Multiple sequence alignment - TraesCS7D01G277800

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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 TraesCS7D01G277800 chr7D 100.000 5826 0 0 1 5826 266887535 266881710 0.000000e+00 10759.0
1 TraesCS7D01G277800 chr7D 97.552 572 11 1 5258 5826 169479828 169479257 0.000000e+00 976.0
2 TraesCS7D01G277800 chr7D 97.378 572 7 5 5262 5826 21765545 21764975 0.000000e+00 966.0
3 TraesCS7D01G277800 chr7D 97.317 559 12 1 5271 5826 602020328 602020886 0.000000e+00 946.0
4 TraesCS7D01G277800 chr7D 91.954 261 21 0 3468 3728 231549744 231550004 3.320000e-97 366.0
5 TraesCS7D01G277800 chr7D 82.407 108 9 9 651 754 15898320 15898421 1.040000e-12 86.1
6 TraesCS7D01G277800 chr7A 94.910 3399 82 23 913 4255 292829559 292826196 0.000000e+00 5234.0
7 TraesCS7D01G277800 chr7A 90.194 1030 32 15 4251 5272 292821127 292820159 0.000000e+00 1279.0
8 TraesCS7D01G277800 chr7A 87.500 504 51 8 1 495 292845721 292845221 6.550000e-159 571.0
9 TraesCS7D01G277800 chr7A 79.116 249 34 12 509 753 292832651 292832417 7.820000e-34 156.0
10 TraesCS7D01G277800 chr7B 92.290 3411 155 29 107 3453 247258076 247261442 0.000000e+00 4743.0
11 TraesCS7D01G277800 chr7B 94.948 1841 43 16 3451 5272 247261582 247263391 0.000000e+00 2839.0
12 TraesCS7D01G277800 chr7B 88.312 231 25 2 4462 4692 141816141 141815913 5.750000e-70 276.0
13 TraesCS7D01G277800 chr7B 97.872 47 1 0 1 47 247258028 247258074 1.350000e-11 82.4
14 TraesCS7D01G277800 chr4D 98.211 559 7 1 5271 5826 51347227 51346669 0.000000e+00 974.0
15 TraesCS7D01G277800 chr4D 90.187 214 21 0 4476 4689 206060848 206061061 4.450000e-71 279.0
16 TraesCS7D01G277800 chr4D 95.238 105 4 1 2895 2998 498396840 498396736 1.300000e-36 165.0
17 TraesCS7D01G277800 chr4D 82.353 119 14 6 625 742 97971629 97971741 4.810000e-16 97.1
18 TraesCS7D01G277800 chrUn 98.032 559 7 2 5272 5826 108986237 108985679 0.000000e+00 968.0
19 TraesCS7D01G277800 chrUn 80.189 106 16 5 329 432 36560597 36560495 2.250000e-09 75.0
20 TraesCS7D01G277800 chr1D 97.535 568 11 1 5262 5826 226959272 226958705 0.000000e+00 968.0
21 TraesCS7D01G277800 chr1D 97.849 558 9 1 5272 5826 57219069 57218512 0.000000e+00 961.0
22 TraesCS7D01G277800 chr1D 91.954 261 21 0 3468 3728 254471924 254472184 3.320000e-97 366.0
23 TraesCS7D01G277800 chr1D 90.393 229 22 0 4464 4692 268963510 268963282 9.490000e-78 302.0
24 TraesCS7D01G277800 chr1D 92.373 118 7 2 2881 2998 494470806 494470921 3.610000e-37 167.0
25 TraesCS7D01G277800 chr1D 80.469 128 19 6 286 412 247133140 247133018 6.220000e-15 93.5
26 TraesCS7D01G277800 chr5D 97.312 558 12 1 5272 5826 42565820 42565263 0.000000e+00 944.0
27 TraesCS7D01G277800 chr5D 91.571 261 22 0 3468 3728 503326017 503326277 1.540000e-95 361.0
28 TraesCS7D01G277800 chr5D 90.909 264 24 0 3468 3731 432309866 432309603 7.180000e-94 355.0
29 TraesCS7D01G277800 chr5D 76.440 191 43 2 242 430 520431667 520431477 1.030000e-17 102.0
30 TraesCS7D01G277800 chr5D 83.333 96 11 5 274 366 219512668 219512761 3.740000e-12 84.2
31 TraesCS7D01G277800 chr3D 96.237 558 16 2 5272 5826 562379666 562380221 0.000000e+00 909.0
32 TraesCS7D01G277800 chr3D 91.954 261 21 0 3468 3728 24160677 24160937 3.320000e-97 366.0
33 TraesCS7D01G277800 chr3D 80.769 130 19 5 274 400 3992231 3992105 4.810000e-16 97.1
34 TraesCS7D01G277800 chr3D 77.966 118 20 5 338 452 322518697 322518811 1.050000e-07 69.4
35 TraesCS7D01G277800 chr3B 91.571 261 22 0 3468 3728 201488238 201488498 1.540000e-95 361.0
36 TraesCS7D01G277800 chr1A 91.255 263 23 0 3469 3731 554452704 554452442 5.550000e-95 359.0
37 TraesCS7D01G277800 chr1A 83.178 107 13 4 262 367 282543342 282543444 6.220000e-15 93.5
38 TraesCS7D01G277800 chr4B 90.187 214 21 0 4479 4692 258771566 258771353 4.450000e-71 279.0
39 TraesCS7D01G277800 chr4B 88.739 222 23 2 4469 4689 252007320 252007540 2.680000e-68 270.0
40 TraesCS7D01G277800 chr4B 75.912 137 28 5 332 466 374717235 374717102 1.360000e-06 65.8
41 TraesCS7D01G277800 chr2D 89.908 218 20 2 4472 4689 388833658 388833873 4.450000e-71 279.0
42 TraesCS7D01G277800 chr2D 81.875 160 22 6 625 780 320182437 320182281 1.700000e-25 128.0
43 TraesCS7D01G277800 chr2D 81.752 137 25 0 308 444 554304624 554304760 1.330000e-21 115.0
44 TraesCS7D01G277800 chr2D 80.986 142 19 6 637 777 17796990 17797124 7.980000e-19 106.0
45 TraesCS7D01G277800 chr2D 76.136 176 41 1 274 448 101690579 101690754 2.240000e-14 91.6
46 TraesCS7D01G277800 chr5B 88.053 226 25 2 4465 4689 400094347 400094571 3.460000e-67 267.0
47 TraesCS7D01G277800 chr5B 97.059 102 3 0 2898 2999 625959562 625959461 7.760000e-39 172.0
48 TraesCS7D01G277800 chr5B 79.042 167 33 2 241 405 655707998 655707832 4.770000e-21 113.0
49 TraesCS7D01G277800 chr5B 84.314 102 11 5 269 367 241975276 241975375 1.730000e-15 95.3
50 TraesCS7D01G277800 chr5B 78.992 119 23 2 336 452 5056323 5056205 4.840000e-11 80.5
51 TraesCS7D01G277800 chr6B 97.000 100 3 0 2899 2998 219879346 219879445 1.000000e-37 169.0
52 TraesCS7D01G277800 chr6B 82.955 88 11 3 643 730 402200976 402200893 6.260000e-10 76.8
53 TraesCS7D01G277800 chr3A 97.000 100 3 0 2899 2998 287684683 287684782 1.000000e-37 169.0
54 TraesCS7D01G277800 chr3A 75.691 181 33 11 278 452 730091156 730090981 4.840000e-11 80.5
55 TraesCS7D01G277800 chr2A 97.000 100 3 0 2899 2998 416627573 416627474 1.000000e-37 169.0
56 TraesCS7D01G277800 chr2A 84.906 106 13 3 625 729 411086112 411086215 2.870000e-18 104.0
57 TraesCS7D01G277800 chr6A 95.876 97 4 0 2902 2998 507116916 507117012 2.170000e-34 158.0
58 TraesCS7D01G277800 chr1B 80.374 107 19 2 308 413 378855142 378855037 4.840000e-11 80.5
59 TraesCS7D01G277800 chr5A 81.308 107 11 7 625 729 687938281 687938380 1.740000e-10 78.7
60 TraesCS7D01G277800 chr6D 91.667 48 2 2 683 729 330106409 330106363 1.360000e-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 TraesCS7D01G277800 chr7D 266881710 266887535 5825 True 10759.0 10759 100.000000 1 5826 1 chr7D.!!$R3 5825
1 TraesCS7D01G277800 chr7D 169479257 169479828 571 True 976.0 976 97.552000 5258 5826 1 chr7D.!!$R2 568
2 TraesCS7D01G277800 chr7D 21764975 21765545 570 True 966.0 966 97.378000 5262 5826 1 chr7D.!!$R1 564
3 TraesCS7D01G277800 chr7D 602020328 602020886 558 False 946.0 946 97.317000 5271 5826 1 chr7D.!!$F3 555
4 TraesCS7D01G277800 chr7A 292826196 292832651 6455 True 2695.0 5234 87.013000 509 4255 2 chr7A.!!$R3 3746
5 TraesCS7D01G277800 chr7A 292820159 292821127 968 True 1279.0 1279 90.194000 4251 5272 1 chr7A.!!$R1 1021
6 TraesCS7D01G277800 chr7A 292845221 292845721 500 True 571.0 571 87.500000 1 495 1 chr7A.!!$R2 494
7 TraesCS7D01G277800 chr7B 247258028 247263391 5363 False 2554.8 4743 95.036667 1 5272 3 chr7B.!!$F1 5271
8 TraesCS7D01G277800 chr4D 51346669 51347227 558 True 974.0 974 98.211000 5271 5826 1 chr4D.!!$R1 555
9 TraesCS7D01G277800 chrUn 108985679 108986237 558 True 968.0 968 98.032000 5272 5826 1 chrUn.!!$R2 554
10 TraesCS7D01G277800 chr1D 226958705 226959272 567 True 968.0 968 97.535000 5262 5826 1 chr1D.!!$R2 564
11 TraesCS7D01G277800 chr1D 57218512 57219069 557 True 961.0 961 97.849000 5272 5826 1 chr1D.!!$R1 554
12 TraesCS7D01G277800 chr5D 42565263 42565820 557 True 944.0 944 97.312000 5272 5826 1 chr5D.!!$R1 554
13 TraesCS7D01G277800 chr3D 562379666 562380221 555 False 909.0 909 96.237000 5272 5826 1 chr3D.!!$F3 554

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
780 811 0.033781 TTTACTGTTCACCCGACCCG 59.966 55.000 0.00 0.00 0.00 5.28 F
2241 5031 0.178967 TCCTTGCAATGGACAGGCAA 60.179 50.000 12.03 11.85 44.50 4.52 F
3428 6264 1.067142 TGACCGTACTGTTCATGAGCC 60.067 52.381 7.13 0.00 0.00 4.70 F
4471 7467 0.179132 CAGCAGCTGCAACAACAACA 60.179 50.000 38.24 0.00 45.16 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2387 5179 0.191064 TGGGCCCACTATCTAGGAGG 59.809 60.000 24.45 0.00 0.00 4.30 R
3717 6695 1.609208 AGCGCCTATTTAATGGCCTG 58.391 50.000 2.29 2.64 45.90 4.85 R
4756 7752 1.734137 GCATGCATCTTCCAGCAGG 59.266 57.895 14.21 0.00 44.94 4.85 R
5381 8387 4.247267 TCTACTTCCTTTGTGTACCACG 57.753 45.455 0.00 0.00 37.14 4.94 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
49 50 9.793259 ATTATTTGTAGGAAGAACACTCAAGAA 57.207 29.630 0.00 0.00 0.00 2.52
53 54 4.138487 AGGAAGAACACTCAAGAACGTT 57.862 40.909 0.00 0.00 0.00 3.99
148 151 1.094073 CATTTGGGAGCAGGAGAGCG 61.094 60.000 0.00 0.00 40.15 5.03
161 164 0.248458 GAGAGCGCTTTCGGAGAGAG 60.248 60.000 13.26 0.00 42.17 3.20
164 167 0.963355 AGCGCTTTCGGAGAGAGAGT 60.963 55.000 2.64 0.00 41.78 3.24
167 170 1.200252 CGCTTTCGGAGAGAGAGTGAA 59.800 52.381 0.00 0.00 41.78 3.18
168 171 2.601804 GCTTTCGGAGAGAGAGTGAAC 58.398 52.381 0.00 0.00 41.78 3.18
169 172 2.029828 GCTTTCGGAGAGAGAGTGAACA 60.030 50.000 0.00 0.00 41.78 3.18
187 196 6.888088 AGTGAACATGATGAAAATGGATGAGA 59.112 34.615 0.00 0.00 0.00 3.27
219 228 7.035004 GCAAACTCACTATTATTCCAAATGCA 58.965 34.615 0.00 0.00 0.00 3.96
221 230 6.382869 ACTCACTATTATTCCAAATGCAGC 57.617 37.500 0.00 0.00 0.00 5.25
231 240 3.609853 TCCAAATGCAGCGAACTAAGAT 58.390 40.909 0.00 0.00 0.00 2.40
255 264 4.082125 AGCTCAAATGGTTAGGTTCTTGG 58.918 43.478 0.00 0.00 0.00 3.61
260 269 0.774908 TGGTTAGGTTCTTGGGGTGG 59.225 55.000 0.00 0.00 0.00 4.61
267 276 2.171003 GGTTCTTGGGGTGGAATCAAG 58.829 52.381 0.00 0.00 39.20 3.02
298 307 4.772624 AGTTCATGTCCTAGACTTGCACTA 59.227 41.667 12.02 0.00 40.24 2.74
299 308 4.720649 TCATGTCCTAGACTTGCACTAC 57.279 45.455 5.90 0.00 37.54 2.73
306 315 1.329256 AGACTTGCACTACTGGTCGT 58.671 50.000 0.00 0.00 32.86 4.34
314 323 3.676172 TGCACTACTGGTCGTATTTTTCG 59.324 43.478 0.00 0.00 0.00 3.46
353 362 3.549467 GCGATGTGCGTTCAGTGA 58.451 55.556 0.00 0.00 43.41 3.41
369 378 0.448593 GTGAGAGGAGACGTTCTCGG 59.551 60.000 9.74 0.00 44.28 4.63
370 379 0.036448 TGAGAGGAGACGTTCTCGGT 59.964 55.000 9.74 0.96 44.28 4.69
398 407 2.158959 GGCGTCCGTGATGACTTCG 61.159 63.158 0.00 0.00 32.97 3.79
404 413 2.599082 GTCCGTGATGACTTCGTCAATC 59.401 50.000 2.65 1.32 45.96 2.67
416 425 5.650543 ACTTCGTCAATCCCAAAATATTGC 58.349 37.500 0.00 0.00 35.10 3.56
433 442 3.120105 CGCCGGCTCAGTATCTCA 58.880 61.111 26.68 0.00 0.00 3.27
434 443 1.662608 CGCCGGCTCAGTATCTCAT 59.337 57.895 26.68 0.00 0.00 2.90
498 507 1.746470 TCTAATCCGAGCTCACGTGA 58.254 50.000 18.88 18.88 0.00 4.35
502 511 0.603569 ATCCGAGCTCACGTGAGTTT 59.396 50.000 38.11 28.92 46.40 2.66
519 528 6.206498 GTGAGTTTGGGTGAACAGTAAAATC 58.794 40.000 0.00 0.00 31.94 2.17
523 532 6.153680 AGTTTGGGTGAACAGTAAAATCAACA 59.846 34.615 0.00 0.00 32.38 3.33
588 617 7.894376 ATTGACAAATGTTTTGATAGCTTGG 57.106 32.000 6.96 0.00 0.00 3.61
629 658 4.318333 CGATATTCGTGAAAGACATGGCAG 60.318 45.833 0.00 0.00 34.72 4.85
630 659 0.874390 TTCGTGAAAGACATGGCAGC 59.126 50.000 0.00 0.00 36.29 5.25
632 661 0.806868 CGTGAAAGACATGGCAGCAT 59.193 50.000 0.00 0.00 32.38 3.79
633 662 1.202110 CGTGAAAGACATGGCAGCATC 60.202 52.381 0.00 0.00 32.38 3.91
634 663 1.089112 TGAAAGACATGGCAGCATCG 58.911 50.000 0.00 0.00 0.00 3.84
636 665 1.945394 GAAAGACATGGCAGCATCGAT 59.055 47.619 0.00 0.00 0.00 3.59
637 666 2.048444 AAGACATGGCAGCATCGATT 57.952 45.000 0.00 0.00 0.00 3.34
639 668 3.413846 AGACATGGCAGCATCGATTAT 57.586 42.857 0.00 0.00 0.00 1.28
640 669 3.072211 AGACATGGCAGCATCGATTATG 58.928 45.455 0.00 0.00 38.74 1.90
642 671 3.216800 ACATGGCAGCATCGATTATGTT 58.783 40.909 0.00 0.00 37.93 2.71
643 672 3.633525 ACATGGCAGCATCGATTATGTTT 59.366 39.130 0.00 0.00 37.93 2.83
644 673 4.098349 ACATGGCAGCATCGATTATGTTTT 59.902 37.500 0.00 0.00 37.93 2.43
683 714 8.522542 TCATGAAATGTCATATGGTGATGAAA 57.477 30.769 0.00 0.00 46.80 2.69
684 715 8.968969 TCATGAAATGTCATATGGTGATGAAAA 58.031 29.630 0.00 0.00 46.80 2.29
685 716 9.758651 CATGAAATGTCATATGGTGATGAAAAT 57.241 29.630 0.00 0.00 42.88 1.82
777 808 9.896263 TTATTTTTATTTTACTGTTCACCCGAC 57.104 29.630 0.00 0.00 0.00 4.79
778 809 5.945466 TTTATTTTACTGTTCACCCGACC 57.055 39.130 0.00 0.00 0.00 4.79
779 810 2.259266 TTTTACTGTTCACCCGACCC 57.741 50.000 0.00 0.00 0.00 4.46
780 811 0.033781 TTTACTGTTCACCCGACCCG 59.966 55.000 0.00 0.00 0.00 5.28
781 812 0.827089 TTACTGTTCACCCGACCCGA 60.827 55.000 0.00 0.00 0.00 5.14
782 813 1.246056 TACTGTTCACCCGACCCGAG 61.246 60.000 0.00 0.00 0.00 4.63
783 814 2.522436 TGTTCACCCGACCCGAGT 60.522 61.111 0.00 0.00 0.00 4.18
784 815 2.095978 CTGTTCACCCGACCCGAGTT 62.096 60.000 0.00 0.00 0.00 3.01
785 816 1.373873 GTTCACCCGACCCGAGTTC 60.374 63.158 0.00 0.00 0.00 3.01
786 817 1.833492 TTCACCCGACCCGAGTTCA 60.833 57.895 0.00 0.00 0.00 3.18
787 818 1.189524 TTCACCCGACCCGAGTTCAT 61.190 55.000 0.00 0.00 0.00 2.57
788 819 0.323633 TCACCCGACCCGAGTTCATA 60.324 55.000 0.00 0.00 0.00 2.15
789 820 0.179119 CACCCGACCCGAGTTCATAC 60.179 60.000 0.00 0.00 0.00 2.39
790 821 0.324091 ACCCGACCCGAGTTCATACT 60.324 55.000 0.00 0.00 37.31 2.12
791 822 1.064463 ACCCGACCCGAGTTCATACTA 60.064 52.381 0.00 0.00 33.84 1.82
792 823 1.336125 CCCGACCCGAGTTCATACTAC 59.664 57.143 0.00 0.00 33.84 2.73
801 832 5.803967 CCCGAGTTCATACTACTGTTTGTAC 59.196 44.000 0.00 0.00 33.84 2.90
805 836 7.594015 CGAGTTCATACTACTGTTTGTACTGTT 59.406 37.037 0.00 0.00 36.50 3.16
858 889 4.702131 GGAAGCAAGATAAAAGAGGAAGCA 59.298 41.667 0.00 0.00 0.00 3.91
1168 3938 0.820871 GAGTCTCCGCCAGATTCACT 59.179 55.000 0.00 0.00 37.72 3.41
1179 3949 1.107114 AGATTCACTCTCGCGACCAT 58.893 50.000 3.71 0.00 0.00 3.55
1216 3986 2.960129 CCCTATTCGTGGCGTCGC 60.960 66.667 9.22 9.22 0.00 5.19
1247 4017 2.579684 GAAGCGGAAGAGATGGCCGT 62.580 60.000 0.00 0.00 46.38 5.68
1517 4288 6.744537 CACATGAGAATCGGATTTCTTGTTTC 59.255 38.462 19.49 4.58 38.61 2.78
1532 4304 3.992943 TGTTTCCATGATTACCGTCCT 57.007 42.857 0.00 0.00 0.00 3.85
1553 4325 3.283751 TGACGTCCCATTTGTTTCAGTT 58.716 40.909 14.12 0.00 0.00 3.16
1599 4371 2.063266 CATTTTGGTGTCACAGCATGC 58.937 47.619 11.21 10.51 41.53 4.06
1627 4399 1.714794 CTCGACTTGGTAGGTGCAAG 58.285 55.000 0.00 0.00 0.00 4.01
1770 4545 8.993121 AGCATGCTTAATAAGTGTACATACATC 58.007 33.333 16.30 0.00 38.63 3.06
1798 4586 5.599359 TCGTTTATCTTTGTGCGATTGAA 57.401 34.783 0.00 0.00 0.00 2.69
2060 4850 7.036220 CCTAGTTACCTTTCTCATGTGTACAG 58.964 42.308 0.00 0.00 0.00 2.74
2062 4852 6.456501 AGTTACCTTTCTCATGTGTACAGTC 58.543 40.000 0.00 0.00 0.00 3.51
2109 4899 4.541085 TTGACGATGCATCACATGAATC 57.459 40.909 25.70 11.20 41.16 2.52
2241 5031 0.178967 TCCTTGCAATGGACAGGCAA 60.179 50.000 12.03 11.85 44.50 4.52
2387 5179 4.898607 TGGCAACACAAGGAGACC 57.101 55.556 0.00 0.00 46.17 3.85
2402 5194 2.225167 GGAGACCCTCCTAGATAGTGGG 60.225 59.091 5.78 11.45 46.41 4.61
2801 5636 1.338200 GCTCTGTAATGGGGATAGCCG 60.338 57.143 0.00 0.00 33.83 5.52
3317 6153 7.789349 AGTTTATAATTATCCCCAACTGGCATT 59.211 33.333 0.00 0.00 0.00 3.56
3392 6228 2.752903 CACAGCCCCTATGTTAAACCAC 59.247 50.000 0.00 0.00 0.00 4.16
3428 6264 1.067142 TGACCGTACTGTTCATGAGCC 60.067 52.381 7.13 0.00 0.00 4.70
3482 6460 7.454225 AGCTAATCAAGTTAAGTTCAAGTCCT 58.546 34.615 0.00 0.00 0.00 3.85
4202 7187 7.551617 GGTATTATGTGCACCTACTTGTAAGTT 59.448 37.037 15.69 0.00 40.37 2.66
4236 7221 5.824904 AGCGTGAAGATGCTTATTTCAAT 57.175 34.783 0.00 0.00 42.10 2.57
4260 7245 9.561069 AATACATTAAGAAAGCGAGACCAATAT 57.439 29.630 0.00 0.00 0.00 1.28
4431 7427 7.420800 GTTTTCTTAATGGAGTGATATGCAGG 58.579 38.462 0.00 0.00 0.00 4.85
4470 7466 2.585263 CAGCAGCTGCAACAACAAC 58.415 52.632 38.24 7.79 45.16 3.32
4471 7467 0.179132 CAGCAGCTGCAACAACAACA 60.179 50.000 38.24 0.00 45.16 3.33
4472 7468 0.531657 AGCAGCTGCAACAACAACAA 59.468 45.000 38.24 0.00 45.16 2.83
4552 7548 6.262193 TGAAACCCATAAAATCTCGAAACC 57.738 37.500 0.00 0.00 0.00 3.27
4626 7622 6.313519 TGGCTAGTTCTTTGGTGATATTCT 57.686 37.500 0.00 0.00 0.00 2.40
4830 7826 5.692814 TGAAAACATTTCTGCTTGATCTCG 58.307 37.500 4.65 0.00 0.00 4.04
4881 7877 9.638239 AAGCGTCACATTTTAATTTGATTGTAT 57.362 25.926 0.00 0.00 28.94 2.29
5005 8002 6.988522 TCACCATGCGTATATATGTGTTAGT 58.011 36.000 3.92 0.00 0.00 2.24
5006 8003 6.866248 TCACCATGCGTATATATGTGTTAGTG 59.134 38.462 3.92 6.06 0.00 2.74
5086 8085 6.603201 CACATATAACCAGGTCATGTCCTTTT 59.397 38.462 8.95 8.07 35.37 2.27
5212 8218 8.698854 CGAGAAAGCTCTTATAATCAGTTGATC 58.301 37.037 0.00 0.00 39.06 2.92
5253 8259 3.694734 ACCGATTTAATTTGATGCGCAG 58.305 40.909 18.32 0.00 0.00 5.18
5348 8354 5.940470 GTGAGAATATTCAGACACCCAAGTT 59.060 40.000 17.56 0.00 0.00 2.66
5493 8499 0.391130 CGCCTTTTCTCACCGGATCA 60.391 55.000 9.46 0.00 0.00 2.92
5637 8643 1.629043 TAGGTGTTGCTCCTCGTCTT 58.371 50.000 0.00 0.00 36.60 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 6.306987 AGGTGAACAGTACATTCCAGAAAAT 58.693 36.000 0.00 0.00 0.00 1.82
99 102 4.164981 ACCTAGGTGAACAGTACATTCCA 58.835 43.478 15.42 0.00 0.00 3.53
100 103 4.820894 ACCTAGGTGAACAGTACATTCC 57.179 45.455 15.42 0.00 0.00 3.01
148 151 2.029828 TGTTCACTCTCTCTCCGAAAGC 60.030 50.000 0.00 0.00 0.00 3.51
161 164 7.066645 TCTCATCCATTTTCATCATGTTCACTC 59.933 37.037 0.00 0.00 0.00 3.51
164 167 6.183360 GCTCTCATCCATTTTCATCATGTTCA 60.183 38.462 0.00 0.00 0.00 3.18
167 170 5.067413 GTGCTCTCATCCATTTTCATCATGT 59.933 40.000 0.00 0.00 0.00 3.21
168 171 5.067283 TGTGCTCTCATCCATTTTCATCATG 59.933 40.000 0.00 0.00 0.00 3.07
169 172 5.198207 TGTGCTCTCATCCATTTTCATCAT 58.802 37.500 0.00 0.00 0.00 2.45
187 196 6.183360 GGAATAATAGTGAGTTTGCATGTGCT 60.183 38.462 6.55 0.00 42.66 4.40
219 228 5.525378 CCATTTGAGCTAATCTTAGTTCGCT 59.475 40.000 8.62 0.00 41.96 4.93
221 230 6.910536 ACCATTTGAGCTAATCTTAGTTCG 57.089 37.500 8.62 0.00 41.96 3.95
231 240 5.710099 CCAAGAACCTAACCATTTGAGCTAA 59.290 40.000 0.00 0.00 0.00 3.09
255 264 3.217626 CTCTAATGGCTTGATTCCACCC 58.782 50.000 0.00 0.00 36.26 4.61
260 269 6.238593 GGACATGAACTCTAATGGCTTGATTC 60.239 42.308 0.00 0.00 32.05 2.52
267 276 5.069781 AGTCTAGGACATGAACTCTAATGGC 59.930 44.000 0.00 0.00 34.60 4.40
298 307 5.952526 AAATTCCGAAAAATACGACCAGT 57.047 34.783 0.00 0.00 0.00 4.00
299 308 7.068692 AGTAAATTCCGAAAAATACGACCAG 57.931 36.000 0.00 0.00 0.00 4.00
314 323 6.072342 TCGCCAAAAGACCTAAAGTAAATTCC 60.072 38.462 0.00 0.00 0.00 3.01
333 342 1.596752 ACTGAACGCACATCGCCAA 60.597 52.632 0.00 0.00 43.23 4.52
351 360 0.036448 ACCGAGAACGTCTCCTCTCA 59.964 55.000 13.79 0.00 40.34 3.27
353 362 0.036448 TCACCGAGAACGTCTCCTCT 59.964 55.000 8.73 0.00 40.34 3.69
369 378 0.172803 ACGGACGCCTTCATAGTCAC 59.827 55.000 0.00 0.00 36.68 3.67
370 379 0.172578 CACGGACGCCTTCATAGTCA 59.827 55.000 0.00 0.00 36.68 3.41
398 407 3.123050 GGCGCAATATTTTGGGATTGAC 58.877 45.455 10.83 0.00 45.88 3.18
404 413 1.591327 GCCGGCGCAATATTTTGGG 60.591 57.895 12.58 8.32 45.79 4.12
416 425 0.881796 TATGAGATACTGAGCCGGCG 59.118 55.000 23.20 9.91 0.00 6.46
434 443 8.633561 GCATATACATACTCCTATGAGCACATA 58.366 37.037 3.74 3.74 42.74 2.29
455 464 0.810648 CCACTTTGGCACGTGCATAT 59.189 50.000 38.60 18.13 44.36 1.78
498 507 6.153680 TGTTGATTTTACTGTTCACCCAAACT 59.846 34.615 0.00 0.00 0.00 2.66
500 509 6.531503 TGTTGATTTTACTGTTCACCCAAA 57.468 33.333 0.00 0.00 0.00 3.28
502 511 6.723298 ATTGTTGATTTTACTGTTCACCCA 57.277 33.333 0.00 0.00 0.00 4.51
588 617 8.895845 CGAATATCGTTTCATGATGAAATTTCC 58.104 33.333 21.91 9.49 46.55 3.13
620 649 2.810274 ACATAATCGATGCTGCCATGTC 59.190 45.455 0.00 0.00 39.39 3.06
644 673 9.281371 TGACATTTCATGAAAAATATGGCAAAA 57.719 25.926 23.91 2.83 33.56 2.44
654 683 9.589111 CATCACCATATGACATTTCATGAAAAA 57.411 29.630 23.91 11.02 42.79 1.94
655 684 8.968969 TCATCACCATATGACATTTCATGAAAA 58.031 29.630 23.91 8.76 42.79 2.29
656 685 8.522542 TCATCACCATATGACATTTCATGAAA 57.477 30.769 22.52 22.52 42.79 2.69
759 790 2.786777 GGGTCGGGTGAACAGTAAAAT 58.213 47.619 0.00 0.00 31.55 1.82
760 791 1.540797 CGGGTCGGGTGAACAGTAAAA 60.541 52.381 0.00 0.00 31.55 1.52
761 792 0.033781 CGGGTCGGGTGAACAGTAAA 59.966 55.000 0.00 0.00 31.55 2.01
762 793 0.827089 TCGGGTCGGGTGAACAGTAA 60.827 55.000 0.00 0.00 31.55 2.24
763 794 1.228521 TCGGGTCGGGTGAACAGTA 60.229 57.895 0.00 0.00 31.55 2.74
765 796 2.095978 AACTCGGGTCGGGTGAACAG 62.096 60.000 0.00 0.00 40.83 3.16
766 797 2.091102 GAACTCGGGTCGGGTGAACA 62.091 60.000 0.00 0.00 40.83 3.18
767 798 1.373873 GAACTCGGGTCGGGTGAAC 60.374 63.158 0.00 0.00 40.83 3.18
768 799 1.189524 ATGAACTCGGGTCGGGTGAA 61.190 55.000 0.00 0.00 40.83 3.18
769 800 0.323633 TATGAACTCGGGTCGGGTGA 60.324 55.000 0.00 0.00 40.83 4.02
770 801 0.179119 GTATGAACTCGGGTCGGGTG 60.179 60.000 0.00 0.00 40.83 4.61
771 802 0.324091 AGTATGAACTCGGGTCGGGT 60.324 55.000 0.00 0.00 44.96 5.28
772 803 1.336125 GTAGTATGAACTCGGGTCGGG 59.664 57.143 0.00 0.00 37.15 5.14
773 804 2.033049 CAGTAGTATGAACTCGGGTCGG 59.967 54.545 0.00 0.00 37.15 4.79
774 805 2.681848 ACAGTAGTATGAACTCGGGTCG 59.318 50.000 0.00 0.00 37.15 4.79
775 806 4.715527 AACAGTAGTATGAACTCGGGTC 57.284 45.455 0.00 0.00 37.15 4.46
776 807 4.282703 ACAAACAGTAGTATGAACTCGGGT 59.717 41.667 0.00 0.00 37.15 5.28
777 808 4.817517 ACAAACAGTAGTATGAACTCGGG 58.182 43.478 0.00 0.00 37.15 5.14
778 809 6.527023 CAGTACAAACAGTAGTATGAACTCGG 59.473 42.308 0.00 0.00 37.15 4.63
779 810 7.082602 ACAGTACAAACAGTAGTATGAACTCG 58.917 38.462 0.00 0.00 37.15 4.18
780 811 8.813643 AACAGTACAAACAGTAGTATGAACTC 57.186 34.615 0.00 0.00 37.15 3.01
812 843 6.698766 TCCGCCGTTTTAAATATACTCTTCTC 59.301 38.462 0.00 0.00 0.00 2.87
817 848 5.006941 TGCTTCCGCCGTTTTAAATATACTC 59.993 40.000 0.00 0.00 34.43 2.59
818 849 4.877251 TGCTTCCGCCGTTTTAAATATACT 59.123 37.500 0.00 0.00 34.43 2.12
819 850 5.159399 TGCTTCCGCCGTTTTAAATATAC 57.841 39.130 0.00 0.00 34.43 1.47
823 854 2.554893 TCTTGCTTCCGCCGTTTTAAAT 59.445 40.909 0.00 0.00 34.43 1.40
827 858 1.816074 TATCTTGCTTCCGCCGTTTT 58.184 45.000 0.00 0.00 34.43 2.43
830 861 1.737793 CTTTTATCTTGCTTCCGCCGT 59.262 47.619 0.00 0.00 34.43 5.68
831 862 2.006888 TCTTTTATCTTGCTTCCGCCG 58.993 47.619 0.00 0.00 34.43 6.46
832 863 2.356069 CCTCTTTTATCTTGCTTCCGCC 59.644 50.000 0.00 0.00 34.43 6.13
833 864 3.270877 TCCTCTTTTATCTTGCTTCCGC 58.729 45.455 0.00 0.00 0.00 5.54
834 865 4.201861 GCTTCCTCTTTTATCTTGCTTCCG 60.202 45.833 0.00 0.00 0.00 4.30
1149 3919 0.820871 AGTGAATCTGGCGGAGACTC 59.179 55.000 1.04 0.00 34.59 3.36
1227 3997 1.524482 GGCCATCTCTTCCGCTTCT 59.476 57.895 0.00 0.00 0.00 2.85
1296 4066 1.587043 CGAGGCAGACGAAGAGGACA 61.587 60.000 0.00 0.00 0.00 4.02
1364 4134 2.283298 CTCGAATCAGTTGGGGTGATG 58.717 52.381 0.00 0.00 34.78 3.07
1476 4247 2.042831 GTGATGTGCACCCAGGCTC 61.043 63.158 15.69 2.33 41.78 4.70
1532 4304 2.925724 ACTGAAACAAATGGGACGTCA 58.074 42.857 18.91 0.00 0.00 4.35
1538 4310 4.501400 GGGAGACAAACTGAAACAAATGGG 60.501 45.833 0.00 0.00 0.00 4.00
1553 4325 3.199946 AGAACAAGACAACAGGGAGACAA 59.800 43.478 0.00 0.00 0.00 3.18
1672 4444 5.964477 ACATAGAGACAAGATGAACCCCTAA 59.036 40.000 0.00 0.00 0.00 2.69
1798 4586 8.147244 AGTAAGGTGGTGTAATGAAACTATCT 57.853 34.615 0.00 0.00 0.00 1.98
2060 4850 1.461127 GCCGTCACTGAACTGATTGAC 59.539 52.381 0.00 0.00 35.93 3.18
2062 4852 1.511850 TGCCGTCACTGAACTGATTG 58.488 50.000 0.00 0.00 0.00 2.67
2109 4899 0.546598 AGTCGGCCTTATTTCCCTGG 59.453 55.000 0.00 0.00 0.00 4.45
2241 5031 6.331307 AGGGAGCTGAGAGATAACCATAATTT 59.669 38.462 0.00 0.00 0.00 1.82
2387 5179 0.191064 TGGGCCCACTATCTAGGAGG 59.809 60.000 24.45 0.00 0.00 4.30
2392 5184 2.293586 ACCTTCTTGGGCCCACTATCTA 60.294 50.000 28.70 7.92 41.11 1.98
2402 5194 5.131067 CCTATAAACCTAACCTTCTTGGGC 58.869 45.833 0.00 0.00 41.11 5.36
2801 5636 9.683069 CCTAAACAATTTATCCAACATCTATGC 57.317 33.333 0.00 0.00 0.00 3.14
2962 5797 7.139392 GTCCCAAAATAAGTGACTCAACTTTC 58.861 38.462 0.00 0.00 40.77 2.62
2979 5814 1.626825 CTTACTCCCTCCGTCCCAAAA 59.373 52.381 0.00 0.00 0.00 2.44
3317 6153 5.952526 CATTCATGCACATATCAAGGCTA 57.047 39.130 0.00 0.00 0.00 3.93
3392 6228 3.181465 ACGGTCATTAGCCACTAAGATGG 60.181 47.826 0.00 0.00 43.26 3.51
3717 6695 1.609208 AGCGCCTATTTAATGGCCTG 58.391 50.000 2.29 2.64 45.90 4.85
4202 7187 7.210174 AGCATCTTCACGCTTTACTATATTCA 58.790 34.615 0.00 0.00 33.81 2.57
4431 7427 2.928731 GCTGCTAGAACACACAGGAGAC 60.929 54.545 0.00 0.00 29.97 3.36
4441 7437 4.291047 GCTGCTGCTGCTAGAACA 57.709 55.556 22.10 0.00 40.48 3.18
4459 7455 3.457234 TGTTGTTGTTGTTGTTGTTGCA 58.543 36.364 0.00 0.00 0.00 4.08
4461 7457 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
4462 7458 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
4463 7459 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
4464 7460 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
4465 7461 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
4466 7462 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
4467 7463 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
4468 7464 6.422776 TTTGTTGTTGTTGTTGTTGTTGTT 57.577 29.167 0.00 0.00 0.00 2.83
4469 7465 5.503194 GCTTTGTTGTTGTTGTTGTTGTTGT 60.503 36.000 0.00 0.00 0.00 3.32
4470 7466 4.903016 GCTTTGTTGTTGTTGTTGTTGTTG 59.097 37.500 0.00 0.00 0.00 3.33
4471 7467 4.024472 GGCTTTGTTGTTGTTGTTGTTGTT 60.024 37.500 0.00 0.00 0.00 2.83
4472 7468 3.496507 GGCTTTGTTGTTGTTGTTGTTGT 59.503 39.130 0.00 0.00 0.00 3.32
4626 7622 8.968969 GTCCATAAAGAGAGACCTAAAGAACTA 58.031 37.037 0.00 0.00 0.00 2.24
4714 7710 3.894427 TGCCCAAAGAATGTTTAGAGCAA 59.106 39.130 0.00 0.00 0.00 3.91
4717 7713 6.271488 TCATTGCCCAAAGAATGTTTAGAG 57.729 37.500 0.00 0.00 32.40 2.43
4756 7752 1.734137 GCATGCATCTTCCAGCAGG 59.266 57.895 14.21 0.00 44.94 4.85
4881 7877 3.245016 ACATCTTTGCAACTGATCCCTGA 60.245 43.478 0.00 0.00 0.00 3.86
5086 8085 3.181469 GCCCTACATGTTATCCTCACGAA 60.181 47.826 2.30 0.00 0.00 3.85
5180 8186 7.556844 TGATTATAAGAGCTTTCTCGGTCTTT 58.443 34.615 10.04 2.91 46.28 2.52
5249 8255 9.849607 CTAGTGTATATTAAATGAACAACTGCG 57.150 33.333 0.00 0.00 0.00 5.18
5381 8387 4.247267 TCTACTTCCTTTGTGTACCACG 57.753 45.455 0.00 0.00 37.14 4.94
5493 8499 9.685276 TCCTTTTGTGATCATGTATCTATGTTT 57.315 29.630 0.00 0.00 35.45 2.83


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

AutoCloner maintained by Alex Coulton.