Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008166.1 Hibiscus syriacus cultivar Beakdansim tig00110747_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: 2544747
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 10
Found at i:443844 original size:45 final size:45
Alignment explanation
Indices: 443768--443998 Score: 311
Period size: 45 Copynumber: 5.1 Consensus size: 45
443758 TATATTAAAT
443768 ATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGAC
1 ATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGAC
* * * *
443813 ATGACTAAAAGATTGACTCCTTTTCATGAGAAAGTCAAGAATGAC
1 ATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGAC
* * * * *
443858 ATCACTAAAAGGTTAAC-CTCTTTTCGCGAGAAAGCCAAGAAGGAC
1 ATCACTAAAAGATTGACTC-CTCTTCACGAGAAAGTCAAGAAGGAC
* * *
443903 AACACTAAAAGATTGACTCCTCTTCACAAGAAAGTGAAGAAGGAC
1 ATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGAC
* * *
443948 TTCACTAAAAGATTGACTCATCTTCAAGAGAAAGTCAAGAAGGAC
1 ATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGAC
443993 ATCACT
1 ATCACT
443999 GTTGAAAACA
Statistics
Matches: 158, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
44 1 0.01
45 156 0.99
46 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (45 bp):
ATCACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGAC
Found at i:446242 original size:19 final size:20
Alignment explanation
Indices: 446201--446246 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
446191 GGATTATGAG
* *
446201 AAATTATTTTTAAAATATAA
1 AAATGATTTTCAAAATATAA
446221 AAATGATTTTCAAAAT-TGAA
1 AAATGATTTTCAAAATAT-AA
446241 AAATGA
1 AAATGA
446247 AAATAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (20 bp):
AAATGATTTTCAAAATATAA
Found at i:450075 original size:23 final size:21
Alignment explanation
Indices: 450023--450084 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
450013 TTTTGGTACA
*
450023 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
450043 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
450064 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
450085 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:452070 original size:19 final size:19
Alignment explanation
Indices: 452043--452079 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
452033 TTTTGGAATG
*
452043 TTTGATTGATTGACTTGAA
1 TTTGATTGATTGAATTGAA
*
452062 TTTGTTTGATTGAATTGA
1 TTTGATTGATTGAATTGA
452080 TCTGGTGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (19 bp):
TTTGATTGATTGAATTGAA
Found at i:452197 original size:17 final size:18
Alignment explanation
Indices: 452175--452213 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
452165 TATTATATAA
452175 TCAA-TTGGCTAATGATT
1 TCAATTTGGCTAATGATT
452192 TCAATTTGGCTAATGATT
1 TCAATTTGGCTAATGATT
452210 TCAA
1 TCAA
452214 ACCTTGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (18 bp):
TCAATTTGGCTAATGATT
Found at i:454118 original size:23 final size:24
Alignment explanation
Indices: 454092--454145 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
454082 TTTCAAGAGG
454092 TGAAAAAGTTTGATG-AAGAAGTT
1 TGAAAAAGTTTGATGAAAGAAGTT
* * *
454115 TGAAAATGTTTTATGAAAGAATTT
1 TGAAAAAGTTTGATGAAAGAAGTT
*
454139 TAAAAAA
1 TGAAAAA
454146 TATTTGAGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (24 bp):
TGAAAAAGTTTGATGAAAGAAGTT
Found at i:455912 original size:12 final size:12
Alignment explanation
Indices: 455895--455925 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
455885 GCATCGATGC
*
455895 ACAGTACCTGCT
1 ACAGTAACTGCT
455907 ACAGTAACTGCT
1 ACAGTAACTGCT
455919 ACAGTAA
1 ACAGTAA
455926 TTCTGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (12 bp):
ACAGTAACTGCT
Found at i:456393 original size:44 final size:44
Alignment explanation
Indices: 456283--456395 Score: 149
Period size: 45 Copynumber: 2.5 Consensus size: 44
456273 TACCATTTAT
*
456283 TTCCATAAGCTCGTAAGCTTA-TTTTACCAAAATAATTACCATT
1 TTCCATAAGCTCGTAAGCTTATTTTTACCAAAATAATTACCATA
* * *
456326 TGTCCCATAAGCTCGTAAGCTTATTTTTACC-ATATACTTGCCAATA
1 T-T-CCATAAGCTCGTAAGCTTATTTTTACCAAAATAATTACC-ATA
456372 TTCCATAAGCTCGTAAGCTTATTT
1 TTCCATAAGCTCGTAAGCTTATTT
456396 GCATACTTAC
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
43 1 0.02
44 23 0.37
45 28 0.45
46 10 0.16
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (44 bp):
TTCCATAAGCTCGTAAGCTTATTTTTACCAAAATAATTACCATA
Found at i:457461 original size:30 final size:30
Alignment explanation
Indices: 457427--457493 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
457417 AACCCATCAA
* * *
457427 TTTTCTAGAATTTAC-AAATTGATCTCCAAC
1 TTTTCTAAAACTTACAAAATTG-TCCCCAAC
*
457457 TTTTC-AAAACTTACAAAATTGTCCCCAAG
1 TTTTCTAAAACTTACAAAATTGTCCCCAAC
457486 TTTTCTAA
1 TTTTCTAA
457494 GGCTTGTAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.39
Consensus pattern (30 bp):
TTTTCTAAAACTTACAAAATTGTCCCCAAC
Found at i:460933 original size:13 final size:13
Alignment explanation
Indices: 460901--460935 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
460891 GATTTTCTAA
*
460901 TTGAAAATAAATT
1 TTGAAATTAAATT
*
460914 TTGAAATTAAGTT
1 TTGAAATTAAATT
460927 TTGAAATTA
1 TTGAAATTA
460936 CTCGCCCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
TTGAAATTAAATT
Found at i:461700 original size:240 final size:240
Alignment explanation
Indices: 461277--461756 Score: 951
Period size: 240 Copynumber: 2.0 Consensus size: 240
461267 ATCCAAAAGC
461277 ATTCAAAATGTTGAAAACAATAAGGTCGAAGCTAAGCAAGAAAACAGGGCCTAATCGCCCATCGG
1 ATTCAAAATGTTGAAAACAATAAGGTCGAAGCTAAGCAAGAAAACAGGGCCTAATCGCCCATCGG
461342 TGGATCAGGAGGAGATAAGTGTGTCCAAATGTTGGCCACATCACATGAAATTGGATCGACCCTCT
66 TGGATCAGGAGGAGATAAGTGTGTCCAAATGTTGGCCACATCACATGAAATTGGATCGACCCTCT
461407 CATCCAAAGTGTCGAAATGATGATTCATCATTTCGTTGGTAGCAGTCATATGTGATTCGATGGAT
131 CATCCAAAGTGTCGAAATGATGATTCATCATTTCGTTGGTAGCAGTCATATGTGATTCGATGGAT
461472 CCAAACCTCATATCAAGATTCTCCATAAATGATCGAAAGTATAGA
196 CCAAACCTCATATCAAGATTCTCCATAAATGATCGAAAGTATAGA
*
461517 ATTCAAAATGTTGAAAACAATAAGGTCGAAGCTAAGCAAGAAAACAGGGCCTAATCGCCTATCGG
1 ATTCAAAATGTTGAAAACAATAAGGTCGAAGCTAAGCAAGAAAACAGGGCCTAATCGCCCATCGG
461582 TGGATCAGGAGGAGATAAGTGTGTCCAAATGTTGGCCACATCACATGAAATTGGATCGACCCTCT
66 TGGATCAGGAGGAGATAAGTGTGTCCAAATGTTGGCCACATCACATGAAATTGGATCGACCCTCT
461647 CATCCAAAGTGTCGAAATGATGATTCATCATTTCGTTGGTAGCAGTCATATGTGATTCGATGGAT
131 CATCCAAAGTGTCGAAATGATGATTCATCATTTCGTTGGTAGCAGTCATATGTGATTCGATGGAT
461712 CCAAACCTCATATCAAGATTCTCCATAAATGATCGAAAGTATAGA
196 CCAAACCTCATATCAAGATTCTCCATAAATGATCGAAAGTATAGA
461757 GGCACTTGAT
Statistics
Matches: 239, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
240 239 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (240 bp):
ATTCAAAATGTTGAAAACAATAAGGTCGAAGCTAAGCAAGAAAACAGGGCCTAATCGCCCATCGG
TGGATCAGGAGGAGATAAGTGTGTCCAAATGTTGGCCACATCACATGAAATTGGATCGACCCTCT
CATCCAAAGTGTCGAAATGATGATTCATCATTTCGTTGGTAGCAGTCATATGTGATTCGATGGAT
CCAAACCTCATATCAAGATTCTCCATAAATGATCGAAAGTATAGA
Found at i:463425 original size:22 final size:21
Alignment explanation
Indices: 463369--463425 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
463359 AGACCCCGTG
*
463369 GGGGGTATCGATT-CCCTCGA
1 GGGGGTATCGATTCCCCTCAA
* *
463389 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGTATCGATTCCCC-TCAA
*
463411 GGTGGTATCGATTCC
1 GGGGGTATCGATTCC
463426 TCCTGTACCA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 11 0.38
21 3 0.10
22 15 0.52
ACGTcount: A:0.16, C:0.25, G:0.33, T:0.26
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCTCAA
Found at i:468972 original size:20 final size:22
Alignment explanation
Indices: 468935--468977 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
468925 AACCATTCAA
468935 GGGGGAATCGGTACCCCT-TGG
1 GGGGGAATCGGTACCCCTCTGG
*
468956 GGGGGAATCGGT-TCCCTCTGG
1 GGGGGAATCGGTACCCCTCTGG
468977 G
1 G
468978 CAATCTGCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.12, C:0.23, G:0.44, T:0.21
Consensus pattern (22 bp):
GGGGGAATCGGTACCCCTCTGG
Found at i:469900 original size:45 final size:45
Alignment explanation
Indices: 469851--470266 Score: 598
Period size: 45 Copynumber: 9.2 Consensus size: 45
469841 GTTTTCATTA
* * * **
469851 CATAAATAAAATGTATAATGGTGCATTAAAGGCATGAAATTATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
469896 CATAAATGAAATTCATAACGGTTCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
** * *
469941 CATAAATGAAATATATAACAGTGCATTAAAGGCATGAAATGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * *
469986 CATAAATGAAATGCATAACGATGTATTAAAGGCATGAAATGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * * *
470031 TATAAATGAAATGCATATCGGTGCATTAAAGGCATGAAAGAATAC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
470076 CATAAATGAAATGCATAATGGTGCATTAAATGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
470121 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
470166 CATAAATGAAATGCATAACGATGCATTAAAGTCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * * *
470211 AATAAATGAAATGCATAACTGTGCATTAAAGGCATGAAATGATGT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
470256 CATAAATGAAA
1 CATAAATGAAA
470267 ATAATGAATA
Statistics
Matches: 330, Mismatches: 41, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 330 1.00
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.24
Consensus pattern (45 bp):
CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
Found at i:469991 original size:21 final size:21
Alignment explanation
Indices: 469967--470036 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
469957 AACAGTGCAT
*
469967 TAAAGGCATGAAATGATGCCA
1 TAAAGGCATGAAATGATGCTA
** *
469988 TAAATGAAATGCATAACGATG-TA
1 TAAA-GGCATG-A-AATGATGCTA
470011 TTAAAGGCATGAAATGATGCTA
1 -TAAAGGCATGAAATGATGCTA
470033 TAAA
1 TAAA
470037 TGAAATGCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
21 14 0.38
22 7 0.19
23 6 0.16
24 10 0.27
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (21 bp):
TAAAGGCATGAAATGATGCTA
Found at i:474535 original size:14 final size:15
Alignment explanation
Indices: 474518--474548 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
474508 ACTTTTGATA
474518 AATTTGATAAAT-TT
1 AATTTGATAAATGTT
474532 AATTTGATAAATGTT
1 AATTTGATAAATGTT
474547 AA
1 AA
474549 AGTATCAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (15 bp):
AATTTGATAAATGTT
Found at i:475910 original size:19 final size:19
Alignment explanation
Indices: 475886--475953 Score: 55
Period size: 25 Copynumber: 3.2 Consensus size: 19
475876 TAAATGAAAT
475886 GCATAACGGTGCATTAAAG
1 GCATAACGGTGCATTAAAG
*
475905 GCATAAAAGGATGCCATAAATAAAG
1 GCAT-AACGG-TG-CAT---TAAAG
*
475930 TGCATAACGGTGCATTAAAA
1 -GCATAACGGTGCATTAAAG
475950 GCAT
1 GCAT
475954 GAAAGGATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
19 8 0.21
20 8 0.21
21 2 0.05
22 3 0.08
23 3 0.08
24 2 0.05
25 9 0.23
26 4 0.10
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.21
Consensus pattern (19 bp):
GCATAACGGTGCATTAAAG
Found at i:476263 original size:45 final size:45
Alignment explanation
Indices: 475784--476240 Score: 736
Period size: 45 Copynumber: 10.2 Consensus size: 45
475774 GTTTTCATTA
*
475784 CATAAATGAAATGCATAACAGTGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
475829 CATAAATGAAATGCATAATGGTGCATTAAAGGCATGAAATGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
*
475874 CATAAATGAAATGCATAACGGTGCATTAAAGGCATAAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
475919 CATAAAT-AAAGTGCATAACGGTGCATTAAAAGCATGAAAGGATGT
1 CATAAATGAAA-TGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * *
475964 CATAAATGAAATGCATAACAGTGTATTAAAGTCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * *
476009 TATAAATGAAATGTATAACAGTGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
476054 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
*
476099 CATAAATGAAATGTATAACGGTGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * *
476144 CATAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGAATGT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
476189 CATAAATGAAATGCACAACTGTGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
476234 CATAAAT
1 CATAAAT
476241 AAAAATAATG
Statistics
Matches: 379, Mismatches: 31, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
44 3 0.01
45 373 0.98
46 3 0.01
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (45 bp):
CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
Found at i:480118 original size:14 final size:14
Alignment explanation
Indices: 480096--480140 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
480086 ATGTAAGTTA
*
480096 AATAT-TAATATTT
1 AATATATAATAATT
480109 AATATATAATAATT
1 AATATATAATAATT
480123 AA-ATAATAATAA-T
1 AATAT-ATAATAATT
480136 AATAT
1 AATAT
480141 CGGACAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATATATAATAATT
Found at i:480358 original size:2 final size:2
Alignment explanation
Indices: 480351--480375 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
480341 TTATTTTTGT
480351 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
480376 TGAATAGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:481372 original size:3 final size:3
Alignment explanation
Indices: 481357--481390 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
481347 GGTTAAAAAA
*
481357 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
481391 AGTGTGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.04
3 27 0.96
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:482811 original size:5 final size:5
Alignment explanation
Indices: 482801--482833 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
482791 TATTAAAGTT
482801 TATTA TATTA TATTA TATTA TA-TA TATATA TAT
1 TATTA TATTA TATTA TATTA TATTA TAT-TA TAT
482834 ACACACATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 17 0.65
6 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:483294 original size:21 final size:20
Alignment explanation
Indices: 483270--483311 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
483260 AATGTCAAGA
483270 TTTCT-TTTCATATTACATAAT
1 TTTCTCTTTCA-ATTA-ATAAT
*
483291 TTTCTCTTTTAATTAATAAT
1 TTTCTCTTTCAATTAATAAT
483311 T
1 T
483312 CAAAACAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTCTCTTTCAATTAATAAT
Found at i:483863 original size:28 final size:26
Alignment explanation
Indices: 483813--483871 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 26
483803 AATTTATTCA
*
483813 TATTATTAAAATATAATATAATATCTTT
1 TATTATTAAAATATAATAGAATA--TTT
* *
483841 TATTATTATAATATAATCGAATATTT
1 TATTATTAAAATATAATAGAATATTT
483867 TATTA
1 TATTA
483872 CAATATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 8 0.29
28 20 0.71
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (26 bp):
TATTATTAAAATATAATAGAATATTT
Found at i:483901 original size:23 final size:24
Alignment explanation
Indices: 483875--483943 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 24
483865 TTTATTACAA
*
483875 TATTAAAAACTA-TAAT-ATTATAT
1 TATTAAAAA-TATTAATAAATATAT
*
483898 TATTAGAAATATTAATAAATATAT
1 TATTAAAAATATTAATAAATATAT
*
483922 T-TTAAATAT-TTAAT-AATATAT
1 TATTAAAAATATTAATAAATATAT
483943 T
1 T
483944 TGATTATATT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 8 0.20
22 7 0.17
23 18 0.45
24 7 0.17
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (24 bp):
TATTAAAAATATTAATAAATATAT
Found at i:483928 original size:21 final size:21
Alignment explanation
Indices: 483904--483962 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 21
483894 ATATTATTAG
483904 AAATA-TTAATAAATATATTTT
1 AAATATTTAAT-AATATATTTT
*
483925 AAATATTTAATAATATATTTG
1 AAATATTTAATAATATATTTT
*
483946 ATTATATTTAATAATAT
1 A-AATATTTAATAATAT
483963 TAAAATGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 15 0.44
22 19 0.56
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
AAATATTTAATAATATATTTT
Found at i:483944 original size:12 final size:12
Alignment explanation
Indices: 483909--483962 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 12
483899 ATTAGAAATA
483909 TTAATAAATATAT
1 TTAAT-AATATAT
483922 TT--TAA-ATAT
1 TTAATAATATAT
483931 TTAATAATATAT
1 TTAATAATATAT
*
483943 TTGAT--TATAT
1 TTAATAATATAT
483953 TTAATAATAT
1 TTAATAATAT
483963 TAAAATGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
9 6 0.18
10 11 0.32
11 4 0.12
12 11 0.32
13 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (12 bp):
TTAATAATATAT
Found at i:483960 original size:22 final size:21
Alignment explanation
Indices: 483898--483962 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 21
483888 AATATTATAT
*
483898 TATTAGAAATA-TTAATAAATA
1 TATTTGAAATATTTAAT-AATA
*
483919 TATTTTAAATATTTAATAATA
1 TATTTGAAATATTTAATAATA
*
483940 TATTTGATTATATTTAATAATA
1 TATTTGA-AATATTTAATAATA
483962 T
1 T
483963 TAAAATGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 19 0.50
22 19 0.50
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (21 bp):
TATTTGAAATATTTAATAATA
Found at i:484125 original size:7 final size:7
Alignment explanation
Indices: 484113--484138 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
484103 ACGAGCTCTA
484113 AGGAGGG
1 AGGAGGG
484120 AGGAGGG
1 AGGAGGG
484127 AGGAGGG
1 AGGAGGG
484134 AGGAG
1 AGGAG
484139 AGCGGGAGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (7 bp):
AGGAGGG
Found at i:484715 original size:20 final size:20
Alignment explanation
Indices: 484690--484730 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
484680 GTTATCTATG
* * *
484690 AATTAAAGAGAAAATATATT
1 AATTAAACAAAAAATAAATT
484710 AATTAAACAAAAAATAAATT
1 AATTAAACAAAAAATAAATT
484730 A
1 A
484731 TATAAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (20 bp):
AATTAAACAAAAAATAAATT
Found at i:484736 original size:20 final size:19
Alignment explanation
Indices: 484690--484740 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
484680 GTTATCTATG
* *
484690 AATTAAAGAGAAAATATATT
1 AATTAAA-AAAAAATAAATT
484710 AATTAAACAAAAAATAAATT
1 AATTAAA-AAAAAATAAATT
484730 -ATATAAAAAAA
1 AAT-TAAAAAAA
484741 TTAAATTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (19 bp):
AATTAAAAAAAAATAAATT
Found at i:488835 original size:19 final size:20
Alignment explanation
Indices: 488800--488837 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
488790 GAGAAATGAT
488800 TGTTACAATGTTGAAATTGA
1 TGTTACAATGTTGAAATTGA
*
488820 TGTTAGAATG-TGAAATTG
1 TGTTACAATGTTGAAATTG
488838 GATCATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.39
Consensus pattern (20 bp):
TGTTACAATGTTGAAATTGA
Found at i:492728 original size:19 final size:20
Alignment explanation
Indices: 492693--492730 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
492683 TGGAAATTAT
*
492693 TGTTAGAGTGTTGAAATTGA
1 TGTTAGAATGTTGAAATTGA
492713 TGTTAGAATG-TGAAATTG
1 TGTTAGAATGTTGAAATTG
492731 TATCATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (20 bp):
TGTTAGAATGTTGAAATTGA
Found at i:493563 original size:26 final size:26
Alignment explanation
Indices: 493531--493583 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
493521 ATTTAGTGTG
*
493531 TATGGTGGGCACGACCTTATGTGTAT
1 TATGGTGGGCACAACCTTATGTGTAT
493557 TATGGTGGGCACAACCTTATGTGTAT
1 TATGGTGGGCACAACCTTATGTGTAT
493583 T
1 T
493584 GGCACTACGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (26 bp):
TATGGTGGGCACAACCTTATGTGTAT
Found at i:499678 original size:33 final size:34
Alignment explanation
Indices: 499641--499711 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
499631 CCTTTACAAA
*
499641 TCCCTAG-TTTTTCACGAGATAAACTAGAACCTT
1 TCCCTAGCTTTTACACGAGATAAACTAGAACCTT
* * * *
499674 TCCCTAGCTTTTACACGGGCTTAGCTAGAACCTT
1 TCCCTAGCTTTTACACGAGATAAACTAGAACCTT
499708 TCCC
1 TCCC
499712 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 7 0.22
34 25 0.78
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGAGATAAACTAGAACCTT
Found at i:500516 original size:13 final size:13
Alignment explanation
Indices: 500484--500518 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
500474 GATTTTCTAA
*
500484 TTGAAAATAAATT
1 TTGAAATTAAATT
*
500497 TTGAAATTAAGTT
1 TTGAAATTAAATT
500510 TTGAAATTA
1 TTGAAATTA
500519 CTCGCCCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
TTGAAATTAAATT
Found at i:502749 original size:23 final size:23
Alignment explanation
Indices: 502713--502756 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
502703 TTCCCTCGAG
502713 GGGGAATGGATTCCCCTTCAAAT
1 GGGGAATGGATTCCCCTTCAAAT
502736 GGGGAATCGG-TTCCCCTTCAA
1 GGGGAAT-GGATTCCCCTTCAA
502757 GGGGGTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (23 bp):
GGGGAATGGATTCCCCTTCAAAT
Found at i:502771 original size:22 final size:23
Alignment explanation
Indices: 502711--502771 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
502701 GATTCCCTCG
**
502711 AGGGGGAATGGATTCCCCTTCAA
1 AGGGGGAATCAATTCCCCTTCAA
* **
502734 ATGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCAATTCCCCTTCAA
*
502756 AGGGGGTATCAATTCC
1 AGGGGGAATCAATTCC
502772 TCATGTACCA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.25
Consensus pattern (23 bp):
AGGGGGAATCAATTCCCCTTCAA
Found at i:504663 original size:15 final size:15
Alignment explanation
Indices: 504628--504665 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
504618 AGGATCTTGA
*
504628 GTTTCCTCATCTTTC
1 GTTTCTTCATCTTTC
*
504643 ATTTCTTCATCTTTC
1 GTTTCTTCATCTTTC
504658 GTTTCTTC
1 GTTTCTTC
504666 CTTTGATGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.29, G:0.05, T:0.58
Consensus pattern (15 bp):
GTTTCTTCATCTTTC
Found at i:508551 original size:22 final size:24
Alignment explanation
Indices: 508512--508556 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
508502 AACCATTCAA
508512 GGGGGAATCGGTACCCCT-TGGGG
1 GGGGGAATCGGTACCCCTCTGGGG
*
508535 GGGGGAATCGGT-TCCCTCTGGG
1 GGGGGAATCGGTACCCCTCTGGG
508557 CAATATGCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.11, C:0.22, G:0.47, T:0.20
Consensus pattern (24 bp):
GGGGGAATCGGTACCCCTCTGGGG
Found at i:509470 original size:21 final size:21
Alignment explanation
Indices: 509446--509513 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
509436 TAAAATGTAT
509446 AATGGTGCATTAAAGGCATGA
1 AATGGTGCATTAAAGGCATGA
* **
509467 AATGATGCCA-TAAATGAAATGTA
1 AATGGTG-CATTAAA-GGCATG-A
*
509490 TAACGGTGCATTAAAGGCATGA
1 -AATGGTGCATTAAAGGCATGA
509512 AA
1 AA
509514 GGATACCATA
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
21 12 0.34
22 7 0.20
23 7 0.20
24 9 0.26
ACGTcount: A:0.43, C:0.10, G:0.24, T:0.24
Consensus pattern (21 bp):
AATGGTGCATTAAAGGCATGA
Found at i:509479 original size:45 final size:45
Alignment explanation
Indices: 509430--509800 Score: 537
Period size: 45 Copynumber: 8.2 Consensus size: 45
509420 GTTTTCATTA
* * *
509430 CATAAATAAAATGTATAATGGTGCATTAAAGGCATGAAATGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGC
* * *
509475 CATAAATGAAATGTATAACGGTGCATTAAAGGCATGAAAGGATAC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGC
* *
509520 CATAAATGAAATACATAACGATGCATTAAAGGCATGAAATGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGC
* *
509565 CATAAATGAAATGCATAACGATGTATTAAAGGCATGAAATGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGC
* * *
509610 TATAAATGAAATGCATATCGGTGCATTAAAGGCATGAAA-GAATAC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATG-ATGC
* * *
509655 CATAAATGAAATGCATAATGGTGCATTAAATGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGC
* *
509700 CATAAATGAAATGCATAACGGTGCATTAAATGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGC
* * *
509745 AATAAATGAAATGCATAACTGTGCATTAAAGGCATGAAATGATGT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGC
509790 CATAAATGAAA
1 CATAAATGAAA
509801 ATAATGAATA
Statistics
Matches: 296, Mismatches: 28, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
44 1 0.00
45 294 0.99
46 1 0.00
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.24
Consensus pattern (45 bp):
CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGC
Found at i:509615 original size:21 final size:21
Alignment explanation
Indices: 509546--509615 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
509536 AACGATGCAT
*
509546 TAAAGGCATGAAATGATGCCA
1 TAAAGGCATGAAATGATGCTA
** *
509567 TAAATGAAATGCATAACGATG-TA
1 TAAA-GGCATG-A-AATGATGCTA
509590 TTAAAGGCATGAAATGATGCTA
1 -TAAAGGCATGAAATGATGCTA
509612 TAAA
1 TAAA
509616 TGAAATGCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
21 14 0.38
22 7 0.19
23 6 0.16
24 10 0.27
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (21 bp):
TAAAGGCATGAAATGATGCTA
Found at i:509687 original size:19 final size:19
Alignment explanation
Indices: 509663--509752 Score: 72
Period size: 19 Copynumber: 4.3 Consensus size: 19
509653 ACCATAAATG
*
509663 AAATGCATAATGGTGCATT
1 AAATGCATAAAGGTGCATT
509682 AAATGCATGAAAGGATGCCATAAAT
1 AAATGCAT-AAAGG-TG-CAT---T
*
509707 GAAATGCATAACGGTGCATT
1 -AAATGCATAAAGGTGCATT
*
509727 AAATGCATGAAAGGATGCAAT
1 AAATGCAT-AAAGG-TGCATT
509748 AAATG
1 AAATG
509753 AAATGCATAA
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
19 16 0.28
20 9 0.16
21 12 0.21
22 3 0.05
23 3 0.05
24 2 0.03
25 5 0.09
26 8 0.14
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.23
Consensus pattern (19 bp):
AAATGCATAAAGGTGCATT
Found at i:509707 original size:21 final size:21
Alignment explanation
Indices: 509681--509752 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
509671 AATGGTGCAT
509681 TAAATGCATGAAAGGATGCCA
1 TAAATGCATGAAAGGATGCCA
*
509702 TAAATGAAATGCATAACGG-TG-CA
1 TAAATG-CATG-A-AA-GGATGCCA
*
509725 TTAAATGCATGAAAGGATGCAA
1 -TAAATGCATGAAAGGATGCCA
509747 TAAATG
1 TAAATG
509753 AAATGCATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
20 2 0.05
21 16 0.39
22 5 0.12
23 6 0.15
24 10 0.24
25 2 0.05
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (21 bp):
TAAATGCATGAAAGGATGCCA
Found at i:509713 original size:26 final size:26
Alignment explanation
Indices: 509682--509760 Score: 91
Period size: 26 Copynumber: 3.3 Consensus size: 26
509672 ATGGTGCATT
509682 AAATGCATGAAAGGATGCCATAAATG
1 AAATGCATGAAAGGATGCCATAAATG
*
509708 AAATGCAT-AACGG-TG-CAT---T-
1 AAATGCATGAAAGGATGCCATAAATG
*
509727 AAATGCATGAAAGGATGCAATAAATG
1 AAATGCATGAAAGGATGCCATAAATG
509753 AAATGCAT
1 AAATGCAT
509761 AACTGTGCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
19 8 0.19
20 5 0.12
21 2 0.05
22 2 0.05
23 3 0.07
24 2 0.05
25 5 0.12
26 16 0.37
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.22
Consensus pattern (26 bp):
AAATGCATGAAAGGATGCCATAAATG
Found at i:516582 original size:19 final size:19
Alignment explanation
Indices: 516558--516625 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 19
516548 TAAATGAAAT
516558 GCATAACGGTGCATTAAAG
1 GCATAACGGTGCATTAAAG
* *
516577 GCATAAAAGGATGCCATAAATGAAG
1 GCAT-AACGG-TG-CAT---TAAAG
516602 TGCATAACGGTGCATTAAAG
1 -GCATAACGGTGCATTAAAG
516622 GCAT
1 GCAT
516626 GAAATGATGC
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
19 8 0.21
20 8 0.21
21 2 0.05
22 3 0.08
23 3 0.08
24 2 0.05
25 8 0.21
26 4 0.11
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.21
Consensus pattern (19 bp):
GCATAACGGTGCATTAAAG
Found at i:516935 original size:45 final size:45
Alignment explanation
Indices: 516456--516912 Score: 779
Period size: 45 Copynumber: 10.2 Consensus size: 45
516446 TGTTTCATTA
* *
516456 CATAAATGAAATGCATAACAGTACATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
516501 CATAAATGAAATGCATAATGGTGCATTAAAGGCATGAAATGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
*
516546 CATAAATGAAATGCATAACGGTGCATTAAAGGCATAAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
516591 CATAAATGAAGTGCATAACGGTGCATTAAAGGCATGAAATGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * * *
516636 CATAAATGAAATACATAACAGTGTATTAAAGTCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
*
516681 TATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
516726 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
516771 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
*
516816 CATAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
516861 CATAAATGAAATGCACAACTGTGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
516906 CATAAAT
1 CATAAAT
516913 TAAAATAATG
Statistics
Matches: 386, Mismatches: 26, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 386 1.00
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (45 bp):
CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
Found at i:521250 original size:13 final size:12
Alignment explanation
Indices: 521212--521242 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
521202 TTACTATATA
521212 ATTTTTTTCTAT
1 ATTTTTTTCTAT
521224 ATTTTTTTCTAT
1 ATTTTTTTCTAT
521236 ATTTTTT
1 ATTTTTT
521243 ATTAATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (12 bp):
ATTTTTTTCTAT
Found at i:522119 original size:21 final size:21
Alignment explanation
Indices: 522093--522145 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
522083 GTTTCCAGAT
522093 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
522114 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
*
522135 TCGCAATGCGA
1 TCGCAACGCGA
522146 TTTACATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:522184 original size:21 final size:21
Alignment explanation
Indices: 522154--522297 Score: 111
Period size: 21 Copynumber: 7.0 Consensus size: 21
522144 GATTTACATA
*
522154 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
** * *
522175 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCGAAG
522196 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
** * *
522215 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCGAAG
*
522236 TT--CGTTTCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
* * *
522255 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCGAAG
522278 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
522297 T
1 T
522298 CGAAGTTCAC
Statistics
Matches: 92, Mismatches: 25, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
19 36 0.39
21 48 0.52
23 8 0.09
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGAAG
Found at i:522289 original size:42 final size:42
Alignment explanation
Indices: 522160--522382 Score: 328
Period size: 40 Copynumber: 5.3 Consensus size: 42
522150 CATATTCGCA
522160 TTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
522200 TTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
522240 TTTCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
522282 TTGCGATAGTCGAAGTCGAAGTTCACGTTGCGATTTATTCAAAATTCG
1 TTGCG--A-T---AGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
522330 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
522372 TTGCGATAGTC
1 TTGCGATAGTC
522383 CAAAATCGCA
Statistics
Matches: 168, Mismatches: 7, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
40 66 0.39
41 2 0.01
42 58 0.35
44 1 0.01
45 2 0.01
46 1 0.01
48 38 0.23
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:522318 original size:48 final size:48
Alignment explanation
Indices: 522242--522382 Score: 213
Period size: 48 Copynumber: 3.0 Consensus size: 48
522232 CAAATTCGTT
522242 TCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
1 TCGA-AGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
* *
522291 TCGAAGTCGAAGTTCACGTTGCGATTTATTCAAAATTCGTTGCGATAG
1 TCGAAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
522339 TC-----C-AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
1 TCGAAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
522381 TC
1 TC
522383 CAAAATCGCA
Statistics
Matches: 88, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
42 39 0.44
43 1 0.01
48 44 0.50
49 4 0.05
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (48 bp):
TCGAAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
Found at i:522333 original size:21 final size:21
Alignment explanation
Indices: 522307--522378 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
522297 TCGAAGTTCA
*
522307 CGTTGCGATTTATTCAAAATT
1 CGTTGCGATTTATTCCAAATT
* *
522328 CGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAATT
522347 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
522370 CGTTGCGAT
1 CGTTGCGAT
522379 AGTCCAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 8 0.19
21 25 0.60
23 9 0.21
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:522358 original size:90 final size:86
Alignment explanation
Indices: 522160--522382 Score: 332
Period size: 90 Copynumber: 2.6 Consensus size: 86
522150 CATATTCGCA
*
522160 TTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTGCG--A-T-AGTCGAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCAGTCGAAGTTCA
*
522219 CGTTGCGATTTTCCAAATTCG
66 CGTTGCGATTTTCAAAATTCG
*
522240 TTTCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTCGAAGTT
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTC--AGTCGAAGTT
522305 CACGTTGCGATTTATTCAAAATTCG
64 CACGTTGCGA-TT-TTCAAAATTCG
*
522330 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
522383 CAAAATCGCA
Statistics
Matches: 128, Mismatches: 5, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
80 26 0.20
81 2 0.02
82 16 0.12
84 1 0.01
85 1 0.01
88 19 0.15
89 2 0.02
90 61 0.48
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.35
Consensus pattern (86 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCAGTCGAAGTTCA
CGTTGCGATTTTCAAAATTCG
Found at i:523140 original size:21 final size:21
Alignment explanation
Indices: 523114--523185 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
523104 ATTTTGGACT
*
523114 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
523135 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
523156 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
523177 ATCGCAACG
1 ATCGCAACG
523186 CGAACTTCGA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 10 0.24
21 23 0.55
23 9 0.21
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:523172 original size:42 final size:42
Alignment explanation
Indices: 523110--523204 Score: 181
Period size: 42 Copynumber: 2.3 Consensus size: 42
523100 TGCGATTTTG
*
523110 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
523152 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
523194 GACTATCGCAA
1 GACTATCGCAA
523205 TGCGAATATG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:523201 original size:21 final size:21
Alignment explanation
Indices: 523135--523210 Score: 93
Period size: 21 Copynumber: 3.6 Consensus size: 21
523125 TTTGGAATAA
523135 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
523156 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTCGACT
523175 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
*
523198 ATCGCAATGCGAA
1 ATCGCAACGCGAA
523211 TATGTAAATC
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
19 10 0.22
21 26 0.57
23 10 0.22
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:525465 original size:21 final size:20
Alignment explanation
Indices: 525441--525482 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
525431 AATGTCAAGA
525441 TTTCT-TTTCATATTACATAAT
1 TTTCTCTTTCA-ATTA-ATAAT
*
525462 TTTCTCTTTTAATTAATAAT
1 TTTCTCTTTCAATTAATAAT
525482 T
1 T
525483 CAAAACAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTCTCTTTCAATTAATAAT
Found at i:526040 original size:23 final size:24
Alignment explanation
Indices: 525987--526046 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
525977 TTTATTCATA
*
525987 TTATTAAAATATAATATAATATCTT
1 TTATTAAAATATAATAGAATA-CTT
* *
526012 TTATTATAATATAATCGAATA-TT
1 TTATTAAAATATAATAGAATACTT
*
526035 TTATTACAATAT
1 TTATTAAAATAT
526047 TAAAAACTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 13 0.42
25 18 0.58
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (24 bp):
TTATTAAAATATAATAGAATACTT
Found at i:526070 original size:23 final size:24
Alignment explanation
Indices: 526044--526113 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 24
526034 TTTATTACAA
*
526044 TATTAAAAACTA-TAAT-ATTATAT
1 TATTAAAAA-TATTAATAAATATAT
*
526067 TATTAGAAATATTAATAAATATAT
1 TATTAAAAATATTAATAAATATAT
* *
526091 T-TTAAATATTTTAAT-AATATAT
1 TATTAAAAATATTAATAAATATAT
526113 T
1 T
526114 TGATTATATT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 10 0.25
23 23 0.57
24 7 0.17
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (24 bp):
TATTAAAAATATTAATAAATATAT
Found at i:526122 original size:23 final size:22
Alignment explanation
Indices: 526078--526133 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
526068 ATTAGAAATA
*
526078 TTAATAAATATATTTTAAATATT
1 TTAAT-AATATATTTGAAATATT
*
526101 TTAATAATATATTTGATTATATT
1 TTAATAATATATTTGA-AATATT
526124 TTAATAATAT
1 TTAATAATAT
526134 TAAAATGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 10 0.33
23 20 0.67
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TTAATAATATATTTGAAATATT
Found at i:526152 original size:53 final size:56
Alignment explanation
Indices: 526060--526163 Score: 128
Period size: 53 Copynumber: 1.9 Consensus size: 56
526050 AAACTATAAT
* *
526060 ATTATATTATTAGAAATATTAATAAATATATTTTAAATATTTTAATAATATATTTG
1 ATTATATTATTAGAAATATTAATAAATATATTTAAAATATTATAATAATATATTTG
*
526116 ATTATATT-TTA-ATAATATT-A-AAATGATA-TTAAAATATTATATTAATAT
1 ATTATATTATTAGA-AATATTAATAAAT-ATATTTAAAATATTATAATAATAT
526164 TAAATTCATA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
53 21 0.49
54 5 0.12
55 9 0.21
56 8 0.19
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (56 bp):
ATTATATTATTAGAAATATTAATAAATATATTTAAAATATTATAATAATATATTTG
Found at i:526295 original size:7 final size:7
Alignment explanation
Indices: 526283--526308 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
526273 ACGAGCTCTA
526283 AGGAGGG
1 AGGAGGG
526290 AGGAGGG
1 AGGAGGG
526297 AGGAGGG
1 AGGAGGG
526304 AGGAG
1 AGGAG
526309 AGCGGGAGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (7 bp):
AGGAGGG
Found at i:526885 original size:20 final size:20
Alignment explanation
Indices: 526860--526900 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
526850 GTTATCTATG
* * *
526860 AATTAAAGAGAAAATATATT
1 AATTAAACAAAAAATAAATT
526880 AATTAAACAAAAAATAAATT
1 AATTAAACAAAAAATAAATT
526900 A
1 A
526901 TATAAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (20 bp):
AATTAAACAAAAAATAAATT
Found at i:526906 original size:20 final size:19
Alignment explanation
Indices: 526860--526910 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
526850 GTTATCTATG
* *
526860 AATTAAAGAGAAAATATATT
1 AATTAAA-AAAAAATAAATT
526880 AATTAAACAAAAAATAAATT
1 AATTAAA-AAAAAATAAATT
526900 -ATATAAAAAAA
1 AAT-TAAAAAAA
526911 TTAAATTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (19 bp):
AATTAAAAAAAAATAAATT
Found at i:535486 original size:19 final size:20
Alignment explanation
Indices: 535451--535488 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
535441 GAGAAATGAC
*
535451 TGTTACAATGTTGAAATTGA
1 TGTTAAAATGTTGAAATTGA
535471 TGTTAAAATG-TGAAATTG
1 TGTTAAAATGTTGAAATTG
535489 GATCATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.39
Consensus pattern (20 bp):
TGTTAAAATGTTGAAATTGA
Found at i:539409 original size:19 final size:20
Alignment explanation
Indices: 539366--539411 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
539356 TACTATGCTG
* *
539366 GAAATTAATGTTAGAGTGTT
1 GAAATTGATGTTAGAATGTT
539386 GAAATTGATGTTAGAATG-T
1 GAAATTGATGTTAGAATGTT
539405 GAAATTG
1 GAAATTG
539412 TATCATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGTT
Found at i:539714 original size:2 final size:2
Alignment explanation
Indices: 539707--539750 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
539697 AGCTGAGGCT
539707 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
539749 TA
1 TA
539751 GTGTCAAGGT
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:540169 original size:26 final size:26
Alignment explanation
Indices: 540137--540189 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
540127 ATTTAGTGTG
540137 TATGGTGGGCACGACCTTATGTGTAT
1 TATGGTGGGCACGACCTTATGTGTAT
540163 TATGGTGGGCACGACCTTATGTGTAT
1 TATGGTGGGCACGACCTTATGTGTAT
540189 T
1 T
540190 GGCACTACGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.30, T:0.36
Consensus pattern (26 bp):
TATGGTGGGCACGACCTTATGTGTAT
Found at i:546323 original size:33 final size:34
Alignment explanation
Indices: 546284--546354 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
546274 CCTTTACAAC
*
546284 TCCCTAG-TTTTTCACGGGATAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
* * *
546317 TCCCTAGCTTTTACACGGGCTTAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
546351 TCCC
1 TCCC
546355 CTTTGCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 7 0.21
34 26 0.79
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
Found at i:546751 original size:20 final size:20
Alignment explanation
Indices: 546726--546773 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
546716 ATGGTTTATG
546726 GATACACTGCAGGGTGTATC
1 GATACACTGCAGGGTGTATC
546746 GATACACTGCAGGGTGTATC
1 GATACACTGCAGGGTGTATC
546766 GATACACT
1 GATACACT
546774 ACTGTATGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (20 bp):
GATACACTGCAGGGTGTATC
Found at i:546786 original size:36 final size:36
Alignment explanation
Indices: 546740--546810 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
546730 CACTGCAGGG
*
546740 TGTATCGATACACTGCA-GGGTGTATC-GATACACTAC
1 TGTATCGATACACT-CATAGGTGTATCAG-TACACTAC
*
546776 TGTATGGATACACTCATAGGTGTATCAGTACACTA
1 TGTATCGATACACTCATAGGTGTATCAGTACACTA
546811 TTTGCATTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 2 0.06
36 28 0.90
37 1 0.03
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (36 bp):
TGTATCGATACACTCATAGGTGTATCAGTACACTAC
Found at i:546900 original size:20 final size:19
Alignment explanation
Indices: 546837--546907 Score: 67
Period size: 16 Copynumber: 3.7 Consensus size: 19
546827 GAGCAGTCAT
546837 AGGTGTATGGATACACGTGCA
1 AGGTGTATGGATACAC-T-CA
* **
546858 GGGTGTATCCATACACT--
1 AGGTGTATGGATACACTCA
546875 -GGTGTATGGATACACTACA
1 AGGTGTATGGATACACT-CA
546894 AGGTGTATGGATAC
1 AGGTGTATGGATAC
546908 CCTTTTACAC
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
16 14 0.34
20 14 0.34
21 13 0.32
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (19 bp):
AGGTGTATGGATACACTCA
Found at i:547156 original size:21 final size:18
Alignment explanation
Indices: 547132--547188 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 18
547122 ATTTTTAATA
547132 AAAAAGATATCAATTGTT
1 AAAAAGATATCAATTGTT
*
547150 GACAAAAGGATATCGATTGTT
1 -A-AAAA-GATATCAATTGTT
547171 AAAAAGATA-CAATTGTT
1 AAAAAGATATCAATTGTT
547188 A
1 A
547189 CCAATTGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 8 0.24
18 4 0.12
19 5 0.15
20 5 0.15
21 12 0.35
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.30
Consensus pattern (18 bp):
AAAAAGATATCAATTGTT
Found at i:547715 original size:13 final size:13
Alignment explanation
Indices: 547697--547721 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
547687 ATATCAATTG
547697 TTAGAGAGATATA
1 TTAGAGAGATATA
547710 TTAGAGAGATAT
1 TTAGAGAGATAT
547722 CATTTTCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (13 bp):
TTAGAGAGATATA
Found at i:550314 original size:16 final size:17
Alignment explanation
Indices: 550292--550344 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 17
550282 TTTCAGCCAG
550292 GGTGTATCGATACACTA
1 GGTGTATCGATACACTA
550309 -GTGTAT-GAATACACTCATA
1 GGTGTATCG-ATACA--C-TA
550328 GGTGTATCGATACACTA
1 GGTGTATCGATACACTA
550345 TTTGCATTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
15 1 0.03
16 11 0.37
17 2 0.07
18 2 0.07
19 2 0.07
20 11 0.37
21 1 0.03
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (17 bp):
GGTGTATCGATACACTA
Found at i:550399 original size:57 final size:57
Alignment explanation
Indices: 550307--550420 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
550297 ATCGATACAC
*
550307 TAGTGTATGAATACACTCATAGGTGTATCGATACACTATTTGCATTCGGTGTTTGAG
1 TAGTGTATGAATACACTCATAGGTGTATCGATACACTATTTACATTCGGTGTTTGAG
* *
550364 TAGTGTATGGATACACTCATAGGTGTATCGGTACACTATTTACATTCGGTGTTTGAG
1 TAGTGTATGAATACACTCATAGGTGTATCGATACACTATTTACATTCGGTGTTTGAG
550421 CAGTCATAGG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (57 bp):
TAGTGTATGAATACACTCATAGGTGTATCGATACACTATTTACATTCGGTGTTTGAG
Found at i:555996 original size:64 final size:66
Alignment explanation
Indices: 555842--556001 Score: 193
Period size: 65 Copynumber: 2.5 Consensus size: 66
555832 AATTAAATTG
* * * *
555842 AACATTGAATGCATTTCATGCATCAATGCA-CATACCATGCACCGATGCAGTGAGGATTTTATGA
1 AACATTGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATGCACTCAGGATTTTATGA
555906 A
66 A
* * * * *
555907 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATGCACTCTGGCTATTT-TG
1 AACATTGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATGCACTCAGGAT-TTTATG
555970 -A
65 AA
*
555971 AACATTGAATGCACTTGATGCATCGATGCAC
1 AACATTGAATGCATTTGATGCATCGATGCAC
556002 TCTTAGTGCA
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 30 0.37
65 47 0.57
66 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (66 bp):
AACATTGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATGCACTCAGGATTTTATGA
A
Found at i:557555 original size:65 final size:65
Alignment explanation
Indices: 557458--557610 Score: 177
Period size: 65 Copynumber: 2.4 Consensus size: 65
557448 TTGAACATTG
* * *
557458 AATGCATTTCATGCATCGATGCA-CATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACAT
1 AATGCATTTGATGCATCGATGCACCATACCATGCACCAATGCACTCAGGATATTT-TG-AAACAT
557521 CA
64 CA
* * * * *
557523 AATGCATTTGATGCATCGATGCACCA-GCCATGCATCAATGCACTCTGGCTATTTTGAAACATCG
1 AATGCATTTGATGCATCGATGCACCATACCATGCACCAATGCACTCAGGATATTTTGAAACATCA
* *
557587 ATTGCACTTGATGCATCGATGCAC
1 AATGCATTTGATGCATCGATGCAC
557611 TCTTAGTGCA
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 29 0.38
65 42 0.55
66 5 0.07
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.27
Consensus pattern (65 bp):
AATGCATTTGATGCATCGATGCACCATACCATGCACCAATGCACTCAGGATATTTTGAAACATCA
Found at i:562051 original size:18 final size:18
Alignment explanation
Indices: 562030--562065 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
562020 TGAAGTTGGA
*
562030 AGAAGTACCTTGTAAAGT
1 AGAAGTACCTTGGAAAGT
562048 AGAAGTACCTTGGAAAGT
1 AGAAGTACCTTGGAAAGT
562066 TTCTTTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (18 bp):
AGAAGTACCTTGGAAAGT
Found at i:562783 original size:58 final size:58
Alignment explanation
Indices: 562715--562850 Score: 150
Period size: 58 Copynumber: 2.3 Consensus size: 58
562705 AATTAAATAT
* * * **
562715 TTTTTATAAATTACATTTA-AGGACAAAGATTTTTATAAATTTTAAT-AATGGACAAATC
1 TTTTTATAAATTACA-ATAGAAGACAAAGATTCTTATAAATTACAATAAAT-GACAAATC
* **
562773 TTTTTATAAATTACAATAGAAGATAAATCTTCTTATAAATTACAATAAATGACAAATC
1 TTTTTATAAATTACAATAGAAGACAAAGATTCTTATAAATTACAATAAATGACAAATC
* *
562831 TTTTTATAATTTAAAATAGA
1 TTTTTATAAATTACAATAGA
562851 GAACAAAACG
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
57 2 0.03
58 61 0.92
59 3 0.05
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (58 bp):
TTTTTATAAATTACAATAGAAGACAAAGATTCTTATAAATTACAATAAATGACAAATC
Found at i:562856 original size:29 final size:29
Alignment explanation
Indices: 562715--562857 Score: 114
Period size: 29 Copynumber: 4.9 Consensus size: 29
562705 AATTAAATAT
* * **
562715 TTTTTATAAATTACATTTA-AGGACAAAGA
1 TTTTTATAAATTACA-ATAGAGAACAAATC
** *
562744 TTTTTATAAATTTTAATA-ATGGACAAATC
1 TTTTTATAAATTACAATAGA-GAACAAATC
*
562773 TTTTTATAAATTACAATAGA-AGATAAATC
1 TTTTTATAAATTACAATAGAGA-ACAAATC
* *
562802 TTCTTATAAATTACAATAAATG-ACAAATC
1 TTTTTATAAATTACAATAGA-GAACAAATC
* *
562831 TTTTTATAATTTAAAATAGAGAACAAA
1 TTTTTATAAATTACAATAGAGAACAAA
562858 ACGTGATATG
Statistics
Matches: 92, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
28 4 0.04
29 87 0.95
30 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (29 bp):
TTTTTATAAATTACAATAGAGAACAAATC
Found at i:564218 original size:18 final size:17
Alignment explanation
Indices: 564179--564230 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
564169 TAAGAGTTTT
**
564179 TTTATTAATGAAAAAAC
1 TTTATTAATGAACTAAC
*
564196 ATTATTCAATGAACTAAC
1 TTTATT-AATGAACTAAC
564214 TTTATTGAATGAACTAA
1 TTTATT-AATGAACTAA
564231 ATGCATGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 5 0.17
18 24 0.83
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.37
Consensus pattern (17 bp):
TTTATTAATGAACTAAC
Found at i:564601 original size:29 final size:27
Alignment explanation
Indices: 564560--564652 Score: 132
Period size: 28 Copynumber: 3.3 Consensus size: 27
564550 CATCAAAACA
*
564560 TTTTACAAATTACAATAACGACATATACT
1 TTTTACAAATTACAATAACAAC-TATA-T
564589 TTTTACAAATTACAATAACAACTCATAT
1 TTTTACAAATTACAATAACAACT-ATAT
*
564617 TTTTACATATTACAATAACAACCTATAT
1 TTTTACAAATTACAATAACAA-CTATAT
564645 TTTTACAA
1 TTTTACAA
564653 TCATTATATT
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
28 33 0.56
29 26 0.44
ACGTcount: A:0.44, C:0.17, G:0.01, T:0.38
Consensus pattern (27 bp):
TTTTACAAATTACAATAACAACTATAT
Found at i:565523 original size:17 final size:17
Alignment explanation
Indices: 565501--565533 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
565491 AGAGCAAAAG
*
565501 GGAAAAGAA-AAAGAAA
1 GGAAAAAAAGAAAGAAA
565517 GGAAAAAAAGAAAGAAA
1 GGAAAAAAAGAAAGAAA
565534 CATACTTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
GGAAAAAAAGAAAGAAA
Found at i:570640 original size:14 final size:15
Alignment explanation
Indices: 570616--570644 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
570606 TTTGGTGCCA
570616 AAAATGTTATATAGT
1 AAAATGTTATATAGT
570631 AAAA-GTTATATAGT
1 AAAATGTTATATAGT
570645 TATTGTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (15 bp):
AAAATGTTATATAGT
Found at i:574323 original size:27 final size:27
Alignment explanation
Indices: 574283--574336 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
574273 TAATTTATGT
**
574283 GTATTTTATATTTAGGTCGTTGATTTA
1 GTATTTTATATTTAGGTCACTGATTTA
*
574310 GTATTTTATGTTTAGGTCACTGATTTA
1 GTATTTTATATTTAGGTCACTGATTTA
574337 TTTCTGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.22, C:0.06, G:0.19, T:0.54
Consensus pattern (27 bp):
GTATTTTATATTTAGGTCACTGATTTA
Found at i:578174 original size:21 final size:21
Alignment explanation
Indices: 578150--578189 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
578140 TATATAAAAT
578150 AAATTAA-CAAATATAGAAAGC
1 AAATTAATC-AATATAGAAAGC
578171 AAATTAATCAATATAGAAA
1 AAATTAATCAATATAGAAA
578190 ATGTCAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.23
Consensus pattern (21 bp):
AAATTAATCAATATAGAAAGC
Found at i:581968 original size:20 final size:20
Alignment explanation
Indices: 581943--581984 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
581933 TCATGTGGCA
*
581943 TTGCATGGTATTTATTCATG
1 TTGCATGGTATTAATTCATG
*
581963 TTGCATTGTATTAATTCATG
1 TTGCATGGTATTAATTCATG
581983 TT
1 TT
581985 ATATTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.17, T:0.52
Consensus pattern (20 bp):
TTGCATGGTATTAATTCATG
Found at i:587080 original size:43 final size:48
Alignment explanation
Indices: 587028--587133 Score: 123
Period size: 50 Copynumber: 2.3 Consensus size: 48
587018 ATAACTAATG
* *
587028 AATAAAATAATAACAAAT-TAAA-CATGTTTTAA-CT-C-TAATTCCT
1 AATAAAATAATAACAAATAAAAATAATGTTTTAACCTACTTAATTCCT
* *
587071 AATAAAATAATAATAACTAAAAATAATGTTTTAACCTAACCTTAATTCCT
1 AATAAAATAATAACAAATAAAAATAATGTTTTAACCT-A-CTTAATTCCT
587121 AATAAAATAATAA
1 AATAAAATAATAA
587134 ATCTAATCCT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
43 16 0.31
44 3 0.06
45 9 0.17
46 2 0.04
49 1 0.02
50 21 0.40
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (48 bp):
AATAAAATAATAACAAATAAAAATAATGTTTTAACCTACTTAATTCCT
Found at i:593398 original size:12 final size:12
Alignment explanation
Indices: 593381--593405 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
593371 TGGGTTAACC
593381 AACAAGTGGAAG
1 AACAAGTGGAAG
593393 AACAAGTGGAAG
1 AACAAGTGGAAG
593405 A
1 A
593406 GAACTATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.32, T:0.08
Consensus pattern (12 bp):
AACAAGTGGAAG
Found at i:594207 original size:22 final size:22
Alignment explanation
Indices: 594182--594223 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
594172 CATAATTTAT
*
594182 TTAGACAAAATAACAAATTAAA
1 TTAGACAAAATAAAAAATTAAA
**
594204 TTAGTTAAAATAAAAAATTA
1 TTAGACAAAATAAAAAATTA
594224 TGTCAAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (22 bp):
TTAGACAAAATAAAAAATTAAA
Found at i:594391 original size:98 final size:94
Alignment explanation
Indices: 594244--594591 Score: 236
Period size: 98 Copynumber: 3.5 Consensus size: 94
594234 ATTTATTCAA
* ** * *
594244 AATATTTTCTCAAAATAACAAATTA-ATACAAATTTAACTAGTTATAATAACAAATTATAATAAA
1 AATATTTT-TCACAATAAC-AATTATA-ACAAATTTATTTAGTCACAATAACAAATTATAATAAA
*
594308 TATTAATTTCTCAATATAAAAAGTTATGACAAAC
63 TATTAATTTCT--ATATAAAAAATTATGACAAAC
*
594342 AATAGTTTTTCACAATAATCAATTATAACAAATTTATTTAGTCACAATAACATATTA-AATTTAG
1 AATA-TTTTTCACAATAA-CAATTATAACAAATTTATTTAGTCACAATAACAAATTATAA--TA-
* * * * * ** **
594406 TCAAAATGAAAATT-TATAT-TAAATTTATTTCGTCAC
61 --AATAT-TAATTTCTATATAAAAAATTATGAC-AAAC
* * * * * *
594442 AATATTTTCTCAAAATAACAACTTTTGACAAATTTATTTAGTCATAATAACAATTTATAACAAAT
1 AATATTTT-TCACAATAACAA-TTATAACAAATTTATTTAGTCACAATAACAAATTATAATAAAT
* *
594507 ATTAATTCCTTGATATAAAAAATTATGACAAAT
64 ATTAATTTC-T-ATATAAAAAATTATGACAAAC
* * * *
594540 AATATTCTTTCACAATAACAAATTGTAATAAATTCATTTAGTTACAATAACA
1 AATATT-TTTCACAATAAC-AATTATAACAAATTTATTTAGTCACAATAACA
594592 TAGTAAATTT
Statistics
Matches: 191, Mismatches: 40, Indels: 38
0.71 0.15 0.14
Matches are distributed among these distances:
95 3 0.02
96 4 0.02
97 3 0.02
98 86 0.45
99 36 0.19
100 48 0.25
101 2 0.01
102 5 0.03
103 4 0.02
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.37
Consensus pattern (94 bp):
AATATTTTTCACAATAACAATTATAACAAATTTATTTAGTCACAATAACAAATTATAATAAATAT
TAATTTCTATATAAAAAATTATGACAAAC
Found at i:594392 original size:22 final size:22
Alignment explanation
Indices: 594366--594422 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
594356 ATAATCAATT
*
594366 ATAACAAATTTATTTAGTCACA
1 ATAACAAATTTATTTAGTCAAA
* *
594388 ATAACATATTAAATTTAGTCAAA
1 ATAACAAATT-TATTTAGTCAAA
*
594411 ATGA-AAATTTAT
1 ATAACAAATTTAT
594423 ATTAAATTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 2 0.07
22 13 0.46
23 13 0.46
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (22 bp):
ATAACAAATTTATTTAGTCAAA
Found at i:594512 original size:198 final size:195
Alignment explanation
Indices: 594175--594963 Score: 828
Period size: 198 Copynumber: 4.1 Consensus size: 195
594165 AAATTATCAT
* * * * *
594175 AATTTATTTAGACAAAATAACAAATTAAA-TTAGTTAAAATAAAAAATTATGTCAAATTTATTTA
1 AATTTATTTAGTCACAATAACATATTAAATTTAGTCAAAAT--AAAATTATATCAAATTTATTT-
* * * * ** * * *
594239 TTCAAAATATTTTCTCAAAATAACAAATTAAT-ACAAATTTAACTAGTTATAATAACAAATTATA
63 GTCACAATATTTTCTCAAAATAAAAAATT-GTGACAAATTTATTTAGTCAAAATAACAATTTATA
* * *
594303 ATAAATATTAATTTCTCAATATAAAAAGTTATGACAAACAATAGTT-TTTCACAATAATC-AATT
127 ACAAATATTAATTTCTCAATATAAAAAATTATGACAAATAATA-TTCTTTCACAATAA-CAAATT
*
594366 ATAACA
190 GTAACA
*
594372 AATTTATTTAGTCACAATAACATATTAAATTTAGTCAAAATGAAAATTTATATTAAATTTATTTC
1 AATTTATTTAGTCACAATAACATATTAAATTTAGTCAAAAT-AAAA-TTATATCAAATTTATTT-
* * * *
594437 GTCACAATATTTTCTCAAAATAACAACTTTTGACAAATTTATTTAGTCATAATAACAATTTATAA
63 GTCACAATATTTTCTCAAAATAAAAAATTGTGACAAATTTATTTAGTCAAAATAACAATTTATAA
* **
594502 CAAATATTAATTCCTTGATATAAAAAATTATGACAAATAATATTCTTTCACAATAACAAATTGTA
128 CAAATATTAATTTCTCAATATAAAAAATTATGACAAATAATATTCTTTCACAATAACAAATTGTA
*
594567 ATA
193 ACA
* * *
594570 AATTCATTTAGTTACAATAACATAGTAAATTTAGTC--------A--A-A-CAAA-TTA--TGTC
1 AATTTATTTAGTCACAATAACATATTAAATTTAGTCAAAATAAAATTATATCAAATTTATTTGTC
* * * *
594620 ACAATATTTTGTCAAAA-AAAAAATTGTGATAAATTTATTTAAG-AAAAATAATAATTTATAACA
66 ACAATATTTTCTCAAAATAAAAAATTGTGACAAATTTATTT-AGTCAAAATAACAATTTATAACA
* * * *
594683 AATATTAATTTCTCAATATAAAAAAGTGTGACAAGTAAAATTCTTTCACAATAACAAATTGGTAA
130 AATATTAATTTCTCAATATAAAAAATTATGACAAATAATATTCTTTCACAATAACAAATT-GTAA
594748 CA
194 CA
* * * * * *
594750 AAATGATTTAGTCACAATAACACATTAAATTTGGTCAAAGTAAAAGGTTATGTCAAATTTATTTT
1 AATTTATTTAGTCACAATAACATATTAAATTTAGTCAAAATAAAA--TTATATCAAATTTA-TTT
* * * * *
594815 ATCACAATATTTTGTAAAAATAAAAAATTGTGACAAATTTGTTTAATCAAAATAACAATTTATAA
63 GTCACAATATTTTCTCAAAATAAAAAATTGTGACAAATTTATTTAGTCAAAATAACAATTTATAA
* * *
594880 CAAATATTAATTTCTCATTATAAAAAATTGTGACAAATAATATTCTTTCACGATAACAAATTGTA
128 CAAATATTAATTTCTCAATATAAAAAATTATGACAAATAATATTCTTTCACAATAACAAATTGTA
594945 ACA
193 ACA
*
594948 AAATTATTTAGTCACA
1 AATTTATTTAGTCACA
594964 GTAAAAAGTT
Statistics
Matches: 501, Mismatches: 64, Indels: 53
0.81 0.10 0.09
Matches are distributed among these distances:
179 89 0.18
180 56 0.11
181 1 0.00
183 3 0.01
184 3 0.01
185 1 0.00
186 1 0.00
188 1 0.00
189 1 0.00
192 1 0.00
194 4 0.01
195 3 0.01
197 34 0.07
198 209 0.42
199 94 0.19
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.36
Consensus pattern (195 bp):
AATTTATTTAGTCACAATAACATATTAAATTTAGTCAAAATAAAATTATATCAAATTTATTTGTC
ACAATATTTTCTCAAAATAAAAAATTGTGACAAATTTATTTAGTCAAAATAACAATTTATAACAA
ATATTAATTTCTCAATATAAAAAATTATGACAAATAATATTCTTTCACAATAACAAATTGTAACA
Found at i:596747 original size:42 final size:43
Alignment explanation
Indices: 596655--596747 Score: 116
Period size: 43 Copynumber: 2.2 Consensus size: 43
596645 AAGATCATAA
*
596655 GTCAGGTTCTTTAGAGGCATTTTGGATACAAACATCACAAAAG
1 GTCAGGTTCTTTAGAGGCATTTAGGATACAAACATCACAAAAG
* ** * * *
596698 GTCAGGTTCTTTAGCGGTGTTTAGTAT-CAATCATCGCAAAAG
1 GTCAGGTTCTTTAGAGGCATTTAGGATACAAACATCACAAAAG
596740 GTCAGGTT
1 GTCAGGTT
596748 GTAACACCCC
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 21 0.49
43 22 0.51
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (43 bp):
GTCAGGTTCTTTAGAGGCATTTAGGATACAAACATCACAAAAG
Found at i:597427 original size:18 final size:18
Alignment explanation
Indices: 597376--597428 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
597366 ACTGAATATT
* *
597376 TGTCCTGAAGGACCAATA
1 TGTCCCGAAGGACCACTA
597394 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
597412 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
597429 GATAATCCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:598092 original size:64 final size:65
Alignment explanation
Indices: 597999--598162 Score: 151
Period size: 64 Copynumber: 2.6 Consensus size: 65
597989 CATCCCTTGA
* * * *
597999 CGGGTGTATCGATGTACTATCTATGCATCGGTACA-TAAATCTCATTCGATGTTTGTATTTT-AA
1 CGGGTGCATCGATGCACTATCTATGCATCGATACACT-AATCGCATTCGATGTTTGTATTTTAAA
598062 G
65 G
* * *
598063 CGGGTGCATCGATGCACTA-CT-TGTACATCGATACACTGATGGCATTCGATGTTTTTATTTTAA
1 CGGGTGCATCGATGCACTATCTATG--CATCGATACACTAATCGCATTCGATGTTTGTATTTTAA
598126 AG
64 AG
* * * *
598128 -GAGTGCATCGATACACT-TCATGTGCATTGATACAC
1 CGGGTGCATCGATGCACTATC-TATGCATCGATACAC
598163 CTTGAACAAT
Statistics
Matches: 83, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
62 2 0.02
63 2 0.02
64 72 0.87
65 5 0.06
66 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (65 bp):
CGGGTGCATCGATGCACTATCTATGCATCGATACACTAATCGCATTCGATGTTTGTATTTTAAAG
Found at i:604308 original size:18 final size:18
Alignment explanation
Indices: 604257--604309 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
604247 ACTGAATATT
*
604257 TGTCCCGAAGGACCAATA
1 TGTCCCGAAGGACCACTA
604275 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
604293 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
604310 GATAATCCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.28, C:0.32, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:604566 original size:2 final size:2
Alignment explanation
Indices: 604559--604592 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
604549 TAACGTTAAC
604559 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
604593 GCATGTGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:604885 original size:20 final size:20
Alignment explanation
Indices: 604855--604907 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
604845 TAATGAAGGT
* * *
604855 ATGCATTGATGCAGTACACT
1 ATGCATCGATGCACTACACC
*
604875 ATGTATCGATGCACTACACC
1 ATGCATCGATGCACTACACC
604895 ATGCATCGATGCA
1 ATGCATCGATGCA
604908 TCCCTTGACG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (20 bp):
ATGCATCGATGCACTACACC
Found at i:605389 original size:19 final size:18
Alignment explanation
Indices: 605347--605387 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
605337 CGATGACAAG
605347 TCAAATTGAACCTCGATT
1 TCAAATTGAACCTCGATT
*
605365 TCAAATATGAA-CTCTATT
1 TCAAAT-TGAACCTCGATT
605383 TCAAA
1 TCAAA
605388 ATTTCATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (18 bp):
TCAAATTGAACCTCGATT
Found at i:608939 original size:9 final size:9
Alignment explanation
Indices: 608925--608961 Score: 51
Period size: 8 Copynumber: 4.2 Consensus size: 9
608915 AAATATCACC
608925 TTTTTCTTT
1 TTTTTCTTT
608934 TTTTTC-TT
1 TTTTTCTTT
608942 TTTTTCATTT
1 TTTTTC-TTT
608952 TTTTT-TTT
1 TTTTTCTTT
608960 TT
1 TT
608962 CATTTTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 13 0.50
9 6 0.23
10 7 0.27
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:608944 original size:15 final size:16
Alignment explanation
Indices: 608924--608977 Score: 67
Period size: 15 Copynumber: 3.4 Consensus size: 16
608914 TAAATATCAC
608924 CTTTTTC-TTTTTTTT
1 CTTTTTCATTTTTTTT
608939 CTTTTTTTCATTTTTTTT
1 C--TTTTTCATTTTTTTT
*
608957 -TTTTTCATTTTTTCT
1 CTTTTTCATTTTTTTT
608972 CTTTTT
1 CTTTTT
608978 AAAATATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
15 15 0.44
16 5 0.15
17 6 0.18
18 8 0.24
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (16 bp):
CTTTTTCATTTTTTTT
Found at i:608952 original size:23 final size:23
Alignment explanation
Indices: 608926--608970 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
608916 AATATCACCT
*
608926 TTTTCTTTTTTTTCTTTTTTTCA
1 TTTTCTTTTTTTTCATTTTTTCA
*
608949 TTTTTTTTTTTTTCATTTTTTC
1 TTTTCTTTTTTTTCATTTTTTC
608971 TCTTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTCTTTTTTTTCATTTTTTCA
Found at i:608967 original size:9 final size:8
Alignment explanation
Indices: 608925--608977 Score: 63
Period size: 9 Copynumber: 6.4 Consensus size: 8
608915 AAATATCACC
608925 TTTTTCTTT
1 TTTTTC-TT
608934 TTTTTCTT
1 TTTTTCTT
*
608942 TTTTTCAT
1 TTTTTCTT
608950 TTTTT-TT
1 TTTTTCTT
608957 TTTTTCATT
1 TTTTTC-TT
608966 TTTTCTCTT
1 TTTT-TCTT
608975 TTT
1 TTT
608978 AAAATATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
7 6 0.15
8 14 0.36
9 17 0.44
10 2 0.05
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTCTT
Found at i:608976 original size:23 final size:23
Alignment explanation
Indices: 608931--608977 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
608921 CACCTTTTTC
* *
608931 TTTTTTTTCTTTTTTTCATTTTT
1 TTTTTTTTCATTTTTTCATCTTT
608954 TTTTTTTTCATTTTTTC-TCTTT
1 TTTTTTTTCATTTTTTCATCTTT
608976 TT
1 TT
608978 AAAATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (23 bp):
TTTTTTTTCATTTTTTCATCTTT
Found at i:609744 original size:75 final size:77
Alignment explanation
Indices: 609615--609769 Score: 242
Period size: 75 Copynumber: 2.0 Consensus size: 77
609605 CTCTACTCTC
609615 CCCCTCACTGCCCTTTTTTTAACAAGAGACCCCTGATTTCGAATCCCCTCTCTCTACCTTGTTTT
1 CCCCTCACTGCCCTTTTTTTAACAAGAGACCCCTGATTTCGAATCCCCTCTCTCTACCTTGTTTT
**
609680 TGTTCGGATGAA
66 TGTTCAAATGAA
** * *
609692 CCCC-CACTGCCC-TTTTTTAATGAGAGACCTCTGATTTCGAATCCCTTCTCTCTACCTTGTTTT
1 CCCCTCACTGCCCTTTTTTTAACAAGAGACCCCTGATTTCGAATCCCCTCTCTCTACCTTGTTTT
609755 TGTTCAAATGAA
66 TGTTCAAATGAA
609767 CCC
1 CCC
609770 TGTATTACAA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
75 60 0.83
76 8 0.11
77 4 0.06
ACGTcount: A:0.19, C:0.32, G:0.12, T:0.37
Consensus pattern (77 bp):
CCCCTCACTGCCCTTTTTTTAACAAGAGACCCCTGATTTCGAATCCCCTCTCTCTACCTTGTTTT
TGTTCAAATGAA
Found at i:610136 original size:3 final size:3
Alignment explanation
Indices: 610123--610170 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
610113 CCTACAAGAA
* * *
610123 AAT ATT AAT AAT AAT TA- AAT AAT AAT AAT ATT AAT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
610169 AA
1 AA
610171 AGACGGGTCC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
2 3 0.08
3 34 0.92
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:610713 original size:133 final size:134
Alignment explanation
Indices: 610324--611094 Score: 963
Period size: 133 Copynumber: 5.8 Consensus size: 134
610314 CTGTTTCTGC
* ** * * *
610324 AGGGTAGATCAGA-TCGAGAAATGTTT-ATTCATTTCGCTGCTCTTCAGGGAAGATTGAATC-TA
1 AGGGGAGATCAGACTCGAGAAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCAGA
* * *
610386 A-CGTGATTTGATTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAACAAAAATCTACTCCACTA
66 ATC--GATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTACTCCACTA
610450 CTCTTT
129 CTCTTT
* *
610456 AGGGGAGATCAGACTCGAGAAAACTTTTGATTCACTTCACTACTCTTCA-GGAAGATTGAAT-TG
1 AGGGGAGATCAGACTCGAGAAAAC-TTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCAG
* * * * *
610519 AACTTGATTTGCTTCACTGCTCTTAAGAAAGACCAAATCTGAAAGAAGAAGAATATGCTCCACTA
65 AA-TCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTACTCCACTA
610584 CTCTTT
129 CTCTTT
* * * *
610590 AGGGGAGATCATACTCGAGAAAAC-TTGATTCACTTCGCTGTTCTTTAGGGAAGATTGAATCAGA
1 AGGGGAGATCAGACTCGAGAAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCAGA
* * *
610654 ATCGATTTGCTTCACTGCTCTTCAGGAATACTAAATCTGAAA-AAAAAGGAATCTACTCCACTAC
66 ATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAA-GAATCTACTCCACTAC
610718 TCTTT
130 TCTTT
* * *
610723 AGGGGAGATCAGGCTCGAGAAAACTTTGATCCACTTTACTGCT-TTCAGGGAAGATTGAATCAGA
1 AGGGGAGATCAGACTCGAGAAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCAGA
* * * * * *
610787 ATCGATTTGCTTCACTTCTTTTCAAGAAGTCCAAATCTGAAAGAAGAAGATTCTTCTCCACTACT
66 ATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTACTCCACTACT
610852 CTTT
131 CTTT
* * *
610856 AAGGGAGATCAGACTCGAGAAAACTTT-AATC-TTTCACTGCTCTTCAGGGAAGATTGAATCAGA
1 AGGGGAGATCAGACTCGAGAAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCAGA
* * * * * * *
610919 ATTGATTTGCTTCGCTGCTCTTCAGGAAAACCGAATCTGAAATAAGAAGAATCTGCTCCACTAAT
66 ATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTACTCCACTACT
610984 CTTT
131 CTTT
* ** *
610988 AGGGGAGA-CTAGACTCAAGAAAACTTTGATTCACTTCGTTGCTTTTCAGGGAAGATTGAATCAG
1 AGGGGAGATC-AGACTCGAGAAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCAG
* * *
611052 AATCGATTTTCTTCGCTGCTCTTTAGGAAGACCAAATCTGAAA
65 AATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAA
611095 ATTAAACATT
Statistics
Matches: 549, Mismatches: 75, Indels: 28
0.84 0.12 0.04
Matches are distributed among these distances:
131 9 0.02
132 138 0.25
133 200 0.36
134 185 0.34
135 17 0.03
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (134 bp):
AGGGGAGATCAGACTCGAGAAAACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCAGA
ATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTACTCCACTACT
CTTT
Found at i:611714 original size:45 final size:45
Alignment explanation
Indices: 611598--612070 Score: 332
Period size: 45 Copynumber: 10.8 Consensus size: 45
611588 CAATATTACA
* * * *
611598 GAAAGATTGTCTTCTCTACACGAGAAAGTCAA-AATGGACAACATT
1 GAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAT-GACAACACT
* * * * *** *
611643 AAAAGATCGACAT-TTTTTTGTGAGAAAGTAAAGAATGACAACACT
1 GAAAGATTGAC-TCCTCTTCACGAGAAAGTCAAGAATGACAACACT
* * * *
611688 AAAAGATTGACTCCTCTTCACAAGAAAGTCAAG---GATAATACT
1 GAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACT
* * * * *
611730 AAAATATTGACTCCTCTTGATGAGAAAGTCAATGAA-GACAACACC
1 GAAAGATTGACTCCTCTTCACGAGAAAGTCAA-GAATGACAACACT
* * * * *
611775 AAAATATTGACTCCTCTTCGCGAGAAAGTCAAGAATGACAAAATT
1 GAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACT
*** *
611820 GAAAGATTGACTCCTCTTTGTGAGAAAGTTAAGAAAAT-ACAACACT
1 GAAAGATTGACTCCTCTTCACGAGAAAGTCAAG--AATGACAACACT
** *
611866 GAAAGATTGACTCCTCTTTGCGAGAAAGTCAAG---GATAACACT
1 GAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACT
* * *
611908 AAAATATTGACT--T-TTCACGAGAAAATCAAGGAA-GACAACACT
1 GAAAGATTGACTCCTCTTCACGAGAAAGTCAA-GAATGACAACACT
* * * * *
611950 GAAAGATTGACTCTTTTTCATGAGGAAGTCAAGAATGACAATACT
1 GAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACT
* * * * * *
611995 GAGAGACTGAATTCTCTTCATGAGAAAGCCAAGAAT---AACACT
1 GAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACT
* *
612037 GAAAGATTGACTTCTCTTCACGAGAAAGCCAAGA
1 GAAAGATTGACTCCTCTTCACGAGAAAGTCAAGA
612071 GTAACAAATA
Statistics
Matches: 342, Mismatches: 69, Indels: 37
0.76 0.15 0.08
Matches are distributed among these distances:
39 13 0.04
40 2 0.01
42 105 0.31
43 1 0.00
44 8 0.02
45 169 0.49
46 41 0.12
47 3 0.01
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (45 bp):
GAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACT
Found at i:611739 original size:42 final size:43
Alignment explanation
Indices: 611664--612693 Score: 369
Period size: 38 Copynumber: 25.4 Consensus size: 43
611654 ATTTTTTTGT
* *
611664 GAGAAAGTAAAGAATGACAACACTAAAAGATTGACTCCTCTTCAC
1 GAGAAAGTCAAG-A-GATAACACTAAAAGATTGACTCCTCTTCAC
* * * * *
611709 AAGAAAGTCAAG-GATAATACTAAAATATTGACTCCTCTTGAT
1 GAGAAAGTCAAGAGATAACACTAAAAGATTGACTCCTCTTCAC
* * * *
611751 GAGAAAGTCAATGAAGACAACACCAAAATATTGACTCCTCTTCGC
1 GAGAAAGTCAA-G-AGATAACACTAAAAGATTGACTCCTCTTCAC
* * * * ***
611796 GAGAAAGTCAAGAATGACAAAATTGAAAGATTGACTCCTCTTTGT
1 GAGAAAGTCAAG-A-GATAACACTAAAAGATTGACTCCTCTTCAC
* * * **
611841 GAGAAAGTTAAGAAAATACAACACTGAAAGATTGACTCCTCTTTGC
1 GAGAAAGTCAAG-AGAT--AACACTAAAAGATTGACTCCTCTTCAC
*
611887 GAGAAAGTCAAG-GATAACACTAAAATATTGACT--T-TTCAC
1 GAGAAAGTCAAGAGATAACACTAAAAGATTGACTCCTCTTCAC
* * * * * *
611926 GAGAAAATCAAGGAAGACAACACTGAAAGATTGACTCTTTTTCAT
1 GAGAAAGTCAA-G-AGATAACACTAAAAGATTGACTCCTCTTCAC
* * * * * * * * *
611971 GAGGAAGTCAAGAATGACAATACTGAGAGACTGAATTCTCTTCAT
1 GAGAAAGTCAAG-A-GATAACACTAAAAGATTGACTCCTCTTCAC
* * *
612016 GAGAAAGCCAAGA-ATAACACTGAAAGATTGACTTCTCTTCAC
1 GAGAAAGTCAAGAGATAACACTAAAAGATTGACTCCTCTTCAC
* * *
612058 GAGAAAGCCAAGAG-T-A-AC--AAATATTGACTTCTCTTCAC
1 GAGAAAGTCAAGAGATAACACTAAAAGATTGACTCCTCTTCAC
** ** * *
612096 GAGAAAGTCAA-TTATAACA--AAGATATTTTGAATTCTCTTCAC
1 GAGAAAGTCAAGAGATAACACTAA-A-AGATTGACTCCTCTTCAC
** * * *
612138 GAGGGAGTCAAGA-AT-A-AC--AGATATTGACTTCTCTTCAC
1 GAGAAAGTCAAGAGATAACACTAAAAGATTGACTCCTCTTCAC
* * * * * **
612176 GAGGAAGCCAAGA-CT-A-AC--AGAGATTAACTTATCTTCAC
1 GAGAAAGTCAAGAGATAACACTAAAAGATTGACTCCTCTTCAC
* ** * * * * *
612214 GCGGGAGTCAAGA-ATAACATTGAAAGTTTAACTCCTCTTCAT
1 GAGAAAGTCAAGAGATAACACTAAAAGATTGACTCCTCTTCAC
* *
612256 GAGAAAGTCAAGA-AT-A-A--AAAAGATCGACTTCTCTTCAC
1 GAGAAAGTCAAGAGATAACACTAAAAGATTGACTCCTCTTCAC
* * * *
612294 GAGGAAGTCAAGA-AT--GAC--AAAGATTGACTTCTCTTCAT
1 GAGAAAGTCAAGAGATAACACTAAAAGATTGACTCCTCTTCAC
* * *
612332 GAGGAAGTCAAGA-AT-A-AC--AAAGATTGACTTCTTTTCAC
1 GAGAAAGTCAAGAGATAACACTAAAAGATTGACTCCTCTTCAC
* * *
612370 GAGGAAGTCAAGA-AT-A-AC--AAAGATTGACTTCTCTTCAT
1 GAGAAAGTCAAGAGATAACACTAAAAGATTGACTCCTCTTCAC
* * * * *
612408 GAGGAAGTCGAGA-ATAACATTAAAAGATTGACTCATCTTCGC
1 GAGAAAGTCAAGAGATAACACTAAAAGATTGACTCCTCTTCAC
** * *
612450 GAGGGAGTCAAGA-AT-A-AC--AAAGATTCACTTCTCTTCAC
1 GAGAAAGTCAAGAGATAACACTAAAAGATTGACTCCTCTTCAC
* * *
612488 GAGGAAGTCAAGAG-T-A-AC--AAAGATTGACTTCTCTTTAC
1 GAGAAAGTCAAGAGATAACACTAAAAGATTGACTCCTCTTCAC
* * * * * *
612526 GAGGAAGTCAAGA-AT-A-AC--AATGTTTGATTTCTCTTCAT
1 GAGAAAGTCAAGAGATAACACTAAAAGATTGACTCCTCTTCAC
* * *
612564 GAGGAAGTCAAGA-AT-A-AC--AAATATTGACTCCTCTTCGC
1 GAGAAAGTCAAGAGATAACACTAAAAGATTGACTCCTCTTCAC
** * *
612602 GAGGGATTCAAGA-AT-A-AC--AAAGATTGACTTCTCTTCAC
1 GAGAAAGTCAAGAGATAACACTAAAAGATTGACTCCTCTTCAC
* * * *
612640 AAGGAAGTCAGGAG-T-A-AC--AAAGATTGACTTCTCTTCAC
1 GAGAAAGTCAAGAGATAACACTAAAAGATTGACTCCTCTTCAC
*
612678 GAGAAAGTTAAG-GATA
1 GAGAAAGTCAAGAGATA
612694 GGAAAGAATG
Statistics
Matches: 807, Mismatches: 140, Indels: 82
0.78 0.14 0.08
Matches are distributed among these distances:
37 1 0.00
38 410 0.51
39 16 0.02
40 12 0.01
41 5 0.01
42 189 0.23
43 1 0.00
44 11 0.01
45 127 0.16
46 35 0.04
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.25
Consensus pattern (43 bp):
GAGAAAGTCAAGAGATAACACTAAAAGATTGACTCCTCTTCAC
Found at i:611770 original size:87 final size:86
Alignment explanation
Indices: 611663--612106 Score: 359
Period size: 87 Copynumber: 5.1 Consensus size: 86
611653 CATTTTTTTG
* * *
611663 TGAGAAAGTAAAGAATGACAACACTAAAAGATTGACTCCTCTTCACAAGAAAGTCAAGGATAATA
1 TGAGAAAGTCAAGAA-GACAACACTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAGGATAATA
*
611728 CTAAAATATTGACTCCTCTTGA
65 CTAAAATATTGACTCCTCTTCA
** * * *
611750 TGAGAAAGTCAATGAAGACAACACCAAAATATTGACTCCTCTTCGCGAGAAAGTCAAGAATGACA
1 TGAGAAAGTCAA-GAAGACAACACTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAG---GATA
* * * * **
611815 AAATTGAAAGATTGACTCCTCTTTG
62 ATACTAAAATATTGACTCCTCTTCA
* * ** *
611840 TGAGAAAGTTAAGAAAATACAACACTGAAAGATTGACTCCTCTTTGCGAGAAAGTCAAGGATAAC
1 TGAGAAAGTCAAG--AAGACAACACTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAGGATAAT
611905 ACTAAAATATTGACT--T-TTCA
64 ACTAAAATATTGACTCCTCTTCA
* * * * * * *
611925 CGAGAAAATCAAGGAAGACAACACTGAAAGATTGACTCTTTTTCATGAGGAAGTCAAGAATGACA
1 TGAGAAAGTCAA-GAAGACAACACTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAG---GATA
* * * * * *
611990 ATACTGAGAGACTGAATTCTCTTCA
62 ATACTAAAATATTGACTCCTCTTCA
* * * *
612015 TGAGAAAGCCAAG-A-ATAACACTGAAAGATTGACTTCTCTTCACGAGAAAGCCAA-GAGT-A-A
1 TGAGAAAGTCAAGAAGACAACACTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAGGA-TAATA
*
612075 C--AAATATTGACTTCTCTTCA
65 CTAAAATATTGACTCCTCTTCA
*
612095 CGAGAAAGTCAA
1 TGAGAAAGTCAA
612107 TTATAACAAA
Statistics
Matches: 284, Mismatches: 59, Indels: 35
0.75 0.16 0.09
Matches are distributed among these distances:
80 25 0.09
82 2 0.01
83 3 0.01
84 37 0.13
85 11 0.04
86 2 0.01
87 96 0.34
88 20 0.07
89 3 0.01
90 46 0.16
91 39 0.14
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (86 bp):
TGAGAAAGTCAAGAAGACAACACTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAGGATAATAC
TAAAATATTGACTCCTCTTCA
Found at i:612093 original size:38 final size:38
Alignment explanation
Indices: 612006--612785 Score: 779
Period size: 38 Copynumber: 20.0 Consensus size: 38
611996 AGAGACTGAA
* * *
612006 TTCTCTTCATGAGAAAGCCAAGAATAACACTGAAAGATTGAC
1 TTCTCTTCACGAGGAAGTCAAGAAT-A-AC--AAAGATTGAC
* * * *
612048 TTCTCTTCACGAGAAAGCCAAGAGTAACAAATATTGAC
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
* ** *
612086 TTCTCTTCACGAGAAAGTCAATTATAACAAAGATATTTTGAA
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAG--A--TTGAC
* * *
612128 TTCTCTTCACGAGGGAGTCAAGAATAACAGATATTGAC
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
* * * *
612166 TTCTCTTCACGAGGAAGCCAAGACTAACAGAGATTAAC
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
* * * * *
612204 TTATCTTCACGCGGGAGTCAAGAATAACATTGAAAGTTTAAC
1 TTCTCTTCACGAGGAAGTCAAGAATAAC----AAAGATTGAC
* * * * *
612246 TCCTCTTCATGAGAAAGTCAAGAATAAAAAAGATCGAC
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
*
612284 TTCTCTTCACGAGGAAGTCAAGAATGACAAAGATTGAC
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
*
612322 TTCTCTTCATGAGGAAGTCAAGAATAACAAAGATTGAC
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
*
612360 TTCTTTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
* *
612398 TTCTCTTCATGAGGAAGTCGAGAATAACATTAAAAGATTGAC
1 TTCTCTTCACGAGGAAGTCAAGAATAAC----AAAGATTGAC
* * *
612440 -TCATCTTCGCGAGGGAGTCAAGAATAACAAAGATTCAC
1 TTC-TCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
*
612478 TTCTCTTCACGAGGAAGTCAAGAGTAACAAAGATTGAC
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
* * * *
612516 TTCTCTTTACGAGGAAGTCAAGAATAACAATGTTTGAT
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
* *
612554 TTCTCTTCATGAGGAAGTCAAGAATAACAAATATTGAC
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
* * * *
612592 TCCTCTTCGCGAGGGATTCAAGAATAACAAAGATTGAC
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
* * *
612630 TTCTCTTCACAAGGAAGTCAGGAGTAACAAAGATTGAC
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
* * * ** *
612668 TTCTCTTCACGAGAAAGTTAAGGATAGGAAAGAATGAC
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
* ** * * *
612706 TTCTCTTTATAAGGAAGTCAATAATGACAAATGAAAGATTGAA
1 TTCTCTTCACGAGGAAGTCAAGAAT----AA-CAAAGATTGAC
* *
612749 TCCTCTTCATGAGGAAGTCAAGAATAACAAAGATTGA
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGA
612786 AGTTTCTAGG
Statistics
Matches: 611, Mismatches: 108, Indels: 42
0.80 0.14 0.06
Matches are distributed among these distances:
38 456 0.75
39 4 0.01
40 4 0.01
41 3 0.00
42 114 0.19
43 30 0.05
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (38 bp):
TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
Found at i:614515 original size:15 final size:15
Alignment explanation
Indices: 614488--614531 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
614478 TGAAATACTT
614488 TATTTATTTTCTTT-C
1 TATTT-TTTTCTTTCC
614503 TATTTTTTCTCTTTCC
1 TATTTTTT-TCTTTCC
614519 TATTTTTCTTCTT
1 TATTTTT-TTCTT
614532 CTTCTTCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 3 0.12
15 10 0.38
16 12 0.46
17 1 0.04
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTTTTTTCTTTCC
Found at i:614558 original size:22 final size:22
Alignment explanation
Indices: 614533--614605 Score: 94
Period size: 22 Copynumber: 3.3 Consensus size: 22
614523 TTTCTTCTTC
* *
614533 TTCTTCTTCTATCTTTTCTATT
1 TTCTTTTTATATCTTTTCTATT
614555 TTCTTTTTATATCTTTTCCCT-TT
1 TTCTTTTTATATCTTTT--CTATT
*
614578 TTCTTTTTTTATCTTTTCTATT
1 TTCTTTTTATATCTTTTCTATT
614600 TTCTTT
1 TTCTTT
614606 ATTTTTATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
21 2 0.04
22 23 0.51
23 18 0.40
24 2 0.04
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (22 bp):
TTCTTTTTATATCTTTTCTATT
Found at i:616205 original size:20 final size:20
Alignment explanation
Indices: 616177--616216 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
616167 GAAATACATA
* *
616177 AATGGAAATGTAAAAGGTGT
1 AATGCAAATGCAAAAGGTGT
*
616197 AATGCAAATGCAAGAGGTGT
1 AATGCAAATGCAAAAGGTGT
616217 CATTCTTGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.05, G:0.30, T:0.23
Consensus pattern (20 bp):
AATGCAAATGCAAAAGGTGT
Found at i:619053 original size:20 final size:20
Alignment explanation
Indices: 619003--619053 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 20
618993 AAGTTTTTAG
* *
619003 ATAAAATACA-TATATTAAA
1 ATAAAATATATTATATGAAA
*
619022 ACAAAA-AT-TTATATGAAA
1 ATAAAATATATTATATGAAA
619040 ATAAAATATATTAT
1 ATAAAATATATTAT
619054 TTTGTGCGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
18 14 0.56
19 7 0.28
20 4 0.16
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (20 bp):
ATAAAATATATTATATGAAA
Found at i:620669 original size:78 final size:78
Alignment explanation
Indices: 620586--620746 Score: 277
Period size: 78 Copynumber: 2.1 Consensus size: 78
620576 TCTCTGCTCT
*
620586 CCCCCCTCACTGCCTTTTTTTTTAACGAGAGACCCCTGATTTCGAATCCCCTCTCTACCTTGTTT
1 CCCCCCTCACTGCCCTTTTTTTTAACGAGAGACCCCTGATTTCGAATCCCCTCTCTACCTTGTTT
*
620651 TTATTCTAATGAA
66 TTATTCGAATGAA
* *
620664 CCCCCCTCACTGCCCTTTTTTTTAACGAGAGACCCCTGATTTTGAATCCTCTCTCTACCTTGTTT
1 CCCCCCTCACTGCCCTTTTTTTTAACGAGAGACCCCTGATTTCGAATCCCCTCTCTACCTTGTTT
*
620729 TTGTTCGAATGAA
66 TTATTCGAATGAA
620742 CCCCC
1 CCCCC
620747 ATTACAATCT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.18, C:0.34, G:0.11, T:0.37
Consensus pattern (78 bp):
CCCCCCTCACTGCCCTTTTTTTTAACGAGAGACCCCTGATTTCGAATCCCCTCTCTACCTTGTTT
TTATTCGAATGAA
Done.