Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008164.1 Hibiscus syriacus cultivar Beakdansim tig00110744_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2577652
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 11
Found at i:466161 original size:22 final size:22
Alignment explanation
Indices: 466109--466161 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
466099 ATTAACTTTT
* *
466109 TGGTCAAAGTCAAAGTTAATGC
1 TGGTCAAAGTCAAAGTAAATGA
* *
466131 GGGTTAAAGTCAAAGTCAAAT-A
1 TGGTCAAAGTCAAAGT-AAATGA
466153 TGGTCAAAG
1 TGGTCAAAG
466162 CCAATAGGTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.25
Consensus pattern (22 bp):
TGGTCAAAGTCAAAGTAAATGA
Found at i:466704 original size:16 final size:16
Alignment explanation
Indices: 466669--466742 Score: 71
Period size: 16 Copynumber: 4.7 Consensus size: 16
466659 GTATGGAATA
*
466669 TATATACTTTATA-GC
1 TATATACTTTATATAC
*
466684 TTATATACTTTATATAG
1 -TATATACTTTATATAC
*
466701 TATATAGTTTATATAC
1 TATATACTTTATATAC
* *
466717 T-TGTACTTTATTTAC
1 TATATACTTTATATAC
*
466732 TTTATACTTTA
1 TATATACTTTA
466743 CATATATGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.25
16 36 0.75
ACGTcount: A:0.31, C:0.09, G:0.05, T:0.54
Consensus pattern (16 bp):
TATATACTTTATATAC
Found at i:466706 original size:25 final size:25
Alignment explanation
Indices: 466669--466718 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
466659 GTATGGAATA
*
466669 TATATACTTTATAGCTTATATACTT
1 TATATACTATATAGCTTATATACTT
* *
466694 TATATAGTATATAGTTTATATACTT
1 TATATACTATATAGCTTATATACTT
466719 GTACTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.52
Consensus pattern (25 bp):
TATATACTATATAGCTTATATACTT
Found at i:466942 original size:2 final size:2
Alignment explanation
Indices: 466891--466922 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
466881 CAATGATAAG
466891 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
466923 TGTAAGTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:467238 original size:55 final size:55
Alignment explanation
Indices: 467174--467315 Score: 257
Period size: 55 Copynumber: 2.6 Consensus size: 55
467164 TTATTTAAAG
*
467174 TATATATATAATTTGATCATTGAATGTTGTTTCTAAATATAAGCTATAAGTATAT
1 TATATATATAATTTGATCATTGAATGTTGTTTCTAAATATAAACTATAAGTATAT
*
467229 TCTATATATAATTTGATCATTGAATGTTGTTTCTAAATATAAACTATAAGTATAT
1 TATATATATAATTTGATCATTGAATGTTGTTTCTAAATATAAACTATAAGTATAT
*
467284 TATATATATAATTTGATCATTGAATATTGTTT
1 TATATATATAATTTGATCATTGAATGTTGTTT
467316 AATTTATTTA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 83 1.00
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (55 bp):
TATATATATAATTTGATCATTGAATGTTGTTTCTAAATATAAACTATAAGTATAT
Found at i:468763 original size:95 final size:95
Alignment explanation
Indices: 468581--468804 Score: 299
Period size: 95 Copynumber: 2.4 Consensus size: 95
468571 ATACCGACTA
* *
468581 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAAAACATCGAATCTAAAACTGGCATCG
1 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAAAACATCAAAACTAAAACTGGCATCG
* * **
468646 ATACCAGAAGGTGTATTTGTACCATAATAT
66 ATACCAAAAGGGGTATCGGTACCATAATAT
* * *
468676 GGTAGTATCGATACCATGGTAAGGGTATCAATACCAGG-AAACATCAAAACTAAAATTGGTATCG
1 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAAAACATCAAAACTAAAACTGGCATCG
468740 ATACCAAAAGGGGTTATCGGTACCATAATAT
66 ATACCAAAAGGGG-TATCGGTACCATAATAT
* * * *
468771 AGAAGTATTGATACCAAGGT-AGTGGTATCGATAC
1 GGTAGTATCGATACCATGGTAAG-GGTATCGATAC
468805 TATTGAGCTG
Statistics
Matches: 113, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
94 35 0.31
95 78 0.69
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (95 bp):
GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAAAACATCAAAACTAAAACTGGCATCG
ATACCAAAAGGGGTATCGGTACCATAATAT
Found at i:469826 original size:68 final size:68
Alignment explanation
Indices: 469712--469968 Score: 379
Period size: 68 Copynumber: 3.8 Consensus size: 68
469702 AAAGATTAAT
* * *
469712 AGGCCTAATTGTGCATTTTACAGAAAAGGTGTCATTTATGCCAGTTAGATGAAATGCTAAGTGCC
1 AGGCCTAACTGTGCATTTGACAG-AAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
469777 TTTG
65 TTTG
* *
469781 AGGCCTAACTGTGCATTTGATAGAAAGGTATCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
469846 TTG
66 TTG
*
469849 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGGGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
469914 TTG
66 TTG
* * * * * * **
469917 AGACCTGACTGTGCAATTGGCATAAAGGTGTCAATTATGTTAGTTAGATGAA
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAA
469969 CTGTTAAATA
Statistics
Matches: 172, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
68 152 0.88
69 20 0.12
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:470124 original size:149 final size:149
Alignment explanation
Indices: 469854--470149 Score: 441
Period size: 149 Copynumber: 2.0 Consensus size: 149
469844 CTTTGAGGCC
469854 TAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGGGCCTTTGAG
1 TAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGGGCCTTTGAG
* * * * ** * *
469919 ACCTGACTGTGCAATTGGCATAAAGGTGTCAATTATGTTAGTTAGATGAACTGTTAAATACCGTG
66 ACCTAACTATGCAATTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAACGGTTAAACACCGTG
469984 GAGTAA-AGAAATAATAGCT
131 GAGTAATAG-AATAATAGCT
* * *
470003 TAACTGTGCATTTGACAGAAATGTGTCATTTATGCCAGTTAGATGTAAGGCTAAGTGCCTTTGAG
1 TAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGGGCCTTTGAG
* * * *
470068 GCCTAACTATGCAATTGGCAGAAAGATGTCAATTATGCCAGTTAGGTGAACGGTTAAACACTGTT
66 ACCTAACTATGCAATTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAACGGTTAAACACCGTG
470133 GAGTAATAGAATAATAG
131 GAGTAATAGAATAATAG
470150 ATTAGCTATT
Statistics
Matches: 131, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
149 129 0.98
150 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (149 bp):
TAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGGGCCTTTGAG
ACCTAACTATGCAATTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAACGGTTAAACACCGTG
GAGTAATAGAATAATAGCT
Found at i:470282 original size:20 final size:20
Alignment explanation
Indices: 470245--470283 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
470235 ATAATGTAAG
*
470245 GTGATATAAATGGTATATAA
1 GTGATATAAATGGAATATAA
470265 GTGATATGAAA-GGAATATA
1 GTGATAT-AAATGGAATATA
470284 TATATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (20 bp):
GTGATATAAATGGAATATAA
Found at i:474722 original size:68 final size:68
Alignment explanation
Indices: 474609--475000 Score: 527
Period size: 68 Copynumber: 5.8 Consensus size: 68
474599 AAAGATTAAT
* *
474609 AGGCCTAACTGTGCATTTGACAGAAAGGTATCATTTATACTAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGGCTAAGTGCCT
474674 TTG
66 TTG
* * * * * * *
474677 AGGCCTAAATATGCATTTGACAGAAATGTGTCATTTATGCAAGTTAGATGAAAGTCTAAGCGTCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGGCTAAGTGCCT
474742 TTG
66 TTG
*
474745 AGGCCTAACTGTGCATTTGACAGAAAGGTGACATTTATGCTAGTTAGAT-AATAGGCTAAGTGCC
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCTAGTTAGATGAA-AGGCTAAGTGCC
474809 TTTG
65 TTTG
* * * *
474813 AGGCCTAACTGTGAATTTGACAGAAAGGTGTCATTTATGCCAGCTAGATGAAAGGTTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGGCTAAGTGCCT
474878 TTG
66 TTG
* * * * * *
474881 AGACCTAACTGTTCATTTGACAGAACA-ATGTCAATTATTCTAGTTAGATGAAAGGATAAGTGCC
1 AGGCCTAACTGTGCATTTGACAGAA-AGGTGTCATTTATGCTAGTTAGATGAAAGGCTAAGTGCC
474945 TTTG
65 TTTG
* * * * *
474949 AGGCCTAACTGTGCAATTGGCATAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCTAGTTAGATGAA
475001 CGATTAAATA
Statistics
Matches: 281, Mismatches: 39, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
67 3 0.01
68 275 0.98
69 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:474959 original size:204 final size:208
Alignment explanation
Indices: 474609--475365 Score: 772
Period size: 216 Copynumber: 3.6 Consensus size: 208
474599 AAAGATTAAT
* * *
474609 AGGCCTAACTGTGCATTTGACAGAAAGGTATCATTTATACTAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
* * * * *
474674 TTGAGGCCTAAATATGCATTTGACAGAAATGTGTCATTTATGCAAGTTAGATGAAAGTCTAAGCG
66 TTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCAAGTTAGATGAAAGGCTAAGTG
* * * * *
474739 TCTTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGACATTTATGCTAGTTAGAT-AATAGGCTA
131 TCTTTGAGGCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA-AGACTA
* *
474803 AGT-GCCTT-T-G-
195 AATAGCATTGTAGA
* * *
474813 AGGCCTAACTGTGAATTTGACAGAAAGGTGTCATTTATGCCAGCTAGATGAAAGGTTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
* * * * * * *
474878 TTGAGACCTAACTGTTCATTTGACAGAACA-ATGTCAATTATTCTAGTTAGATGAAAGGATAAGT
66 TTGAGGCCTAACTGTGCATTTGACAGAA-AGGTGTCATTTATGCAAGTTAGATGAAAGGCTAAGT
* * * * *
474942 GCCTTTGAGGCCTAACTGTGCAATTGGCATAAAGGTGTCAATTATGCCAGTTAGATGAACGATTA
130 GTCTTTGAGGCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTA
*
475007 AATATCATTGAGTAAAAGAATA
195 AATAGCATT--GT---AG---A
* * * * *
475029 ATAGCCTAAATGTGCATTTGATAGAAATGTGCCA-TTATGCCAGTTAGATGAAAGGCTAAGTGCC
1 A-GGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
* *
475093 TTTGAGGCCTATCTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGT
65 TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCAAGTTAGATGAAAGGCTAAGT
* * **
475158 ATCTTTGAGGCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTA
130 GTCTTTGAGGCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTA
* *
475223 AATATCGTTGAGTAAAAGAATA
195 AATAGCATT--GT---AG---A
* * * * * *
475245 ATAGCCTAATTGTGCATTTGACATAAAGGTGTCATTTATGCCAGTTTGATGAAAAGCTAATTGCC
1 A-GGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
* * * * * * *
475310 TTTGAGGCCTAAATGTGCAATTGGCATAAAGGTGTCAATGATGCTAGTTAGATGAA
65 TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCAAGTTAGATGAA
475366 CGATTAAATA
Statistics
Matches: 468, Mismatches: 68, Indels: 21
0.84 0.12 0.04
Matches are distributed among these distances:
204 164 0.35
205 6 0.01
208 1 0.00
212 1 0.00
215 1 0.00
216 194 0.41
217 101 0.22
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (208 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCAAGTTAGATGAAAGGCTAAGTG
TCTTTGAGGCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAA
ATAGCATTGTAGA
Found at i:475018 original size:136 final size:136
Alignment explanation
Indices: 474612--475216 Score: 680
Period size: 136 Copynumber: 4.4 Consensus size: 136
474602 GATTAATAGG
* * *
474612 CCTAACTGTGCATTTGACAGAAAGGTATCATTTATACTAGTTAGATGAAAGGCTAAGTGCCTTTG
1 CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGCTAAGTGCCTTTG
* * * * * **
474677 AGGCCTAAATATGCATTTGACAGAAATGTGTCATTTATGCAAGTTAGATGAAA-GTCTAAGCGTC
66 AGGCCTAACTGTGCAATTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGT-TAAGTATC
*
474741 TTTGAGG
130 TTTGAGA
* *
474748 CCTAACTGTGCATTTGACAGAAAGGTGACATTTATGCTAGTTAGAT-AATAGGCTAAGTGCCTTT
1 CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAA-AGGCTAAGTGCCTTT
* **
474812 GAGGCCTAACTGTG-AATTTGACAGAAAGGTGTCATTTATGCCAGCTAGATGAAAGGTTAAGTGC
65 GAGGCCTAACTGTGCAA-TTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGTTAAGTAT
474876 CTTTGAGA
129 CTTTGAGA
* * * *
474884 CCTAACTGTTCATTTGACAGAACA-ATGTCAATTATTCTAGTTAGATGAAAGGATAAGTGCCTTT
1 CCTAACTGTGCATTTGACAGAA-AGGTGTCAATTATGCTAGTTAGATGAAAGGCTAAGTGCCTTT
* * * * * *
474948 GAGGCCTAACTGTGCAATTGGCATAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAATATC
65 GAGGCCTAACTGTGCAATTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGTTAAGTATC
*
475013 ATTGAGTAAAAGAATAATA
130 -TT---T----G----AGA
* * * * *
475032 GCCTAAATGTGCATTTGATAGAAATGTG-CCATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1 -CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGCTAAGTGCCTTT
* * *
475096 GAGGCCTATCTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTATC
65 GAGGCCTAACTGTGCAATTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGTTAAGTATC
*
475161 TTTGAGG
130 TTTGAGA
* *
475168 CCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAA
475217 CGGTTAAATA
Statistics
Matches: 396, Mismatches: 52, Indels: 42
0.81 0.11 0.09
Matches are distributed among these distances:
135 26 0.07
136 243 0.61
137 9 0.02
140 2 0.01
144 2 0.01
147 2 0.01
148 91 0.23
149 21 0.05
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.30
Consensus pattern (136 bp):
CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGCTAAGTGCCTTTG
AGGCCTAACTGTGCAATTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGTTAAGTATCT
TTGAGA
Found at i:475226 original size:216 final size:217
Alignment explanation
Indices: 474815--475527 Score: 876
Period size: 216 Copynumber: 3.2 Consensus size: 217
474805 TGCCTTTGAG
* * *
474815 GCCTAACTGTGAATTTGACAGAAAGGTGTCATTTATGCCAGCTAGATGAAAGGTTAAGTGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGCCATTTATGCCAGCTAGATGAAAGGCTAAGTGCCTTT
* * * * *
474880 GAGACCTAACTGTTCATTTGACAGAACA-ATGTCAATTATTCTAGTTAGATGAAAGGATAAGTGC
66 GAGGCCTAACTGTGCATTTGACAGAA-AGGTGTCAATTATGCTAGTTAGATGAAAGGATAAGTAC
* *
474944 CTTTGAGGCCTAACTGTGCAATTGGCATAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAA
130 CTTTGAGGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAA
*
475009 TATCATTGAGTAAAAGAATAATA
195 TATCGTTGAGTAAAAGAATAATA
* * * *
475032 GCCTAAATGTGCATTTGATAGAAATGTGCCA-TTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGCCATTTATGCCAGCTAGATGAAAGGCTAAGTGCCTTT
* * * * *
475096 GAGGCCTATCTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTATC
66 GAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGATAAGTACC
*
475161 TTTGAGGCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAT
131 TTTGAGGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAT
475226 ATCGTTGAGTAAAAGAATAATA
196 ATCGTTGAGTAAAAGAATAATA
* * * * * * *
475248 GCCTAATTGTGCATTTGACATAAAGGTGTCATTTATGCCAGTTTGATGAAAAGCTAATTGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGCCATTTATGCCAGCTAGATGAAAGGCTAAGTGCCTTT
* * * * * * *
475313 GAGGCCTAAATGTGCAATTGGCATAAAGGTGTCAATGATGCTAGTTAGATG-AACGATTAAATAC
66 GAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGA-TAAGTAC
* * *
475377 CGTTGAGTAAAAGAATAATAGCCTAACTGTGCAATTGGTAGAAAGGTGTCAATTATGCCAATTAG
130 C-TT---T----G----A-GGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAG
475442 ATGAACGGTTAAATATCGTTGAGTAAAAGAATAATA
182 ATGAACGGTTAAATATCGTTGAGTAAAAGAATAATA
* * * *
475478 GCCTAACTGTGCAATTGGA-AGAAAGGTGTCAATTATGCCAGCTAGGTGAA
1 GCCTAACTGTGC-ATTTGACAGAAAGGTGCCATTTATGCCAGCTAGATGAA
475528 CGGTTAAACA
Statistics
Matches: 427, Mismatches: 52, Indels: 21
0.85 0.10 0.04
Matches are distributed among these distances:
215 1 0.00
216 196 0.46
217 105 0.25
218 2 0.00
221 1 0.00
225 1 0.00
229 1 0.00
230 115 0.27
231 5 0.01
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.29
Consensus pattern (217 bp):
GCCTAACTGTGCATTTGACAGAAAGGTGCCATTTATGCCAGCTAGATGAAAGGCTAAGTGCCTTT
GAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGATAAGTACC
TTTGAGGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAT
ATCGTTGAGTAAAAGAATAATA
Found at i:475234 original size:68 final size:68
Alignment explanation
Indices: 475032--475234 Score: 282
Period size: 68 Copynumber: 3.0 Consensus size: 68
475022 AAGAATAATA
* * * * **
475032 GCCTAAATGTGCATTTGATAGAAATGTG-CCATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTATCTTT
475096 GAG
66 GAG
* *
475099 GCCTATCTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTATCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTATCTTT
475164 GAG
66 GAG
* * * * *
475167 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATATCGTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTATCTTT
475232 GAG
66 GAG
475235 TAAAAGAATA
Statistics
Matches: 120, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 24 0.20
68 96 0.80
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (68 bp):
GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTATCTTT
GAG
Found at i:475286 original size:149 final size:148
Alignment explanation
Indices: 475099--475626 Score: 515
Period size: 149 Copynumber: 3.5 Consensus size: 148
475089 TGCCTTTGAG
* *
475099 GCCTATCTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTATCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAATATCTTT
475164 GAGGCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATATC
66 GAGGCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATA-C
475229 GTTGAGTAAAAGAATAATA
130 GTTGAGTAAAAGAATAATA
* * * * * **
475248 GCCTAATTGTGCATTTGACATAAAGGTGTCATTTATGCCAGTTTGATGAAAAGCTAATTGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAATATCTTT
* * * * * *
475313 GAGGCCTAAATGTGCAATTGGCATAAAGGTGTCAATGATGCTAGTTAGATGAACGATTAAATACC
66 GAGGCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATA-C
475378 GTTGAGTAAAAGAATAATA
130 GTTGAGTAAAAGAATAATA
* ** * * * *
475397 GCCTAACTGTGCAATTGGTAGAAAGGTGTCAATTATGCCAATTAGATGAACGGTTAAATATCGTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAATATC-TT
* * *
475462 GAGTAAAAGAATAATAGCCTAACTGTGCAATTGGA-AGAAAGGTGTCAATTATGCCAGCTAGGTG
65 ---T----G----A-GGCCTAACTGTGCAATT-GACAGAAAGGTGTCAATTATGCCAGTTAGATG
* * *
475526 AACGGTTAAACACTATTGAGTAAAAGAATAATG
117 AACGGTTAAATAC-GTTGAGTAAAAGAATAATA
** * * * * ** * *
475559 GATTAGCTGTGTAATTGACTATAAA-GTGTCAAATATGCAAGTTAAATGGAAA-GCTAAATA-CT
1 GCCTAACTGTGCATTTGAC-AGAAAGGTGTCATTTATGCCAGTTAGAT-GAAAGGCTAAATATCT
475621 TTGAGG
64 TTGAGG
475627 TAGAAGAATA
Statistics
Matches: 307, Mismatches: 55, Indels: 35
0.77 0.14 0.09
Matches are distributed among these distances:
148 1 0.00
149 183 0.60
150 2 0.01
153 2 0.01
157 2 0.01
160 2 0.01
161 3 0.01
162 104 0.34
163 8 0.03
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (148 bp):
GCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAATATCTTT
GAGGCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACG
TTGAGTAAAAGAATAATA
Found at i:475383 original size:68 final size:68
Alignment explanation
Indices: 475248--475383 Score: 148
Period size: 68 Copynumber: 2.0 Consensus size: 68
475238 AAGAATAATA
* * * * * * * *
475248 GCCTAATTGTGCATTTGACATAAAGGTGTCATTTATGCCAGTTTGATGAAAAGCTAATTGCCTTT
1 GCCTAAATGTGCAATTGACATAAAGGTGTCAATGATGCCAGTTAGATGAAAAGCTAAATACCGTT
475313 GAG
66 GAG
* * * *
475316 GCCTAAATGTGCAATTGGCATAAAGGTGTCAATGATGCTAGTTAGATG-AACGATTAAATACCGT
1 GCCTAAATGTGCAATTGACATAAAGGTGTCAATGATGCCAGTTAGATGAAAAG-CTAAATACCGT
475380 TGAG
65 TGAG
475384 TAAAAGAATA
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
67 3 0.05
68 52 0.95
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.32
Consensus pattern (68 bp):
GCCTAAATGTGCAATTGACATAAAGGTGTCAATGATGCCAGTTAGATGAAAAGCTAAATACCGTT
GAG
Found at i:475454 original size:81 final size:81
Alignment explanation
Indices: 475316--475557 Score: 358
Period size: 81 Copynumber: 3.0 Consensus size: 81
475306 TGCCTTTGAG
* * * * * *
475316 GCCTAAATGTGCAATTGGCATAAAGGTGTCAATGATGCTAGTTAGATGAACGATTAAATACCGTT
1 GCCTAACTGTGCAATTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTT
475381 GAGTAAAAGAATAATA
66 GAGTAAAAGAATAATA
* * *
475397 GCCTAACTGTGCAATTGGTAGAAAGGTGTCAATTATGCCAATTAGATGAACGGTTAAATATCGTT
1 GCCTAACTGTGCAATTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTT
475462 GAGTAAAAGAATAATA
66 GAGTAAAAGAATAATA
* * * **
475478 GCCTAACTGTGCAATTGGAAGAAAGGTGTCAATTATGCCAGCTAGGTGAACGGTTAAACACTATT
1 GCCTAACTGTGCAATTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTT
475543 GAGTAAAAGAATAAT
66 GAGTAAAAGAATAAT
475558 GGATTAGCTG
Statistics
Matches: 145, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 145 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (81 bp):
GCCTAACTGTGCAATTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTT
GAGTAAAAGAATAATA
Found at i:475588 original size:81 final size:81
Alignment explanation
Indices: 475316--475637 Score: 330
Period size: 81 Copynumber: 4.0 Consensus size: 81
475306 TGCCTTTGAG
* ** * * * * *
475316 GCCTAAATGTGCAATTGGCATAAAGGTGTCAATGATGCTAGTTAGATGAACGATTAAATACCGTT
1 GCCTAACTGTGCAATTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACTGTT
475381 GAGTAAAAGAATAATA
66 GAGTAAAAGAATAATA
* *
475397 GCCTAACTGTGCAATTGGTAGAAAGGTGTCAATTATGCCAATTAGATGAACGGTTAAATA-TCGT
1 GCCTAACTGTGCAATTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACT-GT
475461 TGAGTAAAAGAATAATA
65 TGAGTAAAAGAATAATA
* * * *
475478 GCCTAACTGTGCAATTGGA-AGAAAGGTGTCAATTATGCCAGCTAGGTGAACGGTTAAACACTAT
1 GCCTAACTGTGCAATT-GATAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACTGT
*
475542 TGAGTAAAAGAATAATG
65 TGAGTAAAAGAATAATA
** * * * * * * * *
475559 GATTAGCTGTGTAATTGACTATAAA-GTGTCAAATATGCAAGTTAAATGGAA-AGCTAAATACT-
1 GCCTAACTGTGCAATTGA-TAGAAAGGTGTCAATTATGCCAGTTAGAT-GAACGGTTAAATACTG
*
475621 TTGAGGTAGAAGAATAA
64 TTGA-GTAAAAGAATAA
475638 AGGAATTATA
Statistics
Matches: 205, Mismatches: 29, Indels: 14
0.83 0.12 0.06
Matches are distributed among these distances:
80 6 0.03
81 190 0.93
82 9 0.04
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (81 bp):
GCCTAACTGTGCAATTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACTGTT
GAGTAAAAGAATAATA
Found at i:475636 original size:162 final size:162
Alignment explanation
Indices: 475316--475637 Score: 364
Period size: 162 Copynumber: 2.0 Consensus size: 162
475306 TGCCTTTGAG
* * * * * *
475316 GCCTAAATGTGCAATTGGCATAAAGGTGTCAATGATGCTAGTTAGATGAACGATTAAATACCGTT
1 GCCTAAATGTGCAATTGGAAGAAAGGTGTCAATGATGCCAGCTAGATGAACGATTAAACACCATT
* * * *
475381 GAGTAAAAGAATAATAGCCTAACTGTGCAATTGGTAGAAAGGTGTCAATTATGCCAATTAGATGA
66 GAGTAAAAGAATAATAGACTAACTGTGCAATTGCTAGAAAGGTGTCAAATATGCCAATTAAATGA
* *
475446 ACGGTTAAATATCGTTGAGTAAAAGAATAATA
131 ACAGCTAAATATCGTTGAGTAAAAGAATAATA
* * * * *
475478 GCCTAACTGTGCAATTGGAAGAAAGGTGTCAATTATGCCAGCTAGGTGAACGGTTAAACACTATT
1 GCCTAAATGTGCAATTGGAAGAAAGGTGTCAATGATGCCAGCTAGATGAACGATTAAACACCATT
* * * * *
475543 GAGTAAAAGAATAATGGATTAGCTGTGTAATTGACTATAAA-GTGTCAAATATG-CAAGTTAAAT
66 GAGTAAAAGAATAATAGACTAACTGTGCAATTG-CTAGAAAGGTGTCAAATATGCCAA-TTAAAT
* *
475606 GGAA-AGCTAAATA-CTTTGAGGTAGAAGAATAA
129 -GAACAGCTAAATATCGTTGA-GTAAAAGAATAA
475638 AGGAATTATA
Statistics
Matches: 132, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
161 8 0.06
162 116 0.88
163 8 0.06
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (162 bp):
GCCTAAATGTGCAATTGGAAGAAAGGTGTCAATGATGCCAGCTAGATGAACGATTAAACACCATT
GAGTAAAAGAATAATAGACTAACTGTGCAATTGCTAGAAAGGTGTCAAATATGCCAATTAAATGA
ACAGCTAAATATCGTTGAGTAAAAGAATAATA
Found at i:475696 original size:2 final size:2
Alignment explanation
Indices: 475689--475715 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
475679 TATGGAAGAA
475689 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
475716 ATGTACAACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:478804 original size:18 final size:20
Alignment explanation
Indices: 478769--478805 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
478759 CACAAAATGT
478769 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
478789 AAGATTACC-G-GGGAATA
1 AAGATTACCAGTGGGAATA
478806 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 1 0.06
20 9 0.53
ACGTcount: A:0.43, C:0.11, G:0.27, T:0.19
Consensus pattern (20 bp):
AAGATTACCAGTGGGAATAA
Found at i:482518 original size:117 final size:114
Alignment explanation
Indices: 482282--482597 Score: 490
Period size: 117 Copynumber: 2.7 Consensus size: 114
482272 TACTATTCAC
* *
482282 GTGAAGGCGCGTTCCTAGGGGGCGCCTTCCATTATTTTATCAGATAATATGTTATCATTGCCCTA
1 GTGAAAGCGCGTTCCT--GGGGCGCCTTCTATTATTTTATCAGATAATATGTTATCATTGCCCTA
482347 TTATGTCACTCATGTCCCTCGTGGGCACTATTCATGTCAGTACCCAAAGTG
64 TTATGTCACTCATGTCCCTCGTGGGCACTATTCATGTCAGTACCCAAAGTG
*
482398 GTGAAAGCGCGTTCCTGGGGACGCAGCTTCTATTATTTTATCAGATAATATGTTATCATTCCCCT
1 GTGAAAGCGCGTTCCTGGGG-CGC--CTTCTATTATTTTATCAGATAATATGTTATCATTGCCCT
*
482463 ATTATGTCACTCATGCCCCTCAG-GGGCACTATTCATGTCAGTACCCAAAGTG
63 ATTATGTCACTCATGTCCCTC-GTGGGCACTATTCATGTCAGTACCCAAAGTG
* * * *
482515 GTGAAAGTGCGTTCCCGGTGGCGCCTTATATTATTTTATCAGAGAATATGTTATCATTGCCCTAT
1 GTGAAAGCGCGTTCCTGG-GGCGCCTTCTATTATTTTATCAGATAATATGTTATCATTGCCCTAT
482580 TATGTCACTCATGTCCCT
65 TATGTCACTCATGTCCCT
482598 TGGGGAATTA
Statistics
Matches: 185, Mismatches: 10, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
114 4 0.02
115 58 0.31
116 15 0.08
117 105 0.57
118 3 0.02
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (114 bp):
GTGAAAGCGCGTTCCTGGGGCGCCTTCTATTATTTTATCAGATAATATGTTATCATTGCCCTATT
ATGTCACTCATGTCCCTCGTGGGCACTATTCATGTCAGTACCCAAAGTG
Found at i:482792 original size:23 final size:23
Alignment explanation
Indices: 482744--482793 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
482734 TGAAGTTTGA
* * *
482744 ATAAATTGGATAAAATGTTATGG
1 ATAAATTGAATAAAATGTGAAGG
482767 ATAAATTGAAT-AAATGTGAAGTG
1 ATAAATTGAATAAAATGTGAAG-G
482790 ATAA
1 ATAA
482794 GTTGGTTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (23 bp):
ATAAATTGAATAAAATGTGAAGG
Found at i:482850 original size:70 final size:70
Alignment explanation
Indices: 482773--483003 Score: 262
Period size: 70 Copynumber: 3.4 Consensus size: 70
482763 ATGGATAAAT
482773 TGAATAAATGTGAAGTGATAAGTTGGTTGTGACATTGAAATTGTATGGAATGATCATCGACATGT
1 TGAATAAATGTGAAGTGATAAGTTGGTTGTGACATTGAAATTGTATGGAATGATCATCGACATGT
**
482838 TTTTA
66 TAATA
* * * * ** * *
482843 TGAATAAATGTGAAGTGATAAGTTGGTTGTTTA-AAT-AAACTGGATAAAATG-TTATGGACA--
1 TGAATAAATGTGAAGTGATAAGTTGGTTG-TGACATTGAAATTGTATGGAATGATCATCGACATG
482903 --AAT-
65 TTAATA
* *
482906 TGAATAAATGTGAAGTGAAAAGTTGGTTGTGACATTGAAATTGTATGGAATGAGCATCGACATGT
1 TGAATAAATGTGAAGTGATAAGTTGGTTGTGACATTGAAATTGTATGGAATGATCATCGACATGT
**
482971 TCCTA
66 TAATA
*
482976 CGAATAAATGTGAAGTGATAAGTTGGTT
1 TGAATAAATGTGAAGTGATAAGTTGGTT
483004 TTAATGTATA
Statistics
Matches: 128, Mismatches: 24, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
62 2 0.02
63 30 0.23
64 12 0.09
65 6 0.05
68 7 0.05
69 12 0.09
70 57 0.45
71 2 0.02
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.34
Consensus pattern (70 bp):
TGAATAAATGTGAAGTGATAAGTTGGTTGTGACATTGAAATTGTATGGAATGATCATCGACATGT
TAATA
Found at i:482981 original size:133 final size:133
Alignment explanation
Indices: 482738--483003 Score: 460
Period size: 133 Copynumber: 2.0 Consensus size: 133
482728 GTTATGTGAA
* * * *
482738 GTTTGAATAAATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGT
1 GTTTAAATAAACTGGATAAAATGTTATGGACAAATTGAATAAATGTGAAGTGAAAAGTTGGTTGT
* ** *
482803 GACATTGAAATTGTATGGAATGATCATCGACATGTTTTTATGAATAAATGTGAAGTGATAAGTTG
66 GACATTGAAATTGTATGGAATGAGCATCGACATGTTCCTACGAATAAATGTGAAGTGATAAGTTG
482868 GTT
131 GTT
482871 GTTTAAATAAACTGGATAAAATGTTATGGACAAATTGAATAAATGTGAAGTGAAAAGTTGGTTGT
1 GTTTAAATAAACTGGATAAAATGTTATGGACAAATTGAATAAATGTGAAGTGAAAAGTTGGTTGT
482936 GACATTGAAATTGTATGGAATGAGCATCGACATGTTCCTACGAATAAATGTGAAGTGATAAGTTG
66 GACATTGAAATTGTATGGAATGAGCATCGACATGTTCCTACGAATAAATGTGAAGTGATAAGTTG
483001 GTT
131 GTT
483004 TTAATGTATA
Statistics
Matches: 125, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
133 125 1.00
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (133 bp):
GTTTAAATAAACTGGATAAAATGTTATGGACAAATTGAATAAATGTGAAGTGAAAAGTTGGTTGT
GACATTGAAATTGTATGGAATGAGCATCGACATGTTCCTACGAATAAATGTGAAGTGATAAGTTG
GTT
Found at i:483020 original size:14 final size:14
Alignment explanation
Indices: 483001--483031 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
482991 TGATAAGTTG
483001 GTTTTAATGTATAT
1 GTTTTAATGTATAT
483015 GTTTTAATGTATAT
1 GTTTTAATGTATAT
483029 GTT
1 GTT
483032 AAGGATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (14 bp):
GTTTTAATGTATAT
Found at i:483178 original size:34 final size:34
Alignment explanation
Indices: 483139--483211 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
483129 TTAAGTTGAA
483139 TTTAATGTTAAATTTCAAATACCATAATTTGTAT
1 TTTAATGTTAAATTTCAAATACCATAATTTGTAT
* * *
483173 TTTAATTTTAAATTTCGAATACTATAATTTGTAT
1 TTTAATGTTAAATTTCAAATACCATAATTTGTAT
*
483207 ATTAA
1 TTTAA
483212 AAACATTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.49
Consensus pattern (34 bp):
TTTAATGTTAAATTTCAAATACCATAATTTGTAT
Found at i:483740 original size:21 final size:21
Alignment explanation
Indices: 483714--483765 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
483704 GGTGTCATAA
483714 AACCCTGCGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
483735 AACCCTGAGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGT
483756 AACCCTGCGG
1 AACCCTGCGG
483766 AGATGGCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.25, G:0.33, T:0.17
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:483789 original size:42 final size:42
Alignment explanation
Indices: 483741--483830 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
483731 ATGTAACCCT
* *
483741 GAGGGCTAGGAATGTAACCCTGCGGAGATGGCATATAAACTG
1 GAGGGCTAGGAATATAACCCTGAGGAGATGGCATATAAACTG
* ** * * * *
483783 GTGGGCTTTGCATATACCCCTGAGGAGATGGCATCTGAACTG
1 GAGGGCTAGGAATATAACCCTGAGGAGATGGCATATAAACTG
483825 GAGGGC
1 GAGGGC
483831 AGGGCATTAT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (42 bp):
GAGGGCTAGGAATATAACCCTGAGGAGATGGCATATAAACTG
Found at i:485400 original size:28 final size:30
Alignment explanation
Indices: 485336--485402 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 30
485326 TCAGTTTCCT
485336 AAATAATATACATTATAAAAATTTATAATTA
1 AAATAATATACATTAT-AAAATTTATAATTA
* *
485367 ATATAA-ATTCATTAT-AAATTTA-AATTAA
1 AAATAATATACATTATAAAATTTATAATT-A
485395 AAATAATA
1 AAATAATA
485403 ATAAATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 4 0.13
28 13 0.42
29 1 0.03
30 8 0.26
31 5 0.16
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (30 bp):
AAATAATATACATTATAAAATTTATAATTA
Found at i:485587 original size:30 final size:31
Alignment explanation
Indices: 485548--485616 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
485538 TAATTAATAA
* *
485548 ATTTAAATAAATAATAATTATATAA-ATATT
1 ATTTTAATAAAAAATAATTATATAATATATT
*
485578 ATTTTAATAAAAAATATTTATATAATTATATT
1 ATTTTAATAAAAAATAATTATATAA-TATATT
*
485610 ACTTTAA
1 ATTTTAA
485617 AATATAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 22 0.67
32 11 0.33
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (31 bp):
ATTTTAATAAAAAATAATTATATAATATATT
Found at i:487563 original size:115 final size:115
Alignment explanation
Indices: 487316--487550 Score: 380
Period size: 115 Copynumber: 2.0 Consensus size: 115
487306 TCATTTCAAT
* * * *
487316 AAAAAAATATCAATTTAATTTATAACGGGATAATGATTCTGTCGGAAATTTTGTTCAACTTTAAT
1 AAAAAAATATCAATTTAATTAATAACGGGACAATGATTCCGTCGGAAATTTTGCTCAACTTTAAT
* **
487381 TAAAATATACCAATTTAATTTGTGATGGAATAATCATTTTGCCAGAAATA
66 TAAAATATACCAATTTAATTTGTGATAGAATAATCATTCCGCCAGAAATA
*
487431 AAAAAAATATCAATTTAATTAATGACGGGACAATGATTCCGTCGGAAATTTTGCTCAACTTTAAT
1 AAAAAAATATCAATTTAATTAATAACGGGACAATGATTCCGTCGGAAATTTTGCTCAACTTTAAT
* *
487496 TAAAATATACCAATTTAATTTGTGATAGAATACTCATTCCGTCAGAAATA
66 TAAAATATACCAATTTAATTTGTGATAGAATAATCATTCCGCCAGAAATA
487546 AAAAA
1 AAAAA
487551 TAACTACATT
Statistics
Matches: 110, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
115 110 1.00
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (115 bp):
AAAAAAATATCAATTTAATTAATAACGGGACAATGATTCCGTCGGAAATTTTGCTCAACTTTAAT
TAAAATATACCAATTTAATTTGTGATAGAATAATCATTCCGCCAGAAATA
Found at i:489562 original size:31 final size:31
Alignment explanation
Indices: 489527--489591 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
489517 ACAAATTTTT
*
489527 AAATTTGTGATGGAATATGTGGACCCATCAC
1 AAATTTGTGACGGAATATGTGGACCCATCAC
* *
489558 AAATTTGTGACGGAATATGTGGATCCGTCAC
1 AAATTTGTGACGGAATATGTGGACCCATCAC
489589 AAA
1 AAA
489592 GTTCTGACAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (31 bp):
AAATTTGTGACGGAATATGTGGACCCATCAC
Found at i:490539 original size:14 final size:13
Alignment explanation
Indices: 490411--490561 Score: 66
Period size: 13 Copynumber: 11.8 Consensus size: 13
490401 AAATAGTAAG
*
490411 TAAA-AAAACAAA
1 TAAATAAAATAAA
*
490423 T-AATAAAATATA
1 TAAATAAAATAAA
*
490435 TATAA-AAAAGAAA
1 TA-AATAAAATAAA
*
490448 -AAGA-AAAAGAAA
1 TAA-ATAAAATAAA
*
490460 TAAATAAAACAAA
1 TAAATAAAATAAA
*
490473 TAAACAAAAT-AA
1 TAAATAAAATAAA
* *
490485 T-AATAACA-AAG
1 TAAATAAAATAAA
* *
490496 TACGAATAATATATA
1 TA--AATAAAATAAA
*
490511 TATATAAAATAAA
1 TAAATAAAATAAA
490524 TAAATAAAAGTAAA
1 TAAATAAAA-TAAA
* *
490538 TATATATAAATTAA
1 TAAATA-AAATAAA
*
490552 TAAATTAAAT
1 TAAATAAAAT
490562 GACGAAAATA
Statistics
Matches: 105, Mismatches: 21, Indels: 25
0.70 0.14 0.17
Matches are distributed among these distances:
11 10 0.10
12 22 0.21
13 43 0.41
14 24 0.23
15 6 0.06
ACGTcount: A:0.70, C:0.03, G:0.04, T:0.23
Consensus pattern (13 bp):
TAAATAAAATAAA
Found at i:490854 original size:2 final size:2
Alignment explanation
Indices: 490786--490838 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
490776 CTTGTGTAGA
490786 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
490828 AT AT AT AT AT A
1 AT AT AT AT AT A
490839 GTAAAATGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:491090 original size:12 final size:11
Alignment explanation
Indices: 491063--491102 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
491053 TAACAAAATA
*
491063 AATAATATAA-
1 AATAATACAAG
491073 AATAATACAAG
1 AATAATACAAG
491084 TAATAATACAAG
1 -AATAATACAAG
491096 AATAATA
1 AATAATA
491103 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 9 0.33
11 7 0.26
12 11 0.41
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (11 bp):
AATAATACAAG
Found at i:491159 original size:20 final size:21
Alignment explanation
Indices: 491118--491221 Score: 60
Period size: 22 Copynumber: 4.9 Consensus size: 21
491108 AAAGAGAAAG
491118 TAAAAAATAATATAATAAAATA
1 TAAAAAATAATATAAT-AAATA
491140 TAAAAAATACATAT-AT-AATA
1 TAAAAAATA-ATATAATAAATA
*
491160 T---AAATAAGTAGAATAAA-A
1 TAAAAAATAA-TATAATAAATA
*
491178 GAAAAATATAATAGTAA-AAATAA
1 TAAAAA-ATAATA-TAATAAAT-A
491201 TAATAAATATAATAGTAATAA
1 TAA-AAA-ATAATA-TAATAA
491222 TAAAAATGCA
Statistics
Matches: 65, Mismatches: 4, Indels: 23
0.71 0.04 0.25
Matches are distributed among these distances:
16 1 0.02
17 7 0.11
18 3 0.05
19 2 0.03
20 5 0.08
21 7 0.11
22 17 0.26
23 7 0.11
24 14 0.22
25 2 0.03
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (21 bp):
TAAAAAATAATATAATAAATA
Found at i:491202 original size:12 final size:12
Alignment explanation
Indices: 491180--491224 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
491170 GAATAAAAGA
491180 AAAATATAATAGT
1 AAAA-ATAATAGT
*
491193 AAAAATAATAAT
1 AAAAATAATAGT
*
491205 AAATATAATAGT
1 AAAAATAATAGT
*
491217 AATAATAA
1 AAAAATAA
491225 AAATGCAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:491841 original size:37 final size:38
Alignment explanation
Indices: 491800--491903 Score: 142
Period size: 36 Copynumber: 2.8 Consensus size: 38
491790 GTGCTTGTGG
* * * *
491800 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTT-T
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAAATTCT
*
491837 ATCCTATTTTTAAGAGTTTGAATCCTA-TA-AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAAATTCT
491873 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
491904 GATGAAAAGG
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
35 4 0.07
36 29 0.50
37 25 0.43
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (38 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAAATTCT
Found at i:492862 original size:106 final size:106
Alignment explanation
Indices: 492573--494051 Score: 2106
Period size: 106 Copynumber: 14.0 Consensus size: 106
492563 GCATTGTTCT
* * ** * * *
492573 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACAGGGAAATTGTTTTTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
* * *
492637 ACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
492679 GAGTCCAATATCCTT-GCTGTGAAGTTGAAATTGACTCTG-AA-TGA-AA--T-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * * * *
492737 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * * *
492779 GA-TTCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTTTGGAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
492843 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
492884 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATT-AGGAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGA-GAAGTTGTTTGTTGACA
*
492948 ACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
492990 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGGTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
493055 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
493096 GAATCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * * *
493161 CCAGCAGTCCTTTCGTCGTGAAGTTGAACTTGCATTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
493202 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
493267 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** *
493308 AAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
493373 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
493414 GAGTCCAAAATCCTTTGTTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * *
493479 CCAGCAGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
493520 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
493585 CCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
493626 GAGTCCAATATCCTTAGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
493691 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
493732 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTGTTGACA
* *
493796 ACCA-CGGTCCCTTCGTCGTGGAGTTGAACTTGTGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
493837 GAGTCCAATATCCTTCGCTGTGAATTTGAAATTGGATATGAAATT-AGGAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGA-GAAGTTGTTTGTTGACA
* *
493901 ACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
493943 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCCGAAATTGAAAAATTG-TTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * ** *
494007 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTTTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
494048 GAGT
1 GAGT
494052 GGCACGATAT
Statistics
Matches: 1241, Mismatches: 114, Indels: 37
0.89 0.08 0.03
Matches are distributed among these distances:
98 1 0.00
99 53 0.04
100 25 0.02
101 2 0.00
102 5 0.00
103 3 0.00
104 2 0.00
105 169 0.14
106 979 0.79
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:494904 original size:22 final size:21
Alignment explanation
Indices: 494878--494929 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 21
494868 TGTTTGGTCA
494878 AAGGTTTGGCATTTGATGCTC
1 AAGGTTTGGCATTTGATGCTC
494899 ATAGGTTTGGCATTTGATGCTC
1 A-AGGTTTGGCATTTGATGCTC
494921 AACGGTTTG
1 AA-GGTTTG
494930 ATGGGGTAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 2 0.07
22 27 0.93
ACGTcount: A:0.19, C:0.13, G:0.29, T:0.38
Consensus pattern (21 bp):
AAGGTTTGGCATTTGATGCTC
Found at i:495549 original size:23 final size:23
Alignment explanation
Indices: 495523--495591 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 23
495513 TTGCATGTGC
495523 TTTTTGTCCCTTTTTCTTTTTGA
1 TTTTTGTCCCTTTTTCTTTTTGA
* *
495546 TTTTTGT-TCTTTCTTTTTTTTGA
1 TTTTTGTCCCTTT-TTCTTTTTGA
* *
495569 TTTTGTTTCTCTTTTTTCTTTTT
1 TTTT-TGTC-CCTTTTTCTTTTT
495592 TTTTCTTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
22 4 0.11
23 20 0.56
24 2 0.06
25 7 0.19
26 3 0.08
ACGTcount: A:0.03, C:0.13, G:0.07, T:0.77
Consensus pattern (23 bp):
TTTTTGTCCCTTTTTCTTTTTGA
Found at i:495577 original size:19 final size:18
Alignment explanation
Indices: 495555--495621 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 18
495545 ATTTTTGTTC
495555 TTTCTTTTTTTTGATTTT
1 TTTCTTTTTTTTGATTTT
*
495573 GTTTCTCTTTTTTCT-TTTTT
1 -TTTCT-TTTTTT-TGATTTT
* * *
495593 TTTC-TTCTTTTGCTTCT
1 TTTCTTTTTTTTGATTTT
495610 TTTCTTTTTTTT
1 TTTCTTTTTTTT
495622 CTTGATTGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
16 1 0.03
17 12 0.31
18 6 0.15
19 9 0.23
20 10 0.26
21 1 0.03
ACGTcount: A:0.01, C:0.13, G:0.04, T:0.81
Consensus pattern (18 bp):
TTTCTTTTTTTTGATTTT
Found at i:495600 original size:22 final size:22
Alignment explanation
Indices: 495546--495623 Score: 56
Period size: 21 Copynumber: 3.6 Consensus size: 22
495536 TTCTTTTTGA
*
495546 TTTTTGTTCTT-TCTTTTTT-T
1 TTTTTTTTCTTCTCTTTTTTCT
* *
495566 TGATTTTGT-TTCTCTTTTTTCT
1 T-TTTTTTTCTTCTCTTTTTTCT
*
495588 TTTTTTTTCTTCT-TTTGCTTCT
1 TTTTTTTTCTTCTCTTT-TTTCT
*
495610 TTTCTTTTTTTTCT
1 TTT-TTTTTCTTCT
495624 TGATTGGATC
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
20 3 0.07
21 20 0.44
22 13 0.29
23 9 0.20
ACGTcount: A:0.01, C:0.14, G:0.05, T:0.79
Consensus pattern (22 bp):
TTTTTTTTCTTCTCTTTTTTCT
Found at i:495621 original size:9 final size:9
Alignment explanation
Indices: 495533--495624 Score: 62
Period size: 9 Copynumber: 9.9 Consensus size: 9
495523 TTTTTGTCCC
495533 TTTTTCTTT
1 TTTTTCTTT
495542 TTGATTT-TTGT
1 TT--TTTCTT-T
*
495553 TCTTTCTTT
1 TTTTTCTTT
*
495562 TTTTTGATTT
1 TTTTT-CTTT
* *
495572 TGTTTCTCT
1 TTTTTCTTT
495581 TTTTTCTTTT
1 TTTTTC-TTT
*
495591 TTTTTCTTC
1 TTTTTCTTT
*
495600 TTTTGC-TT
1 TTTTTCTTT
*
495608 CTTTTCTTT
1 TTTTTCTTT
495617 TTTTTCTT
1 TTTTTCTT
495625 GATTGGATCT
Statistics
Matches: 62, Mismatches: 14, Indels: 14
0.69 0.16 0.16
Matches are distributed among these distances:
8 5 0.08
9 33 0.53
10 19 0.31
11 5 0.08
ACGTcount: A:0.02, C:0.13, G:0.05, T:0.79
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:495965 original size:14 final size:14
Alignment explanation
Indices: 495933--495966 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
495923 AATGCATGAT
*
495933 AGAATTATTTCGGA
1 AGAATTATTTCAGA
495947 AGAATTATTTCAGA
1 AGAATTATTTCAGA
*
495961 TGAATT
1 AGAATT
495967 CTTCTTCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (14 bp):
AGAATTATTTCAGA
Found at i:496784 original size:8 final size:8
Alignment explanation
Indices: 496771--496806 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
496761 GTAAATGAAG
496771 ATGCAAAA
1 ATGCAAAA
496779 ATGCAAAA
1 ATGCAAAA
496787 ATGC-AAA
1 ATGCAAAA
*
496794 ATGCAAGA
1 ATGCAAAA
496802 ATGCA
1 ATGCA
496807 TGAAATGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.14
Consensus pattern (8 bp):
ATGCAAAA
Found at i:496796 original size:15 final size:15
Alignment explanation
Indices: 496771--496806 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
496761 GTAAATGAAG
496771 ATGCAAAAATGCAAAA
1 ATGC-AAAATGCAAAA
*
496787 ATGCAAAATGCAAGA
1 ATGCAAAATGCAAAA
496802 ATGCA
1 ATGCA
496807 TGAAATGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.14
Consensus pattern (15 bp):
ATGCAAAATGCAAAA
Found at i:499406 original size:25 final size:25
Alignment explanation
Indices: 499378--499484 Score: 69
Period size: 27 Copynumber: 4.2 Consensus size: 25
499368 TAGTAAGTAA
499378 AAAAAACAAATAATAAAATATATAT
1 AAAAAACAAATAATAAAATATATAT
* * *
499403 AAAAAAGAAA-AAGAAAA-ATAAAT
1 AAAAAACAAATAATAAAATATATAT
*
499426 AAATAAAACAAATAAACAAAATA-ATAAT
1 -AA-AAAACAAAT-AATAAAATATAT-AT
* *
499454 AACAAAGTACGAATAAT-ATATATATAT
1 AA-AAA--ACAAATAATAAAATATATAT
499481 AAAA
1 AAAA
499485 TAAATAAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
23 5 0.08
24 8 0.13
25 16 0.25
26 2 0.03
27 20 0.32
28 7 0.11
29 5 0.08
ACGTcount: A:0.72, C:0.05, G:0.04, T:0.20
Consensus pattern (25 bp):
AAAAAACAAATAATAAAATATATAT
Found at i:499815 original size:2 final size:2
Alignment explanation
Indices: 499752--499796 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
499742 CTTGTGTAGA
499752 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
499794 AT A
1 AT A
499797 ATAGTAAAAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:499998 original size:2 final size:2
Alignment explanation
Indices: 499991--500047 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
499981 GAACATACGC
499991 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
500033 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
500048 CAAATAATAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:500138 original size:22 final size:23
Alignment explanation
Indices: 500097--500142 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
500087 AAGAGAAAGT
500097 AAAAATATAATAATAAAATATAA
1 AAAAATATAATAATAAAATATAA
* *
500120 AAAAATATACT-ATATAATATAA
1 AAAAATATAATAATAAAATATAA
500142 A
1 A
500143 TAAGTAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAAATATAATAATAAAATATAA
Found at i:500227 original size:61 final size:59
Alignment explanation
Indices: 500074--500227 Score: 145
Period size: 61 Copynumber: 2.5 Consensus size: 59
500064 AATATAAAAG
*
500074 AATAATAAAAAGAAAGAGAAAGTAAAAATATAATAATAAAATATAAAAAAATATACTATAT
1 AATAATAAAAAGAAAGA-AAAGT-AAAATATAATAATAAAATATAAAAAAATATAATATAT
* * * *
500135 AAT-ATAAATAAGTAGAATAAAAGGAAAATATAATAGTAAAA-ATAATAATAAATATAAT-TGT
1 AATAATAAA-AAG-A-AAGAAAAGTAAAATATAATAATAAAATATAA-AA-AAATATAATATAT
500196 AATAATAAAAATGCAAAGAAAA-TAAATATATA
1 AATAATAAAAA-G-AAAGAAAAGTAAA-ATATA
500228 TATATATTGG
Statistics
Matches: 77, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
60 12 0.16
61 42 0.55
62 20 0.26
63 3 0.04
ACGTcount: A:0.66, C:0.01, G:0.08, T:0.25
Consensus pattern (59 bp):
AATAATAAAAAGAAAGAAAAGTAAAATATAATAATAAAATATAAAAAAATATAATATAT
Found at i:500873 original size:37 final size:37
Alignment explanation
Indices: 500775--500875 Score: 148
Period size: 37 Copynumber: 2.7 Consensus size: 37
500765 GTGCTTGTGG
* * * * *
500775 ATCCTATCTTTAGGAGTTTAAATCATAATAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAACAAAACTCT
*
500812 ATCCTATTTTTAGGAGTTTGAATCCTAACAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAACAAAACTCT
500849 ATCCTATTTTTAGGAGTTTGAATCCTA
1 ATCCTATTTTTAGGAGTTTGAATCCTA
500876 GTAGGACGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAACAAAACTCT
Found at i:501208 original size:17 final size:17
Alignment explanation
Indices: 501153--501210 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
501143 GACTTGTTAG
*
501153 TATTATTATT-ATTATCT
1 TATTATT-TTAATTATAT
*
501170 AATT-TTTTAATTA-AT
1 TATTATTTTAATTATAT
501185 GTAATTATTTTAATTATAT
1 -T-ATTATTTTAATTATAT
501204 TATTATT
1 TATTATT
501211 AATTTTTGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
15 3 0.09
16 6 0.18
17 12 0.36
18 10 0.30
19 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
TATTATTTTAATTATAT
Found at i:501596 original size:19 final size:19
Alignment explanation
Indices: 501572--501621 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
501562 CTTCCCTCAG
* *
501572 AAATTCTGTTACTAAACTT
1 AAATTCCGTCACTAAACTT
501591 AAATTCCGTCACTAAACTT
1 AAATTCCGTCACTAAACTT
501610 AAATTCCGTCAC
1 AAATTCCGTCAC
501622 AAATTCCCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (19 bp):
AAATTCCGTCACTAAACTT
Found at i:503318 original size:114 final size:115
Alignment explanation
Indices: 503117--503341 Score: 389
Period size: 114 Copynumber: 2.0 Consensus size: 115
503107 TTAATTTTTT
*
503117 TAATGAACAACAAGCTTAACGAGTAACGAATCGAGTCGAGCAACAAGTTCTTTTAACTAGCATGA
1 TAATGAACAACAAGCTTAACGAGTAACGAATCGAGTCGAGCAACAAGTTCTTTTAACTAGCACGA
* *
503182 GTCGAGAAAAAAATTGACGAGCTTAACGAGCAACGAATCGAGTCGAGCAG
66 GTCAAGAAAAAAATTGACGAGCTTAACGAACAACGAATCGAGTCGAGCAG
503232 TAATGAACAACAAGCTTAACGAGTAACGAATCG-GTCGAGCAACAAGTTCTTTTAACTAGCACGA
1 TAATGAACAACAAGCTTAACGAGTAACGAATCGAGTCGAGCAACAAGTTCTTTTAACTAGCACGA
* * *
503296 GTCAAGAAAAAAATTGATGAGCTTAACGAACAACGAGTTGAGTCGA
66 GTCAAGAAAAAAATTGACGAGCTTAACGAACAACGAATCGAGTCGA
503342 ACACCTAAAA
Statistics
Matches: 104, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
114 71 0.68
115 33 0.32
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (115 bp):
TAATGAACAACAAGCTTAACGAGTAACGAATCGAGTCGAGCAACAAGTTCTTTTAACTAGCACGA
GTCAAGAAAAAAATTGACGAGCTTAACGAACAACGAATCGAGTCGAGCAG
Found at i:504008 original size:102 final size:97
Alignment explanation
Indices: 503827--504084 Score: 272
Period size: 102 Copynumber: 2.6 Consensus size: 97
503817 TCAATCTCTT
* * ** * * *
503827 AAAAATTAATTTAAATATGAATTAACTTTTATTTTTATTTAAT-ATTT-TTAATTAGTCTAATAA
1 AAAAATTAATTTAAATA-AAATTGACTCATATTTTTGTTTAATAATTTATAAATTA-T-TAAAAA
* *
503890 TTTAAATATTATAATATTTTTGTTGAATTCAGTCCCTA
63 TTGAAATATTATAATATTTGTGTTGAATTCAGT--C-A
503928 AAAAATTAATTTAAATTAAAATTGACTCATATTATTTGTTTAATAATTTATAAATTATTAAAAAT
1 AAAAATTAATTTAAA-TAAAATTGACTCATATT-TTTGTTTAATAATTTATAAATTATTAAAAAT
*
503993 TGAAATATTATAATATTTGTGTTGGATTCAGTCA
64 TGAAATATTATAATATTTGTGTTGAATTCAGTCA
* * * *
504027 AAAAATT-ATTTAAACTAAAACTGA-ACACTATTTTTGTTTAATATTTTATAATTTATTA
1 AAAAATTAATTTAAA-TAAAATTGACTCA-TATTTTTGTTTAATAATTTATAAATTATTA
504085 TAATATTTGT
Statistics
Matches: 137, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
97 26 0.19
98 19 0.14
99 8 0.06
100 1 0.01
101 26 0.19
102 46 0.34
103 5 0.04
104 6 0.04
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.47
Consensus pattern (97 bp):
AAAAATTAATTTAAATAAAATTGACTCATATTTTTGTTTAATAATTTATAAATTATTAAAAATTG
AAATATTATAATATTTGTGTTGAATTCAGTCA
Found at i:504611 original size:84 final size:84
Alignment explanation
Indices: 504451--504638 Score: 195
Period size: 84 Copynumber: 2.2 Consensus size: 84
504441 CAATTTATTA
* * * * * *
504451 TAATATTTGAAATATTATAATGTTTTTATTGTATTCAGTCCCTCAAAAATTAATTTGAATCAATA
1 TAATATTTTAAATATTATAATGATTTGATTGGATTCAATCCCTCAAAAATTAATTTAAATCAATA
*
504516 TTAACTACTATT-TTTAGTT
66 TTAACCACTATTATTT-GTT
504535 TAATATTTTAAATATTATAAT-ATTTGAGTTGGATTCAATCCCT-AAATAATTAATTTAAATC-A
1 TAATATTTTAAATATTATAATGATTTGA-TTGGATTCAATCCCTCAAA-AATTAATTTAAATCAA
* *
504597 TAATTGACCCCTATTATTTGTT
64 T-ATTAACCACTATTATTTGTT
*
504619 TATTAATTTATAAATGATTA
1 TAAT-ATTT-TAAAT-ATTA
504639 CATTTGTTAA
Statistics
Matches: 87, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
83 9 0.10
84 62 0.71
85 7 0.08
86 5 0.06
87 4 0.05
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (84 bp):
TAATATTTTAAATATTATAATGATTTGATTGGATTCAATCCCTCAAAAATTAATTTAAATCAATA
TTAACCACTATTATTTGTT
Found at i:508260 original size:57 final size:57
Alignment explanation
Indices: 508162--508270 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 57
508152 GGTAAATAAA
* * *
508162 AATTGAGTATATTATTACTCATTATTATTATAATATAATAATA-TATTATTATAATAT
1 AATTGAGCATATTATTACTCATTATAATTAAAATATAATAATATTA-TATTATAATAT
*
508219 AATTGAGCATATTATTACTCATTATAATATAAAAT-TTATAATATTATATTAT
1 AATTGAGCATATTATTACTCATTATAAT-TAAAATATAATAATATTATATTAT
508271 TAAAATTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
57 39 0.85
58 7 0.15
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.48
Consensus pattern (57 bp):
AATTGAGCATATTATTACTCATTATAATTAAAATATAATAATATTATATTATAATAT
Found at i:508279 original size:22 final size:23
Alignment explanation
Indices: 508230--508284 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
508220 ATTGAGCATA
*
508230 TTATTACTCATTATAATATAAAAT
1 TTATTAAT-ATTATAATATAAAAT
*
508254 TTA-TAATATTATATTATTAAAA-
1 TTATTAATATTATAATA-TAAAAT
508276 TTATTAATA
1 TTATTAATA
508285 AATGTATTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 11 0.41
23 13 0.48
24 3 0.11
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
TTATTAATATTATAATATAAAAT
Found at i:510583 original size:25 final size:25
Alignment explanation
Indices: 510547--510616 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
510537 GAAGATGTGG
510547 TTGTTG-AGGCATTCTGGAGAAA-GA
1 TTGTTGTA-GCATTCTGGAGAAATGA
* *
510571 TATGTTGTAGCATGCTGGAGAAATGG
1 T-TGTTGTAGCATTCTGGAGAAATGA
*
510597 TTGTTGTAGCATTCTAGAGA
1 TTGTTGTAGCATTCTGGAGA
510617 TGGAAAGATA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
24 1 0.03
25 35 0.90
26 3 0.08
ACGTcount: A:0.27, C:0.09, G:0.31, T:0.33
Consensus pattern (25 bp):
TTGTTGTAGCATTCTGGAGAAATGA
Found at i:512436 original size:18 final size:20
Alignment explanation
Indices: 512413--512457 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
512403 AATTGGTACT
512413 GATACTG-AGGC-CAATATC
1 GATACTGAAGGCTCAATATC
512431 GATACTGACAGGCTCAATATC
1 GATACTGA-AGGCTCAATATC
*
512452 AATACT
1 GATACT
512458 AACGAGCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.30
20 4 0.17
21 12 0.52
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (20 bp):
GATACTGAAGGCTCAATATC
Found at i:531534 original size:32 final size:32
Alignment explanation
Indices: 531484--531549 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
531474 ATCTTGGGGA
* *
531484 CTAAGAGCCTACCCAAGGAAGTACCTTAGGGC
1 CTAAAAGCCTACCCAAGGAAGTAACTTAGGGC
* *
531516 CTAAAAGCCTACCTAAGGAAGTAACTTGGGGC
1 CTAAAAGCCTACCCAAGGAAGTAACTTAGGGC
531548 CT
1 CT
531550 TAGAGTCTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (32 bp):
CTAAAAGCCTACCCAAGGAAGTAACTTAGGGC
Found at i:535202 original size:17 final size:16
Alignment explanation
Indices: 535180--535214 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
535170 TTTCTTAATC
535180 AATTTAAACTATAAAAT
1 AATTTAAA-TATAAAAT
*
535197 AATTTATATATAAAAT
1 AATTTAAATATAAAAT
535213 AA
1 AA
535215 AATTTGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTTAAATATAAAAT
Found at i:537214 original size:19 final size:19
Alignment explanation
Indices: 537197--537242 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
537187 TGAAAAGATT
537197 TAATAAAATAAAATAGATAA
1 TAAT-AAATAAAATAGATAA
**
537217 TAATAAATAAAAGGGA-AA
1 TAATAAATAAAATAGATAA
537235 TAATAAAT
1 TAATAAAT
537243 TAATAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 10 0.42
19 10 0.42
20 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (19 bp):
TAATAAATAAAATAGATAA
Found at i:544035 original size:17 final size:18
Alignment explanation
Indices: 544001--544042 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
543991 GTTGTTTTTG
544001 AAATAAAAGATAAGAATT
1 AAATAAAAGATAAGAATT
*
544019 AAATAAAA-ATAATAATT
1 AAATAAAAGATAAGAATT
*
544036 AACTAAA
1 AAATAAA
544043 TAACCTAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:548167 original size:2 final size:2
Alignment explanation
Indices: 548160--548194 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
548150 TTCACCCAGG
548160 TA TA TA TA 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 TA TA TA TA T
548195 CGATCGAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:548561 original size:92 final size:92
Alignment explanation
Indices: 548404--548584 Score: 335
Period size: 92 Copynumber: 2.0 Consensus size: 92
548394 TTGGACCCAG
*
548404 GAGATTGACCTCCGTCCCTCCACCACAAGACTATATTAGCCATTATTCCATATTCCCATTTCCTC
1 GAGATTGACCTCCGTCCCTCCACCACAAGACTATATTAGCCATTATTCAATATTCCCATTTCCTC
548469 AACTTGCTCCTTTTAAACCTTCACAGC
66 AACTTGCTCCTTTTAAACCTTCACAGC
* *
548496 GAGATTGACCTCCGTCCCTCCACCACCAGACTTTATTAGCCATTATTCAATATTCCCATTTCCTC
1 GAGATTGACCTCCGTCCCTCCACCACAAGACTATATTAGCCATTATTCAATATTCCCATTTCCTC
548561 AACTTGCTCCTTTTAAACCTTCAC
66 AACTTGCTCCTTTTAAACCTTCAC
548585 GGCTTCTACT
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 86 1.00
ACGTcount: A:0.24, C:0.35, G:0.08, T:0.33
Consensus pattern (92 bp):
GAGATTGACCTCCGTCCCTCCACCACAAGACTATATTAGCCATTATTCAATATTCCCATTTCCTC
AACTTGCTCCTTTTAAACCTTCACAGC
Found at i:555850 original size:2 final size:2
Alignment explanation
Indices: 555843--555880 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
555833 GTATCCATAG
555843 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
555881 CAAAATATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:565556 original size:17 final size:18
Alignment explanation
Indices: 565536--565574 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
565526 CTTAGGTATA
*
565536 GATAC-TCCTTGAGTACC
1 GATACTTCCATGAGTACC
565553 GATACTTCCATGAGTACC
1 GATACTTCCATGAGTACC
565571 GATA
1 GATA
565575 TCAGGATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (18 bp):
GATACTTCCATGAGTACC
Found at i:569708 original size:19 final size:18
Alignment explanation
Indices: 569684--569724 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
569674 TTTTAATACA
569684 TAAAATATATAAAAATTAT
1 TAAAATATATAAAAATT-T
*
569703 TAAAATATATAATAATTT
1 TAAAATATATAAAAATTT
569721 TAAA
1 TAAA
569725 TTTTGAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATATATAAAAATTT
Found at i:572641 original size:22 final size:22
Alignment explanation
Indices: 572599--572641 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
572589 AAACGGACCC
**
572599 TTAAATTTGAACAATTTAAAAT
1 TTAAATTTGAACAATCGAAAAT
572621 TTAAA-TTGAACAAATCGAAAA
1 TTAAATTTGAAC-AATCGAAAA
572642 CTAATTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (22 bp):
TTAAATTTGAACAATCGAAAAT
Found at i:572762 original size:67 final size:67
Alignment explanation
Indices: 572651--572787 Score: 256
Period size: 67 Copynumber: 2.0 Consensus size: 67
572641 ACTAATTTGT
*
572651 ATCACCAACAATATATAGTCCCAATCATGCAAGGAATGAGGCATCATAATAACAAGTTTTATTTA
1 ATCACCAACAATATATAGTCCCAATCATGCAAGGAATGAAGCATCATAATAACAAGTTTTATTTA
572716 GA
66 GA
*
572718 ATCACCCACAATATATAGTCCCAATCATGCAAGGAATGAAGCATCATAATAACAAGTTTTATTTA
1 ATCACCAACAATATATAGTCCCAATCATGCAAGGAATGAAGCATCATAATAACAAGTTTTATTTA
572783 GA
66 GA
572785 ATC
1 ATC
572788 TATGTATTCA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (67 bp):
ATCACCAACAATATATAGTCCCAATCATGCAAGGAATGAAGCATCATAATAACAAGTTTTATTTA
GA
Found at i:581500 original size:31 final size:31
Alignment explanation
Indices: 581435--581517 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
581425 CCAAAATAAA
*
581435 TAAA-TTTTGGAAATTACACTTTTGGTATCC
1 TAAACTTTTGGAAATTACACTTTTGGTACCC
581465 -AAACTTTTGGAATATTACTA-TTTTGGT-CCC
1 TAAACTTTTGGAA-ATTAC-ACTTTTGGTACCC
** *
581495 TAAACTTTTCTAAATTATACTTT
1 TAAACTTTTGGAAATTACACTTT
581518 AGAAACTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
29 4 0.09
30 17 0.39
31 22 0.50
32 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (31 bp):
TAAACTTTTGGAAATTACACTTTTGGTACCC
Found at i:581967 original size:2 final size:2
Alignment explanation
Indices: 581960--582004 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
581950 TACACTTTCG
581960 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
582002 TA T
1 TA T
582005 CATACACATC
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:583977 original size:27 final size:27
Alignment explanation
Indices: 583943--583996 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
583933 TTTAGGATGA
583943 AATTGCAAGCTTTTGAATGTTTAAGTG
1 AATTGCAAGCTTTTGAATGTTTAAGTG
583970 AATTGCAAGCTTTTGAATGTTTAAGTG
1 AATTGCAAGCTTTTGAATGTTTAAGTG
583997 TTGATTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (27 bp):
AATTGCAAGCTTTTGAATGTTTAAGTG
Found at i:591082 original size:28 final size:26
Alignment explanation
Indices: 591017--591090 Score: 89
Period size: 28 Copynumber: 2.8 Consensus size: 26
591007 AATATAGGTT
*
591017 GTTATTGTAATATGTAAAAA-TATGA
1 GTTATTGTAATTTGTAAAAAGTATGA
*
591042 GTTAATGTAATTTGTAAAAAGTAATGTCA
1 GTTATTGTAATTTGTAAAAAGT-ATG--A
591071 -TTATTGTAATTTGTAAAAAG
1 GTTATTGTAATTTGTAAAAAG
591091 ATTTGTTCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 18 0.43
26 1 0.02
27 3 0.07
28 19 0.45
29 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.16, T:0.41
Consensus pattern (26 bp):
GTTATTGTAATTTGTAAAAAGTATGA
Found at i:591182 original size:87 final size:87
Alignment explanation
Indices: 591072--591231 Score: 207
Period size: 87 Copynumber: 1.8 Consensus size: 87
591062 GTAATGTCAT
* * * * *
591072 TATTGTAATTTGTAAAAAGATTTGTTCT-CTATT-TAAAATTATAAAAAGATTTGTGCTTTATTG
1 TATTATAATTTATAAAAAGATTTG-TCTGCTATTGT-AAATTATAAAAAGATTTGTCCTTAAATG
591135 TAATTTATAAGAAGATTTATCTTC
64 TAATTTATAAGAAGATTTATCTTC
* * **
591159 TATTATAATTTATAAAAAGATTTGTCTGTTATTGTAATTTATAAAAATCTTTGTCCTTAAATGTA
1 TATTATAATTTATAAAAAGATTTGTCTGCTATTGTAAATTATAAAAAGATTTGTCCTTAAATGTA
591224 ATTTATAA
66 ATTTATAA
591232 AAAATTATTT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
86 3 0.05
87 58 0.94
88 1 0.02
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (87 bp):
TATTATAATTTATAAAAAGATTTGTCTGCTATTGTAAATTATAAAAAGATTTGTCCTTAAATGTA
ATTTATAAGAAGATTTATCTTC
Found at i:591211 original size:29 final size:28
Alignment explanation
Indices: 591047--591234 Score: 182
Period size: 29 Copynumber: 6.5 Consensus size: 28
591037 TATGAGTTAA
* * *
591047 TGTAATTTGTAAAAAG-TAATGTCATTAT
1 TGTAATTTATAAAAAGAT-TTGTCTTTAT
* *
591075 TGTAATTTGTAAAAAGATTTGTTCTCTAT
1 TGTAATTTATAAAAAGATTTG-TCTTTAT
*
591104 T-TAAAATTATAAAAAGATTTGTGCTTTAT
1 TGT-AATTTATAAAAAGATTTGT-CTTTAT
* *
591133 TGTAATTTATAAGAAGATTTATCTTCTAT
1 TGTAATTTATAAAAAGATTTGTCTT-TAT
*
591162 TATAATTTATAAAAAGATTTGTCTGTTAT
1 TGTAATTTATAAAAAGATTTGTCT-TTAT
** * *
591191 TGTAATTTATAAAAATCTTTGTCCTTAAA
1 TGTAATTTATAAAAAGATTTGT-CTTTAT
591220 TGTAATTTATAAAAA
1 TGTAATTTATAAAAA
591235 ATTATTTAAT
Statistics
Matches: 135, Mismatches: 17, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
28 23 0.17
29 108 0.80
30 4 0.03
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (28 bp):
TGTAATTTATAAAAAGATTTGTCTTTAT
Found at i:596242 original size:20 final size:21
Alignment explanation
Indices: 596196--596256 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
596186 TTCCCCTGTG
596196 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
596219 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
596239 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
596257 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:606949 original size:23 final size:23
Alignment explanation
Indices: 606915--606959 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
606905 TTATGTTTGA
*
606915 ATAAATATTATTCTAATATATTT
1 ATAAATATTATTATAATATATTT
*
606938 ATAAAT-TATATTATATTATATT
1 ATAAATAT-TATTATAATATATT
606960 ATTATATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
ATAAATATTATTATAATATATTT
Found at i:607311 original size:60 final size:60
Alignment explanation
Indices: 607218--607395 Score: 191
Period size: 60 Copynumber: 3.0 Consensus size: 60
607208 TCCCTCAACC
* * **
607218 ATGACTCTCGTTAC-AAATTAGT-CTTGAAACTTTTAAATACTCCAATTTCATCCTTAAACT
1 ATGACTCTCATT-CTAAATTAGTCCTT-AAACTTTTAAATACTTCAATTTCATCCCCAAACT
* * * *
607278 ATGACTCTCATTCTAAATTAGTCCTTAAACTTTTGAACATTTAAATTTCATCCCCAAACT
1 ATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAATACTTCAATTTCATCCCCAAACT
* * * * *
607338 ATGAATCTCATTCTAAATTGGTCCCTCAACTTTTAGAT-CTTTCAATTTCATCCCCAAA
1 ATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAATAC-TTCAATTTCATCCCCAAA
607396 TTCATTCAAA
Statistics
Matches: 98, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
59 1 0.01
60 94 0.96
61 3 0.03
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (60 bp):
ATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAATACTTCAATTTCATCCCCAAACT
Found at i:609889 original size:27 final size:25
Alignment explanation
Indices: 609853--609902 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
609843 AATATAACAC
*
609853 ACACACATATATATATGCAACACGT
1 ACACACACATATATATGCAACACGT
609878 ACACACACATATATATGCAACACGT
1 ACACACACATATATATGCAACACGT
609903 GCAACTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.26, G:0.08, T:0.22
Consensus pattern (25 bp):
ACACACACATATATATGCAACACGT
Found at i:609941 original size:19 final size:21
Alignment explanation
Indices: 609917--609955 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
609907 CTATAATAAT
*
609917 CAATTA-A-ATAAACATGTAG
1 CAATTATATATAAAAATGTAG
609936 CAATTATATATAAAAATGTA
1 CAATTATATATAAAAATGTA
609956 CAAATATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (21 bp):
CAATTATATATAAAAATGTAG
Found at i:613837 original size:37 final size:38
Alignment explanation
Indices: 613787--613859 Score: 112
Period size: 39 Copynumber: 1.9 Consensus size: 38
613777 TTTCCCTTTT
613787 TTAAAATATA-TTTTTCTTGTTTTCCCTTAGTTTTCAC
1 TTAAAATATATTTTTTCTTGTTTTCCCTTAGTTTTCAC
* *
613824 TTAAAATATATTTTTTTCTTGTTTTGCCTTGGTTTT
1 TTAAAATATA-TTTTTTCTTGTTTTCCCTTAGTTTT
613860 AAGATAGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 10 0.31
39 22 0.69
ACGTcount: A:0.19, C:0.12, G:0.08, T:0.60
Consensus pattern (38 bp):
TTAAAATATATTTTTTCTTGTTTTCCCTTAGTTTTCAC
Found at i:616167 original size:20 final size:20
Alignment explanation
Indices: 616142--616182 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
616132 CAAAAAGCCT
616142 ACTGGAATATTGGTATCGAG
1 ACTGGAATATTGGTATCGAG
* *
616162 ACTGGAATGTTGGTTTCGAG
1 ACTGGAATATTGGTATCGAG
616182 A
1 A
616183 TTGACATGGA
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:0.27, C:0.10, G:0.32, T:0.32
Consensus pattern (20 bp):
ACTGGAATATTGGTATCGAG
Found at i:618509 original size:19 final size:19
Alignment explanation
Indices: 618485--618521 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
618475 ATAACCAACA
*
618485 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
618504 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
618522 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:618639 original size:61 final size:62
Alignment explanation
Indices: 618547--618702 Score: 181
Period size: 61 Copynumber: 2.5 Consensus size: 62
618537 GTTTCCAGAT
* * *** * * * **
618547 TCGCAACGCAATTTTGACTATCGCGTTGCGATTTTAGAAAATCGCAATGCGAAT-AT-GTAAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATTATACAAAATCGCAATG-AAATAATACAAAA
*
618608 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAATCGCAATGAAATAATACAAAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATTATACAAAATCGCAATGAAATAATACAAAA
*
618670 TCGCAACGCGATTCTGACTATCACAACGCGATT
1 TCGCAACGCGATTCTGACTATCGCAACGCGATT
618703 CTGACTATCG
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
60 3 0.04
61 43 0.54
62 34 0.43
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.24
Consensus pattern (62 bp):
TCGCAACGCGATTCTGACTATCGCAACGCGATTATACAAAATCGCAATGAAATAATACAAAA
Found at i:618698 original size:20 final size:20
Alignment explanation
Indices: 618673--618741 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
618663 TACAAAATCG
618673 CAACGCGATTCTGACTATCA
1 CAACGCGATTCTGACTATCA
*
618693 CAACGCGATTCTGACTATCG
1 CAACGCGATTCTGACTATCA
* *
618713 CAACGTGATCCTGACTATCA
1 CAACGCGATTCTGACTATCA
618733 CAACGCGAT
1 CAACGCGAT
618742 AATAAAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.23
Consensus pattern (20 bp):
CAACGCGATTCTGACTATCA
Found at i:618782 original size:21 final size:21
Alignment explanation
Indices: 618758--618804 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
618748 AAATCGCAAC
618758 GCGATAGTCCAAGTTCACGTT
1 GCGATAGTCCAAGTTCACGTT
* *
618779 GCGATAGTCGAAGTTCGCGTT
1 GCGATAGTCCAAGTTCACGTT
618800 GCGAT
1 GCGAT
618805 TTTCCAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (21 bp):
GCGATAGTCCAAGTTCACGTT
Found at i:623768 original size:19 final size:20
Alignment explanation
Indices: 623743--623833 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 20
623733 CTTATTTTGA
623743 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
623763 -TTTTTCACTATCGTAACAACAC
1 ATTTTTCACTATCG---CAACAC
*
623785 ATTTTTCAAACTCTCGCAACAC
1 ATTTTTC--ACTATCGCAACAC
*
623807 A-TTTTAACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
623826 ATTTTTCA
1 ATTTTTCA
623834 AAATCGCATT
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 26 0.43
20 5 0.08
21 4 0.07
22 13 0.22
23 6 0.10
25 6 0.10
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.36
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:623805 original size:44 final size:41
Alignment explanation
Indices: 623754--623835 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 41
623744 TTTTTCACTA
* *
623754 TCGCAACACTTTTTCACTATCGTAACAACACATTTTTCAAACTC
1 TCGCAACACATTTTAACTATCG---CAACACATTTTTCAAACTC
623798 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
1 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
623836 ATCGCATTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 16 0.44
44 20 0.56
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (41 bp):
TCGCAACACATTTTAACTATCGCAACACATTTTTCAAACTC
Found at i:627470 original size:19 final size:19
Alignment explanation
Indices: 627446--627501 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 19
627436 TCTACATTTT
627446 TATGTGTAGATATTATATA
1 TATGTGTAGATATTATATA
627465 TATGTGTAGATATTATATA
1 TATGTGTAGATATTATATA
*
627484 GATGTGTA-ATATT-TATA
1 TATGTGTAGATATTATATA
627501 T
1 T
627502 TTGAGCATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.11
18 5 0.14
19 26 0.74
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (19 bp):
TATGTGTAGATATTATATA
Found at i:627600 original size:19 final size:20
Alignment explanation
Indices: 627572--627612 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
627562 ATTTTATAAA
* *
627572 ATTATTTTTTTATAAT-TTT
1 ATTATGTTTTCATAATATTT
627591 ATTATGTTTTCATAATATTT
1 ATTATGTTTTCATAATATTT
627611 AT
1 AT
627613 AATATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
ATTATGTTTTCATAATATTT
Found at i:627818 original size:29 final size:27
Alignment explanation
Indices: 627767--627837 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
627757 GAAAATTTTA
* * *
627767 TAAAACAATATTATAATATATAATTAT
1 TAAAAAAATATAATAATATATAAATAT
627794 TAAAAAAATATAATTAATATTATAAATAT
1 TAAAAAAATATAA-TAATA-TATAAATAT
*
627823 AACAAAAAACTATAA
1 TA-AAAAAA-TATAA
627838 CATAAAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 11 0.31
28 5 0.14
29 9 0.25
30 6 0.17
31 5 0.14
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (27 bp):
TAAAAAAATATAATAATATATAAATAT
Found at i:630450 original size:29 final size:28
Alignment explanation
Indices: 630403--630468 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
630393 GGCTTGCGTG
*
630403 AAAAAATAATTAGTAATTATAAAAATATA
1 AAAAAATAATTAGAAATTATAAAAATA-A
**
630432 AAAAAATAATT-GAACATTATATTAATAA
1 AAAAAATAATTAGAA-ATTATAAAAATAA
630460 AAAAAATAA
1 AAAAAATAA
630469 ATTAACTTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 12 0.36
29 21 0.64
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.29
Consensus pattern (28 bp):
AAAAAATAATTAGAAATTATAAAAATAA
Found at i:631486 original size:40 final size:41
Alignment explanation
Indices: 631408--631506 Score: 137
Period size: 40 Copynumber: 2.4 Consensus size: 41
631398 AAAAAATAAA
* *
631408 ACTCATTTACCCTTATTTTGAAAAAAAAAACATGTAACATAT
1 ACTCATTTACCCTTATTTTG-AAAAAAAAACATATAACACAT
* *
631450 TCTCATTTTCCCTTATTTTG-AAAAAAAACATATAACACAT
1 ACTCATTTACCCTTATTTTGAAAAAAAAACATATAACACAT
*
631490 ACTCATTTCCCCTTATT
1 ACTCATTTACCCTTATT
631507 GACTTACACC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
40 33 0.65
42 18 0.35
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.37
Consensus pattern (41 bp):
ACTCATTTACCCTTATTTTGAAAAAAAAACATATAACACAT
Found at i:632595 original size:9 final size:9
Alignment explanation
Indices: 632581--632623 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
632571 ATCATTAATT
632581 TTATGTTCA
1 TTATGTTCA
632590 TTATGTTCA
1 TTATGTTCA
*
632599 GTCTAGTGTTGA
1 -T-TA-TGTTCA
632611 TTATGTTCA
1 TTATGTTCA
632620 TTAT
1 TTAT
632624 CTCTTATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
9 18 0.62
10 3 0.10
11 3 0.10
12 5 0.17
ACGTcount: A:0.21, C:0.09, G:0.16, T:0.53
Consensus pattern (9 bp):
TTATGTTCA
Found at i:633448 original size:38 final size:37
Alignment explanation
Indices: 633379--633453 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
633369 ATACTAGACA
* * * *
633379 CATATATTATCATAAATATATTATCTACATATTTATT
1 CATATATTATCATAAACATAATATCAACATATATATT
633416 CATAT-TTATTCAGTAAACATAATATCAACATATATATT
1 CATATATTA-TCA-TAAACATAATATCAACATATATATT
633454 AACCACCTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 3 0.09
37 8 0.25
38 21 0.66
ACGTcount: A:0.43, C:0.12, G:0.01, T:0.44
Consensus pattern (37 bp):
CATATATTATCATAAACATAATATCAACATATATATT
Found at i:633494 original size:27 final size:27
Alignment explanation
Indices: 633445--633496 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
633435 TAATATCAAC
* *
633445 ATATATATTAACCACCTACAATCAGAA
1 ATATATATTAACAACATACAATCAGAA
* *
633472 ATATATATTCACAACATATAATCAG
1 ATATATATTAACAACATACAATCAG
633497 TAAAGCATAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.04, T:0.29
Consensus pattern (27 bp):
ATATATATTAACAACATACAATCAGAA
Found at i:635016 original size:15 final size:15
Alignment explanation
Indices: 634996--635025 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
634986 ATGAGGGAAT
634996 TGAATTCCATCCAAG
1 TGAATTCCATCCAAG
635011 TGAATTCCATCCAAG
1 TGAATTCCATCCAAG
635026 AATGGATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (15 bp):
TGAATTCCATCCAAG
Found at i:635651 original size:268 final size:256
Alignment explanation
Indices: 635111--635697 Score: 808
Period size: 263 Copynumber: 2.2 Consensus size: 256
635101 TTATTCATAC
*
635111 ATTGAATAAAAATATTTTTTTATTATTTC-G--GG-TCGGGTCGGGTTTCTAATTCATATATTCG
1 ATTGAATAAAAATAATTTTTTATTATTTCGGTCGGTTCGGGTC-GGTTTCTAATTCATATATTCG
* * * *
635172 GGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGGG
65 GGTCGGGTGAAACTTTATTTTGGTCAGGTCGGATCGGGTTTTTTAAGTGTGATATTCGGGTCAGG
* * * *
635237 TCGAGTTTGGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATATATT
130 TCGAGTTCGGGTTTAGGGTGAAAAAAACCCGACCCAAAAAAATATATAATTTTACCTTATATATT
* * * * *
635302 TAGGAGTAATTACAATAATATCCCTCTATATATATTTTTTTTTCAATTAAGTCATTGTTTTT
195 TAGGAATAATTACAATAATACCCCTCTATATATATATTTTTTTCAATTAAATCAATGTTTTT
635364 ATTGAATAAAAATAATTTTTTATTATTTCGGGTCGGTTCGGGTCGGATTTCTAATTCATATATCC
1 ATTGAATAAAAATAATTTTTTATTATTTC-GGTCGGTTCGGGTCGG-TTTCTAATTCATATAT--
*
635429 GGGTCGGGTCGGGTGAAACTTTATTTTGTTCAGGTCGGATCGGGTTTTTTAAGTGTGATATTCGG
62 ---TCGGGTCGGGTGAAACTTTATTTTGGTCAGGTCGGATCGGGTTTTTTAAGTGTGATATTCGG
*
635494 GTCAGGTCGGGTTCGGGTTTAGGGTGAAAAAAACTGGACCGACCCAAAAAAAATATATAATTTTA
124 GTCAGGTCGAGTTCGGGTTTAGGGTGAAAAAAAC----CCGACCC-AAAAAAATATATAATTTTA
635559 CCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATA-ATTTTTTTCAATTAAATCA
184 CCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATATATTTTTTTCAATTAAATCA
635623 ATGTTTTT
249 ATGTTTTT
*
635631 ATTGAATAAAAATAAATTTTTATTATTATTTTGTGTC-GTGTCGGGTCAGGTTTCTAATTCATAT
1 ATTGAATAAAAAT-AA-TTTT-TTATTATTTCG-GTCGGT-TCGGGTC-GGTTTCTAATTCATAT
635695 ATT
60 ATT
635698 GAATAAAAAT
Statistics
Matches: 295, Mismatches: 17, Indels: 32
0.86 0.05 0.09
Matches are distributed among these distances:
253 28 0.09
255 1 0.00
257 4 0.01
258 23 0.08
263 88 0.30
265 1 0.00
267 44 0.15
268 62 0.21
269 7 0.02
270 35 0.12
271 2 0.01
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.41
Consensus pattern (256 bp):
ATTGAATAAAAATAATTTTTTATTATTTCGGTCGGTTCGGGTCGGTTTCTAATTCATATATTCGG
GTCGGGTGAAACTTTATTTTGGTCAGGTCGGATCGGGTTTTTTAAGTGTGATATTCGGGTCAGGT
CGAGTTCGGGTTTAGGGTGAAAAAAACCCGACCCAAAAAAATATATAATTTTACCTTATATATTT
AGGAATAATTACAATAATACCCCTCTATATATATATTTTTTTCAATTAAATCAATGTTTTT
Found at i:638559 original size:30 final size:30
Alignment explanation
Indices: 638519--638582 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
638509 TGAATTTGTA
* * * *
638519 TTTTGTTATTTTAGTCATTTAATTTTATGT
1 TTTTGCTATTTAACTCATTTAATTTCATGT
*
638549 TTTTGCTATTTAACTCCTTTAATTTCATGT
1 TTTTGCTATTTAACTCATTTAATTTCATGT
638579 TTTT
1 TTTT
638583 AAAATTTCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.09, G:0.08, T:0.64
Consensus pattern (30 bp):
TTTTGCTATTTAACTCATTTAATTTCATGT
Found at i:641882 original size:6 final size:6
Alignment explanation
Indices: 641867--641924 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
641857 GAACAAGAGC
* * *
641867 AAAAAGG AAAAAG AAAAAG AAATA- AAAGAG -CAAAG AAAAAG AAAAAG
1 AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
*
641914 -CAAAG AAAAAG
1 AAAAAG AAAAAG
641925 GAACAAGAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
5 11 0.27
6 25 0.61
7 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:641917 original size:17 final size:17
Alignment explanation
Indices: 641867--641924 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
641857 GAACAAGAGC
641867 AAAAAGGAAAAAG-AAA-
1 AAAAA-GAAAAAGCAAAG
*
641883 AAGAAATAAAAGAGCAAAG
1 AA-AAAGAAAA-AGCAAAG
641902 AAAAAGAAAAAGCAAAG
1 AAAAAGAAAAAGCAAAG
641919 AAAAAG
1 AAAAAG
641925 GAACAAGAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
16 6 0.17
17 18 0.50
18 10 0.28
19 2 0.06
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.02
Consensus pattern (17 bp):
AAAAAGAAAAAGCAAAG
Found at i:643685 original size:64 final size:64
Alignment explanation
Indices: 643584--643777 Score: 334
Period size: 64 Copynumber: 3.0 Consensus size: 64
643574 AAGCTGTATG
* * * *
643584 TCAACAAAAAACGTTCCAGTTTCATTCAGAGTCAATTTAAACTTCACATCGAAGGATATTGGAC
1 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGAC
*
643648 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGAC
1 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGAC
*
643712 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCAAAGGATATTGGAC
1 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGAC
643776 TC
1 TC
643778 GAAGTGCCAC
Statistics
Matches: 123, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 123 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (64 bp):
TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGAC
Found at i:643997 original size:90 final size:90
Alignment explanation
Indices: 643842--644031 Score: 285
Period size: 90 Copynumber: 2.1 Consensus size: 90
643832 AATTCAAGGC
*
643842 TCAACTTCATAACGAATGGGCCATCCACGATTTCAACTTCACGACGAATGATATCGAGCCCACCA
1 TCAACTTCACAACGAATGGGCCATCCACGATTTCAACTTCACGACGAATGATATCGAGCCCACCA
* *
643907 GCAACATTCATCTTCAGCTTGGATT
66 GCAACATTCATATTCAGATTGGATT
* * *
643932 TTAACTTCACAACGAA-GGGTCCATCCACGATTTCAACTTCACGACGAA-GAATATCGTGTCCAC
1 TCAACTTCACAACGAATGGG-CCATCCACGATTTCAACTTCACGACGAATG-ATATCGAGCCCAC
*
643995 CAGCAACATTCATATTTAGATTGGATT
64 CAGCAACATTCATATTCAGATTGGATT
644022 TCAACTTCAC
1 TCAACTTCAC
644032 GATAAAAGAT
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
89 4 0.04
90 86 0.96
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (90 bp):
TCAACTTCACAACGAATGGGCCATCCACGATTTCAACTTCACGACGAATGATATCGAGCCCACCA
GCAACATTCATATTCAGATTGGATT
Found at i:644508 original size:129 final size:130
Alignment explanation
Indices: 644273--644563 Score: 392
Period size: 129 Copynumber: 2.3 Consensus size: 130
644263 AAGATATCCA
* * * **
644273 ACCTGACTTGATCTCCTCATCATGTAGGAACC-ACGTTAACCCTAGCTAACCAACCGTCCTCATC
1 ACCTGACCTGATCTCCTCATCACGTAGGAGCCGACGTTAACCCTAAATAACCAACCGTCCTCATC
* * * * *
644337 ATATAGTAACAGTGTTATCACCCTTAGATGGCCTGTCGTCCTCATCACGTAAGAA-CTGTGTCAT
66 ACATAGGAACAGTGTTATCACCCTTAGATGACCTGTCATCCTCATCACATAAGAATC-GTGTCAT
644401 C
130 C
*
644402 ACCTGACCTGATCTCCTCATCACGTAGGAGCCGA-GTTAA-CCTCAAATAACCAGCCGTCCTCAT
1 ACCTGACCTGATCTCCTCATCACGTAGGAGCCGACGTTAACCCT-AAATAACCAACCGTCCTCAT
* * * *
644465 CACGTAGGAACCGTGTTATCACCCTTAGATGACTTGTCATCCTCATCACATAGGAATCGTGTCAT
65 CACATAGGAACAGTGTTATCACCCTTAGATGACCTGTCATCCTCATCACATAAGAATCGTGTCAT
644530 C
130 C
*
644531 ACATGACCTGATCTCCTCATCACGTAGGAGCCG
1 ACCTGACCTGATCTCCTCATCACGTAGGAGCCG
644564 TGTCAACCCT
Statistics
Matches: 143, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
128 3 0.02
129 138 0.97
130 2 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (130 bp):
ACCTGACCTGATCTCCTCATCACGTAGGAGCCGACGTTAACCCTAAATAACCAACCGTCCTCATC
ACATAGGAACAGTGTTATCACCCTTAGATGACCTGTCATCCTCATCACATAAGAATCGTGTCATC
Found at i:644537 original size:40 final size:40
Alignment explanation
Indices: 644375--644568 Score: 113
Period size: 40 Copynumber: 4.6 Consensus size: 40
644365 TGGCCTGTCG
* * * *
644375 TCCTCATCACGTAAGAACTGTGTCATCACCTGACCTGATC
1 TCCTCATCACATAGGAACCGTGTCATCACATGACCTGATC
* * * * * * * *
644415 TCCTCATCACGTAGGAGCCGAGTTAACCTCAAATAACCAG-CC
1 TCCTCATCACATAGGAACCGTG-T--CATCACATGACCTGATC
* * *
644457 GTCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGACTTG-TC
1 -TCCTCATCACATAGGAACCGTGTCATCA--C----ATGACCTGATC
*
644503 ATCCTCATCACATAGGAATCGTGTCATCACATGACCTGATC
1 -TCCTCATCACATAGGAACCGTGTCATCACATGACCTGATC
* *
644544 TCCTCATCACGTAGGAGCCGTGTCA
1 TCCTCATCACATAGGAACCGTGTCA
644569 ACCCTTAGAC
Statistics
Matches: 116, Mismatches: 27, Indels: 22
0.70 0.16 0.13
Matches are distributed among these distances:
40 50 0.43
41 3 0.03
42 2 0.02
43 29 0.25
44 1 0.01
46 31 0.27
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (40 bp):
TCCTCATCACATAGGAACCGTGTCATCACATGACCTGATC
Found at i:651653 original size:2 final size:2
Alignment explanation
Indices: 651648--651697 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
651638 AAAAAATTGA
651648 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
651690 AT AT AT AT
1 AT AT AT AT
651698 TAAAAATACT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:651807 original size:2 final size:2
Alignment explanation
Indices: 651800--651866 Score: 102
Period size: 2 Copynumber: 34.0 Consensus size: 2
651790 ATTTTTAAAA
*
651800 AT AT AT AT -T AC AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
651840 AT AT AT AT AT AT AT AT AT AT CAT AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT
651867 GCATATTATC
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
1 2 0.03
2 56 0.93
3 2 0.03
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:652122 original size:25 final size:25
Alignment explanation
Indices: 652067--652123 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
652057 ATAAATTTCA
*
652067 ATTAATCCAAAATTTGTAAGTCCTG
1 ATTAATCCAAAATTTGCAAGTCCTG
* * *
652092 ACTAATTCAAATTTTGCAAGT-CTCG
1 ATTAATCCAAAATTTGCAAGTCCT-G
652117 ATTAATC
1 ATTAATC
652124 TATTAAGAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.37
Consensus pattern (25 bp):
ATTAATCCAAAATTTGCAAGTCCTG
Found at i:656711 original size:65 final size:66
Alignment explanation
Indices: 656614--656742 Score: 199
Period size: 65 Copynumber: 2.0 Consensus size: 66
656604 AAATATTGGT
* *
656614 CAAAAGGTCATATTGGATTTGTTTTTTAAATTAAAGGGTCACATTGAG-AAAAAATAATATGAGG
1 CAAAAGGTCATATTGGATTTATTTTCTAAATTAAAGGGTCACATTGAGAAAAAAATAATATGAGG
656678 A
66 A
* *
656679 CAAAAGGTCATATTAGG-TTTATTTTCTGAATTAAAGGGTCGCATTGAGAAAAAAATAATATGAG
1 CAAAAGGTCATATT-GGATTTATTTTCTAAATTAAAGGGTCACATTGAGAAAAAAATAATATGAG
656743 ACCACATTAG
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
65 41 0.71
66 17 0.29
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (66 bp):
CAAAAGGTCATATTGGATTTATTTTCTAAATTAAAGGGTCACATTGAGAAAAAAATAATATGAGG
A
Found at i:658329 original size:181 final size:182
Alignment explanation
Indices: 657938--658405 Score: 629
Period size: 181 Copynumber: 2.6 Consensus size: 182
657928 GATCCAACTT
* * * * * **
657938 AAAAATGTATCGATCCACAACGATATAACATGTAAAAACTATGATAAGAC-CAGTATTGAAATGA
1 AAAAATGTATCGATCAACAAAGATATAACAGGTAAAAA-TATGATAAAACTGA-TATCAAAATGA
* * * * *
658002 TAAAACCGGTAAAGCGGTACCGAATATATTTAAAA-TGTCGATACTTTAATATAAGGATCGACAC
64 TAAAACCGGTAAAACGATACCGGATATA-TTAAAAGTGTCGAAACATTAATATAAGGATCGACAC
* * * *
658066 TTCGTTAATTTAAAAAAGAAGTAGTTTTAGCGCCTATAAAGTGTCGATGCTTTCA
128 TTCGTGAATTTAAAAAAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
* * *
658121 AATAATATATCGATCAACAAAGATATAACAGGTAAAAATATGATAAAACTGATATCAAAATGATG
1 AAAAATGTATCGATCAACAAAGATATAACAGGTAAAAATATGATAAAACTGATATCAAAATGATA
* * * *
658186 AAACCGGTAAAACGTTATCGGATATATTGAAAGTGTCGAAACATT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGAAACATTAATATAAGGATCGACACTTC
*
658250 GTGAATTTAAAAGAGAAGCA-TTTTAGCGCCTATAAAGTGTCGATACTTTAA
131 GTGAATTTAAAAAAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
* *
658301 AAAAATGTATCGATCAGACAATGATATAACAGGTAAAAATATGATAAAACTGGTATCAAAATGAT
1 AAAAATGTATCGATCA-ACAAAGATATAACAGGTAAAAATATGATAAAACTGATATCAAAATGAT
*
658366 AAAACCGGTAAAATGATACCGGATATATTAAAAGTGTCGA
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGA
658406 TACTTTCGTA
Statistics
Matches: 250, Mismatches: 32, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
180 43 0.17
181 121 0.48
182 52 0.21
183 34 0.14
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCAACAAAGATATAACAGGTAAAAATATGATAAAACTGATATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGAAACATTAATATAAGGATCGACACTTC
GTGAATTTAAAAAAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
Found at i:658346 original size:20 final size:19
Alignment explanation
Indices: 658320--658378 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
658310 TCGATCAGAC
*
658320 AATGATATAACAGGTAAAA
1 AATGATAAAACAGGTAAAA
* *
658339 ATATGATAAAACTGGTATCAA
1 A-ATGATAAAACAGGTA-AAA
*
658360 AATGATAAAACCGGTAAAA
1 AATGATAAAACAGGTAAAA
658379 TGATACCGGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 3 0.09
20 27 0.82
21 3 0.09
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.22
Consensus pattern (19 bp):
AATGATAAAACAGGTAAAA
Found at i:660181 original size:20 final size:21
Alignment explanation
Indices: 660144--660183 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
660134 AAATTAAGTT
660144 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
660165 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
660184 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:661742 original size:182 final size:182
Alignment explanation
Indices: 661220--662108 Score: 1545
Period size: 182 Copynumber: 4.9 Consensus size: 182
661210 TAACTCAACA
*
661220 AAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAATTT
1 AAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTT
* * * *
661285 AAAAGAGAAG-AGTTATAGCGCCAATAAAGTGTGGATAGTTTATAAAAATATATCGATCTATAAC
66 AAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAAC
661349 AATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGT
131 AATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGT
661401 AAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCG--ACTTTTGGAA-TT
1 AAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTT
* *
661463 AATAAGAGAAGAAGTTATAGCGCCAATAACGTGTCGTTACTTTATAAAAATGTATCGATCCATAA
66 AA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAA
* * *
661528 CAATATAACATGTAAAAATATGACAAAACCGGTCTGGAAATGACAACATAGGT
130 CAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGT
661581 AAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTT
1 AAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTT
661646 AAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAAC
66 AAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAAC
* *
661711 AATATAACAGGTAATAATATGACAAAACCGGTCTCGAAATGACAAAACAGGT
131 AATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGT
661763 AAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTT
1 AAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTT
* *
661828 AAAAGAGAAGAAGTTATAGTGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAAC
66 AAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAAC
* *
661893 AATATAACATGTAACAATATGACAAAACCGGTCTCGAAATAACAAAACAGGT
131 AATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGT
*
661945 AAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA-TT
1 AAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTT
*
662009 AATAAGAGAAGAAGTTATAGCGCCAATAAAGTATCGATACTTTATAAAAATGTATCGATCCATAA
66 AA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAA
* *
662074 TAATATAACATGTAAAAATATGATAAAACCGGTCT
130 CAATATAACATGTAAAAATATGACAAAACCGGTCT
662109 ATAAGTGACA
Statistics
Matches: 673, Mismatches: 29, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
178 4 0.01
179 18 0.03
180 147 0.22
181 53 0.08
182 447 0.66
183 4 0.01
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.29
Consensus pattern (182 bp):
AAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTT
AAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAAC
AATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGT
Found at i:662355 original size:87 final size:87
Alignment explanation
Indices: 662257--662419 Score: 308
Period size: 87 Copynumber: 1.9 Consensus size: 87
662247 AAATTGGTCA
662257 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
662322 CTGGTTAAATACTTATTTTATT
66 CTGGTTAAATACTTATTTTATT
* *
662344 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
662409 CTGGTTAAATA
66 CTGGTTAAATA
662420 ATATAACATA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CTGGTTAAATACTTATTTTATT
Found at i:662391 original size:23 final size:23
Alignment explanation
Indices: 662341--662385 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
662331 TACTTATTTT
* *
662341 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
662364 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
662386 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Done.