Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 35
Found at i:522774 original size:43 final size:43
Alignment explanation
Indices: 522727--522903 Score: 230
Period size: 43 Copynumber: 4.1 Consensus size: 43
522717 CATACGTATT
* * *
522727 TTGCGGCGTTTTTGGGAAAAACGCCGCTAAATCTCAAAACCTG
1 TTGCAGCGTTTTTGGGAAAAACGCCGCTAAATCTCAACACCTA
* * * *
522770 TTGCGGC-TTTTGTGGGAAAAACGCCGCTAATTATCAATACCTA
1 TTGCAGCGTTTT-TGGGAAAAACGCCGCTAAATCTCAACACCTA
* * *
522813 TTGCAGCATTTGTGGGATAAACGCCGCTAAATCTCAACACCTA
1 TTGCAGCGTTTTTGGGAAAAACGCCGCTAAATCTCAACACCTA
* *
522856 TTGCAGCGTTTATGGGATAAACGCCGCTAAATCTCAACACCTA
1 TTGCAGCGTTTTTGGGAAAAACGCCGCTAAATCTCAACACCTA
522899 TTGCA
1 TTGCA
522904 ACAAACGCCA
Statistics
Matches: 120, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
42 4 0.03
43 113 0.94
44 3 0.03
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (43 bp):
TTGCAGCGTTTTTGGGAAAAACGCCGCTAAATCTCAACACCTA
Found at i:525932 original size:12 final size:12
Alignment explanation
Indices: 525915--525965 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
525905 TTCAAAGAGG
525915 TTTTATATTTAA
1 TTTTATATTTAA
525927 TTTTATA-TTATA
1 TTTTATATTTA-A
*
525939 TTTGAT-TTTAA
1 TTTTATATTTAA
525950 TTTTA-ATATTAA
1 TTTTATAT-TTAA
525962 TTTT
1 TTTT
525966 TTAAATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:526056 original size:64 final size:63
Alignment explanation
Indices: 525979--526181 Score: 252
Period size: 64 Copynumber: 3.2 Consensus size: 63
525969 AATAAATTAA
*
525979 ATATTAATTTTAATATTAATTTTTTAATATTATATTATAGATATT-TGATTTT-ATATTATATT-
1 ATATTAATTTTAATATTAATTTTTTAA-A-TAAATTA-A-ATATTAT-ATTTTAATATTATATTA
526041 T-G
61 TAG
* * * *
526043 ATTTTAAGTTTAATATTACTTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAG
1 ATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATT-ATATTTTAATATTATATTATAG
*
526107 ATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAG
1 ATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATT-ATATTTTAATATTATATTATAG
526171 ATATTTAATTT
1 ATA-TTAATTT
526182 ATATCATATA
Statistics
Matches: 125, Mismatches: 8, Indels: 11
0.87 0.06 0.08
Matches are distributed among these distances:
60 5 0.04
61 5 0.04
62 17 0.14
63 2 0.02
64 89 0.71
65 7 0.06
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (63 bp):
ATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTATATTTTAATATTATATTATAG
Found at i:526103 original size:26 final size:27
Alignment explanation
Indices: 525948--526125 Score: 98
Period size: 24 Copynumber: 7.0 Consensus size: 27
525938 ATTTGATTTT
*
525948 AATTTTAATATTAATTTTTTAA-A-TA
1 AATTATAATATTAATTTTTTAATATTA
525973 AATTA-AATATTAA--TTTTAATATTA
1 AATTATAATATTAATTTTTTAATATTA
* * * * *
525997 ATTTTTTAATATT-ATATTATAGATATTT
1 A-ATTATAATATTAATTTTTTA-ATATTA
* * * * *
526025 GATT-TTATATT-A-TATTTGATTTTA
1 AATTATAATATTAATTTTTTAATATTA
* *
526049 AGTT-TAATATTACTTTTTTAA-A-TA
1 AATTATAATATTAATTTTTTAATATTA
526073 AATTA-AATATTAATTTTTTAATATTA
1 AATTATAATATTAATTTTTTAATATTA
*
526099 TATTATAGATATTAA--TTTTAATATTA
1 AATTATA-ATATTAATTTTTTAATATTA
526125 A
1 A
526126 TTTTTTAAAT
Statistics
Matches: 114, Mismatches: 25, Indels: 27
0.69 0.15 0.16
Matches are distributed among these distances:
22 6 0.05
23 1 0.01
24 43 0.38
25 10 0.09
26 35 0.31
27 7 0.06
28 12 0.11
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (27 bp):
AATTATAATATTAATTTTTTAATATTA
Found at i:526123 original size:100 final size:99
Alignment explanation
Indices: 525915--526129 Score: 312
Period size: 100 Copynumber: 2.2 Consensus size: 99
525905 TTCAAAGAGG
*
525915 TTTT-ATATTTAATTTTATATTATATTTGATTTTAATTTTAATATTAATTTTTTAAATAAATTAA
1 TTTTAATATTTAATTTTATATTATATTTGATTTTAAGTTTAATATTAATTTTTTAAATAAATTAA
* *
525979 ATATTAATTTTAATATTAATTTTTTAATATTATA
66 ATATTAATTTTAATATTAATATTATAATATTATA
* * *
526013 TTATAGATATTTGATTTTATATTATATTTGATTTTAAGTTTAATATTACTTTTTTAAATAAATTA
1 TTTTA-ATATTTAATTTTATATTATATTTGATTTTAAGTTTAATATTAATTTTTTAAATAAATTA
526078 AATATTAATTTTTTAATATT-ATATTATAGATATTA-A
65 AATATTAA--TTTTAATATTAATATTATA-ATATTATA
526114 TTTTAATA-TTAATTTT
1 TTTTAATATTTAATTTT
526130 TTAAATAAAT
Statistics
Matches: 104, Mismatches: 8, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
98 3 0.03
99 7 0.07
100 67 0.64
101 11 0.11
102 16 0.15
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (99 bp):
TTTTAATATTTAATTTTATATTATATTTGATTTTAAGTTTAATATTAATTTTTTAAATAAATTAA
ATATTAATTTTAATATTAATATTATAATATTATA
Found at i:526127 original size:40 final size:37
Alignment explanation
Indices: 526078--526162 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 37
526068 AAATAAATTA
*
526078 AATATTAATTTTTTAATATTATATTATAGATATTAA-TTTT
1 AATATTAATTTTTTAA-A-TAAATTA-A-ATATTAATTTTT
526118 AATATTAATTTTTTAAATAAATTAAATATTAATTTTTT
1 AATATTAATTTTTTAAATAAATTAAATATTAA-TTTTT
526156 AATATTA
1 AATATTA
526163 TATTATAGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
36 7 0.17
37 1 0.02
38 17 0.40
39 1 0.02
40 16 0.38
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (37 bp):
AATATTAATTTTTTAAATAAATTAAATATTAATTTTT
Found at i:526146 original size:88 final size:87
Alignment explanation
Indices: 525990--526157 Score: 234
Period size: 88 Copynumber: 1.9 Consensus size: 87
525980 TATTAATTTT
* * *
525990 AATATTAATTTTTTAATATTATATTATAGATATTTGATTTTATATTATATTTGATTTTAAGTTTA
1 AATATTAATTTTTTAATATTATATTATAGATATTTAATTTTATATTATATTT-ATTTTAAATTAA
*
526055 ATATTACTTTTTTAAATAAATTA
65 ATATTAATTTTTTAAATAAATTA
526078 AATATTAATTTTTTAATATTATATTATAGATA-TTAATTTTAATATTA-ATTT-TTTAAATAAAT
1 AATATTAATTTTTTAATATTATATTATAGATATTTAATTTT-ATATTATATTTATTT---TAAAT
526140 TAAATATTAATTTTTTAA
62 TAAATATTAATTTTTTAA
526158 TATTATATTA
Statistics
Matches: 72, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
85 3 0.04
87 11 0.15
88 58 0.81
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (87 bp):
AATATTAATTTTTTAATATTATATTATAGATATTTAATTTTATATTATATTTATTTTAAATTAAA
TATTAATTTTTTAAATAAATTA
Found at i:526237 original size:20 final size:19
Alignment explanation
Indices: 526179--526238 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
526169 AGATATTTAA
*
526179 TTTATATCA-TATAAATTAT
1 TTTATAT-ATTATTAATTAT
*
526198 TTTATATATTATTAA-AAT
1 TTTATATATTATTAATTAT
526216 TTTATAT-TTATTTTAATTAT
1 TTTATATATTA--TTAATTAT
526236 TTT
1 TTT
526239 GATTTAAGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 3 0.09
18 10 0.29
19 16 0.47
20 5 0.15
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATATATTATTAATTAT
Found at i:526729 original size:31 final size:31
Alignment explanation
Indices: 526691--526750 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
526681 TAGTTGTATG
* *
526691 AATTATTTAAATTTCAATATTGTAAAACTAC
1 AATTATTTAAATCTCAATATTGCAAAACTAC
*
526722 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAATATTGCAAAACT
526751 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAATATTGCAAAACTAC
Found at i:532151 original size:180 final size:181
Alignment explanation
Indices: 531658--532194 Score: 717
Period size: 182 Copynumber: 2.9 Consensus size: 181
531648 CAGGTACTTA
* *
531658 AAATTGAGAAGAATCCTTCCTGGTAGATGTCTGCCTCATTTTCTTATTATGCATAGCCTAATTTG
1 AAATTGAGAAGAATCCTTCCTGGTAGA--T-TGTCTCATTTTTTTATTATGCATAGCCTAATTTG
* * * *
531723 TTTAATAACTTGTCTAACGGGCTGCAAATGCAATTCATTCACCATGGATAATCTTCTTATTC-TT
63 TTTAATCACTTGTCTAACAGGCTGCAAATGCAAGTCATTTACCATGGATAATCTTCTTATTCTTT
* *
531787 GTATTGGGCGTCAACTCCTATGATTTACCAAGTCTAGCTTAAATAAAGATACATT
128 GTATTAGGC-TCAACTCCAATGATTTACCAAGTCTAGCTTAAATAAAGATACATT
* *
531842 AAATTGAGAAGAATCCTTCCTGGTAGA-TGTCTCCCTCATTTTTTATTTTGCATAG-CTAATTTG
1 AAATTGAGAAGAATCCTTCCTGGTAGATTGTCT-CAT--TTTTTTATTATGCATAGCCTAATTTG
* * * * * * *
531905 TTTAATCACTTTTCTAA-TGATCTGCAAATGCAAGTCACTTACCGTGGATACTCTTTTTATTCTT
63 TTTAATCACTTGTCTAACAG-GCTGCAAATGCAAGTCATTTACCATGGATAATCTTCTTATTCTT
* ** *
531969 TGTATTAGGCTC-ACTCCAATTATTTACGTAGTCTAGCTTAAATAAAGATACTTT
127 TGTATTAGGCTCAACTCCAATGATTTACCAAGTCTAGCTTAAATAAAGATACATT
*
532023 AGATTGAGAAGAAAT-CTTCCTGGTAGATTGTCTCATTTTTTTATTATGCATAGCCTAATTTGTT
1 AAATTGAGAAG-AATCCTTCCTGGTAGATTGTCTCATTTTTTTATTATGCATAGCCTAATTTGTT
*
532087 TAATCACTTGTCTAACAGGCTGCAAATGCAAGTCATTTACCACGGATAATCTTCTTATTCTTTGT
65 TAATCACTTGTCTAACAGGCTGCAAATGCAAGTCATTTACCATGGATAATCTTCTTATTCTTTGT
* *
532152 ATTTGGCCTCAACCCCAATGATTTACCAAGTCTAGCTTAAATA
130 ATTAGG-CTCAACTCCAATGATTTACCAAGTCTAGCTTAAATA
532195 TTTAGGGATG
Statistics
Matches: 306, Mismatches: 36, Indels: 24
0.84 0.10 0.07
Matches are distributed among these distances:
179 16 0.05
180 74 0.24
181 68 0.22
182 96 0.31
183 25 0.08
184 27 0.09
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (181 bp):
AAATTGAGAAGAATCCTTCCTGGTAGATTGTCTCATTTTTTTATTATGCATAGCCTAATTTGTTT
AATCACTTGTCTAACAGGCTGCAAATGCAAGTCATTTACCATGGATAATCTTCTTATTCTTTGTA
TTAGGCTCAACTCCAATGATTTACCAAGTCTAGCTTAAATAAAGATACATT
Found at i:532314 original size:23 final size:23
Alignment explanation
Indices: 532284--532329 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
532274 ATTGCATCCT
*
532284 AAGTTTTGCATTGTCGTGCTATA
1 AAGTTTTGCATTGACGTGCTATA
532307 AAGTTTTGCATTGACGTGCTATA
1 AAGTTTTGCATTGACGTGCTATA
532330 TGTTTTACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.41
Consensus pattern (23 bp):
AAGTTTTGCATTGACGTGCTATA
Found at i:545948 original size:54 final size:54
Alignment explanation
Indices: 545879--545992 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 54
545869 AAAAACGAAA
* *
545879 AAAATAATAAAAATGAGAAAAAGA-AAAAGAAGAAAAGAAG-AAAAGGAAAAATGAG
1 AAAA-AATAAAAATGAGAAAAA-ATAAAA-AAGAAAAAAAGAAAAAGGAAAAAAGAG
* *
545934 AAAAAATAAAAATGAGAAAAAATAAAAATGAAAAAAAGAAAAATGAAAAAAGAG
1 AAAAAATAAAAATGAGAAAAAATAAAAAAGAAAAAAAGAAAAAGGAAAAAAGAG
545988 AAAAA
1 AAAAA
545993 TGAAAAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
53 10 0.19
54 39 0.74
55 4 0.08
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (54 bp):
AAAAAATAAAAATGAGAAAAAATAAAAAAGAAAAAAAGAAAAAGGAAAAAAGAG
Found at i:545969 original size:31 final size:31
Alignment explanation
Indices: 545887--546001 Score: 132
Period size: 31 Copynumber: 3.7 Consensus size: 31
545877 AAAAAATAAT
*
545887 AAAAATGAGAAAAA-GAAAAAGAAG-AAAA-G
1 AAAAAAGAGAAAAATGAAAAA-AAGAAAAATG
*
545916 AAGAAAAG-GAAAAATGAGAAAAAATAAAAATG
1 AA-AAAAGAGAAAAATGA-AAAAAAGAAAAATG
*
545948 AGAAAAA-ATAAAAATGAAAAAAAGAAAAATG
1 A-AAAAAGAGAAAAATGAAAAAAAGAAAAATG
545979 AAAAAAGAGAAAAATGAAAAAAA
1 AAAAAAGAGAAAAATGAAAAAAA
546002 AGAGAAATAA
Statistics
Matches: 73, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
29 8 0.11
30 13 0.18
31 37 0.51
32 14 0.19
33 1 0.01
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (31 bp):
AAAAAAGAGAAAAATGAAAAAAAGAAAAATG
Found at i:546013 original size:15 final size:16
Alignment explanation
Indices: 545894--546013 Score: 124
Period size: 16 Copynumber: 7.8 Consensus size: 16
545884 AATAAAAATG
*
545894 AGAAAAA-GAAAAAGA
1 AGAAAAATGAAAAAAA
*
545909 AG-AAAA-GAAGAAAA
1 AGAAAAATGAAAAAAA
* *
545923 GGAAAAATGAGAAAAA
1 AGAAAAATGAAAAAAA
* *
545939 ATAAAAATGAGAAAAA
1 AGAAAAATGAAAAAAA
*
545955 ATAAAAATG-AAAAAA
1 AGAAAAATGAAAAAAA
*
545970 AGAAAAATGAAAAAAG
1 AGAAAAATGAAAAAAA
545986 AGAAAAATGAAAAAAA
1 AGAAAAATGAAAAAAA
*
546002 AGAGAAAT-AAAA
1 AGAAAAATGAAAA
546014 GGAGAGTTCA
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
14 11 0.12
15 23 0.26
16 56 0.62
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (16 bp):
AGAAAAATGAAAAAAA
Found at i:547210 original size:51 final size:51
Alignment explanation
Indices: 547141--547554 Score: 648
Period size: 51 Copynumber: 8.0 Consensus size: 51
547131 AGTGAAGCAA
*
547141 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
* *
547192 ACAATTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
547243 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
547294 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
547345 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
* *
547396 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGG
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
* * *
547447 ACTAGTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGG
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
** ** * * * *
547498 ACCTGTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAAGAGAGAGCGG
1 ACAAGTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGG
547553 AC
1 AC
547555 CCGTTTTATT
Statistics
Matches: 339, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
51 307 0.91
54 2 0.01
55 30 0.09
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (51 bp):
ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
Found at i:547325 original size:153 final size:153
Alignment explanation
Indices: 547141--547661 Score: 661
Period size: 153 Copynumber: 3.3 Consensus size: 153
547131 AGTGAAGCAA
547141 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAATTTTGTTGAA
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAATTTTGTTGAA
547206 GATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATA
66 GATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATA
*
547271 CTCTCTGAATGAATAGGGAGCGG
131 CTCTCTGAATGAATAGAGAGCGG
* * *
547294 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAA
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAATTTTGTTGAA
547359 GATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATA
66 GATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATA
*
547424 CTCTCTGAAGGAATAGAGAGCGG
131 CTCTCTGAATGAATAGAGAGCGG
* * * * *
547447 ACTAGTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGAC-CTGTTTATTGA
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAT-TTTGTTGA
* * * * ** ** *
547511 AGATTTTTCGAGTTCTATACTCTCTGAAGGAAGAGAGAGCGGACCCGTTTTATTAAAGATTGTCC
65 AGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGATTG---
* *
547576 AAGTCTTATACTCTCTGAATGAATAGAGAGCAG
122 -AGTCCTATACTCTCTGAATGAATAGAGAGCGG
* * *
547609 ACACGTT-TTATGAAGATTGTTCGAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 ACAAGTTCGT-TGAAGA---TT-GAGTCCTATACTCT-CTGAAGGAATAGGGAGC
547662 AGGCTCGTCA
Statistics
Matches: 322, Mismatches: 30, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
153 207 0.64
156 2 0.01
157 32 0.10
158 11 0.03
161 1 0.00
162 40 0.12
165 2 0.01
166 27 0.08
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.29
Consensus pattern (153 bp):
ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAATTTTGTTGAA
GATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATA
CTCTCTGAATGAATAGAGAGCGG
Found at i:547632 original size:111 final size:105
Alignment explanation
Indices: 547144--547653 Score: 467
Period size: 102 Copynumber: 4.9 Consensus size: 105
547134 GAAGCAAACA
* * * * *
547144 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA-ATTTTGTTGAAGA
1 AGTTCATTAAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACACGTTTT-ATGAAGA
* * * * *
547208 --TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
65 TTTTCGAGTTCTATACTCTCTGAAGGAAGAGAGAGCGGACC
* * * *
547246 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGT-TGAAGA
1 AGTTCATTAAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACACGTT-TTATGAAGA
* * * * *
547310 --TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
65 TTTTCGAGTTCTATACTCTCTGAAGGAAGAGAGAGCGGACC
* * * *
547348 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGT-TGAAGA
1 AGTTCATTAAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACACGTT-TTATGAAGA
* * *
547412 --TT-GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACT
65 TTTTCGAGTTCTATACTCTCTGAAGGAAGAGAGAGCGGACC
* * * *
547450 AGTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGAC-C-TGTTTATTGAAG
1 AGTTCATTAAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACACGT-TTTA-TGAAG
547513 ATTTTTCGAGTTCTATACTCTCTGAAGGAAGAGAGAGCGGACC
64 A-TTTTCGAGTTCTATACTCTCTGAAGGAAGAGAGAGCGGACC
* * * * *
547556 CGTTTTATTAAAGATTGTCCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTATG
1 AG-TTCATTAAAGATTG----AGTCCTATACTCTCTGAATGAATAGGGAGCGGACACGTTTTATG
547621 AAGATTGTTCGAG-TCTTATACT-TCCTGAAGGAA
61 AAGATT-TTCGAGTTC-TATACTCT-CTGAAGGAA
547654 TAGGGAGCAG
Statistics
Matches: 367, Mismatches: 22, Indels: 29
0.88 0.05 0.07
Matches are distributed among these distances:
100 2 0.01
101 1 0.00
102 247 0.67
103 2 0.01
104 1 0.00
105 2 0.01
106 34 0.09
107 11 0.03
110 5 0.01
111 56 0.15
112 5 0.01
113 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (105 bp):
AGTTCATTAAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACACGTTTTATGAAGAT
TTTCGAGTTCTATACTCTCTGAAGGAAGAGAGAGCGGACC
Found at i:547655 original size:55 final size:55
Alignment explanation
Indices: 547159--547663 Score: 221
Period size: 51 Copynumber: 9.6 Consensus size: 55
547149 GTTGAAGATT
* * * ** *
547159 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAATTTTGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCGTTTTATTGAAGATTGTTC
* * * * * **
547210 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
* * * * * **
547261 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
* * * * * **
547312 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
* * * * * **
547363 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
* * * **
547414 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACTAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
* * * * * *
547465 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACC-TGTTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCGT-TTTATTGAAGATTGTTC
* * * *
547520 GAGT-TCTATACTCTCTGAAGGAAGAGAGAGCGGACCCGTTTTATTAAAGATTGTCC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGA-CCGTTTTATTGAAGATTGTTC
* *
547576 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTA-TGAAGATTGTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
*
547631 GAGTCTTATACT-TCCTGAAGGAATAGGGAGCAG
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGCAG
547664 GCTCGTCATT
Statistics
Matches: 412, Mismatches: 29, Indels: 22
0.89 0.06 0.05
Matches are distributed among these distances:
51 288 0.70
52 1 0.00
54 3 0.01
55 67 0.16
56 51 0.12
57 2 0.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.29
Consensus pattern (55 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCGTTTTATTGAAGATTGTTC
Found at i:547678 original size:55 final size:55
Alignment explanation
Indices: 547415--547681 Score: 171
Period size: 55 Copynumber: 4.9 Consensus size: 55
547405 TTGAAGATTG
* *
547415 AGTCCTATACTCTCTGAAGGAATAGAGAGCGGACTA-GT-TCGT-TGAAGATTG----
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-ACGTAT--TATGAAGATTGTCCA
* * * * * * * *
547466 AGTCCTATACTCCCTGAAAGAATAGGGAGCGGAC-CTGT-TTATTGAAGATTTTTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACAC-GTATTA-TGAAGATTGTCCA
* * * * *
547521 AGT-TCTATACTCTCTGAAGGAAGAGAGAGCGGACCCGTTTTATTAAAGATTGTCCA
1 AGTCT-TATACTCTCTGAAGGAATAGAGAGCAGACACGTATTA-TGAAGATTGTCCA
* * * *
547577 AGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTATGAAGATTGTTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGTATTATGAAGATTGTCCA
* * *
547632 AGTCTTATACT-TCCTGAAGGAATAGGGAGCAGGCTCGTCATT-TGAAGATT
1 AGTCTTATACTCT-CTGAAGGAATAGAGAGCAGACACGT-ATTATGAAGATT
547682 TTTCAAGTAT
Statistics
Matches: 177, Mismatches: 25, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
49 1 0.01
51 42 0.24
54 1 0.01
55 80 0.45
56 52 0.29
57 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (55 bp):
AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGTATTATGAAGATTGTCCA
Found at i:549328 original size:19 final size:18
Alignment explanation
Indices: 549276--549328 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
549266 GAATTTTACA
*
549276 TTTTTTAAATTTA-GTCC
1 TTTTTTAAATTTATATCC
*
549293 TTATTTTAACATGTATATACC
1 TT-TTTTAA-ATTTATAT-CC
549314 TTTTTTAAATTTATA
1 TTTTTTAAATTTATA
549329 GTTTAGCATG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 2 0.07
18 6 0.21
19 10 0.34
20 7 0.24
21 4 0.14
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (18 bp):
TTTTTTAAATTTATATCC
Found at i:569095 original size:416 final size:416
Alignment explanation
Indices: 568324--569158 Score: 1661
Period size: 416 Copynumber: 2.0 Consensus size: 416
568314 AAAAGGTCCA
568324 CCAGTGCCTCCAGTTGGCTTACTACTGCAACGGAACAGATTTCAATGTATTTCATATGCAAACTC
1 CCAGTGCCTCCAGTTGGCTTACTACTGCAACGGAACAGATTTCAATGTATTTCATATGCAAACTC
568389 AGGGTAGGAAAACGATATATGTTTTATATAATAGAGAGCTTCCTTTCTTTTTCCTTCGTCATCAG
66 AGGGTAGGAAAACGATATATGTTTTATATAATAGAGAGCTTCCTTTCTTTTTCCTTCGTCATCAG
568454 AAATTCAGAATAATGAACAAAAAATGGAGAAAAAGAACGTTTCATTAAATTTAGGACCATATCAA
131 AAATTCAGAATAATGAACAAAAAATGGAGAAAAAGAACGTTTCATTAAATTTAGGACCATATCAA
568519 ATCATCAAGGTACAAAAGCTTTAGATAATATATGTGTGTGTGTATCACTCAATAAACAATAAGAA
196 ATCATCAAGGTACAAAAGCTTTAGATAATATATGTGTGTGTGTATCACTCAATAAACAATAAGAA
568584 CAAGTGATCCTAAAAAAATGTGCGTACAGACATCTAAGGTTTTCTAAGGGAGAAAATATTAGCAA
261 CAAGTGATCCTAAAAAAATGTGCGTACAGACATCTAAGGTTTTCTAAGGGAGAAAATATTAGCAA
568649 TTTCATATTTCTATTGCATGGGGCCTCATAACAGATAAATCCAAAGTTCAAAGCTCACTTATATA
326 TTTCATATTTCTATTGCATGGGGCCTCATAACAGATAAATCCAAAGTTCAAAGCTCACTTATATA
568714 TTCAAATCAGCTCTCTATTTCAGTTT
391 TTCAAATCAGCTCTCTATTTCAGTTT
568740 CCAGTGCCTCCAGTTGGCTTACTACTGCAACGGAACAGATTTCAATGTATTTCATATGCAAACTC
1 CCAGTGCCTCCAGTTGGCTTACTACTGCAACGGAACAGATTTCAATGTATTTCATATGCAAACTC
568805 AGGGTAGGAAAACGATATATGTTTTATATAATAGAGAGCTTCCTTTCTTTTTCCTTCGTCATCAG
66 AGGGTAGGAAAACGATATATGTTTTATATAATAGAGAGCTTCCTTTCTTTTTCCTTCGTCATCAG
568870 AAATTCAGAATAATGAACAAAAAATGGAGAAAAAGAACGTTTCATTAAATTTAGGACCATATCAA
131 AAATTCAGAATAATGAACAAAAAATGGAGAAAAAGAACGTTTCATTAAATTTAGGACCATATCAA
568935 ATCATCAAGGTACAAAAGCTTTAGATAATATATGTGTGTGTGTATCACTCAATAAACAATAAGAA
196 ATCATCAAGGTACAAAAGCTTTAGATAATATATGTGTGTGTGTATCACTCAATAAACAATAAGAA
*
569000 CAAGTGATCCTAAAAAAATGTGCGTACAGACATCTATGGTTTTCTAAGGGAGAAAATATTAGCAA
261 CAAGTGATCCTAAAAAAATGTGCGTACAGACATCTAAGGTTTTCTAAGGGAGAAAATATTAGCAA
569065 TTTCATATTTCTATTGCATGGGGCCTCATAACAGATAAATCCAAAGTTCAAAGCTCACTTATATA
326 TTTCATATTTCTATTGCATGGGGCCTCATAACAGATAAATCCAAAGTTCAAAGCTCACTTATATA
569130 TTCAAATCAGCTCTCTATTTCAGTTT
391 TTCAAATCAGCTCTCTATTTCAGTTT
569156 CCA
1 CCA
569159 TTTTAAGATT
Statistics
Matches: 418, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
416 418 1.00
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (416 bp):
CCAGTGCCTCCAGTTGGCTTACTACTGCAACGGAACAGATTTCAATGTATTTCATATGCAAACTC
AGGGTAGGAAAACGATATATGTTTTATATAATAGAGAGCTTCCTTTCTTTTTCCTTCGTCATCAG
AAATTCAGAATAATGAACAAAAAATGGAGAAAAAGAACGTTTCATTAAATTTAGGACCATATCAA
ATCATCAAGGTACAAAAGCTTTAGATAATATATGTGTGTGTGTATCACTCAATAAACAATAAGAA
CAAGTGATCCTAAAAAAATGTGCGTACAGACATCTAAGGTTTTCTAAGGGAGAAAATATTAGCAA
TTTCATATTTCTATTGCATGGGGCCTCATAACAGATAAATCCAAAGTTCAAAGCTCACTTATATA
TTCAAATCAGCTCTCTATTTCAGTTT
Found at i:572894 original size:20 final size:20
Alignment explanation
Indices: 572866--572905 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
572856 GCCTATTATT
* *
572866 TATTATTAATAATTTAATAA
1 TATTATTAAGAAATTAATAA
*
572886 TATTTTTAAGAAATTAATAA
1 TATTATTAAGAAATTAATAA
572906 ATAATATAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TATTATTAAGAAATTAATAA
Found at i:572981 original size:37 final size:40
Alignment explanation
Indices: 572922--573017 Score: 101
Period size: 38 Copynumber: 2.5 Consensus size: 40
572912 TAACTTTTAT
* *
572922 TAATAAT-TTATTATATATTAATA-AAATAAGAATTTAATAA
1 TAATAATATTATTAT-TA-TAATATAAATAACAATATAATAA
* * *
572962 T-ATCATA-TATTATTATAATATAACTAACTATATAATAA
1 TAATAATATTATTATTATAATATAAATAACAATATAATAA
573000 TAATAATATTATTATTAT
1 TAATAATATTATTATTAT
573018 TATTATTATT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
37 5 0.11
38 16 0.35
39 15 0.33
40 10 0.22
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (40 bp):
TAATAATATTATTATTATAATATAAATAACAATATAATAA
Found at i:573002 original size:52 final size:51
Alignment explanation
Indices: 572942--573040 Score: 119
Period size: 52 Copynumber: 1.9 Consensus size: 51
572932 TTATATATTA
572942 ATAAAATAAGAAT-TTAATAATATCATATATTATTATAATATAACTAACTAT
1 ATAAAATAAGAATATTAATAATATCAT-TATTATTATAATATAACTAACTAT
* * * * * *
572993 ATAATAATAATAATATTATTATTATTATTATTATTATTATATTACTAA
1 ATAA-AATAAGAATATTAATAATATCATTATTATTATAATATAACTAA
573041 AAAATATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
51 4 0.10
52 26 0.65
53 10 0.25
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (51 bp):
ATAAAATAAGAATATTAATAATATCATTATTATTATAATATAACTAACTAT
Found at i:573012 original size:3 final size:3
Alignment explanation
Indices: 573006--573036 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
572996 ATAATAATAA
573006 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
573037 CTAAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:574796 original size:64 final size:65
Alignment explanation
Indices: 574724--574876 Score: 163
Period size: 64 Copynumber: 2.4 Consensus size: 65
574714 TGTCATGTGT
** * * **
574724 ATCGATGCACTGTC-TATGCATCGGTGCA-TAAATCTCATTCGATGTTTGTA-TTTTAAGCGGGT
1 ATCGATGCACTCCCTTATGCATCGATGCACT-AATCACATTCGATGTTTCCATTTTTAA-CGGGT
574786 GC
64 GC
* *
574788 ATCGATGCAC-CCCTTATGCATCGATGCACTAATGACATTCGATGTTTCCATTTTTAATGGGTGC
1 ATCGATGCACTCCCTTATGCATCGATGCACTAATCACATTCGATGTTTCCATTTTTAACGGGTGC
* *
574852 ATCGATGCACTTCC-TGTGCATCGAT
1 ATCGATGCACTCCCTTATGCATCGAT
574877 ACACACTGAA
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
63 1 0.01
64 65 0.87
65 9 0.12
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (65 bp):
ATCGATGCACTCCCTTATGCATCGATGCACTAATCACATTCGATGTTTCCATTTTTAACGGGTGC
Found at i:578771 original size:32 final size:32
Alignment explanation
Indices: 578671--578776 Score: 107
Period size: 32 Copynumber: 3.4 Consensus size: 32
578661 TAGGTCCCGA
*
578671 AGAACCTAGGTAA-ACTGTCCATATGTTCCT-T
1 AGAACATAGGTAATACTGTCCATATGTT-CTGT
*
578702 A-AACATAGGT-ATACTATCCATATG-TCTCG-
1 AGAACATAGGTAATACTGTCCATATGTTCT-GT
* *
578731 AAAGACATAGGTAATTCTGTCCATATGTTCTGT
1 AGA-ACATAGGTAATACTGTCCATATGTTCTGT
578764 AGAACATAGGTAA
1 AGAACATAGGTAA
578777 ACCCTCGACT
Statistics
Matches: 62, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
28 2 0.03
29 3 0.05
30 20 0.32
31 9 0.15
32 23 0.37
33 5 0.08
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (32 bp):
AGAACATAGGTAATACTGTCCATATGTTCTGT
Found at i:582345 original size:23 final size:23
Alignment explanation
Indices: 582314--582366 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
582304 TTGAGGGTTC
* * * *
582314 TACGCGGTCCTTCGGGATATTTT
1 TACGTGGTCCTTCGAGACATTTA
*
582337 TACGTGGTCTTTCGAGACATTTA
1 TACGTGGTCCTTCGAGACATTTA
582360 TACGTGG
1 TACGTGG
582367 CACTTTGGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (23 bp):
TACGTGGTCCTTCGAGACATTTA
Found at i:583245 original size:2 final size:2
Alignment explanation
Indices: 583238--583291 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
583228 TGCACCTTTC
583238 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
583280 AT AT AT AC AT AT
1 AT AT AT AT AT AT
583292 CCACACATAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:583618 original size:30 final size:30
Alignment explanation
Indices: 583565--583744 Score: 317
Period size: 30 Copynumber: 6.0 Consensus size: 30
583555 GGACCTATCT
* * *
583565 AGAGGTCACAAAGA-CCCCGGTAACTATCC
1 AGAGGTCATAAAGATCCTCGGTAACTGTCC
*
583594 AGAGGTCATAAAGATCCTCGGTAACTATCC
1 AGAGGTCATAAAGATCCTCGGTAACTGTCC
583624 AGAGGTCATAAAGATCCTCGGTAACTGTCC
1 AGAGGTCATAAAGATCCTCGGTAACTGTCC
583654 AGAGGTCATAAAGATCCTCGGTAACTGTCC
1 AGAGGTCATAAAGATCCTCGGTAACTGTCC
583684 AGAGGTCATAAAGATCCTCGGTAACTGTCC
1 AGAGGTCATAAAGATCCTCGGTAACTGTCC
583714 AGAGGTCATAAAGATCCTCGGTAACTGTCC
1 AGAGGTCATAAAGATCCTCGGTAACTGTCC
583744 A
1 A
583745 TATGTTCCTT
Statistics
Matches: 147, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
29 13 0.09
30 134 0.91
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (30 bp):
AGAGGTCATAAAGATCCTCGGTAACTGTCC
Found at i:583775 original size:31 final size:30
Alignment explanation
Indices: 583733--583830 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 30
583723 AAAGATCCTC
*
583733 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCATAGAACATA
* *
583763 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCATAGAACATA
*
583794 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT--AACTGTCCATATGTTCCATAGAACATA
583826 GGTAA
1 GGTAA
583831 ACCCTCGACT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
30 6 0.11
31 25 0.44
32 25 0.44
33 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCATAGAACATA
Found at i:584694 original size:21 final size:21
Alignment explanation
Indices: 584664--584708 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
584654 ATTCTGTCGT
* *
584664 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
584685 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
584706 TTG
1 TTG
584709 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:585985 original size:17 final size:18
Alignment explanation
Indices: 585957--585994 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
585947 AAAATGGAAA
585957 CATCGAATGCAGTTAGTG
1 CATCGAATGCAGTTAGTG
585975 CATCG-ATGCAGTTAGTG
1 CATCGAATGCAGTTAGTG
585992 CAT
1 CAT
585995 GGGTAGTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (18 bp):
CATCGAATGCAGTTAGTG
Found at i:587265 original size:2 final size:2
Alignment explanation
Indices: 587253--587287 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
587243 GAACATGTGA
*
587253 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
587288 ATAAGACATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:587745 original size:23 final size:23
Alignment explanation
Indices: 587677--587745 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
587667 CAACCTTATA
* *
587677 TGGCACTTTAGTGCATTTCTACA
1 TGGCACTTCAGTGCATTTCTACG
* * * * *
587700 CGGTACTACGGTGCAATTCTACG
1 TGGCACTTCAGTGCATTTCTACG
*
587723 TGGCACTTCAGTGCATTTATACG
1 TGGCACTTCAGTGCATTTCTACG
587746 AGTGTGGTGA
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (23 bp):
TGGCACTTCAGTGCATTTCTACG
Found at i:588994 original size:19 final size:19
Alignment explanation
Indices: 588938--588997 Score: 111
Period size: 19 Copynumber: 3.2 Consensus size: 19
588928 TTGTCAGTAT
*
588938 GTGGATAAGATAGAATATT
1 GTGGATAAGATAGAATATG
588957 GTGGATAAGATAGAATATG
1 GTGGATAAGATAGAATATG
588976 GTGGATAAGATAGAATATG
1 GTGGATAAGATAGAATATG
588995 GTG
1 GTG
588998 AACAAGTGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (19 bp):
GTGGATAAGATAGAATATG
Found at i:591248 original size:19 final size:19
Alignment explanation
Indices: 591224--591271 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
591214 TTCAGTGTAT
591224 ATCGATGCACAGGAAGTGC
1 ATCGATGCACAGGAAGTGC
591243 ATCGATGCACAGGAAGTGC
1 ATCGATGCACAGGAAGTGC
591262 ATCGATGCAC
1 ATCGATGCAC
591272 CCATTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.31, C:0.23, G:0.29, T:0.17
Consensus pattern (19 bp):
ATCGATGCACAGGAAGTGC
Found at i:591310 original size:64 final size:64
Alignment explanation
Indices: 591238--591399 Score: 195
Period size: 64 Copynumber: 2.5 Consensus size: 64
591228 ATGCACAGGA
* *
591238 AGTGCATCGATGCACAGGAAGTGCATCGATGCAC-CCATTAAAAATGAAAACATCGAATG-CAGT
1 AGTGCATCGATGCAAAGGAAGTGCATCGATGCACTCCATT-AAAATGAAAACATCGAA-GACAAT
591301 T
64 T
* *
591302 AGTGCATCGATGCATAAGG-AGTGCATCGATGCACTCCCTTAAAATGAAAACATCGAAGATAATT
1 AGTGCATCGATGCA-AAGGAAGTGCATCGATGCACTCCATTAAAATGAAAACATCGAAGACAATT
** * **
591366 TTTGTATCGATGCATGGGAAGTGCATCGATGCAC
1 AGTGCATCGATGCAAAGGAAGTGCATCGATGCAC
591400 ATGTTAAAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
63 3 0.04
64 75 0.88
65 7 0.08
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (64 bp):
AGTGCATCGATGCAAAGGAAGTGCATCGATGCACTCCATTAAAATGAAAACATCGAAGACAATT
Found at i:593577 original size:20 final size:20
Alignment explanation
Indices: 593552--593589 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
593542 TTCCCATTGA
**
593552 AGTGCATCGGTGCATTCTAT
1 AGTGCATCAATGCATTCTAT
593572 AGTGCATCAATGCATTCT
1 AGTGCATCAATGCATTCT
593590 TTAACAGGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (20 bp):
AGTGCATCAATGCATTCTAT
Found at i:597716 original size:24 final size:20
Alignment explanation
Indices: 597666--597703 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
597656 TTCCCATTGA
*
597666 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
597686 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
597704 TTAACAGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:599772 original size:23 final size:23
Alignment explanation
Indices: 599746--599805 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
599736 ATGGCACTTT
599746 GGTGCATTTCTACGCGGCACTAC
1 GGTGCATTTCTACGCGGCACTAC
* * **
599769 GGTGCAATTCTACGTGGCACTTT
1 GGTGCATTTCTACGCGGCACTAC
*
599792 GGTGCATTTATACG
1 GGTGCATTTCTACG
599806 AGCTGTGGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (23 bp):
GGTGCATTTCTACGCGGCACTAC
Found at i:602801 original size:2 final size:2
Alignment explanation
Indices: 602794--602860 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
602784 TTATTATGTT
602794 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
602836 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 T
602861 CATAACTTTC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:603628 original size:417 final size:417
Alignment explanation
Indices: 602854--603692 Score: 1536
Period size: 417 Copynumber: 2.0 Consensus size: 417
602844 TATATATATA
*
602854 TATATATCATAACTTTCGATATCTAATCTATTGATCGACTAATATGAATCGGATATTGTAGAGGC
1 TATATATCATAACTTTCGATATCTAATCTATTGATCGACTAATATGAATCGGATACTGTAGAGGC
*
602919 GAGGGCGACACTCCCAATCCAATGTGCTCCATTCGCAAACGTCAAGATTCGAACCTTTAGAATTG
66 GAGGGCGACACTCCCAATCCAATGTGCTCCATTCGCAAACGTCAAGATTCGAACCTCTAGAATTG
* *
602984 CTTAAGGGATTTAGTATCTCATCTCACTAAACCAACTAGTTGTTAGTATTTTTTTATAACACAAT
131 CTTAAGGGATTTAGTACCTCATCTCACTAAACCAACTAGTTGCTAGTATTTTTTTATAACACAAT
*
603049 TATCAAATGAGTAAATTGCTCCAATGACCATTTAACTATAAGATTGGTGTCAACATGATCACTAT
196 TATCAAATGAGTAAATTGCTCCAATGACCATTTAACTATAAGATTGGTGTCAACATGATCACCAT
*
603114 ACTTTCAATTTTGGCAATATAATCACATAACTATTTAAGTGATTTTAATGTAGACACTTGTTATA
261 ACATTCAATTTTGGCAATATAATCACATAACTATTTAAGTGATTTTAATGTAGACACTTGTTATA
* *
603179 AAACAAACGGGATAACTGATGTAGACCTCTGACTCGCCGTTAGTCAATAACAATCACATCAACTA
326 AAACAAACGGGATAACTAATGTAGACCTCTGACTCACCGTTAGTCAATAACAATCACATCAACTA
603244 CGTGTTTGTTTTGTAACGACAAGTAGC
391 CGTGTTTGTTTTGTAACGACAAGTAGC
* * *
603271 TATATATTATAA-TTTCTTATATTTAATCTATTGATCGACTAATATGAATCGGATACTGTAGAGG
1 TATATATCATAACTTTC-GATATCTAATCTATTGATCGACTAATATGAATCGGATACTGTAGAGG
* * *
603335 CGAGGGTGACCCTCCCAATCCAATTTGCTCCATTCGCAAACGTCAAGATTCGAACCTCTAGAATT
65 CGAGGGCGACACTCCCAATCCAATGTGCTCCATTCGCAAACGTCAAGATTCGAACCTCTAGAATT
603400 GCTTAAGGGATTTAGTACCTCATCTCACTAAACCAACTAGTTGCTAGTATTTTTTTATAACACAA
130 GCTTAAGGGATTTAGTACCTCATCTCACTAAACCAACTAGTTGCTAGTATTTTTTTATAACACAA
603465 TTATCAAATGAGTAAATTGCTCCAATGACCATTTAACTATAAGATTGGTGTCAACATGATCACCA
195 TTATCAAATGAGTAAATTGCTCCAATGACCATTTAACTATAAGATTGGTGTCAACATGATCACCA
603530 TACATTCAATTTTGGCAATATAATCACATAACTATTTAAGTGATTTTAATGTAGACACTTGTTAT
260 TACATTCAATTTTGGCAATATAATCACATAACTATTTAAGTGATTTTAATGTAGACACTTGTTAT
603595 AAAACAAACGGGATAACTAATGTAGACCTCTGACTCACCGTTAGTCAATAACAATCACATCAACT
325 AAAACAAACGGGATAACTAATGTAGACCTCTGACTCACCGTTAGTCAATAACAATCACATCAACT
603660 ACGTGTTTGTTTTGTAACGACAAGTAGC
390 ACGTGTTTGTTTTGTAACGACAAGTAGC
603688 TATAT
1 TATAT
603693 TAAAACCACA
Statistics
Matches: 407, Mismatches: 14, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
416 4 0.01
417 403 0.99
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33
Consensus pattern (417 bp):
TATATATCATAACTTTCGATATCTAATCTATTGATCGACTAATATGAATCGGATACTGTAGAGGC
GAGGGCGACACTCCCAATCCAATGTGCTCCATTCGCAAACGTCAAGATTCGAACCTCTAGAATTG
CTTAAGGGATTTAGTACCTCATCTCACTAAACCAACTAGTTGCTAGTATTTTTTTATAACACAAT
TATCAAATGAGTAAATTGCTCCAATGACCATTTAACTATAAGATTGGTGTCAACATGATCACCAT
ACATTCAATTTTGGCAATATAATCACATAACTATTTAAGTGATTTTAATGTAGACACTTGTTATA
AAACAAACGGGATAACTAATGTAGACCTCTGACTCACCGTTAGTCAATAACAATCACATCAACTA
CGTGTTTGTTTTGTAACGACAAGTAGC
Found at i:603756 original size:3 final size:3
Alignment explanation
Indices: 603750--603882 Score: 176
Period size: 3 Copynumber: 43.7 Consensus size: 3
603740 TCATTTAAAG
** *
603750 TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
603798 TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TAA TAA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
603846 TTA TTA TTTA TTA TTA TTA ATA TTA TATA TTA TTA TT
1 TTA TTA -TTA TTA TTA TTA TTA TTA T-TA TTA TTA TT
603883 TAATAAATAA
Statistics
Matches: 116, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
3 110 0.95
4 6 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:604393 original size:17 final size:18
Alignment explanation
Indices: 604363--604400 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
604353 CACACAGCAG
604363 AGAACGACAAAAAAAAAC
1 AGAACGACAAAAAAAAAC
604381 AGAACGA-AAAAAAAAAC
1 AGAACGACAAAAAAAAAC
604398 AGA
1 AGA
604401 GAGGAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.74, C:0.13, G:0.13, T:0.00
Consensus pattern (18 bp):
AGAACGACAAAAAAAAAC
Found at i:604680 original size:13 final size:13
Alignment explanation
Indices: 604662--604690 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
604652 ACCACCGTTA
604662 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
604675 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
604688 CGG
1 CGG
604691 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:605982 original size:20 final size:21
Alignment explanation
Indices: 605959--606010 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
605949 AGAAATTAAA
605959 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
605979 AATTCTTTTCTTTTAAATTTTT
1 AATTCATTT-ATTTAAATTTTT
606001 -ATT-ATTTATT
1 AATTCATTTATT
606011 ATTTTATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 2 0.08
20 11 0.42
21 6 0.23
22 7 0.27
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:610687 original size:9 final size:10
Alignment explanation
Indices: 610669--610706 Score: 67
Period size: 10 Copynumber: 3.7 Consensus size: 10
610659 GCAAAGAAAG
610669 AAGAAAAAAA
1 AAGAAAAAAA
610679 AAGAAAAAAA
1 AAGAAAAAAA
610689 AAGAAAAAAA
1 AAGAAAAAAA
610699 AAGGAAAA
1 AA-GAAAA
610707 TTGAATCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 22 0.81
11 5 0.19
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:610688 original size:11 final size:11
Alignment explanation
Indices: 610672--610706 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
610662 AAGAAAGAAG
610672 AAAAAAAAAG-
1 AAAAAAAAAGA
610682 AAAAAAAAAGA
1 AAAAAAAAAGA
*
610693 AAAAAAAAGGA
1 AAAAAAAAAGA
610704 AAA
1 AAA
610707 TTGAATCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:613047 original size:93 final size:93
Alignment explanation
Indices: 612867--613061 Score: 232
Period size: 93 Copynumber: 2.1 Consensus size: 93
612857 TAGAAATAAG
* * * * * *
612867 GTGCCCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGA
1 GTGCTCATAACATCTTCTGGAAGTGTTCTTTGAATTATCTGATATGATTTGGTATGAACCACAAA
** * *
612932 ACCTGTTATTGAATTTGGAAGATGAA-T
66 ACCAATCATTGAATTTGAAAGATGAATT
*
612959 GTGCTCATAACATCTTTTGGGAAGTGTTCTTTGAATTATCTGATATGATTTGGTATGAACTC-CA
1 GTGCTCATAACATCTTCT-GGAAGTGTTCTTTGAATTATCTGATATGATTTGGTATGAAC-CACA
* *
613023 AAATCAATCATTGGATTTGAAAGATGAATT
64 AAACCAATCATTGAATTTGAAAGATGAATT
*
613053 TTGCTCATA
1 GTGCTCATA
613062 TTAGAAATAA
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
92 15 0.17
93 61 0.71
94 10 0.12
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (93 bp):
GTGCTCATAACATCTTCTGGAAGTGTTCTTTGAATTATCTGATATGATTTGGTATGAACCACAAA
ACCAATCATTGAATTTGAAAGATGAATT
Found at i:614990 original size:52 final size:53
Alignment explanation
Indices: 614908--615080 Score: 188
Period size: 54 Copynumber: 3.3 Consensus size: 53
614898 AAAGAGATTC
* *
614908 AATGTTTGA-GAACATCTGAGCAGAAGCCACA-AAAAAATGAATATGTTGTCA
1 AATGTTTTACGAACATCTGAGCAGAAGCCACAGAAAAAATGAATATATTGTCA
* * * ** *
614959 AATGTTTTACGAACATCTAAACAGAAACCACAGGAAAGGATGAATGTATTGTCA
1 AATGTTTTACGAACATCTGAGCAGAAGCCACA-GAAAAAATGAATATATTGTCA
** ** * *
615013 AATGTTTTACGAACATCTGAGCAGAAGCCACAGTAAAGGATGAATGCACTATCA
1 AATGTTTTACGAACATCTGAGCAGAAGCCACAG-AAAAAATGAATATATTGTCA
615067 AATGTTTTACGAAC
1 AATGTTTTACGAAC
615081 CTGCTATTCT
Statistics
Matches: 104, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
51 8 0.08
52 19 0.18
53 1 0.01
54 76 0.73
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (53 bp):
AATGTTTTACGAACATCTGAGCAGAAGCCACAGAAAAAATGAATATATTGTCA
Found at i:615018 original size:54 final size:54
Alignment explanation
Indices: 614944--615080 Score: 193
Period size: 54 Copynumber: 2.5 Consensus size: 54
614934 CCACAAAAAA
* *
614944 ATGAATATGTTGTCAAATGTTTTACGAACATCTAAACAGAAACCACAGGAAAGG
1 ATGAATGTATTGTCAAATGTTTTACGAACATCTAAACAGAAACCACAGGAAAGG
* * * *
614998 ATGAATGTATTGTCAAATGTTTTACGAACATCTGAGCAGAAGCCACAGTAAAGG
1 ATGAATGTATTGTCAAATGTTTTACGAACATCTAAACAGAAACCACAGGAAAGG
* * *
615052 ATGAATGCACTATCAAATGTTTTACGAAC
1 ATGAATGTATTGTCAAATGTTTTACGAAC
615081 CTGCTATTCT
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 74 1.00
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.26
Consensus pattern (54 bp):
ATGAATGTATTGTCAAATGTTTTACGAACATCTAAACAGAAACCACAGGAAAGG
Found at i:615473 original size:22 final size:22
Alignment explanation
Indices: 615446--615498 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
615436 CTACACTCTT
** *
615446 CAAAGATGATGGATTCTCTTTT
1 CAAAGATGACAGATTCTCTTTC
*
615468 TAAAGATGACAGATTCTCTTTC
1 CAAAGATGACAGATTCTCTTTC
615490 CAAAGATGA
1 CAAAGATGA
615499 AAATTTTATG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (22 bp):
CAAAGATGACAGATTCTCTTTC
Found at i:616295 original size:76 final size:76
Alignment explanation
Indices: 616169--616959 Score: 1501
Period size: 76 Copynumber: 10.4 Consensus size: 76
616159 CTATTTCTCA
*
616169 CATCTGTAAGTCCTTCAGTGCATCATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
616234 ATCCTTCGGGT
66 ATCCTTCGGGT
616245 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
616310 ATCCTTCGGGT
66 ATCCTTCGGGT
*
616321 CATCTGTAAGTCCTTCAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
616386 ATCCTTCGGGT
66 ATCCTTCGGGT
*
616397 CATCTGTAAGTCCTTCAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
616462 ATCCTTCGGGT
66 ATCCTTCGGGT
616473 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
616538 ATCCTTCGGGT
66 ATCCTTCGGGT
*
616549 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
616614 ATCCTTCGGGT
66 ATCCTTCGGGT
*
616625 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
616690 ATCCTTCGGGT
66 ATCCTTCGGGT
616701 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
616766 AGCCTTCGGGT
66 ATCCTTCGGGT
616777 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
616842 ATCCTTCGGGT
66 ATCCTTCGGGT
*
616853 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
616918 AAGCCTTCGGGT
65 AATCCTTCGGGT
616930 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
616960 TCAACATTTC
Statistics
Matches: 704, Mismatches: 10, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
76 632 0.90
77 72 0.10
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ATCCTTCGGGT
Found at i:617098 original size:3 final size:3
Alignment explanation
Indices: 617092--617215 Score: 158
Period size: 3 Copynumber: 40.7 Consensus size: 3
617082 TCATTTAAAG
** * *
617092 TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA GTA GTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
617140 TTA TTA TTA GTA TTA TTA TTA TTA TAA TAA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
617189 TTA TTA TTA ATA TTA TATA TTA TTA TT
1 TTA TTA TTA TTA TTA T-TA TTA TTA TT
617216 TAATAAATAA
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
3 101 0.94
4 6 0.06
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:620371 original size:18 final size:19
Alignment explanation
Indices: 620336--620372 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
620326 CACGGAATGT
620336 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
620356 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
620373 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:622926 original size:23 final size:22
Alignment explanation
Indices: 622896--622938 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
622886 TAAGTTTTTT
622896 AAATTTCAATAATTTTCTATTCA
1 AAATTTCAATAATTTT-TATTCA
622919 AAATTTCAATAATTTTTATT
1 AAATTTCAATAATTTTTATT
622939 TTATGTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATTTCAATAATTTTTATTCA
Found at i:622983 original size:18 final size:19
Alignment explanation
Indices: 622944--622989 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
622934 TTATTTTATG
622944 TTTATAATTTTCTATCATT
1 TTTATAATTTTCTATCATT
*
622963 TTTATAATTTTC-ATGATT
1 TTTATAATTTTCTATCATT
622981 TTTA-AATTT
1 TTTATAATTT
622990 CTACAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 5 0.19
18 9 0.35
19 12 0.46
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTATAATTTTCTATCATT
Found at i:623415 original size:25 final size:26
Alignment explanation
Indices: 623366--623415 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
623356 TCATATTTTG
*
623366 TTTGATTTGCAGACATGTAAGATGAA
1 TTTGATTTGCAGACATGTAAAATGAA
623392 TTTGATTT-CAGTA-ATGTAAAATGA
1 TTTGATTTGCAG-ACATGTAAAATGA
623416 CAGAATTGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (26 bp):
TTTGATTTGCAGACATGTAAAATGAA
Found at i:623458 original size:21 final size:21
Alignment explanation
Indices: 623429--623468 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
623419 AATTGCTCTT
* * *
623429 CTTATTTTTATTTTTTTTTTG
1 CTTAATTTTAGTTTGTTTTTG
623450 CTTAATTTTAGTTTGTTTT
1 CTTAATTTTAGTTTGTTTT
623469 ATAAATTACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.75
Consensus pattern (21 bp):
CTTAATTTTAGTTTGTTTTTG
Found at i:623807 original size:24 final size:22
Alignment explanation
Indices: 623762--623806 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
623752 AAACATTGAC
623762 TTAATTGAAAAAAAATTATATA
1 TTAATTGAAAAAAAATTATATA
623784 TTAATTGAAAAAAAATTATATA
1 TTAATTGAAAAAAAATTATATA
623806 T
1 T
623807 AGAGAGGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
TTAATTGAAAAAAAATTATATA
Found at i:624366 original size:195 final size:195
Alignment explanation
Indices: 624001--624394 Score: 586
Period size: 195 Copynumber: 2.0 Consensus size: 195
623991 TAGAAATCCA
*
624001 ACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTTACTTAATTGAAAAAAA
1 ACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAA
624066 TTATATATAGAGAGGTATTATTGTAATTATTCATAAATATATAAGATAAAATTATATATATTTTC
66 TTATATATAGAGAGGTATTATTGTAATTATTCATAAATATATAAGATAAAATTATATATATTTTC
624131 GGGTCGGGTATTTTTCACCCGAAACCCGAACTCGACTCGACCC-A-AATATCACACTTAAAAAAA
131 GGGTCGGGTATTTTTCACCCGAAACCCGAA--C-ACTCGACCCGACAATATCACACTTAAAAAAA
624194 CTG
193 CTG
624197 ACCCGACCCGAAATAAT-AAAAAA-TATTTTTATTCAAT-AAAACAGTGACTTAATTGAAAAAAA
1 ACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTG--AAAAA
* * *
624259 AATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTT
64 AATTATATATAGAGAGGTATTATTGTAATTATTCATAAATATATAAGATAAAATTATATATATTT
624324 TCAGGTCAGGTCGGGTATTTTTCACCCGAAACCCG-A-ACTCGACCCGACCCGAATATCACACTT
129 TC--G---GGTCGGGTATTTTTCACCCGAAACCCGAACACTCGACCCGA--C-AATATCACACTT
624387 AAAAAAAC
186 AAAAAAAC
624395 CCAACCCGAC
Statistics
Matches: 182, Mismatches: 4, Indels: 20
0.88 0.02 0.10
Matches are distributed among these distances:
193 17 0.09
194 14 0.08
195 84 0.46
196 18 0.10
197 1 0.01
199 1 0.01
200 47 0.26
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (195 bp):
ACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAA
TTATATATAGAGAGGTATTATTGTAATTATTCATAAATATATAAGATAAAATTATATATATTTTC
GGGTCGGGTATTTTTCACCCGAAACCCGAACACTCGACCCGACAATATCACACTTAAAAAAACTG
Found at i:627987 original size:77 final size:76
Alignment explanation
Indices: 627859--628002 Score: 207
Period size: 77 Copynumber: 1.9 Consensus size: 76
627849 GAAAATAAGG
* * * * *
627859 TTTTTTAATATAATAATATTAAAAAATTATACATTTGTAATATTTGGCACCTAGATTGAAAAACA
1 TTTTTTAATATAATAATATTAAAAAATGATACATTTGTAACATTAGACACCTAGATT-AAAAAAA
627924 ATTATAAGGTTT
65 ATTATAAGGTTT
* * *
627936 TTTTTTAATATAATGATATTAAAAAATGGTACATTTGTAACGTTAGACACCTAGATTAAAAAAAA
1 TTTTTTAATATAATAATATTAAAAAATGATACATTTGTAACATTAGACACCTAGATTAAAAAAAA
628001 TT
66 TT
628003 GTAAAGTTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
76 9 0.15
77 50 0.85
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.40
Consensus pattern (76 bp):
TTTTTTAATATAATAATATTAAAAAATGATACATTTGTAACATTAGACACCTAGATTAAAAAAAA
TTATAAGGTTT
Found at i:629889 original size:4 final size:4
Alignment explanation
Indices: 629880--629918 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
629870 GTACCAGGAA
629880 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
629919 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:630969 original size:27 final size:27
Alignment explanation
Indices: 630911--630969 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
630901 TTAACTGATG
* * *
630911 TAGCTGTTTCATTTTCCTCTTCTGTAG
1 TAGCTGTCTCATTTTCCTCTTCTGAAA
630938 TAGCTGTCTCATTTTCCTCTTCT-AAA
1 TAGCTGTCTCATTTTCCTCTTCTGAAA
630964 TCAGCT
1 T-AGCT
630970 ACTACAGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.15, C:0.25, G:0.12, T:0.47
Consensus pattern (27 bp):
TAGCTGTCTCATTTTCCTCTTCTGAAA
Found at i:632350 original size:2 final size:2
Alignment explanation
Indices: 632343--632386 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
632333 TAAAAATAAT
632343 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
632384 TA T
1 TA T
632387 TAATAAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:632390 original size:6 final size:7
Alignment explanation
Indices: 632344--632391 Score: 53
Period size: 8 Copynumber: 6.4 Consensus size: 7
632334 AAAAATAATT
632344 ATATATA
1 ATATATA
632351 TATATATA
1 -ATATATA
632359 TATATATA
1 -ATATATA
632367 TATATATA
1 -ATATATA
632375 TATATATA
1 -ATATATA
632383 ATAT-TA
1 ATATATA
632389 ATA
1 ATA
632392 AATTTAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 5 0.12
7 4 0.10
8 31 0.77
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
ATATATA
Found at i:633327 original size:14 final size:14
Alignment explanation
Indices: 633308--633337 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
633298 GCAACATAAT
633308 AAAGGAGTTAAATG
1 AAAGGAGTTAAATG
633322 AAAGGAGTTAAATG
1 AAAGGAGTTAAATG
633336 AA
1 AA
633338 GGCTTACAAG
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:0.53, C:0.00, G:0.27, T:0.20
Consensus pattern (14 bp):
AAAGGAGTTAAATG
Found at i:638276 original size:37 final size:37
Alignment explanation
Indices: 638234--638305 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
638224 AACGTTTCGT
638234 GTCTTATGTATTTTGTAGGAGTGTTCTTAAGTCTTAA
1 GTCTTATGTATTTTGTAGGAGTGTTCTTAAGTCTTAA
*
638271 GTCTTATGTATTTTGTAGGAGTGTTCTTATGTCTT
1 GTCTTATGTATTTTGTAGGAGTGTTCTTAAGTCTT
638306 TTGTAATTGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.18, C:0.08, G:0.22, T:0.51
Consensus pattern (37 bp):
GTCTTATGTATTTTGTAGGAGTGTTCTTAAGTCTTAA
Found at i:644810 original size:3 final size:3
Alignment explanation
Indices: 644802--644826 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
644792 TTTGTACAAT
644802 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
644827 ATACAATGAA
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:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:650645 original size:57 final size:57
Alignment explanation
Indices: 650572--650686 Score: 194
Period size: 57 Copynumber: 2.0 Consensus size: 57
650562 CTACATACAA
* * * *
650572 AAGGTAAAGAATTGAAGATTATGATTCTAAGACTTTCACCACTCTACCCTATTTCCT
1 AAGGTAAAGAACTGAAGATTATGATTCTAAGACTTGCACAACTCCACCCTATTTCCT
650629 AAGGTAAAGAACTGAAGATTATGATTCTAAGACTTGCACAACTCCACCCTATTTCCT
1 AAGGTAAAGAACTGAAGATTATGATTCTAAGACTTGCACAACTCCACCCTATTTCCT
650686 A
1 A
650687 GAGAACAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (57 bp):
AAGGTAAAGAACTGAAGATTATGATTCTAAGACTTGCACAACTCCACCCTATTTCCT
Found at i:651002 original size:31 final size:31
Alignment explanation
Indices: 650959--651053 Score: 145
Period size: 31 Copynumber: 3.1 Consensus size: 31
650949 CTATTTGTTT
*
650959 ATTGCTCATATCAAACAAGGAAATAATATCA
1 ATTGCTCATATCAAACAAGGAAATAATAACA
* *
650990 ATTGTTCATATCAAACAGGGAAATAATAACA
1 ATTGCTCATATCAAACAAGGAAATAATAACA
* *
651021 ATTGCTCATACCAAACAAGGAAATAATGACA
1 ATTGCTCATATCAAACAAGGAAATAATAACA
651052 AT
1 AT
651054 CTTTTCAAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (31 bp):
ATTGCTCATATCAAACAAGGAAATAATAACA
Found at i:654898 original size:31 final size:31
Alignment explanation
Indices: 654857--654917 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
654847 ATTTTGTTAC
*
654857 AAATCGATAATACTAGCGATCAATATATTAT
1 AAATCAATAATACTAGCGATCAATATATTAT
** * *
654888 AAATCAATAATGTTAGTGATTAATATATTA
1 AAATCAATAATACTAGCGATCAATATATTA
654918 CTTTTAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (31 bp):
AAATCAATAATACTAGCGATCAATATATTAT
Found at i:658459 original size:2 final size:2
Alignment explanation
Indices: 658452--658481 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
658442 TCTTTTATAA
658452 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
658482 GAGATAATGG
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:664244 original size:14 final size:14
Alignment explanation
Indices: 664225--664251 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
664215 AGGCCGACCG
664225 AACCGAATTAACCT
1 AACCGAATTAACCT
664239 AACCGAATTAACC
1 AACCGAATTAACC
664252 AAATTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.30, G:0.07, T:0.19
Consensus pattern (14 bp):
AACCGAATTAACCT
Found at i:664701 original size:183 final size:184
Alignment explanation
Indices: 664378--664764 Score: 638
Period size: 183 Copynumber: 2.1 Consensus size: 184
664368 AATTCTAATT
* * *
664378 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
* *
664442 TATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTATT
* * * *
664507 GGATTTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AGCCCATATGTTA
131 AGATCTTAAATTATTAATTGAGTTTTAAATGATTTGGG-TTGAGCCCATATGTTA
664561 TATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATATATAA
*
664625 TTATAAAATAAAAAATTTATAT-AATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTAT
65 TTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTAT
664689 TAGATCTTAAATTATTAATTGAGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
130 TAGATCTTAAATTATTAATTGAGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
664744 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
664765 AAAATTTAAT
Statistics
Matches: 191, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
182 2 0.01
183 123 0.64
184 66 0.35
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTATT
AGATCTTAAATTATTAATTGAGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
Found at i:665035 original size:15 final size:15
Alignment explanation
Indices: 665015--665066 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
665005 ATAAAAAAAT
665015 TCACCCTTAATGACC
1 TCACCCTTAATGACC
* ** **
665030 TCACCCGTAAAAAAAA
1 TCACCC-TTAATGACC
665046 TCACCCTTAATGACC
1 TCACCCTTAATGACC
665061 TCACCC
1 TCACCC
665067 GTCCCTCACC
Statistics
Matches: 26, Mismatches: 10, Indels: 2
0.68 0.26 0.05
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.35, C:0.38, G:0.06, T:0.21
Consensus pattern (15 bp):
TCACCCTTAATGACC
Found at i:665041 original size:31 final size:31
Alignment explanation
Indices: 665006--665068 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
664996 GCTAAAAGTA
*
665006 TAAAAAAATTCACCCTTAATGACCTCACCCG
1 TAAAAAAAATCACCCTTAATGACCTCACCCG
665037 TAAAAAAAATCACCCTTAATGACCTCACCCG
1 TAAAAAAAATCACCCTTAATGACCTCACCCG
665068 T
1 T
665069 CCCTCACCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.40, C:0.32, G:0.06, T:0.22
Consensus pattern (31 bp):
TAAAAAAAATCACCCTTAATGACCTCACCCG
Found at i:667514 original size:24 final size:24
Alignment explanation
Indices: 667486--667537 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
667476 GACCCGACCC
667486 GACCCGAACCAACCGTTGACCGTT
1 GACCCGAACCAACCGTTGACCGTT
* * * *
667510 GACCCGACCCGATCGTTGACTGTT
1 GACCCGAACCAACCGTTGACCGTT
667534 GACC
1 GACC
667538 TCCTTTGACC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.37, G:0.23, T:0.19
Consensus pattern (24 bp):
GACCCGAACCAACCGTTGACCGTT
Found at i:677264 original size:22 final size:22
Alignment explanation
Indices: 677228--677272 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
677218 AAAATTTCAT
677228 ATTTATATTTGTATAATAACATCA
1 ATTTATATTTGTAT-ATAA-ATCA
677252 ATTTAT-TTT-TATATAAATCA
1 ATTTATATTTGTATATAAATCA
677272 A
1 A
677273 ATCGATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
21 4 0.19
22 3 0.14
23 3 0.14
24 6 0.29
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (22 bp):
ATTTATATTTGTATATAAATCA
Found at i:678790 original size:3 final size:3
Alignment explanation
Indices: 678782--678839 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
678772 ATGACTGTAA
678782 AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
678829 AAT AAT AAT AA
1 AAT AAT AAT AA
678840 ATAAATTCTT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 52 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:679538 original size:22 final size:23
Alignment explanation
Indices: 679513--679557 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
679503 TTTTTACATT
679513 TTAAAAATAAAACTTA-AAAATA
1 TTAAAAATAAAACTTAGAAAATA
679535 TTAAAAATAAAACTTAGAAAATA
1 TTAAAAATAAAACTTAGAAAATA
679558 ACTTTAGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (23 bp):
TTAAAAATAAAACTTAGAAAATA
Found at i:679555 original size:14 final size:13
Alignment explanation
Indices: 679513--679558 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
679503 TTTTTACATT
679513 TTAAAAATAAAAC
1 TTAAAAATAAAAC
679526 TTAAAAAT---A-
1 TTAAAAATAAAAC
679535 TTAAAAATAAAAC
1 TTAAAAATAAAAC
679548 TTAGAAAATAA
1 TTA-AAAATAA
679559 CTTTAGACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
9 8 0.29
10 1 0.04
12 1 0.04
13 11 0.39
14 7 0.25
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.26
Consensus pattern (13 bp):
TTAAAAATAAAAC
Found at i:680979 original size:14 final size:14
Alignment explanation
Indices: 680960--680988 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
680950 AATCATTAAA
680960 AACGGTTAATCGTT
1 AACGGTTAATCGTT
680974 AACGGTTAATCGTT
1 AACGGTTAATCGTT
680988 A
1 A
680989 TTAATAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (14 bp):
AACGGTTAATCGTT
Found at i:681623 original size:32 final size:32
Alignment explanation
Indices: 681555--681623 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
681545 AACACCCCTA
*
681555 ATATATTATATTATTATTTTGAATGATATAAT
1 ATATATTATATTATTATTTTGAATGATATAAC
* * * *
681587 ATATATTATGTTATTATTTTTAATGATTTGAC
1 ATATATTATATTATTATTTTGAATGATATAAC
681619 ATATA
1 ATATA
681624 ATCAATCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.54
Consensus pattern (32 bp):
ATATATTATATTATTATTTTGAATGATATAAC
Found at i:682768 original size:15 final size:15
Alignment explanation
Indices: 682748--682782 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
682738 AATTGCAGTT
682748 AAATAATTATCATAA
1 AAATAATTATCATAA
*
682763 AAATAATTATTATAA
1 AAATAATTATCATAA
682778 AAATA
1 AAATA
682783 TAATTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATAATTATCATAA
Found at i:682788 original size:14 final size:15
Alignment explanation
Indices: 682748--682790 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
682738 AATTGCAGTT
* *
682748 AAATAATTATCATAA
1 AAATAATAATTATAA
*
682763 AAATAATTATTATAA
1 AAATAATAATTATAA
682778 AAAT-ATAATTATA
1 AAATAATAATTATA
682791 TTGATAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 8 0.31
15 18 0.69
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATAATAATTATAA
Found at i:686231 original size:85 final size:85
Alignment explanation
Indices: 686087--686258 Score: 326
Period size: 85 Copynumber: 2.0 Consensus size: 85
686077 ACTAATATCT
*
686087 TTAATAGATTATGTTCTCTTTTTCTTTCCAGCTTTCAAAGTTGTTGATGGTGTCTTCTGGACATA
1 TTAATAGATTATGTTCTCTTTTTCTTTCCAGCTTTCAAAGTTGTTGATGGTGTCCTCTGGACATA
686152 TCCTTTACCTTTACACTTAG
66 TCCTTTACCTTTACACTTAG
*
686172 TTAATAGATTATGTTCTCTTTTTCTTTCCAGCTTTTAAAGTTGTTGATGGTGTCCTCTGGACATA
1 TTAATAGATTATGTTCTCTTTTTCTTTCCAGCTTTCAAAGTTGTTGATGGTGTCCTCTGGACATA
686237 TCCTTTACCTTTACACTTAG
66 TCCTTTACCTTTACACTTAG
686257 TT
1 TT
686259 TCCTTTTTCT
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.48
Consensus pattern (85 bp):
TTAATAGATTATGTTCTCTTTTTCTTTCCAGCTTTCAAAGTTGTTGATGGTGTCCTCTGGACATA
TCCTTTACCTTTACACTTAG
Found at i:700967 original size:30 final size:30
Alignment explanation
Indices: 700933--700990 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
700923 GAAAAAGGGT
700933 TGTGTTTTTGTAAAGTTTACATTTCGGTGC
1 TGTGTTTTTGTAAAGTTTACATTTCGGTGC
*
700963 TGTGTTTTTGTAAAGTTTGCATTTCGGT
1 TGTGTTTTTGTAAAGTTTACATTTCGGT
700991 CATTGAATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.16, C:0.09, G:0.24, T:0.52
Consensus pattern (30 bp):
TGTGTTTTTGTAAAGTTTACATTTCGGTGC
Found at i:701389 original size:16 final size:16
Alignment explanation
Indices: 701363--701405 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
701353 CTTTAACTTA
*
701363 TTTATTAATTTAAGTCT
1 TTTA-TAATTTAAGTAT
**
701380 TTTATAATTTATTTAT
1 TTTATAATTTAAGTAT
701396 TTTATAATTT
1 TTTATAATTT
701406 TATAATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTATAATTTAAGTAT
Found at i:701405 original size:8 final size:8
Alignment explanation
Indices: 701379--701416 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
701369 AATTTAAGTC
701379 TTTTATAA
1 TTTTATAA
*
701387 -TTTATTTA
1 TTTTA-TAA
701395 TTTTATAA
1 TTTTATAA
701403 TTTTATAA
1 TTTTATAA
701411 TTTTAT
1 TTTTAT
701417 TTTTTCTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 4 0.15
8 18 0.69
9 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
TTTTATAA
Found at i:703626 original size:23 final size:23
Alignment explanation
Indices: 703600--703654 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
703590 TTGCTTGTTC
* *
703600 ATATTTTCTTTTTAGTTAGCTTA
1 ATATTTTCTTTTTACTTACCTTA
*
703623 ATATGTTT-TTTTTACTTTCCTTA
1 ATAT-TTTCTTTTTACTTACCTTA
703646 AT-TTTTCTT
1 ATATTTTCTT
703655 CATTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 3 0.11
22 3 0.11
23 18 0.67
24 3 0.11
ACGTcount: A:0.18, C:0.11, G:0.05, T:0.65
Consensus pattern (23 bp):
ATATTTTCTTTTTACTTACCTTA
Found at i:714547 original size:20 final size:21
Alignment explanation
Indices: 714501--714561 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
714491 TTCCCCTGTG
714501 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
714524 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
714544 GGGGGTATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
714562 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:718301 original size:21 final size:21
Alignment explanation
Indices: 718275--718314 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
718265 CAGAACCCCA
*
718275 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
718296 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
718315 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:718349 original size:20 final size:21
Alignment explanation
Indices: 718295--718357 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
718285 GATTCCCCTG
718295 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
718319 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
718339 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
718358 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:721694 original size:22 final size:21
Alignment explanation
Indices: 721668--721714 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
721658 AAGGTCAAAA
*
721668 ATCAAATTGTTTGAAAATTG-AT
1 ATCAAATGGTTT-AAAA-TGAAT
721690 ATC-AATGGTTTAAAATGAAT
1 ATCAAATGGTTTAAAATGAAT
721710 ATCAA
1 ATCAA
721715 TTACGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 9 0.41
21 8 0.36
22 3 0.14
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (21 bp):
ATCAAATGGTTTAAAATGAAT
Found at i:723837 original size:22 final size:22
Alignment explanation
Indices: 723809--723852 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
723799 TCGGAGCCAA
723809 ACCCCCTTGGGGGGGAATCGGT
1 ACCCCCTTGGGGGGGAATCGGT
723831 ACCCCCTTGGGGGGGAATCGGT
1 ACCCCCTTGGGGGGGAATCGGT
723853 TCCCTCTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.27, G:0.41, T:0.18
Consensus pattern (22 bp):
ACCCCCTTGGGGGGGAATCGGT
Found at i:727631 original size:22 final size:21
Alignment explanation
Indices: 727589--727628 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
727579 GAGTTTATTT
*
727589 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
727610 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
727629 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:742543 original size:37 final size:37
Alignment explanation
Indices: 742478--742596 Score: 104
Period size: 36 Copynumber: 3.3 Consensus size: 37
742468 ATAAAGTATC
* *
742478 GTCTCGCTAGA-ACAATTATTC-CTAAAAATCAATTTT
1 GTCTCGCTTGAGACAGTT-TTCTCTAAAAATCAATTTT
*
742514 GTCTCGCTTGAGACAGTTTTCTCTAAAAATAAATTTT
1 GTCTCGCTTGAGACAGTTTTCTCTAAAAATCAATTTT
* * * * *
742551 ATCTTG-TTGAGAC-GATTTCTTTCAAAA-CAAATTTT
1 GTCTCGCTTGAGACAGTTTTCTCTAAAAATC-AATTTT
*
742586 GTCTCGGTTGA
1 GTCTCGCTTGA
742597 TATATTTTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
35 21 0.31
36 24 0.35
37 23 0.34
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (37 bp):
GTCTCGCTTGAGACAGTTTTCTCTAAAAATCAATTTT
Found at i:742596 original size:36 final size:37
Alignment explanation
Indices: 742499--742596 Score: 103
Period size: 35 Copynumber: 2.7 Consensus size: 37
742489 ACAATTATTC
* *
742499 CTAAAAATC-AATTTTGTCTCGCTTGAGACAGTTTTCT
1 CTAAAAA-CAAATTTTGTCTCGGTTGAGACAGATTTCT
* * *
742536 CTAAAAATAAATTTTATCT-TGTTGAGAC-GATTTCT
1 CTAAAAACAAATTTTGTCTCGGTTGAGACAGATTTCT
* *
742571 TTCAAAACAAATTTTGTCTCGGTTGA
1 CTAAAAACAAATTTTGTCTCGGTTGA
742597 TATATTTTTT
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
35 21 0.43
36 12 0.24
37 16 0.33
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (37 bp):
CTAAAAACAAATTTTGTCTCGGTTGAGACAGATTTCT
Found at i:742971 original size:36 final size:36
Alignment explanation
Indices: 742939--743056 Score: 113
Period size: 36 Copynumber: 3.4 Consensus size: 36
742929 CATTGAGATT
742939 GTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACA
* * * ** * **
742975 ATTTCTCTTGAAAC-A----T-ACAATATTGAGATT
1 GTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACA
743005 GTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACA
*
743041 GTTTCTCTTGAAACAA
1 GTTTCCCTTGAAACAA
743057 ATTGTCCCTA
Statistics
Matches: 59, Mismatches: 17, Indels: 12
0.67 0.19 0.14
Matches are distributed among these distances:
30 20 0.34
31 2 0.03
35 2 0.03
36 35 0.59
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACA
Found at i:743025 original size:66 final size:66
Alignment explanation
Indices: 742930--743055 Score: 243
Period size: 66 Copynumber: 1.9 Consensus size: 66
742920 ACATAAAAAC
742930 ATTGAGATTGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATACAA
1 ATTGAGATTGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATACAA
742995 T
66 T
*
742996 ATTGAGATTGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 ATTGAGATTGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACA
743056 AATTGTCCCT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (66 bp):
ATTGAGATTGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATACAA
T
Found at i:745230 original size:23 final size:23
Alignment explanation
Indices: 745183--745245 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
745173 GGAGTCGAAC
* *
745183 TGGAGCATGGGCATGGGTAATAG
1 TGGAACATGGGCATGGGTAACAG
* * *
745206 TGTAACATGGGCGTGGGTGACAG
1 TGGAACATGGGCATGGGTAACAG
* *
745229 TGGATCATGGGCTTGGG
1 TGGAACATGGGCATGGG
745246 CTGCTGCTCG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.21, C:0.11, G:0.44, T:0.24
Consensus pattern (23 bp):
TGGAACATGGGCATGGGTAACAG
Found at i:746092 original size:91 final size:91
Alignment explanation
Indices: 745962--746129 Score: 282
Period size: 91 Copynumber: 1.8 Consensus size: 91
745952 GAATCGAGCT
* * *
745962 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTCCCTCATTGGATAAGTTATTCTCATTAT
746027 GAACTCTCCACTGGAAATATTGATCC
66 GAACTCTCCACTGGAAATATTGATCC
* * *
746053 AAGGTTGAATAAATTCTTCTCATTATGAACTTATTCTCCCTCATTGGATGAGTTATTCTCGTTAT
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTCCCTCATTGGATAAGTTATTCTCATTAT
746118 GAACTCTCCACT
66 GAACTCTCCACT
746130 AAAAATGTTG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 71 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (91 bp):
AAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTCCCTCATTGGATAAGTTATTCTCATTAT
GAACTCTCCACTGGAAATATTGATCC
Found at i:747102 original size:11 final size:12
Alignment explanation
Indices: 747082--747152 Score: 78
Period size: 11 Copynumber: 6.1 Consensus size: 12
747072 GAACCTTCTT
*
747082 TTTTC-TTTTTC
1 TTTTCATTTTTA
*
747093 TTTTTATTTTTA
1 TTTTCATTTTTA
747105 -TTTCATTTTTA
1 TTTTCATTTTTA
747116 -TTTCATTTTTA
1 TTTTCATTTTTA
747127 -TTTCATTTTTTCA
1 TTTTCA-TTTTT-A
747140 TTTTCATTTTTA
1 TTTTCATTTTTA
747152 T
1 T
747153 CTTTTTTTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
11 30 0.57
12 12 0.23
13 6 0.11
14 5 0.09
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCATTTTTA
Found at i:747104 original size:6 final size:6
Alignment explanation
Indices: 747081--747167 Score: 56
Period size: 6 Copynumber: 14.8 Consensus size: 6
747071 TGAACCTTCT
* * * *
747081 TTTTTC TTTTTC TTTTTA TTTTTA -TTTCA TTTTTA -TTTCA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* * * *
747127 TTTCATT- TTTTCA TTTTCA TTTTTA TCTTT- TTTTCA TTTTT
1 TTT--TTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
747168 TTCACTTTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
5 12 0.19
6 47 0.73
7 3 0.05
8 2 0.03
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:747140 original size:8 final size:8
Alignment explanation
Indices: 747127--747181 Score: 60
Period size: 8 Copynumber: 6.9 Consensus size: 8
747117 TTCATTTTTA
747127 TTTCATTT
1 TTTCATTT
747135 TTTCA--T
1 TTTCATTT
747141 TTTCATTT
1 TTTCATTT
*
747149 TTATCTTTT
1 TT-TCATTT
747158 TTTCATTTT
1 TTTCA-TTT
*
747167 TTTCACTT
1 TTTCATTT
747175 TTTCATT
1 TTTCATT
747182 CATTCATTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
6 6 0.15
8 18 0.46
9 15 0.38
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTCATTT
Found at i:747168 original size:11 final size:11
Alignment explanation
Indices: 747080--747169 Score: 73
Period size: 11 Copynumber: 8.4 Consensus size: 11
747070 TTGAACCTTC
747080 TTTTTTC-TTT
1 TTTTTTCATTT
*
747090 TTCTTTTTATTT
1 TT-TTTTCATTT
*
747102 TTATTTCATTT
1 TTTTTTCATTT
*
747113 TTATTTCATTT
1 TTTTTTCATTT
*
747124 TTATTTCA---
1 TTTTTTCATTT
747132 TTTTTTCATTT
1 TTTTTTCATTT
*
747143 TCATTTTT-ATCT
1 T--TTTTTCATTT
747155 TTTTTTCATTT
1 TTTTTTCATTT
747166 TTTT
1 TTTT
747170 CACTTTTTCA
Statistics
Matches: 66, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
8 7 0.11
10 7 0.11
11 38 0.58
12 9 0.14
13 5 0.08
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTCATTT
Found at i:747176 original size:17 final size:16
Alignment explanation
Indices: 747127--747181 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
747117 TTCATTTTTA
747127 TTTCA-TTTTTTCA-T
1 TTTCATTTTTTTCATT
* *
747141 TTTCATTTTTATCTTTT
1 TTTCATTTTTTTC-ATT
747158 TTTCATTTTTTTCACTT
1 TTTCATTTTTTTCA-TT
747175 TTTCATT
1 TTTCATT
747182 CATTCATTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
14 5 0.15
15 6 0.18
17 22 0.67
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTCATTTTTTTCATT
Found at i:747197 original size:53 final size:52
Alignment explanation
Indices: 747084--747195 Score: 133
Period size: 52 Copynumber: 2.2 Consensus size: 52
747074 ACCTTCTTTT
**
747084 TTCTTTTTCTTTTTATTTTTATTTCATTTTTATTTCATTTTTATTTCATTTT
1 TTCTTTTTCTTTTTATTTTTATTTCATTTTTATTTCATTTTTATTTCATTCA
*
747136 TTCATTTTCATTTTTATCTTTT-TTTCA-TTTT-TTTCACTTTTTCA-TTCATTCA
1 TTCTTTTTC-TTTTTAT-TTTTATTTCATTTTTATTTCA-TTTTT-ATTTCATTCA
747188 TTCTTTTT
1 TTCTTTTT
747196 TCCAGGCATA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
51 5 0.10
52 30 0.58
53 13 0.25
54 4 0.08
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (52 bp):
TTCTTTTTCTTTTTATTTTTATTTCATTTTTATTTCATTTTTATTTCATTCA
Found at i:749747 original size:66 final size:66
Alignment explanation
Indices: 749641--749773 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
749631 TCTGGATCCA
749641 TCTCAATTCTTCTTTGACTAACCACAAAGCCTAAGAGTTTCCCAGACATTACCCCGAAAGTACAT
1 TCTCAATTCTTCTTTGACTAACCACAAAGCCTAAGAGTTTCCCAGACATTACCCCGAAAGTACAT
749706 T
66 T
* *
749707 TCTCAATTCTTCTTTGACTAACCACAAAGCCTAAGAGTTTCTCGGACATTACCCCGAAAGTACAT
1 TCTCAATTCTTCTTTGACTAACCACAAAGCCTAAGAGTTTCCCAGACATTACCCCGAAAGTACAT
749772 T
66 T
749773 T
1 T
749774 AGTTGTACTG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.30
Consensus pattern (66 bp):
TCTCAATTCTTCTTTGACTAACCACAAAGCCTAAGAGTTTCCCAGACATTACCCCGAAAGTACAT
T
Found at i:750794 original size:7 final size:7
Alignment explanation
Indices: 750780--750825 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
750770 GAAATGAATG
750780 TAAAGAA
1 TAAAGAA
*
750787 TGAAGAA
1 TAAAGAA
750794 TAAAGAA
1 TAAAGAA
750801 TAAAGAA
1 TAAAGAA
*
750808 TGAA-AA
1 TAAAGAA
*
750814 TATA-AA
1 TAAAGAA
750820 TAAAGA
1 TAAAGA
750826 TGGCCATTCG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
6 9 0.28
7 23 0.72
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.17
Consensus pattern (7 bp):
TAAAGAA
Found at i:750805 original size:21 final size:19
Alignment explanation
Indices: 750780--750825 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 19
750770 GAAATGAATG
750780 TAAAGAATGAAGAATAAAGAA
1 TAAAGAATGAA-AATAAA-AA
*
750801 TAAAGAATGAAAATATAAA
1 TAAAGAATGAAAATAAAAA
750820 TAAAGA
1 TAAAGA
750826 TGGCCATTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 8 0.33
20 5 0.21
21 11 0.46
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.17
Consensus pattern (19 bp):
TAAAGAATGAAAATAAAAA
Found at i:758202 original size:137 final size:137
Alignment explanation
Indices: 757973--758260 Score: 380
Period size: 137 Copynumber: 2.1 Consensus size: 137
757963 CATCGCATAC
* * * *
757973 GAACCATGTTATCTCCATTATCTCTAAAGATGGTCAGACGTCCTCATCACGTAAAAATCATGTCA
1 GAACCATGTTATCTCCATTATCCCAAAAGATGGTCAGACATCCTCATCACGTAAAAACCATGTCA
* * * * ** **
758038 TCCACCGACCAGATCTCCTTATCACGTAGGAGTC-GCGTCATCCTTAGATAGGCAGACTTTGTCA
66 TCCACCGACCAGAACTCCTCATCACGTAGGAG-CAACATCATCCTTAGATAACCAGACTTCCTCA
*
758102 TCATGTAT
130 TCATGTAG
** * **
758110 GAACCATGTTATCTCTTTTATCCCAAAAGATGGTCAGCCATCCTCATCACGTAGGAACCATGTCA
1 GAACCATGTTATCTCCATTATCCCAAAAGATGGTCAGACATCCTCATCACGTAAAAACCATGTCA
758175 TCCACCGACCAGAACTCCTCATCACGTAGGAGCAACATCATCCTTAGATAACCAGACTTCCTCAT
66 TCCACCGACCAGAACTCCTCATCACGTAGGAGCAACATCATCCTTAGATAACCAGACTTCCTCAT
758240 CATGTAG
131 CATGTAG
* *
758247 GAAGCGTGTTATCT
1 GAACCATGTTATCT
758261 ACAAATTTAC
Statistics
Matches: 130, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
136 1 0.01
137 129 0.99
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (137 bp):
GAACCATGTTATCTCCATTATCCCAAAAGATGGTCAGACATCCTCATCACGTAAAAACCATGTCA
TCCACCGACCAGAACTCCTCATCACGTAGGAGCAACATCATCCTTAGATAACCAGACTTCCTCAT
CATGTAG
Found at i:758471 original size:3 final size:3
Alignment explanation
Indices: 758465--758497 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
758455 AATAATAATA
758465 ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
758498 ATAAATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:759624 original size:31 final size:29
Alignment explanation
Indices: 759579--759636 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 29
759569 AAAAGGGGGT
759579 TGTGTTTTGTAAAGTTTACATTTCAGTGC
1 TGTGTTTTGTAAAGTTTACATTTCAGTGC
*
759608 TGTGTTTTATGTAAAGTTTGCATTTCAGT
1 TGTG-TTT-TGTAAAGTTTACATTTCAGT
759637 CATTGAATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 3 0.12
31 19 0.73
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.50
Consensus pattern (29 bp):
TGTGTTTTGTAAAGTTTACATTTCAGTGC
Found at i:760135 original size:12 final size:12
Alignment explanation
Indices: 760114--760147 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
760104 ACCACATTTT
*
760114 CAATACCAAACA
1 CAATATCAAACA
760126 CAATATCAAACA
1 CAATATCAAACA
*
760138 CAATCTCAAA
1 CAATATCAAA
760148 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:762994 original size:64 final size:64
Alignment explanation
Indices: 762925--763089 Score: 285
Period size: 64 Copynumber: 2.6 Consensus size: 64
762915 AATTTAAAAC
762925 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
*** * *
762989 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
763053 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAA
763090 CAAAATGTAC
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 96 1.00
ACGTcount: A:0.53, C:0.18, G:0.02, T:0.27
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
Found at i:764455 original size:21 final size:21
Alignment explanation
Indices: 764429--764506 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
764419 CATGTGAATC
*
764429 GACCTCTTGAACGTTGGAAGG
1 GACCTCTTGAACGATGGAAGG
764450 GACCTCTTGAACGAT-GACAGG
1 GACCTCTTGAACGATGGA-AGG
* * *
764471 GGCCTCTTGAACGGTGGTAGG
1 GACCTCTTGAACGATGGAAGG
*
764492 GGCCTCTTGAACGAT
1 GACCTCTTGAACGAT
764507 AGGAGATGCC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
20 2 0.04
21 47 0.94
22 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.23
Consensus pattern (21 bp):
GACCTCTTGAACGATGGAAGG
Found at i:764518 original size:42 final size:42
Alignment explanation
Indices: 764431--764523 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
764421 TGTGAATCGA
* *
764431 CCTCTTGAACGTTGGAAGGGACCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGGTGGAAGGGACCTCTTGAACGATGACAGAGG
* * * *
764473 CCTCTTGAACGGTGGTAGGGGCCTCTTGAACGAT-AGGAGATG
1 CCTCTTGAACGGTGGAAGGGACCTCTTGAACGATGA-CAGAGG
764515 CCTCTTGAA
1 CCTCTTGAA
764524 TGATGACAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
41 1 0.02
42 43 0.98
ACGTcount: A:0.23, C:0.22, G:0.32, T:0.24
Consensus pattern (42 bp):
CCTCTTGAACGGTGGAAGGGACCTCTTGAACGATGACAGAGG
Done.