Multiple sequence alignment - TraesCS2B01G039400

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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 TraesCS2B01G039400 chr2B 100.000 4250 0 0 1 4250 18095483 18091234 0.000000e+00 7849.0
1 TraesCS2B01G039400 chr2B 83.672 1427 196 21 2823 4236 18124863 18123461 0.000000e+00 1310.0
2 TraesCS2B01G039400 chr2B 87.699 878 99 8 2833 3706 18072504 18071632 0.000000e+00 1014.0
3 TraesCS2B01G039400 chr2B 85.538 809 115 2 934 1741 18128056 18127249 0.000000e+00 845.0
4 TraesCS2B01G039400 chr2B 82.143 924 154 8 998 1916 18074647 18073730 0.000000e+00 782.0
5 TraesCS2B01G039400 chr2B 81.149 870 153 10 878 1743 17931012 17930150 0.000000e+00 688.0
6 TraesCS2B01G039400 chr2B 80.984 752 133 9 998 1745 18114896 18114151 4.730000e-164 588.0
7 TraesCS2B01G039400 chr2B 86.007 536 72 3 3703 4236 18069073 18068539 4.770000e-159 571.0
8 TraesCS2B01G039400 chr2B 85.331 559 55 10 2298 2832 18073283 18072728 1.730000e-153 553.0
9 TraesCS2B01G039400 chr2B 84.385 301 33 7 500 795 18099804 18099513 2.500000e-72 283.0
10 TraesCS2B01G039400 chr2B 81.624 234 19 11 156 383 18100079 18099864 5.650000e-39 172.0
11 TraesCS2B01G039400 chr2B 84.034 119 17 2 156 273 18094803 18094686 3.470000e-21 113.0
12 TraesCS2B01G039400 chr2B 84.034 119 17 2 681 798 18095328 18095211 3.470000e-21 113.0
13 TraesCS2B01G039400 chr2B 90.000 70 5 2 689 757 18100072 18100004 5.850000e-14 89.8
14 TraesCS2B01G039400 chr2B 100.000 28 0 0 356 383 18095100 18095073 8.000000e-03 52.8
15 TraesCS2B01G039400 chr2B 100.000 28 0 0 384 411 18095128 18095101 8.000000e-03 52.8
16 TraesCS2B01G039400 chr2A 89.185 2367 182 26 1916 4236 12224410 12222072 0.000000e+00 2885.0
17 TraesCS2B01G039400 chr2A 86.167 1547 182 24 2717 4236 12201999 12200458 0.000000e+00 1642.0
18 TraesCS2B01G039400 chr2A 92.117 1129 80 8 792 1916 12225572 12224449 0.000000e+00 1583.0
19 TraesCS2B01G039400 chr2A 76.353 1404 264 52 2823 4195 12181060 12179694 0.000000e+00 691.0
20 TraesCS2B01G039400 chr2A 82.772 772 125 8 970 1737 12171849 12171082 0.000000e+00 682.0
21 TraesCS2B01G039400 chr2A 81.744 734 126 8 1008 1737 12209708 12208979 1.310000e-169 606.0
22 TraesCS2B01G039400 chr2A 83.601 311 26 10 487 795 12225907 12225620 7.000000e-68 268.0
23 TraesCS2B01G039400 chr2A 80.000 385 54 12 1 383 12226326 12225963 3.260000e-66 263.0
24 TraesCS2B01G039400 chr2A 81.107 307 39 9 500 798 12237884 12237589 1.190000e-55 228.0
25 TraesCS2B01G039400 chr2A 81.818 121 18 3 680 798 12226191 12226073 9.730000e-17 99.0
26 TraesCS2B01G039400 chr2D 87.456 1427 174 5 2823 4246 11578079 11576655 0.000000e+00 1639.0
27 TraesCS2B01G039400 chr2D 86.143 866 116 4 878 1741 11581210 11580347 0.000000e+00 931.0
28 TraesCS2B01G039400 chr2D 83.418 790 127 3 955 1741 11555140 11554352 0.000000e+00 730.0
29 TraesCS2B01G039400 chrUn 86.536 1426 175 14 2823 4236 230602378 230603798 0.000000e+00 1554.0
30 TraesCS2B01G039400 chrUn 81.597 1565 246 29 2717 4250 1981258 1979705 0.000000e+00 1256.0
31 TraesCS2B01G039400 chr1B 80.738 1111 191 19 2823 3923 486480463 486481560 0.000000e+00 845.0
32 TraesCS2B01G039400 chr1D 80.385 1040 180 21 2823 3850 363122750 363123777 0.000000e+00 769.0
33 TraesCS2B01G039400 chr1D 82.574 746 122 7 1001 1742 363120393 363121134 0.000000e+00 651.0
34 TraesCS2B01G039400 chr7A 80.620 774 134 10 2823 3584 32019857 32019088 6.120000e-163 584.0
35 TraesCS2B01G039400 chr3D 85.484 62 6 3 2253 2313 24217575 24217634 1.280000e-05 62.1


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 TraesCS2B01G039400 chr2B 18091234 18095483 4249 True 1636.12 7849 93.6136 1 4250 5 chr2B.!!$R4 4249
1 TraesCS2B01G039400 chr2B 18123461 18128056 4595 True 1077.50 1310 84.6050 934 4236 2 chr2B.!!$R6 3302
2 TraesCS2B01G039400 chr2B 18068539 18074647 6108 True 730.00 1014 85.2950 998 4236 4 chr2B.!!$R3 3238
3 TraesCS2B01G039400 chr2B 17930150 17931012 862 True 688.00 688 81.1490 878 1743 1 chr2B.!!$R1 865
4 TraesCS2B01G039400 chr2B 18114151 18114896 745 True 588.00 588 80.9840 998 1745 1 chr2B.!!$R2 747
5 TraesCS2B01G039400 chr2A 12200458 12201999 1541 True 1642.00 1642 86.1670 2717 4236 1 chr2A.!!$R3 1519
6 TraesCS2B01G039400 chr2A 12222072 12226326 4254 True 1019.60 2885 85.3442 1 4236 5 chr2A.!!$R6 4235
7 TraesCS2B01G039400 chr2A 12179694 12181060 1366 True 691.00 691 76.3530 2823 4195 1 chr2A.!!$R2 1372
8 TraesCS2B01G039400 chr2A 12171082 12171849 767 True 682.00 682 82.7720 970 1737 1 chr2A.!!$R1 767
9 TraesCS2B01G039400 chr2A 12208979 12209708 729 True 606.00 606 81.7440 1008 1737 1 chr2A.!!$R4 729
10 TraesCS2B01G039400 chr2D 11576655 11581210 4555 True 1285.00 1639 86.7995 878 4246 2 chr2D.!!$R2 3368
11 TraesCS2B01G039400 chr2D 11554352 11555140 788 True 730.00 730 83.4180 955 1741 1 chr2D.!!$R1 786
12 TraesCS2B01G039400 chrUn 230602378 230603798 1420 False 1554.00 1554 86.5360 2823 4236 1 chrUn.!!$F1 1413
13 TraesCS2B01G039400 chrUn 1979705 1981258 1553 True 1256.00 1256 81.5970 2717 4250 1 chrUn.!!$R1 1533
14 TraesCS2B01G039400 chr1B 486480463 486481560 1097 False 845.00 845 80.7380 2823 3923 1 chr1B.!!$F1 1100
15 TraesCS2B01G039400 chr1D 363120393 363123777 3384 False 710.00 769 81.4795 1001 3850 2 chr1D.!!$F1 2849
16 TraesCS2B01G039400 chr7A 32019088 32019857 769 True 584.00 584 80.6200 2823 3584 1 chr7A.!!$R1 761

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
358 360 0.036294 GGGCCTTAGCTGACGACTTT 60.036 55.0 0.84 0.0 39.73 2.66 F
758 760 0.171007 CAACCCATGTTAAGCCAGCG 59.829 55.0 0.00 0.0 32.09 5.18 F
1079 1133 0.179124 GAGGAGTACAAGCTGCCGAG 60.179 60.0 0.00 0.0 0.00 4.63 F
1858 1915 0.888619 TCTGGCAGACAAGAGGTACG 59.111 55.0 14.43 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 1661 1.228276 GCCCAATCCTCCGAATCCC 60.228 63.158 0.0 0.00 0.00 3.85 R
2390 4230 0.119561 TGGCAGTAGGGAGGGGTAAA 59.880 55.000 0.0 0.00 0.00 2.01 R
2964 5831 1.066929 TCATTAGCAGACGAGCAGCAA 60.067 47.619 0.0 0.00 36.85 3.91 R
3659 6535 0.041684 TCACATCTCAGAGGCCTGGA 59.958 55.000 12.0 6.79 40.76 3.86 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
37 38 7.589587 TCACACTATGCACTTTTTATTTTGTCG 59.410 33.333 0.00 0.00 0.00 4.35
46 47 9.284594 GCACTTTTTATTTTGTCGATGCTAATA 57.715 29.630 0.00 0.00 0.00 0.98
131 132 9.527157 TTCAAGTATTTTGAAACATAGGGATCA 57.473 29.630 0.00 0.00 35.69 2.92
132 133 9.699410 TCAAGTATTTTGAAACATAGGGATCAT 57.301 29.630 0.00 0.00 0.00 2.45
140 141 9.739276 TTTGAAACATAGGGATCATATATGTCC 57.261 33.333 18.64 18.64 38.78 4.02
141 142 8.448068 TGAAACATAGGGATCATATATGTCCA 57.552 34.615 23.95 12.82 38.78 4.02
142 143 9.061252 TGAAACATAGGGATCATATATGTCCAT 57.939 33.333 23.95 21.41 38.78 3.41
143 144 9.911788 GAAACATAGGGATCATATATGTCCATT 57.088 33.333 23.95 17.51 38.78 3.16
144 145 9.690913 AAACATAGGGATCATATATGTCCATTG 57.309 33.333 23.95 20.24 38.78 2.82
145 146 7.285566 ACATAGGGATCATATATGTCCATTGC 58.714 38.462 23.95 13.54 35.72 3.56
146 147 4.774124 AGGGATCATATATGTCCATTGCG 58.226 43.478 23.95 0.00 32.90 4.85
147 148 3.879295 GGGATCATATATGTCCATTGCGG 59.121 47.826 23.95 0.00 32.90 5.69
148 149 3.313526 GGATCATATATGTCCATTGCGGC 59.686 47.826 20.53 0.00 32.12 6.53
149 150 3.415457 TCATATATGTCCATTGCGGCA 57.585 42.857 12.42 0.00 33.14 5.69
150 151 3.749226 TCATATATGTCCATTGCGGCAA 58.251 40.909 18.85 18.85 33.14 4.52
151 152 4.140536 TCATATATGTCCATTGCGGCAAA 58.859 39.130 20.48 2.66 33.14 3.68
152 153 4.216042 TCATATATGTCCATTGCGGCAAAG 59.784 41.667 20.48 15.34 33.14 2.77
153 154 1.102154 TATGTCCATTGCGGCAAAGG 58.898 50.000 26.52 26.52 34.03 3.11
154 155 0.899717 ATGTCCATTGCGGCAAAGGT 60.900 50.000 29.56 13.43 34.34 3.50
175 176 1.350071 TTGCCCCTAACCAAGTCGTA 58.650 50.000 0.00 0.00 0.00 3.43
215 216 8.193250 GTACAGAAGTTTTGTACAAGAGACAA 57.807 34.615 24.47 0.00 46.35 3.18
216 217 7.308782 ACAGAAGTTTTGTACAAGAGACAAG 57.691 36.000 8.56 1.79 38.03 3.16
217 218 6.183360 ACAGAAGTTTTGTACAAGAGACAAGC 60.183 38.462 8.56 0.00 38.03 4.01
218 219 4.795970 AGTTTTGTACAAGAGACAAGCG 57.204 40.909 8.56 0.00 38.03 4.68
221 223 1.497991 TGTACAAGAGACAAGCGCAC 58.502 50.000 11.47 0.00 0.00 5.34
239 241 1.291877 ACGTTCAGCCAGCGTTGATC 61.292 55.000 0.00 0.00 35.11 2.92
240 242 1.421485 GTTCAGCCAGCGTTGATCG 59.579 57.895 0.00 0.00 43.12 3.69
259 261 1.800805 GATGCGATCACGGGAATCAT 58.199 50.000 0.00 0.00 40.15 2.45
264 266 1.875514 CGATCACGGGAATCATTGCAT 59.124 47.619 0.00 0.00 35.72 3.96
286 288 2.738846 GTCATGACATGTTCTGAACGCT 59.261 45.455 21.07 3.13 0.00 5.07
288 290 4.388773 GTCATGACATGTTCTGAACGCTTA 59.611 41.667 21.07 0.00 0.00 3.09
297 299 1.272490 TCTGAACGCTTAGGTCTGTGG 59.728 52.381 0.00 0.00 37.49 4.17
300 302 1.001633 GAACGCTTAGGTCTGTGGGAA 59.998 52.381 0.00 0.00 32.63 3.97
311 313 5.155161 AGGTCTGTGGGAATGTATATAGCA 58.845 41.667 0.00 0.00 0.00 3.49
312 314 5.247110 AGGTCTGTGGGAATGTATATAGCAG 59.753 44.000 0.00 0.00 0.00 4.24
331 333 4.330074 AGCAGAATATTACAAGTGCACGTC 59.670 41.667 12.01 0.00 33.24 4.34
348 350 1.995626 TCACTGGGAGGGCCTTAGC 60.996 63.158 7.89 0.00 38.76 3.09
349 351 1.997874 CACTGGGAGGGCCTTAGCT 60.998 63.158 7.89 0.00 39.73 3.32
350 352 1.997874 ACTGGGAGGGCCTTAGCTG 60.998 63.158 7.89 0.00 39.73 4.24
353 355 2.501610 GGAGGGCCTTAGCTGACG 59.498 66.667 7.89 0.00 39.73 4.35
355 357 1.142097 GAGGGCCTTAGCTGACGAC 59.858 63.158 7.89 0.00 39.73 4.34
356 358 1.305381 AGGGCCTTAGCTGACGACT 60.305 57.895 0.00 0.00 39.73 4.18
357 359 0.905337 AGGGCCTTAGCTGACGACTT 60.905 55.000 0.00 0.00 39.73 3.01
358 360 0.036294 GGGCCTTAGCTGACGACTTT 60.036 55.000 0.84 0.00 39.73 2.66
359 361 1.079503 GGCCTTAGCTGACGACTTTG 58.920 55.000 0.00 0.00 39.73 2.77
360 362 1.337823 GGCCTTAGCTGACGACTTTGA 60.338 52.381 0.00 0.00 39.73 2.69
361 363 2.413837 GCCTTAGCTGACGACTTTGAA 58.586 47.619 0.00 0.00 35.50 2.69
362 364 2.806244 GCCTTAGCTGACGACTTTGAAA 59.194 45.455 0.00 0.00 35.50 2.69
363 365 3.437049 GCCTTAGCTGACGACTTTGAAAT 59.563 43.478 0.00 0.00 35.50 2.17
364 366 4.670221 GCCTTAGCTGACGACTTTGAAATG 60.670 45.833 0.00 0.00 35.50 2.32
365 367 2.977405 AGCTGACGACTTTGAAATGC 57.023 45.000 0.00 0.00 0.00 3.56
366 368 2.221169 AGCTGACGACTTTGAAATGCA 58.779 42.857 0.00 0.00 0.00 3.96
367 369 2.816087 AGCTGACGACTTTGAAATGCAT 59.184 40.909 0.00 0.00 0.00 3.96
368 370 4.002982 AGCTGACGACTTTGAAATGCATA 58.997 39.130 0.00 0.00 0.00 3.14
369 371 4.637534 AGCTGACGACTTTGAAATGCATAT 59.362 37.500 0.00 0.00 0.00 1.78
370 372 5.817296 AGCTGACGACTTTGAAATGCATATA 59.183 36.000 0.00 0.00 0.00 0.86
371 373 5.904080 GCTGACGACTTTGAAATGCATATAC 59.096 40.000 0.00 0.00 0.00 1.47
372 374 6.456853 GCTGACGACTTTGAAATGCATATACA 60.457 38.462 0.00 0.00 0.00 2.29
373 375 7.371126 TGACGACTTTGAAATGCATATACAA 57.629 32.000 0.00 4.34 0.00 2.41
374 376 7.463544 TGACGACTTTGAAATGCATATACAAG 58.536 34.615 0.00 3.41 0.00 3.16
375 377 6.258160 ACGACTTTGAAATGCATATACAAGC 58.742 36.000 0.00 1.07 0.00 4.01
376 378 6.128035 ACGACTTTGAAATGCATATACAAGCA 60.128 34.615 0.00 0.00 45.92 3.91
395 397 5.593679 AGCATTCTAGCTTTGAAATGCAT 57.406 34.783 24.42 0.00 43.70 3.96
397 399 7.286215 AGCATTCTAGCTTTGAAATGCATAT 57.714 32.000 24.42 10.93 43.70 1.78
398 400 8.400184 AGCATTCTAGCTTTGAAATGCATATA 57.600 30.769 24.42 0.00 43.70 0.86
435 437 9.388506 AGAAATAAAAGATGTACTCCATGACTG 57.611 33.333 0.00 0.00 32.56 3.51
445 447 2.158769 ACTCCATGACTGTGAACTTGCA 60.159 45.455 0.00 0.00 0.00 4.08
446 448 3.079578 CTCCATGACTGTGAACTTGCAT 58.920 45.455 0.00 0.00 0.00 3.96
447 449 3.076621 TCCATGACTGTGAACTTGCATC 58.923 45.455 0.00 0.00 0.00 3.91
448 450 2.815503 CCATGACTGTGAACTTGCATCA 59.184 45.455 0.00 0.00 0.00 3.07
449 451 3.253921 CCATGACTGTGAACTTGCATCAA 59.746 43.478 0.00 0.00 0.00 2.57
460 462 1.312371 TTGCATCAAGTTAGCGGGCC 61.312 55.000 0.00 0.00 0.00 5.80
461 463 2.823829 GCATCAAGTTAGCGGGCCG 61.824 63.158 24.35 24.35 0.00 6.13
462 464 1.153449 CATCAAGTTAGCGGGCCGA 60.153 57.895 33.44 6.69 0.00 5.54
465 467 2.046604 AAGTTAGCGGGCCGAACC 60.047 61.111 33.44 12.71 37.93 3.62
474 476 4.388499 GGCCGAACCCTCAAGCGA 62.388 66.667 0.00 0.00 0.00 4.93
475 477 2.815647 GCCGAACCCTCAAGCGAG 60.816 66.667 0.00 0.00 39.16 5.03
476 478 2.970639 CCGAACCCTCAAGCGAGA 59.029 61.111 0.00 0.00 42.34 4.04
477 479 1.446272 CCGAACCCTCAAGCGAGAC 60.446 63.158 0.00 0.00 42.34 3.36
478 480 1.801913 CGAACCCTCAAGCGAGACG 60.802 63.158 0.00 0.00 42.34 4.18
479 481 1.585006 GAACCCTCAAGCGAGACGA 59.415 57.895 0.00 0.00 42.34 4.20
480 482 0.173708 GAACCCTCAAGCGAGACGAT 59.826 55.000 0.00 0.00 42.34 3.73
481 483 0.608640 AACCCTCAAGCGAGACGATT 59.391 50.000 0.00 0.00 42.34 3.34
482 484 1.471119 ACCCTCAAGCGAGACGATTA 58.529 50.000 0.00 0.00 42.34 1.75
483 485 1.405821 ACCCTCAAGCGAGACGATTAG 59.594 52.381 0.00 0.00 42.34 1.73
484 486 1.405821 CCCTCAAGCGAGACGATTAGT 59.594 52.381 0.00 0.00 42.34 2.24
485 487 2.159226 CCCTCAAGCGAGACGATTAGTT 60.159 50.000 0.00 0.00 42.34 2.24
496 498 3.635836 AGACGATTAGTTAGCCACCCTAC 59.364 47.826 0.00 0.00 0.00 3.18
505 507 4.096003 CCACCCTACGGCACCCAG 62.096 72.222 0.00 0.00 0.00 4.45
546 548 1.089920 CGGAAGTTCTGCCCAATGAG 58.910 55.000 2.25 0.00 0.00 2.90
584 586 7.942990 TGAAGGTGTAAACGTGGAATTTTTAT 58.057 30.769 0.00 0.00 0.00 1.40
585 587 7.863375 TGAAGGTGTAAACGTGGAATTTTTATG 59.137 33.333 0.00 0.00 0.00 1.90
586 588 7.279750 AGGTGTAAACGTGGAATTTTTATGT 57.720 32.000 0.00 0.00 0.00 2.29
589 591 7.810759 GGTGTAAACGTGGAATTTTTATGTGAT 59.189 33.333 0.00 0.00 0.00 3.06
591 593 9.828852 TGTAAACGTGGAATTTTTATGTGATAC 57.171 29.630 0.00 0.00 0.00 2.24
593 595 8.964420 AAACGTGGAATTTTTATGTGATACTG 57.036 30.769 0.00 0.00 0.00 2.74
594 596 7.083875 ACGTGGAATTTTTATGTGATACTGG 57.916 36.000 0.00 0.00 0.00 4.00
595 597 6.657541 ACGTGGAATTTTTATGTGATACTGGT 59.342 34.615 0.00 0.00 0.00 4.00
596 598 7.148306 ACGTGGAATTTTTATGTGATACTGGTC 60.148 37.037 0.00 0.00 0.00 4.02
597 599 7.186804 GTGGAATTTTTATGTGATACTGGTCG 58.813 38.462 0.00 0.00 0.00 4.79
602 604 8.780846 ATTTTTATGTGATACTGGTCGTAACA 57.219 30.769 0.00 0.00 0.00 2.41
603 605 8.604640 TTTTTATGTGATACTGGTCGTAACAA 57.395 30.769 0.00 0.00 33.41 2.83
608 610 4.322804 GTGATACTGGTCGTAACAAGTTCG 59.677 45.833 0.00 0.00 36.13 3.95
611 613 3.784338 ACTGGTCGTAACAAGTTCGAAA 58.216 40.909 0.00 0.00 36.13 3.46
612 614 4.374399 ACTGGTCGTAACAAGTTCGAAAT 58.626 39.130 0.00 0.00 36.13 2.17
644 646 9.399797 TGATTTGATCATATCTTGTTGCTAACT 57.600 29.630 21.85 0.00 33.59 2.24
649 651 9.196552 TGATCATATCTTGTTGCTAACTAATCG 57.803 33.333 0.00 0.00 0.00 3.34
651 653 6.423905 TCATATCTTGTTGCTAACTAATCGCC 59.576 38.462 0.00 0.00 0.00 5.54
656 658 1.647346 TGCTAACTAATCGCCCGTTG 58.353 50.000 0.00 0.00 0.00 4.10
668 670 1.894881 GCCCGTTGGGTGTTAACTAA 58.105 50.000 7.22 0.00 46.51 2.24
669 671 2.228925 GCCCGTTGGGTGTTAACTAAA 58.771 47.619 7.22 0.00 46.51 1.85
670 672 2.030893 GCCCGTTGGGTGTTAACTAAAC 60.031 50.000 7.22 5.41 46.51 2.01
715 717 9.877178 AACCAAGTCATACTCTTCTACATTAAG 57.123 33.333 0.00 0.00 0.00 1.85
729 731 9.813080 CTTCTACATTAAGTACAGAAGTTTTGC 57.187 33.333 8.13 0.00 37.81 3.68
732 734 7.328277 ACATTAAGTACAGAAGTTTTGCACA 57.672 32.000 0.00 0.00 0.00 4.57
741 743 5.048083 ACAGAAGTTTTGCACAAAGAGACAA 60.048 36.000 0.00 0.00 0.00 3.18
755 757 2.375174 AGAGACAACCCATGTTAAGCCA 59.625 45.455 0.00 0.00 44.12 4.75
758 760 0.171007 CAACCCATGTTAAGCCAGCG 59.829 55.000 0.00 0.00 32.09 5.18
769 771 2.028130 AGCCAGCGCTAATCAATGC 58.972 52.632 10.99 4.42 46.08 3.56
783 785 5.695851 AATCAATGCGATTACAGGAATCC 57.304 39.130 0.00 0.00 42.76 3.01
795 797 3.206150 ACAGGAATCCATGCACGTTATC 58.794 45.455 0.61 0.00 0.00 1.75
796 798 3.205338 CAGGAATCCATGCACGTTATCA 58.795 45.455 0.61 0.00 0.00 2.15
798 800 2.290641 GGAATCCATGCACGTTATCACC 59.709 50.000 0.00 0.00 0.00 4.02
799 801 1.581934 ATCCATGCACGTTATCACCG 58.418 50.000 0.00 0.00 0.00 4.94
800 802 1.087202 TCCATGCACGTTATCACCGC 61.087 55.000 0.00 0.00 0.00 5.68
801 803 1.351707 CATGCACGTTATCACCGCC 59.648 57.895 0.00 0.00 0.00 6.13
802 804 1.078778 ATGCACGTTATCACCGCCA 60.079 52.632 0.00 0.00 0.00 5.69
804 806 3.077705 CACGTTATCACCGCCACG 58.922 61.111 0.00 0.00 38.62 4.94
807 809 0.243365 ACGTTATCACCGCCACGTTA 59.757 50.000 0.00 0.00 43.10 3.18
808 810 0.641783 CGTTATCACCGCCACGTTAC 59.358 55.000 0.00 0.00 0.00 2.50
809 811 0.641783 GTTATCACCGCCACGTTACG 59.358 55.000 2.19 2.19 0.00 3.18
818 820 2.813908 CACGTTACGGGGAGCTGC 60.814 66.667 10.20 0.00 0.00 5.25
819 821 4.430765 ACGTTACGGGGAGCTGCG 62.431 66.667 10.20 0.00 0.00 5.18
821 823 4.452733 GTTACGGGGAGCTGCGCT 62.453 66.667 19.76 9.62 43.88 5.92
838 888 0.301987 GCTCGGCGACTTAAAGATGC 59.698 55.000 4.99 0.00 0.00 3.91
844 894 3.863424 CGGCGACTTAAAGATGCTTTAGA 59.137 43.478 0.00 0.00 0.00 2.10
845 895 4.026475 CGGCGACTTAAAGATGCTTTAGAG 60.026 45.833 0.00 0.00 0.00 2.43
846 896 4.870991 GGCGACTTAAAGATGCTTTAGAGT 59.129 41.667 0.00 0.00 0.00 3.24
847 897 6.040878 GGCGACTTAAAGATGCTTTAGAGTA 58.959 40.000 0.00 0.00 0.00 2.59
848 898 6.019720 GGCGACTTAAAGATGCTTTAGAGTAC 60.020 42.308 0.00 0.00 0.00 2.73
849 899 6.530534 GCGACTTAAAGATGCTTTAGAGTACA 59.469 38.462 0.00 0.00 0.00 2.90
851 901 8.587950 CGACTTAAAGATGCTTTAGAGTACAAG 58.412 37.037 0.00 0.00 0.00 3.16
852 902 8.257830 ACTTAAAGATGCTTTAGAGTACAAGC 57.742 34.615 8.35 8.35 44.87 4.01
876 928 8.844244 AGCATTCTAGAAAAATATGGACATGAC 58.156 33.333 9.71 0.00 0.00 3.06
881 933 6.764308 AGAAAAATATGGACATGACTGTGG 57.236 37.500 0.00 0.00 35.14 4.17
886 938 3.795688 ATGGACATGACTGTGGACTTT 57.204 42.857 0.00 0.00 35.14 2.66
887 939 3.126001 TGGACATGACTGTGGACTTTC 57.874 47.619 0.00 0.00 35.14 2.62
916 968 4.510571 GGCCGAGTTCCTATAAAGAACAA 58.489 43.478 14.54 0.00 44.91 2.83
921 973 6.649557 CCGAGTTCCTATAAAGAACAACAACT 59.350 38.462 14.54 0.00 44.91 3.16
942 994 3.495331 TCTGCACACCCAAACATACATT 58.505 40.909 0.00 0.00 0.00 2.71
968 1020 1.539388 CTGTGCGCTTATCCACCAAAA 59.461 47.619 9.73 0.00 0.00 2.44
1006 1060 1.107538 CAGCAAGGGAGCCATGGATG 61.108 60.000 18.40 0.00 34.23 3.51
1051 1105 3.382803 CTCCCCAAGCTGCTCGAGG 62.383 68.421 15.58 5.68 0.00 4.63
1057 1111 2.355193 AAGCTGCTCGAGGTCCTCC 61.355 63.158 15.58 0.00 0.00 4.30
1076 1130 1.811679 GCGAGGAGTACAAGCTGCC 60.812 63.158 0.00 0.00 0.00 4.85
1079 1133 0.179124 GAGGAGTACAAGCTGCCGAG 60.179 60.000 0.00 0.00 0.00 4.63
1080 1134 0.900647 AGGAGTACAAGCTGCCGAGT 60.901 55.000 0.00 0.00 0.00 4.18
1137 1191 1.449246 GAAGAGCATGCACCTCGCT 60.449 57.895 21.98 6.09 43.06 4.93
1366 1422 2.106938 GCCATGAGATCGCCGACA 59.893 61.111 0.00 0.00 0.00 4.35
1605 1661 5.998454 AGTTGAAGATTGTCTCTGTTGTG 57.002 39.130 0.00 0.00 33.29 3.33
1824 1881 6.073602 TGTTGAATGAAAGACAACTCATCGAG 60.074 38.462 0.00 0.00 42.60 4.04
1845 1902 2.950874 GCTACTCCTAGAAGGTCTGGCA 60.951 54.545 0.00 0.00 36.53 4.92
1858 1915 0.888619 TCTGGCAGACAAGAGGTACG 59.111 55.000 14.43 0.00 0.00 3.67
1922 2046 4.330620 GCAATAATGTGCAAATTGGGTGAG 59.669 41.667 12.62 0.00 44.29 3.51
1928 2052 5.389859 TGTGCAAATTGGGTGAGATTTAG 57.610 39.130 0.00 0.00 0.00 1.85
1959 2083 2.182827 ACTGTCCAATGAGCAGCTCTA 58.817 47.619 23.15 10.19 0.00 2.43
1963 2087 1.134699 TCCAATGAGCAGCTCTAACCG 60.135 52.381 23.15 7.26 0.00 4.44
1964 2088 1.134699 CCAATGAGCAGCTCTAACCGA 60.135 52.381 23.15 1.92 0.00 4.69
1972 2096 6.578944 TGAGCAGCTCTAACCGATTATTTTA 58.421 36.000 23.15 0.00 0.00 1.52
2115 3640 8.567285 AAAGTATTTTCTAAGAGGTCATGTGG 57.433 34.615 0.00 0.00 31.62 4.17
2164 3689 4.965119 ACCAAAGATTTGAATAGCGGTC 57.035 40.909 6.87 0.00 40.55 4.79
2170 3830 7.118390 CCAAAGATTTGAATAGCGGTCTATAGG 59.882 40.741 6.87 0.00 40.55 2.57
2180 3840 2.481449 GCGGTCTATAGGTCAACCACAG 60.481 54.545 8.59 0.00 38.89 3.66
2181 3841 2.481449 CGGTCTATAGGTCAACCACAGC 60.481 54.545 8.59 0.00 38.89 4.40
2199 3987 1.429148 GCGGTTTGAGTAGGATGCCG 61.429 60.000 0.00 0.00 40.52 5.69
2226 4018 6.655078 AATAGAATCCATGTACAATTGCCC 57.345 37.500 5.05 0.00 0.00 5.36
2284 4076 7.022384 GCTATTGCTGATTTCAAGATATGCTC 58.978 38.462 0.00 0.00 36.03 4.26
2285 4077 5.762825 TTGCTGATTTCAAGATATGCTCC 57.237 39.130 0.00 0.00 0.00 4.70
2287 4079 6.178607 TGCTGATTTCAAGATATGCTCCTA 57.821 37.500 0.00 0.00 0.00 2.94
2288 4080 6.776744 TGCTGATTTCAAGATATGCTCCTAT 58.223 36.000 0.00 0.00 0.00 2.57
2289 4081 7.229308 TGCTGATTTCAAGATATGCTCCTATT 58.771 34.615 0.00 0.00 0.00 1.73
2290 4082 7.722728 TGCTGATTTCAAGATATGCTCCTATTT 59.277 33.333 0.00 0.00 0.00 1.40
2291 4083 8.574737 GCTGATTTCAAGATATGCTCCTATTTT 58.425 33.333 0.00 0.00 0.00 1.82
2309 4149 8.107095 TCCTATTTTTCATAGCCCGCTATTTAT 58.893 33.333 6.48 0.44 37.16 1.40
2318 4158 7.934665 TCATAGCCCGCTATTTATAACTTTGAA 59.065 33.333 6.48 0.00 37.16 2.69
2320 4160 9.953565 ATAGCCCGCTATTTATAACTTTGAATA 57.046 29.630 3.31 0.00 35.92 1.75
2390 4230 1.203313 TCTCCCTACTGCCTTGAACCT 60.203 52.381 0.00 0.00 0.00 3.50
2649 5268 8.974292 ACTAGGATGTTTGGACCTATATGTAT 57.026 34.615 0.00 0.00 36.00 2.29
2673 5292 3.749088 TCCGTTGTGACATGGTCATTAAC 59.251 43.478 2.02 9.88 44.63 2.01
2803 5654 6.096673 TCTTTAAATTGACCCTTTGAAGCC 57.903 37.500 0.00 0.00 32.33 4.35
2812 5663 2.094675 CCCTTTGAAGCCTACCATGTG 58.905 52.381 0.00 0.00 0.00 3.21
2866 5733 8.947055 CATCGTAATTGATGACATATGGGATA 57.053 34.615 7.80 0.00 46.98 2.59
2879 5746 7.285172 TGACATATGGGATAAAACATTGTGGAG 59.715 37.037 7.80 0.00 0.00 3.86
2899 5766 6.309980 GTGGAGAGATATCAACTATGCATTCG 59.690 42.308 3.54 0.00 30.79 3.34
2964 5831 9.162764 ACTCGCATAGTTAGTGTATCAAAATTT 57.837 29.630 0.00 0.00 33.35 1.82
2977 5844 3.631144 TCAAAATTTTGCTGCTCGTCTG 58.369 40.909 23.36 0.00 38.05 3.51
3010 5877 9.918630 ATTCAGTTTATCAAATGAAACCTCTTG 57.081 29.630 6.60 0.00 36.41 3.02
3029 5896 6.097839 CCTCTTGGTGATGATGATTCCAAAAT 59.902 38.462 0.00 0.00 37.65 1.82
3077 5944 0.457851 GAGAGTGGATGTCCTCGTGG 59.542 60.000 0.00 0.00 36.82 4.94
3151 6018 3.815401 GGCCACCATTACAATAGCTAGTG 59.185 47.826 19.13 19.13 0.00 2.74
3154 6021 5.007724 GCCACCATTACAATAGCTAGTGTTC 59.992 44.000 29.53 7.65 35.90 3.18
3366 6233 7.440556 CGAGGTCATGAAAGATCAGTTGATATT 59.559 37.037 0.00 0.00 39.39 1.28
3508 6384 0.871722 TTGGATGTGTACGTGCTTGC 59.128 50.000 4.97 0.00 0.00 4.01
3659 6535 8.712228 AAATGGTAGAAAAGAAGAAGGTCAAT 57.288 30.769 0.00 0.00 0.00 2.57
3681 6557 1.829849 CAGGCCTCTGAGATGTGAGAA 59.170 52.381 0.00 0.00 43.49 2.87
3752 9190 1.168714 GCCACCATTCTCGAGCTTTT 58.831 50.000 7.81 0.00 0.00 2.27
3785 9238 7.066887 TGCGTGTGTTAGATTTGGATGAATATT 59.933 33.333 0.00 0.00 0.00 1.28
3799 9252 8.096621 TGGATGAATATTGTGGTACTAAGGAA 57.903 34.615 0.00 0.00 0.00 3.36
3808 9261 4.466370 TGTGGTACTAAGGAAGACCATCTG 59.534 45.833 0.00 0.00 43.61 2.90
3853 9307 7.371159 GTTTACTTCACTTAGGTACCTACGTT 58.629 38.462 24.53 14.75 30.13 3.99
3873 9327 4.269363 CGTTTATCTGGACGTGGAATTACC 59.731 45.833 0.00 0.00 39.54 2.85
3910 9376 6.607198 AGAGATTGGGAAGTTGAAGTTTTTGA 59.393 34.615 0.00 0.00 0.00 2.69
4093 9571 0.387622 CATTGTGCAAGAGTTGGGCG 60.388 55.000 0.00 0.00 0.00 6.13
4125 9603 4.225942 ACACTGAGGGAGCTCAATATTCAA 59.774 41.667 17.19 0.00 32.43 2.69
4168 9652 3.188460 GCAAGCTTTCGTGGAATCACTAA 59.812 43.478 0.00 0.00 41.53 2.24
4200 9684 5.183904 GCCAAAGATCCAGTGTGTAGAAATT 59.816 40.000 0.00 0.00 0.00 1.82
4221 9705 1.071299 TGCCAAGTGTGAGCGTGAT 59.929 52.632 0.00 0.00 0.00 3.06
4237 9721 3.242870 GCGTGATGTTTCAATGGATCTCC 60.243 47.826 0.00 0.00 32.48 3.71
4238 9722 3.313526 CGTGATGTTTCAATGGATCTCCC 59.686 47.826 0.00 0.00 32.48 4.30
4239 9723 3.633986 GTGATGTTTCAATGGATCTCCCC 59.366 47.826 0.00 0.00 32.48 4.81
4246 9730 0.403453 AATGGATCTCCCCGGGGAAT 60.403 55.000 41.16 33.33 44.66 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.243637 GACAAAATAAAAAGTGCATAGTGTGAA 57.756 29.630 0.00 0.00 0.00 3.18
14 15 8.577939 CATCGACAAAATAAAAAGTGCATAGTG 58.422 33.333 0.00 0.00 0.00 2.74
17 18 7.312154 AGCATCGACAAAATAAAAAGTGCATA 58.688 30.769 0.00 0.00 0.00 3.14
20 21 7.561237 TTAGCATCGACAAAATAAAAAGTGC 57.439 32.000 0.00 0.00 0.00 4.40
121 122 6.426025 CGCAATGGACATATATGATCCCTATG 59.574 42.308 19.63 17.40 31.35 2.23
122 123 6.464892 CCGCAATGGACATATATGATCCCTAT 60.465 42.308 19.63 9.56 42.00 2.57
123 124 5.163311 CCGCAATGGACATATATGATCCCTA 60.163 44.000 19.63 7.92 42.00 3.53
124 125 4.384537 CCGCAATGGACATATATGATCCCT 60.385 45.833 19.63 11.64 42.00 4.20
126 127 3.313526 GCCGCAATGGACATATATGATCC 59.686 47.826 19.63 19.52 42.00 3.36
127 128 3.940852 TGCCGCAATGGACATATATGATC 59.059 43.478 19.63 12.07 42.00 2.92
128 129 3.954200 TGCCGCAATGGACATATATGAT 58.046 40.909 19.63 3.75 42.00 2.45
130 131 4.478699 CTTTGCCGCAATGGACATATATG 58.521 43.478 11.29 11.29 42.00 1.78
131 132 3.507233 CCTTTGCCGCAATGGACATATAT 59.493 43.478 26.54 0.00 39.91 0.86
132 133 2.884012 CCTTTGCCGCAATGGACATATA 59.116 45.455 26.54 0.71 39.91 0.86
133 134 1.682854 CCTTTGCCGCAATGGACATAT 59.317 47.619 26.54 0.00 39.91 1.78
134 135 1.102154 CCTTTGCCGCAATGGACATA 58.898 50.000 26.54 2.09 39.91 2.29
135 136 0.899717 ACCTTTGCCGCAATGGACAT 60.900 50.000 33.51 16.27 39.91 3.06
136 137 1.112315 AACCTTTGCCGCAATGGACA 61.112 50.000 33.51 9.25 39.91 4.02
137 138 0.033366 AAACCTTTGCCGCAATGGAC 59.967 50.000 33.51 0.27 39.91 4.02
138 139 0.755686 AAAACCTTTGCCGCAATGGA 59.244 45.000 33.51 9.92 39.91 3.41
139 140 0.867086 CAAAACCTTTGCCGCAATGG 59.133 50.000 28.02 28.02 42.18 3.16
140 141 0.235404 GCAAAACCTTTGCCGCAATG 59.765 50.000 6.64 9.29 39.38 2.82
141 142 2.615774 GCAAAACCTTTGCCGCAAT 58.384 47.368 6.64 0.00 39.38 3.56
142 143 4.116878 GCAAAACCTTTGCCGCAA 57.883 50.000 12.10 0.38 39.38 4.85
147 148 1.270625 GGTTAGGGGCAAAACCTTTGC 60.271 52.381 14.30 14.30 41.63 3.68
148 149 2.043227 TGGTTAGGGGCAAAACCTTTG 58.957 47.619 13.73 0.00 44.55 2.77
149 150 2.480642 TGGTTAGGGGCAAAACCTTT 57.519 45.000 13.73 0.00 44.55 3.11
150 151 2.325484 CTTGGTTAGGGGCAAAACCTT 58.675 47.619 13.73 0.00 44.55 3.50
151 152 1.219469 ACTTGGTTAGGGGCAAAACCT 59.781 47.619 13.73 1.50 44.55 3.50
152 153 1.616865 GACTTGGTTAGGGGCAAAACC 59.383 52.381 7.67 7.67 44.51 3.27
153 154 1.268625 CGACTTGGTTAGGGGCAAAAC 59.731 52.381 0.00 0.00 0.00 2.43
154 155 1.133730 ACGACTTGGTTAGGGGCAAAA 60.134 47.619 0.00 0.00 0.00 2.44
218 219 3.649986 AACGCTGGCTGAACGTGC 61.650 61.111 0.00 0.00 40.44 5.34
221 223 1.421485 GATCAACGCTGGCTGAACG 59.579 57.895 0.00 0.00 0.00 3.95
239 241 0.597377 TGATTCCCGTGATCGCATCG 60.597 55.000 7.12 0.11 35.54 3.84
240 242 1.800805 ATGATTCCCGTGATCGCATC 58.199 50.000 7.12 2.44 35.54 3.91
244 246 1.298602 TGCAATGATTCCCGTGATCG 58.701 50.000 0.00 0.00 0.00 3.69
264 266 2.480037 GCGTTCAGAACATGTCATGACA 59.520 45.455 29.67 29.67 46.44 3.58
282 284 1.066143 CATTCCCACAGACCTAAGCGT 60.066 52.381 0.00 0.00 0.00 5.07
283 285 1.066143 ACATTCCCACAGACCTAAGCG 60.066 52.381 0.00 0.00 0.00 4.68
286 288 6.785466 TGCTATATACATTCCCACAGACCTAA 59.215 38.462 0.00 0.00 0.00 2.69
288 290 5.155161 TGCTATATACATTCCCACAGACCT 58.845 41.667 0.00 0.00 0.00 3.85
311 313 5.779806 GTGACGTGCACTTGTAATATTCT 57.220 39.130 16.19 0.00 44.27 2.40
331 333 1.997874 AGCTAAGGCCCTCCCAGTG 60.998 63.158 0.00 0.00 39.73 3.66
337 339 1.142097 GTCGTCAGCTAAGGCCCTC 59.858 63.158 0.00 0.00 39.73 4.30
348 350 7.003939 TGTATATGCATTTCAAAGTCGTCAG 57.996 36.000 3.54 0.00 0.00 3.51
349 351 6.976636 TGTATATGCATTTCAAAGTCGTCA 57.023 33.333 3.54 0.00 0.00 4.35
350 352 6.412072 GCTTGTATATGCATTTCAAAGTCGTC 59.588 38.462 3.54 0.00 0.00 4.20
373 375 5.593679 ATGCATTTCAAAGCTAGAATGCT 57.406 34.783 24.21 14.24 46.40 3.79
374 376 8.077991 TGTATATGCATTTCAAAGCTAGAATGC 58.922 33.333 20.40 20.40 33.81 3.56
375 377 9.955208 TTGTATATGCATTTCAAAGCTAGAATG 57.045 29.630 3.54 5.05 0.00 2.67
377 379 8.131100 GCTTGTATATGCATTTCAAAGCTAGAA 58.869 33.333 20.65 0.00 0.00 2.10
378 380 7.282901 TGCTTGTATATGCATTTCAAAGCTAGA 59.717 33.333 24.73 11.70 32.67 2.43
379 381 7.420002 TGCTTGTATATGCATTTCAAAGCTAG 58.580 34.615 24.73 11.17 32.67 3.42
380 382 7.332213 TGCTTGTATATGCATTTCAAAGCTA 57.668 32.000 24.73 15.17 32.67 3.32
381 383 6.211587 TGCTTGTATATGCATTTCAAAGCT 57.788 33.333 24.73 0.00 32.67 3.74
414 416 7.239763 TCACAGTCATGGAGTACATCTTTTA 57.760 36.000 0.00 0.00 37.84 1.52
419 421 5.078411 AGTTCACAGTCATGGAGTACATC 57.922 43.478 0.00 0.00 37.84 3.06
425 427 2.497138 TGCAAGTTCACAGTCATGGAG 58.503 47.619 0.00 0.00 0.00 3.86
445 447 0.743345 GTTCGGCCCGCTAACTTGAT 60.743 55.000 0.00 0.00 0.00 2.57
446 448 1.375013 GTTCGGCCCGCTAACTTGA 60.375 57.895 0.00 0.00 0.00 3.02
447 449 2.396157 GGTTCGGCCCGCTAACTTG 61.396 63.158 0.00 0.00 0.00 3.16
448 450 2.046604 GGTTCGGCCCGCTAACTT 60.047 61.111 0.00 0.00 0.00 2.66
457 459 4.388499 TCGCTTGAGGGTTCGGCC 62.388 66.667 0.00 0.00 0.00 6.13
458 460 2.815647 CTCGCTTGAGGGTTCGGC 60.816 66.667 0.00 0.00 36.01 5.54
460 462 1.801913 CGTCTCGCTTGAGGGTTCG 60.802 63.158 0.00 0.00 40.31 3.95
461 463 0.173708 ATCGTCTCGCTTGAGGGTTC 59.826 55.000 0.00 0.00 40.31 3.62
462 464 0.608640 AATCGTCTCGCTTGAGGGTT 59.391 50.000 0.00 0.00 40.31 4.11
465 467 2.853731 ACTAATCGTCTCGCTTGAGG 57.146 50.000 0.00 0.00 40.31 3.86
466 468 3.726730 GCTAACTAATCGTCTCGCTTGAG 59.273 47.826 0.00 0.00 41.33 3.02
467 469 3.488721 GGCTAACTAATCGTCTCGCTTGA 60.489 47.826 0.00 0.00 0.00 3.02
468 470 2.789893 GGCTAACTAATCGTCTCGCTTG 59.210 50.000 0.00 0.00 0.00 4.01
469 471 2.426024 TGGCTAACTAATCGTCTCGCTT 59.574 45.455 0.00 0.00 0.00 4.68
470 472 2.022195 TGGCTAACTAATCGTCTCGCT 58.978 47.619 0.00 0.00 0.00 4.93
471 473 2.117910 GTGGCTAACTAATCGTCTCGC 58.882 52.381 0.00 0.00 0.00 5.03
472 474 2.543238 GGGTGGCTAACTAATCGTCTCG 60.543 54.545 0.00 0.00 0.00 4.04
473 475 2.694109 AGGGTGGCTAACTAATCGTCTC 59.306 50.000 0.00 0.00 0.00 3.36
474 476 2.748388 AGGGTGGCTAACTAATCGTCT 58.252 47.619 0.00 0.00 0.00 4.18
475 477 3.549625 CGTAGGGTGGCTAACTAATCGTC 60.550 52.174 0.00 0.00 0.00 4.20
476 478 2.360165 CGTAGGGTGGCTAACTAATCGT 59.640 50.000 0.00 0.00 0.00 3.73
477 479 3.009301 CGTAGGGTGGCTAACTAATCG 57.991 52.381 0.00 0.00 0.00 3.34
496 498 1.518572 GATGTACGTCTGGGTGCCG 60.519 63.158 7.88 0.00 0.00 5.69
505 507 1.993370 GCAGAGTGGTTGATGTACGTC 59.007 52.381 8.21 8.21 0.00 4.34
561 563 7.650104 CACATAAAAATTCCACGTTTACACCTT 59.350 33.333 0.00 0.00 0.00 3.50
565 567 9.828852 GTATCACATAAAAATTCCACGTTTACA 57.171 29.630 0.00 0.00 0.00 2.41
584 586 4.859304 ACTTGTTACGACCAGTATCACA 57.141 40.909 0.00 0.00 35.45 3.58
585 587 4.322804 CGAACTTGTTACGACCAGTATCAC 59.677 45.833 0.00 0.00 35.45 3.06
586 588 4.216042 TCGAACTTGTTACGACCAGTATCA 59.784 41.667 0.00 0.00 31.10 2.15
589 591 4.566545 TTCGAACTTGTTACGACCAGTA 57.433 40.909 0.00 0.00 31.10 2.74
591 593 4.446385 TCATTTCGAACTTGTTACGACCAG 59.554 41.667 0.00 0.00 35.82 4.00
592 594 4.370049 TCATTTCGAACTTGTTACGACCA 58.630 39.130 0.00 0.00 35.82 4.02
593 595 4.977741 TCATTTCGAACTTGTTACGACC 57.022 40.909 0.00 0.00 35.82 4.79
594 596 7.584847 TCAATTTCATTTCGAACTTGTTACGAC 59.415 33.333 0.00 0.00 42.17 4.34
595 597 7.631822 TCAATTTCATTTCGAACTTGTTACGA 58.368 30.769 0.00 0.00 42.17 3.43
596 598 7.830217 TCAATTTCATTTCGAACTTGTTACG 57.170 32.000 0.00 0.00 42.17 3.18
602 604 9.695526 TGATCAAATCAATTTCATTTCGAACTT 57.304 25.926 0.00 0.00 36.11 2.66
603 605 9.865321 ATGATCAAATCAATTTCATTTCGAACT 57.135 25.926 0.00 0.00 43.50 3.01
633 635 2.004017 CGGGCGATTAGTTAGCAACAA 58.996 47.619 0.00 0.00 0.00 2.83
637 639 1.647346 CAACGGGCGATTAGTTAGCA 58.353 50.000 0.00 0.00 0.00 3.49
638 640 0.935196 CCAACGGGCGATTAGTTAGC 59.065 55.000 0.00 0.00 0.00 3.09
639 641 1.578583 CCCAACGGGCGATTAGTTAG 58.421 55.000 0.00 0.00 35.35 2.34
640 642 3.764658 CCCAACGGGCGATTAGTTA 57.235 52.632 0.00 0.00 35.35 2.24
641 643 4.629779 CCCAACGGGCGATTAGTT 57.370 55.556 0.00 0.00 35.35 2.24
649 651 4.551164 TGTTTAGTTAACACCCAACGGGC 61.551 47.826 8.61 0.00 41.73 6.13
663 665 3.057806 GCCAAAGCCGTACATGTTTAGTT 60.058 43.478 2.30 0.00 0.00 2.24
664 666 2.486592 GCCAAAGCCGTACATGTTTAGT 59.513 45.455 2.30 0.00 0.00 2.24
678 680 1.892474 TGACTTGGTTATGGCCAAAGC 59.108 47.619 10.96 15.50 46.59 3.51
679 681 4.949856 AGTATGACTTGGTTATGGCCAAAG 59.050 41.667 10.96 11.47 46.59 2.77
715 717 5.965918 GTCTCTTTGTGCAAAACTTCTGTAC 59.034 40.000 0.00 0.00 0.00 2.90
729 731 5.762045 CTTAACATGGGTTGTCTCTTTGTG 58.238 41.667 0.00 0.00 37.68 3.33
732 734 3.826729 GGCTTAACATGGGTTGTCTCTTT 59.173 43.478 0.00 0.00 37.68 2.52
741 743 2.046285 GCGCTGGCTTAACATGGGT 61.046 57.895 0.00 0.00 35.83 4.51
769 771 2.221749 CGTGCATGGATTCCTGTAATCG 59.778 50.000 3.95 0.00 44.32 3.34
783 785 1.351707 GGCGGTGATAACGTGCATG 59.648 57.895 3.82 3.82 0.00 4.06
799 801 4.078516 AGCTCCCCGTAACGTGGC 62.079 66.667 0.00 0.00 0.00 5.01
800 802 2.125673 CAGCTCCCCGTAACGTGG 60.126 66.667 0.00 0.00 0.00 4.94
801 803 2.813908 GCAGCTCCCCGTAACGTG 60.814 66.667 0.00 0.00 0.00 4.49
802 804 4.430765 CGCAGCTCCCCGTAACGT 62.431 66.667 0.00 0.00 0.00 3.99
819 821 0.301987 GCATCTTTAAGTCGCCGAGC 59.698 55.000 0.00 0.00 0.00 5.03
820 822 1.927895 AGCATCTTTAAGTCGCCGAG 58.072 50.000 0.00 0.00 0.00 4.63
821 823 2.380084 AAGCATCTTTAAGTCGCCGA 57.620 45.000 5.14 0.00 0.00 5.54
824 874 6.530534 TGTACTCTAAAGCATCTTTAAGTCGC 59.469 38.462 12.70 0.00 0.00 5.19
844 894 9.905713 TCCATATTTTTCTAGAATGCTTGTACT 57.094 29.630 5.89 0.00 0.00 2.73
845 895 9.937175 GTCCATATTTTTCTAGAATGCTTGTAC 57.063 33.333 5.89 0.00 0.00 2.90
846 896 9.679661 TGTCCATATTTTTCTAGAATGCTTGTA 57.320 29.630 5.89 0.00 0.00 2.41
847 897 8.579850 TGTCCATATTTTTCTAGAATGCTTGT 57.420 30.769 5.89 0.00 0.00 3.16
848 898 9.459640 CATGTCCATATTTTTCTAGAATGCTTG 57.540 33.333 5.89 1.59 0.00 4.01
849 899 9.412460 TCATGTCCATATTTTTCTAGAATGCTT 57.588 29.630 5.89 0.00 0.00 3.91
851 901 8.844244 AGTCATGTCCATATTTTTCTAGAATGC 58.156 33.333 5.89 0.00 0.00 3.56
853 903 9.911788 ACAGTCATGTCCATATTTTTCTAGAAT 57.088 29.630 5.89 0.00 32.99 2.40
876 928 1.672356 CGGCCAGGAAAGTCCACAG 60.672 63.158 2.24 0.00 39.61 3.66
916 968 1.102978 GTTTGGGTGTGCAGAGTTGT 58.897 50.000 0.00 0.00 0.00 3.32
921 973 2.647683 TGTATGTTTGGGTGTGCAGA 57.352 45.000 0.00 0.00 0.00 4.26
942 994 1.276705 TGGATAAGCGCACAGTGGTTA 59.723 47.619 11.47 4.92 39.65 2.85
968 1020 4.081420 TGCTGGTAATTGTTTGGTGTGTTT 60.081 37.500 0.00 0.00 0.00 2.83
987 1041 1.107538 CATCCATGGCTCCCTTGCTG 61.108 60.000 6.96 0.00 0.00 4.41
1032 1086 2.283894 TCGAGCAGCTTGGGGAGA 60.284 61.111 9.98 0.00 0.00 3.71
1057 1111 2.161486 GCAGCTTGTACTCCTCGCG 61.161 63.158 0.00 0.00 0.00 5.87
1076 1130 1.313812 ACCTTCCCTGACGCTACTCG 61.314 60.000 0.00 0.00 45.38 4.18
1079 1133 4.099113 ACTTAATACCTTCCCTGACGCTAC 59.901 45.833 0.00 0.00 0.00 3.58
1080 1134 4.284178 ACTTAATACCTTCCCTGACGCTA 58.716 43.478 0.00 0.00 0.00 4.26
1137 1191 2.922503 TCCGCCACCTTGCAGAGA 60.923 61.111 0.00 0.00 0.00 3.10
1177 1231 3.052082 CCAGTGCTTGACCTGCCG 61.052 66.667 0.00 0.00 0.00 5.69
1178 1232 2.674380 CCCAGTGCTTGACCTGCC 60.674 66.667 0.00 0.00 0.00 4.85
1279 1333 5.123027 GCTTCAGCTTATTAGAGTTTGCTGT 59.877 40.000 11.64 0.00 45.39 4.40
1299 1353 1.512926 TCTTCTTTGTGAGCCGCTTC 58.487 50.000 0.00 0.00 0.00 3.86
1366 1422 5.006153 TGTTTATTGATGTCCTCGATCGT 57.994 39.130 15.94 0.00 0.00 3.73
1372 1428 6.655003 TCTTGGACTTGTTTATTGATGTCCTC 59.345 38.462 10.65 0.00 42.96 3.71
1605 1661 1.228276 GCCCAATCCTCCGAATCCC 60.228 63.158 0.00 0.00 0.00 3.85
1710 1766 4.985538 TGTCTATGAAAACCTTCCTTGCT 58.014 39.130 0.00 0.00 0.00 3.91
1824 1881 1.684450 GCCAGACCTTCTAGGAGTAGC 59.316 57.143 0.00 0.00 37.67 3.58
1845 1902 3.699538 TGATATGTGCGTACCTCTTGTCT 59.300 43.478 0.00 0.00 0.00 3.41
1858 1915 4.995487 TCATGAGCAAGAGATGATATGTGC 59.005 41.667 0.00 0.00 0.00 4.57
1928 2052 7.761409 TGCTCATTGGACAGTATTCAAAATAC 58.239 34.615 2.32 2.32 0.00 1.89
2013 2705 8.345565 GCTATTAGATGTGTCATAAAAAGTGGG 58.654 37.037 0.00 0.00 0.00 4.61
2103 3628 4.647564 AATGTCTTTCCACATGACCTCT 57.352 40.909 0.00 0.00 37.07 3.69
2104 3629 7.253422 CAAATAATGTCTTTCCACATGACCTC 58.747 38.462 0.00 0.00 37.07 3.85
2115 3640 5.485662 CGGAGGTCCAAATAATGTCTTTC 57.514 43.478 0.00 0.00 35.14 2.62
2164 3689 2.225068 CCGCTGTGGTTGACCTATAG 57.775 55.000 0.00 0.00 36.82 1.31
2180 3840 1.429148 CGGCATCCTACTCAAACCGC 61.429 60.000 0.00 0.00 31.85 5.68
2181 3841 1.429148 GCGGCATCCTACTCAAACCG 61.429 60.000 0.00 0.00 41.97 4.44
2199 3987 7.809806 GGCAATTGTACATGGATTCTATTTAGC 59.190 37.037 7.40 0.00 0.00 3.09
2226 4018 7.881643 AGCAGAGTTAAATCAAGCTATATCG 57.118 36.000 17.51 0.00 33.00 2.92
2284 4076 6.575162 AAATAGCGGGCTATGAAAAATAGG 57.425 37.500 13.53 0.00 39.03 2.57
2287 4079 9.297037 AGTTATAAATAGCGGGCTATGAAAAAT 57.703 29.630 13.53 6.41 39.03 1.82
2288 4080 8.685838 AGTTATAAATAGCGGGCTATGAAAAA 57.314 30.769 13.53 4.78 39.03 1.94
2289 4081 8.685838 AAGTTATAAATAGCGGGCTATGAAAA 57.314 30.769 13.53 4.48 39.03 2.29
2290 4082 8.564574 CAAAGTTATAAATAGCGGGCTATGAAA 58.435 33.333 13.53 3.68 39.03 2.69
2291 4083 7.934665 TCAAAGTTATAAATAGCGGGCTATGAA 59.065 33.333 13.53 5.93 39.03 2.57
2296 4136 8.685838 TTATTCAAAGTTATAAATAGCGGGCT 57.314 30.769 0.00 0.00 0.00 5.19
2312 4152 8.854979 TGTTGTGATCAGTGTTTTATTCAAAG 57.145 30.769 0.00 0.00 0.00 2.77
2318 4158 6.016276 GGGAGTTGTTGTGATCAGTGTTTTAT 60.016 38.462 0.00 0.00 0.00 1.40
2320 4160 4.097892 GGGAGTTGTTGTGATCAGTGTTTT 59.902 41.667 0.00 0.00 0.00 2.43
2327 4167 2.038952 CAGAGGGGAGTTGTTGTGATCA 59.961 50.000 0.00 0.00 0.00 2.92
2390 4230 0.119561 TGGCAGTAGGGAGGGGTAAA 59.880 55.000 0.00 0.00 0.00 2.01
2649 5268 2.333688 TGACCATGTCACAACGGAAA 57.666 45.000 3.63 0.00 37.67 3.13
2673 5292 1.248101 GGGATGAACCAACCAACGGG 61.248 60.000 0.00 0.00 41.20 5.28
2791 5642 1.710809 ACATGGTAGGCTTCAAAGGGT 59.289 47.619 0.00 0.00 0.00 4.34
2798 5649 5.914033 TCATAAGTACACATGGTAGGCTTC 58.086 41.667 0.00 0.00 31.13 3.86
2800 5651 5.950544 TTCATAAGTACACATGGTAGGCT 57.049 39.130 0.00 0.00 31.13 4.58
2866 5733 9.911788 ATAGTTGATATCTCTCCACAATGTTTT 57.088 29.630 3.98 0.00 0.00 2.43
2879 5746 7.818493 TTAGCGAATGCATAGTTGATATCTC 57.182 36.000 0.00 0.00 46.23 2.75
2899 5766 7.042051 TCGACTGCCAAAATCATTACTATTAGC 60.042 37.037 0.00 0.00 0.00 3.09
2964 5831 1.066929 TCATTAGCAGACGAGCAGCAA 60.067 47.619 0.00 0.00 36.85 3.91
3010 5877 6.400568 ACAACATTTTGGAATCATCATCACC 58.599 36.000 0.00 0.00 37.00 4.02
3029 5896 9.601971 GAGCAAATATACGTTTAAAGAACAACA 57.398 29.630 0.00 0.00 0.00 3.33
3077 5944 1.728971 CTGCAGACACTTCATCGAACC 59.271 52.381 8.42 0.00 0.00 3.62
3134 6001 5.237344 GCCAGAACACTAGCTATTGTAATGG 59.763 44.000 26.96 26.96 35.78 3.16
3151 6018 3.402628 TTTCTGACCACTAGCCAGAAC 57.597 47.619 13.54 0.00 43.90 3.01
3154 6021 3.126001 TGTTTTCTGACCACTAGCCAG 57.874 47.619 0.00 0.00 0.00 4.85
3233 6100 4.536295 TCATCTCATCTACACTGGGGTA 57.464 45.455 0.00 0.00 0.00 3.69
3366 6233 2.799017 AGCTTTCAGCAATCCACATCA 58.201 42.857 0.00 0.00 45.56 3.07
3402 6269 6.635755 ACCTCAAAGAGACTAGTATTTGCTC 58.364 40.000 17.00 10.31 33.64 4.26
3600 6476 0.400213 ACGGACAATGCCCTCTGAAA 59.600 50.000 0.00 0.00 0.00 2.69
3659 6535 0.041684 TCACATCTCAGAGGCCTGGA 59.958 55.000 12.00 6.79 40.76 3.86
3681 6557 5.721960 ACAACAGACCTCACTTGTCCTATAT 59.278 40.000 0.00 0.00 33.09 0.86
3752 9190 5.289675 CCAAATCTAACACACGCAAAACAAA 59.710 36.000 0.00 0.00 0.00 2.83
3785 9238 4.466370 CAGATGGTCTTCCTTAGTACCACA 59.534 45.833 0.00 0.00 44.40 4.17
3799 9252 3.307339 GCTCTTGAAGGTTCAGATGGTCT 60.307 47.826 0.00 0.00 38.61 3.85
3808 9261 0.962855 GCCCCAGCTCTTGAAGGTTC 60.963 60.000 0.00 0.00 31.91 3.62
3853 9307 3.700539 TCGGTAATTCCACGTCCAGATAA 59.299 43.478 0.00 0.00 35.57 1.75
3873 9327 1.002366 CAATCTCTTCGGGCAACTCG 58.998 55.000 0.00 0.00 0.00 4.18
3894 9360 6.866248 TCAACACCTTCAAAAACTTCAACTTC 59.134 34.615 0.00 0.00 0.00 3.01
3910 9376 1.070601 GCCAGGCAAAATCAACACCTT 59.929 47.619 6.55 0.00 0.00 3.50
4093 9571 0.035317 TCCCTCAGTGTGTGCATGTC 59.965 55.000 0.00 0.00 0.00 3.06
4168 9652 3.512724 CACTGGATCTTTGGCATTTTCCT 59.487 43.478 0.00 0.00 0.00 3.36
4200 9684 0.599991 CACGCTCACACTTGGCACTA 60.600 55.000 0.00 0.00 0.00 2.74
4221 9705 1.064758 CCGGGGAGATCCATTGAAACA 60.065 52.381 0.00 0.00 37.91 2.83


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

AutoCloner maintained by Alex Coulton.