Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007988.1 Hibiscus syriacus cultivar Beakdansim tig00110435_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: 847207
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:300551 original size:18 final size:17
Alignment explanation
Indices: 300526--300572 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 17
300516 GGAAACAAAT
300526 AACATAATCATAAAAAC
1 AACATAATCATAAAAAC
*
300543 AACCATAATCATAAAAAG
1 AA-CATAATCATAAAAAC
300561 AA-ATAATCATAA
1 AACATAATCATAA
300573 TCATAAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 10 0.36
17 2 0.07
18 16 0.57
ACGTcount: A:0.64, C:0.15, G:0.02, T:0.19
Consensus pattern (17 bp):
AACATAATCATAAAAAC
Found at i:303085 original size:42 final size:40
Alignment explanation
Indices: 303016--303096 Score: 126
Period size: 42 Copynumber: 2.0 Consensus size: 40
303006 GATTTACATA
* *
303016 TTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAG
1 TTCGCGTCGCGATTTTCCAAATTCGTTGCGATAATCCAAG
303056 TTCGCGTCGCGATTTATTCCAAATTCGTTGCGATAATCCAA
1 TTCGCGTCGCGA-TT-TTCCAAATTCGTTGCGATAATCCAA
303097 AATCGCAACG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 11 0.30
41 2 0.05
42 24 0.65
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (40 bp):
TTCGCGTCGCGATTTTCCAAATTCGTTGCGATAATCCAAG
Found at i:303097 original size:19 final size:19
Alignment explanation
Indices: 303020--303097 Score: 75
Period size: 19 Copynumber: 3.9 Consensus size: 19
303010 TACATATTCG
*
303020 CGTTGCGATTTTCCAAATT
1 CGTTGCGATATTCCAAATT
* *
303039 CGTTGCGATAGTCCAAGTT
1 CGTTGCGATATTCCAAATT
*
303058 CGCGTCGCGATTTATTCCAAATT
1 --CGTTGCGA--TATTCCAAATT
*
303081 CGTTGCGATAATCCAAA
1 CGTTGCGATATTCCAAA
303098 ATCGCAACGA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
19 24 0.51
21 14 0.30
23 9 0.19
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.33
Consensus pattern (19 bp):
CGTTGCGATATTCCAAATT
Found at i:303197 original size:6 final size:6
Alignment explanation
Indices: 303186--303212 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
303176 GACACGTATT
303186 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
303213 CGAGACGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:303937 original size:42 final size:42
Alignment explanation
Indices: 303819--304250 Score: 643
Period size: 42 Copynumber: 10.3 Consensus size: 42
303809 TGCGATTTTG
*
303819 GACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
303861 GACTATCGCAACGGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAAC-GAATTTGGAATAAATCGCAACGCGAACTTC
303904 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
303946 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *** *
303988 GAATAAATCAACGAATTTGGAATAAATTGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
304030 GACTATCGCAACGAACTTGGAATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
304072 GACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
304114 GACTATCGCAACGAACTTGGAATAAATCGCAACGTGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
304156 GACTATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * * *
304198 GACTATCGCAACGCGAACTTCGACT--ATCGCAACGCGAACTTA
1 GACTATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTC
304240 GACTATCGCAA
1 GACTATCGCAA
304251 TGCGAATATG
Statistics
Matches: 357, Mismatches: 30, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
42 308 0.86
43 41 0.11
44 8 0.02
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:304007 original size:19 final size:20
Alignment explanation
Indices: 303912--304189 Score: 92
Period size: 21 Copynumber: 13.2 Consensus size: 20
303902 TCGACTATCG
303912 CAACGAATTTGGAATAAATC
1 CAACGAATTTGGAATAAATC
* * *
303932 GCAACGCGAACTTCGACT--ATC
1 -CAA--CGAATTTGGAATAAATC
303953 GCAACGAATTTGGAATAAATC
1 -CAACGAATTTGGAATAAATC
*
303974 GCAACGCGAACTTGGAATAAAT-
1 -CAA--CGAATTTGGAATAAATC
*
303996 CAACGAATTTGGAATAAATTG
1 CAACGAATTTGGAATAAA-TC
* * *
304017 CAACGCGAACTTCGACT--ATC
1 CAA--CGAATTTGGAATAAATC
*
304037 GCAACGAACTTGGAATAAATC
1 -CAACGAATTTGGAATAAATC
* * *
304058 GCAATGCGAACTTCGACT--ATC
1 -CAA--CGAATTTGGAATAAATC
304079 GCAACGAATTTGGAATAAATC
1 -CAACGAATTTGGAATAAATC
* * *
304100 GCAATGCGAACTTCGACT--ATC
1 -CAA--CGAATTTGGAATAAATC
*
304121 GCAACGAACTTGGAATAAATC
1 -CAACGAATTTGGAATAAATC
* *
304142 GCAACGTGAACTTGGACT--ATC
1 -CAAC--GAATTTGGAATAAATC
*
304163 GCAACAAATTTGGAATAAATC
1 -CAACGAATTTGGAATAAATC
304184 GCAACG
1 -CAACG
304190 CGAACTTGGA
Statistics
Matches: 203, Mismatches: 29, Indels: 50
0.72 0.10 0.18
Matches are distributed among these distances:
19 60 0.30
20 2 0.01
21 79 0.39
23 62 0.31
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
CAACGAATTTGGAATAAATC
Found at i:309748 original size:7 final size:6
Alignment explanation
Indices: 309711--309747 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
309701 CTTAATCGCG
*
309711 AAAATC AAAATT AAAATT AAAATT AAAATTT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAA-TT AAAATT
309748 TTAATTTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:310280 original size:84 final size:81
Alignment explanation
Indices: 310140--310906 Score: 523
Period size: 84 Copynumber: 9.2 Consensus size: 81
310130 CTTAATGGAA
* * * * * *
310140 TCGAACTCGAAGGTCTTTG--G-CAGATAGCCCTTATTGCCTTGAGCTATGCTGCAAATGATAGT
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCT--AAATGAT-GT
* * *
310202 GTCTTTGAGCTGAGTGGAG
63 GCCTTAGAGCTGAGTGTAG
* * *
310221 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGTCATAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATG-C-TAAATGATGTG
* * *
310286 CCCTCGAAGCTGAGTGTAA
64 CCTTAG-AGCTGAGTGTAG
* * * *
310305 TCGGACTAGAGGGTCTTTG--G-CAGATAACCCTTCTCGACTTAAGCTATGCTGTAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGC--TAAATGATGTG
* * *
310367 CCTTGGAGTTGAGCGTAG
64 CCTTAGAGCTGAGTGTAG
* * * * *
310385 TCAAACTCGAAGGTCTTTGGTTGGCATATAACCCTTCTCGACTTAAGTTATGCTGCAAATTATAT
1 TCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGACTTAAGTTATGCT--AAATGATGT
*
310450 GCCTTAGAGCTGAGTGCAG
63 GCCTTAGAGCTGAGTGTAG
* * * * * * *
310469 TCAAACTCGAAGGTCTTTTGGTCACAGATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGC--TAAATGATGT
* * *
310534 GCCCTCGAAGCTGAGTGTAA
63 GCCTTAG-AGCTGAGTGTAG
* * * * * * * *
310554 CCAAACTCG-AGG-GTTT-TTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTGTAAATAATGTG
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGC--TAAATGATGTG
* *
310616 CCTT-GAAGTTGAGCGTAG
64 CCTTAG-AGCTGAGTGTAG
* * *
310634 TCGAACTAGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGACTTAAGTTATGCT--AAATGATGT
*
310699 GCCTTAGAGCTGAGCGTAG
63 GCCTTAGAGCTGAGTGTAG
* * * *
310718 TCGAACTCGAAGGT-TTTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTTTACTG-TAAATGA
1 TCGAACTCGAAGGTCTTTGTT-G--ACAGATAACCCTTCTCGACTTAAG--TTA-TGCTAAATGA
* * *
310781 TGTGCCCTCGAAGCTGAGTGTAA
60 TGTGCCTTAG-AGCTGAGTGTAG
* * * ** *
310804 TCGAACTCTAGGGTCTTCGGTTGGTAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTT-TGTTGACAGATAACCCTTCTCGACTTAAGTTATGCT--AAATGATGT
* * **
310869 GTCTTGGAGCTGAAAGTAG
63 GCCTTAGAGCTGAGTGTAG
* * *
310888 CCGAACTTGAAGGCCTTTG
1 TCGAACTCGAAGGTCTTTG
310907 GTGGGCACAA
Statistics
Matches: 543, Mismatches: 107, Indels: 70
0.75 0.15 0.10
Matches are distributed among these distances:
80 41 0.08
81 100 0.18
82 13 0.02
83 17 0.03
84 249 0.46
85 88 0.16
86 24 0.04
87 7 0.01
88 4 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (81 bp):
TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTAAATGATGTGCC
TTAGAGCTGAGTGTAG
Found at i:310418 original size:165 final size:165
Alignment explanation
Indices: 310121--310906 Score: 692
Period size: 165 Copynumber: 4.7 Consensus size: 165
310111 CGGTTGATAC
* * * * * * * * * *
310121 GCCCTCG-AGCTTAATGGAATCGAACTCGAAGGTC-TTTGGCAGATAGCCCTTATTGCCTTGAGC
1 GCCCTCGAAGCTGAGTGTAATCGAACTAGAAGGTCTTTTGGCAGATAACCCTTCTCGACTTAAGT
* * * * *
310184 TATGCTGCAAATGATAGTGTCTTTGAGCTGAGTGGAGTCGAACTCGAAGGTCTTTGTTGACAGAT
66 TATGCTGCAAATGAT-GTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGAT
* * *
310249 AACCCTTCTAGCCTTGAGTTATG-TCATAAATGATGT
130 AACCCTTCTAGACTTAAGTTATGCT-GTAAATGATGT
* * *
310285 GCCCTCGAAGCTGAGTGTAATCGGACTAGAGGGTC-TTTGGCAGATAACCCTTCTCGACTTAAGC
1 GCCCTCGAAGCTGAGTGTAATCGAACTAGAAGGTCTTTTGGCAGATAACCCTTCTCGACTTAAGT
* * * *
310349 TATGCTGTAAATGATGTGCCTTGGAGTTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCATAT
66 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGAT
* * * *
310414 AACCCTTCTCGACTTAAGTTATGCTGCAAATTATAT
130 AACCCTTCTAGACTTAAGTTATGCTGTAAATGATGT
* * * * * * * * * *
310450 GCCTTAG-AGCTGAGTGCAGTCAAACTCGAAGGTCTTTTGGTCACAGATAACCCTTATAGCCTTG
1 GCCCTCGAAGCTGAGTGTAATCGAACTAGAAGGTCTTTTGG---CAGATAACCCTTCTCGACTTA
* * * * ** * *
310514 AGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAACCAAACTCG-AGG-GTTT-TTGGCA
63 AGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCA
* * * * *
310576 GATAGCTCTTCTCGACTTAAGCTATGCTGTAAATAATGT
127 GATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGT
* * * *
310615 G-CCTTGAAGTTGAGCGTAGTCGAACTAGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
1 GCCCTCGAAGCTGAGTGTAATCGAACTAGAAGGTC-TT--TTGGCAGATAACCCTTCTCGACTTA
* * *
310679 AGTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGT-TTTTTTGGTCA
63 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGG---
* * * *
310743 CAGATAACCCTTCTAGCCTTGAGTTTTACTGTAAATGATGT
125 CAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGT
** * * *
310784 GCCCTCGAAGCTGAGTGTAATCGAACTCTAGGGTCTTCGGTTGGTAGATAACCCTTCTTGACTTA
1 GCCCTCGAAGCTGAGTGTAATCGAACTAGAAGGTCTT---TTGGCAGATAACCCTTCTCGACTTA
* ** * * *
310849 AGTTATGCTGCAAATGATGTGTCTTGGAGCTGAAAGTAGCCGAACTTGAAGGCCTTTG
63 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG
310907 GTGGGCACAA
Statistics
Matches: 500, Mismatches: 101, Indels: 35
0.79 0.16 0.06
Matches are distributed among these distances:
164 84 0.17
165 207 0.41
166 7 0.01
167 3 0.01
168 44 0.09
169 56 0.11
170 96 0.19
171 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (165 bp):
GCCCTCGAAGCTGAGTGTAATCGAACTAGAAGGTCTTTTGGCAGATAACCCTTCTCGACTTAAGT
TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATA
ACCCTTCTAGACTTAAGTTATGCTGTAAATGATGT
Found at i:310628 original size:249 final size:249
Alignment explanation
Indices: 310156--310874 Score: 1019
Period size: 249 Copynumber: 2.9 Consensus size: 249
310146 TCGAAGGTCT
* * * * * * * * *
310156 TTGGCAGATAGCCCTTATTGCCTTGAGCTATGCTGCAAATGATAGTGTCTTTGAGCTGAGTGGAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATA-TGCCTTAGAGCTGAGTGCAG
* * *
310221 TCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATG-TCATAAATGATG
65 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCT-GTAAATGATG
* * *
310284 TGCCCTCGAAGCTGAGTGTAATCGGACTAGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGC
129 TGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTTTTTGGCAGATAACCCTTCTCGACTTAAGC
* *
310349 TATGCTGTAAATGATGTGCCTTGGAGTTGAGCGTAGTCAAACTCGAAGGTCTTTGG
194 TATGCTGTAAATGATGTGCCTTGAAGTTGAGCGTAGTCAAACTAGAAGGTCTTTGG
* *
310405 TTGGCATATAACCCTTCTCGACTTAAGTTATGCTGCAAATTATATGCCTTAGAGCTGAGTGCAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTAGAGCTGAGTGCAGT
* *
310470 CAAACTCGAAGGTCTTTTGGTCACAGATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATGTG
66 CGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
* * * *
310535 CCCTCGAAGCTGAGTGTAACCAAACTCGAGGGTTTTTGGCAGATAGCTCTTCTCGACTTAAGCTA
131 CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTTTTTGGCAGATAACCCTTCTCGACTTAAGCTA
* *
310600 TGCTGTAAATAATGTGCCTTGAAGTTGAGCGTAGTCGAACTAGAAGGTCTTTGG
196 TGCTGTAAATGATGTGCCTTGAAGTTGAGCGTAGTCAAACTAGAAGGTCTTTGG
* *
310654 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTAGAGCTGAGTGCAGT
* * *
310719 CGAACTCGAAGGTTTTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTTTACTGTAAATGATGT
66 CGAACTCGAAGG-TCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
* * *
310784 GCCCTCGAAGCTGAGTGTAATCGAACTCTAGGGTCTTCGGTTGGTAGATAACCCTTCTTGACTTA
130 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGT-TT---TTGGCAGATAACCCTTCTCGACTTA
* * *
310849 AGTTATGCTGCAAATGATGTGTCTTG
191 AGCTATGCTGTAAATGATGTGCCTTG
310875 GAGCTGAAAG
Statistics
Matches: 416, Mismatches: 47, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
248 31 0.07
249 260 0.62
250 80 0.19
251 2 0.00
254 43 0.10
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (249 bp):
TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTAGAGCTGAGTGCAGT
CGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTTTTTGGCAGATAACCCTTCTCGACTTAAGCTA
TGCTGTAAATGATGTGCCTTGAAGTTGAGCGTAGTCAAACTAGAAGGTCTTTGG
Found at i:311235 original size:110 final size:110
Alignment explanation
Indices: 311015--311560 Score: 789
Period size: 110 Copynumber: 5.0 Consensus size: 110
311005 ATCCAAATAT
* * *
311015 TTGTGTTGTTTCGAGGCCAATATCCTTCG-TCGTGAAGTTGAAATTGACTC----TGAAACTGGA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGACTCTGAATGAAACTGAA
* * *
311075 AAGTTGTTTGTTGACAGCCAGCCGCCCCTTCGTTGTGAAGTTGGGC
65 AAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGTTGTGAAGTTGAGC
* * *
311121 TTGTGTTGTCTCGAGTCCAATATCATTCGCTGTAAAGTTGAAATTGAATCTGAATGAAACTGAAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
* * * * *
311186 ATTTGTTTTTTGACAGTCAGTCGCCCATTCGCTATGAAGTTGAGC
66 AGTTGTTTGTTGACAGTCAGTCGCCCCTTCGTTGTGAAGTTGAGC
** * *
311231 TTGTGTTGTCTCGAGTCTGATATCCTTCGTTGTGAAATTGAAATTGACTCTGAATGAAACTGAAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
* * * *
311296 AGTTGTTTATTGACAGTCAGTCACCCCTTCGCTGTAAAGTTGAGC
66 AGTTGTTTGTTGACAGTCAGTCGCCCCTTCGTTGTGAAGTTGAGC
311341 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACT-AAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
311405 ATGTTGTTTGTTGACAGTCAGTCGCCCCTTCGTTGTGAAGTTGAGC
66 A-GTTGTTTGTTGACAGTCAGTCGCCCCTTCGTTGTGAAGTTGAGC
* * *
311451 TTGTGTTGTCTCGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGACTATGAATGAAACTGAAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
* *
311516 AGTTGTTTGATGACCGTCAGTCGCCCCTTCGTTGTGAAGTTGAGC
66 AGTTGTTTGTTGACAGTCAGTCGCCCCTTCGTTGTGAAGTTGAGC
311561 AACCACCATC
Statistics
Matches: 393, Mismatches: 40, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
106 43 0.11
107 1 0.00
109 4 0.01
110 341 0.87
111 4 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (110 bp):
TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
AGTTGTTTGTTGACAGTCAGTCGCCCCTTCGTTGTGAAGTTGAGC
Found at i:314250 original size:16 final size:17
Alignment explanation
Indices: 314221--314253 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
314211 TGAAAAATAA
*
314221 ATGTCTTACTCCACATG
1 ATGTCTTACCCCACATG
314238 ATGT-TTACCCCACATG
1 ATGTCTTACCCCACATG
314254 CTTTAATTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.24, C:0.30, G:0.12, T:0.33
Consensus pattern (17 bp):
ATGTCTTACCCCACATG
Found at i:314630 original size:65 final size:65
Alignment explanation
Indices: 314554--314712 Score: 309
Period size: 65 Copynumber: 2.4 Consensus size: 65
314544 ATTCTCTTAT
*
314554 GCCCATACGGAGAATAAATTCACACGAAGAAATAAGGTATATGAATCTCGAAGGTTACTTGCTAG
1 GCCCATACGGAGAATAAATTCCCACGAAGAAATAAGGTATATGAATCTCGAAGGTTACTTGCTAG
314619 GCCCATACGGAGAATAAATTCCCACGAAGAAATAAGGTATATGAATCTCGAAGGTTACTTGCTAG
1 GCCCATACGGAGAATAAATTCCCACGAAGAAATAAGGTATATGAATCTCGAAGGTTACTTGCTAG
314684 GCCCATACGGAGAATAAATTCCCACGAAG
1 GCCCATACGGAGAATAAATTCCCACGAAG
314713 GCATCACTTT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 93 1.00
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (65 bp):
GCCCATACGGAGAATAAATTCCCACGAAGAAATAAGGTATATGAATCTCGAAGGTTACTTGCTAG
Found at i:314998 original size:21 final size:21
Alignment explanation
Indices: 314974--315044 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
314964 TTGAAAATCG
314974 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * * *
314995 CGTTGC--TATTTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
315013 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
315036 CGTTGCGAT
1 CGTTGCGAT
315045 TTTCCATTTC
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
18 2 0.05
19 6 0.16
20 6 0.16
21 15 0.41
22 6 0.16
23 2 0.05
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.38
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:315017 original size:41 final size:41
Alignment explanation
Indices: 314971--315208 Score: 390
Period size: 41 Copynumber: 5.8 Consensus size: 41
314961 TAGTTGAAAA
*
314971 TCGCGTTGCGATAGTCTACAGTGTCGTTGCTATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
315012 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
* *
315053 TCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCT-ACAGT-GTCGTTGCGATTTTCCATT
* * *
315094 TCGCGTTGCGGTAGTGTACAGTGTCGTTGCGATTTTCCATC
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
315135 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
315176 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGAT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGAT
315209 AGTCTACAGT
Statistics
Matches: 183, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
40 2 0.01
41 179 0.98
42 2 0.01
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
Found at i:315020 original size:20 final size:20
Alignment explanation
Indices: 314995--315187 Score: 101
Period size: 20 Copynumber: 9.4 Consensus size: 20
314985 TCTACAGTGT
*
314995 CGTTGCTATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* * *
315015 CGTTGCGATAGTCTACA-GT-G
1 CGTTGCGAT--TTTCCATTTCG
315035 TCGTTGCGATTTTCCATTTCG
1 -CGTTGCGATTTTCCATTTCG
* ** **
315056 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGAT-TTTCCATTTCG
315077 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* * * *
315097 CGTTGCGGTAGTGTACA-GT-G
1 CGTTGC-G-ATTTTCCATTTCG
*
315117 TCGTTGCGATTTTCCATCTCG
1 -CGTTGCGATTTTCCATTTCG
* * *
315138 CGTTGCGATAGTCTACA-GT-G
1 CGTTGCGAT--TTTCCATTTCG
315158 TCGTTGCGATTTTCCATTTCG
1 -CGTTGCGATTTTCCATTTCG
315179 CGTTGCGAT
1 CGTTGCGAT
315188 AGTCTACAGT
Statistics
Matches: 126, Mismatches: 31, Indels: 32
0.67 0.16 0.17
Matches are distributed among these distances:
19 13 0.10
20 54 0.43
21 46 0.37
22 13 0.10
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCG
Found at i:315164 original size:21 final size:21
Alignment explanation
Indices: 315138--315218 Score: 96
Period size: 21 Copynumber: 3.9 Consensus size: 21
315128 TTCCATCTCG
315138 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
315159 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
315177 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
315200 CGTTGCGATAGTCTACAGT
1 CGTTGCGATAGTCTACAGT
315219 AAATTAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
18 2 0.04
19 4 0.08
20 9 0.18
21 28 0.57
22 4 0.08
23 2 0.04
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:316002 original size:20 final size:20
Alignment explanation
Indices: 315940--316008 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
315930 TAGACTATCA
315940 CAACGCGAAATGGAAAATCG
1 CAACGCGAAATGGAAAATCG
* **
315960 CAA--CGACACTGTAGACTATCG
1 CAACGCGA-AATG--GAAAATCG
315981 CAACGCGAAATGGAAAATCG
1 CAACGCGAAATGGAAAATCG
316001 CAACGCGA
1 CAACGCGA
316009 TTTTCAACTA
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 17 0.45
21 9 0.24
22 3 0.08
23 3 0.08
ACGTcount: A:0.41, C:0.25, G:0.23, T:0.12
Consensus pattern (20 bp):
CAACGCGAAATGGAAAATCG
Found at i:316033 original size:41 final size:41
Alignment explanation
Indices: 315926--316005 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
315916 TTTTTAATTT
*
315926 ACTGTAGACTATCACAACGCGAAATGGAAAATCGCAACGAC
1 ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGAC
315967 ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACG
1 ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACG
316006 CGATTTTCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (41 bp):
ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGAC
Found at i:316037 original size:21 final size:21
Alignment explanation
Indices: 315974--316037 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
315964 GACACTGTAG
*
315974 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
315995 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
316015 ACTATCGCAATGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
316036 AC
1 AC
316038 GCGAATTTGC
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:316729 original size:2 final size:2
Alignment explanation
Indices: 316724--316756 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
316714 AAATGAATAA
*
316724 AT AT AT AT AT GT 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 AT AT AT A
316757 ACAATGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:316837 original size:16 final size:17
Alignment explanation
Indices: 316794--316838 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
316784 AAATTAGGAG
316794 AAAATGAAA-AAATATA
1 AAAATGAAATAAATATA
*
316810 TAAA-GTAAATAAATA-A
1 AAAATG-AAATAAATATA
316826 AAAATGAAATAAA
1 AAAATGAAATAAA
316839 AAGAATAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (17 bp):
AAAATGAAATAAATATA
Found at i:317239 original size:3 final size:3
Alignment explanation
Indices: 317211--317281 Score: 69
Period size: 3 Copynumber: 24.0 Consensus size: 3
317201 TGCGGGGCCT
* *
317211 ATA AAA ATA ATA A-A ATA AAA AT- ATA ATA ATA ATA ATA ATA ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
317258 ATAA ATA TATA AT- ATA ATA A-A ATA
1 AT-A ATA -ATA ATA ATA ATA ATA ATA
317282 TTTTTGTAGA
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
2 8 0.14
3 40 0.69
4 10 0.17
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:317254 original size:31 final size:31
Alignment explanation
Indices: 317216--317281 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 31
317206 GGCCTATAAA
317216 AATAATAAAATAAAAATATAATAATAATAATAAT
1 AATAAT-AAATAAAAATATAAT-ATAATAA-AAT
*
317250 AATAATAAATAAATATATAATATAATAAAAT
1 AATAATAAATAAAAATATAATATAATAAAAT
317281 A
1 A
317282 TTTTTGTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
31 4 0.13
32 7 0.23
33 14 0.45
34 6 0.19
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (31 bp):
AATAATAAATAAAAATATAATATAATAAAAT
Found at i:318504 original size:18 final size:17
Alignment explanation
Indices: 318474--318507 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
318464 GGTTTTCAGC
318474 CGGTTTGAACGGTTCAA
1 CGGTTTGAACGGTTCAA
*
318491 CGGTTCTGACCGGTTCA
1 CGGTT-TGAACGGTTCA
318508 CTAATAACGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (17 bp):
CGGTTTGAACGGTTCAA
Found at i:320141 original size:33 final size:33
Alignment explanation
Indices: 320068--320187 Score: 122
Period size: 33 Copynumber: 3.7 Consensus size: 33
320058 CCTTTGAATC
* *
320068 ATAGATATATTT--TAATTTATTAAAATAACATA
1 ATAGATATATTTCATAATTT-TAAAAATAACATT
*
320100 ATAGATATATTTCATAATTTTAAAAATAATATT
1 ATAGATATATTTCATAATTTTAAAAATAACATT
* * * *
320133 ATATATATA-TGCGT-ATTTTAAAAATAACAGT
1 ATAGATATATTTCATAATTTTAAAAATAACATT
* *
320164 ATAGATACATTTTATAATTTTAAA
1 ATAGATATATTTCATAATTTTAAA
320188 TATCATTGAA
Statistics
Matches: 71, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
31 22 0.31
32 17 0.24
33 26 0.37
34 6 0.08
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.43
Consensus pattern (33 bp):
ATAGATATATTTCATAATTTTAAAAATAACATT
Found at i:321343 original size:90 final size:90
Alignment explanation
Indices: 321186--321359 Score: 258
Period size: 90 Copynumber: 1.9 Consensus size: 90
321176 GTAACTATCC
* * * *
321186 CAATATGATGCTGGATTAAAGTATGGCTGAGAATTTACATCATAAATGCTGATAGTGTCATAACT
1 CAATATGATGCTGGATTAAAGTATGGCTGAGAATTTACATCATAAATGCTGACAATGCCACAACT
321251 CTGACTATGTTCAAATCCACTCCCA
66 CTGACTATGTTCAAATCCACTCCCA
* * * * *
321276 CAATATGTTGGTGGATTAAAGTATGGCTGAGAATTTACATCATAAATGTTGACAATGCCGCATCT
1 CAATATGATGCTGGATTAAAGTATGGCTGAGAATTTACATCATAAATGCTGACAATGCCACAACT
*
321341 CTGATTATGTTCAAATCCA
66 CTGACTATGTTCAAATCCA
321360 TCCGGCTCGG
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
90 74 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (90 bp):
CAATATGATGCTGGATTAAAGTATGGCTGAGAATTTACATCATAAATGCTGACAATGCCACAACT
CTGACTATGTTCAAATCCACTCCCA
Found at i:323108 original size:23 final size:22
Alignment explanation
Indices: 323078--323131 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
323068 TTGTGTTCGG
323078 TTCGTTTATCATTTATAAACATA
1 TTCGTTTAT-ATTTATAAACATA
* * *
323101 TTCGTTTAATGTTTGTCAACATA
1 TTCGTTT-ATATTTATAAACATA
323124 TTCGTTTA
1 TTCGTTTA
323132 GCAGTTATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.04
23 24 0.89
24 2 0.07
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50
Consensus pattern (22 bp):
TTCGTTTATATTTATAAACATA
Found at i:326281 original size:24 final size:24
Alignment explanation
Indices: 326225--326281 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
326215 TTAAATTTTG
* * *
326225 TTAAGATTTTTTTATAAGAATATT
1 TTAAAATTTTTTAATAAAAATATT
*
326249 TATACAATTTTTTAATAAAAATATT
1 T-TAAAATTTTTTAATAAAAATATT
326274 TTAAAATT
1 TTAAAATT
326282 AATAAGATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (24 bp):
TTAAAATTTTTTAATAAAAATATT
Found at i:331657 original size:16 final size:16
Alignment explanation
Indices: 331638--331676 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
331628 TGAAGTCAAA
331638 AAATAAAACAAACAAG
1 AAATAAAACAAACAAG
*
331654 AAAT-AAATAAACAAG
1 AAATAAAACAAACAAG
331669 ATAATAAA
1 A-AATAAA
331677 CGAATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 11 0.55
16 7 0.35
17 2 0.10
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (16 bp):
AAATAAAACAAACAAG
Found at i:331785 original size:19 final size:19
Alignment explanation
Indices: 331735--331807 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 19
331725 AAGCCAAGAA
*
331735 AAAATAAAAAATATGAAAAT
1 AAAATAAAAAATAT-TAAAT
*
331755 ACAAATACAAAATATTAAAT
1 A-AAATAAAAAATATTAAAT
* *
331775 AGAATAAAAAAATAGT-AAT
1 AAAAT-AAAAAATATTAAAT
331794 AAAATAATAAAATA
1 AAAATAA-AAAATA
331808 CGAAAAACTA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
18 2 0.05
19 16 0.36
20 14 0.32
21 12 0.27
ACGTcount: A:0.71, C:0.03, G:0.04, T:0.22
Consensus pattern (19 bp):
AAAATAAAAAATATTAAAT
Found at i:332180 original size:20 final size:19
Alignment explanation
Indices: 332155--332193 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
332145 ATGAACAAAG
332155 CAAATAAAAATAAAATAAAA
1 CAAATAAAAA-AAAATAAAA
*
332175 CAAATATAAAAAAATAAAA
1 CAAATAAAAAAAAATAAAA
332194 GGATTCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.15
Consensus pattern (19 bp):
CAAATAAAAAAAAATAAAA
Found at i:332247 original size:12 final size:12
Alignment explanation
Indices: 332211--332274 Score: 52
Period size: 10 Copynumber: 5.8 Consensus size: 12
332201 AAAAAAAAAA
332211 AATATATAT-AT
1 AATATATATAAT
332222 -ATATAGTAATAAT
1 AATATA-T-ATAAT
332235 AATATATATAAT
1 AATATATATAAT
*
332247 AA-A-ATGTAAT
1 AATATATATAAT
332257 -ATATATA-AA-
1 AATATATATAAT
332266 AATATATAT
1 AATATATAT
332275 GTGATTGAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
9 1 0.02
10 21 0.49
11 4 0.09
12 9 0.21
13 3 0.07
14 5 0.12
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (12 bp):
AATATATATAAT
Found at i:333412 original size:2 final size:2
Alignment explanation
Indices: 333405--333451 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
333395 TAATAATACA
*
333405 AT AT AT AT AT AT AT AT AT AT A- AT -T AT GT AT AT A- 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
*
333444 AA AT AT AT
1 AT AT AT AT
333452 TTTGGTCATA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:334113 original size:18 final size:18
Alignment explanation
Indices: 334090--334125 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
334080 TGCTTGCGTG
334090 CACGATTCCCTTCGTCGT
1 CACGATTCCCTTCGTCGT
334108 CACGATTCCCTTCGTCGT
1 CACGATTCCCTTCGTCGT
334126 GAAGTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.39, G:0.17, T:0.33
Consensus pattern (18 bp):
CACGATTCCCTTCGTCGT
Found at i:334416 original size:106 final size:106
Alignment explanation
Indices: 334225--334705 Score: 721
Period size: 106 Copynumber: 4.5 Consensus size: 106
334215 GTATTGTTCC
* * * ** * *
334225 GAGTCCAATATCCTCCACCGTGAAGTTGAAATTGGCTCTAGAA-CCGGAAAATTATTTGTTAACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAGTTGGGAAATTATTTGTTGACA
* *
334289 GTTAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTT
65 GTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTT
* * * *
334331 GAGCCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTATGAAGTTGGGAAATTATTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACAG
* *
334396 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGCTGTATT
66 TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTT
*
334437 GAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACAG
334502 TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTTGACTCTT
66 TCAGCCGCCCCTTCGCCGTGAAGTTGAGC-T-TG-TG-C-TG--TCTT
**
334550 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGTCATTATTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACAG
334615 TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTT
66 TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTT
334656 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAA
334706 GCCCCTTCGT
Statistics
Matches: 340, Mismatches: 27, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
105 3 0.01
106 227 0.67
107 1 0.00
108 4 0.01
109 3 0.01
110 3 0.01
111 4 0.01
112 1 0.00
113 94 0.28
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACAG
TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTT
Found at i:334637 original size:219 final size:212
Alignment explanation
Indices: 334225--334705 Score: 730
Period size: 219 Copynumber: 2.2 Consensus size: 212
334215 GTATTGTTCC
* * * ** *
334225 GAGTCCAATATCCTCCACCGTGAAGTTGAAATTGGCTCTAGAA-CCGGAAAATTATTTGTTAACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAGTTGGGAAATTATTTGTTAACA
* * *
334289 GTTAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTTGAGCCCAATATCTTTCGTTGTGA
65 GTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTTGAGCCCAATATCCTTCGCTGTGA
*
334354 AGTTGAAATTGGCTATGAAGTTGGGAAATTATTTGTTGACAGTCAGCCGCCCCTTCGTCGTGAAG
130 AGTTGAAATTGGCTATGAAGTTGGGAAATTATTTGTTGACAGTCAGCCGCCCCTTCGCCGTGAAG
334419 TTGAGCTTGTGCTGTATT
195 TTGAGCTTGTGCTGTATT
* *
334437 GAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTAACAG
*
334502 TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTTGACTCTTGAGTCCAATATCCTTCG
66 TCAGCCGCCCCTTCGCCGTGAAGTTGAGC-T-TG-TG--TTG--TCTTGAGCCCAATATCCTTCG
* **
334567 CTGTGAAGTTGAAATTGGCTCTGAAGTTGGGTCATTATTTGTTGACAGTCAGCCGCCCCTTCGCC
124 CTGTGAAGTTGAAATTGGCTATGAAGTTGGGAAATTATTTGTTGACAGTCAGCCGCCCCTTCGCC
*
334632 GTGAAGTTGAGCTTGTGCTGTCTT
189 GTGAAGTTGAGCTTGTGCTGTATT
334656 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAA
334706 GCCCCTTCGT
Statistics
Matches: 243, Mismatches: 18, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
211 3 0.01
212 81 0.33
213 1 0.00
214 2 0.01
215 2 0.01
217 3 0.01
219 151 0.62
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (212 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTAACAG
TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTTGAGCCCAATATCCTTCGCTGTGAA
GTTGAAATTGGCTATGAAGTTGGGAAATTATTTGTTGACAGTCAGCCGCCCCTTCGCCGTGAAGT
TGAGCTTGTGCTGTATT
Found at i:335834 original size:12 final size:13
Alignment explanation
Indices: 335818--335865 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 13
335808 CCCACCTTAT
335818 TTTTCTTTTCTT-
1 TTTTCTTTTCTTC
*
335830 TTTTCTTTTGTTC
1 TTTTCTTTTCTTC
335843 TTTCTCTTTT-TTC
1 TTT-TCTTTTCTTC
*
335856 TTTTTTTTTC
1 TTTTCTTTTC
335866 AATTTAGGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 16 0.52
13 9 0.29
14 6 0.19
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (13 bp):
TTTTCTTTTCTTC
Found at i:335845 original size:8 final size:7
Alignment explanation
Indices: 335823--335861 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
335813 CTTATTTTTC
335823 TTTTCTT
1 TTTTCTT
335830 TTTTCTT
1 TTTTCTT
335837 TTGTTC-T
1 TT-TTCTT
*
335844 TTCTCTT
1 TTTTCTT
335851 TTTTCTT
1 TTTTCTT
335858 TTTT
1 TTTT
335862 TTTCAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 2 0.07
7 23 0.82
8 3 0.11
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (7 bp):
TTTTCTT
Found at i:335852 original size:21 final size:20
Alignment explanation
Indices: 335820--335859 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
335810 CACCTTATTT
335820 TTCTTTTCTTTTTTCTTTTG
1 TTCTTTTCTTTTTTCTTTTG
335840 TTCTTTCTCTTTTTTCTTTT
1 TTCTTT-TCTTTTTTCTTTT
335860 TTTTTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (20 bp):
TTCTTTTCTTTTTTCTTTTG
Found at i:335941 original size:65 final size:68
Alignment explanation
Indices: 335835--335963 Score: 192
Period size: 65 Copynumber: 1.9 Consensus size: 68
335825 TTCTTTTTTC
* * * *
335835 TTTTGTTCTTTCTCTTTTTTCTTTTTTTTTCAATTTAGGACGCCCTTTCGGGTTTTCACCCTAAA
1 TTTTGTTCTTTCTCTTTTTTCTCTTTTTTTCAACTTAGGACGCCCTCTCAGGTTTTCACCCTAAA
335900 CGT
66 CGT
*
335903 TTTTGTT-TTT-TCTTTTTT-TCTTTTTTTCAACTTAGGACGCCCTCTCAGGTTTTCATCCTAA
1 TTTTGTTCTTTCTCTTTTTTCTCTTTTTTTCAACTTAGGACGCCCTCTCAGGTTTTCACCCTAA
335964 GCGAAGTACT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
65 38 0.68
66 8 0.14
67 3 0.05
68 7 0.12
ACGTcount: A:0.12, C:0.22, G:0.11, T:0.55
Consensus pattern (68 bp):
TTTTGTTCTTTCTCTTTTTTCTCTTTTTTTCAACTTAGGACGCCCTCTCAGGTTTTCACCCTAAA
CGT
Found at i:335977 original size:65 final size:66
Alignment explanation
Indices: 335847--335977 Score: 156
Period size: 65 Copynumber: 2.0 Consensus size: 66
335837 TTGTTCTTTC
* * * * *** **
335847 TCTTTTTTCTTTTTTTTTCAATTTAGGACGCCCTTTCGGGTTTTCACCCTAAACGTTTTTGTTTT
1 TCTTTTTTCTCTTTTTTTCAACTTAGGACGCCCTCTCAGGTTTTCACCCTAAACGAAGTACTTTT
335912 T
66 T
* *
335913 TCTTTTTT-TCTTTTTTTCAACTTAGGACGCCCTCTCAGGTTTTCATCCTAAGCGAAGTACTTTT
1 TCTTTTTTCTCTTTTTTTCAACTTAGGACGCCCTCTCAGGTTTTCACCCTAAACGAAGTACTTTT
335977 T
66 T
335978 GACTGCATCC
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
65 46 0.85
66 8 0.15
ACGTcount: A:0.15, C:0.21, G:0.12, T:0.52
Consensus pattern (66 bp):
TCTTTTTTCTCTTTTTTTCAACTTAGGACGCCCTCTCAGGTTTTCACCCTAAACGAAGTACTTTT
T
Found at i:343007 original size:23 final size:23
Alignment explanation
Indices: 342959--343001 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
342949 ATACGAATGT
342959 AAAAACATGGAAAATATAAAATA
1 AAAAACATGGAAAATATAAAATA
342982 AAAAACAT-G-AAATATAAAAT
1 AAAAACATGGAAAATATAAAAT
343002 GCAAAATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 11 0.55
22 1 0.05
23 8 0.40
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.19
Consensus pattern (23 bp):
AAAAACATGGAAAATATAAAATA
Found at i:346305 original size:16 final size:16
Alignment explanation
Indices: 346286--346325 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
346276 TGAAGTCAAA
346286 AAATAAAACAAACAAG
1 AAATAAAACAAACAAG
*
346302 AAAT-AAATAAACAAG
1 AAATAAAACAAACAAG
346317 ATAATAAAA
1 A-AATAAAA
346326 ATAAACAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 11 0.52
16 7 0.33
17 3 0.14
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.12
Consensus pattern (16 bp):
AAATAAAACAAACAAG
Found at i:346309 original size:4 final size:4
Alignment explanation
Indices: 346302--346362 Score: 52
Period size: 4 Copynumber: 15.0 Consensus size: 4
346292 AACAAACAAG
* * * *
346302 AAAT AAAT AAAC AAGAT AATAA AAAT AAAC AAAT AAA- CAAT AAAT AAAT
1 AAAT AAAT AAAT AA-AT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
346351 AAAT AAGT AAAT
1 AAAT AAAT AAAT
346363 TAGAAAAGCC
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
3 2 0.05
4 36 0.82
5 6 0.14
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:346315 original size:15 final size:15
Alignment explanation
Indices: 346295--346353 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 15
346285 AAAATAAAAC
346295 AAACAAGAAATAAAT
1 AAACAAGAAATAAAT
346310 AAACAAG--AT-AAT
1 AAACAAGAAATAAAT
* *
346322 AAA-AATAAACAAAT
1 AAACAAGAAATAAAT
*
346336 AAACAATAAATAAAT
1 AAACAAGAAATAAAT
346351 AAA
1 AAA
346354 TAAGTAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
11 2 0.05
12 6 0.16
13 3 0.08
14 6 0.16
15 20 0.54
ACGTcount: A:0.75, C:0.07, G:0.03, T:0.15
Consensus pattern (15 bp):
AAACAAGAAATAAAT
Found at i:346445 original size:14 final size:13
Alignment explanation
Indices: 346421--346456 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
346411 AAAAAAATTA
346421 AATAGAATAAAAT
1 AATAGAATAAAAT
346434 AATAGTAATAAAAT
1 AATAG-AATAAAAT
*
346448 AATAAAATA
1 AATAGAATA
346457 CGAAAAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (13 bp):
AATAGAATAAAAT
Found at i:346589 original size:21 final size:21
Alignment explanation
Indices: 346548--346589 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
346538 CACCGAAAGT
*
346548 AAAAAAAAAGGTACAGATTTG
1 AAAAAAAAAGGTAAAGATTTG
* *
346569 AAAAAAAAGGGTAAAGGTTTG
1 AAAAAAAAAGGTAAAGATTTG
346590 GTCAGCTAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.02, G:0.24, T:0.19
Consensus pattern (21 bp):
AAAAAAAAAGGTAAAGATTTG
Found at i:346820 original size:12 final size:12
Alignment explanation
Indices: 346803--346829 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
346793 CAAAGCAAAT
346803 AAAAATATAAAA
1 AAAAATATAAAA
346815 AAAAATATAAAA
1 AAAAATATAAAA
346827 AAA
1 AAA
346830 TAAAAGGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAATATAAAA
Found at i:346863 original size:18 final size:17
Alignment explanation
Indices: 346840--346903 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
346830 TAAAAGGATT
346840 TAATAAATATATATATA
1 TAATAAATATATATATA
*
346857 GTAAT-AATA-ATATATC
1 -TAATAAATATATATATA
*
346873 TAATAAAATGTAATATATA
1 TAAT-AAATAT-ATATATA
*
346892 TAAAAAATATAT
1 TAATAAATATAT
346904 GATTGAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
15 4 0.11
16 6 0.16
17 9 0.24
18 9 0.24
19 9 0.24
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (17 bp):
TAATAAATATATATATA
Found at i:346888 original size:19 final size:18
Alignment explanation
Indices: 346864--346899 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
346854 ATAGTAATAA
*
346864 TAATATATCTAATAAAATG
1 TAATATATATAA-AAAATG
346883 TAATATATATAAAAAAT
1 TAATATATATAAAAAAT
346900 ATATGATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (18 bp):
TAATATATATAAAAAATG
Found at i:357214 original size:20 final size:19
Alignment explanation
Indices: 357191--357242 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
357181 TATGAAACTT
*
357191 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACACG-AAATG
* *
357211 AAAATTGCAACATGAAATG
1 AAAATCGCAACACGAAATG
357230 AAAATCGCAACAC
1 AAAATCGCAACAC
357243 AAAACTAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.52, C:0.19, G:0.15, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACACGAAATG
Found at i:357640 original size:22 final size:22
Alignment explanation
Indices: 357610--357667 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
357600 GATGGAGATA
*
357610 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
* *
357632 GATGGATTTCGTCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
*
357654 GACGGATGTCGCCA
1 GACGGATTTCGCCA
357668 TAGAGAGCGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.21, C:0.17, G:0.41, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:357840 original size:20 final size:20
Alignment explanation
Indices: 357815--357865 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
357805 TAAAAGCGAT
*
357815 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGCG
*
357835 TTGCGAATTTGACTTTTGCG
1 TTGCGAATTTGACTTATGCG
357855 TTGCGAATTTG
1 TTGCGAATTTG
357866 GAAACTGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.18, C:0.12, G:0.25, T:0.45
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGCG
Found at i:364336 original size:2 final size:2
Alignment explanation
Indices: 364329--364369 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
364319 GTATTTACAC
364329 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
364370 TAATTATTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:365518 original size:5 final size:5
Alignment explanation
Indices: 365508--365540 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
365498 ATGACTTATC
365508 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
365541 GTTATATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:367044 original size:37 final size:35
Alignment explanation
Indices: 366989--367088 Score: 103
Period size: 35 Copynumber: 2.7 Consensus size: 35
366979 TTTCGTCCTA
366989 CTAGGATTTAAACTTTAAAAAATAGGATAGAATTCTG
1 CTAGGATTTAAACTTT--AAAATAGGATAGAATTCTG
* *
367026 CTAGGA-TTCAACTCTTAAAATAGGATAGAATTTTG
1 CTAGGATTTAAACT-TTAAAATAGGATAGAATTCTG
* * *
367061 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTAGGATTTAAACT-TTAAA-ATAGGAT
367089 CCACAAGCAC
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
35 22 0.41
36 17 0.31
37 15 0.28
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (35 bp):
CTAGGATTTAAACTTTAAAATAGGATAGAATTCTG
Found at i:367504 original size:31 final size:31
Alignment explanation
Indices: 367440--367516 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
367430 ATTATTCTTG
* *
367440 TTATATATGCATATTACTTTCTATTAATTTTA
1 TTATATATGTATA-TACTTTCTATTAATGTTA
* * *
367472 TTATATATGTATATATTTTTTATTAGTGTTA
1 TTATATATGTATATACTTTCTATTAATGTTA
*
367503 TTATATATATATAT
1 TTATATATGTATAT
367517 TTATATATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 27 0.69
32 12 0.31
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.58
Consensus pattern (31 bp):
TTATATATGTATATACTTTCTATTAATGTTA
Found at i:367612 original size:20 final size:20
Alignment explanation
Indices: 367587--367624 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
367577 ATTATTATTA
367587 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
367607 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
367625 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:367656 original size:16 final size:18
Alignment explanation
Indices: 367635--367669 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
367625 TTTACTCATT
367635 TATTTATC-TAT-TTTTA
1 TATTTATCTTATATTTTA
367651 TATTTATCTTATATTTTA
1 TATTTATCTTATATTTTA
367669 T
1 T
367670 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (18 bp):
TATTTATCTTATATTTTA
Found at i:374118 original size:17 final size:18
Alignment explanation
Indices: 374081--374120 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
374071 CCTTAGCCCA
374081 GGGCAGCATGATTGAGAG
1 GGGCAGCATGATTGAGAG
* *
374099 GGGCAGTATGTTTGAG-G
1 GGGCAGCATGATTGAGAG
374116 GGGCA
1 GGGCA
374121 TGAACAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.23, C:0.10, G:0.47, T:0.20
Consensus pattern (18 bp):
GGGCAGCATGATTGAGAG
Found at i:374135 original size:13 final size:13
Alignment explanation
Indices: 374117--374142 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
374107 TGTTTGAGGG
374117 GGCATGAACAAGA
1 GGCATGAACAAGA
374130 GGCATGAACAAGA
1 GGCATGAACAAGA
374143 ATGAAAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.31, T:0.08
Consensus pattern (13 bp):
GGCATGAACAAGA
Found at i:379928 original size:43 final size:42
Alignment explanation
Indices: 379861--380124 Score: 242
Period size: 43 Copynumber: 6.2 Consensus size: 42
379851 AAGTTAACGC
* * *
379861 CGTTTTTTGAACAAACGCCGCAAAAAGTCGAGATCTATAGCGG
1 CGTTTTTGGAACAAACGCCACAAAAGGTC-AGATCTATAGCGG
* * * * *
379904 CGTTTTCGGAACAAACACCACAAAAGGTCGATATCTATAGTGA
1 CGTTTTTGGAACAAACGCCACAAAAGGTC-AGATCTATAGCGG
* ** * * *
379947 CATTTTCAGAACAAACGTCGA-AAAAGGTCAGATTTATAGTGG
1 CGTTTTTGGAACAAACG-CCACAAAAGGTCAGATCTATAGCGG
* * * *
379989 CGTTTTTGGAACAAACGTCACAAAAGCTCTGATCTATAGCGT
1 CGTTTTTGGAACAAACGCCACAAAAGGTCAGATCTATAGCGG
* * * *
380031 CATTTTTTGGATACAAACGCCGCAAAAGGTCATATCTATAGTGG
1 C-GTTTTTGGA-ACAAACGCCACAAAAGGTCAGATCTATAGCGG
* * *
380075 CGTTTTTGAATACAAACGCCGCAAAAGGTTAGATCTATAGCGG
1 CGTTTTTGGA-ACAAACGCCACAAAAGGTCAGATCTATAGCGG
380118 CGTTTTT
1 CGTTTTT
380125 TTTATACAAA
Statistics
Matches: 179, Mismatches: 38, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
41 1 0.01
42 41 0.23
43 109 0.61
44 28 0.16
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (42 bp):
CGTTTTTGGAACAAACGCCACAAAAGGTCAGATCTATAGCGG
Found at i:380075 original size:86 final size:84
Alignment explanation
Indices: 379863--380140 Score: 290
Period size: 86 Copynumber: 3.2 Consensus size: 84
379853 GTTAACGCCG
* * * *
379863 TTTTTTGAACAAACGCCGCAAAAAGTCGAGATCTATAGCGGCGTTTTCGGAACAAACACCACAAA
1 TTTTTTGAACAAACGCCGCAAAAGGTC-AGATCTATAGTGGCGTTTTTGGAACAAACGCCACAAA
*
379928 AGGTC-GATATCTATAGTGACA
65 AGGTCTG--ATCTATAGCGACA
** * * * *
379949 TTTTCAGAACAAACGTCGAAAAAGGTCAGATTTATAGTGGCGTTTTTGGAACAAACGTCACAAAA
1 TTTTTTGAACAAACGCCGCAAAAGGTCAGATCTATAGTGGCGTTTTTGGAACAAACGCCACAAAA
* *
380014 GCTCTGATCTATAGCGTCA
66 GGTCTGATCTATAGCGACA
* * *
380033 TTTTTTGGATACAAACGCCGCAAAAGGTCATATCTATAGTGGCGTTTTTGAATACAAACGCCGCA
1 TTTTTT-GA-ACAAACGCCGCAAAAGGTCAGATCTATAGTGGCGTTTTTGGA-ACAAACGCCACA
* *
380098 AAAGGT-TAGATCTATAGCGGCGT
63 AAAGGTCT-GATCTATAGCGAC-A
*
380121 TTTTTTTATACAAACGCCGC
1 TTTTTTGA-ACAAACGCCGC
380141 CAAATATGCA
Statistics
Matches: 160, Mismatches: 26, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
84 15 0.09
85 38 0.24
86 61 0.38
87 40 0.25
88 6 0.04
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (84 bp):
TTTTTTGAACAAACGCCGCAAAAGGTCAGATCTATAGTGGCGTTTTTGGAACAAACGCCACAAAA
GGTCTGATCTATAGCGACA
Found at i:384068 original size:41 final size:41
Alignment explanation
Indices: 384012--384305 Score: 207
Period size: 41 Copynumber: 7.2 Consensus size: 41
384002 TTTATAAATA
*
384012 AAAAACGCCACTAAAGTACAAGCATTTAGTGGCGTTTGTCT
1 AAAAACGCCACTAAAGTACAAGCATTTAGCGGCGTTTGTCT
* * * *
384053 AAAAATGCCACTAAAGTACGAGTATTTAGCGGCGTTTGT-A
1 AAAAACGCCACTAAAGTACAAGCATTTAGCGGCGTTTGTCT
* * **
384093 AAAAACGCAACTAAAGTACTAGGTTTTAGCGGCGTTTGTCT
1 AAAAACGCCACTAAAGTACAAGCATTTAGCGGCGTTTGTCT
* * * * * *
384134 AAAAATGCCAC--GA-TACATGTATCCTATTGCGGCGTTTGTTT
1 AAAAACGCCACTAAAGTACAAGCAT--T-TAGCGGCGTTTGTCT
* *
384175 AAAAACGCCACTAAAG-A-ACG-ATTCTAAAGCGGCGTTTGTTT
1 AAAAACGCCACTAAAGTACAAGCATT-T--AGCGGCGTTTGTCT
* *
384216 AAAAACGCCACTAAAG-A-ACG-ATTCTAAAGCGGCGTTTGTTT
1 AAAAACGCCACTAAAGTACAAGCATT-T--AGCGGCGTTTGTCT
* * * *
384257 ACAAACGCCACTAAAGTACGAG-TTTTAGCAGCGTTTGT-T
1 AAAAACGCCACTAAAGTACAAGCATTTAGCGGCGTTTGTCT
384296 GAAAAACGCC
1 -AAAAACGCC
384306 GTTAATGTTA
Statistics
Matches: 210, Mismatches: 31, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
38 5 0.02
39 4 0.02
40 54 0.26
41 138 0.66
42 4 0.02
43 5 0.02
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (41 bp):
AAAAACGCCACTAAAGTACAAGCATTTAGCGGCGTTTGTCT
Found at i:384166 original size:81 final size:81
Alignment explanation
Indices: 384010--384294 Score: 244
Period size: 81 Copynumber: 3.5 Consensus size: 81
384000 GGTTTATAAA
*
384010 TAAAAAACGCCACTAAAGTACAAGCATTTAGTGGCGTTTGTCTAAAAATGCCACTAAAGTACGAG
1 TAAAAAACGCCACTAAAGTACAAGCATTTAGCGGCGTTTGTCTAAAAATGCCAC-AAAGTACGAG
384075 TATTTAGCGGCGTTTG-
65 TATTTAGCGGCGTTTGT
* * ** *
384091 TAAAAAACGCAACTAAAGTACTAGGTTTTAGCGGCGTTTGTCTAAAAATGCCAC-GA-TAC-ATG
1 TAAAAAACGCCACTAAAGTACAAGCATTTAGCGGCGTTTGTCTAAAAATGCCACAAAGTACGA-G
*
384153 TATCCTATTGCGGCGTTTGT
65 TAT--T-TAGCGGCGTTTGT
* * * * *
384173 TTAAAAACGCCACTAAAG-A-ACG-ATTCTAAAGCGGCGTTTGTTTAAAAACGCCACTAAAGAAC
1 TAAAAAACGCCACTAAAGTACAAGCATT-T--AGCGGCGTTTGTCTAAAAATGCCAC-AAAGTAC
* * **
384235 GATTCTAAAGCGGCGTTTGT
62 GAGTATTTAGCGGCGTTTGT
* * * * *
384255 TTACAAACGCCACTAAAGTACGAG-TTTTAGCAGCGTTTGT
1 TAAAAAACGCCACTAAAGTACAAGCATTTAGCGGCGTTTGT
384295 TGAAAAACGC
Statistics
Matches: 164, Mismatches: 26, Indels: 28
0.75 0.12 0.13
Matches are distributed among these distances:
77 1 0.01
78 7 0.04
79 3 0.02
80 3 0.02
81 72 0.44
82 67 0.41
83 2 0.01
84 4 0.02
85 4 0.02
86 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (81 bp):
TAAAAAACGCCACTAAAGTACAAGCATTTAGCGGCGTTTGTCTAAAAATGCCACAAAGTACGAGT
ATTTAGCGGCGTTTGT
Found at i:385004 original size:11 final size:11
Alignment explanation
Indices: 384990--385033 Score: 70
Period size: 11 Copynumber: 4.0 Consensus size: 11
384980 AAGCAAACGA
384990 TAAACGAACAC
1 TAAACGAACAC
* *
385001 TAAATGAACAT
1 TAAACGAACAC
385012 TAAACGAACAC
1 TAAACGAACAC
385023 TAAACGAACAC
1 TAAACGAACAC
385034 GTTCGTAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.55, C:0.23, G:0.09, T:0.14
Consensus pattern (11 bp):
TAAACGAACAC
Found at i:385079 original size:24 final size:23
Alignment explanation
Indices: 385052--385096 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
385042 ACGCTAAATG
385052 AACACATTC-ATGAACATATAAACA
1 AACACATTCGA-GAACAT-TAAACA
*
385076 AACACGTTCGAGAACATTAAA
1 AACACATTCGAGAACATTAAA
385097 TGAAGATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 14 0.74
25 1 0.05
ACGTcount: A:0.51, C:0.20, G:0.09, T:0.20
Consensus pattern (23 bp):
AACACATTCGAGAACATTAAACA
Found at i:386000 original size:35 final size:36
Alignment explanation
Indices: 385949--386029 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 36
385939 AACACAGTCA
* * *
385949 TCAATTACATTGTAAACCCCAAATT-TAAAAATGCT
1 TCAATTACATTCTAAACCCCAAATTCCAAAAATACT
*
385984 TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAAATACT
386020 TCAATTACAT
1 TCAATTACAT
386030 GCCTAATCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 23 0.56
36 18 0.44
ACGTcount: A:0.43, C:0.22, G:0.02, T:0.32
Consensus pattern (36 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAAATACT
Found at i:386022 original size:36 final size:35
Alignment explanation
Indices: 385949--386046 Score: 117
Period size: 36 Copynumber: 2.8 Consensus size: 35
385939 AACACAGTCA
* * *
385949 TCAATTACATTGTAAACCCCAAATTTAAAAATGCT
1 TCAATTACATTCTAAACCCCAAATTCAAAAATACT
*
385984 TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
1 TCAATTACATTCTAAACCCCAAATT-CAAAAATACT
* *
386020 TCAATTACATGCCT-AATCCCAAATTCA
1 TCAATTACAT-TCTAAACCCCAAATTCA
386047 TAATACATTC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
35 25 0.46
36 27 0.50
37 2 0.04
ACGTcount: A:0.42, C:0.24, G:0.03, T:0.31
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCAAAAATACT
Found at i:386799 original size:148 final size:148
Alignment explanation
Indices: 386510--386802 Score: 462
Period size: 148 Copynumber: 2.0 Consensus size: 148
386500 AAACTATTTA
* * * * *
386510 AATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACATAAACTCAAA
1 AATTACAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
* * *
386575 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAATTCAAATTGAAAAAATTTCGAGTCAACT
66 AATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAAATTAAAAAAATTTCGAGTCAACT
386640 ATTTTATAAACTGAACTG
131 ATTTTATAAACTGAACTG
* **
386658 AATTACAATAAAATAATTTTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTGGAA
1 AATTACAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
*
386723 AATTCAATTCAATTTGAATTGATTTAAATTTTATAAACTC-AATTAAAAAAATTTCGAGTCAACT
66 AATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAAATTAAAAAAATTTCGAGTCAACT
386787 ATTTTATAAAACTGAA
131 ATTTTAT-AAACTGAA
386803 TTGAGTATTT
Statistics
Matches: 132, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
147 30 0.23
148 102 0.77
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.38
Consensus pattern (148 bp):
AATTACAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
AATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAAATTAAAAAAATTTCGAGTCAACT
ATTTTATAAACTGAACTG
Found at i:387026 original size:35 final size:35
Alignment explanation
Indices: 386987--387066 Score: 115
Period size: 35 Copynumber: 2.3 Consensus size: 35
386977 GGGGTTGGGC
* *
386987 ATGTAATTGAAGTATTTTGGAAGTTGAGGTTTAGA
1 ATGTAATTGAAATATTTTAGAAGTTGAGGTTTAGA
** *
387022 ATGTAATTGAAATATTTTAGATTTTGGGGTTTAGA
1 ATGTAATTGAAATATTTTAGAAGTTGAGGTTTAGA
387057 ATGTAATTGA
1 ATGTAATTGA
387067 TGATGTGTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (35 bp):
ATGTAATTGAAATATTTTAGAAGTTGAGGTTTAGA
Found at i:388378 original size:35 final size:36
Alignment explanation
Indices: 388327--388407 Score: 110
Period size: 35 Copynumber: 2.3 Consensus size: 36
388317 GACACAGACA
* *
388327 TCAATTACATTGTAAACCCCAAATTTC-AAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAAATACT
* *
388362 TCAATTACATTCTAAACCTCAAATTCCAAAAATAGT
1 TCAATTACATTCTAAACCCCAAATTCCAAAAATACT
*
388398 TTAATTACAT
1 TCAATTACAT
388408 GCCCAATCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 24 0.60
36 16 0.40
ACGTcount: A:0.43, C:0.21, G:0.02, T:0.33
Consensus pattern (36 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAAATACT
Found at i:389070 original size:148 final size:148
Alignment explanation
Indices: 388887--389179 Score: 473
Period size: 148 Copynumber: 2.0 Consensus size: 148
388877 AAACTATTTA
* * *
388887 AATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACATAAACTCAAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
* * *
388952 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAA-AATTTTGAGTCAAC
66 AATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTC-AAT-GAAAAGAAATTCGAGTCAAC
389016 TATTTTATAAAA-TGAACTG
129 TATTTTATAAAACTGAACTG
**
389035 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTGGAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
*
389100 AATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAATTAAAAGAAATTCGAGTCAACTA
66 AATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAATGAAAAGAAATTCGAGTCAACTA
389165 TTTTATAAAACTGAA
131 TTTTATAAAACTGAA
389180 TTGAGTATTT
Statistics
Matches: 134, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
146 4 0.03
147 27 0.20
148 103 0.77
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (148 bp):
AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
AATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAATGAAAAGAAATTCGAGTCAACTA
TTTTATAAAACTGAACTG
Found at i:389397 original size:35 final size:35
Alignment explanation
Indices: 389358--389437 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
389348 GGGGTTGGGC
* *
389358 ATGTAATTGAAGTATTTTGGAAGTTGAGGTTTAGA
1 ATGTAATTGAAATATTTTGGAAGTTGAGGTTTAAA
* ** *
389393 ATGTAATTAAAATATTTTGGATTTTGGGGTTTAAA
1 ATGTAATTGAAATATTTTGGAAGTTGAGGTTTAAA
389428 ATGTAATTGA
1 ATGTAATTGA
389438 TGACTGTGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.42
Consensus pattern (35 bp):
ATGTAATTGAAATATTTTGGAAGTTGAGGTTTAAA
Found at i:390752 original size:35 final size:36
Alignment explanation
Indices: 390703--390781 Score: 124
Period size: 35 Copynumber: 2.2 Consensus size: 36
390693 CACAATTATT
* *
390703 AATTATATTGTAAACCCCAAATTTC-AAAATACTTC
1 AATTATATTCTAAACCCCAAATTCCAAAAATACTTC
*
390738 AATTATATTCTAAACCTCAAATTCCAAAAATACTTC
1 AATTATATTCTAAACCCCAAATTCCAAAAATACTTC
390774 AATTATAT
1 AATTATAT
390782 GTCCAATCCT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 22 0.55
36 18 0.45
ACGTcount: A:0.44, C:0.19, G:0.01, T:0.35
Consensus pattern (36 bp):
AATTATATTCTAAACCCCAAATTCCAAAAATACTTC
Found at i:390796 original size:36 final size:36
Alignment explanation
Indices: 390703--390797 Score: 113
Period size: 36 Copynumber: 2.7 Consensus size: 36
390693 CACAATTATT
** * *
390703 AATTATATTGTAAACCCCAAATTTC-AAAATACTTC
1 AATTATATTCCAAACCTCAAATTCCAAAAATACTTC
*
390738 AATTATATTCTAAACCTCAAATTCCAAAAATACTTC
1 AATTATATTCCAAACCTCAAATTCCAAAAATACTTC
*
390774 AATTATATGTCCAATCCT-AAATTC
1 AATTATAT-TCCAAACCTCAAATTC
390798 ATAATACATT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
35 22 0.42
36 24 0.45
37 7 0.13
ACGTcount: A:0.42, C:0.21, G:0.02, T:0.35
Consensus pattern (36 bp):
AATTATATTCCAAACCTCAAATTCCAAAAATACTTC
Found at i:397703 original size:146 final size:146
Alignment explanation
Indices: 397439--397958 Score: 862
Period size: 146 Copynumber: 3.6 Consensus size: 146
397429 TCAGGATCTC
397439 TGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAG
1 TGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAG
** *
397504 GACGATCAGACGGTGGACGGTGACAAATCGGAGAAAACAAATCCGGGTGGTTTTTAGCCTCTTGC
66 GACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGC
*
397569 CGTTGATCGGAATATT
131 CGGTGATCGGAATATT
397585 TGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAG
1 TGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAG
*
397650 GACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTTC
66 GACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGC
397715 CGGTGATCGGAATATT
131 CGGTGATCGGAATATT
397731 TGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAG
1 TGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAG
* * *
397796 GACGATCGGACGGTGGACGGTGACGGATCGGAGAAAATAAATCCGGACGGTTTTTAGCCTCTTGC
66 GACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGC
* *
397861 CGGTGATCGGAATCTG
131 CGGTGATCGGAATATT
* * * * * *
397877 CGATCAATATTCCGAACGGTGAAAAGTTGCGCG-ATGCCAACACAAACAACCTATTGAAAAATCA
1 TGATCAATATTCCGAACGGTCAAAAGTTGCG-GAAGGCCATCACGAACAACATATTGAAAAATCA
* *
397941 GGACAATCGGACGGTGGA
65 GGACGATCAGACGGTGGA
397959 TGACGGCAGA
Statistics
Matches: 355, Mismatches: 18, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
146 354 1.00
147 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (146 bp):
TGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAG
GACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGC
CGGTGATCGGAATATT
Found at i:402721 original size:31 final size:30
Alignment explanation
Indices: 402663--402720 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
402653 GAGCAACGAA
402663 TCAAGTTTTGATCTTGTAATTTTTTTTTCT
1 TCAAGTTTTGATCTTGTAATTTTTTTTTCT
402693 TCAAGTTTTGATCTTGTAATTTTTTTTT
1 TCAAGTTTTGATCTTGTAATTTTTTTTT
402721 TGAGTTAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.17, C:0.09, G:0.10, T:0.64
Consensus pattern (30 bp):
TCAAGTTTTGATCTTGTAATTTTTTTTTCT
Found at i:404920 original size:125 final size:124
Alignment explanation
Indices: 404692--405069 Score: 438
Period size: 125 Copynumber: 3.0 Consensus size: 124
404682 TTAGGATATG
* **
404692 TTGGGGCACGACTGAACCCACATCAGGTTGAGATGACAAGATTCAGACCAATGAGGCATGAAGAA
1 TTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAAAAGGCATGAAG-A
* * * *
404757 TGAGCCTTAGAATTTGAGGTGATGAGGCATTTTAAAGGCCCGTACCAGTATAAGACAATA
65 GGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACAATA
* * * *
404817 TTGGGGCACGACTGAACCCACGTCATGTTGAGATGACAAGATTTAAACCAAAAATGCATGAAGTA
1 TTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAAAAGGCATGAAG-A
** * * *
404882 GGAGCCTTACAATTTGAGGTGATGGGGTTTTTTGAAGGCCCATACCGGTATAAGACACTGA
65 GGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACAAT-A
* * * *
404943 -TGGGGCATGACTGCACCCACATCGTG-TGAAGATGACAAGATTCAGACCAAGAAGGCATTG-AG
1 TTGGGGCACGACTGAACCCACATCATGTTG-AGATGACAAGATTCAGACCAAAAAGGCA-TGAAG
* * * * * * *
405005 AGCAAGCCTTACAATCTGAGATGTTGGGGCATTTTGAAGGCCCGTACCAATGTAAGATAATA
64 AG-GAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACAATA
405067 TTG
1 TTG
405070 CGACACTAGG
Statistics
Matches: 211, Mismatches: 37, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
124 5 0.02
125 203 0.96
126 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (124 bp):
TTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAAAAGGCATGAAGAG
GAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACAATA
Found at i:406336 original size:36 final size:36
Alignment explanation
Indices: 406173--406366 Score: 140
Period size: 36 Copynumber: 5.4 Consensus size: 36
406163 AGCAAAGTCA
* * * ** * *
406173 ATCTTAAGCCTTTACCGAAGAGGAGTGAAGCAGATCA
1 ATCTTAAGTCTTCACCAAAGAATAGTGAAGCA-AACC
* *
406210 ATCTGAAGTCTTCACCAAATAATAGTGAAGC-AACC
1 ATCTTAAGTCTTCACCAAAGAATAGTGAAGCAAACC
* * *
406245 ATCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAACC
1 ATCTTAAGTCTTCACCAAAGAATAGTGAAGCAAACC
* * *
406281 GTCTTAAG-CATGCACCAAAGAATAATGAAGCAAACC
1 ATCTTAAGTC-TTCACCAAAGAATAGTGAAGCAAACC
** * * * *
406317 ATCTTGTGTCTTCATCAAAGAGTCGTGAAGGAAATCC
1 ATCTTAAGTCTTCACCAAAGAATAGTGAAGCAAA-CC
* *
406354 ATTTTAAGCCTTC
1 ATCTTAAGTCTTC
406367 TCATAAGAGT
Statistics
Matches: 121, Mismatches: 32, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
35 29 0.24
36 56 0.46
37 36 0.30
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (36 bp):
ATCTTAAGTCTTCACCAAAGAATAGTGAAGCAAACC
Found at i:406881 original size:54 final size:54
Alignment explanation
Indices: 406736--407631 Score: 1153
Period size: 54 Copynumber: 16.5 Consensus size: 54
406726 AGTGAAGCAA
* *
406736 AAGAAGATTTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* *
406790 AAG-A-TTGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* *
406842 AAGAAGATGTACGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
406896 AAGAAGATGTACGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
406950 AAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
407004 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
407058 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
407112 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
407166 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGTGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* *
407220 AAGAAGATTTCCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * * * *
407274 AAG-AGATATCCGAGTTCCATACTCCTTAAAGAAAGAAGGAGTGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * **
407327 AAG-AGATGTCTGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCCGTAAG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAA-CCCGTTTG
* * *
407381 AAGAAGATGTTCGAGTTCCATACTCCTTGAAAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTG
** * * * * * *
407436 TTGAAGATGGTTCGAG-TCTTATACTCTCT-GCAAGAAATAGAGAGC-AGACACGATTT-
1 AAGAAGAT-GTCCGAGTTC-CATACTCCCTAG--AGAAAGAGGGAGCGA-ACCCG-TTTG
** * ** * * * *
407492 TTGAAGATTGTTCGAGTTTTATACTCCTTGAAAGAAAGATGGAGCGAACCCGTTTT
1 AAGAAGA-TGTCCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTG
* * * * * * * *
407548 CAGAAGATTGTTCGAGTTCTATACTCCCTAAAGCAATAGGGAGCGAACCTGGTTTC
1 AAGAAGA-TGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACC-CGTTTG
* * *
407604 AA-AAGGTTGTTCGAGTTCTATACTCCCT
1 AAGAA-GATGTCCGAGTTCCATACTCCCT
407632 GAAAGAATAG
Statistics
Matches: 762, Mismatches: 61, Indels: 37
0.89 0.07 0.04
Matches are distributed among these distances:
52 49 0.06
53 86 0.11
54 430 0.56
55 79 0.10
56 112 0.15
57 6 0.01
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (54 bp):
AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
Found at i:407727 original size:55 final size:55
Alignment explanation
Indices: 407382--407731 Score: 231
Period size: 55 Copynumber: 6.3 Consensus size: 55
407372 CCCCGTAAGA
* * * *
407382 AGAAGA-TGTTCGAGT-TCCATACTCCTTGAAAGAA-AGAGGGAGCGAACCCGTTTGT-
1 AGAAGATTGTTCGAGTCT-TATACTCCCTGAAAGAATA-A-GGAGCGGACACGTTT-TC
* * * * *
407437 TGAAGATGGTTCGAGTCTTATACTCTCTGCAAGAA-ATAGAGAGCAGACACGATTTT-
1 AGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATA-AG-GAGCGGACACG-TTTTC
* * * * *
407493 TGAAGATTGTTCGAGTTTTATACTCCTTGAAAGAA-AGATGGAGCGAACCCGTTTTC
1 AGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATA-A-GGAGCGGACACGTTTTC
* * *
407549 AGAAGATTGTTCGAGT-TCTATACTCCCT-AAAGCAATAGGGAGCGAAC-CTGGTTTC
1 AGAAGATTGTTCGAGTCT-TATACTCCCTGAAAG-AATAAGGAGCGGACAC-GTTTTC
* * * *
407604 AAAAGGTTGTTCGAGT-TCTATACTCCCTGAAAGAAT-AGGAAGCAGACACGTTGGTC
1 AGAAGATTGTTCGAGTCT-TATACTCCCTGAAAGAATAAGG-AGCGGACACGTT-TTC
* * *
407660 -GAAGATTGTTCAAGTCTTATACTCTCTGAAAGAATAAAGAGCGGACACGTTTTC
1 AGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAAGGAGCGGACACGTTTTC
* * *
407714 CGAAGATTTTTCAAGTCT
1 AGAAGATTGTTCGAGTCT
407732 CATTTAGTTA
Statistics
Matches: 240, Mismatches: 38, Indels: 34
0.77 0.12 0.11
Matches are distributed among these distances:
54 5 0.02
55 121 0.50
56 108 0.45
57 6 0.03
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.28
Consensus pattern (55 bp):
AGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAAGGAGCGGACACGTTTTC
Found at i:408545 original size:146 final size:146
Alignment explanation
Indices: 408300--408818 Score: 851
Period size: 146 Copynumber: 3.6 Consensus size: 146
408290 CAGGATCTCC
408300 GATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGG
1 GATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGG
* *
408365 ACGATCAGACGGTGGACGGTGACGAATCGGAGAAAACAAATCCGGGTGGTTTTTAGCCTCTTGCC
66 ACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGCC
408430 GGTGATCGGAATATTT
131 GGTGATCGGAATATTT
*
408446 GATCAATATTCTGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGG
1 GATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGG
* *
408511 ACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATACGGGCGGTTTTTAGCCTCTTTCC
66 ACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGCC
408576 GGTGATCGGAATATTT
131 GGTGATCGGAATATTT
408592 GATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGG
1 GATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGG
* * *
408657 ACGATCGGACGGTGGACGGTGACGGATCGGAGAAAATAAATCCGGACGGTTTTTAGCCTCTTGCC
66 ACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGCC
* **
408722 GGTGATCGGAATCTGC
131 GGTGATCGGAATATTT
* * * * * *
408738 GATCAATATTTCGAACGGTGAAAAGTTGCGCG-ATGCCAACACAAACAACCTATTGAAAAATCAG
1 GATCAATATTCCGAACGGTCAAAAGTTGCG-GAAGGCCATCACGAACAACATATTGAAAAATCAG
* *
408802 GACAATCGGACGGTGGA
65 GACGATCAGACGGTGGA
408819 TGACGGCAAA
Statistics
Matches: 351, Mismatches: 21, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
146 350 1.00
147 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (146 bp):
GATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGG
ACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTGCC
GGTGATCGGAATATTT
Found at i:414518 original size:111 final size:111
Alignment explanation
Indices: 414374--414700 Score: 531
Period size: 111 Copynumber: 3.0 Consensus size: 111
414364 ATTACAAAAA
* *
414374 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAATTATTACTAACAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
414439 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
414485 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
414550 AATTAAAACGTTAAAATATTACCGTAT---C--A-TGTTGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
* * *
414590 TTAATTTTTAATCTAATAATCATGCATTAAATAAATAAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
414655 AATTAACACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
414701 ATGATTTTCA
Statistics
Matches: 200, Mismatches: 10, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
105 97 0.49
106 1 0.00
108 2 0.01
110 1 0.00
111 99 0.50
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:414648 original size:105 final size:106
Alignment explanation
Indices: 414374--414684 Score: 498
Period size: 105 Copynumber: 2.9 Consensus size: 106
414364 ATTACAAAAA
* *
414374 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAATTATTACTAACAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
414439 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTAT---C--AGTGTCGAGATAT
414485 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
414550 AATTAAAACGTTAAAATATTACCGTATCA-TGTTGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGTGTCGAGATAT
* * *
414590 TTAATTTTTAATCTAATAATCATGCATTAAATAAATAAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
414655 AATTAACACGTTAAAATGTTACCGTATCAG
66 AATTAAAACGTTAAAATGTTACCGTATCAG
414685 CAAAGTGTAG
Statistics
Matches: 190, Mismatches: 9, Indels: 7
0.92 0.04 0.03
Matches are distributed among these distances:
105 99 0.52
106 1 0.01
108 1 0.01
111 89 0.47
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.37
Consensus pattern (106 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGTGTCGAGATAT
Found at i:414784 original size:17 final size:18
Alignment explanation
Indices: 414764--414797 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
414754 ATTATATTAG
414764 TAAAATA-TTAAATAAAA
1 TAAAATACTTAAATAAAA
414781 TAAAATACTTAAATAAA
1 TAAAATACTTAAATAAA
414798 TTATATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAATACTTAAATAAAA
Found at i:415041 original size:50 final size:50
Alignment explanation
Indices: 414987--415112 Score: 173
Period size: 50 Copynumber: 2.5 Consensus size: 50
414977 AGATACTTAG
* * *
414987 GTATAGCACGGATCAGGGGGCGCGCTATACCTACGTGGCGCCAAATCACC
1 GTATAACACGGATCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAAC
* *
415037 GTATATCACGGGA-CAGGGGGCGCACTATACCCACGTGGCGCCAAATCAAC
1 GTATAACAC-GGATCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAAC
* *
415087 GTATAACACGGTTCGGGGGGCGCGCT
1 GTATAACACGGATCAGGGGGCGCGCT
415113 TTACTGCTAC
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
49 2 0.03
50 61 0.92
51 3 0.05
ACGTcount: A:0.24, C:0.29, G:0.32, T:0.16
Consensus pattern (50 bp):
GTATAACACGGATCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAAC
Found at i:415417 original size:60 final size:59
Alignment explanation
Indices: 415331--415507 Score: 187
Period size: 60 Copynumber: 2.9 Consensus size: 59
415321 AAGTATGATT
* ** * *
415331 TTCATTTTAAATTGGTGCAT-AAATTTTTAAATATTTTATTTTCATCCCTAAACTATGATA
1 TTCATTTTAAATTGGT-CCTCAAATTTTTAAATATTCCAATTTCATCCC-AAACTATGACA
* * *
415391 GTT-ATTTTAAATTAGTCCTCAAATTTTTAAACATTCCAATTGCATCCCCAAAACTATGACA
1 -TTCATTTTAAATTGGTCCTCAAATTTTTAAATATTCCAATTTCAT-CCC-AAACTATGACA
* * *
415452 TTCATTCTAAATTGGTCCCCAAACTTTTTTAATATTCCAATTTCATCCCAAACTAT
1 TTCATTTTAAATTGGTCCTCAAA-TTTTTAAATATTCCAATTTCATCCCAAACTAT
415508 ACACATGTAC
Statistics
Matches: 97, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
59 2 0.02
60 41 0.42
61 35 0.36
62 19 0.20
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.42
Consensus pattern (59 bp):
TTCATTTTAAATTGGTCCTCAAATTTTTAAATATTCCAATTTCATCCCAAACTATGACA
Found at i:415502 original size:61 final size:59
Alignment explanation
Indices: 415351--415507 Score: 163
Period size: 61 Copynumber: 2.6 Consensus size: 59
415341 ATTGGTGCAT
* ** * * * *
415351 AAATTTTTAAATATTTTATTTTCATCCCTAAACTATGATAGTTATTTTAAATTAGTCCTC
1 AAATTTTTAAACATTCCAATTTCATCCC-AAACTATGACAGTTATTCTAAATTAGTCCCC
* *
415411 AAATTTTTAAACATTCCAATTGCATCCCCAAAACTATGACA-TTCATTCTAAATTGGTCCCC
1 AAATTTTTAAACATTCCAATTTCAT-CCC-AAACTATGACAGTT-ATTCTAAATTAGTCCCC
* *
415472 AAACTTTTTTAATATTCCAATTTCATCCCAAACTAT
1 AAA-TTTTTAAACATTCCAATTTCATCCCAAACTAT
415508 ACACATGTAC
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
60 29 0.36
61 33 0.41
62 19 0.23
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.41
Consensus pattern (59 bp):
AAATTTTTAAACATTCCAATTTCATCCCAAACTATGACAGTTATTCTAAATTAGTCCCC
Found at i:417638 original size:22 final size:23
Alignment explanation
Indices: 417584--417638 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
417574 CTGCATGTAC
417584 GACACATTTTCATATTGCTTTAT
1 GACACATTTTCATATTGCTTTAT
* * *
417607 AACACGTTTTC-TTTTGTCTTT-T
1 GACACATTTTCATATTG-CTTTAT
417629 GACACATTTT
1 GACACATTTT
417639 TCAGCCGTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.22, C:0.18, G:0.09, T:0.51
Consensus pattern (23 bp):
GACACATTTTCATATTGCTTTAT
Found at i:441796 original size:10 final size:9
Alignment explanation
Indices: 441771--441795 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
441761 TTTTTTACTC
441771 CAAAAAATG
1 CAAAAAATG
441780 CAAAAAATG
1 CAAAAAATG
441789 CAAAAAA
1 CAAAAAA
441796 AAAATGGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.72, C:0.12, G:0.08, T:0.08
Consensus pattern (9 bp):
CAAAAAATG
Found at i:455008 original size:60 final size:60
Alignment explanation
Indices: 454842--455031 Score: 177
Period size: 60 Copynumber: 3.2 Consensus size: 60
454832 TTACATCATA
* * * * * * * * * * *
454842 CATCCCTAAAATATAACCCTCATTTTAAATTAGTTTTTAAGCTTTTAAATATTCTAATTC
1 CATCCCCAAACTATGACTCTCATTCTAAATTAATCTTTAAACTTTTGAACATTCTAATTT
* *
454902 CATCCCCAAACTATGACTCTCATTCTAAATTAATCCTTGAACTTTTGAACATTCTAATTT
1 CATCCCCAAACTATGACTCTCATTCTAAATTAATCTTTAAACTTTTGAACATTCTAATTT
* * * * *
454962 CATCCCTACACTATGAC-CTTCTTTCTAAATTGATCTTTAAACTTTTGAATC-TTCCAATTT
1 CATCCCCAAACTATGACTC-TCATTCTAAATTAATCTTTAAACTTTTGAA-CATTCTAATTT
*
455022 CATCCTCAAA
1 CATCCCCAAA
455032 TGCACCCAAA
Statistics
Matches: 105, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
59 1 0.01
60 103 0.98
61 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.41
Consensus pattern (60 bp):
CATCCCCAAACTATGACTCTCATTCTAAATTAATCTTTAAACTTTTGAACATTCTAATTT
Found at i:455215 original size:29 final size:29
Alignment explanation
Indices: 455160--455215 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
455150 TTTGGGAGAC
* * *
455160 AATTGGAATGTTCAAAAAGTTTTGGATGA
1 AATTGAAATATTCAAAAAGTTTAGGATGA
455189 AATTGAAATATTC-AAAAGTTTAAGGAT
1 AATTGAAATATTCAAAAAGTTT-AGGAT
455216 TAATTTGGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.34
Consensus pattern (29 bp):
AATTGAAATATTCAAAAAGTTTAGGATGA
Found at i:455931 original size:60 final size:60
Alignment explanation
Indices: 455850--456167 Score: 183
Period size: 60 Copynumber: 5.2 Consensus size: 60
455840 ATCTATTATG
* * * * *
455850 TTAAA-TTTTAAATATTCTAATTCTATCCCCAAACTATGACTCTCATTCTAAATTAATCC
1 TTAAACTTTTGAACATTCTAATTCTATCCCTAAACTATAACCCTCATTCTAAATTAATCC
455909 TTAAACTTTTGAACATTCTAATT-TCATCCCTAAACTATAACCCTC-TT-TAATATTGGTGATTT
1 TTAAACTTTTGAACATTCTAATTCT-ATCCCTAAACTATAACCCTCATTCTAA-A-T--T-A---
*
455971 TAT-G
57 -ATCC
* * * * * *
455975 TTAAA--TTTGAGTTA-ATTACATCATAC-ATCCCTAAAGTATAACCCTCATTGTAAATTAGTCT
1 TTAAACTTTTGA---ACATT-C-TAATTCTATCCCTAAACTATAACCCTCATTCTAAATTAATCC
* * * * * * ** **
456036 TTAAGCTTTTAAATATTCTAATTAC-ATCCCCACACTATGATTCTCACACTAAATTAATCC
1 TTAAACTTTTGAACATTCTAATT-CTATCCCTAAACTATAACCCTCATTCTAAATTAATCC
* *
456096 TTAAACTTTTGAACATTCTAATT-TCATCCCTAAACTATAACCCTCTTTCT-AATTGATCC
1 TTAAACTTTTGAACATTCTAATTCT-ATCCCTAAACTATAACCCTCATTCTAAATTAATCC
456155 TTAAACTTTTGAA
1 TTAAACTTTTGAA
456168 TCTTCCAATT
Statistics
Matches: 195, Mismatches: 38, Indels: 52
0.68 0.13 0.18
Matches are distributed among these distances:
58 3 0.02
59 33 0.17
60 98 0.50
61 7 0.04
62 1 0.01
63 5 0.03
64 6 0.03
65 1 0.01
66 8 0.04
67 24 0.12
68 6 0.03
69 3 0.02
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (60 bp):
TTAAACTTTTGAACATTCTAATTCTATCCCTAAACTATAACCCTCATTCTAAATTAATCC
Found at i:456183 original size:29 final size:30
Alignment explanation
Indices: 456092--456184 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 30
456082 CACTAAATTA
456092 ATCCTTAAACTTTTGAA-CATTCTAATTTC
1 ATCCTTAAACTTTTGAATCATTCTAATTTC
* * * *
456121 ATCCCTAAAC-TAT-AACCCTCTTTCTAA-TTG
1 ATCCTTAAACTTTTGAA---TCATTCTAATTTC
*
456151 ATCCTTAAACTTTTGAATC-TTCCAATTTC
1 ATCCTTAAACTTTTGAATCATTCTAATTTC
456180 ATCCT
1 ATCCT
456185 CAAGTGCATC
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
27 2 0.04
28 7 0.14
29 18 0.37
30 11 0.22
31 9 0.18
32 2 0.04
ACGTcount: A:0.29, C:0.26, G:0.03, T:0.42
Consensus pattern (30 bp):
ATCCTTAAACTTTTGAATCATTCTAATTTC
Found at i:456586 original size:60 final size:59
Alignment explanation
Indices: 456508--456671 Score: 145
Period size: 60 Copynumber: 2.7 Consensus size: 59
456498 GGAATGTTCA
** *
456508 AAAAGTTTGGGGACTAATTTAGAATGAAGGTCATAGTTTAAGGATGAAATTGAAATATTT
1 AAAAGTTTAAGGACTAATTTAGAATGAAGGTCATAGTTT-AGGATGAAATTGAAACATTT
* * * *
456568 AAAAGTTTAAGGACTAATTT-GAAATGATA-ATCATAGTTTAGGAATGCAATTGGAGCATTT
1 AAAAGTTTAAGGACTAATTTAG-AATGA-AGGTCATAGTTTAGG-ATGAAATTGAAACATTT
* * * * *
456628 AAAATTTTATGGACCAATTTAAAATG-AGGATCATACTTTGAGGA
1 AAAAGTTTAAGGACTAATTTAGAATGAAGG-TCATAGTTT-AGGA
456672 CACGTGATAC
Statistics
Matches: 84, Mismatches: 13, Indels: 14
0.76 0.12 0.13
Matches are distributed among these distances:
58 1 0.01
59 4 0.05
60 75 0.89
61 4 0.05
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (59 bp):
AAAAGTTTAAGGACTAATTTAGAATGAAGGTCATAGTTTAGGATGAAATTGAAACATTT
Found at i:471752 original size:19 final size:17
Alignment explanation
Indices: 471728--471762 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
471718 ACTAAAAGAT
471728 CAACCTTTCAGTTTTTTGG
1 CAACC-TTCA-TTTTTTGG
471747 CAACCTTCATTTTTTG
1 CAACCTTCATTTTTTG
471763 CTGTTTTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.17, C:0.23, G:0.11, T:0.49
Consensus pattern (17 bp):
CAACCTTCATTTTTTGG
Found at i:474775 original size:25 final size:25
Alignment explanation
Indices: 474749--474796 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
474739 ATATATATTA
474749 AAATA-AATATATTT-TTAATATAAT
1 AAATACAAT-TATTTATTAATATAAT
*
474773 AAATACAATTTTTTATTAATATAA
1 AAATACAATTATTTATTAATATAA
474797 AATGGGCCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATACAATTATTTATTAATATAAT
Found at i:479866 original size:32 final size:32
Alignment explanation
Indices: 479830--479899 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
479820 TCTCAATTTC
*
479830 CCCCCATAAACTACCATTTTAATCCCACTTTG
1 CCCCCATAAACTACCATTTTAATCCCACTTAG
479862 CCCCCATAAACTACCATTTTAATCCCACTTAG
1 CCCCCATAAACTACCATTTTAATCCCACTTAG
479894 CCCCCA
1 CCCCCA
479900 ATATTATAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.29, C:0.41, G:0.03, T:0.27
Consensus pattern (32 bp):
CCCCCATAAACTACCATTTTAATCCCACTTAG
Found at i:482325 original size:2 final size:2
Alignment explanation
Indices: 482318--482375 Score: 84
Period size: 2 Copynumber: 30.0 Consensus size: 2
482308 TTTGATATCG
* *
482318 AT AT AT AT -T AT AA AA 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
482359 AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT
482376 GTGACTAAGA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:482409 original size:19 final size:19
Alignment explanation
Indices: 482387--482439 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
482377 TGACTAAGAT
482387 AATAATAAAATAATAAAGC
1 AATAATAAAATAATAAAGC
*
482406 AATAATTAAAAT-ATAAAGT
1 AATAA-TAAAATAATAAAGC
*
482425 AATAACAAAATAATA
1 AATAATAAAATAATA
482440 TTGTAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 5 0.17
19 19 0.63
20 6 0.20
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (19 bp):
AATAATAAAATAATAAAGC
Found at i:483835 original size:14 final size:13
Alignment explanation
Indices: 483816--483867 Score: 72
Period size: 12 Copynumber: 4.1 Consensus size: 13
483806 TTGGGCTTTG
*
483816 TAATATTTAATAAA
1 TAATATATAAT-AA
483830 TAATATATAATAA
1 TAATATATAATAA
483843 TAAT-TATAATAA
1 TAATATATAATAA
483855 TAATA-ATAATAA
1 TAATATATAATAA
483867 T
1 T
483868 TTTAAATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
12 20 0.56
13 6 0.17
14 10 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATATATAATAA
Found at i:483842 original size:3 final size:3
Alignment explanation
Indices: 483823--483867 Score: 63
Period size: 3 Copynumber: 14.3 Consensus size: 3
483813 TTGTAATATT
*
483823 TAA TAAA TAA TATA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA T
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
483868 TTTAAATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 32 0.84
4 6 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:484064 original size:45 final size:45
Alignment explanation
Indices: 484000--484281 Score: 519
Period size: 45 Copynumber: 6.3 Consensus size: 45
483990 GATAAAAATG
* *
484000 TTGAAAACATCATGCACTGAAGAGCTTATAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTATAGATGACTCGAAGGTT
484045 TTGAAAACATCATGCACTGAAGGGCTTATAGATGACTCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTATAGATGACTCGAAGGTT
*
484090 TTGAAAACATCATGCACTGAAGGGCTTATAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTATAGATGACTCGAAGGTT
*
484135 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACTCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTATAGATGACTCGAAGGTT
484180 TTGAAAACATCATGCACTGAAGGGCTTATAGATGACTCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTATAGATGACTCGAAGGTT
*
484225 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACTCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTATAGATGACTCGAAGGTT
484270 TTGAAAACATCA
1 TTGAAAACATCA
484282 AAAAGCTCCC
Statistics
Matches: 230, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 230 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.25
Consensus pattern (45 bp):
TTGAAAACATCATGCACTGAAGGGCTTATAGATGACTCGAAGGTT
Found at i:484448 original size:73 final size:73
Alignment explanation
Indices: 484346--484795 Score: 828
Period size: 73 Copynumber: 6.2 Consensus size: 73
484336 AAAATTTATG
* *
484346 TTTCGAGTGAAACTATCTCGAGCGAGACAAATTTTGTTTTAAGGAAAACAATCTCAAGTGAGATA
1 TTTCGAGTGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
484411 AATTGCTA
66 AATTGCTA
* *
484419 TTTCAAGTGAAATTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
1 TTTCGAGTGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
484484 AATTGCTA
66 AATTGCTA
484492 TTTCGAGTGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
1 TTTCGAGTGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
484557 AATTGCTA
66 AATTGCTA
* *
484565 TTTCGAGTGAAACTGTCACGAGCGAGACAAATTTTGTTTTAAGAAAAATAATCTCAAGTGAGATA
1 TTTCGAGTGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
484630 AATTGCTA
66 AATTGCTA
*
484638 TTTCGAGTGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGGAAAACAATCTCAAGTGAGATA
1 TTTCGAGTGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
484703 AATTGCTA
66 AATTGCTA
484711 TTTCGAGTGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
1 TTTCGAGTGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
484776 AATTGCTA
66 AATTGCTA
*
484784 TTTCGAGGGAAA
1 TTTCGAGTGAAA
484796 ATGTTTACTA
Statistics
Matches: 364, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 364 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (73 bp):
TTTCGAGTGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
AATTGCTA
Found at i:485087 original size:165 final size:164
Alignment explanation
Indices: 484794--485113 Score: 527
Period size: 165 Copynumber: 1.9 Consensus size: 164
484784 TTTCGAGGGA
484794 AAATGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTCAGA
1 AAATGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTCAGA
** * * * * *
484859 AAAGATTGAATGAGAAACTTTGGAAATCGTTTTCTCATTATGTTTCAAGATAACCTGTTGATTGG
66 AAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATGTTTCAAGATAACATATTGATTGA
484924 GTAACATGCCCCAATCTCAAGATAAGGTTGTTGG
131 GTAACATGCCCCAATCTCAAGATAAGGTTGTTGG
484958 AAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTT-AG
1 AAAT-GTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTCAG
*
485022 AAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATGTTTTTGAA-ATAACATATTGAT
65 AAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATG--TTTCAAGATAACATATTGAT
485086 TGAGTAACATGCCCCAATCTCAAGATAA
128 TGAGTAACATGCCCCAATCTCAAGATAA
485114 TGCTCATTCT
Statistics
Matches: 145, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
164 45 0.31
165 95 0.66
166 5 0.03
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (164 bp):
AAATGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTCAGA
AAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATGTTTCAAGATAACATATTGATTGA
GTAACATGCCCCAATCTCAAGATAAGGTTGTTGG
Found at i:489320 original size:29 final size:29
Alignment explanation
Indices: 489287--489345 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
489277 TATCCCTTTC
*
489287 AGGTTCACAATGTAATCGAATCATAAACA
1 AGGTTCACAATATAATCGAATCATAAACA
489316 AGGTTCACAATATAATCGAATCATAAACA
1 AGGTTCACAATATAATCGAATCATAAACA
489345 A
1 A
489346 TGAGTTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.24
Consensus pattern (29 bp):
AGGTTCACAATATAATCGAATCATAAACA
Found at i:490060 original size:17 final size:18
Alignment explanation
Indices: 490039--490079 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
490029 TAATTTCTCC
490039 CTTTTTCCTTTTTCCTTT
1 CTTTTTCCTTTTTCCTTT
* *
490057 -TTTTTCTTTTTTTCTTT
1 CTTTTTCCTTTTTCCTTT
490074 CTTTTT
1 CTTTTT
490080 TTCATTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
CTTTTTCCTTTTTCCTTT
Found at i:490102 original size:14 final size:13
Alignment explanation
Indices: 490054--490105 Score: 56
Period size: 12 Copynumber: 4.0 Consensus size: 13
490044 TCCTTTTTCC
490054 TTTTT-TTTC-TT
1 TTTTTCTTTCTTT
490065 TTTTTCTTTC-TT
1 TTTTTCTTTCTTT
490077 TTTTTCATTTTCTATT
1 TTTTTC--TTTCT-TT
490093 TTTTTCTTTCTTT
1 TTTTTCTTTCTTT
490106 GATGTCTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
11 5 0.14
12 12 0.33
13 2 0.06
14 9 0.25
16 8 0.22
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTCTTTCTTT
Found at i:493308 original size:8 final size:7
Alignment explanation
Indices: 493279--493328 Score: 66
Period size: 7 Copynumber: 7.0 Consensus size: 7
493269 ATAAAAATAT
493279 AAATGCA
1 AAATGCA
*
493286 AAATGAA
1 AAATGCA
493293 AAATGCA
1 AAATGCA
493300 AAGATGCA
1 AA-ATGCA
493308 AAGATGCA
1 AA-ATGCA
493316 AAATG-A
1 AAATGCA
493322 AAATGCA
1 AAATGCA
493329 TGTATGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 6 0.15
7 18 0.46
8 15 0.38
ACGTcount: A:0.58, C:0.10, G:0.18, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:496321 original size:17 final size:18
Alignment explanation
Indices: 496299--496333 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
496289 ATAAATAAAT
*
496299 GACAAACATTT-TTTTAA
1 GACAAAAATTTATTTTAA
496316 GACAAAAATTTATTTTAA
1 GACAAAAATTTATTTTAA
496334 TATAGTAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (18 bp):
GACAAAAATTTATTTTAA
Found at i:496451 original size:31 final size:31
Alignment explanation
Indices: 496416--496476 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
496406 TTGATATTAA
*
496416 TAAATAAAAATATATTAAAATTTTAATAATT
1 TAAATAAAAATAAATTAAAATTTTAATAATT
* * *
496447 TAAATAAAACTAAATTATAATTTTTATAAT
1 TAAATAAAAATAAATTAAAATTTTAATAAT
496477 ATTTAATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (31 bp):
TAAATAAAAATAAATTAAAATTTTAATAATT
Found at i:498071 original size:14 final size:13
Alignment explanation
Indices: 498052--498100 Score: 66
Period size: 12 Copynumber: 3.8 Consensus size: 13
498042 TTGGGCTTTG
*
498052 TAATATTTAATAAA
1 TAATATATAAT-AA
498066 TAATATATAATAA
1 TAATATATAATAA
498079 TAAT-TATAATAA
1 TAATATATAATAA
498091 TAATA-ATAAT
1 TAATATATAAT
498101 TTTAAATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
12 17 0.52
13 6 0.18
14 10 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TAATATATAATAA
Found at i:498078 original size:3 final size:3
Alignment explanation
Indices: 498059--498100 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
498049 TTGTAATATT
*
498059 TAA TAAA TAA TATA TAA TAA TAA TTA TAA TAA TAA TAA TAA T
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA T
498101 TTTAAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 29 0.83
4 6 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:498211 original size:16 final size:18
Alignment explanation
Indices: 498188--498227 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
498178 ACTAATGGAT
498188 TTTA-ATGA-CAAAT-AA
1 TTTATATGATCAAATGAA
498203 TTTATATGATCAAATGAA
1 TTTATATGATCAAATGAA
*
498221 TCTATAT
1 TTTATAT
498228 ATTATATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 4 0.19
17 5 0.24
18 8 0.38
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (18 bp):
TTTATATGATCAAATGAA
Found at i:501371 original size:28 final size:28
Alignment explanation
Indices: 501340--501397 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
501330 TTATGTGTCT
501340 TATTTAAAG-TTTAAGAACTA-AAATTTTA
1 TATTTAAAGATTT-AGAA-TACAAATTTTA
* *
501368 TATTTTAAGATTTAGAATACTAATTTTA
1 TATTTAAAGATTTAGAATACAAATTTTA
501396 TA
1 TA
501398 CTATCGGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 2 0.08
28 21 0.81
29 3 0.12
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (28 bp):
TATTTAAAGATTTAGAATACAAATTTTA
Found at i:501699 original size:3 final size:3
Alignment explanation
Indices: 501685--501736 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
501675 AATTAAAAAC
*
501685 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
501733 AAT A
1 AAT A
501737 GAAAAATTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:502928 original size:54 final size:54
Alignment explanation
Indices: 502854--502961 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
502844 GTTTGAGGAA
*
502854 GAAACAAAATTATGGCTCACTGAATTGGGGAATTTAAGAAATCAGAAGTTAGGG
1 GAAACAAAATTAGGGCTCACTGAATTGGGGAATTTAAGAAATCAGAAGTTAGGG
* *
502908 GAAACAAAATTAGGGTTCACTGAATTGGGGAATTTGAGAAATCAGAAGTTAGGG
1 GAAACAAAATTAGGGCTCACTGAATTGGGGAATTTAAGAAATCAGAAGTTAGGG
502962 ATTTGGAAGG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.40, C:0.08, G:0.28, T:0.24
Consensus pattern (54 bp):
GAAACAAAATTAGGGCTCACTGAATTGGGGAATTTAAGAAATCAGAAGTTAGGG
Found at i:506127 original size:2 final size:2
Alignment explanation
Indices: 506120--506176 Score: 52
Period size: 2 Copynumber: 31.0 Consensus size: 2
506110 GAAAATATTT
* * *
506120 TA TA TA TA -A T- TA -A TA TA -A AA TA TA TA AA AA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
506157 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
506177 ATCGGGGCGG
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
1 5 0.11
2 42 0.89
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Done.