Multiple sequence alignment - TraesCS3D01G027900

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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 TraesCS3D01G027900 chr3D 100.000 3785 0 0 1 3785 9631330 9635114 0.000000e+00 6990.0
1 TraesCS3D01G027900 chr3D 91.181 2914 244 10 875 3785 4960506 4957603 0.000000e+00 3945.0
2 TraesCS3D01G027900 chr3D 90.634 363 25 6 875 1236 4999635 4999281 1.230000e-129 473.0
3 TraesCS3D01G027900 chr3D 94.828 232 10 2 282 512 581727567 581727337 1.000000e-95 361.0
4 TraesCS3D01G027900 chr3D 96.970 33 1 0 839 871 4999845 4999813 5.280000e-04 56.5
5 TraesCS3D01G027900 chr3A 91.835 3160 247 9 635 3785 10690095 10686938 0.000000e+00 4396.0
6 TraesCS3D01G027900 chr3A 91.146 2914 245 8 874 3785 10885716 10882814 0.000000e+00 3940.0
7 TraesCS3D01G027900 chr3A 88.024 2338 197 38 561 2829 10697703 10695380 0.000000e+00 2689.0
8 TraesCS3D01G027900 chr3A 95.556 315 14 0 1 315 10690410 10690096 4.360000e-139 505.0
9 TraesCS3D01G027900 chr3A 91.336 277 21 3 13 287 10698050 10697775 3.570000e-100 375.0
10 TraesCS3D01G027900 chrUn 90.517 3248 257 23 578 3785 284404255 284401019 0.000000e+00 4244.0
11 TraesCS3D01G027900 chrUn 90.517 3248 257 23 578 3785 284410789 284407553 0.000000e+00 4244.0
12 TraesCS3D01G027900 chrUn 90.517 3248 257 23 578 3785 302994414 302991178 0.000000e+00 4244.0
13 TraesCS3D01G027900 chrUn 90.088 3168 260 21 649 3785 35293758 35296902 0.000000e+00 4061.0
14 TraesCS3D01G027900 chrUn 90.088 3168 260 21 649 3785 229343598 229346742 0.000000e+00 4061.0
15 TraesCS3D01G027900 chrUn 89.944 3192 259 28 596 3785 257888595 257885464 0.000000e+00 4060.0
16 TraesCS3D01G027900 chrUn 88.293 205 14 4 94 289 319857518 319857315 1.760000e-58 237.0
17 TraesCS3D01G027900 chrUn 88.293 205 14 4 94 289 331092624 331092827 1.760000e-58 237.0
18 TraesCS3D01G027900 chrUn 78.049 369 34 17 621 956 319857038 319856684 4.990000e-44 189.0
19 TraesCS3D01G027900 chrUn 78.049 369 34 17 621 956 331093104 331093458 4.990000e-44 189.0
20 TraesCS3D01G027900 chrUn 84.659 176 23 2 26 200 257888892 257888720 5.030000e-39 172.0
21 TraesCS3D01G027900 chrUn 77.931 290 21 13 728 985 35292370 35292648 1.420000e-29 141.0
22 TraesCS3D01G027900 chrUn 77.903 267 17 12 751 985 229342232 229342488 1.100000e-25 128.0
23 TraesCS3D01G027900 chrUn 97.143 35 1 0 504 538 257888693 257888659 4.080000e-05 60.2
24 TraesCS3D01G027900 chr3B 91.161 3066 254 10 721 3785 13813821 13816870 0.000000e+00 4145.0
25 TraesCS3D01G027900 chr3B 93.031 287 20 0 1 287 13813224 13813510 1.630000e-113 420.0
26 TraesCS3D01G027900 chr3B 100.000 49 0 0 536 584 13813564 13813612 1.450000e-14 91.6
27 TraesCS3D01G027900 chr7D 95.909 220 8 1 286 505 548196942 548197160 4.650000e-94 355.0
28 TraesCS3D01G027900 chr7D 95.475 221 9 1 286 505 264838820 264839040 6.020000e-93 351.0
29 TraesCS3D01G027900 chr7D 94.298 228 11 2 286 512 469089062 469088836 7.780000e-92 348.0
30 TraesCS3D01G027900 chr7D 95.000 220 10 1 286 505 470879135 470879353 1.010000e-90 344.0
31 TraesCS3D01G027900 chr5D 95.909 220 8 1 286 505 220494650 220494432 4.650000e-94 355.0
32 TraesCS3D01G027900 chr1D 95.455 220 9 1 286 505 329834119 329833901 2.160000e-92 350.0
33 TraesCS3D01G027900 chr1D 95.000 220 10 1 286 505 194434010 194433792 1.010000e-90 344.0
34 TraesCS3D01G027900 chr5B 95.023 221 10 1 285 505 543783589 543783370 2.800000e-91 346.0


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 TraesCS3D01G027900 chr3D 9631330 9635114 3784 False 6990.000000 6990 100.000000 1 3785 1 chr3D.!!$F1 3784
1 TraesCS3D01G027900 chr3D 4957603 4960506 2903 True 3945.000000 3945 91.181000 875 3785 1 chr3D.!!$R1 2910
2 TraesCS3D01G027900 chr3D 4999281 4999845 564 True 264.750000 473 93.802000 839 1236 2 chr3D.!!$R3 397
3 TraesCS3D01G027900 chr3A 10882814 10885716 2902 True 3940.000000 3940 91.146000 874 3785 1 chr3A.!!$R1 2911
4 TraesCS3D01G027900 chr3A 10686938 10690410 3472 True 2450.500000 4396 93.695500 1 3785 2 chr3A.!!$R2 3784
5 TraesCS3D01G027900 chr3A 10695380 10698050 2670 True 1532.000000 2689 89.680000 13 2829 2 chr3A.!!$R3 2816
6 TraesCS3D01G027900 chrUn 284401019 284410789 9770 True 4244.000000 4244 90.517000 578 3785 2 chrUn.!!$R3 3207
7 TraesCS3D01G027900 chrUn 302991178 302994414 3236 True 4244.000000 4244 90.517000 578 3785 1 chrUn.!!$R1 3207
8 TraesCS3D01G027900 chrUn 35292370 35296902 4532 False 2101.000000 4061 84.009500 649 3785 2 chrUn.!!$F1 3136
9 TraesCS3D01G027900 chrUn 229342232 229346742 4510 False 2094.500000 4061 83.995500 649 3785 2 chrUn.!!$F2 3136
10 TraesCS3D01G027900 chrUn 257885464 257888892 3428 True 1430.733333 4060 90.582000 26 3785 3 chrUn.!!$R2 3759
11 TraesCS3D01G027900 chrUn 319856684 319857518 834 True 213.000000 237 83.171000 94 956 2 chrUn.!!$R4 862
12 TraesCS3D01G027900 chrUn 331092624 331093458 834 False 213.000000 237 83.171000 94 956 2 chrUn.!!$F3 862
13 TraesCS3D01G027900 chr3B 13813224 13816870 3646 False 1552.200000 4145 94.730667 1 3785 3 chr3B.!!$F1 3784

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
477 487 0.241749 CGACCTAGGTACACGTGCAA 59.758 55.0 16.29 0.27 0.00 4.08 F
1232 8384 0.593128 GTTGGTGTCACATGCAGTCC 59.407 55.0 5.12 0.00 0.00 3.85 F
1898 9057 0.178891 TTGGGGCTCTCCTCTTGTCT 60.179 55.0 0.00 0.00 32.58 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 8983 0.039256 TGATCTTTTGCAACGCTGGC 60.039 50.0 0.00 0.00 0.00 4.85 R
2573 9755 0.101759 CAAGCGATTTCCATGCAGGG 59.898 55.0 12.23 12.23 38.24 4.45 R
3164 10346 0.748005 ACGTGAAGCACCACAAAGCT 60.748 50.0 8.80 0.00 44.31 3.74 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 36 2.872557 CATGTGCCAGTTGCTCCG 59.127 61.111 0.00 0.00 42.00 4.63
39 40 3.555324 TGCCAGTTGCTCCGGTGA 61.555 61.111 7.92 0.00 42.00 4.02
44 45 3.414700 GTTGCTCCGGTGACTGCG 61.415 66.667 7.92 0.00 0.00 5.18
114 116 0.452987 CCGCCATGTGAGATTTGGTG 59.547 55.000 0.00 0.00 40.05 4.17
189 198 3.581101 TCATCATCAGTAGGAAGGAGGG 58.419 50.000 0.00 0.00 0.00 4.30
227 236 1.141881 AGTGCTGCCCGTATCGAAG 59.858 57.895 0.00 0.00 0.00 3.79
285 295 9.558396 TGAAAGCAATCCAATTATTTTCTGTTT 57.442 25.926 0.00 0.00 30.99 2.83
289 299 9.860898 AGCAATCCAATTATTTTCTGTTTACTC 57.139 29.630 0.00 0.00 0.00 2.59
290 300 9.087424 GCAATCCAATTATTTTCTGTTTACTCC 57.913 33.333 0.00 0.00 0.00 3.85
291 301 9.586435 CAATCCAATTATTTTCTGTTTACTCCC 57.414 33.333 0.00 0.00 0.00 4.30
292 302 9.547279 AATCCAATTATTTTCTGTTTACTCCCT 57.453 29.630 0.00 0.00 0.00 4.20
293 303 8.575649 TCCAATTATTTTCTGTTTACTCCCTC 57.424 34.615 0.00 0.00 0.00 4.30
294 304 7.614192 TCCAATTATTTTCTGTTTACTCCCTCC 59.386 37.037 0.00 0.00 0.00 4.30
295 305 7.396055 CCAATTATTTTCTGTTTACTCCCTCCA 59.604 37.037 0.00 0.00 0.00 3.86
296 306 8.971073 CAATTATTTTCTGTTTACTCCCTCCAT 58.029 33.333 0.00 0.00 0.00 3.41
297 307 8.753497 ATTATTTTCTGTTTACTCCCTCCATC 57.247 34.615 0.00 0.00 0.00 3.51
298 308 5.843019 TTTTCTGTTTACTCCCTCCATCT 57.157 39.130 0.00 0.00 0.00 2.90
299 309 5.422214 TTTCTGTTTACTCCCTCCATCTC 57.578 43.478 0.00 0.00 0.00 2.75
300 310 4.061131 TCTGTTTACTCCCTCCATCTCA 57.939 45.455 0.00 0.00 0.00 3.27
301 311 4.026744 TCTGTTTACTCCCTCCATCTCAG 58.973 47.826 0.00 0.00 0.00 3.35
302 312 3.772025 CTGTTTACTCCCTCCATCTCAGT 59.228 47.826 0.00 0.00 0.00 3.41
303 313 4.168101 TGTTTACTCCCTCCATCTCAGTT 58.832 43.478 0.00 0.00 0.00 3.16
304 314 4.597507 TGTTTACTCCCTCCATCTCAGTTT 59.402 41.667 0.00 0.00 0.00 2.66
305 315 5.783360 TGTTTACTCCCTCCATCTCAGTTTA 59.217 40.000 0.00 0.00 0.00 2.01
306 316 6.443849 TGTTTACTCCCTCCATCTCAGTTTAT 59.556 38.462 0.00 0.00 0.00 1.40
307 317 7.037586 TGTTTACTCCCTCCATCTCAGTTTATT 60.038 37.037 0.00 0.00 0.00 1.40
308 318 8.483758 GTTTACTCCCTCCATCTCAGTTTATTA 58.516 37.037 0.00 0.00 0.00 0.98
309 319 6.739331 ACTCCCTCCATCTCAGTTTATTAG 57.261 41.667 0.00 0.00 0.00 1.73
310 320 6.206042 ACTCCCTCCATCTCAGTTTATTAGT 58.794 40.000 0.00 0.00 0.00 2.24
311 321 6.325286 ACTCCCTCCATCTCAGTTTATTAGTC 59.675 42.308 0.00 0.00 0.00 2.59
312 322 6.444704 TCCCTCCATCTCAGTTTATTAGTCT 58.555 40.000 0.00 0.00 0.00 3.24
313 323 6.903534 TCCCTCCATCTCAGTTTATTAGTCTT 59.096 38.462 0.00 0.00 0.00 3.01
314 324 6.989169 CCCTCCATCTCAGTTTATTAGTCTTG 59.011 42.308 0.00 0.00 0.00 3.02
315 325 6.481644 CCTCCATCTCAGTTTATTAGTCTTGC 59.518 42.308 0.00 0.00 0.00 4.01
316 326 6.946340 TCCATCTCAGTTTATTAGTCTTGCA 58.054 36.000 0.00 0.00 0.00 4.08
317 327 6.818644 TCCATCTCAGTTTATTAGTCTTGCAC 59.181 38.462 0.00 0.00 0.00 4.57
318 328 6.237942 CCATCTCAGTTTATTAGTCTTGCACG 60.238 42.308 0.00 0.00 0.00 5.34
319 329 5.779922 TCTCAGTTTATTAGTCTTGCACGT 58.220 37.500 0.00 0.00 0.00 4.49
320 330 5.633601 TCTCAGTTTATTAGTCTTGCACGTG 59.366 40.000 12.28 12.28 0.00 4.49
321 331 5.294356 TCAGTTTATTAGTCTTGCACGTGT 58.706 37.500 18.38 0.00 0.00 4.49
322 332 6.448852 TCAGTTTATTAGTCTTGCACGTGTA 58.551 36.000 18.38 10.46 0.00 2.90
323 333 7.094631 TCAGTTTATTAGTCTTGCACGTGTAT 58.905 34.615 18.38 0.00 0.00 2.29
324 334 7.274904 TCAGTTTATTAGTCTTGCACGTGTATC 59.725 37.037 18.38 6.65 0.00 2.24
325 335 7.275779 CAGTTTATTAGTCTTGCACGTGTATCT 59.724 37.037 18.38 13.30 0.00 1.98
326 336 8.464404 AGTTTATTAGTCTTGCACGTGTATCTA 58.536 33.333 18.38 12.37 0.00 1.98
327 337 9.079833 GTTTATTAGTCTTGCACGTGTATCTAA 57.920 33.333 18.38 19.08 0.00 2.10
328 338 8.851960 TTATTAGTCTTGCACGTGTATCTAAG 57.148 34.615 18.38 13.32 0.00 2.18
329 339 4.785511 AGTCTTGCACGTGTATCTAAGT 57.214 40.909 18.38 0.00 0.00 2.24
330 340 4.734917 AGTCTTGCACGTGTATCTAAGTC 58.265 43.478 18.38 11.21 0.00 3.01
331 341 3.542704 GTCTTGCACGTGTATCTAAGTCG 59.457 47.826 18.38 0.00 0.00 4.18
332 342 3.189910 TCTTGCACGTGTATCTAAGTCGT 59.810 43.478 18.38 0.00 35.12 4.34
333 343 3.127081 TGCACGTGTATCTAAGTCGTC 57.873 47.619 18.38 0.00 32.47 4.20
334 344 2.485038 TGCACGTGTATCTAAGTCGTCA 59.515 45.455 18.38 0.00 32.47 4.35
335 345 3.058085 TGCACGTGTATCTAAGTCGTCAA 60.058 43.478 18.38 0.00 32.47 3.18
336 346 4.103357 GCACGTGTATCTAAGTCGTCAAT 58.897 43.478 18.38 0.00 32.47 2.57
337 347 4.561606 GCACGTGTATCTAAGTCGTCAATT 59.438 41.667 18.38 0.00 32.47 2.32
338 348 5.061808 GCACGTGTATCTAAGTCGTCAATTT 59.938 40.000 18.38 0.00 32.47 1.82
339 349 6.252015 GCACGTGTATCTAAGTCGTCAATTTA 59.748 38.462 18.38 0.00 32.47 1.40
340 350 7.201376 GCACGTGTATCTAAGTCGTCAATTTAA 60.201 37.037 18.38 0.00 32.47 1.52
341 351 8.100306 CACGTGTATCTAAGTCGTCAATTTAAC 58.900 37.037 7.58 0.00 32.47 2.01
342 352 8.025445 ACGTGTATCTAAGTCGTCAATTTAACT 58.975 33.333 0.00 0.00 0.00 2.24
343 353 8.857216 CGTGTATCTAAGTCGTCAATTTAACTT 58.143 33.333 0.00 0.00 36.09 2.66
451 461 9.851686 AATGTATGCCTCTTATTAAGTTGATCA 57.148 29.630 3.45 0.00 0.00 2.92
452 462 9.851686 ATGTATGCCTCTTATTAAGTTGATCAA 57.148 29.630 3.38 3.38 0.00 2.57
453 463 9.679661 TGTATGCCTCTTATTAAGTTGATCAAA 57.320 29.630 10.35 0.00 0.00 2.69
466 476 7.611213 AAGTTGATCAAATTAACGACCTAGG 57.389 36.000 18.88 7.41 34.34 3.02
467 477 6.708285 AGTTGATCAAATTAACGACCTAGGT 58.292 36.000 16.26 16.26 34.34 3.08
468 478 7.844009 AGTTGATCAAATTAACGACCTAGGTA 58.156 34.615 16.29 0.00 34.34 3.08
469 479 7.763071 AGTTGATCAAATTAACGACCTAGGTAC 59.237 37.037 16.29 7.83 34.34 3.34
470 480 7.172868 TGATCAAATTAACGACCTAGGTACA 57.827 36.000 16.29 0.00 0.00 2.90
471 481 7.037438 TGATCAAATTAACGACCTAGGTACAC 58.963 38.462 16.29 1.05 0.00 2.90
472 482 5.401550 TCAAATTAACGACCTAGGTACACG 58.598 41.667 16.29 16.96 0.00 4.49
473 483 5.048083 TCAAATTAACGACCTAGGTACACGT 60.048 40.000 16.29 17.67 38.81 4.49
474 484 3.829886 TTAACGACCTAGGTACACGTG 57.170 47.619 23.27 15.48 37.28 4.49
475 485 0.242017 AACGACCTAGGTACACGTGC 59.758 55.000 23.27 6.22 37.28 5.34
476 486 0.890542 ACGACCTAGGTACACGTGCA 60.891 55.000 22.28 0.00 35.91 4.57
477 487 0.241749 CGACCTAGGTACACGTGCAA 59.758 55.000 16.29 0.27 0.00 4.08
478 488 1.731424 CGACCTAGGTACACGTGCAAG 60.731 57.143 16.29 5.88 0.00 4.01
479 489 1.542915 GACCTAGGTACACGTGCAAGA 59.457 52.381 16.29 0.00 0.00 3.02
480 490 1.271656 ACCTAGGTACACGTGCAAGAC 59.728 52.381 14.41 8.65 0.00 3.01
481 491 1.544691 CCTAGGTACACGTGCAAGACT 59.455 52.381 17.22 9.58 0.00 3.24
482 492 2.029290 CCTAGGTACACGTGCAAGACTT 60.029 50.000 17.22 7.83 0.00 3.01
483 493 1.865865 AGGTACACGTGCAAGACTTG 58.134 50.000 17.22 11.02 0.00 3.16
484 494 1.138266 AGGTACACGTGCAAGACTTGT 59.862 47.619 17.22 3.04 40.10 3.16
485 495 2.363038 AGGTACACGTGCAAGACTTGTA 59.637 45.455 17.22 9.51 38.06 2.41
486 496 3.125316 GGTACACGTGCAAGACTTGTAA 58.875 45.455 17.22 3.08 40.07 2.41
487 497 3.556775 GGTACACGTGCAAGACTTGTAAA 59.443 43.478 17.22 0.63 40.07 2.01
488 498 3.668596 ACACGTGCAAGACTTGTAAAC 57.331 42.857 17.22 11.23 35.36 2.01
489 499 3.267483 ACACGTGCAAGACTTGTAAACT 58.733 40.909 17.22 0.00 35.36 2.66
490 500 3.063452 ACACGTGCAAGACTTGTAAACTG 59.937 43.478 17.22 9.92 35.36 3.16
491 501 3.308595 CACGTGCAAGACTTGTAAACTGA 59.691 43.478 16.39 0.00 0.00 3.41
492 502 3.555956 ACGTGCAAGACTTGTAAACTGAG 59.444 43.478 16.39 3.60 0.00 3.35
493 503 3.802139 CGTGCAAGACTTGTAAACTGAGA 59.198 43.478 16.39 0.00 0.00 3.27
494 504 4.449068 CGTGCAAGACTTGTAAACTGAGAT 59.551 41.667 16.39 0.00 0.00 2.75
495 505 5.613360 CGTGCAAGACTTGTAAACTGAGATG 60.613 44.000 16.39 0.00 0.00 2.90
496 506 4.756642 TGCAAGACTTGTAAACTGAGATGG 59.243 41.667 16.39 0.00 0.00 3.51
497 507 4.997395 GCAAGACTTGTAAACTGAGATGGA 59.003 41.667 16.39 0.00 0.00 3.41
498 508 5.121454 GCAAGACTTGTAAACTGAGATGGAG 59.879 44.000 16.39 0.00 0.00 3.86
499 509 5.413309 AGACTTGTAAACTGAGATGGAGG 57.587 43.478 0.00 0.00 0.00 4.30
500 510 4.223923 AGACTTGTAAACTGAGATGGAGGG 59.776 45.833 0.00 0.00 0.00 4.30
501 511 4.168101 ACTTGTAAACTGAGATGGAGGGA 58.832 43.478 0.00 0.00 0.00 4.20
502 512 4.223923 ACTTGTAAACTGAGATGGAGGGAG 59.776 45.833 0.00 0.00 0.00 4.30
584 618 4.976731 GGCATGTAGATGTAGAACGTACTG 59.023 45.833 1.37 0.00 31.50 2.74
586 620 5.733655 GCATGTAGATGTAGAACGTACTGCT 60.734 44.000 1.37 0.00 31.50 4.24
592 648 4.713824 TGTAGAACGTACTGCTTGCTAT 57.286 40.909 0.00 0.00 0.00 2.97
713 7639 5.063564 GTCTCCATTATTTCCTGTTGTCGTC 59.936 44.000 0.00 0.00 0.00 4.20
873 8013 7.913297 CACTAATCCACAAAAATATTACACCGG 59.087 37.037 0.00 0.00 0.00 5.28
991 8143 3.547567 GCACTTGCATCTCTGTCCT 57.452 52.632 0.00 0.00 41.59 3.85
1144 8296 0.829333 TGCCCTGCTTGCTTTCAAAA 59.171 45.000 0.00 0.00 0.00 2.44
1165 8317 2.124693 CAGCTCTCCGACCCTCTCC 61.125 68.421 0.00 0.00 0.00 3.71
1232 8384 0.593128 GTTGGTGTCACATGCAGTCC 59.407 55.000 5.12 0.00 0.00 3.85
1379 8531 2.639839 CCATCCCCGATGATTTAGGACT 59.360 50.000 3.18 0.00 42.09 3.85
1380 8532 3.838317 CCATCCCCGATGATTTAGGACTA 59.162 47.826 3.18 0.00 42.09 2.59
1398 8550 7.565323 AGGACTACTTCGTCGTCTTAAATAT 57.435 36.000 0.00 0.00 34.75 1.28
1460 8612 3.139397 ACCACCATAGGAAACCTCACAAA 59.861 43.478 0.00 0.00 34.61 2.83
1482 8634 2.223479 GCTTCGTGTTCTTTCCTTGCAA 60.223 45.455 0.00 0.00 0.00 4.08
1483 8635 3.621794 CTTCGTGTTCTTTCCTTGCAAG 58.378 45.455 19.93 19.93 0.00 4.01
1546 8705 3.131400 CCTACAGAGTCTTGGCTACTTCC 59.869 52.174 0.00 0.00 0.00 3.46
1547 8706 2.896039 ACAGAGTCTTGGCTACTTCCT 58.104 47.619 0.00 0.00 0.00 3.36
1618 8777 9.670442 TTAATAATACCCCTCTGATAACTCACT 57.330 33.333 0.00 0.00 0.00 3.41
1653 8812 3.009473 ACAACAGCCTGTCAGGACATATT 59.991 43.478 23.77 5.84 41.01 1.28
1709 8868 2.795121 CTTGTCCTTCAAGCGAATCG 57.205 50.000 0.00 0.00 45.37 3.34
1734 8893 2.063979 CGGCCCAGTACCTCCATCA 61.064 63.158 0.00 0.00 0.00 3.07
1789 8948 5.758296 TGGCTTGAACTGAACTACAACTTAG 59.242 40.000 0.00 0.00 0.00 2.18
1790 8949 5.758784 GGCTTGAACTGAACTACAACTTAGT 59.241 40.000 0.00 0.00 0.00 2.24
1824 8983 7.992008 TCCCTAACAACAAAAGTTTTAGTCTG 58.008 34.615 0.00 6.21 0.00 3.51
1898 9057 0.178891 TTGGGGCTCTCCTCTTGTCT 60.179 55.000 0.00 0.00 32.58 3.41
2140 9299 3.326006 ACTCACTGTGTTGGATGTCTCAT 59.674 43.478 7.79 0.00 0.00 2.90
2146 9305 6.818142 CACTGTGTTGGATGTCTCATACAATA 59.182 38.462 10.04 5.55 42.70 1.90
2184 9343 2.567615 TCCTGCTTCTCTTGGTAACCTC 59.432 50.000 0.00 0.00 0.00 3.85
2202 9361 5.799827 ACCTCTCTGAATTAGCATACCTC 57.200 43.478 0.00 0.00 0.00 3.85
2230 9389 9.974980 TCTTAAACAAAAATATGTTCCTTGGAC 57.025 29.630 0.00 0.00 42.49 4.02
2330 9489 9.877178 TCTTAGCTTCTTATCCAGTTTTTCTAG 57.123 33.333 0.00 0.00 0.00 2.43
2331 9490 9.103861 CTTAGCTTCTTATCCAGTTTTTCTAGG 57.896 37.037 0.00 0.00 0.00 3.02
2429 9588 1.515736 GCCAGCTGCAGATTTTCGC 60.516 57.895 20.43 6.10 40.77 4.70
2544 9703 6.008960 GGATAGCAAGATTCCAGAATCCATT 58.991 40.000 15.16 3.51 46.28 3.16
2573 9755 1.377536 GAGAATCTCCAGTGGCTTGC 58.622 55.000 3.51 0.00 0.00 4.01
2619 9801 0.466922 CCATCCCACCTCAGATTGCC 60.467 60.000 0.00 0.00 0.00 4.52
2641 9823 6.432162 TGCCATGCTCAAGAATATAGGAAATC 59.568 38.462 0.00 0.00 0.00 2.17
2782 9964 8.203485 GTCTATTTGATCTTGACAATCTCCTCT 58.797 37.037 0.00 0.00 0.00 3.69
2822 10004 4.357918 ACTTCTTGACTGGCACATTACT 57.642 40.909 0.00 0.00 38.20 2.24
2837 10019 4.516698 CACATTACTGGTTGATATGGGCTC 59.483 45.833 0.00 0.00 0.00 4.70
2983 10165 4.518211 CACTTCCAGAATCTTTCAGCAAGT 59.482 41.667 0.00 0.00 33.66 3.16
3164 10346 4.017222 ACAATCCTTGATGGGGAATTCTGA 60.017 41.667 5.23 0.00 36.37 3.27
3304 10487 8.956533 TGTAGCTTTCTGCATATATGTAACAA 57.043 30.769 14.14 3.17 45.94 2.83
3400 10583 4.106029 GTCTCGTACCATGAGCTTGTTA 57.894 45.455 0.00 0.00 31.39 2.41
3412 10595 3.999001 TGAGCTTGTTAGAGCAACTGATG 59.001 43.478 0.00 0.00 45.12 3.07
3432 10615 6.946340 TGATGATTTTAGTGAGAGCAACCTA 58.054 36.000 0.00 0.00 0.00 3.08
3498 10681 5.549347 AGCAATGGTTTGATTGTTGCAATA 58.451 33.333 0.59 0.00 45.54 1.90
3628 10811 1.886542 CCAACTTGGAGTTTAGGGCAC 59.113 52.381 0.92 0.00 40.96 5.01
3774 10957 4.801330 TCTTCACCATGAACACTACGAT 57.199 40.909 0.00 0.00 32.21 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 0.247814 CCACGACAATTGATGCGCTC 60.248 55.000 13.59 4.27 33.67 5.03
157 159 7.455891 TCCTACTGATGATGATGTGCATTTAT 58.544 34.615 0.00 0.00 37.34 1.40
189 198 5.407995 GCACTGAAAGCATAGACCATATCTC 59.592 44.000 0.00 0.00 36.63 2.75
227 236 7.643579 ACTTTCTAAGACATTTCTTTCAGCAC 58.356 34.615 0.00 0.00 39.17 4.40
285 295 7.363031 ACTAATAAACTGAGATGGAGGGAGTA 58.637 38.462 0.00 0.00 0.00 2.59
286 296 6.206042 ACTAATAAACTGAGATGGAGGGAGT 58.794 40.000 0.00 0.00 0.00 3.85
287 297 6.553100 AGACTAATAAACTGAGATGGAGGGAG 59.447 42.308 0.00 0.00 0.00 4.30
288 298 6.444704 AGACTAATAAACTGAGATGGAGGGA 58.555 40.000 0.00 0.00 0.00 4.20
289 299 6.739331 AGACTAATAAACTGAGATGGAGGG 57.261 41.667 0.00 0.00 0.00 4.30
290 300 6.481644 GCAAGACTAATAAACTGAGATGGAGG 59.518 42.308 0.00 0.00 0.00 4.30
291 301 7.010923 GTGCAAGACTAATAAACTGAGATGGAG 59.989 40.741 0.00 0.00 0.00 3.86
292 302 6.818644 GTGCAAGACTAATAAACTGAGATGGA 59.181 38.462 0.00 0.00 0.00 3.41
293 303 6.237942 CGTGCAAGACTAATAAACTGAGATGG 60.238 42.308 0.00 0.00 0.00 3.51
294 304 6.311445 ACGTGCAAGACTAATAAACTGAGATG 59.689 38.462 6.65 0.00 0.00 2.90
295 305 6.311445 CACGTGCAAGACTAATAAACTGAGAT 59.689 38.462 6.65 0.00 0.00 2.75
296 306 5.633601 CACGTGCAAGACTAATAAACTGAGA 59.366 40.000 6.65 0.00 0.00 3.27
297 307 5.405571 ACACGTGCAAGACTAATAAACTGAG 59.594 40.000 17.22 0.00 0.00 3.35
298 308 5.294356 ACACGTGCAAGACTAATAAACTGA 58.706 37.500 17.22 0.00 0.00 3.41
299 309 5.591643 ACACGTGCAAGACTAATAAACTG 57.408 39.130 17.22 0.00 0.00 3.16
300 310 7.321153 AGATACACGTGCAAGACTAATAAACT 58.679 34.615 17.22 0.00 0.00 2.66
301 311 7.521509 AGATACACGTGCAAGACTAATAAAC 57.478 36.000 17.22 0.00 0.00 2.01
302 312 9.297586 CTTAGATACACGTGCAAGACTAATAAA 57.702 33.333 17.22 0.00 0.00 1.40
303 313 8.464404 ACTTAGATACACGTGCAAGACTAATAA 58.536 33.333 17.22 3.16 0.00 1.40
304 314 7.993101 ACTTAGATACACGTGCAAGACTAATA 58.007 34.615 17.22 0.00 0.00 0.98
305 315 6.864342 ACTTAGATACACGTGCAAGACTAAT 58.136 36.000 17.22 0.00 0.00 1.73
306 316 6.263516 ACTTAGATACACGTGCAAGACTAA 57.736 37.500 17.22 15.79 0.00 2.24
307 317 5.446875 CGACTTAGATACACGTGCAAGACTA 60.447 44.000 17.22 9.60 0.00 2.59
308 318 4.672024 CGACTTAGATACACGTGCAAGACT 60.672 45.833 17.22 10.57 0.00 3.24
309 319 3.542704 CGACTTAGATACACGTGCAAGAC 59.457 47.826 17.22 10.33 0.00 3.01
310 320 3.189910 ACGACTTAGATACACGTGCAAGA 59.810 43.478 17.22 0.00 35.91 3.02
311 321 3.499048 ACGACTTAGATACACGTGCAAG 58.501 45.455 17.22 13.15 35.91 4.01
312 322 3.058085 TGACGACTTAGATACACGTGCAA 60.058 43.478 17.22 4.26 37.32 4.08
313 323 2.485038 TGACGACTTAGATACACGTGCA 59.515 45.455 17.22 2.06 37.32 4.57
314 324 3.127081 TGACGACTTAGATACACGTGC 57.873 47.619 17.22 0.00 37.32 5.34
315 325 6.627690 AAATTGACGACTTAGATACACGTG 57.372 37.500 15.48 15.48 37.32 4.49
316 326 8.025445 AGTTAAATTGACGACTTAGATACACGT 58.975 33.333 0.00 0.00 39.82 4.49
317 327 8.390854 AGTTAAATTGACGACTTAGATACACG 57.609 34.615 0.00 0.00 0.00 4.49
425 435 9.851686 TGATCAACTTAATAAGAGGCATACATT 57.148 29.630 7.06 0.00 0.00 2.71
426 436 9.851686 TTGATCAACTTAATAAGAGGCATACAT 57.148 29.630 3.38 0.00 0.00 2.29
427 437 9.679661 TTTGATCAACTTAATAAGAGGCATACA 57.320 29.630 7.89 0.00 0.00 2.29
440 450 9.158233 CCTAGGTCGTTAATTTGATCAACTTAA 57.842 33.333 20.86 20.86 0.00 1.85
441 451 8.316214 ACCTAGGTCGTTAATTTGATCAACTTA 58.684 33.333 9.21 10.82 0.00 2.24
442 452 7.166167 ACCTAGGTCGTTAATTTGATCAACTT 58.834 34.615 9.21 11.90 0.00 2.66
443 453 6.708285 ACCTAGGTCGTTAATTTGATCAACT 58.292 36.000 9.21 0.00 0.00 3.16
444 454 6.980051 ACCTAGGTCGTTAATTTGATCAAC 57.020 37.500 9.21 0.00 0.00 3.18
445 455 7.546667 GTGTACCTAGGTCGTTAATTTGATCAA 59.453 37.037 20.32 3.38 0.00 2.57
446 456 7.037438 GTGTACCTAGGTCGTTAATTTGATCA 58.963 38.462 20.32 0.00 0.00 2.92
447 457 6.197842 CGTGTACCTAGGTCGTTAATTTGATC 59.802 42.308 20.32 0.00 0.00 2.92
448 458 6.038356 CGTGTACCTAGGTCGTTAATTTGAT 58.962 40.000 20.32 0.00 0.00 2.57
449 459 5.048083 ACGTGTACCTAGGTCGTTAATTTGA 60.048 40.000 20.32 0.00 0.00 2.69
450 460 5.061311 CACGTGTACCTAGGTCGTTAATTTG 59.939 44.000 20.32 5.49 32.47 2.32
451 461 5.163513 CACGTGTACCTAGGTCGTTAATTT 58.836 41.667 20.32 0.00 32.47 1.82
452 462 4.737054 CACGTGTACCTAGGTCGTTAATT 58.263 43.478 20.32 0.00 32.47 1.40
453 463 3.428045 GCACGTGTACCTAGGTCGTTAAT 60.428 47.826 20.32 0.00 32.47 1.40
454 464 2.095263 GCACGTGTACCTAGGTCGTTAA 60.095 50.000 20.32 0.00 32.47 2.01
455 465 1.468520 GCACGTGTACCTAGGTCGTTA 59.531 52.381 20.32 0.00 32.47 3.18
456 466 0.242017 GCACGTGTACCTAGGTCGTT 59.758 55.000 20.32 4.39 32.47 3.85
457 467 0.890542 TGCACGTGTACCTAGGTCGT 60.891 55.000 20.32 19.27 35.12 4.34
458 468 0.241749 TTGCACGTGTACCTAGGTCG 59.758 55.000 20.32 18.55 0.00 4.79
459 469 1.542915 TCTTGCACGTGTACCTAGGTC 59.457 52.381 20.32 10.94 0.00 3.85
460 470 1.271656 GTCTTGCACGTGTACCTAGGT 59.728 52.381 20.57 20.57 0.00 3.08
461 471 1.544691 AGTCTTGCACGTGTACCTAGG 59.455 52.381 18.38 7.41 0.00 3.02
462 472 2.987149 CAAGTCTTGCACGTGTACCTAG 59.013 50.000 18.38 7.46 30.37 3.02
463 473 2.363038 ACAAGTCTTGCACGTGTACCTA 59.637 45.455 18.38 0.00 44.87 3.08
464 474 1.138266 ACAAGTCTTGCACGTGTACCT 59.862 47.619 18.38 5.66 44.87 3.08
465 475 1.578583 ACAAGTCTTGCACGTGTACC 58.421 50.000 18.38 0.49 44.87 3.34
466 476 4.269363 AGTTTACAAGTCTTGCACGTGTAC 59.731 41.667 18.38 10.47 45.99 2.90
467 477 4.269123 CAGTTTACAAGTCTTGCACGTGTA 59.731 41.667 18.38 10.46 44.87 2.90
469 479 3.308595 TCAGTTTACAAGTCTTGCACGTG 59.691 43.478 12.28 12.28 40.14 4.49
470 480 3.527533 TCAGTTTACAAGTCTTGCACGT 58.472 40.909 12.66 0.00 0.00 4.49
471 481 3.802139 TCTCAGTTTACAAGTCTTGCACG 59.198 43.478 12.66 4.68 0.00 5.34
472 482 5.334414 CCATCTCAGTTTACAAGTCTTGCAC 60.334 44.000 12.66 7.19 0.00 4.57
473 483 4.756642 CCATCTCAGTTTACAAGTCTTGCA 59.243 41.667 12.66 0.00 0.00 4.08
474 484 4.997395 TCCATCTCAGTTTACAAGTCTTGC 59.003 41.667 12.66 0.00 0.00 4.01
475 485 5.641209 CCTCCATCTCAGTTTACAAGTCTTG 59.359 44.000 11.17 11.17 0.00 3.02
476 486 5.280215 CCCTCCATCTCAGTTTACAAGTCTT 60.280 44.000 0.00 0.00 0.00 3.01
477 487 4.223923 CCCTCCATCTCAGTTTACAAGTCT 59.776 45.833 0.00 0.00 0.00 3.24
478 488 4.223032 TCCCTCCATCTCAGTTTACAAGTC 59.777 45.833 0.00 0.00 0.00 3.01
479 489 4.168101 TCCCTCCATCTCAGTTTACAAGT 58.832 43.478 0.00 0.00 0.00 3.16
480 490 4.223923 ACTCCCTCCATCTCAGTTTACAAG 59.776 45.833 0.00 0.00 0.00 3.16
481 491 4.168101 ACTCCCTCCATCTCAGTTTACAA 58.832 43.478 0.00 0.00 0.00 2.41
482 492 3.791320 ACTCCCTCCATCTCAGTTTACA 58.209 45.455 0.00 0.00 0.00 2.41
483 493 6.487299 AATACTCCCTCCATCTCAGTTTAC 57.513 41.667 0.00 0.00 0.00 2.01
484 494 8.798975 AATAATACTCCCTCCATCTCAGTTTA 57.201 34.615 0.00 0.00 0.00 2.01
485 495 7.698163 AATAATACTCCCTCCATCTCAGTTT 57.302 36.000 0.00 0.00 0.00 2.66
486 496 7.698163 AAATAATACTCCCTCCATCTCAGTT 57.302 36.000 0.00 0.00 0.00 3.16
487 497 7.348274 TCAAAATAATACTCCCTCCATCTCAGT 59.652 37.037 0.00 0.00 0.00 3.41
488 498 7.659390 GTCAAAATAATACTCCCTCCATCTCAG 59.341 40.741 0.00 0.00 0.00 3.35
489 499 7.509546 GTCAAAATAATACTCCCTCCATCTCA 58.490 38.462 0.00 0.00 0.00 3.27
490 500 6.647067 CGTCAAAATAATACTCCCTCCATCTC 59.353 42.308 0.00 0.00 0.00 2.75
491 501 6.464465 CCGTCAAAATAATACTCCCTCCATCT 60.464 42.308 0.00 0.00 0.00 2.90
492 502 5.701290 CCGTCAAAATAATACTCCCTCCATC 59.299 44.000 0.00 0.00 0.00 3.51
493 503 5.456186 CCCGTCAAAATAATACTCCCTCCAT 60.456 44.000 0.00 0.00 0.00 3.41
494 504 4.141574 CCCGTCAAAATAATACTCCCTCCA 60.142 45.833 0.00 0.00 0.00 3.86
495 505 4.386711 CCCGTCAAAATAATACTCCCTCC 58.613 47.826 0.00 0.00 0.00 4.30
496 506 4.102054 TCCCCGTCAAAATAATACTCCCTC 59.898 45.833 0.00 0.00 0.00 4.30
497 507 4.042174 TCCCCGTCAAAATAATACTCCCT 58.958 43.478 0.00 0.00 0.00 4.20
498 508 4.102054 TCTCCCCGTCAAAATAATACTCCC 59.898 45.833 0.00 0.00 0.00 4.30
499 509 5.286267 TCTCCCCGTCAAAATAATACTCC 57.714 43.478 0.00 0.00 0.00 3.85
500 510 6.238402 GCTTTCTCCCCGTCAAAATAATACTC 60.238 42.308 0.00 0.00 0.00 2.59
501 511 5.589050 GCTTTCTCCCCGTCAAAATAATACT 59.411 40.000 0.00 0.00 0.00 2.12
502 512 5.355910 TGCTTTCTCCCCGTCAAAATAATAC 59.644 40.000 0.00 0.00 0.00 1.89
584 618 2.990066 ACCCACAGACTATAGCAAGC 57.010 50.000 0.00 0.00 0.00 4.01
586 620 9.914834 AAAATATAAACCCACAGACTATAGCAA 57.085 29.630 0.00 0.00 0.00 3.91
713 7639 1.631072 GCACATGCGCACTACTACG 59.369 57.895 14.90 0.00 0.00 3.51
800 7731 3.326006 TGATATAGGAGGCTCCAGCTTTG 59.674 47.826 33.86 0.00 39.61 2.77
873 8013 1.528129 CAGCTTCCAAGTGGTCCTTC 58.472 55.000 0.00 0.00 36.34 3.46
877 8017 0.957888 GCTCCAGCTTCCAAGTGGTC 60.958 60.000 0.00 0.00 38.21 4.02
943 8084 4.352001 TGGCTTTGGGCTGATATCTTATCT 59.648 41.667 3.98 0.00 41.46 1.98
991 8143 4.018870 TCCAAGTGAGGCCATGTATGTTTA 60.019 41.667 5.01 0.00 0.00 2.01
1245 8397 0.317854 GCAGTTTCAAAGCGGTGACC 60.318 55.000 0.00 0.00 0.00 4.02
1398 8550 3.244215 GGCCATTGAATCCGAGATGTAGA 60.244 47.826 0.00 0.00 0.00 2.59
1460 8612 1.604278 GCAAGGAAAGAACACGAAGCT 59.396 47.619 0.00 0.00 0.00 3.74
1618 8777 2.548875 GCTGTTGTTGCCAATGTTCAA 58.451 42.857 0.00 0.00 32.11 2.69
1653 8812 4.141482 GGTAAGGAGCCAATACAAGATGGA 60.141 45.833 0.00 0.00 39.12 3.41
1709 8868 2.038837 GGTACTGGGCCGCTGAAAC 61.039 63.158 0.00 0.00 0.00 2.78
1761 8920 4.318332 TGTAGTTCAGTTCAAGCCAGATG 58.682 43.478 0.00 0.00 0.00 2.90
1789 8948 3.492337 TGTTGTTAGGGATTGGACCAAC 58.508 45.455 9.67 3.70 0.00 3.77
1790 8949 3.885976 TGTTGTTAGGGATTGGACCAA 57.114 42.857 9.92 9.92 0.00 3.67
1824 8983 0.039256 TGATCTTTTGCAACGCTGGC 60.039 50.000 0.00 0.00 0.00 4.85
1852 9011 0.605319 TCACCGGTGAATCTGTTGCC 60.605 55.000 34.60 0.00 36.53 4.52
1898 9057 4.689150 CGAGGGAGATAGTTTGGAGGTAGA 60.689 50.000 0.00 0.00 0.00 2.59
1928 9087 2.481276 GGCACAACACCCTCAAAGAAAC 60.481 50.000 0.00 0.00 0.00 2.78
1959 9118 5.753721 AACTGAGATGAGAAAGCTTACCT 57.246 39.130 0.00 0.00 0.00 3.08
1962 9121 6.365970 AGGAAACTGAGATGAGAAAGCTTA 57.634 37.500 0.00 0.00 41.13 3.09
2140 9299 8.026396 GGAATGGGTCCTACTAGTTTATTGTA 57.974 38.462 0.00 0.00 43.98 2.41
2184 9343 6.418057 AAGAGGAGGTATGCTAATTCAGAG 57.582 41.667 0.00 0.00 0.00 3.35
2202 9361 9.423061 CCAAGGAACATATTTTTGTTTAAGAGG 57.577 33.333 0.00 0.00 39.85 3.69
2230 9389 1.271707 ACCAATTGTTCCTGGTACCGG 60.272 52.381 14.38 14.38 44.28 5.28
2330 9489 7.448748 TGAATAAACTGGAGCTTTCTAAACC 57.551 36.000 0.00 0.00 0.00 3.27
2331 9490 9.914131 ATTTGAATAAACTGGAGCTTTCTAAAC 57.086 29.630 0.00 0.00 0.00 2.01
2573 9755 0.101759 CAAGCGATTTCCATGCAGGG 59.898 55.000 12.23 12.23 38.24 4.45
2619 9801 8.618702 ACAGATTTCCTATATTCTTGAGCATG 57.381 34.615 0.00 0.00 0.00 4.06
2764 9946 5.789643 AGCTAGAGGAGATTGTCAAGATC 57.210 43.478 0.00 0.00 0.00 2.75
2782 9964 7.233389 AGAAGTTTTGAGACACATCTAGCTA 57.767 36.000 0.00 0.00 34.34 3.32
2822 10004 4.272489 CTTCAAAGAGCCCATATCAACCA 58.728 43.478 0.00 0.00 0.00 3.67
2837 10019 7.223387 GGTCCATGCTATAAATTTGCTTCAAAG 59.777 37.037 0.00 0.00 36.76 2.77
2983 10165 3.449018 TCCAAACTTTGCAAGCTGGTTAA 59.551 39.130 14.25 0.00 36.60 2.01
3050 10232 3.367703 GCTGGTCAGGATGGTGAAATTTG 60.368 47.826 0.00 0.00 36.16 2.32
3164 10346 0.748005 ACGTGAAGCACCACAAAGCT 60.748 50.000 8.80 0.00 44.31 3.74
3304 10487 5.414144 GCTGCTTCTTAATCTTCTTTCTGGT 59.586 40.000 0.00 0.00 0.00 4.00
3400 10583 6.705302 TCTCACTAAAATCATCAGTTGCTCT 58.295 36.000 0.00 0.00 0.00 4.09
3412 10595 6.981559 CCTAGTAGGTTGCTCTCACTAAAATC 59.018 42.308 8.17 0.00 0.00 2.17
3432 10615 3.323775 TCCAAAACTTCCAGACCCTAGT 58.676 45.455 0.00 0.00 0.00 2.57
3498 10681 6.042638 TCTAGCTGCATGTCTAGAACTTTT 57.957 37.500 14.39 0.00 38.55 2.27
3628 10811 3.489355 TGGGCATATATTGAAGCACCAG 58.511 45.455 0.00 0.00 0.00 4.00
3669 10852 5.361571 TGTTGTACCTTGAGAGTTGTGTAGA 59.638 40.000 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.