Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007924.1 Hibiscus syriacus cultivar Beakdansim tig00110330_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: 1741266
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 4 of 7
Found at i:809864 original size:181 final size:183
Alignment explanation
Indices: 809449--809884 Score: 644
Period size: 183 Copynumber: 2.4 Consensus size: 183
809439 GATCCAAATT
* * * *
809449 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATA-GAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-ACAAAATGAT
* * * *
809513 AAAACCGGTCAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
65 AAAACCGGTAAAACGCTACCGGATACATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* *
809578 CGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTAA
130 CGTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTTAA
*
809632 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* * * *
809697 AAACCGGTAAAACGTTACCGGATATATTAAAAGTGTCGATACTTT-ATATAAGGATCGGCACTTT
66 AAACCGGTAAAACGCTACCGGATACATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* ** *
809761 GTGAATTTAAAAGAGCAGCAGTTATAGCGCCTATAATGTGTCGATAC-TTTAA
131 GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTTAA
* * *
809813 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
809878 AAACCGG
66 AAACCGG
809885 GTGTCGATAC
Statistics
Matches: 229, Mismatches: 23, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
181 73 0.32
182 59 0.26
183 97 0.42
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (183 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
AAACCGGTAAAACGCTACCGGATACATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTTAA
Found at i:809866 original size:20 final size:20
Alignment explanation
Indices: 809843--809884 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
809833 CGATATAACA
809843 GGTA-AAAATATGATAAAACC
1 GGTATAAAA-ATGATAAAACC
*
809863 GGTATCAAAATGATAAAACC
1 GGTATAAAAATGATAAAACC
809883 GG
1 GG
809885 GTGTCGATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (20 bp):
GGTATAAAAATGATAAAACC
Found at i:812005 original size:15 final size:15
Alignment explanation
Indices: 811985--812017 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
811975 TGGTTGTATT
*
811985 GGGGGATGACGGTGA
1 GGGGGACGACGGTGA
812000 GGGGGACGACGGTGA
1 GGGGGACGACGGTGA
812015 GGG
1 GGG
812018 AAAACAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.09, G:0.64, T:0.09
Consensus pattern (15 bp):
GGGGGACGACGGTGA
Found at i:812127 original size:21 final size:21
Alignment explanation
Indices: 812100--812164 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
812090 AAGACAATCA
*
812100 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
* * *
812121 CGAGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
812142 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
812163 AG
1 AG
812165 GCATAAGGGG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:812240 original size:33 final size:33
Alignment explanation
Indices: 812198--812263 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
812188 AAATAGATGG
*
812198 AGTGGTGAAAGAAGTAGAGGTGTTTAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
812231 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
812264 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.47, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:814076 original size:19 final size:19
Alignment explanation
Indices: 814052--814100 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
814042 AATGTAGGGT
814052 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
814071 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
814090 TAATTTTGTAT
1 TAATTTTGTAT
814101 GTGAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:814550 original size:199 final size:199
Alignment explanation
Indices: 814209--815366 Score: 2077
Period size: 199 Copynumber: 5.8 Consensus size: 199
814199 GGCAAATTTA
* * * *
814209 CCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCAAAAAACATCGAAAACCAAAAGTATAA
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AACCCAAAAGTATAA
* * * * *
814274 TGTAATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGATTTTATGAGAGAATATGTCTAA
65 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAA
* *
814339 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCATAATGAATGGAAAACATGG
130 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGG
814404 TGCAC
195 TGCAC
*
814409 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* *
814474 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACAGGTTTTATGAGATAATATGTCTAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
*
814539 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
*
814604 GAAC
196 GCAC
814608 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
814673 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
*
814738 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCATAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
814803 GCAC
196 GCAC
* *
814807 CCATAAAATGTCGATCCATATATAAAAAGTGTCGATACCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
814872 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
814937 TAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
815001 GCAC
196 GCAC
815005 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
815070 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
*
815135 TAATGTGTCAACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
815199 GCAC
196 GCAC
815203 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* * *
815268 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
*
815333 TCATGTGTCGACACTAATATAGTTTGTGTCGATA
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATA
815367 CTAATTTAAA
Statistics
Matches: 928, Mismatches: 30, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
198 387 0.42
199 495 0.53
200 46 0.05
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (199 bp):
CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
GCAC
Found at i:816852 original size:18 final size:18
Alignment explanation
Indices: 816831--816892 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
816821 AGCGGTCGCA
816831 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
816849 GAAGATGACGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
816867 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
816885 GAAGATGA
1 GAAGATGA
816893 TGACGATGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.10, G:0.35, T:0.18
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:816855 original size:6 final size:6
Alignment explanation
Indices: 816831--816922 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
816821 AGCGGTCGCA
* * * * * *
816831 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * * *
816879 GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
816923 TGATCCAAAC
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:816866 original size:3 final size:3
Alignment explanation
Indices: 816846--816926 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
816836 TGAAGCTGAC
* * * * * ** *
816846 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
816894 GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
816927 CCAAACAAGT
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:816885 original size:36 final size:36
Alignment explanation
Indices: 816834--816910 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
816824 GGTCGCAGAA
*
816834 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
* * *
816870 GATGAAGCTGGCGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
816906 GATGA
1 GATGA
816911 TGATGAAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.21
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGAC
Found at i:816926 original size:12 final size:12
Alignment explanation
Indices: 816834--816922 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
816824 GGTCGCAGAA
*
816834 GATGAAGCTGAC
1 GATGAAGATGAC
816846 GATGAAGATGAC
1 GATGAAGATGAC
*
816858 GATGATGATGAC
1 GATGAAGATGAC
* *
816870 GATGAAGCTGGC
1 GATGAAGATGAC
*
816882 GATGAAGATGAT
1 GATGAAGATGAC
* * *
816894 GACGATGATGAT
1 GATGAAGATGAC
* *
816906 GATGATGATGAA
1 GATGAAGATGAC
816918 GATGA
1 GATGA
816923 TGATCCAAAC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:816926 original size:18 final size:18
Alignment explanation
Indices: 816831--816922 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
816821 AGCGGTCGCA
*
816831 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGACGAT
* *
816849 GAAGATGACGATGATGAT
1 GAAGATGAAGATGACGAT
* * *
816867 GACGATGAAGCTGGCGAT
1 GAAGATGAAGATGACGAT
* * *
816885 GAAGATGATGACGATGAT
1 GAAGATGAAGATGACGAT
* * *
816903 GATGATGATGATGAAGAT
1 GAAGATGAAGATGACGAT
816921 GA
1 GA
816923 TGATCCAAAC
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGACGAT
Found at i:818385 original size:22 final size:22
Alignment explanation
Indices: 818341--818385 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
818331 ATTACATATC
*
818341 TTTAAAAAAAGTATTGATCCTT
1 TTTAAAAAAAGTATTGATACTT
*
818363 TTTATAAAAAGTA-TGTATACTT
1 TTTAAAAAAAGTATTG-ATACTT
818385 T
1 T
818386 CAACATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (22 bp):
TTTAAAAAAAGTATTGATACTT
Found at i:818702 original size:183 final size:182
Alignment explanation
Indices: 818394--819066 Score: 1202
Period size: 183 Copynumber: 3.7 Consensus size: 182
818384 TTCAACATAT
* *
818394 TATAAATATACCGGTTTTGTGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATCTTGTG
1 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
*
818459 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGTTAAAAAGTGTCGACATTT
66 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATT-TAAAAAAGTGTCGACATTT
818524 ACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGG
130 ACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGG
*
818577 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATCTTGTG
1 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
* *
818642 TTGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGTTAAAAAGTGTCGACATTT
66 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATT-TAAAAAAGTGTCGACATTT
818707 ACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGG
130 ACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGG
818760 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
1 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
* *
818825 TCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTATCGACATTT
66 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATAC-ATTTAAAAAAGTGTCGACATTT
* *
818890 ACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGG
130 ACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGG
* *
818943 TATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTG
1 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
819008 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
66 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTTAAAAAAGTGTCG
819067 GTAATTTTAA
Statistics
Matches: 475, Mismatches: 13, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
183 471 0.99
184 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (182 bp):
TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTTAAAAAAGTGTCGACATTTA
CACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGG
Found at i:821569 original size:25 final size:25
Alignment explanation
Indices: 821535--821599 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
821525 TTATCATTAA
821535 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
821560 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
821585 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
821600 TCTTTTAAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:821799 original size:20 final size:22
Alignment explanation
Indices: 821769--821849 Score: 69
Period size: 23 Copynumber: 3.7 Consensus size: 22
821759 TGGACACTTT
*
821769 TAATATAATAGGTA-AAC-ATA
1 TAATGTAATAGGTAGAACTATA
* *
821789 TGATGTAATAGGTAGAGCTTATA
1 TAATGTAATAGGTAGAAC-TATA
**
821812 TAATGTAATAGGTATCG-TTTATA
1 TAATGTAATAGGTA--GAACTATA
821835 TAATGTAATAGGTAG
1 TAATGTAATAGGTAG
821850 TGGTTATATT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 12 0.24
21 3 0.06
23 34 0.68
25 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.36
Consensus pattern (22 bp):
TAATGTAATAGGTAGAACTATA
Found at i:821817 original size:23 final size:23
Alignment explanation
Indices: 821786--821858 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
821776 ATAGGTAAAC
*
821786 ATATGATGTAATAGGTAGAGCTT
1 ATATAATGTAATAGGTAGAGCTT
** *
821809 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGAGCTT
* *
821832 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGAGCTT
821855 ATAT
1 ATAT
821859 TGTAAAGTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGAGCTT
Found at i:822307 original size:18 final size:18
Alignment explanation
Indices: 822286--822322 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
822276 GTAATTGGAG
822286 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
822304 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
822322 T
1 T
822323 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:822330 original size:24 final size:24
Alignment explanation
Indices: 822278--822324 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
822268 TTTCATATGT
* *
822278 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
822302 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
822325 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:822642 original size:34 final size:34
Alignment explanation
Indices: 822595--822660 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
822585 AAATCCAAAG
*
822595 CTCATATGGTGCCAAGCAAAAGGAAATAAAAAAT
1 CTCATATGATGCCAAGCAAAAGGAAATAAAAAAT
*
822629 CTCATATGATGCCAAGCAAAAGGAAATCAAAA
1 CTCATATGATGCCAAGCAAAAGGAAATAAAAA
822661 TCTACAACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (34 bp):
CTCATATGATGCCAAGCAAAAGGAAATAAAAAAT
Found at i:823115 original size:23 final size:23
Alignment explanation
Indices: 823084--823156 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
823074 ATAGGTAAAC
*
823084 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* **
823107 ATATAATGTAATAGGTATCATTT
1 ATATAATGTAATAGGTAGCGCTT
* *
823130 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
823153 ATAT
1 ATAT
823157 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:823663 original size:22 final size:23
Alignment explanation
Indices: 823628--823670 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
823618 TATTGTACTT
**
823628 TATAATATTTCCGGT-TAAATAA
1 TATAATATAACCGGTATAAATAA
823650 TATAATATAACCGGTATAAAT
1 TATAATATAACCGGTATAAAT
823671 TTTAACCGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (23 bp):
TATAATATAACCGGTATAAATAA
Found at i:833399 original size:12 final size:13
Alignment explanation
Indices: 833382--833412 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
833372 GGTATCCATC
833382 GGAAAAGG-AAAA
1 GGAAAAGGAAAAA
833394 GGAAAAGGAAAAA
1 GGAAAAGGAAAAA
833407 GGAAAA
1 GGAAAA
833413 ATCCACAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (13 bp):
GGAAAAGGAAAAA
Found at i:833413 original size:7 final size:6
Alignment explanation
Indices: 833382--833412 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
833372 GGTATCCATC
833382 GGAAAA GGAAAA GGAAAA GGAAAAA GGAAAA
1 GGAAAA GGAAAA GGAAAA GG-AAAA GGAAAA
833413 ATCCACAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
GGAAAA
Found at i:849348 original size:3 final size:3
Alignment explanation
Indices: 849342--849377 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
849332 CCCCGATATC
849342 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
849378 ATTCACCAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:849424 original size:15 final size:16
Alignment explanation
Indices: 849400--849429 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
849390 ACATAAAAAT
849400 AATTATTAAAAAATAA
1 AATTATTAAAAAATAA
849416 AATTA-TAAAAAATA
1 AATTATTAAAAAATA
849430 CTCCTAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATTATTAAAAAATAA
Found at i:855045 original size:21 final size:21
Alignment explanation
Indices: 855019--855063 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
855009 GATTTCTGGG
* *
855019 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
855040 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
855061 CAA
1 CAA
855064 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:856088 original size:2 final size:2
Alignment explanation
Indices: 856081--856124 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
856071 GAACATGTGA
856081 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
856123 AT
1 AT
856125 GTTTAAGAGA
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):
AT
Found at i:856841 original size:23 final size:23
Alignment explanation
Indices: 856775--856833 Score: 93
Period size: 22 Copynumber: 2.6 Consensus size: 23
856765 ATCATTATAT
*
856775 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
*
856797 GGCACTTCGATGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
856820 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
856834 TTTATACGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 19 0.58
23 14 0.42
ACGTcount: A:0.20, C:0.27, G:0.29, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:860030 original size:21 final size:21
Alignment explanation
Indices: 860004--860048 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
859994 GATTTCTGGG
* *
860004 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
860025 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
860046 CAA
1 CAA
860049 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:861802 original size:23 final size:23
Alignment explanation
Indices: 861736--861794 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
861726 ATCATTATAT
*
861736 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
861758 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
861781 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
861795 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:864507 original size:8 final size:8
Alignment explanation
Indices: 864494--864534 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
864484 CTCATTTTCA
864494 GAGAATTT
1 GAGAATTT
864502 GAGAATTT
1 GAGAATTT
*
864510 -AGAGTTT
1 GAGAATTT
*
864517 GGGAATTT
1 GAGAATTT
864525 GAGAATTT
1 GAGAATTT
864533 GA
1 GA
864535 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:864830 original size:128 final size:128
Alignment explanation
Indices: 864602--865233 Score: 1183
Period size: 128 Copynumber: 4.9 Consensus size: 128
864592 CTATAATCGG
* * *
864602 TTCACTATTCACATAAAGGCGCGTTCCCAGGGGCGCGCCTTCTATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
864667 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
* *
864730 TTCACTATTCACATGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATAT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
864795 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
864858 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
864923 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
864986 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
*
865051 TATCATTGCCCTATTATGTCACTCATGTCCCTCGAGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
* *
865114 TTCACTATTCACATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
865179 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
865234 AATCAGGTAA
Statistics
Matches: 491, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
128 491 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.32
Consensus pattern (128 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:865688 original size:26 final size:27
Alignment explanation
Indices: 865625--865682 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
865615 ATTAAGTTGA
*
865625 AATTT-AATGTTAAATTTCGAATACTAT
1 AATTTAAAT-TTAAATTTCGAATAATAT
865652 AATTTAAATTTAAATTT-GAATAATAT
1 AATTTAAATTTAAATTTCGAATAATAT
*
865678 TATTT
1 AATTT
865683 TTATTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 12 0.43
27 13 0.46
28 3 0.11
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (27 bp):
AATTTAAATTTAAATTTCGAATAATAT
Found at i:865697 original size:33 final size:34
Alignment explanation
Indices: 865660--865723 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
865650 ATAATTTAAA
* *
865660 TTTAAATTT-GAATAATATTATTTTTATTTTTAT
1 TTTAAATTTCGAATAATATAATTTGTATTTTTAT
865693 TTTAAATTTCGAATAATATAATTTGTATTTT
1 TTTAAATTTCGAATAATATAATTTGTATTTT
865724 AAAAACATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 9 0.32
34 19 0.68
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (34 bp):
TTTAAATTTCGAATAATATAATTTGTATTTTTAT
Found at i:866313 original size:21 final size:21
Alignment explanation
Indices: 866246--866314 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
866236 TATGGTATAA
*
866246 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
866267 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
866288 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
866309 AACCCT
1 AACCCT
866315 ACGGAGATGG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.07
21 38 0.86
22 3 0.07
ACGTcount: A:0.22, C:0.28, G:0.32, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:866348 original size:21 final size:21
Alignment explanation
Indices: 866322--866369 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
866312 CCTACGGAGA
*
866322 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
866343 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
866364 GGGCAT
1 TGGCAT
866370 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:868139 original size:35 final size:32
Alignment explanation
Indices: 868098--868182 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 32
868088 AATTCTAAAT
868098 AAATAATAATTATATAAATATTATTTTAATAAAAA
1 AAATAATAATTATATAAATA-TA--TTAATAAAAA
* * *
868133 AAATAATATTTACATAAATATATTAATATAAA
1 AAATAATAATTATATAAATATATTAATAAAAA
* *
868165 AAATAATAACTATTTAAA
1 AAATAATAATTATATAAA
868183 AAAATACTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 23 0.53
34 2 0.05
35 18 0.42
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (32 bp):
AAATAATAATTATATAAATATATTAATAAAAA
Found at i:868172 original size:32 final size:34
Alignment explanation
Indices: 868093--868173 Score: 103
Period size: 35 Copynumber: 2.4 Consensus size: 34
868083 TTAATAATTC
*
868093 TAAATAAATAATAATTATATAAATATTATTTTAATA
1 TAAA-AAATAATAATTACATAAATATTA-TTTAATA
* *
868129 AAAAAAATAATATTTACATAAATA-TA-TTAATA
1 TAAAAAATAATAATTACATAAATATTATTTAATA
868161 TAAAAAATAATAA
1 TAAAAAATAATAA
868174 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 17 0.43
34 2 0.05
35 18 0.45
36 3 0.08
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (34 bp):
TAAAAAATAATAATTACATAAATATTATTTAATA
Found at i:868198 original size:34 final size:34
Alignment explanation
Indices: 868126--868205 Score: 92
Period size: 34 Copynumber: 2.3 Consensus size: 34
868116 TATTATTTTA
* * *
868126 ATAAAAAAAATAATATTTACATAAATATATTAAT
1 ATAAAAAAAATAATATTTACATAAAAATACTAAC
868160 ATAAAAAATAATAACTATTTA-A-AAAAATACTAAC
1 ATAAAAAA-AATAA-TATTTACATAAAAATACTAAC
868194 ATAAAAATAAAT
1 ATAAAAA-AAAT
868206 TTCTTACCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 27 0.68
35 7 0.17
36 6 0.15
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (34 bp):
ATAAAAAAAATAATATTTACATAAAAATACTAAC
Found at i:870891 original size:31 final size:32
Alignment explanation
Indices: 870830--870891 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 32
870820 AAAGTACTTA
* *
870830 AATGTAAATAAAAAAATGAAAGAACGGAAATC
1 AATGTAAATAAAAAAATAAAAGAACAGAAATC
*
870862 AATG-AAATAAATAAATAAAA-AGACAGAAAT
1 AATGTAAATAAAAAAATAAAAGA-ACAGAAAT
870892 GTAAATAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 1 0.04
31 21 0.81
32 4 0.15
ACGTcount: A:0.66, C:0.05, G:0.13, T:0.16
Consensus pattern (32 bp):
AATGTAAATAAAAAAATAAAAGAACAGAAATC
Found at i:871094 original size:15 final size:15
Alignment explanation
Indices: 871074--871157 Score: 65
Period size: 15 Copynumber: 5.9 Consensus size: 15
871064 CAAAAAAAAA
871074 AGTAAGTTAGCAATT
1 AGTAAGTTAGCAATT
871089 AGTAAGTTAG-AAGTT
1 AGTAAGTTAGCAA-TT
* *
871104 AGTAGGTTAGTAA--
1 AGTAAGTTAGCAATT
871117 A-TAA-TTAGCAATT
1 AGTAAGTTAGCAATT
*
871130 AGTATGTTAG-AAGTT
1 AGTAAGTTAGCAA-TT
871145 AGTGAA-TTAGCAA
1 AGT-AAGTTAGCAA
871158 ATAAATTAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 17
0.71 0.06 0.22
Matches are distributed among these distances:
11 6 0.11
12 2 0.04
13 2 0.04
14 6 0.11
15 34 0.62
16 5 0.09
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (15 bp):
AGTAAGTTAGCAATT
Found at i:871112 original size:8 final size:8
Alignment explanation
Indices: 871074--871116 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
871064 CAAAAAAAAA
871074 AGTAAGTT
1 AGTAAGTT
*
871082 AGCAA-TT
1 AGTAAGTT
871089 AGTAAGTT
1 AGTAAGTT
871097 AG-AAGTT
1 AGTAAGTT
*
871104 AGTAGGTT
1 AGTAAGTT
871112 AGTAA
1 AGTAA
871117 ATAATTAGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 13 0.45
8 16 0.55
ACGTcount: A:0.40, C:0.02, G:0.26, T:0.33
Consensus pattern (8 bp):
AGTAAGTT
Found at i:871160 original size:41 final size:41
Alignment explanation
Indices: 871080--871161 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
871070 AAAAAGTAAG
* *
871080 TTAGCAATTAGTAAGTTAGAAGTTAGTAGGTTAGTAAATAA
1 TTAGCAATTAGTAAGTTAGAAGTTAGTAGATTAGCAAATAA
*
871121 TTAGCAATTAGTATGTTAGAAGTTAGT-GAATTAGCAAATAA
1 TTAGCAATTAGTAAGTTAGAAGTTAGTAG-ATTAGCAAATAA
871162 ATTAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.03
41 36 0.97
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34
Consensus pattern (41 bp):
TTAGCAATTAGTAAGTTAGAAGTTAGTAGATTAGCAAATAA
Found at i:871834 original size:15 final size:15
Alignment explanation
Indices: 871814--871845 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
871804 TTTCTCCCTT
*
871814 ATATATATTATAAAC
1 ATATATATTAGAAAC
871829 ATATATATTAGAAAC
1 ATATATATTAGAAAC
871844 AT
1 AT
871846 TTAATATAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (15 bp):
ATATATATTAGAAAC
Found at i:873331 original size:2 final size:2
Alignment explanation
Indices: 873324--873355 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
873314 GGAGGTAATA
873324 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
873356 GCGTCGACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:882689 original size:16 final size:17
Alignment explanation
Indices: 882668--882703 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
882658 GTTTTGATAT
882668 ATTTTAA-TTACTTAAA
1 ATTTTAATTTACTTAAA
*
882684 ATTTTAATTTATTTAAA
1 ATTTTAATTTACTTAAA
882701 ATT
1 ATT
882704 ATACTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTAATTTACTTAAA
Found at i:891491 original size:16 final size:16
Alignment explanation
Indices: 891438--891493 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
891428 ATTTAAACAT
891438 ATAAAATTAAAATATAA
1 ATAAAATTAAAAT-TAA
891455 ATAAACAATGAGTAAAA-TAA
1 AT-AA-AAT---TAAAATTAA
891475 ATAAAATTAAAATTAA
1 ATAAAATTAAAATTAA
891491 ATA
1 ATA
891494 TAAAAAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
15 5 0.15
16 6 0.18
17 2 0.06
18 5 0.15
19 5 0.15
20 5 0.15
22 5 0.15
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAATTAA
Found at i:891508 original size:37 final size:34
Alignment explanation
Indices: 891438--891524 Score: 86
Period size: 37 Copynumber: 2.4 Consensus size: 34
891428 ATTTAAACAT
* *
891438 ATAAAATTAAAATATAAATAAACAATGAGTAAAATAA
1 ATAAAATTAAAAT-TAAATAAAAAATGAAT-AAA-AA
*
891475 ATAAAATTAAAATTAAATATAAAAA-GTAATAAAAC
1 ATAAAATTAAAATTAAATA-AAAAATG-AATAAAAA
*
891510 ATATAATTAAAATTA
1 ATAAAATTAAAATTA
891525 GTGACTAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
35 15 0.34
36 10 0.23
37 19 0.43
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (34 bp):
ATAAAATTAAAATTAAATAAAAAATGAATAAAAA
Found at i:891524 original size:35 final size:35
Alignment explanation
Indices: 891432--891524 Score: 93
Period size: 35 Copynumber: 2.5 Consensus size: 35
891422 ATAATAATTT
891432 AAACATATAAAATTAAAATATAAATAAACAATGAGTAAA
1 AAACATAT--AATTAAAAT-TAAATAAACAA-GAGTAAA
*
891471 ATAA-ATAAAATTAAAATTAAATATAA-AA-AGTAATA
1 A-AACATATAATTAAAATTAAATA-AACAAGAGTAA-A
891506 AAACATATAATTAAAATTA
1 AAACATATAATTAAAATTA
891525 GTGACTAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
34 7 0.15
35 16 0.33
36 8 0.17
37 11 0.23
39 4 0.08
40 2 0.04
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (35 bp):
AAACATATAATTAAAATTAAATAAACAAGAGTAAA
Found at i:892757 original size:3 final size:3
Alignment explanation
Indices: 892749--892800 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
892739 GGCTTGTAAT
* *
892749 TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
892795 TAA TAA
1 TAA TAA
892801 CAAAATGAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:899752 original size:108 final size:108
Alignment explanation
Indices: 899613--899979 Score: 346
Period size: 108 Copynumber: 3.3 Consensus size: 108
899603 TAACCGGTTA
* *
899613 TGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACATTTTAGGAGTTACCTAA
1 TGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACCTAA
*
899678 TATGTTGATAATACTAATAACAAATTAAGTAAGTAACGTATTT
66 TATGTTGATAATACTAATAACAAATTAAGTAATTAACGTATTT
* * * ** * * *
899721 TGTTATTGTCGGATTTCTAAGCCCCCATCAGCTTAATAATGCGCTACCTATTATGTTACATAAGC
1 TGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTAA-ACTTTGGTA---A-CAT-TT---TAGGC
* * * * *** * * *
899786 GCTACCTAATATGTT-ATTATGCTTGATAA-TGTTTCCAGTAATTAACCG-GTTA
57 GTTACCTAATATGTTGATAATAC-TAATAACAAATT-AAGTAATTAA-CGTATTT
* * *
899838 TGTTATCGTCGGATTTCTAAGGCTCTATCAGCTTAAACTTTTGTAACATTTTAGGCGTTACCTAA
1 TGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACCTAA
*
899903 TATGTTGATAATACTAATAACAAATTAAGTAATTAACATATTT
66 TATGTTGATAATACTAATAACAAATTAAGTAATTAACGTATTT
**
899946 TGTTATCGTCGGATTT-TCAAAACCCCATCAGCTT
1 TGTTATCGTCGGATTTCT-AAGGCCCCATCAGCTT
899980 TAAAAATGTG
Statistics
Matches: 196, Mismatches: 47, Indels: 32
0.71 0.17 0.12
Matches are distributed among these distances:
107 2 0.01
108 95 0.48
109 12 0.06
111 2 0.01
112 3 0.02
113 3 0.02
114 2 0.01
116 11 0.06
117 64 0.33
118 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (108 bp):
TGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTAAACTTTGGTAACATTTTAGGCGTTACCTAA
TATGTTGATAATACTAATAACAAATTAAGTAATTAACGTATTT
Found at i:899787 original size:23 final size:24
Alignment explanation
Indices: 899756--899801 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
899746 CATCAGCTTA
*
899756 ATAATGCGCTACCTATTATGTTAC
1 ATAATGCGCTACCTAATATGTTAC
899780 ATAA-GCGCTACCTAATATGTTA
1 ATAATGCGCTACCTAATATGTTA
899802 TTATGCTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (24 bp):
ATAATGCGCTACCTAATATGTTAC
Found at i:899840 original size:225 final size:226
Alignment explanation
Indices: 899430--900073 Score: 1067
Period size: 225 Copynumber: 2.9 Consensus size: 226
899420 CCTATTTTTT
* * * *
899430 TAACATTTTAGGCGTTACTTAATATGTTGATAATATTGATAACAAATTAAGTAATTAACCTATTT
1 TAACATTTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACATATTT
* *
899495 TGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAATAATACGCTACCTATTACGTTACATAAG
66 TGTTATCGTCGGATTTCTAAGACCCCATCAGCTTTAATAATGCGCTACCTATTACGTTACATAAG
* *
899560 AGCTACCTAATATGTTATTATGTTTTATAATGTTTCCAGTAATTAACCGGTTATGTTATCGTCGG
131 CGCTACCTAATATGTTATTATGTTTGATAATGTTTCCAGTAATTAACCGGTTATGTTATCGTCGG
899625 ATTTCTAAGGCTCCATCAGCTTAAACTTTGG
196 ATTTCTAAGGCTCCATCAGCTTAAACTTTGG
* * *
899656 TAACATTTTAGGAGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAAGTAACGTATTT
1 TAACATTTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACATATTT
* * *
899721 TGTTATTGTCGGATTTCTAAGCCCCCATCAGC-TTAATAATGCGCTACCTATTATGTTACATAAG
66 TGTTATCGTCGGATTTCTAAGACCCCATCAGCTTTAATAATGCGCTACCTATTACGTTACATAAG
*
899785 CGCTACCTAATATGTTATTATGCTTGATAATGTTTCCAGTAATTAACCGGTTATGTTATCGTCGG
131 CGCTACCTAATATGTTATTATGTTTGATAATGTTTCCAGTAATTAACCGGTTATGTTATCGTCGG
* *
899850 ATTTCTAAGGCTCTATCAGCTTAAACTTTTG
196 ATTTCTAAGGCTCCATCAGCTTAAACTTTGG
899881 TAACATTTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACATATTT
1 TAACATTTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACATATTT
* * * *
899946 TGTTATCGTCGGATTT-TCAAAACCCCATCAGCTTTAAAAATGTGCTACCTATTACGTTATATAA
66 TGTTATCGTCGGATTTCT-AAGACCCCATCAGCTTTAATAATGCGCTACCTATTACGTTACATAA
*
900010 GCGCTACCTAATATGTTATTATGTTTGATAATGTTTCCAGTAATTAACTGGTTATGTTATCGTC
130 GCGCTACCTAATATGTTATTATGTTTGATAATGTTTCCAGTAATTAACCGGTTATGTTATCGTC
900074 TACATTTTTT
Statistics
Matches: 389, Mismatches: 27, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
224 1 0.00
225 210 0.54
226 178 0.46
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (226 bp):
TAACATTTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACATATTT
TGTTATCGTCGGATTTCTAAGACCCCATCAGCTTTAATAATGCGCTACCTATTACGTTACATAAG
CGCTACCTAATATGTTATTATGTTTGATAATGTTTCCAGTAATTAACCGGTTATGTTATCGTCGG
ATTTCTAAGGCTCCATCAGCTTAAACTTTGG
Found at i:909905 original size:4 final size:4
Alignment explanation
Indices: 909896--909926 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
909886 CTCTATGCCC
909896 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
909927 TCCTGTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:911817 original size:20 final size:20
Alignment explanation
Indices: 911789--911826 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
911779 TGGATTTTCA
* *
911789 AAATTTATTTTTGAAATTGT
1 AAATATATTTTTAAAATTGT
911809 AAATATATTTTTAAAATT
1 AAATATATTTTTAAAATT
911827 ATATTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
AAATATATTTTTAAAATTGT
Found at i:912062 original size:27 final size:26
Alignment explanation
Indices: 912012--912073 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
912002 ATTCATATTT
**
912012 TTTAAAAAATAATTATAATTTTATGAA
1 TTTAAAAAATAATTATAAAGTTAT-AA
*
912039 -TTAAAAGATTAATTATAAAGTTATAA
1 TTTAAAA-AATAATTATAAAGTTATAA
912065 TTTAAAAAA
1 TTTAAAAAA
912074 ATACTTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 9 0.31
27 20 0.69
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (26 bp):
TTTAAAAAATAATTATAAAGTTATAA
Found at i:918080 original size:2 final size:2
Alignment explanation
Indices: 918073--918099 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
918063 TAATAATGTT
918073 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
918100 GATGCTCGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:919339 original size:2 final size:2
Alignment explanation
Indices: 919334--919372 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
919324 AAATAAAACT
919334 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
919373 GACATGTGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:923476 original size:18 final size:18
Alignment explanation
Indices: 923453--923497 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
923443 TTGGGTTTCC
*
923453 TCTCAATCATCTTCTTCT
1 TCTCAATCATCATCTTCT
923471 TCTCAATCATCATCTTCT
1 TCTCAATCATCATCTTCT
923489 TCTCAATCA
1 TCTCAATCA
923498 AGCTCTGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.44
Consensus pattern (18 bp):
TCTCAATCATCATCTTCT
Found at i:928762 original size:31 final size:31
Alignment explanation
Indices: 928727--928795 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
928717 ATTGTGTGGA
*
928727 ATGAGTTGCTAGCCATTTATGATCGTTGGGG
1 ATGAGTTGCTAGCCATTTATGAACGTTGGGG
928758 ATGAGTTGCTAGCCATTTATGAACGTTGGGG
1 ATGAGTTGCTAGCCATTTATGAACGTTGGGG
928789 ATGAGTT
1 ATGAGTT
928796 ATAGTCGTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.22, C:0.12, G:0.32, T:0.35
Consensus pattern (31 bp):
ATGAGTTGCTAGCCATTTATGAACGTTGGGG
Found at i:930856 original size:75 final size:76
Alignment explanation
Indices: 930754--930962 Score: 271
Period size: 75 Copynumber: 2.8 Consensus size: 76
930744 CCGTTGTACA
* *
930754 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
** *
930818 CAAAACTGTTT
66 CAAAACCATTC
* * * *
930829 AGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
*
930893 CCAAACCATTC
66 CAAAACCATTC
**
930904 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTATGAGCA-ATCTGGAATT
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGG-ATCGGTTCCCTCCGAGCATA-CTGGAATT
930963 TTTGGCTTTG
Statistics
Matches: 115, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
75 86 0.75
76 6 0.05
77 23 0.20
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.23
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
CAAAACCATTC
Found at i:931370 original size:22 final size:21
Alignment explanation
Indices: 931328--931367 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
931318 GAGTTTGTTT
*
931328 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
931349 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
931368 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:933404 original size:75 final size:75
Alignment explanation
Indices: 933279--933485 Score: 263
Period size: 75 Copynumber: 2.7 Consensus size: 75
933269 CGTTGTACAA
* * * *
933279 GGGGGAATCGGTACCCCCT-TGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAA
1 GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAACAA
** *
933343 AACTGTTTAG
66 AACCATTCAG
* * *
933353 GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCCA
1 GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAACAA
933418 AACCATTCAG
66 AACCATTCAG
** *
933428 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCCTATGAGCAATCTGGAATT
1 GGGGGAATCGGTTCCTCCTAT--GGGGGAATCGGTT-CCCTCCGAGCATTCTGGAATT
933486 TTTGGCTTTG
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
74 17 0.15
75 68 0.59
77 13 0.11
78 17 0.15
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.24
Consensus pattern (75 bp):
GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAACAA
AACCATTCAG
Found at i:933469 original size:22 final size:23
Alignment explanation
Indices: 933427--933471 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
933417 AAACCATTCA
933427 GGGGGGAATCGGTTCCTCCTATG
1 GGGGGGAATCGGTTCCTCCTATG
933450 GGGGGGAATCGGTTCC-CCTATG
1 GGGGGGAATCGGTTCCTCCTATG
933472 AGCAATCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.13, C:0.22, G:0.40, T:0.24
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCTCCTATG
Found at i:935676 original size:20 final size:19
Alignment explanation
Indices: 935650--935687 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
935640 AAACCTTCAA
* *
935650 AGGGGGAATCGGTTCCCTC
1 AGGGGGGATCGATTCCCTC
935669 AGGGGGGATCGATTCCCTC
1 AGGGGGGATCGATTCCCTC
935688 TGCACCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.26, G:0.37, T:0.21
Consensus pattern (19 bp):
AGGGGGGATCGATTCCCTC
Found at i:941561 original size:75 final size:75
Alignment explanation
Indices: 941436--941641 Score: 270
Period size: 75 Copynumber: 2.7 Consensus size: 75
941426 CGTTGTACAA
* * *
941436 GGGGGAATCGGTACCCCCT-TGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAA
1 GGGGGAATCGGTTCCCCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAACAA
** *
941500 AACTGTTTAG
66 AACCATTCAG
* * *
941510 GGGGGAATCGGTTCCCCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCCA
1 GGGGGAATCGGTTCCCCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAACAA
941575 AACCATTCAG
66 AACCATTCAG
* ** *
941585 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTATGAGCAATCTGGAATT
1 GGGGGAATCGGTTCCCCCTAT--GGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
941642 TTTGGCTTTG
Statistics
Matches: 115, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
74 18 0.16
75 67 0.58
77 30 0.26
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.23
Consensus pattern (75 bp):
GGGGGAATCGGTTCCCCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAACAA
AACCATTCAG
Found at i:944546 original size:21 final size:20
Alignment explanation
Indices: 944502--944574 Score: 87
Period size: 19 Copynumber: 3.7 Consensus size: 20
944492 TTTTGGGTGC
944502 AAAGTTTCGAAACT-TTAAA
1 AAAGTTTCGAAACTCTTAAA
*
944521 AAAGTTTTGAAACTCTTAATA
1 AAAGTTTCGAAACTCTTAA-A
* *
944542 AAAGTTTCAAAACTCTT-AC
1 AAAGTTTCGAAACTCTTAAA
*
944561 AAAGTTTCCAAACT
1 AAAGTTTCGAAACT
944575 ATGAATGGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 26 0.55
20 5 0.11
21 16 0.34
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (20 bp):
AAAGTTTCGAAACTCTTAAA
Found at i:962334 original size:31 final size:31
Alignment explanation
Indices: 962299--962378 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
962289 AAAATTTTTG
* *
962299 TGTTCATGTTTGTTCATTAAGGAATATAACT
1 TGTTCATGTTCGTTCATTAAGAAATATAACT
*
962330 TGTTCATGTTCGTTTATTAAGAAATATAACT
1 TGTTCATGTTCGTTCATTAAGAAATATAACT
*
962361 TCTTCATGTTCGTTCATT
1 TGTTCATGTTCGTTCATT
962379 TAAATAATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.47
Consensus pattern (31 bp):
TGTTCATGTTCGTTCATTAAGAAATATAACT
Found at i:963947 original size:21 final size:21
Alignment explanation
Indices: 963921--963975 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
963911 GATTCTGACT
963921 ATTGCAACGCGATAATACAAA
1 ATTGCAACGCGATAATACAAA
963942 ATTGCAACGCGATAATACAAA
1 ATTGCAACGCGATAATACAAA
*
963963 ATCGCAACGCGAT
1 ATTGCAACGCGAT
963976 TCTGACTATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.18
Consensus pattern (21 bp):
ATTGCAACGCGATAATACAAA
Found at i:964466 original size:19 final size:19
Alignment explanation
Indices: 964442--964550 Score: 101
Period size: 19 Copynumber: 5.4 Consensus size: 19
964432 TTATTTTGGA
964442 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
964461 TTTTTCACTATCGCAACAACAC
1 TTTTTCACTATCG---CAACAC
*
964483 GTTTTTCAAACTCTCGCAACAC
1 -TTTTTC--ACTATCGCAACAC
* *
964505 ATTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
* * *
964524 ATTTTAACTATCGCAGCAC
1 TTTTTCACTATCGCAACAC
964543 ATTTTTCA
1 -TTTTTCA
964551 AAATTGTGTT
Statistics
Matches: 76, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
19 43 0.57
20 5 0.07
21 4 0.05
22 12 0.16
23 6 0.08
25 6 0.08
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.35
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:967278 original size:10 final size:10
Alignment explanation
Indices: 967253--967291 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
967243 ATAATAAAAC
967253 ATTAAAAA-T
1 ATTAAAAATT
*
967262 ATAAAAAATT
1 ATTAAAAATT
967272 ATTAAAAATT
1 ATTAAAAATT
*
967282 AATAAAAATT
1 ATTAAAAATT
967292 TGAAGACATC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:967288 original size:19 final size:18
Alignment explanation
Indices: 967236--967288 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
967226 TAAAAACTTG
967236 TATT-AAAA-TAATAAAA
1 TATTAAAAATTAATAAAA
*
967252 CATTAAAAATATAA-AAAA
1 TATTAAAAAT-TAATAAAA
967270 TTATTAAAAATTAATAAAA
1 -TATTAAAAATTAATAAAA
967289 ATTTGAAGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 3 0.10
17 4 0.13
18 7 0.23
19 16 0.53
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
TATTAAAAATTAATAAAA
Found at i:970653 original size:20 final size:20
Alignment explanation
Indices: 970628--970665 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
970618 TTTGGTTCAC
*
970628 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
970648 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
970666 GGAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.21
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:970668 original size:18 final size:19
Alignment explanation
Indices: 970628--970671 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
970618 TTTGGTTCAC
*
970628 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAG-G
970648 GGAATAAAAGATTACCA-G
1 GGAATAAAAGATTACCAGG
970666 GGAATA
1 GGAATA
970672 GGATTACTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.20
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:970810 original size:18 final size:18
Alignment explanation
Indices: 970787--970834 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
970777 AAATTGTCCT
*
970787 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
*
970805 TATTATA-AATTGTAAAA
1 TATTATATATTTGTAAAA
970822 TATTTATATATTT
1 TA-TTATATATTT
970835 TCTTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
18 12 0.48
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:972072 original size:5 final size:5
Alignment explanation
Indices: 972053--972213 Score: 70
Period size: 5 Copynumber: 31.2 Consensus size: 5
972043 GTTATATTAC
* *
972053 ATATT ATAATAT ATATT ATATT ATACT ACTA-T ATAGT ATATGT -TA-T
1 ATATT AT-AT-T ATATT ATATT ATATT A-TATT ATATT ATAT-T ATATT
* *
972099 ATATTT AGTATT ATATT ATAGT ATATT TTATT ATA-T AGTATT -TATT
1 ATA-TT A-TATT ATATT ATATT ATATT ATATT ATATT A-TATT ATATT
* *
972145 ATTAGGCAT ATATT ATAGT ATATT ATATT ATA-T -TATT ACCTATT A-ATT
1 A-TA---TT ATATT ATATT ATATT ATATT ATATT ATATT A--TATT ATATT
*
972193 AATATT ATAGT A-ATT ATATT A
1 -ATATT ATATT ATATT ATATT A
972214 ATAATAAATG
Statistics
Matches: 121, Mismatches: 12, Indels: 46
0.68 0.07 0.26
Matches are distributed among these distances:
3 3 0.02
4 18 0.15
5 68 0.56
6 18 0.15
7 10 0.08
8 2 0.02
9 2 0.02
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (5 bp):
ATATT
Found at i:972134 original size:41 final size:44
Alignment explanation
Indices: 972066--972177 Score: 119
Period size: 43 Copynumber: 2.6 Consensus size: 44
972056 TTATAATATA
* *
972066 TATTATATTATACTACTA-TATAGTATAT-GT-TATA-TATTTA-G
1 TATTATATTATAGTA-TATTATATTATATAGTATATATTA-TTAGG
* *
972107 TATTATATTATAGTATATTTTATTATATAGTATTTATTATTAGG
1 TATTATATTATAGTATATTATATTATATAGTATATATTATTAGG
*
972151 CA-TATATTATAGTATATTATATTATAT
1 TATTATATTATAGTATATTATATTATAT
972178 TATTACCTAT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
40 2 0.03
41 22 0.37
42 2 0.03
43 30 0.50
44 4 0.07
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.54
Consensus pattern (44 bp):
TATTATATTATAGTATATTATATTATATAGTATATATTATTAGG
Found at i:975006 original size:125 final size:125
Alignment explanation
Indices: 974869--975127 Score: 484
Period size: 125 Copynumber: 2.1 Consensus size: 125
974859 AAAATTGACA
974869 TAATT-ATATATTTGACCCTTAATATTTACACATACTATCAATCAATCATTATTTTAATTCAATT
1 TAATTAAT-TATTTGACCCTTAATATTTACACATACTATCAATCAATCATTATTTTAATTCAATT
974933 AAATAAATTTAACCTTTAATTCAGAGATATCATGTGGTTCTATATGACTGGAGGATTAATT
65 AAATAAATTTAACCTTTAATTCAGAGATATCATGTGGTTCTATATGACTGGAGGATTAATT
*
974994 TAATTAATTATTTGACCCTTAATGTTTACACATACTATCAATCAATCATTATTTTAATTCAATTA
1 TAATTAATTATTTGACCCTTAATATTTACACATACTATCAATCAATCATTATTTTAATTCAATTA
*
975059 AATAAATTTAACCTTTAATTCAGAGGTATCATGTGGTTCTATATGACTGGAGGATTAATT
66 AATAAATTTAACCTTTAATTCAGAGATATCATGTGGTTCTATATGACTGGAGGATTAATT
975119 TAATTAATT
1 TAATTAATT
975128 TATTACGTCA
Statistics
Matches: 131, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
125 129 0.98
126 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (125 bp):
TAATTAATTATTTGACCCTTAATATTTACACATACTATCAATCAATCATTATTTTAATTCAATTA
AATAAATTTAACCTTTAATTCAGAGATATCATGTGGTTCTATATGACTGGAGGATTAATT
Found at i:975749 original size:22 final size:22
Alignment explanation
Indices: 975692--975750 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
975682 ACGCGATTCT
975692 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
975714 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
975735 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
975751 ATATGTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:975764 original size:20 final size:20
Alignment explanation
Indices: 975739--975795 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
975729 TTTTCCGACT
975739 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
975759 ATCGCAATGCGGATATGTAA
1 ATCGCAATGCGAATATGTAA
*
975779 ATCGCAATGCGATTATG
1 ATCGCAATGCGAATATG
975796 ACTATCGCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:975802 original size:20 final size:20
Alignment explanation
Indices: 975735--975825 Score: 80
Period size: 20 Copynumber: 4.5 Consensus size: 20
975725 GCGATTTTCC
*
975735 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
*
975755 GTA-AATCGCAATGCGGA-TAT
1 G-ACTATCGCAATGC-GATTAT
*
975775 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
* *
975795 GACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGATTAT
*
975815 GACTGTCGCAA
1 GACTATCGCAA
975826 CACTGAATTT
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
19 3 0.05
20 56 0.90
21 3 0.05
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:976671 original size:24 final size:24
Alignment explanation
Indices: 976639--976692 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
976629 GTATTCGAAA
976639 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
976663 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
976687 TTTGAT
1 TTTGAT
976693 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:979270 original size:139 final size:140
Alignment explanation
Indices: 979019--979287 Score: 504
Period size: 139 Copynumber: 1.9 Consensus size: 140
979009 AAACGTTGTA
*
979019 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
* *
979084 TGATCTGTTCAGTTGTTATCACTTATTACATATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
979149 TATATGTATT
131 TATATGTATT
979159 TTATGTGTAAACTTTTAACA-TTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
979223 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
979288 CGCAACTCAA
Statistics
Matches: 126, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
139 106 0.84
140 20 0.16
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATATGTATT
Found at i:979283 original size:20 final size:20
Alignment explanation
Indices: 979258--979428 Score: 185
Period size: 20 Copynumber: 8.8 Consensus size: 20
979248 TTACACATTC
*
979258 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
979278 ATTTGACTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
979297 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
979312 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
979332 ATATGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
979352 ATCTGTCTATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
979372 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
979392 ATTTGATTATCACAACG-GCT
1 ATTTGACTATCGCAACGCG-A
979412 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
979429 ATTTTGAGTT
Statistics
Matches: 125, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
14 9 0.07
15 3 0.02
19 4 0.03
20 109 0.87
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:979608 original size:14 final size:14
Alignment explanation
Indices: 979571--979609 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
979561 TTAATATTAA
*
979571 ACAAATCAACTTTT
1 ACAAATCAATTTTT
979585 ACAAATCAATTTTT
1 ACAAATCAATTTTT
*
979599 ATAAATCAATT
1 ACAAATCAATT
979610 AAACAAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (14 bp):
ACAAATCAATTTTT
Found at i:981120 original size:42 final size:41
Alignment explanation
Indices: 981015--981124 Score: 105
Period size: 42 Copynumber: 2.6 Consensus size: 41
981005 TAGAATGTTG
* * * *
981015 GGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGGT
1 GGAGGGGCCTCTTAAACGATGACAGGGGCCTCTTGAACGAT
* * ** *
981056 GGAAGGGGGCTCTTGAGGGATGATAGGGGCCTCTTGAACGAT
1 GG-AGGGGCCTCTTAAACGATGACAGGGGCCTCTTGAACGAT
981098 AGG-GGAGGCCTCTTAAACGATGACAGG
1 -GGAGG-GGCCTCTTAAACGATGACAGG
981125 TGAGTCGGGC
Statistics
Matches: 53, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
41 4 0.08
42 47 0.89
43 2 0.04
ACGTcount: A:0.24, C:0.19, G:0.37, T:0.20
Consensus pattern (41 bp):
GGAGGGGCCTCTTAAACGATGACAGGGGCCTCTTGAACGAT
Found at i:981639 original size:18 final size:18
Alignment explanation
Indices: 981613--981675 Score: 72
Period size: 20 Copynumber: 3.3 Consensus size: 18
981603 CTTAAAATCT
* *
981613 CAACACGAATGACTATTG
1 CAACGCGAATGACTATCG
981631 CAACGCGAAAATGACTATCG
1 CAACGCG--AATGACTATCG
981651 CAACGCGAATTTGACTATCG
1 CAACGCGAA--TGACTATCG
981671 CAACG
1 CAACG
981676 AGAGAATCGC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 8 0.21
20 31 0.79
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (18 bp):
CAACGCGAATGACTATCG
Found at i:981645 original size:20 final size:20
Alignment explanation
Indices: 981620--981675 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
981610 TCTCAACACG
*
981620 AATGACTATTGCAACGCGAA
1 AATGACTATCGCAACGCGAA
981640 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
**
981660 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
981676 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:981916 original size:18 final size:18
Alignment explanation
Indices: 981893--981942 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
981883 TTTACTAAGC
981893 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
981911 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
*
981929 AATCTAATTGAAAT
1 AATCTAAGTGAAAT
981943 TACGAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:983714 original size:19 final size:19
Alignment explanation
Indices: 983644--983730 Score: 77
Period size: 19 Copynumber: 4.5 Consensus size: 19
983634 TCTGAAACTT
* * *
983644 AAAATTGCAACACGAAAATA
1 AAAATCGCAACGCG-AAATG
*
983664 AAAATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAA-ATG
** *
983684 ACTATTGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
983703 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAA-TG
983722 AAAATCGCA
1 AAAATCGCA
983731 TTGCGATTCT
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
19 27 0.50
20 27 0.50
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.16
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:984358 original size:20 final size:20
Alignment explanation
Indices: 984330--984440 Score: 168
Period size: 20 Copynumber: 5.5 Consensus size: 20
984320 GAAAATCACA
*
984330 TTGCGATAGTCAGCATCGCG
1 TTGCGATAGTCAGAATCGCG
* *
984350 TTGCAATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
* *
984370 TTGCGATAATCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
984390 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
*
984410 TTGCGATAGTCATAATCGCG
1 TTGCGATAGTCAGAATCGCG
984430 TTGCGATAGTC
1 TTGCGATAGTC
984441 GAAAAATCGT
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:987344 original size:114 final size:110
Alignment explanation
Indices: 987141--987364 Score: 349
Period size: 114 Copynumber: 2.0 Consensus size: 110
987131 CACATGTACC
* * *
987141 AACACGAAATTATTTTTACAAACCCAAAGTAGTTTTTTAGTTTAAAAACCGCGCAGAAGATTAGA
1 AACACGAAATTACTTTTACAAACCCAAAGTACTTTTTTAGTTTAAAAACCGCACAGAAGATTAGA
*
987206 TCAAAACAAAAAGAACCGTTTCCTGCAGTGATTTAGGGCTCGTTT
66 TCAAAACAAAAAGAACCATTTCCTGCAGTGATTTAGGGCTCGTTT
987251 AACACGAAATTACTTTTACAAACCCAAAGTACTTTGTTTAGTTTAAAAACAACCGCACAGAAGAT
1 AACACGAAATTACTTTTACAAACCCAAAGTACTTT-TTTAGTTT--AAA-AACCGCACAGAAGAT
* * *
987316 TAGATCAAAGCAAAGAGAAGCATTTCCTGCAGTGATTTAGGGCTCGTTT
62 TAGATCAAAACAAAAAGAACCATTTCCTGCAGTGATTTAGGGCTCGTTT
987365 CCAGGAAGGC
Statistics
Matches: 103, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
110 33 0.32
111 8 0.08
113 3 0.03
114 59 0.57
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (110 bp):
AACACGAAATTACTTTTACAAACCCAAAGTACTTTTTTAGTTTAAAAACCGCACAGAAGATTAGA
TCAAAACAAAAAGAACCATTTCCTGCAGTGATTTAGGGCTCGTTT
Found at i:988185 original size:2 final size:2
Alignment explanation
Indices: 988178--988215 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
988168 ATCAGGCTCC
988178 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
988216 CACAAACATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:993950 original size:50 final size:50
Alignment explanation
Indices: 993875--993972 Score: 196
Period size: 50 Copynumber: 2.0 Consensus size: 50
993865 AACAAGACTG
993875 TTGGATAGAGTATTGTAGAAACGATAATGATTCTCCCGATTTAATTTAAT
1 TTGGATAGAGTATTGTAGAAACGATAATGATTCTCCCGATTTAATTTAAT
993925 TTGGATAGAGTATTGTAGAAACGATAATGATTCTCCCGATTTAATTTA
1 TTGGATAGAGTATTGTAGAAACGATAATGATTCTCCCGATTTAATTTA
993973 CTCCATGGCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (50 bp):
TTGGATAGAGTATTGTAGAAACGATAATGATTCTCCCGATTTAATTTAAT
Found at i:994713 original size:14 final size:14
Alignment explanation
Indices: 994694--994721 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
994684 TACCCTAACC
994694 TATTAATAACATAT
1 TATTAATAACATAT
994708 TATTAATAACATAT
1 TATTAATAACATAT
994722 GTAACCAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TATTAATAACATAT
Found at i:999541 original size:23 final size:22
Alignment explanation
Indices: 999485--999565 Score: 60
Period size: 23 Copynumber: 3.7 Consensus size: 22
999475 ATGACACGAA
999485 TTTTTTTCTTTCATAACACATT
1 TTTTTTTCTTTCATAACACATT
* * * *
999507 TTTCTCTACTTTCATAATACGTT
1 TTT-TTTTCTTTCATAACACATT
*
999530 TTTTTTGTCTTT--TAGCAC-TT
1 TTTTTT-TCTTTCATAACACATT
*
999550 TTTTTTTATTTTCATA
1 TTTTTTT-CTTTCATA
999566 TAAGGTTAGA
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
19 1 0.02
20 11 0.24
21 4 0.09
22 7 0.16
23 22 0.49
ACGTcount: A:0.19, C:0.16, G:0.04, T:0.62
Consensus pattern (22 bp):
TTTTTTTCTTTCATAACACATT
Found at i:1001565 original size:26 final size:26
Alignment explanation
Indices: 1001535--1001589 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
1001525 GGATTAAATT
*
1001535 AAATAAAAATTAAAGTT-TATATTCTA
1 AAATAAAAATTAAA-TTCTAAATTCTA
*
1001561 AAATAAAGATTAAATTCTAAATTCTA
1 AAATAAAAATTAAATTCTAAATTCTA
1001587 AAA
1 AAA
1001590 GATTTGAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (26 bp):
AAATAAAAATTAAATTCTAAATTCTA
Found at i:1001577 original size:19 final size:20
Alignment explanation
Indices: 1001540--1001581 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1001530 AAATTAAATA
* *
1001540 AAAATTAAAGTTTATATTCT
1 AAAATTAAAGATTAAATTCT
1001560 AAAA-TAAAGATTAAATTCT
1 AAAATTAAAGATTAAATTCT
1001579 AAA
1 AAA
1001582 TTCTAAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAATTAAAGATTAAATTCT
Found at i:1003079 original size:16 final size:16
Alignment explanation
Indices: 1003053--1003095 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
1003043 ACTATAATTA
1003053 TTTTC-ATTATTTAAT
1 TTTTCTATTATTTAAT
1003068 TTTTCTATTATTTAAT
1 TTTTCTATTATTTAAT
1003084 TTTTCTATTATT
1 TTTTCTATTATT
1003096 ATTATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 5 0.19
16 22 0.81
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTCTATTATTTAAT
Found at i:1015312 original size:22 final size:22
Alignment explanation
Indices: 1015284--1015352 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 22
1015274 ATCCGACCTG
1015284 ACCCGAGAGCAAGAGAGCCTCT
1 ACCCGAGAGCAAGAGAGCCTCT
* *
1015306 ACCCGAGATC---CGA--CTCT
1 ACCCGAGAGCAAGAGAGCCTCT
* *
1015323 ACCCGAAAGCAAGAGAGCCTCC
1 ACCCGAGAGCAAGAGAGCCTCT
1015345 ACCCGAGA
1 ACCCGAGA
1015353 TCCGACCCGA
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
17 12 0.34
19 2 0.06
20 2 0.06
22 19 0.54
ACGTcount: A:0.32, C:0.36, G:0.23, T:0.09
Consensus pattern (22 bp):
ACCCGAGAGCAAGAGAGCCTCT
Found at i:1015328 original size:39 final size:38
Alignment explanation
Indices: 1015274--1015369 Score: 138
Period size: 39 Copynumber: 2.4 Consensus size: 38
1015264 TTTTTGGTCT
* *
1015274 ATCCGACCTGACCCGAGAGCAAGAGAGCCTCTACCCGAG
1 ATCCGACCT-ACCCGAAAGCAAGAGAGCCTCCACCCGAG
1015313 ATCCGACTCTACCCGAAAGCAAGAGAGCCTCCACCCGAG
1 ATCCGAC-CTACCCGAAAGCAAGAGAGCCTCCACCCGAG
*
1015352 ATCCGACCCGACCCGAAA
1 ATCCGA-CCTACCCGAAA
1015370 TAAATAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
39 49 0.94
40 3 0.06
ACGTcount: A:0.30, C:0.39, G:0.22, T:0.09
Consensus pattern (38 bp):
ATCCGACCTACCCGAAAGCAAGAGAGCCTCCACCCGAG
Found at i:1015797 original size:2 final size:2
Alignment explanation
Indices: 1015790--1015819 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1015780 ATGTTATAAG
1015790 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
1015820 AATAGAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1016815 original size:23 final size:23
Alignment explanation
Indices: 1016789--1016832 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1016779 CACATATTCT
* *
1016789 TTTGTTATTATGGCTTGTTTTTC
1 TTTGTTATTATGACATGTTTTTC
*
1016812 TTTGTTTTTATGACATGTTTT
1 TTTGTTATTATGACATGTTTT
1016833 CAATCGTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.11, C:0.07, G:0.16, T:0.66
Consensus pattern (23 bp):
TTTGTTATTATGACATGTTTTTC
Found at i:1021830 original size:2 final size:2
Alignment explanation
Indices: 1021823--1021847 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1021813 TTTAATTGAA
1021823 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 A
1021848 GTGATATTGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1022355 original size:21 final size:22
Alignment explanation
Indices: 1022326--1022369 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1022316 CACCAACTCC
1022326 ATAAATTC-TTTGATATTTTTT
1 ATAAATTCTTTTGATATTTTTT
*
1022347 ATAATTTCTTTTTGATATTTTTT
1 ATAAATTC-TTTTGATATTTTTT
1022370 TATTTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
23 13 0.65
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.66
Consensus pattern (22 bp):
ATAAATTCTTTTGATATTTTTT
Found at i:1022511 original size:37 final size:37
Alignment explanation
Indices: 1022470--1022542 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
1022460 GAAACATAAT
1022470 ATTTAATAATAATAATAATTCTTTTAACCATCTAAAC
1 ATTTAATAATAATAATAATTCTTTTAACCATCTAAAC
1022507 ATTTAATAATAATAATAATTCTTTTAACCATCTAAA
1 ATTTAATAATAATAATAATTCTTTTAACCATCTAAA
1022543 TAAATTAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (37 bp):
ATTTAATAATAATAATAATTCTTTTAACCATCTAAAC
Found at i:1025697 original size:14 final size:14
Alignment explanation
Indices: 1025675--1025734 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 14
1025665 CGTTTGTTGT
*
1025675 GTTTGTGTTGGTTC
1 GTTTATGTTGGTTC
*
1025689 GTTTATGTTTGTTC
1 GTTTATGTTGGTTC
1025703 G-TT-TG-T-GTTC
1 GTTTATGTTGGTTC
1025713 GTTTA--TTGTGTTC
1 GTTTATGTTG-GTTC
1025726 GTTTATGTT
1 GTTTATGTT
1025735 CGTTTGTATC
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
10 5 0.14
11 4 0.11
12 2 0.05
13 11 0.30
14 13 0.35
15 2 0.05
ACGTcount: A:0.05, C:0.07, G:0.27, T:0.62
Consensus pattern (14 bp):
GTTTATGTTGGTTC
Found at i:1025713 original size:10 final size:10
Alignment explanation
Indices: 1025698--1025741 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
1025688 CGTTTATGTT
1025698 TGTTCGTTTG
1 TGTTCGTTTG
1025708 TGTTCGTTTATTG
1 TGTTCG--T-TTG
*
1025721 TGTTCGTTTA
1 TGTTCGTTTG
1025731 TGTTCGTTTG
1 TGTTCGTTTG
1025741 T
1 T
1025742 ATCCGCTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 18 0.62
11 1 0.03
12 1 0.03
13 9 0.31
ACGTcount: A:0.05, C:0.09, G:0.25, T:0.61
Consensus pattern (10 bp):
TGTTCGTTTG
Found at i:1025723 original size:13 final size:13
Alignment explanation
Indices: 1025685--1025731 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
1025675 GTTTGTGTTG
*
1025685 GTTCGTTTATGTTT
1 GTTCGTTTAT-TGT
1025699 GTTCG--T-TTGT
1 GTTCGTTTATTGT
1025709 GTTCGTTTATTGT
1 GTTCGTTTATTGT
1025722 GTTCGTTTAT
1 GTTCGTTTAT
1025732 GTTCGTTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
10 7 0.24
11 1 0.03
12 2 0.07
13 14 0.48
14 5 0.17
ACGTcount: A:0.06, C:0.09, G:0.23, T:0.62
Consensus pattern (13 bp):
GTTCGTTTATTGT
Found at i:1025736 original size:47 final size:47
Alignment explanation
Indices: 1025649--1025785 Score: 141
Period size: 47 Copynumber: 2.9 Consensus size: 47
1025639 ATTCATTTGT
* * * * *
1025649 TTTGTTCGATTATGTTCGTTTGTTGTGTTTGTGTT-GGTTCGTTTATG
1 TTTGTTCGTTTATGTTCGTTTATTGTGTTCGT-TTATGTTCGTTTATA
* *
1025696 TTTGTTCGTTTGTGTTCGTTTATTGTGTTCGTTTATGTTCGTTTGTA
1 TTTGTTCGTTTATGTTCGTTTATTGTGTTCGTTTATGTTCGTTTATA
** * * * *
1025743 TCCGCTCATTTATGTTCATTTATTGAGTTCGTTTATGTTCGTT
1 TTTGTTCGTTTATGTTCGTTTATTGTGTTCGTTTATGTTCGTT
1025786 CTTTTATGTT
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
46 2 0.03
47 73 0.97
ACGTcount: A:0.09, C:0.10, G:0.23, T:0.58
Consensus pattern (47 bp):
TTTGTTCGTTTATGTTCGTTTATTGTGTTCGTTTATGTTCGTTTATA
Found at i:1025782 original size:10 final size:10
Alignment explanation
Indices: 1025698--1025785 Score: 50
Period size: 10 Copynumber: 7.8 Consensus size: 10
1025688 CGTTTATGTT
*
1025698 TGTTCGTTTG
1 TGTTCGTTTA
1025708 TGTTCGTTTA
1 TGTTCGTTTA
1025718 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
1025731 TGTTCGTTTGTA
1 TGTTCG-TT-TA
* *
1025743 TCCGCTCATTTA
1 T--GTTCGTTTA
*
1025755 TGTTCATTTA
1 TGTTCGTTTA
1025765 TTGAGTTCGTTTA
1 -T--GTTCGTTTA
1025778 TGTTCGTT
1 TGTTCGTT
1025786 CTTTTATGTT
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
10 30 0.48
11 3 0.05
12 7 0.11
13 20 0.32
14 3 0.05
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.57
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:1026171 original size:11 final size:11
Alignment explanation
Indices: 1026155--1026186 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
1026145 CAAAAATCCA
1026155 TAAACCCTAAG
1 TAAACCCTAAG
1026166 TAAACCCTAAG
1 TAAACCCTAAG
1026177 TAAACCCTAA
1 TAAACCCTAA
1026187 ATCTCAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.47, C:0.28, G:0.06, T:0.19
Consensus pattern (11 bp):
TAAACCCTAAG
Found at i:1029843 original size:2 final size:2
Alignment explanation
Indices: 1029808--1029833 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1029798 ATATTCATTC
1029808 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
1029834 TAACATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1030306 original size:15 final size:13
Alignment explanation
Indices: 1030260--1030306 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1030250 CATTACACAT
1030260 TCACATA-TTCATA
1 TCACATAGTTC-TA
*
1030273 TCACATAGTTCTT
1 TCACATAGTTCTA
1030286 TCACATAGCTCTCTA
1 TCACATAG-T-TCTA
1030301 TCACAT
1 TCACAT
1030307 TTCATATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 16 0.55
14 4 0.14
15 9 0.31
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.38
Consensus pattern (13 bp):
TCACATAGTTCTA
Found at i:1034026 original size:2 final size:2
Alignment explanation
Indices: 1033946--1034014 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
1033936 TTTATTTTTT
1033946 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
1033988 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1034015 GGATGGATAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1040878 original size:163 final size:163
Alignment explanation
Indices: 1040608--1040933 Score: 616
Period size: 163 Copynumber: 2.0 Consensus size: 163
1040598 AGAATCAGAG
*
1040608 CTGCCACTGTAAAGATCGTTGACCCATACAAATTGCTGAAAGATCATCATTGAGGTGTCTCTTAT
1 CTGCCACTGTAAAGATCATTGACCCATACAAATTGCTGAAAGATCATCATTGAGGTGTCTCTTAT
*
1040673 TTCATCTGATATCATTCCCTTGCAATTTCTGGATGTGTTGACTATTGACTTCACTGGTGTTTGCA
66 TTCATCAGATATCATTCCCTTGCAATTTCTGGATGTGTTGACTATTGACTTCACTGGTGTTTGCA
*
1040738 AAGCCATAATTGTTCCAAGAAGTTTTGAGAACC
131 AAGCCATAATGGTTCCAAGAAGTTTTGAGAACC
1040771 CTGCCACTGTAAAGATCATTGACCCATACAAATTGCTGAAAGATCATCATTGAGGTGTCTCTTAT
1 CTGCCACTGTAAAGATCATTGACCCATACAAATTGCTGAAAGATCATCATTGAGGTGTCTCTTAT
*
1040836 TTCATCAGATATCATTTCCTTGCAATTTCTGGATGTGTTGACTATTGACTTCACTGGTGTTTGCA
66 TTCATCAGATATCATTCCCTTGCAATTTCTGGATGTGTTGACTATTGACTTCACTGGTGTTTGCA
1040901 AAGCCATAATGGTTCCAAGAAGTTTTGAGAACC
131 AAGCCATAATGGTTCCAAGAAGTTTTGAGAACC
1040934 TTATGACTCA
Statistics
Matches: 159, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
163 159 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (163 bp):
CTGCCACTGTAAAGATCATTGACCCATACAAATTGCTGAAAGATCATCATTGAGGTGTCTCTTAT
TTCATCAGATATCATTCCCTTGCAATTTCTGGATGTGTTGACTATTGACTTCACTGGTGTTTGCA
AAGCCATAATGGTTCCAAGAAGTTTTGAGAACC
Found at i:1051111 original size:159 final size:159
Alignment explanation
Indices: 1050844--1051699 Score: 914
Period size: 159 Copynumber: 5.4 Consensus size: 159
1050834 CCGCCAACCA
* * *
1050844 AAAAGCCTACTGTTGTTGCTCCTGGAGATGACCTCCTTGCCAACCCTTCTGTTCAACCAGATGTG
1 AAAAGCCTACTGTTCTTGCTCCTGGAGATGACCTCCCTGCAAACCCTTCTGTTCAACCAGATGTG
* * * *
1050909 AAGGTATCTTTGACGTCTGAGTCCGAGATCAATAATAACAGAAGGAATATGGAGAAACGAGAATC
66 AAGGTATCTTTGACGTCTGAGTCCAAGATCACTAATAACAAAAGGAATATGGAGAAACGAAAATC
* *
1050974 AGGCACTGAGGATCCACCGATGCCAACCG
131 AGGCACTGAGGAGCCACCGATGCCAACTG
* * * * *
1051003 AAAAGCCTACTGTTCTTGCTCCTGGAGATGACCTTCTTGCCAATCCTTCTGCTCAACCAGATGTG
1 AAAAGCCTACTGTTCTTGCTCCTGGAGATGACCTCCCTGCAAACCCTTCTGTTCAACCAGATGTG
** *** * *
1051068 AAACTATCTTTGACGTCTGAGTCTGTGATCAGTAATAACAGAAGGAATATGGAGAAACGAAAATC
66 AAGGTATCTTTGACGTCTGAGTCCAAGATCACTAATAACAAAAGGAATATGGAGAAACGAAAATC
* *
1051133 AGGCACTGAGGATCCGCCGATGCCAACTG
131 AGGCACTGAGGAGCCACCGATGCCAACTG
* * ** * * *
1051162 AAAAGCCTGCTGTTCTTGCTCCGGGAGATGACCTATCTGCGAACCCTTCTGTTCAACCGGATGAG
1 AAAAGCCTACTGTTCTTGCTCCTGGAGATGACCTCCCTGCAAACCCTTCTGTTCAACCAGATGTG
* * * * *
1051227 AAGGTATCTTTGACGTCAGAGTCCAAGATCCCTAATAACAAAAGTAAAATGGGGAAACGAAAATC
66 AAGGTATCTTTGACGTCTGAGTCCAAGATCACTAATAACAAAAGGAATATGGAGAAACGAAAATC
* ** * * *
1051292 AGTCACAAATGAGCCACTGATGCCTACTG
131 AGGCACTGAGGAGCCACCGATGCCAACTG
* *
1051321 AAAAACCTACTGTTATTGCT-CTAGGAGATGACCTCCCTGCAAACCCTTCTGTTCAACCAGATGT
1 AAAAGCCTACTGTTCTTGCTCCT-GGAGATGACCTCCCTGCAAACCCTTCTGTTCAACCAGATGT
* ** * * * * * * *
1051385 GAAGGTACCTTCAATGTCCG-GATCCAAGATCCCTAAAAACAAAAGGAAGATGGGGAGACGAAAA
65 GAAGGTATCTTTGACGTCTGAG-TCCAAGATCACTAATAACAAAAGGAATATGGAGAAACGAAAA
* *
1051449 TCAGGCACCGAGGAGCCACTGATGCCAACTG
129 TCAGGCACTGAGGAGCCACCGATGCCAACTG
* * * *
1051480 AAAAGCCTACTCTTCTTGCTCCTGGACATGACCTCCCAGCAAACCCTTCTGTTCAACCAGATATG
1 AAAAGCCTACTGTTCTTGCTCCTGGAGATGACCTCCCTGCAAACCCTTCTGTTCAACCAGATGTG
* * ** * * * *
1051545 AAGCTTTCTTCT--CTGTCCAAATCCAAGGTCCCTAATAACAAAAGGAA-GTGGAGGAAAC-AAA
66 AAGGTATCTT-TGAC-GTCTGAGTCCAAGATCACTAATAACAAAAGGAATATGGA-GAAACGAAA
** ** * * * **
1051606 AGTCAGGCACCAAAAAGCCGCCAATGCCTACCA
128 A-TCAGGCACTGAGGAGCCACCGATGCCAACTG
* *
1051639 AAAAGCCTACTGTTCTTGCTCCTGTAGATGACCTCACTGCAAACCCTTCTGTTCAACCAGA
1 AAAAGCCTACTGTTCTTGCTCCTGGAGATGACCTCCCTGCAAACCCTTCTGTTCAACCAGA
1051700 CGCAGATGTA
Statistics
Matches: 592, Mismatches: 97, Indels: 16
0.84 0.14 0.02
Matches are distributed among these distances:
158 9 0.02
159 581 0.98
160 2 0.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (159 bp):
AAAAGCCTACTGTTCTTGCTCCTGGAGATGACCTCCCTGCAAACCCTTCTGTTCAACCAGATGTG
AAGGTATCTTTGACGTCTGAGTCCAAGATCACTAATAACAAAAGGAATATGGAGAAACGAAAATC
AGGCACTGAGGAGCCACCGATGCCAACTG
Found at i:1061593 original size:16 final size:15
Alignment explanation
Indices: 1061572--1061601 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1061562 TAACTGAAAT
1061572 TATTAAATATTATATA
1 TATTAAATA-TATATA
1061588 TATTAAATATATAT
1 TATTAAATATATAT
1061602 TTTAAGCTAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTAAATATATATA
Done.