Multiple sequence alignment - TraesCS1D01G057800

Loading Multiple Alignment...

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 TraesCS1D01G057800 chr1D 100.000 3092 0 0 1 3092 37965836 37962745 0.000000e+00 5710
1 TraesCS1D01G057800 chr1D 88.099 2462 227 32 665 3092 38260064 38257635 0.000000e+00 2863
2 TraesCS1D01G057800 chr1D 86.699 2248 263 23 872 3092 38368217 38365979 0.000000e+00 2462
3 TraesCS1D01G057800 chr1D 85.841 2246 268 21 879 3092 38584193 38581966 0.000000e+00 2340
4 TraesCS1D01G057800 chr1D 84.879 2103 300 6 1002 3090 36618247 36616149 0.000000e+00 2106
5 TraesCS1D01G057800 chr1D 84.594 2116 300 18 995 3092 36624666 36622559 0.000000e+00 2078
6 TraesCS1D01G057800 chr1D 83.927 1798 278 3 1306 3092 37430434 37432231 0.000000e+00 1709
7 TraesCS1D01G057800 chr1D 88.156 1410 150 9 1697 3092 38559659 38558253 0.000000e+00 1663
8 TraesCS1D01G057800 chr1D 82.425 1394 228 9 1704 3083 50008020 50009410 0.000000e+00 1201
9 TraesCS1D01G057800 chr1D 82.166 1099 181 7 2005 3090 58763324 58762228 0.000000e+00 929
10 TraesCS1D01G057800 chr1D 93.878 490 26 3 1 487 277089122 277088634 0.000000e+00 736
11 TraesCS1D01G057800 chr1D 89.640 222 23 0 444 665 277088615 277088394 1.820000e-72 283
12 TraesCS1D01G057800 chr1B 86.461 2467 276 27 663 3092 57792037 57789592 0.000000e+00 2652
13 TraesCS1D01G057800 chr1B 85.983 2283 262 28 844 3092 58328887 58326629 0.000000e+00 2390
14 TraesCS1D01G057800 chr1B 85.176 2125 287 17 985 3092 56501868 56499755 0.000000e+00 2154
15 TraesCS1D01G057800 chr1A 85.874 2237 253 29 879 3092 37505482 37503286 0.000000e+00 2322
16 TraesCS1D01G057800 chr1A 85.156 2122 298 7 985 3092 36188390 36186272 0.000000e+00 2158
17 TraesCS1D01G057800 chr1A 84.899 2119 294 18 992 3092 36613124 36615234 0.000000e+00 2117
18 TraesCS1D01G057800 chr1A 84.547 1126 159 7 1980 3092 36605769 36606892 0.000000e+00 1101
19 TraesCS1D01G057800 chr6D 80.809 2126 367 29 987 3092 401293730 401295834 0.000000e+00 1628
20 TraesCS1D01G057800 chr6D 94.467 488 25 2 1 487 6551944 6552430 0.000000e+00 750
21 TraesCS1D01G057800 chr3D 89.790 666 67 1 1 665 338544811 338545476 0.000000e+00 852
22 TraesCS1D01G057800 chr3D 94.203 483 27 1 1 482 536145831 536145349 0.000000e+00 736
23 TraesCS1D01G057800 chr4D 88.438 666 61 7 1 665 22228708 22229358 0.000000e+00 789
24 TraesCS1D01G057800 chr4D 90.222 225 21 1 444 668 396622331 396622108 3.020000e-75 292
25 TraesCS1D01G057800 chr4D 90.090 222 21 1 444 665 22556854 22556634 1.400000e-73 287
26 TraesCS1D01G057800 chr4A 87.574 676 73 6 1 665 593831724 593831049 0.000000e+00 773
27 TraesCS1D01G057800 chr7A 93.241 503 29 5 1 501 533034546 533035045 0.000000e+00 736
28 TraesCS1D01G057800 chr7A 85.366 287 41 1 379 665 665968026 665968311 2.330000e-76 296
29 TraesCS1D01G057800 chr7A 86.415 265 33 2 399 663 208408859 208408598 1.400000e-73 287
30 TraesCS1D01G057800 chr2A 93.852 488 27 2 1 487 186361015 186360530 0.000000e+00 732
31 TraesCS1D01G057800 chr7D 93.648 488 30 1 1 487 71620627 71621114 0.000000e+00 728
32 TraesCS1D01G057800 chr7D 89.286 224 23 1 446 669 71621138 71621360 2.350000e-71 279


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 TraesCS1D01G057800 chr1D 37962745 37965836 3091 True 5710.0 5710 100.000 1 3092 1 chr1D.!!$R3 3091
1 TraesCS1D01G057800 chr1D 38257635 38260064 2429 True 2863.0 2863 88.099 665 3092 1 chr1D.!!$R4 2427
2 TraesCS1D01G057800 chr1D 38365979 38368217 2238 True 2462.0 2462 86.699 872 3092 1 chr1D.!!$R5 2220
3 TraesCS1D01G057800 chr1D 38581966 38584193 2227 True 2340.0 2340 85.841 879 3092 1 chr1D.!!$R7 2213
4 TraesCS1D01G057800 chr1D 36616149 36618247 2098 True 2106.0 2106 84.879 1002 3090 1 chr1D.!!$R1 2088
5 TraesCS1D01G057800 chr1D 36622559 36624666 2107 True 2078.0 2078 84.594 995 3092 1 chr1D.!!$R2 2097
6 TraesCS1D01G057800 chr1D 37430434 37432231 1797 False 1709.0 1709 83.927 1306 3092 1 chr1D.!!$F1 1786
7 TraesCS1D01G057800 chr1D 38558253 38559659 1406 True 1663.0 1663 88.156 1697 3092 1 chr1D.!!$R6 1395
8 TraesCS1D01G057800 chr1D 50008020 50009410 1390 False 1201.0 1201 82.425 1704 3083 1 chr1D.!!$F2 1379
9 TraesCS1D01G057800 chr1D 58762228 58763324 1096 True 929.0 929 82.166 2005 3090 1 chr1D.!!$R8 1085
10 TraesCS1D01G057800 chr1D 277088394 277089122 728 True 509.5 736 91.759 1 665 2 chr1D.!!$R9 664
11 TraesCS1D01G057800 chr1B 57789592 57792037 2445 True 2652.0 2652 86.461 663 3092 1 chr1B.!!$R2 2429
12 TraesCS1D01G057800 chr1B 58326629 58328887 2258 True 2390.0 2390 85.983 844 3092 1 chr1B.!!$R3 2248
13 TraesCS1D01G057800 chr1B 56499755 56501868 2113 True 2154.0 2154 85.176 985 3092 1 chr1B.!!$R1 2107
14 TraesCS1D01G057800 chr1A 37503286 37505482 2196 True 2322.0 2322 85.874 879 3092 1 chr1A.!!$R2 2213
15 TraesCS1D01G057800 chr1A 36186272 36188390 2118 True 2158.0 2158 85.156 985 3092 1 chr1A.!!$R1 2107
16 TraesCS1D01G057800 chr1A 36613124 36615234 2110 False 2117.0 2117 84.899 992 3092 1 chr1A.!!$F2 2100
17 TraesCS1D01G057800 chr1A 36605769 36606892 1123 False 1101.0 1101 84.547 1980 3092 1 chr1A.!!$F1 1112
18 TraesCS1D01G057800 chr6D 401293730 401295834 2104 False 1628.0 1628 80.809 987 3092 1 chr6D.!!$F2 2105
19 TraesCS1D01G057800 chr3D 338544811 338545476 665 False 852.0 852 89.790 1 665 1 chr3D.!!$F1 664
20 TraesCS1D01G057800 chr4D 22228708 22229358 650 False 789.0 789 88.438 1 665 1 chr4D.!!$F1 664
21 TraesCS1D01G057800 chr4A 593831049 593831724 675 True 773.0 773 87.574 1 665 1 chr4A.!!$R1 664
22 TraesCS1D01G057800 chr7D 71620627 71621360 733 False 503.5 728 91.467 1 669 2 chr7D.!!$F1 668

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
525 529 0.024619 GATCTAAAACACGCGCGGTC 59.975 55.0 35.22 12.77 0.0 4.79 F
716 720 0.169230 CGACTGAGAAGGTGACCGAG 59.831 60.0 0.00 0.00 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1479 1824 1.077663 AGGAAGGTGGTGGCAATGATT 59.922 47.619 0.0 0.0 0.00 2.57 R
2361 2730 1.079612 CGACAGCATCAGCCAGACA 60.080 57.895 0.0 0.0 43.56 3.41 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
61 62 2.125512 GATGGTGAGGCGACGCTT 60.126 61.111 20.77 13.06 0.00 4.68
88 89 1.183030 TGGTGGACACGACGATCCTT 61.183 55.000 19.05 0.00 35.86 3.36
146 147 4.406173 CGCTGGCTCGACACGTCT 62.406 66.667 0.00 0.00 0.00 4.18
172 173 1.469335 TTCATATCCCGACGAGGCCC 61.469 60.000 0.00 0.00 39.21 5.80
268 269 2.279582 TTCTCGCGAAACCAGATCTC 57.720 50.000 11.33 0.00 0.00 2.75
322 324 1.375523 ACGAAAATCCGAAGCGCCT 60.376 52.632 2.29 0.00 0.00 5.52
369 371 2.418910 GGCAGCGAGGCTAGTGAGA 61.419 63.158 0.00 0.00 36.40 3.27
371 373 1.732917 CAGCGAGGCTAGTGAGAGG 59.267 63.158 0.00 0.00 36.40 3.69
372 374 1.454847 AGCGAGGCTAGTGAGAGGG 60.455 63.158 0.00 0.00 36.99 4.30
375 377 2.041405 AGGCTAGTGAGAGGGGGC 60.041 66.667 0.00 0.00 0.00 5.80
411 413 1.594310 GACAGAGTGTGGAGGGAGC 59.406 63.158 0.00 0.00 0.00 4.70
417 419 3.249189 TGTGGAGGGAGCGCCTTT 61.249 61.111 2.29 0.00 0.00 3.11
434 436 1.662122 CTTTTTATAACGAGCGCCGGT 59.338 47.619 19.73 16.63 43.93 5.28
483 487 2.597217 TGGAGCGCCAAAACCAGG 60.597 61.111 6.75 0.00 42.49 4.45
484 488 3.373565 GGAGCGCCAAAACCAGGG 61.374 66.667 2.29 0.00 0.00 4.45
485 489 4.056125 GAGCGCCAAAACCAGGGC 62.056 66.667 2.29 0.00 46.80 5.19
489 493 2.909965 GCCAAAACCAGGGCGACA 60.910 61.111 0.00 0.00 40.93 4.35
490 494 2.919494 GCCAAAACCAGGGCGACAG 61.919 63.158 0.00 0.00 40.93 3.51
491 495 2.644992 CAAAACCAGGGCGACAGC 59.355 61.111 0.00 0.00 44.18 4.40
509 513 3.023946 AGCATAGACGCTGACATGATC 57.976 47.619 0.00 0.00 41.85 2.92
510 514 2.627221 AGCATAGACGCTGACATGATCT 59.373 45.455 0.00 0.00 41.85 2.75
511 515 3.823304 AGCATAGACGCTGACATGATCTA 59.177 43.478 0.00 0.00 41.85 1.98
512 516 4.279420 AGCATAGACGCTGACATGATCTAA 59.721 41.667 0.00 0.00 41.85 2.10
513 517 4.984785 GCATAGACGCTGACATGATCTAAA 59.015 41.667 0.00 0.00 0.00 1.85
514 518 5.463392 GCATAGACGCTGACATGATCTAAAA 59.537 40.000 0.00 0.00 0.00 1.52
515 519 6.563010 GCATAGACGCTGACATGATCTAAAAC 60.563 42.308 0.00 0.00 0.00 2.43
516 520 4.820897 AGACGCTGACATGATCTAAAACA 58.179 39.130 0.00 0.00 0.00 2.83
517 521 4.627467 AGACGCTGACATGATCTAAAACAC 59.373 41.667 0.00 0.00 0.00 3.32
518 522 3.367932 ACGCTGACATGATCTAAAACACG 59.632 43.478 0.00 0.00 0.00 4.49
519 523 3.674423 GCTGACATGATCTAAAACACGC 58.326 45.455 0.00 0.00 0.00 5.34
520 524 3.782250 GCTGACATGATCTAAAACACGCG 60.782 47.826 3.53 3.53 0.00 6.01
521 525 2.093625 TGACATGATCTAAAACACGCGC 59.906 45.455 5.73 0.00 0.00 6.86
522 526 1.060553 ACATGATCTAAAACACGCGCG 59.939 47.619 30.96 30.96 0.00 6.86
523 527 0.650512 ATGATCTAAAACACGCGCGG 59.349 50.000 35.22 24.36 0.00 6.46
524 528 0.668096 TGATCTAAAACACGCGCGGT 60.668 50.000 35.22 25.06 0.00 5.68
525 529 0.024619 GATCTAAAACACGCGCGGTC 59.975 55.000 35.22 12.77 0.00 4.79
526 530 0.668096 ATCTAAAACACGCGCGGTCA 60.668 50.000 35.22 15.33 0.00 4.02
527 531 0.668096 TCTAAAACACGCGCGGTCAT 60.668 50.000 35.22 20.62 0.00 3.06
528 532 0.518355 CTAAAACACGCGCGGTCATG 60.518 55.000 35.22 24.72 0.00 3.07
529 533 0.944788 TAAAACACGCGCGGTCATGA 60.945 50.000 35.22 12.30 0.00 3.07
530 534 1.777030 AAAACACGCGCGGTCATGAA 61.777 50.000 35.22 0.00 0.00 2.57
531 535 1.777030 AAACACGCGCGGTCATGAAA 61.777 50.000 35.22 0.00 0.00 2.69
532 536 1.573829 AACACGCGCGGTCATGAAAT 61.574 50.000 35.22 6.31 0.00 2.17
534 538 2.023181 CGCGCGGTCATGAAATGG 59.977 61.111 24.84 0.00 46.73 3.16
535 539 2.408835 GCGCGGTCATGAAATGGG 59.591 61.111 8.83 0.00 46.73 4.00
536 540 2.406616 GCGCGGTCATGAAATGGGT 61.407 57.895 8.83 0.00 46.73 4.51
537 541 1.721487 CGCGGTCATGAAATGGGTC 59.279 57.895 0.00 0.00 46.73 4.46
538 542 1.721487 GCGGTCATGAAATGGGTCG 59.279 57.895 0.00 0.00 46.73 4.79
539 543 1.714899 GCGGTCATGAAATGGGTCGG 61.715 60.000 0.00 0.00 46.73 4.79
540 544 1.714899 CGGTCATGAAATGGGTCGGC 61.715 60.000 0.00 0.00 46.73 5.54
541 545 1.384222 GGTCATGAAATGGGTCGGCC 61.384 60.000 0.00 0.00 46.73 6.13
560 564 3.712881 GTTGGACGCACTGCCGAC 61.713 66.667 0.00 0.00 0.00 4.79
561 565 3.923864 TTGGACGCACTGCCGACT 61.924 61.111 0.00 0.00 0.00 4.18
562 566 3.858868 TTGGACGCACTGCCGACTC 62.859 63.158 0.00 0.00 0.00 3.36
563 567 4.357947 GGACGCACTGCCGACTCA 62.358 66.667 0.00 0.00 0.00 3.41
564 568 2.355837 GACGCACTGCCGACTCAA 60.356 61.111 0.00 0.00 0.00 3.02
565 569 1.954146 GACGCACTGCCGACTCAAA 60.954 57.895 0.00 0.00 0.00 2.69
566 570 1.495584 GACGCACTGCCGACTCAAAA 61.496 55.000 0.00 0.00 0.00 2.44
567 571 1.082756 CGCACTGCCGACTCAAAAC 60.083 57.895 0.00 0.00 0.00 2.43
568 572 1.498865 CGCACTGCCGACTCAAAACT 61.499 55.000 0.00 0.00 0.00 2.66
569 573 1.508632 GCACTGCCGACTCAAAACTA 58.491 50.000 0.00 0.00 0.00 2.24
570 574 1.871039 GCACTGCCGACTCAAAACTAA 59.129 47.619 0.00 0.00 0.00 2.24
571 575 2.289547 GCACTGCCGACTCAAAACTAAA 59.710 45.455 0.00 0.00 0.00 1.85
572 576 3.242936 GCACTGCCGACTCAAAACTAAAA 60.243 43.478 0.00 0.00 0.00 1.52
573 577 4.732355 GCACTGCCGACTCAAAACTAAAAA 60.732 41.667 0.00 0.00 0.00 1.94
587 591 3.698765 AAAAAGGGCGGATGGCAG 58.301 55.556 0.00 0.00 46.16 4.85
588 592 1.984026 AAAAAGGGCGGATGGCAGG 60.984 57.895 0.00 0.00 46.16 4.85
609 613 3.122323 GCGGCCGATCCAAACGAA 61.122 61.111 33.48 0.00 34.01 3.85
610 614 2.469516 GCGGCCGATCCAAACGAAT 61.470 57.895 33.48 0.00 34.01 3.34
611 615 1.155424 GCGGCCGATCCAAACGAATA 61.155 55.000 33.48 0.00 34.01 1.75
612 616 1.292061 CGGCCGATCCAAACGAATAA 58.708 50.000 24.07 0.00 34.01 1.40
613 617 1.666700 CGGCCGATCCAAACGAATAAA 59.333 47.619 24.07 0.00 34.01 1.40
614 618 2.096174 CGGCCGATCCAAACGAATAAAA 59.904 45.455 24.07 0.00 34.01 1.52
615 619 3.426426 CGGCCGATCCAAACGAATAAAAA 60.426 43.478 24.07 0.00 34.01 1.94
632 636 2.547913 AAAACGAAGAAAAACGCCGT 57.452 40.000 0.00 0.00 34.35 5.68
633 637 2.095384 AAACGAAGAAAAACGCCGTC 57.905 45.000 0.00 0.00 33.04 4.79
634 638 0.305617 AACGAAGAAAAACGCCGTCC 59.694 50.000 0.00 0.00 33.04 4.79
635 639 1.154727 CGAAGAAAAACGCCGTCCG 60.155 57.895 0.00 0.00 44.21 4.79
644 648 3.467119 CGCCGTCCGTTTGAGTCG 61.467 66.667 0.00 0.00 0.00 4.18
646 650 3.110178 CCGTCCGTTTGAGTCGGC 61.110 66.667 0.00 0.00 46.49 5.54
647 651 3.110178 CGTCCGTTTGAGTCGGCC 61.110 66.667 0.00 0.00 46.49 6.13
648 652 2.741211 GTCCGTTTGAGTCGGCCC 60.741 66.667 0.00 0.00 46.49 5.80
649 653 4.367023 TCCGTTTGAGTCGGCCCG 62.367 66.667 0.00 0.00 46.49 6.13
650 654 4.675029 CCGTTTGAGTCGGCCCGT 62.675 66.667 1.63 0.00 41.48 5.28
651 655 2.663852 CGTTTGAGTCGGCCCGTT 60.664 61.111 1.63 0.00 0.00 4.44
652 656 2.943653 GTTTGAGTCGGCCCGTTG 59.056 61.111 1.63 0.00 0.00 4.10
653 657 2.281208 TTTGAGTCGGCCCGTTGG 60.281 61.111 1.63 0.00 0.00 3.77
654 658 2.809307 TTTGAGTCGGCCCGTTGGA 61.809 57.895 1.63 0.00 0.00 3.53
655 659 2.725203 TTTGAGTCGGCCCGTTGGAG 62.725 60.000 1.63 0.00 0.00 3.86
656 660 3.692406 GAGTCGGCCCGTTGGAGT 61.692 66.667 1.63 0.00 0.00 3.85
657 661 3.236003 GAGTCGGCCCGTTGGAGTT 62.236 63.158 1.63 0.00 0.00 3.01
658 662 3.047877 GTCGGCCCGTTGGAGTTG 61.048 66.667 1.63 0.00 0.00 3.16
659 663 3.552384 TCGGCCCGTTGGAGTTGT 61.552 61.111 1.63 0.00 0.00 3.32
660 664 2.593436 CGGCCCGTTGGAGTTGTT 60.593 61.111 0.00 0.00 0.00 2.83
661 665 2.613506 CGGCCCGTTGGAGTTGTTC 61.614 63.158 0.00 0.00 0.00 3.18
714 718 1.213013 CCGACTGAGAAGGTGACCG 59.787 63.158 0.00 0.00 0.00 4.79
716 720 0.169230 CGACTGAGAAGGTGACCGAG 59.831 60.000 0.00 0.00 0.00 4.63
783 794 4.953667 TCACACTCATCTAATCTGCATCC 58.046 43.478 0.00 0.00 0.00 3.51
784 795 3.739810 CACACTCATCTAATCTGCATCCG 59.260 47.826 0.00 0.00 0.00 4.18
785 796 2.735663 CACTCATCTAATCTGCATCCGC 59.264 50.000 0.00 0.00 39.24 5.54
786 797 2.289320 ACTCATCTAATCTGCATCCGCC 60.289 50.000 0.00 0.00 37.32 6.13
787 798 1.073964 CATCTAATCTGCATCCGCCG 58.926 55.000 0.00 0.00 37.32 6.46
788 799 0.969149 ATCTAATCTGCATCCGCCGA 59.031 50.000 0.00 0.00 37.32 5.54
789 800 0.969149 TCTAATCTGCATCCGCCGAT 59.031 50.000 0.00 0.00 43.14 4.18
790 801 1.067565 TCTAATCTGCATCCGCCGATC 60.068 52.381 0.00 0.00 40.76 3.69
791 802 0.678950 TAATCTGCATCCGCCGATCA 59.321 50.000 0.00 0.00 40.76 2.92
792 803 0.882042 AATCTGCATCCGCCGATCAC 60.882 55.000 0.00 0.00 40.76 3.06
793 804 2.031674 ATCTGCATCCGCCGATCACA 62.032 55.000 0.00 0.00 37.52 3.58
794 805 1.815003 CTGCATCCGCCGATCACAA 60.815 57.895 0.00 0.00 37.32 3.33
795 806 1.368345 CTGCATCCGCCGATCACAAA 61.368 55.000 0.00 0.00 37.32 2.83
796 807 1.353103 GCATCCGCCGATCACAAAG 59.647 57.895 0.00 0.00 0.00 2.77
797 808 2.016961 CATCCGCCGATCACAAAGG 58.983 57.895 0.00 0.00 0.00 3.11
798 809 0.461870 CATCCGCCGATCACAAAGGA 60.462 55.000 0.00 0.00 0.00 3.36
799 810 0.469917 ATCCGCCGATCACAAAGGAT 59.530 50.000 0.00 0.00 34.02 3.24
809 820 4.141937 CGATCACAAAGGATTCTCCCAGTA 60.142 45.833 0.00 0.00 37.19 2.74
826 865 3.244215 CCAGTACAGAGCACAAAGGAAGA 60.244 47.826 0.00 0.00 0.00 2.87
838 877 3.942748 ACAAAGGAAGAAACACTGCGTAA 59.057 39.130 0.00 0.00 0.00 3.18
857 906 1.963338 GCACGCAAAGTCCAGAGCT 60.963 57.895 0.00 0.00 0.00 4.09
867 916 2.185350 CCAGAGCTCGCCGATGTT 59.815 61.111 8.37 0.00 0.00 2.71
1092 1218 4.995058 TCCACCTCCACCCCCACC 62.995 72.222 0.00 0.00 0.00 4.61
1094 1220 2.858974 CACCTCCACCCCCACCTT 60.859 66.667 0.00 0.00 0.00 3.50
1249 1577 2.747686 GCTCCCTGGACGGTTTCA 59.252 61.111 0.00 0.00 0.00 2.69
1380 1725 1.229428 CACCACGCACAATCTTCACT 58.771 50.000 0.00 0.00 0.00 3.41
1408 1753 0.677098 CCTCATGAACTGCTGCTGCT 60.677 55.000 17.00 0.00 40.48 4.24
1465 1810 3.706373 GCTTCCTCAGGACGGGCA 61.706 66.667 0.00 0.00 0.00 5.36
1471 1816 1.153289 CTCAGGACGGGCATGAAGG 60.153 63.158 0.00 0.00 36.79 3.46
1479 1824 0.531657 CGGGCATGAAGGCAAATGAA 59.468 50.000 0.00 0.00 46.44 2.57
1560 1905 4.397417 GTCAACTTGCTGCTTCATAGGATT 59.603 41.667 0.00 0.00 0.00 3.01
1617 1962 4.723309 ACTCCATTGTTCTGAAGAGCTTT 58.277 39.130 0.00 0.00 0.00 3.51
1680 2025 0.392998 TGATGGCGAAAGAAGGAGGC 60.393 55.000 0.00 0.00 0.00 4.70
1799 2145 2.127232 AGCAAGGTGTTGTGCCCAC 61.127 57.895 0.00 0.00 41.88 4.61
1977 2323 8.035394 CAGTTGAGAGAGGCTACTAAAATGTTA 58.965 37.037 9.25 0.00 0.00 2.41
2029 2387 3.557595 AGATATTGTTACTTGCAGCTCGC 59.442 43.478 0.00 1.70 42.89 5.03
2330 2699 6.836007 TGAGTCCTGATGTAGTCACATATTCT 59.164 38.462 0.00 0.00 45.58 2.40
2331 2700 7.343057 TGAGTCCTGATGTAGTCACATATTCTT 59.657 37.037 0.00 0.00 45.58 2.52
2339 2708 7.004555 TGTAGTCACATATTCTTCTGTGGTT 57.995 36.000 3.14 0.00 42.37 3.67
2363 2732 1.069049 GCACTTTGCAGAATGGGTTGT 59.931 47.619 0.00 0.00 44.26 3.32
2426 2796 3.090037 GGAGTACAGCCAGACAGAGTTA 58.910 50.000 0.00 0.00 0.00 2.24
2606 2977 9.187996 TGGATGCACAAGATATCTTTGAATTTA 57.812 29.630 15.49 7.90 33.11 1.40
2675 3046 5.912892 TGATTGACGGATATTGCTTAGTCA 58.087 37.500 0.00 0.00 36.91 3.41
2694 3065 4.820716 AGTCAGCAAGATGGATAAAGCATC 59.179 41.667 0.00 0.00 0.00 3.91
2875 3246 2.244510 TGGCATCATACTGGATGGGTTT 59.755 45.455 0.00 0.00 43.85 3.27
2964 3335 7.939039 ACCAGTGACCATTTCCATATACAATAG 59.061 37.037 0.00 0.00 0.00 1.73
3007 3378 3.764885 AATAATTGTGCAGACGAAGCC 57.235 42.857 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 3.311110 GTGTCCACCAGAGGCGGA 61.311 66.667 0.00 0.00 30.60 5.54
69 70 1.183030 AAGGATCGTCGTGTCCACCA 61.183 55.000 17.43 0.00 36.96 4.17
146 147 4.377021 CTCGTCGGGATATGAATTTTCCA 58.623 43.478 0.00 0.00 0.00 3.53
304 306 0.108520 TAGGCGCTTCGGATTTTCGT 60.109 50.000 7.64 0.00 0.00 3.85
322 324 2.910479 ATGTCGATCCGCCGCCTA 60.910 61.111 0.00 0.00 0.00 3.93
354 356 1.454847 CCCTCTCACTAGCCTCGCT 60.455 63.158 0.00 0.00 43.41 4.93
389 391 2.279069 CCTCCACACTCTGTCCGCT 61.279 63.158 0.00 0.00 0.00 5.52
411 413 1.593793 GGCGCTCGTTATAAAAAGGCG 60.594 52.381 7.64 14.61 37.09 5.52
417 419 0.866906 CGACCGGCGCTCGTTATAAA 60.867 55.000 15.90 0.00 37.11 1.40
490 494 3.023946 AGATCATGTCAGCGTCTATGC 57.976 47.619 0.00 0.00 0.00 3.14
491 495 6.476706 TGTTTTAGATCATGTCAGCGTCTATG 59.523 38.462 0.00 0.00 0.00 2.23
492 496 6.477033 GTGTTTTAGATCATGTCAGCGTCTAT 59.523 38.462 0.00 0.00 0.00 1.98
493 497 5.805486 GTGTTTTAGATCATGTCAGCGTCTA 59.195 40.000 0.00 0.00 0.00 2.59
494 498 4.627467 GTGTTTTAGATCATGTCAGCGTCT 59.373 41.667 0.00 0.00 0.00 4.18
495 499 4.490959 CGTGTTTTAGATCATGTCAGCGTC 60.491 45.833 0.00 0.00 0.00 5.19
496 500 3.367932 CGTGTTTTAGATCATGTCAGCGT 59.632 43.478 0.00 0.00 0.00 5.07
497 501 3.782250 GCGTGTTTTAGATCATGTCAGCG 60.782 47.826 0.00 0.00 0.00 5.18
498 502 3.674423 GCGTGTTTTAGATCATGTCAGC 58.326 45.455 0.00 0.00 0.00 4.26
499 503 3.782250 GCGCGTGTTTTAGATCATGTCAG 60.782 47.826 8.43 0.00 0.00 3.51
500 504 2.093625 GCGCGTGTTTTAGATCATGTCA 59.906 45.455 8.43 0.00 0.00 3.58
501 505 2.694043 GCGCGTGTTTTAGATCATGTC 58.306 47.619 8.43 0.00 0.00 3.06
502 506 1.060553 CGCGCGTGTTTTAGATCATGT 59.939 47.619 24.19 0.00 0.00 3.21
503 507 1.592110 CCGCGCGTGTTTTAGATCATG 60.592 52.381 29.95 3.54 0.00 3.07
504 508 0.650512 CCGCGCGTGTTTTAGATCAT 59.349 50.000 29.95 0.00 0.00 2.45
505 509 0.668096 ACCGCGCGTGTTTTAGATCA 60.668 50.000 29.95 0.00 0.00 2.92
506 510 0.024619 GACCGCGCGTGTTTTAGATC 59.975 55.000 29.95 8.45 0.00 2.75
507 511 0.668096 TGACCGCGCGTGTTTTAGAT 60.668 50.000 29.95 2.01 0.00 1.98
508 512 0.668096 ATGACCGCGCGTGTTTTAGA 60.668 50.000 29.95 9.19 0.00 2.10
509 513 0.518355 CATGACCGCGCGTGTTTTAG 60.518 55.000 29.95 13.89 0.00 1.85
510 514 0.944788 TCATGACCGCGCGTGTTTTA 60.945 50.000 29.95 15.58 0.00 1.52
511 515 1.777030 TTCATGACCGCGCGTGTTTT 61.777 50.000 29.95 13.81 0.00 2.43
512 516 1.777030 TTTCATGACCGCGCGTGTTT 61.777 50.000 29.95 14.15 0.00 2.83
513 517 1.573829 ATTTCATGACCGCGCGTGTT 61.574 50.000 29.95 12.71 0.00 3.32
514 518 2.032634 ATTTCATGACCGCGCGTGT 61.033 52.632 29.95 25.05 0.00 4.49
515 519 1.580893 CATTTCATGACCGCGCGTG 60.581 57.895 29.95 21.87 0.00 5.34
516 520 2.749865 CCATTTCATGACCGCGCGT 61.750 57.895 29.95 17.00 0.00 6.01
517 521 2.023181 CCATTTCATGACCGCGCG 59.977 61.111 25.67 25.67 0.00 6.86
518 522 2.322999 GACCCATTTCATGACCGCGC 62.323 60.000 0.00 0.00 0.00 6.86
519 523 1.721487 GACCCATTTCATGACCGCG 59.279 57.895 0.00 0.00 0.00 6.46
520 524 1.714899 CCGACCCATTTCATGACCGC 61.715 60.000 0.00 0.00 0.00 5.68
521 525 1.714899 GCCGACCCATTTCATGACCG 61.715 60.000 0.00 0.00 0.00 4.79
522 526 1.384222 GGCCGACCCATTTCATGACC 61.384 60.000 0.00 0.00 0.00 4.02
523 527 2.106844 GGCCGACCCATTTCATGAC 58.893 57.895 0.00 0.00 0.00 3.06
524 528 4.655921 GGCCGACCCATTTCATGA 57.344 55.556 0.00 0.00 0.00 3.07
543 547 3.712881 GTCGGCAGTGCGTCCAAC 61.713 66.667 9.45 0.00 0.00 3.77
544 548 3.858868 GAGTCGGCAGTGCGTCCAA 62.859 63.158 9.45 0.00 0.00 3.53
545 549 4.357947 GAGTCGGCAGTGCGTCCA 62.358 66.667 9.45 0.00 0.00 4.02
546 550 3.858868 TTGAGTCGGCAGTGCGTCC 62.859 63.158 9.45 0.00 0.00 4.79
547 551 1.495584 TTTTGAGTCGGCAGTGCGTC 61.496 55.000 9.45 3.84 0.00 5.19
548 552 1.522806 TTTTGAGTCGGCAGTGCGT 60.523 52.632 9.45 0.00 0.00 5.24
549 553 1.082756 GTTTTGAGTCGGCAGTGCG 60.083 57.895 9.45 4.79 0.00 5.34
550 554 1.508632 TAGTTTTGAGTCGGCAGTGC 58.491 50.000 6.55 6.55 0.00 4.40
551 555 4.545823 TTTTAGTTTTGAGTCGGCAGTG 57.454 40.909 0.00 0.00 0.00 3.66
570 574 1.984026 CCTGCCATCCGCCCTTTTT 60.984 57.895 0.00 0.00 36.24 1.94
571 575 2.362889 CCTGCCATCCGCCCTTTT 60.363 61.111 0.00 0.00 36.24 2.27
592 596 1.155424 TATTCGTTTGGATCGGCCGC 61.155 55.000 23.51 7.37 40.66 6.53
593 597 1.292061 TTATTCGTTTGGATCGGCCG 58.708 50.000 22.12 22.12 40.66 6.13
594 598 3.768468 TTTTATTCGTTTGGATCGGCC 57.232 42.857 0.00 0.00 37.10 6.13
612 616 2.847717 GACGGCGTTTTTCTTCGTTTTT 59.152 40.909 16.19 0.00 34.06 1.94
613 617 2.443387 GACGGCGTTTTTCTTCGTTTT 58.557 42.857 16.19 0.00 34.06 2.43
614 618 1.268184 GGACGGCGTTTTTCTTCGTTT 60.268 47.619 16.19 0.00 34.06 3.60
615 619 0.305617 GGACGGCGTTTTTCTTCGTT 59.694 50.000 16.19 0.00 34.06 3.85
616 620 1.824272 CGGACGGCGTTTTTCTTCGT 61.824 55.000 16.19 0.00 36.74 3.85
617 621 1.154727 CGGACGGCGTTTTTCTTCG 60.155 57.895 16.19 6.34 0.00 3.79
618 622 0.305617 AACGGACGGCGTTTTTCTTC 59.694 50.000 16.19 0.00 0.00 2.87
619 623 0.734309 AAACGGACGGCGTTTTTCTT 59.266 45.000 16.19 1.53 36.32 2.52
620 624 0.028374 CAAACGGACGGCGTTTTTCT 59.972 50.000 16.19 0.00 37.45 2.52
621 625 0.027848 TCAAACGGACGGCGTTTTTC 59.972 50.000 16.19 0.00 37.45 2.29
622 626 0.028374 CTCAAACGGACGGCGTTTTT 59.972 50.000 16.19 11.54 37.45 1.94
623 627 1.091197 ACTCAAACGGACGGCGTTTT 61.091 50.000 16.19 8.33 37.45 2.43
624 628 1.493134 GACTCAAACGGACGGCGTTT 61.493 55.000 16.19 0.70 39.72 3.60
625 629 1.952635 GACTCAAACGGACGGCGTT 60.953 57.895 16.19 0.00 0.00 4.84
626 630 2.355481 GACTCAAACGGACGGCGT 60.355 61.111 14.65 14.65 0.00 5.68
627 631 3.467119 CGACTCAAACGGACGGCG 61.467 66.667 4.80 4.80 0.00 6.46
634 638 2.663852 AACGGGCCGACTCAAACG 60.664 61.111 35.78 2.05 0.00 3.60
635 639 2.613506 CCAACGGGCCGACTCAAAC 61.614 63.158 35.78 0.00 0.00 2.93
636 640 2.281208 CCAACGGGCCGACTCAAA 60.281 61.111 35.78 0.00 0.00 2.69
637 641 3.234630 CTCCAACGGGCCGACTCAA 62.235 63.158 35.78 12.55 0.00 3.02
638 642 3.691342 CTCCAACGGGCCGACTCA 61.691 66.667 35.78 12.53 0.00 3.41
639 643 3.236003 AACTCCAACGGGCCGACTC 62.236 63.158 35.78 0.00 0.00 3.36
640 644 3.239253 AACTCCAACGGGCCGACT 61.239 61.111 35.78 16.74 0.00 4.18
641 645 3.047877 CAACTCCAACGGGCCGAC 61.048 66.667 35.78 0.00 0.00 4.79
642 646 2.999739 GAACAACTCCAACGGGCCGA 63.000 60.000 35.78 9.29 0.00 5.54
643 647 2.593436 AACAACTCCAACGGGCCG 60.593 61.111 27.06 27.06 0.00 6.13
644 648 0.822121 AAGAACAACTCCAACGGGCC 60.822 55.000 0.00 0.00 0.00 5.80
645 649 1.886886 TAAGAACAACTCCAACGGGC 58.113 50.000 0.00 0.00 0.00 6.13
646 650 5.671493 AGATATAAGAACAACTCCAACGGG 58.329 41.667 0.00 0.00 0.00 5.28
647 651 6.338146 TGAGATATAAGAACAACTCCAACGG 58.662 40.000 0.00 0.00 0.00 4.44
648 652 7.462856 CGTTGAGATATAAGAACAACTCCAACG 60.463 40.741 0.00 0.00 38.69 4.10
649 653 7.201530 CCGTTGAGATATAAGAACAACTCCAAC 60.202 40.741 0.00 0.00 38.69 3.77
650 654 6.816640 CCGTTGAGATATAAGAACAACTCCAA 59.183 38.462 0.00 0.00 38.69 3.53
651 655 6.338146 CCGTTGAGATATAAGAACAACTCCA 58.662 40.000 0.00 0.00 38.69 3.86
652 656 5.234543 GCCGTTGAGATATAAGAACAACTCC 59.765 44.000 0.00 0.00 38.69 3.85
653 657 5.810587 TGCCGTTGAGATATAAGAACAACTC 59.189 40.000 0.00 0.00 38.69 3.01
654 658 5.730550 TGCCGTTGAGATATAAGAACAACT 58.269 37.500 0.00 0.00 38.69 3.16
655 659 6.417191 TTGCCGTTGAGATATAAGAACAAC 57.583 37.500 0.00 0.00 37.87 3.32
656 660 7.441890 TTTTGCCGTTGAGATATAAGAACAA 57.558 32.000 0.00 0.00 0.00 2.83
657 661 7.465379 CGATTTTGCCGTTGAGATATAAGAACA 60.465 37.037 0.00 0.00 0.00 3.18
658 662 6.846283 CGATTTTGCCGTTGAGATATAAGAAC 59.154 38.462 0.00 0.00 0.00 3.01
659 663 6.759356 TCGATTTTGCCGTTGAGATATAAGAA 59.241 34.615 0.00 0.00 0.00 2.52
660 664 6.277605 TCGATTTTGCCGTTGAGATATAAGA 58.722 36.000 0.00 0.00 0.00 2.10
661 665 6.525121 TCGATTTTGCCGTTGAGATATAAG 57.475 37.500 0.00 0.00 0.00 1.73
714 718 5.954335 ACTTGTATGGTTTTGCTAATGCTC 58.046 37.500 0.00 0.00 40.48 4.26
716 720 6.632834 CGATACTTGTATGGTTTTGCTAATGC 59.367 38.462 0.00 0.00 40.20 3.56
783 794 1.594862 GAGAATCCTTTGTGATCGGCG 59.405 52.381 0.00 0.00 0.00 6.46
797 808 2.497675 TGTGCTCTGTACTGGGAGAATC 59.502 50.000 3.42 0.67 0.00 2.52
798 809 2.540383 TGTGCTCTGTACTGGGAGAAT 58.460 47.619 3.42 0.00 0.00 2.40
799 810 2.009681 TGTGCTCTGTACTGGGAGAA 57.990 50.000 3.42 0.00 0.00 2.87
809 820 3.378427 GTGTTTCTTCCTTTGTGCTCTGT 59.622 43.478 0.00 0.00 0.00 3.41
838 877 1.963338 GCTCTGGACTTTGCGTGCT 60.963 57.895 0.00 0.00 34.66 4.40
840 879 1.621301 CGAGCTCTGGACTTTGCGTG 61.621 60.000 12.85 0.00 0.00 5.34
843 882 2.394563 GGCGAGCTCTGGACTTTGC 61.395 63.158 12.85 4.76 0.00 3.68
846 885 2.055042 ATCGGCGAGCTCTGGACTT 61.055 57.895 17.22 0.00 0.00 3.01
847 886 2.441164 ATCGGCGAGCTCTGGACT 60.441 61.111 17.22 0.00 0.00 3.85
849 888 2.351244 AACATCGGCGAGCTCTGGA 61.351 57.895 17.22 6.43 0.00 3.86
857 906 2.463620 GCAGATGCAACATCGGCGA 61.464 57.895 13.87 13.87 41.59 5.54
1059 1185 1.495574 GTGGAGGTAGAGGAGGAGCTA 59.504 57.143 0.00 0.00 0.00 3.32
1245 1565 3.439540 GCGAGGGCGGCAATGAAA 61.440 61.111 12.47 0.00 38.16 2.69
1365 1710 2.066262 CCGTAAGTGAAGATTGTGCGT 58.934 47.619 0.00 0.00 0.00 5.24
1367 1712 1.804151 TGCCGTAAGTGAAGATTGTGC 59.196 47.619 0.00 0.00 0.00 4.57
1380 1725 2.905075 CAGTTCATGAGGATGCCGTAA 58.095 47.619 0.00 0.00 0.00 3.18
1465 1810 4.879545 GGCAATGATTTCATTTGCCTTCAT 59.120 37.500 24.20 0.00 45.80 2.57
1471 1816 3.125658 GTGGTGGCAATGATTTCATTTGC 59.874 43.478 3.06 9.99 43.48 3.68
1479 1824 1.077663 AGGAAGGTGGTGGCAATGATT 59.922 47.619 0.00 0.00 0.00 2.57
1580 1925 6.058183 ACAATGGAGTATGAGAAGGCATTAC 58.942 40.000 0.00 0.00 0.00 1.89
1617 1962 3.451526 CTGACTCATGCTATTCTCGCAA 58.548 45.455 0.00 0.00 41.26 4.85
1799 2145 3.349488 TCGAGTTATATGTCGCCACAG 57.651 47.619 0.00 0.00 35.41 3.66
1909 2255 6.378848 CCATGGATCATGCAATTATATGTCCA 59.621 38.462 5.56 17.48 40.20 4.02
1910 2256 6.604396 TCCATGGATCATGCAATTATATGTCC 59.396 38.462 11.44 11.51 40.20 4.02
1977 2323 1.967779 CCCCGGGTTGTCATTTTTCTT 59.032 47.619 21.85 0.00 0.00 2.52
2029 2387 1.203994 CTTGCAAAGGGAAGCCATGAG 59.796 52.381 0.00 0.00 41.27 2.90
2330 2699 2.673610 GCAAAGTGCAACAACCACAGAA 60.674 45.455 0.00 0.00 44.26 3.02
2331 2700 1.135141 GCAAAGTGCAACAACCACAGA 60.135 47.619 0.00 0.00 44.26 3.41
2361 2730 1.079612 CGACAGCATCAGCCAGACA 60.080 57.895 0.00 0.00 43.56 3.41
2363 2732 1.216444 GTCGACAGCATCAGCCAGA 59.784 57.895 11.55 0.00 43.56 3.86
2450 2820 5.975693 ACCAAACCACCATGTATACAAAG 57.024 39.130 10.14 6.80 0.00 2.77
2606 2977 8.891985 TCAGGTCTCTCATCTATGCTTATAAT 57.108 34.615 0.00 0.00 0.00 1.28
2675 3046 4.141321 TCCAGATGCTTTATCCATCTTGCT 60.141 41.667 1.42 0.00 45.21 3.91
2694 3065 2.092753 ACCATGGCATCAAGTACTCCAG 60.093 50.000 13.04 0.00 0.00 3.86
2775 3146 8.428852 TCAAACCATCATCGATCCTTCTATTTA 58.571 33.333 0.00 0.00 0.00 1.40
2823 3194 8.974060 AACACTGTCAGGTTTTATTCTCTTAA 57.026 30.769 4.53 0.00 0.00 1.85
2875 3246 1.134220 ACAGTTCTCCCAGCACGAAAA 60.134 47.619 0.00 0.00 0.00 2.29
2976 3347 8.177663 CGTCTGCACAATTATTTCTACAAAGAT 58.822 33.333 0.00 0.00 0.00 2.40
3007 3378 5.991606 TCCTAATTTCTGGAATAGTGCGATG 59.008 40.000 0.00 0.00 0.00 3.84


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

AutoCloner maintained by Alex Coulton.