Multiple sequence alignment - TraesCS6D01G343700

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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 TraesCS6D01G343700 chr6D 100.000 3425 0 0 1 3425 443550087 443553511 0.000000e+00 6325
1 TraesCS6D01G343700 chr6D 97.100 3276 66 5 1 3249 443344208 443347481 0.000000e+00 5496
2 TraesCS6D01G343700 chr6D 97.720 3158 63 4 1 3151 443448376 443451531 0.000000e+00 5424
3 TraesCS6D01G343700 chr6D 96.685 543 17 1 1 543 433239387 433238846 0.000000e+00 902
4 TraesCS6D01G343700 chr6D 78.846 1248 224 27 885 2112 448507102 448508329 0.000000e+00 806
5 TraesCS6D01G343700 chr6D 78.486 1255 222 37 885 2121 448050581 448049357 0.000000e+00 778
6 TraesCS6D01G343700 chr6D 81.137 387 65 6 1701 2082 448032554 448032171 1.540000e-78 303
7 TraesCS6D01G343700 chr6D 97.196 107 3 0 3144 3250 443452216 443452322 7.550000e-42 182
8 TraesCS6D01G343700 chr2D 86.965 1074 121 9 2128 3186 622368277 622369346 0.000000e+00 1190
9 TraesCS6D01G343700 chr2D 88.837 215 22 2 3211 3425 256594440 256594652 2.620000e-66 263
10 TraesCS6D01G343700 chr7D 86.603 1045 115 11 2160 3185 412871394 412870356 0.000000e+00 1131
11 TraesCS6D01G343700 chr7D 96.475 539 19 0 1 539 596907867 596907329 0.000000e+00 891
12 TraesCS6D01G343700 chr7D 96.140 544 20 1 1 544 49812305 49811763 0.000000e+00 887
13 TraesCS6D01G343700 chr7A 84.651 1075 131 23 2130 3184 474281196 474280136 0.000000e+00 1040
14 TraesCS6D01G343700 chr7A 84.314 1071 143 13 2135 3189 219378416 219377355 0.000000e+00 1024
15 TraesCS6D01G343700 chr1D 83.597 1073 159 6 2132 3189 494487565 494486495 0.000000e+00 990
16 TraesCS6D01G343700 chr1D 97.196 535 15 0 4 538 467541404 467540870 0.000000e+00 905
17 TraesCS6D01G343700 chr1D 96.660 539 18 0 1 539 462313517 462312979 0.000000e+00 896
18 TraesCS6D01G343700 chr1D 90.863 197 18 0 3229 3425 295851332 295851136 7.290000e-67 265
19 TraesCS6D01G343700 chr1A 83.473 1071 159 9 2134 3189 260842926 260841859 0.000000e+00 981
20 TraesCS6D01G343700 chr7B 83.569 1059 157 9 2143 3186 33421819 33420763 0.000000e+00 976
21 TraesCS6D01G343700 chr7B 90.686 204 17 2 3223 3425 457354332 457354534 1.570000e-68 270
22 TraesCS6D01G343700 chr7B 90.148 203 20 0 3222 3424 284259721 284259519 7.290000e-67 265
23 TraesCS6D01G343700 chr5B 83.287 1071 161 11 2134 3189 521396356 521395289 0.000000e+00 970
24 TraesCS6D01G343700 chr5B 90.686 204 18 1 3222 3425 401433539 401433337 1.570000e-68 270
25 TraesCS6D01G343700 chr5B 81.288 326 45 9 2133 2443 701544530 701544206 2.040000e-62 250
26 TraesCS6D01G343700 chr5B 77.528 356 69 8 2134 2483 62952634 62952984 1.610000e-48 204
27 TraesCS6D01G343700 chr3B 83.178 1070 160 9 2126 3179 541061612 541062677 0.000000e+00 961
28 TraesCS6D01G343700 chr3B 92.593 189 12 2 3238 3425 653392719 653392532 1.570000e-68 270
29 TraesCS6D01G343700 chr3D 97.032 539 16 0 1 539 560042565 560043103 0.000000e+00 907
30 TraesCS6D01G343700 chr3D 96.475 539 19 0 1 539 4446588 4447126 0.000000e+00 891
31 TraesCS6D01G343700 chr2B 82.166 1071 164 19 2134 3186 206726883 206727944 0.000000e+00 894
32 TraesCS6D01G343700 chr2B 85.309 810 107 6 2377 3186 656580463 656581260 0.000000e+00 826
33 TraesCS6D01G343700 chr6B 84.580 655 48 18 693 1342 42549873 42550479 4.890000e-168 601
34 TraesCS6D01G343700 chr6B 93.671 316 16 4 1692 2005 42550459 42550772 1.440000e-128 470
35 TraesCS6D01G343700 chr6A 90.657 396 36 1 1610 2005 24181281 24181675 3.030000e-145 525
36 TraesCS6D01G343700 chr6A 83.843 229 12 7 700 912 24181063 24181282 9.700000e-46 195
37 TraesCS6D01G343700 chr3A 88.755 249 26 2 2129 2377 177112110 177112356 1.540000e-78 303
38 TraesCS6D01G343700 chr5A 91.371 197 17 0 3229 3425 438570572 438570376 1.570000e-68 270
39 TraesCS6D01G343700 chr5D 90.196 204 20 0 3222 3425 292316898 292316695 2.030000e-67 267
40 TraesCS6D01G343700 chr5D 90.148 203 20 0 3223 3425 387327030 387327232 7.290000e-67 265


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 TraesCS6D01G343700 chr6D 443550087 443553511 3424 False 6325.0 6325 100.0000 1 3425 1 chr6D.!!$F2 3424
1 TraesCS6D01G343700 chr6D 443344208 443347481 3273 False 5496.0 5496 97.1000 1 3249 1 chr6D.!!$F1 3248
2 TraesCS6D01G343700 chr6D 443448376 443452322 3946 False 2803.0 5424 97.4580 1 3250 2 chr6D.!!$F4 3249
3 TraesCS6D01G343700 chr6D 433238846 433239387 541 True 902.0 902 96.6850 1 543 1 chr6D.!!$R1 542
4 TraesCS6D01G343700 chr6D 448507102 448508329 1227 False 806.0 806 78.8460 885 2112 1 chr6D.!!$F3 1227
5 TraesCS6D01G343700 chr6D 448049357 448050581 1224 True 778.0 778 78.4860 885 2121 1 chr6D.!!$R3 1236
6 TraesCS6D01G343700 chr2D 622368277 622369346 1069 False 1190.0 1190 86.9650 2128 3186 1 chr2D.!!$F2 1058
7 TraesCS6D01G343700 chr7D 412870356 412871394 1038 True 1131.0 1131 86.6030 2160 3185 1 chr7D.!!$R2 1025
8 TraesCS6D01G343700 chr7D 596907329 596907867 538 True 891.0 891 96.4750 1 539 1 chr7D.!!$R3 538
9 TraesCS6D01G343700 chr7D 49811763 49812305 542 True 887.0 887 96.1400 1 544 1 chr7D.!!$R1 543
10 TraesCS6D01G343700 chr7A 474280136 474281196 1060 True 1040.0 1040 84.6510 2130 3184 1 chr7A.!!$R2 1054
11 TraesCS6D01G343700 chr7A 219377355 219378416 1061 True 1024.0 1024 84.3140 2135 3189 1 chr7A.!!$R1 1054
12 TraesCS6D01G343700 chr1D 494486495 494487565 1070 True 990.0 990 83.5970 2132 3189 1 chr1D.!!$R4 1057
13 TraesCS6D01G343700 chr1D 467540870 467541404 534 True 905.0 905 97.1960 4 538 1 chr1D.!!$R3 534
14 TraesCS6D01G343700 chr1D 462312979 462313517 538 True 896.0 896 96.6600 1 539 1 chr1D.!!$R2 538
15 TraesCS6D01G343700 chr1A 260841859 260842926 1067 True 981.0 981 83.4730 2134 3189 1 chr1A.!!$R1 1055
16 TraesCS6D01G343700 chr7B 33420763 33421819 1056 True 976.0 976 83.5690 2143 3186 1 chr7B.!!$R1 1043
17 TraesCS6D01G343700 chr5B 521395289 521396356 1067 True 970.0 970 83.2870 2134 3189 1 chr5B.!!$R2 1055
18 TraesCS6D01G343700 chr3B 541061612 541062677 1065 False 961.0 961 83.1780 2126 3179 1 chr3B.!!$F1 1053
19 TraesCS6D01G343700 chr3D 560042565 560043103 538 False 907.0 907 97.0320 1 539 1 chr3D.!!$F2 538
20 TraesCS6D01G343700 chr3D 4446588 4447126 538 False 891.0 891 96.4750 1 539 1 chr3D.!!$F1 538
21 TraesCS6D01G343700 chr2B 206726883 206727944 1061 False 894.0 894 82.1660 2134 3186 1 chr2B.!!$F1 1052
22 TraesCS6D01G343700 chr2B 656580463 656581260 797 False 826.0 826 85.3090 2377 3186 1 chr2B.!!$F2 809
23 TraesCS6D01G343700 chr6B 42549873 42550772 899 False 535.5 601 89.1255 693 2005 2 chr6B.!!$F1 1312
24 TraesCS6D01G343700 chr6A 24181063 24181675 612 False 360.0 525 87.2500 700 2005 2 chr6A.!!$F1 1305

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
664 665 0.107557 AAAACTGGACCACCGACGTT 60.108 50.0 0.00 0.0 39.42 3.99 F
1227 1257 2.005971 GCGGATTACGTGTCCTTCTT 57.994 50.0 16.66 0.0 46.52 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1490 1889 0.179137 GGGAGCACGCAAATAAAGGC 60.179 55.000 0.0 0.0 0.00 4.35 R
2643 3060 1.821136 CCCAAGGCTTCCATGAAAGAC 59.179 52.381 0.0 0.0 34.24 3.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.764237 AAGAACGGGCTTAGAACTGAA 57.236 42.857 0.00 0.00 0.00 3.02
145 146 2.449967 TAAGAGGGTCTGGGCGTGGA 62.450 60.000 0.00 0.00 0.00 4.02
451 452 1.486726 GTGTGGGCTATCTACCTGCTT 59.513 52.381 0.00 0.00 0.00 3.91
641 642 1.153823 CTGGCCGAGTCGTGTAAGG 60.154 63.158 12.31 0.00 0.00 2.69
664 665 0.107557 AAAACTGGACCACCGACGTT 60.108 50.000 0.00 0.00 39.42 3.99
682 683 5.618395 CGACGTTAAAAGAAGCCAAACTTAC 59.382 40.000 0.00 0.00 39.29 2.34
900 917 8.832521 TCACAAAGATTACGTCACAGTTATTTT 58.167 29.630 0.00 0.00 0.00 1.82
908 925 4.636648 ACGTCACAGTTATTTTGTTCACCA 59.363 37.500 0.00 0.00 0.00 4.17
1030 1060 2.622011 GCCCAAAATGTCGCCGTCA 61.622 57.895 0.00 0.00 0.00 4.35
1227 1257 2.005971 GCGGATTACGTGTCCTTCTT 57.994 50.000 16.66 0.00 46.52 2.52
1682 2081 3.073798 TGGAGCCATTAAAGAGGACAACA 59.926 43.478 0.00 0.00 0.00 3.33
2019 2419 2.100631 CACCGACGGCTTCCATCAC 61.101 63.158 15.39 0.00 0.00 3.06
2096 2496 5.583457 CGCATTAGCTGAATGATGGATGATA 59.417 40.000 15.69 0.00 46.94 2.15
2113 2513 7.533967 TGGATGATACCCATGAATATTCCAAA 58.466 34.615 12.90 0.00 35.17 3.28
2239 2639 4.327627 GCTCCTCGAACAAATCTGAAGTAC 59.672 45.833 0.00 0.00 0.00 2.73
2328 2728 7.061441 TCGAATCTAGTCGTAACAAAATCACAC 59.939 37.037 3.05 0.00 41.80 3.82
2643 3060 2.283173 GGGCAAGACCAACCCCTG 60.283 66.667 0.00 0.00 42.05 4.45
2678 3095 3.830755 GCCTTGGGAGATGATGCATTTAT 59.169 43.478 0.00 0.00 0.00 1.40
2838 3275 5.301805 CCCCATAATACACAAATCTTGGTCC 59.698 44.000 0.00 0.00 34.12 4.46
2872 3309 2.168728 AGATACTCCAAAACCGCCTCTC 59.831 50.000 0.00 0.00 0.00 3.20
2911 3350 6.215477 TCGCAAGCTTTATCAATAATCTCG 57.785 37.500 0.00 0.00 37.18 4.04
3227 4365 2.267426 CGCGGTTGATGTAGTCATTGA 58.733 47.619 0.00 0.00 36.54 2.57
3233 4371 6.042777 CGGTTGATGTAGTCATTGATACAGT 58.957 40.000 11.76 0.00 36.54 3.55
3237 4375 8.598924 GTTGATGTAGTCATTGATACAGTGAAG 58.401 37.037 0.00 0.00 36.54 3.02
3250 4388 8.424274 TGATACAGTGAAGTGCTATACAAATG 57.576 34.615 0.00 0.00 0.00 2.32
3251 4389 7.495606 TGATACAGTGAAGTGCTATACAAATGG 59.504 37.037 0.00 0.00 0.00 3.16
3252 4390 5.560724 ACAGTGAAGTGCTATACAAATGGT 58.439 37.500 0.00 0.00 0.00 3.55
3253 4391 6.003950 ACAGTGAAGTGCTATACAAATGGTT 58.996 36.000 0.00 0.00 0.00 3.67
3254 4392 6.490040 ACAGTGAAGTGCTATACAAATGGTTT 59.510 34.615 0.00 0.00 0.00 3.27
3255 4393 7.014230 ACAGTGAAGTGCTATACAAATGGTTTT 59.986 33.333 0.00 0.00 0.00 2.43
3256 4394 7.867403 CAGTGAAGTGCTATACAAATGGTTTTT 59.133 33.333 0.00 0.00 0.00 1.94
3257 4395 9.073475 AGTGAAGTGCTATACAAATGGTTTTTA 57.927 29.630 0.00 0.00 0.00 1.52
3258 4396 9.685828 GTGAAGTGCTATACAAATGGTTTTTAA 57.314 29.630 0.00 0.00 0.00 1.52
3259 4397 9.685828 TGAAGTGCTATACAAATGGTTTTTAAC 57.314 29.630 0.00 0.00 0.00 2.01
3269 4407 2.443887 GGTTTTTAACCCCTTTCCGC 57.556 50.000 0.00 0.00 46.12 5.54
3270 4408 1.336148 GGTTTTTAACCCCTTTCCGCG 60.336 52.381 0.00 0.00 46.12 6.46
3271 4409 1.608109 GTTTTTAACCCCTTTCCGCGA 59.392 47.619 8.23 0.00 0.00 5.87
3272 4410 1.237533 TTTTAACCCCTTTCCGCGAC 58.762 50.000 8.23 0.00 0.00 5.19
3273 4411 0.950071 TTTAACCCCTTTCCGCGACG 60.950 55.000 8.23 0.00 0.00 5.12
3285 4423 2.733593 GCGACGGCGTTCAGAACT 60.734 61.111 16.19 0.00 40.36 3.01
3286 4424 3.000080 GCGACGGCGTTCAGAACTG 62.000 63.158 16.19 6.30 40.36 3.16
3287 4425 1.660575 CGACGGCGTTCAGAACTGT 60.661 57.895 16.19 7.01 0.00 3.55
3288 4426 1.606350 CGACGGCGTTCAGAACTGTC 61.606 60.000 16.19 13.77 0.00 3.51
3289 4427 0.596600 GACGGCGTTCAGAACTGTCA 60.597 55.000 16.19 0.00 0.00 3.58
3290 4428 0.033504 ACGGCGTTCAGAACTGTCAT 59.966 50.000 6.77 0.00 0.00 3.06
3291 4429 0.716108 CGGCGTTCAGAACTGTCATC 59.284 55.000 11.60 0.00 0.00 2.92
3292 4430 1.670087 CGGCGTTCAGAACTGTCATCT 60.670 52.381 11.60 0.00 0.00 2.90
3293 4431 2.415491 CGGCGTTCAGAACTGTCATCTA 60.415 50.000 11.60 0.00 0.00 1.98
3294 4432 3.182967 GGCGTTCAGAACTGTCATCTAG 58.817 50.000 11.60 0.00 0.00 2.43
3295 4433 3.367498 GGCGTTCAGAACTGTCATCTAGT 60.367 47.826 11.60 0.00 0.00 2.57
3296 4434 3.610242 GCGTTCAGAACTGTCATCTAGTG 59.390 47.826 11.60 0.00 0.00 2.74
3297 4435 4.616143 GCGTTCAGAACTGTCATCTAGTGA 60.616 45.833 11.60 0.00 0.00 3.41
3298 4436 5.092105 CGTTCAGAACTGTCATCTAGTGAG 58.908 45.833 11.60 0.00 37.56 3.51
3299 4437 5.335269 CGTTCAGAACTGTCATCTAGTGAGT 60.335 44.000 11.60 0.00 37.56 3.41
3300 4438 5.635417 TCAGAACTGTCATCTAGTGAGTG 57.365 43.478 1.73 0.00 37.56 3.51
3301 4439 5.073428 TCAGAACTGTCATCTAGTGAGTGT 58.927 41.667 1.73 0.00 37.56 3.55
3302 4440 5.048434 TCAGAACTGTCATCTAGTGAGTGTG 60.048 44.000 1.73 0.00 37.56 3.82
3303 4441 4.219507 AGAACTGTCATCTAGTGAGTGTGG 59.780 45.833 0.00 0.00 37.56 4.17
3304 4442 2.828520 ACTGTCATCTAGTGAGTGTGGG 59.171 50.000 0.00 0.00 37.56 4.61
3305 4443 1.550524 TGTCATCTAGTGAGTGTGGGC 59.449 52.381 0.00 0.00 37.56 5.36
3306 4444 0.817654 TCATCTAGTGAGTGTGGGCG 59.182 55.000 0.00 0.00 31.80 6.13
3307 4445 0.817654 CATCTAGTGAGTGTGGGCGA 59.182 55.000 0.00 0.00 0.00 5.54
3308 4446 1.410517 CATCTAGTGAGTGTGGGCGAT 59.589 52.381 0.00 0.00 0.00 4.58
3309 4447 2.430248 TCTAGTGAGTGTGGGCGATA 57.570 50.000 0.00 0.00 0.00 2.92
3310 4448 2.298610 TCTAGTGAGTGTGGGCGATAG 58.701 52.381 0.00 0.00 0.00 2.08
3311 4449 2.092592 TCTAGTGAGTGTGGGCGATAGA 60.093 50.000 0.00 0.00 39.76 1.98
3312 4450 1.781786 AGTGAGTGTGGGCGATAGAT 58.218 50.000 0.00 0.00 39.76 1.98
3313 4451 1.683917 AGTGAGTGTGGGCGATAGATC 59.316 52.381 0.00 0.00 39.76 2.75
3324 4462 1.617322 CGATAGATCGGTCCTTCCCA 58.383 55.000 3.95 0.00 45.93 4.37
3325 4463 1.269998 CGATAGATCGGTCCTTCCCAC 59.730 57.143 3.95 0.00 45.93 4.61
3326 4464 2.317040 GATAGATCGGTCCTTCCCACA 58.683 52.381 0.00 0.00 0.00 4.17
3327 4465 1.481871 TAGATCGGTCCTTCCCACAC 58.518 55.000 0.00 0.00 0.00 3.82
3328 4466 1.153628 GATCGGTCCTTCCCACACG 60.154 63.158 0.00 0.00 0.00 4.49
3329 4467 1.601419 GATCGGTCCTTCCCACACGA 61.601 60.000 0.00 0.00 34.70 4.35
3330 4468 1.885163 ATCGGTCCTTCCCACACGAC 61.885 60.000 0.00 0.00 32.90 4.34
3331 4469 2.346365 GGTCCTTCCCACACGACC 59.654 66.667 0.00 0.00 38.18 4.79
3332 4470 2.346365 GTCCTTCCCACACGACCC 59.654 66.667 0.00 0.00 0.00 4.46
3333 4471 2.122769 TCCTTCCCACACGACCCA 60.123 61.111 0.00 0.00 0.00 4.51
3334 4472 2.214216 TCCTTCCCACACGACCCAG 61.214 63.158 0.00 0.00 0.00 4.45
3335 4473 2.214216 CCTTCCCACACGACCCAGA 61.214 63.158 0.00 0.00 0.00 3.86
3336 4474 1.752198 CTTCCCACACGACCCAGAA 59.248 57.895 0.00 0.00 0.00 3.02
3337 4475 0.107831 CTTCCCACACGACCCAGAAA 59.892 55.000 0.00 0.00 0.00 2.52
3338 4476 0.179040 TTCCCACACGACCCAGAAAC 60.179 55.000 0.00 0.00 0.00 2.78
3339 4477 1.599797 CCCACACGACCCAGAAACC 60.600 63.158 0.00 0.00 0.00 3.27
3340 4478 1.959226 CCACACGACCCAGAAACCG 60.959 63.158 0.00 0.00 0.00 4.44
3341 4479 1.227438 CACACGACCCAGAAACCGT 60.227 57.895 0.00 0.00 35.46 4.83
3342 4480 1.068585 ACACGACCCAGAAACCGTC 59.931 57.895 0.00 0.00 32.50 4.79
3343 4481 1.068417 CACGACCCAGAAACCGTCA 59.932 57.895 0.00 0.00 32.50 4.35
3344 4482 0.944311 CACGACCCAGAAACCGTCAG 60.944 60.000 0.00 0.00 32.50 3.51
3345 4483 1.374252 CGACCCAGAAACCGTCAGG 60.374 63.158 0.00 0.00 45.13 3.86
3351 4489 2.838736 CCAGAAACCGTCAGGGATATG 58.161 52.381 0.00 0.00 43.47 1.78
3352 4490 2.213499 CAGAAACCGTCAGGGATATGC 58.787 52.381 0.00 0.00 43.47 3.14
3353 4491 1.141053 AGAAACCGTCAGGGATATGCC 59.859 52.381 4.83 4.83 43.47 4.40
3364 4502 1.131638 GGATATGCCCTCCTGTCACA 58.868 55.000 0.00 0.00 0.00 3.58
3365 4503 1.202698 GGATATGCCCTCCTGTCACAC 60.203 57.143 0.00 0.00 0.00 3.82
3366 4504 1.486310 GATATGCCCTCCTGTCACACA 59.514 52.381 0.00 0.00 0.00 3.72
3367 4505 0.613260 TATGCCCTCCTGTCACACAC 59.387 55.000 0.00 0.00 0.00 3.82
3368 4506 2.357517 GCCCTCCTGTCACACACG 60.358 66.667 0.00 0.00 0.00 4.49
3369 4507 2.357517 CCCTCCTGTCACACACGC 60.358 66.667 0.00 0.00 0.00 5.34
3370 4508 2.737180 CCTCCTGTCACACACGCT 59.263 61.111 0.00 0.00 0.00 5.07
3371 4509 1.373497 CCTCCTGTCACACACGCTC 60.373 63.158 0.00 0.00 0.00 5.03
3372 4510 1.730902 CTCCTGTCACACACGCTCG 60.731 63.158 0.00 0.00 0.00 5.03
3373 4511 2.734723 CCTGTCACACACGCTCGG 60.735 66.667 0.00 0.00 0.00 4.63
3374 4512 3.406361 CTGTCACACACGCTCGGC 61.406 66.667 0.00 0.00 0.00 5.54
3375 4513 4.214327 TGTCACACACGCTCGGCA 62.214 61.111 0.00 0.00 0.00 5.69
3376 4514 2.964925 GTCACACACGCTCGGCAA 60.965 61.111 0.00 0.00 0.00 4.52
3377 4515 2.202946 TCACACACGCTCGGCAAA 60.203 55.556 0.00 0.00 0.00 3.68
3378 4516 1.815840 TCACACACGCTCGGCAAAA 60.816 52.632 0.00 0.00 0.00 2.44
3379 4517 1.163420 TCACACACGCTCGGCAAAAT 61.163 50.000 0.00 0.00 0.00 1.82
3380 4518 0.998226 CACACACGCTCGGCAAAATG 60.998 55.000 0.00 0.00 0.00 2.32
3381 4519 1.163420 ACACACGCTCGGCAAAATGA 61.163 50.000 0.00 0.00 0.00 2.57
3382 4520 0.453282 CACACGCTCGGCAAAATGAG 60.453 55.000 0.00 0.00 35.30 2.90
3383 4521 1.135315 CACGCTCGGCAAAATGAGG 59.865 57.895 0.00 0.00 32.78 3.86
3384 4522 1.302511 ACGCTCGGCAAAATGAGGT 60.303 52.632 0.00 0.00 32.78 3.85
3385 4523 1.298859 ACGCTCGGCAAAATGAGGTC 61.299 55.000 0.00 0.00 32.78 3.85
3386 4524 1.425428 GCTCGGCAAAATGAGGTCG 59.575 57.895 0.00 0.00 32.78 4.79
3387 4525 1.298859 GCTCGGCAAAATGAGGTCGT 61.299 55.000 0.00 0.00 32.78 4.34
3388 4526 0.443869 CTCGGCAAAATGAGGTCGTG 59.556 55.000 0.00 0.00 0.00 4.35
3389 4527 0.250124 TCGGCAAAATGAGGTCGTGT 60.250 50.000 0.00 0.00 0.00 4.49
3390 4528 0.110238 CGGCAAAATGAGGTCGTGTG 60.110 55.000 0.00 0.00 0.00 3.82
3391 4529 0.387239 GGCAAAATGAGGTCGTGTGC 60.387 55.000 0.00 0.00 0.00 4.57
3392 4530 0.725784 GCAAAATGAGGTCGTGTGCG 60.726 55.000 0.00 0.00 39.92 5.34
3393 4531 0.865111 CAAAATGAGGTCGTGTGCGA 59.135 50.000 0.00 0.00 45.79 5.10
3409 4547 2.738521 GACTGGCGAGCGAGCAAA 60.739 61.111 7.01 0.00 39.27 3.68
3410 4548 2.046892 ACTGGCGAGCGAGCAAAT 60.047 55.556 7.01 0.00 39.27 2.32
3411 4549 0.806102 GACTGGCGAGCGAGCAAATA 60.806 55.000 7.01 0.00 39.27 1.40
3412 4550 1.084370 ACTGGCGAGCGAGCAAATAC 61.084 55.000 7.01 0.00 39.27 1.89
3413 4551 2.082437 CTGGCGAGCGAGCAAATACG 62.082 60.000 8.59 0.00 39.27 3.06
3414 4552 2.621000 GCGAGCGAGCAAATACGG 59.379 61.111 0.00 0.00 37.05 4.02
3415 4553 2.165301 GCGAGCGAGCAAATACGGT 61.165 57.895 0.00 0.00 42.67 4.83
3416 4554 1.693083 GCGAGCGAGCAAATACGGTT 61.693 55.000 0.00 0.00 40.19 4.44
3417 4555 1.552226 CGAGCGAGCAAATACGGTTA 58.448 50.000 0.00 0.00 40.19 2.85
3418 4556 2.124903 CGAGCGAGCAAATACGGTTAT 58.875 47.619 0.00 0.00 40.19 1.89
3419 4557 3.302555 CGAGCGAGCAAATACGGTTATA 58.697 45.455 0.00 0.00 40.19 0.98
3420 4558 3.119136 CGAGCGAGCAAATACGGTTATAC 59.881 47.826 0.00 0.00 40.19 1.47
3421 4559 3.047796 AGCGAGCAAATACGGTTATACG 58.952 45.455 0.00 0.00 36.90 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.527457 AGGGATGGCAAGGCTAGATT 58.473 50.000 0.00 0.00 0.00 2.40
145 146 1.149174 CACAAGGTGCCCTGACTGT 59.851 57.895 0.00 0.00 32.13 3.55
451 452 2.688446 TGGTTGTGGTGCGACAATTTTA 59.312 40.909 3.30 0.00 38.11 1.52
641 642 1.871676 GTCGGTGGTCCAGTTTTTCTC 59.128 52.381 0.00 0.00 0.00 2.87
664 665 4.276431 CCGTGGTAAGTTTGGCTTCTTTTA 59.724 41.667 0.00 0.00 38.57 1.52
682 683 5.006153 AGTTTTCCTTTTTCTTTCCGTGG 57.994 39.130 0.00 0.00 0.00 4.94
804 820 0.732880 CCTGTGTTCGGCTAGACGTG 60.733 60.000 19.41 2.69 34.94 4.49
900 917 4.947147 GCAGGGCGGTGGTGAACA 62.947 66.667 0.00 0.00 0.00 3.18
1227 1257 3.818210 GACATCTTCATCTAGCTCGAGGA 59.182 47.826 15.58 3.19 0.00 3.71
1490 1889 0.179137 GGGAGCACGCAAATAAAGGC 60.179 55.000 0.00 0.00 0.00 4.35
1498 1897 4.695993 TCGCATGGGAGCACGCAA 62.696 61.111 8.63 0.00 41.96 4.85
1669 2068 1.876416 GCGGCAGTGTTGTCCTCTTTA 60.876 52.381 0.00 0.00 0.00 1.85
2096 2496 6.352910 CCACCATTTTTGGAATATTCATGGGT 60.353 38.462 24.69 15.77 36.02 4.51
2201 2601 3.065925 CGAGGAGCCTCCAAATGAAATTC 59.934 47.826 14.46 0.00 39.61 2.17
2239 2639 7.115663 GCTCGCTAGATTACCTAGATTTTCTTG 59.884 40.741 0.00 0.00 46.17 3.02
2328 2728 3.060230 TCGACGATTGTTTTCACTATGCG 59.940 43.478 0.00 0.00 0.00 4.73
2346 2746 2.874315 GCGGCGGCAATTTTCGAC 60.874 61.111 9.78 0.00 39.62 4.20
2373 2773 3.274288 GGAAGTGATTGAGACCATGTCC 58.726 50.000 0.00 0.00 32.18 4.02
2643 3060 1.821136 CCCAAGGCTTCCATGAAAGAC 59.179 52.381 0.00 0.00 34.24 3.01
2678 3095 7.256332 GGATTATAGCCCTCATGTCTAACTTCA 60.256 40.741 0.00 0.00 0.00 3.02
2872 3309 2.511600 GAGGTTGATCGTGCCGGG 60.512 66.667 2.18 0.00 0.00 5.73
2911 3350 2.119495 TGGAAGAGGCTAGGAATGGAC 58.881 52.381 0.00 0.00 0.00 4.02
3227 4365 7.338710 ACCATTTGTATAGCACTTCACTGTAT 58.661 34.615 0.00 0.00 0.00 2.29
3233 4371 9.685828 GTTAAAAACCATTTGTATAGCACTTCA 57.314 29.630 0.00 0.00 0.00 3.02
3251 4389 1.608109 TCGCGGAAAGGGGTTAAAAAC 59.392 47.619 6.13 0.00 0.00 2.43
3252 4390 1.608109 GTCGCGGAAAGGGGTTAAAAA 59.392 47.619 6.13 0.00 0.00 1.94
3253 4391 1.237533 GTCGCGGAAAGGGGTTAAAA 58.762 50.000 6.13 0.00 0.00 1.52
3254 4392 0.950071 CGTCGCGGAAAGGGGTTAAA 60.950 55.000 6.13 0.00 0.00 1.52
3255 4393 1.374505 CGTCGCGGAAAGGGGTTAA 60.375 57.895 6.13 0.00 0.00 2.01
3256 4394 2.262292 CGTCGCGGAAAGGGGTTA 59.738 61.111 6.13 0.00 0.00 2.85
3268 4406 2.733593 AGTTCTGAACGCCGTCGC 60.734 61.111 14.35 0.00 39.84 5.19
3269 4407 1.606350 GACAGTTCTGAACGCCGTCG 61.606 60.000 14.35 0.00 42.43 5.12
3270 4408 0.596600 TGACAGTTCTGAACGCCGTC 60.597 55.000 22.59 22.59 36.23 4.79
3271 4409 0.033504 ATGACAGTTCTGAACGCCGT 59.966 50.000 14.35 12.68 36.23 5.68
3272 4410 0.716108 GATGACAGTTCTGAACGCCG 59.284 55.000 14.35 9.83 36.23 6.46
3273 4411 2.086054 AGATGACAGTTCTGAACGCC 57.914 50.000 14.35 8.48 36.23 5.68
3274 4412 3.610242 CACTAGATGACAGTTCTGAACGC 59.390 47.826 14.35 9.00 36.23 4.84
3275 4413 5.048153 TCACTAGATGACAGTTCTGAACG 57.952 43.478 14.35 11.70 31.61 3.95
3276 4414 5.861251 CACTCACTAGATGACAGTTCTGAAC 59.139 44.000 12.54 12.54 32.37 3.18
3277 4415 5.536538 ACACTCACTAGATGACAGTTCTGAA 59.463 40.000 6.83 0.00 32.37 3.02
3278 4416 5.048434 CACACTCACTAGATGACAGTTCTGA 60.048 44.000 6.83 0.00 32.37 3.27
3279 4417 5.159925 CACACTCACTAGATGACAGTTCTG 58.840 45.833 0.00 0.00 32.37 3.02
3280 4418 4.219507 CCACACTCACTAGATGACAGTTCT 59.780 45.833 0.00 0.00 32.37 3.01
3281 4419 4.489810 CCACACTCACTAGATGACAGTTC 58.510 47.826 0.00 0.00 32.37 3.01
3282 4420 3.259374 CCCACACTCACTAGATGACAGTT 59.741 47.826 0.00 0.00 32.37 3.16
3283 4421 2.828520 CCCACACTCACTAGATGACAGT 59.171 50.000 0.00 0.00 32.37 3.55
3284 4422 2.417924 GCCCACACTCACTAGATGACAG 60.418 54.545 0.00 0.00 32.37 3.51
3285 4423 1.550524 GCCCACACTCACTAGATGACA 59.449 52.381 0.00 0.00 32.37 3.58
3286 4424 1.469940 CGCCCACACTCACTAGATGAC 60.470 57.143 0.00 0.00 32.37 3.06
3287 4425 0.817654 CGCCCACACTCACTAGATGA 59.182 55.000 0.00 0.00 35.45 2.92
3288 4426 0.817654 TCGCCCACACTCACTAGATG 59.182 55.000 0.00 0.00 0.00 2.90
3289 4427 1.781786 ATCGCCCACACTCACTAGAT 58.218 50.000 0.00 0.00 0.00 1.98
3290 4428 2.092592 TCTATCGCCCACACTCACTAGA 60.093 50.000 0.00 0.00 0.00 2.43
3291 4429 2.298610 TCTATCGCCCACACTCACTAG 58.701 52.381 0.00 0.00 0.00 2.57
3292 4430 2.430248 TCTATCGCCCACACTCACTA 57.570 50.000 0.00 0.00 0.00 2.74
3293 4431 1.683917 GATCTATCGCCCACACTCACT 59.316 52.381 0.00 0.00 0.00 3.41
3294 4432 1.600663 CGATCTATCGCCCACACTCAC 60.601 57.143 0.00 0.00 43.84 3.51
3295 4433 0.668535 CGATCTATCGCCCACACTCA 59.331 55.000 0.00 0.00 43.84 3.41
3296 4434 3.481009 CGATCTATCGCCCACACTC 57.519 57.895 0.00 0.00 43.84 3.51
3306 4444 2.036089 GTGTGGGAAGGACCGATCTATC 59.964 54.545 0.00 0.00 40.11 2.08
3307 4445 2.040178 GTGTGGGAAGGACCGATCTAT 58.960 52.381 0.00 0.00 40.11 1.98
3308 4446 1.481871 GTGTGGGAAGGACCGATCTA 58.518 55.000 0.00 0.00 40.11 1.98
3309 4447 1.605058 CGTGTGGGAAGGACCGATCT 61.605 60.000 0.00 0.00 40.11 2.75
3310 4448 1.153628 CGTGTGGGAAGGACCGATC 60.154 63.158 0.00 0.00 40.11 3.69
3311 4449 1.608336 TCGTGTGGGAAGGACCGAT 60.608 57.895 0.00 0.00 40.11 4.18
3312 4450 2.203523 TCGTGTGGGAAGGACCGA 60.204 61.111 0.00 0.00 40.11 4.69
3313 4451 2.048503 GTCGTGTGGGAAGGACCG 60.049 66.667 0.00 0.00 40.11 4.79
3314 4452 2.346365 GGTCGTGTGGGAAGGACC 59.654 66.667 0.78 0.78 45.07 4.46
3315 4453 2.346365 GGGTCGTGTGGGAAGGAC 59.654 66.667 0.00 0.00 34.86 3.85
3316 4454 2.122769 TGGGTCGTGTGGGAAGGA 60.123 61.111 0.00 0.00 0.00 3.36
3317 4455 1.764571 TTCTGGGTCGTGTGGGAAGG 61.765 60.000 0.00 0.00 0.00 3.46
3318 4456 0.107831 TTTCTGGGTCGTGTGGGAAG 59.892 55.000 0.00 0.00 0.00 3.46
3319 4457 0.179040 GTTTCTGGGTCGTGTGGGAA 60.179 55.000 0.00 0.00 0.00 3.97
3320 4458 1.448497 GTTTCTGGGTCGTGTGGGA 59.552 57.895 0.00 0.00 0.00 4.37
3321 4459 1.599797 GGTTTCTGGGTCGTGTGGG 60.600 63.158 0.00 0.00 0.00 4.61
3322 4460 1.959226 CGGTTTCTGGGTCGTGTGG 60.959 63.158 0.00 0.00 0.00 4.17
3323 4461 1.219522 GACGGTTTCTGGGTCGTGTG 61.220 60.000 0.00 0.00 35.91 3.82
3324 4462 1.068585 GACGGTTTCTGGGTCGTGT 59.931 57.895 0.00 0.00 35.91 4.49
3325 4463 0.944311 CTGACGGTTTCTGGGTCGTG 60.944 60.000 0.00 0.00 35.91 4.35
3326 4464 1.366366 CTGACGGTTTCTGGGTCGT 59.634 57.895 0.00 0.00 38.62 4.34
3327 4465 1.374252 CCTGACGGTTTCTGGGTCG 60.374 63.158 0.00 0.00 39.23 4.79
3328 4466 4.695560 CCTGACGGTTTCTGGGTC 57.304 61.111 0.00 0.00 39.23 4.46
3331 4469 2.838736 CATATCCCTGACGGTTTCTGG 58.161 52.381 0.00 0.00 41.94 3.86
3332 4470 2.213499 GCATATCCCTGACGGTTTCTG 58.787 52.381 0.00 0.00 0.00 3.02
3333 4471 1.141053 GGCATATCCCTGACGGTTTCT 59.859 52.381 0.00 0.00 0.00 2.52
3334 4472 1.594331 GGCATATCCCTGACGGTTTC 58.406 55.000 0.00 0.00 0.00 2.78
3335 4473 3.800826 GGCATATCCCTGACGGTTT 57.199 52.632 0.00 0.00 0.00 3.27
3345 4483 1.131638 TGTGACAGGAGGGCATATCC 58.868 55.000 0.00 0.00 37.07 2.59
3346 4484 1.486310 TGTGTGACAGGAGGGCATATC 59.514 52.381 0.00 0.00 0.00 1.63
3347 4485 1.210478 GTGTGTGACAGGAGGGCATAT 59.790 52.381 0.00 0.00 0.00 1.78
3348 4486 0.613260 GTGTGTGACAGGAGGGCATA 59.387 55.000 0.00 0.00 0.00 3.14
3349 4487 1.376466 GTGTGTGACAGGAGGGCAT 59.624 57.895 0.00 0.00 0.00 4.40
3350 4488 2.828868 GTGTGTGACAGGAGGGCA 59.171 61.111 0.00 0.00 0.00 5.36
3351 4489 2.357517 CGTGTGTGACAGGAGGGC 60.358 66.667 0.00 0.00 36.17 5.19
3352 4490 2.357517 GCGTGTGTGACAGGAGGG 60.358 66.667 0.00 0.00 36.17 4.30
3353 4491 1.373497 GAGCGTGTGTGACAGGAGG 60.373 63.158 0.00 0.00 36.17 4.30
3354 4492 1.730902 CGAGCGTGTGTGACAGGAG 60.731 63.158 0.00 0.00 36.17 3.69
3355 4493 2.335011 CGAGCGTGTGTGACAGGA 59.665 61.111 0.00 0.00 36.17 3.86
3356 4494 2.734723 CCGAGCGTGTGTGACAGG 60.735 66.667 0.00 0.00 37.08 4.00
3357 4495 3.406361 GCCGAGCGTGTGTGACAG 61.406 66.667 0.00 0.00 0.00 3.51
3358 4496 3.724914 TTGCCGAGCGTGTGTGACA 62.725 57.895 0.00 0.00 0.00 3.58
3359 4497 2.042520 TTTTGCCGAGCGTGTGTGAC 62.043 55.000 0.00 0.00 0.00 3.67
3360 4498 1.163420 ATTTTGCCGAGCGTGTGTGA 61.163 50.000 0.00 0.00 0.00 3.58
3361 4499 0.998226 CATTTTGCCGAGCGTGTGTG 60.998 55.000 0.00 0.00 0.00 3.82
3362 4500 1.163420 TCATTTTGCCGAGCGTGTGT 61.163 50.000 0.00 0.00 0.00 3.72
3363 4501 0.453282 CTCATTTTGCCGAGCGTGTG 60.453 55.000 0.00 0.00 0.00 3.82
3364 4502 1.577328 CCTCATTTTGCCGAGCGTGT 61.577 55.000 0.00 0.00 0.00 4.49
3365 4503 1.135315 CCTCATTTTGCCGAGCGTG 59.865 57.895 0.00 0.00 0.00 5.34
3366 4504 1.298859 GACCTCATTTTGCCGAGCGT 61.299 55.000 0.00 0.00 0.00 5.07
3367 4505 1.425428 GACCTCATTTTGCCGAGCG 59.575 57.895 0.00 0.00 0.00 5.03
3368 4506 1.298859 ACGACCTCATTTTGCCGAGC 61.299 55.000 0.00 0.00 0.00 5.03
3369 4507 0.443869 CACGACCTCATTTTGCCGAG 59.556 55.000 0.00 0.00 0.00 4.63
3370 4508 0.250124 ACACGACCTCATTTTGCCGA 60.250 50.000 0.00 0.00 0.00 5.54
3371 4509 0.110238 CACACGACCTCATTTTGCCG 60.110 55.000 0.00 0.00 0.00 5.69
3372 4510 0.387239 GCACACGACCTCATTTTGCC 60.387 55.000 0.00 0.00 0.00 4.52
3373 4511 0.725784 CGCACACGACCTCATTTTGC 60.726 55.000 0.00 0.00 43.93 3.68
3374 4512 0.865111 TCGCACACGACCTCATTTTG 59.135 50.000 0.00 0.00 45.12 2.44
3375 4513 3.299050 TCGCACACGACCTCATTTT 57.701 47.368 0.00 0.00 45.12 1.82
3392 4530 0.806102 TATTTGCTCGCTCGCCAGTC 60.806 55.000 0.00 0.00 0.00 3.51
3393 4531 1.084370 GTATTTGCTCGCTCGCCAGT 61.084 55.000 0.00 0.00 0.00 4.00
3394 4532 1.638467 GTATTTGCTCGCTCGCCAG 59.362 57.895 0.00 0.00 0.00 4.85
3395 4533 2.164663 CGTATTTGCTCGCTCGCCA 61.165 57.895 0.00 0.00 0.00 5.69
3396 4534 2.621000 CGTATTTGCTCGCTCGCC 59.379 61.111 0.00 0.00 0.00 5.54
3397 4535 1.693083 AACCGTATTTGCTCGCTCGC 61.693 55.000 0.00 0.00 0.00 5.03
3398 4536 1.552226 TAACCGTATTTGCTCGCTCG 58.448 50.000 0.00 0.00 0.00 5.03
3399 4537 3.119136 CGTATAACCGTATTTGCTCGCTC 59.881 47.826 0.00 0.00 0.00 5.03
3400 4538 3.047796 CGTATAACCGTATTTGCTCGCT 58.952 45.455 0.00 0.00 0.00 4.93
3401 4539 2.791004 ACGTATAACCGTATTTGCTCGC 59.209 45.455 0.00 0.00 39.73 5.03
3402 4540 5.471608 GTACGTATAACCGTATTTGCTCG 57.528 43.478 0.00 0.00 44.27 5.03


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

AutoCloner maintained by Alex Coulton.