Multiple sequence alignment - TraesCS4A01G224100

Loading Multiple Alignment...

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 TraesCS4A01G224100 chr4A 100.000 4739 0 0 1 4739 531681552 531676814 0.000000e+00 8752
1 TraesCS4A01G224100 chr4A 84.760 3189 426 36 954 4122 531386675 531383527 0.000000e+00 3142
2 TraesCS4A01G224100 chr4A 85.308 2566 313 30 1482 4043 532215674 532218179 0.000000e+00 2591
3 TraesCS4A01G224100 chr4A 80.020 996 138 30 958 1926 626302384 626301423 0.000000e+00 680
4 TraesCS4A01G224100 chr4A 79.399 898 159 16 2058 2934 626299911 626299019 1.130000e-170 610
5 TraesCS4A01G224100 chr4A 81.923 520 80 12 4198 4712 430874799 430874289 1.220000e-115 427
6 TraesCS4A01G224100 chr4B 96.493 4135 117 12 1 4128 95068218 95072331 0.000000e+00 6807
7 TraesCS4A01G224100 chr4B 91.130 2965 249 10 994 3956 94791602 94788650 0.000000e+00 4006
8 TraesCS4A01G224100 chr4D 97.651 3405 78 1 725 4129 64537714 64541116 0.000000e+00 5843
9 TraesCS4A01G224100 chr4D 89.175 1478 141 5 1012 2488 64356168 64354709 0.000000e+00 1825
10 TraesCS4A01G224100 chr4D 85.576 1657 191 29 2484 4122 64349333 64347707 0.000000e+00 1692
11 TraesCS4A01G224100 chr4D 93.605 735 33 6 1 726 64536945 64537674 0.000000e+00 1085
12 TraesCS4A01G224100 chr4D 90.130 385 32 6 4357 4739 445477873 445477493 3.290000e-136 496
13 TraesCS4A01G224100 chr2D 83.696 2938 436 21 954 3886 580192054 580194953 0.000000e+00 2732
14 TraesCS4A01G224100 chr2D 90.206 388 31 7 4355 4738 553390943 553390559 2.550000e-137 499
15 TraesCS4A01G224100 chr2D 75.744 437 76 17 288 706 580191431 580191855 4.840000e-45 193
16 TraesCS4A01G224100 chr2B 83.356 2968 444 26 966 3927 699107712 699110635 0.000000e+00 2699
17 TraesCS4A01G224100 chr2A 83.607 1763 250 19 2133 3886 718119194 718120926 0.000000e+00 1618
18 TraesCS4A01G224100 chr2A 81.669 671 107 10 954 1620 718117765 718118423 1.160000e-150 544
19 TraesCS4A01G224100 chr3D 90.956 387 31 4 4355 4739 594310100 594309716 7.030000e-143 518
20 TraesCS4A01G224100 chr3D 90.979 388 28 6 4355 4739 273122275 273122658 2.530000e-142 516
21 TraesCS4A01G224100 chr3D 90.000 390 33 6 4354 4739 247313426 247313813 2.550000e-137 499
22 TraesCS4A01G224100 chr3D 90.155 386 32 6 4355 4738 341185466 341185085 9.160000e-137 497
23 TraesCS4A01G224100 chr3D 89.717 389 36 4 4353 4739 290698147 290697761 1.180000e-135 494
24 TraesCS4A01G224100 chr3D 79.866 447 80 7 954 1395 438451673 438452114 7.650000e-83 318
25 TraesCS4A01G224100 chr3B 89.948 388 33 6 4355 4739 616314959 616314575 3.290000e-136 496
26 TraesCS4A01G224100 chrUn 78.905 493 88 9 1763 2244 358384661 358385148 2.130000e-83 320
27 TraesCS4A01G224100 chrUn 83.784 222 30 5 4126 4347 255520293 255520078 6.220000e-49 206
28 TraesCS4A01G224100 chr3A 86.752 234 24 5 4126 4354 593223142 593222911 2.190000e-63 254
29 TraesCS4A01G224100 chr5B 79.675 369 56 18 4190 4549 427327956 427327598 1.020000e-61 248
30 TraesCS4A01G224100 chr7D 86.087 230 23 5 4126 4354 120510850 120511071 6.130000e-59 239
31 TraesCS4A01G224100 chr7D 86.026 229 24 6 4131 4354 449530484 449530259 6.130000e-59 239
32 TraesCS4A01G224100 chr7D 85.088 228 32 2 4212 4439 339190870 339191095 1.030000e-56 231
33 TraesCS4A01G224100 chr7D 84.685 222 28 5 4127 4347 382503091 382502875 2.870000e-52 217
34 TraesCS4A01G224100 chr6D 84.753 223 27 4 4126 4347 52549223 52549007 2.870000e-52 217
35 TraesCS4A01G224100 chr6B 84.211 228 27 6 4126 4347 221381788 221381564 3.710000e-51 213
36 TraesCS4A01G224100 chr6B 83.784 222 30 5 4126 4347 332365225 332365440 6.220000e-49 206
37 TraesCS4A01G224100 chr6B 83.784 222 30 5 4126 4347 332372447 332372662 6.220000e-49 206


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 TraesCS4A01G224100 chr4A 531676814 531681552 4738 True 8752.0 8752 100.0000 1 4739 1 chr4A.!!$R3 4738
1 TraesCS4A01G224100 chr4A 531383527 531386675 3148 True 3142.0 3142 84.7600 954 4122 1 chr4A.!!$R2 3168
2 TraesCS4A01G224100 chr4A 532215674 532218179 2505 False 2591.0 2591 85.3080 1482 4043 1 chr4A.!!$F1 2561
3 TraesCS4A01G224100 chr4A 626299019 626302384 3365 True 645.0 680 79.7095 958 2934 2 chr4A.!!$R4 1976
4 TraesCS4A01G224100 chr4A 430874289 430874799 510 True 427.0 427 81.9230 4198 4712 1 chr4A.!!$R1 514
5 TraesCS4A01G224100 chr4B 95068218 95072331 4113 False 6807.0 6807 96.4930 1 4128 1 chr4B.!!$F1 4127
6 TraesCS4A01G224100 chr4B 94788650 94791602 2952 True 4006.0 4006 91.1300 994 3956 1 chr4B.!!$R1 2962
7 TraesCS4A01G224100 chr4D 64536945 64541116 4171 False 3464.0 5843 95.6280 1 4129 2 chr4D.!!$F1 4128
8 TraesCS4A01G224100 chr4D 64354709 64356168 1459 True 1825.0 1825 89.1750 1012 2488 1 chr4D.!!$R2 1476
9 TraesCS4A01G224100 chr4D 64347707 64349333 1626 True 1692.0 1692 85.5760 2484 4122 1 chr4D.!!$R1 1638
10 TraesCS4A01G224100 chr2D 580191431 580194953 3522 False 1462.5 2732 79.7200 288 3886 2 chr2D.!!$F1 3598
11 TraesCS4A01G224100 chr2B 699107712 699110635 2923 False 2699.0 2699 83.3560 966 3927 1 chr2B.!!$F1 2961
12 TraesCS4A01G224100 chr2A 718117765 718120926 3161 False 1081.0 1618 82.6380 954 3886 2 chr2A.!!$F1 2932


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
52 53 0.042188 CACTGGTCGTTTGTTCAGCG 60.042 55.000 0.00 0.00 0.00 5.18 F
928 994 0.326264 GTGTCCCTGACCTCTGCATT 59.674 55.000 0.00 0.00 0.00 3.56 F
1160 1228 0.813184 CAACTGACCATGATGGCCAC 59.187 55.000 8.16 2.36 42.67 5.01 F
1479 1571 1.410882 GAGATAGAAAGGCAGCGGTCT 59.589 52.381 0.00 0.00 0.00 3.85 F
1916 2468 1.539165 CTCTCCAGGATCTCCCGGA 59.461 63.158 0.73 1.28 40.87 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1464 1556 0.321122 CTTGAGACCGCTGCCTTTCT 60.321 55.000 0.0 0.0 0.00 2.52 R
2244 4261 1.139853 GGAAGGTCATGGTAGCTCAGG 59.860 57.143 0.0 0.0 0.00 3.86 R
2958 5011 3.995705 GCTTCTCATCAGCATATCTGTCC 59.004 47.826 0.0 0.0 43.32 4.02 R
3669 5728 3.750130 CAGTGTCCCATTGAGTTCTGAAG 59.250 47.826 0.0 0.0 0.00 3.02 R
3959 6044 5.036117 ACAACAGAAACAGTACAGTCCAT 57.964 39.130 0.0 0.0 0.00 3.41 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
52 53 0.042188 CACTGGTCGTTTGTTCAGCG 60.042 55.000 0.00 0.00 0.00 5.18
88 89 3.577919 CCACTCTATAGGCCACCTACTT 58.422 50.000 5.01 0.00 39.10 2.24
112 113 6.122277 TCAAGTCTTCAGAAGGTGAACATTT 58.878 36.000 10.42 0.00 40.45 2.32
157 158 5.707242 ATCATATGCTGCATTTTCAGAGG 57.293 39.130 21.56 3.21 36.19 3.69
159 160 4.577693 TCATATGCTGCATTTTCAGAGGAC 59.422 41.667 21.56 0.00 36.19 3.85
230 232 1.609208 ATCTTGTTCCAAACAGCGCT 58.391 45.000 2.64 2.64 43.27 5.92
231 233 0.662619 TCTTGTTCCAAACAGCGCTG 59.337 50.000 34.89 34.89 43.27 5.18
409 413 6.833933 TGCAGTTCTCTAGTCCAGATTACATA 59.166 38.462 0.00 0.00 31.13 2.29
415 419 9.871238 TTCTCTAGTCCAGATTACATACAAAAC 57.129 33.333 0.00 0.00 31.13 2.43
434 438 1.829222 ACGGGTGACAGTCGGATATTT 59.171 47.619 0.00 0.00 31.00 1.40
607 627 4.689062 TCTCTAGGATTGGGTCTCTGTTT 58.311 43.478 0.00 0.00 0.00 2.83
627 647 6.303054 TGTTTTGGGATATGAGTCAAAGTCA 58.697 36.000 0.00 0.00 31.89 3.41
653 673 2.857483 TGCTTTCCAAATTCGACTGGA 58.143 42.857 6.07 6.07 40.03 3.86
855 921 4.291249 AGGGGGAAAATGCTACTCTTTACA 59.709 41.667 0.00 0.00 0.00 2.41
911 977 4.672899 TCATTCTTTCCTTAAAGGGGGTG 58.327 43.478 0.00 0.00 42.09 4.61
928 994 0.326264 GTGTCCCTGACCTCTGCATT 59.674 55.000 0.00 0.00 0.00 3.56
1157 1225 1.133790 GAAGCAACTGACCATGATGGC 59.866 52.381 12.25 5.15 42.67 4.40
1160 1228 0.813184 CAACTGACCATGATGGCCAC 59.187 55.000 8.16 2.36 42.67 5.01
1377 1463 8.258007 AGTGAAATTACGGATGAGATAGTTGAA 58.742 33.333 0.00 0.00 0.00 2.69
1443 1535 2.971598 GCAGCCCTCCCAGCTTGTA 61.972 63.158 0.00 0.00 38.95 2.41
1464 1556 6.429151 TGTAGCTAACCCACTTACTGAGATA 58.571 40.000 0.00 0.00 0.00 1.98
1479 1571 1.410882 GAGATAGAAAGGCAGCGGTCT 59.589 52.381 0.00 0.00 0.00 3.85
1878 2428 2.286872 GATGTCTGGGAGCAAGATGTG 58.713 52.381 0.00 0.00 0.00 3.21
1884 2436 3.327757 TCTGGGAGCAAGATGTGTACTTT 59.672 43.478 0.00 0.00 0.00 2.66
1916 2468 1.539165 CTCTCCAGGATCTCCCGGA 59.461 63.158 0.73 1.28 40.87 5.14
2064 4081 2.034066 CGGAAGGGCCACATGTGT 59.966 61.111 23.79 5.30 35.94 3.72
2244 4261 6.321717 TGATCATGTCCGAGCAATTTTAAAC 58.678 36.000 0.00 0.00 0.00 2.01
2451 4468 2.942376 CCGCAATATGCTTGAGGTTGTA 59.058 45.455 0.43 0.00 42.25 2.41
2517 4534 5.691754 TGATATTGTGCGTGAACTAGCTATG 59.308 40.000 0.00 0.00 0.00 2.23
2627 4679 4.273480 GTCATTATGTGGATGGAAAGACGG 59.727 45.833 0.00 0.00 0.00 4.79
3466 5525 3.188254 GCACAGTGCAAAAACTTTGGTTT 59.812 39.130 21.22 0.00 44.05 3.27
3497 5556 2.989571 ACTCCTTTCCCAACCTGAAGAT 59.010 45.455 0.00 0.00 0.00 2.40
3669 5728 1.168407 TGCTGAGCTTGCACAAGGAC 61.168 55.000 5.83 0.00 38.80 3.85
3970 6055 4.431416 TTTGTTGACCATGGACTGTACT 57.569 40.909 21.47 0.00 0.00 2.73
4104 6192 7.194607 ACATTGGTATCTTTTGATCTATGCG 57.805 36.000 0.00 0.00 40.19 4.73
4119 6207 0.183492 ATGCGCTATGTCACCCCATT 59.817 50.000 9.73 0.00 0.00 3.16
4122 6210 2.158682 TGCGCTATGTCACCCCATTATT 60.159 45.455 9.73 0.00 0.00 1.40
4129 6217 8.234546 CGCTATGTCACCCCATTATTATTTTAC 58.765 37.037 0.00 0.00 0.00 2.01
4130 6218 8.520351 GCTATGTCACCCCATTATTATTTTACC 58.480 37.037 0.00 0.00 0.00 2.85
4131 6219 9.581289 CTATGTCACCCCATTATTATTTTACCA 57.419 33.333 0.00 0.00 0.00 3.25
4133 6221 8.243961 TGTCACCCCATTATTATTTTACCATG 57.756 34.615 0.00 0.00 0.00 3.66
4134 6222 8.061920 TGTCACCCCATTATTATTTTACCATGA 58.938 33.333 0.00 0.00 0.00 3.07
4135 6223 8.919145 GTCACCCCATTATTATTTTACCATGAA 58.081 33.333 0.00 0.00 0.00 2.57
4136 6224 9.667607 TCACCCCATTATTATTTTACCATGAAT 57.332 29.630 0.00 0.00 0.00 2.57
4177 6265 7.793927 ACAACTTTATTATTGCCTCTAGAGC 57.206 36.000 14.73 10.34 0.00 4.09
4178 6266 7.338710 ACAACTTTATTATTGCCTCTAGAGCA 58.661 34.615 14.73 12.79 38.81 4.26
4179 6267 7.995488 ACAACTTTATTATTGCCTCTAGAGCAT 59.005 33.333 14.73 8.17 40.59 3.79
4180 6268 9.494271 CAACTTTATTATTGCCTCTAGAGCATA 57.506 33.333 14.73 7.24 40.59 3.14
4187 6275 9.804977 ATTATTGCCTCTAGAGCATATTTTCTT 57.195 29.630 14.73 0.00 40.59 2.52
4188 6276 7.742556 ATTGCCTCTAGAGCATATTTTCTTC 57.257 36.000 14.73 0.00 40.59 2.87
4189 6277 6.239217 TGCCTCTAGAGCATATTTTCTTCA 57.761 37.500 14.73 0.00 34.69 3.02
4190 6278 6.653020 TGCCTCTAGAGCATATTTTCTTCAA 58.347 36.000 14.73 0.00 34.69 2.69
4191 6279 7.285566 TGCCTCTAGAGCATATTTTCTTCAAT 58.714 34.615 14.73 0.00 34.69 2.57
4192 6280 8.432013 TGCCTCTAGAGCATATTTTCTTCAATA 58.568 33.333 14.73 0.00 34.69 1.90
4193 6281 8.716909 GCCTCTAGAGCATATTTTCTTCAATAC 58.283 37.037 14.73 0.00 0.00 1.89
4194 6282 9.995003 CCTCTAGAGCATATTTTCTTCAATACT 57.005 33.333 14.73 0.00 0.00 2.12
4229 6317 0.179092 GTTAAGCGTGCGGACCCTAT 60.179 55.000 0.00 0.00 0.00 2.57
4231 6319 1.038681 TAAGCGTGCGGACCCTATGA 61.039 55.000 0.00 0.00 0.00 2.15
4241 6329 2.623889 CGGACCCTATGAGTTCGAGAAT 59.376 50.000 0.00 0.00 38.56 2.40
4242 6330 3.551046 CGGACCCTATGAGTTCGAGAATG 60.551 52.174 0.00 0.00 38.56 2.67
4255 6343 7.048629 AGTTCGAGAATGATGTAGACATGAT 57.951 36.000 0.00 0.00 36.57 2.45
4259 6347 6.017109 TCGAGAATGATGTAGACATGATCGAA 60.017 38.462 0.00 0.00 39.80 3.71
4261 6349 7.328005 CGAGAATGATGTAGACATGATCGAAAT 59.672 37.037 0.00 0.00 38.04 2.17
4262 6350 8.307921 AGAATGATGTAGACATGATCGAAATG 57.692 34.615 0.00 9.30 36.57 2.32
4264 6352 4.751600 TGATGTAGACATGATCGAAATGCC 59.248 41.667 0.00 1.34 36.57 4.40
4271 6359 0.104855 TGATCGAAATGCCTCTCCGG 59.895 55.000 0.00 0.00 0.00 5.14
4273 6361 0.541863 ATCGAAATGCCTCTCCGGTT 59.458 50.000 0.00 0.00 34.25 4.44
4279 6367 4.755123 CGAAATGCCTCTCCGGTTAATAAT 59.245 41.667 0.00 0.00 34.25 1.28
4289 6377 4.571919 TCCGGTTAATAATCAATAGCGGG 58.428 43.478 0.00 0.00 46.54 6.13
4295 6383 7.336396 GGTTAATAATCAATAGCGGGACCTAT 58.664 38.462 0.00 0.00 0.00 2.57
4300 6388 2.500098 TCAATAGCGGGACCTATATGCC 59.500 50.000 0.00 0.00 0.00 4.40
4342 6430 5.340010 TCTACGAAGATCTTTATCGGTCG 57.660 43.478 17.21 13.10 43.94 4.79
4345 6433 4.349501 ACGAAGATCTTTATCGGTCGAAC 58.650 43.478 17.21 0.00 42.42 3.95
4348 6436 5.340439 AAGATCTTTATCGGTCGAACCTT 57.660 39.130 0.88 0.00 35.66 3.50
4349 6437 5.340439 AGATCTTTATCGGTCGAACCTTT 57.660 39.130 0.00 0.00 35.66 3.11
4352 6440 6.924060 AGATCTTTATCGGTCGAACCTTTATG 59.076 38.462 0.00 0.00 35.66 1.90
4364 6452 6.696148 GTCGAACCTTTATGATGATACGTCTT 59.304 38.462 0.00 0.00 0.00 3.01
4483 6572 7.202158 GGATTAACCTATTAACCTAGAGCCCAA 60.202 40.741 0.00 0.00 33.09 4.12
4489 6578 0.257039 AACCTAGAGCCCAATGCCAG 59.743 55.000 0.00 0.00 42.71 4.85
4494 6583 1.260544 AGAGCCCAATGCCAGTTTTC 58.739 50.000 0.00 0.00 42.71 2.29
4495 6584 1.203100 AGAGCCCAATGCCAGTTTTCT 60.203 47.619 0.00 0.00 42.71 2.52
4496 6585 2.041620 AGAGCCCAATGCCAGTTTTCTA 59.958 45.455 0.00 0.00 42.71 2.10
4540 6629 9.893305 AGTTTTACAGAAAAGGAATATCAAACG 57.107 29.630 0.00 0.00 35.21 3.60
4546 6635 6.371548 CAGAAAAGGAATATCAAACGGAGTCA 59.628 38.462 0.00 0.00 45.00 3.41
4549 6638 6.496338 AAGGAATATCAAACGGAGTCAAAC 57.504 37.500 0.00 0.00 45.00 2.93
4550 6639 4.630069 AGGAATATCAAACGGAGTCAAACG 59.370 41.667 0.00 0.00 45.00 3.60
4551 6640 4.628333 GGAATATCAAACGGAGTCAAACGA 59.372 41.667 0.00 0.00 45.00 3.85
4552 6641 5.220416 GGAATATCAAACGGAGTCAAACGAG 60.220 44.000 0.00 0.00 45.00 4.18
4556 6646 0.600255 AACGGAGTCAAACGAGCTGG 60.600 55.000 0.00 0.00 45.00 4.85
4559 6649 1.872237 CGGAGTCAAACGAGCTGGAAA 60.872 52.381 1.44 0.00 0.00 3.13
4562 6652 3.253432 GGAGTCAAACGAGCTGGAAATTT 59.747 43.478 1.44 0.00 0.00 1.82
4564 6654 5.358298 AGTCAAACGAGCTGGAAATTTAC 57.642 39.130 1.44 0.00 0.00 2.01
4567 6657 2.467566 ACGAGCTGGAAATTTACGGT 57.532 45.000 10.97 4.10 0.00 4.83
4572 6662 4.142687 CGAGCTGGAAATTTACGGTGATTT 60.143 41.667 10.97 4.61 0.00 2.17
4594 6684 3.864789 TTATGGATCAGAAGAAGCCCC 57.135 47.619 0.00 0.00 0.00 5.80
4595 6685 1.904440 ATGGATCAGAAGAAGCCCCT 58.096 50.000 0.00 0.00 0.00 4.79
4597 6687 1.207791 GGATCAGAAGAAGCCCCTGA 58.792 55.000 0.00 0.00 40.68 3.86
4600 6690 0.326264 TCAGAAGAAGCCCCTGAAGC 59.674 55.000 0.00 0.00 34.38 3.86
4602 6692 0.037447 AGAAGAAGCCCCTGAAGCAC 59.963 55.000 0.00 0.00 0.00 4.40
4603 6693 0.250901 GAAGAAGCCCCTGAAGCACA 60.251 55.000 0.00 0.00 0.00 4.57
4604 6694 0.185901 AAGAAGCCCCTGAAGCACAA 59.814 50.000 0.00 0.00 0.00 3.33
4605 6695 0.251077 AGAAGCCCCTGAAGCACAAG 60.251 55.000 0.00 0.00 0.00 3.16
4608 6698 1.073897 GCCCCTGAAGCACAAGAGT 59.926 57.895 0.00 0.00 0.00 3.24
4612 6702 1.242076 CCTGAAGCACAAGAGTTGGG 58.758 55.000 0.00 0.00 37.05 4.12
4618 6708 3.419793 CACAAGAGTTGGGCCAGAA 57.580 52.632 6.23 0.00 34.12 3.02
4624 6714 0.035915 GAGTTGGGCCAGAAGAGTCC 60.036 60.000 6.23 0.00 0.00 3.85
4626 6716 2.592993 TTGGGCCAGAAGAGTCCCG 61.593 63.158 6.23 0.00 41.65 5.14
4631 6721 1.984570 CCAGAAGAGTCCCGAGGCA 60.985 63.158 0.00 0.00 0.00 4.75
4634 6724 0.832135 AGAAGAGTCCCGAGGCAACA 60.832 55.000 0.00 0.00 41.41 3.33
4637 6727 1.070786 GAGTCCCGAGGCAACAACA 59.929 57.895 0.00 0.00 41.41 3.33
4645 6735 0.467290 GAGGCAACAACAAGGGTGGA 60.467 55.000 0.00 0.00 41.41 4.02
4651 6741 4.660938 AACAAGGGTGGAGGGCGC 62.661 66.667 0.00 0.00 0.00 6.53
4690 6780 4.368003 CCCCCTACCTTGTCGCTA 57.632 61.111 0.00 0.00 0.00 4.26
4696 6786 1.093159 CTACCTTGTCGCTACCTCGT 58.907 55.000 0.00 0.00 0.00 4.18
4703 6793 2.754658 CGCTACCTCGTGGACCCT 60.755 66.667 11.17 0.00 37.04 4.34
4705 6795 2.424733 GCTACCTCGTGGACCCTCC 61.425 68.421 11.17 0.00 36.96 4.30
4712 6802 0.406750 TCGTGGACCCTCCTGACTTA 59.593 55.000 0.00 0.00 37.46 2.24
4713 6803 1.203087 TCGTGGACCCTCCTGACTTAA 60.203 52.381 0.00 0.00 37.46 1.85
4714 6804 1.621814 CGTGGACCCTCCTGACTTAAA 59.378 52.381 0.00 0.00 37.46 1.52
4715 6805 2.038033 CGTGGACCCTCCTGACTTAAAA 59.962 50.000 0.00 0.00 37.46 1.52
4716 6806 3.409570 GTGGACCCTCCTGACTTAAAAC 58.590 50.000 0.00 0.00 37.46 2.43
4717 6807 2.374170 TGGACCCTCCTGACTTAAAACC 59.626 50.000 0.00 0.00 37.46 3.27
4718 6808 2.614734 GGACCCTCCTGACTTAAAACCG 60.615 54.545 0.00 0.00 32.53 4.44
4719 6809 2.301009 GACCCTCCTGACTTAAAACCGA 59.699 50.000 0.00 0.00 0.00 4.69
4720 6810 2.038164 ACCCTCCTGACTTAAAACCGAC 59.962 50.000 0.00 0.00 0.00 4.79
4721 6811 2.334838 CCTCCTGACTTAAAACCGACG 58.665 52.381 0.00 0.00 0.00 5.12
4722 6812 1.725164 CTCCTGACTTAAAACCGACGC 59.275 52.381 0.00 0.00 0.00 5.19
4723 6813 1.342174 TCCTGACTTAAAACCGACGCT 59.658 47.619 0.00 0.00 0.00 5.07
4724 6814 2.557924 TCCTGACTTAAAACCGACGCTA 59.442 45.455 0.00 0.00 0.00 4.26
4725 6815 3.005684 TCCTGACTTAAAACCGACGCTAA 59.994 43.478 0.00 0.00 0.00 3.09
4726 6816 3.742369 CCTGACTTAAAACCGACGCTAAA 59.258 43.478 0.00 0.00 0.00 1.85
4727 6817 4.211794 CCTGACTTAAAACCGACGCTAAAA 59.788 41.667 0.00 0.00 0.00 1.52
4728 6818 5.277442 CCTGACTTAAAACCGACGCTAAAAA 60.277 40.000 0.00 0.00 0.00 1.94
4729 6819 6.303021 TGACTTAAAACCGACGCTAAAAAT 57.697 33.333 0.00 0.00 0.00 1.82
4730 6820 6.727215 TGACTTAAAACCGACGCTAAAAATT 58.273 32.000 0.00 0.00 0.00 1.82
4731 6821 6.852345 TGACTTAAAACCGACGCTAAAAATTC 59.148 34.615 0.00 0.00 0.00 2.17
4732 6822 6.727215 ACTTAAAACCGACGCTAAAAATTCA 58.273 32.000 0.00 0.00 0.00 2.57
4733 6823 7.364970 ACTTAAAACCGACGCTAAAAATTCAT 58.635 30.769 0.00 0.00 0.00 2.57
4734 6824 8.505625 ACTTAAAACCGACGCTAAAAATTCATA 58.494 29.630 0.00 0.00 0.00 2.15
4735 6825 9.498307 CTTAAAACCGACGCTAAAAATTCATAT 57.502 29.630 0.00 0.00 0.00 1.78
4738 6828 9.843334 AAAACCGACGCTAAAAATTCATATAAA 57.157 25.926 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.012673 GACCAAGTCTGCAGCATAAGG 58.987 52.381 9.47 9.50 0.00 2.69
52 53 4.735132 TGGGACAGCAGCGTACGC 62.735 66.667 32.17 32.17 42.33 4.42
88 89 4.753516 TGTTCACCTTCTGAAGACTTGA 57.246 40.909 18.68 13.82 39.69 3.02
112 113 3.556817 GTGGTCCACATGATCAGCA 57.443 52.632 17.59 0.00 33.82 4.41
157 158 2.464157 ACTACAGGCAAAGAGCTGTC 57.536 50.000 0.00 0.00 44.79 3.51
159 160 2.351157 GCAAACTACAGGCAAAGAGCTG 60.351 50.000 0.00 0.00 44.79 4.24
230 232 7.759489 ATTTAGTCTAGCAAATGAACCAACA 57.241 32.000 0.00 0.00 0.00 3.33
231 233 9.937175 GATATTTAGTCTAGCAAATGAACCAAC 57.063 33.333 6.91 0.00 0.00 3.77
233 235 9.330063 CTGATATTTAGTCTAGCAAATGAACCA 57.670 33.333 6.91 0.00 0.00 3.67
261 263 1.939381 GCAGCATCCACGTAGAACACA 60.939 52.381 0.00 0.00 0.00 3.72
409 413 0.812412 CCGACTGTCACCCGTTTTGT 60.812 55.000 8.73 0.00 0.00 2.83
415 419 2.201732 CAAATATCCGACTGTCACCCG 58.798 52.381 8.73 0.00 0.00 5.28
434 438 2.976882 ACAAACCCACTAGGCTAGAACA 59.023 45.455 27.59 0.00 40.58 3.18
571 589 7.332926 CCAATCCTAGAGATAAATGGAATCACG 59.667 40.741 0.00 0.00 33.71 4.35
577 595 6.393897 AGACCCAATCCTAGAGATAAATGGA 58.606 40.000 9.98 0.00 33.71 3.41
579 597 7.016072 ACAGAGACCCAATCCTAGAGATAAATG 59.984 40.741 0.00 0.00 33.66 2.32
607 627 7.675161 TCTATGACTTTGACTCATATCCCAA 57.325 36.000 0.00 0.00 31.61 4.12
627 647 6.183360 CCAGTCGAATTTGGAAAGCATTCTAT 60.183 38.462 1.19 0.00 36.55 1.98
653 673 7.826252 CGGATGGAATTCCTATATGAACTTGAT 59.174 37.037 24.73 5.49 36.82 2.57
747 813 9.445878 CAGGATGTATCAATCTACAGCATATTT 57.554 33.333 2.44 0.00 39.25 1.40
855 921 5.104900 ACCAAATTAGCTCAGGAACTCGTAT 60.105 40.000 0.00 0.00 34.60 3.06
911 977 0.615331 TCAATGCAGAGGTCAGGGAC 59.385 55.000 0.00 0.00 0.00 4.46
928 994 4.949238 ACTAATGGCTGTGTGCATTAATCA 59.051 37.500 0.00 0.00 45.15 2.57
978 1044 7.975616 GCCATTTGATCTAAACAGCAAAGATAA 59.024 33.333 0.00 0.00 34.21 1.75
1157 1225 4.202357 TGCCTATCTGCCTTATAACAGTGG 60.202 45.833 0.00 5.93 35.37 4.00
1160 1228 3.990469 CGTGCCTATCTGCCTTATAACAG 59.010 47.826 0.00 0.00 35.15 3.16
1377 1463 9.930158 ATAACTAGTTGAATCTCCTTCTCTACT 57.070 33.333 18.56 0.00 34.75 2.57
1443 1535 5.767670 TCTATCTCAGTAAGTGGGTTAGCT 58.232 41.667 0.00 0.00 31.25 3.32
1464 1556 0.321122 CTTGAGACCGCTGCCTTTCT 60.321 55.000 0.00 0.00 0.00 2.52
1479 1571 3.795688 AATTCTGGGAAGCTGTCTTGA 57.204 42.857 0.00 0.00 31.48 3.02
1878 2428 6.644592 GGAGAGCATCATGTATCTGAAAGTAC 59.355 42.308 0.00 0.00 37.82 2.73
1884 2436 3.577415 CCTGGAGAGCATCATGTATCTGA 59.423 47.826 0.00 0.00 37.82 3.27
1916 2468 4.804139 GTGTCGTAATGATGATCCGACTTT 59.196 41.667 18.00 4.48 45.87 2.66
2064 4081 4.688045 GCAATCATCTCAAGATCCTTGGGA 60.688 45.833 11.19 11.19 35.55 4.37
2244 4261 1.139853 GGAAGGTCATGGTAGCTCAGG 59.860 57.143 0.00 0.00 0.00 3.86
2451 4468 4.961730 ACTCTACCAAGCTCATCATTCTCT 59.038 41.667 0.00 0.00 0.00 3.10
2517 4534 7.517321 CAAATCTCTCTTCTTTAGCAACAGAC 58.483 38.462 0.00 0.00 0.00 3.51
2627 4679 4.292977 AGTTTAACTTTCACTGCAGTGC 57.707 40.909 36.76 21.39 45.25 4.40
2958 5011 3.995705 GCTTCTCATCAGCATATCTGTCC 59.004 47.826 0.00 0.00 43.32 4.02
3669 5728 3.750130 CAGTGTCCCATTGAGTTCTGAAG 59.250 47.826 0.00 0.00 0.00 3.02
3959 6044 5.036117 ACAACAGAAACAGTACAGTCCAT 57.964 39.130 0.00 0.00 0.00 3.41
3970 6055 6.373216 AGTGTGTAGCTTAAACAACAGAAACA 59.627 34.615 0.00 0.00 0.00 2.83
4104 6192 8.520351 GGTAAAATAATAATGGGGTGACATAGC 58.480 37.037 0.00 0.00 0.00 2.97
4151 6239 9.326413 GCTCTAGAGGCAATAATAAAGTTGTTA 57.674 33.333 21.23 0.00 0.00 2.41
4152 6240 7.829211 TGCTCTAGAGGCAATAATAAAGTTGTT 59.171 33.333 21.23 0.00 36.71 2.83
4153 6241 7.338710 TGCTCTAGAGGCAATAATAAAGTTGT 58.661 34.615 21.23 0.00 36.71 3.32
4154 6242 7.792374 TGCTCTAGAGGCAATAATAAAGTTG 57.208 36.000 21.23 0.00 36.71 3.16
4161 6249 9.804977 AAGAAAATATGCTCTAGAGGCAATAAT 57.195 29.630 21.23 11.28 43.14 1.28
4162 6250 9.277783 GAAGAAAATATGCTCTAGAGGCAATAA 57.722 33.333 21.23 9.78 43.14 1.40
4163 6251 8.432013 TGAAGAAAATATGCTCTAGAGGCAATA 58.568 33.333 21.23 12.68 43.14 1.90
4164 6252 7.285566 TGAAGAAAATATGCTCTAGAGGCAAT 58.714 34.615 21.23 11.82 43.14 3.56
4165 6253 6.653020 TGAAGAAAATATGCTCTAGAGGCAA 58.347 36.000 21.23 10.37 43.14 4.52
4166 6254 6.239217 TGAAGAAAATATGCTCTAGAGGCA 57.761 37.500 21.23 18.27 44.05 4.75
4167 6255 7.742556 ATTGAAGAAAATATGCTCTAGAGGC 57.257 36.000 21.23 13.48 0.00 4.70
4168 6256 9.995003 AGTATTGAAGAAAATATGCTCTAGAGG 57.005 33.333 21.23 3.52 0.00 3.69
4192 6280 9.109393 ACGCTTAACATTTGTTGATGATATAGT 57.891 29.630 6.21 0.00 38.90 2.12
4193 6281 9.373750 CACGCTTAACATTTGTTGATGATATAG 57.626 33.333 6.21 0.00 38.90 1.31
4194 6282 7.855409 GCACGCTTAACATTTGTTGATGATATA 59.145 33.333 6.21 0.00 38.90 0.86
4195 6283 6.692681 GCACGCTTAACATTTGTTGATGATAT 59.307 34.615 6.21 0.00 38.90 1.63
4196 6284 6.027131 GCACGCTTAACATTTGTTGATGATA 58.973 36.000 6.21 0.00 38.90 2.15
4200 6288 3.233578 CGCACGCTTAACATTTGTTGAT 58.766 40.909 6.21 0.00 38.90 2.57
4204 6292 1.069500 GTCCGCACGCTTAACATTTGT 60.069 47.619 0.00 0.00 0.00 2.83
4206 6294 0.519961 GGTCCGCACGCTTAACATTT 59.480 50.000 0.00 0.00 0.00 2.32
4209 6297 1.534336 TAGGGTCCGCACGCTTAACA 61.534 55.000 0.00 0.00 43.11 2.41
4229 6317 5.897377 TGTCTACATCATTCTCGAACTCA 57.103 39.130 0.00 0.00 0.00 3.41
4231 6319 6.456795 TCATGTCTACATCATTCTCGAACT 57.543 37.500 0.00 0.00 33.61 3.01
4241 6329 4.751600 GGCATTTCGATCATGTCTACATCA 59.248 41.667 6.90 0.00 33.61 3.07
4242 6330 4.993584 AGGCATTTCGATCATGTCTACATC 59.006 41.667 9.84 0.00 34.73 3.06
4255 6343 1.187974 TAACCGGAGAGGCATTTCGA 58.812 50.000 9.46 0.00 46.52 3.71
4259 6347 5.304686 TGATTATTAACCGGAGAGGCATT 57.695 39.130 9.46 0.00 46.52 3.56
4261 6349 4.764050 TTGATTATTAACCGGAGAGGCA 57.236 40.909 9.46 0.00 46.52 4.75
4262 6350 5.351740 GCTATTGATTATTAACCGGAGAGGC 59.648 44.000 9.46 0.00 46.52 4.70
4264 6352 5.577164 CCGCTATTGATTATTAACCGGAGAG 59.423 44.000 9.46 0.00 35.50 3.20
4273 6361 8.148351 GCATATAGGTCCCGCTATTGATTATTA 58.852 37.037 0.00 0.00 0.00 0.98
4279 6367 2.500098 GGCATATAGGTCCCGCTATTGA 59.500 50.000 0.00 0.00 0.00 2.57
4289 6377 5.044846 AGGAACCAATATGGGCATATAGGTC 60.045 44.000 0.00 0.00 43.37 3.85
4295 6383 5.858876 ATGTAGGAACCAATATGGGCATA 57.141 39.130 0.00 0.00 43.37 3.14
4298 6386 6.485171 AGAATATGTAGGAACCAATATGGGC 58.515 40.000 0.00 0.00 43.37 5.36
4300 6388 8.528643 TCGTAGAATATGTAGGAACCAATATGG 58.471 37.037 0.00 0.00 45.02 2.74
4342 6430 8.328864 GTTGAAGACGTATCATCATAAAGGTTC 58.671 37.037 4.53 0.00 32.80 3.62
4345 6433 6.867388 CGTTGAAGACGTATCATCATAAAGG 58.133 40.000 4.53 0.00 46.49 3.11
4456 6544 6.271624 GGGCTCTAGGTTAATAGGTTAATCCA 59.728 42.308 0.00 0.00 39.02 3.41
4459 6547 7.701257 TTGGGCTCTAGGTTAATAGGTTAAT 57.299 36.000 0.00 0.00 32.76 1.40
4460 6548 7.514721 CATTGGGCTCTAGGTTAATAGGTTAA 58.485 38.462 0.00 0.00 0.00 2.01
4473 6562 2.134789 AAACTGGCATTGGGCTCTAG 57.865 50.000 0.00 0.00 44.01 2.43
4517 6606 8.624367 TCCGTTTGATATTCCTTTTCTGTAAA 57.376 30.769 0.00 0.00 0.00 2.01
4519 6608 7.391620 ACTCCGTTTGATATTCCTTTTCTGTA 58.608 34.615 0.00 0.00 0.00 2.74
4520 6609 6.238648 ACTCCGTTTGATATTCCTTTTCTGT 58.761 36.000 0.00 0.00 0.00 3.41
4532 6621 2.991190 GCTCGTTTGACTCCGTTTGATA 59.009 45.455 0.00 0.00 0.00 2.15
4534 6623 1.202486 AGCTCGTTTGACTCCGTTTGA 60.202 47.619 0.00 0.00 0.00 2.69
4539 6628 0.319555 TTCCAGCTCGTTTGACTCCG 60.320 55.000 0.00 0.00 0.00 4.63
4540 6629 1.878953 TTTCCAGCTCGTTTGACTCC 58.121 50.000 0.00 0.00 0.00 3.85
4546 6635 3.058501 CACCGTAAATTTCCAGCTCGTTT 60.059 43.478 0.00 0.00 0.00 3.60
4549 6638 2.343101 TCACCGTAAATTTCCAGCTCG 58.657 47.619 0.00 0.00 0.00 5.03
4550 6639 4.965119 AATCACCGTAAATTTCCAGCTC 57.035 40.909 0.00 0.00 0.00 4.09
4551 6640 5.722021 AAAATCACCGTAAATTTCCAGCT 57.278 34.783 0.00 0.00 0.00 4.24
4572 6662 4.230502 AGGGGCTTCTTCTGATCCATAAAA 59.769 41.667 0.00 0.00 0.00 1.52
4576 6666 1.493871 CAGGGGCTTCTTCTGATCCAT 59.506 52.381 0.00 0.00 0.00 3.41
4581 6671 0.326264 GCTTCAGGGGCTTCTTCTGA 59.674 55.000 0.00 0.00 35.95 3.27
4594 6684 0.595095 GCCCAACTCTTGTGCTTCAG 59.405 55.000 0.00 0.00 31.00 3.02
4595 6685 0.823356 GGCCCAACTCTTGTGCTTCA 60.823 55.000 0.00 0.00 34.31 3.02
4597 6687 0.825010 CTGGCCCAACTCTTGTGCTT 60.825 55.000 0.00 0.00 34.31 3.91
4600 6690 1.202806 TCTTCTGGCCCAACTCTTGTG 60.203 52.381 0.00 0.00 0.00 3.33
4602 6692 1.072965 ACTCTTCTGGCCCAACTCTTG 59.927 52.381 0.00 0.00 0.00 3.02
4603 6693 1.349357 GACTCTTCTGGCCCAACTCTT 59.651 52.381 0.00 0.00 0.00 2.85
4604 6694 0.980423 GACTCTTCTGGCCCAACTCT 59.020 55.000 0.00 0.00 0.00 3.24
4605 6695 0.035915 GGACTCTTCTGGCCCAACTC 60.036 60.000 0.00 0.00 0.00 3.01
4608 6698 2.592993 CGGGACTCTTCTGGCCCAA 61.593 63.158 0.00 0.00 40.71 4.12
4612 6702 2.896443 CCTCGGGACTCTTCTGGC 59.104 66.667 0.00 0.00 0.00 4.85
4618 6708 1.371558 GTTGTTGCCTCGGGACTCT 59.628 57.895 0.00 0.00 0.00 3.24
4624 6714 1.528309 ACCCTTGTTGTTGCCTCGG 60.528 57.895 0.00 0.00 0.00 4.63
4626 6716 0.467290 TCCACCCTTGTTGTTGCCTC 60.467 55.000 0.00 0.00 0.00 4.70
4631 6721 1.152546 GCCCTCCACCCTTGTTGTT 60.153 57.895 0.00 0.00 0.00 2.83
4634 6724 4.660938 GCGCCCTCCACCCTTGTT 62.661 66.667 0.00 0.00 0.00 2.83
4673 6763 1.683418 GGTAGCGACAAGGTAGGGGG 61.683 65.000 0.00 0.00 32.89 5.40
4680 6770 1.153823 CCACGAGGTAGCGACAAGG 60.154 63.158 0.00 0.00 34.83 3.61
4683 6773 2.338015 GGTCCACGAGGTAGCGACA 61.338 63.158 0.00 0.00 35.89 4.35
4686 6776 2.754658 AGGGTCCACGAGGTAGCG 60.755 66.667 0.00 0.00 35.89 4.26
4689 6779 1.000019 CAGGAGGGTCCACGAGGTA 60.000 63.158 0.00 0.00 39.61 3.08
4690 6780 2.283966 CAGGAGGGTCCACGAGGT 60.284 66.667 0.00 0.00 39.61 3.85
4696 6786 2.374170 GGTTTTAAGTCAGGAGGGTCCA 59.626 50.000 0.00 0.00 39.61 4.02
4703 6793 1.342174 AGCGTCGGTTTTAAGTCAGGA 59.658 47.619 0.00 0.00 0.00 3.86
4705 6795 4.977741 TTTAGCGTCGGTTTTAAGTCAG 57.022 40.909 0.65 0.00 0.00 3.51
4712 6802 9.843334 TTTATATGAATTTTTAGCGTCGGTTTT 57.157 25.926 0.65 0.00 0.00 2.43



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

AutoCloner maintained by Alex Coulton.