Multiple sequence alignment - TraesCS2A01G111700

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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 TraesCS2A01G111700 chr2A 100.000 2912 0 0 1 2912 63139254 63136343 0.000000e+00 5378.0
1 TraesCS2A01G111700 chr2A 79.477 497 76 15 1299 1770 63588742 63588247 2.160000e-86 329.0
2 TraesCS2A01G111700 chr2A 80.592 304 47 9 1474 1770 63606776 63606478 1.050000e-54 224.0
3 TraesCS2A01G111700 chr2A 83.000 200 14 8 1043 1226 63607276 63607081 2.320000e-36 163.0
4 TraesCS2A01G111700 chr2B 88.946 2515 167 61 468 2912 97934493 97932020 0.000000e+00 3001.0
5 TraesCS2A01G111700 chr2B 88.832 394 26 9 1 388 97934983 97934602 4.390000e-128 468.0
6 TraesCS2A01G111700 chr2B 78.427 496 65 27 1311 1771 98264413 98263925 4.750000e-73 285.0
7 TraesCS2A01G111700 chr2B 78.834 326 50 14 1299 1607 98256763 98256440 4.920000e-48 202.0
8 TraesCS2A01G111700 chr2B 85.864 191 15 6 1043 1224 98257069 98256882 2.960000e-45 193.0
9 TraesCS2A01G111700 chr2B 81.532 222 26 10 1017 1226 98264729 98264511 4.990000e-38 169.0
10 TraesCS2A01G111700 chr2B 93.396 106 7 0 1666 1771 98256333 98256228 1.080000e-34 158.0
11 TraesCS2A01G111700 chr2B 81.281 203 18 12 1040 1226 98286804 98286606 2.340000e-31 147.0
12 TraesCS2A01G111700 chr2B 82.192 146 24 2 1459 1603 98286320 98286176 1.100000e-24 124.0
13 TraesCS2A01G111700 chr2B 88.119 101 12 0 1671 1771 98286092 98285992 1.420000e-23 121.0
14 TraesCS2A01G111700 chr2B 97.059 34 1 0 436 469 638958231 638958198 1.130000e-04 58.4
15 TraesCS2A01G111700 chr2D 91.284 1893 105 33 1058 2912 62289859 62287989 0.000000e+00 2527.0
16 TraesCS2A01G111700 chr2D 84.956 452 35 19 482 914 62290530 62290093 7.460000e-116 427.0
17 TraesCS2A01G111700 chr2D 76.903 775 129 31 1043 1770 62553321 62552550 7.560000e-106 394.0
18 TraesCS2A01G111700 chr2D 79.573 328 45 15 1463 1771 62559274 62558950 6.320000e-52 215.0
19 TraesCS2A01G111700 chr2D 81.116 233 19 15 1017 1226 62559851 62559621 2.320000e-36 163.0
20 TraesCS2A01G111700 chr2D 80.488 205 16 15 1043 1226 62565143 62564942 5.060000e-28 135.0
21 TraesCS2A01G111700 chr2D 89.796 98 9 1 3 99 62290870 62290773 1.100000e-24 124.0
22 TraesCS2A01G111700 chr2D 83.077 130 22 0 1474 1603 62564621 62564492 5.100000e-23 119.0
23 TraesCS2A01G111700 chr5B 100.000 32 0 0 438 469 271112852 271112821 3.130000e-05 60.2
24 TraesCS2A01G111700 chr5B 94.444 36 1 1 438 472 365139908 365139873 1.000000e-03 54.7
25 TraesCS2A01G111700 chr1B 100.000 32 0 0 438 469 474683067 474683036 3.130000e-05 60.2
26 TraesCS2A01G111700 chr1B 97.059 34 0 1 437 470 73021598 73021630 4.050000e-04 56.5
27 TraesCS2A01G111700 chr3B 97.143 35 0 1 438 471 28259669 28259635 1.130000e-04 58.4
28 TraesCS2A01G111700 chr3B 97.143 35 0 1 440 473 222064704 222064738 1.130000e-04 58.4
29 TraesCS2A01G111700 chr6B 94.595 37 0 2 437 472 444866951 444866986 4.050000e-04 56.5
30 TraesCS2A01G111700 chr7B 96.970 33 0 1 437 469 236596030 236595999 1.000000e-03 54.7


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 TraesCS2A01G111700 chr2A 63136343 63139254 2911 True 5378.0 5378 100.000000 1 2912 1 chr2A.!!$R1 2911
1 TraesCS2A01G111700 chr2B 97932020 97934983 2963 True 1734.5 3001 88.889000 1 2912 2 chr2B.!!$R2 2911
2 TraesCS2A01G111700 chr2B 98263925 98264729 804 True 227.0 285 79.979500 1017 1771 2 chr2B.!!$R4 754
3 TraesCS2A01G111700 chr2D 62287989 62290870 2881 True 1026.0 2527 88.678667 3 2912 3 chr2D.!!$R2 2909
4 TraesCS2A01G111700 chr2D 62552550 62553321 771 True 394.0 394 76.903000 1043 1770 1 chr2D.!!$R1 727

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
411 587 0.036765 GGTCGATGCACCCAAGTACA 60.037 55.0 0.0 0.0 0.0 2.90 F
439 615 0.168788 CGAGGACAATGCACGCAAAT 59.831 50.0 0.0 0.0 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 2257 0.029167 CATCACTTGCACGCACACAA 59.971 50.0 0.0 0.0 0.00 3.33 R
2330 2778 1.512926 GTCGTCAATGGTGAAGCAGT 58.487 50.0 0.0 0.0 34.87 4.40 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
118 288 4.687483 GCATGCATAGCTGAAACAACTTTT 59.313 37.500 14.21 0.00 0.00 2.27
169 343 4.177026 ACGCAGCTATTAACACTGAGAAG 58.823 43.478 10.53 0.00 35.51 2.85
174 348 6.209361 CAGCTATTAACACTGAGAAGCGATA 58.791 40.000 0.00 0.00 33.10 2.92
206 382 9.840427 GCTGTTGTTTTAGTGTTGTATGAATAT 57.160 29.630 0.00 0.00 0.00 1.28
237 413 1.370609 TCCATTTAAATTCCGCGCGA 58.629 45.000 34.63 13.72 0.00 5.87
253 429 1.636570 GCGAGCCCGAAAAGGAAGTC 61.637 60.000 0.00 0.00 45.00 3.01
268 444 2.414691 GGAAGTCCTTTCGAAATGCTGC 60.415 50.000 11.70 8.25 36.62 5.25
274 450 0.889994 TTTCGAAATGCTGCATGGCT 59.110 45.000 17.00 3.81 0.00 4.75
289 465 2.307934 TGGCTTTTCCACTGCAAAAC 57.692 45.000 0.00 0.00 40.72 2.43
290 466 1.830477 TGGCTTTTCCACTGCAAAACT 59.170 42.857 0.00 0.00 40.72 2.66
291 467 2.204237 GGCTTTTCCACTGCAAAACTG 58.796 47.619 0.00 0.00 34.01 3.16
292 468 2.418609 GGCTTTTCCACTGCAAAACTGT 60.419 45.455 0.00 0.00 34.01 3.55
293 469 3.261580 GCTTTTCCACTGCAAAACTGTT 58.738 40.909 0.00 0.00 0.00 3.16
320 496 6.735678 TTTTTCTCTTTTCAAAAAGGTGCC 57.264 33.333 13.68 0.00 44.22 5.01
335 511 1.072332 TGCCGCACACACACCTATT 59.928 52.632 0.00 0.00 0.00 1.73
336 512 1.233950 TGCCGCACACACACCTATTG 61.234 55.000 0.00 0.00 0.00 1.90
337 513 1.922135 GCCGCACACACACCTATTGG 61.922 60.000 0.00 0.00 39.83 3.16
351 527 3.486383 CCTATTGGGTGTTGTGACTTGT 58.514 45.455 0.00 0.00 0.00 3.16
358 534 2.088423 GTGTTGTGACTTGTGACCCAA 58.912 47.619 0.00 0.00 0.00 4.12
373 549 1.180456 CCCAAGATGCTGTGTTGCCA 61.180 55.000 0.00 0.00 30.07 4.92
375 551 1.336517 CCAAGATGCTGTGTTGCCAAG 60.337 52.381 0.00 0.00 30.07 3.61
376 552 1.610038 CAAGATGCTGTGTTGCCAAGA 59.390 47.619 0.00 0.00 0.00 3.02
385 561 2.104622 TGTGTTGCCAAGAGACATGAGA 59.895 45.455 0.00 0.00 0.00 3.27
388 564 3.181451 TGTTGCCAAGAGACATGAGAACT 60.181 43.478 0.00 0.00 0.00 3.01
389 565 3.325293 TGCCAAGAGACATGAGAACTC 57.675 47.619 0.00 2.95 0.00 3.01
390 566 2.266554 GCCAAGAGACATGAGAACTCG 58.733 52.381 0.00 0.00 36.03 4.18
391 567 2.094494 GCCAAGAGACATGAGAACTCGA 60.094 50.000 0.00 0.00 36.03 4.04
392 568 3.768406 CCAAGAGACATGAGAACTCGAG 58.232 50.000 11.84 11.84 36.03 4.04
394 570 3.080300 AGAGACATGAGAACTCGAGGT 57.920 47.619 18.41 11.06 36.03 3.85
395 571 3.013921 AGAGACATGAGAACTCGAGGTC 58.986 50.000 23.21 23.21 36.03 3.85
396 572 1.740585 AGACATGAGAACTCGAGGTCG 59.259 52.381 24.17 12.76 41.45 4.79
406 582 2.264480 CGAGGTCGATGCACCCAA 59.736 61.111 0.00 0.00 43.02 4.12
407 583 1.811266 CGAGGTCGATGCACCCAAG 60.811 63.158 0.00 0.00 43.02 3.61
408 584 1.296715 GAGGTCGATGCACCCAAGT 59.703 57.895 0.00 0.00 37.09 3.16
409 585 0.535335 GAGGTCGATGCACCCAAGTA 59.465 55.000 0.00 0.00 37.09 2.24
410 586 0.249398 AGGTCGATGCACCCAAGTAC 59.751 55.000 0.00 0.00 37.09 2.73
411 587 0.036765 GGTCGATGCACCCAAGTACA 60.037 55.000 0.00 0.00 0.00 2.90
413 589 1.665679 GTCGATGCACCCAAGTACATG 59.334 52.381 0.00 0.00 29.71 3.21
414 590 1.552792 TCGATGCACCCAAGTACATGA 59.447 47.619 0.00 0.00 29.71 3.07
415 591 1.935873 CGATGCACCCAAGTACATGAG 59.064 52.381 0.00 0.00 29.71 2.90
416 592 2.292267 GATGCACCCAAGTACATGAGG 58.708 52.381 0.00 2.14 29.71 3.86
417 593 1.357137 TGCACCCAAGTACATGAGGA 58.643 50.000 0.00 0.00 0.00 3.71
418 594 1.003118 TGCACCCAAGTACATGAGGAC 59.997 52.381 0.00 0.00 0.00 3.85
419 595 1.279271 GCACCCAAGTACATGAGGACT 59.721 52.381 0.00 0.00 0.00 3.85
420 596 2.678190 GCACCCAAGTACATGAGGACTC 60.678 54.545 0.00 0.00 0.00 3.36
421 597 1.825474 ACCCAAGTACATGAGGACTCG 59.175 52.381 0.00 0.00 0.00 4.18
422 598 2.100197 CCCAAGTACATGAGGACTCGA 58.900 52.381 0.00 0.00 0.00 4.04
424 600 2.099921 CCAAGTACATGAGGACTCGAGG 59.900 54.545 18.41 0.00 0.00 4.63
427 603 2.026169 AGTACATGAGGACTCGAGGACA 60.026 50.000 18.41 11.00 0.00 4.02
428 604 1.924731 ACATGAGGACTCGAGGACAA 58.075 50.000 18.41 2.22 0.00 3.18
429 605 2.461695 ACATGAGGACTCGAGGACAAT 58.538 47.619 18.41 4.46 0.00 2.71
430 606 2.167281 ACATGAGGACTCGAGGACAATG 59.833 50.000 18.41 16.79 0.00 2.82
431 607 0.532573 TGAGGACTCGAGGACAATGC 59.467 55.000 18.41 0.00 0.00 3.56
432 608 0.532573 GAGGACTCGAGGACAATGCA 59.467 55.000 18.41 0.00 0.00 3.96
433 609 0.247736 AGGACTCGAGGACAATGCAC 59.752 55.000 18.41 0.00 0.00 4.57
434 610 1.078759 GGACTCGAGGACAATGCACG 61.079 60.000 18.41 0.00 0.00 5.34
435 611 1.687494 GACTCGAGGACAATGCACGC 61.687 60.000 18.41 0.00 0.00 5.34
436 612 1.737735 CTCGAGGACAATGCACGCA 60.738 57.895 3.91 0.00 0.00 5.24
437 613 1.291184 CTCGAGGACAATGCACGCAA 61.291 55.000 3.91 0.00 0.00 4.85
438 614 0.882484 TCGAGGACAATGCACGCAAA 60.882 50.000 0.00 0.00 0.00 3.68
439 615 0.168788 CGAGGACAATGCACGCAAAT 59.831 50.000 0.00 0.00 0.00 2.32
440 616 1.621107 GAGGACAATGCACGCAAATG 58.379 50.000 0.00 1.14 0.00 2.32
441 617 0.961019 AGGACAATGCACGCAAATGT 59.039 45.000 12.05 12.05 34.34 2.71
442 618 2.158559 AGGACAATGCACGCAAATGTA 58.841 42.857 12.15 0.00 32.67 2.29
443 619 2.162208 AGGACAATGCACGCAAATGTAG 59.838 45.455 12.15 0.00 32.67 2.74
444 620 2.095263 GGACAATGCACGCAAATGTAGT 60.095 45.455 12.15 0.00 32.67 2.73
445 621 2.910482 GACAATGCACGCAAATGTAGTG 59.090 45.455 12.15 6.74 36.51 2.74
450 626 2.414058 CACGCAAATGTAGTGCCAAA 57.586 45.000 0.00 0.00 38.86 3.28
451 627 2.736978 CACGCAAATGTAGTGCCAAAA 58.263 42.857 0.00 0.00 38.86 2.44
492 718 4.218200 ACAATGTATGCTGCTGCTTGTAAA 59.782 37.500 17.00 3.30 40.48 2.01
520 746 3.581024 TCTGCGACCGTGTTATTACTT 57.419 42.857 0.00 0.00 0.00 2.24
523 749 5.653507 TCTGCGACCGTGTTATTACTTATT 58.346 37.500 0.00 0.00 0.00 1.40
524 750 6.794374 TCTGCGACCGTGTTATTACTTATTA 58.206 36.000 0.00 0.00 0.00 0.98
526 752 5.748152 TGCGACCGTGTTATTACTTATTACC 59.252 40.000 0.00 0.00 0.00 2.85
528 754 6.198687 CGACCGTGTTATTACTTATTACCGA 58.801 40.000 0.00 0.00 0.00 4.69
529 755 6.140737 CGACCGTGTTATTACTTATTACCGAC 59.859 42.308 0.00 0.00 0.00 4.79
530 756 6.273071 ACCGTGTTATTACTTATTACCGACC 58.727 40.000 0.00 0.00 0.00 4.79
531 757 6.127479 ACCGTGTTATTACTTATTACCGACCA 60.127 38.462 0.00 0.00 0.00 4.02
555 781 2.791158 GCAATAATCGGAAGCGGTGTTG 60.791 50.000 0.00 0.00 0.00 3.33
559 785 2.449031 ATCGGAAGCGGTGTTGCTGA 62.449 55.000 0.00 0.00 46.60 4.26
596 824 2.787473 TGTGAGCTCGGGATCAAAAT 57.213 45.000 3.99 0.00 39.68 1.82
667 895 5.122711 ACTTAAAAGTAAAGCGTGTGTGTGT 59.877 36.000 0.00 0.00 37.52 3.72
675 903 1.366111 GCGTGTGTGTGTTGACCAGT 61.366 55.000 0.00 0.00 0.00 4.00
678 906 2.284150 CGTGTGTGTGTTGACCAGTAAG 59.716 50.000 0.00 0.00 0.00 2.34
692 920 5.297776 TGACCAGTAAGTATCTTACTACGCC 59.702 44.000 17.87 10.50 38.26 5.68
694 922 6.595682 ACCAGTAAGTATCTTACTACGCCTA 58.404 40.000 17.87 0.00 38.26 3.93
695 923 6.484977 ACCAGTAAGTATCTTACTACGCCTAC 59.515 42.308 17.87 0.97 38.26 3.18
696 924 6.709846 CCAGTAAGTATCTTACTACGCCTACT 59.290 42.308 17.87 2.81 38.26 2.57
697 925 7.875041 CCAGTAAGTATCTTACTACGCCTACTA 59.125 40.741 17.87 0.00 38.26 1.82
714 942 5.542779 CCTACTATGGCTAATCACAGGTTC 58.457 45.833 0.00 0.00 0.00 3.62
744 974 5.195379 CAGAAACTGAAAAACTAACGGTCG 58.805 41.667 0.00 0.00 32.44 4.79
746 976 2.553086 ACTGAAAAACTAACGGTCGCA 58.447 42.857 0.00 0.00 0.00 5.10
777 1007 2.113986 GGTTGGCTGAGTGGCTGT 59.886 61.111 0.00 0.00 42.34 4.40
778 1008 1.374947 GGTTGGCTGAGTGGCTGTA 59.625 57.895 0.00 0.00 42.34 2.74
781 1011 1.275291 GTTGGCTGAGTGGCTGTACTA 59.725 52.381 0.00 0.00 42.34 1.82
851 1094 2.124122 GCTAAAACCAACAGCCAAACG 58.876 47.619 0.00 0.00 0.00 3.60
897 1140 2.513897 GCCGCCACCAGTATCCAC 60.514 66.667 0.00 0.00 0.00 4.02
898 1141 3.031417 GCCGCCACCAGTATCCACT 62.031 63.158 0.00 0.00 34.42 4.00
911 1190 4.041321 CAGTATCCACTGTCCATGATCCAT 59.959 45.833 0.00 0.00 46.03 3.41
914 1193 1.491754 CCACTGTCCATGATCCATCCA 59.508 52.381 0.00 0.00 0.00 3.41
915 1194 2.107726 CCACTGTCCATGATCCATCCAT 59.892 50.000 0.00 0.00 0.00 3.41
925 1204 3.707316 TGATCCATCCATTCCGGTTTTT 58.293 40.909 0.00 0.00 35.57 1.94
927 1206 2.175202 TCCATCCATTCCGGTTTTTGG 58.825 47.619 0.00 4.85 35.57 3.28
956 1254 2.099263 CCTATATGTACGCCCCTCGATG 59.901 54.545 0.00 0.00 41.67 3.84
971 1269 1.227468 GATGGCGCTGCTCATCAGA 60.227 57.895 20.28 0.00 45.72 3.27
975 1276 1.497223 GGCGCTGCTCATCAGATCAC 61.497 60.000 7.64 0.00 45.72 3.06
979 1280 1.664659 GCTGCTCATCAGATCACACAC 59.335 52.381 0.00 0.00 45.72 3.82
984 1285 3.332034 CTCATCAGATCACACACAGCAA 58.668 45.455 0.00 0.00 0.00 3.91
1000 1301 1.298602 GCAAACCTGCCAACCAAAAG 58.701 50.000 0.00 0.00 43.26 2.27
1002 1303 0.908198 AAACCTGCCAACCAAAAGCA 59.092 45.000 0.00 0.00 34.79 3.91
1003 1304 0.908198 AACCTGCCAACCAAAAGCAA 59.092 45.000 0.00 0.00 35.79 3.91
1004 1305 1.130777 ACCTGCCAACCAAAAGCAAT 58.869 45.000 0.00 0.00 35.79 3.56
1005 1306 2.324541 ACCTGCCAACCAAAAGCAATA 58.675 42.857 0.00 0.00 35.79 1.90
1008 1333 3.244181 CCTGCCAACCAAAAGCAATAGTT 60.244 43.478 0.00 0.00 35.79 2.24
1010 1335 4.376146 TGCCAACCAAAAGCAATAGTTTC 58.624 39.130 0.00 0.00 32.56 2.78
1013 1338 5.610398 CCAACCAAAAGCAATAGTTTCCTT 58.390 37.500 0.00 0.00 0.00 3.36
1025 1350 1.302913 TTTCCTTGCGATGGCGGAA 60.303 52.632 5.21 5.21 45.68 4.30
1032 1357 2.038269 GCGATGGCGGAAACCAAGA 61.038 57.895 0.00 0.00 44.65 3.02
1220 1572 4.021925 GTCACCTTCGGCAGCCCT 62.022 66.667 5.63 0.00 0.00 5.19
1246 1612 3.897239 CCTGCCATAGACCCATTTTGTA 58.103 45.455 0.00 0.00 0.00 2.41
1248 1614 3.287222 TGCCATAGACCCATTTTGTAGC 58.713 45.455 0.00 0.00 0.00 3.58
1273 1639 5.638530 TTTTTAAGGGGAAAACATGGCTT 57.361 34.783 0.00 0.00 0.00 4.35
1274 1640 4.615588 TTTAAGGGGAAAACATGGCTTG 57.384 40.909 0.00 0.00 0.00 4.01
1275 1641 2.397044 AAGGGGAAAACATGGCTTGA 57.603 45.000 7.45 0.00 0.00 3.02
1277 1643 2.906568 AGGGGAAAACATGGCTTGATT 58.093 42.857 7.45 0.00 0.00 2.57
1279 1645 2.093500 GGGGAAAACATGGCTTGATTCC 60.093 50.000 22.31 22.31 40.76 3.01
1282 1648 3.501950 GAAAACATGGCTTGATTCCGTC 58.498 45.455 7.45 0.00 0.00 4.79
1335 1709 2.592993 CGTGGTGAGGGTGGTGGAT 61.593 63.158 0.00 0.00 0.00 3.41
1453 1849 2.123342 CTCGATCGGAGACATTTGCTC 58.877 52.381 16.41 0.00 46.23 4.26
1455 1851 2.094234 TCGATCGGAGACATTTGCTCAA 60.094 45.455 16.41 0.00 42.51 3.02
1608 2025 5.250200 ACGGTGCAATCAAGAGGTAATTAA 58.750 37.500 0.00 0.00 0.00 1.40
1609 2026 5.123344 ACGGTGCAATCAAGAGGTAATTAAC 59.877 40.000 0.00 0.00 0.00 2.01
1755 2193 1.908619 TGATAGTCAAGCAGCCCAAGA 59.091 47.619 0.00 0.00 0.00 3.02
1787 2225 3.195002 CGTCATTGTGGCGCCGAT 61.195 61.111 23.90 13.05 39.15 4.18
1812 2251 6.816640 TCCTGTTGTATCTCTTGTAAAATCCG 59.183 38.462 0.00 0.00 0.00 4.18
1813 2252 6.594159 CCTGTTGTATCTCTTGTAAAATCCGT 59.406 38.462 0.00 0.00 0.00 4.69
1818 2257 9.715121 TTGTATCTCTTGTAAAATCCGTAGTTT 57.285 29.630 0.00 0.00 0.00 2.66
1845 2285 2.794282 GCGTGCAAGTGATGTCAAACAA 60.794 45.455 0.59 0.00 0.00 2.83
1849 2289 5.340403 CGTGCAAGTGATGTCAAACAAATAG 59.660 40.000 0.00 0.00 0.00 1.73
1850 2290 6.208644 GTGCAAGTGATGTCAAACAAATAGT 58.791 36.000 0.00 0.00 0.00 2.12
1851 2291 7.359595 GTGCAAGTGATGTCAAACAAATAGTA 58.640 34.615 0.00 0.00 0.00 1.82
1852 2292 7.323656 GTGCAAGTGATGTCAAACAAATAGTAC 59.676 37.037 0.00 0.00 0.00 2.73
1901 2341 4.344104 ACCAATACCTCAAATCCAGGTTG 58.656 43.478 0.00 0.00 41.95 3.77
1952 2392 9.529325 TGTTACTGTATTCAAATATCTTCCGAG 57.471 33.333 0.00 0.00 0.00 4.63
1953 2393 9.530633 GTTACTGTATTCAAATATCTTCCGAGT 57.469 33.333 0.00 0.00 0.00 4.18
1998 2442 7.495901 TCCAAGTAAAAATGCTGACAATGAAA 58.504 30.769 0.00 0.00 0.00 2.69
2252 2700 4.695455 ACACTTCCCAATCGACAATAAGTG 59.305 41.667 19.64 19.64 44.83 3.16
2314 2762 0.322816 GTGATGGGCTCTTGCTTGGA 60.323 55.000 0.00 0.00 39.59 3.53
2368 2816 0.385390 CGGGCTGAGCAAAAACAACT 59.615 50.000 6.82 0.00 0.00 3.16
2396 2846 8.612619 AGGTAAGTTTCATAAACAGATATTGCG 58.387 33.333 5.42 0.00 43.79 4.85
2403 2853 9.982291 TTTCATAAACAGATATTGCGAAAGTAC 57.018 29.630 0.00 0.00 0.00 2.73
2447 2897 1.045407 CGACAGGGGATCGGGATTTA 58.955 55.000 0.00 0.00 35.92 1.40
2541 2991 0.983378 AAGAACCTCCATCCTCCCCG 60.983 60.000 0.00 0.00 0.00 5.73
2574 3024 3.673902 GCCAAATGCAAGTAAAATGGGT 58.326 40.909 0.00 0.00 40.77 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.503399 AAACATAAAAACCTCAGGAACTACTAG 57.497 33.333 0.00 0.00 36.02 2.57
14 15 6.748132 ACATGTCAAACATAAAAACCTCAGG 58.252 36.000 0.00 0.00 36.53 3.86
96 97 7.381948 TGTTAAAAGTTGTTTCAGCTATGCATG 59.618 33.333 10.16 0.26 0.00 4.06
118 288 5.838529 TCTCGTCAGATGTTTGTCTTGTTA 58.161 37.500 0.00 0.00 0.00 2.41
169 343 4.616181 AAAACAACAGCTATGGTATCGC 57.384 40.909 3.96 0.00 0.00 4.58
174 348 5.592688 ACAACACTAAAACAACAGCTATGGT 59.407 36.000 3.96 0.00 0.00 3.55
216 392 2.032377 TCGCGCGGAATTTAAATGGATC 60.032 45.455 31.69 0.00 0.00 3.36
237 413 2.464582 AGGACTTCCTTTTCGGGCT 58.535 52.632 0.00 0.00 46.09 5.19
253 429 1.917273 CCATGCAGCATTTCGAAAGG 58.083 50.000 17.74 17.74 0.00 3.11
299 475 4.429108 CGGCACCTTTTTGAAAAGAGAAA 58.571 39.130 15.79 0.00 46.39 2.52
302 478 2.127251 GCGGCACCTTTTTGAAAAGAG 58.873 47.619 15.79 9.85 46.39 2.85
320 496 2.170738 CCCAATAGGTGTGTGTGCG 58.829 57.895 0.00 0.00 0.00 5.34
331 507 4.024048 GTCACAAGTCACAACACCCAATAG 60.024 45.833 0.00 0.00 0.00 1.73
332 508 3.880490 GTCACAAGTCACAACACCCAATA 59.120 43.478 0.00 0.00 0.00 1.90
333 509 2.687935 GTCACAAGTCACAACACCCAAT 59.312 45.455 0.00 0.00 0.00 3.16
335 511 1.680555 GGTCACAAGTCACAACACCCA 60.681 52.381 0.00 0.00 0.00 4.51
336 512 1.021968 GGTCACAAGTCACAACACCC 58.978 55.000 0.00 0.00 0.00 4.61
337 513 1.021968 GGGTCACAAGTCACAACACC 58.978 55.000 0.00 0.00 0.00 4.16
351 527 1.608055 CAACACAGCATCTTGGGTCA 58.392 50.000 0.00 0.00 32.38 4.02
373 549 3.426615 ACCTCGAGTTCTCATGTCTCTT 58.573 45.455 12.31 0.00 0.00 2.85
375 551 2.223157 CGACCTCGAGTTCTCATGTCTC 60.223 54.545 12.31 0.00 43.02 3.36
376 552 1.740585 CGACCTCGAGTTCTCATGTCT 59.259 52.381 12.31 0.00 43.02 3.41
389 565 1.811266 CTTGGGTGCATCGACCTCG 60.811 63.158 0.00 0.00 36.14 4.63
390 566 0.535335 TACTTGGGTGCATCGACCTC 59.465 55.000 0.00 0.00 36.14 3.85
391 567 0.249398 GTACTTGGGTGCATCGACCT 59.751 55.000 0.00 0.00 36.14 3.85
392 568 0.036765 TGTACTTGGGTGCATCGACC 60.037 55.000 0.00 0.00 33.35 4.79
394 570 1.552792 TCATGTACTTGGGTGCATCGA 59.447 47.619 8.74 0.00 44.68 3.59
395 571 1.935873 CTCATGTACTTGGGTGCATCG 59.064 52.381 8.74 0.00 44.68 3.84
396 572 2.092968 TCCTCATGTACTTGGGTGCATC 60.093 50.000 7.77 0.00 44.68 3.91
398 574 1.003118 GTCCTCATGTACTTGGGTGCA 59.997 52.381 7.77 0.00 41.85 4.57
400 576 2.417379 CGAGTCCTCATGTACTTGGGTG 60.417 54.545 7.77 0.42 0.00 4.61
402 578 2.099921 CTCGAGTCCTCATGTACTTGGG 59.900 54.545 3.62 5.32 0.00 4.12
403 579 2.099921 CCTCGAGTCCTCATGTACTTGG 59.900 54.545 12.31 0.67 0.00 3.61
404 580 3.017442 TCCTCGAGTCCTCATGTACTTG 58.983 50.000 12.31 2.36 0.00 3.16
406 582 2.026169 TGTCCTCGAGTCCTCATGTACT 60.026 50.000 12.31 0.00 0.00 2.73
407 583 2.366533 TGTCCTCGAGTCCTCATGTAC 58.633 52.381 12.31 0.00 0.00 2.90
408 584 2.801077 TGTCCTCGAGTCCTCATGTA 57.199 50.000 12.31 0.00 0.00 2.29
409 585 1.924731 TTGTCCTCGAGTCCTCATGT 58.075 50.000 12.31 0.00 0.00 3.21
410 586 2.819115 CATTGTCCTCGAGTCCTCATG 58.181 52.381 12.31 3.34 0.00 3.07
411 587 1.137872 GCATTGTCCTCGAGTCCTCAT 59.862 52.381 12.31 0.00 0.00 2.90
413 589 0.532573 TGCATTGTCCTCGAGTCCTC 59.467 55.000 12.31 0.00 0.00 3.71
414 590 0.247736 GTGCATTGTCCTCGAGTCCT 59.752 55.000 12.31 0.00 0.00 3.85
415 591 1.078759 CGTGCATTGTCCTCGAGTCC 61.079 60.000 12.31 1.44 0.00 3.85
416 592 1.687494 GCGTGCATTGTCCTCGAGTC 61.687 60.000 12.31 4.82 0.00 3.36
417 593 1.738099 GCGTGCATTGTCCTCGAGT 60.738 57.895 12.31 0.00 0.00 4.18
418 594 1.291184 TTGCGTGCATTGTCCTCGAG 61.291 55.000 5.13 5.13 0.00 4.04
419 595 0.882484 TTTGCGTGCATTGTCCTCGA 60.882 50.000 0.00 0.00 0.00 4.04
420 596 0.168788 ATTTGCGTGCATTGTCCTCG 59.831 50.000 0.00 0.00 0.00 4.63
421 597 1.068333 ACATTTGCGTGCATTGTCCTC 60.068 47.619 0.00 0.00 0.00 3.71
422 598 0.961019 ACATTTGCGTGCATTGTCCT 59.039 45.000 0.00 0.00 0.00 3.85
424 600 2.910482 CACTACATTTGCGTGCATTGTC 59.090 45.455 12.44 0.00 0.00 3.18
431 607 2.414058 TTTGGCACTACATTTGCGTG 57.586 45.000 0.00 0.00 41.18 5.34
432 608 3.444703 TTTTTGGCACTACATTTGCGT 57.555 38.095 0.00 0.00 41.18 5.24
449 625 8.573035 ACATTGTCCATAATGTAAGACGTTTTT 58.427 29.630 0.00 0.00 46.40 1.94
450 626 8.106247 ACATTGTCCATAATGTAAGACGTTTT 57.894 30.769 2.56 0.00 46.40 2.43
451 627 7.681939 ACATTGTCCATAATGTAAGACGTTT 57.318 32.000 2.56 0.00 46.40 3.60
465 641 1.679680 GCAGCAGCATACATTGTCCAT 59.320 47.619 0.00 0.00 41.58 3.41
475 701 3.125146 CGAAGTTTACAAGCAGCAGCATA 59.875 43.478 3.17 0.00 45.49 3.14
520 746 4.986034 CGATTATTGCAGTGGTCGGTAATA 59.014 41.667 9.25 0.00 0.00 0.98
523 749 2.482316 CCGATTATTGCAGTGGTCGGTA 60.482 50.000 21.13 0.00 42.54 4.02
524 750 1.651987 CGATTATTGCAGTGGTCGGT 58.348 50.000 9.25 0.00 0.00 4.69
526 752 1.934589 TCCGATTATTGCAGTGGTCG 58.065 50.000 9.91 9.91 0.00 4.79
528 754 2.017049 GCTTCCGATTATTGCAGTGGT 58.983 47.619 0.00 0.00 0.00 4.16
529 755 1.003545 CGCTTCCGATTATTGCAGTGG 60.004 52.381 0.00 0.00 36.29 4.00
530 756 1.003545 CCGCTTCCGATTATTGCAGTG 60.004 52.381 0.00 0.00 36.29 3.66
531 757 1.299541 CCGCTTCCGATTATTGCAGT 58.700 50.000 0.00 0.00 36.29 4.40
565 791 4.864334 CTCACATGCCCCCGCCTC 62.864 72.222 0.00 0.00 0.00 4.70
667 895 6.183360 GGCGTAGTAAGATACTTACTGGTCAA 60.183 42.308 24.98 9.53 40.14 3.18
675 903 7.335422 GCCATAGTAGGCGTAGTAAGATACTTA 59.665 40.741 5.15 0.00 46.12 2.24
678 906 5.878133 GCCATAGTAGGCGTAGTAAGATAC 58.122 45.833 5.15 0.00 46.12 2.24
692 920 5.542779 GGAACCTGTGATTAGCCATAGTAG 58.457 45.833 0.00 0.00 0.00 2.57
694 922 3.181465 CGGAACCTGTGATTAGCCATAGT 60.181 47.826 0.00 0.00 0.00 2.12
695 923 3.393800 CGGAACCTGTGATTAGCCATAG 58.606 50.000 0.00 0.00 0.00 2.23
696 924 2.104111 CCGGAACCTGTGATTAGCCATA 59.896 50.000 0.00 0.00 0.00 2.74
697 925 1.134098 CCGGAACCTGTGATTAGCCAT 60.134 52.381 0.00 0.00 0.00 4.40
712 940 0.762418 TTCAGTTTCTGCTCCCGGAA 59.238 50.000 0.73 0.00 34.59 4.30
714 942 1.604604 TTTTCAGTTTCTGCTCCCGG 58.395 50.000 0.00 0.00 0.00 5.73
744 974 3.720193 CCAGTGCGTGCTGACTGC 61.720 66.667 9.40 0.00 38.64 4.40
746 976 1.889105 CAACCAGTGCGTGCTGACT 60.889 57.895 9.40 0.00 38.70 3.41
851 1094 2.981350 TGCCCCGGTTTTCGCTTC 60.981 61.111 0.00 0.00 37.59 3.86
878 1121 2.203070 GGATACTGGTGGCGGCAG 60.203 66.667 13.91 2.93 0.00 4.85
897 1140 3.418995 GGAATGGATGGATCATGGACAG 58.581 50.000 0.00 0.00 0.00 3.51
898 1141 2.224597 CGGAATGGATGGATCATGGACA 60.225 50.000 0.00 0.00 0.00 4.02
899 1142 2.430465 CGGAATGGATGGATCATGGAC 58.570 52.381 0.00 0.00 0.00 4.02
900 1143 1.352017 CCGGAATGGATGGATCATGGA 59.648 52.381 0.00 0.00 42.00 3.41
901 1144 1.074405 ACCGGAATGGATGGATCATGG 59.926 52.381 9.46 0.00 42.00 3.66
902 1145 2.574006 ACCGGAATGGATGGATCATG 57.426 50.000 9.46 0.00 42.00 3.07
903 1146 3.600448 AAACCGGAATGGATGGATCAT 57.400 42.857 9.46 0.00 42.00 2.45
904 1147 3.380471 AAAACCGGAATGGATGGATCA 57.620 42.857 9.46 0.00 42.00 2.92
905 1148 3.181476 CCAAAAACCGGAATGGATGGATC 60.181 47.826 9.46 0.00 42.00 3.36
906 1149 2.765699 CCAAAAACCGGAATGGATGGAT 59.234 45.455 9.46 0.00 42.00 3.41
911 1190 2.356992 GGCCAAAAACCGGAATGGA 58.643 52.632 9.46 0.00 42.00 3.41
927 1206 0.389426 CGTACATATAGGGCCACGGC 60.389 60.000 6.18 0.00 41.06 5.68
930 1209 3.527434 GGCGTACATATAGGGCCAC 57.473 57.895 6.18 0.00 43.23 5.01
937 1235 2.097036 CCATCGAGGGGCGTACATATA 58.903 52.381 8.61 0.00 41.80 0.86
956 1254 1.227468 TGATCTGATGAGCAGCGCC 60.227 57.895 2.29 0.00 44.52 6.53
971 1269 0.670162 GCAGGTTTGCTGTGTGTGAT 59.330 50.000 0.00 0.00 46.95 3.06
984 1285 0.908198 TTGCTTTTGGTTGGCAGGTT 59.092 45.000 0.00 0.00 37.28 3.50
992 1293 5.056480 GCAAGGAAACTATTGCTTTTGGTT 58.944 37.500 2.80 0.00 43.76 3.67
998 1299 3.129287 CCATCGCAAGGAAACTATTGCTT 59.871 43.478 8.13 0.00 46.71 3.91
1000 1301 2.796032 GCCATCGCAAGGAAACTATTGC 60.796 50.000 0.00 0.00 46.53 3.56
1002 1303 1.670811 CGCCATCGCAAGGAAACTATT 59.329 47.619 0.00 0.00 42.68 1.73
1003 1304 1.299541 CGCCATCGCAAGGAAACTAT 58.700 50.000 0.00 0.00 42.68 2.12
1004 1305 0.742990 CCGCCATCGCAAGGAAACTA 60.743 55.000 0.00 0.00 42.68 2.24
1008 1333 1.302913 TTTCCGCCATCGCAAGGAA 60.303 52.632 0.00 0.00 40.60 3.36
1010 1335 2.485122 GTTTCCGCCATCGCAAGG 59.515 61.111 0.00 0.00 38.47 3.61
1013 1338 2.281831 TTGGTTTCCGCCATCGCA 60.282 55.556 0.00 0.00 38.48 5.10
1025 1350 2.980233 GCAGGCGCAGTCTTGGTT 60.980 61.111 10.83 0.00 45.33 3.67
1052 1392 0.895530 CCGTCTTCTTCCTACTGCCA 59.104 55.000 0.00 0.00 0.00 4.92
1220 1572 2.679342 GGGTCTATGGCAGGCACCA 61.679 63.158 0.00 1.44 45.82 4.17
1262 1628 3.157087 AGACGGAATCAAGCCATGTTTT 58.843 40.909 0.00 0.00 0.00 2.43
1264 1630 2.026822 AGAGACGGAATCAAGCCATGTT 60.027 45.455 0.00 0.00 0.00 2.71
1265 1631 1.556911 AGAGACGGAATCAAGCCATGT 59.443 47.619 0.00 0.00 0.00 3.21
1271 1637 2.957491 AGCAGAGAGACGGAATCAAG 57.043 50.000 0.00 0.00 0.00 3.02
1272 1638 2.416027 CGAAGCAGAGAGACGGAATCAA 60.416 50.000 0.00 0.00 0.00 2.57
1273 1639 1.133216 CGAAGCAGAGAGACGGAATCA 59.867 52.381 0.00 0.00 0.00 2.57
1274 1640 1.535015 CCGAAGCAGAGAGACGGAATC 60.535 57.143 0.00 0.00 45.31 2.52
1275 1641 0.457851 CCGAAGCAGAGAGACGGAAT 59.542 55.000 0.00 0.00 45.31 3.01
1277 1643 3.592070 CCGAAGCAGAGAGACGGA 58.408 61.111 0.00 0.00 45.31 4.69
1279 1645 2.285827 AATTCCGAAGCAGAGAGACG 57.714 50.000 0.00 0.00 0.00 4.18
1282 1648 3.181512 GCTGAAAATTCCGAAGCAGAGAG 60.182 47.826 0.00 0.00 34.01 3.20
1347 1721 3.066233 GACGTCCTCGGCCCTCTTC 62.066 68.421 3.51 0.00 39.49 2.87
1421 1795 1.420641 CGATCGAGCAATGCGGTGAA 61.421 55.000 10.26 0.00 0.00 3.18
1424 1799 2.586079 CCGATCGAGCAATGCGGT 60.586 61.111 18.66 0.00 37.35 5.68
1453 1849 2.153645 TGGCATGAGCAGTACACTTTG 58.846 47.619 0.00 0.00 44.61 2.77
1455 1851 2.566833 TTGGCATGAGCAGTACACTT 57.433 45.000 0.00 0.00 44.61 3.16
1608 2025 2.558378 CATGCGGAACAGATCATCAGT 58.442 47.619 0.00 0.00 0.00 3.41
1609 2026 1.263484 GCATGCGGAACAGATCATCAG 59.737 52.381 0.00 0.00 0.00 2.90
1755 2193 2.093306 TGACGCGATCATTTCTTGGT 57.907 45.000 15.93 0.00 29.99 3.67
1787 2225 6.816640 CGGATTTTACAAGAGATACAACAGGA 59.183 38.462 0.00 0.00 0.00 3.86
1812 2251 2.108700 CTTGCACGCACACAAAACTAC 58.891 47.619 0.00 0.00 0.00 2.73
1813 2252 1.740585 ACTTGCACGCACACAAAACTA 59.259 42.857 0.00 0.00 0.00 2.24
1818 2257 0.029167 CATCACTTGCACGCACACAA 59.971 50.000 0.00 0.00 0.00 3.33
1845 2285 6.690098 CGCGACACTGTTTACATAGTACTATT 59.310 38.462 12.87 7.55 0.00 1.73
1849 2289 4.406069 TCGCGACACTGTTTACATAGTAC 58.594 43.478 3.71 0.00 0.00 2.73
1850 2290 4.683501 TCGCGACACTGTTTACATAGTA 57.316 40.909 3.71 0.00 0.00 1.82
1851 2291 3.564235 TCGCGACACTGTTTACATAGT 57.436 42.857 3.71 0.00 0.00 2.12
1852 2292 4.896562 TTTCGCGACACTGTTTACATAG 57.103 40.909 9.15 0.00 0.00 2.23
1901 2341 5.157781 TGCCGTTTGTAATGCTGAAAATAC 58.842 37.500 0.00 0.00 0.00 1.89
1952 2392 8.827177 TTGGATTATTATCTATGGTCGTTGAC 57.173 34.615 0.00 0.00 0.00 3.18
1953 2393 8.647796 ACTTGGATTATTATCTATGGTCGTTGA 58.352 33.333 0.00 0.00 0.00 3.18
2226 2674 3.980646 TTGTCGATTGGGAAGTGTTTG 57.019 42.857 0.00 0.00 0.00 2.93
2227 2675 5.768164 ACTTATTGTCGATTGGGAAGTGTTT 59.232 36.000 0.00 0.00 0.00 2.83
2330 2778 1.512926 GTCGTCAATGGTGAAGCAGT 58.487 50.000 0.00 0.00 34.87 4.40
2384 2834 6.533723 TCAATCGTACTTTCGCAATATCTGTT 59.466 34.615 0.00 0.00 0.00 3.16
2396 2846 9.784680 TCTGTAAGTATTCTCAATCGTACTTTC 57.215 33.333 2.45 0.00 38.14 2.62
2403 2853 6.346439 GCTGCATCTGTAAGTATTCTCAATCG 60.346 42.308 0.00 0.00 33.76 3.34
2447 2897 2.590821 ACTTTTTGCAGATCACCAGCT 58.409 42.857 0.00 0.00 0.00 4.24
2541 2991 2.401320 GCATTTGGCGATTGGAATGCC 61.401 52.381 8.32 0.00 45.20 4.40
2574 3024 9.248291 GAACTGATTGCTTTTAATTTCTGTGAA 57.752 29.630 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.