Multiple sequence alignment - TraesCS2B01G170400

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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 TraesCS2B01G170400 chr2B 100.000 3128 0 0 1 3128 143283018 143279891 0.000000e+00 5777.0
1 TraesCS2B01G170400 chr2B 75.068 1464 208 98 881 2284 143483799 143485165 1.280000e-148 536.0
2 TraesCS2B01G170400 chr2B 93.701 254 12 4 2568 2819 143776867 143776616 8.190000e-101 377.0
3 TraesCS2B01G170400 chr2B 94.000 150 4 2 2979 3128 143776341 143776197 4.060000e-54 222.0
4 TraesCS2B01G170400 chr2D 95.986 1943 47 9 930 2870 90523218 90521305 0.000000e+00 3127.0
5 TraesCS2B01G170400 chr2D 75.523 1769 261 112 592 2284 89216434 89214762 0.000000e+00 710.0
6 TraesCS2B01G170400 chr2D 89.529 573 24 12 2580 3128 90716946 90716386 0.000000e+00 693.0
7 TraesCS2B01G170400 chr2D 75.628 1235 185 75 592 1787 104876158 104877315 1.000000e-139 507.0
8 TraesCS2B01G170400 chr2D 95.000 220 7 1 654 873 90523431 90523216 2.990000e-90 342.0
9 TraesCS2B01G170400 chr2D 96.000 150 2 1 2979 3128 90521278 90521133 1.120000e-59 241.0
10 TraesCS2B01G170400 chr2D 88.725 204 7 8 481 672 90523643 90523444 5.220000e-58 235.0
11 TraesCS2B01G170400 chr2D 92.537 134 8 2 276 408 95519663 95519531 1.150000e-44 191.0
12 TraesCS2B01G170400 chr2D 94.915 118 6 0 282 399 13599771 13599654 5.330000e-43 185.0
13 TraesCS2B01G170400 chr2A 92.133 2250 85 34 927 3128 90428984 90426779 0.000000e+00 3090.0
14 TraesCS2B01G170400 chr2A 75.144 1388 196 96 899 2227 90509689 90508392 5.980000e-142 514.0
15 TraesCS2B01G170400 chr2A 91.843 331 17 5 2568 2893 90525538 90525213 1.320000e-123 453.0
16 TraesCS2B01G170400 chr2A 92.473 279 7 4 395 662 90429494 90429219 1.360000e-103 387.0
17 TraesCS2B01G170400 chr2A 89.753 283 23 3 1 283 90429767 90429491 1.070000e-94 357.0
18 TraesCS2B01G170400 chr2A 89.372 207 12 5 654 859 90429197 90429000 5.180000e-63 252.0
19 TraesCS2B01G170400 chr2A 96.000 150 5 1 2979 3128 90524869 90524721 3.120000e-60 243.0
20 TraesCS2B01G170400 chr7A 96.398 944 22 6 1666 2601 570183066 570182127 0.000000e+00 1544.0
21 TraesCS2B01G170400 chr7A 97.391 115 3 0 2635 2749 570181791 570181677 2.460000e-46 196.0
22 TraesCS2B01G170400 chr7A 97.015 67 2 0 197 263 570183220 570183154 2.550000e-21 113.0
23 TraesCS2B01G170400 chr3D 91.096 146 13 0 1 146 93478398 93478253 6.840000e-47 198.0
24 TraesCS2B01G170400 chr3D 89.286 140 12 3 264 402 7308190 7308053 4.150000e-39 172.0
25 TraesCS2B01G170400 chr7B 81.328 241 43 2 1543 1782 424537164 424537403 8.850000e-46 195.0
26 TraesCS2B01G170400 chr7B 90.511 137 11 2 263 399 310416196 310416330 2.480000e-41 180.0
27 TraesCS2B01G170400 chr7B 87.261 157 17 1 1 157 128073413 128073566 3.210000e-40 176.0
28 TraesCS2B01G170400 chr7B 75.824 273 53 10 1175 1441 399174192 399173927 3.270000e-25 126.0
29 TraesCS2B01G170400 chr5D 90.909 143 13 0 1 143 457669207 457669349 3.180000e-45 193.0
30 TraesCS2B01G170400 chr5D 86.957 161 20 1 1 161 446678902 446679061 2.480000e-41 180.0
31 TraesCS2B01G170400 chr1B 90.278 144 13 1 1 144 384211120 384210978 1.480000e-43 187.0
32 TraesCS2B01G170400 chr1D 89.655 145 15 0 1 145 398872724 398872580 5.330000e-43 185.0
33 TraesCS2B01G170400 chr3B 93.443 122 8 0 278 399 637086325 637086446 6.890000e-42 182.0
34 TraesCS2B01G170400 chr3B 87.342 158 18 2 1 157 47793992 47794148 2.480000e-41 180.0
35 TraesCS2B01G170400 chr3B 87.342 158 18 2 1 157 48063724 48063880 2.480000e-41 180.0
36 TraesCS2B01G170400 chr3A 92.800 125 9 0 277 401 750495664 750495540 6.890000e-42 182.0
37 TraesCS2B01G170400 chr3A 85.714 63 8 1 583 645 722182094 722182033 7.240000e-07 65.8
38 TraesCS2B01G170400 chr6B 92.063 126 10 0 281 406 27078088 27077963 8.910000e-41 178.0
39 TraesCS2B01G170400 chr4D 92.683 123 9 0 282 404 428946495 428946373 8.910000e-41 178.0
40 TraesCS2B01G170400 chr4B 92.126 127 9 1 280 406 165306627 165306502 8.910000e-41 178.0
41 TraesCS2B01G170400 chr7D 81.019 216 37 4 1546 1759 411018125 411017912 5.370000e-38 169.0


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 TraesCS2B01G170400 chr2B 143279891 143283018 3127 True 5777.000000 5777 100.000000 1 3128 1 chr2B.!!$R1 3127
1 TraesCS2B01G170400 chr2B 143483799 143485165 1366 False 536.000000 536 75.068000 881 2284 1 chr2B.!!$F1 1403
2 TraesCS2B01G170400 chr2B 143776197 143776867 670 True 299.500000 377 93.850500 2568 3128 2 chr2B.!!$R2 560
3 TraesCS2B01G170400 chr2D 90521133 90523643 2510 True 986.250000 3127 93.927750 481 3128 4 chr2D.!!$R5 2647
4 TraesCS2B01G170400 chr2D 89214762 89216434 1672 True 710.000000 710 75.523000 592 2284 1 chr2D.!!$R2 1692
5 TraesCS2B01G170400 chr2D 90716386 90716946 560 True 693.000000 693 89.529000 2580 3128 1 chr2D.!!$R3 548
6 TraesCS2B01G170400 chr2D 104876158 104877315 1157 False 507.000000 507 75.628000 592 1787 1 chr2D.!!$F1 1195
7 TraesCS2B01G170400 chr2A 90426779 90429767 2988 True 1021.500000 3090 90.932750 1 3128 4 chr2A.!!$R2 3127
8 TraesCS2B01G170400 chr2A 90508392 90509689 1297 True 514.000000 514 75.144000 899 2227 1 chr2A.!!$R1 1328
9 TraesCS2B01G170400 chr2A 90524721 90525538 817 True 348.000000 453 93.921500 2568 3128 2 chr2A.!!$R3 560
10 TraesCS2B01G170400 chr7A 570181677 570183220 1543 True 617.666667 1544 96.934667 197 2749 3 chr7A.!!$R1 2552

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
842 906 1.414919 TCGGGTTGAGTTGCAGTAAGT 59.585 47.619 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2641 3130 1.064979 GTCCATCGGCCCCTAAAAGAA 60.065 52.381 0.0 0.0 0.0 2.52 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
52 53 2.341760 GCTTTAGTGCTTGTAGTCGTCG 59.658 50.000 0.00 0.00 0.00 5.12
65 66 1.669779 AGTCGTCGCTATGTGGTCTAC 59.330 52.381 0.00 0.00 0.00 2.59
72 73 2.159282 CGCTATGTGGTCTACGGAACTT 60.159 50.000 0.00 0.00 0.00 2.66
73 74 3.187700 GCTATGTGGTCTACGGAACTTG 58.812 50.000 0.00 0.00 0.00 3.16
75 76 4.441634 GCTATGTGGTCTACGGAACTTGAT 60.442 45.833 0.00 0.00 0.00 2.57
76 77 3.313012 TGTGGTCTACGGAACTTGATG 57.687 47.619 0.00 0.00 0.00 3.07
79 80 4.281435 TGTGGTCTACGGAACTTGATGTAA 59.719 41.667 0.00 0.00 0.00 2.41
85 86 8.938906 GGTCTACGGAACTTGATGTAATTTTTA 58.061 33.333 0.00 0.00 0.00 1.52
86 87 9.750882 GTCTACGGAACTTGATGTAATTTTTAC 57.249 33.333 0.00 0.00 0.00 2.01
87 88 8.938906 TCTACGGAACTTGATGTAATTTTTACC 58.061 33.333 0.00 0.00 0.00 2.85
88 89 6.604930 ACGGAACTTGATGTAATTTTTACCG 58.395 36.000 0.00 0.00 39.90 4.02
92 93 8.908678 GGAACTTGATGTAATTTTTACCGTTTC 58.091 33.333 0.00 0.00 0.00 2.78
102 103 4.713854 TTTTACCGTTTCTAGTGTTCGC 57.286 40.909 0.00 0.00 0.00 4.70
110 111 5.330295 CGTTTCTAGTGTTCGCTGTACTAT 58.670 41.667 0.00 0.00 0.00 2.12
128 129 9.987272 CTGTACTATCATTGTTGGAGATGAATA 57.013 33.333 0.00 0.00 36.03 1.75
134 135 7.812690 TCATTGTTGGAGATGAATAGATTGG 57.187 36.000 0.00 0.00 29.82 3.16
195 196 4.142337 TGTTCATGTTAAGCTCATGCATGG 60.142 41.667 25.97 17.21 41.40 3.66
261 262 4.574599 ATTTGCGGGATCAGCTATTTTC 57.425 40.909 12.59 0.00 35.28 2.29
293 294 5.513233 TGATTACTAAGTACTCCCTCCGTT 58.487 41.667 0.00 0.00 0.00 4.44
294 295 5.591877 TGATTACTAAGTACTCCCTCCGTTC 59.408 44.000 0.00 0.00 0.00 3.95
295 296 2.363683 ACTAAGTACTCCCTCCGTTCG 58.636 52.381 0.00 0.00 0.00 3.95
296 297 1.674962 CTAAGTACTCCCTCCGTTCGG 59.325 57.143 4.74 4.74 0.00 4.30
301 302 1.856629 ACTCCCTCCGTTCGGAAATA 58.143 50.000 14.79 2.82 33.41 1.40
302 303 1.479730 ACTCCCTCCGTTCGGAAATAC 59.520 52.381 14.79 0.00 33.41 1.89
303 304 1.755380 CTCCCTCCGTTCGGAAATACT 59.245 52.381 14.79 0.00 33.41 2.12
304 305 2.167900 CTCCCTCCGTTCGGAAATACTT 59.832 50.000 14.79 0.00 33.41 2.24
305 306 2.093869 TCCCTCCGTTCGGAAATACTTG 60.094 50.000 14.79 1.97 33.41 3.16
306 307 2.354403 CCCTCCGTTCGGAAATACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
307 308 2.928116 CCTCCGTTCGGAAATACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
308 309 2.597305 CTCCGTTCGGAAATACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
309 310 1.657094 CCGTTCGGAAATACTTGTCGG 59.343 52.381 5.19 0.00 0.00 4.79
310 311 2.598589 CGTTCGGAAATACTTGTCGGA 58.401 47.619 0.00 0.00 0.00 4.55
311 312 2.597305 CGTTCGGAAATACTTGTCGGAG 59.403 50.000 0.00 0.00 0.00 4.63
312 313 2.928116 GTTCGGAAATACTTGTCGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
313 314 2.449464 TCGGAAATACTTGTCGGAGGA 58.551 47.619 0.00 0.00 0.00 3.71
314 315 2.827322 TCGGAAATACTTGTCGGAGGAA 59.173 45.455 0.00 0.00 0.00 3.36
315 316 3.449737 TCGGAAATACTTGTCGGAGGAAT 59.550 43.478 0.00 0.00 0.00 3.01
316 317 3.555956 CGGAAATACTTGTCGGAGGAATG 59.444 47.826 0.00 0.00 0.00 2.67
317 318 4.679639 CGGAAATACTTGTCGGAGGAATGA 60.680 45.833 0.00 0.00 0.00 2.57
318 319 5.183228 GGAAATACTTGTCGGAGGAATGAA 58.817 41.667 0.00 0.00 0.00 2.57
319 320 5.823045 GGAAATACTTGTCGGAGGAATGAAT 59.177 40.000 0.00 0.00 0.00 2.57
320 321 6.238484 GGAAATACTTGTCGGAGGAATGAATG 60.238 42.308 0.00 0.00 0.00 2.67
321 322 3.703001 ACTTGTCGGAGGAATGAATGT 57.297 42.857 0.00 0.00 0.00 2.71
322 323 4.819105 ACTTGTCGGAGGAATGAATGTA 57.181 40.909 0.00 0.00 0.00 2.29
323 324 5.359194 ACTTGTCGGAGGAATGAATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
324 325 5.360591 ACTTGTCGGAGGAATGAATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
325 326 5.129485 ACTTGTCGGAGGAATGAATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
326 327 6.323996 ACTTGTCGGAGGAATGAATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
327 328 6.332735 TGTCGGAGGAATGAATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
328 329 6.068670 TGTCGGAGGAATGAATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
329 330 6.721668 TGTCGGAGGAATGAATGTATCTAGAT 59.278 38.462 10.73 10.73 0.00 1.98
330 331 7.888546 TGTCGGAGGAATGAATGTATCTAGATA 59.111 37.037 8.44 8.44 0.00 1.98
331 332 8.908903 GTCGGAGGAATGAATGTATCTAGATAT 58.091 37.037 15.43 0.00 0.00 1.63
371 372 6.275335 ACATCCAATTTTATGCATTTCTCCG 58.725 36.000 3.54 0.00 0.00 4.63
372 373 6.096705 ACATCCAATTTTATGCATTTCTCCGA 59.903 34.615 3.54 0.00 0.00 4.55
373 374 5.890334 TCCAATTTTATGCATTTCTCCGAC 58.110 37.500 3.54 0.00 0.00 4.79
374 375 5.417266 TCCAATTTTATGCATTTCTCCGACA 59.583 36.000 3.54 0.00 0.00 4.35
375 376 6.071672 TCCAATTTTATGCATTTCTCCGACAA 60.072 34.615 3.54 0.00 0.00 3.18
376 377 6.254157 CCAATTTTATGCATTTCTCCGACAAG 59.746 38.462 3.54 0.00 0.00 3.16
377 378 5.957842 TTTTATGCATTTCTCCGACAAGT 57.042 34.783 3.54 0.00 0.00 3.16
378 379 7.624360 ATTTTATGCATTTCTCCGACAAGTA 57.376 32.000 3.54 0.00 0.00 2.24
379 380 7.624360 TTTTATGCATTTCTCCGACAAGTAT 57.376 32.000 3.54 0.00 0.00 2.12
380 381 7.624360 TTTATGCATTTCTCCGACAAGTATT 57.376 32.000 3.54 0.00 0.00 1.89
381 382 7.624360 TTATGCATTTCTCCGACAAGTATTT 57.376 32.000 3.54 0.00 0.00 1.40
382 383 5.545658 TGCATTTCTCCGACAAGTATTTC 57.454 39.130 0.00 0.00 0.00 2.17
383 384 5.245531 TGCATTTCTCCGACAAGTATTTCT 58.754 37.500 0.00 0.00 0.00 2.52
384 385 5.122239 TGCATTTCTCCGACAAGTATTTCTG 59.878 40.000 0.00 0.00 0.00 3.02
385 386 5.447818 GCATTTCTCCGACAAGTATTTCTGG 60.448 44.000 0.00 0.00 0.00 3.86
386 387 5.477607 TTTCTCCGACAAGTATTTCTGGA 57.522 39.130 0.00 0.00 0.00 3.86
387 388 4.451629 TCTCCGACAAGTATTTCTGGAC 57.548 45.455 0.00 0.00 0.00 4.02
388 389 3.119602 TCTCCGACAAGTATTTCTGGACG 60.120 47.826 0.00 0.00 35.64 4.79
389 390 2.268298 CCGACAAGTATTTCTGGACGG 58.732 52.381 0.00 0.00 45.37 4.79
390 391 3.226346 CGACAAGTATTTCTGGACGGA 57.774 47.619 0.00 0.00 33.12 4.69
391 392 3.782046 CGACAAGTATTTCTGGACGGAT 58.218 45.455 0.00 0.00 33.12 4.18
392 393 3.551890 CGACAAGTATTTCTGGACGGATG 59.448 47.826 0.00 0.00 33.12 3.51
393 394 3.871594 GACAAGTATTTCTGGACGGATGG 59.128 47.826 0.00 0.00 0.00 3.51
450 451 9.609950 GCATTTAGCATCAAAGCAAAAATAAAA 57.390 25.926 0.00 0.00 44.79 1.52
756 800 3.119291 CTGCACCATCTTCGATCTGTAC 58.881 50.000 0.00 0.00 0.00 2.90
840 904 2.851263 ATCGGGTTGAGTTGCAGTAA 57.149 45.000 0.00 0.00 0.00 2.24
842 906 1.414919 TCGGGTTGAGTTGCAGTAAGT 59.585 47.619 0.00 0.00 0.00 2.24
843 907 2.629137 TCGGGTTGAGTTGCAGTAAGTA 59.371 45.455 0.00 0.00 0.00 2.24
876 940 5.973565 GGGCTTGATTGATTTCTATTTGACG 59.026 40.000 0.00 0.00 0.00 4.35
877 941 6.183360 GGGCTTGATTGATTTCTATTTGACGA 60.183 38.462 0.00 0.00 0.00 4.20
879 943 7.377928 GGCTTGATTGATTTCTATTTGACGATG 59.622 37.037 0.00 0.00 0.00 3.84
1094 1190 2.940971 GCCATGGATATAGCATCCGCAA 60.941 50.000 18.40 0.00 41.03 4.85
1127 1223 3.257561 CGGCGAGAACCATCAGCG 61.258 66.667 0.00 0.00 33.86 5.18
1254 1350 2.440980 GGCACCAGGATCTTGGCC 60.441 66.667 23.05 15.50 42.18 5.36
1416 1536 7.213678 AGCTATTCACTATGAGCTTTTACTCC 58.786 38.462 0.00 0.00 42.59 3.85
1417 1537 7.070571 AGCTATTCACTATGAGCTTTTACTCCT 59.929 37.037 0.00 0.00 42.59 3.69
1418 1538 7.713073 GCTATTCACTATGAGCTTTTACTCCTT 59.287 37.037 0.00 0.00 35.72 3.36
1419 1539 9.255304 CTATTCACTATGAGCTTTTACTCCTTC 57.745 37.037 0.00 0.00 35.72 3.46
1420 1540 5.651530 TCACTATGAGCTTTTACTCCTTCG 58.348 41.667 0.00 0.00 35.72 3.79
1421 1541 5.417894 TCACTATGAGCTTTTACTCCTTCGA 59.582 40.000 0.00 0.00 35.72 3.71
1422 1542 5.746245 CACTATGAGCTTTTACTCCTTCGAG 59.254 44.000 0.00 0.00 42.32 4.04
1423 1543 5.652891 ACTATGAGCTTTTACTCCTTCGAGA 59.347 40.000 0.00 0.00 38.52 4.04
1424 1544 5.606348 ATGAGCTTTTACTCCTTCGAGAT 57.394 39.130 0.00 0.00 38.52 2.75
1425 1545 4.748892 TGAGCTTTTACTCCTTCGAGATG 58.251 43.478 0.00 0.00 38.52 2.90
1426 1546 3.526534 AGCTTTTACTCCTTCGAGATGC 58.473 45.455 0.00 0.00 38.52 3.91
1427 1547 3.196685 AGCTTTTACTCCTTCGAGATGCT 59.803 43.478 0.00 0.00 38.52 3.79
1428 1548 3.553917 GCTTTTACTCCTTCGAGATGCTC 59.446 47.826 0.00 0.00 38.52 4.26
1429 1549 4.679372 GCTTTTACTCCTTCGAGATGCTCT 60.679 45.833 0.00 0.00 38.52 4.09
1430 1550 4.377839 TTTACTCCTTCGAGATGCTCTG 57.622 45.455 0.00 0.00 38.52 3.35
1431 1551 0.459489 ACTCCTTCGAGATGCTCTGC 59.541 55.000 0.00 0.00 38.52 4.26
1432 1552 0.746063 CTCCTTCGAGATGCTCTGCT 59.254 55.000 0.00 0.00 38.52 4.24
1433 1553 1.136695 CTCCTTCGAGATGCTCTGCTT 59.863 52.381 0.00 0.00 38.52 3.91
1434 1554 1.134877 TCCTTCGAGATGCTCTGCTTG 60.135 52.381 0.00 0.00 0.00 4.01
1435 1555 1.288350 CTTCGAGATGCTCTGCTTGG 58.712 55.000 0.00 0.00 0.00 3.61
1436 1556 0.897621 TTCGAGATGCTCTGCTTGGA 59.102 50.000 0.00 0.00 0.00 3.53
1437 1557 0.459078 TCGAGATGCTCTGCTTGGAG 59.541 55.000 0.00 0.00 36.50 3.86
1438 1558 0.175302 CGAGATGCTCTGCTTGGAGT 59.825 55.000 0.00 0.00 35.89 3.85
1489 1609 1.961277 GCCAAGGTATCGCATCGGG 60.961 63.158 0.00 0.00 0.00 5.14
1603 1726 1.681166 CCTTCCTCATCAGCACCAAGG 60.681 57.143 0.00 0.00 0.00 3.61
1626 1749 2.040606 ACCACCGAGGCCACCTAT 59.959 61.111 5.01 0.00 43.14 2.57
1629 1752 0.759436 CCACCGAGGCCACCTATAGT 60.759 60.000 5.01 0.00 31.76 2.12
2141 2303 6.985188 TTGGATGTAGAATGCTGAAAGTAC 57.015 37.500 0.00 0.00 35.30 2.73
2162 2328 8.768501 AGTACTGTCATGATAATCAGTTCCTA 57.231 34.615 18.52 2.21 40.77 2.94
2203 2375 2.616524 ACCCTGTTGCCTTCTACAGTA 58.383 47.619 0.00 0.00 42.08 2.74
2204 2376 2.302157 ACCCTGTTGCCTTCTACAGTAC 59.698 50.000 0.00 0.00 42.08 2.73
2205 2377 2.567615 CCCTGTTGCCTTCTACAGTACT 59.432 50.000 0.00 0.00 42.08 2.73
2270 2451 7.913297 TGTACTGTCTTTTGTTTTCATGTTAGC 59.087 33.333 0.00 0.00 0.00 3.09
2297 2478 7.035004 TGCAACAAGAAAGTATTCCATTATGC 58.965 34.615 0.00 0.00 36.12 3.14
2307 2488 8.825667 AAGTATTCCATTATGCGTTTGTTTTT 57.174 26.923 0.00 0.00 0.00 1.94
2365 2546 4.408821 CGGGGGTGCTGCTGCTAA 62.409 66.667 17.00 0.00 40.48 3.09
2424 2605 7.276658 TGCATCGTTTTAATCTGTTTTTGTTGT 59.723 29.630 0.00 0.00 0.00 3.32
2428 2609 7.968956 TCGTTTTAATCTGTTTTTGTTGTGCTA 59.031 29.630 0.00 0.00 0.00 3.49
2487 2668 1.229975 TGCCAGCGTGTGATGTTCTG 61.230 55.000 0.00 0.00 0.00 3.02
2516 2697 6.544650 TCATACTTTAGGCCTTGTTTGGTAA 58.455 36.000 12.58 0.00 0.00 2.85
2641 3130 3.269381 TGGGAAAGAATGGGCTGTTCTAT 59.731 43.478 5.58 0.00 34.97 1.98
2761 3256 3.444805 GAGACCGGCGACTCTGCT 61.445 66.667 20.42 5.20 34.52 4.24
2781 3280 3.704061 GCTAGTGGTTCTCTCCTCTGATT 59.296 47.826 0.00 0.00 33.97 2.57
2817 3316 2.356793 CCCTGATCTCGGCGATGC 60.357 66.667 11.27 3.23 30.84 3.91
2865 3364 2.032681 GCCCTCTTCACCAGCGTT 59.967 61.111 0.00 0.00 0.00 4.84
2902 3415 3.590574 AAACCACAGCCCTCCCCC 61.591 66.667 0.00 0.00 0.00 5.40
3056 3813 3.306166 CAGATGTACGCCCGTTTTCTTAG 59.694 47.826 0.00 0.00 0.00 2.18
3061 3818 1.869132 ACGCCCGTTTTCTTAGTTCAC 59.131 47.619 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.291877 ACAAGCACTAAAGCGAGCCG 61.292 55.000 0.00 0.00 40.15 5.52
30 31 2.325761 ACGACTACAAGCACTAAAGCG 58.674 47.619 0.00 0.00 40.15 4.68
52 53 3.119245 TCAAGTTCCGTAGACCACATAGC 60.119 47.826 0.00 0.00 0.00 2.97
65 66 6.604930 ACGGTAAAAATTACATCAAGTTCCG 58.395 36.000 0.00 0.00 36.05 4.30
72 73 9.275398 ACACTAGAAACGGTAAAAATTACATCA 57.725 29.630 0.00 0.00 0.00 3.07
75 76 8.274939 CGAACACTAGAAACGGTAAAAATTACA 58.725 33.333 0.00 0.00 0.00 2.41
76 77 7.266966 GCGAACACTAGAAACGGTAAAAATTAC 59.733 37.037 0.00 0.00 0.00 1.89
79 80 5.467735 AGCGAACACTAGAAACGGTAAAAAT 59.532 36.000 0.00 0.00 33.21 1.82
85 86 1.068127 ACAGCGAACACTAGAAACGGT 59.932 47.619 0.00 0.00 35.19 4.83
86 87 1.779569 ACAGCGAACACTAGAAACGG 58.220 50.000 0.00 0.00 0.00 4.44
87 88 3.562505 AGTACAGCGAACACTAGAAACG 58.437 45.455 0.00 0.00 0.00 3.60
88 89 6.320171 TGATAGTACAGCGAACACTAGAAAC 58.680 40.000 0.00 0.00 0.00 2.78
92 93 6.266323 ACAATGATAGTACAGCGAACACTAG 58.734 40.000 0.00 0.00 0.00 2.57
102 103 8.899427 ATTCATCTCCAACAATGATAGTACAG 57.101 34.615 0.00 0.00 32.24 2.74
110 111 7.576403 TCCAATCTATTCATCTCCAACAATGA 58.424 34.615 0.00 0.00 0.00 2.57
195 196 8.721478 AGTAAACATGTCATCTCAACATACAAC 58.279 33.333 0.00 0.00 35.62 3.32
279 280 0.038744 TTCCGAACGGAGGGAGTACT 59.961 55.000 15.34 0.00 46.06 2.73
280 281 0.890683 TTTCCGAACGGAGGGAGTAC 59.109 55.000 15.34 0.00 46.06 2.73
281 282 1.856629 ATTTCCGAACGGAGGGAGTA 58.143 50.000 15.34 0.00 46.06 2.59
282 283 1.479730 GTATTTCCGAACGGAGGGAGT 59.520 52.381 15.34 1.96 46.06 3.85
293 294 2.449464 TCCTCCGACAAGTATTTCCGA 58.551 47.619 0.00 0.00 0.00 4.55
294 295 2.953466 TCCTCCGACAAGTATTTCCG 57.047 50.000 0.00 0.00 0.00 4.30
295 296 4.766375 TCATTCCTCCGACAAGTATTTCC 58.234 43.478 0.00 0.00 0.00 3.13
296 297 6.316390 ACATTCATTCCTCCGACAAGTATTTC 59.684 38.462 0.00 0.00 0.00 2.17
301 302 3.703001 ACATTCATTCCTCCGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
302 303 5.605534 AGATACATTCATTCCTCCGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
303 304 5.614324 AGATACATTCATTCCTCCGACAA 57.386 39.130 0.00 0.00 0.00 3.18
304 305 6.068670 TCTAGATACATTCATTCCTCCGACA 58.931 40.000 0.00 0.00 0.00 4.35
305 306 6.576662 TCTAGATACATTCATTCCTCCGAC 57.423 41.667 0.00 0.00 0.00 4.79
345 346 8.084073 CGGAGAAATGCATAAAATTGGATGTAT 58.916 33.333 0.00 1.11 30.71 2.29
346 347 7.284261 TCGGAGAAATGCATAAAATTGGATGTA 59.716 33.333 0.00 0.00 0.00 2.29
347 348 6.096705 TCGGAGAAATGCATAAAATTGGATGT 59.903 34.615 0.00 0.00 0.00 3.06
348 349 6.418819 GTCGGAGAAATGCATAAAATTGGATG 59.581 38.462 0.00 0.00 39.69 3.51
349 350 6.096705 TGTCGGAGAAATGCATAAAATTGGAT 59.903 34.615 0.00 0.00 39.69 3.41
350 351 5.417266 TGTCGGAGAAATGCATAAAATTGGA 59.583 36.000 0.00 0.00 39.69 3.53
351 352 5.649557 TGTCGGAGAAATGCATAAAATTGG 58.350 37.500 0.00 0.00 39.69 3.16
352 353 6.808212 ACTTGTCGGAGAAATGCATAAAATTG 59.192 34.615 0.00 0.00 39.69 2.32
353 354 6.924111 ACTTGTCGGAGAAATGCATAAAATT 58.076 32.000 0.00 0.00 39.69 1.82
354 355 6.515272 ACTTGTCGGAGAAATGCATAAAAT 57.485 33.333 0.00 0.00 39.69 1.82
355 356 5.957842 ACTTGTCGGAGAAATGCATAAAA 57.042 34.783 0.00 0.00 39.69 1.52
356 357 7.624360 AATACTTGTCGGAGAAATGCATAAA 57.376 32.000 0.00 0.00 39.69 1.40
357 358 7.552687 AGAAATACTTGTCGGAGAAATGCATAA 59.447 33.333 0.00 0.00 39.69 1.90
358 359 7.011389 CAGAAATACTTGTCGGAGAAATGCATA 59.989 37.037 0.00 0.00 39.69 3.14
359 360 5.882557 AGAAATACTTGTCGGAGAAATGCAT 59.117 36.000 0.00 0.00 39.69 3.96
360 361 5.122239 CAGAAATACTTGTCGGAGAAATGCA 59.878 40.000 0.00 0.00 39.69 3.96
361 362 5.447818 CCAGAAATACTTGTCGGAGAAATGC 60.448 44.000 0.00 0.00 39.69 3.56
362 363 5.874810 TCCAGAAATACTTGTCGGAGAAATG 59.125 40.000 0.00 0.00 39.69 2.32
363 364 5.875359 GTCCAGAAATACTTGTCGGAGAAAT 59.125 40.000 0.00 0.00 39.69 2.17
364 365 5.235516 GTCCAGAAATACTTGTCGGAGAAA 58.764 41.667 0.00 0.00 39.69 2.52
365 366 4.617530 CGTCCAGAAATACTTGTCGGAGAA 60.618 45.833 0.00 0.00 39.69 2.87
366 367 3.119602 CGTCCAGAAATACTTGTCGGAGA 60.120 47.826 0.00 0.00 0.00 3.71
367 368 3.179830 CGTCCAGAAATACTTGTCGGAG 58.820 50.000 0.00 0.00 0.00 4.63
368 369 2.094390 CCGTCCAGAAATACTTGTCGGA 60.094 50.000 0.00 0.00 42.19 4.55
369 370 2.094390 TCCGTCCAGAAATACTTGTCGG 60.094 50.000 0.00 0.00 41.47 4.79
370 371 3.226346 TCCGTCCAGAAATACTTGTCG 57.774 47.619 0.00 0.00 0.00 4.35
371 372 3.871594 CCATCCGTCCAGAAATACTTGTC 59.128 47.826 0.00 0.00 0.00 3.18
372 373 3.517901 TCCATCCGTCCAGAAATACTTGT 59.482 43.478 0.00 0.00 0.00 3.16
373 374 4.122776 CTCCATCCGTCCAGAAATACTTG 58.877 47.826 0.00 0.00 0.00 3.16
374 375 3.775316 ACTCCATCCGTCCAGAAATACTT 59.225 43.478 0.00 0.00 0.00 2.24
375 376 3.375699 ACTCCATCCGTCCAGAAATACT 58.624 45.455 0.00 0.00 0.00 2.12
376 377 3.821421 ACTCCATCCGTCCAGAAATAC 57.179 47.619 0.00 0.00 0.00 1.89
377 378 6.494666 AAATACTCCATCCGTCCAGAAATA 57.505 37.500 0.00 0.00 0.00 1.40
378 379 5.373812 AAATACTCCATCCGTCCAGAAAT 57.626 39.130 0.00 0.00 0.00 2.17
379 380 4.837093 AAATACTCCATCCGTCCAGAAA 57.163 40.909 0.00 0.00 0.00 2.52
380 381 4.019681 ACAAAATACTCCATCCGTCCAGAA 60.020 41.667 0.00 0.00 0.00 3.02
381 382 3.517901 ACAAAATACTCCATCCGTCCAGA 59.482 43.478 0.00 0.00 0.00 3.86
382 383 3.873910 ACAAAATACTCCATCCGTCCAG 58.126 45.455 0.00 0.00 0.00 3.86
383 384 3.992943 ACAAAATACTCCATCCGTCCA 57.007 42.857 0.00 0.00 0.00 4.02
384 385 5.667466 TCTAACAAAATACTCCATCCGTCC 58.333 41.667 0.00 0.00 0.00 4.79
385 386 7.605410 TTTCTAACAAAATACTCCATCCGTC 57.395 36.000 0.00 0.00 0.00 4.79
386 387 7.989416 TTTTCTAACAAAATACTCCATCCGT 57.011 32.000 0.00 0.00 0.00 4.69
387 388 9.855021 AAATTTTCTAACAAAATACTCCATCCG 57.145 29.630 0.00 0.00 30.38 4.18
479 480 9.921637 TTTTTCCTTGCTCATCGTAATTTATTT 57.078 25.926 0.00 0.00 0.00 1.40
540 541 5.277634 GCTGTTCGCAAGGAAAAACTAACTA 60.278 40.000 0.00 0.00 36.14 2.24
545 557 1.067060 GGCTGTTCGCAAGGAAAAACT 59.933 47.619 0.00 0.00 41.67 2.66
623 636 0.609131 AGCGAAGGGTTTGGTGGATG 60.609 55.000 0.00 0.00 0.00 3.51
756 800 1.194495 GGAAATCGCAGGTACGTACG 58.806 55.000 18.98 15.01 0.00 3.67
840 904 4.166725 TCAATCAAGCCCAATCATCCTACT 59.833 41.667 0.00 0.00 0.00 2.57
842 906 4.794311 TCAATCAAGCCCAATCATCCTA 57.206 40.909 0.00 0.00 0.00 2.94
843 907 3.675348 TCAATCAAGCCCAATCATCCT 57.325 42.857 0.00 0.00 0.00 3.24
876 940 5.728351 TTTGAATACGAACCGAATCCATC 57.272 39.130 0.00 0.00 0.00 3.51
877 941 6.693315 AATTTGAATACGAACCGAATCCAT 57.307 33.333 0.00 0.00 0.00 3.41
879 943 7.007313 TGTAATTTGAATACGAACCGAATCC 57.993 36.000 0.00 0.00 0.00 3.01
891 956 5.833131 GCCCTTGATCCCTGTAATTTGAATA 59.167 40.000 0.00 0.00 0.00 1.75
1094 1190 1.176619 GCCGGGCAACAAGTTTACCT 61.177 55.000 15.62 0.00 39.74 3.08
1127 1223 2.037772 TCTTGGTCTGAGAAAGCAGTCC 59.962 50.000 0.00 0.00 42.19 3.85
1254 1350 0.389556 CGGGATCTCTCGGATGCATG 60.390 60.000 2.46 0.00 43.34 4.06
1422 1542 0.540923 AGGACTCCAAGCAGAGCATC 59.459 55.000 0.00 0.00 37.39 3.91
1423 1543 0.990374 AAGGACTCCAAGCAGAGCAT 59.010 50.000 0.00 0.00 37.39 3.79
1424 1544 0.322975 GAAGGACTCCAAGCAGAGCA 59.677 55.000 0.00 0.00 37.39 4.26
1425 1545 0.739112 CGAAGGACTCCAAGCAGAGC 60.739 60.000 0.00 0.00 37.39 4.09
1426 1546 0.891373 TCGAAGGACTCCAAGCAGAG 59.109 55.000 0.00 0.00 39.91 3.35
1427 1547 0.891373 CTCGAAGGACTCCAAGCAGA 59.109 55.000 0.00 0.00 0.00 4.26
1428 1548 0.891373 TCTCGAAGGACTCCAAGCAG 59.109 55.000 0.00 0.00 0.00 4.24
1429 1549 1.205655 CATCTCGAAGGACTCCAAGCA 59.794 52.381 0.00 0.00 0.00 3.91
1430 1550 1.933247 CATCTCGAAGGACTCCAAGC 58.067 55.000 0.00 0.00 0.00 4.01
1431 1551 1.480137 AGCATCTCGAAGGACTCCAAG 59.520 52.381 0.00 0.00 0.00 3.61
1432 1552 1.478510 GAGCATCTCGAAGGACTCCAA 59.521 52.381 0.00 0.00 0.00 3.53
1433 1553 1.107114 GAGCATCTCGAAGGACTCCA 58.893 55.000 0.00 0.00 0.00 3.86
1434 1554 3.957383 GAGCATCTCGAAGGACTCC 57.043 57.895 0.00 0.00 0.00 3.85
1489 1609 1.734465 CGACCACTCTTTGCTGGAATC 59.266 52.381 0.00 0.00 0.00 2.52
1603 1726 4.083862 GGCCTCGGTGGTGTCCTC 62.084 72.222 0.00 0.00 38.35 3.71
1626 1749 1.689813 TGCCTCTCCGTGTCAAAACTA 59.310 47.619 0.00 0.00 0.00 2.24
1629 1752 2.151202 GAATGCCTCTCCGTGTCAAAA 58.849 47.619 0.00 0.00 0.00 2.44
2162 2328 8.576442 CAGGGTTGTAACTGAGTGAAAATAAAT 58.424 33.333 0.00 0.00 36.86 1.40
2203 2375 8.893727 GGAGTGCAGACATTATTAAAACATAGT 58.106 33.333 0.00 0.00 0.00 2.12
2204 2376 9.113838 AGGAGTGCAGACATTATTAAAACATAG 57.886 33.333 0.00 0.00 0.00 2.23
2205 2377 8.892723 CAGGAGTGCAGACATTATTAAAACATA 58.107 33.333 0.00 0.00 0.00 2.29
2270 2451 9.079833 CATAATGGAATACTTTCTTGTTGCAAG 57.920 33.333 0.00 2.71 32.16 4.01
2297 2478 9.256715 GGAAAACAAAAGACATAAAAACAAACG 57.743 29.630 0.00 0.00 0.00 3.60
2307 2488 7.499895 ACTTCTTACCGGAAAACAAAAGACATA 59.500 33.333 9.46 0.00 0.00 2.29
2364 2545 2.092103 TGCCAGGTGACAGGTTTACTTT 60.092 45.455 0.00 0.00 39.66 2.66
2365 2546 1.493022 TGCCAGGTGACAGGTTTACTT 59.507 47.619 0.00 0.00 39.66 2.24
2424 2605 6.435430 ACGCATGTTAGAAAAATCATAGCA 57.565 33.333 0.00 0.00 0.00 3.49
2428 2609 6.071391 AGGGAAACGCATGTTAGAAAAATCAT 60.071 34.615 0.00 0.00 37.31 2.45
2487 2668 6.759497 AACAAGGCCTAAAGTATGATTCAC 57.241 37.500 5.16 0.00 0.00 3.18
2516 2697 3.339742 ACCAATCCCCTCAAAAACCCTAT 59.660 43.478 0.00 0.00 0.00 2.57
2578 2760 4.283467 GGAGGTTCCCTTTTAAAGCAACAT 59.717 41.667 15.10 10.52 31.76 2.71
2641 3130 1.064979 GTCCATCGGCCCCTAAAAGAA 60.065 52.381 0.00 0.00 0.00 2.52
2761 3256 5.584913 AGAAATCAGAGGAGAGAACCACTA 58.415 41.667 0.00 0.00 30.29 2.74
2865 3364 1.890489 TGGAAGCTTACTACGTGCTCA 59.110 47.619 10.74 0.00 35.85 4.26
2870 3369 3.181463 TGTGGTTTGGAAGCTTACTACGT 60.181 43.478 10.74 0.00 0.00 3.57
2902 3415 2.278596 CAGATGTACGGGCGGTCG 60.279 66.667 0.00 0.00 0.00 4.79
2904 3417 3.387091 TGCAGATGTACGGGCGGT 61.387 61.111 2.46 2.46 0.00 5.68
3056 3813 7.467403 GCATATAAACTTAAGAGGCAGGTGAAC 60.467 40.741 10.09 0.00 0.00 3.18
3061 3818 6.942532 TTGCATATAAACTTAAGAGGCAGG 57.057 37.500 10.09 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.