Multiple sequence alignment - TraesCS5D01G141200

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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 TraesCS5D01G141200 chr5D 100.000 5716 0 0 1 5716 224951703 224945988 0.000000e+00 10556.0
1 TraesCS5D01G141200 chr5D 100.000 33 0 0 5187 5219 224946485 224946453 1.720000e-05 62.1
2 TraesCS5D01G141200 chr5D 100.000 33 0 0 5219 5251 224946517 224946485 1.720000e-05 62.1
3 TraesCS5D01G141200 chr5B 92.491 2930 122 37 542 3430 246136558 246139430 0.000000e+00 4102.0
4 TraesCS5D01G141200 chr5B 94.670 1182 32 11 3422 4590 246139716 246140879 0.000000e+00 1805.0
5 TraesCS5D01G141200 chr5B 97.260 584 14 2 4636 5219 246140873 246141454 0.000000e+00 989.0
6 TraesCS5D01G141200 chr5B 92.336 548 36 6 1 546 246135855 246136398 0.000000e+00 774.0
7 TraesCS5D01G141200 chr5B 94.574 258 13 1 5459 5716 246147480 246147736 1.150000e-106 398.0
8 TraesCS5D01G141200 chr5B 95.885 243 8 1 5219 5461 246141422 246141662 5.370000e-105 392.0
9 TraesCS5D01G141200 chr5B 82.114 123 17 5 5231 5352 593435967 593435849 3.640000e-17 100.0
10 TraesCS5D01G141200 chr5A 94.752 2401 96 17 1 2392 299602558 299600179 0.000000e+00 3709.0
11 TraesCS5D01G141200 chr5A 95.635 1810 50 10 3254 5050 299599455 299597662 0.000000e+00 2878.0
12 TraesCS5D01G141200 chr5A 90.593 776 36 11 2312 3066 299600215 299599456 0.000000e+00 994.0
13 TraesCS5D01G141200 chr5A 94.800 500 22 4 5219 5716 299597570 299597073 0.000000e+00 776.0
14 TraesCS5D01G141200 chr5A 95.420 131 6 0 5089 5219 299597668 299597538 5.800000e-50 209.0
15 TraesCS5D01G141200 chr5A 81.600 125 18 5 5231 5354 603776988 603776868 1.310000e-16 99.0
16 TraesCS5D01G141200 chr3D 84.491 432 43 13 37 450 567901918 567901493 6.900000e-109 405.0
17 TraesCS5D01G141200 chr3A 76.941 425 62 25 2 423 731429945 731429554 5.800000e-50 209.0
18 TraesCS5D01G141200 chr7D 95.890 73 3 0 870 942 193192330 193192258 1.010000e-22 119.0
19 TraesCS5D01G141200 chr4D 96.078 51 2 0 892 942 107698816 107698866 3.670000e-12 84.2
20 TraesCS5D01G141200 chr4A 75.138 181 38 7 5235 5415 290367444 290367271 1.710000e-10 78.7
21 TraesCS5D01G141200 chr6D 90.196 51 2 3 454 502 161249825 161249776 4.780000e-06 63.9
22 TraesCS5D01G141200 chr7B 90.476 42 1 2 463 503 136549251 136549290 1.000000e-02 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G141200 chr5D 224945988 224951703 5715 True 10556.0 10556 100.0000 1 5716 1 chr5D.!!$R1 5715
1 TraesCS5D01G141200 chr5B 246135855 246141662 5807 False 1612.4 4102 94.5284 1 5461 5 chr5B.!!$F2 5460
2 TraesCS5D01G141200 chr5A 299597073 299602558 5485 True 1713.2 3709 94.2400 1 5716 5 chr5A.!!$R2 5715

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
400 402 0.033228 TTGCAAAGATTGGTTGGCCG 59.967 50.000 0.00 0.0 37.67 6.13 F
775 945 0.248012 TCGTGCGAGGCCTTCAAATA 59.752 50.000 6.77 0.0 0.00 1.40 F
1132 1306 0.689412 CTCCAACCCCTCTCCTCTCC 60.689 65.000 0.00 0.0 0.00 3.71 F
2701 2943 1.005450 GGATTACCACTGGGAGCCAAA 59.995 52.381 0.00 0.0 38.05 3.28 F
3868 4430 0.179189 GGTACGCATGACTTTGCTGC 60.179 55.000 0.00 0.0 40.54 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2208 2397 0.942962 GGCTCTGCAAGATGAATCCG 59.057 55.000 0.00 0.00 45.62 4.18 R
2532 2766 2.292828 AGCACTATGGCCAAAACAGT 57.707 45.000 10.96 8.27 0.00 3.55 R
2907 3149 3.068307 ACAGAGCTACAACTAATAGGCGG 59.932 47.826 0.00 0.00 0.00 6.13 R
4682 5258 0.452987 CCATCAATCCGCCTGTTGTG 59.547 55.000 0.00 0.00 0.00 3.33 R
5466 6051 0.773644 TTCTTTCTCCCTTGCTGGCT 59.226 50.000 0.00 0.00 0.00 4.75 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
33 34 4.515567 GCACACTATAAACCTAAGGATGGC 59.484 45.833 0.00 0.00 0.00 4.40
42 43 1.281867 CCTAAGGATGGCAGTCAACCA 59.718 52.381 3.83 0.00 40.40 3.67
53 54 4.122776 GGCAGTCAACCATGTCTATACTG 58.877 47.826 0.00 0.00 36.74 2.74
69 70 7.336176 TGTCTATACTGGATTATAGTACCGCAG 59.664 40.741 0.00 0.00 34.72 5.18
117 118 6.422223 GCACATGCTTGATTATAGTACACAC 58.578 40.000 6.60 0.00 38.21 3.82
220 221 4.621068 TGGCAGAAGAAATTATGCTTCG 57.379 40.909 7.44 0.00 43.94 3.79
313 315 7.110155 TGTTAGAGATGATTGTCTTTAACCCC 58.890 38.462 12.10 0.00 41.50 4.95
318 320 7.394641 AGAGATGATTGTCTTTAACCCCTTTTC 59.605 37.037 0.00 0.00 0.00 2.29
320 322 7.730332 AGATGATTGTCTTTAACCCCTTTTCTT 59.270 33.333 0.00 0.00 0.00 2.52
321 323 7.669089 TGATTGTCTTTAACCCCTTTTCTTT 57.331 32.000 0.00 0.00 0.00 2.52
355 357 6.002704 TGTCTTTAACCTAACCCGCAAATTA 58.997 36.000 0.00 0.00 0.00 1.40
399 401 1.872952 GTTTGCAAAGATTGGTTGGCC 59.127 47.619 13.26 0.00 0.00 5.36
400 402 0.033228 TTGCAAAGATTGGTTGGCCG 59.967 50.000 0.00 0.00 37.67 6.13
403 405 1.934849 GCAAAGATTGGTTGGCCGAAC 60.935 52.381 0.00 0.00 37.67 3.95
446 448 4.282449 ACATTCCCATCACCATGCATATTG 59.718 41.667 0.00 0.00 0.00 1.90
449 451 2.600790 CCATCACCATGCATATTGGGT 58.399 47.619 9.58 5.24 38.64 4.51
473 475 1.134220 AGGAGCGTGTGTTTTTCTCCA 60.134 47.619 8.99 0.00 44.29 3.86
558 725 8.720562 ACATCAAAATACTTTTTATTGCAAGGC 58.279 29.630 4.94 0.00 33.29 4.35
559 726 7.665561 TCAAAATACTTTTTATTGCAAGGCC 57.334 32.000 4.94 0.00 33.29 5.19
632 799 3.425758 CGGGTTAAGAATCAAAGCGGTTC 60.426 47.826 0.00 0.00 0.00 3.62
697 867 4.873746 TTTGAATTTTGAATGGGCCGTA 57.126 36.364 0.00 0.00 0.00 4.02
698 868 4.873746 TTGAATTTTGAATGGGCCGTAA 57.126 36.364 0.00 0.00 0.00 3.18
725 895 4.099170 CTGGCAGCAGCAACGAGC 62.099 66.667 0.00 0.00 44.61 5.03
741 911 2.951458 GCGTGGGCTTGGTGTTAC 59.049 61.111 0.00 0.00 35.83 2.50
759 929 1.006102 CGGCTCACAAGTTCCTCGT 60.006 57.895 0.00 0.00 0.00 4.18
775 945 0.248012 TCGTGCGAGGCCTTCAAATA 59.752 50.000 6.77 0.00 0.00 1.40
1132 1306 0.689412 CTCCAACCCCTCTCCTCTCC 60.689 65.000 0.00 0.00 0.00 3.71
1239 1413 3.414700 CCTGCTCACCGTTGCGTC 61.415 66.667 0.00 0.00 0.00 5.19
1405 1581 6.398095 GTTGGTTTTGATTTTCTCCCCTATG 58.602 40.000 0.00 0.00 0.00 2.23
1463 1639 2.351738 GCCTAATTTCGTGCAGCTTTGT 60.352 45.455 0.00 0.00 0.00 2.83
1468 1644 2.404265 TTCGTGCAGCTTTGTTGATG 57.596 45.000 0.00 0.00 0.00 3.07
1550 1726 7.979444 TTTTTCTCCACGAATTAGTCTGAAT 57.021 32.000 0.00 0.00 0.00 2.57
1585 1761 1.672881 GAGCTGCCATGCGTTTAATCT 59.327 47.619 0.00 0.00 38.13 2.40
1691 1867 1.464521 CCAATTACGGACGCGTTTTCC 60.465 52.381 15.53 9.66 0.00 3.13
1729 1905 3.497332 GGGTTTTAAGCCTGTCTTCCTT 58.503 45.455 3.52 0.00 43.15 3.36
1920 2109 5.941058 TGAATTTGAATCCTAAGCCGTAACA 59.059 36.000 0.00 0.00 0.00 2.41
1921 2110 6.601613 TGAATTTGAATCCTAAGCCGTAACAT 59.398 34.615 0.00 0.00 0.00 2.71
1922 2111 7.122055 TGAATTTGAATCCTAAGCCGTAACATT 59.878 33.333 0.00 0.00 0.00 2.71
1923 2112 6.431198 TTTGAATCCTAAGCCGTAACATTC 57.569 37.500 0.00 0.00 0.00 2.67
1924 2113 4.448210 TGAATCCTAAGCCGTAACATTCC 58.552 43.478 0.00 0.00 0.00 3.01
1925 2114 4.163458 TGAATCCTAAGCCGTAACATTCCT 59.837 41.667 0.00 0.00 0.00 3.36
1926 2115 4.772886 ATCCTAAGCCGTAACATTCCTT 57.227 40.909 0.00 0.00 0.00 3.36
1927 2116 3.869065 TCCTAAGCCGTAACATTCCTTG 58.131 45.455 0.00 0.00 0.00 3.61
1928 2117 3.262405 TCCTAAGCCGTAACATTCCTTGT 59.738 43.478 0.00 0.00 41.53 3.16
1929 2118 4.467082 TCCTAAGCCGTAACATTCCTTGTA 59.533 41.667 0.00 0.00 37.68 2.41
1930 2119 5.046448 TCCTAAGCCGTAACATTCCTTGTAA 60.046 40.000 0.00 0.00 37.68 2.41
1931 2120 5.064325 CCTAAGCCGTAACATTCCTTGTAAC 59.936 44.000 0.00 0.00 37.68 2.50
2110 2299 4.892433 TCCCTAAAATTTGTGGTTGCATG 58.108 39.130 0.00 0.00 0.00 4.06
2153 2342 5.803461 GCACGACACATGACTGTTATTAGTA 59.197 40.000 0.00 0.00 31.62 1.82
2256 2445 1.808411 TTAAGGGCTTGTCTGAAGCG 58.192 50.000 0.00 0.00 43.89 4.68
2274 2463 4.744795 AGCGAAGGTTGATAAGATCTGT 57.255 40.909 0.00 0.00 27.67 3.41
2406 2639 1.344114 TGCCATCTGTGCTATGCGATA 59.656 47.619 0.00 0.00 0.00 2.92
2409 2642 3.862264 GCCATCTGTGCTATGCGATAGAA 60.862 47.826 7.19 0.00 34.77 2.10
2419 2652 6.089283 GTGCTATGCGATAGAATCTTCTGAAG 59.911 42.308 11.18 11.18 38.19 3.02
2425 2658 6.091305 TGCGATAGAATCTTCTGAAGTTTGTG 59.909 38.462 16.21 4.76 38.19 3.33
2427 2660 7.275779 GCGATAGAATCTTCTGAAGTTTGTGTA 59.724 37.037 16.21 7.39 38.19 2.90
2572 2814 8.746530 AGTGCTACTATGCTAAACTTACTGTAA 58.253 33.333 0.00 0.00 0.00 2.41
2573 2815 9.362539 GTGCTACTATGCTAAACTTACTGTAAA 57.637 33.333 1.46 0.00 0.00 2.01
2701 2943 1.005450 GGATTACCACTGGGAGCCAAA 59.995 52.381 0.00 0.00 38.05 3.28
2735 2977 4.769688 CTGCTTGGAGGTAACATATGTCA 58.230 43.478 9.23 0.00 41.41 3.58
2759 3001 9.334947 TCATCCTTGATTCTGTTCTGATTATTC 57.665 33.333 0.00 0.00 0.00 1.75
2785 3027 7.933577 CCTGATGTTATGCTCTAACCTATTCAA 59.066 37.037 7.12 0.00 0.00 2.69
2794 3036 7.639039 TGCTCTAACCTATTCAAATATTTGCG 58.361 34.615 21.15 10.30 38.05 4.85
2866 3108 2.745821 GTTCCGGTGAGTAAATGTTCCC 59.254 50.000 0.00 0.00 0.00 3.97
2883 3125 5.134661 TGTTCCCGTTACCATTTTCTTCTT 58.865 37.500 0.00 0.00 0.00 2.52
2885 3127 4.076394 TCCCGTTACCATTTTCTTCTTGG 58.924 43.478 0.00 0.00 36.56 3.61
2889 3131 5.918576 CCGTTACCATTTTCTTCTTGGTTTC 59.081 40.000 0.00 0.00 40.87 2.78
2890 3132 6.238925 CCGTTACCATTTTCTTCTTGGTTTCT 60.239 38.462 0.00 0.00 40.87 2.52
2891 3133 7.200455 CGTTACCATTTTCTTCTTGGTTTCTT 58.800 34.615 0.00 0.00 40.87 2.52
2892 3134 7.378728 CGTTACCATTTTCTTCTTGGTTTCTTC 59.621 37.037 0.00 0.00 40.87 2.87
2923 3165 2.963782 AGGGACCGCCTATTAGTTGTAG 59.036 50.000 0.00 0.00 0.00 2.74
3001 3255 7.900782 TTTAGTACATGGTGCTAAAACTCTC 57.099 36.000 14.45 0.00 43.65 3.20
3027 3281 5.568620 AGCTTCTTTCACCTCCTTTTCTA 57.431 39.130 0.00 0.00 0.00 2.10
3055 3309 5.835819 TCTAGTCTTCCAGAGGTATTGATGG 59.164 44.000 0.00 0.00 0.00 3.51
3068 3322 8.535335 AGAGGTATTGATGGTAGTGCATATAAG 58.465 37.037 0.00 0.00 0.00 1.73
3071 3325 9.672673 GGTATTGATGGTAGTGCATATAAGAAT 57.327 33.333 0.00 0.00 0.00 2.40
3074 3328 7.889589 TGATGGTAGTGCATATAAGAATTCG 57.110 36.000 0.00 0.00 0.00 3.34
3075 3329 7.666623 TGATGGTAGTGCATATAAGAATTCGA 58.333 34.615 0.00 0.00 0.00 3.71
3116 3370 8.210265 TGATGCTAACATTGAATACTGGATACA 58.790 33.333 0.00 0.00 40.33 2.29
3132 3386 3.618150 GGATACATGTTGCATGCCAAAAC 59.382 43.478 16.68 13.58 34.68 2.43
3140 3394 3.257469 TGCATGCCAAAACTCAAACAA 57.743 38.095 16.68 0.00 0.00 2.83
3183 3438 3.009723 ACTATTTCCCTGATGCAACACG 58.990 45.455 0.00 0.00 0.00 4.49
3221 3483 6.579666 ATTGAGCACAGTTGTAATGTTGAT 57.420 33.333 0.00 0.00 0.00 2.57
3246 3508 5.587289 TCCAAAGCACATTTGTTACTCAAC 58.413 37.500 0.23 0.00 45.78 3.18
3273 3540 4.894784 TCTCAATTCCAACTTTCTAGCGT 58.105 39.130 0.00 0.00 0.00 5.07
3373 3641 4.222810 GGTCCATTTCCTGCCTTGTATTTT 59.777 41.667 0.00 0.00 0.00 1.82
3374 3642 5.420739 GGTCCATTTCCTGCCTTGTATTTTA 59.579 40.000 0.00 0.00 0.00 1.52
3378 3646 6.039270 CCATTTCCTGCCTTGTATTTTATCGA 59.961 38.462 0.00 0.00 0.00 3.59
3392 3660 9.529325 TGTATTTTATCGATGAAACCTCACTAG 57.471 33.333 16.57 0.00 33.30 2.57
3415 3683 9.474920 CTAGAACAGAATCCATGAATAACTCTC 57.525 37.037 0.00 0.00 0.00 3.20
3417 3685 6.566079 ACAGAATCCATGAATAACTCTCCA 57.434 37.500 0.00 0.00 0.00 3.86
3676 4238 3.758023 TGCTGTTCTTGACAATGTATGGG 59.242 43.478 0.00 0.00 37.93 4.00
3694 4256 6.443849 TGTATGGGTCCTTTTACATCTCTCTT 59.556 38.462 0.00 0.00 0.00 2.85
3695 4257 7.622081 TGTATGGGTCCTTTTACATCTCTCTTA 59.378 37.037 0.00 0.00 0.00 2.10
3721 4283 9.726438 ATAACCCATTTAAGGAAGAATAGATCG 57.274 33.333 0.00 0.00 0.00 3.69
3774 4336 6.368791 TGTTTTAGATCATATATGCTCGTGCC 59.631 38.462 7.92 0.04 38.71 5.01
3868 4430 0.179189 GGTACGCATGACTTTGCTGC 60.179 55.000 0.00 0.00 40.54 5.25
3877 4445 4.751060 CATGACTTTGCTGCCATGTAAAT 58.249 39.130 0.00 0.00 33.62 1.40
3912 4480 2.916702 TCTCAACTGTGCTCATGTGT 57.083 45.000 0.00 0.00 0.00 3.72
3923 4491 4.157472 TGTGCTCATGTGTTCTTTGTTTGA 59.843 37.500 0.00 0.00 0.00 2.69
3961 4529 1.089112 TGGATTCTGTGATTGCGCTG 58.911 50.000 9.73 0.00 0.00 5.18
4068 4636 4.867047 AGCAACTCATGAAGTAGTCGAATG 59.133 41.667 0.00 0.00 37.17 2.67
4069 4637 4.493220 GCAACTCATGAAGTAGTCGAATGC 60.493 45.833 0.00 0.00 37.17 3.56
4070 4638 4.727507 ACTCATGAAGTAGTCGAATGCT 57.272 40.909 0.00 0.00 36.07 3.79
4093 4661 5.782047 TGCTTGCATTTTATACACTTGCTT 58.218 33.333 0.00 0.00 34.47 3.91
4124 4692 1.335689 GCTCTGGAACTGCAGCAAAAG 60.336 52.381 15.27 7.18 33.45 2.27
4492 5067 4.813296 ACTACTTGTTTACTGCTTGTGC 57.187 40.909 0.00 0.00 40.20 4.57
4493 5068 2.755836 ACTTGTTTACTGCTTGTGCG 57.244 45.000 0.00 0.00 43.34 5.34
4522 5097 7.856145 TCATTGCTTTAATTTGTTTGGTTGT 57.144 28.000 0.00 0.00 0.00 3.32
4628 5204 3.659735 CTTCACGTAGCACAAATTAGCG 58.340 45.455 0.00 0.00 35.48 4.26
4630 5206 2.664568 TCACGTAGCACAAATTAGCGAC 59.335 45.455 0.00 0.00 35.48 5.19
4682 5258 2.031157 CCACCAACACGTTTTCCAGATC 60.031 50.000 0.00 0.00 0.00 2.75
4753 5329 4.272504 CGCTTCCTGTCTTAAACTGTTGAA 59.727 41.667 0.00 0.00 0.00 2.69
4802 5378 2.614829 ACTGCACCGTTACTCTGTTT 57.385 45.000 0.00 0.00 0.00 2.83
4865 5441 1.061546 TACCTCCTGTTGGGTGTTCC 58.938 55.000 0.00 0.00 37.07 3.62
4917 5499 4.245660 CTGAGGACAAAAGTTATCTCGCA 58.754 43.478 0.00 0.00 0.00 5.10
4972 5554 7.231467 AGTGGAGATGTAAGGTTAACATGTTT 58.769 34.615 17.78 0.09 37.69 2.83
5053 5635 7.596749 TCTTTGAAGAATGAAATAGTCCGTC 57.403 36.000 0.00 0.00 30.73 4.79
5154 5736 8.774546 TTCCATTCTCTCTCTGTATGAGTAAT 57.225 34.615 0.00 0.00 43.13 1.89
5196 5778 4.092675 GCATGGATCGAGCTCTAAATAAGC 59.907 45.833 12.85 5.02 40.14 3.09
5215 5797 9.729281 AAATAAGCATTGAAGTGAATTCCATTT 57.271 25.926 2.27 0.00 37.08 2.32
5216 5798 9.729281 AATAAGCATTGAAGTGAATTCCATTTT 57.271 25.926 2.27 0.00 37.08 1.82
5217 5799 9.729281 ATAAGCATTGAAGTGAATTCCATTTTT 57.271 25.926 2.27 0.00 37.08 1.94
5244 5826 9.241919 TCTAAATAAGCATTGAAGTGAATTCCA 57.758 29.630 2.27 0.00 37.08 3.53
5293 5875 4.063689 TGGCAGCAATTACAACATTTTGG 58.936 39.130 0.00 0.00 37.00 3.28
5300 5882 8.063630 CAGCAATTACAACATTTTGGAGTTTTC 58.936 33.333 0.00 0.00 37.00 2.29
5412 5994 4.406003 ACATCGGCTGGTTTATTCTACTCT 59.594 41.667 0.00 0.00 0.00 3.24
5413 5995 5.104900 ACATCGGCTGGTTTATTCTACTCTT 60.105 40.000 0.00 0.00 0.00 2.85
5454 6039 0.935942 TCCATTTGGCAGGGGATGAT 59.064 50.000 0.38 0.00 34.44 2.45
5466 6051 3.392285 CAGGGGATGATTCCTACATGTCA 59.608 47.826 0.00 0.00 42.20 3.58
5526 6111 1.301479 GTGTGGTCAGGGTTCGGAC 60.301 63.158 0.00 0.00 37.37 4.79
5528 6113 1.125093 TGTGGTCAGGGTTCGGACAT 61.125 55.000 0.00 0.00 39.36 3.06
5565 6150 3.133365 AACCCTGCCTCCGCAACTT 62.133 57.895 0.00 0.00 46.66 2.66
5567 6152 1.224592 CCCTGCCTCCGCAACTTAT 59.775 57.895 0.00 0.00 46.66 1.73
5588 6173 3.750371 TGGTTGATTGTGTTCCCTACAG 58.250 45.455 0.00 0.00 37.45 2.74
5674 6259 4.099266 TGTTTAATTGTCAGCTTGCTTGGT 59.901 37.500 0.00 0.00 0.00 3.67
5686 6271 3.445096 GCTTGCTTGGTGTCCAATAATCT 59.555 43.478 1.58 0.00 43.07 2.40
5692 6277 4.665833 TGGTGTCCAATAATCTAGTCGG 57.334 45.455 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 5.598416 TCCAGTATAGACATGGTTGACTG 57.402 43.478 0.00 4.03 35.51 3.51
42 43 7.832685 TGCGGTACTATAATCCAGTATAGACAT 59.167 37.037 7.83 0.00 37.46 3.06
50 51 5.336531 GCATACTGCGGTACTATAATCCAGT 60.337 44.000 7.76 0.00 36.24 4.00
318 320 7.745620 AGGTTAAAGACAATCACCTACAAAG 57.254 36.000 0.00 0.00 36.02 2.77
320 322 7.662669 GGTTAGGTTAAAGACAATCACCTACAA 59.337 37.037 0.00 0.00 39.37 2.41
321 323 7.163441 GGTTAGGTTAAAGACAATCACCTACA 58.837 38.462 0.00 0.00 39.37 2.74
355 357 6.094881 ACGGCTAACAAACTTATGCATTGTAT 59.905 34.615 3.54 0.00 36.33 2.29
399 401 4.692625 ACATGAAGGAGAATTGTGAGTTCG 59.307 41.667 0.00 0.00 0.00 3.95
400 402 6.650807 TGTACATGAAGGAGAATTGTGAGTTC 59.349 38.462 0.00 0.00 0.00 3.01
403 405 7.201679 GGAATGTACATGAAGGAGAATTGTGAG 60.202 40.741 9.63 0.00 0.00 3.51
446 448 1.601166 AACACACGCTCCTAAAACCC 58.399 50.000 0.00 0.00 0.00 4.11
449 451 4.035909 GGAGAAAAACACACGCTCCTAAAA 59.964 41.667 0.00 0.00 41.44 1.52
502 504 4.307032 AAGTGTACCCTCTCGTTAGGTA 57.693 45.455 5.33 0.00 34.56 3.08
540 543 6.340522 GTGATGGCCTTGCAATAAAAAGTAT 58.659 36.000 3.32 0.00 0.00 2.12
578 745 6.599356 ACCAACTCTTTTGTAAAAGGTGTT 57.401 33.333 14.99 15.62 44.22 3.32
609 776 1.400494 CCGCTTTGATTCTTAACCCGG 59.600 52.381 0.00 0.00 0.00 5.73
632 799 5.503031 CGTGCCAATCAAGCAATCTAGTAAG 60.503 44.000 0.00 0.00 43.02 2.34
685 855 2.573920 GCCTTTTACGGCCCATTCA 58.426 52.632 0.00 0.00 44.41 2.57
697 867 0.540365 TGCTGCCAGCTAAGCCTTTT 60.540 50.000 18.96 0.00 42.97 2.27
698 868 0.964358 CTGCTGCCAGCTAAGCCTTT 60.964 55.000 18.96 0.00 42.97 3.11
725 895 2.322081 CCGTAACACCAAGCCCACG 61.322 63.158 0.00 0.00 0.00 4.94
728 898 2.033602 AGCCGTAACACCAAGCCC 59.966 61.111 0.00 0.00 0.00 5.19
730 900 0.882927 TGTGAGCCGTAACACCAAGC 60.883 55.000 0.00 0.00 36.35 4.01
731 901 1.531149 CTTGTGAGCCGTAACACCAAG 59.469 52.381 0.00 0.00 36.35 3.61
732 902 1.134340 ACTTGTGAGCCGTAACACCAA 60.134 47.619 0.00 0.00 36.35 3.67
733 903 0.466543 ACTTGTGAGCCGTAACACCA 59.533 50.000 0.00 0.00 36.35 4.17
734 904 1.529865 GAACTTGTGAGCCGTAACACC 59.470 52.381 0.00 0.00 36.35 4.16
735 905 1.529865 GGAACTTGTGAGCCGTAACAC 59.470 52.381 0.00 0.00 37.51 3.32
736 906 1.414919 AGGAACTTGTGAGCCGTAACA 59.585 47.619 0.00 0.00 27.25 2.41
737 907 2.067013 GAGGAACTTGTGAGCCGTAAC 58.933 52.381 0.00 0.00 41.55 2.50
738 908 1.336517 CGAGGAACTTGTGAGCCGTAA 60.337 52.381 0.00 0.00 41.55 3.18
739 909 0.242825 CGAGGAACTTGTGAGCCGTA 59.757 55.000 0.00 0.00 41.55 4.02
740 910 1.006102 CGAGGAACTTGTGAGCCGT 60.006 57.895 0.00 0.00 41.55 5.68
741 911 3.862124 CGAGGAACTTGTGAGCCG 58.138 61.111 0.00 0.00 41.55 5.52
759 929 1.459450 GGTTATTTGAAGGCCTCGCA 58.541 50.000 5.23 4.63 0.00 5.10
885 1059 4.035843 CCTGTAAGAGGCGGAGGT 57.964 61.111 0.00 0.00 34.01 3.85
896 1070 1.340795 GGAGGAGGACGAGACCTGTAA 60.341 57.143 0.00 0.00 40.73 2.41
944 1118 4.363990 AGCGAGCACTGGGACACG 62.364 66.667 0.00 0.00 0.00 4.49
946 1120 3.695606 GGAGCGAGCACTGGGACA 61.696 66.667 0.00 0.00 0.00 4.02
1062 1236 1.760480 GCACTCCTCCTCCTCCTCC 60.760 68.421 0.00 0.00 0.00 4.30
1374 1550 4.566360 AGAAAATCAAAACCAACGCAACAG 59.434 37.500 0.00 0.00 0.00 3.16
1405 1581 2.325583 TAATCCCCAGATTGCACGAC 57.674 50.000 0.00 0.00 42.78 4.34
1538 1714 7.978099 AATTGGGGCTAAATTCAGACTAATT 57.022 32.000 0.00 0.00 0.00 1.40
1550 1726 2.028203 GCAGCTCAAAATTGGGGCTAAA 60.028 45.455 0.00 0.00 36.49 1.85
1585 1761 2.494445 CCAGTGATCGCTACGGCA 59.506 61.111 8.81 0.00 38.60 5.69
1691 1867 1.517257 CCTACGCCTCGAAGTGCAG 60.517 63.158 0.00 0.00 0.00 4.41
1920 2109 7.064253 GTGATTAGTTACAGCGTTACAAGGAAT 59.936 37.037 1.90 0.00 0.00 3.01
1921 2110 6.366877 GTGATTAGTTACAGCGTTACAAGGAA 59.633 38.462 1.90 0.00 0.00 3.36
1922 2111 5.865552 GTGATTAGTTACAGCGTTACAAGGA 59.134 40.000 1.90 0.00 0.00 3.36
1923 2112 5.867716 AGTGATTAGTTACAGCGTTACAAGG 59.132 40.000 1.90 0.00 0.00 3.61
1924 2113 6.237227 CGAGTGATTAGTTACAGCGTTACAAG 60.237 42.308 1.90 0.00 0.00 3.16
1925 2114 5.570206 CGAGTGATTAGTTACAGCGTTACAA 59.430 40.000 1.90 0.00 0.00 2.41
1926 2115 5.090757 CGAGTGATTAGTTACAGCGTTACA 58.909 41.667 1.90 0.00 0.00 2.41
1927 2116 5.091431 ACGAGTGATTAGTTACAGCGTTAC 58.909 41.667 0.00 0.00 0.00 2.50
1928 2117 5.300969 ACGAGTGATTAGTTACAGCGTTA 57.699 39.130 0.00 0.00 0.00 3.18
1929 2118 4.164294 GACGAGTGATTAGTTACAGCGTT 58.836 43.478 0.00 0.00 31.83 4.84
1930 2119 3.427233 GGACGAGTGATTAGTTACAGCGT 60.427 47.826 0.00 0.00 33.39 5.07
1931 2120 3.106672 GGACGAGTGATTAGTTACAGCG 58.893 50.000 0.00 0.00 0.00 5.18
2110 2299 2.294233 TGCACCAGAAATCAACTTCAGC 59.706 45.455 0.00 0.00 0.00 4.26
2153 2342 8.629158 TGTGTTGAAACTTGAATACATAAAGCT 58.371 29.630 0.00 0.00 0.00 3.74
2208 2397 0.942962 GGCTCTGCAAGATGAATCCG 59.057 55.000 0.00 0.00 45.62 4.18
2256 2445 4.813697 GCCTCACAGATCTTATCAACCTTC 59.186 45.833 0.00 0.00 0.00 3.46
2274 2463 2.620115 CAGAAGTTTTTCAGCAGCCTCA 59.380 45.455 0.00 0.00 35.70 3.86
2409 2642 9.778741 TCAAATAGTACACAAACTTCAGAAGAT 57.221 29.630 17.56 1.55 0.00 2.40
2425 2658 7.824779 ACCCTGACTCTGAAAATCAAATAGTAC 59.175 37.037 0.00 0.00 0.00 2.73
2427 2660 6.784031 ACCCTGACTCTGAAAATCAAATAGT 58.216 36.000 0.00 0.00 0.00 2.12
2484 2717 4.645588 TCAGTAGCTTAGCTCCTAAACCTC 59.354 45.833 11.09 0.00 40.44 3.85
2509 2743 8.743085 AGTACTAAACTGTATGATCGTCCTTA 57.257 34.615 0.00 0.00 36.93 2.69
2532 2766 2.292828 AGCACTATGGCCAAAACAGT 57.707 45.000 10.96 8.27 0.00 3.55
2544 2778 8.915036 ACAGTAAGTTTAGCATAGTAGCACTAT 58.085 33.333 3.78 3.78 41.82 2.12
2574 2816 9.474920 CAAGCAGATTCCAAAAACAAACTATTA 57.525 29.630 0.00 0.00 0.00 0.98
2575 2817 8.203485 TCAAGCAGATTCCAAAAACAAACTATT 58.797 29.630 0.00 0.00 0.00 1.73
2735 2977 8.501070 AGGAATAATCAGAACAGAATCAAGGAT 58.499 33.333 0.00 0.00 0.00 3.24
2759 3001 7.445121 TGAATAGGTTAGAGCATAACATCAGG 58.555 38.462 12.28 0.00 0.00 3.86
2785 3027 6.605594 TCCCTCCTTCAAATTACGCAAATATT 59.394 34.615 0.00 0.00 0.00 1.28
2792 3034 3.945285 TCAATCCCTCCTTCAAATTACGC 59.055 43.478 0.00 0.00 0.00 4.42
2794 3036 7.039714 AGTGTTTCAATCCCTCCTTCAAATTAC 60.040 37.037 0.00 0.00 0.00 1.89
2853 3095 6.505044 AAATGGTAACGGGAACATTTACTC 57.495 37.500 11.77 0.00 40.56 2.59
2866 3108 6.735130 AGAAACCAAGAAGAAAATGGTAACG 58.265 36.000 0.00 0.00 46.46 3.18
2907 3149 3.068307 ACAGAGCTACAACTAATAGGCGG 59.932 47.826 0.00 0.00 0.00 6.13
2923 3165 5.066375 TGGCACAAATCATACATAACAGAGC 59.934 40.000 0.00 0.00 31.92 4.09
2983 3237 5.355350 GCTTATGAGAGTTTTAGCACCATGT 59.645 40.000 0.00 0.00 0.00 3.21
2984 3238 5.587844 AGCTTATGAGAGTTTTAGCACCATG 59.412 40.000 0.00 0.00 0.00 3.66
2985 3239 5.749462 AGCTTATGAGAGTTTTAGCACCAT 58.251 37.500 0.00 0.00 0.00 3.55
2986 3240 5.165961 AGCTTATGAGAGTTTTAGCACCA 57.834 39.130 0.00 0.00 0.00 4.17
2987 3241 5.877564 AGAAGCTTATGAGAGTTTTAGCACC 59.122 40.000 0.00 0.00 0.00 5.01
2988 3242 6.976636 AGAAGCTTATGAGAGTTTTAGCAC 57.023 37.500 0.00 0.00 0.00 4.40
2991 3245 8.447053 GGTGAAAGAAGCTTATGAGAGTTTTAG 58.553 37.037 0.00 0.00 0.00 1.85
3001 3255 6.432472 AGAAAAGGAGGTGAAAGAAGCTTATG 59.568 38.462 0.00 0.00 0.00 1.90
3027 3281 3.818295 ACCTCTGGAAGACTAGACAGT 57.182 47.619 0.00 0.00 38.67 3.55
3055 3309 7.851508 TGCTTTCGAATTCTTATATGCACTAC 58.148 34.615 0.00 0.00 0.00 2.73
3116 3370 3.472283 TTGAGTTTTGGCATGCAACAT 57.528 38.095 21.36 5.66 0.00 2.71
3121 3375 4.512571 AGATTTGTTTGAGTTTTGGCATGC 59.487 37.500 9.90 9.90 0.00 4.06
3157 3411 6.017605 GTGTTGCATCAGGGAAATAGTGATAG 60.018 42.308 0.00 0.00 29.64 2.08
3207 3469 6.701400 GTGCTTTGGAAATCAACATTACAACT 59.299 34.615 0.00 0.00 34.67 3.16
3246 3508 7.031975 GCTAGAAAGTTGGAATTGAGAAATGG 58.968 38.462 0.00 0.00 0.00 3.16
3373 3641 6.602009 TCTGTTCTAGTGAGGTTTCATCGATA 59.398 38.462 0.00 0.00 35.39 2.92
3374 3642 5.419155 TCTGTTCTAGTGAGGTTTCATCGAT 59.581 40.000 0.00 0.00 35.39 3.59
3378 3646 6.013379 TGGATTCTGTTCTAGTGAGGTTTCAT 60.013 38.462 0.00 0.00 35.39 2.57
3392 3660 7.050377 TGGAGAGTTATTCATGGATTCTGTTC 58.950 38.462 0.00 0.00 0.00 3.18
3394 3662 6.566079 TGGAGAGTTATTCATGGATTCTGT 57.434 37.500 0.00 0.00 0.00 3.41
3534 4096 9.558648 TGTAAATGAATTCATCGAACAAATCAG 57.441 29.630 20.95 0.00 35.10 2.90
3572 4134 2.735134 CCGTTAAGGGAACAGTTTCGAG 59.265 50.000 8.58 0.00 37.99 4.04
3676 4238 8.483758 TGGGTTATAAGAGAGATGTAAAAGGAC 58.516 37.037 0.00 0.00 0.00 3.85
3695 4257 9.726438 CGATCTATTCTTCCTTAAATGGGTTAT 57.274 33.333 0.00 0.00 0.00 1.89
3765 4327 0.459899 CATAGGTGTAGGCACGAGCA 59.540 55.000 7.26 0.00 46.13 4.26
3774 4336 3.699538 TGTACTGGTGCTCATAGGTGTAG 59.300 47.826 0.00 0.00 0.00 2.74
3912 4480 9.130661 TCTATCATTTCCAAGTCAAACAAAGAA 57.869 29.630 0.00 0.00 0.00 2.52
3923 4491 5.614324 TCCACGATCTATCATTTCCAAGT 57.386 39.130 0.00 0.00 0.00 3.16
3961 4529 2.616842 ACCACTGAAATCAACACGGAAC 59.383 45.455 0.00 0.00 0.00 3.62
4057 4625 1.363744 GCAAGCAGCATTCGACTACT 58.636 50.000 0.00 0.00 44.79 2.57
4068 4636 4.032104 GCAAGTGTATAAAATGCAAGCAGC 59.968 41.667 0.00 0.00 45.96 5.25
4069 4637 5.404946 AGCAAGTGTATAAAATGCAAGCAG 58.595 37.500 0.00 0.00 39.42 4.24
4070 4638 5.389859 AGCAAGTGTATAAAATGCAAGCA 57.610 34.783 0.00 0.00 39.42 3.91
4093 4661 4.318332 CAGTTCCAGAGCACATCACTTAA 58.682 43.478 0.00 0.00 0.00 1.85
4124 4692 1.080298 GGACAGCATTTGTGCCAGC 60.080 57.895 0.00 0.00 41.83 4.85
4492 5067 7.899330 CCAAACAAATTAAAGCAATGAATAGCG 59.101 33.333 0.00 0.00 35.48 4.26
4493 5068 8.720562 ACCAAACAAATTAAAGCAATGAATAGC 58.279 29.630 0.00 0.00 0.00 2.97
4522 5097 7.231317 AGCAAAACAATCCTATCAAGAGTTCAA 59.769 33.333 0.00 0.00 0.00 2.69
4600 5176 1.068588 TGTGCTACGTGAAGCTTCAGT 59.931 47.619 29.13 26.49 43.19 3.41
4628 5204 4.800993 ACAATTTCTCGACATCTGATCGTC 59.199 41.667 1.15 5.65 40.50 4.20
4630 5206 5.709011 AACAATTTCTCGACATCTGATCG 57.291 39.130 0.00 0.00 41.00 3.69
4682 5258 0.452987 CCATCAATCCGCCTGTTGTG 59.547 55.000 0.00 0.00 0.00 3.33
4753 5329 5.419542 TGTCGATTTTGCTAGCAGAACTAT 58.580 37.500 21.70 7.51 0.00 2.12
4816 5392 4.081476 GCATAGAGGTTGCCCAATTTCTTT 60.081 41.667 3.64 0.00 33.95 2.52
4865 5441 4.873827 TCCTTAAGGCATTACAAGCTTACG 59.126 41.667 17.32 0.00 34.44 3.18
4917 5499 5.843421 AGGCTAAGGTCTTATGATGAGTCAT 59.157 40.000 4.98 4.98 46.54 3.06
4972 5554 1.214175 TGGTGTCTCCCTGAAGCAAAA 59.786 47.619 0.00 0.00 34.77 2.44
5053 5635 8.709386 TGCAGTTTTTAAGCTAGAATCTAGAG 57.291 34.615 20.58 0.00 0.00 2.43
5154 5736 5.455183 CCATGCAAGATAATGGAGTCCACTA 60.455 44.000 15.86 8.77 45.29 2.74
5218 5800 9.241919 TGGAATTCACTTCAATGCTTATTTAGA 57.758 29.630 7.93 0.00 35.41 2.10
5221 5803 9.729281 AAATGGAATTCACTTCAATGCTTATTT 57.271 25.926 7.93 0.00 33.67 1.40
5222 5804 9.729281 AAAATGGAATTCACTTCAATGCTTATT 57.271 25.926 7.93 0.00 33.67 1.40
5223 5805 9.729281 AAAAATGGAATTCACTTCAATGCTTAT 57.271 25.926 7.93 0.00 33.67 1.73
5293 5875 8.445275 AAATTGGTAAAAACATGGGAAAACTC 57.555 30.769 0.00 0.00 0.00 3.01
5300 5882 7.736447 TGCTTAAAATTGGTAAAAACATGGG 57.264 32.000 0.00 0.00 0.00 4.00
5391 5973 5.615925 AAGAGTAGAATAAACCAGCCGAT 57.384 39.130 0.00 0.00 0.00 4.18
5454 6039 0.983467 TGCTGGCTGACATGTAGGAA 59.017 50.000 0.00 0.00 0.00 3.36
5466 6051 0.773644 TTCTTTCTCCCTTGCTGGCT 59.226 50.000 0.00 0.00 0.00 4.75
5507 6092 1.458777 TCCGAACCCTGACCACACT 60.459 57.895 0.00 0.00 0.00 3.55
5508 6093 1.301479 GTCCGAACCCTGACCACAC 60.301 63.158 0.00 0.00 0.00 3.82
5509 6094 1.125093 ATGTCCGAACCCTGACCACA 61.125 55.000 0.00 0.00 0.00 4.17
5510 6095 0.899720 TATGTCCGAACCCTGACCAC 59.100 55.000 0.00 0.00 0.00 4.16
5511 6096 1.760613 GATATGTCCGAACCCTGACCA 59.239 52.381 0.00 0.00 0.00 4.02
5512 6097 2.036089 GAGATATGTCCGAACCCTGACC 59.964 54.545 0.00 0.00 0.00 4.02
5513 6098 2.693591 TGAGATATGTCCGAACCCTGAC 59.306 50.000 0.00 0.00 0.00 3.51
5515 6100 4.342862 AATGAGATATGTCCGAACCCTG 57.657 45.455 0.00 0.00 0.00 4.45
5516 6101 5.602978 ACTAAATGAGATATGTCCGAACCCT 59.397 40.000 0.00 0.00 0.00 4.34
5526 6111 5.406780 GGTTGAGCGGACTAAATGAGATATG 59.593 44.000 0.00 0.00 0.00 1.78
5528 6113 4.202223 GGGTTGAGCGGACTAAATGAGATA 60.202 45.833 0.00 0.00 0.00 1.98
5565 6150 5.249622 TCTGTAGGGAACACAATCAACCATA 59.750 40.000 0.00 0.00 33.45 2.74
5567 6152 3.392947 TCTGTAGGGAACACAATCAACCA 59.607 43.478 0.00 0.00 33.45 3.67
5577 6162 8.225863 AGATATCTCTATCTCTGTAGGGAACA 57.774 38.462 0.00 0.00 40.02 3.18
5674 6259 4.343814 TCATGCCGACTAGATTATTGGACA 59.656 41.667 0.00 0.00 0.00 4.02
5686 6271 3.978855 CGTCGATATTTTCATGCCGACTA 59.021 43.478 0.00 0.00 42.64 2.59


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

AutoCloner maintained by Alex Coulton.