Multiple sequence alignment - TraesCS7B01G052200

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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 TraesCS7B01G052200 chr7B 100.000 5447 0 0 1 5447 54724172 54729618 0.000000e+00 10059.0
1 TraesCS7B01G052200 chr7B 93.103 87 4 2 576 660 638921349 638921263 5.730000e-25 126.0
2 TraesCS7B01G052200 chr7D 96.055 4715 169 4 249 4947 99461465 99466178 0.000000e+00 7661.0
3 TraesCS7B01G052200 chr7D 72.863 2948 706 83 1062 3965 164406712 164409609 0.000000e+00 926.0
4 TraesCS7B01G052200 chr7D 94.422 251 12 2 1 250 99461055 99461304 8.560000e-103 385.0
5 TraesCS7B01G052200 chr7D 89.362 188 3 12 4943 5114 99466206 99466392 2.550000e-53 220.0
6 TraesCS7B01G052200 chr7D 86.486 111 8 2 5342 5447 618173663 618173555 1.240000e-21 115.0
7 TraesCS7B01G052200 chr7D 91.111 45 3 1 5281 5325 118829568 118829525 5.890000e-05 60.2
8 TraesCS7B01G052200 chr7A 95.090 4460 206 8 1 4455 101857898 101862349 0.000000e+00 7011.0
9 TraesCS7B01G052200 chr7A 90.909 429 29 4 4497 4915 101862349 101862777 7.920000e-158 568.0
10 TraesCS7B01G052200 chr7A 95.000 80 4 0 573 652 509222371 509222450 5.730000e-25 126.0
11 TraesCS7B01G052200 chr7A 86.607 112 8 3 5340 5447 156271606 156271714 3.450000e-22 117.0
12 TraesCS7B01G052200 chr3A 91.111 90 7 1 579 668 597181251 597181163 2.660000e-23 121.0
13 TraesCS7B01G052200 chr3A 97.297 37 1 0 5290 5326 556370121 556370085 4.550000e-06 63.9
14 TraesCS7B01G052200 chr1B 90.909 88 8 0 573 660 156850443 156850356 9.580000e-23 119.0
15 TraesCS7B01G052200 chr3D 86.792 106 12 1 5342 5447 442760538 442760435 3.450000e-22 117.0
16 TraesCS7B01G052200 chr3D 85.455 110 10 3 5340 5447 16644282 16644387 5.770000e-20 110.0
17 TraesCS7B01G052200 chr3D 85.965 57 8 0 5270 5326 341460519 341460463 1.640000e-05 62.1
18 TraesCS7B01G052200 chr4D 86.364 110 10 2 5342 5447 77230436 77230544 1.240000e-21 115.0
19 TraesCS7B01G052200 chr5D 86.239 109 9 5 5342 5447 497016444 497016549 4.460000e-21 113.0
20 TraesCS7B01G052200 chr4B 90.698 86 7 1 569 654 41531414 41531498 4.460000e-21 113.0
21 TraesCS7B01G052200 chr4B 89.130 92 9 1 567 658 41531506 41531416 4.460000e-21 113.0
22 TraesCS7B01G052200 chr2D 86.792 106 9 4 5342 5447 59142815 59142715 4.460000e-21 113.0
23 TraesCS7B01G052200 chr5A 85.586 111 10 2 5342 5447 643449699 643449590 1.600000e-20 111.0
24 TraesCS7B01G052200 chr1A 85.455 110 11 2 5342 5447 348727810 348727918 5.770000e-20 110.0
25 TraesCS7B01G052200 chr1A 86.598 97 12 1 573 669 11940814 11940909 7.460000e-19 106.0


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 TraesCS7B01G052200 chr7B 54724172 54729618 5446 False 10059.000000 10059 100.000000 1 5447 1 chr7B.!!$F1 5446
1 TraesCS7B01G052200 chr7D 99461055 99466392 5337 False 2755.333333 7661 93.279667 1 5114 3 chr7D.!!$F2 5113
2 TraesCS7B01G052200 chr7D 164406712 164409609 2897 False 926.000000 926 72.863000 1062 3965 1 chr7D.!!$F1 2903
3 TraesCS7B01G052200 chr7A 101857898 101862777 4879 False 3789.500000 7011 92.999500 1 4915 2 chr7A.!!$F3 4914

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
498 662 1.202302 TCGAGTCTAGGAATGCTTGCG 60.202 52.381 0.00 0.00 0.00 4.85 F
1508 1672 0.175760 CAGGACGTGTACCTCCATGG 59.824 60.000 4.97 4.97 42.93 3.66 F
2708 2872 0.979665 TCTAGTTGCTCCAAGCTGCT 59.020 50.000 0.00 0.00 42.97 4.24 F
4314 4488 1.074775 CTTGGCCCTTAGGTGCACA 59.925 57.895 20.43 0.00 34.57 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2409 2573 0.395862 TTCGTTCCAAACCTGGGCAA 60.396 50.0 0.0 0.0 43.71 4.52 R
2931 3098 0.445436 GTCCGTTGCTGCTGAGATTG 59.555 55.0 0.0 0.0 0.00 2.67 R
4350 4524 0.730834 CAGTCAGCTCCTTCACGACG 60.731 60.0 0.0 0.0 0.00 5.12 R
5353 5592 0.039256 TCGCAGAAGCAAAACCATGC 60.039 50.0 0.0 0.0 46.78 4.06 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
103 104 8.634335 TCCATTTGTTTCTCTGTTTATCATGA 57.366 30.769 0.00 0.00 0.00 3.07
306 470 4.220602 GGGCCTCAATTTAATTGACACTGT 59.779 41.667 15.46 0.00 43.84 3.55
332 496 7.735326 TCTTACTAATAGCCTCAGTTTCCTT 57.265 36.000 0.00 0.00 0.00 3.36
416 580 3.306472 AACAACAAGCTGTAGGGGAAA 57.694 42.857 0.00 0.00 0.00 3.13
438 602 9.772973 GGAAACCCTGACAGTAAAATAATTTTT 57.227 29.630 0.93 0.00 38.56 1.94
498 662 1.202302 TCGAGTCTAGGAATGCTTGCG 60.202 52.381 0.00 0.00 0.00 4.85
549 713 1.609783 GTTGGAGGGACCTCATGGG 59.390 63.158 19.30 0.00 44.40 4.00
582 746 5.013258 ACCCTCAGATATTACTACCTCCC 57.987 47.826 0.00 0.00 0.00 4.30
598 762 8.865244 ACTACCTCCCTACCAAAATATAAGAA 57.135 34.615 0.00 0.00 0.00 2.52
769 933 5.648092 GCTCTTGTTAGGATGTACACCATTT 59.352 40.000 14.39 0.00 32.56 2.32
805 969 5.609533 ACTTGGAGTGTACATGGTATACC 57.390 43.478 15.50 15.50 0.00 2.73
852 1016 5.129485 TCCTTCTAAAGTATGAGAAGCCTGG 59.871 44.000 6.19 0.00 44.89 4.45
905 1069 4.101430 TGTGCTCAGGATGTAATATCTGCA 59.899 41.667 0.00 0.00 37.40 4.41
924 1088 2.223203 GCAAGACAATTCTGAGCATCGG 60.223 50.000 0.00 0.00 44.94 4.18
965 1129 9.903682 ATCAGTTTGAGAAAACATACAATCTTG 57.096 29.630 4.34 0.00 35.20 3.02
977 1141 7.369803 ACATACAATCTTGTGCTAACTTCTG 57.630 36.000 5.84 0.00 42.31 3.02
1051 1215 7.394923 TGTTTCTCTTCTTAAGTTTGGTTTCCA 59.605 33.333 1.63 0.00 0.00 3.53
1080 1244 3.181506 GGAGTTTGAATTCAGATGGTCGC 60.182 47.826 8.41 0.00 0.00 5.19
1240 1404 2.632996 TCGTCTGGAGTTTCTGGTTCAT 59.367 45.455 0.00 0.00 0.00 2.57
1257 1421 7.027874 TGGTTCATTAGGAGTTCAAATAGGT 57.972 36.000 0.00 0.00 0.00 3.08
1508 1672 0.175760 CAGGACGTGTACCTCCATGG 59.824 60.000 4.97 4.97 42.93 3.66
1515 1679 3.714798 ACGTGTACCTCCATGGGAATAAT 59.285 43.478 13.02 0.00 41.11 1.28
1579 1743 4.394920 GCCTTAGATCATTTTGGTTGACGA 59.605 41.667 0.00 0.00 0.00 4.20
1819 1983 3.582647 TCATATGAGTGGCGGTATTCCAT 59.417 43.478 0.00 0.00 35.81 3.41
1838 2002 2.057137 TCATGGCTAGGGAATTGCAC 57.943 50.000 0.00 0.00 0.00 4.57
1849 2013 2.162408 GGGAATTGCACTAGCTTGACAC 59.838 50.000 1.04 0.00 42.74 3.67
1864 2028 1.396648 TGACACAACTTGCACTTGTCG 59.603 47.619 6.05 5.56 39.59 4.35
1876 2040 1.661617 CACTTGTCGACAACCGTTTCA 59.338 47.619 26.53 4.45 39.75 2.69
1981 2145 3.264450 CCCTCCTGAGATTGGTAACTGTT 59.736 47.826 0.00 0.00 37.61 3.16
2375 2539 3.383185 GTGTTGGTTTTGGGTCTCAATCA 59.617 43.478 0.00 0.00 34.98 2.57
2409 2573 2.832643 TCCCATCCAATGTTGCAGAT 57.167 45.000 0.00 0.00 0.00 2.90
2547 2711 2.511218 AGATATTCCAGCAAGCTTGGGA 59.489 45.455 27.10 21.97 0.00 4.37
2682 2846 1.127567 TACAGGGTGCACTTCCAGCT 61.128 55.000 17.98 1.64 33.88 4.24
2708 2872 0.979665 TCTAGTTGCTCCAAGCTGCT 59.020 50.000 0.00 0.00 42.97 4.24
2727 2891 7.219322 AGCTGCTTATTTTGGATTTGAGTTTT 58.781 30.769 0.00 0.00 0.00 2.43
2889 3053 1.538047 GCAACATTCTTGGAGGCAGA 58.462 50.000 0.00 0.00 0.00 4.26
3032 3199 4.870991 GTCAGTTAATAACCTCACTGGAGC 59.129 45.833 0.00 0.00 39.96 4.70
3048 3215 2.663188 GCTCTCGGCGCATTAGGG 60.663 66.667 10.83 3.77 0.00 3.53
3066 3233 3.878778 AGGGAGTCTACATTCATTGCAC 58.121 45.455 0.00 0.00 0.00 4.57
3540 3707 4.675146 GCCATAAAGAAGCTTGCGATTTCA 60.675 41.667 2.10 0.00 0.00 2.69
3669 3836 6.127310 ACTCTGGGTTCATACTGTATGACTTC 60.127 42.308 25.76 18.72 44.32 3.01
4125 4299 2.569134 GTCGTCCTGCTCGAGCTT 59.431 61.111 35.27 0.00 42.66 3.74
4131 4305 2.223502 CGTCCTGCTCGAGCTTATAACA 60.224 50.000 35.27 14.62 42.66 2.41
4181 4355 1.398390 GGAGAACATGGACATTGTCGC 59.602 52.381 10.56 4.79 32.65 5.19
4314 4488 1.074775 CTTGGCCCTTAGGTGCACA 59.925 57.895 20.43 0.00 34.57 4.57
4533 4711 6.038985 CAGAATGTACAGTCAGATTCATCGT 58.961 40.000 23.89 0.00 32.14 3.73
4581 4764 6.294176 GCTGGTAACTGAGTTTTGATGATTGT 60.294 38.462 1.97 0.00 37.83 2.71
4664 4847 0.479815 TGGATGGATGGGGCAGATTC 59.520 55.000 0.00 0.00 0.00 2.52
4985 5209 1.952621 TCGATCTGTTCCCTTCCCTT 58.047 50.000 0.00 0.00 0.00 3.95
5071 5308 8.918202 TTTGAAGTGTATGAGGTAGAAACATT 57.082 30.769 0.00 0.00 0.00 2.71
5129 5368 6.560253 ATTTAAAACTAGCAGATATGCCCG 57.440 37.500 9.09 2.67 34.90 6.13
5130 5369 3.560636 AAAACTAGCAGATATGCCCGT 57.439 42.857 9.09 3.36 34.90 5.28
5131 5370 3.560636 AAACTAGCAGATATGCCCGTT 57.439 42.857 9.09 9.68 34.90 4.44
5132 5371 2.821991 ACTAGCAGATATGCCCGTTC 57.178 50.000 9.09 0.00 34.90 3.95
5133 5372 1.000163 ACTAGCAGATATGCCCGTTCG 60.000 52.381 9.09 0.00 34.90 3.95
5134 5373 1.000163 CTAGCAGATATGCCCGTTCGT 60.000 52.381 9.09 0.00 34.90 3.85
5135 5374 0.178068 AGCAGATATGCCCGTTCGTT 59.822 50.000 9.09 0.00 34.90 3.85
5136 5375 0.304705 GCAGATATGCCCGTTCGTTG 59.695 55.000 0.00 0.00 0.00 4.10
5137 5376 0.304705 CAGATATGCCCGTTCGTTGC 59.695 55.000 0.00 0.00 0.00 4.17
5138 5377 0.107897 AGATATGCCCGTTCGTTGCA 60.108 50.000 8.54 8.54 39.68 4.08
5139 5378 0.730265 GATATGCCCGTTCGTTGCAA 59.270 50.000 0.00 0.00 38.69 4.08
5140 5379 0.450184 ATATGCCCGTTCGTTGCAAC 59.550 50.000 19.89 19.89 38.69 4.17
5153 5392 3.643159 GTTGCAACGGGAGAGAAAATT 57.357 42.857 14.90 0.00 0.00 1.82
5154 5393 3.308530 GTTGCAACGGGAGAGAAAATTG 58.691 45.455 14.90 0.00 0.00 2.32
5155 5394 2.857483 TGCAACGGGAGAGAAAATTGA 58.143 42.857 0.00 0.00 0.00 2.57
5156 5395 2.552315 TGCAACGGGAGAGAAAATTGAC 59.448 45.455 0.00 0.00 0.00 3.18
5157 5396 2.412847 GCAACGGGAGAGAAAATTGACG 60.413 50.000 0.00 0.00 0.00 4.35
5158 5397 1.439679 ACGGGAGAGAAAATTGACGC 58.560 50.000 0.00 0.00 0.00 5.19
5159 5398 0.370273 CGGGAGAGAAAATTGACGCG 59.630 55.000 3.53 3.53 0.00 6.01
5160 5399 1.439679 GGGAGAGAAAATTGACGCGT 58.560 50.000 13.85 13.85 0.00 6.01
5161 5400 1.393883 GGGAGAGAAAATTGACGCGTC 59.606 52.381 31.66 31.66 0.00 5.19
5162 5401 2.338500 GGAGAGAAAATTGACGCGTCT 58.662 47.619 36.27 18.90 0.00 4.18
5163 5402 2.092838 GGAGAGAAAATTGACGCGTCTG 59.907 50.000 36.27 0.00 0.00 3.51
5164 5403 1.461127 AGAGAAAATTGACGCGTCTGC 59.539 47.619 36.27 17.72 37.91 4.26
5165 5404 1.461127 GAGAAAATTGACGCGTCTGCT 59.539 47.619 36.27 22.17 39.65 4.24
5166 5405 1.461127 AGAAAATTGACGCGTCTGCTC 59.539 47.619 36.27 24.16 39.65 4.26
5167 5406 1.461127 GAAAATTGACGCGTCTGCTCT 59.539 47.619 36.27 19.90 39.65 4.09
5168 5407 1.512926 AAATTGACGCGTCTGCTCTT 58.487 45.000 36.27 20.22 39.65 2.85
5169 5408 1.512926 AATTGACGCGTCTGCTCTTT 58.487 45.000 36.27 18.57 39.65 2.52
5170 5409 1.071605 ATTGACGCGTCTGCTCTTTC 58.928 50.000 36.27 11.22 39.65 2.62
5171 5410 0.249280 TTGACGCGTCTGCTCTTTCA 60.249 50.000 36.27 13.86 39.65 2.69
5172 5411 0.249280 TGACGCGTCTGCTCTTTCAA 60.249 50.000 36.27 12.45 39.65 2.69
5173 5412 0.161870 GACGCGTCTGCTCTTTCAAC 59.838 55.000 31.12 0.44 39.65 3.18
5174 5413 1.222115 ACGCGTCTGCTCTTTCAACC 61.222 55.000 5.58 0.00 39.65 3.77
5175 5414 1.221466 CGCGTCTGCTCTTTCAACCA 61.221 55.000 0.00 0.00 39.65 3.67
5176 5415 0.944386 GCGTCTGCTCTTTCAACCAA 59.056 50.000 0.00 0.00 38.39 3.67
5177 5416 1.333619 GCGTCTGCTCTTTCAACCAAA 59.666 47.619 0.00 0.00 38.39 3.28
5178 5417 2.223479 GCGTCTGCTCTTTCAACCAAAA 60.223 45.455 0.00 0.00 38.39 2.44
5179 5418 3.733684 GCGTCTGCTCTTTCAACCAAAAA 60.734 43.478 0.00 0.00 38.39 1.94
5180 5419 4.610945 CGTCTGCTCTTTCAACCAAAAAT 58.389 39.130 0.00 0.00 0.00 1.82
5181 5420 5.757886 CGTCTGCTCTTTCAACCAAAAATA 58.242 37.500 0.00 0.00 0.00 1.40
5182 5421 6.205784 CGTCTGCTCTTTCAACCAAAAATAA 58.794 36.000 0.00 0.00 0.00 1.40
5183 5422 6.360681 CGTCTGCTCTTTCAACCAAAAATAAG 59.639 38.462 0.00 0.00 0.00 1.73
5184 5423 7.425606 GTCTGCTCTTTCAACCAAAAATAAGA 58.574 34.615 0.00 0.00 0.00 2.10
5185 5424 7.920682 GTCTGCTCTTTCAACCAAAAATAAGAA 59.079 33.333 0.00 0.00 0.00 2.52
5186 5425 8.641541 TCTGCTCTTTCAACCAAAAATAAGAAT 58.358 29.630 0.00 0.00 0.00 2.40
5187 5426 8.592105 TGCTCTTTCAACCAAAAATAAGAATG 57.408 30.769 0.00 0.00 0.00 2.67
5188 5427 7.656948 TGCTCTTTCAACCAAAAATAAGAATGG 59.343 33.333 0.00 0.00 38.91 3.16
5189 5428 7.118245 GCTCTTTCAACCAAAAATAAGAATGGG 59.882 37.037 0.00 0.00 37.26 4.00
5190 5429 7.449247 TCTTTCAACCAAAAATAAGAATGGGG 58.551 34.615 0.00 0.00 37.26 4.96
5191 5430 6.755542 TTCAACCAAAAATAAGAATGGGGT 57.244 33.333 0.00 0.00 37.26 4.95
5192 5431 6.353404 TCAACCAAAAATAAGAATGGGGTC 57.647 37.500 0.00 0.00 37.26 4.46
5193 5432 5.841237 TCAACCAAAAATAAGAATGGGGTCA 59.159 36.000 0.00 0.00 37.26 4.02
5194 5433 6.500049 TCAACCAAAAATAAGAATGGGGTCAT 59.500 34.615 0.00 0.00 37.26 3.06
5195 5434 7.676043 TCAACCAAAAATAAGAATGGGGTCATA 59.324 33.333 0.00 0.00 37.26 2.15
5196 5435 7.660030 ACCAAAAATAAGAATGGGGTCATAG 57.340 36.000 0.00 0.00 37.26 2.23
5197 5436 7.418378 ACCAAAAATAAGAATGGGGTCATAGA 58.582 34.615 0.00 0.00 37.26 1.98
5198 5437 7.561356 ACCAAAAATAAGAATGGGGTCATAGAG 59.439 37.037 0.00 0.00 37.26 2.43
5199 5438 7.779798 CCAAAAATAAGAATGGGGTCATAGAGA 59.220 37.037 0.00 0.00 32.44 3.10
5200 5439 8.844244 CAAAAATAAGAATGGGGTCATAGAGAG 58.156 37.037 0.00 0.00 32.44 3.20
5201 5440 7.937700 AAATAAGAATGGGGTCATAGAGAGA 57.062 36.000 0.00 0.00 32.44 3.10
5202 5441 7.552050 AATAAGAATGGGGTCATAGAGAGAG 57.448 40.000 0.00 0.00 32.44 3.20
5203 5442 3.238597 AGAATGGGGTCATAGAGAGAGC 58.761 50.000 0.00 0.00 32.44 4.09
5204 5443 1.626686 ATGGGGTCATAGAGAGAGCG 58.373 55.000 0.00 0.00 34.46 5.03
5205 5444 1.109920 TGGGGTCATAGAGAGAGCGC 61.110 60.000 0.00 0.00 43.88 5.92
5206 5445 1.109920 GGGGTCATAGAGAGAGCGCA 61.110 60.000 11.47 0.00 43.32 6.09
5207 5446 0.965439 GGGTCATAGAGAGAGCGCAT 59.035 55.000 11.47 0.00 34.46 4.73
5208 5447 2.163509 GGGTCATAGAGAGAGCGCATA 58.836 52.381 11.47 0.00 34.46 3.14
5209 5448 2.757868 GGGTCATAGAGAGAGCGCATAT 59.242 50.000 11.47 0.00 34.46 1.78
5210 5449 3.428725 GGGTCATAGAGAGAGCGCATATG 60.429 52.174 11.47 8.14 34.46 1.78
5211 5450 3.441922 GGTCATAGAGAGAGCGCATATGA 59.558 47.826 11.47 10.30 32.04 2.15
5212 5451 4.082517 GGTCATAGAGAGAGCGCATATGAA 60.083 45.833 11.47 0.00 35.32 2.57
5213 5452 5.465051 GTCATAGAGAGAGCGCATATGAAA 58.535 41.667 11.47 0.00 35.32 2.69
5214 5453 6.098679 GTCATAGAGAGAGCGCATATGAAAT 58.901 40.000 11.47 0.00 35.32 2.17
5215 5454 6.253298 GTCATAGAGAGAGCGCATATGAAATC 59.747 42.308 11.47 0.00 35.32 2.17
5216 5455 4.597404 AGAGAGAGCGCATATGAAATCA 57.403 40.909 11.47 0.00 0.00 2.57
5217 5456 5.149973 AGAGAGAGCGCATATGAAATCAT 57.850 39.130 11.47 1.01 40.22 2.45
5218 5457 4.930405 AGAGAGAGCGCATATGAAATCATG 59.070 41.667 11.47 0.00 37.15 3.07
5219 5458 3.436015 AGAGAGCGCATATGAAATCATGC 59.564 43.478 11.47 2.87 43.30 4.06
5220 5459 3.143728 AGAGCGCATATGAAATCATGCA 58.856 40.909 11.47 0.00 46.32 3.96
5221 5460 3.566742 AGAGCGCATATGAAATCATGCAA 59.433 39.130 11.47 0.00 46.32 4.08
5222 5461 4.217767 AGAGCGCATATGAAATCATGCAAT 59.782 37.500 11.47 0.00 46.32 3.56
5223 5462 4.482386 AGCGCATATGAAATCATGCAATC 58.518 39.130 11.47 0.00 46.32 2.67
5224 5463 4.022676 AGCGCATATGAAATCATGCAATCA 60.023 37.500 11.47 0.00 46.32 2.57
5225 5464 4.682401 GCGCATATGAAATCATGCAATCAA 59.318 37.500 6.97 0.00 46.32 2.57
5226 5465 5.164090 GCGCATATGAAATCATGCAATCAAG 60.164 40.000 6.97 0.00 46.32 3.02
5227 5466 5.918576 CGCATATGAAATCATGCAATCAAGT 59.081 36.000 6.97 0.00 46.32 3.16
5228 5467 7.079475 CGCATATGAAATCATGCAATCAAGTA 58.921 34.615 6.97 0.00 46.32 2.24
5229 5468 7.753580 CGCATATGAAATCATGCAATCAAGTAT 59.246 33.333 6.97 0.00 46.32 2.12
5230 5469 9.073368 GCATATGAAATCATGCAATCAAGTATC 57.927 33.333 6.97 0.00 45.51 2.24
5234 5473 7.430441 TGAAATCATGCAATCAAGTATCATGG 58.570 34.615 0.00 0.00 36.22 3.66
5235 5474 5.977489 ATCATGCAATCAAGTATCATGGG 57.023 39.130 0.00 0.00 36.22 4.00
5236 5475 4.795469 TCATGCAATCAAGTATCATGGGT 58.205 39.130 0.00 0.00 36.22 4.51
5237 5476 4.581409 TCATGCAATCAAGTATCATGGGTG 59.419 41.667 0.00 0.00 36.22 4.61
5238 5477 3.966979 TGCAATCAAGTATCATGGGTGT 58.033 40.909 0.00 0.00 0.00 4.16
5239 5478 3.695556 TGCAATCAAGTATCATGGGTGTG 59.304 43.478 0.00 0.00 0.00 3.82
5240 5479 3.696051 GCAATCAAGTATCATGGGTGTGT 59.304 43.478 0.00 0.00 0.00 3.72
5241 5480 4.881273 GCAATCAAGTATCATGGGTGTGTA 59.119 41.667 0.00 0.00 0.00 2.90
5242 5481 5.532406 GCAATCAAGTATCATGGGTGTGTAT 59.468 40.000 0.00 0.00 0.00 2.29
5243 5482 6.513884 GCAATCAAGTATCATGGGTGTGTATG 60.514 42.308 0.00 0.00 0.00 2.39
5244 5483 5.034852 TCAAGTATCATGGGTGTGTATGG 57.965 43.478 0.00 0.00 0.00 2.74
5245 5484 3.492102 AGTATCATGGGTGTGTATGGC 57.508 47.619 0.00 0.00 0.00 4.40
5246 5485 3.048600 AGTATCATGGGTGTGTATGGCT 58.951 45.455 0.00 0.00 0.00 4.75
5247 5486 2.645838 ATCATGGGTGTGTATGGCTC 57.354 50.000 0.00 0.00 0.00 4.70
5248 5487 1.284313 TCATGGGTGTGTATGGCTCA 58.716 50.000 0.00 0.00 0.00 4.26
5249 5488 1.632920 TCATGGGTGTGTATGGCTCAA 59.367 47.619 0.00 0.00 0.00 3.02
5250 5489 2.019249 CATGGGTGTGTATGGCTCAAG 58.981 52.381 0.00 0.00 0.00 3.02
5251 5490 0.327924 TGGGTGTGTATGGCTCAAGG 59.672 55.000 0.00 0.00 0.00 3.61
5252 5491 1.032114 GGGTGTGTATGGCTCAAGGC 61.032 60.000 0.00 0.00 41.50 4.35
5262 5501 2.706555 GGCTCAAGGCAAGTAAACAC 57.293 50.000 0.00 0.00 44.01 3.32
5263 5502 1.269723 GGCTCAAGGCAAGTAAACACC 59.730 52.381 0.00 0.00 44.01 4.16
5264 5503 1.953686 GCTCAAGGCAAGTAAACACCA 59.046 47.619 0.00 0.00 41.35 4.17
5265 5504 2.287608 GCTCAAGGCAAGTAAACACCAC 60.288 50.000 0.00 0.00 41.35 4.16
5266 5505 1.944024 TCAAGGCAAGTAAACACCACG 59.056 47.619 0.00 0.00 0.00 4.94
5267 5506 1.001815 CAAGGCAAGTAAACACCACGG 60.002 52.381 0.00 0.00 0.00 4.94
5268 5507 0.181824 AGGCAAGTAAACACCACGGT 59.818 50.000 0.00 0.00 0.00 4.83
5269 5508 1.417145 AGGCAAGTAAACACCACGGTA 59.583 47.619 0.00 0.00 0.00 4.02
5270 5509 1.802365 GGCAAGTAAACACCACGGTAG 59.198 52.381 0.00 0.00 0.00 3.18
5271 5510 2.548493 GGCAAGTAAACACCACGGTAGA 60.548 50.000 0.00 0.00 0.00 2.59
5272 5511 2.735134 GCAAGTAAACACCACGGTAGAG 59.265 50.000 0.00 0.00 0.00 2.43
5273 5512 3.553508 GCAAGTAAACACCACGGTAGAGA 60.554 47.826 0.00 0.00 0.00 3.10
5274 5513 3.930634 AGTAAACACCACGGTAGAGAC 57.069 47.619 0.00 0.00 0.00 3.36
5275 5514 3.225104 AGTAAACACCACGGTAGAGACA 58.775 45.455 0.00 0.00 0.00 3.41
5276 5515 3.830755 AGTAAACACCACGGTAGAGACAT 59.169 43.478 0.00 0.00 0.00 3.06
5277 5516 2.743636 AACACCACGGTAGAGACATG 57.256 50.000 0.00 0.00 0.00 3.21
5278 5517 1.919240 ACACCACGGTAGAGACATGA 58.081 50.000 0.00 0.00 0.00 3.07
5279 5518 2.457598 ACACCACGGTAGAGACATGAT 58.542 47.619 0.00 0.00 0.00 2.45
5280 5519 2.832129 ACACCACGGTAGAGACATGATT 59.168 45.455 0.00 0.00 0.00 2.57
5281 5520 3.260884 ACACCACGGTAGAGACATGATTT 59.739 43.478 0.00 0.00 0.00 2.17
5282 5521 4.253685 CACCACGGTAGAGACATGATTTT 58.746 43.478 0.00 0.00 0.00 1.82
5283 5522 4.695455 CACCACGGTAGAGACATGATTTTT 59.305 41.667 0.00 0.00 0.00 1.94
5284 5523 4.935808 ACCACGGTAGAGACATGATTTTTC 59.064 41.667 0.00 0.00 0.00 2.29
5285 5524 5.178797 CCACGGTAGAGACATGATTTTTCT 58.821 41.667 0.00 0.00 0.00 2.52
5286 5525 5.643777 CCACGGTAGAGACATGATTTTTCTT 59.356 40.000 0.00 0.00 0.00 2.52
5287 5526 6.149474 CCACGGTAGAGACATGATTTTTCTTT 59.851 38.462 0.00 0.00 0.00 2.52
5288 5527 7.308589 CCACGGTAGAGACATGATTTTTCTTTT 60.309 37.037 0.00 0.00 0.00 2.27
5289 5528 7.535258 CACGGTAGAGACATGATTTTTCTTTTG 59.465 37.037 0.00 0.00 0.00 2.44
5290 5529 6.524586 CGGTAGAGACATGATTTTTCTTTTGC 59.475 38.462 0.00 0.00 0.00 3.68
5291 5530 6.524586 GGTAGAGACATGATTTTTCTTTTGCG 59.475 38.462 0.00 0.00 0.00 4.85
5292 5531 6.317789 AGAGACATGATTTTTCTTTTGCGA 57.682 33.333 0.00 0.00 0.00 5.10
5293 5532 6.376978 AGAGACATGATTTTTCTTTTGCGAG 58.623 36.000 0.00 0.00 0.00 5.03
5294 5533 6.205464 AGAGACATGATTTTTCTTTTGCGAGA 59.795 34.615 0.00 0.00 0.00 4.04
5295 5534 6.376978 AGACATGATTTTTCTTTTGCGAGAG 58.623 36.000 0.00 0.00 0.00 3.20
5296 5535 5.464168 ACATGATTTTTCTTTTGCGAGAGG 58.536 37.500 0.00 0.00 0.00 3.69
5297 5536 5.241506 ACATGATTTTTCTTTTGCGAGAGGA 59.758 36.000 0.00 0.00 0.00 3.71
5298 5537 5.766150 TGATTTTTCTTTTGCGAGAGGAA 57.234 34.783 0.00 0.00 40.67 3.36
5299 5538 5.519722 TGATTTTTCTTTTGCGAGAGGAAC 58.480 37.500 0.00 0.00 42.67 3.62
5300 5539 3.602390 TTTTCTTTTGCGAGAGGAACG 57.398 42.857 0.00 0.00 42.67 3.95
5301 5540 2.519377 TTCTTTTGCGAGAGGAACGA 57.481 45.000 0.00 0.00 42.67 3.85
5302 5541 2.743636 TCTTTTGCGAGAGGAACGAT 57.256 45.000 0.00 0.00 42.67 3.73
5303 5542 3.040147 TCTTTTGCGAGAGGAACGATT 57.960 42.857 0.00 0.00 42.67 3.34
5304 5543 3.399330 TCTTTTGCGAGAGGAACGATTT 58.601 40.909 0.00 0.00 42.67 2.17
5305 5544 3.813166 TCTTTTGCGAGAGGAACGATTTT 59.187 39.130 0.00 0.00 42.67 1.82
5306 5545 3.536158 TTTGCGAGAGGAACGATTTTG 57.464 42.857 0.00 0.00 42.67 2.44
5307 5546 0.796312 TGCGAGAGGAACGATTTTGC 59.204 50.000 0.00 0.00 0.00 3.68
5308 5547 1.079503 GCGAGAGGAACGATTTTGCT 58.920 50.000 0.00 0.00 0.00 3.91
5309 5548 1.464997 GCGAGAGGAACGATTTTGCTT 59.535 47.619 0.00 0.00 0.00 3.91
5310 5549 2.474691 GCGAGAGGAACGATTTTGCTTC 60.475 50.000 0.00 0.00 0.00 3.86
5311 5550 2.094417 CGAGAGGAACGATTTTGCTTCC 59.906 50.000 0.00 0.00 34.69 3.46
5312 5551 2.076863 AGAGGAACGATTTTGCTTCCG 58.923 47.619 0.00 0.00 38.84 4.30
5313 5552 0.521735 AGGAACGATTTTGCTTCCGC 59.478 50.000 0.00 0.00 38.84 5.54
5314 5553 0.793104 GGAACGATTTTGCTTCCGCG 60.793 55.000 0.00 0.00 39.65 6.46
5315 5554 0.165079 GAACGATTTTGCTTCCGCGA 59.835 50.000 8.23 0.00 39.65 5.87
5316 5555 0.165944 AACGATTTTGCTTCCGCGAG 59.834 50.000 8.23 0.00 39.65 5.03
5317 5556 0.669318 ACGATTTTGCTTCCGCGAGA 60.669 50.000 8.23 0.00 39.65 4.04
5318 5557 0.025513 CGATTTTGCTTCCGCGAGAG 59.974 55.000 8.23 5.93 39.65 3.20
5319 5558 0.375106 GATTTTGCTTCCGCGAGAGG 59.625 55.000 8.23 4.88 39.65 3.69
5329 5568 4.373116 GCGAGAGGCACGGAACCA 62.373 66.667 0.00 0.00 42.87 3.67
5330 5569 2.342279 CGAGAGGCACGGAACCAA 59.658 61.111 0.00 0.00 0.00 3.67
5331 5570 1.301401 CGAGAGGCACGGAACCAAA 60.301 57.895 0.00 0.00 0.00 3.28
5332 5571 0.882927 CGAGAGGCACGGAACCAAAA 60.883 55.000 0.00 0.00 0.00 2.44
5333 5572 1.314730 GAGAGGCACGGAACCAAAAA 58.685 50.000 0.00 0.00 0.00 1.94
5356 5595 5.722021 AAAAATTCTTCCGTAAGTGGCAT 57.278 34.783 0.00 0.00 34.13 4.40
5357 5596 4.701956 AAATTCTTCCGTAAGTGGCATG 57.298 40.909 0.00 0.00 34.13 4.06
5358 5597 2.107950 TTCTTCCGTAAGTGGCATGG 57.892 50.000 0.00 0.00 34.13 3.66
5359 5598 0.981183 TCTTCCGTAAGTGGCATGGT 59.019 50.000 0.00 0.00 34.13 3.55
5360 5599 1.349688 TCTTCCGTAAGTGGCATGGTT 59.650 47.619 0.00 0.00 34.13 3.67
5361 5600 2.159382 CTTCCGTAAGTGGCATGGTTT 58.841 47.619 0.00 0.00 0.00 3.27
5362 5601 2.279935 TCCGTAAGTGGCATGGTTTT 57.720 45.000 0.00 0.00 0.00 2.43
5363 5602 1.883275 TCCGTAAGTGGCATGGTTTTG 59.117 47.619 0.00 0.00 0.00 2.44
5364 5603 1.668628 CCGTAAGTGGCATGGTTTTGC 60.669 52.381 0.00 0.00 42.01 3.68
5365 5604 1.269448 CGTAAGTGGCATGGTTTTGCT 59.731 47.619 0.00 0.00 42.38 3.91
5366 5605 2.288152 CGTAAGTGGCATGGTTTTGCTT 60.288 45.455 0.00 0.00 42.38 3.91
5367 5606 2.531522 AAGTGGCATGGTTTTGCTTC 57.468 45.000 0.00 0.00 42.38 3.86
5368 5607 1.708341 AGTGGCATGGTTTTGCTTCT 58.292 45.000 0.00 0.00 42.38 2.85
5369 5608 1.342174 AGTGGCATGGTTTTGCTTCTG 59.658 47.619 0.00 0.00 42.38 3.02
5370 5609 0.033781 TGGCATGGTTTTGCTTCTGC 59.966 50.000 0.00 0.00 42.38 4.26
5371 5610 1.010419 GGCATGGTTTTGCTTCTGCG 61.010 55.000 0.00 0.00 42.38 5.18
5372 5611 0.039256 GCATGGTTTTGCTTCTGCGA 60.039 50.000 0.00 0.00 43.34 5.10
5373 5612 1.973138 CATGGTTTTGCTTCTGCGAG 58.027 50.000 0.00 0.00 43.34 5.03
5374 5613 1.536766 CATGGTTTTGCTTCTGCGAGA 59.463 47.619 0.00 0.00 43.34 4.04
5375 5614 1.229428 TGGTTTTGCTTCTGCGAGAG 58.771 50.000 0.00 0.00 43.34 3.20
5376 5615 0.519077 GGTTTTGCTTCTGCGAGAGG 59.481 55.000 0.00 0.00 43.34 3.69
5377 5616 0.110010 GTTTTGCTTCTGCGAGAGGC 60.110 55.000 11.53 11.53 46.21 4.70
5397 5636 2.358247 GGCCGTGCCTCTCGAAAA 60.358 61.111 7.58 0.00 46.69 2.29
5398 5637 2.677979 GGCCGTGCCTCTCGAAAAC 61.678 63.158 7.58 0.00 46.69 2.43
5399 5638 3.011760 GCCGTGCCTCTCGAAAACG 62.012 63.158 0.00 0.00 0.00 3.60
5400 5639 1.372499 CCGTGCCTCTCGAAAACGA 60.372 57.895 0.00 0.00 36.38 3.85
5401 5640 0.942410 CCGTGCCTCTCGAAAACGAA 60.942 55.000 0.00 0.00 36.38 3.85
5402 5641 0.856641 CGTGCCTCTCGAAAACGAAA 59.143 50.000 0.00 0.00 36.38 3.46
5403 5642 1.259507 CGTGCCTCTCGAAAACGAAAA 59.740 47.619 0.00 0.00 36.38 2.29
5404 5643 2.285950 CGTGCCTCTCGAAAACGAAAAA 60.286 45.455 0.00 0.00 36.38 1.94
5442 5681 2.513159 TTTTTCGCGAGAGTCACGG 58.487 52.632 9.59 2.55 43.69 4.94
5443 5682 0.249155 TTTTTCGCGAGAGTCACGGT 60.249 50.000 9.59 0.00 43.69 4.83
5444 5683 0.249155 TTTTCGCGAGAGTCACGGTT 60.249 50.000 9.59 0.00 43.69 4.44
5445 5684 0.249155 TTTCGCGAGAGTCACGGTTT 60.249 50.000 9.59 0.00 43.69 3.27
5446 5685 0.249155 TTCGCGAGAGTCACGGTTTT 60.249 50.000 9.59 0.00 43.69 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 8.634335 TCATGATAAACAGAGAAACAAATGGA 57.366 30.769 0.00 0.00 0.00 3.41
103 104 3.064931 GTCGAAGTGGTCCGAAATTCTT 58.935 45.455 0.00 0.00 36.50 2.52
306 470 8.147244 AGGAAACTGAGGCTATTAGTAAGAAA 57.853 34.615 0.00 0.00 41.13 2.52
549 713 3.914426 ATCTGAGGGTTGTGGTCATAC 57.086 47.619 0.00 0.00 0.00 2.39
565 729 7.850935 TTTGGTAGGGAGGTAGTAATATCTG 57.149 40.000 0.00 0.00 0.00 2.90
688 852 5.645056 TTCATGGTTTATGGCTCCTATCA 57.355 39.130 0.00 0.00 37.39 2.15
781 945 5.815740 GGTATACCATGTACACTCCAAGTTG 59.184 44.000 17.44 0.00 35.64 3.16
805 969 0.250038 ACGCTATGTGCTATGGCCTG 60.250 55.000 3.32 0.00 40.11 4.85
905 1069 3.340814 ACCGATGCTCAGAATTGTCTT 57.659 42.857 0.00 0.00 28.78 3.01
917 1081 1.265905 GGAAACGAAACAACCGATGCT 59.734 47.619 0.00 0.00 0.00 3.79
924 1088 6.721321 TCAAACTGATAGGAAACGAAACAAC 58.279 36.000 0.00 0.00 0.00 3.32
977 1141 2.349155 CCGTTCCTGCAAAAGTTCGTAC 60.349 50.000 0.00 0.00 0.00 3.67
1051 1215 4.641396 TCTGAATTCAAACTCCATGACGT 58.359 39.130 9.88 0.00 0.00 4.34
1080 1244 1.743252 GGACAGAGCAAGAAGGGCG 60.743 63.158 0.00 0.00 36.08 6.13
1363 1527 6.434340 GGTATTTCACCAGAAAGGAAGTTCAT 59.566 38.462 5.01 0.00 46.13 2.57
1364 1528 5.768164 GGTATTTCACCAGAAAGGAAGTTCA 59.232 40.000 5.01 0.00 46.13 3.18
1423 1587 4.147321 AGGGAGTTAGTGTACAACGAGAA 58.853 43.478 0.00 0.00 0.00 2.87
1508 1672 6.271159 AGGGATAGAACCACTGAGATTATTCC 59.729 42.308 0.00 0.00 0.00 3.01
1515 1679 4.061131 TGAAGGGATAGAACCACTGAGA 57.939 45.455 0.00 0.00 0.00 3.27
1579 1743 5.374921 CAGACCTCCAGATAATGCATTCTT 58.625 41.667 16.86 4.72 0.00 2.52
1677 1841 5.833131 TCCTTTGACATAGCTCAAGGTTTTT 59.167 36.000 0.00 0.00 31.76 1.94
1800 1964 2.969262 TGATGGAATACCGCCACTCATA 59.031 45.455 0.00 0.00 38.44 2.15
1819 1983 1.565759 AGTGCAATTCCCTAGCCATGA 59.434 47.619 0.00 0.00 0.00 3.07
1838 2002 2.874701 AGTGCAAGTTGTGTCAAGCTAG 59.125 45.455 4.48 0.00 0.00 3.42
1864 2028 1.098712 TGGCCAGTGAAACGGTTGTC 61.099 55.000 0.00 0.00 45.86 3.18
1981 2145 0.835971 TCTAGCCACTCCAGCAACCA 60.836 55.000 0.00 0.00 0.00 3.67
2375 2539 5.501263 TGGATGGGATGCTACCATTCAGAT 61.501 45.833 10.58 0.00 46.56 2.90
2409 2573 0.395862 TTCGTTCCAAACCTGGGCAA 60.396 50.000 0.00 0.00 43.71 4.52
2614 2778 7.489160 ACTTCCAAATTCACCAAGTTTCTAAC 58.511 34.615 0.00 0.00 0.00 2.34
2617 2781 6.381133 AGAACTTCCAAATTCACCAAGTTTCT 59.619 34.615 0.00 0.00 37.41 2.52
2682 2846 3.807209 GCTTGGAGCAACTAGAAACCTGA 60.807 47.826 0.00 0.00 41.89 3.86
2727 2891 0.824109 CCGGACCATGCAGAGAGTTA 59.176 55.000 0.00 0.00 0.00 2.24
2743 2907 0.732880 CTTACTGTCGTGAGTGCCGG 60.733 60.000 0.00 0.00 0.00 6.13
2889 3053 3.260128 ACTTTCCTAACGACGAAGGGATT 59.740 43.478 17.09 0.00 33.40 3.01
2931 3098 0.445436 GTCCGTTGCTGCTGAGATTG 59.555 55.000 0.00 0.00 0.00 2.67
3032 3199 1.006805 CTCCCTAATGCGCCGAGAG 60.007 63.158 4.18 0.00 0.00 3.20
3048 3215 2.030946 GGCGTGCAATGAATGTAGACTC 59.969 50.000 0.00 0.00 0.00 3.36
3471 3638 1.453155 CCTTGTACACAGTCCCATGC 58.547 55.000 0.00 0.00 0.00 4.06
3552 3719 5.668471 TCTCTGATCATGCTTTTGTAGGAG 58.332 41.667 0.00 0.00 0.00 3.69
3585 3752 2.218603 CTGTGCCGAACTTTACCAAGT 58.781 47.619 0.00 0.00 45.89 3.16
3669 3836 0.763652 AGAGGCTACCATGCTCCATG 59.236 55.000 0.00 0.00 41.10 3.66
3867 4037 3.565482 TGATCTTTGCTATGCCGAAATCC 59.435 43.478 0.00 0.00 0.00 3.01
3936 4106 2.373169 ACCTGGTGCCATATATCCAGTG 59.627 50.000 14.13 9.63 43.96 3.66
4125 4299 1.826720 ACCGCCGTCTTTCCTGTTATA 59.173 47.619 0.00 0.00 0.00 0.98
4131 4305 2.240162 GATCCACCGCCGTCTTTCCT 62.240 60.000 0.00 0.00 0.00 3.36
4155 4329 1.285280 TGTCCATGTTCTCCGGGAAT 58.715 50.000 0.00 0.00 36.24 3.01
4297 4471 1.074775 CTGTGCACCTAAGGGCCAA 59.925 57.895 15.69 0.00 35.63 4.52
4314 4488 2.276116 TTGACTCGGCTCCTTCGCT 61.276 57.895 0.00 0.00 0.00 4.93
4350 4524 0.730834 CAGTCAGCTCCTTCACGACG 60.731 60.000 0.00 0.00 0.00 5.12
4488 4662 3.247411 TGCGTTTCACACAGTTCACTATG 59.753 43.478 0.00 0.00 0.00 2.23
4494 4672 3.242739 ACATTCTGCGTTTCACACAGTTC 60.243 43.478 0.00 0.00 30.74 3.01
4495 4673 2.682856 ACATTCTGCGTTTCACACAGTT 59.317 40.909 0.00 0.00 30.74 3.16
4497 4675 3.247411 TGTACATTCTGCGTTTCACACAG 59.753 43.478 0.00 0.00 29.93 3.66
4509 4687 6.038985 ACGATGAATCTGACTGTACATTCTG 58.961 40.000 13.66 12.89 0.00 3.02
4581 4764 4.458989 GCATCCAGTTAGAAATCACCACAA 59.541 41.667 0.00 0.00 0.00 3.33
5118 5357 0.304705 GCAACGAACGGGCATATCTG 59.695 55.000 0.00 0.00 0.00 2.90
5119 5358 0.107897 TGCAACGAACGGGCATATCT 60.108 50.000 10.58 0.00 31.58 1.98
5120 5359 0.730265 TTGCAACGAACGGGCATATC 59.270 50.000 14.09 0.00 37.39 1.63
5121 5360 0.450184 GTTGCAACGAACGGGCATAT 59.550 50.000 14.90 0.00 37.39 1.78
5122 5361 1.870383 GTTGCAACGAACGGGCATA 59.130 52.632 14.90 5.70 37.39 3.14
5123 5362 2.642700 GTTGCAACGAACGGGCAT 59.357 55.556 14.90 0.00 37.39 4.40
5133 5372 3.004315 TCAATTTTCTCTCCCGTTGCAAC 59.996 43.478 19.89 19.89 0.00 4.17
5134 5373 3.004315 GTCAATTTTCTCTCCCGTTGCAA 59.996 43.478 0.00 0.00 0.00 4.08
5135 5374 2.552315 GTCAATTTTCTCTCCCGTTGCA 59.448 45.455 0.00 0.00 0.00 4.08
5136 5375 2.412847 CGTCAATTTTCTCTCCCGTTGC 60.413 50.000 0.00 0.00 0.00 4.17
5137 5376 2.412847 GCGTCAATTTTCTCTCCCGTTG 60.413 50.000 0.00 0.00 0.00 4.10
5138 5377 1.804748 GCGTCAATTTTCTCTCCCGTT 59.195 47.619 0.00 0.00 0.00 4.44
5139 5378 1.439679 GCGTCAATTTTCTCTCCCGT 58.560 50.000 0.00 0.00 0.00 5.28
5140 5379 0.370273 CGCGTCAATTTTCTCTCCCG 59.630 55.000 0.00 0.00 0.00 5.14
5141 5380 1.393883 GACGCGTCAATTTTCTCTCCC 59.606 52.381 33.09 1.28 0.00 4.30
5142 5381 2.092838 CAGACGCGTCAATTTTCTCTCC 59.907 50.000 37.85 9.82 0.00 3.71
5143 5382 2.473049 GCAGACGCGTCAATTTTCTCTC 60.473 50.000 37.85 10.03 0.00 3.20
5144 5383 1.461127 GCAGACGCGTCAATTTTCTCT 59.539 47.619 37.85 13.87 0.00 3.10
5145 5384 1.461127 AGCAGACGCGTCAATTTTCTC 59.539 47.619 37.85 17.62 45.49 2.87
5146 5385 1.461127 GAGCAGACGCGTCAATTTTCT 59.539 47.619 37.85 23.61 45.49 2.52
5147 5386 1.461127 AGAGCAGACGCGTCAATTTTC 59.539 47.619 37.85 25.54 45.49 2.29
5148 5387 1.512926 AGAGCAGACGCGTCAATTTT 58.487 45.000 37.85 19.68 45.49 1.82
5149 5388 1.512926 AAGAGCAGACGCGTCAATTT 58.487 45.000 37.85 21.42 45.49 1.82
5150 5389 1.461127 GAAAGAGCAGACGCGTCAATT 59.539 47.619 37.85 23.18 45.49 2.32
5151 5390 1.071605 GAAAGAGCAGACGCGTCAAT 58.928 50.000 37.85 24.03 45.49 2.57
5152 5391 0.249280 TGAAAGAGCAGACGCGTCAA 60.249 50.000 37.85 11.04 45.49 3.18
5153 5392 0.249280 TTGAAAGAGCAGACGCGTCA 60.249 50.000 37.85 14.52 45.49 4.35
5154 5393 0.161870 GTTGAAAGAGCAGACGCGTC 59.838 55.000 31.30 31.30 45.49 5.19
5155 5394 1.222115 GGTTGAAAGAGCAGACGCGT 61.222 55.000 13.85 13.85 45.49 6.01
5156 5395 1.221466 TGGTTGAAAGAGCAGACGCG 61.221 55.000 3.53 3.53 45.49 6.01
5157 5396 0.944386 TTGGTTGAAAGAGCAGACGC 59.056 50.000 0.00 0.00 38.99 5.19
5158 5397 3.691049 TTTTGGTTGAAAGAGCAGACG 57.309 42.857 0.00 0.00 0.00 4.18
5159 5398 7.425606 TCTTATTTTTGGTTGAAAGAGCAGAC 58.574 34.615 0.00 0.00 0.00 3.51
5160 5399 7.581213 TCTTATTTTTGGTTGAAAGAGCAGA 57.419 32.000 0.00 0.00 0.00 4.26
5161 5400 8.706035 CATTCTTATTTTTGGTTGAAAGAGCAG 58.294 33.333 0.00 0.00 0.00 4.24
5162 5401 7.656948 CCATTCTTATTTTTGGTTGAAAGAGCA 59.343 33.333 0.00 0.00 0.00 4.26
5163 5402 7.118245 CCCATTCTTATTTTTGGTTGAAAGAGC 59.882 37.037 0.00 0.00 0.00 4.09
5164 5403 7.603784 CCCCATTCTTATTTTTGGTTGAAAGAG 59.396 37.037 0.00 0.00 0.00 2.85
5165 5404 7.071824 ACCCCATTCTTATTTTTGGTTGAAAGA 59.928 33.333 0.00 0.00 0.00 2.52
5166 5405 7.223584 ACCCCATTCTTATTTTTGGTTGAAAG 58.776 34.615 0.00 0.00 0.00 2.62
5167 5406 7.142995 ACCCCATTCTTATTTTTGGTTGAAA 57.857 32.000 0.00 0.00 0.00 2.69
5168 5407 6.327626 TGACCCCATTCTTATTTTTGGTTGAA 59.672 34.615 0.00 0.00 0.00 2.69
5169 5408 5.841237 TGACCCCATTCTTATTTTTGGTTGA 59.159 36.000 0.00 0.00 0.00 3.18
5170 5409 6.107901 TGACCCCATTCTTATTTTTGGTTG 57.892 37.500 0.00 0.00 0.00 3.77
5171 5410 6.950860 ATGACCCCATTCTTATTTTTGGTT 57.049 33.333 0.00 0.00 0.00 3.67
5172 5411 7.418378 TCTATGACCCCATTCTTATTTTTGGT 58.582 34.615 0.00 0.00 34.31 3.67
5173 5412 7.779798 TCTCTATGACCCCATTCTTATTTTTGG 59.220 37.037 0.00 0.00 34.31 3.28
5174 5413 8.752005 TCTCTATGACCCCATTCTTATTTTTG 57.248 34.615 0.00 0.00 34.31 2.44
5175 5414 8.781951 TCTCTCTATGACCCCATTCTTATTTTT 58.218 33.333 0.00 0.00 34.31 1.94
5176 5415 8.337118 TCTCTCTATGACCCCATTCTTATTTT 57.663 34.615 0.00 0.00 34.31 1.82
5177 5416 7.474079 GCTCTCTCTATGACCCCATTCTTATTT 60.474 40.741 0.00 0.00 34.31 1.40
5178 5417 6.013812 GCTCTCTCTATGACCCCATTCTTATT 60.014 42.308 0.00 0.00 34.31 1.40
5179 5418 5.483583 GCTCTCTCTATGACCCCATTCTTAT 59.516 44.000 0.00 0.00 34.31 1.73
5180 5419 4.835615 GCTCTCTCTATGACCCCATTCTTA 59.164 45.833 0.00 0.00 34.31 2.10
5181 5420 3.645687 GCTCTCTCTATGACCCCATTCTT 59.354 47.826 0.00 0.00 34.31 2.52
5182 5421 3.238597 GCTCTCTCTATGACCCCATTCT 58.761 50.000 0.00 0.00 34.31 2.40
5183 5422 2.029470 CGCTCTCTCTATGACCCCATTC 60.029 54.545 0.00 0.00 34.31 2.67
5184 5423 1.967066 CGCTCTCTCTATGACCCCATT 59.033 52.381 0.00 0.00 34.31 3.16
5185 5424 1.626686 CGCTCTCTCTATGACCCCAT 58.373 55.000 0.00 0.00 36.81 4.00
5186 5425 1.109920 GCGCTCTCTCTATGACCCCA 61.110 60.000 0.00 0.00 0.00 4.96
5187 5426 1.109920 TGCGCTCTCTCTATGACCCC 61.110 60.000 9.73 0.00 0.00 4.95
5188 5427 0.965439 ATGCGCTCTCTCTATGACCC 59.035 55.000 9.73 0.00 0.00 4.46
5189 5428 3.441922 TCATATGCGCTCTCTCTATGACC 59.558 47.826 9.73 0.00 0.00 4.02
5190 5429 4.693538 TCATATGCGCTCTCTCTATGAC 57.306 45.455 9.73 0.00 0.00 3.06
5191 5430 5.712152 TTTCATATGCGCTCTCTCTATGA 57.288 39.130 9.73 8.76 0.00 2.15
5192 5431 6.098017 TGATTTCATATGCGCTCTCTCTATG 58.902 40.000 9.73 6.64 0.00 2.23
5193 5432 6.278172 TGATTTCATATGCGCTCTCTCTAT 57.722 37.500 9.73 0.00 0.00 1.98
5194 5433 5.712152 TGATTTCATATGCGCTCTCTCTA 57.288 39.130 9.73 0.00 0.00 2.43
5195 5434 4.597404 TGATTTCATATGCGCTCTCTCT 57.403 40.909 9.73 0.00 0.00 3.10
5196 5435 4.435784 GCATGATTTCATATGCGCTCTCTC 60.436 45.833 9.73 0.00 40.09 3.20
5197 5436 3.436015 GCATGATTTCATATGCGCTCTCT 59.564 43.478 9.73 0.00 40.09 3.10
5198 5437 3.744987 GCATGATTTCATATGCGCTCTC 58.255 45.455 9.73 0.00 40.09 3.20
5199 5438 3.826236 GCATGATTTCATATGCGCTCT 57.174 42.857 9.73 0.00 40.09 4.09
5208 5447 8.088365 CCATGATACTTGATTGCATGATTTCAT 58.912 33.333 0.00 0.00 38.82 2.57
5209 5448 7.430441 CCATGATACTTGATTGCATGATTTCA 58.570 34.615 0.00 0.00 38.82 2.69
5210 5449 6.866770 CCCATGATACTTGATTGCATGATTTC 59.133 38.462 0.00 0.00 38.82 2.17
5211 5450 6.325545 ACCCATGATACTTGATTGCATGATTT 59.674 34.615 0.00 0.00 38.82 2.17
5212 5451 5.836898 ACCCATGATACTTGATTGCATGATT 59.163 36.000 0.00 0.00 38.82 2.57
5213 5452 5.243060 CACCCATGATACTTGATTGCATGAT 59.757 40.000 0.00 0.00 38.82 2.45
5214 5453 4.581409 CACCCATGATACTTGATTGCATGA 59.419 41.667 0.00 0.00 38.82 3.07
5215 5454 4.340097 ACACCCATGATACTTGATTGCATG 59.660 41.667 0.00 0.00 36.87 4.06
5216 5455 4.340097 CACACCCATGATACTTGATTGCAT 59.660 41.667 0.00 0.00 0.00 3.96
5217 5456 3.695556 CACACCCATGATACTTGATTGCA 59.304 43.478 0.00 0.00 0.00 4.08
5218 5457 3.696051 ACACACCCATGATACTTGATTGC 59.304 43.478 0.00 0.00 0.00 3.56
5219 5458 6.016860 CCATACACACCCATGATACTTGATTG 60.017 42.308 0.00 0.00 0.00 2.67
5220 5459 6.064060 CCATACACACCCATGATACTTGATT 58.936 40.000 0.00 0.00 0.00 2.57
5221 5460 5.624159 CCATACACACCCATGATACTTGAT 58.376 41.667 0.00 0.00 0.00 2.57
5222 5461 4.685848 GCCATACACACCCATGATACTTGA 60.686 45.833 0.00 0.00 0.00 3.02
5223 5462 3.565482 GCCATACACACCCATGATACTTG 59.435 47.826 0.00 0.00 0.00 3.16
5224 5463 3.459598 AGCCATACACACCCATGATACTT 59.540 43.478 0.00 0.00 0.00 2.24
5225 5464 3.048600 AGCCATACACACCCATGATACT 58.951 45.455 0.00 0.00 0.00 2.12
5226 5465 3.181455 TGAGCCATACACACCCATGATAC 60.181 47.826 0.00 0.00 0.00 2.24
5227 5466 3.044894 TGAGCCATACACACCCATGATA 58.955 45.455 0.00 0.00 0.00 2.15
5228 5467 1.845791 TGAGCCATACACACCCATGAT 59.154 47.619 0.00 0.00 0.00 2.45
5229 5468 1.284313 TGAGCCATACACACCCATGA 58.716 50.000 0.00 0.00 0.00 3.07
5230 5469 2.019249 CTTGAGCCATACACACCCATG 58.981 52.381 0.00 0.00 0.00 3.66
5231 5470 1.064463 CCTTGAGCCATACACACCCAT 60.064 52.381 0.00 0.00 0.00 4.00
5232 5471 0.327924 CCTTGAGCCATACACACCCA 59.672 55.000 0.00 0.00 0.00 4.51
5233 5472 1.032114 GCCTTGAGCCATACACACCC 61.032 60.000 0.00 0.00 34.35 4.61
5234 5473 0.322456 TGCCTTGAGCCATACACACC 60.322 55.000 0.00 0.00 42.71 4.16
5235 5474 1.470098 CTTGCCTTGAGCCATACACAC 59.530 52.381 0.00 0.00 42.71 3.82
5236 5475 1.073763 ACTTGCCTTGAGCCATACACA 59.926 47.619 0.00 0.00 42.71 3.72
5237 5476 1.826385 ACTTGCCTTGAGCCATACAC 58.174 50.000 0.00 0.00 42.71 2.90
5238 5477 3.712016 TTACTTGCCTTGAGCCATACA 57.288 42.857 0.00 0.00 42.71 2.29
5239 5478 3.756434 TGTTTACTTGCCTTGAGCCATAC 59.244 43.478 0.00 0.00 42.71 2.39
5240 5479 3.756434 GTGTTTACTTGCCTTGAGCCATA 59.244 43.478 0.00 0.00 42.71 2.74
5241 5480 2.558359 GTGTTTACTTGCCTTGAGCCAT 59.442 45.455 0.00 0.00 42.71 4.40
5242 5481 1.953686 GTGTTTACTTGCCTTGAGCCA 59.046 47.619 0.00 0.00 42.71 4.75
5243 5482 1.269723 GGTGTTTACTTGCCTTGAGCC 59.730 52.381 0.00 0.00 42.71 4.70
5244 5483 1.953686 TGGTGTTTACTTGCCTTGAGC 59.046 47.619 0.00 0.00 44.14 4.26
5245 5484 2.032030 CGTGGTGTTTACTTGCCTTGAG 60.032 50.000 0.00 0.00 0.00 3.02
5246 5485 1.944024 CGTGGTGTTTACTTGCCTTGA 59.056 47.619 0.00 0.00 0.00 3.02
5247 5486 1.001815 CCGTGGTGTTTACTTGCCTTG 60.002 52.381 0.00 0.00 0.00 3.61
5248 5487 1.314730 CCGTGGTGTTTACTTGCCTT 58.685 50.000 0.00 0.00 0.00 4.35
5249 5488 0.181824 ACCGTGGTGTTTACTTGCCT 59.818 50.000 0.00 0.00 0.00 4.75
5250 5489 1.802365 CTACCGTGGTGTTTACTTGCC 59.198 52.381 0.72 0.00 0.00 4.52
5251 5490 2.735134 CTCTACCGTGGTGTTTACTTGC 59.265 50.000 0.72 0.00 0.00 4.01
5252 5491 3.985925 GTCTCTACCGTGGTGTTTACTTG 59.014 47.826 0.72 0.00 0.00 3.16
5253 5492 3.638160 TGTCTCTACCGTGGTGTTTACTT 59.362 43.478 0.72 0.00 0.00 2.24
5254 5493 3.225104 TGTCTCTACCGTGGTGTTTACT 58.775 45.455 0.72 0.00 0.00 2.24
5255 5494 3.648339 TGTCTCTACCGTGGTGTTTAC 57.352 47.619 0.72 0.00 0.00 2.01
5256 5495 3.827876 TCATGTCTCTACCGTGGTGTTTA 59.172 43.478 0.72 0.00 0.00 2.01
5257 5496 2.631062 TCATGTCTCTACCGTGGTGTTT 59.369 45.455 0.72 0.00 0.00 2.83
5258 5497 2.244695 TCATGTCTCTACCGTGGTGTT 58.755 47.619 0.72 0.00 0.00 3.32
5259 5498 1.919240 TCATGTCTCTACCGTGGTGT 58.081 50.000 0.72 0.00 0.00 4.16
5260 5499 3.526931 AATCATGTCTCTACCGTGGTG 57.473 47.619 0.72 0.00 0.00 4.17
5261 5500 4.553330 AAAATCATGTCTCTACCGTGGT 57.447 40.909 0.00 0.00 0.00 4.16
5262 5501 5.178797 AGAAAAATCATGTCTCTACCGTGG 58.821 41.667 0.00 0.00 0.00 4.94
5263 5502 6.727824 AAGAAAAATCATGTCTCTACCGTG 57.272 37.500 0.00 0.00 0.00 4.94
5264 5503 7.584987 CAAAAGAAAAATCATGTCTCTACCGT 58.415 34.615 0.00 0.00 0.00 4.83
5265 5504 6.524586 GCAAAAGAAAAATCATGTCTCTACCG 59.475 38.462 0.00 0.00 0.00 4.02
5266 5505 6.524586 CGCAAAAGAAAAATCATGTCTCTACC 59.475 38.462 0.00 0.00 0.00 3.18
5267 5506 7.298122 TCGCAAAAGAAAAATCATGTCTCTAC 58.702 34.615 0.00 0.00 0.00 2.59
5268 5507 7.387673 TCTCGCAAAAGAAAAATCATGTCTCTA 59.612 33.333 0.00 0.00 0.00 2.43
5269 5508 6.205464 TCTCGCAAAAGAAAAATCATGTCTCT 59.795 34.615 0.00 0.00 0.00 3.10
5270 5509 6.373779 TCTCGCAAAAGAAAAATCATGTCTC 58.626 36.000 0.00 0.00 0.00 3.36
5271 5510 6.317789 TCTCGCAAAAGAAAAATCATGTCT 57.682 33.333 0.00 0.00 0.00 3.41
5272 5511 5.570589 CCTCTCGCAAAAGAAAAATCATGTC 59.429 40.000 0.00 0.00 0.00 3.06
5273 5512 5.241506 TCCTCTCGCAAAAGAAAAATCATGT 59.758 36.000 0.00 0.00 0.00 3.21
5274 5513 5.702865 TCCTCTCGCAAAAGAAAAATCATG 58.297 37.500 0.00 0.00 0.00 3.07
5275 5514 5.964958 TCCTCTCGCAAAAGAAAAATCAT 57.035 34.783 0.00 0.00 0.00 2.45
5276 5515 5.519722 GTTCCTCTCGCAAAAGAAAAATCA 58.480 37.500 0.00 0.00 0.00 2.57
5277 5516 4.613031 CGTTCCTCTCGCAAAAGAAAAATC 59.387 41.667 0.00 0.00 0.00 2.17
5278 5517 4.274950 TCGTTCCTCTCGCAAAAGAAAAAT 59.725 37.500 0.00 0.00 0.00 1.82
5279 5518 3.623960 TCGTTCCTCTCGCAAAAGAAAAA 59.376 39.130 0.00 0.00 0.00 1.94
5280 5519 3.199677 TCGTTCCTCTCGCAAAAGAAAA 58.800 40.909 0.00 0.00 0.00 2.29
5281 5520 2.828877 TCGTTCCTCTCGCAAAAGAAA 58.171 42.857 0.00 0.00 0.00 2.52
5282 5521 2.519377 TCGTTCCTCTCGCAAAAGAA 57.481 45.000 0.00 0.00 0.00 2.52
5283 5522 2.743636 ATCGTTCCTCTCGCAAAAGA 57.256 45.000 0.00 0.00 0.00 2.52
5284 5523 3.813529 AAATCGTTCCTCTCGCAAAAG 57.186 42.857 0.00 0.00 0.00 2.27
5285 5524 3.851838 GCAAAATCGTTCCTCTCGCAAAA 60.852 43.478 0.00 0.00 0.00 2.44
5286 5525 2.350388 GCAAAATCGTTCCTCTCGCAAA 60.350 45.455 0.00 0.00 0.00 3.68
5287 5526 1.196808 GCAAAATCGTTCCTCTCGCAA 59.803 47.619 0.00 0.00 0.00 4.85
5288 5527 0.796312 GCAAAATCGTTCCTCTCGCA 59.204 50.000 0.00 0.00 0.00 5.10
5289 5528 1.079503 AGCAAAATCGTTCCTCTCGC 58.920 50.000 0.00 0.00 0.00 5.03
5290 5529 2.094417 GGAAGCAAAATCGTTCCTCTCG 59.906 50.000 0.00 0.00 37.38 4.04
5291 5530 2.094417 CGGAAGCAAAATCGTTCCTCTC 59.906 50.000 0.00 0.00 38.09 3.20
5292 5531 2.076863 CGGAAGCAAAATCGTTCCTCT 58.923 47.619 0.00 0.00 38.09 3.69
5293 5532 2.527442 CGGAAGCAAAATCGTTCCTC 57.473 50.000 0.00 0.00 38.09 3.71
5312 5551 3.876589 TTGGTTCCGTGCCTCTCGC 62.877 63.158 0.00 0.00 38.31 5.03
5313 5552 0.882927 TTTTGGTTCCGTGCCTCTCG 60.883 55.000 0.00 0.00 0.00 4.04
5314 5553 1.314730 TTTTTGGTTCCGTGCCTCTC 58.685 50.000 0.00 0.00 0.00 3.20
5315 5554 3.505835 TTTTTGGTTCCGTGCCTCT 57.494 47.368 0.00 0.00 0.00 3.69
5334 5573 5.469479 CATGCCACTTACGGAAGAATTTTT 58.531 37.500 16.06 0.00 36.45 1.94
5335 5574 4.082245 CCATGCCACTTACGGAAGAATTTT 60.082 41.667 16.06 0.00 36.45 1.82
5336 5575 3.443681 CCATGCCACTTACGGAAGAATTT 59.556 43.478 16.06 0.00 36.45 1.82
5337 5576 3.016736 CCATGCCACTTACGGAAGAATT 58.983 45.455 16.06 0.00 36.45 2.17
5338 5577 2.026262 ACCATGCCACTTACGGAAGAAT 60.026 45.455 16.06 0.00 36.45 2.40
5339 5578 1.349688 ACCATGCCACTTACGGAAGAA 59.650 47.619 16.06 0.00 36.45 2.52
5340 5579 0.981183 ACCATGCCACTTACGGAAGA 59.019 50.000 16.06 0.00 36.45 2.87
5341 5580 1.821216 AACCATGCCACTTACGGAAG 58.179 50.000 5.64 5.64 38.76 3.46
5342 5581 2.279935 AAACCATGCCACTTACGGAA 57.720 45.000 0.00 0.00 0.00 4.30
5343 5582 1.883275 CAAAACCATGCCACTTACGGA 59.117 47.619 0.00 0.00 0.00 4.69
5344 5583 1.668628 GCAAAACCATGCCACTTACGG 60.669 52.381 0.00 0.00 40.49 4.02
5345 5584 1.696988 GCAAAACCATGCCACTTACG 58.303 50.000 0.00 0.00 40.49 3.18
5353 5592 0.039256 TCGCAGAAGCAAAACCATGC 60.039 50.000 0.00 0.00 46.78 4.06
5354 5593 1.536766 TCTCGCAGAAGCAAAACCATG 59.463 47.619 0.00 0.00 42.27 3.66
5355 5594 1.808945 CTCTCGCAGAAGCAAAACCAT 59.191 47.619 0.00 0.00 42.27 3.55
5356 5595 1.229428 CTCTCGCAGAAGCAAAACCA 58.771 50.000 0.00 0.00 42.27 3.67
5357 5596 0.519077 CCTCTCGCAGAAGCAAAACC 59.481 55.000 0.00 0.00 42.27 3.27
5358 5597 0.110010 GCCTCTCGCAGAAGCAAAAC 60.110 55.000 2.95 0.00 42.27 2.43
5359 5598 0.534877 TGCCTCTCGCAGAAGCAAAA 60.535 50.000 6.89 0.00 44.64 2.44
5360 5599 1.071299 TGCCTCTCGCAGAAGCAAA 59.929 52.632 6.89 0.00 44.64 3.68
5361 5600 2.743060 TGCCTCTCGCAGAAGCAA 59.257 55.556 6.89 0.00 44.64 3.91
5381 5620 2.861006 GTTTTCGAGAGGCACGGC 59.139 61.111 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.