Multiple sequence alignment - TraesCS7A01G183200

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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 TraesCS7A01G183200 chr7A 100.000 3140 0 0 1 3140 138165076 138161937 0.000000e+00 5799.0
1 TraesCS7A01G183200 chr7D 91.164 2535 178 16 1 2530 138194881 138192388 0.000000e+00 3398.0
2 TraesCS7A01G183200 chr7D 84.505 697 87 8 1 681 511647775 511648466 0.000000e+00 669.0
3 TraesCS7A01G183200 chr7D 83.588 524 48 20 2641 3136 138192384 138191871 1.030000e-124 457.0
4 TraesCS7A01G183200 chr7B 95.565 1601 60 4 928 2527 103573059 103571469 0.000000e+00 2553.0
5 TraesCS7A01G183200 chr7B 84.835 699 84 14 17 696 544408704 544409399 0.000000e+00 684.0
6 TraesCS7A01G183200 chr7B 96.259 294 10 1 2632 2925 103571470 103571178 6.090000e-132 481.0
7 TraesCS7A01G183200 chr7B 95.434 219 10 0 2922 3140 103571029 103570811 1.790000e-92 350.0
8 TraesCS7A01G183200 chr7B 94.400 125 4 3 2526 2647 201497398 201497274 4.130000e-44 189.0
9 TraesCS7A01G183200 chr7B 88.636 132 3 4 755 886 103574572 103574453 1.950000e-32 150.0
10 TraesCS7A01G183200 chr2D 84.182 727 103 10 39 756 552067674 552066951 0.000000e+00 695.0
11 TraesCS7A01G183200 chr4B 84.441 707 89 14 1 694 634182153 634182851 0.000000e+00 676.0
12 TraesCS7A01G183200 chr2B 84.897 682 84 15 18 694 491707747 491707080 0.000000e+00 671.0
13 TraesCS7A01G183200 chr2B 99.123 114 0 1 2526 2638 456339449 456339336 1.480000e-48 204.0
14 TraesCS7A01G183200 chr4D 82.937 756 113 10 11 756 295426466 295427215 0.000000e+00 667.0
15 TraesCS7A01G183200 chr4A 83.471 726 107 9 33 750 595822869 595823589 0.000000e+00 664.0
16 TraesCS7A01G183200 chr1D 82.438 763 110 14 1 756 303021070 303020325 0.000000e+00 645.0
17 TraesCS7A01G183200 chrUn 95.902 122 5 0 2526 2647 223726651 223726772 6.870000e-47 198.0
18 TraesCS7A01G183200 chrUn 95.902 122 5 0 2526 2647 308507633 308507512 6.870000e-47 198.0
19 TraesCS7A01G183200 chrUn 95.902 122 5 0 2526 2647 308511720 308511599 6.870000e-47 198.0
20 TraesCS7A01G183200 chr6B 84.925 199 22 6 1067 1258 41410317 41410120 8.890000e-46 195.0
21 TraesCS7A01G183200 chr6B 100.000 36 0 0 715 750 251380684 251380649 2.020000e-07 67.6
22 TraesCS7A01G183200 chr1B 77.904 353 50 24 1067 1402 683538591 683538250 8.890000e-46 195.0
23 TraesCS7A01G183200 chr5B 95.082 122 5 1 2517 2638 669302706 669302586 1.150000e-44 191.0
24 TraesCS7A01G183200 chr3A 95.082 122 3 3 2514 2635 642924947 642924829 4.130000e-44 189.0
25 TraesCS7A01G183200 chr1A 94.355 124 6 1 2516 2639 533667884 533667762 4.130000e-44 189.0
26 TraesCS7A01G183200 chr3B 94.215 121 6 1 2514 2633 308390926 308391046 1.920000e-42 183.0


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 TraesCS7A01G183200 chr7A 138161937 138165076 3139 True 5799.0 5799 100.0000 1 3140 1 chr7A.!!$R1 3139
1 TraesCS7A01G183200 chr7D 138191871 138194881 3010 True 1927.5 3398 87.3760 1 3136 2 chr7D.!!$R1 3135
2 TraesCS7A01G183200 chr7D 511647775 511648466 691 False 669.0 669 84.5050 1 681 1 chr7D.!!$F1 680
3 TraesCS7A01G183200 chr7B 103570811 103574572 3761 True 883.5 2553 93.9735 755 3140 4 chr7B.!!$R2 2385
4 TraesCS7A01G183200 chr7B 544408704 544409399 695 False 684.0 684 84.8350 17 696 1 chr7B.!!$F1 679
5 TraesCS7A01G183200 chr2D 552066951 552067674 723 True 695.0 695 84.1820 39 756 1 chr2D.!!$R1 717
6 TraesCS7A01G183200 chr4B 634182153 634182851 698 False 676.0 676 84.4410 1 694 1 chr4B.!!$F1 693
7 TraesCS7A01G183200 chr2B 491707080 491707747 667 True 671.0 671 84.8970 18 694 1 chr2B.!!$R2 676
8 TraesCS7A01G183200 chr4D 295426466 295427215 749 False 667.0 667 82.9370 11 756 1 chr4D.!!$F1 745
9 TraesCS7A01G183200 chr4A 595822869 595823589 720 False 664.0 664 83.4710 33 750 1 chr4A.!!$F1 717
10 TraesCS7A01G183200 chr1D 303020325 303021070 745 True 645.0 645 82.4380 1 756 1 chr1D.!!$R1 755

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
503 539 0.107508 AAGGGCAGTCGTGGATGATG 60.108 55.0 0.0 0.0 0.0 3.07 F
1327 2725 0.036952 CGATGTGGAGCTGAACCTGT 60.037 55.0 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 3412 0.528017 TTCTTCTCAGTCAGCGCGAT 59.472 50.000 12.1 0.0 0.0 4.58 R
2176 3574 1.004044 CCAGAAACATGCTCCCAGACT 59.996 52.381 0.0 0.0 0.0 3.24 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 1.003580 ACTCCATTGTGTCGGCTCAAT 59.996 47.619 11.30 11.30 38.78 2.57
123 124 3.753797 GACAGCCGAAAAATCTCTCCTTT 59.246 43.478 0.00 0.00 0.00 3.11
135 136 1.452108 CTCCTTTCCCATCACCGGC 60.452 63.158 0.00 0.00 0.00 6.13
191 193 3.253838 CCGTGGGAAGGGGTGGAA 61.254 66.667 0.00 0.00 0.00 3.53
193 195 1.303317 CGTGGGAAGGGGTGGAAAG 60.303 63.158 0.00 0.00 0.00 2.62
270 283 2.743718 CGGCCGCATAGGAGGAAT 59.256 61.111 14.67 0.00 45.00 3.01
318 332 3.616721 AGCGGAGGAACACGTGCT 61.617 61.111 17.22 2.15 33.72 4.40
320 334 2.651361 CGGAGGAACACGTGCTCT 59.349 61.111 17.22 10.57 43.96 4.09
324 338 0.885196 GAGGAACACGTGCTCTCTCT 59.115 55.000 17.22 5.66 41.36 3.10
390 425 0.248134 GAAGGAGGACATCGACGACG 60.248 60.000 0.00 0.00 41.26 5.12
470 506 2.970639 CGAGAAGGACGGCAAGGA 59.029 61.111 0.00 0.00 0.00 3.36
503 539 0.107508 AAGGGCAGTCGTGGATGATG 60.108 55.000 0.00 0.00 0.00 3.07
573 609 4.436242 AGTGTAGTGTGATGGAGTAACG 57.564 45.455 0.00 0.00 0.00 3.18
591 628 1.165907 CGGGTGATGTGTGTGCAACT 61.166 55.000 0.00 0.00 38.04 3.16
909 1114 1.100463 TCAGCGGCACAGCAAGAAAA 61.100 50.000 1.45 0.00 40.15 2.29
972 2367 4.760757 GCCTAGCGGTCAATCCTC 57.239 61.111 0.00 0.00 0.00 3.71
973 2368 1.069935 GCCTAGCGGTCAATCCTCC 59.930 63.158 0.00 0.00 0.00 4.30
974 2369 1.403687 GCCTAGCGGTCAATCCTCCT 61.404 60.000 0.00 0.00 0.00 3.69
975 2370 0.676736 CCTAGCGGTCAATCCTCCTC 59.323 60.000 0.00 0.00 0.00 3.71
976 2371 0.676736 CTAGCGGTCAATCCTCCTCC 59.323 60.000 0.00 0.00 0.00 4.30
1059 2457 2.681778 CGCACACCCTCCCTCTCT 60.682 66.667 0.00 0.00 0.00 3.10
1264 2662 2.040442 TCGGCATCTCCCCCTCAA 59.960 61.111 0.00 0.00 0.00 3.02
1265 2663 2.190578 CGGCATCTCCCCCTCAAC 59.809 66.667 0.00 0.00 0.00 3.18
1327 2725 0.036952 CGATGTGGAGCTGAACCTGT 60.037 55.000 0.00 0.00 0.00 4.00
1360 2758 2.755876 AGCTCACGGATCTCGGCA 60.756 61.111 8.20 0.00 44.45 5.69
1577 2975 0.937304 CAATGCGGGATAAGTGTCCG 59.063 55.000 0.00 0.00 45.84 4.79
1615 3013 0.974010 CCTTACCCGGGTGCTCACTA 60.974 60.000 36.97 11.79 0.00 2.74
1684 3082 2.368192 TGCCCCGGGATTCCTCAT 60.368 61.111 26.32 0.00 0.00 2.90
1752 3150 5.425196 AAATTGACAGGAAAATGGGGATG 57.575 39.130 0.00 0.00 0.00 3.51
1893 3291 4.435977 TGGGCTGGAGATACCCTATATT 57.564 45.455 0.00 0.00 44.56 1.28
1908 3306 3.567164 CCTATATTGCTCAAAGGCCAGTG 59.433 47.826 5.01 1.58 0.00 3.66
2011 3409 5.336150 TCCTGAGCTTGACTTCTATTCTG 57.664 43.478 0.00 0.00 0.00 3.02
2014 3412 6.437477 TCCTGAGCTTGACTTCTATTCTGTTA 59.563 38.462 0.00 0.00 0.00 2.41
2157 3555 8.923270 TCTACCTGAAAAGACAAAATGGAAAAT 58.077 29.630 0.00 0.00 0.00 1.82
2176 3574 3.900966 ATGAGACTCTGTGCATGCTTA 57.099 42.857 20.33 6.77 0.00 3.09
2192 3590 2.040278 TGCTTAGTCTGGGAGCATGTTT 59.960 45.455 0.00 0.00 41.15 2.83
2251 3649 1.061735 ACCCCCTTGACCCATGTTTTT 60.062 47.619 0.00 0.00 0.00 1.94
2265 3663 9.968870 GACCCATGTTTTTAATGTTAAACAGTA 57.031 29.630 8.64 0.00 44.61 2.74
2313 3712 6.392625 TCGCTAGTTAATGAATAGCAGAGT 57.607 37.500 5.42 0.00 41.60 3.24
2394 3793 7.558161 TCCAGTGAACATGCTTGATTTATAG 57.442 36.000 6.60 0.00 0.00 1.31
2395 3794 7.112122 TCCAGTGAACATGCTTGATTTATAGT 58.888 34.615 6.60 0.00 0.00 2.12
2422 3821 7.540299 TGAATTAATTTGGCCTTAGGTTTACG 58.460 34.615 3.32 0.00 0.00 3.18
2464 3863 1.913778 ATGGACTTGTCTGCAATGCA 58.086 45.000 7.99 7.99 36.92 3.96
2521 3920 7.278135 TGCTCTGCAGAGATGAGTTTATTTAT 58.722 34.615 41.20 0.00 44.74 1.40
2525 3924 9.842775 TCTGCAGAGATGAGTTTATTTATTCAT 57.157 29.630 13.74 0.00 33.23 2.57
2535 3934 8.148351 TGAGTTTATTTATTCATACTCCCTCCG 58.852 37.037 0.00 0.00 32.96 4.63
2536 3935 8.030913 AGTTTATTTATTCATACTCCCTCCGT 57.969 34.615 0.00 0.00 0.00 4.69
2537 3936 8.491958 AGTTTATTTATTCATACTCCCTCCGTT 58.508 33.333 0.00 0.00 0.00 4.44
2538 3937 8.771766 GTTTATTTATTCATACTCCCTCCGTTC 58.228 37.037 0.00 0.00 0.00 3.95
2539 3938 5.943349 TTTATTCATACTCCCTCCGTTCA 57.057 39.130 0.00 0.00 0.00 3.18
2540 3939 3.821421 ATTCATACTCCCTCCGTTCAC 57.179 47.619 0.00 0.00 0.00 3.18
2541 3940 2.526888 TCATACTCCCTCCGTTCACT 57.473 50.000 0.00 0.00 0.00 3.41
2542 3941 2.816411 TCATACTCCCTCCGTTCACTT 58.184 47.619 0.00 0.00 0.00 3.16
2543 3942 3.170717 TCATACTCCCTCCGTTCACTTT 58.829 45.455 0.00 0.00 0.00 2.66
2544 3943 3.581332 TCATACTCCCTCCGTTCACTTTT 59.419 43.478 0.00 0.00 0.00 2.27
2545 3944 4.773674 TCATACTCCCTCCGTTCACTTTTA 59.226 41.667 0.00 0.00 0.00 1.52
2546 3945 5.424252 TCATACTCCCTCCGTTCACTTTTAT 59.576 40.000 0.00 0.00 0.00 1.40
2547 3946 6.608405 TCATACTCCCTCCGTTCACTTTTATA 59.392 38.462 0.00 0.00 0.00 0.98
2548 3947 5.750352 ACTCCCTCCGTTCACTTTTATAA 57.250 39.130 0.00 0.00 0.00 0.98
2549 3948 5.731591 ACTCCCTCCGTTCACTTTTATAAG 58.268 41.667 0.00 0.00 37.40 1.73
2550 3949 5.247792 ACTCCCTCCGTTCACTTTTATAAGT 59.752 40.000 0.00 0.00 45.40 2.24
2551 3950 5.727434 TCCCTCCGTTCACTTTTATAAGTC 58.273 41.667 0.00 0.00 42.67 3.01
2552 3951 4.565564 CCCTCCGTTCACTTTTATAAGTCG 59.434 45.833 0.00 0.00 42.67 4.18
2553 3952 5.166398 CCTCCGTTCACTTTTATAAGTCGT 58.834 41.667 0.00 0.00 42.67 4.34
2554 3953 5.636543 CCTCCGTTCACTTTTATAAGTCGTT 59.363 40.000 0.00 0.00 42.67 3.85
2555 3954 6.146673 CCTCCGTTCACTTTTATAAGTCGTTT 59.853 38.462 0.00 0.00 42.67 3.60
2556 3955 7.109006 TCCGTTCACTTTTATAAGTCGTTTC 57.891 36.000 0.00 0.00 42.67 2.78
2557 3956 6.700960 TCCGTTCACTTTTATAAGTCGTTTCA 59.299 34.615 0.00 0.00 42.67 2.69
2558 3957 7.007697 CCGTTCACTTTTATAAGTCGTTTCAG 58.992 38.462 0.00 0.00 42.67 3.02
2559 3958 7.095940 CCGTTCACTTTTATAAGTCGTTTCAGA 60.096 37.037 0.00 0.00 42.67 3.27
2560 3959 7.734726 CGTTCACTTTTATAAGTCGTTTCAGAC 59.265 37.037 0.00 0.00 42.67 3.51
2561 3960 8.545420 GTTCACTTTTATAAGTCGTTTCAGACA 58.455 33.333 0.00 0.00 42.67 3.41
2562 3961 8.651391 TCACTTTTATAAGTCGTTTCAGACAA 57.349 30.769 0.00 0.00 42.67 3.18
2563 3962 8.761497 TCACTTTTATAAGTCGTTTCAGACAAG 58.239 33.333 0.00 0.00 42.67 3.16
2564 3963 8.548721 CACTTTTATAAGTCGTTTCAGACAAGT 58.451 33.333 0.00 0.00 42.67 3.16
2565 3964 8.548721 ACTTTTATAAGTCGTTTCAGACAAGTG 58.451 33.333 0.00 0.00 40.60 3.16
2566 3965 8.651391 TTTTATAAGTCGTTTCAGACAAGTGA 57.349 30.769 0.00 0.00 43.24 3.41
2567 3966 8.651391 TTTATAAGTCGTTTCAGACAAGTGAA 57.349 30.769 0.00 0.00 43.24 3.18
2568 3967 8.651391 TTATAAGTCGTTTCAGACAAGTGAAA 57.349 30.769 0.00 0.00 42.79 2.69
2569 3968 7.730364 ATAAGTCGTTTCAGACAAGTGAAAT 57.270 32.000 2.59 0.00 45.71 2.17
2570 3969 6.436843 AAGTCGTTTCAGACAAGTGAAATT 57.563 33.333 2.59 0.00 45.71 1.82
2571 3970 5.810525 AGTCGTTTCAGACAAGTGAAATTG 58.189 37.500 2.59 0.24 45.71 2.32
2572 3971 5.354234 AGTCGTTTCAGACAAGTGAAATTGT 59.646 36.000 2.59 0.00 45.71 2.71
2573 3972 5.452302 GTCGTTTCAGACAAGTGAAATTGTG 59.548 40.000 0.20 0.00 45.71 3.33
2574 3973 4.204978 CGTTTCAGACAAGTGAAATTGTGC 59.795 41.667 0.20 0.00 45.71 4.57
2575 3974 5.343249 GTTTCAGACAAGTGAAATTGTGCT 58.657 37.500 0.20 0.00 45.71 4.40
2576 3975 4.556942 TCAGACAAGTGAAATTGTGCTG 57.443 40.909 0.20 8.31 43.32 4.41
2577 3976 3.947196 TCAGACAAGTGAAATTGTGCTGT 59.053 39.130 0.20 0.00 43.32 4.40
2578 3977 4.398988 TCAGACAAGTGAAATTGTGCTGTT 59.601 37.500 0.20 0.00 43.32 3.16
2579 3978 5.104374 CAGACAAGTGAAATTGTGCTGTTT 58.896 37.500 0.20 0.00 43.32 2.83
2580 3979 5.577945 CAGACAAGTGAAATTGTGCTGTTTT 59.422 36.000 0.20 0.00 43.32 2.43
2581 3980 5.577945 AGACAAGTGAAATTGTGCTGTTTTG 59.422 36.000 0.20 0.00 43.32 2.44
2582 3981 4.093261 ACAAGTGAAATTGTGCTGTTTTGC 59.907 37.500 0.00 0.00 41.76 3.68
2583 3982 3.859443 AGTGAAATTGTGCTGTTTTGCA 58.141 36.364 0.00 0.00 41.05 4.08
2591 3990 1.462616 TGCTGTTTTGCACACTGTCT 58.537 45.000 0.00 0.00 38.12 3.41
2592 3991 1.132834 TGCTGTTTTGCACACTGTCTG 59.867 47.619 0.00 0.00 38.12 3.51
2593 3992 1.401552 GCTGTTTTGCACACTGTCTGA 59.598 47.619 0.00 0.00 0.00 3.27
2594 3993 2.159393 GCTGTTTTGCACACTGTCTGAA 60.159 45.455 0.00 0.00 0.00 3.02
2595 3994 3.673052 GCTGTTTTGCACACTGTCTGAAA 60.673 43.478 0.00 0.00 0.00 2.69
2596 3995 3.832276 TGTTTTGCACACTGTCTGAAAC 58.168 40.909 0.00 0.00 0.00 2.78
2597 3996 2.823196 TTTGCACACTGTCTGAAACG 57.177 45.000 0.00 0.00 0.00 3.60
2598 3997 1.732941 TTGCACACTGTCTGAAACGT 58.267 45.000 0.00 0.00 0.00 3.99
2599 3998 1.286501 TGCACACTGTCTGAAACGTC 58.713 50.000 0.00 0.00 0.00 4.34
2600 3999 1.134818 TGCACACTGTCTGAAACGTCT 60.135 47.619 0.00 0.00 0.00 4.18
2601 4000 2.100087 TGCACACTGTCTGAAACGTCTA 59.900 45.455 0.00 0.00 0.00 2.59
2602 4001 2.471743 GCACACTGTCTGAAACGTCTAC 59.528 50.000 0.00 0.00 0.00 2.59
2603 4002 3.702330 CACACTGTCTGAAACGTCTACA 58.298 45.455 0.00 0.00 0.00 2.74
2604 4003 4.109766 CACACTGTCTGAAACGTCTACAA 58.890 43.478 0.00 0.00 0.00 2.41
2605 4004 4.565166 CACACTGTCTGAAACGTCTACAAA 59.435 41.667 0.00 0.00 0.00 2.83
2606 4005 4.804139 ACACTGTCTGAAACGTCTACAAAG 59.196 41.667 0.00 0.00 0.00 2.77
2607 4006 3.802685 ACTGTCTGAAACGTCTACAAAGC 59.197 43.478 0.00 0.00 0.00 3.51
2608 4007 3.128349 TGTCTGAAACGTCTACAAAGCC 58.872 45.455 0.00 0.00 0.00 4.35
2609 4008 3.181469 TGTCTGAAACGTCTACAAAGCCT 60.181 43.478 0.00 0.00 0.00 4.58
2610 4009 3.808174 GTCTGAAACGTCTACAAAGCCTT 59.192 43.478 0.00 0.00 0.00 4.35
2611 4010 4.986659 GTCTGAAACGTCTACAAAGCCTTA 59.013 41.667 0.00 0.00 0.00 2.69
2612 4011 5.638234 GTCTGAAACGTCTACAAAGCCTTAT 59.362 40.000 0.00 0.00 0.00 1.73
2613 4012 6.810182 GTCTGAAACGTCTACAAAGCCTTATA 59.190 38.462 0.00 0.00 0.00 0.98
2614 4013 7.330208 GTCTGAAACGTCTACAAAGCCTTATAA 59.670 37.037 0.00 0.00 0.00 0.98
2615 4014 7.874016 TCTGAAACGTCTACAAAGCCTTATAAA 59.126 33.333 0.00 0.00 0.00 1.40
2616 4015 8.380743 TGAAACGTCTACAAAGCCTTATAAAA 57.619 30.769 0.00 0.00 0.00 1.52
2617 4016 8.500773 TGAAACGTCTACAAAGCCTTATAAAAG 58.499 33.333 0.00 0.00 0.00 2.27
2618 4017 7.974482 AACGTCTACAAAGCCTTATAAAAGT 57.026 32.000 0.00 0.00 0.00 2.66
2619 4018 7.360575 ACGTCTACAAAGCCTTATAAAAGTG 57.639 36.000 0.00 0.00 0.00 3.16
2620 4019 7.156673 ACGTCTACAAAGCCTTATAAAAGTGA 58.843 34.615 0.00 0.00 0.00 3.41
2621 4020 7.658575 ACGTCTACAAAGCCTTATAAAAGTGAA 59.341 33.333 0.00 0.00 0.00 3.18
2622 4021 7.955864 CGTCTACAAAGCCTTATAAAAGTGAAC 59.044 37.037 0.00 0.00 0.00 3.18
2623 4022 8.780249 GTCTACAAAGCCTTATAAAAGTGAACA 58.220 33.333 0.00 0.00 0.00 3.18
2624 4023 8.999431 TCTACAAAGCCTTATAAAAGTGAACAG 58.001 33.333 0.00 0.00 0.00 3.16
2625 4024 7.817418 ACAAAGCCTTATAAAAGTGAACAGA 57.183 32.000 0.00 0.00 0.00 3.41
2626 4025 7.875971 ACAAAGCCTTATAAAAGTGAACAGAG 58.124 34.615 0.00 0.00 0.00 3.35
2627 4026 7.040409 ACAAAGCCTTATAAAAGTGAACAGAGG 60.040 37.037 0.00 0.00 0.00 3.69
2628 4027 5.501156 AGCCTTATAAAAGTGAACAGAGGG 58.499 41.667 0.00 0.00 0.00 4.30
2629 4028 5.250774 AGCCTTATAAAAGTGAACAGAGGGA 59.749 40.000 0.00 0.00 0.00 4.20
2630 4029 5.586643 GCCTTATAAAAGTGAACAGAGGGAG 59.413 44.000 0.00 0.00 0.00 4.30
2810 4210 1.874019 CCGCCGACTCTGATTCACG 60.874 63.158 0.00 0.00 0.00 4.35
2855 4255 6.560253 ACCCAATTATATCGCTTTGTGATC 57.440 37.500 0.00 0.00 34.45 2.92
2893 4293 4.514816 GTGAACCCAATCATTTTGGTTTGG 59.485 41.667 3.16 0.00 40.09 3.28
2904 4306 6.690530 TCATTTTGGTTTGGCATAAAGAGAG 58.309 36.000 0.00 0.00 0.00 3.20
2905 4307 6.267471 TCATTTTGGTTTGGCATAAAGAGAGT 59.733 34.615 0.00 0.00 0.00 3.24
2937 4514 7.547227 ACCAGCAAAATACTAAGCTAAATTGG 58.453 34.615 0.00 0.00 35.19 3.16
2966 4543 5.334802 GGTTGCAAAATTGGCTTAATGGAAC 60.335 40.000 0.00 0.00 35.86 3.62
3011 4588 2.174210 AGCCCATGAGCTTATGTGTCAT 59.826 45.455 16.48 0.00 41.41 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 3.425162 AAGGAGAGATTTTTCGGCTGT 57.575 42.857 0.00 0.00 0.00 4.40
135 136 1.742768 GGACTCATAGTCTGCCCGG 59.257 63.158 6.99 0.00 44.46 5.73
173 174 4.585216 TCCACCCCTTCCCACGGT 62.585 66.667 0.00 0.00 0.00 4.83
185 187 1.080025 CTCGACGACCCTTTCCACC 60.080 63.158 0.00 0.00 0.00 4.61
187 189 2.939261 GCCTCGACGACCCTTTCCA 61.939 63.158 0.00 0.00 0.00 3.53
193 195 2.085042 GATAAGGGCCTCGACGACCC 62.085 65.000 6.46 14.26 44.62 4.46
261 274 1.816863 GCGCGGATGGATTCCTCCTA 61.817 60.000 8.83 0.00 42.99 2.94
270 283 4.108299 AATGTGGGCGCGGATGGA 62.108 61.111 8.83 0.00 0.00 3.41
503 539 1.134946 GCATGTTTGGCTATGGTGGAC 59.865 52.381 0.00 0.00 0.00 4.02
573 609 1.535462 GTAGTTGCACACACATCACCC 59.465 52.381 0.00 0.00 0.00 4.61
591 628 7.334858 TCCATACAAACTCATGCAACTATGTA 58.665 34.615 0.00 0.00 0.00 2.29
714 756 0.612732 TGCAAATCTGGCCCCTCAAG 60.613 55.000 0.00 0.00 0.00 3.02
909 1114 2.902423 TTTGCACTCCAAGTGGCCGT 62.902 55.000 9.01 0.00 46.01 5.68
1059 2457 4.667935 TGGAGCGGGGAAAGGGGA 62.668 66.667 0.00 0.00 0.00 4.81
1352 2750 1.593750 GAGCGCTTGATGCCGAGAT 60.594 57.895 13.26 0.00 38.78 2.75
1360 2758 1.068753 CGATCTGGGAGCGCTTGAT 59.931 57.895 13.26 13.28 34.07 2.57
1402 2800 4.021925 GGAGCTGCGGAAGGTGGT 62.022 66.667 0.00 0.00 36.52 4.16
1440 2838 1.677552 GAAGACCGGGAGCCAGAAA 59.322 57.895 6.32 0.00 0.00 2.52
1577 2975 9.274206 GGGTAAGGTATGTATCTGAAAATTCTC 57.726 37.037 0.00 0.00 0.00 2.87
1615 3013 2.439883 GACGTACTCGGGGAGCCT 60.440 66.667 0.00 0.00 41.85 4.58
1633 3031 1.594862 GATGTACAGCACGGCATTCTC 59.405 52.381 6.17 0.00 0.00 2.87
1712 3110 4.581309 ATTTTCTCCTGGCTCTGAATCA 57.419 40.909 0.00 0.00 0.00 2.57
1714 3112 4.704057 GTCAATTTTCTCCTGGCTCTGAAT 59.296 41.667 0.00 0.00 0.00 2.57
1752 3150 2.224018 TGACCAACCAAGCATTTCAAGC 60.224 45.455 0.00 0.00 0.00 4.01
1893 3291 1.900016 CAGCACTGGCCTTTGAGCA 60.900 57.895 3.32 0.00 42.56 4.26
1908 3306 4.180057 GCTCATAGCTATACATGACCAGC 58.820 47.826 5.77 4.34 38.45 4.85
2011 3409 1.849219 CTTCTCAGTCAGCGCGATAAC 59.151 52.381 12.10 0.00 0.00 1.89
2014 3412 0.528017 TTCTTCTCAGTCAGCGCGAT 59.472 50.000 12.10 0.00 0.00 4.58
2157 3555 2.564504 ACTAAGCATGCACAGAGTCTCA 59.435 45.455 21.98 0.00 0.00 3.27
2176 3574 1.004044 CCAGAAACATGCTCCCAGACT 59.996 52.381 0.00 0.00 0.00 3.24
2192 3590 2.920724 TTCCAACACGACAATCCAGA 57.079 45.000 0.00 0.00 0.00 3.86
2251 3649 8.268605 TCACCCATAGCATACTGTTTAACATTA 58.731 33.333 0.00 0.00 0.00 1.90
2265 3663 3.939740 ACACAAGATCACCCATAGCAT 57.060 42.857 0.00 0.00 0.00 3.79
2301 3700 2.760650 ACATCCGTCACTCTGCTATTCA 59.239 45.455 0.00 0.00 0.00 2.57
2313 3712 3.441244 GTGCTGATCACATCCGTCA 57.559 52.632 0.00 0.00 44.98 4.35
2336 3735 3.367498 GGCACTCCACGATCCATATCTAC 60.367 52.174 0.00 0.00 0.00 2.59
2361 3760 3.304928 GCATGTTCACTGGAAAACTGGAG 60.305 47.826 0.00 0.00 34.13 3.86
2422 3821 9.362539 CCATATCCAAATTTATCAATTAGCTGC 57.637 33.333 0.00 0.00 31.89 5.25
2464 3863 9.444668 ACATATAATATAGCATCAGGTCCAGAT 57.555 33.333 0.00 0.00 0.00 2.90
2521 3920 2.816411 AGTGAACGGAGGGAGTATGAA 58.184 47.619 0.00 0.00 0.00 2.57
2525 3924 6.438425 ACTTATAAAAGTGAACGGAGGGAGTA 59.562 38.462 0.00 0.00 44.40 2.59
2526 3925 5.247792 ACTTATAAAAGTGAACGGAGGGAGT 59.752 40.000 0.00 0.00 44.40 3.85
2527 3926 5.731591 ACTTATAAAAGTGAACGGAGGGAG 58.268 41.667 0.00 0.00 44.40 4.30
2528 3927 5.622914 CGACTTATAAAAGTGAACGGAGGGA 60.623 44.000 0.00 0.00 46.09 4.20
2529 3928 4.565564 CGACTTATAAAAGTGAACGGAGGG 59.434 45.833 0.00 0.00 46.09 4.30
2530 3929 5.166398 ACGACTTATAAAAGTGAACGGAGG 58.834 41.667 0.00 0.00 46.09 4.30
2531 3930 6.701432 AACGACTTATAAAAGTGAACGGAG 57.299 37.500 0.00 0.00 46.09 4.63
2532 3931 6.700960 TGAAACGACTTATAAAAGTGAACGGA 59.299 34.615 0.00 0.00 46.09 4.69
2533 3932 6.879962 TGAAACGACTTATAAAAGTGAACGG 58.120 36.000 0.00 0.00 46.09 4.44
2534 3933 7.734726 GTCTGAAACGACTTATAAAAGTGAACG 59.265 37.037 0.00 0.00 46.09 3.95
2535 3934 8.545420 TGTCTGAAACGACTTATAAAAGTGAAC 58.455 33.333 0.00 0.00 46.09 3.18
2536 3935 8.651391 TGTCTGAAACGACTTATAAAAGTGAA 57.349 30.769 0.00 0.00 46.09 3.18
2537 3936 8.651391 TTGTCTGAAACGACTTATAAAAGTGA 57.349 30.769 0.00 0.00 46.09 3.41
2538 3937 8.548721 ACTTGTCTGAAACGACTTATAAAAGTG 58.451 33.333 0.00 0.00 46.09 3.16
2540 3939 8.761497 TCACTTGTCTGAAACGACTTATAAAAG 58.239 33.333 0.00 0.00 38.77 2.27
2541 3940 8.651391 TCACTTGTCTGAAACGACTTATAAAA 57.349 30.769 0.00 0.00 35.00 1.52
2542 3941 8.651391 TTCACTTGTCTGAAACGACTTATAAA 57.349 30.769 0.00 0.00 35.00 1.40
2543 3942 8.651391 TTTCACTTGTCTGAAACGACTTATAA 57.349 30.769 0.00 0.00 35.63 0.98
2544 3943 8.827177 ATTTCACTTGTCTGAAACGACTTATA 57.173 30.769 0.00 0.00 41.76 0.98
2545 3944 7.730364 ATTTCACTTGTCTGAAACGACTTAT 57.270 32.000 0.00 0.00 41.76 1.73
2546 3945 7.065324 ACAATTTCACTTGTCTGAAACGACTTA 59.935 33.333 0.00 0.00 41.76 2.24
2547 3946 6.128007 ACAATTTCACTTGTCTGAAACGACTT 60.128 34.615 0.00 0.00 41.76 3.01
2548 3947 5.354234 ACAATTTCACTTGTCTGAAACGACT 59.646 36.000 0.00 0.00 41.76 4.18
2549 3948 5.452302 CACAATTTCACTTGTCTGAAACGAC 59.548 40.000 0.00 0.00 41.76 4.34
2550 3949 5.568482 CACAATTTCACTTGTCTGAAACGA 58.432 37.500 0.00 0.00 41.76 3.85
2551 3950 4.204978 GCACAATTTCACTTGTCTGAAACG 59.795 41.667 0.00 0.00 41.76 3.60
2552 3951 5.230726 CAGCACAATTTCACTTGTCTGAAAC 59.769 40.000 0.00 0.00 41.76 2.78
2553 3952 5.105797 ACAGCACAATTTCACTTGTCTGAAA 60.106 36.000 16.18 0.00 42.83 2.69
2554 3953 4.398988 ACAGCACAATTTCACTTGTCTGAA 59.601 37.500 16.18 0.00 37.25 3.02
2555 3954 3.947196 ACAGCACAATTTCACTTGTCTGA 59.053 39.130 16.18 0.00 37.25 3.27
2556 3955 4.297299 ACAGCACAATTTCACTTGTCTG 57.703 40.909 11.40 11.40 37.25 3.51
2557 3956 4.989279 AACAGCACAATTTCACTTGTCT 57.011 36.364 0.00 0.00 37.25 3.41
2558 3957 5.724769 GCAAAACAGCACAATTTCACTTGTC 60.725 40.000 0.00 0.00 37.25 3.18
2559 3958 4.093261 GCAAAACAGCACAATTTCACTTGT 59.907 37.500 0.00 0.00 39.91 3.16
2560 3959 4.093115 TGCAAAACAGCACAATTTCACTTG 59.907 37.500 0.00 0.00 40.11 3.16
2561 3960 4.252073 TGCAAAACAGCACAATTTCACTT 58.748 34.783 0.00 0.00 40.11 3.16
2562 3961 3.859443 TGCAAAACAGCACAATTTCACT 58.141 36.364 0.00 0.00 40.11 3.41
2572 3971 1.132834 CAGACAGTGTGCAAAACAGCA 59.867 47.619 0.00 0.00 40.26 4.41
2573 3972 1.401552 TCAGACAGTGTGCAAAACAGC 59.598 47.619 0.00 0.00 40.26 4.40
2574 3973 3.763097 TTCAGACAGTGTGCAAAACAG 57.237 42.857 0.00 0.00 40.26 3.16
2575 3974 3.669290 CGTTTCAGACAGTGTGCAAAACA 60.669 43.478 0.00 0.00 36.04 2.83
2576 3975 2.845967 CGTTTCAGACAGTGTGCAAAAC 59.154 45.455 0.00 7.16 0.00 2.43
2577 3976 2.486203 ACGTTTCAGACAGTGTGCAAAA 59.514 40.909 0.00 0.00 0.00 2.44
2578 3977 2.080693 ACGTTTCAGACAGTGTGCAAA 58.919 42.857 0.00 0.00 0.00 3.68
2579 3978 1.663643 GACGTTTCAGACAGTGTGCAA 59.336 47.619 0.00 0.00 0.00 4.08
2580 3979 1.134818 AGACGTTTCAGACAGTGTGCA 60.135 47.619 0.00 0.00 0.00 4.57
2581 3980 1.571919 AGACGTTTCAGACAGTGTGC 58.428 50.000 0.00 0.00 0.00 4.57
2582 3981 3.702330 TGTAGACGTTTCAGACAGTGTG 58.298 45.455 0.00 0.00 0.00 3.82
2583 3982 4.380841 TTGTAGACGTTTCAGACAGTGT 57.619 40.909 0.00 0.00 0.00 3.55
2584 3983 4.318121 GCTTTGTAGACGTTTCAGACAGTG 60.318 45.833 0.00 0.00 0.00 3.66
2585 3984 3.802685 GCTTTGTAGACGTTTCAGACAGT 59.197 43.478 0.00 0.00 0.00 3.55
2586 3985 3.184581 GGCTTTGTAGACGTTTCAGACAG 59.815 47.826 0.00 0.00 0.00 3.51
2587 3986 3.128349 GGCTTTGTAGACGTTTCAGACA 58.872 45.455 0.00 0.00 0.00 3.41
2588 3987 3.391049 AGGCTTTGTAGACGTTTCAGAC 58.609 45.455 0.00 0.00 33.24 3.51
2589 3988 3.746045 AGGCTTTGTAGACGTTTCAGA 57.254 42.857 0.00 0.00 33.24 3.27
2590 3989 7.591006 TTATAAGGCTTTGTAGACGTTTCAG 57.409 36.000 4.45 0.00 33.24 3.02
2591 3990 7.966246 TTTATAAGGCTTTGTAGACGTTTCA 57.034 32.000 4.45 0.00 33.24 2.69
2592 3991 8.501580 ACTTTTATAAGGCTTTGTAGACGTTTC 58.498 33.333 4.45 0.00 35.61 2.78
2593 3992 8.287503 CACTTTTATAAGGCTTTGTAGACGTTT 58.712 33.333 4.45 0.00 35.61 3.60
2594 3993 7.658575 TCACTTTTATAAGGCTTTGTAGACGTT 59.341 33.333 4.45 0.00 35.61 3.99
2595 3994 7.156673 TCACTTTTATAAGGCTTTGTAGACGT 58.843 34.615 4.45 0.00 35.61 4.34
2596 3995 7.591006 TCACTTTTATAAGGCTTTGTAGACG 57.409 36.000 4.45 0.00 35.61 4.18
2597 3996 8.780249 TGTTCACTTTTATAAGGCTTTGTAGAC 58.220 33.333 4.45 0.00 35.61 2.59
2598 3997 8.911918 TGTTCACTTTTATAAGGCTTTGTAGA 57.088 30.769 4.45 0.00 35.61 2.59
2599 3998 8.999431 TCTGTTCACTTTTATAAGGCTTTGTAG 58.001 33.333 4.45 0.00 35.61 2.74
2600 3999 8.911918 TCTGTTCACTTTTATAAGGCTTTGTA 57.088 30.769 4.45 0.00 35.61 2.41
2601 4000 7.040409 CCTCTGTTCACTTTTATAAGGCTTTGT 60.040 37.037 4.45 0.00 35.61 2.83
2602 4001 7.308435 CCTCTGTTCACTTTTATAAGGCTTTG 58.692 38.462 4.45 0.00 35.61 2.77
2603 4002 6.434340 CCCTCTGTTCACTTTTATAAGGCTTT 59.566 38.462 4.45 0.00 35.61 3.51
2604 4003 5.946377 CCCTCTGTTCACTTTTATAAGGCTT 59.054 40.000 4.58 4.58 35.61 4.35
2605 4004 5.250774 TCCCTCTGTTCACTTTTATAAGGCT 59.749 40.000 0.00 0.00 35.61 4.58
2606 4005 5.497474 TCCCTCTGTTCACTTTTATAAGGC 58.503 41.667 0.00 0.00 35.61 4.35
2607 4006 6.712276 ACTCCCTCTGTTCACTTTTATAAGG 58.288 40.000 0.00 0.00 35.61 2.69
2608 4007 9.892130 AATACTCCCTCTGTTCACTTTTATAAG 57.108 33.333 0.00 0.00 37.40 1.73
2616 4015 9.838339 CAAATTATAATACTCCCTCTGTTCACT 57.162 33.333 0.00 0.00 0.00 3.41
2617 4016 9.614792 ACAAATTATAATACTCCCTCTGTTCAC 57.385 33.333 0.00 0.00 0.00 3.18
2620 4019 9.975218 ACAACAAATTATAATACTCCCTCTGTT 57.025 29.630 0.00 0.00 0.00 3.16
2621 4020 9.614792 GACAACAAATTATAATACTCCCTCTGT 57.385 33.333 0.00 0.00 0.00 3.41
2622 4021 9.613428 TGACAACAAATTATAATACTCCCTCTG 57.387 33.333 0.00 0.00 0.00 3.35
2623 4022 9.614792 GTGACAACAAATTATAATACTCCCTCT 57.385 33.333 0.00 0.00 0.00 3.69
2624 4023 9.614792 AGTGACAACAAATTATAATACTCCCTC 57.385 33.333 0.00 0.00 0.00 4.30
2625 4024 9.396022 CAGTGACAACAAATTATAATACTCCCT 57.604 33.333 0.00 0.00 0.00 4.20
2626 4025 9.174166 ACAGTGACAACAAATTATAATACTCCC 57.826 33.333 0.00 0.00 0.00 4.30
2672 4071 8.980610 CATGATTTCAACAATTGCAAGTTTCTA 58.019 29.630 4.94 0.00 0.00 2.10
2728 4128 5.652014 CCAGCAAAATGGGAAGTGTCTAATA 59.348 40.000 0.00 0.00 36.64 0.98
2810 4210 7.065324 TGGGTTCACGAGTCAAATAATATGTTC 59.935 37.037 0.00 0.00 0.00 3.18
2855 4255 3.119849 GGGTTCACGAATCAACATCCAAG 60.120 47.826 0.00 0.00 0.00 3.61
2893 4293 5.023533 TGGTATGGTCACTCTCTTTATGC 57.976 43.478 0.00 0.00 0.00 3.14
2904 4306 6.458342 GCTTAGTATTTTGCTGGTATGGTCAC 60.458 42.308 0.00 0.00 0.00 3.67
2905 4307 5.588648 GCTTAGTATTTTGCTGGTATGGTCA 59.411 40.000 0.00 0.00 0.00 4.02
2954 4531 3.442273 TCCATTCGTTGTTCCATTAAGCC 59.558 43.478 0.00 0.00 0.00 4.35
2966 4543 5.996219 TGTTGTTTATCAGTCCATTCGTTG 58.004 37.500 0.00 0.00 0.00 4.10
2978 4555 3.193267 GCTCATGGGCTTGTTGTTTATCA 59.807 43.478 11.30 0.00 0.00 2.15
3031 4609 8.769359 AGCAAAAAGGTACCTATACTGAAGTAT 58.231 33.333 16.67 8.02 43.15 2.12


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

AutoCloner maintained by Alex Coulton.