Multiple sequence alignment - TraesCS4A01G179800

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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 TraesCS4A01G179800 chr4A 100.000 8293 0 0 1 8293 453604061 453612353 0.000000e+00 15315.0
1 TraesCS4A01G179800 chr4A 86.990 392 32 11 250 624 19654901 19655290 2.770000e-114 424.0
2 TraesCS4A01G179800 chr4A 95.455 44 0 1 6051 6094 453609945 453609986 1.490000e-07 69.4
3 TraesCS4A01G179800 chr4A 95.455 44 0 1 5885 5926 453610111 453610154 1.490000e-07 69.4
4 TraesCS4A01G179800 chr4B 95.160 3306 108 18 2455 5741 184235187 184238459 0.000000e+00 5171.0
5 TraesCS4A01G179800 chr4B 96.362 2611 73 7 5702 8293 184238458 184241065 0.000000e+00 4276.0
6 TraesCS4A01G179800 chr4B 94.615 947 26 6 737 1679 184233224 184234149 0.000000e+00 1443.0
7 TraesCS4A01G179800 chr4B 93.252 815 31 5 1671 2462 184234337 184235150 0.000000e+00 1179.0
8 TraesCS4A01G179800 chr4B 89.669 242 23 2 1 241 184231140 184231380 2.910000e-79 307.0
9 TraesCS4A01G179800 chr4B 95.455 44 0 1 6051 6094 184238641 184238682 1.490000e-07 69.4
10 TraesCS4A01G179800 chr4B 100.000 31 0 0 5933 5963 184238840 184238870 3.230000e-04 58.4
11 TraesCS4A01G179800 chr4D 96.529 2622 60 14 5702 8293 121437635 121440255 0.000000e+00 4309.0
12 TraesCS4A01G179800 chr4D 96.113 1955 50 10 2455 4404 121434177 121436110 0.000000e+00 3166.0
13 TraesCS4A01G179800 chr4D 96.211 950 28 5 737 1679 121432357 121433305 0.000000e+00 1548.0
14 TraesCS4A01G179800 chr4D 95.137 802 22 9 1671 2455 121433333 121434134 0.000000e+00 1249.0
15 TraesCS4A01G179800 chr4D 97.286 737 18 2 4140 4875 121436100 121436835 0.000000e+00 1249.0
16 TraesCS4A01G179800 chr4D 96.371 744 23 3 5000 5741 121436895 121437636 0.000000e+00 1221.0
17 TraesCS4A01G179800 chr4D 88.136 236 24 3 1 234 121432112 121432345 2.280000e-70 278.0
18 TraesCS4A01G179800 chr4D 95.455 44 0 1 6051 6094 121437820 121437861 1.490000e-07 69.4
19 TraesCS4A01G179800 chr4D 100.000 35 0 0 5885 5919 121437990 121438024 1.930000e-06 65.8
20 TraesCS4A01G179800 chr4D 92.500 40 2 1 1 39 121432058 121432097 1.000000e-03 56.5
21 TraesCS4A01G179800 chr4D 100.000 28 0 0 5933 5960 121438019 121438046 1.500000e-02 52.8
22 TraesCS4A01G179800 chr1A 88.295 393 29 9 250 625 303010087 303010479 9.810000e-124 455.0
23 TraesCS4A01G179800 chr1A 85.870 92 12 1 139 230 108075942 108075852 6.850000e-16 97.1
24 TraesCS4A01G179800 chr1A 90.164 61 6 0 623 683 282160882 282160942 6.900000e-11 80.5
25 TraesCS4A01G179800 chr5A 87.940 398 30 10 245 625 554060886 554061282 3.530000e-123 453.0
26 TraesCS4A01G179800 chr5A 82.727 330 46 9 5104 5425 445201607 445201933 4.900000e-72 283.0
27 TraesCS4A01G179800 chr5A 94.643 56 2 1 4719 4773 546715167 546715112 1.480000e-12 86.1
28 TraesCS4A01G179800 chr6A 87.224 407 30 14 238 626 423807120 423807522 2.120000e-120 444.0
29 TraesCS4A01G179800 chr6A 84.536 97 11 3 136 230 127617570 127617476 8.860000e-15 93.5
30 TraesCS4A01G179800 chr6A 92.982 57 3 1 628 683 12317646 12317702 1.920000e-11 82.4
31 TraesCS4A01G179800 chrUn 87.500 392 33 12 239 625 259672135 259671755 9.880000e-119 438.0
32 TraesCS4A01G179800 chrUn 91.379 58 5 0 629 686 31617063 31617006 6.900000e-11 80.5
33 TraesCS4A01G179800 chrUn 88.889 63 7 0 620 682 76130726 76130788 2.480000e-10 78.7
34 TraesCS4A01G179800 chr2A 91.720 314 22 4 250 560 71266182 71266494 4.600000e-117 433.0
35 TraesCS4A01G179800 chr2A 91.401 314 23 4 250 560 71216509 71216821 2.140000e-115 427.0
36 TraesCS4A01G179800 chr2A 85.442 419 38 13 230 628 165863162 165863577 1.670000e-111 414.0
37 TraesCS4A01G179800 chr2A 89.877 326 26 5 256 576 281661064 281660741 5.990000e-111 412.0
38 TraesCS4A01G179800 chr2A 91.358 81 5 1 4638 4716 502836150 502836230 8.800000e-20 110.0
39 TraesCS4A01G179800 chr7A 87.195 328 37 3 5104 5427 128783370 128783044 1.310000e-97 368.0
40 TraesCS4A01G179800 chr7A 84.375 128 10 7 4644 4765 708614929 708614806 5.260000e-22 117.0
41 TraesCS4A01G179800 chr7A 92.208 77 5 1 4644 4719 636917342 636917266 3.170000e-19 108.0
42 TraesCS4A01G179800 chr7A 81.633 147 9 7 4644 4773 671487616 671487471 1.140000e-18 106.0
43 TraesCS4A01G179800 chr7A 85.263 95 13 1 136 230 646081295 646081202 6.850000e-16 97.1
44 TraesCS4A01G179800 chr6B 89.855 276 26 2 5152 5427 625367862 625368135 3.680000e-93 353.0
45 TraesCS4A01G179800 chr6B 87.059 85 9 1 4637 4719 535451849 535451765 2.460000e-15 95.3
46 TraesCS4A01G179800 chr6D 89.170 277 28 2 5152 5427 414780998 414781273 2.220000e-90 344.0
47 TraesCS4A01G179800 chr6D 78.261 161 11 12 4644 4784 3744099 3743943 1.920000e-11 82.4
48 TraesCS4A01G179800 chr3B 88.043 276 28 5 5153 5427 159569241 159568970 1.040000e-83 322.0
49 TraesCS4A01G179800 chr3B 79.861 144 10 8 4654 4779 561746795 561746653 4.120000e-13 87.9
50 TraesCS4A01G179800 chr3B 92.727 55 4 0 4719 4773 156722518 156722572 6.900000e-11 80.5
51 TraesCS4A01G179800 chr5D 83.271 269 40 4 5147 5411 259443887 259443620 8.320000e-60 243.0
52 TraesCS4A01G179800 chr5D 81.818 110 13 4 136 243 450380573 450380469 1.480000e-12 86.1
53 TraesCS4A01G179800 chr5B 80.308 325 56 7 5105 5427 653711356 653711674 1.080000e-58 239.0
54 TraesCS4A01G179800 chr5B 81.481 108 18 2 123 230 360418645 360418750 4.120000e-13 87.9
55 TraesCS4A01G179800 chr2D 83.448 145 6 8 4641 4769 192744284 192744142 1.460000e-22 119.0
56 TraesCS4A01G179800 chr2D 86.316 95 13 0 136 230 615978187 615978281 4.090000e-18 104.0
57 TraesCS4A01G179800 chr2D 88.889 72 8 0 3707 3778 169039707 169039636 1.150000e-13 89.8
58 TraesCS4A01G179800 chr2B 83.688 141 8 6 4638 4763 247928124 247928264 1.460000e-22 119.0
59 TraesCS4A01G179800 chr2B 90.278 72 7 0 3707 3778 228984866 228984937 2.460000e-15 95.3
60 TraesCS4A01G179800 chr3A 87.368 95 11 1 136 230 25233200 25233107 3.170000e-19 108.0
61 TraesCS4A01G179800 chr3A 87.692 65 8 0 619 683 569166094 569166158 8.930000e-10 76.8
62 TraesCS4A01G179800 chr3D 82.353 136 7 10 4641 4759 580990219 580990084 1.470000e-17 102.0
63 TraesCS4A01G179800 chr7D 88.235 68 6 2 620 686 63467314 63467248 6.900000e-11 80.5
64 TraesCS4A01G179800 chr7D 77.564 156 17 6 4644 4781 499063967 499063812 2.480000e-10 78.7
65 TraesCS4A01G179800 chr1D 91.525 59 3 2 629 686 290446587 290446530 6.900000e-11 80.5
66 TraesCS4A01G179800 chr1D 86.765 68 9 0 616 683 387944207 387944274 8.930000e-10 76.8
67 TraesCS4A01G179800 chr1B 87.324 71 7 2 613 683 27291081 27291149 6.900000e-11 80.5


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 TraesCS4A01G179800 chr4A 453604061 453612353 8292 False 5151.266667 15315 96.970000 1 8293 3 chr4A.!!$F2 8292
1 TraesCS4A01G179800 chr4B 184231140 184241065 9925 False 1786.257143 5171 94.930429 1 8293 7 chr4B.!!$F1 8292
2 TraesCS4A01G179800 chr4D 121432058 121440255 8197 False 1205.863636 4309 95.794364 1 8293 11 chr4D.!!$F1 8292

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
487 555 0.252761 TGGCAGAGAAATCATGGCGA 59.747 50.000 0.00 0.00 42.03 5.54 F
619 687 0.306533 ACAACGCACGGACAATTGTC 59.693 50.000 27.16 27.16 44.04 3.18 F
620 688 0.586319 CAACGCACGGACAATTGTCT 59.414 50.000 31.81 15.30 44.20 3.41 F
623 691 1.000506 ACGCACGGACAATTGTCTAGT 59.999 47.619 31.81 27.63 44.20 2.57 F
1114 2656 1.139947 CTTTCGTCTCCCTCTCCGC 59.860 63.158 0.00 0.00 0.00 5.54 F
2505 4324 0.756903 AACAACACTAGGCACCGTCT 59.243 50.000 0.00 0.00 0.00 4.18 F
3131 4953 2.101575 GCTGTGGCATGCATCGTG 59.898 61.111 21.36 6.31 38.54 4.35 F
4095 5922 1.806542 CATTGTTCACCGTGGAGGAAG 59.193 52.381 0.00 0.00 45.00 3.46 F
4214 6041 2.821366 CCAGCTCGGTCCACATGC 60.821 66.667 0.00 0.00 0.00 4.06 F
5064 7150 0.845102 AATTCGACCCCCACCTCCTT 60.845 55.000 0.00 0.00 0.00 3.36 F
5769 7897 1.000506 TGTAGTCGGTGCCTTGTTCTC 59.999 52.381 0.00 0.00 0.00 2.87 F
6818 8956 1.352622 TTGTTGGTCCTGCCCTCACT 61.353 55.000 0.00 0.00 36.04 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1350 2892 0.315568 GGCCTAGGCACGTCTATCTG 59.684 60.000 34.09 0.0 44.11 2.90 R
1613 3155 0.319555 TGAGTGTTGCCTACTCGTGC 60.320 55.000 0.00 0.0 45.82 5.34 R
1819 3586 0.611896 AACCTCGGGGCAGGAATTTG 60.612 55.000 0.00 0.0 36.96 2.32 R
2472 4291 1.748493 TGTTGTTTGGTTCACCTCAGC 59.252 47.619 0.00 0.0 36.82 4.26 R
2893 4714 2.068519 GCCAATGCCAGCAACTTTTAC 58.931 47.619 0.00 0.0 0.00 2.01 R
4095 5922 0.035820 TATGGTGGGAACGCAGGAAC 60.036 55.000 0.00 0.0 44.70 3.62 R
4164 5991 0.108138 GAGTACTTGCGGTGCATCCT 60.108 55.000 0.00 0.0 38.76 3.24 R
4912 6997 1.271488 GGGGGTTATCACGTGGTTTGA 60.271 52.381 17.00 0.0 0.00 2.69 R
5145 7235 1.302271 GAGGACGTGGGGTTGGTTC 60.302 63.158 0.00 0.0 0.00 3.62 R
6818 8956 0.111639 GGGTAAACAAGTGAGGGCCA 59.888 55.000 6.18 0.0 0.00 5.36 R
6833 8971 0.331278 CCATCCACAGCCAAAGGGTA 59.669 55.000 0.00 0.0 36.17 3.69 R
7652 9812 1.702182 TTGCAAGGGAAACTGATGCA 58.298 45.000 0.00 0.0 44.54 3.96 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 90 5.500234 ACTAGTCATGAATTAAAGCCTGCA 58.500 37.500 0.00 0.00 0.00 4.41
67 122 8.454106 AGTTGAATCTTATGTGCAAGTATGAAC 58.546 33.333 0.00 0.00 35.44 3.18
153 211 4.829872 TTGCTCCCTCCGTTCTTAAATA 57.170 40.909 0.00 0.00 0.00 1.40
285 343 5.422214 ACGTAAGGTTCCATTTCATCTCT 57.578 39.130 0.00 0.00 46.39 3.10
286 344 5.420409 ACGTAAGGTTCCATTTCATCTCTC 58.580 41.667 0.00 0.00 46.39 3.20
287 345 5.187967 ACGTAAGGTTCCATTTCATCTCTCT 59.812 40.000 0.00 0.00 46.39 3.10
288 346 6.109359 CGTAAGGTTCCATTTCATCTCTCTT 58.891 40.000 0.00 0.00 0.00 2.85
289 347 6.595716 CGTAAGGTTCCATTTCATCTCTCTTT 59.404 38.462 0.00 0.00 0.00 2.52
291 349 5.181748 AGGTTCCATTTCATCTCTCTTTCG 58.818 41.667 0.00 0.00 0.00 3.46
292 350 4.938226 GGTTCCATTTCATCTCTCTTTCGT 59.062 41.667 0.00 0.00 0.00 3.85
293 351 5.064071 GGTTCCATTTCATCTCTCTTTCGTC 59.936 44.000 0.00 0.00 0.00 4.20
294 352 4.759782 TCCATTTCATCTCTCTTTCGTCC 58.240 43.478 0.00 0.00 0.00 4.79
295 353 4.222810 TCCATTTCATCTCTCTTTCGTCCA 59.777 41.667 0.00 0.00 0.00 4.02
296 354 4.937620 CCATTTCATCTCTCTTTCGTCCAA 59.062 41.667 0.00 0.00 0.00 3.53
297 355 5.163814 CCATTTCATCTCTCTTTCGTCCAAC 60.164 44.000 0.00 0.00 0.00 3.77
298 356 3.594603 TCATCTCTCTTTCGTCCAACC 57.405 47.619 0.00 0.00 0.00 3.77
299 357 3.165875 TCATCTCTCTTTCGTCCAACCT 58.834 45.455 0.00 0.00 0.00 3.50
300 358 3.578716 TCATCTCTCTTTCGTCCAACCTT 59.421 43.478 0.00 0.00 0.00 3.50
301 359 3.662247 TCTCTCTTTCGTCCAACCTTC 57.338 47.619 0.00 0.00 0.00 3.46
302 360 2.299297 TCTCTCTTTCGTCCAACCTTCC 59.701 50.000 0.00 0.00 0.00 3.46
303 361 2.037251 CTCTCTTTCGTCCAACCTTCCA 59.963 50.000 0.00 0.00 0.00 3.53
304 362 2.637872 TCTCTTTCGTCCAACCTTCCAT 59.362 45.455 0.00 0.00 0.00 3.41
307 365 5.659525 TCTCTTTCGTCCAACCTTCCATATA 59.340 40.000 0.00 0.00 0.00 0.86
309 367 7.507956 TCTCTTTCGTCCAACCTTCCATATATA 59.492 37.037 0.00 0.00 0.00 0.86
310 368 7.439381 TCTTTCGTCCAACCTTCCATATATAC 58.561 38.462 0.00 0.00 0.00 1.47
311 369 5.381174 TCGTCCAACCTTCCATATATACG 57.619 43.478 0.00 0.00 0.00 3.06
312 370 4.828939 TCGTCCAACCTTCCATATATACGT 59.171 41.667 0.00 0.00 0.00 3.57
313 371 5.048504 TCGTCCAACCTTCCATATATACGTC 60.049 44.000 0.00 0.00 0.00 4.34
314 372 5.048224 CGTCCAACCTTCCATATATACGTCT 60.048 44.000 0.00 0.00 0.00 4.18
315 373 6.388278 GTCCAACCTTCCATATATACGTCTC 58.612 44.000 0.00 0.00 0.00 3.36
316 374 6.015688 GTCCAACCTTCCATATATACGTCTCA 60.016 42.308 0.00 0.00 0.00 3.27
317 375 6.015688 TCCAACCTTCCATATATACGTCTCAC 60.016 42.308 0.00 0.00 0.00 3.51
319 377 6.821031 ACCTTCCATATATACGTCTCACTC 57.179 41.667 0.00 0.00 0.00 3.51
320 378 6.544650 ACCTTCCATATATACGTCTCACTCT 58.455 40.000 0.00 0.00 0.00 3.24
322 380 7.506261 ACCTTCCATATATACGTCTCACTCTTT 59.494 37.037 0.00 0.00 0.00 2.52
324 382 9.400638 CTTCCATATATACGTCTCACTCTTTTC 57.599 37.037 0.00 0.00 0.00 2.29
325 383 7.582352 TCCATATATACGTCTCACTCTTTTCG 58.418 38.462 0.00 0.00 0.00 3.46
327 385 8.501580 CCATATATACGTCTCACTCTTTTCGTA 58.498 37.037 0.00 0.00 37.96 3.43
330 388 4.094090 ACGTCTCACTCTTTTCGTATCC 57.906 45.455 0.00 0.00 0.00 2.59
332 390 4.142643 ACGTCTCACTCTTTTCGTATCCTC 60.143 45.833 0.00 0.00 0.00 3.71
333 391 4.095185 CGTCTCACTCTTTTCGTATCCTCT 59.905 45.833 0.00 0.00 0.00 3.69
334 392 5.392165 CGTCTCACTCTTTTCGTATCCTCTT 60.392 44.000 0.00 0.00 0.00 2.85
335 393 6.391537 GTCTCACTCTTTTCGTATCCTCTTT 58.608 40.000 0.00 0.00 0.00 2.52
336 394 6.309251 GTCTCACTCTTTTCGTATCCTCTTTG 59.691 42.308 0.00 0.00 0.00 2.77
337 395 6.208797 TCTCACTCTTTTCGTATCCTCTTTGA 59.791 38.462 0.00 0.00 0.00 2.69
338 396 6.936279 TCACTCTTTTCGTATCCTCTTTGAT 58.064 36.000 0.00 0.00 0.00 2.57
339 397 7.386851 TCACTCTTTTCGTATCCTCTTTGATT 58.613 34.615 0.00 0.00 0.00 2.57
340 398 7.878127 TCACTCTTTTCGTATCCTCTTTGATTT 59.122 33.333 0.00 0.00 0.00 2.17
341 399 8.507249 CACTCTTTTCGTATCCTCTTTGATTTT 58.493 33.333 0.00 0.00 0.00 1.82
342 400 9.067986 ACTCTTTTCGTATCCTCTTTGATTTTT 57.932 29.630 0.00 0.00 0.00 1.94
369 437 9.532494 TTCCTTCCATATTTGATTTTTCTCTCA 57.468 29.630 0.00 0.00 0.00 3.27
370 438 9.705103 TCCTTCCATATTTGATTTTTCTCTCAT 57.295 29.630 0.00 0.00 0.00 2.90
389 457 9.676861 TCTCTCATTTATTCAATTGTCTCATGT 57.323 29.630 5.13 0.00 0.00 3.21
403 471 9.787435 AATTGTCTCATGTTTAGTAACTTACCA 57.213 29.630 0.00 0.00 35.24 3.25
404 472 9.787435 ATTGTCTCATGTTTAGTAACTTACCAA 57.213 29.630 0.00 0.00 35.24 3.67
405 473 9.616156 TTGTCTCATGTTTAGTAACTTACCAAA 57.384 29.630 0.00 0.00 35.24 3.28
406 474 9.616156 TGTCTCATGTTTAGTAACTTACCAAAA 57.384 29.630 0.00 0.00 35.24 2.44
426 494 9.620259 ACCAAAATAAACATACATTTTGTTGGT 57.380 25.926 14.99 0.00 44.80 3.67
474 542 8.845413 AAAATGCTTAACAATAAAATGGCAGA 57.155 26.923 0.00 0.00 32.04 4.26
475 543 8.483307 AAATGCTTAACAATAAAATGGCAGAG 57.517 30.769 0.00 0.00 32.04 3.35
476 544 6.832520 TGCTTAACAATAAAATGGCAGAGA 57.167 33.333 0.00 0.00 0.00 3.10
477 545 7.225784 TGCTTAACAATAAAATGGCAGAGAA 57.774 32.000 0.00 0.00 0.00 2.87
478 546 7.665690 TGCTTAACAATAAAATGGCAGAGAAA 58.334 30.769 0.00 0.00 0.00 2.52
479 547 8.313292 TGCTTAACAATAAAATGGCAGAGAAAT 58.687 29.630 0.00 0.00 0.00 2.17
480 548 8.811378 GCTTAACAATAAAATGGCAGAGAAATC 58.189 33.333 0.00 0.00 0.00 2.17
481 549 9.859427 CTTAACAATAAAATGGCAGAGAAATCA 57.141 29.630 0.00 0.00 0.00 2.57
483 551 8.712285 AACAATAAAATGGCAGAGAAATCATG 57.288 30.769 0.00 0.00 0.00 3.07
484 552 7.270047 ACAATAAAATGGCAGAGAAATCATGG 58.730 34.615 0.00 0.00 0.00 3.66
485 553 3.814005 AAATGGCAGAGAAATCATGGC 57.186 42.857 0.00 5.58 39.75 4.40
486 554 1.315690 ATGGCAGAGAAATCATGGCG 58.684 50.000 0.00 0.00 42.03 5.69
487 555 0.252761 TGGCAGAGAAATCATGGCGA 59.747 50.000 0.00 0.00 42.03 5.54
488 556 0.659957 GGCAGAGAAATCATGGCGAC 59.340 55.000 0.00 0.00 0.00 5.19
489 557 1.661341 GCAGAGAAATCATGGCGACT 58.339 50.000 0.00 0.00 0.00 4.18
490 558 1.329906 GCAGAGAAATCATGGCGACTG 59.670 52.381 0.00 0.00 0.00 3.51
491 559 1.329906 CAGAGAAATCATGGCGACTGC 59.670 52.381 0.00 0.00 41.71 4.40
492 560 1.065926 AGAGAAATCATGGCGACTGCA 60.066 47.619 0.00 0.00 45.35 4.41
493 561 1.945394 GAGAAATCATGGCGACTGCAT 59.055 47.619 0.00 0.00 45.35 3.96
494 562 3.133691 GAGAAATCATGGCGACTGCATA 58.866 45.455 0.00 0.00 45.35 3.14
495 563 2.874701 AGAAATCATGGCGACTGCATAC 59.125 45.455 0.00 0.00 45.35 2.39
496 564 2.330440 AATCATGGCGACTGCATACA 57.670 45.000 0.00 0.00 45.35 2.29
497 565 2.330440 ATCATGGCGACTGCATACAA 57.670 45.000 0.00 0.00 45.35 2.41
498 566 2.106477 TCATGGCGACTGCATACAAA 57.894 45.000 0.00 0.00 45.35 2.83
499 567 2.009051 TCATGGCGACTGCATACAAAG 58.991 47.619 0.00 0.00 45.35 2.77
500 568 2.009051 CATGGCGACTGCATACAAAGA 58.991 47.619 0.00 0.00 45.35 2.52
501 569 2.401583 TGGCGACTGCATACAAAGAT 57.598 45.000 0.00 0.00 45.35 2.40
502 570 2.710377 TGGCGACTGCATACAAAGATT 58.290 42.857 0.00 0.00 45.35 2.40
503 571 3.081061 TGGCGACTGCATACAAAGATTT 58.919 40.909 0.00 0.00 45.35 2.17
504 572 3.119884 TGGCGACTGCATACAAAGATTTG 60.120 43.478 3.79 3.79 45.35 2.32
505 573 3.429085 GCGACTGCATACAAAGATTTGG 58.571 45.455 9.91 0.00 40.81 3.28
506 574 3.119849 GCGACTGCATACAAAGATTTGGT 60.120 43.478 9.91 0.00 40.81 3.67
507 575 4.094294 GCGACTGCATACAAAGATTTGGTA 59.906 41.667 9.91 1.38 40.81 3.25
508 576 5.391523 GCGACTGCATACAAAGATTTGGTAA 60.392 40.000 9.91 0.00 40.81 2.85
509 577 6.250819 CGACTGCATACAAAGATTTGGTAAG 58.749 40.000 9.91 3.23 42.34 2.34
510 578 6.092122 CGACTGCATACAAAGATTTGGTAAGA 59.908 38.462 9.91 0.00 42.34 2.10
511 579 7.201644 CGACTGCATACAAAGATTTGGTAAGAT 60.202 37.037 9.91 0.00 42.34 2.40
512 580 8.353423 ACTGCATACAAAGATTTGGTAAGATT 57.647 30.769 9.91 0.00 42.34 2.40
513 581 8.806146 ACTGCATACAAAGATTTGGTAAGATTT 58.194 29.630 9.91 0.00 42.34 2.17
514 582 9.643693 CTGCATACAAAGATTTGGTAAGATTTT 57.356 29.630 9.91 0.00 42.34 1.82
519 587 7.882179 ACAAAGATTTGGTAAGATTTTAGCGT 58.118 30.769 9.91 0.00 42.34 5.07
520 588 9.005777 ACAAAGATTTGGTAAGATTTTAGCGTA 57.994 29.630 9.91 0.00 42.34 4.42
523 591 8.958119 AGATTTGGTAAGATTTTAGCGTATCA 57.042 30.769 15.42 0.00 39.55 2.15
524 592 9.391006 AGATTTGGTAAGATTTTAGCGTATCAA 57.609 29.630 15.42 0.00 39.55 2.57
587 655 8.865590 AAAAGACGTGCAGTTATTAAAATGTT 57.134 26.923 0.00 0.00 33.27 2.71
588 656 8.865590 AAAGACGTGCAGTTATTAAAATGTTT 57.134 26.923 0.00 0.00 33.27 2.83
606 674 5.954434 TGTTTATACTCCGATTACAACGC 57.046 39.130 0.00 0.00 0.00 4.84
607 675 5.409211 TGTTTATACTCCGATTACAACGCA 58.591 37.500 0.00 0.00 0.00 5.24
608 676 5.289193 TGTTTATACTCCGATTACAACGCAC 59.711 40.000 0.00 0.00 0.00 5.34
610 678 0.734942 ACTCCGATTACAACGCACGG 60.735 55.000 0.00 0.00 44.09 4.94
611 679 4.172346 CCGATTACAACGCACGGA 57.828 55.556 0.00 0.00 45.31 4.69
612 680 0.733566 TCCGATTACAACGCACGGAC 60.734 55.000 0.00 0.00 45.87 4.79
613 681 1.009903 CCGATTACAACGCACGGACA 61.010 55.000 0.00 0.00 45.31 4.02
614 682 0.785378 CGATTACAACGCACGGACAA 59.215 50.000 0.00 0.00 0.00 3.18
615 683 1.392168 CGATTACAACGCACGGACAAT 59.608 47.619 0.00 0.00 0.00 2.71
616 684 2.159761 CGATTACAACGCACGGACAATT 60.160 45.455 0.00 0.00 0.00 2.32
617 685 2.672188 TTACAACGCACGGACAATTG 57.328 45.000 3.24 3.24 0.00 2.32
618 686 1.584175 TACAACGCACGGACAATTGT 58.416 45.000 11.78 11.78 37.30 2.71
619 687 0.306533 ACAACGCACGGACAATTGTC 59.693 50.000 27.16 27.16 44.04 3.18
620 688 0.586319 CAACGCACGGACAATTGTCT 59.414 50.000 31.81 15.30 44.20 3.41
621 689 1.795872 CAACGCACGGACAATTGTCTA 59.204 47.619 31.81 0.00 44.20 2.59
622 690 1.710013 ACGCACGGACAATTGTCTAG 58.290 50.000 31.81 27.09 44.20 2.43
623 691 1.000506 ACGCACGGACAATTGTCTAGT 59.999 47.619 31.81 27.63 44.20 2.57
624 692 2.229543 ACGCACGGACAATTGTCTAGTA 59.770 45.455 31.81 0.00 44.20 1.82
625 693 3.119245 ACGCACGGACAATTGTCTAGTAT 60.119 43.478 31.81 19.03 44.20 2.12
626 694 3.863424 CGCACGGACAATTGTCTAGTATT 59.137 43.478 31.81 12.47 44.20 1.89
627 695 4.328983 CGCACGGACAATTGTCTAGTATTT 59.671 41.667 31.81 12.18 44.20 1.40
628 696 5.500290 CGCACGGACAATTGTCTAGTATTTC 60.500 44.000 31.81 19.84 44.20 2.17
631 699 6.594159 CACGGACAATTGTCTAGTATTTCCTT 59.406 38.462 31.81 9.02 44.20 3.36
632 700 6.817140 ACGGACAATTGTCTAGTATTTCCTTC 59.183 38.462 31.81 13.64 44.20 3.46
636 704 8.252964 ACAATTGTCTAGTATTTCCTTCGTTC 57.747 34.615 4.92 0.00 0.00 3.95
637 705 8.095169 ACAATTGTCTAGTATTTCCTTCGTTCT 58.905 33.333 4.92 0.00 0.00 3.01
638 706 9.582431 CAATTGTCTAGTATTTCCTTCGTTCTA 57.418 33.333 0.00 0.00 0.00 2.10
650 718 8.446599 TTTCCTTCGTTCTAAAATTCTTGTCT 57.553 30.769 0.00 0.00 0.00 3.41
651 719 8.446599 TTCCTTCGTTCTAAAATTCTTGTCTT 57.553 30.769 0.00 0.00 0.00 3.01
652 720 9.550406 TTCCTTCGTTCTAAAATTCTTGTCTTA 57.450 29.630 0.00 0.00 0.00 2.10
653 721 9.204570 TCCTTCGTTCTAAAATTCTTGTCTTAG 57.795 33.333 0.00 0.00 0.00 2.18
670 738 8.919777 TTGTCTTAGATTCATCTAGATACGGA 57.080 34.615 4.54 0.00 40.23 4.69
757 2293 1.168714 ACAAAGGGAGCAGAATTCGC 58.831 50.000 12.44 12.44 0.00 4.70
778 2314 2.223377 CGAGGAAACGAAAAGGAAGTGG 59.777 50.000 0.00 0.00 35.09 4.00
1114 2656 1.139947 CTTTCGTCTCCCTCTCCGC 59.860 63.158 0.00 0.00 0.00 5.54
1262 2804 4.214327 CCCTCCTCTTCGAGCGCC 62.214 72.222 2.29 0.00 0.00 6.53
1323 2865 2.169789 CATCTCGCACGCCTCTTGG 61.170 63.158 0.00 0.00 0.00 3.61
1350 2892 7.892609 TGATTGATTGATTTGATCCATCCATC 58.107 34.615 8.24 8.24 35.70 3.51
1488 3030 2.779755 TGCAACCTATGATTGGACGT 57.220 45.000 0.00 0.00 0.00 4.34
1552 3094 2.229302 AGCAAGACTGACGAGTAAGACC 59.771 50.000 0.00 0.00 30.16 3.85
1607 3149 7.753580 TCTTTATATTGCGTCGTACTGATATGG 59.246 37.037 0.00 0.00 0.00 2.74
1613 3155 3.629058 CGTCGTACTGATATGGACCAAG 58.371 50.000 0.00 0.00 0.00 3.61
1854 3621 7.175990 GCCCCGAGGTTATGATTTCAAAATATA 59.824 37.037 0.00 0.00 34.57 0.86
1937 3704 4.657504 ACTCTGGGAATCAATCTCTGCATA 59.342 41.667 0.00 0.00 0.00 3.14
2005 3778 4.106197 GGTCTGCTCTTAACTATGTCACG 58.894 47.826 0.00 0.00 0.00 4.35
2006 3779 4.380655 GGTCTGCTCTTAACTATGTCACGT 60.381 45.833 0.00 0.00 0.00 4.49
2150 3925 6.470278 GGTAACCAAACCTTCTTCTAAGCTA 58.530 40.000 0.00 0.00 36.53 3.32
2226 4001 4.201950 CCCAAGCAAGGAAGAAATGTATCG 60.202 45.833 0.00 0.00 0.00 2.92
2235 4010 9.884465 CAAGGAAGAAATGTATCGGATTTATTC 57.116 33.333 0.00 0.00 39.02 1.75
2274 4049 2.158534 TGGACCAAACAACACTAGGCAT 60.159 45.455 0.00 0.00 0.00 4.40
2375 4150 4.986054 ACTTACACCTCACACCCAAATA 57.014 40.909 0.00 0.00 0.00 1.40
2381 4156 6.493189 ACACCTCACACCCAAATAAAAATT 57.507 33.333 0.00 0.00 0.00 1.82
2472 4291 9.619316 TCGAAAAGTTATTTCAATTGTATGGTG 57.381 29.630 5.13 0.00 0.00 4.17
2503 4322 1.305201 CAAACAACACTAGGCACCGT 58.695 50.000 0.00 0.00 0.00 4.83
2505 4324 0.756903 AACAACACTAGGCACCGTCT 59.243 50.000 0.00 0.00 0.00 4.18
2589 4409 7.591165 AGAGATTCAAATTCAGACATGTTGTG 58.409 34.615 0.00 0.84 0.00 3.33
2672 4492 6.372937 GCTCCTGTTTAAGAAGCTATTTCTGT 59.627 38.462 0.00 0.00 45.41 3.41
2893 4714 9.890085 CATAAAATGCAATAAAACATGAAGTCG 57.110 29.630 0.00 0.00 0.00 4.18
2955 4777 6.943146 TCCTACTTGCAACATGTAACCATTTA 59.057 34.615 0.00 0.00 0.00 1.40
3008 4830 2.301870 CACCCTGTTGCCTCTTGTACTA 59.698 50.000 0.00 0.00 0.00 1.82
3130 4952 3.136123 GGCTGTGGCATGCATCGT 61.136 61.111 21.36 0.00 40.87 3.73
3131 4953 2.101575 GCTGTGGCATGCATCGTG 59.898 61.111 21.36 6.31 38.54 4.35
3132 4954 2.101575 CTGTGGCATGCATCGTGC 59.898 61.111 21.36 0.00 44.69 5.34
3261 5084 3.490761 GGTGGACATTTTTGTGGACACAG 60.491 47.826 5.21 0.00 42.94 3.66
3428 5251 4.010349 GGTGTGCTTCCTTAGTTAGCAAT 58.990 43.478 7.01 0.00 45.54 3.56
3654 5478 9.294030 CAAGCTAACAAATCTTTGGAATATGAC 57.706 33.333 7.51 0.00 42.34 3.06
3697 5521 2.223203 CGGAGTCAAATGCTGCATCTTC 60.223 50.000 16.55 6.44 0.00 2.87
3952 5779 2.139323 ATGCTGCATCCACATTGAGT 57.861 45.000 9.81 0.00 0.00 3.41
4095 5922 1.806542 CATTGTTCACCGTGGAGGAAG 59.193 52.381 0.00 0.00 45.00 3.46
4164 5991 5.375773 TCATCACACAAACCTCTTCATTCA 58.624 37.500 0.00 0.00 0.00 2.57
4214 6041 2.821366 CCAGCTCGGTCCACATGC 60.821 66.667 0.00 0.00 0.00 4.06
4296 6379 8.454106 CAGAACGATCAAATAGGAGATGTTTTT 58.546 33.333 0.00 0.00 0.00 1.94
4356 6439 3.947196 CTGCACTTTTATATGTCTGCCCA 59.053 43.478 0.00 0.00 0.00 5.36
4434 6517 2.957576 CTTTGAAGGACAGCGAAGTG 57.042 50.000 0.00 0.00 0.00 3.16
4580 6663 4.279169 TGTTGAGATTCCAAGCCAAGAAAG 59.721 41.667 0.00 0.00 0.00 2.62
4591 6674 3.167485 AGCCAAGAAAGCATCCATTTCA 58.833 40.909 1.73 0.00 38.79 2.69
4592 6675 3.773119 AGCCAAGAAAGCATCCATTTCAT 59.227 39.130 1.73 0.00 38.79 2.57
4671 6756 8.612619 CAAAATATAAGGTAAATCACGAGCAGT 58.387 33.333 0.00 0.00 0.00 4.40
4811 6896 7.640630 CGTGATTACGCTAGAGCTATATTAAGG 59.359 40.741 0.00 0.00 44.11 2.69
4971 7056 1.600916 GCGCCTCCTTGTTTCTGGT 60.601 57.895 0.00 0.00 0.00 4.00
4974 7059 2.076863 CGCCTCCTTGTTTCTGGTAAG 58.923 52.381 0.00 0.00 0.00 2.34
4978 7063 4.811063 GCCTCCTTGTTTCTGGTAAGGAAT 60.811 45.833 0.00 0.00 46.67 3.01
4979 7064 5.572885 GCCTCCTTGTTTCTGGTAAGGAATA 60.573 44.000 0.00 0.00 46.67 1.75
5064 7150 0.845102 AATTCGACCCCCACCTCCTT 60.845 55.000 0.00 0.00 0.00 3.36
5072 7158 1.691163 CCCCCACCTCCTTGTTTTTGT 60.691 52.381 0.00 0.00 0.00 2.83
5145 7235 7.040271 ACGATAACCCCCATTAATTTATTTCCG 60.040 37.037 0.00 0.00 0.00 4.30
5157 7247 2.203470 TATTTCCGAACCAACCCCAC 57.797 50.000 0.00 0.00 0.00 4.61
5358 7448 8.663167 ACATCATATCTCAATCTCAACCCAATA 58.337 33.333 0.00 0.00 0.00 1.90
5462 7552 7.831690 TGCATTATTGGTAATAGGAAACTGACA 59.168 33.333 0.00 0.00 43.88 3.58
5566 7656 6.588204 ACATACTGTCTGACCAGTTTTACAA 58.412 36.000 14.82 1.50 42.99 2.41
5741 7831 3.106242 TGCTTGTTTCGAGCTGTAAGA 57.894 42.857 9.86 0.00 41.18 2.10
5769 7897 1.000506 TGTAGTCGGTGCCTTGTTCTC 59.999 52.381 0.00 0.00 0.00 2.87
5960 8090 1.671850 GCTTTCCAGTGTGCGCTAGTA 60.672 52.381 9.73 0.00 0.00 1.82
6087 8221 7.776030 TGTTACTGATTTTGTTCCCAGTTTCTA 59.224 33.333 0.00 0.00 40.07 2.10
6100 8234 4.451900 CCAGTTTCTACTTTCCAGTGTGT 58.548 43.478 0.00 0.00 34.06 3.72
6479 8613 7.016268 AGGATAACTAAAGACTCAAGTGGAACA 59.984 37.037 0.00 0.00 41.43 3.18
6818 8956 1.352622 TTGTTGGTCCTGCCCTCACT 61.353 55.000 0.00 0.00 36.04 3.41
6833 8971 0.550914 TCACTGGCCCTCACTTGTTT 59.449 50.000 0.00 0.00 0.00 2.83
6965 9103 8.816640 AAGTAAACTAGAATTTGCAAATGTGG 57.183 30.769 24.74 18.20 0.00 4.17
6993 9131 6.768381 CCTGATGGTAGGGAAGTTCTATTTTC 59.232 42.308 2.25 0.00 34.06 2.29
6994 9132 7.366011 CCTGATGGTAGGGAAGTTCTATTTTCT 60.366 40.741 2.25 0.00 34.06 2.52
7063 9201 3.181467 GCAGCTCTGACTTCCATGACTAT 60.181 47.826 0.29 0.00 0.00 2.12
7238 9377 2.286772 CGTTAGGTTGTTTGGCACAGAC 60.287 50.000 0.00 0.00 44.33 3.51
7244 9383 1.363807 GTTTGGCACAGACAAGGGC 59.636 57.895 0.00 0.00 43.46 5.19
7619 9779 7.254227 TGTTTTGCAAGTCGAGTAAATAACT 57.746 32.000 0.00 0.00 42.80 2.24
7652 9812 9.382275 AGATTTGTCTGTGCTTTATTTGTTTTT 57.618 25.926 0.00 0.00 0.00 1.94
7655 9815 5.871524 TGTCTGTGCTTTATTTGTTTTTGCA 59.128 32.000 0.00 0.00 0.00 4.08
7678 9838 3.318839 TCAGTTTCCCTTGCAAACTCATG 59.681 43.478 0.00 0.00 41.25 3.07
7753 9915 4.396166 GCAAAACTTAGCTTCTAGCCATGA 59.604 41.667 0.00 0.00 43.77 3.07
7838 10000 1.598130 GCATATGACCTGGCCCGTC 60.598 63.158 6.97 12.14 0.00 4.79
8233 10395 1.077501 CGAGGTTGGTGGCCATGAT 60.078 57.895 9.72 0.00 31.53 2.45
8234 10396 1.378882 CGAGGTTGGTGGCCATGATG 61.379 60.000 9.72 0.00 31.53 3.07
8243 10405 3.349006 GCCATGATGCGGGCGTAG 61.349 66.667 0.00 0.00 40.93 3.51
8282 10444 2.444256 GGCCGCCTTGTAGAGGGAT 61.444 63.158 0.71 0.00 46.40 3.85
8283 10445 1.527370 GCCGCCTTGTAGAGGGATT 59.473 57.895 0.00 0.00 46.40 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 5.990120 AGATTCAACTAATTTTGCAGGCT 57.010 34.783 0.00 0.00 0.00 4.58
134 192 6.522946 ACTTATATTTAAGAACGGAGGGAGC 58.477 40.000 9.58 0.00 38.56 4.70
259 317 7.230712 AGAGATGAAATGGAACCTTACGTTTTT 59.769 33.333 0.00 0.00 33.74 1.94
261 319 6.238648 AGAGATGAAATGGAACCTTACGTTT 58.761 36.000 0.00 0.00 33.74 3.60
263 321 5.187967 AGAGAGATGAAATGGAACCTTACGT 59.812 40.000 0.00 0.00 0.00 3.57
264 322 5.665459 AGAGAGATGAAATGGAACCTTACG 58.335 41.667 0.00 0.00 0.00 3.18
265 323 7.201565 CGAAAGAGAGATGAAATGGAACCTTAC 60.202 40.741 0.00 0.00 0.00 2.34
267 325 5.645497 CGAAAGAGAGATGAAATGGAACCTT 59.355 40.000 0.00 0.00 0.00 3.50
270 328 5.064071 GGACGAAAGAGAGATGAAATGGAAC 59.936 44.000 0.00 0.00 0.00 3.62
271 329 5.178797 GGACGAAAGAGAGATGAAATGGAA 58.821 41.667 0.00 0.00 0.00 3.53
272 330 4.222810 TGGACGAAAGAGAGATGAAATGGA 59.777 41.667 0.00 0.00 0.00 3.41
273 331 4.507710 TGGACGAAAGAGAGATGAAATGG 58.492 43.478 0.00 0.00 0.00 3.16
274 332 5.163814 GGTTGGACGAAAGAGAGATGAAATG 60.164 44.000 0.00 0.00 0.00 2.32
275 333 4.938226 GGTTGGACGAAAGAGAGATGAAAT 59.062 41.667 0.00 0.00 0.00 2.17
277 335 3.578716 AGGTTGGACGAAAGAGAGATGAA 59.421 43.478 0.00 0.00 0.00 2.57
279 337 3.601443 AGGTTGGACGAAAGAGAGATG 57.399 47.619 0.00 0.00 0.00 2.90
281 339 2.299297 GGAAGGTTGGACGAAAGAGAGA 59.701 50.000 0.00 0.00 0.00 3.10
282 340 2.037251 TGGAAGGTTGGACGAAAGAGAG 59.963 50.000 0.00 0.00 0.00 3.20
283 341 2.043992 TGGAAGGTTGGACGAAAGAGA 58.956 47.619 0.00 0.00 0.00 3.10
284 342 2.543777 TGGAAGGTTGGACGAAAGAG 57.456 50.000 0.00 0.00 0.00 2.85
285 343 4.837093 ATATGGAAGGTTGGACGAAAGA 57.163 40.909 0.00 0.00 0.00 2.52
286 344 6.365247 CGTATATATGGAAGGTTGGACGAAAG 59.635 42.308 0.00 0.00 0.00 2.62
287 345 6.183360 ACGTATATATGGAAGGTTGGACGAAA 60.183 38.462 6.89 0.00 0.00 3.46
288 346 5.302568 ACGTATATATGGAAGGTTGGACGAA 59.697 40.000 6.89 0.00 0.00 3.85
289 347 4.828939 ACGTATATATGGAAGGTTGGACGA 59.171 41.667 6.89 0.00 0.00 4.20
291 349 6.015688 TGAGACGTATATATGGAAGGTTGGAC 60.016 42.308 6.89 0.00 0.00 4.02
292 350 6.015688 GTGAGACGTATATATGGAAGGTTGGA 60.016 42.308 6.89 0.00 0.00 3.53
293 351 6.015350 AGTGAGACGTATATATGGAAGGTTGG 60.015 42.308 6.89 0.00 0.00 3.77
294 352 6.982852 AGTGAGACGTATATATGGAAGGTTG 58.017 40.000 6.89 0.00 0.00 3.77
295 353 7.005296 AGAGTGAGACGTATATATGGAAGGTT 58.995 38.462 6.89 0.00 0.00 3.50
296 354 6.544650 AGAGTGAGACGTATATATGGAAGGT 58.455 40.000 6.89 0.00 0.00 3.50
297 355 7.455641 AAGAGTGAGACGTATATATGGAAGG 57.544 40.000 6.89 0.00 0.00 3.46
298 356 9.400638 GAAAAGAGTGAGACGTATATATGGAAG 57.599 37.037 6.89 0.00 0.00 3.46
299 357 8.074370 CGAAAAGAGTGAGACGTATATATGGAA 58.926 37.037 6.89 0.00 0.00 3.53
300 358 7.228108 ACGAAAAGAGTGAGACGTATATATGGA 59.772 37.037 6.89 0.00 32.42 3.41
301 359 7.361127 ACGAAAAGAGTGAGACGTATATATGG 58.639 38.462 6.89 0.00 32.42 2.74
304 362 8.715998 GGATACGAAAAGAGTGAGACGTATATA 58.284 37.037 0.00 0.00 43.47 0.86
307 365 5.589452 AGGATACGAAAAGAGTGAGACGTAT 59.411 40.000 0.00 0.00 45.13 3.06
309 367 3.757493 AGGATACGAAAAGAGTGAGACGT 59.243 43.478 0.00 0.00 46.39 4.34
310 368 4.095185 AGAGGATACGAAAAGAGTGAGACG 59.905 45.833 0.00 0.00 46.39 4.18
311 369 5.570234 AGAGGATACGAAAAGAGTGAGAC 57.430 43.478 0.00 0.00 46.39 3.36
312 370 6.208797 TCAAAGAGGATACGAAAAGAGTGAGA 59.791 38.462 0.00 0.00 46.39 3.27
313 371 6.390721 TCAAAGAGGATACGAAAAGAGTGAG 58.609 40.000 0.00 0.00 46.39 3.51
314 372 6.340962 TCAAAGAGGATACGAAAAGAGTGA 57.659 37.500 0.00 0.00 46.39 3.41
315 373 7.602517 AATCAAAGAGGATACGAAAAGAGTG 57.397 36.000 0.00 0.00 46.39 3.51
316 374 8.622948 AAAATCAAAGAGGATACGAAAAGAGT 57.377 30.769 0.00 0.00 46.39 3.24
343 401 9.532494 TGAGAGAAAAATCAAATATGGAAGGAA 57.468 29.630 0.00 0.00 0.00 3.36
344 402 9.705103 ATGAGAGAAAAATCAAATATGGAAGGA 57.295 29.630 0.00 0.00 0.00 3.36
363 431 9.676861 ACATGAGACAATTGAATAAATGAGAGA 57.323 29.630 13.59 0.00 0.00 3.10
377 445 9.787435 TGGTAAGTTACTAAACATGAGACAATT 57.213 29.630 12.65 0.00 38.12 2.32
378 446 9.787435 TTGGTAAGTTACTAAACATGAGACAAT 57.213 29.630 12.65 0.00 38.12 2.71
379 447 9.616156 TTTGGTAAGTTACTAAACATGAGACAA 57.384 29.630 17.67 5.07 38.12 3.18
380 448 9.616156 TTTTGGTAAGTTACTAAACATGAGACA 57.384 29.630 20.38 4.77 38.58 3.41
448 516 9.282569 TCTGCCATTTTATTGTTAAGCATTTTT 57.717 25.926 0.00 0.00 0.00 1.94
449 517 8.845413 TCTGCCATTTTATTGTTAAGCATTTT 57.155 26.923 0.00 0.00 0.00 1.82
450 518 8.313292 TCTCTGCCATTTTATTGTTAAGCATTT 58.687 29.630 0.00 0.00 0.00 2.32
451 519 7.839907 TCTCTGCCATTTTATTGTTAAGCATT 58.160 30.769 0.00 0.00 0.00 3.56
452 520 7.408756 TCTCTGCCATTTTATTGTTAAGCAT 57.591 32.000 0.00 0.00 0.00 3.79
453 521 6.832520 TCTCTGCCATTTTATTGTTAAGCA 57.167 33.333 0.00 0.00 0.00 3.91
454 522 8.707938 ATTTCTCTGCCATTTTATTGTTAAGC 57.292 30.769 0.00 0.00 0.00 3.09
455 523 9.859427 TGATTTCTCTGCCATTTTATTGTTAAG 57.141 29.630 0.00 0.00 0.00 1.85
457 525 9.806203 CATGATTTCTCTGCCATTTTATTGTTA 57.194 29.630 0.00 0.00 0.00 2.41
458 526 7.767198 CCATGATTTCTCTGCCATTTTATTGTT 59.233 33.333 0.00 0.00 0.00 2.83
459 527 7.270047 CCATGATTTCTCTGCCATTTTATTGT 58.730 34.615 0.00 0.00 0.00 2.71
460 528 6.202188 GCCATGATTTCTCTGCCATTTTATTG 59.798 38.462 0.00 0.00 0.00 1.90
461 529 6.285990 GCCATGATTTCTCTGCCATTTTATT 58.714 36.000 0.00 0.00 0.00 1.40
462 530 5.508489 CGCCATGATTTCTCTGCCATTTTAT 60.508 40.000 0.00 0.00 0.00 1.40
463 531 4.202040 CGCCATGATTTCTCTGCCATTTTA 60.202 41.667 0.00 0.00 0.00 1.52
464 532 3.429822 CGCCATGATTTCTCTGCCATTTT 60.430 43.478 0.00 0.00 0.00 1.82
465 533 2.100252 CGCCATGATTTCTCTGCCATTT 59.900 45.455 0.00 0.00 0.00 2.32
466 534 1.679680 CGCCATGATTTCTCTGCCATT 59.320 47.619 0.00 0.00 0.00 3.16
467 535 1.134007 TCGCCATGATTTCTCTGCCAT 60.134 47.619 0.00 0.00 0.00 4.40
468 536 0.252761 TCGCCATGATTTCTCTGCCA 59.747 50.000 0.00 0.00 0.00 4.92
469 537 0.659957 GTCGCCATGATTTCTCTGCC 59.340 55.000 0.00 0.00 0.00 4.85
470 538 1.329906 CAGTCGCCATGATTTCTCTGC 59.670 52.381 0.00 0.00 0.00 4.26
471 539 1.329906 GCAGTCGCCATGATTTCTCTG 59.670 52.381 0.00 0.00 0.00 3.35
472 540 1.065926 TGCAGTCGCCATGATTTCTCT 60.066 47.619 0.00 0.00 37.32 3.10
473 541 1.372582 TGCAGTCGCCATGATTTCTC 58.627 50.000 0.00 0.00 37.32 2.87
474 542 2.048444 ATGCAGTCGCCATGATTTCT 57.952 45.000 0.00 0.00 37.32 2.52
475 543 2.613595 TGTATGCAGTCGCCATGATTTC 59.386 45.455 0.00 0.00 37.32 2.17
476 544 2.642427 TGTATGCAGTCGCCATGATTT 58.358 42.857 0.00 0.00 37.32 2.17
477 545 2.330440 TGTATGCAGTCGCCATGATT 57.670 45.000 0.00 0.00 37.32 2.57
478 546 2.330440 TTGTATGCAGTCGCCATGAT 57.670 45.000 0.00 0.00 37.32 2.45
479 547 2.009051 CTTTGTATGCAGTCGCCATGA 58.991 47.619 0.00 0.00 37.32 3.07
480 548 2.009051 TCTTTGTATGCAGTCGCCATG 58.991 47.619 0.00 0.00 37.32 3.66
481 549 2.401583 TCTTTGTATGCAGTCGCCAT 57.598 45.000 0.00 0.00 37.32 4.40
482 550 2.401583 ATCTTTGTATGCAGTCGCCA 57.598 45.000 0.00 0.00 37.32 5.69
483 551 3.429085 CAAATCTTTGTATGCAGTCGCC 58.571 45.455 0.00 0.00 33.47 5.54
484 552 3.119849 ACCAAATCTTTGTATGCAGTCGC 60.120 43.478 0.00 0.00 36.45 5.19
485 553 4.685169 ACCAAATCTTTGTATGCAGTCG 57.315 40.909 0.00 0.00 36.45 4.18
486 554 7.377766 TCTTACCAAATCTTTGTATGCAGTC 57.622 36.000 0.00 0.00 36.45 3.51
487 555 7.944729 ATCTTACCAAATCTTTGTATGCAGT 57.055 32.000 0.00 0.00 36.45 4.40
488 556 9.643693 AAAATCTTACCAAATCTTTGTATGCAG 57.356 29.630 0.00 0.00 36.45 4.41
493 561 9.005777 ACGCTAAAATCTTACCAAATCTTTGTA 57.994 29.630 2.29 0.00 36.45 2.41
494 562 7.882179 ACGCTAAAATCTTACCAAATCTTTGT 58.118 30.769 2.29 0.00 36.45 2.83
497 565 9.391006 TGATACGCTAAAATCTTACCAAATCTT 57.609 29.630 0.00 0.00 0.00 2.40
498 566 8.958119 TGATACGCTAAAATCTTACCAAATCT 57.042 30.769 0.00 0.00 0.00 2.40
583 651 6.019318 GTGCGTTGTAATCGGAGTATAAACAT 60.019 38.462 11.75 0.00 0.00 2.71
584 652 5.289193 GTGCGTTGTAATCGGAGTATAAACA 59.711 40.000 11.75 5.40 0.00 2.83
585 653 5.553211 CGTGCGTTGTAATCGGAGTATAAAC 60.553 44.000 0.00 1.28 0.00 2.01
587 655 4.037021 CGTGCGTTGTAATCGGAGTATAA 58.963 43.478 0.00 0.00 0.00 0.98
588 656 3.548616 CCGTGCGTTGTAATCGGAGTATA 60.549 47.826 0.00 0.00 43.22 1.47
590 658 1.467883 CCGTGCGTTGTAATCGGAGTA 60.468 52.381 0.00 0.00 43.22 2.59
591 659 0.734942 CCGTGCGTTGTAATCGGAGT 60.735 55.000 0.00 0.00 43.22 3.85
593 661 0.733566 GTCCGTGCGTTGTAATCGGA 60.734 55.000 0.00 0.00 46.14 4.55
594 662 1.009903 TGTCCGTGCGTTGTAATCGG 61.010 55.000 0.00 0.00 42.12 4.18
596 664 3.160545 CAATTGTCCGTGCGTTGTAATC 58.839 45.455 0.00 0.00 0.00 1.75
599 667 1.527736 GACAATTGTCCGTGCGTTGTA 59.472 47.619 25.26 0.00 39.07 2.41
601 669 0.586319 AGACAATTGTCCGTGCGTTG 59.414 50.000 30.34 0.00 45.85 4.10
602 670 2.066262 CTAGACAATTGTCCGTGCGTT 58.934 47.619 30.34 15.45 45.85 4.84
603 671 1.000506 ACTAGACAATTGTCCGTGCGT 59.999 47.619 30.34 18.48 45.85 5.24
605 673 5.220605 GGAAATACTAGACAATTGTCCGTGC 60.221 44.000 30.34 18.18 45.85 5.34
606 674 6.106673 AGGAAATACTAGACAATTGTCCGTG 58.893 40.000 30.34 22.61 45.85 4.94
607 675 6.295719 AGGAAATACTAGACAATTGTCCGT 57.704 37.500 30.34 27.43 45.85 4.69
608 676 6.019801 CGAAGGAAATACTAGACAATTGTCCG 60.020 42.308 30.34 23.99 45.85 4.79
610 678 7.829378 ACGAAGGAAATACTAGACAATTGTC 57.171 36.000 27.69 27.69 45.08 3.18
611 679 8.095169 AGAACGAAGGAAATACTAGACAATTGT 58.905 33.333 11.78 11.78 0.00 2.71
612 680 8.480643 AGAACGAAGGAAATACTAGACAATTG 57.519 34.615 3.24 3.24 0.00 2.32
615 683 9.985730 TTTTAGAACGAAGGAAATACTAGACAA 57.014 29.630 0.00 0.00 0.00 3.18
624 692 9.067986 AGACAAGAATTTTAGAACGAAGGAAAT 57.932 29.630 0.00 0.00 0.00 2.17
625 693 8.446599 AGACAAGAATTTTAGAACGAAGGAAA 57.553 30.769 0.00 0.00 0.00 3.13
626 694 8.446599 AAGACAAGAATTTTAGAACGAAGGAA 57.553 30.769 0.00 0.00 0.00 3.36
627 695 9.204570 CTAAGACAAGAATTTTAGAACGAAGGA 57.795 33.333 0.00 0.00 0.00 3.36
628 696 9.204570 TCTAAGACAAGAATTTTAGAACGAAGG 57.795 33.333 0.00 0.00 31.26 3.46
643 711 9.004717 CCGTATCTAGATGAATCTAAGACAAGA 57.995 37.037 15.79 0.00 38.80 3.02
644 712 9.004717 TCCGTATCTAGATGAATCTAAGACAAG 57.995 37.037 15.79 0.00 38.80 3.16
645 713 8.919777 TCCGTATCTAGATGAATCTAAGACAA 57.080 34.615 15.79 0.00 38.80 3.18
646 714 8.951243 CATCCGTATCTAGATGAATCTAAGACA 58.049 37.037 15.79 0.00 42.04 3.41
647 715 8.952278 ACATCCGTATCTAGATGAATCTAAGAC 58.048 37.037 15.79 1.20 42.04 3.01
729 797 5.923733 TCTGCTCCCTTTGTTTTGTAAAA 57.076 34.783 0.00 0.00 0.00 1.52
730 798 5.923733 TTCTGCTCCCTTTGTTTTGTAAA 57.076 34.783 0.00 0.00 0.00 2.01
731 799 6.478512 AATTCTGCTCCCTTTGTTTTGTAA 57.521 33.333 0.00 0.00 0.00 2.41
732 800 5.278266 CGAATTCTGCTCCCTTTGTTTTGTA 60.278 40.000 3.52 0.00 0.00 2.41
733 801 4.499696 CGAATTCTGCTCCCTTTGTTTTGT 60.500 41.667 3.52 0.00 0.00 2.83
735 803 3.552890 GCGAATTCTGCTCCCTTTGTTTT 60.553 43.478 12.90 0.00 0.00 2.43
741 2277 0.460987 CTCGCGAATTCTGCTCCCTT 60.461 55.000 11.33 0.00 0.00 3.95
757 2293 2.223377 CCACTTCCTTTTCGTTTCCTCG 59.777 50.000 0.00 0.00 0.00 4.63
810 2346 0.394762 ACACCCGGACTAGATGCGTA 60.395 55.000 0.73 0.00 41.28 4.42
1098 2640 2.754658 GGCGGAGAGGGAGACGAA 60.755 66.667 0.00 0.00 0.00 3.85
1262 2804 0.809385 TACTTGGCGAAGAGTCCGAG 59.191 55.000 16.00 0.00 39.32 4.63
1323 2865 7.494211 TGGATGGATCAAATCAATCAATCAAC 58.506 34.615 6.64 0.00 40.77 3.18
1350 2892 0.315568 GGCCTAGGCACGTCTATCTG 59.684 60.000 34.09 0.00 44.11 2.90
1552 3094 1.078426 ATCCCTTTCTGGTTCGGCG 60.078 57.895 0.00 0.00 0.00 6.46
1607 3149 0.320421 TTGCCTACTCGTGCTTGGTC 60.320 55.000 0.00 0.00 0.00 4.02
1613 3155 0.319555 TGAGTGTTGCCTACTCGTGC 60.320 55.000 0.00 0.00 45.82 5.34
1789 3556 6.758886 AGCTTGATCAAGTAATAGAAGGTTCG 59.241 38.462 30.88 6.58 40.45 3.95
1802 3569 8.680903 CAGGAATTTGTTATAGCTTGATCAAGT 58.319 33.333 30.88 21.29 40.45 3.16
1819 3586 0.611896 AACCTCGGGGCAGGAATTTG 60.612 55.000 0.00 0.00 36.96 2.32
1937 3704 6.610075 AGGCATTTGTTTGTCCTGATAAAT 57.390 33.333 0.00 0.00 0.00 1.40
2005 3778 2.424956 GTGGAAGGATCAATCAAGGCAC 59.575 50.000 0.00 0.00 0.00 5.01
2006 3779 2.309755 AGTGGAAGGATCAATCAAGGCA 59.690 45.455 0.00 0.00 0.00 4.75
2255 4030 3.146066 TGATGCCTAGTGTTGTTTGGTC 58.854 45.455 0.00 0.00 0.00 4.02
2274 4049 4.335315 AGAACGTGAAATGAAAACAGCTGA 59.665 37.500 23.35 0.00 0.00 4.26
2375 4150 5.631119 TCCTTCTCCTCGGAAGAAATTTTT 58.369 37.500 5.89 0.00 43.70 1.94
2381 4156 4.910458 ATTTTCCTTCTCCTCGGAAGAA 57.090 40.909 5.89 0.00 43.70 2.52
2472 4291 1.748493 TGTTGTTTGGTTCACCTCAGC 59.252 47.619 0.00 0.00 36.82 4.26
2589 4409 9.416794 CTCTTGTATGGTTCATATCAGTATCAC 57.583 37.037 0.00 0.00 0.00 3.06
2618 4438 6.937436 AACTAACCGAAAATGAGTGTTTCT 57.063 33.333 0.00 0.00 33.63 2.52
2672 4492 8.982723 ACTTTATAAATCTCTAACAGCAGAGGA 58.017 33.333 0.00 0.00 42.05 3.71
2893 4714 2.068519 GCCAATGCCAGCAACTTTTAC 58.931 47.619 0.00 0.00 0.00 2.01
2919 4741 2.197577 GCAAGTAGGATCTTCTGTCGC 58.802 52.381 0.00 0.00 0.00 5.19
2955 4777 8.166061 ACCCAACTGATATCTAAATGCATACAT 58.834 33.333 0.00 0.00 38.49 2.29
3024 4846 4.846168 TGACAGAGGAGCTAGACTAGAA 57.154 45.455 13.91 0.00 0.00 2.10
3029 4851 3.699038 AGTGATTGACAGAGGAGCTAGAC 59.301 47.826 0.00 0.00 0.00 2.59
3133 4955 2.781595 AATCTCGACCCGCACCACAC 62.782 60.000 0.00 0.00 0.00 3.82
3261 5084 3.509659 GCCTGGGCCAATACGTTC 58.490 61.111 8.04 0.00 34.56 3.95
3283 5106 1.134401 GGACGCCTCCTTGATTCATCA 60.134 52.381 0.00 0.00 33.07 3.07
3404 5227 3.003480 GCTAACTAAGGAAGCACACCTG 58.997 50.000 0.00 0.00 37.85 4.00
3428 5251 3.076182 GGTATCCATCCTAGGTCTCCAGA 59.924 52.174 9.08 0.00 0.00 3.86
3697 5521 1.429148 GCCAATCTGGGAGCGTTACG 61.429 60.000 0.00 0.00 38.19 3.18
3779 5603 1.699656 ATGAATCTGACGCGCACTGC 61.700 55.000 5.73 0.00 41.47 4.40
3952 5779 8.624367 TGAAACCGAGGAAAGATTATGTAAAA 57.376 30.769 0.00 0.00 0.00 1.52
4095 5922 0.035820 TATGGTGGGAACGCAGGAAC 60.036 55.000 0.00 0.00 44.70 3.62
4135 5962 0.883833 GGTTTGTGTGATGAGGCAGG 59.116 55.000 0.00 0.00 0.00 4.85
4164 5991 0.108138 GAGTACTTGCGGTGCATCCT 60.108 55.000 0.00 0.00 38.76 3.24
4214 6041 6.824553 TGATGAAGTCATTAGGAGATCTTGG 58.175 40.000 0.00 0.00 36.57 3.61
4296 6379 2.806745 GCAAGGGCGATGCTGATACTAA 60.807 50.000 5.95 0.00 40.64 2.24
4356 6439 2.693591 TCCCTTGTCGAGCGATTCTTAT 59.306 45.455 0.00 0.00 0.00 1.73
4433 6516 0.464735 CGTGGGGAACAGTTTGGACA 60.465 55.000 0.00 0.00 0.00 4.02
4434 6517 0.464916 ACGTGGGGAACAGTTTGGAC 60.465 55.000 0.00 0.00 0.00 4.02
4548 6631 5.279657 GCTTGGAATCTCAACAAAAGGGAAT 60.280 40.000 0.00 0.00 0.00 3.01
4580 6663 4.828939 TCTCCCAACATATGAAATGGATGC 59.171 41.667 20.88 0.00 34.82 3.91
4591 6674 1.625818 GCGATCCCTCTCCCAACATAT 59.374 52.381 0.00 0.00 0.00 1.78
4592 6675 1.048601 GCGATCCCTCTCCCAACATA 58.951 55.000 0.00 0.00 0.00 2.29
4844 6929 0.179272 GCGACGAGAGCAAAACGAAG 60.179 55.000 0.00 0.00 34.19 3.79
4912 6997 1.271488 GGGGGTTATCACGTGGTTTGA 60.271 52.381 17.00 0.00 0.00 2.69
4952 7037 2.680913 CCAGAAACAAGGAGGCGCG 61.681 63.158 0.00 0.00 0.00 6.86
5048 7134 2.606519 CAAGGAGGTGGGGGTCGA 60.607 66.667 0.00 0.00 0.00 4.20
5064 7150 6.169094 TGCAAGGATTTCTTTCACAAAAACA 58.831 32.000 0.00 0.00 32.41 2.83
5072 7158 4.669206 TGCTTTGCAAGGATTTCTTTCA 57.331 36.364 13.48 0.00 34.76 2.69
5120 7210 7.175293 TCGGAAATAAATTAATGGGGGTTATCG 59.825 37.037 0.00 0.00 0.00 2.92
5145 7235 1.302271 GAGGACGTGGGGTTGGTTC 60.302 63.158 0.00 0.00 0.00 3.62
5157 7247 1.798813 CTTTTCCCAGAAACGAGGACG 59.201 52.381 0.00 0.00 45.75 4.79
5173 7263 3.233507 TGCTTTGCAAGGGATCTCTTTT 58.766 40.909 4.67 0.00 34.76 2.27
5236 7326 4.861389 TGATTTTGTTGTTTGCTTGCAG 57.139 36.364 0.00 0.00 0.00 4.41
5270 7360 9.788889 ATGATGTGATTGAGATTGTGTACATAT 57.211 29.630 0.00 0.00 0.00 1.78
5566 7656 3.764434 TGTTCTTAGCGAGGAGATTCTGT 59.236 43.478 0.00 0.00 0.00 3.41
5741 7831 3.219281 AGGCACCGACTACAAACATTTT 58.781 40.909 0.00 0.00 0.00 1.82
6087 8221 3.560636 AACTAGCACACACTGGAAAGT 57.439 42.857 0.00 0.00 0.00 2.66
6188 8322 5.294734 AGGAAACCAGTTACGTAAGGAAA 57.705 39.130 17.81 0.00 45.67 3.13
6479 8613 6.071165 AGCATTAGCAAGTTAAGCAATTTCCT 60.071 34.615 0.00 0.00 45.49 3.36
6818 8956 0.111639 GGGTAAACAAGTGAGGGCCA 59.888 55.000 6.18 0.00 0.00 5.36
6833 8971 0.331278 CCATCCACAGCCAAAGGGTA 59.669 55.000 0.00 0.00 36.17 3.69
6993 9131 6.742718 CAGTTAAACGCAACCTATCAAATGAG 59.257 38.462 0.00 0.00 0.00 2.90
6994 9132 6.428465 TCAGTTAAACGCAACCTATCAAATGA 59.572 34.615 0.00 0.00 0.00 2.57
7244 9383 3.544834 CGATGGCTTTTGTCTTGCGATAG 60.545 47.826 0.00 0.00 0.00 2.08
7422 9562 4.097135 AGAGACTCAACGACATGTAGGATG 59.903 45.833 10.86 8.91 0.00 3.51
7619 9779 4.548451 AGCACAGACAAATCTCATCTCA 57.452 40.909 0.00 0.00 30.42 3.27
7652 9812 1.702182 TTGCAAGGGAAACTGATGCA 58.298 45.000 0.00 0.00 44.54 3.96
7655 9815 3.565307 TGAGTTTGCAAGGGAAACTGAT 58.435 40.909 18.43 0.00 42.42 2.90
7678 9838 2.036256 ACTTGCACCATGCTCCCC 59.964 61.111 2.02 0.00 45.31 4.81
7762 9924 4.250464 ACAATACACATGTAACCGTGAGG 58.750 43.478 0.00 0.00 44.54 3.86


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

AutoCloner maintained by Alex Coulton.