Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold71
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: 5741892
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 121862 characters in sequence are not A, C, G, or T
File 9 of 33
Found at i:1418399 original size:171 final size:170
Alignment explanation
Indices: 1418049--1418455 Score: 430
Period size: 171 Copynumber: 2.4 Consensus size: 170
1418039 GGACAAAGCA
*
1418049 GACAGGTCACCAAGGGTAAGAAA-TTTACCAGGGACATAGCTGACAAGTAAACAAAGGGTAAGAA
1 GACAGGTCACCAAGGGTAA-AAAGTTTA-CAGGGACATAGCTGACAGGTAAACAAAGGGTAAGAA
* *
1418113 AGGCTGACCAGCGACAAAGCCAATAGGTCACCAAGGGATAAGAAGTTTACCAAGGACATAGCCGA
64 AGGCTGACCAGCGACAAAGCCAATAGGTCACCAAGCGATAAGAAGTTTACCAAGGACATAGCCAA
* * * * *
1418178 CAGCTAAACAAAGGGTAAGAAAGGTCGACTAGGGATAAAATC
129 CAGCTAAAAAAAAGATAAGAAAGGTCGACGAGGGACAAAATC
* * *
1418220 GACAGGTCACCAAGAGGTAAAAAGTTTATCAGGGACAT-GGTGACAGGTAAACAAAAGGTAATAA
1 GACAGGTCACCAAG-GGTAAAAAGTTTA-CAGGGACATAGCTGACAGGTAAACAAAGGGTAAGAA
* * * * * ** * ** *
1418284 TGGTTGATCGGGGACAAAGCTGATAGGTCACTAAGCGATAAGAAGTTTACCGGGGACATAGCTAA
64 AGGCTGACCAGCGACAAAGCCAATAGGTCACCAAGCGATAAGAAGTTTACCAAGGACATAGCCAA
* * *
1418349 CAAG-TAAAAAAAAGATAAGAATA-GTTGATCGA-GGACATAGTC
129 C-AGCTAAAAAAAAGATAAGAA-AGGTCGA-CGAGGGACAAAATC
* * * *
1418391 GGCAGGTCACCAAGGAATAAGAAGTTTACTA-GGACATAGCCGACAGGTAAACAAAGGGTAAGAA
1 GACAGGTCACCAAGG-GTAAAAAGTTTAC-AGGGACATAGCTGACAGGTAAACAAAGGGTAAGAA
1418455 A
64 A
1418456 AGATAAAAAA
Statistics
Matches: 194, Mismatches: 34, Indels: 16
0.80 0.14 0.07
Matches are distributed among these distances:
170 8 0.04
171 163 0.84
172 23 0.12
ACGTcount: A:0.42, C:0.15, G:0.27, T:0.16
Consensus pattern (170 bp):
GACAGGTCACCAAGGGTAAAAAGTTTACAGGGACATAGCTGACAGGTAAACAAAGGGTAAGAAAG
GCTGACCAGCGACAAAGCCAATAGGTCACCAAGCGATAAGAAGTTTACCAAGGACATAGCCAACA
GCTAAAAAAAAGATAAGAAAGGTCGACGAGGGACAAAATC
Found at i:1418821 original size:42 final size:42
Alignment explanation
Indices: 1418775--1418886 Score: 109
Period size: 42 Copynumber: 2.7 Consensus size: 42
1418765 AGAAGTTTTT
*
1418775 TCGGGTCTGAGCCGATGGGCAGACAAAAGATGAAGGAA-TCTC
1 TCGGGTCTGAGCCGATGGGCAGACAAAAGATGAA-AAAGTCTC
* * * * **
1418817 TCGGGTCTGAGTCGACGGGTAGACGATTGATGAAAAAGTCTC
1 TCGGGTCTGAGCCGATGGGCAGACAAAAGATGAAAAAGTCTC
* * * *
1418859 CCGGGTCTAAGCTGATGGGCAAACAAAA
1 TCGGGTCTGAGCCGATGGGCAGACAAAA
1418887 AGGTAAGAAA
Statistics
Matches: 52, Mismatches: 17, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
41 2 0.04
42 50 0.96
ACGTcount: A:0.30, C:0.19, G:0.32, T:0.19
Consensus pattern (42 bp):
TCGGGTCTGAGCCGATGGGCAGACAAAAGATGAAAAAGTCTC
Found at i:1419004 original size:44 final size:43
Alignment explanation
Indices: 1418888--1420338 Score: 768
Period size: 43 Copynumber: 33.8 Consensus size: 43
1418878 CAAACAAAAA
* ** * *
1418888 GGTAAGAAAGTCTCCAAAGTCAAAGCCGACAGACAGACTTGAG
1 GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
** * *
1418931 GGTAAAGAAA-TCTCCAATGTCAAAGTCGATAGGCAGACTTAAG
1 GGTAAA-AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
** * * *
1418974 GGTATAAAAAGTCTCCAGGGTCAAAATCGATATGCAGACTTAAA
1 GGTA-AAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* ** * *
1419018 AGTAAGGAAGTCTCTAGGGTCAAAGCCGACAGACAGACTTAAG
1 GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* * * * ** * * * *
1419061 GATAAAGGAAGTCTCCAAGATCAAAGTTGACAAGTAGATTTAAA
1 GGTAAA-AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* ** * * *
1419105 GATAAAGAAAGTCTTTAGGGTTAAAGCCAACAGGCAAACTTAAG
1 GGTAAA-AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* ** * ** *
1419149 GGTGATGAAGTCTCTAGAATCAAAGCCGACAGGCAAACTTAAG
1 GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* ** * * *
1419192 GGTGAGGAAGTTTCCAAGGTCAAAGTCGACAGGCAGACTTAAG
1 GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* ** * *
1419235 GGTGAGGAAGTCTCAAGGGTCAAAGTCGACAGGCAGACTTAAG
1 GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* * * ** * *
1419278 GATAAAGGAAGTCTCTAGGGTCAAAGCTAACAGACAGACTTAAA
1 GGTAAA-AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* * ** * *
1419322 GATAAAGAAAGTCTCTAGGGTCAAAGTTGACAAGCAAACTTAAG
1 GGTAAA-AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
** * **
1419366 GGTAATGAAGTCT-C-GGGTCAAAGCCGATAAACAGACTTAAG
1 GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* ** * * **
1419407 GGTGAGGAAGTCTCTAGGGTCAAAGCCAACAAACAGACTTAAG
1 GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* * *
1419450 GATAAAGGAAA-TATCCAGGGTCAAAGCCGACAGACAGACTTAAG
1 GGTAAA--AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
** * * * * *
1419494 AATAAAAAAGTCTGCAAGGTCAAAACCGATAGGCAAACTTAAG
1 GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* ** * * *
1419537 GATAATGAAGTCTCCAAGGTCAAAGTCGGCAGGCAGA-TATAAG
1 GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACT-TAAG
* * * * *
1419580 GGTAAATAAAGTCTCTAGGGTCAAAGTCGATAAGCAGATTTAAG
1 GGTAAA-AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
** * * *
1419624 GGTAAGGAAGTCTCTAAGGTCAAAACCGACAGGCAGACTTAAG
1 GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* * * * * * *
1419667 GATAAAGAAGTTTTCAGGGTCAACGCCAATAGGCAG----AAG
1 GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* * * * * *
1419706 GATGAAGAATGTCTCCATGGTCAAAGCCGACAAGCAAACTTAAG
1 GGT-AAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* * ** *
1419750 TGTGAGGAAGTCTCTAGGGTCAAAGCCGACAGGC-GAACTTAAG
1 GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAG-ACTTAAG
* * * * *
1419793 GATAAAGGAAGTC-CCTAGGGTCAAAGTCGACAAGC-GAACTTAAA
1 GGTAAA-AAAGTCTCC-AGGGTCAAAGCCGACAGGCAG-ACTTAAG
* * * ** *
1419837 GATAAAGAAGTTTCCAAAGTCATAA-CCGATAGGCAGACTTAAG
1 GGTAAAAAAGTCTCCAGGGTCA-AAGCCGACAGGCAGACTTAAG
* * * * * *
1419880 GATAAAGAAGTCTCAAGGGTCACAGCTGACAAGCAGACTTAAG
1 GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* * ** * * * *
1419923 GATTAGGAAGTCTTCAAGGTCGAAA-TCGATAGGCAGACTTAAG
1 GGTAAAAAAGTCTCCAGGGTC-AAAGCCGACAGGCAGACTTAAG
* * * * * *
1419966 GATAAAGAAGTCTCTAGGGTCGAAGCAGACAGGTAGACTTAAG
1 GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* ** ** * * *
1420009 GATAATGAAGTCTCCAAAGCCAAAGCTGACAAGCAGACTTAAG
1 GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* * * * * * *
1420052 GGTAAATAAGTATTCAGGGTCAAACCCAATAGGTAGACTTAAG
1 GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* ** * *
1420095 GATAAAAGAAGTCTCCAAAGTCAAAGCTGACAAGCAGACTTAAG
1 GGTAAAA-AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* * * * * *
1420139 GATAATAAAGTCTCTAGGGTTAAAGCCGACAAGCAAACTTAAG
1 GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* * *
1420182 GGT---AAA-----CAAGGTCAAAGCCGACAAGCAGACTTAAA
1 GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* * * * * * *
1420217 GGTGATAAAGTTTGCAAGGTCAAAGTCGACAGGTAGACTTAAG
1 GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
** * * * * *
1420260 AATAAAGGAAGTCTCTAGGGTCAAAACCGACAAGTAGACTTAAG
1 GGTAAA-AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
* * * * *
1420304 GATAAAGAAGTCTCTAGGGTTAAAACCGACAGGCA
1 GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCA
1420339 AACTGAAGAA
Statistics
Matches: 1091, Mismatches: 280, Indels: 74
0.76 0.19 0.05
Matches are distributed among these distances:
35 27 0.02
38 3 0.00
39 6 0.01
40 25 0.02
41 33 0.03
42 7 0.01
43 637 0.58
44 350 0.32
45 3 0.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.19
Consensus pattern (43 bp):
GGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAAG
Found at i:1419040 original size:87 final size:88
Alignment explanation
Indices: 1418949--1420338 Score: 681
Period size: 87 Copynumber: 16.2 Consensus size: 88
1418939 AATCTCCAAT
* * * * *
1418949 GTCAAAGTCGATAGGCAGACTTAAGGGTATAAAAAGTCTCCAGGGTCAAAATCGATATGCAGACT
1 GTCAAAGCCGACAGGCAGACTTAAGGGTATAAAAAGTCTCCAGGGTCAAAGTCGACAAGCAGACT
*
1419014 TAAAAG-TAAGGAAGTCTCTAGG
66 TAAAGGATAAGGAAGTCTCTAGG
* * * * *
1419036 GTCAAAGCCGACAGACAGACTTAA-GG-ATAAAGGAAGTCTCCAAGATCAAAGTTGACAAGTAGA
1 GTCAAAGCCGACAGGCAGACTTAAGGGTATAAA--AAGTCTCCAGGGTCAAAGTCGACAAGCAGA
* * *
1419099 TTTAAA-GATAAAGAAAGTCTTTAGG
64 CTTAAAGGAT-AAGGAAGTCTCTAGG
* * * * * ** * * *
1419124 GTTAAAGCCAACAGGCAAACTTAAGGGTGAT--GAAGTCTCTAGAATCAAAGCCGACAGGCAAAC
1 GTCAAAGCCGACAGGCAGACTTAAGGGT-ATAAAAAGTCTCCAGGGTCAAAGTCGACAAGCAGAC
* * * * *
1419187 TT-AAGGGTGAGGAAGTTTCCAAG
65 TTAAAGGATAAGGAAGTCTCTAGG
* * ** * *
1419210 GTCAAAGTCGACAGGCAGACTTAAGGGT-GAGGAAGTCTCAAGGGTCAAAGTCGACAGGCAGACT
1 GTCAAAGCCGACAGGCAGACTTAAGGGTATAAAAAGTCTCCAGGGTCAAAGTCGACAAGCAGACT
1419274 T-AAGGATAAAGGAAGTCTCTAGG
66 TAAAGGAT-AAGGAAGTCTCTAGG
** * * * * * *
1419297 GTCAAAGCTAACAGACAGACTTAAAGATA-AAGAAAGTCTCTAGGGTCAAAGTTGACAAGCAAAC
1 GTCAAAGCCGACAGGCAGACTTAAGGGTATAA-AAAGTCTCCAGGGTCAAAGTCGACAAGCAGAC
* *
1419361 TT-AAGGGTAATGAAGTCTC--GG
65 TTAAAGGATAAGGAAGTCTCTAGG
* ** * ** * * * *
1419382 GTCAAAGCCGATAAACAGACTTAAGGGT-GAGGAAGTCTCTAGGGTCAAAGCCAACAAACAGACT
1 GTCAAAGCCGACAGGCAGACTTAAGGGTATAAAAAGTCTCCAGGGTCAAAGTCGACAAGCAGACT
* * *
1419446 T-AAGGATAAAGGAAATATCCAGG
66 TAAAGGAT-AAGGAAGTCTCTAGG
* ** * * ** * * *
1419469 GTCAAAGCCGACAGACAGACTTAAGAATA-AAAAAGTCTGCAAGGTCAAAACCGATAGGCAAACT
1 GTCAAAGCCGACAGGCAGACTTAAGGGTATAAAAAGTCTCCAGGGTCAAAGTCGACAAGCAGACT
* * *
1419533 T-AAGGATAATGAAGTCTCCAAG
66 TAAAGGATAAGGAAGTCTCTAGG
* * * *
1419555 GTCAAAGTCGGCAGGCAGA-TATAAGGGTA-AATAAAGTCTCTAGGGTCAAAGTCGATAAGCAGA
1 GTCAAAGCCGACAGGCAGACT-TAAGGGTATAA-AAAGTCTCCAGGGTCAAAGTCGACAAGCAGA
* * *
1419618 -TTTAAGGGTAAGGAAGTCTCTAAG
64 CTTAAAGGATAAGGAAGTCTCTAGG
* * * * * *
1419642 GTCAAAACCGACAGGCAGACTTAA-GG-ATAAAGAAGTTTTCAGGGTC-AA--CGCCAA-TAGGC
1 GTCAAAGCCGACAGGCAGACTTAAGGGTATAAA-AAGTCTCCAGGGTCAAAGTCGACAAGCAGAC
* *
1419701 --AGAAGGATGAA-GAATGTCTCCATG
65 TTA-AAGGAT-AAGGAA-GTCTCTAGG
* * * * ** * * *
1419725 GTCAAAGCCGACAAGCAAACTTAAGTGT-GAGGAAGTCTCTAGGGTCAAAGCCGACAGGC-GAAC
1 GTCAAAGCCGACAGGCAGACTTAAGGGTATAAAAAGTCTCCAGGGTCAAAGTCGACAAGCAG-AC
*
1419788 TT-AAGGATAAAGGAAGTCCCTAGG
65 TTAAAGGAT-AAGGAAGTCTCTAGG
* * * * ** * * *
1419812 GTCAAAGTCGACAAGC-GAACTTAA-AG-ATAAAGAAGTTTCCAAAGTCATAA-CCGATAGGCAG
1 GTCAAAGCCGACAGGCAG-ACTTAAGGGTATAAA-AAGTCTCCAGGGTCA-AAGTCGACAAGCAG
* *
1419873 ACTT-AAGGATAAAGAAGTCTCAAGG
63 ACTTAAAGGATAAGGAAGTCTCTAGG
* * * * ** * * * *
1419898 GTCACAGCTGACAAGCAGACTTAAGGAT-TAGGAAGTCTTCAAGGTCGAAA-TCGATAGGCAGAC
1 GTCAAAGCCGACAGGCAGACTTAAGGGTATAAAAAGTCTCCAGGGTC-AAAGTCGACAAGCAGAC
*
1419961 TT-AAGGATAAAGAAGTCTCTAGG
65 TTAAAGGATAAGGAAGTCTCTAGG
* * * * ** *
1419984 GTCGAAGCAGACAGGTAGACTTAA-GG-ATAATGAAGTCTCCAAAGCCAAAG-CTGACAAGCAGA
1 GTCAAAGCCGACAGGCAGACTTAAGGGTATAA-AAAGTCTCCAGGGTCAAAGTC-GACAAGCAGA
* ** *
1420046 CTT-AAGGGTAAATAAGTAT-TCAGG
64 CTTAAAGGATAAGGAAGTCTCT-AGG
* * * * * **
1420070 GTCAAACCCAATAGGTAGACTTAAGGATA-AAAGAAGTCTCCAAAGTCAAAG-CTGACAAGCAGA
1 GTCAAAGCCGACAGGCAGACTTAAGGGTATAAA-AAGTCTCCAGGGTCAAAGTC-GACAAGCAGA
**
1420133 CTT-AAGGATAATAAAGTCTCTAGG
64 CTTAAAGGATAAGGAAGTCTCTAGG
* * * * *
1420157 GTTAAAGCCGACAAGCAAACTTAAGGG--T--AAA-----CAAGGTCAAAGCCGACAAGCAGACT
1 GTCAAAGCCGACAGGCAGACTTAAGGGTATAAAAAGTCTCCAGGGTCAAAGTCGACAAGCAGACT
* ** * *
1420213 TAAAGG-TGATAAAGTTTGC-AAG
66 TAAAGGATAAGGAAGTCT-CTAGG
* * * * ** *
1420235 GTCAAAGTCGACAGGTAGACTTAA--GAATAAAGGAAGTCTCTAGGGTCAAAACCGACAAGTAGA
1 GTCAAAGCCGACAGGCAGACTTAAGGGTATAAA--AAGTCTCCAGGGTCAAAGTCGACAAGCAGA
*
1420298 CTT-AAGGATAAAGAAGTCTCTAGG
64 CTTAAAGGATAAGGAAGTCTCTAGG
* *
1420322 GTTAAAACCGACAGGCA
1 GTCAAAGCCGACAGGCA
1420339 AACTGAAGAA
Statistics
Matches: 1001, Mismatches: 229, Indels: 146
0.73 0.17 0.11
Matches are distributed among these distances:
76 1 0.00
78 54 0.05
79 6 0.01
80 1 0.00
82 12 0.01
83 47 0.05
84 38 0.04
85 51 0.05
86 291 0.29
87 420 0.42
88 76 0.08
89 2 0.00
91 2 0.00
ACGTcount: A:0.40, C:0.16, G:0.25, T:0.19
Consensus pattern (88 bp):
GTCAAAGCCGACAGGCAGACTTAAGGGTATAAAAAGTCTCCAGGGTCAAAGTCGACAAGCAGACT
TAAAGGATAAGGAAGTCTCTAGG
Found at i:1419258 original size:217 final size:215
Alignment explanation
Indices: 1418891--1420143 Score: 689
Period size: 217 Copynumber: 5.8 Consensus size: 215
1418881 ACAAAAAGGT
* ** * * * * * *
1418891 AAGAAAGTCTCCAAAGTCAAAGCCGAC-AGACAGACTTGAGGGTAAAGAAATCTCCAATGTCAAA
1 AAGAAAGTCTCTAGGGTCAAAGCCAACAAG-CAAACTTAAGGGTAATGAAGTCTCGAA--TCAAA
* * ** * * * **
1418955 GTCGATAGGCAGACTTAAGGGTATAAAAAGTCTCCAGGGTCAAAATCGATATGCAGACTTAAAAG
63 GCCGATAGGCAGACTTAAGGGT-GAGGAAGTCTCCAGGGTCAAAGTCGACAAGCAGACTTAAGGG
* *
1419020 TAAGGAAGTCTCTAGGGTCAAAGCCGACAGACAGACTTAAGGATAAAGGAAGTCTCCAAGATCAA
127 TAAGGAAGTCTCAAGGGTCAAAGCCGACAGACAGACTTAAGGATAAAGGAAGTCTCCAAGGTCAA
* * * *
1419085 AGTTGACA-AGTAGATTTAAAGATA
192 AGCTAACAGA-CAGACTTAAAGATA
* * * *
1419109 AAGAAAGTCTTTAGGGTTAAAGCCAACAGGCAAACTTAAGGGTGATGAAGTCTCTAGAATCAAAG
1 AAGAAAGTCTCTAGGGTCAAAGCCAACAAGCAAACTTAAGGGTAATGAAGTCTC--GAATCAAAG
* * * * * *
1419174 CCGACAGGCAAACTTAAGGGTGAGGAAGTTTCCAAGGTCAAAGTCGACAGGCAGACTTAAGGGTG
64 CCGATAGGCAGACTTAAGGGTGAGGAAGTCTCCAGGGTCAAAGTCGACAAGCAGACTTAAGGGTA
* * * *
1419239 AGGAAGTCTCAAGGGTCAAAGTCGACAGGCAGACTTAAGGATAAAGGAAGTCTCTAGGGTCAAAG
129 AGGAAGTCTCAAGGGTCAAAGCCGACAGACAGACTTAAGGATAAAGGAAGTCTCCAAGGTCAAAG
1419304 CTAACAGACAGACTTAAAGATA
194 CTAACAGACAGACTTAAAGATA
*** **
1419326 AAGAAAGTCTCTAGGGTCAAAGTTGACAAGCAAACTTAAGGGTAATGAAGTCTCGGGTCAAAGCC
1 AAGAAAGTCTCTAGGGTCAAAGCCAACAAGCAAACTTAAGGGTAATGAAGTCTCGAATCAAAGCC
** * * * * *
1419391 GATAAACAGACTTAAGGGTGAGGAAGTCTCTAGGGTCAAAGCCAACAAACAGACTTAAGGATAAA
66 GATAGGCAGACTTAAGGGTGAGGAAGTCTCCAGGGTCAAAGTCGACAAGCAGACTTAAGGGT-AA
* * * * * * *
1419456 GGAAATATCCAGGGTCAAAGCCGACAGACAGACTTAAGAATAAA-AAAGTCTGCAAGGTCAAAAC
130 GGAAGTCTCAAGGGTCAAAGCCGACAGACAGACTTAAGGATAAAGGAAGTCTCCAAGGTCAAAGC
** * * * *
1419520 CGATAGGCAAACTTAAGGATA
195 TAACAGACAGACTTAAAGATA
* * * * ** * * * **
1419541 ATG-AAGTCTCCAAGGTCAAAGTCGGCAGGCAGA-TATAAGGGTAAATAAAGTCTCTAGGGTCAA
1 AAGAAAGTCTCTAGGGTCAAAGCCAACAAGCAAACT-TAAGGGT-AATGAAGTCTC--GAATCAA
* * * * * * ** * *
1419604 AGTCGATAAGCAGATTTAAGGGTAAGGAAGTCTCTAAGGTCAAAACCGACAGGCAGACTTAAGGA
62 AGCCGATAGGCAGACTTAAGGGTGAGGAAGTCTCCAGGGTCAAAGTCGACAAGCAGACTTAAGGG
* * * * * * * *
1419669 TAAAGAAGTTTTC-AGGGTCAACGCCAATAGGCAG----AAGGATGAA-GAATGTCTCCATGGTC
127 TAAGGAAG-TCTCAAGGGTCAAAGCCGACAGACAGACTTAAGGATAAAGGAA-GTCTCCAAGGTC
** * *
1419728 AAAGCCGACA-AGCAAACTT-AAG-TGT
190 AAAGCTAACAGA-CAGACTTAAAGAT-A
* * * * * * * * **
1419753 GAGGAAGTCTCTAGGGTCAAAGCCGACAGGCGAACTTAAGGATAAAGGAAGTCCCTAGGGTCAAA
1 AAGAAAGTCTCTAGGGTCAAAGCCAACAAGCAAACTTAAGGGT-AATGAAGT--CTCGAATCAAA
* * * * * * * * ** * * *
1419818 GTCGACAAGC-GAACTTAAAGATAAAGAAGTTTCCAAAGTCATAA-CCGATAGGCAGACTTAAGG
63 GCCGATAGGCAG-ACTTAAGGGTGAGGAAGTCTCCAGGGTCA-AAGTCGACAAGCAGACTTAAGG
* * * * * *
1419881 ATAAAGAAGTCTCAAGGGTCACAGCTGACA-AGCAGACTTAAGGAT-TAGGAAGTCTTCAAGGTC
126 GTAAGGAAGTCTCAAGGGTCAAAGCCGACAGA-CAGACTTAAGGATAAAGGAAGTCTCCAAGGTC
* * * * *
1419944 GAAATC-GATAGGCAGACTTAAGGATA
190 -AAAGCTAACAGACAGACTTAAAGATA
* * * * * * *
1419970 AAG-AAGTCTCTAGGGTCGAAG-CAGACAGGTAGACTTAAGGATAATGAAGTCTCCAAAGCCAAA
1 AAGAAAGTCTCTAGGGTCAAAGCCA-ACAAGCAAACTTAAGGGTAATGAAGTCT-CGAA-TCAAA
* * * * ** * * ** * * * * *
1420033 GCTGACAAGCAGACTTAAGGGTAAATAAGTATTCAGGGTCAAACCCAATAGGTAGACTTAAGGAT
63 GCCGATAGGCAGACTTAAGGGTGAGGAAGTCTCCAGGGTCAAAGTCGACAAGCAGACTTAAGGGT
* * *
1420098 AAAAGAAGTCTCCAA-AGTCAAAGCTGACA-AGCAGACTTAAGGATAA
128 -AAGGAAGTCT-CAAGGGTCAAAGCCGACAGA-CAGACTTAAGGATAA
1420144 TAAAGTCTCT
Statistics
Matches: 824, Mismatches: 173, Indels: 77
0.77 0.16 0.07
Matches are distributed among these distances:
211 1 0.00
212 16 0.02
213 145 0.18
214 36 0.04
215 164 0.20
216 151 0.18
217 242 0.29
218 66 0.08
219 1 0.00
220 2 0.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.19
Consensus pattern (215 bp):
AAGAAAGTCTCTAGGGTCAAAGCCAACAAGCAAACTTAAGGGTAATGAAGTCTCGAATCAAAGCC
GATAGGCAGACTTAAGGGTGAGGAAGTCTCCAGGGTCAAAGTCGACAAGCAGACTTAAGGGTAAG
GAAGTCTCAAGGGTCAAAGCCGACAGACAGACTTAAGGATAAAGGAAGTCTCCAAGGTCAAAGCT
AACAGACAGACTTAAAGATA
Found at i:1420301 original size:165 final size:165
Alignment explanation
Indices: 1420029--1420342 Score: 418
Period size: 165 Copynumber: 1.9 Consensus size: 165
1420019 TCTCCAAAGC
* * * *
1420029 CAAAGCTGACAAGCAGACTTAAGGGTAAATAAGTATTCAGGGTCAAACCCAATAGGTAGACTTAA
1 CAAAGCCGACAAGCAGACTTAAAGGTAAATAAGTATTCAAGGTCAAACCCAACAGGTAGACTTAA
* * *
1420094 GGATAAAAGAAGTCTCCAAAGTCAAAGCTGACAAGCAGACTTAAGGATAATA-AAGTCTCTAGGG
66 GAATAAAAGAAGTCTCCAAAGTCAAAACCGACAAGCAGACTTAAGGATAA-AGAAGTCTCTAGGG
*
1420158 TTAAAGCCGACAAGCAAACTTAAGGGTAAACAAGGT
130 TTAAAACCGACAAGCAAACTTAAGGGTAAACAAGGT
* ** *
1420194 CAAAGCCGACAAGCAGACTTAAAGGT-GATAAAGT-TTGCAAGGTCAAAGTCGACAGGTAGACTT
1 CAAAGCCGACAAGCAGACTTAAAGGTAAAT-AAGTATT-CAAGGTCAAACCCAACAGGTAGACTT
* * ** *
1420257 AAGAATAAAGGAAGTCTCTAGGGTCAAAACCGACAAGTAGACTTAAGGATAAAGAAGTCTCTAGG
64 AAGAATAAAAGAAGTCTCCAAAGTCAAAACCGACAAGCAGACTTAAGGATAAAGAAGTCTCTAGG
*
1420322 GTTAAAACCGACAGGCAAACT
129 GTTAAAACCGACAAGCAAACT
1420343 GAAGAATCAA
Statistics
Matches: 128, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
164 5 0.04
165 123 0.96
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (165 bp):
CAAAGCCGACAAGCAGACTTAAAGGTAAATAAGTATTCAAGGTCAAACCCAACAGGTAGACTTAA
GAATAAAAGAAGTCTCCAAAGTCAAAACCGACAAGCAGACTTAAGGATAAAGAAGTCTCTAGGGT
TAAAACCGACAAGCAAACTTAAGGGTAAACAAGGT
Found at i:1420544 original size:44 final size:44
Alignment explanation
Indices: 1420436--1420741 Score: 277
Period size: 44 Copynumber: 7.0 Consensus size: 44
1420426 TTTGACCATA
* *
1420436 GTGGTAACCATACGTCAAAT-AGGAA--AAAAGCAGATTTGACCATG
1 GTGGTAACCATACGTCAAATCA-GAATGAAAAG-A-ATTTGACTAGG
* * * * * *
1420480 GTTGTAAACATATGTTAAATCAGAATGAAAAGAATGTGACCAGG
1 GTGGTAACCATACGTCAAATCAGAATGAAAAGAATTTGACTAGG
* * * * *
1420524 GTGGTAACAATACATCAAATCAAAACGAAAAGAGTTTGACTAGG
1 GTGGTAACCATACGTCAAATCAGAATGAAAAGAATTTGACTAGG
** * * *
1420568 GTGGTAACCATGTGTCAAA-CATGAATGAAAAG-ACTTGACCAAG
1 GTGGTAACCATACGTCAAATCA-GAATGAAAAGAATTTGACTAGG
* * *
1420611 GTGGTAACTATACGTC-AAGCAGAATGAAAAGAATCTGACTAGG
1 GTGGTAACCATACGTCAAATCAGAATGAAAAGAATTTGACTAGG
** *
1420654 GTGGTAACCATACGTCAAA-CATGAATGAGGAGGATTTGACTAGG
1 GTGGTAACCATACGTCAAATCA-GAATGAAAAGAATTTGACTAGG
*
1420698 GTGGTAACCATACGTCAAATC-GAAATGAAAAGAGTTTGACTAGG
1 GTGGTAACCATACGTCAAATCAG-AATGAAAAGAATTTGACTAGG
1420742 CCTTAACACC
Statistics
Matches: 209, Mismatches: 43, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
42 12 0.06
43 49 0.23
44 140 0.67
45 3 0.01
46 5 0.02
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (44 bp):
GTGGTAACCATACGTCAAATCAGAATGAAAAGAATTTGACTAGG
Found at i:1421889 original size:7 final size:6
Alignment explanation
Indices: 1421873--1421925 Score: 56
Period size: 6 Copynumber: 8.8 Consensus size: 6
1421863 AGTATTATAT
* *
1421873 TTTTTG TTTTTG CTTTTTTG TTTTT- TTTTTG TTTTTA TTTTT- TTGTTG
1 TTTTTG TTTTTG --TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
1421921 TTTTT
1 TTTTT
1421926 TGTGTAAGCC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 9 0.22
6 25 0.62
8 6 0.15
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:1421890 original size:8 final size:7
Alignment explanation
Indices: 1421872--1421928 Score: 50
Period size: 7 Copynumber: 8.1 Consensus size: 7
1421862 AAGTATTATA
1421872 TTTTTTG
1 TTTTTTG
1421879 -TTTTTG
1 TTTTTTG
1421885 CTTTTTTG
1 -TTTTTTG
1421893 TTTTTT-
1 TTTTTTG
1421899 TTTTGTT-
1 TTTT-TTG
1421906 TTTATTT-
1 TTT-TTTG
1421913 TTTTGTTG
1 TTTT-TTG
1421921 TTTTTTG
1 TTTTTTG
1421928 T
1 T
1421929 GTAAGCCTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
6 11 0.25
7 22 0.50
8 11 0.25
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.84
Consensus pattern (7 bp):
TTTTTTG
Found at i:1421891 original size:14 final size:12
Alignment explanation
Indices: 1421872--1421926 Score: 58
Period size: 14 Copynumber: 4.2 Consensus size: 12
1421862 AAGTATTATA
1421872 TTTTTTGTTTTT
1 TTTTTTGTTTTT
1421884 GCTTTTTTG-TTTT
1 --TTTTTTGTTTTT
1421897 TTTTTTGTTTTTAT
1 TTTTTTG-TTTT-T
1421911 TTTTTTGTTGTTT
1 TTTTTTGTT-TTT
1421924 TTT
1 TTT
1421927 GTGTAAGCCT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
11 7 0.19
13 13 0.35
14 17 0.46
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (12 bp):
TTTTTTGTTTTT
Found at i:1421905 original size:25 final size:25
Alignment explanation
Indices: 1421872--1421926 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
1421862 AAGTATTATA
* *
1421872 TTTTTTGTTTTTGCTTTTTTGTTTT
1 TTTTTTGTTTTTACTTTTTTGTTGT
*
1421897 TTTTTTGTTTTTATTTTTTTGTTGT
1 TTTTTTGTTTTTACTTTTTTGTTGT
1421922 TTTTT
1 TTTTT
1421927 GTGTAAGCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (25 bp):
TTTTTTGTTTTTACTTTTTTGTTGT
Found at i:1421907 original size:17 final size:17
Alignment explanation
Indices: 1421873--1421925 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
1421863 AGTATTATAT
*
1421873 TTTTTGTTTTTGCTTTTTTG
1 TTTTT-TTTTTG--TTTTTA
1421893 TTTTTTTTTTGTTTTTA
1 TTTTTTTTTTGTTTTTA
*
1421910 TTTTTTTGTTGTTTTT
1 TTTTTTTTTTGTTTTT
1421926 TGTGTAAGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 20 0.65
19 6 0.19
20 5 0.16
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (17 bp):
TTTTTTTTTTGTTTTTA
Found at i:1422277 original size:112 final size:112
Alignment explanation
Indices: 1422151--1422389 Score: 239
Period size: 112 Copynumber: 2.1 Consensus size: 112
1422141 TTTAGAATCC
** * * ** * *
1422151 AACAAATTTAATGTTACGGGGCTCAAAGATTTCAAAACTGATAAGATACGTACTCTA-TTTCCTA
1 AACAAATTCGATGTTACGGAGCTCAAAAAGATCAAAACTGACAAGATACGTAC-CCAGTTTCCTA
* ***
1422215 GGCACGAATGGATCGAAACGAATAAAGTGTGAATTTCTTCAAAAATTA
65 GGCACGAATGGATCAAAACGAATAAAACATGAATTTCTTCAAAAATTA
* ** * * * *
1422263 AGCAAATAT-GATGTTGTGGAGTTTAAAAAGATCAAAACTGACAAGATATGTGCCCAGTTTCCTA
1 AACAAAT-TCGATGTTACGGAGCTCAAAAAGATCAAAACTGACAAGATACGTACCCAGTTTCCTA
* * **
1422327 GGCACGAATGGATCAAAATGTATAAAACATGAATTTCTTTGAAAATTA
65 GGCACGAATGGATCAAAACGAATAAAACATGAATTTCTTCAAAAATTA
1422375 AACAAATTCGATGTT
1 AACAAATTCGATGTT
1422390 CTTCCAAGTT
Statistics
Matches: 101, Mismatches: 23, Indels: 6
0.78 0.18 0.05
Matches are distributed among these distances:
111 3 0.03
112 97 0.96
113 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.29
Consensus pattern (112 bp):
AACAAATTCGATGTTACGGAGCTCAAAAAGATCAAAACTGACAAGATACGTACCCAGTTTCCTAG
GCACGAATGGATCAAAACGAATAAAACATGAATTTCTTCAAAAATTA
Found at i:1422673 original size:21 final size:21
Alignment explanation
Indices: 1422648--1422699 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1422638 TAGAGCCTCA
1422648 TTCTTTCTTTTCTTTC-CATT
1 TTCTTTCTTTTCTTTCTCATT
1422668 TCTCTTT-TTCTTCTTTCTCATT
1 T-TCTTTCTT-TTCTTTCTCATT
*
1422690 TTTTTTCTTT
1 TTCTTTCTTT
1422700 CACAATCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 3 0.11
21 17 0.63
22 7 0.26
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (21 bp):
TTCTTTCTTTTCTTTCTCATT
Found at i:1422684 original size:15 final size:16
Alignment explanation
Indices: 1422666--1422700 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1422656 TTTCTTTCCA
1422666 TTTCTC-TTTTTCTTC
1 TTTCTCATTTTTCTTC
*
1422681 TTTCTCATTTTTTTTC
1 TTTCTCATTTTTCTTC
1422697 TTTC
1 TTTC
1422701 ACAATCTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCTCATTTTTCTTC
Found at i:1426647 original size:157 final size:156
Alignment explanation
Indices: 1426366--1426662 Score: 361
Period size: 157 Copynumber: 1.9 Consensus size: 156
1426356 AAAATACTTT
* *
1426366 TAGGGGATACCTTTGACGTAGAAGTACCTGATACCCCTAAAAGACTTAAAAAAGACTATAGATGA
1 TAGGGGATACCTTTGACGTAGAAGTACCTGATACCCCTAAAAGACTTAAAAAAGACTATAAAAGA
** * * * * *
1426431 GACGAACCTATTTTAAATATCTATCATTGGCATTAAAGTGGACCCGGTGATAACCTAGGACTTGA
66 GACGAACCTATCCTAAAAATCTATCATTGGCATAAAAGCGGACCCGATGATAACCTAGGACTCGA
1426496 TTCTAAAAAAATTACCCAAATACCCC
131 TTCTAAAAAAATTACCCAAATACCCC
* *
1426522 TAGGGGATACCTTTGACGT-GAAAGTATCTCGATACCCCT-AAAGAACTTAAAAATGACTATAAA
1 TAGGGGATACCTTTGACGTAG-AAGTACCT-GATACCCCTAAAAG-ACTTAAAAAAGACTATAAA
* * * *
1426585 AGGGATC-AACCTATCCTAAAAA-CTCA-CTTTCGGCATAAAAGCGGATCCGATGATAACTTAGG
63 AGAGA-CGAACCTATCCTAAAAATCT-ATCATT-GGCATAAAAGCGGACCCGATGATAACCTAGG
*
1426647 ACTCGATTTTAAAAAA
125 ACTCGATTCTAAAAAA
1426663 TTATAAAAGG
Statistics
Matches: 119, Mismatches: 16, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
155 1 0.01
156 35 0.29
157 82 0.69
158 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (156 bp):
TAGGGGATACCTTTGACGTAGAAGTACCTGATACCCCTAAAAGACTTAAAAAAGACTATAAAAGA
GACGAACCTATCCTAAAAATCTATCATTGGCATAAAAGCGGACCCGATGATAACCTAGGACTCGA
TTCTAAAAAAATTACCCAAATACCCC
Found at i:1426807 original size:146 final size:146
Alignment explanation
Indices: 1426525--1426795 Score: 345
Period size: 146 Copynumber: 1.9 Consensus size: 146
1426515 ATACCCCTAG
* *
1426525 GGGATACCTTTGACGTGAAAGTATCTCGATACCCCTAAAGAACTTAAAAATGACTATAAAAGGGA
1 GGGATACCTTCGACGTGAAAGTATCTCGATACCCCTAAAGAACGTAAAAATGACTATAAAAGGGA
* ** * * *
1426590 TCAACCTATCCTAAAAACTCACTTTCGGCATAAAAGCGGATCCGATGATAACTTAGGACTCGATT
66 TCAACCTATCCTAAAAACTCACCTTCAACATAAAAGCAGATCCGATAATAACCTAGGACTCGATT
*
1426655 TTAAAAAATTATAAAA
131 TAAAAAAATTATAAAA
* *
1426671 GGGATACCTTCGACGTGAAAGTATC-CTGGTACCCCTAAA-AGTCGTAAAAATGA-TCATAAAAG
1 GGGATACCTTCGACGTGAAAGTATCTC-GATACCCCTAAAGA-ACGTAAAAATGACT-ATAAAAG
* * *
1426733 GGGTGAACCTATCCTAAATAC-CACCTTCAACATAAAAGCAGA-CTCGATAATAACCTAGGACTC
63 GGATCAACCTATCCTAAAAACTCACCTTCAACATAAAAGCAGATC-CGATAATAACCTAGGACTC
1426796 AGTTCTAAAA
Statistics
Matches: 108, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
144 1 0.01
145 37 0.34
146 70 0.65
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.24
Consensus pattern (146 bp):
GGGATACCTTCGACGTGAAAGTATCTCGATACCCCTAAAGAACGTAAAAATGACTATAAAAGGGA
TCAACCTATCCTAAAAACTCACCTTCAACATAAAAGCAGATCCGATAATAACCTAGGACTCGATT
TAAAAAAATTATAAAA
Found at i:1435614 original size:2 final size:2
Alignment explanation
Indices: 1435609--1435638 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1435599 AAAAGAGATT
1435609 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1435639 ACAAATTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1436654 original size:14 final size:15
Alignment explanation
Indices: 1436624--1436656 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1436614 ACAAATAAAA
1436624 AATAAAAAAATATTT
1 AATAAAAAAATATTT
*
1436639 AATAAAAAATTA-TT
1 AATAAAAAAATATTT
1436653 AATA
1 AATA
1436657 CTATTATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AATAAAAAAATATTT
Found at i:1439423 original size:16 final size:16
Alignment explanation
Indices: 1439402--1439433 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1439392 AACATTACAT
*
1439402 GTTAATGTAAATTTTA
1 GTTAATATAAATTTTA
1439418 GTTAATATAAATTTTA
1 GTTAATATAAATTTTA
1439434 TTTATTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (16 bp):
GTTAATATAAATTTTA
Found at i:1440675 original size:16 final size:16
Alignment explanation
Indices: 1440651--1440682 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1440641 TTTTTTTATA
1440651 AAATCATAATAAAGTT
1 AAATCATAATAAAGTT
*
1440667 AAATTATAATAAAGTT
1 AAATCATAATAAAGTT
1440683 TTTTAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.34
Consensus pattern (16 bp):
AAATCATAATAAAGTT
Found at i:1441684 original size:18 final size:17
Alignment explanation
Indices: 1441658--1441693 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1441648 AATAAATTTA
*
1441658 TAAATTAAATTAAAAAT
1 TAAATTAAATAAAAAAT
1441675 TAAATATAAATAAAAAAT
1 TAAAT-TAAATAAAAAAT
1441693 T
1 T
1441694 TTAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAATTAAATAAAAAAT
Found at i:1442011 original size:22 final size:21
Alignment explanation
Indices: 1441976--1442026 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
1441966 TTATTTGAAA
*
1441976 TAAAATATTTATTTATTAAAT
1 TAAAATATTTATTTAATAAAT
*
1441997 TAAATTATTTAATTTAATAAAT
1 TAAAATATTT-ATTTAATAAAT
*
1442019 AAAAATAT
1 TAAAATAT
1442027 ACTATATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAAATATTTATTTAATAAAT
Found at i:1442021 original size:21 final size:20
Alignment explanation
Indices: 1441973--1442022 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
1441963 ATTTTATTTG
*
1441973 AAATAAAATATTTATTTATT
1 AAATAAAATATTTATTTAAT
*
1441993 AAATTAAATTATTTAATTTAAT
1 AAA-TAAAATATTT-ATTTAAT
1442015 AAATAAAA
1 AAATAAAA
1442023 ATATACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 13 0.52
22 9 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATAAAATATTTATTTAAT
Found at i:1442108 original size:15 final size:15
Alignment explanation
Indices: 1442078--1442122 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1442068 AATATTAAAA
1442078 AAAT-TTTA-AATATT
1 AAATATTTATAAT-TT
1442092 AAATATTTATAATTT
1 AAATATTTATAATTT
*
1442107 AAAAATTTATAATTT
1 AAATATTTATAATTT
1442122 A
1 A
1442123 TATAAAACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 4 0.14
15 21 0.75
16 3 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATATTTATAATTT
Found at i:1443273 original size:2 final size:2
Alignment explanation
Indices: 1443268--1443307 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1443258 AAAGTACCCC
*
1443268 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1443308 GATTTGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1444356 original size:2 final size:2
Alignment explanation
Indices: 1444349--1444384 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1444339 ATTCTCAAAT
1444349 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1444385 AATTCAAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1444908 original size:16 final size:16
Alignment explanation
Indices: 1444889--1444934 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
1444879 TATTCATTTG
1444889 ATATTTAAAAATTTTA
1 ATATTTAAAAATTTTA
*
1444905 ATA-TTAAATATTTATA
1 ATATTTAAAAATTT-TA
1444921 AT-TTT-AAAATTTTA
1 ATATTTAAAAATTTTA
1444935 TAGTATGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 2 0.08
15 15 0.58
16 9 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATTTAAAAATTTTA
Found at i:1447346 original size:34 final size:33
Alignment explanation
Indices: 1447298--1447518 Score: 266
Period size: 34 Copynumber: 6.5 Consensus size: 33
1447288 TGGTAAAAAC
*
1447298 CACCATTTAATCAACAATGGGAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
1447331 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
1447365 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
1447399 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
1447433 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
1447467 CACCTATTTAATCAACAATGGTAAACTACCAAAT
1 CACC-ATTTAATCAACAATGGTAACCTACCAAAT
1447501 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1447519 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
33 23 0.14
34 133 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:1447477 original size:102 final size:101
Alignment explanation
Indices: 1447298--1447518 Score: 343
Period size: 102 Copynumber: 2.2 Consensus size: 101
1447288 TGGTAAAAAC
* *
1447298 CACCATTTAATCAACAATGGGAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGGAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
1447363 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * *
1447399 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGGAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
*
1447464 AATCACCTATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1447501 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1447519 TCTCCCACTT
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 16 0.15
102 91 0.85
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGGAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:1451976 original size:34 final size:33
Alignment explanation
Indices: 1451928--1452147 Score: 237
Period size: 34 Copynumber: 6.5 Consensus size: 33
1451918 TGGTAAAAAC
*
1451928 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
1451961 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* * *
1451995 CACCCATTTAATCAATAATGGTAAGCTATCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
1452029 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * **
1452063 CTCCCATTTAGTCAACAATGACAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATG-GTAACCTACCAAAT
*
1452097 CACCTATTTAATCAACAATAGGTAAACTACCAAAT
1 CACC-ATTTAATCAACAAT-GGTAACCTACCAAAT
1452132 CACCATTTAATCAACA
1 CACCATTTAATCAACA
1452148 CGACGTAGAT
Statistics
Matches: 156, Mismatches: 21, Indels: 19
0.80 0.11 0.10
Matches are distributed among these distances:
33 6 0.04
34 132 0.85
35 18 0.12
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:1452044 original size:68 final size:67
Alignment explanation
Indices: 1451930--1452147 Score: 267
Period size: 68 Copynumber: 3.2 Consensus size: 67
1451920 GTAAAAACCA
* * *
1451930 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
1451995 CAC
65 CAC
* * * * *
1451998 CCATTTAATCAATAATGGTAAGCTATCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
1452063 CTC
65 CAC
* * * * *
1452066 CCATTTAGTCAACAATGACAAACCACCAAATCACCTATTTAATCAACAATAGGTAAACTACCAAA
1 CCATTTAATCAACAATGGCAAACTACCAAATTACC-ATTTAATCAACAAT-GGTAAGCTACCAAA
1452131 TCA-
64 TCAC
1452134 CCATTTAATCAACA
1 CCATTTAATCAACA
1452148 CGACGTAGAT
Statistics
Matches: 127, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
67 3 0.02
68 109 0.86
69 15 0.12
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:1452107 original size:102 final size:102
Alignment explanation
Indices: 1451928--1452147 Score: 316
Period size: 102 Copynumber: 2.2 Consensus size: 102
1451918 TGGTAAAAAC
** *
1451928 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGACAAACCACCAA
* * *
1451993 ATCACCCATTTAATCAATAAT-GGTAAGCTATCAAAT
66 ATCACCCATTTAATCAACAATAGGTAAACTACCAAAT
** * * *
1452029 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGACAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGACAAACCACCA
*
1452094 AATCACCTATTTAATCAACAATAGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATAGGTAAACTACCAAAT
1452132 CACCATTTAATCAACA
1 CACCATTTAATCAACA
1452148 CGACGTAGAT
Statistics
Matches: 103, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
101 1 0.01
102 88 0.85
103 14 0.14
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (102 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGACAAACCACCAA
ATCACCCATTTAATCAACAATAGGTAAACTACCAAAT
Found at i:1453674 original size:23 final size:24
Alignment explanation
Indices: 1453648--1453700 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1453638 GGTTAAACTT
*
1453648 AAAATATTATTT-AATTTAATAAA
1 AAAATATTATTTAAATCTAATAAA
* *
1453671 AAAATTTTATTTAAATCTAATTAA
1 AAAATATTATTTAAATCTAATAAA
1453695 AAAATA
1 AAAATA
1453701 ATTAAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
AAAATATTATTTAAATCTAATAAA
Found at i:1457001 original size:21 final size:22
Alignment explanation
Indices: 1456961--1457008 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
1456951 AAAATTTTTT
* *
1456961 TATTTTAATTTATTTATAAAAA
1 TATTTTAAATTATGTATAAAAA
1456983 TATTTTAAATTA-GTATAAAAA
1 TATTTTAAATTATGTATAAAAA
1457004 TATTT
1 TATTT
1457009 GTGACATCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TATTTTAAATTATGTATAAAAA
Found at i:1460027 original size:2 final size:2
Alignment explanation
Indices: 1460020--1460056 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1460010 TTTGAAGTAT
1460020 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1460057 TAATTACGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1460503 original size:3 final size:3
Alignment explanation
Indices: 1460495--1460519 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1460485 ATTTTACGTG
1460495 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
1460520 GATAATTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1460893 original size:19 final size:19
Alignment explanation
Indices: 1460871--1460929 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
1460861 ATTTAAAAAT
1460871 TATTATATTATTTAATTAA
1 TATTATATTATTTAATTAA
*
1460890 TATTTTA-TATTTTAATATAGA
1 TATTATATTA-TTTAAT-TA-A
* *
1460911 T-TTAAATTTTTTAATTAA
1 TATTATATTATTTAATTAA
1460929 T
1 T
1460930 TTTTTATGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
18 4 0.12
19 14 0.44
20 11 0.34
21 3 0.09
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TATTATATTATTTAATTAA
Found at i:1460943 original size:19 final size:19
Alignment explanation
Indices: 1460881--1460944 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
1460871 TATTATATTA
*
1460881 TTTAATTAATATTTTATAT
1 TTTAATTAATTTTTTATAT
** *
1460900 TTTAATATAGA-TTTAAATTT
1 TTTAAT-TA-ATTTTTTATAT
*
1460920 TTTAATTAATTTTTTATGT
1 TTTAATTAATTTTTTATAT
1460939 TTTAAT
1 TTTAAT
1460945 ATACTGAAGA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
18 1 0.03
19 20 0.57
20 13 0.37
21 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTAATTAATTTTTTATAT
Found at i:1469671 original size:51 final size:51
Alignment explanation
Indices: 1469603--1469703 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 51
1469593 ATTTCAACTA
*
1469603 AAGCTATCCTTAATAACTATTCTTGGGCCTTATCATTTAGATTCCAATTTG
1 AAGCTATCCTTAATAACTATTCTTGGGCCTTATCATTTAGATGCCAATTTG
* ** *
1469654 AAGCTATCTCTT-CTAACTATTCTTGGGTTTTTTCATTTAGATGCCAATTT
1 AAGCTATC-CTTAATAACTATTCTTGGGCCTTATCATTTAGATGCCAATTT
1469704 CAACTAAAGC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 41 0.93
52 3 0.07
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.45
Consensus pattern (51 bp):
AAGCTATCCTTAATAACTATTCTTGGGCCTTATCATTTAGATGCCAATTTG
Found at i:1469880 original size:57 final size:56
Alignment explanation
Indices: 1469655--1469972 Score: 153
Period size: 56 Copynumber: 5.7 Consensus size: 56
1469645 TCCAATTTGA
* * * * * * *
1469655 AGCTATCTCTT-CTAACTA-TTCTTGGGTTTTTTCATTTAGATGCCAATTTCAACTAA
1 AGCTATCT-TTACTAGCTACTT-TTGGGCTTTCTCATTTTGGTGACAATTTCAACTAG
* * * * *** * *
1469711 AGCTATCCTTACCAGCTAATCTTAAACTTT-TCCATTTTAGTG-CAAATTTCAACTGG
1 AGCTATCTTTACTAGCTACTTTTGGGCTTTCT-CATTTTGGTGAC-AATTTCAACTAG
** * * * ** * * ** *
1469767 AGCTATCCGTGCTAGTTACTCTTAAGCTTTCTCAATTGGGTGTGAATTTCACCTAG
1 AGCTATCTTTACTAGCTACTTTTGGGCTTTCTCATTTTGGTGACAATTTCAACTAG
* *
1469823 AGCTATCTTTATTAGCTACTTTTGGGCTATTCTCATTTTGGT-ACTAATTTTAACTAG
1 AGCTATCTTTACTAGCTACTTTTGGGCT-TTCTCATTTTGGTGAC-AATTTCAACTAG
* * * ** * * ** *
1469880 AGTTATCATTACCAATTACTCTTGGGCTTTCTTATTTTGGTGACAATTTCAGTTAA
1 AGCTATCTTTACTAGCTACTTTTGGGCTTTCTCATTTTGGTGACAATTTCAACTAG
* *
1469936 AGCTATCTTTGCTGGCTA-TTATTGGGCTTTCTCATTT
1 AGCTATCTTTACTAGCTACTT-TTGGGCTTTCTCATTT
1469973 AAAATTTGAT
Statistics
Matches: 192, Mismatches: 60, Indels: 20
0.71 0.22 0.07
Matches are distributed among these distances:
55 5 0.03
56 141 0.73
57 46 0.24
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.43
Consensus pattern (56 bp):
AGCTATCTTTACTAGCTACTTTTGGGCTTTCTCATTTTGGTGACAATTTCAACTAG
Found at i:1472518 original size:19 final size:18
Alignment explanation
Indices: 1472451--1472520 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 18
1472441 CAAATAATTA
1472451 TTTTAATATTTAAAATATT
1 TTTTAATA-TTAAAATATT
*
1472470 TTTACTCAATATTAAAATATAG
1 TTT--T-AATATTAAAATAT-T
**
1472492 TTAAAATATTAAAATAATT
1 TTTTAATATTAAAAT-ATT
1472511 TTTTAATATT
1 TTTTAATATT
1472521 TTATATTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 22 0.55
20 2 0.05
21 10 0.25
22 6 0.15
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (18 bp):
TTTTAATATTAAAATATT
Found at i:1472792 original size:22 final size:22
Alignment explanation
Indices: 1472777--1472823 Score: 78
Period size: 21 Copynumber: 2.1 Consensus size: 22
1472767 TATAGTATAA
1472777 TTATTATTTAAATATATATTAAT
1 TTATTA-TTAAATATATATTAAT
1472800 TTATTATTAAATATA-ATTAAT
1 TTATTATTAAATATATATTAAT
1472821 TTA
1 TTA
1472824 AGTATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 9 0.38
22 9 0.38
23 6 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATTATTAAATATATATTAAT
Found at i:1474936 original size:21 final size:21
Alignment explanation
Indices: 1474912--1474957 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1474902 TTTAATATAA
1474912 TAATAATAATTAT-TTAAATTT
1 TAAT-ATAATTATATTAAATTT
* *
1474933 TAATATATTTATATTATATTT
1 TAATATAATTATATTAAATTT
1474954 TAAT
1 TAAT
1474958 TATTTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATATAATTATATTAAATTT
Found at i:1476453 original size:19 final size:19
Alignment explanation
Indices: 1476429--1476468 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1476419 GTAAAGTAAG
1476429 ATAAATATTAATAATAATA
1 ATAAATATTAATAATAATA
* *
1476448 ATAAATATTTATAATGATA
1 ATAAATATTAATAATAATA
1476467 AT
1 AT
1476469 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (19 bp):
ATAAATATTAATAATAATA
Found at i:1479071 original size:21 final size:22
Alignment explanation
Indices: 1479030--1479086 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
1479020 TTGATATTTC
1479030 AAATTTTAAATTTTATTTTTTA
1 AAATTTTAAATTTTATTTTTTA
*
1479052 AAATTTT-TATTTT-TTATTTTA
1 AAATTTTAAATTTTATT-TTTTA
1479073 AAATTTATAAATTT
1 AAATTT-TAAATTT
1479087 CAAGAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 2 0.07
21 16 0.53
22 8 0.27
23 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
AAATTTTAAATTTTATTTTTTA
Found at i:1479172 original size:26 final size:26
Alignment explanation
Indices: 1479125--1479180 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1479115 CTTTGGAAAT
* *
1479125 TTTTTATTTTAATGTACATTTTTCAA
1 TTTTTATTTTAATATACATTTTTAAA
*
1479151 TTTTTATTTTACATATA-TTTTTTAAA
1 TTTTTATTTTA-ATATACATTTTTAAA
1479177 TTTT
1 TTTT
1479181 CAAAATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (26 bp):
TTTTTATTTTAATATACATTTTTAAA
Found at i:1479292 original size:18 final size:19
Alignment explanation
Indices: 1479269--1479306 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1479259 TTTTTTAAAA
1479269 AAAATACTTTGA-AAATTT
1 AAAATACTTTGAGAAATTT
* *
1479287 AAAATATTTTTAGAAATTT
1 AAAATACTTTGAGAAATTT
1479306 A
1 A
1479307 TTTTGAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (19 bp):
AAAATACTTTGAGAAATTT
Found at i:1479533 original size:9 final size:9
Alignment explanation
Indices: 1479519--1479548 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1479509 AATTTAGATT
1479519 ATATTTAAA
1 ATATTTAAA
1479528 ATATTTAAAA
1 ATATTT-AAA
1479538 ATATTTAAA
1 ATATTTAAA
1479547 AT
1 AT
1479549 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
ATATTTAAA
Found at i:1479540 original size:10 final size:10
Alignment explanation
Indices: 1479519--1479547 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1479509 AATTTAGATT
1479519 ATATTT-AAA
1 ATATTTAAAA
1479528 ATATTTAAAA
1 ATATTTAAAA
1479538 ATATTTAAAA
1 ATATTTAAAA
1479548 TTTTTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATTTAAAA
Found at i:1480102 original size:17 final size:17
Alignment explanation
Indices: 1480054--1480102 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1480044 TAAATCAGCC
1480054 TTTCTTTATTTGTTTCTTA
1 TTTCTTT-TTT-TTTCTTA
* * *
1480073 TTCCTATTTTTTTCTTG
1 TTTCTTTTTTTTTCTTA
1480090 TTTCTTTTTTTTT
1 TTTCTTTTTTTTT
1480103 TTTTTTTGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 17 0.68
18 3 0.12
19 5 0.20
ACGTcount: A:0.06, C:0.12, G:0.04, T:0.78
Consensus pattern (17 bp):
TTTCTTTTTTTTTCTTA
Found at i:1480537 original size:28 final size:26
Alignment explanation
Indices: 1480489--1480554 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 26
1480479 GGGATAATTT
*
1480489 TAATATAAAAAAATTAAAATATAATA
1 TAATATAAAAAAAATAAAATATAATA
*
1480515 TAATATAAAAAATAATATAAATATGATA
1 TAATATAAAAAA-AATA-AAATATAATA
1480543 TAAATATAAAAA
1 T-AATATAAAAA
1480555 TTTATTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 12 0.34
27 3 0.09
28 10 0.29
29 10 0.29
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (26 bp):
TAATATAAAAAAAATAAAATATAATA
Found at i:1480555 original size:28 final size:27
Alignment explanation
Indices: 1480489--1480579 Score: 89
Period size: 28 Copynumber: 3.3 Consensus size: 27
1480479 GGGATAATTT
1480489 TAATATAAAAA-AATTAAAATATAATA
1 TAATATAAAAATAATTAAAATATAATA
*
1480515 TAATATAAAAAATAA-TATAAATATGATA
1 TAATAT-AAAAATAATTA-AAATATAATA
* *
1480543 TAAATATAAAAATTTATTAAAAT-TTATA
1 T-AATATAAAAA-TAATTAAAATATAATA
*
1480571 TAACATAAA
1 TAATATAAA
1480580 TTAATAATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
26 6 0.11
27 14 0.25
28 22 0.40
29 11 0.20
30 2 0.04
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (27 bp):
TAATATAAAAATAATTAAAATATAATA
Found at i:1480605 original size:16 final size:16
Alignment explanation
Indices: 1480558--1480607 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
1480548 ATAAAAATTT
1480558 ATTAAAATTTATATAA
1 ATTAAAATTTATATAA
*
1480574 CA-T-AAATTAATAATAA
1 -ATTAAAATTTAT-ATAA
1480590 ATTAAAATTTATATAA
1 ATTAAAATTTATATAA
1480606 AT
1 AT
1480608 ATGTAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 8 0.29
16 12 0.43
17 8 0.29
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTAAAATTTATATAA
Found at i:1480794 original size:21 final size:21
Alignment explanation
Indices: 1480764--1480803 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1480754 TTATCTAAAT
*
1480764 TATATATATATATTTAAAAAA
1 TATATATATAAATTTAAAAAA
*
1480785 TATATTTATAAATTTAAAA
1 TATATATATAAATTTAAAA
1480804 CAACACGTAA
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATATATATAAATTTAAAAAA
Found at i:1482159 original size:3 final size:3
Alignment explanation
Indices: 1482151--1482201 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
1482141 CTCAAAAGTC
1482151 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1482199 TAT
1 TAT
1482202 ATGAATGTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1482216 original size:2 final size:2
Alignment explanation
Indices: 1482209--1482239 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1482199 TATATGAATG
*
1482209 TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1482240 TTCTTTTACG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1483564 original size:17 final size:16
Alignment explanation
Indices: 1483519--1483555 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1483509 AATTAATTAA
1483519 TATTTAATAA-AA-TTT
1 TATTTAA-AATAATTTT
1483534 TATTTAAAATAATTTT
1 TATTTAAAATAATTTT
1483550 TATTTA
1 TATTTA
1483556 TAATTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.10
15 9 0.45
16 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTTAAAATAATTTT
Found at i:1484365 original size:29 final size:31
Alignment explanation
Indices: 1484331--1484403 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
1484321 AAAGTTTTTA
1484331 AAATAAATTTTT-GTGCTTTTATTT-TATTC
1 AAATAAATTTTTAGTGCTTTTATTTATATTC
* ** *
1484360 AAATAAATTTTTATTTTTTTTATTTATATTT
1 AAATAAATTTTTAGTGCTTTTATTTATATTC
*
1484391 AAATAAATCTTTA
1 AAATAAATTTTTA
1484404 TTTTAAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 12 0.32
30 9 0.24
31 16 0.43
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (31 bp):
AAATAAATTTTTAGTGCTTTTATTTATATTC
Found at i:1484398 original size:31 final size:30
Alignment explanation
Indices: 1484347--1484407 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 30
1484337 ATTTTTGTGC
*
1484347 TTTTATTTTATTCAAATAAATTTTTATTTT
1 TTTTATTTTATTCAAATAAATCTTTATTTT
*
1484377 TTTTATTTATATTTAAATAAATCTTTATTTT
1 TTTTATTT-TATTCAAATAAATCTTTATTTT
1484408 AAATAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 8 0.29
31 20 0.71
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (30 bp):
TTTTATTTTATTCAAATAAATCTTTATTTT
Found at i:1485004 original size:18 final size:18
Alignment explanation
Indices: 1484949--1485005 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
1484939 TATTATATTG
**
1484949 AATAATTAATTAATAAAA
1 AATAATTAATTAATTTAA
*
1484967 AATTATTAA-TAATTTTTAA
1 AATAATTAATTAA--TTTAA
1484986 AATAATTAATTAATTTAA
1 AATAATTAATTAATTTAA
1485004 AA
1 AA
1485006 AAAAGCAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
17 3 0.09
18 15 0.47
19 11 0.34
20 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATAATTAATTAATTTAA
Found at i:1486621 original size:2 final size:2
Alignment explanation
Indices: 1486614--1486639 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1486604 ATACTAGTGT
1486614 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1486640 GTACAGAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1487570 original size:14 final size:14
Alignment explanation
Indices: 1487551--1487585 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1487541 TAACTAATTA
1487551 ATTTTAATAAAAAT
1 ATTTTAATAAAAAT
**
1487565 ATTTTAATAAATTT
1 ATTTTAATAAAAAT
1487579 ATTTTAA
1 ATTTTAA
1487586 AATTAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTTTAATAAAAAT
Found at i:1487668 original size:16 final size:16
Alignment explanation
Indices: 1487649--1487680 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1487639 AATTAGAATA
*
1487649 TAATTTAATAATAATT
1 TAATTTAAAAATAATT
1487665 TAATTTAAAAATAATT
1 TAATTTAAAAATAATT
1487681 AAATATAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAATTTAAAAATAATT
Found at i:1487866 original size:28 final size:26
Alignment explanation
Indices: 1487843--1487907 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 26
1487833 CAAATTTTAA
1487843 AAAAATAAATATTTTTTA-AAAA-TT
1 AAAAATAAATATTTTTTATAAAATTT
1487867 AAAAATAAATTTATTTTTTATAAAAATTT
1 AAAAATAAA--TATTTTTTAT-AAAATTT
1487896 AAAAATAAATAT
1 AAAAATAAATAT
1487908 CAATTACCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
24 9 0.25
26 9 0.25
27 3 0.08
28 4 0.11
29 11 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AAAAATAAATATTTTTTATAAAATTT
Found at i:1488708 original size:2 final size:2
Alignment explanation
Indices: 1488703--1488736 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1488693 TCTCTCTCTC
*
1488703 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1488737 CACTTAATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1489203 original size:19 final size:20
Alignment explanation
Indices: 1489157--1489203 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
1489147 AATATTAAAA
* *
1489157 ATAAAATTTATTTTTTAATG
1 ATAAAATATATTTTTAAATG
* *
1489177 TTATAATATA-TTTTAAATG
1 ATAAAATATATTTTTAAATG
1489196 ATAAAATA
1 ATAAAATA
1489204 AGCTTTTCAA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
ATAAAATATATTTTTAAATG
Found at i:1489282 original size:19 final size:20
Alignment explanation
Indices: 1489250--1489289 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
1489240 AAGTAACTTT
1489250 TTTATTATCTAAAT-TTTAA
1 TTTATTATCTAAATATTTAA
1489269 TTTATTAT-TAAAATATTTAA
1 TTTATTATCT-AAATATTTAA
1489289 T
1 T
1489290 CTCACTATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.05
19 12 0.63
20 6 0.32
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTATTATCTAAATATTTAA
Found at i:1490187 original size:25 final size:24
Alignment explanation
Indices: 1490159--1490212 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
1490149 TAATCAAGTA
1490159 TTAAATATTAAA-ATTTAATTATGAT
1 TTAAATATTAAATA-TTAATTATG-T
* *
1490184 TTAATTATTAATTATTAATTATGT
1 TTAAATATTAAATATTAATTATGT
1490208 TTAAA
1 TTAAA
1490213 ATTTTAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 5 0.20
25 19 0.76
26 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
TTAAATATTAAATATTAATTATGT
Found at i:1490603 original size:13 final size:13
Alignment explanation
Indices: 1490585--1490638 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 13
1490575 ATTTTTAATT
1490585 TTATTAAATTATA
1 TTATTAAATTATA
1490598 TTATTAAATTATTA
1 TTATTAAATTA-TA
1490612 TTATT--ATTA-A
1 TTATTAAATTATA
1490622 TTAATTAAATTAT-
1 TT-ATTAAATTATA
1490635 TTAT
1 TTAT
1490639 ATTAATTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
10 3 0.08
11 3 0.08
12 6 0.17
13 17 0.47
14 7 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATTAAATTATA
Found at i:1490623 original size:16 final size:16
Alignment explanation
Indices: 1490592--1490635 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
1490582 ATTTTATTAA
1490592 ATTATATTATTAAATT
1 ATTATATTATTAAATT
1490608 ATTATTATTATT-AATT
1 ATTA-TATTATTAAATT
*
1490624 AATTAAATTATT
1 -ATTATATTATT
1490636 TATATTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTATATTATTAAATT
Found at i:1490657 original size:13 final size:13
Alignment explanation
Indices: 1490580--1490671 Score: 59
Period size: 13 Copynumber: 7.4 Consensus size: 13
1490570 TGTAAATTTT
1490580 TAATTTTATTAAA
1 TAATTTTATTAAA
* *
1490593 TTATATTATTAAA
1 TAATTTTATTAAA
* *
1490606 TTATTATTATT-AT
1 TAATT-TTATTAAA
*
1490619 TAA-TTAATTAAA
1 TAATTTTATTAAA
* *
1490631 TTA-TTTA-T-AT
1 TAATTTTATTAAA
1490641 TAATTTTATTAAA
1 TAATTTTATTAAA
*
1490654 TAATTTTAATAAA
1 TAATTTTATTAAA
*
1490667 AAATT
1 TAATT
1490672 AACATATATA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
10 3 0.05
11 9 0.15
12 8 0.13
13 35 0.58
14 5 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAATTTTATTAAA
Found at i:1490804 original size:13 final size:14
Alignment explanation
Indices: 1490775--1490818 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1490765 ACTTAATTTA
1490775 TTAATAATAAAAAT
1 TTAATAATAAAAAT
*
1490789 TTAATAAT-ATAAT
1 TTAATAATAAAAAT
*
1490802 TTAATAAATTAAAAT
1 TTAAT-AATAAAAAT
1490817 TT
1 TT
1490819 TAAAATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 9 0.35
14 11 0.42
15 6 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAATAATAAAAAT
Found at i:1491189 original size:17 final size:16
Alignment explanation
Indices: 1491167--1491202 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1491157 AAAATTAATT
1491167 ATTTATTTAACATAAAA
1 ATTTATTTAA-ATAAAA
*
1491184 ATTTATTTAAATATAA
1 ATTTATTTAAATAAAA
1491200 ATT
1 ATT
1491203 AAATATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTATTTAAATAAAA
Found at i:1491427 original size:14 final size:15
Alignment explanation
Indices: 1491387--1491430 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
1491377 GATTACAAAA
1491387 AAAAATTAATTTTATT
1 AAAAA-TAATTTTATT
* *
1491403 AAATATTATTTT-TT
1 AAAAATAATTTTATT
1491417 AAAAATAATTTTAT
1 AAAAATAATTTTAT
1491431 AAGTAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 12 0.52
15 7 0.30
16 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AAAAATAATTTTATT
Found at i:1491575 original size:8 final size:8
Alignment explanation
Indices: 1491562--1491590 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1491552 ATATTATATT
1491562 ATAAAATA
1 ATAAAATA
1491570 ATAAAA-A
1 ATAAAATA
1491577 ATAAAATA
1 ATAAAATA
1491585 ATAAAA
1 ATAAAA
1491591 ATATATTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
ATAAAATA
Found at i:1491580 original size:15 final size:15
Alignment explanation
Indices: 1491562--1491591 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1491552 ATATTATATT
1491562 ATAAAATAATAAAAA
1 ATAAAATAATAAAAA
1491577 ATAAAATAATAAAAA
1 ATAAAATAATAAAAA
1491592 TATATTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (15 bp):
ATAAAATAATAAAAA
Found at i:1492900 original size:29 final size:29
Alignment explanation
Indices: 1492865--1492964 Score: 134
Period size: 28 Copynumber: 3.4 Consensus size: 29
1492855 AGGTAATTGA
1492865 TATTTATTTTTAAATTTTTATAAAAA-ATT
1 TATTTATTTTTAAATTTTTA-AAAAATATT
1492894 TATTTATTTTT-AATTTTTAAAAAATATT
1 TATTTATTTTTAAATTTTTAAAAAATATT
*
1492922 TATTT-TTTTAAAATTTGATTAAAAATATATT
1 TATTTATTTTTAAATTT--TTAAAAA-ATATT
1492953 TATTTATTTTTA
1 TATTTATTTTTA
1492965 TATTAATTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
27 9 0.14
28 21 0.33
29 11 0.17
30 7 0.11
31 10 0.16
32 5 0.08
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (29 bp):
TATTTATTTTTAAATTTTTAAAAAATATT
Found at i:1492969 original size:27 final size:26
Alignment explanation
Indices: 1492886--1492970 Score: 66
Period size: 27 Copynumber: 3.0 Consensus size: 26
1492876 AAATTTTTAT
*
1492886 AAAAA-ATTTATTTATTTTTAATTTTTA
1 AAAAATATTTATTTATTTTT-A-TATTA
*
1492913 AAAAATATTTATTT-TTTTAAAATTTGATTA
1 AAAAATATTTATTTATTTT----TAT-ATTA
1492943 AAAATATATTTATTTATTTTTATATTA
1 AAAA-ATATTTATTTATTTTTATATTA
1492970 A
1 A
1492971 TTTTAAATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 16
0.71 0.05 0.24
Matches are distributed among these distances:
27 14 0.30
28 10 0.21
29 1 0.02
30 7 0.15
31 11 0.23
32 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (26 bp):
AAAAATATTTATTTATTTTTATATTA
Found at i:1493188 original size:14 final size:14
Alignment explanation
Indices: 1493169--1493213 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
1493159 TATATTAATT
1493169 TTAAAATAAATTTA
1 TTAAAATAAATTTA
**
1493183 TTAAAATATTTTTA
1 TTAAAATAAATTTA
* *
1493197 TTAAAATTAATTAA
1 TTAAAATAAATTTA
1493211 TTA
1 TTA
1493214 CTATTGTTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAAAATAAATTTA
Found at i:1496180 original size:17 final size:16
Alignment explanation
Indices: 1496131--1496189 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
1496121 AGTCATTGTG
*
1496131 AATTTGAATTATTTTGA
1 AATTTG-ATTATTTTTA
**
1496148 GTTTTGATTA-TTTTA
1 AATTTGATTATTTTTA
1496163 AATTTGAGTTATTTTTA
1 AATTTGA-TTATTTTTA
1496180 AATTTAGATT
1 AATTT-GATT
1496190 GATTAGTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 9 0.26
16 7 0.21
17 16 0.47
18 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.58
Consensus pattern (16 bp):
AATTTGATTATTTTTA
Found at i:1501708 original size:78 final size:73
Alignment explanation
Indices: 1501568--1501781 Score: 182
Period size: 78 Copynumber: 2.8 Consensus size: 73
1501558 ACGAGACCCT
* * **
1501568 AAACTCGGTATTAATGCAATATTACGTACATAACCATAAT-AGACATATATCAACATGAAAATTC
1 AAACTTGGTATTAATGCAATATTAC-TA-ATAACCCTAATGA-ACATATATTGACATG-AAATTC
1501632 TCACAA-GACCTTA
62 -C-CAATGACCTTA
*
1501645 GAAACTTGGTATTAATGCAATATTATCTCAATAACCCTAATGAACATATTTTGACATTGAAATTC
1 -AAACTTGGTATTAATGCAATATTA-CT-AATAACCCTAATGAACATATATTGACA-TGAAATTC
*
1501710 CCAATGACTTTA
62 CCAATGACCTTA
* * * * * *
1501722 AAGACTTGATTTTAA-GTAATATTACCTAAATAACTCTAGTGGACATATATTGACATGAAA
1 AA-ACTTGGTATTAATGCAATATTA-CT-AATAACCCTAATGAACATATATTGACATGAAA
1501782 ATTGCCACAT
Statistics
Matches: 115, Mismatches: 15, Indels: 15
0.79 0.10 0.10
Matches are distributed among these distances:
75 5 0.04
76 38 0.33
77 17 0.15
78 50 0.43
79 5 0.04
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (73 bp):
AAACTTGGTATTAATGCAATATTACTAATAACCCTAATGAACATATATTGACATGAAATTCCCAA
TGACCTTA
Found at i:1501784 original size:76 final size:78
Alignment explanation
Indices: 1501576--1501784 Score: 212
Period size: 76 Copynumber: 2.7 Consensus size: 78
1501566 CTAAACTCGG
* * * * **
1501576 TATTAATGCAATATTACGTACATAACCATAATAGACATATATCAACATGAAAATTCTCACAAGAC
1 TATTAATGCAATATTACCTAAATAACCCTAATGGACATATATTGACATGAAAATTCTCACAAGAC
*
1501641 CTTAGAAACTTGG
66 CTTAGAAACTTGA
* * * *
1501654 TATTAATGCAATATTATCTCAATAACCCTAATGAACATATTTTGACATTG-AAATTC-C-CAATG
1 TATTAATGCAATATTACCTAAATAACCCTAATGGACATATATTGACA-TGAAAATTCTCACAA-G
*
1501716 ACTTTA-AAGACTTGA
64 ACCTTAGAA-ACTTGA
* * * *
1501731 TTTTAA-GTAATATTACCTAAATAACTCTAGTGGACATATATTGACATGAAAATT
1 TATTAATGCAATATTACCTAAATAACCCTAATGGACATATATTGACATGAAAATT
1501785 GCCACATAAC
Statistics
Matches: 107, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
75 2 0.02
76 43 0.40
77 17 0.16
78 43 0.40
79 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (78 bp):
TATTAATGCAATATTACCTAAATAACCCTAATGGACATATATTGACATGAAAATTCTCACAAGAC
CTTAGAAACTTGA
Found at i:1508217 original size:21 final size:22
Alignment explanation
Indices: 1508193--1508233 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1508183 GACATGCTGT
1508193 AAATGCATGAAACAT-AGCTCA
1 AAATGCATGAAACATGAGCTCA
* *
1508214 AAATGTATGAATCATGAGCT
1 AAATGCATGAAACATGAGCT
1508234 GTTAGCATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (22 bp):
AAATGCATGAAACATGAGCTCA
Found at i:1510333 original size:55 final size:55
Alignment explanation
Indices: 1510198--1510906 Score: 946
Period size: 55 Copynumber: 12.9 Consensus size: 55
1510188 CGCATTTTTT
* * * *
1510198 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTT--AGTCCTCAAAAAGCAGGACGC
1 CTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACAC
* * * * *
1510252 CTTCTCCTTTTAAAGCCCACAAAAGTTGGTAGCA-CTTCCTAGTTCTCAAAGAGCAGGACGC
1 CTT-T-C----AAAGCCCACACAAGTTGGTGGCATTTTCC-AGTCCTCAAAGAGCAGGACAC
*
1510313 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
*
1510368 CTCTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
*
1510423 CTTTCAAAGCCCACCCAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* *
1510478 CTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCAAAGAGCAGGACAC
1 CT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACAC
1510533 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* *
1510588 CTCTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACCC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* * *
1510643 CTTTCGAAGCCCACACAAGTTGGTGGCATTTTCCAGTTCTCAAAGAGCAGGACCC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* *
1510698 CTTTCGAAGCCCACACAAGTTGGTGGCATTTTCCAGTTCTCAAAGAGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
1510753 CTTTCAAAGCCCACACAAGTTGGTGG-------CA-TCCTCAAAGAGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* * *
1510800 CTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGTAGGACGC
1 CT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACAC
* * *
1510855 CTTTCAAAGCCCACACCAGTTGGTGGCACTTTT-TAGTCCTCAATGAGCAGGA
1 CTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA
1510907 TACACTTTAT
Statistics
Matches: 595, Mismatches: 36, Indels: 47
0.88 0.05 0.07
Matches are distributed among these distances:
47 41 0.07
48 4 0.01
54 12 0.02
55 483 0.81
56 9 0.02
58 2 0.00
60 22 0.04
61 22 0.04
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (55 bp):
CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
Found at i:1510809 original size:47 final size:47
Alignment explanation
Indices: 1510736--1510882 Score: 179
Period size: 47 Copynumber: 3.0 Consensus size: 47
1510726 TTTTCCAGTT
1510736 CTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATC
1 CTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATC
1510783 CTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
1 CTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGG-------CA-TC
* * *
1510838 CTCAAAGAGTAGGACGCCTTTCAAAGCCCACACCAGTTGGTGGCA
1 CTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1510883 CTTTTTAGTC
Statistics
Matches: 87, Mismatches: 3, Indels: 19
0.80 0.03 0.17
Matches are distributed among these distances:
47 40 0.46
48 4 0.05
54 4 0.05
55 39 0.45
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (47 bp):
CTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATC
Found at i:1511732 original size:33 final size:33
Alignment explanation
Indices: 1511690--1511754 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
1511680 CAAAGAAATG
***
1511690 TATCGATACATTTTTCTGTGTATCGATACATTA
1 TATCGATACATGGATCTGTGTATCGATACATTA
*
1511723 TATCGATACATGGATCTTTGTATCGATACATT
1 TATCGATACATGGATCTGTGTATCGATACATT
1511755 TGGAAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (33 bp):
TATCGATACATGGATCTGTGTATCGATACATTA
Found at i:1514165 original size:51 final size:51
Alignment explanation
Indices: 1514104--1514201 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
1514094 AATTCTCCGC
* *
1514104 AATCAGGGATA-TCCCAACTTCGATTTCATTTTTAAAACA-CTAATTTTCTGT
1 AATCAGGGATACT-CCAACTCCGATTTCATTTCTAAAACATC-AATTTTCTGT
* *
1514155 AATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAATTTT
1 AATCAGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTT
1514202 TCATCGAGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
51 39 0.95
52 2 0.05
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (51 bp):
AATCAGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTCTGT
Found at i:1514240 original size:27 final size:27
Alignment explanation
Indices: 1514202--1514254 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1514192 CATCAATTTT
*
1514202 TCATCGAGGATACTCCACCCCCGTTAA
1 TCATCGAGGATACTCCAACCCCGTTAA
*
1514229 TCATCGGGGATACTCCAACCCCGTTA
1 TCATCGAGGATACTCCAACCCCGTTA
1514255 TTTTCAAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.36, G:0.17, T:0.23
Consensus pattern (27 bp):
TCATCGAGGATACTCCAACCCCGTTAA
Found at i:1514265 original size:28 final size:27
Alignment explanation
Indices: 1514209--1514277 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
1514199 TTTTCATCGA
* *
1514209 GGATACTCCACCCCCGTTAATCATCGG
1 GGATACTCCAACCCCGTTAATCATAGG
*
1514236 GGATACTCCAACCCCGTTATTTTCA-AGG
1 GGATACTCCAACCCCGTTA--ATCATAGG
1514264 GGATACTCCAACCC
1 GGATACTCCAACCC
1514278 TCGACTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 18 0.49
28 16 0.43
29 3 0.08
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (27 bp):
GGATACTCCAACCCCGTTAATCATAGG
Found at i:1514384 original size:80 final size:79
Alignment explanation
Indices: 1514231--1514593 Score: 316
Period size: 80 Copynumber: 4.6 Consensus size: 79
1514221 CCCGTTAATC
* * *
1514231 ATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCTCGACTTTATTTCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATCTCCAAGGGGATACTCCAACCC-CGACTTTATTTCCAAAA
* * *
1514296 TATTAATTTCTCATA
65 CATCAATTTCTCACA
* * *
1514311 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACTCCGATTTTATTTCCAAAAA
1 ATCGGGGATACTCCAACCCCGTTATCTCCAAGGGGATACTCCAACCCCGACTTTATTTCC-AAAA
* *
1514376 CACCAATTTTTCACA
65 CATCAATTTCTCACA
* * ** * * * *
1514391 ATTGAGGATACTCCAACCTTGTTAT-TTCATCGGGGATACTCCAACCCCGGCTTTATTCCCAAAA
1 ATCGGGGATACTCCAACCCCGTTATCTCCA-AGGGGATACTCCAACCCCGACTTTATTTCCAAAA
* ** *
1514455 TATTGATTTCTCATA
65 CATCAATTTCTCACA
** * * * * *** * * *
1514470 ATTAGGGATACTCCAACCCTGTTACCTCCGAGGGGATACTCTAATTTCGATTTTATTTCCTAATC
1 ATCGGGGATACTCCAACCCCGTTATCTCCAAGGGGATACTCCAACCCCGACTTTATTTCCAAAAC
* *
1514535 ATCGATTTTTCACA
66 ATCAATTTCTCACA
* * **
1514549 ACCGGAGATACTCCAACCCCGTTAT-TTTAAGGGGATACTCCAACC
1 ATCGGGGATACTCCAACCCCGTTATCTCCAAGGGGATACTCCAACC
1514594 TCGTTATTAT
Statistics
Matches: 220, Mismatches: 60, Indels: 8
0.76 0.21 0.03
Matches are distributed among these distances:
78 14 0.06
79 101 0.46
80 105 0.48
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATCTCCAAGGGGATACTCCAACCCCGACTTTATTTCCAAAAC
ATCAATTTCTCACA
Found at i:1514478 original size:159 final size:157
Alignment explanation
Indices: 1514235--1514626 Score: 486
Period size: 159 Copynumber: 2.5 Consensus size: 157
1514225 TTAATCATCG
* *
1514235 GGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCTCGACTTTATTTCTAAAATATT
1 GGGATACTCCAACCCCGTTA-TTTCAAGGGGATACTCCAACCCTCGACTTTATTCCCAAAATATT
* *
1514300 AATTTCTCATAATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACTCCGATTTT
65 AATTTCTCATAATCAGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACTCCGATTTT
**
1514365 ATTTCCAAAAACACCAATTTTTCACAATT
130 ATTTCC-AAAACACCAATTTTTCACAACC
** * *
1514394 GAGGATACTCCAACCTTGTTATTTCATCGGGGATACTCCAACCC-CGGCTTTATTCCCAAAATAT
1 G-GGATACTCCAACCCCGTTATTTCA-AGGGGATACTCCAACCCTCGACTTTATTCCCAAAATAT
* * * * * *
1514458 TGATTTCTCATAATTAGGGATACTCCAACCCTGTTACCTCCGAGGGGATACTCTAATTTCGATTT
64 TAATTTCTCATAATCAGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACTCCGATTT
* * * *
1514523 TATTTCCTAATCATCGATTTTTCACAACC
129 TATTTCCAAAACACCAATTTTTCACAACC
* *
1514552 GGAGATACTCCAACCCCGTTATTTTAAGGGGATACTCCAA-CCTCG-TTATTA-TCTCCAAAATA
1 GG-GATACTCCAACCCCGTTATTTCAAGGGGATACTCCAACCCTCGACT-TTATTC-CCAAAATA
1514614 TTAAATTTCTCAT
63 TT-AATTTCTCAT
1514627 CGGGACATAT
Statistics
Matches: 200, Mismatches: 26, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
156 5 0.03
157 29 0.14
158 46 0.23
159 87 0.44
160 33 0.17
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (157 bp):
GGGATACTCCAACCCCGTTATTTCAAGGGGATACTCCAACCCTCGACTTTATTCCCAAAATATTA
ATTTCTCATAATCAGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACTCCGATTTTA
TTTCCAAAACACCAATTTTTCACAACC
Found at i:1518096 original size:20 final size:20
Alignment explanation
Indices: 1518043--1518097 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1518033 TTCTCCAATT
* *
1518043 TGTATCGATACAATAAGTTAA
1 TGTATCGATAC-ATGAGTGAA
*
1518064 TGTATTGATACATGAGTGAA
1 TGTATCGATACATGAGTGAA
*
1518084 TGTATCAATACATG
1 TGTATCGATACATG
1518098 CTTGAAATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATGAGTGAA
Found at i:1520739 original size:53 final size:53
Alignment explanation
Indices: 1520681--1521323 Score: 521
Period size: 52 Copynumber: 12.4 Consensus size: 53
1520671 CCCAAAACAT
1520681 ATATAAAATATTTTTTAATTTTTTATTATTTTTAAATAGTAATTCAAGATTTA
1 ATATAAAATATTTTTTAATTTTTTATTATTTTTAAATAGTAATTCAAGATTTA
* **** * * * *
1520734 ATAT--AA-CTTTTTT-A-TTTTTA--AAAAGTAATTTG-AGTT-TA-A--TA
1 ATATAAAATATTTTTTAATTTTTTATTATTTTTAAATAGTAATTCAAGATTTA
* * *
1520775 ---TAAAATATTTTTAAATTTTTTATT-TTTTTAAATAGTAAATT-GAGATTTC
1 ATATAAAATATTTTTTAATTTTTTATTATTTTTAAATAGT-AATTCAAGATTTA
* * * *
1520824 ATATAAAATATTTTTAAATTTTTTATTATTTTTTAAAAAATAATTCAGGATTTA
1 ATATAAAATATTTTTTAATTTTTTATTA-TTTTTAAATAGTAATTCAAGATTTA
* * * * * * **
1520878 ACATCAAATA-TTTTTAATATGTTA--CTTTTTAAATAGTGATTTGAGATTTA
1 ATATAAAATATTTTTTAATTTTTTATTATTTTTAAATAGTAATTCAAGATTTA
** * *
1520928 ATATAAAATATATTTTTTAA-TTTTTATTA-TTTTAAATAGTGGTTTAAGATTTT
1 ATAT-AAA-ATATTTTTTAATTTTTTATTATTTTTAAATAGTAATTCAAGATTTA
** * * * *
1520981 ATATAAAATATTTTAAAATATTTTATTATTTTTAACA-A-TAATTTAGGATTCA
1 ATATAAAATATTTTTTAATTTTTTATTATTTTTAA-ATAGTAATTCAAGATTTA
* * *
1521033 ATATAAAATATTTTTT-ATTTTTTATTTTTTTTAAATAATAATTTAAGATTTA
1 ATATAAAATATTTTTTAATTTTTTATTATTTTTAAATAGTAATTCAAGATTTA
* * * *
1521085 ATATAAAATAGCTTTTAAAATTTTTATTATTTTTAAATAGTATTTCAAGATTTA
1 ATATAAAATA-TTTTTTAATTTTTTATTATTTTTAAATAGTAATTCAAGATTTA
* * *
1521139 ATATAAAATA-TTTATAAATTTTT-TTATTTTTTAAATAGTAATTCATGATTTA
1 ATATAAAATATTTTTTAATTTTTTATTA-TTTTTAAATAGTAATTCAAGATTTA
* * * **
1521191 ATGTAAAATGTTTTTAAATTTTTTATTATTTTTAAATAGTAATTTTAGATTTA
1 ATATAAAATATTTTTTAATTTTTTATTATTTTTAAATAGTAATTCAAGATTTA
* *
1521244 ATATAAAATATTTTTAAAAATTTTTTATTATTTTTTAAATAATAATTCAAGATTTA
1 ATATAAAATATTTTT--TAATTTTTTATTA-TTTTTAAATAGTAATTCAAGATTTA
* *
1521300 AAATAAAATATTTTTATTATTTTT
1 ATATAAAATATTTTT-TAATTTTT
1521324 AAATAATAAT
Statistics
Matches: 468, Mismatches: 86, Indels: 70
0.75 0.14 0.11
Matches are distributed among these distances:
38 1 0.00
40 2 0.00
41 7 0.01
42 1 0.00
43 7 0.01
44 6 0.01
45 3 0.01
46 10 0.02
47 1 0.00
48 6 0.01
49 2 0.00
50 29 0.06
51 33 0.07
52 129 0.28
53 107 0.23
54 68 0.15
55 20 0.04
56 36 0.08
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (53 bp):
ATATAAAATATTTTTTAATTTTTTATTATTTTTAAATAGTAATTCAAGATTTA
Found at i:1520753 original size:39 final size:39
Alignment explanation
Indices: 1520701--1520777 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
1520691 TTTTTTAATT
*
1520701 TTTTATTATTTTTAAATAGTAATTCAAGATTTAATATAAC
1 TTTTATTATTTTTAAAAAGTAATTCAAG-TTTAATATAAC
**
1520741 TTTT-TTATTTTTAAAAAGTAATTTGAGTTTAATATAA
1 TTTTATTATTTTTAAAAAGTAATTCAAGTTTAATATAA
1520778 AATATTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 10 0.29
39 20 0.59
40 4 0.12
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (39 bp):
TTTTATTATTTTTAAAAAGTAATTCAAGTTTAATATAAC
Found at i:1520841 original size:52 final size:51
Alignment explanation
Indices: 1520741--1521315 Score: 522
Period size: 52 Copynumber: 11.0 Consensus size: 51
1520731 TTAATATAAC
* *
1520741 TTTTTTA--TTTTTAAAAAGTAATTTGAG-TTTAATATAAAATATTTTTAAA
1 TTTTTTATTTTTTTAAATAGT-ATTTAAGATTTAATATAAAATATTTTTAAA
* * *
1520790 TTTTTTATTTTTTTAAATAGTAAATTGAGATTTCATATAAAATATTTTTAAA
1 TTTTTTATTTTTTTAAATAGT-ATTTAAGATTTAATATAAAATATTTTTAAA
* * * * * *
1520842 TTTTTTATTATTTTTTAAAAAATAATTCAGGATTTAACATCAAATATTTTT-AA
1 TTTTTTA-T-TTTTTTAAATAGT-ATTTAAGATTTAATATAAAATATTTTTAAA
* * * * *
1520895 TATGTTA-CTTTTTAAATAGTGATTTGAGATTTAATATAAAATATATTTTTTAA
1 TTTTTTATTTTTTTAAATAGT-ATTTAAGATTTAATAT-AAA-ATATTTTTAAA
* * * *
1520948 -TTTTTATTATTTTAAATAGTGGTTTAAGATTTTATATAAAATATTTTAAAA
1 TTTTTTATTTTTTTAAATAGT-ATTTAAGATTTAATATAAAATATTTTTAAA
* * * *
1520999 TATTTTATTATTTTTAACA-A-TAATTTAGGATTCAATATAAAATATTTTT-TA
1 TTTTTTATT-TTTTTAA-ATAGT-ATTTAAGATTTAATATAAAATATTTTTAAA
* *
1521050 TTTTTTATTTTTTTTAAATAATAATTTAAGATTTAATATAAAATAGCTTTTAAA
1 TTTTTTA-TTTTTTTAAATAGT-ATTTAAGATTTAATATAAAATA-TTTTTAAA
* *
1521104 ATTTTTATTATTTTTAAATAGTATTTCAAGATTTAATATAAAATATTTATAAA
1 TTTTTTATT-TTTTTAAATAGTATTT-AAGATTTAATATAAAATATTTTTAAA
* * * *
1521157 TTTTTT-TATTTTTTAAATAGTAATTCATGATTTAATGTAAAATGTTTTTAAA
1 TTTTTTAT-TTTTTTAAATAGT-ATTTAAGATTTAATATAAAATATTTTTAAA
*
1521209 TTTTTTATTATTTTTAAATAGTAATTTTAGATTTAATATAAAATATTTTTAAAAA
1 TTTTTTATT-TTTTTAAATAGT-ATTTAAGATTTAATATAAAATATTTTT--AAA
* * *
1521264 TTTTTTATTATTTTTTAAATAATAATTCAAGATTTAAAATAAAATATTTTTA
1 TTTTTTA-T-TTTTTTAAATAGT-ATTTAAGATTTAATATAAAATATTTTTA
1521316 TTATTTTTAA
Statistics
Matches: 434, Mismatches: 65, Indels: 49
0.79 0.12 0.09
Matches are distributed among these distances:
49 7 0.02
50 23 0.05
51 44 0.10
52 139 0.32
53 103 0.24
54 70 0.16
55 10 0.02
56 37 0.09
57 1 0.00
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (51 bp):
TTTTTTATTTTTTTAAATAGTATTTAAGATTTAATATAAAATATTTTTAAA
Found at i:1520868 original size:105 final size:106
Alignment explanation
Indices: 1520741--1521315 Score: 619
Period size: 105 Copynumber: 5.5 Consensus size: 106
1520731 TTAATATAAC
*
1520741 TTTT-TTA-TTTTTAAA-AAGTAATTTGAG-TTTAATATAAAATATTTTTAAATTTTTTATT-TT
1 TTTTATTATTTTTTAAATAA-TAATTTAAGATTTAATATAAAATATTTTTAAATTTTTTATTATT
* *
1520801 TTTAAATAGTAAATTGAGATTTCATATAAAATATTTTTAAATT
65 TTTAAATAGT-ATTTGAGATTTAATATAAAATATTTTTAAATT
* * * * * * * *
1520844 TTTTATTATTTTTTAAAAAATAATTCAGGATTTAACATCAAATATTTTT-AATATGTTA--CTTT
1 TTTTATTATTTTTTAAATAATAATTTAAGATTTAATATAAAATATTTTTAAATTTTTTATTATTT
*
1520906 TTAAATAGTGATTTGAGATTTAATATAAAATATATTTTTTAA-T
66 TTAAATAGT-ATTTGAGATTTAATAT-AAA-ATATTTTTAAATT
* ** * * *
1520949 TTTTATTA--TTTTAAATAGTGGTTTAAGATTTTATATAAAATATTTTAAAATATTTTATTATTT
1 TTTTATTATTTTTTAAATAATAATTTAAGATTTAATATAAAATATTTTTAAATTTTTTATTATTT
* *
1521012 TTAACA-A-TAATTT-AGGATTCAATATAAAATATTTTT-TATT
66 TTAA-ATAGT-ATTTGA-GATTTAATATAAAATATTTTTAAATT
* *
1521052 TTTTATT-TTTTTTAAATAATAATTTAAGATTTAATATAAAATAGCTTTTAAAATTTTTATTATT
1 TTTTATTATTTTTTAAATAATAATTTAAGATTTAATATAAAATA-TTTTTAAATTTTTTATTATT
* *
1521116 TTTAAATAGTATTTCAAGATTTAATATAAAATATTTATAAA-T
65 TTTAAATAGTATTT-GAGATTTAATATAAAATATTTTTAAATT
* * * * *
1521158 TTTT-TTATTTTTTAAATAGTAATTCATGATTTAATGTAAAATGTTTTTAAATTTTTTATTATTT
1 TTTTATTATTTTTTAAATAATAATTTAAGATTTAATATAAAATATTTTTAAATTTTTTATTATTT
*
1521222 TTAAATAGTAATTTTAGATTTAATATAAAATATTTTTAAAAATT
66 TTAAATAGT-ATTTGAGATTTAATATAAAATATTTTT--AAATT
* *
1521266 TTTTATTATTTTTTAAATAATAATTCAAGATTTAAAATAAAATATTTTTA
1 TTTTATTATTTTTTAAATAATAATTTAAGATTTAATATAAAATATTTTTA
1521316 TTATTTTTAA
Statistics
Matches: 394, Mismatches: 51, Indels: 48
0.80 0.10 0.10
Matches are distributed among these distances:
102 1 0.00
103 49 0.12
104 72 0.18
105 124 0.31
106 97 0.25
107 6 0.02
108 5 0.01
109 40 0.10
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (106 bp):
TTTTATTATTTTTTAAATAATAATTTAAGATTTAATATAAAATATTTTTAAATTTTTTATTATTT
TTAAATAGTATTTGAGATTTAATATAAAATATTTTTAAATT
Found at i:1520978 original size:157 final size:160
Alignment explanation
Indices: 1520741--1521315 Score: 667
Period size: 157 Copynumber: 3.6 Consensus size: 160
1520731 TTAATATAAC
*
1520741 TTTTT-TATTTTTAAAAAGTAATTTGAG-TTTAATATAAAATAT-TTTT-AAATTTTTTATT-TT
1 TTTTTATATTTTTAAATAGTAATTTGAGATTTAATATAAAATATATTTTAAAATTTTTTATTATT
* * *
1520801 TTTAAATAGTAAATTGAGATTTCATATAAAATATTTTTAAATTTTTTATTATTTTTTAAAAAATA
66 TTTAAATAGTAATTTAAGATTTAATATAAAATATTTTTAAATTTTTTATTATTTTTTAAAAAATA
* *
1520866 ATTCAGGATTTAACATCAAATATTTTTAAT
131 ATTCAGGATTTAATATAAAATATTTTTAAT
* * * * **
1520896 ATGTTA-CTTTTTAAATAGTGATTTGAGATTTAATATAAAATATATTTTTTAA-TTTTTATTA-T
1 TTTTTATATTTTTAAATAGTAATTTGAGATTTAATATAAAATATATTTTAAAATTTTTTATTATT
** * * * *
1520958 TTTAAATAGTGGTTTAAGATTTTATATAAAATATTTTAAAATATTTTATTA-TTTTT-AACAATA
66 TTTAAATAGTAATTTAAGATTTAATATAAAATATTTTTAAATTTTTTATTATTTTTTAAAAAATA
* * *
1521021 ATTTAGGATTCAATATAAAATATTTTTTAT
131 ATTCAGGATTTAATATAAAATATTTTTAAT
* * * **
1521051 TTTTTATTTTTTTTAAATAATAATTTAAGATTTAATATAAAATAGCTTTTAAAA-TTTTTATTAT
1 TTTTTA-TATTTTTAAATAGTAATTTGAGATTTAATATAAAATATATTTTAAAATTTTTTATTAT
* * *
1521115 TTTTAAATAGT-ATTTCAAGATTTAATATAAAATATTTATAAA-TTTTT-TTATTTTTTAAATAG
65 TTTTAAATAGTAATTT-AAGATTTAATATAAAATATTTTTAAATTTTTTATTATTTTTTAAAAAA
* * *
1521177 TAATTCATGATTTAATGTAAAATGTTTTTAAAT
129 TAATTCAGGATTTAATATAAAATATTTTT-AAT
*
1521210 TTTTTATTATTTTTAAATAGTAATTTTAGATTTAATATAAAATAT-TTTTAAAAATTTTTTATTA
1 TTTTTA-TATTTTTAAATAGTAATTTGAGATTTAATATAAAATATATTTT-AAAATTTTTTATTA
* * *
1521274 TTTTTTAAATAATAATTCAAGATTTAAAATAAAATATTTTTA
64 -TTTTTAAATAGTAATTTAAGATTTAATATAAAATATTTTTA
1521316 TTATTTTTAA
Statistics
Matches: 354, Mismatches: 50, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
155 56 0.16
156 23 0.06
157 116 0.33
158 67 0.19
159 47 0.13
160 9 0.03
161 33 0.09
162 3 0.01
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (160 bp):
TTTTTATATTTTTAAATAGTAATTTGAGATTTAATATAAAATATATTTTAAAATTTTTTATTATT
TTTAAATAGTAATTTAAGATTTAATATAAAATATTTTTAAATTTTTTATTATTTTTTAAAAAATA
ATTCAGGATTTAATATAAAATATTTTTAAT
Found at i:1521258 original size:44 final size:44
Alignment explanation
Indices: 1521258--1521364 Score: 146
Period size: 44 Copynumber: 2.4 Consensus size: 44
1521248 AAAATATTTT
* *
1521258 TAAAA-ATTTTTTATTATTTTTTAAATAATAATTCAAGATTTAAAA
1 TAAAATATT-TTTATTA-TTTTTAAATAATAATTTAAGATTTAATA
*
1521303 TAAAATATTTTTATTATTTTTAAATAATAATTTAAAATTTAATA
1 TAAAATATTTTTATTATTTTTAAATAATAATTTAAGATTTAATA
*
1521347 TAAAATATTTAT-TTATTT
1 TAAAATATTTTTATTATTT
1521365 ATTGATGGGT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
43 6 0.11
44 36 0.63
45 12 0.21
46 3 0.05
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (44 bp):
TAAAATATTTTTATTATTTTTAAATAATAATTTAAGATTTAATA
Found at i:1521668 original size:10 final size:10
Alignment explanation
Indices: 1521653--1521699 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 10
1521643 TAAATATTAT
1521653 ATATATTTTA
1 ATATATTTTA
1521663 ATATA-TTT-
1 ATATATTTTA
1521671 ATATATTTATA
1 ATATATTT-TA
*
1521682 TTATATTTTA
1 ATATATTTTA
1521692 AT-TATTTT
1 ATATATTTT
1521700 TAAAAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
8 5 0.16
9 11 0.34
10 9 0.28
11 7 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
ATATATTTTA
Found at i:1521686 original size:19 final size:18
Alignment explanation
Indices: 1521646--1521689 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
1521636 TTAATAATAA
1521646 ATATTATATATATTTTAAT
1 ATATT-TATATATTTTAAT
*
1521665 ATATTTATATATTTATATT
1 ATATTTATATATTT-TAAT
1521684 ATATTT
1 ATATTT
1521690 TAATTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATTTATATATTTTAAT
Found at i:1521696 original size:16 final size:16
Alignment explanation
Indices: 1521648--1521696 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 16
1521638 AATAATAAAT
1521648 ATTATA-TATATTTTA
1 ATTATATTATATTTTA
*
1521663 A-TATATT-TA-TATA
1 ATTATATTATATTTTA
*
1521676 TTTATATTATATTTTA
1 ATTATATTATATTTTA
1521692 ATTAT
1 ATTAT
1521697 TTTTAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 3 0.12
14 12 0.46
15 4 0.15
16 7 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATATTATATTTTA
Found at i:1524296 original size:33 final size:32
Alignment explanation
Indices: 1524218--1524394 Score: 104
Period size: 33 Copynumber: 5.6 Consensus size: 32
1524208 TATATAACAT
* *
1524218 AAATATAATAATTATCAATATA-AAA-ATA-TA
1 AAATAT-ATAAATATAAATATATAAATATATTA
* * *
1524248 ATATATAT-GACATAAATATATAAATATATTA
1 AAATATATAAATATAAATATATAAATATATTA
* *
1524279 AAATTTATATAATATAAAT-TATTAATATAATTA
1 AAATATATA-AATATAAATATATAAATAT-ATTA
*
1524312 AAATATATAAATATATAATATTTTAAATATAATTA
1 AAATATATAAATATA-AATA-TATAAATAT-ATTA
* * *
1524347 TAATACT-T-AA-A-AAATAT-TTAATATAATA
1 AAATA-TATAAATATAAATATATAAATATATTA
*
1524375 TAAATATATAAAAATAAATA
1 -AAATATATAAATATAAATA
1524395 ACAAATTTTT
Statistics
Matches: 115, Mismatches: 17, Indels: 28
0.72 0.11 0.17
Matches are distributed among these distances:
28 12 0.10
29 16 0.14
30 11 0.10
31 13 0.11
32 20 0.17
33 23 0.20
34 2 0.02
35 17 0.15
36 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.39
Consensus pattern (32 bp):
AAATATATAAATATAAATATATAAATATATTA
Found at i:1524306 original size:13 final size:14
Alignment explanation
Indices: 1524196--1524332 Score: 56
Period size: 15 Copynumber: 9.6 Consensus size: 14
1524186 TTAACTTTAA
*
1524196 ATATAATAT-GATT
1 ATATAATATAAATT
*
1524209 ATATAACATAAA-T
1 ATATAATATAAATT
*
1524222 ATAATAATTATCAA-T
1 AT-ATAA-TATAAATT
*
1524237 ATA-AAAATATAATAT
1 ATATAATATA-AAT-T
* *
1524252 ATATGACATAAATAT
1 ATATAATATAAAT-T
*
1524267 ATAAATATATTAAAATTT
1 ATATA-ATA-T-AAA-TT
1524285 ATATAATATAAATT
1 ATATAATATAAATT
1524299 AT-TAATAT-AATT
1 ATATAATATAAATT
*
1524311 A-A-AATATATAAAT
1 ATATAATATA-AATT
1524324 ATATAATAT
1 ATATAATAT
1524333 TTTAAATATA
Statistics
Matches: 95, Mismatches: 13, Indels: 30
0.69 0.09 0.22
Matches are distributed among these distances:
11 5 0.05
12 7 0.07
13 25 0.26
14 11 0.12
15 27 0.28
16 7 0.07
17 4 0.04
18 8 0.08
19 1 0.01
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (14 bp):
ATATAATATAAATT
Found at i:1524316 original size:24 final size:22
Alignment explanation
Indices: 1524260--1524358 Score: 76
Period size: 24 Copynumber: 4.2 Consensus size: 22
1524250 ATATATGACA
*
1524260 TAAATATATAAATATATTAAAATT
1 TAAA-ATATAAAT-TATTAATATT
1524284 TATATAATATAAATTATTAATATAAT
1 TA-A-AATATAAATTATTAATAT--T
*
1524310 TAAAATATATAAATATATAATATT
1 TAAAATATA-AATTAT-TAATATT
* *
1524334 TTAAATAT-AATTA-TAATACT
1 TAAAATATAAATTATTAATATT
1524354 TAAAA
1 TAAAA
1524359 AATATTTAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
20 10 0.16
22 4 0.06
24 24 0.38
25 15 0.24
26 10 0.16
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAATATAAATTATTAATATT
Found at i:1524346 original size:35 final size:34
Alignment explanation
Indices: 1524247--1524351 Score: 110
Period size: 33 Copynumber: 3.1 Consensus size: 34
1524237 ATAAAAATAT
* *
1524247 AATATATATGACATAAA-TATATAAATAT-ATTAA
1 AATATATATAATATAAATTAT-TAAATATAATTAA
*
1524280 AATTTATATAATATAAATTATT-AATATAATTAA
1 AATATATATAATATAAATTATTAAATATAATTAA
* *
1524313 AATATATA-AATATATAATATTTTAAATATAATTAT
1 AATATATATAATATA-AAT-TATTAAATATAATTAA
1524348 AATA
1 AATA
1524352 CTTAAAAAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
32 11 0.18
33 30 0.49
34 6 0.10
35 14 0.23
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (34 bp):
AATATATATAATATAAATTATTAAATATAATTAA
Found at i:1524380 original size:29 final size:31
Alignment explanation
Indices: 1524302--1524388 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 31
1524292 ATAAATTATT
*
1524302 AATATAATTAAAATATATAAATATATAATATTTTA
1 AATATAATTATAATATAT-AA-A-A-AATATTTTA
1524337 AATATAATTATAATACT-TAAAAAATA-TTT-
1 AATATAATTATAATA-TATAAAAAATATTTTA
1524366 AATATAA-TATAAATATATAAAAA
1 AATATAATTAT-AATATATAAAAA
1524389 TAAATAACAA
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
28 4 0.08
29 17 0.35
30 3 0.06
31 4 0.08
32 1 0.02
33 1 0.02
34 2 0.04
35 15 0.31
36 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (31 bp):
AATATAATTATAATATATAAAAAATATTTTA
Found at i:1524602 original size:6 final size:6
Alignment explanation
Indices: 1524591--1524633 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
1524581 TATGTAATTT
*
1524591 TTTATA TTTATA TTTATA -TTATT TTTATA -TTATA TTTA-A TTTA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTA
1524634 AAGTATTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 14 0.42
6 19 0.58
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTATA
Found at i:1524617 original size:11 final size:11
Alignment explanation
Indices: 1524591--1524628 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
1524581 TATGTAATTT
1524591 TTTATATTTATA
1 TTTATA-TTATA
*
1524603 TTTATATTATT
1 TTTATATTATA
1524614 TTTATATTATA
1 TTTATATTATA
1524625 TTTA
1 TTTA
1524629 ATTTAAAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 18 0.75
12 6 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTATATTATA
Found at i:1524617 original size:17 final size:16
Alignment explanation
Indices: 1524592--1524626 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1524582 ATGTAATTTT
1524592 TTATATTTATATTTATA
1 TTATATTTATA-TTATA
*
1524609 TTATTTTTATATTATA
1 TTATATTTATATTATA
1524625 TT
1 TT
1524627 TAATTTAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATATTTATATTATA
Found at i:1525328 original size:11 final size:12
Alignment explanation
Indices: 1525289--1525330 Score: 61
Period size: 13 Copynumber: 3.6 Consensus size: 12
1525279 CACAAATAAA
1525289 AAATTATAAAAT
1 AAATTATAAAAT
1525301 AATATTATAAAAT
1 AA-ATTATAAAAT
1525314 -AATTA-AAAAT
1 AAATTATAAAAT
1525324 AAATTAT
1 AAATTAT
1525331 TAACACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 5 0.19
11 9 0.33
12 3 0.11
13 10 0.37
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAATTATAAAAT
Found at i:1527014 original size:4 final size:4
Alignment explanation
Indices: 1527005--1527035 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1526995 TAAATTTTCT
1527005 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1527036 GATTGAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1527916 original size:29 final size:29
Alignment explanation
Indices: 1527874--1527975 Score: 70
Period size: 29 Copynumber: 3.7 Consensus size: 29
1527864 ATACAATCTC
**
1527874 AATATAAAAAAATAATTAAAATATGATAT
1 AATATAAATTAATAATTAAAATATGATAT
** *
1527903 AATATAAATTAAT-A--CGAATAAGATA-
1 AATATAAATTAATAATTAAAATATGATAT
* * *
1527928 AAAATATATTAATATATTAAAAT-TTATAT
1 AATATAAATTAATA-ATTAAAATATGATAT
* *
1527957 AACACAAATTAATAATTAA
1 AATATAAATTAATAATTAA
1527976 TTAAAATTTA
Statistics
Matches: 54, Mismatches: 14, Indels: 11
0.68 0.18 0.14
Matches are distributed among these distances:
25 11 0.20
26 8 0.15
27 1 0.02
28 9 0.17
29 25 0.46
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (29 bp):
AATATAAATTAATAATTAAAATATGATAT
Found at i:1528073 original size:15 final size:15
Alignment explanation
Indices: 1528055--1528113 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
1528045 TTTATTTTTA
1528055 TTTTATATTTAAAAT
1 TTTTATATTTAAAAT
* *
1528070 TTTTAAATATAAAAT
1 TTTTATATTTAAAAT
*
1528085 ATTTATAATTTTAAAA-
1 TTTTAT-A-TTTAAAAT
*
1528101 TTTTATACTTAAA
1 TTTTATATTTAAA
1528114 TAAACATACA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
14 5 0.14
15 18 0.51
16 6 0.17
17 6 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTATATTTAAAAT
Found at i:1528079 original size:17 final size:18
Alignment explanation
Indices: 1528059--1528104 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
1528049 TTTTTATTTT
1528059 ATATTTAAAATTTTTA-A
1 ATATTTAAAATTTTTATA
*
1528076 ATA--TAAAATATTTATA
1 ATATTTAAAATTTTTATA
1528092 AT-TTTAAAATTTT
1 ATATTTAAAATTTT
1528105 ATACTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
15 10 0.42
16 3 0.12
17 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATTTAAAATTTTTATA
Found at i:1528323 original size:20 final size:20
Alignment explanation
Indices: 1528298--1528343 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1528288 AAGAATTGAA
*
1528298 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
* **
1528318 GAGGGATGCTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
1528338 GAGGGA
1 GAGGGA
1528344 GCCTTTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.52, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:1528484 original size:27 final size:27
Alignment explanation
Indices: 1528419--1528489 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
1528409 AAACAAGCTT
* *
1528419 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
*
1528447 CCATTTTTGACAAACACAAA-ATAACTA
1 CCATTTTTGACAAACACAAAGA-AACCA
1528474 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
1528490 AATGGGTGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.24
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:1530411 original size:21 final size:22
Alignment explanation
Indices: 1530373--1530418 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1530363 ATCTGTTGAA
* **
1530373 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
1530394 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
1530416 ACT
1 ACT
1530419 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:1532897 original size:20 final size:20
Alignment explanation
Indices: 1532872--1532917 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1532862 AAGAATTGAA
*
1532872 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
* **
1532892 GAGGGATGCTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
1532912 GAGGGA
1 GAGGGA
1532918 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.52, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:1533068 original size:24 final size:27
Alignment explanation
Indices: 1532994--1533064 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
1532984 AAACAAGTCT
* *
1532994 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
1533022 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
1533049 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
1533065 AATAGATGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Done.