Multiple sequence alignment - TraesCS1D01G254600

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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 TraesCS1D01G254600 chr1D 100.000 3512 0 0 1 3512 346879166 346875655 0.000000e+00 6486.0
1 TraesCS1D01G254600 chr1D 92.672 232 14 3 1 230 467103883 467104113 7.270000e-87 331.0
2 TraesCS1D01G254600 chr1B 95.507 2537 57 19 575 3075 467207334 467204819 0.000000e+00 4000.0
3 TraesCS1D01G254600 chr1B 96.166 313 2 4 3207 3512 467204819 467204510 1.460000e-138 503.0
4 TraesCS1D01G254600 chr1A 96.274 2362 79 6 717 3075 447120346 447117991 0.000000e+00 3866.0
5 TraesCS1D01G254600 chr1A 91.829 257 12 3 3207 3456 447117991 447117737 2.010000e-92 350.0
6 TraesCS1D01G254600 chr1A 91.845 233 19 0 1 233 577316334 577316102 3.380000e-85 326.0
7 TraesCS1D01G254600 chr1A 91.057 123 9 2 3386 3507 447117363 447117242 7.800000e-37 165.0
8 TraesCS1D01G254600 chr1A 92.857 98 7 0 575 672 447121830 447121733 3.650000e-30 143.0
9 TraesCS1D01G254600 chr1A 96.250 80 3 0 3077 3156 554470835 554470914 7.910000e-27 132.0
10 TraesCS1D01G254600 chr3D 91.392 395 29 5 187 576 512695463 512695857 1.430000e-148 536.0
11 TraesCS1D01G254600 chr3D 93.506 231 14 1 1 230 512695312 512695542 3.360000e-90 342.0
12 TraesCS1D01G254600 chr5D 91.071 392 30 5 187 573 65105043 65105434 3.110000e-145 525.0
13 TraesCS1D01G254600 chr5D 89.394 396 34 7 187 575 436783882 436783488 3.150000e-135 492.0
14 TraesCS1D01G254600 chr5D 89.460 389 35 5 187 569 212564049 212563661 1.470000e-133 486.0
15 TraesCS1D01G254600 chr5D 93.939 231 13 1 1 230 65104892 65105122 7.220000e-92 348.0
16 TraesCS1D01G254600 chr5D 93.506 231 14 1 1 230 65995256 65995486 3.360000e-90 342.0
17 TraesCS1D01G254600 chr5D 92.647 68 5 0 576 643 212625112 212625045 8.020000e-17 99.0
18 TraesCS1D01G254600 chr4D 89.848 394 34 6 187 574 489155285 489154892 5.230000e-138 501.0
19 TraesCS1D01G254600 chr4D 89.250 400 37 4 187 580 485393625 485393226 2.430000e-136 496.0
20 TraesCS1D01G254600 chr4D 89.086 394 33 8 187 574 461842552 461842163 6.820000e-132 481.0
21 TraesCS1D01G254600 chr4D 93.191 235 14 2 1 233 461842704 461842470 9.330000e-91 344.0
22 TraesCS1D01G254600 chr4D 93.191 235 14 2 1 233 489155437 489155203 9.330000e-91 344.0
23 TraesCS1D01G254600 chr4D 92.340 235 16 2 1 233 485393777 485393543 2.020000e-87 333.0
24 TraesCS1D01G254600 chr4D 100.000 52 0 0 3155 3206 30386664 30386715 2.890000e-16 97.1
25 TraesCS1D01G254600 chr5B 89.974 389 31 8 187 569 139154416 139154030 2.430000e-136 496.0
26 TraesCS1D01G254600 chr5B 96.429 84 2 1 3073 3156 548607136 548607054 1.700000e-28 137.0
27 TraesCS1D01G254600 chr2B 88.889 396 36 8 187 576 230219839 230219446 6.820000e-132 481.0
28 TraesCS1D01G254600 chr2A 92.340 235 14 4 1 233 378557482 378557250 7.270000e-87 331.0
29 TraesCS1D01G254600 chr2A 94.048 84 3 1 3073 3156 41099929 41099848 3.680000e-25 126.0
30 TraesCS1D01G254600 chr6D 95.238 84 2 1 3073 3156 354356135 354356054 7.910000e-27 132.0
31 TraesCS1D01G254600 chr6D 100.000 52 0 0 3155 3206 135463109 135463160 2.890000e-16 97.1
32 TraesCS1D01G254600 chr6D 100.000 52 0 0 3155 3206 168256260 168256209 2.890000e-16 97.1
33 TraesCS1D01G254600 chr3A 96.250 80 3 0 3077 3156 593321165 593321244 7.910000e-27 132.0
34 TraesCS1D01G254600 chr7B 98.611 72 1 0 3085 3156 300902878 300902949 1.020000e-25 128.0
35 TraesCS1D01G254600 chr7B 94.048 84 2 1 3073 3156 149444960 149444880 1.320000e-24 124.0
36 TraesCS1D01G254600 chr6B 98.611 72 1 0 3085 3156 204449303 204449374 1.020000e-25 128.0
37 TraesCS1D01G254600 chr7A 95.833 72 2 1 3085 3156 712250459 712250389 7.970000e-22 115.0
38 TraesCS1D01G254600 chr7A 100.000 53 0 0 3155 3207 352180536 352180588 8.020000e-17 99.0
39 TraesCS1D01G254600 chrUn 100.000 52 0 0 3155 3206 93408298 93408349 2.890000e-16 97.1
40 TraesCS1D01G254600 chrUn 100.000 52 0 0 3155 3206 195875547 195875598 2.890000e-16 97.1
41 TraesCS1D01G254600 chrUn 100.000 52 0 0 3155 3206 195881337 195881388 2.890000e-16 97.1
42 TraesCS1D01G254600 chrUn 100.000 52 0 0 3155 3206 389360469 389360418 2.890000e-16 97.1
43 TraesCS1D01G254600 chrUn 100.000 52 0 0 3155 3206 444245098 444245149 2.890000e-16 97.1


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 TraesCS1D01G254600 chr1D 346875655 346879166 3511 True 6486.0 6486 100.00000 1 3512 1 chr1D.!!$R1 3511
1 TraesCS1D01G254600 chr1B 467204510 467207334 2824 True 2251.5 4000 95.83650 575 3512 2 chr1B.!!$R1 2937
2 TraesCS1D01G254600 chr1A 447117242 447121830 4588 True 1131.0 3866 93.00425 575 3507 4 chr1A.!!$R2 2932
3 TraesCS1D01G254600 chr3D 512695312 512695857 545 False 439.0 536 92.44900 1 576 2 chr3D.!!$F1 575
4 TraesCS1D01G254600 chr5D 65104892 65105434 542 False 436.5 525 92.50500 1 573 2 chr5D.!!$F2 572
5 TraesCS1D01G254600 chr4D 489154892 489155437 545 True 422.5 501 91.51950 1 574 2 chr4D.!!$R3 573
6 TraesCS1D01G254600 chr4D 485393226 485393777 551 True 414.5 496 90.79500 1 580 2 chr4D.!!$R2 579
7 TraesCS1D01G254600 chr4D 461842163 461842704 541 True 412.5 481 91.13850 1 574 2 chr4D.!!$R1 573

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
880 2253 0.039708 GTTGTCAGCTTGCTCAAGGC 60.040 55.0 11.15 4.36 38.8 4.35 F
963 2336 0.818040 ATCCCTAAAACCCATCGCGC 60.818 55.0 0.00 0.00 0.0 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2181 3563 0.533032 TTATGACGGACCGCATCACA 59.467 50.0 21.7 12.14 0.00 3.58 R
2935 4318 1.769098 CTGCTCGGATTGTGATGCCG 61.769 60.0 0.0 0.00 46.08 5.69 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
157 161 1.134228 AAAACACAGGACCCTACCGT 58.866 50.000 0.00 0.00 34.73 4.83
215 219 4.704833 CCCCATGGCGATAGGGCG 62.705 72.222 6.09 0.00 46.04 6.13
216 220 3.625897 CCCATGGCGATAGGGCGA 61.626 66.667 6.09 0.00 46.04 5.54
217 221 2.425592 CCATGGCGATAGGGCGAA 59.574 61.111 0.00 0.00 46.04 4.70
218 222 1.961277 CCATGGCGATAGGGCGAAC 60.961 63.158 0.00 0.00 46.04 3.95
219 223 1.961277 CATGGCGATAGGGCGAACC 60.961 63.158 0.00 0.00 46.04 3.62
323 327 4.338710 GCCACACCCTACCGCCAA 62.339 66.667 0.00 0.00 0.00 4.52
468 473 3.494332 CGGTAGGCTGTATAACCCTACT 58.506 50.000 17.50 0.00 46.54 2.57
652 658 1.264288 GAGGTTTGCCAGAAACGAGTG 59.736 52.381 0.00 0.00 37.19 3.51
704 733 0.865111 CAAACGTCAACCGCATCTCA 59.135 50.000 0.00 0.00 41.42 3.27
724 2059 5.529581 TCAAAAACCCTGGATTTGAGAAC 57.470 39.130 14.26 0.00 37.95 3.01
759 2122 4.641645 TGACCAGCAAGGCCCGTG 62.642 66.667 0.00 0.00 43.14 4.94
773 2136 2.100631 CCGTGAAGCCGACATCACC 61.101 63.158 1.46 0.00 40.58 4.02
877 2250 1.677576 CCAAGTTGTCAGCTTGCTCAA 59.322 47.619 20.62 0.00 41.27 3.02
879 2252 1.602311 AGTTGTCAGCTTGCTCAAGG 58.398 50.000 11.15 0.00 38.80 3.61
880 2253 0.039708 GTTGTCAGCTTGCTCAAGGC 60.040 55.000 11.15 4.36 38.80 4.35
961 2334 1.202604 TCGATCCCTAAAACCCATCGC 60.203 52.381 0.00 0.00 37.00 4.58
962 2335 1.226746 GATCCCTAAAACCCATCGCG 58.773 55.000 0.00 0.00 0.00 5.87
963 2336 0.818040 ATCCCTAAAACCCATCGCGC 60.818 55.000 0.00 0.00 0.00 6.86
964 2337 2.478033 CCCTAAAACCCATCGCGCC 61.478 63.158 0.00 0.00 0.00 6.53
965 2338 2.707039 CTAAAACCCATCGCGCCG 59.293 61.111 0.00 0.00 0.00 6.46
966 2339 3.449095 CTAAAACCCATCGCGCCGC 62.449 63.158 0.00 0.00 0.00 6.53
1318 2700 1.001503 GCCCATTCATTCCCCACCA 59.998 57.895 0.00 0.00 0.00 4.17
1332 2714 1.607801 CCACCATCCTCGCAGTCTCA 61.608 60.000 0.00 0.00 0.00 3.27
1447 2829 2.207924 ACGCTCCCCGAGTTTGTCT 61.208 57.895 0.00 0.00 41.02 3.41
1710 3092 2.982130 GTCGACCACATGGAGGCT 59.018 61.111 3.51 0.00 38.94 4.58
2094 3476 6.071952 CCTGGCTCAATGTGTTGTTAATTAGT 60.072 38.462 0.00 0.00 36.69 2.24
2181 3563 1.064758 ACCACAGTCACCACAACACAT 60.065 47.619 0.00 0.00 0.00 3.21
2493 3875 1.073098 ACGGTTTTGGATCCCCTTCT 58.927 50.000 9.90 0.00 0.00 2.85
2503 3885 2.422945 GGATCCCCTTCTGGCGTATTTT 60.423 50.000 0.00 0.00 0.00 1.82
2662 4044 3.632145 ACAACAAAGACAAGGACACATCC 59.368 43.478 0.00 0.00 46.69 3.51
2864 4246 5.031066 TGTATATTTTCAGCCGCTTACCT 57.969 39.130 0.00 0.00 0.00 3.08
2935 4318 5.612351 TGGTTATTTGTTTTTAAGCCACCC 58.388 37.500 0.00 0.00 0.00 4.61
2996 4379 8.937634 AAATGAAGCCTAAATCATTGATTCAC 57.062 30.769 12.15 3.27 43.54 3.18
3075 4459 1.594862 CATAACTGGCTGCGAGTTAGC 59.405 52.381 31.03 3.79 37.88 3.09
3076 4460 0.606096 TAACTGGCTGCGAGTTAGCA 59.394 50.000 26.55 12.46 45.96 3.49
3077 4461 0.036010 AACTGGCTGCGAGTTAGCAT 60.036 50.000 25.40 4.28 46.97 3.79
3078 4462 0.036010 ACTGGCTGCGAGTTAGCATT 60.036 50.000 11.73 0.00 46.97 3.56
3079 4463 1.089920 CTGGCTGCGAGTTAGCATTT 58.910 50.000 3.25 0.00 46.97 2.32
3080 4464 1.470098 CTGGCTGCGAGTTAGCATTTT 59.530 47.619 3.25 0.00 46.97 1.82
3081 4465 1.199789 TGGCTGCGAGTTAGCATTTTG 59.800 47.619 0.00 0.00 46.97 2.44
3082 4466 1.468520 GGCTGCGAGTTAGCATTTTGA 59.531 47.619 0.00 0.00 46.97 2.69
3083 4467 2.095263 GGCTGCGAGTTAGCATTTTGAA 60.095 45.455 0.00 0.00 46.97 2.69
3084 4468 3.564511 GCTGCGAGTTAGCATTTTGAAA 58.435 40.909 0.00 0.00 46.97 2.69
3085 4469 3.980775 GCTGCGAGTTAGCATTTTGAAAA 59.019 39.130 0.00 0.00 46.97 2.29
3086 4470 4.444056 GCTGCGAGTTAGCATTTTGAAAAA 59.556 37.500 0.00 0.00 46.97 1.94
3121 4505 5.459110 TTTTTACACACAGTTCGAGTCAC 57.541 39.130 0.00 0.00 0.00 3.67
3122 4506 4.380841 TTTACACACAGTTCGAGTCACT 57.619 40.909 0.00 0.00 0.00 3.41
3123 4507 2.961526 ACACACAGTTCGAGTCACTT 57.038 45.000 0.00 0.00 0.00 3.16
3124 4508 2.540515 ACACACAGTTCGAGTCACTTG 58.459 47.619 0.00 0.00 0.00 3.16
3125 4509 2.094182 ACACACAGTTCGAGTCACTTGT 60.094 45.455 0.00 0.00 0.00 3.16
3126 4510 2.930040 CACACAGTTCGAGTCACTTGTT 59.070 45.455 0.00 0.00 0.00 2.83
3127 4511 2.930040 ACACAGTTCGAGTCACTTGTTG 59.070 45.455 0.00 0.00 0.00 3.33
3128 4512 3.186909 CACAGTTCGAGTCACTTGTTGA 58.813 45.455 0.00 0.00 0.00 3.18
3140 4524 4.939271 TCACTTGTTGACTCACGATTACA 58.061 39.130 0.00 0.00 0.00 2.41
3141 4525 4.743151 TCACTTGTTGACTCACGATTACAC 59.257 41.667 0.00 0.00 0.00 2.90
3142 4526 4.056050 ACTTGTTGACTCACGATTACACC 58.944 43.478 0.00 0.00 0.00 4.16
3143 4527 4.202223 ACTTGTTGACTCACGATTACACCT 60.202 41.667 0.00 0.00 0.00 4.00
3144 4528 3.649073 TGTTGACTCACGATTACACCTG 58.351 45.455 0.00 0.00 0.00 4.00
3145 4529 3.069016 TGTTGACTCACGATTACACCTGT 59.931 43.478 0.00 0.00 0.00 4.00
3146 4530 4.056050 GTTGACTCACGATTACACCTGTT 58.944 43.478 0.00 0.00 0.00 3.16
3147 4531 5.221283 TGTTGACTCACGATTACACCTGTTA 60.221 40.000 0.00 0.00 0.00 2.41
3148 4532 5.456548 TGACTCACGATTACACCTGTTAA 57.543 39.130 0.00 0.00 0.00 2.01
3149 4533 5.845103 TGACTCACGATTACACCTGTTAAA 58.155 37.500 0.00 0.00 0.00 1.52
3150 4534 6.282167 TGACTCACGATTACACCTGTTAAAA 58.718 36.000 0.00 0.00 0.00 1.52
3151 4535 6.422701 TGACTCACGATTACACCTGTTAAAAG 59.577 38.462 0.00 0.00 0.00 2.27
3152 4536 6.285990 ACTCACGATTACACCTGTTAAAAGT 58.714 36.000 0.00 0.00 0.00 2.66
3153 4537 6.764560 ACTCACGATTACACCTGTTAAAAGTT 59.235 34.615 0.00 0.00 0.00 2.66
3154 4538 7.281549 ACTCACGATTACACCTGTTAAAAGTTT 59.718 33.333 0.00 0.00 0.00 2.66
3155 4539 7.632721 TCACGATTACACCTGTTAAAAGTTTC 58.367 34.615 0.00 0.00 0.00 2.78
3156 4540 6.854381 CACGATTACACCTGTTAAAAGTTTCC 59.146 38.462 0.00 0.00 0.00 3.13
3157 4541 6.016860 ACGATTACACCTGTTAAAAGTTTCCC 60.017 38.462 0.00 0.00 0.00 3.97
3158 4542 6.206048 CGATTACACCTGTTAAAAGTTTCCCT 59.794 38.462 0.00 0.00 0.00 4.20
3159 4543 6.947644 TTACACCTGTTAAAAGTTTCCCTC 57.052 37.500 0.00 0.00 0.00 4.30
3160 4544 5.125367 ACACCTGTTAAAAGTTTCCCTCT 57.875 39.130 0.00 0.00 0.00 3.69
3161 4545 5.131067 ACACCTGTTAAAAGTTTCCCTCTC 58.869 41.667 0.00 0.00 0.00 3.20
3162 4546 5.130350 CACCTGTTAAAAGTTTCCCTCTCA 58.870 41.667 0.00 0.00 0.00 3.27
3163 4547 5.592688 CACCTGTTAAAAGTTTCCCTCTCAA 59.407 40.000 0.00 0.00 0.00 3.02
3164 4548 6.265422 CACCTGTTAAAAGTTTCCCTCTCAAT 59.735 38.462 0.00 0.00 0.00 2.57
3165 4549 6.490381 ACCTGTTAAAAGTTTCCCTCTCAATC 59.510 38.462 0.00 0.00 0.00 2.67
3166 4550 6.717084 CCTGTTAAAAGTTTCCCTCTCAATCT 59.283 38.462 0.00 0.00 0.00 2.40
3167 4551 7.094592 CCTGTTAAAAGTTTCCCTCTCAATCTC 60.095 40.741 0.00 0.00 0.00 2.75
3168 4552 7.518188 TGTTAAAAGTTTCCCTCTCAATCTCT 58.482 34.615 0.00 0.00 0.00 3.10
3169 4553 7.661847 TGTTAAAAGTTTCCCTCTCAATCTCTC 59.338 37.037 0.00 0.00 0.00 3.20
3170 4554 6.446909 AAAAGTTTCCCTCTCAATCTCTCT 57.553 37.500 0.00 0.00 0.00 3.10
3171 4555 6.446909 AAAGTTTCCCTCTCAATCTCTCTT 57.553 37.500 0.00 0.00 0.00 2.85
3172 4556 6.446909 AAGTTTCCCTCTCAATCTCTCTTT 57.553 37.500 0.00 0.00 0.00 2.52
3173 4557 6.048732 AGTTTCCCTCTCAATCTCTCTTTC 57.951 41.667 0.00 0.00 0.00 2.62
3174 4558 5.545723 AGTTTCCCTCTCAATCTCTCTTTCA 59.454 40.000 0.00 0.00 0.00 2.69
3175 4559 6.043706 AGTTTCCCTCTCAATCTCTCTTTCAA 59.956 38.462 0.00 0.00 0.00 2.69
3176 4560 6.633325 TTCCCTCTCAATCTCTCTTTCAAT 57.367 37.500 0.00 0.00 0.00 2.57
3177 4561 6.633325 TCCCTCTCAATCTCTCTTTCAATT 57.367 37.500 0.00 0.00 0.00 2.32
3178 4562 6.648192 TCCCTCTCAATCTCTCTTTCAATTC 58.352 40.000 0.00 0.00 0.00 2.17
3179 4563 5.523188 CCCTCTCAATCTCTCTTTCAATTCG 59.477 44.000 0.00 0.00 0.00 3.34
3180 4564 6.336566 CCTCTCAATCTCTCTTTCAATTCGA 58.663 40.000 0.00 0.00 0.00 3.71
3181 4565 6.476380 CCTCTCAATCTCTCTTTCAATTCGAG 59.524 42.308 0.00 0.00 0.00 4.04
3182 4566 6.336566 TCTCAATCTCTCTTTCAATTCGAGG 58.663 40.000 0.00 0.00 0.00 4.63
3183 4567 6.153510 TCTCAATCTCTCTTTCAATTCGAGGA 59.846 38.462 0.00 0.00 0.00 3.71
3184 4568 6.882656 TCAATCTCTCTTTCAATTCGAGGAT 58.117 36.000 0.00 0.00 0.00 3.24
3185 4569 6.983307 TCAATCTCTCTTTCAATTCGAGGATC 59.017 38.462 0.00 0.00 0.00 3.36
3186 4570 5.269505 TCTCTCTTTCAATTCGAGGATCC 57.730 43.478 2.48 2.48 0.00 3.36
3187 4571 4.711846 TCTCTCTTTCAATTCGAGGATCCA 59.288 41.667 15.82 0.00 0.00 3.41
3188 4572 5.016051 TCTCTTTCAATTCGAGGATCCAG 57.984 43.478 15.82 7.77 0.00 3.86
3189 4573 4.711846 TCTCTTTCAATTCGAGGATCCAGA 59.288 41.667 15.82 10.27 0.00 3.86
3190 4574 5.016051 TCTTTCAATTCGAGGATCCAGAG 57.984 43.478 15.82 4.59 0.00 3.35
3191 4575 4.711846 TCTTTCAATTCGAGGATCCAGAGA 59.288 41.667 15.82 7.13 0.00 3.10
3192 4576 4.662468 TTCAATTCGAGGATCCAGAGAG 57.338 45.455 15.82 6.87 0.00 3.20
3193 4577 2.961741 TCAATTCGAGGATCCAGAGAGG 59.038 50.000 15.82 6.22 39.47 3.69
3194 4578 2.697751 CAATTCGAGGATCCAGAGAGGT 59.302 50.000 15.82 0.00 39.02 3.85
3195 4579 1.769026 TTCGAGGATCCAGAGAGGTG 58.231 55.000 15.82 0.00 39.02 4.00
3196 4580 0.626382 TCGAGGATCCAGAGAGGTGT 59.374 55.000 15.82 0.00 39.02 4.16
3197 4581 1.006043 TCGAGGATCCAGAGAGGTGTT 59.994 52.381 15.82 0.00 39.02 3.32
3198 4582 1.827969 CGAGGATCCAGAGAGGTGTTT 59.172 52.381 15.82 0.00 39.02 2.83
3199 4583 2.234908 CGAGGATCCAGAGAGGTGTTTT 59.765 50.000 15.82 0.00 39.02 2.43
3200 4584 3.677424 CGAGGATCCAGAGAGGTGTTTTC 60.677 52.174 15.82 0.00 39.02 2.29
3201 4585 3.251484 AGGATCCAGAGAGGTGTTTTCA 58.749 45.455 15.82 0.00 39.02 2.69
3202 4586 3.848975 AGGATCCAGAGAGGTGTTTTCAT 59.151 43.478 15.82 0.00 39.02 2.57
3203 4587 5.032846 AGGATCCAGAGAGGTGTTTTCATA 58.967 41.667 15.82 0.00 39.02 2.15
3204 4588 5.130145 AGGATCCAGAGAGGTGTTTTCATAG 59.870 44.000 15.82 0.00 39.02 2.23
3205 4589 5.104735 GGATCCAGAGAGGTGTTTTCATAGT 60.105 44.000 6.95 0.00 39.02 2.12
3206 4590 5.152623 TCCAGAGAGGTGTTTTCATAGTG 57.847 43.478 0.00 0.00 39.02 2.74
3494 5334 3.936453 GCACCCGTATTGTTCTGTATCAA 59.064 43.478 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
214 218 4.867599 GGCCTCGCGGTAGGTTCG 62.868 72.222 14.64 0.00 39.02 3.95
215 219 4.525949 GGGCCTCGCGGTAGGTTC 62.526 72.222 14.64 7.92 39.02 3.62
219 223 4.609018 CATGGGGCCTCGCGGTAG 62.609 72.222 6.13 0.00 0.00 3.18
232 236 4.169696 TTCGCCCTACCGCCATGG 62.170 66.667 7.63 7.63 46.41 3.66
233 237 2.895372 GTTCGCCCTACCGCCATG 60.895 66.667 0.00 0.00 0.00 3.66
234 238 4.171103 GGTTCGCCCTACCGCCAT 62.171 66.667 0.00 0.00 0.00 4.40
235 239 3.961225 TAGGTTCGCCCTACCGCCA 62.961 63.158 0.00 0.00 43.87 5.69
236 240 3.149648 TAGGTTCGCCCTACCGCC 61.150 66.667 0.00 0.00 43.87 6.13
524 530 8.413309 TTTGACAAAGAATTTCAGGATCTGAT 57.587 30.769 0.00 0.00 40.39 2.90
669 675 7.962964 TGACGTTTGTCTCAGAAAATATTCT 57.037 32.000 0.00 0.00 44.94 2.40
672 678 6.347402 CGGTTGACGTTTGTCTCAGAAAATAT 60.347 38.462 0.00 0.00 45.70 1.28
673 679 5.050634 CGGTTGACGTTTGTCTCAGAAAATA 60.051 40.000 0.00 0.00 45.70 1.40
674 680 4.260620 CGGTTGACGTTTGTCTCAGAAAAT 60.261 41.667 0.00 0.00 45.70 1.82
676 682 2.605818 CGGTTGACGTTTGTCTCAGAAA 59.394 45.455 0.00 0.00 45.70 2.52
679 685 0.232303 GCGGTTGACGTTTGTCTCAG 59.768 55.000 0.00 0.00 45.70 3.35
681 687 0.865769 ATGCGGTTGACGTTTGTCTC 59.134 50.000 0.00 0.00 45.70 3.36
682 688 0.865769 GATGCGGTTGACGTTTGTCT 59.134 50.000 0.00 0.00 45.70 3.41
683 689 0.865769 AGATGCGGTTGACGTTTGTC 59.134 50.000 0.00 0.00 46.52 3.18
704 733 4.202253 GCAGTTCTCAAATCCAGGGTTTTT 60.202 41.667 0.00 0.00 0.00 1.94
723 2058 0.114168 AGACCAGTGAGAGAGGCAGT 59.886 55.000 0.00 0.00 0.00 4.40
724 2059 0.531657 CAGACCAGTGAGAGAGGCAG 59.468 60.000 0.00 0.00 0.00 4.85
759 2122 2.434185 TGCGGTGATGTCGGCTTC 60.434 61.111 0.00 0.00 35.27 3.86
812 2185 1.444553 GAGTGCTCTTGACGGACCG 60.445 63.158 13.61 13.61 0.00 4.79
880 2253 4.001329 CGTAGCGTTTTTGCGTCG 57.999 55.556 0.00 0.00 40.67 5.12
1318 2700 3.069980 GCGGTGAGACTGCGAGGAT 62.070 63.158 0.00 0.00 41.08 3.24
1447 2829 2.819595 GGCAAGCGAGATGGCGAA 60.820 61.111 0.00 0.00 38.18 4.70
2094 3476 0.844661 ACCCCTCCTTGGCATACACA 60.845 55.000 0.00 0.00 0.00 3.72
2181 3563 0.533032 TTATGACGGACCGCATCACA 59.467 50.000 21.70 12.14 0.00 3.58
2503 3885 5.761234 GGTGTGTACTGACCTGTTATTGAAA 59.239 40.000 6.62 0.00 0.00 2.69
2662 4044 8.018520 TGCACTACTACCGTAATTCAAATTTTG 58.981 33.333 2.59 2.59 0.00 2.44
2935 4318 1.769098 CTGCTCGGATTGTGATGCCG 61.769 60.000 0.00 0.00 46.08 5.69
2996 4379 6.649973 ACTCTGAGACACTGAAATTGAGAATG 59.350 38.462 12.44 0.00 0.00 2.67
3099 4483 5.172934 AGTGACTCGAACTGTGTGTAAAAA 58.827 37.500 0.00 0.00 0.00 1.94
3100 4484 4.751060 AGTGACTCGAACTGTGTGTAAAA 58.249 39.130 0.00 0.00 0.00 1.52
3101 4485 4.380841 AGTGACTCGAACTGTGTGTAAA 57.619 40.909 0.00 0.00 0.00 2.01
3102 4486 4.109766 CAAGTGACTCGAACTGTGTGTAA 58.890 43.478 0.00 0.00 0.00 2.41
3103 4487 3.129813 ACAAGTGACTCGAACTGTGTGTA 59.870 43.478 0.00 0.00 0.00 2.90
3104 4488 2.094182 ACAAGTGACTCGAACTGTGTGT 60.094 45.455 0.00 0.00 0.00 3.72
3105 4489 2.540515 ACAAGTGACTCGAACTGTGTG 58.459 47.619 0.00 0.00 0.00 3.82
3106 4490 2.930040 CAACAAGTGACTCGAACTGTGT 59.070 45.455 0.00 0.00 0.00 3.72
3107 4491 3.186909 TCAACAAGTGACTCGAACTGTG 58.813 45.455 0.00 0.00 0.00 3.66
3108 4492 3.520290 TCAACAAGTGACTCGAACTGT 57.480 42.857 0.00 0.00 0.00 3.55
3118 4502 4.743151 GTGTAATCGTGAGTCAACAAGTGA 59.257 41.667 0.00 0.00 0.00 3.41
3119 4503 4.084537 GGTGTAATCGTGAGTCAACAAGTG 60.085 45.833 0.00 0.00 0.00 3.16
3120 4504 4.056050 GGTGTAATCGTGAGTCAACAAGT 58.944 43.478 0.00 0.00 0.00 3.16
3121 4505 4.150627 CAGGTGTAATCGTGAGTCAACAAG 59.849 45.833 0.00 0.00 0.00 3.16
3122 4506 4.055360 CAGGTGTAATCGTGAGTCAACAA 58.945 43.478 0.00 0.00 0.00 2.83
3123 4507 3.069016 ACAGGTGTAATCGTGAGTCAACA 59.931 43.478 0.00 0.00 0.00 3.33
3124 4508 3.650139 ACAGGTGTAATCGTGAGTCAAC 58.350 45.455 0.00 0.00 0.00 3.18
3125 4509 4.330944 AACAGGTGTAATCGTGAGTCAA 57.669 40.909 0.00 0.00 0.00 3.18
3126 4510 5.456548 TTAACAGGTGTAATCGTGAGTCA 57.543 39.130 0.00 0.00 0.00 3.41
3127 4511 6.423001 ACTTTTAACAGGTGTAATCGTGAGTC 59.577 38.462 0.00 0.00 0.00 3.36
3128 4512 6.285990 ACTTTTAACAGGTGTAATCGTGAGT 58.714 36.000 0.00 0.00 0.00 3.41
3129 4513 6.780706 ACTTTTAACAGGTGTAATCGTGAG 57.219 37.500 0.00 0.00 0.00 3.51
3130 4514 7.254863 GGAAACTTTTAACAGGTGTAATCGTGA 60.255 37.037 0.00 0.00 0.00 4.35
3131 4515 6.854381 GGAAACTTTTAACAGGTGTAATCGTG 59.146 38.462 0.00 0.00 0.00 4.35
3132 4516 6.016860 GGGAAACTTTTAACAGGTGTAATCGT 60.017 38.462 0.00 0.00 0.00 3.73
3133 4517 6.206048 AGGGAAACTTTTAACAGGTGTAATCG 59.794 38.462 0.00 0.00 0.00 3.34
3134 4518 7.447545 AGAGGGAAACTTTTAACAGGTGTAATC 59.552 37.037 0.00 0.00 0.00 1.75
3135 4519 7.295340 AGAGGGAAACTTTTAACAGGTGTAAT 58.705 34.615 0.00 0.00 0.00 1.89
3136 4520 6.665695 AGAGGGAAACTTTTAACAGGTGTAA 58.334 36.000 0.00 0.00 0.00 2.41
3137 4521 6.126710 TGAGAGGGAAACTTTTAACAGGTGTA 60.127 38.462 0.00 0.00 0.00 2.90
3138 4522 5.125367 AGAGGGAAACTTTTAACAGGTGT 57.875 39.130 0.00 0.00 0.00 4.16
3139 4523 5.130350 TGAGAGGGAAACTTTTAACAGGTG 58.870 41.667 0.00 0.00 0.00 4.00
3140 4524 5.382664 TGAGAGGGAAACTTTTAACAGGT 57.617 39.130 0.00 0.00 0.00 4.00
3141 4525 6.717084 AGATTGAGAGGGAAACTTTTAACAGG 59.283 38.462 0.00 0.00 0.00 4.00
3142 4526 7.663493 AGAGATTGAGAGGGAAACTTTTAACAG 59.337 37.037 0.00 0.00 0.00 3.16
3143 4527 7.518188 AGAGATTGAGAGGGAAACTTTTAACA 58.482 34.615 0.00 0.00 0.00 2.41
3144 4528 7.880713 AGAGAGATTGAGAGGGAAACTTTTAAC 59.119 37.037 0.00 0.00 0.00 2.01
3145 4529 7.978925 AGAGAGATTGAGAGGGAAACTTTTAA 58.021 34.615 0.00 0.00 0.00 1.52
3146 4530 7.560796 AGAGAGATTGAGAGGGAAACTTTTA 57.439 36.000 0.00 0.00 0.00 1.52
3147 4531 6.446909 AGAGAGATTGAGAGGGAAACTTTT 57.553 37.500 0.00 0.00 0.00 2.27
3148 4532 6.446909 AAGAGAGATTGAGAGGGAAACTTT 57.553 37.500 0.00 0.00 0.00 2.66
3149 4533 6.043706 TGAAAGAGAGATTGAGAGGGAAACTT 59.956 38.462 0.00 0.00 0.00 2.66
3150 4534 5.545723 TGAAAGAGAGATTGAGAGGGAAACT 59.454 40.000 0.00 0.00 0.00 2.66
3151 4535 5.799213 TGAAAGAGAGATTGAGAGGGAAAC 58.201 41.667 0.00 0.00 0.00 2.78
3152 4536 6.439636 TTGAAAGAGAGATTGAGAGGGAAA 57.560 37.500 0.00 0.00 0.00 3.13
3153 4537 6.633325 ATTGAAAGAGAGATTGAGAGGGAA 57.367 37.500 0.00 0.00 0.00 3.97
3154 4538 6.629068 CGAATTGAAAGAGAGATTGAGAGGGA 60.629 42.308 0.00 0.00 0.00 4.20
3155 4539 5.523188 CGAATTGAAAGAGAGATTGAGAGGG 59.477 44.000 0.00 0.00 0.00 4.30
3156 4540 6.336566 TCGAATTGAAAGAGAGATTGAGAGG 58.663 40.000 0.00 0.00 0.00 3.69
3157 4541 6.476380 CCTCGAATTGAAAGAGAGATTGAGAG 59.524 42.308 0.00 0.00 34.13 3.20
3158 4542 6.153510 TCCTCGAATTGAAAGAGAGATTGAGA 59.846 38.462 0.00 0.00 34.13 3.27
3159 4543 6.336566 TCCTCGAATTGAAAGAGAGATTGAG 58.663 40.000 0.00 0.00 34.13 3.02
3160 4544 6.286240 TCCTCGAATTGAAAGAGAGATTGA 57.714 37.500 0.00 0.00 34.13 2.57
3161 4545 6.202570 GGATCCTCGAATTGAAAGAGAGATTG 59.797 42.308 3.84 0.00 34.13 2.67
3162 4546 6.126940 TGGATCCTCGAATTGAAAGAGAGATT 60.127 38.462 14.23 0.00 34.13 2.40
3163 4547 5.365025 TGGATCCTCGAATTGAAAGAGAGAT 59.635 40.000 14.23 0.00 34.13 2.75
3164 4548 4.711846 TGGATCCTCGAATTGAAAGAGAGA 59.288 41.667 14.23 0.00 34.13 3.10
3165 4549 5.016051 TGGATCCTCGAATTGAAAGAGAG 57.984 43.478 14.23 0.00 34.13 3.20
3166 4550 4.711846 TCTGGATCCTCGAATTGAAAGAGA 59.288 41.667 14.23 0.00 34.13 3.10
3167 4551 5.016051 TCTGGATCCTCGAATTGAAAGAG 57.984 43.478 14.23 0.00 0.00 2.85
3168 4552 4.711846 TCTCTGGATCCTCGAATTGAAAGA 59.288 41.667 14.23 2.13 0.00 2.52
3169 4553 5.016051 TCTCTGGATCCTCGAATTGAAAG 57.984 43.478 14.23 0.00 0.00 2.62
3170 4554 4.141846 CCTCTCTGGATCCTCGAATTGAAA 60.142 45.833 14.23 0.00 38.35 2.69
3171 4555 3.386078 CCTCTCTGGATCCTCGAATTGAA 59.614 47.826 14.23 0.00 38.35 2.69
3172 4556 2.961741 CCTCTCTGGATCCTCGAATTGA 59.038 50.000 14.23 3.15 38.35 2.57
3173 4557 2.697751 ACCTCTCTGGATCCTCGAATTG 59.302 50.000 14.23 3.49 39.71 2.32
3174 4558 2.697751 CACCTCTCTGGATCCTCGAATT 59.302 50.000 14.23 0.00 39.71 2.17
3175 4559 2.315176 CACCTCTCTGGATCCTCGAAT 58.685 52.381 14.23 0.00 39.71 3.34
3176 4560 1.006043 ACACCTCTCTGGATCCTCGAA 59.994 52.381 14.23 0.00 39.71 3.71
3177 4561 0.626382 ACACCTCTCTGGATCCTCGA 59.374 55.000 14.23 8.63 39.71 4.04
3178 4562 1.479709 AACACCTCTCTGGATCCTCG 58.520 55.000 14.23 4.22 39.71 4.63
3179 4563 3.261897 TGAAAACACCTCTCTGGATCCTC 59.738 47.826 14.23 0.00 39.71 3.71
3180 4564 3.251484 TGAAAACACCTCTCTGGATCCT 58.749 45.455 14.23 0.00 39.71 3.24
3181 4565 3.703001 TGAAAACACCTCTCTGGATCC 57.297 47.619 4.20 4.20 39.71 3.36
3182 4566 5.814705 CACTATGAAAACACCTCTCTGGATC 59.185 44.000 0.00 0.00 39.71 3.36
3183 4567 5.338708 CCACTATGAAAACACCTCTCTGGAT 60.339 44.000 0.00 0.00 39.71 3.41
3184 4568 4.020218 CCACTATGAAAACACCTCTCTGGA 60.020 45.833 0.00 0.00 39.71 3.86
3185 4569 4.256920 CCACTATGAAAACACCTCTCTGG 58.743 47.826 0.00 0.00 42.93 3.86
3186 4570 4.899502 ACCACTATGAAAACACCTCTCTG 58.100 43.478 0.00 0.00 0.00 3.35
3187 4571 5.568620 AACCACTATGAAAACACCTCTCT 57.431 39.130 0.00 0.00 0.00 3.10
3188 4572 5.763204 TGAAACCACTATGAAAACACCTCTC 59.237 40.000 0.00 0.00 0.00 3.20
3189 4573 5.690865 TGAAACCACTATGAAAACACCTCT 58.309 37.500 0.00 0.00 0.00 3.69
3190 4574 5.531287 ACTGAAACCACTATGAAAACACCTC 59.469 40.000 0.00 0.00 0.00 3.85
3191 4575 5.299279 CACTGAAACCACTATGAAAACACCT 59.701 40.000 0.00 0.00 0.00 4.00
3192 4576 5.067283 ACACTGAAACCACTATGAAAACACC 59.933 40.000 0.00 0.00 0.00 4.16
3193 4577 6.131544 ACACTGAAACCACTATGAAAACAC 57.868 37.500 0.00 0.00 0.00 3.32
3194 4578 6.767524 AACACTGAAACCACTATGAAAACA 57.232 33.333 0.00 0.00 0.00 2.83
3195 4579 7.378728 GCTAAACACTGAAACCACTATGAAAAC 59.621 37.037 0.00 0.00 0.00 2.43
3196 4580 7.067615 TGCTAAACACTGAAACCACTATGAAAA 59.932 33.333 0.00 0.00 0.00 2.29
3197 4581 6.544197 TGCTAAACACTGAAACCACTATGAAA 59.456 34.615 0.00 0.00 0.00 2.69
3198 4582 6.058833 TGCTAAACACTGAAACCACTATGAA 58.941 36.000 0.00 0.00 0.00 2.57
3199 4583 5.616270 TGCTAAACACTGAAACCACTATGA 58.384 37.500 0.00 0.00 0.00 2.15
3200 4584 5.940192 TGCTAAACACTGAAACCACTATG 57.060 39.130 0.00 0.00 0.00 2.23
3201 4585 6.570378 GCAATGCTAAACACTGAAACCACTAT 60.570 38.462 0.00 0.00 0.00 2.12
3202 4586 5.278266 GCAATGCTAAACACTGAAACCACTA 60.278 40.000 0.00 0.00 0.00 2.74
3203 4587 4.499696 GCAATGCTAAACACTGAAACCACT 60.500 41.667 0.00 0.00 0.00 4.00
3204 4588 3.735746 GCAATGCTAAACACTGAAACCAC 59.264 43.478 0.00 0.00 0.00 4.16
3205 4589 3.382865 TGCAATGCTAAACACTGAAACCA 59.617 39.130 6.82 0.00 0.00 3.67
3206 4590 3.976169 TGCAATGCTAAACACTGAAACC 58.024 40.909 6.82 0.00 0.00 3.27
3258 4642 6.968904 CCAGTGTGAAAATATATGCAGTTGTC 59.031 38.462 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.