Multiple sequence alignment - TraesCS3B01G041000

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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 TraesCS3B01G041000 chr3B 100.000 3251 0 0 1 3251 20377573 20380823 0.000000e+00 6004.0
1 TraesCS3B01G041000 chr3B 87.081 627 73 4 1003 1622 20277982 20278607 0.000000e+00 702.0
2 TraesCS3B01G041000 chr3B 86.106 547 72 2 1620 2165 20283790 20284333 1.300000e-163 586.0
3 TraesCS3B01G041000 chr3B 83.750 160 13 7 2155 2313 20285046 20285193 4.370000e-29 139.0
4 TraesCS3B01G041000 chr3A 90.192 1509 108 21 907 2407 22806550 22805074 0.000000e+00 1930.0
5 TraesCS3B01G041000 chr3A 85.455 825 83 18 6 797 22807439 22806619 0.000000e+00 824.0
6 TraesCS3B01G041000 chr3A 80.432 833 96 24 2467 3251 20561187 20560374 1.010000e-159 573.0
7 TraesCS3B01G041000 chr1A 84.340 894 86 14 2410 3251 309468394 309467503 0.000000e+00 826.0
8 TraesCS3B01G041000 chr6B 86.528 720 72 13 2553 3248 31745532 31746250 0.000000e+00 769.0
9 TraesCS3B01G041000 chr6B 82.444 900 96 25 2408 3251 544058833 544059726 0.000000e+00 730.0
10 TraesCS3B01G041000 chr7B 83.860 855 82 19 2436 3251 23076860 23076023 0.000000e+00 763.0
11 TraesCS3B01G041000 chr7B 81.897 696 96 14 2574 3248 750018348 750019034 7.880000e-156 560.0
12 TraesCS3B01G041000 chr7B 81.804 654 70 26 2632 3251 295509341 295508703 1.350000e-138 503.0
13 TraesCS3B01G041000 chr7D 83.220 882 90 15 2410 3251 76562355 76561492 0.000000e+00 756.0
14 TraesCS3B01G041000 chr7D 84.777 808 61 17 2403 3163 119099451 119098659 0.000000e+00 754.0
15 TraesCS3B01G041000 chr6D 83.794 833 85 21 2443 3246 100357159 100357970 0.000000e+00 745.0
16 TraesCS3B01G041000 chr6D 78.832 137 25 4 1386 1518 18098433 18098569 4.470000e-14 89.8
17 TraesCS3B01G041000 chr7A 83.214 840 84 16 2441 3248 80572956 80572142 0.000000e+00 717.0
18 TraesCS3B01G041000 chr5D 84.000 525 62 9 2743 3248 37154215 37154736 4.880000e-133 484.0
19 TraesCS3B01G041000 chr4B 82.600 500 70 2 2766 3248 362137101 362137600 3.000000e-115 425.0
20 TraesCS3B01G041000 chr2D 79.640 555 100 9 2701 3248 284965504 284966052 1.410000e-103 387.0
21 TraesCS3B01G041000 chr2B 78.445 566 96 17 2701 3251 367030318 367029764 2.400000e-91 346.0
22 TraesCS3B01G041000 chr2B 81.818 132 22 2 1396 1526 11038 10908 3.430000e-20 110.0
23 TraesCS3B01G041000 chr2B 78.226 124 25 2 1396 1518 31301428 31301550 9.670000e-11 78.7
24 TraesCS3B01G041000 chr2A 80.165 121 20 2 1410 1528 32265556 32265674 1.610000e-13 87.9
25 TraesCS3B01G041000 chr2A 100.000 31 0 0 2072 2102 32230780 32230750 1.260000e-04 58.4


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 TraesCS3B01G041000 chr3B 20377573 20380823 3250 False 6004.0 6004 100.0000 1 3251 1 chr3B.!!$F2 3250
1 TraesCS3B01G041000 chr3B 20277982 20278607 625 False 702.0 702 87.0810 1003 1622 1 chr3B.!!$F1 619
2 TraesCS3B01G041000 chr3B 20283790 20285193 1403 False 362.5 586 84.9280 1620 2313 2 chr3B.!!$F3 693
3 TraesCS3B01G041000 chr3A 22805074 22807439 2365 True 1377.0 1930 87.8235 6 2407 2 chr3A.!!$R2 2401
4 TraesCS3B01G041000 chr3A 20560374 20561187 813 True 573.0 573 80.4320 2467 3251 1 chr3A.!!$R1 784
5 TraesCS3B01G041000 chr1A 309467503 309468394 891 True 826.0 826 84.3400 2410 3251 1 chr1A.!!$R1 841
6 TraesCS3B01G041000 chr6B 31745532 31746250 718 False 769.0 769 86.5280 2553 3248 1 chr6B.!!$F1 695
7 TraesCS3B01G041000 chr6B 544058833 544059726 893 False 730.0 730 82.4440 2408 3251 1 chr6B.!!$F2 843
8 TraesCS3B01G041000 chr7B 23076023 23076860 837 True 763.0 763 83.8600 2436 3251 1 chr7B.!!$R1 815
9 TraesCS3B01G041000 chr7B 750018348 750019034 686 False 560.0 560 81.8970 2574 3248 1 chr7B.!!$F1 674
10 TraesCS3B01G041000 chr7B 295508703 295509341 638 True 503.0 503 81.8040 2632 3251 1 chr7B.!!$R2 619
11 TraesCS3B01G041000 chr7D 76561492 76562355 863 True 756.0 756 83.2200 2410 3251 1 chr7D.!!$R1 841
12 TraesCS3B01G041000 chr7D 119098659 119099451 792 True 754.0 754 84.7770 2403 3163 1 chr7D.!!$R2 760
13 TraesCS3B01G041000 chr6D 100357159 100357970 811 False 745.0 745 83.7940 2443 3246 1 chr6D.!!$F2 803
14 TraesCS3B01G041000 chr7A 80572142 80572956 814 True 717.0 717 83.2140 2441 3248 1 chr7A.!!$R1 807
15 TraesCS3B01G041000 chr5D 37154215 37154736 521 False 484.0 484 84.0000 2743 3248 1 chr5D.!!$F1 505
16 TraesCS3B01G041000 chr2D 284965504 284966052 548 False 387.0 387 79.6400 2701 3248 1 chr2D.!!$F1 547
17 TraesCS3B01G041000 chr2B 367029764 367030318 554 True 346.0 346 78.4450 2701 3251 1 chr2B.!!$R2 550

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
225 226 0.032540 GAAGGCCCTTTGCAACACAG 59.967 55.0 0.0 0.0 43.89 3.66 F
410 411 0.107654 GCTGGTCGGATTAGGTTGCT 60.108 55.0 0.0 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1402 1441 0.108186 TCGGTGACCTGCATCATCAC 60.108 55.0 13.89 13.89 41.68 3.06 R
2377 3143 0.106708 ATACATGAATCTGCCCGCGT 59.893 50.0 4.92 0.00 0.00 6.01 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
29 30 7.095910 CCATTTTCACCAAACTATGCATTGTA 58.904 34.615 14.19 0.00 0.00 2.41
38 39 7.176515 ACCAAACTATGCATTGTATGACTTCAA 59.823 33.333 14.19 0.00 0.00 2.69
39 40 8.028354 CCAAACTATGCATTGTATGACTTCAAA 58.972 33.333 14.19 0.00 0.00 2.69
57 58 7.703328 ACTTCAAACAAATTATATAGGGCGTG 58.297 34.615 0.00 0.00 0.00 5.34
65 66 2.386661 ATATAGGGCGTGTGCTATGC 57.613 50.000 0.00 0.00 42.25 3.14
72 73 3.508840 GTGTGCTATGCGTGGGCC 61.509 66.667 0.00 0.00 38.85 5.80
74 75 2.749839 GTGCTATGCGTGGGCCAA 60.750 61.111 8.40 0.00 38.85 4.52
77 78 1.153249 GCTATGCGTGGGCCAACTA 60.153 57.895 8.40 0.00 38.85 2.24
80 81 1.873591 CTATGCGTGGGCCAACTAATC 59.126 52.381 8.40 0.00 38.85 1.75
94 95 6.967199 GGCCAACTAATCTTTGTAAAAGATCG 59.033 38.462 13.97 11.12 36.07 3.69
132 133 2.639926 GAATCGGTGCGATCGAGCG 61.640 63.158 20.40 20.40 46.30 5.03
162 163 2.281484 TCGTGAGGCCCTTGCAAC 60.281 61.111 0.00 0.00 40.13 4.17
177 178 0.936600 GCAACACCAACAACATTGCC 59.063 50.000 0.00 0.00 39.78 4.52
185 186 1.130777 AACAACATTGCCAAGGCCTT 58.869 45.000 13.78 13.78 41.09 4.35
188 189 0.250424 AACATTGCCAAGGCCTTTGC 60.250 50.000 29.90 29.90 41.09 3.68
193 194 1.301165 GCCAAGGCCTTTGCAACAG 60.301 57.895 31.15 12.58 40.13 3.16
194 195 2.031674 GCCAAGGCCTTTGCAACAGT 62.032 55.000 31.15 0.00 40.13 3.55
197 198 2.299867 CCAAGGCCTTTGCAACAGTAAT 59.700 45.455 17.61 0.00 40.13 1.89
199 200 2.875296 AGGCCTTTGCAACAGTAATGA 58.125 42.857 0.00 0.00 40.13 2.57
200 201 2.558359 AGGCCTTTGCAACAGTAATGAC 59.442 45.455 0.00 0.00 40.13 3.06
207 208 2.810852 TGCAACAGTAATGACATTGCGA 59.189 40.909 11.05 4.80 45.81 5.10
217 218 0.109132 GACATTGCGAAGGCCCTTTG 60.109 55.000 6.34 6.34 38.85 2.77
225 226 0.032540 GAAGGCCCTTTGCAACACAG 59.967 55.000 0.00 0.00 43.89 3.66
237 238 1.921573 GCAACACAGACGACATTGCAC 60.922 52.381 2.54 0.00 44.01 4.57
240 241 1.599071 ACACAGACGACATTGCACAAG 59.401 47.619 0.00 0.00 0.00 3.16
241 242 0.588252 ACAGACGACATTGCACAAGC 59.412 50.000 0.00 0.00 42.57 4.01
242 243 0.451628 CAGACGACATTGCACAAGCG 60.452 55.000 0.00 0.00 46.23 4.68
243 244 1.154413 GACGACATTGCACAAGCGG 60.154 57.895 0.00 0.00 46.23 5.52
254 255 1.200020 GCACAAGCGGAAAGTAGCAAT 59.800 47.619 0.00 0.00 35.48 3.56
259 260 3.266510 AGCGGAAAGTAGCAATGATGA 57.733 42.857 0.00 0.00 35.48 2.92
260 261 2.939103 AGCGGAAAGTAGCAATGATGAC 59.061 45.455 0.00 0.00 35.48 3.06
276 277 3.008266 TGATGACTGTTGCTTGGATCAGA 59.992 43.478 7.11 0.00 0.00 3.27
278 279 2.079925 GACTGTTGCTTGGATCAGACC 58.920 52.381 7.11 0.00 0.00 3.85
283 284 2.109126 GCTTGGATCAGACCGCCAC 61.109 63.158 0.00 0.00 0.00 5.01
307 308 4.587584 TGGTAACACAGATGACGTTGTA 57.412 40.909 0.00 0.00 46.17 2.41
314 315 2.224426 ACAGATGACGTTGTAAAGGCCA 60.224 45.455 5.01 0.00 34.48 5.36
326 327 0.249826 AAAGGCCATTTGCAACACGG 60.250 50.000 5.01 0.47 43.89 4.94
328 329 1.372872 GGCCATTTGCAACACGGAC 60.373 57.895 11.27 5.25 43.89 4.79
388 389 2.273370 GCACAGAGCAACAATGATGG 57.727 50.000 0.00 0.00 44.79 3.51
389 390 1.734707 GCACAGAGCAACAATGATGGC 60.735 52.381 0.00 0.00 44.79 4.40
390 391 1.135199 CACAGAGCAACAATGATGGCC 60.135 52.381 0.00 0.00 0.00 5.36
395 396 1.140161 CAACAATGATGGCCGCTGG 59.860 57.895 0.00 0.00 0.00 4.85
410 411 0.107654 GCTGGTCGGATTAGGTTGCT 60.108 55.000 0.00 0.00 0.00 3.91
423 424 1.165270 GGTTGCTACCATGGTGACAC 58.835 55.000 28.17 16.97 44.36 3.67
424 425 1.544537 GGTTGCTACCATGGTGACACA 60.545 52.381 28.17 16.11 44.36 3.72
425 426 3.450877 GGTTGCTACCATGGTGACACAG 61.451 54.545 28.17 16.97 44.36 3.66
434 435 1.023502 TGGTGACACAGACGTCGTTA 58.976 50.000 10.46 0.00 38.84 3.18
441 442 2.295349 ACACAGACGTCGTTATGAAGGT 59.705 45.455 10.46 9.25 0.00 3.50
442 443 3.243636 ACACAGACGTCGTTATGAAGGTT 60.244 43.478 10.46 0.00 0.00 3.50
458 459 1.937899 AGGTTCTTTTCAACACGGACG 59.062 47.619 0.00 0.00 0.00 4.79
461 462 2.296831 TCTTTTCAACACGGACGACA 57.703 45.000 0.00 0.00 0.00 4.35
465 466 1.942677 TTCAACACGGACGACATTGT 58.057 45.000 0.00 0.00 0.00 2.71
466 467 1.213491 TCAACACGGACGACATTGTG 58.787 50.000 0.00 0.00 38.28 3.33
474 475 1.464997 GGACGACATTGTGAAGCCTTC 59.535 52.381 0.00 0.00 0.00 3.46
491 493 2.719046 CCTTCGCAAAACAAACGACATC 59.281 45.455 0.00 0.00 35.20 3.06
543 545 3.468780 GCAGCAGCAAAGTTCTGTC 57.531 52.632 0.00 0.00 41.58 3.51
547 549 1.576421 CAGCAAAGTTCTGTCGCCC 59.424 57.895 0.00 0.00 0.00 6.13
586 588 0.108615 CGCGAGGAGAATGGACTGTT 60.109 55.000 0.00 0.00 0.00 3.16
604 606 3.705579 CTGTTCAGAGGAGATGGATGAGT 59.294 47.826 0.00 0.00 0.00 3.41
609 611 3.959449 CAGAGGAGATGGATGAGTGAGAA 59.041 47.826 0.00 0.00 0.00 2.87
614 616 3.814283 GAGATGGATGAGTGAGAAATGGC 59.186 47.826 0.00 0.00 0.00 4.40
621 623 2.290260 TGAGTGAGAAATGGCGGTCAAT 60.290 45.455 0.00 0.00 0.00 2.57
622 624 2.086869 AGTGAGAAATGGCGGTCAATG 58.913 47.619 0.00 0.00 0.00 2.82
624 626 0.248215 GAGAAATGGCGGTCAATGCG 60.248 55.000 0.00 0.00 0.00 4.73
625 627 0.960364 AGAAATGGCGGTCAATGCGT 60.960 50.000 0.00 0.00 0.00 5.24
626 628 0.523335 GAAATGGCGGTCAATGCGTC 60.523 55.000 0.00 0.00 0.00 5.19
693 725 5.542779 AGTCTTCTGACACCTTGTATTGAC 58.457 41.667 0.00 0.00 45.20 3.18
732 764 3.010420 TGTCAACGGAAACATGTTCACA 58.990 40.909 12.39 3.94 0.00 3.58
733 765 3.440522 TGTCAACGGAAACATGTTCACAA 59.559 39.130 12.39 0.00 0.00 3.33
735 767 4.440758 GTCAACGGAAACATGTTCACAATG 59.559 41.667 12.39 9.10 0.00 2.82
751 783 9.179909 TGTTCACAATGGTTTTTCTAAGACTTA 57.820 29.630 0.00 0.00 0.00 2.24
799 831 2.840296 GCTAAGCCACTTGCATTCTC 57.160 50.000 0.00 0.00 44.83 2.87
800 832 2.086869 GCTAAGCCACTTGCATTCTCA 58.913 47.619 0.00 0.00 44.83 3.27
801 833 2.489329 GCTAAGCCACTTGCATTCTCAA 59.511 45.455 0.00 0.00 44.83 3.02
802 834 3.671702 GCTAAGCCACTTGCATTCTCAAC 60.672 47.826 0.00 0.00 44.83 3.18
803 835 1.985473 AGCCACTTGCATTCTCAACA 58.015 45.000 0.00 0.00 44.83 3.33
804 836 2.522185 AGCCACTTGCATTCTCAACAT 58.478 42.857 0.00 0.00 44.83 2.71
805 837 2.490903 AGCCACTTGCATTCTCAACATC 59.509 45.455 0.00 0.00 44.83 3.06
806 838 2.416431 GCCACTTGCATTCTCAACATCC 60.416 50.000 0.00 0.00 40.77 3.51
807 839 3.087031 CCACTTGCATTCTCAACATCCT 58.913 45.455 0.00 0.00 0.00 3.24
808 840 3.508793 CCACTTGCATTCTCAACATCCTT 59.491 43.478 0.00 0.00 0.00 3.36
809 841 4.380233 CCACTTGCATTCTCAACATCCTTC 60.380 45.833 0.00 0.00 0.00 3.46
810 842 4.458295 CACTTGCATTCTCAACATCCTTCT 59.542 41.667 0.00 0.00 0.00 2.85
811 843 4.699257 ACTTGCATTCTCAACATCCTTCTC 59.301 41.667 0.00 0.00 0.00 2.87
812 844 4.290711 TGCATTCTCAACATCCTTCTCA 57.709 40.909 0.00 0.00 0.00 3.27
813 845 4.259356 TGCATTCTCAACATCCTTCTCAG 58.741 43.478 0.00 0.00 0.00 3.35
814 846 4.260170 GCATTCTCAACATCCTTCTCAGT 58.740 43.478 0.00 0.00 0.00 3.41
815 847 4.699257 GCATTCTCAACATCCTTCTCAGTT 59.301 41.667 0.00 0.00 0.00 3.16
816 848 5.877012 GCATTCTCAACATCCTTCTCAGTTA 59.123 40.000 0.00 0.00 0.00 2.24
817 849 6.372659 GCATTCTCAACATCCTTCTCAGTTAA 59.627 38.462 0.00 0.00 0.00 2.01
818 850 7.625185 GCATTCTCAACATCCTTCTCAGTTAAC 60.625 40.741 0.00 0.00 0.00 2.01
819 851 6.672266 TCTCAACATCCTTCTCAGTTAACT 57.328 37.500 1.12 1.12 0.00 2.24
820 852 7.776618 TCTCAACATCCTTCTCAGTTAACTA 57.223 36.000 8.04 0.00 0.00 2.24
821 853 8.190326 TCTCAACATCCTTCTCAGTTAACTAA 57.810 34.615 8.04 0.00 0.00 2.24
822 854 8.816894 TCTCAACATCCTTCTCAGTTAACTAAT 58.183 33.333 8.04 0.00 0.00 1.73
823 855 9.442047 CTCAACATCCTTCTCAGTTAACTAATT 57.558 33.333 8.04 0.00 0.00 1.40
824 856 9.793259 TCAACATCCTTCTCAGTTAACTAATTT 57.207 29.630 8.04 0.00 0.00 1.82
825 857 9.831737 CAACATCCTTCTCAGTTAACTAATTTG 57.168 33.333 8.04 0.00 0.00 2.32
826 858 9.793259 AACATCCTTCTCAGTTAACTAATTTGA 57.207 29.630 8.04 0.99 0.00 2.69
831 863 9.346725 CCTTCTCAGTTAACTAATTTGAATTGC 57.653 33.333 8.04 0.00 0.00 3.56
846 878 0.255890 ATTGCTGTCGGTGCCCTTAT 59.744 50.000 0.00 0.00 0.00 1.73
849 881 1.134521 TGCTGTCGGTGCCCTTATTAG 60.135 52.381 0.00 0.00 0.00 1.73
850 882 1.134491 GCTGTCGGTGCCCTTATTAGT 60.134 52.381 0.00 0.00 0.00 2.24
851 883 2.101917 GCTGTCGGTGCCCTTATTAGTA 59.898 50.000 0.00 0.00 0.00 1.82
853 885 4.021719 GCTGTCGGTGCCCTTATTAGTATA 60.022 45.833 0.00 0.00 0.00 1.47
856 888 4.022849 GTCGGTGCCCTTATTAGTATACGT 60.023 45.833 0.00 0.00 0.00 3.57
857 889 5.181245 GTCGGTGCCCTTATTAGTATACGTA 59.819 44.000 0.00 0.00 0.00 3.57
858 890 5.181245 TCGGTGCCCTTATTAGTATACGTAC 59.819 44.000 0.00 0.00 0.00 3.67
859 891 5.048782 CGGTGCCCTTATTAGTATACGTACA 60.049 44.000 0.00 0.00 33.09 2.90
860 892 6.349611 CGGTGCCCTTATTAGTATACGTACAT 60.350 42.308 0.00 0.00 33.09 2.29
861 893 7.031975 GGTGCCCTTATTAGTATACGTACATC 58.968 42.308 0.00 0.00 33.09 3.06
862 894 6.744537 GTGCCCTTATTAGTATACGTACATCG 59.255 42.308 0.00 0.00 46.00 3.84
863 895 6.654582 TGCCCTTATTAGTATACGTACATCGA 59.345 38.462 0.00 0.00 42.86 3.59
866 898 9.897744 CCCTTATTAGTATACGTACATCGAAAA 57.102 33.333 0.00 0.00 42.86 2.29
873 905 8.792831 AGTATACGTACATCGAAAATACCTTG 57.207 34.615 0.00 0.00 42.86 3.61
874 906 8.623903 AGTATACGTACATCGAAAATACCTTGA 58.376 33.333 0.00 0.00 42.86 3.02
875 907 7.689953 ATACGTACATCGAAAATACCTTGAC 57.310 36.000 0.00 0.00 42.86 3.18
876 908 4.866486 ACGTACATCGAAAATACCTTGACC 59.134 41.667 0.00 0.00 42.86 4.02
877 909 4.865925 CGTACATCGAAAATACCTTGACCA 59.134 41.667 0.00 0.00 42.86 4.02
878 910 5.349270 CGTACATCGAAAATACCTTGACCAA 59.651 40.000 0.00 0.00 42.86 3.67
879 911 6.036735 CGTACATCGAAAATACCTTGACCAAT 59.963 38.462 0.00 0.00 42.86 3.16
880 912 7.223193 CGTACATCGAAAATACCTTGACCAATA 59.777 37.037 0.00 0.00 42.86 1.90
883 915 8.621286 ACATCGAAAATACCTTGACCAATAATC 58.379 33.333 0.00 0.00 0.00 1.75
885 917 6.259167 TCGAAAATACCTTGACCAATAATCCG 59.741 38.462 0.00 0.00 0.00 4.18
890 922 3.278574 CCTTGACCAATAATCCGAAGCA 58.721 45.455 0.00 0.00 0.00 3.91
892 924 4.201950 CCTTGACCAATAATCCGAAGCAAG 60.202 45.833 0.00 0.00 0.00 4.01
895 927 3.545703 ACCAATAATCCGAAGCAAGAGG 58.454 45.455 0.00 0.00 0.00 3.69
897 929 3.947834 CCAATAATCCGAAGCAAGAGGTT 59.052 43.478 0.00 0.00 38.36 3.50
915 947 7.729124 AGAGGTTGCCATAGTTAGTTAAGTA 57.271 36.000 0.00 0.00 0.00 2.24
916 948 7.783042 AGAGGTTGCCATAGTTAGTTAAGTAG 58.217 38.462 0.00 0.00 0.00 2.57
917 949 6.885922 AGGTTGCCATAGTTAGTTAAGTAGG 58.114 40.000 0.00 0.00 0.00 3.18
918 950 6.442885 AGGTTGCCATAGTTAGTTAAGTAGGT 59.557 38.462 0.00 0.00 0.00 3.08
920 952 6.862469 TGCCATAGTTAGTTAAGTAGGTGT 57.138 37.500 0.00 0.00 0.00 4.16
922 954 5.975939 GCCATAGTTAGTTAAGTAGGTGTCG 59.024 44.000 0.00 0.00 0.00 4.35
923 955 6.183360 GCCATAGTTAGTTAAGTAGGTGTCGA 60.183 42.308 0.00 0.00 0.00 4.20
925 957 8.074972 CCATAGTTAGTTAAGTAGGTGTCGATC 58.925 40.741 0.00 0.00 0.00 3.69
926 958 6.116680 AGTTAGTTAAGTAGGTGTCGATCG 57.883 41.667 9.36 9.36 0.00 3.69
927 959 5.065731 AGTTAGTTAAGTAGGTGTCGATCGG 59.934 44.000 16.41 0.00 0.00 4.18
929 961 1.027357 TAAGTAGGTGTCGATCGGCC 58.973 55.000 18.47 15.61 0.00 6.13
930 962 0.683504 AAGTAGGTGTCGATCGGCCT 60.684 55.000 18.47 21.31 35.28 5.19
932 964 1.102222 GTAGGTGTCGATCGGCCTCT 61.102 60.000 23.01 18.97 32.90 3.69
934 966 0.395311 AGGTGTCGATCGGCCTCTAA 60.395 55.000 18.47 0.00 0.00 2.10
941 973 1.067283 CGATCGGCCTCTAATCTGCAT 60.067 52.381 7.38 0.00 0.00 3.96
946 978 1.615883 GGCCTCTAATCTGCATCGAGA 59.384 52.381 0.00 0.00 0.00 4.04
963 995 1.803519 GAGAGCGACCAGTTGAGCG 60.804 63.158 0.00 0.00 34.34 5.03
974 1006 2.478134 CCAGTTGAGCGAAAGAGACAAG 59.522 50.000 0.00 0.00 0.00 3.16
975 1007 2.478134 CAGTTGAGCGAAAGAGACAAGG 59.522 50.000 0.00 0.00 0.00 3.61
976 1008 2.365617 AGTTGAGCGAAAGAGACAAGGA 59.634 45.455 0.00 0.00 0.00 3.36
977 1009 3.131396 GTTGAGCGAAAGAGACAAGGAA 58.869 45.455 0.00 0.00 0.00 3.36
991 1024 2.701951 ACAAGGAAACCTAGTCCACGAA 59.298 45.455 0.00 0.00 37.65 3.85
992 1025 3.135167 ACAAGGAAACCTAGTCCACGAAA 59.865 43.478 0.00 0.00 37.65 3.46
999 1032 1.134965 CCTAGTCCACGAAAGAGCAGG 60.135 57.143 0.00 0.00 0.00 4.85
1000 1033 1.819288 CTAGTCCACGAAAGAGCAGGA 59.181 52.381 0.00 0.00 0.00 3.86
1001 1034 1.270907 AGTCCACGAAAGAGCAGGAT 58.729 50.000 0.00 0.00 0.00 3.24
1008 1041 3.063180 CACGAAAGAGCAGGATGATGAAC 59.937 47.826 0.00 0.00 39.69 3.18
1021 1054 2.054021 TGATGAACTTCCCTGTGACCA 58.946 47.619 0.00 0.00 0.00 4.02
1028 1061 0.179020 TTCCCTGTGACCAAGTGCTG 60.179 55.000 0.00 0.00 0.00 4.41
1138 1171 2.851104 CGTCGCTCCACGTTTTCC 59.149 61.111 0.00 0.00 44.19 3.13
1360 1393 1.755783 CCTCTGGATGCCTTTGCCC 60.756 63.158 0.00 0.00 36.33 5.36
1476 1515 4.467084 AACCATGCCGTCGCCGAT 62.467 61.111 0.00 0.00 35.63 4.18
1593 1632 1.153349 GGAGATCCCGCACCTGTTC 60.153 63.158 0.00 0.00 0.00 3.18
1649 1688 2.577911 GTACGCCTACACGGACGC 60.578 66.667 0.00 0.00 37.10 5.19
1673 1712 2.573369 CATCCCTTGGAGCTTCATCAG 58.427 52.381 0.00 0.00 34.05 2.90
1694 1733 3.768632 CGTCAAGGCAGAGTACGC 58.231 61.111 0.00 0.00 0.00 4.42
1975 2017 3.266772 ACCTTGCATCCTTGGAGATTACA 59.733 43.478 0.00 0.00 0.00 2.41
1980 2022 3.686691 GCATCCTTGGAGATTACAAGCCT 60.687 47.826 0.00 0.00 42.98 4.58
2218 2984 3.371063 GGGAGGAGCACGTCGACA 61.371 66.667 17.16 0.00 0.00 4.35
2256 3022 1.557443 CGACGCTCCACTGAACCAAC 61.557 60.000 0.00 0.00 0.00 3.77
2259 3025 0.817634 CGCTCCACTGAACCAACCAA 60.818 55.000 0.00 0.00 0.00 3.67
2263 3029 1.110442 CCACTGAACCAACCAAGCAA 58.890 50.000 0.00 0.00 0.00 3.91
2276 3042 0.040958 CAAGCAACCTGTTCGAGTGC 60.041 55.000 0.00 0.00 0.00 4.40
2277 3043 1.166531 AAGCAACCTGTTCGAGTGCC 61.167 55.000 0.00 0.00 0.00 5.01
2278 3044 2.617274 GCAACCTGTTCGAGTGCCC 61.617 63.158 0.00 0.00 0.00 5.36
2279 3045 1.071471 CAACCTGTTCGAGTGCCCT 59.929 57.895 0.00 0.00 0.00 5.19
2280 3046 1.071471 AACCTGTTCGAGTGCCCTG 59.929 57.895 0.00 0.00 0.00 4.45
2281 3047 2.743928 CCTGTTCGAGTGCCCTGC 60.744 66.667 0.00 0.00 0.00 4.85
2287 3053 2.046023 CGAGTGCCCTGCCATTCA 60.046 61.111 0.00 0.00 0.00 2.57
2308 3074 4.625742 TCATTCTCCTCGATTCGTTGTTTC 59.374 41.667 5.89 0.00 0.00 2.78
2313 3079 4.124238 TCCTCGATTCGTTGTTTCAAGTT 58.876 39.130 5.89 0.00 0.00 2.66
2315 3081 4.670621 CCTCGATTCGTTGTTTCAAGTTTG 59.329 41.667 5.89 0.00 0.00 2.93
2316 3082 5.472320 TCGATTCGTTGTTTCAAGTTTGA 57.528 34.783 5.89 0.00 34.92 2.69
2317 3083 6.055231 TCGATTCGTTGTTTCAAGTTTGAT 57.945 33.333 5.89 0.00 37.00 2.57
2318 3084 6.133392 TCGATTCGTTGTTTCAAGTTTGATC 58.867 36.000 5.89 0.00 37.00 2.92
2319 3085 5.056807 CGATTCGTTGTTTCAAGTTTGATCG 59.943 40.000 0.00 0.00 37.00 3.69
2320 3086 3.613563 TCGTTGTTTCAAGTTTGATCGC 58.386 40.909 0.00 0.00 37.00 4.58
2321 3087 3.311322 TCGTTGTTTCAAGTTTGATCGCT 59.689 39.130 0.00 0.00 37.00 4.93
2322 3088 4.035017 CGTTGTTTCAAGTTTGATCGCTT 58.965 39.130 0.00 0.00 37.00 4.68
2323 3089 4.499040 CGTTGTTTCAAGTTTGATCGCTTT 59.501 37.500 0.00 0.00 37.00 3.51
2324 3090 5.004345 CGTTGTTTCAAGTTTGATCGCTTTT 59.996 36.000 0.00 0.00 37.00 2.27
2325 3091 5.947503 TGTTTCAAGTTTGATCGCTTTTG 57.052 34.783 0.00 0.00 37.00 2.44
2326 3092 5.406649 TGTTTCAAGTTTGATCGCTTTTGT 58.593 33.333 0.00 0.00 37.00 2.83
2327 3093 5.288232 TGTTTCAAGTTTGATCGCTTTTGTG 59.712 36.000 0.00 0.00 37.00 3.33
2328 3094 4.891627 TCAAGTTTGATCGCTTTTGTGA 57.108 36.364 0.00 0.00 43.70 3.58
2367 3133 5.277825 CAACGGCAGATGTTTAAGTTTCAA 58.722 37.500 0.00 0.00 0.00 2.69
2375 3141 4.098055 TGTTTAAGTTTCAACGCTGCAA 57.902 36.364 0.00 0.00 0.00 4.08
2376 3142 3.854809 TGTTTAAGTTTCAACGCTGCAAC 59.145 39.130 0.00 0.00 0.00 4.17
2377 3143 3.766676 TTAAGTTTCAACGCTGCAACA 57.233 38.095 4.25 0.00 31.83 3.33
2378 3144 1.908065 AAGTTTCAACGCTGCAACAC 58.092 45.000 4.25 0.00 31.83 3.32
2395 3161 0.809636 CACGCGGGCAGATTCATGTA 60.810 55.000 12.47 0.00 0.00 2.29
2399 3165 2.602933 CGCGGGCAGATTCATGTATTTG 60.603 50.000 0.00 0.00 0.00 2.32
2400 3166 2.358898 GCGGGCAGATTCATGTATTTGT 59.641 45.455 5.03 0.00 0.00 2.83
2401 3167 3.181487 GCGGGCAGATTCATGTATTTGTT 60.181 43.478 5.03 0.00 0.00 2.83
2405 3171 7.202526 CGGGCAGATTCATGTATTTGTTATTT 58.797 34.615 5.03 0.00 0.00 1.40
2433 3199 0.250467 ATCTCCAATAGGCGCGCAAT 60.250 50.000 34.42 22.47 33.74 3.56
2434 3200 0.391228 TCTCCAATAGGCGCGCAATA 59.609 50.000 34.42 24.49 33.74 1.90
2551 3317 3.282745 GAGCCGCTCCAACAGACGA 62.283 63.158 9.42 0.00 0.00 4.20
2713 3568 5.106237 CCTCCTCCTACGATAGATAAAACGG 60.106 48.000 0.00 0.00 41.38 4.44
2750 3624 3.401332 TCGTCCTCCTCCGACTCT 58.599 61.111 0.00 0.00 0.00 3.24
2818 3692 1.734748 GATCGTCTTCGGAGTCCCC 59.265 63.158 2.80 0.00 37.69 4.81
2850 3724 2.815478 CTCCTAGCTCGATGTTGAACC 58.185 52.381 0.00 0.00 0.00 3.62
2872 3746 3.845259 GTCCGCCTCCCGCATACA 61.845 66.667 0.00 0.00 37.30 2.29
3004 3904 1.667154 TTCCATCTCGACGAGGCTGG 61.667 60.000 27.73 27.73 35.62 4.85
3053 3953 0.450583 CGATCCTCGTCGGTGAGAAA 59.549 55.000 6.42 0.00 38.28 2.52
3125 4025 1.779061 AAGTTCATGTCCCGGCAGGT 61.779 55.000 1.11 0.00 36.75 4.00
3194 4094 0.884704 GCTGTCTCAAAGGTGCCGAA 60.885 55.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.295950 TGCATAGTTTGGTGAAAATGGTTG 58.704 37.500 0.00 0.00 0.00 3.77
2 3 5.543507 TGCATAGTTTGGTGAAAATGGTT 57.456 34.783 0.00 0.00 0.00 3.67
3 4 5.743636 ATGCATAGTTTGGTGAAAATGGT 57.256 34.783 0.00 0.00 0.00 3.55
4 5 5.933463 ACAATGCATAGTTTGGTGAAAATGG 59.067 36.000 0.00 0.00 0.00 3.16
12 13 6.658816 TGAAGTCATACAATGCATAGTTTGGT 59.341 34.615 0.00 0.00 0.00 3.67
17 18 7.686438 TGTTTGAAGTCATACAATGCATAGT 57.314 32.000 0.00 0.00 35.45 2.12
29 30 8.567948 CGCCCTATATAATTTGTTTGAAGTCAT 58.432 33.333 0.00 0.00 0.00 3.06
38 39 5.130350 AGCACACGCCCTATATAATTTGTT 58.870 37.500 0.00 0.00 39.83 2.83
39 40 4.714632 AGCACACGCCCTATATAATTTGT 58.285 39.130 0.00 0.00 39.83 2.83
52 53 3.864686 CCACGCATAGCACACGCC 61.865 66.667 0.00 0.00 39.83 5.68
57 58 2.749839 TTGGCCCACGCATAGCAC 60.750 61.111 0.00 0.00 36.38 4.40
65 66 2.159382 ACAAAGATTAGTTGGCCCACG 58.841 47.619 0.00 0.00 0.00 4.94
72 73 7.898309 CGACCGATCTTTTACAAAGATTAGTTG 59.102 37.037 12.00 11.75 37.14 3.16
74 75 6.534079 CCGACCGATCTTTTACAAAGATTAGT 59.466 38.462 12.00 11.88 37.14 2.24
77 78 4.634443 CCCGACCGATCTTTTACAAAGATT 59.366 41.667 12.00 0.00 37.14 2.40
80 81 3.332034 ACCCGACCGATCTTTTACAAAG 58.668 45.455 0.00 0.00 0.00 2.77
94 95 0.815615 GAATGGCTCATGACCCGACC 60.816 60.000 2.59 0.00 0.00 4.79
113 114 2.639926 GCTCGATCGCACCGATTCG 61.640 63.158 11.09 0.00 47.00 3.34
132 133 3.097728 CACGACGTGACGCTGACC 61.098 66.667 23.39 0.00 35.23 4.02
134 135 2.251371 CTCACGACGTGACGCTGA 59.749 61.111 26.04 5.62 37.67 4.26
139 140 3.222354 AAGGGCCTCACGACGTGAC 62.222 63.158 26.04 17.10 37.67 3.67
162 163 1.868469 CCTTGGCAATGTTGTTGGTG 58.132 50.000 0.00 0.00 0.00 4.17
177 178 3.005684 TCATTACTGTTGCAAAGGCCTTG 59.994 43.478 21.33 14.33 40.13 3.61
185 186 3.251972 TCGCAATGTCATTACTGTTGCAA 59.748 39.130 15.79 0.00 42.70 4.08
188 189 4.406069 CCTTCGCAATGTCATTACTGTTG 58.594 43.478 0.00 0.00 0.00 3.33
193 194 1.065551 GGGCCTTCGCAATGTCATTAC 59.934 52.381 0.84 0.00 36.38 1.89
194 195 1.064758 AGGGCCTTCGCAATGTCATTA 60.065 47.619 0.00 0.00 36.38 1.90
197 198 0.539438 AAAGGGCCTTCGCAATGTCA 60.539 50.000 21.20 0.00 36.38 3.58
199 200 1.966762 CAAAGGGCCTTCGCAATGT 59.033 52.632 21.20 0.00 36.38 2.71
200 201 1.446618 GCAAAGGGCCTTCGCAATG 60.447 57.895 23.96 16.53 36.38 2.82
207 208 0.396974 TCTGTGTTGCAAAGGGCCTT 60.397 50.000 14.48 14.48 43.89 4.35
217 218 0.307453 TGCAATGTCGTCTGTGTTGC 59.693 50.000 0.00 0.00 43.93 4.17
225 226 1.154413 CCGCTTGTGCAATGTCGTC 60.154 57.895 0.00 0.00 39.64 4.20
237 238 3.374988 TCATCATTGCTACTTTCCGCTTG 59.625 43.478 0.00 0.00 0.00 4.01
240 241 2.939103 AGTCATCATTGCTACTTTCCGC 59.061 45.455 0.00 0.00 0.00 5.54
241 242 3.935203 ACAGTCATCATTGCTACTTTCCG 59.065 43.478 0.00 0.00 0.00 4.30
242 243 5.634896 CAACAGTCATCATTGCTACTTTCC 58.365 41.667 0.00 0.00 0.00 3.13
243 244 5.091431 GCAACAGTCATCATTGCTACTTTC 58.909 41.667 1.06 0.00 44.26 2.62
254 255 3.008266 TCTGATCCAAGCAACAGTCATCA 59.992 43.478 0.00 0.00 0.00 3.07
259 260 1.609061 CGGTCTGATCCAAGCAACAGT 60.609 52.381 0.00 0.00 0.00 3.55
260 261 1.081892 CGGTCTGATCCAAGCAACAG 58.918 55.000 0.00 0.00 0.00 3.16
267 268 1.561769 ATGGTGGCGGTCTGATCCAA 61.562 55.000 0.00 0.00 0.00 3.53
276 277 1.302993 GTGTTACCATGGTGGCGGT 60.303 57.895 28.17 0.93 42.67 5.68
278 279 0.321210 TCTGTGTTACCATGGTGGCG 60.321 55.000 28.17 9.51 42.67 5.69
283 284 2.972625 ACGTCATCTGTGTTACCATGG 58.027 47.619 11.19 11.19 0.00 3.66
307 308 0.249826 CCGTGTTGCAAATGGCCTTT 60.250 50.000 3.32 0.00 43.89 3.11
314 315 1.234821 ATGTCGTCCGTGTTGCAAAT 58.765 45.000 0.00 0.00 0.00 2.32
326 327 2.726241 GCAAAGGCTTCAAAATGTCGTC 59.274 45.455 0.00 0.00 36.96 4.20
328 329 2.741612 TGCAAAGGCTTCAAAATGTCG 58.258 42.857 0.00 0.00 41.91 4.35
371 372 1.180029 GGCCATCATTGTTGCTCTGT 58.820 50.000 0.00 0.00 0.00 3.41
373 374 1.660560 GCGGCCATCATTGTTGCTCT 61.661 55.000 2.24 0.00 0.00 4.09
390 391 1.429148 GCAACCTAATCCGACCAGCG 61.429 60.000 0.00 0.00 40.47 5.18
395 396 2.973694 TGGTAGCAACCTAATCCGAC 57.026 50.000 0.00 0.00 46.91 4.79
410 411 1.271379 GACGTCTGTGTCACCATGGTA 59.729 52.381 19.28 0.00 38.75 3.25
418 419 3.561503 CTTCATAACGACGTCTGTGTCA 58.438 45.455 14.70 3.64 38.84 3.58
419 420 2.915463 CCTTCATAACGACGTCTGTGTC 59.085 50.000 14.70 0.00 35.49 3.67
423 424 3.834610 AGAACCTTCATAACGACGTCTG 58.165 45.455 14.70 9.79 0.00 3.51
424 425 4.516365 AAGAACCTTCATAACGACGTCT 57.484 40.909 14.70 0.00 0.00 4.18
425 426 5.176223 TGAAAAGAACCTTCATAACGACGTC 59.824 40.000 5.18 5.18 0.00 4.34
429 430 6.510478 CGTGTTGAAAAGAACCTTCATAACGA 60.510 38.462 11.84 0.00 40.64 3.85
430 431 5.619607 CGTGTTGAAAAGAACCTTCATAACG 59.380 40.000 0.00 0.00 36.51 3.18
434 435 4.036380 GTCCGTGTTGAAAAGAACCTTCAT 59.964 41.667 0.00 0.00 32.98 2.57
441 442 2.619147 TGTCGTCCGTGTTGAAAAGAA 58.381 42.857 0.00 0.00 0.00 2.52
442 443 2.296831 TGTCGTCCGTGTTGAAAAGA 57.703 45.000 0.00 0.00 0.00 2.52
458 459 0.874390 TGCGAAGGCTTCACAATGTC 59.126 50.000 25.66 7.16 40.82 3.06
461 462 2.100584 TGTTTTGCGAAGGCTTCACAAT 59.899 40.909 26.07 0.00 40.82 2.71
465 466 2.535331 GTTTGTTTTGCGAAGGCTTCA 58.465 42.857 25.66 6.29 40.82 3.02
466 467 1.516864 CGTTTGTTTTGCGAAGGCTTC 59.483 47.619 17.33 17.33 40.82 3.86
511 513 3.751246 CTGCAACACCGGGCCATG 61.751 66.667 6.32 3.38 0.00 3.66
586 588 3.203934 TCTCACTCATCCATCTCCTCTGA 59.796 47.826 0.00 0.00 0.00 3.27
604 606 0.810648 GCATTGACCGCCATTTCTCA 59.189 50.000 0.00 0.00 0.00 3.27
609 611 2.749865 CGACGCATTGACCGCCATT 61.750 57.895 0.00 0.00 0.00 3.16
614 616 4.483683 CACGCGACGCATTGACCG 62.484 66.667 21.35 3.75 0.00 4.79
664 679 6.767524 ACAAGGTGTCAGAAGACTATCTAG 57.232 41.667 0.00 0.00 45.20 2.43
693 725 0.179235 CAACGCACAAATACCGGACG 60.179 55.000 9.46 0.74 0.00 4.79
722 754 7.920682 GTCTTAGAAAAACCATTGTGAACATGT 59.079 33.333 0.00 0.00 0.00 3.21
732 764 6.657541 TCGCCATAAGTCTTAGAAAAACCATT 59.342 34.615 0.00 0.00 0.00 3.16
733 765 6.177610 TCGCCATAAGTCTTAGAAAAACCAT 58.822 36.000 0.00 0.00 0.00 3.55
735 767 6.490566 TTCGCCATAAGTCTTAGAAAAACC 57.509 37.500 0.00 0.00 0.00 3.27
751 783 7.710475 CCATTTTTCCTATACAAAATTCGCCAT 59.290 33.333 0.00 0.00 31.54 4.40
793 825 7.605691 AGTTAACTGAGAAGGATGTTGAGAATG 59.394 37.037 7.48 0.00 0.00 2.67
794 826 7.684529 AGTTAACTGAGAAGGATGTTGAGAAT 58.315 34.615 7.48 0.00 0.00 2.40
795 827 7.067496 AGTTAACTGAGAAGGATGTTGAGAA 57.933 36.000 7.48 0.00 0.00 2.87
796 828 6.672266 AGTTAACTGAGAAGGATGTTGAGA 57.328 37.500 7.48 0.00 0.00 3.27
797 829 9.442047 AATTAGTTAACTGAGAAGGATGTTGAG 57.558 33.333 18.56 0.00 0.00 3.02
798 830 9.793259 AAATTAGTTAACTGAGAAGGATGTTGA 57.207 29.630 18.56 0.00 0.00 3.18
799 831 9.831737 CAAATTAGTTAACTGAGAAGGATGTTG 57.168 33.333 18.56 4.52 0.00 3.33
800 832 9.793259 TCAAATTAGTTAACTGAGAAGGATGTT 57.207 29.630 18.56 0.00 0.00 2.71
801 833 9.793259 TTCAAATTAGTTAACTGAGAAGGATGT 57.207 29.630 18.56 0.00 0.00 3.06
805 837 9.346725 GCAATTCAAATTAGTTAACTGAGAAGG 57.653 33.333 18.56 10.94 0.00 3.46
807 839 9.897744 CAGCAATTCAAATTAGTTAACTGAGAA 57.102 29.630 18.56 13.51 0.00 2.87
808 840 9.066892 ACAGCAATTCAAATTAGTTAACTGAGA 57.933 29.630 18.56 4.63 0.00 3.27
809 841 9.334693 GACAGCAATTCAAATTAGTTAACTGAG 57.665 33.333 18.56 3.69 0.00 3.35
810 842 8.015087 CGACAGCAATTCAAATTAGTTAACTGA 58.985 33.333 18.56 10.67 0.00 3.41
811 843 7.271223 CCGACAGCAATTCAAATTAGTTAACTG 59.729 37.037 18.56 1.85 0.00 3.16
812 844 7.040686 ACCGACAGCAATTCAAATTAGTTAACT 60.041 33.333 13.68 13.68 0.00 2.24
813 845 7.060633 CACCGACAGCAATTCAAATTAGTTAAC 59.939 37.037 0.00 0.00 0.00 2.01
814 846 7.081349 CACCGACAGCAATTCAAATTAGTTAA 58.919 34.615 0.00 0.00 0.00 2.01
815 847 6.607689 CACCGACAGCAATTCAAATTAGTTA 58.392 36.000 0.00 0.00 0.00 2.24
816 848 5.460646 CACCGACAGCAATTCAAATTAGTT 58.539 37.500 0.00 0.00 0.00 2.24
817 849 4.615912 GCACCGACAGCAATTCAAATTAGT 60.616 41.667 0.00 0.00 0.00 2.24
818 850 3.853671 GCACCGACAGCAATTCAAATTAG 59.146 43.478 0.00 0.00 0.00 1.73
819 851 3.366883 GGCACCGACAGCAATTCAAATTA 60.367 43.478 0.00 0.00 0.00 1.40
820 852 2.610232 GGCACCGACAGCAATTCAAATT 60.610 45.455 0.00 0.00 0.00 1.82
821 853 1.067635 GGCACCGACAGCAATTCAAAT 60.068 47.619 0.00 0.00 0.00 2.32
822 854 0.313672 GGCACCGACAGCAATTCAAA 59.686 50.000 0.00 0.00 0.00 2.69
823 855 1.523154 GGGCACCGACAGCAATTCAA 61.523 55.000 0.00 0.00 40.86 2.69
824 856 1.971167 GGGCACCGACAGCAATTCA 60.971 57.895 0.00 0.00 40.86 2.57
825 857 2.877691 GGGCACCGACAGCAATTC 59.122 61.111 0.00 0.00 40.86 2.17
849 881 8.685536 GTCAAGGTATTTTCGATGTACGTATAC 58.314 37.037 0.00 0.00 43.13 1.47
850 882 7.862372 GGTCAAGGTATTTTCGATGTACGTATA 59.138 37.037 0.00 0.00 43.13 1.47
851 883 6.698766 GGTCAAGGTATTTTCGATGTACGTAT 59.301 38.462 0.00 0.00 43.13 3.06
853 885 4.866486 GGTCAAGGTATTTTCGATGTACGT 59.134 41.667 0.00 0.00 43.13 3.57
856 888 9.621629 ATTATTGGTCAAGGTATTTTCGATGTA 57.378 29.630 0.00 0.00 0.00 2.29
857 889 7.931578 TTATTGGTCAAGGTATTTTCGATGT 57.068 32.000 0.00 0.00 0.00 3.06
858 890 8.076178 GGATTATTGGTCAAGGTATTTTCGATG 58.924 37.037 0.00 0.00 0.00 3.84
859 891 7.041372 CGGATTATTGGTCAAGGTATTTTCGAT 60.041 37.037 0.00 0.00 0.00 3.59
860 892 6.259167 CGGATTATTGGTCAAGGTATTTTCGA 59.741 38.462 0.00 0.00 0.00 3.71
861 893 6.259167 TCGGATTATTGGTCAAGGTATTTTCG 59.741 38.462 0.00 0.00 0.00 3.46
862 894 7.562454 TCGGATTATTGGTCAAGGTATTTTC 57.438 36.000 0.00 0.00 0.00 2.29
863 895 7.416326 GCTTCGGATTATTGGTCAAGGTATTTT 60.416 37.037 0.00 0.00 0.00 1.82
866 898 5.063880 GCTTCGGATTATTGGTCAAGGTAT 58.936 41.667 0.00 0.00 0.00 2.73
870 902 4.635765 TCTTGCTTCGGATTATTGGTCAAG 59.364 41.667 0.00 0.00 0.00 3.02
871 903 4.584874 TCTTGCTTCGGATTATTGGTCAA 58.415 39.130 0.00 0.00 0.00 3.18
872 904 4.191544 CTCTTGCTTCGGATTATTGGTCA 58.808 43.478 0.00 0.00 0.00 4.02
873 905 3.561725 CCTCTTGCTTCGGATTATTGGTC 59.438 47.826 0.00 0.00 0.00 4.02
874 906 3.054361 ACCTCTTGCTTCGGATTATTGGT 60.054 43.478 0.00 0.00 0.00 3.67
875 907 3.545703 ACCTCTTGCTTCGGATTATTGG 58.454 45.455 0.00 0.00 0.00 3.16
876 908 4.913376 CAACCTCTTGCTTCGGATTATTG 58.087 43.478 0.00 0.00 0.00 1.90
890 922 7.017319 ACTTAACTAACTATGGCAACCTCTT 57.983 36.000 0.00 0.00 0.00 2.85
892 924 6.985059 CCTACTTAACTAACTATGGCAACCTC 59.015 42.308 0.00 0.00 0.00 3.85
895 927 7.101700 ACACCTACTTAACTAACTATGGCAAC 58.898 38.462 0.00 0.00 0.00 4.17
897 929 6.405065 CGACACCTACTTAACTAACTATGGCA 60.405 42.308 0.00 0.00 0.00 4.92
908 940 2.457970 GCCGATCGACACCTACTTAAC 58.542 52.381 18.66 0.00 0.00 2.01
909 941 1.406539 GGCCGATCGACACCTACTTAA 59.593 52.381 18.66 0.00 0.00 1.85
912 944 1.076923 AGGCCGATCGACACCTACT 60.077 57.895 18.66 0.00 0.00 2.57
915 947 0.395311 TTAGAGGCCGATCGACACCT 60.395 55.000 18.66 19.43 34.43 4.00
916 948 0.674534 ATTAGAGGCCGATCGACACC 59.325 55.000 18.66 14.82 0.00 4.16
917 949 1.609555 AGATTAGAGGCCGATCGACAC 59.390 52.381 18.66 7.86 0.00 3.67
918 950 1.609072 CAGATTAGAGGCCGATCGACA 59.391 52.381 18.66 0.00 0.00 4.35
920 952 0.598562 GCAGATTAGAGGCCGATCGA 59.401 55.000 18.66 0.00 0.00 3.59
922 954 2.615869 GATGCAGATTAGAGGCCGATC 58.384 52.381 0.00 0.00 0.00 3.69
923 955 1.067283 CGATGCAGATTAGAGGCCGAT 60.067 52.381 0.00 0.00 0.00 4.18
925 957 0.315251 TCGATGCAGATTAGAGGCCG 59.685 55.000 0.00 0.00 0.00 6.13
926 958 1.615883 TCTCGATGCAGATTAGAGGCC 59.384 52.381 0.00 0.00 0.00 5.19
927 959 2.556189 TCTCTCGATGCAGATTAGAGGC 59.444 50.000 14.55 0.00 35.47 4.70
929 961 3.667695 CGCTCTCTCGATGCAGATTAGAG 60.668 52.174 10.39 10.39 35.23 2.43
930 962 2.225255 CGCTCTCTCGATGCAGATTAGA 59.775 50.000 0.00 0.00 0.00 2.10
932 964 2.031595 GTCGCTCTCTCGATGCAGATTA 60.032 50.000 0.00 0.00 40.84 1.75
934 966 0.310543 GTCGCTCTCTCGATGCAGAT 59.689 55.000 0.00 0.00 40.84 2.90
941 973 0.605589 TCAACTGGTCGCTCTCTCGA 60.606 55.000 0.00 0.00 35.95 4.04
946 978 1.806461 TTCGCTCAACTGGTCGCTCT 61.806 55.000 0.00 0.00 0.00 4.09
949 981 0.944311 TCTTTCGCTCAACTGGTCGC 60.944 55.000 0.00 0.00 0.00 5.19
974 1006 3.586892 CTCTTTCGTGGACTAGGTTTCC 58.413 50.000 0.00 0.00 0.00 3.13
975 1007 2.994578 GCTCTTTCGTGGACTAGGTTTC 59.005 50.000 0.00 0.00 0.00 2.78
976 1008 2.367567 TGCTCTTTCGTGGACTAGGTTT 59.632 45.455 0.00 0.00 0.00 3.27
977 1009 1.968493 TGCTCTTTCGTGGACTAGGTT 59.032 47.619 0.00 0.00 0.00 3.50
991 1024 3.371380 GGGAAGTTCATCATCCTGCTCTT 60.371 47.826 5.01 0.00 34.66 2.85
992 1025 2.172293 GGGAAGTTCATCATCCTGCTCT 59.828 50.000 5.01 0.00 34.66 4.09
999 1032 3.274288 GGTCACAGGGAAGTTCATCATC 58.726 50.000 5.01 0.00 0.00 2.92
1000 1033 2.644299 TGGTCACAGGGAAGTTCATCAT 59.356 45.455 5.01 0.00 0.00 2.45
1001 1034 2.054021 TGGTCACAGGGAAGTTCATCA 58.946 47.619 5.01 0.00 0.00 3.07
1008 1041 0.109342 AGCACTTGGTCACAGGGAAG 59.891 55.000 0.00 0.00 0.00 3.46
1086 1119 1.673665 GCAGCCCTTGTCAGTGGAG 60.674 63.158 0.00 0.00 0.00 3.86
1138 1171 4.873129 CTCGTGGATCGGGCGGTG 62.873 72.222 3.13 0.00 40.32 4.94
1161 1194 2.954868 GCACGCCGTATGGTCTCG 60.955 66.667 2.17 0.20 37.67 4.04
1191 1224 1.335882 GGGGGTAGTAGTGGACCAGC 61.336 65.000 0.00 0.00 37.47 4.85
1298 1331 1.203237 ACCTGACATCCTCCAGAGTGT 60.203 52.381 0.00 0.00 32.37 3.55
1392 1425 2.184830 CATCATCACCAGCGGGCAG 61.185 63.158 1.46 0.00 37.90 4.85
1402 1441 0.108186 TCGGTGACCTGCATCATCAC 60.108 55.000 13.89 13.89 41.68 3.06
1789 1831 2.542907 CCGTGAAAACCAGCAGCGT 61.543 57.895 0.00 0.00 0.00 5.07
1956 1998 3.696051 GCTTGTAATCTCCAAGGATGCAA 59.304 43.478 0.00 0.00 39.72 4.08
2106 2148 0.830023 TCCACGTCACCTCCATGTCA 60.830 55.000 0.00 0.00 0.00 3.58
2148 2914 1.664306 GTCCTTCCTCGAACACGGT 59.336 57.895 0.00 0.00 0.00 4.83
2218 2984 1.147824 CCAGCTCGGCATGGAATCT 59.852 57.895 0.00 0.00 39.02 2.40
2256 3022 0.588252 CACTCGAACAGGTTGCTTGG 59.412 55.000 0.00 0.00 0.00 3.61
2259 3025 1.598130 GGCACTCGAACAGGTTGCT 60.598 57.895 0.00 0.00 0.00 3.91
2263 3029 2.743718 CAGGGCACTCGAACAGGT 59.256 61.111 0.00 0.00 0.00 4.00
2276 3042 1.813092 CGAGGAGAATGAATGGCAGGG 60.813 57.143 0.00 0.00 0.00 4.45
2277 3043 1.139654 TCGAGGAGAATGAATGGCAGG 59.860 52.381 0.00 0.00 0.00 4.85
2278 3044 2.609427 TCGAGGAGAATGAATGGCAG 57.391 50.000 0.00 0.00 0.00 4.85
2279 3045 3.470709 GAATCGAGGAGAATGAATGGCA 58.529 45.455 0.00 0.00 0.00 4.92
2280 3046 2.478134 CGAATCGAGGAGAATGAATGGC 59.522 50.000 0.00 0.00 0.00 4.40
2281 3047 3.722147 ACGAATCGAGGAGAATGAATGG 58.278 45.455 10.55 0.00 0.00 3.16
2287 3053 4.566004 TGAAACAACGAATCGAGGAGAAT 58.434 39.130 10.55 0.00 0.00 2.40
2308 3074 5.686841 TGAATCACAAAAGCGATCAAACTTG 59.313 36.000 0.00 0.00 0.00 3.16
2313 3079 5.412286 TCTGATGAATCACAAAAGCGATCAA 59.588 36.000 0.00 0.00 32.50 2.57
2315 3081 5.475273 TCTGATGAATCACAAAAGCGATC 57.525 39.130 0.00 0.00 32.50 3.69
2316 3082 5.821470 AGATCTGATGAATCACAAAAGCGAT 59.179 36.000 0.00 0.00 32.50 4.58
2317 3083 5.181009 AGATCTGATGAATCACAAAAGCGA 58.819 37.500 0.00 0.00 32.50 4.93
2318 3084 5.481200 AGATCTGATGAATCACAAAAGCG 57.519 39.130 0.00 0.00 32.50 4.68
2319 3085 5.515626 GCAAGATCTGATGAATCACAAAAGC 59.484 40.000 0.00 0.00 32.50 3.51
2320 3086 6.034591 GGCAAGATCTGATGAATCACAAAAG 58.965 40.000 0.00 0.00 32.50 2.27
2321 3087 5.477637 TGGCAAGATCTGATGAATCACAAAA 59.522 36.000 0.00 0.00 32.50 2.44
2322 3088 5.011586 TGGCAAGATCTGATGAATCACAAA 58.988 37.500 0.00 0.00 32.50 2.83
2323 3089 4.591929 TGGCAAGATCTGATGAATCACAA 58.408 39.130 0.00 0.00 32.50 3.33
2324 3090 4.224991 TGGCAAGATCTGATGAATCACA 57.775 40.909 0.00 0.00 32.50 3.58
2325 3091 4.495349 CGTTGGCAAGATCTGATGAATCAC 60.495 45.833 0.00 0.00 32.50 3.06
2326 3092 3.624410 CGTTGGCAAGATCTGATGAATCA 59.376 43.478 0.00 0.00 35.16 2.57
2327 3093 3.003068 CCGTTGGCAAGATCTGATGAATC 59.997 47.826 0.00 0.00 0.00 2.52
2328 3094 2.947652 CCGTTGGCAAGATCTGATGAAT 59.052 45.455 0.00 0.00 0.00 2.57
2329 3095 2.358957 CCGTTGGCAAGATCTGATGAA 58.641 47.619 0.00 0.00 0.00 2.57
2330 3096 2.028420 CCGTTGGCAAGATCTGATGA 57.972 50.000 0.00 0.00 0.00 2.92
2356 3122 3.854809 GTGTTGCAGCGTTGAAACTTAAA 59.145 39.130 21.91 0.98 42.45 1.52
2359 3125 1.793714 CGTGTTGCAGCGTTGAAACTT 60.794 47.619 21.91 0.00 42.45 2.66
2375 3141 2.108514 CATGAATCTGCCCGCGTGT 61.109 57.895 4.92 0.00 0.00 4.49
2376 3142 0.809636 TACATGAATCTGCCCGCGTG 60.810 55.000 4.92 0.00 0.00 5.34
2377 3143 0.106708 ATACATGAATCTGCCCGCGT 59.893 50.000 4.92 0.00 0.00 6.01
2378 3144 1.229428 AATACATGAATCTGCCCGCG 58.771 50.000 0.00 0.00 0.00 6.46
2400 3166 9.672673 GCCTATTGGAGATGCTCTAATAAATAA 57.327 33.333 12.31 0.00 41.15 1.40
2401 3167 7.981789 CGCCTATTGGAGATGCTCTAATAAATA 59.018 37.037 12.31 0.00 41.15 1.40
2405 3171 4.382040 GCGCCTATTGGAGATGCTCTAATA 60.382 45.833 11.19 11.19 40.95 0.98
2551 3317 7.902387 ATATGTGTATCGAGTCGTAGTACAT 57.098 36.000 21.49 21.60 0.00 2.29
2657 3506 8.355272 ACTATCTACGCACTATCTATGTATCG 57.645 38.462 0.00 0.00 0.00 2.92
2750 3624 1.826921 GGAGGACATCGCCGAGGTA 60.827 63.158 3.67 0.00 0.00 3.08
2758 3632 2.049475 GACGTCGGAGGAGGACATCG 62.049 65.000 0.00 0.00 34.04 3.84
2818 3692 1.007964 CTAGGAGCAGCGTCATCCG 60.008 63.158 0.00 0.00 38.20 4.18
2863 3737 3.441011 GAGGACCGGTGTATGCGGG 62.441 68.421 14.63 0.00 35.32 6.13
2872 3746 2.905880 CCTATCGCGAGGACCGGT 60.906 66.667 16.66 6.92 39.15 5.28
3173 4073 2.328099 GGCACCTTTGAGACAGCCG 61.328 63.158 0.00 0.00 31.88 5.52


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

AutoCloner maintained by Alex Coulton.