Multiple sequence alignment - TraesCS7A01G434200

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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 TraesCS7A01G434200 chr7A 100.000 7040 0 0 1 7040 628006126 628013165 0.000000e+00 13001.0
1 TraesCS7A01G434200 chr7A 85.358 1564 169 39 814 2354 628242400 628240874 0.000000e+00 1565.0
2 TraesCS7A01G434200 chr7A 90.765 693 47 6 6361 7040 516923350 516922662 0.000000e+00 909.0
3 TraesCS7A01G434200 chr7A 87.061 626 64 7 2446 3067 628240877 628240265 0.000000e+00 691.0
4 TraesCS7A01G434200 chr7A 81.975 638 57 30 3118 3737 628240253 628239656 8.210000e-134 488.0
5 TraesCS7A01G434200 chr7A 80.945 656 76 21 5436 6067 628236512 628235882 2.300000e-129 473.0
6 TraesCS7A01G434200 chr7A 80.565 283 37 12 3728 4007 628237974 628237707 1.200000e-47 202.0
7 TraesCS7A01G434200 chr7A 96.262 107 4 0 2350 2456 511927414 511927308 7.260000e-40 176.0
8 TraesCS7A01G434200 chr7B 97.172 3288 72 11 2876 6159 589347801 589344531 0.000000e+00 5537.0
9 TraesCS7A01G434200 chr7B 92.335 1683 68 16 815 2455 589349976 589348313 0.000000e+00 2337.0
10 TraesCS7A01G434200 chr7B 98.051 513 10 0 2408 2920 589348313 589347801 0.000000e+00 893.0
11 TraesCS7A01G434200 chr7B 81.297 1064 123 44 676 1702 589401770 589400746 0.000000e+00 793.0
12 TraesCS7A01G434200 chr7B 87.982 674 53 15 1696 2354 589400477 589399817 0.000000e+00 771.0
13 TraesCS7A01G434200 chr7B 86.465 628 66 10 2446 3067 589399820 589399206 0.000000e+00 671.0
14 TraesCS7A01G434200 chr7B 97.326 187 5 0 6178 6364 589344483 589344297 1.140000e-82 318.0
15 TraesCS7A01G434200 chr7B 77.679 336 28 19 3394 3710 589398866 589398559 2.030000e-35 161.0
16 TraesCS7A01G434200 chr7B 86.458 96 11 2 5130 5224 242674280 242674186 3.470000e-18 104.0
17 TraesCS7A01G434200 chr7D 96.904 2713 67 13 3467 6171 545394077 545391374 0.000000e+00 4529.0
18 TraesCS7A01G434200 chr7D 91.896 1814 72 28 688 2455 545399316 545397532 0.000000e+00 2466.0
19 TraesCS7A01G434200 chr7D 98.331 599 10 0 2876 3474 545397020 545396422 0.000000e+00 1051.0
20 TraesCS7A01G434200 chr7D 98.051 513 10 0 2408 2920 545397532 545397020 0.000000e+00 893.0
21 TraesCS7A01G434200 chr7D 89.368 696 51 7 6364 7040 78290553 78291244 0.000000e+00 854.0
22 TraesCS7A01G434200 chr7D 88.369 662 54 15 2 652 523543774 523543125 0.000000e+00 774.0
23 TraesCS7A01G434200 chr7D 88.944 606 52 13 3 600 206841621 206842219 0.000000e+00 734.0
24 TraesCS7A01G434200 chr7D 87.685 609 53 15 3 605 8472583 8471991 0.000000e+00 689.0
25 TraesCS7A01G434200 chr7D 84.091 176 27 1 4931 5106 334924792 334924618 1.210000e-37 169.0
26 TraesCS7A01G434200 chr7D 91.667 120 7 3 2338 2457 370726306 370726190 5.650000e-36 163.0
27 TraesCS7A01G434200 chr3D 93.218 693 31 4 6361 7040 602047882 602048571 0.000000e+00 1005.0
28 TraesCS7A01G434200 chr3D 92.743 689 36 6 6363 7040 80220420 80219735 0.000000e+00 983.0
29 TraesCS7A01G434200 chr2D 92.475 691 35 9 6363 7040 642825485 642826171 0.000000e+00 972.0
30 TraesCS7A01G434200 chr2D 91.416 699 37 10 6361 7040 453731597 453730903 0.000000e+00 937.0
31 TraesCS7A01G434200 chr2D 91.228 684 39 11 6361 7040 30144772 30144106 0.000000e+00 911.0
32 TraesCS7A01G434200 chr2D 85.629 167 21 3 4938 5103 28882466 28882302 9.390000e-39 172.0
33 TraesCS7A01G434200 chr5D 92.330 691 35 5 6363 7040 84382307 84381622 0.000000e+00 966.0
34 TraesCS7A01G434200 chr5D 91.751 691 33 7 6363 7040 374626809 374627488 0.000000e+00 939.0
35 TraesCS7A01G434200 chr5D 91.429 700 32 9 6363 7040 559113385 559114078 0.000000e+00 935.0
36 TraesCS7A01G434200 chr5D 89.291 691 42 15 6363 7040 391321334 391320663 0.000000e+00 837.0
37 TraesCS7A01G434200 chr5D 90.370 135 4 6 6915 7040 407315189 407315323 1.210000e-37 169.0
38 TraesCS7A01G434200 chr5D 93.043 115 7 1 2353 2467 521371581 521371694 4.370000e-37 167.0
39 TraesCS7A01G434200 chr6D 92.063 693 36 5 6361 7040 108455742 108455056 0.000000e+00 957.0
40 TraesCS7A01G434200 chr6D 91.787 694 35 8 6363 7040 451668340 451667653 0.000000e+00 946.0
41 TraesCS7A01G434200 chr6D 86.989 661 61 18 3 651 126627081 126627728 0.000000e+00 721.0
42 TraesCS7A01G434200 chr4D 92.133 661 31 6 6361 7009 439874001 439874652 0.000000e+00 913.0
43 TraesCS7A01G434200 chr4D 90.072 695 52 6 6359 7040 386122963 386123653 0.000000e+00 885.0
44 TraesCS7A01G434200 chr4D 86.047 172 22 2 4938 5109 424471641 424471810 4.340000e-42 183.0
45 TraesCS7A01G434200 chr4D 87.500 96 10 2 5130 5224 65943872 65943778 7.470000e-20 110.0
46 TraesCS7A01G434200 chr4D 94.545 55 3 0 5136 5190 295573758 295573704 1.260000e-12 86.1
47 TraesCS7A01G434200 chr3A 90.476 588 36 7 6466 7040 461844042 461844622 0.000000e+00 758.0
48 TraesCS7A01G434200 chr3A 90.625 64 6 0 3606 3669 15288795 15288732 1.260000e-12 86.1
49 TraesCS7A01G434200 chr4A 88.245 621 55 12 17 625 5703093 5703707 0.000000e+00 726.0
50 TraesCS7A01G434200 chr4A 75.466 644 72 60 52 652 729264003 729264603 1.180000e-57 235.0
51 TraesCS7A01G434200 chr4A 86.420 162 21 1 4949 5110 40247391 40247231 7.260000e-40 176.0
52 TraesCS7A01G434200 chr4A 89.655 58 6 0 5130 5187 195969228 195969285 2.720000e-09 75.0
53 TraesCS7A01G434200 chr1D 88.739 595 46 18 2 582 397645998 397646585 0.000000e+00 708.0
54 TraesCS7A01G434200 chr1B 90.149 538 43 8 3 532 530486934 530486399 0.000000e+00 691.0
55 TraesCS7A01G434200 chr1B 96.226 106 2 2 2353 2458 606612826 606612929 9.390000e-39 172.0
56 TraesCS7A01G434200 chr1B 92.373 118 7 2 2346 2462 259511945 259511829 4.370000e-37 167.0
57 TraesCS7A01G434200 chr1B 85.417 96 12 2 5130 5224 82181128 82181222 1.620000e-16 99.0
58 TraesCS7A01G434200 chr1B 90.323 62 6 0 3604 3665 487408961 487409022 1.630000e-11 82.4
59 TraesCS7A01G434200 chr5B 86.625 643 63 17 3 631 529529650 529529017 0.000000e+00 689.0
60 TraesCS7A01G434200 chr5B 74.021 485 108 13 3602 4073 84476934 84477413 1.560000e-41 182.0
61 TraesCS7A01G434200 chr5A 87.922 563 52 12 3 555 699056582 699056026 0.000000e+00 649.0
62 TraesCS7A01G434200 chr5A 91.597 119 7 3 2342 2458 68548458 68548575 2.030000e-35 161.0
63 TraesCS7A01G434200 chr5A 89.062 64 7 0 3602 3665 104255597 104255660 5.850000e-11 80.5
64 TraesCS7A01G434200 chr3B 79.852 541 60 32 131 652 620856285 620856795 4.040000e-92 350.0
65 TraesCS7A01G434200 chr2B 78.232 611 79 36 62 652 655207159 655206583 6.760000e-90 342.0
66 TraesCS7A01G434200 chr2B 89.231 65 7 0 3601 3665 695514385 695514321 1.630000e-11 82.4
67 TraesCS7A01G434200 chr2A 76.373 601 77 42 85 643 200338222 200337645 5.420000e-66 263.0
68 TraesCS7A01G434200 chr2A 87.500 80 10 0 5130 5209 438523795 438523874 7.520000e-15 93.5
69 TraesCS7A01G434200 chr4B 85.227 176 25 1 4933 5108 654063660 654063486 5.610000e-41 180.0
70 TraesCS7A01G434200 chr4B 89.655 58 6 0 5130 5187 364043504 364043561 2.720000e-09 75.0
71 TraesCS7A01G434200 chr1A 84.746 177 26 1 4933 5109 33779423 33779248 7.260000e-40 176.0
72 TraesCS7A01G434200 chr1A 96.226 106 4 0 2344 2449 351606753 351606858 2.610000e-39 174.0
73 TraesCS7A01G434200 chr1A 84.091 176 27 1 4933 5108 328366255 328366429 1.210000e-37 169.0
74 TraesCS7A01G434200 chr1A 90.323 62 6 0 3603 3664 508152254 508152315 1.630000e-11 82.4
75 TraesCS7A01G434200 chr6B 72.835 508 116 15 3602 4094 431235848 431235348 3.400000e-33 154.0


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 TraesCS7A01G434200 chr7A 628006126 628013165 7039 False 13001.00 13001 100.00000 1 7040 1 chr7A.!!$F1 7039
1 TraesCS7A01G434200 chr7A 516922662 516923350 688 True 909.00 909 90.76500 6361 7040 1 chr7A.!!$R2 679
2 TraesCS7A01G434200 chr7A 628235882 628242400 6518 True 683.80 1565 83.18080 814 6067 5 chr7A.!!$R3 5253
3 TraesCS7A01G434200 chr7B 589344297 589349976 5679 True 2271.25 5537 96.22100 815 6364 4 chr7B.!!$R2 5549
4 TraesCS7A01G434200 chr7B 589398559 589401770 3211 True 599.00 793 83.35575 676 3710 4 chr7B.!!$R3 3034
5 TraesCS7A01G434200 chr7D 545391374 545399316 7942 True 2234.75 4529 96.29550 688 6171 4 chr7D.!!$R5 5483
6 TraesCS7A01G434200 chr7D 78290553 78291244 691 False 854.00 854 89.36800 6364 7040 1 chr7D.!!$F1 676
7 TraesCS7A01G434200 chr7D 523543125 523543774 649 True 774.00 774 88.36900 2 652 1 chr7D.!!$R4 650
8 TraesCS7A01G434200 chr7D 206841621 206842219 598 False 734.00 734 88.94400 3 600 1 chr7D.!!$F2 597
9 TraesCS7A01G434200 chr7D 8471991 8472583 592 True 689.00 689 87.68500 3 605 1 chr7D.!!$R1 602
10 TraesCS7A01G434200 chr3D 602047882 602048571 689 False 1005.00 1005 93.21800 6361 7040 1 chr3D.!!$F1 679
11 TraesCS7A01G434200 chr3D 80219735 80220420 685 True 983.00 983 92.74300 6363 7040 1 chr3D.!!$R1 677
12 TraesCS7A01G434200 chr2D 642825485 642826171 686 False 972.00 972 92.47500 6363 7040 1 chr2D.!!$F1 677
13 TraesCS7A01G434200 chr2D 453730903 453731597 694 True 937.00 937 91.41600 6361 7040 1 chr2D.!!$R3 679
14 TraesCS7A01G434200 chr2D 30144106 30144772 666 True 911.00 911 91.22800 6361 7040 1 chr2D.!!$R2 679
15 TraesCS7A01G434200 chr5D 84381622 84382307 685 True 966.00 966 92.33000 6363 7040 1 chr5D.!!$R1 677
16 TraesCS7A01G434200 chr5D 374626809 374627488 679 False 939.00 939 91.75100 6363 7040 1 chr5D.!!$F1 677
17 TraesCS7A01G434200 chr5D 559113385 559114078 693 False 935.00 935 91.42900 6363 7040 1 chr5D.!!$F4 677
18 TraesCS7A01G434200 chr5D 391320663 391321334 671 True 837.00 837 89.29100 6363 7040 1 chr5D.!!$R2 677
19 TraesCS7A01G434200 chr6D 108455056 108455742 686 True 957.00 957 92.06300 6361 7040 1 chr6D.!!$R1 679
20 TraesCS7A01G434200 chr6D 451667653 451668340 687 True 946.00 946 91.78700 6363 7040 1 chr6D.!!$R2 677
21 TraesCS7A01G434200 chr6D 126627081 126627728 647 False 721.00 721 86.98900 3 651 1 chr6D.!!$F1 648
22 TraesCS7A01G434200 chr4D 439874001 439874652 651 False 913.00 913 92.13300 6361 7009 1 chr4D.!!$F3 648
23 TraesCS7A01G434200 chr4D 386122963 386123653 690 False 885.00 885 90.07200 6359 7040 1 chr4D.!!$F1 681
24 TraesCS7A01G434200 chr3A 461844042 461844622 580 False 758.00 758 90.47600 6466 7040 1 chr3A.!!$F1 574
25 TraesCS7A01G434200 chr4A 5703093 5703707 614 False 726.00 726 88.24500 17 625 1 chr4A.!!$F1 608
26 TraesCS7A01G434200 chr4A 729264003 729264603 600 False 235.00 235 75.46600 52 652 1 chr4A.!!$F3 600
27 TraesCS7A01G434200 chr1D 397645998 397646585 587 False 708.00 708 88.73900 2 582 1 chr1D.!!$F1 580
28 TraesCS7A01G434200 chr1B 530486399 530486934 535 True 691.00 691 90.14900 3 532 1 chr1B.!!$R2 529
29 TraesCS7A01G434200 chr5B 529529017 529529650 633 True 689.00 689 86.62500 3 631 1 chr5B.!!$R1 628
30 TraesCS7A01G434200 chr5A 699056026 699056582 556 True 649.00 649 87.92200 3 555 1 chr5A.!!$R1 552
31 TraesCS7A01G434200 chr3B 620856285 620856795 510 False 350.00 350 79.85200 131 652 1 chr3B.!!$F1 521
32 TraesCS7A01G434200 chr2B 655206583 655207159 576 True 342.00 342 78.23200 62 652 1 chr2B.!!$R1 590
33 TraesCS7A01G434200 chr2A 200337645 200338222 577 True 263.00 263 76.37300 85 643 1 chr2A.!!$R1 558

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
979 1151 0.107831 CTCCGGCGATATTCCCCAAA 59.892 55.000 9.30 0.00 0.00 3.28 F
1976 2485 0.658897 TTGCCCGTCGTTTTCTTCAC 59.341 50.000 0.00 0.00 0.00 3.18 F
2478 3035 2.160219 TGCTTTGTTGCGCTCTTCTATG 59.840 45.455 9.73 0.00 35.36 2.23 F
3173 3780 2.289694 CCAGTTGGTTGATCCTCGAACT 60.290 50.000 8.15 8.15 37.07 3.01 F
4323 9079 0.035630 CCTCTCCCTTGACCAAGCTG 60.036 60.000 4.31 0.00 37.11 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2357 2867 2.418976 GACACTTATTTTGGGACGGAGC 59.581 50.000 0.0 0.0 0.00 4.70 R
3015 3622 2.105766 AGGAAAGGGCAAGCATCATTC 58.894 47.619 0.0 0.0 0.00 2.67 R
3991 8747 0.455410 TGCGGAAATGCCTATGTTGC 59.545 50.000 0.0 0.0 0.00 4.17 R
4380 9136 1.338484 GGAATGAGAGCAGTGACAGCA 60.338 52.381 2.1 0.0 0.00 4.41 R
6212 11198 1.002624 TCGTGGAAATGCCTCACCC 60.003 57.895 0.0 0.0 37.63 4.61 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
43 44 8.870160 TTGAAAAGAAATGTTCACGATTCAAT 57.130 26.923 0.00 0.00 33.58 2.57
44 45 8.870160 TGAAAAGAAATGTTCACGATTCAATT 57.130 26.923 0.00 0.00 0.00 2.32
45 46 9.311916 TGAAAAGAAATGTTCACGATTCAATTT 57.688 25.926 0.00 0.00 0.00 1.82
327 409 4.822036 TGTTCGTGGGTTATCAAAAGTG 57.178 40.909 0.00 0.00 0.00 3.16
329 411 3.134574 TCGTGGGTTATCAAAAGTGCT 57.865 42.857 0.00 0.00 0.00 4.40
332 414 3.440173 CGTGGGTTATCAAAAGTGCTCAT 59.560 43.478 0.00 0.00 0.00 2.90
333 415 4.672542 CGTGGGTTATCAAAAGTGCTCATG 60.673 45.833 0.00 0.00 0.00 3.07
334 416 3.763360 TGGGTTATCAAAAGTGCTCATGG 59.237 43.478 0.00 0.00 0.00 3.66
336 418 4.220602 GGGTTATCAAAAGTGCTCATGGTT 59.779 41.667 0.00 0.00 0.00 3.67
338 420 6.322491 GGTTATCAAAAGTGCTCATGGTTAC 58.678 40.000 0.00 0.00 0.00 2.50
643 774 0.951558 CCGGCCCATATTAACAGCAC 59.048 55.000 0.00 0.00 0.00 4.40
644 775 0.586319 CGGCCCATATTAACAGCACG 59.414 55.000 0.00 0.00 0.00 5.34
673 804 2.278013 CGCTAGTTCGCTCCCGAC 60.278 66.667 0.00 0.00 44.30 4.79
674 805 2.278013 GCTAGTTCGCTCCCGACG 60.278 66.667 0.00 0.00 44.30 5.12
675 806 2.408022 CTAGTTCGCTCCCGACGG 59.592 66.667 6.99 6.99 44.30 4.79
676 807 2.046023 TAGTTCGCTCCCGACGGA 60.046 61.111 17.49 0.15 44.30 4.69
677 808 2.320339 CTAGTTCGCTCCCGACGGAC 62.320 65.000 17.49 4.00 44.30 4.79
678 809 4.047059 GTTCGCTCCCGACGGACA 62.047 66.667 17.49 0.00 44.30 4.02
679 810 3.296836 TTCGCTCCCGACGGACAA 61.297 61.111 17.49 0.00 44.30 3.18
680 811 3.277211 TTCGCTCCCGACGGACAAG 62.277 63.158 17.49 10.82 44.30 3.16
682 813 4.373116 GCTCCCGACGGACAAGCA 62.373 66.667 17.49 0.00 33.32 3.91
812 948 2.941025 CACCCCACCCACCTCCAT 60.941 66.667 0.00 0.00 0.00 3.41
813 949 2.121042 ACCCCACCCACCTCCATT 60.121 61.111 0.00 0.00 0.00 3.16
829 965 2.955859 ATTCCCGACCCTCCTCCCA 61.956 63.158 0.00 0.00 0.00 4.37
830 970 3.918328 TTCCCGACCCTCCTCCCAC 62.918 68.421 0.00 0.00 0.00 4.61
836 976 4.455137 CCCTCCTCCCACCCCCAT 62.455 72.222 0.00 0.00 0.00 4.00
842 982 4.309689 TCCCACCCCCATCCCCAA 62.310 66.667 0.00 0.00 0.00 4.12
979 1151 0.107831 CTCCGGCGATATTCCCCAAA 59.892 55.000 9.30 0.00 0.00 3.28
987 1159 4.262894 GGCGATATTCCCCAAATACTCTCA 60.263 45.833 0.00 0.00 32.68 3.27
990 1162 6.128172 GCGATATTCCCCAAATACTCTCATTG 60.128 42.308 0.00 0.00 32.68 2.82
1156 1331 1.138069 TCTCTCGCTCTGTCTCGATCT 59.862 52.381 0.00 0.00 33.98 2.75
1254 1441 4.647654 GTCTTCTTGGACGTGCGA 57.352 55.556 1.60 0.00 0.00 5.10
1300 1487 4.388499 GGTGGAAGGAGGCGCGAA 62.388 66.667 12.10 0.00 0.00 4.70
1313 1500 1.289109 GCGCGAAAGTACTTGAGCCA 61.289 55.000 22.16 0.00 0.00 4.75
1341 1528 1.064946 GTGCCAGGACGAGATCGAG 59.935 63.158 9.58 0.00 43.02 4.04
1343 1530 2.122167 GCCAGGACGAGATCGAGGT 61.122 63.158 9.58 0.00 43.02 3.85
1362 1549 2.978010 CCCACCGCGCTCAGTTTT 60.978 61.111 5.56 0.00 0.00 2.43
1470 1657 2.683742 CGCTATCCCTTCCACCATGTTT 60.684 50.000 0.00 0.00 0.00 2.83
1778 2275 2.367241 GGGTTTGGGTAAGTGCAACATT 59.633 45.455 0.00 0.00 41.43 2.71
1845 2354 3.099438 CTGCATGAGAAGCCGCAG 58.901 61.111 0.00 0.00 45.17 5.18
1964 2473 4.625800 GCATCTCTTCTTGCCCGT 57.374 55.556 0.00 0.00 32.66 5.28
1976 2485 0.658897 TTGCCCGTCGTTTTCTTCAC 59.341 50.000 0.00 0.00 0.00 3.18
2005 2514 5.243954 AGAGGTATGTATATCGTGTGCACAT 59.756 40.000 24.69 9.98 34.40 3.21
2068 2577 9.661187 GTTGTAAAGTTTAGAGCTTTTAACCTC 57.339 33.333 2.81 0.00 37.37 3.85
2187 2696 9.546909 GTTTATAACCATGCTAATTGATGATCG 57.453 33.333 0.00 0.00 0.00 3.69
2317 2827 6.698329 CACAAGCTGTTTTTCTGAATGAATCA 59.302 34.615 0.00 0.00 34.24 2.57
2357 2867 5.005107 GGCCTTCGTTTGTTATAAGTACTCG 59.995 44.000 0.00 0.00 0.00 4.18
2478 3035 2.160219 TGCTTTGTTGCGCTCTTCTATG 59.840 45.455 9.73 0.00 35.36 2.23
2519 3076 9.386010 AGTGTATTTGGTTCGTTTGCTATAATA 57.614 29.630 0.00 0.00 0.00 0.98
2575 3132 4.263462 ACATGCTGTGGGAAGAATTAGTCA 60.263 41.667 0.00 0.00 0.00 3.41
2633 3191 7.702348 GCAATCAGTGTTTTCAAAACTAGAAGT 59.298 33.333 14.10 0.00 0.00 3.01
3015 3622 4.330074 CAGGGTACTCTTTGCTAATGAACG 59.670 45.833 0.00 0.00 0.00 3.95
3096 3703 5.491078 TGGTTCTCCTGTTGGGTTATCTATT 59.509 40.000 0.00 0.00 36.25 1.73
3173 3780 2.289694 CCAGTTGGTTGATCCTCGAACT 60.290 50.000 8.15 8.15 37.07 3.01
3357 4047 5.473504 ACCTGGCAGTGTTCTTTTACTTATG 59.526 40.000 14.43 0.00 0.00 1.90
3621 6674 6.019779 AGAAACAACAACAACAGCAAAGTA 57.980 33.333 0.00 0.00 0.00 2.24
3673 6734 3.138468 AGAGTTAAAACCCAACAGGAGCT 59.862 43.478 0.00 0.00 39.89 4.09
3730 6793 3.378112 CACACTCCTGTTCAAGCAGAAAA 59.622 43.478 0.00 0.00 38.13 2.29
3840 8594 3.181465 CGTGGCTTAGGATTCCACTATGT 60.181 47.826 5.29 0.00 45.99 2.29
3947 8701 4.098044 CCCTAGCCGATCACGTATATCATT 59.902 45.833 9.87 0.00 37.88 2.57
3991 8747 4.757799 TGTATGACCACAAATCCAAACG 57.242 40.909 0.00 0.00 0.00 3.60
4188 8944 0.037232 GTTGGGTTGAGGAGTCGGAG 60.037 60.000 0.00 0.00 0.00 4.63
4313 9069 1.306568 GACTCTGCCCCTCTCCCTT 60.307 63.158 0.00 0.00 0.00 3.95
4322 9078 1.204113 CCCTCTCCCTTGACCAAGCT 61.204 60.000 4.31 0.00 37.11 3.74
4323 9079 0.035630 CCTCTCCCTTGACCAAGCTG 60.036 60.000 4.31 0.00 37.11 4.24
4401 9157 1.066286 GCTGTCACTGCTCTCATTCCT 60.066 52.381 0.00 0.00 0.00 3.36
4607 9363 1.134220 TCTGCAACAAGGAAGAACGGT 60.134 47.619 0.00 0.00 0.00 4.83
4625 9381 4.118410 ACGGTAACAACGATTGTGTGTTA 58.882 39.130 12.84 12.84 44.59 2.41
4745 9501 5.547465 TCGATTTGGTGACTGTTTCTGTAT 58.453 37.500 0.00 0.00 0.00 2.29
4818 9574 1.202867 TGGCTGCTGTTGTATTCACCA 60.203 47.619 0.00 0.00 0.00 4.17
4819 9575 1.885887 GGCTGCTGTTGTATTCACCAA 59.114 47.619 0.00 0.00 0.00 3.67
4820 9576 2.493278 GGCTGCTGTTGTATTCACCAAT 59.507 45.455 0.00 0.00 0.00 3.16
5017 9773 4.367039 TCCATTCCTCCGAAATATTCCC 57.633 45.455 0.00 0.00 0.00 3.97
5067 9823 3.931907 TCTAGTGGAATGGAACCATGG 57.068 47.619 11.19 11.19 39.69 3.66
5384 10141 6.715264 AGTTTCCTATTTCCAGGTAACAACTG 59.285 38.462 12.35 0.00 44.28 3.16
5475 10398 4.157840 GGGGAATTGCGTTTATTCAGTCTT 59.842 41.667 0.00 0.00 34.43 3.01
5516 10439 2.025887 AGGGCCACCTCAAGTTTAGATG 60.026 50.000 6.18 0.00 46.95 2.90
5518 10441 3.010420 GGCCACCTCAAGTTTAGATGAC 58.990 50.000 0.00 0.00 0.00 3.06
5519 10442 3.559171 GGCCACCTCAAGTTTAGATGACA 60.559 47.826 0.00 0.00 0.00 3.58
5718 10663 3.655615 ACCACCTCTGTTTACAAACCA 57.344 42.857 2.55 0.00 38.11 3.67
5736 10681 7.035004 ACAAACCATCATACATACAATGCAAC 58.965 34.615 0.00 0.00 0.00 4.17
6139 11092 7.874016 TGTTTTCTTATACGCTTTACCAGAAGA 59.126 33.333 0.00 0.00 0.00 2.87
6156 11109 5.426504 CAGAAGAGCAATGGTGTCTTATCT 58.573 41.667 0.00 0.00 30.55 1.98
6157 11110 5.879223 CAGAAGAGCAATGGTGTCTTATCTT 59.121 40.000 0.00 0.00 30.55 2.40
6158 11111 6.373774 CAGAAGAGCAATGGTGTCTTATCTTT 59.626 38.462 0.00 0.00 30.55 2.52
6159 11112 6.373774 AGAAGAGCAATGGTGTCTTATCTTTG 59.626 38.462 0.00 0.00 30.55 2.77
6171 11124 9.665264 GGTGTCTTATCTTTGTTTTTGTAAGAG 57.335 33.333 0.00 0.00 31.98 2.85
6174 11127 9.730420 GTCTTATCTTTGTTTTTGTAAGAGCAA 57.270 29.630 0.00 0.00 31.98 3.91
6195 11181 3.955650 TGGTAGGACTGTAGAAAGCAC 57.044 47.619 0.00 0.00 0.00 4.40
6285 11271 2.671177 CGAGCAACACAGCCTTCCG 61.671 63.158 0.00 0.00 34.23 4.30
6286 11272 1.301716 GAGCAACACAGCCTTCCGA 60.302 57.895 0.00 0.00 34.23 4.55
6288 11274 1.301716 GCAACACAGCCTTCCGAGA 60.302 57.895 0.00 0.00 0.00 4.04
6464 11459 2.046314 AGCGGGCGTGCAATAACT 60.046 55.556 3.15 0.00 37.31 2.24
6527 11531 0.604073 TCTCGCGTGGTGTATTTGGA 59.396 50.000 5.77 0.00 0.00 3.53
6669 11673 1.633774 CGCTCACCCCATCCTATAGT 58.366 55.000 0.00 0.00 0.00 2.12
6672 11676 2.877866 CTCACCCCATCCTATAGTCGT 58.122 52.381 0.00 0.00 0.00 4.34
6861 11902 0.034186 ATCAAAGCTCCCCAATGCGA 60.034 50.000 0.00 0.00 0.00 5.10
7025 12076 0.384230 ACGCGCACAAAATGTTCGAG 60.384 50.000 5.73 5.80 39.26 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 63 7.922505 TTCAAATTCGTGAACATTTTTCGAT 57.077 28.000 0.00 0.00 32.56 3.59
306 380 3.003897 GCACTTTTGATAACCCACGAACA 59.996 43.478 0.00 0.00 0.00 3.18
307 381 3.252458 AGCACTTTTGATAACCCACGAAC 59.748 43.478 0.00 0.00 0.00 3.95
309 383 3.071479 GAGCACTTTTGATAACCCACGA 58.929 45.455 0.00 0.00 0.00 4.35
310 384 2.811431 TGAGCACTTTTGATAACCCACG 59.189 45.455 0.00 0.00 0.00 4.94
313 387 3.763897 ACCATGAGCACTTTTGATAACCC 59.236 43.478 0.00 0.00 0.00 4.11
314 388 5.391312 AACCATGAGCACTTTTGATAACC 57.609 39.130 0.00 0.00 0.00 2.85
319 401 5.843673 TTTGTAACCATGAGCACTTTTGA 57.156 34.783 0.00 0.00 0.00 2.69
320 402 6.900568 TTTTTGTAACCATGAGCACTTTTG 57.099 33.333 0.00 0.00 0.00 2.44
352 435 9.661563 ACTAATTCGTGTACATTCTCCAAAATA 57.338 29.630 0.00 0.00 0.00 1.40
551 676 4.447290 CCTGAACCGGGTTTTTCATTTTT 58.553 39.130 14.69 0.00 31.41 1.94
552 677 3.181459 CCCTGAACCGGGTTTTTCATTTT 60.181 43.478 14.69 0.00 39.51 1.82
553 678 2.367241 CCCTGAACCGGGTTTTTCATTT 59.633 45.455 14.69 0.00 39.51 2.32
556 685 0.551879 TCCCTGAACCGGGTTTTTCA 59.448 50.000 14.69 6.87 44.95 2.69
656 787 2.278013 GTCGGGAGCGAACTAGCG 60.278 66.667 0.00 0.00 43.00 4.26
657 788 2.278013 CGTCGGGAGCGAACTAGC 60.278 66.667 0.00 0.00 37.41 3.42
658 789 2.110967 TCCGTCGGGAGCGAACTAG 61.111 63.158 12.29 0.00 37.43 2.57
659 790 2.046023 TCCGTCGGGAGCGAACTA 60.046 61.111 12.29 0.00 37.43 2.24
660 791 3.745803 GTCCGTCGGGAGCGAACT 61.746 66.667 12.29 0.00 44.97 3.01
661 792 3.562779 TTGTCCGTCGGGAGCGAAC 62.563 63.158 12.29 1.14 44.97 3.95
662 793 3.277211 CTTGTCCGTCGGGAGCGAA 62.277 63.158 12.29 0.00 44.97 4.70
663 794 3.744719 CTTGTCCGTCGGGAGCGA 61.745 66.667 12.29 1.57 44.97 4.93
665 796 4.373116 TGCTTGTCCGTCGGGAGC 62.373 66.667 20.92 20.92 44.97 4.70
666 797 2.432628 GTGCTTGTCCGTCGGGAG 60.433 66.667 12.29 8.51 44.97 4.30
667 798 4.351938 CGTGCTTGTCCGTCGGGA 62.352 66.667 12.29 0.00 41.08 5.14
671 802 3.712881 GTGCCGTGCTTGTCCGTC 61.713 66.667 0.00 0.00 0.00 4.79
672 803 4.539083 TGTGCCGTGCTTGTCCGT 62.539 61.111 0.00 0.00 0.00 4.69
673 804 3.716006 CTGTGCCGTGCTTGTCCG 61.716 66.667 0.00 0.00 0.00 4.79
674 805 3.357079 CCTGTGCCGTGCTTGTCC 61.357 66.667 0.00 0.00 0.00 4.02
675 806 3.357079 CCCTGTGCCGTGCTTGTC 61.357 66.667 0.00 0.00 0.00 3.18
796 932 2.121042 AATGGAGGTGGGTGGGGT 60.121 61.111 0.00 0.00 0.00 4.95
798 934 2.683475 GGAATGGAGGTGGGTGGG 59.317 66.667 0.00 0.00 0.00 4.61
801 937 2.124085 TCGGGAATGGAGGTGGGT 59.876 61.111 0.00 0.00 0.00 4.51
803 939 2.590092 GGTCGGGAATGGAGGTGG 59.410 66.667 0.00 0.00 0.00 4.61
804 940 1.972660 GAGGGTCGGGAATGGAGGTG 61.973 65.000 0.00 0.00 0.00 4.00
805 941 1.689582 GAGGGTCGGGAATGGAGGT 60.690 63.158 0.00 0.00 0.00 3.85
806 942 2.444256 GGAGGGTCGGGAATGGAGG 61.444 68.421 0.00 0.00 0.00 4.30
807 943 1.383248 AGGAGGGTCGGGAATGGAG 60.383 63.158 0.00 0.00 0.00 3.86
808 944 1.382695 GAGGAGGGTCGGGAATGGA 60.383 63.158 0.00 0.00 0.00 3.41
809 945 2.444256 GGAGGAGGGTCGGGAATGG 61.444 68.421 0.00 0.00 0.00 3.16
810 946 2.444256 GGGAGGAGGGTCGGGAATG 61.444 68.421 0.00 0.00 0.00 2.67
811 947 2.040779 GGGAGGAGGGTCGGGAAT 60.041 66.667 0.00 0.00 0.00 3.01
812 948 3.607299 TGGGAGGAGGGTCGGGAA 61.607 66.667 0.00 0.00 0.00 3.97
813 949 4.393778 GTGGGAGGAGGGTCGGGA 62.394 72.222 0.00 0.00 0.00 5.14
860 1028 3.157949 GGCGGGAGGAAGGAGGAG 61.158 72.222 0.00 0.00 0.00 3.69
861 1029 4.798682 GGGCGGGAGGAAGGAGGA 62.799 72.222 0.00 0.00 0.00 3.71
979 1151 1.863267 GCGCTCTGCAATGAGAGTAT 58.137 50.000 7.13 0.00 45.45 2.12
987 1159 3.580193 GCCATCGCGCTCTGCAAT 61.580 61.111 5.56 0.00 46.97 3.56
1126 1298 1.066303 AGAGCGAGAGATTAAGCCGTG 59.934 52.381 0.00 0.00 0.00 4.94
1141 1313 0.316937 GAGCAGATCGAGACAGAGCG 60.317 60.000 0.00 0.00 0.00 5.03
1156 1331 2.238701 GGGGAGGAAAAGGGGAGCA 61.239 63.158 0.00 0.00 0.00 4.26
1211 1398 2.743928 CGTGCTTCAGCCTGGACC 60.744 66.667 0.00 0.00 41.18 4.46
1288 1475 0.320697 AAGTACTTTCGCGCCTCCTT 59.679 50.000 0.00 0.00 0.00 3.36
1300 1487 2.551071 GCAGGAAGTGGCTCAAGTACTT 60.551 50.000 1.12 1.12 37.36 2.24
1313 1500 4.335647 CCTGGCACGGCAGGAAGT 62.336 66.667 30.43 0.00 40.95 3.01
1359 1546 1.202486 ACGTTGAGGCGAGTGAGAAAA 60.202 47.619 0.00 0.00 35.59 2.29
1362 1549 0.039437 GAACGTTGAGGCGAGTGAGA 60.039 55.000 5.00 0.00 35.59 3.27
1499 1686 1.230635 CCAGAACAAGACTGTGCGGG 61.231 60.000 0.00 0.00 39.75 6.13
1534 1721 6.142498 AGATGATAGATGAAGGAGACCAGTT 58.858 40.000 0.00 0.00 0.00 3.16
1778 2275 7.451731 AATAAAGTCATAACTGAGGATGGGA 57.548 36.000 0.00 0.00 35.36 4.37
1845 2354 5.914635 GGCCCGTTAAAAGTTTAACTGTAAC 59.085 40.000 19.31 15.98 46.33 2.50
1964 2473 4.766375 ACCTCTCTTTGTGAAGAAAACGA 58.234 39.130 0.00 0.00 41.19 3.85
1976 2485 6.363626 GCACACGATATACATACCTCTCTTTG 59.636 42.308 0.00 0.00 0.00 2.77
2005 2514 4.391830 GTGGAACAACGAGAGCATCAATTA 59.608 41.667 0.00 0.00 44.16 1.40
2158 2667 9.183368 TCATCAATTAGCATGGTTATAAACACA 57.817 29.630 5.07 0.00 0.00 3.72
2187 2696 5.512788 CGATGAACCTGCAATTGAAACATAC 59.487 40.000 10.34 0.00 0.00 2.39
2317 2827 4.142687 CGAAGGCCATAACGAAATTCAAGT 60.143 41.667 5.01 0.00 0.00 3.16
2357 2867 2.418976 GACACTTATTTTGGGACGGAGC 59.581 50.000 0.00 0.00 0.00 4.70
2478 3035 7.173390 ACCAAATACACTAAAGCAGTTCTTCTC 59.827 37.037 0.00 0.00 34.26 2.87
2519 3076 5.534654 TGTTACAAATGCTGTCCTTTAAGCT 59.465 36.000 0.00 0.00 39.64 3.74
2575 3132 5.934935 ATCGACTTAAAACAAACGGACAT 57.065 34.783 0.00 0.00 0.00 3.06
2640 3198 6.110411 TGGGAAGTAGACTACTGAAAAAGG 57.890 41.667 15.88 0.00 39.39 3.11
2737 3300 7.121168 CCCAGCTAACATAGTTTCATCTGAAAA 59.879 37.037 6.92 0.00 44.58 2.29
2845 3408 5.476599 TGGGGAACATCAACAATGAAAGTAG 59.523 40.000 0.00 0.00 39.49 2.57
3015 3622 2.105766 AGGAAAGGGCAAGCATCATTC 58.894 47.619 0.00 0.00 0.00 2.67
3096 3703 4.382147 GGTGCAGTTCCAAAACTTTTACCA 60.382 41.667 0.00 0.00 43.28 3.25
3173 3780 9.823647 TTCAATTAAGTAACAGGCAATGAAAAA 57.176 25.926 0.00 0.00 0.00 1.94
3357 4047 9.453325 TTTTTACTGGAATGTGAAACGTAATTC 57.547 29.630 0.00 0.00 42.39 2.17
3533 6585 8.731275 TCAATAAACCTGGTGTATTGATACAG 57.269 34.615 33.76 17.49 43.56 2.74
3621 6674 3.571401 CCCAACTTGCTTGAGACTGAAAT 59.429 43.478 0.00 0.00 30.42 2.17
3673 6734 7.239763 TCATGTGTCTGAACCTTGATTAGTA 57.760 36.000 0.00 0.00 0.00 1.82
3947 8701 2.632996 AGAATGGGTCGAGTTCAGAACA 59.367 45.455 15.85 0.00 0.00 3.18
3991 8747 0.455410 TGCGGAAATGCCTATGTTGC 59.545 50.000 0.00 0.00 0.00 4.17
4188 8944 2.651135 GTTCTAGGGAACGAGTGGAC 57.349 55.000 0.00 0.00 41.70 4.02
4313 9069 1.675801 CTGGAGCTCAGCTTGGTCA 59.324 57.895 17.19 0.19 39.88 4.02
4380 9136 1.338484 GGAATGAGAGCAGTGACAGCA 60.338 52.381 2.10 0.00 0.00 4.41
4401 9157 2.679619 ATAGGGAGAGGGCGGCATCA 62.680 60.000 25.80 4.62 0.00 3.07
4607 9363 4.118410 ACGGTAACACACAATCGTTGTTA 58.882 39.130 1.37 0.00 43.23 2.41
4625 9381 4.452733 GCTCGCCTAGGCAACGGT 62.453 66.667 32.47 0.00 46.39 4.83
4660 9416 1.374190 CAACTGCTGCTCCCTGTCT 59.626 57.895 0.00 0.00 0.00 3.41
4714 9470 4.022068 ACAGTCACCAAATCGATGCAAATT 60.022 37.500 0.00 0.00 0.00 1.82
4745 9501 5.122239 CGCACCAAATTTCACTAATCTCTCA 59.878 40.000 0.00 0.00 0.00 3.27
5017 9773 7.295930 GTCGGTTCTGTTTTTCTATTTGGTAG 58.704 38.462 0.00 0.00 0.00 3.18
5067 9823 3.588955 GGAACAAAGTGGAATGGAATGC 58.411 45.455 0.00 0.00 0.00 3.56
5428 10317 5.594725 CACCTGGTACTACATCTACTGACAT 59.405 44.000 0.00 0.00 0.00 3.06
5475 10398 3.118629 CCTGCTCTGCTCACCATAACTAA 60.119 47.826 0.00 0.00 0.00 2.24
5516 10439 9.485591 CCTTTGATAACGTGTAATGTTTATGTC 57.514 33.333 0.00 0.00 45.42 3.06
5571 10495 2.550208 CCACCCCACTGTCAAGAAGTAC 60.550 54.545 0.00 0.00 0.00 2.73
5622 10547 2.995466 ACACACAAAATCATGGAGCG 57.005 45.000 0.00 0.00 0.00 5.03
6125 11073 2.096496 CCATTGCTCTTCTGGTAAAGCG 59.904 50.000 0.00 0.00 37.57 4.68
6139 11092 6.655078 AAACAAAGATAAGACACCATTGCT 57.345 33.333 0.00 0.00 0.00 3.91
6156 11109 7.068839 TCCTACCATTGCTCTTACAAAAACAAA 59.931 33.333 0.00 0.00 32.27 2.83
6157 11110 6.547880 TCCTACCATTGCTCTTACAAAAACAA 59.452 34.615 0.00 0.00 32.27 2.83
6158 11111 6.016610 GTCCTACCATTGCTCTTACAAAAACA 60.017 38.462 0.00 0.00 32.27 2.83
6159 11112 6.206829 AGTCCTACCATTGCTCTTACAAAAAC 59.793 38.462 0.00 0.00 32.27 2.43
6171 11124 3.623510 GCTTTCTACAGTCCTACCATTGC 59.376 47.826 0.00 0.00 0.00 3.56
6174 11127 3.119101 CGTGCTTTCTACAGTCCTACCAT 60.119 47.826 0.00 0.00 0.00 3.55
6175 11128 2.230508 CGTGCTTTCTACAGTCCTACCA 59.769 50.000 0.00 0.00 0.00 3.25
6176 11129 2.877335 CGTGCTTTCTACAGTCCTACC 58.123 52.381 0.00 0.00 0.00 3.18
6212 11198 1.002624 TCGTGGAAATGCCTCACCC 60.003 57.895 0.00 0.00 37.63 4.61
6285 11271 3.059120 CCATTGACATCGACATGCATCTC 60.059 47.826 0.00 0.00 32.57 2.75
6286 11272 2.876550 CCATTGACATCGACATGCATCT 59.123 45.455 0.00 0.00 32.57 2.90
6288 11274 2.921821 TCCATTGACATCGACATGCAT 58.078 42.857 0.00 0.00 32.57 3.96
6400 11386 3.832276 CGCTAAACTGGCTAAATTTGCA 58.168 40.909 0.00 0.00 0.00 4.08
6464 11459 2.583868 CCTTATACCGCACGCGCA 60.584 61.111 5.73 0.00 38.40 6.09
6515 11519 1.377987 GGGCGCTCCAAATACACCA 60.378 57.895 7.64 0.00 35.00 4.17
6575 11579 1.728672 CGTAGGAGGCGGAGAAGAC 59.271 63.158 0.00 0.00 0.00 3.01
6836 11877 0.914644 TGGGGAGCTTTGATGAGGAG 59.085 55.000 0.00 0.00 0.00 3.69
7016 12067 1.474330 GGGGCATTTCCTCGAACATT 58.526 50.000 0.00 0.00 34.39 2.71


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

AutoCloner maintained by Alex Coulton.