Multiple sequence alignment - TraesCS7D01G357800

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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 TraesCS7D01G357800 chr7D 100.000 3203 0 0 1 3203 461126002 461129204 0.000000e+00 5915.0
1 TraesCS7D01G357800 chr7D 85.199 277 33 5 2923 3192 232475881 232476156 8.750000e-71 278.0
2 TraesCS7D01G357800 chr7B 94.535 2507 70 24 1 2487 483754324 483756783 0.000000e+00 3808.0
3 TraesCS7D01G357800 chr7B 87.970 532 36 8 2675 3203 483757256 483757762 1.270000e-168 603.0
4 TraesCS7D01G357800 chr7B 92.727 110 6 1 2485 2594 483756845 483756952 1.190000e-34 158.0
5 TraesCS7D01G357800 chr7B 100.000 50 0 0 2628 2677 483756999 483756950 3.400000e-15 93.5
6 TraesCS7D01G357800 chr4A 91.809 1819 99 23 706 2487 250524415 250526220 0.000000e+00 2488.0
7 TraesCS7D01G357800 chr4A 84.946 279 32 2 2923 3192 535471537 535471814 1.130000e-69 274.0
8 TraesCS7D01G357800 chr4A 85.057 261 14 12 67 314 250519093 250519341 3.190000e-60 243.0
9 TraesCS7D01G357800 chr4A 91.824 159 8 3 2686 2839 250890851 250891009 1.930000e-52 217.0
10 TraesCS7D01G357800 chr4A 88.024 167 18 2 3015 3181 508005368 508005532 2.520000e-46 196.0
11 TraesCS7D01G357800 chr4A 88.312 77 8 1 2492 2567 250526271 250526347 1.220000e-14 91.6
12 TraesCS7D01G357800 chr4D 91.720 1703 84 23 829 2487 152820094 152818405 0.000000e+00 2311.0
13 TraesCS7D01G357800 chr4D 86.405 331 18 11 289 605 152893982 152893665 1.420000e-88 337.0
14 TraesCS7D01G357800 chr4D 83.636 275 34 4 2920 3184 488164778 488165051 6.860000e-62 248.0
15 TraesCS7D01G357800 chr4D 90.476 147 4 3 2676 2815 152818209 152818066 5.460000e-43 185.0
16 TraesCS7D01G357800 chr4D 87.786 131 12 2 2879 3007 12712668 12712540 1.990000e-32 150.0
17 TraesCS7D01G357800 chr4D 94.186 86 5 0 167 252 152894074 152893989 7.210000e-27 132.0
18 TraesCS7D01G357800 chr4D 91.954 87 7 0 2923 3009 297071068 297071154 4.340000e-24 122.0
19 TraesCS7D01G357800 chr4D 92.208 77 2 3 2492 2567 152818351 152818278 4.370000e-19 106.0
20 TraesCS7D01G357800 chr1B 95.211 710 30 2 1572 2281 60351477 60352182 0.000000e+00 1120.0
21 TraesCS7D01G357800 chr1B 91.667 744 45 10 846 1577 60345466 60346204 0.000000e+00 1014.0
22 TraesCS7D01G357800 chr1B 80.332 361 52 17 2492 2842 60352369 60352720 4.100000e-64 255.0
23 TraesCS7D01G357800 chr2D 85.921 277 29 2 2923 3190 543288032 543287757 1.450000e-73 287.0
24 TraesCS7D01G357800 chr2D 84.496 258 25 8 2938 3193 611209097 611208853 1.150000e-59 241.0
25 TraesCS7D01G357800 chr6B 85.357 280 31 4 2920 3190 674978516 674978794 6.760000e-72 281.0
26 TraesCS7D01G357800 chr3D 85.039 254 27 3 2941 3184 300116904 300117156 6.860000e-62 248.0
27 TraesCS7D01G357800 chr5D 84.810 158 15 3 2920 3068 519215134 519215291 1.990000e-32 150.0
28 TraesCS7D01G357800 chr5D 90.323 93 9 0 2920 3012 418625208 418625300 4.340000e-24 122.0
29 TraesCS7D01G357800 chr2B 83.636 165 13 4 2903 3067 65879937 65879787 3.330000e-30 143.0
30 TraesCS7D01G357800 chr4B 92.222 90 7 0 2923 3012 659687493 659687404 9.330000e-26 128.0
31 TraesCS7D01G357800 chr2A 83.221 149 12 4 2920 3067 649006942 649007078 1.210000e-24 124.0
32 TraesCS7D01G357800 chr3A 91.954 87 7 0 2923 3009 174950049 174950135 4.340000e-24 122.0


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 TraesCS7D01G357800 chr7D 461126002 461129204 3202 False 5915.000000 5915 100.0000 1 3203 1 chr7D.!!$F2 3202
1 TraesCS7D01G357800 chr7B 483754324 483757762 3438 False 1523.000000 3808 91.7440 1 3203 3 chr7B.!!$F1 3202
2 TraesCS7D01G357800 chr4A 250524415 250526347 1932 False 1289.800000 2488 90.0605 706 2567 2 chr4A.!!$F5 1861
3 TraesCS7D01G357800 chr4D 152818066 152820094 2028 True 867.333333 2311 91.4680 829 2815 3 chr4D.!!$R2 1986
4 TraesCS7D01G357800 chr1B 60345466 60346204 738 False 1014.000000 1014 91.6670 846 1577 1 chr1B.!!$F1 731
5 TraesCS7D01G357800 chr1B 60351477 60352720 1243 False 687.500000 1120 87.7715 1572 2842 2 chr1B.!!$F2 1270

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
512 521 0.033228 AGCGCAGTGGAGATAGATGC 59.967 55.0 11.47 0.0 0.00 3.91 F
513 522 0.033228 GCGCAGTGGAGATAGATGCT 59.967 55.0 0.30 0.0 34.75 3.79 F
1499 1561 1.056660 AAGAACTCCTTCTCCGGCAA 58.943 50.0 0.00 0.0 35.52 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1499 1561 1.448922 GAGCAGCGACGAGGGTATCT 61.449 60.000 0.0 0.0 0.00 1.98 R
1614 1676 1.616865 CCGGATAGGCGATTGTTCCTA 59.383 52.381 0.0 0.0 39.11 2.94 R
2631 2803 0.110486 CCTAGTTGTGCAGGGTGGTT 59.890 55.000 0.0 0.0 0.00 3.67 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
26 27 6.902224 AAAAAGAAACAACAATGTACCTGC 57.098 33.333 0.00 0.00 39.40 4.85
48 49 2.508439 GCGTCGAGATCGGGCAAA 60.508 61.111 12.21 0.00 40.29 3.68
49 50 2.799540 GCGTCGAGATCGGGCAAAC 61.800 63.158 12.21 0.00 40.29 2.93
51 52 0.736325 CGTCGAGATCGGGCAAACTT 60.736 55.000 1.91 0.00 40.29 2.66
56 57 3.066342 TCGAGATCGGGCAAACTTAGTAG 59.934 47.826 1.91 0.00 40.29 2.57
104 105 2.370281 GCAGCTGCACTTACAGTCTA 57.630 50.000 33.36 0.00 39.96 2.59
156 157 8.142994 ACGCTTTAGAGTTGGATTATGTATTG 57.857 34.615 0.00 0.00 0.00 1.90
194 195 7.805163 TCTCTGTATTTGGATGGATTACATGT 58.195 34.615 2.69 2.69 40.72 3.21
195 196 7.716560 TCTCTGTATTTGGATGGATTACATGTG 59.283 37.037 9.11 0.00 40.72 3.21
196 197 7.572814 TCTGTATTTGGATGGATTACATGTGA 58.427 34.615 9.11 0.00 40.72 3.58
197 198 7.498900 TCTGTATTTGGATGGATTACATGTGAC 59.501 37.037 9.11 0.00 40.72 3.67
198 199 5.756195 ATTTGGATGGATTACATGTGACG 57.244 39.130 9.11 0.00 40.72 4.35
199 200 3.192541 TGGATGGATTACATGTGACGG 57.807 47.619 9.11 0.00 40.72 4.79
200 201 2.503765 TGGATGGATTACATGTGACGGT 59.496 45.455 9.11 0.00 40.72 4.83
257 262 5.182001 GTCTTTGTGATTTGTCATAGCACCT 59.818 40.000 8.84 0.00 0.00 4.00
268 273 5.208890 TGTCATAGCACCTATGGACTTAGT 58.791 41.667 11.19 0.00 42.71 2.24
287 292 6.314648 ACTTAGTATCATGTCATGCACACTTG 59.685 38.462 8.03 0.00 38.04 3.16
317 322 1.902508 TGCACTGGAAGCTAGCTAAGT 59.097 47.619 19.70 18.35 37.60 2.24
511 520 2.133553 CAAGCGCAGTGGAGATAGATG 58.866 52.381 11.47 0.00 0.00 2.90
512 521 0.033228 AGCGCAGTGGAGATAGATGC 59.967 55.000 11.47 0.00 0.00 3.91
513 522 0.033228 GCGCAGTGGAGATAGATGCT 59.967 55.000 0.30 0.00 34.75 3.79
516 525 2.482664 CGCAGTGGAGATAGATGCTTGT 60.483 50.000 0.00 0.00 34.75 3.16
517 526 3.129871 GCAGTGGAGATAGATGCTTGTC 58.870 50.000 0.00 0.00 34.10 3.18
519 528 2.703007 AGTGGAGATAGATGCTTGTCCC 59.297 50.000 0.00 0.00 0.00 4.46
520 529 2.435805 GTGGAGATAGATGCTTGTCCCA 59.564 50.000 0.00 0.00 0.00 4.37
521 530 2.702478 TGGAGATAGATGCTTGTCCCAG 59.298 50.000 0.00 0.00 0.00 4.45
610 628 2.069430 GCCTCTCTTCTCCCCAGGG 61.069 68.421 0.00 0.00 0.00 4.45
650 668 4.475747 AGGACCAGGACCCGAATTAAAATA 59.524 41.667 4.04 0.00 0.00 1.40
808 831 1.734477 CTTGTCCGTGAGCGACAGG 60.734 63.158 0.00 0.00 40.56 4.00
825 848 2.668632 GATGCAGTCGGGTGGGAA 59.331 61.111 0.00 0.00 0.00 3.97
848 871 2.045829 ACACCACACCACACGCAA 60.046 55.556 0.00 0.00 0.00 4.85
856 879 1.202710 ACACCACACGCAAGGTTATCA 60.203 47.619 0.00 0.00 46.39 2.15
888 915 3.682292 ATCCCCAGCGCGTTCTTCC 62.682 63.158 8.43 0.00 0.00 3.46
925 955 4.306471 CAACGCCGCGCTGAACAA 62.306 61.111 13.88 0.00 0.00 2.83
942 972 3.251479 ACAATGCGATTCACTGAGCTA 57.749 42.857 0.00 0.00 0.00 3.32
944 974 3.193263 CAATGCGATTCACTGAGCTACT 58.807 45.455 0.00 0.00 0.00 2.57
945 975 4.142160 ACAATGCGATTCACTGAGCTACTA 60.142 41.667 0.00 0.00 0.00 1.82
947 977 2.099263 TGCGATTCACTGAGCTACTACC 59.901 50.000 0.00 0.00 0.00 3.18
948 978 2.359531 GCGATTCACTGAGCTACTACCT 59.640 50.000 0.00 0.00 0.00 3.08
959 989 1.335496 GCTACTACCTCGCTCTCCTTG 59.665 57.143 0.00 0.00 0.00 3.61
1047 1080 2.435059 GTGTTCCTGCTCCTCGCC 60.435 66.667 0.00 0.00 38.05 5.54
1185 1218 3.524648 TTCGTGGGACTTCACCGGC 62.525 63.158 0.00 0.00 34.36 6.13
1470 1532 2.182030 CCTGCTCTTCGGACGGTC 59.818 66.667 0.00 0.00 0.00 4.79
1499 1561 1.056660 AAGAACTCCTTCTCCGGCAA 58.943 50.000 0.00 0.00 35.52 4.52
1680 1742 0.321387 TCGTGTACCTCAGTCTCGCT 60.321 55.000 0.00 0.00 0.00 4.93
2217 2282 4.140543 AGGGGGTAAGGAAGGAAATGTTTT 60.141 41.667 0.00 0.00 0.00 2.43
2426 2520 1.035923 TGCAAAGAAATGTTCGGCCA 58.964 45.000 2.24 0.00 34.02 5.36
2594 2766 3.498397 CGGTTTCAGAATGTAGCAACTGT 59.502 43.478 0.00 0.00 37.40 3.55
2595 2767 4.611355 CGGTTTCAGAATGTAGCAACTGTG 60.611 45.833 0.00 0.00 37.40 3.66
2597 2769 5.207768 GTTTCAGAATGTAGCAACTGTGTG 58.792 41.667 0.00 0.00 37.40 3.82
2598 2770 4.071961 TCAGAATGTAGCAACTGTGTGT 57.928 40.909 0.00 0.00 37.40 3.72
2599 2771 4.450976 TCAGAATGTAGCAACTGTGTGTT 58.549 39.130 0.00 0.00 36.96 3.32
2601 2773 5.356751 TCAGAATGTAGCAACTGTGTGTTTT 59.643 36.000 0.00 0.00 35.13 2.43
2602 2774 6.035843 CAGAATGTAGCAACTGTGTGTTTTT 58.964 36.000 0.00 0.00 36.63 1.94
2603 2775 6.020440 CAGAATGTAGCAACTGTGTGTTTTTG 60.020 38.462 0.00 0.00 36.63 2.44
2607 2779 5.986135 TGTAGCAACTGTGTGTTTTTGTTTT 59.014 32.000 0.00 0.00 36.63 2.43
2608 2780 6.480320 TGTAGCAACTGTGTGTTTTTGTTTTT 59.520 30.769 0.00 0.00 36.63 1.94
2630 2802 8.667076 TTTTTCTACTTCCAAACTACTGTACC 57.333 34.615 0.00 0.00 0.00 3.34
2631 2803 6.982160 TTCTACTTCCAAACTACTGTACCA 57.018 37.500 0.00 0.00 0.00 3.25
2632 2804 6.982160 TCTACTTCCAAACTACTGTACCAA 57.018 37.500 0.00 0.00 0.00 3.67
2633 2805 6.752168 TCTACTTCCAAACTACTGTACCAAC 58.248 40.000 0.00 0.00 0.00 3.77
2634 2806 4.711399 ACTTCCAAACTACTGTACCAACC 58.289 43.478 0.00 0.00 0.00 3.77
2635 2807 4.164604 ACTTCCAAACTACTGTACCAACCA 59.835 41.667 0.00 0.00 0.00 3.67
2636 2808 4.075963 TCCAAACTACTGTACCAACCAC 57.924 45.455 0.00 0.00 0.00 4.16
2637 2809 3.143728 CCAAACTACTGTACCAACCACC 58.856 50.000 0.00 0.00 0.00 4.61
2638 2810 3.143728 CAAACTACTGTACCAACCACCC 58.856 50.000 0.00 0.00 0.00 4.61
2640 2812 1.975680 ACTACTGTACCAACCACCCTG 59.024 52.381 0.00 0.00 0.00 4.45
2641 2813 0.688487 TACTGTACCAACCACCCTGC 59.312 55.000 0.00 0.00 0.00 4.85
2642 2814 1.349542 ACTGTACCAACCACCCTGCA 61.350 55.000 0.00 0.00 0.00 4.41
2643 2815 0.889186 CTGTACCAACCACCCTGCAC 60.889 60.000 0.00 0.00 0.00 4.57
2644 2816 1.149627 GTACCAACCACCCTGCACA 59.850 57.895 0.00 0.00 0.00 4.57
2645 2817 0.466555 GTACCAACCACCCTGCACAA 60.467 55.000 0.00 0.00 0.00 3.33
2646 2818 0.466555 TACCAACCACCCTGCACAAC 60.467 55.000 0.00 0.00 0.00 3.32
2647 2819 1.455587 CCAACCACCCTGCACAACT 60.456 57.895 0.00 0.00 0.00 3.16
2648 2820 0.179004 CCAACCACCCTGCACAACTA 60.179 55.000 0.00 0.00 0.00 2.24
2650 2822 0.110486 AACCACCCTGCACAACTAGG 59.890 55.000 0.00 0.00 0.00 3.02
2651 2823 0.766674 ACCACCCTGCACAACTAGGA 60.767 55.000 0.00 0.00 36.11 2.94
2652 2824 0.620556 CCACCCTGCACAACTAGGAT 59.379 55.000 0.00 0.00 36.11 3.24
2653 2825 1.004745 CCACCCTGCACAACTAGGATT 59.995 52.381 0.00 0.00 36.11 3.01
2654 2826 2.359900 CACCCTGCACAACTAGGATTC 58.640 52.381 0.00 0.00 36.11 2.52
2655 2827 1.066143 ACCCTGCACAACTAGGATTCG 60.066 52.381 0.00 0.00 36.11 3.34
2657 2829 2.544685 CCTGCACAACTAGGATTCGAG 58.455 52.381 0.00 0.00 36.11 4.04
2658 2830 2.166459 CCTGCACAACTAGGATTCGAGA 59.834 50.000 0.00 0.00 36.11 4.04
2659 2831 3.182967 CTGCACAACTAGGATTCGAGAC 58.817 50.000 0.00 0.00 0.00 3.36
2660 2832 2.094182 TGCACAACTAGGATTCGAGACC 60.094 50.000 0.00 2.35 0.00 3.85
2661 2833 2.094182 GCACAACTAGGATTCGAGACCA 60.094 50.000 11.48 0.00 0.00 4.02
2662 2834 3.616560 GCACAACTAGGATTCGAGACCAA 60.617 47.826 11.48 0.00 0.00 3.67
2663 2835 4.566004 CACAACTAGGATTCGAGACCAAA 58.434 43.478 11.48 0.56 0.00 3.28
2665 2837 5.063944 CACAACTAGGATTCGAGACCAAATG 59.936 44.000 11.48 7.64 0.00 2.32
2666 2838 5.178797 CAACTAGGATTCGAGACCAAATGT 58.821 41.667 11.48 3.34 0.00 2.71
2667 2839 6.070995 ACAACTAGGATTCGAGACCAAATGTA 60.071 38.462 11.48 0.00 0.00 2.29
2668 2840 6.150396 ACTAGGATTCGAGACCAAATGTAG 57.850 41.667 11.48 7.02 0.00 2.74
2669 2841 3.798202 AGGATTCGAGACCAAATGTAGC 58.202 45.455 11.48 0.00 0.00 3.58
2673 2845 4.742438 TTCGAGACCAAATGTAGCAAAC 57.258 40.909 0.00 0.00 0.00 2.93
2821 3228 2.290641 CCTTTCTCCTTTCCACAACACG 59.709 50.000 0.00 0.00 0.00 4.49
2822 3229 1.305201 TTCTCCTTTCCACAACACGC 58.695 50.000 0.00 0.00 0.00 5.34
2823 3230 0.468226 TCTCCTTTCCACAACACGCT 59.532 50.000 0.00 0.00 0.00 5.07
2824 3231 0.588252 CTCCTTTCCACAACACGCTG 59.412 55.000 0.00 0.00 0.00 5.18
2825 3232 0.817634 TCCTTTCCACAACACGCTGG 60.818 55.000 0.00 0.00 0.00 4.85
2826 3233 1.654220 CTTTCCACAACACGCTGGG 59.346 57.895 0.00 0.00 0.00 4.45
2827 3234 0.817634 CTTTCCACAACACGCTGGGA 60.818 55.000 0.00 0.00 0.00 4.37
2828 3235 0.394488 TTTCCACAACACGCTGGGAA 60.394 50.000 0.00 0.00 35.93 3.97
2829 3236 0.817634 TTCCACAACACGCTGGGAAG 60.818 55.000 0.00 0.00 32.95 3.46
2830 3237 1.525995 CCACAACACGCTGGGAAGT 60.526 57.895 0.00 0.00 0.00 3.01
2831 3238 1.648720 CACAACACGCTGGGAAGTG 59.351 57.895 0.00 0.00 43.46 3.16
2832 3239 1.525995 ACAACACGCTGGGAAGTGG 60.526 57.895 0.00 0.00 42.25 4.00
2833 3240 1.227823 CAACACGCTGGGAAGTGGA 60.228 57.895 0.00 0.00 42.25 4.02
2834 3241 1.071471 AACACGCTGGGAAGTGGAG 59.929 57.895 0.00 0.00 42.25 3.86
2835 3242 1.407656 AACACGCTGGGAAGTGGAGA 61.408 55.000 0.00 0.00 42.25 3.71
2836 3243 1.371183 CACGCTGGGAAGTGGAGAA 59.629 57.895 0.00 0.00 34.93 2.87
2837 3244 0.671781 CACGCTGGGAAGTGGAGAAG 60.672 60.000 0.00 0.00 34.93 2.85
2838 3245 0.832135 ACGCTGGGAAGTGGAGAAGA 60.832 55.000 0.00 0.00 0.00 2.87
2839 3246 0.108424 CGCTGGGAAGTGGAGAAGAG 60.108 60.000 0.00 0.00 0.00 2.85
2840 3247 0.392327 GCTGGGAAGTGGAGAAGAGC 60.392 60.000 0.00 0.00 0.00 4.09
2850 3257 0.251634 GGAGAAGAGCTGGGAAGTGG 59.748 60.000 0.00 0.00 0.00 4.00
2863 3270 2.610727 GGGAAGTGGAGAAGAACTCACG 60.611 54.545 0.00 0.00 46.54 4.35
2876 3283 5.508200 AGAACTCACGAGAATGATCTACC 57.492 43.478 0.00 0.00 35.54 3.18
2877 3284 3.972950 ACTCACGAGAATGATCTACCG 57.027 47.619 0.00 0.00 35.54 4.02
2878 3285 3.280295 ACTCACGAGAATGATCTACCGT 58.720 45.455 0.00 0.00 36.80 4.83
2879 3286 3.695060 ACTCACGAGAATGATCTACCGTT 59.305 43.478 0.00 0.00 34.88 4.44
2880 3287 4.880120 ACTCACGAGAATGATCTACCGTTA 59.120 41.667 0.00 0.00 34.88 3.18
2881 3288 5.007823 ACTCACGAGAATGATCTACCGTTAG 59.992 44.000 0.00 0.00 34.88 2.34
2884 3291 3.612004 CGAGAATGATCTACCGTTAGGGC 60.612 52.174 0.00 0.00 37.75 5.19
2894 3301 0.810031 CCGTTAGGGCATCTCCAACG 60.810 60.000 0.00 0.00 39.09 4.10
2896 3303 1.202533 CGTTAGGGCATCTCCAACGAT 60.203 52.381 0.00 0.00 40.37 3.73
2899 3306 2.622064 AGGGCATCTCCAACGATAAC 57.378 50.000 0.00 0.00 36.21 1.89
2903 3310 3.181458 GGGCATCTCCAACGATAACCTAA 60.181 47.826 0.00 0.00 36.21 2.69
2959 3368 4.778143 GAGGCGGCCATCCAACGT 62.778 66.667 23.09 0.00 0.00 3.99
2962 3371 2.469516 GGCGGCCATCCAACGTTAG 61.470 63.158 15.62 0.00 0.00 2.34
2963 3372 3.098555 CGGCCATCCAACGTTAGC 58.901 61.111 2.24 0.00 0.00 3.09
2965 3374 2.469516 GGCCATCCAACGTTAGCCG 61.470 63.158 0.00 0.00 44.03 5.52
2994 3403 7.962917 ACATTTTCACAACAACTCAAATCAAC 58.037 30.769 0.00 0.00 0.00 3.18
3030 3439 2.477825 CAGGATTACATGCAGACTCGG 58.522 52.381 0.00 0.00 0.00 4.63
3088 3497 3.949113 ACCAGACACAAACGGTTACATTT 59.051 39.130 0.00 0.00 0.00 2.32
3132 3542 5.505165 AGTTAAAACTATGTGCACGTACG 57.495 39.130 14.85 15.01 37.52 3.67
3158 3568 2.574399 GAGCTCCACTCCCACGAC 59.426 66.667 0.87 0.00 39.75 4.34
3161 3571 4.778415 CTCCACTCCCACGACGCG 62.778 72.222 3.53 3.53 0.00 6.01
3184 3594 5.996513 CGGATACACTACACTAGTCTATGGT 59.003 44.000 0.00 0.00 36.76 3.55
3191 3601 0.464452 ACTAGTCTATGGTTGGCCGC 59.536 55.000 0.00 0.00 37.67 6.53
3192 3602 0.464036 CTAGTCTATGGTTGGCCGCA 59.536 55.000 0.00 0.00 37.67 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.735132 GACGCGGCTGCAGGTACA 62.735 66.667 19.50 0.00 42.97 2.90
24 25 4.854784 GATCTCGACGCGGCTGCA 62.855 66.667 19.50 0.00 42.97 4.41
48 49 8.534954 TTGATCTATGGCTGTTACTACTAAGT 57.465 34.615 0.00 0.00 39.91 2.24
49 50 8.085296 CCTTGATCTATGGCTGTTACTACTAAG 58.915 40.741 0.00 0.00 0.00 2.18
51 52 6.015350 GCCTTGATCTATGGCTGTTACTACTA 60.015 42.308 14.08 0.00 44.17 1.82
123 124 8.556213 AATCCAACTCTAAAGCGTACAATTTA 57.444 30.769 0.00 0.00 0.00 1.40
156 157 8.467598 TCCAAATACAGAGATCAACACTACTAC 58.532 37.037 0.00 0.00 0.00 2.73
159 160 7.225538 CCATCCAAATACAGAGATCAACACTAC 59.774 40.741 0.00 0.00 0.00 2.73
160 161 7.125659 TCCATCCAAATACAGAGATCAACACTA 59.874 37.037 0.00 0.00 0.00 2.74
161 162 6.070021 TCCATCCAAATACAGAGATCAACACT 60.070 38.462 0.00 0.00 0.00 3.55
162 163 6.115446 TCCATCCAAATACAGAGATCAACAC 58.885 40.000 0.00 0.00 0.00 3.32
194 195 3.140073 AATGCAACCCCCACCGTCA 62.140 57.895 0.00 0.00 0.00 4.35
195 196 2.282887 AATGCAACCCCCACCGTC 60.283 61.111 0.00 0.00 0.00 4.79
196 197 2.282887 GAATGCAACCCCCACCGT 60.283 61.111 0.00 0.00 0.00 4.83
197 198 2.282816 TGAATGCAACCCCCACCG 60.283 61.111 0.00 0.00 0.00 4.94
198 199 2.635443 CGTGAATGCAACCCCCACC 61.635 63.158 0.00 0.00 0.00 4.61
199 200 2.961768 CGTGAATGCAACCCCCAC 59.038 61.111 0.00 0.00 0.00 4.61
200 201 2.988684 GCGTGAATGCAACCCCCA 60.989 61.111 0.00 0.00 34.15 4.96
257 262 7.154656 GTGCATGACATGATACTAAGTCCATA 58.845 38.462 19.76 0.00 0.00 2.74
268 273 3.054508 TCCCAAGTGTGCATGACATGATA 60.055 43.478 19.76 4.23 36.78 2.15
287 292 0.108585 TTCCAGTGCAGTGAACTCCC 59.891 55.000 23.34 0.00 0.00 4.30
511 520 1.930908 GCACAGCATCTGGGACAAGC 61.931 60.000 0.00 0.00 36.97 4.01
512 521 1.310933 GGCACAGCATCTGGGACAAG 61.311 60.000 0.00 0.00 43.56 3.16
513 522 1.303561 GGCACAGCATCTGGGACAA 60.304 57.895 0.00 0.00 43.56 3.18
516 525 0.040058 ATTTGGCACAGCATCTGGGA 59.960 50.000 0.00 0.00 42.39 4.37
517 526 0.458669 GATTTGGCACAGCATCTGGG 59.541 55.000 0.00 0.00 42.39 4.45
519 528 1.404391 GAGGATTTGGCACAGCATCTG 59.596 52.381 0.00 0.00 42.39 2.90
520 529 1.284198 AGAGGATTTGGCACAGCATCT 59.716 47.619 0.00 0.00 42.39 2.90
521 530 1.674962 GAGAGGATTTGGCACAGCATC 59.325 52.381 0.00 0.00 42.39 3.91
610 628 2.941720 GTCCTGATGATTGTCCAGCTTC 59.058 50.000 0.00 0.00 0.00 3.86
650 668 5.564550 AGTGAATAGCAAGAGAACAACCAT 58.435 37.500 0.00 0.00 0.00 3.55
808 831 1.745489 GTTCCCACCCGACTGCATC 60.745 63.158 0.00 0.00 0.00 3.91
825 848 2.274104 GTGGTGTGGTGTGGTGGT 59.726 61.111 0.00 0.00 0.00 4.16
828 851 2.124901 CGTGTGGTGTGGTGTGGT 60.125 61.111 0.00 0.00 0.00 4.16
848 871 2.426842 GGCTCTGCCTTTGATAACCT 57.573 50.000 0.73 0.00 46.69 3.50
888 915 3.625897 TGGTGTGAGCTGGTCGGG 61.626 66.667 0.00 0.00 0.00 5.14
891 918 2.032681 GGGTGGTGTGAGCTGGTC 59.967 66.667 0.00 0.00 0.00 4.02
894 921 2.253758 CGTTGGGTGGTGTGAGCTG 61.254 63.158 0.00 0.00 0.00 4.24
925 955 3.243569 GGTAGTAGCTCAGTGAATCGCAT 60.244 47.826 5.73 0.00 0.00 4.73
942 972 0.323908 AGCAAGGAGAGCGAGGTAGT 60.324 55.000 0.00 0.00 37.01 2.73
944 974 0.323451 TCAGCAAGGAGAGCGAGGTA 60.323 55.000 0.00 0.00 37.01 3.08
945 975 0.975040 ATCAGCAAGGAGAGCGAGGT 60.975 55.000 0.00 0.00 37.01 3.85
947 977 1.406898 TGTATCAGCAAGGAGAGCGAG 59.593 52.381 0.00 0.00 37.01 5.03
948 978 1.135139 GTGTATCAGCAAGGAGAGCGA 59.865 52.381 0.00 0.00 37.01 4.93
953 983 1.740380 CGGTGGTGTATCAGCAAGGAG 60.740 57.143 3.26 0.00 43.50 3.69
959 989 1.521681 GAGGCGGTGGTGTATCAGC 60.522 63.158 0.00 0.00 0.00 4.26
1028 1061 2.125912 CGAGGAGCAGGAACACGG 60.126 66.667 0.00 0.00 0.00 4.94
1470 1532 2.957491 AGGAGTTCTTGCTGAGATCG 57.043 50.000 0.00 0.00 33.49 3.69
1499 1561 1.448922 GAGCAGCGACGAGGGTATCT 61.449 60.000 0.00 0.00 0.00 1.98
1614 1676 1.616865 CCGGATAGGCGATTGTTCCTA 59.383 52.381 0.00 0.00 39.11 2.94
1680 1742 3.003173 CCGGAGAGCCTGTTCCCA 61.003 66.667 0.00 0.00 0.00 4.37
2217 2282 2.480642 AAACCACCCCAAAAGCCTTA 57.519 45.000 0.00 0.00 0.00 2.69
2394 2481 6.532657 ACATTTCTTTGCACAAAGTTTCTCTG 59.467 34.615 19.61 12.86 45.88 3.35
2426 2520 7.671302 ACAAATCGGTAGAGATAACATAGCAT 58.329 34.615 0.00 0.00 0.00 3.79
2607 2779 7.364149 TGGTACAGTAGTTTGGAAGTAGAAA 57.636 36.000 0.00 0.00 0.00 2.52
2608 2780 6.982160 TGGTACAGTAGTTTGGAAGTAGAA 57.018 37.500 0.00 0.00 0.00 2.10
2612 2784 4.164604 TGGTTGGTACAGTAGTTTGGAAGT 59.835 41.667 0.00 0.00 42.39 3.01
2613 2785 4.514066 GTGGTTGGTACAGTAGTTTGGAAG 59.486 45.833 0.00 0.00 42.39 3.46
2614 2786 4.453751 GTGGTTGGTACAGTAGTTTGGAA 58.546 43.478 0.00 0.00 42.39 3.53
2615 2787 3.181452 GGTGGTTGGTACAGTAGTTTGGA 60.181 47.826 0.00 0.00 42.39 3.53
2616 2788 3.143728 GGTGGTTGGTACAGTAGTTTGG 58.856 50.000 0.00 0.00 42.39 3.28
2618 2790 3.050835 AGGGTGGTTGGTACAGTAGTTT 58.949 45.455 0.00 0.00 42.39 2.66
2619 2791 2.370849 CAGGGTGGTTGGTACAGTAGTT 59.629 50.000 0.00 0.00 42.39 2.24
2621 2793 1.338769 GCAGGGTGGTTGGTACAGTAG 60.339 57.143 0.00 0.00 42.39 2.57
2623 2795 1.349542 TGCAGGGTGGTTGGTACAGT 61.350 55.000 0.00 0.00 42.39 3.55
2624 2796 0.889186 GTGCAGGGTGGTTGGTACAG 60.889 60.000 0.00 0.00 42.39 2.74
2627 2799 0.466555 GTTGTGCAGGGTGGTTGGTA 60.467 55.000 0.00 0.00 0.00 3.25
2629 2801 0.179004 TAGTTGTGCAGGGTGGTTGG 60.179 55.000 0.00 0.00 0.00 3.77
2630 2802 1.238439 CTAGTTGTGCAGGGTGGTTG 58.762 55.000 0.00 0.00 0.00 3.77
2631 2803 0.110486 CCTAGTTGTGCAGGGTGGTT 59.890 55.000 0.00 0.00 0.00 3.67
2632 2804 0.766674 TCCTAGTTGTGCAGGGTGGT 60.767 55.000 0.00 0.00 32.40 4.16
2633 2805 0.620556 ATCCTAGTTGTGCAGGGTGG 59.379 55.000 0.00 0.00 32.40 4.61
2634 2806 2.359900 GAATCCTAGTTGTGCAGGGTG 58.640 52.381 0.00 0.00 32.40 4.61
2635 2807 1.066143 CGAATCCTAGTTGTGCAGGGT 60.066 52.381 0.00 0.00 32.40 4.34
2636 2808 1.207089 TCGAATCCTAGTTGTGCAGGG 59.793 52.381 0.00 0.00 32.40 4.45
2637 2809 2.166459 TCTCGAATCCTAGTTGTGCAGG 59.834 50.000 0.00 0.00 0.00 4.85
2638 2810 3.182967 GTCTCGAATCCTAGTTGTGCAG 58.817 50.000 0.00 0.00 0.00 4.41
2640 2812 2.094182 TGGTCTCGAATCCTAGTTGTGC 60.094 50.000 7.01 0.00 0.00 4.57
2641 2813 3.868757 TGGTCTCGAATCCTAGTTGTG 57.131 47.619 7.01 0.00 0.00 3.33
2642 2814 4.884668 TTTGGTCTCGAATCCTAGTTGT 57.115 40.909 7.01 0.00 0.00 3.32
2643 2815 5.178797 ACATTTGGTCTCGAATCCTAGTTG 58.821 41.667 7.01 4.68 0.00 3.16
2644 2816 5.422214 ACATTTGGTCTCGAATCCTAGTT 57.578 39.130 7.01 0.00 0.00 2.24
2645 2817 5.452077 GCTACATTTGGTCTCGAATCCTAGT 60.452 44.000 7.01 3.79 0.00 2.57
2646 2818 4.985409 GCTACATTTGGTCTCGAATCCTAG 59.015 45.833 7.01 0.00 0.00 3.02
2647 2819 4.404394 TGCTACATTTGGTCTCGAATCCTA 59.596 41.667 7.01 0.00 0.00 2.94
2648 2820 3.197766 TGCTACATTTGGTCTCGAATCCT 59.802 43.478 7.01 0.00 0.00 3.24
2650 2822 5.324697 GTTTGCTACATTTGGTCTCGAATC 58.675 41.667 0.00 0.00 0.00 2.52
2651 2823 4.156008 GGTTTGCTACATTTGGTCTCGAAT 59.844 41.667 0.00 0.00 0.00 3.34
2652 2824 3.500680 GGTTTGCTACATTTGGTCTCGAA 59.499 43.478 0.00 0.00 0.00 3.71
2653 2825 3.071479 GGTTTGCTACATTTGGTCTCGA 58.929 45.455 0.00 0.00 0.00 4.04
2654 2826 2.811431 TGGTTTGCTACATTTGGTCTCG 59.189 45.455 0.00 0.00 0.00 4.04
2655 2827 4.072131 TCTGGTTTGCTACATTTGGTCTC 58.928 43.478 0.00 0.00 0.00 3.36
2657 2829 4.218417 ACATCTGGTTTGCTACATTTGGTC 59.782 41.667 0.00 0.00 0.00 4.02
2658 2830 4.151883 ACATCTGGTTTGCTACATTTGGT 58.848 39.130 0.00 0.00 0.00 3.67
2659 2831 4.789012 ACATCTGGTTTGCTACATTTGG 57.211 40.909 0.00 0.00 0.00 3.28
2660 2832 7.315142 ACAATACATCTGGTTTGCTACATTTG 58.685 34.615 0.00 0.00 0.00 2.32
2661 2833 7.466746 ACAATACATCTGGTTTGCTACATTT 57.533 32.000 0.00 0.00 0.00 2.32
2662 2834 7.394359 AGAACAATACATCTGGTTTGCTACATT 59.606 33.333 0.00 0.00 0.00 2.71
2663 2835 6.886459 AGAACAATACATCTGGTTTGCTACAT 59.114 34.615 0.00 0.00 0.00 2.29
2665 2837 6.743575 AGAACAATACATCTGGTTTGCTAC 57.256 37.500 0.00 0.00 0.00 3.58
2666 2838 7.119699 CAGAAGAACAATACATCTGGTTTGCTA 59.880 37.037 0.00 0.00 35.11 3.49
2667 2839 6.006449 AGAAGAACAATACATCTGGTTTGCT 58.994 36.000 0.00 0.00 0.00 3.91
2668 2840 6.088824 CAGAAGAACAATACATCTGGTTTGC 58.911 40.000 0.00 0.00 35.11 3.68
2669 2841 7.206981 ACAGAAGAACAATACATCTGGTTTG 57.793 36.000 0.00 0.00 41.34 2.93
2673 2845 9.778993 CAAATTACAGAAGAACAATACATCTGG 57.221 33.333 0.00 0.00 41.34 3.86
2821 3228 0.392327 GCTCTTCTCCACTTCCCAGC 60.392 60.000 0.00 0.00 0.00 4.85
2822 3229 1.066286 CAGCTCTTCTCCACTTCCCAG 60.066 57.143 0.00 0.00 0.00 4.45
2823 3230 0.979665 CAGCTCTTCTCCACTTCCCA 59.020 55.000 0.00 0.00 0.00 4.37
2824 3231 0.251634 CCAGCTCTTCTCCACTTCCC 59.748 60.000 0.00 0.00 0.00 3.97
2825 3232 0.251634 CCCAGCTCTTCTCCACTTCC 59.748 60.000 0.00 0.00 0.00 3.46
2826 3233 1.270907 TCCCAGCTCTTCTCCACTTC 58.729 55.000 0.00 0.00 0.00 3.01
2827 3234 1.627834 CTTCCCAGCTCTTCTCCACTT 59.372 52.381 0.00 0.00 0.00 3.16
2828 3235 1.274712 CTTCCCAGCTCTTCTCCACT 58.725 55.000 0.00 0.00 0.00 4.00
2829 3236 0.980423 ACTTCCCAGCTCTTCTCCAC 59.020 55.000 0.00 0.00 0.00 4.02
2830 3237 0.979665 CACTTCCCAGCTCTTCTCCA 59.020 55.000 0.00 0.00 0.00 3.86
2831 3238 0.251634 CCACTTCCCAGCTCTTCTCC 59.748 60.000 0.00 0.00 0.00 3.71
2832 3239 1.206849 CTCCACTTCCCAGCTCTTCTC 59.793 57.143 0.00 0.00 0.00 2.87
2833 3240 1.203237 TCTCCACTTCCCAGCTCTTCT 60.203 52.381 0.00 0.00 0.00 2.85
2834 3241 1.270907 TCTCCACTTCCCAGCTCTTC 58.729 55.000 0.00 0.00 0.00 2.87
2835 3242 1.627834 CTTCTCCACTTCCCAGCTCTT 59.372 52.381 0.00 0.00 0.00 2.85
2836 3243 1.203237 TCTTCTCCACTTCCCAGCTCT 60.203 52.381 0.00 0.00 0.00 4.09
2837 3244 1.270907 TCTTCTCCACTTCCCAGCTC 58.729 55.000 0.00 0.00 0.00 4.09
2838 3245 1.349357 GTTCTTCTCCACTTCCCAGCT 59.651 52.381 0.00 0.00 0.00 4.24
2839 3246 1.349357 AGTTCTTCTCCACTTCCCAGC 59.651 52.381 0.00 0.00 0.00 4.85
2840 3247 2.634940 TGAGTTCTTCTCCACTTCCCAG 59.365 50.000 0.00 0.00 42.12 4.45
2850 3257 5.890334 AGATCATTCTCGTGAGTTCTTCTC 58.110 41.667 0.00 0.00 43.03 2.87
2863 3270 3.321111 TGCCCTAACGGTAGATCATTCTC 59.679 47.826 9.67 0.00 33.17 2.87
2876 3283 0.174845 TCGTTGGAGATGCCCTAACG 59.825 55.000 0.00 0.00 39.61 3.18
2877 3284 2.622064 ATCGTTGGAGATGCCCTAAC 57.378 50.000 0.00 0.00 34.97 2.34
2878 3285 3.181458 GGTTATCGTTGGAGATGCCCTAA 60.181 47.826 0.00 0.00 34.97 2.69
2879 3286 2.367567 GGTTATCGTTGGAGATGCCCTA 59.632 50.000 0.00 0.00 34.97 3.53
2880 3287 1.141053 GGTTATCGTTGGAGATGCCCT 59.859 52.381 0.00 0.00 34.97 5.19
2881 3288 1.141053 AGGTTATCGTTGGAGATGCCC 59.859 52.381 0.00 0.00 34.97 5.36
2942 3351 2.862674 TAACGTTGGATGGCCGCCTC 62.863 60.000 11.99 5.68 36.79 4.70
2947 3356 2.469516 CGGCTAACGTTGGATGGCC 61.470 63.158 16.60 16.05 37.93 5.36
2959 3368 4.216472 TGTTGTGAAAATGTATGCGGCTAA 59.784 37.500 0.00 0.00 0.00 3.09
2962 3371 2.940147 TGTTGTGAAAATGTATGCGGC 58.060 42.857 0.00 0.00 0.00 6.53
2963 3372 4.545610 AGTTGTTGTGAAAATGTATGCGG 58.454 39.130 0.00 0.00 0.00 5.69
2965 3374 7.462109 TTTGAGTTGTTGTGAAAATGTATGC 57.538 32.000 0.00 0.00 0.00 3.14
3017 3426 4.457496 CCGGCCGAGTCTGCATGT 62.457 66.667 30.73 0.00 0.00 3.21
3024 3433 1.202486 TGTATGAAATCCGGCCGAGTC 60.202 52.381 30.73 17.80 0.00 3.36
3030 3439 4.142491 TGTCATGTTTGTATGAAATCCGGC 60.142 41.667 0.00 0.00 38.69 6.13
3110 3520 4.386652 CCGTACGTGCACATAGTTTTAACT 59.613 41.667 18.64 0.29 42.91 2.24
3155 3565 0.376152 AGTGTAGTGTATCCGCGTCG 59.624 55.000 4.92 0.00 0.00 5.12
3157 3567 2.611292 GACTAGTGTAGTGTATCCGCGT 59.389 50.000 4.92 0.00 39.59 6.01
3158 3568 2.871022 AGACTAGTGTAGTGTATCCGCG 59.129 50.000 0.00 0.00 39.59 6.46
3161 3571 7.255520 CCAACCATAGACTAGTGTAGTGTATCC 60.256 44.444 0.00 0.00 41.62 2.59


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

AutoCloner maintained by Alex Coulton.