Multiple sequence alignment - TraesCS3A01G209800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G209800 chr3A 100.000 2408 0 0 1 2408 374445026 374447433 0.000000e+00 4447
1 TraesCS3A01G209800 chr3A 100.000 212 0 0 2676 2887 374447701 374447912 2.700000e-105 392
2 TraesCS3A01G209800 chr3A 87.037 108 14 0 1621 1728 78710686 78710793 3.910000e-24 122
3 TraesCS3A01G209800 chr3B 95.622 1462 44 5 425 1869 379171636 379173094 0.000000e+00 2327
4 TraesCS3A01G209800 chr3B 88.220 382 43 2 2026 2406 379173418 379173798 3.390000e-124 455
5 TraesCS3A01G209800 chr3B 96.914 162 5 0 1867 2028 379173135 379173296 3.670000e-69 272
6 TraesCS3A01G209800 chr3B 93.631 157 9 1 143 298 379171492 379171648 1.730000e-57 233
7 TraesCS3A01G209800 chr3B 85.047 214 16 4 2676 2887 379173814 379174013 1.360000e-48 204
8 TraesCS3A01G209800 chr3B 87.273 110 14 0 1619 1728 111943249 111943358 3.020000e-25 126
9 TraesCS3A01G209800 chr3B 81.884 138 21 4 2272 2408 692958614 692958480 2.350000e-21 113
10 TraesCS3A01G209800 chr3D 93.490 1444 42 22 434 1869 286189022 286190421 0.000000e+00 2098
11 TraesCS3A01G209800 chr3D 89.167 360 34 4 1867 2223 286190462 286190819 7.340000e-121 444
12 TraesCS3A01G209800 chr3D 92.157 153 9 3 143 293 286187543 286187694 2.250000e-51 213
13 TraesCS3A01G209800 chr3D 84.360 211 31 2 2676 2884 295293132 295293342 3.770000e-49 206
14 TraesCS3A01G209800 chr3D 87.963 108 13 0 1621 1728 67351483 67351590 8.400000e-26 128
15 TraesCS3A01G209800 chr4D 84.507 213 31 2 2676 2886 74409779 74409991 2.920000e-50 209
16 TraesCS3A01G209800 chr4D 84.076 157 22 3 2039 2194 401599485 401599331 6.450000e-32 148
17 TraesCS3A01G209800 chr5D 89.286 140 11 3 297 433 443898183 443898321 3.820000e-39 172
18 TraesCS3A01G209800 chr4A 88.971 136 13 2 291 425 591874454 591874588 1.780000e-37 167
19 TraesCS3A01G209800 chr6A 89.394 132 11 2 297 425 249162484 249162353 2.300000e-36 163
20 TraesCS3A01G209800 chr6A 89.600 125 12 1 301 425 147454387 147454510 1.070000e-34 158
21 TraesCS3A01G209800 chr2A 89.231 130 14 0 296 425 32548140 32548269 2.300000e-36 163
22 TraesCS3A01G209800 chr7D 89.147 129 12 2 297 425 75800723 75800849 2.980000e-35 159
23 TraesCS3A01G209800 chr1D 89.600 125 13 0 301 425 470555241 470555117 2.980000e-35 159
24 TraesCS3A01G209800 chr1A 88.636 132 13 2 301 431 436420389 436420519 2.980000e-35 159
25 TraesCS3A01G209800 chr1A 85.714 112 14 2 1618 1728 135182800 135182690 1.820000e-22 117
26 TraesCS3A01G209800 chr5A 86.207 145 18 2 287 429 649804805 649804661 3.850000e-34 156


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G209800 chr3A 374445026 374447912 2886 False 2419.500000 4447 100.000000 1 2887 2 chr3A.!!$F2 2886
1 TraesCS3A01G209800 chr3B 379171492 379174013 2521 False 698.200000 2327 91.886800 143 2887 5 chr3B.!!$F2 2744
2 TraesCS3A01G209800 chr3D 286187543 286190819 3276 False 918.333333 2098 91.604667 143 2223 3 chr3D.!!$F3 2080

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
42 43 0.106708 AGCCATACTGCCATACACGG 59.893 55.000 0.00 0.00 0.0 4.94 F
43 44 0.179056 GCCATACTGCCATACACGGT 60.179 55.000 0.00 0.00 0.0 4.83 F
45 46 1.134521 CCATACTGCCATACACGGTGT 60.135 52.381 18.89 18.89 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1224 2425 1.855213 TACTTGCTGCTTTGCCGCTG 61.855 55.000 0.00 3.62 39.43 5.18 R
1875 3128 4.971939 TCCTGAACATGTCAATTGTCAGA 58.028 39.130 19.80 7.44 35.22 3.27 R
2047 3426 5.132897 AGCGAATGCATTTGTAGGAAAAA 57.867 34.783 24.39 0.00 46.23 1.94 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.794687 CAACAAAGTTCATACCGATAGCA 57.205 39.130 0.00 0.00 0.00 3.49
23 24 6.176975 CAACAAAGTTCATACCGATAGCAA 57.823 37.500 0.00 0.00 0.00 3.91
24 25 6.250819 CAACAAAGTTCATACCGATAGCAAG 58.749 40.000 0.00 0.00 0.00 4.01
25 26 4.332819 ACAAAGTTCATACCGATAGCAAGC 59.667 41.667 0.00 0.00 0.00 4.01
26 27 3.113260 AGTTCATACCGATAGCAAGCC 57.887 47.619 0.00 0.00 0.00 4.35
27 28 2.434336 AGTTCATACCGATAGCAAGCCA 59.566 45.455 0.00 0.00 0.00 4.75
28 29 3.071602 AGTTCATACCGATAGCAAGCCAT 59.928 43.478 0.00 0.00 0.00 4.40
29 30 4.283467 AGTTCATACCGATAGCAAGCCATA 59.717 41.667 0.00 0.00 0.00 2.74
30 31 4.188247 TCATACCGATAGCAAGCCATAC 57.812 45.455 0.00 0.00 0.00 2.39
31 32 3.832490 TCATACCGATAGCAAGCCATACT 59.168 43.478 0.00 0.00 0.00 2.12
32 33 2.533266 ACCGATAGCAAGCCATACTG 57.467 50.000 0.00 0.00 0.00 2.74
33 34 1.151668 CCGATAGCAAGCCATACTGC 58.848 55.000 0.00 0.00 0.00 4.40
34 35 1.151668 CGATAGCAAGCCATACTGCC 58.848 55.000 0.00 0.00 0.00 4.85
35 36 1.541015 CGATAGCAAGCCATACTGCCA 60.541 52.381 0.00 0.00 0.00 4.92
36 37 2.787994 GATAGCAAGCCATACTGCCAT 58.212 47.619 0.00 0.00 0.00 4.40
37 38 3.617288 CGATAGCAAGCCATACTGCCATA 60.617 47.826 0.00 0.00 0.00 2.74
38 39 1.972872 AGCAAGCCATACTGCCATAC 58.027 50.000 0.00 0.00 0.00 2.39
39 40 1.212688 AGCAAGCCATACTGCCATACA 59.787 47.619 0.00 0.00 0.00 2.29
40 41 1.334869 GCAAGCCATACTGCCATACAC 59.665 52.381 0.00 0.00 0.00 2.90
41 42 1.599071 CAAGCCATACTGCCATACACG 59.401 52.381 0.00 0.00 0.00 4.49
42 43 0.106708 AGCCATACTGCCATACACGG 59.893 55.000 0.00 0.00 0.00 4.94
43 44 0.179056 GCCATACTGCCATACACGGT 60.179 55.000 0.00 0.00 0.00 4.83
44 45 1.581934 CCATACTGCCATACACGGTG 58.418 55.000 6.58 6.58 0.00 4.94
45 46 1.134521 CCATACTGCCATACACGGTGT 60.135 52.381 18.89 18.89 0.00 4.16
46 47 2.101750 CCATACTGCCATACACGGTGTA 59.898 50.000 22.05 22.05 37.24 2.90
47 48 3.244078 CCATACTGCCATACACGGTGTAT 60.244 47.826 24.33 24.33 43.81 2.29
48 49 4.377021 CATACTGCCATACACGGTGTATT 58.623 43.478 26.73 16.53 40.40 1.89
49 50 5.510009 CCATACTGCCATACACGGTGTATTA 60.510 44.000 26.73 17.90 40.40 0.98
50 51 4.682778 ACTGCCATACACGGTGTATTAT 57.317 40.909 26.73 9.80 40.40 1.28
51 52 4.377021 ACTGCCATACACGGTGTATTATG 58.623 43.478 26.73 19.59 40.40 1.90
52 53 3.734463 TGCCATACACGGTGTATTATGG 58.266 45.455 26.73 26.57 40.40 2.74
53 54 3.071479 GCCATACACGGTGTATTATGGG 58.929 50.000 29.26 25.66 40.40 4.00
54 55 3.071479 CCATACACGGTGTATTATGGGC 58.929 50.000 26.73 0.00 40.40 5.36
55 56 3.244422 CCATACACGGTGTATTATGGGCT 60.244 47.826 26.73 6.06 40.40 5.19
56 57 4.385825 CATACACGGTGTATTATGGGCTT 58.614 43.478 26.73 5.39 40.40 4.35
57 58 5.511716 CCATACACGGTGTATTATGGGCTTA 60.512 44.000 26.73 2.97 40.40 3.09
58 59 4.699925 ACACGGTGTATTATGGGCTTAT 57.300 40.909 12.96 0.00 0.00 1.73
59 60 4.385825 ACACGGTGTATTATGGGCTTATG 58.614 43.478 12.96 0.00 0.00 1.90
60 61 3.751175 CACGGTGTATTATGGGCTTATGG 59.249 47.826 0.00 0.00 0.00 2.74
61 62 2.747446 CGGTGTATTATGGGCTTATGGC 59.253 50.000 0.00 0.00 40.90 4.40
81 82 3.469008 CCATAGACGGCCAACTTATGA 57.531 47.619 2.24 0.00 0.00 2.15
82 83 3.131396 CCATAGACGGCCAACTTATGAC 58.869 50.000 2.24 0.00 0.00 3.06
83 84 3.181465 CCATAGACGGCCAACTTATGACT 60.181 47.826 2.24 0.00 0.00 3.41
84 85 4.038763 CCATAGACGGCCAACTTATGACTA 59.961 45.833 2.24 0.00 0.00 2.59
85 86 5.452776 CCATAGACGGCCAACTTATGACTAA 60.453 44.000 2.24 0.00 0.00 2.24
86 87 3.858247 AGACGGCCAACTTATGACTAAC 58.142 45.455 2.24 0.00 0.00 2.34
87 88 3.259876 AGACGGCCAACTTATGACTAACA 59.740 43.478 2.24 0.00 0.00 2.41
88 89 3.998341 GACGGCCAACTTATGACTAACAA 59.002 43.478 2.24 0.00 0.00 2.83
89 90 4.585879 ACGGCCAACTTATGACTAACAAT 58.414 39.130 2.24 0.00 0.00 2.71
90 91 4.394920 ACGGCCAACTTATGACTAACAATG 59.605 41.667 2.24 0.00 0.00 2.82
91 92 4.394920 CGGCCAACTTATGACTAACAATGT 59.605 41.667 2.24 0.00 0.00 2.71
92 93 5.106317 CGGCCAACTTATGACTAACAATGTT 60.106 40.000 2.24 3.43 0.00 2.71
93 94 6.322491 GGCCAACTTATGACTAACAATGTTC 58.678 40.000 0.22 0.00 0.00 3.18
94 95 6.151144 GGCCAACTTATGACTAACAATGTTCT 59.849 38.462 0.22 0.00 0.00 3.01
95 96 7.023575 GCCAACTTATGACTAACAATGTTCTG 58.976 38.462 0.22 0.00 0.00 3.02
96 97 7.094805 GCCAACTTATGACTAACAATGTTCTGA 60.095 37.037 0.22 0.00 0.00 3.27
97 98 8.446273 CCAACTTATGACTAACAATGTTCTGAG 58.554 37.037 0.22 0.00 0.00 3.35
98 99 9.208022 CAACTTATGACTAACAATGTTCTGAGA 57.792 33.333 0.22 0.00 0.00 3.27
99 100 8.994429 ACTTATGACTAACAATGTTCTGAGAG 57.006 34.615 0.22 0.00 0.00 3.20
100 101 7.547370 ACTTATGACTAACAATGTTCTGAGAGC 59.453 37.037 0.22 0.00 0.00 4.09
101 102 4.237724 TGACTAACAATGTTCTGAGAGCG 58.762 43.478 0.22 0.00 0.00 5.03
102 103 4.022329 TGACTAACAATGTTCTGAGAGCGA 60.022 41.667 0.22 0.00 0.00 4.93
103 104 4.238514 ACTAACAATGTTCTGAGAGCGAC 58.761 43.478 0.22 0.00 0.00 5.19
104 105 3.393089 AACAATGTTCTGAGAGCGACT 57.607 42.857 0.00 0.00 0.00 4.18
105 106 4.521130 AACAATGTTCTGAGAGCGACTA 57.479 40.909 0.00 0.00 0.00 2.59
106 107 3.839293 ACAATGTTCTGAGAGCGACTAC 58.161 45.455 0.00 0.00 0.00 2.73
107 108 3.255888 ACAATGTTCTGAGAGCGACTACA 59.744 43.478 0.00 0.00 0.00 2.74
108 109 3.773860 ATGTTCTGAGAGCGACTACAG 57.226 47.619 0.00 0.00 0.00 2.74
109 110 2.505405 TGTTCTGAGAGCGACTACAGT 58.495 47.619 0.00 0.00 0.00 3.55
110 111 3.671716 TGTTCTGAGAGCGACTACAGTA 58.328 45.455 0.00 0.00 0.00 2.74
111 112 4.070009 TGTTCTGAGAGCGACTACAGTAA 58.930 43.478 0.00 0.00 0.00 2.24
112 113 4.517832 TGTTCTGAGAGCGACTACAGTAAA 59.482 41.667 0.00 0.00 0.00 2.01
113 114 5.183331 TGTTCTGAGAGCGACTACAGTAAAT 59.817 40.000 0.00 0.00 0.00 1.40
114 115 6.373495 TGTTCTGAGAGCGACTACAGTAAATA 59.627 38.462 0.00 0.00 0.00 1.40
115 116 6.997239 TCTGAGAGCGACTACAGTAAATAA 57.003 37.500 0.00 0.00 0.00 1.40
116 117 7.387119 TCTGAGAGCGACTACAGTAAATAAA 57.613 36.000 0.00 0.00 0.00 1.40
117 118 7.823665 TCTGAGAGCGACTACAGTAAATAAAA 58.176 34.615 0.00 0.00 0.00 1.52
118 119 7.968956 TCTGAGAGCGACTACAGTAAATAAAAG 59.031 37.037 0.00 0.00 0.00 2.27
119 120 7.823665 TGAGAGCGACTACAGTAAATAAAAGA 58.176 34.615 0.00 0.00 0.00 2.52
120 121 8.301720 TGAGAGCGACTACAGTAAATAAAAGAA 58.698 33.333 0.00 0.00 0.00 2.52
121 122 9.136952 GAGAGCGACTACAGTAAATAAAAGAAA 57.863 33.333 0.00 0.00 0.00 2.52
122 123 9.654663 AGAGCGACTACAGTAAATAAAAGAAAT 57.345 29.630 0.00 0.00 0.00 2.17
123 124 9.903185 GAGCGACTACAGTAAATAAAAGAAATC 57.097 33.333 0.00 0.00 0.00 2.17
124 125 9.654663 AGCGACTACAGTAAATAAAAGAAATCT 57.345 29.630 0.00 0.00 0.00 2.40
125 126 9.903185 GCGACTACAGTAAATAAAAGAAATCTC 57.097 33.333 0.00 0.00 0.00 2.75
130 131 8.581253 ACAGTAAATAAAAGAAATCTCCCTGG 57.419 34.615 0.00 0.00 0.00 4.45
131 132 8.170730 ACAGTAAATAAAAGAAATCTCCCTGGT 58.829 33.333 0.00 0.00 0.00 4.00
132 133 9.681062 CAGTAAATAAAAGAAATCTCCCTGGTA 57.319 33.333 0.00 0.00 0.00 3.25
133 134 9.907229 AGTAAATAAAAGAAATCTCCCTGGTAG 57.093 33.333 0.00 0.00 0.00 3.18
134 135 7.646548 AAATAAAAGAAATCTCCCTGGTAGC 57.353 36.000 0.00 0.00 0.00 3.58
135 136 2.990066 AAGAAATCTCCCTGGTAGCG 57.010 50.000 0.00 0.00 0.00 4.26
136 137 2.160721 AGAAATCTCCCTGGTAGCGA 57.839 50.000 0.00 0.00 0.00 4.93
137 138 2.035632 AGAAATCTCCCTGGTAGCGAG 58.964 52.381 0.00 0.00 0.00 5.03
138 139 2.032620 GAAATCTCCCTGGTAGCGAGA 58.967 52.381 3.36 3.36 37.08 4.04
139 140 2.390225 AATCTCCCTGGTAGCGAGAT 57.610 50.000 7.20 7.20 43.56 2.75
140 141 2.390225 ATCTCCCTGGTAGCGAGATT 57.610 50.000 7.20 0.00 39.75 2.40
141 142 2.160721 TCTCCCTGGTAGCGAGATTT 57.839 50.000 0.00 0.00 0.00 2.17
154 155 3.562973 AGCGAGATTTATGGATGTTGCAG 59.437 43.478 0.00 0.00 33.35 4.41
171 172 1.669211 GCAGTCGGTAGGAAGACACAC 60.669 57.143 0.00 0.00 39.67 3.82
221 223 1.515020 GCTGGACGATGCTCTGTCT 59.485 57.895 0.00 0.00 35.45 3.41
258 260 4.982999 TGCACTCGACTGAGACTTAATAC 58.017 43.478 0.00 0.00 45.57 1.89
259 261 4.700692 TGCACTCGACTGAGACTTAATACT 59.299 41.667 0.00 0.00 45.57 2.12
280 282 5.688807 ACTAGATACCGTAAGCTAAGGACA 58.311 41.667 8.77 0.00 0.00 4.02
293 295 5.675538 AGCTAAGGACATCGAGCTTAAATT 58.324 37.500 0.00 0.00 42.59 1.82
299 301 6.879400 AGGACATCGAGCTTAAATTAGACTT 58.121 36.000 0.00 0.00 0.00 3.01
300 302 8.008513 AGGACATCGAGCTTAAATTAGACTTA 57.991 34.615 0.00 0.00 0.00 2.24
301 303 8.475639 AGGACATCGAGCTTAAATTAGACTTAA 58.524 33.333 0.00 0.00 0.00 1.85
302 304 9.262358 GGACATCGAGCTTAAATTAGACTTAAT 57.738 33.333 0.00 0.00 0.00 1.40
350 352 6.994421 AAAAGAAAATACCCACACCAATCT 57.006 33.333 0.00 0.00 0.00 2.40
351 353 6.994421 AAAGAAAATACCCACACCAATCTT 57.006 33.333 0.00 0.00 0.00 2.40
353 355 5.640147 AGAAAATACCCACACCAATCTTCA 58.360 37.500 0.00 0.00 0.00 3.02
354 356 6.256053 AGAAAATACCCACACCAATCTTCAT 58.744 36.000 0.00 0.00 0.00 2.57
356 358 1.549203 ACCCACACCAATCTTCATGC 58.451 50.000 0.00 0.00 0.00 4.06
357 359 1.203038 ACCCACACCAATCTTCATGCA 60.203 47.619 0.00 0.00 0.00 3.96
358 360 1.894466 CCCACACCAATCTTCATGCAA 59.106 47.619 0.00 0.00 0.00 4.08
359 361 2.094390 CCCACACCAATCTTCATGCAAG 60.094 50.000 0.00 0.00 0.00 4.01
360 362 2.821378 CCACACCAATCTTCATGCAAGA 59.179 45.455 9.18 9.18 45.60 3.02
361 363 3.366679 CCACACCAATCTTCATGCAAGAC 60.367 47.826 9.00 0.00 44.28 3.01
363 365 2.821378 CACCAATCTTCATGCAAGACCA 59.179 45.455 9.00 0.00 44.28 4.02
364 366 3.256383 CACCAATCTTCATGCAAGACCAA 59.744 43.478 9.00 0.00 44.28 3.67
369 1418 6.040054 CCAATCTTCATGCAAGACCAATGATA 59.960 38.462 9.00 0.00 44.28 2.15
371 1420 8.789762 CAATCTTCATGCAAGACCAATGATATA 58.210 33.333 9.00 0.00 44.28 0.86
374 1423 8.212995 TCTTCATGCAAGACCAATGATATAAGA 58.787 33.333 0.00 0.00 36.08 2.10
385 1434 8.839310 ACCAATGATATAAGACTTAGATGTGC 57.161 34.615 7.07 0.00 0.00 4.57
386 1435 8.432013 ACCAATGATATAAGACTTAGATGTGCA 58.568 33.333 7.07 0.45 0.00 4.57
387 1436 9.276590 CCAATGATATAAGACTTAGATGTGCAA 57.723 33.333 7.07 0.00 0.00 4.08
397 1446 8.879342 AGACTTAGATGTGCAATACTTATGAC 57.121 34.615 0.00 0.00 0.00 3.06
398 1447 8.478066 AGACTTAGATGTGCAATACTTATGACA 58.522 33.333 0.00 0.00 0.00 3.58
399 1448 8.425577 ACTTAGATGTGCAATACTTATGACAC 57.574 34.615 0.00 0.00 0.00 3.67
400 1449 8.040727 ACTTAGATGTGCAATACTTATGACACA 58.959 33.333 0.00 0.00 38.34 3.72
401 1450 8.962884 TTAGATGTGCAATACTTATGACACAT 57.037 30.769 13.39 13.39 42.56 3.21
403 1452 7.488187 GATGTGCAATACTTATGACACATCT 57.512 36.000 22.83 7.26 45.69 2.90
404 1453 8.593492 GATGTGCAATACTTATGACACATCTA 57.407 34.615 22.83 2.36 45.69 1.98
405 1454 8.599055 ATGTGCAATACTTATGACACATCTAG 57.401 34.615 9.84 0.00 39.26 2.43
406 1455 7.781056 TGTGCAATACTTATGACACATCTAGA 58.219 34.615 0.00 0.00 33.26 2.43
407 1456 8.424133 TGTGCAATACTTATGACACATCTAGAT 58.576 33.333 0.00 0.00 33.26 1.98
442 1631 7.172361 GCAAAACTGCTTAAATTACCCATGAAA 59.828 33.333 0.00 0.00 0.00 2.69
443 1632 9.050601 CAAAACTGCTTAAATTACCCATGAAAA 57.949 29.630 0.00 0.00 0.00 2.29
458 1647 2.778299 TGAAAAGGATGAGGAACACGG 58.222 47.619 0.00 0.00 0.00 4.94
670 1867 4.170449 TGGATCCCACATCATACAGCTAT 58.830 43.478 9.90 0.00 0.00 2.97
674 1872 2.039480 CCCACATCATACAGCTATGCCT 59.961 50.000 0.00 0.00 31.18 4.75
722 1923 4.523173 TGATACCAGTATACCACTAGCTGC 59.477 45.833 0.00 0.00 34.98 5.25
723 1924 2.747177 ACCAGTATACCACTAGCTGCA 58.253 47.619 1.02 0.00 34.98 4.41
923 2124 4.922791 GCTTTGTGCTCGTCAACC 57.077 55.556 0.00 0.00 38.95 3.77
1183 2384 2.746277 CCTACCCCTTGCACGCAC 60.746 66.667 0.00 0.00 0.00 5.34
1184 2385 2.031919 CTACCCCTTGCACGCACA 59.968 61.111 0.00 0.00 0.00 4.57
1185 2386 2.031919 TACCCCTTGCACGCACAG 59.968 61.111 0.00 0.00 0.00 3.66
1388 2598 1.815003 CAATTGTCCAGGAGCTTGACC 59.185 52.381 0.00 0.00 0.00 4.02
1856 3066 3.340928 TCTTGACACCATGAAGATGCAG 58.659 45.455 0.00 0.00 0.00 4.41
1892 3145 6.457392 GCGTGATATCTGACAATTGACATGTT 60.457 38.462 13.59 2.92 0.00 2.71
2047 3426 3.903530 AACAAGGGTTCCAGAGGAAAT 57.096 42.857 0.00 0.00 43.86 2.17
2068 3447 6.407475 AATTTTTCCTACAAATGCATTCGC 57.593 33.333 13.38 0.00 39.24 4.70
2083 3462 2.087501 TTCGCTTCGTAGGAAATGCA 57.912 45.000 9.27 0.00 0.00 3.96
2137 3517 5.535333 TCCTGTGTTTTAGAGGAAACTACG 58.465 41.667 0.00 0.00 45.23 3.51
2150 3530 3.500680 GGAAACTACGCATCCACTCAAAA 59.499 43.478 0.00 0.00 33.30 2.44
2182 3562 3.542875 CGCGTAGAAATGATGCAAGTCAG 60.543 47.826 0.00 0.00 0.00 3.51
2194 3574 8.757982 ATGATGCAAGTCAGTTCCTTATAATT 57.242 30.769 0.00 0.00 0.00 1.40
2205 3585 7.446931 TCAGTTCCTTATAATTGCAAGTGTCAA 59.553 33.333 10.14 0.00 0.00 3.18
2206 3586 8.246180 CAGTTCCTTATAATTGCAAGTGTCAAT 58.754 33.333 10.14 0.00 35.83 2.57
2207 3587 8.806146 AGTTCCTTATAATTGCAAGTGTCAATT 58.194 29.630 10.14 14.02 43.89 2.32
2208 3588 9.423061 GTTCCTTATAATTGCAAGTGTCAATTT 57.577 29.630 10.14 0.00 42.27 1.82
2270 3650 5.480205 GTTTCCTCTAAACCGAATGAGACT 58.520 41.667 0.00 0.00 41.44 3.24
2278 3658 9.204570 CTCTAAACCGAATGAGACTTTAAAAGA 57.795 33.333 0.00 0.00 0.00 2.52
2298 3678 7.716799 AAAGATTTAATCATTACACCTGGCA 57.283 32.000 7.74 0.00 0.00 4.92
2306 3686 2.512692 TTACACCTGGCATCTGCATT 57.487 45.000 4.33 0.00 44.36 3.56
2310 3690 1.674441 CACCTGGCATCTGCATTACTG 59.326 52.381 4.33 0.00 44.36 2.74
2312 3692 2.219458 CCTGGCATCTGCATTACTGAG 58.781 52.381 4.33 0.00 44.36 3.35
2327 3707 6.404623 GCATTACTGAGATGCACATAACCAAA 60.405 38.462 12.60 0.00 46.96 3.28
2397 3778 4.491234 ACATGTAGAGTCTGTATAGCGC 57.509 45.455 0.00 0.00 0.00 5.92
2406 3787 2.033801 GTCTGTATAGCGCCTAAACCGA 59.966 50.000 2.29 0.00 0.00 4.69
2701 4082 7.616528 TCCTAAGATCATGTTGTCATCCATA 57.383 36.000 0.00 0.00 31.15 2.74
2702 4083 7.445121 TCCTAAGATCATGTTGTCATCCATAC 58.555 38.462 0.00 0.00 31.15 2.39
2707 4088 2.418368 TGTTGTCATCCATACTGGGC 57.582 50.000 0.00 0.00 38.32 5.36
2714 4095 4.018870 TGTCATCCATACTGGGCAAAGTTA 60.019 41.667 0.00 0.00 38.32 2.24
2722 4104 2.290960 ACTGGGCAAAGTTATCCTCACC 60.291 50.000 0.00 0.00 0.00 4.02
2731 4113 2.370189 AGTTATCCTCACCATAGCCTGC 59.630 50.000 0.00 0.00 0.00 4.85
2748 4130 3.531538 CCTGCAATCGTGTACATACCTT 58.468 45.455 0.00 0.00 0.00 3.50
2756 4138 4.402583 TCGTGTACATACCTTCGTAAACG 58.597 43.478 0.00 6.04 46.13 3.60
2757 4139 3.543494 CGTGTACATACCTTCGTAAACGG 59.457 47.826 0.00 0.00 42.80 4.44
2760 4143 3.236632 ACATACCTTCGTAAACGGGTC 57.763 47.619 6.70 0.00 40.29 4.46
2771 4154 3.674410 CGTAAACGGGTCTTAGTTCTCCC 60.674 52.174 0.00 0.00 36.82 4.30
2774 4157 0.535797 CGGGTCTTAGTTCTCCCCAC 59.464 60.000 0.00 0.00 36.84 4.61
2775 4158 0.535797 GGGTCTTAGTTCTCCCCACG 59.464 60.000 0.00 0.00 35.32 4.94
2776 4159 1.264295 GGTCTTAGTTCTCCCCACGT 58.736 55.000 0.00 0.00 0.00 4.49
2777 4160 1.622312 GGTCTTAGTTCTCCCCACGTT 59.378 52.381 0.00 0.00 0.00 3.99
2778 4161 2.612221 GGTCTTAGTTCTCCCCACGTTG 60.612 54.545 0.00 0.00 0.00 4.10
2779 4162 2.036862 GTCTTAGTTCTCCCCACGTTGT 59.963 50.000 0.00 0.00 0.00 3.32
2780 4163 3.256631 GTCTTAGTTCTCCCCACGTTGTA 59.743 47.826 0.00 0.00 0.00 2.41
2781 4164 3.508793 TCTTAGTTCTCCCCACGTTGTAG 59.491 47.826 0.00 0.00 0.00 2.74
2782 4165 2.005370 AGTTCTCCCCACGTTGTAGA 57.995 50.000 0.00 0.00 0.00 2.59
2783 4166 1.893801 AGTTCTCCCCACGTTGTAGAG 59.106 52.381 0.00 0.00 0.00 2.43
2784 4167 1.891150 GTTCTCCCCACGTTGTAGAGA 59.109 52.381 3.37 3.37 0.00 3.10
2785 4168 1.542492 TCTCCCCACGTTGTAGAGAC 58.458 55.000 3.37 0.00 0.00 3.36
2786 4169 1.202964 TCTCCCCACGTTGTAGAGACA 60.203 52.381 3.37 0.00 0.00 3.41
2787 4170 1.616865 CTCCCCACGTTGTAGAGACAA 59.383 52.381 0.00 0.00 43.41 3.18
2804 4187 9.431887 GTAGAGACAACCATAAATAAAGTGTCA 57.568 33.333 0.00 0.00 0.00 3.58
2805 4188 8.324163 AGAGACAACCATAAATAAAGTGTCAC 57.676 34.615 0.00 0.00 0.00 3.67
2828 4211 4.547532 GGTACATCTGTAGATAACCTGCG 58.452 47.826 14.05 0.00 37.07 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.794687 TGCTATCGGTATGAACTTTGTTG 57.205 39.130 0.00 0.00 0.00 3.33
1 2 5.163754 GCTTGCTATCGGTATGAACTTTGTT 60.164 40.000 0.00 0.00 0.00 2.83
2 3 4.332819 GCTTGCTATCGGTATGAACTTTGT 59.667 41.667 0.00 0.00 0.00 2.83
3 4 4.260784 GGCTTGCTATCGGTATGAACTTTG 60.261 45.833 0.00 0.00 0.00 2.77
4 5 3.877508 GGCTTGCTATCGGTATGAACTTT 59.122 43.478 0.00 0.00 0.00 2.66
5 6 3.118408 TGGCTTGCTATCGGTATGAACTT 60.118 43.478 0.00 0.00 0.00 2.66
6 7 2.434336 TGGCTTGCTATCGGTATGAACT 59.566 45.455 0.00 0.00 0.00 3.01
7 8 2.833794 TGGCTTGCTATCGGTATGAAC 58.166 47.619 0.00 0.00 0.00 3.18
8 9 3.769739 ATGGCTTGCTATCGGTATGAA 57.230 42.857 0.00 0.00 0.00 2.57
9 10 3.832490 AGTATGGCTTGCTATCGGTATGA 59.168 43.478 0.00 0.00 0.00 2.15
10 11 3.928992 CAGTATGGCTTGCTATCGGTATG 59.071 47.826 0.00 0.00 0.00 2.39
11 12 3.617531 GCAGTATGGCTTGCTATCGGTAT 60.618 47.826 0.00 0.00 35.86 2.73
12 13 2.288825 GCAGTATGGCTTGCTATCGGTA 60.289 50.000 0.00 0.00 35.86 4.02
13 14 1.541233 GCAGTATGGCTTGCTATCGGT 60.541 52.381 0.00 0.00 35.86 4.69
14 15 1.151668 GCAGTATGGCTTGCTATCGG 58.848 55.000 0.00 0.00 35.86 4.18
25 26 1.134521 ACACCGTGTATGGCAGTATGG 60.135 52.381 1.18 0.00 35.86 2.74
26 27 2.309528 ACACCGTGTATGGCAGTATG 57.690 50.000 1.18 0.00 40.87 2.39
27 28 4.682778 AATACACCGTGTATGGCAGTAT 57.317 40.909 22.08 4.74 42.29 2.12
28 29 5.510009 CCATAATACACCGTGTATGGCAGTA 60.510 44.000 22.08 12.18 42.29 2.74
29 30 4.377021 CATAATACACCGTGTATGGCAGT 58.623 43.478 22.08 10.56 42.29 4.40
30 31 3.745975 CCATAATACACCGTGTATGGCAG 59.254 47.826 22.08 13.27 42.29 4.85
31 32 3.495276 CCCATAATACACCGTGTATGGCA 60.495 47.826 22.08 12.39 42.29 4.92
32 33 3.071479 CCCATAATACACCGTGTATGGC 58.929 50.000 22.08 0.00 42.29 4.40
33 34 3.071479 GCCCATAATACACCGTGTATGG 58.929 50.000 22.08 20.47 42.29 2.74
34 35 4.002906 AGCCCATAATACACCGTGTATG 57.997 45.455 22.08 13.75 42.29 2.39
35 36 4.699925 AAGCCCATAATACACCGTGTAT 57.300 40.909 16.95 16.95 44.79 2.29
36 37 5.511716 CCATAAGCCCATAATACACCGTGTA 60.512 44.000 13.69 13.69 37.24 2.90
37 38 4.385825 CATAAGCCCATAATACACCGTGT 58.614 43.478 9.58 9.58 0.00 4.49
38 39 3.751175 CCATAAGCCCATAATACACCGTG 59.249 47.826 0.00 0.00 0.00 4.94
39 40 3.809324 GCCATAAGCCCATAATACACCGT 60.809 47.826 0.00 0.00 34.35 4.83
40 41 2.747446 GCCATAAGCCCATAATACACCG 59.253 50.000 0.00 0.00 34.35 4.94
61 62 3.131396 GTCATAAGTTGGCCGTCTATGG 58.869 50.000 0.00 0.00 0.00 2.74
62 63 4.060038 AGTCATAAGTTGGCCGTCTATG 57.940 45.455 0.00 2.98 0.00 2.23
63 64 5.128171 TGTTAGTCATAAGTTGGCCGTCTAT 59.872 40.000 0.00 0.00 0.00 1.98
64 65 4.463539 TGTTAGTCATAAGTTGGCCGTCTA 59.536 41.667 0.00 0.00 0.00 2.59
65 66 3.259876 TGTTAGTCATAAGTTGGCCGTCT 59.740 43.478 0.00 0.00 0.00 4.18
66 67 3.592059 TGTTAGTCATAAGTTGGCCGTC 58.408 45.455 0.00 0.00 0.00 4.79
67 68 3.688694 TGTTAGTCATAAGTTGGCCGT 57.311 42.857 0.00 0.00 0.00 5.68
68 69 4.394920 ACATTGTTAGTCATAAGTTGGCCG 59.605 41.667 0.00 0.00 0.00 6.13
69 70 5.897377 ACATTGTTAGTCATAAGTTGGCC 57.103 39.130 0.00 0.00 0.00 5.36
70 71 7.023575 CAGAACATTGTTAGTCATAAGTTGGC 58.976 38.462 1.15 0.00 0.00 4.52
71 72 8.322906 TCAGAACATTGTTAGTCATAAGTTGG 57.677 34.615 1.15 0.00 0.00 3.77
72 73 9.208022 TCTCAGAACATTGTTAGTCATAAGTTG 57.792 33.333 1.15 0.00 0.00 3.16
73 74 9.429359 CTCTCAGAACATTGTTAGTCATAAGTT 57.571 33.333 1.15 0.00 0.00 2.66
74 75 7.547370 GCTCTCAGAACATTGTTAGTCATAAGT 59.453 37.037 1.15 0.00 0.00 2.24
75 76 7.253917 CGCTCTCAGAACATTGTTAGTCATAAG 60.254 40.741 1.15 0.00 0.00 1.73
76 77 6.531594 CGCTCTCAGAACATTGTTAGTCATAA 59.468 38.462 1.15 0.00 0.00 1.90
77 78 6.036470 CGCTCTCAGAACATTGTTAGTCATA 58.964 40.000 1.15 0.00 0.00 2.15
78 79 4.867047 CGCTCTCAGAACATTGTTAGTCAT 59.133 41.667 1.15 0.00 0.00 3.06
79 80 4.022329 TCGCTCTCAGAACATTGTTAGTCA 60.022 41.667 1.15 0.00 0.00 3.41
80 81 4.324936 GTCGCTCTCAGAACATTGTTAGTC 59.675 45.833 1.15 0.00 0.00 2.59
81 82 4.021894 AGTCGCTCTCAGAACATTGTTAGT 60.022 41.667 1.15 0.00 0.00 2.24
82 83 4.489810 AGTCGCTCTCAGAACATTGTTAG 58.510 43.478 1.15 0.00 0.00 2.34
83 84 4.521130 AGTCGCTCTCAGAACATTGTTA 57.479 40.909 1.15 0.00 0.00 2.41
84 85 3.393089 AGTCGCTCTCAGAACATTGTT 57.607 42.857 0.63 0.63 0.00 2.83
85 86 3.255888 TGTAGTCGCTCTCAGAACATTGT 59.744 43.478 0.00 0.00 0.00 2.71
86 87 3.838120 TGTAGTCGCTCTCAGAACATTG 58.162 45.455 0.00 0.00 0.00 2.82
87 88 3.508012 ACTGTAGTCGCTCTCAGAACATT 59.492 43.478 13.91 0.00 0.00 2.71
88 89 3.085533 ACTGTAGTCGCTCTCAGAACAT 58.914 45.455 13.91 0.00 0.00 2.71
89 90 2.505405 ACTGTAGTCGCTCTCAGAACA 58.495 47.619 13.91 0.00 0.00 3.18
90 91 4.681835 TTACTGTAGTCGCTCTCAGAAC 57.318 45.455 13.91 0.00 0.00 3.01
91 92 5.899120 ATTTACTGTAGTCGCTCTCAGAA 57.101 39.130 13.91 4.96 0.00 3.02
92 93 6.997239 TTATTTACTGTAGTCGCTCTCAGA 57.003 37.500 13.91 0.00 0.00 3.27
93 94 7.968956 TCTTTTATTTACTGTAGTCGCTCTCAG 59.031 37.037 0.00 0.00 0.00 3.35
94 95 7.823665 TCTTTTATTTACTGTAGTCGCTCTCA 58.176 34.615 0.00 0.00 0.00 3.27
95 96 8.684973 TTCTTTTATTTACTGTAGTCGCTCTC 57.315 34.615 0.00 0.00 0.00 3.20
96 97 9.654663 ATTTCTTTTATTTACTGTAGTCGCTCT 57.345 29.630 0.00 0.00 0.00 4.09
97 98 9.903185 GATTTCTTTTATTTACTGTAGTCGCTC 57.097 33.333 0.00 0.00 0.00 5.03
98 99 9.654663 AGATTTCTTTTATTTACTGTAGTCGCT 57.345 29.630 0.00 0.00 0.00 4.93
99 100 9.903185 GAGATTTCTTTTATTTACTGTAGTCGC 57.097 33.333 0.00 0.00 0.00 5.19
104 105 9.681062 CCAGGGAGATTTCTTTTATTTACTGTA 57.319 33.333 0.00 0.00 0.00 2.74
105 106 8.170730 ACCAGGGAGATTTCTTTTATTTACTGT 58.829 33.333 0.00 0.00 0.00 3.55
106 107 8.581253 ACCAGGGAGATTTCTTTTATTTACTG 57.419 34.615 0.00 0.00 0.00 2.74
107 108 9.907229 CTACCAGGGAGATTTCTTTTATTTACT 57.093 33.333 0.00 0.00 0.00 2.24
108 109 8.622157 GCTACCAGGGAGATTTCTTTTATTTAC 58.378 37.037 1.25 0.00 0.00 2.01
109 110 7.497909 CGCTACCAGGGAGATTTCTTTTATTTA 59.502 37.037 1.25 0.00 0.00 1.40
110 111 6.318900 CGCTACCAGGGAGATTTCTTTTATTT 59.681 38.462 1.25 0.00 0.00 1.40
111 112 5.823045 CGCTACCAGGGAGATTTCTTTTATT 59.177 40.000 1.25 0.00 0.00 1.40
112 113 5.130477 TCGCTACCAGGGAGATTTCTTTTAT 59.870 40.000 1.25 0.00 31.82 1.40
113 114 4.468510 TCGCTACCAGGGAGATTTCTTTTA 59.531 41.667 1.25 0.00 31.82 1.52
114 115 3.263425 TCGCTACCAGGGAGATTTCTTTT 59.737 43.478 1.25 0.00 31.82 2.27
115 116 2.838202 TCGCTACCAGGGAGATTTCTTT 59.162 45.455 1.25 0.00 31.82 2.52
116 117 2.467880 TCGCTACCAGGGAGATTTCTT 58.532 47.619 1.25 0.00 31.82 2.52
117 118 2.160721 TCGCTACCAGGGAGATTTCT 57.839 50.000 1.25 0.00 31.82 2.52
124 125 2.632996 CCATAAATCTCGCTACCAGGGA 59.367 50.000 0.00 0.00 35.75 4.20
125 126 2.632996 TCCATAAATCTCGCTACCAGGG 59.367 50.000 0.00 0.00 0.00 4.45
126 127 4.248859 CATCCATAAATCTCGCTACCAGG 58.751 47.826 0.00 0.00 0.00 4.45
127 128 4.887748 ACATCCATAAATCTCGCTACCAG 58.112 43.478 0.00 0.00 0.00 4.00
128 129 4.955811 ACATCCATAAATCTCGCTACCA 57.044 40.909 0.00 0.00 0.00 3.25
129 130 4.083802 GCAACATCCATAAATCTCGCTACC 60.084 45.833 0.00 0.00 0.00 3.18
130 131 4.511454 TGCAACATCCATAAATCTCGCTAC 59.489 41.667 0.00 0.00 0.00 3.58
131 132 4.702831 TGCAACATCCATAAATCTCGCTA 58.297 39.130 0.00 0.00 0.00 4.26
132 133 3.544684 TGCAACATCCATAAATCTCGCT 58.455 40.909 0.00 0.00 0.00 4.93
133 134 3.313526 ACTGCAACATCCATAAATCTCGC 59.686 43.478 0.00 0.00 0.00 5.03
134 135 4.318333 CGACTGCAACATCCATAAATCTCG 60.318 45.833 0.00 0.00 0.00 4.04
135 136 4.024556 CCGACTGCAACATCCATAAATCTC 60.025 45.833 0.00 0.00 0.00 2.75
136 137 3.879295 CCGACTGCAACATCCATAAATCT 59.121 43.478 0.00 0.00 0.00 2.40
137 138 3.627577 ACCGACTGCAACATCCATAAATC 59.372 43.478 0.00 0.00 0.00 2.17
138 139 3.620488 ACCGACTGCAACATCCATAAAT 58.380 40.909 0.00 0.00 0.00 1.40
139 140 3.066291 ACCGACTGCAACATCCATAAA 57.934 42.857 0.00 0.00 0.00 1.40
140 141 2.779755 ACCGACTGCAACATCCATAA 57.220 45.000 0.00 0.00 0.00 1.90
141 142 2.102420 CCTACCGACTGCAACATCCATA 59.898 50.000 0.00 0.00 0.00 2.74
154 155 1.669211 GCAGTGTGTCTTCCTACCGAC 60.669 57.143 0.00 0.00 0.00 4.79
171 172 5.163992 GCACATTTTGTCTCATCATTTGCAG 60.164 40.000 0.00 0.00 0.00 4.41
221 223 1.482182 AGTGCATGGAGATTCGTGCTA 59.518 47.619 6.85 0.00 46.57 3.49
258 260 6.402334 CGATGTCCTTAGCTTACGGTATCTAG 60.402 46.154 0.00 0.00 0.00 2.43
259 261 5.410746 CGATGTCCTTAGCTTACGGTATCTA 59.589 44.000 0.00 0.00 0.00 1.98
270 272 4.737855 TTTAAGCTCGATGTCCTTAGCT 57.262 40.909 0.00 0.00 46.96 3.32
326 328 7.373617 AGATTGGTGTGGGTATTTTCTTTTT 57.626 32.000 0.00 0.00 0.00 1.94
327 329 6.994421 AGATTGGTGTGGGTATTTTCTTTT 57.006 33.333 0.00 0.00 0.00 2.27
328 330 6.553100 TGAAGATTGGTGTGGGTATTTTCTTT 59.447 34.615 0.00 0.00 0.00 2.52
329 331 6.074648 TGAAGATTGGTGTGGGTATTTTCTT 58.925 36.000 0.00 0.00 0.00 2.52
330 332 5.640147 TGAAGATTGGTGTGGGTATTTTCT 58.360 37.500 0.00 0.00 0.00 2.52
331 333 5.975693 TGAAGATTGGTGTGGGTATTTTC 57.024 39.130 0.00 0.00 0.00 2.29
332 334 5.337491 GCATGAAGATTGGTGTGGGTATTTT 60.337 40.000 0.00 0.00 0.00 1.82
333 335 4.160252 GCATGAAGATTGGTGTGGGTATTT 59.840 41.667 0.00 0.00 0.00 1.40
334 336 3.701040 GCATGAAGATTGGTGTGGGTATT 59.299 43.478 0.00 0.00 0.00 1.89
335 337 3.290710 GCATGAAGATTGGTGTGGGTAT 58.709 45.455 0.00 0.00 0.00 2.73
336 338 2.040947 TGCATGAAGATTGGTGTGGGTA 59.959 45.455 0.00 0.00 0.00 3.69
337 339 1.203038 TGCATGAAGATTGGTGTGGGT 60.203 47.619 0.00 0.00 0.00 4.51
339 341 2.821378 TCTTGCATGAAGATTGGTGTGG 59.179 45.455 0.00 0.00 35.64 4.17
341 343 2.821969 GGTCTTGCATGAAGATTGGTGT 59.178 45.455 3.51 0.00 42.82 4.16
342 344 2.821378 TGGTCTTGCATGAAGATTGGTG 59.179 45.455 3.51 0.00 42.82 4.17
343 345 3.159213 TGGTCTTGCATGAAGATTGGT 57.841 42.857 3.51 0.00 42.82 3.67
344 346 4.158949 TCATTGGTCTTGCATGAAGATTGG 59.841 41.667 3.51 0.00 42.82 3.16
346 348 7.834881 ATATCATTGGTCTTGCATGAAGATT 57.165 32.000 3.51 0.00 42.82 2.40
347 349 8.929260 TTATATCATTGGTCTTGCATGAAGAT 57.071 30.769 3.51 6.07 42.82 2.40
348 350 8.212995 TCTTATATCATTGGTCTTGCATGAAGA 58.787 33.333 3.51 0.00 38.45 2.87
349 351 8.288208 GTCTTATATCATTGGTCTTGCATGAAG 58.712 37.037 3.51 0.00 30.79 3.02
350 352 7.994911 AGTCTTATATCATTGGTCTTGCATGAA 59.005 33.333 3.51 0.00 30.79 2.57
351 353 7.512130 AGTCTTATATCATTGGTCTTGCATGA 58.488 34.615 0.00 0.00 0.00 3.07
353 355 9.499479 CTAAGTCTTATATCATTGGTCTTGCAT 57.501 33.333 0.00 0.00 0.00 3.96
354 356 8.704668 TCTAAGTCTTATATCATTGGTCTTGCA 58.295 33.333 0.00 0.00 0.00 4.08
359 361 8.930760 GCACATCTAAGTCTTATATCATTGGTC 58.069 37.037 0.00 0.00 0.00 4.02
360 362 8.432013 TGCACATCTAAGTCTTATATCATTGGT 58.568 33.333 0.00 0.00 0.00 3.67
361 363 8.837788 TGCACATCTAAGTCTTATATCATTGG 57.162 34.615 0.00 0.00 0.00 3.16
371 1420 9.319143 GTCATAAGTATTGCACATCTAAGTCTT 57.681 33.333 0.00 0.00 0.00 3.01
374 1423 8.040727 TGTGTCATAAGTATTGCACATCTAAGT 58.959 33.333 0.00 0.00 32.79 2.24
383 1432 8.822652 CATCTAGATGTGTCATAAGTATTGCA 57.177 34.615 22.42 0.00 34.23 4.08
419 1468 7.877612 CCTTTTCATGGGTAATTTAAGCAGTTT 59.122 33.333 0.00 0.00 0.00 2.66
420 1469 7.234577 TCCTTTTCATGGGTAATTTAAGCAGTT 59.765 33.333 0.00 0.00 0.00 3.16
422 1471 7.169158 TCCTTTTCATGGGTAATTTAAGCAG 57.831 36.000 0.00 0.00 0.00 4.24
424 1473 7.781056 TCATCCTTTTCATGGGTAATTTAAGC 58.219 34.615 0.00 0.00 0.00 3.09
425 1474 8.416329 CCTCATCCTTTTCATGGGTAATTTAAG 58.584 37.037 0.00 0.00 0.00 1.85
426 1475 8.119246 TCCTCATCCTTTTCATGGGTAATTTAA 58.881 33.333 0.00 0.00 0.00 1.52
427 1476 7.647827 TCCTCATCCTTTTCATGGGTAATTTA 58.352 34.615 0.00 0.00 0.00 1.40
428 1477 6.502138 TCCTCATCCTTTTCATGGGTAATTT 58.498 36.000 0.00 0.00 0.00 1.82
430 1479 5.732331 TCCTCATCCTTTTCATGGGTAAT 57.268 39.130 0.00 0.00 0.00 1.89
431 1480 5.222233 TGTTCCTCATCCTTTTCATGGGTAA 60.222 40.000 0.00 0.00 0.00 2.85
432 1481 4.290985 TGTTCCTCATCCTTTTCATGGGTA 59.709 41.667 0.00 0.00 0.00 3.69
442 1631 0.840722 ACCCCGTGTTCCTCATCCTT 60.841 55.000 0.00 0.00 0.00 3.36
443 1632 1.229529 ACCCCGTGTTCCTCATCCT 60.230 57.895 0.00 0.00 0.00 3.24
475 1664 2.906354 CTCGGAAGGATCACGGAATTT 58.094 47.619 0.00 0.00 0.00 1.82
571 1760 2.661866 GTCTGTTCGCGTGGCAGT 60.662 61.111 19.96 0.00 0.00 4.40
670 1867 0.036732 AATCGCTTTCTGTCCAGGCA 59.963 50.000 0.00 0.00 0.00 4.75
674 1872 1.298157 CCGCAATCGCTTTCTGTCCA 61.298 55.000 0.00 0.00 35.30 4.02
722 1923 2.023318 GCAAGCTGCTATGAGGCTG 58.977 57.895 0.90 0.00 40.96 4.85
723 1924 4.555610 GCAAGCTGCTATGAGGCT 57.444 55.556 0.90 0.00 40.96 4.58
801 2002 3.243535 CCAAGACTTTGCCTGGAAAACTC 60.244 47.826 0.00 0.00 32.79 3.01
923 2124 1.154413 GCATGGCAACTCGTGTTCG 60.154 57.895 0.00 0.00 33.52 3.95
1224 2425 1.855213 TACTTGCTGCTTTGCCGCTG 61.855 55.000 0.00 3.62 39.43 5.18
1563 2773 7.439356 CAGAGAAGAGGATTAAAATGCGTATCA 59.561 37.037 0.00 0.00 0.00 2.15
1875 3128 4.971939 TCCTGAACATGTCAATTGTCAGA 58.028 39.130 19.80 7.44 35.22 3.27
2047 3426 5.132897 AGCGAATGCATTTGTAGGAAAAA 57.867 34.783 24.39 0.00 46.23 1.94
2056 3435 2.351418 TCCTACGAAGCGAATGCATTTG 59.649 45.455 20.60 20.60 46.23 2.32
2068 3447 6.603237 TTCATGTATGCATTTCCTACGAAG 57.397 37.500 3.54 0.00 31.99 3.79
2125 3505 2.166664 GAGTGGATGCGTAGTTTCCTCT 59.833 50.000 0.00 0.00 37.28 3.69
2137 3517 6.454186 GCGTAAAATGATTTTTGAGTGGATGC 60.454 38.462 8.60 2.56 35.82 3.91
2173 3553 5.709631 TGCAATTATAAGGAACTGACTTGCA 59.290 36.000 11.37 11.37 42.73 4.08
2182 3562 8.986477 AATTGACACTTGCAATTATAAGGAAC 57.014 30.769 0.00 0.00 42.39 3.62
2194 3574 8.149647 AGGAATTTGATAAAATTGACACTTGCA 58.850 29.630 5.44 0.00 32.92 4.08
2278 3658 6.239120 GCAGATGCCAGGTGTAATGATTAAAT 60.239 38.462 0.00 0.00 34.31 1.40
2286 3666 2.742428 ATGCAGATGCCAGGTGTAAT 57.258 45.000 1.72 0.00 41.18 1.89
2292 3672 2.158856 TCTCAGTAATGCAGATGCCAGG 60.159 50.000 1.72 0.00 41.18 4.45
2293 3673 3.189618 TCTCAGTAATGCAGATGCCAG 57.810 47.619 1.72 0.00 41.18 4.85
2294 3674 3.473625 CATCTCAGTAATGCAGATGCCA 58.526 45.455 14.93 0.00 37.73 4.92
2306 3686 5.555966 TGTTTGGTTATGTGCATCTCAGTA 58.444 37.500 0.00 0.00 0.00 2.74
2310 3690 5.314923 ACATGTTTGGTTATGTGCATCTC 57.685 39.130 0.00 0.00 36.26 2.75
2312 3692 5.345741 GTGAACATGTTTGGTTATGTGCATC 59.654 40.000 13.36 0.00 42.95 3.91
2320 3700 7.094162 TGTTTTCAGAGTGAACATGTTTGGTTA 60.094 33.333 13.36 0.00 35.89 2.85
2364 3745 9.026121 ACAGACTCTACATGTTTACTTGTATCT 57.974 33.333 2.30 6.80 36.38 1.98
2369 3750 9.239002 GCTATACAGACTCTACATGTTTACTTG 57.761 37.037 2.30 0.00 0.00 3.16
2701 4082 2.290960 GGTGAGGATAACTTTGCCCAGT 60.291 50.000 0.00 0.00 0.00 4.00
2702 4083 2.290896 TGGTGAGGATAACTTTGCCCAG 60.291 50.000 0.00 0.00 0.00 4.45
2707 4088 4.818546 CAGGCTATGGTGAGGATAACTTTG 59.181 45.833 0.00 0.00 0.00 2.77
2714 4095 1.216064 TTGCAGGCTATGGTGAGGAT 58.784 50.000 0.00 0.00 0.00 3.24
2722 4104 2.549926 TGTACACGATTGCAGGCTATG 58.450 47.619 0.00 0.00 0.00 2.23
2731 4113 6.505265 CGTTTACGAAGGTATGTACACGATTG 60.505 42.308 0.00 0.00 43.61 2.67
2748 4130 3.191371 GGAGAACTAAGACCCGTTTACGA 59.809 47.826 3.46 0.00 43.02 3.43
2756 4138 0.535797 CGTGGGGAGAACTAAGACCC 59.464 60.000 0.00 0.00 41.84 4.46
2757 4139 1.264295 ACGTGGGGAGAACTAAGACC 58.736 55.000 0.00 0.00 0.00 3.85
2760 4143 2.833631 ACAACGTGGGGAGAACTAAG 57.166 50.000 0.00 0.00 0.00 2.18
2776 4159 9.787435 ACACTTTATTTATGGTTGTCTCTACAA 57.213 29.630 0.00 0.00 43.32 2.41
2777 4160 9.431887 GACACTTTATTTATGGTTGTCTCTACA 57.568 33.333 0.00 0.00 0.00 2.74
2778 4161 9.431887 TGACACTTTATTTATGGTTGTCTCTAC 57.568 33.333 0.00 0.00 0.00 2.59
2779 4162 9.431887 GTGACACTTTATTTATGGTTGTCTCTA 57.568 33.333 0.00 0.00 0.00 2.43
2780 4163 7.117812 CGTGACACTTTATTTATGGTTGTCTCT 59.882 37.037 3.68 0.00 0.00 3.10
2781 4164 7.234384 CGTGACACTTTATTTATGGTTGTCTC 58.766 38.462 3.68 0.00 0.00 3.36
2782 4165 6.148811 CCGTGACACTTTATTTATGGTTGTCT 59.851 38.462 3.68 0.00 0.00 3.41
2783 4166 6.072893 ACCGTGACACTTTATTTATGGTTGTC 60.073 38.462 3.68 0.00 0.00 3.18
2784 4167 5.766174 ACCGTGACACTTTATTTATGGTTGT 59.234 36.000 3.68 0.00 0.00 3.32
2785 4168 6.249035 ACCGTGACACTTTATTTATGGTTG 57.751 37.500 3.68 0.00 0.00 3.77
2786 4169 6.935771 TGTACCGTGACACTTTATTTATGGTT 59.064 34.615 3.68 0.00 0.00 3.67
2787 4170 6.465948 TGTACCGTGACACTTTATTTATGGT 58.534 36.000 3.68 2.89 0.00 3.55
2795 4178 4.859304 ACAGATGTACCGTGACACTTTA 57.141 40.909 3.68 0.00 30.52 1.85
2796 4179 3.746045 ACAGATGTACCGTGACACTTT 57.254 42.857 3.68 0.00 30.52 2.66
2804 4187 4.037684 GCAGGTTATCTACAGATGTACCGT 59.962 45.833 14.58 6.00 41.46 4.83
2805 4188 4.547532 GCAGGTTATCTACAGATGTACCG 58.452 47.826 14.58 12.01 41.46 4.02
2866 4249 2.083774 CTGGTCGCTTTGGCTATTTGA 58.916 47.619 0.00 0.00 36.09 2.69


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.