Multiple sequence alignment - TraesCS3B01G131300

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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 TraesCS3B01G131300 chr3B 100.000 2489 0 0 1 2489 113513557 113511069 0.000000e+00 4597.0
1 TraesCS3B01G131300 chr3B 89.474 684 54 7 810 1491 112465805 112465138 0.000000e+00 848.0
2 TraesCS3B01G131300 chr3B 95.914 514 19 2 980 1491 113503706 113504219 0.000000e+00 832.0
3 TraesCS3B01G131300 chr3B 88.712 691 52 12 803 1491 112948555 112947889 0.000000e+00 821.0
4 TraesCS3B01G131300 chr3B 87.959 681 54 11 803 1480 113483336 113483991 0.000000e+00 778.0
5 TraesCS3B01G131300 chr3B 98.000 50 1 0 1895 1944 61984849 61984800 1.230000e-13 87.9
6 TraesCS3B01G131300 chr3D 92.261 1473 84 15 774 2230 68170048 68171506 0.000000e+00 2061.0
7 TraesCS3B01G131300 chr3D 89.007 1219 70 16 713 1896 68273536 68274725 0.000000e+00 1450.0
8 TraesCS3B01G131300 chr3D 89.003 682 49 9 810 1490 68335962 68335306 0.000000e+00 821.0
9 TraesCS3B01G131300 chr3D 88.252 698 49 15 796 1491 68325755 68325089 0.000000e+00 804.0
10 TraesCS3B01G131300 chr3D 88.647 643 51 14 850 1490 68833132 68833754 0.000000e+00 763.0
11 TraesCS3B01G131300 chr3D 92.383 512 31 5 980 1491 68842912 68843415 0.000000e+00 723.0
12 TraesCS3B01G131300 chr3D 80.114 704 120 16 1 694 610476229 610476922 7.940000e-140 507.0
13 TraesCS3B01G131300 chr3D 89.062 320 27 6 2169 2485 68171506 68171820 8.350000e-105 390.0
14 TraesCS3B01G131300 chr3D 86.463 229 18 8 2258 2485 68274801 68275017 3.200000e-59 239.0
15 TraesCS3B01G131300 chr3D 87.805 82 6 3 1945 2026 68274727 68274804 2.640000e-15 93.5
16 TraesCS3B01G131300 chr3D 97.917 48 0 1 1898 1944 421143403 421143450 5.710000e-12 82.4
17 TraesCS3B01G131300 chr3D 100.000 28 0 0 738 765 68170024 68170051 4.000000e-03 52.8
18 TraesCS3B01G131300 chr3A 90.501 979 53 19 774 1713 80225581 80226558 0.000000e+00 1256.0
19 TraesCS3B01G131300 chr3A 89.451 692 46 10 803 1491 80412937 80413604 0.000000e+00 848.0
20 TraesCS3B01G131300 chr3A 89.067 686 47 13 806 1491 80289624 80288967 0.000000e+00 826.0
21 TraesCS3B01G131300 chr3A 92.166 217 15 2 2269 2485 80279533 80279747 3.110000e-79 305.0
22 TraesCS3B01G131300 chr3A 87.619 210 18 7 2063 2267 80279114 80279320 1.150000e-58 237.0
23 TraesCS3B01G131300 chr3A 91.018 167 13 1 1730 1896 80226615 80226779 8.960000e-55 224.0
24 TraesCS3B01G131300 chr2B 95.063 709 26 4 1 701 72752933 72752226 0.000000e+00 1107.0
25 TraesCS3B01G131300 chr2B 100.000 47 0 0 1898 1944 610937903 610937949 1.230000e-13 87.9
26 TraesCS3B01G131300 chr2B 100.000 46 0 0 1899 1944 586683526 586683481 4.410000e-13 86.1
27 TraesCS3B01G131300 chr4B 91.907 729 27 10 1 697 65949357 65948629 0.000000e+00 990.0
28 TraesCS3B01G131300 chr4B 93.489 599 20 8 1 590 507981906 507982494 0.000000e+00 872.0
29 TraesCS3B01G131300 chr4B 94.393 321 14 4 381 699 55299664 55299982 8.000000e-135 490.0
30 TraesCS3B01G131300 chr6B 93.548 651 28 5 1 638 117762976 117762327 0.000000e+00 957.0
31 TraesCS3B01G131300 chr2A 90.833 720 43 9 1 697 10222036 10222755 0.000000e+00 942.0
32 TraesCS3B01G131300 chr5A 89.444 720 46 14 1 697 512765344 512764632 0.000000e+00 881.0
33 TraesCS3B01G131300 chr7B 89.943 696 48 11 796 1491 603657069 603657742 0.000000e+00 878.0
34 TraesCS3B01G131300 chr7B 84.562 719 83 16 1 700 591216462 591215753 0.000000e+00 688.0
35 TraesCS3B01G131300 chr4D 89.086 678 57 8 816 1491 134550540 134549878 0.000000e+00 826.0
36 TraesCS3B01G131300 chr4D 87.927 439 37 9 2049 2485 134626404 134625980 1.030000e-138 503.0
37 TraesCS3B01G131300 chr4D 94.643 112 5 1 1788 1899 134626582 134626472 3.290000e-39 172.0
38 TraesCS3B01G131300 chr4D 100.000 47 0 0 1898 1944 363960571 363960525 1.230000e-13 87.9
39 TraesCS3B01G131300 chr4D 97.959 49 0 1 1898 1945 220605112 220605160 1.590000e-12 84.2
40 TraesCS3B01G131300 chr4D 95.652 46 1 1 1899 1944 463541330 463541374 3.430000e-09 73.1
41 TraesCS3B01G131300 chr6A 86.584 723 63 19 1 697 21342920 21343634 0.000000e+00 767.0
42 TraesCS3B01G131300 chr6A 100.000 46 0 0 1899 1944 273874164 273874209 4.410000e-13 86.1
43 TraesCS3B01G131300 chr7D 85.167 627 68 18 1 613 156212411 156211796 9.780000e-174 619.0
44 TraesCS3B01G131300 chr7D 82.582 643 87 22 76 703 134832525 134833157 6.050000e-151 544.0
45 TraesCS3B01G131300 chr7D 100.000 46 0 0 1899 1944 325580935 325580890 4.410000e-13 86.1
46 TraesCS3B01G131300 chr5B 100.000 47 0 0 1898 1944 211004093 211004047 1.230000e-13 87.9
47 TraesCS3B01G131300 chr7A 96.154 52 2 0 1893 1944 547642650 547642599 4.410000e-13 86.1
48 TraesCS3B01G131300 chr2D 100.000 46 0 0 1899 1944 278714549 278714504 4.410000e-13 86.1
49 TraesCS3B01G131300 chr5D 97.872 47 1 0 1898 1944 22835690 22835644 5.710000e-12 82.4
50 TraesCS3B01G131300 chr5D 97.826 46 1 0 1899 1944 29506396 29506441 2.050000e-11 80.5
51 TraesCS3B01G131300 chr5D 95.833 48 2 0 1897 1944 22278786 22278739 7.380000e-11 78.7
52 TraesCS3B01G131300 chr1A 97.872 47 1 0 1898 1944 120017861 120017815 5.710000e-12 82.4
53 TraesCS3B01G131300 chr6D 97.872 47 0 1 1900 1945 135141360 135141406 2.050000e-11 80.5
54 TraesCS3B01G131300 chr6D 95.652 46 1 1 1899 1944 347890176 347890220 3.430000e-09 73.1
55 TraesCS3B01G131300 chr1D 97.872 47 0 1 1898 1944 356186836 356186791 2.050000e-11 80.5
56 TraesCS3B01G131300 chr1D 95.652 46 2 0 1899 1944 491604738 491604783 9.550000e-10 75.0
57 TraesCS3B01G131300 chrUn 94.118 51 2 1 1894 1943 321532975 321532925 2.650000e-10 76.8


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 TraesCS3B01G131300 chr3B 113511069 113513557 2488 True 4597.000000 4597 100.000000 1 2489 1 chr3B.!!$R4 2488
1 TraesCS3B01G131300 chr3B 112465138 112465805 667 True 848.000000 848 89.474000 810 1491 1 chr3B.!!$R2 681
2 TraesCS3B01G131300 chr3B 113503706 113504219 513 False 832.000000 832 95.914000 980 1491 1 chr3B.!!$F2 511
3 TraesCS3B01G131300 chr3B 112947889 112948555 666 True 821.000000 821 88.712000 803 1491 1 chr3B.!!$R3 688
4 TraesCS3B01G131300 chr3B 113483336 113483991 655 False 778.000000 778 87.959000 803 1480 1 chr3B.!!$F1 677
5 TraesCS3B01G131300 chr3D 68170024 68171820 1796 False 834.600000 2061 93.774333 738 2485 3 chr3D.!!$F5 1747
6 TraesCS3B01G131300 chr3D 68335306 68335962 656 True 821.000000 821 89.003000 810 1490 1 chr3D.!!$R2 680
7 TraesCS3B01G131300 chr3D 68325089 68325755 666 True 804.000000 804 88.252000 796 1491 1 chr3D.!!$R1 695
8 TraesCS3B01G131300 chr3D 68833132 68833754 622 False 763.000000 763 88.647000 850 1490 1 chr3D.!!$F1 640
9 TraesCS3B01G131300 chr3D 68842912 68843415 503 False 723.000000 723 92.383000 980 1491 1 chr3D.!!$F2 511
10 TraesCS3B01G131300 chr3D 68273536 68275017 1481 False 594.166667 1450 87.758333 713 2485 3 chr3D.!!$F6 1772
11 TraesCS3B01G131300 chr3D 610476229 610476922 693 False 507.000000 507 80.114000 1 694 1 chr3D.!!$F4 693
12 TraesCS3B01G131300 chr3A 80412937 80413604 667 False 848.000000 848 89.451000 803 1491 1 chr3A.!!$F1 688
13 TraesCS3B01G131300 chr3A 80288967 80289624 657 True 826.000000 826 89.067000 806 1491 1 chr3A.!!$R1 685
14 TraesCS3B01G131300 chr3A 80225581 80226779 1198 False 740.000000 1256 90.759500 774 1896 2 chr3A.!!$F2 1122
15 TraesCS3B01G131300 chr3A 80279114 80279747 633 False 271.000000 305 89.892500 2063 2485 2 chr3A.!!$F3 422
16 TraesCS3B01G131300 chr2B 72752226 72752933 707 True 1107.000000 1107 95.063000 1 701 1 chr2B.!!$R1 700
17 TraesCS3B01G131300 chr4B 65948629 65949357 728 True 990.000000 990 91.907000 1 697 1 chr4B.!!$R1 696
18 TraesCS3B01G131300 chr4B 507981906 507982494 588 False 872.000000 872 93.489000 1 590 1 chr4B.!!$F2 589
19 TraesCS3B01G131300 chr6B 117762327 117762976 649 True 957.000000 957 93.548000 1 638 1 chr6B.!!$R1 637
20 TraesCS3B01G131300 chr2A 10222036 10222755 719 False 942.000000 942 90.833000 1 697 1 chr2A.!!$F1 696
21 TraesCS3B01G131300 chr5A 512764632 512765344 712 True 881.000000 881 89.444000 1 697 1 chr5A.!!$R1 696
22 TraesCS3B01G131300 chr7B 603657069 603657742 673 False 878.000000 878 89.943000 796 1491 1 chr7B.!!$F1 695
23 TraesCS3B01G131300 chr7B 591215753 591216462 709 True 688.000000 688 84.562000 1 700 1 chr7B.!!$R1 699
24 TraesCS3B01G131300 chr4D 134549878 134550540 662 True 826.000000 826 89.086000 816 1491 1 chr4D.!!$R1 675
25 TraesCS3B01G131300 chr4D 134625980 134626582 602 True 337.500000 503 91.285000 1788 2485 2 chr4D.!!$R3 697
26 TraesCS3B01G131300 chr6A 21342920 21343634 714 False 767.000000 767 86.584000 1 697 1 chr6A.!!$F1 696
27 TraesCS3B01G131300 chr7D 156211796 156212411 615 True 619.000000 619 85.167000 1 613 1 chr7D.!!$R1 612
28 TraesCS3B01G131300 chr7D 134832525 134833157 632 False 544.000000 544 82.582000 76 703 1 chr7D.!!$F1 627

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
441 460 0.105039 CCTCCTCGGCATGTAGAACC 59.895 60.0 0.0 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1627 2086 0.104304 ACAACACTCTCGGACACCAC 59.896 55.0 0.0 0.0 0.0 4.16 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
229 242 4.147449 CGAGATGGTCCGGCAGCA 62.147 66.667 0.00 1.90 36.77 4.41
365 381 3.411517 CCGGGGGAGGAATGCAGT 61.412 66.667 0.00 0.00 0.00 4.40
378 394 4.208686 GCAGTAGGGACGGCGGAG 62.209 72.222 13.24 0.00 37.03 4.63
379 395 3.528370 CAGTAGGGACGGCGGAGG 61.528 72.222 13.24 0.00 0.00 4.30
420 439 0.523072 TGACTACACGCGGTTCTACC 59.477 55.000 12.47 0.00 34.05 3.18
429 448 2.806237 GGTTCTACCGCCTCCTCG 59.194 66.667 0.00 0.00 0.00 4.63
441 460 0.105039 CCTCCTCGGCATGTAGAACC 59.895 60.000 0.00 0.00 0.00 3.62
444 463 2.202690 TCGGCATGTAGAACCGCG 60.203 61.111 0.00 0.00 46.49 6.46
445 464 2.508439 CGGCATGTAGAACCGCGT 60.508 61.111 4.92 0.00 40.55 6.01
449 471 2.125269 ATGTAGAACCGCGTGGGC 60.125 61.111 21.14 11.05 40.62 5.36
475 497 3.804638 GAGGGAGACGGCGGGGATA 62.805 68.421 13.24 0.00 0.00 2.59
476 498 3.303928 GGGAGACGGCGGGGATAG 61.304 72.222 13.24 0.00 0.00 2.08
477 499 3.992317 GGAGACGGCGGGGATAGC 61.992 72.222 13.24 0.00 0.00 2.97
487 509 3.135814 GGGATAGCCCGCGTAGTT 58.864 61.111 0.00 0.00 46.48 2.24
530 559 2.699954 AGTTTGAATGAACTCGCCGAT 58.300 42.857 0.00 0.00 34.94 4.18
536 565 0.447801 ATGAACTCGCCGATGTTTGC 59.552 50.000 0.00 0.00 0.00 3.68
547 576 3.670991 GCCGATGTTTGCGTTAAATTTGA 59.329 39.130 0.00 0.00 0.00 2.69
549 578 4.915085 CCGATGTTTGCGTTAAATTTGAGT 59.085 37.500 0.00 0.00 0.00 3.41
551 580 5.623264 CGATGTTTGCGTTAAATTTGAGTCA 59.377 36.000 0.00 0.00 0.00 3.41
553 582 7.148983 CGATGTTTGCGTTAAATTTGAGTCATT 60.149 33.333 0.00 0.00 0.00 2.57
561 590 7.062848 CGTTAAATTTGAGTCATTTTTGTGCC 58.937 34.615 0.00 0.00 0.00 5.01
563 592 3.791973 TTTGAGTCATTTTTGTGCCGT 57.208 38.095 0.00 0.00 0.00 5.68
564 593 2.772568 TGAGTCATTTTTGTGCCGTG 57.227 45.000 0.00 0.00 0.00 4.94
568 597 3.186119 AGTCATTTTTGTGCCGTGTTTG 58.814 40.909 0.00 0.00 0.00 2.93
569 598 3.119316 AGTCATTTTTGTGCCGTGTTTGA 60.119 39.130 0.00 0.00 0.00 2.69
574 603 5.613358 TTTTTGTGCCGTGTTTGATTTTT 57.387 30.435 0.00 0.00 0.00 1.94
593 622 3.887335 TTGACTAACCGTGGGCGCC 62.887 63.158 21.18 21.18 36.67 6.53
622 651 2.897350 GCATCACGCCCCTAGTGC 60.897 66.667 0.00 0.00 39.31 4.40
630 659 2.580276 CCCCTAGTGCGCGGTTTA 59.420 61.111 8.83 0.00 0.00 2.01
631 660 1.520787 CCCCTAGTGCGCGGTTTAG 60.521 63.158 8.83 1.59 0.00 1.85
632 661 2.171725 CCCTAGTGCGCGGTTTAGC 61.172 63.158 8.83 0.00 0.00 3.09
658 687 3.647771 GTCCTCAGGGGGCGGTTT 61.648 66.667 0.00 0.00 35.33 3.27
659 688 2.856988 TCCTCAGGGGGCGGTTTT 60.857 61.111 0.00 0.00 35.33 2.43
660 689 2.117423 CCTCAGGGGGCGGTTTTT 59.883 61.111 0.00 0.00 0.00 1.94
681 710 2.993853 CTCTCCTGGAGGGCCAAC 59.006 66.667 23.00 0.00 45.41 3.77
682 711 3.003173 TCTCCTGGAGGGCCAACG 61.003 66.667 23.00 0.00 45.41 4.10
683 712 4.101448 CTCCTGGAGGGCCAACGG 62.101 72.222 16.19 2.33 45.41 4.44
699 728 4.887615 GGCTGGAGATGCCCTTAC 57.112 61.111 0.00 0.00 44.32 2.34
700 729 1.915228 GGCTGGAGATGCCCTTACA 59.085 57.895 0.00 0.00 44.32 2.41
701 730 0.464554 GGCTGGAGATGCCCTTACAC 60.465 60.000 0.00 0.00 44.32 2.90
702 731 0.253044 GCTGGAGATGCCCTTACACA 59.747 55.000 0.00 0.00 34.97 3.72
703 732 2.014068 GCTGGAGATGCCCTTACACAC 61.014 57.143 0.00 0.00 34.97 3.82
704 733 0.618458 TGGAGATGCCCTTACACACC 59.382 55.000 0.00 0.00 34.97 4.16
705 734 0.912486 GGAGATGCCCTTACACACCT 59.088 55.000 0.00 0.00 0.00 4.00
706 735 1.407437 GGAGATGCCCTTACACACCTG 60.407 57.143 0.00 0.00 0.00 4.00
707 736 0.620556 AGATGCCCTTACACACCTGG 59.379 55.000 0.00 0.00 0.00 4.45
708 737 1.000896 ATGCCCTTACACACCTGGC 60.001 57.895 0.00 0.00 42.49 4.85
709 738 2.361230 GCCCTTACACACCTGGCC 60.361 66.667 0.00 0.00 36.07 5.36
710 739 2.355115 CCCTTACACACCTGGCCC 59.645 66.667 0.00 0.00 0.00 5.80
711 740 2.046314 CCTTACACACCTGGCCCG 60.046 66.667 0.00 0.00 0.00 6.13
732 761 2.932187 GCCAAACCAGCCATTCAACATC 60.932 50.000 0.00 0.00 0.00 3.06
765 796 3.771577 AAGAAAGACCGTTGATGGAGT 57.228 42.857 0.00 0.00 0.00 3.85
766 797 3.320673 AGAAAGACCGTTGATGGAGTC 57.679 47.619 0.00 0.00 0.00 3.36
767 798 2.028020 AGAAAGACCGTTGATGGAGTCC 60.028 50.000 0.73 0.73 0.00 3.85
768 799 0.613777 AAGACCGTTGATGGAGTCCC 59.386 55.000 6.74 0.00 0.00 4.46
769 800 1.221021 GACCGTTGATGGAGTCCCC 59.779 63.158 6.74 0.00 0.00 4.81
890 939 2.029290 CCACCGATATAAACTCCCTCCG 60.029 54.545 0.00 0.00 0.00 4.63
893 942 1.067071 CGATATAAACTCCCTCCGCCC 60.067 57.143 0.00 0.00 0.00 6.13
1007 1085 2.964389 GCGAGCGAGAATGGAGGC 60.964 66.667 0.00 0.00 0.00 4.70
1518 1962 0.959372 GGACGACCGAACCAGAGAGA 60.959 60.000 0.00 0.00 0.00 3.10
1548 1993 1.446792 CTGCACGCCTGATCGAAGT 60.447 57.895 0.00 0.00 0.00 3.01
1608 2067 2.168326 TGATGCGTGATGTGTCTGTT 57.832 45.000 0.00 0.00 0.00 3.16
1658 2117 3.467803 AGAGTGTTGTGTGGCTAGTTTC 58.532 45.455 0.00 0.00 0.00 2.78
1692 2151 4.884707 CGCAATTTCAATGAAATTTCGGG 58.115 39.130 30.94 23.35 46.07 5.14
1703 2162 8.570488 TCAATGAAATTTCGGGAATATCATCAG 58.430 33.333 13.34 0.00 31.22 2.90
1745 2265 1.065491 TCAGTAATCTTGGTGGCGCAT 60.065 47.619 10.83 0.00 0.00 4.73
1764 2284 6.414987 GGCGCATACAACTTCAAATAATTCTC 59.585 38.462 10.83 0.00 0.00 2.87
1765 2285 7.189512 GCGCATACAACTTCAAATAATTCTCT 58.810 34.615 0.30 0.00 0.00 3.10
1889 2412 8.522830 GGATTTCAATGGAAGTCAGTTAATTCA 58.477 33.333 7.57 0.00 40.45 2.57
1896 2419 5.222027 TGGAAGTCAGTTAATTCACCCATGA 60.222 40.000 0.00 0.00 0.00 3.07
1933 2458 7.816640 TGTTGATTGTTTTTGAGATAGCTACC 58.183 34.615 0.00 0.00 0.00 3.18
1934 2459 7.094377 TGTTGATTGTTTTTGAGATAGCTACCC 60.094 37.037 0.00 0.00 0.00 3.69
1949 2474 3.275999 GCTACCCGCTTATTCCTTGAAA 58.724 45.455 0.00 0.00 35.14 2.69
1954 2479 2.159379 CCGCTTATTCCTTGAAAGGTGC 60.159 50.000 8.91 6.41 46.54 5.01
1960 2485 1.981256 TCCTTGAAAGGTGCCTGTTC 58.019 50.000 8.91 0.00 46.54 3.18
1962 2487 0.593128 CTTGAAAGGTGCCTGTTCGG 59.407 55.000 0.00 0.00 0.00 4.30
1977 2502 3.475575 TGTTCGGGGTGGTTTTTACTAC 58.524 45.455 0.00 0.00 0.00 2.73
1980 2505 1.799994 CGGGGTGGTTTTTACTACGTG 59.200 52.381 0.00 0.00 0.00 4.49
2038 2574 9.716507 GATACAATTGAGCATTACGTTTATGTT 57.283 29.630 13.59 0.00 0.00 2.71
2039 2575 9.716507 ATACAATTGAGCATTACGTTTATGTTC 57.283 29.630 13.59 15.51 34.84 3.18
2040 2576 7.027161 ACAATTGAGCATTACGTTTATGTTCC 58.973 34.615 13.59 7.65 33.76 3.62
2041 2577 7.094377 ACAATTGAGCATTACGTTTATGTTCCT 60.094 33.333 13.59 6.67 33.76 3.36
2042 2578 6.417191 TTGAGCATTACGTTTATGTTCCTC 57.583 37.500 17.98 12.99 33.76 3.71
2267 2867 9.668497 ACATTGGAATAGAGGAAGTAACTTTAC 57.332 33.333 0.00 0.00 0.00 2.01
2425 3237 6.043411 AGCATCGTAGTTCAAGGTTAGATTC 58.957 40.000 0.00 0.00 0.00 2.52
2475 3288 2.223805 GGGTGCTTTCTTGGTCAAACAG 60.224 50.000 0.00 0.00 0.00 3.16
2485 3298 4.038642 TCTTGGTCAAACAGGTAAATTGCC 59.961 41.667 0.00 0.00 0.00 4.52
2486 3299 3.300388 TGGTCAAACAGGTAAATTGCCA 58.700 40.909 2.39 0.00 32.06 4.92
2487 3300 3.706594 TGGTCAAACAGGTAAATTGCCAA 59.293 39.130 2.39 0.00 31.79 4.52
2488 3301 4.346418 TGGTCAAACAGGTAAATTGCCAAT 59.654 37.500 2.39 0.00 31.79 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
358 374 2.186903 CGCCGTCCCTACTGCATT 59.813 61.111 0.00 0.00 35.74 3.56
401 417 0.523072 GGTAGAACCGCGTGTAGTCA 59.477 55.000 4.92 0.00 0.00 3.41
412 431 2.783288 CCGAGGAGGCGGTAGAACC 61.783 68.421 0.00 0.00 46.07 3.62
422 441 0.105039 GGTTCTACATGCCGAGGAGG 59.895 60.000 0.00 0.00 44.97 4.30
429 448 2.461110 CCACGCGGTTCTACATGCC 61.461 63.158 12.47 0.00 0.00 4.40
471 493 1.660167 AAAAACTACGCGGGCTATCC 58.340 50.000 12.47 0.00 0.00 2.59
505 534 4.611366 CGGCGAGTTCATTCAAACTTAAAC 59.389 41.667 0.00 0.00 39.55 2.01
510 539 2.163818 TCGGCGAGTTCATTCAAACT 57.836 45.000 4.99 0.00 42.10 2.66
511 540 2.159627 ACATCGGCGAGTTCATTCAAAC 59.840 45.455 17.22 0.00 0.00 2.93
513 542 2.093306 ACATCGGCGAGTTCATTCAA 57.907 45.000 17.22 0.00 0.00 2.69
516 545 1.135689 GCAAACATCGGCGAGTTCATT 60.136 47.619 17.22 3.07 0.00 2.57
530 559 7.763172 AAATGACTCAAATTTAACGCAAACA 57.237 28.000 0.00 0.00 0.00 2.83
536 565 7.062848 GGCACAAAAATGACTCAAATTTAACG 58.937 34.615 0.00 0.00 0.00 3.18
537 566 7.062848 CGGCACAAAAATGACTCAAATTTAAC 58.937 34.615 0.00 0.00 0.00 2.01
538 567 6.758886 ACGGCACAAAAATGACTCAAATTTAA 59.241 30.769 0.00 0.00 0.00 1.52
539 568 6.199908 CACGGCACAAAAATGACTCAAATTTA 59.800 34.615 0.00 0.00 0.00 1.40
540 569 5.006552 CACGGCACAAAAATGACTCAAATTT 59.993 36.000 0.00 0.00 0.00 1.82
547 576 3.119316 TCAAACACGGCACAAAAATGACT 60.119 39.130 0.00 0.00 0.00 3.41
549 578 3.510388 TCAAACACGGCACAAAAATGA 57.490 38.095 0.00 0.00 0.00 2.57
551 580 5.809719 AAAATCAAACACGGCACAAAAAT 57.190 30.435 0.00 0.00 0.00 1.82
574 603 1.962306 GCGCCCACGGTTAGTCAAA 60.962 57.895 0.00 0.00 40.57 2.69
575 604 2.357760 GCGCCCACGGTTAGTCAA 60.358 61.111 0.00 0.00 40.57 3.18
576 605 4.382320 GGCGCCCACGGTTAGTCA 62.382 66.667 18.11 0.00 40.57 3.41
641 670 2.708593 AAAAACCGCCCCCTGAGGAC 62.709 60.000 0.00 0.00 38.24 3.85
642 671 2.466186 AAAAACCGCCCCCTGAGGA 61.466 57.895 0.00 0.00 38.24 3.71
643 672 2.117423 AAAAACCGCCCCCTGAGG 59.883 61.111 0.00 0.00 40.30 3.86
664 693 2.993853 GTTGGCCCTCCAGGAGAG 59.006 66.667 19.21 5.68 44.53 3.20
665 694 3.003173 CGTTGGCCCTCCAGGAGA 61.003 66.667 19.21 0.00 44.53 3.71
666 695 4.101448 CCGTTGGCCCTCCAGGAG 62.101 72.222 9.90 9.90 44.53 3.69
683 712 0.253044 TGTGTAAGGGCATCTCCAGC 59.747 55.000 0.00 0.00 36.21 4.85
684 713 1.407437 GGTGTGTAAGGGCATCTCCAG 60.407 57.143 0.00 0.00 36.21 3.86
685 714 0.618458 GGTGTGTAAGGGCATCTCCA 59.382 55.000 0.00 0.00 36.21 3.86
686 715 0.912486 AGGTGTGTAAGGGCATCTCC 59.088 55.000 0.00 0.00 0.00 3.71
687 716 1.407437 CCAGGTGTGTAAGGGCATCTC 60.407 57.143 0.00 0.00 0.00 2.75
688 717 0.620556 CCAGGTGTGTAAGGGCATCT 59.379 55.000 0.00 0.00 0.00 2.90
689 718 1.032114 GCCAGGTGTGTAAGGGCATC 61.032 60.000 0.00 0.00 44.01 3.91
690 719 1.000896 GCCAGGTGTGTAAGGGCAT 60.001 57.895 0.00 0.00 44.01 4.40
691 720 2.434331 GCCAGGTGTGTAAGGGCA 59.566 61.111 0.00 0.00 44.01 5.36
692 721 2.361230 GGCCAGGTGTGTAAGGGC 60.361 66.667 0.00 0.00 43.86 5.19
693 722 2.355115 GGGCCAGGTGTGTAAGGG 59.645 66.667 4.39 0.00 0.00 3.95
694 723 2.046314 CGGGCCAGGTGTGTAAGG 60.046 66.667 4.39 0.00 0.00 2.69
695 724 2.746277 GCGGGCCAGGTGTGTAAG 60.746 66.667 4.39 0.00 0.00 2.34
696 725 4.338710 GGCGGGCCAGGTGTGTAA 62.339 66.667 4.39 0.00 35.81 2.41
708 737 2.996734 AATGGCTGGTTTGGCGGG 60.997 61.111 0.00 0.00 35.06 6.13
709 738 1.814772 TTGAATGGCTGGTTTGGCGG 61.815 55.000 0.00 0.00 35.06 6.13
710 739 0.667184 GTTGAATGGCTGGTTTGGCG 60.667 55.000 0.00 0.00 35.06 5.69
711 740 0.392336 TGTTGAATGGCTGGTTTGGC 59.608 50.000 0.00 0.00 0.00 4.52
766 797 1.381327 TTCTAGAGCTCCCGTGGGG 60.381 63.158 10.93 0.00 46.11 4.96
767 798 0.684805 AGTTCTAGAGCTCCCGTGGG 60.685 60.000 10.93 0.00 0.00 4.61
768 799 1.187087 AAGTTCTAGAGCTCCCGTGG 58.813 55.000 10.93 0.00 0.00 4.94
769 800 2.417515 GGAAAGTTCTAGAGCTCCCGTG 60.418 54.545 10.93 0.00 0.00 4.94
770 801 1.826096 GGAAAGTTCTAGAGCTCCCGT 59.174 52.381 10.93 0.00 0.00 5.28
771 802 1.202313 CGGAAAGTTCTAGAGCTCCCG 60.202 57.143 24.73 24.73 0.00 5.14
772 803 1.471851 GCGGAAAGTTCTAGAGCTCCC 60.472 57.143 10.93 12.50 0.00 4.30
812 843 2.413310 AACTTCTGAAACGTGGTGGT 57.587 45.000 0.00 0.00 0.00 4.16
893 942 2.588877 GGTGATGATGCGACGGGG 60.589 66.667 0.00 0.00 0.00 5.73
1007 1085 2.124570 CCAGCCCGAACATCCTGG 60.125 66.667 0.00 0.00 38.93 4.45
1223 1322 2.885644 CCTTGATGTCGCCGGACG 60.886 66.667 5.05 9.12 46.49 4.79
1518 1962 1.898574 CGTGCAGGCAAAGGACCTT 60.899 57.895 0.00 0.00 34.42 3.50
1548 1993 3.361786 TCATCGATCACTACCCACTCAA 58.638 45.455 0.00 0.00 0.00 3.02
1587 2043 2.004733 ACAGACACATCACGCATCATG 58.995 47.619 0.00 0.00 0.00 3.07
1588 2044 2.391616 ACAGACACATCACGCATCAT 57.608 45.000 0.00 0.00 0.00 2.45
1589 2045 2.168326 AACAGACACATCACGCATCA 57.832 45.000 0.00 0.00 0.00 3.07
1608 2067 4.245660 CCACACGAGCAGAGATAGAAAAA 58.754 43.478 0.00 0.00 0.00 1.94
1627 2086 0.104304 ACAACACTCTCGGACACCAC 59.896 55.000 0.00 0.00 0.00 4.16
1692 2151 8.055279 TGGAAGAACCAAAACTGATGATATTC 57.945 34.615 0.00 0.00 46.75 1.75
1723 2243 1.398390 GCGCCACCAAGATTACTGAAG 59.602 52.381 0.00 0.00 0.00 3.02
1773 2293 9.715123 CCAAACCAATATTTTGAAGAAACAAAC 57.285 29.630 0.00 0.00 39.08 2.93
1781 2301 6.945218 TGGGATCCAAACCAATATTTTGAAG 58.055 36.000 15.23 0.00 36.24 3.02
1949 2474 3.953775 CACCCCGAACAGGCACCT 61.954 66.667 0.00 0.00 39.21 4.00
1954 2479 1.610038 GTAAAAACCACCCCGAACAGG 59.390 52.381 0.00 0.00 40.63 4.00
1960 2485 1.799994 CACGTAGTAAAAACCACCCCG 59.200 52.381 0.00 0.00 41.61 5.73
1962 2487 4.881920 TCTACACGTAGTAAAAACCACCC 58.118 43.478 4.22 0.00 41.61 4.61
1977 2502 7.076842 ACATCCAAAATTCTGATTCTACACG 57.923 36.000 0.00 0.00 0.00 4.49
2038 2574 0.984230 ACGCTGAAATTGAGGGAGGA 59.016 50.000 3.30 0.00 0.00 3.71
2039 2575 2.691409 TACGCTGAAATTGAGGGAGG 57.309 50.000 3.30 0.00 0.00 4.30
2040 2576 3.134458 GGATACGCTGAAATTGAGGGAG 58.866 50.000 3.30 0.00 0.00 4.30
2041 2577 2.158813 GGGATACGCTGAAATTGAGGGA 60.159 50.000 3.30 0.00 37.60 4.20
2042 2578 2.222027 GGGATACGCTGAAATTGAGGG 58.778 52.381 0.00 0.00 37.60 4.30
2124 2663 9.350357 CTTCTTTTGAATATGAATTCTGTGGTG 57.650 33.333 7.05 0.00 41.83 4.17
2204 2744 8.172484 CACGGATATCGAAATTTAACTTTGACA 58.828 33.333 0.00 0.00 42.43 3.58
2220 2760 2.394545 TAAGACGTGCACGGATATCG 57.605 50.000 39.21 16.33 44.95 2.92
2223 2763 4.841443 ATGTATAAGACGTGCACGGATA 57.159 40.909 39.21 27.97 44.95 2.59
2459 3272 6.200854 GCAATTTACCTGTTTGACCAAGAAAG 59.799 38.462 0.00 0.00 0.00 2.62
2460 3273 6.045955 GCAATTTACCTGTTTGACCAAGAAA 58.954 36.000 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.