Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 95 of 132
Found at i:29240612 original size:59 final size:59
Alignment explanation
Indices: 29240370--29240619 Score: 229
Period size: 60 Copynumber: 4.2 Consensus size: 59
29240360 TTTGAACCTC
* * * *
29240370 AAACTTTCTAAAAATCAGATTTTGACCCCAAACTCTT-TAAAAATTACATTTTAA-CCTCT
1 AAACTTTCCAAAAATCAAATTTTGACCCCAAACT-TTCCAAAAATTTCATTTTAACCCT-T
** * * * * *
29240429 AATTTTTCCAAAAATCATATCTTAACCCCTAAACTTTCCAAAAATTAT-ATTTTGACCCCT
1 AAACTTTCCAAAAATCAAATTTTGACCCC-AAACTTTCCAAAAATT-TCATTTTAACCCTT
* * * * *
29240489 AAACTTTCCAAAAATTAAAATTTGACCCCCAAACTTTCCAAAACTTTGATTTTGACCCTT
1 AAACTTTCCAAAAATCAAATTTTGA-CCCCAAACTTTCCAAAAATTTCATTTTAACCCTT
* * ** *
29240549 AAACTTTCTAAAAATCACATTTTGACTTCGAACTCTT-CAAAAATTTCATTTTAACCCTT
1 AAACTTTCCAAAAATCAAATTTTGACCCCAAACT-TTCCAAAAATTTCATTTTAACCCTT
29240608 AAACTTTCCAAA
1 AAACTTTCCAAA
29240620 TTTACATTTT
Statistics
Matches: 154, Mismatches: 30, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
59 62 0.40
60 86 0.56
61 6 0.04
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.36
Consensus pattern (59 bp):
AAACTTTCCAAAAATCAAATTTTGACCCCAAACTTTCCAAAAATTTCATTTTAACCCTT
Found at i:29246862 original size:50 final size:50
Alignment explanation
Indices: 29246800--29247286 Score: 279
Period size: 50 Copynumber: 9.9 Consensus size: 50
29246790 CATAACGACG
* * **
29246800 AACCTGGTACCTTAAAAGATGTGAAGGGAAAGGTTGAGGCCGTAATGGCG
1 AACCTGGTACCTTAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGAA
** * * *
29246850 AATTTGGTACCTTAGAAGATGTGATGGGAAAGGTTAAGGCCGCAACGGAA
1 AACCTGGTACCTTAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGAA
**
29246900 AACCTGGTACCTTAAAAGATGTGATA-GGAAAGGTTGAGGCCGCAACGGTG
1 AACCTGGTACCTTAAAAGATGTGA-AGGGAAAGGTTGAGGCCGCAACGGAA
* * * * *
29246950 AACCCGATACC-------ATTTGAAGGGAAAGGTTAAGGTCGCAAC-GACGA
1 AACCTGGTACCTTAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGA--A
* * * * * * **
29246994 ACCCT-GTACCTTAGAAGATATGAAGTGAAAGGTTGAGTCCACAACGGCG
1 AACCTGGTACCTTAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGAA
* * * * * * **
29247043 AACCCGGTACCAT-GAAGATATGAAGGGAAAGGTTAAGGCTGCAACGGTG
1 AACCTGGTACCTTAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGAA
* * * * * * * * *
29247092 AACCCGGTACCAT-GAAGATATAAAGGGAAGGGTTAAGGCCGTAACGGTA
1 AACCTGGTACCTTAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGAA
* * ** * * * **
29247141 AACCCGGTACCTTAGAAGACATGATGGGAAAGGTCGAGGCCACAACGGTG
1 AACCTGGTACCTTAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGAA
* * * * *
29247191 AACCCGATACCATT--AAGATTTGAAGGGAAAGGTTGAGGCCGCAATGGCGA
1 AACCTGGTACC-TTAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGG-AA
* *
29247241 ACCCT-GTACCTTAAAAGATGTGATA-GG-AAGGATTGAGGCCACAACG
1 AACCTGGTACCTTAAAAGATGTGA-AGGGAAAGG-TTGAGGCCGCAACG
29247287 ATAAATCTTA
Statistics
Matches: 344, Mismatches: 73, Indels: 40
0.75 0.16 0.09
Matches are distributed among these distances:
42 2 0.01
43 27 0.08
44 3 0.01
48 2 0.01
49 124 0.36
50 182 0.53
51 4 0.01
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.18
Consensus pattern (50 bp):
AACCTGGTACCTTAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGAA
Found at i:29247024 original size:93 final size:91
Alignment explanation
Indices: 29246875--29247151 Score: 263
Period size: 93 Copynumber: 2.9 Consensus size: 91
29246865 AAGATGTGAT
* * *
29246875 GGGAAAGGTTAAGGCCGCAACGGAAAACCTGGTACCTTAAAAGATGTGATAGGAAAGGTTGAGGC
1 GGGAAAGGTTAAGG-CGCAACGG-AACCCT-GTACCTTAGAAGATATGA-AGGAAAGGTTGAGGC
*
29246940 CGCAACGGTGAACCCGATACCAT-T-TGAA
62 CGCAACGGTGAACCCGGTACCATATATGAA
*
29246968 GGGAAAGGTTAAGGTCGCAACGACGAACCCTGTACCTTAGAAGATATGAAGTGAAAGGTTGAGTC
1 GGGAAAGGTTAAGG-CGCAACG--GAACCCTGTACCTTAGAAGATATGAAG-GAAAGGTTGAGGC
* *
29247033 CACAACGGCGAACCCGGTACCATGAAGATATGAA
62 CGCAACGGTGAACCCGGTACCAT----ATATGAA
* * * * *
29247067 GGGAAAGGTTAAGGCTGCAACGGTGAACCCGGTACCAT-GAAGATATAAAGGGAAGGGTTAAGGC
1 GGGAAAGGTTAAGGC-GCAAC-G-GAACCCTGTACCTTAGAAGATATGAA-GGAAAGGTTGAGGC
* *
29247131 CGTAACGGTAAACCCGGTACC
62 CGCAACGGTGAACCCGGTACC
29247152 TTAGAAGACA
Statistics
Matches: 153, Mismatches: 19, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
92 2 0.01
93 69 0.45
94 5 0.03
95 1 0.01
98 39 0.25
99 36 0.24
100 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.30, T:0.17
Consensus pattern (91 bp):
GGGAAAGGTTAAGGCGCAACGGAACCCTGTACCTTAGAAGATATGAAGGAAAGGTTGAGGCCGCA
ACGGTGAACCCGGTACCATATATGAA
Found at i:29247088 original size:49 final size:50
Alignment explanation
Indices: 29246964--29247286 Score: 305
Period size: 49 Copynumber: 6.5 Consensus size: 50
29246954 CGATACCATT
* * * * *
29246964 TGAAGGGAAAGGTTAAGGTCGCAACGACGAACCCTGTACCTTAGAAGATA
1 TGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATAGAAGATA
* * *
29247014 TGAAGTGAAAGGTTGAGTCCACAACGGCGAACCCGGTACCAT-GAAGATA
1 TGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATAGAAGATA
* * *
29247063 TGAAGGGAAAGGTTAAGGCTGCAACGGTGAACCCGGTACCAT-GAAGATA
1 TGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATAGAAGATA
* * * * ** * *
29247112 TAAAGGGAAGGGTTAAGGCCGTAACGGTAAACCCGGTACCTTAGAAGACA
1 TGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATAGAAGATA
* * * * * * *
29247162 TGATGGGAAAGGTCGAGGCCACAACGGTGAACCCGATACCAT-TAAGATT
1 TGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATAGAAGATA
* * * * *
29247211 TGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCTGTACCTTAAAAGATG
1 TGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATAGAAGATA
*
29247261 TGATA-GG-AAGGATTGAGGCCACAACG
1 TGA-AGGGAAAGG-TTGAGGCCGCAACG
29247287 ATAAATCTTA
Statistics
Matches: 223, Mismatches: 46, Indels: 8
0.81 0.17 0.03
Matches are distributed among these distances:
49 128 0.57
50 94 0.42
51 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.30, T:0.17
Consensus pattern (50 bp):
TGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATAGAAGATA
Found at i:29247184 original size:148 final size:142
Alignment explanation
Indices: 29246855--29247250 Score: 425
Period size: 148 Copynumber: 2.7 Consensus size: 142
29246845 TGGCGAATTT
* * * * * *
29246855 GGTACCTTAGAAGATGTGATGGGAAAGGTTAAGGCCGCAACGGAAAACCTGGTACCTTAAAAGAT
1 GGTACCTTAGAAGATATGATGGGAAAGGTTGAGGCCACAACGGAGAACCCGGTACCAT-AAAGAT
* * * *
29246920 GTGATA-GGAAAGGTTGAGGCCGCAACGGTGAACCCGATACCATTTGAAGGGAAAGGTTAAGGTC
65 ATGA-AGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCATTTAAAGGGAAAGGTTAAGGCC
*
29246984 GCAACGACGAACCC
129 GCAACGACAAACCC
* * * * * *
29246998 TGTACCTTAGAAGATATGAAGTGAAAGGTTGAGTCCACAACGGCGAACCCGGTACCATGAAGATA
1 GGTACCTTAGAAGATATGATGGGAAAGGTTGAGGCCACAACGGAGAACCCGGTACCATAAAGATA
* * *
29247063 TGAAGGGAAAGGTTAAGGCTGCAACGGTGAACCCGGTACCATGAAGATATAAAGGGAAGGGTTAA
66 TGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCAT-----T-TAAAGGGAAAGGTTAA
* **
29247128 GGCCGTAACGGTAAACCC
125 GGCCGCAACGACAAACCC
* * * * * *
29247146 GGTACCTTAGAAGACATGATGGGAAAGGTCGAGGCCACAACGGTGAACCCGATACCATTAAGATT
1 GGTACCTTAGAAGATATGATGGGAAAGGTTGAGGCCACAACGGAGAACCCGGTACCATAAAGATA
* * *
29247211 TGAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCTGTACC
66 TGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACC
29247251 TTAAAAGATG
Statistics
Matches: 208, Mismatches: 38, Indels: 9
0.82 0.15 0.04
Matches are distributed among these distances:
141 1 0.00
142 42 0.20
143 47 0.23
147 1 0.00
148 117 0.56
ACGTcount: A:0.34, C:0.19, G:0.30, T:0.17
Consensus pattern (142 bp):
GGTACCTTAGAAGATATGATGGGAAAGGTTGAGGCCACAACGGAGAACCCGGTACCATAAAGATA
TGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCATTTAAAGGGAAAGGTTAAGGCCGC
AACGACAAACCC
Found at i:29247279 original size:99 final size:98
Alignment explanation
Indices: 29246730--29247286 Score: 417
Period size: 99 Copynumber: 5.7 Consensus size: 98
29246720 GATGTAATGC
* * *
29246730 GAAAGGTTGAGGCCGCAACGGCGGACCCGATA-CTAAGAAGATGTGAT-GGGAA-GTTAAGGCCA
1 GAAAGGTTGAGGCCGCAACGGCGAACCCG-TACCTTAGAAGATGTGATAGGAAAGGTTAAGGCCA
* * * *
29246792 TAACGACGAACCTGGTACCTTAAAAGATGTGAAGG
65 CAACGGCGAACCCGGTACCTT-AAAGATATGAAGG
* * *** * *
29246827 GAAAGGTTGAGGCCGTAATGGCGAATTTGGTACCTTAGAAGATGTGATGGGAAAGGTTAAGGCCG
1 GAAAGGTTGAGGCCGCAACGGCGAA-CCCGTACCTTAGAAGATGTGATAGGAAAGGTTAAGGCCA
** * *
29246892 CAACGGAAAACCTGGTACCTTAAAAGATGTGATA-G
65 CAACGGCGAACCCGGTACCTT-AAAGATATGA-AGG
* * *
29246927 GAAAGGTTGAGGCCGCAACGGTGAACCCGATACC-------ATTTGA-AGGGAAAGGTTAAGGTC
1 GAAAGGTTGAGGCCGCAACGGCGAACCCG-TACCTTAGAAGATGTGATA-GGAAAGGTTAAGGCC
* * * *
29246984 GCAACGACGAACCCTGTACCTTAGAAGATATGAAGT
64 ACAACGGCGAACCCGGTACCTTA-AAGATATGAAGG
* * * * *
29247020 GAAAGGTTGAGTCCACAACGGCGAACCCGGTACCAT-GAAGATATGA-AGGGAAAGGTTAAGGCT
1 GAAAGGTTGAGGCCGCAACGGCGAACCC-GTACCTTAGAAGATGTGATA-GGAAAGGTTAAGGCC
* * * * *
29247083 GCAACGGTGAACCCGGTACCATGAAGATATAAAGG
64 ACAACGGCGAACCCGGTACCTTAAAGATATGAAGG
* * * ** ** * **
29247118 GAAGGGTTAAGGCCGTAACGGTAAACCCGGTACCTTAGAAGACATGATGGGAAAGGTCGAGGCCA
1 GAAAGGTTGAGGCCGCAACGGCGAACCC-GTACCTTAGAAGATGTGATAGGAAAGGTTAAGGCCA
* * *
29247183 CAACGGTGAACCCGATACCATT-AAGATTTGAAGG
65 CAACGGCGAACCCGGTACC-TTAAAGATATGAAGG
* * *
29247217 GAAAGGTTGAGGCCGCAATGGCGAACCCTGTACCTTAAAAGATGTGATAGG-AAGGATTGAGGCC
1 GAAAGGTTGAGGCCGCAACGGCGAACCC-GTACCTTAGAAGATGTGATAGGAAAGG-TTAAGGCC
29247281 ACAACG
64 ACAACG
29247287 ATAAATCTTA
Statistics
Matches: 368, Mismatches: 72, Indels: 38
0.77 0.15 0.08
Matches are distributed among these distances:
92 2 0.01
93 73 0.20
94 1 0.00
97 24 0.07
98 57 0.15
99 145 0.39
100 65 0.18
101 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.31, T:0.18
Consensus pattern (98 bp):
GAAAGGTTGAGGCCGCAACGGCGAACCCGTACCTTAGAAGATGTGATAGGAAAGGTTAAGGCCAC
AACGGCGAACCCGGTACCTTAAAGATATGAAGG
Found at i:29247582 original size:39 final size:39
Alignment explanation
Indices: 29247530--29247659 Score: 165
Period size: 39 Copynumber: 3.4 Consensus size: 39
29247520 ACGTCACCAT
29247530 CCAATCTCTTACCTCGACCATGGGCCAAATTGAAGCACA
1 CCAATCTCTTACCTCGACCATGGGCCAAATTGAAGCACA
*
29247569 CCAATCTCTTACCTCGACCATGGGCCAAATTGAAGTACA
1 CCAATCTCTTACCTCGACCATGGGCCAAATTGAAGCACA
* * * * * *
29247608 CCAATCTCTCACC-CTAATCATGGGGCAGATTGAAGCA-T
1 CCAATCTCTTACCTC-GACCATGGGCCAAATTGAAGCACA
*
29247646 CCAATCTTTTACCT
1 CCAATCTCTTACCT
29247660 TAATTAGAAG
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
38 12 0.15
39 67 0.85
ACGTcount: A:0.29, C:0.32, G:0.15, T:0.25
Consensus pattern (39 bp):
CCAATCTCTTACCTCGACCATGGGCCAAATTGAAGCACA
Found at i:29247692 original size:78 final size:78
Alignment explanation
Indices: 29247530--29248459 Score: 1184
Period size: 78 Copynumber: 11.9 Consensus size: 78
29247520 ACGTCACCAT
* * * * * * ** *
29247530 CCAATCTCTTACCTCGACCATGGGCCAAATTGAAGCACACCAATCTCTTACCTCGACCATG--GG
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCA-TCCAATCTTTTACCTTAATCA-GAAGG
* *
29247593 CCAAATTGAAG-TACA
64 -CAGATTGAAGACACA
* ** *
29247608 CCAATCTCTCACCCTAATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATTAGAAGGCA
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAAGGCA
*
29247673 GATCGAAGACACA
66 GATTGAAGACACA
* *
29247686 CTAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAAGGTA
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAAGGCA
*
29247751 GATTGAAGATACA
66 GATTGAAGACACA
* * * * *
29247764 CCAATCTCTTACCCCGATCATAGGGAAAATTTAAGCATCCAATCTTTTACCTTAATCAGAAGGAA
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAAGGCA
29247829 GATTGAAGACACA
66 GATTGAAGACACA
* *
29247842 CCAATCTCTTACCCCGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCTTAATCATAAGGCA
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAAGGCA
**
29247907 GATTGAAGATGCA
66 GATTGAAGACACA
* *
29247920 CCAATCTCTTACCCCGATCATGGGGCAGACTGAAGCATCCAATCTTTTACCTTAATTAGAAGGCA
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAAGGCA
*
29247985 GATTGAAGACGCA
66 GATTGAAGACACA
* * *
29247998 CCAATCTCTTACCCTGATCATGGGGCAGATTGAAACATTCAATCTTTTACCTTAATCAGAAGGCA
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAAGGCA
29248063 GATT-AACGACACA
66 GATTGAA-GACACA
* * * * * *
29248076 ACAATCTCTTACCTCGATCATGGGGCATATTGAAGCATCTAATATTTTACCTTAATTAGAAGGCA
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAAGGCA
* *
29248141 GATTGAAGGCGCA
66 GATTGAAGACACA
* *
29248154 CCAAATCTCTTACCCCGATCATGGGGCAGATTAAAGCATCCAATCTTTTACCTTAATCAGAAGGA
1 CC-AATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAAGGC
* *
29248219 AGATTGAAAACGCA
65 AGATTGAAGACACA
* *
29248233 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAAAAGGTA
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAAGGCA
**
29248298 GATTGAAGATGCA
66 GATTGAAGACACA
* * * * * * *
29248311 CCAATCTCTTACCCTGGTCATGAGACAAATTGAAGCATCTAATCTTTTACCTTAATCAGAGGGCA
1 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAAGGCA
*
29248376 GAGTGAAGACACA
66 GATTGAAGACACA
* * * * * * *
29248389 CCAATCTATTACCTCGGTCATGGGGCAGATTGAAACCATCCAATCTTTTTACCTCAATTAGAGGG
1 CCAATCTCTTACCCCGATCATGGGGCAGATTG-AAGCATCCAATC-TTTTACCTTAATCAGAAGG
29248454 CAGATT
64 CAGATT
29248460 AAAGCCACGC
Statistics
Matches: 744, Mismatches: 100, Indels: 14
0.87 0.12 0.02
Matches are distributed among these distances:
76 1 0.00
77 25 0.03
78 615 0.83
79 81 0.11
80 22 0.03
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (78 bp):
CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAAGGCA
GATTGAAGACACA
Found at i:29249995 original size:29 final size:28
Alignment explanation
Indices: 29249769--29250044 Score: 221
Period size: 30 Copynumber: 9.4 Consensus size: 28
29249759 TTGACTCCCG
* * *
29249769 AACTTTCCAAAACTTAGACTTTGACCCTAA
1 AACTTTCCAAAAATTA-ATTTTAACCCT-A
* *
29249799 AACTTTCTAAAAATTGCATTTTAACCC-A
1 AACTTTCCAAAAATT-AATTTTAACCCTA
* *
29249827 AACTCTCTAAAAATTGAATTTTAACCCTTA
1 AACTTTCCAAAAATT-AATTTTAACCC-TA
* *
29249857 AATTTTCCAAAAATCATATTTTAACCCCTA
1 AACTTTCCAAAAATTA-ATTTTAA-CCCTA
*
29249887 AAGTTTCCAAAAATTATATTTTAACCTCTA
1 AACTTTCCAAAAATTA-ATTTTAACC-CTA
* *
29249917 AACTTTCCAAAAATTAACTTTTGACCCCA
1 AACTTTCCAAAAATTAA-TTTTAACCCTA
* *
29249946 AACTTTCCAAAACTTCAATTTTGACCCTA
1 AACTTTCCAAAAATT-AATTTTAACCCTA
* * * * *
29249975 AACTTTCTAAAAATCACATTTTGACCTTG
1 AACTTTCCAAAAATTA-ATTTTAACCCTA
* * *
29250004 AACTCTCTAAAAATTTTATTTTAACCCTCA
1 AACTTTCCAAAAA-TTAATTTTAACCCT-A
29250034 AACTTTCCAAA
1 AACTTTCCAAA
29250045 TTTACATTTT
Statistics
Matches: 204, Mismatches: 31, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
28 27 0.13
29 73 0.36
30 101 0.50
31 3 0.01
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (28 bp):
AACTTTCCAAAAATTAATTTTAACCCTA
Found at i:29250053 original size:29 final size:30
Alignment explanation
Indices: 29249747--29250060 Score: 211
Period size: 30 Copynumber: 10.6 Consensus size: 30
29249737 GTTTTTATTT
* *
29249747 AAAAATTACATTTTGACTCC-CGAACTTTCC
1 AAAAATTACATTTTAAC-CCTCAAACTTTCC
* * * * * *
29249777 AAAACTTAGACTTTGACCCTAAAACTTTCT
1 AAAAATTACATTTTAACCCTCAAACTTTCC
* * *
29249807 AAAAATTGCATTTTAA-CC-CAAACTCTCT
1 AAAAATTACATTTTAACCCTCAAACTTTCC
* *
29249835 AAAAATTGA-ATTTTAACCCTTAAATTTTCC
1 AAAAATT-ACATTTTAACCCTCAAACTTTCC
* * *
29249865 AAAAATCATATTTTAACCC-CTAAAGTTTCC
1 AAAAATTACATTTTAACCCTC-AAACTTTCC
*
29249895 AAAAATTATATTTTAA-CCTCTAAACTTTCC
1 AAAAATTACATTTTAACCCTC-AAACTTTCC
*
29249925 AAAAATTA-ACTTTTGACCC-CAAACTTTCC
1 AAAAATTACA-TTTTAACCCTCAAACTTTCC
* * *
29249954 AAAACTT-CAATTTTGACCCT-AAACTTTCT
1 AAAAATTAC-ATTTTAACCCTCAAACTTTCC
* * ** * *
29249983 AAAAATCACATTTTGA-CCTTGAACTCTCT
1 AAAAATTACATTTTAACCCTCAAACTTTCC
**
29250012 AAAAATTTTATTTTAACCCTCAAACTTTCC
1 AAAAATTACATTTTAACCCTCAAACTTTCC
*
29250042 -AAATTTACATTTTTAACCC
1 AAAAATTACA-TTTTAACCC
29250061 CATTTTTCTT
Statistics
Matches: 227, Mismatches: 41, Indels: 32
0.76 0.14 0.11
Matches are distributed among these distances:
28 25 0.11
29 79 0.35
30 121 0.53
31 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAAATTACATTTTAACCCTCAAACTTTCC
Found at i:29250054 original size:58 final size:59
Alignment explanation
Indices: 29249747--29250044 Score: 226
Period size: 58 Copynumber: 5.1 Consensus size: 59
29249737 GTTTTTATTT
* ** * * * * * * *
29249747 AAAAATTACATTTTGACTCCCGAACTTTCCAAAACTTAGACTTTGACCCTAAAACTTTCT
1 AAAAATCACATTTTGAC-CCTAAACTCTCCAAAAATTAAATTTTAACCCTCAAACTTTCC
** * * * * *
29249807 AAAAATTGCATTTTAACCC-AAACTCTCTAAAAATTGAATTTTAACCCTTAAATTTTCC
1 AAAAATCACATTTTGACCCTAAACTCTCCAAAAATTAAATTTTAACCCTCAAACTTTCC
* * * * *
29249865 AAAAATCATATTTTAACCCCTAAAGTTTCCAAAAATTATATTTTAA-CCTCTAAACTTTCC
1 AAAAATCACATTTTGA-CCCTAAACTCTCCAAAAATTAAATTTTAACCCTC-AAACTTTCC
* * * * * * *
29249925 AAAAATTA-ACTTTTGACCCCAAACTTTCCAAAACTTCAATTTTGACCCT-AAACTTTCT
1 AAAAATCACA-TTTTGACCCTAAACTCTCCAAAAATTAAATTTTAACCCTCAAACTTTCC
* * * **
29249983 AAAAATCACATTTTGACCTTGAACTCTCTAAAAATTTTATTTTAACCCTCAAACTTTCC
1 AAAAATCACATTTTGACCCTAAACTCTCCAAAAATTAAATTTTAACCCTCAAACTTTCC
29250042 AAA
1 AAA
29250045 TTTACATTTT
Statistics
Matches: 188, Mismatches: 43, Indels: 15
0.76 0.17 0.06
Matches are distributed among these distances:
58 86 0.46
59 44 0.23
60 58 0.31
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.35
Consensus pattern (59 bp):
AAAAATCACATTTTGACCCTAAACTCTCCAAAAATTAAATTTTAACCCTCAAACTTTCC
Found at i:29252993 original size:21 final size:19
Alignment explanation
Indices: 29252967--29253017 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 19
29252957 ATACAAGAAG
*
29252967 TATCGATACCAATATGATTTT
1 TATCGATACCAATAT--TTTC
29252988 TATCGATACC-ATATTTTC
1 TATCGATACCAATATTTTC
29253006 TATCGATACCAA
1 TATCGATACCAA
29253018 AATTGCTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 13 0.46
19 1 0.04
20 4 0.14
21 10 0.36
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (19 bp):
TATCGATACCAATATTTTC
Found at i:29256639 original size:63 final size:63
Alignment explanation
Indices: 29256540--29256666 Score: 245
Period size: 63 Copynumber: 2.0 Consensus size: 63
29256530 GGGGGATGAG
*
29256540 ATCTCCTTAATGGAAGAAGAACTCGCTTAACTGTCTGTCAAAAGCTTAAAAGTGGTGCTGAAT
1 ATCTCCTTAATGGAAGAAGAACTCGCTCAACTGTCTGTCAAAAGCTTAAAAGTGGTGCTGAAT
29256603 ATCTCCTTAATGGAAGAAGAACTCGCTCAACTGTCTGTCAAAAGCTTAAAAGTGGTGCTGAAT
1 ATCTCCTTAATGGAAGAAGAACTCGCTCAACTGTCTGTCAAAAGCTTAAAAGTGGTGCTGAAT
29256666 A
1 A
29256667 ATGCTTATAC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (63 bp):
ATCTCCTTAATGGAAGAAGAACTCGCTCAACTGTCTGTCAAAAGCTTAAAAGTGGTGCTGAAT
Found at i:29258218 original size:16 final size:16
Alignment explanation
Indices: 29258199--29258229 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29258189 TATTGCAACC
29258199 CGTTTCTATAACACCT
1 CGTTTCTATAACACCT
*
29258215 CGTTTCTGTAACACC
1 CGTTTCTATAACACC
29258230 CTTATACTCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.32, G:0.10, T:0.35
Consensus pattern (16 bp):
CGTTTCTATAACACCT
Found at i:29259288 original size:21 final size:18
Alignment explanation
Indices: 29259239--29259290 Score: 50
Period size: 21 Copynumber: 2.6 Consensus size: 18
29259229 CAACTAAACT
29259239 TCACCTTAAATAAATTAAC
1 TCACCTT-AATAAATTAAC
*
29259258 TTACCTTTAATAATTATTAAGC
1 TCACC-TTAATAA--ATTAA-C
29259280 TCACCTTAATA
1 TCACCTTAATA
29259291 CTATGATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 9 0.33
20 2 0.07
21 11 0.41
22 5 0.19
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (18 bp):
TCACCTTAATAAATTAAC
Found at i:29259434 original size:22 final size:22
Alignment explanation
Indices: 29259402--29259495 Score: 116
Period size: 22 Copynumber: 4.0 Consensus size: 22
29259392 TGCACTAATG
* *
29259402 AACGGAAAGCACAAAGGTGCTA
1 AACGGAGAGCACAAACGTGCTA
*
29259424 GACGGAGAGCACAAACGTGCTA
1 AACGGAGAGCACAAACGTGCTA
29259446 AACGGAGAGCACTAAACGTGCTAATA
1 AACGGAGAGCAC-AAACGTGC---TA
29259472 AACGGAGAGCACTAAACGTGCTA
1 AACGGAGAGCAC-AAACGTGCTA
29259495 A
1 A
29259496 TAAACGGAGA
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
22 30 0.47
23 11 0.17
26 23 0.36
ACGTcount: A:0.41, C:0.20, G:0.27, T:0.12
Consensus pattern (22 bp):
AACGGAGAGCACAAACGTGCTA
Found at i:29259480 original size:26 final size:26
Alignment explanation
Indices: 29259425--29259507 Score: 138
Period size: 26 Copynumber: 3.3 Consensus size: 26
29259415 AAGGTGCTAG
29259425 ACGGAGAGCAC-AAACGTGC---TAA
1 ACGGAGAGCACTAAACGTGCTAATAA
29259447 ACGGAGAGCACTAAACGTGCTAATAA
1 ACGGAGAGCACTAAACGTGCTAATAA
29259473 ACGGAGAGCACTAAACGTGCTAATAA
1 ACGGAGAGCACTAAACGTGCTAATAA
29259499 ACGGAGAGC
1 ACGGAGAGC
29259508 GCGTTAGGGT
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
22 11 0.19
23 8 0.14
26 38 0.67
ACGTcount: A:0.41, C:0.20, G:0.27, T:0.12
Consensus pattern (26 bp):
ACGGAGAGCACTAAACGTGCTAATAA
Found at i:29263564 original size:44 final size:44
Alignment explanation
Indices: 29263501--29263589 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
29263491 AATTCGTGTT
29263501 AAAATTACCAACATATTGATTTTTAATTATTTTTATAAATATTG
1 AAAATTACCAACATATTGATTTTTAATTATTTTTATAAATATTG
29263545 AAAATTACCAACATATTGATTTTTAATTATTTTTATAAATATTG
1 AAAATTACCAACATATTGATTTTTAATTATTTTTATAAATATTG
29263589 A
1 A
29263590 GCATAAATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (44 bp):
AAAATTACCAACATATTGATTTTTAATTATTTTTATAAATATTG
Found at i:29266731 original size:19 final size:20
Alignment explanation
Indices: 29266684--29266731 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
29266674 TTGATAATAC
29266684 TTAA-TATTA-AATTATAAA
1 TTAATTATTATAATTATAAA
*
29266702 TTAAATT-TTATAATT-TATA
1 TT-AATTATTATAATTATAAA
29266721 TTAATTATTAT
1 TTAATTATTAT
29266732 CAAGAGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.24
19 14 0.56
20 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTATTATAATTATAAA
Found at i:29268313 original size:18 final size:18
Alignment explanation
Indices: 29268269--29268313 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
29268259 AGCAAGCTGA
*
29268269 AGAAGAAGAGGAAGAGCC
1 AGAAGAAGAAGAAGAGCC
* *
29268287 TGAAGAAGAAGAAGATCC
1 AGAAGAAGAAGAAGAGCC
*
29268305 AGAATAAGA
1 AGAAGAAGA
29268314 TCCTAAGGAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.53, C:0.09, G:0.31, T:0.07
Consensus pattern (18 bp):
AGAAGAAGAAGAAGAGCC
Found at i:29269791 original size:52 final size:53
Alignment explanation
Indices: 29269699--29269807 Score: 211
Period size: 52 Copynumber: 2.1 Consensus size: 53
29269689 AGCATGAGCA
29269699 TGAGCATGCAAAGTTCGAAAAAAAGTTGGTGAAATTGAAGGTCTGCTGCAAAC
1 TGAGCATGCAAAGTTCGAAAAAAAGTTGGTGAAATTGAAGGTCTGCTGCAAAC
29269752 TGAGCATGCAAAGTTCG-AAAAAAGTTGGTGAAATTGAAGGTCTGCTGCAAAC
1 TGAGCATGCAAAGTTCGAAAAAAAGTTGGTGAAATTGAAGGTCTGCTGCAAAC
29269804 TGAG
1 TGAG
29269808 TCTAGGGTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 39 0.70
53 17 0.30
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.23
Consensus pattern (53 bp):
TGAGCATGCAAAGTTCGAAAAAAAGTTGGTGAAATTGAAGGTCTGCTGCAAAC
Found at i:29271209 original size:12 final size:12
Alignment explanation
Indices: 29271192--29271216 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29271182 TGTTATGATG
29271192 ATGAATGCTATT
1 ATGAATGCTATT
29271204 ATGAATGCTATT
1 ATGAATGCTATT
29271216 A
1 A
29271217 ATTCTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:29274513 original size:37 final size:37
Alignment explanation
Indices: 29274454--29274530 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
29274444 GTCAAAGGTT
*
29274454 TATAATAATCGGCCAAATCGAGAAAGCTTCTTACTTC
1 TATAATAATCGGCCAAACCGAGAAAGCTTCTTACTTC
* *
29274491 TATAATAATCGGTCAAACCGAGAATGCTTCTTACTTC
1 TATAATAATCGGCCAAACCGAGAAAGCTTCTTACTTC
29274528 TAT
1 TAT
29274531 CACATTCTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (37 bp):
TATAATAATCGGCCAAACCGAGAAAGCTTCTTACTTC
Found at i:29278493 original size:22 final size:22
Alignment explanation
Indices: 29278465--29278529 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
29278455 ATTAATGAAT
* *
29278465 GGAGAGCATAAAGGTGCTAGAC
1 GGAGAGCATAAACGTGCTAAAC
*
29278487 GGAGAGCACAAACGTGCTAAAC
1 GGAGAGCATAAACGTGCTAAAC
* * *
29278509 GAAAAGCACTAAATGTGCTAA
1 GGAGAGCA-TAAACGTGCTAA
29278530 TAAATGGAGA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
22 25 0.71
23 10 0.29
ACGTcount: A:0.42, C:0.17, G:0.28, T:0.14
Consensus pattern (22 bp):
GGAGAGCATAAACGTGCTAAAC
Found at i:29284046 original size:29 final size:28
Alignment explanation
Indices: 29283964--29284052 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 28
29283954 AAAACACATA
*
29283964 AATATAATACAAAAGTATGCAAATCACAAT
1 AATAT-ATACAAAAG-ATACAAATCACAAT
*
29283994 AATA-ATA-AAAA-ATA-ATATCACAAT
1 AATATATACAAAAGATACAAATCACAAT
29284018 AATATATACAAAAGCATACAAATCACAAT
1 AATATATACAAAAG-ATACAAATCACAAT
29284047 AATATA
1 AATATA
29284053 ACTTAAACTT
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
24 13 0.25
25 5 0.10
26 4 0.08
27 4 0.08
28 6 0.12
29 15 0.29
30 4 0.08
ACGTcount: A:0.61, C:0.12, G:0.03, T:0.24
Consensus pattern (28 bp):
AATATATACAAAAGATACAAATCACAAT
Found at i:29293535 original size:769 final size:769
Alignment explanation
Indices: 29292485--29294034 Score: 3091
Period size: 769 Copynumber: 2.0 Consensus size: 769
29292475 CCATCAGAAA
29292485 CATCTAGATTTTGATATTTAAAAAAAAATATTTTTAAATTTTGTAATTAGGTTAAATATTGCCAA
1 CATCTAGATTTTGATATTTAAAAAAAAATATTTTTAAATTTTGTAATTAGGTTAAATATTGCCAA
29292550 ACATTATAGTTTATTTAATACAAATCACCTGCTCACTCCACGTGTGAAAATAATATTAGTCTATA
66 ACATTATAGTTTATTTAATACAAATCACCTGCTCACTCCACGTGTGAAAATAATATTAGTCTATA
29292615 TCAATCACGAACGTCTTCATCAAGAAAATCAAACGGTCGTCAATCTCCAACATATGAAACGGTTC
131 TCAATCACGAACGTCTTCATCAAGAAAATCAAACGGTCGTCAATCTCCAACATATGAAACGGTTC
29292680 AGATTTAAAGCACCTTCGTTAAACGGTCTAGATTAAATCTAACGTGTACTTACACTCACGCTCTC
196 AGATTTAAAGCACCTTCGTTAAACGGTCTAGATTAAATCTAACGTGTACTTACACTCACGCTCTC
29292745 TATAGCCACAAAACCCGATACTAAGAGCTTCAAAGAAAACAAGTCAAACAACACTGAAATCTTAC
261 TATAGCCACAAAACCCGATACTAAGAGCTTCAAAGAAAACAAGTCAAACAACACTGAAATCTTAC
29292810 ATTTCTCCTCTTTTTTTTTCTTTCAATCTTCAAAAACGTTTCAAAGCGAGTAGTTGGGGTTTTTT
326 ATTTCTCCTCTTTTTTTTTCTTTCAATCTTCAAAAACGTTTCAAAGCGAGTAGTTGGGGTTTTTT
29292875 TTAAGAATTTGTGTGGAAAAAATAAATAAAAAAATGGCTGAGCACGAAGAGAAGAAGCACGAGGA
391 TTAAGAATTTGTGTGGAAAAAATAAATAAAAAAATGGCTGAGCACGAAGAGAAGAAGCACGAGGA
29292940 ATCGTTGATGGAAAAGATAGCGGAGAAGATCCATGGTCATGATTCATCGTCATCGTCGTCGGATT
456 ATCGTTGATGGAAAAGATAGCGGAGAAGATCCATGGTCATGATTCATCGTCATCGTCGTCGGATT
29293005 CCGATGACGACAAGCCATCTGAATCTTCGATCAAGGACAAGGTGTTTCGTCTCTTTGGAAGAGAA
521 CCGATGACGACAAGCCATCTGAATCTTCGATCAAGGACAAGGTGTTTCGTCTCTTTGGAAGAGAA
29293070 AAGCCCGTCCACCATGTTTTCGGTGGAGGCAAACGTATGTTACAAGGACCCCCTTTTTCTTCATT
586 AAGCCCGTCCACCATGTTTTCGGTGGAGGCAAACGTATGTTACAAGGACCCCCTTTTTCTTCATT
29293135 TCTTAAATTAGGGTCTTTTACAAGTCTGGGTTTTTAAATTTTCTAATTTTCATTTATAATCAGAT
651 TCTTAAATTAGGGTCTTTTACAAGTCTGGGTTTTTAAATTTTCTAATTTTCATTTATAATCAGAT
29293200 GTTATTTTTATTTTGTGGTCATGGGAGAGTAATTAGATCTGACTTAGTGATTTG
716 GTTATTTTTATTTTGTGGTCATGGGAGAGTAATTAGATCTGACTTAGTGATTTG
29293254 CATCTAGATTTTGATATTTAAAAAAAAATATTTTTAAATTTTGTAATTAGGTTAAATATTGCCAA
1 CATCTAGATTTTGATATTTAAAAAAAAATATTTTTAAATTTTGTAATTAGGTTAAATATTGCCAA
29293319 ACATTATAGTTTATTTAATACAAATCACCTGCTCACTCCACGTGTGAAAATAATATTAGTCTATA
66 ACATTATAGTTTATTTAATACAAATCACCTGCTCACTCCACGTGTGAAAATAATATTAGTCTATA
29293384 TCAATCACGAACGTCTTCATCAAGAAAATCAAACGGTCGTCAATCTCCAACATATGAAACGGTTC
131 TCAATCACGAACGTCTTCATCAAGAAAATCAAACGGTCGTCAATCTCCAACATATGAAACGGTTC
29293449 AGATTTAAAGCACCTTCGTTAAACGGTCTAGATTAAATCTAACGTGTACTTACACTCACGCTCTC
196 AGATTTAAAGCACCTTCGTTAAACGGTCTAGATTAAATCTAACGTGTACTTACACTCACGCTCTC
29293514 TATAGCCACAAAACCCGATACTAAGAGCTTCAAAGAAAACAAGTCAAACAACACTGAAATCTTAC
261 TATAGCCACAAAACCCGATACTAAGAGCTTCAAAGAAAACAAGTCAAACAACACTGAAATCTTAC
29293579 ATTTCTCCTCTTTTTTTTTCTTTCAATCTTCAAAAACGTTTCAAAGCGAGTAGTTGGGGTTTTTT
326 ATTTCTCCTCTTTTTTTTTCTTTCAATCTTCAAAAACGTTTCAAAGCGAGTAGTTGGGGTTTTTT
29293644 TTAAGAATTTGTGTGGAAAAAATAAATAAAAAAATGGCTGAGCACGAAGAGAAGAAGCACGAGGA
391 TTAAGAATTTGTGTGGAAAAAATAAATAAAAAAATGGCTGAGCACGAAGAGAAGAAGCACGAGGA
29293709 ATCGTTGATGGAAAAGATAGCGGAGAAGATCCATGGTCATGATTCATCGTCATCGTCGTCGGATT
456 ATCGTTGATGGAAAAGATAGCGGAGAAGATCCATGGTCATGATTCATCGTCATCGTCGTCGGATT
29293774 CCGATGACGACAAGCCATCTGAATCTTCGATCAAGGACAAGGTGTTTCGTCTCTTTGGAAGAGAA
521 CCGATGACGACAAGCCATCTGAATCTTCGATCAAGGACAAGGTGTTTCGTCTCTTTGGAAGAGAA
29293839 AAGCCCGTCCACCATGTTTTCGGTGGAGGCAAACGTATGTTACAAGGACCCCCTTTTTCTTCATT
586 AAGCCCGTCCACCATGTTTTCGGTGGAGGCAAACGTATGTTACAAGGACCCCCTTTTTCTTCATT
29293904 TCTTAAATTAGGGTCTTTTACAAGTCTGGGTTTTTAAATTTTCTAATTTTCATTTATAATCAGAT
651 TCTTAAATTAGGGTCTTTTACAAGTCTGGGTTTTTAAATTTTCTAATTTTCATTTATAATCAGAT
29293969 GTTATTTTTATTTTGTGGTCATGGGAGAGTAATTAGATCTGACTTAGTGATTTG
716 GTTATTTTTATTTTGTGGTCATGGGAGAGTAATTAGATCTGACTTAGTGATTTG
*
29294023 CATCTAGCTTTT
1 CATCTAGATTTT
29294035 AATTTTGATT
Statistics
Matches: 780, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
769 780 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (769 bp):
CATCTAGATTTTGATATTTAAAAAAAAATATTTTTAAATTTTGTAATTAGGTTAAATATTGCCAA
ACATTATAGTTTATTTAATACAAATCACCTGCTCACTCCACGTGTGAAAATAATATTAGTCTATA
TCAATCACGAACGTCTTCATCAAGAAAATCAAACGGTCGTCAATCTCCAACATATGAAACGGTTC
AGATTTAAAGCACCTTCGTTAAACGGTCTAGATTAAATCTAACGTGTACTTACACTCACGCTCTC
TATAGCCACAAAACCCGATACTAAGAGCTTCAAAGAAAACAAGTCAAACAACACTGAAATCTTAC
ATTTCTCCTCTTTTTTTTTCTTTCAATCTTCAAAAACGTTTCAAAGCGAGTAGTTGGGGTTTTTT
TTAAGAATTTGTGTGGAAAAAATAAATAAAAAAATGGCTGAGCACGAAGAGAAGAAGCACGAGGA
ATCGTTGATGGAAAAGATAGCGGAGAAGATCCATGGTCATGATTCATCGTCATCGTCGTCGGATT
CCGATGACGACAAGCCATCTGAATCTTCGATCAAGGACAAGGTGTTTCGTCTCTTTGGAAGAGAA
AAGCCCGTCCACCATGTTTTCGGTGGAGGCAAACGTATGTTACAAGGACCCCCTTTTTCTTCATT
TCTTAAATTAGGGTCTTTTACAAGTCTGGGTTTTTAAATTTTCTAATTTTCATTTATAATCAGAT
GTTATTTTTATTTTGTGGTCATGGGAGAGTAATTAGATCTGACTTAGTGATTTG
Found at i:29301302 original size:29 final size:29
Alignment explanation
Indices: 29301219--29301303 Score: 77
Period size: 29 Copynumber: 2.9 Consensus size: 29
29301209 ATGTTTCGGT
* *
29301219 TATAAAAATAAA-ATTATTTGTGTATCAG
1 TATAAAAATAAATTTTATTTGTATATCAG
**
29301247 TATTTAAATCAAATTTT-TATTGATATATCA-
1 TATAAAAAT-AAATTTTAT-TTG-TATATCAG
29301277 TATAAAAATAAATTTTAATTTGTATAT
1 TATAAAAATAAATTTT-ATTTGTATAT
29301304 AAGAGGAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
28 7 0.16
29 16 0.36
30 15 0.33
31 7 0.16
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (29 bp):
TATAAAAATAAATTTTATTTGTATATCAG
Found at i:29302151 original size:6 final size:6
Alignment explanation
Indices: 29302119--29302181 Score: 55
Period size: 6 Copynumber: 11.2 Consensus size: 6
29302109 CAACTTGAAT
* *
29302119 TTTAAA -TTAAG TTTGAAA -TTAAT TTTAAA TTT--A TTTAAA TTTAAA
1 TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
29302164 TTT-AT TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA T
29302182 ACATTTGAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
4 4 0.09
5 10 0.22
6 29 0.64
7 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:29302159 original size:17 final size:17
Alignment explanation
Indices: 29302137--29302181 Score: 74
Period size: 16 Copynumber: 2.7 Consensus size: 17
29302127 AAGTTTGAAA
*
29302137 TTAATTTTAAATTTA-T
1 TTAAATTTAAATTTATT
29302153 TTAAATTTAAATTTATT
1 TTAAATTTAAATTTATT
29302170 TTAAATTTAAAT
1 TTAAATTTAAAT
29302182 ACATTTGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATTTAAATTTATT
Found at i:29302165 original size:27 final size:28
Alignment explanation
Indices: 29302125--29302201 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 28
29302115 GAATTTTAAA
*
29302125 TTAAGTTTGAAATTAATTTTAAATTTAT
1 TTAAATTTGAAATTAATTTTAAATTTAT
* *
29302153 TTAAATTT-AAATTTATTTTAAATTTAA
1 TTAAATTTGAAATTAATTTTAAATTTAT
* * *
29302180 ATACATTTGAAA-TAACTTTAAA
1 TTAAATTTGAAATTAATTTTAAA
29302202 CTTAAAATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
27 31 0.76
28 10 0.24
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (28 bp):
TTAAATTTGAAATTAATTTTAAATTTAT
Found at i:29302178 original size:11 final size:11
Alignment explanation
Indices: 29302116--29302159 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
29302106 GCCCAACTTG
29302116 AATTTTAAATT
1 AATTTTAAATT
*
29302127 AAGTTTGAAATT
1 AA-TTTTAAATT
29302139 AATTTTAAATT
1 AATTTTAAATT
*
29302150 TA-TTTAAATT
1 AATTTTAAATT
29302160 TAAATTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
10 8 0.28
11 11 0.38
12 10 0.34
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (11 bp):
AATTTTAAATT
Found at i:29302187 original size:17 final size:17
Alignment explanation
Indices: 29302152--29302192 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
29302142 TTTAAATTTA
**
29302152 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATACAT
29302169 TTTAAATTTAAATACAT
1 TTTAAATTTAAATACAT
*
29302186 TTGAAAT
1 TTTAAAT
29302193 AACTTTAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTAAATTTAAATACAT
Found at i:29303512 original size:29 final size:28
Alignment explanation
Indices: 29303478--29303581 Score: 115
Period size: 30 Copynumber: 3.6 Consensus size: 28
29303468 CCCGATTTTA
*
29303478 CCAAAATTACCGTTTTACCCCTAAACTT
1 CCAAAATTACCATTTTACCCCTAAACTT
29303506 CCTAAAATT-CCATTTTTGA-CCCTAAAACTT
1 CC-AAAATTACCA-TTTT-ACCCCT-AAACTT
29303536 CCAAAAATTACCATTTTACCCCTAAACTTT
1 CC-AAAATTACCATTTTACCCCTAAAC-TT
*
29303566 CCAAAA-TCCCATTTTA
1 CCAAAATTACCATTTTA
29303582 ACCTCGATTT
Statistics
Matches: 66, Mismatches: 3, Indels: 14
0.80 0.04 0.17
Matches are distributed among these distances:
28 13 0.20
29 23 0.35
30 27 0.41
31 3 0.05
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.34
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCCTAAACTT
Found at i:29303536 original size:30 final size:28
Alignment explanation
Indices: 29303447--29303580 Score: 105
Period size: 29 Copynumber: 4.6 Consensus size: 28
29303437 TCCTCGAACT
* * **
29303447 TTCCAAAATTCCTTTTTTAACCCC-GATT
1 TTCCAAAATTCCATTTTT-ACCCCTAAAC
*
29303475 TTACCAAAATTACC-GTTTTACCCCTAAAC
1 TT-CCAAAATT-CCATTTTTACCCCTAAAC
29303504 TTCCTAAAATTCCATTTTTGA-CCCTAAAAC
1 TTCC-AAAATTCCATTTTT-ACCCCT-AAAC
29303534 TTCCAAAAATTACCA-TTTTACCCCTAAAC
1 TTCC-AAAATT-CCATTTTTACCCCTAAAC
*
29303563 TTTCCAAAATCCCATTTT
1 -TTCCAAAATTCCATTTT
29303581 AACCTCGATT
Statistics
Matches: 88, Mismatches: 7, Indels: 21
0.76 0.06 0.18
Matches are distributed among these distances:
28 14 0.16
29 42 0.48
30 29 0.33
31 3 0.03
ACGTcount: A:0.32, C:0.29, G:0.02, T:0.37
Consensus pattern (28 bp):
TTCCAAAATTCCATTTTTACCCCTAAAC
Found at i:29303599 original size:28 final size:28
Alignment explanation
Indices: 29303568--29303709 Score: 99
Period size: 28 Copynumber: 4.9 Consensus size: 28
29303558 TAAACTTTCC
*
29303568 AAAATCCCATTTTAACCTCGATTTCAAT
1 AAAATCCCATTTTAACCCCGATTTCAAT
* ** ***
29303596 AAAAATTACCATTTT-ACCCTCGAACTCTCC
1 -AAAA-TCCCATTTTAACCC-CGATTTCAAT
29303626 AAAATCCCATTTTAACCCCGATTTCACCA-
1 AAAATCCCATTTTAACCCCGATTTCA--AT
* * ** **
29303655 AAAATTACCATTTTACCCCCGAACTCTCT
1 AAAA-TCCCATTTTAACCCCGATTTCAAT
29303684 AAAATCCCATTTTAACCCCGATTTCA
1 AAAATCCCATTTTAACCCCGATTTCA
29303710 CCAAAACTTA
Statistics
Matches: 83, Mismatches: 23, Indels: 15
0.69 0.19 0.12
Matches are distributed among these distances:
28 30 0.36
29 23 0.28
30 30 0.36
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.31
Consensus pattern (28 bp):
AAAATCCCATTTTAACCCCGATTTCAAT
Found at i:29303609 original size:30 final size:30
Alignment explanation
Indices: 29303574--29303784 Score: 140
Period size: 30 Copynumber: 7.2 Consensus size: 30
29303564 TTCCAAAATC
* *
29303574 CCATTTTAACCTCGATTTCAATAAAAATTA
1 CCATTTTAACCCCGATTTCACTAAAAATTA
** * * *
29303604 CCATTTT-ACCCTCGAACTCTC-CAAAA-TC
1 CCATTTTAACCC-CGATTTCACTAAAAATTA
*
29303632 CCATTTTAACCCCGATTTCACCAAAAATTA
1 CCATTTTAACCCCGATTTCACTAAAAATTA
* ** * *
29303662 CCATTTTACCCCCGAACTCTCT-AAAA-TC
1 CCATTTTAACCCCGATTTCACTAAAAATTA
* *
29303690 CCATTTTAACCCCGATTTCACCAAAACTTA
1 CCATTTTAACCCCGATTTCACTAAAAATTA
29303720 CCATTTT-ACCCTCGAACTTTC-C--AAAA-T-
1 CCATTTTAACCC-CG-A-TTTCACTAAAAATTA
*
29303747 CTCATTTTAACCCTGATTTCA-TCAAAAATTA
1 C-CATTTTAACCCCGATTTCACT-AAAAATTA
29303778 CCATTTT
1 CCATTTT
29303785 CCCCCGGGCA
Statistics
Matches: 137, Mismatches: 27, Indels: 34
0.69 0.14 0.17
Matches are distributed among these distances:
26 4 0.03
27 2 0.01
28 40 0.29
29 37 0.27
30 47 0.34
31 3 0.02
32 4 0.03
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (30 bp):
CCATTTTAACCCCGATTTCACTAAAAATTA
Found at i:29303627 original size:58 final size:58
Alignment explanation
Indices: 29303438--29303784 Score: 364
Period size: 58 Copynumber: 6.0 Consensus size: 58
29303428 CCTCTCTAGT
* ** * * *
29303438 CCTCGAACTTTCCAAAATTCCTTTTTTAACCCCGATTT-TACCAAAATTACCGTTTTAC
1 CCTCGAACTCTCCAAAA-TCCCATTTTAACCCCGATTTCAACAAAAATTACCATTTTAC
* * * ** *
29303496 CC-CTAAACT-TCCTAAAATTCCATTTTTGACCCTAAAACTTC--CAAAAATTACCATTTTAC
1 CCTC-GAACTCTCC-AAAATCCCA-TTTTAACCC--CGATTTCAACAAAAATTACCATTTTAC
* * * *
29303555 CC-CTAAACTTTCCAAAATCCCATTTTAACCTCGATTTCAATAAAAATTACCATTTTAC
1 CCTC-GAACTCTCCAAAATCCCATTTTAACCCCGATTTCAACAAAAATTACCATTTTAC
*
29303613 CCTCGAACTCTCCAAAATCCCATTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
1 CCTCGAACTCTCCAAAATCCCATTTTAACCCCGATTTCAACAAAAATTACCATTTTAC
* * * *
29303671 CCCCGAACTCTCTAAAATCCCATTTTAACCCCGATTTCACCAAAACTTACCATTTTAC
1 CCTCGAACTCTCCAAAATCCCATTTTAACCCCGATTTCAACAAAAATTACCATTTTAC
* * * *
29303729 CCTCGAACTTTCCAAAATCTCATTTTAACCCTGATTTCATCAAAAATTACCATTTT
1 CCTCGAACTCTCCAAAATCCCATTTTAACCCCGATTTCAACAAAAATTACCATTTT
29303785 CCCCCGGGCA
Statistics
Matches: 247, Mismatches: 32, Indels: 20
0.83 0.11 0.07
Matches are distributed among these distances:
56 4 0.02
57 6 0.02
58 197 0.80
59 34 0.14
60 6 0.02
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.34
Consensus pattern (58 bp):
CCTCGAACTCTCCAAAATCCCATTTTAACCCCGATTTCAACAAAAATTACCATTTTAC
Found at i:29303746 original size:174 final size:174
Alignment explanation
Indices: 29303438--29303784 Score: 438
Period size: 174 Copynumber: 2.0 Consensus size: 174
29303428 CCTCTCTAGT
* ** * * *
29303438 CCTCGAACTTTCCAAAATTCCTTTTTTAACCCCGATTTTACCAAAATTACCGTTTTACCCCTAAA
1 CCTCGAACTCTCCAAAATTCCCATTTTAACCCCGATTTCACCAAAATTACCATTTTACCCCCAAA
* *
29303503 CTTCCTAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACCATTTTACCCCTAAACTTTCC
66 CTTCCTAAAATCCCATTTTTAACCC-AAAACTTCCAAAAATTACCATTTTACCCCTAAACTTTCC
29303568 AAAATCCCATTTTAA-CCTCGATTTCAAT-AAAAATTACCATTTTAC
130 AAAATCCCATTTTAACCCT-GATTTC-ATCAAAAATTACCATTTTAC
*
29303613 CCTCGAACTCTCCAAAA-TCCCATTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGA
1 CCTCGAACTCTCCAAAATTCCCATTTTAACCCCGATTTCACC-AAAATTACCATTTTACCCCCAA
** * * *
29303677 AC-TCTCTAAAATCCCA-TTTTAACCC-CGATTTCACCAAAACTTACCATTTTA-CCCTCGAACT
65 ACTTC-CTAAAATCCCATTTTTAACCCAAAACTT--CCAAAAATTACCATTTTACCCCT-AAACT
*
29303738 TTCCAAAATCTCATTTTAACCCTGATTTCATCAAAAATTACCATTTT
126 TTCCAAAATCCCATTTTAACCCTGATTTCATCAAAAATTACCATTTT
29303785 CCCCCGGGCA
Statistics
Matches: 150, Mismatches: 15, Indels: 15
0.83 0.08 0.08
Matches are distributed among these distances:
172 3 0.02
173 6 0.04
174 91 0.61
175 50 0.33
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.34
Consensus pattern (174 bp):
CCTCGAACTCTCCAAAATTCCCATTTTAACCCCGATTTCACCAAAATTACCATTTTACCCCCAAA
CTTCCTAAAATCCCATTTTTAACCCAAAACTTCCAAAAATTACCATTTTACCCCTAAACTTTCCA
AAATCCCATTTTAACCCTGATTTCATCAAAAATTACCATTTTAC
Found at i:29306521 original size:22 final size:23
Alignment explanation
Indices: 29306492--29306545 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
29306482 AAAAGCTATC
29306492 TACAAATCCA-ATC-TCT-AAGAT
1 TACAAAT-CATATCTTCTAAAGAT
29306513 TACAGAATCATATCTTCTAAAGAT
1 TACA-AATCATATCTTCTAAAGAT
*
29306537 TACATATCA
1 TACAAATCA
29306546 AATCCAAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 6 0.21
22 6 0.21
23 7 0.25
24 9 0.32
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (23 bp):
TACAAATCATATCTTCTAAAGAT
Found at i:29308599 original size:21 final size:21
Alignment explanation
Indices: 29308538--29308610 Score: 83
Period size: 21 Copynumber: 3.2 Consensus size: 21
29308528 ACCTCATACA
29308538 GCTTCAAATAATCCAGTAAAG
1 GCTTCAAATAATCCAGTAAAG
*
29308559 CCTTCTTCAACAAGTAATCCAGTAAAG
1 ---GCTTC-A-AA-TAATCCAGTAAAG
29308586 GCTTCAAATAATCCAGTAAAG
1 GCTTCAAATAATCCAGTAAAG
29308607 GCTT
1 GCTT
29308611 TCTCACATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
21 17 0.39
22 2 0.05
23 1 0.02
24 8 0.18
25 1 0.02
26 2 0.05
27 13 0.30
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (21 bp):
GCTTCAAATAATCCAGTAAAG
Found at i:29318642 original size:15 final size:15
Alignment explanation
Indices: 29318623--29318657 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
29318613 TGTGAAAGCA
*
29318623 TAAAAATAAAA-AGG
1 TAAAAATAAAATAAG
29318637 TAAAAATAAAATAAG
1 TAAAAATAAAATAAG
29318652 TAAAAA
1 TAAAAA
29318658 AGAGAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (15 bp):
TAAAAATAAAATAAG
Found at i:29320141 original size:25 final size:27
Alignment explanation
Indices: 29320107--29320219 Score: 92
Period size: 25 Copynumber: 4.3 Consensus size: 27
29320097 AAATAAGCCT
*
29320107 AGACAGAATATCGCTCATACGATC-A-
1 AGACAGAATATCGCTCATACGAGCTAG
* * * *
29320132 AGACGGAATATTGCTCTTACAAGCTAG
1 AGACAGAATATCGCTCATACGAGCTAG
* *
29320159 AGTCAGAATATCGCTCATACGAGCCA-
1 AGACAGAATATCGCTCATACGAGCTAG
* *
29320185 A-ACAGAAT-TACGCTCTTACGAGCCAG
1 AGACAGAATAT-CGCTCATACGAGCTAG
*
29320211 AAACAGAAT
1 AGACAGAAT
29320220 TACGTTTTTA
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
24 1 0.01
25 39 0.56
26 3 0.04
27 27 0.39
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (27 bp):
AGACAGAATATCGCTCATACGAGCTAG
Found at i:29320200 original size:52 final size:54
Alignment explanation
Indices: 29320144--29320406 Score: 215
Period size: 52 Copynumber: 5.0 Consensus size: 54
29320134 ACGGAATATT
* * *
29320144 GCTCTTACAAGCTAGAGTCAGAATATCGCTCATACGAGCC-AAA-CAGAATTAC
1 GCTCTTACAAGCCAGAATCAGAATATCGCTCTTACGAGCCAAAATCAGAATTAC
* * * * * *
29320196 GCTCTTACGAGCCAGAAACAGAAT-TACGTTTTTATGAGCCAAAATCAGAATTAT
1 GCTCTTACAAGCCAGAATCAGAATAT-CGCTCTTACGAGCCAAAATCAGAATTAC
* *
29320250 GCTCTTACGAGCCAG-A-CAGAAT-TACGCTCTTAAGAGCCAAAATCAGAATTAC
1 GCTCTTACAAGCCAGAATCAGAATAT-CGCTCTTACGAGCCAAAATCAGAATTAC
* * * *
29320302 ACTCTTACAAGCCAAAATCAGAATTAT-GCTCTTACGAG--ATAAAT-AAAATTAT
1 GCTCTTACAAGCCAGAATCAGAA-TATCGCTCTTACGAGCCA-AAATCAGAATTAC
* * * * *
29320354 GCTCTTACGAGCCAGAAATCAAAAT-TAAGCTCTTACGAGCTAGAATCAGAATT
1 GCTCTTACAAGCCAG-AATCAGAATAT-CGCTCTTACGAGCCAAAATCAGAATT
29320407 CCTTCATCTT
Statistics
Matches: 172, Mismatches: 25, Indels: 25
0.77 0.11 0.11
Matches are distributed among these distances:
51 2 0.01
52 94 0.55
53 27 0.16
54 41 0.24
55 7 0.04
56 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (54 bp):
GCTCTTACAAGCCAGAATCAGAATATCGCTCTTACGAGCCAAAATCAGAATTAC
Found at i:29320222 original size:27 final size:27
Alignment explanation
Indices: 29320144--29320406 Score: 222
Period size: 27 Copynumber: 9.9 Consensus size: 27
29320134 ACGGAATATT
* * **
29320144 GCTCTTACAAGCTAGAGTCAGAA-TATC
1 GCTCTTACGAGCCAGAAACAGAATTA-C
*
29320171 GCTCATACGAGCC--AAACAGAATTAC
1 GCTCTTACGAGCCAGAAACAGAATTAC
29320196 GCTCTTACGAGCCAGAAACAGAATTAC
1 GCTCTTACGAGCCAGAAACAGAATTAC
* * * *
29320223 GTTTTTATGAGCCA-AAATCAGAATTAT
1 GCTCTTACGAGCCAGAAA-CAGAATTAC
29320250 GCTCTTACGAGCCAG--ACAGAATTAC
1 GCTCTTACGAGCCAGAAACAGAATTAC
*
29320275 GCTCTTAAGAGCCA-AAATCAGAATTAC
1 GCTCTTACGAGCCAGAAA-CAGAATTAC
* * *
29320302 ACTCTTACAAGCCA-AAATCAGAATTAT
1 GCTCTTACGAGCCAGAAA-CAGAATTAC
* * * *
29320329 GCTCTTACGAG--ATAAATAAAATTAT
1 GCTCTTACGAGCCAGAAACAGAATTAC
* *
29320354 GCTCTTACGAGCCAGAAATCAAAATTAA
1 GCTCTTACGAGCCAGAAA-CAGAATTAC
* *
29320382 GCTCTTACGAGCTAGAATCAGAATT
1 GCTCTTACGAGCCAGAAACAGAATT
29320407 CCTTCATCTT
Statistics
Matches: 195, Mismatches: 29, Indels: 24
0.79 0.12 0.10
Matches are distributed among these distances:
25 59 0.30
26 10 0.05
27 103 0.53
28 23 0.12
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (27 bp):
GCTCTTACGAGCCAGAAACAGAATTAC
Found at i:29320269 original size:79 final size:80
Alignment explanation
Indices: 29320145--29320406 Score: 298
Period size: 79 Copynumber: 3.3 Consensus size: 80
29320135 CGGAATATTG
* * * *
29320145 CTCTTACAAGCTAGAGTCAGAA-TATCGCTCATACGAGCCAAACAGAATTACGCTCTTACGAGCC
1 CTCTTACAAGCCAAAATCAGAATTAT-GCTCTTACGAGCCAAACAGAATTACGCTCTTACGAGCC
*
29320209 AGAAA-CAGAATTACG
65 AGAAATCAGAATTACA
* * ** * *
29320224 TTTTTATGAGCCAAAATCAGAATTATGCTCTTACGAGCCAGACAGAATTACGCTCTTAAGAGCCA
1 CTCTTACAAGCCAAAATCAGAATTATGCTCTTACGAGCCAAACAGAATTACGCTCTTACGAGCCA
29320289 -AAATCAGAATTACA
66 GAAATCAGAATTACA
** * * *
29320303 CTCTTACAAGCCAAAATCAGAATTATGCTCTTACGAGATAAATAAAATTATGCTCTTACGAGCCA
1 CTCTTACAAGCCAAAATCAGAATTATGCTCTTACGAGCCAAACAGAATTACGCTCTTACGAGCCA
*
29320368 GAAATCAAAATTA-A
66 GAAATCAGAATTACA
* * *
29320382 GCTCTTACGAGCTAGAATCAGAATT
1 -CTCTTACAAGCCAAAATCAGAATT
29320407 CCTTCATCTT
Statistics
Matches: 153, Mismatches: 26, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
78 3 0.02
79 115 0.75
80 35 0.23
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (80 bp):
CTCTTACAAGCCAAAATCAGAATTATGCTCTTACGAGCCAAACAGAATTACGCTCTTACGAGCCA
GAAATCAGAATTACA
Found at i:29322679 original size:23 final size:25
Alignment explanation
Indices: 29322653--29322704 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 25
29322643 TTTTAACACT
29322653 TTTTCTTACTC-TTTT-TTTTTG-TA
1 TTTT-TTACTCATTTTCTTTTTGATA
29322676 -TTTTTACTCATTTTCTTTTTGATA
1 TTTTTTACTCATTTTCTTTTTGATA
29322700 TTTTT
1 TTTTT
29322705 CACTTGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 6 0.24
22 7 0.28
23 6 0.24
24 2 0.08
25 4 0.16
ACGTcount: A:0.12, C:0.12, G:0.04, T:0.73
Consensus pattern (25 bp):
TTTTTTACTCATTTTCTTTTTGATA
Found at i:29322682 original size:21 final size:24
Alignment explanation
Indices: 29322658--29322704 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
29322648 ACACTTTTTC
29322658 TTACTC-TTTT-TTTTTG-TATTT
1 TTACTCATTTTCTTTTTGATATTT
29322679 TTACTCATTTTCTTTTTGATATTT
1 TTACTCATTTTCTTTTTGATATTT
29322703 TT
1 TT
29322705 CACTTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.26
22 4 0.17
23 6 0.26
24 7 0.30
ACGTcount: A:0.13, C:0.11, G:0.04, T:0.72
Consensus pattern (24 bp):
TTACTCATTTTCTTTTTGATATTT
Found at i:29323440 original size:19 final size:17
Alignment explanation
Indices: 29323416--29323450 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
29323406 CAACAATTAC
29323416 AAGTCTTTAAATAAAAATA
1 AAGTC-TTAAA-AAAAATA
29323435 AAGTCTTAAAAAAAAT
1 AAGTCTTAAAAAAAAT
29323451 TCAATCATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.29
Consensus pattern (17 bp):
AAGTCTTAAAAAAAATA
Found at i:29334989 original size:30 final size:31
Alignment explanation
Indices: 29334931--29334995 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
29334921 TTAAGTTAGT
* * *
29334931 ATTTTTATAAGAGTTAAAATATATTTTTATA
1 ATTTTTAAAAGAGTTAAAATAAAATTTTATA
* *
29334962 ATTTTTAAAAGA-TTAAATTAAAATTTTATT
1 ATTTTTAAAAGAGTTAAAATAAAATTTTATA
29334992 ATTT
1 ATTT
29334996 GGAGGTAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 18 0.62
31 11 0.38
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (31 bp):
ATTTTTAAAAGAGTTAAAATAAAATTTTATA
Found at i:29335203 original size:25 final size:25
Alignment explanation
Indices: 29335170--29335229 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
29335160 AAATTTAAAT
* *
29335170 TTCAA-AAAATTGTTCCAATTTTGA
1 TTCAATAAAATTGGTCCAATTTCGA
* *
29335194 TTCAATAAAATTGGTCGAGTTTCGA
1 TTCAATAAAATTGGTCCAATTTCGA
*
29335219 TTCAATCAAAT
1 TTCAATAAAAT
29335230 CGAAATTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 5 0.17
25 25 0.83
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (25 bp):
TTCAATAAAATTGGTCCAATTTCGA
Found at i:29343669 original size:19 final size:18
Alignment explanation
Indices: 29343641--29343679 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
29343631 TAATATTTAG
*
29343641 TAATTTTATATTTACATTA
1 TAATTATATATTTA-ATTA
29343660 TAATTATATATTTAATTA
1 TAATTATATATTTAATTA
29343678 TA
1 TA
29343680 TAATGCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATTATATATTTAATTA
Found at i:29348750 original size:15 final size:15
Alignment explanation
Indices: 29348730--29348775 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
29348720 TATTGTATTA
*
29348730 TTTATAAATTTGATT
1 TTTATAAATTTAATT
*
29348745 TTTAT--ATTTTATT
1 TTTATAAATTTAATT
*
29348758 TTTAAAAATTTAATT
1 TTTATAAATTTAATT
29348773 TTT
1 TTT
29348776 CTATTTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 11 0.42
15 15 0.58
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TTTATAAATTTAATT
Found at i:29348768 original size:28 final size:29
Alignment explanation
Indices: 29348720--29348782 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
29348710 TGCTATAGAT
* * *
29348720 TATTGTATTATTTATAAATTTGATTTTTA
1 TATTTTATTATTTAAAAATTTAATTTTTA
*
29348749 TATTTTATT-TTTAAAAATTTAATTTTTC
1 TATTTTATTATTTAAAAATTTAATTTTTA
29348777 TATTTT
1 TATTTT
29348783 TAAATATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 22 0.73
29 8 0.27
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (29 bp):
TATTTTATTATTTAAAAATTTAATTTTTA
Found at i:29348775 original size:29 final size:30
Alignment explanation
Indices: 29348720--29348784 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
29348710 TGCTATAGAT
* * *
29348720 TATTGTATTATTTATAAATTTGATTTT-TA
1 TATTTTATTATTTAAAAATTTAATTTTCTA
29348749 TATTTTATT-TTTAAAAATTTAATTTTTCTA
1 TATTTTATTATTTAAAAATTTAA-TTTTCTA
29348779 T-TTTTA
1 TATTTTA
29348785 AATATTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 11 0.35
29 17 0.55
30 3 0.10
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (30 bp):
TATTTTATTATTTAAAAATTTAATTTTCTA
Found at i:29355280 original size:17 final size:17
Alignment explanation
Indices: 29355258--29355297 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
29355248 TCCCCACCTT
* *
29355258 GACAAGAATTCTCTACG
1 GACAAGAACTCTCAACG
29355275 GACAAGAACTCTCAACG
1 GACAAGAACTCTCAACG
*
29355292 AACAAG
1 GACAAG
29355298 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.15
Consensus pattern (17 bp):
GACAAGAACTCTCAACG
Found at i:29357319 original size:24 final size:24
Alignment explanation
Indices: 29357283--29357330 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
29357273 TTTCCATTAT
*
29357283 TAACATGAGCATAAGCAGGACACC
1 TAACATGACCATAAGCAGGACACC
29357307 TAACATGACCATAAGCAGGACACC
1 TAACATGACCATAAGCAGGACACC
29357331 CAAAAATCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.27, G:0.19, T:0.12
Consensus pattern (24 bp):
TAACATGACCATAAGCAGGACACC
Found at i:29361811 original size:24 final size:24
Alignment explanation
Indices: 29361779--29361826 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
29361769 TTTCCATTAT
29361779 TAACATGAGCATAAGCAGGACACC
1 TAACATGAGCATAAGCAGGACACC
29361803 TAACATGAGCATAAGCAGGACACC
1 TAACATGAGCATAAGCAGGACACC
29361827 CAAAAATCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.25, G:0.21, T:0.12
Consensus pattern (24 bp):
TAACATGAGCATAAGCAGGACACC
Found at i:29365293 original size:11 final size:11
Alignment explanation
Indices: 29365277--29365309 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
29365267 GTATACTTGT
29365277 GTATAATTTGA
1 GTATAATTTGA
29365288 GTATAATTTGA
1 GTATAATTTGA
*
29365299 GCATAATTTGA
1 GTATAATTTGA
29365310 AATACTAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.42
Consensus pattern (11 bp):
GTATAATTTGA
Found at i:29365455 original size:31 final size:30
Alignment explanation
Indices: 29365420--29365488 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
29365410 AACCTAAATG
29365420 ATTACAGGGTACGAAAATGTAAATGT-GATCA
1 ATTACAGGGTACG-AAATGTAAATGTGGAT-A
* ** *
29365451 ATTACAAGGTGTGATATGTAAATGTGGATA
1 ATTACAGGGTACGAAATGTAAATGTGGATA
29365481 ATTACAGG
1 ATTACAGG
29365489 ATATAAACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
30 19 0.59
31 13 0.41
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.29
Consensus pattern (30 bp):
ATTACAGGGTACGAAATGTAAATGTGGATA
Found at i:29366945 original size:40 final size:39
Alignment explanation
Indices: 29366890--29367085 Score: 209
Period size: 40 Copynumber: 4.9 Consensus size: 39
29366880 GTTAAATTCG
* * *
29366890 GTGTTAATGTTCAAGCTTTAGCTTAGCATGCTATGAGCCA
1 GTGTTAATATTCAAGCTTCAGCTTAGCA-GCTATGAGTCA
**
29366930 GTGTTAATATTCAAGCTTCAGCTTAGCAAGCTATGAGTTG
1 GTGTTAATATTCAAGCTTCAGCTTAGC-AGCTATGAGTCA
*
29366970 GTGTTAATATTCAAGCTTCGGCTTAGCAGCCTATGAG-CA
1 GTGTTAATATTCAAGCTTCAGCTTAGCAG-CTATGAGTCA
** * *
29367009 GGTGTTAATATTCAAGCTTTGGCTTAGCAGGCCATGAGTTA
1 -GTGTTAATATTCAAGCTTCAGCTTAGCA-GCTATGAGTCA
*
29367050 GTG-TAATATTCAAGCTTC-GACTTAGTAGGCTATGAG
1 GTGTTAATATTCAAGCTTCAG-CTTAGCA-GCTATGAG
29367086 CCGGTGAATA
Statistics
Matches: 136, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
38 1 0.01
39 30 0.22
40 102 0.75
41 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (39 bp):
GTGTTAATATTCAAGCTTCAGCTTAGCAGCTATGAGTCA
Found at i:29367022 original size:80 final size:79
Alignment explanation
Indices: 29366889--29367091 Score: 257
Period size: 80 Copynumber: 2.5 Consensus size: 79
29366879 TGTTAAATTC
* **
29366889 GGTGTTAATGTTCAAGCTTTAGCTTAGCATGCTATGAGCCA-GTGTTAATATTCAAGCTTCAGCT
1 GGTGTTAATATTCAAGCTTCGGCTTAGCA-GCTATGAG-CAGGTGTTAATATTCAAGCTTCAGCT
*
29366953 TAGCAAGCTATGAGTT
64 TAGCAAGCCATGAGTT
**
29366969 GGTGTTAATATTCAAGCTTCGGCTTAGCAGCCTATGAGCAGGTGTTAATATTCAAGCTTTGGCTT
1 GGTGTTAATATTCAAGCTTCGGCTTAGCAG-CTATGAGCAGGTGTTAATATTCAAGCTTCAGCTT
*
29367034 AGCAGGCCATGAGTT
65 AGCAAGCCATGAGTT
* * * *
29367049 AGTG-TAATATTCAAGCTTCGACTTAGTAGGCTATGAGCCGGTG
1 GGTGTTAATATTCAAGCTTCGGCTTAGCA-GCTATGAGCAGGTG
29367092 AATATGTAAG
Statistics
Matches: 109, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
79 37 0.34
80 72 0.66
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (79 bp):
GGTGTTAATATTCAAGCTTCGGCTTAGCAGCTATGAGCAGGTGTTAATATTCAAGCTTCAGCTTA
GCAAGCCATGAGTT
Found at i:29367736 original size:2 final size:2
Alignment explanation
Indices: 29367731--29367755 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29367721 TATATATATA
29367731 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
29367756 ATTGAAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:29380711 original size:3 final size:3
Alignment explanation
Indices: 29380703--29380751 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
29380693 AGCAAGAGCA
29380703 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29380751 A
1 A
29380752 ATTGGAATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:29382160 original size:15 final size:15
Alignment explanation
Indices: 29382140--29382169 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29382130 TTCATTTAAC
*
29382140 AAAATTAATCAAATT
1 AAAATTAACCAAATT
29382155 AAAATTAACCAAATT
1 AAAATTAACCAAATT
29382170 CGTAATATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATTAACCAAATT
Found at i:29394478 original size:2 final size:2
Alignment explanation
Indices: 29394465--29394505 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
29394455 AACATGCATA
*
29394465 TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
29394506 CAGGAAAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.02, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:29397644 original size:195 final size:195
Alignment explanation
Indices: 29397302--29397744 Score: 554
Period size: 195 Copynumber: 2.3 Consensus size: 195
29397292 AACCGACGCG
* * * *
29397302 ATGGCTGAGGTATCGCTTATGTTACGAGAT-CTCGACAGCTCGTGTGAGCAGCATCGTGAGTCGG
1 ATGGCTGAGGTATCGCATATGTTGCGAG-TCCTCGATAGCTCGTGTGAGCAGCATCGTGAGTCGA
* * * * * * * * *
29397366 GAAATGAGTAAATGATCCAAGAATGGATTACAGGCCTTATGATGGTTGAGATTTATGCATAAGTG
65 AAAAAGAGTAAATGATCCAAGAATAGATTACAAGCCCTACGATAGCTGAGACTTATGCATAAGTG
** *
29397431 CATATTCTCAACAGCTCGTGTGAGCAGCATCATTAGG-GAACAGTTATATACACAGACACCGTA-
130 CATACACCCAACAGCTCGTGTGAGCAGCATCATTAGGAG-ACAGTTATATACACAGACACCGTAC
29397494 TCA
194 T-A
* * *
29397497 ATGGCTGAGGTA-CTGCATATGTTGCGAGTCCTTGATAGCTTGTATGAGCAGCATCGTGAGTCGA
1 ATGGCTGAGGTATC-GCATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGAGTCGA
* *
29397561 AAAAAGAG-ATATGAATCCAAGAATAGATTACAAGCCCTGCGATAGCTGAGACTTATGCATAAGT
65 AAAAAGAGTAAATG-ATCCAAGAATAGATTACAAGCCCTACGATAGCTGAGACTTATGCATAAGT
* * *
29397625 GCATACACCCAATAGCTCGTGTGAGCAGCATCGTTAGGAGACAGTTATATAGACAGACACCGTAC
129 GCATACACCCAACAGCTCGTGTGAGCAGCATCATTAGGAGACAGTTATATACACAGACACCGTAC
*
29397690 TG
194 TA
* * *
29397692 ATGGTTGGGGTATCACATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCA
1 ATGGCTGAGGTATCGCATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCA
29397745 CCGAGTACTA
Statistics
Matches: 211, Mismatches: 31, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
194 6 0.03
195 202 0.96
196 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (195 bp):
ATGGCTGAGGTATCGCATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGAGTCGAA
AAAAGAGTAAATGATCCAAGAATAGATTACAAGCCCTACGATAGCTGAGACTTATGCATAAGTGC
ATACACCCAACAGCTCGTGTGAGCAGCATCATTAGGAGACAGTTATATACACAGACACCGTACTA
Found at i:29398545 original size:21 final size:21
Alignment explanation
Indices: 29398497--29398548 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
29398487 GGAATTTTTG
*
29398497 GTATCGGTAGACGTATGACAT
1 GTATCGGTAGACGTATCACAT
* * * *
29398518 GTTTCGGTAGAGGTCTCACTT
1 GTATCGGTAGACGTATCACAT
29398539 GTATCGGTAG
1 GTATCGGTAG
29398549 TACTGCCTCA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGACGTATCACAT
Found at i:29415067 original size:16 final size:17
Alignment explanation
Indices: 29415046--29415092 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
29415036 CATTGTCCCC
*
29415046 AATGCACTAAC-ATTAA
1 AATGCAATAACAATTAA
*
29415062 AATGCAATGACAATTAA
1 AATGCAATAACAATTAA
*
29415079 AATGCAATGACAAT
1 AATGCAATAACAAT
29415093 GTGCACTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 9 0.32
17 19 0.68
ACGTcount: A:0.51, C:0.15, G:0.11, T:0.23
Consensus pattern (17 bp):
AATGCAATAACAATTAA
Found at i:29415079 original size:17 final size:17
Alignment explanation
Indices: 29415057--29415092 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
29415047 ATGCACTAAC
29415057 ATTAAAATGCAATGACA
1 ATTAAAATGCAATGACA
29415074 ATTAAAATGCAATGACA
1 ATTAAAATGCAATGACA
29415091 AT
1 AT
29415093 GTGCACTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.25
Consensus pattern (17 bp):
ATTAAAATGCAATGACA
Found at i:29428276 original size:20 final size:19
Alignment explanation
Indices: 29428219--29428267 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
29428209 AAATGCAAAA
*
29428219 AAAAATCAAAATAATTT-TT
1 AAAATTCAAAAT-ATTTATT
29428238 AAAATTCAAAATATTTATT
1 AAAATTCAAAATATTTATT
29428257 AAAATTTCAAA
1 AAAA-TTCAAA
29428268 TTTTTTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 4 0.15
19 17 0.63
20 6 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATTCAAAATATTTATT
Found at i:29428320 original size:22 final size:20
Alignment explanation
Indices: 29428288--29428331 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
29428278 TAAAAAATAT
29428288 AAAA-ATATA-AAAAATTCTA
1 AAAATATATATAAAAATT-TA
29428307 AAAATATATATAAAAATTTA
1 AAAATATATATAAAAATTTA
29428327 AAAAT
1 AAAAT
29428332 TTTCTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.17
20 12 0.52
21 7 0.30
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAATATATATAAAAATTTA
Found at i:29428321 original size:20 final size:18
Alignment explanation
Indices: 29428279--29428331 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 18
29428269 TTTTTATTTT
*
29428279 AAAAAATATAAAAATAT-
1 AAAAAATTTAAAAATATA
29428296 AAAAAATTCTAAAAATATA
1 AAAAAATT-TAAAAATATA
29428315 TATAAAAATTTAAAAAT
1 -A-AAAAATTTAAAAAT
29428332 TTTCTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 7 0.23
18 9 0.29
20 8 0.26
21 7 0.23
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAAATTTAAAAATATA
Found at i:29443576 original size:21 final size:21
Alignment explanation
Indices: 29443547--29443586 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
29443537 ATGAATAGAT
29443547 ACTACCATGAACATTCATGTC
1 ACTACCATGAACATTCATGTC
*
29443568 ACTATCATGAACATTCATG
1 ACTACCATGAACATTCATG
29443587 ATGAATTCAA
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:0.35, C:0.25, G:0.10, T:0.30
Consensus pattern (21 bp):
ACTACCATGAACATTCATGTC
Found at i:29448358 original size:42 final size:40
Alignment explanation
Indices: 29448287--29448438 Score: 182
Period size: 40 Copynumber: 3.8 Consensus size: 40
29448277 GAACTAAAGT
* * * *
29448287 GCCGCAAAAGATAAAGCAATAGTGACGTTTTCCCATAAAC
1 GCCGCAAAAGGTAAAGCAATAGCGGCGTTTTACCATAAAC
* * *
29448327 ACCGAAAAAGGTAAAGAGCAATAGCGGCGTTTATGA-GA-AAAC
1 GCCGCAAAAGGT-AA-AGCAATAGCGGCGTTT-T-ACCATAAAC
*
29448369 GCCGCAAAAGGTAAAGCAATAGTGGCGTTTTACCATAAAC
1 GCCGCAAAAGGTAAAGCAATAGCGGCGTTTTACCATAAAC
29448409 GCCGCAAAAGGTAAAGCAATAGCGGCGTTT
1 GCCGCAAAAGGTAAAGCAATAGCGGCGTTT
29448439 ATGGAAAAAT
Statistics
Matches: 94, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
38 1 0.01
39 2 0.02
40 57 0.61
41 4 0.04
42 28 0.30
43 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (40 bp):
GCCGCAAAAGGTAAAGCAATAGCGGCGTTTTACCATAAAC
Found at i:29448424 original size:82 final size:81
Alignment explanation
Indices: 29448287--29448465 Score: 263
Period size: 82 Copynumber: 2.2 Consensus size: 81
29448277 GAACTAAAGT
* *
29448287 GCCGCAAAAGATAAAGCAATAGTGACGTTTTCCCATAAACACCGAAAAAGGTAAAGAGCAATAGC
1 GCCGCAAAAGGTAAAGCAATAGTGACGTTTTACCATAAACACCGAAAAAGGT-AA-AGCAATAGC
29448352 GGCGTTTAT-GAGAAAA-C
64 GGCGTTTATGGA-AAAATC
* * *
29448369 GCCGCAAAAGGTAAAGCAATAGTGGCGTTTTACCATAAACGCCGCAAAAGGTAAAGCAATAGCGG
1 GCCGCAAAAGGTAAAGCAATAGTGACGTTTTACCATAAACACCGAAAAAGGTAAAGCAATAGCGG
29448434 CGTTTATGGAAAAATC
66 CGTTTATGGAAAAATC
*
29448450 GCTGCAAAAGGTAAAG
1 GCCGCAAAAGGTAAAG
29448466 AGCATTAGCG
Statistics
Matches: 89, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
80 22 0.25
81 20 0.22
82 47 0.53
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (81 bp):
GCCGCAAAAGGTAAAGCAATAGTGACGTTTTACCATAAACACCGAAAAAGGTAAAGCAATAGCGG
CGTTTATGGAAAAATC
Found at i:29455076 original size:40 final size:41
Alignment explanation
Indices: 29454993--29455110 Score: 125
Period size: 40 Copynumber: 2.9 Consensus size: 41
29454983 TAATCGCCGC
* * *
29454993 AAAGGTAAA-A-CAATAGCGACGCTTATGGGAAAACGCCGTA
1 AAAGGTAAAGAGCAATAGCGACGTTTATGGAAAAACGACG-A
* *
29455033 AAAGGTAAAGAGCAATAGCGACGTTTGTGGAAAAACTAC-A
1 AAAGGTAAAGAGCAATAGCGACGTTTATGGAAAAACGACGA
* * *
29455073 AAAGGTAAGGAGCATTAGCGGCGTTTATAGGAAAAACG
1 AAAGGTAAAGAGCAATAGCGACGTTTAT-GGAAAAACG
29455111 TCAGCAAAGG
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
40 34 0.52
41 9 0.14
42 22 0.34
ACGTcount: A:0.42, C:0.14, G:0.27, T:0.17
Consensus pattern (41 bp):
AAAGGTAAAGAGCAATAGCGACGTTTATGGAAAAACGACGA
Found at i:29457594 original size:16 final size:16
Alignment explanation
Indices: 29457573--29457604 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29457563 AGAAACAACC
29457573 TAAATATTCAATTATT
1 TAAATATTCAATTATT
*
29457589 TAAATATTTAATTATT
1 TAAATATTCAATTATT
29457605 AAAAACAACT
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:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAATATTCAATTATT
Found at i:29457619 original size:26 final size:26
Alignment explanation
Indices: 29457589--29457704 Score: 118
Period size: 26 Copynumber: 4.6 Consensus size: 26
29457579 TTCAATTATT
29457589 TAAATATTTAATTATTAAAAACAA-C
1 TAAATATTTAATTATTAAAAACAACC
* * **
29457614 TCAAATATTT-A--ATTCAAAA-TATT
1 T-AAATATTTAATTATTAAAAACAACC
*
29457637 TAATTATTTAATTACTT-AAAACAACC
1 TAAATATTTAATTA-TTAAAAACAACC
*
29457663 TAAATATTTAATTATTAAAAATAACC
1 TAAATATTTAATTATTAAAAACAACC
29457689 TAAATATTTAATTATT
1 TAAATATTTAATTATT
29457705 TAATTATTAA
Statistics
Matches: 74, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
22 8 0.11
23 9 0.12
25 9 0.12
26 48 0.65
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (26 bp):
TAAATATTTAATTATTAAAAACAACC
Found at i:29457623 original size:34 final size:34
Alignment explanation
Indices: 29457580--29457730 Score: 101
Period size: 34 Copynumber: 4.3 Consensus size: 34
29457570 ACCTAAATAT
*
29457580 TCAATTATTTAAATATTTAATTATTAAAAACAAC
1 TCAAATATTTAAATATTTAATTATTAAAAACAAC
** *
29457614 TCAAATATTTAATTCAAAATATTTAATTATTTAATTAC--T
1 TCAAATA--T--TT--AAATATTTAATTA-TTAAAAACAAC
* * ** *
29457653 TAAAACAACCTAAATATTTAATTATTAAAAATAAC
1 TCAAA-TATTTAAATATTTAATTATTAAAAACAAC
*
29457688 -CTAAATATTTAATTATTTAATTATTAAAAACAAC
1 TC-AAATATTTAAATATTTAATTATTAAAAACAAC
*
29457722 CCAAATATT
1 TCAAATATT
29457731 CGGTTCAAAT
Statistics
Matches: 87, Mismatches: 18, Indels: 24
0.67 0.14 0.19
Matches are distributed among these distances:
33 5 0.06
34 50 0.57
35 4 0.05
36 2 0.02
38 2 0.02
39 4 0.05
40 14 0.16
41 6 0.07
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (34 bp):
TCAAATATTTAAATATTTAATTATTAAAAACAAC
Found at i:29457966 original size:12 final size:12
Alignment explanation
Indices: 29457946--29457984 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
29457936 AAGAATGATG
*
29457946 AAATATAAATAT
1 AAATATAAATCT
*
29457958 AAATCTAAATCT
1 AAATATAAATCT
*
29457970 AAATATAATTCT
1 AAATATAAATCT
29457982 AAA
1 AAA
29457985 CATATATCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATATAAATCT
Found at i:29457972 original size:18 final size:18
Alignment explanation
Indices: 29457946--29457984 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
29457936 AAGAATGATG
29457946 AAATATAAATATAAATCT
1 AAATATAAATATAAATCT
* *
29457964 AAATCTAAATATAATTCT
1 AAATATAAATATAAATCT
29457982 AAA
1 AAA
29457985 CATATATCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATATAAATATAAATCT
Found at i:29470111 original size:66 final size:66
Alignment explanation
Indices: 29469980--29470104 Score: 153
Period size: 66 Copynumber: 1.9 Consensus size: 66
29469970 GCAAATTGCT
** * * * *
29469980 CAACTTAAAGCGGAGGCAGCAGTGAGAGAAGTAGAGGCTCAAAGAAAATATGATGAACTTCAGCT
1 CAACTTAAAGCCAAGGAAGCAGCGAGAGAAGCAGAGGCTCAAAGAAAATATGACGAACTTCAGCT
29470045 A
66 A
* * *
29470046 CAACTTAAAGCCAAGGAAGCAGCGAGGGAAGCAGAGTCTCAAA-AAAAGTATTACGAACT
1 CAACTTAAAGCCAAGGAAGCAGCGAGAGAAGCAGAGGCTCAAAGAAAA-TATGACGAACT
29470105 ATAGCTATAG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 4 0.08
66 45 0.92
ACGTcount: A:0.42, C:0.17, G:0.26, T:0.15
Consensus pattern (66 bp):
CAACTTAAAGCCAAGGAAGCAGCGAGAGAAGCAGAGGCTCAAAGAAAATATGACGAACTTCAGCT
A
Found at i:29470518 original size:43 final size:43
Alignment explanation
Indices: 29470390--29470519 Score: 163
Period size: 43 Copynumber: 3.0 Consensus size: 43
29470380 CAATGTTAGT
* * *
29470390 GGCATTTGTGGGAAAAACGCCACTAAAGATCATGCTCTATAGT
1 GGCATTTGTGGGAAAAACGCCGCTAAAGACCATGCTCTATAGC
* * *
29470433 GGCGTTTGT-GGAAAAAGCACCGGTAAAGACCATGCTCTATAGC
1 GGCATTTGTGGGAAAAA-CGCCGCTAAAGACCATGCTCTATAGC
* * *
29470476 GGCATTTGTGGGAAAAACGCTGTTAAAGACCATGTTCTATAGC
1 GGCATTTGTGGGAAAAACGCCGCTAAAGACCATGCTCTATAGC
29470519 G
1 G
29470520 ATGTTTTCCC
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
42 7 0.09
43 60 0.81
44 7 0.09
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (43 bp):
GGCATTTGTGGGAAAAACGCCGCTAAAGACCATGCTCTATAGC
Found at i:29494228 original size:58 final size:57
Alignment explanation
Indices: 29494154--29494415 Score: 210
Period size: 59 Copynumber: 4.5 Consensus size: 57
29494144 TGGATACCTA
* * ** * *
29494154 GGGGCAAAACGATAATTTTGGTCACTTCGAGGTCAAAAATAGAATCTTTGGAAGTTCG
1 GGGGTAAAATGATAATTTTGGAAAGTTCGAGGTCAAAAATGGAAT-TTTGGAAGTTCG
* **
29494212 GGGGTAAAATGATAATTTTTAGG-AAGTT-TAGGGTCAAAAATGGAATTTTTGGAAGTTTA
1 GGGGTAAAATGATAA-TTTT-GGAAAGTTCGA-GGTCAAAAATGGAA-TTTTGGAAGTTCG
* * * * *
29494271 GGGGTAAAATGGTAAATTTTAGAAAGTTTG-GAATCAAAAATGGAATTTTTGAGAGTTCG
1 GGGGTAAAATGAT-AATTTTGGAAAGTTCGAG-GTCAAAAATGGAATTTTGGA-AGTTCG
* * *
29494330 GGGGTAAAATGGTAATTTTTGGAAAATTCGGGGTC-AAAATGGAATTTTGGAAAGTTCG
1 GGGGTAAAATGATAA-TTTTGGAAAGTTCGAGGTCAAAAATGGAATTTTGG-AAGTTCG
* *
29494388 AGGGTAAAAATG-TAATTTTTGGACAGTT
1 GGGGT-AAAATGATAA-TTTTGGAAAGTT
29494416 TAGGGACCTT
Statistics
Matches: 168, Mismatches: 23, Indels: 26
0.77 0.11 0.12
Matches are distributed among these distances:
58 62 0.37
59 100 0.60
60 6 0.04
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (57 bp):
GGGGTAAAATGATAATTTTGGAAAGTTCGAGGTCAAAAATGGAATTTTGGAAGTTCG
Found at i:29494263 original size:59 final size:58
Alignment explanation
Indices: 29494184--29494420 Score: 259
Period size: 59 Copynumber: 4.0 Consensus size: 58
29494174 GTCACTTCGA
* * *
29494184 GGTCAAAAATAGAATCTTTGGAAGTTCGGGGGTAAAATGATAATTTTTAGGAAGTTTAG
1 GGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTT-GGAAGTTTAG
** * *
29494243 GGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGGTAAATTTTAGAAAGTTT-G
1 GGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGGT-AATTTTTGGAAGTTTAG
* * **
29494301 GAATCAAAAATGGAATTTTT-GAGAGTTCGGGGGTAAAATGGTAATTTTTGGAAAATTCGG
1 G-GTCAAAAATGGAATTTTTGGA-AGTTCGGGGGTAAAATGGTAATTTTTGG-AAGTTTAG
*
29494361 GGTC-AAAATGGAA-TTTTGGAAAGTTCGAGGGTAAAAAT-GTAATTTTTGGACAGTTTAG
1 GGTCAAAAATGGAATTTTTGG-AAGTTCGGGGGT-AAAATGGTAATTTTTGGA-AGTTTAG
29494419 GG
1 GG
29494421 ACCTTCAAGG
Statistics
Matches: 150, Mismatches: 19, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
57 5 0.03
58 48 0.32
59 89 0.59
60 8 0.05
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.32
Consensus pattern (58 bp):
GGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGTTTAG
Found at i:29494348 original size:28 final size:30
Alignment explanation
Indices: 29494188--29494415 Score: 163
Period size: 29 Copynumber: 7.8 Consensus size: 30
29494178 CTTCGAGGTC
* *
29494188 AAAAATAGAATCTTTGG-AAGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAAGTTCGGGGGT
* **
29494217 -AAAATGATAATTTTTAGG-AAGTT-TAGGGT
1 AAAAATG-GAATTTTT-GGAAAGTTCGGGGGT
**
29494246 CAAAAATGGAATTTTTGG-AAGTTTAGGGGT
1 -AAAAATGGAATTTTTGGAAAGTTCGGGGGT
* * * **
29494276 -AAAATGGTAAATTTTAGAAAGTT-TGGAAT
1 AAAAATGG-AATTTTTGGAAAGTTCGGGGGT
*
29494305 CAAAAATGGAATTTTT-GAGAGTTCGGGGGT
1 -AAAAATGGAATTTTTGGAAAGTTCGGGGGT
*
29494335 -AAAATGGTAATTTTTGGAAAATTC-GGGGT
1 AAAAATGG-AATTTTTGGAAAGTTCGGGGGT
* *
29494364 CAAAATGGAA-TTTTGGAAAGTTCGAGGGT
1 AAAAATGGAATTTTTGGAAAGTTCGGGGGT
* *
29494393 AAAAATGTAATTTTTGGACAGTT
1 AAAAATGGAATTTTTGGAAAGTT
29494416 TAGGGACCTT
Statistics
Matches: 159, Mismatches: 25, Indels: 29
0.75 0.12 0.14
Matches are distributed among these distances:
28 31 0.19
29 59 0.37
30 56 0.35
31 13 0.08
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAAGTTCGGGGGT
Found at i:29496253 original size:17 final size:17
Alignment explanation
Indices: 29496245--29496324 Score: 99
Period size: 17 Copynumber: 4.7 Consensus size: 17
29496235 AAATAAATTT
*
29496245 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAGAA
**
29496262 TAAATTTAAATTTCCAA
1 TAAATTTAAATTTAGAA
29496279 TAAATTTAAATTTAGAA
1 TAAATTTAAATTTAGAA
*
29496296 TAAATTTAATTTTA-AGA
1 TAAATTTAAATTTAGA-A
*
29496313 TAAATTCAAATT
1 TAAATTTAAATT
29496325 CTGTTGGGCC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
16 1 0.02
17 54 0.98
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAGAA
Found at i:29496254 original size:6 final size:6
Alignment explanation
Indices: 29496238--29496310 Score: 50
Period size: 6 Copynumber: 12.5 Consensus size: 6
29496228 ATTATTTAAA
*
29496238 TAAATTT TAAATT TAAATT TATAA-- TAAATT TAAATT TCCAA-- TAAATT
1 TAAA-TT TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT
*
29496285 TAAATT TAGAA-- TAAATT TAATTT TAA
1 TAAATT TA-AATT TAAATT TAAATT TAA
29496311 GATAAATTCA
Statistics
Matches: 54, Mismatches: 3, Indels: 19
0.71 0.04 0.25
Matches are distributed among these distances:
4 6 0.11
5 5 0.09
6 33 0.61
7 10 0.19
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (6 bp):
TAAATT
Found at i:29496257 original size:23 final size:23
Alignment explanation
Indices: 29496231--29496274 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
29496221 ATTGGACATT
29496231 ATTTA-AATAAATTTTAAATTTAA
1 ATTTATAATAAA-TTTAAATTTAA
29496254 ATTTATAATAAATTTAAATTT
1 ATTTATAATAAATTTAAATTT
29496275 CCAATAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTTATAATAAATTTAAATTTAA
Found at i:29496855 original size:48 final size:49
Alignment explanation
Indices: 29496753--29496967 Score: 167
Period size: 48 Copynumber: 4.4 Consensus size: 49
29496743 GCCATTGCGA
* ** * *
29496753 CTTAAACCTTTCCCTTTTGTGTCTTCGTGGTACTGGATTCGCCGTTG-AGG
1 CTTAAATCTTTCCC-TTCATGTCTTCGTGGTACTGGATTCACTGTTGCA-G
* *
29496803 CTTAAATCTTTCCCTTCATG-CTTTGTGGTACTGGATTCACTGTTGCAA
1 CTTAAATCTTTCCCTTCATGTCTTCGTGGTACTGGATTCACTGTTGCAG
* * *
29496851 CTTAAATATTTCCCTTCATG-CTTCTGAGGTA-TAAGG-TTGC-C-GTTGCGG
1 CTTAAATCTTTCCCTTCATGTCTTC-GTGGTACT--GGATT-CACTGTTGCAG
* ** * *
29496899 CTTAAACCTTTCCCTTTTGTGTCTTCGTGGTATTGGATTCA-TCGTTACAG
1 CTTAAATCTTTCCC-TTCATGTCTTCGTGGTACTGGATTCACT-GTTGCAG
29496949 CTTAAATCTTTCCCTTCAT
1 CTTAAATCTTTCCCTTCAT
29496968 CCTCATGTAA
Statistics
Matches: 131, Mismatches: 22, Indels: 25
0.74 0.12 0.14
Matches are distributed among these distances:
48 65 0.50
49 27 0.21
50 39 0.30
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (49 bp):
CTTAAATCTTTCCCTTCATGTCTTCGTGGTACTGGATTCACTGTTGCAG
Found at i:29496952 original size:146 final size:147
Alignment explanation
Indices: 29496704--29496967 Score: 415
Period size: 146 Copynumber: 1.8 Consensus size: 147
29496694 GCCGTTGCGG
* * * *
29496704 CTTAAATTTTTCCTTTCATGCTTTTGAGGTGTAAGGTTTGCCATTGCGACTTAAACCTTTCCCTT
1 CTTAAATATTTCCCTTCATGCTTCTGAGGTATAAGGTTTGCCATTGCGACTTAAACCTTTCCCTT
* *
29496769 TTGTGTCTTCGTGGTACTGGATTCGCCGTTGAGGCTTAAATCTTTCCCTTCATGCTTTGTGGTAC
66 TTGTGTCTTCGTGGTACTGGATTCACCGTTGAAGCTTAAATCTTTCCCTTCATGCTTTGTGGTAC
29496834 TGGATTCACTGTTGCAA
131 TGGATTCACTGTTGCAA
* *
29496851 CTTAAATATTTCCCTTCATGCTTCTGAGGTATAAGG-TTGCCGTTGCGGCTTAAACCTTTCCCTT
1 CTTAAATATTTCCCTTCATGCTTCTGAGGTATAAGGTTTGCCATTGCGACTTAAACCTTTCCCTT
* *
29496915 TTGTGTCTTCGTGGTATTGGATTCATCGTT-ACAGCTTAAATCTTTCCCTTCAT
66 TTGTGTCTTCGTGGTACTGGATTCACCGTTGA-AGCTTAAATCTTTCCCTTCAT
29496968 CCTCATGTAA
Statistics
Matches: 106, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
145 1 0.01
146 73 0.69
147 32 0.30
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (147 bp):
CTTAAATATTTCCCTTCATGCTTCTGAGGTATAAGGTTTGCCATTGCGACTTAAACCTTTCCCTT
TTGTGTCTTCGTGGTACTGGATTCACCGTTGAAGCTTAAATCTTTCCCTTCATGCTTTGTGGTAC
TGGATTCACTGTTGCAA
Found at i:29497027 original size:146 final size:147
Alignment explanation
Indices: 29496736--29497209 Score: 372
Period size: 146 Copynumber: 3.2 Consensus size: 147
29496726 TTTGAGGTGT
* *
29496736 AAGGTTTGCCATTGCGACTTAAACCTTTCCCTTTTGTGTCTTCGTGGTACTGGATTCGCCGTTGA
1 AAGGTTCGCCATTGCGGCTTAAACCTTTCCCTTTTGTGTCTTCGTGGTACTGGATTCGCCGTT-A
* * * * * ** * * **
29496801 -GGCTTAAATCTTTCCCTTCATGCT-TTGTGGTACTGGA-TTCACTGTTGCAACTTAAATATTTC
65 CGGCTTAAATCTTTCCCTTCATCCTCATGT--AACCGGATTTAAC-GTTGCGGCCTCAATCCTTC
* * * * * *
29496863 CCTTCAT-GCTTCTGAGGTAT
127 CCATAATATCTACTAAGGTAC
* * **
29496883 AAGGTT-GCCGTTGCGGCTTAAACCTTTCCCTTTTGTGTCTTCGTGGTATTGGATTCATCGTTAC
1 AAGGTTCGCCATTGCGGCTTAAACCTTTCCCTTTTGTGTCTTCGTGGTACTGGATTCGCCGTTAC
* **
29496947 AGCTTAAATCTTTCCCTTCATCCTCATGTAACCGGATTTGTCGTTGCGGCCTCAATCCTTCCCAT
66 GGCTTAAATCTTTCCCTTCATCCTCATGTAACCGGATTTAACGTTGCGGCCTCAATCCTTCCCAT
29497012 AATATCTACTAAGGTAC
131 AATATCTACTAAGGTAC
** ** **** * *
29497029 CGGGTTCGCCGCTGCGGCCTT-AACCTTTCCC-TTCAAATCTTCATGGTACCAGG-TTCGCCGTT
1 AAGGTTCGCCATTGCGG-CTTAAACCTTTCCCTTTTGTGTCTTCGTGGTA-CTGGATTCGCCGTT
* * * * * * * * *
29497091 GCGGCCTCAACCTTTCCCATTTATTCCTCATGGAATCGGATTTACCGTTGCGGCCTCAATCCTTT
64 ACGGCTTAAATCTTTCCC-TTCA-TCCTCATGTAACCGGATTTAACGTTGCGGCCTCAATCCTTC
*
29497156 CCATAATATCTGCTAAGGTACC
127 CCATAATATCTACTAAGGTA-C
* *
29497178 AA-GTTCGCCATTGCGGCCTCAACCTTTCCCTT
1 AAGGTTCGCCATTGCGGCTTAAACCTTTCCCTT
29497210 CAAATCTTCA
Statistics
Matches: 262, Mismatches: 53, Indels: 22
0.78 0.16 0.07
Matches are distributed among these distances:
145 24 0.09
146 121 0.46
147 35 0.13
148 80 0.31
149 2 0.01
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.36
Consensus pattern (147 bp):
AAGGTTCGCCATTGCGGCTTAAACCTTTCCCTTTTGTGTCTTCGTGGTACTGGATTCGCCGTTAC
GGCTTAAATCTTTCCCTTCATCCTCATGTAACCGGATTTAACGTTGCGGCCTCAATCCTTCCCAT
AATATCTACTAAGGTAC
Found at i:29497086 original size:49 final size:49
Alignment explanation
Indices: 29496988--29497273 Score: 246
Period size: 49 Copynumber: 5.8 Consensus size: 49
29496978 CCGGATTTGT
* * * *
29496988 CGTTGCGGCCTCAATCC-TTCCCAT-AATATCTACTAAGGTACCGGGTTCGC
1 CGTTGCGGCCTCAA-CCTTTCCCTTCAA-ATCTTC-ATGGTACCAGGTTCGC
* *
29497038 CGCTGCGGCCTTAACCTTTCCCTTCAAATCTTCATGGTACCAGGTTCGC
1 CGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCAGGTTCGC
* * * * * **
29497087 CGTTGCGGCCTCAACCTTTCCCATT-TATTCCTCATGGAATC-GGATTTAC
1 CGTTGCGGCCTCAACCTTTCCC-TTCAAATCTTCATGGTACCAGG-TTCGC
* * * *
29497136 CGTTGCGGCCTCAATCCTTT-CCAT-AATATCTGCTAAGGTACCAAGTTCGC
1 CGTTGCGGCCTCAA-CCTTTCCCTTCAA-ATCTTC-ATGGTACCAGGTTCGC
* *
29497186 CATTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGGTTCGC
1 CGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCAGGTTCGC
*
29497235 CATTGCGGCCTCAACCTTTCCCATTTC--ATCTTCATGGTA
1 CGTTGCGGCCTCAACCTTTCCC--TTCAAATCTTCATGGTA
29497274 TTAGATTCAC
Statistics
Matches: 192, Mismatches: 32, Indels: 25
0.77 0.13 0.10
Matches are distributed among these distances:
48 4 0.02
49 121 0.63
50 59 0.31
51 8 0.04
ACGTcount: A:0.19, C:0.33, G:0.17, T:0.31
Consensus pattern (49 bp):
CGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCAGGTTCGC
Found at i:29497098 original size:99 final size:99
Alignment explanation
Indices: 29496988--29497273 Score: 275
Period size: 99 Copynumber: 2.9 Consensus size: 99
29496978 CCGGATTTGT
* * *
29496988 CGTTGCGGCCTCAATCC-TTCCCATAATATCTACTAAGGTACCGGGTTCGCCGCTGCGGCCTTAA
1 CGTTGCGGCCTCAA-CCTTTCCCATAATATCTACTATGGTACCGGGTTCGCCGTTGCGGCCTCAA
*
29497052 CCTTTCCCTTCAAATCTTCATGGTACCAGGTTCGC
65 CCTTTCCCTTCAAATCTTCATGGTACCAAGTTCGC
* * * * * **
29497087 CGTTGCGGCCTCAACCTTTCCCAT-TTAT-TCCTCATGGAATCGGATTTACCGTTGCGGCCTCAA
1 CGTTGCGGCCTCAACCTTTCCCATAATATCTACT-ATGGTACCGGGTTCGCCGTTGCGGCCTCAA
* * *
29497150 TCCTTT-CCAT-AATATCTGCTAAGGTACCAAGTTCGC
65 -CCTTTCCCTTCAA-ATCTTC-ATGGTACCAAGTTCGC
* * * *
29497186 CATTGCGGCCTCAACCTTTCCCTTCAA-ATCTTC-ATGGTACCGGGTTCGCCATTGCGGCCTCAA
1 CGTTGCGGCCTCAACCTTTCCCAT-AATATCTACTATGGTACCGGGTTCGCCGTTGCGGCCTCAA
29497249 CCTTTCCCATTTC--ATCTTCATGGTA
65 CCTTTCCC--TTCAAATCTTCATGGTA
29497274 TTAGATTCAC
Statistics
Matches: 148, Mismatches: 27, Indels: 25
0.74 0.14 0.12
Matches are distributed among these distances:
97 5 0.03
98 45 0.30
99 93 0.63
100 2 0.01
101 3 0.02
ACGTcount: A:0.19, C:0.33, G:0.17, T:0.31
Consensus pattern (99 bp):
CGTTGCGGCCTCAACCTTTCCCATAATATCTACTATGGTACCGGGTTCGCCGTTGCGGCCTCAAC
CTTTCCCTTCAAATCTTCATGGTACCAAGTTCGC
Found at i:29497270 original size:148 final size:148
Alignment explanation
Indices: 29496956--29497271 Score: 476
Period size: 148 Copynumber: 2.1 Consensus size: 148
29496946 CAGCTTAAAT
* **
29496956 CTTTCCC--TTCATCCTCATGTAACCGGATTTGTCGTTGCGGCCTCAATCCTTCCCATAATATCT
1 CTTTCCCATTTCATCCTCATGGAACCGGATTTACCGTTGCGGCCTCAATCCTTCCCATAATATCT
** * *
29497019 ACTAAGGTACCGGGTTCGCCGCTGCGGCCTTAACCTTTCCCTTCAAATCTTCATGGTACCAGGTT
66 ACTAAGGTACCAAGTTCGCCACTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCAGGTT
*
29497084 CGCCGTTGCGGCCTCAAC
131 CGCCATTGCGGCCTCAAC
* *
29497102 CTTTCCCATTT-ATTCCTCATGGAATCGGATTTACCGTTGCGGCCTCAATCCTTTCCATAATATC
1 CTTTCCCATTTCA-TCCTCATGGAACCGGATTTACCGTTGCGGCCTCAATCCTTCCCATAATATC
* * *
29497166 TGCTAAGGTACCAAGTTCGCCATTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGGT
65 TACTAAGGTACCAAGTTCGCCACTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCAGGT
29497231 TCGCCATTGCGGCCTCAAC
130 TCGCCATTGCGGCCTCAAC
*
29497250 CTTTCCCATTTCATCTTCATGG
1 CTTTCCCATTTCATCCTCATGG
29497272 TATTAGATTC
Statistics
Matches: 152, Mismatches: 14, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
146 7 0.05
147 1 0.01
148 143 0.94
149 1 0.01
ACGTcount: A:0.18, C:0.33, G:0.17, T:0.32
Consensus pattern (148 bp):
CTTTCCCATTTCATCCTCATGGAACCGGATTTACCGTTGCGGCCTCAATCCTTCCCATAATATCT
ACTAAGGTACCAAGTTCGCCACTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCAGGTT
CGCCATTGCGGCCTCAAC
Found at i:29498019 original size:42 final size:44
Alignment explanation
Indices: 29497960--29498072 Score: 131
Period size: 42 Copynumber: 2.6 Consensus size: 44
29497950 GAATTTGAGT
** *
29497960 CGCCCTTTGTGGGTTTTCAACTCAAAAC-CTTTGGTT-TCAAGA
1 CGCCCTTTACGGGTTTTCATCTCAAAACTCTTTGGTTATCAAGA
* ** *
29498002 CGCCCTTTACGGGTTTTCATCTCAAACCTCTTTTTTTAATCGAGA
1 CGCCCTTTACGGGTTTTCATCTCAAAACTCTTTGGTT-ATCAAGA
29498047 CGCCCTTTTACGGGTTTTCATCTCAA
1 CGCCC-TTTACGGGTTTTCATCTCAA
29498073 TCTTTTTTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
42 24 0.40
43 6 0.10
45 10 0.17
46 20 0.33
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.38
Consensus pattern (44 bp):
CGCCCTTTACGGGTTTTCATCTCAAAACTCTTTGGTTATCAAGA
Found at i:29507596 original size:30 final size:29
Alignment explanation
Indices: 29507562--29507735 Score: 119
Period size: 29 Copynumber: 5.9 Consensus size: 29
29507552 GTCACTTCAA
*
29507562 GGTCAAAAATGAAATATTTGGAAGTTCGGG
1 GGTCAAAAATGAAATTTTTGGAAGTTC-GG
*
29507592 GGTC--AAATGGTAATTTTTGGGAAGTTCGG
1 GGTCAAAAAT-GAAATTTTT-GGAAGTTCGG
* *
29507621 GGTCAAAAATGGAATTTTTGGAAGTTTGAG
1 GGTCAAAAATGAAATTTTTGGAAGTTCG-G
* * *
29507651 GGT--AAAATGGTAATTTTTAGAAAATTCGG
1 GGTCAAAAAT-GAAATTTTT-GGAAGTTCGG
* *
29507680 GGAT-GAAAATGGAA-TTTTGGAAAGTTCGAG
1 GG-TCAAAAATGAAATTTTTGG-AAGTTCG-G
*
29507710 GGT-AAAAATGTAATTTTTGGATAGTT
1 GGTCAAAAATGAAATTTTTGGA-AGTT
29507736 TAGGGACCTT
Statistics
Matches: 118, Mismatches: 13, Indels: 26
0.75 0.08 0.17
Matches are distributed among these distances:
28 10 0.08
29 52 0.44
30 47 0.40
31 9 0.08
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (29 bp):
GGTCAAAAATGAAATTTTTGGAAGTTCGG
Found at i:29507622 original size:29 final size:29
Alignment explanation
Indices: 29507581--29507729 Score: 137
Period size: 29 Copynumber: 5.0 Consensus size: 29
29507571 TGAAATATTT
*
29507581 GGAAGTTCGGGGGTCAAATGGTAATTTTTG
1 GGAAGTTC-GGGGTAAAATGGTAATTTTTG
29507611 GGAAGTTCGGGGTCAAAAATGG-AATTTTT-
1 GGAAGTTCGGGGT--AAAATGGTAATTTTTG
* *
29507640 GGAAGTTTGAGGGTAAAATGGTAATTTTTA
1 GGAAGTTCG-GGGTAAAATGGTAATTTTTG
* *
29507670 GAAAATTCGGGGATGAAAATGG-AA-TTTTG
1 GGAAGTTCGGGG-T-AAAATGGTAATTTTTG
*
29507699 GAAAGTTCGAGGGTAAAAAT-GTAATTTTTG
1 GGAAGTTCG-GGGT-AAAATGGTAATTTTTG
29507729 G
1 G
29507730 ATAGTTTAGG
Statistics
Matches: 101, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
28 8 0.08
29 43 0.43
30 37 0.37
31 13 0.13
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.32
Consensus pattern (29 bp):
GGAAGTTCGGGGTAAAATGGTAATTTTTG
Found at i:29507630 original size:59 final size:58
Alignment explanation
Indices: 29507562--29507730 Score: 207
Period size: 59 Copynumber: 2.9 Consensus size: 58
29507552 GTCACTTCAA
* * * * *
29507562 GGTCAAAAATGAAATATTTGGAAGTTCGGGGGTCAAATGGTAATTTTTGGGAAGTTCGG
1 GGTCAAAAATGGAAT-TTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAATTCGG
* *
29507621 GGTCAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTAGAAAATTCGG
1 GGTCAAAAATGGAA-TTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAATTCGG
*
29507680 GGAT-GAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAAT-GTAATTTTTGGA
1 GG-TCAAAAATGGAATTTTGG-AAGTTCGAGGGT-AAAATGGTAATTTTTGGA
29507731 TAGTTTAGGG
Statistics
Matches: 96, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
58 6 0.06
59 83 0.86
60 7 0.07
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (58 bp):
GGTCAAAAATGGAATTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAATTCGG
Found at i:29509538 original size:17 final size:17
Alignment explanation
Indices: 29509516--29509585 Score: 52
Period size: 17 Copynumber: 3.7 Consensus size: 17
29509506 ATTGGACATT
29509516 ATTTAAATAAATTTTAA
1 ATTTAAATAAATTTTAA
29509533 ATTTAAATTCATAATAAATTTAA
1 ATTTAAA-T-A-AAT---TTTAA
*
29509556 ATTTCCAATAAA-TTTAA
1 ATTT-AAATAAATTTTAA
29509573 ATTTAGAATAAAT
1 ATTTA-AATAAAT
29509586 AAATAAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 17
0.69 0.03 0.28
Matches are distributed among these distances:
17 22 0.52
18 1 0.02
19 1 0.02
20 3 0.07
21 2 0.05
22 1 0.02
23 10 0.24
24 2 0.05
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (17 bp):
ATTTAAATAAATTTTAA
Found at i:29509573 original size:23 final size:21
Alignment explanation
Indices: 29509521--29509577 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 21
29509511 ACATTATTTA
29509521 AATAAATTTTAAATTTAAATTC
1 AATAAA-TTTAAATTTAAATTC
29509543 -AT-AA--TAAATTTAAATTTCC
1 AATAAATTTAAATTTAAA-TT-C
29509562 AATAAATTTAAATTTA
1 AATAAATTTAAATTTA
29509578 GAATAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
17 10 0.34
18 2 0.07
19 1 0.03
20 4 0.14
21 4 0.14
23 8 0.28
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
AATAAATTTAAATTTAAATTC
Found at i:29510948 original size:30 final size:30
Alignment explanation
Indices: 29510912--29511046 Score: 98
Period size: 30 Copynumber: 4.5 Consensus size: 30
29510902 TATTTTTTAA
* *
29510912 AAAAATTATGTTTTGACCCCTAAACTATCC
1 AAAAATTATGATTTGACCCCTAAACTTTCC
* * * * *
29510942 AAAAATTCA-AATTTAACCTGTCTGAATTTTCC
1 AAAAATT-ATGATTTGACC--CCTAAACTTTCC
* *
29510974 AAAAATTATGTTTTGAACCCC-AAACTTTTC
1 AAAAATTATGATTTG-ACCCCTAAACTTTCC
*
29511004 AAAAATT-TGGATTTGA-CCCTAAACTTTTC
1 AAAAATTAT-GATTTGACCCCTAAACTTTCC
*
29511033 AAAAATTATAATTT
1 AAAAATTATGATTT
29511047 AGCCTCCAAA
Statistics
Matches: 81, Mismatches: 16, Indels: 17
0.71 0.14 0.15
Matches are distributed among these distances:
28 3 0.04
29 22 0.27
30 32 0.40
31 3 0.04
32 18 0.22
33 3 0.04
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.37
Consensus pattern (30 bp):
AAAAATTATGATTTGACCCCTAAACTTTCC
Found at i:29511022 original size:29 final size:30
Alignment explanation
Indices: 29510968--29511068 Score: 102
Period size: 29 Copynumber: 3.4 Consensus size: 30
29510958 CCTGTCTGAA
*
29510968 TTTTCCAAAAATTATGTTTTGAACCCCAAAC
1 TTTT-CAAAAATTATGATTTGAACCCCAAAC
*
29510999 TTTTCAAAAATT-TGGATTTG-ACCCTAAAC
1 TTTTCAAAAATTAT-GATTTGAACCCCAAAC
* *
29511028 TTTTCAAAAATTATAATTT-AGCCTCCAAA-
1 TTTTCAAAAATTATGATTTGAACC-CCAAAC
*
29511057 TTTTCCAAAATT
1 TTTTCAAAAATT
29511069 TCATTTTTGA
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
29 38 0.63
30 18 0.30
31 4 0.07
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.39
Consensus pattern (30 bp):
TTTTCAAAAATTATGATTTGAACCCCAAAC
Found at i:29511149 original size:30 final size:34
Alignment explanation
Indices: 29511115--29511189 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 34
29511105 TTACCCCAAA
29511115 ATTTTCATTTTTGCTT-TAA-TTTAAT-CT-TTT
1 ATTTTCATTTTTGCTTCTAATTTTAATCCTGTTT
*
29511145 ATTTT--TTATTGCTTCTAATTTTAATCCTGTTT
1 ATTTTCATTTTTGCTTCTAATTTTAATCCTGTTT
29511177 ATTTATCTATTTT
1 ATTT-TC-ATTTT
29511190 ATCTTTCGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
28 8 0.23
29 3 0.09
30 11 0.31
31 2 0.06
32 7 0.20
33 1 0.03
36 3 0.09
ACGTcount: A:0.20, C:0.11, G:0.04, T:0.65
Consensus pattern (34 bp):
ATTTTCATTTTTGCTTCTAATTTTAATCCTGTTT
Found at i:29512911 original size:263 final size:263
Alignment explanation
Indices: 29511940--29513107 Score: 1926
Period size: 263 Copynumber: 4.4 Consensus size: 263
29511930 TGTTTCGACA
*
29511940 TACTATATTCTGATTCTATATATGCTTTCTAATTTTTATCTCTTTTTTCTTGAATCTTTACTGTT
1 TACTATATTCTGATTCTATATATGCTTTCTAATTTTTATCTCTTTTTCCTTGAATCTTTACTGTT
* * *
29512005 GATGGGTTGTTCTTGAATCAAAATTTACTTTTAGGATAGTTTTTTTTAAATGAATTTCTATATTC
66 GATGGGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATAG-TTTTTTTAAATGAATTTCTATATTC
* * * * * *
29512070 TTTTGGATTCTTCTTATTATTGGTTGTTCTAAGAAGTGAAAAATATGAAAGTAAATACACACAAA
130 TTTTGGGTTCGTCTTCTTATTAGTTGTTCTAAGCAGTGAAAAAGATGAAAGTAAATACACACAAA
* * * *
29512135 AACAAGTAGACTGATTTTCTTCTTGTTTATTTTCAGATTGTATTTACAATGATTAATTTTAATTT
195 AACAAGTAGACTAATTTTATTCTTGTTTATTTTCAGATTTTATTTATAATGATTAATTTTAATTT
29512200 TAAT
260 TAAT
* * *
29512204 TACTATATTCTGATTCTATATATGCTTTCTAATTTTTATCTTTTTTTTCCTTGAATCTTTATTAT
1 TACTATATTCTGATTCTATATATGCTTTCTAATTTTTATC-TCTTTTTCCTTGAATCTTTACTGT
*
29512269 TGATGGGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATAGTTTTTTTAAATGAATTTTTATATTC
65 TGATGGGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATAGTTTTTTTAAATGAATTTCTATATTC
* *
29512334 TTTTGGGTTAGTCTTCTTATTAGTTGTTCTAAGCAGTGAAAAAGATTAAAGTAAATACACACAAA
130 TTTTGGGTTCGTCTTCTTATTAGTTGTTCTAAGCAGTGAAAAAGATGAAAGTAAATACACACAAA
* *
29512399 AACAAGTAGACTAATTTTATTCTTGTTTATTTTCAGATCTTATTTATAATCATTAATTTTAATTT
195 AACAAGTAGACTAATTTTATTCTTGTTTATTTTCAGATTTTATTTATAATGATTAATTTTAATTT
29512464 TAAT
260 TAAT
* *
29512468 TACTATATTCTGATTCTATATATGCTTTTTAATTTTTATCTTTTTTTTCCCTTGAATCTTTACTG
1 TACTATATTCTGATTCTATATATGCTTTCTAATTTTTATC-TCTTTTT-CCTTGAATCTTTACTG
* *
29512533 TTGATGGGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATAATTTTTTTAAATGAATTTCTATTTT
64 TTGATGGGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATAGTTTTTTTAAATGAATTTCTATATT
* *
29512598 TTTTTGGGTTCGTCTTCTTATT-GATTGTTCTAAGCAGTGAAAAAGATGAAAGTAAATACAAACA
129 CTTTTGGGTTCGTCTTCTTATTAG-TTGTTCTAAGCAGTGAAAAAGATGAAAGTAAATACACACA
*
29512662 AAAATAAGTAGACTAATTTTATTCTT-TTTCATTTTCAGATTTTATTTATAATGATTAATTTTAA
193 AAAACAAGTAGACTAATTTTATTCTTGTTT-ATTTTCAGATTTTATTTATAATGATTAATTTTAA
29512726 TTTTAAT
257 TTTTAAT
* *
29512733 TACTATATTCTGATTCTATATATGCTTTTTAATTTTTATCTCTTTTTCCTTGAATCTTTATTGTT
1 TACTATATTCTGATTCTATATATGCTTTCTAATTTTTATCTCTTTTTCCTTGAATCTTTACTGTT
29512798 GATGGGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATAGTTTTTTTAAATGAATTTCTATATTCT
66 GATGGGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATAGTTTTTTTAAATGAATTTCTATATTCT
*
29512863 TTTGGGTTCGTCTTCTTATTAGTTGTTCTAAGCAGTGAAAATGATGAAAGTAAATACACACAAAA
131 TTTGGGTTCGTCTTCTTATTAGTTGTTCTAAGCAGTGAAAAAGATGAAAGTAAATACACACAAAA
* *
29512928 ACAAGTAGACTGATTTTATTCTTGTTCATTTTCAGATTTTATTTATAATGATTAATTTTAATTTT
196 ACAAGTAGACTAATTTTATTCTTGTTTATTTTCAGATTTTATTTATAATGATTAATTTTAATTTT
29512993 AAT
261 AAT
* * *
29512996 TACTATATTTTGATTCTATATATGCTTTCTAATTTTTAACTCTTTTTCCTTGAATTTTTACTGTT
1 TACTATATTCTGATTCTATATATGCTTTCTAATTTTTATCTCTTTTTCCTTGAATCTTTACTGTT
*
29513061 GATGAGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATAGTTTTTTTA
66 GATGGGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATAGTTTTTTTA
29513108 TTTATAATGA
Statistics
Matches: 847, Mismatches: 51, Indels: 13
0.93 0.06 0.01
Matches are distributed among these distances:
263 308 0.36
264 244 0.29
265 295 0.35
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (263 bp):
TACTATATTCTGATTCTATATATGCTTTCTAATTTTTATCTCTTTTTCCTTGAATCTTTACTGTT
GATGGGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATAGTTTTTTTAAATGAATTTCTATATTCT
TTTGGGTTCGTCTTCTTATTAGTTGTTCTAAGCAGTGAAAAAGATGAAAGTAAATACACACAAAA
ACAAGTAGACTAATTTTATTCTTGTTTATTTTCAGATTTTATTTATAATGATTAATTTTAATTTT
AAT
Found at i:29512936 original size:528 final size:528
Alignment explanation
Indices: 29511940--29513107 Score: 1948
Period size: 528 Copynumber: 2.2 Consensus size: 528
29511930 TGTTTCGACA
*
29511940 TACTATATTCTGATTCTATATATGCTTTCTAATTTTTATCTCTTTTTT-CTTGAATCTTTACTGT
1 TACTATATTCTGATTCTATATATGCTTTCTAATTTTTATCTTTTTTTTCCTTGAATCTTTACTGT
* * * *
29512004 TGATGGGTTGTTCTTGAATCAAAATTTACTTTTAGGATAGTTTTTTTTAAATGAATTTCTATATT
66 TGATGGGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATA-ATTTTTTTAAATGAATTTCTATATT
* * * *
29512069 CTTTTGGATTCTTCTTATTATTGGTTGTTCTAAGAAGTGAAAAATATGAAAGTAAATACACACAA
130 CTTTTGGATTCGTCTTATTATTGATTGTTCTAAGAAGTGAAAAAGATGAAAGTAAATACAAACAA
* *
29512134 AAACAAGTAGACTGATTTTCTTCTTGTTTATTTTCAGATTGTATTTACAATGATTAATTTTAATT
195 AAACAAGTAGACTAATTTTATTCTTGTTTATTTTCAGATTGTATTTACAATGATTAATTTTAATT
*
29512199 TTAATTACTATATTCTGATTCTATATATGCTTTCTAATTTTTATCTTTTTTTTCCTTGAATCTTT
260 TTAATTACTATATTCTGATTCTATATATGCTTTCTAATTTTTATCTTCTTTTTCCTTGAATCTTT
*
29512264 ATTATTGATGGGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATAGTTTTTTTAAATGAATTTTTA
325 ATTATTGATGGGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATAGTTTTTTTAAATGAATTTCTA
*
29512329 TATTCTTTTGGGTTAGTCTTCTTATTAGTTGTTCTAAGCAGTGAAAAAGATTAAAGTAAATACAC
390 TATTCTTTTGGGTTAGTCTTCTTATTAGTTGTTCTAAGCAGTGAAAAAGATGAAAGTAAATACAC
*
29512394 ACAAAAACAAGTAGACTAATTTTATTCTTGTTTATTTTCAGATCTTATTTATAATCATTAATTTT
455 ACAAAAACAAGTAGACTAATTTTATTCTTGTTCATTTTCAGATCTTATTTATAATCATTAATTTT
29512459 AATTTTAAT
520 AATTTTAAT
*
29512468 TACTATATTCTGATTCTATATATGCTTTTTAATTTTTATCTTTTTTTTCCCTTGAATCTTTACTG
1 TACTATATTCTGATTCTATATATGCTTTCTAATTTTTATCTTTTTTTT-CCTTGAATCTTTACTG
*
29512533 TTGATGGGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATAATTTTTTTAAATGAATTTCTATTTT
65 TTGATGGGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATAATTTTTTTAAATGAATTTCTATATT
* * * *
29512598 TTTTTGGGTTCGTCTTCTTATTGATTGTTCTAAGCAGTGAAAAAGATGAAAGTAAATACAAACAA
130 CTTTTGGATTCGTCTTATTATTGATTGTTCTAAGAAGTGAAAAAGATGAAAGTAAATACAAACAA
* * *
29512663 AAATAAGTAGACTAATTTTATTCTT-TTTCATTTTCAGATTTTATTTATAATGATTAATTTTAAT
195 AAACAAGTAGACTAATTTTATTCTTGTTT-ATTTTCAGATTGTATTTACAATGATTAATTTTAAT
*
29512727 TTTAATTACTATATTCTGATTCTATATATGCTTTTTAATTTTTATC-TCTTTTTCCTTGAATCTT
259 TTTAATTACTATATTCTGATTCTATATATGCTTTCTAATTTTTATCTTCTTTTTCCTTGAATCTT
*
29512791 TATTGTTGATGGGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATAGTTTTTTTAAATGAATTTCT
324 TATTATTGATGGGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATAGTTTTTTTAAATGAATTTCT
* *
29512856 ATATTCTTTTGGGTTCGTCTTCTTATTAGTTGTTCTAAGCAGTGAAAATGATGAAAGTAAATACA
389 ATATTCTTTTGGGTTAGTCTTCTTATTAGTTGTTCTAAGCAGTGAAAAAGATGAAAGTAAATACA
* * *
29512921 CACAAAAACAAGTAGACTGATTTTATTCTTGTTCATTTTCAGATTTTATTTATAATGATTAATTT
454 CACAAAAACAAGTAGACTAATTTTATTCTTGTTCATTTTCAGATCTTATTTATAATCATTAATTT
29512986 TAATTTTAAT
519 TAATTTTAAT
* * * *
29512996 TACTATATTTTGATTCTATATATGCTTTCTAATTTTTAAC-TCTTTTTCCTTGAATTTTTACTGT
1 TACTATATTCTGATTCTATATATGCTTTCTAATTTTTATCTTTTTTTTCCTTGAATCTTTACTGT
* *
29513060 TGATGAGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATAGTTTTTTTA
66 TGATGGGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATAATTTTTTTA
29513108 TTTATAATGA
Statistics
Matches: 599, Mismatches: 38, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
526 62 0.10
527 6 0.01
528 299 0.50
529 180 0.30
530 52 0.09
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (528 bp):
TACTATATTCTGATTCTATATATGCTTTCTAATTTTTATCTTTTTTTTCCTTGAATCTTTACTGT
TGATGGGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATAATTTTTTTAAATGAATTTCTATATTC
TTTTGGATTCGTCTTATTATTGATTGTTCTAAGAAGTGAAAAAGATGAAAGTAAATACAAACAAA
AACAAGTAGACTAATTTTATTCTTGTTTATTTTCAGATTGTATTTACAATGATTAATTTTAATTT
TAATTACTATATTCTGATTCTATATATGCTTTCTAATTTTTATCTTCTTTTTCCTTGAATCTTTA
TTATTGATGGGTTGTTCTTGAATCAAAGTTTGCTTTTGGGATAGTTTTTTTAAATGAATTTCTAT
ATTCTTTTGGGTTAGTCTTCTTATTAGTTGTTCTAAGCAGTGAAAAAGATGAAAGTAAATACACA
CAAAAACAAGTAGACTAATTTTATTCTTGTTCATTTTCAGATCTTATTTATAATCATTAATTTTA
ATTTTAAT
Found at i:29515450 original size:11 final size:11
Alignment explanation
Indices: 29515421--29515493 Score: 55
Period size: 11 Copynumber: 6.7 Consensus size: 11
29515411 TTTTGAAGGT
29515421 TGTT-TTTTG-
1 TGTTGTTTTGA
*
29515430 TGTTGATTTGA
1 TGTTGTTTTGA
*
29515441 TGTTGTTTTGG
1 TGTTGTTTTGA
29515452 TGTTGTTTT-A
1 TGTTGTTTTGA
*
29515462 -GTAATGTTTTGG
1 TGT--TGTTTTGA
*
29515474 TGCTGTTTTGGA
1 TGTTGTTTT-GA
29515486 TGTTGTTT
1 TGTTGTTT
29515494 CGCAATTATT
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
9 6 0.12
10 4 0.08
11 30 0.61
12 8 0.16
13 1 0.02
ACGTcount: A:0.08, C:0.01, G:0.29, T:0.62
Consensus pattern (11 bp):
TGTTGTTTTGA
Found at i:29515454 original size:22 final size:21
Alignment explanation
Indices: 29515419--29515493 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 21
29515409 CATTTTGAAG
*
29515419 GTTGTTTTTTGTGTTGATTTGAT
1 GTTG-TTTTGGTGTTG-TTTGAT
*
29515442 GTTGTTTTGGTGTTGTTTTA-
1 GTTGTTTTGGTGTTGTTTGAT
*
29515462 GTAATGTTTTGGTGCTGTTTTGGAT
1 GT--TGTTTTGGTGTTG-TTT-GAT
29515487 GTTGTTT
1 GTTGTTT
29515494 CGCAATTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
20 2 0.05
21 4 0.09
22 22 0.51
23 12 0.28
24 1 0.02
25 2 0.05
ACGTcount: A:0.08, C:0.01, G:0.29, T:0.61
Consensus pattern (21 bp):
GTTGTTTTGGTGTTGTTTGAT
Found at i:29522530 original size:27 final size:25
Alignment explanation
Indices: 29522488--29522542 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 25
29522478 TATATCTAAA
*
29522488 AAAACCCAATTGATATTTTACTTTAAC
1 AAAACCCAATTAATATTTTA--TTAAC
*
29522515 AAAACTCAATTAATATTTTATTAAC
1 AAAACCCAATTAATATTTTATTAAC
29522540 AAA
1 AAA
29522543 GCTATATGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 8 0.31
27 18 0.69
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.36
Consensus pattern (25 bp):
AAAACCCAATTAATATTTTATTAAC
Found at i:29524489 original size:18 final size:18
Alignment explanation
Indices: 29524455--29524489 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29524445 ACAGACATAA
*
29524455 TTTAAAAATTTAAAAATC
1 TTTAAAAATATAAAAATC
*
29524473 TTTAAAAATATATAAAT
1 TTTAAAAATATAAAAAT
29524490 TAATAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTAAAAATATAAAAATC
Found at i:29524762 original size:17 final size:17
Alignment explanation
Indices: 29524725--29524762 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
29524715 ATTTTAGTTA
**
29524725 TTTTATAAATTTATATT
1 TTTTATAAATTTATAAC
29524742 TTTTATAAATTTATAAC
1 TTTTATAAATTTATAAC
29524759 TTTT
1 TTTT
29524763 TAATTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTATAAATTTATAAC
Found at i:29524809 original size:45 final size:46
Alignment explanation
Indices: 29524741--29524828 Score: 115
Period size: 45 Copynumber: 1.9 Consensus size: 46
29524731 AAATTTATAT
* * ** *
29524741 TTTTTATAAATTTATAACTTTTTAATTTTTTTATATAT-TATTGTA
1 TTTTCATAAAGTTATAAAATTTTAAATTTTTTATATATATATTGTA
*
29524786 TTTTCATAAAGTTATAAAATTTTAAATTTTTTATTTATATATT
1 TTTTCATAAAGTTATAAAATTTTAAATTTTTTATATATATATT
29524829 ATATATAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 32 0.89
46 4 0.11
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (46 bp):
TTTTCATAAAGTTATAAAATTTTAAATTTTTTATATATATATTGTA
Found at i:29524840 original size:45 final size:45
Alignment explanation
Indices: 29524746--29524849 Score: 111
Period size: 45 Copynumber: 2.3 Consensus size: 45
29524736 TATATTTTTT
** * * * *
29524746 ATAAATTTATAACTTTTTAATTTTTTTATATATTATTGTATTTTC
1 ATAAATTTATAAAATTTTAAATTTTTTATATATTATTATATTATA
* *
29524791 ATAAAGTTATAAAATTTTAAATTTTTTATTTATATATTATA-TATA
1 ATAAATTTATAAAATTTTAAATTTTTTATATAT-TATTATATTATA
*
29524836 ATAAATTTTTAAAA
1 ATAAATTTATAAAA
29524850 ATATTGTAAG
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
45 42 0.88
46 6 0.12
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (45 bp):
ATAAATTTATAAAATTTTAAATTTTTTATATATTATTATATTATA
Found at i:29527187 original size:43 final size:43
Alignment explanation
Indices: 29527125--29527464 Score: 371
Period size: 43 Copynumber: 8.0 Consensus size: 43
29527115 GGAAAACACT
* * *
29527125 GCTATAGAACATGATCTTTAGCAGCGCTTTTCTCACAAACGCC
1 GCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* ** * * * *
29527168 TCTATAGAACATGGTCTTTAGCCACACTTTCCCCACAAACACT
1 GCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* * * *
29527211 GCTATAAAACATGGTTTTTAGCGGTGCTTTTCCCACAAACGGC
1 GCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* * * * *
29527254 GCTATA-AAGCTTGGTCTTTAGCAGCGTTTTTACCACAAACACC
1 GCTATAGAA-CATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* *
29527297 GCTATAGAACATGATATTTAGCGGCGCTTTTCCCACAAACGCC
1 GCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* * *
29527340 ACTATAGAACAT-GTCTTTAGCGGTG-TTTTCCTACAAACGCC
1 GCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* * * * *
29527381 GCTATAAAACATGGTCTTTAGCGGCGTTTTTCCCTCAAATGTC
1 GCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* *
29527424 GTTATAGAACATGATCTTTAGCGGCGCTTTTCCCACAAACG
1 GCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACG
29527465 TCACTAACAT
Statistics
Matches: 240, Mismatches: 53, Indels: 8
0.80 0.18 0.03
Matches are distributed among these distances:
41 25 0.10
42 24 0.10
43 189 0.79
44 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (43 bp):
GCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
Found at i:29527430 original size:127 final size:128
Alignment explanation
Indices: 29527125--29527470 Score: 408
Period size: 127 Copynumber: 2.7 Consensus size: 128
29527115 GGAAAACACT
* * * * * *
29527125 GCTATAGAACATGATCTTTAGCAGCGCTTTTCTCACAAACGCCTCTATAGAACATGGTCTTTAGC
1 GCTATAAAACATGGTCTTTAGCAGCGTTTTTCCCACAAACGCGT-TATAGAACATGATCTTTAGC
** * * * ** * *
29527190 CACACTTTCCCCACAAACACTGCTATAAAACATGGTTTTTAGCGGTGCTTTTCCCACAAACGGC
65 GGCGCTTTTCCCACAAACGCCACTATAAAACATGGTCTTTAGCGGTGCTTTTCCCACAAACGCC
* * * * * *
29527254 GCTATAAAGCTTGGTCTTTAGCAGCGTTTTTACCACAAACACCGCTATAGAACATGATATTTAGC
1 GCTATAAAACATGGTCTTTAGCAGCGTTTTTCCCACAAAC-GCGTTATAGAACATGATCTTTAGC
* *
29527319 GGCGCTTTTCCCACAAACGCCACTATAGAACAT-GTCTTTAGCGGTG-TTTTCCTACAAACGCC
65 GGCGCTTTTCCCACAAACGCCACTATAAAACATGGTCTTTAGCGGTGCTTTTCCCACAAACGCC
* * *
29527381 GCTATAAAACATGGTCTTTAGCGGCGTTTTTCCCTCAAATGTCGTTATAGAACATGATCTTTAGC
1 GCTATAAAACATGGTCTTTAGCAGCGTTTTTCCCACAAACG-CGTTATAGAACATGATCTTTAGC
*
29527446 GGCGCTTTTCCCACAAACGTCACTA
65 GGCGCTTTTCCCACAAACGCCACTA
29527471 ACATTAACAA
Statistics
Matches: 182, Mismatches: 33, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
127 93 0.51
128 12 0.07
129 76 0.42
130 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (128 bp):
GCTATAAAACATGGTCTTTAGCAGCGTTTTTCCCACAAACGCGTTATAGAACATGATCTTTAGCG
GCGCTTTTCCCACAAACGCCACTATAAAACATGGTCTTTAGCGGTGCTTTTCCCACAAACGCC
Found at i:29531121 original size:30 final size:30
Alignment explanation
Indices: 29531087--29531284 Score: 229
Period size: 30 Copynumber: 6.6 Consensus size: 30
29531077 ATTTTATTTT
** * *
29531087 AAAATTATGTTTTAGCCCCTAAACATTCTA
1 AAAATTACATTTTAACCCCTAAACTTTCTA
* * *
29531117 AAAATT-CAAATTTAACCTCTAAACTTTTTA
1 AAAATTAC-ATTTTAACCCCTAAACTTTCTA
* * *
29531147 TAAATTACA-TTTAGGCCTCTAAACTTTCTA
1 AAAATTACATTTTA-ACCCCTAAACTTTCTA
* *
29531177 AAAATTACATTCTAACCCATAAACTTTCTA
1 AAAATTACATTTTAACCCCTAAACTTTCTA
29531207 AAAATTACATTTTAACCCCTAAACTTTCTA
1 AAAATTACATTTTAACCCCTAAACTTTCTA
29531237 AAAATTACATTTTAACCCCTAAACTTTCTA
1 AAAATTACATTTTAACCCCTAAACTTTCTA
* **
29531267 AAATTTTGATTTTAACCC
1 AAAATTACATTTTAACCC
29531285 TTGTTTTCCT
Statistics
Matches: 144, Mismatches: 20, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
29 4 0.03
30 136 0.94
31 4 0.03
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCTAAACTTTCTA
Found at i:29542970 original size:49 final size:49
Alignment explanation
Indices: 29542859--29543968 Score: 496
Period size: 49 Copynumber: 22.8 Consensus size: 49
29542849 TACAGGTTTG
* * * * * *
29542859 GAGGGAAAGGTTGAAGCCGCAATGGCGAA-CCTTTTTTCC-T-TAGATGT
1 GAGGGAAAGATTGAAGCCGCAACGGCGAATCC-TTATACCATAGAGATAT
* * * *
29542906 GATGGGAAAGATTGAAGCCGTAACGGTGAATCATT-TACCATGGAGATAT
1 GA-GGGAAAGATTGAAGCCGCAACGGCGAATCCTTATACCATAGAGATAT
* * * * * *
29542955 GGAGGGAAAGGTTGAAG-CGTAATGACGAA-CCTTATACCTTAGA-AAAT
1 -GAGGGAAAGATTGAAGCCGCAACGGCGAATCCTTATACCATAGAGATAT
* * ** **
29543002 AATGGGAAAGATTGAAGCCGCAACGACGAAT-CTTGCACCACGGAGATAT
1 GA-GGGAAAGATTGAAGCCGCAACGGCGAATCCTTATACCATAGAGATAT
* * * *
29543051 GGAAGGAAAGGA-TAAAGCCGCAACGGCGAA-CCTTATACC-T-TAGATGT
1 -GAGGGAAA-GATTGAAGCCGCAACGGCGAATCCTTATACCATAGAGATAT
* * * *
29543098 GATGGGAAAAATTGAAGCCGCAACGACGAAT-CGTGTACCAT-GAAGATAT
1 GA-GGGAAAGATTGAAGCCGCAACGGCGAATCCTTATACCATAG-AGATAT
* * * * * * *
29543147 GGAGGGAAAGGTTCAAGCCGCAATGACGAA-CCTTATACCTTAGAAAAAT
1 -GAGGGAAAGATTGAAGCCGCAACGGCGAATCCTTATACCATAGAGATAT
* * ** *
29543196 AATGGGAAAGATTGAAGCCGCAACGACGAAT-CTTGCACCACAGAGATAT
1 GA-GGGAAAGATTGAAGCCGCAACGGCGAATCCTTATACCATAGAGATAT
* * * * * * *
29543245 GGAGGAAAAGGTTGAAGCCTCAATGGC-AAACCTTATACC-T-TAGATGT
1 -GAGGGAAAGATTGAAGCCGCAACGGCGAATCCTTATACCATAGAGATAT
* * * *
29543292 GATGGGAAAGATTGAAGCCGCAACGGCGAAT-CGTGTACTATGGAGATAT
1 GA-GGGAAAGATTGAAGCCGCAACGGCGAATCCTTATACCATAGAGATAT
* * * * * * * * *
29543341 AGAGAGAAAGGTTGAAGTCACAAACTGCGAA-CCCTATACCTTAGAAAAAT
1 -GAGGGAAAGATTGAAGCCGC-AACGGCGAATCCTTATACCATAGAGATAT
* * *
29543391 AATGGGAAAGATTGAAGCCGCAACGACGAAT-CTTGTACCACT-GAGATAT
1 GA-GGGAAAGATTGAAGCCGCAACGGCGAATCCTTATACCA-TAGAGATAT
* * * * * **
29543440 GGAGGGAAAGGTTGAAGCTGCAACGGTGAA-CCTTATACCTTAGTGAGGT
1 -GAGGGAAAGATTGAAGCCGCAACGGCGAATCCTTATACCATAGAGATAT
* * * *
29543489 GATGGGAAAGATTGAAGCCGCAATGGCGAAT-CGTGTACCATGGAGATAT
1 GA-GGGAAAGATTGAAGCCGCAACGGCGAATCCTTATACCATAGAGATAT
* * * * * * * * *
29543538 AGAGGGAAAGGTTAAAGCTGCAATGGTGAA-CCTTATACCTTAGAAAAAA
1 -GAGGGAAAGATTGAAGCCGCAACGGCGAATCCTTATACCATAGAGATAT
* * * * * **
29543587 AATAGGAAAGATTGAAGTCGCAACGACGAAT-CTTGTACCACGGAGATAT
1 GA-GGGAAAGATTGAAGCCGCAACGGCGAATCCTTATACCATAGAGATAT
* * * **
29543636 GGAGGGAAATG-TTGAAGCGGCAACGGCGAA-CCTTATACCTTAGTGAGGT
1 -GAGGGAAA-GATTGAAGCCGCAACGGCGAATCCTTATACCATAGAGATAT
* * * * *
29543685 GATGGGAAAGATTGAAGCCGCAATGGTGAAT-CGTGTACCATGGAGATAT
1 GA-GGGAAAGATTGAAGCCGCAACGGCGAATCCTTATACCATAGAGATAT
* * * * * * *
29543734 GGAGGGAAA-AGTTAAAGCTGCAATGGTGAA-CCTTATACCTTAGAAAAAT
1 -GAGGGAAAGA-TTGAAGCCGCAACGGCGAATCCTTATACCATAGAGATAT
* * * * * * *
29543783 AATGGGAAAGATTGAAGCTGTAACAGCGAAT-CGTGTACCATGGAGATAT
1 GA-GGGAAAGATTGAAGCCGCAACGGCGAATCCTTATACCATAGAGATAT
* * ** * * *
29543832 GGAGGGAAAGGTTAAAGCCATAATGGCGAA-CCTTATACCTTAGAGATGT
1 -GAGGGAAAGATTGAAGCCGCAACGGCGAATCCTTATACCATAGAGATAT
** * * *
29543881 GATGGGAAAGATTGAAGCTTCAACGACGAAT-CTTATACCCTAAAG-T-T
1 GA-GGGAAAGATTGAAGCCGCAACGGCGAATCCTTATACCATAGAGATAT
* * *
29543928 GAAGAGGAGCAGATTAAAGCCGCAATGGCGAAT-CTTATACC
1 G-AG-GGA-AAGATTGAAGCCGCAACGGCGAATCCTTATACC
29543969 TCAAAGTTGT
Statistics
Matches: 775, Mismatches: 225, Indels: 124
0.69 0.20 0.11
Matches are distributed among these distances:
46 6 0.01
47 89 0.11
48 83 0.11
49 543 0.70
50 54 0.07
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.21
Consensus pattern (49 bp):
GAGGGAAAGATTGAAGCCGCAACGGCGAATCCTTATACCATAGAGATAT
Found at i:29543245 original size:98 final size:98
Alignment explanation
Indices: 29542857--29543919 Score: 1214
Period size: 98 Copynumber: 10.9 Consensus size: 98
29542847 TCTACAGGTT
* * *
29542857 TGGAGGGAAAGGTTGAAGCCGCAATGGCGAACCTTTTTTCCTTAG--ATGTGATGGGAAAGATTG
1 TGGAGGGAAAGGTTGAAGCCGCAATGGCGAACC-TTATACCTTAGAAAAGTGATGGGAAAGATTG
* **
29542920 AAGCCGTAACGGTGAATCATT-TACCATGGAGATA
65 AAGCCGCAACGACGAATC-TTGTACCATGGAGATA
* * *
29542954 TGGAGGGAAAGGTTGAAG-CGTAATGACGAACCTTATACCTTAGAAAA-TAATGGGAAAGATTGA
1 TGGAGGGAAAGGTTGAAGCCGCAATGGCGAACCTTATACCTTAGAAAAGTGATGGGAAAGATTGA
* *
29543017 AGCCGCAACGACGAATCTTGCACCACGGAGATA
66 AGCCGCAACGACGAATCTTGTACCATGGAGATA
* * * * * *
29543050 TGGAAGGAAAGGATAAAGCCGCAACGGCGAACCTTATACCTTAG--ATGTGATGGGAAAAATTGA
1 TGGAGGGAAAGGTTGAAGCCGCAATGGCGAACCTTATACCTTAGAAAAGTGATGGGAAAGATTGA
* *
29543113 AGCCGCAACGACGAATCGTGTACCATGAAGATA
66 AGCCGCAACGACGAATCTTGTACCATGGAGATA
* * * *
29543146 TGGAGGGAAAGGTTCAAGCCGCAATGACGAACCTTATACCTTAGAAAAATAATGGGAAAGATTGA
1 TGGAGGGAAAGGTTGAAGCCGCAATGGCGAACCTTATACCTTAGAAAAGTGATGGGAAAGATTGA
* **
29543211 AGCCGCAACGACGAATCTTGCACCACAGAGATA
66 AGCCGCAACGACGAATCTTGTACCATGGAGATA
* * * *
29543244 TGGAGGAAAAGGTTGAAGCCTCAATGGCAAACCTTATACCTTAG--ATGTGATGGGAAAGATTGA
1 TGGAGGGAAAGGTTGAAGCCGCAATGGCGAACCTTATACCTTAGAAAAGTGATGGGAAAGATTGA
* * *
29543307 AGCCGCAACGGCGAATCGTGTACTATGGAGATA
66 AGCCGCAACGACGAATCTTGTACCATGGAGATA
* * * * * * *
29543340 TAGAGAGAAAGGTTGAAGTCACAAACT-GCGAACCCTATACCTTAGAAAAATAATGGGAAAGATT
1 TGGAGGGAAAGGTTGAAGCCGC-AA-TGGCGAACCTTATACCTTAGAAAAGTGATGGGAAAGATT
29543404 GAAGCCGCAACGACGAATCTTGTACCACT-GAGATA
64 GAAGCCGCAACGACGAATCTTGTACCA-TGGAGATA
* * * ** *
29543439 TGGAGGGAAAGGTTGAAGCTGCAACGGTGAACCTTATACCTTAGTGAGGTGATGGGAAAGATTGA
1 TGGAGGGAAAGGTTGAAGCCGCAATGGCGAACCTTATACCTTAGAAAAGTGATGGGAAAGATTGA
* * *
29543504 AGCCGCAATGGCGAATCGTGTACCATGGAGATA
66 AGCCGCAACGACGAATCTTGTACCATGGAGATA
* * * * *** *
29543537 TAGAGGGAAAGGTTAAAGCTGCAATGGTGAACCTTATACCTTAGAAAAAAAATAGGAAAGATTGA
1 TGGAGGGAAAGGTTGAAGCCGCAATGGCGAACCTTATACCTTAGAAAAGTGATGGGAAAGATTGA
* *
29543602 AGTCGCAACGACGAATCTTGTACCACGGAGATA
66 AGCCGCAACGACGAATCTTGTACCATGGAGATA
* * * ** *
29543635 TGGAGGGAAATGTTGAAGCGGCAACGGCGAACCTTATACCTTAGTGAGGTGATGGGAAAGATTGA
1 TGGAGGGAAAGGTTGAAGCCGCAATGGCGAACCTTATACCTTAGAAAAGTGATGGGAAAGATTGA
* ** *
29543700 AGCCGCAATGGTGAATCGTGTACCATGGAGATA
66 AGCCGCAACGACGAATCTTGTACCATGGAGATA
* * * * * *
29543733 TGGAGGGAAAAGTTAAAGCTGCAATGGTGAACCTTATACCTTAGAAAAATAATGGGAAAGATTGA
1 TGGAGGGAAAGGTTGAAGCCGCAATGGCGAACCTTATACCTTAGAAAAGTGATGGGAAAGATTGA
* * *
29543798 AGCTGTAAC-AGCGAATCGTGTACCATGGAGATA
66 AGCCGCAACGA-CGAATCTTGTACCATGGAGATA
* ** * *
29543831 TGGAGGGAAAGGTTAAAGCCATAATGGCGAACCTTATACCTTAGAGATGTGATGGGAAAGATTGA
1 TGGAGGGAAAGGTTGAAGCCGCAATGGCGAACCTTATACCTTAGAAAAGTGATGGGAAAGATTGA
** *
29543896 AGCTTCAACGACGAATCTTATACC
66 AGCCGCAACGACGAATCTTGTACC
29543920 CTAAAGTTGA
Statistics
Matches: 807, Mismatches: 143, Indels: 31
0.82 0.15 0.03
Matches are distributed among these distances:
95 12 0.01
96 209 0.26
97 60 0.07
98 463 0.57
99 62 0.08
100 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.21
Consensus pattern (98 bp):
TGGAGGGAAAGGTTGAAGCCGCAATGGCGAACCTTATACCTTAGAAAAGTGATGGGAAAGATTGA
AGCCGCAACGACGAATCTTGTACCATGGAGATA
Found at i:29543638 original size:196 final size:194
Alignment explanation
Indices: 29542857--29543912 Score: 1438
Period size: 196 Copynumber: 5.4 Consensus size: 194
29542847 TCTACAGGTT
* * *
29542857 TGGAGGGAAAGGTTGAAGCCGCAATGGCGAACCTTTTTTCCTTAGATGTGATGGGAAAGATTGAA
1 TGGAGGGAAAGGTTGAAGCCGCAACGGCGAACC-TTATACCTTAGATGTGATGGGAAAGATTGAA
* * * * * * *
29542922 GCCGTAACGGTGAATCATTTACCATGGAGATATGGAGGGAAAGGTTGAAGC-GTAATGACGAACC
65 GCCGCAACGGCGAATCGTGTACCATGGAGATATGGAGGGAAAGGTTAAAGCTGCAATGGCGAACC
*
29542986 TTATACCTTAG-AAAATAATGGGAAAGATTGAAGCCGCAACGACGAATCTTGCACCACGGAGATA
130 TTATACCTTAGAAAAATAATGGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCACGGAGATA
* * * *
29543050 TGGAAGGAAAGGATAAAGCCGCAACGGCGAACCTTATACCTTAGATGTGATGGGAAAAATTGAAG
1 TGGAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTATACCTTAGATGTGATGGGAAAGATTGAAG
* * * * *
29543115 CCGCAACGACGAATCGTGTACCATGAAGATATGGAGGGAAAGGTTCAAGCCGCAATGACGAACCT
66 CCGCAACGGCGAATCGTGTACCATGGAGATATGGAGGGAAAGGTTAAAGCTGCAATGGCGAACCT
* *
29543180 TATACCTTAGAAAAATAATGGGAAAGATTGAAGCCGCAACGACGAATCTTGCACCACAGAGATA
131 TATACCTTAGAAAAATAATGGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCACGGAGATA
* * * *
29543244 TGGAGGAAAAGGTTGAAGCCTCAATGGCAAACCTTATACCTTAGATGTGATGGGAAAGATTGAAG
1 TGGAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTATACCTTAGATGTGATGGGAAAGATTGAAG
* * * * *
29543309 CCGCAACGGCGAATCGTGTACTATGGAGATATAGAGAGAAAGGTTGAAG-TCACAAACT-GCGAA
66 CCGCAACGGCGAATCGTGTACCATGGAGATATGGAGGGAAAGGTTAAAGCT-GC-AA-TGGCGAA
* *
29543372 CCCTATACCTTAGAAAAATAATGGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCACTGAGA
128 CCTTATACCTTAGAAAAATAATGGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCACGGAGA
29543437 TA
193 TA
* * *
29543439 TGGAGGGAAAGGTTGAAGCTGCAACGGTGAACCTTATACCTTAGTGAGGTGATGGGAAAGATTGA
1 TGGAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTATACCTTA--GATGTGATGGGAAAGATTGA
* * *
29543504 AGCCGCAATGGCGAATCGTGTACCATGGAGATATAGAGGGAAAGGTTAAAGCTGCAATGGTGAAC
64 AGCCGCAACGGCGAATCGTGTACCATGGAGATATGGAGGGAAAGGTTAAAGCTGCAATGGCGAAC
* * *
29543569 CTTATACCTTAGAAAAAAAATAGGAAAGATTGAAGTCGCAACGACGAATCTTGTACCACGGAGAT
129 CTTATACCTTAGAAAAATAATGGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCACGGAGAT
29543634 A
194 A
* * *
29543635 TGGAGGGAAATGTTGAAGCGGCAACGGCGAACCTTATACCTTAGTGAGGTGATGGGAAAGATTGA
1 TGGAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTATACCTTA--GATGTGATGGGAAAGATTGA
* * * *
29543700 AGCCGCAATGGTGAATCGTGTACCATGGAGATATGGAGGGAAAAGTTAAAGCTGCAATGGTGAAC
64 AGCCGCAACGGCGAATCGTGTACCATGGAGATATGGAGGGAAAGGTTAAAGCTGCAATGGCGAAC
* * * *
29543765 CTTATACCTTAGAAAAATAATGGGAAAGATTGAAGCTGTAAC-AGCGAATCGTGTACCATGGAGA
129 CTTATACCTTAGAAAAATAATGGGAAAGATTGAAGCCGCAACGA-CGAATCTTGTACCACGGAGA
29543829 TA
193 TA
* ** *
29543831 TGGAGGGAAAGGTTAAAGCCATAATGGCGAACCTTATACCTTAGAGATGTGATGGGAAAGATTGA
1 TGGAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTATACCTT--AGATGTGATGGGAAAGATTGA
** *
29543896 AGCTTCAACGACGAATC
64 AGCCGCAACGGCGAATC
29543913 TTATACCCTA
Statistics
Matches: 772, Mismatches: 79, Indels: 21
0.89 0.09 0.02
Matches are distributed among these distances:
192 72 0.09
193 52 0.07
194 153 0.20
195 109 0.14
196 317 0.41
197 67 0.09
198 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.21
Consensus pattern (194 bp):
TGGAGGGAAAGGTTGAAGCCGCAACGGCGAACCTTATACCTTAGATGTGATGGGAAAGATTGAAG
CCGCAACGGCGAATCGTGTACCATGGAGATATGGAGGGAAAGGTTAAAGCTGCAATGGCGAACCT
TATACCTTAGAAAAATAATGGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCACGGAGATA
Found at i:29545733 original size:58 final size:57
Alignment explanation
Indices: 29545638--29545840 Score: 162
Period size: 58 Copynumber: 3.4 Consensus size: 57
29545628 TATGTTTTGC
* ** * *
29545638 CCCCAAACTTTCCAAAAATTTAAATTTGGCCTTCAAACTTTGTAGAAATTAT-ATTTT-A
1 CCCCAAACTTTCTAAAAATTT--ATTTGGCCCACAAACTTTCTAAAAATT-TCATTTTAA
*
29545696 GCCCAAACTTTCTAAAAATTGTATTATGGCCCACAAACTTTCTAAAAATTTCATTTTAA
1 CCCCAAACTTTCTAAAAATT-TATT-TGGCCCACAAACTTTCTAAAAATTTCATTTTAA
** * *
29545755 CCCCTAAACTTTCTAAAAATTATATTTTAATCCC-TAAACTTT-TAAAAATTACATTTTAA
1 CCCC-AAACTTTCTAAAAATT-TA-TTT-GGCCCACAAACTTTCTAAAAATTTCATTTTAA
* * *
29545814 CACCTAAACTTTCCAAAATTTTGATTT
1 C-CCCAAACTTTCTAAAAATTT-ATTT
29545841 TAACCCTATT
Statistics
Matches: 121, Mismatches: 15, Indels: 18
0.79 0.10 0.12
Matches are distributed among these distances:
57 4 0.03
58 47 0.39
59 37 0.31
60 28 0.23
61 5 0.04
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.38
Consensus pattern (57 bp):
CCCCAAACTTTCTAAAAATTTATTTGGCCCACAAACTTTCTAAAAATTTCATTTTAA
Done.