Multiple sequence alignment - TraesCS1A01G189400

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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 TraesCS1A01G189400 chr1A 100.000 2724 0 0 1 2724 342598058 342595335 0.000000e+00 5031
1 TraesCS1A01G189400 chr6B 97.578 2147 42 4 582 2724 37126719 37124579 0.000000e+00 3668
2 TraesCS1A01G189400 chr6B 91.224 433 14 4 1 422 37127135 37126716 3.940000e-158 568
3 TraesCS1A01G189400 chr6B 97.661 171 4 0 417 587 703948893 703948723 7.380000e-76 294
4 TraesCS1A01G189400 chrUn 98.229 1468 17 3 1260 2724 305968983 305967522 0.000000e+00 2558
5 TraesCS1A01G189400 chrUn 98.229 1468 17 3 1260 2724 344607958 344609419 0.000000e+00 2558
6 TraesCS1A01G189400 chrUn 98.567 349 5 0 1 349 305965171 305964823 3.850000e-173 617
7 TraesCS1A01G189400 chr3B 92.332 1265 82 12 623 1886 709749795 709751045 0.000000e+00 1784
8 TraesCS1A01G189400 chr3B 96.067 178 5 2 417 593 732837622 732837798 3.430000e-74 289
9 TraesCS1A01G189400 chr3B 95.055 182 7 2 406 585 160359000 160359181 4.440000e-73 285
10 TraesCS1A01G189400 chr3B 93.194 191 9 3 420 609 599893746 599893933 7.430000e-71 278
11 TraesCS1A01G189400 chr3B 90.576 191 17 1 1 191 709740264 709740453 4.500000e-63 252
12 TraesCS1A01G189400 chr5B 85.987 1206 137 18 691 1886 447400078 447398895 0.000000e+00 1262
13 TraesCS1A01G189400 chr5B 88.800 500 53 3 2227 2724 447398699 447398201 6.450000e-171 610
14 TraesCS1A01G189400 chr5B 88.778 499 54 2 2227 2724 680793335 680792838 6.450000e-171 610
15 TraesCS1A01G189400 chr5B 98.204 167 3 0 427 593 217679210 217679044 2.650000e-75 292
16 TraesCS1A01G189400 chr5B 96.571 175 6 0 412 586 200416055 200415881 9.540000e-75 291
17 TraesCS1A01G189400 chr2D 85.762 899 95 14 833 1724 651035418 651036290 0.000000e+00 920
18 TraesCS1A01G189400 chr2D 84.897 629 78 10 2112 2724 651036513 651037140 1.070000e-173 619
19 TraesCS1A01G189400 chr6A 81.021 1038 150 38 1020 2040 16623133 16622126 0.000000e+00 782
20 TraesCS1A01G189400 chr6A 88.153 498 59 0 2227 2724 16622073 16621576 6.490000e-166 593
21 TraesCS1A01G189400 chr6A 90.029 341 32 2 684 1024 16628026 16627688 8.950000e-120 440
22 TraesCS1A01G189400 chr6A 85.135 148 11 2 272 408 562296389 562296242 1.020000e-29 141
23 TraesCS1A01G189400 chr3A 98.567 349 5 0 1 349 237061546 237061198 3.850000e-173 617
24 TraesCS1A01G189400 chr3A 76.931 997 177 41 729 1700 577245898 577246866 4.020000e-143 518
25 TraesCS1A01G189400 chr2B 77.455 998 170 41 729 1700 776589577 776590545 1.840000e-151 545
26 TraesCS1A01G189400 chr2B 81.048 496 86 8 2233 2724 776590800 776591291 3.290000e-104 388
27 TraesCS1A01G189400 chr2B 98.810 168 2 0 421 588 182011274 182011107 1.590000e-77 300
28 TraesCS1A01G189400 chr3D 77.232 997 174 39 729 1700 41716826 41717794 3.990000e-148 534
29 TraesCS1A01G189400 chr3D 81.452 496 84 8 2233 2724 41718049 41718540 1.520000e-107 399
30 TraesCS1A01G189400 chr4D 77.131 997 172 43 729 1700 40415548 40414583 6.680000e-146 527
31 TraesCS1A01G189400 chr5D 76.196 920 168 36 805 1699 502406062 502405169 3.220000e-119 438
32 TraesCS1A01G189400 chr6D 78.978 509 87 15 805 1307 14145913 14146407 2.020000e-86 329
33 TraesCS1A01G189400 chr7B 98.214 168 3 0 418 585 707639860 707640027 7.380000e-76 294
34 TraesCS1A01G189400 chr7B 84.459 148 12 8 272 409 500239155 500239301 4.730000e-28 135
35 TraesCS1A01G189400 chr7B 93.056 72 4 1 304 375 180033817 180033887 1.330000e-18 104
36 TraesCS1A01G189400 chr4B 97.093 172 4 1 414 585 492223130 492222960 3.430000e-74 289
37 TraesCS1A01G189400 chr7D 91.743 109 8 1 272 379 476066100 476066208 1.690000e-32 150
38 TraesCS1A01G189400 chr2A 82.313 147 15 5 273 408 676374666 676374812 1.710000e-22 117


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 TraesCS1A01G189400 chr1A 342595335 342598058 2723 True 5031.0 5031 100.0000 1 2724 1 chr1A.!!$R1 2723
1 TraesCS1A01G189400 chr6B 37124579 37127135 2556 True 2118.0 3668 94.4010 1 2724 2 chr6B.!!$R2 2723
2 TraesCS1A01G189400 chrUn 344607958 344609419 1461 False 2558.0 2558 98.2290 1260 2724 1 chrUn.!!$F1 1464
3 TraesCS1A01G189400 chrUn 305964823 305968983 4160 True 1587.5 2558 98.3980 1 2724 2 chrUn.!!$R1 2723
4 TraesCS1A01G189400 chr3B 709749795 709751045 1250 False 1784.0 1784 92.3320 623 1886 1 chr3B.!!$F4 1263
5 TraesCS1A01G189400 chr5B 447398201 447400078 1877 True 936.0 1262 87.3935 691 2724 2 chr5B.!!$R4 2033
6 TraesCS1A01G189400 chr2D 651035418 651037140 1722 False 769.5 920 85.3295 833 2724 2 chr2D.!!$F1 1891
7 TraesCS1A01G189400 chr6A 16621576 16623133 1557 True 687.5 782 84.5870 1020 2724 2 chr6A.!!$R3 1704
8 TraesCS1A01G189400 chr3A 577245898 577246866 968 False 518.0 518 76.9310 729 1700 1 chr3A.!!$F1 971
9 TraesCS1A01G189400 chr2B 776589577 776591291 1714 False 466.5 545 79.2515 729 2724 2 chr2B.!!$F1 1995
10 TraesCS1A01G189400 chr3D 41716826 41718540 1714 False 466.5 534 79.3420 729 2724 2 chr3D.!!$F1 1995
11 TraesCS1A01G189400 chr4D 40414583 40415548 965 True 527.0 527 77.1310 729 1700 1 chr4D.!!$R1 971
12 TraesCS1A01G189400 chr5D 502405169 502406062 893 True 438.0 438 76.1960 805 1699 1 chr5D.!!$R1 894

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
356 357 0.931202 CCAATGTATGCGCGCATGTG 60.931 55.0 46.79 35.81 37.82 3.21 F
908 922 2.712057 AAGAAAGCATGGCGTGAAAG 57.288 45.0 11.71 0.00 0.00 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 1478 1.599071 GCTTTTGCCCTTTTGAAGTGC 59.401 47.619 0.0 0.0 40.15 4.40 R
2664 2775 2.940994 TCGTTGGGAACTTCATTGGA 57.059 45.000 0.0 0.0 0.00 3.53 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
42 43 7.675062 AGCCTACAGGTAAGATTCATAATCAG 58.325 38.462 2.74 0.00 37.69 2.90
64 65 8.087982 TCAGAAACTGATGAACATACTCAAAC 57.912 34.615 0.00 0.00 35.39 2.93
65 66 7.933577 TCAGAAACTGATGAACATACTCAAACT 59.066 33.333 0.00 0.00 35.39 2.66
66 67 8.562892 CAGAAACTGATGAACATACTCAAACTT 58.437 33.333 0.00 0.00 32.44 2.66
67 68 9.778741 AGAAACTGATGAACATACTCAAACTTA 57.221 29.630 0.00 0.00 0.00 2.24
148 149 4.757149 AGTTCTGCCAACATGTCTTTACTC 59.243 41.667 0.00 0.00 0.00 2.59
243 244 9.997482 TCAGTACAAAGTTGACAATTCTTTTAC 57.003 29.630 0.00 7.65 30.41 2.01
263 264 6.605471 TTACAGATGCGATACCCTTGATAT 57.395 37.500 0.00 0.00 0.00 1.63
304 305 2.664185 CGATCCTGCTGCCCGATG 60.664 66.667 0.00 0.00 0.00 3.84
356 357 0.931202 CCAATGTATGCGCGCATGTG 60.931 55.000 46.79 35.81 37.82 3.21
417 429 8.147642 GTGTATAGCACAGCTCTATTGATTTT 57.852 34.615 0.00 0.00 46.91 1.82
418 430 9.261180 GTGTATAGCACAGCTCTATTGATTTTA 57.739 33.333 0.00 0.00 46.91 1.52
419 431 9.481340 TGTATAGCACAGCTCTATTGATTTTAG 57.519 33.333 0.00 0.00 40.44 1.85
420 432 9.482627 GTATAGCACAGCTCTATTGATTTTAGT 57.517 33.333 0.00 0.00 40.44 2.24
422 434 7.778470 AGCACAGCTCTATTGATTTTAGTAC 57.222 36.000 0.00 0.00 30.62 2.73
423 435 7.560368 AGCACAGCTCTATTGATTTTAGTACT 58.440 34.615 0.00 0.00 30.62 2.73
424 436 7.708752 AGCACAGCTCTATTGATTTTAGTACTC 59.291 37.037 0.00 0.00 30.62 2.59
425 437 7.708752 GCACAGCTCTATTGATTTTAGTACTCT 59.291 37.037 0.00 0.00 0.00 3.24
426 438 9.243637 CACAGCTCTATTGATTTTAGTACTCTC 57.756 37.037 0.00 0.00 0.00 3.20
427 439 9.196139 ACAGCTCTATTGATTTTAGTACTCTCT 57.804 33.333 0.00 0.00 0.00 3.10
428 440 9.677567 CAGCTCTATTGATTTTAGTACTCTCTC 57.322 37.037 0.00 0.00 0.00 3.20
429 441 8.856103 AGCTCTATTGATTTTAGTACTCTCTCC 58.144 37.037 0.00 0.00 0.00 3.71
430 442 7.806014 GCTCTATTGATTTTAGTACTCTCTCCG 59.194 40.741 0.00 0.00 0.00 4.63
431 443 8.749026 TCTATTGATTTTAGTACTCTCTCCGT 57.251 34.615 0.00 0.00 0.00 4.69
432 444 9.186837 TCTATTGATTTTAGTACTCTCTCCGTT 57.813 33.333 0.00 0.00 0.00 4.44
433 445 9.453325 CTATTGATTTTAGTACTCTCTCCGTTC 57.547 37.037 0.00 0.00 0.00 3.95
434 446 6.205101 TGATTTTAGTACTCTCTCCGTTCC 57.795 41.667 0.00 0.00 0.00 3.62
435 447 5.950549 TGATTTTAGTACTCTCTCCGTTCCT 59.049 40.000 0.00 0.00 0.00 3.36
436 448 7.114754 TGATTTTAGTACTCTCTCCGTTCCTA 58.885 38.462 0.00 0.00 0.00 2.94
437 449 7.613022 TGATTTTAGTACTCTCTCCGTTCCTAA 59.387 37.037 0.00 0.00 0.00 2.69
438 450 7.765695 TTTTAGTACTCTCTCCGTTCCTAAA 57.234 36.000 0.00 0.00 0.00 1.85
439 451 7.951347 TTTAGTACTCTCTCCGTTCCTAAAT 57.049 36.000 0.00 0.00 0.00 1.40
440 452 9.466497 TTTTAGTACTCTCTCCGTTCCTAAATA 57.534 33.333 0.00 0.00 0.00 1.40
441 453 9.466497 TTTAGTACTCTCTCCGTTCCTAAATAA 57.534 33.333 0.00 0.00 0.00 1.40
442 454 9.638176 TTAGTACTCTCTCCGTTCCTAAATAAT 57.362 33.333 0.00 0.00 0.00 1.28
443 455 8.536340 AGTACTCTCTCCGTTCCTAAATAATT 57.464 34.615 0.00 0.00 0.00 1.40
444 456 8.414778 AGTACTCTCTCCGTTCCTAAATAATTG 58.585 37.037 0.00 0.00 0.00 2.32
445 457 7.184067 ACTCTCTCCGTTCCTAAATAATTGT 57.816 36.000 0.00 0.00 0.00 2.71
446 458 7.266400 ACTCTCTCCGTTCCTAAATAATTGTC 58.734 38.462 0.00 0.00 0.00 3.18
447 459 7.124448 ACTCTCTCCGTTCCTAAATAATTGTCT 59.876 37.037 0.00 0.00 0.00 3.41
448 460 7.848128 TCTCTCCGTTCCTAAATAATTGTCTT 58.152 34.615 0.00 0.00 0.00 3.01
449 461 8.319146 TCTCTCCGTTCCTAAATAATTGTCTTT 58.681 33.333 0.00 0.00 0.00 2.52
450 462 8.488651 TCTCCGTTCCTAAATAATTGTCTTTC 57.511 34.615 0.00 0.00 0.00 2.62
451 463 8.319146 TCTCCGTTCCTAAATAATTGTCTTTCT 58.681 33.333 0.00 0.00 0.00 2.52
452 464 9.595823 CTCCGTTCCTAAATAATTGTCTTTCTA 57.404 33.333 0.00 0.00 0.00 2.10
453 465 9.595823 TCCGTTCCTAAATAATTGTCTTTCTAG 57.404 33.333 0.00 0.00 0.00 2.43
454 466 8.336080 CCGTTCCTAAATAATTGTCTTTCTAGC 58.664 37.037 0.00 0.00 0.00 3.42
455 467 8.336080 CGTTCCTAAATAATTGTCTTTCTAGCC 58.664 37.037 0.00 0.00 0.00 3.93
456 468 9.174166 GTTCCTAAATAATTGTCTTTCTAGCCA 57.826 33.333 0.00 0.00 0.00 4.75
457 469 9.920946 TTCCTAAATAATTGTCTTTCTAGCCAT 57.079 29.630 0.00 0.00 0.00 4.40
458 470 9.561069 TCCTAAATAATTGTCTTTCTAGCCATC 57.439 33.333 0.00 0.00 0.00 3.51
459 471 9.566432 CCTAAATAATTGTCTTTCTAGCCATCT 57.434 33.333 0.00 0.00 0.00 2.90
462 474 9.466497 AAATAATTGTCTTTCTAGCCATCTCAA 57.534 29.630 0.00 0.00 0.00 3.02
463 475 9.466497 AATAATTGTCTTTCTAGCCATCTCAAA 57.534 29.630 0.00 0.00 0.00 2.69
464 476 7.951347 AATTGTCTTTCTAGCCATCTCAAAT 57.049 32.000 0.00 0.00 0.00 2.32
465 477 6.748333 TTGTCTTTCTAGCCATCTCAAATG 57.252 37.500 0.00 0.00 0.00 2.32
466 478 5.188434 TGTCTTTCTAGCCATCTCAAATGG 58.812 41.667 0.00 0.00 41.99 3.16
467 479 5.045651 TGTCTTTCTAGCCATCTCAAATGGA 60.046 40.000 8.23 0.00 41.64 3.41
468 480 5.295540 GTCTTTCTAGCCATCTCAAATGGAC 59.704 44.000 8.23 0.19 41.64 4.02
469 481 5.190528 TCTTTCTAGCCATCTCAAATGGACT 59.809 40.000 8.23 7.12 41.64 3.85
470 482 6.384015 TCTTTCTAGCCATCTCAAATGGACTA 59.616 38.462 8.23 7.79 41.64 2.59
471 483 5.537300 TCTAGCCATCTCAAATGGACTAC 57.463 43.478 8.23 0.00 41.64 2.73
472 484 4.962362 TCTAGCCATCTCAAATGGACTACA 59.038 41.667 8.23 0.00 41.64 2.74
473 485 4.574674 AGCCATCTCAAATGGACTACAA 57.425 40.909 8.23 0.00 41.64 2.41
474 486 4.265073 AGCCATCTCAAATGGACTACAAC 58.735 43.478 8.23 0.00 41.64 3.32
475 487 4.009675 GCCATCTCAAATGGACTACAACA 58.990 43.478 8.23 0.00 41.64 3.33
476 488 4.641989 GCCATCTCAAATGGACTACAACAT 59.358 41.667 8.23 0.00 41.64 2.71
477 489 5.822519 GCCATCTCAAATGGACTACAACATA 59.177 40.000 8.23 0.00 41.64 2.29
478 490 6.238484 GCCATCTCAAATGGACTACAACATAC 60.238 42.308 8.23 0.00 41.64 2.39
479 491 6.018751 CCATCTCAAATGGACTACAACATACG 60.019 42.308 0.00 0.00 41.64 3.06
480 492 5.416083 TCTCAAATGGACTACAACATACGG 58.584 41.667 0.00 0.00 0.00 4.02
481 493 5.186215 TCTCAAATGGACTACAACATACGGA 59.814 40.000 0.00 0.00 0.00 4.69
482 494 5.984725 TCAAATGGACTACAACATACGGAT 58.015 37.500 0.00 0.00 0.00 4.18
483 495 5.815222 TCAAATGGACTACAACATACGGATG 59.185 40.000 5.94 5.94 39.16 3.51
485 497 6.474140 AATGGACTACAACATACGGATGTA 57.526 37.500 15.10 0.00 45.93 2.29
486 498 6.665992 ATGGACTACAACATACGGATGTAT 57.334 37.500 15.10 8.21 45.93 2.29
503 515 9.692749 ACGGATGTATGTAGACATGTTTTATAG 57.307 33.333 0.00 0.00 40.18 1.31
504 516 9.692749 CGGATGTATGTAGACATGTTTTATAGT 57.307 33.333 0.00 0.00 40.18 2.12
524 536 9.890629 TTATAGTGTAGATTCACTCATTTTGCT 57.109 29.630 2.59 0.00 45.79 3.91
525 537 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
526 538 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
527 539 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
528 540 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
529 541 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
530 542 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
531 543 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
532 544 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
533 545 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
534 546 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
535 547 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
536 548 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
537 549 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
538 550 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
539 551 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
540 552 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
541 553 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
542 554 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
543 555 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
544 556 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
545 557 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
546 558 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
547 559 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
548 560 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
549 561 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
550 562 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
551 563 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
552 564 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
553 565 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
554 566 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
555 567 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
556 568 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
557 569 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
558 570 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
559 571 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
560 572 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
561 573 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
562 574 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
563 575 9.566432 ACTTGTTGAAATCTCTAGAAAGACAAT 57.434 29.630 0.00 0.00 0.00 2.71
576 588 9.595823 TCTAGAAAGACAATTATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
577 589 9.595823 CTAGAAAGACAATTATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
578 590 8.494016 AGAAAGACAATTATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
579 591 7.553044 AGAAAGACAATTATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
580 592 5.681639 AGACAATTATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
601 613 7.455008 GGAGGGAGTAGATCATAATTACTTCCA 59.545 40.741 15.43 0.00 42.97 3.53
659 671 5.990668 AGTACAGATAAGTAGGGCCAAAAG 58.009 41.667 6.18 0.00 0.00 2.27
664 676 6.069029 ACAGATAAGTAGGGCCAAAAGGTAAT 60.069 38.462 6.18 0.00 0.00 1.89
908 922 2.712057 AAGAAAGCATGGCGTGAAAG 57.288 45.000 11.71 0.00 0.00 2.62
1007 1021 4.588899 AGTTGTTATGCTAGCATGGACAA 58.411 39.130 34.13 34.13 39.30 3.18
1347 1379 9.194972 TGATCTGAATGAGATAGTAGAAGTTGT 57.805 33.333 0.00 0.00 41.91 3.32
1446 1478 0.314935 AATGCAAGTGGGTCGCAAAG 59.685 50.000 0.00 0.00 39.48 2.77
1522 1554 2.298610 CTGGCAGATGCATCACTGATT 58.701 47.619 27.81 3.64 44.36 2.57
1761 1807 6.979817 TGTAGCGTACTGTTTAGTTTTCTGAA 59.020 34.615 0.00 0.00 38.36 3.02
1916 1994 9.077885 AGAACTTGGATTTATATTTGTGTGTGT 57.922 29.630 0.00 0.00 0.00 3.72
1917 1995 9.128107 GAACTTGGATTTATATTTGTGTGTGTG 57.872 33.333 0.00 0.00 0.00 3.82
1918 1996 8.177119 ACTTGGATTTATATTTGTGTGTGTGT 57.823 30.769 0.00 0.00 0.00 3.72
1919 1997 8.081633 ACTTGGATTTATATTTGTGTGTGTGTG 58.918 33.333 0.00 0.00 0.00 3.82
1920 1998 7.517614 TGGATTTATATTTGTGTGTGTGTGT 57.482 32.000 0.00 0.00 0.00 3.72
1921 1999 7.366513 TGGATTTATATTTGTGTGTGTGTGTG 58.633 34.615 0.00 0.00 0.00 3.82
2103 2185 4.399303 ACCGAAATCATTCAATGTTCTCCC 59.601 41.667 0.00 0.00 35.15 4.30
2483 2594 5.142061 TGTGCGAGAGGAATTTACTTACA 57.858 39.130 0.00 0.00 0.00 2.41
2664 2775 5.518847 CGTGATGTTTACATAACAGATCCGT 59.481 40.000 10.25 0.00 37.53 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.706594 TCTTACCTGTAGGCTCATGAAGG 59.293 47.826 7.23 7.23 39.32 3.46
15 16 7.290014 TGATTATGAATCTTACCTGTAGGCTCA 59.710 37.037 0.00 0.00 38.72 4.26
59 60 9.979578 ACATGAACAATTTTGCTATAAGTTTGA 57.020 25.926 0.00 0.00 0.00 2.69
63 64 9.630098 CAGAACATGAACAATTTTGCTATAAGT 57.370 29.630 0.00 0.00 0.00 2.24
64 65 9.844790 TCAGAACATGAACAATTTTGCTATAAG 57.155 29.630 0.00 0.00 34.02 1.73
65 66 9.844790 CTCAGAACATGAACAATTTTGCTATAA 57.155 29.630 0.00 0.00 37.52 0.98
66 67 8.461222 CCTCAGAACATGAACAATTTTGCTATA 58.539 33.333 0.00 0.00 37.52 1.31
67 68 7.177216 TCCTCAGAACATGAACAATTTTGCTAT 59.823 33.333 0.00 0.00 37.52 2.97
116 117 3.871485 TGTTGGCAGAACTTTGCAATTT 58.129 36.364 0.00 0.00 45.86 1.82
148 149 6.102663 AGAAGGTTTGTCTATTCATCACTCG 58.897 40.000 0.00 0.00 0.00 4.18
236 237 5.105106 TCAAGGGTATCGCATCTGTAAAAGA 60.105 40.000 0.00 0.00 39.94 2.52
237 238 5.116180 TCAAGGGTATCGCATCTGTAAAAG 58.884 41.667 0.00 0.00 0.00 2.27
242 243 5.012046 TCAATATCAAGGGTATCGCATCTGT 59.988 40.000 0.00 0.00 0.00 3.41
243 244 5.482006 TCAATATCAAGGGTATCGCATCTG 58.518 41.667 0.00 0.00 0.00 2.90
339 340 0.248175 CACACATGCGCGCATACATT 60.248 50.000 42.66 25.25 34.91 2.71
356 357 4.201980 GGACTATGTTTAAAATCCGGCCAC 60.202 45.833 2.24 0.00 0.00 5.01
410 422 6.436532 AGGAACGGAGAGAGTACTAAAATCAA 59.563 38.462 0.00 0.00 0.00 2.57
417 429 9.638176 AATTATTTAGGAACGGAGAGAGTACTA 57.362 33.333 0.00 0.00 0.00 1.82
418 430 8.414778 CAATTATTTAGGAACGGAGAGAGTACT 58.585 37.037 0.00 0.00 0.00 2.73
419 431 8.196103 ACAATTATTTAGGAACGGAGAGAGTAC 58.804 37.037 0.00 0.00 0.00 2.73
420 432 8.302515 ACAATTATTTAGGAACGGAGAGAGTA 57.697 34.615 0.00 0.00 0.00 2.59
421 433 7.124448 AGACAATTATTTAGGAACGGAGAGAGT 59.876 37.037 0.00 0.00 0.00 3.24
422 434 7.493367 AGACAATTATTTAGGAACGGAGAGAG 58.507 38.462 0.00 0.00 0.00 3.20
423 435 7.419711 AGACAATTATTTAGGAACGGAGAGA 57.580 36.000 0.00 0.00 0.00 3.10
424 436 8.494016 AAAGACAATTATTTAGGAACGGAGAG 57.506 34.615 0.00 0.00 0.00 3.20
425 437 8.319146 AGAAAGACAATTATTTAGGAACGGAGA 58.681 33.333 0.00 0.00 0.00 3.71
426 438 8.494016 AGAAAGACAATTATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
427 439 9.595823 CTAGAAAGACAATTATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
428 440 8.336080 GCTAGAAAGACAATTATTTAGGAACGG 58.664 37.037 0.00 0.00 0.00 4.44
429 441 8.336080 GGCTAGAAAGACAATTATTTAGGAACG 58.664 37.037 0.00 0.00 0.00 3.95
430 442 9.174166 TGGCTAGAAAGACAATTATTTAGGAAC 57.826 33.333 0.00 0.00 38.01 3.62
431 443 9.920946 ATGGCTAGAAAGACAATTATTTAGGAA 57.079 29.630 0.00 0.00 46.32 3.36
432 444 9.561069 GATGGCTAGAAAGACAATTATTTAGGA 57.439 33.333 0.00 0.00 46.32 2.94
433 445 9.566432 AGATGGCTAGAAAGACAATTATTTAGG 57.434 33.333 0.00 0.00 46.32 2.69
436 448 9.466497 TTGAGATGGCTAGAAAGACAATTATTT 57.534 29.630 0.00 0.00 46.32 1.40
437 449 9.466497 TTTGAGATGGCTAGAAAGACAATTATT 57.534 29.630 0.00 0.00 46.32 1.40
438 450 9.638176 ATTTGAGATGGCTAGAAAGACAATTAT 57.362 29.630 0.00 0.00 46.32 1.28
439 451 8.896744 CATTTGAGATGGCTAGAAAGACAATTA 58.103 33.333 0.00 0.00 46.32 1.40
440 452 7.147949 CCATTTGAGATGGCTAGAAAGACAATT 60.148 37.037 0.00 0.00 46.32 2.32
441 453 6.320672 CCATTTGAGATGGCTAGAAAGACAAT 59.679 38.462 0.00 0.00 46.32 2.71
442 454 5.649395 CCATTTGAGATGGCTAGAAAGACAA 59.351 40.000 0.00 0.00 46.32 3.18
444 456 5.295540 GTCCATTTGAGATGGCTAGAAAGAC 59.704 44.000 0.00 0.00 39.01 3.01
445 457 5.190528 AGTCCATTTGAGATGGCTAGAAAGA 59.809 40.000 0.00 0.00 39.01 2.52
446 458 5.435291 AGTCCATTTGAGATGGCTAGAAAG 58.565 41.667 0.00 0.00 39.01 2.62
447 459 5.441718 AGTCCATTTGAGATGGCTAGAAA 57.558 39.130 0.00 0.00 39.01 2.52
448 460 5.425217 TGTAGTCCATTTGAGATGGCTAGAA 59.575 40.000 0.00 0.00 39.01 2.10
449 461 4.962362 TGTAGTCCATTTGAGATGGCTAGA 59.038 41.667 0.00 0.00 39.01 2.43
450 462 5.282055 TGTAGTCCATTTGAGATGGCTAG 57.718 43.478 0.00 0.00 39.01 3.42
451 463 5.045942 TGTTGTAGTCCATTTGAGATGGCTA 60.046 40.000 0.00 0.33 39.01 3.93
452 464 4.263462 TGTTGTAGTCCATTTGAGATGGCT 60.263 41.667 0.00 1.24 39.01 4.75
453 465 4.009675 TGTTGTAGTCCATTTGAGATGGC 58.990 43.478 0.00 0.00 39.01 4.40
454 466 6.018751 CGTATGTTGTAGTCCATTTGAGATGG 60.019 42.308 0.00 0.00 40.48 3.51
455 467 6.018751 CCGTATGTTGTAGTCCATTTGAGATG 60.019 42.308 0.00 0.00 0.00 2.90
456 468 6.049149 CCGTATGTTGTAGTCCATTTGAGAT 58.951 40.000 0.00 0.00 0.00 2.75
457 469 5.186215 TCCGTATGTTGTAGTCCATTTGAGA 59.814 40.000 0.00 0.00 0.00 3.27
458 470 5.416083 TCCGTATGTTGTAGTCCATTTGAG 58.584 41.667 0.00 0.00 0.00 3.02
459 471 5.408880 TCCGTATGTTGTAGTCCATTTGA 57.591 39.130 0.00 0.00 0.00 2.69
460 472 5.584649 ACATCCGTATGTTGTAGTCCATTTG 59.415 40.000 0.00 0.00 44.07 2.32
461 473 5.741011 ACATCCGTATGTTGTAGTCCATTT 58.259 37.500 0.00 0.00 44.07 2.32
462 474 5.353394 ACATCCGTATGTTGTAGTCCATT 57.647 39.130 0.00 0.00 44.07 3.16
463 475 6.455647 CATACATCCGTATGTTGTAGTCCAT 58.544 40.000 0.00 0.00 46.70 3.41
464 476 5.838529 CATACATCCGTATGTTGTAGTCCA 58.161 41.667 0.00 0.00 46.70 4.02
477 489 9.692749 CTATAAAACATGTCTACATACATCCGT 57.307 33.333 0.00 0.00 38.01 4.69
478 490 9.692749 ACTATAAAACATGTCTACATACATCCG 57.307 33.333 0.00 0.00 38.01 4.18
503 515 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
504 516 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
505 517 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
506 518 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
507 519 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
508 520 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
509 521 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
510 522 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
511 523 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
512 524 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
513 525 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
514 526 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
515 527 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
516 528 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
517 529 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
518 530 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
519 531 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
520 532 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
521 533 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
522 534 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
523 535 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
524 536 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
525 537 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
526 538 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
527 539 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
529 541 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
530 542 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
531 543 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
532 544 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
533 545 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
534 546 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
535 547 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
536 548 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
537 549 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
550 562 9.595823 CCGTTCCTAAATAATTGTCTTTCTAGA 57.404 33.333 0.00 0.00 0.00 2.43
551 563 9.595823 TCCGTTCCTAAATAATTGTCTTTCTAG 57.404 33.333 0.00 0.00 0.00 2.43
552 564 9.595823 CTCCGTTCCTAAATAATTGTCTTTCTA 57.404 33.333 0.00 0.00 0.00 2.10
553 565 7.553044 CCTCCGTTCCTAAATAATTGTCTTTCT 59.447 37.037 0.00 0.00 0.00 2.52
554 566 7.201705 CCCTCCGTTCCTAAATAATTGTCTTTC 60.202 40.741 0.00 0.00 0.00 2.62
555 567 6.602009 CCCTCCGTTCCTAAATAATTGTCTTT 59.398 38.462 0.00 0.00 0.00 2.52
556 568 6.069847 TCCCTCCGTTCCTAAATAATTGTCTT 60.070 38.462 0.00 0.00 0.00 3.01
557 569 5.427481 TCCCTCCGTTCCTAAATAATTGTCT 59.573 40.000 0.00 0.00 0.00 3.41
558 570 5.677567 TCCCTCCGTTCCTAAATAATTGTC 58.322 41.667 0.00 0.00 0.00 3.18
559 571 5.191124 ACTCCCTCCGTTCCTAAATAATTGT 59.809 40.000 0.00 0.00 0.00 2.71
560 572 5.681639 ACTCCCTCCGTTCCTAAATAATTG 58.318 41.667 0.00 0.00 0.00 2.32
561 573 5.970501 ACTCCCTCCGTTCCTAAATAATT 57.029 39.130 0.00 0.00 0.00 1.40
562 574 6.379579 TCTACTCCCTCCGTTCCTAAATAAT 58.620 40.000 0.00 0.00 0.00 1.28
563 575 5.769835 TCTACTCCCTCCGTTCCTAAATAA 58.230 41.667 0.00 0.00 0.00 1.40
564 576 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
565 577 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
566 578 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
567 579 3.203710 TGATCTACTCCCTCCGTTCCTAA 59.796 47.826 0.00 0.00 0.00 2.69
568 580 2.781757 TGATCTACTCCCTCCGTTCCTA 59.218 50.000 0.00 0.00 0.00 2.94
569 581 1.569548 TGATCTACTCCCTCCGTTCCT 59.430 52.381 0.00 0.00 0.00 3.36
570 582 2.068834 TGATCTACTCCCTCCGTTCC 57.931 55.000 0.00 0.00 0.00 3.62
571 583 5.986501 ATTATGATCTACTCCCTCCGTTC 57.013 43.478 0.00 0.00 0.00 3.95
572 584 7.011382 AGTAATTATGATCTACTCCCTCCGTT 58.989 38.462 0.00 0.00 0.00 4.44
573 585 6.553857 AGTAATTATGATCTACTCCCTCCGT 58.446 40.000 0.00 0.00 0.00 4.69
574 586 7.363094 GGAAGTAATTATGATCTACTCCCTCCG 60.363 44.444 0.00 0.00 0.00 4.63
575 587 7.455008 TGGAAGTAATTATGATCTACTCCCTCC 59.545 40.741 0.00 0.00 0.00 4.30
576 588 8.423906 TGGAAGTAATTATGATCTACTCCCTC 57.576 38.462 0.00 0.00 0.00 4.30
577 589 8.980832 ATGGAAGTAATTATGATCTACTCCCT 57.019 34.615 0.00 0.00 0.00 4.20
578 590 8.816894 TGATGGAAGTAATTATGATCTACTCCC 58.183 37.037 0.00 0.00 0.00 4.30
908 922 4.569943 TGACTCATTGAACTGTTCTAGGC 58.430 43.478 20.18 14.33 0.00 3.93
1007 1021 3.577805 ACCCTGTGTGCTTTAGAAGTT 57.422 42.857 0.00 0.00 0.00 2.66
1347 1379 6.070656 GGGGAATCATTTGTTCCATCAGATA 58.929 40.000 7.16 0.00 45.56 1.98
1446 1478 1.599071 GCTTTTGCCCTTTTGAAGTGC 59.401 47.619 0.00 0.00 40.15 4.40
1522 1554 7.148540 GCTGCATTTTTCTTTGATTCAGCAATA 60.149 33.333 0.00 0.00 42.59 1.90
1916 1994 5.875359 TGTATTTGTAGAACACACACACACA 59.125 36.000 0.00 0.00 36.69 3.72
1917 1995 6.352682 TGTATTTGTAGAACACACACACAC 57.647 37.500 0.00 0.00 36.69 3.82
1918 1996 8.664211 TTATGTATTTGTAGAACACACACACA 57.336 30.769 0.00 0.00 36.69 3.72
1919 1997 7.744715 GCTTATGTATTTGTAGAACACACACAC 59.255 37.037 0.00 0.00 36.69 3.82
1920 1998 7.659799 AGCTTATGTATTTGTAGAACACACACA 59.340 33.333 0.00 0.00 36.69 3.72
1921 1999 8.029642 AGCTTATGTATTTGTAGAACACACAC 57.970 34.615 0.00 0.00 36.69 3.82
2023 2104 4.159693 TGGAGATATGTACTGACGCAAAGT 59.840 41.667 0.00 0.00 0.00 2.66
2103 2185 7.067129 AGGACAAGAATCATTGAATGAGTGATG 59.933 37.037 13.23 12.90 43.53 3.07
2483 2594 3.056393 TGACGTCCATCCGTTTTGTATCT 60.056 43.478 14.12 0.00 41.98 1.98
2664 2775 2.940994 TCGTTGGGAACTTCATTGGA 57.059 45.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.