Multiple sequence alignment - TraesCS6B01G221000

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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 TraesCS6B01G221000 chr6B 100.000 3437 0 0 1 3437 316461612 316458176 0.000000e+00 6348.0
1 TraesCS6B01G221000 chr6D 97.921 2164 29 7 745 2896 203749447 203747288 0.000000e+00 3733.0
2 TraesCS6B01G221000 chr6D 95.588 544 22 1 2896 3437 203747248 203746705 0.000000e+00 870.0
3 TraesCS6B01G221000 chr6D 93.182 44 3 0 520 563 413031450 413031407 7.960000e-07 65.8
4 TraesCS6B01G221000 chr6D 93.182 44 2 1 520 563 307786947 307786905 2.860000e-06 63.9
5 TraesCS6B01G221000 chr6A 97.878 2121 30 4 788 2896 289027799 289025682 0.000000e+00 3653.0
6 TraesCS6B01G221000 chr6A 95.413 545 20 2 2896 3437 289025642 289025100 0.000000e+00 863.0
7 TraesCS6B01G221000 chr6A 89.159 535 51 7 2 531 289028691 289029223 0.000000e+00 660.0
8 TraesCS6B01G221000 chr3D 89.405 538 48 9 1 531 159769081 159768546 0.000000e+00 669.0
9 TraesCS6B01G221000 chr3D 86.928 153 19 1 562 713 474589703 474589551 1.640000e-38 171.0
10 TraesCS6B01G221000 chr2A 89.219 538 49 7 1 534 122003845 122003313 0.000000e+00 664.0
11 TraesCS6B01G221000 chr2A 88.235 153 17 1 562 713 37039484 37039636 7.580000e-42 182.0
12 TraesCS6B01G221000 chr2A 90.566 53 5 0 511 563 70652502 70652450 1.710000e-08 71.3
13 TraesCS6B01G221000 chr1D 88.497 539 50 12 1 531 296280168 296280702 2.890000e-180 641.0
14 TraesCS6B01G221000 chr1D 90.909 154 13 1 561 713 393473060 393472907 4.500000e-49 206.0
15 TraesCS6B01G221000 chr1D 89.474 152 13 2 563 713 118476836 118476985 4.530000e-44 189.0
16 TraesCS6B01G221000 chr1D 90.769 130 12 0 584 713 157726692 157726563 1.270000e-39 174.0
17 TraesCS6B01G221000 chr3A 86.995 569 64 8 1 563 747601917 747601353 1.740000e-177 632.0
18 TraesCS6B01G221000 chr5B 87.127 536 62 6 1 531 321482003 321482536 4.910000e-168 601.0
19 TraesCS6B01G221000 chr5B 79.167 816 165 5 1510 2323 234903947 234903135 8.330000e-156 560.0
20 TraesCS6B01G221000 chr5B 87.500 208 17 4 3023 3221 184769499 184769706 7.420000e-57 231.0
21 TraesCS6B01G221000 chr5B 88.304 171 15 5 3268 3437 184769877 184770043 2.090000e-47 200.0
22 TraesCS6B01G221000 chr5B 88.889 153 16 1 561 712 690872263 690872415 1.630000e-43 187.0
23 TraesCS6B01G221000 chr5B 93.333 45 2 1 2766 2810 184766101 184766144 7.960000e-07 65.8
24 TraesCS6B01G221000 chr7B 86.617 538 64 7 1 531 240940493 240939957 3.820000e-164 588.0
25 TraesCS6B01G221000 chr7B 93.182 44 3 0 520 563 721689702 721689659 7.960000e-07 65.8
26 TraesCS6B01G221000 chr5D 79.950 798 159 1 1510 2307 218260976 218260180 1.370000e-163 586.0
27 TraesCS6B01G221000 chr5D 90.845 142 5 7 3268 3407 173753622 173753487 2.110000e-42 183.0
28 TraesCS6B01G221000 chr5D 84.768 151 10 8 2766 2906 173756413 173756266 4.630000e-29 139.0
29 TraesCS6B01G221000 chr5A 79.850 799 158 3 1510 2307 291271966 291271170 6.390000e-162 580.0
30 TraesCS6B01G221000 chr5A 90.116 172 11 5 3268 3437 195632100 195631933 5.780000e-53 219.0
31 TraesCS6B01G221000 chr5A 91.139 158 14 0 3031 3188 195632473 195632316 7.470000e-52 215.0
32 TraesCS6B01G221000 chr1B 86.406 537 65 7 1 531 211628183 211627649 6.390000e-162 580.0
33 TraesCS6B01G221000 chr1B 89.474 152 15 1 561 711 654215366 654215215 1.260000e-44 191.0
34 TraesCS6B01G221000 chr1B 85.417 144 18 3 563 705 608051891 608052032 2.760000e-31 147.0
35 TraesCS6B01G221000 chr7D 86.059 538 65 9 1 531 154169801 154170335 1.380000e-158 569.0
36 TraesCS6B01G221000 chr4D 84.283 579 66 10 1 563 309495546 309494977 3.020000e-150 542.0
37 TraesCS6B01G221000 chr1A 87.582 153 18 1 562 713 224971930 224971778 3.530000e-40 176.0
38 TraesCS6B01G221000 chr4A 76.613 124 18 3 448 560 740754375 740754498 1.330000e-04 58.4


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 TraesCS6B01G221000 chr6B 316458176 316461612 3436 True 6348.0 6348 100.0000 1 3437 1 chr6B.!!$R1 3436
1 TraesCS6B01G221000 chr6D 203746705 203749447 2742 True 2301.5 3733 96.7545 745 3437 2 chr6D.!!$R3 2692
2 TraesCS6B01G221000 chr6A 289025100 289027799 2699 True 2258.0 3653 96.6455 788 3437 2 chr6A.!!$R1 2649
3 TraesCS6B01G221000 chr6A 289028691 289029223 532 False 660.0 660 89.1590 2 531 1 chr6A.!!$F1 529
4 TraesCS6B01G221000 chr3D 159768546 159769081 535 True 669.0 669 89.4050 1 531 1 chr3D.!!$R1 530
5 TraesCS6B01G221000 chr2A 122003313 122003845 532 True 664.0 664 89.2190 1 534 1 chr2A.!!$R2 533
6 TraesCS6B01G221000 chr1D 296280168 296280702 534 False 641.0 641 88.4970 1 531 1 chr1D.!!$F2 530
7 TraesCS6B01G221000 chr3A 747601353 747601917 564 True 632.0 632 86.9950 1 563 1 chr3A.!!$R1 562
8 TraesCS6B01G221000 chr5B 321482003 321482536 533 False 601.0 601 87.1270 1 531 1 chr5B.!!$F1 530
9 TraesCS6B01G221000 chr5B 234903135 234903947 812 True 560.0 560 79.1670 1510 2323 1 chr5B.!!$R1 813
10 TraesCS6B01G221000 chr7B 240939957 240940493 536 True 588.0 588 86.6170 1 531 1 chr7B.!!$R1 530
11 TraesCS6B01G221000 chr5D 218260180 218260976 796 True 586.0 586 79.9500 1510 2307 1 chr5D.!!$R1 797
12 TraesCS6B01G221000 chr5A 291271170 291271966 796 True 580.0 580 79.8500 1510 2307 1 chr5A.!!$R1 797
13 TraesCS6B01G221000 chr5A 195631933 195632473 540 True 217.0 219 90.6275 3031 3437 2 chr5A.!!$R2 406
14 TraesCS6B01G221000 chr1B 211627649 211628183 534 True 580.0 580 86.4060 1 531 1 chr1B.!!$R1 530
15 TraesCS6B01G221000 chr7D 154169801 154170335 534 False 569.0 569 86.0590 1 531 1 chr7D.!!$F1 530
16 TraesCS6B01G221000 chr4D 309494977 309495546 569 True 542.0 542 84.2830 1 563 1 chr4D.!!$R1 562

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
453 465 0.107116 TACGCCGGCAAATATGGGTT 60.107 50.0 28.98 1.01 0.00 4.11 F
478 490 0.179001 GTTGGGTGTACTGCCAACCT 60.179 55.0 0.00 0.00 43.01 3.50 F
664 677 0.603975 AGAAAGCTCGTCCAACCAGC 60.604 55.0 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1650 1685 1.954146 GTTGTCGAGGTGCGCAAGA 60.954 57.895 14.00 6.87 40.61 3.02 R
1839 1874 3.197549 AGTGCTTCTCAAAGAGGAGATCC 59.802 47.826 6.51 0.00 43.10 3.36 R
2657 2701 3.746045 ACTTGTCCTGCGAGAAAGTAA 57.254 42.857 0.00 0.00 32.82 2.24 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
48 49 8.522830 TCATGCACAATATGATCGTAGAAGATA 58.477 33.333 0.41 0.00 43.58 1.98
80 81 1.135460 CGTCTCTACGGTCAAGGGTTC 60.135 57.143 0.00 0.00 45.50 3.62
87 88 0.951558 CGGTCAAGGGTTCCAGTTTG 59.048 55.000 0.00 0.00 0.00 2.93
89 90 2.661718 GGTCAAGGGTTCCAGTTTGAA 58.338 47.619 4.95 0.00 31.98 2.69
205 207 4.272991 GCAACTGCAAAATGATTGGTTGAA 59.727 37.500 12.28 0.00 41.59 2.69
211 213 7.879160 ACTGCAAAATGATTGGTTGAACATATT 59.121 29.630 0.00 0.00 0.00 1.28
222 224 4.114794 GTTGAACATATTTGGGCTCATGC 58.885 43.478 0.00 0.00 38.76 4.06
235 237 1.477700 GCTCATGCTGGCAACCAATAA 59.522 47.619 0.00 0.00 36.03 1.40
269 272 8.850454 TTTTATTCGGCTTGCAAAACTATATC 57.150 30.769 0.00 0.00 0.00 1.63
422 434 6.969993 TTTGTGCTATTTGTTAAAGAGGGT 57.030 33.333 0.00 0.00 30.60 4.34
453 465 0.107116 TACGCCGGCAAATATGGGTT 60.107 50.000 28.98 1.01 0.00 4.11
465 477 1.901654 TATGGGTTAGCGCGTTGGGT 61.902 55.000 8.43 0.00 0.00 4.51
467 479 2.667199 GGTTAGCGCGTTGGGTGT 60.667 61.111 8.43 0.00 0.00 4.16
478 490 0.179001 GTTGGGTGTACTGCCAACCT 60.179 55.000 0.00 0.00 43.01 3.50
483 495 3.181427 TGGGTGTACTGCCAACCTAAATT 60.181 43.478 8.82 0.00 43.01 1.82
496 508 3.227614 ACCTAAATTTCAAACAGGGCGT 58.772 40.909 8.47 0.00 0.00 5.68
540 553 4.084888 GGACAAAAGCGCCGTCCG 62.085 66.667 16.93 0.65 39.86 4.79
563 576 4.413800 GCCGGCGCGTTGGATTTT 62.414 61.111 12.58 0.00 0.00 1.82
564 577 2.257067 CCGGCGCGTTGGATTTTT 59.743 55.556 8.43 0.00 0.00 1.94
585 598 5.562298 TTTTTAGGGAAGACTACACTGCT 57.438 39.130 0.00 0.00 0.00 4.24
586 599 6.675413 TTTTTAGGGAAGACTACACTGCTA 57.325 37.500 0.00 0.00 0.00 3.49
587 600 5.916661 TTTAGGGAAGACTACACTGCTAG 57.083 43.478 0.00 0.00 0.00 3.42
588 601 3.459710 AGGGAAGACTACACTGCTAGT 57.540 47.619 0.00 0.00 0.00 2.57
589 602 3.780626 AGGGAAGACTACACTGCTAGTT 58.219 45.455 0.00 0.00 0.00 2.24
590 603 4.161102 AGGGAAGACTACACTGCTAGTTT 58.839 43.478 0.00 0.00 0.00 2.66
591 604 4.593634 AGGGAAGACTACACTGCTAGTTTT 59.406 41.667 0.00 0.00 0.00 2.43
592 605 5.778750 AGGGAAGACTACACTGCTAGTTTTA 59.221 40.000 0.00 0.00 0.00 1.52
593 606 6.440965 AGGGAAGACTACACTGCTAGTTTTAT 59.559 38.462 0.00 0.00 0.00 1.40
594 607 7.038231 AGGGAAGACTACACTGCTAGTTTTATT 60.038 37.037 0.00 0.00 0.00 1.40
595 608 7.064728 GGGAAGACTACACTGCTAGTTTTATTG 59.935 40.741 0.00 0.00 0.00 1.90
596 609 7.817962 GGAAGACTACACTGCTAGTTTTATTGA 59.182 37.037 0.00 0.00 0.00 2.57
597 610 9.204570 GAAGACTACACTGCTAGTTTTATTGAA 57.795 33.333 0.00 0.00 0.00 2.69
598 611 9.555727 AAGACTACACTGCTAGTTTTATTGAAA 57.444 29.630 0.00 0.00 0.00 2.69
599 612 8.989980 AGACTACACTGCTAGTTTTATTGAAAC 58.010 33.333 0.00 0.00 46.42 2.78
620 633 9.959749 TGAAACTCAAAATAGGTTTACATTGTC 57.040 29.630 0.00 0.00 34.00 3.18
624 637 8.932791 ACTCAAAATAGGTTTACATTGTCTACG 58.067 33.333 0.00 0.00 0.00 3.51
625 638 9.146984 CTCAAAATAGGTTTACATTGTCTACGA 57.853 33.333 0.00 0.00 0.00 3.43
626 639 9.146984 TCAAAATAGGTTTACATTGTCTACGAG 57.853 33.333 0.00 0.00 0.00 4.18
627 640 7.535489 AAATAGGTTTACATTGTCTACGAGC 57.465 36.000 0.00 0.00 0.00 5.03
628 641 4.803098 AGGTTTACATTGTCTACGAGCT 57.197 40.909 0.00 0.00 0.00 4.09
629 642 5.148651 AGGTTTACATTGTCTACGAGCTT 57.851 39.130 0.00 0.00 0.00 3.74
630 643 4.929808 AGGTTTACATTGTCTACGAGCTTG 59.070 41.667 0.00 0.00 0.00 4.01
631 644 4.435651 GGTTTACATTGTCTACGAGCTTGC 60.436 45.833 0.00 0.00 0.00 4.01
632 645 2.751166 ACATTGTCTACGAGCTTGCT 57.249 45.000 0.00 0.00 0.00 3.91
633 646 3.045601 ACATTGTCTACGAGCTTGCTT 57.954 42.857 0.00 0.00 0.00 3.91
634 647 4.188247 ACATTGTCTACGAGCTTGCTTA 57.812 40.909 0.00 0.00 0.00 3.09
635 648 3.927142 ACATTGTCTACGAGCTTGCTTAC 59.073 43.478 0.00 0.00 0.00 2.34
636 649 3.653539 TTGTCTACGAGCTTGCTTACA 57.346 42.857 0.00 0.00 0.00 2.41
637 650 3.653539 TGTCTACGAGCTTGCTTACAA 57.346 42.857 0.00 0.00 0.00 2.41
638 651 3.314553 TGTCTACGAGCTTGCTTACAAC 58.685 45.455 0.00 0.00 0.00 3.32
639 652 3.243602 TGTCTACGAGCTTGCTTACAACA 60.244 43.478 0.00 0.00 0.00 3.33
640 653 3.739300 GTCTACGAGCTTGCTTACAACAA 59.261 43.478 0.00 0.00 0.00 2.83
641 654 4.389077 GTCTACGAGCTTGCTTACAACAAT 59.611 41.667 0.00 0.00 0.00 2.71
642 655 3.542712 ACGAGCTTGCTTACAACAATG 57.457 42.857 0.00 0.00 0.00 2.82
643 656 2.878406 ACGAGCTTGCTTACAACAATGT 59.122 40.909 0.00 0.00 43.74 2.71
644 657 3.058914 ACGAGCTTGCTTACAACAATGTC 60.059 43.478 0.00 0.00 41.05 3.06
645 658 3.058983 CGAGCTTGCTTACAACAATGTCA 60.059 43.478 0.00 0.00 41.05 3.58
646 659 4.470462 GAGCTTGCTTACAACAATGTCAG 58.530 43.478 0.00 0.00 41.05 3.51
647 660 4.136796 AGCTTGCTTACAACAATGTCAGA 58.863 39.130 0.00 0.00 41.05 3.27
648 661 4.580167 AGCTTGCTTACAACAATGTCAGAA 59.420 37.500 0.00 0.00 41.05 3.02
649 662 5.067674 AGCTTGCTTACAACAATGTCAGAAA 59.932 36.000 0.00 0.00 41.05 2.52
650 663 5.400485 GCTTGCTTACAACAATGTCAGAAAG 59.600 40.000 6.54 6.54 44.37 2.62
651 664 4.858935 TGCTTACAACAATGTCAGAAAGC 58.141 39.130 12.64 12.64 43.18 3.51
652 665 4.580167 TGCTTACAACAATGTCAGAAAGCT 59.420 37.500 17.34 0.00 43.24 3.74
653 666 5.149977 GCTTACAACAATGTCAGAAAGCTC 58.850 41.667 12.40 0.00 41.21 4.09
654 667 3.885484 ACAACAATGTCAGAAAGCTCG 57.115 42.857 0.00 0.00 33.41 5.03
655 668 3.206150 ACAACAATGTCAGAAAGCTCGT 58.794 40.909 0.00 0.00 33.41 4.18
656 669 3.248602 ACAACAATGTCAGAAAGCTCGTC 59.751 43.478 0.00 0.00 33.41 4.20
657 670 2.417719 ACAATGTCAGAAAGCTCGTCC 58.582 47.619 0.00 0.00 0.00 4.79
658 671 2.224281 ACAATGTCAGAAAGCTCGTCCA 60.224 45.455 0.00 0.00 0.00 4.02
659 672 2.807967 CAATGTCAGAAAGCTCGTCCAA 59.192 45.455 0.00 0.00 0.00 3.53
660 673 1.865865 TGTCAGAAAGCTCGTCCAAC 58.134 50.000 0.00 0.00 0.00 3.77
661 674 1.149148 GTCAGAAAGCTCGTCCAACC 58.851 55.000 0.00 0.00 0.00 3.77
662 675 0.756294 TCAGAAAGCTCGTCCAACCA 59.244 50.000 0.00 0.00 0.00 3.67
663 676 1.151668 CAGAAAGCTCGTCCAACCAG 58.848 55.000 0.00 0.00 0.00 4.00
664 677 0.603975 AGAAAGCTCGTCCAACCAGC 60.604 55.000 0.00 0.00 0.00 4.85
665 678 0.603975 GAAAGCTCGTCCAACCAGCT 60.604 55.000 0.00 0.00 45.69 4.24
666 679 0.685097 AAAGCTCGTCCAACCAGCTA 59.315 50.000 0.00 0.00 42.86 3.32
667 680 0.685097 AAGCTCGTCCAACCAGCTAA 59.315 50.000 0.00 0.00 42.86 3.09
668 681 0.685097 AGCTCGTCCAACCAGCTAAA 59.315 50.000 0.00 0.00 41.84 1.85
669 682 1.071699 AGCTCGTCCAACCAGCTAAAA 59.928 47.619 0.00 0.00 41.84 1.52
670 683 1.877443 GCTCGTCCAACCAGCTAAAAA 59.123 47.619 0.00 0.00 0.00 1.94
704 717 8.964420 TTACAATAACAAAAATGAGCTAGCAC 57.036 30.769 18.83 11.88 0.00 4.40
705 718 6.086222 ACAATAACAAAAATGAGCTAGCACG 58.914 36.000 18.83 0.00 0.00 5.34
706 719 5.880054 ATAACAAAAATGAGCTAGCACGT 57.120 34.783 18.83 9.57 0.00 4.49
707 720 3.542712 ACAAAAATGAGCTAGCACGTG 57.457 42.857 18.83 12.28 0.00 4.49
708 721 2.226437 ACAAAAATGAGCTAGCACGTGG 59.774 45.455 18.83 1.27 0.00 4.94
709 722 1.453155 AAAATGAGCTAGCACGTGGG 58.547 50.000 18.83 0.00 0.00 4.61
710 723 1.026718 AAATGAGCTAGCACGTGGGC 61.027 55.000 18.83 3.25 0.00 5.36
711 724 2.876368 AATGAGCTAGCACGTGGGCC 62.876 60.000 18.83 0.00 0.00 5.80
726 739 4.481112 GCCGGCGCATTGGAGTTG 62.481 66.667 12.58 0.00 34.03 3.16
727 740 4.481112 CCGGCGCATTGGAGTTGC 62.481 66.667 10.83 0.00 36.74 4.17
728 741 3.434319 CGGCGCATTGGAGTTGCT 61.434 61.111 10.83 0.00 37.96 3.91
729 742 2.486966 GGCGCATTGGAGTTGCTC 59.513 61.111 10.83 0.00 37.96 4.26
730 743 2.042831 GGCGCATTGGAGTTGCTCT 61.043 57.895 10.83 0.00 37.96 4.09
731 744 0.744414 GGCGCATTGGAGTTGCTCTA 60.744 55.000 10.83 0.00 37.96 2.43
732 745 1.086696 GCGCATTGGAGTTGCTCTAA 58.913 50.000 0.30 0.00 37.96 2.10
733 746 1.672881 GCGCATTGGAGTTGCTCTAAT 59.327 47.619 0.30 2.55 41.23 1.73
734 747 2.872245 GCGCATTGGAGTTGCTCTAATA 59.128 45.455 0.30 0.00 39.14 0.98
735 748 3.499918 GCGCATTGGAGTTGCTCTAATAT 59.500 43.478 0.30 0.00 39.14 1.28
736 749 4.023707 GCGCATTGGAGTTGCTCTAATATT 60.024 41.667 0.30 0.00 39.14 1.28
737 750 5.179368 GCGCATTGGAGTTGCTCTAATATTA 59.821 40.000 0.30 0.00 39.14 0.98
738 751 6.619446 GCGCATTGGAGTTGCTCTAATATTAG 60.619 42.308 15.25 15.25 39.14 1.73
739 752 6.425114 CGCATTGGAGTTGCTCTAATATTAGT 59.575 38.462 19.58 2.07 39.14 2.24
740 753 7.570140 CGCATTGGAGTTGCTCTAATATTAGTG 60.570 40.741 19.58 18.08 39.14 2.74
741 754 7.579726 CATTGGAGTTGCTCTAATATTAGTGC 58.420 38.462 29.78 29.78 45.54 4.40
824 847 3.265995 GTCTACCTCTTCCAAATCCCCAA 59.734 47.826 0.00 0.00 0.00 4.12
840 863 1.530655 CAACCCGCCCCACTTTTCT 60.531 57.895 0.00 0.00 0.00 2.52
931 966 3.560251 ACGCTCTGCAACCCACCT 61.560 61.111 0.00 0.00 0.00 4.00
1650 1685 3.108881 CGACATCGAGATCGTTCACAAT 58.891 45.455 11.81 0.00 43.02 2.71
1839 1874 4.697514 ACCTCATCATTCACGGTTATCAG 58.302 43.478 0.00 0.00 0.00 2.90
2211 2246 3.520569 GCCATTTGTGACACACTTTGTT 58.479 40.909 8.05 0.00 39.17 2.83
2277 2312 2.423892 GTGTCTCAAGAGTATGGAGCGA 59.576 50.000 0.00 0.00 0.00 4.93
2657 2701 9.301153 GTTTTGTACTCAATTTCATTTCAGTGT 57.699 29.630 0.00 0.00 33.32 3.55
2666 2710 9.950680 TCAATTTCATTTCAGTGTTACTTTCTC 57.049 29.630 0.00 0.00 0.00 2.87
2669 2713 5.053811 TCATTTCAGTGTTACTTTCTCGCA 58.946 37.500 0.00 0.00 0.00 5.10
2682 2726 1.153823 CTCGCAGGACAAGTACCCG 60.154 63.158 0.00 0.00 0.00 5.28
2695 2739 4.040217 ACAAGTACCCGTAATGTGGTGTTA 59.960 41.667 0.00 0.00 36.04 2.41
2937 3021 6.822170 GGAGGGAGTAGTTCATTTCGTATTTT 59.178 38.462 0.00 0.00 0.00 1.82
2954 3038 3.363341 TTTTTCTTGTTCGATGGTGGC 57.637 42.857 0.00 0.00 0.00 5.01
3000 3084 7.380423 AGTGCCTAGATATGTTAGTCCAAAT 57.620 36.000 0.00 0.00 0.00 2.32
3001 3085 7.806180 AGTGCCTAGATATGTTAGTCCAAATT 58.194 34.615 0.00 0.00 0.00 1.82
3003 3087 8.903820 GTGCCTAGATATGTTAGTCCAAATTTT 58.096 33.333 0.00 0.00 0.00 1.82
3027 3111 8.436046 TTTTTCATGGAACCATTGAAGAAAAG 57.564 30.769 19.29 4.03 36.69 2.27
3104 3188 6.438425 CCACCTAGGTTACAGTCCTAAACTTA 59.562 42.308 13.15 0.00 37.15 2.24
3171 3255 2.224523 ACGATGTGTCCATGGTCACTTT 60.225 45.455 32.63 23.51 35.37 2.66
3249 3429 8.480133 TTTAAGAGAAGATAGTATCTCACCCC 57.520 38.462 13.10 6.28 43.62 4.95
3263 3443 4.599041 TCTCACCCCCTTGTAATGAATTG 58.401 43.478 0.00 0.00 0.00 2.32
3264 3444 4.044065 TCTCACCCCCTTGTAATGAATTGT 59.956 41.667 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 1.870055 TAGAGACGTTTCGGGCGCTT 61.870 55.000 7.64 0.00 0.00 4.68
70 71 2.623416 CCTTCAAACTGGAACCCTTGAC 59.377 50.000 0.00 0.00 0.00 3.18
80 81 4.339247 ACAACATTCTCACCTTCAAACTGG 59.661 41.667 0.00 0.00 0.00 4.00
87 88 4.380531 TCAGACACAACATTCTCACCTTC 58.619 43.478 0.00 0.00 0.00 3.46
89 90 3.805108 GCTCAGACACAACATTCTCACCT 60.805 47.826 0.00 0.00 0.00 4.00
205 207 2.313317 CCAGCATGAGCCCAAATATGT 58.687 47.619 0.00 0.00 43.56 2.29
211 213 2.117858 TTGCCAGCATGAGCCCAA 59.882 55.556 0.00 0.00 43.56 4.12
222 224 8.776376 AAAAAGATACATTTATTGGTTGCCAG 57.224 30.769 0.00 0.00 33.81 4.85
235 237 6.862209 TGCAAGCCGAATAAAAAGATACATT 58.138 32.000 0.00 0.00 0.00 2.71
434 446 0.107116 AACCCATATTTGCCGGCGTA 60.107 50.000 23.90 15.05 0.00 4.42
453 465 1.080366 CAGTACACCCAACGCGCTA 60.080 57.895 5.73 0.00 0.00 4.26
465 477 6.096987 TGTTTGAAATTTAGGTTGGCAGTACA 59.903 34.615 0.00 0.00 0.00 2.90
467 479 6.239176 CCTGTTTGAAATTTAGGTTGGCAGTA 60.239 38.462 0.00 0.00 0.00 2.74
478 490 3.365164 GCGTACGCCCTGTTTGAAATTTA 60.365 43.478 29.51 0.00 34.56 1.40
483 495 3.645286 GCGTACGCCCTGTTTGAA 58.355 55.556 29.51 0.00 34.56 2.69
516 529 1.357334 GCGCTTTTGTCCGTTTGGA 59.643 52.632 0.00 0.00 43.88 3.53
547 560 2.257067 AAAAATCCAACGCGCCGG 59.743 55.556 5.73 7.13 0.00 6.13
563 576 5.562298 AGCAGTGTAGTCTTCCCTAAAAA 57.438 39.130 0.00 0.00 0.00 1.94
564 577 5.778750 ACTAGCAGTGTAGTCTTCCCTAAAA 59.221 40.000 0.00 0.00 0.00 1.52
565 578 5.331069 ACTAGCAGTGTAGTCTTCCCTAAA 58.669 41.667 0.00 0.00 0.00 1.85
566 579 4.931914 ACTAGCAGTGTAGTCTTCCCTAA 58.068 43.478 0.00 0.00 0.00 2.69
567 580 4.587976 ACTAGCAGTGTAGTCTTCCCTA 57.412 45.455 0.00 0.00 0.00 3.53
568 581 3.459710 ACTAGCAGTGTAGTCTTCCCT 57.540 47.619 0.00 0.00 0.00 4.20
569 582 4.538746 AAACTAGCAGTGTAGTCTTCCC 57.461 45.455 6.04 0.00 31.73 3.97
570 583 7.817962 TCAATAAAACTAGCAGTGTAGTCTTCC 59.182 37.037 6.04 0.00 31.73 3.46
571 584 8.758633 TCAATAAAACTAGCAGTGTAGTCTTC 57.241 34.615 6.04 0.00 31.73 2.87
572 585 9.555727 TTTCAATAAAACTAGCAGTGTAGTCTT 57.444 29.630 6.04 2.74 31.73 3.01
573 586 8.989980 GTTTCAATAAAACTAGCAGTGTAGTCT 58.010 33.333 6.04 1.65 43.30 3.24
594 607 9.959749 GACAATGTAAACCTATTTTGAGTTTCA 57.040 29.630 0.00 0.00 35.45 2.69
598 611 8.932791 CGTAGACAATGTAAACCTATTTTGAGT 58.067 33.333 0.00 0.00 0.00 3.41
599 612 9.146984 TCGTAGACAATGTAAACCTATTTTGAG 57.853 33.333 0.00 0.00 0.00 3.02
600 613 9.146984 CTCGTAGACAATGTAAACCTATTTTGA 57.853 33.333 0.00 0.00 0.00 2.69
601 614 7.903431 GCTCGTAGACAATGTAAACCTATTTTG 59.097 37.037 0.00 0.00 0.00 2.44
602 615 7.822822 AGCTCGTAGACAATGTAAACCTATTTT 59.177 33.333 0.00 0.00 0.00 1.82
603 616 7.328737 AGCTCGTAGACAATGTAAACCTATTT 58.671 34.615 0.00 0.00 0.00 1.40
604 617 6.875076 AGCTCGTAGACAATGTAAACCTATT 58.125 36.000 0.00 0.00 0.00 1.73
605 618 6.466885 AGCTCGTAGACAATGTAAACCTAT 57.533 37.500 0.00 0.00 0.00 2.57
606 619 5.909621 AGCTCGTAGACAATGTAAACCTA 57.090 39.130 0.00 0.00 0.00 3.08
607 620 4.803098 AGCTCGTAGACAATGTAAACCT 57.197 40.909 0.00 0.00 0.00 3.50
608 621 4.435651 GCAAGCTCGTAGACAATGTAAACC 60.436 45.833 0.00 0.00 0.00 3.27
609 622 4.389077 AGCAAGCTCGTAGACAATGTAAAC 59.611 41.667 0.00 0.00 0.00 2.01
610 623 4.566004 AGCAAGCTCGTAGACAATGTAAA 58.434 39.130 0.00 0.00 0.00 2.01
611 624 4.188247 AGCAAGCTCGTAGACAATGTAA 57.812 40.909 0.00 0.00 0.00 2.41
612 625 3.868757 AGCAAGCTCGTAGACAATGTA 57.131 42.857 0.00 0.00 0.00 2.29
613 626 2.751166 AGCAAGCTCGTAGACAATGT 57.249 45.000 0.00 0.00 0.00 2.71
614 627 3.926527 TGTAAGCAAGCTCGTAGACAATG 59.073 43.478 0.00 0.00 0.00 2.82
615 628 4.188247 TGTAAGCAAGCTCGTAGACAAT 57.812 40.909 0.00 0.00 0.00 2.71
616 629 3.653539 TGTAAGCAAGCTCGTAGACAA 57.346 42.857 0.00 0.00 0.00 3.18
617 630 3.243602 TGTTGTAAGCAAGCTCGTAGACA 60.244 43.478 0.00 0.00 34.94 3.41
618 631 3.314553 TGTTGTAAGCAAGCTCGTAGAC 58.685 45.455 0.00 0.00 34.94 2.59
619 632 3.653539 TGTTGTAAGCAAGCTCGTAGA 57.346 42.857 0.00 0.00 34.94 2.59
620 633 4.152402 ACATTGTTGTAAGCAAGCTCGTAG 59.848 41.667 0.00 0.00 34.94 3.51
621 634 4.062293 ACATTGTTGTAAGCAAGCTCGTA 58.938 39.130 0.00 0.00 34.94 3.43
622 635 2.878406 ACATTGTTGTAAGCAAGCTCGT 59.122 40.909 0.00 0.00 34.94 4.18
623 636 3.058983 TGACATTGTTGTAAGCAAGCTCG 60.059 43.478 0.00 0.00 35.79 5.03
624 637 4.214119 TCTGACATTGTTGTAAGCAAGCTC 59.786 41.667 0.00 0.00 34.65 4.09
625 638 4.136796 TCTGACATTGTTGTAAGCAAGCT 58.863 39.130 0.00 0.00 34.65 3.74
626 639 4.488126 TCTGACATTGTTGTAAGCAAGC 57.512 40.909 0.00 0.00 34.65 4.01
627 640 5.400485 GCTTTCTGACATTGTTGTAAGCAAG 59.600 40.000 19.65 10.98 40.78 4.01
628 641 5.067674 AGCTTTCTGACATTGTTGTAAGCAA 59.932 36.000 23.10 6.39 42.34 3.91
629 642 4.580167 AGCTTTCTGACATTGTTGTAAGCA 59.420 37.500 23.10 5.94 42.34 3.91
630 643 5.113502 AGCTTTCTGACATTGTTGTAAGC 57.886 39.130 18.21 18.21 41.14 3.09
631 644 5.050091 ACGAGCTTTCTGACATTGTTGTAAG 60.050 40.000 0.00 0.00 35.84 2.34
632 645 4.814234 ACGAGCTTTCTGACATTGTTGTAA 59.186 37.500 0.00 0.00 35.79 2.41
633 646 4.377021 ACGAGCTTTCTGACATTGTTGTA 58.623 39.130 0.00 0.00 35.79 2.41
634 647 3.206150 ACGAGCTTTCTGACATTGTTGT 58.794 40.909 0.00 0.00 39.32 3.32
635 648 3.364366 GGACGAGCTTTCTGACATTGTTG 60.364 47.826 0.00 0.00 0.00 3.33
636 649 2.808543 GGACGAGCTTTCTGACATTGTT 59.191 45.455 0.00 0.00 0.00 2.83
637 650 2.224281 TGGACGAGCTTTCTGACATTGT 60.224 45.455 0.00 0.00 0.00 2.71
638 651 2.416747 TGGACGAGCTTTCTGACATTG 58.583 47.619 0.00 0.00 0.00 2.82
639 652 2.808543 GTTGGACGAGCTTTCTGACATT 59.191 45.455 0.00 0.00 0.00 2.71
640 653 2.417719 GTTGGACGAGCTTTCTGACAT 58.582 47.619 0.00 0.00 0.00 3.06
641 654 1.540363 GGTTGGACGAGCTTTCTGACA 60.540 52.381 0.00 0.00 0.00 3.58
642 655 1.149148 GGTTGGACGAGCTTTCTGAC 58.851 55.000 0.00 0.00 0.00 3.51
643 656 0.756294 TGGTTGGACGAGCTTTCTGA 59.244 50.000 0.00 0.00 0.00 3.27
644 657 1.151668 CTGGTTGGACGAGCTTTCTG 58.848 55.000 0.00 0.00 0.00 3.02
645 658 0.603975 GCTGGTTGGACGAGCTTTCT 60.604 55.000 7.67 0.00 44.94 2.52
646 659 1.869690 GCTGGTTGGACGAGCTTTC 59.130 57.895 7.67 0.00 44.94 2.62
647 660 4.065110 GCTGGTTGGACGAGCTTT 57.935 55.556 7.67 0.00 44.94 3.51
678 691 9.573133 GTGCTAGCTCATTTTTGTTATTGTAAT 57.427 29.630 17.23 0.00 0.00 1.89
679 692 7.748683 CGTGCTAGCTCATTTTTGTTATTGTAA 59.251 33.333 17.23 0.00 0.00 2.41
680 693 7.094975 ACGTGCTAGCTCATTTTTGTTATTGTA 60.095 33.333 17.23 0.00 0.00 2.41
681 694 6.086222 CGTGCTAGCTCATTTTTGTTATTGT 58.914 36.000 17.23 0.00 0.00 2.71
682 695 6.032775 CACGTGCTAGCTCATTTTTGTTATTG 59.967 38.462 17.23 0.00 0.00 1.90
683 696 6.086222 CACGTGCTAGCTCATTTTTGTTATT 58.914 36.000 17.23 0.00 0.00 1.40
684 697 5.391950 CCACGTGCTAGCTCATTTTTGTTAT 60.392 40.000 17.23 0.00 0.00 1.89
685 698 4.083537 CCACGTGCTAGCTCATTTTTGTTA 60.084 41.667 17.23 0.00 0.00 2.41
686 699 3.304659 CCACGTGCTAGCTCATTTTTGTT 60.305 43.478 17.23 0.00 0.00 2.83
687 700 2.226437 CCACGTGCTAGCTCATTTTTGT 59.774 45.455 17.23 1.67 0.00 2.83
688 701 2.414559 CCCACGTGCTAGCTCATTTTTG 60.415 50.000 17.23 1.01 0.00 2.44
689 702 1.812571 CCCACGTGCTAGCTCATTTTT 59.187 47.619 17.23 0.00 0.00 1.94
690 703 1.453155 CCCACGTGCTAGCTCATTTT 58.547 50.000 17.23 0.00 0.00 1.82
691 704 1.026718 GCCCACGTGCTAGCTCATTT 61.027 55.000 17.23 0.00 0.00 2.32
692 705 1.450312 GCCCACGTGCTAGCTCATT 60.450 57.895 17.23 0.00 0.00 2.57
693 706 2.187946 GCCCACGTGCTAGCTCAT 59.812 61.111 17.23 0.00 0.00 2.90
694 707 4.082523 GGCCCACGTGCTAGCTCA 62.083 66.667 17.23 0.00 0.00 4.26
709 722 4.481112 CAACTCCAATGCGCCGGC 62.481 66.667 19.07 19.07 40.52 6.13
710 723 4.481112 GCAACTCCAATGCGCCGG 62.481 66.667 4.18 0.00 33.57 6.13
713 726 8.901016 ACTAATATTAGAGCAACTCCAATGCGC 61.901 40.741 25.83 0.00 42.90 6.09
714 727 6.425114 ACTAATATTAGAGCAACTCCAATGCG 59.575 38.462 25.83 0.00 40.06 4.73
715 728 7.579726 CACTAATATTAGAGCAACTCCAATGC 58.420 38.462 25.83 0.00 37.83 3.56
716 729 7.579726 GCACTAATATTAGAGCAACTCCAATG 58.420 38.462 29.06 14.84 43.76 2.82
717 730 7.736447 GCACTAATATTAGAGCAACTCCAAT 57.264 36.000 29.06 4.54 43.76 3.16
783 796 1.543358 ACGGACGGAGAAAGGAGTAAC 59.457 52.381 0.00 0.00 0.00 2.50
824 847 2.434774 GAGAAAAGTGGGGCGGGT 59.565 61.111 0.00 0.00 0.00 5.28
840 863 3.311110 GACGCTGGGTGGAGTGGA 61.311 66.667 0.70 0.00 0.00 4.02
1650 1685 1.954146 GTTGTCGAGGTGCGCAAGA 60.954 57.895 14.00 6.87 40.61 3.02
1839 1874 3.197549 AGTGCTTCTCAAAGAGGAGATCC 59.802 47.826 6.51 0.00 43.10 3.36
2277 2312 5.971763 TGGTTATCGGCAAAATTAAATGCT 58.028 33.333 9.72 0.00 42.20 3.79
2657 2701 3.746045 ACTTGTCCTGCGAGAAAGTAA 57.254 42.857 0.00 0.00 32.82 2.24
2666 2710 0.244450 TTACGGGTACTTGTCCTGCG 59.756 55.000 0.00 0.00 34.93 5.18
2669 2713 2.235402 CCACATTACGGGTACTTGTCCT 59.765 50.000 0.00 0.00 0.00 3.85
2682 2726 9.084164 CACTACAAGATACTAACACCACATTAC 57.916 37.037 0.00 0.00 0.00 1.89
2937 3021 2.198827 ATGCCACCATCGAACAAGAA 57.801 45.000 0.00 0.00 0.00 2.52
2954 3038 6.692681 CACTAAAGATGGCAATTCGGTAAATG 59.307 38.462 0.00 0.00 0.00 2.32
3003 3087 7.790027 TCTTTTCTTCAATGGTTCCATGAAAA 58.210 30.769 18.15 18.15 30.86 2.29
3027 3111 6.019720 CACTTATGATATGCTCAGATCGCATC 60.020 42.308 9.48 0.00 44.24 3.91
3047 3131 3.844211 ACCACAAGGAATCTAGCCACTTA 59.156 43.478 0.00 0.00 38.69 2.24
3104 3188 0.968405 AAAATGCGAACACCCATGCT 59.032 45.000 0.00 0.00 0.00 3.79
3171 3255 8.648698 TCCAAATGGAAATCTTTAGATTGACA 57.351 30.769 5.78 8.31 43.41 3.58
3401 3622 3.245122 ACAAAATACGGATTGTCCCCAGT 60.245 43.478 0.00 0.00 34.84 4.00


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

AutoCloner maintained by Alex Coulton.