Multiple sequence alignment - TraesCS1B01G477400

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 TraesCS1B01G477400 chr1B 100.000 6106 0 0 1 6106 685650392 685644287 0.000000e+00 11276.0
1 TraesCS1B01G477400 chr1B 78.682 258 39 14 3348 3592 32399653 32399907 2.280000e-34 158.0
2 TraesCS1B01G477400 chr1A 95.495 2997 74 13 2116 5054 591614487 591611494 0.000000e+00 4730.0
3 TraesCS1B01G477400 chr1A 84.326 1863 117 70 1 1742 591616567 591614759 0.000000e+00 1661.0
4 TraesCS1B01G477400 chr1A 94.373 1084 37 10 5040 6106 591611468 591610392 0.000000e+00 1642.0
5 TraesCS1B01G477400 chr1A 93.970 199 12 0 1782 1980 591614760 591614562 9.950000e-78 302.0
6 TraesCS1B01G477400 chr1D 94.648 1775 38 13 3338 5057 493486117 493484345 0.000000e+00 2699.0
7 TraesCS1B01G477400 chr1D 96.908 1229 31 2 2116 3338 493487649 493486422 0.000000e+00 2052.0
8 TraesCS1B01G477400 chr1D 86.199 1268 71 37 1 1228 493492171 493490968 0.000000e+00 1277.0
9 TraesCS1B01G477400 chr1D 95.277 487 14 4 5629 6106 493483444 493482958 0.000000e+00 763.0
10 TraesCS1B01G477400 chr1D 85.736 666 49 24 1497 2134 493488319 493487672 0.000000e+00 662.0
11 TraesCS1B01G477400 chr1D 94.344 389 15 3 5206 5594 493483825 493483444 1.900000e-164 590.0
12 TraesCS1B01G477400 chr1D 91.875 320 11 7 1085 1404 493488643 493488339 3.380000e-117 433.0
13 TraesCS1B01G477400 chr1D 85.530 387 13 11 725 1093 493489295 493488934 1.250000e-96 364.0
14 TraesCS1B01G477400 chr1D 93.038 158 6 2 5055 5208 493484287 493484131 6.160000e-55 226.0
15 TraesCS1B01G477400 chr2B 84.674 261 22 7 3347 3592 225571375 225571632 1.700000e-60 244.0
16 TraesCS1B01G477400 chr2B 90.132 152 14 1 3347 3498 106941230 106941380 4.830000e-46 196.0
17 TraesCS1B01G477400 chr4B 84.400 250 23 2 3347 3581 358476439 358476191 1.320000e-56 231.0
18 TraesCS1B01G477400 chr4A 84.000 250 24 9 3347 3581 329186944 329187192 6.160000e-55 226.0
19 TraesCS1B01G477400 chr4A 82.587 201 20 8 3392 3578 352273207 352273008 4.900000e-36 163.0
20 TraesCS1B01G477400 chr4A 93.023 43 2 1 3294 3336 597138346 597138305 1.840000e-05 62.1
21 TraesCS1B01G477400 chr3A 83.083 266 19 13 3345 3591 714645285 714645543 1.030000e-52 219.0
22 TraesCS1B01G477400 chr4D 83.200 250 26 9 3347 3581 281294812 281294564 1.330000e-51 215.0
23 TraesCS1B01G477400 chr4D 89.720 107 10 1 3486 3591 500283969 500284075 1.070000e-27 135.0
24 TraesCS1B01G477400 chr5D 83.200 250 25 2 3347 3580 517846688 517846936 4.790000e-51 213.0
25 TraesCS1B01G477400 chr2D 89.542 153 14 2 3347 3498 70525551 70525702 6.250000e-45 193.0
26 TraesCS1B01G477400 chr2A 81.893 243 28 9 3362 3591 626580189 626580428 2.250000e-44 191.0
27 TraesCS1B01G477400 chr5A 88.462 104 11 1 3489 3591 380272082 380271979 2.310000e-24 124.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G477400 chr1B 685644287 685650392 6105 True 11276.000000 11276 100.000000 1 6106 1 chr1B.!!$R1 6105
1 TraesCS1B01G477400 chr1A 591610392 591616567 6175 True 2083.750000 4730 92.041000 1 6106 4 chr1A.!!$R1 6105
2 TraesCS1B01G477400 chr1D 493482958 493492171 9213 True 1007.333333 2699 91.506111 1 6106 9 chr1D.!!$R1 6105

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
759 2949 0.028747 AGGATCCCATGTCATCCCCA 60.029 55.000 8.55 0.0 39.73 4.96 F
952 3175 0.180406 ATTTCTCCCCAACCGATCGG 59.820 55.000 32.20 32.2 42.03 4.18 F
1736 4337 0.100682 TATGCTTGGCTCTCGACGAC 59.899 55.000 0.00 0.0 0.00 4.34 F
1902 4503 0.374758 CACAGCGTTGATGATTCCCG 59.625 55.000 6.16 0.0 0.00 5.14 F
3703 6678 0.457443 TCGAGCTGCATCGACTGATT 59.543 50.000 16.36 0.0 46.20 2.57 F
4735 7727 1.311403 CAGCCCCAGGTCTCCTCTA 59.689 63.158 0.00 0.0 0.00 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1661 4262 1.025812 ACAAAACGGGCGTTTCATCA 58.974 45.000 0.00 0.00 46.22 3.07 R
2854 5507 1.078918 GCCCATTTCCAGCCTTTGC 60.079 57.895 0.00 0.00 37.95 3.68 R
3703 6678 0.320421 GGTGGCGCAGACTCACTTTA 60.320 55.000 10.83 0.00 34.59 1.85 R
3885 6877 2.866156 CGTCTTCTTCTTGCTTGTCACA 59.134 45.455 0.00 0.00 0.00 3.58 R
4890 7882 0.103937 TTTTCTTTGTGCCGGCCAAG 59.896 50.000 26.77 22.23 0.00 3.61 R
5819 9212 1.134670 GTCCAGAATAGAGCGCCAGTT 60.135 52.381 2.29 0.00 0.00 3.16 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
44 45 5.160641 GGCTCTTTTTCATTGCATACGAAA 58.839 37.500 0.00 0.00 0.00 3.46
58 59 7.231705 TGCATACGAAATTTTAAATGCATGG 57.768 32.000 21.54 0.00 43.32 3.66
112 113 8.299570 GGGTTCACATGCATAAAAAGGATATAG 58.700 37.037 0.00 0.00 0.00 1.31
134 136 0.251742 ACTGCCCATGCCTAGCAAAA 60.252 50.000 0.00 0.00 43.62 2.44
194 196 5.080969 TGAAACCGTTCCCTCAACTATAG 57.919 43.478 0.00 0.00 32.28 1.31
217 219 4.621510 GCCCTTCCTCATTGGTGAAATTTC 60.622 45.833 11.41 11.41 37.07 2.17
218 220 4.527816 CCCTTCCTCATTGGTGAAATTTCA 59.472 41.667 16.91 16.91 37.07 2.69
265 267 8.652463 CCAACTTTTGAACACGTTTTCTTATTT 58.348 29.630 14.99 0.80 0.00 1.40
285 287 9.185192 CTTATTTTTGGAAGAGCTTTACACAAG 57.815 33.333 0.00 0.00 0.00 3.16
302 304 4.141321 ACACAAGATACAGGATGGATGCAT 60.141 41.667 0.00 0.00 42.17 3.96
305 307 4.017177 AGATACAGGATGGATGCATGTG 57.983 45.455 2.46 4.50 42.17 3.21
350 352 5.057149 GTCGTATTGGATAAAGCTGGATGT 58.943 41.667 0.00 0.00 0.00 3.06
359 361 5.357878 GGATAAAGCTGGATGTGATGACAAA 59.642 40.000 0.00 0.00 35.11 2.83
360 362 6.040166 GGATAAAGCTGGATGTGATGACAAAT 59.960 38.462 0.00 0.00 35.11 2.32
367 369 5.184711 TGGATGTGATGACAAATTCGATGA 58.815 37.500 0.00 0.00 35.11 2.92
368 370 5.065090 TGGATGTGATGACAAATTCGATGAC 59.935 40.000 0.00 0.00 35.11 3.06
387 401 3.483235 CTTTTGTGGCGCGCTTGGT 62.483 57.895 32.29 0.00 0.00 3.67
395 409 2.102161 CGCGCTTGGTATTTGCCC 59.898 61.111 5.56 0.00 0.00 5.36
410 424 3.158648 CCCCCGCCGGAGATACAA 61.159 66.667 5.05 0.00 0.00 2.41
419 433 2.031683 GCCGGAGATACAACCAAAATCG 59.968 50.000 5.05 0.00 0.00 3.34
432 446 6.206634 ACAACCAAAATCGAGTGTTGATGTAT 59.793 34.615 17.84 0.00 38.81 2.29
437 451 7.271223 CCAAAATCGAGTGTTGATGTATGTTTC 59.729 37.037 6.99 0.00 0.00 2.78
438 452 7.433708 AAATCGAGTGTTGATGTATGTTTCA 57.566 32.000 0.00 0.00 0.00 2.69
515 549 2.102252 GTGGGGAAAAGAACATGCACAA 59.898 45.455 0.00 0.00 0.00 3.33
532 566 7.277760 ACATGCACAAATGATGAATGAATCTTG 59.722 33.333 0.00 0.00 0.00 3.02
539 573 2.008752 TGAATGAATCTTGAGCGCGA 57.991 45.000 12.10 0.00 0.00 5.87
581 615 2.525629 TCAAGCCAGGGTGGACGA 60.526 61.111 0.00 0.00 40.96 4.20
727 2917 2.098614 TCATTTGCAGTGGTGTTGTGT 58.901 42.857 0.00 0.00 0.00 3.72
728 2918 2.495270 TCATTTGCAGTGGTGTTGTGTT 59.505 40.909 0.00 0.00 0.00 3.32
729 2919 2.360553 TTTGCAGTGGTGTTGTGTTG 57.639 45.000 0.00 0.00 0.00 3.33
730 2920 1.252175 TTGCAGTGGTGTTGTGTTGT 58.748 45.000 0.00 0.00 0.00 3.32
731 2921 0.808125 TGCAGTGGTGTTGTGTTGTC 59.192 50.000 0.00 0.00 0.00 3.18
758 2948 0.695347 GAGGATCCCATGTCATCCCC 59.305 60.000 8.55 2.17 39.73 4.81
759 2949 0.028747 AGGATCCCATGTCATCCCCA 60.029 55.000 8.55 0.00 39.73 4.96
760 2950 1.078955 GGATCCCATGTCATCCCCAT 58.921 55.000 0.00 0.00 33.55 4.00
761 2951 1.430464 GGATCCCATGTCATCCCCATT 59.570 52.381 0.00 0.00 33.55 3.16
766 2956 1.063038 CCATGTCATCCCCATTCCCAA 60.063 52.381 0.00 0.00 0.00 4.12
772 2962 1.158963 ATCCCCATTCCCAACCCCAA 61.159 55.000 0.00 0.00 0.00 4.12
778 2968 1.679969 ATTCCCAACCCCAACCCCAA 61.680 55.000 0.00 0.00 0.00 4.12
782 2972 3.036959 AACCCCAACCCCAACCCA 61.037 61.111 0.00 0.00 0.00 4.51
783 2973 3.094751 AACCCCAACCCCAACCCAG 62.095 63.158 0.00 0.00 0.00 4.45
793 3006 1.752310 CCAACCCAGCACACACACA 60.752 57.895 0.00 0.00 0.00 3.72
796 3009 0.748005 AACCCAGCACACACACACTC 60.748 55.000 0.00 0.00 0.00 3.51
800 3013 1.372582 CAGCACACACACACTCTTGT 58.627 50.000 0.00 0.00 35.84 3.16
802 3015 2.162208 CAGCACACACACACTCTTGTTT 59.838 45.455 0.00 0.00 31.66 2.83
816 3029 3.601685 GTTTGTGGTGGGCGTGGG 61.602 66.667 0.00 0.00 0.00 4.61
951 3174 2.902705 TATTTCTCCCCAACCGATCG 57.097 50.000 8.51 8.51 0.00 3.69
952 3175 0.180406 ATTTCTCCCCAACCGATCGG 59.820 55.000 32.20 32.20 42.03 4.18
953 3176 1.906105 TTTCTCCCCAACCGATCGGG 61.906 60.000 35.87 20.10 42.67 5.14
954 3177 2.762459 CTCCCCAACCGATCGGGA 60.762 66.667 35.87 22.01 46.34 5.14
955 3178 2.041301 TCCCCAACCGATCGGGAT 60.041 61.111 35.87 22.51 46.34 3.85
956 3179 2.100879 CTCCCCAACCGATCGGGATC 62.101 65.000 35.87 0.00 46.34 3.36
1038 3261 1.731098 CGAAAAATCCGCCCTTTTCCG 60.731 52.381 7.88 0.00 37.98 4.30
1128 3667 1.964891 CATGATGGCGGCCTAGCTG 60.965 63.158 21.46 9.00 38.08 4.24
1419 3978 4.263683 CCTCTCACCCATCTTCTCCTTTTT 60.264 45.833 0.00 0.00 0.00 1.94
1510 4069 5.617528 TTGGATTGGATTGGATTGGATTG 57.382 39.130 0.00 0.00 0.00 2.67
1522 4081 6.091076 TGGATTGGATTGGAAACCTAGATT 57.909 37.500 0.00 0.00 0.00 2.40
1555 4114 2.511600 GCCGGCGATTACTGCTGT 60.512 61.111 12.58 0.66 36.99 4.40
1556 4115 2.813179 GCCGGCGATTACTGCTGTG 61.813 63.158 12.58 0.00 36.99 3.66
1557 4116 2.703409 CGGCGATTACTGCTGTGC 59.297 61.111 0.00 0.82 33.99 4.57
1597 4184 2.450476 CCTCTATTGGCTTGGCTTGTT 58.550 47.619 0.00 0.00 0.00 2.83
1599 4186 3.084039 CTCTATTGGCTTGGCTTGTTGA 58.916 45.455 0.00 0.00 0.00 3.18
1630 4221 3.303659 GCCGCTCTATTGATGCTCTTTTC 60.304 47.826 0.00 0.00 0.00 2.29
1638 4229 7.868775 TCTATTGATGCTCTTTTCATGTATGC 58.131 34.615 0.00 0.00 0.00 3.14
1671 4272 1.501741 ACGCATGGTGATGAAACGC 59.498 52.632 0.00 0.00 0.00 4.84
1672 4273 1.226379 CGCATGGTGATGAAACGCC 60.226 57.895 0.00 0.00 40.43 5.68
1673 4274 1.139520 GCATGGTGATGAAACGCCC 59.860 57.895 0.00 0.00 39.42 6.13
1674 4275 1.429021 CATGGTGATGAAACGCCCG 59.571 57.895 0.00 0.00 39.42 6.13
1675 4276 1.002624 ATGGTGATGAAACGCCCGT 60.003 52.632 0.00 0.00 39.42 5.28
1676 4277 0.608035 ATGGTGATGAAACGCCCGTT 60.608 50.000 0.00 0.00 39.42 4.44
1696 4297 4.092237 CGTTTTGTATGATTACGAGTGCCA 59.908 41.667 0.00 0.00 34.36 4.92
1708 4309 2.103771 ACGAGTGCCATGAGATGCTTAT 59.896 45.455 0.00 0.00 0.00 1.73
1710 4311 3.474600 GAGTGCCATGAGATGCTTATGT 58.525 45.455 0.00 0.00 0.00 2.29
1711 4312 4.635223 GAGTGCCATGAGATGCTTATGTA 58.365 43.478 0.00 0.00 0.00 2.29
1712 4313 4.384056 AGTGCCATGAGATGCTTATGTAC 58.616 43.478 0.00 0.00 0.00 2.90
1721 4322 6.379386 TGAGATGCTTATGTACTACGTATGC 58.621 40.000 15.00 15.00 39.67 3.14
1736 4337 0.100682 TATGCTTGGCTCTCGACGAC 59.899 55.000 0.00 0.00 0.00 4.34
1739 4340 1.803519 CTTGGCTCTCGACGACTGC 60.804 63.158 8.35 8.35 0.00 4.40
1756 4357 1.478510 CTGCTTGTCGGGTATCTGACT 59.521 52.381 15.92 0.00 46.66 3.41
1761 4362 1.005569 TGTCGGGTATCTGACTGAGGT 59.994 52.381 15.92 0.00 46.66 3.85
1780 4381 4.397348 ACCGGAAATGGTCACTGC 57.603 55.556 9.46 0.00 37.91 4.40
1799 4400 9.757227 GTCACTGCTTCTTTATCTGTTAGATAT 57.243 33.333 0.00 0.00 37.09 1.63
1832 4433 2.561373 GCTTTCCGGAGTTTGGCG 59.439 61.111 3.34 0.00 0.00 5.69
1902 4503 0.374758 CACAGCGTTGATGATTCCCG 59.625 55.000 6.16 0.00 0.00 5.14
1991 4592 2.824936 AGATGATGAGATGGAGCCTACG 59.175 50.000 0.00 0.00 0.00 3.51
1997 4598 5.952347 TGATGAGATGGAGCCTACGTATTAT 59.048 40.000 0.00 0.00 0.00 1.28
2007 4608 6.238022 GGAGCCTACGTATTATTGTTTGACAC 60.238 42.308 0.00 0.00 0.00 3.67
2071 4672 5.240623 TCCACGAATAATTCAAGTTGCTTGT 59.759 36.000 8.48 0.00 41.66 3.16
2072 4673 5.920273 CCACGAATAATTCAAGTTGCTTGTT 59.080 36.000 8.48 0.00 41.66 2.83
2073 4674 6.129115 CCACGAATAATTCAAGTTGCTTGTTG 60.129 38.462 8.48 0.00 41.66 3.33
2084 4685 2.247790 GCTTGTTGCACGGATGAGT 58.752 52.632 0.00 0.00 42.31 3.41
2116 4717 1.238439 CACGACTGGGCAATGTCTTT 58.762 50.000 0.00 0.00 0.00 2.52
2120 4721 4.634004 CACGACTGGGCAATGTCTTTATTA 59.366 41.667 0.00 0.00 0.00 0.98
2121 4722 4.634443 ACGACTGGGCAATGTCTTTATTAC 59.366 41.667 0.00 0.00 0.00 1.89
2125 4726 7.465513 CGACTGGGCAATGTCTTTATTACTAAC 60.466 40.741 0.00 0.00 0.00 2.34
2127 4728 7.888546 ACTGGGCAATGTCTTTATTACTAACTT 59.111 33.333 0.00 0.00 0.00 2.66
2128 4729 8.050778 TGGGCAATGTCTTTATTACTAACTTG 57.949 34.615 0.00 0.00 0.00 3.16
2129 4730 7.668052 TGGGCAATGTCTTTATTACTAACTTGT 59.332 33.333 0.00 0.00 0.00 3.16
2130 4731 9.169592 GGGCAATGTCTTTATTACTAACTTGTA 57.830 33.333 0.00 0.00 0.00 2.41
2184 4828 4.704057 AGACCTCTCTTTCCATCATTTTGC 59.296 41.667 0.00 0.00 0.00 3.68
2196 4840 3.383620 TCATTTTGCGTGCCTTCAAAT 57.616 38.095 0.00 0.00 32.92 2.32
2258 4902 3.958860 GCGGGATGGCCAGGCTAT 61.959 66.667 10.72 10.72 33.72 2.97
2349 4993 3.014604 AGTTCACAGCGTAGAGACAAC 57.985 47.619 0.00 0.00 0.00 3.32
2354 4998 2.863740 CACAGCGTAGAGACAACAACAA 59.136 45.455 0.00 0.00 0.00 2.83
2358 5002 4.024893 CAGCGTAGAGACAACAACAACAAT 60.025 41.667 0.00 0.00 0.00 2.71
2360 5007 5.405571 AGCGTAGAGACAACAACAACAATAG 59.594 40.000 0.00 0.00 0.00 1.73
2363 5010 6.128553 CGTAGAGACAACAACAACAATAGCAT 60.129 38.462 0.00 0.00 0.00 3.79
2479 5132 4.163839 AGGAAGTGAGGATCCAAGAGAATG 59.836 45.833 15.82 0.00 38.23 2.67
2665 5318 5.290386 ACACAACGACAAACTTTTTGGAAA 58.710 33.333 3.82 0.00 0.00 3.13
2724 5377 7.108847 CAGAGAAGACAATGGGTAAAAGAGAT 58.891 38.462 0.00 0.00 0.00 2.75
2733 5386 5.319043 TGGGTAAAAGAGATGACAAAGGT 57.681 39.130 0.00 0.00 0.00 3.50
3003 5656 2.027653 GGATGATTCCTCGGATTCCTCC 60.028 54.545 13.00 13.00 39.14 4.30
3093 5746 5.171339 TCTGGAAAGCAAGAAGAGCTATT 57.829 39.130 0.00 0.00 42.53 1.73
3255 5908 5.089970 TCATCTCAAATCACCCTACTGTG 57.910 43.478 0.00 0.00 37.59 3.66
3372 6330 5.381757 TCCCATCCGTTCCAAAATATAAGG 58.618 41.667 0.00 0.00 0.00 2.69
3373 6331 5.103855 TCCCATCCGTTCCAAAATATAAGGT 60.104 40.000 0.00 0.00 0.00 3.50
3477 6435 9.559732 AAATTTGTATCATTAGATCCATGACGA 57.440 29.630 7.23 0.00 33.42 4.20
3651 6626 8.499162 AGTAATCACTTTTCTTTGAACTCGATG 58.501 33.333 0.00 0.00 0.00 3.84
3703 6678 0.457443 TCGAGCTGCATCGACTGATT 59.543 50.000 16.36 0.00 46.20 2.57
3735 6710 5.929992 GTCTGCGCCACCAAATATATAGTAA 59.070 40.000 4.18 0.00 0.00 2.24
3763 6755 3.389983 AGCGGGTGGTTAGCTTATTGATA 59.610 43.478 0.00 0.00 38.13 2.15
3936 6928 3.314553 CAATGTGGAAAAGCAGCTTCTG 58.685 45.455 8.48 0.00 34.12 3.02
4044 7036 4.142730 GCTTCACCATCTCAAGACAATGAC 60.143 45.833 0.00 0.00 0.00 3.06
4353 7345 2.874648 CTATGCCTCACCAGCCGCAA 62.875 60.000 0.00 0.00 34.38 4.85
4368 7360 2.358125 CAACACATGGGCGTCGGA 60.358 61.111 0.00 0.00 0.00 4.55
4443 7435 2.435693 CCCGGTGGTCTCATCCTCC 61.436 68.421 0.00 0.00 37.66 4.30
4734 7726 2.040278 CAGCCCCAGGTCTCCTCT 59.960 66.667 0.00 0.00 0.00 3.69
4735 7727 1.311403 CAGCCCCAGGTCTCCTCTA 59.689 63.158 0.00 0.00 0.00 2.43
5069 8130 9.989296 AGCAGGACTTGTATCTATCTATCTATT 57.011 33.333 0.00 0.00 0.00 1.73
5108 8180 8.188139 CCACAATGAAAACTGTAACTGTTAGTT 58.812 33.333 0.00 1.77 41.97 2.24
5155 8231 2.057922 AGTGAAACCTGGGAGTGATGT 58.942 47.619 0.00 0.00 37.80 3.06
5168 8244 4.118410 GGAGTGATGTCTCTGCTGTATTG 58.882 47.826 0.00 0.00 35.11 1.90
5298 8682 0.458669 GCCAACCTGCCAGATGATTG 59.541 55.000 0.00 0.00 0.00 2.67
5306 8690 2.167693 CTGCCAGATGATTGTTGCCAAT 59.832 45.455 0.00 0.00 43.97 3.16
5323 8707 0.329596 AATCCCAGGAAGTGAGCCAC 59.670 55.000 0.00 0.00 34.10 5.01
5345 8729 7.117379 GCCACTACCTTACTGTTACAGTTTTAG 59.883 40.741 23.52 18.07 42.59 1.85
5368 8752 9.528018 TTAGATTTGTGTTTGAACTTGGATTTC 57.472 29.630 0.00 0.00 0.00 2.17
5469 8854 6.010850 TGACAGGTCAGATGTAGACTAAACT 58.989 40.000 0.00 0.00 36.29 2.66
5568 8953 8.854614 AGTTTGTAGCTTCTCAAGTCATTTAT 57.145 30.769 0.00 0.00 0.00 1.40
5569 8954 9.944376 AGTTTGTAGCTTCTCAAGTCATTTATA 57.056 29.630 0.00 0.00 0.00 0.98
5837 9230 1.134699 TCAACTGGCGCTCTATTCTGG 60.135 52.381 7.64 0.00 0.00 3.86
6016 9416 0.865769 CGCACCTACACACAAACTCC 59.134 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 6.875926 ATTTCGTATGCAATGAAAAAGAGC 57.124 33.333 15.45 0.00 44.30 4.09
112 113 0.107214 TGCTAGGCATGGGCAGTTAC 60.107 55.000 0.00 0.00 43.71 2.50
136 138 3.441922 TGCTATGTGTGTGTGTGTGTTTT 59.558 39.130 0.00 0.00 0.00 2.43
137 139 3.013219 TGCTATGTGTGTGTGTGTGTTT 58.987 40.909 0.00 0.00 0.00 2.83
138 140 2.637947 TGCTATGTGTGTGTGTGTGTT 58.362 42.857 0.00 0.00 0.00 3.32
194 196 1.923356 TTTCACCAATGAGGAAGGGC 58.077 50.000 0.00 0.00 41.22 5.19
217 219 1.023513 GGTGCAGCTAGGCTCTTGTG 61.024 60.000 9.07 0.00 36.40 3.33
218 220 1.298014 GGTGCAGCTAGGCTCTTGT 59.702 57.895 9.07 0.00 36.40 3.16
265 267 6.995686 TGTATCTTGTGTAAAGCTCTTCCAAA 59.004 34.615 0.00 0.00 0.00 3.28
268 270 5.582665 CCTGTATCTTGTGTAAAGCTCTTCC 59.417 44.000 0.00 0.00 0.00 3.46
285 287 3.501062 CACACATGCATCCATCCTGTATC 59.499 47.826 0.00 0.00 0.00 2.24
302 304 4.580995 CCTTTGTATGGGTAAACACACACA 59.419 41.667 0.00 0.00 35.98 3.72
305 307 3.508402 CCCCTTTGTATGGGTAAACACAC 59.492 47.826 0.00 0.00 43.09 3.82
330 332 6.712095 TCATCACATCCAGCTTTATCCAATAC 59.288 38.462 0.00 0.00 0.00 1.89
350 352 6.016360 ACAAAAGGTCATCGAATTTGTCATCA 60.016 34.615 0.00 0.00 39.31 3.07
359 361 1.468520 CGCCACAAAAGGTCATCGAAT 59.531 47.619 0.00 0.00 0.00 3.34
360 362 0.871722 CGCCACAAAAGGTCATCGAA 59.128 50.000 0.00 0.00 0.00 3.71
367 369 3.216292 AAGCGCGCCACAAAAGGT 61.216 55.556 30.33 1.73 0.00 3.50
368 370 2.730604 CAAGCGCGCCACAAAAGG 60.731 61.111 30.33 4.42 0.00 3.11
387 401 4.183858 CTCCGGCGGGGGCAAATA 62.184 66.667 27.98 2.24 36.01 1.40
395 409 2.108362 GGTTGTATCTCCGGCGGG 59.892 66.667 27.98 17.02 0.00 6.13
409 423 6.206634 ACATACATCAACACTCGATTTTGGTT 59.793 34.615 0.00 0.00 0.00 3.67
410 424 5.705441 ACATACATCAACACTCGATTTTGGT 59.295 36.000 0.00 0.00 0.00 3.67
419 433 7.584123 GCGATATTGAAACATACATCAACACTC 59.416 37.037 0.00 0.00 38.29 3.51
432 446 4.023963 TCAACAAACGGCGATATTGAAACA 60.024 37.500 16.62 1.08 0.00 2.83
437 451 4.536364 ATCTCAACAAACGGCGATATTG 57.464 40.909 16.62 17.54 0.00 1.90
438 452 5.989168 TCATATCTCAACAAACGGCGATATT 59.011 36.000 16.62 2.26 0.00 1.28
492 526 1.686052 TGCATGTTCTTTTCCCCACAC 59.314 47.619 0.00 0.00 0.00 3.82
495 529 2.079170 TGTGCATGTTCTTTTCCCCA 57.921 45.000 0.00 0.00 0.00 4.96
496 530 3.467374 TTTGTGCATGTTCTTTTCCCC 57.533 42.857 0.00 0.00 0.00 4.81
515 549 4.554134 CGCGCTCAAGATTCATTCATCATT 60.554 41.667 5.56 0.00 0.00 2.57
532 566 1.060191 CGCCTTTCTTTTTCGCGCTC 61.060 55.000 5.56 0.00 36.02 5.03
758 2948 1.612146 GGGGTTGGGGTTGGGAATG 60.612 63.158 0.00 0.00 0.00 2.67
759 2949 1.679969 TTGGGGTTGGGGTTGGGAAT 61.680 55.000 0.00 0.00 0.00 3.01
760 2950 2.333462 TTGGGGTTGGGGTTGGGAA 61.333 57.895 0.00 0.00 0.00 3.97
761 2951 2.704198 TTGGGGTTGGGGTTGGGA 60.704 61.111 0.00 0.00 0.00 4.37
766 2956 3.517497 CTGGGTTGGGGTTGGGGT 61.517 66.667 0.00 0.00 0.00 4.95
772 2962 3.425014 TGTGTGCTGGGTTGGGGT 61.425 61.111 0.00 0.00 0.00 4.95
778 2968 1.153168 GAGTGTGTGTGTGCTGGGT 60.153 57.895 0.00 0.00 0.00 4.51
782 2972 2.113860 AACAAGAGTGTGTGTGTGCT 57.886 45.000 0.00 0.00 38.27 4.40
783 2973 2.518949 CAAACAAGAGTGTGTGTGTGC 58.481 47.619 0.00 0.00 38.08 4.57
793 3006 1.101049 CGCCCACCACAAACAAGAGT 61.101 55.000 0.00 0.00 0.00 3.24
796 3009 1.065600 CACGCCCACCACAAACAAG 59.934 57.895 0.00 0.00 0.00 3.16
816 3029 2.574399 GTCTGGTGGAGGAGACGC 59.426 66.667 0.00 0.00 29.86 5.19
953 3176 2.735100 GCGAGCGGGATTCGGATC 60.735 66.667 0.00 0.00 38.45 3.36
954 3177 4.301027 GGCGAGCGGGATTCGGAT 62.301 66.667 0.00 0.00 38.45 4.18
1038 3261 2.482839 CCGAATCAAGAAGAGGAGGAGC 60.483 54.545 0.00 0.00 0.00 4.70
1393 3940 2.472029 GAGAAGATGGGTGAGAGGGAA 58.528 52.381 0.00 0.00 0.00 3.97
1444 4003 8.372459 AGCGGACAGGATAAAAATACATACATA 58.628 33.333 0.00 0.00 0.00 2.29
1446 4005 6.481976 CAGCGGACAGGATAAAAATACATACA 59.518 38.462 0.00 0.00 0.00 2.29
1451 4010 6.430451 CAATCAGCGGACAGGATAAAAATAC 58.570 40.000 0.00 0.00 0.00 1.89
1460 4019 0.911769 AATCCAATCAGCGGACAGGA 59.088 50.000 10.69 10.69 34.69 3.86
1510 4069 2.644676 GCAGGTGGAATCTAGGTTTCC 58.355 52.381 14.91 14.91 42.52 3.13
1551 4110 2.447244 AGTCTAACACTGAGCACAGC 57.553 50.000 11.37 0.00 46.95 4.40
1553 4112 3.763057 TCCTAGTCTAACACTGAGCACA 58.237 45.455 0.00 0.00 36.43 4.57
1555 4114 3.131223 GCATCCTAGTCTAACACTGAGCA 59.869 47.826 0.00 0.00 36.43 4.26
1556 4115 3.491792 GGCATCCTAGTCTAACACTGAGC 60.492 52.174 0.00 0.00 36.43 4.26
1557 4116 3.957497 AGGCATCCTAGTCTAACACTGAG 59.043 47.826 0.00 0.00 36.43 3.35
1597 4184 4.742201 GAGCGGCAAGGCGAGTCA 62.742 66.667 20.47 0.00 38.18 3.41
1599 4186 1.961180 AATAGAGCGGCAAGGCGAGT 61.961 55.000 20.47 5.61 38.18 4.18
1630 4221 4.142924 TGTGTCGCTAAGTTTGCATACATG 60.143 41.667 10.02 0.00 31.72 3.21
1661 4262 1.025812 ACAAAACGGGCGTTTCATCA 58.974 45.000 0.00 0.00 46.22 3.07
1662 4263 2.973419 TACAAAACGGGCGTTTCATC 57.027 45.000 0.00 0.00 46.22 2.92
1663 4264 2.814919 TCATACAAAACGGGCGTTTCAT 59.185 40.909 0.00 0.00 46.22 2.57
1664 4265 2.219458 TCATACAAAACGGGCGTTTCA 58.781 42.857 0.00 0.00 46.22 2.69
1665 4266 2.973419 TCATACAAAACGGGCGTTTC 57.027 45.000 0.00 0.00 46.22 2.78
1667 4268 3.181518 CGTAATCATACAAAACGGGCGTT 60.182 43.478 0.00 0.00 34.44 4.84
1668 4269 2.349275 CGTAATCATACAAAACGGGCGT 59.651 45.455 0.00 0.00 32.02 5.68
1669 4270 2.604011 TCGTAATCATACAAAACGGGCG 59.396 45.455 0.00 0.00 34.47 6.13
1670 4271 3.619929 ACTCGTAATCATACAAAACGGGC 59.380 43.478 0.00 0.00 37.56 6.13
1671 4272 4.493545 GCACTCGTAATCATACAAAACGGG 60.494 45.833 0.00 0.00 39.85 5.28
1672 4273 4.493545 GGCACTCGTAATCATACAAAACGG 60.494 45.833 0.00 0.00 34.47 4.44
1673 4274 4.092237 TGGCACTCGTAATCATACAAAACG 59.908 41.667 0.00 0.00 34.99 3.60
1674 4275 5.539582 TGGCACTCGTAATCATACAAAAC 57.460 39.130 0.00 0.00 32.02 2.43
1675 4276 5.877564 TCATGGCACTCGTAATCATACAAAA 59.122 36.000 0.00 0.00 32.02 2.44
1676 4277 5.423886 TCATGGCACTCGTAATCATACAAA 58.576 37.500 0.00 0.00 32.02 2.83
1712 4313 1.333931 TCGAGAGCCAAGCATACGTAG 59.666 52.381 0.08 0.00 0.00 3.51
1721 4322 1.803519 GCAGTCGTCGAGAGCCAAG 60.804 63.158 0.00 0.00 0.00 3.61
1736 4337 1.478510 AGTCAGATACCCGACAAGCAG 59.521 52.381 0.00 0.00 34.48 4.24
1739 4340 2.099921 CCTCAGTCAGATACCCGACAAG 59.900 54.545 0.00 0.00 34.48 3.16
1756 4357 2.458892 ACCATTTCCGGTCACCTCA 58.541 52.632 0.00 0.00 32.11 3.86
1799 4400 3.869246 GGAAAGCGATAATCAACGGAAGA 59.131 43.478 0.00 0.00 0.00 2.87
1832 4433 5.205565 CACTAGCGTTCAGAAAAGAAAACC 58.794 41.667 0.00 0.00 0.00 3.27
1902 4503 1.890979 CATCCCTGATGCCACTCGC 60.891 63.158 0.00 0.00 33.17 5.03
2184 4828 1.608590 ACAGGTTCATTTGAAGGCACG 59.391 47.619 0.00 0.00 34.27 5.34
2196 4840 2.485795 GGGCAAACGCACAGGTTCA 61.486 57.895 0.00 0.00 31.06 3.18
2253 4897 2.026729 GGAAAGCCTCCCAGATATAGCC 60.027 54.545 0.00 0.00 38.44 3.93
2258 4902 1.213296 GGTGGAAAGCCTCCCAGATA 58.787 55.000 0.10 0.00 44.69 1.98
2349 4993 8.752766 AAGAATTCTTCATGCTATTGTTGTTG 57.247 30.769 15.11 0.00 0.00 3.33
2479 5132 2.602676 TAGCTGGGAAGGGTGTGGC 61.603 63.158 0.00 0.00 0.00 5.01
2603 5256 4.284746 CCCTGATAATACTTGGAGAGTCCC 59.715 50.000 0.00 0.00 39.86 4.46
2685 5338 5.009010 TGTCTTCTCTGCAGAAAATTGGAAC 59.991 40.000 18.85 7.01 38.23 3.62
2688 5341 5.443185 TTGTCTTCTCTGCAGAAAATTGG 57.557 39.130 18.85 4.89 38.23 3.16
2724 5377 6.127535 CCCTACTATACGAAGAACCTTTGTCA 60.128 42.308 3.09 0.00 0.00 3.58
2733 5386 8.897752 GTCTCTTTTACCCTACTATACGAAGAA 58.102 37.037 0.00 0.00 0.00 2.52
2854 5507 1.078918 GCCCATTTCCAGCCTTTGC 60.079 57.895 0.00 0.00 37.95 3.68
3003 5656 1.411977 AGATCTGGCAGAGATTCCACG 59.588 52.381 23.24 0.00 41.91 4.94
3093 5746 7.383687 CCTAAGTGGTGAATACTTACTTGACA 58.616 38.462 0.00 0.00 39.06 3.58
3176 5829 1.945354 CTGCCTGGCTCATTTGCTGG 61.945 60.000 21.03 0.00 0.00 4.85
3273 5926 2.679450 ACATGACAAATGTGCATGTGC 58.321 42.857 19.04 0.00 44.05 4.57
3532 6507 6.939551 TTCGTGCAAGTCTAACTTATGTAC 57.060 37.500 0.00 0.00 36.03 2.90
3625 6600 8.499162 CATCGAGTTCAAAGAAAAGTGATTACT 58.501 33.333 0.00 0.00 39.32 2.24
3651 6626 2.075426 AAAAACCCGCTGCTGACTGC 62.075 55.000 0.00 0.00 43.25 4.40
3703 6678 0.320421 GGTGGCGCAGACTCACTTTA 60.320 55.000 10.83 0.00 34.59 1.85
3763 6755 7.844493 ATATCAGCATCCCAACACAAAATAT 57.156 32.000 0.00 0.00 0.00 1.28
3885 6877 2.866156 CGTCTTCTTCTTGCTTGTCACA 59.134 45.455 0.00 0.00 0.00 3.58
3936 6928 4.152402 TCGTCATCTTTGCTTTTAGCTGAC 59.848 41.667 0.00 7.53 42.97 3.51
4044 7036 2.478890 ATGCCGGACCTCGACTACG 61.479 63.158 5.05 0.00 42.43 3.51
4353 7345 4.082523 CCTCCGACGCCCATGTGT 62.083 66.667 0.00 0.00 38.09 3.72
4443 7435 2.433838 CTCACCTGCTCCACTGCG 60.434 66.667 0.00 0.00 35.36 5.18
4471 7463 4.235762 AGTGTTGGGTCGCGCTGT 62.236 61.111 5.56 0.00 0.00 4.40
4677 7669 2.045131 GGCTGACGACGTAGGGAGT 61.045 63.158 0.00 0.00 0.00 3.85
4734 7726 2.359169 CGGGTTCTCCTGGCTGCTA 61.359 63.158 0.00 0.00 36.50 3.49
4735 7727 3.710722 CGGGTTCTCCTGGCTGCT 61.711 66.667 0.00 0.00 36.50 4.24
4890 7882 0.103937 TTTTCTTTGTGCCGGCCAAG 59.896 50.000 26.77 22.23 0.00 3.61
5069 8130 9.851686 AGTTTTCATTGTGGCATAGATAGATAA 57.148 29.630 0.00 0.00 0.00 1.75
5108 8180 4.901197 TTGCCTGAGACATACACCTAAA 57.099 40.909 0.00 0.00 0.00 1.85
5155 8231 7.428826 CACATACATAGACAATACAGCAGAGA 58.571 38.462 0.00 0.00 0.00 3.10
5168 8244 6.036517 GGCAATATAGCTGCACATACATAGAC 59.963 42.308 1.02 0.00 41.78 2.59
5298 8682 0.890683 CACTTCCTGGGATTGGCAAC 59.109 55.000 0.00 0.00 0.00 4.17
5306 8690 0.116342 TAGTGGCTCACTTCCTGGGA 59.884 55.000 12.22 0.00 42.59 4.37
5345 8729 6.760770 TGGAAATCCAAGTTCAAACACAAATC 59.239 34.615 0.00 0.00 44.35 2.17
5418 8803 6.978080 ACAAATCAAAATGTGGTAACTGTGTC 59.022 34.615 0.00 0.00 37.61 3.67
5485 8870 7.535997 GCGTTCCCTTTCACTAGAAAATAATT 58.464 34.615 0.00 0.00 42.78 1.40
5717 9109 7.129457 TCCAATATAGTGAGAAAGCAGATGT 57.871 36.000 0.79 0.00 0.00 3.06
5819 9212 1.134670 GTCCAGAATAGAGCGCCAGTT 60.135 52.381 2.29 0.00 0.00 3.16
5837 9230 4.570930 TCTTTGTGTTTTGGTTTTGGGTC 58.429 39.130 0.00 0.00 0.00 4.46
5975 9375 1.750341 TTCGGTCGCAGGAACAGGAA 61.750 55.000 0.00 0.00 0.00 3.36
6059 9459 4.175337 TATGACCCTGCAGGCCGC 62.175 66.667 28.39 17.83 40.58 6.53


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

AutoCloner maintained by Alex Coulton.