Multiple sequence alignment - TraesCS1D01G000300

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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 TraesCS1D01G000300 chr1D 100.000 3221 0 0 1 3221 98275 101495 0.000000e+00 5949.0
1 TraesCS1D01G000300 chr1D 92.487 1677 102 16 1356 3021 84815 86478 0.000000e+00 2377.0
2 TraesCS1D01G000300 chr1D 88.206 1221 103 23 736 1940 7156969 7155774 0.000000e+00 1419.0
3 TraesCS1D01G000300 chr1D 86.893 1236 104 33 736 1937 4341406 4342617 0.000000e+00 1332.0
4 TraesCS1D01G000300 chr1D 87.314 1009 84 30 480 1471 84072 85053 0.000000e+00 1114.0
5 TraesCS1D01G000300 chr1D 86.404 1015 102 24 424 1432 5356113 5357097 0.000000e+00 1077.0
6 TraesCS1D01G000300 chr1D 84.230 818 95 8 1945 2733 4342661 4343473 0.000000e+00 765.0
7 TraesCS1D01G000300 chr1D 84.586 798 86 10 1966 2733 7155712 7154922 0.000000e+00 758.0
8 TraesCS1D01G000300 chr1D 82.789 796 89 24 1945 2700 5357469 5358256 0.000000e+00 667.0
9 TraesCS1D01G000300 chr1D 85.439 570 61 14 1394 1962 3710391 3709843 1.000000e-159 573.0
10 TraesCS1D01G000300 chr1D 86.534 401 46 5 422 821 7157371 7156978 4.930000e-118 435.0
11 TraesCS1D01G000300 chr1D 92.015 263 17 3 1 260 83628 83889 1.830000e-97 366.0
12 TraesCS1D01G000300 chr1D 85.375 253 20 13 1 238 5137565 5137815 2.480000e-61 246.0
13 TraesCS1D01G000300 chr1D 96.512 86 3 0 3136 3221 86477 86562 3.350000e-30 143.0
14 TraesCS1D01G000300 chr1D 92.857 84 4 1 2799 2882 3707346 3707265 1.570000e-23 121.0
15 TraesCS1D01G000300 chr1B 93.994 2148 107 13 357 2483 5688419 5686273 0.000000e+00 3232.0
16 TraesCS1D01G000300 chr1B 94.322 1814 79 14 680 2483 5521158 5519359 0.000000e+00 2758.0
17 TraesCS1D01G000300 chr1B 96.549 1420 46 3 1354 2772 5584955 5583538 0.000000e+00 2348.0
18 TraesCS1D01G000300 chr1B 86.953 1234 109 18 736 1962 22185384 22186572 0.000000e+00 1339.0
19 TraesCS1D01G000300 chr1B 85.797 1211 99 35 739 1940 6437816 6436670 0.000000e+00 1216.0
20 TraesCS1D01G000300 chr1B 95.152 722 32 2 671 1389 5585887 5585166 0.000000e+00 1136.0
21 TraesCS1D01G000300 chr1B 84.127 819 92 12 1945 2733 22186594 22187404 0.000000e+00 758.0
22 TraesCS1D01G000300 chr1B 86.500 400 46 5 422 820 6438223 6437831 1.770000e-117 433.0
23 TraesCS1D01G000300 chr1B 84.897 437 31 17 1 408 5688764 5688334 2.990000e-110 409.0
24 TraesCS1D01G000300 chr1B 89.407 236 23 2 391 625 5586121 5585887 2.430000e-76 296.0
25 TraesCS1D01G000300 chr1B 86.822 258 24 5 7 263 5521726 5521478 2.450000e-71 279.0
26 TraesCS1D01G000300 chr1B 96.512 86 3 0 3136 3221 5583466 5583381 3.350000e-30 143.0
27 TraesCS1D01G000300 chr1B 98.701 77 0 1 2946 3021 5583541 5583465 5.610000e-28 135.0
28 TraesCS1D01G000300 chr1B 95.349 43 2 0 2979 3021 5944190 5944148 5.770000e-08 69.4
29 TraesCS1D01G000300 chr1A 89.286 1680 121 27 1389 3021 4203001 4201334 0.000000e+00 2050.0
30 TraesCS1D01G000300 chr1A 90.903 1539 110 12 1507 3021 4096380 4094848 0.000000e+00 2039.0
31 TraesCS1D01G000300 chr1A 87.552 956 90 17 393 1325 4204284 4203335 0.000000e+00 1079.0
32 TraesCS1D01G000300 chr1A 87.083 929 90 24 486 1408 6561199 6562103 0.000000e+00 1024.0
33 TraesCS1D01G000300 chr1A 90.728 755 63 4 391 1142 4097514 4096764 0.000000e+00 1000.0
34 TraesCS1D01G000300 chr1A 87.453 534 63 4 1945 2477 6518137 6518667 2.120000e-171 612.0
35 TraesCS1D01G000300 chr1A 88.430 121 10 3 3020 3137 13260748 13260629 3.350000e-30 143.0
36 TraesCS1D01G000300 chrUn 81.462 383 43 2 2266 2620 480721451 480721833 4.070000e-74 289.0
37 TraesCS1D01G000300 chr7D 94.215 121 6 1 3020 3140 158994450 158994331 1.970000e-42 183.0
38 TraesCS1D01G000300 chr7B 92.373 118 6 2 3020 3137 209402356 209402242 7.150000e-37 165.0
39 TraesCS1D01G000300 chr3D 91.129 124 7 1 3015 3138 184458790 184458671 7.150000e-37 165.0
40 TraesCS1D01G000300 chr4D 94.340 106 4 2 3034 3138 362603708 362603604 9.250000e-36 161.0
41 TraesCS1D01G000300 chr6A 88.889 126 10 3 3020 3141 558188545 558188670 5.570000e-33 152.0
42 TraesCS1D01G000300 chr3B 89.516 124 7 5 3020 3138 696734033 696733911 5.570000e-33 152.0
43 TraesCS1D01G000300 chr5D 88.800 125 9 4 3017 3137 79434665 79434542 7.200000e-32 148.0
44 TraesCS1D01G000300 chr6D 87.302 126 14 2 3013 3137 149031808 149031932 3.350000e-30 143.0


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 TraesCS1D01G000300 chr1D 98275 101495 3220 False 5949.000000 5949 100.0000 1 3221 1 chr1D.!!$F1 3220
1 TraesCS1D01G000300 chr1D 4341406 4343473 2067 False 1048.500000 1332 85.5615 736 2733 2 chr1D.!!$F4 1997
2 TraesCS1D01G000300 chr1D 83628 86562 2934 False 1000.000000 2377 92.0820 1 3221 4 chr1D.!!$F3 3220
3 TraesCS1D01G000300 chr1D 5356113 5358256 2143 False 872.000000 1077 84.5965 424 2700 2 chr1D.!!$F5 2276
4 TraesCS1D01G000300 chr1D 7154922 7157371 2449 True 870.666667 1419 86.4420 422 2733 3 chr1D.!!$R2 2311
5 TraesCS1D01G000300 chr1D 3707265 3710391 3126 True 347.000000 573 89.1480 1394 2882 2 chr1D.!!$R1 1488
6 TraesCS1D01G000300 chr1B 5686273 5688764 2491 True 1820.500000 3232 89.4455 1 2483 2 chr1B.!!$R4 2482
7 TraesCS1D01G000300 chr1B 5519359 5521726 2367 True 1518.500000 2758 90.5720 7 2483 2 chr1B.!!$R2 2476
8 TraesCS1D01G000300 chr1B 22185384 22187404 2020 False 1048.500000 1339 85.5400 736 2733 2 chr1B.!!$F1 1997
9 TraesCS1D01G000300 chr1B 6436670 6438223 1553 True 824.500000 1216 86.1485 422 1940 2 chr1B.!!$R5 1518
10 TraesCS1D01G000300 chr1B 5583381 5586121 2740 True 811.600000 2348 95.2642 391 3221 5 chr1B.!!$R3 2830
11 TraesCS1D01G000300 chr1A 4201334 4204284 2950 True 1564.500000 2050 88.4190 393 3021 2 chr1A.!!$R3 2628
12 TraesCS1D01G000300 chr1A 4094848 4097514 2666 True 1519.500000 2039 90.8155 391 3021 2 chr1A.!!$R2 2630
13 TraesCS1D01G000300 chr1A 6561199 6562103 904 False 1024.000000 1024 87.0830 486 1408 1 chr1A.!!$F2 922
14 TraesCS1D01G000300 chr1A 6518137 6518667 530 False 612.000000 612 87.4530 1945 2477 1 chr1A.!!$F1 532

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
253 260 0.252197 ACGTTGGGCCTAATCACTCC 59.748 55.000 4.25 0.0 0.00 3.85 F
994 1324 0.555769 AAGAAAAGAGGTGGTGCCCA 59.444 50.000 0.00 0.0 38.26 5.36 F
1199 1529 2.607771 GCAGCAACAACCATTACCACTG 60.608 50.000 0.00 0.0 0.00 3.66 F
1905 3127 2.599578 AGCAGCAGCAACCCCAAG 60.600 61.111 3.17 0.0 45.49 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1789 2990 0.977108 GGATTGCTGGGGGATTTGCA 60.977 55.000 0.0 0.0 0.00 4.08 R
1905 3127 1.000843 GGAAACACATTGGCCCAACTC 59.999 52.381 0.0 0.0 0.00 3.01 R
2057 3327 1.959226 GACACGGCACATCGTTGGT 60.959 57.895 0.0 0.0 41.86 3.67 R
3119 6077 2.314071 TCTACTCCCTCCGTTCCAAA 57.686 50.000 0.0 0.0 0.00 3.28 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
18 19 2.285368 ATGCGGAGGGTGGAAGGA 60.285 61.111 0.00 0.00 0.00 3.36
197 202 2.414612 TGGGGCCTCCGAAAACTATAT 58.585 47.619 0.00 0.00 38.76 0.86
230 237 0.548989 TGGTGCCCTAACACACAACT 59.451 50.000 0.00 0.00 42.55 3.16
249 256 2.835764 ACTCTTACGTTGGGCCTAATCA 59.164 45.455 4.25 0.00 0.00 2.57
253 260 0.252197 ACGTTGGGCCTAATCACTCC 59.748 55.000 4.25 0.00 0.00 3.85
262 316 1.694048 CCTAATCACTCCCTCCTGGCT 60.694 57.143 0.00 0.00 0.00 4.75
279 354 1.988107 GGCTCCATCTATCATTCCCCA 59.012 52.381 0.00 0.00 0.00 4.96
309 384 5.089970 TCCTTCACACATAGATGGAACTG 57.910 43.478 0.00 0.00 36.66 3.16
310 385 4.777366 TCCTTCACACATAGATGGAACTGA 59.223 41.667 0.00 0.00 36.66 3.41
312 387 5.526479 CCTTCACACATAGATGGAACTGATG 59.474 44.000 0.00 0.00 33.42 3.07
313 388 5.937975 TCACACATAGATGGAACTGATGA 57.062 39.130 0.00 0.00 0.00 2.92
315 390 6.892485 TCACACATAGATGGAACTGATGATT 58.108 36.000 0.00 0.00 0.00 2.57
316 391 6.988580 TCACACATAGATGGAACTGATGATTC 59.011 38.462 0.00 0.00 0.00 2.52
317 392 6.990939 CACACATAGATGGAACTGATGATTCT 59.009 38.462 0.00 0.00 0.00 2.40
318 393 7.171167 CACACATAGATGGAACTGATGATTCTC 59.829 40.741 0.00 0.00 0.00 2.87
323 398 7.627298 AGATGGAACTGATGATTCTCAAAAG 57.373 36.000 0.00 0.00 0.00 2.27
324 399 7.400439 AGATGGAACTGATGATTCTCAAAAGA 58.600 34.615 0.00 0.00 0.00 2.52
325 400 7.886970 AGATGGAACTGATGATTCTCAAAAGAA 59.113 33.333 0.00 0.00 45.36 2.52
326 401 7.822161 TGGAACTGATGATTCTCAAAAGAAA 57.178 32.000 0.00 0.00 44.49 2.52
327 402 8.236585 TGGAACTGATGATTCTCAAAAGAAAA 57.763 30.769 0.00 0.00 44.49 2.29
328 403 8.694540 TGGAACTGATGATTCTCAAAAGAAAAA 58.305 29.630 0.00 0.00 44.49 1.94
329 404 9.189723 GGAACTGATGATTCTCAAAAGAAAAAG 57.810 33.333 0.00 0.00 44.49 2.27
330 405 9.956720 GAACTGATGATTCTCAAAAGAAAAAGA 57.043 29.630 0.00 0.00 44.49 2.52
331 406 9.962783 AACTGATGATTCTCAAAAGAAAAAGAG 57.037 29.630 0.00 0.00 44.49 2.85
332 407 9.347240 ACTGATGATTCTCAAAAGAAAAAGAGA 57.653 29.630 0.00 0.00 44.49 3.10
335 410 9.570488 GATGATTCTCAAAAGAAAAAGAGATGG 57.430 33.333 0.00 0.00 44.49 3.51
336 411 8.696043 TGATTCTCAAAAGAAAAAGAGATGGA 57.304 30.769 0.00 0.00 44.49 3.41
337 412 9.135189 TGATTCTCAAAAGAAAAAGAGATGGAA 57.865 29.630 0.00 0.00 44.49 3.53
338 413 9.404348 GATTCTCAAAAGAAAAAGAGATGGAAC 57.596 33.333 0.00 0.00 44.49 3.62
339 414 8.525290 TTCTCAAAAGAAAAAGAGATGGAACT 57.475 30.769 0.00 0.00 38.58 3.01
340 415 7.934457 TCTCAAAAGAAAAAGAGATGGAACTG 58.066 34.615 0.00 0.00 32.57 3.16
341 416 7.775093 TCTCAAAAGAAAAAGAGATGGAACTGA 59.225 33.333 0.00 0.00 32.57 3.41
342 417 8.469309 TCAAAAGAAAAAGAGATGGAACTGAT 57.531 30.769 0.00 0.00 0.00 2.90
343 418 8.917088 TCAAAAGAAAAAGAGATGGAACTGATT 58.083 29.630 0.00 0.00 0.00 2.57
344 419 8.975439 CAAAAGAAAAAGAGATGGAACTGATTG 58.025 33.333 0.00 0.00 0.00 2.67
345 420 7.830099 AAGAAAAAGAGATGGAACTGATTGT 57.170 32.000 0.00 0.00 0.00 2.71
346 421 7.211966 AGAAAAAGAGATGGAACTGATTGTG 57.788 36.000 0.00 0.00 0.00 3.33
347 422 6.774656 AGAAAAAGAGATGGAACTGATTGTGT 59.225 34.615 0.00 0.00 0.00 3.72
348 423 6.566197 AAAAGAGATGGAACTGATTGTGTC 57.434 37.500 0.00 0.00 0.00 3.67
349 424 4.897509 AGAGATGGAACTGATTGTGTCA 57.102 40.909 0.00 0.00 35.05 3.58
350 425 5.432680 AGAGATGGAACTGATTGTGTCAT 57.567 39.130 0.00 0.00 35.97 3.06
351 426 5.183969 AGAGATGGAACTGATTGTGTCATG 58.816 41.667 0.00 0.00 35.97 3.07
352 427 4.914983 AGATGGAACTGATTGTGTCATGT 58.085 39.130 0.00 0.00 35.97 3.21
353 428 4.940046 AGATGGAACTGATTGTGTCATGTC 59.060 41.667 0.00 0.00 35.97 3.06
354 429 4.356405 TGGAACTGATTGTGTCATGTCT 57.644 40.909 0.00 0.00 35.97 3.41
355 430 4.717877 TGGAACTGATTGTGTCATGTCTT 58.282 39.130 0.00 0.00 35.97 3.01
360 435 8.134895 GGAACTGATTGTGTCATGTCTTAAAAA 58.865 33.333 0.00 0.00 35.97 1.94
415 524 9.381033 CATAGATGGAACTGATGATTTATCTCC 57.619 37.037 0.00 0.00 36.71 3.71
416 525 6.462500 AGATGGAACTGATGATTTATCTCCG 58.538 40.000 0.00 0.00 36.71 4.63
543 664 4.023365 TCGATGAGTCATGTCATGCTCTAG 60.023 45.833 24.82 18.89 37.29 2.43
709 834 3.443099 ACACAAGCTTTGCCTTTCTTC 57.557 42.857 0.00 0.00 0.00 2.87
857 1172 5.900865 TTGTGTGTGATCATATGCACAAT 57.099 34.783 18.55 0.00 45.53 2.71
915 1237 2.921754 GTGTAGCTAGTGCAACCTAACG 59.078 50.000 0.00 0.00 42.74 3.18
951 1279 4.359971 TCATTTCAGATGCATCCAAACG 57.640 40.909 23.06 14.41 0.00 3.60
956 1284 4.149511 TCAGATGCATCCAAACGGAATA 57.850 40.909 23.06 0.00 35.74 1.75
994 1324 0.555769 AAGAAAAGAGGTGGTGCCCA 59.444 50.000 0.00 0.00 38.26 5.36
1199 1529 2.607771 GCAGCAACAACCATTACCACTG 60.608 50.000 0.00 0.00 0.00 3.66
1236 1566 2.992543 CACCAACAACAACAACAACCTG 59.007 45.455 0.00 0.00 0.00 4.00
1630 2831 5.049680 CAGTTCTACCGCAACAACAAATACT 60.050 40.000 0.00 0.00 0.00 2.12
1905 3127 2.599578 AGCAGCAGCAACCCCAAG 60.600 61.111 3.17 0.00 45.49 3.61
2057 3327 1.440060 CATTGCGCTCCGTACCCTA 59.560 57.895 9.73 0.00 0.00 3.53
2337 3609 1.255882 TTGGCATTGTGTGGATGTCC 58.744 50.000 0.00 0.00 0.00 4.02
2415 3687 6.701400 GCAACCTGGTGCCTTAATTAATTATG 59.299 38.462 8.70 10.66 38.66 1.90
2483 3778 9.974980 TGTAAAATTTGGGTTGAACTCTTTATC 57.025 29.630 0.00 0.00 0.00 1.75
2581 3886 9.061610 CAATCACAACCAGTTTTATCGTTAATC 57.938 33.333 0.00 0.00 0.00 1.75
2611 3925 7.585286 TGCTTTCTTGCAAATACATTCATTC 57.415 32.000 0.00 0.00 40.29 2.67
2813 5768 6.536582 CGGTCATGTCAAGAACTAAATCAGAT 59.463 38.462 0.00 0.00 0.00 2.90
2933 5889 9.571816 AAAAATCATCAAAGAATGCCCTAAAAA 57.428 25.926 0.00 0.00 0.00 1.94
3021 5979 8.944029 AGATAGATGCTGCACATTATCATTTAC 58.056 33.333 21.61 5.14 39.84 2.01
3022 5980 8.859236 ATAGATGCTGCACATTATCATTTACT 57.141 30.769 3.57 0.00 39.84 2.24
3023 5981 7.199541 AGATGCTGCACATTATCATTTACTC 57.800 36.000 3.57 0.00 39.84 2.59
3024 5982 5.756195 TGCTGCACATTATCATTTACTCC 57.244 39.130 0.00 0.00 0.00 3.85
3025 5983 4.580167 TGCTGCACATTATCATTTACTCCC 59.420 41.667 0.00 0.00 0.00 4.30
3026 5984 4.823989 GCTGCACATTATCATTTACTCCCT 59.176 41.667 0.00 0.00 0.00 4.20
3027 5985 5.049129 GCTGCACATTATCATTTACTCCCTC 60.049 44.000 0.00 0.00 0.00 4.30
3028 5986 5.376625 TGCACATTATCATTTACTCCCTCC 58.623 41.667 0.00 0.00 0.00 4.30
3029 5987 5.104151 TGCACATTATCATTTACTCCCTCCA 60.104 40.000 0.00 0.00 0.00 3.86
3030 5988 6.006449 GCACATTATCATTTACTCCCTCCAT 58.994 40.000 0.00 0.00 0.00 3.41
3031 5989 6.491403 GCACATTATCATTTACTCCCTCCATT 59.509 38.462 0.00 0.00 0.00 3.16
3032 5990 7.308830 GCACATTATCATTTACTCCCTCCATTC 60.309 40.741 0.00 0.00 0.00 2.67
3033 5991 7.175641 CACATTATCATTTACTCCCTCCATTCC 59.824 40.741 0.00 0.00 0.00 3.01
3034 5992 6.840090 TTATCATTTACTCCCTCCATTCCA 57.160 37.500 0.00 0.00 0.00 3.53
3035 5993 5.732331 ATCATTTACTCCCTCCATTCCAA 57.268 39.130 0.00 0.00 0.00 3.53
3036 5994 5.528600 TCATTTACTCCCTCCATTCCAAA 57.471 39.130 0.00 0.00 0.00 3.28
3037 5995 5.898120 TCATTTACTCCCTCCATTCCAAAA 58.102 37.500 0.00 0.00 0.00 2.44
3038 5996 6.502138 TCATTTACTCCCTCCATTCCAAAAT 58.498 36.000 0.00 0.00 0.00 1.82
3039 5997 7.647827 TCATTTACTCCCTCCATTCCAAAATA 58.352 34.615 0.00 0.00 0.00 1.40
3040 5998 7.779798 TCATTTACTCCCTCCATTCCAAAATAG 59.220 37.037 0.00 0.00 0.00 1.73
3041 5999 6.901615 TTACTCCCTCCATTCCAAAATAGA 57.098 37.500 0.00 0.00 0.00 1.98
3042 6000 7.465900 TTACTCCCTCCATTCCAAAATAGAT 57.534 36.000 0.00 0.00 0.00 1.98
3043 6001 5.699143 ACTCCCTCCATTCCAAAATAGATG 58.301 41.667 0.00 0.00 0.00 2.90
3044 6002 5.433051 ACTCCCTCCATTCCAAAATAGATGA 59.567 40.000 0.00 0.00 0.00 2.92
3045 6003 5.694995 TCCCTCCATTCCAAAATAGATGAC 58.305 41.667 0.00 0.00 0.00 3.06
3046 6004 5.433051 TCCCTCCATTCCAAAATAGATGACT 59.567 40.000 0.00 0.00 0.00 3.41
3047 6005 5.767168 CCCTCCATTCCAAAATAGATGACTC 59.233 44.000 0.00 0.00 0.00 3.36
3048 6006 6.359804 CCTCCATTCCAAAATAGATGACTCA 58.640 40.000 0.00 0.00 0.00 3.41
3049 6007 6.830324 CCTCCATTCCAAAATAGATGACTCAA 59.170 38.462 0.00 0.00 0.00 3.02
3050 6008 7.504911 CCTCCATTCCAAAATAGATGACTCAAT 59.495 37.037 0.00 0.00 0.00 2.57
3051 6009 8.827832 TCCATTCCAAAATAGATGACTCAATT 57.172 30.769 0.00 0.00 0.00 2.32
3052 6010 9.258629 TCCATTCCAAAATAGATGACTCAATTT 57.741 29.630 0.00 0.00 0.00 1.82
3053 6011 9.880157 CCATTCCAAAATAGATGACTCAATTTT 57.120 29.630 0.00 0.00 33.07 1.82
3123 6081 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
3124 6082 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
3125 6083 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
3126 6084 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
3127 6085 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
3128 6086 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
3129 6087 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
3130 6088 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
3131 6089 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
3132 6090 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
3133 6091 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
3134 6092 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
3135 6093 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
3136 6094 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
3192 6150 9.672086 GCGGCTCATAATTCTATAAGACTATAG 57.328 37.037 0.00 0.00 38.86 1.31
3212 6170 3.019564 AGCAGGCTGTCCAATCATTTAC 58.980 45.455 17.16 0.00 33.74 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
197 202 1.243902 GCACCAAATTCGAACTGGGA 58.756 50.000 24.70 0.0 34.31 4.37
230 237 2.835764 AGTGATTAGGCCCAACGTAAGA 59.164 45.455 0.00 0.0 43.62 2.10
249 256 1.383803 GATGGAGCCAGGAGGGAGT 60.384 63.158 0.00 0.0 40.01 3.85
253 260 2.021262 TGATAGATGGAGCCAGGAGG 57.979 55.000 0.00 0.0 38.23 4.30
295 370 7.370905 TGAGAATCATCAGTTCCATCTATGT 57.629 36.000 0.00 0.0 42.56 2.29
312 387 9.404348 GTTCCATCTCTTTTTCTTTTGAGAATC 57.596 33.333 0.00 0.0 38.77 2.52
313 388 9.140874 AGTTCCATCTCTTTTTCTTTTGAGAAT 57.859 29.630 0.00 0.0 38.77 2.40
315 390 7.775093 TCAGTTCCATCTCTTTTTCTTTTGAGA 59.225 33.333 0.00 0.0 39.47 3.27
316 391 7.934457 TCAGTTCCATCTCTTTTTCTTTTGAG 58.066 34.615 0.00 0.0 0.00 3.02
317 392 7.880160 TCAGTTCCATCTCTTTTTCTTTTGA 57.120 32.000 0.00 0.0 0.00 2.69
318 393 8.975439 CAATCAGTTCCATCTCTTTTTCTTTTG 58.025 33.333 0.00 0.0 0.00 2.44
323 398 6.974965 ACACAATCAGTTCCATCTCTTTTTC 58.025 36.000 0.00 0.0 0.00 2.29
324 399 6.547141 TGACACAATCAGTTCCATCTCTTTTT 59.453 34.615 0.00 0.0 31.91 1.94
325 400 6.064060 TGACACAATCAGTTCCATCTCTTTT 58.936 36.000 0.00 0.0 31.91 2.27
326 401 5.624159 TGACACAATCAGTTCCATCTCTTT 58.376 37.500 0.00 0.0 31.91 2.52
327 402 5.233083 TGACACAATCAGTTCCATCTCTT 57.767 39.130 0.00 0.0 31.91 2.85
328 403 4.897509 TGACACAATCAGTTCCATCTCT 57.102 40.909 0.00 0.0 31.91 3.10
329 404 4.940046 ACATGACACAATCAGTTCCATCTC 59.060 41.667 0.00 0.0 41.91 2.75
330 405 4.914983 ACATGACACAATCAGTTCCATCT 58.085 39.130 0.00 0.0 41.91 2.90
331 406 4.940046 AGACATGACACAATCAGTTCCATC 59.060 41.667 0.00 0.0 41.91 3.51
332 407 4.914983 AGACATGACACAATCAGTTCCAT 58.085 39.130 0.00 0.0 41.91 3.41
333 408 4.356405 AGACATGACACAATCAGTTCCA 57.644 40.909 0.00 0.0 41.91 3.53
334 409 6.801539 TTAAGACATGACACAATCAGTTCC 57.198 37.500 0.00 0.0 41.91 3.62
389 464 9.381033 GGAGATAAATCATCAGTTCCATCTATG 57.619 37.037 0.00 0.0 35.96 2.23
513 634 2.797156 GACATGACTCATCGAATTCCCG 59.203 50.000 0.00 0.0 0.00 5.14
543 664 4.046938 TGATAAGATGAACTGACGCCTC 57.953 45.455 0.00 0.0 0.00 4.70
588 710 8.908903 TCTAGAGTTGGTTGCTTTTCATAAAAA 58.091 29.630 0.00 0.0 33.42 1.94
737 862 2.750166 TCACTTTTGCAACCGAGTTTGA 59.250 40.909 0.00 0.0 0.00 2.69
857 1172 9.206870 GGATTGATCATCAAAGTTGCTTTTTAA 57.793 29.630 3.63 0.0 40.12 1.52
994 1324 7.560796 ACTTCATGCCTATTTATAGTAGCCT 57.439 36.000 0.00 0.0 0.00 4.58
1199 1529 2.940147 TGGTGCGATAATGTTTGTTGC 58.060 42.857 0.00 0.0 0.00 4.17
1236 1566 1.546476 TGGTTGTGGTTGTTGTTGGAC 59.454 47.619 0.00 0.0 0.00 4.02
1630 2831 7.040892 GCTGCAAGATAGATGGATGAACAAATA 60.041 37.037 0.00 0.0 34.07 1.40
1789 2990 0.977108 GGATTGCTGGGGGATTTGCA 60.977 55.000 0.00 0.0 0.00 4.08
1905 3127 1.000843 GGAAACACATTGGCCCAACTC 59.999 52.381 0.00 0.0 0.00 3.01
2057 3327 1.959226 GACACGGCACATCGTTGGT 60.959 57.895 0.00 0.0 41.86 3.67
2124 3394 2.436115 GTAGGCACCAACTCCGGC 60.436 66.667 0.00 0.0 0.00 6.13
2337 3609 3.378911 TGCAAGCATGGCAATCATATG 57.621 42.857 0.00 0.0 46.27 1.78
2483 3778 4.256920 ACAAGATCTCAAATCTCCAACCG 58.743 43.478 0.00 0.0 0.00 4.44
2623 3937 8.770828 TGGTCTTTTCTCGACAAATAAGTTAAG 58.229 33.333 0.00 0.0 33.11 1.85
3021 5979 5.767168 GTCATCTATTTTGGAATGGAGGGAG 59.233 44.000 0.00 0.0 36.39 4.30
3022 5980 5.433051 AGTCATCTATTTTGGAATGGAGGGA 59.567 40.000 0.00 0.0 36.39 4.20
3023 5981 5.699143 AGTCATCTATTTTGGAATGGAGGG 58.301 41.667 0.00 0.0 36.39 4.30
3024 5982 6.359804 TGAGTCATCTATTTTGGAATGGAGG 58.640 40.000 0.00 0.0 36.39 4.30
3025 5983 7.870509 TTGAGTCATCTATTTTGGAATGGAG 57.129 36.000 0.00 0.0 36.39 3.86
3026 5984 8.827832 AATTGAGTCATCTATTTTGGAATGGA 57.172 30.769 0.00 0.0 37.20 3.41
3027 5985 9.880157 AAAATTGAGTCATCTATTTTGGAATGG 57.120 29.630 11.47 0.0 44.08 3.16
3097 6055 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.0 0.00 2.73
3098 6056 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.0 0.00 2.90
3099 6057 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.0 0.00 2.41
3100 6058 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.0 0.00 2.83
3101 6059 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.0 0.00 2.77
3102 6060 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.0 0.00 2.66
3103 6061 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.0 0.00 2.66
3104 6062 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.0 0.00 3.16
3105 6063 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.0 0.00 3.18
3106 6064 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.0 0.00 3.02
3107 6065 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.0 0.00 3.41
3108 6066 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.0 0.00 3.36
3109 6067 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.0 0.00 3.41
3110 6068 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.0 0.00 3.06
3111 6069 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.0 0.00 2.92
3112 6070 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.0 0.00 2.90
3113 6071 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.0 0.00 1.98
3114 6072 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.0 0.00 1.98
3115 6073 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.0 0.00 1.73
3116 6074 4.355549 TCTACTCCCTCCGTTCCAAAATA 58.644 43.478 0.00 0.0 0.00 1.40
3117 6075 3.178865 TCTACTCCCTCCGTTCCAAAAT 58.821 45.455 0.00 0.0 0.00 1.82
3118 6076 2.612000 TCTACTCCCTCCGTTCCAAAA 58.388 47.619 0.00 0.0 0.00 2.44
3119 6077 2.314071 TCTACTCCCTCCGTTCCAAA 57.686 50.000 0.00 0.0 0.00 3.28
3120 6078 2.314071 TTCTACTCCCTCCGTTCCAA 57.686 50.000 0.00 0.0 0.00 3.53
3121 6079 2.314071 TTTCTACTCCCTCCGTTCCA 57.686 50.000 0.00 0.0 0.00 3.53
3122 6080 3.908643 AATTTCTACTCCCTCCGTTCC 57.091 47.619 0.00 0.0 0.00 3.62
3123 6081 5.451659 GGTCTAATTTCTACTCCCTCCGTTC 60.452 48.000 0.00 0.0 0.00 3.95
3124 6082 4.405036 GGTCTAATTTCTACTCCCTCCGTT 59.595 45.833 0.00 0.0 0.00 4.44
3125 6083 3.959449 GGTCTAATTTCTACTCCCTCCGT 59.041 47.826 0.00 0.0 0.00 4.69
3126 6084 3.958798 TGGTCTAATTTCTACTCCCTCCG 59.041 47.826 0.00 0.0 0.00 4.63
3127 6085 5.661759 TCTTGGTCTAATTTCTACTCCCTCC 59.338 44.000 0.00 0.0 0.00 4.30
3128 6086 6.608002 TCTCTTGGTCTAATTTCTACTCCCTC 59.392 42.308 0.00 0.0 0.00 4.30
3129 6087 6.503944 TCTCTTGGTCTAATTTCTACTCCCT 58.496 40.000 0.00 0.0 0.00 4.20
3130 6088 6.793505 TCTCTTGGTCTAATTTCTACTCCC 57.206 41.667 0.00 0.0 0.00 4.30
3131 6089 9.103861 CATTTCTCTTGGTCTAATTTCTACTCC 57.896 37.037 0.00 0.0 0.00 3.85
3132 6090 9.660180 ACATTTCTCTTGGTCTAATTTCTACTC 57.340 33.333 0.00 0.0 0.00 2.59
3133 6091 9.442047 CACATTTCTCTTGGTCTAATTTCTACT 57.558 33.333 0.00 0.0 0.00 2.57
3134 6092 8.669243 CCACATTTCTCTTGGTCTAATTTCTAC 58.331 37.037 0.00 0.0 0.00 2.59
3135 6093 8.602424 TCCACATTTCTCTTGGTCTAATTTCTA 58.398 33.333 0.00 0.0 0.00 2.10
3136 6094 7.461749 TCCACATTTCTCTTGGTCTAATTTCT 58.538 34.615 0.00 0.0 0.00 2.52
3192 6150 2.754552 TGTAAATGATTGGACAGCCTGC 59.245 45.455 0.00 0.0 34.31 4.85


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

AutoCloner maintained by Alex Coulton.