Multiple sequence alignment - TraesCS6A01G051300

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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 TraesCS6A01G051300 chr6A 100.000 3488 0 0 1 3488 26733230 26736717 0.000000e+00 6442.0
1 TraesCS6A01G051300 chr6A 89.796 1568 145 11 967 2525 26717930 26719491 0.000000e+00 1995.0
2 TraesCS6A01G051300 chr6A 80.151 398 58 18 7 394 119192244 119192630 9.540000e-71 278.0
3 TraesCS6A01G051300 chr6B 89.911 2597 213 18 1 2564 45982426 45985006 0.000000e+00 3299.0
4 TraesCS6A01G051300 chr6B 91.807 1599 120 8 960 2552 46390153 46391746 0.000000e+00 2217.0
5 TraesCS6A01G051300 chr6B 91.108 1507 115 9 1024 2524 46072323 46073816 0.000000e+00 2023.0
6 TraesCS6A01G051300 chr6B 89.732 1568 143 9 967 2525 46092811 46094369 0.000000e+00 1988.0
7 TraesCS6A01G051300 chr6B 84.594 727 56 36 737 1447 46026483 46027169 0.000000e+00 671.0
8 TraesCS6A01G051300 chr6B 89.344 366 36 2 2158 2523 46081996 46082358 1.140000e-124 457.0
9 TraesCS6A01G051300 chr6B 87.923 207 15 3 1973 2169 46074126 46074332 5.820000e-58 235.0
10 TraesCS6A01G051300 chr6B 100.000 28 0 0 1174 1201 46083006 46083033 6.000000e-03 52.8
11 TraesCS6A01G051300 chr6B 100.000 28 0 0 934 961 46390108 46390135 6.000000e-03 52.8
12 TraesCS6A01G051300 chrUn 93.874 1665 87 2 921 2570 95385225 95386889 0.000000e+00 2495.0
13 TraesCS6A01G051300 chrUn 89.632 733 58 12 1 725 95314364 95315086 0.000000e+00 917.0
14 TraesCS6A01G051300 chrUn 92.233 206 8 1 719 924 95385002 95385199 5.700000e-73 285.0
15 TraesCS6A01G051300 chrUn 91.542 201 17 0 202 402 98220343 98220143 9.540000e-71 278.0
16 TraesCS6A01G051300 chr5B 87.779 761 59 16 2729 3484 469211471 469210740 0.000000e+00 859.0
17 TraesCS6A01G051300 chr5B 86.156 809 67 16 2693 3484 469352953 469352173 0.000000e+00 832.0
18 TraesCS6A01G051300 chr5B 84.770 847 88 24 2658 3488 588687970 588688791 0.000000e+00 811.0
19 TraesCS6A01G051300 chr5B 83.562 146 24 0 594 739 676206711 676206566 1.690000e-28 137.0
20 TraesCS6A01G051300 chr1D 85.851 834 82 23 2653 3483 114632110 114632910 0.000000e+00 854.0
21 TraesCS6A01G051300 chr1D 84.138 145 23 0 594 738 298438805 298438661 1.310000e-29 141.0
22 TraesCS6A01G051300 chr6D 85.124 847 73 21 2662 3470 54661888 54661057 0.000000e+00 817.0
23 TraesCS6A01G051300 chr6D 86.343 432 55 3 3059 3488 54661369 54660940 5.270000e-128 468.0
24 TraesCS6A01G051300 chr6D 87.619 210 19 6 7 209 445651473 445651264 1.620000e-58 237.0
25 TraesCS6A01G051300 chr7D 84.826 804 85 14 2659 3459 92422669 92421900 0.000000e+00 774.0
26 TraesCS6A01G051300 chr7D 92.891 211 14 1 199 408 92137960 92137750 4.370000e-79 305.0
27 TraesCS6A01G051300 chr7D 87.793 213 18 5 1 209 165480367 165480575 3.480000e-60 243.0
28 TraesCS6A01G051300 chr4D 88.156 591 60 7 2901 3488 197768552 197769135 0.000000e+00 695.0
29 TraesCS6A01G051300 chr4D 87.899 595 53 13 2875 3464 418434657 418435237 0.000000e+00 682.0
30 TraesCS6A01G051300 chr4D 91.266 229 14 6 2659 2883 418434409 418434635 1.220000e-79 307.0
31 TraesCS6A01G051300 chr4D 89.394 198 17 3 2659 2853 197768349 197768545 2.690000e-61 246.0
32 TraesCS6A01G051300 chr4D 80.952 168 27 4 576 740 504041931 504042096 1.020000e-25 128.0
33 TraesCS6A01G051300 chr4D 84.000 75 12 0 2087 2161 14561860 14561934 4.830000e-09 73.1
34 TraesCS6A01G051300 chr1A 87.919 596 62 9 2895 3488 526735830 526735243 0.000000e+00 693.0
35 TraesCS6A01G051300 chr1A 87.437 199 21 3 2657 2853 526736041 526735845 3.500000e-55 226.0
36 TraesCS6A01G051300 chr5D 83.683 429 39 11 1 402 438336167 438336591 3.290000e-100 375.0
37 TraesCS6A01G051300 chr5D 91.262 206 12 3 199 402 189169970 189170171 3.430000e-70 276.0
38 TraesCS6A01G051300 chr5D 82.738 168 25 2 577 740 302824249 302824082 2.810000e-31 147.0
39 TraesCS6A01G051300 chr7A 91.071 224 19 1 174 397 80566595 80566373 5.660000e-78 302.0
40 TraesCS6A01G051300 chr2D 90.640 203 18 1 202 404 36380177 36380378 5.740000e-68 268.0
41 TraesCS6A01G051300 chr2D 87.619 210 19 5 7 209 375356389 375356180 1.620000e-58 237.0
42 TraesCS6A01G051300 chr3D 88.517 209 17 5 7 208 501791980 501791772 2.690000e-61 246.0
43 TraesCS6A01G051300 chr3D 87.678 211 17 5 7 209 517006840 517007049 1.620000e-58 237.0
44 TraesCS6A01G051300 chr3D 87.923 207 18 6 7 208 569980327 569980123 1.620000e-58 237.0
45 TraesCS6A01G051300 chr3D 89.024 164 11 6 2695 2853 43020430 43020269 2.750000e-46 196.0
46 TraesCS6A01G051300 chr4A 85.714 147 21 0 593 739 142446824 142446678 4.660000e-34 156.0
47 TraesCS6A01G051300 chr4A 87.023 131 17 0 611 741 84371030 84370900 7.800000e-32 148.0
48 TraesCS6A01G051300 chr2B 83.537 164 23 4 582 741 416833801 416833638 2.170000e-32 150.0
49 TraesCS6A01G051300 chr4B 83.333 150 21 3 594 739 20587506 20587357 6.070000e-28 135.0
50 TraesCS6A01G051300 chr3A 92.000 50 4 0 2102 2151 488108728 488108679 1.740000e-08 71.3


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 TraesCS6A01G051300 chr6A 26733230 26736717 3487 False 6442.0 6442 100.0000 1 3488 1 chr6A.!!$F2 3487
1 TraesCS6A01G051300 chr6A 26717930 26719491 1561 False 1995.0 1995 89.7960 967 2525 1 chr6A.!!$F1 1558
2 TraesCS6A01G051300 chr6B 45982426 45985006 2580 False 3299.0 3299 89.9110 1 2564 1 chr6B.!!$F1 2563
3 TraesCS6A01G051300 chr6B 46092811 46094369 1558 False 1988.0 1988 89.7320 967 2525 1 chr6B.!!$F3 1558
4 TraesCS6A01G051300 chr6B 46390108 46391746 1638 False 1134.9 2217 95.9035 934 2552 2 chr6B.!!$F6 1618
5 TraesCS6A01G051300 chr6B 46072323 46074332 2009 False 1129.0 2023 89.5155 1024 2524 2 chr6B.!!$F4 1500
6 TraesCS6A01G051300 chr6B 46026483 46027169 686 False 671.0 671 84.5940 737 1447 1 chr6B.!!$F2 710
7 TraesCS6A01G051300 chr6B 46081996 46083033 1037 False 254.9 457 94.6720 1174 2523 2 chr6B.!!$F5 1349
8 TraesCS6A01G051300 chrUn 95385002 95386889 1887 False 1390.0 2495 93.0535 719 2570 2 chrUn.!!$F2 1851
9 TraesCS6A01G051300 chrUn 95314364 95315086 722 False 917.0 917 89.6320 1 725 1 chrUn.!!$F1 724
10 TraesCS6A01G051300 chr5B 469210740 469211471 731 True 859.0 859 87.7790 2729 3484 1 chr5B.!!$R1 755
11 TraesCS6A01G051300 chr5B 469352173 469352953 780 True 832.0 832 86.1560 2693 3484 1 chr5B.!!$R2 791
12 TraesCS6A01G051300 chr5B 588687970 588688791 821 False 811.0 811 84.7700 2658 3488 1 chr5B.!!$F1 830
13 TraesCS6A01G051300 chr1D 114632110 114632910 800 False 854.0 854 85.8510 2653 3483 1 chr1D.!!$F1 830
14 TraesCS6A01G051300 chr6D 54660940 54661888 948 True 642.5 817 85.7335 2662 3488 2 chr6D.!!$R2 826
15 TraesCS6A01G051300 chr7D 92421900 92422669 769 True 774.0 774 84.8260 2659 3459 1 chr7D.!!$R2 800
16 TraesCS6A01G051300 chr4D 418434409 418435237 828 False 494.5 682 89.5825 2659 3464 2 chr4D.!!$F4 805
17 TraesCS6A01G051300 chr4D 197768349 197769135 786 False 470.5 695 88.7750 2659 3488 2 chr4D.!!$F3 829
18 TraesCS6A01G051300 chr1A 526735243 526736041 798 True 459.5 693 87.6780 2657 3488 2 chr1A.!!$R1 831

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
70 72 0.032678 CTTGACGCCTATGCTCCGAT 59.967 55.0 0.00 0.00 34.43 4.18 F
306 308 0.243365 TTAATTTGTGGCGGCAGCTG 59.757 50.0 13.91 10.11 44.37 4.24 F
853 863 0.608308 ACCTCCCGTTGGCTTAAAGC 60.608 55.0 0.00 0.00 41.46 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1615 1682 2.221299 CCAAGGACAGGAACCCGGA 61.221 63.158 0.73 0.0 0.0 5.14 R
2142 2230 1.216710 CTCCAGGCTCGAGTTCCAC 59.783 63.158 15.13 0.0 0.0 4.02 R
2606 2801 0.034896 GGTTTTCAGTGCGAGGGAGA 59.965 55.000 0.00 0.0 0.0 3.71 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
19 20 0.818296 AACGAAGCGCTAGGAGATGT 59.182 50.000 12.05 0.00 0.00 3.06
70 72 0.032678 CTTGACGCCTATGCTCCGAT 59.967 55.000 0.00 0.00 34.43 4.18
102 104 2.418910 ATCACCGAGGCAGAGTCCG 61.419 63.158 0.00 0.00 0.00 4.79
107 109 2.041115 CGAGGCAGAGTCCGAGTCA 61.041 63.158 6.01 0.00 0.00 3.41
117 119 1.275856 AGTCCGAGTCAGACGAGTAGT 59.724 52.381 0.83 0.00 39.31 2.73
118 120 2.495270 AGTCCGAGTCAGACGAGTAGTA 59.505 50.000 0.83 0.00 39.31 1.82
119 121 2.859538 GTCCGAGTCAGACGAGTAGTAG 59.140 54.545 0.00 0.00 0.00 2.57
191 193 7.893124 ACTGGTTTATCTATCGTAGGAGAAA 57.107 36.000 0.00 0.00 0.00 2.52
237 239 8.242053 ACCAAATATGTATCGAATCGTAGTAGG 58.758 37.037 1.52 0.00 0.00 3.18
295 297 1.404477 GTGTGCGCGCTTTAATTTGT 58.596 45.000 33.29 0.00 0.00 2.83
302 304 0.387878 CGCTTTAATTTGTGGCGGCA 60.388 50.000 7.97 7.97 41.77 5.69
306 308 0.243365 TTAATTTGTGGCGGCAGCTG 59.757 50.000 13.91 10.11 44.37 4.24
358 360 2.891112 CTAACCCGGCGTTGTATTGTA 58.109 47.619 15.93 0.00 35.79 2.41
367 369 5.106987 CCGGCGTTGTATTGTAACTTTTAGT 60.107 40.000 6.01 0.00 0.00 2.24
372 374 5.926214 TGTATTGTAACTTTTAGTGCGCA 57.074 34.783 5.66 5.66 0.00 6.09
402 404 0.809241 CGGCTGTTGGAGATGCTCTC 60.809 60.000 5.01 5.01 42.66 3.20
420 422 2.639347 TCTCAAGCAGGGAGATGACAAA 59.361 45.455 0.00 0.00 36.52 2.83
426 428 4.410099 AGCAGGGAGATGACAAATTTCAA 58.590 39.130 0.00 0.00 0.00 2.69
443 445 3.998099 TCAATGCAATTTGACACGGAA 57.002 38.095 0.00 0.00 31.22 4.30
446 448 4.022503 TCAATGCAATTTGACACGGAATGA 60.023 37.500 0.00 0.00 31.22 2.57
452 454 2.743636 TTGACACGGAATGAGGTCTC 57.256 50.000 0.00 0.00 0.00 3.36
471 473 4.026052 TCTCTTCAGATATGCCAGACACA 58.974 43.478 0.00 0.00 0.00 3.72
472 474 4.118410 CTCTTCAGATATGCCAGACACAC 58.882 47.826 0.00 0.00 0.00 3.82
513 515 7.716612 AGAAACCTCACTGTATTTTGAAAAGG 58.283 34.615 0.00 0.00 0.00 3.11
534 536 1.153489 CCTCCTGTCCAGCATCACG 60.153 63.158 0.00 0.00 0.00 4.35
589 591 5.163499 CCAGATTCTATTATACTCCCTCCGC 60.163 48.000 0.00 0.00 0.00 5.54
592 594 5.723672 TTCTATTATACTCCCTCCGCTTG 57.276 43.478 0.00 0.00 0.00 4.01
593 595 4.737578 TCTATTATACTCCCTCCGCTTGT 58.262 43.478 0.00 0.00 0.00 3.16
595 597 6.491383 TCTATTATACTCCCTCCGCTTGTAT 58.509 40.000 0.00 0.00 0.00 2.29
597 599 8.111545 TCTATTATACTCCCTCCGCTTGTATAA 58.888 37.037 0.00 0.00 39.10 0.98
598 600 6.585695 TTATACTCCCTCCGCTTGTATAAG 57.414 41.667 0.00 0.00 33.71 1.73
633 640 8.402798 ACATTCCAACAAATGACTACATACAA 57.597 30.769 3.78 0.00 38.64 2.41
634 641 8.855110 ACATTCCAACAAATGACTACATACAAA 58.145 29.630 3.78 0.00 38.64 2.83
635 642 9.689976 CATTCCAACAAATGACTACATACAAAA 57.310 29.630 0.00 0.00 38.64 2.44
816 826 4.487714 ACTCCTCGAGATGCCAAATTTA 57.512 40.909 15.71 0.00 33.32 1.40
853 863 0.608308 ACCTCCCGTTGGCTTAAAGC 60.608 55.000 0.00 0.00 41.46 3.51
897 913 3.274095 AGGGACAGCTGCTCTAATTTC 57.726 47.619 15.27 0.31 0.00 2.17
1026 1093 2.360475 GAGCCAGGCAACCAGGAC 60.360 66.667 15.80 0.00 34.28 3.85
1347 1414 3.381983 ATCGCCTGGTCGCTGACA 61.382 61.111 10.14 0.00 33.68 3.58
1348 1415 3.362399 ATCGCCTGGTCGCTGACAG 62.362 63.158 0.00 0.00 33.68 3.51
1467 1534 2.981302 CCGTGGATGCTCCTGTCA 59.019 61.111 4.21 0.00 37.46 3.58
1615 1682 2.567049 GGAGCAGCGACACGTACT 59.433 61.111 0.00 0.00 0.00 2.73
1866 1948 4.856607 CTCTCGTTCGGGAGCGGC 62.857 72.222 9.14 0.00 35.70 6.53
2084 2172 2.989824 CGTCCTCCTGTCGTGGGT 60.990 66.667 0.00 0.00 0.00 4.51
2223 2311 0.459237 CCGAGCAGAAGATGAACGCT 60.459 55.000 0.00 0.00 35.14 5.07
2401 2596 0.881796 CAGAGACAGAGCCACACGTA 59.118 55.000 0.00 0.00 0.00 3.57
2494 2689 8.758633 TTCTAGTGACGAAAAATAGAGGAAAG 57.241 34.615 0.00 0.00 0.00 2.62
2533 2728 1.996786 GCAAGCCACCGATCACCATG 61.997 60.000 0.00 0.00 0.00 3.66
2570 2765 2.548920 CGGGATTTGGTAGGCTGAGATC 60.549 54.545 0.00 0.00 0.00 2.75
2571 2766 2.224646 GGGATTTGGTAGGCTGAGATCC 60.225 54.545 0.00 3.14 0.00 3.36
2572 2767 2.439507 GGATTTGGTAGGCTGAGATCCA 59.560 50.000 0.00 0.00 33.48 3.41
2573 2768 3.471680 GATTTGGTAGGCTGAGATCCAC 58.528 50.000 0.00 0.00 0.00 4.02
2574 2769 1.951209 TTGGTAGGCTGAGATCCACA 58.049 50.000 0.00 0.00 0.00 4.17
2575 2770 1.489481 TGGTAGGCTGAGATCCACAG 58.511 55.000 11.63 11.63 38.27 3.66
2576 2771 1.273267 TGGTAGGCTGAGATCCACAGT 60.273 52.381 15.64 3.70 37.64 3.55
2577 2772 1.834263 GGTAGGCTGAGATCCACAGTT 59.166 52.381 15.64 9.28 37.64 3.16
2578 2773 2.237392 GGTAGGCTGAGATCCACAGTTT 59.763 50.000 15.64 9.02 37.64 2.66
2579 2774 3.451178 GGTAGGCTGAGATCCACAGTTTA 59.549 47.826 15.64 8.31 37.64 2.01
2580 2775 4.101741 GGTAGGCTGAGATCCACAGTTTAT 59.898 45.833 15.64 5.72 37.64 1.40
2581 2776 4.851639 AGGCTGAGATCCACAGTTTATT 57.148 40.909 15.64 0.32 37.64 1.40
2582 2777 5.184892 AGGCTGAGATCCACAGTTTATTT 57.815 39.130 15.64 0.00 37.64 1.40
2583 2778 5.574188 AGGCTGAGATCCACAGTTTATTTT 58.426 37.500 15.64 0.00 37.64 1.82
2584 2779 5.649831 AGGCTGAGATCCACAGTTTATTTTC 59.350 40.000 15.64 1.30 37.64 2.29
2585 2780 5.447818 GGCTGAGATCCACAGTTTATTTTCG 60.448 44.000 15.64 0.00 37.64 3.46
2586 2781 5.122396 GCTGAGATCCACAGTTTATTTTCGT 59.878 40.000 15.64 0.00 37.64 3.85
2587 2782 6.673316 GCTGAGATCCACAGTTTATTTTCGTC 60.673 42.308 15.64 0.00 37.64 4.20
2588 2783 6.464222 TGAGATCCACAGTTTATTTTCGTCT 58.536 36.000 0.00 0.00 0.00 4.18
2589 2784 6.590292 TGAGATCCACAGTTTATTTTCGTCTC 59.410 38.462 0.00 0.00 0.00 3.36
2590 2785 6.464222 AGATCCACAGTTTATTTTCGTCTCA 58.536 36.000 0.00 0.00 0.00 3.27
2591 2786 7.106239 AGATCCACAGTTTATTTTCGTCTCAT 58.894 34.615 0.00 0.00 0.00 2.90
2592 2787 6.721571 TCCACAGTTTATTTTCGTCTCATC 57.278 37.500 0.00 0.00 0.00 2.92
2593 2788 6.227522 TCCACAGTTTATTTTCGTCTCATCA 58.772 36.000 0.00 0.00 0.00 3.07
2594 2789 6.147164 TCCACAGTTTATTTTCGTCTCATCAC 59.853 38.462 0.00 0.00 0.00 3.06
2595 2790 6.073276 CCACAGTTTATTTTCGTCTCATCACA 60.073 38.462 0.00 0.00 0.00 3.58
2596 2791 6.792250 CACAGTTTATTTTCGTCTCATCACAC 59.208 38.462 0.00 0.00 0.00 3.82
2597 2792 6.706270 ACAGTTTATTTTCGTCTCATCACACT 59.294 34.615 0.00 0.00 0.00 3.55
2598 2793 7.870954 ACAGTTTATTTTCGTCTCATCACACTA 59.129 33.333 0.00 0.00 0.00 2.74
2599 2794 8.873830 CAGTTTATTTTCGTCTCATCACACTAT 58.126 33.333 0.00 0.00 0.00 2.12
2600 2795 9.436957 AGTTTATTTTCGTCTCATCACACTATT 57.563 29.630 0.00 0.00 0.00 1.73
2619 2814 2.169832 TTTTTCTCTCCCTCGCACTG 57.830 50.000 0.00 0.00 0.00 3.66
2620 2815 1.338107 TTTTCTCTCCCTCGCACTGA 58.662 50.000 0.00 0.00 0.00 3.41
2621 2816 1.338107 TTTCTCTCCCTCGCACTGAA 58.662 50.000 0.00 0.00 0.00 3.02
2622 2817 1.338107 TTCTCTCCCTCGCACTGAAA 58.662 50.000 0.00 0.00 0.00 2.69
2623 2818 1.338107 TCTCTCCCTCGCACTGAAAA 58.662 50.000 0.00 0.00 0.00 2.29
2624 2819 1.000955 TCTCTCCCTCGCACTGAAAAC 59.999 52.381 0.00 0.00 0.00 2.43
2625 2820 0.034896 TCTCCCTCGCACTGAAAACC 59.965 55.000 0.00 0.00 0.00 3.27
2626 2821 0.250295 CTCCCTCGCACTGAAAACCA 60.250 55.000 0.00 0.00 0.00 3.67
2627 2822 0.181587 TCCCTCGCACTGAAAACCAA 59.818 50.000 0.00 0.00 0.00 3.67
2628 2823 1.028905 CCCTCGCACTGAAAACCAAA 58.971 50.000 0.00 0.00 0.00 3.28
2629 2824 1.613437 CCCTCGCACTGAAAACCAAAT 59.387 47.619 0.00 0.00 0.00 2.32
2630 2825 2.351738 CCCTCGCACTGAAAACCAAATC 60.352 50.000 0.00 0.00 0.00 2.17
2631 2826 2.574322 CTCGCACTGAAAACCAAATCG 58.426 47.619 0.00 0.00 0.00 3.34
2632 2827 2.214347 TCGCACTGAAAACCAAATCGA 58.786 42.857 0.00 0.00 0.00 3.59
2633 2828 2.811431 TCGCACTGAAAACCAAATCGAT 59.189 40.909 0.00 0.00 0.00 3.59
2634 2829 3.252215 TCGCACTGAAAACCAAATCGATT 59.748 39.130 4.39 4.39 0.00 3.34
2635 2830 3.980775 CGCACTGAAAACCAAATCGATTT 59.019 39.130 17.60 17.60 0.00 2.17
2636 2831 4.143556 CGCACTGAAAACCAAATCGATTTG 60.144 41.667 34.03 34.03 45.04 2.32
2645 2840 2.719798 CAAATCGATTTGGCCGATCAC 58.280 47.619 33.59 1.64 44.85 3.06
2646 2841 2.332063 AATCGATTTGGCCGATCACT 57.668 45.000 16.47 3.08 44.85 3.41
2647 2842 1.871080 ATCGATTTGGCCGATCACTC 58.129 50.000 16.47 2.10 42.35 3.51
2648 2843 0.824109 TCGATTTGGCCGATCACTCT 59.176 50.000 16.47 0.00 0.00 3.24
2649 2844 1.207089 TCGATTTGGCCGATCACTCTT 59.793 47.619 16.47 0.00 0.00 2.85
2650 2845 2.009774 CGATTTGGCCGATCACTCTTT 58.990 47.619 16.47 0.00 0.00 2.52
2651 2846 2.420022 CGATTTGGCCGATCACTCTTTT 59.580 45.455 16.47 0.00 0.00 2.27
2652 2847 3.728864 CGATTTGGCCGATCACTCTTTTG 60.729 47.826 16.47 0.00 0.00 2.44
2653 2848 2.270352 TTGGCCGATCACTCTTTTGT 57.730 45.000 0.00 0.00 0.00 2.83
2654 2849 2.270352 TGGCCGATCACTCTTTTGTT 57.730 45.000 0.00 0.00 0.00 2.83
2655 2850 2.582052 TGGCCGATCACTCTTTTGTTT 58.418 42.857 0.00 0.00 0.00 2.83
2665 2860 6.102897 TCACTCTTTTGTTTTTGGGAAACA 57.897 33.333 0.55 0.55 38.26 2.83
2681 2876 0.465460 AACATTATGTGCCGGCGGAT 60.465 50.000 33.44 17.40 0.00 4.18
2749 2945 4.132336 ACGATCTATGGCTAACACGTCTA 58.868 43.478 0.00 0.00 0.00 2.59
2750 2946 4.024218 ACGATCTATGGCTAACACGTCTAC 60.024 45.833 0.00 0.00 0.00 2.59
2807 3009 3.384532 CCCACCACATGCCCTTGC 61.385 66.667 0.00 0.00 38.26 4.01
2827 3327 2.109774 CCCCATCATGGCTGCTTTTTA 58.890 47.619 0.00 0.00 35.79 1.52
2940 3478 1.076024 TCCCGGTGTACTAGAACCAGT 59.924 52.381 0.00 0.00 36.14 4.00
3021 3559 0.940833 TTTGCTGCAATCGTCGTCAA 59.059 45.000 16.77 0.00 0.00 3.18
3027 3565 3.058129 GCTGCAATCGTCGTCAATTTTTC 59.942 43.478 0.00 0.00 0.00 2.29
3055 3593 7.752695 ACAATTAGCGAGAAAATTTCCTACAG 58.247 34.615 1.57 0.00 0.00 2.74
3057 3595 7.923414 ATTAGCGAGAAAATTTCCTACAGTT 57.077 32.000 1.57 0.00 0.00 3.16
3066 3604 9.533831 AGAAAATTTCCTACAGTTATTCATGGT 57.466 29.630 1.57 0.00 0.00 3.55
3082 3620 0.681887 TGGTAGAGATGCGACCCGAA 60.682 55.000 0.00 0.00 41.17 4.30
3140 3685 2.018542 TTTTTGCTACTAGCGGCGAT 57.981 45.000 12.98 7.15 46.26 4.58
3165 3710 6.015603 TGTTGTTTTGCTACATCCATTCATGA 60.016 34.615 0.00 0.00 0.00 3.07
3273 3837 2.359848 CACATTCATTCATGGCGGTGAT 59.640 45.455 0.00 0.00 0.00 3.06
3279 3843 0.892814 TTCATGGCGGTGATGCAACA 60.893 50.000 0.00 0.00 36.28 3.33
3285 3948 1.745115 CGGTGATGCAACACGGGAT 60.745 57.895 22.01 0.00 41.12 3.85
3310 3973 0.958099 CGACGACGATTTTTGTTGCG 59.042 50.000 0.00 0.00 42.66 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 72 0.970937 GGTGATGTCCTCCTCCGACA 60.971 60.000 0.00 0.00 44.00 4.35
102 104 6.795399 ACTACTACTACTACTCGTCTGACTC 58.205 44.000 6.21 0.00 0.00 3.36
107 109 7.600752 ACGAAAAACTACTACTACTACTCGTCT 59.399 37.037 0.00 0.00 29.40 4.18
160 162 4.202223 ACGATAGATAAACCAGTTCGGCAT 60.202 41.667 0.00 0.00 38.05 4.40
164 166 6.204301 TCTCCTACGATAGATAAACCAGTTCG 59.796 42.308 0.00 0.00 41.38 3.95
207 209 5.404366 ACGATTCGATACATATTTGGTTCCG 59.596 40.000 13.95 0.00 0.00 4.30
279 281 1.006314 GCCACAAATTAAAGCGCGCA 61.006 50.000 35.10 13.52 0.00 6.09
382 384 2.437359 AGCATCTCCAACAGCCGC 60.437 61.111 0.00 0.00 0.00 6.53
402 404 4.219070 TGAAATTTGTCATCTCCCTGCTTG 59.781 41.667 0.00 0.00 0.00 4.01
420 422 4.880759 TCCGTGTCAAATTGCATTGAAAT 58.119 34.783 4.34 0.00 40.76 2.17
426 428 3.119388 CCTCATTCCGTGTCAAATTGCAT 60.119 43.478 0.00 0.00 0.00 3.96
443 445 4.229639 TGGCATATCTGAAGAGACCTCAT 58.770 43.478 0.00 0.00 0.00 2.90
446 448 3.640967 GTCTGGCATATCTGAAGAGACCT 59.359 47.826 0.00 0.00 0.00 3.85
452 454 3.865446 TGTGTGTCTGGCATATCTGAAG 58.135 45.455 0.00 0.00 0.00 3.02
471 473 5.432060 AGGTTTCTATTATTAGTGGCCCTGT 59.568 40.000 0.00 0.00 0.00 4.00
472 474 5.941788 AGGTTTCTATTATTAGTGGCCCTG 58.058 41.667 0.00 0.00 0.00 4.45
505 507 2.512056 TGGACAGGAGGTTCCTTTTCAA 59.488 45.455 0.00 0.00 46.91 2.69
513 515 0.615331 TGATGCTGGACAGGAGGTTC 59.385 55.000 1.01 0.00 30.57 3.62
561 563 6.875469 AGGGAGTATAATAGAATCTGGTCCA 58.125 40.000 0.00 0.00 0.00 4.02
564 566 5.952947 CGGAGGGAGTATAATAGAATCTGGT 59.047 44.000 0.00 0.00 0.00 4.00
568 570 6.071278 ACAAGCGGAGGGAGTATAATAGAATC 60.071 42.308 0.00 0.00 0.00 2.52
577 579 4.481072 ACTTATACAAGCGGAGGGAGTAT 58.519 43.478 0.00 0.00 34.94 2.12
606 613 8.511321 TGTATGTAGTCATTTGTTGGAATGTTC 58.489 33.333 0.00 0.00 38.04 3.18
607 614 8.402798 TGTATGTAGTCATTTGTTGGAATGTT 57.597 30.769 0.00 0.00 38.04 2.71
816 826 4.221041 GGAGGTAGTGAAGAGCTACAAGTT 59.779 45.833 0.00 0.00 40.24 2.66
853 863 2.404789 GCGTCATGGTTGGCATCG 59.595 61.111 0.00 0.00 0.00 3.84
897 913 2.028476 TCACTTGGTTGTACGATGGGAG 60.028 50.000 0.00 0.00 0.00 4.30
1467 1534 2.883828 CGGGAGGTGCAGGAACAGT 61.884 63.158 0.00 0.00 0.00 3.55
1615 1682 2.221299 CCAAGGACAGGAACCCGGA 61.221 63.158 0.73 0.00 0.00 5.14
2142 2230 1.216710 CTCCAGGCTCGAGTTCCAC 59.783 63.158 15.13 0.00 0.00 4.02
2494 2689 7.360861 GGCTTGCAAACATAGTTTTATTTTCCC 60.361 37.037 0.00 0.00 0.00 3.97
2506 2701 1.164411 TCGGTGGCTTGCAAACATAG 58.836 50.000 0.00 1.94 0.00 2.23
2533 2728 5.595257 AATCCCGTTTTAGGAGTAGAGAC 57.405 43.478 0.00 0.00 36.67 3.36
2570 2765 6.073276 TGTGATGAGACGAAAATAAACTGTGG 60.073 38.462 0.00 0.00 0.00 4.17
2571 2766 6.792250 GTGTGATGAGACGAAAATAAACTGTG 59.208 38.462 0.00 0.00 0.00 3.66
2572 2767 6.706270 AGTGTGATGAGACGAAAATAAACTGT 59.294 34.615 0.00 0.00 0.00 3.55
2573 2768 7.121974 AGTGTGATGAGACGAAAATAAACTG 57.878 36.000 0.00 0.00 0.00 3.16
2574 2769 9.436957 AATAGTGTGATGAGACGAAAATAAACT 57.563 29.630 0.00 0.00 0.00 2.66
2600 2795 1.691976 TCAGTGCGAGGGAGAGAAAAA 59.308 47.619 0.00 0.00 0.00 1.94
2601 2796 1.338107 TCAGTGCGAGGGAGAGAAAA 58.662 50.000 0.00 0.00 0.00 2.29
2602 2797 1.338107 TTCAGTGCGAGGGAGAGAAA 58.662 50.000 0.00 0.00 0.00 2.52
2603 2798 1.338107 TTTCAGTGCGAGGGAGAGAA 58.662 50.000 0.00 0.00 0.00 2.87
2604 2799 1.000955 GTTTTCAGTGCGAGGGAGAGA 59.999 52.381 0.00 0.00 0.00 3.10
2605 2800 1.433534 GTTTTCAGTGCGAGGGAGAG 58.566 55.000 0.00 0.00 0.00 3.20
2606 2801 0.034896 GGTTTTCAGTGCGAGGGAGA 59.965 55.000 0.00 0.00 0.00 3.71
2607 2802 0.250295 TGGTTTTCAGTGCGAGGGAG 60.250 55.000 0.00 0.00 0.00 4.30
2608 2803 0.181587 TTGGTTTTCAGTGCGAGGGA 59.818 50.000 0.00 0.00 0.00 4.20
2609 2804 1.028905 TTTGGTTTTCAGTGCGAGGG 58.971 50.000 0.00 0.00 0.00 4.30
2610 2805 2.665519 CGATTTGGTTTTCAGTGCGAGG 60.666 50.000 0.00 0.00 0.00 4.63
2611 2806 2.223144 TCGATTTGGTTTTCAGTGCGAG 59.777 45.455 0.00 0.00 0.00 5.03
2612 2807 2.214347 TCGATTTGGTTTTCAGTGCGA 58.786 42.857 0.00 0.00 0.00 5.10
2613 2808 2.679355 TCGATTTGGTTTTCAGTGCG 57.321 45.000 0.00 0.00 0.00 5.34
2614 2809 5.254669 CAAATCGATTTGGTTTTCAGTGC 57.745 39.130 33.59 0.00 42.51 4.40
2625 2820 2.355756 AGTGATCGGCCAAATCGATTTG 59.644 45.455 34.03 34.03 45.81 2.32
2626 2821 2.614057 GAGTGATCGGCCAAATCGATTT 59.386 45.455 17.60 17.60 45.81 2.17
2627 2822 2.158900 AGAGTGATCGGCCAAATCGATT 60.159 45.455 4.39 4.39 45.81 3.34
2629 2824 0.824109 AGAGTGATCGGCCAAATCGA 59.176 50.000 2.24 0.00 41.04 3.59
2630 2825 1.656652 AAGAGTGATCGGCCAAATCG 58.343 50.000 2.24 0.00 0.00 3.34
2631 2826 3.191371 ACAAAAGAGTGATCGGCCAAATC 59.809 43.478 2.24 5.80 0.00 2.17
2632 2827 3.157087 ACAAAAGAGTGATCGGCCAAAT 58.843 40.909 2.24 0.00 0.00 2.32
2633 2828 2.582052 ACAAAAGAGTGATCGGCCAAA 58.418 42.857 2.24 0.00 0.00 3.28
2634 2829 2.270352 ACAAAAGAGTGATCGGCCAA 57.730 45.000 2.24 0.00 0.00 4.52
2635 2830 2.270352 AACAAAAGAGTGATCGGCCA 57.730 45.000 2.24 0.00 0.00 5.36
2636 2831 3.643159 AAAACAAAAGAGTGATCGGCC 57.357 42.857 0.00 0.00 0.00 6.13
2637 2832 3.735746 CCAAAAACAAAAGAGTGATCGGC 59.264 43.478 0.00 0.00 0.00 5.54
2638 2833 4.037446 TCCCAAAAACAAAAGAGTGATCGG 59.963 41.667 0.00 0.00 0.00 4.18
2639 2834 5.181690 TCCCAAAAACAAAAGAGTGATCG 57.818 39.130 0.00 0.00 0.00 3.69
2640 2835 6.816140 TGTTTCCCAAAAACAAAAGAGTGATC 59.184 34.615 1.09 0.00 37.22 2.92
2641 2836 6.706295 TGTTTCCCAAAAACAAAAGAGTGAT 58.294 32.000 1.09 0.00 37.22 3.06
2642 2837 6.102897 TGTTTCCCAAAAACAAAAGAGTGA 57.897 33.333 1.09 0.00 37.22 3.41
2643 2838 6.983474 ATGTTTCCCAAAAACAAAAGAGTG 57.017 33.333 7.36 0.00 42.57 3.51
2644 2839 9.108284 CATAATGTTTCCCAAAAACAAAAGAGT 57.892 29.630 7.36 0.00 42.57 3.24
2645 2840 9.108284 ACATAATGTTTCCCAAAAACAAAAGAG 57.892 29.630 7.36 1.36 42.57 2.85
2646 2841 8.887717 CACATAATGTTTCCCAAAAACAAAAGA 58.112 29.630 7.36 0.00 42.57 2.52
2647 2842 7.643371 GCACATAATGTTTCCCAAAAACAAAAG 59.357 33.333 7.36 2.21 42.57 2.27
2648 2843 7.415653 GGCACATAATGTTTCCCAAAAACAAAA 60.416 33.333 7.36 0.40 42.57 2.44
2649 2844 6.038714 GGCACATAATGTTTCCCAAAAACAAA 59.961 34.615 7.36 0.71 42.57 2.83
2650 2845 5.529060 GGCACATAATGTTTCCCAAAAACAA 59.471 36.000 7.36 0.00 42.57 2.83
2651 2846 5.059833 GGCACATAATGTTTCCCAAAAACA 58.940 37.500 5.87 5.87 43.33 2.83
2652 2847 4.151512 CGGCACATAATGTTTCCCAAAAAC 59.848 41.667 0.00 0.00 0.00 2.43
2653 2848 4.310769 CGGCACATAATGTTTCCCAAAAA 58.689 39.130 0.00 0.00 0.00 1.94
2654 2849 3.306364 CCGGCACATAATGTTTCCCAAAA 60.306 43.478 0.00 0.00 0.00 2.44
2655 2850 2.232452 CCGGCACATAATGTTTCCCAAA 59.768 45.455 0.00 0.00 0.00 3.28
2665 2860 1.667830 CGATCCGCCGGCACATAAT 60.668 57.895 28.98 11.47 0.00 1.28
2749 2945 3.988379 ACGCAAACAATGAATCTGTGT 57.012 38.095 0.00 0.00 0.00 3.72
2750 2946 4.043750 ACAACGCAAACAATGAATCTGTG 58.956 39.130 0.00 0.00 0.00 3.66
2807 3009 0.906775 AAAAAGCAGCCATGATGGGG 59.093 50.000 14.26 0.00 38.19 4.96
2827 3327 3.209410 GACGCATTGGAGGATGAGAAAT 58.791 45.455 0.00 0.00 32.15 2.17
2967 3505 2.805546 GCGGTCGTAGCTCCATCA 59.194 61.111 0.00 0.00 0.00 3.07
3000 3538 1.535028 TGACGACGATTGCAGCAAAAT 59.465 42.857 12.97 0.00 0.00 1.82
3027 3565 9.704098 GTAGGAAATTTTCTCGCTAATTGTAAG 57.296 33.333 1.07 0.00 0.00 2.34
3055 3593 4.686554 GGTCGCATCTCTACCATGAATAAC 59.313 45.833 0.00 0.00 33.28 1.89
3057 3595 3.258372 GGGTCGCATCTCTACCATGAATA 59.742 47.826 0.00 0.00 34.83 1.75
3066 3604 0.099968 CGTTTCGGGTCGCATCTCTA 59.900 55.000 0.00 0.00 0.00 2.43
3082 3620 1.095228 AAATCATCATCGCCGCCGTT 61.095 50.000 0.00 0.00 35.54 4.44
3093 3631 1.818060 CGGGTCCAGCAAAAATCATCA 59.182 47.619 0.00 0.00 0.00 3.07
3133 3678 0.109964 TAGCAAAACAACATCGCCGC 60.110 50.000 0.00 0.00 0.00 6.53
3140 3685 5.781210 TGAATGGATGTAGCAAAACAACA 57.219 34.783 0.00 0.00 32.02 3.33
3165 3710 1.102222 GTCCCTAGTCGCATCTCCGT 61.102 60.000 0.00 0.00 0.00 4.69
3249 3813 1.744522 CCGCCATGAATGAATGTGACA 59.255 47.619 0.00 0.00 0.00 3.58
3250 3814 1.745087 ACCGCCATGAATGAATGTGAC 59.255 47.619 0.00 0.00 0.00 3.67
3251 3815 1.744522 CACCGCCATGAATGAATGTGA 59.255 47.619 0.00 0.00 0.00 3.58
3252 3816 1.744522 TCACCGCCATGAATGAATGTG 59.255 47.619 0.00 0.00 0.00 3.21
3285 3948 4.728102 AAATCGTCGTCGCCGCCA 62.728 61.111 0.00 0.00 36.96 5.69


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

AutoCloner maintained by Alex Coulton.