Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 94 of 378
Found at i:25519848 original size:17 final size:15
Alignment explanation
Indices: 25519823--25519861 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
25519813 GAAACAAGGG
25519823 AAGGAAAGAAGGAAAAA
1 AAGGAAAGAA--AAAAA
*
25519840 AAGGGAAGAAAAAAA
1 AAGGAAAGAAAAAAA
25519855 AAGGAAA
1 AAGGAAA
25519862 AATTGGGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 11 0.55
17 9 0.45
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (15 bp):
AAGGAAAGAAAAAAA
Found at i:25521248 original size:2 final size:2
Alignment explanation
Indices: 25521241--25521270 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25521231 TGAATAATTG
25521241 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25521271 TGAATTGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25521612 original size:45 final size:48
Alignment explanation
Indices: 25521516--25521635 Score: 129
Period size: 45 Copynumber: 2.5 Consensus size: 48
25521506 TAGGCACTTA
* * *
25521516 TGTGTCGACTACTGTTACTGTTACCGTTACTATTACCGATTCGGCATTTTG
1 TGTGTCGAATACTGTTACTGTTACCGTTA-TATT--CGATTCAGCACTTTG
* *
25521567 TGTGTCGATTACTGTTACTGTTACCG-T-TATT-GATTTAGCACTTTG
1 TGTGTCGAATACTGTTACTGTTACCGTTATATTCGATTCAGCACTTTG
* *
25521612 TATGTTGAATACTGTTACTGTTAC
1 TGTGTCGAATACTGTTACTGTTAC
25521636 TGCTTCGGAT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
45 32 0.52
48 4 0.06
50 1 0.02
51 25 0.40
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.44
Consensus pattern (48 bp):
TGTGTCGAATACTGTTACTGTTACCGTTATATTCGATTCAGCACTTTG
Found at i:25521873 original size:18 final size:18
Alignment explanation
Indices: 25521815--25522005 Score: 113
Period size: 18 Copynumber: 10.6 Consensus size: 18
25521805 CAACTGATTA
*
25521815 TTACTGAATAATTGACTG
1 TTACTGGATAATTGACTG
*
25521833 TTACCGGATAATTGACTG
1 TTACTGGATAATTGACTG
25521851 TTACTGGAT-ATTAGACTG
1 TTACTGGATAATT-GACTG
* * * *
25521869 TTACTGAATAACTGAATA
1 TTACTGGATAATTGACTG
* *
25521887 TTACTGAATAATTGA-TCA
1 TTACTGGATAATTGACT-G
* * * *
25521905 TTACAGAATAACTGATTG
1 TTACTGGATAATTGACTG
** *
25521923 TCGCTGAATGAA-TGACTG
1 TTACTGGAT-AATTGACTG
* * *
25521941 TTACTGAATAACTTAATTG
1 TTACTGGATAA-TTGACTG
* *
25521960 TTACTGAAT-ATCTGA-TT
1 TTACTGGATAAT-TGACTG
*
25521977 TTACTGAATAATTGACTG
1 TTACTGGATAATTGACTG
25521995 TTACTGGATAA
1 TTACTGGATAA
25522006 CCGATCAATT
Statistics
Matches: 140, Mismatches: 23, Indels: 20
0.77 0.13 0.11
Matches are distributed among these distances:
17 20 0.14
18 102 0.73
19 18 0.13
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTACTGGATAATTGACTG
Found at i:25521879 original size:54 final size:51
Alignment explanation
Indices: 25521815--25522005 Score: 159
Period size: 54 Copynumber: 3.6 Consensus size: 51
25521805 CAACTGATTA
* * *
25521815 TTACTGAATAATTGACTGTTACCGGATAATTGACTGTTACTGGATATTAGACTG
1 TTACTGAATAATTGACTGTTACTGAATAATTGA-TGTTACTGAATATT-GA-TG
* * * * * *
25521869 TTACTGAATAACTGAATATTACTGAATAATTGATCATTACAGAATAACTGATTG
1 TTACTGAATAATTGACTGTTACTGAATAATTGAT-GTTACTGAAT-ATTGA-TG
** * *
25521923 TCGCTGAATGAA-TGACTGTTACTGAATAACTTAATTGTTACTGAATATCTGATT
1 TTACTGAAT-AATTGACTGTTACTGAATAA-TTGA-TGTTACTGAATAT-TGATG
*
25521977 TTACTGAATAATTGACTGTTACTGGATAA
1 TTACTGAATAATTGACTGTTACTGAATAA
25522006 CCGATCAATT
Statistics
Matches: 108, Mismatches: 22, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
53 3 0.03
54 86 0.80
55 18 0.17
56 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (51 bp):
TTACTGAATAATTGACTGTTACTGAATAATTGATGTTACTGAATATTGATG
Found at i:25521891 original size:36 final size:36
Alignment explanation
Indices: 25521806--25522005 Score: 158
Period size: 36 Copynumber: 5.6 Consensus size: 36
25521796 GGTATAAAAC
* * * *
25521806 AACTGATTATTACTGAATAATTGACTGTTACCGGAT
1 AACTGAATGTTACTGAATAATTGACTGTTACTGAAT
* * *
25521842 AATTGACTGTTACTGGAT-ATTAGACTGTTACTGAAT
1 AACTGAATGTTACTGAATAATT-GACTGTTACTGAAT
* * *
25521878 AACTGAATATTACTGAATAATTGA-TCATTACAGAAT
1 AACTGAATGTTACTGAATAATTGACT-GTTACTGAAT
* **
25521914 AACTGATTGTCGCTGAATGAA-TGACTGTTACTGAAT
1 AACTGAATGTTACTGAAT-AATTGACTGTTACTGAAT
* *
25521950 AACTTAATTGTTACTGAAT-ATCTGA-TTTTACTGAAT
1 AACTGAA-TGTTACTGAATAAT-TGACTGTTACTGAAT
* * *
25521986 AATTGACTGTTACTGGATAA
1 AACTGAATGTTACTGAATAA
25522006 CCGATCAATT
Statistics
Matches: 128, Mismatches: 27, Indels: 18
0.74 0.16 0.10
Matches are distributed among these distances:
35 15 0.12
36 95 0.74
37 18 0.14
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (36 bp):
AACTGAATGTTACTGAATAATTGACTGTTACTGAAT
Found at i:25523727 original size:6 final size:6
Alignment explanation
Indices: 25523679--25523737 Score: 57
Period size: 6 Copynumber: 9.8 Consensus size: 6
25523669 AAGTCTTCAA
* * * * *
25523679 AAAAAA AAAAAG AAAAAT AAAATT AAAATT AAAAAT AATAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
25523727 AATAAA- AAAAA
1 AA-AAAT AAAAA
25523738 AACTCAAAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
5 3 0.07
6 40 0.87
7 3 0.07
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:25527788 original size:18 final size:18
Alignment explanation
Indices: 25527757--25527859 Score: 116
Period size: 18 Copynumber: 5.7 Consensus size: 18
25527747 AGTTTCATTT
*
25527757 AGTAACATTCAGTTATTC
1 AGTAACAATCAGTTATTC
* *
25527775 AGTAGCAATTAGTTATTC
1 AGTAACAATCAGTTATTC
* **
25527793 AGTAACAATCATTTGCTC
1 AGTAACAATCAGTTATTC
*
25527811 AGTAGCAATCAGTTATTC
1 AGTAACAATCAGTTATTC
* *
25527829 AGTAACATTCAATTATTC
1 AGTAACAATCAGTTATTC
*
25527847 AGTAACAGTCAGT
1 AGTAACAATCAGT
25527860 CTTTCAGACT
Statistics
Matches: 68, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (18 bp):
AGTAACAATCAGTTATTC
Found at i:25527866 original size:36 final size:36
Alignment explanation
Indices: 25527757--25527859 Score: 134
Period size: 36 Copynumber: 2.9 Consensus size: 36
25527747 AGTTTCATTT
* *
25527757 AGTAACATTCAGTTATTCAGTAGCAATTAGTTATTC
1 AGTAACATTCAATTATTCAGTAGCAATCAGTTATTC
* * **
25527793 AGTAACAATCATTTGCTCAGTAGCAATCAGTTATTC
1 AGTAACATTCAATTATTCAGTAGCAATCAGTTATTC
* *
25527829 AGTAACATTCAATTATTCAGTAACAGTCAGT
1 AGTAACATTCAATTATTCAGTAGCAATCAGT
25527860 CTTTCAGACT
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (36 bp):
AGTAACATTCAATTATTCAGTAGCAATCAGTTATTC
Found at i:25527917 original size:8 final size:8
Alignment explanation
Indices: 25527904--25527928 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
25527894 TCGAAAACTG
25527904 ACGGATTC
1 ACGGATTC
25527912 ACGGATTC
1 ACGGATTC
25527920 ACGGATTC
1 ACGGATTC
25527928 A
1 A
25527929 ACCATCACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (8 bp):
ACGGATTC
Found at i:25534969 original size:20 final size:21
Alignment explanation
Indices: 25534939--25534984 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
25534929 TAAGACATGG
*
25534939 CAGGTGGTGGTGGGCCTGCCA
1 CAGGCGGTGGTGGGCCTGCCA
25534960 -AGGCGGTGGTGGGCCTGCCA
1 CAGGCGGTGGTGGGCCTGCCA
25534980 CAGGC
1 CAGGC
25534985 TGCACTGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.11, C:0.26, G:0.48, T:0.15
Consensus pattern (21 bp):
CAGGCGGTGGTGGGCCTGCCA
Found at i:25535149 original size:3 final size:3
Alignment explanation
Indices: 25535121--25535183 Score: 53
Period size: 3 Copynumber: 22.0 Consensus size: 3
25535111 TTTCAGGTAG
* *
25535121 GAA GAAA GAA GGA GAA GAA -AA AAA GAA G-A GAA GAA GAA -AA G-A
1 GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
25535163 CAA GAA GAA GAA GAA GGA GAA
1 GAA GAA GAA GAA GAA GAA GAA
25535184 AGAGGCGGCA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
2 7 0.15
3 38 0.79
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:25535157 original size:19 final size:20
Alignment explanation
Indices: 25535122--25535178 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 20
25535112 TTCAGGTAGG
25535122 AAGAAAGAAG-G-AGAAGAA
1 AAGAAAGAAGAGAAGAAGAA
25535140 AA-AAAGAAGAGAAGAAGAA
1 AAGAAAGAAGAGAAGAAGAA
25535159 AAGACAAGAAGAAGAAGAAG
1 AAGA-AAGAAG-AGAAGAAG
25535179 GAGAAAGAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.21
18 3 0.09
19 9 0.26
20 1 0.03
21 6 0.18
22 8 0.24
ACGTcount: A:0.68, C:0.02, G:0.30, T:0.00
Consensus pattern (20 bp):
AAGAAAGAAGAGAAGAAGAA
Found at i:25535172 original size:16 final size:16
Alignment explanation
Indices: 25535121--25535174 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
25535111 TTTCAGGTAG
25535121 GAAG-AAAGAAGGAGAA
1 GAAGAAAAGAA-GAGAA
*
25535137 GAAAAAAAGAAGAGAA
1 GAAGAAAAGAAGAGAA
25535153 GAAGAAAAGACA-AGAA
1 GAAGAAAAGA-AGAGAA
25535169 GAAGAA
1 GAAGAA
25535175 GAAGGAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 27 0.79
17 7 0.21
ACGTcount: A:0.69, C:0.02, G:0.30, T:0.00
Consensus pattern (16 bp):
GAAGAAAAGAAGAGAA
Found at i:25535806 original size:148 final size:147
Alignment explanation
Indices: 25535628--25536148 Score: 652
Period size: 148 Copynumber: 3.6 Consensus size: 147
25535618 GTGGGTTTTT
25535628 TACT-AAATAATAT-AAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTCGAGAAT-
1 TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTCGAGAATA
*
25535690 AAAAAATACAAA-AAATGGCCAAAATCAGGATTTTTTACTAAATTAATATAAAAAATACTAAAAT
66 AAAAAATACAAACAAAGGGCCAAAATCAGGATTTTTTACTAAATTAATAT-AAAAA-ACTAAAAT
25535754 AATACATTTGAAACACTATG
129 AATACATTTGAAACA-TATG
* *
25535774 TACTAAAATAATATAAAAAATAAAATATGAAAATAGTATATTTTAAAAAATAAAATTAGAGAATA
1 TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTCGAGAATA
* * * *
25535839 AAAAAATAGAAACAAAGGGCTAAAATTCAGGGTTTTTTTACTAAATTAATAT-AAAAA-TAAAGT
66 AAAAAATACAAACAAAGGGCCAAAA-TCA-GGATTTTTTACTAAATTAATATAAAAAACTAAAAT
25535902 AATACATTTG----A-A--
129 AATACATTTGAAACATATG
* * * * *
25535914 -ACTAAAATAATATAAAAACTAAAATA-AAAAATAGTATATTTTAGAGAATAAAA-TC-CG---A
1 TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTCGAGAATA
* * *
25535972 AAAAAATACAAAACAAAGGGGCAAAATCAGAATTTTTTATTAAATT-ATATAAAAAACTAAAATA
66 AAAAAATAC-AAACAAAGGGCCAAAATCAGGATTTTTTACTAAATTAATATAAAAAACTAAAATA
25536036 ATACATTTGAAACATTATG
130 ATACATTTGAAACA-TATG
* * * *
25536055 TACTAAAGTAATATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCTAAAAT
1 TACTAAAATAATAT-AAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTCGAGAAT
25536120 AAAAAAATACAAACAAAGGGCCAAAATCA
65 AAAAAAATACAAACAAAGGGCCAAAATCA
25536149 TCGAACAGAA
Statistics
Matches: 321, Mismatches: 29, Indels: 48
0.81 0.07 0.12
Matches are distributed among these distances:
131 4 0.01
132 19 0.06
133 27 0.08
134 14 0.04
136 1 0.00
137 2 0.01
138 24 0.07
139 26 0.08
142 13 0.04
143 12 0.04
144 25 0.08
145 1 0.00
146 4 0.01
147 9 0.03
148 80 0.25
149 22 0.07
150 14 0.04
151 3 0.01
152 21 0.07
ACGTcount: A:0.58, C:0.07, G:0.08, T:0.27
Consensus pattern (147 bp):
TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTCGAGAATA
AAAAAATACAAACAAAGGGCCAAAATCAGGATTTTTTACTAAATTAATATAAAAAACTAAAATAA
TACATTTGAAACATATG
Found at i:25536059 original size:281 final size:286
Alignment explanation
Indices: 25535632--25536146 Score: 789
Period size: 282 Copynumber: 1.8 Consensus size: 286
25535622 GTTTTTTACT
*
25535632 AAATAATATAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTCGAGAATAAAAAAT
1 AAATAATATAAAAATAAAATACAAAAATAGTATATTTTAAAAAATAAAATTCGAGAATAAAAAAT
* *
25535697 ACAAAAAATGGCCAAAATCAGGATTTTTTACTAAATTAATATAAAAAATACTAAAATAATACATT
66 ACAAAAAAGGGCCAAAATCAGAATTTTTTACTAAATTAATATAAAAAATACTAAAATAATACATT
*
25535762 TGAAACACTATGTACTAAAATAATAT-AAAAAATAAAATATGAAAATAGTATATTTTAAAAAATA
131 TGAAACACTATGTACTAAAATAATATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATA
* *
25535826 AAAT-TAGAGAATAAAAAAATAGAAACAAAGGGCTAAAATTCAGGGTTTTTTTACTAAATTAATA
196 AAATCTA-A-AATAAAAAAATACAAACAAAGGGCCAAAATTCAGGGTTTTTTTACTAAATTAATA
25535890 TAAAAATAAAGTAATACATTTGAAACTA
259 TAAAAATAAAGTAATACATTTGAAACTA
* * *
25535918 AAATAATATAAAAACTAAAATA-AAAAATAGTATATTTTAGAGAATAAAA-TC-CG-A-AAAAAA
1 AAATAATATAAAAA-TAAAATACAAAAATAGTATATTTTAAAAAATAAAATTCGAGAATAAAAAA
* *
25535978 TACAAAACAAAGGGGCAAAATCAGAATTTTTTATTAAATT-ATAT-AAAAA-ACTAAAATAATAC
65 TAC-AAA-AAAGGGCCAAAATCAGAATTTTTTACTAAATTAATATAAAAAATACTAAAATAATAC
* *
25536040 ATTTGAAACATTATGTACTAAAGTAATATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAA
128 ATTTGAAACACTATGTACTAAAATAATATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAA
25536105 ATAAAATCCTAAAATAAAAAAATACAAACAAAGGGCCAAAAT
193 ATAAAAT-CTAAAATAAAAAAATACAAACAAAGGGCCAAAAT
25536147 CATCGAACAG
Statistics
Matches: 210, Mismatches: 13, Indels: 16
0.88 0.05 0.07
Matches are distributed among these distances:
281 40 0.19
282 83 0.40
283 9 0.04
284 31 0.15
285 2 0.01
286 38 0.18
287 7 0.03
ACGTcount: A:0.58, C:0.07, G:0.08, T:0.27
Consensus pattern (286 bp):
AAATAATATAAAAATAAAATACAAAAATAGTATATTTTAAAAAATAAAATTCGAGAATAAAAAAT
ACAAAAAAGGGCCAAAATCAGAATTTTTTACTAAATTAATATAAAAAATACTAAAATAATACATT
TGAAACACTATGTACTAAAATAATATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATA
AAATCTAAAATAAAAAAATACAAACAAAGGGCCAAAATTCAGGGTTTTTTTACTAAATTAATATA
AAAATAAAGTAATACATTTGAAACTA
Found at i:25537864 original size:15 final size:15
Alignment explanation
Indices: 25537844--25537873 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25537834 TAATAAAAAG
*
25537844 GAAAAATAAAGCTAA
1 GAAAAAGAAAGCTAA
25537859 GAAAAAGAAAGCTAA
1 GAAAAAGAAAGCTAA
25537874 AATCAACCAT
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:0.67, C:0.07, G:0.17, T:0.10
Consensus pattern (15 bp):
GAAAAAGAAAGCTAA
Found at i:25546880 original size:46 final size:48
Alignment explanation
Indices: 25546813--25547035 Score: 245
Period size: 47 Copynumber: 4.8 Consensus size: 48
25546803 TGTAACCCGC
* *
25546813 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG-G-C-GTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGAGCCAGTT-ACAT
*
25546859 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA-GCC-AGTTACAT
*
25546909 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA-GCC-AGTTACAT
* *
25546956 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA--CA-TTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGAGCCAGTT-ACAT
*
25546999 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
25547036 TGCTCAACCA
Statistics
Matches: 160, Mismatches: 8, Indels: 18
0.86 0.04 0.10
Matches are distributed among these distances:
42 2 0.01
43 4 0.03
44 2 0.01
45 2 0.01
46 63 0.39
47 76 0.47
48 3 0.02
49 2 0.01
50 3 0.02
51 3 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (48 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGAGCCAGTTACAT
Found at i:25546921 original size:27 final size:27
Alignment explanation
Indices: 25546891--25546969 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 27
25546881 CTCAACGAGT
25546891 TCGGATGCCTAGTTACATCTCACGAAC
1 TCGGATGCCTAGTTACATCTCACGAAC
* **
25546918 TCGGA---CTCA---AC-TC-AACGAGT
1 TCGGATGCCT-AGTTACATCTCACGAAC
25546938 TCGGATGCCTAGTTACATCTCACGAAC
1 TCGGATGCCTAGTTACATCTCACGAAC
25546965 TCGGA
1 TCGGA
25546970 CTCAACTCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 18
0.61 0.10 0.30
Matches are distributed among these distances:
20 9 0.24
21 2 0.05
22 3 0.08
23 2 0.05
24 2 0.05
25 3 0.08
26 2 0.05
27 14 0.38
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (27 bp):
TCGGATGCCTAGTTACATCTCACGAAC
Found at i:25546935 original size:47 final size:47
Alignment explanation
Indices: 25546867--25547038 Score: 246
Period size: 47 Copynumber: 3.7 Consensus size: 47
25546857 ATCCATAAGT
25546867 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
25546914 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
* * *
25546961 GAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-TCA-C
25547007 GAACTCGGACTCAACTCAACGAGTTCGGATGC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGC
25547039 TCAACCATCC
Statistics
Matches: 115, Mismatches: 3, Indels: 12
0.88 0.02 0.09
Matches are distributed among these distances:
42 2 0.02
43 4 0.03
44 2 0.02
45 2 0.02
46 29 0.25
47 76 0.66
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:25549049 original size:18 final size:17
Alignment explanation
Indices: 25549007--25549050 Score: 79
Period size: 17 Copynumber: 2.5 Consensus size: 17
25548997 TGGTAAAGGA
25549007 TACTTATTCTTGATAGT
1 TACTTATTCTTGATAGT
25549024 TACTTATTCTTGATAGT
1 TACTTATTCTTGATAGT
25549041 TACCTTATTC
1 TA-CTTATTC
25549051 AGCTATTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 19 0.73
18 7 0.27
ACGTcount: A:0.23, C:0.16, G:0.09, T:0.52
Consensus pattern (17 bp):
TACTTATTCTTGATAGT
Found at i:25555038 original size:18 final size:18
Alignment explanation
Indices: 25555017--25555055 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
25555007 CGAGCCATAA
*
25555017 CCAGATCCCAAGCCTGAG
1 CCAGAGCCCAAGCCTGAG
25555035 CCAGAGCCCAAGCCTGAG
1 CCAGAGCCCAAGCCTGAG
25555053 CCA
1 CCA
25555056 CAGTCGGAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.41, G:0.23, T:0.08
Consensus pattern (18 bp):
CCAGAGCCCAAGCCTGAG
Found at i:25555667 original size:38 final size:38
Alignment explanation
Indices: 25555624--25555715 Score: 143
Period size: 38 Copynumber: 2.4 Consensus size: 38
25555614 TTGTAATATA
*
25555624 AATTGGAACAAACTTTAAATACATTACAACATTAATCT
1 AATTGGAACAAACTTTAAATACATTAAAACATTAATCT
25555662 AATTGGAACATTAA--TTAAATACATTAAAACATTAATCT
1 AATTGGAACA--AACTTTAAATACATTAAAACATTAATCT
25555700 AATTGGAACAAACTTT
1 AATTGGAACAAACTTT
25555716 GCAATATAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
36 2 0.04
38 45 0.92
40 2 0.04
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (38 bp):
AATTGGAACAAACTTTAAATACATTAAAACATTAATCT
Found at i:25555671 original size:17 final size:17
Alignment explanation
Indices: 25555651--25555709 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
25555641 AATACATTAC
25555651 AACATTAATCTAATTGG
1 AACATTAATCTAATTGG
* **
25555668 AACATTAATTAAATACATTAA
1 AACATTAA-T--CTA-ATTGG
25555689 AACATTAATCTAATTGG
1 AACATTAATCTAATTGG
25555706 AACA
1 AACA
25555710 AACTTTGCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 15 0.47
18 3 0.09
20 3 0.09
21 11 0.34
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (17 bp):
AACATTAATCTAATTGG
Found at i:25556936 original size:55 final size:55
Alignment explanation
Indices: 25556870--25556979 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
25556860 ATGCAAATAT
25556870 TATCGTTTCTAATAACATACCTTCGCAGGTTGGTAAGGAAGAATTCCCACAATTC
1 TATCGTTTCTAATAACATACCTTCGCAGGTTGGTAAGGAAGAATTCCCACAATTC
25556925 TATCGTTTCTAATAACATACCTTCGCAGGTTGGTAAGGAAGAATTCCCACAATTC
1 TATCGTTTCTAATAACATACCTTCGCAGGTTGGTAAGGAAGAATTCCCACAATTC
25556980 CATGTTCTCC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (55 bp):
TATCGTTTCTAATAACATACCTTCGCAGGTTGGTAAGGAAGAATTCCCACAATTC
Found at i:25559804 original size:26 final size:27
Alignment explanation
Indices: 25559768--25559829 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 27
25559758 CATCCACCTC
25559768 TATATTTTTAT-TTTTTAAGCTTTTAT
1 TATATTTTTATATTTTTAAGCTTTTAT
*
25559794 TATATTTTTATATTTTTCAGCTTTTAT
1 TATATTTTTATATTTTTAAGCTTTTAT
*
25559821 T-TTTTTTTA
1 TATATTTTTA
25559830 CTGTTTATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 18 0.55
27 15 0.45
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (27 bp):
TATATTTTTATATTTTTAAGCTTTTAT
Found at i:25559842 original size:19 final size:19
Alignment explanation
Indices: 25559817--25559858 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
25559807 TTTTCAGCTT
*
25559817 TTAT-TTTTTTTT-ACTGT
1 TTATGTTTTTTTTAACTGA
25559834 TTATGTTTTTTTTAACTGA
1 TTATGTTTTTTTTAACTGA
25559853 TTATGT
1 TTATGT
25559859 CCGAAACCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.18
18 8 0.36
19 10 0.45
ACGTcount: A:0.17, C:0.05, G:0.10, T:0.69
Consensus pattern (19 bp):
TTATGTTTTTTTTAACTGA
Found at i:25565625 original size:16 final size:17
Alignment explanation
Indices: 25565604--25565637 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
25565594 AATTAGAGAA
25565604 TTCTATTTAA-TTCTAT
1 TTCTATTTAATTTCTAT
25565620 TTCTATTTAATTTCTAT
1 TTCTATTTAATTTCTAT
25565637 T
1 T
25565638 AAATCCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (17 bp):
TTCTATTTAATTTCTAT
Found at i:25566199 original size:21 final size:23
Alignment explanation
Indices: 25566157--25566212 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
25566147 TTTATTTATC
25566157 TATTTA-ATATTATATTCAA-TT
1 TATTTATATATTATATTCAATTT
*
25566178 TATTTATATATTATA-TCTATTT
1 TATTTATATATTATATTCAATTT
25566200 TATTATATATATT
1 TATT-TATATATT
25566213 CTAAATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 9 0.29
22 14 0.45
23 8 0.26
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTTATATATTATATTCAATTT
Found at i:25566221 original size:23 final size:22
Alignment explanation
Indices: 25566176--25566225 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
25566166 TTATATTCAA
**
25566176 TTTATTTATATATTATATCTAT
1 TTTATTTATATATTATAAATAT
*
25566198 TTTATTATATATATTCTAAATAT
1 TTTATT-TATATATTATAAATAT
25566221 TTTAT
1 TTTAT
25566226 ATCTAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTATTTATATATTATAAATAT
Found at i:25566232 original size:15 final size:15
Alignment explanation
Indices: 25566207--25566254 Score: 87
Period size: 15 Copynumber: 3.1 Consensus size: 15
25566197 TTTTATTATA
25566207 TATATTCTAAATATTT
1 TATA-TCTAAATATTT
25566223 TATATCTAAATATTT
1 TATATCTAAATATTT
25566238 TATATCTAAATATTT
1 TATATCTAAATATTT
25566253 TA
1 TA
25566255 GTCTTTTGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 28 0.88
16 4 0.12
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATCTAAATATTT
Found at i:25568245 original size:17 final size:17
Alignment explanation
Indices: 25568220--25568253 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
25568210 TTTAGAAATT
25568220 GTTGATTAGAATCATTA
1 GTTGATTAGAATCATTA
*
25568237 GTTGGTTAGAATCATTA
1 GTTGATTAGAATCATTA
25568254 TTTTTGGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (17 bp):
GTTGATTAGAATCATTA
Found at i:25573129 original size:20 final size:20
Alignment explanation
Indices: 25573104--25573176 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 20
25573094 ATTCCAAAAA
25573104 TAATATTATTTTAATAAATT
1 TAATATTATTTTAATAAATT
25573124 TAATATTTATCTTGTAAATAAATAT
1 TAATA-TTAT-TT-T-AATAAAT-T
* *
25573149 T-CTATTAATTTAATAAGATT
1 TAATATTATTTTAATAA-ATT
25573169 TAATATTA
1 TAATATTA
25573177 AAGTGATTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
20 12 0.28
21 12 0.28
22 4 0.09
23 4 0.09
24 9 0.21
25 2 0.05
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (20 bp):
TAATATTATTTTAATAAATT
Found at i:25573561 original size:20 final size:20
Alignment explanation
Indices: 25573536--25573576 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
25573526 AGATAACAAG
25573536 ACCAAGATTTTGTTTTGGAA
1 ACCAAGATTTTGTTTTGGAA
* *
25573556 ACCAAGTTTTTGTTTTTGAA
1 ACCAAGATTTTGTTTTGGAA
25573576 A
1 A
25573577 ATTTTTCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (20 bp):
ACCAAGATTTTGTTTTGGAA
Found at i:25574881 original size:5 final size:5
Alignment explanation
Indices: 25574871--25574898 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
25574861 CTGTGTGTTC
25574871 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
25574899 CACAAATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:25578965 original size:29 final size:29
Alignment explanation
Indices: 25578885--25578965 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 29
25578875 GAAGAGGTGG
* * *
25578885 AGAACTTGTTCGTTGAGAGTTCACGATGA
1 AGAACTTGTTCATTGAGAATTCGCGATGA
* * *
25578914 AGAATTTATTCATTGAGATTTCGCGATGA
1 AGAACTTGTTCATTGAGAATTCGCGATGA
25578943 AGAACTTGTTCATTGAGAATTCG
1 AGAACTTGTTCATTGAGAATTCG
25578966 TGTCAATGTG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (29 bp):
AGAACTTGTTCATTGAGAATTCGCGATGA
Found at i:25582059 original size:18 final size:20
Alignment explanation
Indices: 25582036--25582074 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
25582026 TAACTCGAAA
25582036 TTTAAAA-AAAATCGA-TTT
1 TTTAAAATAAAATCGAGTTT
*
25582054 TTTAAAATAGAATCGAGTTT
1 TTTAAAATAAAATCGAGTTT
25582074 T
1 T
25582075 ACTCCCCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 7 0.39
20 4 0.22
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTAAAATAAAATCGAGTTT
Found at i:25583924 original size:22 final size:22
Alignment explanation
Indices: 25583890--25583933 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
25583880 TACTAACATG
*
25583890 TATATATACTATATATTTTTAT
1 TATATATACTATACATTTTTAT
*
25583912 TATAT-TACGTATACGTTTTTAT
1 TATATATAC-TATACATTTTTAT
25583934 ATACGCCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.57
Consensus pattern (22 bp):
TATATATACTATACATTTTTAT
Found at i:25588460 original size:18 final size:18
Alignment explanation
Indices: 25588433--25588476 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
25588423 TGAGTTCAGA
* * *
25588433 TTTAATTTTAAATTTTTT
1 TTTAAATTTAAACTTATT
25588451 TTTAAATTTAAACTTATT
1 TTTAAATTTAAACTTATT
*
25588469 TTCAAATT
1 TTTAAATT
25588477 ATCAGTTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAAATTTAAACTTATT
Found at i:25592461 original size:8 final size:8
Alignment explanation
Indices: 25592450--25592477 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
25592440 TTATAATTGC
25592450 TAAAGGAT
1 TAAAGGAT
25592458 TAAAGGAT
1 TAAAGGAT
25592466 TAAAGGAT
1 TAAAGGAT
25592474 TAAA
1 TAAA
25592478 ATAACAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.21, T:0.25
Consensus pattern (8 bp):
TAAAGGAT
Found at i:25593649 original size:25 final size:26
Alignment explanation
Indices: 25593621--25593690 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 26
25593611 GTGAATTCTC
*
25593621 TGAAGCTAGTGTTAGCAGCATCGT-A
1 TGAAGCTAGTGTTAGCAGCATCCTGA
*
25593646 TGAAGCTAGTGTTAG-A-AATCCTGA
1 TGAAGCTAGTGTTAGCAGCATCCTGA
25593670 TCAGAAGCTAGTGTTAGCAGC
1 T--GAAGCTAGTGTTAGCAGC
25593691 CCAAATATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
23 4 0.11
24 3 0.08
25 15 0.41
26 14 0.38
27 1 0.03
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (26 bp):
TGAAGCTAGTGTTAGCAGCATCCTGA
Found at i:25600415 original size:28 final size:27
Alignment explanation
Indices: 25600375--25600443 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 27
25600365 TTTTAGAAAA
25600375 TTTTTAAACTTTTAACTTTCTTATAAAT
1 TTTTTAAA-TTTTAACTTTCTTATAAAT
* *
25600403 TTTTTAGAATTTTAACTTTTTTATATAT
1 TTTTTA-AATTTTAACTTTCTTATAAAT
25600431 TTTTTAAAATTTT
1 TTTTT-AAATTTT
25600444 TATAATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 34 0.92
29 3 0.08
ACGTcount: A:0.30, C:0.06, G:0.01, T:0.62
Consensus pattern (27 bp):
TTTTTAAATTTTAACTTTCTTATAAAT
Found at i:25600424 original size:9 final size:9
Alignment explanation
Indices: 25600375--25600529 Score: 59
Period size: 10 Copynumber: 16.6 Consensus size: 9
25600365 TTTTAGAAAA
25600375 TTTTTAAA-
1 TTTTTAAAT
* *
25600383 CTTTTAACT
1 TTTTTAAAT
25600392 TTCTTATAAAT
1 TT-TT-TAAAT
25600403 TTTTTAGAA-
1 TTTTTA-AAT
*
25600412 -TTTTAACT
1 TTTTTAAAT
25600420 TTTTTATATAT
1 TTTTTA-A-AT
*
25600431 TTTTTAAAA
1 TTTTTAAAT
25600440 TTTTTATAAT
1 TTTTTA-AAT
25600450 TTTTTAAA-
1 TTTTTAAAT
* * *
25600458 -ATATATAT
1 TTTTTAAAT
25600466 TTTTTGAAAT
1 TTTTT-AAAT
25600476 TTTTATAAAT
1 TTTT-TAAAT
* *
25600486 ATTTTGAAT
1 TTTTTAAAT
**
25600495 TTTAAAAAT
1 TTTTTAAAT
*
25600504 TATTTTGAAT
1 T-TTTTAAAT
*
25600514 TATTTTGTAAT
1 T-TTTT-AAAT
25600525 TTTTT
1 TTTTT
25600530 TTTAGAGAGA
Statistics
Matches: 108, Mismatches: 24, Indels: 28
0.68 0.15 0.17
Matches are distributed among these distances:
7 5 0.05
8 11 0.10
9 29 0.27
10 45 0.42
11 18 0.17
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:25600437 original size:20 final size:19
Alignment explanation
Indices: 25600420--25600483 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
25600410 AATTTTAACT
25600420 TTTTTATATATTTTTTAAAA
1 TTTTTATA-ATTTTTTAAAA
25600440 TTTTTATAATTTTTTAAAA
1 TTTTTATAATTTTTTAAAA
* *
25600459 --TATAT-ATTTTTTGAAA
1 TTTTTATAATTTTTTAAAA
25600475 TTTTTATAA
1 TTTTTATAA
25600484 ATATTTTGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 10 0.26
17 4 0.11
18 4 0.11
19 12 0.32
20 8 0.21
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTTATAATTTTTTAAAA
Found at i:25600452 original size:28 final size:28
Alignment explanation
Indices: 25600363--25600443 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 28
25600353 CTAAAATTAT
* * *
25600363 TATTTTAGAAAATTTTTAAACTTTTAAC
1 TATTTTATAAATTTTTTAAAATTTTAAC
*
25600391 T-TTCTTATAAATTTTTTAGAATTTTAAC
1 TATT-TTATAAATTTTTTAAAATTTTAAC
* *
25600419 TTTTTTATATATTTTTTAAAATTTT
1 TATTTTATAAATTTTTTAAAATTTT
25600444 TATAATTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
27 2 0.04
28 41 0.91
29 2 0.04
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.59
Consensus pattern (28 bp):
TATTTTATAAATTTTTTAAAATTTTAAC
Found at i:25600497 original size:19 final size:20
Alignment explanation
Indices: 25600467--25600514 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
25600457 AATATATATT
*
25600467 TTTTGAAATTTTTATAAA-TA
1 TTTTG-AATTTTTAAAAATTA
25600487 TTTTGAA-TTTTAAAAATTA
1 TTTTGAATTTTTAAAAATTA
25600506 TTTTGAATT
1 TTTTGAATT
25600515 ATTTTGTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 8 0.32
19 11 0.44
20 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (20 bp):
TTTTGAATTTTTAAAAATTA
Found at i:25600752 original size:16 final size:17
Alignment explanation
Indices: 25600726--25600760 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
25600716 GCAACCAAAG
*
25600726 AGAAGTTCATGCACGTA
1 AGAAGTTCATGCACATA
25600743 AGAA-TTCATGCACATA
1 AGAAGTTCATGCACATA
25600759 AG
1 AG
25600761 TCTTGCGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (17 bp):
AGAAGTTCATGCACATA
Found at i:25609771 original size:21 final size:21
Alignment explanation
Indices: 25609747--25609788 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
25609737 AGCCAAAGAA
25609747 AAAATTGCGATTGAATCGACG
1 AAAATTGCGATTGAATCGACG
25609768 AAAATTGCGATTGAATCGACG
1 AAAATTGCGATTGAATCGACG
25609789 GCAGAGCACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (21 bp):
AAAATTGCGATTGAATCGACG
Found at i:25612467 original size:23 final size:24
Alignment explanation
Indices: 25612441--25612488 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
25612431 AAATTTAATA
*
25612441 TTTTTT-AATATAATATTTTTATT
1 TTTTTTCAATATAATATTTGTATT
* *
25612464 TTTTTTCATTATGATATTTGTATT
1 TTTTTTCAATATAATATTTGTATT
25612488 T
1 T
25612489 GTCAAAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (24 bp):
TTTTTTCAATATAATATTTGTATT
Found at i:25620533 original size:28 final size:28
Alignment explanation
Indices: 25620497--25620553 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
25620487 TGTGAATAGG
25620497 AGAGAAATTAAACCTAAGATTTGAAGAC
1 AGAGAAATTAAACCTAAGATTTGAAGAC
25620525 AGAGAAATTAAACCTAAGATTTGAAGAC
1 AGAGAAATTAAACCTAAGATTTGAAGAC
25620553 A
1 A
25620554 AACCCACTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.51, C:0.11, G:0.18, T:0.21
Consensus pattern (28 bp):
AGAGAAATTAAACCTAAGATTTGAAGAC
Found at i:25620724 original size:13 final size:13
Alignment explanation
Indices: 25620706--25620730 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25620696 AATTTTTTTA
25620706 TTTTTAATTAATG
1 TTTTTAATTAATG
25620719 TTTTTAATTAAT
1 TTTTTAATTAAT
25620731 AAATATATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:25623955 original size:67 final size:64
Alignment explanation
Indices: 25623836--25623985 Score: 160
Period size: 67 Copynumber: 2.3 Consensus size: 64
25623826 ATACAGATAG
* * * *
25623836 TATGTAGCTAGGTCACATGTATGGTGCTAAGTGCACATCATGTGTACAAGAGAGCTACAAGACAT
1 TATGTAGCTAGGTCGCATGGATGATGCTAAGTGCACACCATGTGTACAAGAGAGCTAC--GACA-
25623901 TA
63 TA
* * * **
25623903 TGATGTAGCTAGGTCGCATGGGTGAT-CTATGTGTACACCATGTAG-ACAAGAGAGCTACGGGAT
1 T-ATGTAGCTAGGTCGCATGGATGATGCTAAGTGCACACCATGT-GTACAAGAGAGCTACGACAT
25623966 A
64 A
25623967 TATGTAGCTAGGTCGCATG
1 TATGTAGCTAGGTCGCATG
25623986 TGTAGTACTA
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
63 18 0.25
64 3 0.04
65 2 0.03
67 28 0.39
68 21 0.29
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (64 bp):
TATGTAGCTAGGTCGCATGGATGATGCTAAGTGCACACCATGTGTACAAGAGAGCTACGACATA
Found at i:25624105 original size:50 final size:50
Alignment explanation
Indices: 25623975--25624159 Score: 246
Period size: 50 Copynumber: 3.7 Consensus size: 50
25623965 TATATGTAGC
* * * *
25623975 TAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACT
1 TAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T
* * * **
25624026 TCGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATAAT
1 TAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAAT
* *
25624076 TAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAAT
1 TAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAAT
*
25624126 T-GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 TAGGTCACATGTGTAGTACTAAGTGCAGGCTACTA
25624160 TGCGTACTAG
Statistics
Matches: 118, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
49 31 0.26
50 47 0.40
51 40 0.34
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (50 bp):
TAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAAT
Found at i:25625261 original size:2 final size:2
Alignment explanation
Indices: 25625254--25625280 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25625244 TCATGACATG
25625254 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
25625281 GACTAGTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25627833 original size:24 final size:24
Alignment explanation
Indices: 25627801--25627850 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
25627791 GCCTACCCGA
25627801 AACAAAAGCACATTGAGAATCATC
1 AACAAAAGCACATTGAGAATCATC
*
25627825 AACAAAAGCACATTGAGAATCGTC
1 AACAAAAGCACATTGAGAATCATC
25627849 AA
1 AA
25627851 TACACTCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.20, G:0.14, T:0.16
Consensus pattern (24 bp):
AACAAAAGCACATTGAGAATCATC
Found at i:25630759 original size:22 final size:24
Alignment explanation
Indices: 25630716--25630759 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
25630706 AAACCTTAAG
*
25630716 AAACGTGCCAAAGACAGTAGACAT
1 AAACGTGCCAAAGACAGCAGACAT
25630740 AAACGTGCC-AA-ACAGCAGAC
1 AAACGTGCCAAAGACAGCAGAC
25630760 CTAATCTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 2 0.11
24 9 0.47
ACGTcount: A:0.45, C:0.25, G:0.20, T:0.09
Consensus pattern (24 bp):
AAACGTGCCAAAGACAGCAGACAT
Found at i:25631023 original size:19 final size:19
Alignment explanation
Indices: 25630982--25631070 Score: 67
Period size: 19 Copynumber: 4.5 Consensus size: 19
25630972 CAAAATTACT
* *
25630982 AAAAATTCAAAATA-ATATT
1 AAAAATT-AAAATATTTATA
25631001 AAAAATTAAAATATTTATAA
1 AAAAATTAAAATATTTAT-A
*
25631021 AAAAATCACAAAT-TTTATA
1 AAAAATTA-AAATATTTATA
*
25631040 AAAAA-TAAAGTATAGATTATA
1 AAAAATTAAA--ATA-TTTATA
25631061 AAAAATTAAA
1 AAAAATTAAA
25631071 TTTCAAATGT
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
17 2 0.04
18 7 0.12
19 18 0.32
20 12 0.21
21 14 0.25
22 4 0.07
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAATTAAAATATTTATA
Found at i:25631634 original size:20 final size:20
Alignment explanation
Indices: 25631593--25631635 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
25631583 ATGATTGTTA
* *
25631593 ATATCAATATTTATATAAAT
1 ATATCAATATTTAAAGAAAT
25631613 ATAT-AATATTTAAAGAAGAT
1 ATATCAATATTTAAAGAA-AT
25631633 ATA
1 ATA
25631636 GTATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (20 bp):
ATATCAATATTTAAAGAAAT
Found at i:25633693 original size:42 final size:42
Alignment explanation
Indices: 25633624--25633738 Score: 101
Period size: 42 Copynumber: 2.7 Consensus size: 42
25633614 AAGTGCTTAA
* *
25633624 AGAAACCCATAAGGGTTGAA-TGAAAGCTCGTA-AGAACTGAAT
1 AGAAACCCAT-AGGGTTAAACAG-AAGCTCGTATAGAACTGAAT
* * * *
25633666 GGAAACCCATGAGGGTTTAACAGAAGCTC-AATAGAGCTGAAT
1 AGAAACCCAT-AGGGTTAAACAGAAGCTCGTATAGAACTGAAT
* *
25633708 AGAAACTCATATGAGTTAAACAGAAGCTCGT
1 AGAAACCCATA-GGGTTAAACAGAAGCTCGT
25633739 GAGAGCTAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 7
0.76 0.14 0.09
Matches are distributed among these distances:
41 2 0.03
42 55 0.95
43 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (42 bp):
AGAAACCCATAGGGTTAAACAGAAGCTCGTATAGAACTGAAT
Found at i:25636750 original size:35 final size:35
Alignment explanation
Indices: 25636698--25636769 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
25636688 ACACTTTTGC
25636698 AATAGAGTCCTTTGAATTTGTGCAACCTAAAGGAT
1 AATAGAGTCCTTTGAATTTGTGCAACCTAAAGGAT
*
25636733 AATAGAGT-CTTTCGAATTTGTGCAATCTAAAGGAT
1 AATAGAGTCCTTT-GAATTTGTGCAACCTAAAGGAT
25636768 AA
1 AA
25636770 GAAAAATGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 4 0.11
35 31 0.89
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (35 bp):
AATAGAGTCCTTTGAATTTGTGCAACCTAAAGGAT
Found at i:25641429 original size:19 final size:19
Alignment explanation
Indices: 25641384--25641422 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
25641374 TGATCCTAAT
25641384 TATA-AAAAATTAAAGAAA
1 TATATAAAAATTAAAGAAA
*
25641402 TATATAAAAA-TAAATAAA
1 TATATAAAAATTAAAGAAA
25641420 TAT
1 TAT
25641423 TCTAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (19 bp):
TATATAAAAATTAAAGAAA
Found at i:25641512 original size:16 final size:15
Alignment explanation
Indices: 25641484--25641522 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
25641474 AAAAATAAAA
*
25641484 TAAAAATTAAAAACTTT
1 TAAAAAGTAAAAA--TT
25641501 TAAAAAGTAAAAATT
1 TAAAAAGTAAAAATT
25641516 TAAAAAG
1 TAAAAAG
25641523 AATATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
17 12 0.57
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (15 bp):
TAAAAAGTAAAAATT
Found at i:25642183 original size:19 final size:19
Alignment explanation
Indices: 25642140--25642201 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
25642130 TATAATAATA
* *
25642140 TTTTTTTACAAATTTATAAC
1 TTTTTTTAAAAATTTA-AAT
*
25642160 ATTTTTTAAAAATTTAAAT
1 TTTTTTTAAAAATTTAAAT
*
25642179 TTTTTTAAAAAATTTAAAT
1 TTTTTTTAAAAATTTAAAT
25642198 TTTT
1 TTTT
25642202 AAAAGAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 23 0.62
20 14 0.38
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTTTTAAAAATTTAAAT
Found at i:25642210 original size:18 final size:17
Alignment explanation
Indices: 25642160--25642213 Score: 72
Period size: 19 Copynumber: 3.0 Consensus size: 17
25642150 AATTTATAAC
*
25642160 ATTTTTTAAAAATTTAA
1 ATTTTTAAAAAATTTAA
25642177 ATTTTTTTAAAAAATTTAA
1 A--TTTTTAAAAAATTTAA
25642196 ATTTTTAAAAGAATTTAA
1 ATTTTTAAAA-AATTTAA
25642214 TATTCCTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
17 10 0.30
18 7 0.21
19 16 0.48
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
ATTTTTAAAAAATTTAA
Found at i:25642236 original size:36 final size:34
Alignment explanation
Indices: 25642196--25642263 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 34
25642186 AAAAATTTAA
*
25642196 ATTTTT-AAAAGAATTTAATATTCCTTTTATTTTTTT
1 ATTTTTCAAAA-AAATTAA-ATT-CTTTTATTTTTTT
*
25642232 ATTTTTCAAAAAAATTAAATTTTTTTATTTTT
1 ATTTTTCAAAAAAATTAAATTCTTTTATTTTT
25642264 GTTGACATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 10 0.34
35 3 0.10
36 12 0.41
37 4 0.14
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (34 bp):
ATTTTTCAAAAAAATTAAATTCTTTTATTTTTTT
Found at i:25643898 original size:48 final size:48
Alignment explanation
Indices: 25643827--25643923 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
25643817 GGAGCCCAGT
25643827 TCAATTATACAAAGATAAACTAAGGACCTCTAGTTTTGTTGTTACTAA
1 TCAATTATACAAAGATAAACTAAGGACCTCTAGTTTTGTTGTTACTAA
25643875 TCAATTATACAAAGATAAACTAAGGACCTCTAGTTTTGTTGTTACTAA
1 TCAATTATACAAAGATAAACTAAGGACCTCTAGTTTTGTTGTTACTAA
25643923 T
1 T
25643924 AAAAATATCC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.36
Consensus pattern (48 bp):
TCAATTATACAAAGATAAACTAAGGACCTCTAGTTTTGTTGTTACTAA
Found at i:25646535 original size:40 final size:40
Alignment explanation
Indices: 25646408--25646537 Score: 163
Period size: 40 Copynumber: 3.2 Consensus size: 40
25646398 ATGCTGGAAA
* * *
25646408 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * **
25646448 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
*
25646488 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
25646528 TTATATCCGG
1 TTATATCCGG
25646538 TTATATTCTG
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 73 0.99
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:25648270 original size:23 final size:24
Alignment explanation
Indices: 25648240--25648286 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
25648230 CAAACGAAGC
*
25648240 TAAAACATATTATTCATG-GAAAT
1 TAAAACATATTATACATGTGAAAT
*
25648263 TAAAACATGTTATACATGTGAAAT
1 TAAAACATATTATACATGTGAAAT
25648287 GAACTTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.34
Consensus pattern (24 bp):
TAAAACATATTATACATGTGAAAT
Found at i:25649973 original size:47 final size:46
Alignment explanation
Indices: 25649922--25650048 Score: 152
Period size: 45 Copynumber: 2.8 Consensus size: 46
25649912 GAATTATGAG
25649922 GCATCCGAACTCGTTGAGTTTCGTTTCGAGTTCACCTATGGATGC-AA
1 GCATCCGAACTCGTTGAGTTTCGTTTCGAGTTCA--TATGGATGCGAA
* * *
25649969 GCATCTGAACTCGTTGAGTTGT-GTTCCGAGTTCATTTGGATGCGAA
1 GCATCCGAACTCGTTGAGTT-TCGTTTCGAGTTCATATGGATGCGAA
* * *
25650015 -CACCCGAGCTCGTTGAGTTGCGTTTCGAGTTCAT
1 GCATCCGAACTCGTTGAGTTTCGTTTCGAGTTCAT
25650049 TATAGGTGAA
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
45 36 0.52
46 2 0.03
47 30 0.43
48 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.33
Consensus pattern (46 bp):
GCATCCGAACTCGTTGAGTTTCGTTTCGAGTTCATATGGATGCGAA
Found at i:25650366 original size:13 final size:13
Alignment explanation
Indices: 25650348--25650373 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25650338 ATTTTTTACT
25650348 TAGCCAGTTAGTA
1 TAGCCAGTTAGTA
25650361 TAGCCAGTTAGTA
1 TAGCCAGTTAGTA
25650374 CAGTTTATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
TAGCCAGTTAGTA
Found at i:25651502 original size:19 final size:19
Alignment explanation
Indices: 25651456--25651503 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
25651446 GTATATATTT
25651456 TAAA-TTTATTTAGATAGA
1 TAAATTTTATTTAGATAGA
* *
25651474 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGATAGA
25651493 TAAATTTTATT
1 TAAATTTTATT
25651504 CATATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGATAGA
Found at i:25661488 original size:22 final size:22
Alignment explanation
Indices: 25661415--25661491 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
25661405 ACCAAAATTG
*
25661415 ATAATTAAAAATAAAATTATAAA
1 ATAA-TAAAAATAAAATAATAAA
* **
25661438 ATCTAATAAAAAT-AAATAGTAGTT
1 A--TAATAAAAATAAAATAATA-AA
*
25661462 TTAATAAAAATAAAATAATAAA
1 ATAATAAAAATAAAATAATAAA
25661484 ATAATAAA
1 ATAATAAA
25661492 TAAATGTTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 9
0.69 0.15 0.15
Matches are distributed among these distances:
22 17 0.41
23 14 0.34
24 7 0.17
25 3 0.07
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (22 bp):
ATAATAAAAATAAAATAATAAA
Found at i:25662934 original size:28 final size:28
Alignment explanation
Indices: 25662902--25662959 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
25662892 AAGGCATGAG
25662902 TATGTCTATTGTTCTAATCATAAATATT
1 TATGTCTATTGTTCTAATCATAAATATT
* *
25662930 TATGTTTATTGTTCTAATCATGAATATT
1 TATGTCTATTGTTCTAATCATAAATATT
25662958 TA
1 TA
25662960 GTTCTAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.52
Consensus pattern (28 bp):
TATGTCTATTGTTCTAATCATAAATATT
Found at i:25669961 original size:20 final size:20
Alignment explanation
Indices: 25669936--25669975 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
25669926 CGGCCTCGAG
25669936 ACGTAAGCTAGTGTAAGACA
1 ACGTAAGCTAGTGTAAGACA
25669956 ACGTAAGCTAGTGTAAGACA
1 ACGTAAGCTAGTGTAAGACA
25669976 TGTCTGGGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (20 bp):
ACGTAAGCTAGTGTAAGACA
Found at i:25671562 original size:16 final size:16
Alignment explanation
Indices: 25671543--25671576 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
25671533 ATAATTGCGC
25671543 GGCTTATTAATTCCAT
1 GGCTTATTAATTCCAT
25671559 GGCTTATTAATTCCAT
1 GGCTTATTAATTCCAT
25671575 GG
1 GG
25671577 AAGCGTCCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (16 bp):
GGCTTATTAATTCCAT
Found at i:25674647 original size:14 final size:14
Alignment explanation
Indices: 25674628--25674657 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
25674618 CTATATACAA
*
25674628 ATAAACTTATCAAC
1 ATAAACTTATAAAC
25674642 ATAAACTTATAAAC
1 ATAAACTTATAAAC
25674656 AT
1 AT
25674658 CAAGAATACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAACTTATAAAC
Found at i:25675032 original size:44 final size:40
Alignment explanation
Indices: 25674925--25675050 Score: 126
Period size: 44 Copynumber: 3.0 Consensus size: 40
25674915 GTAATCAAAC
* * * *
25674925 ATCGATGCCACTGTCCCAGACAGGGTCCTACACGAAATCAG
1 ATCGATGCCAATGT-CCAGACATGGTCTTACACGAAAACAG
* *
25674966 ATACGATGACGATGTCCTAGACATGGTCTTACACGTAAAACAG
1 AT-CGATGCCAATGTCC-AGACATGGTCTTACACG-AAAACAG
*
25675009 AAGTCGATGCCAATGTCACAGACATGGTCTTACACGATAACA
1 -A-TCGATGCCAATGTC-CAGACATGGTCTTACACGAAAACA
25675051 CATATCGAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
41 4 0.06
42 24 0.34
43 11 0.16
44 29 0.41
45 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (40 bp):
ATCGATGCCAATGTCCAGACATGGTCTTACACGAAAACAG
Found at i:25678725 original size:18 final size:18
Alignment explanation
Indices: 25678702--25678737 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
25678692 AAAAACATAG
25678702 TATAACAAAATTAAGCAA
1 TATAACAAAATTAAGCAA
* *
25678720 TATAACATACTTAAGCAA
1 TATAACAAAATTAAGCAA
25678738 CAACATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.25
Consensus pattern (18 bp):
TATAACAAAATTAAGCAA
Found at i:25688077 original size:64 final size:63
Alignment explanation
Indices: 25687996--25688179 Score: 190
Period size: 67 Copynumber: 2.9 Consensus size: 63
25687986 AGACATTATG
*
25687996 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATA
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATA
* * * * * * *
25688059 TATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGTTACGAGA
1 -ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGA
25688124 TA
62 TA
** * * * *
25688126 AACTAGCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
25688180 CGAACTATAT
Statistics
Matches: 96, Mismatches: 20, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
62 1 0.01
63 18 0.19
64 21 0.22
65 8 0.08
66 19 0.20
67 29 0.30
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.23
Consensus pattern (63 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATA
Found at i:25689266 original size:2 final size:2
Alignment explanation
Indices: 25689259--25689283 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25689249 TCATGACATG
25689259 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
25689284 GACTAGTCTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25691481 original size:13 final size:13
Alignment explanation
Indices: 25691463--25691487 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25691453 CCGAGCACAC
25691463 GCCCGTGTCCCTG
1 GCCCGTGTCCCTG
25691476 GCCCGTGTCCCT
1 GCCCGTGTCCCT
25691488 CACACTGCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.48, G:0.28, T:0.24
Consensus pattern (13 bp):
GCCCGTGTCCCTG
Found at i:25697475 original size:7 final size:7
Alignment explanation
Indices: 25697463--25697489 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
25697453 CACCTTCCCA
25697463 TTTCTTC
1 TTTCTTC
25697470 TTTCTTC
1 TTTCTTC
25697477 TTTCTTC
1 TTTCTTC
25697484 TTTCTT
1 TTTCTT
25697490 TCTGTTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTCTTC
Found at i:25706462 original size:17 final size:18
Alignment explanation
Indices: 25706432--25706465 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
25706422 AATTTCTATT
25706432 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
25706450 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
25706466 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:25707004 original size:7 final size:7
Alignment explanation
Indices: 25706976--25707022 Score: 69
Period size: 7 Copynumber: 6.6 Consensus size: 7
25706966 GTTTTTATTA
25706976 ATATAAT
1 ATATAAT
25706983 AATATAAT
1 -ATATAAT
25706991 AATATAAT
1 -ATATAAT
25706999 ATATAAT
1 ATATAAT
25707006 ATATAAT
1 ATATAAT
25707013 ATATAA-
1 ATATAAT
25707019 ATAT
1 ATAT
25707023 CTTTACTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 4 0.10
7 20 0.51
8 15 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATATAAT
Found at i:25708410 original size:20 final size:19
Alignment explanation
Indices: 25708385--25708500 Score: 65
Period size: 20 Copynumber: 5.8 Consensus size: 19
25708375 CATAATAGAG
25708385 GAGGCATCGAAGTGCAAACA
1 GAGGCA-CGAAGTGCAAACA
* ** *
25708405 GAGGCACAAATGTGTGATCA
1 GAGGCACGAA-GTGCAAACA
25708425 GAGGCACCGAAGTGCAAACA
1 GAGGCA-CGAAGTGCAAACA
* * *
25708445 AAGACACCGAAGTGTGAAA-A
1 GAGGCA-CGAAGTG-CAAACA
* *
25708465 -AGGCATCAAAGTGCAAATA
1 GAGGCA-CGAAGTGCAAACA
*
25708484 GAGACACTGAAGTGCAA
1 GAGGCAC-GAAGTGCAA
25708501 TCCCGTACAA
Statistics
Matches: 73, Mismatches: 17, Indels: 12
0.72 0.17 0.12
Matches are distributed among these distances:
18 3 0.04
19 15 0.21
20 49 0.67
21 6 0.08
ACGTcount: A:0.42, C:0.18, G:0.28, T:0.12
Consensus pattern (19 bp):
GAGGCACGAAGTGCAAACA
Found at i:25708460 original size:40 final size:39
Alignment explanation
Indices: 25708385--25708497 Score: 120
Period size: 39 Copynumber: 2.9 Consensus size: 39
25708375 CATAATAGAG
* * *
25708385 GAGGCATCGAAGTGCAAACAGAGGCA-CAAATGTGTGATCA
1 GAGGCATCGAAGTGCAAACAGAGACACCGAA-GTGTGA-AA
* *
25708425 GAGGCACCGAAGTGCAAACAAAGACACCGAAGTGTGAAA
1 GAGGCATCGAAGTGCAAACAGAGACACCGAAGTGTGAAA
* * * *
25708464 AAGGCATCAAAGTGCAAATAGAGACACTGAAGTG
1 GAGGCATCGAAGTGCAAACAGAGACACCGAAGTG
25708498 CAATCCCGTA
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
39 29 0.48
40 29 0.48
41 3 0.05
ACGTcount: A:0.42, C:0.18, G:0.28, T:0.12
Consensus pattern (39 bp):
GAGGCATCGAAGTGCAAACAGAGACACCGAAGTGTGAAA
Found at i:25712738 original size:20 final size:20
Alignment explanation
Indices: 25712713--25712756 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
25712703 GAACATGCCT
25712713 GTGTGCTTTAGGACACGCCC
1 GTGTGCTTTAGGACACGCCC
*
25712733 GTGTGCTTTAGGACACGTCC
1 GTGTGCTTTAGGACACGCCC
25712753 GTGT
1 GTGT
25712757 CCCTAACCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.25, G:0.32, T:0.30
Consensus pattern (20 bp):
GTGTGCTTTAGGACACGCCC
Found at i:25722281 original size:68 final size:70
Alignment explanation
Indices: 25722209--25722406 Score: 294
Period size: 71 Copynumber: 2.8 Consensus size: 70
25722199 ACACCCTGTA
* * * *
25722209 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
25722271 ATAAAT
65 ATAAAT
*
25722277 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
25722342 ATAAAT
65 ATAAAT
*
25722348 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
25722407 AGACAAATCG
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 24 0.20
69 3 0.02
70 1 0.01
71 93 0.77
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:25722320 original size:41 final size:41
Alignment explanation
Indices: 25722275--25722392 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
25722265 TGAAAGATAA
25722275 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
25722316 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
25722346 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
25722387 ATGTAG
1 ATGTAG
25722393 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:25722332 original size:71 final size:71
Alignment explanation
Indices: 25722243--25722406 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
25722233 GAGATGTATC
25722243 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
25722308 AGGACA
66 AGGACA
25722314 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
25722379 AGGACA
66 AGGACA
25722385 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
25722407 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:25742395 original size:27 final size:29
Alignment explanation
Indices: 25742365--25742429 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
25742355 AAGCATACTC
*
25742365 CAAACAAAAAGAGTAA-AAAAAA-AAAAT
1 CAAACAAAAAGAGAAACAAAAAAGAAAAT
*
25742392 CAAACAAATAGAGAAACAAAAAAGAAAAT
1 CAAACAAAAAGAGAAACAAAAAAGAAAAT
25742421 -AAATCAAAA
1 CAAA-CAAAA
25742430 GAATTGGCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 14 0.44
28 9 0.28
29 9 0.28
ACGTcount: A:0.75, C:0.09, G:0.08, T:0.08
Consensus pattern (29 bp):
CAAACAAAAAGAGAAACAAAAAAGAAAAT
Found at i:25744357 original size:2 final size:2
Alignment explanation
Indices: 25744350--25744404 Score: 62
Period size: 2 Copynumber: 29.0 Consensus size: 2
25744340 TTTTAATGTT
* * *
25744350 TA TA TA TA -A TA TA -A TA TA CA TA TG CA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25744390 TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA
25744405 AGTGTGGGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:25747102 original size:20 final size:20
Alignment explanation
Indices: 25747077--25747114 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
25747067 CTCTCTCTAG
25747077 GGTTAGGGTTTTTATTTTTA
1 GGTTAGGGTTTTTATTTTTA
25747097 GGTTAGGGTTTTTATTTT
1 GGTTAGGGTTTTTATTTT
25747115 ATCAGCGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.00, G:0.26, T:0.61
Consensus pattern (20 bp):
GGTTAGGGTTTTTATTTTTA
Found at i:25749921 original size:26 final size:26
Alignment explanation
Indices: 25749885--25749938 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
25749875 AGGTTGGATG
*
25749885 AATCTCTTCCTCATATGACAAATATT
1 AATCTCTTCCTCATATGACAAACATT
25749911 AATCTCTTCCTCATATGACAAACATT
1 AATCTCTTCCTCATATGACAAACATT
25749937 AA
1 AA
25749939 CCTATCGGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (26 bp):
AATCTCTTCCTCATATGACAAACATT
Found at i:25756507 original size:18 final size:19
Alignment explanation
Indices: 25756486--25756522 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
25756476 ACAAAAAAAG
*
25756486 GAGAGA-TTTAATAAAACA
1 GAGAGATTTTAAAAAAACA
25756504 GAGAGATTTTAAAAAAACA
1 GAGAGATTTTAAAAAAACA
25756523 ACAAATAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.57, C:0.05, G:0.16, T:0.22
Consensus pattern (19 bp):
GAGAGATTTTAAAAAAACA
Found at i:25756618 original size:20 final size:21
Alignment explanation
Indices: 25756579--25756622 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
25756569 GTTACTGATT
*
25756579 ATTTTTTTTTCTTTCTCTTTC
1 ATTTTATTTTCTTTCTCTTTC
25756600 ATTTTATTTTCTTTC-CTTTC
1 ATTTTATTTTCTTTCTCTTTC
25756620 ATT
1 ATT
25756623 CCGAATCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (21 bp):
ATTTTATTTTCTTTCTCTTTC
Found at i:25757786 original size:2 final size:2
Alignment explanation
Indices: 25757779--25757823 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
25757769 TAAACCAATT
25757779 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25757821 TA T
1 TA T
25757824 CCTTTCAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25764544 original size:64 final size:64
Alignment explanation
Indices: 25764476--25764603 Score: 220
Period size: 64 Copynumber: 2.0 Consensus size: 64
25764466 CATATAATAA
* * *
25764476 CACATCTAGTTAGGAGTATTTGATTCATTTCGATCATAGCATCCTAATTATTTGATATAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
*
25764540 CACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGGCATAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
25764604 AGATACATGA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (64 bp):
CACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
Found at i:25764886 original size:132 final size:132
Alignment explanation
Indices: 25764683--25765413 Score: 860
Period size: 132 Copynumber: 5.6 Consensus size: 132
25764673 AGCCTTAACC
** * * * * * *
25764683 CCCTAAGCAGTAG-GGTAACAGGCTAAGGATTGTAGATCTTGCCTCCCTGAAGTTGAAATGGAGC
1 CCCTAAGCAGTAGTGG-AGTAGGCTAAAGATTGCAGATCTTGTCTCCCTGAAGTTGCAGTGGAAC
* *
25764747 AGATCAAAGATGGCAAATCTTGTCT-TCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCT
65 AGATCAAAGACGGCGAATCTTGTCTCT-CTGAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCT
25764811 ATCT
129 ATCT
* * * * *
25764815 CCCTAAGCAGTTGTGGAGTAGGCTAAAGATTGTAGATCTTATCTCCTTAAAGTTGCAGTGGAACA
1 CCCTAAGCAGTAGTGGAGTAGGCTAAAGATTGCAGATCTTGTCTCCCTGAAGTTGCAGTGGAACA
** * * * *
25764880 GATCAAAGATTGTGAATCTTGTCTCTCTGAAGTTGCAGT-AGAGTAGATTTAAGCCACTATTCTA
66 GATCAAAGACGGCGAATCTTGTCTCTCTGAAGTTGCAGTGA-AGCAGATTTAAGCCACCATCCTA
25764944 TCT
130 TCT
* * *
25764947 CCCTAAGCAGTAGTAGAGTAGGCTGAAGATTGCAGATCTTGTCTCCCTGAAGTTGCAGTGAAACA
1 CCCTAAGCAGTAGTGGAGTAGGCTAAAGATTGCAGATCTTGTCTCCCTGAAGTTGCAGTGGAACA
* * *
25765012 GGTCGAAGACGGTGAATCTTGTCTCTCTGAAGTTGCAGTG-AGCAGATTTAAGCCACCATCCTAT
66 GATCAAAGACGGCGAATCTTGTCTCTCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCTAT
25765076 CT
131 CT
* * * * **
25765078 CCCTAAGAAATAGTGGAGTAGACTAAAGATTGTAGATCTTGTCTCTTTGAAGTTGCAGTGGAACA
1 CCCTAAGCAGTAGTGGAGTAGGCTAAAGATTGCAGATCTTGTCTCCCTGAAGTTGCAGTGGAACA
* * * * *
25765143 GATCGAAGACGGCGAATCTTGTCTTTCTGAAGTTGCAGTGGAGCAGATTTAAGCCACTATTCTAT
66 GATCAAAGACGGCGAATCTTGTCTCTCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCTAT
25765208 CT
131 CT
* * * *
25765210 CCCTAAGCAGTAGTAGAATAGGCTAAAGATTGCAGATCTTGTCTCCCTGAAGTTGCAGTGAAATA
1 CCCTAAGCAGTAGTGGAGTAGGCTAAAGATTGCAGATCTTGTCTCCCTGAAGTTGCAGTGGAACA
* * ** * * * * *
25765275 GGTCGAAGACAACGAATCTTGTCTCTTTGAAGTTACAGCGGAGCAAATTTAAGCCACCATCCTAT
66 GATCAAAGACGGCGAATCTTGTCTCTCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCTAT
25765340 C-
131 CT
* * * * * * * *
25765341 CCTTAAGCAGTAATGGAGTAGGCTGAAGATAGCAAATCTTATTTCCCTGAAGATGCAGTGGAACA
1 CCCTAAGCAGTAGTGGAGTAGGCTAAAGATTGCAGATCTTGTCTCCCTGAAGTTGCAGTGGAACA
*
25765406 GATTAAAG
66 GATCAAAG
25765414 CTACAAATCA
Statistics
Matches: 513, Mismatches: 81, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
131 175 0.34
132 335 0.65
133 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (132 bp):
CCCTAAGCAGTAGTGGAGTAGGCTAAAGATTGCAGATCTTGTCTCCCTGAAGTTGCAGTGGAACA
GATCAAAGACGGCGAATCTTGTCTCTCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCTAT
CT
Found at i:25765162 original size:263 final size:262
Alignment explanation
Indices: 25764683--25765413 Score: 973
Period size: 263 Copynumber: 2.8 Consensus size: 262
25764673 AGCCTTAACC
* * * * * * * *
25764683 CCCTAAGCAGTAG-GGTAACAGGCTAAGGATTGTAGATCTTGCCTCCCTGAAGTTGAAATGGAGC
1 CCCTAAGCAGTAGTAG-AATAGGCTAA-GATTGCAGATCTTGTCTCCCTGAAGTTGCAGTGAAAC
* * * *
25764747 AGATCAAAGATGGCAAATCTTGTCT-TCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCT
64 AGGTCGAAGACGGCGAATCTTGTCTCT-CTGAAGTTGCAGTG-AGCAGATTTAAGCCACCATCCT
* *
25764811 ATCTCCCTAAGCAGTTGTGGAGTAGGCTAAAGATTGTAGATCTTATCTCCTTAAAGTTGCAGTGG
127 ATCTCCCTAAGCAGTAGTGGAGTAGGCTAAAGATTGTAGATCTTATCTCCTTGAAGTTGCAGTGG
** * *
25764876 AACAGATCAAAGATTGTGAATCTTGTCTCTCTGAAGTTGCAGTAGAGTAGATTTAAGCCACTATT
192 AACAGATCAAAGACGGCGAATCTTGTCTCTCTGAAGTTGCAGTAGAGCAGATTTAAGCCACTATT
25764941 CTATCT
257 CTATCT
*
25764947 CCCTAAGCAGTAGTAGAGTAGGCTGAAGATTGCAGATCTTGTCTCCCTGAAGTTGCAGTGAAACA
1 CCCTAAGCAGTAGTAGAATAGGCT-AAGATTGCAGATCTTGTCTCCCTGAAGTTGCAGTGAAACA
*
25765012 GGTCGAAGACGGTGAATCTTGTCTCTCTGAAGTTGCAGTGAGCAGATTTAAGCCACCATCCTATC
65 GGTCGAAGACGGCGAATCTTGTCTCTCTGAAGTTGCAGTGAGCAGATTTAAGCCACCATCCTATC
* * * * *
25765077 TCCCTAAGAAATAGTGGAGTAGACTAAAGATTGTAGATCTTGTCTCTTTGAAGTTGCAGTGGAAC
130 TCCCTAAGCAGTAGTGGAGTAGGCTAAAGATTGTAGATCTTATCTCCTTGAAGTTGCAGTGGAAC
* * *
25765142 AGATCGAAGACGGCGAATCTTGTCTTTCTGAAGTTGCAGTGGAGCAGATTTAAGCCACTATTCTA
195 AGATCAAAGACGGCGAATCTTGTCTCTCTGAAGTTGCAGTAGAGCAGATTTAAGCCACTATTCTA
25765207 TCT
260 TCT
*
25765210 CCCTAAGCAGTAGTAGAATAGGCTAAAGATTGCAGATCTTGTCTCCCTGAAGTTGCAGTGAAATA
1 CCCTAAGCAGTAGTAGAATAGGCT-AAGATTGCAGATCTTGTCTCCCTGAAGTTGCAGTGAAACA
** * * * *
25765275 GGTCGAAGACAACGAATCTTGTCTCTTTGAAGTTACAGCGGAGCAAATTTAAGCCACCATCCTAT
65 GGTCGAAGACGGCGAATCTTGTCTCTCTGAAGTTGCAG-TGAGCAGATTTAAGCCACCATCCTAT
* * * * * * * * *
25765340 C-CCTTAAGCAGTAATGGAGTAGGCTGAAGATAGCAAATCTTATTTCCCTGAAGATGCAGTGGAA
129 CTCCCTAAGCAGTAGTGGAGTAGGCTAAAGATTGTAGATCTTATCTCCTTGAAGTTGCAGTGGAA
*
25765404 CAGATTAAAG
194 CAGATCAAAG
25765414 CTACAAATCA
Statistics
Matches: 409, Mismatches: 54, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
263 296 0.72
264 109 0.27
265 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (262 bp):
CCCTAAGCAGTAGTAGAATAGGCTAAGATTGCAGATCTTGTCTCCCTGAAGTTGCAGTGAAACAG
GTCGAAGACGGCGAATCTTGTCTCTCTGAAGTTGCAGTGAGCAGATTTAAGCCACCATCCTATCT
CCCTAAGCAGTAGTGGAGTAGGCTAAAGATTGTAGATCTTATCTCCTTGAAGTTGCAGTGGAACA
GATCAAAGACGGCGAATCTTGTCTCTCTGAAGTTGCAGTAGAGCAGATTTAAGCCACTATTCTAT
CT
Found at i:25765421 original size:44 final size:44
Alignment explanation
Indices: 25765373--25766015 Score: 337
Period size: 44 Copynumber: 14.1 Consensus size: 44
25765363 CTGAAGATAG
* * *
25765373 CAAATCTTATTTCCCTGAAGATGCAGTGGAACAGATTAAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
* * * *
25765417 CAAATCACAAACCTTATCTTCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTA
1 CAAAT-------CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
* * * * *
25765468 CGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
** *
25765512 GCAAATCTTATCTCTTTGAAGTTGCAGTAGAGCAGATTAAAGCTA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
* * * * * *
25765557 CAAATCCTATAC-CTCTGAAGTTGCAGTAGG-TCGGATCAAATCTA
1 CAAATCTTAT-CTCCCTGAAGTTGCAGT-GGAGCAGATTAAAGCTA
* * * * * *
25765601 CTATGGTGGATCTTATCTCCCTAAAGTTGTAGTGGAGTAGATTGAAGCCA
1 C-A-----AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
* * * * *
25765651 CAAA-CTTTATCCCCCTGAAGTTGCAGTGGGGCAGGTCGAAA-TTA
1 CAAATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGAT-TAAAGCTA
* * ** * *
25765695 CAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGCCTGAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
* * * *
25765739 GCTAATCTTATCTCTCTGAAGTTGCAGTAGAGCAAATTAAAGCTA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
* * * * * *
25765784 CAAATCCTATAC-CTCTGAAGTTGCAGTAGG-TCGGATCAAATCTA
1 CAAATCTTAT-CTCCCTGAAGTTGCAGT-GGAGCAGATTAAAGCTA
* * * * *
25765828 CCATGTTAAATCTTATCTCTCTGAAGTTGTAGTGGAGTAGATTGAAGCCA
1 -C-----AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
* * * * * *
25765878 CAAACCTTATCCCCCTGAAGTTGCAGTGGGGCAGGTCGAAA-TTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT-TAAAGCTA
* **** *
25765922 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGCCCGAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
* * * * *
25765966 TCAAATCTTATTTCCCTGAAGTTGTAGTAGAACAGATTGAAGCTA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
*
25766011 TAAAT
1 CAAAT
25766016 TACAGATCTT
Statistics
Matches: 446, Mismatches: 117, Indels: 72
0.70 0.18 0.11
Matches are distributed among these distances:
43 5 0.01
44 227 0.51
45 116 0.26
49 8 0.02
50 55 0.12
51 35 0.08
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
Found at i:25765703 original size:227 final size:227
Alignment explanation
Indices: 25765422--25766015 Score: 954
Period size: 227 Copynumber: 2.6 Consensus size: 227
25765412 AGCTACAAAT
** * * * *
25765422 CACAAACCTTATCTTCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACGAGTCTTATCTCCCTGAA
1 CACAAACCTTATCCCCCTGAAGTTGCAGTGGGGCAGGTCGAAATTACAAGTCTTATCTCCCTGAA
* *
25765487 GTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCTTTGAAGTTGCAGTAGAGCAGATTAA
66 GTTGCAGTGGAGCAGCCTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAA
* **
25765552 AGCTACAAATCCTATACCTCTGAAGTTGCAGTAGGTCGGATCAAATCTACTATGGTGGATCTTAT
131 AGCTACAAATCCTATACCTCTGAAGTTGCAGTAGGTCGGATCAAATCTACCATGGTAAATCTTAT
25765617 CTCCCTAAAGTTGTAGTGGAGTAGATTGAAGC
196 CTCCCTAAAGTTGTAGTGGAGTAGATTGAAGC
*
25765649 CACAAACTTTATCCCCCTGAAGTTGCAGTGGGGCAGGTCGAAATTACAAGTCTTATCTCCCTGAA
1 CACAAACCTTATCCCCCTGAAGTTGCAGTGGGGCAGGTCGAAATTACAAGTCTTATCTCCCTGAA
* * *
25765714 GTTGCAATGGAGCAGCCTGAAGATAGCTAATCTTATCTCTCTGAAGTTGCAGTAGAGCAAATTAA
66 GTTGCAGTGGAGCAGCCTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAA
*
25765779 AGCTACAAATCCTATACCTCTGAAGTTGCAGTAGGTCGGATCAAATCTACCATGTTAAATCTTAT
131 AGCTACAAATCCTATACCTCTGAAGTTGCAGTAGGTCGGATCAAATCTACCATGGTAAATCTTAT
* *
25765844 CTCTCTGAAGTTGTAGTGGAGTAGATTGAAGC
196 CTCCCTAAAGTTGTAGTGGAGTAGATTGAAGC
25765876 CACAAACCTTATCCCCCTGAAGTTGCAGTGGGGCAGGTCGAAATTACAAGTCTTATCTCCCTGAA
1 CACAAACCTTATCCCCCTGAAGTTGCAGTGGGGCAGGTCGAAATTACAAGTCTTATCTCCCTGAA
* * * * * * *
25765941 GTTGCAGTGGAGCAGCCCGAAGATATCAAATCTTATTTCCCTGAAGTTGTAGTAGAACAGATTGA
66 GTTGCAGTGGAGCAGCCTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAA
*
25766006 AGCTATAAAT
131 AGCTACAAAT
25766016 TACAGATCTT
Statistics
Matches: 337, Mismatches: 30, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
227 337 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (227 bp):
CACAAACCTTATCCCCCTGAAGTTGCAGTGGGGCAGGTCGAAATTACAAGTCTTATCTCCCTGAA
GTTGCAGTGGAGCAGCCTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAA
AGCTACAAATCCTATACCTCTGAAGTTGCAGTAGGTCGGATCAAATCTACCATGGTAAATCTTAT
CTCCCTAAAGTTGTAGTGGAGTAGATTGAAGC
Found at i:25767779 original size:28 final size:27
Alignment explanation
Indices: 25767747--25767825 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 27
25767737 TTAAACCACC
* *
25767747 ATACATATTATTATTTTGAAGTTTTTTT
1 ATACATATTATTATTTT-AAATTATTTT
* *
25767775 TTACATATCTTTTATTTTAAATTATTTT
1 ATACATAT-TATTATTTTAAATTATTTT
*
25767803 ATACATAATATATATTTTAAATT
1 ATACATATTAT-TATTTTAAATT
25767826 TTCGTATATG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
27 2 0.05
28 32 0.76
29 8 0.19
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (27 bp):
ATACATATTATTATTTTAAATTATTTT
Found at i:25778597 original size:18 final size:18
Alignment explanation
Indices: 25778571--25778609 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
25778561 CCTAAGAAAC
* *
25778571 TTTATATCCTTTTGGGAT
1 TTTAAATCCTTTAGGGAT
25778589 TTTAAATCCTTTAGGGAT
1 TTTAAATCCTTTAGGGAT
25778607 TTT
1 TTT
25778610 CATATAAATT
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:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (18 bp):
TTTAAATCCTTTAGGGAT
Found at i:25780662 original size:29 final size:29
Alignment explanation
Indices: 25780629--25780789 Score: 178
Period size: 29 Copynumber: 5.6 Consensus size: 29
25780619 GTGACGAGAT
*
25780629 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
25780658 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
25780687 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* * **
25780716 TGACACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* ** * * ***
25780745 CGGCACTGGGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
25780774 TGGCACTATGTGTGCG
1 TGGCACTAAGTGTGCG
25780790 GGCTTAAATT
Statistics
Matches: 115, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 115 1.00
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAAAATA
Found at i:25788477 original size:29 final size:29
Alignment explanation
Indices: 25788444--25788604 Score: 178
Period size: 29 Copynumber: 5.6 Consensus size: 29
25788434 GTGACGAGAT
*
25788444 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
25788473 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
25788502 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* * **
25788531 TGACACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* ** * * ***
25788560 CGGCACTGGGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
25788589 TGGCACTATGTGTGCG
1 TGGCACTAAGTGTGCG
25788605 GGCTTAAATT
Statistics
Matches: 115, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 115 1.00
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAAAATA
Found at i:25790825 original size:43 final size:43
Alignment explanation
Indices: 25790762--25791080 Score: 423
Period size: 43 Copynumber: 7.5 Consensus size: 43
25790752 AAAACAATGA
* * *
25790762 CGCTATAGAACATGATCTTTAGCGGCGCTTTTCCCATAAACGC
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGC
* *
25790805 CGCTAAAGAACGTGACCTTTAGCGGCGCTTTT-CCACAAAAGC
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGC
* *
25790847 CGCTAAAGAATATGACCTTTAGCGGCACTTTT-CCACAAACGC
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGC
25790889 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGC
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGC
* * *
25790932 CGCTAAAGAACATGACCTTTAGCGGCACTTTTCCTATAAACGC
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGC
* * *
25790975 CGCTAAAGAATC-TGACCTTTAGCGACACTTTTCCCACGAACGC
1 CGCTAAAGAA-CATGACCTTTAGCGGCGCTTTTCCCACAAACGC
* * * * *
25791018 CACTATA-AA-ATAGACCTTTAGCGGCGCTTTTCTCACAAGCAC
1 CGCTAAAGAACAT-GACCTTTAGCGGCGCTTTTCCCACAAACGC
25791060 CGCTAAAGAACATGACCTTTA
1 CGCTAAAGAACATGACCTTTA
25791081 AAAATATATA
Statistics
Matches: 242, Mismatches: 28, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
41 1 0.00
42 107 0.44
43 131 0.54
44 3 0.01
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (43 bp):
CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGC
Found at i:25790879 original size:85 final size:86
Alignment explanation
Indices: 25790762--25791080 Score: 423
Period size: 85 Copynumber: 3.7 Consensus size: 86
25790752 AAAACAATGA
* * * * *
25790762 CGCTATAGAACATGATCTTTAGCGGCGCTTTTCCCATAAACGCCGCTAAAGAACGTGACCTTTAG
1 CGCTAAAGAACATGACCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAG
*
25790827 CGGCGCTTTT-CCACAAAAGC
66 CGGCGCTTTTCCCACAAACGC
*
25790847 CGCTAAAGAATATGACCTTTAGCGGCACTTTT-CCACAAACGCCGCTAAAGAACATGACCTTTAG
1 CGCTAAAGAACATGACCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAG
25790911 CGGCGCTTTTCCCACAAACGC
66 CGGCGCTTTTCCCACAAACGC
* *
25790932 CGCTAAAGAACATGACCTTTAGCGGCACTTTTCCTATAAACGCCGCTAAAGAATC-TGACCTTTA
1 CGCTAAAGAACATGACCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGAA-CATGACCTTTA
* * *
25790996 GCGACACTTTTCCCACGAACGC
65 GCGGCGCTTTTCCCACAAACGC
* * * * * *
25791018 CACTATA-AA-ATAGACCTTTAGCGGCGCTTTTCTCACAAGCACCGCTAAAGAACATGACCTTTA
1 CGCTAAAGAACAT-GACCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGAACATGACCTTTA
25791081 AAAATATATA
Statistics
Matches: 208, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
84 43 0.21
85 113 0.54
86 51 0.25
87 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (86 bp):
CGCTAAAGAACATGACCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGAACATGACCTTTAG
CGGCGCTTTTCCCACAAACGC
Found at i:25791188 original size:22 final size:22
Alignment explanation
Indices: 25791160--25791204 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
25791150 TTTGAACTTT
*
25791160 AACTATATACTTTTAAGGATAA
1 AACTATATAATTTTAAGGATAA
25791182 AACTATATAATTTTAAGGATAA
1 AACTATATAATTTTAAGGATAA
25791204 A
1 A
25791205 TAAAAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.36
Consensus pattern (22 bp):
AACTATATAATTTTAAGGATAA
Found at i:25796041 original size:16 final size:15
Alignment explanation
Indices: 25796009--25796051 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
25795999 AAATCGAAGG
*
25796009 AGAAGAAAAATAGAGA
1 AGAAGAAAAA-AAAGA
25796025 AGAAGGAAAAAAAAGA
1 AGAA-GAAAAAAAAGA
25796041 A-AAGAAAAAAA
1 AGAAGAAAAAAA
25796052 TTTTGGCAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 8 0.32
15 2 0.08
16 9 0.36
17 6 0.24
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (15 bp):
AGAAGAAAAAAAAGA
Found at i:25796873 original size:11 final size:11
Alignment explanation
Indices: 25796859--25796883 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25796849 GAGTAAAATG
25796859 AGATGAGAAGA
1 AGATGAGAAGA
25796870 AGATGAGAAGA
1 AGATGAGAAGA
25796881 AGA
1 AGA
25796884 GGGAGTAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.36, T:0.08
Consensus pattern (11 bp):
AGATGAGAAGA
Found at i:25797903 original size:21 final size:21
Alignment explanation
Indices: 25797877--25797923 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
25797867 CCCAAACCCC
25797877 AAACCCCAAATCCTAGACCAT
1 AAACCCCAAATCCTAGACCAT
* * *
25797898 AAACCCTAATTCTTAGACCAT
1 AAACCCCAAATCCTAGACCAT
25797919 AAACC
1 AAACC
25797924 TACACCTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.34, G:0.04, T:0.19
Consensus pattern (21 bp):
AAACCCCAAATCCTAGACCAT
Found at i:25798323 original size:21 final size:21
Alignment explanation
Indices: 25798296--25798431 Score: 78
Period size: 21 Copynumber: 6.4 Consensus size: 21
25798286 TCCCCTATCC
25798296 CCATAAACCTTAAATCATAAA
1 CCATAAACCTTAAATCATAAA
* * *
25798317 ACATAAACCATAAATCCTAAA
1 CCATAAACCTTAAATCATAAA
* * ** *
25798338 CCCCTAACCCTTAACCCATAAT
1 -CCATAAACCTTAAATCATAAA
*
25798360 CCATAAACCTTAAAATAAT-AA
1 CCATAAACCTT-AAATCATAAA
* * * *
25798381 CTCCTAAAGCTTAAACCCTAAA
1 C-CATAAACCTTAAATCATAAA
* *
25798403 CCATATATCTTAAA-CTATAAA
1 CCATAAACCTTAAATC-ATAAA
*
25798424 CCCTAAAC
1 CCATAAAC
25798432 TATAATGATA
Statistics
Matches: 81, Mismatches: 29, Indels: 10
0.68 0.24 0.08
Matches are distributed among these distances:
20 1 0.01
21 52 0.64
22 28 0.35
ACGTcount: A:0.47, C:0.29, G:0.01, T:0.24
Consensus pattern (21 bp):
CCATAAACCTTAAATCATAAA
Found at i:25798430 original size:14 final size:14
Alignment explanation
Indices: 25798383--25798436 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
25798373 AATAATAACT
25798383 CCTAAAGCT-TAAAC
1 CCTAAA-CTATAAAC
* * *
25798397 CCTAAACCATATAT
1 CCTAAACTATAAAC
*
25798411 CTTAAACTATAAAC
1 CCTAAACTATAAAC
25798425 CCTAAACTATAA
1 CCTAAACTATAA
25798437 TGATAATTAA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
13 1 0.03
14 30 0.97
ACGTcount: A:0.46, C:0.26, G:0.02, T:0.26
Consensus pattern (14 bp):
CCTAAACTATAAAC
Found at i:25798830 original size:40 final size:40
Alignment explanation
Indices: 25798786--25798881 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
25798776 TTTTTTTGCG
* * *
25798786 GCGTTTTTCAAAAAGTGCCGCTAATGGTCGACCTATAGCA
1 GCGTTTTTCAAAAAGCGCCGCTAATGCTCAACCTATAGCA
* *
25798826 GCGTTTTTTAAAAAGCGCCGCTAATGCTCAATCTATAGCA
1 GCGTTTTTCAAAAAGCGCCGCTAATGCTCAACCTATAGCA
25798866 GCGTTTTTCAAAAAGC
1 GCGTTTTTCAAAAAGC
25798882 AAAACTACTG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (40 bp):
GCGTTTTTCAAAAAGCGCCGCTAATGCTCAACCTATAGCA
Found at i:25798994 original size:40 final size:40
Alignment explanation
Indices: 25798938--25799043 Score: 149
Period size: 40 Copynumber: 2.6 Consensus size: 40
25798928 TAATTTTTTT
* *
25798938 GCGGCGTTTTTCAAAAAGCGCCGCTAATGGTCGACCTATA
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCAACCTATA
* * *
25798978 GCGGCGTTTTTTAAAAAGCGCTGCTAATGCTCAATCTATA
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCAACCTATA
* *
25799018 GCGGTGGTTTTCAAAAAGCGCCGCTA
1 GCGGCGTTTTTCAAAAAGCGCCGCTA
25799044 GTGCCGCTAC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (40 bp):
GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCAACCTATA
Found at i:25799192 original size:155 final size:155
Alignment explanation
Indices: 25798668--25799198 Score: 697
Period size: 155 Copynumber: 3.4 Consensus size: 155
25798658 AACGTTTTTT
* * * * * *
25798668 GCGGCGTTTTTGATAAAGCGCCGCTAA-AGCTCGATCTATAGCGGCATTTTTCAAAAAGCACTGT
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATA-CTCAATCTATAGCGGCGTTTTTCAAAAAGCACCGC
* * *
25798732 TAATGTCACTAAAGCTCAACACAAAACGAC-AGCATTGTGCTTAATTTTTTTGCGGCGTTTTTCA
65 TAATGCCACTAAAGCTCAACATAAAACGACGA-CGTTGTGCTTAATTTTTTTGCGGCGTTTTTCA
*
25798796 AAAAGTGCCGCTAATGGTCGACCTATA
129 AAAAGCGCCGCTAATGGTCGACCTATA
* * * ***
25798823 GCAGCGTTTTTTAAAAAGCGCCGCTAATGCTCAATCTATAGCAGCGTTTTTCAAAAAGCAAAACT
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATACTCAATCTATAGCGGCGTTTTTCAAAAAGCACCGCT
* * *
25798888 ACTGCCACTAAAGCTCAACATAAAACGACGATGTTTTGCTTAATTTTTTTGCGGCGTTTTTCAAA
66 AATGCCACTAAAGCTCAACATAAAACGACGACGTTGTGCTTAATTTTTTTGCGGCGTTTTTCAAA
25798953 AAGCGCCGCTAATGGTCGACCTATA
131 AAGCGCCGCTAATGGTCGACCTATA
* * * * *
25798978 GCGGCGTTTTTTAAAAAGCGCTGCTAATGCTCAATCTATAGCGGTGGTTTTCAAAAAGCGCCGCT
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATACTCAATCTATAGCGGCGTTTTTCAAAAAGCACCGCT
* * * * * *
25799043 AGTGCCGCTACATCTCAACATAAAACGACGACGTTGTGCTTAATTTTTTTGTGGCGTTTGTCAAA
66 AATGCCACTAAAGCTCAACATAAAACGACGACGTTGTGCTTAATTTTTTTGCGGCGTTTTTCAAA
**
25799108 AAGCATCGCTAATGGTCGACCTATA
131 AAGCGCCGCTAATGGTCGACCTATA
* * * * *
25799133 ACGGCATTTTTTGAAAAGCTCCGCTAATACTCAATCTATAGCGGCGTTTTTCAAAAAGCGCCGCT
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATACTCAATCTATAGCGGCGTTTTTCAAAAAGCACCGCT
25799198 A
66 A
25799199 CTGTTCGAGA
Statistics
Matches: 329, Mismatches: 45, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
155 328 1.00
156 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (155 bp):
GCGGCGTTTTTTAAAAAGCGCCGCTAATACTCAATCTATAGCGGCGTTTTTCAAAAAGCACCGCT
AATGCCACTAAAGCTCAACATAAAACGACGACGTTGTGCTTAATTTTTTTGCGGCGTTTTTCAAA
AAGCGCCGCTAATGGTCGACCTATA
Found at i:25808251 original size:44 final size:45
Alignment explanation
Indices: 25808203--25808294 Score: 150
Period size: 44 Copynumber: 2.0 Consensus size: 45
25808193 TATTAAGTTA
* *
25808203 AAATTTAATATAGTTATCAAATAGAATT-AAAAAAAATTAAATGT
1 AAATTTAAAATAGTTATCAAACAGAATTAAAAAAAAATTAAATGT
25808247 AAATTTAAAATAGTTATCAAACAGAATTAAAAAAAAAATTAAATGT
1 AAATTTAAAATAGTTATCAAACAGAATT-AAAAAAAAATTAAATGT
25808293 AA
1 AA
25808295 TTTTTTTTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 26 0.59
46 18 0.41
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (45 bp):
AAATTTAAAATAGTTATCAAACAGAATTAAAAAAAAATTAAATGT
Found at i:25816488 original size:23 final size:23
Alignment explanation
Indices: 25816462--25816509 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
25816452 TCCGAGATCA
25816462 TAATAGCTTTAATCTAGCTATCT
1 TAATAGCTTTAATCTAGCTATCT
25816485 TAATAGCTTTAATCTAGCTATCT
1 TAATAGCTTTAATCTAGCTATCT
25816508 TA
1 TA
25816510 GGGATTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.08, T:0.44
Consensus pattern (23 bp):
TAATAGCTTTAATCTAGCTATCT
Found at i:25816856 original size:21 final size:21
Alignment explanation
Indices: 25816832--25816871 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25816822 TTTGCCTAAG
*
25816832 ATATGAATTGAATTGAATTAA
1 ATATGAATTGAATTAAATTAA
*
25816853 ATATGAATTGTATTAAATT
1 ATATGAATTGAATTAAATT
25816872 GATGTTCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (21 bp):
ATATGAATTGAATTAAATTAA
Done.