Multiple sequence alignment - TraesCS4A01G378400

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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 TraesCS4A01G378400 chr4A 100.000 5288 0 0 1 5288 655628287 655623000 0.000000e+00 9766.0
1 TraesCS4A01G378400 chr4A 79.762 168 25 3 197 363 724319845 724320004 4.330000e-21 113.0
2 TraesCS4A01G378400 chr4A 79.762 168 25 3 197 363 724330961 724331120 4.330000e-21 113.0
3 TraesCS4A01G378400 chr4A 94.444 36 2 0 4446 4481 655623728 655623693 7.400000e-04 56.5
4 TraesCS4A01G378400 chr4A 94.444 36 2 0 4560 4595 655623842 655623807 7.400000e-04 56.5
5 TraesCS4A01G378400 chr7D 92.901 4691 193 66 555 5198 44526324 44521727 0.000000e+00 6689.0
6 TraesCS4A01G378400 chr7D 85.692 1929 225 28 1709 3628 567659145 567657259 0.000000e+00 1986.0
7 TraesCS4A01G378400 chr7D 84.370 659 57 32 966 1614 567659827 567659205 5.860000e-169 604.0
8 TraesCS4A01G378400 chr7D 84.840 376 50 3 3950 4318 567657077 567656702 6.470000e-99 372.0
9 TraesCS4A01G378400 chr7D 97.222 36 1 0 4446 4481 44522336 44522301 1.590000e-05 62.1
10 TraesCS4A01G378400 chr7D 97.222 36 1 0 4560 4595 44522454 44522419 1.590000e-05 62.1
11 TraesCS4A01G378400 chr7A 95.497 3509 132 14 1697 5197 46969119 46965629 0.000000e+00 5581.0
12 TraesCS4A01G378400 chr7A 86.809 1880 209 27 1755 3628 654206384 654204538 0.000000e+00 2061.0
13 TraesCS4A01G378400 chr7A 87.303 1142 78 40 555 1681 46970356 46969267 0.000000e+00 1243.0
14 TraesCS4A01G378400 chr7A 83.689 656 68 30 966 1614 654207155 654206532 2.740000e-162 582.0
15 TraesCS4A01G378400 chr7A 83.550 231 36 2 134 363 46971041 46970812 1.150000e-51 215.0
16 TraesCS4A01G378400 chr7A 77.019 161 23 8 4846 5005 46965488 46965341 4.390000e-11 80.5
17 TraesCS4A01G378400 chr7A 97.222 36 1 0 4560 4595 46966374 46966339 1.590000e-05 62.1
18 TraesCS4A01G378400 chr7B 86.322 1835 216 20 1799 3628 621475005 621473201 0.000000e+00 1965.0
19 TraesCS4A01G378400 chr7B 83.155 653 70 29 966 1614 621475802 621475186 1.290000e-155 560.0
20 TraesCS4A01G378400 chr7B 84.946 372 48 5 3952 4318 621473001 621472633 2.330000e-98 370.0
21 TraesCS4A01G378400 chrUn 81.938 227 37 4 5023 5247 15528875 15529099 6.990000e-44 189.0
22 TraesCS4A01G378400 chrUn 81.938 227 37 4 5023 5247 212997445 212997669 6.990000e-44 189.0
23 TraesCS4A01G378400 chrUn 81.938 227 37 4 5023 5247 222050333 222050557 6.990000e-44 189.0
24 TraesCS4A01G378400 chrUn 81.938 227 37 4 5023 5247 224609619 224609843 6.990000e-44 189.0
25 TraesCS4A01G378400 chrUn 81.938 227 37 4 5023 5247 255474776 255475000 6.990000e-44 189.0
26 TraesCS4A01G378400 chrUn 81.938 227 37 4 5023 5247 268968563 268968339 6.990000e-44 189.0
27 TraesCS4A01G378400 chrUn 89.922 129 13 0 4214 4342 43317359 43317487 3.280000e-37 167.0
28 TraesCS4A01G378400 chr2B 81.938 227 37 4 5023 5247 8363152 8363376 6.990000e-44 189.0
29 TraesCS4A01G378400 chr3A 92.913 127 9 0 4214 4340 514598 514724 9.040000e-43 185.0
30 TraesCS4A01G378400 chr3A 94.017 117 7 0 4214 4330 80369 80485 1.510000e-40 178.0
31 TraesCS4A01G378400 chr3B 93.069 101 7 0 3 103 785200663 785200763 1.190000e-31 148.0
32 TraesCS4A01G378400 chr3B 85.437 103 4 6 1 103 633132606 633132697 4.360000e-16 97.1
33 TraesCS4A01G378400 chr3B 87.324 71 8 1 33 102 534172098 534172168 4.390000e-11 80.5
34 TraesCS4A01G378400 chr3D 92.233 103 7 1 1 103 45667776 45667877 1.530000e-30 145.0
35 TraesCS4A01G378400 chr3D 89.320 103 10 1 1 102 506006057 506006159 1.550000e-25 128.0
36 TraesCS4A01G378400 chr4B 86.239 109 9 2 1 103 105725535 105725643 4.330000e-21 113.0
37 TraesCS4A01G378400 chr4B 89.583 48 5 0 55 102 13375805 13375852 1.590000e-05 62.1
38 TraesCS4A01G378400 chr5A 87.143 70 8 1 33 102 632050544 632050476 1.580000e-10 78.7
39 TraesCS4A01G378400 chr2D 80.583 103 14 6 4 102 548672395 548672295 2.040000e-09 75.0


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 TraesCS4A01G378400 chr4A 655623000 655628287 5287 True 9766.000000 9766 100.000000 1 5288 1 chr4A.!!$R1 5287
1 TraesCS4A01G378400 chr7D 44521727 44526324 4597 True 6689.000000 6689 92.901000 555 5198 1 chr7D.!!$R1 4643
2 TraesCS4A01G378400 chr7D 567656702 567659827 3125 True 987.333333 1986 84.967333 966 4318 3 chr7D.!!$R3 3352
3 TraesCS4A01G378400 chr7A 46965341 46971041 5700 True 1436.320000 5581 88.118200 134 5197 5 chr7A.!!$R1 5063
4 TraesCS4A01G378400 chr7A 654204538 654207155 2617 True 1321.500000 2061 85.249000 966 3628 2 chr7A.!!$R2 2662
5 TraesCS4A01G378400 chr7B 621472633 621475802 3169 True 965.000000 1965 84.807667 966 4318 3 chr7B.!!$R1 3352

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
790 1128 0.178990 ACTGCAACTCCCAACTTCCC 60.179 55.000 0.00 0.00 0.0 3.97 F
1119 1464 0.033991 GCTTTCTTTCCCTCCCTCCC 60.034 60.000 0.00 0.00 0.0 4.30 F
1937 2495 0.674581 TTCCAGGCAGCATCGAAGTG 60.675 55.000 0.00 0.00 0.0 3.16 F
2076 2634 1.120530 ACTTCTCAGTTGGACACGGT 58.879 50.000 0.00 0.00 0.0 4.83 F
2077 2635 1.202533 ACTTCTCAGTTGGACACGGTG 60.203 52.381 6.58 6.58 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1917 2475 0.254178 ACTTCGATGCTGCCTGGAAT 59.746 50.000 0.00 0.0 0.0 3.01 R
2206 2764 2.124320 GCATAGCTTTCCGGGCCA 60.124 61.111 4.39 0.0 0.0 5.36 R
3885 4475 0.572590 CGAAGAGATGCGCGTAAAGG 59.427 55.000 8.43 0.0 0.0 3.11 R
4142 4743 2.367202 GCCTTCCCGTCATCCTCCA 61.367 63.158 0.00 0.0 0.0 3.86 R
4474 5079 6.753107 TCCGAATTAAAACCAAGGATTCTC 57.247 37.500 0.00 0.0 0.0 2.87 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
35 36 5.660629 CAAGCATGCAAAACATTTCTCAA 57.339 34.783 21.98 0.00 36.64 3.02
36 37 6.050454 CAAGCATGCAAAACATTTCTCAAA 57.950 33.333 21.98 0.00 36.64 2.69
37 38 5.917541 AGCATGCAAAACATTTCTCAAAG 57.082 34.783 21.98 0.00 36.64 2.77
38 39 5.362263 AGCATGCAAAACATTTCTCAAAGT 58.638 33.333 21.98 0.00 36.64 2.66
39 40 5.818857 AGCATGCAAAACATTTCTCAAAGTT 59.181 32.000 21.98 0.00 36.64 2.66
40 41 6.316890 AGCATGCAAAACATTTCTCAAAGTTT 59.683 30.769 21.98 0.00 36.64 2.66
41 42 7.495279 AGCATGCAAAACATTTCTCAAAGTTTA 59.505 29.630 21.98 0.00 36.64 2.01
42 43 8.284693 GCATGCAAAACATTTCTCAAAGTTTAT 58.715 29.630 14.21 0.00 36.64 1.40
43 44 9.801714 CATGCAAAACATTTCTCAAAGTTTATC 57.198 29.630 0.00 0.00 36.64 1.75
44 45 8.060020 TGCAAAACATTTCTCAAAGTTTATCG 57.940 30.769 0.00 0.00 33.45 2.92
45 46 7.704472 TGCAAAACATTTCTCAAAGTTTATCGT 59.296 29.630 0.00 0.00 33.45 3.73
46 47 9.176181 GCAAAACATTTCTCAAAGTTTATCGTA 57.824 29.630 0.00 0.00 33.45 3.43
110 111 8.256611 TCTGATTTTACTGTTCACAATCTAGC 57.743 34.615 0.00 0.00 0.00 3.42
111 112 8.097038 TCTGATTTTACTGTTCACAATCTAGCT 58.903 33.333 0.00 0.00 0.00 3.32
112 113 8.621532 TGATTTTACTGTTCACAATCTAGCTT 57.378 30.769 0.00 0.00 0.00 3.74
113 114 8.506437 TGATTTTACTGTTCACAATCTAGCTTG 58.494 33.333 4.78 4.78 0.00 4.01
114 115 7.801716 TTTTACTGTTCACAATCTAGCTTGT 57.198 32.000 6.14 6.14 39.91 3.16
122 123 5.868043 CACAATCTAGCTTGTGTGAATGA 57.132 39.130 24.72 0.00 46.97 2.57
123 124 5.866075 CACAATCTAGCTTGTGTGAATGAG 58.134 41.667 24.72 3.71 46.97 2.90
124 125 4.394300 ACAATCTAGCTTGTGTGAATGAGC 59.606 41.667 11.05 0.00 37.93 4.26
125 126 2.610433 TCTAGCTTGTGTGAATGAGCG 58.390 47.619 0.00 0.00 39.99 5.03
126 127 1.662629 CTAGCTTGTGTGAATGAGCGG 59.337 52.381 0.00 0.00 39.99 5.52
127 128 0.957395 AGCTTGTGTGAATGAGCGGG 60.957 55.000 0.00 0.00 39.99 6.13
128 129 1.237285 GCTTGTGTGAATGAGCGGGT 61.237 55.000 0.00 0.00 0.00 5.28
129 130 1.238439 CTTGTGTGAATGAGCGGGTT 58.762 50.000 0.00 0.00 0.00 4.11
130 131 1.608590 CTTGTGTGAATGAGCGGGTTT 59.391 47.619 0.00 0.00 0.00 3.27
131 132 0.950836 TGTGTGAATGAGCGGGTTTG 59.049 50.000 0.00 0.00 0.00 2.93
132 133 0.387239 GTGTGAATGAGCGGGTTTGC 60.387 55.000 0.00 0.00 0.00 3.68
148 149 7.920682 AGCGGGTTTGCTTGAAATTTAATATAG 59.079 33.333 0.00 0.00 44.46 1.31
194 196 6.380095 TGCTTGAAGTTTTAATGTAACCGT 57.620 33.333 0.00 0.00 0.00 4.83
196 198 7.259161 TGCTTGAAGTTTTAATGTAACCGTTT 58.741 30.769 0.00 0.00 0.00 3.60
200 202 7.194962 TGAAGTTTTAATGTAACCGTTTGGAC 58.805 34.615 0.00 0.00 39.21 4.02
202 204 7.098074 AGTTTTAATGTAACCGTTTGGACAA 57.902 32.000 0.00 0.00 39.21 3.18
207 209 8.943909 TTAATGTAACCGTTTGGACAAAAATT 57.056 26.923 0.00 0.00 39.21 1.82
210 212 5.811100 TGTAACCGTTTGGACAAAAATTTCC 59.189 36.000 0.00 0.00 39.21 3.13
211 213 3.449632 ACCGTTTGGACAAAAATTTCCG 58.550 40.909 0.00 0.00 39.21 4.30
221 223 5.278758 GGACAAAAATTTCCGTTCTCATGGA 60.279 40.000 0.00 0.00 36.15 3.41
236 238 8.119226 CGTTCTCATGGAAGAATTATCTTGTTC 58.881 37.037 0.63 0.00 45.91 3.18
239 241 7.554118 TCTCATGGAAGAATTATCTTGTTCCAC 59.446 37.037 16.05 0.00 45.91 4.02
355 357 4.882427 TGAACCGTGAAAGGTAAAATGTCA 59.118 37.500 0.00 0.00 45.21 3.58
363 365 7.573096 CGTGAAAGGTAAAATGTCATAGCTTGT 60.573 37.037 0.00 0.00 39.18 3.16
364 366 7.538678 GTGAAAGGTAAAATGTCATAGCTTGTG 59.461 37.037 0.00 0.00 39.18 3.33
365 367 7.446931 TGAAAGGTAAAATGTCATAGCTTGTGA 59.553 33.333 0.00 0.00 39.18 3.58
367 369 9.461312 AAAGGTAAAATGTCATAGCTTGTGATA 57.539 29.630 0.00 0.00 39.18 2.15
368 370 8.668510 AGGTAAAATGTCATAGCTTGTGATAG 57.331 34.615 0.00 0.00 0.00 2.08
369 371 8.486210 AGGTAAAATGTCATAGCTTGTGATAGA 58.514 33.333 0.00 0.00 0.00 1.98
370 372 9.277783 GGTAAAATGTCATAGCTTGTGATAGAT 57.722 33.333 0.00 0.00 0.00 1.98
373 375 8.969260 AAATGTCATAGCTTGTGATAGATTCA 57.031 30.769 0.00 0.00 0.00 2.57
374 376 9.570468 AAATGTCATAGCTTGTGATAGATTCAT 57.430 29.630 0.00 0.00 36.54 2.57
375 377 8.774890 ATGTCATAGCTTGTGATAGATTCATC 57.225 34.615 0.00 0.00 36.54 2.92
376 378 7.157347 TGTCATAGCTTGTGATAGATTCATCC 58.843 38.462 0.00 0.00 36.54 3.51
377 379 6.309980 GTCATAGCTTGTGATAGATTCATCCG 59.690 42.308 0.00 0.00 36.54 4.18
378 380 4.679373 AGCTTGTGATAGATTCATCCGT 57.321 40.909 0.00 0.00 36.54 4.69
380 382 6.352016 AGCTTGTGATAGATTCATCCGTAT 57.648 37.500 0.00 0.00 36.54 3.06
381 383 6.393990 AGCTTGTGATAGATTCATCCGTATC 58.606 40.000 0.00 0.00 36.54 2.24
383 385 7.394641 AGCTTGTGATAGATTCATCCGTATCTA 59.605 37.037 0.00 0.00 36.36 1.98
384 386 7.700234 GCTTGTGATAGATTCATCCGTATCTAG 59.300 40.741 0.00 0.00 35.66 2.43
387 389 7.883311 TGTGATAGATTCATCCGTATCTAGACA 59.117 37.037 0.00 0.00 35.66 3.41
388 390 8.731605 GTGATAGATTCATCCGTATCTAGACAA 58.268 37.037 0.00 0.00 35.66 3.18
389 391 9.297037 TGATAGATTCATCCGTATCTAGACAAA 57.703 33.333 0.00 0.00 35.66 2.83
390 392 9.562583 GATAGATTCATCCGTATCTAGACAAAC 57.437 37.037 0.00 0.00 35.66 2.93
391 393 7.589958 AGATTCATCCGTATCTAGACAAACT 57.410 36.000 0.00 0.00 28.31 2.66
393 395 8.478877 AGATTCATCCGTATCTAGACAAACTTT 58.521 33.333 0.00 0.00 28.31 2.66
396 398 9.932207 TTCATCCGTATCTAGACAAACTTTTTA 57.068 29.630 0.00 0.00 0.00 1.52
397 399 9.582431 TCATCCGTATCTAGACAAACTTTTTAG 57.418 33.333 0.00 0.00 0.00 1.85
398 400 8.818057 CATCCGTATCTAGACAAACTTTTTAGG 58.182 37.037 0.00 0.00 0.00 2.69
399 401 8.125978 TCCGTATCTAGACAAACTTTTTAGGA 57.874 34.615 0.00 0.00 0.00 2.94
401 403 7.008992 CCGTATCTAGACAAACTTTTTAGGACG 59.991 40.741 0.00 0.00 0.00 4.79
402 404 7.008992 CGTATCTAGACAAACTTTTTAGGACGG 59.991 40.741 0.00 0.00 0.00 4.79
403 405 6.409524 TCTAGACAAACTTTTTAGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
404 406 6.819284 TCTAGACAAACTTTTTAGGACGGAA 58.181 36.000 0.00 0.00 0.00 4.30
405 407 6.927381 TCTAGACAAACTTTTTAGGACGGAAG 59.073 38.462 0.00 0.00 0.00 3.46
406 408 4.820173 AGACAAACTTTTTAGGACGGAAGG 59.180 41.667 0.00 0.00 0.00 3.46
407 409 4.529897 ACAAACTTTTTAGGACGGAAGGT 58.470 39.130 0.00 0.00 0.00 3.50
410 412 6.774170 ACAAACTTTTTAGGACGGAAGGTAAT 59.226 34.615 0.00 0.00 0.00 1.89
412 414 8.785946 CAAACTTTTTAGGACGGAAGGTAATAA 58.214 33.333 0.00 0.00 0.00 1.40
417 419 8.667076 TTTTAGGACGGAAGGTAATAATAAGC 57.333 34.615 0.00 0.00 0.00 3.09
418 420 5.881923 AGGACGGAAGGTAATAATAAGCA 57.118 39.130 0.00 0.00 0.00 3.91
419 421 6.435292 AGGACGGAAGGTAATAATAAGCAT 57.565 37.500 0.00 0.00 0.00 3.79
421 423 7.970102 AGGACGGAAGGTAATAATAAGCATTA 58.030 34.615 0.00 0.00 33.48 1.90
422 424 8.434392 AGGACGGAAGGTAATAATAAGCATTAA 58.566 33.333 0.00 0.00 32.17 1.40
446 768 8.650143 AATATTTTGGAACTGTTATGTCTGGT 57.350 30.769 0.00 0.00 0.00 4.00
448 770 4.698201 TTGGAACTGTTATGTCTGGTGA 57.302 40.909 0.00 0.00 0.00 4.02
449 771 4.271696 TGGAACTGTTATGTCTGGTGAG 57.728 45.455 0.00 0.00 0.00 3.51
450 772 3.003480 GGAACTGTTATGTCTGGTGAGC 58.997 50.000 0.00 0.00 0.00 4.26
451 773 2.770164 ACTGTTATGTCTGGTGAGCC 57.230 50.000 0.00 0.00 0.00 4.70
452 774 1.279271 ACTGTTATGTCTGGTGAGCCC 59.721 52.381 0.00 0.00 0.00 5.19
460 782 4.908333 TGGTGAGCCCAGATGGTA 57.092 55.556 0.00 0.00 38.72 3.25
461 783 3.340064 TGGTGAGCCCAGATGGTAT 57.660 52.632 0.00 0.00 38.72 2.73
462 784 2.487746 TGGTGAGCCCAGATGGTATA 57.512 50.000 0.00 0.00 38.72 1.47
466 788 4.167892 TGGTGAGCCCAGATGGTATAAAAT 59.832 41.667 0.00 0.00 38.72 1.82
467 789 4.762251 GGTGAGCCCAGATGGTATAAAATC 59.238 45.833 0.00 0.00 36.04 2.17
518 840 9.931210 CAATCAAATATAGTACTTTTTCCGTCC 57.069 33.333 0.00 0.00 0.00 4.79
519 841 8.672823 ATCAAATATAGTACTTTTTCCGTCCC 57.327 34.615 0.00 0.00 0.00 4.46
520 842 7.622713 TCAAATATAGTACTTTTTCCGTCCCA 58.377 34.615 0.00 0.00 0.00 4.37
521 843 8.102047 TCAAATATAGTACTTTTTCCGTCCCAA 58.898 33.333 0.00 0.00 0.00 4.12
522 844 8.732531 CAAATATAGTACTTTTTCCGTCCCAAA 58.267 33.333 0.00 0.00 0.00 3.28
523 845 8.866970 AATATAGTACTTTTTCCGTCCCAAAA 57.133 30.769 0.00 0.00 0.00 2.44
524 846 9.470399 AATATAGTACTTTTTCCGTCCCAAAAT 57.530 29.630 0.00 0.00 0.00 1.82
526 848 8.866970 ATAGTACTTTTTCCGTCCCAAAATAA 57.133 30.769 0.00 0.00 0.00 1.40
527 849 7.210718 AGTACTTTTTCCGTCCCAAAATAAG 57.789 36.000 0.00 0.00 0.00 1.73
528 850 6.774170 AGTACTTTTTCCGTCCCAAAATAAGT 59.226 34.615 0.00 0.00 0.00 2.24
529 851 5.838529 ACTTTTTCCGTCCCAAAATAAGTG 58.161 37.500 0.00 0.00 0.00 3.16
530 852 5.361571 ACTTTTTCCGTCCCAAAATAAGTGT 59.638 36.000 0.00 0.00 0.00 3.55
531 853 5.441709 TTTTCCGTCCCAAAATAAGTGTC 57.558 39.130 0.00 0.00 0.00 3.67
532 854 2.690786 TCCGTCCCAAAATAAGTGTCG 58.309 47.619 0.00 0.00 0.00 4.35
533 855 2.299582 TCCGTCCCAAAATAAGTGTCGA 59.700 45.455 0.00 0.00 0.00 4.20
534 856 2.414138 CCGTCCCAAAATAAGTGTCGAC 59.586 50.000 9.11 9.11 0.00 4.20
535 857 3.061322 CGTCCCAAAATAAGTGTCGACA 58.939 45.455 15.76 15.76 0.00 4.35
536 858 3.682858 CGTCCCAAAATAAGTGTCGACAT 59.317 43.478 23.12 9.40 0.00 3.06
537 859 4.153475 CGTCCCAAAATAAGTGTCGACATT 59.847 41.667 23.12 15.55 0.00 2.71
538 860 5.334569 CGTCCCAAAATAAGTGTCGACATTT 60.335 40.000 26.46 26.46 0.00 2.32
539 861 6.443792 GTCCCAAAATAAGTGTCGACATTTT 58.556 36.000 28.03 22.37 32.29 1.82
540 862 6.921307 GTCCCAAAATAAGTGTCGACATTTTT 59.079 34.615 28.03 22.08 30.27 1.94
570 892 7.720074 TGACTGAGGGAGTAATACACAGTATAG 59.280 40.741 4.85 0.00 37.27 1.31
573 895 7.002879 TGAGGGAGTAATACACAGTATAGGTC 58.997 42.308 0.00 0.00 0.00 3.85
574 896 7.147177 TGAGGGAGTAATACACAGTATAGGTCT 60.147 40.741 0.00 0.00 0.00 3.85
664 991 6.530019 AGACTCCACAATGTTGTTCTTTTT 57.470 33.333 0.00 0.00 39.91 1.94
696 1029 8.420222 TGAGAATACCACAATGTTTGTTTCAAT 58.580 29.630 0.00 0.00 43.23 2.57
697 1030 8.592105 AGAATACCACAATGTTTGTTTCAATG 57.408 30.769 0.00 0.00 43.23 2.82
709 1042 2.817258 TGTTTCAATGATGGTTCGTCCC 59.183 45.455 0.00 0.00 34.77 4.46
710 1043 2.817258 GTTTCAATGATGGTTCGTCCCA 59.183 45.455 0.00 0.00 39.27 4.37
712 1045 0.726827 CAATGATGGTTCGTCCCACG 59.273 55.000 0.00 0.00 44.19 4.94
767 1105 2.590859 GGCCCGCCCGATTTAGTC 60.591 66.667 0.00 0.00 0.00 2.59
768 1106 2.590859 GCCCGCCCGATTTAGTCC 60.591 66.667 0.00 0.00 0.00 3.85
769 1107 2.279918 CCCGCCCGATTTAGTCCG 60.280 66.667 0.00 0.00 0.00 4.79
785 1123 2.639286 CGCACTGCAACTCCCAAC 59.361 61.111 1.11 0.00 0.00 3.77
786 1124 1.893808 CGCACTGCAACTCCCAACT 60.894 57.895 1.11 0.00 0.00 3.16
787 1125 1.447317 CGCACTGCAACTCCCAACTT 61.447 55.000 1.11 0.00 0.00 2.66
788 1126 0.312102 GCACTGCAACTCCCAACTTC 59.688 55.000 0.00 0.00 0.00 3.01
789 1127 0.954452 CACTGCAACTCCCAACTTCC 59.046 55.000 0.00 0.00 0.00 3.46
790 1128 0.178990 ACTGCAACTCCCAACTTCCC 60.179 55.000 0.00 0.00 0.00 3.97
791 1129 0.178992 CTGCAACTCCCAACTTCCCA 60.179 55.000 0.00 0.00 0.00 4.37
792 1130 0.260230 TGCAACTCCCAACTTCCCAA 59.740 50.000 0.00 0.00 0.00 4.12
810 1148 2.350134 GGTCCAAACCCTCGTCCC 59.650 66.667 0.00 0.00 39.93 4.46
816 1154 0.905357 CAAACCCTCGTCCCATCTCT 59.095 55.000 0.00 0.00 0.00 3.10
948 1287 3.917760 CCAGTCGATCTCGCCCCC 61.918 72.222 0.00 0.00 39.60 5.40
964 1303 1.701024 CCCCTCCCATTCCCCATCA 60.701 63.158 0.00 0.00 0.00 3.07
979 1320 3.293337 CCCATCAATCAATCAAGGAGCA 58.707 45.455 0.00 0.00 0.00 4.26
1096 1438 2.681064 ACTACCCGCCGTAAGCCA 60.681 61.111 0.00 0.00 38.78 4.75
1111 1453 1.588597 GCCAGCTGCTTTCTTTCCC 59.411 57.895 8.66 0.00 36.87 3.97
1116 1461 0.038890 GCTGCTTTCTTTCCCTCCCT 59.961 55.000 0.00 0.00 0.00 4.20
1119 1464 0.033991 GCTTTCTTTCCCTCCCTCCC 60.034 60.000 0.00 0.00 0.00 4.30
1120 1465 1.675007 CTTTCTTTCCCTCCCTCCCT 58.325 55.000 0.00 0.00 0.00 4.20
1400 1761 3.237741 CTCCCTCCCTCCGCATCC 61.238 72.222 0.00 0.00 0.00 3.51
1459 1829 1.133792 GTCCTGGTTATGATGGGTGGG 60.134 57.143 0.00 0.00 0.00 4.61
1461 1831 2.131854 CCTGGTTATGATGGGTGGGTA 58.868 52.381 0.00 0.00 0.00 3.69
1462 1832 2.512056 CCTGGTTATGATGGGTGGGTAA 59.488 50.000 0.00 0.00 0.00 2.85
1463 1833 3.551846 CTGGTTATGATGGGTGGGTAAC 58.448 50.000 0.00 0.00 0.00 2.50
1495 1865 1.238439 CAAACAATGCAGGTCGAGGT 58.762 50.000 0.00 0.00 0.00 3.85
1649 2032 4.317671 GAGCATCTGCAGCCAATTAATT 57.682 40.909 9.47 0.00 45.16 1.40
1658 2041 6.434028 TCTGCAGCCAATTAATTAGTTGAAGT 59.566 34.615 19.18 3.74 0.00 3.01
1695 2210 7.293073 AGACTCATGGGATATTTGCAACTTAT 58.707 34.615 0.00 0.00 0.00 1.73
1705 2220 9.331282 GGATATTTGCAACTTATCAGTAAGAGT 57.669 33.333 21.46 0.00 39.77 3.24
1720 2236 6.606395 TCAGTAAGAGTAGGGGAGTGAAATAC 59.394 42.308 0.00 0.00 0.00 1.89
1925 2483 2.167075 CAGGGATTGTGAAATTCCAGGC 59.833 50.000 0.00 0.00 29.73 4.85
1927 2485 2.167075 GGGATTGTGAAATTCCAGGCAG 59.833 50.000 0.00 0.00 30.98 4.85
1932 2490 1.097232 TGAAATTCCAGGCAGCATCG 58.903 50.000 0.00 0.00 0.00 3.84
1937 2495 0.674581 TTCCAGGCAGCATCGAAGTG 60.675 55.000 0.00 0.00 0.00 3.16
2076 2634 1.120530 ACTTCTCAGTTGGACACGGT 58.879 50.000 0.00 0.00 0.00 4.83
2077 2635 1.202533 ACTTCTCAGTTGGACACGGTG 60.203 52.381 6.58 6.58 0.00 4.94
2465 3026 7.147976 GTGACAAAATATGCTGTCTCCTTTTT 58.852 34.615 15.05 0.00 42.06 1.94
2466 3027 7.115378 GTGACAAAATATGCTGTCTCCTTTTTG 59.885 37.037 15.05 0.00 42.06 2.44
2467 3028 6.458210 ACAAAATATGCTGTCTCCTTTTTGG 58.542 36.000 9.27 0.00 37.07 3.28
2468 3029 4.725790 AATATGCTGTCTCCTTTTTGGC 57.274 40.909 0.00 0.00 35.26 4.52
2469 3030 1.999648 ATGCTGTCTCCTTTTTGGCA 58.000 45.000 0.00 0.00 35.26 4.92
2470 3031 1.999648 TGCTGTCTCCTTTTTGGCAT 58.000 45.000 0.00 0.00 35.26 4.40
2495 3056 2.273370 TGTCTTTCATACGACCTCGC 57.727 50.000 0.00 0.00 44.43 5.03
2496 3057 1.542472 TGTCTTTCATACGACCTCGCA 59.458 47.619 0.00 0.00 44.43 5.10
2502 3063 2.362736 TCATACGACCTCGCACTTAGT 58.637 47.619 0.00 0.00 44.43 2.24
2842 3403 5.310409 ACATTCTCAGAAAAGTCAGGGAA 57.690 39.130 0.00 0.00 34.57 3.97
2909 3470 2.999355 GAGTCTGCAGGTGAAGATTGTC 59.001 50.000 15.13 0.00 31.17 3.18
3374 3940 8.094798 TCTGATAAACAGTTACAATTGTGACC 57.905 34.615 25.05 11.75 45.86 4.02
3556 4126 2.017049 GGATAGCGCATGAACCACTTT 58.983 47.619 11.47 0.00 0.00 2.66
3635 4216 2.030701 GCCGTTGTTCAGTCGTTTACAA 59.969 45.455 0.00 0.00 0.00 2.41
3748 4338 3.641436 TGAGTTCAGCCTGACTTCAGTTA 59.359 43.478 0.00 0.00 42.27 2.24
3763 4353 7.098074 ACTTCAGTTAAGAGAATAGGTACGG 57.902 40.000 0.00 0.00 38.67 4.02
3772 4362 5.858381 AGAGAATAGGTACGGTGATACGTA 58.142 41.667 0.00 0.00 46.58 3.57
3885 4475 4.319177 AGATTTACTCAACTGACTGGTGC 58.681 43.478 0.00 0.00 32.28 5.01
4315 4920 1.673337 TGTGCTGCAGTGCTGGATC 60.673 57.895 21.74 14.23 30.50 3.36
4525 5133 7.224297 AGCCGTGTATTATTATGGAAGACAAT 58.776 34.615 0.00 0.00 30.39 2.71
4680 5290 1.076727 TCTCCTGGCTCCGTTCTCA 59.923 57.895 0.00 0.00 0.00 3.27
4800 5412 3.686016 ACAGTTCTGTTTTGTGACACCT 58.314 40.909 2.45 0.00 0.00 4.00
4828 5440 6.462500 ACTTATGCCATGTTATTGTTGCAAA 58.538 32.000 0.00 0.00 31.81 3.68
4834 5446 7.157347 TGCCATGTTATTGTTGCAAAGAATAA 58.843 30.769 15.89 15.89 45.96 1.40
4908 5520 9.256477 TGTCAAATGGCTTACTAACTTATATCG 57.744 33.333 0.00 0.00 0.00 2.92
4953 5567 9.970395 TGAAATATATTTATTTGAGCTTGCTGG 57.030 29.630 10.68 0.00 37.98 4.85
4954 5568 8.822652 AAATATATTTATTTGAGCTTGCTGGC 57.177 30.769 8.99 0.00 36.80 4.85
4955 5569 3.531934 ATTTATTTGAGCTTGCTGGCC 57.468 42.857 0.00 0.00 0.00 5.36
4967 5581 1.717032 TGCTGGCCCTACTATAGGTG 58.283 55.000 0.00 0.00 44.73 4.00
5079 5694 3.947834 GCATTATTGTCCTGCTACCTGTT 59.052 43.478 0.00 0.00 33.15 3.16
5123 5738 2.032799 GTGTGTCATTTTGCGAACCAGA 59.967 45.455 0.00 0.00 0.00 3.86
5166 5781 8.837099 ATCACAAATGATAATAACCTCCCAAA 57.163 30.769 0.00 0.00 44.11 3.28
5229 5987 3.812053 CAGTTCCATGCTATGCTTACTCC 59.188 47.826 0.00 0.00 0.00 3.85
5240 5998 7.561251 TGCTATGCTTACTCCACTGTTAATTA 58.439 34.615 0.00 0.00 0.00 1.40
5241 5999 8.044309 TGCTATGCTTACTCCACTGTTAATTAA 58.956 33.333 0.00 0.00 0.00 1.40
5246 6004 7.393234 TGCTTACTCCACTGTTAATTAATTGCT 59.607 33.333 11.05 0.00 0.00 3.91
5247 6005 8.244113 GCTTACTCCACTGTTAATTAATTGCTT 58.756 33.333 11.05 0.00 0.00 3.91
5269 6027 6.431234 GCTTATGGGAATATAGGGTCTTTGTG 59.569 42.308 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.660629 TTGAGAAATGTTTTGCATGCTTG 57.339 34.783 20.33 0.00 37.96 4.01
14 15 5.818857 ACTTTGAGAAATGTTTTGCATGCTT 59.181 32.000 20.33 2.06 37.96 3.91
15 16 5.362263 ACTTTGAGAAATGTTTTGCATGCT 58.638 33.333 20.33 0.00 37.96 3.79
16 17 5.662211 ACTTTGAGAAATGTTTTGCATGC 57.338 34.783 11.82 11.82 37.96 4.06
17 18 9.801714 GATAAACTTTGAGAAATGTTTTGCATG 57.198 29.630 7.49 0.00 37.96 4.06
18 19 8.702438 CGATAAACTTTGAGAAATGTTTTGCAT 58.298 29.630 7.49 0.00 40.03 3.96
19 20 7.704472 ACGATAAACTTTGAGAAATGTTTTGCA 59.296 29.630 7.49 0.00 34.88 4.08
20 21 8.061125 ACGATAAACTTTGAGAAATGTTTTGC 57.939 30.769 7.49 0.00 34.88 3.68
84 85 8.721478 GCTAGATTGTGAACAGTAAAATCAGAA 58.279 33.333 0.00 0.00 31.96 3.02
85 86 8.097038 AGCTAGATTGTGAACAGTAAAATCAGA 58.903 33.333 0.00 0.00 31.15 3.27
86 87 8.261492 AGCTAGATTGTGAACAGTAAAATCAG 57.739 34.615 0.00 0.00 31.15 2.90
87 88 8.506437 CAAGCTAGATTGTGAACAGTAAAATCA 58.494 33.333 12.62 0.00 31.15 2.57
88 89 8.507249 ACAAGCTAGATTGTGAACAGTAAAATC 58.493 33.333 24.72 0.00 41.76 2.17
89 90 8.396272 ACAAGCTAGATTGTGAACAGTAAAAT 57.604 30.769 24.72 0.00 41.76 1.82
90 91 7.801716 ACAAGCTAGATTGTGAACAGTAAAA 57.198 32.000 24.72 0.00 41.76 1.52
101 102 4.394300 GCTCATTCACACAAGCTAGATTGT 59.606 41.667 20.32 20.32 44.12 2.71
102 103 4.493708 CGCTCATTCACACAAGCTAGATTG 60.494 45.833 18.88 18.88 36.22 2.67
103 104 3.620374 CGCTCATTCACACAAGCTAGATT 59.380 43.478 0.00 0.00 32.55 2.40
104 105 3.193263 CGCTCATTCACACAAGCTAGAT 58.807 45.455 0.00 0.00 32.55 1.98
105 106 2.610433 CGCTCATTCACACAAGCTAGA 58.390 47.619 0.00 0.00 32.55 2.43
106 107 1.662629 CCGCTCATTCACACAAGCTAG 59.337 52.381 0.00 0.00 32.55 3.42
107 108 1.675714 CCCGCTCATTCACACAAGCTA 60.676 52.381 0.00 0.00 32.55 3.32
108 109 0.957395 CCCGCTCATTCACACAAGCT 60.957 55.000 0.00 0.00 32.55 3.74
109 110 1.237285 ACCCGCTCATTCACACAAGC 61.237 55.000 0.00 0.00 0.00 4.01
110 111 1.238439 AACCCGCTCATTCACACAAG 58.762 50.000 0.00 0.00 0.00 3.16
111 112 1.336440 CAAACCCGCTCATTCACACAA 59.664 47.619 0.00 0.00 0.00 3.33
112 113 0.950836 CAAACCCGCTCATTCACACA 59.049 50.000 0.00 0.00 0.00 3.72
113 114 0.387239 GCAAACCCGCTCATTCACAC 60.387 55.000 0.00 0.00 0.00 3.82
114 115 0.537143 AGCAAACCCGCTCATTCACA 60.537 50.000 0.00 0.00 37.91 3.58
115 116 0.598065 AAGCAAACCCGCTCATTCAC 59.402 50.000 0.00 0.00 42.89 3.18
116 117 0.597568 CAAGCAAACCCGCTCATTCA 59.402 50.000 0.00 0.00 42.89 2.57
117 118 0.881118 TCAAGCAAACCCGCTCATTC 59.119 50.000 0.00 0.00 42.89 2.67
118 119 1.327303 TTCAAGCAAACCCGCTCATT 58.673 45.000 0.00 0.00 42.89 2.57
119 120 1.327303 TTTCAAGCAAACCCGCTCAT 58.673 45.000 0.00 0.00 42.89 2.90
120 121 1.327303 ATTTCAAGCAAACCCGCTCA 58.673 45.000 0.00 0.00 42.89 4.26
121 122 2.438868 AATTTCAAGCAAACCCGCTC 57.561 45.000 0.00 0.00 42.89 5.03
122 123 2.908688 AAATTTCAAGCAAACCCGCT 57.091 40.000 0.00 0.00 46.67 5.52
123 124 6.902224 ATATTAAATTTCAAGCAAACCCGC 57.098 33.333 0.00 0.00 0.00 6.13
124 125 9.796120 TTCTATATTAAATTTCAAGCAAACCCG 57.204 29.630 0.00 0.00 0.00 5.28
175 177 7.148120 TGTCCAAACGGTTACATTAAAACTTCA 60.148 33.333 0.00 0.00 0.00 3.02
176 178 7.194962 TGTCCAAACGGTTACATTAAAACTTC 58.805 34.615 0.00 0.00 0.00 3.01
179 181 7.752557 TTTGTCCAAACGGTTACATTAAAAC 57.247 32.000 0.00 0.00 0.00 2.43
182 184 8.943909 AATTTTTGTCCAAACGGTTACATTAA 57.056 26.923 0.00 0.00 0.00 1.40
191 193 3.449632 ACGGAAATTTTTGTCCAAACGG 58.550 40.909 0.00 0.00 33.10 4.44
194 196 5.967088 TGAGAACGGAAATTTTTGTCCAAA 58.033 33.333 0.00 0.00 33.10 3.28
196 198 5.508825 CCATGAGAACGGAAATTTTTGTCCA 60.509 40.000 0.00 0.00 33.10 4.02
200 202 6.446318 TCTTCCATGAGAACGGAAATTTTTG 58.554 36.000 0.00 0.00 40.71 2.44
202 204 6.648879 TTCTTCCATGAGAACGGAAATTTT 57.351 33.333 0.00 0.00 40.71 1.82
207 209 6.889198 AGATAATTCTTCCATGAGAACGGAA 58.111 36.000 0.00 0.00 38.39 4.30
210 212 7.545362 ACAAGATAATTCTTCCATGAGAACG 57.455 36.000 0.00 0.00 40.28 3.95
211 213 8.401709 GGAACAAGATAATTCTTCCATGAGAAC 58.598 37.037 0.00 0.00 40.28 3.01
261 263 8.725405 TCAGAATATAACGCAAATAAAGACCA 57.275 30.769 0.00 0.00 0.00 4.02
273 275 8.408743 AGTTTCAGTACTTCAGAATATAACGC 57.591 34.615 0.00 0.00 0.00 4.84
322 324 6.270064 ACCTTTCACGGTTCAAATACTTTTG 58.730 36.000 0.00 0.00 42.98 2.44
323 325 6.459670 ACCTTTCACGGTTCAAATACTTTT 57.540 33.333 0.00 0.00 31.94 2.27
325 327 7.571080 TTTACCTTTCACGGTTCAAATACTT 57.429 32.000 0.00 0.00 38.49 2.24
332 334 4.882427 TGACATTTTACCTTTCACGGTTCA 59.118 37.500 0.00 0.00 38.49 3.18
336 338 5.354234 AGCTATGACATTTTACCTTTCACGG 59.646 40.000 0.00 0.00 0.00 4.94
337 339 6.422776 AGCTATGACATTTTACCTTTCACG 57.577 37.500 0.00 0.00 0.00 4.35
355 357 6.352016 ACGGATGAATCTATCACAAGCTAT 57.648 37.500 0.00 0.00 41.93 2.97
363 365 8.863872 TTGTCTAGATACGGATGAATCTATCA 57.136 34.615 0.00 0.00 43.67 2.15
364 366 9.562583 GTTTGTCTAGATACGGATGAATCTATC 57.437 37.037 0.00 0.00 34.91 2.08
365 367 9.303116 AGTTTGTCTAGATACGGATGAATCTAT 57.697 33.333 0.00 0.00 34.91 1.98
367 369 7.589958 AGTTTGTCTAGATACGGATGAATCT 57.410 36.000 0.00 0.00 36.45 2.40
368 370 8.649973 AAAGTTTGTCTAGATACGGATGAATC 57.350 34.615 0.00 0.00 0.00 2.52
369 371 9.449719 AAAAAGTTTGTCTAGATACGGATGAAT 57.550 29.630 0.00 0.00 0.00 2.57
370 372 8.842358 AAAAAGTTTGTCTAGATACGGATGAA 57.158 30.769 0.00 0.00 0.00 2.57
372 374 8.818057 CCTAAAAAGTTTGTCTAGATACGGATG 58.182 37.037 0.00 0.00 0.00 3.51
373 375 8.755977 TCCTAAAAAGTTTGTCTAGATACGGAT 58.244 33.333 0.00 0.00 0.00 4.18
374 376 8.031277 GTCCTAAAAAGTTTGTCTAGATACGGA 58.969 37.037 0.00 0.00 0.00 4.69
375 377 7.008992 CGTCCTAAAAAGTTTGTCTAGATACGG 59.991 40.741 0.00 0.00 0.00 4.02
376 378 7.008992 CCGTCCTAAAAAGTTTGTCTAGATACG 59.991 40.741 0.00 5.18 0.00 3.06
377 379 8.031277 TCCGTCCTAAAAAGTTTGTCTAGATAC 58.969 37.037 0.00 0.00 0.00 2.24
378 380 8.125978 TCCGTCCTAAAAAGTTTGTCTAGATA 57.874 34.615 0.00 0.00 0.00 1.98
380 382 6.409524 TCCGTCCTAAAAAGTTTGTCTAGA 57.590 37.500 0.00 0.00 0.00 2.43
381 383 6.147328 CCTTCCGTCCTAAAAAGTTTGTCTAG 59.853 42.308 0.00 0.00 0.00 2.43
383 385 4.820173 CCTTCCGTCCTAAAAAGTTTGTCT 59.180 41.667 0.00 0.00 0.00 3.41
384 386 4.577693 ACCTTCCGTCCTAAAAAGTTTGTC 59.422 41.667 0.00 0.00 0.00 3.18
387 389 8.922931 TTATTACCTTCCGTCCTAAAAAGTTT 57.077 30.769 0.00 0.00 0.00 2.66
391 393 9.112725 GCTTATTATTACCTTCCGTCCTAAAAA 57.887 33.333 0.00 0.00 0.00 1.94
393 395 7.794041 TGCTTATTATTACCTTCCGTCCTAAA 58.206 34.615 0.00 0.00 0.00 1.85
396 398 5.881923 TGCTTATTATTACCTTCCGTCCT 57.118 39.130 0.00 0.00 0.00 3.85
397 399 8.611654 TTAATGCTTATTATTACCTTCCGTCC 57.388 34.615 0.00 0.00 0.00 4.79
421 423 8.522830 CACCAGACATAACAGTTCCAAAATATT 58.477 33.333 0.00 0.00 0.00 1.28
422 424 7.888021 TCACCAGACATAACAGTTCCAAAATAT 59.112 33.333 0.00 0.00 0.00 1.28
424 426 6.068010 TCACCAGACATAACAGTTCCAAAAT 58.932 36.000 0.00 0.00 0.00 1.82
430 752 3.003480 GGCTCACCAGACATAACAGTTC 58.997 50.000 0.00 0.00 35.26 3.01
446 768 5.645056 TGATTTTATACCATCTGGGCTCA 57.355 39.130 0.54 0.00 42.05 4.26
448 770 4.829492 GCTTGATTTTATACCATCTGGGCT 59.171 41.667 0.54 0.00 42.05 5.19
449 771 4.584325 TGCTTGATTTTATACCATCTGGGC 59.416 41.667 0.54 0.00 42.05 5.36
450 772 6.713762 TTGCTTGATTTTATACCATCTGGG 57.286 37.500 0.54 0.00 44.81 4.45
451 773 7.775120 AGTTTGCTTGATTTTATACCATCTGG 58.225 34.615 0.00 0.00 42.17 3.86
452 774 9.643693 AAAGTTTGCTTGATTTTATACCATCTG 57.356 29.630 0.00 0.00 34.71 2.90
492 814 9.931210 GGACGGAAAAAGTACTATATTTGATTG 57.069 33.333 0.00 0.00 0.00 2.67
493 815 9.117183 GGGACGGAAAAAGTACTATATTTGATT 57.883 33.333 0.00 0.00 0.00 2.57
495 817 7.622713 TGGGACGGAAAAAGTACTATATTTGA 58.377 34.615 0.00 0.00 0.00 2.69
496 818 7.852971 TGGGACGGAAAAAGTACTATATTTG 57.147 36.000 0.00 0.00 0.00 2.32
497 819 8.866970 TTTGGGACGGAAAAAGTACTATATTT 57.133 30.769 0.00 0.00 0.00 1.40
500 822 9.956640 TTATTTTGGGACGGAAAAAGTACTATA 57.043 29.630 0.00 0.00 0.00 1.31
501 823 8.866970 TTATTTTGGGACGGAAAAAGTACTAT 57.133 30.769 0.00 0.00 0.00 2.12
502 824 7.938490 ACTTATTTTGGGACGGAAAAAGTACTA 59.062 33.333 0.00 0.00 0.00 1.82
503 825 6.774170 ACTTATTTTGGGACGGAAAAAGTACT 59.226 34.615 0.00 0.00 0.00 2.73
504 826 6.859508 CACTTATTTTGGGACGGAAAAAGTAC 59.140 38.462 0.00 0.00 0.00 2.73
505 827 6.546772 ACACTTATTTTGGGACGGAAAAAGTA 59.453 34.615 0.00 0.00 0.00 2.24
506 828 5.361571 ACACTTATTTTGGGACGGAAAAAGT 59.638 36.000 0.00 0.00 0.00 2.66
507 829 5.838529 ACACTTATTTTGGGACGGAAAAAG 58.161 37.500 0.00 0.00 0.00 2.27
508 830 5.505985 CGACACTTATTTTGGGACGGAAAAA 60.506 40.000 0.00 0.00 0.00 1.94
509 831 4.023878 CGACACTTATTTTGGGACGGAAAA 60.024 41.667 0.00 0.00 0.00 2.29
510 832 3.499157 CGACACTTATTTTGGGACGGAAA 59.501 43.478 0.00 0.00 0.00 3.13
511 833 3.068560 CGACACTTATTTTGGGACGGAA 58.931 45.455 0.00 0.00 0.00 4.30
512 834 2.299582 TCGACACTTATTTTGGGACGGA 59.700 45.455 0.00 0.00 0.00 4.69
513 835 2.414138 GTCGACACTTATTTTGGGACGG 59.586 50.000 11.55 0.00 0.00 4.79
514 836 3.061322 TGTCGACACTTATTTTGGGACG 58.939 45.455 15.76 0.00 0.00 4.79
515 837 5.622770 AATGTCGACACTTATTTTGGGAC 57.377 39.130 22.71 0.00 0.00 4.46
516 838 6.642707 AAAATGTCGACACTTATTTTGGGA 57.357 33.333 22.71 0.00 33.05 4.37
540 862 6.833041 TGTGTATTACTCCCTCAGTCAAAAA 58.167 36.000 0.00 0.00 36.43 1.94
541 863 6.042781 ACTGTGTATTACTCCCTCAGTCAAAA 59.957 38.462 0.00 0.00 36.43 2.44
542 864 5.542635 ACTGTGTATTACTCCCTCAGTCAAA 59.457 40.000 0.00 0.00 36.43 2.69
543 865 5.084519 ACTGTGTATTACTCCCTCAGTCAA 58.915 41.667 0.00 0.00 36.43 3.18
544 866 4.673968 ACTGTGTATTACTCCCTCAGTCA 58.326 43.478 0.00 0.00 36.43 3.41
545 867 6.963083 ATACTGTGTATTACTCCCTCAGTC 57.037 41.667 0.00 0.00 36.43 3.51
546 868 7.005296 CCTATACTGTGTATTACTCCCTCAGT 58.995 42.308 0.00 0.00 39.41 3.41
547 869 7.005296 ACCTATACTGTGTATTACTCCCTCAG 58.995 42.308 0.00 0.00 0.00 3.35
548 870 6.919158 ACCTATACTGTGTATTACTCCCTCA 58.081 40.000 0.00 0.00 0.00 3.86
549 871 7.175293 CAGACCTATACTGTGTATTACTCCCTC 59.825 44.444 0.00 0.00 0.00 4.30
550 872 7.005296 CAGACCTATACTGTGTATTACTCCCT 58.995 42.308 0.00 0.00 0.00 4.20
551 873 7.002879 TCAGACCTATACTGTGTATTACTCCC 58.997 42.308 0.00 0.00 36.81 4.30
552 874 8.638629 ATCAGACCTATACTGTGTATTACTCC 57.361 38.462 0.00 0.00 36.81 3.85
667 994 9.092876 GAAACAAACATTGTGGTATTCTCAAAA 57.907 29.630 0.00 0.00 44.59 2.44
671 998 8.702438 CATTGAAACAAACATTGTGGTATTCTC 58.298 33.333 0.00 0.00 44.59 2.87
673 1000 8.586570 TCATTGAAACAAACATTGTGGTATTC 57.413 30.769 0.00 0.00 44.59 1.75
676 1003 6.927936 CCATCATTGAAACAAACATTGTGGTA 59.072 34.615 0.00 0.00 44.59 3.25
678 1005 5.759273 ACCATCATTGAAACAAACATTGTGG 59.241 36.000 0.00 0.00 44.59 4.17
679 1006 6.847956 ACCATCATTGAAACAAACATTGTG 57.152 33.333 0.00 0.00 44.59 3.33
681 1008 6.200665 ACGAACCATCATTGAAACAAACATTG 59.799 34.615 0.00 0.00 0.00 2.82
682 1009 6.279882 ACGAACCATCATTGAAACAAACATT 58.720 32.000 0.00 0.00 0.00 2.71
683 1010 5.841810 ACGAACCATCATTGAAACAAACAT 58.158 33.333 0.00 0.00 0.00 2.71
685 1012 4.679654 GGACGAACCATCATTGAAACAAAC 59.320 41.667 0.00 0.00 38.79 2.93
689 1016 2.817258 TGGGACGAACCATCATTGAAAC 59.183 45.455 0.00 0.00 41.20 2.78
690 1017 2.817258 GTGGGACGAACCATCATTGAAA 59.183 45.455 6.15 0.00 43.59 2.69
691 1018 2.432444 GTGGGACGAACCATCATTGAA 58.568 47.619 6.15 0.00 43.59 2.69
696 1029 2.660206 CCGTGGGACGAACCATCA 59.340 61.111 6.15 0.00 46.05 3.07
697 1030 2.125269 CCCGTGGGACGAACCATC 60.125 66.667 0.00 0.93 46.05 3.51
709 1042 1.207593 CGAAGAAAGCAAGCCCGTG 59.792 57.895 0.00 0.00 0.00 4.94
710 1043 1.966451 CCGAAGAAAGCAAGCCCGT 60.966 57.895 0.00 0.00 0.00 5.28
712 1045 2.568612 GCCGAAGAAAGCAAGCCC 59.431 61.111 0.00 0.00 0.00 5.19
749 1087 4.540735 ACTAAATCGGGCGGGCCG 62.541 66.667 34.28 34.28 36.85 6.13
750 1088 2.590859 GACTAAATCGGGCGGGCC 60.591 66.667 11.17 11.17 0.00 5.80
752 1090 2.279918 CGGACTAAATCGGGCGGG 60.280 66.667 0.00 0.00 0.00 6.13
757 1095 0.739462 TGCAGTGCGGACTAAATCGG 60.739 55.000 10.03 0.00 0.00 4.18
759 1097 2.076863 AGTTGCAGTGCGGACTAAATC 58.923 47.619 18.97 1.35 0.00 2.17
761 1099 1.508632 GAGTTGCAGTGCGGACTAAA 58.491 50.000 20.02 4.66 30.08 1.85
762 1100 0.320421 GGAGTTGCAGTGCGGACTAA 60.320 55.000 20.02 0.00 30.08 2.24
763 1101 1.292223 GGAGTTGCAGTGCGGACTA 59.708 57.895 20.02 0.00 30.08 2.59
764 1102 2.031163 GGAGTTGCAGTGCGGACT 59.969 61.111 20.08 20.08 31.99 3.85
765 1103 3.050275 GGGAGTTGCAGTGCGGAC 61.050 66.667 11.20 11.75 0.00 4.79
766 1104 3.113514 TTGGGAGTTGCAGTGCGGA 62.114 57.895 11.20 0.00 0.00 5.54
767 1105 2.594303 TTGGGAGTTGCAGTGCGG 60.594 61.111 11.20 0.00 0.00 5.69
768 1106 1.447317 AAGTTGGGAGTTGCAGTGCG 61.447 55.000 11.20 0.00 0.00 5.34
769 1107 0.312102 GAAGTTGGGAGTTGCAGTGC 59.688 55.000 8.58 8.58 0.00 4.40
785 1123 0.482887 AGGGTTTGGACCTTGGGAAG 59.517 55.000 0.00 0.00 45.75 3.46
786 1124 0.481128 GAGGGTTTGGACCTTGGGAA 59.519 55.000 0.00 0.00 45.75 3.97
787 1125 1.774894 CGAGGGTTTGGACCTTGGGA 61.775 60.000 0.00 0.00 45.75 4.37
788 1126 1.303317 CGAGGGTTTGGACCTTGGG 60.303 63.158 0.00 0.00 45.75 4.12
789 1127 0.605589 GACGAGGGTTTGGACCTTGG 60.606 60.000 0.00 0.00 45.75 3.61
790 1128 0.605589 GGACGAGGGTTTGGACCTTG 60.606 60.000 0.00 0.00 45.75 3.61
791 1129 1.759236 GGACGAGGGTTTGGACCTT 59.241 57.895 0.00 0.00 45.75 3.50
792 1130 2.222013 GGGACGAGGGTTTGGACCT 61.222 63.158 0.00 0.00 45.75 3.85
807 1145 1.074926 GGAGGCAGGAGAGATGGGA 60.075 63.158 0.00 0.00 0.00 4.37
810 1148 3.136750 CCGGAGGCAGGAGAGATG 58.863 66.667 0.00 0.00 46.14 2.90
948 1287 1.500303 TGATTGATGGGGAATGGGAGG 59.500 52.381 0.00 0.00 0.00 4.30
950 1289 3.207093 TGATTGATTGATGGGGAATGGGA 59.793 43.478 0.00 0.00 0.00 4.37
954 1293 5.145564 CTCCTTGATTGATTGATGGGGAAT 58.854 41.667 0.00 0.00 0.00 3.01
961 1300 3.958798 CCCTTGCTCCTTGATTGATTGAT 59.041 43.478 0.00 0.00 0.00 2.57
964 1303 2.743553 CCCCTTGCTCCTTGATTGATT 58.256 47.619 0.00 0.00 0.00 2.57
1096 1438 0.038890 GGGAGGGAAAGAAAGCAGCT 59.961 55.000 0.00 0.00 0.00 4.24
1099 1441 0.698818 GGAGGGAGGGAAAGAAAGCA 59.301 55.000 0.00 0.00 0.00 3.91
1105 1447 1.694525 GGGAGGGAGGGAGGGAAAG 60.695 68.421 0.00 0.00 0.00 2.62
1106 1448 2.459710 GGGAGGGAGGGAGGGAAA 59.540 66.667 0.00 0.00 0.00 3.13
1107 1449 3.707189 GGGGAGGGAGGGAGGGAA 61.707 72.222 0.00 0.00 0.00 3.97
1108 1450 4.761304 AGGGGAGGGAGGGAGGGA 62.761 72.222 0.00 0.00 0.00 4.20
1109 1451 4.179599 GAGGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
1110 1452 4.179599 GGAGGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
1111 1453 4.179599 GGGAGGGGAGGGAGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
1401 1762 1.499049 GTCAATTATCGTCGGGCTCC 58.501 55.000 0.00 0.00 0.00 4.70
1462 1832 8.772705 CCTGCATTGTTTGTTAATTGTTATTGT 58.227 29.630 0.00 0.00 0.00 2.71
1463 1833 8.772705 ACCTGCATTGTTTGTTAATTGTTATTG 58.227 29.630 0.00 0.00 0.00 1.90
1551 1924 0.755698 ACGGCCATGTCTACGAGGAT 60.756 55.000 2.24 0.00 0.00 3.24
1646 2029 5.716228 TCATTCCATGCCACTTCAACTAATT 59.284 36.000 0.00 0.00 0.00 1.40
1647 2030 5.263599 TCATTCCATGCCACTTCAACTAAT 58.736 37.500 0.00 0.00 0.00 1.73
1648 2031 4.661222 TCATTCCATGCCACTTCAACTAA 58.339 39.130 0.00 0.00 0.00 2.24
1649 2032 4.019411 TCTCATTCCATGCCACTTCAACTA 60.019 41.667 0.00 0.00 0.00 2.24
1658 2041 2.422377 CCATGAGTCTCATTCCATGCCA 60.422 50.000 12.88 0.00 34.28 4.92
1674 2064 7.062322 ACTGATAAGTTGCAAATATCCCATGA 58.938 34.615 21.71 9.20 0.00 3.07
1695 2210 4.669866 TTCACTCCCCTACTCTTACTGA 57.330 45.455 0.00 0.00 0.00 3.41
1720 2236 5.577945 ACTCAAAACATTTTGTTCTGCAGTG 59.422 36.000 14.67 5.09 45.77 3.66
1917 2475 0.254178 ACTTCGATGCTGCCTGGAAT 59.746 50.000 0.00 0.00 0.00 3.01
1932 2490 2.778299 TGGTACAAGCATCACCACTTC 58.222 47.619 0.00 0.00 37.42 3.01
1937 2495 3.616219 TGGTTATGGTACAAGCATCACC 58.384 45.455 13.10 13.10 45.64 4.02
2206 2764 2.124320 GCATAGCTTTCCGGGCCA 60.124 61.111 4.39 0.00 0.00 5.36
2496 3057 7.822822 CCTACAAAGGCATACACTAAACTAAGT 59.177 37.037 0.00 0.00 35.64 2.24
2688 3249 5.645497 AGATTCGCCTCTGAATTATTATGCC 59.355 40.000 0.00 0.00 38.65 4.40
2842 3403 9.263538 TGGTAGCGAACAATATTACGATATTTT 57.736 29.630 11.24 0.00 36.53 1.82
2909 3470 2.160219 TGCAGAAATGACTTAGCAAGCG 59.840 45.455 0.00 0.00 0.00 4.68
3444 4010 2.069273 AGTGCATATCGGCGATAAAGC 58.931 47.619 32.64 32.64 36.28 3.51
3643 4224 6.488683 GCAAGGCTTTACCATGGTATATACAA 59.511 38.462 25.12 14.57 43.14 2.41
3649 4230 3.023832 GTGCAAGGCTTTACCATGGTAT 58.976 45.455 25.12 7.30 43.14 2.73
3654 4235 2.584835 TCAGTGCAAGGCTTTACCAT 57.415 45.000 0.00 0.00 43.14 3.55
3658 4239 5.009631 ACATACATTCAGTGCAAGGCTTTA 58.990 37.500 0.00 0.00 0.00 1.85
3748 4338 5.128919 ACGTATCACCGTACCTATTCTCTT 58.871 41.667 0.00 0.00 39.73 2.85
3763 4353 6.163476 TGGCAATGATCCTAATACGTATCAC 58.837 40.000 8.86 0.00 31.56 3.06
3772 4362 1.785208 AGCCCTGGCAATGATCCTAAT 59.215 47.619 11.38 0.00 44.88 1.73
3885 4475 0.572590 CGAAGAGATGCGCGTAAAGG 59.427 55.000 8.43 0.00 0.00 3.11
4142 4743 2.367202 GCCTTCCCGTCATCCTCCA 61.367 63.158 0.00 0.00 0.00 3.86
4474 5079 6.753107 TCCGAATTAAAACCAAGGATTCTC 57.247 37.500 0.00 0.00 0.00 2.87
4515 5123 4.728772 ACCAGAAATCACATTGTCTTCCA 58.271 39.130 0.00 0.00 0.00 3.53
4525 5133 6.053632 ACATGTCAGATACCAGAAATCACA 57.946 37.500 0.00 0.00 0.00 3.58
4589 5198 3.117813 TGCATCACCATCTCCATGATTCA 60.118 43.478 0.00 0.00 30.58 2.57
4632 5242 3.335356 ATCAAGTCCAGCTGGCCGG 62.335 63.158 28.91 14.84 34.44 6.13
4680 5290 2.594592 GGTGCGGTGGTGCTTCTT 60.595 61.111 0.00 0.00 35.36 2.52
4702 5312 2.356665 TTGGCTAACAACAGCTTCCA 57.643 45.000 0.00 0.00 41.50 3.53
4704 5314 6.923508 AGTTTTTATTGGCTAACAACAGCTTC 59.076 34.615 0.00 0.00 42.94 3.86
4800 5412 7.067981 TGCAACAATAACATGGCATAAGTATCA 59.932 33.333 0.00 0.00 0.00 2.15
4834 5446 6.672593 TGAGGCATCTAGGGACAATAAAAAT 58.327 36.000 0.00 0.00 0.00 1.82
4908 5520 4.537135 TCACTTCACCTCTCATAACACC 57.463 45.455 0.00 0.00 0.00 4.16
4967 5581 7.907214 TGCTAATTTCAAGGTAAGAAGTCTC 57.093 36.000 0.00 0.00 0.00 3.36
5079 5694 4.835284 TGATTAGAGGGCATGTGTACAA 57.165 40.909 0.00 0.00 0.00 2.41
5240 5998 7.348680 AGACCCTATATTCCCATAAGCAATT 57.651 36.000 0.00 0.00 0.00 2.32
5241 5999 6.977244 AGACCCTATATTCCCATAAGCAAT 57.023 37.500 0.00 0.00 0.00 3.56
5244 6002 6.431234 CACAAAGACCCTATATTCCCATAAGC 59.569 42.308 0.00 0.00 0.00 3.09
5246 6004 6.391649 ACCACAAAGACCCTATATTCCCATAA 59.608 38.462 0.00 0.00 0.00 1.90
5247 6005 5.914716 ACCACAAAGACCCTATATTCCCATA 59.085 40.000 0.00 0.00 0.00 2.74
5248 6006 4.731929 ACCACAAAGACCCTATATTCCCAT 59.268 41.667 0.00 0.00 0.00 4.00
5249 6007 4.080015 CACCACAAAGACCCTATATTCCCA 60.080 45.833 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.