Multiple sequence alignment - TraesCS4A01G234000

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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 TraesCS4A01G234000 chr4A 100.000 3301 0 0 1 3301 542826942 542830242 0.000000e+00 6096
1 TraesCS4A01G234000 chr4B 94.287 1628 63 14 698 2321 79738374 79736773 0.000000e+00 2464
2 TraesCS4A01G234000 chr4B 88.889 702 60 13 2609 3300 79736777 79736084 0.000000e+00 848
3 TraesCS4A01G234000 chr4B 88.506 348 32 5 1 343 481525372 481525028 6.590000e-112 414
4 TraesCS4A01G234000 chr4B 96.330 109 3 1 589 697 79738534 79738427 9.410000e-41 178
5 TraesCS4A01G234000 chr4D 93.919 1628 57 12 589 2185 54128211 54126595 0.000000e+00 2420
6 TraesCS4A01G234000 chr4D 90.917 1145 72 19 2183 3301 54126435 54125297 0.000000e+00 1509
7 TraesCS4A01G234000 chr3D 87.262 526 50 4 1 510 342802709 342802185 4.750000e-163 584
8 TraesCS4A01G234000 chr3D 86.842 152 18 2 1297 1447 61703549 61703399 5.660000e-38 169
9 TraesCS4A01G234000 chrUn 89.462 446 40 4 1 440 86405984 86406428 1.030000e-154 556
10 TraesCS4A01G234000 chr2B 85.985 528 54 9 1 512 239813048 239812525 6.230000e-152 547
11 TraesCS4A01G234000 chr2B 85.488 441 47 9 1 425 554452004 554452443 8.410000e-121 444
12 TraesCS4A01G234000 chr2B 81.958 521 72 13 4 510 239625131 239624619 3.940000e-114 422
13 TraesCS4A01G234000 chr2B 88.732 142 11 5 1295 1433 777618672 777618533 5.660000e-38 169
14 TraesCS4A01G234000 chr1A 88.470 451 47 2 1 447 370025877 370025428 1.040000e-149 540
15 TraesCS4A01G234000 chr1A 80.556 216 39 3 2385 2598 23418719 23418933 2.640000e-36 163
16 TraesCS4A01G234000 chr6B 87.500 464 39 7 1 447 159695654 159695193 4.880000e-143 518
17 TraesCS4A01G234000 chr6B 77.778 234 40 9 2324 2548 211811054 211811284 2.070000e-27 134
18 TraesCS4A01G234000 chr6D 84.645 521 64 9 1 512 386297581 386297068 3.800000e-139 505
19 TraesCS4A01G234000 chr7D 81.818 253 40 4 2339 2586 123454840 123454589 1.200000e-49 207
20 TraesCS4A01G234000 chr7D 81.224 245 36 8 2366 2601 199400972 199400729 4.350000e-44 189
21 TraesCS4A01G234000 chr2D 90.141 142 10 4 1295 1434 634556345 634556206 7.280000e-42 182
22 TraesCS4A01G234000 chr1B 78.723 282 49 9 2324 2596 136920969 136921248 9.410000e-41 178
23 TraesCS4A01G234000 chr3B 87.500 152 17 2 1297 1447 99171521 99171371 1.220000e-39 174
24 TraesCS4A01G234000 chr3A 87.500 152 17 2 1297 1447 70730649 70730499 1.220000e-39 174
25 TraesCS4A01G234000 chr2A 78.007 291 53 9 2321 2601 706508564 706508275 4.380000e-39 172
26 TraesCS4A01G234000 chr2A 88.732 142 12 4 1295 1434 778827534 778827673 1.580000e-38 171
27 TraesCS4A01G234000 chr5B 78.417 278 49 6 2324 2599 705077678 705077946 1.580000e-38 171
28 TraesCS4A01G234000 chr5B 79.439 214 35 8 2339 2548 702263729 702263521 3.430000e-30 143
29 TraesCS4A01G234000 chr6A 82.723 191 32 1 257 447 531401374 531401185 5.660000e-38 169
30 TraesCS4A01G234000 chr5D 85.526 152 19 3 1285 1434 365992569 365992719 4.410000e-34 156


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 TraesCS4A01G234000 chr4A 542826942 542830242 3300 False 6096.000000 6096 100.000000 1 3301 1 chr4A.!!$F1 3300
1 TraesCS4A01G234000 chr4B 79736084 79738534 2450 True 1163.333333 2464 93.168667 589 3300 3 chr4B.!!$R2 2711
2 TraesCS4A01G234000 chr4D 54125297 54128211 2914 True 1964.500000 2420 92.418000 589 3301 2 chr4D.!!$R1 2712
3 TraesCS4A01G234000 chr3D 342802185 342802709 524 True 584.000000 584 87.262000 1 510 1 chr3D.!!$R2 509
4 TraesCS4A01G234000 chr2B 239812525 239813048 523 True 547.000000 547 85.985000 1 512 1 chr2B.!!$R2 511
5 TraesCS4A01G234000 chr2B 239624619 239625131 512 True 422.000000 422 81.958000 4 510 1 chr2B.!!$R1 506
6 TraesCS4A01G234000 chr6D 386297068 386297581 513 True 505.000000 505 84.645000 1 512 1 chr6D.!!$R1 511

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
946 1043 0.312102 CTCGCTCACTCACACACTCA 59.688 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2893 3177 0.391661 GAGCTCTTTCCATCGCACCA 60.392 55.0 6.43 0.0 0.0 4.17 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
47 48 7.704047 GCATAATATGATCGTAGAAGATGAGCA 59.296 37.037 4.14 0.00 43.42 4.26
55 56 2.777832 AGAAGATGAGCACCCAGAAC 57.222 50.000 0.00 0.00 0.00 3.01
105 106 2.229792 GGTGAGAATGTTGTGCCTGAA 58.770 47.619 0.00 0.00 0.00 3.02
110 111 3.489355 AGAATGTTGTGCCTGAACATGA 58.511 40.909 0.00 0.00 42.04 3.07
117 118 0.694771 TGCCTGAACATGAAGGAGCT 59.305 50.000 15.18 0.00 35.40 4.09
137 138 1.326245 TGCAACGTTCGAACAGTTCAG 59.674 47.619 26.71 18.73 0.00 3.02
153 155 5.421056 ACAGTTCAGCCAATTTCATCATGAT 59.579 36.000 1.18 1.18 0.00 2.45
172 174 4.269183 TGATATGCGTGATTGGGAAACTT 58.731 39.130 0.00 0.00 0.00 2.66
183 185 7.319646 GTGATTGGGAAACTTACATGCAATTA 58.680 34.615 0.00 0.00 0.00 1.40
236 243 5.822519 TGTTGGCAACCAATAGATGTATCTC 59.177 40.000 26.31 0.00 45.80 2.75
394 406 3.216292 ACGCCGGCAAATATGGGC 61.216 61.111 28.98 0.00 42.14 5.36
401 413 3.215568 CAAATATGGGCCGGCGCA 61.216 61.111 43.00 43.00 42.90 6.09
443 455 3.883744 CTCAAACCTGGCGGACGCT 62.884 63.158 16.72 0.00 41.60 5.07
455 488 2.049802 GACGCTCGACCCAAACGA 60.050 61.111 0.00 0.00 38.11 3.85
457 490 1.005394 ACGCTCGACCCAAACGAAT 60.005 52.632 0.00 0.00 39.23 3.34
487 520 0.871722 CCAAAGCGTCATCCGTTTGA 59.128 50.000 0.00 0.00 39.19 2.69
490 523 2.734606 CAAAGCGTCATCCGTTTGAGTA 59.265 45.455 0.00 0.00 39.19 2.59
491 524 2.961526 AGCGTCATCCGTTTGAGTAT 57.038 45.000 0.00 0.00 39.32 2.12
493 526 2.094182 AGCGTCATCCGTTTGAGTATGT 60.094 45.455 0.00 0.00 39.32 2.29
512 545 1.871039 GTGCGTTGGAGTTGCTCTAAA 59.129 47.619 0.00 0.00 33.06 1.85
513 546 2.289547 GTGCGTTGGAGTTGCTCTAAAA 59.710 45.455 0.00 0.00 33.06 1.52
514 547 2.946329 TGCGTTGGAGTTGCTCTAAAAA 59.054 40.909 0.00 0.00 33.06 1.94
515 548 3.242936 TGCGTTGGAGTTGCTCTAAAAAC 60.243 43.478 0.00 0.00 33.06 2.43
516 549 3.541711 CGTTGGAGTTGCTCTAAAAACG 58.458 45.455 0.00 0.00 33.06 3.60
517 550 3.606153 CGTTGGAGTTGCTCTAAAAACGG 60.606 47.826 13.44 0.00 33.06 4.44
518 551 3.478857 TGGAGTTGCTCTAAAAACGGA 57.521 42.857 0.00 0.00 0.00 4.69
519 552 3.135994 TGGAGTTGCTCTAAAAACGGAC 58.864 45.455 0.00 0.00 0.00 4.79
520 553 2.483106 GGAGTTGCTCTAAAAACGGACC 59.517 50.000 0.00 0.00 0.00 4.46
521 554 2.483106 GAGTTGCTCTAAAAACGGACCC 59.517 50.000 0.00 0.00 0.00 4.46
522 555 2.158726 AGTTGCTCTAAAAACGGACCCA 60.159 45.455 0.00 0.00 0.00 4.51
523 556 2.619646 GTTGCTCTAAAAACGGACCCAA 59.380 45.455 0.00 0.00 0.00 4.12
524 557 2.933573 TGCTCTAAAAACGGACCCAAA 58.066 42.857 0.00 0.00 0.00 3.28
525 558 3.492337 TGCTCTAAAAACGGACCCAAAT 58.508 40.909 0.00 0.00 0.00 2.32
526 559 3.254657 TGCTCTAAAAACGGACCCAAATG 59.745 43.478 0.00 0.00 0.00 2.32
527 560 3.833442 CTCTAAAAACGGACCCAAATGC 58.167 45.455 0.00 0.00 0.00 3.56
528 561 3.223435 TCTAAAAACGGACCCAAATGCA 58.777 40.909 0.00 0.00 0.00 3.96
529 562 2.990066 AAAAACGGACCCAAATGCAA 57.010 40.000 0.00 0.00 0.00 4.08
530 563 2.524569 AAAACGGACCCAAATGCAAG 57.475 45.000 0.00 0.00 0.00 4.01
531 564 1.408969 AAACGGACCCAAATGCAAGT 58.591 45.000 0.00 0.00 0.00 3.16
532 565 1.408969 AACGGACCCAAATGCAAGTT 58.591 45.000 0.00 0.00 0.00 2.66
533 566 0.673437 ACGGACCCAAATGCAAGTTG 59.327 50.000 0.00 0.00 42.43 3.16
534 567 0.673437 CGGACCCAAATGCAAGTTGT 59.327 50.000 4.48 0.00 40.94 3.32
535 568 1.602668 CGGACCCAAATGCAAGTTGTG 60.603 52.381 4.48 4.13 40.94 3.33
536 569 1.270252 GGACCCAAATGCAAGTTGTGG 60.270 52.381 4.48 12.99 40.94 4.17
537 570 1.412343 GACCCAAATGCAAGTTGTGGT 59.588 47.619 18.32 18.32 44.18 4.16
538 571 2.625790 GACCCAAATGCAAGTTGTGGTA 59.374 45.455 18.30 0.00 42.52 3.25
539 572 2.627699 ACCCAAATGCAAGTTGTGGTAG 59.372 45.455 17.48 0.00 41.36 3.18
540 573 2.627699 CCCAAATGCAAGTTGTGGTAGT 59.372 45.455 4.48 0.00 40.94 2.73
541 574 3.552684 CCCAAATGCAAGTTGTGGTAGTG 60.553 47.826 4.48 0.00 40.94 2.74
542 575 3.052036 CAAATGCAAGTTGTGGTAGTGC 58.948 45.455 4.48 0.00 37.10 4.40
543 576 3.485764 TGCAAGTTGTGGTAGTGCA 57.514 47.368 4.48 0.00 42.62 4.57
544 577 1.308047 TGCAAGTTGTGGTAGTGCAG 58.692 50.000 4.48 0.00 40.14 4.41
545 578 1.134250 TGCAAGTTGTGGTAGTGCAGA 60.134 47.619 4.48 0.00 40.14 4.26
546 579 1.532868 GCAAGTTGTGGTAGTGCAGAG 59.467 52.381 4.48 0.00 35.28 3.35
547 580 2.838736 CAAGTTGTGGTAGTGCAGAGT 58.161 47.619 0.00 0.00 0.00 3.24
548 581 3.206150 CAAGTTGTGGTAGTGCAGAGTT 58.794 45.455 0.00 0.00 0.00 3.01
549 582 3.113260 AGTTGTGGTAGTGCAGAGTTC 57.887 47.619 0.00 0.00 0.00 3.01
550 583 2.434336 AGTTGTGGTAGTGCAGAGTTCA 59.566 45.455 0.00 0.00 0.00 3.18
551 584 2.526304 TGTGGTAGTGCAGAGTTCAC 57.474 50.000 0.00 0.00 34.80 3.18
552 585 2.039418 TGTGGTAGTGCAGAGTTCACT 58.961 47.619 0.00 1.18 45.71 3.41
553 586 2.434336 TGTGGTAGTGCAGAGTTCACTT 59.566 45.455 0.77 0.00 41.61 3.16
554 587 3.118408 TGTGGTAGTGCAGAGTTCACTTT 60.118 43.478 0.77 0.00 41.61 2.66
555 588 3.248602 GTGGTAGTGCAGAGTTCACTTTG 59.751 47.826 0.77 0.00 41.61 2.77
556 589 2.808543 GGTAGTGCAGAGTTCACTTTGG 59.191 50.000 0.77 0.00 41.61 3.28
557 590 1.312815 AGTGCAGAGTTCACTTTGGC 58.687 50.000 0.00 0.00 41.61 4.52
558 591 1.024271 GTGCAGAGTTCACTTTGGCA 58.976 50.000 0.00 0.00 0.00 4.92
559 592 1.405105 GTGCAGAGTTCACTTTGGCAA 59.595 47.619 0.00 0.00 31.74 4.52
560 593 1.677576 TGCAGAGTTCACTTTGGCAAG 59.322 47.619 0.00 0.00 35.92 4.01
561 594 1.678101 GCAGAGTTCACTTTGGCAAGT 59.322 47.619 0.00 0.00 44.72 3.16
562 595 2.099756 GCAGAGTTCACTTTGGCAAGTT 59.900 45.455 0.00 0.00 40.66 2.66
563 596 3.429410 GCAGAGTTCACTTTGGCAAGTTT 60.429 43.478 0.00 0.00 40.66 2.66
564 597 4.747810 CAGAGTTCACTTTGGCAAGTTTT 58.252 39.130 0.00 0.00 40.66 2.43
565 598 5.678616 GCAGAGTTCACTTTGGCAAGTTTTA 60.679 40.000 0.00 0.00 40.66 1.52
566 599 6.329496 CAGAGTTCACTTTGGCAAGTTTTAA 58.671 36.000 0.00 0.00 40.66 1.52
567 600 6.811170 CAGAGTTCACTTTGGCAAGTTTTAAA 59.189 34.615 0.00 0.00 40.66 1.52
568 601 6.811665 AGAGTTCACTTTGGCAAGTTTTAAAC 59.188 34.615 0.00 0.00 40.66 2.01
569 602 5.872617 AGTTCACTTTGGCAAGTTTTAAACC 59.127 36.000 4.01 0.00 40.66 3.27
570 603 5.407407 TCACTTTGGCAAGTTTTAAACCA 57.593 34.783 4.01 0.00 40.66 3.67
571 604 5.794894 TCACTTTGGCAAGTTTTAAACCAA 58.205 33.333 4.01 3.71 40.66 3.67
572 605 6.231211 TCACTTTGGCAAGTTTTAAACCAAA 58.769 32.000 15.35 15.35 45.55 3.28
573 606 6.881602 TCACTTTGGCAAGTTTTAAACCAAAT 59.118 30.769 16.13 7.75 46.27 2.32
574 607 7.065204 TCACTTTGGCAAGTTTTAAACCAAATC 59.935 33.333 16.13 0.00 46.27 2.17
575 608 6.881602 ACTTTGGCAAGTTTTAAACCAAATCA 59.118 30.769 16.13 0.91 46.27 2.57
576 609 7.555914 ACTTTGGCAAGTTTTAAACCAAATCAT 59.444 29.630 16.13 6.67 46.27 2.45
577 610 7.489574 TTGGCAAGTTTTAAACCAAATCATC 57.510 32.000 4.01 0.00 37.45 2.92
578 611 6.586344 TGGCAAGTTTTAAACCAAATCATCA 58.414 32.000 4.01 0.00 0.00 3.07
579 612 6.481644 TGGCAAGTTTTAAACCAAATCATCAC 59.518 34.615 4.01 0.00 0.00 3.06
580 613 6.481644 GGCAAGTTTTAAACCAAATCATCACA 59.518 34.615 4.01 0.00 0.00 3.58
581 614 7.173047 GGCAAGTTTTAAACCAAATCATCACAT 59.827 33.333 4.01 0.00 0.00 3.21
582 615 8.558700 GCAAGTTTTAAACCAAATCATCACATT 58.441 29.630 4.01 0.00 0.00 2.71
585 618 9.696917 AGTTTTAAACCAAATCATCACATTCTC 57.303 29.630 4.01 0.00 0.00 2.87
586 619 9.696917 GTTTTAAACCAAATCATCACATTCTCT 57.303 29.630 0.00 0.00 0.00 3.10
589 622 9.513906 TTAAACCAAATCATCACATTCTCTACA 57.486 29.630 0.00 0.00 0.00 2.74
590 623 8.408043 AAACCAAATCATCACATTCTCTACAA 57.592 30.769 0.00 0.00 0.00 2.41
591 624 7.621428 ACCAAATCATCACATTCTCTACAAG 57.379 36.000 0.00 0.00 0.00 3.16
592 625 7.170965 ACCAAATCATCACATTCTCTACAAGT 58.829 34.615 0.00 0.00 0.00 3.16
593 626 8.321353 ACCAAATCATCACATTCTCTACAAGTA 58.679 33.333 0.00 0.00 0.00 2.24
670 703 3.799420 GCATGTTGCTGTAGTACTAGCTC 59.201 47.826 16.62 11.03 40.96 4.09
714 799 9.998106 GCAGTAGTATATAGAATGGGAGAAAAA 57.002 33.333 0.00 0.00 0.00 1.94
732 817 9.244799 GGAGAAAAACCATTTACTTTTACTGTG 57.755 33.333 0.00 0.00 0.00 3.66
905 992 2.102420 CCATCACCTACAACGCCTATCA 59.898 50.000 0.00 0.00 0.00 2.15
906 993 3.384668 CATCACCTACAACGCCTATCAG 58.615 50.000 0.00 0.00 0.00 2.90
909 996 2.427453 CACCTACAACGCCTATCAGACT 59.573 50.000 0.00 0.00 0.00 3.24
910 997 2.427453 ACCTACAACGCCTATCAGACTG 59.573 50.000 0.00 0.00 0.00 3.51
930 1027 0.730834 CACACACCTTCTCTCGCTCG 60.731 60.000 0.00 0.00 0.00 5.03
940 1037 1.916697 CTCTCGCTCGCTCACTCACA 61.917 60.000 0.00 0.00 0.00 3.58
945 1042 1.006314 GCTCGCTCACTCACACACTC 61.006 60.000 0.00 0.00 0.00 3.51
946 1043 0.312102 CTCGCTCACTCACACACTCA 59.688 55.000 0.00 0.00 0.00 3.41
951 1048 2.861750 GCTCACTCACACACTCACTCTG 60.862 54.545 0.00 0.00 0.00 3.35
1009 1106 2.167487 TCCCAAAACAGCAAAACTCACC 59.833 45.455 0.00 0.00 0.00 4.02
1045 1142 2.378028 GCTCGAGCTCCATTGTCAC 58.622 57.895 29.88 0.00 38.21 3.67
1055 1152 2.267426 TCCATTGTCACAATACGAGCG 58.733 47.619 1.72 0.00 0.00 5.03
1078 1175 0.823356 ACACACCCACATTGCACCTC 60.823 55.000 0.00 0.00 0.00 3.85
1082 1179 1.679977 CCCACATTGCACCTCCAGG 60.680 63.158 0.00 0.00 42.17 4.45
1083 1180 1.679977 CCACATTGCACCTCCAGGG 60.680 63.158 0.00 0.00 40.27 4.45
1084 1181 2.036256 ACATTGCACCTCCAGGGC 59.964 61.111 0.00 0.00 40.27 5.19
1085 1182 2.757099 CATTGCACCTCCAGGGCC 60.757 66.667 0.00 0.00 40.27 5.80
1086 1183 3.267233 ATTGCACCTCCAGGGCCA 61.267 61.111 6.18 0.00 40.27 5.36
1112 1209 2.435938 TCGAACGCCATGGAAGCC 60.436 61.111 18.40 0.00 0.00 4.35
1748 1848 4.147449 CCGATGCTCTGGCCGACA 62.147 66.667 0.00 0.00 37.74 4.35
1928 2029 1.682323 TGGTCAGTAGTTGTGTGCGTA 59.318 47.619 0.00 0.00 0.00 4.42
1954 2055 0.248907 GTGATGGCTCATGCATGTGC 60.249 55.000 34.70 34.70 44.16 4.57
1979 2080 3.871594 GCTGGATTATGTGTGTGTAGGTC 59.128 47.826 0.00 0.00 0.00 3.85
2022 2123 0.928229 GCTCGTGTCGTGTCTTGTTT 59.072 50.000 0.00 0.00 0.00 2.83
2048 2149 3.350833 AGTACGTAGTGGTACAAGGAGG 58.649 50.000 1.10 0.00 45.73 4.30
2155 2259 4.585162 TGGTGTTATTTGTTGGGTACTTGG 59.415 41.667 0.00 0.00 0.00 3.61
2156 2260 4.021807 GGTGTTATTTGTTGGGTACTTGGG 60.022 45.833 0.00 0.00 0.00 4.12
2293 2559 4.340950 TCAAAGAATTGTTCAGACCCAACC 59.659 41.667 0.00 0.00 37.79 3.77
2321 2587 8.574196 AAAAAGAAATGTCCAAACAATCGTAG 57.426 30.769 0.00 0.00 39.30 3.51
2326 2592 5.705609 ATGTCCAAACAATCGTAGCTTTT 57.294 34.783 0.00 0.00 39.30 2.27
2375 2641 8.883954 GCTCATATATATGTGCATACACTCAT 57.116 34.615 30.93 0.00 46.63 2.90
2389 2655 2.435805 ACACTCATCCCTATGAACGCAT 59.564 45.455 0.00 0.00 41.57 4.73
2396 2662 2.895404 TCCCTATGAACGCATACCCTAC 59.105 50.000 0.00 0.00 35.94 3.18
2411 2677 2.022918 ACCCTACTCCTATGAGCACCTT 60.023 50.000 0.00 0.00 42.74 3.50
2415 2681 3.902881 ACTCCTATGAGCACCTTTGAG 57.097 47.619 0.00 0.00 42.74 3.02
2417 2683 3.450457 ACTCCTATGAGCACCTTTGAGAG 59.550 47.826 0.00 0.00 42.74 3.20
2424 2690 2.298729 GAGCACCTTTGAGAGACTGAGT 59.701 50.000 0.00 0.00 0.00 3.41
2430 2696 3.192422 CCTTTGAGAGACTGAGTCGACAT 59.808 47.826 19.50 2.45 37.67 3.06
2449 2715 7.063426 GTCGACATGTCATCTTGAGATTTTACA 59.937 37.037 24.93 0.00 26.66 2.41
2465 2731 7.965045 AGATTTTACAAAGTCATCTTAGACGC 58.035 34.615 0.86 0.00 43.24 5.19
2467 2733 3.678056 ACAAAGTCATCTTAGACGCCA 57.322 42.857 0.00 0.00 43.24 5.69
2472 2738 2.751259 AGTCATCTTAGACGCCACGTAA 59.249 45.455 0.00 0.00 41.37 3.18
2474 2740 3.729716 GTCATCTTAGACGCCACGTAATC 59.270 47.826 0.00 0.00 41.37 1.75
2477 2743 2.615447 TCTTAGACGCCACGTAATCGAT 59.385 45.455 9.68 0.00 41.37 3.59
2485 2751 0.575390 CACGTAATCGATGGGAACGC 59.425 55.000 17.47 0.00 40.62 4.84
2488 2754 1.499049 GTAATCGATGGGAACGCCTC 58.501 55.000 0.00 0.00 0.00 4.70
2491 2757 1.338136 ATCGATGGGAACGCCTCCTT 61.338 55.000 0.00 0.00 44.68 3.36
2493 2759 1.153147 GATGGGAACGCCTCCTTCC 60.153 63.158 4.28 0.00 44.68 3.46
2495 2761 1.281925 ATGGGAACGCCTCCTTCCAT 61.282 55.000 4.36 0.00 44.68 3.41
2497 2763 1.032114 GGGAACGCCTCCTTCCATTG 61.032 60.000 4.36 0.00 44.68 2.82
2512 2778 4.009370 TCCATTGAACGTGTATCACCAA 57.991 40.909 0.00 0.00 0.00 3.67
2526 2792 9.219603 CGTGTATCACCAAAAATCCTGATATAT 57.780 33.333 0.00 0.00 30.33 0.86
2574 2840 4.785301 GATTTGAATCCTGATGGACTGGA 58.215 43.478 0.00 0.00 46.51 3.86
2579 2845 5.684704 TGAATCCTGATGGACTGGAATAAC 58.315 41.667 0.00 0.00 46.51 1.89
2582 2848 4.104086 TCCTGATGGACTGGAATAACACT 58.896 43.478 0.00 0.00 42.27 3.55
2586 2852 4.532126 TGATGGACTGGAATAACACTGTCT 59.468 41.667 0.00 0.00 36.29 3.41
2587 2853 4.271696 TGGACTGGAATAACACTGTCTG 57.728 45.455 0.00 0.00 36.29 3.51
2601 2867 4.081420 ACACTGTCTGCCTAACCATCTAAG 60.081 45.833 0.00 0.00 0.00 2.18
2605 2871 4.404715 TGTCTGCCTAACCATCTAAGTACC 59.595 45.833 0.00 0.00 0.00 3.34
2621 2904 4.724074 AGTACCCGTCGTAATTGAATCA 57.276 40.909 0.00 0.00 0.00 2.57
2693 2976 8.721478 CAGTCTGTAACAGTATTGCATTACTTT 58.279 33.333 16.66 15.44 29.93 2.66
2809 3093 6.699642 GGATCAACAAAATTCCTTTTCGTTCA 59.300 34.615 0.00 0.00 32.21 3.18
2893 3177 4.472690 AGGGACCTCCTATTTATCGACT 57.527 45.455 0.00 0.00 45.98 4.18
2898 3182 3.069729 ACCTCCTATTTATCGACTGGTGC 59.930 47.826 0.00 0.00 0.00 5.01
3056 3346 9.502091 AAGGCTCATAAAATTTTAGAAAAACCC 57.498 29.630 15.45 9.22 0.00 4.11
3058 3348 9.278978 GGCTCATAAAATTTTAGAAAAACCCAA 57.721 29.630 15.45 0.00 0.00 4.12
3291 3586 8.828644 TCAAACATGAACAAGAAATGAAAATGG 58.171 29.630 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.741647 TCATCTTCTACGATCATATTATGCATC 57.258 33.333 0.19 3.33 0.00 3.91
78 79 3.743521 CACAACATTCTCACCCTGAAGA 58.256 45.455 0.00 0.00 0.00 2.87
79 80 2.227388 GCACAACATTCTCACCCTGAAG 59.773 50.000 0.00 0.00 0.00 3.02
105 106 0.250467 ACGTTGCAGCTCCTTCATGT 60.250 50.000 0.00 0.00 0.00 3.21
110 111 0.531974 TTCGAACGTTGCAGCTCCTT 60.532 50.000 5.00 0.00 0.00 3.36
117 118 1.326245 CTGAACTGTTCGAACGTTGCA 59.674 47.619 29.53 24.68 0.00 4.08
137 138 4.619760 CACGCATATCATGATGAAATTGGC 59.380 41.667 18.72 9.51 0.00 4.52
153 155 4.580868 TGTAAGTTTCCCAATCACGCATA 58.419 39.130 0.00 0.00 0.00 3.14
172 174 9.149225 GACCAAATCATTTTGTAATTGCATGTA 57.851 29.630 0.00 0.00 40.55 2.29
183 185 6.642430 CCCACATATGACCAAATCATTTTGT 58.358 36.000 10.38 0.00 46.54 2.83
236 243 8.011106 CACATAGTTTTGCAAGCCAAATAAAAG 58.989 33.333 0.00 0.00 42.63 2.27
244 252 2.954989 TGTCACATAGTTTTGCAAGCCA 59.045 40.909 0.00 0.00 0.00 4.75
412 424 1.260544 GTTTGAGATTTGGGCTGGCT 58.739 50.000 0.00 0.00 0.00 4.75
416 428 1.928868 CCAGGTTTGAGATTTGGGCT 58.071 50.000 0.00 0.00 0.00 5.19
417 429 0.247460 GCCAGGTTTGAGATTTGGGC 59.753 55.000 0.00 0.00 0.00 5.36
463 496 0.744414 CGGATGACGCTTTGGTCCAT 60.744 55.000 0.00 0.00 36.07 3.41
464 497 1.375396 CGGATGACGCTTTGGTCCA 60.375 57.895 0.00 0.00 36.07 4.02
487 520 1.156736 GCAACTCCAACGCACATACT 58.843 50.000 0.00 0.00 0.00 2.12
490 523 0.250467 AGAGCAACTCCAACGCACAT 60.250 50.000 0.00 0.00 0.00 3.21
491 524 0.391228 TAGAGCAACTCCAACGCACA 59.609 50.000 0.00 0.00 0.00 4.57
493 526 2.248280 TTTAGAGCAACTCCAACGCA 57.752 45.000 0.00 0.00 0.00 5.24
512 545 1.408969 ACTTGCATTTGGGTCCGTTT 58.591 45.000 0.00 0.00 0.00 3.60
513 546 1.068434 CAACTTGCATTTGGGTCCGTT 59.932 47.619 0.00 0.00 0.00 4.44
514 547 0.673437 CAACTTGCATTTGGGTCCGT 59.327 50.000 0.00 0.00 0.00 4.69
515 548 0.673437 ACAACTTGCATTTGGGTCCG 59.327 50.000 11.99 0.00 0.00 4.79
516 549 1.270252 CCACAACTTGCATTTGGGTCC 60.270 52.381 11.99 0.00 0.00 4.46
517 550 1.412343 ACCACAACTTGCATTTGGGTC 59.588 47.619 11.99 0.00 0.00 4.46
518 551 1.494960 ACCACAACTTGCATTTGGGT 58.505 45.000 11.99 12.15 0.00 4.51
519 552 2.627699 ACTACCACAACTTGCATTTGGG 59.372 45.455 11.99 8.31 0.00 4.12
520 553 3.641648 CACTACCACAACTTGCATTTGG 58.358 45.455 11.99 2.05 0.00 3.28
521 554 3.052036 GCACTACCACAACTTGCATTTG 58.948 45.455 6.96 6.96 33.24 2.32
522 555 2.692557 TGCACTACCACAACTTGCATTT 59.307 40.909 0.00 0.00 38.25 2.32
523 556 2.294233 CTGCACTACCACAACTTGCATT 59.706 45.455 0.00 0.00 42.09 3.56
524 557 1.881973 CTGCACTACCACAACTTGCAT 59.118 47.619 0.00 0.00 42.09 3.96
525 558 1.134250 TCTGCACTACCACAACTTGCA 60.134 47.619 0.00 0.00 40.81 4.08
526 559 1.532868 CTCTGCACTACCACAACTTGC 59.467 52.381 0.00 0.00 0.00 4.01
527 560 2.838736 ACTCTGCACTACCACAACTTG 58.161 47.619 0.00 0.00 0.00 3.16
528 561 3.118408 TGAACTCTGCACTACCACAACTT 60.118 43.478 0.00 0.00 0.00 2.66
529 562 2.434336 TGAACTCTGCACTACCACAACT 59.566 45.455 0.00 0.00 0.00 3.16
530 563 2.544267 GTGAACTCTGCACTACCACAAC 59.456 50.000 0.00 0.00 33.57 3.32
531 564 2.434336 AGTGAACTCTGCACTACCACAA 59.566 45.455 0.00 0.00 44.27 3.33
532 565 2.039418 AGTGAACTCTGCACTACCACA 58.961 47.619 0.00 0.00 44.27 4.17
533 566 2.821991 AGTGAACTCTGCACTACCAC 57.178 50.000 0.00 0.00 44.27 4.16
534 567 3.466836 CAAAGTGAACTCTGCACTACCA 58.533 45.455 0.00 0.00 45.27 3.25
535 568 2.808543 CCAAAGTGAACTCTGCACTACC 59.191 50.000 0.00 0.00 45.27 3.18
536 569 2.224314 GCCAAAGTGAACTCTGCACTAC 59.776 50.000 0.00 0.00 45.27 2.73
537 570 2.158827 TGCCAAAGTGAACTCTGCACTA 60.159 45.455 0.00 0.00 45.27 2.74
539 572 1.024271 TGCCAAAGTGAACTCTGCAC 58.976 50.000 0.00 0.00 36.53 4.57
540 573 1.677576 CTTGCCAAAGTGAACTCTGCA 59.322 47.619 0.00 0.00 0.00 4.41
541 574 1.678101 ACTTGCCAAAGTGAACTCTGC 59.322 47.619 0.00 0.00 45.12 4.26
542 575 4.376340 AAACTTGCCAAAGTGAACTCTG 57.624 40.909 0.00 0.00 46.15 3.35
543 576 6.524101 TTAAAACTTGCCAAAGTGAACTCT 57.476 33.333 0.00 0.00 46.15 3.24
544 577 6.035650 GGTTTAAAACTTGCCAAAGTGAACTC 59.964 38.462 0.00 0.00 46.15 3.01
545 578 5.872617 GGTTTAAAACTTGCCAAAGTGAACT 59.127 36.000 0.00 0.00 46.15 3.01
546 579 5.639931 TGGTTTAAAACTTGCCAAAGTGAAC 59.360 36.000 4.60 0.00 46.15 3.18
547 580 5.794894 TGGTTTAAAACTTGCCAAAGTGAA 58.205 33.333 4.60 0.00 46.15 3.18
548 581 5.407407 TGGTTTAAAACTTGCCAAAGTGA 57.593 34.783 4.60 0.00 46.15 3.41
549 582 6.487689 TTTGGTTTAAAACTTGCCAAAGTG 57.512 33.333 13.23 0.00 46.15 3.16
553 586 7.011857 GTGATGATTTGGTTTAAAACTTGCCAA 59.988 33.333 4.60 4.09 37.42 4.52
554 587 6.481644 GTGATGATTTGGTTTAAAACTTGCCA 59.518 34.615 4.60 0.00 0.00 4.92
555 588 6.481644 TGTGATGATTTGGTTTAAAACTTGCC 59.518 34.615 4.60 0.00 0.00 4.52
556 589 7.475771 TGTGATGATTTGGTTTAAAACTTGC 57.524 32.000 4.60 0.00 0.00 4.01
559 592 9.696917 GAGAATGTGATGATTTGGTTTAAAACT 57.303 29.630 4.60 0.00 0.00 2.66
560 593 9.696917 AGAGAATGTGATGATTTGGTTTAAAAC 57.303 29.630 0.00 0.00 0.00 2.43
563 596 9.513906 TGTAGAGAATGTGATGATTTGGTTTAA 57.486 29.630 0.00 0.00 0.00 1.52
564 597 9.513906 TTGTAGAGAATGTGATGATTTGGTTTA 57.486 29.630 0.00 0.00 0.00 2.01
565 598 8.408043 TTGTAGAGAATGTGATGATTTGGTTT 57.592 30.769 0.00 0.00 0.00 3.27
566 599 7.667219 ACTTGTAGAGAATGTGATGATTTGGTT 59.333 33.333 0.00 0.00 0.00 3.67
567 600 7.170965 ACTTGTAGAGAATGTGATGATTTGGT 58.829 34.615 0.00 0.00 0.00 3.67
568 601 7.621428 ACTTGTAGAGAATGTGATGATTTGG 57.379 36.000 0.00 0.00 0.00 3.28
572 605 8.887717 GCTTTTACTTGTAGAGAATGTGATGAT 58.112 33.333 0.00 0.00 0.00 2.45
573 606 7.334421 GGCTTTTACTTGTAGAGAATGTGATGA 59.666 37.037 0.00 0.00 0.00 2.92
574 607 7.119699 TGGCTTTTACTTGTAGAGAATGTGATG 59.880 37.037 0.00 0.00 0.00 3.07
575 608 7.168219 TGGCTTTTACTTGTAGAGAATGTGAT 58.832 34.615 0.00 0.00 0.00 3.06
576 609 6.530120 TGGCTTTTACTTGTAGAGAATGTGA 58.470 36.000 0.00 0.00 0.00 3.58
577 610 6.650807 TCTGGCTTTTACTTGTAGAGAATGTG 59.349 38.462 0.00 0.00 0.00 3.21
578 611 6.769512 TCTGGCTTTTACTTGTAGAGAATGT 58.230 36.000 0.00 0.00 0.00 2.71
579 612 6.314896 CCTCTGGCTTTTACTTGTAGAGAATG 59.685 42.308 0.00 0.00 33.76 2.67
580 613 6.410540 CCTCTGGCTTTTACTTGTAGAGAAT 58.589 40.000 0.00 0.00 33.76 2.40
581 614 5.794894 CCTCTGGCTTTTACTTGTAGAGAA 58.205 41.667 0.00 0.00 33.76 2.87
582 615 4.322801 GCCTCTGGCTTTTACTTGTAGAGA 60.323 45.833 0.73 0.00 46.69 3.10
583 616 3.935828 GCCTCTGGCTTTTACTTGTAGAG 59.064 47.826 0.73 0.00 46.69 2.43
584 617 3.939066 GCCTCTGGCTTTTACTTGTAGA 58.061 45.455 0.73 0.00 46.69 2.59
632 665 5.532557 CAACATGCTACTGCTAGCTATACA 58.467 41.667 17.23 8.27 45.20 2.29
670 703 1.649815 CTACGTAGGAGCTCTGCCG 59.350 63.158 15.07 14.69 0.00 5.69
714 799 5.069518 ACCCCACAGTAAAAGTAAATGGT 57.930 39.130 0.00 0.00 0.00 3.55
732 817 2.100749 CACCAGACAGTTTTGAAACCCC 59.899 50.000 3.14 0.00 39.71 4.95
905 992 1.342819 GAGAGAAGGTGTGTGCAGTCT 59.657 52.381 0.00 0.00 0.00 3.24
906 993 1.789506 GAGAGAAGGTGTGTGCAGTC 58.210 55.000 0.00 0.00 0.00 3.51
909 996 1.300931 GCGAGAGAAGGTGTGTGCA 60.301 57.895 0.00 0.00 0.00 4.57
910 997 1.005630 AGCGAGAGAAGGTGTGTGC 60.006 57.895 0.00 0.00 0.00 4.57
930 1027 1.339610 AGAGTGAGTGTGTGAGTGAGC 59.660 52.381 0.00 0.00 0.00 4.26
940 1037 1.662608 CGTGAGCCAGAGTGAGTGT 59.337 57.895 0.00 0.00 0.00 3.55
1009 1106 3.609644 CGAGCTAACTTGGCTAGATACCG 60.610 52.174 2.20 0.00 40.40 4.02
1045 1142 2.182825 GGTGTGTAGACGCTCGTATTG 58.817 52.381 3.36 0.00 32.78 1.90
1055 1152 1.535462 GTGCAATGTGGGTGTGTAGAC 59.465 52.381 0.00 0.00 0.00 2.59
1156 1253 0.871057 GTGCTTGCAGTTCTGAGGAC 59.129 55.000 3.84 1.36 0.00 3.85
1160 1257 1.215014 CGTCGTGCTTGCAGTTCTGA 61.215 55.000 3.84 0.00 0.00 3.27
1313 1413 0.464036 AGCAGAACTTGGTGTCGTGA 59.536 50.000 0.00 0.00 35.85 4.35
1553 1653 4.847444 GAGCTGAGAAGGCCGCCC 62.847 72.222 5.55 0.00 0.00 6.13
1748 1848 2.251642 GCCGTTGTCCAAGAACGCT 61.252 57.895 4.07 0.00 43.83 5.07
1928 2029 0.528466 CATGAGCCATCACGTACGCT 60.528 55.000 16.72 2.28 38.57 5.07
1954 2055 2.715046 ACACACACATAATCCAGCAGG 58.285 47.619 0.00 0.00 0.00 4.85
2155 2259 6.794374 TCATAACATCAACATGCATGTAACC 58.206 36.000 31.55 0.00 40.80 2.85
2156 2260 8.748582 CAATCATAACATCAACATGCATGTAAC 58.251 33.333 31.55 0.00 40.80 2.50
2326 2592 7.333423 AGCTCTTGCGTCTGTATTATGTTAAAA 59.667 33.333 0.00 0.00 45.42 1.52
2370 2636 3.006967 GGTATGCGTTCATAGGGATGAGT 59.993 47.826 0.00 0.00 43.03 3.41
2375 2641 2.097110 AGGGTATGCGTTCATAGGGA 57.903 50.000 0.00 0.00 35.96 4.20
2389 2655 2.789992 AGGTGCTCATAGGAGTAGGGTA 59.210 50.000 6.23 0.00 43.37 3.69
2396 2662 3.703556 TCTCTCAAAGGTGCTCATAGGAG 59.296 47.826 0.00 0.00 44.33 3.69
2411 2677 3.149981 ACATGTCGACTCAGTCTCTCAA 58.850 45.455 17.92 0.00 0.00 3.02
2415 2681 3.376859 AGATGACATGTCGACTCAGTCTC 59.623 47.826 24.85 20.45 0.00 3.36
2417 2683 3.773860 AGATGACATGTCGACTCAGTC 57.226 47.619 20.54 19.76 0.00 3.51
2424 2690 7.096551 TGTAAAATCTCAAGATGACATGTCGA 58.903 34.615 20.54 10.19 34.49 4.20
2430 2696 8.675705 TGACTTTGTAAAATCTCAAGATGACA 57.324 30.769 0.00 0.00 34.49 3.58
2449 2715 2.029290 ACGTGGCGTCTAAGATGACTTT 60.029 45.455 0.00 0.00 33.69 2.66
2465 2731 1.205657 CGTTCCCATCGATTACGTGG 58.794 55.000 0.00 0.00 40.69 4.94
2467 2733 0.529119 GGCGTTCCCATCGATTACGT 60.529 55.000 15.86 0.00 40.69 3.57
2472 2738 2.822399 GGAGGCGTTCCCATCGAT 59.178 61.111 0.00 0.00 40.37 3.59
2485 2751 2.185004 ACACGTTCAATGGAAGGAGG 57.815 50.000 9.51 3.95 40.47 4.30
2488 2754 3.374058 GGTGATACACGTTCAATGGAAGG 59.626 47.826 0.85 0.85 42.95 3.46
2491 2757 3.686916 TGGTGATACACGTTCAATGGA 57.313 42.857 0.00 0.00 34.83 3.41
2493 2759 6.307800 GGATTTTTGGTGATACACGTTCAATG 59.692 38.462 0.00 0.00 34.83 2.82
2495 2761 5.533154 AGGATTTTTGGTGATACACGTTCAA 59.467 36.000 0.00 0.00 34.83 2.69
2497 2763 5.180492 TCAGGATTTTTGGTGATACACGTTC 59.820 40.000 0.00 0.00 34.83 3.95
2526 2792 9.288576 CCTCATGCTTGTATTTATCCTTGAATA 57.711 33.333 0.00 0.00 0.00 1.75
2565 2831 4.836825 CAGACAGTGTTATTCCAGTCCAT 58.163 43.478 0.00 0.00 0.00 3.41
2574 2840 4.634012 TGGTTAGGCAGACAGTGTTATT 57.366 40.909 0.00 0.00 0.00 1.40
2579 2845 4.081420 ACTTAGATGGTTAGGCAGACAGTG 60.081 45.833 0.00 0.00 0.00 3.66
2582 2848 4.404715 GGTACTTAGATGGTTAGGCAGACA 59.595 45.833 0.00 0.00 0.00 3.41
2586 2852 2.696707 CGGGTACTTAGATGGTTAGGCA 59.303 50.000 0.00 0.00 0.00 4.75
2587 2853 2.697229 ACGGGTACTTAGATGGTTAGGC 59.303 50.000 0.00 0.00 0.00 3.93
2601 2867 5.783100 TTTGATTCAATTACGACGGGTAC 57.217 39.130 0.00 0.00 0.00 3.34
2605 2871 6.599437 AGACTTTTTGATTCAATTACGACGG 58.401 36.000 0.00 0.00 0.00 4.79
2643 2926 5.006165 GTCCGCTCATGAAAAAGTGAGATAG 59.994 44.000 6.56 0.00 43.50 2.08
2826 3110 8.562892 ACCGAGCAAGAAAATAATATCTTCATG 58.437 33.333 0.00 0.00 33.73 3.07
2837 3121 5.414454 AGTGCAATAACCGAGCAAGAAAATA 59.586 36.000 0.00 0.00 40.35 1.40
2893 3177 0.391661 GAGCTCTTTCCATCGCACCA 60.392 55.000 6.43 0.00 0.00 4.17
2898 3182 1.329906 GTGCATGAGCTCTTTCCATCG 59.670 52.381 16.19 0.00 42.74 3.84
3000 3289 6.809976 ATCCCGAACTAGATTTAAGGAAGT 57.190 37.500 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.