Multiple sequence alignment - TraesCS2B01G583100

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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 TraesCS2B01G583100 chr2B 100.000 3791 0 0 1 3791 770678168 770674378 0.000000e+00 7001
1 TraesCS2B01G583100 chr2B 86.111 864 57 23 829 1675 748355955 748356772 0.000000e+00 872
2 TraesCS2B01G583100 chr2B 84.899 841 68 20 2503 3320 748365160 748365964 0.000000e+00 795
3 TraesCS2B01G583100 chr2B 84.527 866 62 28 829 1675 748202542 748203354 0.000000e+00 791
4 TraesCS2B01G583100 chr2B 84.679 842 71 28 2503 3320 748214184 748214991 0.000000e+00 787
5 TraesCS2B01G583100 chr2B 86.544 327 26 14 3410 3732 748366089 748366401 1.010000e-90 344
6 TraesCS2B01G583100 chr2B 85.276 326 32 11 3410 3732 748215116 748215428 4.720000e-84 322
7 TraesCS2B01G583100 chr2B 86.139 303 22 6 1663 1963 748212985 748213269 3.680000e-80 309
8 TraesCS2B01G583100 chr2D 88.243 3904 234 103 1 3791 627918712 627914921 0.000000e+00 4458
9 TraesCS2B01G583100 chr2A 88.508 2628 143 63 738 3321 758394323 758391811 0.000000e+00 3033
10 TraesCS2B01G583100 chr2A 95.137 473 18 2 3320 3791 758390220 758389752 0.000000e+00 741
11 TraesCS2B01G583100 chr2A 94.926 473 19 2 3320 3791 758391687 758391219 0.000000e+00 736
12 TraesCS2B01G583100 chr2A 85.897 546 22 20 1 537 758395025 758394526 7.210000e-147 531
13 TraesCS2B01G583100 chr2A 84.274 496 30 18 2842 3321 758390807 758390344 1.250000e-119 440
14 TraesCS2B01G583100 chr7A 75.983 458 57 32 1595 2048 96199431 96199839 1.800000e-43 187


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 TraesCS2B01G583100 chr2B 770674378 770678168 3790 True 7001.000000 7001 100.000000 1 3791 1 chr2B.!!$R1 3790
1 TraesCS2B01G583100 chr2B 748355955 748356772 817 False 872.000000 872 86.111000 829 1675 1 chr2B.!!$F2 846
2 TraesCS2B01G583100 chr2B 748202542 748203354 812 False 791.000000 791 84.527000 829 1675 1 chr2B.!!$F1 846
3 TraesCS2B01G583100 chr2B 748365160 748366401 1241 False 569.500000 795 85.721500 2503 3732 2 chr2B.!!$F4 1229
4 TraesCS2B01G583100 chr2B 748212985 748215428 2443 False 472.666667 787 85.364667 1663 3732 3 chr2B.!!$F3 2069
5 TraesCS2B01G583100 chr2D 627914921 627918712 3791 True 4458.000000 4458 88.243000 1 3791 1 chr2D.!!$R1 3790
6 TraesCS2B01G583100 chr2A 758389752 758395025 5273 True 1096.200000 3033 89.748400 1 3791 5 chr2A.!!$R1 3790

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
579 608 0.108138 AAGAAGAGGCCACCGAATCG 60.108 55.0 5.01 0.0 0.00 3.34 F
1639 1757 0.031178 CAGGTCTGCTTTGTTGTGCC 59.969 55.0 0.00 0.0 0.00 5.01 F
1724 1852 0.246086 TGATGGTTTGGCCGCAATTC 59.754 50.0 0.00 0.0 41.21 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1724 1852 0.037326 TTCTCGCCTTACACCTGCAG 60.037 55.000 6.78 6.78 0.00 4.41 R
2720 3268 0.606673 GGCCTGGACAAAGGAGTGTC 60.607 60.000 0.00 0.00 45.99 3.67 R
3323 4046 1.229177 TCACAGAGGCTGCCTACCA 60.229 57.895 23.44 0.89 34.37 3.25 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 6.092748 GTGTTTCAATAATCGAGCAACCATT 58.907 36.000 0.00 0.00 0.00 3.16
54 55 7.819415 TCAATAATCGAGCAACCATTCCTATAG 59.181 37.037 0.00 0.00 0.00 1.31
61 62 7.232737 TCGAGCAACCATTCCTATAGAAATCTA 59.767 37.037 0.00 0.00 38.21 1.98
62 63 7.543868 CGAGCAACCATTCCTATAGAAATCTAG 59.456 40.741 0.00 0.00 38.21 2.43
63 64 8.268878 AGCAACCATTCCTATAGAAATCTAGT 57.731 34.615 0.00 0.00 38.21 2.57
139 140 3.550820 TGTCCAAACATAACAGCACACT 58.449 40.909 0.00 0.00 0.00 3.55
144 145 4.629634 CCAAACATAACAGCACACTCGATA 59.370 41.667 0.00 0.00 0.00 2.92
145 146 5.294306 CCAAACATAACAGCACACTCGATAT 59.706 40.000 0.00 0.00 0.00 1.63
153 159 6.149129 ACAGCACACTCGATATTGATAAGA 57.851 37.500 0.00 0.00 0.00 2.10
157 163 5.861251 GCACACTCGATATTGATAAGAGAGG 59.139 44.000 11.35 7.31 33.53 3.69
158 164 6.385843 CACACTCGATATTGATAAGAGAGGG 58.614 44.000 11.35 7.30 34.19 4.30
159 165 6.015856 CACACTCGATATTGATAAGAGAGGGT 60.016 42.308 11.35 7.75 40.99 4.34
160 166 7.175119 CACACTCGATATTGATAAGAGAGGGTA 59.825 40.741 11.35 0.00 38.64 3.69
161 167 7.891183 ACACTCGATATTGATAAGAGAGGGTAT 59.109 37.037 11.35 0.00 38.87 2.73
162 168 9.397280 CACTCGATATTGATAAGAGAGGGTATA 57.603 37.037 11.35 0.00 33.53 1.47
341 347 1.685224 CTGCCAGCCCTTGAGGTTA 59.315 57.895 0.00 0.00 38.26 2.85
377 383 1.008538 GACGCTGCAAACACCAAGG 60.009 57.895 0.00 0.00 0.00 3.61
379 385 2.848858 CGCTGCAAACACCAAGGCT 61.849 57.895 0.00 0.00 0.00 4.58
381 387 1.458639 GCTGCAAACACCAAGGCTCT 61.459 55.000 0.00 0.00 0.00 4.09
382 388 0.595095 CTGCAAACACCAAGGCTCTC 59.405 55.000 0.00 0.00 0.00 3.20
383 389 0.183492 TGCAAACACCAAGGCTCTCT 59.817 50.000 0.00 0.00 0.00 3.10
384 390 1.322442 GCAAACACCAAGGCTCTCTT 58.678 50.000 0.00 0.00 35.79 2.85
385 391 2.158682 TGCAAACACCAAGGCTCTCTTA 60.159 45.455 0.00 0.00 33.68 2.10
386 392 2.485814 GCAAACACCAAGGCTCTCTTAG 59.514 50.000 0.00 0.00 33.68 2.18
398 404 6.025793 AGGCTCTCTTAGGATAAGAACTCT 57.974 41.667 1.28 0.00 0.00 3.24
399 405 7.156694 AGGCTCTCTTAGGATAAGAACTCTA 57.843 40.000 1.28 0.00 0.00 2.43
400 406 7.002276 AGGCTCTCTTAGGATAAGAACTCTAC 58.998 42.308 1.28 0.00 0.00 2.59
401 407 6.773685 GGCTCTCTTAGGATAAGAACTCTACA 59.226 42.308 1.28 0.00 0.00 2.74
402 408 7.040686 GGCTCTCTTAGGATAAGAACTCTACAG 60.041 44.444 1.28 0.00 0.00 2.74
403 409 7.501225 GCTCTCTTAGGATAAGAACTCTACAGT 59.499 40.741 1.28 0.00 0.00 3.55
404 410 8.967664 TCTCTTAGGATAAGAACTCTACAGTC 57.032 38.462 1.28 0.00 29.93 3.51
405 411 8.774183 TCTCTTAGGATAAGAACTCTACAGTCT 58.226 37.037 1.28 0.00 29.93 3.24
406 412 8.740123 TCTTAGGATAAGAACTCTACAGTCTG 57.260 38.462 0.00 0.00 29.93 3.51
407 413 8.549731 TCTTAGGATAAGAACTCTACAGTCTGA 58.450 37.037 6.91 0.00 29.93 3.27
408 414 9.349713 CTTAGGATAAGAACTCTACAGTCTGAT 57.650 37.037 6.91 0.00 29.93 2.90
409 415 7.581213 AGGATAAGAACTCTACAGTCTGATG 57.419 40.000 6.91 0.00 29.93 3.07
410 416 7.350382 AGGATAAGAACTCTACAGTCTGATGA 58.650 38.462 6.91 3.32 29.93 2.92
411 417 7.284489 AGGATAAGAACTCTACAGTCTGATGAC 59.716 40.741 6.91 0.00 43.22 3.06
435 441 4.857871 TTTACAACAGCATCATACGAGC 57.142 40.909 0.00 0.00 0.00 5.03
463 469 4.272018 CAGCCACATAGTTAAGCAGTGATC 59.728 45.833 0.00 0.00 32.14 2.92
567 596 2.863153 CGCACGGGCAAAGAAGAG 59.137 61.111 11.77 0.00 41.24 2.85
569 598 2.982744 GCACGGGCAAAGAAGAGGC 61.983 63.158 3.77 0.00 40.72 4.70
570 599 2.034221 ACGGGCAAAGAAGAGGCC 59.966 61.111 0.00 0.00 46.99 5.19
573 602 3.686760 GGCAAAGAAGAGGCCACC 58.313 61.111 5.01 0.00 46.92 4.61
576 605 0.889186 GCAAAGAAGAGGCCACCGAA 60.889 55.000 5.01 0.00 0.00 4.30
577 606 1.826385 CAAAGAAGAGGCCACCGAAT 58.174 50.000 5.01 0.00 0.00 3.34
579 608 0.108138 AAGAAGAGGCCACCGAATCG 60.108 55.000 5.01 0.00 0.00 3.34
580 609 2.125106 AAGAGGCCACCGAATCGC 60.125 61.111 5.01 0.00 0.00 4.58
581 610 2.579684 GAAGAGGCCACCGAATCGCT 62.580 60.000 5.01 0.00 0.00 4.93
582 611 2.859273 AAGAGGCCACCGAATCGCTG 62.859 60.000 5.01 0.00 0.00 5.18
583 612 4.473520 AGGCCACCGAATCGCTGG 62.474 66.667 12.32 12.32 35.89 4.85
586 615 3.197790 CCACCGAATCGCTGGCAG 61.198 66.667 10.94 10.94 0.00 4.85
587 616 2.125552 CACCGAATCGCTGGCAGA 60.126 61.111 20.86 0.00 0.00 4.26
588 617 1.522355 CACCGAATCGCTGGCAGAT 60.522 57.895 20.86 0.07 0.00 2.90
589 618 1.091771 CACCGAATCGCTGGCAGATT 61.092 55.000 20.86 10.36 40.63 2.40
590 619 0.464036 ACCGAATCGCTGGCAGATTA 59.536 50.000 20.86 2.10 38.32 1.75
591 620 1.070758 ACCGAATCGCTGGCAGATTAT 59.929 47.619 20.86 4.70 38.32 1.28
592 621 1.462283 CCGAATCGCTGGCAGATTATG 59.538 52.381 20.86 6.47 38.32 1.90
593 622 2.407090 CGAATCGCTGGCAGATTATGA 58.593 47.619 20.86 7.46 38.32 2.15
594 623 2.411069 CGAATCGCTGGCAGATTATGAG 59.589 50.000 20.86 0.00 38.32 2.90
595 624 1.805869 ATCGCTGGCAGATTATGAGC 58.194 50.000 20.86 0.00 0.00 4.26
597 626 0.585357 CGCTGGCAGATTATGAGCAC 59.415 55.000 20.86 0.00 30.03 4.40
599 628 1.602311 CTGGCAGATTATGAGCACCC 58.398 55.000 9.42 0.00 0.00 4.61
601 630 0.886490 GGCAGATTATGAGCACCCGG 60.886 60.000 0.00 0.00 0.00 5.73
602 631 0.886490 GCAGATTATGAGCACCCGGG 60.886 60.000 22.25 22.25 0.00 5.73
604 633 1.073199 GATTATGAGCACCCGGGGG 59.927 63.158 27.92 25.22 42.03 5.40
606 635 0.991355 ATTATGAGCACCCGGGGGAA 60.991 55.000 32.21 12.57 38.96 3.97
607 636 0.991355 TTATGAGCACCCGGGGGAAT 60.991 55.000 32.21 19.15 38.96 3.01
608 637 1.415672 TATGAGCACCCGGGGGAATC 61.416 60.000 32.21 24.26 38.96 2.52
609 638 4.547367 GAGCACCCGGGGGAATCG 62.547 72.222 32.21 7.48 38.96 3.34
632 662 4.500116 GCTCGCTCCTCCGGTCAC 62.500 72.222 0.00 0.00 0.00 3.67
640 670 2.657237 CTCCGGTCACCACACTCC 59.343 66.667 0.00 0.00 0.00 3.85
641 671 3.282745 CTCCGGTCACCACACTCCG 62.283 68.421 0.00 0.00 42.22 4.63
642 672 3.612681 CCGGTCACCACACTCCGT 61.613 66.667 0.00 0.00 41.17 4.69
643 673 2.049433 CGGTCACCACACTCCGTC 60.049 66.667 0.00 0.00 38.45 4.79
644 674 2.342648 GGTCACCACACTCCGTCC 59.657 66.667 0.00 0.00 0.00 4.79
646 676 3.299977 TCACCACACTCCGTCCCG 61.300 66.667 0.00 0.00 0.00 5.14
657 687 2.356553 CGTCCCGCGGAAGTGAAA 60.357 61.111 30.73 0.00 46.66 2.69
658 688 1.740296 CGTCCCGCGGAAGTGAAAT 60.740 57.895 30.73 0.00 46.66 2.17
659 689 0.458889 CGTCCCGCGGAAGTGAAATA 60.459 55.000 30.73 0.00 46.66 1.40
660 690 1.287425 GTCCCGCGGAAGTGAAATAG 58.713 55.000 30.73 5.39 46.66 1.73
661 691 1.134907 GTCCCGCGGAAGTGAAATAGA 60.135 52.381 30.73 8.18 46.66 1.98
662 692 1.136305 TCCCGCGGAAGTGAAATAGAG 59.864 52.381 30.73 4.53 46.66 2.43
663 693 1.136305 CCCGCGGAAGTGAAATAGAGA 59.864 52.381 30.73 0.00 46.66 3.10
664 694 2.464865 CCGCGGAAGTGAAATAGAGAG 58.535 52.381 24.07 0.00 46.66 3.20
665 695 1.855360 CGCGGAAGTGAAATAGAGAGC 59.145 52.381 0.00 0.00 46.66 4.09
667 697 2.863137 GCGGAAGTGAAATAGAGAGCAG 59.137 50.000 0.00 0.00 0.00 4.24
668 698 3.429547 GCGGAAGTGAAATAGAGAGCAGA 60.430 47.826 0.00 0.00 0.00 4.26
669 699 4.748892 CGGAAGTGAAATAGAGAGCAGAA 58.251 43.478 0.00 0.00 0.00 3.02
670 700 5.171476 CGGAAGTGAAATAGAGAGCAGAAA 58.829 41.667 0.00 0.00 0.00 2.52
671 701 5.062809 CGGAAGTGAAATAGAGAGCAGAAAC 59.937 44.000 0.00 0.00 0.00 2.78
672 702 6.169800 GGAAGTGAAATAGAGAGCAGAAACT 58.830 40.000 0.00 0.00 0.00 2.66
674 704 5.406649 AGTGAAATAGAGAGCAGAAACTCG 58.593 41.667 0.00 0.00 41.77 4.18
679 709 0.522180 GAGAGCAGAAACTCGGACGA 59.478 55.000 0.00 0.00 41.77 4.20
695 725 1.941734 CGAGAGCCGAGACGAATGC 60.942 63.158 0.00 0.00 41.76 3.56
699 729 2.202623 GCCGAGACGAATGCGAGT 60.203 61.111 0.00 0.00 41.64 4.18
701 731 0.524816 GCCGAGACGAATGCGAGTAA 60.525 55.000 0.00 0.00 41.64 2.24
702 732 1.904144 CCGAGACGAATGCGAGTAAA 58.096 50.000 0.00 0.00 41.64 2.01
703 733 1.846782 CCGAGACGAATGCGAGTAAAG 59.153 52.381 0.00 0.00 41.64 1.85
704 734 1.846782 CGAGACGAATGCGAGTAAAGG 59.153 52.381 0.00 0.00 41.64 3.11
705 735 2.731341 CGAGACGAATGCGAGTAAAGGT 60.731 50.000 0.00 0.00 41.64 3.50
707 737 1.060698 GACGAATGCGAGTAAAGGTGC 59.939 52.381 0.00 0.00 41.64 5.01
727 764 1.815421 CCTTGCGAGGAATGTCGGG 60.815 63.158 15.76 0.00 46.74 5.14
762 799 3.967335 GCCGGAGAGGGATCGTCG 61.967 72.222 5.05 0.00 41.48 5.12
764 801 2.203167 CGGAGAGGGATCGTCGGA 60.203 66.667 0.00 0.00 0.00 4.55
765 802 2.255172 CGGAGAGGGATCGTCGGAG 61.255 68.421 0.00 0.00 0.00 4.63
766 803 1.152922 GGAGAGGGATCGTCGGAGT 60.153 63.158 0.00 0.00 0.00 3.85
767 804 1.167781 GGAGAGGGATCGTCGGAGTC 61.168 65.000 0.00 0.00 0.00 3.36
768 805 1.500512 GAGAGGGATCGTCGGAGTCG 61.501 65.000 0.00 0.00 41.01 4.18
769 806 1.818785 GAGGGATCGTCGGAGTCGT 60.819 63.158 0.00 0.00 40.43 4.34
770 807 1.774046 GAGGGATCGTCGGAGTCGTC 61.774 65.000 0.00 0.00 40.43 4.20
771 808 2.323790 GGATCGTCGGAGTCGTCG 59.676 66.667 0.00 0.00 45.99 5.12
772 809 2.350985 GATCGTCGGAGTCGTCGC 60.351 66.667 0.00 0.00 44.74 5.19
773 810 3.786918 GATCGTCGGAGTCGTCGCC 62.787 68.421 0.00 0.00 44.74 5.54
816 862 3.447944 GGAGAGAGTCCCGAGTTGTTTAT 59.552 47.826 0.00 0.00 39.88 1.40
817 863 4.425520 GAGAGAGTCCCGAGTTGTTTATG 58.574 47.826 0.00 0.00 0.00 1.90
818 864 2.930682 GAGAGTCCCGAGTTGTTTATGC 59.069 50.000 0.00 0.00 0.00 3.14
819 865 2.007608 GAGTCCCGAGTTGTTTATGCC 58.992 52.381 0.00 0.00 0.00 4.40
820 866 1.092348 GTCCCGAGTTGTTTATGCCC 58.908 55.000 0.00 0.00 0.00 5.36
821 867 0.391927 TCCCGAGTTGTTTATGCCCG 60.392 55.000 0.00 0.00 0.00 6.13
822 868 1.427819 CCGAGTTGTTTATGCCCGC 59.572 57.895 0.00 0.00 0.00 6.13
823 869 1.060308 CGAGTTGTTTATGCCCGCG 59.940 57.895 0.00 0.00 0.00 6.46
824 870 1.226295 GAGTTGTTTATGCCCGCGC 60.226 57.895 0.00 0.00 0.00 6.86
964 1020 5.554822 TTTATTTATTTGCGAGCCTCGTT 57.445 34.783 16.50 1.39 42.81 3.85
988 1044 1.271871 TGTCCAAGCCGTTCCATCATT 60.272 47.619 0.00 0.00 0.00 2.57
989 1045 1.401905 GTCCAAGCCGTTCCATCATTC 59.598 52.381 0.00 0.00 0.00 2.67
997 1057 4.038162 AGCCGTTCCATCATTCTACTACTC 59.962 45.833 0.00 0.00 0.00 2.59
1511 1615 7.549839 TCCTTTTTCTTCAGAATAATGCCATG 58.450 34.615 0.00 0.00 33.54 3.66
1599 1717 0.754217 CAATGGATGCTCCTGGTGGG 60.754 60.000 0.00 0.00 37.46 4.61
1639 1757 0.031178 CAGGTCTGCTTTGTTGTGCC 59.969 55.000 0.00 0.00 0.00 5.01
1657 1780 1.886542 GCCGAATTTGGTTGGAGAACT 59.113 47.619 13.49 0.00 32.15 3.01
1658 1781 3.078837 GCCGAATTTGGTTGGAGAACTA 58.921 45.455 13.49 0.00 32.15 2.24
1659 1782 3.127030 GCCGAATTTGGTTGGAGAACTAG 59.873 47.826 13.49 0.00 32.15 2.57
1660 1783 3.127030 CCGAATTTGGTTGGAGAACTAGC 59.873 47.826 3.21 0.00 32.15 3.42
1702 1830 1.627329 TGAACTCTGATGAGCTTGGCT 59.373 47.619 0.00 0.00 43.85 4.75
1716 1844 0.392336 TTGGCTTGTGATGGTTTGGC 59.608 50.000 0.00 0.00 0.00 4.52
1724 1852 0.246086 TGATGGTTTGGCCGCAATTC 59.754 50.000 0.00 0.00 41.21 2.17
1749 1877 2.431057 AGGTGTAAGGCGAGAATAGTGG 59.569 50.000 0.00 0.00 0.00 4.00
1850 1978 6.572519 TGTAAATTGAGCTCTTTTGCTTGTT 58.427 32.000 16.19 0.00 44.17 2.83
1851 1979 6.697019 TGTAAATTGAGCTCTTTTGCTTGTTC 59.303 34.615 16.19 3.47 44.17 3.18
1852 1980 4.924305 ATTGAGCTCTTTTGCTTGTTCA 57.076 36.364 16.19 0.00 44.17 3.18
1853 1981 3.976793 TGAGCTCTTTTGCTTGTTCAG 57.023 42.857 16.19 0.00 44.17 3.02
1854 1982 2.620115 TGAGCTCTTTTGCTTGTTCAGG 59.380 45.455 16.19 0.00 44.17 3.86
1855 1983 2.880890 GAGCTCTTTTGCTTGTTCAGGA 59.119 45.455 6.43 0.00 44.17 3.86
1856 1984 3.290710 AGCTCTTTTGCTTGTTCAGGAA 58.709 40.909 0.00 0.00 40.93 3.36
1889 2022 7.717568 ACTACATCCTTAGTTAGCTATGTGTG 58.282 38.462 0.00 2.90 33.53 3.82
1937 2071 3.319122 GTGGCCATTTTCTGTCAGAAACT 59.681 43.478 24.48 17.80 43.25 2.66
1945 2082 0.588252 CTGTCAGAAACTTGTGCCGG 59.412 55.000 0.00 0.00 0.00 6.13
1990 2288 2.851045 GTTGGGGAAAGCCAGGGA 59.149 61.111 0.00 0.00 35.15 4.20
2043 2341 3.194005 ACCATTTAGTATGCCTGACCG 57.806 47.619 0.00 0.00 0.00 4.79
2114 2553 8.607441 TCTGATGATTAACTTATATGTGCACC 57.393 34.615 15.69 0.00 0.00 5.01
2152 2604 6.074088 CGATATCAAAGGCAGTGTAATCTCAC 60.074 42.308 3.12 0.00 38.46 3.51
2193 2645 6.258727 GCTGCACTATGTACTGATAAATGTGT 59.741 38.462 0.00 0.00 0.00 3.72
2194 2646 7.201644 GCTGCACTATGTACTGATAAATGTGTT 60.202 37.037 0.00 0.00 0.00 3.32
2227 2679 5.009010 CACAATTGTAATCATGGACCTAGGC 59.991 44.000 11.53 1.17 0.00 3.93
2228 2680 3.857157 TTGTAATCATGGACCTAGGCC 57.143 47.619 9.30 11.95 0.00 5.19
2376 2873 6.706295 TCTGAATGTGTAATGTGTCCATGTA 58.294 36.000 0.00 0.00 0.00 2.29
2644 3192 5.277825 TCAAGGTTAGTGTTGAAAAATGCG 58.722 37.500 0.00 0.00 29.66 4.73
2647 3195 3.425193 GGTTAGTGTTGAAAAATGCGCTG 59.575 43.478 9.73 0.00 0.00 5.18
2678 3226 3.125658 GCATTTCATGGTTCCAATTGCAC 59.874 43.478 0.00 0.00 0.00 4.57
2714 3262 2.863137 GCTGCGGACTTTCTATTCTGAG 59.137 50.000 0.00 0.00 0.00 3.35
2715 3263 3.677424 GCTGCGGACTTTCTATTCTGAGT 60.677 47.826 0.00 0.00 0.00 3.41
2716 3264 4.499183 CTGCGGACTTTCTATTCTGAGTT 58.501 43.478 0.00 0.00 0.00 3.01
2717 3265 4.894784 TGCGGACTTTCTATTCTGAGTTT 58.105 39.130 0.00 0.00 0.00 2.66
2718 3266 4.929808 TGCGGACTTTCTATTCTGAGTTTC 59.070 41.667 0.00 0.00 0.00 2.78
2719 3267 5.172205 GCGGACTTTCTATTCTGAGTTTCT 58.828 41.667 0.00 0.00 0.00 2.52
2720 3268 5.062809 GCGGACTTTCTATTCTGAGTTTCTG 59.937 44.000 0.00 0.00 0.00 3.02
2721 3269 6.390721 CGGACTTTCTATTCTGAGTTTCTGA 58.609 40.000 0.00 0.00 0.00 3.27
2728 3276 6.013379 TCTATTCTGAGTTTCTGACACTCCT 58.987 40.000 18.45 6.23 40.12 3.69
2751 3299 2.206536 CCAGGCCCGCTTGGAAAAA 61.207 57.895 12.24 0.00 44.80 1.94
2780 3328 1.262683 GAAGCTTGTCAGTGTCAGCAC 59.737 52.381 2.10 0.00 45.57 4.40
2819 3370 6.597614 CACTGAAAACTGCACTTCTAAGATC 58.402 40.000 0.00 0.00 0.00 2.75
2914 3465 4.611310 CAACCTCTGCAAGTGTCATATG 57.389 45.455 0.00 0.00 33.76 1.78
2967 3518 4.558226 TGCAGTGTACAATGATCTTCCT 57.442 40.909 26.35 0.00 0.00 3.36
2990 3541 6.435904 CCTTTGACTCCTTAGAAGAAGAGAGA 59.564 42.308 8.74 0.00 0.00 3.10
2993 3544 4.266714 ACTCCTTAGAAGAAGAGAGACGG 58.733 47.826 8.74 0.00 0.00 4.79
3024 3584 3.181484 CCATCATTGTTGTGCCCATGTAG 60.181 47.826 0.00 0.00 0.00 2.74
3032 3592 4.343526 TGTTGTGCCCATGTAGTTTTGAAT 59.656 37.500 0.00 0.00 0.00 2.57
3037 3597 4.083003 TGCCCATGTAGTTTTGAATTCGAC 60.083 41.667 0.04 0.00 0.00 4.20
3043 3603 8.070171 CCATGTAGTTTTGAATTCGACATATCC 58.930 37.037 0.04 0.00 0.00 2.59
3088 3651 4.944619 TCAGATGTAGGCTATGGAGTTG 57.055 45.455 0.00 0.00 0.00 3.16
3142 3731 5.353123 TCCCATTTGTGAACTACTATTTCGC 59.647 40.000 0.00 0.00 34.63 4.70
3166 3764 6.183360 GCTATACCATACTGGCATTGGTTTTT 60.183 38.462 18.33 9.42 42.67 1.94
3337 4060 5.310594 TGATAATAATTGGTAGGCAGCCTCT 59.689 40.000 20.38 0.00 34.61 3.69
3363 4086 4.396854 GATGCCGTACGTCCAGAC 57.603 61.111 15.21 6.07 0.00 3.51
3507 5700 7.222417 TGTCACATTTTTGCACTATTTGTTCAG 59.778 33.333 0.00 0.00 0.00 3.02
3640 5833 3.100817 CGACATTCGAATTTGGTCATGC 58.899 45.455 20.59 2.29 43.74 4.06
3743 5937 2.537633 TAACCGAGGACTACCATGGT 57.462 50.000 23.55 23.55 44.15 3.55
3777 5971 8.044309 TCCTTCATAATATCTTTGTCGGTGAAA 58.956 33.333 0.00 0.00 0.00 2.69
3783 5977 7.921786 AATATCTTTGTCGGTGAAAATCTGA 57.078 32.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 159 5.554034 AGCCCACACTATATATACCCTCT 57.446 43.478 0.00 0.00 0.00 3.69
254 260 3.366273 CGAAGAGAGCTGATCTGATAGCC 60.366 52.174 0.00 7.15 38.84 3.93
299 305 1.363807 GGCTGTTGCAGTTGGTTCC 59.636 57.895 0.00 0.00 41.91 3.62
377 383 7.501225 ACTGTAGAGTTCTTATCCTAAGAGAGC 59.499 40.741 0.00 0.00 0.00 4.09
379 385 8.774183 AGACTGTAGAGTTCTTATCCTAAGAGA 58.226 37.037 0.00 0.00 30.16 3.10
381 387 8.549731 TCAGACTGTAGAGTTCTTATCCTAAGA 58.450 37.037 1.59 0.00 30.16 2.10
382 388 8.740123 TCAGACTGTAGAGTTCTTATCCTAAG 57.260 38.462 1.59 0.00 30.16 2.18
383 389 9.126151 CATCAGACTGTAGAGTTCTTATCCTAA 57.874 37.037 1.59 0.00 30.16 2.69
384 390 8.495260 TCATCAGACTGTAGAGTTCTTATCCTA 58.505 37.037 1.59 0.00 30.16 2.94
385 391 7.284489 GTCATCAGACTGTAGAGTTCTTATCCT 59.716 40.741 1.59 0.00 41.64 3.24
386 392 7.422399 GTCATCAGACTGTAGAGTTCTTATCC 58.578 42.308 1.59 0.00 41.64 2.59
402 408 6.060028 TGCTGTTGTAAAAAGTCATCAGAC 57.940 37.500 0.00 0.00 45.31 3.51
403 409 6.486320 TGATGCTGTTGTAAAAAGTCATCAGA 59.514 34.615 10.57 0.00 43.35 3.27
404 410 6.671190 TGATGCTGTTGTAAAAAGTCATCAG 58.329 36.000 10.57 0.00 43.35 2.90
405 411 6.631971 TGATGCTGTTGTAAAAAGTCATCA 57.368 33.333 10.57 10.57 44.62 3.07
406 412 7.426456 CGTATGATGCTGTTGTAAAAAGTCATC 59.574 37.037 0.00 0.00 41.22 2.92
407 413 7.119116 TCGTATGATGCTGTTGTAAAAAGTCAT 59.881 33.333 0.00 0.00 33.16 3.06
408 414 6.425417 TCGTATGATGCTGTTGTAAAAAGTCA 59.575 34.615 0.00 0.00 32.25 3.41
409 415 6.827641 TCGTATGATGCTGTTGTAAAAAGTC 58.172 36.000 0.00 0.00 32.25 3.01
410 416 6.620733 GCTCGTATGATGCTGTTGTAAAAAGT 60.621 38.462 0.00 0.00 32.25 2.66
411 417 5.734498 GCTCGTATGATGCTGTTGTAAAAAG 59.266 40.000 0.00 0.00 33.02 2.27
412 418 5.180304 TGCTCGTATGATGCTGTTGTAAAAA 59.820 36.000 7.57 0.00 0.00 1.94
413 419 4.693095 TGCTCGTATGATGCTGTTGTAAAA 59.307 37.500 7.57 0.00 0.00 1.52
414 420 4.092821 GTGCTCGTATGATGCTGTTGTAAA 59.907 41.667 7.57 0.00 0.00 2.01
415 421 3.616821 GTGCTCGTATGATGCTGTTGTAA 59.383 43.478 7.57 0.00 0.00 2.41
435 441 1.665679 CTTAACTATGTGGCTGCCGTG 59.334 52.381 14.98 4.55 0.00 4.94
463 469 1.128692 GTTTGATGAAACGCCTCTCCG 59.871 52.381 0.00 0.00 32.49 4.63
553 582 2.034221 GGCCTCTTCTTTGCCCGT 59.966 61.111 0.00 0.00 39.30 5.28
556 585 2.335712 CGGTGGCCTCTTCTTTGCC 61.336 63.158 3.32 0.00 45.56 4.52
559 588 1.676014 CGATTCGGTGGCCTCTTCTTT 60.676 52.381 3.32 0.00 0.00 2.52
571 600 0.464036 TAATCTGCCAGCGATTCGGT 59.536 50.000 4.68 4.68 38.40 4.69
572 601 1.462283 CATAATCTGCCAGCGATTCGG 59.538 52.381 8.34 0.00 33.47 4.30
573 602 2.407090 TCATAATCTGCCAGCGATTCG 58.593 47.619 0.62 0.62 33.47 3.34
576 605 1.071228 TGCTCATAATCTGCCAGCGAT 59.929 47.619 0.00 0.00 32.43 4.58
577 606 0.465287 TGCTCATAATCTGCCAGCGA 59.535 50.000 0.00 0.00 32.43 4.93
579 608 0.950116 GGTGCTCATAATCTGCCAGC 59.050 55.000 0.00 0.00 0.00 4.85
580 609 1.602311 GGGTGCTCATAATCTGCCAG 58.398 55.000 0.00 0.00 0.00 4.85
581 610 0.179048 CGGGTGCTCATAATCTGCCA 60.179 55.000 0.00 0.00 0.00 4.92
582 611 0.886490 CCGGGTGCTCATAATCTGCC 60.886 60.000 0.00 0.00 0.00 4.85
583 612 0.886490 CCCGGGTGCTCATAATCTGC 60.886 60.000 14.18 0.00 0.00 4.26
585 614 1.418908 CCCCCGGGTGCTCATAATCT 61.419 60.000 21.85 0.00 0.00 2.40
586 615 1.073199 CCCCCGGGTGCTCATAATC 59.927 63.158 21.85 0.00 0.00 1.75
587 616 0.991355 TTCCCCCGGGTGCTCATAAT 60.991 55.000 21.85 0.00 36.47 1.28
588 617 0.991355 ATTCCCCCGGGTGCTCATAA 60.991 55.000 21.85 0.00 36.47 1.90
589 618 1.385347 ATTCCCCCGGGTGCTCATA 60.385 57.895 21.85 0.00 36.47 2.15
590 619 2.696125 ATTCCCCCGGGTGCTCAT 60.696 61.111 21.85 0.46 36.47 2.90
591 620 3.407967 GATTCCCCCGGGTGCTCA 61.408 66.667 21.85 0.00 36.47 4.26
592 621 4.547367 CGATTCCCCCGGGTGCTC 62.547 72.222 21.85 9.54 36.47 4.26
623 652 2.657237 GGAGTGTGGTGACCGGAG 59.343 66.667 9.46 0.00 0.00 4.63
641 671 1.134907 TCTATTTCACTTCCGCGGGAC 60.135 52.381 27.83 0.00 0.00 4.46
642 672 1.136305 CTCTATTTCACTTCCGCGGGA 59.864 52.381 27.83 17.96 0.00 5.14
643 673 1.136305 TCTCTATTTCACTTCCGCGGG 59.864 52.381 27.83 13.23 0.00 6.13
644 674 2.464865 CTCTCTATTTCACTTCCGCGG 58.535 52.381 22.12 22.12 0.00 6.46
646 676 2.863137 CTGCTCTCTATTTCACTTCCGC 59.137 50.000 0.00 0.00 0.00 5.54
649 679 6.034470 CGAGTTTCTGCTCTCTATTTCACTTC 59.966 42.308 0.00 0.00 33.55 3.01
650 680 5.866633 CGAGTTTCTGCTCTCTATTTCACTT 59.133 40.000 0.00 0.00 33.55 3.16
652 682 4.564769 CCGAGTTTCTGCTCTCTATTTCAC 59.435 45.833 0.00 0.00 33.55 3.18
653 683 4.462834 TCCGAGTTTCTGCTCTCTATTTCA 59.537 41.667 0.00 0.00 33.55 2.69
654 684 4.801516 GTCCGAGTTTCTGCTCTCTATTTC 59.198 45.833 0.00 0.00 33.55 2.17
655 685 4.675671 CGTCCGAGTTTCTGCTCTCTATTT 60.676 45.833 0.00 0.00 33.55 1.40
656 686 3.181495 CGTCCGAGTTTCTGCTCTCTATT 60.181 47.826 0.00 0.00 33.55 1.73
657 687 2.356382 CGTCCGAGTTTCTGCTCTCTAT 59.644 50.000 0.00 0.00 33.55 1.98
658 688 1.738350 CGTCCGAGTTTCTGCTCTCTA 59.262 52.381 0.00 0.00 33.55 2.43
659 689 0.523966 CGTCCGAGTTTCTGCTCTCT 59.476 55.000 0.00 0.00 33.55 3.10
660 690 0.522180 TCGTCCGAGTTTCTGCTCTC 59.478 55.000 0.00 0.00 33.55 3.20
661 691 0.523966 CTCGTCCGAGTTTCTGCTCT 59.476 55.000 8.50 0.00 37.47 4.09
662 692 0.522180 TCTCGTCCGAGTTTCTGCTC 59.478 55.000 15.59 0.00 42.49 4.26
663 693 0.523966 CTCTCGTCCGAGTTTCTGCT 59.476 55.000 15.59 0.00 42.49 4.24
664 694 1.073768 GCTCTCGTCCGAGTTTCTGC 61.074 60.000 15.59 9.93 42.49 4.26
665 695 0.456995 GGCTCTCGTCCGAGTTTCTG 60.457 60.000 15.59 4.86 42.49 3.02
667 697 4.480031 GGCTCTCGTCCGAGTTTC 57.520 61.111 15.59 6.78 42.49 2.78
674 704 1.716826 ATTCGTCTCGGCTCTCGTCC 61.717 60.000 0.00 0.00 40.32 4.79
679 709 2.103143 CGCATTCGTCTCGGCTCT 59.897 61.111 0.00 0.00 0.00 4.09
689 719 1.075542 TGCACCTTTACTCGCATTCG 58.924 50.000 0.00 0.00 0.00 3.34
703 733 1.675641 ATTCCTCGCAAGGTGCACC 60.676 57.895 29.22 29.22 45.36 5.01
704 734 1.237285 ACATTCCTCGCAAGGTGCAC 61.237 55.000 8.80 8.80 45.36 4.57
705 735 0.955428 GACATTCCTCGCAAGGTGCA 60.955 55.000 0.61 0.00 45.36 4.57
707 737 1.361668 CCGACATTCCTCGCAAGGTG 61.362 60.000 0.00 0.00 43.82 4.00
768 805 3.519930 GTCTCCTCCTCCGGCGAC 61.520 72.222 9.30 0.00 32.30 5.19
824 870 4.873129 CTCCCGTCCACGCCATCG 62.873 72.222 0.00 0.00 42.43 3.84
940 996 6.854496 ACGAGGCTCGCAAATAAATAAATA 57.146 33.333 34.76 0.00 45.12 1.40
941 997 5.751243 ACGAGGCTCGCAAATAAATAAAT 57.249 34.783 34.76 9.39 45.12 1.40
942 998 5.122554 TGAACGAGGCTCGCAAATAAATAAA 59.877 36.000 34.76 6.39 45.12 1.40
943 999 4.632251 TGAACGAGGCTCGCAAATAAATAA 59.368 37.500 34.76 7.68 45.12 1.40
955 1011 0.033504 TTGGACAGTGAACGAGGCTC 59.966 55.000 3.87 3.87 0.00 4.70
964 1020 1.070786 GGAACGGCTTGGACAGTGA 59.929 57.895 0.00 0.00 0.00 3.41
988 1044 1.669265 CGTCGCCATGTGAGTAGTAGA 59.331 52.381 0.00 0.00 0.00 2.59
989 1045 1.268589 CCGTCGCCATGTGAGTAGTAG 60.269 57.143 0.00 0.00 0.00 2.57
997 1057 3.928769 CATCGCCGTCGCCATGTG 61.929 66.667 0.00 0.00 35.26 3.21
1599 1717 0.605860 CTCCATAGGCCAGATGCAGC 60.606 60.000 5.01 0.00 43.89 5.25
1630 1748 2.544685 CAACCAAATTCGGCACAACAA 58.455 42.857 0.00 0.00 0.00 2.83
1633 1751 1.339610 CTCCAACCAAATTCGGCACAA 59.660 47.619 0.00 0.00 0.00 3.33
1635 1753 1.243902 TCTCCAACCAAATTCGGCAC 58.756 50.000 0.00 0.00 0.00 5.01
1639 1757 4.003648 AGCTAGTTCTCCAACCAAATTCG 58.996 43.478 0.00 0.00 32.22 3.34
1657 1780 1.822506 ACACTGTCAGACGCTAGCTA 58.177 50.000 13.93 0.00 0.00 3.32
1658 1781 1.822506 TACACTGTCAGACGCTAGCT 58.177 50.000 13.93 0.00 0.00 3.32
1659 1782 2.631418 TTACACTGTCAGACGCTAGC 57.369 50.000 6.91 4.06 0.00 3.42
1660 1783 4.324669 CACATTTACACTGTCAGACGCTAG 59.675 45.833 6.91 0.00 0.00 3.42
1702 1830 1.395045 TTGCGGCCAAACCATCACAA 61.395 50.000 2.24 0.00 39.03 3.33
1724 1852 0.037326 TTCTCGCCTTACACCTGCAG 60.037 55.000 6.78 6.78 0.00 4.41
1850 1978 7.862274 AAGGATGTAGTATCATGATTCCTGA 57.138 36.000 20.19 7.66 0.00 3.86
1851 1979 8.811017 ACTAAGGATGTAGTATCATGATTCCTG 58.189 37.037 20.19 13.34 32.42 3.86
1852 1980 8.964533 ACTAAGGATGTAGTATCATGATTCCT 57.035 34.615 14.65 15.28 32.42 3.36
1856 1984 9.540538 AGCTAACTAAGGATGTAGTATCATGAT 57.459 33.333 13.81 13.81 33.05 2.45
1884 2012 6.453943 CCATCCAATTCATAAACAACACACA 58.546 36.000 0.00 0.00 0.00 3.72
1889 2022 5.964758 TGAGCCATCCAATTCATAAACAAC 58.035 37.500 0.00 0.00 0.00 3.32
1937 2071 2.612567 CGCAAAGCTACCGGCACAA 61.613 57.895 0.00 0.00 44.79 3.33
1945 2082 4.151867 ACTTGCTAGTTAACGCAAAGCTAC 59.848 41.667 17.79 0.00 44.54 3.58
1990 2288 4.225042 TCACTTTACTGTCATATGCACCCT 59.775 41.667 0.00 0.00 0.00 4.34
1995 2293 6.968131 TCAGTTCACTTTACTGTCATATGC 57.032 37.500 0.00 0.00 42.77 3.14
2043 2341 5.036737 CGATTTTGTAATTCATGGGCTCAC 58.963 41.667 0.00 0.00 0.00 3.51
2114 2553 5.344396 CCTTTGATATCGACATGATCTCACG 59.656 44.000 0.00 0.00 39.21 4.35
2152 2604 1.532505 GCAGCCTCGCAAATGTATGTG 60.533 52.381 0.00 0.00 0.00 3.21
2161 2613 0.534873 TACATAGTGCAGCCTCGCAA 59.465 50.000 0.00 0.00 45.14 4.85
2227 2679 3.350833 AGCTTCAAATGGAGCTTACTGG 58.649 45.455 10.48 0.00 33.34 4.00
2228 2680 5.048504 TCAAAGCTTCAAATGGAGCTTACTG 60.049 40.000 25.21 20.60 45.49 2.74
2376 2873 3.751518 ACGGCCATAAAAGAGAACAACT 58.248 40.909 2.24 0.00 0.00 3.16
2426 2923 1.321474 TCAAGAAAGGCAAGCACCAG 58.679 50.000 0.00 0.00 0.00 4.00
2571 3095 1.227943 ATCCAAGGCGCGTGCATAT 60.228 52.632 24.18 3.07 45.35 1.78
2644 3192 3.928375 CCATGAAATGCCAAAACTACAGC 59.072 43.478 0.00 0.00 44.97 4.40
2647 3195 4.929211 GGAACCATGAAATGCCAAAACTAC 59.071 41.667 0.00 0.00 44.97 2.73
2720 3268 0.606673 GGCCTGGACAAAGGAGTGTC 60.607 60.000 0.00 0.00 45.99 3.67
2721 3269 1.456287 GGCCTGGACAAAGGAGTGT 59.544 57.895 0.00 0.00 40.02 3.55
2728 3276 2.597217 CAAGCGGGCCTGGACAAA 60.597 61.111 15.02 0.00 0.00 2.83
2751 3299 1.546476 CTGACAAGCTTCTCCCGTAGT 59.454 52.381 0.00 0.00 0.00 2.73
2780 3328 5.885230 TTTCAGTGCCAACTATGATGAAG 57.115 39.130 0.00 0.00 33.79 3.02
2914 3465 2.607187 TGAACGAGCAAAGCTAGCTAC 58.393 47.619 19.70 10.91 43.58 3.58
2957 3508 7.401493 TCTTCTAAGGAGTCAAAGGAAGATCAT 59.599 37.037 11.26 0.00 34.70 2.45
2967 3518 6.072397 CGTCTCTCTTCTTCTAAGGAGTCAAA 60.072 42.308 0.00 0.00 33.18 2.69
2990 3541 1.879380 CAATGATGGTCAACACACCGT 59.121 47.619 0.00 0.00 39.62 4.83
2993 3544 4.043750 CACAACAATGATGGTCAACACAC 58.956 43.478 0.00 0.00 0.00 3.82
3115 3692 7.119262 CGAAATAGTAGTTCACAAATGGGAAGT 59.881 37.037 10.38 10.38 43.11 3.01
3166 3764 8.424918 TGGCACAAAATTAATCTTAACCTGAAA 58.575 29.630 0.00 0.00 31.92 2.69
3323 4046 1.229177 TCACAGAGGCTGCCTACCA 60.229 57.895 23.44 0.89 34.37 3.25
3337 4060 1.594833 GTACGGCATCCACCTCACA 59.405 57.895 0.00 0.00 0.00 3.58
3363 4086 1.517832 CCGGAGAAGTACCAGCTGG 59.482 63.158 31.60 31.60 42.17 4.85
3403 4129 3.984193 GAAGAGGTGCGGCATGGCT 62.984 63.158 18.09 0.43 0.00 4.75
3507 5700 4.505324 AACAGTTATCTTAAGGCCCCTC 57.495 45.455 0.00 0.00 0.00 4.30
3640 5833 8.932945 ACACAATTCATACTACACATGAGTAG 57.067 34.615 23.67 23.67 45.44 2.57
3727 5921 1.144057 GCACCATGGTAGTCCTCGG 59.856 63.158 19.28 3.37 34.23 4.63
3743 5937 9.797642 ACAAAGATATTATGAAGGATATGTGCA 57.202 29.630 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.