Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 181 of 182
Found at i:55261170 original size:65 final size:65
Alignment explanation
Indices: 55261077--55261400 Score: 503
Period size: 65 Copynumber: 5.0 Consensus size: 65
55261067 ATTGTAAGTT
* * * *
55261077 ATGTAAG-T-TGTAAGTT-ATGTATAATATTAATTAACTAACTTATGTAATTTAAGTATAATATT
1 ATGTAAGTTATGTAA-TTAATGTATAATATTAATTAATTAAGTCATGTAATTTATGTATAATATT
55261139 A
65 A
*
55261140 ATGTAAGTTATGTAATTAACGTATAATATTAATTAATTAAGTCATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTAATTAATGTATAATATTAATTAATTAAGTCATGTAATTTATGTATAATATTA
* *
55261205 ATGTAAATTATGTAATTAATGTATAATATTAATTAATTAAGTCATATAATTTATGTATAATATTA
1 ATGTAAGTTATGTAATTAATGTATAATATTAATTAATTAAGTCATGTAATTTATGTATAATATTA
* *
55261270 ATGTAAGTTATGTAATTAATGTATAATATTAATCAATTAAGTCATATAATTTATGTATAATATTA
1 ATGTAAGTTATGTAATTAATGTATAATATTAATTAATTAAGTCATGTAATTTATGTATAATATTA
* *
55261335 ATGCAAGTTATGTAA-TATATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATT
1 ATGTAAGTTATGTAATTA-ATGTATAATATTAATTAATTAAGTCATGTAATTTATGTATAATATT
55261399 A
65 A
55261400 A
1 A
55261401 ATAATCAAGT
Statistics
Matches: 243, Mismatches: 14, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
63 7 0.03
64 5 0.02
65 231 0.95
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (65 bp):
ATGTAAGTTATGTAATTAATGTATAATATTAATTAATTAAGTCATGTAATTTATGTATAATATTA
Found at i:55261405 original size:21 final size:22
Alignment explanation
Indices: 55261381--55261425 Score: 56
Period size: 25 Copynumber: 2.0 Consensus size: 22
55261371 TTAAGTTATG
55261381 TAAT-TTATGTATAATATTAAA
1 TAATATTATGTATAATATTAAA
55261402 TAATCAAGTTATGTATAATATTAA
1 TAAT--A-TTATGTATAATATTAA
55261426 TTTTTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.20
25 16 0.80
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (22 bp):
TAATATTATGTATAATATTAAA
Found at i:55264194 original size:20 final size:20
Alignment explanation
Indices: 55264156--55264195 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
55264146 TAAATTTTTG
55264156 TTTTTTATTTCCTTTTTATAA
1 TTTTTTATTT-CTTTTTATAA
55264177 TTTTTTATTT-TTTCTTATA
1 TTTTTTATTTCTTT-TTATA
55264196 CTTTGGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 5 0.28
21 10 0.56
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTTATTTCTTTTTATAA
Found at i:55264684 original size:90 final size:89
Alignment explanation
Indices: 55264534--55264770 Score: 406
Period size: 90 Copynumber: 2.7 Consensus size: 89
55264524 CACCCATAAA
* *
55264534 CCCTAAACACTATTTAATATATAATTTAAAAAACACTAATTAATCTAAA-CCTTAAACCCTAACT
1 CCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCC-TAAACCCTAACT
55264598 CGACCACGAATCACTAACCCCCAAC
65 CGACCACGAATCACTAACCCCCAAC
55264623 CCCTAAACATTATTTAATATATAAATTAAAAAAACACTAATTAATCTAAATCCTAAACCCTAACT
1 CCCTAAACATTATTTAATATATAAATT-AAAAAACACTAATTAATCTAAATCCTAAACCCTAACT
* *
55264688 CGACCCCGAATCACTAACCCCTAAC
65 CGACCACGAATCACTAACCCCCAAC
55264713 CCCTAAACATTATTTAATATATAAA-TAAAAAACACTAATTAATCTAAATCCTAAACCC
1 CCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACCC
55264771 CTAGCTAACC
Statistics
Matches: 142, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
88 32 0.23
89 26 0.18
90 82 0.58
91 2 0.01
ACGTcount: A:0.46, C:0.27, G:0.02, T:0.26
Consensus pattern (89 bp):
CCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACCCTAACTC
GACCACGAATCACTAACCCCCAAC
Found at i:55264793 original size:88 final size:87
Alignment explanation
Indices: 55264525--55264813 Score: 387
Period size: 90 Copynumber: 3.3 Consensus size: 87
55264515 CCCAAACCCC
* * * *
55264525 ACCCATAAACCCTAAACACTATTTAATATATAATTTAAAAAACACTAATTAATCTAAA-CCTTAA
1 ACCCCTAACCCCTAAACATTATTTAATATATAA-ATAAAAAACACTAATTAATCTAAATCC-TAA
55264589 ACCCTAACTCGACCACGAATCACTA
64 ACCCTAACTCGACC-CGAATCACTA
*
55264614 ACCCCCAACCCCTAAACATTATTTAATATATAAATTAAAAAAACACTAATTAATCTAAATCCTAA
1 ACCCCTAACCCCTAAACATTATTTAATATATAAA-T-AAAAAACACTAATTAATCTAAATCCTAA
55264679 ACCCTAACTCGACCCCGAATCACTA
64 ACCCTAACTCGA-CCCGAATCACTA
55264704 ACCCCTAACCCCTAAACATTATTTAATATATAAATAAAAAACACTAATTAATCTAAATCCTAAAC
1 ACCCCTAACCCCTAAACATTATTTAATATATAAATAAAAAACACTAATTAATCTAAATCCTAAA-
* *
55264769 CCCTAGCT-AACCC---T-A--A
65 CCCTAACTCGACCCGAATCACTA
*
55264785 ATCCCTAACCCCTAAACATTATTTAATAT
1 ACCCCTAACCCCTAAACATTATTTAATAT
55264814 TATATAATTT
Statistics
Matches: 186, Mismatches: 9, Indels: 18
0.87 0.04 0.08
Matches are distributed among these distances:
81 29 0.16
83 1 0.01
84 1 0.01
87 3 0.02
88 30 0.16
89 38 0.20
90 80 0.43
91 4 0.02
ACGTcount: A:0.45, C:0.27, G:0.02, T:0.26
Consensus pattern (87 bp):
ACCCCTAACCCCTAAACATTATTTAATATATAAATAAAAAACACTAATTAATCTAAATCCTAAAC
CCTAACTCGACCCGAATCACTA
Found at i:55264883 original size:85 final size:81
Alignment explanation
Indices: 55264713--55264886 Score: 183
Period size: 85 Copynumber: 2.1 Consensus size: 81
55264703 AACCCCTAAC
*
55264713 CCCTAAACATTATTTAATATATAAATAAAAAACACTAATTAATCTAAATCCTAAACCCCTAGCTA
1 CCCTAAACATTATTTAATATATAAATAAAAAACACTAATTAATCTAAATCCTAAACCCCTACCTA
* *
55264778 ACCCTAAATCCCTAAC
66 ACCCTAAATCCATAAA
* * * * *
55264794 CCCTAAACATTATTTAATATTATATAATTTAAAATATATTAATTAGTCTAAA-CACTAAA-CTCT
1 CCCTAAACATTATTTAATA-TATA-AA--TAAAAAACACTAATTAATCTAAATC-CTAAACCCCT
*
55264857 AACCTAACACC-GAATCCATAAA
61 -ACCTAAC-CCTAAATCCATAAA
55264879 CCCTAAAC
1 CCCTAAAC
55264887 TTCTAACATT
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
81 19 0.25
82 4 0.05
83 2 0.03
84 4 0.05
85 46 0.60
86 2 0.03
ACGTcount: A:0.45, C:0.24, G:0.02, T:0.29
Consensus pattern (81 bp):
CCCTAAACATTATTTAATATATAAATAAAAAACACTAATTAATCTAAATCCTAAACCCCTACCTA
ACCCTAAATCCATAAA
Found at i:55265540 original size:113 final size:114
Alignment explanation
Indices: 55265341--55266166 Score: 1134
Period size: 113 Copynumber: 7.3 Consensus size: 114
55265331 AGATAAAATG
* * * * * *
55265341 TTTTTGCGGCGC-TTTACAAAAAACGCCGCTAAAGGCATCAACATTAGCGGCGCTTATTCA-GAA
1 TTTTTGCGGCGCATTTA-AAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTT-TACATAAA
* * *
55265404 ACGCCGCTAAAGTCCCCAAAAACTCAGAAAACGGTGACGTTAGGCTTAGGC
64 ACGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
*
55265455 -TTTTGCGGCGCATTTAAAAAAACGCCACTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAAC
1 TTTTTGCGGCGCATTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAAC
*
55265519 GCCACTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
66 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
55265568 -TTTTGCGGCGCATTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAAC
1 TTTTTGCGGCGCATTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAAC
* * *
55265632 GCCACTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGCGTTTAGGC
66 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * * * *
55265681 TTTTTGCGGCGCTTTTGAGAAAACGCCGCTAAAGACCTCAGCATTAGCGGCGCTTT--ATAAATG
1 TTTTTGCGGCGCATTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAA-A
*
55265744 CGCCGCTAAAGACCCCCAAAAACTCAGAAAACGATGCCGTTGGGCTTAGGC
65 CGCCGCTAAAGA-CCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* *
55265795 TTTTTGCGGCGCATTTAAAAAAACGCCACTAAAGACCTGAACATTAGCGGCGCTTTACAT-AAAC
1 TTTTTGCGGCGCATTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAAC
* * *
55265859 GCCGCGAAAGACCCCAAAAACTCAGAAAATGGTGCCGTTGAGCTTAGGC
66 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * * *
55265908 TTTTTTGCGGCGC-TTTAAAAAAAATGCCGCTAAAGACATGATCATTAGCGGCACTTTACAT-AA
1 -TTTTTGCGGCGCATTT-AAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAA
* * *
55265971 ACGCCACTAAAGACCCC-AAAACTCAGAAAACGGTGCCGTTGGGTTTAGAC
64 ACGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * *
55266021 TTTTTGTGGCGCATTTAAAACAACGCCGCTAAAGACCTGA-CATTAGCGGCGCTTTTACAGAAAA
1 TTTTTGCGGCGCATTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGC-TTTACATAAAA
* * * *
55266085 CGCCGCTAAAGACCCCAAAAAATCAGAAAACGGTGCCGTTTGTCTTTGGC
65 CGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * *
55266135 TTTTTGCGGCGCTTTTATAAAAATGCCGCTAA
1 TTTTTGCGGCGCATTTAAAAAAACGCCGCTAA
55266167 TGCTTATTTT
Statistics
Matches: 636, Mismatches: 63, Indels: 26
0.88 0.09 0.04
Matches are distributed among these distances:
111 11 0.02
112 46 0.07
113 302 0.47
114 273 0.43
115 2 0.00
116 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (114 bp):
TTTTTGCGGCGCATTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAAC
GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
Found at i:55265994 original size:340 final size:338
Alignment explanation
Indices: 55265341--55266166 Score: 1189
Period size: 340 Copynumber: 2.4 Consensus size: 338
55265331 AGATAAAATG
* * *
55265341 TTTTTGCGGCGCTTTACAAAAAACGCCGCTAAAGGCATCAACATTAGCGGCGC-TTATTCAGAAA
1 TTTTTGCGGCGCTTT-TAAAAAACGCCGCTAAAGACCTC-ACATTAGCGGCGCTTTA-T-AGAAA
* *
55265405 CGCCGCTAAAGTCCCCAAAAACTCAGAAAACGGTGACGTTAGGCTTAGGC-TTTTGCGGCGCATT
62 CGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTAGGCTTAGGCTTTTTGCGGCGCATT
* *
55265469 TAAAAAAACGCCACTAAAGACCTGAGCATTAGCGGCGCTTTACATAAAACGCCACTAAAGACCCC
127 TAAAAAAACGCCACTAAAGACCTGAACATTAGCGGCGCTTTACATAAAACGCCACGAAAGACCCC
*
55265534 AAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTGCGGCGCATTTAAAAAAACGCCGCTAA
192 AAAAACTCAGAAAACGGTGCCGTTGAGCTTAGGCTTTTGCGGCGCATTTAAAAAAACGCCGCTAA
* *
55265599 AGACCTGAGCATTAGCGGCGCTTTACATAAAACGCCACTAAAGACCCCAAAAACTCAGAAAACGG
257 AGACATGAGCATTAGCGGCACTTTACATAAAACGCCACTAAAGACCCCAAAAACTCAGAAAACGG
*
55265664 TGCCGTTGCGTTTAGGC
322 TGCCGTTGCGTTTAGAC
* *
55265681 TTTTTGCGGCGCTTTTGAGAAAACGCCGCTAAAGACCTCAGCATTAGCGGCGCTTTATA-AATGC
1 TTTTTGCGGCGCTTTT-AAAAAACGCCGCTAAAGACCTCA-CATTAGCGGCGCTTTATAGAA-AC
* *
55265745 GCCGCTAAAGACCCCCAAAAACTCAGAAAACGATGCCGTTGGGCTTAGGCTTTTTGCGGCGCATT
63 GCCGCTAAAGA-CCCCAAAAACTCAGAAAACGGTGCCGTTAGGCTTAGGCTTTTTGCGGCGCATT
*
55265810 TAAAAAAACGCCACTAAAGACCTGAACATTAGCGGCGCTTTACAT-AAACGCCGCGAAAGACCCC
127 TAAAAAAACGCCACTAAAGACCTGAACATTAGCGGCGCTTTACATAAAACGCCACGAAAGACCCC
* *
55265874 AAAAACTCAGAAAATGGTGCCGTTGAGCTTAGGCTTTTTTGCGGCGC-TTTAAAAAAAATGCCGC
192 AAAAACTCAGAAAACGGTGCCGTTGAGCTTAGGC--TTTTGCGGCGCATTT-AAAAAAACGCCGC
*
55265938 TAAAGACATGATCATTAGCGGCACTTTACAT-AAACGCCACTAAAGACCCC-AAAACTCAGAAAA
254 TAAAGACATGAGCATTAGCGGCACTTTACATAAAACGCCACTAAAGACCCCAAAAACTCAGAAAA
*
55266001 CGGTGCCGTTGGGTTTAGAC
319 CGGTGCCGTTGCGTTTAGAC
* * * *
55266021 TTTTTGTGGCGCATTTAAAACAACGCCGCTAAAGACCTGACATTAGCGGCGCTTTTACAGAAAAC
1 TTTTTGCGGCGCTTTTAAAA-AACGCCGCTAAAGACCTCACATTAGCGGCGC-TTTATAG-AAAC
* * * * *
55266086 GCCGCTAAAGACCCCAAAAAATCAGAAAACGGTGCCGTTTGTCTTTGGCTTTTTGCGGCGCTTTT
63 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTAGGCTTAGGCTTTTTGCGGCGCATTT
* * *
55266151 ATAAAAATGCCGCTAA
128 AAAAAAACGCCACTAA
55266167 TGCTTATTTT
Statistics
Matches: 438, Mismatches: 35, Indels: 26
0.88 0.07 0.05
Matches are distributed among these distances:
338 2 0.00
339 28 0.06
340 260 0.59
341 95 0.22
342 53 0.12
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (338 bp):
TTTTTGCGGCGCTTTTAAAAAACGCCGCTAAAGACCTCACATTAGCGGCGCTTTATAGAAACGCC
GCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTAGGCTTAGGCTTTTTGCGGCGCATTTAAA
AAAACGCCACTAAAGACCTGAACATTAGCGGCGCTTTACATAAAACGCCACGAAAGACCCCAAAA
ACTCAGAAAACGGTGCCGTTGAGCTTAGGCTTTTGCGGCGCATTTAAAAAAACGCCGCTAAAGAC
ATGAGCATTAGCGGCACTTTACATAAAACGCCACTAAAGACCCCAAAAACTCAGAAAACGGTGCC
GTTGCGTTTAGAC
Found at i:55270692 original size:3 final size:3
Alignment explanation
Indices: 55270684--55270716 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
55270674 AACCGTAGGT
55270684 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
55270717 GCAGAGCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:55271893 original size:16 final size:16
Alignment explanation
Indices: 55271849--55271896 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
55271839 AACTACAATT
55271849 TATTAAATAAAA-ATTA
1 TATT-AATAAAATATTA
55271865 TATTAATTAAAATATTA
1 TATTAA-TAAAATATTA
*
55271882 TTTTAATAAAATATT
1 TATTAATAAAATATT
55271897 TAATTTCATG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 2 0.07
16 18 0.62
17 9 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATTAATAAAATATTA
Found at i:55271950 original size:18 final size:18
Alignment explanation
Indices: 55271927--55271965 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
55271917 TATTAATAAT
*
55271927 ATTTTATTAAATAAAAAA
1 ATTTTAATAAATAAAAAA
* *
55271945 ATTTTAATAATTAAAATA
1 ATTTTAATAAATAAAAAA
55271963 ATT
1 ATT
55271966 AACTATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTTAATAAATAAAAAA
Found at i:55276743 original size:24 final size:24
Alignment explanation
Indices: 55276714--55276767 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
55276704 CTGATGAAAG
* *
55276714 ATGAACTGTTAAATACATGCAGAA
1 ATGAACTGTTAAACACATACAGAA
* *
55276738 ATGAACCGTTCAACACATACAGAA
1 ATGAACTGTTAAACACATACAGAA
55276762 A-GAACT
1 ATGAACT
55276768 TACTTTTCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.20
Consensus pattern (24 bp):
ATGAACTGTTAAACACATACAGAA
Found at i:55281084 original size:24 final size:26
Alignment explanation
Indices: 55281026--55281084 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 26
55281016 AGCAATTGGC
* *
55281026 AAATGGTTAACTCAACAATATTAGTA
1 AAATTGTTAACTCAACAATATTACTA
* *
55281052 AAAAT-TTAACT-AACAATTTTACT-
1 AAATTGTTAACTCAACAATATTACTA
55281075 AAATTGTTAA
1 AAATTGTTAA
55281085 AATTACTCTC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
23 4 0.15
24 14 0.52
25 6 0.22
26 3 0.11
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (26 bp):
AAATTGTTAACTCAACAATATTACTA
Found at i:55282155 original size:21 final size:20
Alignment explanation
Indices: 55282125--55282164 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
55282115 TATAAAGCTT
*
55282125 ATTGAAGAGTGTTTTTATATA
1 ATTGAAGAGT-ATTTTATATA
*
55282146 ATTGATGAGTATTTTATAT
1 ATTGAAGAGTATTTTATAT
55282165 TTAAAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (20 bp):
ATTGAAGAGTATTTTATATA
Found at i:55282837 original size:3 final size:3
Alignment explanation
Indices: 55282829--55282874 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
55282819 TTCTCCGTCA
* *
55282829 CTC CTC CT- CTC CT- CTG CTC CTC CTC CTC CTC CTC CTC TTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
55282875 AGCATCCACG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.00, C:0.61, G:0.02, T:0.37
Consensus pattern (3 bp):
CTC
Found at i:55284890 original size:64 final size:65
Alignment explanation
Indices: 55284789--55284917 Score: 251
Period size: 64 Copynumber: 2.0 Consensus size: 65
55284779 TCTTTTAAAT
55284789 TTAAATTTGTTTTAATCAAATCTCTCCTCTTTCATATGTCGAAGATGTTTG-TTTTGTTGGACCG
1 TTAAATTTGTTTTAATCAAATCTCTCCTCTTTCATATGTCGAAGATGTTTGTTTTTGTTGGACCG
55284853 TTAAATTTGTTTTAATCAAATCTCTCCTCTTTCATATGTCGAAGATGTTTGTTTTTGTTGGACCG
1 TTAAATTTGTTTTAATCAAATCTCTCCTCTTTCATATGTCGAAGATGTTTGTTTTTGTTGGACCG
55284918 ATTGTCAATG
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
64 51 0.80
65 13 0.20
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.47
Consensus pattern (65 bp):
TTAAATTTGTTTTAATCAAATCTCTCCTCTTTCATATGTCGAAGATGTTTGTTTTTGTTGGACCG
Found at i:55291798 original size:13 final size:13
Alignment explanation
Indices: 55291780--55291805 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55291770 ATAATACTGG
55291780 GTTTTTGTTTTTT
1 GTTTTTGTTTTTT
55291793 GTTTTTGTTTTTT
1 GTTTTTGTTTTTT
55291806 TACCTTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (13 bp):
GTTTTTGTTTTTT
Found at i:55298442 original size:28 final size:28
Alignment explanation
Indices: 55298410--55298470 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
55298400 TAGTAATGAT
* * *
55298410 AAAAATTAAACTTAAATTT-TGAAATTTA
1 AAAAATAAAAC-TAAATTTCTGAAAATAA
55298438 AAAAATAAAACTAAATTTCTGAAAATAA
1 AAAAATAAAACTAAATTTCTGAAAATAA
55298466 AAAAA
1 AAAAA
55298471 AACTGTGGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (28 bp):
AAAAATAAAACTAAATTTCTGAAAATAA
Found at i:55301315 original size:21 final size:21
Alignment explanation
Indices: 55301291--55301334 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
55301281 ACATAAAAAG
*
55301291 ATAAAAATA-CCTTTAAATAAT
1 ATAAAAATATCC-TAAAATAAT
55301312 ATAAAAATATCCTAAAATAAT
1 ATAAAAATATCCTAAAATAAT
55301333 AT
1 AT
55301335 TTAATCTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAAAAATATCCTAAAATAAT
Found at i:55302111 original size:26 final size:26
Alignment explanation
Indices: 55302075--55302126 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
55302065 AAAATATAGA
55302075 GAGAGAATTCCTCTAAGAGTAATTTG
1 GAGAGAATTCCTCTAAGAGTAATTTG
55302101 GAGAGAATTCCTCTAAGAGTAATTTG
1 GAGAGAATTCCTCTAAGAGTAATTTG
55302127 AACTTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.31
Consensus pattern (26 bp):
GAGAGAATTCCTCTAAGAGTAATTTG
Found at i:55305084 original size:17 final size:18
Alignment explanation
Indices: 55305073--55305105 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55305063 TTTATATATG
55305073 GATATT-AATTATA-AAA
1 GATATTGAATTATATAAA
55305089 GATATTGAATTATATAA
1 GATATTGAATTATATAA
55305106 TTTTACATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 7 0.47
18 2 0.13
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (18 bp):
GATATTGAATTATATAAA
Found at i:55309054 original size:7 final size:7
Alignment explanation
Indices: 55309042--55309071 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
55309032 GAGGGGTTTT
55309042 AAAATTA
1 AAAATTA
55309049 AAAATTA
1 AAAATTA
55309056 AAAATT-
1 AAAATTA
55309062 AAAATTA
1 AAAATTA
55309069 AAA
1 AAA
55309072 CCATGTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTA
Found at i:55309058 original size:13 final size:14
Alignment explanation
Indices: 55309042--55309071 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
55309032 GAGGGGTTTT
55309042 AAAATTAAAAATTA
1 AAAATTAAAAATTA
55309056 AAAATT-AAAATTA
1 AAAATTAAAAATTA
55309069 AAA
1 AAA
55309072 CCATGTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAATTAAAAATTA
Found at i:55313744 original size:83 final size:83
Alignment explanation
Indices: 55313648--55313815 Score: 318
Period size: 83 Copynumber: 2.0 Consensus size: 83
55313638 AATTGATTTT
*
55313648 AACCTCATTTTAATCTGTTAATTTAGTTGATTATTAGTTTTTGAATAAATCGATTTATTTTATAT
1 AACCTCATCTTAATCTGTTAATTTAGTTGATTATTAGTTTTTGAATAAATCGATTTATTTTATAT
55313713 AATTTTTAAATGAATTAA
66 AATTTTTAAATGAATTAA
55313731 AACCTCATCTTAATCTGTTAATTTAGTTGATTATTAGTTTTTGAATAAATCGATTTATTTTATAT
1 AACCTCATCTTAATCTGTTAATTTAGTTGATTATTAGTTTTTGAATAAATCGATTTATTTTATAT
*
55313796 TATTTTTAAATGAATTAA
66 AATTTTTAAATGAATTAA
55313814 AA
1 AA
55313816 TATATTTATA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.35, C:0.07, G:0.08, T:0.50
Consensus pattern (83 bp):
AACCTCATCTTAATCTGTTAATTTAGTTGATTATTAGTTTTTGAATAAATCGATTTATTTTATAT
AATTTTTAAATGAATTAA
Found at i:55321181 original size:7 final size:7
Alignment explanation
Indices: 55321169--55321193 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
55321159 GTATAGGGAC
55321169 TAAATTT
1 TAAATTT
55321176 TAAATTT
1 TAAATTT
55321183 TAAATTT
1 TAAATTT
55321190 TAAA
1 TAAA
55321194 AGAGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TAAATTT
Found at i:55321691 original size:31 final size:31
Alignment explanation
Indices: 55321656--55321721 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
55321646 TTAATATGCC
* * *
55321656 ATTTGGTACTTGCATTTGACTTTAATGTTTA
1 ATTTGGTACTTGAATTTAACTTTAATGTTAA
55321687 ATTTGGTACTTGAATTTAACTTTAATGTTAA
1 ATTTGGTACTTGAATTTAACTTTAATGTTAA
55321718 ATTT
1 ATTT
55321722 AATACCCGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.52
Consensus pattern (31 bp):
ATTTGGTACTTGAATTTAACTTTAATGTTAA
Found at i:55325842 original size:23 final size:24
Alignment explanation
Indices: 55325808--55325867 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
55325798 ATCAGCTCAT
*
55325808 AAATATATTTGTT-TTATTATTAG
1 AAATATATTTGTTATTATAATTAG
*
55325831 AAATAT-TCTTGTTATTATAATTTG
1 AAATATAT-TTGTTATTATAATTAG
*
55325855 AAAAAATATTTGT
1 -AAATATATTTGT
55325868 AGGAAAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 1 0.03
23 11 0.37
24 8 0.27
25 9 0.30
26 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (24 bp):
AAATATATTTGTTATTATAATTAG
Found at i:55330713 original size:16 final size:16
Alignment explanation
Indices: 55330692--55330761 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
55330682 TTTGGTTCGC
*
55330692 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
55330708 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
55330724 TGTAATGGATTAGAGG
1 TGTAATGGATTAGAGG
* *
55330740 TGTAATAGAATAGAGG
1 TGTAATGGATTAGAGG
55330756 TGTAAT
1 TGTAAT
55330762 AGCAAATCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:55330796 original size:45 final size:41
Alignment explanation
Indices: 55330740--55330849 Score: 116
Period size: 45 Copynumber: 2.6 Consensus size: 41
55330730 GGATTAGAGG
*
55330740 TGTAATAGAATAGAGGTGTAATAGCAAATCAAATGTTTGGTT
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAAATGTTTGG-T
* * ***
55330782 GAATGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGT
1 ---TGTAATGGAATAGAGGTGTAATAGCAAATCAAATGTTTGGT
55330825 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
55330850 TAATGGAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
39 20 0.36
40 2 0.04
43 1 0.02
44 11 0.20
45 22 0.39
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (41 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAAATGTTTGGT
Found at i:55333816 original size:19 final size:19
Alignment explanation
Indices: 55333792--55333828 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
55333782 TTGTGTTTGT
*
55333792 TTAATGAAAAATGATTTAA
1 TTAATGAAAAATAATTTAA
*
55333811 TTAATGGAAAATAATTTA
1 TTAATGAAAAATAATTTA
55333829 TTGGTTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
TTAATGAAAAATAATTTAA
Found at i:55334128 original size:32 final size:36
Alignment explanation
Indices: 55334055--55334135 Score: 84
Period size: 35 Copynumber: 2.4 Consensus size: 36
55334045 TATTAATATA
* * *
55334055 ATTAAAATAATTATTTATTTTAATGAAATTAATGAAT
1 ATTAAAATAATTATTTATCTTAATAAAATT-ATGAAC
55334092 ATTAAAAT-ATTATTT-TCTTAATAAAATT-T-AAC
1 ATTAAAATAATTATTTATCTTAATAAAATTATGAAC
55334124 ATT--AATAATTAT
1 ATTAAAATAATTAT
55334136 AAAATGGAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
30 3 0.08
31 5 0.12
32 5 0.12
33 1 0.03
35 11 0.28
36 7 0.17
37 8 0.20
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.47
Consensus pattern (36 bp):
ATTAAAATAATTATTTATCTTAATAAAATTATGAAC
Found at i:55341700 original size:25 final size:27
Alignment explanation
Indices: 55341653--55341702 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
55341643 TTATTATTAT
*
55341653 TATTTAAAATATTTTATTTCATTTTAA
1 TATTTAAAATATTTTATTACATTTTAA
*
55341680 TATTTAATA-ATTTTA-TACATTTT
1 TATTTAAAATATTTTATTACATTTT
55341703 TTATTTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 6 0.29
27 8 0.38
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (27 bp):
TATTTAAAATATTTTATTACATTTTAA
Found at i:55343135 original size:30 final size:30
Alignment explanation
Indices: 55343101--55343158 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
55343091 AACATAATTT
*
55343101 AATAATATAAAAT-TATTAAAAATATATCAC
1 AATAA-ATAAAATATATTAAAAAAATATCAC
*
55343131 AATAACTAAAATATATTAAAAAAATATC
1 AATAAATAAAATATATTAAAAAAATATC
55343159 TTATTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (30 bp):
AATAAATAAAATATATTAAAAAAATATCAC
Found at i:55345118 original size:8 final size:8
Alignment explanation
Indices: 55345105--55345141 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
55345095 ACATGCATAT
55345105 ATATATAC
1 ATATATAC
55345113 ATATATAC
1 ATATATAC
*
55345121 ATACATAC
1 ATATATAC
*
55345129 ATATATAT
1 ATATATAC
55345137 ATATA
1 ATATA
55345142 AAGAAAAGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATATAC
Found at i:55352403 original size:19 final size:19
Alignment explanation
Indices: 55352379--55352417 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
55352369 ACTGATAAGC
*
55352379 TGAAGCTTAAT-TTAATATT
1 TGAAGCTCAATATT-ATATT
55352398 TGAAGCTCAATATTATATT
1 TGAAGCTCAATATTATATT
55352417 T
1 T
55352418 AAACTTGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (19 bp):
TGAAGCTCAATATTATATT
Found at i:55365200 original size:16 final size:15
Alignment explanation
Indices: 55365179--55365226 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
55365169 GATGTGAATA
55365179 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
55365195 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
55365210 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
55365226 A
1 A
55365227 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:55365202 original size:24 final size:24
Alignment explanation
Indices: 55365175--55365230 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
55365165 TAATGATGTG
*
55365175 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
55365199 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
55365223 AATAATAA
1 AATAATAA
55365231 TAATTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:55365209 original size:8 final size:8
Alignment explanation
Indices: 55365175--55365226 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
55365165 TAATGATGTG
*
55365175 AATAATAA
1 AATATTAA
55365183 AATATATAA
1 AATAT-TAA
55365192 AATA-TAA
1 AATATTAA
55365199 AATATTAA
1 AATATTAA
*
55365207 AATATCAA
1 AATATTAA
*
55365215 AATATTAG
1 AATATTAA
55365223 AATA
1 AATA
55365227 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:55365442 original size:22 final size:24
Alignment explanation
Indices: 55365379--55365443 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
55365369 CGTGATAATA
*
55365379 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAG-G
*
55365404 TTAAAAATACATACATAATATA-G
1 TTAAAAATATATACATAATATAGG
*
55365427 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
55365444 GATAACATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 13 0.36
23 3 0.08
25 20 0.56
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (24 bp):
TTAAAAATATATACATAATATAGG
Found at i:55365492 original size:27 final size:25
Alignment explanation
Indices: 55365462--55365545 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
55365452 GTAAAAAAAT
*
55365462 ATATATATATATAATATAATATTAA
1 ATATATATATATAATATAATATAAA
* * * *
55365487 AGATATATAAATAAAATAGTATAAA
1 ATATATATATATAATATAATATAAA
*
55365512 ATATATATATACGTAATATAGAATTTAAA
1 ATATATATATA--TAATAT--AATATAAA
55365541 ATATA
1 ATATA
55365546 CCTAATATAT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
25 29 0.64
27 5 0.11
29 11 0.24
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.37
Consensus pattern (25 bp):
ATATATATATATAATATAATATAAA
Found at i:55365500 original size:25 final size:25
Alignment explanation
Indices: 55365464--55365597 Score: 77
Period size: 25 Copynumber: 5.6 Consensus size: 25
55365454 AAAAAAATAT
*
55365464 ATATATATATAATATAATATTAAAG
1 ATATATAAATAATATAATATTAAAG
* * * *
55365489 ATATATAAATAAAATAGTATAAAAT
1 ATATATAAATAATATAATATTAAAG
* *
55365514 ATATATATACGTAATATAGA-ATTTAA-
1 ATATATA-A-ATAATATA-ATATTAAAG
** *
55365540 A-ATATACCTAATAT-AT-TAAAAG
1 ATATATAAATAATATAATATTAAAG
*
55365562 A-ATATATATAATATAATATT-AAG
1 ATATATAAATAATATAATATTAAAG
*
55365585 AAATAT-AATAATA
1 ATATATAAATAATA
55365598 ACAAAAAAGG
Statistics
Matches: 83, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
21 4 0.05
22 12 0.14
23 18 0.22
24 5 0.06
25 32 0.39
26 2 0.02
27 10 0.12
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.36
Consensus pattern (25 bp):
ATATATAAATAATATAATATTAAAG
Found at i:55366121 original size:30 final size:30
Alignment explanation
Indices: 55366085--55366259 Score: 305
Period size: 30 Copynumber: 5.8 Consensus size: 30
55366075 TAGGTACAAG
* *
55366085 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
55366115 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
55366145 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
55366175 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
55366205 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
55366235 TGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGT
55366260 TGAGAAAAGT
Statistics
Matches: 137, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 137 1.00
ACGTcount: A:0.22, C:0.03, G:0.50, T:0.25
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
Found at i:55378402 original size:7 final size:8
Alignment explanation
Indices: 55378390--55378423 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
55378380 ATAATAAAAT
55378390 ATAT-AAA
1 ATATCAAA
55378397 ATAT-AAA
1 ATATCAAA
55378404 ATATCAAA
1 ATATCAAA
55378412 ATATCAAA
1 ATATCAAA
55378420 ATAT
1 ATAT
55378424 TAGAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 11 0.42
8 15 0.58
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (8 bp):
ATATCAAA
Found at i:55378406 original size:24 final size:24
Alignment explanation
Indices: 55378379--55378434 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
55378369 TAATGATGTG
*
55378379 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
*
55378403 AAT-ATCAAAATATCAAAATATTAG
1 AATAAT-AAAATATCAAAATATTAA
55378427 AATAATAA
1 AATAATAA
55378435 TAATTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 8 0.30
24 17 0.63
25 2 0.07
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.29
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:55378430 original size:16 final size:15
Alignment explanation
Indices: 55378383--55378430 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
55378373 GATGTGAATA
55378383 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
*
55378399 ATAAAATATCAAAAT
1 ATAAAATATTAAAAT
*
55378414 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
55378430 A
1 A
55378431 ATAATAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 7 0.25
16 21 0.75
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:55378648 original size:22 final size:24
Alignment explanation
Indices: 55378585--55378649 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
55378575 CGTGATAATA
*
55378585 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAG-G
*
55378610 TTAAAAATACATACATAATATA-G
1 TTAAAAATATATACATAATATAGG
*
55378633 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
55378650 GATAACATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 13 0.36
23 3 0.08
25 20 0.56
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (24 bp):
TTAAAAATATATACATAATATAGG
Found at i:55378698 original size:27 final size:25
Alignment explanation
Indices: 55378668--55378751 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
55378658 GTAAAAAAAT
*
55378668 ATATATATATATAATATAATATTAA
1 ATATATATATATAATATAATATAAA
* * * *
55378693 AGATATATACATAAAATAGTATAAA
1 ATATATATATATAATATAATATAAA
*
55378718 ATATATATATACGTAATATAGAATTTAAA
1 ATATATATATA--TAATAT--AATATAAA
55378747 ATATA
1 ATATA
55378752 CCTAATATAT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
25 29 0.64
27 5 0.11
29 11 0.24
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (25 bp):
ATATATATATATAATATAATATAAA
Found at i:55378706 original size:25 final size:25
Alignment explanation
Indices: 55378670--55378803 Score: 86
Period size: 23 Copynumber: 5.6 Consensus size: 25
55378660 AAAAAAATAT
*
55378670 ATATATATATAATATAATATTAAAG
1 ATATATACATAATATAATATTAAAG
* * * *
55378695 ATATATACATAAAATAGTATAAAATAT
1 ATATATACATAATATAATAT-TAA-AG
* *
55378722 ATATATACGTAATATAGA-ATTTAA-
1 ATATATACATAATATA-ATATTAAAG
* *
55378746 A-ATATACCTAATAT-AT-TAAAAG
1 ATATATACATAATATAATATTAAAG
*
55378768 A-ATATATATAATATAATATT-AAG
1 ATATATACATAATATAATATTAAAG
*
55378791 AAATATA-ATAATA
1 ATATATACATAATA
55378804 ACAAAAAAGG
Statistics
Matches: 85, Mismatches: 16, Indels: 18
0.71 0.13 0.15
Matches are distributed among these distances:
21 4 0.05
22 12 0.14
23 24 0.28
24 7 0.08
25 18 0.21
26 3 0.04
27 17 0.20
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (25 bp):
ATATATACATAATATAATATTAAAG
Found at i:55379330 original size:30 final size:30
Alignment explanation
Indices: 55379294--55379408 Score: 203
Period size: 30 Copynumber: 3.8 Consensus size: 30
55379284 TAGGTACAAG
*
55379294 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
* *
55379324 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
55379354 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
55379384 TGGTGGTGGAAAAGGTGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGT
55379409 TGAGAAAAGT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 80 1.00
ACGTcount: A:0.21, C:0.03, G:0.50, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:55386394 original size:24 final size:24
Alignment explanation
Indices: 55386367--55386418 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
55386357 TTAGTAAGTC
*
55386367 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
55386391 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
55386415 AAAT
1 AAAT
55386419 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:55388364 original size:24 final size:24
Alignment explanation
Indices: 55388337--55388388 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
55388327 TTAGTAAGTC
*
55388337 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
55388361 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
55388385 AAAT
1 AAAT
55388389 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:55395094 original size:18 final size:18
Alignment explanation
Indices: 55395071--55395112 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
55395061 TTCAAGGTGT
*
55395071 AATTAATTTAAAATATTC
1 AATTAATTAAAAATATTC
*
55395089 AATTAATTAAAAATATTT
1 AATTAATTAAAAATATTC
55395107 AATTAA
1 AATTAA
55395113 AAATCTATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTAATTAAAAATATTC
Found at i:55402322 original size:20 final size:21
Alignment explanation
Indices: 55402299--55402341 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
55402289 TTTAACTTTC
*
55402299 TTTAT-ATATTTTTTAGAATT
1 TTTATAATATTTTTTAAAATT
55402319 TTTATAAATATTTTTTAAAATT
1 TTTAT-AATATTTTTTAAAATT
55402341 T
1 T
55402342 AAAAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
22 15 0.75
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTATAATATTTTTTAAAATT
Found at i:55419465 original size:141 final size:141
Alignment explanation
Indices: 55419263--55419967 Score: 1040
Period size: 142 Copynumber: 5.0 Consensus size: 141
55419253 CAAAAGTCTC
*
55419263 GAAGAACGTGAA-TTTGAATTCAAATCTAGAATTACAAAAGCATTCGCATTGGAATCGGACTCAT
1 GAAGAACGT-AATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCAT
* *
55419327 GAATTCAAATTTCAACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACA
65 GAATTCAAATTTCCACGTAATTTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACA
55419392 CACAGATCAAAA
130 CACAGATCAAAA
* *
55419404 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCACATTGAAATCGGACTCATG
1 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATG
* *
55419469 AATTCAAATTTCCGCGTAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAACTCAATTACA
66 AATTCAAATTTCCACGTAATTTTGAAGAACTTTG-ATGAAAAATGAGGTAAAGAACTCAATTACA
55419534 CACAGATCAAAA
130 CACAGATCAAAA
* * * * *
55419546 GAAGAACGCAATTTCGAATTCAAATCTAAAATTACAAAAGCGTTCCCATTGGAACCGGACTCATG
1 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATG
* * * * *
55419611 AATTCAAATTTCCACGTAAATTTGAAGAATTTTGATGAAAACTGAGGCAAAGCACTCAATTACAC
66 AATTCAAATTTCCACGTAATTTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACAC
55419676 ACAGATC--AA
131 ACAGATCAAAA
* * * * *
55419685 -AAGAACGTAATTTTGAATTCAAATCTAAACTTACAAAAGCATTCGCATTGAAACCAGACTCGTG
1 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATG
* * *
55419749 AATTCAAATTTCGACGTAATTTTGAAGAACTTGGAATGAAAAATGAGCTAAAGAACTCAAATTAC
66 AATTCAAATTTCCACGTAATTTTGAAGAACTTTG-ATGAAAAATGAGGTAAAGAACTC-AATTAC
55419814 ACACAGATCAAAA
129 ACACAGATCAAAA
* * * * * * *
55419827 CAAGAACGTGACTTTAAATTCAAATCTAAAGTTACAAATGCATTCGCATTGGAATCCGACTCATG
1 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATG
* *
55419892 AATTCAAATTTCCACGTAATTTTGAAGAACTATAATGAAAAATGAGGTAAAGAACTCAATTACAC
66 AATTCAAATTTCCACGTAATTTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACAC
55419957 ACAGATCAAAA
131 ACAGATCAAAA
55419968 AGGAGAAAAC
Statistics
Matches: 507, Mismatches: 50, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
138 86 0.17
139 21 0.04
140 17 0.03
141 143 0.28
142 155 0.31
143 85 0.17
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (141 bp):
GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATG
AATTCAAATTTCCACGTAATTTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACAC
ACAGATCAAAA
Found at i:55419956 original size:281 final size:279
Alignment explanation
Indices: 55419264--55419967 Score: 1099
Period size: 281 Copynumber: 2.5 Consensus size: 279
55419254 AAAAGTCTCG
*
55419264 AAGAACGTGAATTTGAATTCAAATCTAGAATTACAAAAGCATTCGCATTGGAATCGGACTCATGA
1 AAGAACGTGAATTTGAATTCAAATCTA-AATTACAAAAGCATTCGCATTGGAATCCGACTCATGA
*
55419329 ATTCAAATTTCAACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACACA
65 ATTCAAATTTCCACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACACA
*
55419394 CAGATCAAAAGAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCACATTGAAAT
130 CAGATC--AA-AAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCACATTGAAAC
* *
55419459 CGGACTCATGAATTCAAATTTCCGCGTAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAA
192 CAGACTCATGAATTCAAATTTCCGCGTAATTTTGAAGAACTTGGAATGAAAAATGAGCTAAAGAA
*
55419524 CTCAATTACACACAGATCAAAAG
257 CTCAATTACACACAGATCAAAAC
* * *
55419547 AAGAACG-CAATTTCGAATTCAAATCTAAAATTACAAAAGCGTTCCCATTGGAA-CCGGACTCAT
1 AAGAACGTGAATTT-GAATTCAAATCT-AAATTACAAAAGCATTCGCATTGGAATCC-GACTCAT
* * * *
55419610 GAATTCAAATTTCCACGTAAATTTGAAGAATTTTGATGAAAACTGAGGCAAAGCACTCAATTACA
63 GAATTCAAATTTCCACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACA
* *
55419675 CACAGATCAAAAGAACGTAATTTTGAATTCAAATCTAAACTTACAAAAGCATTCGCATTGAAACC
128 CACAGATCAAAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCACATTGAAACC
*
55419740 AGACTCGTGAATTCAAATTT-CGACGTAATTTTGAAGAACTTGGAATGAAAAATGAGCTAAAGAA
193 AGACTCATGAATTCAAATTTCCG-CGTAATTTTGAAGAACTTGGAATGAAAAATGAGCTAAAGAA
55419804 CTCAAATTACACACAGATCAAAAC
257 CTC-AATTACACACAGATCAAAAC
* * *
55419828 AAGAACGTGACTTTAAATTCAAATCTAAAGTTACAAATGCATTCGCATTGGAATCCGACTCATGA
1 AAGAACGTGAATTTGAATTCAAATCTAAA-TTACAAAAGCATTCGCATTGGAATCCGACTCATGA
* * *
55419893 ATTCAAATTTCCACGTAATTTTGAAGAACTATAATGAAAAATGAGGTAAAGAACTCAATTACACA
65 ATTCAAATTTCCACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACACA
55419958 CAGATCAAAA
130 CAGATCAAAA
55419968 AGGAGAAAAC
Statistics
Matches: 384, Mismatches: 29, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
279 2 0.01
280 116 0.30
281 136 0.35
282 12 0.03
283 117 0.30
284 1 0.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (279 bp):
AAGAACGTGAATTTGAATTCAAATCTAAATTACAAAAGCATTCGCATTGGAATCCGACTCATGAA
TTCAAATTTCCACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACACAC
AGATCAAAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCACATTGAAACCAGA
CTCATGAATTCAAATTTCCGCGTAATTTTGAAGAACTTGGAATGAAAAATGAGCTAAAGAACTCA
ATTACACACAGATCAAAAC
Found at i:55420037 original size:10 final size:10
Alignment explanation
Indices: 55420022--55420048 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
55420012 AAAAAATGAG
55420022 CAGATCCGAA
1 CAGATCCGAA
55420032 CAGATCCGAA
1 CAGATCCGAA
55420042 CAGATCC
1 CAGATCC
55420049 AATTCATAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.37, C:0.33, G:0.19, T:0.11
Consensus pattern (10 bp):
CAGATCCGAA
Found at i:55420973 original size:22 final size:21
Alignment explanation
Indices: 55420950--55420999 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 21
55420940 TTAAATTTTA
55420950 AAATT-TTAAAAATAAAAAATT
1 AAATTCTT-AAAATAAAAAATT
55420971 AAATTCGTTAAAATAAAAATATAT
1 AAATTC-TTAAAATAAAAA-AT-T
55420995 AAATT
1 AAATT
55421000 AAATTCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.20
22 10 0.40
23 4 0.16
24 6 0.24
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (21 bp):
AAATTCTTAAAATAAAAAATT
Found at i:55421015 original size:28 final size:28
Alignment explanation
Indices: 55420955--55421016 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
55420945 TTTTAAAATT
*
55420955 TTAAAAATAAAAAATTAAATTCGTTAAAA
1 TTAAAAATAAAAAATTAAATTCG-AAAAA
*
55420984 -TAAAAATATATAAATTAAATTC-AAAAA
1 TTAAAAATA-AAAAATTAAATTCGAAAAA
55421011 TTAAAA
1 TTAAAA
55421017 GAAAAACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
27 4 0.14
28 13 0.45
29 12 0.41
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.31
Consensus pattern (28 bp):
TTAAAAATAAAAAATTAAATTCGAAAAA
Found at i:55421432 original size:24 final size:25
Alignment explanation
Indices: 55421387--55421441 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
55421377 AAATCGAAGT
55421387 ATTTTTAATATAATAATAAATTT-A
1 ATTTTTAATATAATAATAAATTTAA
** * *
55421411 ATTTTTAATATTTTTATTAATTTAA
1 ATTTTTAATATAATAATAAATTTAA
55421436 ATTTTT
1 ATTTTT
55421442 GAGCCAATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTTTTAATATAATAATAAATTTAA
Found at i:55435570 original size:22 final size:21
Alignment explanation
Indices: 55435519--55435570 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
55435509 GAGCAAGCTA
*
55435519 GTCCTTTTTATTAAAAATGTT
1 GTCCTTTTTATTAAAAATCTT
*
55435540 ATCCATTTTTATGTTAAAAA-CTT
1 GTCC-TTTTTA--TTAAAAATCTT
55435563 GTCCTTTT
1 GTCCTTTT
55435571 AAGTCATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 3 0.12
22 10 0.40
23 5 0.20
24 7 0.28
ACGTcount: A:0.27, C:0.13, G:0.08, T:0.52
Consensus pattern (21 bp):
GTCCTTTTTATTAAAAATCTT
Found at i:55451729 original size:14 final size:16
Alignment explanation
Indices: 55451710--55451749 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
55451700 ATTAATCTTT
55451710 AAATTTAAAA-TTT-A
1 AAATTTAAAATTTTAA
55451724 AAATTTAAAATTTTAA
1 AAATTTAAAATTTTAA
55451740 AAATTTAAAA
1 AAATTTAAAA
55451750 AAGTCTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 11 0.46
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATTTAAAATTTTAA
Found at i:55451740 original size:8 final size:7
Alignment explanation
Indices: 55451710--55451749 Score: 62
Period size: 7 Copynumber: 5.4 Consensus size: 7
55451700 ATTAATCTTT
55451710 AAATTTA
1 AAATTTA
55451717 AAATTTA
1 AAATTTA
55451724 AAATTTA
1 AAATTTA
55451731 AAATTTTAA
1 AAA-TTT-A
55451740 AAATTTA
1 AAATTTA
55451747 AAA
1 AAA
55451750 AAGTCTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 21 0.68
8 6 0.19
9 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTTA
Found at i:55451750 original size:8 final size:8
Alignment explanation
Indices: 55451710--55451750 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
55451700 ATTAATCTTT
55451710 AAATTT-A
1 AAATTTAA
55451717 AAATTT-A
1 AAATTTAA
55451724 AAATTTAA
1 AAATTTAA
*
55451732 AATTTTAA
1 AAATTTAA
55451740 AAATTTAA
1 AAATTTAA
55451748 AAA
1 AAA
55451751 AGTCTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 13 0.42
8 18 0.58
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AAATTTAA
Found at i:55453203 original size:25 final size:25
Alignment explanation
Indices: 55453145--55453206 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
55453135 AAATTTCAAT
** *
55453145 AAATAAAAAAT-GTATAAAATTATT
1 AAATAAAAAATAAAATAAAATTATA
*
55453169 AAATATAAAATAAAATAAAATTA-A
1 AAATAAAAAATAAAATAAAATTATA
55453193 AAATTAAAAAATAA
1 AAA-TAAAAAATAA
55453207 TATGAGCGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 13 0.42
25 18 0.58
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (25 bp):
AAATAAAAAATAAAATAAAATTATA
Found at i:55454122 original size:27 final size:27
Alignment explanation
Indices: 55454084--55454135 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
55454074 TTGAAAAACA
55454084 AATTTCCTTGTAGAAGGTGTAAAGACT
1 AATTTCCTTGTAGAAGGTGTAAAGACT
*
55454111 AATTTTCTTGTAGAAGGTGTAAAGA
1 AATTTCCTTGTAGAAGGTGTAAAGA
55454136 TAAACTTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (27 bp):
AATTTCCTTGTAGAAGGTGTAAAGACT
Found at i:55454342 original size:36 final size:36
Alignment explanation
Indices: 55454294--55454402 Score: 200
Period size: 36 Copynumber: 3.0 Consensus size: 36
55454284 AGTTTCACAA
*
55454294 AGATACTATTAATGATCTTGAAATATTATATCAATG
1 AGATACTCTTAATGATCTTGAAATATTATATCAATG
55454330 AGATACTCTTAATGATCTTGAAATATTATATCAATG
1 AGATACTCTTAATGATCTTGAAATATTATATCAATG
*
55454366 AGATACTCTTAATGATCTTGAAATATTGTATCAATG
1 AGATACTCTTAATGATCTTGAAATATTATATCAATG
55454402 A
1 A
55454403 CTATGACATG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (36 bp):
AGATACTCTTAATGATCTTGAAATATTATATCAATG
Found at i:55460476 original size:14 final size:14
Alignment explanation
Indices: 55460447--55460498 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
55460437 ATATGAGATT
* *
55460447 AGTAGAAACCAGAA
1 AGTAGAAAGCAAAA
*
55460461 AGCAGAAAGCAAAA
1 AGTAGAAAGCAAAA
* *
55460475 AGTAAAAAGTAAAA
1 AGTAGAAAGCAAAA
55460489 AGTAGAAAGC
1 AGTAGAAAGC
55460499 GGGATCAAAC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.62, C:0.10, G:0.21, T:0.08
Consensus pattern (14 bp):
AGTAGAAAGCAAAA
Found at i:55464160 original size:14 final size:14
Alignment explanation
Indices: 55464141--55464170 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
55464131 ATAAGTTTGG
55464141 AATAAATAATATAT
1 AATAAATAATATAT
55464155 AATAAATAATATAT
1 AATAAATAATATAT
55464169 AA
1 AA
55464171 ATGAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAAATAATATAT
Found at i:55465451 original size:17 final size:19
Alignment explanation
Indices: 55465417--55465458 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
55465407 GATCCATACC
55465417 TTTTTTAAAAGTACATAATT
1 TTTTTTAAAAG-ACATAATT
55465437 TTTTTTAAAA-A-ATAATT
1 TTTTTTAAAAGACATAATT
55465454 TTTTT
1 TTTTT
55465459 CTTATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.50
18 1 0.05
20 10 0.45
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTTTTAAAAGACATAATT
Found at i:55465532 original size:23 final size:24
Alignment explanation
Indices: 55465505--55465552 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
55465495 AAAAATATGA
* *
55465505 AAAAAATATTTAAAATTAAAAAAT
1 AAAAAGTATTTAAAATAAAAAAAT
*
55465529 AAAAAGTTTTTAAAATAAAAAAAT
1 AAAAAGTATTTAAAATAAAAAAAT
55465553 CTAAAATTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (24 bp):
AAAAAGTATTTAAAATAAAAAAAT
Found at i:55466047 original size:16 final size:17
Alignment explanation
Indices: 55466009--55466047 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
55465999 AAGAGTTTCT
55466009 ATTTTTAAAAAATTATA
1 ATTTTTAAAAAATTATA
55466026 ATTTTT-AAAAATTATA
1 ATTTTTAAAAAATTATA
*
55466042 GTTTTT
1 ATTTTT
55466048 TATTTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTTTAAAAAATTATA
Found at i:55469303 original size:35 final size:35
Alignment explanation
Indices: 55469241--55469326 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
55469231 TTTTATTTGT
*
55469241 TTTA-ATTATATAATTAATGATATTTAAA-TATAA
1 TTTATATTATATAATTAATGATAATTAAATTATAA
*
55469274 TTTATATTATATGAATTTATGATAATTAAATTATAA
1 TTTATATTATAT-AATTAATGATAATTAAATTATAA
* *
55469310 -TGATATTATATTATTAA
1 TTTATATTATATAATTAA
55469327 ATAAATAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 4 0.09
34 11 0.24
35 25 0.56
36 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (35 bp):
TTTATATTATATAATTAATGATAATTAAATTATAA
Found at i:55469312 original size:25 final size:23
Alignment explanation
Indices: 55469268--55469328 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
55469258 TGATATTTAA
*
55469268 ATATAATTTATATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
55469292 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
55469317 ATATTATTAAAT
1 ATATAATTAAAT
55469329 AAATAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:55495723 original size:12 final size:12
Alignment explanation
Indices: 55495706--55495730 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55495696 AACAATTGTC
55495706 ATTTGCATTAAG
1 ATTTGCATTAAG
55495718 ATTTGCATTAAG
1 ATTTGCATTAAG
55495730 A
1 A
55495731 CTTAAATTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATTTGCATTAAG
Found at i:55499232 original size:29 final size:29
Alignment explanation
Indices: 55499200--55499271 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 29
55499190 AAATTAAACC
55499200 ATATAAGGAATAGGATCTAAAAGGAAATT
1 ATATAAGGAATAGGATCTAAAAGGAAATT
* * *
55499229 ATATAAAAGAATAGGATCTAAATGTAAATT
1 ATAT-AAGGAATAGGATCTAAAAGGAAATT
*
55499259 ATACAAGGAATAG
1 ATATAAGGAATAG
55499272 TTTGGCCAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 12 0.32
30 25 0.68
ACGTcount: A:0.53, C:0.04, G:0.18, T:0.25
Consensus pattern (29 bp):
ATATAAGGAATAGGATCTAAAAGGAAATT
Found at i:55499250 original size:15 final size:16
Alignment explanation
Indices: 55499204--55499250 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
55499194 TAAACCATAT
55499204 AAGGAATAGGATCTAA
1 AAGGAATAGGATCTAA
** *
55499220 AAGGAA-ATTATATAA
1 AAGGAATAGGATCTAA
55499235 AA-GAATAGGATCTAA
1 AAGGAATAGGATCTAA
55499250 A
1 A
55499251 TGTAAATTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
14 3 0.12
15 15 0.62
16 6 0.25
ACGTcount: A:0.55, C:0.04, G:0.19, T:0.21
Consensus pattern (16 bp):
AAGGAATAGGATCTAA
Found at i:55499871 original size:31 final size:31
Alignment explanation
Indices: 55499813--55499877 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
55499803 GAGCAATTTG
* * *
55499813 ACTCTTTTTTAAAGGTTGATGGTCAAATTCA
1 ACTCTTTCTAAAAGGTTGATGGCCAAATTCA
*
55499844 ACTCTTTCTAAAAGGTTGA-GGACCAAATTTA
1 ACTCTTTCTAAAAGGTTGATGG-CCAAATTCA
55499875 ACT
1 ACT
55499878 AAAAAAATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 2 0.07
31 27 0.93
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (31 bp):
ACTCTTTCTAAAAGGTTGATGGCCAAATTCA
Found at i:55501447 original size:51 final size:51
Alignment explanation
Indices: 55501329--55501440 Score: 134
Period size: 51 Copynumber: 2.2 Consensus size: 51
55501319 TATGTAAATG
* * * * * * * *
55501329 TTGACAAAATATGTAAATTTTGTGAGTTAATTTTGTTAAATCAGGATCAAA
1 TTGACAGAATATGTAAATATAGTGAGCTAAATTTATTAAATCAAGATAAAA
**
55501380 TTGGTAGAATATGTAAATATAGTGAGCTAAATTTATTAAATCAAGATAAAA
1 TTGACAGAATATGTAAATATAGTGAGCTAAATTTATTAAATCAAGATAAAA
55501431 TTGACAGAAT
1 TTGACAGAAT
55501441 GAGTAAACTT
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (51 bp):
TTGACAGAATATGTAAATATAGTGAGCTAAATTTATTAAATCAAGATAAAA
Found at i:55502332 original size:20 final size:20
Alignment explanation
Indices: 55502307--55502356 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
55502297 TGGCTTAAAA
55502307 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
55502327 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
55502344 GTGGTAGTGGATT
1 TTGGTAGTGGATT
55502357 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:55506971 original size:20 final size:20
Alignment explanation
Indices: 55506946--55506995 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
55506936 TGGCTTAAAA
55506946 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
55506966 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
55506983 GTGGTAGTGGATT
1 TTGGTAGTGGATT
55506996 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:55515721 original size:14 final size:14
Alignment explanation
Indices: 55515700--55515733 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
55515690 TGGTATGGGT
55515700 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
55515713 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
55515727 TTATAGG
1 TTATAGG
55515734 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:55519995 original size:21 final size:21
Alignment explanation
Indices: 55519969--55520024 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
55519959 AATAGCGGTG
*
55519969 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
55519990 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
55520011 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
55520025 AACAATGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:55520255 original size:30 final size:30
Alignment explanation
Indices: 55520193--55520343 Score: 213
Period size: 30 Copynumber: 5.2 Consensus size: 30
55520183 ATTCATTTAA
*
55520193 TAAAATACACTACATATA----TATA-TTT
1 TAAAATACACTACATATATTTTTTTATTTT
*
55520218 TAAAATACACTACATATATTTTTTTATTTC
1 TAAAATACACTACATATATTTTTTTATTTT
*
55520248 TAGAATACACTACATATATTTTTTTATTTT
1 TAAAATACACTACATATATTTTTTTATTTT
*
55520278 TAAAATACACTACATGTATTTTTTTATTTT
1 TAAAATACACTACATATATTTTTTTATTTT
* *
55520308 TAAAATCCATTACATATATTTTTTTATTTT
1 TAAAATACACTACATATATTTTTTTATTTT
55520338 TAAAAT
1 TAAAAT
55520344 TTTAAATACA
Statistics
Matches: 112, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
25 18 0.16
29 3 0.03
30 91 0.81
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.50
Consensus pattern (30 bp):
TAAAATACACTACATATATTTTTTTATTTT
Found at i:55520535 original size:6 final size:6
Alignment explanation
Indices: 55520524--55520561 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
55520514 CGTTCCCTCC
55520524 TCCCAT TCCCAT TCCCATT TCCCAT TCCCAT TCCCAT T
1 TCCCAT TCCCAT TCCCA-T TCCCAT TCCCAT TCCCAT T
55520562 ATCAACAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.16, C:0.47, G:0.00, T:0.37
Consensus pattern (6 bp):
TCCCAT
Found at i:55520546 original size:19 final size:19
Alignment explanation
Indices: 55520524--55520561 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
55520514 CGTTCCCTCC
55520524 TCCCATTCCCATTCCCATT
1 TCCCATTCCCATTCCCATT
55520543 TCCCATTCCCATTCCCATT
1 TCCCATTCCCATTCCCATT
55520562 ATCAACAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.47, G:0.00, T:0.37
Consensus pattern (19 bp):
TCCCATTCCCATTCCCATT
Found at i:55524768 original size:31 final size:31
Alignment explanation
Indices: 55524700--55524783 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
55524690 GGTTTGAGTG
* * *
55524700 ACTGATTTGTTACTTTCCGAAAACGTTAGTA
1 ACTGATTTGTCACTTTTCGAAAACGTTAATA
* * * *
55524731 ATTGATTTGTCACTTTTCGTAAATGTTAATT
1 ACTGATTTGTCACTTTTCGAAAACGTTAATA
55524762 ACTGATTTGTCACTTTT-GAAAA
1 ACTGATTTGTCACTTTTCGAAAA
55524784 TTTAGTGACT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 4 0.09
31 40 0.91
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (31 bp):
ACTGATTTGTCACTTTTCGAAAACGTTAATA
Found at i:55530778 original size:25 final size:26
Alignment explanation
Indices: 55530733--55530790 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
55530723 GGTCCTTCTG
55530733 TTAAAAATTTCATCCATTTTCTACTA
1 TTAAAAATTTCATCCATTTTCTACTA
* * * *
55530759 TTAAAATTTTCATTCA-TTTCTATTG
1 TTAAAAATTTCATCCATTTTCTACTA
55530784 TTAAAAA
1 TTAAAAA
55530791 CTGGTCTCTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (26 bp):
TTAAAAATTTCATCCATTTTCTACTA
Found at i:55547491 original size:25 final size:24
Alignment explanation
Indices: 55547463--55547522 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 24
55547453 CATTTTTATT
* **
55547463 AAAAAAATAATTTAATATTTTTTAA
1 AAAAAAATAA-TTAAAATTAATTAA
*
55547488 AAAATTAATAATTAAAATTAATTAA
1 AAAA-AAATAATTAAAATTAATTAA
*
55547513 AAAAATATAA
1 AAAAAAATAA
55547523 GGATTAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 4 0.14
25 19 0.68
26 5 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAAAAATAATTAAAATTAATTAA
Found at i:55547515 original size:26 final size:26
Alignment explanation
Indices: 55547486--55547535 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
55547476 AATATTTTTT
*
55547486 AAAAAAT-TAATAATTAAAATTAATTA
1 AAAAAATATAAGAATT-AAATTAATTA
*
55547512 AAAAAATATAAGGATTAAATTAAT
1 AAAAAATATAAGAATTAAATTAAT
55547536 AGAAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (26 bp):
AAAAAATATAAGAATTAAATTAATTA
Found at i:55553785 original size:25 final size:24
Alignment explanation
Indices: 55553742--55553801 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
55553732 TAATGTCATT
* *
55553742 TTATTATTATGTTGTTACTATTTTG
1 TTATTATTAT-TTATTACTATCTTG
*
55553767 TTATTATTATTTATATACTGTCTTG
1 TTATTATTATTTAT-TACTATCTTG
55553792 TT-TTATTATT
1 TTATTATTATT
55553802 ATTTTTGCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.35
25 20 0.65
ACGTcount: A:0.22, C:0.05, G:0.08, T:0.65
Consensus pattern (24 bp):
TTATTATTATTTATTACTATCTTG
Found at i:55557154 original size:43 final size:44
Alignment explanation
Indices: 55557076--55557165 Score: 164
Period size: 43 Copynumber: 2.1 Consensus size: 44
55557066 AACCACCTCC
*
55557076 GGATATGCGACAAGTATTCAAGGATTGCATTCAAGACTTTGGTG
1 GGATATGCCACAAGTATTCAAGGATTGCATTCAAGACTTTGGTG
55557120 GGATATGCCACAAGTATT-AAGGATTGCATTCAAGACTTTGGTG
1 GGATATGCCACAAGTATTCAAGGATTGCATTCAAGACTTTGGTG
55557163 GGA
1 GGA
55557166 GTGAAATAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 28 0.62
44 17 0.38
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.29
Consensus pattern (44 bp):
GGATATGCCACAAGTATTCAAGGATTGCATTCAAGACTTTGGTG
Found at i:55557919 original size:19 final size:19
Alignment explanation
Indices: 55557892--55557928 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
55557882 AGTATATTCG
* *
55557892 TTAACAATTAATTAATTTT
1 TTAAAAATTAATAAATTTT
55557911 TTAAAAATTAATAAATTT
1 TTAAAAATTAATAAATTT
55557929 AAAAAATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAAAAATTAATAAATTTT
Found at i:55560866 original size:22 final size:22
Alignment explanation
Indices: 55560835--55560877 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
55560825 TTGTTGTTCA
*
55560835 TTGCTGCTATTTTGCTGTTATG
1 TTGCTACTATTTTGCTGTTATG
*
55560857 TTGCTACTATTTTGTTGTTAT
1 TTGCTACTATTTTGCTGTTAT
55560878 TGTTTGGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.58
Consensus pattern (22 bp):
TTGCTACTATTTTGCTGTTATG
Found at i:55570616 original size:18 final size:18
Alignment explanation
Indices: 55570580--55570618 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
55570570 CTTTGGACAT
*
55570580 TTTGGTTTAATTTTTGAA
1 TTTGGTTTAATTTTGGAA
55570598 TTTGGATTTAA-TTTGGAA
1 TTTGG-TTTAATTTTGGAA
55570616 TTT
1 TTT
55570619 TTGGCACGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.23, C:0.00, G:0.18, T:0.59
Consensus pattern (18 bp):
TTTGGTTTAATTTTGGAA
Found at i:55587173 original size:31 final size:29
Alignment explanation
Indices: 55587138--55587207 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
55587128 ATATCAAAAT
*
55587138 TATACATGAATTATGGTTTAATGTGTAATTG
1 TATACATGAATTATGATTT--TGTGTAATTG
* * *
55587169 TATACATAAATTTTGATTTTGTGTAATTT
1 TATACATGAATTATGATTTTGTGTAATTG
55587198 TATACATGAA
1 TATACATGAA
55587208 ATTTTAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.34, C:0.04, G:0.14, T:0.47
Consensus pattern (29 bp):
TATACATGAATTATGATTTTGTGTAATTG
Found at i:55587191 original size:29 final size:30
Alignment explanation
Indices: 55587159--55587217 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
55587149 TATGGTTTAA
*
55587159 TGTGTAATTGTATACAT-AAATTTTGATTT
1 TGTGTAATTGTATACATGAAATTTTAATTT
*
55587188 TGTGTAATTTTATACATGAAATTTTAATTT
1 TGTGTAATTGTATACATGAAATTTTAATTT
55587218 GATCCAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (30 bp):
TGTGTAATTGTATACATGAAATTTTAATTT
Found at i:55587702 original size:43 final size:44
Alignment explanation
Indices: 55587655--55587738 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
55587645 ATATTATTTT
* *
55587655 ATATATTTAATG-AATTTTTAAATTCGAACAAATTAATATCCTA
1 ATATATTTAATGAAAATTTTAAATTCAAACAAATTAATATCCTA
*
55587698 ATATATTTAATGAAAATTTTAAATTTAAACAAATTAATATC
1 ATATATTTAATGAAAATTTTAAATTCAAACAAATTAATATC
55587739 AAGTTTGATT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
43 12 0.32
44 25 0.68
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.42
Consensus pattern (44 bp):
ATATATTTAATGAAAATTTTAAATTCAAACAAATTAATATCCTA
Found at i:55591383 original size:21 final size:22
Alignment explanation
Indices: 55591347--55591391 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 22
55591337 GTCACGAGTG
55591347 AATTTTATAATTTAT-ATTAGCTT
1 AATTTTAT-ATTTATAATTA-CTT
55591370 AATTTTAT-TTTATAATTACTT
1 AATTTTATATTTATAATTACTT
55591391 A
1 A
55591392 GACATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 9 0.43
22 4 0.19
23 8 0.38
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (22 bp):
AATTTTATATTTATAATTACTT
Found at i:55594495 original size:88 final size:88
Alignment explanation
Indices: 55594346--55594506 Score: 322
Period size: 88 Copynumber: 1.8 Consensus size: 88
55594336 TGAAAAATTA
55594346 AAACATGCAAGGGAAGAGAAACAAACTTGAGTCTCAAAAACAATTTCACTAATACTTAACCAACA
1 AAACATGCAAGGGAAGAGAAACAAACTTGAGTCTCAAAAACAATTTCACTAATACTTAACCAACA
55594411 GATCAGTAACTTATTTTTTATAT
66 GATCAGTAACTTATTTTTTATAT
55594434 AAACATGCAAGGGAAGAGAAACAAACTTGAGTCTCAAAAACAATTTCACTAATACTTAACCAACA
1 AAACATGCAAGGGAAGAGAAACAAACTTGAGTCTCAAAAACAATTTCACTAATACTTAACCAACA
55594499 GATCAGTA
66 GATCAGTA
55594507 GAAATAGGTC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 73 1.00
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.24
Consensus pattern (88 bp):
AAACATGCAAGGGAAGAGAAACAAACTTGAGTCTCAAAAACAATTTCACTAATACTTAACCAACA
GATCAGTAACTTATTTTTTATAT
Found at i:55599092 original size:11 final size:11
Alignment explanation
Indices: 55599076--55599127 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
55599066 ATTATAGCTT
*
55599076 ATTAGTGAGGG
1 ATTAGTGATGG
55599087 ATTAGTGATGG
1 ATTAGTGATGG
* *
55599098 ATTAGTGTAAGC
1 ATTAGTG-ATGG
*
55599110 ATAAGTGATGG
1 ATTAGTGATGG
55599121 ATTAGTG
1 ATTAGTG
55599128 TTTTTGTCAC
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
11 25 0.76
12 8 0.24
ACGTcount: A:0.31, C:0.02, G:0.35, T:0.33
Consensus pattern (11 bp):
ATTAGTGATGG
Found at i:55599327 original size:18 final size:18
Alignment explanation
Indices: 55599306--55599359 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
55599296 ACATAATTAT
55599306 TTTAAATATAATAATAAA
1 TTTAAATATAATAATAAA
* *
55599324 TTTAAAT-TTAT-ATTAA
1 TTTAAATATAATAATAAA
*
55599340 TATTAAATAAAATAA-AAA
1 T-TTAAATATAATAATAAA
55599358 TT
1 TT
55599360 GCCCACCCTG
Statistics
Matches: 28, Mismatches: 5, Indels: 7
0.70 0.12 0.17
Matches are distributed among these distances:
16 5 0.18
17 10 0.36
18 12 0.43
19 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTAAATATAATAATAAA
Found at i:55599707 original size:18 final size:18
Alignment explanation
Indices: 55599663--55599707 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
55599653 GATTTTTATT
*
55599663 TTATTTAATATTATTATAA
1 TTATTAAAT-TTATTATAA
55599682 TTATTAAATTTATTATTAA
1 TTATTAAATTTATTA-TAA
55599701 TT-TTAAA
1 TTATTAAA
55599708 AAAATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATTAAATTTATTATAA
Found at i:55600703 original size:31 final size:31
Alignment explanation
Indices: 55600654--55600713 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
55600644 ATTTGGTCAC
*
55600654 TGAACTATTTCAATGTTTTCATTCAAGTCGT
1 TGAACTATTTCAAAGTTTTCATTCAAGTCGT
* *
55600685 TGAACTA-TTCAAAAGTTTTTATTTAAGTC
1 TGAACTATTTC-AAAGTTTTCATTCAAGTC
55600714 ACTAGTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (31 bp):
TGAACTATTTCAAAGTTTTCATTCAAGTCGT
Found at i:55602275 original size:31 final size:30
Alignment explanation
Indices: 55602251--55602639 Score: 466
Period size: 31 Copynumber: 12.8 Consensus size: 30
55602241 GTATATGTTT
*
55602251 TATACATTGCCGAA-TTGATTTGTATAAAGA
1 TATACATTGCCGAATTTGATTTGTAT-ATGA
* *
55602281 TATACATTGTCGAATTTGATTTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATAT-GA
55602312 TATACATTGCCGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATAT-GA
* *
55602342 TATACATTGCCGAATTTGAATTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATAT-GA
* *
55602373 TGTACATTGCCGAA-TTGATTTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATAT-GA
* *
55602403 TATACATTGTCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATAT-GA
*
55602434 TATACATTACCGAATTTGATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATAT-GA
55602465 TATACATTGCCGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATAT-GA
* *
55602495 TATACATTGCTGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATAT-GA
*
55602526 TATACATTGCCGAATTTTATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATAT-GA
*
55602557 TATACATTGCCGAA-TTGATTTGTATGTAGA
1 TATACATTGCCGAATTTGATTTGTATAT-GA
* *
55602587 TATTCATTGCCGAATTTGATTCGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATAT-GA
* *
55602618 TATATATTACCGAA-TTGATTTG
1 TATACATTGCCGAATTTGATTTG
55602640 AGCATTGTAT
Statistics
Matches: 317, Mismatches: 36, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
30 131 0.41
31 186 0.59
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (30 bp):
TATACATTGCCGAATTTGATTTGTATATGA
Found at i:55602326 original size:61 final size:61
Alignment explanation
Indices: 55602251--55602639 Score: 546
Period size: 61 Copynumber: 6.4 Consensus size: 61
55602241 GTATATGTTT
* * *
55602251 TATACATTGCCGAATTGATTTGTATAAAGATATACATTGTCGAATTTGATTTGTTTATAGA
1 TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* *
55602312 TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGAATTGTTTATAGA
1 TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * * * *
55602373 TGTACATTGCCGAATTGATTTGTTTATAGATATACATTGTCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* *
55602434 TATACATTACCGAATTTGATTTGTATATGGATATACATTGCCGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAA-TTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * * * *
55602495 TATACATTGCTGAATTTGATTTGTATATGGTTATACATTGCCGAATTTTATTTGTATATGGA
1 TATACATTGCCGAA-TTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * * *
55602557 TATACATTGCCGAATTGATTTGTATGTAGATATTCATTGCCGAATTTGATTCGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* *
55602618 TATATATTACCGAATTGATTTG
1 TATACATTGCCGAATTGATTTG
55602640 AGCATTGTAT
Statistics
Matches: 295, Mismatches: 31, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
61 241 0.82
62 54 0.18
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (61 bp):
TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
Found at i:55602388 original size:92 final size:92
Alignment explanation
Indices: 55602251--55602639 Score: 559
Period size: 92 Copynumber: 4.2 Consensus size: 92
55602241 GTATATGTTT
* * *
55602251 TATACATTGCCGAA-TTGATTTGTATAAAGATATACATTGTCGAATTTGATTTGTTTATAGATAT
1 TATACATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAA-TTGATTTGTATATAGATAT
*
55602315 ACATTGCCGAA-TTGATTTGTATATAGA
65 ACATTGCCGAATTTGATTTGTATATGGA
* * * *
55602342 TATACATTGCCGAATTTGAATTGTTTATAGATGTACATTGCCGAATTGATTTGTTTATAGATATA
1 TATACATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTGATTTGTATATAGATATA
* *
55602407 CATTGTCGAATTTGATTTGTATATGGT
66 CATTGCCGAATTTGATTTGTATATGGA
* *
55602434 TATACATTACCGAATTTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATAGATATA
1 TATACATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTGATTTGTATATAGATATA
* *
55602499 CATTGCTGAATTTGATTTGTATATGGT
66 CATTGCCGAATTTGATTTGTATATGGA
* * * *
55602526 TATACATTGCCGAATTTTATTTGTATATGGATATACATTGCCGAATTGATTTGTATGTAGATATT
1 TATACATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTGATTTGTATATAGATATA
*
55602591 CATTGCCGAATTTGATTCGTATATGGA
66 CATTGCCGAATTTGATTTGTATATGGA
* *
55602618 TATATATTACCGAA-TTGATTTG
1 TATACATTGCCGAATTTGATTTG
55602640 AGCATTGTAT
Statistics
Matches: 270, Mismatches: 26, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
91 50 0.19
92 220 0.81
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (92 bp):
TATACATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTGATTTGTATATAGATATA
CATTGCCGAATTTGATTTGTATATGGA
Found at i:55604007 original size:19 final size:19
Alignment explanation
Indices: 55603983--55604019 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
55603973 TTAAAATATT
55603983 ATTTTA-ATAAAATATTTAA
1 ATTTTATATAAAA-ATTTAA
55604002 ATTTTATATAAAAATTTA
1 ATTTTATATAAAAATTTA
55604020 TTAATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTATATAAAAATTTAA
Found at i:55604058 original size:20 final size:19
Alignment explanation
Indices: 55604030--55604071 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
55604020 TTAATTATAT
*
55604030 TTTATTGAATGAATATAATA
1 TTTAATGAATGAA-ATAATA
*
55604050 TTTAATGAATGAAATTATA
1 TTTAATGAATGAAATAATA
55604069 TTT
1 TTT
55604072 GTAAATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (19 bp):
TTTAATGAATGAAATAATA
Found at i:55611822 original size:7 final size:7
Alignment explanation
Indices: 55611810--55611834 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
55611800 AATTAGATAA
55611810 TAACATG
1 TAACATG
55611817 TAACATG
1 TAACATG
55611824 TAACATG
1 TAACATG
55611831 TAAC
1 TAAC
55611835 GTACGACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (7 bp):
TAACATG
Found at i:55617701 original size:19 final size:18
Alignment explanation
Indices: 55617677--55617735 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 18
55617667 TTTTTGTTGC
55617677 TAATTTTTATGATTTTTTA
1 TAATTTTTAT-ATTTTTTA
55617696 TAATTTATT-TA-TTTTTA
1 TAATTT-TTATATTTTTTA
*
55617713 -AATATTTTATAATTTTTA
1 TAAT-TTTTATATTTTTTA
*
55617731 AAATT
1 TAATT
55617736 ATTTGTTAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
16 5 0.14
17 10 0.29
18 8 0.23
19 10 0.29
20 2 0.06
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TAATTTTTATATTTTTTA
Found at i:55617729 original size:9 final size:9
Alignment explanation
Indices: 55617677--55617735 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
55617667 TTTTTGTTGC
55617677 TAATTTTTA
1 TAATTTTTA
*
55617686 TGATTTTTTA
1 T-AATTTTTA
55617696 TAATTTATT-
1 TAATTT-TTA
55617705 T-ATTTTTA
1 TAATTTTTA
55617713 -AATATTTTA
1 TAAT-TTTTA
55617722 TAATTTTTA
1 TAATTTTTA
*
55617731 AAATT
1 TAATT
55617736 ATTTGTTAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
7 2 0.05
8 6 0.15
9 20 0.49
10 13 0.32
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (9 bp):
TAATTTTTA
Found at i:55618172 original size:2 final size:2
Alignment explanation
Indices: 55618165--55618195 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
55618155 AAGTATGCTT
55618165 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 T
55618196 TTGTCAGGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55618917 original size:31 final size:31
Alignment explanation
Indices: 55618879--55618943 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
55618869 TTCCTTCAAG
55618879 TATGTTTTCAAATCAAAGTTAAAAGTATATC
1 TATGTTTTCAAATCAAAGTTAAAAGTATATC
55618910 TATGTTTTCAAATCAAAGTTAAAAGTATATC
1 TATGTTTTCAAATCAAAGTTAAAAGTATATC
55618941 TAT
1 TAT
55618944 TTTGTTGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (31 bp):
TATGTTTTCAAATCAAAGTTAAAAGTATATC
Found at i:55620988 original size:31 final size:31
Alignment explanation
Indices: 55620940--55621006 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
55620930 GAAAATCCTA
* *
55620940 AAGTTTAGGCTCTAATGTGGGAACAACTGCC
1 AAGTTCAGGCTCTAATGTAGGAACAACTGCC
* *
55620971 AAGTTCAGGACTC-AATGTAGGAGCAATTGCC
1 AAGTTCAGG-CTCTAATGTAGGAACAACTGCC
55621002 AAGTT
1 AAGTT
55621007 TAGGGACTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (31 bp):
AAGTTCAGGCTCTAATGTAGGAACAACTGCC
Found at i:55639064 original size:20 final size:19
Alignment explanation
Indices: 55639036--55639079 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
55639026 AAAAAAAAAG
*
55639036 TTTAGGTACCACCTTGATGA
1 TTTAAGTACCA-CTTGATGA
* *
55639056 TTTAAGTACCATTTTATGA
1 TTTAAGTACCACTTGATGA
55639075 TTTAA
1 TTTAA
55639080 ACCTTATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (19 bp):
TTTAAGTACCACTTGATGA
Found at i:55645780 original size:31 final size:31
Alignment explanation
Indices: 55645745--55645831 Score: 81
Period size: 29 Copynumber: 2.9 Consensus size: 31
55645735 TTGGTACGTA
55645745 AGTTTGGTTTTAATGTTCAATTTGATACTTG
1 AGTTTGGTTTTAATGTTCAATTTGATACTTG
* * * *
55645776 AGTTT-CTTTT--TGTCCCAATTTGGTACTTT
1 AGTTTGGTTTTAATGT-TCAATTTGATACTTG
* * *
55645805 AGTTTGGCTTCAATGTTTAATTTGATA
1 AGTTTGGTTTTAATGTTCAATTTGATA
55645832 TCCAGACCAT
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
28 3 0.07
29 17 0.40
30 6 0.14
31 13 0.31
32 3 0.07
ACGTcount: A:0.21, C:0.10, G:0.17, T:0.52
Consensus pattern (31 bp):
AGTTTGGTTTTAATGTTCAATTTGATACTTG
Found at i:55646068 original size:55 final size:57
Alignment explanation
Indices: 55645929--55646077 Score: 153
Period size: 58 Copynumber: 2.6 Consensus size: 57
55645919 TATCAAATTG
* * *
55645929 AAAAAATTCAGGTACCAAATTAAATATTGAAGTCAAACTCAGGTATCAGATTGGACGA
1 AAAAAACTCAGGTACCAAATTAAACATTGAAG-CCAACTCAGGTATCAGATTGGACGA
* * * * *
55645987 AAAAAACTTAGGTCCCAAATTAAACATTGAAGCCAACTCATGTA-CTA-ATTTGG-GGG
1 AAAAAACTCAGGTACCAAATTAAACATTGAAGCCAACTCAGGTATC-AGA-TTGGACGA
* *
55646043 GAAAAA-TCAGGTACCAAATTAAACATTGAAACCAA
1 AAAAAACTCAGGTACCAAATTAAACATTGAAGCCAA
55646078 AATTAGATAC
Statistics
Matches: 77, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
55 26 0.34
56 8 0.10
57 15 0.19
58 28 0.36
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (57 bp):
AAAAAACTCAGGTACCAAATTAAACATTGAAGCCAACTCAGGTATCAGATTGGACGA
Found at i:55653881 original size:25 final size:25
Alignment explanation
Indices: 55653834--55653882 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
55653824 TAGGTTAATC
*
55653834 AGAGTTTAAATGGAGAACTAAAAAT
1 AGAGTTTAAATGGAGAACGAAAAAT
*
55653859 AGAGTTTAATTGGGAGAA-GAAAAA
1 AGAGTTTAAAT-GGAGAACGAAAAA
55653883 AACCAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.51, C:0.02, G:0.24, T:0.22
Consensus pattern (25 bp):
AGAGTTTAAATGGAGAACGAAAAAT
Found at i:55653882 original size:26 final size:25
Alignment explanation
Indices: 55653834--55653883 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
55653824 TAGGTTAATC
*
55653834 AGAGTTTAAATGGAGAACTAAAAAT
1 AGAGTTTAAATGGAGAACAAAAAAT
* *
55653859 AGAGTTTAATTGGGAGAAGAAAAAA
1 AGAGTTTAAAT-GGAGAACAAAAAA
55653884 ACCAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.52, C:0.02, G:0.24, T:0.22
Consensus pattern (25 bp):
AGAGTTTAAATGGAGAACAAAAAAT
Found at i:55659371 original size:14 final size:13
Alignment explanation
Indices: 55659336--55659365 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
55659326 ATAAGCAAAC
55659336 AAAA-ATATTTTA
1 AAAATATATTTTA
55659348 AAAATATATTTTA
1 AAAATATATTTTA
55659361 AAAAT
1 AAAAT
55659366 TGTATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATATATTTTA
Done.