Multiple sequence alignment - TraesCS5A01G489200

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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 TraesCS5A01G489200 chr5A 100.000 3440 0 0 1 3440 659174413 659170974 0.000000e+00 6353.0
1 TraesCS5A01G489200 chr5A 92.612 1340 88 6 1461 2797 697282833 697284164 0.000000e+00 1916.0
2 TraesCS5A01G489200 chr5A 93.066 1298 86 4 1503 2797 697068348 697069644 0.000000e+00 1895.0
3 TraesCS5A01G489200 chr5A 92.989 1298 87 4 1503 2797 697200310 697201606 0.000000e+00 1890.0
4 TraesCS5A01G489200 chr5A 87.869 1220 120 10 1519 2731 697552500 697553698 0.000000e+00 1408.0
5 TraesCS5A01G489200 chr5A 93.261 742 47 3 2058 2797 697132988 697133728 0.000000e+00 1090.0
6 TraesCS5A01G489200 chr5A 85.791 929 68 31 524 1416 697281822 697282722 0.000000e+00 926.0
7 TraesCS5A01G489200 chr5A 92.910 536 37 1 1503 2037 697132121 697132656 0.000000e+00 778.0
8 TraesCS5A01G489200 chr5A 84.204 766 71 17 573 1310 697548126 697548869 0.000000e+00 699.0
9 TraesCS5A01G489200 chr5A 80.392 357 38 17 1 333 697065179 697065527 3.430000e-60 243.0
10 TraesCS5A01G489200 chr5A 80.392 357 39 16 1 333 697198323 697198672 3.430000e-60 243.0
11 TraesCS5A01G489200 chr5A 80.392 357 38 17 1 333 697280304 697280652 3.430000e-60 243.0
12 TraesCS5A01G489200 chr5A 94.000 50 3 0 524 573 697067827 697067876 3.680000e-10 76.8
13 TraesCS5A01G489200 chr5A 94.000 50 3 0 524 573 697199841 697199890 3.680000e-10 76.8
14 TraesCS5A01G489200 chrUn 92.577 1711 116 10 1547 3250 100284568 100282862 0.000000e+00 2446.0
15 TraesCS5A01G489200 chrUn 92.681 1298 87 7 1558 2848 100314428 100313132 0.000000e+00 1864.0
16 TraesCS5A01G489200 chrUn 86.347 1084 61 25 477 1497 100315485 100314426 0.000000e+00 1101.0
17 TraesCS5A01G489200 chrUn 86.763 763 55 8 576 1310 100290035 100289291 0.000000e+00 808.0
18 TraesCS5A01G489200 chrUn 80.989 647 80 21 692 1309 30086980 30087612 1.120000e-129 473.0
19 TraesCS5A01G489200 chrUn 82.051 312 27 13 5 293 30356976 30357281 4.440000e-59 239.0
20 TraesCS5A01G489200 chrUn 80.112 357 40 16 1 333 270873521 270873172 1.600000e-58 237.0
21 TraesCS5A01G489200 chrUn 95.745 47 2 0 527 573 270872000 270871954 3.680000e-10 76.8
22 TraesCS5A01G489200 chr4D 90.803 1370 102 6 1547 2893 491003175 491001807 0.000000e+00 1810.0
23 TraesCS5A01G489200 chr4D 85.276 978 57 24 578 1497 491004132 491003184 0.000000e+00 928.0
24 TraesCS5A01G489200 chr4D 80.488 656 87 16 682 1309 503920946 503920304 6.720000e-127 464.0
25 TraesCS5A01G489200 chr4D 84.110 472 69 6 2969 3438 342830293 342830760 5.240000e-123 451.0
26 TraesCS5A01G489200 chr4D 87.692 390 42 6 3053 3440 491001366 491000981 1.880000e-122 449.0
27 TraesCS5A01G489200 chr4D 82.222 90 16 0 1 90 172013113 172013024 1.020000e-10 78.7
28 TraesCS5A01G489200 chr4D 81.928 83 13 2 252 333 354039045 354039126 6.160000e-08 69.4
29 TraesCS5A01G489200 chr4D 92.500 40 3 0 51 90 38360154 38360193 1.330000e-04 58.4
30 TraesCS5A01G489200 chr4B 90.297 1247 116 4 1558 2800 671750969 671752214 0.000000e+00 1628.0
31 TraesCS5A01G489200 chr4B 86.364 968 62 23 478 1397 671749898 671750843 0.000000e+00 992.0
32 TraesCS5A01G489200 chr4B 82.636 478 76 7 2967 3440 563827539 563828013 1.910000e-112 416.0
33 TraesCS5A01G489200 chr4B 89.394 66 1 3 1430 1493 671750905 671750966 1.020000e-10 78.7
34 TraesCS5A01G489200 chr4B 80.220 91 16 2 1 90 55782651 55782740 2.220000e-07 67.6
35 TraesCS5A01G489200 chr7B 82.560 1078 176 9 1585 2654 409749074 409748001 0.000000e+00 939.0
36 TraesCS5A01G489200 chr7B 81.818 704 78 25 652 1326 409750138 409749456 2.330000e-151 545.0
37 TraesCS5A01G489200 chr3A 84.402 577 79 9 2869 3440 500997631 500998201 1.080000e-154 556.0
38 TraesCS5A01G489200 chr3A 91.597 119 7 2 331 448 182625838 182625722 9.880000e-36 161.0
39 TraesCS5A01G489200 chr3A 86.429 140 17 2 333 471 486364362 486364500 5.950000e-33 152.0
40 TraesCS5A01G489200 chr7D 80.398 704 88 20 652 1326 400185896 400185214 1.110000e-134 490.0
41 TraesCS5A01G489200 chr5D 83.043 460 71 6 2983 3440 525970634 525970180 8.890000e-111 411.0
42 TraesCS5A01G489200 chr5D 90.196 51 5 0 243 293 435770526 435770476 2.220000e-07 67.6
43 TraesCS5A01G489200 chr3B 79.097 598 110 10 2850 3440 61981691 61982280 6.920000e-107 398.0
44 TraesCS5A01G489200 chr3D 81.391 489 82 9 2956 3440 39155228 39155711 1.160000e-104 390.0
45 TraesCS5A01G489200 chr5B 77.907 602 109 17 2849 3440 17975798 17976385 1.520000e-93 353.0
46 TraesCS5A01G489200 chr5B 88.618 123 7 5 331 448 317702847 317702967 3.580000e-30 143.0
47 TraesCS5A01G489200 chr2D 80.115 347 39 16 1 333 639422409 639422079 7.420000e-57 231.0
48 TraesCS5A01G489200 chr6B 94.286 140 8 0 331 470 92564192 92564053 7.480000e-52 215.0
49 TraesCS5A01G489200 chr4A 96.610 118 4 0 331 448 91757228 91757111 2.710000e-46 196.0
50 TraesCS5A01G489200 chr4A 92.035 113 7 2 337 448 699969244 699969133 1.280000e-34 158.0
51 TraesCS5A01G489200 chr2B 91.150 113 8 2 337 448 250711877 250711766 5.950000e-33 152.0
52 TraesCS5A01G489200 chr6D 82.883 111 13 5 109 215 385749894 385749786 1.020000e-15 95.3
53 TraesCS5A01G489200 chr6D 82.883 111 13 5 109 215 385754802 385754694 1.020000e-15 95.3
54 TraesCS5A01G489200 chr7A 89.286 56 6 0 239 294 57623258 57623203 1.710000e-08 71.3


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 TraesCS5A01G489200 chr5A 659170974 659174413 3439 True 6353.000000 6353 100.000000 1 3440 1 chr5A.!!$R1 3439
1 TraesCS5A01G489200 chr5A 697548126 697553698 5572 False 1053.500000 1408 86.036500 573 2731 2 chr5A.!!$F5 2158
2 TraesCS5A01G489200 chr5A 697280304 697284164 3860 False 1028.333333 1916 86.265000 1 2797 3 chr5A.!!$F4 2796
3 TraesCS5A01G489200 chr5A 697132121 697133728 1607 False 934.000000 1090 93.085500 1503 2797 2 chr5A.!!$F2 1294
4 TraesCS5A01G489200 chr5A 697065179 697069644 4465 False 738.266667 1895 89.152667 1 2797 3 chr5A.!!$F1 2796
5 TraesCS5A01G489200 chr5A 697198323 697201606 3283 False 736.600000 1890 89.127000 1 2797 3 chr5A.!!$F3 2796
6 TraesCS5A01G489200 chrUn 100282862 100284568 1706 True 2446.000000 2446 92.577000 1547 3250 1 chrUn.!!$R1 1703
7 TraesCS5A01G489200 chrUn 100313132 100315485 2353 True 1482.500000 1864 89.514000 477 2848 2 chrUn.!!$R3 2371
8 TraesCS5A01G489200 chrUn 100289291 100290035 744 True 808.000000 808 86.763000 576 1310 1 chrUn.!!$R2 734
9 TraesCS5A01G489200 chrUn 30086980 30087612 632 False 473.000000 473 80.989000 692 1309 1 chrUn.!!$F1 617
10 TraesCS5A01G489200 chr4D 491000981 491004132 3151 True 1062.333333 1810 87.923667 578 3440 3 chr4D.!!$R3 2862
11 TraesCS5A01G489200 chr4D 503920304 503920946 642 True 464.000000 464 80.488000 682 1309 1 chr4D.!!$R2 627
12 TraesCS5A01G489200 chr4B 671749898 671752214 2316 False 899.566667 1628 88.685000 478 2800 3 chr4B.!!$F3 2322
13 TraesCS5A01G489200 chr7B 409748001 409750138 2137 True 742.000000 939 82.189000 652 2654 2 chr7B.!!$R1 2002
14 TraesCS5A01G489200 chr3A 500997631 500998201 570 False 556.000000 556 84.402000 2869 3440 1 chr3A.!!$F2 571
15 TraesCS5A01G489200 chr7D 400185214 400185896 682 True 490.000000 490 80.398000 652 1326 1 chr7D.!!$R1 674
16 TraesCS5A01G489200 chr3B 61981691 61982280 589 False 398.000000 398 79.097000 2850 3440 1 chr3B.!!$F1 590
17 TraesCS5A01G489200 chr5B 17975798 17976385 587 False 353.000000 353 77.907000 2849 3440 1 chr5B.!!$F1 591

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
448 472 0.034337 GGCCTTCGTTGTGACTACCA 59.966 55.0 0.00 0.00 0.0 3.25 F
1628 7439 0.036388 ATGTTCAAGCGGTCCGTCAT 60.036 50.0 13.94 5.89 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 7497 0.671796 TCATGTCACCGAACTCGTGT 59.328 50.000 0.0 0.0 37.74 4.49 R
3316 9804 1.003118 TGAAACCCTCTTGGATGACCG 59.997 52.381 0.0 0.0 39.42 4.79 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 4.895297 TGGAGGGAATTTCTCATAAATGCC 59.105 41.667 0.00 0.00 35.06 4.40
41 42 4.895297 GGGAATTTCTCATAAATGCCAGGA 59.105 41.667 9.23 0.00 37.11 3.86
72 73 5.733226 TTTATACAATGGTGTGATGAGCG 57.267 39.130 0.00 0.00 38.82 5.03
83 84 4.037690 GTGTGATGAGCGCAAAAATATCC 58.962 43.478 11.47 0.00 39.02 2.59
86 87 4.972440 GTGATGAGCGCAAAAATATCCTTC 59.028 41.667 11.47 0.00 0.00 3.46
90 91 4.214437 GAGCGCAAAAATATCCTTCATCG 58.786 43.478 11.47 0.00 0.00 3.84
95 96 5.617751 CGCAAAAATATCCTTCATCGGATCC 60.618 44.000 0.00 0.00 42.69 3.36
113 114 1.151668 CCTTGCTCTCCAACACGAAG 58.848 55.000 0.00 0.00 0.00 3.79
119 120 2.670414 GCTCTCCAACACGAAGAATGAG 59.330 50.000 0.00 0.00 0.00 2.90
120 121 3.615110 GCTCTCCAACACGAAGAATGAGA 60.615 47.826 0.00 0.00 0.00 3.27
121 122 4.560128 CTCTCCAACACGAAGAATGAGAA 58.440 43.478 0.00 0.00 0.00 2.87
122 123 4.956085 TCTCCAACACGAAGAATGAGAAA 58.044 39.130 0.00 0.00 0.00 2.52
123 124 4.991056 TCTCCAACACGAAGAATGAGAAAG 59.009 41.667 0.00 0.00 0.00 2.62
138 153 9.571816 AGAATGAGAAAGAAACAAAAGAGAGAT 57.428 29.630 0.00 0.00 0.00 2.75
176 191 8.662141 GGTAAAAAGTAGTAGATGAATTTGCGA 58.338 33.333 0.00 0.00 0.00 5.10
181 196 8.942338 AAGTAGTAGATGAATTTGCGATTGTA 57.058 30.769 0.00 0.00 0.00 2.41
212 227 6.266131 TCTAATTGGCCATCACCTCTAATT 57.734 37.500 6.09 2.03 0.00 1.40
215 230 6.715347 AATTGGCCATCACCTCTAATTTAC 57.285 37.500 6.09 0.00 0.00 2.01
216 231 3.804036 TGGCCATCACCTCTAATTTACG 58.196 45.455 0.00 0.00 0.00 3.18
219 234 3.139077 CCATCACCTCTAATTTACGGGC 58.861 50.000 0.00 0.00 0.00 6.13
220 235 2.994186 TCACCTCTAATTTACGGGCC 57.006 50.000 0.00 0.00 0.00 5.80
221 236 1.137479 TCACCTCTAATTTACGGGCCG 59.863 52.381 27.06 27.06 0.00 6.13
222 237 1.134610 CACCTCTAATTTACGGGCCGT 60.135 52.381 35.91 35.91 44.35 5.68
223 238 1.556451 ACCTCTAATTTACGGGCCGTT 59.444 47.619 38.73 21.94 41.54 4.44
224 239 1.937899 CCTCTAATTTACGGGCCGTTG 59.062 52.381 38.73 19.06 41.54 4.10
239 263 2.482721 GCCGTTGTTGTAGTGCACTATT 59.517 45.455 28.37 6.05 0.00 1.73
242 266 5.334260 GCCGTTGTTGTAGTGCACTATTTTA 60.334 40.000 28.37 13.55 0.00 1.52
256 280 8.476925 GTGCACTATTTTAGTTGTAACTTTTGC 58.523 33.333 10.32 3.27 40.37 3.68
257 281 8.191446 TGCACTATTTTAGTTGTAACTTTTGCA 58.809 29.630 2.20 5.41 40.37 4.08
293 317 8.776470 GGATTGAGATGATTCAAAAAGCAAAAA 58.224 29.630 0.00 0.00 40.21 1.94
296 320 5.977731 AGATGATTCAAAAAGCAAAAACGC 58.022 33.333 0.00 0.00 33.87 4.84
308 332 2.780993 CAAAAACGCTTGTCTTGACGT 58.219 42.857 0.00 0.00 41.16 4.34
322 346 7.310072 TGTCTTGACGTGACAAAGAATTTTA 57.690 32.000 4.84 0.00 40.89 1.52
323 347 7.925993 TGTCTTGACGTGACAAAGAATTTTAT 58.074 30.769 4.84 0.00 40.89 1.40
324 348 7.855409 TGTCTTGACGTGACAAAGAATTTTATG 59.145 33.333 4.84 0.00 40.89 1.90
325 349 6.855914 TCTTGACGTGACAAAGAATTTTATGC 59.144 34.615 0.00 0.00 35.03 3.14
326 350 6.066054 TGACGTGACAAAGAATTTTATGCA 57.934 33.333 0.00 0.00 35.03 3.96
328 352 6.017523 TGACGTGACAAAGAATTTTATGCAGA 60.018 34.615 0.00 0.00 35.03 4.26
330 354 6.636850 ACGTGACAAAGAATTTTATGCAGAAC 59.363 34.615 0.00 0.00 35.03 3.01
331 355 6.636447 CGTGACAAAGAATTTTATGCAGAACA 59.364 34.615 0.00 0.00 35.03 3.18
332 356 7.357532 CGTGACAAAGAATTTTATGCAGAACAC 60.358 37.037 0.00 0.00 35.03 3.32
333 357 6.636447 TGACAAAGAATTTTATGCAGAACACG 59.364 34.615 0.00 0.00 35.03 4.49
334 358 5.920273 ACAAAGAATTTTATGCAGAACACGG 59.080 36.000 0.00 0.00 35.03 4.94
336 360 5.046910 AGAATTTTATGCAGAACACGGTG 57.953 39.130 6.58 6.58 0.00 4.94
337 361 2.697431 TTTTATGCAGAACACGGTGC 57.303 45.000 8.30 0.00 40.29 5.01
338 362 0.515127 TTTATGCAGAACACGGTGCG 59.485 50.000 8.30 0.00 42.96 5.34
339 363 1.295357 TTATGCAGAACACGGTGCGG 61.295 55.000 8.30 0.00 42.96 5.69
340 364 2.443260 TATGCAGAACACGGTGCGGT 62.443 55.000 8.30 0.00 42.96 5.68
341 365 4.012895 GCAGAACACGGTGCGGTG 62.013 66.667 8.30 8.09 43.54 4.94
360 384 4.134623 TTTTTCTGCTCGCGTGGT 57.865 50.000 5.77 0.00 0.00 4.16
361 385 1.646540 TTTTTCTGCTCGCGTGGTG 59.353 52.632 5.77 0.00 0.00 4.17
362 386 2.387125 TTTTTCTGCTCGCGTGGTGC 62.387 55.000 5.77 7.59 41.47 5.01
398 422 4.760047 GGCACGGTGCGGTGATCT 62.760 66.667 25.24 0.00 46.21 2.75
399 423 2.742372 GCACGGTGCGGTGATCTT 60.742 61.111 18.35 0.00 40.38 2.40
401 425 1.852067 GCACGGTGCGGTGATCTTTT 61.852 55.000 18.35 0.00 40.38 2.27
418 442 1.729284 TTTTTCCCTCGCGTGATACC 58.271 50.000 10.21 0.00 0.00 2.73
419 443 0.458889 TTTTCCCTCGCGTGATACCG 60.459 55.000 10.21 0.00 0.00 4.02
420 444 1.597797 TTTCCCTCGCGTGATACCGT 61.598 55.000 10.21 0.00 0.00 4.83
421 445 0.747644 TTCCCTCGCGTGATACCGTA 60.748 55.000 10.21 0.00 0.00 4.02
422 446 1.009222 CCCTCGCGTGATACCGTAC 60.009 63.158 10.21 0.00 0.00 3.67
423 447 1.368493 CCTCGCGTGATACCGTACG 60.368 63.158 8.69 8.69 42.79 3.67
427 451 4.184735 CGTGATACCGTACGCTCG 57.815 61.111 10.49 5.25 33.25 5.03
428 452 1.637934 CGTGATACCGTACGCTCGA 59.362 57.895 10.49 0.00 33.25 4.04
429 453 0.382758 CGTGATACCGTACGCTCGAG 60.383 60.000 10.49 8.45 33.25 4.04
431 455 1.082235 GATACCGTACGCTCGAGGC 60.082 63.158 15.58 5.67 37.64 4.70
432 456 2.455183 GATACCGTACGCTCGAGGCC 62.455 65.000 15.58 0.00 37.74 5.19
433 457 2.955022 ATACCGTACGCTCGAGGCCT 62.955 60.000 15.58 3.86 37.74 5.19
435 459 2.278013 CGTACGCTCGAGGCCTTC 60.278 66.667 15.58 0.00 37.74 3.46
443 467 3.550656 CGAGGCCTTCGTTGTGAC 58.449 61.111 6.77 0.00 44.27 3.67
444 468 1.006102 CGAGGCCTTCGTTGTGACT 60.006 57.895 6.77 0.00 44.27 3.41
446 470 1.711206 GAGGCCTTCGTTGTGACTAC 58.289 55.000 6.77 0.00 0.00 2.73
447 471 0.320697 AGGCCTTCGTTGTGACTACC 59.679 55.000 0.00 0.00 0.00 3.18
448 472 0.034337 GGCCTTCGTTGTGACTACCA 59.966 55.000 0.00 0.00 0.00 3.25
450 474 2.423577 GCCTTCGTTGTGACTACCATT 58.576 47.619 0.00 0.00 0.00 3.16
452 476 3.864921 GCCTTCGTTGTGACTACCATTCT 60.865 47.826 0.00 0.00 0.00 2.40
453 477 4.619863 GCCTTCGTTGTGACTACCATTCTA 60.620 45.833 0.00 0.00 0.00 2.10
454 478 5.103000 CCTTCGTTGTGACTACCATTCTAG 58.897 45.833 0.00 0.00 0.00 2.43
455 479 5.105877 CCTTCGTTGTGACTACCATTCTAGA 60.106 44.000 0.00 0.00 0.00 2.43
456 480 5.970317 TCGTTGTGACTACCATTCTAGAA 57.030 39.130 7.82 7.82 0.00 2.10
457 481 5.950883 TCGTTGTGACTACCATTCTAGAAG 58.049 41.667 11.53 0.67 0.00 2.85
458 482 5.103000 CGTTGTGACTACCATTCTAGAAGG 58.897 45.833 11.53 10.84 0.00 3.46
461 485 4.777896 TGTGACTACCATTCTAGAAGGCTT 59.222 41.667 11.65 0.00 0.00 4.35
462 486 5.248477 TGTGACTACCATTCTAGAAGGCTTT 59.752 40.000 11.65 1.09 0.00 3.51
463 487 6.439375 TGTGACTACCATTCTAGAAGGCTTTA 59.561 38.462 11.65 2.16 0.00 1.85
464 488 7.125811 TGTGACTACCATTCTAGAAGGCTTTAT 59.874 37.037 11.65 0.00 0.00 1.40
466 490 9.381038 TGACTACCATTCTAGAAGGCTTTATAT 57.619 33.333 11.65 0.00 0.00 0.86
467 491 9.646427 GACTACCATTCTAGAAGGCTTTATATG 57.354 37.037 11.65 1.17 0.00 1.78
468 492 9.160412 ACTACCATTCTAGAAGGCTTTATATGT 57.840 33.333 11.65 4.45 0.00 2.29
480 2635 9.160496 GAAGGCTTTATATGTTAGATGAGGATG 57.840 37.037 0.00 0.00 0.00 3.51
508 2687 4.190772 TCGATCGTACGTGGCCATATATA 58.809 43.478 9.72 0.00 34.70 0.86
509 2688 4.818005 TCGATCGTACGTGGCCATATATAT 59.182 41.667 9.72 2.91 34.70 0.86
510 2689 5.990996 TCGATCGTACGTGGCCATATATATA 59.009 40.000 9.72 0.00 34.70 0.86
511 2690 6.482973 TCGATCGTACGTGGCCATATATATAA 59.517 38.462 9.72 0.00 34.70 0.98
512 2691 6.795593 CGATCGTACGTGGCCATATATATAAG 59.204 42.308 9.72 0.00 0.00 1.73
513 2692 5.824429 TCGTACGTGGCCATATATATAAGC 58.176 41.667 9.72 8.83 0.00 3.09
514 2693 5.357596 TCGTACGTGGCCATATATATAAGCA 59.642 40.000 9.72 4.39 0.00 3.91
515 2694 6.040054 TCGTACGTGGCCATATATATAAGCAT 59.960 38.462 9.72 5.29 0.00 3.79
516 2695 6.362551 CGTACGTGGCCATATATATAAGCATC 59.637 42.308 9.72 9.41 0.00 3.91
517 2696 6.485830 ACGTGGCCATATATATAAGCATCT 57.514 37.500 9.72 0.00 0.00 2.90
518 2697 6.889198 ACGTGGCCATATATATAAGCATCTT 58.111 36.000 9.72 4.09 0.00 2.40
519 2698 6.986817 ACGTGGCCATATATATAAGCATCTTC 59.013 38.462 9.72 0.00 0.00 2.87
520 2699 7.147655 ACGTGGCCATATATATAAGCATCTTCT 60.148 37.037 9.72 0.00 0.00 2.85
521 2700 7.383572 CGTGGCCATATATATAAGCATCTTCTC 59.616 40.741 9.72 0.00 0.00 2.87
522 2701 8.206867 GTGGCCATATATATAAGCATCTTCTCA 58.793 37.037 9.72 4.64 0.00 3.27
523 2702 8.771286 TGGCCATATATATAAGCATCTTCTCAA 58.229 33.333 0.00 0.00 0.00 3.02
524 2703 9.790344 GGCCATATATATAAGCATCTTCTCAAT 57.210 33.333 15.97 0.00 0.00 2.57
535 2714 7.418840 AGCATCTTCTCAATTTATTAGCTCG 57.581 36.000 0.00 0.00 0.00 5.03
592 2796 2.412847 GCAACACTCGCATTCAAGTACC 60.413 50.000 0.00 0.00 0.00 3.34
607 2811 0.526954 GTACCGTACGTCCATGCCTG 60.527 60.000 15.21 0.00 0.00 4.85
608 2812 2.287457 TACCGTACGTCCATGCCTGC 62.287 60.000 15.21 0.00 0.00 4.85
609 2813 2.890474 CGTACGTCCATGCCTGCC 60.890 66.667 7.22 0.00 0.00 4.85
639 2847 1.817911 GCCCTACGTAGATGGAGGCC 61.818 65.000 24.15 0.00 0.00 5.19
648 2856 2.611800 ATGGAGGCCAGCAGGTCA 60.612 61.111 5.01 0.00 43.99 4.02
774 2982 2.743928 GACTGCACCCTCGCCAAG 60.744 66.667 0.00 0.00 0.00 3.61
775 2983 3.240134 GACTGCACCCTCGCCAAGA 62.240 63.158 0.00 0.00 0.00 3.02
776 2984 2.743928 CTGCACCCTCGCCAAGAC 60.744 66.667 0.00 0.00 0.00 3.01
777 2985 4.680237 TGCACCCTCGCCAAGACG 62.680 66.667 0.00 0.00 0.00 4.18
781 2989 4.697756 CCCTCGCCAAGACGCCAA 62.698 66.667 0.00 0.00 0.00 4.52
797 3005 0.037605 CCAACGTCTACGGCTCCTTT 60.038 55.000 7.50 0.00 44.95 3.11
798 3006 1.607251 CCAACGTCTACGGCTCCTTTT 60.607 52.381 7.50 0.00 44.95 2.27
1149 3384 3.249189 AGCTCGCTGTGGGGGAAA 61.249 61.111 0.00 0.00 36.45 3.13
1224 3459 3.881104 AACCAGGGGTTCGCCGTT 61.881 61.111 0.00 0.00 43.05 4.44
1227 3462 3.353836 CAGGGGTTCGCCGTTGTG 61.354 66.667 0.41 0.00 38.45 3.33
1330 3569 4.826274 ACCTACTCCTACACGTGTAGTA 57.174 45.455 39.47 30.84 44.88 1.82
1369 6122 0.892755 ATGCCAATGTGCTGAAGTGG 59.107 50.000 0.00 0.00 0.00 4.00
1379 6132 2.094234 GTGCTGAAGTGGGTTTTGTGTT 60.094 45.455 0.00 0.00 0.00 3.32
1495 7059 3.322369 TCGCTTCGATGTACACAAATGT 58.678 40.909 0.00 0.00 43.30 2.71
1496 7060 3.743911 TCGCTTCGATGTACACAAATGTT 59.256 39.130 0.00 0.00 40.48 2.71
1497 7061 4.081761 CGCTTCGATGTACACAAATGTTC 58.918 43.478 0.00 0.00 40.48 3.18
1498 7062 4.376920 CGCTTCGATGTACACAAATGTTCA 60.377 41.667 0.00 0.00 40.01 3.18
1499 7063 4.846137 GCTTCGATGTACACAAATGTTCAC 59.154 41.667 0.00 0.00 38.73 3.18
1500 7064 5.559991 GCTTCGATGTACACAAATGTTCACA 60.560 40.000 0.00 0.88 38.73 3.58
1501 7065 6.552859 TTCGATGTACACAAATGTTCACAT 57.447 33.333 0.00 8.69 39.62 3.21
1594 7405 4.473643 TGCTTGCGCAGGTTACTT 57.526 50.000 21.36 0.00 42.25 2.24
1628 7439 0.036388 ATGTTCAAGCGGTCCGTCAT 60.036 50.000 13.94 5.89 0.00 3.06
1647 7458 3.449227 TTCCTGGAGCGCGACGAT 61.449 61.111 12.10 0.00 0.00 3.73
1862 7676 1.213926 GGAGGAGCATGTGGAGGAAAT 59.786 52.381 0.00 0.00 0.00 2.17
1878 7692 1.463056 GAAATCAACGACATGGCACGA 59.537 47.619 14.08 0.60 0.00 4.35
1955 7769 0.974383 AACGACGGTTCCTCCTTCAT 59.026 50.000 0.00 0.00 34.59 2.57
2012 7826 2.242572 CGTCCAGCTCATGCATCGG 61.243 63.158 0.00 0.00 42.74 4.18
2044 7861 3.381333 CTGCTCCGCTCCTCATGCA 62.381 63.158 0.00 0.00 0.00 3.96
2085 8213 3.428316 GGAGCCTCTTCTTCTACAACTCG 60.428 52.174 0.00 0.00 0.00 4.18
2116 8244 4.082523 CGCTCTCCAAAGCCCCGA 62.083 66.667 0.00 0.00 39.17 5.14
2142 8270 2.667318 CGCCGACATGCAACGACTT 61.667 57.895 11.69 0.00 0.00 3.01
2253 8381 4.436368 ACGGAGGACTCGGTCAAT 57.564 55.556 6.70 0.00 38.53 2.57
2341 8469 2.939103 GAGCTCGAACATATGGCTTTGT 59.061 45.455 7.80 0.00 33.13 2.83
2342 8470 3.347216 AGCTCGAACATATGGCTTTGTT 58.653 40.909 7.80 0.00 38.71 2.83
2353 8501 2.785562 TGGCTTTGTTAAGTATGGCGT 58.214 42.857 0.00 0.00 33.74 5.68
2377 8525 2.274645 CGCAATGGGGCAAGAACCA 61.275 57.895 0.00 0.00 41.76 3.67
2386 8534 0.310854 GGCAAGAACCACAACTTCGG 59.689 55.000 0.00 0.00 0.00 4.30
2459 8607 0.927767 AGGAGAGGTACGACCCAGAT 59.072 55.000 0.00 0.00 39.75 2.90
2474 8622 3.039252 CCAGATGGGGTCTTCTCTAGT 57.961 52.381 0.00 0.00 34.00 2.57
2475 8623 3.379452 CCAGATGGGGTCTTCTCTAGTT 58.621 50.000 0.00 0.00 34.00 2.24
2522 8670 2.355115 GGGAGCCCCAACATCGTT 59.645 61.111 5.45 0.00 44.65 3.85
2558 8706 1.413118 TCGAAGGGCTCTGCATATGA 58.587 50.000 6.97 0.00 0.00 2.15
2670 8818 2.892914 CACACCGCGACCACAACA 60.893 61.111 8.23 0.00 0.00 3.33
2677 8825 0.922111 CGCGACCACAACAACGAAAC 60.922 55.000 0.00 0.00 0.00 2.78
2685 8833 4.097135 ACCACAACAACGAAACATGAATCA 59.903 37.500 0.00 0.00 0.00 2.57
2896 9052 2.656069 CCGGTCCCCTATATGCCCG 61.656 68.421 0.00 0.00 35.32 6.13
2897 9053 2.669240 GGTCCCCTATATGCCCGC 59.331 66.667 0.00 0.00 0.00 6.13
2938 9098 0.969149 CCGGCCTCTCATATGTGCTA 59.031 55.000 0.00 0.00 0.00 3.49
2963 9123 5.220912 CCGCACATTCATATGTCTCAAATGT 60.221 40.000 11.84 11.84 43.07 2.71
3061 9543 8.196771 ACAAGCAAAGAAAATCATAGTTCAACA 58.803 29.630 0.00 0.00 0.00 3.33
3113 9595 4.796231 GCGTGACGGATGCCTCGT 62.796 66.667 7.25 0.00 44.03 4.18
3272 9759 1.598924 CGTCGCCTCGTATTTCCTACC 60.599 57.143 0.00 0.00 0.00 3.18
3274 9761 0.033090 CGCCTCGTATTTCCTACCCC 59.967 60.000 0.00 0.00 0.00 4.95
3275 9762 1.421480 GCCTCGTATTTCCTACCCCT 58.579 55.000 0.00 0.00 0.00 4.79
3303 9791 2.245714 CTTCTTCTTCGCCGCAAGCC 62.246 60.000 0.00 0.00 38.78 4.35
3316 9804 0.598419 GCAAGCCCACTTCTTTGCAC 60.598 55.000 3.43 0.00 32.29 4.57
3336 9824 1.003118 CGGTCATCCAAGAGGGTTTCA 59.997 52.381 0.00 0.00 38.11 2.69
3343 9831 1.078426 AAGAGGGTTTCATCCGCCG 60.078 57.895 0.00 0.00 0.00 6.46
3344 9832 2.513897 GAGGGTTTCATCCGCCGG 60.514 66.667 0.00 0.00 0.00 6.13
3375 9863 1.679305 ATCCTCCGTGTCTCGTGCT 60.679 57.895 0.00 0.00 37.94 4.40
3382 9870 1.278172 CGTGTCTCGTGCTGAGTTGG 61.278 60.000 6.46 0.00 45.46 3.77
3389 9877 0.951040 CGTGCTGAGTTGGAACCTCC 60.951 60.000 0.00 0.00 36.96 4.30
3390 9878 0.398318 GTGCTGAGTTGGAACCTCCT 59.602 55.000 0.00 0.00 37.46 3.69
3399 9887 3.071747 AGTTGGAACCTCCTCTTCTCAAC 59.928 47.826 0.00 0.00 37.46 3.18
3429 9917 3.160269 CTCCAAATGTCTTGGCCTTCTT 58.840 45.455 3.32 0.00 39.38 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.042437 GGCATTTATGAGAAATTCCCTCCAAT 59.958 38.462 5.64 0.89 0.00 3.16
14 15 4.895297 GGCATTTATGAGAAATTCCCTCCA 59.105 41.667 5.64 0.00 0.00 3.86
19 20 6.661304 ATCCTGGCATTTATGAGAAATTCC 57.339 37.500 0.00 0.00 0.00 3.01
22 23 9.370930 TGAATAATCCTGGCATTTATGAGAAAT 57.629 29.630 0.00 0.00 0.00 2.17
35 36 9.643693 CCATTGTATAAAATGAATAATCCTGGC 57.356 33.333 16.02 0.00 39.46 4.85
54 55 1.338579 TGCGCTCATCACACCATTGTA 60.339 47.619 9.73 0.00 33.30 2.41
59 60 1.028130 TTTTTGCGCTCATCACACCA 58.972 45.000 9.73 0.00 0.00 4.17
83 84 2.547642 GGAGAGCAAGGATCCGATGAAG 60.548 54.545 20.77 4.68 0.00 3.02
86 87 0.755079 TGGAGAGCAAGGATCCGATG 59.245 55.000 14.30 14.30 35.78 3.84
90 91 1.743996 GTGTTGGAGAGCAAGGATCC 58.256 55.000 2.48 2.48 0.00 3.36
95 96 2.154854 TCTTCGTGTTGGAGAGCAAG 57.845 50.000 0.00 0.00 0.00 4.01
157 172 9.547753 AATACAATCGCAAATTCATCTACTACT 57.452 29.630 0.00 0.00 0.00 2.57
187 202 4.591321 AGAGGTGATGGCCAATTAGAAA 57.409 40.909 10.96 0.00 0.00 2.52
188 203 5.708736 TTAGAGGTGATGGCCAATTAGAA 57.291 39.130 10.96 0.00 0.00 2.10
189 204 5.912149 ATTAGAGGTGATGGCCAATTAGA 57.088 39.130 10.96 0.00 0.00 2.10
190 205 6.966534 AAATTAGAGGTGATGGCCAATTAG 57.033 37.500 10.96 0.00 0.00 1.73
212 227 0.392336 ACTACAACAACGGCCCGTAA 59.608 50.000 10.30 0.00 39.99 3.18
215 230 2.961669 GCACTACAACAACGGCCCG 61.962 63.158 0.00 0.00 0.00 6.13
216 231 1.894756 TGCACTACAACAACGGCCC 60.895 57.895 0.00 0.00 0.00 5.80
219 234 4.742438 AAATAGTGCACTACAACAACGG 57.258 40.909 28.28 0.00 0.00 4.44
220 235 6.884187 ACTAAAATAGTGCACTACAACAACG 58.116 36.000 28.28 15.17 37.69 4.10
221 236 8.126700 ACAACTAAAATAGTGCACTACAACAAC 58.873 33.333 28.28 0.00 39.39 3.32
222 237 8.215926 ACAACTAAAATAGTGCACTACAACAA 57.784 30.769 28.28 8.06 39.39 2.83
223 238 7.795482 ACAACTAAAATAGTGCACTACAACA 57.205 32.000 28.28 8.88 39.39 3.33
224 239 9.590088 GTTACAACTAAAATAGTGCACTACAAC 57.410 33.333 28.28 14.04 39.39 3.32
242 266 7.867403 CCAAGATTGTATGCAAAAGTTACAACT 59.133 33.333 11.06 8.42 38.31 3.16
256 280 9.063615 TGAATCATCTCAATCCAAGATTGTATG 57.936 33.333 15.03 17.22 31.05 2.39
257 281 9.636789 TTGAATCATCTCAATCCAAGATTGTAT 57.363 29.630 15.03 8.81 31.05 2.29
260 284 9.647797 TTTTTGAATCATCTCAATCCAAGATTG 57.352 29.630 10.42 10.42 35.31 2.67
261 285 9.871238 CTTTTTGAATCATCTCAATCCAAGATT 57.129 29.630 0.00 0.00 35.31 2.40
293 317 0.179121 TGTCACGTCAAGACAAGCGT 60.179 50.000 4.84 0.00 42.57 5.07
303 327 6.017523 TCTGCATAAAATTCTTTGTCACGTCA 60.018 34.615 0.00 0.00 0.00 4.35
308 332 6.636447 CGTGTTCTGCATAAAATTCTTTGTCA 59.364 34.615 0.00 0.00 0.00 3.58
317 341 2.414029 CGCACCGTGTTCTGCATAAAAT 60.414 45.455 0.00 0.00 32.57 1.82
322 346 3.049674 CCGCACCGTGTTCTGCAT 61.050 61.111 0.00 0.00 32.57 3.96
323 347 4.539083 ACCGCACCGTGTTCTGCA 62.539 61.111 0.00 0.00 32.57 4.41
324 348 4.012895 CACCGCACCGTGTTCTGC 62.013 66.667 0.00 0.00 0.00 4.26
325 349 2.587753 ACACCGCACCGTGTTCTG 60.588 61.111 0.00 0.00 44.57 3.02
344 368 2.892334 GCACCACGCGAGCAGAAAA 61.892 57.895 15.93 0.00 0.00 2.29
345 369 3.345808 GCACCACGCGAGCAGAAA 61.346 61.111 15.93 0.00 0.00 2.52
382 406 1.852067 AAAAGATCACCGCACCGTGC 61.852 55.000 13.81 13.81 40.69 5.34
383 407 0.591170 AAAAAGATCACCGCACCGTG 59.409 50.000 0.00 0.00 34.93 4.94
405 429 1.368493 CGTACGGTATCACGCGAGG 60.368 63.158 15.93 4.29 37.37 4.63
406 430 4.184735 CGTACGGTATCACGCGAG 57.815 61.111 15.93 4.59 37.37 5.03
410 434 0.382758 CTCGAGCGTACGGTATCACG 60.383 60.000 21.38 18.80 41.04 4.35
411 435 0.041488 CCTCGAGCGTACGGTATCAC 60.041 60.000 21.38 6.89 0.00 3.06
412 436 1.779025 GCCTCGAGCGTACGGTATCA 61.779 60.000 21.38 6.14 0.00 2.15
413 437 1.082235 GCCTCGAGCGTACGGTATC 60.082 63.158 21.38 8.05 0.00 2.24
415 439 3.204827 GGCCTCGAGCGTACGGTA 61.205 66.667 21.38 4.71 45.17 4.02
417 441 3.753070 GAAGGCCTCGAGCGTACGG 62.753 68.421 18.39 0.00 45.17 4.02
418 442 2.278013 GAAGGCCTCGAGCGTACG 60.278 66.667 5.23 11.84 45.17 3.67
427 451 1.672145 GGTAGTCACAACGAAGGCCTC 60.672 57.143 5.23 0.00 0.00 4.70
428 452 0.320697 GGTAGTCACAACGAAGGCCT 59.679 55.000 0.00 0.00 0.00 5.19
429 453 0.034337 TGGTAGTCACAACGAAGGCC 59.966 55.000 0.00 0.00 0.00 5.19
431 455 3.926616 AGAATGGTAGTCACAACGAAGG 58.073 45.455 0.00 0.00 0.00 3.46
432 456 5.950883 TCTAGAATGGTAGTCACAACGAAG 58.049 41.667 0.00 0.00 0.00 3.79
433 457 5.970317 TCTAGAATGGTAGTCACAACGAA 57.030 39.130 0.00 0.00 0.00 3.85
435 459 5.103000 CCTTCTAGAATGGTAGTCACAACG 58.897 45.833 5.44 0.00 0.00 4.10
436 460 4.870991 GCCTTCTAGAATGGTAGTCACAAC 59.129 45.833 5.44 0.00 0.00 3.32
437 461 4.777896 AGCCTTCTAGAATGGTAGTCACAA 59.222 41.667 10.28 0.00 0.00 3.33
438 462 4.353777 AGCCTTCTAGAATGGTAGTCACA 58.646 43.478 10.28 0.00 0.00 3.58
439 463 5.346181 AAGCCTTCTAGAATGGTAGTCAC 57.654 43.478 12.06 1.16 0.00 3.67
440 464 7.676683 ATAAAGCCTTCTAGAATGGTAGTCA 57.323 36.000 12.06 0.69 0.00 3.41
441 465 9.646427 CATATAAAGCCTTCTAGAATGGTAGTC 57.354 37.037 12.06 2.01 0.00 2.59
442 466 9.160412 ACATATAAAGCCTTCTAGAATGGTAGT 57.840 33.333 12.06 6.98 0.00 2.73
452 476 9.601810 TCCTCATCTAACATATAAAGCCTTCTA 57.398 33.333 0.00 0.00 0.00 2.10
453 477 8.497910 TCCTCATCTAACATATAAAGCCTTCT 57.502 34.615 0.00 0.00 0.00 2.85
454 478 9.160496 CATCCTCATCTAACATATAAAGCCTTC 57.840 37.037 0.00 0.00 0.00 3.46
455 479 8.664079 ACATCCTCATCTAACATATAAAGCCTT 58.336 33.333 0.00 0.00 0.00 4.35
456 480 8.212259 ACATCCTCATCTAACATATAAAGCCT 57.788 34.615 0.00 0.00 0.00 4.58
457 481 8.097038 TGACATCCTCATCTAACATATAAAGCC 58.903 37.037 0.00 0.00 0.00 4.35
458 482 9.664332 ATGACATCCTCATCTAACATATAAAGC 57.336 33.333 0.00 0.00 34.07 3.51
463 487 9.413734 TCGATATGACATCCTCATCTAACATAT 57.586 33.333 0.00 0.00 40.38 1.78
464 488 8.807948 TCGATATGACATCCTCATCTAACATA 57.192 34.615 0.00 0.00 40.38 2.29
466 490 7.414540 CGATCGATATGACATCCTCATCTAACA 60.415 40.741 10.26 0.00 40.38 2.41
467 491 6.909895 CGATCGATATGACATCCTCATCTAAC 59.090 42.308 10.26 0.00 40.38 2.34
468 492 6.599638 ACGATCGATATGACATCCTCATCTAA 59.400 38.462 24.34 0.00 40.38 2.10
470 494 4.946772 ACGATCGATATGACATCCTCATCT 59.053 41.667 24.34 0.00 40.38 2.90
471 495 5.242069 ACGATCGATATGACATCCTCATC 57.758 43.478 24.34 0.00 40.38 2.92
474 498 4.093115 ACGTACGATCGATATGACATCCTC 59.907 45.833 24.34 0.00 34.70 3.71
475 499 4.001652 ACGTACGATCGATATGACATCCT 58.998 43.478 24.34 0.00 34.70 3.24
480 2635 2.240040 GCCACGTACGATCGATATGAC 58.760 52.381 24.34 10.02 34.70 3.06
509 2688 8.982685 CGAGCTAATAAATTGAGAAGATGCTTA 58.017 33.333 0.00 0.00 0.00 3.09
510 2689 7.519649 GCGAGCTAATAAATTGAGAAGATGCTT 60.520 37.037 0.00 0.00 0.00 3.91
511 2690 6.073331 GCGAGCTAATAAATTGAGAAGATGCT 60.073 38.462 0.00 0.00 0.00 3.79
512 2691 6.073331 AGCGAGCTAATAAATTGAGAAGATGC 60.073 38.462 0.00 0.00 0.00 3.91
513 2692 7.170489 TGAGCGAGCTAATAAATTGAGAAGATG 59.830 37.037 0.00 0.00 0.00 2.90
514 2693 7.170658 GTGAGCGAGCTAATAAATTGAGAAGAT 59.829 37.037 0.00 0.00 0.00 2.40
515 2694 6.477033 GTGAGCGAGCTAATAAATTGAGAAGA 59.523 38.462 0.00 0.00 0.00 2.87
516 2695 6.478344 AGTGAGCGAGCTAATAAATTGAGAAG 59.522 38.462 0.00 0.00 0.00 2.85
517 2696 6.341316 AGTGAGCGAGCTAATAAATTGAGAA 58.659 36.000 0.00 0.00 0.00 2.87
518 2697 5.907207 AGTGAGCGAGCTAATAAATTGAGA 58.093 37.500 0.00 0.00 0.00 3.27
519 2698 6.144724 GGTAGTGAGCGAGCTAATAAATTGAG 59.855 42.308 0.00 0.00 0.00 3.02
520 2699 5.983720 GGTAGTGAGCGAGCTAATAAATTGA 59.016 40.000 0.00 0.00 0.00 2.57
521 2700 6.216750 GGTAGTGAGCGAGCTAATAAATTG 57.783 41.667 0.00 0.00 0.00 2.32
535 2714 1.134560 CTTGGGTAGACGGTAGTGAGC 59.865 57.143 0.00 0.00 0.00 4.26
592 2796 2.890474 GGCAGGCATGGACGTACG 60.890 66.667 15.01 15.01 0.00 3.67
622 2826 0.962489 CTGGCCTCCATCTACGTAGG 59.038 60.000 22.01 9.09 30.82 3.18
623 2827 0.315568 GCTGGCCTCCATCTACGTAG 59.684 60.000 16.73 16.73 30.82 3.51
639 2847 1.959899 GCAACGACGATGACCTGCTG 61.960 60.000 9.52 0.00 0.00 4.41
648 2856 2.813908 GCCGGAAGCAACGACGAT 60.814 61.111 5.05 0.00 42.97 3.73
778 2986 0.037605 AAAGGAGCCGTAGACGTTGG 60.038 55.000 0.85 0.00 37.74 3.77
779 2987 1.725164 GAAAAGGAGCCGTAGACGTTG 59.275 52.381 0.85 0.00 37.74 4.10
780 2988 1.668047 CGAAAAGGAGCCGTAGACGTT 60.668 52.381 0.85 0.00 37.74 3.99
781 2989 0.109412 CGAAAAGGAGCCGTAGACGT 60.109 55.000 0.85 0.00 37.74 4.34
844 3052 3.691342 CCACCAACTCCGCCTCGA 61.691 66.667 0.00 0.00 0.00 4.04
924 3132 4.351054 AGCTTGGGGAAGCCGTGG 62.351 66.667 3.19 0.00 46.61 4.94
925 3133 3.058160 CAGCTTGGGGAAGCCGTG 61.058 66.667 3.19 0.00 46.61 4.94
926 3134 4.351054 CCAGCTTGGGGAAGCCGT 62.351 66.667 3.19 0.00 46.61 5.68
1125 3360 4.056125 CACAGCGAGCTCCCGTGA 62.056 66.667 16.09 0.00 0.00 4.35
1208 3443 4.636435 CAACGGCGAACCCCTGGT 62.636 66.667 16.62 0.00 37.65 4.00
1369 6122 2.863740 GGCAAGCAAGTAACACAAAACC 59.136 45.455 0.00 0.00 0.00 3.27
1379 6132 2.073816 GCTTTCGTAGGCAAGCAAGTA 58.926 47.619 13.72 0.00 41.67 2.24
1628 7439 4.717629 CGTCGCGCTCCAGGAACA 62.718 66.667 5.56 0.00 0.00 3.18
1686 7497 0.671796 TCATGTCACCGAACTCGTGT 59.328 50.000 0.00 0.00 37.74 4.49
1862 7676 1.634757 GCATCGTGCCATGTCGTTGA 61.635 55.000 13.44 0.00 37.42 3.18
1905 7719 3.291611 GCCTGCATGGGGAACTTG 58.708 61.111 0.00 0.00 36.00 3.16
2142 8270 4.351938 CGTGGGTTGAGGTCGCGA 62.352 66.667 3.71 3.71 36.65 5.87
2253 8381 5.484715 CTCCGGTAATAGGTGAAGTCAAAA 58.515 41.667 0.00 0.00 0.00 2.44
2268 8396 0.899720 CTTGGGTGTAGCTCCGGTAA 59.100 55.000 0.00 0.00 0.00 2.85
2331 8459 4.519213 ACGCCATACTTAACAAAGCCATA 58.481 39.130 0.00 0.00 0.00 2.74
2459 8607 3.335786 TCCACTAACTAGAGAAGACCCCA 59.664 47.826 0.00 0.00 0.00 4.96
2522 8670 1.971167 GATGGCGCAACCCTTGTGA 60.971 57.895 10.83 0.00 43.66 3.58
2558 8706 2.670635 GCAATGCGAGTCGTGAGAT 58.329 52.632 15.08 0.00 45.19 2.75
2685 8833 3.331889 ACTTCTTGACCCATCCATGACTT 59.668 43.478 0.00 0.00 0.00 3.01
2838 8992 7.916914 TTTAGATGCTCTTAAACCTACAACC 57.083 36.000 0.00 0.00 0.00 3.77
2839 8993 8.328864 CGATTTAGATGCTCTTAAACCTACAAC 58.671 37.037 0.00 0.00 0.00 3.32
2863 9019 2.749839 CGGATTTGCCAAGCCCGA 60.750 61.111 12.38 0.00 42.49 5.14
2867 9023 2.710902 GGGACCGGATTTGCCAAGC 61.711 63.158 9.46 0.00 35.94 4.01
2938 9098 3.541996 TGAGACATATGAATGTGCGGT 57.458 42.857 10.38 0.00 46.49 5.68
2963 9123 4.889409 GGATTACATGGATTTGAGGCTTCA 59.111 41.667 0.00 0.00 0.00 3.02
2965 9125 4.870636 TGGATTACATGGATTTGAGGCTT 58.129 39.130 0.00 0.00 0.00 4.35
3045 9206 6.921307 GTCCGGTTTTGTTGAACTATGATTTT 59.079 34.615 0.00 0.00 0.00 1.82
3061 9543 2.366916 TCATTTTGGCATGTCCGGTTTT 59.633 40.909 0.00 0.00 37.80 2.43
3113 9595 3.329889 AGTGATCCGGCCAGCCAA 61.330 61.111 9.78 0.00 35.37 4.52
3254 9741 1.035139 GGGTAGGAAATACGAGGCGA 58.965 55.000 0.00 0.00 34.99 5.54
3272 9759 3.669536 GAAGAAGAAGGAGACAACAGGG 58.330 50.000 0.00 0.00 0.00 4.45
3274 9761 2.734079 GCGAAGAAGAAGGAGACAACAG 59.266 50.000 0.00 0.00 0.00 3.16
3275 9762 2.548067 GGCGAAGAAGAAGGAGACAACA 60.548 50.000 0.00 0.00 0.00 3.33
3303 9791 1.197721 GATGACCGTGCAAAGAAGTGG 59.802 52.381 0.00 0.00 0.00 4.00
3316 9804 1.003118 TGAAACCCTCTTGGATGACCG 59.997 52.381 0.00 0.00 39.42 4.79
3336 9824 1.598962 CAAGATCATGCCGGCGGAT 60.599 57.895 33.44 27.51 0.00 4.18
3343 9831 1.245732 GAGGATGCCAAGATCATGCC 58.754 55.000 0.00 0.00 33.48 4.40
3344 9832 1.245732 GGAGGATGCCAAGATCATGC 58.754 55.000 0.00 0.00 33.24 4.06
3375 9863 2.900546 GAGAAGAGGAGGTTCCAACTCA 59.099 50.000 12.68 0.00 39.61 3.41
3382 9870 2.900546 TGAGGTTGAGAAGAGGAGGTTC 59.099 50.000 0.00 0.00 0.00 3.62
3389 9877 4.465660 TGGAGAGATTGAGGTTGAGAAGAG 59.534 45.833 0.00 0.00 0.00 2.85
3390 9878 4.420206 TGGAGAGATTGAGGTTGAGAAGA 58.580 43.478 0.00 0.00 0.00 2.87
3399 9887 4.639310 CCAAGACATTTGGAGAGATTGAGG 59.361 45.833 0.00 0.00 42.06 3.86


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

AutoCloner maintained by Alex Coulton.