Multiple sequence alignment - TraesCS7B01G196900

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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 TraesCS7B01G196900 chr7B 100.000 7516 0 0 1 7516 339604969 339612484 0.000000e+00 13880.0
1 TraesCS7B01G196900 chr7B 85.349 587 52 14 2284 2844 450597049 450596471 1.820000e-160 577.0
2 TraesCS7B01G196900 chr7B 84.812 586 58 14 2284 2844 255044562 255045141 1.830000e-155 560.0
3 TraesCS7B01G196900 chr7B 84.471 586 60 14 2284 2844 152480912 152480333 3.960000e-152 549.0
4 TraesCS7B01G196900 chr7B 84.471 586 60 14 2284 2844 155728607 155729186 3.960000e-152 549.0
5 TraesCS7B01G196900 chr7B 90.698 129 9 3 3535 3663 687302844 687302969 1.300000e-37 169.0
6 TraesCS7B01G196900 chr7B 100.000 34 0 0 3460 3493 339607276 339607309 6.300000e-06 63.9
7 TraesCS7B01G196900 chr7B 94.286 35 2 0 845 879 348991995 348992029 4.000000e-03 54.7
8 TraesCS7B01G196900 chr7D 97.142 2274 44 11 3535 5794 296500251 296502517 0.000000e+00 3819.0
9 TraesCS7B01G196900 chr7D 96.202 2238 55 13 869 3105 296496886 296499094 0.000000e+00 3635.0
10 TraesCS7B01G196900 chr7D 95.011 922 17 8 5792 6691 296502700 296503614 0.000000e+00 1421.0
11 TraesCS7B01G196900 chr7D 91.527 838 35 10 6690 7512 296503763 296504579 0.000000e+00 1122.0
12 TraesCS7B01G196900 chr7D 93.750 368 14 2 3100 3458 296499200 296499567 1.840000e-150 544.0
13 TraesCS7B01G196900 chr7D 90.960 177 13 2 4360 4534 397555078 397554903 1.260000e-57 235.0
14 TraesCS7B01G196900 chr7D 97.561 82 2 0 3459 3540 296499636 296499717 2.830000e-29 141.0
15 TraesCS7B01G196900 chr7D 97.059 34 1 0 3460 3493 296498321 296498354 2.930000e-04 58.4
16 TraesCS7B01G196900 chrUn 96.269 2305 39 12 4240 6520 116287037 116289318 0.000000e+00 3736.0
17 TraesCS7B01G196900 chrUn 97.714 1531 30 4 893 2422 116282615 116284141 0.000000e+00 2628.0
18 TraesCS7B01G196900 chrUn 97.179 709 19 1 3535 4242 116286217 116286925 0.000000e+00 1197.0
19 TraesCS7B01G196900 chrUn 95.748 729 30 1 2378 3105 116284138 116284866 0.000000e+00 1173.0
20 TraesCS7B01G196900 chrUn 84.812 586 58 14 2284 2844 427461532 427460953 1.830000e-155 560.0
21 TraesCS7B01G196900 chrUn 94.220 346 18 1 7169 7512 116291562 116291907 1.860000e-145 527.0
22 TraesCS7B01G196900 chrUn 92.683 369 17 3 3100 3458 116284974 116285342 2.400000e-144 523.0
23 TraesCS7B01G196900 chrUn 87.368 475 23 12 6708 7170 116289341 116289790 1.870000e-140 510.0
24 TraesCS7B01G196900 chrUn 81.690 355 50 11 527 879 23395029 23395370 1.600000e-71 281.0
25 TraesCS7B01G196900 chrUn 81.690 355 50 11 527 879 267109036 267109377 1.600000e-71 281.0
26 TraesCS7B01G196900 chrUn 81.690 355 50 11 527 879 267126629 267126970 1.600000e-71 281.0
27 TraesCS7B01G196900 chrUn 86.957 253 11 8 6966 7217 231560634 231560865 1.610000e-66 265.0
28 TraesCS7B01G196900 chrUn 86.957 253 11 8 6966 7217 273327493 273327262 1.610000e-66 265.0
29 TraesCS7B01G196900 chrUn 86.957 253 11 8 6966 7217 403938322 403938091 1.610000e-66 265.0
30 TraesCS7B01G196900 chrUn 97.561 82 2 0 3459 3540 116285411 116285492 2.830000e-29 141.0
31 TraesCS7B01G196900 chrUn 97.059 34 1 0 3460 3493 116284027 116284060 2.930000e-04 58.4
32 TraesCS7B01G196900 chr3B 98.155 867 16 0 1 867 387433040 387433906 0.000000e+00 1513.0
33 TraesCS7B01G196900 chr3B 97.468 869 22 0 1 869 369405658 369404790 0.000000e+00 1483.0
34 TraesCS7B01G196900 chr3B 87.457 869 78 8 1 869 512523215 512524052 0.000000e+00 972.0
35 TraesCS7B01G196900 chr3B 87.199 789 71 4 81 869 511159818 511160576 0.000000e+00 870.0
36 TraesCS7B01G196900 chr3B 89.452 493 52 0 1 493 511289584 511289092 2.300000e-174 623.0
37 TraesCS7B01G196900 chr3B 86.201 558 49 12 2310 2844 141751302 141750750 5.060000e-161 579.0
38 TraesCS7B01G196900 chr3B 89.737 419 35 5 2430 2844 400324024 400323610 5.160000e-146 529.0
39 TraesCS7B01G196900 chr3B 93.373 166 8 2 4360 4523 269252151 269251987 7.530000e-60 243.0
40 TraesCS7B01G196900 chr5D 91.638 873 52 3 1 871 374382080 374382933 0.000000e+00 1188.0
41 TraesCS7B01G196900 chr5D 97.087 103 3 0 3535 3637 485382773 485382875 2.790000e-39 174.0
42 TraesCS7B01G196900 chr5D 97.917 48 1 0 3204 3251 107536161 107536208 4.830000e-12 84.2
43 TraesCS7B01G196900 chr2D 90.219 869 58 10 1 869 106351106 106350265 0.000000e+00 1109.0
44 TraesCS7B01G196900 chr2D 78.615 491 76 20 394 874 409259002 409259473 1.590000e-76 298.0
45 TraesCS7B01G196900 chr2D 92.941 170 9 2 4355 4522 299891549 299891717 2.090000e-60 244.0
46 TraesCS7B01G196900 chr2D 98.000 100 2 0 3538 3637 163016977 163016878 2.790000e-39 174.0
47 TraesCS7B01G196900 chr4A 88.827 895 62 12 1 872 722662202 722661323 0.000000e+00 1064.0
48 TraesCS7B01G196900 chr4A 84.812 586 58 14 2284 2844 611034305 611033726 1.830000e-155 560.0
49 TraesCS7B01G196900 chr4A 78.155 206 43 2 1278 1482 552699306 552699510 6.120000e-26 130.0
50 TraesCS7B01G196900 chr2B 84.932 876 106 12 4 868 526388299 526387439 0.000000e+00 863.0
51 TraesCS7B01G196900 chr2B 86.071 560 48 12 2310 2844 338746603 338746049 6.540000e-160 575.0
52 TraesCS7B01G196900 chr1B 89.744 585 41 5 296 880 614177630 614178195 0.000000e+00 730.0
53 TraesCS7B01G196900 chr1B 88.449 303 29 2 1 303 614175143 614175439 1.990000e-95 361.0
54 TraesCS7B01G196900 chr1B 85.827 254 14 7 6966 7218 619185814 619186046 4.500000e-62 250.0
55 TraesCS7B01G196900 chr4B 85.664 565 50 13 2310 2848 28228313 28227754 3.940000e-157 566.0
56 TraesCS7B01G196900 chr4B 87.352 253 10 8 6966 7217 495578730 495578961 3.460000e-68 270.0
57 TraesCS7B01G196900 chr4B 85.771 253 14 9 6966 7217 209116030 209115799 1.620000e-61 248.0
58 TraesCS7B01G196900 chr4B 76.699 206 46 2 1278 1482 67772063 67772267 6.160000e-21 113.0
59 TraesCS7B01G196900 chr2A 85.613 563 51 11 2307 2844 116437896 116438453 1.420000e-156 564.0
60 TraesCS7B01G196900 chr2A 85.613 563 51 11 2307 2844 448501784 448502341 1.420000e-156 564.0
61 TraesCS7B01G196900 chr1A 84.812 586 58 14 2284 2844 440454779 440454200 1.830000e-155 560.0
62 TraesCS7B01G196900 chr1A 85.714 252 16 6 6966 7217 278533457 278533226 1.620000e-61 248.0
63 TraesCS7B01G196900 chr1D 81.317 653 77 25 2223 2844 409490645 409491283 8.770000e-134 488.0
64 TraesCS7B01G196900 chr4D 86.842 380 48 2 473 851 470773381 470773759 2.510000e-114 424.0
65 TraesCS7B01G196900 chr4D 97.087 103 3 0 3535 3637 121406634 121406736 2.790000e-39 174.0
66 TraesCS7B01G196900 chr4D 77.670 206 44 2 1278 1482 46292090 46291886 2.850000e-24 124.0
67 TraesCS7B01G196900 chr4D 100.000 28 0 0 845 872 366707966 366707939 1.400000e-02 52.8
68 TraesCS7B01G196900 chr3D 86.957 253 11 8 6966 7217 48693669 48693438 1.610000e-66 265.0
69 TraesCS7B01G196900 chr3D 93.373 166 9 1 4360 4523 187836470 187836305 2.090000e-60 244.0
70 TraesCS7B01G196900 chr3D 92.771 166 10 1 4361 4524 87926161 87925996 9.750000e-59 239.0
71 TraesCS7B01G196900 chr7A 77.485 493 75 25 394 869 592058929 592058456 5.780000e-66 263.0
72 TraesCS7B01G196900 chr7A 86.561 253 12 8 6966 7217 60221248 60221479 7.480000e-65 259.0
73 TraesCS7B01G196900 chr6B 86.166 253 13 8 6966 7217 311355549 311355318 3.480000e-63 254.0
74 TraesCS7B01G196900 chr6B 85.317 252 18 6 6966 7217 633591800 633591568 7.530000e-60 243.0
75 TraesCS7B01G196900 chr6B 92.814 167 8 3 4360 4523 481858013 481857848 9.750000e-59 239.0
76 TraesCS7B01G196900 chr6B 98.000 100 2 0 3538 3637 487538401 487538302 2.790000e-39 174.0
77 TraesCS7B01G196900 chr3A 93.373 166 9 1 4360 4523 238686209 238686374 2.090000e-60 244.0
78 TraesCS7B01G196900 chr6A 97.087 103 3 0 3535 3637 263902236 263902338 2.790000e-39 174.0
79 TraesCS7B01G196900 chr5B 97.087 103 3 0 3535 3637 270439131 270439233 2.790000e-39 174.0


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 TraesCS7B01G196900 chr7B 339604969 339612484 7515 False 13880.000000 13880 100.000000 1 7516 1 chr7B.!!$F3 7515
1 TraesCS7B01G196900 chr7B 450596471 450597049 578 True 577.000000 577 85.349000 2284 2844 1 chr7B.!!$R2 560
2 TraesCS7B01G196900 chr7B 255044562 255045141 579 False 560.000000 560 84.812000 2284 2844 1 chr7B.!!$F2 560
3 TraesCS7B01G196900 chr7B 152480333 152480912 579 True 549.000000 549 84.471000 2284 2844 1 chr7B.!!$R1 560
4 TraesCS7B01G196900 chr7B 155728607 155729186 579 False 549.000000 549 84.471000 2284 2844 1 chr7B.!!$F1 560
5 TraesCS7B01G196900 chr7D 296496886 296504579 7693 False 1534.342857 3819 95.464571 869 7512 7 chr7D.!!$F1 6643
6 TraesCS7B01G196900 chrUn 116282615 116291907 9292 False 1165.933333 3736 95.089000 893 7512 9 chrUn.!!$F5 6619
7 TraesCS7B01G196900 chrUn 427460953 427461532 579 True 560.000000 560 84.812000 2284 2844 1 chrUn.!!$R3 560
8 TraesCS7B01G196900 chr3B 387433040 387433906 866 False 1513.000000 1513 98.155000 1 867 1 chr3B.!!$F1 866
9 TraesCS7B01G196900 chr3B 369404790 369405658 868 True 1483.000000 1483 97.468000 1 869 1 chr3B.!!$R3 868
10 TraesCS7B01G196900 chr3B 512523215 512524052 837 False 972.000000 972 87.457000 1 869 1 chr3B.!!$F3 868
11 TraesCS7B01G196900 chr3B 511159818 511160576 758 False 870.000000 870 87.199000 81 869 1 chr3B.!!$F2 788
12 TraesCS7B01G196900 chr3B 141750750 141751302 552 True 579.000000 579 86.201000 2310 2844 1 chr3B.!!$R1 534
13 TraesCS7B01G196900 chr5D 374382080 374382933 853 False 1188.000000 1188 91.638000 1 871 1 chr5D.!!$F2 870
14 TraesCS7B01G196900 chr2D 106350265 106351106 841 True 1109.000000 1109 90.219000 1 869 1 chr2D.!!$R1 868
15 TraesCS7B01G196900 chr4A 722661323 722662202 879 True 1064.000000 1064 88.827000 1 872 1 chr4A.!!$R2 871
16 TraesCS7B01G196900 chr4A 611033726 611034305 579 True 560.000000 560 84.812000 2284 2844 1 chr4A.!!$R1 560
17 TraesCS7B01G196900 chr2B 526387439 526388299 860 True 863.000000 863 84.932000 4 868 1 chr2B.!!$R2 864
18 TraesCS7B01G196900 chr2B 338746049 338746603 554 True 575.000000 575 86.071000 2310 2844 1 chr2B.!!$R1 534
19 TraesCS7B01G196900 chr1B 614175143 614178195 3052 False 545.500000 730 89.096500 1 880 2 chr1B.!!$F2 879
20 TraesCS7B01G196900 chr4B 28227754 28228313 559 True 566.000000 566 85.664000 2310 2848 1 chr4B.!!$R1 538
21 TraesCS7B01G196900 chr2A 116437896 116438453 557 False 564.000000 564 85.613000 2307 2844 1 chr2A.!!$F1 537
22 TraesCS7B01G196900 chr2A 448501784 448502341 557 False 564.000000 564 85.613000 2307 2844 1 chr2A.!!$F2 537
23 TraesCS7B01G196900 chr1A 440454200 440454779 579 True 560.000000 560 84.812000 2284 2844 1 chr1A.!!$R2 560
24 TraesCS7B01G196900 chr1D 409490645 409491283 638 False 488.000000 488 81.317000 2223 2844 1 chr1D.!!$F1 621

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
494 2704 0.183014 TTCTGGTGGCGTTTGGGTTA 59.817 50.000 0.00 0.0 0.00 2.85 F
816 3062 0.690762 AACAGCCACATTCGGGTAGT 59.309 50.000 0.00 0.0 34.17 2.73 F
2266 4513 0.687354 AGACAATGCCGAACACCTCT 59.313 50.000 0.00 0.0 0.00 3.69 F
3101 5417 0.034960 GCCTCCTCTTCCCTTTCCAC 60.035 60.000 0.00 0.0 0.00 4.02 F
4346 8241 0.249447 TCACAAGGTCTGCGTGTCAG 60.249 55.000 0.00 0.0 44.21 3.51 F
5072 8969 2.046285 CGGGGCCAACAATGAGGTC 61.046 63.158 4.39 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2237 4484 0.908198 GGCATTGTCTCCCAGAGAGT 59.092 55.000 0.00 0.0 43.71 3.24 R
2570 4881 0.036858 GGAAGGCGCTCTTGAGAGTT 60.037 55.000 14.63 0.0 43.85 3.01 R
3722 7499 1.202879 ACCAACTGCCAGGATTTTCGA 60.203 47.619 0.00 0.0 0.00 3.71 R
4692 8589 2.450476 CAAGTCCTGAATTTGAGGGGG 58.550 52.381 1.85 0.0 0.00 5.40 R
5927 10022 1.980765 AGCCTGAGAATCTGTCCAACA 59.019 47.619 0.00 0.0 34.92 3.33 R
6908 11174 0.874390 TTGCAGCCGAACACAAGATC 59.126 50.000 0.00 0.0 0.00 2.75 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
220 223 0.532573 GGAGTGAGATGTCGAGGCAA 59.467 55.000 0.00 0.00 0.00 4.52
494 2704 0.183014 TTCTGGTGGCGTTTGGGTTA 59.817 50.000 0.00 0.00 0.00 2.85
816 3062 0.690762 AACAGCCACATTCGGGTAGT 59.309 50.000 0.00 0.00 34.17 2.73
826 3072 2.107950 TTCGGGTAGTCAAATGCCAG 57.892 50.000 0.00 0.00 0.00 4.85
891 3137 6.376018 CGTTAGGGTTATTTCTGGGAATTTGA 59.624 38.462 0.00 0.00 0.00 2.69
1010 3256 3.201363 TCCCAATCCAATCTTCCCTCTT 58.799 45.455 0.00 0.00 0.00 2.85
1068 3314 2.122167 CCCTTCCTCGTCCTCCTCG 61.122 68.421 0.00 0.00 0.00 4.63
1629 3875 2.285220 GCATTGTGCTATGACTGTACCG 59.715 50.000 0.00 0.00 40.96 4.02
1692 3938 2.969821 AGGGTGGCAATGTTCTGTTA 57.030 45.000 0.00 0.00 0.00 2.41
1721 3968 5.008911 TGCTAATGACGCTTGAATGCAATAT 59.991 36.000 0.00 0.00 32.68 1.28
1898 4145 1.669115 CCAGTGCAGAGGGACGTTG 60.669 63.158 0.00 0.00 40.77 4.10
2049 4296 7.445402 AGTTGGGTATAAAATGCTATACTGCAG 59.555 37.037 13.48 13.48 46.71 4.41
2125 4372 4.278170 TGAGTTGGCACTGAATTTGTTAGG 59.722 41.667 0.00 0.00 31.22 2.69
2174 4421 6.070538 ACATGTAGTTCTATCTCCTTGCACTT 60.071 38.462 0.00 0.00 0.00 3.16
2215 4462 1.509923 GGTAGCGTACCAGCTCGTT 59.490 57.895 0.00 0.00 45.67 3.85
2220 4467 1.145803 GCGTACCAGCTCGTTTTCTT 58.854 50.000 0.00 0.00 0.00 2.52
2221 4468 1.136336 GCGTACCAGCTCGTTTTCTTG 60.136 52.381 0.00 0.00 0.00 3.02
2234 4481 3.120338 CGTTTTCTTGTGTGTGTGTGTCT 60.120 43.478 0.00 0.00 0.00 3.41
2237 4484 1.085893 CTTGTGTGTGTGTGTCTGCA 58.914 50.000 0.00 0.00 0.00 4.41
2266 4513 0.687354 AGACAATGCCGAACACCTCT 59.313 50.000 0.00 0.00 0.00 3.69
2374 4624 6.806217 AGATGGGTGGTAGTAGATAGCTATT 58.194 40.000 7.87 0.96 32.85 1.73
2570 4881 4.085357 AGCTGACTGATTGTAACACCAA 57.915 40.909 0.00 0.00 0.00 3.67
2582 4893 4.127171 TGTAACACCAAACTCTCAAGAGC 58.873 43.478 6.94 0.00 45.79 4.09
2750 5062 3.137544 TCCTCCCACAAACACACAATAGT 59.862 43.478 0.00 0.00 0.00 2.12
2751 5063 3.888930 CCTCCCACAAACACACAATAGTT 59.111 43.478 0.00 0.00 0.00 2.24
2798 5110 4.526970 ACAACTTGCCCGATTAGAATCAT 58.473 39.130 3.31 0.00 35.11 2.45
2835 5150 0.670546 AGATGTCCACTCGCAAACCG 60.671 55.000 0.00 0.00 38.61 4.44
2854 5169 1.205460 GCAACCCTTCCCCCTCTACA 61.205 60.000 0.00 0.00 0.00 2.74
2863 5178 3.421394 TCCCCCTCTACATTGATGTCT 57.579 47.619 0.00 0.00 41.97 3.41
2916 5231 0.037697 TGTTGAGGAACGATGTCCCG 60.038 55.000 0.00 0.00 38.59 5.14
2974 5289 1.002544 ACAGCCTCAGCAAGTCCTTAC 59.997 52.381 0.00 0.00 43.56 2.34
2996 5312 3.077359 GTTCACCCATCTTTCTGACCAG 58.923 50.000 0.00 0.00 0.00 4.00
3003 5319 2.724977 TCTTTCTGACCAGCTACACG 57.275 50.000 0.00 0.00 0.00 4.49
3101 5417 0.034960 GCCTCCTCTTCCCTTTCCAC 60.035 60.000 0.00 0.00 0.00 4.02
3116 5545 4.164988 CCTTTCCACTCATCTTCCTACCAT 59.835 45.833 0.00 0.00 0.00 3.55
3128 5557 0.322816 CCTACCATGCAGGCAACAGT 60.323 55.000 0.00 0.00 43.14 3.55
3163 5592 1.029408 AGCAACAACACCGTCAGCAA 61.029 50.000 0.00 0.00 0.00 3.91
3333 5771 4.007644 CCGGCTCACAGGACTGCA 62.008 66.667 0.00 0.00 0.00 4.41
3342 5780 1.196766 ACAGGACTGCAGCTGATCCA 61.197 55.000 25.40 12.18 33.33 3.41
3475 5982 0.321122 CGAAGATAGATGGGCAGGGC 60.321 60.000 0.00 0.00 0.00 5.19
3561 7337 3.118261 TGGTGATACTCCAATCCTTCAGC 60.118 47.826 0.00 0.00 33.47 4.26
3632 7408 1.014044 TTGACATTCTCCGCACGCTC 61.014 55.000 0.00 0.00 0.00 5.03
3645 7421 1.262683 GCACGCTCTAGCATTGGAATC 59.737 52.381 2.44 0.00 42.21 2.52
3793 7570 4.454504 TCGGTTCCATCTTTTACTTGAAGC 59.545 41.667 0.00 0.00 0.00 3.86
3926 7704 6.494893 TGTCGAGGAAAAAGGTTCATAATG 57.505 37.500 0.00 0.00 0.00 1.90
4059 7838 3.183172 CGAATTCTATGTCATGCTGTCCG 59.817 47.826 3.52 0.00 0.00 4.79
4098 7877 6.278172 TGCATTGGCTTTTTGACATACATA 57.722 33.333 0.00 0.00 41.91 2.29
4138 7919 8.085296 CAGGGTTAACTAGCAAGTATGAGATAG 58.915 40.741 5.42 0.00 33.75 2.08
4346 8241 0.249447 TCACAAGGTCTGCGTGTCAG 60.249 55.000 0.00 0.00 44.21 3.51
4370 8265 4.971282 AGATGATCAAACATACTCCCTCCA 59.029 41.667 0.00 0.00 0.00 3.86
4480 8375 4.587262 TGCTCCGTATGTAGTCCATATTGT 59.413 41.667 0.00 0.00 38.29 2.71
4692 8589 5.646606 TGCCAGTTTTTCTAACACACTTTC 58.353 37.500 0.00 0.00 0.00 2.62
4814 8711 6.561294 AGAAGGAAATTCAGGGGACATTTTA 58.439 36.000 0.00 0.00 40.67 1.52
5072 8969 2.046285 CGGGGCCAACAATGAGGTC 61.046 63.158 4.39 0.00 0.00 3.85
5294 9191 7.042389 GGATTTAGACAGACGAATGGATTTCTC 60.042 40.741 0.00 0.00 31.73 2.87
5372 9269 7.496920 CCATACTATGATGCAATGGACGATAAT 59.503 37.037 5.54 0.00 39.60 1.28
5373 9270 9.533253 CATACTATGATGCAATGGACGATAATA 57.467 33.333 0.00 0.00 0.00 0.98
5641 9550 2.269940 AGGTTATCTGAAGCTGGTGGT 58.730 47.619 0.00 0.00 0.00 4.16
5811 9905 5.841957 ATTTACTTGCCCTGATTAAGCAG 57.158 39.130 13.85 13.85 37.89 4.24
5892 9987 5.897377 ATGTTAACTTGGATGTTGTAGCC 57.103 39.130 7.22 0.00 34.64 3.93
6379 10487 0.464036 TGTGTGTTGAGGCGAGAACT 59.536 50.000 0.00 0.00 0.00 3.01
6427 10535 1.479323 GGCATTGCATGACATGACCTT 59.521 47.619 19.76 0.00 38.49 3.50
6432 10540 0.883153 GCATGACATGACCTTGTGCA 59.117 50.000 19.76 0.00 0.00 4.57
6456 10564 7.677276 GCATCTGTTAAATTCGACAGCATTAGT 60.677 37.037 13.53 0.00 42.27 2.24
6474 10582 1.149627 TGGTACCGTTTTGCAGCCT 59.850 52.632 7.57 0.00 0.00 4.58
6476 10584 0.887387 GGTACCGTTTTGCAGCCTGA 60.887 55.000 0.00 0.00 0.00 3.86
6477 10585 0.517316 GTACCGTTTTGCAGCCTGAG 59.483 55.000 0.00 0.00 0.00 3.35
6478 10586 0.394938 TACCGTTTTGCAGCCTGAGA 59.605 50.000 0.00 0.00 0.00 3.27
6479 10587 0.886490 ACCGTTTTGCAGCCTGAGAG 60.886 55.000 0.00 0.00 0.00 3.20
6617 10733 6.613233 TGTAAATACAAATACCAAGTTGGCG 58.387 36.000 22.25 7.93 35.39 5.69
6624 10740 0.887387 TACCAAGTTGGCGGCTGAAC 60.887 55.000 22.25 7.35 42.67 3.18
6649 10765 1.942677 CTCAGGATGCTTCAGCTCTG 58.057 55.000 0.00 5.85 42.66 3.35
6650 10766 1.207570 CTCAGGATGCTTCAGCTCTGT 59.792 52.381 0.00 0.00 42.66 3.41
6660 10776 3.124297 GCTTCAGCTCTGTATGTGTTGTC 59.876 47.826 0.00 0.00 38.21 3.18
6679 10795 5.651387 TGTCATTTGTCAGGTTTGAACAA 57.349 34.783 0.00 0.00 34.49 2.83
6756 11022 5.161358 GCCTGCCTTTAACATAGTGTTTTC 58.839 41.667 0.20 0.00 41.45 2.29
6820 11086 2.853542 TGGAAGAGCAGGGTGCCA 60.854 61.111 0.00 0.00 46.52 4.92
6872 11138 3.892200 CAACACAAGGGGATGTTGC 57.108 52.632 4.34 0.00 46.53 4.17
6908 11174 2.720758 CTGAGCGAAACGGCTGACG 61.721 63.158 0.00 0.00 44.93 4.35
6977 11255 2.351738 GCACTCCCATTTCCGTTTCTTG 60.352 50.000 0.00 0.00 0.00 3.02
7030 11308 0.764890 AGTTCCAACAGTGCCAGCTA 59.235 50.000 0.00 0.00 0.00 3.32
7037 11315 0.108138 ACAGTGCCAGCTACGGAATC 60.108 55.000 0.00 0.00 0.00 2.52
7051 11329 6.070538 AGCTACGGAATCTGCTATTGGATTAT 60.071 38.462 0.00 0.00 33.05 1.28
7052 11330 6.595716 GCTACGGAATCTGCTATTGGATTATT 59.404 38.462 0.00 0.00 33.05 1.40
7053 11331 7.119846 GCTACGGAATCTGCTATTGGATTATTT 59.880 37.037 0.00 0.00 33.05 1.40
7054 11332 7.823745 ACGGAATCTGCTATTGGATTATTTT 57.176 32.000 0.00 0.00 33.05 1.82
7077 11355 5.873179 TTTTTCGAAACGGAATCTGCTAT 57.127 34.783 10.79 0.00 0.00 2.97
7078 11356 5.873179 TTTTCGAAACGGAATCTGCTATT 57.127 34.783 10.79 0.00 0.00 1.73
7079 11357 4.857871 TTCGAAACGGAATCTGCTATTG 57.142 40.909 0.00 0.00 0.00 1.90
7080 11358 3.194861 TCGAAACGGAATCTGCTATTGG 58.805 45.455 0.00 0.00 0.00 3.16
7081 11359 3.118920 TCGAAACGGAATCTGCTATTGGA 60.119 43.478 0.00 0.00 0.00 3.53
7082 11360 3.809832 CGAAACGGAATCTGCTATTGGAT 59.190 43.478 0.00 0.00 0.00 3.41
7083 11361 4.273480 CGAAACGGAATCTGCTATTGGATT 59.727 41.667 0.00 0.00 35.23 3.01
7084 11362 5.220854 CGAAACGGAATCTGCTATTGGATTT 60.221 40.000 0.00 0.00 33.05 2.17
7085 11363 6.530019 AAACGGAATCTGCTATTGGATTTT 57.470 33.333 0.00 0.00 33.05 1.82
7086 11364 6.530019 AACGGAATCTGCTATTGGATTTTT 57.470 33.333 0.00 0.00 33.05 1.94
7087 11365 7.639113 AACGGAATCTGCTATTGGATTTTTA 57.361 32.000 0.00 0.00 33.05 1.52
7088 11366 7.027778 ACGGAATCTGCTATTGGATTTTTAC 57.972 36.000 0.00 0.00 33.05 2.01
7098 11376 7.389330 TGCTATTGGATTTTTACTTTCGAGTCA 59.611 33.333 0.00 0.00 0.00 3.41
7116 11394 2.497675 GTCAGAGGGACTATTGCTGTCA 59.502 50.000 0.00 0.00 41.55 3.58
7177 13228 7.778382 ACAGGAGAGTTACCAAATACAAAGTTT 59.222 33.333 0.00 0.00 0.00 2.66
7178 13229 8.290325 CAGGAGAGTTACCAAATACAAAGTTTC 58.710 37.037 0.00 0.00 0.00 2.78
7234 13285 1.895798 CCTAGCCGATCATAGCTTCCA 59.104 52.381 7.15 0.00 40.56 3.53
7272 13325 5.801531 TCTCTGCTGTAAGTAAACCTCAA 57.198 39.130 0.00 0.00 35.30 3.02
7327 13380 3.694566 GGTTTTAGCGATTTGATGGACCT 59.305 43.478 0.00 0.00 0.00 3.85
7396 13449 7.164122 TGTGAAGAAGATGCAAAAGAGATACT 58.836 34.615 0.00 0.00 0.00 2.12
7404 13457 6.709846 AGATGCAAAAGAGATACTTGCTATCC 59.290 38.462 7.45 0.00 44.57 2.59
7464 13517 4.759516 TTTGACACGAAAGGCTTATTCC 57.240 40.909 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
220 223 1.101049 CGGCAATAACCATCGGCCTT 61.101 55.000 0.00 0.00 42.43 4.35
494 2704 2.282462 CAGCGGTTGGCCCTCTTT 60.282 61.111 0.00 0.00 45.17 2.52
816 3062 5.527214 CGTAGAATTGGATACTGGCATTTGA 59.473 40.000 0.00 0.00 37.61 2.69
826 3072 4.506654 ACATTCGCACGTAGAATTGGATAC 59.493 41.667 13.65 0.00 36.30 2.24
891 3137 1.376812 GGGCGTTTTCGGGACATCT 60.377 57.895 0.00 0.00 44.29 2.90
964 3210 3.238597 TGGATTGGGGAAAGTTTTGGAG 58.761 45.455 0.00 0.00 0.00 3.86
1010 3256 1.622725 GGCTTAGGGTTCCAGGAGAGA 60.623 57.143 0.00 0.00 0.00 3.10
1629 3875 1.079503 CTCGCAGTAGCAAAAGACCC 58.920 55.000 0.00 0.00 42.27 4.46
1692 3938 5.504665 GCATTCAAGCGTCATTAGCAACTAT 60.505 40.000 0.00 0.00 37.01 2.12
1721 3968 3.755905 TGGTTTGAAAATCAGCATCGCTA 59.244 39.130 0.00 0.00 36.40 4.26
2021 4268 9.280174 GCAGTATAGCATTTTATACCCAACTAA 57.720 33.333 0.00 0.00 37.26 2.24
2049 4296 5.922544 AGCATGCAACATAAACTGACTTTTC 59.077 36.000 21.98 0.00 0.00 2.29
2087 4334 5.118990 GCCAACTCAAGCTGATCTATGTAA 58.881 41.667 0.00 0.00 0.00 2.41
2125 4372 9.102757 TGTGTTATTATCTTCAGATTCAGAAGC 57.897 33.333 12.58 0.00 41.68 3.86
2163 4410 3.614092 ACATATGGACAAGTGCAAGGAG 58.386 45.455 7.80 0.00 33.77 3.69
2168 4415 4.020662 TGACTGTACATATGGACAAGTGCA 60.021 41.667 21.15 13.31 34.81 4.57
2174 4421 3.960755 CCTCCTGACTGTACATATGGACA 59.039 47.826 19.75 19.75 0.00 4.02
2215 4462 2.161410 GCAGACACACACACACAAGAAA 59.839 45.455 0.00 0.00 0.00 2.52
2220 4467 2.465774 GTGCAGACACACACACACA 58.534 52.632 0.00 0.00 46.61 3.72
2234 4481 1.277273 CATTGTCTCCCAGAGAGTGCA 59.723 52.381 0.00 0.00 43.71 4.57
2237 4484 0.908198 GGCATTGTCTCCCAGAGAGT 59.092 55.000 0.00 0.00 43.71 3.24
2266 4513 3.706594 CCCATGTGCTAGACCTAGAAGAA 59.293 47.826 8.16 0.00 35.21 2.52
2374 4624 2.620367 GGCATGTGACAAGATGGGGTTA 60.620 50.000 0.00 0.00 0.00 2.85
2570 4881 0.036858 GGAAGGCGCTCTTGAGAGTT 60.037 55.000 14.63 0.00 43.85 3.01
2798 5110 2.832838 TCTTGAGGTGGATGGCTAGAA 58.167 47.619 0.00 0.00 0.00 2.10
2835 5150 1.205460 TGTAGAGGGGGAAGGGTTGC 61.205 60.000 0.00 0.00 0.00 4.17
2854 5169 2.738846 GTTGTCGCTCACAGACATCAAT 59.261 45.455 0.00 0.00 46.44 2.57
2863 5178 0.881796 AGATCGAGTTGTCGCTCACA 59.118 50.000 0.00 0.00 46.39 3.58
2974 5289 2.076863 GGTCAGAAAGATGGGTGAACG 58.923 52.381 0.00 0.00 0.00 3.95
3003 5319 1.208293 AGAAGGGTAAGTAGCTGCTGC 59.792 52.381 13.43 11.60 40.05 5.25
3101 5417 2.809665 GCCTGCATGGTAGGAAGATGAG 60.810 54.545 4.45 0.00 37.52 2.90
3116 5545 1.275291 GTACTCCTACTGTTGCCTGCA 59.725 52.381 0.00 0.00 0.00 4.41
3128 5557 1.266178 TGCTTGCTGCTGTACTCCTA 58.734 50.000 0.00 0.00 43.37 2.94
3361 5799 2.583441 CGGGACCTGACAGAAGGCA 61.583 63.158 3.32 0.00 41.46 4.75
3365 5803 3.691342 CGGCGGGACCTGACAGAA 61.691 66.667 7.04 0.00 35.61 3.02
3390 5829 6.136155 TCCTGATTCTACATGGTATCAGACA 58.864 40.000 20.71 10.49 44.19 3.41
3475 5982 2.862738 GGTGTTGAACCGGTATGGG 58.137 57.895 8.00 0.00 44.64 4.00
3561 7337 2.946990 GGAGGAGTCCGTTAAGAGAGAG 59.053 54.545 2.76 0.00 31.37 3.20
3632 7408 5.413499 CACCCAAAAAGATTCCAATGCTAG 58.587 41.667 0.00 0.00 0.00 3.42
3645 7421 1.739049 TGCGAAGGCACCCAAAAAG 59.261 52.632 0.00 0.00 46.21 2.27
3722 7499 1.202879 ACCAACTGCCAGGATTTTCGA 60.203 47.619 0.00 0.00 0.00 3.71
3724 7501 3.429410 GCATACCAACTGCCAGGATTTTC 60.429 47.826 0.00 0.00 33.44 2.29
3725 7502 2.497273 GCATACCAACTGCCAGGATTTT 59.503 45.455 0.00 0.00 33.44 1.82
3726 7503 2.102578 GCATACCAACTGCCAGGATTT 58.897 47.619 0.00 0.00 33.44 2.17
3926 7704 4.970003 GTGACACAAAACATGCTCAGTAAC 59.030 41.667 0.00 0.00 0.00 2.50
4138 7919 4.060900 ACATCATGACTCTTGTGTGTCAC 58.939 43.478 0.00 0.00 45.53 3.67
4346 8241 5.070981 TGGAGGGAGTATGTTTGATCATCTC 59.929 44.000 0.00 0.00 0.00 2.75
4509 8404 8.808092 GCTTAGAATACATATGTACTCCCTTCT 58.192 37.037 22.77 22.77 32.70 2.85
4561 8456 9.337396 CCTGTGTGGATAAATAGTATGCTAAAA 57.663 33.333 0.00 0.00 38.35 1.52
4692 8589 2.450476 CAAGTCCTGAATTTGAGGGGG 58.550 52.381 1.85 0.00 0.00 5.40
5171 9068 6.194967 TGTAATAGAAGAGTGTGGGAGATCA 58.805 40.000 0.00 0.00 0.00 2.92
5294 9191 3.944250 AATGGTTGCTGGGGAGCCG 62.944 63.158 0.00 0.00 0.00 5.52
5474 9371 5.063186 GTGCAGTGAGTTCATCTCTTACATG 59.937 44.000 0.00 0.00 43.13 3.21
5475 9372 5.046735 AGTGCAGTGAGTTCATCTCTTACAT 60.047 40.000 0.00 0.00 43.13 2.29
5476 9373 4.281941 AGTGCAGTGAGTTCATCTCTTACA 59.718 41.667 0.00 0.00 43.13 2.41
5618 9527 3.452627 CCACCAGCTTCAGATAACCTAGT 59.547 47.826 0.00 0.00 0.00 2.57
5641 9550 7.976734 CCTGGTAAAACAACACAATTTAACTGA 59.023 33.333 0.00 0.00 30.99 3.41
5774 9683 6.804783 GGCAAGTAAATATAACTGCAAACGTT 59.195 34.615 0.00 0.00 0.00 3.99
5917 10012 6.248433 AGAATCTGTCCAACACAATTACCAT 58.752 36.000 0.00 0.00 33.31 3.55
5923 10018 4.330250 CCTGAGAATCTGTCCAACACAAT 58.670 43.478 0.00 0.00 33.31 2.71
5925 10020 2.550855 GCCTGAGAATCTGTCCAACACA 60.551 50.000 0.00 0.00 34.92 3.72
5926 10021 2.079925 GCCTGAGAATCTGTCCAACAC 58.920 52.381 0.00 0.00 34.92 3.32
5927 10022 1.980765 AGCCTGAGAATCTGTCCAACA 59.019 47.619 0.00 0.00 34.92 3.33
5928 10023 2.777832 AGCCTGAGAATCTGTCCAAC 57.222 50.000 0.00 0.00 34.92 3.77
5930 10025 3.713003 TCTTAGCCTGAGAATCTGTCCA 58.287 45.455 0.00 0.00 34.92 4.02
5931 10026 4.744795 TTCTTAGCCTGAGAATCTGTCC 57.255 45.455 0.00 0.00 34.92 4.02
6379 10487 2.692368 GCCATCAGGAGGTCCCCA 60.692 66.667 0.00 0.00 36.89 4.96
6427 10535 4.378356 GCTGTCGAATTTAACAGATGCACA 60.378 41.667 19.66 0.00 44.54 4.57
6432 10540 7.201644 CCACTAATGCTGTCGAATTTAACAGAT 60.202 37.037 19.66 10.56 44.54 2.90
6456 10564 1.149627 AGGCTGCAAAACGGTACCA 59.850 52.632 13.54 0.00 0.00 3.25
6474 10582 4.600062 TGATACAGCACTAACTCCTCTCA 58.400 43.478 0.00 0.00 0.00 3.27
6476 10584 5.658634 TCATTGATACAGCACTAACTCCTCT 59.341 40.000 0.00 0.00 0.00 3.69
6477 10585 5.907207 TCATTGATACAGCACTAACTCCTC 58.093 41.667 0.00 0.00 0.00 3.71
6478 10586 5.939764 TCATTGATACAGCACTAACTCCT 57.060 39.130 0.00 0.00 0.00 3.69
6479 10587 7.254932 GGAATTCATTGATACAGCACTAACTCC 60.255 40.741 7.93 0.00 0.00 3.85
6617 10733 1.676967 CCTGAGCTTGGGTTCAGCC 60.677 63.158 4.70 0.00 45.41 4.85
6649 10765 5.689383 ACCTGACAAATGACAACACATAC 57.311 39.130 0.00 0.00 0.00 2.39
6650 10766 6.319911 TCAAACCTGACAAATGACAACACATA 59.680 34.615 0.00 0.00 0.00 2.29
6660 10776 8.200364 AGAATTTTGTTCAAACCTGACAAATG 57.800 30.769 2.24 0.00 34.98 2.32
6679 10795 4.033358 CGAGAGCATGCGAGTTTAGAATTT 59.967 41.667 13.01 0.00 0.00 1.82
6825 11091 1.980772 GGACAAGCAGCCAGGCAAT 60.981 57.895 15.80 0.00 35.83 3.56
6872 11138 3.153130 TCAGAGGGAGAGATAATCAGCG 58.847 50.000 0.00 0.00 0.00 5.18
6908 11174 0.874390 TTGCAGCCGAACACAAGATC 59.126 50.000 0.00 0.00 0.00 2.75
6977 11255 5.183530 TGATTGACCCATCATATCATCCC 57.816 43.478 0.00 0.00 33.85 3.85
7030 11308 7.823745 AAAATAATCCAATAGCAGATTCCGT 57.176 32.000 0.00 0.00 34.60 4.69
7059 11337 3.118920 TCCAATAGCAGATTCCGTTTCGA 60.119 43.478 0.00 0.00 0.00 3.71
7060 11338 3.194861 TCCAATAGCAGATTCCGTTTCG 58.805 45.455 0.00 0.00 0.00 3.46
7061 11339 5.757850 AATCCAATAGCAGATTCCGTTTC 57.242 39.130 0.00 0.00 0.00 2.78
7062 11340 6.530019 AAAATCCAATAGCAGATTCCGTTT 57.470 33.333 0.00 0.00 31.54 3.60
7064 11342 6.828785 AGTAAAAATCCAATAGCAGATTCCGT 59.171 34.615 0.00 0.00 31.54 4.69
7065 11343 7.264373 AGTAAAAATCCAATAGCAGATTCCG 57.736 36.000 0.00 0.00 31.54 4.30
7066 11344 9.521503 GAAAGTAAAAATCCAATAGCAGATTCC 57.478 33.333 0.00 0.00 31.54 3.01
7067 11345 9.226345 CGAAAGTAAAAATCCAATAGCAGATTC 57.774 33.333 0.00 0.00 31.54 2.52
7068 11346 8.956426 TCGAAAGTAAAAATCCAATAGCAGATT 58.044 29.630 0.00 0.00 34.18 2.40
7069 11347 8.506168 TCGAAAGTAAAAATCCAATAGCAGAT 57.494 30.769 0.00 0.00 0.00 2.90
7070 11348 7.606456 ACTCGAAAGTAAAAATCCAATAGCAGA 59.394 33.333 0.00 0.00 32.59 4.26
7071 11349 7.752695 ACTCGAAAGTAAAAATCCAATAGCAG 58.247 34.615 0.00 0.00 32.59 4.24
7072 11350 7.389330 TGACTCGAAAGTAAAAATCCAATAGCA 59.611 33.333 0.00 0.00 35.28 3.49
7073 11351 7.748847 TGACTCGAAAGTAAAAATCCAATAGC 58.251 34.615 0.00 0.00 35.28 2.97
7074 11352 9.151471 TCTGACTCGAAAGTAAAAATCCAATAG 57.849 33.333 0.00 0.00 35.28 1.73
7075 11353 9.151471 CTCTGACTCGAAAGTAAAAATCCAATA 57.849 33.333 0.00 0.00 35.28 1.90
7076 11354 7.119846 CCTCTGACTCGAAAGTAAAAATCCAAT 59.880 37.037 0.00 0.00 35.28 3.16
7077 11355 6.426937 CCTCTGACTCGAAAGTAAAAATCCAA 59.573 38.462 0.00 0.00 35.28 3.53
7078 11356 5.932303 CCTCTGACTCGAAAGTAAAAATCCA 59.068 40.000 0.00 0.00 35.28 3.41
7079 11357 5.351740 CCCTCTGACTCGAAAGTAAAAATCC 59.648 44.000 0.00 0.00 35.28 3.01
7080 11358 6.091034 GTCCCTCTGACTCGAAAGTAAAAATC 59.909 42.308 0.00 0.00 41.03 2.17
7081 11359 5.932883 GTCCCTCTGACTCGAAAGTAAAAAT 59.067 40.000 0.00 0.00 41.03 1.82
7082 11360 5.295152 GTCCCTCTGACTCGAAAGTAAAAA 58.705 41.667 0.00 0.00 41.03 1.94
7083 11361 4.879598 GTCCCTCTGACTCGAAAGTAAAA 58.120 43.478 0.00 0.00 41.03 1.52
7084 11362 4.516365 GTCCCTCTGACTCGAAAGTAAA 57.484 45.455 0.00 0.00 41.03 2.01
7098 11376 4.472833 AGATTTGACAGCAATAGTCCCTCT 59.527 41.667 0.00 0.00 35.15 3.69
7149 11427 8.434392 ACTTTGTATTTGGTAACTCTCCTGTAA 58.566 33.333 0.00 0.00 37.61 2.41
7177 13228 3.568853 AGAAGAGAACGAAAGGAGAACGA 59.431 43.478 0.00 0.00 0.00 3.85
7178 13229 3.903360 AGAAGAGAACGAAAGGAGAACG 58.097 45.455 0.00 0.00 0.00 3.95
7234 13285 6.939163 ACAGCAGAGAAACAGAAATATTGAGT 59.061 34.615 0.00 0.00 0.00 3.41
7272 13325 6.551227 TGAGTATATGGAGCAGAGTGTTACAT 59.449 38.462 0.00 0.00 36.13 2.29
7327 13380 2.574369 ACATCCCAGGTTTCCGTAATCA 59.426 45.455 0.00 0.00 0.00 2.57
7396 13449 3.433598 GCCACTATCAACAGGGATAGCAA 60.434 47.826 9.48 0.00 46.95 3.91
7404 13457 2.292267 GTCCATGCCACTATCAACAGG 58.708 52.381 0.00 0.00 0.00 4.00
7451 13504 5.654209 AGATTTCACAGGGAATAAGCCTTTC 59.346 40.000 0.00 0.00 34.91 2.62
7464 13517 5.220989 CCAAGTGATATGCAGATTTCACAGG 60.221 44.000 15.39 12.63 40.89 4.00


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

AutoCloner maintained by Alex Coulton.