Multiple sequence alignment - TraesCS7A01G250400

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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 TraesCS7A01G250400 chr7A 100.000 3458 0 0 1 3458 232741244 232744701 0.000000e+00 6386.0
1 TraesCS7A01G250400 chr7A 79.577 710 118 14 1 704 625146154 625146842 1.870000e-132 483.0
2 TraesCS7A01G250400 chr7A 97.348 264 7 0 2561 2824 566529875 566530138 1.890000e-122 449.0
3 TraesCS7A01G250400 chr7A 97.348 264 6 1 2559 2822 559187100 559187362 6.810000e-122 448.0
4 TraesCS7A01G250400 chr7D 95.337 1780 67 6 788 2563 220507035 220508802 0.000000e+00 2813.0
5 TraesCS7A01G250400 chr7D 93.767 722 42 3 1 721 220504105 220504824 0.000000e+00 1081.0
6 TraesCS7A01G250400 chr7D 92.638 652 33 7 2819 3458 220508799 220509447 0.000000e+00 924.0
7 TraesCS7A01G250400 chr7B 96.337 819 29 1 1745 2563 178419392 178418575 0.000000e+00 1345.0
8 TraesCS7A01G250400 chr7B 94.773 727 24 3 960 1683 178420109 178419394 0.000000e+00 1120.0
9 TraesCS7A01G250400 chr7B 92.085 657 33 6 2819 3458 178418578 178417924 0.000000e+00 907.0
10 TraesCS7A01G250400 chr7B 88.404 664 57 7 16 678 629584881 629584237 0.000000e+00 782.0
11 TraesCS7A01G250400 chr7B 80.169 590 95 8 1 589 87824779 87824211 4.130000e-114 422.0
12 TraesCS7A01G250400 chr7B 94.964 139 7 0 804 942 178420533 178420395 5.810000e-53 219.0
13 TraesCS7A01G250400 chr3D 81.163 722 111 14 3 720 462451925 462451225 1.080000e-154 556.0
14 TraesCS7A01G250400 chr3D 81.077 650 109 9 1830 2474 523840268 523840908 1.110000e-139 507.0
15 TraesCS7A01G250400 chr3D 81.051 628 96 9 1 626 592003992 592004598 2.410000e-131 479.0
16 TraesCS7A01G250400 chr4B 80.083 723 116 16 1 721 424745628 424744932 2.380000e-141 512.0
17 TraesCS7A01G250400 chr2B 80.143 700 109 13 33 721 793385264 793385944 2.400000e-136 496.0
18 TraesCS7A01G250400 chr3B 81.864 590 88 6 1 589 815472676 815472105 2.410000e-131 479.0
19 TraesCS7A01G250400 chr3B 82.968 411 60 9 998 1405 691351157 691351560 2.540000e-96 363.0
20 TraesCS7A01G250400 chr6A 98.872 266 3 0 2558 2823 586802511 586802246 3.120000e-130 475.0
21 TraesCS7A01G250400 chr6A 97.736 265 6 0 2561 2825 13387535 13387271 1.130000e-124 457.0
22 TraesCS7A01G250400 chr6A 97.348 264 7 0 2561 2824 421525106 421524843 1.890000e-122 449.0
23 TraesCS7A01G250400 chr6A 84.483 58 6 2 742 797 170757795 170757851 2.000000e-03 54.7
24 TraesCS7A01G250400 chr4A 98.084 261 5 0 2562 2822 212811753 212812013 4.070000e-124 455.0
25 TraesCS7A01G250400 chr4A 97.348 264 7 0 2559 2822 577858449 577858712 1.890000e-122 449.0
26 TraesCS7A01G250400 chr5A 96.691 272 6 2 2551 2822 618310012 618310280 1.890000e-122 449.0
27 TraesCS7A01G250400 chr3A 94.792 288 11 4 2539 2826 652219291 652219574 2.450000e-121 446.0
28 TraesCS7A01G250400 chr3A 81.818 429 75 3 2048 2474 658750428 658750855 1.180000e-94 357.0


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 TraesCS7A01G250400 chr7A 232741244 232744701 3457 False 6386.00 6386 100.00000 1 3458 1 chr7A.!!$F1 3457
1 TraesCS7A01G250400 chr7A 625146154 625146842 688 False 483.00 483 79.57700 1 704 1 chr7A.!!$F4 703
2 TraesCS7A01G250400 chr7D 220504105 220509447 5342 False 1606.00 2813 93.91400 1 3458 3 chr7D.!!$F1 3457
3 TraesCS7A01G250400 chr7B 178417924 178420533 2609 True 897.75 1345 94.53975 804 3458 4 chr7B.!!$R3 2654
4 TraesCS7A01G250400 chr7B 629584237 629584881 644 True 782.00 782 88.40400 16 678 1 chr7B.!!$R2 662
5 TraesCS7A01G250400 chr7B 87824211 87824779 568 True 422.00 422 80.16900 1 589 1 chr7B.!!$R1 588
6 TraesCS7A01G250400 chr3D 462451225 462451925 700 True 556.00 556 81.16300 3 720 1 chr3D.!!$R1 717
7 TraesCS7A01G250400 chr3D 523840268 523840908 640 False 507.00 507 81.07700 1830 2474 1 chr3D.!!$F1 644
8 TraesCS7A01G250400 chr3D 592003992 592004598 606 False 479.00 479 81.05100 1 626 1 chr3D.!!$F2 625
9 TraesCS7A01G250400 chr4B 424744932 424745628 696 True 512.00 512 80.08300 1 721 1 chr4B.!!$R1 720
10 TraesCS7A01G250400 chr2B 793385264 793385944 680 False 496.00 496 80.14300 33 721 1 chr2B.!!$F1 688
11 TraesCS7A01G250400 chr3B 815472105 815472676 571 True 479.00 479 81.86400 1 589 1 chr3B.!!$R1 588

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
829 3015 0.175531 CAAATGACGGAAATGCCCCC 59.824 55.0 0.0 0.0 0.0 5.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2505 4971 1.162181 GCGGATGCAAGATAGCTGCA 61.162 55.0 1.02 7.4 43.04 4.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 2.700371 TGCTTGACATCGTATCTCCCAT 59.300 45.455 0.00 0.00 0.00 4.00
66 70 2.233676 TCTTTTCTCAGCCATGCTCGTA 59.766 45.455 0.00 0.00 36.40 3.43
87 92 1.447317 CGGAGTTGCCACTTGTTGCT 61.447 55.000 0.00 0.00 35.94 3.91
166 194 2.516906 TCAAATGGCATCAGCACTCAA 58.483 42.857 0.00 0.00 44.61 3.02
167 195 2.892215 TCAAATGGCATCAGCACTCAAA 59.108 40.909 0.00 0.00 44.61 2.69
178 206 6.449698 CATCAGCACTCAAAAACACCTATTT 58.550 36.000 0.00 0.00 0.00 1.40
190 218 8.940952 CAAAAACACCTATTTCCAAGTGAAAAA 58.059 29.630 0.00 0.00 45.67 1.94
226 254 2.413142 GGCAGAGGTTGATGCAGGC 61.413 63.158 0.00 0.00 44.37 4.85
376 412 5.163509 CCTCACGAGATTGACCTCAAGAATA 60.164 44.000 0.00 0.00 39.47 1.75
428 465 0.615261 GAGAGGGAGAAGAACGGGGT 60.615 60.000 0.00 0.00 0.00 4.95
614 651 1.506718 CGTCGCTAGCAAGAGGTCA 59.493 57.895 16.45 0.00 0.00 4.02
652 692 1.817099 CTCCTGCCATTCGCCAGAC 60.817 63.158 0.00 0.00 36.24 3.51
721 763 6.098124 AGGGGAATCAATTTGCATCGATTTTA 59.902 34.615 0.00 0.00 0.00 1.52
757 958 1.666888 GGCGAACGTAAGAGGAAACGA 60.667 52.381 1.45 0.00 41.55 3.85
783 984 9.987272 AAACACTACGTTTCTTTTAGGTAGTAT 57.013 29.630 0.00 0.00 44.78 2.12
829 3015 0.175531 CAAATGACGGAAATGCCCCC 59.824 55.000 0.00 0.00 0.00 5.40
945 3131 4.308458 CGAAGCCCACCACCGACA 62.308 66.667 0.00 0.00 0.00 4.35
947 3133 1.527380 GAAGCCCACCACCGACAAA 60.527 57.895 0.00 0.00 0.00 2.83
949 3135 2.203294 GCCCACCACCGACAAACT 60.203 61.111 0.00 0.00 0.00 2.66
1042 3496 1.148273 TTTCTGCTCCTGTTGGCGT 59.852 52.632 0.00 0.00 0.00 5.68
1231 3685 2.656069 GCCGGCTTCTGGGACTACA 61.656 63.158 22.15 0.00 0.00 2.74
1336 3790 3.691342 CCTTCCTCGGCCACGTCA 61.691 66.667 2.24 0.00 41.85 4.35
1415 3869 5.187186 GTGCCTTCCGGGATATAGAGAAATA 59.813 44.000 0.00 0.00 37.23 1.40
1416 3870 5.422331 TGCCTTCCGGGATATAGAGAAATAG 59.578 44.000 0.00 0.00 37.23 1.73
1433 3887 6.711277 AGAAATAGACATCTGCCAGTAACAA 58.289 36.000 0.00 0.00 0.00 2.83
1442 3896 7.370383 ACATCTGCCAGTAACAATTTTAACTG 58.630 34.615 0.00 4.54 39.22 3.16
1509 3963 1.202065 CCGGATGCAACGAAATGTGAG 60.202 52.381 14.75 0.00 0.00 3.51
1517 3976 4.688879 TGCAACGAAATGTGAGTTAGGTAG 59.311 41.667 0.00 0.00 0.00 3.18
1518 3977 4.689345 GCAACGAAATGTGAGTTAGGTAGT 59.311 41.667 0.00 0.00 0.00 2.73
1519 3978 5.865552 GCAACGAAATGTGAGTTAGGTAGTA 59.134 40.000 0.00 0.00 0.00 1.82
1520 3979 6.183360 GCAACGAAATGTGAGTTAGGTAGTAC 60.183 42.308 0.00 0.00 0.00 2.73
1521 3980 6.579666 ACGAAATGTGAGTTAGGTAGTACA 57.420 37.500 2.06 0.00 0.00 2.90
1540 3999 9.106070 GTAGTACAGTATTTAGTTTCCATTGGG 57.894 37.037 2.09 0.00 0.00 4.12
1693 4155 8.489489 TCAGAAGATTCATTCTACTAATTGCCT 58.511 33.333 0.00 0.00 37.43 4.75
1722 4184 2.969262 TCACTGGGAGTGTAACACATCA 59.031 45.455 3.75 0.00 46.03 3.07
1730 4192 7.857456 TGGGAGTGTAACACATCATATAGTTT 58.143 34.615 0.00 0.00 41.43 2.66
1769 4231 5.059833 CCTAAAGGTGATAATCAGGAGTGC 58.940 45.833 0.00 0.00 0.00 4.40
1770 4232 4.574674 AAAGGTGATAATCAGGAGTGCA 57.425 40.909 0.00 0.00 0.00 4.57
1797 4259 6.497259 TCTCATATTACTGGATGGTTACTCCC 59.503 42.308 0.00 0.00 34.77 4.30
2006 4472 5.239963 CAGTTGTTGTTAATTAGGAACCGGT 59.760 40.000 0.00 0.00 0.00 5.28
2033 4499 7.154656 GGGTTTAGCTGTTGATTTTGAATCTT 58.845 34.615 0.00 0.00 0.00 2.40
2463 4929 2.537143 AGTCCCGACTCATAACCAAGT 58.463 47.619 0.00 0.00 36.92 3.16
2487 4953 7.389884 AGTTGCATGTCAGATCCATGTATATTC 59.610 37.037 10.81 0.00 41.38 1.75
2488 4954 6.175471 TGCATGTCAGATCCATGTATATTCC 58.825 40.000 10.81 0.00 41.38 3.01
2496 4962 5.726793 AGATCCATGTATATTCCCCCTGTAC 59.273 44.000 0.00 0.00 0.00 2.90
2505 4971 2.053747 TCCCCCTGTACATTTGAGGT 57.946 50.000 0.00 0.00 0.00 3.85
2522 4988 0.950116 GGTGCAGCTATCTTGCATCC 59.050 55.000 9.07 3.68 40.84 3.51
2524 4990 1.162181 TGCAGCTATCTTGCATCCGC 61.162 55.000 0.00 0.00 39.24 5.54
2542 5008 4.109766 TCCGCAACGATAGAAGTATTGTG 58.890 43.478 0.00 0.00 34.01 3.33
2548 5014 6.675486 GCAACGATAGAAGTATTGTGTGCAAT 60.675 38.462 0.00 0.00 43.30 3.56
2565 5031 9.914131 TGTGTGCAATTCTATATGATAGTACTC 57.086 33.333 0.00 0.00 0.00 2.59
2566 5032 9.360093 GTGTGCAATTCTATATGATAGTACTCC 57.640 37.037 0.00 0.00 0.00 3.85
2567 5033 8.531982 TGTGCAATTCTATATGATAGTACTCCC 58.468 37.037 0.00 0.00 0.00 4.30
2568 5034 8.754080 GTGCAATTCTATATGATAGTACTCCCT 58.246 37.037 0.00 0.00 0.00 4.20
2569 5035 8.972127 TGCAATTCTATATGATAGTACTCCCTC 58.028 37.037 0.00 0.00 0.00 4.30
2570 5036 8.417884 GCAATTCTATATGATAGTACTCCCTCC 58.582 40.741 0.00 0.00 0.00 4.30
2571 5037 8.625651 CAATTCTATATGATAGTACTCCCTCCG 58.374 40.741 0.00 0.00 0.00 4.63
2572 5038 6.887886 TCTATATGATAGTACTCCCTCCGT 57.112 41.667 0.00 0.00 0.00 4.69
2573 5039 7.268212 TCTATATGATAGTACTCCCTCCGTT 57.732 40.000 0.00 0.00 0.00 4.44
2574 5040 7.696981 TCTATATGATAGTACTCCCTCCGTTT 58.303 38.462 0.00 0.00 0.00 3.60
2575 5041 8.168725 TCTATATGATAGTACTCCCTCCGTTTT 58.831 37.037 0.00 0.00 0.00 2.43
2576 5042 5.952347 ATGATAGTACTCCCTCCGTTTTT 57.048 39.130 0.00 0.00 0.00 1.94
2577 5043 8.716674 ATATGATAGTACTCCCTCCGTTTTTA 57.283 34.615 0.00 0.00 0.00 1.52
2578 5044 7.613551 ATGATAGTACTCCCTCCGTTTTTAT 57.386 36.000 0.00 0.00 0.00 1.40
2579 5045 7.427989 TGATAGTACTCCCTCCGTTTTTATT 57.572 36.000 0.00 0.00 0.00 1.40
2580 5046 7.854337 TGATAGTACTCCCTCCGTTTTTATTT 58.146 34.615 0.00 0.00 0.00 1.40
2581 5047 8.980596 TGATAGTACTCCCTCCGTTTTTATTTA 58.019 33.333 0.00 0.00 0.00 1.40
2582 5048 9.473640 GATAGTACTCCCTCCGTTTTTATTTAG 57.526 37.037 0.00 0.00 0.00 1.85
2583 5049 7.250032 AGTACTCCCTCCGTTTTTATTTAGT 57.750 36.000 0.00 0.00 0.00 2.24
2584 5050 7.326454 AGTACTCCCTCCGTTTTTATTTAGTC 58.674 38.462 0.00 0.00 0.00 2.59
2585 5051 5.494724 ACTCCCTCCGTTTTTATTTAGTCC 58.505 41.667 0.00 0.00 0.00 3.85
2586 5052 4.506758 TCCCTCCGTTTTTATTTAGTCCG 58.493 43.478 0.00 0.00 0.00 4.79
2587 5053 3.064408 CCCTCCGTTTTTATTTAGTCCGC 59.936 47.826 0.00 0.00 0.00 5.54
2588 5054 3.685756 CCTCCGTTTTTATTTAGTCCGCA 59.314 43.478 0.00 0.00 0.00 5.69
2589 5055 4.334481 CCTCCGTTTTTATTTAGTCCGCAT 59.666 41.667 0.00 0.00 0.00 4.73
2590 5056 5.524646 CCTCCGTTTTTATTTAGTCCGCATA 59.475 40.000 0.00 0.00 0.00 3.14
2591 5057 6.204108 CCTCCGTTTTTATTTAGTCCGCATAT 59.796 38.462 0.00 0.00 0.00 1.78
2592 5058 7.255001 CCTCCGTTTTTATTTAGTCCGCATATT 60.255 37.037 0.00 0.00 0.00 1.28
2593 5059 8.659925 TCCGTTTTTATTTAGTCCGCATATTA 57.340 30.769 0.00 0.00 0.00 0.98
2594 5060 8.767085 TCCGTTTTTATTTAGTCCGCATATTAG 58.233 33.333 0.00 0.00 0.00 1.73
2595 5061 7.532884 CCGTTTTTATTTAGTCCGCATATTAGC 59.467 37.037 0.00 0.00 0.00 3.09
2596 5062 8.280497 CGTTTTTATTTAGTCCGCATATTAGCT 58.720 33.333 0.00 0.00 0.00 3.32
2597 5063 9.946165 GTTTTTATTTAGTCCGCATATTAGCTT 57.054 29.630 0.00 0.00 0.00 3.74
2599 5065 9.944663 TTTTATTTAGTCCGCATATTAGCTTTG 57.055 29.630 0.00 0.00 0.00 2.77
2600 5066 6.560253 ATTTAGTCCGCATATTAGCTTTGG 57.440 37.500 0.00 0.00 0.00 3.28
2601 5067 3.560636 AGTCCGCATATTAGCTTTGGT 57.439 42.857 0.00 0.00 0.00 3.67
2602 5068 3.467803 AGTCCGCATATTAGCTTTGGTC 58.532 45.455 0.00 0.00 0.00 4.02
2603 5069 3.118408 AGTCCGCATATTAGCTTTGGTCA 60.118 43.478 0.00 0.00 0.00 4.02
2604 5070 3.625764 GTCCGCATATTAGCTTTGGTCAA 59.374 43.478 0.00 0.00 0.00 3.18
2605 5071 4.095782 GTCCGCATATTAGCTTTGGTCAAA 59.904 41.667 0.00 0.00 0.00 2.69
2627 5093 7.812309 AAAGTCAAGCTTTGTAAACTTTGAC 57.188 32.000 14.76 14.88 45.00 3.18
2628 5094 6.759497 AGTCAAGCTTTGTAAACTTTGACT 57.241 33.333 17.37 17.37 32.23 3.41
2629 5095 7.859325 AGTCAAGCTTTGTAAACTTTGACTA 57.141 32.000 19.57 0.00 33.77 2.59
2630 5096 8.276252 AGTCAAGCTTTGTAAACTTTGACTAA 57.724 30.769 19.57 0.00 33.77 2.24
2631 5097 8.398665 AGTCAAGCTTTGTAAACTTTGACTAAG 58.601 33.333 19.57 3.76 39.87 2.18
2767 5233 9.823647 TTTCTATAAATTTGGTCAAACTTTGCA 57.176 25.926 0.00 0.00 32.51 4.08
2768 5234 9.823647 TTCTATAAATTTGGTCAAACTTTGCAA 57.176 25.926 0.00 0.00 32.51 4.08
2769 5235 9.823647 TCTATAAATTTGGTCAAACTTTGCAAA 57.176 25.926 12.14 12.14 32.51 3.68
2781 5247 3.769536 ACTTTGCAAAGTTTGACTTCGG 58.230 40.909 33.85 11.40 46.52 4.30
2782 5248 3.192633 ACTTTGCAAAGTTTGACTTCGGT 59.807 39.130 33.85 12.02 46.52 4.69
2783 5249 3.414549 TTGCAAAGTTTGACTTCGGTC 57.585 42.857 19.82 0.00 37.47 4.79
2796 5262 5.405331 GACTTCGGTCAAACCTAATATGC 57.595 43.478 0.00 0.00 43.91 3.14
2797 5263 4.839121 ACTTCGGTCAAACCTAATATGCA 58.161 39.130 0.00 0.00 35.66 3.96
2798 5264 4.876107 ACTTCGGTCAAACCTAATATGCAG 59.124 41.667 0.00 0.00 35.66 4.41
2799 5265 4.746535 TCGGTCAAACCTAATATGCAGA 57.253 40.909 0.00 0.00 35.66 4.26
2800 5266 4.439057 TCGGTCAAACCTAATATGCAGAC 58.561 43.478 0.00 0.00 35.66 3.51
2801 5267 4.161565 TCGGTCAAACCTAATATGCAGACT 59.838 41.667 0.00 0.00 35.66 3.24
2802 5268 4.271049 CGGTCAAACCTAATATGCAGACTG 59.729 45.833 0.00 0.00 35.66 3.51
2803 5269 5.428253 GGTCAAACCTAATATGCAGACTGA 58.572 41.667 6.65 0.00 34.73 3.41
2804 5270 5.880332 GGTCAAACCTAATATGCAGACTGAA 59.120 40.000 6.65 0.00 34.73 3.02
2805 5271 6.543831 GGTCAAACCTAATATGCAGACTGAAT 59.456 38.462 6.65 3.39 34.73 2.57
2806 5272 7.715249 GGTCAAACCTAATATGCAGACTGAATA 59.285 37.037 6.65 6.06 34.73 1.75
2807 5273 9.109393 GTCAAACCTAATATGCAGACTGAATAA 57.891 33.333 7.25 0.00 0.00 1.40
2808 5274 9.679661 TCAAACCTAATATGCAGACTGAATAAA 57.320 29.630 7.25 0.00 0.00 1.40
2812 5278 8.612619 ACCTAATATGCAGACTGAATAAAAACG 58.387 33.333 7.25 0.00 0.00 3.60
2813 5279 8.070171 CCTAATATGCAGACTGAATAAAAACGG 58.930 37.037 7.25 1.34 0.00 4.44
2814 5280 7.624360 AATATGCAGACTGAATAAAAACGGA 57.376 32.000 7.25 0.00 0.00 4.69
2815 5281 5.551760 ATGCAGACTGAATAAAAACGGAG 57.448 39.130 6.65 0.00 0.00 4.63
2816 5282 3.751175 TGCAGACTGAATAAAAACGGAGG 59.249 43.478 6.65 0.00 0.00 4.30
2817 5283 3.127030 GCAGACTGAATAAAAACGGAGGG 59.873 47.826 6.65 0.00 0.00 4.30
2818 5284 4.575885 CAGACTGAATAAAAACGGAGGGA 58.424 43.478 0.00 0.00 0.00 4.20
2819 5285 4.631813 CAGACTGAATAAAAACGGAGGGAG 59.368 45.833 0.00 0.00 0.00 4.30
2820 5286 4.286291 AGACTGAATAAAAACGGAGGGAGT 59.714 41.667 0.00 0.00 0.00 3.85
2852 5318 0.315251 CTCTGAGGACGACTGTTGCA 59.685 55.000 0.00 0.00 0.00 4.08
2854 5320 2.164422 CTCTGAGGACGACTGTTGCATA 59.836 50.000 0.00 0.00 0.00 3.14
2861 5327 3.930229 GGACGACTGTTGCATATGTGTAA 59.070 43.478 4.29 0.00 0.00 2.41
2902 5371 2.572104 AGCCCGTAACCTTCTCTCATTT 59.428 45.455 0.00 0.00 0.00 2.32
3028 5505 4.396790 CGTGGCCCTTTGCTTTTATAAGTA 59.603 41.667 0.00 0.00 40.92 2.24
3029 5506 5.106078 CGTGGCCCTTTGCTTTTATAAGTAA 60.106 40.000 0.00 0.00 40.92 2.24
3084 5561 2.453983 GCAAAAACCTGCCATTGCTA 57.546 45.000 2.33 0.00 43.58 3.49
3222 5701 4.222588 TGGCATTTTCTCTATTTTGGGGTG 59.777 41.667 0.00 0.00 0.00 4.61
3249 5731 5.295431 TGTGATGTTAATTTTCAGAGGCG 57.705 39.130 0.00 0.00 0.00 5.52
3301 5787 1.491754 ACAGACATATGGGAGCATGCA 59.508 47.619 21.98 0.00 0.00 3.96
3334 5820 5.652744 AGATATCACGGCGAACATAAAAC 57.347 39.130 16.62 3.43 0.00 2.43
3366 5852 9.132521 CAACACCTCAAAATCTATTGTGAATTC 57.867 33.333 0.00 0.00 33.86 2.17
3393 5879 5.071788 AGAGATAACAAGTGTGGGAGTTCAA 59.928 40.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 3.873361 CGAGCATGGCTGAGAAAAGAATA 59.127 43.478 0.00 0.00 39.88 1.75
66 70 0.738389 CAACAAGTGGCAACTCCGTT 59.262 50.000 0.00 0.00 34.77 4.44
76 80 2.086869 CACTATCCCAGCAACAAGTGG 58.913 52.381 0.00 0.00 32.60 4.00
87 92 5.269189 TCTTCTACACATGTCACTATCCCA 58.731 41.667 0.00 0.00 0.00 4.37
190 218 2.031870 GCCTGAACAACCTCCAACTTT 58.968 47.619 0.00 0.00 0.00 2.66
376 412 2.632537 TGCTCCTTTAACTCTTCCCCT 58.367 47.619 0.00 0.00 0.00 4.79
614 651 4.473520 CGCGCACTCCCCTTCCAT 62.474 66.667 8.75 0.00 0.00 3.41
642 679 3.470888 CTCCCCCGTCTGGCGAAT 61.471 66.667 1.87 0.00 44.77 3.34
671 711 0.326904 ATCCCACCTCTGATCTGGCA 60.327 55.000 0.00 0.00 0.00 4.92
721 763 1.375326 GCCCTCTTCGTCCAACCTT 59.625 57.895 0.00 0.00 0.00 3.50
783 984 8.318412 CAGCAGGAGTATCTCTACTTCTCTATA 58.682 40.741 0.00 0.00 41.17 1.31
785 986 6.530120 CAGCAGGAGTATCTCTACTTCTCTA 58.470 44.000 0.00 0.00 41.17 2.43
797 2983 2.286294 CGTCATTTGCAGCAGGAGTATC 59.714 50.000 0.00 0.00 0.00 2.24
800 2986 0.957395 CCGTCATTTGCAGCAGGAGT 60.957 55.000 0.00 0.00 0.00 3.85
801 2987 0.674581 TCCGTCATTTGCAGCAGGAG 60.675 55.000 0.00 0.00 0.00 3.69
802 2988 0.250684 TTCCGTCATTTGCAGCAGGA 60.251 50.000 0.00 0.00 0.00 3.86
945 3131 2.304470 GCTGGAAGAGAAGGAGGAGTTT 59.696 50.000 0.00 0.00 34.07 2.66
947 3133 1.078656 AGCTGGAAGAGAAGGAGGAGT 59.921 52.381 0.00 0.00 34.07 3.85
949 3135 2.183679 GAAGCTGGAAGAGAAGGAGGA 58.816 52.381 0.00 0.00 34.07 3.71
1231 3685 2.044946 GGCGGTGATGAAGGCCTT 60.045 61.111 20.65 20.65 42.29 4.35
1336 3790 2.273179 TACACGAGGTCTTGGCGCT 61.273 57.895 7.64 0.00 0.00 5.92
1415 3869 7.448469 AGTTAAAATTGTTACTGGCAGATGTCT 59.552 33.333 23.66 0.00 0.00 3.41
1416 3870 7.538678 CAGTTAAAATTGTTACTGGCAGATGTC 59.461 37.037 23.66 8.92 35.51 3.06
1433 3887 9.860898 GAAATTCATGAAGCCTACAGTTAAAAT 57.139 29.630 14.54 0.00 0.00 1.82
1517 3976 8.747538 ATCCCAATGGAAACTAAATACTGTAC 57.252 34.615 0.00 0.00 45.98 2.90
1519 3978 8.557450 ACTATCCCAATGGAAACTAAATACTGT 58.443 33.333 0.00 0.00 45.98 3.55
1520 3979 8.840321 CACTATCCCAATGGAAACTAAATACTG 58.160 37.037 0.00 0.00 45.98 2.74
1521 3980 8.557450 ACACTATCCCAATGGAAACTAAATACT 58.443 33.333 0.00 0.00 45.98 2.12
1540 3999 6.825721 AGGAACCATTCTGATGAAACACTATC 59.174 38.462 0.00 0.00 35.63 2.08
1683 4145 5.415701 CCAGTGAACATGTAAGGCAATTAGT 59.584 40.000 0.00 0.00 0.00 2.24
1684 4146 5.163622 CCCAGTGAACATGTAAGGCAATTAG 60.164 44.000 0.00 0.00 0.00 1.73
1769 4231 9.429359 GAGTAACCATCCAGTAATATGAGATTG 57.571 37.037 0.00 0.00 0.00 2.67
1770 4232 8.598041 GGAGTAACCATCCAGTAATATGAGATT 58.402 37.037 0.00 0.00 36.79 2.40
1797 4259 5.048364 GTCAGCTAGACTATATCCACCTGTG 60.048 48.000 0.00 0.00 44.09 3.66
2006 4472 5.860941 TCAAAATCAACAGCTAAACCCAA 57.139 34.783 0.00 0.00 0.00 4.12
2012 4478 8.632679 ACAAGAAGATTCAAAATCAACAGCTAA 58.367 29.630 2.79 0.00 0.00 3.09
2133 4599 2.385013 TCGCTGCTTCAAATGCTAGA 57.615 45.000 0.00 0.00 0.00 2.43
2458 4924 2.439409 TGGATCTGACATGCAACTTGG 58.561 47.619 0.00 0.00 0.00 3.61
2487 4953 1.955208 GCACCTCAAATGTACAGGGGG 60.955 57.143 0.33 5.52 30.48 5.40
2488 4954 1.271871 TGCACCTCAAATGTACAGGGG 60.272 52.381 0.33 0.00 33.33 4.79
2496 4962 3.488721 GCAAGATAGCTGCACCTCAAATG 60.489 47.826 1.02 0.00 0.00 2.32
2505 4971 1.162181 GCGGATGCAAGATAGCTGCA 61.162 55.000 1.02 7.40 43.04 4.41
2522 4988 4.779082 GCACACAATACTTCTATCGTTGCG 60.779 45.833 0.00 0.00 0.00 4.85
2524 4990 5.778161 TGCACACAATACTTCTATCGTTG 57.222 39.130 0.00 0.00 0.00 4.10
2542 5008 8.754080 AGGGAGTACTATCATATAGAATTGCAC 58.246 37.037 0.00 0.00 0.00 4.57
2548 5014 7.268212 ACGGAGGGAGTACTATCATATAGAA 57.732 40.000 0.00 0.00 0.00 2.10
2562 5028 5.494724 GGACTAAATAAAAACGGAGGGAGT 58.505 41.667 0.00 0.00 0.00 3.85
2563 5029 4.569564 CGGACTAAATAAAAACGGAGGGAG 59.430 45.833 0.00 0.00 0.00 4.30
2564 5030 4.506758 CGGACTAAATAAAAACGGAGGGA 58.493 43.478 0.00 0.00 0.00 4.20
2565 5031 3.064408 GCGGACTAAATAAAAACGGAGGG 59.936 47.826 0.00 0.00 0.00 4.30
2566 5032 3.685756 TGCGGACTAAATAAAAACGGAGG 59.314 43.478 0.00 0.00 0.00 4.30
2567 5033 4.932268 TGCGGACTAAATAAAAACGGAG 57.068 40.909 0.00 0.00 0.00 4.63
2568 5034 7.556733 AATATGCGGACTAAATAAAAACGGA 57.443 32.000 0.00 0.00 0.00 4.69
2569 5035 7.532884 GCTAATATGCGGACTAAATAAAAACGG 59.467 37.037 0.00 0.00 0.00 4.44
2570 5036 8.280497 AGCTAATATGCGGACTAAATAAAAACG 58.720 33.333 0.00 0.00 38.13 3.60
2571 5037 9.946165 AAGCTAATATGCGGACTAAATAAAAAC 57.054 29.630 0.00 0.00 38.13 2.43
2573 5039 9.944663 CAAAGCTAATATGCGGACTAAATAAAA 57.055 29.630 0.00 0.00 38.13 1.52
2574 5040 8.564574 CCAAAGCTAATATGCGGACTAAATAAA 58.435 33.333 0.00 0.00 38.13 1.40
2575 5041 7.717875 ACCAAAGCTAATATGCGGACTAAATAA 59.282 33.333 0.00 0.00 38.13 1.40
2576 5042 7.221450 ACCAAAGCTAATATGCGGACTAAATA 58.779 34.615 0.00 0.00 38.13 1.40
2577 5043 6.062095 ACCAAAGCTAATATGCGGACTAAAT 58.938 36.000 0.00 0.00 38.13 1.40
2578 5044 5.433526 ACCAAAGCTAATATGCGGACTAAA 58.566 37.500 0.00 0.00 38.13 1.85
2579 5045 5.031066 ACCAAAGCTAATATGCGGACTAA 57.969 39.130 0.00 0.00 38.13 2.24
2580 5046 4.100344 TGACCAAAGCTAATATGCGGACTA 59.900 41.667 0.00 0.00 38.13 2.59
2581 5047 3.118408 TGACCAAAGCTAATATGCGGACT 60.118 43.478 0.00 0.00 38.13 3.85
2582 5048 3.202906 TGACCAAAGCTAATATGCGGAC 58.797 45.455 0.00 0.00 38.13 4.79
2583 5049 3.552132 TGACCAAAGCTAATATGCGGA 57.448 42.857 0.00 0.00 38.13 5.54
2584 5050 4.601019 CTTTGACCAAAGCTAATATGCGG 58.399 43.478 9.25 0.00 40.94 5.69
2604 5070 7.158099 AGTCAAAGTTTACAAAGCTTGACTT 57.842 32.000 17.55 3.36 42.47 3.01
2605 5071 6.759497 AGTCAAAGTTTACAAAGCTTGACT 57.241 33.333 17.55 17.55 41.47 3.41
2606 5072 8.182227 ACTTAGTCAAAGTTTACAAAGCTTGAC 58.818 33.333 0.00 14.97 46.61 3.18
2607 5073 8.276252 ACTTAGTCAAAGTTTACAAAGCTTGA 57.724 30.769 0.00 0.00 46.61 3.02
2741 5207 9.823647 TGCAAAGTTTGACCAAATTTATAGAAA 57.176 25.926 19.82 0.00 31.37 2.52
2742 5208 9.823647 TTGCAAAGTTTGACCAAATTTATAGAA 57.176 25.926 19.82 0.00 31.37 2.10
2743 5209 9.823647 TTTGCAAAGTTTGACCAAATTTATAGA 57.176 25.926 19.82 0.00 31.37 1.98
2745 5211 9.606631 ACTTTGCAAAGTTTGACCAAATTTATA 57.393 25.926 33.85 0.00 46.52 0.98
2746 5212 8.504812 ACTTTGCAAAGTTTGACCAAATTTAT 57.495 26.923 33.85 10.04 46.52 1.40
2747 5213 7.913674 ACTTTGCAAAGTTTGACCAAATTTA 57.086 28.000 33.85 0.00 46.52 1.40
2748 5214 6.816134 ACTTTGCAAAGTTTGACCAAATTT 57.184 29.167 33.85 11.08 46.52 1.82
2759 5225 6.128842 GACCGAAGTCAAACTTTGCAAAGTT 61.129 40.000 39.24 39.24 45.31 2.66
2760 5226 4.674362 GACCGAAGTCAAACTTTGCAAAGT 60.674 41.667 33.85 33.85 45.47 2.66
2761 5227 3.769536 ACCGAAGTCAAACTTTGCAAAG 58.230 40.909 32.53 32.53 38.80 2.77
2762 5228 3.765026 GACCGAAGTCAAACTTTGCAAA 58.235 40.909 12.14 12.14 38.80 3.68
2763 5229 3.414549 GACCGAAGTCAAACTTTGCAA 57.585 42.857 0.00 0.00 38.80 4.08
2774 5240 4.873827 TGCATATTAGGTTTGACCGAAGTC 59.126 41.667 0.00 0.00 44.90 3.01
2775 5241 4.839121 TGCATATTAGGTTTGACCGAAGT 58.161 39.130 0.00 0.00 44.90 3.01
2776 5242 5.006746 GTCTGCATATTAGGTTTGACCGAAG 59.993 44.000 0.00 0.00 44.90 3.79
2777 5243 4.873827 GTCTGCATATTAGGTTTGACCGAA 59.126 41.667 0.00 0.00 44.90 4.30
2778 5244 4.161565 AGTCTGCATATTAGGTTTGACCGA 59.838 41.667 0.00 0.00 44.90 4.69
2779 5245 4.271049 CAGTCTGCATATTAGGTTTGACCG 59.729 45.833 0.00 0.00 44.90 4.79
2780 5246 5.428253 TCAGTCTGCATATTAGGTTTGACC 58.572 41.667 0.00 0.00 38.99 4.02
2781 5247 6.985188 TTCAGTCTGCATATTAGGTTTGAC 57.015 37.500 0.00 0.00 0.00 3.18
2782 5248 9.679661 TTTATTCAGTCTGCATATTAGGTTTGA 57.320 29.630 0.00 0.00 0.00 2.69
2786 5252 8.612619 CGTTTTTATTCAGTCTGCATATTAGGT 58.387 33.333 0.00 0.00 0.00 3.08
2787 5253 8.070171 CCGTTTTTATTCAGTCTGCATATTAGG 58.930 37.037 0.00 0.00 0.00 2.69
2788 5254 8.826710 TCCGTTTTTATTCAGTCTGCATATTAG 58.173 33.333 0.00 0.00 0.00 1.73
2789 5255 8.725405 TCCGTTTTTATTCAGTCTGCATATTA 57.275 30.769 0.00 0.00 0.00 0.98
2790 5256 7.201732 CCTCCGTTTTTATTCAGTCTGCATATT 60.202 37.037 0.00 0.00 0.00 1.28
2791 5257 6.260936 CCTCCGTTTTTATTCAGTCTGCATAT 59.739 38.462 0.00 0.00 0.00 1.78
2792 5258 5.584649 CCTCCGTTTTTATTCAGTCTGCATA 59.415 40.000 0.00 0.00 0.00 3.14
2793 5259 4.396166 CCTCCGTTTTTATTCAGTCTGCAT 59.604 41.667 0.00 0.00 0.00 3.96
2794 5260 3.751175 CCTCCGTTTTTATTCAGTCTGCA 59.249 43.478 0.00 0.00 0.00 4.41
2795 5261 3.127030 CCCTCCGTTTTTATTCAGTCTGC 59.873 47.826 0.00 0.00 0.00 4.26
2796 5262 4.575885 TCCCTCCGTTTTTATTCAGTCTG 58.424 43.478 0.00 0.00 0.00 3.51
2797 5263 4.286291 ACTCCCTCCGTTTTTATTCAGTCT 59.714 41.667 0.00 0.00 0.00 3.24
2798 5264 4.576879 ACTCCCTCCGTTTTTATTCAGTC 58.423 43.478 0.00 0.00 0.00 3.51
2799 5265 4.635699 ACTCCCTCCGTTTTTATTCAGT 57.364 40.909 0.00 0.00 0.00 3.41
2800 5266 7.625828 AAATACTCCCTCCGTTTTTATTCAG 57.374 36.000 0.00 0.00 0.00 3.02
2801 5267 9.689501 AATAAATACTCCCTCCGTTTTTATTCA 57.310 29.630 0.00 0.00 35.52 2.57
2806 5272 9.828039 CTACTAATAAATACTCCCTCCGTTTTT 57.172 33.333 0.00 0.00 0.00 1.94
2807 5273 7.930325 GCTACTAATAAATACTCCCTCCGTTTT 59.070 37.037 0.00 0.00 0.00 2.43
2808 5274 7.289549 AGCTACTAATAAATACTCCCTCCGTTT 59.710 37.037 0.00 0.00 0.00 3.60
2809 5275 6.781507 AGCTACTAATAAATACTCCCTCCGTT 59.218 38.462 0.00 0.00 0.00 4.44
2810 5276 6.313324 AGCTACTAATAAATACTCCCTCCGT 58.687 40.000 0.00 0.00 0.00 4.69
2811 5277 6.660094 AGAGCTACTAATAAATACTCCCTCCG 59.340 42.308 0.00 0.00 0.00 4.63
2812 5278 7.670559 TCAGAGCTACTAATAAATACTCCCTCC 59.329 40.741 0.00 0.00 0.00 4.30
2813 5279 8.638629 TCAGAGCTACTAATAAATACTCCCTC 57.361 38.462 0.00 0.00 0.00 4.30
2814 5280 7.672239 CCTCAGAGCTACTAATAAATACTCCCT 59.328 40.741 0.00 0.00 0.00 4.20
2815 5281 7.670559 TCCTCAGAGCTACTAATAAATACTCCC 59.329 40.741 0.00 0.00 0.00 4.30
2816 5282 8.517056 GTCCTCAGAGCTACTAATAAATACTCC 58.483 40.741 0.00 0.00 0.00 3.85
2817 5283 8.231837 CGTCCTCAGAGCTACTAATAAATACTC 58.768 40.741 0.00 0.00 0.00 2.59
2818 5284 7.937942 TCGTCCTCAGAGCTACTAATAAATACT 59.062 37.037 0.00 0.00 0.00 2.12
2819 5285 8.016801 GTCGTCCTCAGAGCTACTAATAAATAC 58.983 40.741 0.00 0.00 0.00 1.89
2820 5286 7.937942 AGTCGTCCTCAGAGCTACTAATAAATA 59.062 37.037 0.00 0.00 0.00 1.40
2861 5327 7.159372 CGGGCTTACATAAATAGGTTACAGAT 58.841 38.462 0.00 0.00 0.00 2.90
2912 5381 7.366847 AGTTCTCTGCTGTAATATACATGGT 57.633 36.000 0.00 0.00 38.15 3.55
3008 5483 6.931838 AGTTTACTTATAAAAGCAAAGGGCC 58.068 36.000 0.00 0.00 46.50 5.80
3028 5505 3.142174 GACAGGAGCAAAGCAGTAGTTT 58.858 45.455 0.00 0.00 0.00 2.66
3029 5506 2.104792 TGACAGGAGCAAAGCAGTAGTT 59.895 45.455 0.00 0.00 0.00 2.24
3084 5561 5.533903 AGCAGTCATTTTCACAGAACAAGAT 59.466 36.000 0.00 0.00 0.00 2.40
3222 5701 8.650714 GCCTCTGAAAATTAACATCACAAAATC 58.349 33.333 0.00 0.00 0.00 2.17
3249 5731 7.759433 CCATAACAAAGTATGGTCAATGTTTCC 59.241 37.037 3.50 0.00 43.84 3.13
3315 5801 3.995048 TGTGTTTTATGTTCGCCGTGATA 59.005 39.130 0.00 0.00 0.00 2.15
3334 5820 6.808008 ATAGATTTTGAGGTGTTGACTGTG 57.192 37.500 0.00 0.00 0.00 3.66
3366 5852 4.248859 CTCCCACACTTGTTATCTCTGTG 58.751 47.826 0.00 0.00 33.45 3.66
3371 5857 4.974645 TGAACTCCCACACTTGTTATCT 57.025 40.909 0.00 0.00 0.00 1.98
3393 5879 5.989477 TGTAGTGCTGTAAGAATATGCCTT 58.011 37.500 0.00 0.00 34.07 4.35


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

AutoCloner maintained by Alex Coulton.