Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008031.1 Hibiscus syriacus cultivar Beakdansim tig00110511_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: 1788856
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:413050 original size:316 final size:314
Alignment explanation
Indices: 412466--413114 Score: 951
Period size: 316 Copynumber: 2.1 Consensus size: 314
412456 CCAGAATTGG
* * * * * *
412466 TAAGTCCTTTGAGCTATCAGTAAGTCTTTCGATCATGATTCTTAAATCCTTCGGGTTATCGTAAG
1 TAAGTCC-TTGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCAACGTAAG
* * * * *
412531 TCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCACAAGACCTTCGGGCAGGATGTTTTCATA
65 TCTATCAAGCAAGATGATAAGTCCTTCGAGCCATCCACAAGACCTTCGGGCAAGATGTTTTCACA
* * *
412596 TATTTTTAGAAAAATGAGAAAATTTTCTCATTTAAATATGAAAATTGAAATTTTTGAAAAGTAAG
130 TATTTTTACAAAAATGAGAAAAGTTTCACATTTAAATATGAAAATTGAAATTTTTGAAAAGTAAG
* * * *
412661 AAACGTTTCTTACCTAGTAAACTGTTTCCAAAATTGGTAAGCCTTTCGGGCTATCAGTAAGCCTT
195 AAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGCCTTTCGAGCCATCAGTAAGCCTT
412726 TCGAGCATGATGCTTAAATCCTTAAAGTCAAT-TGTAAGTCTTTCGAGCAAGATGA
260 TCGAGCATGATGCTTAAATCCTTAAAGTC-ATCTGTAAGTCTTTCGAGCAAGATGA
*
412781 TAAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCCTTCGGGTCAACTGTAA
1 TAAGTCCTT-GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCAAC-GTAA
* * *
412846 GTCTATCAAGCAAGATGATAAGTCCTTCGATCCATCCACAAGATCTTTGGGCAAGATGTTTTCAC
64 GTCTATCAAGCAAGATGATAAGTCCTTCGAGCCATCCACAAGACCTTCGGGCAAGATGTTTTCAC
* * *
412911 ATGTTTTTCCAAAAATGAGAAAAGTTTCACATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAA
129 ATATTTTTACAAAAATGAGAAAAGTTTCACATTTAAATATGAAAATTGAAATTTTTGAAAAGTAA
**
412976 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTT-GAGCCATCAGTAAGTG
194 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAG-CCTTTCGAGCCATCAGTAAGCC
* * * *
413040 TTTTGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGCAGGATGA
258 TTTCGAGCATGATGCTTAAATCCTTAAAGTCATCTGTAAGTCTTTCGAGCAAGATGA
413097 TAAGTCCATTGGGCCATC
1 TAAGTCC-TTGGGCCATC
413115 CACAAGACCT
Statistics
Matches: 298, Mismatches: 31, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
314 2 0.01
315 52 0.17
316 237 0.80
317 7 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (314 bp):
TAAGTCCTTGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCAACGTAAGT
CTATCAAGCAAGATGATAAGTCCTTCGAGCCATCCACAAGACCTTCGGGCAAGATGTTTTCACAT
ATTTTTACAAAAATGAGAAAAGTTTCACATTTAAATATGAAAATTGAAATTTTTGAAAAGTAAGA
AAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGCCTTTCGAGCCATCAGTAAGCCTTT
CGAGCATGATGCTTAAATCCTTAAAGTCATCTGTAAGTCTTTCGAGCAAGATGA
Found at i:413255 original size:234 final size:233
Alignment explanation
Indices: 412781--413859 Score: 1486
Period size: 233 Copynumber: 4.6 Consensus size: 233
412771 AGCAAGATGA
* * *
412781 TAAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCCTTCGGGTCAACTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAA
* * ** * *
412846 GTCTATCAAGCAAGATGATAAGTCCTTCGATCCATCCACAAGATCTTTGGGCAAGATGTTTTCAC
66 GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCACAAGACCTTCGGGCAAGATGTTTTCAC
* * *
412911 ATGTTTTTCCAAAAATGAGAAAAGTTTCACATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAA
131 ATTTTTTTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAA
412976 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGG
196 GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGG
* * * *
413014 TAAGTCCTTTGAGCCATCAGTAAGTGTTTTGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAA
* *
413079 GTCTTTCGAGCAGGATGATAAGTCCATT-GGGCCATCCACAAGACCTTCGGGCAGGATGTTTTCA
66 GTCTTTCGAGCAAGATGATAAGTCC-TTCGGGCCATCCACAAGACCTTCGGGCAAGATGTTTTCA
*
413143 CATATTTTTTTGAAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGT
130 CAT-TTTTTTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGT
* * *
413208 ACGAAACGTTTCTTACCTATTAAACTATTTCCAAAATTGG
194 AAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGG
* * * *
413248 TAAGTCCTTCGGGCTATTAGTAAGTCTTTGGAGCATGATGCTTAAATCCTTC-GAGTAATCTGTA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAG-GTCATCTGTA
** * * *
413312 AGTCTTTCGAGCAAGATGATAAGTCCTTCTAGCCATCCACAAGACCTTCGGACATGATATTTTCA
65 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCACAAGACCTTCGGGCAAGATGTTTTCA
*
413377 TATGTTTTTT-GAAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGT
130 CAT-TTTTTTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGT
413441 AAGAAAAGTTTCTTACCTAGTAAACTATTT-CAAAATTTGG
194 AAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAA-TTGG
* * * * * * * *
413481 TAAGTCCTTCGGGCCATCAATAATTGTTTCAAGCATGATGTTTAAATCCTTCGGGTCATTTATAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAA
* * * *
413546 GTCTTTCGAGCAAGATAATAAAGTCTTTCGGGCCATCCACAAGACCTTCGGGCAGGATG-TGTCA
66 GTCTTTCGAGCAAGATGAT-AAGTCCTTCGGGCCATCCACAAGACCTTCGGGCAAGATGTTTTCA
* * *
413610 CATGTTTTTCGAAAAATGAGAAAAGTTTCTCATTTTAATCTAAAAATTGAAATTTTTGAAAAGTA
130 CATTTTTTTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTA
* *
413675 CGAAAAGTTTCTTACATAGTAAACTATTTCCAAAATTGG
195 AGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGG
** * *
413714 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGAGTAAATCCTTCAGGTCATTTATAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAA
* * * * * * * *
413779 G-CATTTTGAGGAAGATGATAAGGCCTTCGGGCCATTCATAAGACCATCAGGTAAGATGTTTTCA
66 GTC-TTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCACAAGACCTTCGGGCAAGATGTTTTCA
*
413843 CATGTTTCTTCGAAAAA
130 CAT-TTTTTTCGAAAAA
413860 AAGACAATTT
Statistics
Matches: 750, Mismatches: 84, Indels: 23
0.88 0.10 0.03
Matches are distributed among these distances:
232 42 0.06
233 443 0.59
234 265 0.35
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (233 bp):
TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAA
GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCACAAGACCTTCGGGCAAGATGTTTTCAC
ATTTTTTTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAA
GAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGG
Found at i:414556 original size:3 final size:3
Alignment explanation
Indices: 414548--414577 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
414538 CGCCCGGACC
414548 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
414578 TTTGTGGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:419339 original size:21 final size:21
Alignment explanation
Indices: 419278--419336 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
419268 TTTTCTGGCT
*
419278 CAAAGAATCGATCTCTTTGAC
1 CAAAGGATCGATCTCTTTGAC
* *
419299 TAAAGGATCGATCTCGTTGAC
1 CAAAGGATCGATCTCTTTGAC
419320 CAAAGGATCGATC-CTTT
1 CAAAGGATCGATCTCTTT
419337 TGATTCCAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
20 3 0.09
21 30 0.91
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.29
Consensus pattern (21 bp):
CAAAGGATCGATCTCTTTGAC
Found at i:423074 original size:13 final size:13
Alignment explanation
Indices: 423027--423079 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
423017 TATGTCTGAG
423027 AAGAAAA-ATAAAA
1 AAGAAAAGA-AAAA
* *
423040 TAGAAATAGAAATA
1 AAGAAA-AGAAAAA
423054 AA-AAAAGAAAAA
1 AAGAAAAGAAAAA
423066 AAGAAAAGAAAAA
1 AAGAAAAGAAAAA
423079 A
1 A
423080 TAGAGAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 8 0.24
13 19 0.58
14 5 0.15
15 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (13 bp):
AAGAAAAGAAAAA
Found at i:424213 original size:132 final size:132
Alignment explanation
Indices: 423983--424315 Score: 416
Period size: 132 Copynumber: 2.5 Consensus size: 132
423973 TTCACTCAAA
* * * * * * *
423983 TCTATCACAGAATGAGATAGATCAGCACCAATATCTCGTTCGATT-CATCACAAAAGGAGGTGGA
1 TCTATCAAAGAAGGAGGTAGATCAGCAACGACATCTCGTTCGATTCCATCACAGAAGGAGGTGGA
* * * * * **
424047 TCGACATTTTTATTTCGCTCAAATCCATCGCATAAGGAGTTGGATCAACATCAACTTTTTGCTTT
66 TCAACATTTTCATTTCACTCAAATCCAACACATAAGGAGTTGGATCAACATCAACTTTTTGCTCG
424112 AT
131 AT
* * * *
424114 TCTATCAAAGAAGGAGGTAGATCAGCATCGACATTTCGTTCGATTCCATCATAGAAGGAGGCGGA
1 TCTATCAAAGAAGGAGGTAGATCAGCAACGACATCTCGTTCGATTCCATCACAGAAGGAGGTGGA
* * * * * *
424179 TCAATATTTTCATTTCACTCAAATCCAACACATAAGGAGTTGGATGAGCTTTAATTTTTTGCTCG
66 TCAACATTTTCATTTCACTCAAATCCAACACATAAGGAGTTGGATCAACATCAACTTTTTGCTCG
424244 AT
131 AT
* * *
424246 TCTATCATAGAAGGAGGTAAATCAGCAACGGCATCTCGTTCGATTCCATCACAGAAGGAGGTGGA
1 TCTATCAAAGAAGGAGGTAGATCAGCAACGACATCTCGTTCGATTCCATCACAGAAGGAGGTGGA
424311 TCAAC
66 TCAAC
424316 GTTTCAATGG
Statistics
Matches: 170, Mismatches: 31, Indels: 1
0.84 0.15 0.00
Matches are distributed among these distances:
131 38 0.22
132 132 0.78
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (132 bp):
TCTATCAAAGAAGGAGGTAGATCAGCAACGACATCTCGTTCGATTCCATCACAGAAGGAGGTGGA
TCAACATTTTCATTTCACTCAAATCCAACACATAAGGAGTTGGATCAACATCAACTTTTTGCTCG
AT
Found at i:427805 original size:21 final size:19
Alignment explanation
Indices: 427790--427840 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
427780 GAGAAGTTAT
427790 TTTCAAAATACAAGAAAAGTA
1 TTTCAAAATACAAG--AAGTA
427811 TTTCAAAATACAAGAAAAGTA
1 TTTCAAAATACAAG--AAGTA
*
427832 TTTTAAAAT
1 TTTCAAAAT
427841 TGAAAAATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (19 bp):
TTTCAAAATACAAGAAGTA
Found at i:429552 original size:22 final size:22
Alignment explanation
Indices: 429525--429572 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
429515 TTGAGGGAAA
429525 AATAGCTTTTGAATAGGAAAAC
1 AATAGCTTTTGAATAGGAAAAC
429547 AATAGCTTTTGAATAGGAAAAC
1 AATAGCTTTTGAATAGGAAAAC
429569 AATA
1 AATA
429573 TCTATACGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (22 bp):
AATAGCTTTTGAATAGGAAAAC
Found at i:429636 original size:21 final size:20
Alignment explanation
Indices: 429596--429646 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
429586 TTTTTAGCGG
*
429596 TTTACTGCTAGGAACATTGT
1 TTTACTGCTTGGAACATTGT
*
429616 TTTACTGCTTGAGAGCATTGT
1 TTTACTGCTTG-GAACATTGT
429637 TTTACTGCTT
1 TTTACTGCTT
429647 TAGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.45
Consensus pattern (20 bp):
TTTACTGCTTGGAACATTGT
Found at i:439198 original size:21 final size:21
Alignment explanation
Indices: 439180--439251 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
439170 ATGAAGCAAG
* *
439180 GGAAGCAGAGAGAGCAGCAGC
1 GGAAGCAGACAGAGTAGCAGC
* *
439201 GGAAGCAGCCAGAGTAGCAAC
1 GGAAGCAGACAGAGTAGCAGC
439222 GGAAGCAG-CTAGAGTAGCAGC
1 GGAAGCAGAC-AGAGTAGCAGC
439243 GGAAGCAGA
1 GGAAGCAGA
439252 TAAAGAAGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
20 1 0.02
21 43 0.98
ACGTcount: A:0.38, C:0.19, G:0.39, T:0.04
Consensus pattern (21 bp):
GGAAGCAGACAGAGTAGCAGC
Found at i:439208 original size:42 final size:41
Alignment explanation
Indices: 439161--439259 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 41
439151 GCTAACTTGA
*
439161 AAGCAGAAAATGAAGCAAGGGAAGCAGAGAGAGCAGCAGCGG
1 AAGCAGAAAA-GAAGCAACGGAAGCAGAGAGAGCAGCAGCGG
* * * ** *
439203 AAGCAGCCAGAGTAGCAACGGAAGCAGCTAGAGTAGCAGCGG
1 AAGCAG-AAAAGAAGCAACGGAAGCAGAGAGAGCAGCAGCGG
439245 AAGCAGATAAAGAAG
1 AAGCAGA-AAAGAAG
439260 TAGCAGCAGC
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
42 43 0.96
43 2 0.04
ACGTcount: A:0.43, C:0.16, G:0.35, T:0.05
Consensus pattern (41 bp):
AAGCAGAAAAGAAGCAACGGAAGCAGAGAGAGCAGCAGCGG
Found at i:439785 original size:43 final size:42
Alignment explanation
Indices: 439738--440013 Score: 139
Period size: 43 Copynumber: 6.4 Consensus size: 42
439728 AAATGCCAAG
** * * *
439738 AAATCTCAACATCTATTGCGGGGTTTGCGATAAAAATGCCGCT
1 AAATCTCAACA-CTATTGCGGCATTTGTGAGAAAAACGCCGCT
* * **
439781 AAATCTCAACACTTATTGCAGCATTT-TAGATAAAAACGCAACT
1 AAATCTCAACAC-TATTGCGGCATTTGT-GAGAAAAACGCCGCT
* * * *
439824 AAATCTCAAAACCTACTGCGGAATTTGTGGGAAAAACGCCGCT
1 AAATCTCAACA-CTATTGCGGCATTTGTGAGAAAAACGCCGCT
* * * *
439867 AAA-CATCAACACTTACTGCGGCGTTTGTGGGAAAAATGCCGCT
1 AAATC-TCAACAC-TATTGCGGCATTTGTGAGAAAAACGCCGCT
* * * * * * *
439910 AAATATCAACACCTATTACGACGTTTATTGA-ACAAACGCCACT
1 AAATCTCAACA-CTATTGCGGCATTT-GTGAGAAAAACGCCGCT
* * * * *
439953 ATATATCGTC-AC-CTACTACGGCGTTTGTGGGAAAAATGCCGCT
1 A-A-ATC-TCAACACTATTGCGGCATTTGTGAGAAAAACGCCGCT
*
439996 AAATATCAACACCTATTG
1 AAATCTCAACA-CTATTG
440014 TAGCGTTCGT
Statistics
Matches: 178, Mismatches: 39, Indels: 32
0.71 0.16 0.13
Matches are distributed among these distances:
40 2 0.01
41 4 0.02
42 6 0.03
43 154 0.87
44 6 0.03
45 4 0.02
46 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (42 bp):
AAATCTCAACACTATTGCGGCATTTGTGAGAAAAACGCCGCT
Found at i:439912 original size:86 final size:86
Alignment explanation
Indices: 439822--440010 Score: 220
Period size: 86 Copynumber: 2.2 Consensus size: 86
439812 AAAAACGCAA
* * * * * * *
439822 CTAAATCTCAAAACCTACTGCGGA-ATTTGTGGGAA-AAACGCCGCTAAACATCAACACTTACTG
1 CTAAATATCAACACCTACTAC-GACATTTAT-GGAACAAACGCCACTAAACATCAACACCTACTA
439885 CGGCGTTTGTGGGAAAAATGCCG
64 CGGCGTTTGTGGGAAAAATGCCG
* * * * * **
439908 CTAAATATCAACACCTATTACGACGTTTATTGAACAAACGCCACTATATATCGTCACCTACTACG
1 CTAAATATCAACACCTACTACGACATTTATGGAACAAACGCCACTAAACATCAACACCTACTACG
439973 GCGTTTGTGGGAAAAATGCCG
66 GCGTTTGTGGGAAAAATGCCG
439994 CTAAATATCAACACCTA
1 CTAAATATCAACACCTA
440011 TTGTAGCGTT
Statistics
Matches: 87, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
85 5 0.06
86 82 0.94
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (86 bp):
CTAAATATCAACACCTACTACGACATTTATGGAACAAACGCCACTAAACATCAACACCTACTACG
GCGTTTGTGGGAAAAATGCCG
Found at i:440020 original size:43 final size:43
Alignment explanation
Indices: 439769--440020 Score: 177
Period size: 43 Copynumber: 5.9 Consensus size: 43
439759 GGTTTGCGAT
* * * * * **
439769 AAAAATGCCGCTAAATCTCAACACTTATTGCAGCATTT-TAGAT
1 AAAAACGCCGCTAAATATCAACACCTACTGCAGCGTTTGT-GGG
** * * * **
439812 AAAAACGCAACTAAATCTCAAAACCTACTGCGGAATTTGTGGG
1 AAAAACGCCGCTAAATATCAACACCTACTGCAGCGTTTGTGGG
* * *
439855 AAAAACGCCGCTAAACATCAACACTTACTGCGGCGTTTGTGGG
1 AAAAACGCCGCTAAATATCAACACCTACTGCAGCGTTTGTGGG
* * * * *
439898 AAAAATGCCGCTAAATATCAACACCTATTAC-GACGTTTAT-TG
1 AAAAACGCCGCTAAATATCAACACCTACTGCAG-CGTTTGTGGG
* * ** * *
439940 AACAAACGCCACTATATATCGTCACCTACTACGGCGTTTGTGGG
1 AA-AAACGCCGCTAAATATCAACACCTACTGCAGCGTTTGTGGG
* * *
439984 AAAAATGCCGCTAAATATCAACACCTATTGTAGCGTT
1 AAAAACGCCGCTAAATATCAACACCTACTGCAGCGTT
440021 CGTTGAACTA
Statistics
Matches: 162, Mismatches: 42, Indels: 10
0.76 0.20 0.05
Matches are distributed among these distances:
42 4 0.02
43 153 0.94
44 5 0.03
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (43 bp):
AAAAACGCCGCTAAATATCAACACCTACTGCAGCGTTTGTGGG
Found at i:445394 original size:2 final size:2
Alignment explanation
Indices: 445387--445430 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
445377 TCTTAGCAGC
445387 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
445429 TA
1 TA
445431 ATTTGACTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:446082 original size:44 final size:44
Alignment explanation
Indices: 446033--446124 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
446023 TTCAGCATCA
* * * * *
446033 ATACTACTATACATAGTAGTATTGATACTTCTTG-GACGATATCG
1 ATACTACCACACATAATAGTATCGATACTCCTTGAGA-GATATCG
*
446077 ATACTACCACACATAATAGTATCGATACTCCTTGAGAGGTATCG
1 ATACTACCACACATAATAGTATCGATACTCCTTGAGAGATATCG
446121 ATAC
1 ATAC
446125 CGTTGGGTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 39 0.95
45 2 0.05
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (44 bp):
ATACTACCACACATAATAGTATCGATACTCCTTGAGAGATATCG
Found at i:449992 original size:2 final size:2
Alignment explanation
Indices: 449987--450018 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
449977 TTTTTTATGT
449987 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
450019 ATGGGTACCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:452010 original size:7 final size:7
Alignment explanation
Indices: 451998--452039 Score: 75
Period size: 7 Copynumber: 6.0 Consensus size: 7
451988 CCCTACATTC
451998 AAACCCT
1 AAACCCT
452005 AAACCCT
1 AAACCCT
452012 AAACCCT
1 AAACCCT
*
452019 AAACCTT
1 AAACCCT
452026 AAACCCT
1 AAACCCT
452033 AAACCCT
1 AAACCCT
452040 GACTTAGAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.43, C:0.40, G:0.00, T:0.17
Consensus pattern (7 bp):
AAACCCT
Found at i:452681 original size:2 final size:2
Alignment explanation
Indices: 452674--452716 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
452664 ATAGTACACT
*
452674 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
452716 T
1 T
452717 TCGAGTGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:462785 original size:19 final size:20
Alignment explanation
Indices: 462761--462798 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
462751 TTAAAAAATG
*
462761 ACCGAAATTATTAT-TTTTA
1 ACCGAAAATATTATGTTTTA
462780 ACCGAAAATATTATGTTTT
1 ACCGAAAATATTATGTTTT
462799 TTATCAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (20 bp):
ACCGAAAATATTATGTTTTA
Found at i:464386 original size:30 final size:30
Alignment explanation
Indices: 464276--464394 Score: 107
Period size: 30 Copynumber: 3.8 Consensus size: 30
464266 AAAGGTTATA
* *
464276 TTCGTGTTCGTTTATTTATTTTTGAAGATG
1 TTCGTGTTCGTTTATTTATTTTTAAAGGTG
* * *
464306 TTCG-GTTCGTGTTCGTTTAAATTTTCAATATTGTG
1 TTCGTGTTCGT-TT-ATTT--ATTTTTAA-A-GGTG
*
464341 TTCATGTTC-TTTATTTATTTTTAAAGGTG
1 TTCGTGTTCGTTTATTTATTTTTAAAGGTG
*
464370 TTCGTGTTCGTTTATTTATTGTTAA
1 TTCGTGTTCGTTTATTTATTTTTAA
464395 TGAAGATGTT
Statistics
Matches: 70, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
29 17 0.24
30 21 0.30
31 10 0.14
33 9 0.13
34 3 0.04
35 6 0.09
36 4 0.06
ACGTcount: A:0.18, C:0.08, G:0.18, T:0.56
Consensus pattern (30 bp):
TTCGTGTTCGTTTATTTATTTTTAAAGGTG
Found at i:464446 original size:24 final size:24
Alignment explanation
Indices: 464372--464452 Score: 76
Period size: 24 Copynumber: 3.3 Consensus size: 24
464362 TAAAGGTGTT
*
464372 CGTGTTCGTTTATTTATTGTTAATGAA
1 CGTGTTCGTTTA--TA-TGTTCATGAA
* **
464399 -GATGTTCATTTA-ATGTTCGCGAA
1 CG-TGTTCGTTTATATGTTCATGAA
464422 CGTGTTCGTTTATATGTTCATGAA
1 CGTGTTCGTTTATATGTTCATGAA
464446 CGTGTTC
1 CGTGTTC
464453 ATAAATATGT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
23 16 0.36
24 18 0.41
26 1 0.02
27 9 0.20
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.46
Consensus pattern (24 bp):
CGTGTTCGTTTATATGTTCATGAA
Found at i:464528 original size:59 final size:59
Alignment explanation
Indices: 464388--464529 Score: 176
Period size: 59 Copynumber: 2.4 Consensus size: 59
464378 CGTTTATTTA
* * * * * *
464388 TTGTTAATGAAGATGTTCATTTAATGTTCGCGAACGTGTTCGTTTATATGTTCATGAAC
1 TTGTTCATGAACATGTTCGTTTAATGTTCGCGAACGTGTTCATTTATAAGTTCACGAAC
* * * * *
464447 GTGTTCATAAATATGTTTGTTTAATGTTCGTGAACGTGTTCATTTATAAGTTCACGAAC
1 TTGTTCATGAACATGTTCGTTTAATGTTCGCGAACGTGTTCATTTATAAGTTCACGAAC
*
464506 TTGTTCATGAACATATTCGTTTAA
1 TTGTTCATGAACATGTTCGTTTAA
464530 CGTTTTTAGT
Statistics
Matches: 68, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
59 68 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (59 bp):
TTGTTCATGAACATGTTCGTTTAATGTTCGCGAACGTGTTCATTTATAAGTTCACGAAC
Found at i:476358 original size:16 final size:17
Alignment explanation
Indices: 476327--476361 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
476317 CGTATTGCCG
476327 ACAAAATTTCACTATTC
1 ACAAAATTTCACTATTC
476344 ACAAAATTT-ACTATTC
1 ACAAAATTTCACTATTC
476360 AC
1 AC
476362 GTGAATAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:477899 original size:15 final size:16
Alignment explanation
Indices: 477879--477908 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
477869 TTCACATAAA
477879 TAAAT-ATTTATATCG
1 TAAATAATTTATATCG
477894 TAAATAATTTATATC
1 TAAATAATTTATATC
477909 AATGTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (16 bp):
TAAATAATTTATATCG
Found at i:478710 original size:26 final size:24
Alignment explanation
Indices: 478661--478705 Score: 69
Period size: 21 Copynumber: 2.0 Consensus size: 24
478651 ATTTATTAAA
478661 TAAAATATATATTATATTTAATTT
1 TAAAATATATATTATATTTAATTT
478685 TAAAATAT-TA-T-TATTTAATTT
1 TAAAATATATATTATATTTAATTT
478706 AATTTACTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.48
22 1 0.05
23 2 0.10
24 8 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TAAAATATATATTATATTTAATTT
Found at i:483937 original size:16 final size:16
Alignment explanation
Indices: 483916--483949 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
483906 TATTTGTTTT
*
483916 TTTTAAAATACAAATA
1 TTTTAAAATAAAAATA
*
483932 TTTTAAATTAAAAATA
1 TTTTAAAATAAAAATA
483948 TT
1 TT
483950 AAAATATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTTAAAATAAAAATA
Found at i:487674 original size:26 final size:26
Alignment explanation
Indices: 487645--487722 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 26
487635 GGTATCGATA
*
487645 CTTCTTCAAGTAT-GAATACTCTACCC
1 CTTCTGCAAGTATCG-ATACTCTACCC
**
487671 CTTCTGGGAGTATCGATACTCTACCC
1 CTTCTGCAAGTATCGATACTCTACCC
** *
487697 CTTCTGGGACTATCGATACTCTACCC
1 CTTCTGCAAGTATCGATACTCTACCC
487723 TAAATATTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
26 46 0.98
27 1 0.02
ACGTcount: A:0.22, C:0.32, G:0.14, T:0.32
Consensus pattern (26 bp):
CTTCTGCAAGTATCGATACTCTACCC
Found at i:487773 original size:20 final size:20
Alignment explanation
Indices: 487707--487775 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
487697 CTTCTGGGAC
* *
487707 TATCGATACTCTACCCTAAA
1 TATCGATACTATTCCCTAAA
* *
487727 TATTGATAC---TCCCATAAC
1 TATCGATACTATTCCC-TAAA
* *
487745 TATCAATACTATTCCCTAAG
1 TATCGATACTATTCCCTAAA
487765 TATCGATACTA
1 TATCGATACTA
487776 CCTAAGCAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.26
20 21 0.55
21 4 0.11
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.33
Consensus pattern (20 bp):
TATCGATACTATTCCCTAAA
Found at i:490794 original size:18 final size:18
Alignment explanation
Indices: 490781--490819 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
490771 AGCCTTGTGT
490781 GTGATGACTCCCTTGATG
1 GTGATGACTCCCTTGATG
* *
490799 GTGTTGACTCCCTTAATG
1 GTGATGACTCCCTTGATG
490817 GTG
1 GTG
490820 GCTAGGACCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.21, G:0.28, T:0.36
Consensus pattern (18 bp):
GTGATGACTCCCTTGATG
Found at i:494421 original size:18 final size:17
Alignment explanation
Indices: 494363--494424 Score: 67
Period size: 18 Copynumber: 3.7 Consensus size: 17
494353 ATTAATCAAC
494363 ACAT-TAATATCCCACCA
1 ACATATAATAT-CCACCA
* *
494380 ACATATACTATCCAACAA
1 ACATATAATATCC-ACCA
494398 ACATATAATATCCACC-
1 ACATATAATATCCACCA
494414 ACATAT-ATATC
1 ACATATAATATC
494425 ATTGTATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 5 0.13
16 6 0.15
17 8 0.21
18 20 0.51
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (17 bp):
ACATATAATATCCACCA
Found at i:509284 original size:42 final size:41
Alignment explanation
Indices: 509212--509318 Score: 124
Period size: 42 Copynumber: 2.6 Consensus size: 41
509202 ACTATTTCCG
* * *
509212 AAGATAATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGACC
1 AAGATGATAAATCCTTCAGGCCATCAGTAAGTCTTTCGACC
* * * *
509253 ATGATGATTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGC
1 AAGATGA-TAAATCCTTCAGGCCATCAGTAAGTCTTTCGACC
* *
509295 AAGATGATAAGTCCTTCGGGCCAT
1 AAGATGATAAATCCTTCAGGCCAT
509319 TCATAAGACC
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 19 0.35
42 35 0.65
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (41 bp):
AAGATGATAAATCCTTCAGGCCATCAGTAAGTCTTTCGACC
Found at i:509363 original size:257 final size:252
Alignment explanation
Indices: 508863--510123 Score: 1364
Period size: 257 Copynumber: 5.1 Consensus size: 252
508853 AAAGAAATTC
*
508863 CAAAGTTTCTCATTTAAATATTTTCA-AGAAATTAAATTTTTGAAAAGTAAGAAAGCGATTTCCA
1 CAAAGTTTCTCATTT-AATATTTTCAGA-AAATGAAATTTTTGAAAAGTAAGAAAGCGATTTCCA
* * * *
508927 AAGTTTCTTACTTAGTAGACTATTTTCGAAGATGACAAGTCCGTCGGACCATCAATAAGTCTTTC
64 AAGTTTCTTAC-TAGTAGACTA-TTTC-AAGAT--TAAGTCCTTCGGGCCATCAGTAAGTCTTTC
* * * **
508992 AAGCATGATGATTAAATTCTTCGGGTCATCTGTAAGTCTTTTGAGCAAGATGATAAGTCCTTTAG
124 GAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGG
* * * * * * *
509057 GCCATCCATAAGACCTTCAGGTAGGACGTTTTCACATGAATTAGAAAAATCAGAAAGTGATTTT
189 GCCATTCATAAGACCTTCAGGCAAGATGTTTTCACATGAATTTGAAAAATGAGAAAGCGATTTT
* *
509121 CAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATCTTTGAAAAGTAAGAAAGCGATTTCCAAA
1 CAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATTTCCAAA
509186 GTTTCTTACTTAGTAGACTATTTCCGAAGATAATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGA
66 GTTTCTTAC-TAGTAGACTATTT-C-AAGAT--TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGA
* *
509251 CCATGATGATTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGC
126 GCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGC
* *
509316 CATTCATAAGACCTTCAGGTAAGATGTTTTCACATGAATTTGAAAAATGAGAAAGCAATTTT
191 CATTCATAAGACCTTCAGGCAAGATGTTTTCACATGAATTTGAAAAATGAGAAAGCGATTTT
* * * *
509378 CAAACTTTCTCATTTAATTTTTTCAGAAAATGAAATATTTGAAAAGTAAGAAAGTGATTTCC-AA
1 CAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATTTCCAAA
* * *
509442 -TAT-TT-CT--T--AC---TT--AG--TAAGTCCTTCGGGCCATCAGTAAGTCTTTTTGAGGAT
66 GTTTCTTACTAGTAGACTATTTCAAGATTAAGTCCTTCGGGCCATCAGTAAGTC-TTTCGAGCAT
* * * *
509493 GATGATTAAATCCTTCGGGTCATCCGTAAGCCTTTCGAGCAATATGATAAGTCATTCGGGCCATA
130 GATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCAT-
* * *
509558 T-ATAAAACCTTCGGGCATGATGTTTTCACATGAATTTGAAAAATGAGAAAGCGATTTT
194 TCATAAGACCTTCAGGCAAGATGTTTTCACATGAATTTGAAAAATGAGAAAGCGATTTT
*
509616 CAAAGTTTCTCATTTAATATTTTTAGAAAAT---A------AAAAGTAAGAAAGCGATTTCC-AA
1 CAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATTTCCAAA
* *
509671 G-GT-TT-CT--T--AC---TT--AG--TAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATG
66 GTTTCTTACTAGTAGACTATTTCAAGATTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
* * * *
509722 ATGATTAAACCCTTTGGGTCACCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCC
131 ATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATTC
* * ** * * *
509787 ATAAGACCTTCGGGCAGGATGTTTTCATGTGATTTTTGAAAAATGAGAAAGTGATTTC
196 ATAAGACCTTCAGGCAAGATGTTTTCACATGA-ATTTGAAAAATGAGAAAGCGATTTT
* * * *
509845 CAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGTGGTTTTCAAA
1 CAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATTTCCAAA
* * * * *
509910 GTTTCTTACCTAGTAGATTATTTCCAAAAATCGGTAAGTCATTCGGGCGATCAGTAAGCCTTTCG
66 GTTTCTTA-CTAGTAGACTATTT-C-AAGAT---TAAGTCCTTCGGGCCATCAGTAAGTCTTTCG
* * * * * *
509975 AGCATGATGATTTAATCCCTCGGGTCATCTGTTAGGCTTTGGAGCAAGATGATAAGTCCTTTGGG
125 AGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGG
* * *
510040 CCA-TCTATAAGACCTTCAGGCAAGATGCTTTCATATGGTATTTGTAAAAAAATGAGAAAGCGAT
190 CCATTC-ATAAGACCTTCAGGCAAGATGTTTTCACAT-GAATTTG---AAAAATGAGAAAGCGAT
510104 TTT
250 TTT
*
510107 CAAAGTTTCTCTTTTAA
1 CAAAGTTTCTCATTTAA
510124 AGTAAAAAGA
Statistics
Matches: 866, Mismatches: 95, Indels: 80
0.83 0.09 0.08
Matches are distributed among these distances:
228 93 0.11
229 110 0.13
232 1 0.00
235 1 0.00
237 26 0.03
238 164 0.19
239 4 0.00
240 1 0.00
241 4 0.00
243 2 0.00
245 3 0.00
247 1 0.00
248 2 0.00
250 3 0.00
252 1 0.00
253 1 0.00
254 3 0.00
255 2 0.00
256 5 0.01
257 272 0.31
258 17 0.02
259 116 0.13
260 1 0.00
262 33 0.04
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (252 bp):
CAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATTTCCAAA
GTTTCTTACTAGTAGACTATTTCAAGATTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
ATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATTC
ATAAGACCTTCAGGCAAGATGTTTTCACATGAATTTGAAAAATGAGAAAGCGATTTT
Found at i:509646 original size:238 final size:235
Alignment explanation
Indices: 509219--509924 Score: 957
Period size: 238 Copynumber: 3.0 Consensus size: 235
509209 CCGAAGATAA
* * *
509219 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGACCATGATGATTAAATCCTTCAGGTCATCTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCCGTAA
* *
509284 GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATTCATAAGACCTTCAGGTAAGATGTTTTCAC
66 GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATT-ATAAGACCTTCGGGCAAGATGTTTTCAC
* *
509349 ATGAATTTGAAAAATGAGAAAGCAATTTTCAAACTTTCTCATTTAAT-TTTTTCAGAAAATGAAA
130 ATGAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATATTTTT-AGAAAATGAAA
509413 TATTTGAAAAGTAAGAAAGTGATTTCCAATATTTCTTACTTAG
194 TATTTGAAAAGTAAGAAAGTGATTTCCAA-ATTTCTTACTTAG
* *
509456 TAAGTCCTTCGGGCCATCAGTAAGTCTTTTTGAGGATGATGATTAAATCCTTCGGGTCATCCGTA
1 TAAGTCCTTCGGGCCATCAGTAAGTC-TTTCGAGCATGATGATTAAATCCTTCGGGTCATCCGTA
* * * * *
509521 AGCCTTTCGAGCAATATGATAAGTCATTCGGGCCATATATAAAACCTTCGGGCATGATGTTTTCA
65 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCAT-TATAAGACCTTCGGGCAAGATGTTTTCA
509586 CATGAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATATTTTTAG---A--AAA
129 CATGAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATATTTTTAGAAAATGAAA
* *
509646 TA----AAAAGTAAGAAAGCGATTTCCAAGGTTTCTTACTTAG
194 TATTTGAAAAGTAAGAAAGTGATTTCCAA-ATTTCTTACTTAG
* * *
509685 TAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAACCCTTTGGGTCA-CCTGTA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCC-GTA
* *
509749 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCA
65 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCAT-TATAAGACCTTCGGGCAAGATGTTTTCA
** * * * * *
509814 TGTGATTTTTGAAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAA
129 CATGA-ATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATATTTTTAGAAAATGAA
* * * *
509879 ATTTTTGAAAAGTAAGAAAGTGGTTTTCAAAGTTTCTTACCTAG
193 ATATTTGAAAAGTAAGAAAGTGATTTCCAAA-TTTCTTACTTAG
509923 TA
1 TA
509925 GATTATTTCC
Statistics
Matches: 412, Mismatches: 42, Indels: 29
0.85 0.09 0.06
Matches are distributed among these distances:
227 2 0.00
228 92 0.22
229 105 0.25
232 1 0.00
233 5 0.01
234 4 0.01
235 1 0.00
237 26 0.06
238 170 0.41
239 6 0.01
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (235 bp):
TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCCGTAA
GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATTATAAGACCTTCGGGCAAGATGTTTTCACA
TGAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATATTTTTAGAAAATGAAATA
TTTGAAAAGTAAGAAAGTGATTTCCAAATTTCTTACTTAG
Found at i:510168 original size:23 final size:24
Alignment explanation
Indices: 510122--510186 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 24
510112 TTTCTCTTTT
510122 AAAGTAAAAAGAAAAAAATAATAA
1 AAAGTAAAAAGAAAAAAATAATAA
* *
510146 AAAGAAAAAAAATAAAATAATAATAA
1 AAAGTAAAAAGA-AAAA-AATAATAA
*
510172 AAAGATAAAGAGAAA
1 AAAG-TAAAAAGAAA
510187 GAATAAACAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
24 10 0.30
25 4 0.12
26 14 0.42
27 5 0.15
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (24 bp):
AAAGTAAAAAGAAAAAAATAATAA
Found at i:511806 original size:16 final size:17
Alignment explanation
Indices: 511782--511818 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
511772 TTTAGGTGTG
511782 TTTAGTTTAGG-TTTAT
1 TTTAGTTTAGGTTTTAT
*
511798 TTTATTTTAGGTTTTAT
1 TTTAGTTTAGGTTTTAT
511815 TTTA
1 TTTA
511819 AAAGGTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.19, C:0.00, G:0.14, T:0.68
Consensus pattern (17 bp):
TTTAGTTTAGGTTTTAT
Found at i:511815 original size:17 final size:16
Alignment explanation
Indices: 511767--511818 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
511757 CGGCCATATG
* *
511767 TTTAGTTTAGGTGT-G
1 TTTAGTTTAGGTTTAT
511782 TTTAGTTTAGGTTTAT
1 TTTAGTTTAGGTTTAT
*
511798 TTTATTTTAGGTTTTAT
1 TTTAGTTTAGG-TTTAT
511815 TTTA
1 TTTA
511819 AAAGGTTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
15 13 0.41
16 10 0.31
17 9 0.28
ACGTcount: A:0.17, C:0.00, G:0.19, T:0.63
Consensus pattern (16 bp):
TTTAGTTTAGGTTTAT
Found at i:515251 original size:29 final size:29
Alignment explanation
Indices: 515209--515276 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
515199 ATATTTGTAC
*
515209 GTGGGTTTAAGGTGTACCCGACGTTAATT
1 GTGGCTTTAAGGTGTACCCGACGTTAATT
515238 GTGGCTTTAAGGTGTACCCGACGTTAATT
1 GTGGCTTTAAGGTGTACCCGACGTTAATT
*
515267 GAGGCTTTAA
1 GTGGCTTTAA
515277 TTGAACGTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (29 bp):
GTGGCTTTAAGGTGTACCCGACGTTAATT
Found at i:519072 original size:11 final size:11
Alignment explanation
Indices: 519056--519120 Score: 50
Period size: 11 Copynumber: 6.1 Consensus size: 11
519046 TGAGGGTGAC
519056 ATACGAGCCAT
1 ATACGAGCCAT
519067 ATACGAGCC--
1 ATACGAGCCAT
519076 ATACGAGCCA-
1 ATACGAGCCAT
**
519086 ATGGGGAG-CAT
1 AT-ACGAGCCAT
519097 GCA-ACGAGCCAT
1 --ATACGAGCCAT
519109 ATACGAGCCAT
1 ATACGAGCCAT
519120 A
1 A
519121 CGAGCCAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
9 9 0.21
10 5 0.12
11 25 0.58
12 3 0.07
13 1 0.02
ACGTcount: A:0.35, C:0.26, G:0.25, T:0.14
Consensus pattern (11 bp):
ATACGAGCCAT
Found at i:519105 original size:42 final size:42
Alignment explanation
Indices: 519058--519211 Score: 183
Period size: 42 Copynumber: 4.0 Consensus size: 42
519048 AGGGTGACAT
519058 ACGAGCCATATACGAGCCATACGAGCCAATGGGGAGCATGCA
1 ACGAGCCATATACGAGCCATACGAGCCAATGGGGAGCATGCA
519100 ACGAGCCATATACGAGCCATACGAGCCAATGGGGAGCATGC-
1 ACGAGCCATATACGAGCCATACGAGCCAATGGGGAGCATGCA
* * *
519141 A-G-G--A-ATA-GAG--A-GCCA----ATGGGGAGCATTCA
1 ACGAGCCATATACGAGCCATACGAGCCAATGGGGAGCATGCA
519170 ACGAGCCATATACGAGCCATACGAGCCAATGGGGAGCATGCA
1 ACGAGCCATATACGAGCCATACGAGCCAATGGGGAGCATGCA
519212 GGAATAGAGA
Statistics
Matches: 92, Mismatches: 6, Indels: 28
0.73 0.05 0.22
Matches are distributed among these distances:
28 12 0.13
29 1 0.01
30 1 0.01
31 1 0.01
32 2 0.02
33 2 0.02
34 3 0.03
35 6 0.07
36 3 0.03
37 2 0.02
38 2 0.02
39 1 0.01
40 1 0.01
41 1 0.01
42 54 0.59
ACGTcount: A:0.34, C:0.24, G:0.30, T:0.12
Consensus pattern (42 bp):
ACGAGCCATATACGAGCCATACGAGCCAATGGGGAGCATGCA
Found at i:519161 original size:70 final size:70
Alignment explanation
Indices: 519080--519222 Score: 277
Period size: 70 Copynumber: 2.0 Consensus size: 70
519070 CGAGCCATAC
519080 GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCCATACGAGCCAATGGGGAGCATGCAGGA
1 GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCCATACGAGCCAATGGGGAGCATGCAGGA
519145 ATAGA
66 ATAGA
*
519150 GAGCCAATGGGGAGCATTCAACGAGCCATATACGAGCCATACGAGCCAATGGGGAGCATGCAGGA
1 GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCCATACGAGCCAATGGGGAGCATGCAGGA
519215 ATAGA
66 ATAGA
519220 GAG
1 GAG
519223 GTCGCCATGC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.34, C:0.21, G:0.33, T:0.12
Consensus pattern (70 bp):
GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCCATACGAGCCAATGGGGAGCATGCAGGA
ATAGA
Found at i:519271 original size:29 final size:29
Alignment explanation
Indices: 519221--519320 Score: 157
Period size: 29 Copynumber: 3.4 Consensus size: 29
519211 AGGAATAGAG
* *
519221 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
519250 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
*
519279 AGGTCGCCATGTAGTCCCGACGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
519308 AGGTCGCCATGTA
1 AGGTCGCCATGTA
519321 CATGCACAGC
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
29 65 0.97
30 2 0.03
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:519407 original size:27 final size:27
Alignment explanation
Indices: 519375--519427 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
519365 CCTACAGCTC
519375 CCAATGCATGCATGTGAACCATTTGAG
1 CCAATGCATGCATGTGAACCATTTGAG
519402 CCAATGCATGCATGTGAACCATTTGA
1 CCAATGCATGCATGTGAACCATTTGA
519428 TTATTGGTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (27 bp):
CCAATGCATGCATGTGAACCATTTGAG
Found at i:519566 original size:23 final size:23
Alignment explanation
Indices: 519538--519583 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
519528 TAAAGAAAGA
519538 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
519561 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
519584 CCGAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:519598 original size:25 final size:23
Alignment explanation
Indices: 519538--519598 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
519528 TAAAGAAAGA
**
519538 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
519561 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
519584 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
519599 AGGGAGAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 23 0.70
25 10 0.30
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:519612 original size:21 final size:21
Alignment explanation
Indices: 519588--519640 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
519578 TTGCAGCCGA
519588 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
519609 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
*
519630 GAAAGTAAGAA
1 GAAAGAAAGAA
519641 GAAAAAGGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (21 bp):
GAAAGAAAGAAAGGGAGAAAG
Found at i:519634 original size:17 final size:16
Alignment explanation
Indices: 519586--519617 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
519576 GATTGCAGCC
519586 GAGAAAGAAAGAAAGG
1 GAGAAAGAAAGAAAGG
519602 GAGAAAGGAAAGAAAG
1 GAGAAA-GAAAGAAAG
519618 AAAGGGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAGAAAGAAAGAAAGG
Found at i:519785 original size:20 final size:21
Alignment explanation
Indices: 519747--519786 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
519737 GTTAATTAGT
*
519747 TTGTTAGTTTAGGGTTATAGA
1 TTGTTAGTTTAGAGTTATAGA
519768 TTGTTAGTTTA-AGTTATAG
1 TTGTTAGTTTAGAGTTATAG
519787 TATACATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (21 bp):
TTGTTAGTTTAGAGTTATAGA
Found at i:519816 original size:41 final size:41
Alignment explanation
Indices: 519771--519859 Score: 92
Period size: 41 Copynumber: 2.2 Consensus size: 41
519761 TTATAGATTG
* *
519771 TTAGTTTAAG-TT-ATAGTATACATAAATTAAAAATTATTTAA
1 TTAGTTTAAGTTTGATAGT-TACAT-AATTAAAAAATAATTAA
* * * *
519812 TTAGTATATGTTTGATAGTTATATAGTTAAAAAATAATTAA
1 TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
519853 TTAGTTT
1 TTAGTTT
519860 GTTTTGTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 28 0.72
42 6 0.15
43 5 0.13
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (41 bp):
TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
Found at i:519903 original size:46 final size:48
Alignment explanation
Indices: 519840--519931 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 48
519830 TTATATAGTT
*
519840 AAAAAATAATTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATATAA
1 AAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATATAA
*
519885 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
519932 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 6 0.15
46 15 0.37
47 5 0.12
48 7 0.17
49 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (48 bp):
AAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATATAA
Found at i:520008 original size:32 final size:33
Alignment explanation
Indices: 519972--520048 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 33
519962 TTAGTTAGTA
519972 AGTTTATTAGTAG-TATA-TTATAATGAAAA-AAT
1 AGTTTATTAGTAGTTATAGTTAT-AT-AAAAGAAT
*
520004 AGTTTATTAGTTAGTTTTAGTTATATAAAAGAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAGAAT
*
520038 ATTTTATTAGT
1 AGTTTATTAGT
520049 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
32 10 0.26
33 8 0.21
34 17 0.44
35 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (33 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAGAAT
Found at i:520319 original size:26 final size:24
Alignment explanation
Indices: 520261--520319 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
520251 CTAATAAACC
*
520261 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
520285 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
520313 TAATAAT
1 TAATAAT
520320 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:521096 original size:41 final size:46
Alignment explanation
Indices: 521051--521204 Score: 167
Period size: 50 Copynumber: 3.3 Consensus size: 46
521041 GTTTAAAGAC
* *
521051 ACTAACAAATTAATTAA-T-ATTTTTTATAT-T-TA-ATAACTTAA
1 ACTAAGAAACTAATTAACTAATTTTTTATATATATATATAACTTAA
521092 ACTAAGAAACTAATTAACTAATTTTTTATATAATATAATATATAACTTAA
1 ACTAAGAAACTAATTAACTAA-TTTTT-TAT-ATAT-ATATATAACTTAA
521142 ACTAAGAAACTAATTAACTAATTTTTTATATAATATAATATATAACTTAA
1 ACTAAGAAACTAATTAACTAA-TTTTT-TAT-ATAT-ATATATAACTTAA
*
521192 ACTAA-TAACTAAT
1 ACTAAGAAACTAAT
521205 AATATAACTT
Statistics
Matches: 101, Mismatches: 3, Indels: 10
0.89 0.03 0.09
Matches are distributed among these distances:
41 15 0.15
42 1 0.01
43 1 0.01
44 5 0.05
45 3 0.03
46 2 0.02
47 1 0.01
49 9 0.09
50 64 0.63
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.41
Consensus pattern (46 bp):
ACTAAGAAACTAATTAACTAATTTTTTATATATATATATAACTTAA
Found at i:521142 original size:50 final size:50
Alignment explanation
Indices: 521083--521204 Score: 228
Period size: 50 Copynumber: 2.5 Consensus size: 50
521073 TTTATATTTA
521083 ATAACTTAAACTAAGAAACTAATTAACTAATTTTTTATATAATATAATAT
1 ATAACTTAAACTAAGAAACTAATTAACTAATTTTTTATATAATATAATAT
521133 ATAACTTAAACTAAGAAACTAATTAACTAATTTTTTATATAATATAATAT
1 ATAACTTAAACTAAGAAACTAATTAACTAATTTTTTATATAATATAATAT
*
521183 ATAACTTAAACTAA-TAACTAAT
1 ATAACTTAAACTAAGAAACTAAT
521205 AATATAACTT
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
49 7 0.10
50 64 0.90
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.39
Consensus pattern (50 bp):
ATAACTTAAACTAAGAAACTAATTAACTAATTTTTTATATAATATAATAT
Found at i:521241 original size:21 final size:21
Alignment explanation
Indices: 521208--521256 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
521198 AACTAATAAT
521208 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
521229 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
521250 ATTAACT
1 A-TAACT
521257 AGATTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:521256 original size:29 final size:25
Alignment explanation
Indices: 521177--521257 Score: 74
Period size: 25 Copynumber: 3.1 Consensus size: 25
521167 TTATATAATA
*
521177 TAAT-ATATAACTTAAACTAATAAC
1 TAATAATATAACTCAAACTAATAAC
* *
521201 TAATAATATAACTTAAACTAACAAAC
1 TAATAATATAACTCAAACTAA-TAAC
*
521227 TAATAATTTATACTAACAAACTAATTAAC
1 TAATAATATA-ACT--CAAACTAA-TAAC
521256 TA
1 TA
521258 GATTTTAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
24 4 0.09
25 16 0.34
26 12 0.26
27 3 0.06
29 12 0.26
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (25 bp):
TAATAATATAACTCAAACTAATAAC
Found at i:521738 original size:25 final size:25
Alignment explanation
Indices: 521710--521789 Score: 66
Period size: 25 Copynumber: 3.4 Consensus size: 25
521700 ACACCGTTCG
521710 ACGTGCATGGCCATGCACAGTTCCC
1 ACGTGCATGGCCATGCACAGTTCCC
* *
521735 ACGT-C----CCATGCACAGCAT-GC
1 ACGTGCATGGCCATGCACAG-TTCCC
521755 ATC-TGCATGGCCATGCACAGTTCCC
1 A-CGTGCATGGCCATGCACAGTTCCC
521780 ACGTCGCATG
1 ACGT-GCATG
521790 CACAGCATGC
Statistics
Matches: 41, Mismatches: 4, Indels: 19
0.64 0.06 0.30
Matches are distributed among these distances:
20 13 0.32
21 3 0.07
24 3 0.07
25 17 0.41
26 5 0.12
ACGTcount: A:0.21, C:0.36, G:0.23, T:0.20
Consensus pattern (25 bp):
ACGTGCATGGCCATGCACAGTTCCC
Found at i:521763 original size:45 final size:45
Alignment explanation
Indices: 521713--521801 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
521703 CCGTTCGACG
521713 TGCATGGCCATGCACAGTTCCCACGTCCCATGCACAGCATGCATC
1 TGCATGGCCATGCACAGTTCCCACGTCCCATGCACAGCATGCATC
*
521758 TGCATGGCCATGCACAGTTCCCACGTCGCATGCACAGCATGCAT
1 TGCATGGCCATGCACAGTTCCCACGTCCCATGCACAGCATGCAT
521802 GCATGCATCC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.22, C:0.36, G:0.21, T:0.20
Consensus pattern (45 bp):
TGCATGGCCATGCACAGTTCCCACGTCCCATGCACAGCATGCATC
Found at i:521920 original size:28 final size:29
Alignment explanation
Indices: 521888--521951 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
521878 GCCCTGATGC
***
521888 CATGGCGACCTTGGAGGTCGCC-GGATTG
1 CATGGCGACCTCCAAGGTCGCCTGGATTG
521916 CATGGCGACCTCCAAGGTCGCCTGGATTG
1 CATGGCGACCTCCAAGGTCGCCTGGATTG
521945 CATGGCG
1 CATGGCG
521952 TCCTATGGCG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 19 0.59
29 13 0.41
ACGTcount: A:0.16, C:0.28, G:0.36, T:0.20
Consensus pattern (29 bp):
CATGGCGACCTCCAAGGTCGCCTGGATTG
Found at i:524168 original size:59 final size:60
Alignment explanation
Indices: 524084--524212 Score: 143
Period size: 59 Copynumber: 2.2 Consensus size: 60
524074 AAACATAGAA
* * * * * *
524084 ACATACCTACACTAATATAATTATGTGTTTATTGTTATGTATCAAGATATT-AAAGATGT
1 ACATACTTACACCAATATAAGTATGTGTTAATTGTTAGGTACCAAGATATTGAAAGATGT
* * * * **
524143 ACATATTTACACCAATGTAAGTATGTGTTAATTTTTGGGTACCAAGATATTGAGTGATGT
1 ACATACTTACACCAATATAAGTATGTGTTAATTGTTAGGTACCAAGATATTGAAAGATGT
524203 ACATACTTAC
1 ACATACTTAC
524213 TCTGGTACAA
Statistics
Matches: 56, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
59 41 0.73
60 15 0.27
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.39
Consensus pattern (60 bp):
ACATACTTACACCAATATAAGTATGTGTTAATTGTTAGGTACCAAGATATTGAAAGATGT
Found at i:535831 original size:27 final size:29
Alignment explanation
Indices: 535801--535854 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
535791 AATTAATCAT
535801 AAAAAT-AAACGT-AATAAAACACATACC
1 AAAAATAAAACGTGAATAAAACACATACC
*
535828 AAAAATAAAACTTGAATAAAACACATA
1 AAAAATAAAACGTGAATAAAACACATA
535855 TATAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 6 0.25
28 5 0.21
29 13 0.54
ACGTcount: A:0.65, C:0.15, G:0.04, T:0.17
Consensus pattern (29 bp):
AAAAATAAAACGTGAATAAAACACATACC
Found at i:539824 original size:2 final size:2
Alignment explanation
Indices: 539811--539851 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
539801 TAAGACCATG
539811 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
539852 AGTATGCATG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:543017 original size:41 final size:41
Alignment explanation
Indices: 542972--543053 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
542962 GCTAGATGAT
*
542972 GTAAAGGAACATATAAGGGAAAAAAAAAGAACCTAAAGCAA
1 GTAAAGGAACAAATAAGGGAAAAAAAAAGAACCTAAAGCAA
* *
543013 GTAAAGGAACAAATAAGGGAAAACAAAAGAACCTGAAGCAA
1 GTAAAGGAACAAATAAGGGAAAAAAAAAGAACCTAAAGCAA
543054 TAAGAATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.60, C:0.11, G:0.21, T:0.09
Consensus pattern (41 bp):
GTAAAGGAACAAATAAGGGAAAAAAAAAGAACCTAAAGCAA
Found at i:543588 original size:15 final size:15
Alignment explanation
Indices: 543570--543603 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
543560 TTTGGGATAT
543570 TTTTTTAGCTTTTTC
1 TTTTTTAGCTTTTTC
**
543585 TTTTTTCTCTTTTTC
1 TTTTTTAGCTTTTTC
543600 TTTT
1 TTTT
543604 ATTTTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTTTAGCTTTTTC
Found at i:544597 original size:15 final size:15
Alignment explanation
Indices: 544564--544598 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
544554 GATTACGATT
*
544564 AAGATTAAGACAATG
1 AAGATTAAGACAATA
*
544579 AAGATTAAGACACTA
1 AAGATTAAGACAATA
544594 AAGAT
1 AAGAT
544599 AAACGGTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.20
Consensus pattern (15 bp):
AAGATTAAGACAATA
Found at i:547507 original size:2 final size:2
Alignment explanation
Indices: 547500--547529 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
547490 TTTCTTTTCA
547500 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
547530 TTGTACTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:548504 original size:33 final size:33
Alignment explanation
Indices: 548466--548736 Score: 153
Period size: 33 Copynumber: 8.3 Consensus size: 33
548456 GGAGGTAACC
*
548466 TTTGGTGAAGAGATATAACTTTTGGAGGCATCA
1 TTTGGTGAAGAGATATAACTTTTGGAGGCACCA
* * * *
548499 ATTGGTGAAGAG-TCATATCTTTTAGAGGCACCC
1 TTTGGTGAAGAGAT-ATAACTTTTGGAGGCACCA
* * * * *
548532 TTTGATGAAGAGAAAAAACTTTTGGTGGCATTC-
1 TTTGGTGAAGAGATATAACTTTTGGAGGCA-CCA
* *
548565 GTTGGTGAAGAG--ACAACTTTTGGAGGCACCA
1 TTTGGTGAAGAGATATAACTTTTGGAGGCACCA
* *
548596 TTTAGTGAAGAGACT-TGACTTTTGGAGGCA-CA
1 TTTGGTGAAGAGA-TATAACTTTTGGAGGCACCA
* * ** * * *
548628 CCTTGGTGAAGAGACACGACTCTTAGAGGCACCT
1 -TTTGGTGAAGAGATATAACTTTTGGAGGCACCA
** * * *
548662 TTTCATGAGGAGACA-AGACTTTTCGAGGCACC-
1 TTTGGTGAAGAGATATA-ACTTTTGGAGGCACCA
* * * * *
548694 TATTGGTGAAGAGAAACAACTTTTGGAGGTATCT
1 T-TTGGTGAAGAGATATAACTTTTGGAGGCACCA
548728 TTTGGTGAA
1 TTTGGTGAA
548737 ACATTATGAC
Statistics
Matches: 181, Mismatches: 43, Indels: 28
0.72 0.17 0.11
Matches are distributed among these distances:
30 1 0.01
31 24 0.13
32 4 0.02
33 148 0.82
34 4 0.02
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (33 bp):
TTTGGTGAAGAGATATAACTTTTGGAGGCACCA
Found at i:548544 original size:66 final size:64
Alignment explanation
Indices: 548464--548722 Score: 213
Period size: 66 Copynumber: 4.0 Consensus size: 64
548454 CTGGAGGTAA
* *
548464 CCTTTGGTGAAGAGATATAACTTTTGGAGGCATCAATTGGTGAAGAGTCATATCTTTTAGAGGCA
1 CCTTTGATGAAGAGATATAACTTTTGGAGGCATCAATTGGTGAAGAGACA-A-CTTTTAGAGGCA
548529 C
64 C
* * * * *
548530 CCTTTGATGAAGAGAAAAAACTTTTGGTGGCATTC-GTTGGTGAAGAGACAACTTTTGGAGGCAC
1 CCTTTGATGAAGAGATATAACTTTTGGAGGCA-TCAATTGGTGAAGAGACAACTTTTAGAGGCAC
* * * *
548594 CATTT-AGTGAAGAGACT-TGACTTTTGGAGGCA-CACCTTGGTGAAGAGACACGACTCTTAGAG
1 CCTTTGA-TGAAGAGA-TATAACTTTTGGAGGCATCA-ATTGGTGAAGAGACA--ACTTTTAGAG
548656 GCAC
61 GCAC
* * * * * * * *
548660 CTTTTCATGAGGAGACA-AGACTTTTCGAGGCACCTATTGGTGAAGAGAAACAACTTTTGGAGG
1 CCTTTGATGAAGAGATATA-ACTTTTGGAGGCATCAATTGGTGAAGAG--ACAACTTTTAGAGG
548723 TATCTTTTGG
Statistics
Matches: 156, Mismatches: 24, Indels: 26
0.76 0.12 0.13
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 50 0.32
65 1 0.01
66 96 0.62
67 4 0.03
68 3 0.02
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (64 bp):
CCTTTGATGAAGAGATATAACTTTTGGAGGCATCAATTGGTGAAGAGACAACTTTTAGAGGCAC
Found at i:548637 original size:130 final size:131
Alignment explanation
Indices: 548470--548722 Score: 300
Period size: 130 Copynumber: 1.9 Consensus size: 131
548460 GTAACCTTTG
* * *
548470 GTGAAGAGATATAACTTTTGGAGGCATCAATTGGTGAAGAGTCA-TATCTTTTAGAGGCACCCTT
1 GTGAAGAGATATAACTTTTGGAGGCATCAATTGGTGAAGAGACACGA-CTCTTAGAGGCACCCTT
* * * * *
548534 TGATGAAGAGAAAAAACTTTTGGTGGCA-TTCGTTGGTGAAGAG-ACAACTTTTGGAGGCACCAT
65 TCATGAAGAGAAAAAACTTTTCGAGGCACCT-ATTGGTGAAGAGAACAACTTTTGGAGGCACCAT
548597 TTA
129 TTA
* * *
548600 GTGAAGAGACT-TGACTTTTGGAGGCA-CACCTTGGTGAAGAGACACGACTCTTAGAGGCACCTT
1 GTGAAGAGA-TATAACTTTTGGAGGCATCA-ATTGGTGAAGAGACACGACTCTTAGAGGCACCCT
* * *
548663 TTCATGAGGAGACAAGACTTTTCGAGGCACCTATTGGTGAAGAGAAACAACTTTTGGAGG
64 TTCATGAAGAGAAAAAACTTTTCGAGGCACCTATTGGTGAAGAG-AACAACTTTTGGAGG
548723 TATCTTTTGG
Statistics
Matches: 103, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
129 2 0.02
130 84 0.82
131 3 0.03
132 14 0.14
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.27
Consensus pattern (131 bp):
GTGAAGAGATATAACTTTTGGAGGCATCAATTGGTGAAGAGACACGACTCTTAGAGGCACCCTTT
CATGAAGAGAAAAAACTTTTCGAGGCACCTATTGGTGAAGAGAACAACTTTTGGAGGCACCATTT
A
Found at i:554149 original size:3 final size:3
Alignment explanation
Indices: 554141--554212 Score: 78
Period size: 3 Copynumber: 24.7 Consensus size: 3
554131 CTACAAAATG
* * *
554141 TAA TAA TAA TTAA TAA -AA TAA TGA TAA TAA TAA TAA TTA -AA TAC
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
554185 TAA TAA TAA TAG TAA TAA TAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
554213 CCCGGACAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
2 5 0.09
3 49 0.86
4 3 0.05
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:554200 original size:29 final size:29
Alignment explanation
Indices: 554140--554213 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
554130 CCTACAAAAT
*
554140 GTAATAATAATT-AATA-AAATAATGATA
1 GTAATAATAATTAAATACAAATAATAATA
* *
554167 ATAATAATAATTAAATACTAATAATAATA
1 GTAATAATAATTAAATACAAATAATAATA
*
554196 GTAATAATAATAAAATAC
1 GTAATAATAATTAAATAC
554214 CCGGACAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 11 0.28
28 4 0.10
29 25 0.62
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (29 bp):
GTAATAATAATTAAATACAAATAATAATA
Found at i:554681 original size:136 final size:136
Alignment explanation
Indices: 554488--554938 Score: 432
Period size: 137 Copynumber: 3.3 Consensus size: 136
554478 GATGGCATTA
* * * * * * *
554488 TTCCTACGCGATGAGGACGTCTTGAACATCTTTAGGGATAATGTAAATAACATGGTTCTTACATG
1 TTCCTACGTGATGAGGAAG-CTTGACCATCTTTAGGGATAATATAGATAACACGGTTCCTACATG
** * * *
554553 ATGAGGA-AGTCTGGCTATCTAAGGGTGAAGCGGCTTCTATGTGATGAGAGATATAGTCGATGGA
65 ATGAGGAGAGT-TGATTATCTAAGGTTGACGCGGCTTCTATGTGATGAGAGATATGGTCGATGGA
554617 TGACACGG
129 TGACACGG
*
554625 TTCCTACGTGATGAGGAAGGTTGACCATCTTTAGGGATAATATAGATAACACGGTTCCTACATGA
1 TTCCTACGTGATGAGGAAGCTTGACCATCTTTAGGGATAATATAGATAACACGGTTCCTACATGA
* * * * * * *
554690 TGAGGAGAATTGATTATCTAAGGTTGACGCGACTTCTACGTGATAAGTAGTTCTGGTCGGTGGAT
66 TGAGGAGAGTTGATTATCTAAGGTTGACGCGGCTTCTATGTGATGAG-AGATATGGTCGATGGAT
554755 GACACGG
130 GACACGG
* * * * * *
554762 TTCCTATGTGAAGAGGATAGCTAGA-CATCTTTATGGATAA-ATGGTGATAACACGGTTCCTACG
1 TTCCTACGTGATGAGGA-AGCTTGACCATCTTTAGGGATAATAT--AGATAACACGGTTCCTACA
* * * *
554825 TAATGAGGATG-GTTGATTATTTAAGGTTGACGCAGC-TCATACATGTTA-G-GAGATATGGTC-
63 TGATGAGGA-GAGTTGATTATCTAAGGTTGACGCGGCTTC-T--ATGTGATGAGAGATATGGTCG
*
554885 AGTGGATGACATGG
124 A-TGGATGACACGG
* * * *
554899 TTCCTACGTGATGAGGATGGTTGGCCATCTCTAGGGATAA
1 TTCCTACGTGATGAGGAAGCTTGACCATCTTTAGGGATAA
554939 ATTGTTTCAA
Statistics
Matches: 256, Mismatches: 47, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
136 81 0.32
137 117 0.46
138 53 0.21
139 1 0.00
140 4 0.02
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.29
Consensus pattern (136 bp):
TTCCTACGTGATGAGGAAGCTTGACCATCTTTAGGGATAATATAGATAACACGGTTCCTACATGA
TGAGGAGAGTTGATTATCTAAGGTTGACGCGGCTTCTATGTGATGAGAGATATGGTCGATGGATG
ACACGG
Found at i:554984 original size:21 final size:20
Alignment explanation
Indices: 554952--555021 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 20
554942 GTTTCAAGAG
*
554952 AAACTGTATCAAGAGAGACA
1 AAACTGTTTCAAGAGAGACA
554972 AAACATGTTTCAAG-G-G---
1 AAAC-TGTTTCAAGAGAGACA
*
554988 AAACTGTCTCAAGAGAGACA
1 AAACTGTTTCAAGAGAGACA
*
555008 AAATATGTTTCAAG
1 AAA-CTGTTTCAAG
555022 GGAAACTGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
15 8 0.21
16 5 0.13
17 1 0.03
19 1 0.03
20 8 0.21
21 16 0.41
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.21
Consensus pattern (20 bp):
AAACTGTTTCAAGAGAGACA
Found at i:555091 original size:35 final size:36
Alignment explanation
Indices: 554937--555098 Score: 229
Period size: 36 Copynumber: 4.6 Consensus size: 36
554927 CTCTAGGGAT
* *
554937 AAAT-TGTTTCAAGAGAAACTGTATCAAGAGAGACA
1 AAATATGTTTCAAGGGAAACTGTCTCAAGAGAGACA
*
554972 AAACATGTTTCAAGGGAAACTGTCTCAAGAGAGACA
1 AAATATGTTTCAAGGGAAACTGTCTCAAGAGAGACA
*
555008 AAATATGTTTCAAGGGAAACTGTCTCAAGAGAGATA
1 AAATATGTTTCAAGGGAAACTGTCTCAAGAGAGACA
* * * *
555044 AAATATCTTTCAAGGGAAATTGTCTTAAAAGAGA-A
1 AAATATGTTTCAAGGGAAACTGTCTCAAGAGAGACA
*
555079 AAATATGGTTCAAGGGAAAC
1 AAATATGTTTCAAGGGAAAC
555099 AATCTCTAAT
Statistics
Matches: 114, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
35 21 0.18
36 93 0.82
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (36 bp):
AAATATGTTTCAAGGGAAACTGTCTCAAGAGAGACA
Found at i:567350 original size:35 final size:36
Alignment explanation
Indices: 567302--567385 Score: 91
Period size: 35 Copynumber: 2.4 Consensus size: 36
567292 ATTTATAAGT
* * * *
567302 TGGTGATAATATAGGCTTG-ATATGGTAATGGAATA
1 TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
* * *
567337 TGGTGATGTTATAGGCGTGAAAATGGTGATGGAAGG
1 TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
567373 TGGTGATGA-ATAG
1 TGGTGATGATATAG
567386 ATAGTATCTT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
35 20 0.50
36 20 0.50
ACGTcount: A:0.31, C:0.02, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
Found at i:567773 original size:19 final size:20
Alignment explanation
Indices: 567726--567776 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
567716 GAAACCCTTT
**
567726 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
567746 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
567765 TGAAGATACATG
1 TGAAAATACATG
567777 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:593096 original size:11 final size:12
Alignment explanation
Indices: 593051--593105 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
593041 AAATTATTAT
593051 TAATAAT-AATA
1 TAATAATAAATA
*
593062 CTAATAAT-ATTA
1 -TAATAATAAATA
*
593074 TTAATTATAAATA
1 -TAATAATAAATA
593087 TAA-AATAAATA
1 TAATAATAAATA
593098 TAATAATA
1 TAATAATA
593106 TATTATTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 10 0.28
12 23 0.64
13 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (12 bp):
TAATAATAAATA
Found at i:593506 original size:89 final size:89
Alignment explanation
Indices: 593337--593578 Score: 357
Period size: 89 Copynumber: 2.7 Consensus size: 89
593327 GCATCTTTCC
*
593337 GAAGGTCTTATGG-TGGCCCGAATGACTTAAAAATCAAGAAACCCCCGAAGG-TTCAG-TTCTTA
1 GAAGGTCTTATGGATGGCCCGAAGGACTTAAAAATCAAGAAA-CCCCGAAGGCTT-AGTTTCTTA
593399 GATCTCATTTGAAAACATCCTGCACT
64 GATCTCATTTGAAAACATCCTGCACT
* *
593425 GAAGGTCTTATGGATGTCCCAAAGGACTT-AAAATCAAGAAACTCCCGAAGGCTTAGTTTCTTAG
1 GAAGGTCTTATGGATGGCCCGAAGGACTTAAAAATCAAGAAAC-CCCGAAGGCTTAGTTTCTTAG
593489 ATCTCATTTGAAAACATCCTGCACT
65 ATCTCATTTGAAAACATCCTGCACT
* * *
593514 GAAGGTCTTATGGATGGCCCGACGGACTTAAAAAATCAAGAAACCCCTGAAGTCTCAGTTTCTTA
1 GAAGGTCTTATGGATGGCCCGAAGGACTT-AAAAATCAAGAAACCCC-GAAGGCTTAGTTTCTTA
593579 ATTGTCACCA
Statistics
Matches: 139, Mismatches: 8, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
87 1 0.01
88 35 0.25
89 72 0.52
90 3 0.02
91 28 0.20
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (89 bp):
GAAGGTCTTATGGATGGCCCGAAGGACTTAAAAATCAAGAAACCCCGAAGGCTTAGTTTCTTAGA
TCTCATTTGAAAACATCCTGCACT
Found at i:593768 original size:41 final size:42
Alignment explanation
Indices: 593587--593851 Score: 272
Period size: 43 Copynumber: 6.3 Consensus size: 42
593577 TAATTGTCAC
* * *
593587 CAAAGAACCCCTACATATCACGATGGTCCCTCAAACCTTTCAT
1 CAAAAAACCCCTACATATCACGATGGTCCTTC-AAGCTTTCAT
593630 CAAAAAACCCCTACATATCACGATGGT-CTCTCAAGCTTTTCAT
1 CAAAAAACCCCTACATATCACGATGGTCCT-TCAAGC-TTTCAT
* * *
593673 CAATAAACCCCTACATATCACGATGGT-TTCTCAAGCTGTCAT
1 CAAAAAACCCCTACATATCACGATGGTCCT-TCAAGCTTTCAT
*
593715 CAAAGAACCCCTACATATCACGATGGTCCTTCAAGC-TTCAT
1 CAAAAAACCCCTACATATCACGATGGTCCTTCAAGCTTTCAT
** * * * *
593756 CAAGGAACCCCTACATAT--TGATGGCCCTTAAAACTTATCAT
1 CAAAAAACCCCTACATATCACGATGGTCCTTCAAGCTT-TCAT
* * *
593797 CAAGAAACCCCTACATATCACGATGGT-CTCTCAAGGTTTTCTT
1 CAAAAAACCCCTACATATCACGATGGTCCT-TCAA-GCTTTCAT
*
593840 CAAGAAACCCCT
1 CAAAAAACCCCT
593852 GAAATCAGGC
Statistics
Matches: 191, Mismatches: 22, Indels: 18
0.83 0.10 0.08
Matches are distributed among these distances:
39 12 0.06
40 1 0.01
41 42 0.22
42 42 0.22
43 92 0.48
44 2 0.01
ACGTcount: A:0.32, C:0.31, G:0.11, T:0.26
Consensus pattern (42 bp):
CAAAAAACCCCTACATATCACGATGGTCCTTCAAGCTTTCAT
Found at i:593845 original size:124 final size:127
Alignment explanation
Indices: 593581--593831 Score: 348
Period size: 124 Copynumber: 2.0 Consensus size: 127
593571 GTTTCTTAAT
*
593581 TGTCACCAAAGAACCCCTACATATCACGATGGTCCCTCAAACCTTTCATCAAAAAACCCCTACAT
1 TGTCATCAAAGAACCCCTACATATCACGATGGTCCCTCAAACCTTTCATCAAAAAACCCCTACAT
* * * * * *
593646 ATCACGATGGTCTCTCAAGCTTTTCATCAATAAACCCCTACATATCACGATGGTTTCTCAAGC
66 AT-ACGATGGCCTCTAAAACTTATCATCAAGAAACCCCTACATATCACGATGGTCTCTCAAGC
* * **
593709 TGTCATCAAAGAACCCCTACATATCACGATGGTCCTTC-AAGC-TTCATCAAGGAACCCCTACAT
1 TGTCATCAAAGAACCCCTACATATCACGATGGTCCCTCAAACCTTTCATCAAAAAACCCCTACAT
*
593772 AT-TGATGGCC-CTTAAAACTTATCATCAAGAAACCCCTACATATCACGATGGTCTCTCAAG
66 ATACGATGGCCTC-TAAAACTTATCATCAAGAAACCCCTACATATCACGATGGTCTCTCAAG
593832 GTTTTCTTCA
Statistics
Matches: 110, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
123 1 0.01
124 49 0.45
126 21 0.19
127 3 0.03
128 36 0.33
ACGTcount: A:0.32, C:0.31, G:0.12, T:0.25
Consensus pattern (127 bp):
TGTCATCAAAGAACCCCTACATATCACGATGGTCCCTCAAACCTTTCATCAAAAAACCCCTACAT
ATACGATGGCCTCTAAAACTTATCATCAAGAAACCCCTACATATCACGATGGTCTCTCAAGC
Found at i:594076 original size:79 final size:80
Alignment explanation
Indices: 593903--594348 Score: 669
Period size: 79 Copynumber: 5.7 Consensus size: 80
593893 TATCTCAAGG
* * **
593903 GAGATAAAATCTTCTGTTTCAAGG-AAAATAATCTTGAATGAG--AAAATCTTCTGTTTCAAATA
1 GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGA
593965 AAAAC-ATCTTGAGT
66 AAAACAATCTTGAGT
* * *
593979 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATATTGAA-GAGATAAAATCTTCTATTTCAAGGA
1 GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGA
594043 AAAACAATCTTGAGT
66 AAAACAATCTTGAGT
*
594058 GAGATAAAATCTTATGTTTCAAGGAAAAATAATCTTG-ATGAGATAAAATCTTCTGTTTCAAGGA
1 GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGA
594122 AAAACAATCTTGAGT
66 AAAACAATCTTGAGT
* *
594137 GAGAAAAAATCTTATGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATATTCTGTTTCAAGGA
1 GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGA
*
594202 AAAACAATCTTGAAT
66 AAAACAATCTTGAGT
* * *
594217 GAGATAAAATCTTTTGTTTCAAGG--AAA-AA-CTTGAGTGAGATAAAATCTTCTATTTCAAGGA
1 GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGA
*
594278 AAAACAATCTTGAAT
66 AAAACAATCTTGAGT
*
594293 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAATTGAGATAAAATCTTCT
1 GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAA-TGAGATAAAATCTTCT
594349 TATCTCGAGT
Statistics
Matches: 338, Mismatches: 21, Indels: 17
0.90 0.06 0.05
Matches are distributed among these distances:
76 93 0.28
77 14 0.04
78 29 0.09
79 119 0.35
80 67 0.20
81 16 0.05
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (80 bp):
GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGA
AAAACAATCTTGAGT
Found at i:594078 original size:40 final size:40
Alignment explanation
Indices: 593903--594348 Score: 660
Period size: 40 Copynumber: 11.4 Consensus size: 40
593893 TATCTCAAGG
*
593903 GAGATAAAATCTTCTGTTTCAAGG-AAAATAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
** *
593942 GAG--AAAATCTTCTGTTTCAAATAAAAAC-ATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
* *
593979 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATATTGAA-
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
* *
594018 GAGATAAAATCTTCTATTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
* *
594058 GAGATAAAATCTTATGTTTCAAGGAAAAATAATCTTG-AT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
*
594097 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
* *
594137 GAGAAAAAATCTTATGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
*
594177 GAGATAAAATATTCTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
* *
594217 GAGATAAAATCTTTTGTTTCAAGG--AAA-AA-CTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
*
594253 GAGATAAAATCTTCTATTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
594293 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAATT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAA-T
594334 GAGATAAAATCTTCT
1 GAGATAAAATCTTCT
594349 TATCTCGAGT
Statistics
Matches: 363, Mismatches: 33, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
36 28 0.08
37 30 0.08
38 10 0.03
39 98 0.27
40 181 0.50
41 16 0.04
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (40 bp):
GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
Found at i:594130 original size:23 final size:22
Alignment explanation
Indices: 594104--594172 Score: 58
Period size: 23 Copynumber: 3.3 Consensus size: 22
594094 GATGAGATAA
594104 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTT-TGTTTCAAGGAAAAAC
** *
594127 AATC-TTGAGT-GA-G-AAAA-
1 AATCTTTGTTTCAAGGAAAAAC
594144 AATCTTATGTTTCAAGGAAAAAC
1 AATCTT-TGTTTCAAGGAAAAAC
594167 AATCTT
1 AATCTT
594173 GAATGAGATA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
17 4 0.12
18 5 0.15
19 4 0.12
20 2 0.06
21 4 0.12
22 5 0.15
23 10 0.29
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.30
Consensus pattern (22 bp):
AATCTTTGTTTCAAGGAAAAAC
Found at i:594293 original size:116 final size:116
Alignment explanation
Indices: 593903--594346 Score: 639
Period size: 116 Copynumber: 3.8 Consensus size: 116
593893 TATCTCAAGG
* * **
593903 GAGATAAAATCTTCTGTTTCAAGG-AAAATAATCTTGAATGAG--AAAATCTTCTGTTTCAAATA
1 GAGATAAAATCTTCTATTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGA
* *
593965 AAAAC-ATCTTGAGTGAGATAAAATCTTTTGTTTCAAGGAAAAACAATATTGA-A
66 AAAACAATCTTGAATGAGATAAAATCTTTTGTTTCAAGGAAAAAC----TTGAGT
* *
594018 GAGATAAAATCTTCTATTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTATGTTTCAAGGA
1 GAGATAAAATCTTCTATTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGA
* *
594083 AAAATAATCTTG-ATGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
66 AAAACAATCTTGAATGAGATAAAATCTTTTGTTTCAAGG--AAA-AA-CTTGAGT
* * * *
594137 GAGAAAAAATCTTATGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATATTCTGTTTCAAGGA
1 GAGATAAAATCTTCTATTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGA
594202 AAAACAATCTTGAATGAGATAAAATCTTTTGTTTCAAGGAAAAACTTGAGT
66 AAAACAATCTTGAATGAGATAAAATCTTTTGTTTCAAGGAAAAACTTGAGT
594253 GAGATAAAATCTTCTATTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGA
1 GAGATAAAATCTTCTATTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGA
594318 AAAACAATCTTGAATTGAGATAAAATCTT
66 AAAACAATCTTGAA-TGAGATAAAATCTT
594347 CTTATCTCGA
Statistics
Matches: 296, Mismatches: 22, Indels: 20
0.88 0.07 0.06
Matches are distributed among these distances:
115 23 0.08
116 98 0.33
117 16 0.05
118 52 0.18
119 76 0.26
120 28 0.09
121 2 0.01
122 1 0.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (116 bp):
GAGATAAAATCTTCTATTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTCAAGGA
AAAACAATCTTGAATGAGATAAAATCTTTTGTTTCAAGGAAAAACTTGAGT
Found at i:594527 original size:74 final size:74
Alignment explanation
Indices: 594377--594553 Score: 191
Period size: 74 Copynumber: 2.4 Consensus size: 74
594367 TCTCAAGCAC
* * * * * *
594377 ACAAATGTTGTTTTAAGAAAAA-ATAACATGTAGTGAAATGAAATGTCTTGTTTTGATAAAATCT
1 ACAAATCTTGTTTTAAGAAAAACA-ATC-TGTAGTCAAATGAAATGTCTTCTTTAGATAAAATCA
594441 GTCTCAGCGAG
64 GTCTCAGCGAG
*
594452 ACAAATCTTGTTTTAAGAAAAACAATCTTTAGTCAAATGAAATGTCTTCTTTCAG-TAAAA-CAG
1 ACAAATCTTGTTTTAAGAAAAACAATCTGTAGTCAAATGAAATGTCTTCTTT-AGATAAAATCAG
*
594515 TCTCAAGTGAG
65 TCTC-AGCGAG
* *
594526 ACGAAGTC-TATTTTAAGAAAAACAATCT
1 AC-AAATCTTGTTTTAAGAAAAACAATCT
594554 CCAGTGAGAT
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
73 6 0.07
74 53 0.60
75 28 0.32
76 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (74 bp):
ACAAATCTTGTTTTAAGAAAAACAATCTGTAGTCAAATGAAATGTCTTCTTTAGATAAAATCAGT
CTCAGCGAG
Found at i:595888 original size:88 final size:85
Alignment explanation
Indices: 595767--595941 Score: 264
Period size: 88 Copynumber: 2.0 Consensus size: 85
595757 CACATGAATC
*
595767 ATTTTTGTCTGAAATGGGCCTTCAAAATGCCCATATGGATCATTTCTATTATTTCATGCTGATGT
1 ATTTTTGTCTGAAATGGGCCTTCAAAATGCCCATATGGATCATTTCTATCATTTCA---TGATGT
*
595832 GAGCCTTCAGGATACTTCA-ATGG
63 GAGCCTTCAAGATAC-TCACATGG
*
595855 ATTTTTGTCTGAAATGGGCCTTC-AAATGCCCCATATGGATCATTTCTGTCATTTCATGATGTGA
1 ATTTTTGTCTGAAATGGGCCTTCAAAATG-CCCATATGGATCATTTCTATCATTTCATGATGTGA
595919 GCCTTCAAGATACTCACATGG
65 GCCTTCAAGATACTCACATGG
595940 AT
1 AT
595942 AATATAGACT
Statistics
Matches: 82, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
84 3 0.04
85 26 0.32
87 5 0.06
88 48 0.59
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (85 bp):
ATTTTTGTCTGAAATGGGCCTTCAAAATGCCCATATGGATCATTTCTATCATTTCATGATGTGAG
CCTTCAAGATACTCACATGG
Found at i:601954 original size:19 final size:20
Alignment explanation
Indices: 601918--601968 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
601908 GAATATAATG
* * *
601918 TTAAAATATGATTCATTTA-
1 TTAAAATTTAATTAATTTAC
601937 TTAAAATTTAATTAATTTAC
1 TTAAAATTTAATTAATTTAC
*
601957 TTCAAA-TTAATT
1 TTAAAATTTAATT
601969 GTTAAAAGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 22 0.81
20 5 0.19
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (20 bp):
TTAAAATTTAATTAATTTAC
Found at i:603652 original size:20 final size:20
Alignment explanation
Indices: 603627--603666 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
603617 GACTCGACGA
603627 TGACTCGACGGTGGTTTGGT
1 TGACTCGACGGTGGTTTGGT
**
603647 TGACTCGGTGGTGGTTTGGT
1 TGACTCGACGGTGGTTTGGT
603667 CAACGTGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.07, C:0.12, G:0.42, T:0.38
Consensus pattern (20 bp):
TGACTCGACGGTGGTTTGGT
Found at i:603925 original size:3 final size:3
Alignment explanation
Indices: 603919--603983 Score: 75
Period size: 3 Copynumber: 22.7 Consensus size: 3
603909 CCAAAATTAT
* *
603919 TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA -ATA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
603964 T-A TAA T-A TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
603984 TTTTTTTAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
2 7 0.13
3 46 0.85
4 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:608778 original size:43 final size:42
Alignment explanation
Indices: 608682--609133 Score: 347
Period size: 42 Copynumber: 10.6 Consensus size: 42
608672 CCGCTAATGT
* * *
608682 TAGCGGCGTTTGTGAAATAAAAACGCCGCAAAAAGTCAAGATCTA
1 TAGCGGCGTTT-TGGAA-ACAAACGCCGCAAAAGGTC-AGATCTA
* * *
608727 TAGCGGCGTTTTGGAAACAAACACCGCCAAAGGTCGAGATATA
1 TAGCGGCGTTTTGGAAACAAACGCCGCAAAAGGTC-AGATCTA
* * ** *
608770 TAGCGGCGTTTT-TATACAAACGCCATAAAAGATCGAGATCTA
1 TAGCGGCGTTTTGGAAACAAACGCCGCAAAAGGTC-AGATCTA
* ** * ** *
608812 TAGTGGTATTTTTGG-AACAAACACTACAAAAGGTCAGATTTA
1 TAGCGG-CGTTTTGGAAACAAACGCCGCAAAAGGTCAGATCTA
* * * * *
608854 TAGCGGCGTTTTTGTATACAAACGCCGTAAAAGGTCAGATATG
1 TAGCGGCG-TTTTGGAAACAAACGCCGCAAAAGGTCAGATCTA
* ** * *
608897 TAGCGGCGTTTTTGCTACAAACGCCGTAAAAGATCGAGATCTA
1 TAGCGGCGTTTTGGAAACAAACGCCGCAAAAGGTC-AGATCTA
* * * **
608940 TAGAGGCATTTTGG-AATAAACGCCGCAAAAGGTTGGATCTA
1 TAGCGGCGTTTTGGAAACAAACGCCGCAAAAGGTCAGATCTA
* *
608981 TAGCGACGTTTTTGGAAA-AAACGCCGCAAAATGTCAGATCTA
1 TAGCGGCG-TTTTGGAAACAAACGCCGCAAAAGGTCAGATCTA
* * *
609023 TAGCAGCGATTTTGGATACAAACGCCGCAAAAGGTCAGATCTG
1 TAGCGGCG-TTTTGGAAACAAACGCCGCAAAAGGTCAGATCTA
* * * * * *
609066 TAGCAGCGTTTT-TAGAACAAACACCGCAAAACGTCATAACTA
1 TAGCGGCGTTTTGGA-AACAAACGCCGCAAAAGGTCAGATCTA
* *
609108 TAACGGCGTTTTTGGATACAAACGCC
1 TAGCGGCG-TTTTGGAAACAAACGCC
609134 ACTAATTACC
Statistics
Matches: 321, Mismatches: 75, Indels: 24
0.76 0.18 0.06
Matches are distributed among these distances:
41 12 0.04
42 153 0.48
43 140 0.44
44 5 0.02
45 11 0.03
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (42 bp):
TAGCGGCGTTTTGGAAACAAACGCCGCAAAAGGTCAGATCTA
Found at i:608917 original size:85 final size:85
Alignment explanation
Indices: 608682--609133 Score: 437
Period size: 85 Copynumber: 5.3 Consensus size: 85
608672 CCGCTAATGT
* * * *
608682 TAGCGGCGTTTGTGAAATAAAAACGCCGCAAAAAGTCAAGATCTATAGCGGCG-TTTTGGAAACA
1 TAGCGGCGTTTTTG-GATACAAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGG-AACA
* *
608746 AACACCGCCAAAGGTCGAGATATA
63 AACACCGCAAAAGGTC-AGATCTA
** * * **
608770 TAGCGGCGTTTTT--ATACAAACGCCATAAAAGATCGAGATCTATAGTGGTATTTTTGGAACAAA
1 TAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAA
** *
608833 CACTACAAAAGGTCAGATTTA
65 CACCGCAAAAGGTCAGATCTA
* * * * **
608854 TAGCGGCGTTTTTGTATACAAACGCCGTAAAAGGTCAGATATGTAGCGGCGTTTTTGCTACAAAC
1 TAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAAC
* * *
608919 GCCGTAAAAGATCGAGATCTA
66 ACCGCAAAAGGTC-AGATCTA
* * * ** * *
608940 TAGAGGC-ATTTTGGA-ATAAACGCCGCAAAAGGTTGGATCTATAGCGACGTTTTTGGAAAAAAC
1 TAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAAC
* *
609003 GCCGCAAAATGTCAGATCTA
66 ACCGCAAAAGGTCAGATCTA
* * * * *
609023 TAGCAGCGATTTTGGATACAAACGCCGCAAAAGGTCAGATCTGTAGCAGCGTTTTTAGAACAAAC
1 TAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAAC
* * *
609088 ACCGCAAAACGTCATAACTA
66 ACCGCAAAAGGTCAGATCTA
*
609108 TAACGGCGTTTTTGGATACAAACGCC
1 TAGCGGCGTTTTTGGATACAAACGCC
609134 ACTAATTACC
Statistics
Matches: 296, Mismatches: 62, Indels: 15
0.79 0.17 0.04
Matches are distributed among these distances:
83 12 0.04
84 75 0.25
85 160 0.54
86 37 0.12
88 12 0.04
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (85 bp):
TAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAAC
ACCGCAAAAGGTCAGATCTA
Found at i:609263 original size:18 final size:19
Alignment explanation
Indices: 609231--609266 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
609221 TTTATATAAA
*
609231 TAACAACAACTATAAATTT
1 TAACAACAACAATAAATTT
609250 TAACAACAA-AATAAATT
1 TAACAACAACAATAAATT
609267 AAAATATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (19 bp):
TAACAACAACAATAAATTT
Found at i:612913 original size:83 final size:82
Alignment explanation
Indices: 612814--613126 Score: 367
Period size: 83 Copynumber: 3.8 Consensus size: 82
612804 GTTTGGTACT
* * * * * *
612814 AAAACGCCACTGAAGTACGTGTTTGTAGCGGCGTTTGGTATTAAAACGCCA-TAAAAGTACAAGT
1 AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTT-GTATAAAAACGCCACT-AAAGTACGAGT
612878 CTATAGCGGCGTTTATATA
64 CTATAGCGGCGTTTATATA
* * *
612897 AAAACGCCACTAAAGTATGAGTCTATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGCGTCT
1 AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCT
* *
612962 ATAGCGGCGTTTGGTATT
66 ATAGCGGCGTTT-ATATA
* * * * *
612980 AAAATGCCACAAAAGTACGAGTCTATAGCGGTGTTTATATAAAAACGCCACTAAAGTACGAGTTT
1 AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCT
* *
613045 ATAGCGGCGTTTTTGTA
66 ATAGCGGCGTTTATATA
* * * * * * *
613062 AAACCGTCACTATAGTATGAGTCTATAGCAGCGTTTGTATAAAAACGCCACTAAAGAAAGAGTCT
1 AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCT
613127 TTTGCGGTGT
Statistics
Matches: 194, Mismatches: 34, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
82 90 0.46
83 104 0.54
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.27
Consensus pattern (82 bp):
AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCT
ATAGCGGCGTTTATATA
Found at i:612969 original size:124 final size:124
Alignment explanation
Indices: 612799--613116 Score: 415
Period size: 124 Copynumber: 2.6 Consensus size: 124
612789 TATGACAATT
* * * *
612799 GCGGCGTTTGGTACT-AAAACGCCACTGAAGTACGTGTTTGTAGCGGCGTTTGGTATTAAAACGC
1 GCGGCGTTT-GTA-TAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGC
*
612863 CATAAAAGTACAAGTCTATAGCGGCGTTTATATAAAAACGCCACTAAAGTATGAGTCTATA
64 CATAAAAGTACAAGTCTATAGCGGCGTTTATATAAAAACGCCACTAAAGTACGAGTCTATA
* * *
612924 GCGGCGTTTGTATAAAAATGCCACTAAAGTACGCGTCTATAGCGGCGTTTGGTATTAAAATGCCA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCA
* * * *
612989 CAAAAGTACGAGTCTATAGCGGTGTTTATATAAAAACGCCACTAAAGTACGAGTTTATA
66 TAAAAGTACAAGTCTATAGCGGCGTTTATATAAAAACGCCACTAAAGTACGAGTCTATA
* * * * * * * *
613048 GCGGCGTTTTTGTAAAACCGTCACTATAGTATGAGTCTATAGCAGCGTTT-GTATAAAAACGCCA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCA
613112 CTAAA
66 -TAAA
613117 GAAAGAGTCT
Statistics
Matches: 168, Mismatches: 23, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
123 13 0.08
124 146 0.87
125 9 0.05
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28
Consensus pattern (124 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCA
TAAAAGTACAAGTCTATAGCGGCGTTTATATAAAAACGCCACTAAAGTACGAGTCTATA
Found at i:613147 original size:41 final size:41
Alignment explanation
Indices: 612799--613140 Score: 373
Period size: 41 Copynumber: 8.3 Consensus size: 41
612789 TATGACAATT
* * * *
612799 GCGGCGTTTGGTACT-AAAACGCCACTGAAGTACGTGTTTGTA
1 GCGGCGTTT-GTA-TAAAAACGCCACTAAAGTACGAGTCTATA
* *
612841 GCGGCGTTTGGTATTAAAACGCCA-TAAAAGTACAAGTCTATA
1 GCGGCGTTT-GTATAAAAACGCCACT-AAAGTACGAGTCTATA
* *
612883 GCGGCGTTTATATAAAAACGCCACTAAAGTATGAGTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATA
* *
612924 GCGGCGTTTGTATAAAAATGCCACTAAAGTACGCGTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATA
* * *
612965 GCGGCGTTTGGTATTAAAATGCCACAAAAGTACGAGTCTATA
1 GCGGCGTTT-GTATAAAAACGCCACTAAAGTACGAGTCTATA
* * *
613007 GCGGTGTTTATATAAAAACGCCACTAAAGTACGAGTTTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATA
* * * * * *
613048 GCGGCGTTTTTGTAAAACCGTCACTATAGTATGAGTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATA
* * * * *
613089 GCAGCGTTTGTATAAAAACGCCACTAAAGAAAGAGTCTTTT
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATA
*
613130 GCGGTGTTTGT
1 GCGGCGTTTGT
613141 TCAAAAAACG
Statistics
Matches: 254, Mismatches: 42, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
41 174 0.69
42 80 0.31
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.29
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATA
Found at i:613408 original size:21 final size:21
Alignment explanation
Indices: 613380--613436 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
613370 AGTTTAACAA
*
613380 TATCGATACTTCAACTATGGG
1 TATCGATACTTCAACTAGGGG
*
613401 TATTGATACTTCAACTAGGGG
1 TATCGATACTTCAACTAGGGG
613422 TATCGATACTATCAA
1 TATCGATACT-TCAA
613437 TCCTATTAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 28 0.88
22 4 0.12
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (21 bp):
TATCGATACTTCAACTAGGGG
Found at i:617331 original size:30 final size:28
Alignment explanation
Indices: 617307--617374 Score: 111
Period size: 30 Copynumber: 2.4 Consensus size: 28
617297 AAAACTTACT
617307 TAAA-CTTTAATAATCATTCTAAAACCC
1 TAAACCTTTAATAATCATTCTAAAACCC
617334 TAAACCTCTTTAATAATCATTCTAAAACCC
1 TAAA-C-CTTTAATAATCATTCTAAAACCC
617364 TAAACCTTTAA
1 TAAACCTTTAA
617375 GGTAAGGTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
27 4 0.11
28 6 0.16
29 1 0.03
30 27 0.71
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.34
Consensus pattern (28 bp):
TAAACCTTTAATAATCATTCTAAAACCC
Found at i:619566 original size:20 final size:20
Alignment explanation
Indices: 619518--619576 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
619508 AATCATATTC
*
619518 ACTGGTAATCTTTTATTCCT
1 ACTGGTAATCTTTTATTTCT
* * *
619538 ATTGATAATCTTTTATTTTT
1 ACTGGTAATCTTTTATTTCT
*
619558 ACTGGTAATCTTATATTTC
1 ACTGGTAATCTTTTATTTC
619577 GTAAATCAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.24, C:0.14, G:0.08, T:0.54
Consensus pattern (20 bp):
ACTGGTAATCTTTTATTTCT
Found at i:620929 original size:2 final size:2
Alignment explanation
Indices: 620922--620954 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
620912 CCCATTAACC
620922 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
620955 GCTCTATAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:628144 original size:8 final size:8
Alignment explanation
Indices: 628128--628178 Score: 93
Period size: 8 Copynumber: 6.4 Consensus size: 8
628118 TCCATCTAGC
*
628128 TATATATA
1 TATACATA
628136 TATACATA
1 TATACATA
628144 TATACATA
1 TATACATA
628152 TATACATA
1 TATACATA
628160 TATACATA
1 TATACATA
628168 TATACATA
1 TATACATA
628176 TAT
1 TAT
628179 GTTGGGCAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
8 42 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (8 bp):
TATACATA
Found at i:630765 original size:14 final size:15
Alignment explanation
Indices: 630740--630768 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
630730 AATTTAATTT
630740 AATTTAAGAATTTAG
1 AATTTAAGAATTTAG
630755 AATTT-AGAATTTAG
1 AATTTAAGAATTTAG
630769 TATATTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (15 bp):
AATTTAAGAATTTAG
Found at i:635231 original size:30 final size:31
Alignment explanation
Indices: 635164--635232 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
635154 TAAGTCTTTT
* *
635164 AAATTTTATTTTTATTCAGTTTAATTATTTT
1 AAATTTTATTTTTATTCAGTTTAATTACTTA
635195 AAATTTTATTTTTATTCAGTTTAATT-CTTA
1 AAATTTTATTTTTATTCAGTTTAATTACTTA
635225 AAATTTTA
1 AAATTTTA
635233 GTTAAATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 10 0.28
31 26 0.72
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (31 bp):
AAATTTTATTTTTATTCAGTTTAATTACTTA
Found at i:635232 original size:37 final size:31
Alignment explanation
Indices: 635160--635220 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
635150 ATGTTAAGTC
635160 TTTTAAATTTTATTTTTATTCAGTTTAATTA
1 TTTTAAATTTTATTTTTATTCAGTTTAATTA
635191 TTTTAAATTTTATTTTTATTCAGTTTAATT
1 TTTTAAATTTTATTTTTATTCAGTTTAATT
635221 CTTAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (31 bp):
TTTTAAATTTTATTTTTATTCAGTTTAATTA
Found at i:635920 original size:16 final size:17
Alignment explanation
Indices: 635899--635937 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
635889 AAGTATTCAT
635899 AATATTTT-TTTA-ATAA
1 AATATTTTATTTATA-AA
635915 AATATTTTATTTATAAA
1 AATATTTTATTTATAAA
635932 AATATT
1 AATATT
635938 ATTAATGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
17 12 0.57
18 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATATTTTATTTATAAA
Found at i:639116 original size:21 final size:21
Alignment explanation
Indices: 639090--639142 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
639080 ACTTTTTAAA
639090 AAAAAATTAAATTAACATTAG
1 AAAAAATTAAATTAACATTAG
*
639111 AAAAAATAAAATTAACATTAG
1 AAAAAATTAAATTAACATTAG
639132 AAAAAA-TAAAT
1 AAAAAATTAAAT
639143 AATATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (21 bp):
AAAAAATTAAATTAACATTAG
Found at i:639220 original size:10 final size:10
Alignment explanation
Indices: 639187--639235 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
639177 GTGTATTAGT
639187 TTAAATAAAA
1 TTAAATAAAA
* *
639197 TTAAACATAA
1 TTAAATAAAA
*
639207 -TAAATAGAA
1 TTAAATAAAA
639216 TTAAATAAAA
1 TTAAATAAAA
639226 TTGAAATAAA
1 TT-AAATAAA
639236 GGACAAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
9 7 0.22
10 18 0.56
11 7 0.22
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (10 bp):
TTAAATAAAA
Found at i:640598 original size:18 final size:19
Alignment explanation
Indices: 640557--640601 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
640547 ATATATATAT
*
640557 ATATATATAGTCTTCATAA
1 ATATATATAGTCTTCAAAA
* *
640576 CTATATAT-GTTTTCAAAA
1 ATATATATAGTCTTCAAAA
640594 ATATATAT
1 ATATATAT
640602 TATATTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.44
Consensus pattern (19 bp):
ATATATATAGTCTTCAAAA
Found at i:640614 original size:20 final size:21
Alignment explanation
Indices: 640577--640672 Score: 86
Period size: 22 Copynumber: 4.4 Consensus size: 21
640567 TCTTCATAAC
* *
640577 TATATATGTTTTCAAAA-ATA
1 TATATATATTTTTAAAATATA
*
640597 TATATTATATTTTTAAAAAATTA
1 TATA-TATATTTTTAAAATA-TA
* * *
640620 TATATATATATATATATATATA
1 TATATATATTTTTA-AAATATA
640642 TATATATATATTTTAAAATATA
1 TATATATAT-TTTTAAAATATA
*
640664 TATTTATAT
1 TATATATAT
640673 AATAAAACTA
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
20 4 0.07
21 11 0.18
22 34 0.56
23 12 0.20
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (21 bp):
TATATATATTTTTAAAATATA
Found at i:640678 original size:20 final size:20
Alignment explanation
Indices: 640591--640686 Score: 77
Period size: 20 Copynumber: 4.5 Consensus size: 20
640581 TATGTTTTCA
*
640591 AAAATATATATTATATTTTTAA-
1 AAAATATATA-TATA--TATAAT
640613 AAAATTATATATATATATATAT
1 AAAA-TATATATATATATA-AT
* **
640635 ATATATATATATATATATTTT
1 A-AAATATATATATATATAAT
*
640656 AAAATATATATTTATATAAT
1 AAAATATATATATATATAAT
640676 AAAACTATATA
1 AAAA-TATATA
640687 CATAATTATA
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
20 22 0.36
21 9 0.15
22 22 0.36
23 8 0.13
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAATATATATATATATAAT
Found at i:640686 original size:2 final size:2
Alignment explanation
Indices: 640618--640673 Score: 71
Period size: 2 Copynumber: 29.0 Consensus size: 2
640608 TTTAAAAAAT
*
640618 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TT TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
640658 AA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA
640674 ATAAAACTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:641727 original size:64 final size:64
Alignment explanation
Indices: 641653--641839 Score: 164
Period size: 64 Copynumber: 2.9 Consensus size: 64
641643 GCATCAATCC
*
641653 ATGCATCGATGCACCATT-GAATAAATT-GAACATCGAATGCATTTCATGCATCAATGCACTCTC
1 ATGCATCGATGCA-C-TTGGAATAAATTAAAACATCGAATGCATTTCATGCATCAATGCACTCTC
641716 T
64 T
** ** * *** *
641717 ATGCATCGATGCACTTGGGTTTTATTAAAACATCGAATGCATTTCATGCATCGATGCACAAGCA
1 ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATGCATCAATGCACTCTCT
* * * ** * * *
641781 ATGCACCGATGCACTCAGG-CTATTTTCAAACATCGAATGCATTTTATGCATCGATGCAC
1 ATGCATCGATGCACT-TGGAATAAATTAAAACATCGAATGCATTTCATGCATCAATGCAC
641840 ACTTGGTGAA
Statistics
Matches: 103, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
62 2 0.02
63 6 0.06
64 93 0.90
65 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (64 bp):
ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATGCATCAATGCACTCTCT
Found at i:641840 original size:64 final size:64
Alignment explanation
Indices: 641681--641840 Score: 205
Period size: 64 Copynumber: 2.5 Consensus size: 64
641671 GAATAAATTG
* *** * * * * *
641681 AACATCGAATGCATTTCATGCATCAATGCACTCTCTATGCATCGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTAGGCTATTATTAA
*
641745 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTCAGGCTATT-TTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACT-AGGCTATTATTAA
*
641809 AACATCGAATGCATTTTATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
641841 CTTGGTGAAC
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
64 79 0.94
65 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTAGGCTATTATTAA
Found at i:641853 original size:64 final size:63
Alignment explanation
Indices: 641681--641860 Score: 202
Period size: 64 Copynumber: 2.8 Consensus size: 63
641671 GAATAAATTG
* * * * * *
641681 AACATCGAATGCATTTCATGCATCAATGCACTCTCTATGCATCGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACT-TATGCACCGATGCACTAGGCTATTATTAA
* *
641745 AACATCGAATGCATTTCATGCATCGATGCACAAGC-AATGCACCGATGCACTCAGGCTATT-TTC
1 AACATCGAATGCATTTCATGCATCGATGCAC-A-CTTATGCACCGATGCACT-AGGCTATTATTA
641808 A
63 A
* * *
641809 AACATCGAATGCATTTTATGCATCGATGCACACTTGGTGAACCGATGCACTA
1 AACATCGAATGCATTTCATGCATCGATGCACACTT-ATGCACCGATGCACTA
641861 AGTGTTCCAA
Statistics
Matches: 99, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 90 0.91
65 5 0.05
66 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTATGCACCGATGCACTAGGCTATTATTAA
Found at i:647633 original size:24 final size:25
Alignment explanation
Indices: 647551--647631 Score: 77
Period size: 24 Copynumber: 3.5 Consensus size: 25
647541 ACATTTAATA
*
647551 GTGCATCGATGCATC-CCTTTGAAT
1 GTGCATCGATGCATCACCCTTGAAT
* *
647575 GTGCATCGATACATCA-GC-TG-A-
1 GTGCATCGATGCATCACCCTTGAAT
*
647596 -TGCACCGATGCA-CACCCTTGAAT
1 GTGCATCGATGCATCACCCTTGAAT
647619 GTGCATCGATGCA
1 GTGCATCGATGCA
647632 CAAGAGACAT
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
19 2 0.05
20 11 0.25
21 2 0.05
22 2 0.05
23 2 0.05
24 25 0.57
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (25 bp):
GTGCATCGATGCATCACCCTTGAAT
Found at i:649198 original size:21 final size:21
Alignment explanation
Indices: 649156--649199 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
649146 ACTCCGGGAG
* *
649156 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
649177 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
649198 CT
1 CT
649200 CCTCCACCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:649899 original size:15 final size:15
Alignment explanation
Indices: 649879--649909 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
649869 TAAGGGGGAG
649879 TAATAGTAATTTTGA
1 TAATAGTAATTTTGA
649894 TAATAGTAATTTTGA
1 TAATAGTAATTTTGA
649909 T
1 T
649910 TTCAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (15 bp):
TAATAGTAATTTTGA
Found at i:650327 original size:64 final size:64
Alignment explanation
Indices: 650254--650413 Score: 214
Period size: 64 Copynumber: 2.5 Consensus size: 64
650244 GAATAAATTG
*** * * * * *
650254 AACATCGAATGCATTTCATGCATCGATGCACTCTCTATGCATCGATGCACT-TGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTCAGGCTATT-TTAA
*
650318 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTCAGGCTATTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTCAGGCTATTTTAA
*
650382 AACATCGAATGCATTTTATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
650414 CTTGGTGCAT
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
64 80 0.94
65 5 0.06
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTCAGGCTATTTTAA
Found at i:650430 original size:64 final size:63
Alignment explanation
Indices: 650254--650433 Score: 211
Period size: 64 Copynumber: 2.8 Consensus size: 63
650244 GAATAAATTG
* * * *
650254 AACATCGAATGCATTTCATGCATCGATGCACTCTCTATGCATCGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACT-TATGCATCGATGCACTAGGCTATTATTAA
* * *
650318 AACATCGAATGCATTTCATGCATCGATGCACAAGC-AATGCACCGATGCACTCAGGCTATT-TTC
1 AACATCGAATGCATTTCATGCATCGATGCAC-A-CTTATGCATCGATGCACT-AGGCTATTATTA
650381 A
63 A
* * *
650382 AACATCGAATGCATTTTATGCATCGATGCACACTTGGTGCATCAATGCACTA
1 AACATCGAATGCATTTCATGCATCGATGCACACTT-ATGCATCGATGCACTA
650434 AGTGTTCCAA
Statistics
Matches: 99, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 90 0.91
65 5 0.05
66 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTATGCATCGATGCACTAGGCTATTATTAA
Found at i:654279 original size:14 final size:14
Alignment explanation
Indices: 654262--654307 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
654252 GATTTATGTT
*
654262 AAATGGATTACCTA
1 AAATGGATTACATA
*
654276 AAATTGATTACATA
1 AAATGGATTACATA
* *
654290 AAATGAATTACATC
1 AAATGGATTACATA
654304 AAAT
1 AAAT
654308 ATATTTTACA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (14 bp):
AAATGGATTACATA
Found at i:654718 original size:21 final size:20
Alignment explanation
Indices: 654668--654721 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
654658 AGTACATATT
654668 AATATAATATTATTAAAATTA
1 AATATAATATTA-TAAAATTA
*
654689 TATAATAATATTA-AATAATTA
1 AAT-ATAATATTATAA-AATTA
654710 AATATTAATATT
1 AATA-TAATATT
654722 TTTATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 3 0.11
21 16 0.57
22 9 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATAATATTATAAAATTA
Done.