Multiple sequence alignment - TraesCS4A01G409400

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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 TraesCS4A01G409400 chr4A 100.000 5105 0 0 1 5105 681921636 681916532 0.000000e+00 9428.0
1 TraesCS4A01G409400 chr4A 86.866 769 87 8 1040 1795 629294194 629293427 0.000000e+00 848.0
2 TraesCS4A01G409400 chr4A 80.058 692 102 22 2479 3161 629293438 629292774 9.940000e-132 481.0
3 TraesCS4A01G409400 chr4A 100.000 55 0 0 4477 4531 681916785 681916731 9.040000e-18 102.0
4 TraesCS4A01G409400 chr4A 100.000 55 0 0 4852 4906 681917160 681917106 9.040000e-18 102.0
5 TraesCS4A01G409400 chr4A 82.301 113 20 0 3503 3615 501124396 501124284 1.170000e-16 99.0
6 TraesCS4A01G409400 chr4D 95.632 4693 157 25 260 4926 475179836 475175166 0.000000e+00 7487.0
7 TraesCS4A01G409400 chr4D 96.622 148 5 0 1 148 475179980 475179833 3.950000e-61 246.0
8 TraesCS4A01G409400 chr4D 85.124 242 10 12 4547 4784 475175908 475175689 1.850000e-54 224.0
9 TraesCS4A01G409400 chr4D 81.405 242 17 16 4200 4419 475175543 475175308 6.800000e-39 172.0
10 TraesCS4A01G409400 chr4D 82.301 113 20 0 3503 3615 88142352 88142240 1.170000e-16 99.0
11 TraesCS4A01G409400 chr4B 94.668 4295 145 27 266 4531 599887885 599883646 0.000000e+00 6586.0
12 TraesCS4A01G409400 chr4B 87.319 552 38 15 4556 5105 599883968 599883447 2.030000e-168 603.0
13 TraesCS4A01G409400 chr4B 100.000 119 0 0 146 264 422040253 422040371 2.390000e-53 220.0
14 TraesCS4A01G409400 chr4B 92.086 139 8 2 147 283 183844330 183844467 5.220000e-45 193.0
15 TraesCS4A01G409400 chr5B 85.443 2157 279 24 1021 3161 680993561 680995698 0.000000e+00 2211.0
16 TraesCS4A01G409400 chr5B 78.169 142 29 2 3660 3800 11306314 11306174 7.040000e-14 89.8
17 TraesCS4A01G409400 chr5D 86.430 1997 240 17 1057 3033 539453810 539455795 0.000000e+00 2158.0
18 TraesCS4A01G409400 chr5D 78.169 142 29 2 3660 3800 10776010 10776150 7.040000e-14 89.8
19 TraesCS4A01G409400 chr6B 78.942 983 159 35 3072 4036 25924608 25923656 4.340000e-175 625.0
20 TraesCS4A01G409400 chr6A 78.888 971 157 37 3072 4024 15438442 15439382 9.390000e-172 614.0
21 TraesCS4A01G409400 chr6A 73.508 1525 352 44 1373 2871 15436758 15438256 9.730000e-147 531.0
22 TraesCS4A01G409400 chr6A 96.032 126 5 0 141 266 601207347 601207222 6.700000e-49 206.0
23 TraesCS4A01G409400 chr6D 78.351 970 164 35 3072 4024 14077688 14078628 2.050000e-163 586.0
24 TraesCS4A01G409400 chr7A 99.160 119 1 0 145 263 681620048 681619930 1.110000e-51 215.0
25 TraesCS4A01G409400 chr7A 96.774 124 3 1 147 270 491263278 491263156 6.700000e-49 206.0
26 TraesCS4A01G409400 chr2B 99.153 118 1 0 147 264 761993720 761993603 4.000000e-51 213.0
27 TraesCS4A01G409400 chr7D 97.521 121 3 0 143 263 579147037 579147157 1.860000e-49 207.0
28 TraesCS4A01G409400 chr2D 96.032 126 5 0 145 270 363524024 363523899 6.700000e-49 206.0
29 TraesCS4A01G409400 chr3B 95.276 127 6 0 137 263 667389993 667390119 8.670000e-48 202.0
30 TraesCS4A01G409400 chr5A 78.873 142 28 2 3660 3800 8904552 8904412 1.510000e-15 95.3
31 TraesCS4A01G409400 chr1A 96.970 33 1 0 1885 1917 22869071 22869103 7.140000e-04 56.5
32 TraesCS4A01G409400 chr7B 96.875 32 1 0 2684 2715 57680410 57680379 3.000000e-03 54.7


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 TraesCS4A01G409400 chr4A 681916532 681921636 5104 True 9428.0 9428 100.0000 1 5105 1 chr4A.!!$R2 5104
1 TraesCS4A01G409400 chr4A 629292774 629294194 1420 True 664.5 848 83.4620 1040 3161 2 chr4A.!!$R3 2121
2 TraesCS4A01G409400 chr4D 475175166 475179836 4670 True 7487.0 7487 95.6320 260 4926 1 chr4D.!!$R2 4666
3 TraesCS4A01G409400 chr4D 475175308 475179980 4672 True 214.0 246 87.7170 1 4784 3 chr4D.!!$R3 4783
4 TraesCS4A01G409400 chr4B 599883447 599887885 4438 True 3594.5 6586 90.9935 266 5105 2 chr4B.!!$R1 4839
5 TraesCS4A01G409400 chr5B 680993561 680995698 2137 False 2211.0 2211 85.4430 1021 3161 1 chr5B.!!$F1 2140
6 TraesCS4A01G409400 chr5D 539453810 539455795 1985 False 2158.0 2158 86.4300 1057 3033 1 chr5D.!!$F2 1976
7 TraesCS4A01G409400 chr6B 25923656 25924608 952 True 625.0 625 78.9420 3072 4036 1 chr6B.!!$R1 964
8 TraesCS4A01G409400 chr6A 15436758 15439382 2624 False 572.5 614 76.1980 1373 4024 2 chr6A.!!$F1 2651
9 TraesCS4A01G409400 chr6D 14077688 14078628 940 False 586.0 586 78.3510 3072 4024 1 chr6D.!!$F1 952

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
165 166 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.0 5.23 0.0 44.66 2.17 F
166 167 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.0 5.23 0.0 44.66 1.40 F
168 169 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 F
707 712 0.108585 CCCACCAACACACACTAGCT 59.891 55.0 0.00 0.0 0.00 3.32 F
912 920 0.394352 AATGGAAGCCCGCAACTAGG 60.394 55.0 0.00 0.0 34.29 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 1891 2.265904 TGACGAGGGACGACAGGTG 61.266 63.158 0.00 0.0 45.77 4.00 R
2262 2289 1.666553 CACTGTGCCGTTAAGCCGA 60.667 57.895 0.00 0.0 0.00 5.54 R
2955 2988 3.830994 GAGCGCGATCGAGATGCCA 62.831 63.158 23.47 0.0 38.10 4.92 R
3045 3090 0.888736 TCCCGTCTTCGTCCACGTTA 60.889 55.000 0.00 0.0 40.80 3.18 R
4156 4210 4.030529 ACGTATACAAAACATACACGTCGC 59.969 41.667 3.32 0.0 36.51 5.19 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
77 78 5.213891 ACAAACTTTATGGCAAAAGGAGG 57.786 39.130 19.22 12.84 40.16 4.30
78 79 3.961480 AACTTTATGGCAAAAGGAGGC 57.039 42.857 19.22 0.00 40.16 4.70
86 87 0.813821 GCAAAAGGAGGCCATCTGTC 59.186 55.000 5.01 0.00 0.00 3.51
132 133 6.182627 TGCTGGAAATTCAGTATGTTCATCT 58.817 36.000 0.00 0.00 37.12 2.90
140 141 5.268118 TCAGTATGTTCATCTAGTGCAGG 57.732 43.478 0.00 0.00 37.40 4.85
144 145 4.558226 ATGTTCATCTAGTGCAGGACAA 57.442 40.909 0.00 0.00 0.00 3.18
145 146 3.930336 TGTTCATCTAGTGCAGGACAAG 58.070 45.455 0.00 0.00 0.00 3.16
146 147 3.324846 TGTTCATCTAGTGCAGGACAAGT 59.675 43.478 0.00 0.00 0.00 3.16
147 148 4.526650 TGTTCATCTAGTGCAGGACAAGTA 59.473 41.667 0.00 0.00 0.00 2.24
148 149 4.720649 TCATCTAGTGCAGGACAAGTAC 57.279 45.455 0.00 0.00 0.00 2.73
149 150 4.344978 TCATCTAGTGCAGGACAAGTACT 58.655 43.478 0.00 0.00 36.00 2.73
150 151 4.399618 TCATCTAGTGCAGGACAAGTACTC 59.600 45.833 0.00 0.00 33.87 2.59
151 152 3.090037 TCTAGTGCAGGACAAGTACTCC 58.910 50.000 0.00 0.00 33.87 3.85
152 153 0.977395 AGTGCAGGACAAGTACTCCC 59.023 55.000 0.00 0.00 0.00 4.30
153 154 0.977395 GTGCAGGACAAGTACTCCCT 59.023 55.000 0.00 0.40 0.00 4.20
154 155 1.066787 GTGCAGGACAAGTACTCCCTC 60.067 57.143 0.00 0.00 0.00 4.30
155 156 0.537653 GCAGGACAAGTACTCCCTCC 59.462 60.000 0.00 0.40 0.00 4.30
156 157 0.818296 CAGGACAAGTACTCCCTCCG 59.182 60.000 0.00 0.00 0.00 4.63
157 158 0.408700 AGGACAAGTACTCCCTCCGT 59.591 55.000 0.00 0.00 0.00 4.69
158 159 0.816373 GGACAAGTACTCCCTCCGTC 59.184 60.000 0.00 0.00 0.00 4.79
159 160 0.816373 GACAAGTACTCCCTCCGTCC 59.184 60.000 0.00 0.00 0.00 4.79
160 161 0.964358 ACAAGTACTCCCTCCGTCCG 60.964 60.000 0.00 0.00 0.00 4.79
161 162 1.379576 AAGTACTCCCTCCGTCCGG 60.380 63.158 0.00 0.00 0.00 5.14
162 163 1.856539 AAGTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
163 164 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
164 165 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
165 166 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
166 167 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
167 168 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
168 169 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
169 170 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
170 171 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
171 172 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
172 173 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
173 174 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
174 175 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
175 176 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
176 177 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
177 178 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
178 179 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
179 180 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
180 181 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
181 182 7.201574 CGTCCGGAAATACTTGTCATCAAAATA 60.202 37.037 5.23 0.00 32.87 1.40
182 183 8.122952 GTCCGGAAATACTTGTCATCAAAATAG 58.877 37.037 5.23 0.00 32.87 1.73
183 184 8.044309 TCCGGAAATACTTGTCATCAAAATAGA 58.956 33.333 0.00 0.00 32.87 1.98
184 185 8.840321 CCGGAAATACTTGTCATCAAAATAGAT 58.160 33.333 0.00 0.00 32.87 1.98
185 186 9.655769 CGGAAATACTTGTCATCAAAATAGATG 57.344 33.333 0.00 0.00 45.28 2.90
237 238 8.211030 ACATCTAGATACATCCATTCCAATGA 57.789 34.615 4.54 0.00 38.70 2.57
238 239 8.099537 ACATCTAGATACATCCATTCCAATGAC 58.900 37.037 4.54 0.00 38.70 3.06
239 240 7.616528 TCTAGATACATCCATTCCAATGACA 57.383 36.000 0.56 0.00 38.70 3.58
240 241 8.033178 TCTAGATACATCCATTCCAATGACAA 57.967 34.615 0.56 0.00 38.70 3.18
241 242 8.152898 TCTAGATACATCCATTCCAATGACAAG 58.847 37.037 0.56 0.00 38.70 3.16
242 243 6.666678 AGATACATCCATTCCAATGACAAGT 58.333 36.000 0.56 0.00 38.70 3.16
243 244 7.805163 AGATACATCCATTCCAATGACAAGTA 58.195 34.615 0.56 0.18 38.70 2.24
244 245 8.443176 AGATACATCCATTCCAATGACAAGTAT 58.557 33.333 0.56 4.32 38.70 2.12
245 246 9.071276 GATACATCCATTCCAATGACAAGTATT 57.929 33.333 0.56 0.00 38.70 1.89
246 247 7.722949 ACATCCATTCCAATGACAAGTATTT 57.277 32.000 0.56 0.00 38.70 1.40
247 248 7.775120 ACATCCATTCCAATGACAAGTATTTC 58.225 34.615 0.56 0.00 38.70 2.17
248 249 6.773976 TCCATTCCAATGACAAGTATTTCC 57.226 37.500 0.56 0.00 38.70 3.13
249 250 5.356751 TCCATTCCAATGACAAGTATTTCCG 59.643 40.000 0.56 0.00 38.70 4.30
250 251 5.450412 CCATTCCAATGACAAGTATTTCCGG 60.450 44.000 0.00 0.00 38.70 5.14
251 252 4.561500 TCCAATGACAAGTATTTCCGGA 57.438 40.909 0.00 0.00 0.00 5.14
252 253 4.258543 TCCAATGACAAGTATTTCCGGAC 58.741 43.478 1.83 0.00 0.00 4.79
253 254 3.063452 CCAATGACAAGTATTTCCGGACG 59.937 47.826 1.83 0.00 0.00 4.79
254 255 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
255 256 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
256 257 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
257 258 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
258 259 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
284 285 8.924511 AGTAGGTGTTTCCATTATTCCATATG 57.075 34.615 0.00 0.00 39.02 1.78
287 288 6.783977 AGGTGTTTCCATTATTCCATATGCAT 59.216 34.615 3.79 3.79 39.02 3.96
288 289 7.290714 AGGTGTTTCCATTATTCCATATGCATT 59.709 33.333 3.54 0.00 39.02 3.56
289 290 7.933033 GGTGTTTCCATTATTCCATATGCATTT 59.067 33.333 3.54 0.00 35.97 2.32
290 291 9.979578 GTGTTTCCATTATTCCATATGCATTTA 57.020 29.630 3.54 0.00 0.00 1.40
291 292 9.979578 TGTTTCCATTATTCCATATGCATTTAC 57.020 29.630 3.54 0.00 0.00 2.01
292 293 9.423061 GTTTCCATTATTCCATATGCATTTACC 57.577 33.333 3.54 0.00 0.00 2.85
293 294 8.718158 TTCCATTATTCCATATGCATTTACCA 57.282 30.769 3.54 0.00 0.00 3.25
294 295 8.898303 TCCATTATTCCATATGCATTTACCAT 57.102 30.769 3.54 0.00 0.00 3.55
295 296 9.987726 TCCATTATTCCATATGCATTTACCATA 57.012 29.630 3.54 0.00 0.00 2.74
301 302 8.579850 TTCCATATGCATTTACCATAATCTCC 57.420 34.615 3.54 0.00 0.00 3.71
311 312 6.742559 TTACCATAATCTCCCCTTCAGTAC 57.257 41.667 0.00 0.00 0.00 2.73
341 342 6.811665 ACCTTTCTTAACTGCAAAAACAAGTC 59.188 34.615 0.00 0.00 0.00 3.01
351 352 3.119495 GCAAAAACAAGTCTGTCCACACT 60.119 43.478 0.00 0.00 33.45 3.55
498 499 5.010282 TCTCCAATAACCAAAGCCTTCTTC 58.990 41.667 0.00 0.00 0.00 2.87
509 510 1.283321 AGCCTTCTTCTCCCCACATTC 59.717 52.381 0.00 0.00 0.00 2.67
590 591 4.195334 ATGTCCATGCCGCCTCCC 62.195 66.667 0.00 0.00 0.00 4.30
654 655 5.911752 ACCTAATGAGCTCACTAATCACTG 58.088 41.667 20.97 0.00 0.00 3.66
676 677 4.127171 GGCCATGTGTATACCTAACACTG 58.873 47.826 0.00 4.15 45.95 3.66
697 698 0.685785 AACACATGCACCCACCAACA 60.686 50.000 0.00 0.00 0.00 3.33
701 702 1.076412 ATGCACCCACCAACACACA 60.076 52.632 0.00 0.00 0.00 3.72
706 711 0.179029 ACCCACCAACACACACTAGC 60.179 55.000 0.00 0.00 0.00 3.42
707 712 0.108585 CCCACCAACACACACTAGCT 59.891 55.000 0.00 0.00 0.00 3.32
708 713 1.229428 CCACCAACACACACTAGCTG 58.771 55.000 0.00 0.00 0.00 4.24
709 714 1.229428 CACCAACACACACTAGCTGG 58.771 55.000 0.00 0.00 0.00 4.85
734 739 3.479489 CATCACCAATGCTATGCTACCA 58.521 45.455 0.00 0.00 0.00 3.25
735 740 3.643199 TCACCAATGCTATGCTACCAA 57.357 42.857 0.00 0.00 0.00 3.67
737 742 3.054434 TCACCAATGCTATGCTACCAAGT 60.054 43.478 0.00 0.00 0.00 3.16
738 743 4.163268 TCACCAATGCTATGCTACCAAGTA 59.837 41.667 0.00 0.00 0.00 2.24
740 745 5.532406 CACCAATGCTATGCTACCAAGTAAT 59.468 40.000 0.00 0.00 0.00 1.89
741 746 5.532406 ACCAATGCTATGCTACCAAGTAATG 59.468 40.000 0.00 0.00 0.00 1.90
742 747 5.455392 CAATGCTATGCTACCAAGTAATGC 58.545 41.667 0.00 0.00 0.00 3.56
746 751 6.353323 TGCTATGCTACCAAGTAATGCTAAA 58.647 36.000 0.00 0.00 0.00 1.85
788 796 6.874134 AGGAGTACATTATTCGTTATCATGGC 59.126 38.462 0.00 0.00 0.00 4.40
789 797 6.183360 GGAGTACATTATTCGTTATCATGGCG 60.183 42.308 0.00 0.00 0.00 5.69
796 804 3.936902 TCGTTATCATGGCGCTTAAAC 57.063 42.857 7.64 3.12 0.00 2.01
804 812 1.099689 TGGCGCTTAAACTAATGGCC 58.900 50.000 7.64 0.00 36.80 5.36
810 818 4.320275 GCGCTTAAACTAATGGCCTAATCC 60.320 45.833 3.32 0.00 0.00 3.01
902 910 1.134610 CCAAGGCAATCAATGGAAGCC 60.135 52.381 8.53 8.53 44.30 4.35
912 920 0.394352 AATGGAAGCCCGCAACTAGG 60.394 55.000 0.00 0.00 34.29 3.02
922 930 1.402968 CCGCAACTAGGACGTAGCTAA 59.597 52.381 0.00 0.00 30.92 3.09
933 941 3.556513 GACGTAGCTAAGTGATCATCCG 58.443 50.000 17.36 4.36 0.00 4.18
953 961 2.508887 GCAGAGACCAGCTGAGCG 60.509 66.667 17.39 0.15 35.39 5.03
1860 1887 1.064389 GGCAAGATACCCAAGGAGCTT 60.064 52.381 0.00 0.00 0.00 3.74
2124 2151 1.794785 CGTCTCGACAAACGCGCTA 60.795 57.895 5.73 0.00 42.26 4.26
2358 2385 2.043349 TCCGGCGAGATCCCAGAA 60.043 61.111 9.30 0.00 0.00 3.02
2571 2598 2.965462 CTTTCCGGCGCGATACCC 60.965 66.667 12.10 0.00 0.00 3.69
2617 2644 0.658829 CGTATCGCTGAGCCTTCGAG 60.659 60.000 0.00 0.00 35.61 4.04
2982 3021 4.166888 ATCGCGCTCCTGGCATGT 62.167 61.111 5.56 0.00 41.91 3.21
2987 3026 2.034687 GCTCCTGGCATGTGGTGT 59.965 61.111 0.00 0.00 41.35 4.16
3000 3039 1.562008 TGTGGTGTTGTCTTCCTTGGA 59.438 47.619 0.00 0.00 0.00 3.53
3045 3090 1.596203 CCATGGATGCTGCGACGAT 60.596 57.895 5.56 0.00 0.00 3.73
4156 4210 2.611518 GGAGACGTGACCAAGATTCAG 58.388 52.381 0.00 0.00 0.00 3.02
4182 4236 7.111455 GCGACGTGTATGTTTTGTATACGTATA 59.889 37.037 11.27 11.27 45.52 1.47
4183 4237 9.106286 CGACGTGTATGTTTTGTATACGTATAT 57.894 33.333 17.86 4.48 45.52 0.86
4185 4239 9.398170 ACGTGTATGTTTTGTATACGTATATCC 57.602 33.333 17.86 7.32 44.34 2.59
4439 4495 1.065551 GGTGTTGCCACTGTCTTTGAC 59.934 52.381 0.00 0.00 41.53 3.18
4498 4566 6.818644 TCCAGAGATAGTTGTTCATTGTTAGC 59.181 38.462 0.00 0.00 0.00 3.09
4508 4582 3.634568 TCATTGTTAGCGTTGTTTGGG 57.365 42.857 0.00 0.00 0.00 4.12
4527 4601 1.464734 GCCCTCTTTGCTTTACCCTC 58.535 55.000 0.00 0.00 0.00 4.30
4528 4602 1.739067 CCCTCTTTGCTTTACCCTCG 58.261 55.000 0.00 0.00 0.00 4.63
4529 4603 1.003233 CCCTCTTTGCTTTACCCTCGT 59.997 52.381 0.00 0.00 0.00 4.18
4537 4611 0.801251 CTTTACCCTCGTCGTCGTCT 59.199 55.000 1.33 0.00 38.33 4.18
4543 4617 1.082038 CTCGTCGTCGTCTGCACTT 60.082 57.895 1.33 0.00 38.33 3.16
4544 4618 0.660595 CTCGTCGTCGTCTGCACTTT 60.661 55.000 1.33 0.00 38.33 2.66
4589 4663 9.323985 CTTTTTCACATAGTTTTGAATTTGGGA 57.676 29.630 0.00 0.00 31.87 4.37
4591 4665 9.844257 TTTTCACATAGTTTTGAATTTGGGATT 57.156 25.926 0.00 0.00 31.87 3.01
4685 4759 7.110155 TGTATGTAAAGGAATTGGTCTCTTCC 58.890 38.462 0.00 0.00 41.07 3.46
4821 4895 2.579207 TCTAATTCCTTGGTCTCGCG 57.421 50.000 0.00 0.00 0.00 5.87
4838 4912 4.478195 GACTGTCGTCGACATGGG 57.522 61.111 27.10 18.19 41.94 4.00
4873 4947 7.044798 AGGAGAGATAGTTGTTCATTGTTAGC 58.955 38.462 0.00 0.00 0.00 3.09
4914 4988 1.045407 TTACCCTCGTCTGCACTTGT 58.955 50.000 0.00 0.00 0.00 3.16
4918 4992 1.272490 CCCTCGTCTGCACTTGTCTTA 59.728 52.381 0.00 0.00 0.00 2.10
4952 5026 9.219603 CATTTCTTCACTATCACAACTTTAGGA 57.780 33.333 0.00 0.00 0.00 2.94
4959 5033 9.653287 TCACTATCACAACTTTAGGATGTAAAG 57.347 33.333 3.50 3.50 39.65 1.85
4961 5035 8.322091 ACTATCACAACTTTAGGATGTAAAGCT 58.678 33.333 4.75 0.00 37.89 3.74
4966 5040 8.184192 CACAACTTTAGGATGTAAAGCTATTGG 58.816 37.037 4.75 0.00 37.89 3.16
4972 5046 4.103311 AGGATGTAAAGCTATTGGTCCCTC 59.897 45.833 0.00 0.00 0.00 4.30
4992 5066 9.325198 GTCCCTCAAATTGAAATAACAAGTTTT 57.675 29.630 0.00 0.00 36.23 2.43
5040 5114 9.851686 ATTATAGTGGCTGAATCATGAACTAAA 57.148 29.630 0.00 0.26 0.00 1.85
5078 5152 1.617850 CTCGGAGATTGGAGAGGGATG 59.382 57.143 0.00 0.00 33.89 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 6.494893 TTAGTGTTAAACATGACAGATGGC 57.505 37.500 0.00 0.00 0.00 4.40
78 79 8.267620 TGATTAGTGTTAAACATGACAGATGG 57.732 34.615 0.00 0.00 0.00 3.51
132 133 2.176889 GGGAGTACTTGTCCTGCACTA 58.823 52.381 0.00 0.00 34.16 2.74
140 141 0.816373 GGACGGAGGGAGTACTTGTC 59.184 60.000 0.00 0.00 0.00 3.18
144 145 1.856539 TTCCGGACGGAGGGAGTACT 61.857 60.000 13.64 0.00 46.06 2.73
145 146 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
146 147 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
147 148 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
148 149 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
149 150 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
150 151 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
151 152 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
152 153 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
153 154 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
154 155 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
155 156 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
156 157 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
157 158 8.044309 TCTATTTTGATGACAAGTATTTCCGGA 58.956 33.333 0.00 0.00 37.32 5.14
158 159 8.208718 TCTATTTTGATGACAAGTATTTCCGG 57.791 34.615 0.00 0.00 37.32 5.14
159 160 9.655769 CATCTATTTTGATGACAAGTATTTCCG 57.344 33.333 0.00 0.00 44.71 4.30
211 212 9.325248 TCATTGGAATGGATGTATCTAGATGTA 57.675 33.333 15.79 4.44 37.03 2.29
212 213 8.099537 GTCATTGGAATGGATGTATCTAGATGT 58.900 37.037 15.79 1.25 37.03 3.06
213 214 8.098912 TGTCATTGGAATGGATGTATCTAGATG 58.901 37.037 15.79 0.00 37.03 2.90
214 215 8.211030 TGTCATTGGAATGGATGTATCTAGAT 57.789 34.615 10.73 10.73 37.03 1.98
215 216 7.616528 TGTCATTGGAATGGATGTATCTAGA 57.383 36.000 0.00 0.00 37.03 2.43
216 217 7.935755 ACTTGTCATTGGAATGGATGTATCTAG 59.064 37.037 0.00 0.00 37.03 2.43
217 218 7.805163 ACTTGTCATTGGAATGGATGTATCTA 58.195 34.615 0.00 0.00 37.03 1.98
218 219 6.666678 ACTTGTCATTGGAATGGATGTATCT 58.333 36.000 0.00 0.00 37.03 1.98
219 220 6.949352 ACTTGTCATTGGAATGGATGTATC 57.051 37.500 0.00 0.00 37.03 2.24
220 221 9.425248 AAATACTTGTCATTGGAATGGATGTAT 57.575 29.630 0.00 3.54 37.03 2.29
221 222 8.821686 AAATACTTGTCATTGGAATGGATGTA 57.178 30.769 0.00 1.74 37.03 2.29
222 223 7.147846 GGAAATACTTGTCATTGGAATGGATGT 60.148 37.037 0.00 0.00 37.03 3.06
223 224 7.205297 GGAAATACTTGTCATTGGAATGGATG 58.795 38.462 0.00 0.00 37.03 3.51
224 225 6.039717 CGGAAATACTTGTCATTGGAATGGAT 59.960 38.462 0.00 0.00 37.03 3.41
225 226 5.356751 CGGAAATACTTGTCATTGGAATGGA 59.643 40.000 0.00 0.00 37.03 3.41
226 227 5.450412 CCGGAAATACTTGTCATTGGAATGG 60.450 44.000 0.00 0.00 37.03 3.16
227 228 5.356751 TCCGGAAATACTTGTCATTGGAATG 59.643 40.000 0.00 0.00 37.75 2.67
228 229 5.357032 GTCCGGAAATACTTGTCATTGGAAT 59.643 40.000 5.23 0.00 0.00 3.01
229 230 4.698304 GTCCGGAAATACTTGTCATTGGAA 59.302 41.667 5.23 0.00 0.00 3.53
230 231 4.258543 GTCCGGAAATACTTGTCATTGGA 58.741 43.478 5.23 0.00 0.00 3.53
231 232 3.063452 CGTCCGGAAATACTTGTCATTGG 59.937 47.826 5.23 0.00 0.00 3.16
232 233 3.063452 CCGTCCGGAAATACTTGTCATTG 59.937 47.826 5.23 0.00 37.50 2.82
233 234 3.055675 TCCGTCCGGAAATACTTGTCATT 60.056 43.478 5.23 0.00 42.05 2.57
234 235 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
235 236 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
236 237 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
237 238 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
238 239 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
239 240 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
240 241 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
241 242 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
242 243 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
243 244 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
244 245 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
245 246 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
246 247 2.593978 CTACTCCCTCCGTCCGGA 59.406 66.667 0.00 0.00 42.90 5.14
247 248 2.518825 CCTACTCCCTCCGTCCGG 60.519 72.222 0.00 0.00 0.00 5.14
248 249 2.119655 CACCTACTCCCTCCGTCCG 61.120 68.421 0.00 0.00 0.00 4.79
249 250 0.614134 AACACCTACTCCCTCCGTCC 60.614 60.000 0.00 0.00 0.00 4.79
250 251 1.204231 GAAACACCTACTCCCTCCGTC 59.796 57.143 0.00 0.00 0.00 4.79
251 252 1.264295 GAAACACCTACTCCCTCCGT 58.736 55.000 0.00 0.00 0.00 4.69
252 253 0.535797 GGAAACACCTACTCCCTCCG 59.464 60.000 0.00 0.00 35.41 4.63
253 254 1.652947 TGGAAACACCTACTCCCTCC 58.347 55.000 0.00 0.00 39.86 4.30
284 285 5.385198 TGAAGGGGAGATTATGGTAAATGC 58.615 41.667 0.00 0.00 0.00 3.56
287 288 6.674861 TGTACTGAAGGGGAGATTATGGTAAA 59.325 38.462 0.00 0.00 0.00 2.01
288 289 6.206787 TGTACTGAAGGGGAGATTATGGTAA 58.793 40.000 0.00 0.00 0.00 2.85
289 290 5.784023 TGTACTGAAGGGGAGATTATGGTA 58.216 41.667 0.00 0.00 0.00 3.25
290 291 4.631234 TGTACTGAAGGGGAGATTATGGT 58.369 43.478 0.00 0.00 0.00 3.55
291 292 5.630415 TTGTACTGAAGGGGAGATTATGG 57.370 43.478 0.00 0.00 0.00 2.74
292 293 7.661847 GGTTATTGTACTGAAGGGGAGATTATG 59.338 40.741 0.00 0.00 0.00 1.90
293 294 7.572861 AGGTTATTGTACTGAAGGGGAGATTAT 59.427 37.037 0.00 0.00 0.00 1.28
294 295 6.906901 AGGTTATTGTACTGAAGGGGAGATTA 59.093 38.462 0.00 0.00 0.00 1.75
295 296 5.731678 AGGTTATTGTACTGAAGGGGAGATT 59.268 40.000 0.00 0.00 0.00 2.40
296 297 5.289510 AGGTTATTGTACTGAAGGGGAGAT 58.710 41.667 0.00 0.00 0.00 2.75
297 298 4.695606 AGGTTATTGTACTGAAGGGGAGA 58.304 43.478 0.00 0.00 0.00 3.71
298 299 5.437191 AAGGTTATTGTACTGAAGGGGAG 57.563 43.478 0.00 0.00 0.00 4.30
299 300 5.550403 AGAAAGGTTATTGTACTGAAGGGGA 59.450 40.000 0.00 0.00 0.00 4.81
300 301 5.816682 AGAAAGGTTATTGTACTGAAGGGG 58.183 41.667 0.00 0.00 0.00 4.79
301 302 8.727910 GTTAAGAAAGGTTATTGTACTGAAGGG 58.272 37.037 0.00 0.00 0.00 3.95
311 312 9.092876 TGTTTTTGCAGTTAAGAAAGGTTATTG 57.907 29.630 0.00 0.00 0.00 1.90
341 342 8.771920 TTCTATGTGTTAATTAGTGTGGACAG 57.228 34.615 0.00 0.00 0.00 3.51
498 499 0.034089 GTGAAGGGGAATGTGGGGAG 60.034 60.000 0.00 0.00 0.00 4.30
509 510 2.362889 GCCCATGTGGTGAAGGGG 60.363 66.667 0.00 0.00 41.75 4.79
590 591 2.416547 CGGCATGAGAGTGTAAAGGTTG 59.583 50.000 0.00 0.00 0.00 3.77
654 655 4.127171 CAGTGTTAGGTATACACATGGCC 58.873 47.826 5.01 0.00 46.42 5.36
697 698 2.093973 GTGATGCTACCAGCTAGTGTGT 60.094 50.000 0.00 0.00 42.97 3.72
701 702 1.866015 TGGTGATGCTACCAGCTAGT 58.134 50.000 4.30 0.00 45.46 2.57
727 732 9.402320 TGAATAATTTAGCATTACTTGGTAGCA 57.598 29.630 0.00 0.00 39.36 3.49
777 785 3.944422 AGTTTAAGCGCCATGATAACG 57.056 42.857 2.29 0.00 0.00 3.18
788 796 4.215613 GGGATTAGGCCATTAGTTTAAGCG 59.784 45.833 5.01 0.00 0.00 4.68
789 797 5.137551 TGGGATTAGGCCATTAGTTTAAGC 58.862 41.667 5.01 0.00 0.00 3.09
796 804 5.779241 TTAGGATGGGATTAGGCCATTAG 57.221 43.478 5.01 0.00 0.00 1.73
804 812 8.037758 GTGTGTCTATGATTAGGATGGGATTAG 58.962 40.741 0.00 0.00 0.00 1.73
810 818 5.465051 CGAGTGTGTCTATGATTAGGATGG 58.535 45.833 0.00 0.00 0.00 3.51
902 910 1.019673 TAGCTACGTCCTAGTTGCGG 58.980 55.000 0.00 0.00 45.07 5.69
912 920 3.003482 ACGGATGATCACTTAGCTACGTC 59.997 47.826 0.00 0.00 0.00 4.34
922 930 0.383590 CTCTGCGACGGATGATCACT 59.616 55.000 0.00 0.00 0.00 3.41
933 941 1.153862 CTCAGCTGGTCTCTGCGAC 60.154 63.158 15.13 0.00 41.81 5.19
953 961 4.785453 CCTCCACTCCTTGGCGCC 62.785 72.222 22.73 22.73 46.47 6.53
970 978 1.048160 CCTCTGCTCCCCTTCTCCTC 61.048 65.000 0.00 0.00 0.00 3.71
974 982 0.032217 CTCTCCTCTGCTCCCCTTCT 60.032 60.000 0.00 0.00 0.00 2.85
1799 1826 2.416244 GAACACCGTGTCGAGCTCCA 62.416 60.000 8.47 0.00 0.00 3.86
1860 1887 4.954118 AGGGACGACAGGTGGCCA 62.954 66.667 0.00 0.00 0.00 5.36
1864 1891 2.265904 TGACGAGGGACGACAGGTG 61.266 63.158 0.00 0.00 45.77 4.00
2262 2289 1.666553 CACTGTGCCGTTAAGCCGA 60.667 57.895 0.00 0.00 0.00 5.54
2955 2988 3.830994 GAGCGCGATCGAGATGCCA 62.831 63.158 23.47 0.00 38.10 4.92
2979 3012 2.174639 TCCAAGGAAGACAACACCACAT 59.825 45.455 0.00 0.00 0.00 3.21
2982 3021 3.287222 CTTTCCAAGGAAGACAACACCA 58.713 45.455 1.32 0.00 35.38 4.17
2987 3026 1.956477 GCAGCTTTCCAAGGAAGACAA 59.044 47.619 1.32 0.00 35.38 3.18
3045 3090 0.888736 TCCCGTCTTCGTCCACGTTA 60.889 55.000 0.00 0.00 40.80 3.18
4156 4210 4.030529 ACGTATACAAAACATACACGTCGC 59.969 41.667 3.32 0.00 36.51 5.19
4182 4236 8.798402 GTTGTAGTAGATTACATGAGCTAGGAT 58.202 37.037 0.00 0.00 33.81 3.24
4183 4237 7.041303 CGTTGTAGTAGATTACATGAGCTAGGA 60.041 40.741 0.00 0.00 33.81 2.94
4184 4238 7.078851 CGTTGTAGTAGATTACATGAGCTAGG 58.921 42.308 0.00 0.00 33.81 3.02
4185 4239 6.579292 GCGTTGTAGTAGATTACATGAGCTAG 59.421 42.308 0.00 0.00 33.81 3.42
4264 4318 3.061322 TGTTTACATTGGTTCCTCGTCG 58.939 45.455 0.00 0.00 0.00 5.12
4265 4319 5.048991 ACATTGTTTACATTGGTTCCTCGTC 60.049 40.000 8.95 0.00 33.04 4.20
4406 4462 4.622701 GGCAACACCAATGAGTTAGATC 57.377 45.455 0.00 0.00 38.86 2.75
4439 4495 4.552166 ACAACTTTGTTCTTCGTCCATG 57.448 40.909 0.00 0.00 38.47 3.66
4466 4522 5.662657 TGAACAACTATCTCTGGATCATGGA 59.337 40.000 0.00 0.00 33.71 3.41
4498 4566 0.031994 CAAAGAGGGCCCAAACAACG 59.968 55.000 27.56 1.36 0.00 4.10
4508 4582 1.464734 GAGGGTAAAGCAAAGAGGGC 58.535 55.000 0.00 0.00 0.00 5.19
4527 4601 0.701303 GTAAAGTGCAGACGACGACG 59.299 55.000 5.58 5.58 45.75 5.12
4528 4602 2.047679 AGTAAAGTGCAGACGACGAC 57.952 50.000 0.00 0.00 0.00 4.34
4529 4603 2.810274 AGTAGTAAAGTGCAGACGACGA 59.190 45.455 0.00 0.00 0.00 4.20
4537 4611 5.771666 AGTGTAGGTGTAGTAGTAAAGTGCA 59.228 40.000 0.00 0.00 0.00 4.57
4544 4618 9.573166 TGAAAAAGTAGTGTAGGTGTAGTAGTA 57.427 33.333 0.00 0.00 0.00 1.82
4613 4687 1.693627 TGTTTACATTGGTTGCCCGT 58.306 45.000 0.00 0.00 0.00 5.28
4615 4689 4.001618 ACATTGTTTACATTGGTTGCCC 57.998 40.909 8.95 0.00 33.04 5.36
4616 4690 7.665561 ATAAACATTGTTTACATTGGTTGCC 57.334 32.000 21.07 0.00 37.60 4.52
4789 4863 4.250464 AGGAATTAGATGTGTTTTCGCGA 58.750 39.130 3.71 3.71 0.00 5.87
4793 4867 7.454260 AGACCAAGGAATTAGATGTGTTTTC 57.546 36.000 0.00 0.00 0.00 2.29
4821 4895 1.805945 GCCCATGTCGACGACAGTC 60.806 63.158 31.72 17.94 46.04 3.51
4838 4912 2.703007 ACTATCTCTCCTTGGTCCATGC 59.297 50.000 0.00 0.00 0.00 4.06
4873 4947 0.031994 CAAAGAGGGCCCAAACAACG 59.968 55.000 27.56 1.36 0.00 4.10
4918 4992 8.463930 TGTGATAGTGAAGAAATGGAGTTTTT 57.536 30.769 0.00 0.00 0.00 1.94
4952 5026 5.450818 TTGAGGGACCAATAGCTTTACAT 57.549 39.130 0.00 0.00 0.00 2.29
4959 5033 5.659440 TTTCAATTTGAGGGACCAATAGC 57.341 39.130 0.00 0.00 0.00 2.97
4961 5035 8.657387 TGTTATTTCAATTTGAGGGACCAATA 57.343 30.769 0.00 0.00 0.00 1.90
4966 5040 8.887036 AAACTTGTTATTTCAATTTGAGGGAC 57.113 30.769 0.00 0.00 0.00 4.46
5012 5086 6.713903 AGTTCATGATTCAGCCACTATAATGG 59.286 38.462 0.00 0.00 43.26 3.16
5040 5114 6.439636 TCCGAGATTATGGGAGAAATCAAT 57.560 37.500 0.00 0.00 35.07 2.57
5068 5142 2.696864 TGGACAACCATCCCTCTCC 58.303 57.895 0.00 0.00 41.77 3.71
5078 5152 2.418368 TGATGCTACCATGGACAACC 57.582 50.000 21.47 10.12 0.00 3.77


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

AutoCloner maintained by Alex Coulton.