Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008940.1 Hibiscus syriacus cultivar Beakdansim tig00112259_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: 476028
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:148840 original size:63 final size:63
Alignment explanation
Indices: 148725--148897 Score: 199
Period size: 63 Copynumber: 2.7 Consensus size: 63
148715 AATTTGTTTT
148725 AAGAGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAA-GGAAAGCAGATTCAAAGATTT-TATT
1 AAGAGAAACTGTCTCAAGAGAGA--AAATTTGTTTCAAGGGAAAG-AGATTCAAAG-TTTATATT
148788 TC
62 TC
* * * * *
148790 AAGGGAAACTGTCTCAAGAGAGAAAATTTATTTCAAGGGAAATG-GTTTCAATGTTTATGTTTC
1 AAGAGAAACTGTCTCAAGAGAGAAAATTTGTTTCAAGGGAAA-GAGATTCAAAGTTTATATTTC
*
148853 AAGAGAAACTGTCTCAAGGGAGATAAAATTTTGTTTCAAGGGAAA
1 AAGAGAAACTGTCTCAA--GAGAGAAAA-TTTGTTTCAAGGGAAA
148898 CTATCTCAAG
Statistics
Matches: 94, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
62 3 0.03
63 40 0.43
64 5 0.05
65 31 0.33
66 15 0.16
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (63 bp):
AAGAGAAACTGTCTCAAGAGAGAAAATTTGTTTCAAGGGAAAGAGATTCAAAGTTTATATTTC
Found at i:148898 original size:37 final size:37
Alignment explanation
Indices: 148847--149018 Score: 118
Period size: 37 Copynumber: 4.9 Consensus size: 37
148837 TCAATGTTTA
*
148847 TGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGATAAAATTT
* * *
148884 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGATAAAATTT
** *
148920 CATTTCAAGGGAAA-TGTTTTC-----A-AT---ATTT
1 TGTTTCAAGGGAAACTG-TCTCAAGGGAGATAAAATTT
** * *
148948 ATGTTTCAAGAAAAACTGTCTCAA-GGA-AGACAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGGGAGATAAAATTT
* *
148984 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGATAAAAT
149019 CTTCTTTTTA
Statistics
Matches: 101, Mismatches: 21, Indels: 26
0.68 0.14 0.18
Matches are distributed among these distances:
27 1 0.01
28 2 0.02
29 13 0.13
30 3 0.03
31 1 0.01
33 2 0.02
35 21 0.21
36 23 0.23
37 35 0.35
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.30
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGGGAGATAAAATTT
Found at i:148954 original size:102 final size:99
Alignment explanation
Indices: 148780--149018 Score: 354
Period size: 100 Copynumber: 2.4 Consensus size: 99
148770 AGATTCAAAG
* * * *
148780 ATTTTATTTCAAGGGAAACTGTCTCAAGAGAG-AAAATTTATTTCAAGGGAAATGGTTTCAATGT
1 ATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAAAAATTCATTTCAAGGGAAATGGTTTCAATAT
* *
148844 TTATGTTTCAAGAGAAACTGTCTCAAGGGAGATAAA
66 TTATGTTTCAAGAAAAACTGTCTCAA-GGA-AGAAA
*
148880 ATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATA
1 ATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA-AAAATTCATTTCAAGGGAAATGGTTTCAATA
*
148945 TTTATGTTTCAAGAAAAACTGTCTCAAGGAAGACA
65 TTTATGTTTCAAGAAAAACTGTCTCAAGGAAGAAA
*
148980 ATTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 ATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA-AAAAT
149019 CTTCTTTTTA
Statistics
Matches: 127, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
100 70 0.55
101 3 0.02
102 54 0.43
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (99 bp):
ATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAAAAATTCATTTCAAGGGAAATGGTTTCAATAT
TTATGTTTCAAGAAAAACTGTCTCAAGGAAGAAA
Found at i:148957 original size:165 final size:164
Alignment explanation
Indices: 148683--148997 Score: 386
Period size: 165 Copynumber: 1.9 Consensus size: 164
148673 TCAAAGATTT
* * * *
148683 TGTTTCACGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGA
* ** **
148748 CGAAATTTGTTTCAAGGAAAGCAGATTCAAAGATTTTATTTCAAGGGAAACTGTCTCAA-GAGAG
66 CAAAATTCATTTCAAGGAAAG-AGATTCAAAGATTTTATTTCAAGAAAAACTGTCTCAAGGA-AG
148812 A-AAATTTATTTCAAGGGAAATGGTTTCAATGTTTA
129 ACAAATTTATTTCAAGGGAAATGGTTTCAATGTTTA
* * *
148847 TGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTATCTCAAGAGAG
** * *
148912 ACAAAATTCATTTCAAGGGAAATG-TTTTC-AATATTTATGTTTCAAGAAAAACTGTCTCAAGGA
65 ACAAAATTCATTTCAA-GGAAA-GAGATTCAAAGATTT-TATTTCAAGAAAAACTGTCTCAAGGA
* *
148975 AGACAATTTTGTTTCAAGGGAAA
127 AGACAAATTTATTTCAAGGGAAA
148998 CTATCTCAAG
Statistics
Matches: 127, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
164 36 0.28
165 66 0.52
166 24 0.19
167 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (164 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGA
CAAAATTCATTTCAAGGAAAGAGATTCAAAGATTTTATTTCAAGAAAAACTGTCTCAAGGAAGAC
AAATTTATTTCAAGGGAAATGGTTTCAATGTTTA
Found at i:150910 original size:20 final size:21
Alignment explanation
Indices: 150885--150939 Score: 94
Period size: 20 Copynumber: 2.7 Consensus size: 21
150875 TTGCAGCCTT
*
150885 GATGCATGGATGCATGGC-AG
1 GATGCATCGATGCATGGCAAG
150905 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
150926 GATGCATCGATGCA
1 GATGCATCGATGCA
150940 CTAATTGCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.27, C:0.18, G:0.35, T:0.20
Consensus pattern (21 bp):
GATGCATCGATGCATGGCAAG
Found at i:150985 original size:20 final size:22
Alignment explanation
Indices: 150960--151015 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
150950 TCGATGTTTG
*
150960 GATGCATGGATGCATT-G-CCT
1 GATGCATGGATGCATTAGTCCA
* *
150980 GATGCATCGATGCATTAGTGCA
1 GATGCATGGATGCATTAGTCCA
151002 GATGCATGGATGCA
1 GATGCATGGATGCA
151016 CTGCAGGGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 15 0.50
21 1 0.03
22 14 0.47
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (22 bp):
GATGCATGGATGCATTAGTCCA
Found at i:151006 original size:42 final size:42
Alignment explanation
Indices: 150959--151059 Score: 118
Period size: 42 Copynumber: 2.4 Consensus size: 42
150949 TTCGATGTTT
* * *
150959 GGATGCATGGATGCATTGC-CTGATGCATCGATGCA-T-TAG
1 GGATGCATGGATGCACTGCACGGATGCATAGATGCACTGTAG
*
150998 TGCAGATGCATGGATGCACTGCAGGGATGCATAGATGCACTGTAG
1 -G--GATGCATGGATGCACTGCACGGATGCATAGATGCACTGTAG
151043 GGATGCATGGATGCACT
1 GGATGCATGGATGCACT
151060 TTGACACCCT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
40 1 0.02
42 33 0.63
43 13 0.25
44 2 0.04
45 3 0.06
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.25
Consensus pattern (42 bp):
GGATGCATGGATGCACTGCACGGATGCATAGATGCACTGTAG
Found at i:151028 original size:21 final size:21
Alignment explanation
Indices: 151002--151059 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
150992 CATTAGTGCA
151002 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
* *
151023 GATGCATAGATGCACTGTAGG
1 GATGCATGGATGCACTGCAGG
151044 GATGCATGGATGCACT
1 GATGCATGGATGCACT
151060 TTGACACCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.26, C:0.17, G:0.34, T:0.22
Consensus pattern (21 bp):
GATGCATGGATGCACTGCAGG
Found at i:151174 original size:30 final size:30
Alignment explanation
Indices: 151140--151199 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
151130 AACTTTGAAT
151140 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
151170 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
151200 CTTAAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:151333 original size:21 final size:21
Alignment explanation
Indices: 151309--151348 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
151299 ATGTTTAATG
151309 AAAAAGATATCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
*
151330 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
151349 TCAATTGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:152529 original size:19 final size:20
Alignment explanation
Indices: 152486--152533 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
152476 TCTAAATCAT
*
152486 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
152506 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
152525 TTTTCAAAA
1 TTTTCAAAA
152534 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:153854 original size:20 final size:21
Alignment explanation
Indices: 153829--153883 Score: 94
Period size: 20 Copynumber: 2.7 Consensus size: 21
153819 TTGCAGCCTT
*
153829 GATGCATGGATGCATGGC-AG
1 GATGCATCGATGCATGGCAAG
153849 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
153870 GATGCATCGATGCA
1 GATGCATCGATGCA
153884 CTAATTGCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.27, C:0.18, G:0.35, T:0.20
Consensus pattern (21 bp):
GATGCATCGATGCATGGCAAG
Found at i:153972 original size:21 final size:21
Alignment explanation
Indices: 153946--154003 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
153936 CATTAGTGCA
153946 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
153967 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
153988 GATGCATGGATGCACT
1 GATGCATGGATGCACT
154004 TTGACACCCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (21 bp):
GATGCATGGATGCACTGCAGG
Found at i:154118 original size:30 final size:30
Alignment explanation
Indices: 154084--154143 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
154074 AACTTTGAAT
154084 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
154114 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
154144 CTTAAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:160444 original size:15 final size:15
Alignment explanation
Indices: 160424--160457 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
160414 GTTTCTCTAA
160424 ATATAATAAA-TTGAT
1 ATATAATAAACTT-AT
160439 ATATAATAAACTTAT
1 ATATAATAAACTTAT
160454 ATAT
1 ATAT
160458 GAATCCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (15 bp):
ATATAATAAACTTAT
Found at i:169637 original size:9 final size:9
Alignment explanation
Indices: 169623--169652 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
169613 AAAATGGCTT
169623 AAAATGAAG
1 AAAATGAAG
169632 AAAATGAAG
1 AAAATGAAG
169641 -AAATGAAG
1 AAAATGAAG
169649 AAAA
1 AAAA
169653 CTTACATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (9 bp):
AAAATGAAG
Found at i:172125 original size:117 final size:116
Alignment explanation
Indices: 171946--172546 Score: 601
Period size: 117 Copynumber: 5.1 Consensus size: 116
171936 TTTTAAATAA
* *
171946 TCAAATCCATCACAAAAAGAGTTGGATCAACATTTTCAAT-AGAGAGTTCATAATGAGAAGAACT
1 TCAAATCCATCAC-AGAAGAGTTGGATTAACA-TTTCAATGAGAGAGTTCATAATGAGAAGAACT
* * * * **
172010 C-GCCTACGAAGAGAGAATAAGTTCATAATGAGAAGAATTTGTTTAACCTTATGC
64 CATCC-ACGAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTT-TGC
* * *
172064 TCAAATCCATCACAGAATGAGCTAGATTAACATTTCAATGAG-GAGCTCATAATGAGAAGAACTC
1 TCAAATCCATCACAGAA-GAGTTGGATTAACATTTCAATGAGAGAGTTCATAATGAGAAGAACTC
* * *
172128 ATCCACGGAGGGAGAAGAAGTTCATAATGAGAATAACTTGTTCGACCTTTTGT
65 ATCCACGAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACC-TTTGC
* * * *
172181 TCAAATGCATCACAGAAGGAGTTTGATTAACATTTCCAATG-GAGAGTTCA-AATAAGAATAACT
1 TCAAATCCATCACAGAA-GAGTTGGATTAACATTT-CAATGAGAGAGTTCATAATGAGAAGAACT
* * *
172244 CATCCAAG-AGGGAGAAGAAGTTCATACTGAGAAAAACTTGTTCGACCTTTCGC
64 CATCCACGAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTT-GC
* * * * *
172297 TCAAATCCATCACAGAAGAAGGTGGATTAACATTTCATTCAGA-AGTTCATATTTAGAAGAACTC
1 TCAAATCCATCACAGAAG-AGTTGGATTAACATTTCAATGAGAGAGTTCATAATGAGAAGAACTC
* * * * *
172361 ATCTACGAAGGGAGAAAAATTTCATAATAAGAAGAACTTGTTCGACCTTTCGT
65 ATCCACGAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTT-GC
* * * * * ** *
172414 TTAAATACATCACAAAAGGAGTTGGATCAATATTTCCAAT-AGAGAGTTTGTAATGAAAAGAACT
1 TCAAATCCATCACAGAA-GAGTTGGATTAACATTT-CAATGAGAGAGTTCATAATGAGAAGAACT
* * ** *
172478 CATCAAAGAA-GGAGAAGAAGTTCATAATGAGAAGAGTTTG-TCGACCTTTCAC
64 CATCCACGAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTT-GC
*
172530 TCAAATTCATCACAGAA
1 TCAAATCCATCACAGAA
172547 AGAGGAGGAT
Statistics
Matches: 404, Mismatches: 65, Indels: 30
0.81 0.13 0.06
Matches are distributed among these distances:
115 13 0.03
116 110 0.27
117 213 0.53
118 68 0.17
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (116 bp):
TCAAATCCATCACAGAAGAGTTGGATTAACATTTCAATGAGAGAGTTCATAATGAGAAGAACTCA
TCCACGAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTTGC
Found at i:172362 original size:233 final size:233
Alignment explanation
Indices: 171946--172546 Score: 717
Period size: 233 Copynumber: 2.6 Consensus size: 233
171936 TTTTAAATAA
* * * *
171946 TCAAATCCATCACAAAAAGAGTTGGATCAACATTTTCAATAGAGAGTTCATAATGAGAAGAACTC
1 TCAAATACATCACAAAAGGAGTTGGATCAACATTTCCAATAGAGAGTTCA-AATAAGAAGAACTC
* * * * **
172011 -GCCTACGAAGAGAGAATAAGTTCATAATGAGAAGAATTTGTTTAACCTTAT-GCTCAAATCCAT
65 ATCC-AAG-AGGGAGAAGAAGTTCATAATGAGAAGAATTTGTTCGACCTT-TCGCTCAAATCCAT
* * *
172074 CACAGAATGAGCTAGATTAACATTTCAATGAGGAGCTCATAATGAGAAGAACTCATCCACGGAGG
127 CACAGAATGAGCTAGATTAACATTTCAATCAGAAGCTCATAATGAGAAGAACTCATCCACGAAGG
* * * *
172139 GAGAAGAAGTTCATAATGAGAATAACTTGTTCGACCTTTTGT
192 GAGAAAAAGTTCATAATAAGAAGAACTTGTTCGACCTTTCGT
* * * * * *
172181 TCAAATGCATCACAGAAGGAGTTTGATTAACATTTCCAATGGAGAGTTCAAATAAGAATAACTCA
1 TCAAATACATCACAAAAGGAGTTGGATCAACATTTCCAATAGAGAGTTCAAATAAGAAGAACTCA
* * *
172246 TCCAAGAGGGAGAAGAAGTTCATACTGAGAAAAACTTGTTCGACCTTTCGCTCAAATCCATCACA
66 TCCAAGAGGGAGAAGAAGTTCATAATGAGAAGAATTTGTTCGACCTTTCGCTCAAATCCATCACA
* * * * * * *
172311 GAA-GAAGGTGGATTAACATTTCATTCAGAAGTTCATATTTAGAAGAACTCATCTACGAAGGGAG
131 GAATG-AGCTAGATTAACATTTCAATCAGAAGCTCATAATGAGAAGAACTCATCCACGAAGGGAG
*
172375 AAAAATTTCATAATAAGAAGAACTTGTTCGACCTTTCGT
195 AAAAAGTTCATAATAAGAAGAACTTGTTCGACCTTTCGT
* * **
172414 TTAAATACATCACAAAAGGAGTTGGATCAATATTTCCAATAGAGAGTTTGTAATGAA-AAGAACT
1 TCAAATACATCACAAAAGGAGTTGGATCAACATTTCCAATAGAGAG-TTCAAAT-AAGAAGAACT
* * * * *
172478 CATCAAAGAAGGAGAAGAAGTTCATAATGAGAAGAGTTTG-TCGACCTTTCACTCAAATTCATCA
64 CATCCAAGAGGGAGAAGAAGTTCATAATGAGAAGAATTTGTTCGACCTTTCGCTCAAATCCATCA
172542 CAGAA
129 CAGAA
172547 AGAGGAGGAT
Statistics
Matches: 310, Mismatches: 51, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
232 2 0.01
233 202 0.65
234 59 0.19
235 47 0.15
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (233 bp):
TCAAATACATCACAAAAGGAGTTGGATCAACATTTCCAATAGAGAGTTCAAATAAGAAGAACTCA
TCCAAGAGGGAGAAGAAGTTCATAATGAGAAGAATTTGTTCGACCTTTCGCTCAAATCCATCACA
GAATGAGCTAGATTAACATTTCAATCAGAAGCTCATAATGAGAAGAACTCATCCACGAAGGGAGA
AAAAGTTCATAATAAGAAGAACTTGTTCGACCTTTCGT
Found at i:172966 original size:5 final size:5
Alignment explanation
Indices: 172926--173082 Score: 50
Period size: 5 Copynumber: 32.2 Consensus size: 5
172916 TATTTCTTAT
* * *
172926 TATT- TATTA T-TTAA TATTA T-TTT TATTA CAATTA TATTA TAATAA
1 TATTA TATTA TATT-A TATTA TATTA TATTA -TATTA TATTA T-ATTA
* * * *
172971 TATTA TTATTA CATAA TATTA T-TTA -CTTA TATTA TATCA TA-TA TCA-TA
1 TATTA -TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA T-ATTA
* * * * *
173019 TATTA TAATTA TGTTA T-GTA TCA-CA TTTTA TATTA GATTA TATT- TATTA
1 TATTA T-ATTA TATTA TATTA T-ATTA TATTA TATTA TATTA TATTA TATTA
173068 TA-TA GTATTA T-TTA T
1 TATTA -TATTA TATTA T
173083 GTAGTTATTA
Statistics
Matches: 114, Mismatches: 21, Indels: 36
0.67 0.12 0.21
Matches are distributed among these distances:
4 31 0.27
5 61 0.54
6 22 0.19
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.55
Consensus pattern (5 bp):
TATTA
Found at i:172986 original size:16 final size:15
Alignment explanation
Indices: 172929--172993 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 15
172919 TTCTTATTAT
*
172929 TTATTATTTAATATTA
1 TTATTA-TTAATAATA
* *
172945 TTTTTATT-ACAAT-
1 TTATTATTAATAATA
172958 TATATTA-TAATAATA
1 T-TATTATTAATAATA
172973 TTATTATTACATAATA
1 TTATTATTA-ATAATA
172989 TTATT
1 TTATT
172994 TACTTATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
13 2 0.05
14 16 0.41
15 5 0.13
16 16 0.41
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTATTAATAATA
Found at i:176251 original size:16 final size:17
Alignment explanation
Indices: 176232--176263 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
176222 ACATTTTAAG
176232 ATTTTCTC-TTAATTTT
1 ATTTTCTCATTAATTTT
176248 ATTTTCTCATTAATTT
1 ATTTTCTCATTAATTT
176264 ATGTCACATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.22, C:0.12, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTTCTCATTAATTTT
Found at i:188986 original size:21 final size:21
Alignment explanation
Indices: 188960--188999 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
188950 CCCCCTTTGA
*
188960 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
188981 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
189000 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:196000 original size:15 final size:16
Alignment explanation
Indices: 195969--196002 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
195959 CCTCTCAGAA
195969 TCTTCTGCTTACCTTT
1 TCTTCTGCTTACCTTT
*
195985 TCTTCTG-TTACTTTT
1 TCTTCTGCTTACCTTT
196000 TCT
1 TCT
196003 CGTAACCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.06, C:0.26, G:0.06, T:0.62
Consensus pattern (16 bp):
TCTTCTGCTTACCTTT
Found at i:197124 original size:144 final size:144
Alignment explanation
Indices: 196889--197161 Score: 510
Period size: 144 Copynumber: 1.9 Consensus size: 144
196879 TTATTCACTG
*
196889 TAAACCGTCGTCGATCGTCGTAGGTGGCCCTTTAAGCTCTGTTGAAAACCTAAAAACCCACCGTT
1 TAAACCGTCGTCGATCGTCGTAGGTGGCCCTTTAAGCTCCGTTGAAAACCTAAAAACCCACCGTT
196954 GATATTCTTCATGATTCTGGCCACCGTAGGCGTTCGTAGGTCGTAACGTCGCCACCAAAGTGACT
66 GATATTCTTCATGATTCTGGCCACCGTAGGCGTTCGTAGGTCGTAACGTCGCCACCAAAGTGACT
197019 GTCGTCCGCCCCTA
131 GTCGTCCGCCCCTA
*
197033 TAAACTGTCGTCGATCGTCGTAGGTGGCCCTTTAAGCTCCGTTGAAAACCTAAAAACCCACCGTT
1 TAAACCGTCGTCGATCGTCGTAGGTGGCCCTTTAAGCTCCGTTGAAAACCTAAAAACCCACCGTT
* *
197098 GATATTCTTCATGATTCTGGCTACCGTAGGCGTTCGTAGGTCGTAACGTCGCCACCAACGTGAC
66 GATATTCTTCATGATTCTGGCCACCGTAGGCGTTCGTAGGTCGTAACGTCGCCACCAAAGTGAC
197162 CGCTGTCCGC
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 125 1.00
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (144 bp):
TAAACCGTCGTCGATCGTCGTAGGTGGCCCTTTAAGCTCCGTTGAAAACCTAAAAACCCACCGTT
GATATTCTTCATGATTCTGGCCACCGTAGGCGTTCGTAGGTCGTAACGTCGCCACCAAAGTGACT
GTCGTCCGCCCCTA
Found at i:198099 original size:24 final size:25
Alignment explanation
Indices: 198072--198119 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
198062 TTATCTTATA
198072 TTAAT-AAAAAATCTATTTGAGTGC
1 TTAATAAAAAAATCTATTTGAGTGC
198096 TTAATAAAAAAAATCTATTTGAGT
1 TTAAT-AAAAAAATCTATTTGAGT
198120 AAAGGAGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 5 0.23
26 17 0.77
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (25 bp):
TTAATAAAAAAATCTATTTGAGTGC
Found at i:203687 original size:22 final size:22
Alignment explanation
Indices: 203662--203710 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
203652 AGCCTTCTGA
203662 TCAATGAGTAGCTGAATTTCTT
1 TCAATGAGTAGCTGAATTTCTT
203684 TCAATGAGTAGCTGAATTTCTT
1 TCAATGAGTAGCTGAATTTCTT
203706 TCAAT
1 TCAAT
203711 TCGTCTGGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (22 bp):
TCAATGAGTAGCTGAATTTCTT
Found at i:204585 original size:4 final size:4
Alignment explanation
Indices: 204576--204602 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
204566 ACTAATGCTA
204576 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
204603 ACATTCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:205811 original size:2 final size:2
Alignment explanation
Indices: 205795--205841 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
205785 TTTAAATTAT
*
205795 TA TA TA TG TA T- TA TA TA TA TA TA TA TA TA TA 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
205836 TA TA TA
1 TA TA TA
205842 ATAATATGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:206930 original size:34 final size:34
Alignment explanation
Indices: 206892--206960 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
206882 AGACATAACT
* *
206892 ATAGATGTTATATTATATATGATGATGAATGTCA
1 ATAGATATTATATTATATATGATGATGAATATCA
206926 ATAGATATTATATTATATATGATGATGAATATCA
1 ATAGATATTATATTATATATGATGATGAATATCA
206960 A
1 A
206961 CTTAACATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.42, C:0.03, G:0.14, T:0.41
Consensus pattern (34 bp):
ATAGATATTATATTATATATGATGATGAATATCA
Found at i:207981 original size:79 final size:80
Alignment explanation
Indices: 207834--207983 Score: 284
Period size: 79 Copynumber: 1.9 Consensus size: 80
207824 AATTATGGCC
207834 TCAAAAATATTTTGAAATATACCGTTGATGAAAAATCTATTTTGAGATCTTTTGATATTTAATAT
1 TCAAAAATATTTTGAAATATACCGTTGATGAAAAATCTATTTTGAGATCTTTTGATATTTAATAT
207899 AATGCTACTATGGGA
66 AATGCTACTATGGGA
*
207914 TCAAAAATATTTTGAAATATACGGTTGATG-AAAATCTATTTTGAGATCTTTTGATATTTAATAT
1 TCAAAAATATTTTGAAATATACCGTTGATGAAAAATCTATTTTGAGATCTTTTGATATTTAATAT
207978 AATGCT
66 AATGCT
207984 TACATGACTA
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
79 40 0.58
80 29 0.42
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.41
Consensus pattern (80 bp):
TCAAAAATATTTTGAAATATACCGTTGATGAAAAATCTATTTTGAGATCTTTTGATATTTAATAT
AATGCTACTATGGGA
Found at i:210538 original size:138 final size:136
Alignment explanation
Indices: 210370--210686 Score: 323
Period size: 138 Copynumber: 2.3 Consensus size: 136
210360 TAATTAGGAT
* * * * *
210370 TAATATTAGAGCTTCCATCTTAGGCCTAATTTCACATTTAGTCATTAAAT-TAGGAGACTTCTT-
1 TAATATTAGAGCCTCCATTTTAGG-TTAATTTCA-ATTTAGTCATTAAATCTAAGAGAATT-TTC
* * * * * *
210433 AATTTGGTCCTCGCTTTTGCTCGATGTTCCAATTTAATTCTTCGAATTGCATAATTGATTAAAAT
63 AATTTGGTCCTCACTTTTACTCGAGGTTCCAATTTAATTATTCGAATTGCACAATTAATTAAAAT
*
210498 CGAATAGGG
128 CGAATAAGG
* * * * * *
210507 TAATGTTTAGAGCCTCCATTTTAGGTTTAATTTGAACTTAGTCCTTTAATCTAAGAGAATTTTCG
1 TAAT-ATTAGAGCCTCCATTTTAGG-TTAATTTCAATTTAGTCATTAAATCTAAGAGAATTTTCA
* * * *
210572 ATTTGGTCTTCACTTTTACTCGAGGTTCCAATTTAATTATTTGAATTTCACAATTAATTAAAATT
64 ATTTGGTCCTCACTTTTACTCGAGGTTCCAATTTAATTATTCGAATTGCACAATTAATTAAAATC
* *
210637 GAGTAAGT
129 GAATAAGG
* * *
210645 TAATATTAAAGCCACCACTTTAGGTTAGATTTCAATTTAGTC
1 TAATATTAGAGCCTCCATTTTAGGTTA-ATTTCAATTTAGTC
210687 CCTTTAATTT
Statistics
Matches: 145, Mismatches: 31, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
136 3 0.02
137 46 0.32
138 96 0.66
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (136 bp):
TAATATTAGAGCCTCCATTTTAGGTTAATTTCAATTTAGTCATTAAATCTAAGAGAATTTTCAAT
TTGGTCCTCACTTTTACTCGAGGTTCCAATTTAATTATTCGAATTGCACAATTAATTAAAATCGA
ATAAGG
Found at i:212189 original size:29 final size:30
Alignment explanation
Indices: 212147--212206 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
212137 TGAATAATAA
212147 TTTTGACTAACTTGATTCT-TTTTGTCTTG
1 TTTTGACTAACTTGATTCTCTTTTGTCTTG
* * *
212176 TTTTTACTAACTTGATTTTCTTTTGTTTTG
1 TTTTGACTAACTTGATTCTCTTTTGTCTTG
212206 T
1 T
212207 CTTGTCTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.13, C:0.12, G:0.12, T:0.63
Consensus pattern (30 bp):
TTTTGACTAACTTGATTCTCTTTTGTCTTG
Found at i:214036 original size:17 final size:17
Alignment explanation
Indices: 214016--214058 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
214006 AAGATATAAC
*
214016 AAAAAGAATAAAAAAAT
1 AAAAAGAATAAAAAAAG
*
214033 AAAAAAAATAAAAAAAG
1 AAAAAGAATAAAAAAAG
214050 AGAAAAGAA
1 A-AAAAGAA
214059 AGAAAGAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.07
Consensus pattern (17 bp):
AAAAAGAATAAAAAAAG
Found at i:214037 original size:9 final size:9
Alignment explanation
Indices: 214016--214048 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
214006 AAGATATAAC
*
214016 AAAAAGAAT
1 AAAAAAAAT
214025 -AAAAAAAT
1 AAAAAAAAT
214033 AAAAAAAAT
1 AAAAAAAAT
214042 AAAAAAA
1 AAAAAAA
214049 GAGAAAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:214197 original size:5 final size:5
Alignment explanation
Indices: 214187--214220 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
214177 ATAGAACACC
214187 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
214221 GACACACAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:215802 original size:138 final size:139
Alignment explanation
Indices: 215616--215907 Score: 326
Period size: 138 Copynumber: 2.1 Consensus size: 139
215606 ATTTGATTCT
* *
215616 ATAATTGACTAAAAT-TAATTAGGATTAGTATTAGAGCCTCCATATTAGGCCTAAATT-CACATT
1 ATAATTGATTAAAATCTAATTAGGATAAGTATTAGAGCCTCCATATTAGGCCTAAATTGCAC--T
*
215679 TAGTCC-TTAAATTAGGAGAATTCTTAATTTGGTCCTT-GCTTTTGCTCGAGGTTCCAAAAAAAT
64 TAGTCCTTTAAATTAAGAGAATTCTTAATTTGGT-CTTCGCTTTTGCTCGAGGTTCCAAAAAAAT
* *
215742 TCTTCGAATTGG
128 TATTCGAATTGC
* * * ** * *
215754 ATAATTGATTAAAATCTAA-TAGGGTAATGT-TTATAGCCTCCATTTTAGGTTTAATTTGGACTT
1 ATAATTGATTAAAATCTAATTAGGATAA-GTATTAGAGCCTCCATATTAGGCCTAAATTGCACTT
* * * ***
215817 AGTCCTTTAATTTAAGAGAATTTTTGATTTGGTCTTCGCTTTTGCTCGAGGTTCCAATTTAATTA
65 AGTCCTTTAAATTAAGAGAATTCTTAATTTGGTCTTCGCTTTTGCTCGAGGTTCCAAAAAAATTA
*
215882 TTCGAATTTC
130 TTCGAATTGC
*
215892 ATAATTAATTAAAATC
1 ATAATTGATTAAAATC
215908 GAGTAAGTTA
Statistics
Matches: 129, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
137 10 0.08
138 112 0.87
139 7 0.05
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (139 bp):
ATAATTGATTAAAATCTAATTAGGATAAGTATTAGAGCCTCCATATTAGGCCTAAATTGCACTTA
GTCCTTTAAATTAAGAGAATTCTTAATTTGGTCTTCGCTTTTGCTCGAGGTTCCAAAAAAATTAT
TCGAATTGC
Found at i:215962 original size:138 final size:138
Alignment explanation
Indices: 215671--215968 Score: 325
Period size: 138 Copynumber: 2.2 Consensus size: 138
215661 TAGGCCTAAA
* *
215671 TTCACATTTAGTCC-TTAAATTAGGAGAATTCTTAATTTGGTCCTTGCTTTTGCTCGAGGTTCCA
1 TTCA-ATTTAGTCCTTTAATTTAAGAGAATTCTTAATTTGGTCCTTGCTTTTGCTCGAGGTTCCA
* * * * * * * *
215735 AAAAAATTCTTCGAATTGGATAATTGATTAAAATCTAATAGGGTAATGTTTATAGCCTCCATTTT
65 AAAAAATTATTCGAATTGCATAATTAATTAAAATCGAATAAGGTAATATTAATAGCCTCCACTTT
215800 AGGTTTAAT
130 AGGTTTAAT
** * * *
215809 TTGGACTTAGTCCTTTAATTTAAGAGAATTTTTGATTTGGT-CTTCGCTTTTGCTCGAGGTTCCA
1 TTCAATTTAGTCCTTTAATTTAAGAGAATTCTTAATTTGGTCCTT-GCTTTTGCTCGAGGTTCCA
*** * * * **
215873 ATTTAATTATTCGAATTTCATAATTAATTAAAATCGAGTAAGTTAATATTAAT-TTCTCCACTTT
65 AAAAAATTATTCGAATTGCATAATTAATTAAAATCGAATAAGGTAATATTAATAGCCTCCACTTT
215937 AGG-TTAGAT
130 AGGTTTA-AT
215946 TTCAATTTAGTCCCTTTAATTTA
1 TTCAATTTAGT-CCTTTAATTTA
215969 GGGAGTAATC
Statistics
Matches: 130, Mismatches: 26, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
136 3 0.02
137 32 0.25
138 95 0.73
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.43
Consensus pattern (138 bp):
TTCAATTTAGTCCTTTAATTTAAGAGAATTCTTAATTTGGTCCTTGCTTTTGCTCGAGGTTCCAA
AAAAATTATTCGAATTGCATAATTAATTAAAATCGAATAAGGTAATATTAATAGCCTCCACTTTA
GGTTTAAT
Found at i:216854 original size:23 final size:24
Alignment explanation
Indices: 216802--216855 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
216792 AAAAATATTG
216802 TAATTA-ATATTTTAAATAATTTA
1 TAATTATATATTTTAAATAATTTA
** *
216825 TGTTTATAT-TTTTAACTAATTTA
1 TAATTATATATTTTAAATAATTTA
216848 TAATTATA
1 TAATTATA
216856 CGTTGAGTAC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
TAATTATATATTTTAAATAATTTA
Found at i:222784 original size:3 final size:3
Alignment explanation
Indices: 222776--222829 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
222766 TGCTCTCCTT
222776 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
222824 TAA TAA
1 TAA TAA
222830 ATTATTTTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:224468 original size:23 final size:23
Alignment explanation
Indices: 224442--224489 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
224432 ATAAAGTACA
*
224442 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
224465 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
224488 AT
1 AT
224490 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:225238 original size:18 final size:18
Alignment explanation
Indices: 225215--225251 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
225205 CGAAATATAT
225215 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
225233 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
225251 A
1 A
225252 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:225481 original size:23 final size:23
Alignment explanation
Indices: 225455--225519 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
225445 ATGCGAGATA
225455 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
**
225478 GATACCTATTACATTATATAAGG
1 GATACCTATTACATTATATAAAC
* *
225501 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
225520 GTTTACCTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:225914 original size:23 final size:23
Alignment explanation
Indices: 225884--225946 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
225874 AATATAACCC
225884 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
225907 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
225930 TACCTATTACATCATAT
1 TACCTATTACATTATAT
225947 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:229221 original size:184 final size:181
Alignment explanation
Indices: 228493--229335 Score: 1497
Period size: 181 Copynumber: 4.7 Consensus size: 181
228483 TTTTAAATGG
* *
228493 TATGGACATAAAGTACCGACACAATATTATAAAGTGTCG--ATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
* *
228556 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGACC-
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTCCG
228620 -TGGAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 ATGGAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
228670 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
228735 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGG-ACG
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTCCG
*
228799 CTCGGAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 AT-GGAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
228851 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
228916 TAAGAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTC
66 TAAG-ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGG-TC
228981 CGATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
129 CGATG-G-AAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
229036 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
229101 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGG-TCC
229166 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
130 GATG-G-AAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
229220 TATGGACATAAAGTACCG--ACAATATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
229282 TAAGACCGGTATATTTATACCGGTTATATTAC-AAATTATCTATTACATTATAAT
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
229336 ATGTTGAAAG
Statistics
Matches: 650, Mismatches: 6, Indels: 17
0.97 0.01 0.03
Matches are distributed among these distances:
177 38 0.06
178 1 0.00
179 83 0.13
180 23 0.04
181 186 0.29
182 65 0.10
183 1 0.00
184 137 0.21
185 116 0.18
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (181 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTCCG
ATGGAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
Found at i:229252 original size:366 final size:359
Alignment explanation
Indices: 228493--229335 Score: 1484
Period size: 366 Copynumber: 2.3 Consensus size: 359
228483 TTTTAAATGG
*
228493 TATGGACATAAAGTACCGACACAATATTATAAAGTGTCG--ATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGA-ACAATATTA-AAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
228556 TAA-AACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGACC
64 TAAGAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGACC
228620 TGGAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTA
129 TGGAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTA
228685 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATT
194 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATT
*
228750 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGACGCTCGGAAAATGTCGAC
259 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGACGATCGGAAAATGTCGAC
228815 ACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
324 ACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
228851 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGA-ACAATATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
228916 TAAGAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTC
64 TAAGAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGG-AC
228981 CGATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATA
128 C--TG-G-AAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATA
229046 AAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGT
189 AAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGT
*
229111 ATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGAT-GTGTAA
254 ATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGG--ACGATCG-G-AA
229175 AATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
315 AATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
229220 TATGGACATAAAGTACCG-ACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATA
1 TATGGACATAAAGTACCGAACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATA
229284 AG-ACCGGTATATTTATACCGGTTATATTAC-AAATTATCTATTACATTATAAT
66 AGAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
229336 ATGTTGAAAG
Statistics
Matches: 468, Mismatches: 4, Indels: 20
0.95 0.01 0.04
Matches are distributed among these distances:
358 37 0.08
359 1 0.00
360 26 0.06
361 58 0.12
362 2 0.00
364 24 0.05
365 29 0.06
366 213 0.46
367 9 0.02
368 4 0.01
369 65 0.14
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (359 bp):
TATGGACATAAAGTACCGAACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATA
AGAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGACCTG
GAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACC
GACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTA
TACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGACGATCGGAAAATGTCGACAC
TTTTTTAAATCGTATCGACACATTTTTCTTCCAA
Found at i:230706 original size:3 final size:3
Alignment explanation
Indices: 230698--230784 Score: 75
Period size: 3 Copynumber: 29.0 Consensus size: 3
230688 ACTTGTTTGG
* * * * **
230698 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC AGC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
230746 AGC TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
230785 TTCAGCTTCA
Statistics
Matches: 63, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.24, C:0.34, G:0.07, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:230721 original size:18 final size:18
Alignment explanation
Indices: 230698--230799 Score: 78
Period size: 18 Copynumber: 5.7 Consensus size: 18
230688 ACTTGTTTGG
230698 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* * *
230716 ATCATCATCATCGTCAGC
1 ATCATCATCTTCATCATC
* ** * *
230734 ATCTTCATCGCCAGCTTC
1 ATCATCATCTTCATCATC
* *
230752 ATCGTCATCATCATCATC
1 ATCATCATCTTCATCATC
* *
230770 ATCGTCATCTTCATCTTC
1 ATCATCATCTTCATCATC
* *
230788 AGCTTCATCTTC
1 ATCATCATCTTC
230800 TGCGACCGAT
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:230765 original size:42 final size:42
Alignment explanation
Indices: 230706--230796 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
230696 GGATCATCAT
*
230706 CTTCATCATCATCATCATCATCGTCAG-CATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATC-GTCATCTTCATCGCCAG
* **
230748 CTTCATCGTCATCATCATCATCATCGTCATCTTCATCTTCAG
1 CTTCATCATCATCATCATCATCATCGTCATCTTCATCGCCAG
230790 CTTCATC
1 CTTCATC
230797 TTCTGCGACC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 1 0.02
42 43 0.98
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCGTCATCTTCATCGCCAG
Found at i:230785 original size:6 final size:6
Alignment explanation
Indices: 230702--230799 Score: 70
Period size: 6 Copynumber: 16.3 Consensus size: 6
230692 GTTTGGATCA
* * * * * * * * *
230702 TCATCT TCATCA TCATCA TCATCA TCGTCA GCATCT TCATCG CCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * *
230750 TCATCG TCATCA TCATCA TCATCG TCATCT TCATCT TCAGCT TCATCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
230798 TC
1 TC
230800 TGCGACCGAT
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.21, C:0.35, G:0.07, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:233107 original size:199 final size:199
Alignment explanation
Indices: 232259--233682 Score: 2597
Period size: 199 Copynumber: 7.1 Consensus size: 199
232249 TTTAAATTAG
* *
232259 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
232324 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
232389 CGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
232452 AAAA
196 AAAA
*
232456 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
232521 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
232586 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
232651 AAAA
196 AAAA
232655 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
232719 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
232784 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
232848 AAAA
196 AAAA
232852 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
232917 ACTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
232981 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
233046 AAAAA
195 AAAAA
233051 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
233116 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
233181 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
233246 AAAAA
195 AAAAA
233251 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
* * *
233316 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTGGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
233381 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
233446 AAAA
196 AAAA
233450 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
233515 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
233580 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCGTGCACCTTGTTTTTAATTCATTCTG
131 CGACAC-TTTTTATATATGGATCGACACTTTAT--G-G-GTGCACCTTGTTTTTAATTCATTCTG
*
233645 GAAAAAATA
191 GAAAAAAAA
* *
233654 TTTCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
233683 TGACCCTTAA
Statistics
Matches: 1195, Mismatches: 21, Indels: 15
0.97 0.02 0.01
Matches are distributed among these distances:
197 264 0.22
198 187 0.16
199 407 0.34
200 276 0.23
203 1 0.00
204 60 0.05
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
AAAA
Found at i:233398 original size:399 final size:398
Alignment explanation
Indices: 232259--233682 Score: 2624
Period size: 399 Copynumber: 3.6 Consensus size: 398
232249 TTTAAATTAG
* *
232259 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
232324 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
232389 CGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
*
232452 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
232517 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
232582 GGATCGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGG
326 GGATCGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGG
*
232647 GAAAAAAA
391 AAAAAAAA
232655 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
232719 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
232784 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
232848 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
*
232913 TATAACTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
*
232977 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
326 GGATCGACAC-TTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTG
233042 GAAAAAAAA
390 GAAAAAAAA
233051 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
233116 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
233181 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
233246 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
195 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
* *
233311 GTATAATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTG
260 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
*
233376 GGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTG
325 GGGATCGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTG
233441 GAAAAAAAA
390 GAAAAAAAA
233450 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
233515 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
233580 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCGTGCACCTTGTTTTTAATTCATTCTG
131 CGACAC-TTTTTATATATGGATCGACACTTTAT--G-G-GTGCACCTTGTTTTTAATTCATTCTG
* * *
233645 GAAAAAATATTTCGACACAAACTATATTAGTATCGACA
191 GAAAAAAAATATCGACACAAACTATATTAGTGTCGACA
233683 TGACCCTTAA
Statistics
Matches: 1001, Mismatches: 16, Indels: 15
0.97 0.02 0.01
Matches are distributed among these distances:
395 134 0.13
396 272 0.27
397 114 0.11
398 38 0.04
399 329 0.33
400 51 0.05
401 1 0.00
402 1 0.00
403 61 0.06
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (398 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
GGATCGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGG
AAAAAAAA
Found at i:233791 original size:19 final size:19
Alignment explanation
Indices: 233764--233808 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
233754 ATTCACATAA
* *
233764 AAAAATATAAATCGTATAC
1 AAAATTATAAATAGTATAC
*
233783 AAAATTATAAATATTATAC
1 AAAATTATAAATAGTATAC
233802 AAAATTA
1 AAAATTA
233809 ACTCGACATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATAGTATAC
Found at i:235636 original size:33 final size:33
Alignment explanation
Indices: 235599--235664 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
235589 CATCTTAATA
*
235599 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
235632 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
235665 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:237821 original size:24 final size:24
Alignment explanation
Indices: 237784--237836 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
237774 CCGTTCTATC
237784 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
237808 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
237832 TATTT
1 TATTT
237837 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:238026 original size:20 final size:19
Alignment explanation
Indices: 237980--238026 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
237970 TCCGGTATCA
*
237980 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
237999 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
238020 TTTTACC
1 TTTTACC
238027 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:238173 original size:20 final size:20
Alignment explanation
Indices: 238147--238192 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
238137 CACTTTTAAA
238147 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
238166 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
238187 TTTACC
1 TTTACC
238193 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:238673 original size:228 final size:227
Alignment explanation
Indices: 238257--238704 Score: 776
Period size: 229 Copynumber: 2.0 Consensus size: 227
238247 TTAAAACTGC
238257 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
**
238322 TTAATTTATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTATT
66 TTAATTTATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATT
* *
238387 TAGCATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAAG
131 TAGCATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAG
*
238452 TATGGACACTTTTATAAAAATGATATATACTT
196 TATGGACACTTTTATAAAAAGGATATATACTT
238484 TTTTGAAAGTTATGTAATTTATGTTTCAAATTT-TTTAATAGTGTTTCATGTTTTCCACCTACAA
1 TTTT-AAAGTTATGTAATTTATGTTTC-AATTTATTTAATAGTGTTTCATGTTTTCCACCTACAA
*
238548 TATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATT
64 TATTAATTT-ATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATT
*
238613 ATTTAG-ATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTC-ACAGTGAAA
128 ATTTAGCA-TTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAA
238676 TAAGTATGGACACTTTTATAAAAAGGATA
192 TAAGTATGGACACTTTTATAAAAAGGATA
238705 GATAATTTAC
Statistics
Matches: 210, Mismatches: 7, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
227 4 0.02
228 100 0.48
229 106 0.50
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (227 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATT
TAGCATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAG
TATGGACACTTTTATAAAAAGGATATATACTT
Found at i:241271 original size:21 final size:21
Alignment explanation
Indices: 241245--241287 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
241235 TTTCTGGGTT
* *
241245 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
241266 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
241287 A
1 A
241288 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:241362 original size:67 final size:69
Alignment explanation
Indices: 241267--241419 Score: 202
Period size: 68 Copynumber: 2.2 Consensus size: 69
241257 ACCCATTCAA
* * * *
241267 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGGTACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCACA
241331 -GGG
66 GGGG
* * * * *
241334 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCATA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCACA
241399 GGGG
66 GGGG
*
241403 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
241420 ATGAGAAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
67 26 0.35
68 29 0.39
69 19 0.26
ACGTcount: A:0.27, C:0.26, G:0.28, T:0.19
Consensus pattern (69 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCACA
GGGG
Found at i:241819 original size:30 final size:31
Alignment explanation
Indices: 241779--241837 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
241769 AGAAAAGTTC
*
241779 TATGCACTATGTGATAAAGGTATGTAAATGA
1 TATGCACTATGTGATAAAGGTATGGAAATGA
*
241810 TATGC-CTATGTGTTAAAGGTATGGAAAT
1 TATGCACTATGTGATAAAGGTATGGAAAT
241838 ACTATGTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.34
Consensus pattern (31 bp):
TATGCACTATGTGATAAAGGTATGGAAATGA
Found at i:242131 original size:22 final size:22
Alignment explanation
Indices: 242057--242123 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
242047 TTATGGACAT
242057 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
*
242079 AATTCTACGGGCACTTCGGTAC
1 AATTCTACGGGCACTTCGGTGC
242101 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
242123 A
1 A
242124 TTTATACGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:244018 original size:4 final size:4
Alignment explanation
Indices: 244009--244042 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
243999 CTTTAATGGT
244009 ATAC ATAC ATAC ATAC --AC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
244043 GTAGGGAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
4 26 0.93
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:244030 original size:14 final size:14
Alignment explanation
Indices: 244011--244039 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
244001 TTAATGGTAT
244011 ACATACATACATAC
1 ACATACATACATAC
244025 ACATACATACATAC
1 ACATACATACATAC
244039 A
1 A
244040 TACGTAGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.21
Consensus pattern (14 bp):
ACATACATACATAC
Found at i:250728 original size:14 final size:14
Alignment explanation
Indices: 250709--250735 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
250699 ATAGAAGATT
250709 ATTTAATTGAAATG
1 ATTTAATTGAAATG
250723 ATTTAATTGAAAT
1 ATTTAATTGAAAT
250736 CTTTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (14 bp):
ATTTAATTGAAATG
Found at i:251257 original size:59 final size:60
Alignment explanation
Indices: 251191--251336 Score: 150
Period size: 59 Copynumber: 2.5 Consensus size: 60
251181 AATTAATTCT
* * * * *
251191 CAAACTTTTTAATATTCTAATTTCATCTTTAGATTATGAATCTCATTTTAAATTGGT-CC
1 CAAACTTTTGAATATTCTAATTTCATCTTCAAACTATGAATCTCATTCTAAATTGGTCCC
** * * * * *
251250 CAAACTTTTGAGCATTCCAAATTCATATTCAAACTATGACTCTCATTCTATATTGGTCCC
1 CAAACTTTTGAATATTCTAATTTCATCTTCAAACTATGAATCTCATTCTAAATTGGTCCC
* * *
251310 CTAACTTTTGAATATTTTAATTCCATC
1 CAAACTTTTGAATATTCTAATTTCATC
251337 CCCACAATTT
Statistics
Matches: 66, Mismatches: 20, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
59 45 0.68
60 21 0.32
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (60 bp):
CAAACTTTTGAATATTCTAATTTCATCTTCAAACTATGAATCTCATTCTAAATTGGTCCC
Found at i:251763 original size:27 final size:27
Alignment explanation
Indices: 251717--251784 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
251707 TATTAGTCTC
* *
251717 TAAAA-TATTTTTTTGGTCAAAGTACA
1 TAAAATTATCTTTTTGCTCAAAGTACA
* *
251743 TAAAGTTATCTTTTTGCTCAAAGTACT
1 TAAAATTATCTTTTTGCTCAAAGTACA
251770 TAAAATTATCTTTTT
1 TAAAATTATCTTTTT
251785 AATTAAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
26 4 0.11
27 32 0.89
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.47
Consensus pattern (27 bp):
TAAAATTATCTTTTTGCTCAAAGTACA
Found at i:254107 original size:42 final size:42
Alignment explanation
Indices: 254048--254132 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
254038 GATTTTAGAG
* * *
254048 ATAGACTTGGAAATATCAATTAACCTGAGAGAAAAGTTAACT
1 ATAGACTTGAAAATATCAATTAACATGAGAGAAAAATTAACT
254090 ATAGACTTGAAAATATCAATTAACATGAGAGAAAAATTAACT
1 ATAGACTTGAAAATATCAATTAACATGAGAGAAAAATTAACT
254132 A
1 A
254133 CAAGAGTTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.26
Consensus pattern (42 bp):
ATAGACTTGAAAATATCAATTAACATGAGAGAAAAATTAACT
Found at i:254281 original size:21 final size:21
Alignment explanation
Indices: 254252--254295 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
254242 TCAAATTCTT
254252 TTATCTTATTTACTCTT-ATTC
1 TTATCTTATTTACT-TTAATTC
*
254273 TTATTTTATTTACTTTAATTC
1 TTATCTTATTTACTTTAATTC
254294 TT
1 TT
254296 TCTAAAACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.66
Consensus pattern (21 bp):
TTATCTTATTTACTTTAATTC
Found at i:258165 original size:20 final size:20
Alignment explanation
Indices: 258140--258214 Score: 141
Period size: 20 Copynumber: 3.8 Consensus size: 20
258130 ATGAGACCGG
258140 CACGATATATACTGGCTGGA
1 CACGATATATACTGGCTGGA
258160 CACGATATATACTGGCTGGA
1 CACGATATATACTGGCTGGA
258180 CACGATATATACTGGCTGGA
1 CACGATATATACTGGCTGGA
*
258200 CATGATATATACTGG
1 CACGATATATACTGG
258215 ACGGTATGGC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (20 bp):
CACGATATATACTGGCTGGA
Found at i:259062 original size:23 final size:23
Alignment explanation
Indices: 259036--259104 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
259026 CACCACAGCT
*
259036 CGTATAAATACACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* * *
259059 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATACACCGAAGTGCCA
259082 CGTAGAAATACACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
259105 TATAAAATGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.16
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:259213 original size:20 final size:20
Alignment explanation
Indices: 259175--259227 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
259165 ACCAAGTATG
* *
259175 TGTCTCAAAAGATCTCATAGA
1 TGTCTCAAAGGAT-ACATAGA
*
259196 TGT-TCCAAAGGATACATATA
1 TGTCT-CAAAGGATACATAGA
259216 TGTCTCAAAGGA
1 TGTCTCAAAGGA
259228 CAGCGTAGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (20 bp):
TGTCTCAAAGGATACATAGA
Found at i:260600 original size:20 final size:20
Alignment explanation
Indices: 260577--260616 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
260567 TTCCTTTAGG
*
260577 GGGTATCGGTACCCTTATTA
1 GGGTATCGGTACCCTCATTA
*
260597 GGGTATTGGTACCCTCATTA
1 GGGTATCGGTACCCTCATTA
260617 CATTCTGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
GGGTATCGGTACCCTCATTA
Found at i:263079 original size:21 final size:20
Alignment explanation
Indices: 263041--263079 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
263031 ATAATAATTA
*
263041 ATAAATTTACTAACTATTCT
1 ATAAATTTAATAACTATTCT
*
263061 ATAAATTTTAATAATTATT
1 ATAAA-TTTAATAACTATT
263080 TAATTATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (20 bp):
ATAAATTTAATAACTATTCT
Found at i:267301 original size:30 final size:30
Alignment explanation
Indices: 267260--267324 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
267250 TTGCTACAGT
* *
267260 GACCACTATAGGTCTCCAGGAGCACACAAC
1 GACCTCTATAGGTCTCCAAGAGCACACAAC
267290 GACCTCTATAGGTCTCCAAGAGCACACAAC
1 GACCTCTATAGGTCTCCAAGAGCACACAAC
267320 GACCT
1 GACCT
267325 ATGGAGCTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.32, C:0.34, G:0.18, T:0.15
Consensus pattern (30 bp):
GACCTCTATAGGTCTCCAAGAGCACACAAC
Found at i:267987 original size:42 final size:42
Alignment explanation
Indices: 267935--268101 Score: 257
Period size: 42 Copynumber: 4.0 Consensus size: 42
267925 GAGCCTAGGA
*
267935 AAACTGTAAGGTTTATCCTT-GCACACAGCAAAGGGACCTGGG
1 AAACTGTAAGGCTTA-CCTTCGCACACAGCAAAGGGACCTGGG
* *
267977 AAACTGTAAGGCTTACCCTT-GCACACAACAAAGGGACCTGGT
1 AAACTGTAAGGCTTA-CCTTCGCACACAGCAAAGGGACCTGGG
268019 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGG
1 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGG
*
268061 AAACTGTAAGGCTTACCTTCGCACACAGCAAAAGGAACCTG
1 AAACTGTAAGGCTTACCTTCGCACACAGC-AAAGGGACCTG
268102 ATAATACTTC
Statistics
Matches: 116, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
41 4 0.03
42 102 0.88
43 10 0.09
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (42 bp):
AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGG
Found at i:269142 original size:28 final size:29
Alignment explanation
Indices: 269054--269209 Score: 183
Period size: 29 Copynumber: 5.4 Consensus size: 29
269044 TTTTTAAAAT
* *
269054 AATTGCCAAAATAGCACCTTTTCGAATGA
1 AATTCCCAAAATAGCACCTTTTCGAATTA
* *
269083 AATTCCCAAAATATCACATTTTTCGAATTA
1 AATTCCCAAAATAGCAC-CTTTTCGAATTA
*
269113 AATTCCCAAAATAGCA-CTTTTTGAATTA
1 AATTCCCAAAATAGCACCTTTTCGAATTA
*
269141 AATTCCCAAAATATCACCTTTTCGAATT-
1 AATTCCCAAAATAGCACCTTTTCGAATTA
* * * *
269169 AATTACCAAAATAACACCCATTTCAAATT-
1 AATTCCCAAAATAGCA-CCTTTTCGAATTA
269198 AATTCCCAAAAT
1 AATTCCCAAAAT
269210 GTCACTCGGT
Statistics
Matches: 110, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
28 39 0.35
29 46 0.42
30 25 0.23
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.32
Consensus pattern (29 bp):
AATTCCCAAAATAGCACCTTTTCGAATTA
Found at i:269192 original size:29 final size:28
Alignment explanation
Indices: 269033--269209 Score: 176
Period size: 29 Copynumber: 6.1 Consensus size: 28
269023 TATTTTACAG
** * *
269033 AAATAGCACCTTTTTTAAAATAATTGCCA
1 AAATAGCACC-TTTTCGAATTAATTCCCA
*
269062 AAATAGCACCTTTTCGAATGAAATTCCCA
1 AAATAGCACCTTTTCGAAT-TAATTCCCA
* *
269091 AAATATCACATTTTTCGAATTAAATTCCCA
1 AAATAGCAC-CTTTTCGAATT-AATTCCCA
*
269121 AAATAGCA-CTTTTTGAATTAAATTCCCA
1 AAATAGCACCTTTTCGAATT-AATTCCCA
* *
269149 AAATATCACCTTTTCGAATTAATTACCA
1 AAATAGCACCTTTTCGAATTAATTCCCA
* * *
269177 AAATAACACCCATTTCAAATTAATTCCCA
1 AAATAGCA-CCTTTTCGAATTAATTCCCA
269206 AAAT
1 AAAT
269210 GTCACTCGGT
Statistics
Matches: 125, Mismatches: 18, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
28 45 0.36
29 56 0.45
30 24 0.19
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (28 bp):
AAATAGCACCTTTTCGAATTAATTCCCA
Found at i:269247 original size:13 final size:13
Alignment explanation
Indices: 269229--269253 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
269219 TCAACGGTCA
269229 GGTCGGGTCAAAG
1 GGTCGGGTCAAAG
269242 GGTCGGGTCAAA
1 GGTCGGGTCAAA
269254 CCGGTCAACC
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:0.24, C:0.16, G:0.44, T:0.16
Consensus pattern (13 bp):
GGTCGGGTCAAAG
Found at i:269831 original size:2 final size:2
Alignment explanation
Indices: 269824--269872 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
269814 AGAAAACCAC
269824 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
269866 AT AT AT A
1 AT AT AT A
269873 AACCAATATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:275501 original size:42 final size:42
Alignment explanation
Indices: 275439--275602 Score: 215
Period size: 42 Copynumber: 3.9 Consensus size: 42
275429 GAGCCTAGGA
* * *
275439 AAACTGTAAAGTTTATCCTT-GCACACAACAAAGGGACATGGG
1 AAACTGTAAGGCTTA-CCTTCGCACACAACAAAGGGACCTGGG
* *
275481 AAACTGTAAGGCTTACCCTT-GCACACAGCAAAGGGACCTGGT
1 AAACTGTAAGGCTTA-CCTTCGCACACAACAAAGGGACCTGGG
* *
275523 AAACTGTAAGGCTTACCTTCGCACACAATAAAAGGACCTGGG
1 AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCTGGG
*
275565 AAACTGTAAGGCTTACCTTCGCACACAGCAAAAGGGAC
1 AAACTGTAAGGCTTACCTTCGCACACAAC-AAAGGGAC
275603 TTGATAATAC
Statistics
Matches: 107, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
41 4 0.04
42 96 0.90
43 7 0.07
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (42 bp):
AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCTGGG
Found at i:275547 original size:84 final size:84
Alignment explanation
Indices: 275400--275602 Score: 250
Period size: 84 Copynumber: 2.4 Consensus size: 84
275390 CTATACACCA
* * *
275400 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACTGTAAAGTTTATCCTTGCACA
1 GTAAGGCTT-ACCT-TGCACACAGCAAAGGGA-CCTAGGAAAACTGTAAAGCTTATCCTTGCACA
*
275464 CAACAAAGGGACATGGGAAACT
63 CAACAAAAGGACATGGGAAACT
* *
275486 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCT-GGTAAACTGTAAGGCTTA-CCTTCGCACAC
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTAGGAAAACTGTAAAGCTTATCCTT-GCACAC
* *
275549 AATAAAAGGACCTGGGAAACT
64 AACAAAAGGACATGGGAAACT
275570 GTAAGGCTTACCTTCGCACACAGCAAAAGGGAC
1 GTAAGGCTTACCTT-GCACACAGC-AAAGGGAC
275603 TTGATAATAC
Statistics
Matches: 104, Mismatches: 8, Indels: 11
0.85 0.07 0.09
Matches are distributed among these distances:
83 8 0.08
84 58 0.56
85 23 0.22
86 15 0.14
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (84 bp):
GTAAGGCTTACCTTGCACACAGCAAAGGGACCTAGGAAAACTGTAAAGCTTATCCTTGCACACAA
CAAAAGGACATGGGAAACT
Found at i:276574 original size:29 final size:27
Alignment explanation
Indices: 276541--276669 Score: 125
Period size: 29 Copynumber: 4.4 Consensus size: 27
276531 CTTTTTAAAA
*
276541 TAATTACCAAAATAGCACATTTTCGAAT
1 TAATT-CCAAAATAGCACCTTTTCGAAT
*
276569 TAAATTCCTAAAATAGCACCTTTTTTGAAT
1 T-AATTCC-AAAATAGCACC-TTTTCGAAT
* *
276599 TAAATTCCCAAAATATCACCTTTTTG-AT
1 T-AATT-CCAAAATAGCACCTTTTCGAAT
276627 GTAATTCCTAAAATAGCACCTATTTCGAAT
1 -TAATTCC-AAAATAGCACCT-TTTCGAAT
276657 TAATTCCCAAAAT
1 TAATT-CCAAAAT
276670 GTCACTCGAT
Statistics
Matches: 87, Mismatches: 5, Indels: 17
0.80 0.05 0.16
Matches are distributed among these distances:
27 2 0.02
28 20 0.23
29 35 0.40
30 28 0.32
31 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (27 bp):
TAATTCCAAAATAGCACCTTTTCGAAT
Found at i:276601 original size:30 final size:29
Alignment explanation
Indices: 276541--276669 Score: 147
Period size: 30 Copynumber: 4.4 Consensus size: 29
276531 CTTTTTAAAA
* *
276541 TAATTACCAAAATAGCA-CATTTTCGAAT
1 TAATTCCCAAAATAGCACCTTTTTCGAAT
* *
276569 TAAATTCCTAAAATAGCACCTTTTTTGAAT
1 T-AATTCCCAAAATAGCACCTTTTTCGAAT
*
276599 TAAATTCCCAAAATATCACCTTTTT-G-AT
1 T-AATTCCCAAAATAGCACCTTTTTCGAAT
* *
276627 GTAATTCCTAAAATAGCACCTATTTCGAAT
1 -TAATTCCCAAAATAGCACCTTTTTCGAAT
276657 TAATTCCCAAAAT
1 TAATTCCCAAAAT
276670 GTCACTCGAT
Statistics
Matches: 86, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
28 23 0.27
29 29 0.34
30 34 0.40
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (29 bp):
TAATTCCCAAAATAGCACCTTTTTCGAAT
Found at i:276701 original size:12 final size:13
Alignment explanation
Indices: 276684--276714 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
276674 CTCGATCAAC
276684 GGTCAAC-GGTCG
1 GGTCAACTGGTCG
276696 GGTCAACTGGTCG
1 GGTCAACTGGTCG
276709 GGTCAA
1 GGTCAA
276715 ACCGATCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.19, C:0.23, G:0.39, T:0.19
Consensus pattern (13 bp):
GGTCAACTGGTCG
Found at i:278778 original size:4 final size:4
Alignment explanation
Indices: 278769--278796 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
278759 GTGATTACTA
278769 GTTT GTTT GTTT GTTT GTTT GTTT GTTT
1 GTTT GTTT GTTT GTTT GTTT GTTT GTTT
278797 TCATTGGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.25, T:0.75
Consensus pattern (4 bp):
GTTT
Found at i:284527 original size:198 final size:203
Alignment explanation
Indices: 284209--284615 Score: 734
Period size: 198 Copynumber: 2.0 Consensus size: 203
284199 TAATTCAATC
284209 TCAATCTCATCCGAATGTTAAATTGGTCTCGTTTCTCGGGCACTCGTAAACTTCCGAAACAAACC
1 TCAATCTCATCCGAATGTTAAATTGGTCTCGTTTCTCGGGCACTCGTAAACTTCCGAAACAAACC
284274 CAAGTTATCTTTCCCTTGCATTAAATAAAAGGATTTTTGCTCATGATCAATTCAAAATAATTAGA
66 CAAGTTATCTTTCCCTTGCATTAAATAAAAGGATTTTTGCTCATGATCAATTCAAAATAATTAGA
284339 ATAATC-TTTTTTTTTATGGTTAGTCATGCTCGTG-CTC-GTCC-A-GAGCATATCATATAGGTA
131 ATAATCTTTTTTTTTTATGGTTAGTCATGCTCGTGACTCAGTCCAACGAGCATATCATATAGGTA
284399 ATATTGAT
196 ATATTGAT
284407 TCAATCTCATCCGAATGTTAAATTGGTCTCGTTTCTCGGGCACTCGTAAACTTCCGAAACAAACC
1 TCAATCTCATCCGAATGTTAAATTGGTCTCGTTTCTCGGGCACTCGTAAACTTCCGAAACAAACC
284472 CAAGTTATCTTTCCCTTGCATTAAATAAAAGGATTTTTGCTCATGATCAATTCAAAATAATTAGA
66 CAAGTTATCTTTCCCTTGCATTAAATAAAAGGATTTTTGCTCATGATCAATTCAAAATAATTAGA
284537 ATAATCTTTTTTTTTTTATGGTTAGTCATGCTCGTGACTCAGTCCAAGTTACGAGCATATCATAT
131 ATAATC-TTTTTTTTTTATGGTTAGTCATGCTCGTGACTCAGTCC-A---ACGAGCATATCATAT
284602 AGGTAATATTGAT
191 AGGTAATATTGAT
284615 T
1 T
284616 GTTGTGGAAC
Statistics
Matches: 199, Mismatches: 0, Indels: 10
0.95 0.00 0.05
Matches are distributed among these distances:
198 136 0.68
200 28 0.14
201 3 0.02
202 4 0.02
207 1 0.01
208 27 0.14
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (203 bp):
TCAATCTCATCCGAATGTTAAATTGGTCTCGTTTCTCGGGCACTCGTAAACTTCCGAAACAAACC
CAAGTTATCTTTCCCTTGCATTAAATAAAAGGATTTTTGCTCATGATCAATTCAAAATAATTAGA
ATAATCTTTTTTTTTTATGGTTAGTCATGCTCGTGACTCAGTCCAACGAGCATATCATATAGGTA
ATATTGAT
Found at i:285087 original size:5 final size:5
Alignment explanation
Indices: 285079--285126 Score: 69
Period size: 5 Copynumber: 9.6 Consensus size: 5
285069 CAAAAAACGA
* * *
285079 AAAGA AAAGA AAACG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAA
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAA
285127 ATAATTATCT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:285093 original size:16 final size:16
Alignment explanation
Indices: 285072--285106 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
285062 ATGTGATCAA
285072 AAAACGAAAAGAAAAG
1 AAAACGAAAAGAAAAG
* *
285088 AAAACGAAAGGAAAGG
1 AAAACGAAAAGAAAAG
285104 AAA
1 AAA
285107 GGAAAGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.06, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAACGAAAAGAAAAG
Found at i:285102 original size:15 final size:15
Alignment explanation
Indices: 285072--285117 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
285062 ATGTGATCAA
*
285072 AAAACGAAAAGAAAAG
1 AAAACG-AAAGGAAAG
285088 AAAACGAAAGGAAAG
1 AAAACGAAAGGAAAG
* *
285103 GAAAGGAAAGGAAAG
1 AAAACGAAAGGAAAG
285118 GAAAGGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 21 0.78
16 6 0.22
ACGTcount: A:0.67, C:0.04, G:0.28, T:0.00
Consensus pattern (15 bp):
AAAACGAAAGGAAAG
Found at i:289029 original size:29 final size:29
Alignment explanation
Indices: 288987--289045 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
288977 CTTTCTAGTT
288987 TGGACTATTCATCAACTAAATGAAATATA
1 TGGACTATTCATCAACTAAATGAAATATA
289016 TGGACTATTCATCAACTAAATGAAATATA
1 TGGACTATTCATCAACTAAATGAAATATA
289045 T
1 T
289046 CCGGATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (29 bp):
TGGACTATTCATCAACTAAATGAAATATA
Found at i:294928 original size:154 final size:159
Alignment explanation
Indices: 294646--294965 Score: 589
Period size: 154 Copynumber: 2.0 Consensus size: 159
294636 ATGACCTCAA
294646 TAATTTTGATAGGTTAAATCATTTCACATGATGCTCCTGTGAAATCTGTGTACCATTATTCTTGG
1 TAATTTTGATAGGTTAAATCATTTCACATGATGCTCCTGTGAAATCTGTGTACCATTATTCTTGG
294711 GAAATAAAATGAGTAAATTTTACTATAACTAAATTAGTGAGAATGTCAAATAAAAGTGG-AAAA-
66 GAAATAAAATGAGTAAATTTTACTATAACTAAATTAGTGAGAATGTCAAATAAAAGTGGAAAAAT
294774 AATACTCCGAAATTG-TAAC-G-GTTCAGC
131 AATACT-CGAAATTGATAACGGAGTTCAGC
294801 T-ATTTTGATAGGTTAAATCATTTCACATGATGCTCCTGTGAAATCTGTGTACCATTATTCTTGG
1 TAATTTTGATAGGTTAAATCATTTCACATGATGCTCCTGTGAAATCTGTGTACCATTATTCTTGG
294865 GAAATAAAATGAGTAAATTTTACTATAACTAAATTAGTGAGAATGTCAAATAAAAGTGGAAAAAT
66 GAAATAAAATGAGTAAATTTTACTATAACTAAATTAGTGAGAATGTCAAATAAAAGTGGAAAAAT
294930 AATACTCGAAATTGATAACGGAGTTCAGC
131 AATACTCGAAATTGATAACGGAGTTCAGC
294959 TAATTTT
1 TAATTTT
294966 ACCTACGTCT
Statistics
Matches: 159, Mismatches: 0, Indels: 8
0.95 0.00 0.05
Matches are distributed among these distances:
154 122 0.77
155 13 0.08
156 10 0.06
157 1 0.01
158 8 0.05
159 5 0.03
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.34
Consensus pattern (159 bp):
TAATTTTGATAGGTTAAATCATTTCACATGATGCTCCTGTGAAATCTGTGTACCATTATTCTTGG
GAAATAAAATGAGTAAATTTTACTATAACTAAATTAGTGAGAATGTCAAATAAAAGTGGAAAAAT
AATACTCGAAATTGATAACGGAGTTCAGC
Found at i:298858 original size:16 final size:16
Alignment explanation
Indices: 298834--298865 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
298824 TGTCGCCGAC
*
298834 CAAATTTCACTATTCA
1 CAAAATTCACTATTCA
298850 CAAAATTCACTATTCA
1 CAAAATTCACTATTCA
298866 AGTGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.34
Consensus pattern (16 bp):
CAAAATTCACTATTCA
Found at i:299813 original size:31 final size:31
Alignment explanation
Indices: 299775--299868 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
299765 CCCGAAGGAC
* * *
299775 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
299806 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
299837 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
299868 C
1 C
299869 CCTCGACCCT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:310252 original size:104 final size:105
Alignment explanation
Indices: 310119--310329 Score: 415
Period size: 104 Copynumber: 2.0 Consensus size: 105
310109 GATTTGTTTA
310119 ATGATTGGGTTGTTTATTTGGTTTATATGAGCCAATTTATAATGGAGATTTTATGAATTTGCATC
1 ATGATTGGGTTGTTTATTTGGTTTATATGAGCCAATTTATAATGGAGATTTTATGAATTTGCATC
310184 GATTAAATCAAATGTAGATTAATAATTAAT-ATAATTTTT
66 GATTAAATCAAATGTAGATTAATAATTAATAATAATTTTT
310223 ATGATTGGGTTGTTTATTTGGTTTATATGAGCCAATTTATAATGGAGATTTTATGAATTTGCATC
1 ATGATTGGGTTGTTTATTTGGTTTATATGAGCCAATTTATAATGGAGATTTTATGAATTTGCATC
310288 GATTAAATCAAATGTAGATTAATAATTAATAATAATTTTT
66 GATTAAATCAAATGTAGATTAATAATTAATAATAATTTTT
310328 AT
1 AT
310330 TTAAATTTAA
Statistics
Matches: 106, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
104 95 0.90
105 11 0.10
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (105 bp):
ATGATTGGGTTGTTTATTTGGTTTATATGAGCCAATTTATAATGGAGATTTTATGAATTTGCATC
GATTAAATCAAATGTAGATTAATAATTAATAATAATTTTT
Found at i:310326 original size:52 final size:52
Alignment explanation
Indices: 310166--310326 Score: 116
Period size: 52 Copynumber: 3.1 Consensus size: 52
310156 TATAATGGAG
310166 ATTTTATGAATTTGCATCGATTAAATCAAATGTAGATTAATAATTAAT-ATA
1 ATTTTATGAATTTGCATCGATTAAATCAAATGTAGATTAATAATTAATAATA
** * * **** * * * ** *
310217 ATTTTTATG-A-TTGGGTTG-TT-TATTTGGTTTATATGAGCCAATTTATAATGGA
1 A-TTTTATGAATTTGCATCGATTAAATCAAATGTAGATTA-ATAATTAATAAT--A
310269 GATTTTATGAATTTGCATCGATTAAATCAAATGTAGATTAATAATTAATAATA
1 -ATTTTATGAATTTGCATCGATTAAATCAAATGTAGATTAATAATTAATAATA
310322 ATTTT
1 ATTTT
310327 TATTTAAATT
Statistics
Matches: 72, Mismatches: 28, Indels: 19
0.61 0.24 0.16
Matches are distributed among these distances:
48 8 0.11
49 8 0.11
50 7 0.10
51 2 0.03
52 20 0.28
53 3 0.04
54 5 0.07
55 11 0.15
56 8 0.11
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.45
Consensus pattern (52 bp):
ATTTTATGAATTTGCATCGATTAAATCAAATGTAGATTAATAATTAATAATA
Found at i:310716 original size:2 final size:2
Alignment explanation
Indices: 310709--310734 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
310699 AATTATAATG
310709 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
310735 TGATTAGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:315088 original size:30 final size:30
Alignment explanation
Indices: 315045--315102 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
315035 AATTTAGGGG
* * *
315045 GTCAAAATGATATTTTATCTAAATTTTATA
1 GTCAAAATAATATTCTATCTAAAGTTTATA
*
315075 GTCAAATTAATATTCTATCTAAAGTTTA
1 GTCAAAATAATATTCTATCTAAAGTTTA
315103 AGGGTTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.45
Consensus pattern (30 bp):
GTCAAAATAATATTCTATCTAAAGTTTATA
Found at i:319823 original size:101 final size:101
Alignment explanation
Indices: 319648--319850 Score: 406
Period size: 101 Copynumber: 2.0 Consensus size: 101
319638 TGGGGTCCAG
319648 TACGTTGCACTTTGCCATGTACATATTAATTGCAAATATCTTGAATTTTGTGTAATCATAAAAAA
1 TACGTTGCACTTTGCCATGTACATATTAATTGCAAATATCTTGAATTTTGTGTAATCATAAAAAA
319713 TCATGGTATCTCTCTTGTCTGGTGTGATTCTAATCT
66 TCATGGTATCTCTCTTGTCTGGTGTGATTCTAATCT
319749 TACGTTGCACTTTGCCATGTACATATTAATTGCAAATATCTTGAATTTTGTGTAATCATAAAAAA
1 TACGTTGCACTTTGCCATGTACATATTAATTGCAAATATCTTGAATTTTGTGTAATCATAAAAAA
319814 TCATGGTATCTCTCTTGTCTGGTGTGATTCTAATCT
66 TCATGGTATCTCTCTTGTCTGGTGTGATTCTAATCT
319850 T
1 T
319851 GTTGTCGATG
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.42
Consensus pattern (101 bp):
TACGTTGCACTTTGCCATGTACATATTAATTGCAAATATCTTGAATTTTGTGTAATCATAAAAAA
TCATGGTATCTCTCTTGTCTGGTGTGATTCTAATCT
Found at i:323675 original size:20 final size:20
Alignment explanation
Indices: 323639--323676 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
323629 ATTAAAAATT
323639 AAAGAAAATGTAAAATAATG
1 AAAGAAAATGTAAAATAATG
*
323659 AAAGACAAA-GTATAATAA
1 AAAGA-AAATGTAAAATAA
323677 AGTCGGGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.66, C:0.03, G:0.13, T:0.18
Consensus pattern (20 bp):
AAAGAAAATGTAAAATAATG
Found at i:328412 original size:43 final size:44
Alignment explanation
Indices: 328321--328412 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
328311 TAATCTATCG
* * * *
328321 TCATACTATTTGTTTTTTTCTTCAAAAGTGATCTTAGTCTGTCG
1 TCATACAATTAGTTTTTTCCTTCAAAAGTGATCTTAGTCTGTCC
* *
328365 TCATACAATTAGTTTTTTCCTTCGAAAGTGATCTTA-TTTGTCC
1 TCATACAATTAGTTTTTTCCTTCAAAAGTGATCTTAGTCTGTCC
328408 TCATA
1 TCATA
328413 TATGACAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 10 0.24
44 32 0.76
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.48
Consensus pattern (44 bp):
TCATACAATTAGTTTTTTCCTTCAAAAGTGATCTTAGTCTGTCC
Found at i:331442 original size:31 final size:31
Alignment explanation
Indices: 331401--331479 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 31
331391 TACAATAAAA
* *
331401 TAAAAATAATATTTTAGGTATTAAAAT-TGAT
1 TAAAATTAATAGTTTAGGTATTAAAATAT-AT
*
331432 TAAAATTAATAGTTTAAGTATTAAAATATAT
1 TAAAATTAATAGTTTAGGTATTAAAATATAT
331463 TAAAATTAATAGTTTAG
1 TAAAATTAATAGTTTAG
331480 ATACTTAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 42 0.98
32 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (31 bp):
TAAAATTAATAGTTTAGGTATTAAAATATAT
Found at i:331492 original size:30 final size:30
Alignment explanation
Indices: 331401--331494 Score: 95
Period size: 31 Copynumber: 3.1 Consensus size: 30
331391 TACAATAAAA
* * *
331401 TAAAAATAATATTTTAGGTATTAAA-ATTGAT
1 TAAAATTAATAGTTTAAGTATTAAATA-T-AT
331432 TAAAATTAATAGTTTAAGTATTAAAATATAT
1 TAAAATTAATAGTTTAAGTATT-AAATATAT
331463 TAAAATTAATAGTTT-AGATACTT-AATATAT
1 TAAAATTAATAGTTTAAG-TA-TTAAATATAT
331493 TA
1 TA
331495 TTTACCCTGT
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
30 11 0.20
31 38 0.68
32 6 0.11
33 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.43
Consensus pattern (30 bp):
TAAAATTAATAGTTTAAGTATTAAATATAT
Found at i:332057 original size:12 final size:12
Alignment explanation
Indices: 332042--332068 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
332032 ATTTAAAATT
332042 ATATTTTAAAAA
1 ATATTTTAAAAA
332054 ATATTTTAAAAA
1 ATATTTTAAAAA
332066 ATA
1 ATA
332069 AACCAACTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATTTTAAAAA
Found at i:352814 original size:21 final size:21
Alignment explanation
Indices: 352790--352831 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
352780 GTAGTTTTAC
* *
352790 GTTTCACGAGTTTTGAGTTGA
1 GTTTCACGAATTTTAAGTTGA
*
352811 GTTTCATGAATTTTAAGTTGA
1 GTTTCACGAATTTTAAGTTGA
352832 TTTAAGTACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.45
Consensus pattern (21 bp):
GTTTCACGAATTTTAAGTTGA
Found at i:353257 original size:24 final size:25
Alignment explanation
Indices: 353230--353276 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
353220 TCATGGTGTT
*
353230 TTTCCTCTATATTCT-TTCCACAGA
1 TTTCCTCCATATTCTCTTCCACAGA
* *
353254 TTTCGTCCATATTTTCTTCCACA
1 TTTCCTCCATATTCTCTTCCACA
353277 AGCCAAGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.19, C:0.30, G:0.04, T:0.47
Consensus pattern (25 bp):
TTTCCTCCATATTCTCTTCCACAGA
Found at i:355979 original size:36 final size:36
Alignment explanation
Indices: 355932--356011 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
355922 ATGGTACATC
*
355932 TGTAATCTTAATAATTAAGATTATAATTGAATGACT
1 TGTAATCTTAATAATTAAGATCATAATTGAATGACT
*
355968 TGTAATCTTAATATTTAAGATCATAATTGAATGACT
1 TGTAATCTTAATAATTAAGATCATAATTGAATGACT
356004 TGTAATCT
1 TGTAATCT
356012 CACTATAGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.42
Consensus pattern (36 bp):
TGTAATCTTAATAATTAAGATCATAATTGAATGACT
Found at i:356902 original size:13 final size:13
Alignment explanation
Indices: 356876--356910 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
356866 CAATCCAGGC
356876 GACATACG-GGGT
1 GACATACGAGGGT
356888 GACATACGAGGGT
1 GACATACGAGGGT
356901 GACATACGAG
1 GACATACGAG
356911 CCATATACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.31, C:0.17, G:0.37, T:0.14
Consensus pattern (13 bp):
GACATACGAGGGT
Found at i:356920 original size:11 final size:11
Alignment explanation
Indices: 356904--356968 Score: 59
Period size: 11 Copynumber: 6.1 Consensus size: 11
356894 CGAGGGTGAC
356904 ATACGAGCCAT
1 ATACGAGCCAT
356915 ATACGAGCC--
1 ATACGAGCCAT
356924 ATACGAGCCA-
1 ATACGAGCCAT
*
356934 ATAGGGAG-CAT
1 ATA-CGAGCCAT
356945 GCA-ACGAGCCAT
1 --ATACGAGCCAT
356957 ATACGAGCCAT
1 ATACGAGCCAT
356968 A
1 A
356969 CGAGCCAATG
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
9 9 0.20
10 6 0.13
11 25 0.56
12 4 0.09
13 1 0.02
ACGTcount: A:0.37, C:0.26, G:0.23, T:0.14
Consensus pattern (11 bp):
ATACGAGCCAT
Found at i:356953 original size:42 final size:42
Alignment explanation
Indices: 356906--356989 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
356896 AGGGTGACAT
356906 ACGAGCCATATACGAGCCATACGAGCCAATAGGGAGCATGCA
1 ACGAGCCATATACGAGCCATACGAGCCAATAGGGAGCATGCA
*
356948 ACGAGCCATATACGAGCCATACGAGCCAATGGGGAGCATGCA
1 ACGAGCCATATACGAGCCATACGAGCCAATAGGGAGCATGCA
356990 GGAATAGAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.35, C:0.26, G:0.27, T:0.12
Consensus pattern (42 bp):
ACGAGCCATATACGAGCCATACGAGCCAATAGGGAGCATGCA
Found at i:357010 original size:28 final size:28
Alignment explanation
Indices: 356970--357028 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
356960 CGAGCCATAC
356970 GAGCCAATGGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAGGAATAGA
356998 GAGCCAATGGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAGGAATAGA
357026 GAG
1 GAG
357029 GTCGCCATGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.36, C:0.14, G:0.41, T:0.10
Consensus pattern (28 bp):
GAGCCAATGGGGAGCATGCAGGAATAGA
Found at i:357077 original size:29 final size:29
Alignment explanation
Indices: 357027--357102 Score: 118
Period size: 29 Copynumber: 2.6 Consensus size: 29
357017 AGGAATAGAG
* *
357027 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
357056 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
357085 AGGTCGCCATGTAGTCCC
1 AGGTCGCCATGTAGTCCC
357103 AGCGCCATTC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 42 0.95
30 2 0.05
ACGTcount: A:0.16, C:0.32, G:0.30, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:357213 original size:27 final size:27
Alignment explanation
Indices: 357181--357233 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
357171 CCTACAGCTC
357181 CCAATGCATGCATGTGAACCATTTGAG
1 CCAATGCATGCATGTGAACCATTTGAG
357208 CCAATGCATGCATGTGAACCATTTGA
1 CCAATGCATGCATGTGAACCATTTGA
357234 TTATTGGTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (27 bp):
CCAATGCATGCATGTGAACCATTTGAG
Found at i:357373 original size:23 final size:23
Alignment explanation
Indices: 357345--357390 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
357335 AAAAGAAAGA
357345 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
357368 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
357391 CCGAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:357405 original size:25 final size:23
Alignment explanation
Indices: 357345--357405 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
357335 AAAAGAAAGA
**
357345 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
357368 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
357391 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
357406 AGGGAGAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 23 0.70
25 10 0.30
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:357420 original size:21 final size:21
Alignment explanation
Indices: 357396--357447 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
357386 TGCAGCCGAG
357396 AAAGAAAGAAAGGGAGAAAGA
1 AAAGAAAGAAAGGGAGAAAGA
*
357417 AAAGAAAGAAAGGGAGAAAGG
1 AAAGAAAGAAAGGGAGAAAGA
*
357438 AAAGTAAGAA
1 AAAGAAAGAA
357448 GAAGAAAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (21 bp):
AAAGAAAGAAAGGGAGAAAGA
Found at i:357436 original size:16 final size:17
Alignment explanation
Indices: 357393--357424 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
357383 GATTGCAGCC
357393 GAGAAAG-AAAGAAAGG
1 GAGAAAGAAAAGAAAGG
357409 GAGAAAGAAAAGAAAG
1 GAGAAAGAAAAGAAAG
357425 AAAGGGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (17 bp):
GAGAAAGAAAAGAAAGG
Found at i:357440 original size:13 final size:12
Alignment explanation
Indices: 357398--357460 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
357388 CAGCCGAGAA
357398 AGAAAGAAAGGG
1 AGAAAGAAAGGG
357410 AGAAAGAAA---
1 AGAAAGAAAGGG
357419 AGAAAGAAAGGG
1 AGAAAGAAAGGG
**
357431 AGAAAGGAAAGTA
1 AGAAA-GAAAGGG
357444 AGAAGAAGAAAGGG
1 AG-A-AAGAAAGGG
357458 AGA
1 AGA
357461 TAAGGTAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
9 9 0.22
12 14 0.34
13 8 0.20
14 8 0.20
15 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.37, T:0.02
Consensus pattern (12 bp):
AGAAAGAAAGGG
Found at i:357627 original size:41 final size:41
Alignment explanation
Indices: 357582--357670 Score: 92
Period size: 41 Copynumber: 2.2 Consensus size: 41
357572 TATATGATTG
* *
357582 TTAGTTTAAG-TT-ATAGTATACATAAATTAAAAATTATTTAA
1 TTAGTTTAAGTTTGATAGT-TACAT-AATTAAAAAATAATTAA
* * * *
357623 TTAGTATATGTTTGATAGTTATATAGTTAAAAAATAATTAA
1 TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
357664 TTAGTTT
1 TTAGTTT
357671 GTTTTGTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 28 0.72
42 6 0.15
43 5 0.13
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (41 bp):
TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
Found at i:357713 original size:45 final size:45
Alignment explanation
Indices: 357610--357741 Score: 134
Period size: 45 Copynumber: 3.0 Consensus size: 45
357600 TACATAAATT
*
357610 AAAAATTATTTAATTAGTATATG-TTTG---ATAGTTA--TATAGTTA
1 AAAAATTATTTAATTAGT-T-TGTTTTGTTAATAGTTAGTTATA-TAA
*
357652 AAAAA-TAATTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
1 AAAAATTATTTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
*
357696 AAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAATTATTTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATAT
357742 TTGTTTGTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
39 2 0.03
40 5 0.07
41 11 0.14
42 5 0.07
43 7 0.09
44 7 0.09
45 19 0.25
46 5 0.07
47 7 0.09
48 8 0.11
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (45 bp):
AAAAATTATTTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
Found at i:357817 original size:32 final size:33
Alignment explanation
Indices: 357781--357857 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 33
357771 TTAGTTAGTA
357781 AGTTTATTAGTAG-TATA-TTATAATGAAAA-AAT
1 AGTTTATTAGTAGTTATAGTTAT-AT-AAAAGAAT
*
357813 AGTTTATTAGTTAGTTTTAGTTATATAAAAGAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAGAAT
*
357847 ATTTTATTAGT
1 AGTTTATTAGT
357858 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
32 10 0.26
33 8 0.21
34 17 0.44
35 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (33 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAGAAT
Done.