Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007937.1 Hibiscus syriacus cultivar Beakdansim tig00110347_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: 820613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:487812 original size:229 final size:229
Alignment explanation
Indices: 487510--488521 Score: 1434
Period size: 229 Copynumber: 4.4 Consensus size: 229
487500 TAGCAAAGAT
* * * *
487510 TCAAATCCATCATTTGATGGATTAGCATTTTCCAATTCGAGTTCATAATGAGAAGAACTCAGCAT
1 TCAAATCCATCACTTGATGGATCAGC-TTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCAT
*
487575 TTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAATCCATCAC
65 CTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAATCCATCAC
487640 TTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGA
130 TTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGA
* *
487705 AATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
195 AATTCATAATGAGAAGAACTTGTTTAACCTTTTAC
* *
487740 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAATTCATAATGAGAAGAACTCATCATT
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCATC
487805 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAATCCATCACT
66 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAATCCATCACT
487870 TGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAA
131 TGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAA
* *
487935 ATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
196 ATTCATAATGAGAAGAACTTGTTTAACCTTTTAC
487969 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAA-T--TCATC
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCATC
* *
488031 TGAAGAAGGAATAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAATTCATCACT
66 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAATCCATCACT
488096 TGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAA
131 TGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAA
* *
488161 GTTCATAATGAGAAGAACTTGTTTAACCTTTTAT
196 ATTCATAATGAGAAGAACTTGTTTAACCTTTTAC
* * * **** *
488195 TCAAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATAAGAAGAACT--T-ATC
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCATC
* * * ** *
488257 TAAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTATTCAAATTCATCACT
66 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAATCCATCACT
* * **** *
488321 TGATGGATCAACATTTCCAGAGAAAGTTCATAATAAGAAGAACTT-ATCTGAAG-AGGAAGAAGA
131 TGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAA-TTCATCTGAAGAAGGAAGAAGA
* * * * *
488384 AGTTCACAATGAGAAGAGCCTGTTCAACCTTTTAC
195 AATTCATAATGAGAAGAACTTGTTTAACCTTTTAC
* * * *
488419 AT-AATTTTATCACAT-ACATGTTAGCATCAGCTTTTGCAGTTCGAGTTCATAATGAGAAGAACT
1 -TCAA----ATC-CATCACTTGAT-GGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACT
* * *
488482 CATCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGA
59 CATCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGA
488522 GCTTATTCAA
Statistics
Matches: 715, Mismatches: 54, Indels: 23
0.90 0.07 0.03
Matches are distributed among these distances:
224 42 0.06
225 98 0.14
226 219 0.31
227 2 0.00
228 8 0.01
229 289 0.40
230 24 0.03
231 1 0.00
232 6 0.01
233 26 0.04
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (229 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCATC
TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAATCCATCACT
TGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAA
ATTCATAATGAGAAGAACTTGTTTAACCTTTTAC
Found at i:487948 original size:24 final size:23
Alignment explanation
Indices: 487905--487949 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
487895 GTTCATAATG
*
487905 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
487928 AGAAGAAATTCATAATG-AGAAG
1 AGAAG-AATTCAT-ATGAAGAAG
487950 AATTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:488174 original size:24 final size:23
Alignment explanation
Indices: 488131--488175 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
488121 GTTCATAATG
*
488131 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
488154 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
488176 AACTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:488773 original size:3 final size:3
Alignment explanation
Indices: 488767--488811 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
488757 TTTACTCATT
* * *
488767 TTA TTA TTA TTA TTA TAA TAA TTA TTA TTA TAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
488812 AAAAAATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:488792 original size:15 final size:15
Alignment explanation
Indices: 488772--488811 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
488762 TCATTTTATT
488772 ATTATTATTATAATA
1 ATTATTATTATAATA
*
488787 ATTATTATTATAATT
1 ATTATTATTATAATA
488802 ATTATTATTA
1 ATTATTATTA
488812 AAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTATTATTATAATA
Found at i:491613 original size:26 final size:28
Alignment explanation
Indices: 491569--491620 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
491559 TAAATTGTAC
491569 CATGGTGATTATATTATAAAT-TTTTCT
1 CATGGTGATTATATTATAAATATTTTCT
491596 CATGG-GA-TATATTGATAAATATTTT
1 CATGGTGATTATATT-ATAAATATTTT
491621 GATATATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 6 0.26
26 8 0.35
27 9 0.39
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (28 bp):
CATGGTGATTATATTATAAATATTTTCT
Found at i:498672 original size:31 final size:31
Alignment explanation
Indices: 498601--498688 Score: 115
Period size: 31 Copynumber: 2.9 Consensus size: 31
498591 ATTTGACCCC
* * * * *
498601 TAAATTTTATATAAAGTATTAATTT-GATCT
1 TAAACTTTAAATAAAATATTAATTTAAATAT
*
498631 TAGACTTTAAATAAAATATTAATTTAAATAT
1 TAAACTTTAAATAAAATATTAATTTAAATAT
498662 TAAACTTTAAATAAAATATTAATTTAA
1 TAAACTTTAAATAAAATATTAATTTAA
498689 CTTATAAATC
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 21 0.42
31 29 0.58
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (31 bp):
TAAACTTTAAATAAAATATTAATTTAAATAT
Found at i:501523 original size:21 final size:20
Alignment explanation
Indices: 501488--501526 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
501478 GAACCAGAAT
*
501488 ATATGTTTCGAAATATTTGA
1 ATATGTTTAGAAATATTTGA
501508 ATATGCTTTAGAAATATTT
1 ATATG-TTTAGAAATATTT
501527 TTATTCGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (20 bp):
ATATGTTTAGAAATATTTGA
Found at i:512010 original size:22 final size:21
Alignment explanation
Indices: 511927--512031 Score: 69
Period size: 22 Copynumber: 5.0 Consensus size: 21
511917 GATAATAGTT
* *
511927 TTAATATTTTTAATATGTATAT
1 TTAAT-TTTTTAATATTTATAA
**
511949 TTAATTTTTTAATAATTTATTT
1 TTAATTTTTTAAT-ATTTATAA
* *
511971 TTTA-TTTTTAGTACATTTATAA
1 TTAATTTTTTA--ATATTTATAA
511993 TTAATTTTTTAAATATTTA-AA
1 TTAATTTTTT-AATATTTATAA
512014 -TAA--TTTT-ATATTTATAA
1 TTAATTTTTTAATATTTATAA
512031 T
1 T
512032 ATAAAATAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
16 7 0.10
17 2 0.03
18 4 0.06
20 3 0.04
21 16 0.24
22 29 0.43
23 6 0.09
24 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (21 bp):
TTAATTTTTTAATATTTATAA
Found at i:512065 original size:27 final size:24
Alignment explanation
Indices: 512009--512067 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
511999 TTTTAAATAT
* *
512009 TTAAATAATTTTATATTTATAATA
1 TTAAATAATTTTAAATTTATAAAA
*
512033 TAAAATAATTTTAAACTTTTGATAAAA
1 TTAAATAATTTTAAA--TTT-ATAAAA
512060 TTAAATAA
1 TTAAATAA
512068 GCCTTAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 13 0.46
26 3 0.11
27 12 0.43
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
TTAAATAATTTTAAATTTATAAAA
Found at i:513052 original size:39 final size:42
Alignment explanation
Indices: 513000--513107 Score: 114
Period size: 47 Copynumber: 2.5 Consensus size: 42
512990 AAAAGTAGTT
*
513000 TAAACTTTGAGTTATTAAAATAT-T-A-ATAAAATAAATAAAA
1 TAAA-TTTGAGTTATTAAAATATGTCATAAAAAATAAATAAAA
*
513040 TAAATTTGAGTTATTAATAGATGCCATGTCATAAAAAATTAATAAAA
1 TAAATTTGAGTTATTAA-A-AT---ATGTCATAAAAAATAAATAAAA
*
513087 TAAATTTAAGTTATTAAAATA
1 TAAATTTGAGTTATTAAAATA
513108 AGAGTAATTC
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
39 13 0.23
40 5 0.09
41 2 0.04
42 1 0.02
44 2 0.04
45 3 0.05
46 2 0.04
47 29 0.51
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (42 bp):
TAAATTTGAGTTATTAAAATATGTCATAAAAAATAAATAAAA
Found at i:519593 original size:15 final size:14
Alignment explanation
Indices: 519573--519684 Score: 50
Period size: 14 Copynumber: 8.0 Consensus size: 14
519563 CATGCATGCA
519573 TTTGCATTTCACATT
1 TTTGCATTT-ACATT
*
519588 TTTGCATTTTCATT
1 TTTGCATTTACATT
* * * *
519602 TTTGTATTCATACT
1 TTTGCATTTACATT
** *
519616 TTTGTGTTT--GTT
1 TTTGCATTTACATT
**
519628 TTTGCATTT-CAAG
1 TTTGCATTTACATT
**
519641 TTTGCATTTTTATT
1 TTTGCATTTACATT
519655 TTTGCATTTATGCATT
1 TTTGCATTTA--CATT
**
519671 TTCACATTTACATT
1 TTTGCATTTACATT
519685 ACATTTTTTA
Statistics
Matches: 71, Mismatches: 22, Indels: 9
0.70 0.22 0.09
Matches are distributed among these distances:
12 8 0.11
13 9 0.13
14 34 0.48
15 9 0.13
16 11 0.15
ACGTcount: A:0.18, C:0.13, G:0.10, T:0.59
Consensus pattern (14 bp):
TTTGCATTTACATT
Found at i:524352 original size:24 final size:20
Alignment explanation
Indices: 524295--524352 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
524285 TTTCCCTTGA
*
524295 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
524315 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
524338 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
524353 CTCCATATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
21 1 0.03
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:528996 original size:75 final size:75
Alignment explanation
Indices: 528869--529011 Score: 180
Period size: 75 Copynumber: 1.9 Consensus size: 75
528859 CAACAAGAAG
* * * *
528869 CAAATACTGGGGTATGCTAAAAACCCATTTCAATCATAATCAGGAATATTGACGCCTTTTGAATG
1 CAAATACTGGGGCATGCTAAAAACCCATTTCAATCAAAATCAGGAATATTGACGCATTTTGAAAG
528934 TTCACGTCAA
66 TTCACGTCAA
* * * * * *
528944 CAAATGCTGGGGCATGCTGAAAGCCTATTTCAATCAGAAAT-ATGAATGTTGACGCATTTTGAAA
1 CAAATACTGGGGCATGCTAAAAACCCATTTCAATCA-AAATCAGGAATATTGACGCATTTTGAAA
529008 GTTC
65 GTTC
529012 GTATCAGCAA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
75 54 0.95
76 3 0.05
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (75 bp):
CAAATACTGGGGCATGCTAAAAACCCATTTCAATCAAAATCAGGAATATTGACGCATTTTGAAAG
TTCACGTCAA
Found at i:529994 original size:54 final size:53
Alignment explanation
Indices: 529914--530073 Score: 214
Period size: 54 Copynumber: 3.0 Consensus size: 53
529904 GATCAGAAAT
*
529914 CTGTGCAGAAACCACAGAAAATGATGAATGTGTTGTCAAATGCTTTACGAACAC
1 CTGTGCAGAAACCACAG-AAATGATGAATGTGTTGTCAAATGTTTTACGAACAC
* * * *
529968 CTG-GTCAGAAGCCACAAGAAAGGATGAATGTGTTATCAAATGTTTTACGAACAT
1 CTGTG-CAGAAACCAC-AGAAATGATGAATGTGTTGTCAAATGTTTTACGAACAC
* *
530022 CTGTGCAGAAACCACGAGAAATGATGAATGTATTGTCACATGTTTTACGAAC
1 CTGTGCAGAAACCAC-AGAAATGATGAATGTGTTGTCAAATGTTTTACGAAC
530074 CAGTGATTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
53 1 0.01
54 88 0.96
55 3 0.03
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (53 bp):
CTGTGCAGAAACCACAGAAATGATGAATGTGTTGTCAAATGTTTTACGAACAC
Found at i:531218 original size:45 final size:45
Alignment explanation
Indices: 531154--531344 Score: 339
Period size: 45 Copynumber: 4.3 Consensus size: 45
531144 TTTCCACATA
*
531154 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCGTC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
*
531199 TGTAAGCCCTTCAGTGCATGATGATTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
*
531244 TGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTT-GGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
531288 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
*
531333 TGTAAGACCTTC
1 TGTAAGCCCTTC
531345 GGGTCATCTG
Statistics
Matches: 139, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
44 43 0.31
45 96 0.69
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (45 bp):
TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
Found at i:531316 original size:89 final size:90
Alignment explanation
Indices: 531154--531344 Score: 348
Period size: 89 Copynumber: 2.1 Consensus size: 90
531144 TTTCCACATA
* *
531154 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCGTCTGTAAGCCCTTCAGTGCATG
1 TGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
531219 ATGATTTCAAAACCTTCGGGTCATC
66 ATGATTTCAAAACCTTCGGGTCATC
531244 TGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTT-GGGTCATCTGTAAGCCCTTCAGTGCATG
1 TGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
*
531308 ATGTTTTCAAAACCTTCGGGTCATC
66 ATGATTTCAAAACCTTCGGGTCATC
531333 TGTAAGACCTTC
1 TGTAAGACCTTC
531345 GGGTCATCTG
Statistics
Matches: 98, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
89 63 0.64
90 35 0.36
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (90 bp):
TGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
ATGATTTCAAAACCTTCGGGTCATC
Found at i:531344 original size:20 final size:20
Alignment explanation
Indices: 531319--531364 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
531309 TGTTTTCAAA
531319 ACCTTCGGGTCATCTGTAAG
1 ACCTTCGGGTCATCTGTAAG
531339 ACCTTCGGGTCATCTGTAAG
1 ACCTTCGGGTCATCTGTAAG
531359 ACCTTC
1 ACCTTC
531365 AGTGCATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.30
Consensus pattern (20 bp):
ACCTTCGGGTCATCTGTAAG
Found at i:531354 original size:65 final size:65
Alignment explanation
Indices: 531275--531409 Score: 236
Period size: 65 Copynumber: 2.1 Consensus size: 65
531265 TGTTTTCAAA
*
531275 ACCTT-GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAG
1 ACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAG
*
531339 ACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTGATCTGTAAG
1 ACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAG
*
531404 CCCTTC
1 ACCTTC
531410 AGTGCATGAT
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
64 5 0.07
65 62 0.93
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.33
Consensus pattern (65 bp):
ACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAG
Found at i:531403 original size:45 final size:45
Alignment explanation
Indices: 531339--531469 Score: 244
Period size: 45 Copynumber: 2.9 Consensus size: 45
531329 CATCTGTAAG
*
531339 ACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAA
1 ACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
*
531384 ACCTTCGGGTGATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 ACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
531429 ACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTT
1 ACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTT
531470 AACATTTCCA
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 83 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.34
Consensus pattern (45 bp):
ACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
Found at i:531433 original size:25 final size:25
Alignment explanation
Indices: 531359--531434 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
531349 CATCTGTAAG
531359 ACCTTCAGTGCATGATGTTTTCAAA
1 ACCTTCAGTGCATGATGTTTTCAAA
* * * *
531384 ACCTTC-G-G-GTGAT-CTGT-AAG
1 ACCTTCAGTGCATGATGTTTTCAAA
*
531404 CCCTTCAGTGCATGATGTTTTCAAA
1 ACCTTCAGTGCATGATGTTTTCAAA
531429 ACCTTC
1 ACCTTC
531435 GGGTCATCTG
Statistics
Matches: 36, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
20 7 0.19
21 3 0.08
22 5 0.14
23 5 0.14
24 3 0.08
25 13 0.36
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (25 bp):
ACCTTCAGTGCATGATGTTTTCAAA
Found at i:531444 original size:110 final size:109
Alignment explanation
Indices: 531230--531454 Score: 423
Period size: 110 Copynumber: 2.1 Consensus size: 109
531220 TGATTTCAAA
531230 ACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTGGGTCATCTGTAAGC
1 ACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTGGGTCATCTGTAAGC
531295 CCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAG
66 CCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAG
*
531339 ACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTGATCTGTAAG
1 ACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTT-GGGTCATCTGTAAG
531404 CCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAG
65 CCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAG
*
531449 CCCTTC
1 ACCTTC
531455 AGTGCATGAT
Statistics
Matches: 113, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
109 50 0.44
110 63 0.56
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (109 bp):
ACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTGGGTCATCTGTAAGC
CCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAG
Found at i:531605 original size:3 final size:3
Alignment explanation
Indices: 531599--531659 Score: 68
Period size: 3 Copynumber: 19.7 Consensus size: 3
531589 TCATTTGATT
** * *
531599 TTA TTA TTA TTA TTA TTA AAA TTA TCA TCA TTA TTA TATA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA T-TA
531646 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
531660 TAAATAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
3 44 0.88
4 6 0.12
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:532669 original size:13 final size:13
Alignment explanation
Indices: 532651--532675 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
532641 TCGACCTTTA
532651 AGTATTTTAATTC
1 AGTATTTTAATTC
532664 AGTATTTTAATT
1 AGTATTTTAATT
532676 TTATTTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (13 bp):
AGTATTTTAATTC
Found at i:533134 original size:2 final size:2
Alignment explanation
Indices: 533127--533189 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
533117 TATGCTTAAA
533127 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
533169 AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT A
533190 AATTATTTTA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:538344 original size:59 final size:59
Alignment explanation
Indices: 538280--538391 Score: 215
Period size: 59 Copynumber: 1.9 Consensus size: 59
538270 GGTAATTCGT
538280 GTTTTTCTCCAATGCATCAATCAACGGGATATTGATTGTTAATTATTTAAGCAATTCAA
1 GTTTTTCTCCAATGCATCAATCAACGGGATATTGATTGTTAATTATTTAAGCAATTCAA
*
538339 GTTTTTCTCCAATGCATCAATCAACTGGATATTGATTGTTAATTATTTAAGCA
1 GTTTTTCTCCAATGCATCAATCAACGGGATATTGATTGTTAATTATTTAAGCA
538392 CACTTATGAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (59 bp):
GTTTTTCTCCAATGCATCAATCAACGGGATATTGATTGTTAATTATTTAAGCAATTCAA
Found at i:543023 original size:21 final size:21
Alignment explanation
Indices: 542997--543037 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
542987 CCGAATTGTG
542997 CCCCCTTTATTGAAAATCACT
1 CCCCCTTTATTGAAAATCACT
*
543018 CCCCCTTTGTTGAAAATCAC
1 CCCCCTTTATTGAAAATCAC
543038 CCGGCGGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.34, G:0.07, T:0.32
Consensus pattern (21 bp):
CCCCCTTTATTGAAAATCACT
Found at i:544366 original size:22 final size:22
Alignment explanation
Indices: 544340--544390 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
544330 TTTTTCTTGT
544340 CTGCCTCTATGAAGCCTTCTGG
1 CTGCCTCTATGAAGCCTTCTGG
*
544362 TTGCCTCTATGAAGCCTTCTGG
1 CTGCCTCTATGAAGCCTTCTGG
544384 CTGCCTC
1 CTGCCTC
544391 ATATAGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.12, C:0.33, G:0.22, T:0.33
Consensus pattern (22 bp):
CTGCCTCTATGAAGCCTTCTGG
Found at i:547646 original size:21 final size:21
Alignment explanation
Indices: 547622--547661 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
547612 CCGAATTGTG
*
547622 CCCCTTTGTTGAAAATCACTC
1 CCCCTTCGTTGAAAATCACTC
547643 CCCCTTCGTTGAAAATCAC
1 CCCCTTCGTTGAAAATCAC
547662 CCGGCGGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.10, T:0.30
Consensus pattern (21 bp):
CCCCTTCGTTGAAAATCACTC
Found at i:548012 original size:37 final size:37
Alignment explanation
Indices: 547945--548051 Score: 114
Period size: 37 Copynumber: 2.9 Consensus size: 37
547935 ATAAAAAATT
* *
547945 TAAA-AATATAATCATATTTTAATTAAATATAAAT-TCA
1 TAAATAATATATTCATA-TTTAATCAAATATAAATGT-A
*
547982 TAAATAATATATTTATATTTAATCAAATATAAATGTA
1 TAAATAATATATTCATATTTAATCAAATATAAATGTA
* *
548019 TAAAT-A-CTATTCATATTTCAATCGAATATAAAT
1 TAAATAATATATTCATATTT-AATCAAATATAAAT
548052 CCTTATATAA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
35 10 0.16
36 14 0.23
37 26 0.43
38 11 0.18
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (37 bp):
TAAATAATATATTCATATTTAATCAAATATAAATGTA
Found at i:568895 original size:20 final size:20
Alignment explanation
Indices: 568853--568895 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
568843 GGAGAAGGAA
* *
568853 AAAGAGAAGTGAAAATGAAG
1 AAAGAGAAGAGAAAAAGAAG
* *
568873 AAAGTGAAGAGAAAAAGATG
1 AAAGAGAAGAGAAAAAGAAG
568893 AAA
1 AAA
568896 ATAGATATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.28, T:0.09
Consensus pattern (20 bp):
AAAGAGAAGAGAAAAAGAAG
Found at i:573088 original size:23 final size:23
Alignment explanation
Indices: 573041--573088 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
573031 ATTATCTTTA
*
573041 TTTATTATTTTATTATTTTTCTT
1 TTTATTATTTTATTATTTTTATT
573064 TTTATT-TATTTATT-TATTTTATT
1 TTTATTAT-TTTATTAT-TTTTATT
573087 TT
1 TT
573089 ACTCTATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTATTATTTTATTATTTTTATT
Found at i:573249 original size:87 final size:86
Alignment explanation
Indices: 573099--573273 Score: 323
Period size: 87 Copynumber: 2.0 Consensus size: 86
573089 ACTCTATCTT
*
573099 CTCACATTTATCTGAAATTCTATCTTCTTCTAAAATTAAGAAACAAATTCACTAAATCGGAAACA
1 CTCACATTTATCTGAAATTCTATCTTCTTCTAAAATTAAGAAACAAATTCACTAAATCAGAAACA
573164 AAATTTCTATGGATCGACCCTG
66 AAA-TTCTATGGATCGACCCTG
*
573186 CTCACCTTTATCTGAAATTCTATCTTCTTCTAAAATTAAGAAACAAATTCACTAAATCAGAAACA
1 CTCACATTTATCTGAAATTCTATCTTCTTCTAAAATTAAGAAACAAATTCACTAAATCAGAAACA
573251 AAATTCTATGGATCGACCCTG
66 AAATTCTATGGATCGACCCTG
573272 CT
1 CT
573274 TCACTATACT
Statistics
Matches: 86, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
86 20 0.23
87 66 0.77
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.32
Consensus pattern (86 bp):
CTCACATTTATCTGAAATTCTATCTTCTTCTAAAATTAAGAAACAAATTCACTAAATCAGAAACA
AAATTCTATGGATCGACCCTG
Found at i:575968 original size:13 final size:13
Alignment explanation
Indices: 575901--575961 Score: 113
Period size: 13 Copynumber: 4.7 Consensus size: 13
575891 TGCGTCATAA
*
575901 ATTTATGACGCGC
1 ATTTATGACACGC
575914 ATTTATGACACGC
1 ATTTATGACACGC
575927 ATTTATGACACGC
1 ATTTATGACACGC
575940 ATTTATGACACGC
1 ATTTATGACACGC
575953 ATTTATGAC
1 ATTTATGAC
575962 GCTCATTGCG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (13 bp):
ATTTATGACACGC
Found at i:575968 original size:26 final size:26
Alignment explanation
Indices: 575901--575968 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
575891 TGCGTCATAA
575901 ATTTATGACGCGCATTTATGACACGC
1 ATTTATGACGCGCATTTATGACACGC
*
575927 ATTTATGACACGCATTTATGACACGC
1 ATTTATGACGCGCATTTATGACACGC
*
575953 ATTTATGACGCTCATT
1 ATTTATGACGCGCATT
575969 GCGCATCATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (26 bp):
ATTTATGACGCGCATTTATGACACGC
Found at i:576011 original size:57 final size:57
Alignment explanation
Indices: 575944--576069 Score: 164
Period size: 57 Copynumber: 2.2 Consensus size: 57
575934 ACACGCATTT
* *
575944 ATGACACGCATTTATGACGCT-CATTGCGCATCATTGAAGCCCCCGTCATAAATAAAG
1 ATGACACGCATTTATGAC-CTACATTGCACATCATTGAAGCCCCCATCATAAATAAAG
* * * * *
576001 ATGACACGCATGTATGACTTACATTGCATATCATTGAAGCCCCTATCATAAATGAAG
1 ATGACACGCATTTATGACCTACATTGCACATCATTGAAGCCCCCATCATAAATAAAG
*
576058 ATGACACACATT
1 ATGACACGCATT
576070 GTGTGTCAGA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
56 1 0.02
57 58 0.98
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (57 bp):
ATGACACGCATTTATGACCTACATTGCACATCATTGAAGCCCCCATCATAAATAAAG
Found at i:579023 original size:2 final size:2
Alignment explanation
Indices: 579016--579046 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
579006 TGTGTTGCAA
579016 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
579047 CTTCTTACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:580375 original size:45 final size:45
Alignment explanation
Indices: 580319--580455 Score: 210
Period size: 44 Copynumber: 3.1 Consensus size: 45
580309 AAGAACAGGG
*
580319 GAAATCGAATAACAAGCTAAGCGGGAAAGGATGAAAATAATGGGA
1 GAAATCAAATAACAAGCTAAGCGGGAAAGGATGAAAATAATGGGA
*
580364 GAAATCAAATAACAAGCTAA-CCGGAAAGGATGAAAATAATAGGG-
1 GAAATCAAATAACAAGCTAAGCGGGAAAGGATGAAAATAAT-GGGA
*
580408 TAAATCAAATAACAAGCTAAGCGGG-AAGGATGAAAATAATGGGA
1 GAAATCAAATAACAAGCTAAGCGGGAAAGGATGAAAATAATGGGA
580452 -AAAT
1 GAAAT
580456 TAAAAGACGA
Statistics
Matches: 85, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
43 7 0.08
44 53 0.62
45 25 0.29
ACGTcount: A:0.51, C:0.09, G:0.25, T:0.15
Consensus pattern (45 bp):
GAAATCAAATAACAAGCTAAGCGGGAAAGGATGAAAATAATGGGA
Found at i:580885 original size:19 final size:19
Alignment explanation
Indices: 580863--580909 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
580853 TATAAATTCA
580863 TAAATAATATATACGA-ATT
1 TAAATAATATATA-GATATT
580882 TAAATTAA-ATATAGATATT
1 TAAA-TAATATATAGATATT
*
580901 TGAATAATA
1 TAAATAATA
580910 GAATATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 5 0.21
19 16 0.67
20 3 0.12
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.38
Consensus pattern (19 bp):
TAAATAATATATAGATATT
Found at i:585413 original size:18 final size:18
Alignment explanation
Indices: 585390--585452 Score: 90
Period size: 18 Copynumber: 3.5 Consensus size: 18
585380 TAGGAATTTA
585390 TTCGGGACATAGTGGTCC
1 TTCGGGACATAGTGGTCC
*
585408 TTCGGGACATAGTGGTCA
1 TTCGGGACATAGTGGTCC
* *
585426 TTCGGGACAAAGTGCTCC
1 TTCGGGACATAGTGGTCC
*
585444 TTTGGGACA
1 TTCGGGACA
585453 AATTTTAAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.27
Consensus pattern (18 bp):
TTCGGGACATAGTGGTCC
Found at i:586546 original size:22 final size:22
Alignment explanation
Indices: 586518--586560 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
586508 GAATTTGGGA
586518 TCTTTCAACACAAACCAAATTT
1 TCTTTCAACACAAACCAAATTT
*
586540 TCTTTCAGCACAAACCAAATT
1 TCTTTCAACACAAACCAAATT
586561 ATTTTCGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.28, G:0.02, T:0.30
Consensus pattern (22 bp):
TCTTTCAACACAAACCAAATTT
Found at i:594533 original size:24 final size:25
Alignment explanation
Indices: 594501--594557 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 25
594491 AAATATATAT
594501 TTTCAACCACA-CAAGTTATATTCG
1 TTTCAACCACAGCAAGTTATATTCG
* *
594525 TTTCGACCACAGTTAAGTTATATTCG
1 TTTCAACCACAG-CAAGTTATATTCG
594551 TTTCAAC
1 TTTCAAC
594558 AATAAGGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 10 0.36
26 18 0.64
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.37
Consensus pattern (25 bp):
TTTCAACCACAGCAAGTTATATTCG
Found at i:595145 original size:15 final size:15
Alignment explanation
Indices: 595125--595156 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
595115 TAAATGATAG
595125 CACCTTGTCATCAAT
1 CACCTTGTCATCAAT
595140 CACCTTGTCATCAAT
1 CACCTTGTCATCAAT
595155 CA
1 CA
595157 ACTACATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.34, G:0.06, T:0.31
Consensus pattern (15 bp):
CACCTTGTCATCAAT
Found at i:596785 original size:32 final size:32
Alignment explanation
Indices: 596748--596810 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
596738 GCATAAATAG
596748 TTGACTAACAAGTTATGCTTAAAACAACGTCA
1 TTGACTAACAAGTTATGCTTAAAACAACGTCA
596780 TTGACTAACAAGTTATGCTTAAAACAACGTC
1 TTGACTAACAAGTTATGCTTAAAACAACGTC
596811 TTTATTTGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.29
Consensus pattern (32 bp):
TTGACTAACAAGTTATGCTTAAAACAACGTCA
Found at i:599513 original size:13 final size:13
Alignment explanation
Indices: 599495--599544 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
599485 CTTAGCATGT
599495 TTAAAAATAAAAC
1 TTAAAAATAAAAC
599508 TT-AAAATAAAA-
1 TTAAAAATAAAAC
*
599519 TAAAAAATGAAAAC
1 TTAAAAAT-AAAAC
* *
599533 TTGAAAAGAAAA
1 TTAAAAATAAAA
599545 GAAAAGAGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
11 1 0.03
12 14 0.47
13 10 0.33
14 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.06, T:0.20
Consensus pattern (13 bp):
TTAAAAATAAAAC
Found at i:599531 original size:25 final size:25
Alignment explanation
Indices: 599497--599549 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
599487 TAGCATGTTT
* *
599497 AAAAATAAAACTT-AAAATAAAATA
1 AAAAATAAAACTTGAAAAGAAAAGA
599521 AAAAATGAAAACTTGAAAAGAAAAGA
1 AAAAAT-AAAACTTGAAAAGAAAAGA
599547 AAA
1 AAA
599550 GAGAGAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 6 0.24
25 7 0.28
26 12 0.48
ACGTcount: A:0.74, C:0.04, G:0.08, T:0.15
Consensus pattern (25 bp):
AAAAATAAAACTTGAAAAGAAAAGA
Found at i:602062 original size:6 final size:6
Alignment explanation
Indices: 602027--602085 Score: 55
Period size: 6 Copynumber: 9.3 Consensus size: 6
602017 GAAAAATAAA
* * * *
602027 AAAAAT AAATAAG AAAAAT AAAATT GAAAAT AAAAAT AAAAATT GGAAAAT
1 AAAAAT AAA-AAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA-T -AAAAAT
602078 AAAAAT AA
1 AAAAAT AA
602086 TAATGGGTTG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
6 31 0.74
7 7 0.17
8 4 0.10
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.19
Consensus pattern (6 bp):
AAAAAT
Found at i:602062 original size:19 final size:20
Alignment explanation
Indices: 602040--602085 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
602030 AATAAATAAG
602040 AAAAAT-AAAATT-GAAAAT
1 AAAAATAAAAATTGGAAAAT
602058 AAAAATAAAAATTGGAAAAT
1 AAAAATAAAAATTGGAAAAT
602078 AAAAATAA
1 AAAAATAA
602086 TAATGGGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 6 0.23
19 6 0.23
20 14 0.54
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (20 bp):
AAAAATAAAAATTGGAAAAT
Found at i:605260 original size:14 final size:14
Alignment explanation
Indices: 605241--605269 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
605231 TCGGTTTGTG
605241 AATTGATCTAAGCA
1 AATTGATCTAAGCA
605255 AATTGATCTAAGCA
1 AATTGATCTAAGCA
605269 A
1 A
605270 CAATAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (14 bp):
AATTGATCTAAGCA
Found at i:606581 original size:32 final size:32
Alignment explanation
Indices: 606545--606692 Score: 140
Period size: 32 Copynumber: 4.6 Consensus size: 32
606535 GTAACTGATA
* * *
606545 TGCATTATCTAAATGTGATACTGACACTCTTG
1 TGCATTATCTAAATGTAACACTGACTCTCTTG
* * * *
606577 TGCATTATATAAAT-TCAAAAATGA-TCTTGTTG
1 TGCATTATCTAAATGT-AACACTGACTC-TCTTG
* * *
606609 TGAATTATCTAAATGCAACACTGACTCTATTG
1 TGCATTATCTAAATGTAACACTGACTCTCTTG
*
606641 TGCATTATCTAAATGTAACACTAACTCTGCTT-
1 TGCATTATCTAAATGTAACACTGACTCT-CTTG
*
606673 TGCATTATCTAAATGCAACA
1 TGCATTATCTAAATGTAACA
606693 TTAACATTAC
Statistics
Matches: 94, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
31 2 0.02
32 88 0.94
33 4 0.04
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (32 bp):
TGCATTATCTAAATGTAACACTGACTCTCTTG
Found at i:608351 original size:45 final size:44
Alignment explanation
Indices: 608289--608610 Score: 401
Period size: 45 Copynumber: 7.2 Consensus size: 44
608279 TATACTTTAT
* * * *
608289 TTTCATTTATAGTATCCTTTCATGCTTATAATGCACCGTTATGTA
1 TTTCATTTATGGCATCCTTTCATGCGT-TAATGCACCGTTATGCA
* *
608334 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATG-CGTTAATGCACCGTTATGCA
*
608379 TTTCTTTTATGGCATCCTTTCATGTCGTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATG-CGTTAATGCACCGTTATGCA
* * **
608424 TTTCATTTATGACATCCTTTCATGTGGTTAATGCACATTTATGCA
1 TTTCATTTATGGCATCCTTTCATG-CGTTAATGCACCGTTATGCA
*
608469 TTTCATTTATGGCATCCTTTCATGTCGTTAATGCACCGTTATGCG
1 TTTCATTTATGGCATCCTTTCATG-CGTTAATGCACCGTTATGCA
* **
608514 TTTCATTTATGGCATCCTTTCATATCGTTAATGCACCGTTACACA
1 TTTCATTTATGGCATCCTTTCAT-GCGTTAATGCACCGTTATGCA
* * * * *
608559 TTTCATTTATGGCATCATTTCATGCCATTAATACACTGTTATGTA
1 TTTCATTTATGGCATCCTTTCATG-CGTTAATGCACCGTTATGCA
608604 TTTCATT
1 TTTCATT
608611 CATTCATTTT
Statistics
Matches: 242, Mismatches: 32, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
45 241 1.00
46 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.44
Consensus pattern (44 bp):
TTTCATTTATGGCATCCTTTCATGCGTTAATGCACCGTTATGCA
Found at i:614342 original size:45 final size:45
Alignment explanation
Indices: 614291--614660 Score: 499
Period size: 45 Copynumber: 8.2 Consensus size: 45
614281 TATCCTTTAT
* * *
614291 TTTCATTTATAACATCTTTTCAT-CCTTATAATGCACCGTTATGCA
1 TTTCATTTATGACATCCTTTCATGCCGT-TAATGCACCGTTATGCA
* * *
614336 TTTCATTTATGACATCATTTCATGCCGATAATGCACAGTTATGCA
1 TTTCATTTATGACATCCTTTCATGCCGTTAATGCACCGTTATGCA
*
614381 TTTCATTTATGACATCCTTTCATGTCGTTAATGCACCGTTATGCA
1 TTTCATTTATGACATCCTTTCATGCCGTTAATGCACCGTTATGCA
* * *
614426 TTTCATATATGACATTCTTTCATGTCGTTAATGCACCGTTATGCA
1 TTTCATTTATGACATCCTTTCATGCCGTTAATGCACCGTTATGCA
* * * * *
614471 TTTCATTTATGGCATCATTTTATACCGTTAATGCACCATTATGCA
1 TTTCATTTATGACATCCTTTCATGCCGTTAATGCACCGTTATGCA
* *
614516 TTTCATTTAGGACATCCTTTCATCCCGTTAATGCACCGTTATGCA
1 TTTCATTTATGACATCCTTTCATGCCGTTAATGCACCGTTATGCA
* * * *
614561 TTTCGTTTATGGCATCCTTTCATGTCGTTAATGCACTGTTATGCA
1 TTTCATTTATGACATCCTTTCATGCCGTTAATGCACCGTTATGCA
* * *
614606 TTTCATTTATGGCATCCTTTCATCCCGTTAATGCACCGTTATGTA
1 TTTCATTTATGACATCCTTTCATGCCGTTAATGCACCGTTATGCA
*
614651 TTTTATTTAT
1 TTTCATTTAT
614661 TTATTCATTT
Statistics
Matches: 287, Mismatches: 37, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 285 0.99
46 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (45 bp):
TTTCATTTATGACATCCTTTCATGCCGTTAATGCACCGTTATGCA
Found at i:615129 original size:41 final size:41
Alignment explanation
Indices: 615084--615228 Score: 103
Period size: 41 Copynumber: 3.2 Consensus size: 41
615074 CCCTACCATG
615084 GTATCGATATTTCTATACTATGGTATCGATACTCCCTTTCA
1 GTATCGATATTTCTATACTATGGTATCGATACTCCCTTTCA
* * **
615125 GTATCGATGCCATTTCTACATTTTGTAATTCATGGTATTGATACATTTCTCTT-A
1 GTATCGAT---ATTTCT--A-----T-ACT-ATGGTATCGATAC-TCCCT-TTCA
* *
615179 GTATCGATACTTCTATACTATGGTACCGATACTCCCTTTCA
1 GTATCGATATTTCTATACTATGGTATCGATACTCCCTTTCA
615220 GTATCGATA
1 GTATCGATA
615229 CCATTTCTAC
Statistics
Matches: 79, Mismatches: 10, Indels: 30
0.66 0.08 0.25
Matches are distributed among these distances:
40 2 0.03
41 21 0.27
42 11 0.14
43 2 0.03
44 7 0.09
46 1 0.01
49 1 0.01
51 6 0.08
52 2 0.03
53 12 0.15
54 12 0.15
55 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (41 bp):
GTATCGATATTTCTATACTATGGTATCGATACTCCCTTTCA
Found at i:620961 original size:81 final size:81
Alignment explanation
Indices: 620860--621124 Score: 320
Period size: 82 Copynumber: 3.2 Consensus size: 81
620850 CCAAATAATG
* * * * *
620860 GTGGTGCATTATCATCTTTTGCAACGTTTCATATGTCATTCAATGCATAATTCAAACAA-ATTTC
1 GTGGTGCATTATCATCTTTTGCAACTTTTCAAAGGTCATTCAATGCATAATTTAAACAACTTTTC
* *
620924 AATCATCGAGTAAAATA
66 AA-CAACGAGTGAAATA
* * * *
620941 GTGGTGCATTATCATATTTTGCAACTTTTCAAAGGTCATTCAATACATAGTTTAAATAACTTTTC
1 GTGGTGCATTATCATCTTTTGCAACTTTTCAAAGGTCATTCAATGCATAATTTAAACAACTTTTC
621006 AGACAAC-AGGTGAAATA
66 A-ACAACGA-GTGAAATA
* * *
621023 ATGGTGTATTATCATCTTCTAG-AACTTTTCAAAGGTCATTCAATGCATAATTTAAACAACTTTT
1 GTGGTGCATTATCATCTT-TTGCAACTTTTCAAAGGTCATTCAATGCATAATTTAAACAACTTTT
* *
621087 CAAAAAACGGGTGAAATA
65 C-AACAACGAGTGAAATA
621105 GTGGTGCATTATCATCTTTT
1 GTGGTGCATTATCATCTTTT
621125 TCAGTGATGT
Statistics
Matches: 155, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
81 53 0.34
82 98 0.63
83 4 0.03
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (81 bp):
GTGGTGCATTATCATCTTTTGCAACTTTTCAAAGGTCATTCAATGCATAATTTAAACAACTTTTC
AACAACGAGTGAAATA
Found at i:622528 original size:11 final size:11
Alignment explanation
Indices: 622507--622536 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
622497 CTATGAGTAG
622507 ATATT-ATCTT
1 ATATTAATCTT
622517 ATATTAATCTT
1 ATATTAATCTT
622528 ATATTAATC
1 ATATTAATC
622537 AAAACTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (11 bp):
ATATTAATCTT
Found at i:628428 original size:18 final size:18
Alignment explanation
Indices: 628405--628442 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
628395 AGATTGATAA
*
628405 AAAAAAGGGATCACACAG
1 AAAAAAGGGAGCACACAG
*
628423 AAAAAAGGGAGGACACAG
1 AAAAAAGGGAGCACACAG
628441 AA
1 AA
628443 CAGAAAAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.58, C:0.13, G:0.26, T:0.03
Consensus pattern (18 bp):
AAAAAAGGGAGCACACAG
Found at i:634146 original size:45 final size:45
Alignment explanation
Indices: 634096--634188 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
634086 GTGCACATTA
*
634096 ATCCAATCGGTGATTCTGTTAACGTACAGCCTGGATCTAGCTCGT
1 ATCCAATCGGTGATTCTGTTAACGTACAACCTGGATCTAGCTCGT
*
634141 ATCCAATCGGTGATTCTGTTAACGTACAACCTGGATCTAGTTCGT
1 ATCCAATCGGTGATTCTGTTAACGTACAACCTGGATCTAGCTCGT
634186 ATC
1 ATC
634189 AGAAGAACAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (45 bp):
ATCCAATCGGTGATTCTGTTAACGTACAACCTGGATCTAGCTCGT
Found at i:640911 original size:9 final size:9
Alignment explanation
Indices: 640894--641012 Score: 69
Period size: 9 Copynumber: 13.8 Consensus size: 9
640884 TTTCGCTTAA
*
640894 AGAAGAAAT
1 AGAAAAAAT
640903 AGAAAAAAT
1 AGAAAAAAT
640912 --AAAAAAT
1 AGAAAAAAT
640919 -GAGAAAAAT
1 AGA-AAAAAT
640928 -GAAAAAA-
1 AGAAAAAAT
*
640935 AGAAGAAGA-
1 AGAA-AAAAT
640944 AGAAAAAAAT
1 AG-AAAAAAT
640954 A-ATAAAAA-
1 AGA-AAAAAT
*
640962 AGAAAAAAA
1 AGAAAAAAT
* *
640971 AGAAGAAAG
1 AGAAAAAAT
640980 AGAAAAAAAT
1 AG-AAAAAAT
640990 A-AAAAAAT
1 AGAAAAAAT
*
640998 -GAAAAAAG
1 AGAAAAAAT
641006 AGAAAAA
1 AGAAAAA
641013 GAAAAGGAAA
Statistics
Matches: 90, Mismatches: 8, Indels: 24
0.74 0.07 0.20
Matches are distributed among these distances:
7 7 0.08
8 29 0.32
9 45 0.50
10 9 0.10
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (9 bp):
AGAAAAAAT
Found at i:640925 original size:17 final size:17
Alignment explanation
Indices: 640899--641012 Score: 53
Period size: 17 Copynumber: 6.7 Consensus size: 17
640889 CTTAAAGAAG
640899 AAAT-AGAAAAAATAAA
1 AAATGAGAAAAAATAAA
640915 AAATGAG-AAAAATGAAA
1 AAATGAGAAAAAAT-AAA
* *
640932 AAAAGAAGAAGAAGA-AAA
1 AAATG-AGAA-AAAATAAA
* * *
640950 AAATAATAAAAAAGAAA
1 AAATGAGAAAAAATAAA
* *
640967 AAA-AAGAAGAAAGAGAAAA
1 AAATGAGAA-AAA-A-TAAA
640986 AAAT-A-AAAAAATGAAA
1 AAATGAGAAAAAAT-AAA
641002 AAA-GAGAAAAA
1 AAATGAGAAAAA
641013 GAAAAGGAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 25
0.69 0.08 0.23
Matches are distributed among these distances:
16 25 0.33
17 29 0.38
18 11 0.14
19 8 0.11
20 3 0.04
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (17 bp):
AAATGAGAAAAAATAAA
Found at i:640933 original size:18 final size:17
Alignment explanation
Indices: 640899--641017 Score: 88
Period size: 18 Copynumber: 7.0 Consensus size: 17
640889 CTTAAAGAAG
640899 AAAT-AGAAAAA-ATAAA
1 AAATGAGAAAAAGA-AAA
640915 AAATGAGAAAAATGAAAA
1 AAATGAGAAAAA-GAAAA
*
640933 AAA-GAAGAAGAAGAAAA
1 AAATG-AGAAAAAGAAAA
* *
640950 AAATAATAAAAAAGAAAA
1 AAATGA-GAAAAAGAAAA
* *
640968 AAAAGAAGAAAGAGAAAA
1 AAATG-AGAAAAAGAAAA
*
640986 AAAT-AAAAAAATG-AAA
1 AAATGAGAAAAA-GAAAA
641002 AAA-GAGAAAAAGAAAA
1 AAATGAGAAAAAGAAAA
641018 GGAAAATGGA
Statistics
Matches: 81, Mismatches: 12, Indels: 20
0.72 0.11 0.18
Matches are distributed among these distances:
15 1 0.01
16 24 0.30
17 18 0.22
18 36 0.44
19 2 0.02
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (17 bp):
AAATGAGAAAAAGAAAA
Found at i:640961 original size:44 final size:42
Alignment explanation
Indices: 640892--641015 Score: 126
Period size: 41 Copynumber: 3.1 Consensus size: 42
640882 TATTTCGCTT
640892 AAAGAAGAA-ATAG-AAAAAAT-AAAAAATGAGAAAAATGAAAA
1 AAAGAAGAAGA-AGAAAAAAATAAAAAAATGAGAAAAA-GAAAA
640933 AAAGAAGAAGAAGAAAAAAATAATAAAAA--AG-AAAA-AAAA
1 AAAGAAGAAGAAGAAAAAAATAA-AAAAATGAGAAAAAGAAAA
* *
640972 GAAG-A-AAG-AGAAAAAAATAAAAAAATGA-AAAAAGAGAA
1 AAAGAAGAAGAAGAAAAAAATAAAAAAATGAGAAAAAGAAAA
641010 AAAGAA
1 AAAGAA
641016 AAGGAAAATG
Statistics
Matches: 71, Mismatches: 3, Indels: 20
0.76 0.03 0.21
Matches are distributed among these distances:
35 5 0.07
36 12 0.17
37 8 0.11
38 7 0.10
39 8 0.11
41 15 0.21
42 10 0.14
43 1 0.01
44 5 0.07
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.06
Consensus pattern (42 bp):
AAAGAAGAAGAAGAAAAAAATAAAAAAATGAGAAAAAGAAAA
Found at i:640962 original size:36 final size:34
Alignment explanation
Indices: 640912--641015 Score: 129
Period size: 35 Copynumber: 2.9 Consensus size: 34
640902 TAGAAAAAAT
*
640912 AAAAAATGAGAAAAATGAAAAAAAGAAGAAGAAGA
1 AAAAAAT-AAAAAAATGAAAAAAAGAAGAAGAAGA
*
640947 AAAAAATAATAAAAAAGAAAAAAAAGAAGAA-AGAGA
1 AAAAAATAA-AAAAATG-AAAAAAAGAAGAAGA-AGA
*
640983 AAAAAATAAAAAAATGAAAAAAGAGAAAAAGAA
1 AAAAAATAAAAAAATGAAAAAA-AGAAGAAGAA
641016 AAGGAAAATG
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
34 7 0.12
35 27 0.45
36 26 0.43
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (34 bp):
AAAAAATAAAAAAATGAAAAAAAGAAGAAGAAGA
Found at i:641002 original size:7 final size:7
Alignment explanation
Indices: 640892--641017 Score: 64
Period size: 7 Copynumber: 17.1 Consensus size: 7
640882 TATTTCGCTT
640892 AAAGAAGA
1 AAAGAA-A
640900 AATAGAAA
1 AA-AGAAA
*
640908 AAATAAA
1 AAAGAAA
640915 AAATGAGAA
1 AAA-GA-AA
640924 AAATGAAAA
1 AAA-G-AAA
640933 AAAGAAGA
1 AAAGAA-A
640941 AGAAGAAA
1 A-AAGAAA
640949 AAA-ATAA
1 AAAGA-AA
640956 TAAA-AAA
1 -AAAGAAA
*
640963 GAA-AAA
1 AAAGAAA
*
640969 AAAGAAG
1 AAAGAAA
*
640976 AAAGAGA
1 AAAGAAA
640983 AAA-AAA
1 AAAGAAA
*
640989 TAA-AAA
1 AAAGAAA
*
640995 AATGAAA
1 AAAGAAA
641002 AAAGAGAA
1 AAAGA-AA
641010 AAAGAAA
1 AAAGAAA
641017 A
1 A
641018 GGAAAATGGA
Statistics
Matches: 95, Mismatches: 12, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
6 16 0.17
7 35 0.37
8 22 0.23
9 21 0.22
10 1 0.01
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (7 bp):
AAAGAAA
Found at i:641022 original size:21 final size:22
Alignment explanation
Indices: 640892--641038 Score: 67
Period size: 23 Copynumber: 6.7 Consensus size: 22
640882 TATTTCGCTT
* **
640892 AAAGAAGAAATAGAAAAAATAAA
1 AAAGAAGAAAAAG-AAAAGGAAA
*
640915 AAATG-AGAAAAATGAAAA-AAAGA
1 AAA-GAAGAAAAA-GAAAAGGAA-A
*
640938 AGAAGAAGAAAAA-AATAA-TAAA
1 A-AAGAAGAAAAAGAA-AAGGAAA
* * *
640960 AAAGAAAAAAAAGAAGAAAGAGA
1 AAAGAAGAAAAAGAA-AAGGAAA
* *
640983 AAA-AA-ATAAA-AAAATGAAA
1 AAAGAAGAAAAAGAAAAGGAAA
641002 AAAG-AGAAAAAGAAAAGGAAA
1 AAAGAAGAAAAAGAAAAGGAAA
**
641023 ATGGAAGAAAAAGAAA
1 AAAGAAGAAAAAGAAA
641039 TGAAAATGAT
Statistics
Matches: 98, Mismatches: 14, Indels: 25
0.72 0.10 0.18
Matches are distributed among these distances:
19 9 0.09
20 6 0.06
21 24 0.24
22 23 0.23
23 25 0.26
24 11 0.11
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (22 bp):
AAAGAAGAAAAAGAAAAGGAAA
Found at i:641031 original size:22 final size:21
Alignment explanation
Indices: 641006--641046 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
640996 ATGAAAAAAG
641006 AGAAAAAGAAAAGGAAAATGGA
1 AGAAAAAG-AAAGGAAAATGGA
*
641028 AGAAAAAGAAATGAAAATG
1 AGAAAAAGAAAGGAAAATG
641047 ATGAATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.07
Consensus pattern (21 bp):
AGAAAAAGAAAGGAAAATGGA
Found at i:641043 original size:21 final size:20
Alignment explanation
Indices: 640990--641046 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
640980 AGAAAAAAAT
**
640990 AAAA-AAATGAAAAAAGAGA
1 AAAAGAAATGAAAATGGAGA
*
641009 AAAAGAAAAGGAAAATGGAAGA
1 AAAAG-AAATGAAAATGG-AGA
641031 AAAAGAAATGAAAATG
1 AAAAGAAATGAAAATG
641047 ATGAATGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 4 0.13
21 19 0.61
22 8 0.26
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (20 bp):
AAAAGAAATGAAAATGGAGA
Found at i:642402 original size:37 final size:37
Alignment explanation
Indices: 642344--642452 Score: 202
Period size: 37 Copynumber: 3.0 Consensus size: 37
642334 AAACAAGTTA
*
642344 ATCT-TAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
1 ATCTATAAGCCTTCACGAAAGAGTAGTGAAGCAAATC
642380 ATCTATAAGCCTTCACGAAAGAGTAGTGAAGCAAATC
1 ATCTATAAGCCTTCACGAAAGAGTAGTGAAGCAAATC
642417 ATCTATAAGCCTTCACGAAAGAGTAGTGAAGCAAAT
1 ATCTATAAGCCTTCACGAAAGAGTAGTGAAGCAAAT
642453 TTATTTTATG
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
36 4 0.06
37 67 0.94
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.22
Consensus pattern (37 bp):
ATCTATAAGCCTTCACGAAAGAGTAGTGAAGCAAATC
Found at i:642526 original size:55 final size:55
Alignment explanation
Indices: 642467--643102 Score: 579
Period size: 55 Copynumber: 11.6 Consensus size: 55
642457 TTTATGAAGA
* * * * *
642467 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGTGGATACATTAGTTGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * * * *
642522 TCGAGTCTTATACTCCCT-AAATGAATAGGGGGCAGACACGTTCGTTGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAA-GAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * * * * *
642577 TCGAGTTCTATACTCTCTGAAAGATTAGGGAGTGAACCCGTTTGCTGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * * *
642632 TAGAGTCTTATACTC-CTTGAAAGAATAGGGAGCGGAC-CGTTTATTGAAGATTGA
1 TCGAGTCCTATACTCTC-TGAAAGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * * * *
642686 TCGAGTCTTATACTC-CTTGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTAT
1 TCGAGTCCTATACTCTC-TGAAAGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * * * * *
642741 TCGAGTTCTATACTATCTGAAAGAATAGAGAGCGGACTCGTTTGTTGAAGCTGGT
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * * * * * * *
642796 TTGAGTTCTATACTCTCTGAAGGAATTGGGAGCAGACTCATTTGTTGAATATTGT
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* * * * *
642851 TCGAGTTCTATACTCTCTGAATGAATAGAGAGCGGACCCAC-TTT-ATGAAGATTAT
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGA--CACGTTTGTTGAAGATTGT
* * * * *
642906 TCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACACATTTATTGAAGATTAT
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
* *
642961 TC-AGGTCTTATACTCTCTGAAAGAATAGGGAGTGGACACGTTTGTT-AGAGATTGT
1 TCGA-GTCCTATACTCTCTGAAAGAATAGGGAGCGGACACGTTTGTTGA-AGATTGT
* * * * * * *
643016 TTGAATCTTATACTC-CTTGAACGAATAGGGAGCAGACATGTTTGCTGAAGATTGT
1 TCGAGTCCTATACTCTC-TGAAAGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
** * *
643071 TCGAGTTTTATACTCCCTGAAGGAATAGGGAG
1 TCGAGTCCTATACTCTCTGAAAGAATAGGGAG
643103 GAAACCCGTC
Statistics
Matches: 479, Mismatches: 87, Indels: 30
0.80 0.15 0.05
Matches are distributed among these distances:
53 3 0.01
54 57 0.12
55 407 0.85
56 10 0.02
57 2 0.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.31
Consensus pattern (55 bp):
TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACACGTTTGTTGAAGATTGT
Found at i:642975 original size:165 final size:163
Alignment explanation
Indices: 642475--643102 Score: 671
Period size: 165 Copynumber: 3.8 Consensus size: 163
642465 GATCGAGTCC
* * * *
642475 TATACTCTCTGAAGGAATAGGGAGTGGA-TACATTAGTTGAAGATTGTTCGAGTCTTATACTCCC
1 TATACTCTCTGAAAGAATAGGGAGCGGACT-CATTTGTTGAAGATTGTTCGAGTCTTATACTCCT
* * * * * * *
642539 TAAATGAATAGGGGGCAGACACGTTCGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAAGATTA
65 TGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTATTCGAGTTCTATACTCTCTGAAAGAATA
* * * *
642604 GGGAGTGAACCCGTTTGCTGAAGATTGTTAGAGTCT
130 GGGAGCGGACACGTTTGTTGAAGATT-TTAG-GTCT
* * *
642640 TATACTC-CTTGAAAGAATAGGGAGCGGAC-CGTTTATTGAAGATTGATCGAGTCTTATACTCCT
1 TATACTCTC-TGAAAGAATAGGGAGCGGACTCATTTGTTGAAGATTGTTCGAGTCTTATACTCCT
*
642703 TGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTATTCGAGTTCTATACTATCTGAAAGAATA
65 TGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTATTCGAGTTCTATACTCTCTGAAAGAATA
* * * *
642768 GAGAGCGGACTCGTTTGTTGAAGCTGGTTTGAGTTC-
130 GGGAGCGGACACGTTTGTTGAAGAT--TTT-AGGTCT
* * * *
642804 TATACTCTCTGAAGGAATTGGGAGCAGACTCATTTGTTGAATATTGTTCGAGT-TCTATACT-CT
1 TATACTCTCTGAAAGAATAGGGAGCGGACTCATTTGTTGAAGATTGTTCGAGTCT-TATACTCCT
* * * * *
642867 CTGAATGAATAGAGAGCGGACCCAC-TTT-ATGAAGATTATTCGAGTTCTATACTCTCTGAAGGA
65 -TGAACGAATAGGGAGCAGA--CACGTTTGCTGAAGATTATTCGAGTTCTATACTCTCTGAAAGA
* *
642930 ATAGGGAGCGGACACATTTATTGAAGATTATTCAGGTCT
127 ATAGGGAGCGGACACGTTTGTTGAAGATT-TT-AGGTCT
* * * * *
642969 TATACTCTCTGAAAGAATAGGGAGTGGACACGTTTGTT-AGAGATTGTTTGAATCTTATACTCCT
1 TATACTCTCTGAAAGAATAGGGAGCGGACTCATTTGTTGA-AGATTGTTCGAGTCTTATACTCCT
* * * * *
643033 TGAACGAATAGGGAGCAGACATGTTTGCTGAAGATTGTTCGAGTTTTATACTCCCTGAAGGAATA
65 TGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTATTCGAGTTCTATACTCTCTGAAAGAATA
643098 GGGAG
130 GGGAG
643103 GAAACCCGTC
Statistics
Matches: 386, Mismatches: 59, Indels: 36
0.80 0.12 0.07
Matches are distributed among these distances:
163 3 0.01
164 143 0.37
165 228 0.59
166 9 0.02
167 3 0.01
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.32
Consensus pattern (163 bp):
TATACTCTCTGAAAGAATAGGGAGCGGACTCATTTGTTGAAGATTGTTCGAGTCTTATACTCCTT
GAACGAATAGGGAGCAGACACGTTTGCTGAAGATTATTCGAGTTCTATACTCTCTGAAAGAATAG
GGAGCGGACACGTTTGTTGAAGATTTTAGGTCT
Found at i:643603 original size:20 final size:20
Alignment explanation
Indices: 643558--643596 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
643548 AGATTGATAA
643558 AAAAAAGGGGGATCACACAG
1 AAAAAAGGGGGATCACACAG
643578 AAAAAAGGGAGGA-CACACA
1 AAAAAAGGG-GGATCACACA
643597 ACAAAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.54, C:0.15, G:0.28, T:0.03
Consensus pattern (20 bp):
AAAAAAGGGGGATCACACAG
Found at i:648165 original size:20 final size:20
Alignment explanation
Indices: 648133--648170 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
648123 TGATAAAGTG
648133 ATCAATTAATTA-TAAATCA
1 ATCAATTAATTATTAAATCA
*
648152 ATCACATTAGTTATTAAAT
1 ATCA-ATTAATTATTAAAT
648171 TAATATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 7 0.44
21 5 0.31
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (20 bp):
ATCAATTAATTATTAAATCA
Found at i:649980 original size:13 final size:13
Alignment explanation
Indices: 649945--649982 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
649935 GATATTAAAG
649945 AATAAATA-TTAA
1 AATAAATATTTAA
*
649957 AATAATTTATTTAA
1 AATAA-ATATTTAA
649971 AATAAATATTTA
1 AATAAATATTTA
649983 TTTATTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 5 0.23
13 8 0.36
14 9 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AATAAATATTTAA
Found at i:651279 original size:3 final size:3
Alignment explanation
Indices: 651256--651296 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
651246 TTTGGGCTTG
*
651256 TAT T-T TAT T-T TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
651297 TATATATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TAT
Found at i:651326 original size:3 final size:3
Alignment explanation
Indices: 651318--651395 Score: 120
Period size: 3 Copynumber: 26.0 Consensus size: 3
651308 TTAATATATT
* * *
651318 TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
651366 TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
651396 ATAAATCAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:651741 original size:36 final size:36
Alignment explanation
Indices: 651647--651741 Score: 145
Period size: 36 Copynumber: 2.6 Consensus size: 36
651637 TTGAATAAGC
* *
651647 TCTTCTTATTATGAACTTTCTGTTCTTCAAATGAGT
1 TCTTCTCATTATGAACTTTCTTTTCTTCAAATGAGT
*
651683 TCTTCTCATTATGAACTTTCTTTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTTCTTTTCTTCAAATGAGT
* *
651719 TCTTCTCATTACGAACTCTCTTT
1 TCTTCTCATTATGAACTTTCTTT
651742 GGCGCTTCTG
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.20, C:0.21, G:0.09, T:0.49
Consensus pattern (36 bp):
TCTTCTCATTATGAACTTTCTTTTCTTCAAATGAGT
Found at i:652295 original size:113 final size:113
Alignment explanation
Indices: 651789--652266 Score: 922
Period size: 113 Copynumber: 4.2 Consensus size: 113
651779 GGGTTAAACA
* *
651789 AGTTCTTCTCATTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGGTTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAG
651854 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
651902 AGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAG
651967 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
652015 AGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGC-AAAG
1 AGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAG
652079 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
*
652127 AATTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAG
652192 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
652240 AGTTCTTCTCATTATGAACTCGAACTG
1 AGTTCTTCTCATTATGAACTCGAACTG
652267 ACACTGTTGA
Statistics
Matches: 360, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
112 111 0.31
113 249 0.69
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAG
GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:652295 original size:225 final size:226
Alignment explanation
Indices: 651789--652266 Score: 922
Period size: 225 Copynumber: 2.1 Consensus size: 226
651779 GGGTTAAACA
*
651789 AGTTCTTCTCATTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGGTTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAG
*
651854 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
66 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGA
651919 ACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT
131 ACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT
651984 CATTATGAACTTCTTCTTCCTTCTTCAGATG
196 CATTATGAACTTCTTCTTCCTTCTTCAGATG
*
652015 AGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGC-AAAG
1 AGTTCTTCTCATTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAG
652079 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGA
66 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGA
652144 ACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT
131 ACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT
652209 CATTATGAACTTCTTCTTCCTTCTTCAGATG
196 CATTATGAACTTCTTCTTCCTTCTTCAGATG
652240 AGTTCTTCTCATTATGAACTCGAACTG
1 AGTTCTTCTCATTATGAACTCGAACTG
652267 ACACTGTTGA
Statistics
Matches: 249, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
225 191 0.77
226 58 0.23
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (226 bp):
AGTTCTTCTCATTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAG
GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGA
ACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCT
CATTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:653089 original size:93 final size:85
Alignment explanation
Indices: 653015--653411 Score: 542
Period size: 83 Copynumber: 4.6 Consensus size: 85
653005 GTGGTTTCAG
*
653015 ACCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGAGCACA-TTATTCTTCC
1 ACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTA-TCTTCC
*
653079 AAATTCAATGACTGGTTCTGTAGTTT
65 AAATTCAATGA-T--TGCTGT--TTT
653105 CAGACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTATCTT
1 ---ACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTATCTT
*
653170 TCAAATTCAATGATTG--GTTTT
63 CCAAATTCAATGATTGCTGTTTT
* *
653191 ACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTTATCTTTCA
1 ACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTATCTTCCA
*
653256 AATTCAATGATTG--ATTTT
66 AATTCAATGATTGCTGTTTT
* * * *
653274 ACCAAATCAGATCAGATAACTCAAATACCACTTCTAGAAGATGCTATGAGCACA-TTATTCTTCC
1 ACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTA-TCTTCC
653338 AAATTCAATGA---CTGATTTT
65 AAATTCAATGATTGCTG-TTTT
653357 ACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
1 ACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
653412 GACATTTATT
Statistics
Matches: 282, Mismatches: 16, Indels: 21
0.88 0.05 0.07
Matches are distributed among these distances:
82 3 0.01
83 200 0.71
86 3 0.01
88 2 0.01
90 1 0.00
92 1 0.00
93 69 0.24
94 3 0.01
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.27
Consensus pattern (85 bp):
ACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTATCTTCCA
AATTCAATGATTGCTGTTTT
Found at i:654580 original size:7 final size:7
Alignment explanation
Indices: 654569--654621 Score: 67
Period size: 7 Copynumber: 7.9 Consensus size: 7
654559 TTTTTCTTCT
654569 TTTTTCTC
1 TTTTT-TC
654577 TTTTTTC
1 TTTTTTC
654584 TTTTTT-
1 TTTTTTC
*
654590 TTTCTT-
1 TTTTTTC
654596 TTTTTT-
1 TTTTTTC
654602 TTTTTTC
1 TTTTTTC
654609 TTTTTTC
1 TTTTTTC
654616 TTTTTT
1 TTTTTT
654622 TTCTTCAAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
6 16 0.38
7 21 0.50
8 5 0.12
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:654581 original size:1 final size:1
Alignment explanation
Indices: 654577--654623 Score: 58
Period size: 1 Copynumber: 47.0 Consensus size: 1
654567 CTTTTTTCTC
* * * *
654577 TTTTTTCTTTTTTTTTCTTTTTTTTTTTTTTCTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
654624 CTTCAAGCAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:654581 original size:19 final size:17
Alignment explanation
Indices: 654559--654623 Score: 98
Period size: 15 Copynumber: 3.8 Consensus size: 17
654549 TGACCCCCCC
654559 TTTTTCTTCTTTTTTCTCT
1 TTTTTCTT-TTTTTT-TCT
654578 TTTTTCTTTTTTTTTC-
1 TTTTTCTTTTTTTTTCT
654594 TTTTT-TTTTTTTTTCT
1 TTTTTCTTTTTTTTTCT
654610 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
654624 CTTCAAGCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.23
16 10 0.23
17 10 0.23
18 6 0.14
19 8 0.18
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTCTTTTTTTTTCT
Found at i:654586 original size:16 final size:16
Alignment explanation
Indices: 654560--654626 Score: 100
Period size: 17 Copynumber: 4.1 Consensus size: 16
654550 GACCCCCCCT
*
654560 TTTTCTTCTTTTTTCTC
1 TTTT-TTCTTTTTTTTC
654577 TTTTTTCTTTTTTTTTC
1 TTTTTTC-TTTTTTTTC
654594 TTTTTT-TTTTTTTTC
1 TTTTTTCTTTTTTTTC
654609 TTTTTTCTTTTTTTTC
1 TTTTTTCTTTTTTTTC
654625 TT
1 TT
654627 CAAGCATAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
15 15 0.32
16 14 0.30
17 18 0.38
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTCTTTTTTTTC
Found at i:654623 original size:9 final size:9
Alignment explanation
Indices: 654559--654626 Score: 81
Period size: 9 Copynumber: 7.9 Consensus size: 9
654549 TGACCCCCCC
654559 TTTTTCTTCT
1 TTTTTCTT-T
*
654569 TTTTTCTCT
1 TTTTTCTTT
654578 TTTTTCTTT
1 TTTTTCTTT
*
654587 TTTTT-TCT
1 TTTTTCTTT
654595 TTTTT-TTT
1 TTTTTCTTT
654603 TTTTTC--T
1 TTTTTCTTT
654610 TTTTTCTTT
1 TTTTTCTTT
654619 TTTTTCTT
1 TTTTTCTT
654627 CAAGCATAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
7 7 0.14
8 14 0.27
9 23 0.45
10 7 0.14
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:667313 original size:17 final size:16
Alignment explanation
Indices: 667284--667316 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
667274 TGGGCTTGTA
667284 TTTTATTTTATTATTT
1 TTTTATTTTATTATTT
667300 TTTTATTATTATTATTT
1 TTTTATT-TTATTATTT
667317 ATATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTATTTTATTATTT
Found at i:667343 original size:12 final size:11
Alignment explanation
Indices: 667325--667421 Score: 75
Period size: 12 Copynumber: 9.2 Consensus size: 11
667315 TTATATATAT
667325 ATTTAAT-AT-
1 ATTTAATAATA
667334 ATTTAATAATA
1 ATTTAATAATA
667345 A--TAATAATA
1 ATTTAATAATA
667354 A--TAATAATA
1 ATTTAATAATA
*
667363 ATATTTATAATA
1 AT-TTAATAATA
667375 ATTATAATAATA
1 ATT-TAATAATA
667387 A--TAATAATA
1 ATTTAATAATA
*
667396 ATAATAATAATA
1 AT-TTAATAATA
*
667408 ATAATAATAATA
1 AT-TTAATAATA
667420 AT
1 AT
667422 AAATAAATCA
Statistics
Matches: 77, Mismatches: 2, Indels: 15
0.82 0.02 0.16
Matches are distributed among these distances:
9 34 0.44
10 2 0.03
11 2 0.03
12 39 0.51
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:667345 original size:3 final size:3
Alignment explanation
Indices: 667337--667423 Score: 147
Period size: 3 Copynumber: 29.0 Consensus size: 3
667327 TTAATATATT
* * *
667337 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
667385 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
667424 ATAAATCAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:668917 original size:20 final size:20
Alignment explanation
Indices: 668888--668934 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
668878 ATGCGGCCCT
*
668888 TTGACCAATGGTTTCCGTCA
1 TTGACTAATGGTTTCCGTCA
668908 TTGACTAATGGTTTCCGTCA
1 TTGACTAATGGTTTCCGTCA
668928 TTGACTA
1 TTGACTA
668935 TTACCTTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (20 bp):
TTGACTAATGGTTTCCGTCA
Found at i:669132 original size:24 final size:24
Alignment explanation
Indices: 669105--669189 Score: 70
Period size: 24 Copynumber: 3.6 Consensus size: 24
669095 AAAATATTTT
669105 AAATAAAAAATATAAAATTATTCA
1 AAATAAAAAATATAAAATTATTCA
*** *
669129 AAATCTTAAATATAATAA-TA-CCTA
1 AAATAAAAAATATAA-AATTATTC-A
*
669153 AAAT-AAAAAT-TAAATTTATTCA
1 AAATAAAAAATATAAAATTATTCA
669175 AAATAAAAATATATA
1 AAATAAAAA-ATATA
669190 TTAAAAAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 13
0.69 0.12 0.19
Matches are distributed among these distances:
21 1 0.02
22 10 0.22
23 10 0.22
24 21 0.46
25 4 0.09
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (24 bp):
AAATAAAAAATATAAAATTATTCA
Found at i:671642 original size:22 final size:22
Alignment explanation
Indices: 671573--671656 Score: 66
Period size: 22 Copynumber: 3.7 Consensus size: 22
671563 ATCTTAAATT
*
671573 TAAAATATAAATTTATTCAAAAAC
1 TAAAATATAAA-TTATT-AAAAAA
* *
671597 TTAAATAT-AA-TAATACCAAAAA
1 TAAAATATAAATTATTA--AAAAA
671619 TATAAAT-TAAATTATTAAAAAA
1 TA-AAATATAAATTATTAAAAAA
*
671641 TAAAATATATATTATT
1 TAAAATATAAATTATT
671657 TTGTTATAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
20 1 0.02
21 7 0.15
22 21 0.44
23 8 0.17
24 11 0.23
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAAATATAAATTATTAAAAAA
Found at i:673838 original size:183 final size:184
Alignment explanation
Indices: 673517--673902 Score: 620
Period size: 183 Copynumber: 2.1 Consensus size: 184
673507 TTTTCTAATT
* * *
673517 TATATAA-AAATTAAATA-TTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
673580 TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATT
66 TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATT
* * *
673645 GGATCTTAAATTATTAATTGAGTTTTAAATTGTTTGGGCTTAGCCCAAATGTTA
131 AGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTA
673699 TATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATATATAA
* *
673763 TTATAAAATAAAAAATTT-ATAT-AATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
65 TTATAAAAT-AAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTA
* *
673826 TTAGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
129 TTAGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTA
*
673882 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
673903 AAAATTTAAT
Statistics
Matches: 189, Mismatches: 11, Indels: 7
0.91 0.05 0.03
Matches are distributed among these distances:
182 7 0.04
183 125 0.66
184 49 0.26
185 8 0.04
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATT
AGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTA
Found at i:675336 original size:2 final size:2
Alignment explanation
Indices: 675329--675356 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
675319 TAGCAAATGC
675329 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
675357 CTCATGTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:675909 original size:28 final size:28
Alignment explanation
Indices: 675869--675945 Score: 127
Period size: 28 Copynumber: 2.8 Consensus size: 28
675859 GACCACTATG
675869 TCCCGAAGGACCACATAGAACACATATA
1 TCCCGAAGGACCACATAGAACACATATA
*
675897 TCCCGAAGGACCACATAGAACACATATG
1 TCCCGAAGGACCACATAGAACACATATA
* *
675925 TCCCGAAAGACCACGTAGAAC
1 TCCCGAAGGACCACATAGAAC
675946 CCTCCACTCT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.40, C:0.30, G:0.17, T:0.13
Consensus pattern (28 bp):
TCCCGAAGGACCACATAGAACACATATA
Found at i:678670 original size:24 final size:24
Alignment explanation
Indices: 678619--678682 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
678609 AAATGGATAT
* ** *
678619 ATCAGAAATCAAAACAGAATTTAG
1 ATCAGAAATCAGAACAGAATCCAA
*
678643 ATCAGATATCAGAACAGAATCCAA
1 ATCAGAAATCAGAACAGAATCCAA
678667 ATCAGAAATCAGAACA
1 ATCAGAAATCAGAACA
678683 AAATTCAGGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.53, C:0.17, G:0.12, T:0.17
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATCCAA
Found at i:680496 original size:594 final size:594
Alignment explanation
Indices: 679368--680543 Score: 2325
Period size: 594 Copynumber: 2.0 Consensus size: 594
679358 CAGGATTTTC
679368 CAGAGTAATTCATACTTTTCTGAATTTCGATACATATTATACTCCTGTTCCGTTCAATTTGGTCT
1 CAGAGTAATTCATACTTTTCTGAATTTCGATACATATTATACTCCTGTTCCGTTCAATTTGGTCT
679433 TCATGGTTGATTTGTCTAATGAATATATCCTTCTTAGTATAGAATACCATCTAGAATTGAGCTGA
66 TCATGGTTGATTTGTCTAATGAATATATCCTTCTTAGTATAGAATACCATCTAGAATTGAGCTGA
*
679498 GCTGAATTCTTCCAAAATTATTATCGAATCTAACTTGATAAGTCGAACACGCATTCAAGTGACAT
131 GCTGAATTCTTCCAAAATTATTATCGAATCTAACTTGAGAAGTCGAACACGCATTCAAGTGACAT
679563 CTATGTCGTTCTGGTACTGATATAACACTAGCATTGGTTGCTTGACTTAATATGTGATCCATAAC
196 CTATGTCGTTCTGGTACTGATATAACACTAGCATTGGTTGCTTGACTTAATATGTGATCCATAAC
679628 TTTTAAGACCAGTACCACACCCATGTTTATTTGGATTCCTTAATTAATCCAACACCTCTACTTAG
261 TTTTAAGACCAGTACCACACCCATGTTTATTTGGATTCCTTAATTAATCCAACACCTCTACTTAG
679693 TTTAGGTTATAAGGGTATTTTGGTAATTATGGTGCTCATTTTCATTCCATTCTTTTCAGAGCTCA
326 TTTAGGTTATAAGGGTATTTTGGTAATTATGGTGCTCATTTTCATTCCATTCTTTTCAGAGCTCA
679758 AGGATATCCAATCATTCCTGAGCTTGGTGATATTCTTGAATAATTTTCATTACAGGGGTATTTGG
391 AGGATATCCAATCATTCCTGAGCTTGGTGATATTCTTGAATAATTTTCATTACAGGGGTATTTGG
679823 TCATTTTACAGATTCAGTGTACTTTAATTATTTCATTCCGTCTGATCTTACTATTATATTCAATC
456 TCATTTTACAGATTCAGTGTACTTTAATTATTTCATTCCGTCTGATCTTACTATTATATTCAATC
679888 TTATCATTTATTTCAGTCCTTTCGAACAATTCTGACAACAGAACACCCCTGACAAATTGTTCCGT
521 TTATCATTTATTTCAGTCCTTTCGAACAATTCTGACAACAGAACACCCCTGACAAATTGTTCCGT
679953 TCAATTTGT
586 TCAATTTGT
679962 CAGAGTAATTCATACTTTTCTGAATTTCGATACATATTATACTCCTGTTCCGTTCAATTTGGTCT
1 CAGAGTAATTCATACTTTTCTGAATTTCGATACATATTATACTCCTGTTCCGTTCAATTTGGTCT
* *
680027 TCATGGTTGATTTGTCTAATGAATATATCCTTCTTAGTATCGAATGCCATCTAGAATTGAGCTGA
66 TCATGGTTGATTTGTCTAATGAATATATCCTTCTTAGTATAGAATACCATCTAGAATTGAGCTGA
680092 GCTGAATTCTTCCAAAATTATTATCGAATCTAACTTGAGAAGTCGAACACGCATTCAAGTGACAT
131 GCTGAATTCTTCCAAAATTATTATCGAATCTAACTTGAGAAGTCGAACACGCATTCAAGTGACAT
680157 CTATGTCGTTCTGGTACTGATATAACACTAGCATTGGTTGCTTGACTTAATATGTGATCCATAAC
196 CTATGTCGTTCTGGTACTGATATAACACTAGCATTGGTTGCTTGACTTAATATGTGATCCATAAC
680222 TTTTAAGACCAGTACCACACCCATGTTTATTTGGATTCCTTAATTAATCCAACACCTCTACTTAG
261 TTTTAAGACCAGTACCACACCCATGTTTATTTGGATTCCTTAATTAATCCAACACCTCTACTTAG
680287 TTTAGGTTATAAGGGTATTTTGGTAATTATGGTGCTCATTTTCATTCCATTCTTTTCAGAGCTCA
326 TTTAGGTTATAAGGGTATTTTGGTAATTATGGTGCTCATTTTCATTCCATTCTTTTCAGAGCTCA
680352 AGGATATCCAATCATTCCTGAGCTTGGTGATATTCTTGAATAATTTTCATTACAGGGGTATTTGG
391 AGGATATCCAATCATTCCTGAGCTTGGTGATATTCTTGAATAATTTTCATTACAGGGGTATTTGG
680417 TCATTTTACAGATTCAGTGTACTTTAATTATTTCATTCCGTCTGATCTTACTATTATATTCAATC
456 TCATTTTACAGATTCAGTGTACTTTAATTATTTCATTCCGTCTGATCTTACTATTATATTCAATC
680482 TTATCATTTATTTCAGTCCTTTCGAACAATTCTGACAACAGAACACCCCTGACAAATTGTTC
521 TTATCATTTATTTCAGTCCTTTCGAACAATTCTGACAACAGAACACCCCTGACAAATTGTTC
680544 TTCAGGTATT
Statistics
Matches: 579, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
594 579 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (594 bp):
CAGAGTAATTCATACTTTTCTGAATTTCGATACATATTATACTCCTGTTCCGTTCAATTTGGTCT
TCATGGTTGATTTGTCTAATGAATATATCCTTCTTAGTATAGAATACCATCTAGAATTGAGCTGA
GCTGAATTCTTCCAAAATTATTATCGAATCTAACTTGAGAAGTCGAACACGCATTCAAGTGACAT
CTATGTCGTTCTGGTACTGATATAACACTAGCATTGGTTGCTTGACTTAATATGTGATCCATAAC
TTTTAAGACCAGTACCACACCCATGTTTATTTGGATTCCTTAATTAATCCAACACCTCTACTTAG
TTTAGGTTATAAGGGTATTTTGGTAATTATGGTGCTCATTTTCATTCCATTCTTTTCAGAGCTCA
AGGATATCCAATCATTCCTGAGCTTGGTGATATTCTTGAATAATTTTCATTACAGGGGTATTTGG
TCATTTTACAGATTCAGTGTACTTTAATTATTTCATTCCGTCTGATCTTACTATTATATTCAATC
TTATCATTTATTTCAGTCCTTTCGAACAATTCTGACAACAGAACACCCCTGACAAATTGTTCCGT
TCAATTTGT
Found at i:690441 original size:19 final size:19
Alignment explanation
Indices: 690417--690457 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
690407 AACCTTTTTA
690417 CATTGCATCATCATCATAG
1 CATTGCATCATCATCATAG
*
690436 CATTGCATCATCATCGTAG
1 CATTGCATCATCATCATAG
690455 CAT
1 CAT
690458 AACATGAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (19 bp):
CATTGCATCATCATCATAG
Found at i:690725 original size:6 final size:5
Alignment explanation
Indices: 690703--690754 Score: 50
Period size: 6 Copynumber: 9.4 Consensus size: 5
690693 AGTAAACTAG
*
690703 ATAAA ATAAA ATAAA ATTAAA ATAACG ATAACA ATAACA ATAACA ATAAA
1 ATAAA ATAAA ATAAA A-TAAA ATAA-A ATAA-A ATAA-A ATAA-A ATAAA
690753 AT
1 AT
690755 TAAGAAAAGT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
5 17 0.40
6 26 0.60
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:691541 original size:29 final size:29
Alignment explanation
Indices: 691512--691569 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
691502 TAAAGAAAAT
691512 AAAATACCTAAAG-AAAATAAAATCCTAATA
1 AAAAT-CCT-AAGCAAAATAAAATCCTAATA
* *
691542 AAAATCCTTAGCAAACTAAAATCCTAAT
1 AAAATCCTAAGCAAAATAAAATCCTAAT
691570 GAATTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 18 0.72
30 5 0.20
ACGTcount: A:0.57, C:0.17, G:0.03, T:0.22
Consensus pattern (29 bp):
AAAATCCTAAGCAAAATAAAATCCTAATA
Found at i:691546 original size:17 final size:18
Alignment explanation
Indices: 691499--691539 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
691489 GCTTGAGAAA
691499 ACCTAAAGAAAATAAAAT
1 ACCTAAAGAAAATAAAAT
691517 ACCTAAAGAAAATAAAAT
1 ACCTAAAGAAAATAAAAT
691535 -CCTAA
1 ACCTAA
691540 TAAAAATCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.63, C:0.15, G:0.05, T:0.17
Consensus pattern (18 bp):
ACCTAAAGAAAATAAAAT
Found at i:694229 original size:32 final size:33
Alignment explanation
Indices: 694182--694261 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
694172 AATTTTGACA
*
694182 CTACCTCTCTCTGAGGCA-CCAAAGTCAT-ATT
1 CTACCTCTCTTTGAGGCATCCAAAGTCATCATT
* *
694213 GCTACATCTCTTTGAGGCATCCAAATTCATCATT
1 -CTACCTCTCTTTGAGGCATCCAAAGTCATCATT
*
694247 TTACCTCTCTTTGAG
1 CTACCTCTCTTTGAG
694262 ATAATAAAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
32 16 0.39
33 22 0.54
34 3 0.07
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (33 bp):
CTACCTCTCTTTGAGGCATCCAAAGTCATCATT
Found at i:695896 original size:24 final size:23
Alignment explanation
Indices: 695844--695901 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
695834 TAAGGGGCAC
*
695844 CATTTTTCAAAAACTTCATCAAT
1 CATTTTTCAAAAACTTCATCAAA
* *
695867 CATTTTTCAAAAGCTTCATTAAA
1 CATTTTTCAAAAACTTCATCAAA
695890 CATTTTT-AAAAA
1 CATTTTTCAAAAA
695902 TTATTTCTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 4 0.13
23 27 0.87
ACGTcount: A:0.41, C:0.17, G:0.02, T:0.40
Consensus pattern (23 bp):
CATTTTTCAAAAACTTCATCAAA
Found at i:695943 original size:25 final size:24
Alignment explanation
Indices: 695881--695956 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 24
695871 TTTCAAAAGC
695881 TTCATTAAACATTTTTAAAAATTAT
1 TTCA-TAAACATTTTTAAAAATTAT
* *
695906 TTCTTCAAACATTATTT-AAAATTCT
1 TTCAT-AAACATT-TTTAAAAATTAT
* *
695931 TTCATAAAGCATTTTCAAAACTTAT
1 TTCATAAA-CATTTTTAAAAATTAT
695956 T
1 T
695957 CGTAAAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
24 6 0.15
25 32 0.78
26 3 0.07
ACGTcount: A:0.39, C:0.13, G:0.01, T:0.46
Consensus pattern (24 bp):
TTCATAAACATTTTTAAAAATTAT
Found at i:696333 original size:30 final size:30
Alignment explanation
Indices: 696296--696443 Score: 154
Period size: 30 Copynumber: 4.9 Consensus size: 30
696286 CGACTAAGCA
* * *
696296 CCAAATAGTACAGGGACTTGGCCACCACTT
1 CCAAATAGTACAGGGACTGGGCCACCAATG
* * *
696326 TCAAATAGTATAAGGACTGGGCCACCAATG
1 CCAAATAGTACAGGGACTGGGCCACCAATG
* *
696356 CCAAATAGTATAAGGACTAGGGCC-CCAATG
1 CCAAATAGTACAGGGACT-GGGCCACCAATG
** * * *
696386 TTAAATAATACAGGGACTGGGCTATCAATG
1 CCAAATAGTACAGGGACTGGGCCACCAATG
*
696416 CCAAATAGTACAGGGACTTGGCCACCAA
1 CCAAATAGTACAGGGACTGGGCCACCAA
696444 GGTTAAATAG
Statistics
Matches: 96, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
29 4 0.04
30 87 0.91
31 5 0.05
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (30 bp):
CCAAATAGTACAGGGACTGGGCCACCAATG
Found at i:696373 original size:60 final size:60
Alignment explanation
Indices: 696296--696452 Score: 192
Period size: 60 Copynumber: 2.6 Consensus size: 60
696286 CGACTAAGCA
* * *
696296 CCAAATAGTACAGGGACTTGGCCACCACT-TTCAAATAGTATAAGGACTGGGCCACCAATG
1 CCAAATAGTACAGGGACTTGGCCACCAATGTT-AAATAATACAAGGACTGGGCCACCAATG
* * * * * *
696356 CCAAATAGTATAAGGACTAGGGCC-CCAATGTTAAATAATACAGGGACTGGGCTATCAATG
1 CCAAATAGTACAGGGACT-TGGCCACCAATGTTAAATAATACAAGGACTGGGCCACCAATG
*
696416 CCAAATAGTACAGGGACTTGGCCACCAAGGTTAAATA
1 CCAAATAGTACAGGGACTTGGCCACCAATGTTAAATA
696453 GTTAAGGACC
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
59 4 0.05
60 71 0.88
61 6 0.07
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (60 bp):
CCAAATAGTACAGGGACTTGGCCACCAATGTTAAATAATACAAGGACTGGGCCACCAATG
Found at i:697741 original size:3 final size:3
Alignment explanation
Indices: 697721--697788 Score: 70
Period size: 3 Copynumber: 23.7 Consensus size: 3
697711 TCGTTTGGGT
* * *
697721 TTA TT- TTA TTA TTG TTA TTA TTA -TA GTA TTA TTT TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
697766 TTA TTA ATA TTT TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
697789 TTGTTTGTAG
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
2 6 0.11
3 47 0.89
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:697763 original size:34 final size:35
Alignment explanation
Indices: 697720--697790 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 35
697710 TTCGTTTGGG
* *
697720 TTTATTTTATTATTGTTATTA-TTATAGTATTATT
1 TTTATTTTATTATTATTAATATTTATAGTATTATT
* *
697754 TTTATTTTATTATTATTAATATTTTTATTATTATT
1 TTTATTTTATTATTATTAATATTTATAGTATTATT
697789 TT
1 TT
697791 GTTTGTAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 19 0.59
35 13 0.41
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (35 bp):
TTTATTTTATTATTATTAATATTTATAGTATTATT
Found at i:697776 original size:17 final size:17
Alignment explanation
Indices: 697721--697788 Score: 82
Period size: 17 Copynumber: 3.9 Consensus size: 17
697711 TCGTTTGGGT
*
697721 TTATTTTATTATTGTTA
1 TTATTTTATTATTATTA
* * *
697738 TTATTATAGTATTATTT
1 TTATTTTATTATTATTA
697755 TTATTTTATTATTATTA
1 TTATTTTATTATTATTA
*
697772 ATATTTTTATTATTATT
1 TTA-TTTTATTATTATT
697789 TTGTTTGTAG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
17 29 0.69
18 13 0.31
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
TTATTTTATTATTATTA
Found at i:725768 original size:45 final size:46
Alignment explanation
Indices: 725719--725809 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
725709 AAACATCGAA
* *
725719 TGCATTTTATGCATCGACGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGACGCACAAGACCATGCATCGATGCACTCAG
*
725764 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGACGCACAAGACCATGCATCGATGCACTCAG
725810 GCTTTTTCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 20 0.48
46 22 0.52
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (46 bp):
TGCATTTGATGCATCGACGCACAAGACCATGCATCGATGCACTCAG
Found at i:728641 original size:17 final size:18
Alignment explanation
Indices: 728619--728661 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
728609 ACTGGTGACT
728619 TTTTAT-TCTTTGATTTG
1 TTTTATATCTTTGATTTG
728636 TTTTATTACTCTTTGATTTG
1 TTTTA-TA-TCTTTGATTTG
*
728656 GTTTAT
1 TTTTAT
728662 CTCGATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.23
18 1 0.05
19 1 0.05
20 15 0.68
ACGTcount: A:0.14, C:0.07, G:0.12, T:0.67
Consensus pattern (18 bp):
TTTTATATCTTTGATTTG
Found at i:729157 original size:24 final size:24
Alignment explanation
Indices: 729112--729160 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
729102 GCTGCTACGC
* *
729112 TCCCGATCTCGATCTCGATCCCGT
1 TCCCGACCTCGATCTCCATCCCGT
729136 TCCCGACCTCGATC-CCATTCCCGT
1 TCCCGACCTCGATCTCCA-TCCCGT
729160 T
1 T
729161 GCCTTGATCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.12, C:0.45, G:0.14, T:0.29
Consensus pattern (24 bp):
TCCCGACCTCGATCTCCATCCCGT
Found at i:740284 original size:17 final size:18
Alignment explanation
Indices: 740262--740296 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
740252 CACATTTTAA
740262 TCTATAA-TATAAATAAT
1 TCTATAATTATAAATAAT
*
740279 TCTATAATTTTAAATAAT
1 TCTATAATTATAAATAAT
740297 ATTTTAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (18 bp):
TCTATAATTATAAATAAT
Found at i:743732 original size:15 final size:15
Alignment explanation
Indices: 743714--743743 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
743704 CAATCTCTTT
743714 TTCGTTATCTAAACC
1 TTCGTTATCTAAACC
743729 TTCGTTATCTAAACC
1 TTCGTTATCTAAACC
743744 AAATGTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.40
Consensus pattern (15 bp):
TTCGTTATCTAAACC
Found at i:747827 original size:23 final size:24
Alignment explanation
Indices: 747798--747846 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
747788 ATTCCCTAAA
*
747798 GGGGAATCGGTTCCCATTCAA-AG
1 GGGGAATAGGTTCCCATTCAAGAG
* *
747821 GGGGAATATGTTCCCCTTCAAGAG
1 GGGGAATAGGTTCCCATTCAAGAG
747845 GG
1 GG
747847 TATCGATTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.22
Consensus pattern (24 bp):
GGGGAATAGGTTCCCATTCAAGAG
Found at i:754011 original size:24 final size:24
Alignment explanation
Indices: 753979--754026 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
753969 AAAACATCAA
*
753979 ATTTTAAAATCAAAACATTTTTTT
1 ATTTCAAAATCAAAACATTTTTTT
* **
754003 ATTTCAAAATGAAAATTTTTTTTT
1 ATTTCAAAATCAAAACATTTTTTT
754027 GATAAAATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (24 bp):
ATTTCAAAATCAAAACATTTTTTT
Found at i:756178 original size:20 final size:20
Alignment explanation
Indices: 756153--756195 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
756143 TACCAGGTTT
756153 TTCAACTAATCATAATTTAC
1 TTCAACTAATCATAATTTAC
*
756173 TTCAACTAATCATACTTTAC
1 TTCAACTAATCATAATTTAC
756193 TTC
1 TTC
756196 TCTCAAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (20 bp):
TTCAACTAATCATAATTTAC
Found at i:757320 original size:16 final size:15
Alignment explanation
Indices: 757294--757323 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
757284 TTAGATCATG
757294 CATTACAAATTTTAT
1 CATTACAAATTTTAT
757309 CATTATCAAATTTTA
1 CATTA-CAAATTTTA
757324 GCTTTGGAAA
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:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (15 bp):
CATTACAAATTTTAT
Found at i:766676 original size:46 final size:45
Alignment explanation
Indices: 766623--766738 Score: 121
Period size: 46 Copynumber: 2.5 Consensus size: 45
766613 GGTATATTTT
766623 CTCCACTACTCTTCAGAGAAGATTAAATCTTGGAAAAA-TAT-A-TCTA
1 CTCCACTACTCTTCAG-GAAGATTAAATC-T-GAAAAATTATGATTC-A
* * *
766669 CTCCACTACTCTTTAGGGAAGATCAGATCTGAAAAATTATGATTCA
1 CTCCACTACTCTTCA-GGAAGATTAAATCTGAAAAATTATGATTCA
*
766715 CTTCACTACTCTTCAGGAAAGATT
1 CTCCACTACTCTTCAGG-AAGATT
766739 GAATTGAGGT
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
44 6 0.10
45 6 0.10
46 44 0.75
47 3 0.05
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (45 bp):
CTCCACTACTCTTCAGGAAGATTAAATCTGAAAAATTATGATTCA
Found at i:766687 original size:134 final size:133
Alignment explanation
Indices: 766536--766790 Score: 352
Period size: 134 Copynumber: 1.9 Consensus size: 133
766526 AGAAATCTTT
* * *
766536 TCCACTATTCTTTAGGGAAGATCATATATGAAAAATTATGATTCACTT-AATGACTCTCCATGAA
1 TCCACTACTCTTTAGGGAAGATCAGATATGAAAAATTATGATTCACTTCAAT-ACTCTCCAGGAA
* * *
766600 AGATTGAATCTGAGGTATATTTTCTCCAC-TACTCTTCAGAGAAGATTAAATCTTGGAAAAATAT
65 AGATTGAAT-TGAGGTAGATTTGCTCCACTTA-TCTTCAGAGAAGATCAAATCTTGGAAAAATAT
766664 ATCTAC
128 ATCTAC
* * *
766670 TCCACTACTCTTTAGGGAAGATCAGATCTGAAAAATTATGATTCACTTCACTACTCTTCAGGAAA
1 TCCACTACTCTTTAGGGAAGATCAGATATGAAAAATTATGATTCACTTCAATACTCTCCAGGAAA
** * *
766735 GATTGAATTGAGGTAGATTTGCTGTACTTATCTTCAGGGAATATCAAATCTTGGAA
66 GATTGAATTGAGGTAGATTTGCTCCACTTATCTTCAGAGAAGATCAAATCTTGGAA
766791 GAAGGGGTAT
Statistics
Matches: 106, Mismatches: 13, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
133 38 0.36
134 66 0.62
135 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (133 bp):
TCCACTACTCTTTAGGGAAGATCAGATATGAAAAATTATGATTCACTTCAATACTCTCCAGGAAA
GATTGAATTGAGGTAGATTTGCTCCACTTATCTTCAGAGAAGATCAAATCTTGGAAAAATATATC
TAC
Found at i:767739 original size:17 final size:17
Alignment explanation
Indices: 767717--767784 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
767707 GACCGGTCAC
*
767717 GACCCGACCCGATAGTT
1 GACCCGACCCGACAGTT
*
767734 GACCCGACCCGACCGTT
1 GACCCGACCCGACAGTT
767751 GACCCGA-CC--C-GTT
1 GACCCGACCCGACAGTT
*
767764 GACCCGACCCGACCGTT
1 GACCCGACCCGACAGTT
767781 GACC
1 GACC
767785 GGTGCTATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
13 10 0.22
14 3 0.07
16 3 0.07
17 29 0.64
ACGTcount: A:0.19, C:0.44, G:0.24, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACAGTT
Found at i:767764 original size:13 final size:13
Alignment explanation
Indices: 767739--767774 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
767729 TAGTTGACCC
767739 GACCCGA-CCGTT
1 GACCCGACCCGTT
767751 GACCCGACCCGTT
1 GACCCGACCCGTT
767764 GACCCGACCCG
1 GACCCGACCCG
767775 ACCGTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.17, C:0.47, G:0.25, T:0.11
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:767827 original size:29 final size:29
Alignment explanation
Indices: 767785--767866 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
767775 ACCGTTGACC
*
767785 GGTGCTATTTTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
767814 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
767843 GGTGCTATTCTGGTAAATAATTCG
1 GGTGCTATTCTGGTAAATAATTCG
767867 AAAAAGGGTG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.44
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTT
Done.