Multiple sequence alignment - TraesCS4D01G327000

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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 TraesCS4D01G327000 chr4D 100.000 3545 0 0 1 3545 486620737 486624281 0.000000e+00 6547.0
1 TraesCS4D01G327000 chr4D 77.709 1458 279 38 1034 2474 486433857 486432429 0.000000e+00 850.0
2 TraesCS4D01G327000 chr5A 92.133 2682 131 29 1 2620 666871578 666874241 0.000000e+00 3711.0
3 TraesCS4D01G327000 chr5A 94.550 1578 71 7 943 2514 667069108 667067540 0.000000e+00 2423.0
4 TraesCS4D01G327000 chr5A 84.161 1490 222 11 996 2478 666823693 666825175 0.000000e+00 1432.0
5 TraesCS4D01G327000 chr5A 88.667 803 44 23 2608 3389 667067510 667066734 0.000000e+00 935.0
6 TraesCS4D01G327000 chr5A 77.967 1466 277 37 999 2450 666750474 666751907 0.000000e+00 876.0
7 TraesCS4D01G327000 chr5A 87.633 283 23 8 2630 2909 666825815 666826088 5.710000e-83 318.0
8 TraesCS4D01G327000 chr5A 86.667 240 32 0 2629 2868 666843844 666844083 2.100000e-67 267.0
9 TraesCS4D01G327000 chr5A 97.656 128 3 0 2616 2743 666876377 666876504 1.660000e-53 220.0
10 TraesCS4D01G327000 chr5A 84.656 189 11 4 2736 2921 666886442 666886615 4.700000e-39 172.0
11 TraesCS4D01G327000 chr4B 92.411 2451 116 26 947 3368 621191553 621189144 0.000000e+00 3432.0
12 TraesCS4D01G327000 chr4B 91.684 1912 117 21 947 2849 621281274 621279396 0.000000e+00 2612.0
13 TraesCS4D01G327000 chr4B 84.059 1493 226 6 994 2480 620965789 620967275 0.000000e+00 1428.0
14 TraesCS4D01G327000 chr4B 77.078 1492 288 44 1001 2474 620945333 620946788 0.000000e+00 811.0
15 TraesCS4D01G327000 chr4B 89.277 401 33 6 276 666 621095175 621095575 8.840000e-136 494.0
16 TraesCS4D01G327000 chr4B 93.929 280 14 1 1 277 621094867 621095146 1.520000e-113 420.0
17 TraesCS4D01G327000 chr4B 87.226 274 20 10 2630 2900 620967680 620967941 7.440000e-77 298.0
18 TraesCS4D01G327000 chr4B 86.076 237 33 0 2629 2865 620971375 620971611 4.540000e-64 255.0
19 TraesCS4D01G327000 chr4B 77.528 178 34 4 712 886 621095675 621095849 6.260000e-18 102.0
20 TraesCS4D01G327000 chr6A 79.539 1129 193 29 1035 2141 31367931 31369043 0.000000e+00 771.0
21 TraesCS4D01G327000 chr6A 87.500 104 13 0 2352 2455 31369278 31369381 1.730000e-23 121.0
22 TraesCS4D01G327000 chr6A 79.389 131 23 4 3380 3507 532157449 532157578 4.870000e-14 89.8
23 TraesCS4D01G327000 chr6B 78.654 1129 205 28 1035 2142 56049027 56050140 0.000000e+00 717.0
24 TraesCS4D01G327000 chrUn 78.083 1127 213 26 1035 2141 103933161 103934273 0.000000e+00 682.0
25 TraesCS4D01G327000 chrUn 81.646 158 27 2 2299 2455 103934449 103934605 2.870000e-26 130.0
26 TraesCS4D01G327000 chr3B 89.535 258 27 0 4 261 133819932 133819675 9.490000e-86 327.0
27 TraesCS4D01G327000 chr3D 89.189 259 27 1 4 261 84911695 84911437 4.410000e-84 322.0
28 TraesCS4D01G327000 chr3A 89.147 258 28 0 4 261 101894637 101894380 4.410000e-84 322.0
29 TraesCS4D01G327000 chr1D 83.636 165 19 6 3380 3542 194469889 194470047 7.930000e-32 148.0


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 TraesCS4D01G327000 chr4D 486620737 486624281 3544 False 6547.000000 6547 100.000000 1 3545 1 chr4D.!!$F1 3544
1 TraesCS4D01G327000 chr4D 486432429 486433857 1428 True 850.000000 850 77.709000 1034 2474 1 chr4D.!!$R1 1440
2 TraesCS4D01G327000 chr5A 666871578 666876504 4926 False 1965.500000 3711 94.894500 1 2743 2 chr5A.!!$F5 2742
3 TraesCS4D01G327000 chr5A 667066734 667069108 2374 True 1679.000000 2423 91.608500 943 3389 2 chr5A.!!$R1 2446
4 TraesCS4D01G327000 chr5A 666750474 666751907 1433 False 876.000000 876 77.967000 999 2450 1 chr5A.!!$F1 1451
5 TraesCS4D01G327000 chr5A 666823693 666826088 2395 False 875.000000 1432 85.897000 996 2909 2 chr5A.!!$F4 1913
6 TraesCS4D01G327000 chr4B 621189144 621191553 2409 True 3432.000000 3432 92.411000 947 3368 1 chr4B.!!$R1 2421
7 TraesCS4D01G327000 chr4B 621279396 621281274 1878 True 2612.000000 2612 91.684000 947 2849 1 chr4B.!!$R2 1902
8 TraesCS4D01G327000 chr4B 620945333 620946788 1455 False 811.000000 811 77.078000 1001 2474 1 chr4B.!!$F1 1473
9 TraesCS4D01G327000 chr4B 620965789 620971611 5822 False 660.333333 1428 85.787000 994 2900 3 chr4B.!!$F2 1906
10 TraesCS4D01G327000 chr4B 621094867 621095849 982 False 338.666667 494 86.911333 1 886 3 chr4B.!!$F3 885
11 TraesCS4D01G327000 chr6A 31367931 31369381 1450 False 446.000000 771 83.519500 1035 2455 2 chr6A.!!$F2 1420
12 TraesCS4D01G327000 chr6B 56049027 56050140 1113 False 717.000000 717 78.654000 1035 2142 1 chr6B.!!$F1 1107
13 TraesCS4D01G327000 chrUn 103933161 103934605 1444 False 406.000000 682 79.864500 1035 2455 2 chrUn.!!$F1 1420

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
498 540 0.179234 TCAGGTTCACTCAAACGCCA 59.821 50.0 0.0 0.0 0.0 5.69 F
1107 1176 0.179097 GTCGAGGTCTTGGGCAGATC 60.179 60.0 0.0 0.0 32.6 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2155 2289 0.174389 GTCTCATCAAGAGCGCTCCA 59.826 55.0 32.94 18.17 44.35 3.86 R
2947 5855 0.728129 GCGCGTTTACTTCTTTGCCC 60.728 55.0 8.43 0.00 0.00 5.36 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
25 26 2.019249 CCATGCATCATTCGTGGAGTT 58.981 47.619 0.00 0.00 41.91 3.01
26 27 3.205338 CCATGCATCATTCGTGGAGTTA 58.795 45.455 0.00 0.00 41.91 2.24
56 57 6.906659 TCCGAGAACGATATATGTCTTTACC 58.093 40.000 0.00 0.00 42.66 2.85
113 114 2.731451 CACAACATGGATACCGATAGCG 59.269 50.000 0.00 0.00 37.24 4.26
143 144 1.303643 CCCGCTGCCTTTCTTCCTT 60.304 57.895 0.00 0.00 0.00 3.36
209 210 0.620556 ATGACTTGCGGGAACTGGAT 59.379 50.000 0.00 0.00 32.89 3.41
300 334 1.135859 GTTTCATTCTCTGCAGTGCCG 60.136 52.381 14.67 6.40 0.00 5.69
368 410 1.684386 CGCAGGAGGAAGATGGCTCT 61.684 60.000 0.00 0.00 0.00 4.09
416 458 4.438148 TCGACGCTGAAATATTGGATGAA 58.562 39.130 0.00 0.00 0.00 2.57
419 461 5.490139 ACGCTGAAATATTGGATGAACTG 57.510 39.130 0.00 0.00 0.00 3.16
431 473 2.210116 GATGAACTGACAACACACCGT 58.790 47.619 0.00 0.00 0.00 4.83
434 476 0.746563 AACTGACAACACACCGTGGG 60.747 55.000 0.00 0.00 37.94 4.61
498 540 0.179234 TCAGGTTCACTCAAACGCCA 59.821 50.000 0.00 0.00 0.00 5.69
503 545 2.034053 GGTTCACTCAAACGCCATTCAA 59.966 45.455 0.00 0.00 0.00 2.69
533 575 3.523157 TCTGAAGATAGAACAATGGCCCA 59.477 43.478 0.00 0.00 0.00 5.36
553 595 0.613853 AGGACCGACCGAGGATTTCA 60.614 55.000 0.00 0.00 44.74 2.69
593 638 3.111265 AGGGAAATCCTCAGGCAGT 57.889 52.632 0.00 0.00 44.06 4.40
606 651 2.109126 GGCAGTAGCTCTTTGCCGG 61.109 63.158 17.12 0.00 46.82 6.13
623 668 2.799207 GCCGGATGCACCATTATTGTTG 60.799 50.000 5.05 0.00 40.77 3.33
648 693 6.351371 GGCTGATATGCATATGGTACTGTAGT 60.351 42.308 23.76 0.00 34.04 2.73
742 787 4.873259 GGTGAGGAGTTGAAAGATTAGCTC 59.127 45.833 0.00 0.00 0.00 4.09
745 790 4.749976 AGGAGTTGAAAGATTAGCTCGTC 58.250 43.478 0.00 0.00 0.00 4.20
831 881 2.811855 TGTTTGAGCGTACGAGTTTGA 58.188 42.857 21.65 0.00 0.00 2.69
833 883 3.617706 TGTTTGAGCGTACGAGTTTGAAA 59.382 39.130 21.65 4.86 0.00 2.69
842 892 5.448162 GCGTACGAGTTTGAAAATATTGCTC 59.552 40.000 21.65 0.00 0.00 4.26
847 897 6.147164 ACGAGTTTGAAAATATTGCTCGAGAA 59.853 34.615 18.75 1.15 44.58 2.87
905 967 1.202687 TGTGTGTGCTTAGCTTGCTCT 60.203 47.619 5.60 0.00 0.00 4.09
925 987 7.375053 TGCTCTGTTTGAGTGTAAAAAGTTTT 58.625 30.769 0.00 0.00 44.41 2.43
1019 1085 2.712057 ATGTTACAGTTTGCTGCTGC 57.288 45.000 8.89 8.89 46.30 5.25
1107 1176 0.179097 GTCGAGGTCTTGGGCAGATC 60.179 60.000 0.00 0.00 32.60 2.75
1108 1177 1.144936 CGAGGTCTTGGGCAGATCC 59.855 63.158 0.00 0.00 32.08 3.36
1216 1288 1.673033 CCGTCCTTCAGCTTCACGAAT 60.673 52.381 0.00 0.00 32.08 3.34
1445 1520 3.665675 ATGGACTCCTTGGTCGCGC 62.666 63.158 0.00 0.00 37.12 6.86
1453 1528 1.446792 CTTGGTCGCGCTGATGTCT 60.447 57.895 5.56 0.00 0.00 3.41
2155 2289 2.355108 CCACCGGATGTCAAACTCAGAT 60.355 50.000 9.46 0.00 0.00 2.90
2187 2324 1.102222 ATGAGACCCTCGTAGTCCGC 61.102 60.000 0.00 0.00 34.67 5.54
2189 2326 3.885521 GACCCTCGTAGTCCGCCG 61.886 72.222 0.00 0.00 36.19 6.46
2407 2574 3.858868 GAACGTGCAGAGGACGGCA 62.859 63.158 15.07 0.00 43.99 5.69
2521 3219 5.889289 ACAGAGAAGTTCCTACTATCACTCC 59.111 44.000 0.00 0.00 33.17 3.85
2535 3270 6.338937 ACTATCACTCCGACTATTTTTCACC 58.661 40.000 0.00 0.00 0.00 4.02
2543 3278 5.659525 TCCGACTATTTTTCACCCTGAGATA 59.340 40.000 0.00 0.00 0.00 1.98
2544 3279 5.986135 CCGACTATTTTTCACCCTGAGATAG 59.014 44.000 0.00 0.00 0.00 2.08
2873 5756 1.841103 GCCTCCTCCTCCTGATCCC 60.841 68.421 0.00 0.00 0.00 3.85
3005 5913 3.520691 GGGTGGGATTAGAATAACCCC 57.479 52.381 0.00 0.00 41.23 4.95
3041 5949 4.864334 GGTGGCGGATCAGCTGGG 62.864 72.222 17.48 2.23 37.29 4.45
3200 8570 2.685017 AGGAGGATCACGCAGGCA 60.685 61.111 0.00 0.00 36.25 4.75
3202 8572 2.202987 GAGGATCACGCAGGCAGG 60.203 66.667 0.00 0.00 33.17 4.85
3203 8573 4.479993 AGGATCACGCAGGCAGGC 62.480 66.667 0.00 0.00 0.00 4.85
3291 9061 1.142936 CACTGATGGGATGGGATGGA 58.857 55.000 0.00 0.00 0.00 3.41
3331 9103 1.356938 GTGCTTGCTACGGAAGTACC 58.643 55.000 5.33 0.00 46.88 3.34
3333 9105 1.067142 TGCTTGCTACGGAAGTACCTG 60.067 52.381 0.00 0.00 46.88 4.00
3335 9107 1.204941 CTTGCTACGGAAGTACCTGCT 59.795 52.381 0.00 0.00 46.88 4.24
3340 9112 0.320697 ACGGAAGTACCTGCTCCAAC 59.679 55.000 0.00 0.00 46.88 3.77
3384 9159 6.017687 ACAAAACTAGCGTCGGTTTTTAAGAT 60.018 34.615 0.65 0.00 41.70 2.40
3393 9168 6.143278 GCGTCGGTTTTTAAGATTTTCATGTT 59.857 34.615 0.00 0.00 0.00 2.71
3394 9169 7.490055 CGTCGGTTTTTAAGATTTTCATGTTG 58.510 34.615 0.00 0.00 0.00 3.33
3395 9170 7.166804 CGTCGGTTTTTAAGATTTTCATGTTGT 59.833 33.333 0.00 0.00 0.00 3.32
3398 9173 8.599774 CGGTTTTTAAGATTTTCATGTTGTTGT 58.400 29.630 0.00 0.00 0.00 3.32
3407 9182 9.480053 AGATTTTCATGTTGTTGTAAGGATTTG 57.520 29.630 0.00 0.00 0.00 2.32
3408 9183 9.260002 GATTTTCATGTTGTTGTAAGGATTTGT 57.740 29.630 0.00 0.00 0.00 2.83
3409 9184 8.641499 TTTTCATGTTGTTGTAAGGATTTGTC 57.359 30.769 0.00 0.00 0.00 3.18
3410 9185 6.951062 TCATGTTGTTGTAAGGATTTGTCA 57.049 33.333 0.00 0.00 0.00 3.58
3411 9186 7.523293 TCATGTTGTTGTAAGGATTTGTCAT 57.477 32.000 0.00 0.00 0.00 3.06
3413 9188 5.527951 TGTTGTTGTAAGGATTTGTCATGC 58.472 37.500 0.00 0.00 0.00 4.06
3414 9189 5.301551 TGTTGTTGTAAGGATTTGTCATGCT 59.698 36.000 0.00 0.00 0.00 3.79
3415 9190 5.627499 TGTTGTAAGGATTTGTCATGCTC 57.373 39.130 0.00 0.00 0.00 4.26
3418 9193 6.939730 TGTTGTAAGGATTTGTCATGCTCTAA 59.060 34.615 0.00 0.00 0.00 2.10
3420 9195 7.615582 TGTAAGGATTTGTCATGCTCTAAAG 57.384 36.000 0.00 0.00 0.00 1.85
3422 9197 6.998968 AAGGATTTGTCATGCTCTAAAGAG 57.001 37.500 2.47 2.47 44.75 2.85
3424 9199 6.715280 AGGATTTGTCATGCTCTAAAGAGAA 58.285 36.000 11.20 0.00 44.74 2.87
3425 9200 7.170965 AGGATTTGTCATGCTCTAAAGAGAAA 58.829 34.615 11.20 2.08 44.74 2.52
3426 9201 7.667219 AGGATTTGTCATGCTCTAAAGAGAAAA 59.333 33.333 11.20 2.22 44.74 2.29
3427 9202 8.299570 GGATTTGTCATGCTCTAAAGAGAAAAA 58.700 33.333 11.20 0.00 44.74 1.94
3428 9203 9.852091 GATTTGTCATGCTCTAAAGAGAAAAAT 57.148 29.630 11.20 3.56 44.74 1.82
3429 9204 9.635520 ATTTGTCATGCTCTAAAGAGAAAAATG 57.364 29.630 11.20 8.16 44.74 2.32
3430 9205 6.615088 TGTCATGCTCTAAAGAGAAAAATGC 58.385 36.000 11.20 0.00 44.74 3.56
3431 9206 6.032717 GTCATGCTCTAAAGAGAAAAATGCC 58.967 40.000 11.20 0.00 44.74 4.40
3440 9309 9.023962 TCTAAAGAGAAAAATGCCATGTGTTAT 57.976 29.630 0.00 0.00 0.00 1.89
3444 9313 9.995003 AAGAGAAAAATGCCATGTGTTATAAAA 57.005 25.926 0.00 0.00 0.00 1.52
3447 9316 9.995003 AGAAAAATGCCATGTGTTATAAAAAGA 57.005 25.926 0.00 0.00 0.00 2.52
3452 9321 9.723601 AATGCCATGTGTTATAAAAAGAATTGT 57.276 25.926 0.00 0.00 0.00 2.71
3454 9323 9.632807 TGCCATGTGTTATAAAAAGAATTGTAC 57.367 29.630 0.00 0.00 0.00 2.90
3455 9324 9.632807 GCCATGTGTTATAAAAAGAATTGTACA 57.367 29.630 0.00 0.00 0.00 2.90
3468 9337 6.843069 AGAATTGTACAAAAATTGCCACAC 57.157 33.333 13.23 0.00 31.21 3.82
3469 9338 6.581712 AGAATTGTACAAAAATTGCCACACT 58.418 32.000 13.23 0.00 31.21 3.55
3470 9339 6.479660 AGAATTGTACAAAAATTGCCACACTG 59.520 34.615 13.23 0.00 31.21 3.66
3471 9340 3.452474 TGTACAAAAATTGCCACACTGC 58.548 40.909 0.00 0.00 0.00 4.40
3472 9341 2.687700 ACAAAAATTGCCACACTGCA 57.312 40.000 0.00 0.00 40.07 4.41
3473 9342 2.278854 ACAAAAATTGCCACACTGCAC 58.721 42.857 0.00 0.00 41.88 4.57
3474 9343 2.277969 CAAAAATTGCCACACTGCACA 58.722 42.857 0.00 0.00 41.88 4.57
3476 9345 1.401761 AAATTGCCACACTGCACAGA 58.598 45.000 4.31 0.00 41.88 3.41
3477 9346 0.956633 AATTGCCACACTGCACAGAG 59.043 50.000 4.31 0.00 41.88 3.35
3479 9348 0.467804 TTGCCACACTGCACAGAGTA 59.532 50.000 4.31 0.00 41.88 2.59
3480 9349 0.467804 TGCCACACTGCACAGAGTAA 59.532 50.000 4.31 0.00 36.04 2.24
3481 9350 1.072173 TGCCACACTGCACAGAGTAAT 59.928 47.619 4.31 0.00 36.04 1.89
3482 9351 2.154462 GCCACACTGCACAGAGTAATT 58.846 47.619 4.31 0.00 31.13 1.40
3487 9356 2.751259 CACTGCACAGAGTAATTGCCAT 59.249 45.455 4.31 0.00 35.26 4.40
3488 9357 2.751259 ACTGCACAGAGTAATTGCCATG 59.249 45.455 4.31 0.00 35.26 3.66
3489 9358 1.473677 TGCACAGAGTAATTGCCATGC 59.526 47.619 0.00 0.00 35.26 4.06
3490 9359 1.473677 GCACAGAGTAATTGCCATGCA 59.526 47.619 0.00 0.00 36.47 3.96
3491 9360 2.100252 GCACAGAGTAATTGCCATGCAT 59.900 45.455 0.00 0.00 38.76 3.96
3492 9361 3.429822 GCACAGAGTAATTGCCATGCATT 60.430 43.478 0.00 0.00 38.76 3.56
3493 9362 4.357142 CACAGAGTAATTGCCATGCATTC 58.643 43.478 0.00 0.00 38.76 2.67
3494 9363 3.065786 ACAGAGTAATTGCCATGCATTCG 59.934 43.478 0.00 0.00 38.76 3.34
3495 9364 3.313249 CAGAGTAATTGCCATGCATTCGA 59.687 43.478 0.00 0.00 38.76 3.71
3497 9366 4.581824 AGAGTAATTGCCATGCATTCGATT 59.418 37.500 0.00 6.45 38.76 3.34
3498 9367 4.613944 AGTAATTGCCATGCATTCGATTG 58.386 39.130 16.18 2.92 38.76 2.67
3499 9368 2.519377 ATTGCCATGCATTCGATTGG 57.481 45.000 9.21 0.00 38.76 3.16
3500 9369 0.460722 TTGCCATGCATTCGATTGGG 59.539 50.000 9.21 0.00 38.76 4.12
3502 9371 0.963962 GCCATGCATTCGATTGGGAT 59.036 50.000 9.21 0.00 0.00 3.85
3503 9372 1.068055 GCCATGCATTCGATTGGGATC 60.068 52.381 9.21 0.00 0.00 3.36
3505 9374 2.228103 CCATGCATTCGATTGGGATCTG 59.772 50.000 9.21 0.00 0.00 2.90
3508 9377 1.528586 GCATTCGATTGGGATCTGACG 59.471 52.381 9.21 0.00 0.00 4.35
3510 9379 1.191535 TTCGATTGGGATCTGACGGT 58.808 50.000 0.00 0.00 0.00 4.83
3511 9380 0.744874 TCGATTGGGATCTGACGGTC 59.255 55.000 0.00 0.00 0.00 4.79
3513 9382 0.460311 GATTGGGATCTGACGGTCGT 59.540 55.000 3.34 0.00 0.00 4.34
3514 9383 1.679680 GATTGGGATCTGACGGTCGTA 59.320 52.381 3.34 0.00 0.00 3.43
3515 9384 1.548081 TTGGGATCTGACGGTCGTAA 58.452 50.000 3.34 0.00 0.00 3.18
3516 9385 1.100510 TGGGATCTGACGGTCGTAAG 58.899 55.000 3.34 1.58 0.00 2.34
3517 9386 0.384669 GGGATCTGACGGTCGTAAGG 59.615 60.000 7.90 0.00 38.47 2.69
3518 9387 0.384669 GGATCTGACGGTCGTAAGGG 59.615 60.000 7.90 0.00 38.47 3.95
3520 9389 2.001361 ATCTGACGGTCGTAAGGGCG 62.001 60.000 7.90 0.00 38.47 6.13
3521 9390 2.985282 TGACGGTCGTAAGGGCGT 60.985 61.111 3.34 0.00 38.47 5.68
3522 9391 2.259511 GACGGTCGTAAGGGCGTT 59.740 61.111 0.00 0.00 38.47 4.84
3523 9392 1.803117 GACGGTCGTAAGGGCGTTC 60.803 63.158 0.00 0.00 38.47 3.95
3524 9393 2.877582 CGGTCGTAAGGGCGTTCG 60.878 66.667 0.00 0.76 38.47 3.95
3525 9394 2.259511 GGTCGTAAGGGCGTTCGT 59.740 61.111 0.00 0.00 38.47 3.85
3526 9395 1.373371 GGTCGTAAGGGCGTTCGTT 60.373 57.895 0.00 0.00 38.47 3.85
3529 9398 2.385091 CGTAAGGGCGTTCGTTGGG 61.385 63.158 0.00 0.00 0.00 4.12
3530 9399 1.004679 GTAAGGGCGTTCGTTGGGA 60.005 57.895 0.00 0.00 0.00 4.37
3531 9400 0.392060 GTAAGGGCGTTCGTTGGGAT 60.392 55.000 0.00 0.00 0.00 3.85
3532 9401 0.325602 TAAGGGCGTTCGTTGGGATT 59.674 50.000 0.00 0.00 0.00 3.01
3534 9403 2.178273 GGCGTTCGTTGGGATTGC 59.822 61.111 0.00 0.00 0.00 3.56
3535 9404 2.332654 GGCGTTCGTTGGGATTGCT 61.333 57.895 0.00 0.00 0.00 3.91
3536 9405 1.579429 GCGTTCGTTGGGATTGCTT 59.421 52.632 0.00 0.00 0.00 3.91
3537 9406 0.800012 GCGTTCGTTGGGATTGCTTA 59.200 50.000 0.00 0.00 0.00 3.09
3538 9407 1.198178 GCGTTCGTTGGGATTGCTTAA 59.802 47.619 0.00 0.00 0.00 1.85
3539 9408 2.350964 GCGTTCGTTGGGATTGCTTAAA 60.351 45.455 0.00 0.00 0.00 1.52
3540 9409 3.854045 GCGTTCGTTGGGATTGCTTAAAA 60.854 43.478 0.00 0.00 0.00 1.52
3541 9410 4.291783 CGTTCGTTGGGATTGCTTAAAAA 58.708 39.130 0.00 0.00 0.00 1.94
3542 9411 4.920927 CGTTCGTTGGGATTGCTTAAAAAT 59.079 37.500 0.00 0.00 0.00 1.82
3543 9412 5.060446 CGTTCGTTGGGATTGCTTAAAAATC 59.940 40.000 3.08 3.08 34.00 2.17
3544 9413 5.713792 TCGTTGGGATTGCTTAAAAATCA 57.286 34.783 10.94 0.00 36.03 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.228995 ACATATATCGTTCTCGGAGACACTA 58.771 40.000 7.33 2.65 37.69 2.74
26 27 5.064558 ACATATATCGTTCTCGGAGACACT 58.935 41.667 7.33 0.00 37.69 3.55
119 120 1.746991 GAAAGGCAGCGGGAAGAGG 60.747 63.158 0.00 0.00 0.00 3.69
209 210 2.628696 TTCTTCGTACTCCGCCGCA 61.629 57.895 0.00 0.00 36.19 5.69
277 281 3.057033 GGCACTGCAGAGAATGAAACAAT 60.057 43.478 23.35 0.00 0.00 2.71
300 334 0.601558 TAGGACGACAGACACCTTGC 59.398 55.000 0.00 0.00 34.42 4.01
310 344 6.931838 AGTTTCAGATTAACATAGGACGACA 58.068 36.000 0.00 0.00 0.00 4.35
340 378 2.852495 TTCCTCCTGCGTGCGGAATC 62.852 60.000 1.35 0.00 31.00 2.52
341 379 2.859273 CTTCCTCCTGCGTGCGGAAT 62.859 60.000 1.35 0.00 35.21 3.01
346 384 1.817099 CCATCTTCCTCCTGCGTGC 60.817 63.158 0.00 0.00 0.00 5.34
368 410 1.406898 CTGTCGCAGCTTCCTGAGATA 59.593 52.381 0.75 0.00 46.98 1.98
416 458 1.153249 CCCACGGTGTGTTGTCAGT 60.153 57.895 7.45 0.00 0.00 3.41
419 461 1.597027 CTCCCCACGGTGTGTTGTC 60.597 63.158 7.45 0.00 0.00 3.18
431 473 2.752358 CTGTGCTTCAGCTCCCCA 59.248 61.111 0.00 0.00 42.66 4.96
434 476 1.073897 AACCCTGTGCTTCAGCTCC 59.926 57.895 0.00 0.00 42.38 4.70
485 527 1.606668 GGTTGAATGGCGTTTGAGTGA 59.393 47.619 0.00 0.00 0.00 3.41
488 530 2.664916 CTTGGTTGAATGGCGTTTGAG 58.335 47.619 0.00 0.00 0.00 3.02
498 540 3.126001 TCTTCAGACGCTTGGTTGAAT 57.874 42.857 0.00 0.00 30.66 2.57
503 545 3.258372 TGTTCTATCTTCAGACGCTTGGT 59.742 43.478 0.00 0.00 0.00 3.67
533 575 0.535797 GAAATCCTCGGTCGGTCCTT 59.464 55.000 0.00 0.00 0.00 3.36
553 595 6.462500 CCTCATTTCTGATAGAATCATCGGT 58.538 40.000 0.00 0.00 38.85 4.69
593 638 4.540153 GCATCCGGCAAAGAGCTA 57.460 55.556 0.00 0.00 44.79 3.32
606 651 3.130869 TCAGCCAACAATAATGGTGCATC 59.869 43.478 0.00 0.00 43.22 3.91
613 658 7.704899 CCATATGCATATCAGCCAACAATAATG 59.295 37.037 16.46 2.40 0.00 1.90
623 668 4.836825 ACAGTACCATATGCATATCAGCC 58.163 43.478 16.46 5.68 0.00 4.85
648 693 5.131977 TGCCTGACTTATGGGAAAAGCTATA 59.868 40.000 0.00 0.00 0.00 1.31
651 696 2.041620 TGCCTGACTTATGGGAAAAGCT 59.958 45.455 0.00 0.00 0.00 3.74
745 790 1.269448 ACAGTTTTGCGGCAATACCTG 59.731 47.619 25.69 24.54 35.61 4.00
807 857 2.132762 ACTCGTACGCTCAAACAAAGG 58.867 47.619 11.24 0.00 0.00 3.11
810 860 3.188492 TCAAACTCGTACGCTCAAACAA 58.812 40.909 11.24 0.00 0.00 2.83
831 881 8.944029 CATCCATAGATTCTCGAGCAATATTTT 58.056 33.333 7.81 0.00 0.00 1.82
833 883 6.538021 GCATCCATAGATTCTCGAGCAATATT 59.462 38.462 7.81 4.03 0.00 1.28
842 892 2.288457 ACACGGCATCCATAGATTCTCG 60.288 50.000 0.00 0.00 0.00 4.04
847 897 3.281727 AAACACACGGCATCCATAGAT 57.718 42.857 0.00 0.00 0.00 1.98
938 1000 4.095782 GCCATTCGGTTGTTAATTAGAGCA 59.904 41.667 0.00 0.00 33.28 4.26
940 1002 6.436843 AAGCCATTCGGTTGTTAATTAGAG 57.563 37.500 0.00 0.00 33.28 2.43
941 1003 6.431198 GAAGCCATTCGGTTGTTAATTAGA 57.569 37.500 0.00 0.00 30.54 2.10
974 1036 7.697352 TGTTTGAAAATGATGTGACATGTTC 57.303 32.000 1.23 2.17 41.93 3.18
975 1037 8.489990 TTTGTTTGAAAATGATGTGACATGTT 57.510 26.923 1.23 0.00 31.34 2.71
1019 1085 1.376037 GCCTGACCAAGACCGGAAG 60.376 63.158 9.46 0.00 0.00 3.46
1107 1176 2.261671 CGGTGGTGTTCGAGGAGG 59.738 66.667 0.00 0.00 0.00 4.30
1108 1177 1.080705 GACGGTGGTGTTCGAGGAG 60.081 63.158 0.00 0.00 0.00 3.69
1445 1520 3.119101 AGCGGGTACTACAAAGACATCAG 60.119 47.826 0.00 0.00 0.00 2.90
1453 1528 2.416296 CGTCATGAGCGGGTACTACAAA 60.416 50.000 0.00 0.00 0.00 2.83
1699 1818 3.832492 GAGGAGCTCGGCTTCGCT 61.832 66.667 7.83 0.00 39.54 4.93
1800 1931 0.178767 CATGATCCTCAACGCTCCCA 59.821 55.000 0.00 0.00 0.00 4.37
1804 1935 2.625737 CTCAACATGATCCTCAACGCT 58.374 47.619 0.00 0.00 0.00 5.07
1812 1943 0.729116 CACGGTGCTCAACATGATCC 59.271 55.000 0.00 0.00 0.00 3.36
2155 2289 0.174389 GTCTCATCAAGAGCGCTCCA 59.826 55.000 32.94 18.17 44.35 3.86
2509 2960 7.648510 GGTGAAAAATAGTCGGAGTGATAGTAG 59.351 40.741 0.00 0.00 0.00 2.57
2521 3219 6.806751 TCTATCTCAGGGTGAAAAATAGTCG 58.193 40.000 0.00 0.00 0.00 4.18
2535 3270 4.693566 GTCCGTGATCTACTCTATCTCAGG 59.306 50.000 0.00 0.00 0.00 3.86
2543 3278 1.102222 GCCCGTCCGTGATCTACTCT 61.102 60.000 0.00 0.00 0.00 3.24
2544 3279 1.359475 GCCCGTCCGTGATCTACTC 59.641 63.158 0.00 0.00 0.00 2.59
2873 5756 4.740822 CCTGGTTGGAAGGGGCGG 62.741 72.222 0.00 0.00 38.35 6.13
2947 5855 0.728129 GCGCGTTTACTTCTTTGCCC 60.728 55.000 8.43 0.00 0.00 5.36
2948 5856 1.058057 CGCGCGTTTACTTCTTTGCC 61.058 55.000 24.19 0.00 0.00 4.52
2950 5858 1.378360 CGCGCGCGTTTACTTCTTTG 61.378 55.000 42.49 12.54 34.35 2.77
3005 5913 4.072131 CACCATTATTCTAATCCCCACCG 58.928 47.826 0.00 0.00 0.00 4.94
3041 5949 2.111878 CATCGGATCACCCCAGCC 59.888 66.667 0.00 0.00 0.00 4.85
3144 7592 1.340991 ACTCTCACTCTCAGAGGAGGC 60.341 57.143 16.07 0.00 41.66 4.70
3146 7594 3.055167 TCTCACTCTCACTCTCAGAGGAG 60.055 52.174 6.64 9.91 41.66 3.69
3149 7597 3.686241 CACTCTCACTCTCACTCTCAGAG 59.314 52.174 0.00 0.00 42.84 3.35
3150 7598 3.326297 TCACTCTCACTCTCACTCTCAGA 59.674 47.826 0.00 0.00 0.00 3.27
3151 7599 3.673902 TCACTCTCACTCTCACTCTCAG 58.326 50.000 0.00 0.00 0.00 3.35
3206 8576 4.720902 TGCATCCCACACAGCCCG 62.721 66.667 0.00 0.00 0.00 6.13
3291 9061 4.217550 CACGAAGTAATCCAACAACCCATT 59.782 41.667 0.00 0.00 41.61 3.16
3331 9103 5.964958 TTCCTCTAATTTTGTTGGAGCAG 57.035 39.130 0.00 0.00 0.00 4.24
3333 9105 6.691508 ACATTTCCTCTAATTTTGTTGGAGC 58.308 36.000 0.00 0.00 0.00 4.70
3335 9107 9.137459 TGTAACATTTCCTCTAATTTTGTTGGA 57.863 29.630 0.00 0.00 0.00 3.53
3384 9159 8.253810 TGACAAATCCTTACAACAACATGAAAA 58.746 29.630 0.00 0.00 0.00 2.29
3393 9168 5.316167 AGAGCATGACAAATCCTTACAACA 58.684 37.500 0.00 0.00 0.00 3.33
3394 9169 5.886960 AGAGCATGACAAATCCTTACAAC 57.113 39.130 0.00 0.00 0.00 3.32
3395 9170 7.882791 TCTTTAGAGCATGACAAATCCTTACAA 59.117 33.333 0.00 0.00 0.00 2.41
3398 9173 7.851228 TCTCTTTAGAGCATGACAAATCCTTA 58.149 34.615 0.00 0.00 41.80 2.69
3399 9174 6.715280 TCTCTTTAGAGCATGACAAATCCTT 58.285 36.000 0.00 0.00 41.80 3.36
3400 9175 6.305272 TCTCTTTAGAGCATGACAAATCCT 57.695 37.500 0.00 0.00 41.80 3.24
3402 9177 9.852091 ATTTTTCTCTTTAGAGCATGACAAATC 57.148 29.630 0.00 0.00 41.80 2.17
3403 9178 9.635520 CATTTTTCTCTTTAGAGCATGACAAAT 57.364 29.630 0.00 0.00 41.80 2.32
3405 9180 7.086376 GCATTTTTCTCTTTAGAGCATGACAA 58.914 34.615 0.00 0.00 41.80 3.18
3407 9182 6.032717 GGCATTTTTCTCTTTAGAGCATGAC 58.967 40.000 0.00 1.28 41.80 3.06
3408 9183 5.711506 TGGCATTTTTCTCTTTAGAGCATGA 59.288 36.000 0.00 0.00 41.80 3.07
3409 9184 5.957798 TGGCATTTTTCTCTTTAGAGCATG 58.042 37.500 1.79 0.00 41.80 4.06
3410 9185 6.154021 ACATGGCATTTTTCTCTTTAGAGCAT 59.846 34.615 0.00 0.00 41.80 3.79
3411 9186 5.477984 ACATGGCATTTTTCTCTTTAGAGCA 59.522 36.000 0.00 0.00 41.80 4.26
3413 9188 6.917533 ACACATGGCATTTTTCTCTTTAGAG 58.082 36.000 0.00 0.15 43.36 2.43
3414 9189 6.899393 ACACATGGCATTTTTCTCTTTAGA 57.101 33.333 0.00 0.00 0.00 2.10
3418 9193 9.995003 TTTTATAACACATGGCATTTTTCTCTT 57.005 25.926 0.00 0.00 0.00 2.85
3426 9201 9.723601 ACAATTCTTTTTATAACACATGGCATT 57.276 25.926 0.00 0.00 0.00 3.56
3428 9203 9.632807 GTACAATTCTTTTTATAACACATGGCA 57.367 29.630 0.00 0.00 0.00 4.92
3429 9204 9.632807 TGTACAATTCTTTTTATAACACATGGC 57.367 29.630 0.00 0.00 0.00 4.40
3444 9313 7.011295 CAGTGTGGCAATTTTTGTACAATTCTT 59.989 33.333 9.56 0.43 33.82 2.52
3447 9316 5.007528 GCAGTGTGGCAATTTTTGTACAATT 59.992 36.000 9.56 0.00 33.82 2.32
3448 9317 4.511082 GCAGTGTGGCAATTTTTGTACAAT 59.489 37.500 9.56 0.00 33.82 2.71
3449 9318 3.868077 GCAGTGTGGCAATTTTTGTACAA 59.132 39.130 3.59 3.59 33.82 2.41
3450 9319 3.118992 TGCAGTGTGGCAATTTTTGTACA 60.119 39.130 0.00 0.00 41.65 2.90
3451 9320 3.245048 GTGCAGTGTGGCAATTTTTGTAC 59.755 43.478 0.00 0.00 46.93 2.90
3452 9321 3.118992 TGTGCAGTGTGGCAATTTTTGTA 60.119 39.130 0.00 0.00 46.93 2.41
3453 9322 2.278854 GTGCAGTGTGGCAATTTTTGT 58.721 42.857 0.00 0.00 46.93 2.83
3454 9323 2.277969 TGTGCAGTGTGGCAATTTTTG 58.722 42.857 0.00 0.00 46.93 2.44
3455 9324 2.168106 TCTGTGCAGTGTGGCAATTTTT 59.832 40.909 0.00 0.00 46.93 1.94
3456 9325 1.755959 TCTGTGCAGTGTGGCAATTTT 59.244 42.857 0.00 0.00 46.93 1.82
3457 9326 1.338973 CTCTGTGCAGTGTGGCAATTT 59.661 47.619 0.00 0.00 46.93 1.82
3459 9328 0.179009 ACTCTGTGCAGTGTGGCAAT 60.179 50.000 6.16 0.00 46.93 3.56
3463 9332 2.095567 GCAATTACTCTGTGCAGTGTGG 60.096 50.000 14.76 5.49 38.19 4.17
3464 9333 2.095567 GGCAATTACTCTGTGCAGTGTG 60.096 50.000 14.76 2.45 40.12 3.82
3465 9334 2.154462 GGCAATTACTCTGTGCAGTGT 58.846 47.619 10.98 10.98 40.12 3.55
3466 9335 2.153645 TGGCAATTACTCTGTGCAGTG 58.846 47.619 0.00 0.00 40.12 3.66
3468 9337 2.479049 GCATGGCAATTACTCTGTGCAG 60.479 50.000 0.00 0.00 40.12 4.41
3469 9338 1.473677 GCATGGCAATTACTCTGTGCA 59.526 47.619 0.00 0.00 40.12 4.57
3470 9339 1.473677 TGCATGGCAATTACTCTGTGC 59.526 47.619 0.00 0.00 34.76 4.57
3471 9340 4.357142 GAATGCATGGCAATTACTCTGTG 58.643 43.478 0.00 0.00 43.62 3.66
3472 9341 3.065786 CGAATGCATGGCAATTACTCTGT 59.934 43.478 0.00 0.00 43.62 3.41
3473 9342 3.313249 TCGAATGCATGGCAATTACTCTG 59.687 43.478 0.00 0.00 43.62 3.35
3474 9343 3.544684 TCGAATGCATGGCAATTACTCT 58.455 40.909 0.00 0.00 43.62 3.24
3476 9345 4.500205 CCAATCGAATGCATGGCAATTACT 60.500 41.667 0.00 0.00 43.62 2.24
3477 9346 3.737266 CCAATCGAATGCATGGCAATTAC 59.263 43.478 0.00 0.00 43.62 1.89
3479 9348 2.484065 CCCAATCGAATGCATGGCAATT 60.484 45.455 0.00 0.00 43.62 2.32
3480 9349 1.069513 CCCAATCGAATGCATGGCAAT 59.930 47.619 0.00 0.00 43.62 3.56
3481 9350 0.460722 CCCAATCGAATGCATGGCAA 59.539 50.000 0.00 0.00 43.62 4.52
3482 9351 0.395448 TCCCAATCGAATGCATGGCA 60.395 50.000 0.00 0.00 44.86 4.92
3487 9356 2.564771 GTCAGATCCCAATCGAATGCA 58.435 47.619 0.00 0.00 36.97 3.96
3488 9357 1.528586 CGTCAGATCCCAATCGAATGC 59.471 52.381 0.00 0.00 36.97 3.56
3489 9358 2.138320 CCGTCAGATCCCAATCGAATG 58.862 52.381 0.00 0.00 36.97 2.67
3490 9359 1.762957 ACCGTCAGATCCCAATCGAAT 59.237 47.619 0.00 0.00 36.97 3.34
3491 9360 1.136305 GACCGTCAGATCCCAATCGAA 59.864 52.381 0.00 0.00 36.97 3.71
3492 9361 0.744874 GACCGTCAGATCCCAATCGA 59.255 55.000 0.00 0.00 36.97 3.59
3493 9362 0.595053 CGACCGTCAGATCCCAATCG 60.595 60.000 0.00 0.00 36.97 3.34
3494 9363 0.460311 ACGACCGTCAGATCCCAATC 59.540 55.000 0.00 0.00 0.00 2.67
3495 9364 1.771565 TACGACCGTCAGATCCCAAT 58.228 50.000 0.00 0.00 0.00 3.16
3497 9366 1.100510 CTTACGACCGTCAGATCCCA 58.899 55.000 0.00 0.00 0.00 4.37
3498 9367 0.384669 CCTTACGACCGTCAGATCCC 59.615 60.000 5.43 0.00 0.00 3.85
3499 9368 0.384669 CCCTTACGACCGTCAGATCC 59.615 60.000 5.43 0.00 0.00 3.36
3500 9369 0.248949 GCCCTTACGACCGTCAGATC 60.249 60.000 5.43 0.00 0.00 2.75
3502 9371 2.693762 CGCCCTTACGACCGTCAGA 61.694 63.158 5.43 0.00 34.06 3.27
3503 9372 2.202570 CGCCCTTACGACCGTCAG 60.203 66.667 0.00 0.00 34.06 3.51
3505 9374 1.803117 GAACGCCCTTACGACCGTC 60.803 63.158 0.00 0.00 36.70 4.79
3508 9377 1.373371 AACGAACGCCCTTACGACC 60.373 57.895 0.00 0.00 36.70 4.79
3510 9379 1.373246 CCAACGAACGCCCTTACGA 60.373 57.895 0.00 0.00 36.70 3.43
3511 9380 2.385091 CCCAACGAACGCCCTTACG 61.385 63.158 0.00 0.00 39.50 3.18
3513 9382 0.325602 AATCCCAACGAACGCCCTTA 59.674 50.000 0.00 0.00 0.00 2.69
3514 9383 1.074248 AATCCCAACGAACGCCCTT 59.926 52.632 0.00 0.00 0.00 3.95
3515 9384 1.674322 CAATCCCAACGAACGCCCT 60.674 57.895 0.00 0.00 0.00 5.19
3516 9385 2.874751 CAATCCCAACGAACGCCC 59.125 61.111 0.00 0.00 0.00 6.13
3517 9386 1.862602 AAGCAATCCCAACGAACGCC 61.863 55.000 0.00 0.00 0.00 5.68
3518 9387 0.800012 TAAGCAATCCCAACGAACGC 59.200 50.000 0.00 0.00 0.00 4.84
3520 9389 5.923684 TGATTTTTAAGCAATCCCAACGAAC 59.076 36.000 0.00 0.00 30.64 3.95
3521 9390 6.090483 TGATTTTTAAGCAATCCCAACGAA 57.910 33.333 0.00 0.00 30.64 3.85
3522 9391 5.713792 TGATTTTTAAGCAATCCCAACGA 57.286 34.783 0.00 0.00 30.64 3.85


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

AutoCloner maintained by Alex Coulton.