Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 179 of 185
Found at i:54396175 original size:142 final size:142
Alignment explanation
Indices: 54395993--54396287 Score: 475
Period size: 142 Copynumber: 2.1 Consensus size: 142
54395983 TGCTGTTGTA
* * * *
54395993 GCTTCAATTTGATGTGATCTATAATACTGTAACTTTAGAGAGATAAGATCCTTTGTTTTAATCTG
1 GCTTCAATCTGATATGATCTATAATACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCG
* * ** *
54396058 CTCTACTGTAATCTTAGGGAGATAGGATTACTAGCTTCAATCTGCTTTGCTGTAATCTCAGGGAG
66 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAAGGAG
54396123 ATAAGATTTCTG
131 ATAAGATTTCTG
*
54396135 GCTTCAATCTGATATGATCTACT-ATACTGTAAGTTCAGAGAGATAAGATCCTTTGTTTTAATCC
1 GCTTCAATCTGATATGATCTA-TAATACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCC
54396199 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAAGGA
65 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAAGGA
54396264 GATAAGATTTCTG
130 GATAAGATTTCTG
*
54396277 GCTTCAGTCTG
1 GCTTCAATCTG
54396288 CCACACTGTG
Statistics
Matches: 141, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
142 140 0.99
143 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (142 bp):
GCTTCAATCTGATATGATCTATAATACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCG
CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAAGGAG
ATAAGATTTCTG
Found at i:54396281 original size:44 final size:44
Alignment explanation
Indices: 54396194--54396296 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 44
54396184 CCTTTGTTTT
* * *
54396194 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAAGGAGATAAGATTACTAGCTTC
* * *
54396238 AATCTGCTCCGCTGTAATCTCAAGGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAATCTCAAGGAGATAAGATTACTAGCTTC
*
54396282 AGTCTGC-CACACTGT
1 AATCTGCTC-CACTGT
54396297 GACCTCAGAG
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
43 1 0.02
44 49 0.98
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAAGGAGATAAGATTACTAGCTTC
Found at i:54407820 original size:66 final size:66
Alignment explanation
Indices: 54407710--54407840 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 66
54407700 TCAATCTTCG
54407710 AAGTTAAATTCGTCCCTTTTTTAAAATTTAAAATTCAAACATTTTGAGAAGGATATTTGGTTATT
1 AAGTTAAATTCGTCCCTTTTTTAAAATTTAAAATTCAAACATTTTGAGAAGGATATTTGGTTATT
54407775 A
66 A
* * * *
54407776 AAGTTAGATTCGTCCCTTTTTTAAAATTTAAAATTCAAATATTTTGATAATGATATTTGGTTATT
1 AAGTTAAATTCGTCCCTTTTTTAAAATTTAAAATTCAAACATTTTGAGAAGGATATTTGGTTATT
54407841 TAGATTGATC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.45
Consensus pattern (66 bp):
AAGTTAAATTCGTCCCTTTTTTAAAATTTAAAATTCAAACATTTTGAGAAGGATATTTGGTTATT
A
Found at i:54410656 original size:44 final size:43
Alignment explanation
Indices: 54410593--54410847 Score: 118
Period size: 44 Copynumber: 5.6 Consensus size: 43
54410583 TGATCTATAA
* * * * *
54410593 TACTGTAA-CTTTAGAGAGATAAGATCCTTTGTTTTAATCTGCTC
1 TACTGTAATC-TTAGGGAGATAAGATAC-TAGCTTCAATCTGCTC
* *
54410637 TACTGTAATCTTAGGGAGATAGGATTACTAGCTTCAATCTGCTT
1 TACTGTAATCTTAGGGAGATAAGA-TACTAGCTTCAATCTGCTC
* * * *
54410681 TGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATATGATCTAC
1 TACTGTAATCTTAGGGAGATAAGA-TACTAGCTTCAATC-----TG--CT-C
* * * * * * *
54410733 TATACTGTAAGT-TCAGAGAGATAAGATCCTTTGTTTTAATCCGCTC
1 --TACTGTAA-TCTTAGGGAGATAAGATAC-TAGCTTCAATCTGCTC
* * *
54410779 CACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTC
1 TACTGTAATCTTAGGGAGATAAGA-TACTAGCTTCAATCTGCTC
** * *
54410823 CGCTGTAATCTCAAGGAGATAAGAT
1 TACTGTAATCTTAGGGAGATAAGAT
54410848 TTCTGGCTTC
Statistics
Matches: 164, Mismatches: 31, Indels: 33
0.72 0.14 0.14
Matches are distributed among these distances:
43 2 0.01
44 118 0.72
45 5 0.03
46 1 0.01
47 2 0.01
49 3 0.02
51 2 0.01
53 2 0.01
54 28 0.17
55 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (43 bp):
TACTGTAATCTTAGGGAGATAAGATACTAGCTTCAATCTGCTC
Found at i:54410751 original size:142 final size:142
Alignment explanation
Indices: 54410569--54410863 Score: 475
Period size: 142 Copynumber: 2.1 Consensus size: 142
54410559 TGCTGTTGTA
* * * *
54410569 GCTTCAATTTGATGTGATCTATAATACTGTAACTTTAGAGAGATAAGATCCTTTGTTTTAATCTG
1 GCTTCAATCTGATATGATCTATAATACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCG
* * ** *
54410634 CTCTACTGTAATCTTAGGGAGATAGGATTACTAGCTTCAATCTGCTTTGCTGTAATCTCAGGGAG
66 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAAGGAG
54410699 ATAAGATTTCTG
131 ATAAGATTTCTG
*
54410711 GCTTCAATCTGATATGATCTACT-ATACTGTAAGTTCAGAGAGATAAGATCCTTTGTTTTAATCC
1 GCTTCAATCTGATATGATCTA-TAATACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCC
54410775 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAAGGA
65 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAAGGA
54410840 GATAAGATTTCTG
130 GATAAGATTTCTG
*
54410853 GCTTCAGTCTG
1 GCTTCAATCTG
54410864 CCACACTGTG
Statistics
Matches: 141, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
142 140 0.99
143 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (142 bp):
GCTTCAATCTGATATGATCTATAATACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCG
CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAAGGAG
ATAAGATTTCTG
Found at i:54410857 original size:44 final size:44
Alignment explanation
Indices: 54410770--54410872 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 44
54410760 CCTTTGTTTT
* * *
54410770 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAAGGAGATAAGATTACTAGCTTC
* * *
54410814 AATCTGCTCCGCTGTAATCTCAAGGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAATCTCAAGGAGATAAGATTACTAGCTTC
*
54410858 AGTCTGC-CACACTGT
1 AATCTGCTC-CACTGT
54410873 GACCTCAGAG
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
43 1 0.02
44 49 0.98
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAAGGAGATAAGATTACTAGCTTC
Found at i:54422982 original size:215 final size:215
Alignment explanation
Indices: 54422611--54423039 Score: 777
Period size: 215 Copynumber: 2.0 Consensus size: 215
54422601 AAGACTTACC
54422611 TACTTTAAAGAAATAAATCGTCATACTCAGTAAGTTAGAGTGCAACGATTCAATCTTCAAAGTTA
1 TACTTTAAAGAAATAAATCGTCATACTCAGTAAGTTAGAGTGCAACGATTCAATCTTCAAAGTTA
* * * *
54422676 GATTCGTCCCTTTTTTAAAATTTAAAATTCAAATATTTTGATAATGATATTTGGTTATTTAGATT
66 AATTCGTCCCTTTTTTAAAATTTAAAATTCAAACATTTTGAGAAGGATATTTGGTTATTTAGATT
*
54422741 GATCGAGAAAATCAAAATCCAGTAAGTTAGAGTTCAATTTTCTTAAAATTCTTAAACACCAAATA
131 GATCGAGAAAATCAAAACCCAGTAAGTTAGAGTTCAATTTTCTTAAAATTCTTAAACACCAAATA
54422806 TTTCCTTTATTTAAAAAACT
196 TTTCCTTTATTTAAAAAACT
*
54422826 TACTTTAAAGAAATAAATCGTCATACTCAGTAAGTTAGAGTGCAACGATTCAATCTTCGAAGTTA
1 TACTTTAAAGAAATAAATCGTCATACTCAGTAAGTTAGAGTGCAACGATTCAATCTTCAAAGTTA
54422891 AATTCGTCCCTTTTTTAAAATTTAAAATTCAAACATTTTGAGAAGGATATTTGGTTATTTAGATT
66 AATTCGTCCCTTTTTTAAAATTTAAAATTCAAACATTTTGAGAAGGATATTTGGTTATTTAGATT
* * *
54422956 GATCGAGAAAATCAAAACCCAGTAAGTTAGGGTTCGATTTTCTTAAAATTCTTGAACACCAAATA
131 GATCGAGAAAATCAAAACCCAGTAAGTTAGAGTTCAATTTTCTTAAAATTCTTAAACACCAAATA
54423021 TTTCCTTTATTTAAAAAAC
196 TTTCCTTTATTTAAAAAAC
54423040 GAGATAACAA
Statistics
Matches: 205, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
215 205 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.37
Consensus pattern (215 bp):
TACTTTAAAGAAATAAATCGTCATACTCAGTAAGTTAGAGTGCAACGATTCAATCTTCAAAGTTA
AATTCGTCCCTTTTTTAAAATTTAAAATTCAAACATTTTGAGAAGGATATTTGGTTATTTAGATT
GATCGAGAAAATCAAAACCCAGTAAGTTAGAGTTCAATTTTCTTAAAATTCTTAAACACCAAATA
TTTCCTTTATTTAAAAAACT
Found at i:54423863 original size:179 final size:178
Alignment explanation
Indices: 54423564--54423920 Score: 696
Period size: 179 Copynumber: 2.0 Consensus size: 178
54423554 AGTTTAATCA
54423564 TATAAACTTGAATATCAATAAATATGCGAATAATGGATCCAATAAAAAAAATGCTTAAACAACTA
1 TATAAACTTGAATATCAATAAATATGCGAATAATGGATCCAATAAAAAAAATGCTTAAACAACTA
54423629 AATGATTATGTTTAAAACTATGTAGAAGAAAAAGGTTCAAAGTTAATACAACATTTTCGTACATA
66 AATGATTATGTTTAAAACTATGTAGAAGAAAAAGGTTCAAAGTTAATACAACATTTTCGTACATA
*
54423694 TGTTATGAATACTAAAATGTTTGCATATAAATTATATATGTATATATT
131 TATTATGAATACTAAAATGTTTGCATATAAATTATATATGTATATATT
54423742 TATAAACTTGAATATCAATAAATATGCGAATAATGGATCCAATAAAATAAAATGCTTAAACAACT
1 TATAAACTTGAATATCAATAAATATGCGAATAATGGATCCAATAAAA-AAAATGCTTAAACAACT
54423807 AAATGATTATGTTTAAAACTATGTAGAAGAAAAAGGTTCAAAGTTAATACAACATTTTCGTACAT
65 AAATGATTATGTTTAAAACTATGTAGAAGAAAAAGGTTCAAAGTTAATACAACATTTTCGTACAT
54423872 ATATTATGAATACTAAAATGTTTGCATATAAATTATATATGTATATATT
130 ATATTATGAATACTAAAATGTTTGCATATAAATTATATATGTATATATT
54423921 AAAAAAAACT
Statistics
Matches: 177, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
178 47 0.27
179 130 0.73
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (178 bp):
TATAAACTTGAATATCAATAAATATGCGAATAATGGATCCAATAAAAAAAATGCTTAAACAACTA
AATGATTATGTTTAAAACTATGTAGAAGAAAAAGGTTCAAAGTTAATACAACATTTTCGTACATA
TATTATGAATACTAAAATGTTTGCATATAAATTATATATGTATATATT
Found at i:54429823 original size:17 final size:16
Alignment explanation
Indices: 54429791--54429838 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
54429781 ATCATAAATC
*
54429791 TATAATAAATTATTAACA
1 TATAA-AAATTTTTAA-A
54429809 TATAAAAATTTTTAAA
1 TATAAAAATTTTTAAA
*
54429825 TAAAAAAATATTTT
1 TATAAAAAT-TTTT
54429839 TTTAATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 9 0.33
17 13 0.48
18 5 0.19
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
TATAAAAATTTTTAAA
Found at i:54436609 original size:44 final size:43
Alignment explanation
Indices: 54436539--54437133 Score: 225
Period size: 44 Copynumber: 13.5 Consensus size: 43
54436529 AGTCCCATCT
* * *
54436539 CCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCA
1 CCCTAAGCAGTAGTGGAGCAGATTGAAGATTG-AGATTCTATCA
* * * * *
54436583 CCCTAAGCAGTAGTGGAGCAAATTGAAGATGGTGAATCTTATCT
1 CCCTAAGCAGTAGTGGAGCAGATTGAAGATTGAGATTC-TATCA
* * * * * * *
54436627 TCCTAAGACAGTGGAGAAGCAGATTTAAGCCATT-AG-TCCTATCT
1 CCCTAAG-CAGTAGTGGAGCAGATTGAAG--ATTGAGATTCTATCA
* * * *
54436671 CCCTAAACAGTAGTGGAGTAGGTTGAAGATTGTAGATTCTGTCA
1 CCCTAAGCAGTAGTGGAGCAGATTGAAGATTG-AGATTCTATCA
* * * * *
54436715 CCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTT
1 CCCTAAGCAGTAGTGGAGCAGATTGAAGATTGAGATTC-TATC-A
* * * * *
54436760 CCC-AAGACAGTGGAGAAGCAGAATT-AAGCCATT-AG-TCCTATCC
1 CCCTAAG-CAGTAGTGGAGCAG-ATTGAAG--ATTGAGATTCTATCA
** * * *
54436803 CCCTAAGCAGTAGTGGAATAGGTCGAAGATTGCAGATTCTGTCA
1 CCCTAAGCAGTAGTGGAGCAGATTGAAGATTG-AGATTCTATCA
* * * * *
54436847 CCCTAAGCAATAGTGGAGCAGATCGAAGATGGTGAATCTTATC-
1 CCCTAAGCAGTAGTGGAGCAGATTGAAGATTGAGATTC-TATCA
** * * * *
54436890 TTCTCAAG-A-TAGTGGAGAAGCATATTTAAGCCATT-AG-TCCTATCT
1 CCCT-AAGCAGTAGT-G-G-AGCAGATTGAAG--ATTGAGATTCTATCA
* * * *
54436935 CCCTAAGCAGTAGTGGAGTAGGTAGAAGATTGCAGATTCTGTCA
1 CCCTAAGCAGTAGTGGAGCAGATTGAAGATTG-AGATTCTATCA
* * * * *
54436979 CCCTAAGCAGTAGTGGAGTAGATTGAAGATGGTGAATCTTATCTT
1 CCCTAAGCAGTAGTGGAGCAGATTGAAGATTGAGATTC-TATC-A
* * *
54437024 CCC-AAG-A-TAGTGGAGAAGCAGATTTAAACCATT-AG-TCCTATCA
1 CCCTAAGCAGTAGT-G-G-AGCAGA-TTGAA-GATTGAGATTCTATCA
* ** * ** *
54437067 CTCTAAGCAGTAGTGGAATAGGTCAAAGATTGTAGATTCTGT-A
1 CCCTAAGCAGTAGTGGAGCAGATTGAAGATTG-AGATTCTATCA
54437110 TCCCTAAGCAGTAGTGGAGCAGAT
1 -CCCTAAGCAGTAGTGGAGCAGAT
54437134 CAAATACGGT
Statistics
Matches: 395, Mismatches: 111, Indels: 90
0.66 0.19 0.15
Matches are distributed among these distances:
41 12 0.03
42 13 0.03
43 73 0.18
44 211 0.53
45 60 0.15
46 18 0.05
47 8 0.02
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (43 bp):
CCCTAAGCAGTAGTGGAGCAGATTGAAGATTGAGATTCTATCA
Found at i:54437163 original size:132 final size:132
Alignment explanation
Indices: 54436529--54437165 Score: 1006
Period size: 132 Copynumber: 4.8 Consensus size: 132
54436519 AAAAATAGTA
* *
54436529 AGTCCCATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
1 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGT
* * * *
54436594 AGTGGAGCAAATTGAAGATGGTGAATCTTATCTTCCTAAGACAGTGGAGAAGCAGATTTAAGCCA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCA
54436659 TT
131 TT
* * *
54436661 AGTCCTATCTCCCTAAACAGTAGTGGAGTAGGTTGAAGATTGTAGATTCTGTCACCCTAAGCAGT
1 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGT
* *
54436726 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGTGGAGAAGCAGAATTAAGCCA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCA
54436791 TT
131 TT
* * *
54436793 AGTCCTATCCCCCTAAGCAGTAGTGGAATAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAAT
1 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGT
* *
54436858 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCTCAAGATAGTGGAGAAGCATATTTAAGCCA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCA
54436923 TT
131 TT
*
54436925 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTAGAAGATTGCAGATTCTGTCACCCTAAGCAGT
1 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGT
* * *
54436990 AGTGGAGTAGATTGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAACCA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCA
54437055 TT
131 TT
* * * * *
54437057 AGTCCTATCACTCTAAGCAGTAGTGGAATAGGTCAAAGATTGTAGATTCTGT-ATCCCTAAGCAG
1 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTCTGTCA-CCCTAAGCAG
* * *
54437121 TAGTGGAGCAGATCAAATACGGTGAATCTTATCTTCCCAAGATAG
65 TAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAG
54437166 AAGGGTAGTA
Statistics
Matches: 467, Mismatches: 37, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
131 1 0.00
132 466 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (132 bp):
AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGT
AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCA
TT
Found at i:54438972 original size:12 final size:12
Alignment explanation
Indices: 54438949--54439042 Score: 54
Period size: 12 Copynumber: 8.0 Consensus size: 12
54438939 TTTACATACG
*
54438949 TATATATATATA
1 TATATTTATATA
54438961 CT-TATTTATATA
1 -TATATTTATATA
54438973 TATATTTATATA
1 TATATTTATATA
54438985 -ATAATTT-TA-A
1 TAT-ATTTATATA
* * *
54438995 AATATGTACATA
1 TATATTTATATA
* *
54439007 TGTTTTTATAT-
1 TATATTTATATA
*
54439018 TTTATATTATATA
1 TATAT-TTATATA
*
54439031 TATATGTATATA
1 TATATTTATATA
54439043 CGTGAATACA
Statistics
Matches: 62, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
10 4 0.06
11 11 0.18
12 42 0.68
13 5 0.08
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.54
Consensus pattern (12 bp):
TATATTTATATA
Found at i:54438972 original size:16 final size:16
Alignment explanation
Indices: 54438951--54438981 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54438941 TACATACGTA
54438951 TATATATATACTTATT
1 TATATATATACTTATT
*
54438967 TATATATATATTTAT
1 TATATATATACTTAT
54438982 ATAATAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TATATATATACTTATT
Found at i:54439197 original size:8 final size:8
Alignment explanation
Indices: 54439186--54439216 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
54439176 TATATATATC
*
54439186 TTTTATAT
1 TTTTATAG
54439194 TTTTATAG
1 TTTTATAG
54439202 TTTTATAG
1 TTTTATAG
54439210 TTTTATA
1 TTTTATA
54439217 CATTTTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (8 bp):
TTTTATAG
Found at i:54447707 original size:35 final size:35
Alignment explanation
Indices: 54447656--54447727 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
54447646 AAATAATTTC
54447656 ACTCTTTCCCAACATGTTGATCTCAAGGAAATCTT
1 ACTCTTTCCCAACATGTTGATCTCAAGGAAATCTT
*
54447691 ACTCTTTCCCATCATGTTGATCTCAAGGAAATCTT
1 ACTCTTTCCCAACATGTTGATCTCAAGGAAATCTT
54447726 AC
1 AC
54447728 CAGAGTGGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (35 bp):
ACTCTTTCCCAACATGTTGATCTCAAGGAAATCTT
Found at i:54457496 original size:13 final size:13
Alignment explanation
Indices: 54457480--54457504 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54457470 AAAAGATTTC
54457480 GTGAAAATTTCGT
1 GTGAAAATTTCGT
54457493 GTGAAAATTTCG
1 GTGAAAATTTCG
54457505 ACGTTTGGGA
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:0.08, G:0.24, T:0.36
Consensus pattern (13 bp):
GTGAAAATTTCGT
Found at i:54458608 original size:26 final size:26
Alignment explanation
Indices: 54458572--54458624 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
54458562 TTGAATGTAA
*
54458572 AGGGGTCGCTAAGTGCAGATTTCCTG
1 AGGGGTCGCTAAGTGCAGATTCCCTG
* *
54458598 AGGGGTTGCTAAGTGCTGATTCCCTG
1 AGGGGTCGCTAAGTGCAGATTCCCTG
54458624 A
1 A
54458625 ATTATTGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (26 bp):
AGGGGTCGCTAAGTGCAGATTCCCTG
Found at i:54460031 original size:23 final size:23
Alignment explanation
Indices: 54460005--54460081 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
54459995 CCAAGTAGAA
* * **
54460005 CCTTTGTGTCGTACTCCATTTGG
1 CCTTTGTGGCGTATTCTGTTTGG
* *
54460028 CCTTTGTGGCGTATTTTGTTTAG
1 CCTTTGTGGCGTATTCTGTTTGG
54460051 CCTTTGTGGCGTATTCTGTTTGG
1 CCTTTGTGGCGTATTCTGTTTGG
54460074 CCTTTGTG
1 CCTTTGTG
54460082 CCATAATATG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.06, C:0.19, G:0.26, T:0.48
Consensus pattern (23 bp):
CCTTTGTGGCGTATTCTGTTTGG
Found at i:54460127 original size:24 final size:24
Alignment explanation
Indices: 54460050--54460128 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 24
54460040 ATTTTGTTTA
* * *
54460050 GCCTTTGTGGCGTATTCTGTTTG-
1 GCCTTTGTGGCATAATCTGTATGT
* * *
54460073 GCCTTTGTGCCATAATATGTAAGT
1 GCCTTTGTGGCATAATCTGTATGT
** *
54460097 GTTTTTGTGGCATAATCTGCATGT
1 GCCTTTGTGGCATAATCTGTATGT
54460121 GCCTTTGT
1 GCCTTTGT
54460129 AGCGAATTCT
Statistics
Matches: 41, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
23 17 0.41
24 24 0.59
ACGTcount: A:0.14, C:0.16, G:0.25, T:0.44
Consensus pattern (24 bp):
GCCTTTGTGGCATAATCTGTATGT
Found at i:54471138 original size:16 final size:16
Alignment explanation
Indices: 54471117--54471148 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
54471107 GTGTAAAAAA
54471117 TAATAATAAGTAATAT
1 TAATAATAAGTAATAT
54471133 TAATAATAAGTAATAT
1 TAATAATAAGTAATAT
54471149 AAGGGCACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
TAATAATAAGTAATAT
Found at i:54474501 original size:40 final size:40
Alignment explanation
Indices: 54474441--54474743 Score: 534
Period size: 40 Copynumber: 7.6 Consensus size: 40
54474431 CAAGCTCAAT
* * * * *
54474441 TGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
*
54474481 TGCCTTCGTGTCTTAGCCCGGATATATCAACTTGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
54474521 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
54474561 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
* *
54474601 TGCCTTCGGGTCTTAGCCCGTATATATCAACTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
54474641 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
54474681 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
54474721 TGCCTTCGGGTCTTAGCCCGGAT
1 TGCCTTCGGGTCTTAGCCCGGAT
54474744 GTATTCAAAT
Statistics
Matches: 252, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 252 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.27
Consensus pattern (40 bp):
TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
Found at i:54478009 original size:709 final size:708
Alignment explanation
Indices: 54476652--54478066 Score: 2001
Period size: 709 Copynumber: 2.0 Consensus size: 708
54476642 TATTTTCATA
*
54476652 ACTCGGTTTTGTGGTCCCGAAACCACTTCCCGACTAGGGTCACATTAGAGCTGTCACAACTCTCC
1 ACTCGGTTTTGTGGTCCCGAAACCACTCCCCGACTAGGGTCACATTAGAGCTGTCACAACTCTCC
* *
54476717 CCCACATAAGAAATTTTCGTCCCCGAAAATCTTACCGCTGAATAATTTTGGATATCGGTCCTTCA
66 CCCACATAAGAAATTTTCGTCCCCGAAAATCTTACCGCTAAATAAGTTTGGATATCGGTCCTTCA
* * *
54476782 TAGAGTCCTCAAGTTCCCAAGTGGCTTCTTCAATTCCGTGTTTATGCCACAACACCTTCACTAAT
131 TAGAGTCCTCAAGTTCCCAAGTAGCTTCTTCAATCCCGTGTTTATGCCACAACACCTTCACTAAC
* ** * * * * *
54476847 GGGATTTTCTTATTTCGCAACTCTTTTACTTCTCGCATCAAAATGCGAACCGGTTCTTCTTCATA
196 GGAACCTTCTTATTTCGCAACTCCTTCACTTCACGCAGCAAAATACGAACCGGTTCTTCTTCATA
* * * * * *
54476912 ACTCAAGTTAGGTTGAATTTCGATCTCAGATGCAGCGATTACATGCGACAGGTCGGATCTATATC
261 ACTCAAG-TAGGTTGAATTTCAACCTCAGATGCAGCAATTACATGCGACAGGTCAGATCGATAGC
* * * *
54476977 GTCGAAGCATCGAGACATGGAAAACGTTGTGAATCTTTTCAAGTTCAGGGGGCAAAATCAATCTA
325 GTCGAAGCATCGAAACATGGAAAACGTCGTAAATCTTTTCAAGCTCAGGGGGCAAAATCAATCTA
* * *
54477042 TACGCAACTGGACCAACTCGTCCGGAGATTTCGTACGGCCCAATGAATCTCGGACTCAATTTTCC
390 TACGCAACCGGACCAACTCGTCCGGAGATTTCGTACGGCCCAATGAATCTCGGACTCAACTTGCC
* * * *
54477107 CTTACGGCCAAATCTGAGTATCTTTTTCCAAGGTGAAACCTTAAGGAACACTTTGTCTCCCACCT
455 CTTACGGCCAAACCTGAGTACCTTTTTCCAAGGCGAAACCTTAAGGAACACTTTATCTCCCACCT
* * * * *
54477172 GATACTCGATGTCTTTTCGTTTCAAATCCGCGTATGACTTCTGGCGATCTGTGGCTGCCTTCAGA
520 GATACTCAATGTCCTTTCGTTTCAAATCCGCATACGACTTCTGACGATCTGTGGCTGCCTTCAGA
*
54477237 CTTTCACGGATTACTTTTACTTTCCGTTCGGCATCTTTAATCAAATCAACTCCGAAAATTTTACT
585 CTTTCACGGATTACCTTTACTTTCCGTTCGGCATCTTTAATCAAATCAACTCCGAAAATTTTACT
*
54477302 TTCACCGAGCTCGGTCCAAAACAATGGTGTACGGCATTTACGCCCGTACAAAGCCTTTG
650 TTCACCGAGCTCGGTCCAAAACAATGGTGTACGGCATTTACGACCGTACAAAGCCTTTG
* * *
54477361 ACTCGGTTTTGTGGTCCCGAAACCACTCCCCGACTAGGGTCA-ATTTTGGGCTGTTACAACTCTC
1 ACTCGGTTTTGTGGTCCCGAAACCACTCCCCGACTAGGGTCACA-TTAGAGCTGTCACAACTCTC
* * * * *
54477425 CCCCACTTAAGAAATTTTCGTCCCCGAAAATCTTACCGGTAAATAGGTTTGGGTATCGTTCCTTC
65 CCCCACATAAGAAATTTTCGTCCCCGAAAATCTTACCGCTAAATAAGTTTGGATATCGGTCCTTC
* * * *
54477490 ATCGAG-CTCTC-GGTTTCCCAAGTAGCTTCCTT-GATCCCGTGTTTGA-GCCATAACACCTTCA
130 ATAGAGTC-CTCAAG-TTCCCAAGTAGCTT-CTTCAATCCCGTGTTT-ATGCCACAACACCTTCA
* ** * *
54477551 CTAACGGAACCCTT-TTGTTTCGCAACTCCTTCACTTCACG-AGCTAGGATACGCATCGGTTCTT
191 CTAACGGAA-CCTTCTTATTTCGCAACTCCTTCACTTCACGCAGC-AAAATACGAACCGGTTCTT
* * * *
54477614 CTTCATAACTCATA-TCGGCTTGAATTTCAACCTCTGATG-GGCTAATTA-AGTGCGA-TGGATC
254 CTTCATAACTCA-AGTAGG-TTGAATTTCAACCTCAGATGCAGC-AATTACA-TGCGACAGG-TC
54477675 AGATCGATAGCGTCGAAGCATCGAAACAT-GAAAGACGTCGTAAATCTTTTCAAGCTCAGGGGGC
314 AGATCGATAGCGTCGAAGCATCGAAACATGGAAA-ACGTCGTAAATCTTTTCAAGCTCAGGGGGC
*
54477739 AAAATCAATCTATACGCAACCGGACCAACTCGTTCGGAGATTTCGTACGGCCCAATGAATCTCGG
378 AAAATCAATCTATACGCAACCGGACCAACTCGTCCGGAGATTTCGTACGGCCCAATGAATCTCGG
* *
54477804 GCTCAACTTGCCCTTACGGCCAAACCTGAGTACCTTTTTCCAAGGCGAAACTTTAAGGAACACTT
443 ACTCAACTTGCCCTTACGGCCAAACCTGAGTACCTTTTTCCAAGGCGAAACCTTAAGGAACACTT
** * *
54477869 TATCTCCCACCTGATGTTCAATGTCCTTTCGTTTCAAGTCCGCATACGATTTCTGACGATCTGTG
508 TATCTCCCACCTGATACTCAATGTCCTTTCGTTTCAAATCCGCATACGACTTCTGACGATCTGTG
*
54477934 GCTGCCTTCAGACTTTCACGGATTACCTTTACTTTCTC-TTTGGCATCTTTAATCAAATCAACTC
573 GCTGCCTTCAGACTTTCACGGATTACCTTTACTTTC-CGTTCGGCATCTTTAATCAAATCAACTC
54477998 CGAAAATTTTACTTTCACCGAGCTCGGTCCAAAACAATGGTGTACGGCATTTACGACCGTACAAA
637 CGAAAATTTTACTTTCACCGAGCTCGGTCCAAAACAATGGTGTACGGCATTTACGACCGTACAAA
54478063 GCCT
702 GCCT
54478067 CGTAAGGTGC
Statistics
Matches: 625, Mismatches: 67, Indels: 28
0.87 0.09 0.04
Matches are distributed among these distances:
708 17 0.03
709 600 0.96
710 8 0.01
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (708 bp):
ACTCGGTTTTGTGGTCCCGAAACCACTCCCCGACTAGGGTCACATTAGAGCTGTCACAACTCTCC
CCCACATAAGAAATTTTCGTCCCCGAAAATCTTACCGCTAAATAAGTTTGGATATCGGTCCTTCA
TAGAGTCCTCAAGTTCCCAAGTAGCTTCTTCAATCCCGTGTTTATGCCACAACACCTTCACTAAC
GGAACCTTCTTATTTCGCAACTCCTTCACTTCACGCAGCAAAATACGAACCGGTTCTTCTTCATA
ACTCAAGTAGGTTGAATTTCAACCTCAGATGCAGCAATTACATGCGACAGGTCAGATCGATAGCG
TCGAAGCATCGAAACATGGAAAACGTCGTAAATCTTTTCAAGCTCAGGGGGCAAAATCAATCTAT
ACGCAACCGGACCAACTCGTCCGGAGATTTCGTACGGCCCAATGAATCTCGGACTCAACTTGCCC
TTACGGCCAAACCTGAGTACCTTTTTCCAAGGCGAAACCTTAAGGAACACTTTATCTCCCACCTG
ATACTCAATGTCCTTTCGTTTCAAATCCGCATACGACTTCTGACGATCTGTGGCTGCCTTCAGAC
TTTCACGGATTACCTTTACTTTCCGTTCGGCATCTTTAATCAAATCAACTCCGAAAATTTTACTT
TCACCGAGCTCGGTCCAAAACAATGGTGTACGGCATTTACGACCGTACAAAGCCTTTG
Found at i:54483608 original size:27 final size:27
Alignment explanation
Indices: 54483578--54483755 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54483568 ATATTGAGTC
* * * *
54483578 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54483605 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54483632 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54483660 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54483687 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54483714 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54483741 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54483756 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:54483717 original size:82 final size:81
Alignment explanation
Indices: 54483599--54483754 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54483589 TGCTATATAA
* *
54483599 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54483664 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54483681 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54483745 CACTTAGTGC
65 CACTTAGTGC
54483755 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54491999 original size:40 final size:40
Alignment explanation
Indices: 54491939--54492121 Score: 312
Period size: 40 Copynumber: 4.6 Consensus size: 40
54491929 CAAGCTCAAT
* * * *
54491939 TGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
*
54491979 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
54492019 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
*
54492059 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
54492099 TGCCTTCGGGTCTTAGCCCGGAT
1 TGCCTTCGGGTCTTAGCCCGGAT
54492122 GTATTCAAAT
Statistics
Matches: 136, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 136 1.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.26
Consensus pattern (40 bp):
TGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAA
Found at i:54509567 original size:20 final size:19
Alignment explanation
Indices: 54509539--54509580 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
54509529 ACTTTATATA
54509539 ATTTAAAATAACGTAAACAT
1 ATTTAAAATAACGTAAA-AT
* *
54509559 ATTTCAAATAACTTAAAAT
1 ATTTAAAATAACGTAAAAT
54509578 ATT
1 ATT
54509581 ACTTGATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (19 bp):
ATTTAAAATAACGTAAAAT
Found at i:54540403 original size:14 final size:14
Alignment explanation
Indices: 54540384--54540415 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
54540374 ACCTTATTAT
54540384 AAAGATAAAGAAAC
1 AAAGATAAAGAAAC
54540398 AAAGATAAAGAAAC
1 AAAGATAAAGAAAC
54540412 AAAG
1 AAAG
54540416 GAAGAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.72, C:0.06, G:0.16, T:0.06
Consensus pattern (14 bp):
AAAGATAAAGAAAC
Found at i:54541298 original size:35 final size:37
Alignment explanation
Indices: 54541252--54541343 Score: 107
Period size: 35 Copynumber: 2.5 Consensus size: 37
54541242 CTTAACACTC
* *
54541252 AAAATAGGTGAATTATTCGCAAGTT-CCA-ATTATCT
1 AAAATAGGTGAATTATTCGCAAGTTGCCACAGTAGCT
* *
54541287 AAAATAGGTGAACTATTCGCATGTTAGGCCACCAGTAGCT
1 AAAATAGGTGAATTATTCGCAAGTT--GCCA-CAGTAGCT
54541327 AAAATAGGTGAATTATT
1 AAAATAGGTGAATTATT
54541344 AAGCTAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
35 23 0.49
38 3 0.06
40 21 0.45
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.30
Consensus pattern (37 bp):
AAAATAGGTGAATTATTCGCAAGTTGCCACAGTAGCT
Found at i:54545069 original size:28 final size:27
Alignment explanation
Indices: 54545033--54545095 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
54545023 AATATAAAAA
* * *
54545033 AATAAAAATCTA-AAATATATTTTTTAT
1 AATAAAAATATATAAATAGATATTTT-T
54545060 AATATAAAATATATAAATAGATATTTTT
1 AATA-AAAATATATAAATAGATATTTTT
54545088 AATAAAAA
1 AATAAAAA
54545096 ATTCAAGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 8 0.26
28 12 0.39
29 11 0.35
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (27 bp):
AATAAAAATATATAAATAGATATTTTT
Found at i:54547787 original size:11 final size:11
Alignment explanation
Indices: 54547757--54547815 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
54547747 AAACTAATCC
54547757 CCTCTCAATTAT
1 CCTCTCAATT-T
**
54547769 TTTCTCAATTT
1 CCTCTCAATTT
54547780 CCTCTCAATTT
1 CCTCTCAATTT
*
54547791 -GTCCTCAATTT
1 CCT-CTCAATTT
*
54547802 GCTCTCAATTT
1 CCTCTCAATTT
54547813 CCT
1 CCT
54547816 TCCAAATTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
10 1 0.03
11 28 0.74
12 9 0.24
ACGTcount: A:0.19, C:0.31, G:0.03, T:0.47
Consensus pattern (11 bp):
CCTCTCAATTT
Found at i:54547800 original size:22 final size:22
Alignment explanation
Indices: 54547757--54547812 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
54547747 AAACTAATCC
* *
54547757 CCTCTCAATTATTTTCTCAATTT
1 CCTCTCAATT-TGTCCTCAATTT
54547780 CCTCTCAATTTGTCCTCAATTT
1 CCTCTCAATTTGTCCTCAATTT
*
54547802 GCTCTCAATTT
1 CCTCTCAATTT
54547813 CCTTCCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 20 0.67
23 10 0.33
ACGTcount: A:0.20, C:0.29, G:0.04, T:0.48
Consensus pattern (22 bp):
CCTCTCAATTTGTCCTCAATTT
Found at i:54549730 original size:7 final size:7
Alignment explanation
Indices: 54549710--54549749 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
54549700 ATTTATTAAA
54549710 AATTTAT
1 AATTTAT
54549717 AAATTTAT
1 -AATTTAT
54549725 AATTTAT
1 AATTTAT
54549732 AA-TTA-
1 AATTTAT
54549737 AATTTAT
1 AATTTAT
54549744 AATTTA
1 AATTTA
54549750 ATTGACAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 2 0.07
6 6 0.20
7 15 0.50
8 7 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
AATTTAT
Found at i:54549807 original size:22 final size:22
Alignment explanation
Indices: 54549781--54549887 Score: 132
Period size: 21 Copynumber: 5.0 Consensus size: 22
54549771 CCCTAACCCT
*
54549781 AACCCTAAACCTTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
54549803 AACCCTAAACCCTTAACTTAAT
1 AACCCTAAACCCTTAACTTAAA
54549825 AACCCT-AACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
54549846 AACCTTAAA-TCTTAACTT-AA
1 AACCCTAAACCCTTAACTTAAA
54549866 AACCCTAAAACCC-TAATCTTAA
1 AACCCT-AAACCCTTAA-CTTAA
54549888 CAAAAACCCT
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
20 7 0.10
21 33 0.45
22 32 0.44
23 1 0.01
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (22 bp):
AACCCTAAACCCTTAACTTAAA
Found at i:54549878 original size:43 final size:44
Alignment explanation
Indices: 54549780--54549887 Score: 143
Period size: 43 Copynumber: 2.5 Consensus size: 44
54549770 ACCCTAACCC
*
54549780 TAACCCTAAACCTTTAACTTAAAAACCCTAAACCCTTAACTTAA
1 TAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* *
54549824 TAACCCT-AACCCTTAACTTAAAAACCTTAAA-TCTTAACTTAA
1 TAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
54549866 -AACCCTAAAACCC-TAATCTTAA
1 TAACCCT-AAACCCTTAA-CTTAA
54549888 CAAAAACCCT
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
41 6 0.10
42 13 0.22
43 32 0.55
44 7 0.12
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.28
Consensus pattern (44 bp):
TAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
Found at i:54549912 original size:24 final size:25
Alignment explanation
Indices: 54549864--54549912 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
54549854 ATCTTAACTT
* *
54549864 AAAACCCTAAAACCCTAATCTTAACA
1 AAAACCCT-AAACCCTAAACCTAACA
54549890 AAAACCCT-AACCCTAAACCTAAC
1 AAAACCCTAAACCCTAAACCTAAC
54549913 CCTAATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
26 8 0.38
ACGTcount: A:0.49, C:0.35, G:0.00, T:0.16
Consensus pattern (25 bp):
AAAACCCTAAACCCTAAACCTAACA
Found at i:54553357 original size:125 final size:125
Alignment explanation
Indices: 54553026--54553464 Score: 681
Period size: 125 Copynumber: 3.5 Consensus size: 125
54553016 CCCAAACATG
* * *
54553026 CTACTATAGCAAAAGCGCGTCCACGA-GGGCGCGATTTCAAAAATTCTTCTGAAAAAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCAC-ATGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTG
* * *
54553090 CTTGAAGCATTTTTTATACTATTCACTCAGAAACGTCAACTCGAAATTATTTTTTTAGGAC
65 CTTGAAGCGTTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
*
54553151 CTACTGTAGCAAAAGCGCGT-C-CATGTG-GCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACATGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
* *
54553213 TTGAAGCGTTTTTTATACTATTCGCTCAGAAGCGACAACTCGAAATTATTTTTTCAGGAC
66 TTGAAGCGTTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
* *
54553273 CTATTGTAGCAAAAGCGCGTCCACATGGGCGTGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACATGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
*
54553338 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTA-TTTTTCAGGAC
66 TTGAAGCGTTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
* * * *
54553397 CAACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTTAGAAATTCTTCTGATACAAGCTTCCTG
1 CTACTGTAGCAAAAGCGCGTCCACATGGGCGCGATTTCAGAAATTCTTCTGATA-AAGCATCCTG
54553462 CTT
65 CTT
54553465 TGATTTTATC
Statistics
Matches: 288, Mismatches: 21, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
122 108 0.38
123 4 0.01
124 66 0.23
125 110 0.38
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACATGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCGTTTTTTATACTATTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
Found at i:54553637 original size:21 final size:22
Alignment explanation
Indices: 54553599--54553639 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
54553589 CTAAATATCT
* *
54553599 TAAAAACCTTAAACCCTAACCC
1 TAAAAACCTCAAAACCTAACCC
54553621 TAAAAACC-CAAAACCTAAC
1 TAAAAACCTCAAAACCTAAC
54553640 GTGGGAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.51, C:0.34, G:0.00, T:0.15
Consensus pattern (22 bp):
TAAAAACCTCAAAACCTAACCC
Found at i:54557064 original size:14 final size:13
Alignment explanation
Indices: 54557045--54557084 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
54557035 GAGCATTCTC
*
54557045 TTTATTTCCTTCAT
1 TTTATTTCATT-AT
54557059 TTTATTTCATTAT
1 TTTATTTCATTAT
54557072 TTATATTTCATTA
1 TT-TATTTCATTA
54557085 ACTTGATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTATTTCATTAT
Found at i:54559227 original size:15 final size:16
Alignment explanation
Indices: 54559202--54559245 Score: 74
Period size: 15 Copynumber: 2.9 Consensus size: 16
54559192 TCTCTTTTGA
54559202 ATTTAGTTTATTTTTC
1 ATTTAGTTTATTTTTC
54559218 ATTT-GTTTA-TTTTC
1 ATTTAGTTTATTTTTC
54559232 ATTTAGTTTATTTT
1 ATTTAGTTTATTTT
54559246 AAGTCCTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.35
15 10 0.38
16 7 0.27
ACGTcount: A:0.18, C:0.05, G:0.07, T:0.70
Consensus pattern (16 bp):
ATTTAGTTTATTTTTC
Found at i:54561366 original size:25 final size:25
Alignment explanation
Indices: 54561338--54561388 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
54561328 TTATTTTCAA
54561338 TCAATTTATGATTTTATATTTCATT
1 TCAATTTATGATTTTATATTTCATT
54561363 TCAATTTATGATTTTATATTTCATT
1 TCAATTTATGATTTTATATTTCATT
54561388 T
1 T
54561389 TCAGTACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (25 bp):
TCAATTTATGATTTTATATTTCATT
Found at i:54562990 original size:34 final size:34
Alignment explanation
Indices: 54562944--54563009 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
54562934 CTCAAAAGAC
54562944 GTTGCACAAGTACGCCTTACCTACATTAGATGTA
1 GTTGCACAAGTACGCCTTACCTACATTAGATGTA
*
54562978 GTTGCACGAGTACGCCTTACCTACATTAGATG
1 GTTGCACAAGTACGCCTTACCTACATTAGATG
54563010 CAGTGTAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (34 bp):
GTTGCACAAGTACGCCTTACCTACATTAGATGTA
Found at i:54572066 original size:16 final size:17
Alignment explanation
Indices: 54572045--54572077 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
54572035 AATAAATATC
*
54572045 AAAATAATAAAA-ATAA
1 AAAATAAGAAAACATAA
54572061 AAAATAAGAAAACATAA
1 AAAATAAGAAAACATAA
54572078 TTTTCTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (17 bp):
AAAATAAGAAAACATAA
Found at i:54572646 original size:14 final size:14
Alignment explanation
Indices: 54572627--54572654 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54572617 TTGAATAAAA
54572627 TTATTAATTTAGAT
1 TTATTAATTTAGAT
54572641 TTATTAATTTAGAT
1 TTATTAATTTAGAT
54572655 CAAGATATAG
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:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
TTATTAATTTAGAT
Found at i:54574668 original size:23 final size:23
Alignment explanation
Indices: 54574625--54574671 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
54574615 TTTAAAGTGT
*
54574625 AAATGAAAACATAAATCAATAAA
1 AAATGAAAACATAAAACAATAAA
*
54574648 AAATGAAAA-ATATAAAGAATAAA
1 AAATGAAAACATA-AAACAATAAA
54574671 A
1 A
54574672 GGTACATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.17
Consensus pattern (23 bp):
AAATGAAAACATAAAACAATAAA
Found at i:54574748 original size:39 final size:39
Alignment explanation
Indices: 54574701--54574778 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
54574691 GAAATTATAA
54574701 AGAATAAAAGACATACACATGGGTTTACATATAAAATTT
1 AGAATAAAAGACATACACATGGGTTTACATATAAAATTT
*
54574740 AGAATAAAAGACATCCACATGGGTTTACATATAAAATTT
1 AGAATAAAAGACATACACATGGGTTTACATATAAAATTT
54574779 TGGACTATAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (39 bp):
AGAATAAAAGACATACACATGGGTTTACATATAAAATTT
Found at i:54575164 original size:14 final size:14
Alignment explanation
Indices: 54575144--54575176 Score: 57
Period size: 14 Copynumber: 2.3 Consensus size: 14
54575134 GCGCATGAAT
54575144 ATAAAAAAACTAATA
1 ATAAAAAAA-TAATA
54575159 ATAAAAAAATAATA
1 ATAAAAAAATAATA
54575173 ATAA
1 ATAA
54575177 TGATACAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (14 bp):
ATAAAAAAATAATA
Found at i:54575686 original size:22 final size:23
Alignment explanation
Indices: 54575644--54575688 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
54575634 AAATTAAAAC
54575644 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTACAAAATCATATCT
*
54575667 TCTAAGATTAC-ATATCATATCT
1 TCTAAGATTACAAAATCATATCT
54575689 AAGATTGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (23 bp):
TCTAAGATTACAAAATCATATCT
Found at i:54575691 original size:19 final size:20
Alignment explanation
Indices: 54575644--54575701 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 20
54575634 AAATTAAAAC
*
54575644 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-ATATCATA--T
54575667 TCTAAGATTACATATCATA-
1 TCTAAGATTACATATCATAT
*
54575686 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
54575702 CTTGAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.45
22 7 0.21
23 11 0.33
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (20 bp):
TCTAAGATTACATATCATAT
Found at i:54576417 original size:44 final size:44
Alignment explanation
Indices: 54576315--54576692 Score: 282
Period size: 44 Copynumber: 8.7 Consensus size: 44
54576305 CTTTCTTGAG
* * *
54576315 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGAT-G---TGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTG-TGGTTTTAA
* * *
54576356 TCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
* * * *
54576400 TCCGCTCCACTGCAACTTCAGGGAGATAGGAT-TATTGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCT-GTGGTTTTAA
*** * *
54576444 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TCGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCT-GTGGT-TTTAA
* *
54576489 TCTGC-CTCACTGCAACTTCA-GGAGGATAAGA-CT-TGCTTACTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGATCTGTGGTT--TTAA
* * * ***
54576533 TCTGCTCCACTGCAACTTCAGAGAGATAAGA-C--TAGATGCGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
* * * *
54576574 TCTGCTCTA-TGCAACTTCAGAGAGATAAAATCTGTGATTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
* * *
54576617 TCTGCTCCACTGCAACTTCAGGGAGATAGGAT-TATTGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCT-GTGGTTTTAA
* *
54576661 TCTACTCCATTGCAACTTCAGGGAGATAAGAT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT
54576693 TCTCCATCTT
Statistics
Matches: 266, Mismatches: 53, Indels: 33
0.76 0.15 0.09
Matches are distributed among these distances:
40 21 0.08
41 40 0.15
42 1 0.00
43 16 0.06
44 156 0.59
45 32 0.12
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAA
Found at i:54576508 original size:45 final size:44
Alignment explanation
Indices: 54576230--54576691 Score: 237
Period size: 44 Copynumber: 10.6 Consensus size: 44
54576220 CTCTAATCCA
* * * * * ** *
54576230 CTCCACTACAACTTTAGGGAGACAGGATTTGTTTATTTAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCATACTTAGTCTG
* * * * * * *
54576274 CCCCACTGTAATTTCAGGGGGATAAGACCTGCTTTCTTGAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCATACTT-AGTCTG
** * * *
54576319 CTCCACTGCAACTTCAGGGAGATAAGACCCG-AT-GTGA-TCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCATACTTAGTCTG
* * * * * *
54576360 CTCTACTGCAACTTCAGAGAGATAAGATCTGTG-GT-TTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCATACTTAGTCTG
* * *
54576404 CTCCACTGCAACTTCAGGGAGATAGGA-TT--ATTGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCA-T-AC-TTAGTCTG
54576448 CTCCACTGCAACTTCAGGGAGATAAGA-TTCGCCAT-CTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTT-G-CATACTT-AGTCTG
*
54576493 C-CTCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTGCATACTTAGTCTG
* * * *
54576537 CTCCACTGCAACTTCAGAGAGATAAGACTAG-ATGC-GA-TCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCATACTTAGTCTG
* * * * *
54576578 CTCTA-TGCAACTTCAGAGAGATAAAATCTGTG-AT-TTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCATACTTAGTCTG
* * * *
54576621 CTCCACTGCAACTTCAGGGAGATAGGA-TT--ATTGGCTTTAATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCA-T-AC-TTAGTCTG
*
54576665 CTCCATTGCAACTTCAGGGAGATAAGA
1 CTCCACTGCAACTTCAGGGAGATAAGA
54576692 TTCTCCATCT
Statistics
Matches: 332, Mismatches: 58, Indels: 56
0.74 0.13 0.13
Matches are distributed among these distances:
40 21 0.06
41 42 0.13
42 9 0.03
43 15 0.05
44 175 0.53
45 66 0.20
46 2 0.01
47 1 0.00
48 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGCATACTTAGTCTG
Found at i:54576542 original size:133 final size:129
Alignment explanation
Indices: 54576315--54576560 Score: 313
Period size: 133 Copynumber: 1.9 Consensus size: 129
54576305 CTTTCTTGAG
*
54576315 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGATGTGATCTACTCTACTGCAACTTCAGAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGATGTCATCTACTCTACTGCAACTTCAGAGA
* *
54576380 GATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
66 GATAAGATCTGTGCTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTATTGGCTTTAA
* *
54576444 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCC-ATCTTCAGTCTGC-CTCACTGCAACTT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA--C-CCGAT-GTCA-TCTACTCT-ACTGCAACTT
* *
54576507 CAG-GAGGATAAGA-CT-TGCTTACTTAGTCTGCTCCACTGCAACTTCAGAGAGATA
60 CAGAGA-GATAAGATCTGTGCTT--TTAATCCGCTCCACTGCAACTTCAGAGAGATA
54576561 AGACTAGATG
Statistics
Matches: 101, Mismatches: 7, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
129 31 0.31
131 7 0.07
132 10 0.10
133 53 0.52
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (129 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGATGTCATCTACTCTACTGCAACTTCAGAGA
GATAAGATCTGTGCTTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTATTGGCTTTAA
Found at i:54576630 original size:84 final size:85
Alignment explanation
Indices: 54576439--54576644 Score: 226
Period size: 84 Copynumber: 2.4 Consensus size: 85
54576429 GATTATTGGC
* *
54576439 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCTCACTGCAA
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTAG-CATC-TCAGTCTGCCTCACTGCAA
* *
54576504 CTTCAGGAGGATAAGACTTGCT
64 CTTCAGGAGGATAAAACTTGAT
* * *
54576526 TACTTAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTAG-AT-GC-GATCTG-CTCTA-TGC
1 T--TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGCATCTCAG-TCTGCCTC-ACTGC
54576586 AACTTCA-GAGAGATAAAATCTGTGAT
62 AACTTCAGGAG-GATAAAA-CT-TGAT
54576612 TTTAATCTGCTCCACTGCAACTTCAGGGAGATA
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATA
54576645 GGATTATTGG
Statistics
Matches: 103, Mismatches: 9, Indels: 17
0.80 0.07 0.13
Matches are distributed among these distances:
83 3 0.03
84 50 0.49
85 8 0.08
86 4 0.04
87 3 0.03
89 35 0.34
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (85 bp):
TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGCATCTCAGTCTGCCTCACTGCAACT
TCAGGAGGATAAAACTTGAT
Found at i:54576632 original size:217 final size:219
Alignment explanation
Indices: 54576268--54576708 Score: 715
Period size: 217 Copynumber: 2.0 Consensus size: 219
54576258 TTGTTTATTT
* * * *
54576268 AGTCTGCCCCACTGTAATTTCAGGGGGATAAGACCTGCTTTCTTGAGTCTGCTCCACTGCAACTT
1 AGTCTGCCCCACTGCAACTTCAGGAGGATAAGACCTGCTTACTTGAGTCTGCTCCACTGCAACTT
* * * * *
54576333 CAGGGAGATAAGACCCGATGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTT
66 CAGAGAGATAAGACCAGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAAATCTGTGATTTT
*
54576398 AATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAACTTC
131 AATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTACTCCACTGCAACTTC
54576463 AGGGAGATAAGATTCGCCATCTTC
196 AGGGAGATAAGATTCGCCATCTTC
* *
54576487 AGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTT-AGTCTGCTCCACTGCAACTT
1 AGTCTGCCCCACTGCAACTTCAGGAGGATAAGACCTGCTTACTTGAGTCTGCTCCACTGCAACTT
* *
54576551 CAGAGAGATAAGACTAGATGCGATCTGCTCTA-TGCAACTTCAGAGAGATAAAATCTGTGATTTT
66 CAGAGAGATAAGACCAGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAAATCTGTGATTTT
* *
54576615 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTACTCCATTGCAACTTC
131 AATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTACTCCACTGCAACTTC
*
54576680 AGGGAGATAAGATTCTCCATCTTC
196 AGGGAGATAAGATTCGCCATCTTC
54576704 AGTCT
1 AGTCT
54576709 TTTAAATTGC
Statistics
Matches: 205, Mismatches: 17, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
217 120 0.59
218 47 0.23
219 38 0.19
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (219 bp):
AGTCTGCCCCACTGCAACTTCAGGAGGATAAGACCTGCTTACTTGAGTCTGCTCCACTGCAACTT
CAGAGAGATAAGACCAGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAAATCTGTGATTTT
AATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTACTCCACTGCAACTTC
AGGGAGATAAGATTCGCCATCTTC
Found at i:54576780 original size:50 final size:50
Alignment explanation
Indices: 54576726--54576908 Score: 150
Period size: 50 Copynumber: 3.7 Consensus size: 50
54576716 TGCAATGTTG
54576726 GGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCA
1 GGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCA
** * * ** * ** * * ** ***
54576776 GGGAAGTAAGATTCGTCGTTGCGGCTTCAATCTTTTTAATTGCAATGTTG
1 GGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCA
* *
54576826 GGGAAACAAGATTTGCTGTCGTAGCTTCAATCTGTTCCACTACACCGCCA
1 GGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCA
* ** * * *
54576876 GGGGAGTAAGATTCGCTGTTGTGGCTTCAATCT
1 GGGAAACAAGATTCGCCGTCGTAGCTTCAATCT
54576909 TTTTAATTGC
Statistics
Matches: 93, Mismatches: 40, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
50 93 1.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (50 bp):
GGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCA
Found at i:54576827 original size:100 final size:100
Alignment explanation
Indices: 54576700--54576922 Score: 376
Period size: 100 Copynumber: 2.2 Consensus size: 100
54576690 GATTCTCCAT
* *
54576700 CTTCAGTCTTTTAAATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
54576765 CTACACCGCCAGGGAAGTAAGATTCG-TCGTTGCGG
66 CTACACCGCCAGGGAAGTAAGATTCGCT-GTTGCGG
* *
54576800 CTTCAATCTTTTTAATTGCAATGTTGGGGAAACAAGATTTGCTGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
* *
54576865 CTACACCGCCAGGGGAGTAAGATTCGCTGTTGTGG
66 CTACACCGCCAGGGAAGTAAGATTCGCTGTTGCGG
54576900 CTTCAATCTTTTTAATTGCAATG
1 CTTCAATCTTTTTAATTGCAATG
54576923 AAGATTCACC
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
100 115 0.99
101 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (100 bp):
CTTCAATCTTTTTAATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
CTACACCGCCAGGGAAGTAAGATTCGCTGTTGCGG
Found at i:54576938 original size:40 final size:40
Alignment explanation
Indices: 54576883--54576962 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
54576873 CCAGGGGAGT
* *
54576883 AAGATTCGCTGTTGTGGCTTCAATCTTTTTAATTGCAATG
1 AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATG
54576923 AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATG
1 AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATG
54576963 TTAGAGAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (40 bp):
AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATG
Found at i:54577042 original size:140 final size:140
Alignment explanation
Indices: 54576783--54577062 Score: 461
Period size: 140 Copynumber: 2.0 Consensus size: 140
54576773 CCAGGGAAGT
** * * * *
54576783 AAGATTCGTCGTTGCGGCTTCAATCTTTTTAATTGCAATGTTGGGGAAACAAGATTTGCTGTCGT
1 AAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTTAGAGAAACAAGATTAGCCGTCGT
** *
54576848 AGCTTCAATCTGTTCCACTACACCGCCAGGGGAGTAAGATTCGCTGTTGTGGCTTCAATCTTTTT
66 AGCTTCAATCTGTTCCACTACACCGCCAGGGGAGTAAGATTCGCCATTGCGGCTTCAATCTTTTT
54576913 AATTGCAATG
131 AATTGCAATG
*
54576923 AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTTAGAGAAACAAGATTAGCCGTCGT
1 AAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTTAGAGAAACAAGATTAGCCGTCGT
*
54576988 AGCTTCAATCTGTTCCACTACACTGCCAGGGGAGTAAGATTCGCCATTGCGGCTTCAATCTTTTT
66 AGCTTCAATCTGTTCCACTACACCGCCAGGGGAGTAAGATTCGCCATTGCGGCTTCAATCTTTTT
54577053 AATTGCAATG
131 AATTGCAATG
54577063 TTGGGGAAAC
Statistics
Matches: 129, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
140 129 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (140 bp):
AAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTTAGAGAAACAAGATTAGCCGTCGT
AGCTTCAATCTGTTCCACTACACCGCCAGGGGAGTAAGATTCGCCATTGCGGCTTCAATCTTTTT
AATTGCAATG
Found at i:54577093 original size:50 final size:49
Alignment explanation
Indices: 54576924--54577094 Score: 121
Period size: 50 Copynumber: 3.4 Consensus size: 49
54576914 ATTGCAATGA
* * * *
54576924 AGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTTAGAGAAAC
1 AGATTCACCGTCGTAGCTTCAATCTTTTTAATTGCAATGTTGGGGAAAC
* ** * * * ** *
54576973 AAGATT-AGCCGTCGTAGCTTCAATCTGTTCCACTACACTGCCAGGGGAGTA-
1 -AGATTCA-CCGTCGTAGCTTCAATCTTTTTAATTGCAATG-TTGGGGA-AAC
* * * **
54577024 AGATTCGCCATTGCGGCTTCAATCTTTTTAATTGCAATGTTGGGGAAAC
1 AGATTCACCGTCGTAGCTTCAATCTTTTTAATTGCAATGTTGGGGAAAC
54577073 GAGATTCACCGTCGTAGCTTCA
1 -AGATTCACCGTCGTAGCTTCA
54577095 TTCTATTCCA
Statistics
Matches: 83, Mismatches: 32, Indels: 12
0.65 0.25 0.09
Matches are distributed among these distances:
48 1 0.01
49 6 0.07
50 72 0.87
51 3 0.04
52 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (49 bp):
AGATTCACCGTCGTAGCTTCAATCTTTTTAATTGCAATGTTGGGGAAAC
Found at i:54577145 original size:100 final size:100
Alignment explanation
Indices: 54576923--54577148 Score: 312
Period size: 100 Copynumber: 2.3 Consensus size: 100
54576913 AATTGCAATG
*
54576923 AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTTAGAGAAACAAGATTAGCCGTCGT
1 AAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTTAGAGAAACAAGATTAGCCGTCGT
* *
54576988 AGCTTCAATCTGTTCCACTACACTGCCAGGGGAGT
66 AGCTTCAATCTATTCCACTACACTGCCAAGGGAGT
* * * * *
54577023 AAGATTCGCCATTGCGGCTTCAATCTTTTTAATTGCAATGTTGGGGAAACGAGATTCA-CCGTCG
1 AAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTTAGAGAAACAAGATT-AGCCGTCG
* *
54577087 TAGCTTCATTCTATTCCACTACA-TCGTCAAGGGAGT
65 TAGCTTCAATCTATTCCACTACACT-GCCAAGGGAGT
* *
54577123 AAGATTCGCCGTGGTGGTTTCAATCT
1 AAGATTCGCCGTTGTGGCTTCAATCT
54577149 GTTCCACTGT
Statistics
Matches: 110, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
99 1 0.01
100 108 0.98
101 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (100 bp):
AAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTTAGAGAAACAAGATTAGCCGTCGT
AGCTTCAATCTATTCCACTACACTGCCAAGGGAGT
Found at i:54577147 original size:240 final size:240
Alignment explanation
Indices: 54576700--54577148 Score: 709
Period size: 240 Copynumber: 1.9 Consensus size: 240
54576690 GATTCTCCAT
* * * *
54576700 CTTCAGTCTTTTAAATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTAAATTGCAATGTTAGAGAAACAAGATTAGCCGTCGTAGCTTCAATCTGTTCCA
* *
54576765 CTACACCGCCAGGGAAGTAAGATTCGTCGTTGCGGCTTCAATCTTTTTAATTGCAATGTTGGGGA
66 CTACACCGCCAGGGAAGTAAGATTCGCCATTGCGGCTTCAATCTTTTTAATTGCAATGTTGGGGA
** * * * *
54576830 AACAAGATTTGCTGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGGAGTAAGATTCGCTGT
131 AACAAGATTCACCGTCGTAGCTTCAATCTATTCCACTACACCGCCAAGGGAGTAAGATTCGCCGT
*
54576895 TGTGGCTTCAATCTTTTTAATTGCAATGAAGATTCACCGTTGTGG
196 GGTGGCTTCAATCTTTTTAATTGCAATGAAGATTCACCGTTGTGG
*
54576940 CTTCAATCTTTTTAATTGCAATGTTAGAGAAACAAGATTAGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTAAATTGCAATGTTAGAGAAACAAGATTAGCCGTCGTAGCTTCAATCTGTTCCA
* *
54577005 CTACACTGCCAGGGGAGTAAGATTCGCCATTGCGGCTTCAATCTTTTTAATTGCAATGTTGGGGA
66 CTACACCGCCAGGGAAGTAAGATTCGCCATTGCGGCTTCAATCTTTTTAATTGCAATGTTGGGGA
* * * *
54577070 AACGAGATTCACCGTCGTAGCTTCATTCTATTCCACTACATCGTCAAGGGAGTAAGATTCGCCGT
131 AACAAGATTCACCGTCGTAGCTTCAATCTATTCCACTACACCGCCAAGGGAGTAAGATTCGCCGT
*
54577135 GGTGGTTTCAATCT
196 GGTGGCTTCAATCT
54577149 GTTCCACTGT
Statistics
Matches: 188, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
240 188 1.00
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.32
Consensus pattern (240 bp):
CTTCAATCTTTTAAATTGCAATGTTAGAGAAACAAGATTAGCCGTCGTAGCTTCAATCTGTTCCA
CTACACCGCCAGGGAAGTAAGATTCGCCATTGCGGCTTCAATCTTTTTAATTGCAATGTTGGGGA
AACAAGATTCACCGTCGTAGCTTCAATCTATTCCACTACACCGCCAAGGGAGTAAGATTCGCCGT
GGTGGCTTCAATCTTTTTAATTGCAATGAAGATTCACCGTTGTGG
Found at i:54577307 original size:50 final size:50
Alignment explanation
Indices: 54577226--54577320 Score: 127
Period size: 50 Copynumber: 1.9 Consensus size: 50
54577216 TCCAAGCCTT
*
54577226 AACGCCAGGGAGATAAGATTCACCGTCGTGGCTTCAATCTCTTCCGCTAC
1 AACGCCAGGGAAATAAGATTCACCGTCGTGGCTTCAATCTCTTCCGCTAC
* ** * * *
54577276 AACGTCAGGGAAATAAGATTTGCTGTTGTGGCTTCAATCTTTTCC
1 AACGCCAGGGAAATAAGATTCACCGTCGTGGCTTCAATCTCTTCC
54577321 ATTGTAACGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 38 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (50 bp):
AACGCCAGGGAAATAAGATTCACCGTCGTGGCTTCAATCTCTTCCGCTAC
Found at i:54577330 original size:50 final size:50
Alignment explanation
Indices: 54577225--54577332 Score: 117
Period size: 50 Copynumber: 2.2 Consensus size: 50
54577215 ATCCAAGCCT
* * *
54577225 TAACGCCAGGGAGATAAGATTCACCGTCGTGGCTTCAATCTCTTCCGCTA
1 TAACGTCAGGGAAATAAGATTCACCGTCGTGGCTTCAATCTCTTCCACTA
* ** * * * * *
54577275 CAACGTCAGGGAAATAAGATTTGCTGTTGTGGCTTCAATCTTTTCCATTG
1 TAACGTCAGGGAAATAAGATTCACCGTCGTGGCTTCAATCTCTTCCACTA
54577325 TAACGTCA
1 TAACGTCA
54577333 AGGTGGTAAG
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (50 bp):
TAACGTCAGGGAAATAAGATTCACCGTCGTGGCTTCAATCTCTTCCACTA
Found at i:54577511 original size:44 final size:44
Alignment explanation
Indices: 54577384--54577511 Score: 114
Period size: 43 Copynumber: 2.9 Consensus size: 44
54577374 ACAGGAAGGT
* * *
54577384 AAGATCTGCTATTTTCAACCTACTCCACTACTGCTCAGGGAGAC
1 AAGATCTGCTATTTTCAACCTACTCCACTGCTGCTTAGGGAAAC
* * * * * ** ***
54577428 AAG-GCTGGTATCTTCAATCTACTTCGTTGCCAATATAGGGAAAC
1 AAGATCTGCTATTTTCAACCTACTCCACTGCTGCT-TAGGGAAAC
*
54577472 AAGATCTGCTATTTTCAACCTACTCCACTGGTGCTTAGGG
1 AAGATCTGCTATTTTCAACCTACTCCACTGCTGCTTAGGG
54577512 TGATAGGATT
Statistics
Matches: 58, Mismatches: 24, Indels: 4
0.67 0.28 0.05
Matches are distributed among these distances:
43 20 0.34
44 18 0.31
45 20 0.34
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (44 bp):
AAGATCTGCTATTTTCAACCTACTCCACTGCTGCTTAGGGAAAC
Found at i:54577533 original size:44 final size:44
Alignment explanation
Indices: 54577485--54577913 Score: 585
Period size: 44 Copynumber: 9.7 Consensus size: 44
54577475 ATCTGCTATT
* * * *
54577485 TTCAACCTACTCCACTGGTG-CTTAGGGTGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATC
* *
54577529 TTCAACCTATTCCATTGCTGACTAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
*
54577573 TTCAACCTATTCCACTGCTGACCAGGGAGAAAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
** *
54577617 TTCAACCTATTCCAACTGCTGACTGGGGAGATA-GATCTTACAATC
1 TTCAACCTATTCC-ACTGCTGACCAGGGAGATAGGAT-TCACAATC
* *
54577662 TTCAACCTATTTCACTGCTGACCAAGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
*
54577706 TTCAACCTATTCCACTACTGACCAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* * * * *
54577750 TTCAACCTATTCTACTGCTGACCAAGGAGATAAGACTCACAATT
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
*
54577794 TTCAACCTATTCCACTGTTGACCAGGGAGATAGGACTT-ACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGA-TTCACAATC
* *
54577838 TTCAACCTATTCCACTACTGACCAGGGAGATAGGATTTACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* * *
54577882 TTCAACATATTCCACTGTTGCCCAGGGAGATA
1 TTCAACCTATTCCACTGCTGACCAGGGAGATA
54577914 AAGCTTTGTG
Statistics
Matches: 342, Mismatches: 37, Indels: 12
0.87 0.09 0.03
Matches are distributed among these distances:
43 2 0.01
44 300 0.88
45 40 0.12
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
Found at i:54579141 original size:6 final size:6
Alignment explanation
Indices: 54579132--54579162 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
54579122 TTTCTTTTTG
*
54579132 TCATTT TCATTT TCATTT TCATTT TGATTT T
1 TCATTT TCATTT TCATTT TCATTT TCATTT T
54579163 TTTTTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.13, G:0.03, T:0.68
Consensus pattern (6 bp):
TCATTT
Found at i:54584153 original size:23 final size:23
Alignment explanation
Indices: 54584110--54584156 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
54584100 TTTAAAGTGT
*
54584110 AAATGAAAACATAAATCAATAAA
1 AAATGAAAACATAAAACAATAAA
*
54584133 AAATGAAAA-ATATAAAGAATAAA
1 AAATGAAAACATA-AAACAATAAA
54584156 A
1 A
54584157 GGTACATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.17
Consensus pattern (23 bp):
AAATGAAAACATAAAACAATAAA
Found at i:54585008 original size:23 final size:22
Alignment explanation
Indices: 54584963--54585020 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
54584953 AAAGGGTATC
* *
54584963 TACAAATTAAATC-TCTAAAAT
1 TACAAATCATATCTTCTAAAAT
*
54584984 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAAAT
*
54585007 TACATATCATATCT
1 TACAAATCATATCT
54585021 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAAAT
Found at i:54588166 original size:15 final size:15
Alignment explanation
Indices: 54588146--54588226 Score: 67
Period size: 15 Copynumber: 5.4 Consensus size: 15
54588136 TTTATCGAAA
54588146 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
54588161 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
54588175 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
54588191 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
54588205 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
54588221 ATCAAA
1 ATCAAA
54588227 TATTAGAAAG
Statistics
Matches: 48, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
14 8 0.17
15 32 0.67
16 8 0.17
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.25
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:54588183 original size:30 final size:30
Alignment explanation
Indices: 54588142--54588251 Score: 184
Period size: 30 Copynumber: 3.7 Consensus size: 30
54588132 CATATTTATC
* *
54588142 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATATTA
*
54588172 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATATTA
54588202 GAAAGTCAAAGATATGGGTATCAAATATTA
1 GAAAGTCAAAGATATGGGTATCAAATATTA
*
54588232 GAAAGTCAAAGAGATGGGTA
1 GAAAGTCAAAGATATGGGTA
54588252 CCGAGATATT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 75 1.00
ACGTcount: A:0.47, C:0.06, G:0.23, T:0.24
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATATTA
Found at i:54592863 original size:15 final size:15
Alignment explanation
Indices: 54592843--54592918 Score: 57
Period size: 15 Copynumber: 5.1 Consensus size: 15
54592833 TTTATGGAAA
54592843 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
54592858 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
54592872 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
54592888 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
54592902 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
54592918 A
1 A
54592919 CCGAGATATT
Statistics
Matches: 43, Mismatches: 14, Indels: 7
0.67 0.22 0.11
Matches are distributed among these distances:
14 8 0.19
15 27 0.63
16 8 0.19
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.25
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:54592880 original size:30 final size:30
Alignment explanation
Indices: 54592839--54592918 Score: 133
Period size: 30 Copynumber: 2.7 Consensus size: 30
54592829 CATATTTATG
*
54592839 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* *
54592869 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
54592899 GAAAGTCAAAGATATGGGTA
1 GAAAGTCAAAGATATGGGTA
54592919 CCGAGATATT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.47, C:0.06, G:0.23, T:0.24
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:54595426 original size:15 final size:15
Alignment explanation
Indices: 54595406--54595437 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
54595396 TATTTCACTA
*
54595406 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
54595421 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
54595436 TT
1 TT
54595438 TGCATCCATA
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:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:54605981 original size:22 final size:21
Alignment explanation
Indices: 54605956--54605999 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
54605946 TGATAAACTT
54605956 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
54605978 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
54605999 T
1 T
54606000 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:54607509 original size:17 final size:16
Alignment explanation
Indices: 54607489--54607521 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
54607479 TTCTTGTAGA
54607489 AAAATAATTAATATTAT
1 AAAATAATTAA-ATTAT
54607506 AAAATAATTAAATTAT
1 AAAATAATTAAATTAT
54607522 GTTAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATAATTAAATTAT
Found at i:54610446 original size:62 final size:61
Alignment explanation
Indices: 54610374--54610554 Score: 206
Period size: 62 Copynumber: 2.9 Consensus size: 61
54610364 ATTTTAATAT
* * * *
54610374 TTTAATATTAAATTTAATTTAATACTTATCTTAAT-AGTATTTTATTAATATAATATAATC
1 TTTAATATTAAATTTAATTTAATATTTATCTTAATAAATATTTTATTAATTTAATATAAGC
* *
54610434 AATTTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAATATTTTATT-ATTTTA-ATAAG
1 --TTTAATATTAAATTTAATTTAATATTTATC-T-TA-ATAAATATTTTATTAATTTAATATAAG
54610497 C
61 C
* * * *
54610498 TTTAATGTTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATAT
1 TTTAATATTAAATTTAATTTAATATTTATCTTAATAAATATTTTATTAATTTAATAT
54610555 TAAAGTTATT
Statistics
Matches: 101, Mismatches: 12, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
59 13 0.13
60 6 0.06
61 3 0.03
62 55 0.54
63 1 0.01
64 7 0.07
65 6 0.06
66 10 0.10
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (61 bp):
TTTAATATTAAATTTAATTTAATATTTATCTTAATAAATATTTTATTAATTTAATATAAGC
Found at i:54617253 original size:3 final size:3
Alignment explanation
Indices: 54617245--54617283 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
54617235 AGGGCGTCGG
*
54617245 TGA TGA TGA TGA TGA CT-A GGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA -TGA TGA TGA TGA TGA TGA TGA TGA
54617284 GACCTTTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 31 0.97
4 1 0.03
ACGTcount: A:0.33, C:0.03, G:0.33, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:54619750 original size:8 final size:8
Alignment explanation
Indices: 54619739--54619775 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
54619729 ATTTAGTTCA
54619739 TTTTTTAT
1 TTTTTTAT
54619747 TTTTCTTAT
1 TTTT-TTAT
*
54619756 TTATTTAT
1 TTTTTTAT
54619764 TTTTTTAT
1 TTTTTTAT
54619772 TTTT
1 TTTT
54619776 ATCTCTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTAT
Found at i:54620960 original size:29 final size:29
Alignment explanation
Indices: 54620927--54620985 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
54620917 AGGAATAGGG
* *
54620927 AATTCTATTAGGATATCTTAGGTTAATTA
1 AATTCCATTAGGATATCTTAAGTTAATTA
* *
54620956 AATTCCATTAGGTTATTTTAAGTTAATTA
1 AATTCCATTAGGATATCTTAAGTTAATTA
54620985 A
1 A
54620986 TTTACTCATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.46
Consensus pattern (29 bp):
AATTCCATTAGGATATCTTAAGTTAATTA
Found at i:54622360 original size:52 final size:52
Alignment explanation
Indices: 54622282--54622386 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
54622272 AAGTGAATAC
54622282 CAAACTATAATGTTTTACATTTTTACCCCAAACTTCCAAACCTATTTATTTT
1 CAAACTATAATGTTTTACATTTTTACCCCAAACTTCCAAACCTATTTATTTT
54622334 CAAACTATAATGTTTTACATTTTTACCCCAAACTTCCAAACCTATTTATTTT
1 CAAACTATAATGTTTTACATTTTTACCCCAAACTTCCAAACCTATTTATTTT
54622386 C
1 C
54622387 TCCCAAAACT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.32, C:0.24, G:0.02, T:0.42
Consensus pattern (52 bp):
CAAACTATAATGTTTTACATTTTTACCCCAAACTTCCAAACCTATTTATTTT
Found at i:54632038 original size:15 final size:15
Alignment explanation
Indices: 54632018--54632048 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
54632008 GTCATGTAAG
54632018 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
54632033 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
54632048 T
1 T
54632049 ATATTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:54632238 original size:17 final size:17
Alignment explanation
Indices: 54632205--54632243 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
54632195 TAAGCTTTTG
54632205 ATTTTATATGAGAGAAC
1 ATTTTATATGAGAGAAC
*
54632222 AATTTTATAT-TGAGAAC
1 -ATTTTATATGAGAGAAC
54632239 ATTTT
1 ATTTT
54632244 CCACAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (17 bp):
ATTTTATATGAGAGAAC
Found at i:54633009 original size:15 final size:15
Alignment explanation
Indices: 54632985--54633014 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54632975 TGGAGATCGA
*
54632985 GGAAATGGTCGTGGT
1 GGAAAAGGTCGTGGT
54633000 GGAAAAGGTCGTGGT
1 GGAAAAGGTCGTGGT
54633015 CAAGAAGGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.07, G:0.47, T:0.23
Consensus pattern (15 bp):
GGAAAAGGTCGTGGT
Found at i:54636221 original size:15 final size:15
Alignment explanation
Indices: 54636201--54636231 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
54636191 GTTATGTAAG
54636201 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
54636216 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
54636231 T
1 T
54636232 ATGTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:54638100 original size:15 final size:15
Alignment explanation
Indices: 54638061--54638135 Score: 52
Period size: 15 Copynumber: 5.0 Consensus size: 15
54638051 TAATAGTTTA
54638061 TATATATTCATTAATGAT
1 TATATATT-A-TAAT-AT
*
54638079 TAAATATTATAATAT
1 TATATATTATAATAT
54638094 TATATATT-T--TAT
1 TATATATTATAATAT
54638106 TATA-ATGTATAATAT
1 TATATAT-TATAATAT
*
54638121 AATA-ATTATATATAT
1 TATATATTATA-ATAT
54638136 ATCATGTATT
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
11 2 0.04
12 8 0.16
13 1 0.02
14 5 0.10
15 21 0.43
16 4 0.08
17 1 0.02
18 7 0.14
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (15 bp):
TATATATTATAATAT
Found at i:54638739 original size:22 final size:21
Alignment explanation
Indices: 54638714--54638769 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
54638704 GCTATAATAA
54638714 TATATAATATATTTATTATCAT
1 TATATAATATATTTATTAT-AT
* *
54638736 TATATATTATTGTTTATTATAT
1 TATATAATA-TATTTATTATAT
* *
54638758 TAGATAAAATAT
1 TATATAATATAT
54638770 GTTTTAAGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
21 2 0.07
22 16 0.59
23 9 0.33
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (21 bp):
TATATAATATATTTATTATAT
Found at i:54638772 original size:23 final size:24
Alignment explanation
Indices: 54638719--54638773 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
54638709 AATAATATAT
* * *
54638719 AATATATTTATTATCATTATATAT
1 AATATGTTTATTATCATTAGATAA
*
54638743 TAT-TGTTTATTAT-ATTAGATAA
1 AATATGTTTATTATCATTAGATAA
54638765 AATATGTTT
1 AATATGTTT
54638774 TAAGTCCTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 9 0.36
23 14 0.56
24 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (24 bp):
AATATGTTTATTATCATTAGATAA
Found at i:54642352 original size:43 final size:42
Alignment explanation
Indices: 54642291--54642449 Score: 165
Period size: 43 Copynumber: 4.0 Consensus size: 42
54642281 CCGGAGTACA
* *
54642291 TTGAATATAAAAGGGGTTGCTAAGTGCTGATTCCACCGTATCT
1 TTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCC-CCGTATCT
* * *
54642334 TTGAATGTGAAAGGGGTTGCTAAGTGTTGATTTCCCGAATCT
1 TTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGTATCT
*
54642376 TT--A-GT------GGTTGCTAAGTGTTGATTCCACCGTATCT
1 TTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCC-CCGTATCT
* *
54642410 TTGAATGTGAAAGGGGTTGCTATGTGCTAATTCCCCGTAT
1 TTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGTAT
54642450 TACTGAATAT
Statistics
Matches: 96, Mismatches: 10, Indels: 21
0.76 0.08 0.17
Matches are distributed among these distances:
33 19 0.20
34 9 0.09
36 1 0.01
37 2 0.02
39 2 0.02
40 1 0.01
42 15 0.16
43 47 0.49
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (42 bp):
TTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGTATCT
Found at i:54643815 original size:24 final size:24
Alignment explanation
Indices: 54643768--54643815 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
54643758 ACAGTCCCTC
* * *
54643768 TGGTTTGTTGTTGGGCTTCCACTT
1 TGGTTTGTTCTCGGGCCTCCACTT
*
54643792 TGGTTTGTTCTCGGGCCTCTACTT
1 TGGTTTGTTCTCGGGCCTCCACTT
54643816 CCCATTATTT
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:0.04, C:0.21, G:0.27, T:0.48
Consensus pattern (24 bp):
TGGTTTGTTCTCGGGCCTCCACTT
Found at i:54647493 original size:103 final size:103
Alignment explanation
Indices: 54647314--54647519 Score: 322
Period size: 103 Copynumber: 2.0 Consensus size: 103
54647304 TTCAAACACG
* *
54647314 CAATTCATTTCTAGTTTCAACGAGCTAGCAGAGGGACCGATTAAACATATGTAGTTTAGAATCAA
1 CAATTCAGTTCTAGTTTCAACAAGCTAGCAGAGGGACCGATTAAACATATGTAGTTTAGAATCAA
* *
54647379 ATGATTTATAATTAAGTTCCTACTTTTCGCCTATTAAT
66 ATGATATATAATTAAGTTCCTACTTTTCACCTATTAAT
* **
54647417 CAATTCAGTTCTAGTTTCAACAAGCTAGCGGAGGGACCGATTAAACATATGTAGTTTAGGCTCAA
1 CAATTCAGTTCTAGTTTCAACAAGCTAGCAGAGGGACCGATTAAACATATGTAGTTTAGAATCAA
* * *
54647482 ATGGTATATAATTAATTTCCTGCTTTTCACCTATTAAT
66 ATGATATATAATTAAGTTCCTACTTTTCACCTATTAAT
54647520 TATAAACTCA
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
103 93 1.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (103 bp):
CAATTCAGTTCTAGTTTCAACAAGCTAGCAGAGGGACCGATTAAACATATGTAGTTTAGAATCAA
ATGATATATAATTAAGTTCCTACTTTTCACCTATTAAT
Found at i:54653430 original size:20 final size:20
Alignment explanation
Indices: 54653389--54653431 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
54653379 AAATCAGCTC
*
54653389 ATTTGAGCTTCTTTCAGCTT
1 ATTTGAGCTTCTTTCAACTT
*
54653409 ATTTGAGC-TCATTTCAATTT
1 ATTTGAGCTTC-TTTCAACTT
54653429 ATT
1 ATT
54653432 CCCAGCTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (20 bp):
ATTTGAGCTTCTTTCAACTT
Found at i:54659189 original size:14 final size:13
Alignment explanation
Indices: 54659148--54659191 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
54659138 GTCCATTTTT
54659148 ATTTTT-ATTATA
1 ATTTTTAATTATA
*
54659160 ATTTTTAGTT-TA
1 ATTTTTAATTATA
54659172 ATTTTTACATTATA
1 ATTTTTA-ATTATA
54659186 ATTTTT
1 ATTTTT
54659192 CTTTTATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 15 0.56
13 4 0.15
14 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (13 bp):
ATTTTTAATTATA
Found at i:54661657 original size:43 final size:42
Alignment explanation
Indices: 54661586--54661732 Score: 134
Period size: 43 Copynumber: 3.4 Consensus size: 42
54661576 CAAAAAGCTC
* * *** *
54661586 ATACAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAA
1 ATACGATGCCAATGTCCCAGATAAGGTCTTACACGTAATCAA
* *
54661628 ATAACGATGCCACTGTCCCAGATAAGGTCTTACACGTAATCAT
1 AT-ACGATGCCAATGTCCCAGATAAGGTCTTACACGTAATCAA
* * * *
54661671 ATACGATGTCAATGTCCTAGATATGGTCTTACACATAAATCGCAA
1 ATACGATGCCAATGTCCCAGATAAGGTCTTACACGT-AAT--CAA
*
54661716 AT-CGATGCCAACGTCCC
1 ATACGATGCCAATGTCCC
54661733 TGACGTGCTC
Statistics
Matches: 84, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
42 31 0.37
43 37 0.44
44 12 0.14
45 4 0.05
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (42 bp):
ATACGATGCCAATGTCCCAGATAAGGTCTTACACGTAATCAA
Found at i:54663479 original size:22 final size:22
Alignment explanation
Indices: 54663435--54663502 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 22
54663425 GACCATTGAG
*
54663435 TTTATTTTTTTCTTTTTAGATTTT
1 TTTATTTTTTTATTTTT--ATTTT
*
54663459 TTTATTTTTTTATTGTTA--TT
1 TTTATTTTTTTATTTTTATTTT
54663479 TTTAGTTCTTTTTATTTTTATTTT
1 TTTA-TT-TTTTTATTTTTATTTT
54663503 CTTAGCCTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 6 0.16
21 2 0.05
22 12 0.32
24 17 0.46
ACGTcount: A:0.13, C:0.03, G:0.04, T:0.79
Consensus pattern (22 bp):
TTTATTTTTTTATTTTTATTTT
Found at i:54663495 original size:16 final size:15
Alignment explanation
Indices: 54663435--54663502 Score: 63
Period size: 16 Copynumber: 4.6 Consensus size: 15
54663425 GACCATTGAG
*
54663435 TTTA-TTTTTTTCTT
1 TTTAGTTTTTTTATT
54663449 TTTAGATTTTTTTATT
1 TTTAG-TTTTTTTATT
*
54663465 TTT--TTATTGTTATT
1 TTTAGTT-TTTTTATT
54663479 TTTAGTTCTTTTTATT
1 TTTAGTT-TTTTTATT
54663495 TTTA-TTTT
1 TTTAGTTTT
54663503 CTTAGCCTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
13 2 0.04
14 16 0.36
15 2 0.04
16 25 0.56
ACGTcount: A:0.13, C:0.03, G:0.04, T:0.79
Consensus pattern (15 bp):
TTTAGTTTTTTTATT
Found at i:54665170 original size:19 final size:19
Alignment explanation
Indices: 54665146--54665183 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
54665136 TATAAATACC
54665146 CATTAGAAGAAGACATAAG
1 CATTAGAAGAAGACATAAG
54665165 CATTAGAAGAAGACATAAG
1 CATTAGAAGAAGACATAAG
54665184 AGGGTAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.11, G:0.21, T:0.16
Consensus pattern (19 bp):
CATTAGAAGAAGACATAAG
Found at i:54666557 original size:98 final size:98
Alignment explanation
Indices: 54666383--54666579 Score: 358
Period size: 98 Copynumber: 2.0 Consensus size: 98
54666373 GTACAATAAA
*
54666383 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
54666448 CCTCTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
54666481 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* *
54666546 CCTTTAAAATCCCAACCTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
54666579 A
1 A
54666580 TTATTTTTTA
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 95 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:54667273 original size:23 final size:24
Alignment explanation
Indices: 54667245--54667299 Score: 85
Period size: 25 Copynumber: 2.3 Consensus size: 24
54667235 ATATACATAT
*
54667245 AAATAT-GAAAATATTCTTTAAAA
1 AAATATAGAAAATATTCGTTAAAA
54667268 AAATATAGGAAAATATTCGTTAAAA
1 AAATATA-GAAAATATTCGTTAAAA
54667293 AAATATA
1 AAATATA
54667300 CATGTACATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 6 0.21
25 23 0.79
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (24 bp):
AAATATAGAAAATATTCGTTAAAA
Found at i:54667310 original size:27 final size:25
Alignment explanation
Indices: 54667251--54667299 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
54667241 ATATAAATAT
*
54667251 GAAAATATTCTTTAAAAAAATATAG
1 GAAAATATTCGTTAAAAAAATATAG
54667276 GAAAATATTCGTTAAAAAAATATA
1 GAAAATATTCGTTAAAAAAATATA
54667300 CATGTACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.31
Consensus pattern (25 bp):
GAAAATATTCGTTAAAAAAATATAG
Found at i:54668070 original size:19 final size:19
Alignment explanation
Indices: 54668046--54668158 Score: 163
Period size: 19 Copynumber: 5.8 Consensus size: 19
54668036 AATCATATAT
54668046 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
54668065 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
54668084 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
54668103 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
**
54668124 TCTTGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
54668143 TCTAATATTGCATATC
1 TCTAAGATTGCATATC
54668159 CTCAAAAATT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
19 66 0.80
21 17 0.20
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:54668133 original size:40 final size:40
Alignment explanation
Indices: 54668046--54668157 Score: 183
Period size: 40 Copynumber: 2.9 Consensus size: 40
54668036 AATCATATAT
54668046 TCTAAGATTGCATATCATATCTAAGATT--ATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
54668084 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
** *
54668124 TCTTGGATTGCATATCATATCTAATATTGCATAT
1 TCTAAGATTGCATATCATATCTAAGATTGCATAT
54668158 CCTCAAAAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
38 28 0.41
40 41 0.59
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (40 bp):
TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
Found at i:54668637 original size:44 final size:44
Alignment explanation
Indices: 54668588--54668735 Score: 208
Period size: 44 Copynumber: 3.4 Consensus size: 44
54668578 CGCTCTACTG
*
54668588 CAACTTCAGGGAGATAGGATCTATTACTTCAATCCGCTCCAATA
1 CAACTTCAGGGAGATAGGATCTATTACTTTAATCCGCTCCAATA
* *
54668632 TAACTTCAGGGAGATAGGATCTATTAGTTTAATCCGCTCCAATA
1 CAACTTCAGGGAGATAGGATCTATTACTTTAATCCGCTCCAATA
** * * *
54668676 CAACTTCAGGGAGATAGGAT-TATCGGCTTTAATCTGCTCCACTG
1 CAACTTCAGGGAGATAGGATCTAT-TACTTTAATCCGCTCCAATA
54668720 CAACTTCAGGGAGATA
1 CAACTTCAGGGAGATA
54668736 AGACTTGCCA
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
43 3 0.03
44 90 0.97
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (44 bp):
CAACTTCAGGGAGATAGGATCTATTACTTTAATCCGCTCCAATA
Found at i:54668762 original size:44 final size:42
Alignment explanation
Indices: 54668708--54668828 Score: 145
Period size: 44 Copynumber: 2.7 Consensus size: 42
54668698 TCGGCTTTAA
54668708 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCAT-CTTCAG
1 TCTGC-CCACTGCAACTTCA-GGAGATAAGACTTG-CATACTT-AG
* *
54668753 TCTGCCCACTGCAACTTCAGGAGGATAAGACATGCTTACTTAG
1 TCTGCCCACTGCAACTTCAGGA-GATAAGACTTGCATACTTAG
*
54668796 TCTGATCCACTGCAACTTCAAGGAGATAAGACT
1 TCTG-CCCACTGCAACTTC-AGGAGATAAGACT
54668829 AGATGCGATA
Statistics
Matches: 68, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
43 11 0.16
44 48 0.71
45 9 0.13
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (42 bp):
TCTGCCCACTGCAACTTCAGGAGATAAGACTTGCATACTTAG
Found at i:54669039 original size:44 final size:44
Alignment explanation
Indices: 54668991--54669419 Score: 123
Period size: 44 Copynumber: 9.8 Consensus size: 44
54668981 TATCTTGGAA
*
54668991 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** * * * * *
54669035 AGATAAGA-TCTACAATCTTCAACCTTCTCCGCTGCTGCTGAGGG
1 AGATAAGATTC-GCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * *
54669079 AGACAAGGCTT-GGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* ** *
54669123 AGATAAGATTCGCCATCTTTGATCTGGTCCACTACTGCTTAGGG
1 AGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
**** * * ** * * *
54669167 AGATAAGA-TCTATAATCTTCAACCTTCTCCGTTGCTGCTGAAGG
1 AGATAAGATTC-GCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * *
54669211 AGACAAGGCTT-GGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
*
54669255 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** * * * * *
54669299 AGATAAGA-TCTACAATCTTCAACCTTCTCCGCTGCTGCTGAGGG
1 AGATAAGATTC-GCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * *
54669343 AGACAAGGCTT-GGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
*
54669387 AGATAAGATTCGCCGTCTTCGATCTGCTCCACT
1 AGATAAGATTCGCCGTCTTCAATCTGCTCCACT
54669420 GTCAATGCAG
Statistics
Matches: 258, Mismatches: 100, Indels: 56
0.62 0.24 0.14
Matches are distributed among these distances:
42 17 0.07
43 25 0.10
44 189 0.73
45 13 0.05
46 14 0.05
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (44 bp):
AGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:54669079 original size:132 final size:132
Alignment explanation
Indices: 54668899--54669419 Score: 961
Period size: 132 Copynumber: 3.9 Consensus size: 132
54668889 CTGCAACTTC
* * *
54668899 AGGGAGATAGGATTTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
1 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTGAGGGAGACAAGGCTTGGTGGC
54668964 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
66 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
54669029 TT
131 TT
54669031 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTGAGGGAGACAAGGCTTGGTGGC
1 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTGAGGGAGACAAGGCTTGGTGGC
* * *
54669096 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCATCTTTGATCTGGTCCACTACTGC
66 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
54669161 TT
131 TT
* * *
54669163 AGGGAGATAAGATCTATAATCTTCAACCTTCTCCGTTGCTGCTGAAGGAGACAAGGCTTGGTGGC
1 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTGAGGGAGACAAGGCTTGGTGGC
54669228 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
66 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
54669293 TT
131 TT
54669295 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTGAGGGAGACAAGGCTTGGTGGC
1 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTGAGGGAGACAAGGCTTGGTGGC
54669360 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACT
66 TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACT
54669420 GTCAATGCAG
Statistics
Matches: 374, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 374 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (132 bp):
AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTGAGGGAGACAAGGCTTGGTGGC
TTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
TT
Found at i:54674892 original size:24 final size:25
Alignment explanation
Indices: 54674863--54674910 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
54674853 ATATAAATAT
*
54674863 GAAAATATTC-TTTAAAAAATATAG
1 GAAAATATTCGTTAAAAAAATATAG
54674887 GAAAATATTCGTTAAAAAAATATA
1 GAAAATATTCGTTAAAAAAATATA
54674911 CATGTACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.31
Consensus pattern (25 bp):
GAAAATATTCGTTAAAAAAATATAG
Found at i:54675680 original size:19 final size:19
Alignment explanation
Indices: 54675656--54675768 Score: 172
Period size: 19 Copynumber: 5.8 Consensus size: 19
54675646 AATCATATAT
54675656 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
54675675 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
54675694 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
54675713 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
**
54675734 TCTTGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
54675753 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
54675769 CTCAAAAATT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
19 67 0.80
21 17 0.20
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:54675743 original size:40 final size:40
Alignment explanation
Indices: 54675656--54675767 Score: 192
Period size: 40 Copynumber: 2.9 Consensus size: 40
54675646 AATCATATAT
54675656 TCTAAGATTGCATATCATATCTAAGATT--ATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
54675694 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
**
54675734 TCTTGGATTGCATATCATATCTAAGATTGCATAT
1 TCTAAGATTGCATATCATATCTAAGATTGCATAT
54675768 CCTCAAAAAT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
38 28 0.40
40 42 0.60
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (40 bp):
TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
Found at i:54675749 original size:59 final size:56
Alignment explanation
Indices: 54675649--54675768 Score: 170
Period size: 59 Copynumber: 2.1 Consensus size: 56
54675639 ATTACAAAAT
*
54675649 CATAT-ATTCTAAGATTGCATATCATATCTAAGATTATATATCATATCTAAGATTG
1 CATATCATTCTAAGATTGCATATCATATCTAAGATTACATATCATATCTAAGATTG
** *
54675704 CATATCATATCTAAGATTGCATATATCATATCTTGGATTGCATATCATATCTAAGATTG
1 CATATCAT-TCTAAGATTGC--ATATCATATCTAAGATTACATATCATATCTAAGATTG
54675763 CATATC
1 CATATC
54675769 CTCAAAAATT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
55 5 0.09
56 2 0.04
57 11 0.19
59 39 0.68
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (56 bp):
CATATCATTCTAAGATTGCATATCATATCTAAGATTACATATCATATCTAAGATTG
Found at i:54682525 original size:27 final size:28
Alignment explanation
Indices: 54682466--54682519 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
54682456 AAAATAATTA
*
54682466 AAATTAAATATGTTAATAATTTAAGTGC
1 AAATTAAATATGTTAATAATTAAAGTGC
* *
54682494 AAATTAATTAT-TTTATAATTAAAGTG
1 AAATTAAATATGTTAATAATTAAAGTG
54682520 TGAATTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (28 bp):
AAATTAAATATGTTAATAATTAAAGTGC
Found at i:54687424 original size:53 final size:53
Alignment explanation
Indices: 54687367--54687472 Score: 135
Period size: 53 Copynumber: 2.0 Consensus size: 53
54687357 TATATTATGA
*
54687367 TTTTAGTAAATT-TATATAAGAATAATTATATTAAGAAT-TTCATTAAATTATTT
1 TTTTAGTAAATTATATATAAGAATAATTAAATTAA-AATATT-ATTAAATTATTT
* * * *
54687420 TTTTATTAAATTATATTTAATACTAATTAAATTAAAATATTATTAAATTATTT
1 TTTTAGTAAATTATATATAAGAATAATTAAATTAAAATATTATTAAATTATTT
54687473 ATTATTTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
53 26 0.57
54 20 0.43
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (53 bp):
TTTTAGTAAATTATATATAAGAATAATTAAATTAAAATATTATTAAATTATTT
Found at i:54687689 original size:16 final size:16
Alignment explanation
Indices: 54687668--54687708 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
54687658 TTGAATTACT
54687668 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
54687684 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
54687700 ATTACAGCT
1 ATTACAGCT
54687709 AGGGGTGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.27, C:0.32, G:0.05, T:0.37
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:54688255 original size:9 final size:9
Alignment explanation
Indices: 54688241--54688285 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
54688231 TATAGTTTGA
54688241 TATTCGAAT
1 TATTCGAAT
54688250 TATTCGAAT
1 TATTCGAAT
54688259 TATTCGAAT
1 TATTCGAAT
*
54688268 TATTCGAGT
1 TATTCGAAT
54688277 TA-TCGAAT
1 TATTCGAAT
54688285 T
1 T
54688286 CGAAAACTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
8 6 0.18
9 28 0.82
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.44
Consensus pattern (9 bp):
TATTCGAAT
Found at i:54696584 original size:11 final size:11
Alignment explanation
Indices: 54696570--54696635 Score: 63
Period size: 11 Copynumber: 6.4 Consensus size: 11
54696560 TTATTTTTAA
54696570 TTTTAAAATAT
1 TTTTAAAATAT
54696581 TTTTAAAATACT
1 TTTTAAAATA-T
*
54696593 TTTTAAACT-T
1 TTTTAAAATAT
54696603 TTTT---A-A-
1 TTTTAAAATAT
54696609 TTTTAAAATAT
1 TTTTAAAATAT
54696620 TTTTAAAATACT
1 TTTTAAAATA-T
54696632 TTTT
1 TTTT
54696636 TTAATTTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
6 4 0.09
9 1 0.02
10 6 0.13
11 20 0.44
12 14 0.31
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:54696644 original size:39 final size:39
Alignment explanation
Indices: 54696552--54696644 Score: 143
Period size: 39 Copynumber: 2.4 Consensus size: 39
54696542 AATATATTTA
*
54696552 TTTTTTTATTATTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTTAAT-TTTTTAATTTTAAAATATTTTTAAAATAC
*
54696592 -TTTTTAAACTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTTAA-TTTTTTAATTTTAAAATATTTTTAAAATAC
54696631 TTTTTTTAATTTTT
1 TTTTTTTAATTTTT
54696645 AAAATAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
39 40 0.83
40 8 0.17
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (39 bp):
TTTTTTTAATTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:54696656 original size:21 final size:21
Alignment explanation
Indices: 54696618--54696657 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54696608 ATTTTAAAAT
**
54696618 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
54696639 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
54696658 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:54696664 original size:22 final size:21
Alignment explanation
Indices: 54696617--54696675 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
54696607 AATTTTAAAA
* *
54696617 TATTTTTAAAAT-ACTTTTTT
1 TATTTTTAAAATAAATTTTTG
54696637 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAATAAATTTTT-G
54696660 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
54696676 GGGCCGGGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.33
22 14 0.42
23 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:54697238 original size:54 final size:54
Alignment explanation
Indices: 54697175--54697343 Score: 180
Period size: 65 Copynumber: 2.9 Consensus size: 54
54697165 TTGATTAGGT
* *
54697175 TTTATGAAAAATTAAATTAGGGTATTATGTTTTTAATTG-TATAGGGTTTTAAGG
1 TTTAGGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTA-AGGGTTTTAAGG
54697229 TTTAGGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTAAGGGTTTCTGGGCTTAATTAGGG
1 TTTAGGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTAAGGG--T-T----TT-A--A-GG
*
54697294 TTTAGGAAAAATTAAATCAGGGTATTAGGTTTTTAATTGTTTAA-GGTTTT
1 TTTAGGAAAAATTAAATTAGGGTATTAGGTTTTTAATTG-TTAAGGGTTTT
54697344 GGGATTTGAT
Statistics
Matches: 99, Mismatches: 3, Indels: 22
0.80 0.02 0.18
Matches are distributed among these distances:
54 41 0.41
55 2 0.02
56 1 0.01
57 1 0.01
58 2 0.02
61 2 0.02
62 2 0.02
63 1 0.01
64 1 0.01
65 42 0.42
66 4 0.04
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.44
Consensus pattern (54 bp):
TTTAGGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTAAGGGTTTTAAGG
Found at i:54697377 original size:130 final size:130
Alignment explanation
Indices: 54697228--54697472 Score: 382
Period size: 130 Copynumber: 1.9 Consensus size: 130
54697218 GGGTTTTAAG
* * *
54697228 GTTTAGGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTAAGGGTTTCTGGGCTTAATTAGG
1 GTTTAGGAAAAATTAAATTACGGTATTAAGTTTTTAATTGTTAAGGGTTTCTGGGCTTAATTAAG
* *
54697293 GTTTAGGAAAAATTAAATCAGGGTATTAGGTTTTTAATTGTTTAAGGTTTTGGGATTTGATTAGT
66 GATTAGAAAAAATTAAATCAGGGTATTAGGTTTTTAATTGTTTAAGGTTTTGGGATTTGATTAGT
** * * * *
54697358 GTTTAGGAAATTTTAAATTACGGTATTAAGTTTTTAATTGTTTAGGGTTTTTGGGTTTGATTAAG
1 GTTTAGGAAAAATTAAATTACGGTATTAAGTTTTTAATTGTTAAGGGTTTCTGGGCTTAATTAAG
*
54697423 GATTAGAAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAAGGTTT
66 GATTAGAAAAAATTAAATCAGGGTATTAGGTTTTTAATTGTTTAAGGTTT
54697473 AATTACTTTT
Statistics
Matches: 103, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
130 103 1.00
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.45
Consensus pattern (130 bp):
GTTTAGGAAAAATTAAATTACGGTATTAAGTTTTTAATTGTTAAGGGTTTCTGGGCTTAATTAAG
GATTAGAAAAAATTAAATCAGGGTATTAGGTTTTTAATTGTTTAAGGTTTTGGGATTTGATTAGT
Found at i:54697472 original size:65 final size:65
Alignment explanation
Indices: 54697223--54697472 Score: 344
Period size: 65 Copynumber: 3.8 Consensus size: 65
54697213 GTATAGGGTT
* * *
54697223 TTAAGGTTTAGGAAAAATTAAATTAGGGTATTAGGTTTTTAATTG-TTAAGGGTTTCTGGGCTTA
1 TTAAGGTTTAGGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAA-GGTTTTTGGGTTTG
54697287 A
65 A
* *
54697288 TTAGGGTTTAGGAAAAATTAAATCAGGGTATTAGGTTTTTAATTGTTTAAGG-TTTTGGGATTTG
1 TTAAGGTTTAGGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAAGGTTTTTGGG-TTTG
54697352 A
65 A
** * * *
54697353 TT-AGTGTTTAGGAAATTTTAAATTACGGTATTAAGTTTTTAATTGTTTAGGGTTTTTGGGTTTG
1 TTAAG-GTTTAGGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAAGGTTTTTGGGTTTG
54697417 A
65 A
* *
54697418 TTAAGGATTAGAAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAAGGTTT
1 TTAAGGTTTAGGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAAGGTTT
54697473 AATTACTTTT
Statistics
Matches: 161, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
64 7 0.04
65 141 0.88
66 13 0.08
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.45
Consensus pattern (65 bp):
TTAAGGTTTAGGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAAGGTTTTTGGGTTTGA
Found at i:54701454 original size:113 final size:113
Alignment explanation
Indices: 54701296--54701518 Score: 301
Period size: 114 Copynumber: 2.0 Consensus size: 113
54701286 GATTCACAAA
54701296 AAGCGCCGCAAAAAAATAAGGCCAACAACGTCGTTTATTGAG-TTTTTGGGCCATTAGCGGCGTT
1 AAGCGCCGCAAAAAAATAAGGCCAACAACGTCGTTTATTGAGTTTTTTGGGCCATTAGCGGCGTT
*
54701360 TT-TACAAAAGCGCCGCTAATGCTCTTG-TCTTTAGCGGCGTTTTTTGAG
66 TTCT-CAAAAGCGCCGCTAATGAT-TTGTTCTTTAGCGGCGTTTTTTGAG
* * ** *
54701408 AAGCGCCGCAAAAAACCTAAGGGCAACAACGTCGTTT-TCTTTGTTTTTTGGGCCTTTAGCGGCG
1 AAGCGCCGCAAAAAA-ATAAGGCCAACAACGTCGTTTAT-TGAGTTTTTTGGGCCATTAGCGGCG
* * *
54701472 TTTTCTTAAAAGCGCTGCTAATGATTTGTTTTTTAGCGGCGTTTTTT
64 TTTTCTCAAAAGCGCCGCTAATGATTTGTTCTTTAGCGGCGTTTTTT
54701519 TGTAAGTTTT
Statistics
Matches: 97, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
112 16 0.16
113 24 0.25
114 56 0.58
115 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (113 bp):
AAGCGCCGCAAAAAAATAAGGCCAACAACGTCGTTTATTGAGTTTTTTGGGCCATTAGCGGCGTT
TTCTCAAAAGCGCCGCTAATGATTTGTTCTTTAGCGGCGTTTTTTGAG
Done.