Multiple sequence alignment - TraesCS7D01G436800

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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 TraesCS7D01G436800 chr7D 100.000 4911 0 0 1 4911 556119912 556124822 0.000000e+00 9070.0
1 TraesCS7D01G436800 chr7D 81.922 874 83 40 3868 4719 555628168 555627348 0.000000e+00 669.0
2 TraesCS7D01G436800 chr7D 82.566 717 66 25 4204 4911 555828459 555827793 1.190000e-160 577.0
3 TraesCS7D01G436800 chr7D 80.671 507 55 20 4205 4709 555535158 555534693 2.170000e-93 353.0
4 TraesCS7D01G436800 chr7D 97.222 72 2 0 3312 3383 509193996 509194067 6.680000e-24 122.0
5 TraesCS7D01G436800 chr7D 89.412 85 8 1 3142 3226 555628780 555628697 6.720000e-19 106.0
6 TraesCS7D01G436800 chr7B 90.816 3419 127 74 5 3311 602937340 602940683 0.000000e+00 4401.0
7 TraesCS7D01G436800 chr7B 88.097 1529 103 35 3386 4899 602940686 602942150 0.000000e+00 1742.0
8 TraesCS7D01G436800 chr7B 87.258 620 49 14 4062 4664 602570901 602570295 0.000000e+00 680.0
9 TraesCS7D01G436800 chr7A 94.124 2723 79 28 651 3311 641581719 641579016 0.000000e+00 4067.0
10 TraesCS7D01G436800 chr7A 86.325 1053 89 29 3681 4701 641578593 641577564 0.000000e+00 1096.0
11 TraesCS7D01G436800 chr7A 89.791 431 37 5 3384 3812 641579015 641578590 3.340000e-151 545.0
12 TraesCS7D01G436800 chr7A 92.825 223 10 5 4189 4410 641949899 641950116 7.930000e-83 318.0
13 TraesCS7D01G436800 chr7A 88.085 235 22 4 4477 4706 641950141 641950374 1.740000e-69 274.0
14 TraesCS7D01G436800 chr7A 84.926 272 23 13 3745 4014 641453248 641452993 4.880000e-65 259.0
15 TraesCS7D01G436800 chr7A 93.827 81 1 1 470 550 641581831 641581755 8.640000e-23 119.0
16 TraesCS7D01G436800 chr1A 81.453 647 89 20 1058 1675 278141927 278142571 7.340000e-138 501.0
17 TraesCS7D01G436800 chr1A 86.842 76 10 0 2534 2609 278144855 278144930 8.760000e-13 86.1
18 TraesCS7D01G436800 chr1D 81.298 647 90 20 1058 1675 217143023 217143667 3.410000e-136 496.0
19 TraesCS7D01G436800 chr1D 100.000 68 0 0 3316 3383 212427242 212427309 5.160000e-25 126.0
20 TraesCS7D01G436800 chr1D 86.842 76 10 0 2534 2609 217145985 217146060 8.760000e-13 86.1
21 TraesCS7D01G436800 chr2A 81.135 652 88 23 1044 1675 623564703 623564067 1.590000e-134 490.0
22 TraesCS7D01G436800 chr1B 80.763 655 88 25 1058 1675 310927107 310927760 1.240000e-130 477.0
23 TraesCS7D01G436800 chr1B 100.000 72 0 0 3312 3383 135175032 135175103 3.080000e-27 134.0
24 TraesCS7D01G436800 chr1B 100.000 72 0 0 3312 3383 135179150 135179221 3.080000e-27 134.0
25 TraesCS7D01G436800 chr1B 98.611 72 1 0 3312 3383 135140578 135140507 1.430000e-25 128.0
26 TraesCS7D01G436800 chr1B 98.611 72 1 0 3312 3383 135144567 135144638 1.430000e-25 128.0
27 TraesCS7D01G436800 chr1B 98.611 72 1 0 3312 3383 135150807 135150878 1.430000e-25 128.0
28 TraesCS7D01G436800 chr1B 85.526 76 11 0 2534 2609 310930097 310930172 4.070000e-11 80.5
29 TraesCS7D01G436800 chr6A 80.800 625 103 11 1064 1675 415907619 415906999 1.600000e-129 473.0
30 TraesCS7D01G436800 chr2D 79.911 677 100 23 1021 1675 480778644 480777982 9.630000e-127 464.0
31 TraesCS7D01G436800 chr2B 80.093 648 98 21 1045 1675 563924047 563923414 2.080000e-123 453.0
32 TraesCS7D01G436800 chr4D 100.000 72 0 0 3312 3383 35780678 35780607 3.080000e-27 134.0
33 TraesCS7D01G436800 chr6B 98.611 72 1 0 3312 3383 562110263 562110334 1.430000e-25 128.0


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 TraesCS7D01G436800 chr7D 556119912 556124822 4910 False 9070.00 9070 100.00000 1 4911 1 chr7D.!!$F2 4910
1 TraesCS7D01G436800 chr7D 555827793 555828459 666 True 577.00 577 82.56600 4204 4911 1 chr7D.!!$R2 707
2 TraesCS7D01G436800 chr7D 555627348 555628780 1432 True 387.50 669 85.66700 3142 4719 2 chr7D.!!$R3 1577
3 TraesCS7D01G436800 chr7B 602937340 602942150 4810 False 3071.50 4401 89.45650 5 4899 2 chr7B.!!$F1 4894
4 TraesCS7D01G436800 chr7B 602570295 602570901 606 True 680.00 680 87.25800 4062 4664 1 chr7B.!!$R1 602
5 TraesCS7D01G436800 chr7A 641577564 641581831 4267 True 1456.75 4067 91.01675 470 4701 4 chr7A.!!$R2 4231
6 TraesCS7D01G436800 chr1A 278141927 278144930 3003 False 293.55 501 84.14750 1058 2609 2 chr1A.!!$F1 1551
7 TraesCS7D01G436800 chr1D 217143023 217146060 3037 False 291.05 496 84.07000 1058 2609 2 chr1D.!!$F2 1551
8 TraesCS7D01G436800 chr2A 623564067 623564703 636 True 490.00 490 81.13500 1044 1675 1 chr2A.!!$R1 631
9 TraesCS7D01G436800 chr1B 310927107 310930172 3065 False 278.75 477 83.14450 1058 2609 2 chr1B.!!$F5 1551
10 TraesCS7D01G436800 chr6A 415906999 415907619 620 True 473.00 473 80.80000 1064 1675 1 chr6A.!!$R1 611
11 TraesCS7D01G436800 chr2D 480777982 480778644 662 True 464.00 464 79.91100 1021 1675 1 chr2D.!!$R1 654
12 TraesCS7D01G436800 chr2B 563923414 563924047 633 True 453.00 453 80.09300 1045 1675 1 chr2B.!!$R1 630

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
47 48 0.108898 AGAGCGAGAGTCACACATGC 60.109 55.000 0.00 0.0 0.00 4.06 F
327 348 0.173481 TGAACTGCTACTGCTAGGCG 59.827 55.000 0.00 0.0 40.48 5.52 F
667 712 0.255318 CTTTGGAGGGATCTGCTGCT 59.745 55.000 0.00 0.0 32.15 4.24 F
841 907 0.586319 TTTCTCTTGTGCCTTTCGCG 59.414 50.000 0.00 0.0 42.08 5.87 F
2387 4159 2.053865 CATGCCGGCCATTCACCTT 61.054 57.895 26.77 0.0 29.71 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 1997 1.228063 CCTCGCCCCCATCATCTTG 60.228 63.158 0.00 0.0 0.00 3.02 R
2270 3488 1.668419 GCACAAGGCCATAGTACCAG 58.332 55.000 5.01 0.0 36.11 4.00 R
2402 4174 1.893786 GCAGAGCTTCTTCCGAGGA 59.106 57.895 0.00 0.0 0.00 3.71 R
2423 4195 2.363406 AGGTCGGGGTAGAACGGG 60.363 66.667 0.00 0.0 32.02 5.28 R
4385 6552 0.253894 CCAGCCATGTCCACATCTCA 59.746 55.000 0.00 0.0 33.61 3.27 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
41 42 0.527385 GCCATGAGAGCGAGAGTCAC 60.527 60.000 0.00 0.00 0.00 3.67
42 43 0.813821 CCATGAGAGCGAGAGTCACA 59.186 55.000 0.00 0.00 0.00 3.58
43 44 1.468908 CCATGAGAGCGAGAGTCACAC 60.469 57.143 0.00 0.00 0.00 3.82
44 45 1.200948 CATGAGAGCGAGAGTCACACA 59.799 52.381 0.00 0.00 0.00 3.72
45 46 1.539157 TGAGAGCGAGAGTCACACAT 58.461 50.000 0.00 0.00 0.00 3.21
46 47 1.200948 TGAGAGCGAGAGTCACACATG 59.799 52.381 0.00 0.00 0.00 3.21
47 48 0.108898 AGAGCGAGAGTCACACATGC 60.109 55.000 0.00 0.00 0.00 4.06
49 50 1.374631 GCGAGAGTCACACATGCCA 60.375 57.895 0.00 0.00 0.00 4.92
50 51 0.742281 GCGAGAGTCACACATGCCAT 60.742 55.000 0.00 0.00 0.00 4.40
52 53 1.134877 CGAGAGTCACACATGCCATCT 60.135 52.381 0.00 0.00 0.00 2.90
54 55 1.134877 AGAGTCACACATGCCATCTCG 60.135 52.381 0.00 0.00 0.00 4.04
55 56 0.897621 AGTCACACATGCCATCTCGA 59.102 50.000 0.00 0.00 0.00 4.04
56 57 1.483827 AGTCACACATGCCATCTCGAT 59.516 47.619 0.00 0.00 0.00 3.59
57 58 2.093288 AGTCACACATGCCATCTCGATT 60.093 45.455 0.00 0.00 0.00 3.34
58 59 2.679837 GTCACACATGCCATCTCGATTT 59.320 45.455 0.00 0.00 0.00 2.17
59 60 2.938451 TCACACATGCCATCTCGATTTC 59.062 45.455 0.00 0.00 0.00 2.17
60 61 2.032550 CACACATGCCATCTCGATTTCC 59.967 50.000 0.00 0.00 0.00 3.13
62 63 2.882761 CACATGCCATCTCGATTTCCAT 59.117 45.455 0.00 0.00 0.00 3.41
85 86 3.334691 CTTTTCCGATGAGTAACAGGCA 58.665 45.455 0.00 0.00 0.00 4.75
91 92 0.321671 ATGAGTAACAGGCAGTGCGT 59.678 50.000 9.45 6.79 0.00 5.24
94 95 0.600255 AGTAACAGGCAGTGCGTGAC 60.600 55.000 36.86 26.63 45.68 3.67
124 125 5.839517 TGGATACTACTCCTACTCCTACC 57.160 47.826 0.00 0.00 36.20 3.18
125 126 5.229966 TGGATACTACTCCTACTCCTACCA 58.770 45.833 0.00 0.00 36.20 3.25
134 135 0.612732 TACTCCTACCACCACCACCG 60.613 60.000 0.00 0.00 0.00 4.94
147 148 0.748005 ACCACCGCCACTAATGATGC 60.748 55.000 0.00 0.00 0.00 3.91
156 157 5.213913 GCCACTAATGATGCGATGATTAG 57.786 43.478 11.11 11.11 40.73 1.73
158 159 4.934001 CCACTAATGATGCGATGATTAGCT 59.066 41.667 12.01 0.00 39.22 3.32
159 160 5.410746 CCACTAATGATGCGATGATTAGCTT 59.589 40.000 12.01 0.00 39.22 3.74
209 230 3.947132 CTGGCGAGGCAGTGGACTG 62.947 68.421 17.16 2.19 46.40 3.51
217 238 0.955919 GGCAGTGGACTGGTGTTAGC 60.956 60.000 8.82 0.00 43.94 3.09
223 244 2.561419 GTGGACTGGTGTTAGCAGAGTA 59.439 50.000 14.20 0.00 45.98 2.59
224 245 2.561419 TGGACTGGTGTTAGCAGAGTAC 59.439 50.000 14.20 0.00 45.98 2.73
225 246 2.826725 GGACTGGTGTTAGCAGAGTACT 59.173 50.000 14.20 0.00 45.98 2.73
226 247 3.119424 GGACTGGTGTTAGCAGAGTACTC 60.119 52.174 15.41 15.41 45.98 2.59
227 248 2.826725 ACTGGTGTTAGCAGAGTACTCC 59.173 50.000 19.38 5.15 45.98 3.85
228 249 3.093057 CTGGTGTTAGCAGAGTACTCCT 58.907 50.000 19.38 12.45 45.98 3.69
229 250 4.263816 ACTGGTGTTAGCAGAGTACTCCTA 60.264 45.833 19.38 11.46 45.98 2.94
230 251 4.015084 TGGTGTTAGCAGAGTACTCCTAC 58.985 47.826 19.38 9.08 0.00 3.18
231 252 3.380954 GGTGTTAGCAGAGTACTCCTACC 59.619 52.174 19.38 10.64 0.00 3.18
248 269 3.502211 CCTACCAGTAGCACCTTTTTGTG 59.498 47.826 0.00 0.00 39.29 3.33
261 282 1.034838 TTTTGTGCACGCTGGGAACT 61.035 50.000 13.13 0.00 0.00 3.01
267 288 1.569479 GCACGCTGGGAACTGAACTC 61.569 60.000 0.00 0.00 0.00 3.01
271 292 1.810031 CGCTGGGAACTGAACTCAACA 60.810 52.381 0.00 0.00 0.00 3.33
272 293 1.604278 GCTGGGAACTGAACTCAACAC 59.396 52.381 0.00 0.00 0.00 3.32
273 294 2.917933 CTGGGAACTGAACTCAACACA 58.082 47.619 0.00 0.00 0.00 3.72
274 295 3.278574 CTGGGAACTGAACTCAACACAA 58.721 45.455 0.00 0.00 0.00 3.33
275 296 3.013921 TGGGAACTGAACTCAACACAAC 58.986 45.455 0.00 0.00 0.00 3.32
298 319 0.793861 TCCGATCCGAAACAAAAGCG 59.206 50.000 0.00 0.00 0.00 4.68
322 343 1.517242 GCAACTGAACTGCTACTGCT 58.483 50.000 0.00 0.00 40.48 4.24
323 344 2.688507 GCAACTGAACTGCTACTGCTA 58.311 47.619 0.00 0.00 40.48 3.49
324 345 2.670414 GCAACTGAACTGCTACTGCTAG 59.330 50.000 0.00 0.00 40.48 3.42
325 346 3.257393 CAACTGAACTGCTACTGCTAGG 58.743 50.000 0.00 0.00 40.48 3.02
326 347 1.205893 ACTGAACTGCTACTGCTAGGC 59.794 52.381 0.00 0.00 40.48 3.93
327 348 0.173481 TGAACTGCTACTGCTAGGCG 59.827 55.000 0.00 0.00 40.48 5.52
328 349 0.456221 GAACTGCTACTGCTAGGCGA 59.544 55.000 0.00 0.00 40.48 5.54
329 350 0.457851 AACTGCTACTGCTAGGCGAG 59.542 55.000 0.00 0.00 40.48 5.03
358 379 9.599322 GTCCATAGTTTATTCATTCATTAAGCG 57.401 33.333 0.00 0.00 0.00 4.68
364 385 4.558538 ATTCATTCATTAAGCGGCTCAC 57.441 40.909 1.45 0.00 0.00 3.51
365 386 2.984562 TCATTCATTAAGCGGCTCACA 58.015 42.857 1.45 0.00 0.00 3.58
367 388 3.755905 TCATTCATTAAGCGGCTCACAAA 59.244 39.130 1.45 0.00 0.00 2.83
368 389 3.829886 TTCATTAAGCGGCTCACAAAG 57.170 42.857 1.45 0.00 0.00 2.77
369 390 2.778299 TCATTAAGCGGCTCACAAAGT 58.222 42.857 1.45 0.00 0.00 2.66
372 393 2.380084 TAAGCGGCTCACAAAGTAGG 57.620 50.000 1.45 0.00 0.00 3.18
373 394 0.321653 AAGCGGCTCACAAAGTAGGG 60.322 55.000 1.45 0.00 0.00 3.53
391 421 0.318784 GGTACTCGCCTAATCCGCTG 60.319 60.000 0.00 0.00 0.00 5.18
409 439 0.328258 TGCCCTTTAGCCTTGACCTC 59.672 55.000 0.00 0.00 0.00 3.85
410 440 0.394488 GCCCTTTAGCCTTGACCTCC 60.394 60.000 0.00 0.00 0.00 4.30
411 441 0.256177 CCCTTTAGCCTTGACCTCCC 59.744 60.000 0.00 0.00 0.00 4.30
412 442 1.290134 CCTTTAGCCTTGACCTCCCT 58.710 55.000 0.00 0.00 0.00 4.20
413 443 1.210722 CCTTTAGCCTTGACCTCCCTC 59.789 57.143 0.00 0.00 0.00 4.30
431 461 3.066814 CCCTTTGCTGCTGCCCTC 61.067 66.667 13.47 0.00 38.71 4.30
432 462 3.066814 CCTTTGCTGCTGCCCTCC 61.067 66.667 13.47 0.00 38.71 4.30
433 463 3.437795 CTTTGCTGCTGCCCTCCG 61.438 66.667 13.47 0.00 38.71 4.63
564 605 4.038804 CAGGGGAGGGGAGGGGAA 62.039 72.222 0.00 0.00 0.00 3.97
570 611 3.711782 AGGGGAGGGGAAGGAGGG 61.712 72.222 0.00 0.00 0.00 4.30
648 693 4.838486 CTGTCCGTCCTCGCTCGC 62.838 72.222 0.00 0.00 35.54 5.03
667 712 0.255318 CTTTGGAGGGATCTGCTGCT 59.745 55.000 0.00 0.00 32.15 4.24
756 818 4.736896 GTCGGGGCTCGCTTTCGT 62.737 66.667 0.00 0.00 39.05 3.85
757 819 4.735132 TCGGGGCTCGCTTTCGTG 62.735 66.667 0.00 0.00 39.05 4.35
768 830 2.384899 GCTTTCGTGCGTTCTTCTTT 57.615 45.000 0.00 0.00 0.00 2.52
812 878 3.307059 CGTCTCTGACCCCAAAATTCTCT 60.307 47.826 0.00 0.00 0.00 3.10
813 879 4.257731 GTCTCTGACCCCAAAATTCTCTC 58.742 47.826 0.00 0.00 0.00 3.20
814 880 4.019771 GTCTCTGACCCCAAAATTCTCTCT 60.020 45.833 0.00 0.00 0.00 3.10
815 881 4.599241 TCTCTGACCCCAAAATTCTCTCTT 59.401 41.667 0.00 0.00 0.00 2.85
841 907 0.586319 TTTCTCTTGTGCCTTTCGCG 59.414 50.000 0.00 0.00 42.08 5.87
957 1041 5.744887 GCCTAATTCTGGTGGGATTATTCGA 60.745 44.000 0.00 0.00 0.00 3.71
1758 1967 2.418669 GGGGGATTCTCCATGTTCCTA 58.581 52.381 4.63 0.00 38.64 2.94
1785 1997 3.723348 GAGGACGGCGGCAACAAC 61.723 66.667 17.61 0.00 0.00 3.32
1786 1998 4.555709 AGGACGGCGGCAACAACA 62.556 61.111 17.61 0.00 0.00 3.33
1929 2165 2.343758 GAGTTCTGCGTGAGGGCA 59.656 61.111 0.00 0.00 41.45 5.36
2137 2477 4.828387 TCTCCATCACTCATCTCATCTCTG 59.172 45.833 0.00 0.00 0.00 3.35
2387 4159 2.053865 CATGCCGGCCATTCACCTT 61.054 57.895 26.77 0.00 29.71 3.50
2402 4174 2.262915 CTTGCTCCGTTCTCGCCT 59.737 61.111 0.00 0.00 35.54 5.52
2423 4195 0.800300 CTCGGAAGAAGCTCTGCGTC 60.800 60.000 0.00 0.00 41.32 5.19
2751 4538 1.337703 GCAATCACCAGAGCAACAACA 59.662 47.619 0.00 0.00 0.00 3.33
2752 4539 2.223782 GCAATCACCAGAGCAACAACAA 60.224 45.455 0.00 0.00 0.00 2.83
2753 4540 3.635331 CAATCACCAGAGCAACAACAAG 58.365 45.455 0.00 0.00 0.00 3.16
2777 4564 2.670414 GTCAGATGTCAAGAAGGCTTCG 59.330 50.000 20.78 8.58 31.75 3.79
2851 4638 2.491675 GGTAACTCTGGGGGTTTCTG 57.508 55.000 0.00 0.00 0.00 3.02
2874 4661 0.758123 ATCTGCTGCTAGGAAGAGCC 59.242 55.000 0.00 0.00 42.11 4.70
2882 4669 1.761009 GCTAGGAAGAGCCCCTCTGAT 60.761 57.143 0.00 0.00 40.28 2.90
2958 4745 2.673368 CAGAATGGCACTACGAAGAACC 59.327 50.000 0.00 0.00 0.00 3.62
3075 4862 2.510238 GGCGCACGCTTGATCTCT 60.510 61.111 15.36 0.00 41.60 3.10
3140 4927 3.823873 ACATGTTCGGTATGGAAAAAGCA 59.176 39.130 0.00 0.00 0.00 3.91
3312 5103 9.643693 AATGCTTGGTAAGTCATTTTAGAATTG 57.356 29.630 0.00 0.00 34.12 2.32
3313 5104 8.402798 TGCTTGGTAAGTCATTTTAGAATTGA 57.597 30.769 0.00 0.00 0.00 2.57
3314 5105 9.023962 TGCTTGGTAAGTCATTTTAGAATTGAT 57.976 29.630 0.00 0.00 0.00 2.57
3315 5106 9.508567 GCTTGGTAAGTCATTTTAGAATTGATC 57.491 33.333 0.00 0.00 0.00 2.92
3318 5109 9.739276 TGGTAAGTCATTTTAGAATTGATCACT 57.261 29.630 0.00 0.00 0.00 3.41
3319 5110 9.994432 GGTAAGTCATTTTAGAATTGATCACTG 57.006 33.333 0.00 0.00 0.00 3.66
3323 5114 8.734386 AGTCATTTTAGAATTGATCACTGAACC 58.266 33.333 0.00 0.00 0.00 3.62
3324 5115 8.734386 GTCATTTTAGAATTGATCACTGAACCT 58.266 33.333 0.00 0.00 0.00 3.50
3325 5116 9.300681 TCATTTTAGAATTGATCACTGAACCTT 57.699 29.630 0.00 0.00 0.00 3.50
3326 5117 9.918630 CATTTTAGAATTGATCACTGAACCTTT 57.081 29.630 0.00 0.00 0.00 3.11
3328 5119 9.748708 TTTTAGAATTGATCACTGAACCTTTTG 57.251 29.630 0.00 0.00 0.00 2.44
3329 5120 8.690203 TTAGAATTGATCACTGAACCTTTTGA 57.310 30.769 0.00 0.00 0.00 2.69
3330 5121 7.771927 AGAATTGATCACTGAACCTTTTGAT 57.228 32.000 0.00 0.00 0.00 2.57
3331 5122 8.868522 AGAATTGATCACTGAACCTTTTGATA 57.131 30.769 0.00 0.00 0.00 2.15
3332 5123 8.954350 AGAATTGATCACTGAACCTTTTGATAG 58.046 33.333 0.00 0.00 0.00 2.08
3333 5124 6.500684 TTGATCACTGAACCTTTTGATAGC 57.499 37.500 0.00 0.00 0.00 2.97
3334 5125 4.631377 TGATCACTGAACCTTTTGATAGCG 59.369 41.667 0.00 0.00 0.00 4.26
3335 5126 4.265904 TCACTGAACCTTTTGATAGCGA 57.734 40.909 0.00 0.00 0.00 4.93
3336 5127 4.832248 TCACTGAACCTTTTGATAGCGAT 58.168 39.130 0.00 0.00 0.00 4.58
3337 5128 4.631377 TCACTGAACCTTTTGATAGCGATG 59.369 41.667 0.00 0.00 0.00 3.84
3338 5129 4.631377 CACTGAACCTTTTGATAGCGATGA 59.369 41.667 0.00 0.00 0.00 2.92
3339 5130 4.872691 ACTGAACCTTTTGATAGCGATGAG 59.127 41.667 0.00 0.00 0.00 2.90
3340 5131 4.832248 TGAACCTTTTGATAGCGATGAGT 58.168 39.130 0.00 0.00 0.00 3.41
3341 5132 5.245531 TGAACCTTTTGATAGCGATGAGTT 58.754 37.500 0.00 0.00 0.00 3.01
3342 5133 5.122239 TGAACCTTTTGATAGCGATGAGTTG 59.878 40.000 0.00 0.00 0.00 3.16
3343 5134 4.579869 ACCTTTTGATAGCGATGAGTTGT 58.420 39.130 0.00 0.00 0.00 3.32
3344 5135 5.003804 ACCTTTTGATAGCGATGAGTTGTT 58.996 37.500 0.00 0.00 0.00 2.83
3345 5136 5.106555 ACCTTTTGATAGCGATGAGTTGTTG 60.107 40.000 0.00 0.00 0.00 3.33
3346 5137 4.340894 TTTGATAGCGATGAGTTGTTGC 57.659 40.909 0.00 0.00 0.00 4.17
3347 5138 3.251479 TGATAGCGATGAGTTGTTGCT 57.749 42.857 0.00 0.00 39.57 3.91
3348 5139 2.931969 TGATAGCGATGAGTTGTTGCTG 59.068 45.455 0.00 0.00 36.95 4.41
3349 5140 2.741759 TAGCGATGAGTTGTTGCTGA 57.258 45.000 0.00 0.00 36.95 4.26
3350 5141 1.882912 AGCGATGAGTTGTTGCTGAA 58.117 45.000 0.00 0.00 35.05 3.02
3351 5142 1.802960 AGCGATGAGTTGTTGCTGAAG 59.197 47.619 0.00 0.00 35.05 3.02
3352 5143 1.532868 GCGATGAGTTGTTGCTGAAGT 59.467 47.619 0.00 0.00 0.00 3.01
3353 5144 2.412065 GCGATGAGTTGTTGCTGAAGTC 60.412 50.000 0.00 0.00 0.00 3.01
3354 5145 3.062763 CGATGAGTTGTTGCTGAAGTCT 58.937 45.455 0.00 0.00 0.00 3.24
3355 5146 3.122613 CGATGAGTTGTTGCTGAAGTCTC 59.877 47.826 0.00 0.00 0.00 3.36
3356 5147 3.827008 TGAGTTGTTGCTGAAGTCTCT 57.173 42.857 0.00 0.00 0.00 3.10
3357 5148 3.722147 TGAGTTGTTGCTGAAGTCTCTC 58.278 45.455 0.00 0.00 0.00 3.20
3358 5149 2.728839 GAGTTGTTGCTGAAGTCTCTCG 59.271 50.000 0.00 0.00 0.00 4.04
3359 5150 1.795286 GTTGTTGCTGAAGTCTCTCGG 59.205 52.381 0.00 0.00 0.00 4.63
3360 5151 1.040646 TGTTGCTGAAGTCTCTCGGT 58.959 50.000 0.00 0.00 0.00 4.69
3361 5152 1.412710 TGTTGCTGAAGTCTCTCGGTT 59.587 47.619 0.00 0.00 0.00 4.44
3362 5153 2.158957 TGTTGCTGAAGTCTCTCGGTTT 60.159 45.455 0.00 0.00 0.00 3.27
3363 5154 2.872858 GTTGCTGAAGTCTCTCGGTTTT 59.127 45.455 0.00 0.00 0.00 2.43
3364 5155 2.755650 TGCTGAAGTCTCTCGGTTTTC 58.244 47.619 0.00 0.00 0.00 2.29
3365 5156 2.365617 TGCTGAAGTCTCTCGGTTTTCT 59.634 45.455 0.00 0.00 0.00 2.52
3366 5157 3.181465 TGCTGAAGTCTCTCGGTTTTCTT 60.181 43.478 0.00 0.00 0.00 2.52
3367 5158 3.185391 GCTGAAGTCTCTCGGTTTTCTTG 59.815 47.826 0.00 0.00 0.00 3.02
3368 5159 4.621991 CTGAAGTCTCTCGGTTTTCTTGA 58.378 43.478 0.00 0.00 0.00 3.02
3369 5160 5.018539 TGAAGTCTCTCGGTTTTCTTGAA 57.981 39.130 0.00 0.00 0.00 2.69
3370 5161 5.424757 TGAAGTCTCTCGGTTTTCTTGAAA 58.575 37.500 0.00 0.00 0.00 2.69
3371 5162 5.293569 TGAAGTCTCTCGGTTTTCTTGAAAC 59.706 40.000 0.00 0.00 45.53 2.78
3372 5163 5.024785 AGTCTCTCGGTTTTCTTGAAACT 57.975 39.130 0.00 0.00 45.55 2.66
3373 5164 5.429130 AGTCTCTCGGTTTTCTTGAAACTT 58.571 37.500 0.00 0.00 45.55 2.66
3374 5165 5.294552 AGTCTCTCGGTTTTCTTGAAACTTG 59.705 40.000 0.00 0.00 45.55 3.16
3375 5166 4.574828 TCTCTCGGTTTTCTTGAAACTTGG 59.425 41.667 0.00 0.00 45.55 3.61
3376 5167 3.066203 TCTCGGTTTTCTTGAAACTTGGC 59.934 43.478 0.00 0.00 45.55 4.52
3377 5168 3.020984 TCGGTTTTCTTGAAACTTGGCT 58.979 40.909 0.00 0.00 45.55 4.75
3378 5169 3.445805 TCGGTTTTCTTGAAACTTGGCTT 59.554 39.130 0.00 0.00 45.55 4.35
3379 5170 4.081917 TCGGTTTTCTTGAAACTTGGCTTT 60.082 37.500 0.00 0.00 45.55 3.51
3380 5171 4.032786 CGGTTTTCTTGAAACTTGGCTTTG 59.967 41.667 0.00 0.00 45.55 2.77
3381 5172 4.332543 GGTTTTCTTGAAACTTGGCTTTGG 59.667 41.667 0.00 0.00 45.55 3.28
3382 5173 2.888834 TCTTGAAACTTGGCTTTGGC 57.111 45.000 0.00 0.00 37.82 4.52
3401 5192 3.268334 TGGCCAGTTAGGTATTTGGTCAT 59.732 43.478 0.00 0.00 40.17 3.06
3402 5193 3.632145 GGCCAGTTAGGTATTTGGTCATG 59.368 47.826 0.00 0.00 40.61 3.07
3431 5226 6.096846 ACTCTTCAAATGTAAGTGGCAGTTTT 59.903 34.615 13.62 0.00 0.00 2.43
3523 5319 3.623848 TTGACCTCAACATCACCCG 57.376 52.632 0.00 0.00 0.00 5.28
3707 5504 1.409427 GTTCCCTCCGATGACCACTAG 59.591 57.143 0.00 0.00 0.00 2.57
3737 5534 6.626302 CCTTACTGTTGAAGGAAACAAAACA 58.374 36.000 3.69 0.00 45.52 2.83
3739 5536 7.435192 CCTTACTGTTGAAGGAAACAAAACATC 59.565 37.037 3.69 0.00 45.52 3.06
3740 5537 6.279513 ACTGTTGAAGGAAACAAAACATCA 57.720 33.333 0.00 0.00 39.47 3.07
3742 5539 6.980397 ACTGTTGAAGGAAACAAAACATCATC 59.020 34.615 0.00 0.00 39.47 2.92
3743 5540 5.976534 TGTTGAAGGAAACAAAACATCATCG 59.023 36.000 0.00 0.00 37.12 3.84
3745 5542 5.757886 TGAAGGAAACAAAACATCATCGTC 58.242 37.500 0.00 0.00 0.00 4.20
3746 5543 5.530915 TGAAGGAAACAAAACATCATCGTCT 59.469 36.000 0.00 0.00 0.00 4.18
3747 5544 6.039270 TGAAGGAAACAAAACATCATCGTCTT 59.961 34.615 0.00 0.00 0.00 3.01
3749 5738 5.765182 AGGAAACAAAACATCATCGTCTTCT 59.235 36.000 0.00 0.00 0.00 2.85
3752 5741 4.067896 ACAAAACATCATCGTCTTCTGCT 58.932 39.130 0.00 0.00 0.00 4.24
3779 5768 6.088616 GTGCAATTTTCTTTCTCATTTCTCCG 59.911 38.462 0.00 0.00 0.00 4.63
3802 5791 6.528423 CCGTTTCTTGTTCAGACTAGATACTG 59.472 42.308 0.00 3.47 37.41 2.74
3824 5934 7.875971 ACTGACCTATTTAGAAAACTTTGCTG 58.124 34.615 0.00 0.00 0.00 4.41
3954 6069 0.388134 CGCCACTTGTACGTACAGCT 60.388 55.000 26.04 13.80 37.52 4.24
3959 6074 1.690352 ACTTGTACGTACAGCTGGGTT 59.310 47.619 26.04 0.00 37.52 4.11
3962 6077 1.000060 TGTACGTACAGCTGGGTTGAC 60.000 52.381 24.10 10.70 0.00 3.18
4015 6133 1.543802 GAGAGCATAGATAGCGTGGCT 59.456 52.381 0.00 0.00 43.41 4.75
4021 6139 1.388837 TAGATAGCGTGGCTGCGGAA 61.389 55.000 0.00 0.00 40.10 4.30
4023 6141 1.153168 ATAGCGTGGCTGCGGAATT 60.153 52.632 0.00 0.00 40.10 2.17
4151 6288 4.520111 TGGTGATCCATGAACAGTTTTCTG 59.480 41.667 0.00 0.00 44.90 3.02
4250 6395 0.959372 CTTGCTGCAAGTCCTGGGAG 60.959 60.000 29.38 6.04 36.79 4.30
4270 6415 5.890419 GGGAGGAATGAATGTCTGAATCTTT 59.110 40.000 0.00 0.00 0.00 2.52
4272 6417 7.416101 GGGAGGAATGAATGTCTGAATCTTTTC 60.416 40.741 0.00 0.00 0.00 2.29
4281 6426 7.814264 ATGTCTGAATCTTTTCTTGTTCTGT 57.186 32.000 0.00 0.00 32.78 3.41
4282 6427 7.019774 TGTCTGAATCTTTTCTTGTTCTGTG 57.980 36.000 0.00 0.00 32.78 3.66
4283 6428 6.823182 TGTCTGAATCTTTTCTTGTTCTGTGA 59.177 34.615 0.00 0.00 32.78 3.58
4454 6621 4.785453 GGCCAGCTCTCCGGTTGG 62.785 72.222 0.00 4.39 0.00 3.77
4541 6708 1.000359 TGGCGATCTGGACTGGAGA 60.000 57.895 0.00 0.00 0.00 3.71
4543 6710 1.739049 GCGATCTGGACTGGAGAGG 59.261 63.158 0.00 0.00 0.00 3.69
4544 6711 1.739049 CGATCTGGACTGGAGAGGC 59.261 63.158 0.00 0.00 0.00 4.70
4545 6712 1.039785 CGATCTGGACTGGAGAGGCA 61.040 60.000 0.00 0.00 0.00 4.75
4547 6714 0.690411 ATCTGGACTGGAGAGGCAGG 60.690 60.000 0.00 0.00 0.00 4.85
4548 6715 2.284921 TGGACTGGAGAGGCAGGG 60.285 66.667 0.00 0.00 0.00 4.45
4550 6717 1.383803 GGACTGGAGAGGCAGGGAT 60.384 63.158 0.00 0.00 0.00 3.85
4555 6726 2.509916 GAGAGGCAGGGATGGCAG 59.490 66.667 4.56 0.00 36.76 4.85
4567 6738 2.605873 TGGCAGGCCAACAAAGGA 59.394 55.556 11.25 0.00 44.12 3.36
4658 6841 1.669760 CACGGCGCTTTCCTAACCA 60.670 57.895 6.90 0.00 0.00 3.67
4681 6864 0.322816 ATGTGTGTAGGCCAAGGCTG 60.323 55.000 5.01 0.00 39.30 4.85
4724 6907 2.671682 GGACAGGCCCTGGTTCTC 59.328 66.667 16.70 2.90 35.51 2.87
4725 6908 1.920835 GGACAGGCCCTGGTTCTCT 60.921 63.158 16.70 0.00 35.51 3.10
4726 6909 1.492993 GGACAGGCCCTGGTTCTCTT 61.493 60.000 16.70 0.00 35.51 2.85
4727 6910 0.402121 GACAGGCCCTGGTTCTCTTT 59.598 55.000 16.70 0.00 35.51 2.52
4728 6911 0.853530 ACAGGCCCTGGTTCTCTTTT 59.146 50.000 16.70 0.00 35.51 2.27
4729 6912 1.217942 ACAGGCCCTGGTTCTCTTTTT 59.782 47.619 16.70 0.00 35.51 1.94
4760 6943 5.010282 GGGTGTCATATCTTGTTCTTTGGT 58.990 41.667 0.00 0.00 0.00 3.67
4767 6950 6.265196 TCATATCTTGTTCTTTGGTTGCTGTT 59.735 34.615 0.00 0.00 0.00 3.16
4789 6972 8.835467 TGTTGAAAGTCGTTTTTATCTTGAAG 57.165 30.769 0.00 0.00 0.00 3.02
4790 6973 8.670135 TGTTGAAAGTCGTTTTTATCTTGAAGA 58.330 29.630 0.00 0.00 0.00 2.87
4797 6980 8.088981 AGTCGTTTTTATCTTGAAGAGAGCTTA 58.911 33.333 0.00 0.00 37.93 3.09
4819 7003 0.923358 TGTGAAGTGTGAACCCCCTT 59.077 50.000 0.00 0.00 0.00 3.95
4836 7020 1.705186 CCTTCCTTTTCACCCCTCTCA 59.295 52.381 0.00 0.00 0.00 3.27
4843 7027 3.874383 TTTCACCCCTCTCATTTGTCA 57.126 42.857 0.00 0.00 0.00 3.58
4844 7028 3.423539 TTCACCCCTCTCATTTGTCAG 57.576 47.619 0.00 0.00 0.00 3.51
4881 7065 2.234908 CCTCTCTCCTTTGATCGGTGTT 59.765 50.000 0.00 0.00 0.00 3.32
4884 7068 2.996621 CTCTCCTTTGATCGGTGTTGTC 59.003 50.000 0.00 0.00 0.00 3.18
4899 7083 3.067106 TGTTGTCTCGATCTTCTTTGCC 58.933 45.455 0.00 0.00 0.00 4.52
4901 7085 1.066143 TGTCTCGATCTTCTTTGCCCC 60.066 52.381 0.00 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.511373 GGCTATGCTGTGATCACCAACTATA 60.511 44.000 22.85 12.50 0.00 1.31
1 2 4.384056 GCTATGCTGTGATCACCAACTAT 58.616 43.478 22.85 12.07 0.00 2.12
2 3 3.432186 GGCTATGCTGTGATCACCAACTA 60.432 47.826 22.85 8.83 0.00 2.24
3 4 2.636830 GCTATGCTGTGATCACCAACT 58.363 47.619 22.85 8.16 0.00 3.16
7 8 1.878088 CATGGCTATGCTGTGATCACC 59.122 52.381 22.85 9.16 0.00 4.02
16 17 0.317799 CTCGCTCTCATGGCTATGCT 59.682 55.000 4.95 0.00 34.21 3.79
21 22 0.682532 TGACTCTCGCTCTCATGGCT 60.683 55.000 0.00 0.00 0.00 4.75
41 42 2.291365 TGGAAATCGAGATGGCATGTG 58.709 47.619 3.81 0.00 0.00 3.21
42 43 2.715749 TGGAAATCGAGATGGCATGT 57.284 45.000 3.81 0.00 0.00 3.21
43 44 2.351447 GCATGGAAATCGAGATGGCATG 60.351 50.000 3.81 0.00 0.00 4.06
44 45 1.884579 GCATGGAAATCGAGATGGCAT 59.115 47.619 0.00 0.00 0.00 4.40
45 46 1.134007 AGCATGGAAATCGAGATGGCA 60.134 47.619 0.00 0.00 0.00 4.92
46 47 1.602311 AGCATGGAAATCGAGATGGC 58.398 50.000 0.00 0.00 0.00 4.40
47 48 4.498682 GGAAAAGCATGGAAATCGAGATGG 60.499 45.833 0.00 0.00 0.00 3.51
49 50 3.313526 CGGAAAAGCATGGAAATCGAGAT 59.686 43.478 0.00 0.00 0.00 2.75
50 51 2.677836 CGGAAAAGCATGGAAATCGAGA 59.322 45.455 0.00 0.00 0.00 4.04
52 53 2.705730 TCGGAAAAGCATGGAAATCGA 58.294 42.857 0.00 0.00 0.00 3.59
54 55 4.096984 ACTCATCGGAAAAGCATGGAAATC 59.903 41.667 0.00 0.00 0.00 2.17
55 56 4.019174 ACTCATCGGAAAAGCATGGAAAT 58.981 39.130 0.00 0.00 0.00 2.17
56 57 3.420893 ACTCATCGGAAAAGCATGGAAA 58.579 40.909 0.00 0.00 0.00 3.13
57 58 3.071874 ACTCATCGGAAAAGCATGGAA 57.928 42.857 0.00 0.00 0.00 3.53
58 59 2.787473 ACTCATCGGAAAAGCATGGA 57.213 45.000 0.00 0.00 0.00 3.41
59 60 3.689161 TGTTACTCATCGGAAAAGCATGG 59.311 43.478 0.00 0.00 0.00 3.66
60 61 4.201851 CCTGTTACTCATCGGAAAAGCATG 60.202 45.833 0.00 0.00 0.00 4.06
62 63 3.334691 CCTGTTACTCATCGGAAAAGCA 58.665 45.455 0.00 0.00 0.00 3.91
85 86 1.080501 CATCACTCCGTCACGCACT 60.081 57.895 0.00 0.00 0.00 4.40
91 92 4.135306 GAGTAGTATCCATCACTCCGTCA 58.865 47.826 0.00 0.00 32.93 4.35
101 102 5.856160 TGGTAGGAGTAGGAGTAGTATCCAT 59.144 44.000 0.00 0.00 42.26 3.41
110 111 1.006878 GGTGGTGGTAGGAGTAGGAGT 59.993 57.143 0.00 0.00 0.00 3.85
114 115 1.192428 GGTGGTGGTGGTAGGAGTAG 58.808 60.000 0.00 0.00 0.00 2.57
115 116 0.612732 CGGTGGTGGTGGTAGGAGTA 60.613 60.000 0.00 0.00 0.00 2.59
116 117 1.911766 CGGTGGTGGTGGTAGGAGT 60.912 63.158 0.00 0.00 0.00 3.85
124 125 1.002624 ATTAGTGGCGGTGGTGGTG 60.003 57.895 0.00 0.00 0.00 4.17
125 126 1.002624 CATTAGTGGCGGTGGTGGT 60.003 57.895 0.00 0.00 0.00 4.16
134 135 4.436584 GCTAATCATCGCATCATTAGTGGC 60.437 45.833 0.00 0.00 34.06 5.01
147 148 1.845809 GCGGGCCAAGCTAATCATCG 61.846 60.000 14.33 0.38 0.00 3.84
184 201 4.166888 TGCCTCGCCAGCTGATCC 62.167 66.667 17.39 1.86 0.00 3.36
185 202 2.588314 CTGCCTCGCCAGCTGATC 60.588 66.667 17.39 5.53 0.00 2.92
187 204 4.383861 CACTGCCTCGCCAGCTGA 62.384 66.667 17.39 0.00 36.29 4.26
192 213 4.007644 CAGTCCACTGCCTCGCCA 62.008 66.667 0.00 0.00 37.15 5.69
196 217 0.685097 TAACACCAGTCCACTGCCTC 59.315 55.000 0.76 0.00 42.47 4.70
209 230 3.380954 GGTAGGAGTACTCTGCTAACACC 59.619 52.174 21.88 11.95 46.77 4.16
217 238 3.628487 GTGCTACTGGTAGGAGTACTCTG 59.372 52.174 21.88 8.44 34.15 3.35
223 244 2.625282 AAGGTGCTACTGGTAGGAGT 57.375 50.000 9.43 0.00 34.15 3.85
224 245 3.983044 AAAAGGTGCTACTGGTAGGAG 57.017 47.619 9.43 0.00 34.15 3.69
225 246 3.393278 ACAAAAAGGTGCTACTGGTAGGA 59.607 43.478 9.43 4.10 33.87 2.94
226 247 3.502211 CACAAAAAGGTGCTACTGGTAGG 59.498 47.826 9.43 0.00 33.87 3.18
227 248 4.749245 CACAAAAAGGTGCTACTGGTAG 57.251 45.455 3.62 3.62 36.29 3.18
248 269 1.569479 GAGTTCAGTTCCCAGCGTGC 61.569 60.000 0.00 0.00 0.00 5.34
250 271 0.468226 TTGAGTTCAGTTCCCAGCGT 59.532 50.000 0.00 0.00 0.00 5.07
261 282 3.130633 CGGATCAGTTGTGTTGAGTTCA 58.869 45.455 0.00 0.00 0.00 3.18
267 288 1.660607 CGGATCGGATCAGTTGTGTTG 59.339 52.381 18.99 0.00 0.00 3.33
271 292 2.028476 TGTTTCGGATCGGATCAGTTGT 60.028 45.455 18.99 0.00 0.00 3.32
272 293 2.616960 TGTTTCGGATCGGATCAGTTG 58.383 47.619 18.99 6.41 0.00 3.16
273 294 3.328382 TTGTTTCGGATCGGATCAGTT 57.672 42.857 18.99 0.00 0.00 3.16
274 295 3.328382 TTTGTTTCGGATCGGATCAGT 57.672 42.857 18.99 0.00 0.00 3.41
275 296 3.485877 GCTTTTGTTTCGGATCGGATCAG 60.486 47.826 18.99 15.15 0.00 2.90
298 319 2.558313 GCAGTTCAGTTGCTCGCC 59.442 61.111 0.00 0.00 38.51 5.54
321 342 1.323412 ACTATGGACTGCTCGCCTAG 58.677 55.000 0.00 0.00 0.00 3.02
322 343 1.776662 AACTATGGACTGCTCGCCTA 58.223 50.000 0.00 0.00 0.00 3.93
323 344 0.905357 AAACTATGGACTGCTCGCCT 59.095 50.000 0.00 0.00 0.00 5.52
324 345 2.596904 TAAACTATGGACTGCTCGCC 57.403 50.000 0.00 0.00 0.00 5.54
325 346 4.119862 TGAATAAACTATGGACTGCTCGC 58.880 43.478 0.00 0.00 0.00 5.03
326 347 6.479990 TGAATGAATAAACTATGGACTGCTCG 59.520 38.462 0.00 0.00 0.00 5.03
327 348 7.792374 TGAATGAATAAACTATGGACTGCTC 57.208 36.000 0.00 0.00 0.00 4.26
328 349 8.757982 AATGAATGAATAAACTATGGACTGCT 57.242 30.769 0.00 0.00 0.00 4.24
332 353 9.599322 CGCTTAATGAATGAATAAACTATGGAC 57.401 33.333 0.00 0.00 0.00 4.02
333 354 8.783093 CCGCTTAATGAATGAATAAACTATGGA 58.217 33.333 0.00 0.00 0.00 3.41
334 355 7.538678 GCCGCTTAATGAATGAATAAACTATGG 59.461 37.037 0.00 0.00 0.00 2.74
335 356 8.292448 AGCCGCTTAATGAATGAATAAACTATG 58.708 33.333 0.00 0.00 0.00 2.23
358 379 2.416972 CGAGTACCCTACTTTGTGAGCC 60.417 54.545 0.00 0.00 39.59 4.70
364 385 4.501058 GGATTAGGCGAGTACCCTACTTTG 60.501 50.000 0.00 0.00 39.59 2.77
365 386 3.640498 GGATTAGGCGAGTACCCTACTTT 59.360 47.826 0.00 0.00 39.59 2.66
367 388 2.813354 CGGATTAGGCGAGTACCCTACT 60.813 54.545 0.00 0.00 42.86 2.57
368 389 1.538950 CGGATTAGGCGAGTACCCTAC 59.461 57.143 0.00 0.00 34.78 3.18
369 390 1.901591 CGGATTAGGCGAGTACCCTA 58.098 55.000 0.00 0.00 33.88 3.53
372 393 0.318784 CAGCGGATTAGGCGAGTACC 60.319 60.000 0.00 0.00 35.00 3.34
373 394 0.940047 GCAGCGGATTAGGCGAGTAC 60.940 60.000 0.00 0.00 35.00 2.73
391 421 0.394488 GGAGGTCAAGGCTAAAGGGC 60.394 60.000 0.00 0.00 41.20 5.19
409 439 2.362120 CAGCAGCAAAGGGGAGGG 60.362 66.667 0.00 0.00 0.00 4.30
410 440 3.066814 GCAGCAGCAAAGGGGAGG 61.067 66.667 0.00 0.00 41.58 4.30
411 441 3.066814 GGCAGCAGCAAAGGGGAG 61.067 66.667 2.65 0.00 44.61 4.30
412 442 4.684134 GGGCAGCAGCAAAGGGGA 62.684 66.667 2.65 0.00 44.61 4.81
413 443 4.691359 AGGGCAGCAGCAAAGGGG 62.691 66.667 2.65 0.00 44.61 4.79
441 471 3.546714 CTAAATAGGGGCGGGGCGG 62.547 68.421 0.00 0.00 0.00 6.13
442 472 2.032071 CTAAATAGGGGCGGGGCG 59.968 66.667 0.00 0.00 0.00 6.13
443 473 2.282251 GCTAAATAGGGGCGGGGC 60.282 66.667 0.00 0.00 0.00 5.80
444 474 2.434774 GGCTAAATAGGGGCGGGG 59.565 66.667 0.00 0.00 0.00 5.73
445 475 2.125766 GAGGGCTAAATAGGGGCGGG 62.126 65.000 0.00 0.00 0.00 6.13
446 476 1.375326 GAGGGCTAAATAGGGGCGG 59.625 63.158 0.00 0.00 0.00 6.13
447 477 1.128188 AGGAGGGCTAAATAGGGGCG 61.128 60.000 0.00 0.00 0.00 6.13
448 478 0.402121 CAGGAGGGCTAAATAGGGGC 59.598 60.000 0.00 0.00 0.00 5.80
449 479 0.402121 GCAGGAGGGCTAAATAGGGG 59.598 60.000 0.00 0.00 0.00 4.79
450 480 0.035458 CGCAGGAGGGCTAAATAGGG 59.965 60.000 0.00 0.00 0.00 3.53
451 481 3.614399 CGCAGGAGGGCTAAATAGG 57.386 57.895 0.00 0.00 0.00 2.57
579 620 3.499929 TATGCGCCTCTGCTACGGC 62.500 63.158 4.18 0.00 42.86 5.68
583 624 0.179111 GTGTGTATGCGCCTCTGCTA 60.179 55.000 4.18 0.00 35.36 3.49
648 693 0.255318 AGCAGCAGATCCCTCCAAAG 59.745 55.000 0.00 0.00 0.00 2.77
755 817 4.273724 AGAGGAAAAGAAAGAAGAACGCAC 59.726 41.667 0.00 0.00 0.00 5.34
756 818 4.273480 CAGAGGAAAAGAAAGAAGAACGCA 59.727 41.667 0.00 0.00 0.00 5.24
757 819 4.777823 CAGAGGAAAAGAAAGAAGAACGC 58.222 43.478 0.00 0.00 0.00 4.84
758 820 4.609336 CGCAGAGGAAAAGAAAGAAGAACG 60.609 45.833 0.00 0.00 0.00 3.95
759 821 4.319839 CCGCAGAGGAAAAGAAAGAAGAAC 60.320 45.833 0.00 0.00 45.00 3.01
760 822 3.815401 CCGCAGAGGAAAAGAAAGAAGAA 59.185 43.478 0.00 0.00 45.00 2.52
761 823 3.403038 CCGCAGAGGAAAAGAAAGAAGA 58.597 45.455 0.00 0.00 45.00 2.87
762 824 2.095516 GCCGCAGAGGAAAAGAAAGAAG 60.096 50.000 0.00 0.00 45.00 2.85
763 825 1.880027 GCCGCAGAGGAAAAGAAAGAA 59.120 47.619 0.00 0.00 45.00 2.52
764 826 1.202758 TGCCGCAGAGGAAAAGAAAGA 60.203 47.619 0.00 0.00 45.00 2.52
768 830 1.672356 GCTGCCGCAGAGGAAAAGA 60.672 57.895 24.80 0.00 45.00 2.52
788 850 3.072476 AGAATTTTGGGGTCAGAGACGAA 59.928 43.478 0.00 0.00 32.65 3.85
789 851 2.637872 AGAATTTTGGGGTCAGAGACGA 59.362 45.455 0.00 0.00 32.65 4.20
812 878 5.440610 AGGCACAAGAGAAAGAAAGAAAGA 58.559 37.500 0.00 0.00 0.00 2.52
813 879 5.764487 AGGCACAAGAGAAAGAAAGAAAG 57.236 39.130 0.00 0.00 0.00 2.62
814 880 6.530019 AAAGGCACAAGAGAAAGAAAGAAA 57.470 33.333 0.00 0.00 0.00 2.52
815 881 5.220854 CGAAAGGCACAAGAGAAAGAAAGAA 60.221 40.000 0.00 0.00 0.00 2.52
841 907 2.748843 GCTCGCTGAGAAAGGCTGC 61.749 63.158 9.32 0.00 0.00 5.25
957 1041 4.409218 CGGCACAGCAGCGCAAAT 62.409 61.111 11.47 0.00 34.64 2.32
977 1064 3.314331 CCTCCACTCACCGCACCT 61.314 66.667 0.00 0.00 0.00 4.00
1784 1996 1.528824 CTCGCCCCCATCATCTTGT 59.471 57.895 0.00 0.00 0.00 3.16
1785 1997 1.228063 CCTCGCCCCCATCATCTTG 60.228 63.158 0.00 0.00 0.00 3.02
1786 1998 2.455565 CCCTCGCCCCCATCATCTT 61.456 63.158 0.00 0.00 0.00 2.40
2137 2477 9.915629 TGGATTTGTACACAATTTAATACAACC 57.084 29.630 0.00 5.52 37.28 3.77
2270 3488 1.668419 GCACAAGGCCATAGTACCAG 58.332 55.000 5.01 0.00 36.11 4.00
2387 4159 3.760035 GGAGGCGAGAACGGAGCA 61.760 66.667 0.00 0.00 40.15 4.26
2402 4174 1.893786 GCAGAGCTTCTTCCGAGGA 59.106 57.895 0.00 0.00 0.00 3.71
2423 4195 2.363406 AGGTCGGGGTAGAACGGG 60.363 66.667 0.00 0.00 32.02 5.28
2751 4538 4.041444 AGCCTTCTTGACATCTGACTTCTT 59.959 41.667 0.00 0.00 0.00 2.52
2752 4539 3.582208 AGCCTTCTTGACATCTGACTTCT 59.418 43.478 0.00 0.00 0.00 2.85
2753 4540 3.936564 AGCCTTCTTGACATCTGACTTC 58.063 45.455 0.00 0.00 0.00 3.01
2851 4638 1.759445 TCTTCCTAGCAGCAGATGGAC 59.241 52.381 0.00 0.00 0.00 4.02
2882 4669 1.355563 CGACTTCTCGGCGCTCATA 59.644 57.895 7.64 0.00 36.16 2.15
3140 4927 2.803030 AAACATGGCTCATCAGCTCT 57.197 45.000 0.00 0.00 46.03 4.09
3238 5028 4.469657 ACCTAATGCCTGAACAGAAACAA 58.530 39.130 3.19 0.00 0.00 2.83
3297 5088 8.734386 GGTTCAGTGATCAATTCTAAAATGACT 58.266 33.333 0.00 0.00 0.00 3.41
3311 5102 4.631377 CGCTATCAAAAGGTTCAGTGATCA 59.369 41.667 0.00 0.00 32.99 2.92
3312 5103 4.870426 TCGCTATCAAAAGGTTCAGTGATC 59.130 41.667 0.00 0.00 32.99 2.92
3313 5104 4.832248 TCGCTATCAAAAGGTTCAGTGAT 58.168 39.130 0.00 0.00 35.05 3.06
3314 5105 4.265904 TCGCTATCAAAAGGTTCAGTGA 57.734 40.909 0.00 0.00 0.00 3.41
3315 5106 4.631377 TCATCGCTATCAAAAGGTTCAGTG 59.369 41.667 0.00 0.00 0.00 3.66
3316 5107 4.832248 TCATCGCTATCAAAAGGTTCAGT 58.168 39.130 0.00 0.00 0.00 3.41
3317 5108 4.872691 ACTCATCGCTATCAAAAGGTTCAG 59.127 41.667 0.00 0.00 0.00 3.02
3318 5109 4.832248 ACTCATCGCTATCAAAAGGTTCA 58.168 39.130 0.00 0.00 0.00 3.18
3319 5110 5.122396 ACAACTCATCGCTATCAAAAGGTTC 59.878 40.000 0.00 0.00 0.00 3.62
3320 5111 5.003804 ACAACTCATCGCTATCAAAAGGTT 58.996 37.500 0.00 0.00 0.00 3.50
3321 5112 4.579869 ACAACTCATCGCTATCAAAAGGT 58.420 39.130 0.00 0.00 0.00 3.50
3322 5113 5.327091 CAACAACTCATCGCTATCAAAAGG 58.673 41.667 0.00 0.00 0.00 3.11
3323 5114 4.790140 GCAACAACTCATCGCTATCAAAAG 59.210 41.667 0.00 0.00 0.00 2.27
3324 5115 4.455533 AGCAACAACTCATCGCTATCAAAA 59.544 37.500 0.00 0.00 0.00 2.44
3325 5116 4.002982 AGCAACAACTCATCGCTATCAAA 58.997 39.130 0.00 0.00 0.00 2.69
3326 5117 3.371898 CAGCAACAACTCATCGCTATCAA 59.628 43.478 0.00 0.00 0.00 2.57
3327 5118 2.931969 CAGCAACAACTCATCGCTATCA 59.068 45.455 0.00 0.00 0.00 2.15
3328 5119 3.190079 TCAGCAACAACTCATCGCTATC 58.810 45.455 0.00 0.00 0.00 2.08
3329 5120 3.251479 TCAGCAACAACTCATCGCTAT 57.749 42.857 0.00 0.00 0.00 2.97
3330 5121 2.741759 TCAGCAACAACTCATCGCTA 57.258 45.000 0.00 0.00 0.00 4.26
3331 5122 1.802960 CTTCAGCAACAACTCATCGCT 59.197 47.619 0.00 0.00 0.00 4.93
3332 5123 1.532868 ACTTCAGCAACAACTCATCGC 59.467 47.619 0.00 0.00 0.00 4.58
3333 5124 3.062763 AGACTTCAGCAACAACTCATCG 58.937 45.455 0.00 0.00 0.00 3.84
3334 5125 4.314121 AGAGACTTCAGCAACAACTCATC 58.686 43.478 0.00 0.00 0.00 2.92
3335 5126 4.314121 GAGAGACTTCAGCAACAACTCAT 58.686 43.478 0.00 0.00 0.00 2.90
3336 5127 3.722147 GAGAGACTTCAGCAACAACTCA 58.278 45.455 0.00 0.00 0.00 3.41
3337 5128 2.728839 CGAGAGACTTCAGCAACAACTC 59.271 50.000 0.00 0.00 0.00 3.01
3338 5129 2.546795 CCGAGAGACTTCAGCAACAACT 60.547 50.000 0.00 0.00 0.00 3.16
3339 5130 1.795286 CCGAGAGACTTCAGCAACAAC 59.205 52.381 0.00 0.00 0.00 3.32
3340 5131 1.412710 ACCGAGAGACTTCAGCAACAA 59.587 47.619 0.00 0.00 0.00 2.83
3341 5132 1.040646 ACCGAGAGACTTCAGCAACA 58.959 50.000 0.00 0.00 0.00 3.33
3342 5133 2.156343 AACCGAGAGACTTCAGCAAC 57.844 50.000 0.00 0.00 0.00 4.17
3343 5134 2.910688 AAACCGAGAGACTTCAGCAA 57.089 45.000 0.00 0.00 0.00 3.91
3344 5135 2.365617 AGAAAACCGAGAGACTTCAGCA 59.634 45.455 0.00 0.00 0.00 4.41
3345 5136 3.033368 AGAAAACCGAGAGACTTCAGC 57.967 47.619 0.00 0.00 0.00 4.26
3346 5137 4.621991 TCAAGAAAACCGAGAGACTTCAG 58.378 43.478 0.00 0.00 0.00 3.02
3347 5138 4.665833 TCAAGAAAACCGAGAGACTTCA 57.334 40.909 0.00 0.00 0.00 3.02
3348 5139 5.739387 GTTTCAAGAAAACCGAGAGACTTC 58.261 41.667 0.00 0.00 41.23 3.01
3349 5140 5.736486 GTTTCAAGAAAACCGAGAGACTT 57.264 39.130 0.00 0.00 41.23 3.01
3359 5150 4.201812 GCCAAAGCCAAGTTTCAAGAAAAC 60.202 41.667 0.00 0.00 46.36 2.43
3360 5151 3.938334 GCCAAAGCCAAGTTTCAAGAAAA 59.062 39.130 0.00 0.00 31.33 2.29
3361 5152 3.530535 GCCAAAGCCAAGTTTCAAGAAA 58.469 40.909 0.00 0.00 0.00 2.52
3362 5153 3.177997 GCCAAAGCCAAGTTTCAAGAA 57.822 42.857 0.00 0.00 0.00 2.52
3363 5154 2.888834 GCCAAAGCCAAGTTTCAAGA 57.111 45.000 0.00 0.00 0.00 3.02
3375 5166 3.119137 CCAAATACCTAACTGGCCAAAGC 60.119 47.826 7.01 0.00 40.22 3.51
3376 5167 4.086457 ACCAAATACCTAACTGGCCAAAG 58.914 43.478 7.01 4.53 40.22 2.77
3377 5168 4.083565 GACCAAATACCTAACTGGCCAAA 58.916 43.478 7.01 0.00 40.22 3.28
3378 5169 3.074687 TGACCAAATACCTAACTGGCCAA 59.925 43.478 7.01 0.00 40.22 4.52
3379 5170 2.645297 TGACCAAATACCTAACTGGCCA 59.355 45.455 4.71 4.71 40.22 5.36
3380 5171 3.359695 TGACCAAATACCTAACTGGCC 57.640 47.619 0.00 0.00 40.22 5.36
3381 5172 4.270008 ACATGACCAAATACCTAACTGGC 58.730 43.478 0.00 0.00 40.22 4.85
3382 5173 4.881850 GGACATGACCAAATACCTAACTGG 59.118 45.833 9.48 0.00 42.93 4.00
3431 5226 8.995027 ACCAACAATGCTAATGGAATATTAGA 57.005 30.769 10.06 0.00 36.75 2.10
3551 5348 4.092279 TGATACAAATGTGGCCATTTCCA 58.908 39.130 9.72 1.34 45.92 3.53
3733 5530 4.867047 CACTAGCAGAAGACGATGATGTTT 59.133 41.667 0.00 0.00 0.00 2.83
3734 5531 4.428209 CACTAGCAGAAGACGATGATGTT 58.572 43.478 0.00 0.00 0.00 2.71
3736 5533 2.793790 GCACTAGCAGAAGACGATGATG 59.206 50.000 0.00 0.00 41.58 3.07
3737 5534 3.090952 GCACTAGCAGAAGACGATGAT 57.909 47.619 0.00 0.00 41.58 2.45
3752 5741 8.299570 GGAGAAATGAGAAAGAAAATTGCACTA 58.700 33.333 0.00 0.00 0.00 2.74
3758 5747 8.633561 AGAAACGGAGAAATGAGAAAGAAAATT 58.366 29.630 0.00 0.00 0.00 1.82
3763 5752 6.055588 ACAAGAAACGGAGAAATGAGAAAGA 58.944 36.000 0.00 0.00 0.00 2.52
3766 5755 5.820423 TGAACAAGAAACGGAGAAATGAGAA 59.180 36.000 0.00 0.00 0.00 2.87
3767 5756 5.364778 TGAACAAGAAACGGAGAAATGAGA 58.635 37.500 0.00 0.00 0.00 3.27
3768 5757 5.466728 TCTGAACAAGAAACGGAGAAATGAG 59.533 40.000 0.00 0.00 29.54 2.90
3769 5758 5.236478 GTCTGAACAAGAAACGGAGAAATGA 59.764 40.000 0.00 0.00 36.40 2.57
3770 5759 5.237344 AGTCTGAACAAGAAACGGAGAAATG 59.763 40.000 0.00 0.00 36.40 2.32
3771 5760 5.368989 AGTCTGAACAAGAAACGGAGAAAT 58.631 37.500 0.00 0.00 36.40 2.17
3779 5768 7.542824 GGTCAGTATCTAGTCTGAACAAGAAAC 59.457 40.741 18.09 6.70 44.74 2.78
3802 5791 7.040686 TCACCAGCAAAGTTTTCTAAATAGGTC 60.041 37.037 0.00 0.00 0.00 3.85
3824 5934 4.044426 GTGAAGTCACTGCAAAATTCACC 58.956 43.478 18.52 7.44 43.25 4.02
3903 6013 3.303938 CTTCCTCATTCCTCCTAGCTCA 58.696 50.000 0.00 0.00 0.00 4.26
4021 6139 1.669999 GCATCCAGGCTGCGGAAAAT 61.670 55.000 9.56 0.00 35.77 1.82
4023 6141 2.751436 GCATCCAGGCTGCGGAAA 60.751 61.111 9.56 0.00 35.77 3.13
4173 6313 5.912149 ACATCATCATAATGGGTGGTAGT 57.088 39.130 0.00 0.00 33.42 2.73
4250 6395 8.302438 ACAAGAAAAGATTCAGACATTCATTCC 58.698 33.333 0.00 0.00 38.06 3.01
4270 6415 5.978919 GCATGTTTTCATCACAGAACAAGAA 59.021 36.000 0.00 0.00 38.64 2.52
4272 6417 4.380678 CGCATGTTTTCATCACAGAACAAG 59.619 41.667 0.00 0.00 38.64 3.16
4281 6426 1.952990 ACCACACGCATGTTTTCATCA 59.047 42.857 0.00 0.00 38.64 3.07
4282 6427 2.584791 GACCACACGCATGTTTTCATC 58.415 47.619 0.00 0.00 38.64 2.92
4283 6428 1.269448 GGACCACACGCATGTTTTCAT 59.731 47.619 0.00 0.00 41.78 2.57
4385 6552 0.253894 CCAGCCATGTCCACATCTCA 59.746 55.000 0.00 0.00 33.61 3.27
4410 6577 3.849951 CTCGTCCCGTCCCATGGG 61.850 72.222 26.30 26.30 46.17 4.00
4421 6588 4.530857 CCGGCACCCATCTCGTCC 62.531 72.222 0.00 0.00 0.00 4.79
4453 6620 2.358247 ACATCACGCCGTGGAACC 60.358 61.111 18.32 0.00 33.87 3.62
4454 6621 1.225376 TTCACATCACGCCGTGGAAC 61.225 55.000 18.32 0.00 33.87 3.62
4543 6710 4.764771 TTGGCCTGCCATCCCTGC 62.765 66.667 12.40 0.00 46.64 4.85
4544 6711 2.757099 GTTGGCCTGCCATCCCTG 60.757 66.667 12.40 0.00 46.64 4.45
4545 6712 2.384933 TTTGTTGGCCTGCCATCCCT 62.385 55.000 12.40 0.00 46.64 4.20
4547 6714 1.593265 CTTTGTTGGCCTGCCATCC 59.407 57.895 12.40 6.55 46.64 3.51
4548 6715 0.899717 TCCTTTGTTGGCCTGCCATC 60.900 55.000 12.40 11.87 46.64 3.51
4550 6717 1.531365 CTCCTTTGTTGGCCTGCCA 60.531 57.895 6.80 6.80 45.63 4.92
4555 6726 1.531602 ACAGGCTCCTTTGTTGGCC 60.532 57.895 0.00 0.00 44.38 5.36
4567 6738 3.023949 GCTCCATCGACCACAGGCT 62.024 63.158 0.00 0.00 0.00 4.58
4658 6841 2.238521 CCTTGGCCTACACACATGTTT 58.761 47.619 3.32 0.00 40.48 2.83
4709 6892 0.853530 AAAAGAGAACCAGGGCCTGT 59.146 50.000 30.68 14.83 0.00 4.00
4727 6910 8.415950 ACAAGATATGACACCCATAACAAAAA 57.584 30.769 0.00 0.00 40.79 1.94
4728 6911 8.415950 AACAAGATATGACACCCATAACAAAA 57.584 30.769 0.00 0.00 40.79 2.44
4729 6912 7.888021 AGAACAAGATATGACACCCATAACAAA 59.112 33.333 0.00 0.00 40.79 2.83
4730 6913 7.402054 AGAACAAGATATGACACCCATAACAA 58.598 34.615 0.00 0.00 40.79 2.83
4731 6914 6.957631 AGAACAAGATATGACACCCATAACA 58.042 36.000 0.00 0.00 40.79 2.41
4732 6915 7.865706 AAGAACAAGATATGACACCCATAAC 57.134 36.000 0.00 0.00 40.79 1.89
4733 6916 7.339212 CCAAAGAACAAGATATGACACCCATAA 59.661 37.037 0.00 0.00 40.79 1.90
4734 6917 6.828273 CCAAAGAACAAGATATGACACCCATA 59.172 38.462 0.00 0.00 41.58 2.74
4735 6918 5.653769 CCAAAGAACAAGATATGACACCCAT 59.346 40.000 0.00 0.00 39.25 4.00
4736 6919 5.009631 CCAAAGAACAAGATATGACACCCA 58.990 41.667 0.00 0.00 0.00 4.51
4737 6920 5.010282 ACCAAAGAACAAGATATGACACCC 58.990 41.667 0.00 0.00 0.00 4.61
4738 6921 6.381801 CAACCAAAGAACAAGATATGACACC 58.618 40.000 0.00 0.00 0.00 4.16
4739 6922 5.858581 GCAACCAAAGAACAAGATATGACAC 59.141 40.000 0.00 0.00 0.00 3.67
4760 6943 6.791303 AGATAAAAACGACTTTCAACAGCAA 58.209 32.000 0.00 0.00 0.00 3.91
4767 6950 8.657074 TCTCTTCAAGATAAAAACGACTTTCA 57.343 30.769 0.00 0.00 0.00 2.69
4789 6972 3.005897 TCACACTTCACACCTAAGCTCTC 59.994 47.826 0.00 0.00 0.00 3.20
4790 6973 2.965831 TCACACTTCACACCTAAGCTCT 59.034 45.455 0.00 0.00 0.00 4.09
4797 6980 0.182775 GGGGTTCACACTTCACACCT 59.817 55.000 0.00 0.00 30.51 4.00
4819 7003 3.140144 ACAAATGAGAGGGGTGAAAAGGA 59.860 43.478 0.00 0.00 0.00 3.36
4852 7036 2.824388 AAAGGAGAGAGGGGACGGGG 62.824 65.000 0.00 0.00 0.00 5.73
4855 7039 1.410882 GATCAAAGGAGAGAGGGGACG 59.589 57.143 0.00 0.00 0.00 4.79
4856 7040 1.410882 CGATCAAAGGAGAGAGGGGAC 59.589 57.143 0.00 0.00 0.00 4.46
4857 7041 1.689575 CCGATCAAAGGAGAGAGGGGA 60.690 57.143 0.00 0.00 0.00 4.81
4858 7042 0.755686 CCGATCAAAGGAGAGAGGGG 59.244 60.000 0.00 0.00 0.00 4.79
4881 7065 1.066143 GGGGCAAAGAAGATCGAGACA 60.066 52.381 0.00 0.00 0.00 3.41
4884 7068 2.409948 AAGGGGCAAAGAAGATCGAG 57.590 50.000 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.