Multiple sequence alignment - TraesCS3D01G299600

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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 TraesCS3D01G299600 chr3D 100.000 2923 0 0 1 2923 414638976 414636054 0.000000e+00 5398.0
1 TraesCS3D01G299600 chr3A 87.940 1932 118 54 353 2219 535726758 535728639 0.000000e+00 2170.0
2 TraesCS3D01G299600 chr3A 80.807 719 71 34 1002 1688 18462402 18463085 4.350000e-138 501.0
3 TraesCS3D01G299600 chr3A 88.318 428 25 9 2499 2923 535806536 535806941 9.410000e-135 490.0
4 TraesCS3D01G299600 chr3A 91.860 172 8 5 2218 2389 535728877 535729042 4.870000e-58 235.0
5 TraesCS3D01G299600 chr3B 90.749 1589 77 34 683 2239 540477190 540475640 0.000000e+00 2056.0
6 TraesCS3D01G299600 chr3B 92.606 284 12 5 2267 2550 540475518 540475244 1.630000e-107 399.0
7 TraesCS3D01G299600 chr3B 86.486 333 26 11 353 680 540477786 540477468 6.000000e-92 348.0
8 TraesCS3D01G299600 chr3B 87.708 301 27 4 5 296 540481085 540480786 2.790000e-90 342.0
9 TraesCS3D01G299600 chr3B 91.371 197 13 2 2727 2923 540463529 540463337 1.730000e-67 267.0
10 TraesCS3D01G299600 chr3B 91.071 168 14 1 2571 2738 540465193 540465027 2.930000e-55 226.0
11 TraesCS3D01G299600 chr6D 80.083 241 39 7 1192 1429 62270814 62271048 1.390000e-38 171.0
12 TraesCS3D01G299600 chr2B 78.151 238 43 6 1192 1426 184409254 184409023 3.040000e-30 143.0
13 TraesCS3D01G299600 chr2B 78.519 135 24 4 1293 1426 637576687 637576817 1.870000e-12 84.2
14 TraesCS3D01G299600 chr2A 78.151 238 43 6 1192 1426 136951321 136951090 3.040000e-30 143.0
15 TraesCS3D01G299600 chr2A 78.519 135 24 4 1293 1426 678965480 678965610 1.870000e-12 84.2
16 TraesCS3D01G299600 chr2D 77.731 238 44 6 1192 1426 130843139 130842908 1.410000e-28 137.0
17 TraesCS3D01G299600 chr1D 76.210 248 44 12 1185 1427 480609546 480609309 1.840000e-22 117.0
18 TraesCS3D01G299600 chr1B 75.403 248 46 12 1185 1427 668982708 668982471 3.980000e-19 106.0
19 TraesCS3D01G299600 chr1A 75.403 248 46 12 1185 1427 577079994 577079757 3.980000e-19 106.0


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 TraesCS3D01G299600 chr3D 414636054 414638976 2922 True 5398.00 5398 100.00000 1 2923 1 chr3D.!!$R1 2922
1 TraesCS3D01G299600 chr3A 535726758 535729042 2284 False 1202.50 2170 89.90000 353 2389 2 chr3A.!!$F3 2036
2 TraesCS3D01G299600 chr3A 18462402 18463085 683 False 501.00 501 80.80700 1002 1688 1 chr3A.!!$F1 686
3 TraesCS3D01G299600 chr3B 540475244 540481085 5841 True 786.25 2056 89.38725 5 2550 4 chr3B.!!$R2 2545
4 TraesCS3D01G299600 chr3B 540463337 540465193 1856 True 246.50 267 91.22100 2571 2923 2 chr3B.!!$R1 352

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
334 369 0.178998 CATGAGCTCAATGGAGGGGG 60.179 60.0 22.5 0.0 41.67 5.40 F
664 3624 0.398664 ACCCGGCCTAGCTAGAACAT 60.399 55.0 22.7 0.0 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1153 4427 1.063488 GCCGGAAACACACACACAC 59.937 57.895 5.05 0.0 0.00 3.82 R
2552 6206 0.176680 CTTCATGCTGGTCGGTAGCT 59.823 55.000 0.00 0.0 41.66 3.32 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
49 50 0.753262 TCTCCGCCCTCTGATAAAGC 59.247 55.000 0.00 0.00 0.00 3.51
52 53 1.070758 TCCGCCCTCTGATAAAGCATC 59.929 52.381 0.00 0.00 0.00 3.91
78 79 4.277921 GGGTATAAAGTCAGACCTACCGAG 59.722 50.000 0.00 0.00 31.41 4.63
139 147 4.975147 AGGAATCTACCAACCATACCATCA 59.025 41.667 0.00 0.00 0.00 3.07
153 161 9.676861 AACCATACCATCATATGATTGATACAG 57.323 33.333 20.52 6.83 34.59 2.74
166 174 2.019249 TGATACAGCTTTGCCATGAGC 58.981 47.619 0.00 0.00 44.14 4.26
179 187 2.569059 CCATGAGCATCCCTACACTTG 58.431 52.381 0.00 0.00 0.00 3.16
186 194 2.684881 GCATCCCTACACTTGACATTGG 59.315 50.000 0.00 0.00 0.00 3.16
196 204 3.318839 CACTTGACATTGGGTTGACACAT 59.681 43.478 0.00 0.00 0.00 3.21
197 205 3.318839 ACTTGACATTGGGTTGACACATG 59.681 43.478 0.00 0.00 0.00 3.21
207 215 2.421424 GGTTGACACATGATGAAGAGGC 59.579 50.000 0.00 0.00 0.00 4.70
223 231 1.798813 GAGGCTTGACACCGTAACAAG 59.201 52.381 0.00 0.00 42.33 3.16
224 232 0.872388 GGCTTGACACCGTAACAAGG 59.128 55.000 14.50 0.00 40.57 3.61
225 233 0.237498 GCTTGACACCGTAACAAGGC 59.763 55.000 14.50 7.02 40.57 4.35
229 237 1.202710 TGACACCGTAACAAGGCATGT 60.203 47.619 0.00 0.00 46.82 3.21
230 238 1.196808 GACACCGTAACAAGGCATGTG 59.803 52.381 0.00 0.00 42.99 3.21
239 247 3.581024 ACAAGGCATGTGCTATTTGTG 57.419 42.857 16.21 5.83 41.93 3.33
253 261 1.433053 TTTGTGGCGTCGAGGTGTTG 61.433 55.000 7.01 0.00 0.00 3.33
263 271 1.552792 TCGAGGTGTTGACATGGCATA 59.447 47.619 0.00 0.00 0.00 3.14
280 289 2.223665 GCATACAAGGAATGCTTGAGGC 60.224 50.000 21.10 15.59 45.05 4.70
281 290 2.128771 TACAAGGAATGCTTGAGGCC 57.871 50.000 21.10 0.00 40.92 5.19
299 308 2.574399 GGGACGAGGTGTGAGCTC 59.426 66.667 6.82 6.82 39.24 4.09
301 310 0.680280 GGGACGAGGTGTGAGCTCTA 60.680 60.000 16.19 0.75 40.38 2.43
302 311 0.736053 GGACGAGGTGTGAGCTCTAG 59.264 60.000 16.19 0.00 40.38 2.43
303 312 1.679336 GGACGAGGTGTGAGCTCTAGA 60.679 57.143 16.19 0.00 40.38 2.43
304 313 2.294074 GACGAGGTGTGAGCTCTAGAT 58.706 52.381 16.19 0.00 40.38 1.98
306 315 3.878103 GACGAGGTGTGAGCTCTAGATTA 59.122 47.826 16.19 0.00 40.38 1.75
307 316 3.880490 ACGAGGTGTGAGCTCTAGATTAG 59.120 47.826 16.19 4.62 40.38 1.73
308 317 3.252215 CGAGGTGTGAGCTCTAGATTAGG 59.748 52.174 16.19 0.00 40.38 2.69
309 318 3.571590 AGGTGTGAGCTCTAGATTAGGG 58.428 50.000 16.19 0.00 0.00 3.53
315 324 2.003196 GCTCTAGATTAGGGCGATGC 57.997 55.000 0.00 0.00 43.30 3.91
316 325 1.273606 GCTCTAGATTAGGGCGATGCA 59.726 52.381 0.00 0.00 43.30 3.96
317 326 2.093764 GCTCTAGATTAGGGCGATGCAT 60.094 50.000 0.00 0.00 43.30 3.96
319 328 3.165071 TCTAGATTAGGGCGATGCATGA 58.835 45.455 2.46 0.00 0.00 3.07
321 330 0.801251 GATTAGGGCGATGCATGAGC 59.199 55.000 2.46 9.78 42.57 4.26
322 331 0.399454 ATTAGGGCGATGCATGAGCT 59.601 50.000 19.30 7.08 42.74 4.09
323 332 0.250038 TTAGGGCGATGCATGAGCTC 60.250 55.000 19.30 16.82 42.74 4.09
324 333 1.402107 TAGGGCGATGCATGAGCTCA 61.402 55.000 20.79 20.79 42.74 4.26
325 334 1.820906 GGGCGATGCATGAGCTCAA 60.821 57.895 22.50 4.47 42.74 3.02
326 335 1.170919 GGGCGATGCATGAGCTCAAT 61.171 55.000 22.50 10.07 42.74 2.57
329 364 1.589803 CGATGCATGAGCTCAATGGA 58.410 50.000 22.50 19.51 42.74 3.41
334 369 0.178998 CATGAGCTCAATGGAGGGGG 60.179 60.000 22.50 0.00 41.67 5.40
362 397 1.974236 CCTGGCTCCACCCTCTAATAG 59.026 57.143 0.00 0.00 37.83 1.73
367 402 4.654262 TGGCTCCACCCTCTAATAGTAAAG 59.346 45.833 0.00 0.00 37.83 1.85
379 3330 8.598041 CCTCTAATAGTAAAGCATTGGAGGTAT 58.402 37.037 14.96 0.00 46.71 2.73
396 3347 8.888836 TGGAGGTATAAATTCATATCTACCGA 57.111 34.615 0.00 0.00 0.00 4.69
397 3348 8.967918 TGGAGGTATAAATTCATATCTACCGAG 58.032 37.037 0.00 0.00 0.00 4.63
398 3349 8.968969 GGAGGTATAAATTCATATCTACCGAGT 58.031 37.037 0.00 0.00 0.00 4.18
400 3351 8.968969 AGGTATAAATTCATATCTACCGAGTCC 58.031 37.037 0.00 0.00 0.00 3.85
401 3352 7.914346 GGTATAAATTCATATCTACCGAGTCCG 59.086 40.741 0.00 0.00 0.00 4.79
402 3353 7.698506 ATAAATTCATATCTACCGAGTCCGA 57.301 36.000 0.00 0.00 38.22 4.55
404 3355 3.766068 TCATATCTACCGAGTCCGACT 57.234 47.619 0.00 0.00 38.22 4.18
406 3357 5.417754 TCATATCTACCGAGTCCGACTAT 57.582 43.478 0.00 0.00 38.22 2.12
407 3358 6.535963 TCATATCTACCGAGTCCGACTATA 57.464 41.667 0.00 0.00 38.22 1.31
408 3359 7.122138 TCATATCTACCGAGTCCGACTATAT 57.878 40.000 0.00 0.00 38.22 0.86
409 3360 6.985059 TCATATCTACCGAGTCCGACTATATG 59.015 42.308 15.06 15.06 38.22 1.78
410 3361 4.613925 TCTACCGAGTCCGACTATATGT 57.386 45.455 0.00 0.00 38.22 2.29
411 3362 5.728637 TCTACCGAGTCCGACTATATGTA 57.271 43.478 0.00 0.75 38.22 2.29
412 3363 6.101650 TCTACCGAGTCCGACTATATGTAA 57.898 41.667 0.00 0.00 38.22 2.41
413 3364 6.162079 TCTACCGAGTCCGACTATATGTAAG 58.838 44.000 0.00 0.00 38.22 2.34
414 3365 4.965814 ACCGAGTCCGACTATATGTAAGA 58.034 43.478 0.00 0.00 38.22 2.10
415 3366 5.558818 ACCGAGTCCGACTATATGTAAGAT 58.441 41.667 0.00 0.00 38.22 2.40
455 3407 9.706691 TTCTTTCTGACAAAAGAACGTATCTAT 57.293 29.630 15.53 0.00 45.60 1.98
462 3414 8.692710 TGACAAAAGAACGTATCTATCATACCT 58.307 33.333 0.00 0.00 37.42 3.08
469 3421 9.742144 AGAACGTATCTATCATACCTTCATAGT 57.258 33.333 0.00 0.00 36.32 2.12
526 3481 2.752903 CCACGGAAAAGAATACAAGGGG 59.247 50.000 0.00 0.00 0.00 4.79
661 3621 1.629043 CATACCCGGCCTAGCTAGAA 58.371 55.000 22.70 0.00 0.00 2.10
664 3624 0.398664 ACCCGGCCTAGCTAGAACAT 60.399 55.000 22.70 0.00 0.00 2.71
824 4063 3.733960 GGAAAAGGACGTGGCCGC 61.734 66.667 6.11 6.11 37.70 6.53
848 4087 2.095567 GGCTGCCGATATAAAGCACATG 60.096 50.000 1.35 0.00 37.40 3.21
1153 4427 0.793250 TTGTGTCGTGTGTGTGTGTG 59.207 50.000 0.00 0.00 0.00 3.82
1155 4429 0.094558 GTGTCGTGTGTGTGTGTGTG 59.905 55.000 0.00 0.00 0.00 3.82
1156 4430 0.319986 TGTCGTGTGTGTGTGTGTGT 60.320 50.000 0.00 0.00 0.00 3.72
1158 4432 0.319986 TCGTGTGTGTGTGTGTGTGT 60.320 50.000 0.00 0.00 0.00 3.72
1168 4442 1.537638 TGTGTGTGTGTGTGTGTTTCC 59.462 47.619 0.00 0.00 0.00 3.13
1172 4446 2.115911 TGTGTGTGTGTTTCCGGCC 61.116 57.895 0.00 0.00 0.00 6.13
1446 4720 1.229082 TACCGTGCCTTCTCACCCT 60.229 57.895 0.00 0.00 33.57 4.34
1448 4722 2.743718 CGTGCCTTCTCACCCTGT 59.256 61.111 0.00 0.00 33.57 4.00
1450 4724 1.754745 GTGCCTTCTCACCCTGTCA 59.245 57.895 0.00 0.00 0.00 3.58
1456 4730 0.673985 TTCTCACCCTGTCACTCGTG 59.326 55.000 0.00 0.00 0.00 4.35
1466 4740 3.356814 TCACTCGTGACTCCATCCA 57.643 52.632 0.00 0.00 34.14 3.41
1467 4741 1.852633 TCACTCGTGACTCCATCCAT 58.147 50.000 0.00 0.00 34.14 3.41
1468 4742 1.751351 TCACTCGTGACTCCATCCATC 59.249 52.381 0.00 0.00 34.14 3.51
1477 4751 2.617308 GACTCCATCCATCAGCATGTTG 59.383 50.000 2.65 2.65 37.40 3.33
1495 4795 6.403636 GCATGTTGGTTTCTTGTTCTATCGAT 60.404 38.462 2.16 2.16 0.00 3.59
1508 4813 4.184079 TCTATCGATCTCACCATGCATG 57.816 45.455 20.19 20.19 0.00 4.06
1515 4820 2.153645 TCTCACCATGCATGTGTGTTC 58.846 47.619 30.53 0.00 33.55 3.18
1516 4821 1.881324 CTCACCATGCATGTGTGTTCA 59.119 47.619 30.53 19.41 33.55 3.18
1521 4826 3.119884 ACCATGCATGTGTGTTCATAACG 60.120 43.478 24.58 7.48 0.00 3.18
1603 4910 3.245284 CGGGCAAATCATAACGAGTACTG 59.755 47.826 0.00 0.00 0.00 2.74
1604 4911 4.189231 GGGCAAATCATAACGAGTACTGT 58.811 43.478 0.00 0.00 0.00 3.55
1605 4912 5.353938 GGGCAAATCATAACGAGTACTGTA 58.646 41.667 0.00 0.00 0.00 2.74
1606 4913 5.462398 GGGCAAATCATAACGAGTACTGTAG 59.538 44.000 0.00 0.00 0.00 2.74
1607 4914 6.040878 GGCAAATCATAACGAGTACTGTAGT 58.959 40.000 0.00 0.00 0.00 2.73
1608 4915 7.198390 GGCAAATCATAACGAGTACTGTAGTA 58.802 38.462 0.00 0.00 0.00 1.82
1666 4977 7.337184 TGACGTATTTTCCCTATGTAAATTGCA 59.663 33.333 0.00 0.00 0.00 4.08
1712 5023 4.416738 GGCACAGGGACAGGCTCC 62.417 72.222 0.00 0.00 38.55 4.70
1983 5294 9.374838 GTGCATTCTTTTTAATCATCTCCAATT 57.625 29.630 0.00 0.00 0.00 2.32
1985 5296 9.038803 GCATTCTTTTTAATCATCTCCAATTCC 57.961 33.333 0.00 0.00 0.00 3.01
2011 5322 1.268539 CGTTGTTGCTTTGGTGGAGAC 60.269 52.381 0.00 0.00 0.00 3.36
2112 5427 1.681264 TGCCTCATGTCGATGTCGTAT 59.319 47.619 2.04 0.00 40.80 3.06
2225 5781 9.474313 AACCAAGCTCACTTTATATATCCAAAA 57.526 29.630 0.00 0.00 32.29 2.44
2226 5782 8.903820 ACCAAGCTCACTTTATATATCCAAAAC 58.096 33.333 0.00 0.00 32.29 2.43
2227 5783 8.070171 CCAAGCTCACTTTATATATCCAAAACG 58.930 37.037 0.00 0.00 32.29 3.60
2231 5787 6.902408 TCACTTTATATATCCAAAACGGGGT 58.098 36.000 0.00 0.00 34.36 4.95
2253 5880 7.759886 GGGGTTTGCTAAGATTGAAACTTAATC 59.240 37.037 0.00 0.00 35.32 1.75
2356 6010 5.497474 AGGCGCTTAAAGAGGAAAAGATAA 58.503 37.500 7.64 0.00 0.00 1.75
2357 6011 5.944007 AGGCGCTTAAAGAGGAAAAGATAAA 59.056 36.000 7.64 0.00 0.00 1.40
2358 6012 6.603599 AGGCGCTTAAAGAGGAAAAGATAAAT 59.396 34.615 7.64 0.00 0.00 1.40
2359 6013 7.773690 AGGCGCTTAAAGAGGAAAAGATAAATA 59.226 33.333 7.64 0.00 0.00 1.40
2360 6014 8.568794 GGCGCTTAAAGAGGAAAAGATAAATAT 58.431 33.333 7.64 0.00 0.00 1.28
2399 6053 1.093496 AGCGCCTATTAACCCAACGC 61.093 55.000 2.29 0.00 44.79 4.84
2404 6058 1.940613 CCTATTAACCCAACGCTGAGC 59.059 52.381 0.00 0.00 0.00 4.26
2415 6069 2.705826 GCTGAGCGCTGTACATGC 59.294 61.111 18.48 8.84 35.14 4.06
2416 6070 2.817423 GCTGAGCGCTGTACATGCC 61.817 63.158 18.48 0.00 35.14 4.40
2417 6071 2.125147 TGAGCGCTGTACATGCCC 60.125 61.111 18.48 0.00 0.00 5.36
2418 6072 2.187946 GAGCGCTGTACATGCCCT 59.812 61.111 18.48 9.58 0.00 5.19
2458 6112 2.809696 CTGATCAATCACTGCACACACA 59.190 45.455 0.00 0.00 32.50 3.72
2459 6113 2.549329 TGATCAATCACTGCACACACAC 59.451 45.455 0.00 0.00 0.00 3.82
2460 6114 2.035530 TCAATCACTGCACACACACA 57.964 45.000 0.00 0.00 0.00 3.72
2461 6115 1.670295 TCAATCACTGCACACACACAC 59.330 47.619 0.00 0.00 0.00 3.82
2473 6127 1.864711 CACACACACGGTTTCTACAGG 59.135 52.381 0.00 0.00 0.00 4.00
2485 6139 4.035909 GGTTTCTACAGGCACGAAGAAAAA 59.964 41.667 0.00 0.00 39.08 1.94
2550 6204 2.389715 AGGCGTCAGGATTAGTTAGCT 58.610 47.619 0.00 0.00 0.00 3.32
2551 6205 2.766828 AGGCGTCAGGATTAGTTAGCTT 59.233 45.455 0.00 0.00 0.00 3.74
2552 6206 3.958798 AGGCGTCAGGATTAGTTAGCTTA 59.041 43.478 0.00 0.00 0.00 3.09
2553 6207 4.038162 AGGCGTCAGGATTAGTTAGCTTAG 59.962 45.833 0.00 0.00 0.00 2.18
2554 6208 3.736759 GCGTCAGGATTAGTTAGCTTAGC 59.263 47.826 0.00 0.00 0.00 3.09
2555 6209 4.500035 GCGTCAGGATTAGTTAGCTTAGCT 60.500 45.833 12.67 12.67 43.41 3.32
2556 6210 5.278364 GCGTCAGGATTAGTTAGCTTAGCTA 60.278 44.000 10.21 10.21 40.44 3.32
2557 6211 6.144175 CGTCAGGATTAGTTAGCTTAGCTAC 58.856 44.000 14.08 9.24 41.12 3.58
2558 6212 6.448852 GTCAGGATTAGTTAGCTTAGCTACC 58.551 44.000 14.08 7.10 41.12 3.18
2559 6213 5.241064 TCAGGATTAGTTAGCTTAGCTACCG 59.759 44.000 14.08 7.42 41.12 4.02
2560 6214 5.241064 CAGGATTAGTTAGCTTAGCTACCGA 59.759 44.000 14.08 0.00 41.12 4.69
2561 6215 5.241285 AGGATTAGTTAGCTTAGCTACCGAC 59.759 44.000 14.08 9.75 41.12 4.79
2562 6216 4.907879 TTAGTTAGCTTAGCTACCGACC 57.092 45.455 14.08 0.31 41.12 4.79
2563 6217 2.731572 AGTTAGCTTAGCTACCGACCA 58.268 47.619 14.08 0.00 41.12 4.02
2564 6218 2.688958 AGTTAGCTTAGCTACCGACCAG 59.311 50.000 14.08 0.00 41.12 4.00
2565 6219 1.030457 TAGCTTAGCTACCGACCAGC 58.970 55.000 10.21 4.94 40.44 4.85
2566 6220 0.970937 AGCTTAGCTACCGACCAGCA 60.971 55.000 4.30 0.00 41.66 4.41
2567 6221 0.105039 GCTTAGCTACCGACCAGCAT 59.895 55.000 7.77 0.00 41.66 3.79
2568 6222 1.858091 CTTAGCTACCGACCAGCATG 58.142 55.000 0.00 0.00 41.66 4.06
2569 6223 1.409064 CTTAGCTACCGACCAGCATGA 59.591 52.381 0.00 0.00 41.66 3.07
2574 6228 1.207089 CTACCGACCAGCATGAAGGAA 59.793 52.381 10.46 0.00 39.69 3.36
2582 6236 5.505173 ACCAGCATGAAGGAAATAAATCG 57.495 39.130 10.46 0.00 39.69 3.34
2587 6241 5.050091 AGCATGAAGGAAATAAATCGTAGCG 60.050 40.000 0.00 0.00 0.00 4.26
2595 6249 2.298411 TAAATCGTAGCGTTCACCCC 57.702 50.000 0.00 0.00 0.00 4.95
2601 6255 1.679977 TAGCGTTCACCCCTAGCGT 60.680 57.895 0.00 0.00 0.00 5.07
2614 6268 2.287427 CCCTAGCGTCCTATGTTGTACG 60.287 54.545 0.00 0.00 38.34 3.67
2617 6271 0.643820 GCGTCCTATGTTGTACGTGC 59.356 55.000 0.00 0.00 37.64 5.34
2621 6275 2.094390 GTCCTATGTTGTACGTGCCTCA 60.094 50.000 0.00 0.00 0.00 3.86
2625 6279 0.753867 TGTTGTACGTGCCTCAAGGA 59.246 50.000 0.00 0.00 37.39 3.36
2716 6370 3.937778 TCAGATCAAATCATGAGGGCA 57.062 42.857 0.09 0.00 42.53 5.36
2717 6371 4.239428 TCAGATCAAATCATGAGGGCAA 57.761 40.909 0.09 0.00 42.53 4.52
2719 6373 5.018149 TCAGATCAAATCATGAGGGCAAAA 58.982 37.500 0.09 0.00 42.53 2.44
2720 6374 5.105635 TCAGATCAAATCATGAGGGCAAAAC 60.106 40.000 0.09 0.00 42.53 2.43
2721 6375 4.773674 AGATCAAATCATGAGGGCAAAACA 59.226 37.500 0.09 0.00 42.53 2.83
2722 6376 4.255833 TCAAATCATGAGGGCAAAACAC 57.744 40.909 0.09 0.00 33.04 3.32
2724 6378 4.100653 TCAAATCATGAGGGCAAAACACAA 59.899 37.500 0.09 0.00 33.04 3.33
2725 6379 3.947910 ATCATGAGGGCAAAACACAAG 57.052 42.857 0.09 0.00 0.00 3.16
2732 7894 4.202141 TGAGGGCAAAACACAAGATTTCAG 60.202 41.667 0.00 0.00 0.00 3.02
2781 7943 3.142174 GCACATTGTAGCCCTTATCCTC 58.858 50.000 0.00 0.00 0.00 3.71
2797 7959 1.918262 TCCTCATCCTCCAACATTGCT 59.082 47.619 0.00 0.00 0.00 3.91
2802 7964 5.185635 CCTCATCCTCCAACATTGCTTTAAA 59.814 40.000 0.00 0.00 0.00 1.52
2815 7977 9.927668 AACATTGCTTTAAAATATGTGCTAGTT 57.072 25.926 9.12 3.78 30.43 2.24
2906 8068 3.904136 AAGACAAAAGCTCATGAACGG 57.096 42.857 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.101635 TATCAGAGGGCGGAGACACG 61.102 60.000 0.00 0.00 37.00 4.49
49 50 4.656112 AGGTCTGACTTTATACCCCTGATG 59.344 45.833 7.85 0.00 32.10 3.07
52 53 4.344390 GGTAGGTCTGACTTTATACCCCTG 59.656 50.000 7.85 0.00 32.10 4.45
59 60 6.039493 CACATACTCGGTAGGTCTGACTTTAT 59.961 42.308 7.85 0.00 30.44 1.40
78 79 6.699575 AGGGACAATATTTCTTGCACATAC 57.300 37.500 0.00 0.00 0.00 2.39
114 115 5.110814 TGGTATGGTTGGTAGATTCCTTG 57.889 43.478 0.00 0.00 0.00 3.61
117 118 5.304686 TGATGGTATGGTTGGTAGATTCC 57.695 43.478 0.00 0.00 0.00 3.01
139 147 6.717997 TCATGGCAAAGCTGTATCAATCATAT 59.282 34.615 0.00 0.00 0.00 1.78
166 174 3.282021 CCCAATGTCAAGTGTAGGGATG 58.718 50.000 0.00 0.00 36.96 3.51
179 187 3.758023 TCATCATGTGTCAACCCAATGTC 59.242 43.478 0.00 0.00 0.00 3.06
186 194 2.421424 GCCTCTTCATCATGTGTCAACC 59.579 50.000 0.00 0.00 0.00 3.77
196 204 1.338105 CGGTGTCAAGCCTCTTCATCA 60.338 52.381 0.00 0.00 0.00 3.07
197 205 1.338200 ACGGTGTCAAGCCTCTTCATC 60.338 52.381 0.00 0.00 0.00 2.92
207 215 1.588674 TGCCTTGTTACGGTGTCAAG 58.411 50.000 15.29 15.29 38.45 3.02
223 231 0.526096 CGCCACAAATAGCACATGCC 60.526 55.000 0.00 0.00 43.38 4.40
224 232 0.171007 ACGCCACAAATAGCACATGC 59.829 50.000 0.00 0.00 42.49 4.06
225 233 1.529622 CGACGCCACAAATAGCACATG 60.530 52.381 0.00 0.00 0.00 3.21
229 237 0.739462 CCTCGACGCCACAAATAGCA 60.739 55.000 0.00 0.00 0.00 3.49
230 238 0.739813 ACCTCGACGCCACAAATAGC 60.740 55.000 0.00 0.00 0.00 2.97
239 247 1.374252 ATGTCAACACCTCGACGCC 60.374 57.895 0.00 0.00 34.78 5.68
253 261 3.360249 GCATTCCTTGTATGCCATGTC 57.640 47.619 0.00 0.00 41.94 3.06
280 289 4.436998 GCTCACACCTCGTCCCGG 62.437 72.222 0.00 0.00 0.00 5.73
281 290 3.343788 GAGCTCACACCTCGTCCCG 62.344 68.421 9.40 0.00 0.00 5.14
292 301 2.231529 TCGCCCTAATCTAGAGCTCAC 58.768 52.381 17.77 0.00 0.00 3.51
296 305 1.273606 TGCATCGCCCTAATCTAGAGC 59.726 52.381 0.00 0.00 0.00 4.09
297 306 3.194329 TCATGCATCGCCCTAATCTAGAG 59.806 47.826 0.00 0.00 0.00 2.43
299 308 3.519579 CTCATGCATCGCCCTAATCTAG 58.480 50.000 0.00 0.00 0.00 2.43
301 310 1.610102 GCTCATGCATCGCCCTAATCT 60.610 52.381 0.00 0.00 39.41 2.40
302 311 0.801251 GCTCATGCATCGCCCTAATC 59.199 55.000 0.00 0.00 39.41 1.75
303 312 0.399454 AGCTCATGCATCGCCCTAAT 59.601 50.000 12.56 0.00 42.74 1.73
304 313 0.250038 GAGCTCATGCATCGCCCTAA 60.250 55.000 9.40 0.00 42.74 2.69
306 315 2.110627 GAGCTCATGCATCGCCCT 59.889 61.111 9.40 0.43 42.74 5.19
307 316 1.170919 ATTGAGCTCATGCATCGCCC 61.171 55.000 19.04 3.45 42.74 6.13
308 317 0.040336 CATTGAGCTCATGCATCGCC 60.040 55.000 19.04 6.49 42.74 5.54
309 318 0.040336 CCATTGAGCTCATGCATCGC 60.040 55.000 19.04 9.01 42.74 4.58
310 319 1.531578 CTCCATTGAGCTCATGCATCG 59.468 52.381 19.04 0.87 42.74 3.84
311 320 1.880675 CCTCCATTGAGCTCATGCATC 59.119 52.381 19.04 0.00 42.74 3.91
312 321 1.478837 CCCTCCATTGAGCTCATGCAT 60.479 52.381 19.04 5.27 42.74 3.96
313 322 0.106868 CCCTCCATTGAGCTCATGCA 60.107 55.000 19.04 2.52 42.74 3.96
314 323 0.822532 CCCCTCCATTGAGCTCATGC 60.823 60.000 19.04 0.00 37.29 4.06
315 324 0.178998 CCCCCTCCATTGAGCTCATG 60.179 60.000 19.04 16.66 37.29 3.07
316 325 2.238530 CCCCCTCCATTGAGCTCAT 58.761 57.895 19.04 4.99 37.29 2.90
317 326 3.745546 CCCCCTCCATTGAGCTCA 58.254 61.111 13.74 13.74 37.29 4.26
342 377 1.974236 CTATTAGAGGGTGGAGCCAGG 59.026 57.143 0.00 0.00 39.65 4.45
346 381 4.101119 TGCTTTACTATTAGAGGGTGGAGC 59.899 45.833 0.00 0.00 0.00 4.70
349 384 5.765182 CCAATGCTTTACTATTAGAGGGTGG 59.235 44.000 0.00 0.00 0.00 4.61
351 386 6.183361 CCTCCAATGCTTTACTATTAGAGGGT 60.183 42.308 0.00 0.00 38.05 4.34
379 3330 6.713903 AGTCGGACTCGGTAGATATGAATTTA 59.286 38.462 4.45 0.00 36.95 1.40
383 3334 4.082665 AGTCGGACTCGGTAGATATGAA 57.917 45.455 4.45 0.00 36.95 2.57
390 3341 6.162079 TCTTACATATAGTCGGACTCGGTAG 58.838 44.000 15.05 5.10 36.95 3.18
393 3344 7.789273 ATATCTTACATATAGTCGGACTCGG 57.211 40.000 15.05 5.43 36.95 4.63
435 3387 8.969267 GGTATGATAGATACGTTCTTTTGTCAG 58.031 37.037 0.00 0.00 35.79 3.51
436 3388 8.692710 AGGTATGATAGATACGTTCTTTTGTCA 58.307 33.333 0.00 1.33 35.79 3.58
474 3426 9.578576 AGAAGAAATGGCAAAGCTATATATCAA 57.421 29.630 0.00 0.00 0.00 2.57
482 3434 6.183360 TGGAAAAAGAAGAAATGGCAAAGCTA 60.183 34.615 0.00 0.00 0.00 3.32
483 3435 5.059161 GGAAAAAGAAGAAATGGCAAAGCT 58.941 37.500 0.00 0.00 0.00 3.74
526 3481 1.222113 GCTTACCAGACCCAGAGGC 59.778 63.158 0.00 0.00 36.11 4.70
672 3632 0.678048 GGGACACCTGGCAGTTGATC 60.678 60.000 19.55 11.71 0.00 2.92
680 3640 3.936203 TCACACGGGACACCTGGC 61.936 66.667 0.00 0.00 33.40 4.85
721 3958 1.062587 CATGTTTCTTAGGCGCGAAGG 59.937 52.381 12.10 2.52 0.00 3.46
845 4084 0.677731 TGAGCTTTCCTTCGGCCATG 60.678 55.000 2.24 0.00 0.00 3.66
848 4087 2.041115 GGTGAGCTTTCCTTCGGCC 61.041 63.158 0.00 0.00 0.00 6.13
899 4138 1.723273 CTGCTGGTGTGTGTGTGTG 59.277 57.895 0.00 0.00 0.00 3.82
900 4139 2.114670 GCTGCTGGTGTGTGTGTGT 61.115 57.895 0.00 0.00 0.00 3.72
936 4175 2.438075 CTTCTGCTGGCTGGCTCC 60.438 66.667 2.00 0.00 0.00 4.70
949 4194 1.431440 CTAGTGCGCGCTCTCTTCT 59.569 57.895 35.71 21.97 0.00 2.85
1153 4427 1.063488 GCCGGAAACACACACACAC 59.937 57.895 5.05 0.00 0.00 3.82
1155 4429 2.719354 GGCCGGAAACACACACAC 59.281 61.111 5.05 0.00 0.00 3.82
1156 4430 2.517402 GGGCCGGAAACACACACA 60.517 61.111 5.05 0.00 0.00 3.72
1158 4432 4.178169 ACGGGCCGGAAACACACA 62.178 61.111 31.78 0.00 0.00 3.72
1448 4722 1.751351 GATGGATGGAGTCACGAGTGA 59.249 52.381 1.24 1.24 37.24 3.41
1450 4724 1.753649 CTGATGGATGGAGTCACGAGT 59.246 52.381 0.00 0.00 0.00 4.18
1456 4730 2.617308 CAACATGCTGATGGATGGAGTC 59.383 50.000 0.00 0.00 44.78 3.36
1465 4739 4.247267 ACAAGAAACCAACATGCTGATG 57.753 40.909 0.00 0.00 35.49 3.07
1466 4740 4.586001 AGAACAAGAAACCAACATGCTGAT 59.414 37.500 0.00 0.00 0.00 2.90
1467 4741 3.953612 AGAACAAGAAACCAACATGCTGA 59.046 39.130 0.00 0.00 0.00 4.26
1468 4742 4.311816 AGAACAAGAAACCAACATGCTG 57.688 40.909 0.00 0.00 0.00 4.41
1495 4795 2.153645 GAACACACATGCATGGTGAGA 58.846 47.619 35.04 0.00 39.53 3.27
1508 4813 2.157668 CCTGCAGACGTTATGAACACAC 59.842 50.000 17.39 0.00 0.00 3.82
1515 4820 1.148157 CCGAGCCTGCAGACGTTATG 61.148 60.000 17.39 0.00 0.00 1.90
1516 4821 1.141881 CCGAGCCTGCAGACGTTAT 59.858 57.895 17.39 0.00 0.00 1.89
1521 4826 2.435059 GTTCCCGAGCCTGCAGAC 60.435 66.667 17.39 2.52 0.00 3.51
1605 4912 9.019656 TGCAATGATAAATGTTTGGTAAGTACT 57.980 29.630 0.00 0.00 0.00 2.73
1606 4913 9.801873 ATGCAATGATAAATGTTTGGTAAGTAC 57.198 29.630 0.00 0.00 0.00 2.73
1716 5027 4.681978 AGACGAGTTGGTGCCGGC 62.682 66.667 22.73 22.73 0.00 6.13
1730 5041 4.144703 GTCGAGCCCGGGGAAGAC 62.145 72.222 25.28 17.62 36.24 3.01
1983 5294 1.601903 CAAAGCAACAACGCACTAGGA 59.398 47.619 0.00 0.00 0.00 2.94
1985 5296 1.333619 ACCAAAGCAACAACGCACTAG 59.666 47.619 0.00 0.00 0.00 2.57
2011 5322 1.125021 CTAAAGCAGAACGACAGCACG 59.875 52.381 0.00 0.00 39.31 5.34
2112 5427 4.177026 CAAATTGTTTCACGGGACACAAA 58.823 39.130 22.12 7.29 44.33 2.83
2220 5536 1.957877 TCTTAGCAAACCCCGTTTTGG 59.042 47.619 4.23 0.00 37.02 3.28
2225 5781 2.871096 TCAATCTTAGCAAACCCCGT 57.129 45.000 0.00 0.00 0.00 5.28
2226 5782 3.506067 AGTTTCAATCTTAGCAAACCCCG 59.494 43.478 0.00 0.00 30.39 5.73
2227 5783 5.468540 AAGTTTCAATCTTAGCAAACCCC 57.531 39.130 0.00 0.00 30.39 4.95
2305 5955 1.332997 GCCTTTCAATGGAGATGCTCG 59.667 52.381 0.00 0.00 0.00 5.03
2356 6010 9.129209 GCTTCGCAGTTCTTTTCTTTAAATATT 57.871 29.630 0.00 0.00 0.00 1.28
2357 6011 7.481798 CGCTTCGCAGTTCTTTTCTTTAAATAT 59.518 33.333 0.00 0.00 0.00 1.28
2358 6012 6.795114 CGCTTCGCAGTTCTTTTCTTTAAATA 59.205 34.615 0.00 0.00 0.00 1.40
2359 6013 5.625311 CGCTTCGCAGTTCTTTTCTTTAAAT 59.375 36.000 0.00 0.00 0.00 1.40
2360 6014 4.967575 CGCTTCGCAGTTCTTTTCTTTAAA 59.032 37.500 0.00 0.00 0.00 1.52
2363 6017 2.987046 CGCTTCGCAGTTCTTTTCTTT 58.013 42.857 0.00 0.00 0.00 2.52
2399 6053 2.176273 GGGCATGTACAGCGCTCAG 61.176 63.158 7.13 0.00 41.20 3.35
2404 6058 2.992089 CCTAAGGGCATGTACAGCG 58.008 57.895 0.33 0.00 0.00 5.18
2415 6069 1.867166 GCTAGTTTAGCGCCTAAGGG 58.133 55.000 2.29 0.00 42.62 3.95
2458 6112 0.599204 CGTGCCTGTAGAAACCGTGT 60.599 55.000 0.00 0.00 0.00 4.49
2459 6113 0.319211 TCGTGCCTGTAGAAACCGTG 60.319 55.000 0.00 0.00 0.00 4.94
2460 6114 0.390124 TTCGTGCCTGTAGAAACCGT 59.610 50.000 0.00 0.00 0.00 4.83
2461 6115 1.068474 CTTCGTGCCTGTAGAAACCG 58.932 55.000 0.00 0.00 0.00 4.44
2485 6139 1.214325 GGCGGCCGCTTAACATTTT 59.786 52.632 45.23 0.00 41.60 1.82
2550 6204 1.480789 TCATGCTGGTCGGTAGCTAA 58.519 50.000 0.00 0.00 41.66 3.09
2551 6205 1.409064 CTTCATGCTGGTCGGTAGCTA 59.591 52.381 0.00 0.00 41.66 3.32
2552 6206 0.176680 CTTCATGCTGGTCGGTAGCT 59.823 55.000 0.00 0.00 41.66 3.32
2553 6207 0.811616 CCTTCATGCTGGTCGGTAGC 60.812 60.000 0.00 0.00 41.49 3.58
2554 6208 0.824109 TCCTTCATGCTGGTCGGTAG 59.176 55.000 4.20 0.00 0.00 3.18
2555 6209 1.271856 TTCCTTCATGCTGGTCGGTA 58.728 50.000 4.20 0.00 0.00 4.02
2556 6210 0.400213 TTTCCTTCATGCTGGTCGGT 59.600 50.000 4.20 0.00 0.00 4.69
2557 6211 1.755179 ATTTCCTTCATGCTGGTCGG 58.245 50.000 4.20 0.00 0.00 4.79
2558 6212 4.963276 TTTATTTCCTTCATGCTGGTCG 57.037 40.909 4.20 0.00 0.00 4.79
2559 6213 5.066505 ACGATTTATTTCCTTCATGCTGGTC 59.933 40.000 0.00 0.00 0.00 4.02
2560 6214 4.949856 ACGATTTATTTCCTTCATGCTGGT 59.050 37.500 0.00 0.00 0.00 4.00
2561 6215 5.505173 ACGATTTATTTCCTTCATGCTGG 57.495 39.130 0.00 0.00 0.00 4.85
2562 6216 6.138761 GCTACGATTTATTTCCTTCATGCTG 58.861 40.000 0.00 0.00 0.00 4.41
2563 6217 5.050091 CGCTACGATTTATTTCCTTCATGCT 60.050 40.000 0.00 0.00 0.00 3.79
2564 6218 5.140177 CGCTACGATTTATTTCCTTCATGC 58.860 41.667 0.00 0.00 0.00 4.06
2565 6219 6.287107 ACGCTACGATTTATTTCCTTCATG 57.713 37.500 0.00 0.00 0.00 3.07
2566 6220 6.537301 TGAACGCTACGATTTATTTCCTTCAT 59.463 34.615 0.00 0.00 0.00 2.57
2567 6221 5.870433 TGAACGCTACGATTTATTTCCTTCA 59.130 36.000 0.00 0.00 0.00 3.02
2568 6222 6.183324 GTGAACGCTACGATTTATTTCCTTC 58.817 40.000 0.00 0.00 0.00 3.46
2569 6223 5.064325 GGTGAACGCTACGATTTATTTCCTT 59.936 40.000 0.00 0.00 0.00 3.36
2574 6228 3.118519 AGGGGTGAACGCTACGATTTATT 60.119 43.478 0.00 0.00 41.10 1.40
2582 6236 1.226888 CGCTAGGGGTGAACGCTAC 60.227 63.158 0.00 0.00 42.98 3.58
2587 6241 1.068741 CATAGGACGCTAGGGGTGAAC 59.931 57.143 11.95 0.00 0.00 3.18
2595 6249 3.360533 CACGTACAACATAGGACGCTAG 58.639 50.000 0.00 0.00 38.86 3.42
2601 6255 2.172679 TGAGGCACGTACAACATAGGA 58.827 47.619 0.00 0.00 0.00 2.94
2614 6268 3.350219 TTGAATAGGTCCTTGAGGCAC 57.650 47.619 0.00 0.00 34.44 5.01
2617 6271 7.613411 AGAATTTCTTTGAATAGGTCCTTGAGG 59.387 37.037 0.00 0.00 0.00 3.86
2625 6279 8.936864 CGTCAACTAGAATTTCTTTGAATAGGT 58.063 33.333 12.79 0.00 28.49 3.08
2697 6351 4.994907 TTTGCCCTCATGATTTGATCTG 57.005 40.909 0.00 0.00 32.72 2.90
2699 6353 4.866486 GTGTTTTGCCCTCATGATTTGATC 59.134 41.667 0.00 0.00 32.72 2.92
2703 6357 4.344679 TCTTGTGTTTTGCCCTCATGATTT 59.655 37.500 0.00 0.00 0.00 2.17
2716 6370 7.337942 ACTCTCTTGACTGAAATCTTGTGTTTT 59.662 33.333 0.00 0.00 0.00 2.43
2717 6371 6.825721 ACTCTCTTGACTGAAATCTTGTGTTT 59.174 34.615 0.00 0.00 0.00 2.83
2719 6373 5.923204 ACTCTCTTGACTGAAATCTTGTGT 58.077 37.500 0.00 0.00 0.00 3.72
2720 6374 6.259608 ACAACTCTCTTGACTGAAATCTTGTG 59.740 38.462 0.00 0.00 0.00 3.33
2721 6375 6.352516 ACAACTCTCTTGACTGAAATCTTGT 58.647 36.000 0.00 0.00 0.00 3.16
2722 6376 6.857777 ACAACTCTCTTGACTGAAATCTTG 57.142 37.500 0.00 0.00 0.00 3.02
2724 6378 7.872113 AAAACAACTCTCTTGACTGAAATCT 57.128 32.000 0.00 0.00 0.00 2.40
2725 6379 8.401709 AGAAAAACAACTCTCTTGACTGAAATC 58.598 33.333 0.00 0.00 0.00 2.17
2732 7894 6.431278 GGCTTAGAAAAACAACTCTCTTGAC 58.569 40.000 0.00 0.00 0.00 3.18
2781 7943 9.037737 CATATTTTAAAGCAATGTTGGAGGATG 57.962 33.333 0.00 0.00 0.00 3.51
2890 8052 1.135972 CGGTCCGTTCATGAGCTTTTG 60.136 52.381 8.01 0.00 0.00 2.44
2898 8060 1.018752 TGCATCACGGTCCGTTCATG 61.019 55.000 15.97 19.62 38.32 3.07
2904 8066 2.539003 TTTTCTGCATCACGGTCCG 58.461 52.632 10.48 10.48 0.00 4.79


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

AutoCloner maintained by Alex Coulton.