Multiple sequence alignment - TraesCS3B01G447800

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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 TraesCS3B01G447800 chr3B 100.000 5446 0 0 1 5446 687062028 687067473 0.000000e+00 10057.0
1 TraesCS3B01G447800 chr3B 84.000 225 34 2 5058 5282 189009207 189009429 1.190000e-51 215.0
2 TraesCS3B01G447800 chr3A 93.541 3592 107 45 285 3802 656718485 656722025 0.000000e+00 5232.0
3 TraesCS3B01G447800 chr3A 95.205 1147 40 7 3789 4925 656722045 656723186 0.000000e+00 1799.0
4 TraesCS3B01G447800 chr3A 89.516 124 9 2 4949 5072 656723291 656723410 2.630000e-33 154.0
5 TraesCS3B01G447800 chr3A 95.238 63 3 0 5292 5354 656723416 656723478 3.470000e-17 100.0
6 TraesCS3B01G447800 chr3D 91.143 3026 121 55 6 2935 521314984 521317958 0.000000e+00 3967.0
7 TraesCS3B01G447800 chr3D 95.787 1994 55 14 2954 4932 521318079 521320058 0.000000e+00 3190.0
8 TraesCS3B01G447800 chr3D 85.068 221 31 2 5058 5278 314814173 314814391 1.970000e-54 224.0
9 TraesCS3B01G447800 chr3D 96.939 98 3 0 4958 5055 521320141 521320238 1.210000e-36 165.0
10 TraesCS3B01G447800 chr3D 92.157 51 4 0 5396 5446 521320308 521320358 7.570000e-09 73.1
11 TraesCS3B01G447800 chr3D 87.719 57 3 1 5292 5348 521320260 521320312 4.550000e-06 63.9
12 TraesCS3B01G447800 chr5B 91.391 302 25 1 1114 1415 308798995 308799295 3.930000e-111 412.0
13 TraesCS3B01G447800 chr5B 93.103 203 14 0 1517 1719 308799329 308799531 1.150000e-76 298.0
14 TraesCS3B01G447800 chr5B 85.068 221 30 3 5058 5278 336893917 336894134 7.100000e-54 222.0
15 TraesCS3B01G447800 chr5B 97.222 36 1 0 1464 1499 308799296 308799331 1.640000e-05 62.1
16 TraesCS3B01G447800 chr7D 84.874 238 34 2 5058 5295 42814596 42814831 7.050000e-59 239.0
17 TraesCS3B01G447800 chr4B 83.913 230 35 2 5058 5287 460036565 460036338 9.180000e-53 219.0
18 TraesCS3B01G447800 chr2D 84.615 221 32 2 5058 5278 284275092 284274874 9.180000e-53 219.0
19 TraesCS3B01G447800 chr2D 84.615 221 32 2 5058 5278 312629727 312629509 9.180000e-53 219.0
20 TraesCS3B01G447800 chr2D 82.500 240 40 2 5057 5296 112312064 112311827 5.530000e-50 209.0
21 TraesCS3B01G447800 chr6D 84.234 222 33 2 5057 5278 83933545 83933764 1.190000e-51 215.0
22 TraesCS3B01G447800 chrUn 80.162 247 42 6 154 397 103230204 103229962 1.560000e-40 178.0
23 TraesCS3B01G447800 chrUn 79.167 216 41 4 154 366 312335905 312336119 4.400000e-31 147.0
24 TraesCS3B01G447800 chr6A 80.631 222 37 6 154 371 29375678 29375897 3.370000e-37 167.0
25 TraesCS3B01G447800 chr6B 80.093 216 39 4 154 366 52437378 52437164 2.030000e-34 158.0
26 TraesCS3B01G447800 chr6B 85.124 121 17 1 154 274 52445886 52445767 7.410000e-24 122.0
27 TraesCS3B01G447800 chr5D 97.059 34 1 0 1385 1418 490497753 490497786 2.120000e-04 58.4


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 TraesCS3B01G447800 chr3B 687062028 687067473 5445 False 10057.000000 10057 100.000000 1 5446 1 chr3B.!!$F2 5445
1 TraesCS3B01G447800 chr3A 656718485 656723478 4993 False 1821.250000 5232 93.375000 285 5354 4 chr3A.!!$F1 5069
2 TraesCS3B01G447800 chr3D 521314984 521320358 5374 False 1491.800000 3967 92.749000 6 5446 5 chr3D.!!$F2 5440
3 TraesCS3B01G447800 chr5B 308798995 308799531 536 False 257.366667 412 93.905333 1114 1719 3 chr5B.!!$F2 605

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
391 401 0.108851 GTAGGGGCATGCGTTTTTGG 60.109 55.0 12.44 0.0 0.00 3.28 F
539 559 0.660488 TCCGTGCAACATGACACAAC 59.340 50.0 0.00 0.0 36.57 3.32 F
2387 2467 0.250467 GCAGCCACAGAAAGGAGTCA 60.250 55.0 0.00 0.0 0.00 3.41 F
2640 2749 0.956633 ATTTCATGGGCGCATGCTAG 59.043 50.0 32.60 14.5 42.25 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2374 2454 0.108615 CGCGGATGACTCCTTTCTGT 60.109 55.000 0.00 0.0 39.65 3.41 R
2443 2523 0.941542 CGGGCTGTTTGAACTCGAAA 59.058 50.000 0.00 0.0 0.00 3.46 R
4157 4424 3.692406 GGCGAGAAGACCACGGGT 61.692 66.667 0.00 0.0 39.44 5.28 R
4449 4719 2.429236 CTCGCCGCGTGCCTATAG 60.429 66.667 13.39 0.0 36.24 1.31 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
23 24 2.754375 CCACCTAAGCCCCGTGTT 59.246 61.111 0.00 0.00 0.00 3.32
25 26 1.072505 CACCTAAGCCCCGTGTTGT 59.927 57.895 0.00 0.00 0.00 3.32
37 38 1.380403 CGTGTTGTTGCCCAAGTCCA 61.380 55.000 0.00 0.00 32.51 4.02
49 50 0.999406 CAAGTCCATTGTCGTAGGCG 59.001 55.000 0.00 0.00 39.92 5.52
50 51 0.739813 AAGTCCATTGTCGTAGGCGC 60.740 55.000 0.00 0.00 38.14 6.53
53 54 1.141881 CCATTGTCGTAGGCGCTCT 59.858 57.895 7.64 5.38 38.14 4.09
55 56 1.064296 ATTGTCGTAGGCGCTCTCG 59.936 57.895 7.64 9.79 38.14 4.04
76 77 4.641645 CCCAGCTGTCGGTGCCAA 62.642 66.667 13.81 0.00 37.32 4.52
77 78 3.357079 CCAGCTGTCGGTGCCAAC 61.357 66.667 13.81 0.00 37.32 3.77
78 79 3.357079 CAGCTGTCGGTGCCAACC 61.357 66.667 5.25 0.00 43.76 3.77
106 107 2.050168 CCGTGCAATGCGCTTTGT 60.050 55.556 29.60 3.85 43.06 2.83
108 109 1.483806 CGTGCAATGCGCTTTGTTG 59.516 52.632 29.60 19.64 43.06 3.33
115 116 2.332514 GCGCTTTGTTGCAGAGCA 59.667 55.556 0.00 0.00 40.90 4.26
121 122 1.034838 TTTGTTGCAGAGCACCGGTT 61.035 50.000 2.97 0.00 38.71 4.44
123 124 2.594303 TTGCAGAGCACCGGTTGG 60.594 61.111 2.97 0.00 38.71 3.77
135 143 2.440247 GGTTGGGCCCTCATTCCG 60.440 66.667 25.70 0.00 0.00 4.30
139 147 3.090532 GGGCCCTCATTCCGGTCT 61.091 66.667 17.04 0.00 0.00 3.85
141 149 2.190578 GCCCTCATTCCGGTCTGG 59.809 66.667 0.00 0.00 40.09 3.86
170 178 2.037136 GTGCTCATGGCGAGTTGCT 61.037 57.895 1.51 0.00 44.33 3.91
172 180 1.300971 TGCTCATGGCGAGTTGCTTC 61.301 55.000 1.51 0.00 44.33 3.86
186 195 0.319555 TGCTTCGTTGAGGTCTTCGG 60.320 55.000 0.00 0.00 0.00 4.30
187 196 1.014564 GCTTCGTTGAGGTCTTCGGG 61.015 60.000 0.00 0.00 0.00 5.14
222 231 9.528489 TTGTAATCTAGCTTTTGATTTTAGGGT 57.472 29.630 12.34 0.00 35.01 4.34
225 234 6.817765 TCTAGCTTTTGATTTTAGGGTGTG 57.182 37.500 0.00 0.00 0.00 3.82
226 235 6.303839 TCTAGCTTTTGATTTTAGGGTGTGT 58.696 36.000 0.00 0.00 0.00 3.72
238 247 7.584122 TTTTAGGGTGTGTTGTGCTATTTTA 57.416 32.000 0.00 0.00 0.00 1.52
241 250 9.469097 TTTAGGGTGTGTTGTGCTATTTTATAT 57.531 29.630 0.00 0.00 0.00 0.86
252 261 7.342581 TGTGCTATTTTATATGGACCTTGTCA 58.657 34.615 0.00 0.00 33.68 3.58
269 278 8.324163 ACCTTGTCATAAATTCAACTAGTGAC 57.676 34.615 0.00 0.00 35.39 3.67
275 284 9.856488 GTCATAAATTCAACTAGTGACTAGTGA 57.144 33.333 24.52 19.44 45.28 3.41
277 286 9.862371 CATAAATTCAACTAGTGACTAGTGAGT 57.138 33.333 24.52 16.73 45.28 3.41
282 292 3.345414 ACTAGTGACTAGTGAGTTCCCG 58.655 50.000 23.37 0.00 44.47 5.14
286 296 2.095161 GTGACTAGTGAGTTCCCGTCTG 60.095 54.545 0.00 0.00 35.45 3.51
304 314 7.011669 TCCCGTCTGATCGAAATAATTTTTACC 59.988 37.037 0.00 0.00 0.00 2.85
317 327 5.952526 AATTTTTACCGGATCTGTTTCGT 57.047 34.783 9.46 0.00 0.00 3.85
334 344 1.227263 GTCTGATGCCACGCGGTAT 60.227 57.895 12.47 0.00 40.87 2.73
357 367 3.694072 CACAAATCCATTTTAGGGCGAGA 59.306 43.478 0.00 0.00 0.00 4.04
359 369 2.640316 ATCCATTTTAGGGCGAGACC 57.360 50.000 0.00 0.00 37.93 3.85
371 381 3.132467 AGGGCGAGACCTATACTGTTTTC 59.868 47.826 0.00 0.00 39.65 2.29
391 401 0.108851 GTAGGGGCATGCGTTTTTGG 60.109 55.000 12.44 0.00 0.00 3.28
443 453 8.604035 TGCAATATCGAGAGTCTTTTACATTTC 58.396 33.333 0.00 0.00 0.00 2.17
472 482 8.201464 CCTAAAACAGGGTTTCATTTTTACAGT 58.799 33.333 0.00 0.00 41.26 3.55
476 486 8.528044 AACAGGGTTTCATTTTTACAGTAGAA 57.472 30.769 0.00 0.00 0.00 2.10
477 487 8.706322 ACAGGGTTTCATTTTTACAGTAGAAT 57.294 30.769 0.00 0.00 0.00 2.40
478 488 9.143155 ACAGGGTTTCATTTTTACAGTAGAATT 57.857 29.630 0.00 0.00 0.00 2.17
539 559 0.660488 TCCGTGCAACATGACACAAC 59.340 50.000 0.00 0.00 36.57 3.32
626 663 2.249309 CGAGCCGCACAACACAAG 59.751 61.111 0.00 0.00 0.00 3.16
629 666 1.436195 GAGCCGCACAACACAAGACA 61.436 55.000 0.00 0.00 0.00 3.41
709 754 1.555533 CCCCCTTGTTCCTGTAGACTC 59.444 57.143 0.00 0.00 0.00 3.36
773 818 1.205460 TAAAAAGAGCTCCCCGCCCT 61.205 55.000 10.93 0.00 40.39 5.19
785 830 1.076339 CCGCCCTTCTCTCTCCTCT 60.076 63.158 0.00 0.00 0.00 3.69
1677 1747 1.413767 CCCTCGTCGTGCTCAATTCG 61.414 60.000 0.00 0.00 0.00 3.34
1722 1792 4.729918 CGCCAGGCCTTCCAAGCT 62.730 66.667 0.00 0.00 32.37 3.74
1760 1830 4.980805 GCACCGAGCCACCGAACA 62.981 66.667 0.00 0.00 37.23 3.18
1781 1851 2.005451 CTTCTCGCCACAATTCTCCTG 58.995 52.381 0.00 0.00 0.00 3.86
1986 2056 1.348594 GCGCACGCAGGTAATTCTC 59.651 57.895 10.65 0.00 41.49 2.87
2089 2166 3.445687 CGACCCATCGTCCCGACA 61.446 66.667 0.00 0.00 43.66 4.35
2387 2467 0.250467 GCAGCCACAGAAAGGAGTCA 60.250 55.000 0.00 0.00 0.00 3.41
2586 2690 2.571757 GTCGTGTCATCCTCCGCA 59.428 61.111 0.00 0.00 0.00 5.69
2640 2749 0.956633 ATTTCATGGGCGCATGCTAG 59.043 50.000 32.60 14.50 42.25 3.42
2690 2804 2.203337 GGCCTTGTGTGCCTGACA 60.203 61.111 0.00 0.00 45.70 3.58
2877 2995 8.174733 ACTATAAGCTGCTGCATTCATATTTT 57.825 30.769 18.42 2.51 42.74 1.82
2882 3000 4.387862 GCTGCTGCATTCATATTTTATGGC 59.612 41.667 11.11 0.00 39.41 4.40
2920 3038 6.366315 ACACACGCTCAATTTACAACTTAA 57.634 33.333 0.00 0.00 0.00 1.85
2959 3178 5.794894 AGTATGAGAAGGTCGTTCAATTGT 58.205 37.500 5.13 0.00 37.67 2.71
3213 3432 2.674954 TGAATTCTTTGGTTGCATGCG 58.325 42.857 14.09 0.00 0.00 4.73
3311 3530 1.157513 GGATCCTCCTCCCTCCCTC 59.842 68.421 3.84 0.00 32.53 4.30
3312 3531 1.157513 GATCCTCCTCCCTCCCTCC 59.842 68.421 0.00 0.00 0.00 4.30
3313 3532 2.395180 GATCCTCCTCCCTCCCTCCC 62.395 70.000 0.00 0.00 0.00 4.30
3314 3533 3.368501 CCTCCTCCCTCCCTCCCA 61.369 72.222 0.00 0.00 0.00 4.37
3708 3934 5.048846 AGCTTTTGACCTCTCCAACTAAA 57.951 39.130 0.00 0.00 0.00 1.85
3713 3939 6.989155 TTTGACCTCTCCAACTAAACTAGA 57.011 37.500 0.00 0.00 0.00 2.43
3714 3940 6.591750 TTGACCTCTCCAACTAAACTAGAG 57.408 41.667 0.00 0.00 34.71 2.43
3715 3941 5.642165 TGACCTCTCCAACTAAACTAGAGT 58.358 41.667 0.00 0.00 33.38 3.24
3716 3942 6.787170 TGACCTCTCCAACTAAACTAGAGTA 58.213 40.000 0.00 0.00 33.38 2.59
3717 3943 7.411808 TGACCTCTCCAACTAAACTAGAGTAT 58.588 38.462 0.00 0.00 33.38 2.12
3718 3944 8.554870 TGACCTCTCCAACTAAACTAGAGTATA 58.445 37.037 0.00 0.00 33.38 1.47
4157 4424 1.699656 GCGACAGCGACGAGTACCTA 61.700 60.000 0.00 0.00 40.82 3.08
4617 4891 0.030369 GAACGACGACAGGAGTGTGT 59.970 55.000 0.00 0.00 36.88 3.72
4803 5082 0.035630 AACTTGGAGCTAGCTGGCTG 60.036 55.000 30.85 17.10 43.20 4.85
4866 5145 7.572502 AATTACAAGTTTTACGTACTCCGAG 57.427 36.000 0.00 0.00 40.70 4.63
4875 5154 1.196354 ACGTACTCCGAGTTTCGACAG 59.804 52.381 23.16 9.58 43.74 3.51
4925 5231 4.758674 CAGATCTCACCATCTCTCTCTCTC 59.241 50.000 0.00 0.00 30.07 3.20
4926 5232 4.662179 AGATCTCACCATCTCTCTCTCTCT 59.338 45.833 0.00 0.00 0.00 3.10
4928 5234 4.040047 TCTCACCATCTCTCTCTCTCTCT 58.960 47.826 0.00 0.00 0.00 3.10
4929 5235 4.101585 TCTCACCATCTCTCTCTCTCTCTC 59.898 50.000 0.00 0.00 0.00 3.20
4947 5325 2.357009 TCTCTCGCCCATTTCGTAGTAC 59.643 50.000 0.00 0.00 0.00 2.73
4972 5359 3.215151 TGCGGGTAATGTTTCAAGTCAA 58.785 40.909 0.00 0.00 0.00 3.18
4984 5371 6.162777 TGTTTCAAGTCAAACCAAAGGAAAG 58.837 36.000 0.00 0.00 35.69 2.62
5055 5442 9.871238 GTAGTTCAATGGAGTATAAAGTCAAGA 57.129 33.333 0.00 0.00 0.00 3.02
5057 5444 9.965902 AGTTCAATGGAGTATAAAGTCAAGATT 57.034 29.630 0.00 0.00 0.00 2.40
5060 5447 9.832445 TCAATGGAGTATAAAGTCAAGATTACC 57.168 33.333 0.00 0.00 0.00 2.85
5064 5451 8.195436 TGGAGTATAAAGTCAAGATTACCTTCG 58.805 37.037 0.00 0.00 31.42 3.79
5065 5452 8.196103 GGAGTATAAAGTCAAGATTACCTTCGT 58.804 37.037 0.00 0.00 31.42 3.85
5066 5453 9.235537 GAGTATAAAGTCAAGATTACCTTCGTC 57.764 37.037 0.00 0.00 31.42 4.20
5070 5457 4.822026 AGTCAAGATTACCTTCGTCTTGG 58.178 43.478 12.70 0.00 45.47 3.61
5071 5458 4.283722 AGTCAAGATTACCTTCGTCTTGGT 59.716 41.667 12.70 3.95 45.47 3.67
5072 5459 4.995487 GTCAAGATTACCTTCGTCTTGGTT 59.005 41.667 12.70 0.00 45.47 3.67
5073 5460 5.469084 GTCAAGATTACCTTCGTCTTGGTTT 59.531 40.000 12.70 0.00 45.47 3.27
5074 5461 6.647895 GTCAAGATTACCTTCGTCTTGGTTTA 59.352 38.462 12.70 0.00 45.47 2.01
5075 5462 7.333672 GTCAAGATTACCTTCGTCTTGGTTTAT 59.666 37.037 12.70 0.40 45.47 1.40
5076 5463 7.881232 TCAAGATTACCTTCGTCTTGGTTTATT 59.119 33.333 12.70 0.00 45.47 1.40
5077 5464 7.611213 AGATTACCTTCGTCTTGGTTTATTG 57.389 36.000 0.00 0.00 37.74 1.90
5078 5465 7.391620 AGATTACCTTCGTCTTGGTTTATTGA 58.608 34.615 0.00 0.00 37.74 2.57
5079 5466 8.047310 AGATTACCTTCGTCTTGGTTTATTGAT 58.953 33.333 0.00 0.00 37.74 2.57
5080 5467 7.605410 TTACCTTCGTCTTGGTTTATTGATC 57.395 36.000 0.00 0.00 37.74 2.92
5081 5468 4.941873 ACCTTCGTCTTGGTTTATTGATCC 59.058 41.667 0.00 0.00 31.62 3.36
5082 5469 5.186198 CCTTCGTCTTGGTTTATTGATCCT 58.814 41.667 0.00 0.00 0.00 3.24
5083 5470 5.648092 CCTTCGTCTTGGTTTATTGATCCTT 59.352 40.000 0.00 0.00 0.00 3.36
5084 5471 6.151144 CCTTCGTCTTGGTTTATTGATCCTTT 59.849 38.462 0.00 0.00 0.00 3.11
5085 5472 7.309194 CCTTCGTCTTGGTTTATTGATCCTTTT 60.309 37.037 0.00 0.00 0.00 2.27
5086 5473 8.624367 TTCGTCTTGGTTTATTGATCCTTTTA 57.376 30.769 0.00 0.00 0.00 1.52
5087 5474 8.263940 TCGTCTTGGTTTATTGATCCTTTTAG 57.736 34.615 0.00 0.00 0.00 1.85
5088 5475 7.881232 TCGTCTTGGTTTATTGATCCTTTTAGT 59.119 33.333 0.00 0.00 0.00 2.24
5089 5476 9.158233 CGTCTTGGTTTATTGATCCTTTTAGTA 57.842 33.333 0.00 0.00 0.00 1.82
5288 5675 5.584551 GGGACCAATAAAGTAGGATGGAT 57.415 43.478 0.00 0.00 35.16 3.41
5289 5676 5.316987 GGGACCAATAAAGTAGGATGGATG 58.683 45.833 0.00 0.00 35.16 3.51
5290 5677 5.163088 GGGACCAATAAAGTAGGATGGATGT 60.163 44.000 0.00 0.00 35.16 3.06
5312 5703 8.834004 ATGTAGTAGGTCCTAAAATACTCACA 57.166 34.615 0.00 2.70 31.25 3.58
5313 5704 8.834004 TGTAGTAGGTCCTAAAATACTCACAT 57.166 34.615 0.00 0.00 31.25 3.21
5317 5708 8.915036 AGTAGGTCCTAAAATACTCACATACTG 58.085 37.037 0.00 0.00 31.94 2.74
5318 5709 7.735326 AGGTCCTAAAATACTCACATACTGT 57.265 36.000 0.00 0.00 0.00 3.55
5354 5745 5.929992 CCTCGAAGTAGTTGTTTAATGTGGA 59.070 40.000 0.00 0.00 0.00 4.02
5355 5746 6.128634 CCTCGAAGTAGTTGTTTAATGTGGAC 60.129 42.308 0.00 0.00 0.00 4.02
5356 5747 6.282167 TCGAAGTAGTTGTTTAATGTGGACA 58.718 36.000 0.00 0.00 0.00 4.02
5357 5748 6.762187 TCGAAGTAGTTGTTTAATGTGGACAA 59.238 34.615 0.00 0.00 0.00 3.18
5358 5749 7.280428 TCGAAGTAGTTGTTTAATGTGGACAAA 59.720 33.333 0.00 0.00 35.31 2.83
5359 5750 7.375017 CGAAGTAGTTGTTTAATGTGGACAAAC 59.625 37.037 0.00 0.00 35.31 2.93
5360 5751 6.721321 AGTAGTTGTTTAATGTGGACAAACG 58.279 36.000 0.00 0.00 35.31 3.60
5361 5752 4.356289 AGTTGTTTAATGTGGACAAACGC 58.644 39.130 0.00 0.00 35.31 4.84
5362 5753 4.106197 GTTGTTTAATGTGGACAAACGCA 58.894 39.130 0.00 0.00 35.31 5.24
5363 5754 4.371855 TGTTTAATGTGGACAAACGCAA 57.628 36.364 0.00 0.00 35.41 4.85
5364 5755 4.106197 TGTTTAATGTGGACAAACGCAAC 58.894 39.130 0.00 0.00 35.41 4.17
5365 5756 4.106197 GTTTAATGTGGACAAACGCAACA 58.894 39.130 0.00 0.00 34.14 3.33
5366 5757 2.202295 AATGTGGACAAACGCAACAC 57.798 45.000 0.00 0.00 34.14 3.32
5367 5758 0.383949 ATGTGGACAAACGCAACACC 59.616 50.000 0.00 0.00 34.14 4.16
5368 5759 0.678366 TGTGGACAAACGCAACACCT 60.678 50.000 0.00 0.00 0.00 4.00
5369 5760 0.248458 GTGGACAAACGCAACACCTG 60.248 55.000 0.00 0.00 0.00 4.00
5370 5761 0.393132 TGGACAAACGCAACACCTGA 60.393 50.000 0.00 0.00 0.00 3.86
5371 5762 0.028902 GGACAAACGCAACACCTGAC 59.971 55.000 0.00 0.00 0.00 3.51
5372 5763 1.014352 GACAAACGCAACACCTGACT 58.986 50.000 0.00 0.00 0.00 3.41
5373 5764 1.400494 GACAAACGCAACACCTGACTT 59.600 47.619 0.00 0.00 0.00 3.01
5374 5765 1.816224 ACAAACGCAACACCTGACTTT 59.184 42.857 0.00 0.00 0.00 2.66
5375 5766 3.011119 ACAAACGCAACACCTGACTTTA 58.989 40.909 0.00 0.00 0.00 1.85
5376 5767 3.630312 ACAAACGCAACACCTGACTTTAT 59.370 39.130 0.00 0.00 0.00 1.40
5377 5768 3.896648 AACGCAACACCTGACTTTATG 57.103 42.857 0.00 0.00 0.00 1.90
5378 5769 2.846193 ACGCAACACCTGACTTTATGT 58.154 42.857 0.00 0.00 0.00 2.29
5379 5770 3.211045 ACGCAACACCTGACTTTATGTT 58.789 40.909 0.00 0.00 35.69 2.71
5380 5771 3.250040 ACGCAACACCTGACTTTATGTTC 59.750 43.478 0.00 0.00 33.05 3.18
5381 5772 3.498397 CGCAACACCTGACTTTATGTTCT 59.502 43.478 0.00 0.00 33.05 3.01
5382 5773 4.688879 CGCAACACCTGACTTTATGTTCTA 59.311 41.667 0.00 0.00 33.05 2.10
5383 5774 5.178623 CGCAACACCTGACTTTATGTTCTAA 59.821 40.000 0.00 0.00 33.05 2.10
5384 5775 6.293190 CGCAACACCTGACTTTATGTTCTAAA 60.293 38.462 0.00 0.00 33.05 1.85
5385 5776 7.422399 GCAACACCTGACTTTATGTTCTAAAA 58.578 34.615 0.00 0.00 33.05 1.52
5386 5777 8.082242 GCAACACCTGACTTTATGTTCTAAAAT 58.918 33.333 0.00 0.00 33.05 1.82
5402 5793 9.715121 TGTTCTAAAATAATCCTGAGTTTACGT 57.285 29.630 0.00 0.00 0.00 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.602676 GGGGCTTAGGTGGCACTGA 61.603 63.158 18.45 2.50 33.03 3.41
2 3 3.717294 CGGGGCTTAGGTGGCACT 61.717 66.667 18.45 6.21 33.39 4.40
4 5 4.028490 CACGGGGCTTAGGTGGCA 62.028 66.667 0.00 0.00 0.00 4.92
5 6 3.562732 AACACGGGGCTTAGGTGGC 62.563 63.158 0.00 0.00 36.02 5.01
7 8 0.536460 AACAACACGGGGCTTAGGTG 60.536 55.000 0.00 0.00 37.67 4.00
9 10 1.862602 GCAACAACACGGGGCTTAGG 61.863 60.000 0.00 0.00 0.00 2.69
10 11 1.579429 GCAACAACACGGGGCTTAG 59.421 57.895 0.00 0.00 0.00 2.18
11 12 1.899534 GGCAACAACACGGGGCTTA 60.900 57.895 0.00 0.00 0.00 3.09
12 13 3.223589 GGCAACAACACGGGGCTT 61.224 61.111 0.00 0.00 0.00 4.35
15 16 2.835431 TTGGGCAACAACACGGGG 60.835 61.111 0.00 0.00 33.18 5.73
23 24 1.327303 GACAATGGACTTGGGCAACA 58.673 50.000 0.00 0.00 39.30 3.33
25 26 0.179004 ACGACAATGGACTTGGGCAA 60.179 50.000 0.00 0.00 39.30 4.52
30 31 0.999406 CGCCTACGACAATGGACTTG 59.001 55.000 0.00 0.00 43.93 3.16
37 38 1.064296 CGAGAGCGCCTACGACAAT 59.936 57.895 2.29 0.00 43.93 2.71
61 62 3.357079 GGTTGGCACCGACAGCTG 61.357 66.667 13.48 13.48 31.60 4.24
69 70 3.615709 GTGGGCTTGGTTGGCACC 61.616 66.667 0.00 0.00 44.56 5.01
96 97 1.080974 GCTCTGCAACAAAGCGCAT 60.081 52.632 11.47 0.00 37.54 4.73
106 107 2.594303 CCAACCGGTGCTCTGCAA 60.594 61.111 8.52 0.00 41.47 4.08
115 116 3.264845 AATGAGGGCCCAACCGGT 61.265 61.111 27.56 0.00 40.62 5.28
121 122 3.407967 GACCGGAATGAGGGCCCA 61.408 66.667 27.56 3.72 0.00 5.36
123 124 2.190578 CAGACCGGAATGAGGGCC 59.809 66.667 9.46 0.00 37.55 5.80
127 128 2.202932 CGCCCAGACCGGAATGAG 60.203 66.667 9.46 0.00 36.56 2.90
147 155 4.758251 TCGCCATGAGCACACCGG 62.758 66.667 0.00 0.00 44.04 5.28
156 164 0.602638 AACGAAGCAACTCGCCATGA 60.603 50.000 0.00 0.00 44.04 3.07
162 170 0.784778 GACCTCAACGAAGCAACTCG 59.215 55.000 0.00 1.82 44.50 4.18
170 178 1.669440 CCCCGAAGACCTCAACGAA 59.331 57.895 0.00 0.00 0.00 3.85
172 180 1.823169 TTCCCCCGAAGACCTCAACG 61.823 60.000 0.00 0.00 0.00 4.10
186 195 4.793201 AGCTAGATTACAATTGGTTCCCC 58.207 43.478 10.83 0.00 0.00 4.81
187 196 6.775594 AAAGCTAGATTACAATTGGTTCCC 57.224 37.500 10.83 0.00 0.00 3.97
222 231 7.116075 AGGTCCATATAAAATAGCACAACACA 58.884 34.615 0.00 0.00 0.00 3.72
225 234 7.996385 ACAAGGTCCATATAAAATAGCACAAC 58.004 34.615 0.00 0.00 0.00 3.32
226 235 7.831690 TGACAAGGTCCATATAAAATAGCACAA 59.168 33.333 0.00 0.00 0.00 3.33
241 250 7.390440 CACTAGTTGAATTTATGACAAGGTCCA 59.610 37.037 0.00 0.00 0.00 4.02
269 278 2.032302 CGATCAGACGGGAACTCACTAG 59.968 54.545 0.00 0.00 0.00 2.57
275 284 4.730949 TTATTTCGATCAGACGGGAACT 57.269 40.909 0.00 0.00 0.00 3.01
277 286 6.995511 AAAATTATTTCGATCAGACGGGAA 57.004 33.333 0.00 0.00 0.00 3.97
282 292 7.912383 TCCGGTAAAAATTATTTCGATCAGAC 58.088 34.615 0.00 0.00 0.00 3.51
286 296 8.557029 ACAGATCCGGTAAAAATTATTTCGATC 58.443 33.333 0.00 0.00 0.00 3.69
304 314 1.590238 GCATCAGACGAAACAGATCCG 59.410 52.381 0.00 0.00 0.00 4.18
317 327 1.067416 GATACCGCGTGGCATCAGA 59.933 57.895 21.03 0.00 37.87 3.27
334 344 3.691575 TCGCCCTAAAATGGATTTGTGA 58.308 40.909 0.00 0.00 32.27 3.58
357 367 3.133542 GCCCCTACGAAAACAGTATAGGT 59.866 47.826 0.00 0.00 32.05 3.08
359 369 4.395959 TGCCCCTACGAAAACAGTATAG 57.604 45.455 0.00 0.00 0.00 1.31
371 381 0.455972 CAAAAACGCATGCCCCTACG 60.456 55.000 13.15 0.00 0.00 3.51
391 401 9.730705 AACTTTAAACAACTCTAGGTTATACCC 57.269 33.333 0.00 0.00 39.75 3.69
480 490 8.812329 GCACTGATTAGATAAGTTCACTGTAAG 58.188 37.037 0.00 0.00 42.29 2.34
500 517 1.260544 TCTTCTAGCTGCTGCACTGA 58.739 50.000 18.42 9.37 42.74 3.41
539 559 3.026630 TCCGAGAGTTTGTTACAGCTG 57.973 47.619 13.48 13.48 0.00 4.24
657 694 2.291043 GGCTGGTCTCGGGAGGAAA 61.291 63.158 0.00 0.00 0.00 3.13
709 754 1.066215 GCAGGTGGGCTTTTATTTGGG 60.066 52.381 0.00 0.00 0.00 4.12
1050 1114 2.151202 GCGTCCAGAATGTTTTGAGGA 58.849 47.619 0.00 0.00 0.00 3.71
1134 1198 3.006756 GCAGTAGAGCTGGTGCGGA 62.007 63.158 0.00 0.00 45.14 5.54
1326 1396 3.052620 CTCGATCTCCGGCGTGTGT 62.053 63.158 6.01 0.00 39.14 3.72
1743 1813 4.980805 TGTTCGGTGGCTCGGTGC 62.981 66.667 0.00 0.00 41.94 5.01
1744 1814 2.989055 AAGTGTTCGGTGGCTCGGTG 62.989 60.000 1.57 0.00 0.00 4.94
1745 1815 2.710724 GAAGTGTTCGGTGGCTCGGT 62.711 60.000 1.57 0.00 0.00 4.69
1746 1816 2.027625 GAAGTGTTCGGTGGCTCGG 61.028 63.158 1.57 0.00 0.00 4.63
1747 1817 1.006102 AGAAGTGTTCGGTGGCTCG 60.006 57.895 0.00 0.00 34.02 5.03
1748 1818 1.009389 CGAGAAGTGTTCGGTGGCTC 61.009 60.000 0.00 0.00 34.56 4.70
1749 1819 1.006102 CGAGAAGTGTTCGGTGGCT 60.006 57.895 0.00 0.00 34.56 4.75
1750 1820 2.668280 GCGAGAAGTGTTCGGTGGC 61.668 63.158 0.00 0.00 38.45 5.01
1760 1830 1.625818 AGGAGAATTGTGGCGAGAAGT 59.374 47.619 0.00 0.00 0.00 3.01
1781 1851 1.199097 CAAACACCAGTCGGGCATTAC 59.801 52.381 0.00 0.00 42.05 1.89
2211 2291 2.657620 GATCGCCCGCGTTAGACC 60.658 66.667 4.92 0.00 40.74 3.85
2374 2454 0.108615 CGCGGATGACTCCTTTCTGT 60.109 55.000 0.00 0.00 39.65 3.41
2443 2523 0.941542 CGGGCTGTTTGAACTCGAAA 59.058 50.000 0.00 0.00 0.00 3.46
2640 2749 4.525912 AGGCAAATCCTTCACACAATTC 57.474 40.909 0.00 0.00 44.75 2.17
2690 2804 2.881074 CGACGAACAAGAGATCACCAT 58.119 47.619 0.00 0.00 0.00 3.55
2877 2995 2.194597 GTGGGATTGGGCGCCATA 59.805 61.111 30.85 16.13 31.53 2.74
2882 3000 2.359354 TGTTCGTGGGATTGGGCG 60.359 61.111 0.00 0.00 0.00 6.13
2930 3048 5.708697 TGAACGACCTTCTCATACTAGAACA 59.291 40.000 0.00 0.00 32.18 3.18
2931 3049 6.192234 TGAACGACCTTCTCATACTAGAAC 57.808 41.667 0.00 0.00 32.18 3.01
2934 3052 7.009631 CACAATTGAACGACCTTCTCATACTAG 59.990 40.741 13.59 0.00 0.00 2.57
2935 3053 6.811665 CACAATTGAACGACCTTCTCATACTA 59.188 38.462 13.59 0.00 0.00 1.82
2936 3054 5.639506 CACAATTGAACGACCTTCTCATACT 59.360 40.000 13.59 0.00 0.00 2.12
2947 3065 6.915843 ACATTTTTCTACCACAATTGAACGAC 59.084 34.615 13.59 0.00 0.00 4.34
2949 3067 6.143758 CCACATTTTTCTACCACAATTGAACG 59.856 38.462 13.59 1.03 0.00 3.95
2959 3178 3.806949 AGCCTCCACATTTTTCTACCA 57.193 42.857 0.00 0.00 0.00 3.25
3584 3809 4.215349 GCACTGATGGCAGGTCTC 57.785 61.111 0.00 0.00 46.60 3.36
3714 3940 9.262358 CCAAGGAAGAGCTACACTATTTTATAC 57.738 37.037 0.00 0.00 27.34 1.47
3715 3941 7.931948 GCCAAGGAAGAGCTACACTATTTTATA 59.068 37.037 0.00 0.00 27.34 0.98
3716 3942 6.768381 GCCAAGGAAGAGCTACACTATTTTAT 59.232 38.462 0.00 0.00 27.34 1.40
3717 3943 6.113411 GCCAAGGAAGAGCTACACTATTTTA 58.887 40.000 0.00 0.00 27.34 1.52
3718 3944 4.944317 GCCAAGGAAGAGCTACACTATTTT 59.056 41.667 0.00 0.00 27.34 1.82
4157 4424 3.692406 GGCGAGAAGACCACGGGT 61.692 66.667 0.00 0.00 39.44 5.28
4447 4717 3.973516 CGCCGCGTGCCTATAGGA 61.974 66.667 23.61 4.91 37.39 2.94
4448 4718 3.898627 CTCGCCGCGTGCCTATAGG 62.899 68.421 15.01 15.01 36.24 2.57
4449 4719 2.429236 CTCGCCGCGTGCCTATAG 60.429 66.667 13.39 0.00 36.24 1.31
4617 4891 6.691508 TCTTTTCTCGAGTCATTTCATCTCA 58.308 36.000 13.13 0.00 0.00 3.27
4732 5006 0.106149 ACCACAAGAACACGACTCCC 59.894 55.000 0.00 0.00 0.00 4.30
4803 5082 5.112686 AGAACGCATGAAGAAGAATAGTCC 58.887 41.667 0.00 0.00 0.00 3.85
4866 5145 0.798776 CCATCACAGGCTGTCGAAAC 59.201 55.000 19.13 0.00 0.00 2.78
4875 5154 4.357918 ACCTATCATTACCATCACAGGC 57.642 45.455 0.00 0.00 0.00 4.85
4925 5231 1.405821 ACTACGAAATGGGCGAGAGAG 59.594 52.381 0.00 0.00 0.00 3.20
4926 5232 1.471119 ACTACGAAATGGGCGAGAGA 58.529 50.000 0.00 0.00 0.00 3.10
4928 5234 2.357009 GAGTACTACGAAATGGGCGAGA 59.643 50.000 0.00 0.00 0.00 4.04
4929 5235 2.098607 TGAGTACTACGAAATGGGCGAG 59.901 50.000 0.00 0.00 0.00 5.03
4947 5325 3.440173 ACTTGAAACATTACCCGCATGAG 59.560 43.478 0.00 0.00 0.00 2.90
4972 5359 3.492482 CCAACGAATGCTTTCCTTTGGTT 60.492 43.478 21.34 11.74 37.05 3.67
4984 5371 9.630098 ATTGATTATAAATCATCCAACGAATGC 57.370 29.630 3.34 0.00 0.00 3.56
5055 5442 7.282450 GGATCAATAAACCAAGACGAAGGTAAT 59.718 37.037 0.00 0.00 37.07 1.89
5057 5444 6.070424 AGGATCAATAAACCAAGACGAAGGTA 60.070 38.462 0.00 0.00 37.07 3.08
5060 5447 6.743575 AAGGATCAATAAACCAAGACGAAG 57.256 37.500 0.00 0.00 0.00 3.79
5062 5449 7.881232 ACTAAAAGGATCAATAAACCAAGACGA 59.119 33.333 0.00 0.00 0.00 4.20
5063 5450 8.040716 ACTAAAAGGATCAATAAACCAAGACG 57.959 34.615 0.00 0.00 0.00 4.18
5251 5638 2.158842 TGGTCCCCTTTTGCAATTTGTG 60.159 45.455 0.00 0.00 0.00 3.33
5252 5639 2.122768 TGGTCCCCTTTTGCAATTTGT 58.877 42.857 0.00 0.00 0.00 2.83
5253 5640 2.926778 TGGTCCCCTTTTGCAATTTG 57.073 45.000 0.00 0.00 0.00 2.32
5254 5641 5.574970 TTATTGGTCCCCTTTTGCAATTT 57.425 34.783 0.00 0.00 0.00 1.82
5255 5642 5.073008 ACTTTATTGGTCCCCTTTTGCAATT 59.927 36.000 0.00 0.00 0.00 2.32
5256 5643 4.597075 ACTTTATTGGTCCCCTTTTGCAAT 59.403 37.500 0.00 0.00 0.00 3.56
5257 5644 3.970640 ACTTTATTGGTCCCCTTTTGCAA 59.029 39.130 0.00 0.00 0.00 4.08
5258 5645 3.582164 ACTTTATTGGTCCCCTTTTGCA 58.418 40.909 0.00 0.00 0.00 4.08
5259 5646 4.159693 CCTACTTTATTGGTCCCCTTTTGC 59.840 45.833 0.00 0.00 0.00 3.68
5260 5647 5.576128 TCCTACTTTATTGGTCCCCTTTTG 58.424 41.667 0.00 0.00 0.00 2.44
5261 5648 5.871324 TCCTACTTTATTGGTCCCCTTTT 57.129 39.130 0.00 0.00 0.00 2.27
5262 5649 5.340863 CCATCCTACTTTATTGGTCCCCTTT 60.341 44.000 0.00 0.00 0.00 3.11
5263 5650 4.168088 CCATCCTACTTTATTGGTCCCCTT 59.832 45.833 0.00 0.00 0.00 3.95
5264 5651 3.722101 CCATCCTACTTTATTGGTCCCCT 59.278 47.826 0.00 0.00 0.00 4.79
5265 5652 3.720002 TCCATCCTACTTTATTGGTCCCC 59.280 47.826 0.00 0.00 0.00 4.81
5266 5653 5.163088 ACATCCATCCTACTTTATTGGTCCC 60.163 44.000 0.00 0.00 0.00 4.46
5267 5654 5.941788 ACATCCATCCTACTTTATTGGTCC 58.058 41.667 0.00 0.00 0.00 4.46
5268 5655 7.736893 ACTACATCCATCCTACTTTATTGGTC 58.263 38.462 0.00 0.00 0.00 4.02
5269 5656 7.691993 ACTACATCCATCCTACTTTATTGGT 57.308 36.000 0.00 0.00 0.00 3.67
5270 5657 8.314751 CCTACTACATCCATCCTACTTTATTGG 58.685 40.741 0.00 0.00 0.00 3.16
5271 5658 8.871125 ACCTACTACATCCATCCTACTTTATTG 58.129 37.037 0.00 0.00 0.00 1.90
5272 5659 9.091220 GACCTACTACATCCATCCTACTTTATT 57.909 37.037 0.00 0.00 0.00 1.40
5273 5660 7.674772 GGACCTACTACATCCATCCTACTTTAT 59.325 40.741 0.00 0.00 32.35 1.40
5274 5661 7.008941 GGACCTACTACATCCATCCTACTTTA 58.991 42.308 0.00 0.00 32.35 1.85
5275 5662 5.839606 GGACCTACTACATCCATCCTACTTT 59.160 44.000 0.00 0.00 32.35 2.66
5276 5663 5.136392 AGGACCTACTACATCCATCCTACTT 59.864 44.000 0.00 0.00 33.29 2.24
5277 5664 4.670727 AGGACCTACTACATCCATCCTACT 59.329 45.833 0.00 0.00 33.29 2.57
5278 5665 5.000570 AGGACCTACTACATCCATCCTAC 57.999 47.826 0.00 0.00 33.29 3.18
5279 5666 6.791847 TTAGGACCTACTACATCCATCCTA 57.208 41.667 0.00 0.00 36.50 2.94
5280 5667 5.681494 TTAGGACCTACTACATCCATCCT 57.319 43.478 0.00 0.00 38.61 3.24
5281 5668 6.742559 TTTTAGGACCTACTACATCCATCC 57.257 41.667 0.00 0.00 34.73 3.51
5282 5669 9.091220 AGTATTTTAGGACCTACTACATCCATC 57.909 37.037 0.00 0.00 34.73 3.51
5283 5670 9.091220 GAGTATTTTAGGACCTACTACATCCAT 57.909 37.037 0.00 0.00 34.73 3.41
5284 5671 8.063153 TGAGTATTTTAGGACCTACTACATCCA 58.937 37.037 0.00 2.10 34.73 3.41
5285 5672 8.358895 GTGAGTATTTTAGGACCTACTACATCC 58.641 40.741 0.00 0.00 0.00 3.51
5286 5673 8.910944 TGTGAGTATTTTAGGACCTACTACATC 58.089 37.037 0.00 4.82 0.00 3.06
5287 5674 8.834004 TGTGAGTATTTTAGGACCTACTACAT 57.166 34.615 0.00 0.00 0.00 2.29
5288 5675 8.834004 ATGTGAGTATTTTAGGACCTACTACA 57.166 34.615 0.00 3.99 0.00 2.74
5354 5745 1.459450 AAGTCAGGTGTTGCGTTTGT 58.541 45.000 0.00 0.00 0.00 2.83
5355 5746 2.559998 AAAGTCAGGTGTTGCGTTTG 57.440 45.000 0.00 0.00 0.00 2.93
5356 5747 3.630312 ACATAAAGTCAGGTGTTGCGTTT 59.370 39.130 0.00 0.00 0.00 3.60
5357 5748 3.211045 ACATAAAGTCAGGTGTTGCGTT 58.789 40.909 0.00 0.00 0.00 4.84
5358 5749 2.846193 ACATAAAGTCAGGTGTTGCGT 58.154 42.857 0.00 0.00 0.00 5.24
5359 5750 3.498397 AGAACATAAAGTCAGGTGTTGCG 59.502 43.478 0.00 0.00 35.15 4.85
5360 5751 6.554334 TTAGAACATAAAGTCAGGTGTTGC 57.446 37.500 0.00 0.00 35.15 4.17
5376 5767 9.715121 ACGTAAACTCAGGATTATTTTAGAACA 57.285 29.630 0.00 0.00 0.00 3.18
5389 5780 9.374838 GGATTATTTTAGAACGTAAACTCAGGA 57.625 33.333 0.00 0.00 0.00 3.86
5390 5781 9.379791 AGGATTATTTTAGAACGTAAACTCAGG 57.620 33.333 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.