Multiple sequence alignment - TraesCS4B01G256100

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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 TraesCS4B01G256100 chr4B 100.000 5370 0 0 843 6212 520907493 520912862 0.000000e+00 9917.0
1 TraesCS4B01G256100 chr4B 92.289 817 48 5 5175 5976 228028771 228029587 0.000000e+00 1146.0
2 TraesCS4B01G256100 chr4B 100.000 459 0 0 1 459 520906651 520907109 0.000000e+00 848.0
3 TraesCS4B01G256100 chr4B 88.750 160 13 4 4124 4278 665401252 665401411 2.290000e-44 191.0
4 TraesCS4B01G256100 chr4B 87.879 66 5 2 4029 4091 364668437 364668502 2.400000e-09 75.0
5 TraesCS4B01G256100 chr4D 95.054 3255 97 9 843 4033 425246053 425249307 0.000000e+00 5060.0
6 TraesCS4B01G256100 chr4D 91.892 1961 96 39 4280 6205 425249347 425251279 0.000000e+00 2682.0
7 TraesCS4B01G256100 chr4D 86.611 478 18 13 22 459 425245458 425245929 2.600000e-133 486.0
8 TraesCS4B01G256100 chr4A 94.020 2040 59 23 843 2839 39523621 39521602 0.000000e+00 3033.0
9 TraesCS4B01G256100 chr4A 93.255 1705 70 28 4493 6168 39520294 39518606 0.000000e+00 2470.0
10 TraesCS4B01G256100 chr4A 92.857 1092 35 8 3083 4148 39521603 39520529 0.000000e+00 1544.0
11 TraesCS4B01G256100 chr4A 88.494 478 29 20 1 459 39524210 39523740 7.040000e-154 555.0
12 TraesCS4B01G256100 chr4A 91.579 190 12 2 4254 4442 39520484 39520298 6.180000e-65 259.0
13 TraesCS4B01G256100 chr4A 95.833 48 2 0 4041 4088 236122162 236122115 1.860000e-10 78.7
14 TraesCS4B01G256100 chr7A 93.390 817 38 6 5175 5976 290243744 290244559 0.000000e+00 1195.0
15 TraesCS4B01G256100 chr7B 92.972 811 42 5 5181 5976 653448086 653448896 0.000000e+00 1168.0
16 TraesCS4B01G256100 chr7B 92.166 817 49 5 5175 5976 653602646 653603462 0.000000e+00 1140.0
17 TraesCS4B01G256100 chr7B 92.109 811 49 5 5181 5976 653515806 653516616 0.000000e+00 1129.0
18 TraesCS4B01G256100 chr7B 100.000 28 0 0 2321 2348 146141106 146141133 1.100000e-02 52.8
19 TraesCS4B01G256100 chr2A 92.485 825 39 6 5175 5976 614698615 614697791 0.000000e+00 1158.0
20 TraesCS4B01G256100 chr2A 94.231 52 2 1 4043 4094 660286809 660286759 1.860000e-10 78.7
21 TraesCS4B01G256100 chr2A 100.000 28 0 0 2321 2348 623542321 623542348 1.100000e-02 52.8
22 TraesCS4B01G256100 chr2B 92.054 818 48 7 5175 5976 693977519 693976703 0.000000e+00 1134.0
23 TraesCS4B01G256100 chr2B 87.225 227 16 6 5175 5388 693990902 693990676 4.810000e-61 246.0
24 TraesCS4B01G256100 chr2B 89.091 165 10 5 4124 4280 693371163 693371327 1.370000e-46 198.0
25 TraesCS4B01G256100 chr2B 100.000 34 0 0 2315 2348 1835074 1835107 5.200000e-06 63.9
26 TraesCS4B01G256100 chr1A 92.767 553 27 6 5281 5820 11267244 11266692 0.000000e+00 787.0
27 TraesCS4B01G256100 chr1A 83.439 157 7 9 5175 5325 11267402 11267259 1.820000e-25 128.0
28 TraesCS4B01G256100 chr1A 100.000 43 0 0 4043 4085 286243052 286243010 5.160000e-11 80.5
29 TraesCS4B01G256100 chr5D 91.358 162 7 4 4124 4278 345684196 345684357 1.360000e-51 215.0
30 TraesCS4B01G256100 chr5D 89.506 162 10 4 4124 4278 399146793 399146632 1.370000e-46 198.0
31 TraesCS4B01G256100 chr5D 88.024 167 12 5 4123 4282 204324446 204324611 2.290000e-44 191.0
32 TraesCS4B01G256100 chr5D 100.000 28 0 0 2321 2348 458874246 458874273 1.100000e-02 52.8
33 TraesCS4B01G256100 chr6B 89.937 159 9 4 4124 4282 585810853 585811004 1.370000e-46 198.0
34 TraesCS4B01G256100 chr2D 88.889 162 11 4 4124 4278 102809578 102809739 6.350000e-45 193.0
35 TraesCS4B01G256100 chr2D 86.517 178 12 6 4121 4287 52690224 52690400 1.060000e-42 185.0
36 TraesCS4B01G256100 chr2D 92.308 52 4 0 4043 4094 539427323 539427272 2.400000e-09 75.0
37 TraesCS4B01G256100 chr2D 97.059 34 1 0 2315 2348 135602703 135602736 2.420000e-04 58.4
38 TraesCS4B01G256100 chr3B 87.719 171 11 6 4124 4286 655304815 655304983 2.290000e-44 191.0
39 TraesCS4B01G256100 chr3B 100.000 28 0 0 2318 2345 674664845 674664872 1.100000e-02 52.8
40 TraesCS4B01G256100 chr6D 100.000 43 0 0 4042 4084 436760970 436761012 5.160000e-11 80.5
41 TraesCS4B01G256100 chr1D 100.000 43 0 0 4043 4085 135931013 135931055 5.160000e-11 80.5
42 TraesCS4B01G256100 chr6A 95.833 48 2 0 4032 4079 74246275 74246322 1.860000e-10 78.7
43 TraesCS4B01G256100 chr5B 95.833 48 2 0 4043 4090 527097748 527097795 1.860000e-10 78.7
44 TraesCS4B01G256100 chr5B 100.000 28 0 0 2321 2348 514682827 514682800 1.100000e-02 52.8
45 TraesCS4B01G256100 chr5A 100.000 28 0 0 2321 2348 447372105 447372078 1.100000e-02 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G256100 chr4B 520906651 520912862 6211 False 5382.500000 9917 100.000000 1 6212 2 chr4B.!!$F4 6211
1 TraesCS4B01G256100 chr4B 228028771 228029587 816 False 1146.000000 1146 92.289000 5175 5976 1 chr4B.!!$F1 801
2 TraesCS4B01G256100 chr4D 425245458 425251279 5821 False 2742.666667 5060 91.185667 22 6205 3 chr4D.!!$F1 6183
3 TraesCS4B01G256100 chr4A 39518606 39524210 5604 True 1572.200000 3033 92.041000 1 6168 5 chr4A.!!$R2 6167
4 TraesCS4B01G256100 chr7A 290243744 290244559 815 False 1195.000000 1195 93.390000 5175 5976 1 chr7A.!!$F1 801
5 TraesCS4B01G256100 chr7B 653448086 653448896 810 False 1168.000000 1168 92.972000 5181 5976 1 chr7B.!!$F2 795
6 TraesCS4B01G256100 chr7B 653602646 653603462 816 False 1140.000000 1140 92.166000 5175 5976 1 chr7B.!!$F4 801
7 TraesCS4B01G256100 chr7B 653515806 653516616 810 False 1129.000000 1129 92.109000 5181 5976 1 chr7B.!!$F3 795
8 TraesCS4B01G256100 chr2A 614697791 614698615 824 True 1158.000000 1158 92.485000 5175 5976 1 chr2A.!!$R1 801
9 TraesCS4B01G256100 chr2B 693976703 693977519 816 True 1134.000000 1134 92.054000 5175 5976 1 chr2B.!!$R1 801
10 TraesCS4B01G256100 chr1A 11266692 11267402 710 True 457.500000 787 88.103000 5175 5820 2 chr1A.!!$R2 645

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
378 422 0.749454 CCGAGCAAAGATCCCCCAAG 60.749 60.000 0.00 0.0 0.00 3.61 F
1710 1772 0.331954 TCTCCTCCGGTAGCAACTCT 59.668 55.000 0.00 0.0 0.00 3.24 F
1788 1850 0.454600 CTAACAGCCGCCTACGAAGA 59.545 55.000 0.00 0.0 43.93 2.87 F
2659 2759 0.890542 GACTGGCATGCACTTGTGGA 60.891 55.000 21.36 0.0 0.00 4.02 F
2940 3041 2.168936 TGTCCTCGTGGTTTGTGTAACT 59.831 45.455 2.99 0.0 36.93 2.24 F
4482 4630 0.736053 TGCCTGGTGTCGTTGTTTTC 59.264 50.000 0.00 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 2063 1.201429 TCTTTGCCCTCCTCACCTCC 61.201 60.000 0.00 0.00 0.00 4.30 R
3683 3786 0.868406 CGAGTCAGCCAAGGTTTGAC 59.132 55.000 14.17 14.17 41.10 3.18 R
3693 3796 2.727777 GGAAAACAAAACGAGTCAGCC 58.272 47.619 0.00 0.00 0.00 4.85 R
4459 4607 1.961277 CAACGACACCAGGCAGACC 60.961 63.158 0.00 0.00 0.00 3.85 R
4839 4993 0.798776 GTTCAAGGACATGCAGACCG 59.201 55.000 0.00 0.00 37.13 4.79 R
6073 6351 1.153509 CGGTCTTAAATCGCCGGGT 60.154 57.895 2.18 0.00 40.45 5.28 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
122 129 4.093408 TCATTCGTTTCAGACATAAGCTGC 59.907 41.667 0.00 0.00 33.45 5.25
125 132 2.738846 CGTTTCAGACATAAGCTGCTGT 59.261 45.455 1.35 0.00 33.44 4.40
185 195 5.215160 CCCATTTCTCGAAAGTTCAAAGTG 58.785 41.667 0.00 0.00 33.32 3.16
220 230 2.224548 ACCCCACTTAGAAGCTGTTGTC 60.225 50.000 0.00 0.00 0.00 3.18
226 236 6.461509 CCCACTTAGAAGCTGTTGTCAAAAAT 60.462 38.462 0.00 0.00 0.00 1.82
229 239 9.683069 CACTTAGAAGCTGTTGTCAAAAATAAT 57.317 29.630 0.00 0.00 0.00 1.28
230 240 9.899226 ACTTAGAAGCTGTTGTCAAAAATAATC 57.101 29.630 0.00 0.00 0.00 1.75
313 334 4.462133 GGCACACCAGAGTAGATAGAGTA 58.538 47.826 0.00 0.00 35.26 2.59
333 354 4.410400 GGAGAAGGCCACACGGGG 62.410 72.222 5.01 0.00 37.04 5.73
377 421 1.302949 CCGAGCAAAGATCCCCCAA 59.697 57.895 0.00 0.00 0.00 4.12
378 422 0.749454 CCGAGCAAAGATCCCCCAAG 60.749 60.000 0.00 0.00 0.00 3.61
1185 1247 1.575576 CCACCTCGTCGACTTCGTCT 61.576 60.000 14.70 0.00 40.80 4.18
1630 1692 1.889530 CGACTCCACCACCTCCTTCC 61.890 65.000 0.00 0.00 0.00 3.46
1710 1772 0.331954 TCTCCTCCGGTAGCAACTCT 59.668 55.000 0.00 0.00 0.00 3.24
1755 1817 3.763356 ATCAGCGTGCCAGCGAGA 61.763 61.111 0.00 0.00 43.00 4.04
1788 1850 0.454600 CTAACAGCCGCCTACGAAGA 59.545 55.000 0.00 0.00 43.93 2.87
1920 1982 3.371097 GACGGCGAGCCCATCAAGA 62.371 63.158 16.62 0.00 0.00 3.02
1974 2036 1.282875 GGTTCAGACGGCAGCAAAC 59.717 57.895 0.00 0.00 0.00 2.93
2001 2063 4.378149 CCATCTATCATTAGCTTTGCTGCG 60.378 45.833 0.00 0.00 40.10 5.18
2508 2608 7.287512 TCTCTGATTGTTGATAGAGGAGATG 57.712 40.000 0.00 0.00 37.76 2.90
2652 2752 2.360852 AGGCTGACTGGCATGCAC 60.361 61.111 21.36 9.64 44.55 4.57
2659 2759 0.890542 GACTGGCATGCACTTGTGGA 60.891 55.000 21.36 0.00 0.00 4.02
2666 2766 2.223641 GCATGCACTTGTGGATGTATGG 60.224 50.000 27.21 9.98 38.80 2.74
2748 2849 5.062528 TCACAGCTCAACATGTATTGTCAA 58.937 37.500 0.00 0.00 37.68 3.18
2869 2970 9.739276 TGATAAATCATGTACTTCCTTTTGAGT 57.261 29.630 0.00 0.00 0.00 3.41
2870 2971 9.994432 GATAAATCATGTACTTCCTTTTGAGTG 57.006 33.333 0.00 0.00 0.00 3.51
2880 2981 4.287238 TCCTTTTGAGTGCGAAGAAAAC 57.713 40.909 0.00 0.00 0.00 2.43
2940 3041 2.168936 TGTCCTCGTGGTTTGTGTAACT 59.831 45.455 2.99 0.00 36.93 2.24
2943 3044 3.070446 TCCTCGTGGTTTGTGTAACTCAT 59.930 43.478 2.99 0.00 36.93 2.90
2983 3084 6.785076 TGGATGTCCTTTTTCATTGGTACTA 58.215 36.000 0.09 0.00 36.82 1.82
3047 3150 3.519510 AGGCTTCAGCTAAATCCTACACA 59.480 43.478 0.00 0.00 41.70 3.72
3070 3173 5.333299 TGTCTACATGTATTTACCGCTGT 57.667 39.130 5.91 0.00 0.00 4.40
3071 3174 5.726397 TGTCTACATGTATTTACCGCTGTT 58.274 37.500 5.91 0.00 0.00 3.16
3081 3184 6.874664 TGTATTTACCGCTGTTAGTGAAATCA 59.125 34.615 0.00 0.00 0.00 2.57
3135 3238 7.928908 ATACACGCTAAAATTGGCAAATATG 57.071 32.000 3.01 0.00 33.91 1.78
3247 3350 4.270084 TGCTTATGCGTAAAAGAATCGGAG 59.730 41.667 0.00 0.00 43.34 4.63
3443 3546 7.371936 GGAGAGGTATGTGATATGAGTTACAC 58.628 42.308 0.00 0.00 0.00 2.90
3683 3786 2.295909 TGCAAAGGTGGGAATTTTCTCG 59.704 45.455 0.00 0.00 0.00 4.04
3693 3796 4.037446 TGGGAATTTTCTCGTCAAACCTTG 59.963 41.667 0.00 0.00 0.00 3.61
4038 4159 6.681729 TTCTCTTATTGTGTTGTACTCCCT 57.318 37.500 0.00 0.00 0.00 4.20
4041 4162 5.091552 TCTTATTGTGTTGTACTCCCTCCT 58.908 41.667 0.00 0.00 0.00 3.69
4042 4163 6.258354 TCTTATTGTGTTGTACTCCCTCCTA 58.742 40.000 0.00 0.00 0.00 2.94
4043 4164 6.727231 TCTTATTGTGTTGTACTCCCTCCTAA 59.273 38.462 0.00 0.00 0.00 2.69
4044 4165 5.836024 ATTGTGTTGTACTCCCTCCTAAA 57.164 39.130 0.00 0.00 0.00 1.85
4045 4166 4.884668 TGTGTTGTACTCCCTCCTAAAG 57.115 45.455 0.00 0.00 0.00 1.85
4046 4167 4.228824 TGTGTTGTACTCCCTCCTAAAGT 58.771 43.478 0.00 0.00 0.00 2.66
4047 4168 4.657039 TGTGTTGTACTCCCTCCTAAAGTT 59.343 41.667 0.00 0.00 0.00 2.66
4069 4215 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
4112 4258 4.161377 TGGCACTATGACTTAGTATGCACA 59.839 41.667 10.97 6.03 39.19 4.57
4114 4260 5.760253 GGCACTATGACTTAGTATGCACATT 59.240 40.000 10.97 0.00 39.19 2.71
4132 4278 6.826741 TGCACATTTTAGTTATTACTCCCTCC 59.173 38.462 0.00 0.00 35.78 4.30
4135 4281 7.551617 CACATTTTAGTTATTACTCCCTCCGTT 59.448 37.037 0.00 0.00 35.78 4.44
4136 4282 7.767659 ACATTTTAGTTATTACTCCCTCCGTTC 59.232 37.037 0.00 0.00 35.78 3.95
4137 4283 5.859205 TTAGTTATTACTCCCTCCGTTCC 57.141 43.478 0.00 0.00 35.78 3.62
4138 4284 3.991683 AGTTATTACTCCCTCCGTTCCT 58.008 45.455 0.00 0.00 0.00 3.36
4148 4294 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
4149 4295 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
4150 4296 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
4151 4297 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
4170 4316 6.706295 AGTCTTTTTAGAGATTCCACTCTGG 58.294 40.000 0.00 0.00 45.33 3.86
4171 4317 6.498651 AGTCTTTTTAGAGATTCCACTCTGGA 59.501 38.462 0.00 0.00 46.61 3.86
4182 4328 4.586306 TCCACTCTGGACTACATACAGA 57.414 45.455 0.00 0.00 42.67 3.41
4190 4336 6.867550 TCTGGACTACATACAGAGTGAAATG 58.132 40.000 0.00 0.00 36.41 2.32
4191 4337 6.663523 TCTGGACTACATACAGAGTGAAATGA 59.336 38.462 0.00 0.00 36.41 2.57
4192 4338 7.343057 TCTGGACTACATACAGAGTGAAATGAT 59.657 37.037 0.00 0.00 36.41 2.45
4193 4339 7.851228 TGGACTACATACAGAGTGAAATGATT 58.149 34.615 0.00 0.00 0.00 2.57
4194 4340 7.765819 TGGACTACATACAGAGTGAAATGATTG 59.234 37.037 0.00 0.00 0.00 2.67
4195 4341 7.981789 GGACTACATACAGAGTGAAATGATTGA 59.018 37.037 0.00 0.00 0.00 2.57
4196 4342 9.371136 GACTACATACAGAGTGAAATGATTGAA 57.629 33.333 0.00 0.00 0.00 2.69
4197 4343 9.896645 ACTACATACAGAGTGAAATGATTGAAT 57.103 29.630 0.00 0.00 0.00 2.57
4199 4345 8.218338 ACATACAGAGTGAAATGATTGAATCC 57.782 34.615 2.26 0.00 0.00 3.01
4200 4346 7.830697 ACATACAGAGTGAAATGATTGAATCCA 59.169 33.333 2.26 0.00 0.00 3.41
4201 4347 8.847196 CATACAGAGTGAAATGATTGAATCCAT 58.153 33.333 2.26 0.00 0.00 3.41
4203 4349 8.991783 ACAGAGTGAAATGATTGAATCCATAT 57.008 30.769 2.26 0.00 0.00 1.78
4204 4350 8.847196 ACAGAGTGAAATGATTGAATCCATATG 58.153 33.333 2.26 0.00 0.00 1.78
4205 4351 8.847196 CAGAGTGAAATGATTGAATCCATATGT 58.153 33.333 2.26 0.00 0.00 2.29
4208 4354 9.857656 AGTGAAATGATTGAATCCATATGTAGT 57.142 29.630 2.26 0.00 0.00 2.73
4238 4384 5.657474 ACATCCGTATGTAGTTTGTAGTGG 58.343 41.667 0.00 0.00 44.66 4.00
4239 4385 5.419788 ACATCCGTATGTAGTTTGTAGTGGA 59.580 40.000 0.00 0.00 44.66 4.02
4240 4386 5.981088 TCCGTATGTAGTTTGTAGTGGAA 57.019 39.130 0.00 0.00 0.00 3.53
4241 4387 6.534475 TCCGTATGTAGTTTGTAGTGGAAT 57.466 37.500 0.00 0.00 0.00 3.01
4243 4389 6.379133 TCCGTATGTAGTTTGTAGTGGAATCT 59.621 38.462 0.00 0.00 0.00 2.40
4246 4392 8.618677 CGTATGTAGTTTGTAGTGGAATCTCTA 58.381 37.037 0.00 0.00 0.00 2.43
4278 4424 7.232330 ACTTATATTTAGGAACGGAGGGAGTAC 59.768 40.741 0.00 0.00 0.00 2.73
4279 4425 3.463048 TTTAGGAACGGAGGGAGTACT 57.537 47.619 0.00 0.00 0.00 2.73
4280 4426 4.591321 TTTAGGAACGGAGGGAGTACTA 57.409 45.455 0.00 0.00 0.00 1.82
4281 4427 4.803329 TTAGGAACGGAGGGAGTACTAT 57.197 45.455 0.00 0.00 0.00 2.12
4288 4434 7.450944 AGGAACGGAGGGAGTACTATTTATTAG 59.549 40.741 0.00 0.00 0.00 1.73
4290 4436 6.856757 ACGGAGGGAGTACTATTTATTAGGA 58.143 40.000 0.00 0.00 31.68 2.94
4306 4452 5.934402 ATTAGGACTCTGTTCGGTATTGT 57.066 39.130 0.00 0.00 0.00 2.71
4311 4457 2.367567 ACTCTGTTCGGTATTGTGGTGT 59.632 45.455 0.00 0.00 0.00 4.16
4474 4622 1.513158 CTAGGTCTGCCTGGTGTCG 59.487 63.158 0.00 0.00 46.47 4.35
4482 4630 0.736053 TGCCTGGTGTCGTTGTTTTC 59.264 50.000 0.00 0.00 0.00 2.29
4485 4633 1.260561 CCTGGTGTCGTTGTTTTCGAG 59.739 52.381 0.00 0.00 37.99 4.04
4642 4796 8.736244 GTTGTAAATACATAATGACAAGTGGGT 58.264 33.333 0.00 0.00 35.89 4.51
4727 4881 5.606505 TGTAATTACACTTGACAGTCTGCA 58.393 37.500 14.35 0.00 0.00 4.41
4763 4917 5.393787 CCTGCGTTCTGTAATAGACCTACAA 60.394 44.000 0.00 0.00 34.43 2.41
4778 4932 5.639506 AGACCTACAATTCTGTTGTCGATTG 59.360 40.000 0.00 0.00 39.38 2.67
4797 4951 2.068519 TGTGAATGTAGTCTGCTTGCG 58.931 47.619 0.00 0.00 0.00 4.85
4811 4965 2.111756 GCTTGCGTCTTTTGTGAACAG 58.888 47.619 0.00 0.00 0.00 3.16
4812 4966 2.477863 GCTTGCGTCTTTTGTGAACAGT 60.478 45.455 0.00 0.00 0.00 3.55
4839 4993 7.282224 TGGCAATAGGATGTAATTACACTTGAC 59.718 37.037 20.26 18.36 39.30 3.18
4840 4994 7.345192 GCAATAGGATGTAATTACACTTGACG 58.655 38.462 20.26 8.06 39.30 4.35
4845 5000 5.291128 GGATGTAATTACACTTGACGGTCTG 59.709 44.000 20.26 2.05 39.30 3.51
4850 5005 0.106708 ACACTTGACGGTCTGCATGT 59.893 50.000 9.88 5.98 0.00 3.21
4969 5124 2.671682 GTGGAGGGGACAAGCTCC 59.328 66.667 0.00 0.00 38.55 4.70
5223 5381 2.621998 ACGGTGGTAGATCAGTTATCCG 59.378 50.000 11.55 11.55 40.94 4.18
5357 5595 4.807631 TCCGCTCGACCGATCCCA 62.808 66.667 0.71 0.00 0.00 4.37
5375 5613 2.499289 CCCACTGAGTGTAGCTGATTCT 59.501 50.000 12.15 0.00 0.00 2.40
5466 5709 3.243134 GCGGGTGTATACAGAGAGAGAAC 60.243 52.174 5.62 0.00 0.00 3.01
5506 5750 9.618890 AAAGATAAGCTTTGCTGTAGATATGAA 57.381 29.630 3.20 0.00 44.89 2.57
5516 5760 9.448438 TTTGCTGTAGATATGAAAAAGCTTAGA 57.552 29.630 0.00 0.00 0.00 2.10
5654 5899 6.524101 TTGTTTTCCTTATCATAACCTGCC 57.476 37.500 0.00 0.00 0.00 4.85
5658 5903 2.775384 TCCTTATCATAACCTGCCCGTT 59.225 45.455 0.00 0.00 0.00 4.44
5771 6027 5.240891 TCTGTGCTTCTATTCTCTTGTTGG 58.759 41.667 0.00 0.00 0.00 3.77
6013 6291 2.111460 GTACGTGCCCACCAACCA 59.889 61.111 0.00 0.00 0.00 3.67
6051 6329 1.436336 CCGGAGAGCGACGGTATTT 59.564 57.895 0.00 0.00 44.85 1.40
6168 6446 2.193536 GGCGTTTGTTGGCTCTGGT 61.194 57.895 0.00 0.00 0.00 4.00
6192 6470 1.571460 GTCGTTGCAGCCTGAACAG 59.429 57.895 0.00 0.00 0.00 3.16
6197 6475 1.678101 GTTGCAGCCTGAACAGAAACT 59.322 47.619 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 129 7.579589 TTTTCTGTTTGACAATGTTGAACAG 57.420 32.000 24.26 24.26 45.17 3.16
125 132 9.868277 ATAGTTTTTCTGTTTGACAATGTTGAA 57.132 25.926 0.00 0.00 0.00 2.69
185 195 4.489306 AGTGGGGTAACTTAGAGAATGC 57.511 45.455 0.00 0.00 0.00 3.56
313 334 4.003788 CGTGTGGCCTTCTCCCGT 62.004 66.667 3.32 0.00 0.00 5.28
341 362 1.557269 GGGAAGCTCTCTCCTTGCCA 61.557 60.000 6.78 0.00 46.40 4.92
377 421 4.822896 TGTTTTACTCGTTTGTATTGGGCT 59.177 37.500 0.00 0.00 0.00 5.19
378 422 5.110940 TGTTTTACTCGTTTGTATTGGGC 57.889 39.130 0.00 0.00 0.00 5.36
1185 1247 4.093952 GCGGACGAGGACGACGAA 62.094 66.667 0.00 0.00 42.10 3.85
1671 1733 3.680786 CTGTCGGTGTCGGAGGCA 61.681 66.667 0.00 0.00 43.93 4.75
1755 1817 3.084786 GCTGTTAGTTTCCTGCCAGAAT 58.915 45.455 0.00 0.00 0.00 2.40
1974 2036 2.001812 AGCTAATGATAGATGGCGCG 57.998 50.000 0.00 0.00 0.00 6.86
2001 2063 1.201429 TCTTTGCCCTCCTCACCTCC 61.201 60.000 0.00 0.00 0.00 4.30
2368 2468 3.081804 CCGTTATCCTGAAAAAGGCAGT 58.918 45.455 0.00 0.00 46.92 4.40
2508 2608 4.083590 GCAGTGTGTTCAAAGATTCTCCTC 60.084 45.833 0.00 0.00 0.00 3.71
2639 2739 1.174078 CCACAAGTGCATGCCAGTCA 61.174 55.000 16.68 0.00 0.00 3.41
2652 2752 9.874205 AAATTTATGTTTCCATACATCCACAAG 57.126 29.630 0.00 0.00 39.39 3.16
2869 2970 2.619646 GGTACCCTTTGTTTTCTTCGCA 59.380 45.455 0.00 0.00 0.00 5.10
2870 2971 2.619646 TGGTACCCTTTGTTTTCTTCGC 59.380 45.455 10.07 0.00 0.00 4.70
2880 2981 2.524306 TGCCTGATTTGGTACCCTTTG 58.476 47.619 10.07 0.00 0.00 2.77
2895 2996 5.068723 AGCTATCATTCTTTTTCCATGCCTG 59.931 40.000 0.00 0.00 0.00 4.85
2983 3084 8.948145 CGCATAGTAATCACTAGAGTAACCTAT 58.052 37.037 0.00 0.00 40.57 2.57
3047 3150 5.914033 ACAGCGGTAAATACATGTAGACAT 58.086 37.500 11.91 0.28 36.96 3.06
3103 3206 7.445707 TGCCAATTTTAGCGTGTATATCCATTA 59.554 33.333 0.00 0.00 0.00 1.90
3135 3238 6.457528 GCAAGTACAAGTGATTAAGCATCTCC 60.458 42.308 0.00 0.00 32.34 3.71
3194 3297 5.972107 ATGCTGCAATGTAAGAAGTTTCT 57.028 34.783 6.36 0.00 39.74 2.52
3247 3350 9.961265 GTTATAATAAAAACATACTGGGCCTTC 57.039 33.333 4.53 0.00 0.00 3.46
3557 3660 5.630121 ACATGAGACCACTCCTCTAGATAG 58.370 45.833 0.00 0.00 41.99 2.08
3683 3786 0.868406 CGAGTCAGCCAAGGTTTGAC 59.132 55.000 14.17 14.17 41.10 3.18
3693 3796 2.727777 GGAAAACAAAACGAGTCAGCC 58.272 47.619 0.00 0.00 0.00 4.85
3974 4095 5.465532 TTTCTGCATTATCACAAAGCCAA 57.534 34.783 0.00 0.00 0.00 4.52
4033 4154 3.835395 AGTGTCTCAACTTTAGGAGGGAG 59.165 47.826 0.00 0.00 34.21 4.30
4038 4159 7.447238 CCCAAAATAAGTGTCTCAACTTTAGGA 59.553 37.037 0.00 0.00 40.77 2.94
4041 4162 7.041644 CGTCCCAAAATAAGTGTCTCAACTTTA 60.042 37.037 0.00 0.00 40.77 1.85
4042 4163 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
4043 4164 5.238650 CGTCCCAAAATAAGTGTCTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
4044 4165 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
4045 4166 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
4046 4167 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
4047 4168 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
4069 4215 7.293535 AGTGCCAAAGATTATCTTATACTCCCT 59.706 37.037 7.98 0.00 35.27 4.20
4112 4258 7.126879 AGGAACGGAGGGAGTAATAACTAAAAT 59.873 37.037 0.00 0.00 35.56 1.82
4114 4260 5.960202 AGGAACGGAGGGAGTAATAACTAAA 59.040 40.000 0.00 0.00 35.56 1.85
4148 4294 6.935240 TCCAGAGTGGAATCTCTAAAAAGA 57.065 37.500 0.00 0.00 45.00 2.52
4161 4307 4.527944 CTCTGTATGTAGTCCAGAGTGGA 58.472 47.826 7.55 0.00 45.98 4.02
4162 4308 4.909696 CTCTGTATGTAGTCCAGAGTGG 57.090 50.000 7.55 0.00 44.54 4.00
4167 4313 6.867550 TCATTTCACTCTGTATGTAGTCCAG 58.132 40.000 0.00 0.00 0.00 3.86
4168 4314 6.850752 TCATTTCACTCTGTATGTAGTCCA 57.149 37.500 0.00 0.00 0.00 4.02
4170 4316 8.932945 TCAATCATTTCACTCTGTATGTAGTC 57.067 34.615 0.00 0.00 0.00 2.59
4171 4317 9.896645 ATTCAATCATTTCACTCTGTATGTAGT 57.103 29.630 0.00 0.00 0.00 2.73
4174 4320 7.830697 TGGATTCAATCATTTCACTCTGTATGT 59.169 33.333 0.00 0.00 0.00 2.29
4175 4321 8.217131 TGGATTCAATCATTTCACTCTGTATG 57.783 34.615 0.00 0.00 0.00 2.39
4180 4326 8.991783 ACATATGGATTCAATCATTTCACTCT 57.008 30.769 7.80 0.00 0.00 3.24
4182 4328 9.857656 ACTACATATGGATTCAATCATTTCACT 57.142 29.630 7.80 0.00 0.00 3.41
4212 4358 8.570488 CCACTACAAACTACATACGGATGTATA 58.430 37.037 20.64 9.08 45.42 1.47
4213 4359 7.286087 TCCACTACAAACTACATACGGATGTAT 59.714 37.037 20.64 8.38 45.42 2.29
4214 4360 6.602803 TCCACTACAAACTACATACGGATGTA 59.397 38.462 19.32 19.32 44.77 2.29
4216 4362 5.898174 TCCACTACAAACTACATACGGATG 58.102 41.667 5.94 5.94 39.16 3.51
4217 4363 6.534475 TTCCACTACAAACTACATACGGAT 57.466 37.500 0.00 0.00 0.00 4.18
4218 4364 5.981088 TTCCACTACAAACTACATACGGA 57.019 39.130 0.00 0.00 0.00 4.69
4219 4365 6.570692 AGATTCCACTACAAACTACATACGG 58.429 40.000 0.00 0.00 0.00 4.02
4220 4366 7.481642 AGAGATTCCACTACAAACTACATACG 58.518 38.462 0.00 0.00 0.00 3.06
4227 4373 9.274206 GTCTTTTTAGAGATTCCACTACAAACT 57.726 33.333 0.00 0.00 0.00 2.66
4228 4374 9.274206 AGTCTTTTTAGAGATTCCACTACAAAC 57.726 33.333 0.00 0.00 0.00 2.93
4229 4375 9.847224 AAGTCTTTTTAGAGATTCCACTACAAA 57.153 29.630 0.00 0.00 0.00 2.83
4246 4392 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
4248 4394 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
4250 4396 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
4251 4397 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
4252 4398 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
4262 4408 3.684408 AATAGTACTCCCTCCGTTCCT 57.316 47.619 0.00 0.00 0.00 3.36
4263 4409 6.416631 AATAAATAGTACTCCCTCCGTTCC 57.583 41.667 0.00 0.00 0.00 3.62
4264 4410 7.449704 TCCTAATAAATAGTACTCCCTCCGTTC 59.550 40.741 0.00 0.00 0.00 3.95
4265 4411 7.232330 GTCCTAATAAATAGTACTCCCTCCGTT 59.768 40.741 0.00 0.00 0.00 4.44
4268 4414 8.172070 AGAGTCCTAATAAATAGTACTCCCTCC 58.828 40.741 0.00 0.00 44.53 4.30
4279 4425 9.976511 CAATACCGAACAGAGTCCTAATAAATA 57.023 33.333 0.00 0.00 0.00 1.40
4280 4426 8.483758 ACAATACCGAACAGAGTCCTAATAAAT 58.516 33.333 0.00 0.00 0.00 1.40
4281 4427 7.762615 CACAATACCGAACAGAGTCCTAATAAA 59.237 37.037 0.00 0.00 0.00 1.40
4288 4434 2.028385 ACCACAATACCGAACAGAGTCC 60.028 50.000 0.00 0.00 0.00 3.85
4290 4436 2.367567 ACACCACAATACCGAACAGAGT 59.632 45.455 0.00 0.00 0.00 3.24
4399 4546 8.610248 TCAACTTATTTTATGAACTGTTCCGA 57.390 30.769 17.26 2.96 0.00 4.55
4459 4607 1.961277 CAACGACACCAGGCAGACC 60.961 63.158 0.00 0.00 0.00 3.85
4474 4622 8.836959 AGAAAAATGTAGTTCTCGAAAACAAC 57.163 30.769 4.14 0.00 27.52 3.32
4501 4649 9.503399 GGCATACAACCTTAAGCTATATAAAGT 57.497 33.333 0.00 0.00 0.00 2.66
4520 4674 5.939764 AGAAGAACAGACTATGGCATACA 57.060 39.130 2.32 0.00 0.00 2.29
4526 4680 6.378564 TCAGGAACTAGAAGAACAGACTATGG 59.621 42.308 0.00 0.00 36.02 2.74
4727 4881 1.000274 GAACGCAGGCCTGTTTTTCAT 60.000 47.619 32.81 13.05 0.00 2.57
4763 4917 5.947228 ACATTCACAATCGACAACAGAAT 57.053 34.783 0.00 0.00 0.00 2.40
4778 4932 2.069273 ACGCAAGCAGACTACATTCAC 58.931 47.619 0.00 0.00 45.62 3.18
4797 4951 3.502191 TGCCAACTGTTCACAAAAGAC 57.498 42.857 0.00 0.00 0.00 3.01
4811 4965 7.568199 AGTGTAATTACATCCTATTGCCAAC 57.432 36.000 20.72 4.07 38.63 3.77
4812 4966 7.831690 TCAAGTGTAATTACATCCTATTGCCAA 59.168 33.333 20.72 4.65 38.63 4.52
4839 4993 0.798776 GTTCAAGGACATGCAGACCG 59.201 55.000 0.00 0.00 37.13 4.79
4840 4994 1.896220 TGTTCAAGGACATGCAGACC 58.104 50.000 0.00 0.00 0.00 3.85
4845 5000 3.429085 CGCTTATTGTTCAAGGACATGC 58.571 45.455 0.00 0.00 0.00 4.06
4850 5005 3.244422 ACAGTCCGCTTATTGTTCAAGGA 60.244 43.478 0.00 0.00 0.00 3.36
4969 5124 0.735978 TCGCAAGCTCATACACCACG 60.736 55.000 0.00 0.00 37.18 4.94
5204 5362 3.305471 GCTCGGATAACTGATCTACCACC 60.305 52.174 0.00 0.00 34.66 4.61
5357 5595 4.881019 ACAAGAATCAGCTACACTCAGT 57.119 40.909 0.00 0.00 0.00 3.41
5466 5709 5.940470 AGCTTATCTTTGGTCAAACACTAGG 59.060 40.000 0.00 0.00 0.00 3.02
5516 5760 1.526887 CAGACGACGACAACAAGCAAT 59.473 47.619 0.00 0.00 0.00 3.56
5654 5899 2.322161 CAGCAGAAGCATGAAAAACGG 58.678 47.619 0.00 0.00 45.49 4.44
5658 5903 1.336517 GCTGCAGCAGAAGCATGAAAA 60.337 47.619 33.36 0.00 46.44 2.29
5682 5927 2.289547 ACACAACGCAGACATAACAACC 59.710 45.455 0.00 0.00 0.00 3.77
6013 6291 2.586792 GAGGCAGCCGAACAGGAT 59.413 61.111 5.55 0.00 45.00 3.24
6073 6351 1.153509 CGGTCTTAAATCGCCGGGT 60.154 57.895 2.18 0.00 40.45 5.28
6168 6446 2.210013 AGGCTGCAACGACCAGAGA 61.210 57.895 0.50 0.00 32.03 3.10


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

AutoCloner maintained by Alex Coulton.