Multiple sequence alignment - TraesCS5B01G171800

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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 TraesCS5B01G171800 chr5B 100.000 5249 0 0 1 5249 316368124 316373372 0.000000e+00 9694.0
1 TraesCS5B01G171800 chr5B 85.821 268 23 4 1848 2110 316369840 316370097 2.410000e-68 270.0
2 TraesCS5B01G171800 chr5B 85.821 268 23 4 1717 1974 316369971 316370233 2.410000e-68 270.0
3 TraesCS5B01G171800 chr5D 95.284 5132 160 35 1 5095 278278466 278283552 0.000000e+00 8061.0
4 TraesCS5B01G171800 chr5D 88.593 263 23 2 1719 1974 278280315 278280577 3.950000e-81 313.0
5 TraesCS5B01G171800 chr5D 87.266 267 23 4 1849 2110 278280184 278280444 1.430000e-75 294.0
6 TraesCS5B01G171800 chr5D 88.618 123 12 1 1717 1837 278280446 278280568 1.180000e-31 148.0
7 TraesCS5B01G171800 chr5A 94.480 5127 155 56 1 5065 367598047 367603107 0.000000e+00 7782.0
8 TraesCS5B01G171800 chr5A 88.679 265 23 2 1717 1974 367599889 367600153 3.050000e-82 316.0
9 TraesCS5B01G171800 chr5A 88.060 268 22 3 1848 2110 367599758 367600020 5.110000e-80 309.0
10 TraesCS5B01G171800 chr5A 88.618 123 12 1 1717 1837 367600022 367600144 1.180000e-31 148.0
11 TraesCS5B01G171800 chr5A 86.029 136 16 3 5115 5249 584945963 584946096 5.480000e-30 143.0
12 TraesCS5B01G171800 chr5A 82.353 136 21 3 5114 5249 562410978 562411110 1.190000e-21 115.0
13 TraesCS5B01G171800 chr5A 91.892 74 6 0 5065 5138 367613823 367613896 2.590000e-18 104.0
14 TraesCS5B01G171800 chr4B 82.381 210 28 7 4683 4885 237949932 237949725 1.940000e-39 174.0
15 TraesCS5B01G171800 chr4B 77.707 157 28 7 4701 4853 631574532 631574379 7.240000e-14 89.8
16 TraesCS5B01G171800 chr3D 86.861 137 15 2 5115 5249 545256380 545256515 3.270000e-32 150.0
17 TraesCS5B01G171800 chr3D 86.131 137 15 2 5115 5249 6302708 6302574 1.520000e-30 145.0
18 TraesCS5B01G171800 chr3D 80.925 173 28 4 4691 4858 4870191 4870019 1.190000e-26 132.0
19 TraesCS5B01G171800 chr2B 80.000 210 32 9 4699 4901 755063241 755063035 4.240000e-31 147.0
20 TraesCS5B01G171800 chr1D 80.000 195 30 9 4680 4869 448243780 448243970 9.170000e-28 135.0
21 TraesCS5B01G171800 chr3A 82.963 135 17 5 5114 5245 370234474 370234605 3.320000e-22 117.0
22 TraesCS5B01G171800 chr3A 92.157 51 4 0 5114 5164 561242942 561242892 7.290000e-09 73.1
23 TraesCS5B01G171800 chr3A 92.157 51 4 0 5114 5164 561286312 561286262 7.290000e-09 73.1
24 TraesCS5B01G171800 chr3A 83.871 62 5 1 4794 4855 16146100 16146156 3.000000e-03 54.7
25 TraesCS5B01G171800 chr7A 82.963 135 16 3 5115 5249 77168771 77168644 1.190000e-21 115.0
26 TraesCS5B01G171800 chr1A 78.061 196 33 9 4680 4869 544128821 544129012 1.190000e-21 115.0
27 TraesCS5B01G171800 chr1B 87.629 97 12 0 5116 5212 181312524 181312620 4.300000e-21 113.0
28 TraesCS5B01G171800 chr4D 76.887 212 36 9 4684 4884 493335211 493335002 2.000000e-19 108.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G171800 chr5B 316368124 316373372 5248 False 3411.333333 9694 90.547333 1 5249 3 chr5B.!!$F1 5248
1 TraesCS5B01G171800 chr5D 278278466 278283552 5086 False 2204.000000 8061 89.940250 1 5095 4 chr5D.!!$F1 5094
2 TraesCS5B01G171800 chr5A 367598047 367603107 5060 False 2138.750000 7782 89.959250 1 5065 4 chr5A.!!$F4 5064

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
254 255 0.037447 GCAAGGCTGAAGAAGAGGGT 59.963 55.000 0.00 0.0 0.00 4.34 F
1166 1189 0.110486 AAGACGCCCCTTGTCATTGT 59.890 50.000 0.00 0.0 38.83 2.71 F
1200 1223 0.456995 CGCTCGAGGTGAAGAAGTCC 60.457 60.000 15.58 0.0 0.00 3.85 F
1290 1313 1.219393 GTTTGGAGCCGAGGAGGAG 59.781 63.158 0.00 0.0 45.00 3.69 F
2430 2468 1.308998 CCATTCAAGTATGACGGCCC 58.691 55.000 0.00 0.0 34.61 5.80 F
3439 3494 0.458543 TCGTCGCTCTGATTGAAGGC 60.459 55.000 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2176 2214 0.038166 TCAACATCCTTCCCAGCCAC 59.962 55.000 0.00 0.00 0.00 5.01 R
2842 2893 2.090267 ACTAGATGAGCTTCCCTGGGAT 60.090 50.000 17.93 0.55 0.00 3.85 R
2956 3009 3.343941 ACATAACATGCGTACCCAACT 57.656 42.857 0.00 0.00 0.00 3.16 R
3222 3277 3.664107 TGAGACAGCATCAACCAACTAC 58.336 45.455 0.00 0.00 0.00 2.73 R
3862 3920 0.476771 GGAAGTGTTCAACAGGGGGA 59.523 55.000 0.00 0.00 0.00 4.81 R
5126 5213 1.376553 GTGAAGCACCCAGGAGCTC 60.377 63.158 9.15 4.71 40.95 4.09 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
59 60 3.814615 ATGGCCGGCAGCGTGATAG 62.815 63.158 30.85 0.00 45.17 2.08
74 75 2.608090 GTGATAGCGGAAAACCTAGTGC 59.392 50.000 0.00 0.00 0.00 4.40
109 110 1.067354 ACAGTCCGAAATGTACCGACC 60.067 52.381 0.00 0.00 0.00 4.79
130 131 3.568007 CCTCTCCAATCTAAGACTCCTCG 59.432 52.174 0.00 0.00 0.00 4.63
191 192 2.005451 CTTCCAGTTCAGCCGATTCAG 58.995 52.381 0.00 0.00 0.00 3.02
198 199 3.470888 AGCCGATTCAGGGACCCG 61.471 66.667 4.40 0.00 0.00 5.28
247 248 2.669569 GGTGCGCAAGGCTGAAGA 60.670 61.111 14.00 0.00 44.05 2.87
249 250 1.208614 GTGCGCAAGGCTGAAGAAG 59.791 57.895 14.00 0.00 44.05 2.85
250 251 1.071299 TGCGCAAGGCTGAAGAAGA 59.929 52.632 8.16 0.00 44.05 2.87
254 255 0.037447 GCAAGGCTGAAGAAGAGGGT 59.963 55.000 0.00 0.00 0.00 4.34
278 279 3.500471 GGGAGGAAAAGGAACTCACCATT 60.500 47.826 0.00 0.00 38.49 3.16
288 289 3.433598 GGAACTCACCATTGCAGGCTATA 60.434 47.826 0.00 0.00 0.00 1.31
431 433 2.740447 GTCGGTTTCGGTTTGCTTCTAT 59.260 45.455 0.00 0.00 36.95 1.98
434 439 4.082081 TCGGTTTCGGTTTGCTTCTATAGA 60.082 41.667 0.00 0.00 36.95 1.98
441 446 3.383825 GGTTTGCTTCTATAGACGAGGGA 59.616 47.826 10.29 0.00 0.00 4.20
456 461 3.053896 GGAGCGTTTTGGACCCCG 61.054 66.667 0.00 0.00 0.00 5.73
457 462 3.053896 GAGCGTTTTGGACCCCGG 61.054 66.667 0.00 0.00 0.00 5.73
591 606 6.718912 TCATTCCATCGTCATATTCTCTCTCT 59.281 38.462 0.00 0.00 0.00 3.10
592 607 6.567687 TTCCATCGTCATATTCTCTCTCTC 57.432 41.667 0.00 0.00 0.00 3.20
593 608 5.875224 TCCATCGTCATATTCTCTCTCTCT 58.125 41.667 0.00 0.00 0.00 3.10
594 609 5.937540 TCCATCGTCATATTCTCTCTCTCTC 59.062 44.000 0.00 0.00 0.00 3.20
612 633 2.690881 CTCCCCGATTCCCCACCA 60.691 66.667 0.00 0.00 0.00 4.17
635 656 1.185315 CCCATCGCACCAAATTCCTT 58.815 50.000 0.00 0.00 0.00 3.36
888 909 7.824779 GGAAGTAAATAAATAGGGATGATCGCT 59.175 37.037 16.41 16.41 42.60 4.93
943 966 5.981915 GGATTATGTTCCGTAGACCTGTTAC 59.018 44.000 0.00 0.00 0.00 2.50
964 987 0.749649 TTTTGTGTGACCACCATGGC 59.250 50.000 13.04 0.00 42.67 4.40
1166 1189 0.110486 AAGACGCCCCTTGTCATTGT 59.890 50.000 0.00 0.00 38.83 2.71
1198 1221 1.587054 CCGCTCGAGGTGAAGAAGT 59.413 57.895 15.58 0.00 0.00 3.01
1200 1223 0.456995 CGCTCGAGGTGAAGAAGTCC 60.457 60.000 15.58 0.00 0.00 3.85
1290 1313 1.219393 GTTTGGAGCCGAGGAGGAG 59.781 63.158 0.00 0.00 45.00 3.69
1428 1451 8.830580 TCATTTGCTGCTATTACTGTATTTCTC 58.169 33.333 0.00 0.00 0.00 2.87
1478 1501 3.046374 CCCTTACCATGGGTAGTAGCTT 58.954 50.000 18.09 0.00 39.52 3.74
1494 1517 4.876679 AGTAGCTTTAAGGGCTTCGAATTC 59.123 41.667 0.00 0.00 40.74 2.17
1545 1570 6.172630 TGTTGTATCTTCTATGCACATGTGT 58.827 36.000 26.01 10.78 0.00 3.72
1546 1571 6.654582 TGTTGTATCTTCTATGCACATGTGTT 59.345 34.615 26.01 16.46 0.00 3.32
1789 1817 3.507233 TGCCTAGCCATGCATAAATTAGC 59.493 43.478 0.00 0.00 31.31 3.09
1842 1870 4.214971 GCATCTAATATGCTCCAACTGGTG 59.785 45.833 2.78 0.00 41.52 4.17
1937 1975 5.755375 AGTAGCTTGTCAAATATGGACATCG 59.245 40.000 10.33 7.06 44.11 3.84
1958 1996 3.306088 CGGTCCTCGGCATCTGTAATATT 60.306 47.826 0.00 0.00 34.75 1.28
2176 2214 7.007546 GCAGCTTATAGATTAACTGTATCGACG 59.992 40.741 0.00 0.00 0.00 5.12
2430 2468 1.308998 CCATTCAAGTATGACGGCCC 58.691 55.000 0.00 0.00 34.61 5.80
2448 2486 3.016736 GCCCTAGCTTTGCTTATCAACA 58.983 45.455 0.00 0.00 40.44 3.33
2483 2524 9.520204 AAATGCTTACATTAAATTTGGAGATCG 57.480 29.630 0.00 0.00 45.90 3.69
2484 2525 7.026631 TGCTTACATTAAATTTGGAGATCGG 57.973 36.000 0.00 0.00 0.00 4.18
2644 2695 3.489416 GGCTTCAAAAATTGGTTCGTGTC 59.511 43.478 0.00 0.00 0.00 3.67
2645 2696 4.109050 GCTTCAAAAATTGGTTCGTGTCA 58.891 39.130 0.00 0.00 0.00 3.58
2646 2697 4.207019 GCTTCAAAAATTGGTTCGTGTCAG 59.793 41.667 0.00 0.00 0.00 3.51
2647 2698 5.568685 TTCAAAAATTGGTTCGTGTCAGA 57.431 34.783 0.00 0.00 0.00 3.27
2706 2757 6.301486 TCTATGCAAGTTCTGATGGCATATT 58.699 36.000 0.00 0.00 43.91 1.28
2824 2875 2.154462 CCTGCTTCCGCTTTATATGGG 58.846 52.381 0.00 0.00 36.97 4.00
2888 2941 5.881923 TGGTAAGTTACTTGAGGTGTCTT 57.118 39.130 12.65 0.00 0.00 3.01
2890 2943 6.053005 TGGTAAGTTACTTGAGGTGTCTTTG 58.947 40.000 12.65 0.00 0.00 2.77
2891 2944 5.049612 GGTAAGTTACTTGAGGTGTCTTTGC 60.050 44.000 12.65 0.00 0.00 3.68
2956 3009 5.076182 TGATTGCTTCCACACTATTCCAAA 58.924 37.500 0.00 0.00 0.00 3.28
2974 3027 3.442273 CCAAAGTTGGGTACGCATGTTAT 59.558 43.478 13.97 0.00 44.70 1.89
3008 3061 1.664965 GTTCGCAGTTCTGCTCCGT 60.665 57.895 20.12 0.00 28.89 4.69
3011 3064 2.375766 CGCAGTTCTGCTCCGTCAC 61.376 63.158 20.12 0.00 0.00 3.67
3068 3123 5.596772 TGGCATGCTCTGTACTGTAGTATTA 59.403 40.000 18.92 0.00 32.54 0.98
3073 3128 8.837389 CATGCTCTGTACTGTAGTATTAGTGTA 58.163 37.037 0.00 0.18 32.54 2.90
3082 3137 8.991783 ACTGTAGTATTAGTGTAGCCTAATGA 57.008 34.615 4.18 0.00 37.97 2.57
3394 3449 1.496429 CCTCCATGCCTTATTCAGGGT 59.504 52.381 0.00 0.00 44.16 4.34
3395 3450 2.711009 CCTCCATGCCTTATTCAGGGTA 59.289 50.000 0.00 0.00 44.16 3.69
3396 3451 3.244700 CCTCCATGCCTTATTCAGGGTAG 60.245 52.174 0.00 0.00 44.16 3.18
3397 3452 2.711009 TCCATGCCTTATTCAGGGTAGG 59.289 50.000 0.00 0.00 44.16 3.18
3398 3453 2.224867 CCATGCCTTATTCAGGGTAGGG 60.225 54.545 0.00 0.00 44.16 3.53
3433 3488 5.351465 ACATTTATTGTTCGTCGCTCTGATT 59.649 36.000 0.00 0.00 33.74 2.57
3439 3494 0.458543 TCGTCGCTCTGATTGAAGGC 60.459 55.000 0.00 0.00 0.00 4.35
3671 3726 1.574263 GCTGGAGGGAAGGTTAGTCT 58.426 55.000 0.00 0.00 0.00 3.24
3750 3806 2.561478 TCTTACTTGGCCTGTTGGAC 57.439 50.000 3.32 0.00 43.36 4.02
3770 3826 9.880064 GTTGGACTCTCTTTTATAACAAGAAAC 57.120 33.333 9.74 7.46 29.74 2.78
3862 3920 0.820891 CATGCATTCCCGCTAGCCTT 60.821 55.000 9.66 0.00 0.00 4.35
3890 3948 0.249868 TGAACACTTCCGCTCAGTGG 60.250 55.000 0.00 0.00 45.20 4.00
4409 4473 7.156876 TGATTTATTCAGCAAGTAACTTGGG 57.843 36.000 0.00 0.00 41.31 4.12
4449 4513 1.078143 CTGGGGTTCTGCAGTAGCC 60.078 63.158 27.89 27.89 41.13 3.93
4501 4566 3.454371 ACTATGAATGTGTCCTACGGC 57.546 47.619 0.00 0.00 0.00 5.68
4557 4622 6.212589 TGGTGATGTATTTCTACCTCTGTTGA 59.787 38.462 0.00 0.00 32.68 3.18
4796 4867 7.719633 ACAAACATTACACTGTGATAACCTCTT 59.280 33.333 15.86 0.00 0.00 2.85
4906 4993 8.589338 AGTACAGAAGACACAATAAACTCAGAT 58.411 33.333 0.00 0.00 0.00 2.90
4920 5007 8.783660 ATAAACTCAGATGGATGGAGTAACTA 57.216 34.615 0.00 0.00 40.80 2.24
4924 5011 8.964533 ACTCAGATGGATGGAGTAACTATTAT 57.035 34.615 0.00 0.00 39.95 1.28
5006 5093 8.820933 ACTACGATGAATTGTATTGATGACTTG 58.179 33.333 0.00 0.00 0.00 3.16
5040 5127 2.503356 GTCATCTGAGGGGAGTGATGTT 59.497 50.000 0.00 0.00 37.93 2.71
5095 5182 7.795534 TGTTACTTTAACCACCCTATAGTGA 57.204 36.000 0.00 0.00 36.97 3.41
5096 5183 8.383374 TGTTACTTTAACCACCCTATAGTGAT 57.617 34.615 0.00 0.00 36.97 3.06
5097 5184 9.491406 TGTTACTTTAACCACCCTATAGTGATA 57.509 33.333 0.00 0.00 36.97 2.15
5105 5192 8.562949 AACCACCCTATAGTGATATAAACAGT 57.437 34.615 0.00 0.00 40.34 3.55
5106 5193 8.191534 ACCACCCTATAGTGATATAAACAGTC 57.808 38.462 0.00 0.00 40.34 3.51
5107 5194 7.787904 ACCACCCTATAGTGATATAAACAGTCA 59.212 37.037 0.00 0.00 40.34 3.41
5108 5195 8.307483 CCACCCTATAGTGATATAAACAGTCAG 58.693 40.741 0.00 0.00 40.34 3.51
5109 5196 8.307483 CACCCTATAGTGATATAAACAGTCAGG 58.693 40.741 0.00 0.00 40.34 3.86
5110 5197 8.011290 ACCCTATAGTGATATAAACAGTCAGGT 58.989 37.037 0.00 0.00 0.00 4.00
5111 5198 8.524487 CCCTATAGTGATATAAACAGTCAGGTC 58.476 40.741 0.00 0.00 0.00 3.85
5112 5199 9.303116 CCTATAGTGATATAAACAGTCAGGTCT 57.697 37.037 0.00 0.00 0.00 3.85
5116 5203 8.824756 AGTGATATAAACAGTCAGGTCTAGAA 57.175 34.615 0.00 0.00 0.00 2.10
5117 5204 9.256228 AGTGATATAAACAGTCAGGTCTAGAAA 57.744 33.333 0.00 0.00 0.00 2.52
5118 5205 9.871238 GTGATATAAACAGTCAGGTCTAGAAAA 57.129 33.333 0.00 0.00 0.00 2.29
5123 5210 7.964604 AAACAGTCAGGTCTAGAAAATACAC 57.035 36.000 0.00 0.00 0.00 2.90
5124 5211 6.665992 ACAGTCAGGTCTAGAAAATACACA 57.334 37.500 0.00 0.00 0.00 3.72
5125 5212 6.692486 ACAGTCAGGTCTAGAAAATACACAG 58.308 40.000 0.00 0.00 0.00 3.66
5126 5213 6.102663 CAGTCAGGTCTAGAAAATACACAGG 58.897 44.000 0.00 0.00 0.00 4.00
5127 5214 6.017192 AGTCAGGTCTAGAAAATACACAGGA 58.983 40.000 0.00 0.00 0.00 3.86
5128 5215 6.153680 AGTCAGGTCTAGAAAATACACAGGAG 59.846 42.308 0.00 0.00 0.00 3.69
5129 5216 5.105310 TCAGGTCTAGAAAATACACAGGAGC 60.105 44.000 0.00 0.00 0.00 4.70
5130 5217 5.026790 AGGTCTAGAAAATACACAGGAGCT 58.973 41.667 0.00 0.00 0.00 4.09
5131 5218 5.128008 AGGTCTAGAAAATACACAGGAGCTC 59.872 44.000 4.71 4.71 0.00 4.09
5132 5219 5.353111 GTCTAGAAAATACACAGGAGCTCC 58.647 45.833 26.22 26.22 0.00 4.70
5141 5228 2.204059 AGGAGCTCCTGGGTGCTT 60.204 61.111 34.74 7.88 46.55 3.91
5142 5229 2.270527 GGAGCTCCTGGGTGCTTC 59.729 66.667 26.25 11.19 43.75 3.86
5143 5230 2.596851 GGAGCTCCTGGGTGCTTCA 61.597 63.158 26.25 0.00 43.75 3.02
5144 5231 1.376553 GAGCTCCTGGGTGCTTCAC 60.377 63.158 15.86 2.24 43.75 3.18
5145 5232 2.116983 GAGCTCCTGGGTGCTTCACA 62.117 60.000 15.86 0.00 43.75 3.58
5156 5243 3.838244 GTGCTTCACACCCCTATATGA 57.162 47.619 0.00 0.00 44.02 2.15
5157 5244 4.150897 GTGCTTCACACCCCTATATGAA 57.849 45.455 0.00 0.00 44.02 2.57
5158 5245 4.718961 GTGCTTCACACCCCTATATGAAT 58.281 43.478 0.00 0.00 44.02 2.57
5159 5246 5.865085 GTGCTTCACACCCCTATATGAATA 58.135 41.667 0.00 0.00 44.02 1.75
5160 5247 5.701290 GTGCTTCACACCCCTATATGAATAC 59.299 44.000 0.00 0.00 44.02 1.89
5161 5248 5.606749 TGCTTCACACCCCTATATGAATACT 59.393 40.000 0.00 0.00 31.00 2.12
5162 5249 6.785466 TGCTTCACACCCCTATATGAATACTA 59.215 38.462 0.00 0.00 31.00 1.82
5163 5250 7.291416 TGCTTCACACCCCTATATGAATACTAA 59.709 37.037 0.00 0.00 31.00 2.24
5164 5251 8.154856 GCTTCACACCCCTATATGAATACTAAA 58.845 37.037 0.00 0.00 31.00 1.85
5167 5254 9.166222 TCACACCCCTATATGAATACTAAATGT 57.834 33.333 0.00 0.00 0.00 2.71
5220 5307 9.918630 AACTGAAATTTGGAGATATCAAACTTG 57.081 29.630 5.32 0.00 37.00 3.16
5221 5308 8.526147 ACTGAAATTTGGAGATATCAAACTTGG 58.474 33.333 5.32 0.00 37.00 3.61
5222 5309 7.839907 TGAAATTTGGAGATATCAAACTTGGG 58.160 34.615 5.32 0.00 37.00 4.12
5223 5310 7.454380 TGAAATTTGGAGATATCAAACTTGGGT 59.546 33.333 5.32 0.00 37.00 4.51
5224 5311 7.797121 AATTTGGAGATATCAAACTTGGGTT 57.203 32.000 5.32 0.00 37.00 4.11
5225 5312 7.797121 ATTTGGAGATATCAAACTTGGGTTT 57.203 32.000 5.32 0.00 45.35 3.27
5226 5313 7.610580 TTTGGAGATATCAAACTTGGGTTTT 57.389 32.000 5.32 0.00 42.96 2.43
5227 5314 6.834168 TGGAGATATCAAACTTGGGTTTTC 57.166 37.500 5.32 0.00 42.96 2.29
5228 5315 6.310941 TGGAGATATCAAACTTGGGTTTTCA 58.689 36.000 5.32 0.00 42.96 2.69
5229 5316 6.780031 TGGAGATATCAAACTTGGGTTTTCAA 59.220 34.615 5.32 0.00 42.96 2.69
5230 5317 7.454380 TGGAGATATCAAACTTGGGTTTTCAAT 59.546 33.333 5.32 0.00 42.96 2.57
5231 5318 7.761249 GGAGATATCAAACTTGGGTTTTCAATG 59.239 37.037 5.32 0.00 42.96 2.82
5232 5319 8.193953 AGATATCAAACTTGGGTTTTCAATGT 57.806 30.769 5.32 0.00 42.96 2.71
5233 5320 9.308000 AGATATCAAACTTGGGTTTTCAATGTA 57.692 29.630 5.32 0.00 42.96 2.29
5236 5323 8.831715 ATCAAACTTGGGTTTTCAATGTATTC 57.168 30.769 0.00 0.00 42.96 1.75
5237 5324 7.213678 TCAAACTTGGGTTTTCAATGTATTCC 58.786 34.615 0.00 0.00 42.96 3.01
5238 5325 5.738619 ACTTGGGTTTTCAATGTATTCCC 57.261 39.130 0.00 0.00 0.00 3.97
5239 5326 4.219725 ACTTGGGTTTTCAATGTATTCCCG 59.780 41.667 0.00 0.00 36.53 5.14
5240 5327 3.768878 TGGGTTTTCAATGTATTCCCGT 58.231 40.909 0.00 0.00 36.53 5.28
5241 5328 3.508012 TGGGTTTTCAATGTATTCCCGTG 59.492 43.478 0.00 0.00 36.53 4.94
5242 5329 3.508402 GGGTTTTCAATGTATTCCCGTGT 59.492 43.478 0.00 0.00 0.00 4.49
5243 5330 4.481463 GGTTTTCAATGTATTCCCGTGTG 58.519 43.478 0.00 0.00 0.00 3.82
5244 5331 4.216687 GGTTTTCAATGTATTCCCGTGTGA 59.783 41.667 0.00 0.00 0.00 3.58
5245 5332 5.278561 GGTTTTCAATGTATTCCCGTGTGAA 60.279 40.000 0.00 0.00 0.00 3.18
5246 5333 6.210078 GTTTTCAATGTATTCCCGTGTGAAA 58.790 36.000 0.00 0.00 33.10 2.69
5247 5334 6.582677 TTTCAATGTATTCCCGTGTGAAAT 57.417 33.333 0.00 0.00 30.73 2.17
5248 5335 6.582677 TTCAATGTATTCCCGTGTGAAATT 57.417 33.333 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 2.396157 CCGGCACTAGGTTTTCCGC 61.396 63.158 0.00 0.00 46.35 5.54
74 75 2.622436 GACTGTGAATCTTCCTTCCGG 58.378 52.381 0.00 0.00 0.00 5.14
109 110 3.568007 CCGAGGAGTCTTAGATTGGAGAG 59.432 52.174 0.00 0.00 0.00 3.20
130 131 2.611224 CGAGGTAGTTGGGTTGTACACC 60.611 54.545 0.00 0.02 46.46 4.16
247 248 0.984995 CTTTTCCTCCCGACCCTCTT 59.015 55.000 0.00 0.00 0.00 2.85
249 250 0.908180 TCCTTTTCCTCCCGACCCTC 60.908 60.000 0.00 0.00 0.00 4.30
250 251 0.475048 TTCCTTTTCCTCCCGACCCT 60.475 55.000 0.00 0.00 0.00 4.34
254 255 1.346722 GTGAGTTCCTTTTCCTCCCGA 59.653 52.381 0.00 0.00 0.00 5.14
369 370 4.736896 GTCTCTCGGCGGGCGTTT 62.737 66.667 23.46 0.00 0.00 3.60
431 433 0.245539 CCAAAACGCTCCCTCGTCTA 59.754 55.000 0.00 0.00 42.46 2.59
434 439 1.301479 GTCCAAAACGCTCCCTCGT 60.301 57.895 0.00 0.00 45.58 4.18
441 446 4.653888 CCCGGGGTCCAAAACGCT 62.654 66.667 14.71 0.00 40.55 5.07
456 461 1.152673 CAATTCCTAGGCAGGCCCC 60.153 63.158 2.96 0.00 42.30 5.80
457 462 1.152673 CCAATTCCTAGGCAGGCCC 60.153 63.158 2.96 0.00 42.30 5.80
555 568 0.752658 ATGGAATGATGCCGACTCGA 59.247 50.000 0.00 0.00 0.00 4.04
591 606 2.285868 GGGGAATCGGGGAGGAGA 59.714 66.667 0.00 0.00 0.00 3.71
592 607 2.040884 TGGGGAATCGGGGAGGAG 60.041 66.667 0.00 0.00 0.00 3.69
593 608 2.366435 GTGGGGAATCGGGGAGGA 60.366 66.667 0.00 0.00 0.00 3.71
594 609 3.489513 GGTGGGGAATCGGGGAGG 61.490 72.222 0.00 0.00 0.00 4.30
612 633 0.541764 AATTTGGTGCGATGGGTGGT 60.542 50.000 0.00 0.00 0.00 4.16
824 845 2.112511 AGCCTCCCCCTCAGAAAAATTT 59.887 45.455 0.00 0.00 0.00 1.82
964 987 1.813513 AAGCTCCAATCAAGACACCG 58.186 50.000 0.00 0.00 0.00 4.94
1105 1128 1.825281 GCAGAGGAGACAGCACCAGT 61.825 60.000 0.00 0.00 0.00 4.00
1166 1189 3.294493 GCGGCCTCTTGTTTGCCA 61.294 61.111 0.00 0.00 45.63 4.92
1200 1223 4.796231 CCCGACAAGACCGAGCCG 62.796 72.222 0.00 0.00 0.00 5.52
1478 1501 4.280436 TGTCAGAATTCGAAGCCCTTAA 57.720 40.909 3.35 0.00 0.00 1.85
1519 1542 7.337689 ACACATGTGCATAGAAGATACAACATT 59.662 33.333 25.68 0.00 0.00 2.71
1545 1570 7.748691 TGAGACAATCTTGATCACAATTGAA 57.251 32.000 25.31 11.93 34.61 2.69
1546 1571 7.748691 TTGAGACAATCTTGATCACAATTGA 57.251 32.000 25.31 9.16 35.37 2.57
1789 1817 5.413833 ACTGAAGTCCATATTTGACAAGCTG 59.586 40.000 0.00 0.00 35.15 4.24
1937 1975 3.963428 ATATTACAGATGCCGAGGACC 57.037 47.619 0.00 0.00 0.00 4.46
2020 2058 2.305009 GATGGCTAGGCAAAAGCAGAT 58.695 47.619 24.12 3.49 41.93 2.90
2141 2179 7.939039 AGTTAATCTATAAGCTGCAGCCATAAA 59.061 33.333 34.39 19.06 43.38 1.40
2176 2214 0.038166 TCAACATCCTTCCCAGCCAC 59.962 55.000 0.00 0.00 0.00 5.01
2430 2468 7.928908 TTTTTGTGTTGATAAGCAAAGCTAG 57.071 32.000 0.00 0.00 38.25 3.42
2644 2695 8.950210 ACCAAAAGTAATGATATTGTCTGTCTG 58.050 33.333 0.00 0.00 0.00 3.51
2706 2757 9.823647 TTGAATTAACTGCATTTTACCAAGAAA 57.176 25.926 0.00 0.00 0.00 2.52
2842 2893 2.090267 ACTAGATGAGCTTCCCTGGGAT 60.090 50.000 17.93 0.55 0.00 3.85
2888 2941 3.486383 AGAAAAGGAAAGTGATCCGCAA 58.514 40.909 0.00 0.00 44.60 4.85
2890 2943 5.622770 TTAAGAAAAGGAAAGTGATCCGC 57.377 39.130 0.00 0.00 44.60 5.54
2891 2944 5.412904 AGCTTAAGAAAAGGAAAGTGATCCG 59.587 40.000 6.67 0.00 44.60 4.18
2956 3009 3.343941 ACATAACATGCGTACCCAACT 57.656 42.857 0.00 0.00 0.00 3.16
2974 3027 5.295787 ACTGCGAACTCAAGAAAACATTACA 59.704 36.000 0.00 0.00 0.00 2.41
3068 3123 7.071196 TGTCCATTCTATTCATTAGGCTACACT 59.929 37.037 0.00 0.00 0.00 3.55
3082 3137 9.182214 GGCACATCATAATATGTCCATTCTATT 57.818 33.333 0.00 0.00 38.01 1.73
3215 3270 6.913170 ACAGCATCAACCAACTACAATTTAG 58.087 36.000 0.00 0.00 0.00 1.85
3222 3277 3.664107 TGAGACAGCATCAACCAACTAC 58.336 45.455 0.00 0.00 0.00 2.73
3395 3450 9.705290 GAACAATAAATGTGAAAAATGTACCCT 57.295 29.630 0.00 0.00 42.99 4.34
3396 3451 8.643752 CGAACAATAAATGTGAAAAATGTACCC 58.356 33.333 0.00 0.00 42.99 3.69
3397 3452 9.187455 ACGAACAATAAATGTGAAAAATGTACC 57.813 29.630 0.00 0.00 42.99 3.34
3433 3488 6.798427 AATATGAAGTCTCTACAGCCTTCA 57.202 37.500 0.00 0.00 45.12 3.02
3439 3494 9.755804 TGAATAGCAAATATGAAGTCTCTACAG 57.244 33.333 0.00 0.00 0.00 2.74
3458 3513 7.972832 CCTGGAAAGAAAGAAAAGATGAATAGC 59.027 37.037 0.00 0.00 0.00 2.97
3671 3726 9.495572 ACTTTGGTGTTTAGTTTTCAATTTGAA 57.504 25.926 7.74 7.74 34.03 2.69
3750 3806 9.846248 CATTGGGTTTCTTGTTATAAAAGAGAG 57.154 33.333 8.88 0.00 35.20 3.20
3770 3826 3.195396 ACGGGATTCATTGTTTCATTGGG 59.805 43.478 0.00 0.00 0.00 4.12
3862 3920 0.476771 GGAAGTGTTCAACAGGGGGA 59.523 55.000 0.00 0.00 0.00 4.81
3916 3975 5.957842 TTTAGCACCTACAACTGAATTGG 57.042 39.130 0.00 0.00 43.20 3.16
4197 4259 7.226441 TCTGCAGGAAATAGCACAACATATAT 58.774 34.615 15.13 0.00 36.62 0.86
4198 4260 6.591001 TCTGCAGGAAATAGCACAACATATA 58.409 36.000 15.13 0.00 36.62 0.86
4409 4473 3.010413 GCCCCAAAGCTGTGGCATC 62.010 63.158 18.48 4.52 43.46 3.91
4449 4513 8.460831 ACTTAAACAAACACTAAAACAGCAAG 57.539 30.769 0.00 0.00 0.00 4.01
4501 4566 3.971150 TCAACTTTGGCATAAAACACCG 58.029 40.909 0.00 0.00 0.00 4.94
4557 4622 8.469200 CCATAATCACAAAGTTACATTGTCCAT 58.531 33.333 2.82 0.00 38.90 3.41
5006 5093 4.175516 CTCAGATGACTTGTCTCTTCAGC 58.824 47.826 2.35 0.00 0.00 4.26
5085 5172 8.423906 ACCTGACTGTTTATATCACTATAGGG 57.576 38.462 4.43 0.00 0.00 3.53
5097 5184 9.654663 GTGTATTTTCTAGACCTGACTGTTTAT 57.345 33.333 0.00 0.00 0.00 1.40
5098 5185 8.644216 TGTGTATTTTCTAGACCTGACTGTTTA 58.356 33.333 0.00 0.00 0.00 2.01
5099 5186 7.506114 TGTGTATTTTCTAGACCTGACTGTTT 58.494 34.615 0.00 0.00 0.00 2.83
5100 5187 7.062749 TGTGTATTTTCTAGACCTGACTGTT 57.937 36.000 0.00 0.00 0.00 3.16
5101 5188 6.295349 CCTGTGTATTTTCTAGACCTGACTGT 60.295 42.308 0.00 0.00 0.00 3.55
5102 5189 6.071334 TCCTGTGTATTTTCTAGACCTGACTG 60.071 42.308 0.00 0.00 0.00 3.51
5103 5190 6.017192 TCCTGTGTATTTTCTAGACCTGACT 58.983 40.000 0.00 0.00 0.00 3.41
5104 5191 6.282199 TCCTGTGTATTTTCTAGACCTGAC 57.718 41.667 0.00 0.00 0.00 3.51
5105 5192 5.105310 GCTCCTGTGTATTTTCTAGACCTGA 60.105 44.000 0.00 0.00 0.00 3.86
5106 5193 5.105146 AGCTCCTGTGTATTTTCTAGACCTG 60.105 44.000 0.00 0.00 0.00 4.00
5107 5194 5.026790 AGCTCCTGTGTATTTTCTAGACCT 58.973 41.667 0.00 0.00 0.00 3.85
5108 5195 5.346181 AGCTCCTGTGTATTTTCTAGACC 57.654 43.478 0.00 0.00 0.00 3.85
5109 5196 5.128008 AGGAGCTCCTGTGTATTTTCTAGAC 59.872 44.000 34.74 0.00 46.55 2.59
5110 5197 5.273208 AGGAGCTCCTGTGTATTTTCTAGA 58.727 41.667 34.74 0.00 46.55 2.43
5111 5198 5.606348 AGGAGCTCCTGTGTATTTTCTAG 57.394 43.478 34.74 0.00 46.55 2.43
5125 5212 2.270527 GAAGCACCCAGGAGCTCC 59.729 66.667 26.22 26.22 40.95 4.70
5126 5213 1.376553 GTGAAGCACCCAGGAGCTC 60.377 63.158 9.15 4.71 40.95 4.09
5127 5214 2.149383 TGTGAAGCACCCAGGAGCT 61.149 57.895 2.45 2.45 43.49 4.09
5128 5215 1.968540 GTGTGAAGCACCCAGGAGC 60.969 63.158 0.00 0.00 42.10 4.70
5129 5216 4.386413 GTGTGAAGCACCCAGGAG 57.614 61.111 0.00 0.00 42.10 3.69
5136 5223 3.838244 TCATATAGGGGTGTGAAGCAC 57.162 47.619 0.00 0.00 46.97 4.40
5137 5224 5.606749 AGTATTCATATAGGGGTGTGAAGCA 59.393 40.000 0.00 0.00 33.62 3.91
5138 5225 6.115448 AGTATTCATATAGGGGTGTGAAGC 57.885 41.667 0.00 0.00 33.62 3.86
5141 5228 9.166222 ACATTTAGTATTCATATAGGGGTGTGA 57.834 33.333 0.00 0.00 0.00 3.58
5194 5281 9.918630 CAAGTTTGATATCTCCAAATTTCAGTT 57.081 29.630 3.98 0.00 36.14 3.16
5195 5282 8.526147 CCAAGTTTGATATCTCCAAATTTCAGT 58.474 33.333 3.98 0.00 36.14 3.41
5196 5283 7.977853 CCCAAGTTTGATATCTCCAAATTTCAG 59.022 37.037 3.98 0.00 36.14 3.02
5197 5284 7.454380 ACCCAAGTTTGATATCTCCAAATTTCA 59.546 33.333 3.98 0.00 36.14 2.69
5198 5285 7.840931 ACCCAAGTTTGATATCTCCAAATTTC 58.159 34.615 3.98 0.00 36.14 2.17
5199 5286 7.797121 ACCCAAGTTTGATATCTCCAAATTT 57.203 32.000 3.98 0.00 36.14 1.82
5200 5287 7.797121 AACCCAAGTTTGATATCTCCAAATT 57.203 32.000 3.98 0.00 36.14 1.82
5201 5288 7.797121 AAACCCAAGTTTGATATCTCCAAAT 57.203 32.000 3.98 0.00 44.57 2.32
5202 5289 7.288852 TGAAAACCCAAGTTTGATATCTCCAAA 59.711 33.333 3.98 0.00 45.54 3.28
5203 5290 6.780031 TGAAAACCCAAGTTTGATATCTCCAA 59.220 34.615 3.98 0.00 45.54 3.53
5204 5291 6.310941 TGAAAACCCAAGTTTGATATCTCCA 58.689 36.000 3.98 0.00 45.54 3.86
5205 5292 6.834168 TGAAAACCCAAGTTTGATATCTCC 57.166 37.500 3.98 0.00 45.54 3.71
5206 5293 8.306761 ACATTGAAAACCCAAGTTTGATATCTC 58.693 33.333 3.98 0.00 45.54 2.75
5207 5294 8.193953 ACATTGAAAACCCAAGTTTGATATCT 57.806 30.769 3.98 0.00 45.54 1.98
5210 5297 9.921637 GAATACATTGAAAACCCAAGTTTGATA 57.078 29.630 0.00 0.00 45.54 2.15
5211 5298 7.877612 GGAATACATTGAAAACCCAAGTTTGAT 59.122 33.333 0.00 0.00 45.54 2.57
5212 5299 7.213678 GGAATACATTGAAAACCCAAGTTTGA 58.786 34.615 0.00 0.00 45.54 2.69
5213 5300 6.426633 GGGAATACATTGAAAACCCAAGTTTG 59.573 38.462 0.00 0.00 45.54 2.93
5215 5302 5.279256 CGGGAATACATTGAAAACCCAAGTT 60.279 40.000 0.00 0.00 38.03 2.66
5216 5303 4.219725 CGGGAATACATTGAAAACCCAAGT 59.780 41.667 0.00 0.00 36.04 3.16
5217 5304 4.219725 ACGGGAATACATTGAAAACCCAAG 59.780 41.667 0.00 0.00 36.04 3.61
5218 5305 4.021894 CACGGGAATACATTGAAAACCCAA 60.022 41.667 0.00 0.00 36.04 4.12
5219 5306 3.508012 CACGGGAATACATTGAAAACCCA 59.492 43.478 0.00 0.00 36.04 4.51
5220 5307 3.508402 ACACGGGAATACATTGAAAACCC 59.492 43.478 0.00 0.00 0.00 4.11
5221 5308 4.216687 TCACACGGGAATACATTGAAAACC 59.783 41.667 0.00 0.00 0.00 3.27
5222 5309 5.365403 TCACACGGGAATACATTGAAAAC 57.635 39.130 0.00 0.00 0.00 2.43
5223 5310 6.392625 TTTCACACGGGAATACATTGAAAA 57.607 33.333 0.00 0.00 30.60 2.29
5224 5311 6.582677 ATTTCACACGGGAATACATTGAAA 57.417 33.333 0.00 0.00 36.30 2.69
5225 5312 6.582677 AATTTCACACGGGAATACATTGAA 57.417 33.333 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.