Multiple sequence alignment - TraesCS7B01G182400

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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 TraesCS7B01G182400 chr7B 100.000 7271 0 0 1 7271 284151127 284143857 0.000000e+00 13428.0
1 TraesCS7B01G182400 chr7B 96.884 353 9 1 3714 4064 129548361 129548009 2.260000e-164 590.0
2 TraesCS7B01G182400 chr7B 95.787 356 12 2 3714 4066 129543020 129542665 8.180000e-159 571.0
3 TraesCS7B01G182400 chr7B 95.751 353 13 1 3714 4064 665685094 665685446 1.060000e-157 568.0
4 TraesCS7B01G182400 chr7B 86.486 74 6 3 253 322 701307778 701307851 2.170000e-10 78.7
5 TraesCS7B01G182400 chr7B 97.500 40 1 0 459 498 532117990 532118029 1.310000e-07 69.4
6 TraesCS7B01G182400 chr7B 97.500 40 0 1 459 498 687299472 687299510 4.710000e-07 67.6
7 TraesCS7B01G182400 chr7D 95.794 2663 68 11 1063 3712 339119662 339117031 0.000000e+00 4257.0
8 TraesCS7B01G182400 chr7D 96.310 2439 70 8 4063 6493 339117034 339114608 0.000000e+00 3988.0
9 TraesCS7B01G182400 chr7D 89.119 772 52 8 6507 7270 339114622 339113875 0.000000e+00 931.0
10 TraesCS7B01G182400 chr7D 93.443 61 4 0 2328 2388 627056733 627056673 2.790000e-14 91.6
11 TraesCS7B01G182400 chr7A 96.550 2435 69 7 4063 6494 344677577 344679999 0.000000e+00 4017.0
12 TraesCS7B01G182400 chr7A 94.118 2669 75 30 1060 3713 344674980 344677581 0.000000e+00 3984.0
13 TraesCS7B01G182400 chr7A 91.192 772 45 11 6507 7270 344679984 344680740 0.000000e+00 1027.0
14 TraesCS7B01G182400 chr7A 91.837 147 10 2 612 757 17708269 17708124 3.440000e-48 204.0
15 TraesCS7B01G182400 chr5A 98.678 1059 10 2 1 1059 472574322 472575376 0.000000e+00 1875.0
16 TraesCS7B01G182400 chr5A 79.528 254 50 2 3427 3679 653289618 653289870 5.800000e-41 180.0
17 TraesCS7B01G182400 chr3B 96.296 567 12 7 500 1062 153539153 153539714 0.000000e+00 922.0
18 TraesCS7B01G182400 chr3B 96.957 460 14 0 1 460 153538710 153539169 0.000000e+00 773.0
19 TraesCS7B01G182400 chr3B 96.317 353 11 1 3714 4064 691361844 691361492 4.890000e-161 579.0
20 TraesCS7B01G182400 chr3B 95.184 353 12 2 3714 4064 691358805 691358456 2.960000e-153 553.0
21 TraesCS7B01G182400 chr3B 83.636 385 39 12 87 448 118133523 118133906 2.510000e-89 340.0
22 TraesCS7B01G182400 chr3B 87.273 275 33 2 584 857 117952739 117952466 5.480000e-81 313.0
23 TraesCS7B01G182400 chr3B 86.598 291 17 9 596 883 118134875 118135146 1.190000e-77 302.0
24 TraesCS7B01G182400 chr3B 87.342 237 24 5 1904 2138 493121872 493121640 4.320000e-67 267.0
25 TraesCS7B01G182400 chr3B 91.720 157 13 0 701 857 153538530 153538374 1.230000e-52 219.0
26 TraesCS7B01G182400 chr3B 83.133 166 21 5 898 1061 153538385 153538225 2.110000e-30 145.0
27 TraesCS7B01G182400 chr6B 96.884 353 9 1 3713 4063 20926131 20925779 2.260000e-164 590.0
28 TraesCS7B01G182400 chr6B 87.917 240 24 5 1902 2138 439062089 439062326 2.000000e-70 278.0
29 TraesCS7B01G182400 chr6B 79.283 251 48 4 3428 3676 701828371 701828123 9.700000e-39 172.0
30 TraesCS7B01G182400 chr6B 77.340 203 29 12 3074 3265 645536753 645536949 3.590000e-18 104.0
31 TraesCS7B01G182400 chrUn 97.289 332 7 1 3735 4064 330454942 330454611 4.930000e-156 562.0
32 TraesCS7B01G182400 chrUn 80.247 162 26 5 3074 3233 17107240 17107083 4.610000e-22 117.0
33 TraesCS7B01G182400 chrUn 80.247 162 26 5 3074 3233 406467407 406467564 4.610000e-22 117.0
34 TraesCS7B01G182400 chrUn 81.250 144 23 3 3092 3233 17086261 17086120 5.960000e-21 113.0
35 TraesCS7B01G182400 chrUn 86.869 99 13 0 12 110 286308276 286308374 2.140000e-20 111.0
36 TraesCS7B01G182400 chrUn 86.869 99 13 0 12 110 286314559 286314657 2.140000e-20 111.0
37 TraesCS7B01G182400 chrUn 87.500 96 12 0 15 110 295781993 295781898 2.140000e-20 111.0
38 TraesCS7B01G182400 chrUn 86.458 96 13 0 15 110 215333212 215333117 9.980000e-19 106.0
39 TraesCS7B01G182400 chrUn 85.859 99 14 0 12 110 396718311 396718409 9.980000e-19 106.0
40 TraesCS7B01G182400 chrUn 87.671 73 5 3 252 322 31324796 31324866 1.680000e-11 82.4
41 TraesCS7B01G182400 chrUn 97.561 41 1 0 458 498 24170238 24170198 3.640000e-08 71.3
42 TraesCS7B01G182400 chr5B 95.211 355 15 1 3712 4064 493651410 493651056 1.770000e-155 560.0
43 TraesCS7B01G182400 chr5B 95.157 351 14 2 3714 4062 493637295 493636946 1.070000e-152 551.0
44 TraesCS7B01G182400 chr5B 92.308 52 4 0 450 501 506972472 506972421 2.810000e-09 75.0
45 TraesCS7B01G182400 chr3D 84.615 403 26 17 499 883 72244260 72244644 1.150000e-97 368.0
46 TraesCS7B01G182400 chr3D 89.818 275 22 3 584 857 72243020 72242751 1.500000e-91 348.0
47 TraesCS7B01G182400 chr3D 81.499 427 53 12 12 414 72243757 72244181 1.960000e-85 327.0
48 TraesCS7B01G182400 chr3D 86.100 259 29 7 1895 2152 394142763 394143015 9.290000e-69 272.0
49 TraesCS7B01G182400 chr3D 83.529 255 41 1 3427 3680 422738343 422738089 3.390000e-58 237.0
50 TraesCS7B01G182400 chr3D 88.764 89 6 4 369 454 72244184 72244271 9.980000e-19 106.0
51 TraesCS7B01G182400 chr3D 87.671 73 6 2 253 325 400740583 400740652 1.680000e-11 82.4
52 TraesCS7B01G182400 chr3A 90.511 274 24 2 584 856 84326263 84325991 1.930000e-95 361.0
53 TraesCS7B01G182400 chr3A 87.395 238 25 4 1907 2143 501225874 501225641 1.200000e-67 268.0
54 TraesCS7B01G182400 chr3A 83.137 255 42 1 3427 3680 566132242 566132496 1.580000e-56 231.0
55 TraesCS7B01G182400 chr3A 87.117 163 16 3 898 1059 84326001 84325843 5.800000e-41 180.0
56 TraesCS7B01G182400 chr5D 88.285 239 23 5 1902 2138 382871966 382871731 1.540000e-71 281.0
57 TraesCS7B01G182400 chr2B 85.606 264 33 5 1894 2155 451836714 451836974 9.290000e-69 272.0
58 TraesCS7B01G182400 chr2B 82.400 250 44 0 3430 3679 494257360 494257609 1.230000e-52 219.0
59 TraesCS7B01G182400 chr2B 81.423 253 45 2 3428 3679 403108004 403107753 9.560000e-49 206.0
60 TraesCS7B01G182400 chr2B 79.866 149 23 7 3090 3233 139078180 139078034 1.290000e-17 102.0
61 TraesCS7B01G182400 chr2B 95.556 45 1 1 459 503 761895268 761895225 3.640000e-08 71.3
62 TraesCS7B01G182400 chr1B 87.083 240 25 2 1904 2138 433422812 433423050 4.320000e-67 267.0
63 TraesCS7B01G182400 chr1B 88.312 154 18 0 4245 4398 546684913 546684760 1.250000e-42 185.0
64 TraesCS7B01G182400 chr1B 90.541 74 7 0 2215 2288 633744819 633744892 1.670000e-16 99.0
65 TraesCS7B01G182400 chr1B 79.070 129 26 1 3073 3201 272107916 272108043 3.610000e-13 87.9
66 TraesCS7B01G182400 chr1B 76.074 163 33 4 3108 3265 456743924 456744085 6.050000e-11 80.5
67 TraesCS7B01G182400 chr1B 100.000 40 0 0 459 498 297337090 297337129 2.810000e-09 75.0
68 TraesCS7B01G182400 chr1A 81.783 258 39 5 3427 3683 541862244 541862494 7.390000e-50 209.0
69 TraesCS7B01G182400 chr1A 97.727 44 1 0 459 502 494154768 494154725 7.820000e-10 76.8
70 TraesCS7B01G182400 chr1A 97.500 40 0 1 459 498 75916218 75916256 4.710000e-07 67.6
71 TraesCS7B01G182400 chr4D 86.239 109 11 2 12 120 371788557 371788661 1.660000e-21 115.0
72 TraesCS7B01G182400 chr4D 93.443 61 4 0 2328 2388 7180639 7180579 2.790000e-14 91.6
73 TraesCS7B01G182400 chr1D 91.026 78 7 0 2215 2292 176206334 176206257 9.980000e-19 106.0
74 TraesCS7B01G182400 chr1D 91.304 46 4 0 453 498 299665940 299665985 6.090000e-06 63.9
75 TraesCS7B01G182400 chr6A 96.552 58 2 0 2328 2385 602045159 602045216 6.000000e-16 97.1
76 TraesCS7B01G182400 chr6A 86.111 72 8 1 254 325 518785632 518785563 7.820000e-10 76.8
77 TraesCS7B01G182400 chr4A 90.278 72 7 0 2215 2286 17098127 17098056 2.160000e-15 95.3
78 TraesCS7B01G182400 chr4A 92.683 41 2 1 459 499 455886855 455886816 2.830000e-04 58.4
79 TraesCS7B01G182400 chr6D 87.500 72 7 1 254 325 377341740 377341671 1.680000e-11 82.4
80 TraesCS7B01G182400 chr2D 85.000 80 8 3 4233 4309 491948941 491948863 2.170000e-10 78.7
81 TraesCS7B01G182400 chr2D 93.182 44 3 0 455 498 354327321 354327278 1.690000e-06 65.8


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 TraesCS7B01G182400 chr7B 284143857 284151127 7270 True 13428.000000 13428 100.000000 1 7271 1 chr7B.!!$R3 7270
1 TraesCS7B01G182400 chr7D 339113875 339119662 5787 True 3058.666667 4257 93.741000 1063 7270 3 chr7D.!!$R2 6207
2 TraesCS7B01G182400 chr7A 344674980 344680740 5760 False 3009.333333 4017 93.953333 1060 7270 3 chr7A.!!$F1 6210
3 TraesCS7B01G182400 chr5A 472574322 472575376 1054 False 1875.000000 1875 98.678000 1 1059 1 chr5A.!!$F1 1058
4 TraesCS7B01G182400 chr3B 153538710 153539714 1004 False 847.500000 922 96.626500 1 1062 2 chr3B.!!$F2 1061
5 TraesCS7B01G182400 chr3B 691358456 691361844 3388 True 566.000000 579 95.750500 3714 4064 2 chr3B.!!$R4 350
6 TraesCS7B01G182400 chr3B 118133523 118135146 1623 False 321.000000 340 85.117000 87 883 2 chr3B.!!$F1 796
7 TraesCS7B01G182400 chr3D 72243757 72244644 887 False 267.000000 368 84.959333 12 883 3 chr3D.!!$F3 871

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
505 579 0.389817 ATGTGTCACGTGATGGACCG 60.390 55.000 23.12 0.0 33.09 4.79 F
1648 2620 1.074752 GCCTCTCACGCTTTCTTCTG 58.925 55.000 0.00 0.0 0.00 3.02 F
2391 3369 1.977854 ACACAGCCAGGATCAGTGTTA 59.022 47.619 0.00 0.0 40.20 2.41 F
3751 4739 0.035739 TACAACCGAAAGAGGCCCAC 59.964 55.000 0.00 0.0 33.69 4.61 F
4269 6708 0.392193 CAGATCGAAGCAGGGCACTT 60.392 55.000 0.00 0.0 0.00 3.16 F
5306 7754 1.480545 GCCCACTTTGGTTTCAGTTGT 59.519 47.619 0.00 0.0 35.17 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1935 2911 0.392998 ATGTTCGGGGTGACATGCTC 60.393 55.000 0.00 0.00 0.00 4.26 R
2591 3569 0.478507 ACCAAAGCCTAGCAGTTGGT 59.521 50.000 17.24 17.24 46.72 3.67 R
4284 6723 1.002033 CTTGTGCACTTGTGCTCCTTC 60.002 52.381 23.53 11.11 35.49 3.46 R
5492 7940 0.027194 CGCTCACATCCTGCAAATCG 59.973 55.000 0.00 0.00 0.00 3.34 R
5546 7994 1.439679 GGCCAGAACTAGGAACAACG 58.560 55.000 0.00 0.00 0.00 4.10 R
7031 9548 1.042003 TGCCAGCTTCTGTGCCAAAA 61.042 50.000 0.00 0.00 30.52 2.44 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
482 556 8.611757 ACTTTTGAAATTGTTTGGATTGCTTAC 58.388 29.630 0.00 0.00 0.00 2.34
498 572 2.749776 CTTACCACATGTGTCACGTGA 58.250 47.619 28.00 15.76 37.29 4.35
505 579 0.389817 ATGTGTCACGTGATGGACCG 60.390 55.000 23.12 0.00 33.09 4.79
979 1951 3.723681 TGGGAATTCTCATATTCTGGCCT 59.276 43.478 3.16 0.00 35.37 5.19
1080 2052 3.226777 CTTCGTATGTCCCATCTCCTCT 58.773 50.000 0.00 0.00 0.00 3.69
1093 2065 2.033757 CCTCTGCACTGCCAAGCT 59.966 61.111 0.00 0.00 0.00 3.74
1295 2267 1.475751 GGTCCGCACCATCTTCATCAT 60.476 52.381 0.00 0.00 43.17 2.45
1488 2460 4.935205 TGTATGGGCTTGTTATATCGATGC 59.065 41.667 8.54 0.07 0.00 3.91
1524 2496 1.212375 TTGGATGGATGTGACCGGAT 58.788 50.000 9.46 0.00 0.00 4.18
1648 2620 1.074752 GCCTCTCACGCTTTCTTCTG 58.925 55.000 0.00 0.00 0.00 3.02
1680 2653 6.591448 GCATAATGTGTCGATCATTAGATGGA 59.409 38.462 21.44 8.39 39.85 3.41
1681 2654 7.201504 GCATAATGTGTCGATCATTAGATGGAG 60.202 40.741 21.44 12.79 39.28 3.86
1682 2655 6.410942 AATGTGTCGATCATTAGATGGAGA 57.589 37.500 14.21 0.00 39.28 3.71
1683 2656 5.188327 TGTGTCGATCATTAGATGGAGAC 57.812 43.478 9.67 9.67 46.50 3.36
1684 2657 4.222886 GTGTCGATCATTAGATGGAGACG 58.777 47.826 0.00 0.00 41.13 4.18
1728 2702 7.561722 AGTCTATAGAGTGAATTTGAGGTAGCA 59.438 37.037 9.37 0.00 0.00 3.49
1770 2744 6.869206 TTAAATGTAGAGTGGGAGCTAACT 57.131 37.500 0.00 0.00 0.00 2.24
1783 2757 4.508662 GGAGCTAACTAGTGATGCTTTGT 58.491 43.478 15.54 0.00 33.83 2.83
1812 2786 4.202040 GGCATGCAAGAATTATGTGCTACA 60.202 41.667 21.36 0.00 39.09 2.74
1872 2848 7.119699 TGTGAACATGTGAACTAATGAGGAATC 59.880 37.037 0.00 0.00 0.00 2.52
1928 2904 2.538449 CCCGATAATTCCTGAACGTTCG 59.462 50.000 22.48 16.45 0.00 3.95
1935 2911 3.889196 TTCCTGAACGTTCGGATTTTG 57.111 42.857 33.55 18.73 35.56 2.44
1945 2921 3.492313 GTTCGGATTTTGAGCATGTCAC 58.508 45.455 0.00 0.00 33.71 3.67
2090 3067 6.701400 GTGTGAACTAAAGTTGCCATGAAAAT 59.299 34.615 0.00 0.00 38.56 1.82
2091 3068 6.700960 TGTGAACTAAAGTTGCCATGAAAATG 59.299 34.615 0.00 0.00 38.56 2.32
2197 3175 9.846248 GTCTTTTCTTATTCATGTTGCTACATT 57.154 29.630 11.24 0.28 42.29 2.71
2243 3221 2.948720 GCTTGACCTCCGTGCTCCT 61.949 63.158 0.00 0.00 0.00 3.69
2293 3271 2.124942 CTTTCTCCTCGGCCCAGC 60.125 66.667 0.00 0.00 0.00 4.85
2336 3314 6.026947 AGCAAGACCGATATAATGTAGGAC 57.973 41.667 0.00 0.00 0.00 3.85
2391 3369 1.977854 ACACAGCCAGGATCAGTGTTA 59.022 47.619 0.00 0.00 40.20 2.41
2594 3572 8.918202 ATCTTTCTCAATTGTTAGTTACACCA 57.082 30.769 5.13 0.00 36.21 4.17
2595 3573 8.740123 TCTTTCTCAATTGTTAGTTACACCAA 57.260 30.769 5.13 0.00 36.21 3.67
2596 3574 8.617809 TCTTTCTCAATTGTTAGTTACACCAAC 58.382 33.333 5.13 0.00 36.21 3.77
2604 3582 2.474410 AGTTACACCAACTGCTAGGC 57.526 50.000 0.00 0.00 46.01 3.93
2605 3583 1.978580 AGTTACACCAACTGCTAGGCT 59.021 47.619 0.00 0.00 46.01 4.58
2606 3584 2.372172 AGTTACACCAACTGCTAGGCTT 59.628 45.455 0.00 0.00 46.01 4.35
2607 3585 3.146847 GTTACACCAACTGCTAGGCTTT 58.853 45.455 0.00 0.00 34.06 3.51
2608 3586 1.609208 ACACCAACTGCTAGGCTTTG 58.391 50.000 0.00 0.00 0.00 2.77
2721 3699 1.092921 AAACGCTTGCGAACTGGTGA 61.093 50.000 22.03 0.00 0.00 4.02
2741 3719 4.442733 GTGAAGACTATACTCATTCTGCGC 59.557 45.833 0.00 0.00 0.00 6.09
2867 3846 7.837202 ACATTCGTCGGTCTTTTATAATGAA 57.163 32.000 0.00 0.00 0.00 2.57
2990 3969 2.556114 CCAATGGCTTCACCTTCTCCTT 60.556 50.000 0.00 0.00 40.22 3.36
3035 4014 4.114058 CCTGTGCAGGTAATCAATTTGG 57.886 45.455 9.96 0.00 43.61 3.28
3128 4108 4.457603 TGTTTGTTTGGATCGTTCCCTATG 59.542 41.667 10.02 0.00 41.83 2.23
3184 4164 8.257306 TCTAGTTCATTTTTCTTGCCAACTTTT 58.743 29.630 0.00 0.00 0.00 2.27
3403 4384 6.665248 ACCTAATAATTTTGCTGCTTCTCCTT 59.335 34.615 0.00 0.00 0.00 3.36
3511 4492 7.338703 ACATCTTAGGTAGGATATTATTCGCGA 59.661 37.037 3.71 3.71 0.00 5.87
3536 4517 7.589395 AGTTAATTATGTGATTTGCGTTGACA 58.411 30.769 0.00 0.00 0.00 3.58
3552 4534 5.914635 GCGTTGACATTGATATTTGGTATGG 59.085 40.000 0.00 0.00 0.00 2.74
3644 4626 2.158957 TGATGGCCGAGATTAGTTGGAC 60.159 50.000 0.00 0.00 0.00 4.02
3706 4694 9.683069 ACTGAAATCTGTATAGTTTGCTTTTTG 57.317 29.630 0.00 0.00 0.00 2.44
3707 4695 8.519492 TGAAATCTGTATAGTTTGCTTTTTGC 57.481 30.769 0.00 0.00 43.25 3.68
3751 4739 0.035739 TACAACCGAAAGAGGCCCAC 59.964 55.000 0.00 0.00 33.69 4.61
4072 5062 7.240167 ACCCTAGTCCTACCAATAAGAGATAC 58.760 42.308 0.00 0.00 0.00 2.24
4152 5142 7.472543 ACAACACTCACTTTTAAGCACTTAAG 58.527 34.615 0.00 0.00 36.52 1.85
4230 6667 3.865164 TCACAGCATAGCACTACAAATCG 59.135 43.478 0.00 0.00 0.00 3.34
4269 6708 0.392193 CAGATCGAAGCAGGGCACTT 60.392 55.000 0.00 0.00 0.00 3.16
4284 6723 3.066760 GGGCACTTGGAATTCCTAAATCG 59.933 47.826 24.73 8.48 36.82 3.34
4437 6876 4.042934 AGAGAGAGCTCCTATCTTAGGGAC 59.957 50.000 10.93 0.00 40.33 4.46
4443 6882 3.764218 CTCCTATCTTAGGGACGCCTTA 58.236 50.000 0.89 0.00 46.24 2.69
4552 6999 7.224297 TCTTATTAATACTGGATCCCTTGCAC 58.776 38.462 9.90 0.00 0.00 4.57
4572 7019 1.827969 CTGGTCTCAGACTTGTAGGGG 59.172 57.143 4.40 0.00 43.49 4.79
4726 7173 8.941995 TGCTACTCTATGGTCTTATATCTTGT 57.058 34.615 0.00 0.00 0.00 3.16
4728 7175 9.015367 GCTACTCTATGGTCTTATATCTTGTCA 57.985 37.037 0.00 0.00 0.00 3.58
4852 7299 6.792250 CAGTTTTGAATAGTGCAGTAAAGACG 59.208 38.462 5.12 0.00 0.00 4.18
4853 7300 6.482308 AGTTTTGAATAGTGCAGTAAAGACGT 59.518 34.615 5.12 0.00 0.00 4.34
4904 7351 4.125703 CTGTAGATGATTCTGACTTGGCC 58.874 47.826 0.00 0.00 33.17 5.36
4985 7432 4.478206 ACTTGATGAATGGACGAGATGT 57.522 40.909 0.00 0.00 0.00 3.06
4999 7446 5.296151 ACGAGATGTCACATGGGATAAAT 57.704 39.130 0.00 0.00 0.00 1.40
5011 7458 5.069516 ACATGGGATAAATGAGAAATGTGCC 59.930 40.000 0.00 0.00 0.00 5.01
5023 7470 2.113860 AATGTGCCGCAGTACTTGAT 57.886 45.000 0.00 0.00 0.00 2.57
5065 7513 9.651913 GTCTATCTTCATTCTTCACTCTTTTCT 57.348 33.333 0.00 0.00 0.00 2.52
5086 7534 7.403312 TTCTCACTGTTCAAGATTTTGGAAA 57.597 32.000 0.00 0.00 34.97 3.13
5215 7663 2.543067 ATTGCGGGGCCTCTTCAGTC 62.543 60.000 0.00 0.00 0.00 3.51
5306 7754 1.480545 GCCCACTTTGGTTTCAGTTGT 59.519 47.619 0.00 0.00 35.17 3.32
5307 7755 2.738321 GCCCACTTTGGTTTCAGTTGTG 60.738 50.000 0.00 0.00 35.17 3.33
5308 7756 2.159114 CCCACTTTGGTTTCAGTTGTGG 60.159 50.000 0.00 0.00 38.17 4.17
5309 7757 2.539476 CACTTTGGTTTCAGTTGTGGC 58.461 47.619 0.00 0.00 0.00 5.01
5310 7758 2.094286 CACTTTGGTTTCAGTTGTGGCA 60.094 45.455 0.00 0.00 0.00 4.92
5311 7759 2.094234 ACTTTGGTTTCAGTTGTGGCAC 60.094 45.455 11.55 11.55 0.00 5.01
5312 7760 1.550327 TTGGTTTCAGTTGTGGCACA 58.450 45.000 17.96 17.96 0.00 4.57
5462 7910 6.699204 TGGTTTAATTATTTATGTGCATGCCG 59.301 34.615 16.68 0.00 0.00 5.69
5546 7994 2.365582 CACCATACTTTACAGGGTGCC 58.634 52.381 0.00 0.00 42.11 5.01
5594 8042 4.082571 GGGATGCGAATCCAATATCCTTTG 60.083 45.833 24.31 0.00 42.49 2.77
5910 8419 3.822735 CCAAATCTGTTCCTGTCATGTGT 59.177 43.478 0.00 0.00 0.00 3.72
5994 8503 7.173722 GGAGTTTCTGGGATATCATCATCATT 58.826 38.462 4.83 0.00 0.00 2.57
6043 8552 3.118956 TCATTGTTGGCGGTTTCAACTTT 60.119 39.130 8.17 0.00 43.36 2.66
6211 8720 7.174426 ACATTATGATCTGGACATGCTGTAATG 59.826 37.037 0.00 0.00 31.10 1.90
6272 8781 1.285962 AGGGATGTTGGGATGGTTCAG 59.714 52.381 0.00 0.00 0.00 3.02
6290 8799 6.183360 TGGTTCAGATCATTATTTGTCATGCC 60.183 38.462 0.00 0.00 0.00 4.40
6330 8839 4.753610 CAGTTAGTAGGCATCATGACATGG 59.246 45.833 15.37 1.62 0.00 3.66
6352 8861 5.357878 TGGCATTACTCATTTGATGAACTCC 59.642 40.000 0.00 0.00 39.11 3.85
6379 8892 0.322816 TCTGTCCCAAGAAGCATGCC 60.323 55.000 15.66 0.00 0.00 4.40
6380 8893 0.609957 CTGTCCCAAGAAGCATGCCA 60.610 55.000 15.66 0.28 0.00 4.92
6386 8899 0.815095 CAAGAAGCATGCCAGCATCA 59.185 50.000 15.66 0.00 34.86 3.07
6449 8962 0.820074 TCCTAGCTGAGAGTAGCCGC 60.820 60.000 0.00 0.00 44.76 6.53
6467 8980 2.752354 CCGCCAGTGTCCATAAAATTGA 59.248 45.455 0.00 0.00 0.00 2.57
6476 8989 5.634859 GTGTCCATAAAATTGAAAGTGCTGG 59.365 40.000 0.00 0.00 0.00 4.85
6592 9105 1.524848 CTCATGATGCTGATGGAGGC 58.475 55.000 0.00 0.00 0.00 4.70
6629 9142 1.066303 GTCGTGCAGATGGAGAGGTAG 59.934 57.143 0.00 0.00 0.00 3.18
6632 9145 0.031716 TGCAGATGGAGAGGTAGGCT 60.032 55.000 0.00 0.00 0.00 4.58
6673 9186 4.021104 TGCGGATAGATAGTTATGCAAGCT 60.021 41.667 0.00 0.00 0.00 3.74
6683 9196 4.518249 AGTTATGCAAGCTAGGAAGGTTC 58.482 43.478 0.00 0.00 41.45 3.62
6719 9232 9.693739 TTATTCTATTATTTGTCCATGTGTGGT 57.306 29.630 0.00 0.00 46.16 4.16
6818 9335 3.741075 GCGGACCATGTGTGAGATGAATA 60.741 47.826 0.00 0.00 0.00 1.75
6827 9344 7.392418 CATGTGTGAGATGAATATGGATAGGT 58.608 38.462 0.00 0.00 0.00 3.08
6843 9360 2.556286 GGTACAAACCTCTGGCTGC 58.444 57.895 0.00 0.00 43.08 5.25
6867 9384 1.078426 GGTCGGCTTGCTGTATGGT 60.078 57.895 1.11 0.00 0.00 3.55
6898 9415 7.408123 TCACGTTTTATGATACAACACGTTTT 58.592 30.769 2.83 0.00 0.00 2.43
6899 9416 7.373703 TCACGTTTTATGATACAACACGTTTTG 59.626 33.333 12.74 12.74 0.00 2.44
6966 9483 2.901249 AGCAGTGAACAGTAACAACGT 58.099 42.857 0.00 0.00 0.00 3.99
6980 9497 2.413837 ACAACGTGGACAAGTATCAGC 58.586 47.619 0.00 0.00 0.00 4.26
6995 9512 5.449304 AGTATCAGCGTAAACTTTTTGTGC 58.551 37.500 0.00 0.00 0.00 4.57
7015 9532 2.592032 TTGGGCGGATGCTGTCTCA 61.592 57.895 0.00 0.00 42.25 3.27
7018 9535 2.581354 GCGGATGCTGTCTCAGGT 59.419 61.111 0.00 0.00 38.39 4.00
7019 9536 1.812922 GCGGATGCTGTCTCAGGTG 60.813 63.158 0.00 0.00 38.39 4.00
7031 9548 3.093057 GTCTCAGGTGTCCATCTGTAGT 58.907 50.000 7.39 0.00 40.38 2.73
7036 9553 3.753272 CAGGTGTCCATCTGTAGTTTTGG 59.247 47.826 0.00 0.00 34.90 3.28
7050 9567 1.042003 TTTTGGCACAGAAGCTGGCA 61.042 50.000 0.00 0.00 42.39 4.92
7085 9602 1.600916 GTGGCCGTCTCCTTTTGCT 60.601 57.895 0.00 0.00 0.00 3.91
7097 9614 7.812669 CCGTCTCCTTTTGCTTATTTTGTTTAT 59.187 33.333 0.00 0.00 0.00 1.40
7114 9984 7.563724 TTGTTTATAGTTCAACTAGAGGGGT 57.436 36.000 3.12 0.00 33.66 4.95
7167 10037 7.716799 AATTGGCACCAGTTTAGATTATTGA 57.283 32.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
498 572 1.401931 CGTAAGTTCGTGACGGTCCAT 60.402 52.381 4.70 0.00 33.01 3.41
505 579 2.937591 TGATGTCCGTAAGTTCGTGAC 58.062 47.619 0.00 0.00 34.34 3.67
917 1889 7.498239 CCAGCCCATTCATTAGATGTATCATAG 59.502 40.741 0.00 0.00 0.00 2.23
1080 2052 2.281970 CTGGAGCTTGGCAGTGCA 60.282 61.111 18.61 0.00 0.00 4.57
1093 2065 0.919289 GGGGGAGATTGGGTTCTGGA 60.919 60.000 0.00 0.00 0.00 3.86
1524 2496 1.829849 CCAGATCCTGCAGAGAGAACA 59.170 52.381 17.39 0.00 0.00 3.18
1648 2620 1.737236 TCGACACATTATGCAACAGCC 59.263 47.619 0.00 0.00 0.00 4.85
1680 2653 1.202557 TGACCCAAAAAGCGTACGTCT 60.203 47.619 17.90 11.56 0.00 4.18
1681 2654 1.193874 CTGACCCAAAAAGCGTACGTC 59.806 52.381 17.90 9.31 0.00 4.34
1682 2655 1.202557 TCTGACCCAAAAAGCGTACGT 60.203 47.619 17.90 0.00 0.00 3.57
1683 2656 1.459592 CTCTGACCCAAAAAGCGTACG 59.540 52.381 11.84 11.84 0.00 3.67
1684 2657 2.479275 GACTCTGACCCAAAAAGCGTAC 59.521 50.000 0.00 0.00 0.00 3.67
1728 2702 8.802267 ACATTTAAACCACAGTTAGCACATAAT 58.198 29.630 0.00 0.00 34.19 1.28
1770 2744 2.293122 GCCAACACACAAAGCATCACTA 59.707 45.455 0.00 0.00 0.00 2.74
1783 2757 4.021280 ACATAATTCTTGCATGCCAACACA 60.021 37.500 16.68 0.00 0.00 3.72
1812 2786 1.376424 CATCTTCCACCGCACAGCT 60.376 57.895 0.00 0.00 0.00 4.24
1906 2882 2.614829 ACGTTCAGGAATTATCGGGG 57.385 50.000 0.00 0.00 0.00 5.73
1928 2904 1.478105 GGGGTGACATGCTCAAAATCC 59.522 52.381 0.00 0.00 0.00 3.01
1935 2911 0.392998 ATGTTCGGGGTGACATGCTC 60.393 55.000 0.00 0.00 0.00 4.26
1966 2942 5.163530 TGTCACCTCGTGTCAACTAAAGTTA 60.164 40.000 0.00 0.00 34.10 2.24
2031 3007 4.624015 ACATGGCAATGTTCTGACAAAAG 58.376 39.130 0.00 0.00 44.94 2.27
2090 3067 2.988684 GCATGGCAACCCGAACCA 60.989 61.111 0.00 0.00 37.99 3.67
2091 3068 0.963355 TAAGCATGGCAACCCGAACC 60.963 55.000 0.00 0.00 0.00 3.62
2165 3143 7.434897 GCAACATGAATAAGAAAAGACACAACA 59.565 33.333 0.00 0.00 0.00 3.33
2243 3221 5.163405 GCAGTAAGAGGATTGTACCATGAGA 60.163 44.000 0.00 0.00 0.00 3.27
2263 3241 1.899142 GGAGAAAGAGGACTCAGCAGT 59.101 52.381 1.75 0.00 35.17 4.40
2320 3298 4.220821 AGCACCAGTCCTACATTATATCGG 59.779 45.833 0.00 0.00 0.00 4.18
2336 3314 2.174363 TGATGAACTGTCAGCACCAG 57.826 50.000 0.00 0.00 45.03 4.00
2350 3328 5.702670 GTGTGAGTTCTTTCTTCCATGATGA 59.297 40.000 0.00 0.00 0.00 2.92
2351 3329 5.471116 TGTGTGAGTTCTTTCTTCCATGATG 59.529 40.000 0.00 0.00 0.00 3.07
2352 3330 5.624159 TGTGTGAGTTCTTTCTTCCATGAT 58.376 37.500 0.00 0.00 0.00 2.45
2391 3369 7.592885 AATTGGTATAATGCATTGAAGCTCT 57.407 32.000 22.27 7.81 34.99 4.09
2483 3461 5.181690 TCAGAAACTTCCAAAATCCAACG 57.818 39.130 0.00 0.00 0.00 4.10
2586 3564 2.474410 AGCCTAGCAGTTGGTGTAAC 57.526 50.000 0.00 0.00 39.65 2.50
2587 3565 3.146066 CAAAGCCTAGCAGTTGGTGTAA 58.854 45.455 0.00 0.00 0.00 2.41
2588 3566 2.552155 CCAAAGCCTAGCAGTTGGTGTA 60.552 50.000 11.78 0.00 39.51 2.90
2589 3567 1.609208 CAAAGCCTAGCAGTTGGTGT 58.391 50.000 0.00 0.00 0.00 4.16
2590 3568 0.883833 CCAAAGCCTAGCAGTTGGTG 59.116 55.000 11.78 0.00 39.51 4.17
2591 3569 0.478507 ACCAAAGCCTAGCAGTTGGT 59.521 50.000 17.24 17.24 46.72 3.67
2592 3570 2.489938 TACCAAAGCCTAGCAGTTGG 57.510 50.000 16.24 16.24 45.36 3.77
2593 3571 4.737054 CAAATACCAAAGCCTAGCAGTTG 58.263 43.478 0.00 0.00 0.00 3.16
2594 3572 3.193479 GCAAATACCAAAGCCTAGCAGTT 59.807 43.478 0.00 0.00 0.00 3.16
2595 3573 2.755103 GCAAATACCAAAGCCTAGCAGT 59.245 45.455 0.00 0.00 0.00 4.40
2596 3574 2.754552 TGCAAATACCAAAGCCTAGCAG 59.245 45.455 0.00 0.00 0.00 4.24
2597 3575 2.801483 TGCAAATACCAAAGCCTAGCA 58.199 42.857 0.00 0.00 0.00 3.49
2598 3576 5.241506 TCATATGCAAATACCAAAGCCTAGC 59.758 40.000 0.00 0.00 0.00 3.42
2599 3577 6.882610 TCATATGCAAATACCAAAGCCTAG 57.117 37.500 0.00 0.00 0.00 3.02
2600 3578 7.838079 ATTCATATGCAAATACCAAAGCCTA 57.162 32.000 0.00 0.00 0.00 3.93
2601 3579 6.736110 ATTCATATGCAAATACCAAAGCCT 57.264 33.333 0.00 0.00 0.00 4.58
2721 3699 4.655762 TGCGCAGAATGAGTATAGTCTT 57.344 40.909 5.66 0.00 39.69 3.01
2741 3719 0.841961 TGGAATGGAGGAGGAGCATG 59.158 55.000 0.00 0.00 0.00 4.06
2963 3942 1.654023 GGTGAAGCCATTGGTACCGC 61.654 60.000 7.57 4.26 37.17 5.68
2990 3969 2.438074 TATGCTGTTGGGCCTGGCAA 62.438 55.000 22.05 3.90 36.49 4.52
3035 4014 4.173256 CGGACCAAACAATTGCCTAAATC 58.827 43.478 5.05 0.00 35.10 2.17
3128 4108 3.893572 GCATGGGCATGGCAAAAC 58.106 55.556 22.06 3.83 40.72 2.43
3511 4492 7.589395 TGTCAACGCAAATCACATAATTAACT 58.411 30.769 0.00 0.00 0.00 2.24
3527 4508 6.459435 CCATACCAAATATCAATGTCAACGCA 60.459 38.462 0.00 0.00 0.00 5.24
3584 4566 9.573166 CCAATGATCTAAATTACTCCAATGGTA 57.427 33.333 0.00 0.00 0.00 3.25
3706 4694 4.438200 CCAAACCGGTCATAACACTTATGC 60.438 45.833 8.04 0.00 42.12 3.14
3707 4695 5.229921 CCAAACCGGTCATAACACTTATG 57.770 43.478 8.04 0.00 43.41 1.90
3734 4722 1.971695 GGTGGGCCTCTTTCGGTTG 60.972 63.158 4.53 0.00 0.00 3.77
3736 4724 4.016706 CGGTGGGCCTCTTTCGGT 62.017 66.667 4.53 0.00 0.00 4.69
3738 4726 4.778143 CCCGGTGGGCCTCTTTCG 62.778 72.222 4.53 0.00 35.35 3.46
3751 4739 1.339727 GCCCCTAATACTAATGCCCGG 60.340 57.143 0.00 0.00 0.00 5.73
3992 4982 4.824515 AGGAGGGAGACGAGGGCG 62.825 72.222 0.00 0.00 44.79 6.13
4171 5161 4.801914 GCATATGCTCTGCCATGTCTAAGA 60.802 45.833 20.64 0.00 38.21 2.10
4230 6667 2.163412 TGTGACTGGTTTTGTGTGCTTC 59.837 45.455 0.00 0.00 0.00 3.86
4269 6708 4.080582 TGCTCCTTCGATTTAGGAATTCCA 60.081 41.667 26.22 9.69 41.13 3.53
4284 6723 1.002033 CTTGTGCACTTGTGCTCCTTC 60.002 52.381 23.53 11.11 35.49 3.46
4427 6866 4.913784 TGTTTTTAAGGCGTCCCTAAGAT 58.086 39.130 0.00 0.00 41.90 2.40
4437 6876 4.047822 TCAAGTGCATTGTTTTTAAGGCG 58.952 39.130 0.00 0.00 39.98 5.52
4443 6882 5.852282 AGGTACTCAAGTGCATTGTTTTT 57.148 34.783 0.00 0.00 40.05 1.94
4552 6999 1.827969 CCCCTACAAGTCTGAGACCAG 59.172 57.143 9.33 4.64 41.74 4.00
4572 7019 4.360563 TCACTTCTCGACAGTTGAACTTC 58.639 43.478 0.00 0.00 0.00 3.01
4658 7105 0.179181 TGTCGATAACGTGCGAGACC 60.179 55.000 8.41 0.00 40.69 3.85
4726 7173 5.931724 CGGCACACATATAAATAGGTCATGA 59.068 40.000 0.00 0.00 0.00 3.07
4728 7175 5.700832 CACGGCACACATATAAATAGGTCAT 59.299 40.000 0.00 0.00 0.00 3.06
4799 7246 5.940470 AGTCTTATCCCAACTGTCATTTCAC 59.060 40.000 0.00 0.00 0.00 3.18
4841 7288 3.057734 ACAGCAACTACGTCTTTACTGC 58.942 45.455 0.00 0.00 0.00 4.40
4852 7299 9.674824 AGTATCGTATAATGTAACAGCAACTAC 57.325 33.333 0.00 0.00 0.00 2.73
4904 7351 2.189594 TTGGCATTCACCAGAGACAG 57.810 50.000 0.00 0.00 41.82 3.51
4985 7432 6.183360 GCACATTTCTCATTTATCCCATGTGA 60.183 38.462 12.05 0.00 41.79 3.58
4999 7446 1.001974 AGTACTGCGGCACATTTCTCA 59.998 47.619 0.00 0.00 0.00 3.27
5011 7458 7.358435 CGGACAATATTCTAATCAAGTACTGCG 60.358 40.741 0.00 0.00 0.00 5.18
5023 7470 9.350951 TGAAGATAGACTCGGACAATATTCTAA 57.649 33.333 0.00 0.00 0.00 2.10
5065 7513 9.748708 CTTATTTTCCAAAATCTTGAACAGTGA 57.251 29.630 0.00 0.00 39.24 3.41
5215 7663 6.884280 ACTTGAAAGGGTTGATTCTTACAG 57.116 37.500 0.00 0.00 0.00 2.74
5306 7754 1.228124 GGTTAGTGCCAGTGTGCCA 60.228 57.895 1.78 0.00 0.00 4.92
5307 7755 0.609131 ATGGTTAGTGCCAGTGTGCC 60.609 55.000 1.78 0.00 42.47 5.01
5308 7756 2.107950 TATGGTTAGTGCCAGTGTGC 57.892 50.000 0.00 0.00 42.47 4.57
5309 7757 3.873361 CAGATATGGTTAGTGCCAGTGTG 59.127 47.826 0.00 0.00 42.47 3.82
5310 7758 3.774766 TCAGATATGGTTAGTGCCAGTGT 59.225 43.478 0.00 0.00 42.47 3.55
5311 7759 4.406648 TCAGATATGGTTAGTGCCAGTG 57.593 45.455 0.00 0.00 42.47 3.66
5312 7760 6.942163 ATATCAGATATGGTTAGTGCCAGT 57.058 37.500 1.76 0.00 42.47 4.00
5313 7761 8.627208 AAAATATCAGATATGGTTAGTGCCAG 57.373 34.615 3.51 0.00 42.47 4.85
5492 7940 0.027194 CGCTCACATCCTGCAAATCG 59.973 55.000 0.00 0.00 0.00 3.34
5546 7994 1.439679 GGCCAGAACTAGGAACAACG 58.560 55.000 0.00 0.00 0.00 4.10
5910 8419 3.284617 CCCAATGAAGATGCTGATGTCA 58.715 45.455 0.00 0.00 0.00 3.58
6211 8720 5.918576 GCAAGCCAAATAAATCGGTTATACC 59.081 40.000 0.00 0.00 31.82 2.73
6272 8781 6.798482 TGAACAGGCATGACAAATAATGATC 58.202 36.000 4.84 0.00 0.00 2.92
6290 8799 2.775890 ACTGTGCTCCTTCATGAACAG 58.224 47.619 17.46 17.46 40.61 3.16
6330 8839 5.504665 CCGGAGTTCATCAAATGAGTAATGC 60.505 44.000 0.00 0.00 40.94 3.56
6386 8899 8.409358 AAGGTCAATTAAGTTAATCAGCAACT 57.591 30.769 8.56 0.00 37.85 3.16
6449 8962 5.634859 GCACTTTCAATTTTATGGACACTGG 59.365 40.000 0.00 0.00 0.00 4.00
6467 8980 1.063183 AGAGAGGCTTCCAGCACTTT 58.937 50.000 0.00 0.00 44.75 2.66
6592 9105 1.883275 CGACCTCTATGGACTAGCCTG 59.117 57.143 5.06 0.00 39.71 4.85
6654 9167 7.978975 CCTTCCTAGCTTGCATAACTATCTATC 59.021 40.741 0.00 0.00 0.00 2.08
6655 9168 7.456269 ACCTTCCTAGCTTGCATAACTATCTAT 59.544 37.037 0.00 0.00 0.00 1.98
6656 9169 6.782988 ACCTTCCTAGCTTGCATAACTATCTA 59.217 38.462 0.00 0.00 0.00 1.98
6657 9170 5.604650 ACCTTCCTAGCTTGCATAACTATCT 59.395 40.000 0.00 0.00 0.00 1.98
6673 9186 8.938883 AGAATAAAGCTGATATGAACCTTCCTA 58.061 33.333 0.00 0.00 0.00 2.94
6718 9231 8.273780 AGATTCAGTCTCCATATGAACAAAAC 57.726 34.615 3.65 0.00 35.89 2.43
6719 9232 8.868522 AAGATTCAGTCTCCATATGAACAAAA 57.131 30.769 3.65 0.00 35.67 2.44
6827 9344 1.133945 TGTTGCAGCCAGAGGTTTGTA 60.134 47.619 0.00 0.00 0.00 2.41
6841 9358 2.918345 GCAAGCCGACCATGTTGCA 61.918 57.895 10.59 0.00 43.86 4.08
6843 9360 1.210931 CAGCAAGCCGACCATGTTG 59.789 57.895 0.00 0.00 0.00 3.33
6909 9426 9.780186 ATATTGTACTTACTTCAAAGGGCTATC 57.220 33.333 0.00 0.00 0.00 2.08
6966 9483 4.530710 AGTTTACGCTGATACTTGTCCA 57.469 40.909 0.00 0.00 0.00 4.02
6980 9497 2.532317 CCCAACGCACAAAAAGTTTACG 59.468 45.455 0.00 0.00 0.00 3.18
6995 9512 3.499737 GACAGCATCCGCCCAACG 61.500 66.667 0.00 0.00 39.83 4.10
7015 9532 3.810743 GCCAAAACTACAGATGGACACCT 60.811 47.826 0.00 0.00 34.82 4.00
7018 9535 3.146066 GTGCCAAAACTACAGATGGACA 58.854 45.455 0.00 0.00 34.82 4.02
7019 9536 3.146066 TGTGCCAAAACTACAGATGGAC 58.854 45.455 0.00 0.00 34.82 4.02
7031 9548 1.042003 TGCCAGCTTCTGTGCCAAAA 61.042 50.000 0.00 0.00 30.52 2.44
7036 9553 4.099170 CGCTGCCAGCTTCTGTGC 62.099 66.667 15.80 0.00 39.60 4.57
7050 9567 3.314331 CCCACACCCTCACTCGCT 61.314 66.667 0.00 0.00 0.00 4.93
7097 9614 4.122337 TGTCACCCCTCTAGTTGAACTA 57.878 45.455 4.81 4.81 0.00 2.24
7167 10037 6.190346 TGGCGGTATGGTACCTTTAATTAT 57.810 37.500 14.36 0.00 46.81 1.28


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

AutoCloner maintained by Alex Coulton.