Multiple sequence alignment - TraesCS5A01G472900

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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 TraesCS5A01G472900 chr5A 100.000 2936 0 0 1 2936 649441604 649444539 0.000000e+00 5422.0
1 TraesCS5A01G472900 chr5A 100.000 282 0 0 663 944 649449684 649449965 3.350000e-144 521.0
2 TraesCS5A01G472900 chr5A 85.000 220 27 5 330 547 537626558 537626773 4.930000e-53 219.0
3 TraesCS5A01G472900 chr5A 80.132 151 24 6 46 193 537626329 537626476 1.110000e-19 108.0
4 TraesCS5A01G472900 chr7B 99.033 2275 20 2 663 2936 648721063 648718790 0.000000e+00 4078.0
5 TraesCS5A01G472900 chr7B 79.646 113 20 3 81 190 590500845 590500733 8.720000e-11 78.7
6 TraesCS5A01G472900 chr7A 95.524 2279 81 9 663 2936 17110603 17112865 0.000000e+00 3624.0
7 TraesCS5A01G472900 chr1A 94.515 2279 115 9 663 2936 561407392 561405119 0.000000e+00 3507.0
8 TraesCS5A01G472900 chr1A 92.948 2283 145 11 659 2934 327713821 327711548 0.000000e+00 3310.0
9 TraesCS5A01G472900 chr2A 93.383 2282 119 16 661 2936 12904850 12902595 0.000000e+00 3349.0
10 TraesCS5A01G472900 chr2A 94.052 1984 96 10 961 2936 677222422 677220453 0.000000e+00 2990.0
11 TraesCS5A01G472900 chr2A 94.826 1469 67 8 1472 2936 70125564 70124101 0.000000e+00 2283.0
12 TraesCS5A01G472900 chr2A 93.056 792 52 3 663 1452 70134931 70134141 0.000000e+00 1155.0
13 TraesCS5A01G472900 chr2A 80.354 509 69 21 53 556 138827108 138826626 1.000000e-94 357.0
14 TraesCS5A01G472900 chr4A 93.383 2282 107 8 664 2936 621705814 621708060 0.000000e+00 3338.0
15 TraesCS5A01G472900 chr4A 92.857 2282 105 22 661 2936 125038526 125036297 0.000000e+00 3258.0
16 TraesCS5A01G472900 chr4A 97.289 332 9 0 663 994 713599907 713600238 5.490000e-157 564.0
17 TraesCS5A01G472900 chr4A 80.961 583 74 28 4 561 68125916 68125346 7.520000e-116 427.0
18 TraesCS5A01G472900 chr4A 76.138 549 86 27 4 547 68141605 68142113 2.260000e-61 246.0
19 TraesCS5A01G472900 chr3D 94.297 1017 50 6 1924 2936 35718570 35719582 0.000000e+00 1550.0
20 TraesCS5A01G472900 chr5B 94.109 662 23 8 1 647 656925940 656926600 0.000000e+00 992.0
21 TraesCS5A01G472900 chr5B 85.000 220 27 4 330 547 512213091 512213306 4.930000e-53 219.0
22 TraesCS5A01G472900 chr5D 96.970 594 3 5 1 594 520910144 520910722 0.000000e+00 983.0
23 TraesCS5A01G472900 chr5D 79.412 170 27 5 46 208 424033501 424033669 2.390000e-21 113.0
24 TraesCS5A01G472900 chr5D 90.476 63 4 2 601 662 520910751 520910812 6.740000e-12 82.4
25 TraesCS5A01G472900 chr2D 80.747 509 67 21 53 556 131777552 131777070 4.620000e-98 368.0
26 TraesCS5A01G472900 chr2B 80.000 515 72 23 47 556 186312074 186312562 4.660000e-93 351.0
27 TraesCS5A01G472900 chr2B 86.522 230 25 5 328 556 185776765 185776541 6.280000e-62 248.0
28 TraesCS5A01G472900 chr4D 75.956 549 87 28 4 547 386831319 386831827 1.050000e-59 241.0
29 TraesCS5A01G472900 chr4B 72.587 518 98 33 42 546 494692163 494691677 2.370000e-26 130.0
30 TraesCS5A01G472900 chr7D 78.761 113 21 3 81 190 547457920 547457808 4.060000e-09 73.1


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 TraesCS5A01G472900 chr5A 649441604 649444539 2935 False 5422.0 5422 100.000 1 2936 1 chr5A.!!$F1 2935
1 TraesCS5A01G472900 chr7B 648718790 648721063 2273 True 4078.0 4078 99.033 663 2936 1 chr7B.!!$R2 2273
2 TraesCS5A01G472900 chr7A 17110603 17112865 2262 False 3624.0 3624 95.524 663 2936 1 chr7A.!!$F1 2273
3 TraesCS5A01G472900 chr1A 561405119 561407392 2273 True 3507.0 3507 94.515 663 2936 1 chr1A.!!$R2 2273
4 TraesCS5A01G472900 chr1A 327711548 327713821 2273 True 3310.0 3310 92.948 659 2934 1 chr1A.!!$R1 2275
5 TraesCS5A01G472900 chr2A 12902595 12904850 2255 True 3349.0 3349 93.383 661 2936 1 chr2A.!!$R1 2275
6 TraesCS5A01G472900 chr2A 677220453 677222422 1969 True 2990.0 2990 94.052 961 2936 1 chr2A.!!$R5 1975
7 TraesCS5A01G472900 chr2A 70124101 70125564 1463 True 2283.0 2283 94.826 1472 2936 1 chr2A.!!$R2 1464
8 TraesCS5A01G472900 chr2A 70134141 70134931 790 True 1155.0 1155 93.056 663 1452 1 chr2A.!!$R3 789
9 TraesCS5A01G472900 chr4A 621705814 621708060 2246 False 3338.0 3338 93.383 664 2936 1 chr4A.!!$F2 2272
10 TraesCS5A01G472900 chr4A 125036297 125038526 2229 True 3258.0 3258 92.857 661 2936 1 chr4A.!!$R2 2275
11 TraesCS5A01G472900 chr4A 68125346 68125916 570 True 427.0 427 80.961 4 561 1 chr4A.!!$R1 557
12 TraesCS5A01G472900 chr4A 68141605 68142113 508 False 246.0 246 76.138 4 547 1 chr4A.!!$F1 543
13 TraesCS5A01G472900 chr3D 35718570 35719582 1012 False 1550.0 1550 94.297 1924 2936 1 chr3D.!!$F1 1012
14 TraesCS5A01G472900 chr5B 656925940 656926600 660 False 992.0 992 94.109 1 647 1 chr5B.!!$F2 646
15 TraesCS5A01G472900 chr5D 520910144 520910812 668 False 532.7 983 93.723 1 662 2 chr5D.!!$F2 661
16 TraesCS5A01G472900 chr4D 386831319 386831827 508 False 241.0 241 75.956 4 547 1 chr4D.!!$F1 543

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
484 485 0.042361 CTACAGCTACGCCTACGACG 60.042 60.0 0.00 0.0 43.93 5.12 F
649 650 0.179004 TGGCTCCCGAAAGCAAAAGA 60.179 50.0 10.53 0.0 44.35 2.52 F
650 651 0.523519 GGCTCCCGAAAGCAAAAGAG 59.476 55.0 10.53 0.0 44.35 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1461 1763 0.816018 ATTCAAACCCGTGTCGCACA 60.816 50.000 9.95 0.0 33.4 4.57 R
1470 1772 1.922135 CTGGGCACGATTCAAACCCG 61.922 60.000 0.00 0.0 44.0 5.28 R
1991 2418 2.986019 TCCAATTCCCCTTCTCTGTTCA 59.014 45.455 0.00 0.0 0.0 3.18 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
129 130 4.681978 ACGCTGGCGGAGTTCACC 62.682 66.667 18.99 0.00 44.69 4.02
130 131 4.680237 CGCTGGCGGAGTTCACCA 62.680 66.667 7.12 0.00 35.56 4.17
132 133 2.401766 GCTGGCGGAGTTCACCATG 61.402 63.158 0.00 0.00 31.79 3.66
139 140 1.003839 GAGTTCACCATGGACGGCA 60.004 57.895 21.47 0.00 0.00 5.69
140 141 0.605319 GAGTTCACCATGGACGGCAA 60.605 55.000 21.47 0.00 0.00 4.52
158 159 0.892755 AACGACGGCATGGACTTCTA 59.107 50.000 0.00 0.00 0.00 2.10
165 166 1.269166 GCATGGACTTCTACGACGTG 58.731 55.000 11.56 0.72 0.00 4.49
171 172 0.522180 ACTTCTACGACGTGAGCCTG 59.478 55.000 11.56 0.00 0.00 4.85
174 175 1.154016 CTACGACGTGAGCCTGGTG 60.154 63.158 11.56 0.00 0.00 4.17
281 282 2.110213 GTGCGTGGTGGACCTGAA 59.890 61.111 0.00 0.00 36.82 3.02
282 283 2.110213 TGCGTGGTGGACCTGAAC 59.890 61.111 0.00 0.00 36.82 3.18
283 284 3.041940 GCGTGGTGGACCTGAACG 61.042 66.667 8.47 8.47 36.42 3.95
284 285 2.357034 CGTGGTGGACCTGAACGG 60.357 66.667 0.00 0.00 36.82 4.44
285 286 2.668550 GTGGTGGACCTGAACGGC 60.669 66.667 0.00 0.00 36.82 5.68
286 287 4.308458 TGGTGGACCTGAACGGCG 62.308 66.667 4.80 4.80 36.82 6.46
314 315 3.470567 CGACCTGCGCGTGTCTTC 61.471 66.667 21.86 4.76 0.00 2.87
315 316 3.470567 GACCTGCGCGTGTCTTCG 61.471 66.667 18.60 0.00 0.00 3.79
316 317 3.891586 GACCTGCGCGTGTCTTCGA 62.892 63.158 18.60 0.00 0.00 3.71
317 318 3.470567 CCTGCGCGTGTCTTCGAC 61.471 66.667 8.43 0.00 0.00 4.20
318 319 3.816920 CTGCGCGTGTCTTCGACG 61.817 66.667 8.43 0.00 39.87 5.12
319 320 4.316571 TGCGCGTGTCTTCGACGA 62.317 61.111 8.43 0.00 39.21 4.20
320 321 3.813688 GCGCGTGTCTTCGACGAC 61.814 66.667 14.69 14.69 39.21 4.34
321 322 3.512452 CGCGTGTCTTCGACGACG 61.512 66.667 16.23 7.99 39.21 5.12
322 323 3.164011 GCGTGTCTTCGACGACGG 61.164 66.667 16.23 11.88 39.21 4.79
323 324 3.164011 CGTGTCTTCGACGACGGC 61.164 66.667 16.23 10.91 39.21 5.68
324 325 3.164011 GTGTCTTCGACGACGGCG 61.164 66.667 19.07 19.07 44.79 6.46
325 326 4.394078 TGTCTTCGACGACGGCGG 62.394 66.667 24.91 8.30 43.17 6.13
398 399 4.801624 CTGCTGCAGCGGCGAGTA 62.802 66.667 33.24 13.43 45.83 2.59
438 439 4.554363 CCGTCGGCCTACTCGCAG 62.554 72.222 5.79 0.00 0.00 5.18
439 440 3.812019 CGTCGGCCTACTCGCAGT 61.812 66.667 5.79 0.00 0.00 4.40
440 441 2.572284 GTCGGCCTACTCGCAGTT 59.428 61.111 0.00 0.00 0.00 3.16
441 442 1.516603 GTCGGCCTACTCGCAGTTC 60.517 63.158 0.00 0.00 0.00 3.01
442 443 1.677966 TCGGCCTACTCGCAGTTCT 60.678 57.895 0.00 0.00 0.00 3.01
443 444 1.215647 CGGCCTACTCGCAGTTCTT 59.784 57.895 0.00 0.00 0.00 2.52
444 445 0.802607 CGGCCTACTCGCAGTTCTTC 60.803 60.000 0.00 0.00 0.00 2.87
445 446 0.246635 GGCCTACTCGCAGTTCTTCA 59.753 55.000 0.00 0.00 0.00 3.02
446 447 1.337823 GGCCTACTCGCAGTTCTTCAA 60.338 52.381 0.00 0.00 0.00 2.69
447 448 1.996191 GCCTACTCGCAGTTCTTCAAG 59.004 52.381 0.00 0.00 0.00 3.02
448 449 2.352814 GCCTACTCGCAGTTCTTCAAGA 60.353 50.000 0.00 0.00 0.00 3.02
449 450 3.861131 GCCTACTCGCAGTTCTTCAAGAA 60.861 47.826 0.00 0.00 0.00 2.52
456 457 3.058457 GTTCTTCAAGAACGCGTGC 57.942 52.632 14.98 12.39 44.22 5.34
457 458 0.384353 GTTCTTCAAGAACGCGTGCC 60.384 55.000 14.98 8.35 44.22 5.01
458 459 1.503818 TTCTTCAAGAACGCGTGCCC 61.504 55.000 14.98 5.35 0.00 5.36
459 460 3.295228 CTTCAAGAACGCGTGCCCG 62.295 63.158 14.98 4.48 37.07 6.13
478 479 4.208686 GCGCCTACAGCTACGCCT 62.209 66.667 0.00 0.00 45.35 5.52
479 480 2.842256 GCGCCTACAGCTACGCCTA 61.842 63.158 0.00 0.00 45.35 3.93
480 481 1.008767 CGCCTACAGCTACGCCTAC 60.009 63.158 0.00 0.00 40.39 3.18
481 482 1.008767 GCCTACAGCTACGCCTACG 60.009 63.158 0.00 0.00 41.72 3.51
482 483 1.442526 GCCTACAGCTACGCCTACGA 61.443 60.000 0.00 0.00 39.36 3.43
483 484 0.307146 CCTACAGCTACGCCTACGAC 59.693 60.000 0.00 0.00 43.93 4.34
484 485 0.042361 CTACAGCTACGCCTACGACG 60.042 60.000 0.00 0.00 43.93 5.12
485 486 0.460109 TACAGCTACGCCTACGACGA 60.460 55.000 0.00 0.00 43.93 4.20
486 487 1.297451 CAGCTACGCCTACGACGAC 60.297 63.158 0.00 0.00 43.93 4.34
487 488 2.350537 GCTACGCCTACGACGACG 60.351 66.667 5.58 5.58 43.93 5.12
488 489 2.350537 CTACGCCTACGACGACGC 60.351 66.667 7.30 0.00 43.93 5.19
489 490 3.780267 CTACGCCTACGACGACGCC 62.780 68.421 7.30 0.00 43.93 5.68
493 494 3.437795 CCTACGACGACGCCACCT 61.438 66.667 7.30 0.00 43.96 4.00
494 495 2.099831 CTACGACGACGCCACCTC 59.900 66.667 7.30 0.00 43.96 3.85
495 496 3.392595 CTACGACGACGCCACCTCC 62.393 68.421 7.30 0.00 43.96 4.30
498 499 4.736896 GACGACGCCACCTCCACC 62.737 72.222 0.00 0.00 0.00 4.61
500 501 4.003788 CGACGCCACCTCCACCTT 62.004 66.667 0.00 0.00 0.00 3.50
501 502 2.047179 GACGCCACCTCCACCTTC 60.047 66.667 0.00 0.00 0.00 3.46
502 503 2.847234 ACGCCACCTCCACCTTCA 60.847 61.111 0.00 0.00 0.00 3.02
503 504 2.358737 CGCCACCTCCACCTTCAC 60.359 66.667 0.00 0.00 0.00 3.18
504 505 2.034221 GCCACCTCCACCTTCACC 59.966 66.667 0.00 0.00 0.00 4.02
505 506 2.529744 GCCACCTCCACCTTCACCT 61.530 63.158 0.00 0.00 0.00 4.00
506 507 1.376466 CCACCTCCACCTTCACCTG 59.624 63.158 0.00 0.00 0.00 4.00
507 508 1.302832 CACCTCCACCTTCACCTGC 60.303 63.158 0.00 0.00 0.00 4.85
508 509 2.046892 CCTCCACCTTCACCTGCG 60.047 66.667 0.00 0.00 0.00 5.18
509 510 2.743928 CTCCACCTTCACCTGCGC 60.744 66.667 0.00 0.00 0.00 6.09
510 511 4.329545 TCCACCTTCACCTGCGCC 62.330 66.667 4.18 0.00 0.00 6.53
533 534 3.900892 CGTCTCCGCCTACGCCAT 61.901 66.667 0.00 0.00 38.22 4.40
534 535 2.027751 GTCTCCGCCTACGCCATC 59.972 66.667 0.00 0.00 38.22 3.51
535 536 2.441348 TCTCCGCCTACGCCATCA 60.441 61.111 0.00 0.00 38.22 3.07
536 537 2.279517 CTCCGCCTACGCCATCAC 60.280 66.667 0.00 0.00 38.22 3.06
537 538 3.792053 CTCCGCCTACGCCATCACC 62.792 68.421 0.00 0.00 38.22 4.02
538 539 3.849951 CCGCCTACGCCATCACCT 61.850 66.667 0.00 0.00 38.22 4.00
539 540 2.186903 CGCCTACGCCATCACCTT 59.813 61.111 0.00 0.00 0.00 3.50
540 541 1.883084 CGCCTACGCCATCACCTTC 60.883 63.158 0.00 0.00 0.00 3.46
541 542 1.522569 GCCTACGCCATCACCTTCT 59.477 57.895 0.00 0.00 0.00 2.85
542 543 0.811616 GCCTACGCCATCACCTTCTG 60.812 60.000 0.00 0.00 0.00 3.02
543 544 0.811616 CCTACGCCATCACCTTCTGC 60.812 60.000 0.00 0.00 0.00 4.26
544 545 0.811616 CTACGCCATCACCTTCTGCC 60.812 60.000 0.00 0.00 0.00 4.85
545 546 2.252072 TACGCCATCACCTTCTGCCC 62.252 60.000 0.00 0.00 0.00 5.36
546 547 2.440980 GCCATCACCTTCTGCCCC 60.441 66.667 0.00 0.00 0.00 5.80
547 548 3.089838 CCATCACCTTCTGCCCCA 58.910 61.111 0.00 0.00 0.00 4.96
548 549 1.077212 CCATCACCTTCTGCCCCAG 60.077 63.158 0.00 0.00 0.00 4.45
549 550 1.751927 CATCACCTTCTGCCCCAGC 60.752 63.158 0.00 0.00 40.48 4.85
551 552 2.490270 ATCACCTTCTGCCCCAGCAC 62.490 60.000 0.00 0.00 46.52 4.40
552 553 3.971702 ACCTTCTGCCCCAGCACC 61.972 66.667 0.00 0.00 46.52 5.01
553 554 3.970410 CCTTCTGCCCCAGCACCA 61.970 66.667 0.00 0.00 46.52 4.17
554 555 2.674380 CTTCTGCCCCAGCACCAC 60.674 66.667 0.00 0.00 46.52 4.16
555 556 4.284550 TTCTGCCCCAGCACCACC 62.285 66.667 0.00 0.00 46.52 4.61
568 569 3.766691 CCACCAGGTACCGTCCGG 61.767 72.222 6.18 8.62 42.03 5.14
584 585 4.112341 GGTCCGACCTCCGACGTG 62.112 72.222 10.59 0.00 41.76 4.49
585 586 3.360340 GTCCGACCTCCGACGTGT 61.360 66.667 0.00 0.00 41.76 4.49
586 587 3.052082 TCCGACCTCCGACGTGTC 61.052 66.667 0.00 0.00 41.76 3.67
595 596 2.705220 CGACGTGTCGCCGAGATA 59.295 61.111 9.68 0.00 46.50 1.98
596 597 1.650536 CGACGTGTCGCCGAGATAC 60.651 63.158 9.68 0.00 46.50 2.24
597 598 1.298190 GACGTGTCGCCGAGATACC 60.298 63.158 0.00 0.00 37.65 2.73
598 599 1.712977 GACGTGTCGCCGAGATACCT 61.713 60.000 0.00 0.00 37.65 3.08
599 600 0.462581 ACGTGTCGCCGAGATACCTA 60.463 55.000 0.00 0.00 37.65 3.08
600 601 0.873054 CGTGTCGCCGAGATACCTAT 59.127 55.000 0.00 0.00 37.65 2.57
601 602 1.266175 CGTGTCGCCGAGATACCTATT 59.734 52.381 0.00 0.00 37.65 1.73
602 603 2.662700 GTGTCGCCGAGATACCTATTG 58.337 52.381 0.00 0.00 35.27 1.90
603 604 2.034305 GTGTCGCCGAGATACCTATTGT 59.966 50.000 0.00 0.00 35.27 2.71
604 605 2.292569 TGTCGCCGAGATACCTATTGTC 59.707 50.000 0.00 0.00 0.00 3.18
605 606 2.292569 GTCGCCGAGATACCTATTGTCA 59.707 50.000 0.00 0.00 0.00 3.58
606 607 2.953648 TCGCCGAGATACCTATTGTCAA 59.046 45.455 0.00 0.00 0.00 3.18
607 608 3.382227 TCGCCGAGATACCTATTGTCAAA 59.618 43.478 0.00 0.00 0.00 2.69
608 609 3.489785 CGCCGAGATACCTATTGTCAAAC 59.510 47.826 0.00 0.00 0.00 2.93
609 610 3.808174 GCCGAGATACCTATTGTCAAACC 59.192 47.826 0.00 0.00 0.00 3.27
610 611 4.682320 GCCGAGATACCTATTGTCAAACCA 60.682 45.833 0.00 0.00 0.00 3.67
611 612 5.424757 CCGAGATACCTATTGTCAAACCAA 58.575 41.667 0.00 0.00 0.00 3.67
612 613 5.878116 CCGAGATACCTATTGTCAAACCAAA 59.122 40.000 0.00 0.00 0.00 3.28
613 614 6.373216 CCGAGATACCTATTGTCAAACCAAAA 59.627 38.462 0.00 0.00 0.00 2.44
614 615 7.414098 CCGAGATACCTATTGTCAAACCAAAAG 60.414 40.741 0.00 0.00 0.00 2.27
615 616 7.333423 CGAGATACCTATTGTCAAACCAAAAGA 59.667 37.037 0.00 0.00 0.00 2.52
616 617 8.336801 AGATACCTATTGTCAAACCAAAAGAC 57.663 34.615 0.00 0.00 0.00 3.01
617 618 7.942341 AGATACCTATTGTCAAACCAAAAGACA 59.058 33.333 0.00 0.00 40.24 3.41
622 623 3.843999 TGTCAAACCAAAAGACAACTGC 58.156 40.909 0.00 0.00 39.15 4.40
623 624 3.186909 GTCAAACCAAAAGACAACTGCC 58.813 45.455 0.00 0.00 32.68 4.85
624 625 3.096092 TCAAACCAAAAGACAACTGCCT 58.904 40.909 0.00 0.00 0.00 4.75
625 626 3.513515 TCAAACCAAAAGACAACTGCCTT 59.486 39.130 0.00 0.00 0.00 4.35
626 627 4.020662 TCAAACCAAAAGACAACTGCCTTT 60.021 37.500 0.00 0.00 34.39 3.11
627 628 3.801114 ACCAAAAGACAACTGCCTTTC 57.199 42.857 0.00 0.00 32.01 2.62
628 629 2.430694 ACCAAAAGACAACTGCCTTTCC 59.569 45.455 0.00 0.00 32.01 3.13
629 630 2.430332 CCAAAAGACAACTGCCTTTCCA 59.570 45.455 0.00 0.00 32.01 3.53
630 631 3.070015 CCAAAAGACAACTGCCTTTCCAT 59.930 43.478 0.00 0.00 32.01 3.41
631 632 4.053295 CAAAAGACAACTGCCTTTCCATG 58.947 43.478 0.00 0.00 32.01 3.66
632 633 1.915141 AGACAACTGCCTTTCCATGG 58.085 50.000 4.97 4.97 0.00 3.66
638 639 2.830370 GCCTTTCCATGGCTCCCG 60.830 66.667 6.96 0.00 46.38 5.14
639 640 2.998097 CCTTTCCATGGCTCCCGA 59.002 61.111 6.96 0.00 0.00 5.14
640 641 1.302949 CCTTTCCATGGCTCCCGAA 59.697 57.895 6.96 0.00 0.00 4.30
641 642 0.323360 CCTTTCCATGGCTCCCGAAA 60.323 55.000 6.96 0.00 0.00 3.46
642 643 1.098050 CTTTCCATGGCTCCCGAAAG 58.902 55.000 6.96 6.91 36.36 2.62
643 644 0.965363 TTTCCATGGCTCCCGAAAGC 60.965 55.000 6.96 0.82 41.73 3.51
644 645 2.045045 CCATGGCTCCCGAAAGCA 60.045 61.111 0.00 0.00 44.35 3.91
645 646 1.678635 CCATGGCTCCCGAAAGCAA 60.679 57.895 0.00 0.38 44.35 3.91
646 647 1.250154 CCATGGCTCCCGAAAGCAAA 61.250 55.000 0.00 0.06 44.35 3.68
647 648 0.602562 CATGGCTCCCGAAAGCAAAA 59.397 50.000 10.53 0.00 44.35 2.44
648 649 0.890683 ATGGCTCCCGAAAGCAAAAG 59.109 50.000 10.53 0.00 44.35 2.27
649 650 0.179004 TGGCTCCCGAAAGCAAAAGA 60.179 50.000 10.53 0.00 44.35 2.52
650 651 0.523519 GGCTCCCGAAAGCAAAAGAG 59.476 55.000 10.53 0.00 44.35 2.85
651 652 1.523758 GCTCCCGAAAGCAAAAGAGA 58.476 50.000 4.37 0.00 42.05 3.10
652 653 1.880027 GCTCCCGAAAGCAAAAGAGAA 59.120 47.619 4.37 0.00 42.05 2.87
653 654 2.095516 GCTCCCGAAAGCAAAAGAGAAG 60.096 50.000 4.37 0.00 42.05 2.85
654 655 1.880027 TCCCGAAAGCAAAAGAGAAGC 59.120 47.619 0.00 0.00 0.00 3.86
655 656 1.608590 CCCGAAAGCAAAAGAGAAGCA 59.391 47.619 0.00 0.00 0.00 3.91
656 657 2.034558 CCCGAAAGCAAAAGAGAAGCAA 59.965 45.455 0.00 0.00 0.00 3.91
657 658 3.045688 CCGAAAGCAAAAGAGAAGCAAC 58.954 45.455 0.00 0.00 0.00 4.17
877 878 5.474578 TCTCACAGAATTGTAACTGCTCT 57.525 39.130 0.00 0.00 37.61 4.09
1461 1763 2.683933 CCTCTGCCCCCGTACTGT 60.684 66.667 0.00 0.00 0.00 3.55
1467 1769 3.687102 CCCCCGTACTGTGTGCGA 61.687 66.667 9.53 0.00 43.77 5.10
1468 1770 2.431942 CCCCGTACTGTGTGCGAC 60.432 66.667 9.53 0.00 43.77 5.19
1469 1771 2.337170 CCCGTACTGTGTGCGACA 59.663 61.111 9.53 0.00 43.77 4.35
1572 1874 0.398522 TCATGCCTCCTGGATACGGT 60.399 55.000 0.00 0.00 43.49 4.83
1991 2418 0.108138 GCGGTGCTGAGTCCAAGTAT 60.108 55.000 0.00 0.00 0.00 2.12
2642 3108 5.194473 TCCACTCTTACTGTGAGGTCTAT 57.806 43.478 0.00 0.00 37.60 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 113 4.681978 GGTGAACTCCGCCAGCGT 62.682 66.667 11.55 0.00 44.82 5.07
119 120 1.447838 CCGTCCATGGTGAACTCCG 60.448 63.158 12.58 4.09 0.00 4.63
129 130 3.487202 CCGTCGTTGCCGTCCATG 61.487 66.667 0.00 0.00 35.01 3.66
139 140 0.892755 TAGAAGTCCATGCCGTCGTT 59.107 50.000 0.00 0.00 0.00 3.85
140 141 0.172803 GTAGAAGTCCATGCCGTCGT 59.827 55.000 0.00 0.00 0.00 4.34
143 144 0.172803 GTCGTAGAAGTCCATGCCGT 59.827 55.000 0.00 0.00 39.69 5.68
158 159 3.991051 CCACCAGGCTCACGTCGT 61.991 66.667 0.00 0.00 0.00 4.34
165 166 2.682494 TACCCGTCCACCAGGCTC 60.682 66.667 0.00 0.00 33.74 4.70
171 172 1.004200 CAGGTTGTACCCGTCCACC 60.004 63.158 0.00 0.00 39.75 4.61
174 175 2.046604 GGCAGGTTGTACCCGTCC 60.047 66.667 0.00 0.00 39.75 4.79
180 181 1.369091 CCAGCATCGGCAGGTTGTAC 61.369 60.000 0.00 0.00 41.48 2.90
263 264 3.469863 TTCAGGTCCACCACGCACC 62.470 63.158 0.00 0.00 38.89 5.01
264 265 2.110213 TTCAGGTCCACCACGCAC 59.890 61.111 0.00 0.00 38.89 5.34
265 266 2.110213 GTTCAGGTCCACCACGCA 59.890 61.111 0.00 0.00 38.89 5.24
266 267 3.041940 CGTTCAGGTCCACCACGC 61.042 66.667 0.00 0.00 38.89 5.34
267 268 2.357034 CCGTTCAGGTCCACCACG 60.357 66.667 0.00 0.00 38.89 4.94
268 269 2.668550 GCCGTTCAGGTCCACCAC 60.669 66.667 0.00 0.00 43.70 4.16
269 270 4.308458 CGCCGTTCAGGTCCACCA 62.308 66.667 0.00 0.00 43.70 4.17
297 298 3.470567 GAAGACACGCGCAGGTCG 61.471 66.667 19.01 0.41 39.01 4.79
298 299 3.470567 CGAAGACACGCGCAGGTC 61.471 66.667 17.88 17.88 0.00 3.85
299 300 3.973516 TCGAAGACACGCGCAGGT 61.974 61.111 5.73 3.95 0.00 4.00
363 364 4.424566 TACTGCGCCGTCCCGAAC 62.425 66.667 8.05 0.00 0.00 3.95
364 365 4.424566 GTACTGCGCCGTCCCGAA 62.425 66.667 8.05 0.00 0.00 4.30
379 380 4.801624 CTCGCCGCTGCAGCAGTA 62.802 66.667 36.03 18.02 42.21 2.74
381 382 4.801624 TACTCGCCGCTGCAGCAG 62.802 66.667 36.03 27.55 42.21 4.24
421 422 4.554363 CTGCGAGTAGGCCGACGG 62.554 72.222 10.29 10.29 0.00 4.79
422 423 3.338126 AACTGCGAGTAGGCCGACG 62.338 63.158 10.60 9.63 0.00 5.12
423 424 1.516603 GAACTGCGAGTAGGCCGAC 60.517 63.158 8.12 8.12 0.00 4.79
424 425 1.248785 AAGAACTGCGAGTAGGCCGA 61.249 55.000 0.00 0.00 0.00 5.54
425 426 0.802607 GAAGAACTGCGAGTAGGCCG 60.803 60.000 0.00 0.00 0.00 6.13
426 427 0.246635 TGAAGAACTGCGAGTAGGCC 59.753 55.000 0.00 0.00 0.00 5.19
427 428 1.996191 CTTGAAGAACTGCGAGTAGGC 59.004 52.381 0.00 0.00 0.00 3.93
428 429 3.577649 TCTTGAAGAACTGCGAGTAGG 57.422 47.619 0.00 0.00 0.00 3.18
439 440 1.503818 GGGCACGCGTTCTTGAAGAA 61.504 55.000 10.22 3.02 0.00 2.52
440 441 1.959226 GGGCACGCGTTCTTGAAGA 60.959 57.895 10.22 0.00 0.00 2.87
441 442 2.556287 GGGCACGCGTTCTTGAAG 59.444 61.111 10.22 0.00 0.00 3.02
442 443 3.342627 CGGGCACGCGTTCTTGAA 61.343 61.111 10.22 0.00 0.00 2.69
476 477 3.392595 GAGGTGGCGTCGTCGTAGG 62.393 68.421 3.66 0.00 39.49 3.18
477 478 2.099831 GAGGTGGCGTCGTCGTAG 59.900 66.667 3.66 0.00 39.49 3.51
478 479 3.434319 GGAGGTGGCGTCGTCGTA 61.434 66.667 3.66 0.00 39.49 3.43
481 482 4.736896 GGTGGAGGTGGCGTCGTC 62.737 72.222 0.00 0.00 0.00 4.20
483 484 3.934391 GAAGGTGGAGGTGGCGTCG 62.934 68.421 0.00 0.00 0.00 5.12
484 485 2.047179 GAAGGTGGAGGTGGCGTC 60.047 66.667 0.00 0.00 0.00 5.19
485 486 2.847234 TGAAGGTGGAGGTGGCGT 60.847 61.111 0.00 0.00 0.00 5.68
486 487 2.358737 GTGAAGGTGGAGGTGGCG 60.359 66.667 0.00 0.00 0.00 5.69
487 488 2.034221 GGTGAAGGTGGAGGTGGC 59.966 66.667 0.00 0.00 0.00 5.01
488 489 1.376466 CAGGTGAAGGTGGAGGTGG 59.624 63.158 0.00 0.00 0.00 4.61
489 490 1.302832 GCAGGTGAAGGTGGAGGTG 60.303 63.158 0.00 0.00 0.00 4.00
490 491 2.883828 CGCAGGTGAAGGTGGAGGT 61.884 63.158 0.00 0.00 0.00 3.85
491 492 2.046892 CGCAGGTGAAGGTGGAGG 60.047 66.667 0.00 0.00 0.00 4.30
492 493 2.743928 GCGCAGGTGAAGGTGGAG 60.744 66.667 0.30 0.00 0.00 3.86
493 494 4.329545 GGCGCAGGTGAAGGTGGA 62.330 66.667 10.83 0.00 0.00 4.02
524 525 0.811616 GCAGAAGGTGATGGCGTAGG 60.812 60.000 0.00 0.00 0.00 3.18
525 526 0.811616 GGCAGAAGGTGATGGCGTAG 60.812 60.000 0.00 0.00 31.92 3.51
526 527 1.220749 GGCAGAAGGTGATGGCGTA 59.779 57.895 0.00 0.00 31.92 4.42
527 528 2.045926 GGCAGAAGGTGATGGCGT 60.046 61.111 0.00 0.00 31.92 5.68
528 529 2.825836 GGGCAGAAGGTGATGGCG 60.826 66.667 0.00 0.00 42.55 5.69
529 530 2.440980 GGGGCAGAAGGTGATGGC 60.441 66.667 0.00 0.00 41.01 4.40
530 531 1.077212 CTGGGGCAGAAGGTGATGG 60.077 63.158 0.00 0.00 32.44 3.51
531 532 1.751927 GCTGGGGCAGAAGGTGATG 60.752 63.158 0.00 0.00 38.54 3.07
532 533 2.233566 TGCTGGGGCAGAAGGTGAT 61.234 57.895 0.00 0.00 44.28 3.06
533 534 2.853542 TGCTGGGGCAGAAGGTGA 60.854 61.111 0.00 0.00 44.28 4.02
551 552 3.766691 CCGGACGGTACCTGGTGG 61.767 72.222 10.23 3.00 39.83 4.61
567 568 4.112341 CACGTCGGAGGTCGGACC 62.112 72.222 19.61 19.61 41.41 4.46
568 569 3.319926 GACACGTCGGAGGTCGGAC 62.320 68.421 0.00 0.00 41.15 4.79
569 570 3.052082 GACACGTCGGAGGTCGGA 61.052 66.667 0.00 0.00 39.77 4.55
579 580 1.298190 GGTATCTCGGCGACACGTC 60.298 63.158 4.99 0.00 34.94 4.34
580 581 0.462581 TAGGTATCTCGGCGACACGT 60.463 55.000 4.99 8.61 34.94 4.49
581 582 0.873054 ATAGGTATCTCGGCGACACG 59.127 55.000 4.99 0.00 0.00 4.49
582 583 2.034305 ACAATAGGTATCTCGGCGACAC 59.966 50.000 4.99 4.11 0.00 3.67
583 584 2.292569 GACAATAGGTATCTCGGCGACA 59.707 50.000 4.99 0.00 0.00 4.35
584 585 2.292569 TGACAATAGGTATCTCGGCGAC 59.707 50.000 4.99 0.00 0.00 5.19
585 586 2.578786 TGACAATAGGTATCTCGGCGA 58.421 47.619 10.14 10.14 0.00 5.54
586 587 3.364889 TTGACAATAGGTATCTCGGCG 57.635 47.619 0.00 0.00 0.00 6.46
587 588 3.808174 GGTTTGACAATAGGTATCTCGGC 59.192 47.826 0.00 0.00 0.00 5.54
588 589 5.018539 TGGTTTGACAATAGGTATCTCGG 57.981 43.478 0.00 0.00 0.00 4.63
589 590 6.978343 TTTGGTTTGACAATAGGTATCTCG 57.022 37.500 0.00 0.00 0.00 4.04
590 591 8.451748 GTCTTTTGGTTTGACAATAGGTATCTC 58.548 37.037 0.00 0.00 32.50 2.75
591 592 7.942341 TGTCTTTTGGTTTGACAATAGGTATCT 59.058 33.333 0.00 0.00 37.71 1.98
592 593 8.106247 TGTCTTTTGGTTTGACAATAGGTATC 57.894 34.615 0.00 0.00 37.71 2.24
593 594 8.472007 TTGTCTTTTGGTTTGACAATAGGTAT 57.528 30.769 0.00 0.00 43.15 2.73
594 595 7.883391 TTGTCTTTTGGTTTGACAATAGGTA 57.117 32.000 0.00 0.00 43.15 3.08
595 596 6.783708 TTGTCTTTTGGTTTGACAATAGGT 57.216 33.333 0.00 0.00 43.15 3.08
600 601 4.241681 GCAGTTGTCTTTTGGTTTGACAA 58.758 39.130 0.00 0.00 44.96 3.18
601 602 3.367910 GGCAGTTGTCTTTTGGTTTGACA 60.368 43.478 0.00 0.00 38.71 3.58
602 603 3.119137 AGGCAGTTGTCTTTTGGTTTGAC 60.119 43.478 0.00 0.00 0.00 3.18
603 604 3.096092 AGGCAGTTGTCTTTTGGTTTGA 58.904 40.909 0.00 0.00 0.00 2.69
604 605 3.525268 AGGCAGTTGTCTTTTGGTTTG 57.475 42.857 0.00 0.00 0.00 2.93
605 606 4.551702 AAAGGCAGTTGTCTTTTGGTTT 57.448 36.364 5.92 0.00 46.68 3.27
612 613 2.242043 CCATGGAAAGGCAGTTGTCTT 58.758 47.619 5.56 0.00 42.58 3.01
613 614 1.915141 CCATGGAAAGGCAGTTGTCT 58.085 50.000 5.56 0.00 0.00 3.41
622 623 0.323360 TTTCGGGAGCCATGGAAAGG 60.323 55.000 18.40 0.00 0.00 3.11
623 624 1.098050 CTTTCGGGAGCCATGGAAAG 58.902 55.000 18.40 11.34 39.33 2.62
624 625 0.965363 GCTTTCGGGAGCCATGGAAA 60.965 55.000 18.40 4.82 36.66 3.13
625 626 1.378514 GCTTTCGGGAGCCATGGAA 60.379 57.895 18.40 0.00 36.66 3.53
626 627 2.135903 TTGCTTTCGGGAGCCATGGA 62.136 55.000 18.40 0.00 42.01 3.41
627 628 1.250154 TTTGCTTTCGGGAGCCATGG 61.250 55.000 7.63 7.63 42.01 3.66
628 629 0.602562 TTTTGCTTTCGGGAGCCATG 59.397 50.000 8.18 0.00 42.01 3.66
629 630 0.890683 CTTTTGCTTTCGGGAGCCAT 59.109 50.000 8.18 0.00 42.01 4.40
630 631 0.179004 TCTTTTGCTTTCGGGAGCCA 60.179 50.000 8.18 0.00 42.01 4.75
631 632 0.523519 CTCTTTTGCTTTCGGGAGCC 59.476 55.000 8.18 0.00 42.01 4.70
632 633 1.523758 TCTCTTTTGCTTTCGGGAGC 58.476 50.000 4.29 4.29 43.00 4.70
633 634 2.095516 GCTTCTCTTTTGCTTTCGGGAG 60.096 50.000 0.00 0.00 0.00 4.30
634 635 1.880027 GCTTCTCTTTTGCTTTCGGGA 59.120 47.619 0.00 0.00 0.00 5.14
635 636 1.608590 TGCTTCTCTTTTGCTTTCGGG 59.391 47.619 0.00 0.00 0.00 5.14
636 637 3.045688 GTTGCTTCTCTTTTGCTTTCGG 58.954 45.455 0.00 0.00 0.00 4.30
637 638 3.957468 AGTTGCTTCTCTTTTGCTTTCG 58.043 40.909 0.00 0.00 0.00 3.46
638 639 6.653273 AAAAGTTGCTTCTCTTTTGCTTTC 57.347 33.333 0.00 0.00 40.73 2.62
639 640 6.427853 ACAAAAAGTTGCTTCTCTTTTGCTTT 59.572 30.769 17.17 0.00 41.17 3.51
640 641 5.934043 ACAAAAAGTTGCTTCTCTTTTGCTT 59.066 32.000 17.17 0.00 41.17 3.91
641 642 5.482006 ACAAAAAGTTGCTTCTCTTTTGCT 58.518 33.333 17.17 9.87 41.17 3.91
642 643 5.784750 ACAAAAAGTTGCTTCTCTTTTGC 57.215 34.783 17.17 0.00 41.17 3.68
643 644 7.759433 TCCTAACAAAAAGTTGCTTCTCTTTTG 59.241 33.333 16.49 16.49 41.17 2.44
644 645 7.836842 TCCTAACAAAAAGTTGCTTCTCTTTT 58.163 30.769 0.00 0.00 42.99 2.27
645 646 7.404671 TCCTAACAAAAAGTTGCTTCTCTTT 57.595 32.000 0.00 0.00 41.50 2.52
646 647 7.404671 TTCCTAACAAAAAGTTGCTTCTCTT 57.595 32.000 0.00 0.00 41.50 2.85
647 648 7.588497 ATTCCTAACAAAAAGTTGCTTCTCT 57.412 32.000 0.00 0.00 41.50 3.10
648 649 8.784043 TCTATTCCTAACAAAAAGTTGCTTCTC 58.216 33.333 0.00 0.00 41.50 2.87
649 650 8.691661 TCTATTCCTAACAAAAAGTTGCTTCT 57.308 30.769 0.00 0.00 41.50 2.85
650 651 9.914131 ATTCTATTCCTAACAAAAAGTTGCTTC 57.086 29.630 0.00 0.00 41.50 3.86
1461 1763 0.816018 ATTCAAACCCGTGTCGCACA 60.816 50.000 9.95 0.00 33.40 4.57
1469 1771 1.969589 GGGCACGATTCAAACCCGT 60.970 57.895 0.00 0.00 36.95 5.28
1470 1772 1.922135 CTGGGCACGATTCAAACCCG 61.922 60.000 0.00 0.00 44.00 5.28
1991 2418 2.986019 TCCAATTCCCCTTCTCTGTTCA 59.014 45.455 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.