size:30
Alignment explanation
Indices: 152763--152825 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
152753 AGCACATAAC
* * *
152763 CCGGTTGAGAACCGGTAAAACCGGGGTGAA
1 CCGGCTGAAAACCGATAAAACCGGGGTGAA
*
152793 CCGGCTGAAAACCGATAAAACCGGTGTGAA
1 CCGGCTGAAAACCGATAAAACCGGGGTGAA
152823 CCG
1 CCG
152826 TCGGTTCTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.32, C:0.24, G:0.32, T:0.13
Consensus pattern (30 bp):
CCGGCTGAAAACCGATAAAACCGGGGTGAA
Found at i:158932 original size:22 final size:24
Alignment explanation
Indices: 158902--158958 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
158892 GGTTCAATTC
*
158902 GGGTCTGG-TTTATTTTGT-AATA
1 GGGTCTGGTTTTATTTTATAAATA
*
158924 GGGTTTGGTTTTATTTTATAAATA
1 GGGTCTGGTTTTATTTTATAAATA
*
158948 -GGTCAGGTTTT
1 GGGTCTGGTTTT
158959 TCTTTTTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 7 0.24
23 18 0.62
24 4 0.14
ACGTcount: A:0.19, C:0.04, G:0.26, T:0.51
Consensus pattern (24 bp):
GGGTCTGGTTTTATTTTATAAATA
Found at i:159944 original size:229 final size:231
Alignment explanation
Indices: 159527--160418 Score: 1128
Period size: 240 Copynumber: 3.8 Consensus size: 231
159517 TTTAGGAAAG
* * * * *
159527 ATTTAAATGAGAAACTTTGGAATTCGCTTTCTCATTTTTCA-AAAATTAAGTGAAAACATCTTGC
1 ATTTAAATGAGAAACTTTGGAAATCACTTTCTCA-TTTT-AGAAAATCATGTGAAAACATCCTGC
* *
159591 CCGAAGGTTTTATGGATGGCCCTAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGACCCGA
64 CCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGACCCGA
* *
159656 AAGATTTAAACATCATGCTCGAAAGACTTACTAATGGCCCGAAGGGCTTACTCAGTAAGAAACTT
129 ATGATTTAAACATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTACTCAGTAAGAAACTT
* *
159721 TGGAAATTGTTTTCTTACCTTTCAAGAAAAATCAA-TT
194 TGGAAATAGTTTTCTTACTTTTCAAGAAAAATCAATTT
* * *
159758 -TTTAAATGAGAAACTTTGGAAAACACTTTCTCATTTTAGAAAATCATGTGAAAATATCGTGCCC
1 ATTTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTAGAAAATCATGTGAAAACATCCTGCCC
* * * *
159822 GAAGGTCTAATGGATGGCCTGAAGGACTTATCACCTTGATCGAAAGACTTATAGATGACCCGAAT
66 GAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGACCCGAAT
* * * * * *
159887 GATTTAAACATCATGCTTGAAAAACTTATTGATGGCCCGAATGACTTACTTAGTAAGAAACTTTG
131 GATTTAAACATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTACTCAGTAAGAAACTTTG
* * *
159952 GAAATCGCTTTCTTACTTTTCAAGAAAAAACAATTTT
196 GAAATAGTTTTCTTACTTTTCAAGAAAAATCAA-TTT
* *
159989 CAGAAAAGATTTAAATGAGAAACTTTAGAAATCACTTTCTCATTTTTGAAAATCATGTGAAAACA
1 --------ATTTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTAGAAAATCATGTGAAAACA
* * *
160054 TCCTGCCTGAAGGTCTTATGGATGGCCCGAATGACTTATCATCTTGTTCGAAAGACTTATAGATG
58 TCCTGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATG
160119 ACCCGAATGATTTAAACATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTACTCAGTAAG
123 ACCCGAATGATTTAAACATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTACTCAGTAAG
* *
160184 AAACTTTGGAAATCACTTTTC-TACTTTTGAAGAAAAATCAATTTT
188 AAACTTTGGAAAT-AGTTTTCTTACTTTTCAAGAAAAATCAA-TTT
* * ** *
160229 CAGCAAAGATTTAAATGAGTAACTTTTGAAATCACTTTCTCATTTTTTAAAATCATGCGAAAACA
1 --------ATTTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTAGAAAATCATGTGAAAACA
* * * * * *
160294 TCCTACCCAAAAGTCTTATGGATGGCCCGAAGTACTTGTCATCTTGCTCGAAAGACTTATAGATA
58 TCCTGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATG
* *
160359 ACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACTAATGGCTC-AAGGGACTTACTCA
123 ACCCGAATGATTTAAACATCATGCTCGAAAGACTTACTAATGGCCCGAA-GGACTTACTCA
160419 TAAATAAACC
Statistics
Matches: 584, Mismatches: 63, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
228 1 0.00
229 170 0.29
230 30 0.05
231 2 0.00
239 2 0.00
240 375 0.64
241 4 0.01
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (231 bp):
ATTTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTAGAAAATCATGTGAAAACATCCTGCCC
GAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGACCCGAAT
GATTTAAACATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTACTCAGTAAGAAACTTTG
GAAATAGTTTTCTTACTTTTCAAGAAAAATCAATTT
Found at i:160154 original size:42 final size:41
Alignment explanation
Indices: 160068--160174 Score: 126
Period size: 42 Copynumber: 2.6 Consensus size: 41
160058 GCCTGAAGGT
* * * *
160068 CTTATGGATGGCCCGAATGACTTATCATCTTGTTCGAAAGA
1 CTTATAGATGGCCCGAATGACTTAACATCATGCTCGAAAGA
* *
160109 CTTATAGATGACCCGAATGATTTAAACATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAATGACTT-AACATCATGCTCGAAAGA
*
160151 CTTACTA-ATGGCCCGAAGGACTTA
1 CTTA-TAGATGGCCCGAATGACTTA
160175 CTCAGTAAGA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 21 0.38
42 32 0.58
43 2 0.04
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28
Consensus pattern (41 bp):
CTTATAGATGGCCCGAATGACTTAACATCATGCTCGAAAGA
Found at i:160555 original size:58 final size:57
Alignment explanation
Indices: 160477--160761 Score: 234
Period size: 53 Copynumber: 5.1 Consensus size: 57
160467 ATTTACAGTT
* * *
160477 ATCATCAAGAAACCCC-AAAAATTAGGCTTAACTTCTTTTTAAAAATCCATTGGAAGTA
1 ATCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAAAT-CATTAGAA-TA
* * *
160535 ATCATCAAG-AACCCCTAAAAATCAGGCTTAGTTTC-TTTAAAAAATCATTTGAA-A
1 ATCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAAATCATTAGAATA
* * * * * *
160589 A-CATCAAGAAACCCTTAAAAAAATAAGCTTAGCTTCTTTCAAAAAATTCTTTAGAAATC
1 ATCATCAAGAAACCCCT-AAAAATTAGGCTTAGCTTCTTTTAAAAAA-TCATTAG-AATA
* * * * * *
160648 ATAATCAAGAAACCCCTAAAAATCATGCGTAG--T-TTCTAAAAAACTCATTTGAA-A
1 ATCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAAA-TCATTAGAATA
* * *
160702 A-CATCAAGAAACTCCTAAAAATTAGGCTTAGCTTC--TTAAAAATTCATTTGAATA
1 ATCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAAATCATTAGAATA
160756 CATCAT
1 -ATCAT
160762 ATCGCTTGGG
Statistics
Matches: 180, Mismatches: 33, Indels: 30
0.74 0.14 0.12
Matches are distributed among these distances:
53 41 0.23
54 16 0.09
55 19 0.11
56 31 0.17
57 21 0.12
58 27 0.15
59 12 0.07
60 13 0.07
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.29
Consensus pattern (57 bp):
ATCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAAATCATTAGAATA
Found at i:162739 original size:22 final size:21
Alignment explanation
Indices: 162714--162789 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 21
162704 TTTTCTTTCA
162714 TCTTCTTCTTTTTTTGTGCTTT
1 TCTTCTTCTTTTTTTGT-CTTT
*
162736 TCTT-TTGCTTTATTT-TCTTT
1 TCTTCTT-CTTTTTTTGTCTTT
162756 TC-TC-TCTTTTTTGTGTTTCTTT
1 TCTTCTTCTTTTTT-TG--TCTTT
162778 T-TTCTTCTTTTT
1 TCTTCTTCTTTTT
162790 GATAATCTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
18 6 0.14
19 3 0.07
20 6 0.14
21 3 0.07
22 19 0.43
23 7 0.16
ACGTcount: A:0.01, C:0.17, G:0.07, T:0.75
Consensus pattern (21 bp):
TCTTCTTCTTTTTTTGTCTTT
Found at i:166746 original size:28 final size:28
Alignment explanation
Indices: 166708--166773 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
166698 AGTAAAGACA
166708 AAATTGAAATAAAATAAAAATAGGAACT
1 AAATTGAAATAAAATAAAAATAGGAACT
* * * * *
166736 AAATTGCAATAAATTAGAATTAGGGACT
1 AAATTGAAATAAAATAAAAATAGGAACT
166764 AAATTGAAAT
1 AAATTGAAAT
166774 TTATAGGAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.56, C:0.05, G:0.14, T:0.26
Consensus pattern (28 bp):
AAATTGAAATAAAATAAAAATAGGAACT
Found at i:168712 original size:45 final size:46
Alignment explanation
Indices: 168663--168753 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
168653 GAACATCGAA
* *
168663 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
168708 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
168754 GCTTTTTCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 21 0.49
46 22 0.51
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:170737 original size:21 final size:21
Alignment explanation
Indices: 170711--170750 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
170701 GAGAAATTGT
170711 TTTTAAAATAT-AAAAATGATG
1 TTTTAAAAT-TGAAAAATGATG
170732 TTTTAAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
170751 AAATAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATG
Found at i:174629 original size:24 final size:24
Alignment explanation
Indices: 174584--174629 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
174574 GCACTTAACA
* *
174584 GTGCATCGATGCATCCTTTTGAAT
1 GTGCATCGATGCATCATGTTGAAT
**
174608 GTGCATCGATTTATCATGTTGA
1 GTGCATCGATGCATCATGTTGA
174630 TGCACTGATG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (24 bp):
GTGCATCGATGCATCATGTTGAAT
Found at i:176955 original size:19 final size:20
Alignment explanation
Indices: 176931--176970 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
176921 GAGAAGTGTA
*
176931 AAATGTTTTA-AAGGGGGAG
1 AAATGTTATAGAAGGGGGAG
176950 AAATGTTATAGTAAGGGGGAG
1 AAATGTTATAG-AAGGGGGAG
176971 CAATTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.25
Consensus pattern (20 bp):
AAATGTTATAGAAGGGGGAG
Found at i:177330 original size:20 final size:20
Alignment explanation
Indices: 177305--177343 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
177295 TTTTCAAGGG
177305 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
177325 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
177344 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:177414 original size:45 final size:45
Alignment explanation
Indices: 177365--177452 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
177355 ACATCGAATG
* *
177365 CATTTTATGCATCGATACAC-ATACCATGCATCGAAGCACTCAGTT
1 CATTTGATGCATCGATACACAAGACCATGCAT-GAAGCACTCAGTT
* *
177410 CATTTGATGCATCGATGCACAAGACCATGCATGATGCACTCAG
1 CATTTGATGCATCGATACACAAGACCATGCATGAAGCACTCAG
177453 GCTTTTTCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 28 0.74
46 10 0.26
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (45 bp):
CATTTGATGCATCGATACACAAGACCATGCATGAAGCACTCAGTT
Found at i:178623 original size:41 final size:42
Alignment explanation
Indices: 178563--178649 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 42
178553 GCCCGAAGGT
* * * * * *
178563 CTTATGGATGGCCCTAAGGACTT-ATCATCTTTCTCAAAAGA
1 CTTATAGATGACCCAAAGGACTTAAACATCATGCTCAAAAGA
*
178604 CTTATAGATGACCCAAAGGATTTAAACATCATGCTCAAAAGA
1 CTTATAGATGACCCAAAGGACTTAAACATCATGCTCAAAAGA
178646 CTTA
1 CTTA
178650 CTGATGGCCC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 19 0.50
42 19 0.50
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.29
Consensus pattern (42 bp):
CTTATAGATGACCCAAAGGACTTAAACATCATGCTCAAAAGA
Found at i:178890 original size:239 final size:240
Alignment explanation
Indices: 178461--178944 Score: 717
Period size: 239 Copynumber: 2.0 Consensus size: 240
178451 AAAAGGACAA
* * *
178461 ACTTTTCAGAAAAATAAGTTTTCAGGAAAGATTTAATTAAGAAACTTTGGAAATCGCTTTCTCAT
1 ACTTTTCAGAAAAATAAGTTTTCAGGAAAGATTTAAATAAGAAACTTTGGAAAACACTTTCTCAT
* * *
178526 TTTTCAAAAATCAAGTGAAAATATCCTGCCCGAAGGTCTTATGGATGGCCCTAAGGACTTATCAT
66 TTTTCAAAAATCAAGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCAT
* *
178591 CTTTCTCAAAAGACTTATAGATGACCCAAAGGATTTAAACATCATGCTCAAAAGACTTACTGATG
131 CTTACTCAAAAGACTTATAGATGACCCAAAGGATTTAAACATCACGCTCAAAAGACTTACTGATG
* *
178656 GCCCGAATGACTTACTCAGTAAAAAACTATGGAAATTGCTTTCTT
196 GCCCGAATGACTTACTCAATAAAAAACTATGGAAATCGCTTTCTT
*
178701 ACTTTTCATGAAAAATCAA-TTTTCAGGAAAGATTTAAATGAGAAA-TTTGGAAAACACTTTCTC
1 ACTTTTCA-GAAAAAT-AAGTTTTCAGGAAAGATTTAAATAAGAAACTTTGGAAAACACTTTCTC
* *
178764 -TTTTTCGAAAATCATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAATAG-CTTAT
64 ATTTTTCAAAAATCAAGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAA-AGACTTAT
* * * **
178827 CTTCTTAAC-CGAAAGACTTATAGATGACCCGAAGGATTTAAACATCACGCTTGAAAGACTTACT
128 CATCTT-ACTCAAAAGACTTATAGATGACCCAAAGGATTTAAACATCACGCTCAAAAGACTTACT
* *
178891 TATGGCCCGAATGACTTACTCAATAAAAAACTATGGAAATCGTTTTCTT
192 GATGGCCCGAATGACTTACTCAATAAAAAACTATGGAAATCGCTTTCTT
178940 ACTTT
1 ACTTT
178945 GTAATAGGGT
Statistics
Matches: 220, Mismatches: 20, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
239 161 0.73
240 26 0.12
241 31 0.14
242 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31
Consensus pattern (240 bp):
ACTTTTCAGAAAAATAAGTTTTCAGGAAAGATTTAAATAAGAAACTTTGGAAAACACTTTCTCAT
TTTTCAAAAATCAAGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCAT
CTTACTCAAAAGACTTATAGATGACCCAAAGGATTTAAACATCACGCTCAAAAGACTTACTGATG
GCCCGAATGACTTACTCAATAAAAAACTATGGAAATCGCTTTCTT
Found at i:179858 original size:30 final size:30
Alignment explanation
Indices: 179822--179891 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
179812 TTTCCAAGGG
*
179822 GAGTTATTAAAATATTAATAAAATACATTT
1 GAGTTATTAAAATATTAATAAAATAAATTT
179852 GAGTTATTAAAATATTAATAAAATAAATTT
1 GAGTTATTAAAATATTAATAAAATAAATTT
*
179882 AAGTTATTAA
1 GAGTTATTAA
179892 TAGATGTCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.40
Consensus pattern (30 bp):
GAGTTATTAAAATATTAATAAAATAAATTT
Found at i:191469 original size:19 final size:21
Alignment explanation
Indices: 191437--191475 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
191427 AGTGCAAAAA
191437 AGATGGCTTAAACCA-ACCAC
1 AGATGGCTTAAACCAGACCAC
*
191457 AGAT-GCTTCAACCAGACCA
1 AGATGGCTTAAACCAGACCA
191476 AGGAACTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.38, C:0.31, G:0.15, T:0.15
Consensus pattern (21 bp):
AGATGGCTTAAACCAGACCAC
Found at i:194266 original size:15 final size:15
Alignment explanation
Indices: 194234--194268 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
194224 TTTTAACCTT
* *
194234 AACCCCATTCACATA
1 AACCCCATTCAAAGA
194249 AACCCCATTCAAAGA
1 AACCCCATTCAAAGA
194264 AACCC
1 AACCC
194269 TAACCCTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.40, G:0.03, T:0.14
Consensus pattern (15 bp):
AACCCCATTCAAAGA
Found at i:195128 original size:14 final size:14
Alignment explanation
Indices: 195109--195161 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
195099 CAACTACAAT
195109 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
195123 AATAAATCAATCTATATT
1 AATAAAT-TAT-T-TA-A
195141 AATAAATTATTTAA
1 AATAAATTATTTAA
195155 AATAAAT
1 AATAAAT
195162 CAATCTATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 14 0.45
15 4 0.13
16 2 0.06
17 4 0.13
18 7 0.23
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:195144 original size:32 final size:32
Alignment explanation
Indices: 195108--195170 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
195098 ACAACTACAA
195108 TAATAAATTATTTAAAATAAATCAATCTATAT
1 TAATAAATTATTTAAAATAAATCAATCTATAT
195140 TAATAAATTATTTAAAATAAATCAATCTATA
1 TAATAAATTATTTAAAATAAATCAATCTATA
195171 CAACTAGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (32 bp):
TAATAAATTATTTAAAATAAATCAATCTATAT
Found at i:195317 original size:14 final size:14
Alignment explanation
Indices: 195300--195353 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
195290 CAATTCATAC
195300 AAATAAATTATTTA
1 AAATAAATTATTTA
*
195314 AAATAAATCAAATTATA
1 AAATAAAT--TATT-TA
*
195331 TTAATAAATTATTTA
1 -AAATAAATTATTTA
195346 AAATAAAT
1 AAATAAAT
195354 CAATCTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 2 0.06
16 6 0.19
17 2 0.06
18 7 0.22
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:195363 original size:32 final size:31
Alignment explanation
Indices: 195278--195364 Score: 129
Period size: 32 Copynumber: 2.7 Consensus size: 31
195268 CAATTTATAT
**
195278 TTTAAAATAAATCAATTCATACAAATAAATTA
1 TTTAAAATAAATCAATT-ATATTAATAAATTA
195310 TTTAAAATAAATCAAATTATATTAATAAATTA
1 TTTAAAATAAATC-AATTATATTAATAAATTA
195342 TTTAAAATAAATCAATCTATATT
1 TTTAAAATAAATCAAT-TATATT
195365 TTAAAATAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
31 3 0.06
32 44 0.86
33 4 0.08
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (31 bp):
TTTAAAATAAATCAATTATATTAATAAATTA
Found at i:195406 original size:22 final size:22
Alignment explanation
Indices: 195342--195406 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
195332 TAATAAATTA
*
195342 TTTAAAATAAATCAA-TCTATAT
1 TTTAAAATAAATCAATTC-ATGT
195364 TTTAAAATAAATCAATTCATGT
1 TTTAAAATAAATCAATTCATGT
195386 TTTAAAATAAATCAATTCATG
1 TTTAAAATAAATCAATTCATG
195407 CTAATAAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 39 0.95
23 2 0.05
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATTCATGT
Found at i:195415 original size:22 final size:22
Alignment explanation
Indices: 195344--195414 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
195334 ATAAATTATT
* **
195344 TAAAATAAATCAA-TCTATATTT
1 TAAAATAAATCAATTC-ATGTAA
**
195366 TAAAATAAATCAATTCATGTTT
1 TAAAATAAATCAATTCATGTAA
195388 TAAAATAAATCAATTCATGCTAA
1 TAAAATAAATCAATTCATG-TAA
195411 TAAA
1 TAAA
195415 TTGTTTAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
22 37 0.84
23 7 0.16
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.37
Consensus pattern (22 bp):
TAAAATAAATCAATTCATGTAA
Found at i:195416 original size:108 final size:108
Alignment explanation
Indices: 195198--195878 Score: 489
Period size: 108 Copynumber: 6.2 Consensus size: 108
195188 TAATCCATAT
* * * **
195198 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATACAACTGCAATAA
1 TTTAAAATAAATCAATCCATATTAATAAATTATTTAAAATAAATCAA-TC-TA-TATTTTAA-AA
*
195263 TAAATCAATTTATATTTTAAAATAAATCAATTCATACAAATAAATTA
62 TAAATCAATTTATATTTTAAAATAAATCAATTCATACTAATAAATTA
*
195310 TTTAAAATAAATCAAAT-TATATTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAA
1 TTTAAAATAAATC-AATCCATATTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAA
* * * *
195374 ATCAATTCATGTTTTAAAATAAATCAATTCATGCTAATAAATTG
65 ATCAATTTATATTTTAAAATAAATCAATTCATACTAATAAATTA
* * *
195418 TTTAAAATAAATCAATCCATATT-TTAAA--A--T-AAATCAATCCATACTAATAAATTATTTAA
1 TTTAAAATAAATCAATCCATATTAATAAATTATTTAAAATAAATCAAT-CT-AT--A-T-TTTAA
* *
195477 AATAAATAAATTTATATTTTAAAATAAATCAATCCATACTAATAAATTA
60 AATAAATCAATTTATATTTTAAAATAAATCAATTCATACTAATAAATTA
* * *
195526 TTTAAAATAAATCAATCCATA-CAACTACA--A--T--AATAAATCAATCCATATTTTAAAATAA
1 TTTAAAATAAATCAATCCATATTAA-TAAATTATTTAAAATAAATCAATCTATATTTTAAAATAA
*
195584 ATCAATTCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTA
65 ATCAATT--T----AT--A-T-TTTAAAATAAATCAATTCATACTAATAAATTA
*
195638 TTTAAAATAAATCAATCC------AT--A-T-TTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATATTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAA
* ** *
195693 TCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATA
66 TCAA--T-T--T-AT--A-T-TTTAAAATAAATCAATTCATACTAATAAATTA
** * * * * * * * **
195745 AAT-CAATACAT-AGTTCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATA
1 TTTAAAATAAATCA-ATCCATATTAATAAATTATTTAAAATAAATCAAT-C-TA-TATTTTAA-A
** *
195808 ATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
61 ATAAATCAATTTATATTTTAAAATAAATCAATTCATACTAATAAATTA
195856 TTTAAAATAAATCAATCCATATT
1 TTTAAAATAAATCAATCCATATT
195879 TTAAATAAAT
Statistics
Matches: 467, Mismatches: 56, Indels: 92
0.76 0.09 0.15
Matches are distributed among these distances:
102 26 0.06
103 4 0.01
104 5 0.01
105 2 0.00
106 13 0.03
107 18 0.04
108 204 0.44
109 9 0.02
110 25 0.05
111 14 0.03
112 106 0.23
113 4 0.01
114 3 0.01
115 1 0.00
116 16 0.03
117 1 0.00
118 2 0.00
119 4 0.01
120 10 0.02
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.36
Consensus pattern (108 bp):
TTTAAAATAAATCAATCCATATTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAA
TCAATTTATATTTTAAAATAAATCAATTCATACTAATAAATTA
Found at i:195422 original size:54 final size:54
Alignment explanation
Indices: 195261--195920 Score: 439
Period size: 54 Copynumber: 12.1 Consensus size: 54
195251 CAACTGCAAT
* * *
195261 AATAAATCAATTTATATTTTAAAATAAATCAATTCATACAAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * *
195315 AATAAATCAAATT-ATATTAATAAATTATTTAAAATAAATCAAT-CT-AT--A-T-TTTAA
1 AATAAATC-AATTCATATT-TTAAA--A--T-AAATCAATCCATACTAATAAATTATTTAA
* * * *
195369 AATAAATCAATTCATGTTTTAAAATAAATCAATTCATGCTAATAAATTGTTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
195423 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
195477 AATAAATAAATTTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * ** ** * ** *
195531 AATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-TTTTAAAATAAAT-C
1 AATAAATCAATTCAT---ATTTTAA-AATAAATCAATCCATACTAATAAATTATTTAA
** * *
195587 AATTCATACAAAT-AAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAAT-CAATTCATA-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * * * *
195643 AATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTAT
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATA--CT--AATAAAT-TATTTAA
* * ** * ** *
195702 ACT-AAT-AAAT--TA-TTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-C
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * ** * * * * *
195749 AATACAT-AGTTCTATACTAATAAATTATTTAAAATAAATCAAT-C-CATACAACTA--CAA
1 AATAAATCAATTC-ATA-TTTTAAA--A--T-AAATCAATCCATACTAATA-AATTATTTAA
*
195806 TAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 -AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
195861 AATAAATCAATCCATATTTT-AAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
195914 AATAAAT
1 AATAAAT
195921 TATTTTAAAA
Statistics
Matches: 470, Mismatches: 87, Indels: 99
0.72 0.13 0.15
Matches are distributed among these distances:
47 2 0.00
48 15 0.03
49 7 0.01
50 2 0.00
51 4 0.01
52 11 0.02
53 59 0.13
54 228 0.49
55 30 0.06
56 15 0.03
57 26 0.06
58 51 0.11
59 11 0.02
60 9 0.02
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.36
Consensus pattern (54 bp):
AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:195425 original size:32 final size:30
Alignment explanation
Indices: 195385--195733 Score: 171
Period size: 32 Copynumber: 12.7 Consensus size: 30
195375 TCAATTCATG
*
195385 TTTTAAAATAAATCAATTCATGCTAATAAAT
1 TTTTAAAATAAATCAATCCAT-CTAATAAAT
195416 TGTTTAAAATAAATCAAT-C--C--AT--A-
1 T-TTTAAAATAAATCAATCCATCTAATAAAT
195439 TTTTAAAATAAATCAATCCATACTAATAAAT
1 TTTTAAAATAAATCAATCCAT-CTAATAAAT
*
195470 TATTTAAAATAAAT-AA---AT-T--TATA-
1 T-TTTAAAATAAATCAATCCATCTAATAAAT
195493 TTTTAAAATAAATCAATCCATACTAATAAAT
1 TTTTAAAATAAATCAATCCAT-CTAATAAAT
195524 TATTTAAAATAAATCAATCCATAC-AACTACAA-
1 T-TTTAAAATAAATCAATCCAT-CTAA-TA-AAT
195556 ---T--AATAAATCAATCCA--T-AT---T
1 TTTTAAAATAAATCAATCCATCTAATAAAT
** * *
195575 TTAAAA--TAAATCAATTCATACAAATAAAT
1 TTTTAAAATAAATCAATCCAT-CTAATAAAT
195604 TATTTAAAATAAATCAATCCATACTAATAAAT
1 T-TTTAAAATAAATCAATCCAT-CTAATAAAT
195636 TATTTAAAATAAATCAAT-C--C--AT--A-
1 T-TTTAAAATAAATCAATCCATCTAATAAAT
195659 TTTTAAAATAAATCAAT-C--C--AT--A-
1 TTTTAAAATAAATCAATCCATCTAATAAAT
*
195681 TTTTAAAATAAATCAATCTATACTAATAAAT
1 TTTTAAAATAAATCAATCCAT-CTAATAAAT
195712 TATTTAAAATAAATCAATCCAT
1 T-TTTAAAATAAATCAATCCAT
195734 ATTTTAAAAT
Statistics
Matches: 257, Mismatches: 11, Indels: 99
0.70 0.03 0.27
Matches are distributed among these distances:
22 78 0.30
23 7 0.03
24 5 0.02
26 25 0.10
28 10 0.04
29 2 0.01
30 8 0.03
31 10 0.04
32 110 0.43
33 2 0.01
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.36
Consensus pattern (30 bp):
TTTTAAAATAAATCAATCCATCTAATAAAT
Found at i:195440 original size:76 final size:76
Alignment explanation
Indices: 195310--195455 Score: 240
Period size: 76 Copynumber: 1.9 Consensus size: 76
195300 AAATAAATTA
* *
195310 TTTAAAATAAATCAAATTATATTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAA
1 TTTAAAATAAATCAAATTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
195375 TCAATTCATGT
66 TCAATTCATGT
* *
195386 TTTAAAATAAATC-AATTCATGCTAATAAATTGTTTAAAATAAATCAATCCATATTTTAAAATAA
1 TTTAAAATAAATCAAATT-ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAA
195450 ATCAAT
65 ATCAAT
195456 CCATACTAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
75 4 0.06
76 61 0.94
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (76 bp):
TTTAAAATAAATCAAATTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
TCAATTCATGT
Found at i:195446 original size:22 final size:22
Alignment explanation
Indices: 195418--195460 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
195408 TAATAAATTG
195418 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
195440 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
195461 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:195469 original size:22 final size:22
Alignment explanation
Indices: 195420--195468 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
195410 ATAAATTGTT
**
195420 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
195442 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
195465 TAAA
1 TAAA
195469 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:195498 original size:76 final size:78
Alignment explanation
Indices: 195418--195756 Score: 394
Period size: 76 Copynumber: 4.3 Consensus size: 78
195408 TAATAAATTG
195418 TTTAAAATAAATCAATCCATA-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATA
1 TTTAAAATAAATCAATCCATATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATA
* **
195481 AATAAATTTATAT
66 AATCAATCCATAT
*
195494 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAAT-C---C--AT--ATTATTTAAAATAAATCAATCCATACTAA-TAAATTA
195556 --T--AATAAATCAATCCATAT
57 TTTAAAATAAATCAATCCATAT
195574 TTTAAAATAAATCAATTCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTAT
1 TTTAAAATAAATCAA-TC---C--AT--ATTATTTAAAATAAATCAATCCATACTAATAAATTAT
195639 TTAAAATAAATCAATCCATAT
58 TTAAAATAAATCAATCCATAT
*
195660 TTTAAAATAAATCAATCCATA-T-TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATA
1 TTTAAAATAAATCAATCCATATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATA
195723 AATCAATCCATAT
66 AATCAATCCATAT
*
195736 TTTAAAATAAATCAATACATA
1 TTTAAAATAAATCAATCCATA
195757 GTTCTATACT
Statistics
Matches: 236, Mismatches: 8, Indels: 38
0.84 0.03 0.13
Matches are distributed among these distances:
76 89 0.38
77 2 0.01
78 1 0.00
80 71 0.30
81 3 0.01
82 5 0.02
84 3 0.01
85 5 0.02
86 57 0.24
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (78 bp):
TTTAAAATAAATCAATCCATATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATA
AATCAATCCATAT
Found at i:195599 original size:18 final size:18
Alignment explanation
Indices: 195578--195635 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
195568 CCATATTTTA
195578 AAATAAATCAATTCATAC
1 AAATAAATCAATTCATAC
*
195596 AAATAAAT-TATT--TA-
1 AAATAAATCAATTCATAC
*
195610 AAATAAATCAATCCATAC
1 AAATAAATCAATTCATAC
*
195628 TAATAAAT
1 AAATAAAT
195636 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 8 0.25
15 4 0.12
17 5 0.16
18 15 0.47
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATAAATCAATTCATAC
Found at i:195646 original size:296 final size:299
Alignment explanation
Indices: 195181--195920 Score: 1031
Period size: 296 Copynumber: 2.5 Consensus size: 299
195171 CAACTAGAAT
*
195181 AATAAATTAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATAAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* * **
195246 TCATACAACTGCAATAATAAATCAATTTATATTTTAAAATAAATCAATTCATACAAATAAATTAT
66 CCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTCATACAAATAAATTAT
* * *
195311 TTAAAATAAATCAAATTATATTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAAT
131 TTAAAATAAATCAAATCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAAT
* * * *
195376 CAATTCATGTTTTAAAATAAATCAAT-TCATGCTAATAAATTGTTTAAAATAAATCAATCCATAT
196 CAATCCATATTTTAAAATAAATCAATCT-ATACTAATAAATTATTTAAAATAAATCAATCCATAT
195440 TTTAAAATAAATCAAT-C-C-ATACTAATAAATTATTTAA
260 TTTAAAATAAATCAATACTCTATACTAATAAATTATTTAA
**
195477 AATAAATAAATTTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATAAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
195542 CCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTCATACAAATAAATTAT
66 CCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTCATACAAATAAATTAT
195607 TTAAAATAAATC-AATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
131 TTAAAATAAATCAAAT-CATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
195671 TCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
195 TCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
195736 TTTAAAATAAATCAATACATAGTTCTATACTAATAAATTATTTAA
260 TTTAAAATAAATCAATAC-----TCTATACTAATAAATTATTTAA
* *** * * * *
195781 AATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAA
1 AATAAATAAATCCATA-TTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
* *
195839 TCCATACTAA-TAAATTATTTAAAATAAATCAATCCATATTTT-AAATAAATCAATTCATACTAA
65 TCCATAC-AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATTCATACAAA
195902 TAAATTATTTAAAATAAAT
123 TAAATTATTTAAAATAAAT
195921 TATTTTAAAA
Statistics
Matches: 400, Mismatches: 26, Indels: 29
0.88 0.06 0.06
Matches are distributed among these distances:
295 3 0.01
296 255 0.64
297 2 0.00
298 25 0.06
299 3 0.01
300 2 0.00
302 3 0.01
303 41 0.10
304 61 0.15
305 5 0.01
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.36
Consensus pattern (299 bp):
AATAAATAAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTCATACAAATAAATTAT
TTAAAATAAATCAAATCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAAT
CAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATT
TTAAAATAAATCAATACTCTATACTAATAAATTATTTAA
Found at i:195740 original size:22 final size:22
Alignment explanation
Indices: 195714--195756 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
195704 TAATAAATTA
*
195714 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATACATAT
195736 TTTAAAATAAATCAATACATA
1 TTTAAAATAAATCAATACATA
195757 GTTCTATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATACATAT
Found at i:195810 original size:40 final size:40
Alignment explanation
Indices: 195736--195813 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
195726 CAATCCATAT
*** * *
195736 TTTAAAATAAATCAATACATAGTTCTATACTAATAAATTA
1 TTTAAAATAAATCAATACATACAACTACAATAATAAATTA
*
195776 TTTAAAATAAATCAATCCATACAACTACAATAATAAAT
1 TTTAAAATAAATCAATACATACAACTACAATAATAAAT
195814 CAATCCATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.33
Consensus pattern (40 bp):
TTTAAAATAAATCAATACATACAACTACAATAATAAATTA
Found at i:195837 original size:88 final size:80
Alignment explanation
Indices: 195490--195876 Score: 450
Period size: 80 Copynumber: 4.7 Consensus size: 80
195480 AAATAAATTT
195490 ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACA
1 ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACA
195555 ATAATAAATCAATCC
66 ATAATAAATCAATCC
* * *
195570 ATATTTTAAAATAAATCAATTCATACAAATAAATTATTTAAAATAAATCAATCCATACTAA-TAA
1 ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC-AACTAC
195634 ATTATTTAAAATAAATCAATCC
65 A--A--T--AATAAATCAATCC
** * * * *
195656 ATATTTTAAAATAAATCAATCCATA-TTTTAAA--A--T-AAATCAATCTATACTAATA-AATTA
1 ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-C-CATACAACTA
*
195714 TTTAA-AATAAATCAATCC
64 --CAATAATAAATCAATCC
195732 ATATTTTAAAATAAATCAATACATAGTTCTATACTAATAAATTATTTAAAATAAATCAATCCATA
1 ATATTTTAAAATAAATCAAT-C------C-ATACTAATAAATTATTTAAAATAAATCAATCCATA
195797 CAACTACAATAATAAATCAATCC
58 CAACTACAATAATAAATCAATCC
195820 ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
1 ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
195877 TTTTAAATAA
Statistics
Matches: 261, Mismatches: 18, Indels: 56
0.78 0.05 0.17
Matches are distributed among these distances:
76 33 0.13
77 1 0.00
80 106 0.41
81 8 0.03
82 4 0.02
83 3 0.01
84 4 0.02
85 9 0.03
86 37 0.14
87 4 0.02
88 36 0.14
89 6 0.02
90 10 0.04
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (80 bp):
ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACA
ATAATAAATCAATCC
Found at i:195844 original size:22 final size:22
Alignment explanation
Indices: 195638--195698 Score: 122
Period size: 22 Copynumber: 2.8 Consensus size: 22
195628 TAATAAATTA
195638 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
195660 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
195682 TTTAAAATAAATCAATC
1 TTTAAAATAAATCAATC
195699 TATACTAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:195853 original size:22 final size:23
Alignment explanation
Indices: 195778--195852 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
195768 ATAAATTATT
195778 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
195800 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
195826 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
195849 TAAA
1 TAAA
195853 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:195876 original size:142 final size:137
Alignment explanation
Indices: 195624--195897 Score: 458
Period size: 142 Copynumber: 2.0 Consensus size: 137
195614 AAATCAATCC
* **
195624 ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAA
1 ATACTAATAAATTATTTAAAATAAATCAATCCATACTACAAAATAAATCAATCCATATTTTAAAA
*
195689 TAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATAC
66 TAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTT-AAATAAATCAATAC
195754 ATAGTTCT
130 ATAGTTCT
195762 ATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTT
1 ATACTAATAAATTATTTAAAATAAATCAATCCAT---ACTACAA-AATAAATCAATCCATATTTT
195827 AAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAATAAATCAA
62 AAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAATAAATCAA
*
195892 TTCATA
127 TACATA
195898 CTAATAAATT
Statistics
Matches: 127, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
138 34 0.27
141 20 0.16
142 73 0.57
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.35
Consensus pattern (137 bp):
ATACTAATAAATTATTTAAAATAAATCAATCCATACTACAAAATAAATCAATCCATATTTTAAAA
TAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAATAAATCAATACA
TAGTTCT
Found at i:195882 original size:22 final size:22
Alignment explanation
Indices: 195856--195955 Score: 76
Period size: 22 Copynumber: 4.5 Consensus size: 22
195846 TAATAAATTA
195856 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
195878 TTT-AAATAAATCAATTCATACT
1 TTTAAAATAAATCAATCCATA-T
** * ** * **
195900 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATCCA-TAT
195924 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
195946 TTTATAATAA
1 TTTAAAATAA
195956 TTTATTTTAA
Statistics
Matches: 56, Mismatches: 18, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
21 16 0.29
22 17 0.30
23 9 0.16
24 12 0.21
25 2 0.04
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:195884 original size:21 final size:21
Alignment explanation
Indices: 195854--195897 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
195844 ACTAATAAAT
195854 TATTTAAAATAAATCAATCCA
1 TATTTAAAATAAATCAATCCA
* *
195875 TATTTTAAATAAATCAATTCA
1 TATTTAAAATAAATCAATCCA
195896 TA
1 TA
195898 CTAATAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (21 bp):
TATTTAAAATAAATCAATCCA
Found at i:195891 original size:53 final size:54
Alignment explanation
Indices: 195807--195920 Score: 212
Period size: 53 Copynumber: 2.1 Consensus size: 54
195797 CAACTACAAT
195807 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
195861 AATAAATCAATCCATATTTT-AAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
195914 AATAAAT
1 AATAAAT
195921 TATTTTAAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
53 39 0.66
54 20 0.34
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:195929 original size:15 final size:15
Alignment explanation
Indices: 195900--196017 Score: 130
Period size: 15 Copynumber: 7.5 Consensus size: 15
195890 AATTCATACT
195900 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
195914 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
195929 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
195951 AATAATTTATTTTAA
1 AATAAATTATTTTAA
* *
195966 AGTAAATTATTTTAT
1 AATAAATTATTTTAA
195981 AATAAATTATTTTAA
1 AATAAATTATTTTAA
195996 AATAAATTATTTTAA
1 AATAAATTATTTTAA
196011 AATAAAT
1 AATAAAT
196018 AACCTTATTA
Statistics
Matches: 88, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
14 9 0.10
15 62 0.70
17 1 0.01
18 2 0.02
19 3 0.03
20 1 0.01
22 10 0.11
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.46
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:195959 original size:47 final size:49
Alignment explanation
Indices: 195769--195987 Score: 159
Period size: 53 Copynumber: 4.4 Consensus size: 49
195759 TCTATACTAA
** *
195769 TAAATTA-TTTAAAATAAATCAATCCATAC-AACTACAATAATAAATCAA-
1 TAAATTATTTTAAAATAAATCAATCCATACTAA-TA-AATAATTTATAAAG
** *
195817 TCCA-TATTTTAAAATAAATCAATCCATACTAATAAATTATTTA-AAA-
1 TAAATTATTTTAAAATAAATCAATCCATACTAATAAATAATTTATAAAG
* * *
195863 TAAATCAATCCATATTTTAAATAAATCAATTCATACTAATAAATTATTTA-AAA-
1 TAAAT---T--AT-TTTAAAATAAATCAATCCATACTAATAAATAATTTATAAAG
**
195916 TAAATTATTTTAAAATAAATCAATCCATA-TTTTATAATAATTTATTTTAAAG
1 TAAATTATTTTAAAATAAATCAATCCATACTAATA-AATAATTTA---TAAAG
*
195968 TAAATTATTTTATAATAAAT
1 TAAATTATTTTAAAATAAAT
195988 TATTTTAAAA
Statistics
Matches: 140, Mismatches: 16, Indels: 26
0.77 0.09 0.14
Matches are distributed among these distances:
46 7 0.05
47 35 0.25
48 28 0.20
49 2 0.01
50 2 0.01
51 3 0.02
52 21 0.15
53 42 0.30
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (49 bp):
TAAATTATTTTAAAATAAATCAATCCATACTAATAAATAATTTATAAAG
Found at i:195991 original size:67 final size:67
Alignment explanation
Indices: 195846--196002 Score: 214
Period size: 67 Copynumber: 2.3 Consensus size: 67
195836 CAATCCATAC
195846 TAATAAATTA-TTTAAAATAAATCAATCCATATTTTAAATAAATCAATTCATACTAATAAATTAT
1 TAATAAATTATTTTAAAATAAATCAATCCATATTTTAAATAAATCAATTCATAC-AATAAATTAT
195910 TTA
65 TTA
* ** *
195913 AAATAAATTATTTTAAAATAAATCAATCCATATTTTATAAT-AATTTATT-TTA-AAGTAAATTA
1 TAATAAATTATTTTAAAATAAATCAATCCATATTTTA-AATAAATCAATTCATACAA-TAAATTA
195975 TTTTA
64 -TTTA
195980 TAATAAATTATTTTAAAATAAAT
1 TAATAAATTATTTTAAAATAAAT
196003 TATTTTAAAA
Statistics
Matches: 81, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
65 2 0.02
66 7 0.09
67 37 0.46
68 32 0.40
69 3 0.04
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (67 bp):
TAATAAATTATTTTAAAATAAATCAATCCATATTTTAAATAAATCAATTCATACAATAAATTATT
TA
Found at i:196825 original size:21 final size:21
Alignment explanation
Indices: 196759--196828 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
196749 TTTAAATGTT
*
196759 ATAA-TAAAATATTAATTATG
1 ATAATTAATATATTAATTATG
*
196779 ATAATTAA-ATTAGTAA--AT-
1 ATAATTAATA-TATTAATTATG
*
196797 ATACTTAATATATTAATTATG
1 ATAATTAATATATTAATTATG
196818 ATAATTAATAT
1 ATAATTAATAT
196829 TCTTTACATT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
18 12 0.30
19 3 0.08
20 7 0.17
21 18 0.45
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (21 bp):
ATAATTAATATATTAATTATG
Found at i:196870 original size:22 final size:21
Alignment explanation
Indices: 196837--196891 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
196827 ATTCTTTACA
196837 TTTAATACTTATATTATATTG
1 TTTAATACTTATATTATATTG
* **
196858 TTTAATATTTTATATTATATAC
1 TTTAATA-CTTATATTATATTG
*
196880 TTTAGTACTTAT
1 TTTAATACTTAT
196892 GTACTTATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (21 bp):
TTTAATACTTATATTATATTG
Found at i:197122 original size:25 final size:24
Alignment explanation
Indices: 197076--197121 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
197066 TGATGAGAGA
197076 TGAAATTGAATTAATTATAAAACG
1 TGAAATTGAATTAATTATAAAACG
*
197100 TGAAGTTGATATTAA-TATAAAA
1 TGAAATTGA-ATTAATTATAAAA
197122 ATGGACTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (24 bp):
TGAAATTGAATTAATTATAAAACG
Found at i:197430 original size:2 final size:2
Alignment explanation
Indices: 197425--197464 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
197415 TAACACACAC
197425 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
197465 GTATGTATGT
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:197694 original size:24 final size:24
Alignment explanation
Indices: 197647--197691 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
197637 TGATGAGGGA
197647 TGAAATTGAATTAATTATAAAATG
1 TGAAATTGAATTAATTATAAAATG
197671 TGAAA-TGATATTAA-TATAAAA
1 TGAAATTGA-ATTAATTATAAAA
197692 ATGGAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (24 bp):
TGAAATTGAATTAATTATAAAATG
Found at i:198158 original size:20 final size:20
Alignment explanation
Indices: 198121--198158 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
198111 TATACAAATA
*
198121 TAAAAATGTATAAGTATATG
1 TAAAAATGTATAACTATATG
198141 TAAAAAGTGTA-AACTATA
1 TAAAAA-TGTATAACTATA
198159 AAGTATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.32
Consensus pattern (20 bp):
TAAAAATGTATAACTATATG
Found at i:198220 original size:27 final size:30
Alignment explanation
Indices: 198155--198224 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 30
198145 AAGTGTAAAC
198155 TATAAAGTATA-TATACTTATAATAATATAA
1 TATAAAGTATACTATAC-TATAATAATATAA
198185 -AGTATAAGTATACTATA-TAT-AT-ATATAA
1 TA-TA-AAGTATACTATACTATAATAATATAA
198213 TATAAAGTATAC
1 TATAAAGTATAC
198225 AAGCAAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
27 8 0.22
28 8 0.22
29 4 0.11
30 5 0.14
31 7 0.19
32 4 0.11
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (30 bp):
TATAAAGTATACTATACTATAATAATATAA
Found at i:198223 original size:22 final size:22
Alignment explanation
Indices: 198198--198484 Score: 137
Period size: 22 Copynumber: 13.0 Consensus size: 22
198188 ATAAGTATAC
198198 TATATATATATATAATATAAAG
1 TATATATATATATAATATAAAG
* * *
198220 TATACAAGCAAATATAAGTATATAAG
1 TATA-TA-TATATATAA-TATA-AAG
*
198246 TAT-TAAATATA-AAGTATATAAG
1 TATATATATATATAA-TATA-AAG
*
198268 TATATATATA-A-ACTATAAAG
1 TATATATATATATAATATAAAG
* * *
198288 TGTGTGTATATATATATATAAAG
1 TATATATATATATA-ATATAAAG
*
198311 T-T-T-TAGTATA-AAGTATATA-
1 TATATATA-TATATAA-TATAAAG
*
198330 TACATATATA-ATAATATAAAG
1 TATATATATATATAATATAAAG
* *
198351 TATA-AGTATATCT-ATATATA-
1 TATATA-TATATATAATATAAAG
198371 TATATATATATATAAAGTATATAAG
1 TATATATATATAT-AA-TATA-AAG
198396 TATATA-ATATA-AACTATATAAG
1 TATATATATATATAA-TATA-AAG
198418 TATATA-AGTATATAATATAAAG
1 TATATATA-TATATAATATAAAG
198440 TATATA-AGTAT-TAAATATAAA-
1 TATATATA-TATAT-AATATAAAG
*
198461 AAT-TATATATATAACCTATAAAG
1 TATATATATATATAA--TATAAAG
198484 T
1 T
198485 GTGTGTGTGT
Statistics
Matches: 211, Mismatches: 23, Indels: 61
0.72 0.08 0.21
Matches are distributed among these distances:
19 2 0.01
20 42 0.20
21 34 0.16
22 71 0.34
23 30 0.14
24 16 0.08
25 10 0.05
26 6 0.03
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.38
Consensus pattern (22 bp):
TATATATATATATAATATAAAG
Found at i:198244 original size:8 final size:8
Alignment explanation
Indices: 198187--198450 Score: 127
Period size: 8 Copynumber: 35.1 Consensus size: 8
198177 TAATATAAAG
198187 TATAAGTA
1 TATAAGTA
198195 TACT-A-TA
1 TA-TAAGTA
198202 TAT-A-TA
1 TATAAGTA
198208 TATAA-TA
1 TATAAGTA
198215 TA-AAGTA
1 TATAAGTA
* *
198222 TACAAGCAAA
1 TATAAG--TA
198232 TATAAGTA
1 TATAAGTA
198240 TATAAGTA
1 TATAAGTA
*
198248 T-TAAATA
1 TATAAGTA
198255 TA-AAGTA
1 TATAAGTA
198262 TATAAGTA
1 TATAAGTA
198270 TAT-A-TA
1 TATAAGTA
*
198276 TA-AACTA
1 TATAAGTA
*
198283 TA-AAGTG
1 TATAAGTA
*
198290 TGT--GTA
1 TATAAGTA
198296 TATATA-TA
1 TATA-AGTA
198304 TATAAAGT-
1 TAT-AAGTA
*
198312 T-TTAGTA
1 TATAAGTA
198319 TA-AAGTA
1 TATAAGTA
*
198326 TATATACATA
1 TATA-A-GTA
198336 TATAA-TAA
1 TATAAGT-A
198344 TATAA--A
1 TATAAGTA
198350 GTATAAGTA
1 -TATAAGTA
*
198359 TAT--CTA
1 TATAAGTA
198365 TATATA-TA
1 TATA-AGTA
198373 TATATA-TA
1 TATA-AGTA
198381 TATAAAGTA
1 TAT-AAGTA
198390 TATAAGTA
1 TATAAGTA
198398 TATAA-TA
1 TATAAGTA
*
198405 TA-AACTA
1 TATAAGTA
198412 TATAAGTA
1 TATAAGTA
198420 TATAAGTA
1 TATAAGTA
198428 TATAA-TA
1 TATAAGTA
198435 TA-AAGTA
1 TATAAGTA
198442 TATAAGTA
1 TATAAGTA
198450 T
1 T
198451 TAAATATAAA
Statistics
Matches: 207, Mismatches: 15, Indels: 68
0.71 0.05 0.23
Matches are distributed among these distances:
6 31 0.15
7 64 0.31
8 88 0.43
9 12 0.06
10 12 0.06
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (8 bp):
TATAAGTA
Found at i:198267 original size:30 final size:30
Alignment explanation
Indices: 198232--198460 Score: 137
Period size: 30 Copynumber: 7.7 Consensus size: 30
198222 TACAAGCAAA
*
198232 TATAAGTATATAAGTATTAAATATA-AAGTA
1 TATAAGTATATAAATA-TAAATATATAAGTA
*
198262 TATAAGTATAT--ATATAAACTATA-AAGTG
1 TATAAGTATATAAATATAAA-TATATAAGTA
* *
198290 TGT--GTATATATATATATAAAGT-T-TTAGTA
1 TATAAGTATATA-A-ATATAAA-TATATAAGTA
198319 TA-AAGTATATATACATATATAATAATATAA--A
1 TATAAGTATATA-A-ATATA-AAT-ATATAAGTA
** *
198350 GTATAAGTATATCTATATATATATATATA-TA
1 -TATAAGTATATAAATATAAATATATA-AGTA
* *
198381 TATAAAGTATATAAGTATATAATATA-AACTA
1 TAT-AAGTATATAAATATA-AATATATAAGTA
*
198412 TATAAGTATATAAGTATATAATATA-AAGTA
1 TATAAGTATATAAATATA-AATATATAAGTA
198442 TATAAGTAT-TAAATATAAA
1 TATAAGTATATAAATATAAA
198461 AATTATATAT
Statistics
Matches: 162, Mismatches: 18, Indels: 40
0.74 0.08 0.18
Matches are distributed among these distances:
26 6 0.04
27 4 0.02
28 14 0.09
29 17 0.10
30 76 0.47
31 27 0.17
32 8 0.05
33 10 0.06
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (30 bp):
TATAAGTATATAAATATAAATATATAAGTA
Found at i:198445 original size:2 final size:2
Alignment explanation
Indices: 198324--198436 Score: 62
Period size: 2 Copynumber: 57.0 Consensus size: 2
198314 TAGTATAAAG
* * *
198324 TA TA TA TA CA TA TA TA -A TA -A TA TA AA GTA TA -A GTA TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
*
198365 TA TA TA TA TA TA TA TA TA TA AA GTA TA TA -A GTA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA
*
198407 AA CTA TA TA -A GTA TA TA -A GTA TA TA -A TA TA
1 TA -TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA
198437 AAGTATATAA
Statistics
Matches: 86, Mismatches: 10, Indels: 30
0.68 0.08 0.24
Matches are distributed among these distances:
1 8 0.09
2 71 0.83
3 7 0.08
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (2 bp):
TA
Found at i:198594 original size:43 final size:46
Alignment explanation
Indices: 198515--198602 Score: 112
Period size: 43 Copynumber: 2.0 Consensus size: 46
198505 ACTTTATATT
*
198515 ATTATATACCTATATAAATTTTATATTTAATACTTATATATTTTAG
1 ATTATATACCTATATAAATTTTATATTTAATACTTATATACTTTAG
* *
198561 ATTATATA-CT-TATTAA-TTTATA-TTATATGCTTATATACTTTA
1 ATTATATACCTATATAAATTTTATATTTA-ATACTTATATACTTTA
198603 TTCTTTATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
42 3 0.08
43 20 0.53
44 5 0.13
45 2 0.05
46 8 0.21
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (46 bp):
ATTATATACCTATATAAATTTTATATTTAATACTTATATACTTTAG
Found at i:198778 original size:22 final size:23
Alignment explanation
Indices: 198500--199080 Score: 211
Period size: 22 Copynumber: 25.9 Consensus size: 23
198490 TGTGTATATA
198500 TATATACTTTATATTATTATATACCT
1 TATATACTTTATA-T-TTATATA-CT
* *
198526 ATATAAATTTTATATTTA-ATACT
1 -TATATACTTTATATTTATATACT
* *
198549 TATATATTTTAGA-TTATATACT
1 TATATACTTTATATTTATATACT
* *
198571 TAT-TAATTTATA-TTATATGCT
1 TATATACTTTATATTTATATACT
*
198592 TATATACTTTATTCTTTATAAATACGT
1 TATATACTTTA-TATTTAT--ATAC-T
* *
198619 TATATA---TATATATATATACA
1 TATATACTTTATATTTATATACT
* * *
198639 CACACACTTTATAGTTTATATA-T
1 TATATACTTTATA-TTTATATACT
* * *
198662 ATACTTTTACTTTATAGTT-TATACA
1 -TA--TATACTTTATATTTATATACT
* * *** *
198687 TATTTA-TATATGCATACATAC-
1 TATATACTTTATATTTATATACT
*
198708 T-TATACTTTATATGTATATATAAT
1 TATATACTTTATAT-T-TATATACT
*
198732 TATATACTTTAGTCTTTATA-A--
1 TATATACTTTA-TATTTATATACT
198753 -ATATACTTTATATTTA-ATACT
1 TATATACTTTATATTTATATACT
* *
198774 TATATATTTTATATTATTATATACA
1 TATATACTTTATA-T-TTATATACT
*
198799 TATATA-TGTATA-TTATATA--
1 TATATACTTTATATTTATATACT
198818 TATATACTTTATATTTA-ATACT
1 TATATACTTTATATTTATATACT
*
198840 TATATATTTTATA-TTATATACT
1 TATATACTTTATATTTATATACT
* *
198862 TATATAATTTATA-TTATATGCT
1 TATATACTTTATATTTATATACT
* *
198884 TATACACTTTAT-TCTT-TATA-A
1 TATATACTTTATAT-TTATATACT
198905 T-TATACTTTATATATATATATA-T
1 TATATACTTTATAT-T-TATATACT
*
198928 AATATAC-TTATATTT-TATA-T
1 TATATACTTTATATTTATATACT
* * *
198948 TAT-TA-TATATGTATATATACT
1 TATATACTTTATATTTATATACT
** *
198969 T-TATA-AATATATATATATA--
1 TATATACTTTATATTTATATACT
* *
198988 TATATA-TATATATATAT-TACT
1 TATATACTTTATATTTATATACT
* **
199009 T-TATAGTTTATACATATATA-T
1 TATATACTTTATATTTATATACT
* *
199030 GTACTTATACTTTATATATATGTATAATT
1 -TA--TATACTTTATAT-T-TATAT-ACT
199059 TATATACTTTTATACTTTATAT
1 TATATAC-TTTATA-TTTATAT
199081 TATATATTTT
Statistics
Matches: 428, Mismatches: 67, Indels: 119
0.70 0.11 0.19
Matches are distributed among these distances:
18 1 0.00
19 22 0.05
20 63 0.15
21 79 0.18
22 99 0.23
23 31 0.07
24 41 0.10
25 35 0.08
26 23 0.05
27 29 0.07
28 4 0.01
29 1 0.00
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATACTTTATATTTATATACT
Found at i:198781 original size:15 final size:14
Alignment explanation
Indices: 198536--199145 Score: 135
Period size: 14 Copynumber: 42.9 Consensus size: 14
198526 ATATAAATTT
198536 TATATTTAATACTTA
1 TATATTT-ATACTTA
*
198551 TATATTT-TAGATTA
1 TATATTTATA-CTTA
* *
198565 TATACTTATTAATT-
1 TATATTTA-TACTTA
*
198579 TATATTATATGCTTA
1 TATATT-TATACTTA
*
198594 TATACTTTATTCTT-
1 TATA-TTTATACTTA
*
198608 TATA--AATACGTTA
1 TATATTTATAC-TTA
*
198621 TATATATATA-TATA
1 TATATTTATACT-TA
* *** *
198635 TACACACACACTT-
1 TATATTTATACTTA
198648 TATAGTTTATA--TA
1 TATA-TTTATACTTA
198661 TATACTTT-TACTT-
1 TATA-TTTATACTTA
*
198674 TATAGTTTATACATA
1 TATA-TTTATACTTA
* * * *
198689 TTTATATATGCATA
1 TATATTTATACTTA
* *
198703 CATACTTATACTTTA
1 TATATTTATAC-TTA
* *
198718 TATGTATATATAATTA
1 TA--TATTTATACTTA
198734 TATACTTTAGT-CTT-
1 TATA-TTTA-TACTTA
**
198748 TATAAATATACTT-
1 TATATTTATACTTA
198761 TATATTTAATACTTA
1 TATATTT-ATACTTA
198776 TATATTT-TA--TA
1 TATATTTATACTTA
*
198787 T-TATTATATACATA
1 TATATT-TATACTTA
*
198801 TATATGTATA-TTA
1 TATATTTATACTTA
*
198814 TATATATATACTT-
1 TATATTTATACTTA
198827 TATATTTAATACTTA
1 TATATTT-ATACTTA
198842 TATATTTTATA-TTA
1 TATA-TTTATACTTA
*
198856 TATACTTATATAATT-
1 TATA-TT-TATACTTA
*
198871 TATATTATATGCTTA
1 TATATT-TATACTTA
* *
198886 TACACTTTATTCTT-
1 TATA-TTTATACTTA
*
198900 TATAATTATACTT-
1 TATATTTATACTTA
*
198913 TATATATATA--TA
1 TATATTTATACTTA
*
198925 TATA-ATATACTTA
1 TATATTTATACTTA
198938 TAT-TTTATA-TTA
1 TATATTTATACTTA
* *
198950 T-TATATAT-GTATA
1 TATATTTATACT-TA
*
198963 TATACTTTATAAATATA
1 TATA-TTTAT-ACT-TA
198980 TATATATATATA-TATA
1 TATAT-T-TATACT-TA
*
198996 TATATATATTACTT-
1 TATATTTA-TACTTA
199010 TATAGTTTATACATATA
1 TATA-TTTATAC-T-TA
*
199027 TATGTACTTATACTTTA
1 TA--TATTTATAC-TTA
*
199044 TATATATGTATAATTTA
1 TATAT-T-TAT-ACTTA
199061 TATACTTTTATACTT-
1 TATA--TTTATACTTA
* *
199076 TATATTATATATTTT
1 TATATT-TATACTTA
199091 TATACTTTAGT-CTT-
1 TATA-TTTA-TACTTA
199105 TATAATTT-TACTTTA
1 TAT-ATTTATAC-TTA
* *
199120 TATATATATA-TAA
1 TATATTTATACTTA
*
199133 TATACTTATACTT
1 TATATTTATACTT
199146 TTTATTATTA
Statistics
Matches: 448, Mismatches: 72, Indels: 151
0.67 0.11 0.23
Matches are distributed among these distances:
10 4 0.01
11 14 0.03
12 22 0.05
13 93 0.21
14 127 0.28
15 102 0.23
16 36 0.08
17 35 0.08
18 12 0.03
19 3 0.01
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (14 bp):
TATATTTATACTTA
Found at i:198796 original size:2 final size:2
Alignment explanation
Indices: 198774--199189 Score: 102
Period size: 2 Copynumber: 213.5 Consensus size: 2
198764 ATTTAATACT
* * *
198774 TA TA TA T- TT TA TA T- TA T- TA TA TA CA TA TA TA TG TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
198812 TA TA TA TA TA TA CTT TA TA TT TA -A TA CT- TA TA TA T- TT TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * *
198853 T- TA TA TA CT- TA TA TA -A TT TA TA T- TA TA TGC T- TA TA CA CTT
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA -TA
* * *
198893 TA T- TC TT TA TA -A T- TA TA CTT TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * *
198932 TA CT- TA TA T- TT TA TA T- TA T- TA TA TA TG TA TA TA TA CTT TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* *
198972 TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA CTT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * * *
199014 GTT TA TA CA TA TA TA TG TA CT- TA TA CTT TA TA TA TA TG TA TA
1 -TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
* * * * * *
199056 -A TT TA TA TA CT- TT TA TA CTT TA TA T- TA TA TA TT TT TA TA CTT
1 TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA
* * * *
199098 TA GTC TT TA TA -A T- TT TA CTT TA TA TA TA TA TA TA -A TA TA CT-
1 TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA
* * * *
199139 TA TA CTT TT TA T- TA T- TA TA TA TG TA TA TA CTT TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
199181 TA TA TA TA T
1 TA TA TA TA T
199190 CTGTTTCAAT
Statistics
Matches: 302, Mismatches: 61, Indels: 102
0.65 0.13 0.22
Matches are distributed among these distances:
1 31 0.10
2 252 0.83
3 19 0.06
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.55
Consensus pattern (2 bp):
TA
Found at i:198866 original size:13 final size:13
Alignment explanation
Indices: 198788--198950 Score: 70
Period size: 13 Copynumber: 13.1 Consensus size: 13
198778 TATTTTATAT
*
198788 TATTATATACATA
1 TATTATATACTTA
*
198801 TATATGTATA-TTA
1 TAT-TATATACTTA
198814 TATATATATACTTTA
1 TAT-TATATAC-TTA
198829 TATT-TAATACTTA
1 TATTAT-ATACTTA
198842 TA-TAT-T--TTA
1 TATTATATACTTA
198851 TATTATATACTTA
1 TATTATATACTTA
198864 TA-TA-AT--TTA
1 TATTATATACTTA
*
198873 TATTATATGCTTA
1 TATTATATACTTA
*
198886 TACACTT-TATTCTT-
1 T--A-TTATATACTTA
*
198900 TATAATTATACTT-
1 TATTA-TATACTTA
198913 TA-TATATA-TATA
1 TATTATATACT-TA
*
198925 TATAATATACTTA
1 TATTATATACTTA
*
198938 TATTTTATA-TTA
1 TATTATATACTTA
198950 T
1 T
198951 TATATATGTA
Statistics
Matches: 118, Mismatches: 10, Indels: 45
0.68 0.06 0.26
Matches are distributed among these distances:
9 10 0.08
10 6 0.05
11 12 0.10
12 11 0.09
13 52 0.44
14 12 0.10
15 13 0.11
16 2 0.02
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (13 bp):
TATTATATACTTA
Found at i:198873 original size:110 final size:110
Alignment explanation
Indices: 198514--199086 Score: 273
Period size: 112 Copynumber: 5.1 Consensus size: 110
198504 TACTTTATAT
* * *
198514 TATTATATACCTATATAAATTTTATATTTA-ATACTTATATATTTTA---GATTATATACTTAT-
1 TATTATATACTTATAT-AA-TTTATATTTATATACTTATATATTTTACTTTATTATATACATATA
* * * *
198574 TAATTTATATTATATGCTTATATACTTTATTCTTTATAAATACGTTATATATATA
64 T-ATGTATATTATAT--ATATATACTTTA-T-ATT-T-AATAC-TTATATATTTA
** * * * * *
198629 TA-TATATACACACACACTTTATAGTTTATATA--TATA-CTTTTACTTTATAGTTTATACATAT
1 TATTATATACTTATATAATTTATA-TTTATATACTTATATATTTTACTTTAT--TATATACATAT
* * * *
198690 -T-TATATATGCATACATACTTATACTTTATATGTATATATAATTATATACTTTA
63 ATATGTATAT-TATATATA--TATACTTTATAT-T-TA-ATACTTATATA-TTTA
* * *
198743 GTCTT-TATA--AATATACTTTATATTTA-ATACTTATATATTTTA-TATTATTATATACATATA
1 -TATTATATACTTATATAATTTATATTTATATACTTATATATTTTACT-TTATTATATACATATA
198803 TATGTATATTATATATATATACTTTATATTTAATACTTATATATTTTA
64 TATGTATATTATATATATATACTTTATATTTAATACTTATATA-TTTA
* * * * *
198851 TATTATATACTTATATAATTTATA-TTATATGCTTATACACTTTATTCTTTATAATTATAC-TTT
1 TATTATATACTTATATAATTTATATTTATATACTTATATA-TTT-TACTTTATTA-TATACATAT
* * *
198914 ATATATATA-TATATA-ATATAC-TTATATTTTATA-TTAT-TATATA
63 ATATGTATATTATATATATATACTTTATATTTAATACTTATATATTTA
* * *
198957 TGTATATATACTT-TATAAATATATATATATATATATA-TATATATATATTACTTTATAGTTTAT
1 TAT-TATATACTTATAT-AAT-T-TATAT-T-TATATACT-TATATATTTTACTTTAT--TATAT
* * *
199020 ACATATATATGTACT-TATACTTTATATATA-TGTATAATTTATATACTTTTATACTTTA
57 ACATATATATGTA-TAT-TA-TATATATATACTTTAT-ATTTA-ATACTTATATA-TTTA
199078 TATTATATA
1 TATTATATA
199087 TTTTTATACT
Statistics
Matches: 354, Mismatches: 53, Indels: 97
0.70 0.11 0.19
Matches are distributed among these distances:
106 8 0.02
107 17 0.05
108 23 0.06
109 20 0.06
110 34 0.10
111 38 0.11
112 58 0.16
113 45 0.13
114 47 0.13
115 22 0.06
116 19 0.05
117 4 0.01
118 3 0.01
119 3 0.01
120 8 0.02
121 5 0.01
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (110 bp):
TATTATATACTTATATAATTTATATTTATATACTTATATATTTTACTTTATTATATACATATATA
TGTATATTATATATATATACTTTATATTTAATACTTATATATTTA
Found at i:198915 original size:7 final size:7
Alignment explanation
Indices: 198820--198916 Score: 58
Period size: 7 Copynumber: 13.6 Consensus size: 7
198810 ATTATATATA
198820 TATACTT
1 TATACTT
198827 TATA-TT
1 TATACTT
198833 TAATACTT
1 T-ATACTT
*
198841 ATATATTT
1 -TATACTT
198849 TATA-TT
1 TATACTT
198855 ATATACTT
1 -TATACTT
*
198863 ATATAATT
1 -TATACTT
198871 TATA-TT
1 TATACTT
*
198877 ATATGCTT
1 -TATACTT
*
198885 ATACACTT
1 -TATACTT
*
198893 TATTCTT
1 TATACTT
*
198900 TATA-AT
1 TATACTT
198906 TATACTT
1 TATACTT
198913 TATA
1 TATA
198917 TATATATATA
Statistics
Matches: 72, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
6 12 0.17
7 35 0.49
8 24 0.33
9 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.01, T:0.56
Consensus pattern (7 bp):
TATACTT
Found at i:199064 original size:9 final size:9
Alignment explanation
Indices: 199035--199080 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
199025 TATATGTACT
199035 TATACTTTA
1 TATACTTTA
* *
199044 TATA-TATG
1 TATACTTTA
*
199052 TATAATTTA
1 TATACTTTA
199061 TATACTTT-
1 TATACTTTA
199069 TATACTTTA
1 TATACTTTA
199078 TAT
1 TAT
199081 TATATATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
8 14 0.47
9 16 0.53
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.57
Consensus pattern (9 bp):
TATACTTTA
Found at i:204036 original size:18 final size:18
Alignment explanation
Indices: 204013--204049 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
204003 TCCCTTCTAT
204013 GGTATCGATACCCCCTTC
1 GGTATCGATACCCCCTTC
204031 GGTATCGATACCCCCTTC
1 GGTATCGATACCCCCTTC
204049 G
1 G
204050 ACACCGATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.38, G:0.19, T:0.27
Consensus pattern (18 bp):
GGTATCGATACCCCCTTC
Found at i:204057 original size:18 final size:18
Alignment explanation
Indices: 204018--204060 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
204008 TCTATGGTAT
** *
204018 CGATACCCCCTTCGGTAT
1 CGATACCCCCTTCGACAC
204036 CGATACCCCCTTCGACAC
1 CGATACCCCCTTCGACAC
204054 CGATACC
1 CGATACC
204061 ATTTTGACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.44, G:0.14, T:0.21
Consensus pattern (18 bp):
CGATACCCCCTTCGACAC
Found at i:205363 original size:36 final size:35
Alignment explanation
Indices: 205322--205409 Score: 140
Period size: 36 Copynumber: 2.5 Consensus size: 35
205312 GCGTAGAATT
*
205322 TGTCCCGTAGGACCACTATGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTATGTCCCGAA-GACCACTG
205358 TGTCCCGAAGGACCACTATGTCCCGAAGACCACTG
1 TGTCCCGAAGGACCACTATGTCCCGAAGACCACTG
* *
205393 TATCTCGAAGGACCACT
1 TGTCCCGAAGGACCACT
205410 GATAATCCCT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 23 0.47
36 26 0.53
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.19
Consensus pattern (35 bp):
TGTCCCGAAGGACCACTATGTCCCGAAGACCACTG
Found at i:205410 original size:18 final size:18
Alignment explanation
Indices: 205322--205410 Score: 126
Period size: 18 Copynumber: 5.0 Consensus size: 18
205312 GCGTAGAATT
* *
205322 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTG
205340 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTG
*
205358 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTG
205376 TGTCCCGAA-GACCACTG
1 TGTCCCGAAGGACCACTG
* *
205393 TATCTCGAAGGACCACTG
1 TGTCCCGAAGGACCACTG
205411 ATAATCCCTC
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
17 14 0.22
18 50 0.78
ACGTcount: A:0.25, C:0.33, G:0.24, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTG
Found at i:213417 original size:30 final size:29
Alignment explanation
Indices: 213379--213435 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
213369 GTTGACAATT
*
213379 TTATTTTTA-GGTTGTTGGTATTATAAATG
1 TTATTTTTATGGTTGTTGG-ACTATAAATG
*
213408 TTATGTTTTATGTTTGTTGGACTATAAA
1 TTAT-TTTTATGGTTGTTGGACTATAAA
213436 ATATATAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 4 0.17
30 12 0.50
31 8 0.33
ACGTcount: A:0.25, C:0.02, G:0.19, T:0.54
Consensus pattern (29 bp):
TTATTTTTATGGTTGTTGGACTATAAATG
Found at i:214911 original size:14 final size:14
Alignment explanation
Indices: 214892--214928 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
214882 ATCCAAACAT
214892 TGGAAAATGTTTTC
1 TGGAAAATGTTTTC
214906 TGGAAAATGTTTTC
1 TGGAAAATGTTTTC
*
214920 TGAAAAATG
1 TGGAAAATG
214929 ATTTATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (14 bp):
TGGAAAATGTTTTC
Found at i:215156 original size:80 final size:80
Alignment explanation
Indices: 215033--215186 Score: 220
Period size: 80 Copynumber: 1.9 Consensus size: 80
215023 ACAATTATCG
* * * *
215033 TTTCGATTCAATTAAATTTTGCGATTCTTAATTATTCACATTTTTCAAATTCAACCTCCAAAATA
1 TTTCAATTCAATTAAATTTTGCAATTCTTAACTATTAACATTTTTCAAATTCAACCTCCAAAATA
*
215098 TAAATTTAATTTTCA
66 CAAATTTAATTTTCA
* * *
215113 TTTCAATTCAATT-GATTTTGCAATTCTTGACTATTAACTATTTTTCAAATTCAACCTCTAAAAT
1 TTTCAATTCAATTAAATTTTGCAATTCTTAACTATTAAC-ATTTTTCAAATTCAACCTCCAAAAT
215177 ACAAATTTAA
65 ACAAATTTAA
215187 AGCTTAAATA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
79 20 0.31
80 45 0.69
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (80 bp):
TTTCAATTCAATTAAATTTTGCAATTCTTAACTATTAACATTTTTCAAATTCAACCTCCAAAATA
CAAATTTAATTTTCA
Found at i:218886 original size:16 final size:16
Alignment explanation
Indices: 218835--218889 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
218825 AATTTTAGAC
*
218835 TTTACGAGTATTATTT
1 TTTATGAGTATTATTT
* *
218851 TTT-TTAGTTATT-TTAA
1 TTTATGAG-TATTATT-T
218867 TTTATGAGTATTATTT
1 TTTATGAGTATTATTT
218883 TTTATGA
1 TTTATGA
218890 TTTAAAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
15 4 0.13
16 21 0.70
17 5 0.17
ACGTcount: A:0.25, C:0.02, G:0.11, T:0.62
Consensus pattern (16 bp):
TTTATGAGTATTATTT
Found at i:220233 original size:2 final size:2
Alignment explanation
Indices: 220228--220274 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
220218 TTACTTTTAT
*
220228 TA TA TA TA TA TA TA TA T- TA T- TA T- TA T- TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
220266 TA TA TA TA T
1 TA TA TA TA T
220275 TTACTTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 4 0.10
2 35 0.90
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (2 bp):
TA
Found at i:220282 original size:26 final size:25
Alignment explanation
Indices: 220212--220276 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 25
220202 ATCTTTTTTT
220212 TATATATTACTTTTATTATATATATA
1 TATATATTA-TTTTATTATATATATA
*
220238 TATATATTATTATTATTATATGTATA
1 TATATATTATT-TTATTATATATATA
220264 TATATATATATTT
1 TATATAT-TATTT
220277 ACTTATTTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.06
26 30 0.83
27 4 0.11
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (25 bp):
TATATATTATTTTATTATATATATA
Found at i:220336 original size:18 final size:18
Alignment explanation
Indices: 220307--220361 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
220297 TTTACCATTT
220307 TTATTT-TATTATTATTA
1 TTATTTATATTATTATTA
* **
220324 TTCTTTATATTATCCTTA
1 TTATTTATATTATTATTA
* *
220342 TTATTTCTATTATTACTA
1 TTATTTATATTATTATTA
220360 TT
1 TT
220362 TTTTTACTTA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
17 5 0.17
18 24 0.83
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTTATATTATTATTA
Found at i:220336 original size:21 final size:21
Alignment explanation
Indices: 220306--220346 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
220296 TTTTACCATT
* *
220306 TTTATTTTATTATTATTATTC
1 TTTATATTATCATTATTATTC
*
220327 TTTATATTATCCTTATTATT
1 TTTATATTATCATTATTATT
220347 TCTATTATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTATATTATCATTATTATTC
Done.