Multiple sequence alignment - TraesCS1D01G425000

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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 TraesCS1D01G425000 chr1D 100.000 6659 0 0 1 6659 479048852 479055510 0.000000e+00 12297
1 TraesCS1D01G425000 chr1D 88.339 283 30 2 1838 2119 417760609 417760889 2.970000e-88 337
2 TraesCS1D01G425000 chr1A 95.249 5851 169 35 1 5798 575362398 575368192 0.000000e+00 9164
3 TraesCS1D01G425000 chr1A 86.020 887 59 31 5798 6656 575368261 575369110 0.000000e+00 891
4 TraesCS1D01G425000 chr1B 94.635 4697 136 53 1 4632 667223737 667228382 0.000000e+00 7171
5 TraesCS1D01G425000 chr1B 91.388 1196 72 11 4630 5798 667228486 667229677 0.000000e+00 1609
6 TraesCS1D01G425000 chr1B 93.990 599 18 9 5798 6383 667229745 667230338 0.000000e+00 891
7 TraesCS1D01G425000 chr1B 92.373 354 26 1 2993 3345 121768910 121769263 2.770000e-138 503
8 TraesCS1D01G425000 chr1B 90.114 263 21 3 1992 2251 121768243 121768503 2.970000e-88 337
9 TraesCS1D01G425000 chr1B 94.702 151 8 0 6509 6659 667230338 667230488 1.120000e-57 235
10 TraesCS1D01G425000 chr3B 89.729 516 46 7 644 1158 34547527 34547018 0.000000e+00 652
11 TraesCS1D01G425000 chr3B 89.494 514 45 8 641 1152 35541541 35542047 5.630000e-180 641
12 TraesCS1D01G425000 chr3B 89.147 516 49 7 641 1155 35725582 35726091 2.620000e-178 636
13 TraesCS1D01G425000 chr3B 88.953 516 50 7 641 1155 35513552 35514061 1.220000e-176 630
14 TraesCS1D01G425000 chr3B 88.953 516 50 7 641 1155 35797272 35797781 1.220000e-176 630
15 TraesCS1D01G425000 chrUn 89.147 516 49 7 644 1158 286898238 286897729 2.620000e-178 636
16 TraesCS1D01G425000 chrUn 89.147 516 49 7 641 1155 378043938 378044447 2.620000e-178 636
17 TraesCS1D01G425000 chr4B 93.094 362 24 1 2993 3353 409740397 409740758 4.570000e-146 529
18 TraesCS1D01G425000 chr4B 92.542 295 21 1 1992 2285 409740103 409740397 7.980000e-114 422
19 TraesCS1D01G425000 chr4B 87.762 286 32 2 1835 2119 222965820 222966103 1.380000e-86 331
20 TraesCS1D01G425000 chr2D 90.909 286 22 2 1834 2119 29450266 29449985 1.360000e-101 381
21 TraesCS1D01G425000 chr2D 89.860 286 26 2 1832 2116 613466868 613467151 1.360000e-96 364
22 TraesCS1D01G425000 chr5D 90.559 286 24 3 1832 2116 52597510 52597793 6.300000e-100 375
23 TraesCS1D01G425000 chr6D 89.510 286 27 2 1835 2119 54632 54349 6.350000e-95 359
24 TraesCS1D01G425000 chr7D 89.046 283 29 1 1832 2114 41331126 41331406 3.820000e-92 350


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 TraesCS1D01G425000 chr1D 479048852 479055510 6658 False 12297.0 12297 100.00000 1 6659 1 chr1D.!!$F2 6658
1 TraesCS1D01G425000 chr1A 575362398 575369110 6712 False 5027.5 9164 90.63450 1 6656 2 chr1A.!!$F1 6655
2 TraesCS1D01G425000 chr1B 667223737 667230488 6751 False 2476.5 7171 93.67875 1 6659 4 chr1B.!!$F2 6658
3 TraesCS1D01G425000 chr1B 121768243 121769263 1020 False 420.0 503 91.24350 1992 3345 2 chr1B.!!$F1 1353
4 TraesCS1D01G425000 chr3B 34547018 34547527 509 True 652.0 652 89.72900 644 1158 1 chr3B.!!$R1 514
5 TraesCS1D01G425000 chr3B 35541541 35542047 506 False 641.0 641 89.49400 641 1152 1 chr3B.!!$F2 511
6 TraesCS1D01G425000 chr3B 35725582 35726091 509 False 636.0 636 89.14700 641 1155 1 chr3B.!!$F3 514
7 TraesCS1D01G425000 chr3B 35513552 35514061 509 False 630.0 630 88.95300 641 1155 1 chr3B.!!$F1 514
8 TraesCS1D01G425000 chr3B 35797272 35797781 509 False 630.0 630 88.95300 641 1155 1 chr3B.!!$F4 514
9 TraesCS1D01G425000 chrUn 286897729 286898238 509 True 636.0 636 89.14700 644 1158 1 chrUn.!!$R1 514
10 TraesCS1D01G425000 chrUn 378043938 378044447 509 False 636.0 636 89.14700 641 1155 1 chrUn.!!$F1 514
11 TraesCS1D01G425000 chr4B 409740103 409740758 655 False 475.5 529 92.81800 1992 3353 2 chr4B.!!$F2 1361

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
583 629 0.257905 AGATGTGCATGGACTGGCAT 59.742 50.000 18.75 3.25 42.75 4.40 F
585 631 0.323999 ATGTGCATGGACTGGCATGT 60.324 50.000 18.75 0.00 42.75 3.21 F
586 632 0.540133 TGTGCATGGACTGGCATGTT 60.540 50.000 18.75 0.00 42.75 2.71 F
587 633 0.604578 GTGCATGGACTGGCATGTTT 59.395 50.000 10.51 0.00 42.75 2.83 F
588 634 1.001181 GTGCATGGACTGGCATGTTTT 59.999 47.619 10.51 0.00 42.75 2.43 F
1365 1412 1.652947 GGGGAGGTAGAGTGAACCAA 58.347 55.000 0.00 0.00 39.64 3.67 F
3054 3477 0.750182 TGGGCCGGCAAAGTAATAGC 60.750 55.000 30.85 6.06 0.00 2.97 F
3288 3712 1.295020 TTATAAGGCTGTGGTGGGCT 58.705 50.000 0.00 0.00 41.37 5.19 F
3471 3895 1.960689 GGTCCTAAAAAGTTGCCTGCA 59.039 47.619 0.00 0.00 0.00 4.41 F
5399 5988 0.254747 TTAATTCCCGTCAGGCCCAG 59.745 55.000 0.00 0.00 35.76 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2031 2081 0.728129 CTGACGCTCGTTGACGCTAA 60.728 55.000 0.00 0.00 39.60 3.09 R
2360 2783 5.030295 CAGATTGCAAAAGCACGGTATAAG 58.970 41.667 1.71 0.00 0.00 1.73 R
2458 2881 5.181245 GTGATAGGCTCTGCAAAGTGTTTAA 59.819 40.000 0.00 0.00 0.00 1.52 R
2539 2962 6.839205 GTTAAGTTAACATGAGCAGTTCCTGC 60.839 42.308 18.82 8.14 45.91 4.85 R
2625 3048 2.485479 GCTCCCATTTAGCTTCGATGGA 60.485 50.000 18.87 8.47 42.31 3.41 R
3279 3703 0.685097 TGTCTCTGTTAGCCCACCAC 59.315 55.000 0.00 0.00 0.00 4.16 R
4560 5000 0.786581 CGAACACACTAGCACAGCAG 59.213 55.000 0.00 0.00 0.00 4.24 R
4674 5221 1.447317 CGCAGTCACACCAAAGCCTT 61.447 55.000 0.00 0.00 0.00 4.35 R
5473 6062 0.465097 ATGGCTGCTGTACCAGATGC 60.465 55.000 0.00 0.00 39.88 3.91 R
6501 7192 1.670791 TCTTTGTTGGTGACGTTCCC 58.329 50.000 7.98 3.29 0.00 3.97 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
115 143 1.067142 GTGCCGTGAGAATGTCCAGTA 60.067 52.381 0.00 0.00 0.00 2.74
116 144 1.831106 TGCCGTGAGAATGTCCAGTAT 59.169 47.619 0.00 0.00 0.00 2.12
117 145 3.028130 TGCCGTGAGAATGTCCAGTATA 58.972 45.455 0.00 0.00 0.00 1.47
118 146 3.449377 TGCCGTGAGAATGTCCAGTATAA 59.551 43.478 0.00 0.00 0.00 0.98
128 170 7.680730 AGAATGTCCAGTATAACTGTTTGACT 58.319 34.615 0.00 0.00 44.50 3.41
188 230 4.088056 TGGAACCGAAATGAGTAACCAA 57.912 40.909 0.00 0.00 0.00 3.67
189 231 3.816523 TGGAACCGAAATGAGTAACCAAC 59.183 43.478 0.00 0.00 0.00 3.77
190 232 4.070009 GGAACCGAAATGAGTAACCAACT 58.930 43.478 0.00 0.00 42.80 3.16
191 233 5.221682 TGGAACCGAAATGAGTAACCAACTA 60.222 40.000 0.00 0.00 39.07 2.24
192 234 5.702209 GGAACCGAAATGAGTAACCAACTAA 59.298 40.000 0.00 0.00 39.07 2.24
193 235 6.128363 GGAACCGAAATGAGTAACCAACTAAG 60.128 42.308 0.00 0.00 39.07 2.18
194 236 4.694037 ACCGAAATGAGTAACCAACTAAGC 59.306 41.667 0.00 0.00 39.07 3.09
195 237 4.693566 CCGAAATGAGTAACCAACTAAGCA 59.306 41.667 0.00 0.00 39.07 3.91
223 265 2.416836 GCACACTACCTGCTTGATCGTA 60.417 50.000 0.00 0.00 0.00 3.43
224 266 3.738281 GCACACTACCTGCTTGATCGTAT 60.738 47.826 0.00 0.00 0.00 3.06
225 267 3.798878 CACACTACCTGCTTGATCGTATG 59.201 47.826 0.00 0.00 0.00 2.39
226 268 2.797156 CACTACCTGCTTGATCGTATGC 59.203 50.000 0.00 0.00 0.00 3.14
227 269 2.054363 CTACCTGCTTGATCGTATGCG 58.946 52.381 0.00 0.00 39.92 4.73
229 271 0.578683 CCTGCTTGATCGTATGCGTG 59.421 55.000 2.37 0.00 39.49 5.34
230 272 1.559831 CTGCTTGATCGTATGCGTGA 58.440 50.000 2.37 0.00 39.49 4.35
232 274 1.277326 GCTTGATCGTATGCGTGACA 58.723 50.000 2.37 0.00 39.49 3.58
235 277 3.242413 GCTTGATCGTATGCGTGACATTT 60.242 43.478 2.37 0.00 40.38 2.32
236 278 3.923827 TGATCGTATGCGTGACATTTG 57.076 42.857 2.37 0.00 40.38 2.32
237 279 3.258228 TGATCGTATGCGTGACATTTGT 58.742 40.909 2.37 0.00 40.38 2.83
238 280 3.682377 TGATCGTATGCGTGACATTTGTT 59.318 39.130 2.37 0.00 40.38 2.83
239 281 3.715618 TCGTATGCGTGACATTTGTTC 57.284 42.857 2.37 0.00 40.38 3.18
240 282 2.413796 TCGTATGCGTGACATTTGTTCC 59.586 45.455 2.37 0.00 40.38 3.62
298 340 6.750963 GGATTGAACTGAGATTTTGAGAATGC 59.249 38.462 0.00 0.00 0.00 3.56
386 431 7.467557 TTTGTAGTTTTACCTTCTGTACACG 57.532 36.000 0.00 0.00 0.00 4.49
400 445 2.474359 TGTACACGCATTTGCAAAATGC 59.526 40.909 24.54 24.54 46.97 3.56
576 622 0.542805 TGCTGCTAGATGTGCATGGA 59.457 50.000 0.00 0.00 39.86 3.41
577 623 0.942962 GCTGCTAGATGTGCATGGAC 59.057 55.000 10.90 10.90 39.86 4.02
579 625 2.210961 CTGCTAGATGTGCATGGACTG 58.789 52.381 18.75 4.99 39.86 3.51
580 626 1.134310 TGCTAGATGTGCATGGACTGG 60.134 52.381 18.75 1.55 35.31 4.00
581 627 1.590932 CTAGATGTGCATGGACTGGC 58.409 55.000 18.75 7.62 0.00 4.85
582 628 0.911053 TAGATGTGCATGGACTGGCA 59.089 50.000 18.75 0.00 37.77 4.92
583 629 0.257905 AGATGTGCATGGACTGGCAT 59.742 50.000 18.75 3.25 42.75 4.40
584 630 0.384309 GATGTGCATGGACTGGCATG 59.616 55.000 18.75 0.00 42.75 4.06
585 631 0.323999 ATGTGCATGGACTGGCATGT 60.324 50.000 18.75 0.00 42.75 3.21
586 632 0.540133 TGTGCATGGACTGGCATGTT 60.540 50.000 18.75 0.00 42.75 2.71
587 633 0.604578 GTGCATGGACTGGCATGTTT 59.395 50.000 10.51 0.00 42.75 2.83
588 634 1.001181 GTGCATGGACTGGCATGTTTT 59.999 47.619 10.51 0.00 42.75 2.43
589 635 2.230992 GTGCATGGACTGGCATGTTTTA 59.769 45.455 10.51 0.00 42.75 1.52
590 636 3.098377 TGCATGGACTGGCATGTTTTAT 58.902 40.909 0.00 0.00 34.58 1.40
591 637 3.119065 TGCATGGACTGGCATGTTTTATG 60.119 43.478 0.00 0.00 34.58 1.90
592 638 3.130869 GCATGGACTGGCATGTTTTATGA 59.869 43.478 0.00 0.00 0.00 2.15
604 650 7.967854 TGGCATGTTTTATGATACGAAAGAAAG 59.032 33.333 0.00 0.00 0.00 2.62
868 914 9.625747 TCATATGATATTGCTCACCTTTTGTTA 57.374 29.630 0.00 0.00 0.00 2.41
871 917 7.333528 TGATATTGCTCACCTTTTGTTATCC 57.666 36.000 0.00 0.00 0.00 2.59
1365 1412 1.652947 GGGGAGGTAGAGTGAACCAA 58.347 55.000 0.00 0.00 39.64 3.67
1405 1452 2.502492 GCTGCTCGCCCTCCTATGA 61.502 63.158 0.00 0.00 0.00 2.15
1515 1562 4.308458 TCACAAGGACCGCCCACG 62.308 66.667 0.00 0.00 37.41 4.94
1808 1855 3.677121 CAGGTCAGTCTGTTTCTTGATCG 59.323 47.826 0.00 0.00 0.00 3.69
1974 2021 5.482526 TGTCCTCTAAGTGCTGTTACCATTA 59.517 40.000 0.00 0.00 0.00 1.90
2031 2081 4.292306 ACCCTGTCCAAAATCCTAACTGAT 59.708 41.667 0.00 0.00 0.00 2.90
2211 2261 8.792830 TCTTATGCAATACAAGCTAAAGTTCT 57.207 30.769 0.00 0.00 0.00 3.01
2288 2711 9.650539 ATCTCAATATGATGTAACTAGCATGTC 57.349 33.333 0.00 0.00 0.00 3.06
2353 2776 9.950680 TTAAATTCTGCTGTTCTTTCTACAAAG 57.049 29.630 0.00 0.00 40.56 2.77
2397 2820 3.755905 TGCAATCTGAGGCGATGTTTTTA 59.244 39.130 0.00 0.00 0.00 1.52
2438 2861 4.734398 TTTGCTCAGGTCAAAACATTGT 57.266 36.364 0.00 0.00 31.27 2.71
2439 2862 3.713858 TGCTCAGGTCAAAACATTGTG 57.286 42.857 0.00 0.00 0.00 3.33
2539 2962 3.777522 AGGACTAGGAATCCAAAGTGAGG 59.222 47.826 11.36 0.00 38.86 3.86
2604 3027 5.649782 AAGGTGTTCCTGCAAAAGATATG 57.350 39.130 0.00 0.00 44.35 1.78
2625 3048 4.858850 TGAAATCTGGTGTGGCAGATAAT 58.141 39.130 0.00 0.00 37.19 1.28
2643 3066 6.093219 CAGATAATCCATCGAAGCTAAATGGG 59.907 42.308 17.35 5.05 40.34 4.00
2651 3074 2.716217 GAAGCTAAATGGGAGCACTGT 58.284 47.619 0.00 0.00 42.69 3.55
2726 3149 1.486310 TGAACGGCCTGAAGCATCTAT 59.514 47.619 0.00 0.00 46.50 1.98
2841 3264 6.647481 CAGCTGATGATTCACAAAATCCAAAA 59.353 34.615 8.42 0.00 0.00 2.44
2957 3380 7.448420 AGAAGTGACTACAATGATGATATGGG 58.552 38.462 0.00 0.00 0.00 4.00
2990 3413 3.685272 GTCCAAGTAAAGCCTGCTTCTAC 59.315 47.826 4.63 9.65 34.84 2.59
3054 3477 0.750182 TGGGCCGGCAAAGTAATAGC 60.750 55.000 30.85 6.06 0.00 2.97
3066 3489 5.686124 GCAAAGTAATAGCAGGACCTCTCAT 60.686 44.000 0.00 0.00 0.00 2.90
3279 3703 4.365899 GGGAAACCGTTTTATAAGGCTG 57.634 45.455 0.00 0.00 43.64 4.85
3288 3712 1.295020 TTATAAGGCTGTGGTGGGCT 58.705 50.000 0.00 0.00 41.37 5.19
3471 3895 1.960689 GGTCCTAAAAAGTTGCCTGCA 59.039 47.619 0.00 0.00 0.00 4.41
3861 4290 2.423577 GTCGCTGGTACACTGGAAAAT 58.576 47.619 0.00 0.00 0.00 1.82
4389 4828 6.882610 ACTGCAGTTTCTTTGTTATGATCA 57.117 33.333 15.25 0.00 0.00 2.92
4392 4831 8.362639 ACTGCAGTTTCTTTGTTATGATCATTT 58.637 29.630 15.25 0.00 0.00 2.32
4483 4923 9.056005 TGGTAATCATGTATGTGCTTAAGATTC 57.944 33.333 6.67 0.00 0.00 2.52
4527 4967 2.584492 TGTCATGCATCCACTCTACG 57.416 50.000 0.00 0.00 0.00 3.51
4537 4977 4.793353 GCATCCACTCTACGGAACAGATAC 60.793 50.000 0.00 0.00 35.77 2.24
4547 4987 8.701908 TCTACGGAACAGATACTTTGGTATAT 57.298 34.615 0.00 0.00 38.60 0.86
4548 4988 9.139734 TCTACGGAACAGATACTTTGGTATATT 57.860 33.333 0.00 0.00 38.60 1.28
4578 5018 2.154854 TCTGCTGTGCTAGTGTGTTC 57.845 50.000 0.00 0.00 0.00 3.18
4636 5182 3.746045 TGGCGAATCCTTGGTATAGTC 57.254 47.619 0.00 0.00 35.26 2.59
4642 5188 5.007724 GCGAATCCTTGGTATAGTCTTTTGG 59.992 44.000 0.00 0.00 0.00 3.28
4694 5241 2.639286 GCTTTGGTGTGACTGCGG 59.361 61.111 0.00 0.00 0.00 5.69
4798 5350 4.415596 TGGCCATGACTCTAATTTTGGTT 58.584 39.130 0.00 0.00 0.00 3.67
4817 5369 3.274288 GTTTTTGTTTGGATGGTTGCCA 58.726 40.909 0.00 0.00 38.19 4.92
4845 5397 0.319813 GGCACGCCAATTGCTCTTTT 60.320 50.000 2.36 0.00 40.07 2.27
4858 5410 7.381323 CAATTGCTCTTTTCCCATTCTAGTTT 58.619 34.615 0.00 0.00 0.00 2.66
4905 5457 6.832520 TGCCAAACATAATCTGTACACAAT 57.167 33.333 0.00 0.00 36.98 2.71
4906 5458 6.619744 TGCCAAACATAATCTGTACACAATG 58.380 36.000 0.00 0.00 36.98 2.82
4996 5549 8.785329 ATTTTCTCCATTCAGAAGAGTAAGAC 57.215 34.615 0.58 0.00 33.85 3.01
5029 5611 5.985911 ACTAAAGCCCGATGTATACTTGTT 58.014 37.500 4.17 0.00 0.00 2.83
5367 5956 4.310769 CTGGCTCTAATAACCAATCGAGG 58.689 47.826 0.00 0.00 31.81 4.63
5399 5988 0.254747 TTAATTCCCGTCAGGCCCAG 59.745 55.000 0.00 0.00 35.76 4.45
5448 6037 0.394899 CATCTGAGTCCCAAAGCCCC 60.395 60.000 0.00 0.00 0.00 5.80
5473 6062 2.533266 GGAAAATTTCATCTGCTGCCG 58.467 47.619 8.09 0.00 0.00 5.69
5542 6131 5.689068 GCAGAAAGTTCAAAGACATTTCCTG 59.311 40.000 0.00 0.00 31.69 3.86
5569 6158 5.163550 GGGATTTCCAAAGAATTACCTTCCG 60.164 44.000 0.00 0.00 34.65 4.30
5570 6159 5.417894 GGATTTCCAAAGAATTACCTTCCGT 59.582 40.000 0.00 0.00 33.32 4.69
5647 6236 0.108945 CGTCTTTACAGACCCGGGTC 60.109 60.000 41.42 41.42 46.19 4.46
5680 6269 2.476241 GGTATGCTGCACTTTTTGTTGC 59.524 45.455 3.57 0.00 0.00 4.17
5698 6287 5.636837 TGTTGCAAAAGAGTTGTAGTTCAC 58.363 37.500 0.00 0.00 0.00 3.18
5798 6401 9.918630 CTGTTGAATAGTTTGAAGGAAATCATT 57.081 29.630 0.00 0.00 0.00 2.57
5803 6406 9.727627 GAATAGTTTGAAGGAAATCATTAGCAG 57.272 33.333 0.00 0.00 0.00 4.24
5804 6407 9.466497 AATAGTTTGAAGGAAATCATTAGCAGA 57.534 29.630 0.00 0.00 0.00 4.26
5914 6594 7.042658 CCGGTAACATTATTTCTAGAAGCAGAC 60.043 40.741 5.12 0.00 0.00 3.51
6058 6738 4.704833 GAGCCGGTTCCAGCTGCA 62.705 66.667 8.66 0.00 40.11 4.41
6059 6739 3.984193 GAGCCGGTTCCAGCTGCAT 62.984 63.158 8.66 0.00 40.11 3.96
6060 6740 3.064324 GCCGGTTCCAGCTGCATT 61.064 61.111 8.66 0.00 0.00 3.56
6061 6741 3.056313 GCCGGTTCCAGCTGCATTC 62.056 63.158 8.66 0.00 0.00 2.67
6062 6742 1.675310 CCGGTTCCAGCTGCATTCA 60.675 57.895 8.66 0.00 0.00 2.57
6072 6752 7.170320 GGTTCCAGCTGCATTCATTTATTTATG 59.830 37.037 8.66 0.00 0.00 1.90
6173 6858 4.928615 CCAAAACAAAACAGTGAAGCTCAA 59.071 37.500 0.00 0.00 0.00 3.02
6271 6960 7.016361 ACGGAAATATTGTGTAAATGAGCTC 57.984 36.000 6.82 6.82 0.00 4.09
6443 7134 5.615289 AGATAAGTCCAGTCAACCATATGC 58.385 41.667 0.00 0.00 0.00 3.14
6444 7135 2.717639 AGTCCAGTCAACCATATGCC 57.282 50.000 0.00 0.00 0.00 4.40
6445 7136 1.212935 AGTCCAGTCAACCATATGCCC 59.787 52.381 0.00 0.00 0.00 5.36
6446 7137 1.212935 GTCCAGTCAACCATATGCCCT 59.787 52.381 0.00 0.00 0.00 5.19
6447 7138 1.922447 TCCAGTCAACCATATGCCCTT 59.078 47.619 0.00 0.00 0.00 3.95
6448 7139 2.092429 TCCAGTCAACCATATGCCCTTC 60.092 50.000 0.00 0.00 0.00 3.46
6449 7140 2.357050 CCAGTCAACCATATGCCCTTCA 60.357 50.000 0.00 0.00 0.00 3.02
6450 7141 3.559069 CAGTCAACCATATGCCCTTCAT 58.441 45.455 0.00 0.00 39.17 2.57
6451 7142 4.446167 CCAGTCAACCATATGCCCTTCATA 60.446 45.833 0.00 0.00 41.52 2.15
6452 7143 4.758674 CAGTCAACCATATGCCCTTCATAG 59.241 45.833 0.00 0.00 40.69 2.23
6453 7144 4.660303 AGTCAACCATATGCCCTTCATAGA 59.340 41.667 0.00 0.00 40.69 1.98
6454 7145 4.999950 GTCAACCATATGCCCTTCATAGAG 59.000 45.833 0.00 0.00 40.69 2.43
6455 7146 4.660303 TCAACCATATGCCCTTCATAGAGT 59.340 41.667 0.00 0.00 40.69 3.24
6456 7147 4.630644 ACCATATGCCCTTCATAGAGTG 57.369 45.455 0.00 0.00 40.69 3.51
6457 7148 3.328931 ACCATATGCCCTTCATAGAGTGG 59.671 47.826 0.00 0.00 40.69 4.00
6458 7149 3.307975 CCATATGCCCTTCATAGAGTGGG 60.308 52.174 0.00 0.00 40.69 4.61
6459 7150 1.898863 ATGCCCTTCATAGAGTGGGT 58.101 50.000 0.00 0.00 41.59 4.51
6460 7151 1.668826 TGCCCTTCATAGAGTGGGTT 58.331 50.000 0.00 0.00 41.59 4.11
6461 7152 2.840511 TGCCCTTCATAGAGTGGGTTA 58.159 47.619 0.00 0.00 41.59 2.85
6462 7153 2.504175 TGCCCTTCATAGAGTGGGTTAC 59.496 50.000 0.00 0.00 41.59 2.50
6463 7154 2.504175 GCCCTTCATAGAGTGGGTTACA 59.496 50.000 0.00 0.00 41.59 2.41
6464 7155 3.054655 GCCCTTCATAGAGTGGGTTACAA 60.055 47.826 0.00 0.00 41.59 2.41
6465 7156 4.514401 CCCTTCATAGAGTGGGTTACAAC 58.486 47.826 0.00 0.00 35.13 3.32
6477 7168 7.458806 AGAGTGGGTTACAACTAGGGTAATTTA 59.541 37.037 11.07 1.33 33.68 1.40
6529 7220 7.596749 ACGTCACCAACAAAGATCTTTATAG 57.403 36.000 20.07 10.93 0.00 1.31
6588 7299 9.080915 GTTATTAAGGTCCTAACTTCTTGTACG 57.919 37.037 0.00 0.00 0.00 3.67
6629 7340 5.308825 ACATGCTATTGAGGCTTACATACC 58.691 41.667 0.00 0.00 0.00 2.73
6632 7343 4.283467 TGCTATTGAGGCTTACATACCGAT 59.717 41.667 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 143 3.317993 GTGGCAACCAGTCAAACAGTTAT 59.682 43.478 0.00 0.00 32.34 1.89
116 144 2.685897 GTGGCAACCAGTCAAACAGTTA 59.314 45.455 0.00 0.00 32.34 2.24
117 145 1.476488 GTGGCAACCAGTCAAACAGTT 59.524 47.619 0.00 0.00 32.34 3.16
118 146 1.102978 GTGGCAACCAGTCAAACAGT 58.897 50.000 0.00 0.00 32.34 3.55
128 170 5.279206 CCATTAAAACATACAGTGGCAACCA 60.279 40.000 0.00 0.00 0.00 3.67
194 236 1.002468 GCAGGTAGTGTGCACAAAGTG 60.002 52.381 23.59 15.24 40.86 3.16
195 237 1.134098 AGCAGGTAGTGTGCACAAAGT 60.134 47.619 23.59 11.94 43.82 2.66
207 249 2.054363 CGCATACGATCAAGCAGGTAG 58.946 52.381 0.00 0.00 43.93 3.18
223 265 1.541147 CCAGGAACAAATGTCACGCAT 59.459 47.619 0.00 0.00 40.03 4.73
224 266 0.950836 CCAGGAACAAATGTCACGCA 59.049 50.000 0.00 0.00 0.00 5.24
225 267 1.234821 TCCAGGAACAAATGTCACGC 58.765 50.000 0.00 0.00 0.00 5.34
226 268 3.980646 TTTCCAGGAACAAATGTCACG 57.019 42.857 0.00 0.00 0.00 4.35
227 269 6.071391 ACCATATTTCCAGGAACAAATGTCAC 60.071 38.462 0.00 0.00 0.00 3.67
229 271 6.530019 ACCATATTTCCAGGAACAAATGTC 57.470 37.500 0.00 0.00 0.00 3.06
230 272 8.429237 TTTACCATATTTCCAGGAACAAATGT 57.571 30.769 0.00 0.00 0.00 2.71
232 274 7.986889 GCATTTACCATATTTCCAGGAACAAAT 59.013 33.333 0.00 0.00 0.00 2.32
235 277 6.194235 AGCATTTACCATATTTCCAGGAACA 58.806 36.000 0.00 0.00 0.00 3.18
236 278 6.715347 AGCATTTACCATATTTCCAGGAAC 57.285 37.500 0.00 0.00 0.00 3.62
237 279 7.732222 AAAGCATTTACCATATTTCCAGGAA 57.268 32.000 0.00 0.00 35.86 3.36
238 280 7.619302 AGAAAAGCATTTACCATATTTCCAGGA 59.381 33.333 0.00 0.00 37.28 3.86
239 281 7.707893 CAGAAAAGCATTTACCATATTTCCAGG 59.292 37.037 0.00 0.00 37.28 4.45
240 282 8.253113 ACAGAAAAGCATTTACCATATTTCCAG 58.747 33.333 0.00 0.00 37.28 3.86
298 340 7.812690 TTCATTGTTCTCATCCTGATTATGG 57.187 36.000 0.00 0.00 0.00 2.74
319 361 9.681692 CTATTTGACAACAGAAACATCATTTCA 57.318 29.630 2.51 0.00 0.00 2.69
320 362 8.642020 GCTATTTGACAACAGAAACATCATTTC 58.358 33.333 0.00 0.00 0.00 2.17
379 424 2.474359 GCATTTTGCAAATGCGTGTACA 59.526 40.909 22.07 0.00 44.26 2.90
386 431 4.845621 ATAAGACGCATTTTGCAAATGC 57.154 36.364 24.54 24.54 45.36 3.56
576 622 6.597672 TCTTTCGTATCATAAAACATGCCAGT 59.402 34.615 0.00 0.00 0.00 4.00
577 623 7.015226 TCTTTCGTATCATAAAACATGCCAG 57.985 36.000 0.00 0.00 0.00 4.85
579 625 7.968405 ACTTTCTTTCGTATCATAAAACATGCC 59.032 33.333 0.00 0.00 0.00 4.40
580 626 8.788813 CACTTTCTTTCGTATCATAAAACATGC 58.211 33.333 0.00 0.00 0.00 4.06
581 627 9.277565 CCACTTTCTTTCGTATCATAAAACATG 57.722 33.333 0.00 0.00 0.00 3.21
582 628 9.226606 TCCACTTTCTTTCGTATCATAAAACAT 57.773 29.630 0.00 0.00 0.00 2.71
583 629 8.610248 TCCACTTTCTTTCGTATCATAAAACA 57.390 30.769 0.00 0.00 0.00 2.83
584 630 8.718734 ACTCCACTTTCTTTCGTATCATAAAAC 58.281 33.333 0.00 0.00 0.00 2.43
585 631 8.842358 ACTCCACTTTCTTTCGTATCATAAAA 57.158 30.769 0.00 0.00 0.00 1.52
586 632 9.582431 CTACTCCACTTTCTTTCGTATCATAAA 57.418 33.333 0.00 0.00 0.00 1.40
587 633 8.195436 CCTACTCCACTTTCTTTCGTATCATAA 58.805 37.037 0.00 0.00 0.00 1.90
588 634 7.201884 CCCTACTCCACTTTCTTTCGTATCATA 60.202 40.741 0.00 0.00 0.00 2.15
589 635 6.407074 CCCTACTCCACTTTCTTTCGTATCAT 60.407 42.308 0.00 0.00 0.00 2.45
590 636 5.105473 CCCTACTCCACTTTCTTTCGTATCA 60.105 44.000 0.00 0.00 0.00 2.15
591 637 5.126707 TCCCTACTCCACTTTCTTTCGTATC 59.873 44.000 0.00 0.00 0.00 2.24
592 638 5.021458 TCCCTACTCCACTTTCTTTCGTAT 58.979 41.667 0.00 0.00 0.00 3.06
604 650 5.871396 TCAGATTTACATCCCTACTCCAC 57.129 43.478 0.00 0.00 0.00 4.02
728 774 9.016438 GTTCCCCTTTCAAATATTAACACACTA 57.984 33.333 0.00 0.00 0.00 2.74
737 783 3.774766 GCCCTGTTCCCCTTTCAAATATT 59.225 43.478 0.00 0.00 0.00 1.28
811 857 5.453567 AAAAGGAGTTTGGAACATAGCAC 57.546 39.130 0.00 0.00 39.30 4.40
868 914 0.395686 CATGAGGCATCAGGACGGAT 59.604 55.000 7.32 0.00 39.62 4.18
871 917 2.827800 ATACATGAGGCATCAGGACG 57.172 50.000 20.84 4.23 39.62 4.79
1365 1412 2.652590 GCAGAAGCTGAATGGAAGGAT 58.347 47.619 0.00 0.00 37.91 3.24
1405 1452 2.995574 CCGTCCTCTTCCCCGTGT 60.996 66.667 0.00 0.00 0.00 4.49
1509 1556 2.256117 ATAAGTTAGGATGCGTGGGC 57.744 50.000 0.00 0.00 40.52 5.36
1515 1562 6.543735 AGGACCCATAAATAAGTTAGGATGC 58.456 40.000 0.00 0.00 0.00 3.91
1554 1601 1.077357 ACCGTTTTGAGCACCACCA 60.077 52.632 0.00 0.00 0.00 4.17
1808 1855 7.877097 AGGATGTAATGCAGAATATTCTCTGAC 59.123 37.037 15.24 9.54 44.82 3.51
1974 2021 9.715121 AGAACATTAATTGCAACTCAAATCATT 57.285 25.926 0.00 0.00 38.34 2.57
1995 2042 3.392947 TGGACAGGGTATTGTGAAGAACA 59.607 43.478 0.00 0.00 36.85 3.18
2031 2081 0.728129 CTGACGCTCGTTGACGCTAA 60.728 55.000 0.00 0.00 39.60 3.09
2183 2233 7.464358 ACTTTAGCTTGTATTGCATAAGAACG 58.536 34.615 0.00 0.00 31.90 3.95
2211 2261 6.596106 ACGCATACAGTAATAATTGTCCACAA 59.404 34.615 0.00 0.00 40.51 3.33
2353 2776 6.584563 TGCAAAAGCACGGTATAAGAAAATTC 59.415 34.615 0.00 0.00 0.00 2.17
2356 2779 5.440234 TGCAAAAGCACGGTATAAGAAAA 57.560 34.783 0.00 0.00 0.00 2.29
2360 2783 5.030295 CAGATTGCAAAAGCACGGTATAAG 58.970 41.667 1.71 0.00 0.00 1.73
2458 2881 5.181245 GTGATAGGCTCTGCAAAGTGTTTAA 59.819 40.000 0.00 0.00 0.00 1.52
2539 2962 6.839205 GTTAAGTTAACATGAGCAGTTCCTGC 60.839 42.308 18.82 8.14 45.91 4.85
2625 3048 2.485479 GCTCCCATTTAGCTTCGATGGA 60.485 50.000 18.87 8.47 42.31 3.41
2643 3066 1.598924 GCAACAGCTGAAACAGTGCTC 60.599 52.381 23.35 0.00 34.51 4.26
2726 3149 5.242615 TCATTAGTATGTGCAAAACCAGCAA 59.757 36.000 0.00 0.00 44.64 3.91
2841 3264 4.385754 GCTATTCTCCCCCAAACAGAAGAT 60.386 45.833 0.00 0.00 29.78 2.40
2957 3380 3.955650 TTACTTGGACAGTGCTAGGAC 57.044 47.619 6.22 6.22 35.97 3.85
2990 3413 4.831155 TGGGTCGACCATTAGTATCCTTAG 59.169 45.833 34.40 0.00 46.80 2.18
3054 3477 4.630111 GAGATGCTTTATGAGAGGTCCTG 58.370 47.826 0.00 0.00 0.00 3.86
3066 3489 4.935205 ACATAAAGTGTGCGAGATGCTTTA 59.065 37.500 0.00 0.00 46.63 1.85
3234 3657 1.618837 ACAGCGTCTGGAGCTTTTAGA 59.381 47.619 10.80 0.00 44.06 2.10
3279 3703 0.685097 TGTCTCTGTTAGCCCACCAC 59.315 55.000 0.00 0.00 0.00 4.16
3288 3712 5.250982 TCGTCAGTAATCCTGTCTCTGTTA 58.749 41.667 0.00 0.00 42.19 2.41
3471 3895 7.499232 GCAGGAGGTATTGATGTTATACTGTTT 59.501 37.037 0.00 0.00 0.00 2.83
3861 4290 4.126520 AGCCAACTCCCCAGAAATTTTA 57.873 40.909 0.00 0.00 0.00 1.52
4389 4828 6.767524 TCCACTGTTGTGTAACTGAAAAAT 57.232 33.333 0.00 0.00 42.34 1.82
4392 4831 5.680619 AGATCCACTGTTGTGTAACTGAAA 58.319 37.500 0.00 0.00 42.34 2.69
4527 4967 9.780186 AGCTAAATATACCAAAGTATCTGTTCC 57.220 33.333 0.00 0.00 39.88 3.62
4547 4987 4.836825 AGCACAGCAGAATAGAAGCTAAA 58.163 39.130 0.00 0.00 36.73 1.85
4548 4988 4.478206 AGCACAGCAGAATAGAAGCTAA 57.522 40.909 0.00 0.00 36.73 3.09
4560 5000 0.786581 CGAACACACTAGCACAGCAG 59.213 55.000 0.00 0.00 0.00 4.24
4578 5018 4.145876 TGCAAGTTAAGCAGAAATGACG 57.854 40.909 0.00 0.00 37.02 4.35
4636 5182 5.333299 TCATCATGAAATGGAGCCAAAAG 57.667 39.130 0.00 0.00 46.73 2.27
4642 5188 7.709947 TCAAAAGTATCATCATGAAATGGAGC 58.290 34.615 0.00 0.00 46.73 4.70
4674 5221 1.447317 CGCAGTCACACCAAAGCCTT 61.447 55.000 0.00 0.00 0.00 4.35
4676 5223 2.639286 CGCAGTCACACCAAAGCC 59.361 61.111 0.00 0.00 0.00 4.35
4694 5241 2.616842 CGGCCACCATCTAAACAATACC 59.383 50.000 2.24 0.00 0.00 2.73
4752 5300 7.909641 CCAAAAACAAAATTTGATGGACAGAAC 59.090 33.333 13.19 0.00 39.56 3.01
4753 5301 7.414984 GCCAAAAACAAAATTTGATGGACAGAA 60.415 33.333 13.19 0.00 39.56 3.02
4771 5319 6.147656 CCAAAATTAGAGTCATGGCCAAAAAC 59.852 38.462 10.96 8.61 0.00 2.43
4798 5350 2.158842 CCTGGCAACCATCCAAACAAAA 60.159 45.455 0.00 0.00 32.41 2.44
4837 5389 8.650143 AAATAAACTAGAATGGGAAAAGAGCA 57.350 30.769 0.00 0.00 0.00 4.26
4845 5397 6.379988 GGCAAGGAAAATAAACTAGAATGGGA 59.620 38.462 0.00 0.00 0.00 4.37
4858 5410 5.010933 TCGGTTATGTTGGCAAGGAAAATA 58.989 37.500 0.00 0.00 0.00 1.40
4905 5457 7.821652 TGTTGAACATGAAAAGACAAGTTACA 58.178 30.769 0.00 0.00 33.03 2.41
4906 5458 8.682128 TTGTTGAACATGAAAAGACAAGTTAC 57.318 30.769 0.00 0.00 33.03 2.50
4965 5518 9.525826 ACTCTTCTGAATGGAGAAAATTAATGT 57.474 29.630 12.11 0.00 31.52 2.71
4996 5549 2.803956 TCGGGCTTTAGTTTCTTCAACG 59.196 45.455 0.00 0.00 40.75 4.10
5029 5611 8.450578 AACATGAACAATCAGTCAAAGTTAGA 57.549 30.769 0.00 0.00 39.39 2.10
5045 5627 3.030291 AGCACAAAAGGGAACATGAACA 58.970 40.909 0.00 0.00 0.00 3.18
5367 5956 4.217767 ACGGGAATTAAACTTTTCTGAGGC 59.782 41.667 0.00 0.00 0.00 4.70
5448 6037 3.922240 CAGCAGATGAAATTTTCCCAACG 59.078 43.478 6.68 0.00 0.00 4.10
5473 6062 0.465097 ATGGCTGCTGTACCAGATGC 60.465 55.000 0.00 0.00 39.88 3.91
5542 6131 7.793944 GGAAGGTAATTCTTTGGAAATCCCAAC 60.794 40.741 0.00 0.00 43.35 3.77
5563 6152 4.342378 TGATGATAGAGAGGAAACGGAAGG 59.658 45.833 0.00 0.00 0.00 3.46
5569 6158 8.498054 TCAACATTTGATGATAGAGAGGAAAC 57.502 34.615 0.00 0.00 34.08 2.78
5570 6159 8.324306 ACTCAACATTTGATGATAGAGAGGAAA 58.676 33.333 0.00 0.00 39.30 3.13
5647 6236 2.625737 CAGCATACCTCACTGTGGAAG 58.374 52.381 8.11 0.00 0.00 3.46
5680 6269 3.311322 TGCCGTGAACTACAACTCTTTTG 59.689 43.478 0.00 0.00 0.00 2.44
5698 6287 5.072040 AGGAAATATTTCAAACCTTGCCG 57.928 39.130 25.55 0.00 38.92 5.69
5798 6401 1.273606 GAGTGACCAGTGCTTCTGCTA 59.726 52.381 4.40 0.00 42.38 3.49
5799 6402 0.034616 GAGTGACCAGTGCTTCTGCT 59.965 55.000 4.40 0.00 42.38 4.24
5800 6403 0.250038 TGAGTGACCAGTGCTTCTGC 60.250 55.000 4.40 0.00 42.38 4.26
5801 6404 1.607509 CCTGAGTGACCAGTGCTTCTG 60.608 57.143 3.18 3.18 43.27 3.02
5803 6406 0.394565 ACCTGAGTGACCAGTGCTTC 59.605 55.000 0.00 0.00 32.43 3.86
5804 6407 2.532854 ACCTGAGTGACCAGTGCTT 58.467 52.632 0.00 0.00 32.43 3.91
5826 6498 2.242043 CCAGTTTTTCAGACCCTGCAT 58.758 47.619 0.00 0.00 0.00 3.96
5914 6594 9.793252 CATCAAACTGGACTCCAAATTATAAAG 57.207 33.333 0.00 0.00 30.80 1.85
6173 6858 7.817418 ATTTTGTGATAAATGCCGTACCTAT 57.183 32.000 0.00 0.00 0.00 2.57
6271 6960 6.039717 CCCAAAGAGGTAACATATCAACCATG 59.960 42.308 0.00 0.00 41.41 3.66
6431 7122 4.973168 TCTATGAAGGGCATATGGTTGAC 58.027 43.478 4.56 0.00 38.72 3.18
6443 7134 4.225267 AGTTGTAACCCACTCTATGAAGGG 59.775 45.833 0.00 0.00 46.96 3.95
6444 7135 5.422214 AGTTGTAACCCACTCTATGAAGG 57.578 43.478 0.00 0.00 0.00 3.46
6445 7136 6.407074 CCCTAGTTGTAACCCACTCTATGAAG 60.407 46.154 0.00 0.00 0.00 3.02
6446 7137 5.424252 CCCTAGTTGTAACCCACTCTATGAA 59.576 44.000 0.00 0.00 0.00 2.57
6447 7138 4.960469 CCCTAGTTGTAACCCACTCTATGA 59.040 45.833 0.00 0.00 0.00 2.15
6448 7139 4.715297 ACCCTAGTTGTAACCCACTCTATG 59.285 45.833 0.00 0.00 0.00 2.23
6449 7140 4.956582 ACCCTAGTTGTAACCCACTCTAT 58.043 43.478 0.00 0.00 0.00 1.98
6450 7141 4.408904 ACCCTAGTTGTAACCCACTCTA 57.591 45.455 0.00 0.00 0.00 2.43
6451 7142 3.271153 ACCCTAGTTGTAACCCACTCT 57.729 47.619 0.00 0.00 0.00 3.24
6452 7143 5.688814 ATTACCCTAGTTGTAACCCACTC 57.311 43.478 4.70 0.00 31.47 3.51
6453 7144 6.458630 AAATTACCCTAGTTGTAACCCACT 57.541 37.500 4.70 0.00 31.47 4.00
6454 7145 8.812513 AATAAATTACCCTAGTTGTAACCCAC 57.187 34.615 4.70 0.00 31.47 4.61
6501 7192 1.670791 TCTTTGTTGGTGACGTTCCC 58.329 50.000 7.98 3.29 0.00 3.97
6502 7193 3.139077 AGATCTTTGTTGGTGACGTTCC 58.861 45.455 0.00 0.00 0.00 3.62
6588 7299 4.094442 GCATGTACCTTAGCACTGTTAACC 59.906 45.833 2.48 0.00 0.00 2.85
6629 7340 5.239087 GGAGGGAGTAGTAAACTAGTCATCG 59.761 48.000 20.98 0.00 45.99 3.84
6632 7343 4.018960 ACGGAGGGAGTAGTAAACTAGTCA 60.019 45.833 20.98 0.00 45.99 3.41


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

AutoCloner maintained by Alex Coulton.