Multiple sequence alignment - TraesCS2D01G435400

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 TraesCS2D01G435400 chr2D 100.000 5660 0 0 1 5660 546448694 546454353 0.000000e+00 10453.0
1 TraesCS2D01G435400 chr2D 91.129 124 8 3 5299 5420 546453540 546453662 1.260000e-36 165.0
2 TraesCS2D01G435400 chr2D 91.129 124 8 3 4847 4969 546453992 546454113 1.260000e-36 165.0
3 TraesCS2D01G435400 chr2B 92.585 5772 219 93 1 5656 653272515 653278193 0.000000e+00 8094.0
4 TraesCS2D01G435400 chr2B 93.496 123 8 0 4847 4969 653277837 653277959 3.480000e-42 183.0
5 TraesCS2D01G435400 chr2A 91.951 3342 141 48 2024 5302 689934060 689930784 0.000000e+00 4564.0
6 TraesCS2D01G435400 chr2A 88.166 338 25 5 996 1329 689935116 689934790 6.880000e-104 388.0
7 TraesCS2D01G435400 chr2A 80.819 537 42 31 1423 1916 689934640 689934122 1.160000e-96 364.0
8 TraesCS2D01G435400 chr2A 89.600 125 10 3 5299 5420 689931246 689931122 7.590000e-34 156.0
9 TraesCS2D01G435400 chr6D 82.237 304 27 14 4184 4463 347681314 347681614 2.640000e-58 237.0
10 TraesCS2D01G435400 chr6D 87.143 140 8 5 3769 3906 347680969 347681100 3.530000e-32 150.0
11 TraesCS2D01G435400 chr6D 95.000 60 1 2 3239 3296 347680426 347680485 6.040000e-15 93.5
12 TraesCS2D01G435400 chr6B 82.392 301 26 11 4187 4463 532344483 532344186 2.640000e-58 237.0
13 TraesCS2D01G435400 chr6B 87.143 140 8 5 3769 3906 532344831 532344700 3.530000e-32 150.0
14 TraesCS2D01G435400 chr6B 95.000 60 1 2 3239 3296 532345383 532345324 6.040000e-15 93.5
15 TraesCS2D01G435400 chr6A 88.439 173 20 0 4291 4463 495693022 495692850 5.750000e-50 209.0
16 TraesCS2D01G435400 chr6A 87.143 140 8 5 3769 3906 495693504 495693373 3.530000e-32 150.0
17 TraesCS2D01G435400 chr6A 89.815 108 7 2 3543 3647 495693701 495693595 9.890000e-28 135.0
18 TraesCS2D01G435400 chr6A 87.755 98 6 2 4187 4281 495693153 495693059 6.000000e-20 110.0
19 TraesCS2D01G435400 chr6A 85.567 97 6 5 3239 3333 495694053 495693963 1.680000e-15 95.3
20 TraesCS2D01G435400 chr7D 81.757 148 23 2 5443 5589 568257289 568257145 2.770000e-23 121.0


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 TraesCS2D01G435400 chr2D 546448694 546454353 5659 False 3594.333333 10453 94.0860 1 5660 3 chr2D.!!$F1 5659
1 TraesCS2D01G435400 chr2B 653272515 653278193 5678 False 4138.500000 8094 93.0405 1 5656 2 chr2B.!!$F1 5655
2 TraesCS2D01G435400 chr2A 689930784 689935116 4332 True 1368.000000 4564 87.6340 996 5420 4 chr2A.!!$R1 4424

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
386 411 0.107897 TGTGTCGCCGCCTAATTCAT 60.108 50.0 0.0 0.00 0.00 2.57 F
1742 1891 0.179215 GCCTCTGCATCGTTGTTTCG 60.179 55.0 0.0 0.00 37.47 3.46 F
2064 2253 0.517316 GCGTGAATGACAGTGGTTCC 59.483 55.0 0.0 0.00 0.00 3.62 F
3220 3463 0.160182 GTTTCGTTCCTGCGTACGTG 59.840 55.0 17.9 10.07 38.79 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 2413 0.033920 CAAGCAAAGGAAAGGTGGCC 59.966 55.0 0.00 0.0 0.00 5.36 R
2874 3092 0.105408 ACAAAGGACCACGCTACGTT 59.895 50.0 0.00 0.0 38.32 3.99 R
3400 3643 0.109458 CTAGTCCTTGTGTACGCGCA 60.109 55.0 5.73 0.0 0.00 6.09 R
5219 5482 0.250727 ATGAAGTGGGTTCCGGTGTG 60.251 55.0 0.00 0.0 33.75 3.82 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
61 62 2.254459 CAGATCAGAGGTCGAACGTTG 58.746 52.381 5.00 0.00 0.00 4.10
168 169 6.770785 ACCTTGTCTTTATAGTGTTTTCTGCA 59.229 34.615 0.00 0.00 0.00 4.41
177 191 0.183492 TGTTTTCTGCAGCCTGGTCT 59.817 50.000 9.47 0.00 0.00 3.85
189 203 4.994471 TGGTCTGCTGCTGGTGCG 62.994 66.667 6.69 0.00 43.34 5.34
232 246 4.462483 AGCAAATCGACATGGGTTAATTGT 59.538 37.500 0.00 0.00 0.00 2.71
237 251 6.877611 ATCGACATGGGTTAATTGTATTCC 57.122 37.500 0.00 0.00 0.00 3.01
269 283 2.215907 ATTAGCAGAGCACTGTAGCG 57.784 50.000 12.89 0.00 45.04 4.26
272 286 2.575993 CAGAGCACTGTAGCGGCT 59.424 61.111 7.98 7.98 41.35 5.52
275 289 1.079819 GAGCACTGTAGCGGCTTCA 60.080 57.895 8.26 8.71 38.15 3.02
277 291 2.391389 GCACTGTAGCGGCTTCACC 61.391 63.158 8.26 0.00 0.00 4.02
294 308 3.228453 TCACCGGAGTACTGTTCTTCTT 58.772 45.455 9.46 0.00 0.00 2.52
349 363 4.455877 GCTCTATTGCGGCCATAGTTAATT 59.544 41.667 17.56 0.00 0.00 1.40
350 364 5.048713 GCTCTATTGCGGCCATAGTTAATTT 60.049 40.000 17.56 0.00 0.00 1.82
360 374 5.336372 GGCCATAGTTAATTTGCACAGTTGA 60.336 40.000 0.00 0.00 0.00 3.18
361 375 5.801947 GCCATAGTTAATTTGCACAGTTGAG 59.198 40.000 0.00 0.00 0.00 3.02
364 378 7.326789 CCATAGTTAATTTGCACAGTTGAGTTG 59.673 37.037 0.00 0.00 0.00 3.16
378 392 4.759096 GTTGCATGTGTCGCCGCC 62.759 66.667 0.00 0.00 0.00 6.13
386 411 0.107897 TGTGTCGCCGCCTAATTCAT 60.108 50.000 0.00 0.00 0.00 2.57
397 422 3.856521 CGCCTAATTCATCTAGATCGCTG 59.143 47.826 1.03 0.00 0.00 5.18
538 567 3.127203 GTGACTGAGCAGTAGTATGACGT 59.873 47.826 2.65 0.00 42.66 4.34
581 610 5.443185 TTGTTACAGACTTACAGTACGCT 57.557 39.130 0.00 0.00 0.00 5.07
615 644 7.434602 GGTACAAATACGTTCTTCTAGATGGAC 59.565 40.741 6.94 6.94 31.40 4.02
617 646 7.036220 ACAAATACGTTCTTCTAGATGGACTG 58.964 38.462 13.63 10.06 0.00 3.51
626 655 7.395525 TCTTCTAGATGGACTGGTAGAGTAT 57.604 40.000 5.84 0.00 33.83 2.12
627 656 8.507582 TCTTCTAGATGGACTGGTAGAGTATA 57.492 38.462 5.84 0.00 33.83 1.47
628 657 8.377034 TCTTCTAGATGGACTGGTAGAGTATAC 58.623 40.741 5.84 0.00 33.83 1.47
629 658 6.699366 TCTAGATGGACTGGTAGAGTATACG 58.301 44.000 0.00 0.00 33.83 3.06
631 660 6.129414 AGATGGACTGGTAGAGTATACGAT 57.871 41.667 0.00 0.00 33.83 3.73
632 661 7.255199 AGATGGACTGGTAGAGTATACGATA 57.745 40.000 0.00 0.00 33.83 2.92
633 662 7.104939 AGATGGACTGGTAGAGTATACGATAC 58.895 42.308 10.43 10.43 33.83 2.24
635 664 6.228995 TGGACTGGTAGAGTATACGATACTG 58.771 44.000 15.65 12.44 33.83 2.74
636 665 6.183361 TGGACTGGTAGAGTATACGATACTGT 60.183 42.308 15.65 14.45 33.83 3.55
637 666 6.147492 GGACTGGTAGAGTATACGATACTGTG 59.853 46.154 15.65 10.61 33.83 3.66
648 677 8.202137 AGTATACGATACTGTGGCATTAAAGTT 58.798 33.333 0.00 0.00 0.00 2.66
678 707 1.875514 TGCAACGTCGTCTACAGTACT 59.124 47.619 0.00 0.00 0.00 2.73
679 708 3.066380 TGCAACGTCGTCTACAGTACTA 58.934 45.455 0.00 0.00 0.00 1.82
680 709 3.686241 TGCAACGTCGTCTACAGTACTAT 59.314 43.478 0.00 0.00 0.00 2.12
733 763 1.197721 CGCAATGTTTGACCCTCTCAC 59.802 52.381 0.00 0.00 0.00 3.51
737 767 4.330250 CAATGTTTGACCCTCTCACATCT 58.670 43.478 0.00 0.00 0.00 2.90
739 769 3.743521 TGTTTGACCCTCTCACATCTTG 58.256 45.455 0.00 0.00 0.00 3.02
819 852 3.653539 AGTTTTAATTTGCACCGTCCC 57.346 42.857 0.00 0.00 0.00 4.46
834 867 1.168714 GTCCCGGTCAACGTAGTACT 58.831 55.000 0.00 0.00 45.00 2.73
850 883 2.359981 TACTATGCCAGTACCGCTCT 57.640 50.000 4.36 0.00 38.80 4.09
866 899 4.393680 ACCGCTCTTGAGATAGATACGATC 59.606 45.833 1.30 0.00 0.00 3.69
867 900 4.493382 CCGCTCTTGAGATAGATACGATCG 60.493 50.000 14.88 14.88 0.00 3.69
892 925 6.494842 ACGTTATTAATGATGAATGCACCAC 58.505 36.000 6.46 0.00 0.00 4.16
905 938 9.091784 GATGAATGCACCACTATATATACACTG 57.908 37.037 0.00 0.00 0.00 3.66
926 959 3.181486 TGCTCTATTCTGTTCTACAGGCG 60.181 47.826 6.96 0.00 45.94 5.52
931 964 1.005037 CTGTTCTACAGGCGGTGCA 60.005 57.895 0.00 0.00 42.35 4.57
946 979 2.555199 GGTGCAGCGAGAAGTGATTAT 58.445 47.619 0.00 0.00 0.00 1.28
964 997 0.534203 ATCCCGTGTTGTTGAGCGTT 60.534 50.000 0.00 0.00 0.00 4.84
1115 1148 2.093106 ACACGTACCATCTGTCTCTCC 58.907 52.381 0.00 0.00 0.00 3.71
1120 1153 2.277008 ACCATCTGTCTCTCCCCAAT 57.723 50.000 0.00 0.00 0.00 3.16
1121 1154 1.842562 ACCATCTGTCTCTCCCCAATG 59.157 52.381 0.00 0.00 0.00 2.82
1215 1249 5.355596 CCAGTACCAGCTCTTCTTTATCTG 58.644 45.833 0.00 0.00 0.00 2.90
1216 1250 5.105146 CCAGTACCAGCTCTTCTTTATCTGT 60.105 44.000 0.00 0.00 0.00 3.41
1232 1266 0.246086 CTGTCTCTCTCCCTGTGCAC 59.754 60.000 10.75 10.75 0.00 4.57
1237 1271 1.670406 CTCTCCCTGTGCACACTGC 60.670 63.158 17.42 0.00 45.29 4.40
1284 1318 3.059884 GTCTCATTTTCTGTCAGCGTGA 58.940 45.455 0.00 0.00 0.00 4.35
1354 1408 1.753078 GGGGAAGAACCGGGAATGC 60.753 63.158 6.32 0.00 40.11 3.56
1360 1414 1.201429 AGAACCGGGAATGCCAGAGT 61.201 55.000 6.32 0.00 35.15 3.24
1438 1555 3.489229 GCATGCCGAATTAAAACCTCCTC 60.489 47.826 6.36 0.00 0.00 3.71
1442 1559 2.351726 CCGAATTAAAACCTCCTCTGCG 59.648 50.000 0.00 0.00 0.00 5.18
1471 1588 1.080025 GGTTATAGGGCTAGGCGCG 60.080 63.158 10.58 0.00 46.18 6.86
1544 1671 6.207213 GGGTTGTTGATCGATGTAGTAGTAG 58.793 44.000 0.54 0.00 0.00 2.57
1742 1891 0.179215 GCCTCTGCATCGTTGTTTCG 60.179 55.000 0.00 0.00 37.47 3.46
1775 1924 3.648339 TTGCATCTCCTTGTTGCTTTC 57.352 42.857 0.00 0.00 40.86 2.62
1809 1958 5.631929 GCACATATGCCATATTTGTGTCATG 59.368 40.000 16.02 0.04 46.97 3.07
1845 2001 4.636249 AGAGGATAATGGATGAGCGAAAC 58.364 43.478 0.00 0.00 0.00 2.78
1881 2058 7.841956 AGTTAGACCCATAATAAGGATCGATG 58.158 38.462 0.54 0.00 0.00 3.84
1949 2137 1.081242 CTTTGGCACGGTGACATGC 60.081 57.895 18.92 0.00 33.90 4.06
1979 2167 0.963225 GCTGCTAGGTAGGAGTAGGC 59.037 60.000 7.30 0.00 42.88 3.93
2022 2210 0.921166 TGGATGGATGCATGACTGGT 59.079 50.000 2.46 0.00 0.00 4.00
2041 2230 1.081906 CGACGCAAAAGCAGTGCAT 60.082 52.632 19.20 1.20 42.33 3.96
2064 2253 0.517316 GCGTGAATGACAGTGGTTCC 59.483 55.000 0.00 0.00 0.00 3.62
2072 2261 0.736325 GACAGTGGTTCCATCGACCG 60.736 60.000 0.00 0.00 40.13 4.79
2161 2353 1.652947 TCCTCGGGAAAAAGCTAGGT 58.347 50.000 0.00 0.00 0.00 3.08
2303 2500 4.141876 CCGGTTCCCCATGGCCAT 62.142 66.667 14.09 14.09 0.00 4.40
2304 2501 2.834505 CGGTTCCCCATGGCCATG 60.835 66.667 34.82 34.82 38.51 3.66
2392 2589 2.094234 CCCTTTGCCGTGGAAATAAAGG 60.094 50.000 0.00 0.00 44.31 3.11
2395 2592 2.871096 TGCCGTGGAAATAAAGGTCT 57.129 45.000 0.00 0.00 0.00 3.85
2396 2593 3.985019 TGCCGTGGAAATAAAGGTCTA 57.015 42.857 0.00 0.00 0.00 2.59
2397 2594 3.869065 TGCCGTGGAAATAAAGGTCTAG 58.131 45.455 0.00 0.00 0.00 2.43
2398 2595 2.612672 GCCGTGGAAATAAAGGTCTAGC 59.387 50.000 0.00 0.00 0.00 3.42
2399 2596 3.869065 CCGTGGAAATAAAGGTCTAGCA 58.131 45.455 0.00 0.00 0.00 3.49
2400 2597 3.871594 CCGTGGAAATAAAGGTCTAGCAG 59.128 47.826 0.00 0.00 0.00 4.24
2404 2601 6.627508 CGTGGAAATAAAGGTCTAGCAGTAGT 60.628 42.308 0.00 0.00 0.00 2.73
2431 2630 2.665089 CCCATGGGTAGCGTGGACA 61.665 63.158 23.93 0.00 34.94 4.02
2432 2631 1.449601 CCATGGGTAGCGTGGACAC 60.450 63.158 2.85 0.00 34.94 3.67
2587 2802 4.090588 CGCTGGTCCCGCCCTTTA 62.091 66.667 0.00 0.00 36.04 1.85
2812 3028 8.689972 CCTTGCTTCAGACAAAAGGATAATAAT 58.310 33.333 0.00 0.00 39.88 1.28
2842 3058 2.076100 GTTGTCAATCCAGCGTGATCA 58.924 47.619 0.00 0.00 0.00 2.92
2865 3083 5.049336 CACTAGCTCGCTGTATGTATGTACT 60.049 44.000 0.85 0.00 0.00 2.73
2866 3084 4.920640 AGCTCGCTGTATGTATGTACTT 57.079 40.909 0.00 0.00 0.00 2.24
2867 3085 5.263968 AGCTCGCTGTATGTATGTACTTT 57.736 39.130 0.00 0.00 0.00 2.66
2868 3086 5.043903 AGCTCGCTGTATGTATGTACTTTG 58.956 41.667 0.00 0.00 0.00 2.77
2869 3087 5.041287 GCTCGCTGTATGTATGTACTTTGA 58.959 41.667 0.00 0.00 0.00 2.69
2870 3088 5.692204 GCTCGCTGTATGTATGTACTTTGAT 59.308 40.000 0.00 0.00 0.00 2.57
2871 3089 6.346120 GCTCGCTGTATGTATGTACTTTGATG 60.346 42.308 0.00 0.00 0.00 3.07
2872 3090 6.569780 TCGCTGTATGTATGTACTTTGATGT 58.430 36.000 0.00 0.00 0.00 3.06
2873 3091 6.475402 TCGCTGTATGTATGTACTTTGATGTG 59.525 38.462 0.00 0.00 0.00 3.21
2874 3092 6.475402 CGCTGTATGTATGTACTTTGATGTGA 59.525 38.462 0.00 0.00 0.00 3.58
2875 3093 7.010091 CGCTGTATGTATGTACTTTGATGTGAA 59.990 37.037 0.00 0.00 0.00 3.18
2876 3094 8.116753 GCTGTATGTATGTACTTTGATGTGAAC 58.883 37.037 0.00 0.00 0.00 3.18
2917 3138 3.810310 AGCAGTAGTAATCTGTGCTCC 57.190 47.619 0.00 0.00 39.48 4.70
2922 3143 5.451937 GCAGTAGTAATCTGTGCTCCACATA 60.452 44.000 0.00 0.00 43.71 2.29
2981 3202 4.751060 TGTGAACTTGTTCGTTAGTCAGT 58.249 39.130 8.68 0.00 0.00 3.41
2982 3203 4.802039 TGTGAACTTGTTCGTTAGTCAGTC 59.198 41.667 8.68 0.00 0.00 3.51
3220 3463 0.160182 GTTTCGTTCCTGCGTACGTG 59.840 55.000 17.90 10.07 38.79 4.49
3324 3567 1.990060 CGGGAGCCCCTCTTTCAGA 60.990 63.158 8.43 0.00 42.67 3.27
3419 3662 0.109458 TGCGCGTACACAAGGACTAG 60.109 55.000 8.43 0.00 0.00 2.57
3429 3672 3.316573 AAGGACTAGTGCGGCAGCC 62.317 63.158 1.18 0.00 44.33 4.85
3752 3995 5.233476 TGTTGAACTGATTAACTCGTGTGAC 59.767 40.000 0.00 0.00 0.00 3.67
3759 4002 1.037493 TAACTCGTGTGACCTGTGCT 58.963 50.000 0.00 0.00 0.00 4.40
3922 4165 2.811317 CTCGCTTCTGGTCGGTGC 60.811 66.667 0.00 0.00 0.00 5.01
3955 4198 3.115098 GCACGTAAAACATTTCGTTCACG 59.885 43.478 0.00 9.25 44.93 4.35
4480 4730 4.021229 TCAGGTATATATGCCTACCACCG 58.979 47.826 20.58 8.78 41.20 4.94
4482 4732 4.649674 CAGGTATATATGCCTACCACCGAT 59.350 45.833 20.58 0.00 41.20 4.18
4483 4733 4.649674 AGGTATATATGCCTACCACCGATG 59.350 45.833 19.77 0.00 41.34 3.84
4498 4748 1.645034 CGATGATCCACGAACTTGCT 58.355 50.000 0.00 0.00 0.00 3.91
4507 4758 2.225727 CCACGAACTTGCTAACCTTTCC 59.774 50.000 0.00 0.00 0.00 3.13
4509 4760 1.810755 CGAACTTGCTAACCTTTCCCC 59.189 52.381 0.00 0.00 0.00 4.81
4535 4788 0.247655 CGGTGCACATTCATACACGC 60.248 55.000 20.43 0.00 33.81 5.34
4559 4812 1.341080 TCAGCCCGATCTCATGCATA 58.659 50.000 0.00 0.00 0.00 3.14
4563 4816 2.570752 AGCCCGATCTCATGCATATTCT 59.429 45.455 0.00 0.00 0.00 2.40
4603 4856 1.079057 GAGAGGTTTGGCGAGGACC 60.079 63.158 0.00 0.00 0.00 4.46
4681 4934 2.108168 TGATCTGGTTAAGCTAGCGGT 58.892 47.619 9.55 3.99 0.00 5.68
4920 5173 2.295909 CCAATGTGGTTCATTCGTTGGT 59.704 45.455 0.00 0.00 43.93 3.67
5022 5279 1.799933 TGGCATGTTTGGGGAAAGTT 58.200 45.000 0.00 0.00 0.00 2.66
5081 5338 2.387757 GGATGCTTATTGGCAGGGAAA 58.612 47.619 0.00 0.00 45.75 3.13
5082 5339 2.363359 GGATGCTTATTGGCAGGGAAAG 59.637 50.000 0.00 0.00 45.75 2.62
5084 5341 3.730215 TGCTTATTGGCAGGGAAAGTA 57.270 42.857 0.00 0.00 37.29 2.24
5085 5342 3.352648 TGCTTATTGGCAGGGAAAGTAC 58.647 45.455 0.00 0.00 37.29 2.73
5086 5343 3.245087 TGCTTATTGGCAGGGAAAGTACA 60.245 43.478 0.00 0.00 37.29 2.90
5087 5344 3.761752 GCTTATTGGCAGGGAAAGTACAA 59.238 43.478 0.00 0.00 0.00 2.41
5143 5406 8.542497 AATTTGAACACATTCATGGAATTCAG 57.458 30.769 7.93 0.00 44.36 3.02
5156 5419 9.904198 TTCATGGAATTCAGAGTTTCATATACA 57.096 29.630 7.93 0.00 0.00 2.29
5199 5462 6.980051 ATAAAACTAGAAATGTCACGGGAC 57.020 37.500 11.93 11.93 44.57 4.46
5219 5482 5.069119 GGGACAGGATTTTTGGAATATGGAC 59.931 44.000 0.00 0.00 0.00 4.02
5281 5544 9.016438 TGTATTTCTATGTTTTGTAAGTTCCCC 57.984 33.333 0.00 0.00 0.00 4.81
5318 5581 6.541907 TCCATATAAACCTGATATGCTTGCA 58.458 36.000 0.00 0.00 36.39 4.08
5333 5596 2.872370 CTTGCATGTCTTTGGCTTAGC 58.128 47.619 0.00 0.00 0.00 3.09
5347 5610 4.579869 TGGCTTAGCTTACCTTTTCTCAG 58.420 43.478 3.59 0.00 0.00 3.35
5429 5693 0.033504 TTGGTCAGGACTCACGAAGC 59.966 55.000 0.00 0.00 0.00 3.86
5461 5725 5.057819 TGTGAACGGATTTGCTACTTTACA 58.942 37.500 0.00 0.00 0.00 2.41
5546 5810 1.879380 CGCTTGGAGGTGTGATTTTCA 59.121 47.619 0.00 0.00 0.00 2.69
5569 5833 2.021457 CTGGTTTTCTGTTTGTCGGGT 58.979 47.619 0.00 0.00 0.00 5.28
5572 5836 1.133407 GTTTTCTGTTTGTCGGGTGCA 59.867 47.619 0.00 0.00 0.00 4.57
5575 5839 0.107410 TCTGTTTGTCGGGTGCAGTT 60.107 50.000 0.00 0.00 0.00 3.16
5657 5921 6.806668 TTTCCCCTTTTGAATTTTCTCTGT 57.193 33.333 0.00 0.00 0.00 3.41
5658 5922 5.789643 TCCCCTTTTGAATTTTCTCTGTG 57.210 39.130 0.00 0.00 0.00 3.66
5659 5923 5.208121 TCCCCTTTTGAATTTTCTCTGTGT 58.792 37.500 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 3.493503 ACAAATCTTCAACGTTCGACCTC 59.506 43.478 0.00 0.00 0.00 3.85
61 62 3.841643 CACCCAGATGCAACAAATCTTC 58.158 45.455 0.00 0.00 31.92 2.87
120 121 2.000447 GTAACAAGACATGGACGGAGC 59.000 52.381 0.00 0.00 0.00 4.70
168 169 4.031129 CCAGCAGCAGACCAGGCT 62.031 66.667 0.00 0.00 43.77 4.58
183 197 3.750155 CCATGCATGCACGCACCA 61.750 61.111 25.37 0.00 46.56 4.17
189 203 2.101575 CAGCGTCCATGCATGCAC 59.898 61.111 25.37 16.36 37.31 4.57
200 214 0.790866 GTCGATTTGCTTGCAGCGTC 60.791 55.000 11.83 5.72 46.26 5.19
237 251 8.310382 AGTGCTCTGCTAATACTATAAGGAATG 58.690 37.037 0.00 0.00 0.00 2.67
269 283 0.320697 AACAGTACTCCGGTGAAGCC 59.679 55.000 11.17 0.00 0.00 4.35
272 286 3.228453 AGAAGAACAGTACTCCGGTGAA 58.772 45.455 11.17 0.00 0.00 3.18
275 289 2.288886 GCAAGAAGAACAGTACTCCGGT 60.289 50.000 0.00 0.00 0.00 5.28
277 291 2.989840 CAGCAAGAAGAACAGTACTCCG 59.010 50.000 0.00 0.00 0.00 4.63
278 292 3.244249 ACCAGCAAGAAGAACAGTACTCC 60.244 47.826 0.00 0.00 0.00 3.85
279 293 3.991121 GACCAGCAAGAAGAACAGTACTC 59.009 47.826 0.00 0.00 0.00 2.59
280 294 3.643792 AGACCAGCAAGAAGAACAGTACT 59.356 43.478 0.00 0.00 0.00 2.73
281 295 3.743396 CAGACCAGCAAGAAGAACAGTAC 59.257 47.826 0.00 0.00 0.00 2.73
321 335 2.586079 GCCGCAATAGAGCTCGCA 60.586 61.111 8.37 0.10 0.00 5.10
349 363 1.750206 ACATGCAACTCAACTGTGCAA 59.250 42.857 1.22 0.00 39.04 4.08
350 364 1.065851 CACATGCAACTCAACTGTGCA 59.934 47.619 1.72 0.00 39.91 4.57
360 374 3.726517 GCGGCGACACATGCAACT 61.727 61.111 12.98 0.00 0.00 3.16
361 375 4.759096 GGCGGCGACACATGCAAC 62.759 66.667 12.98 0.00 0.00 4.17
364 378 1.714899 AATTAGGCGGCGACACATGC 61.715 55.000 18.30 0.00 0.00 4.06
378 392 5.760193 GCACAGCGATCTAGATGAATTAG 57.240 43.478 10.74 0.00 0.00 1.73
414 439 5.393962 GTGGTTATATTAGCTACGTACCCG 58.606 45.833 0.00 0.00 40.83 5.28
418 443 5.107104 CGACCGTGGTTATATTAGCTACGTA 60.107 44.000 0.00 0.00 0.00 3.57
419 444 4.319766 CGACCGTGGTTATATTAGCTACGT 60.320 45.833 0.00 0.00 0.00 3.57
420 445 4.153986 CGACCGTGGTTATATTAGCTACG 58.846 47.826 0.00 0.00 0.00 3.51
421 446 5.113502 ACGACCGTGGTTATATTAGCTAC 57.886 43.478 0.00 0.00 0.00 3.58
422 447 4.083855 CGACGACCGTGGTTATATTAGCTA 60.084 45.833 0.00 0.00 0.00 3.32
423 448 3.304257 CGACGACCGTGGTTATATTAGCT 60.304 47.826 0.00 0.00 0.00 3.32
425 450 3.558505 CCGACGACCGTGGTTATATTAG 58.441 50.000 0.00 0.00 36.31 1.73
426 451 2.287547 GCCGACGACCGTGGTTATATTA 60.288 50.000 0.00 0.00 36.31 0.98
427 452 1.536709 GCCGACGACCGTGGTTATATT 60.537 52.381 0.00 0.00 36.31 1.28
428 453 0.031178 GCCGACGACCGTGGTTATAT 59.969 55.000 0.00 0.00 36.31 0.86
429 454 1.433064 GCCGACGACCGTGGTTATA 59.567 57.895 0.00 0.00 36.31 0.98
430 455 2.182537 GCCGACGACCGTGGTTAT 59.817 61.111 0.00 0.00 36.31 1.89
477 502 0.975544 GACATCACTGTTCGACGACG 59.024 55.000 0.00 0.00 35.14 5.12
538 567 3.262936 CCGCAGGCGTCATTTCAA 58.737 55.556 13.07 0.00 46.14 2.69
581 610 3.574284 ACGTATTTGTACCGCACAGTA 57.426 42.857 0.00 0.00 38.72 2.74
587 616 5.335127 TCTAGAAGAACGTATTTGTACCGC 58.665 41.667 0.00 0.00 0.00 5.68
590 619 8.189460 AGTCCATCTAGAAGAACGTATTTGTAC 58.811 37.037 0.00 0.00 0.00 2.90
615 644 5.106634 GCCACAGTATCGTATACTCTACCAG 60.107 48.000 0.56 2.01 0.00 4.00
617 646 4.758674 TGCCACAGTATCGTATACTCTACC 59.241 45.833 0.56 0.00 0.00 3.18
626 655 6.167685 ACAACTTTAATGCCACAGTATCGTA 58.832 36.000 0.00 0.00 0.00 3.43
627 656 5.001232 ACAACTTTAATGCCACAGTATCGT 58.999 37.500 0.00 0.00 0.00 3.73
628 657 5.545658 ACAACTTTAATGCCACAGTATCG 57.454 39.130 0.00 0.00 0.00 2.92
629 658 6.093495 TGCTACAACTTTAATGCCACAGTATC 59.907 38.462 0.00 0.00 0.00 2.24
631 660 5.180492 GTGCTACAACTTTAATGCCACAGTA 59.820 40.000 0.00 0.00 0.00 2.74
632 661 4.023193 GTGCTACAACTTTAATGCCACAGT 60.023 41.667 0.00 0.00 0.00 3.55
633 662 4.475944 GTGCTACAACTTTAATGCCACAG 58.524 43.478 0.00 0.00 0.00 3.66
635 664 3.366985 GGGTGCTACAACTTTAATGCCAC 60.367 47.826 0.00 0.00 0.00 5.01
636 665 2.823154 GGGTGCTACAACTTTAATGCCA 59.177 45.455 0.00 0.00 0.00 4.92
637 666 3.089284 AGGGTGCTACAACTTTAATGCC 58.911 45.455 0.00 0.00 0.00 4.40
648 677 1.301401 GACGTTGCAGGGTGCTACA 60.301 57.895 12.73 0.00 46.67 2.74
678 707 9.104965 GCAGGTCAACATTAATTGTACTGTATA 57.895 33.333 0.00 0.00 37.68 1.47
679 708 7.067008 GGCAGGTCAACATTAATTGTACTGTAT 59.933 37.037 0.00 0.00 37.68 2.29
680 709 6.373216 GGCAGGTCAACATTAATTGTACTGTA 59.627 38.462 0.00 0.00 37.68 2.74
733 763 8.659491 CGACCAAATGTATATATCCACAAGATG 58.341 37.037 0.00 0.00 36.33 2.90
737 767 9.430623 CATACGACCAAATGTATATATCCACAA 57.569 33.333 0.00 0.00 30.41 3.33
739 769 7.547722 TGCATACGACCAAATGTATATATCCAC 59.452 37.037 0.00 0.00 30.41 4.02
786 816 9.912634 TGCAAATTAAAACTAGTAGTACGTACT 57.087 29.630 29.62 29.62 44.69 2.73
787 817 9.943465 GTGCAAATTAAAACTAGTAGTACGTAC 57.057 33.333 18.10 18.10 0.00 3.67
788 818 9.139174 GGTGCAAATTAAAACTAGTAGTACGTA 57.861 33.333 2.50 0.00 0.00 3.57
790 820 7.148755 ACGGTGCAAATTAAAACTAGTAGTACG 60.149 37.037 2.50 0.00 0.00 3.67
819 852 2.097954 TGGCATAGTACTACGTTGACCG 59.902 50.000 4.31 0.00 44.03 4.79
834 867 1.409064 CTCAAGAGCGGTACTGGCATA 59.591 52.381 3.34 0.00 0.00 3.14
866 899 5.845953 GGTGCATTCATCATTAATAACGTCG 59.154 40.000 0.00 0.00 0.00 5.12
867 900 6.632834 GTGGTGCATTCATCATTAATAACGTC 59.367 38.462 0.00 0.00 35.49 4.34
886 919 6.274157 AGAGCAGTGTATATATAGTGGTGC 57.726 41.667 19.84 12.75 30.33 5.01
926 959 2.010145 TAATCACTTCTCGCTGCACC 57.990 50.000 0.00 0.00 0.00 5.01
931 964 2.032620 ACGGGATAATCACTTCTCGCT 58.967 47.619 0.00 0.00 39.44 4.93
946 979 1.153329 AACGCTCAACAACACGGGA 60.153 52.632 0.00 0.00 0.00 5.14
987 1020 0.813210 CCAGCATCTTCGCTTCCTCC 60.813 60.000 0.00 0.00 41.38 4.30
1026 1059 2.687566 TCCTCCCCGCCTTCCTTC 60.688 66.667 0.00 0.00 0.00 3.46
1097 1130 1.685491 GGGGAGAGACAGATGGTACGT 60.685 57.143 0.00 0.00 0.00 3.57
1098 1131 1.033574 GGGGAGAGACAGATGGTACG 58.966 60.000 0.00 0.00 0.00 3.67
1115 1148 2.418197 CCGTGGTACAGTAGTCATTGGG 60.418 54.545 0.00 0.00 41.80 4.12
1120 1153 0.599558 GCACCGTGGTACAGTAGTCA 59.400 55.000 0.00 0.00 41.80 3.41
1121 1154 0.455633 CGCACCGTGGTACAGTAGTC 60.456 60.000 0.00 0.00 41.80 2.59
1215 1249 0.037790 GTGTGCACAGGGAGAGAGAC 60.038 60.000 22.40 0.00 0.00 3.36
1216 1250 0.178950 AGTGTGCACAGGGAGAGAGA 60.179 55.000 22.40 0.00 0.00 3.10
1284 1318 3.431411 TCCCTCTCTCTCTCTCCTACT 57.569 52.381 0.00 0.00 0.00 2.57
1354 1408 7.941919 TGTGCTGTAATAAGTATAGACTCTGG 58.058 38.462 0.00 0.00 33.58 3.86
1360 1414 6.041637 CCCCACTGTGCTGTAATAAGTATAGA 59.958 42.308 1.29 0.00 0.00 1.98
1438 1555 1.506309 TAACCAACTGTGCAGCGCAG 61.506 55.000 30.51 30.51 46.11 5.18
1442 1559 2.017049 CCCTATAACCAACTGTGCAGC 58.983 52.381 0.00 0.00 0.00 5.25
1471 1588 3.360340 GGCTATCCCTGCATGCGC 61.360 66.667 14.09 8.09 39.24 6.09
1472 1589 3.046087 CGGCTATCCCTGCATGCG 61.046 66.667 14.09 7.87 0.00 4.73
1473 1590 3.360340 GCGGCTATCCCTGCATGC 61.360 66.667 11.82 11.82 34.60 4.06
1474 1591 1.964891 CAGCGGCTATCCCTGCATG 60.965 63.158 0.26 0.00 36.16 4.06
1481 1598 1.062525 CAAAACGCAGCGGCTATCC 59.937 57.895 21.15 0.00 38.10 2.59
1544 1671 2.541762 GCTGATCTACTTTGTCCGCATC 59.458 50.000 0.00 0.00 0.00 3.91
1687 1825 1.062525 GTCACGCCAATTGATCGCC 59.937 57.895 7.12 0.00 0.00 5.54
1742 1891 1.106285 GATGCAATGAACCAGGGACC 58.894 55.000 0.00 0.00 0.00 4.46
1809 1958 5.713792 TTATCCTCTACTGCTCTATGTGC 57.286 43.478 0.00 0.00 0.00 4.57
1949 2137 5.304614 TCCTACCTAGCAGCTAATTAACAGG 59.695 44.000 3.09 3.53 0.00 4.00
1979 2167 3.432252 GGTTCCATCATAATTAGACGCGG 59.568 47.826 12.47 0.00 0.00 6.46
2041 2230 1.374125 CACTGTCATTCACGCGGGA 60.374 57.895 7.15 7.15 0.00 5.14
2064 2253 1.999735 TGCTAAAGAAAGCGGTCGATG 59.000 47.619 0.00 0.00 45.85 3.84
2072 2261 2.159881 CGTACGTGGTGCTAAAGAAAGC 60.160 50.000 7.22 0.00 43.08 3.51
2097 2286 1.467035 CCAGCAACGTACTCTCGGTAC 60.467 57.143 0.00 0.00 45.24 3.34
2098 2287 0.806868 CCAGCAACGTACTCTCGGTA 59.193 55.000 0.00 0.00 34.94 4.02
2100 2289 1.805945 GCCAGCAACGTACTCTCGG 60.806 63.158 0.00 0.00 34.94 4.63
2101 2290 0.450583 TAGCCAGCAACGTACTCTCG 59.549 55.000 0.00 0.00 0.00 4.04
2161 2353 2.273179 CGTGTCCTCCCTTGACCGA 61.273 63.158 0.00 0.00 32.07 4.69
2221 2413 0.033920 CAAGCAAAGGAAAGGTGGCC 59.966 55.000 0.00 0.00 0.00 5.36
2300 2497 3.445687 TCGACGACGGACCCATGG 61.446 66.667 4.14 4.14 40.21 3.66
2301 2498 2.202570 GTCGACGACGGACCCATG 60.203 66.667 12.94 0.00 40.21 3.66
2392 2589 4.516321 GGGCTTCTACTACTACTGCTAGAC 59.484 50.000 0.00 0.00 0.00 2.59
2395 2592 4.515028 TGGGCTTCTACTACTACTGCTA 57.485 45.455 0.00 0.00 0.00 3.49
2396 2593 3.383698 TGGGCTTCTACTACTACTGCT 57.616 47.619 0.00 0.00 0.00 4.24
2397 2594 3.243907 CCATGGGCTTCTACTACTACTGC 60.244 52.174 2.85 0.00 0.00 4.40
2398 2595 3.322254 CCCATGGGCTTCTACTACTACTG 59.678 52.174 20.41 0.00 0.00 2.74
2399 2596 3.052033 ACCCATGGGCTTCTACTACTACT 60.052 47.826 31.73 2.37 39.32 2.57
2400 2597 3.306613 ACCCATGGGCTTCTACTACTAC 58.693 50.000 31.73 0.00 39.32 2.73
2404 2601 2.326428 GCTACCCATGGGCTTCTACTA 58.674 52.381 31.73 12.60 39.32 1.82
2434 2633 4.337060 TGTCGTCGTGGTGCGGAG 62.337 66.667 0.00 0.00 41.72 4.63
2435 2634 4.337060 CTGTCGTCGTGGTGCGGA 62.337 66.667 0.00 0.00 41.72 5.54
2436 2635 4.640855 ACTGTCGTCGTGGTGCGG 62.641 66.667 0.00 0.00 41.72 5.69
2437 2636 3.394874 CACTGTCGTCGTGGTGCG 61.395 66.667 0.00 0.00 43.01 5.34
2681 2896 1.903404 AAAAGCAGGCCCCGTCTTG 60.903 57.895 0.00 0.00 0.00 3.02
2684 2899 1.866853 CTTCAAAAGCAGGCCCCGTC 61.867 60.000 0.00 0.00 0.00 4.79
2812 3028 4.022935 GCTGGATTGACAACAGTGAAATCA 60.023 41.667 0.00 0.00 35.16 2.57
2825 3041 2.015736 AGTGATCACGCTGGATTGAC 57.984 50.000 19.85 0.00 35.40 3.18
2842 3058 5.064558 AGTACATACATACAGCGAGCTAGT 58.935 41.667 0.00 1.64 0.00 2.57
2865 3083 1.795872 CCACGCTACGTTCACATCAAA 59.204 47.619 0.00 0.00 38.32 2.69
2866 3084 1.269883 ACCACGCTACGTTCACATCAA 60.270 47.619 0.00 0.00 38.32 2.57
2867 3085 0.315886 ACCACGCTACGTTCACATCA 59.684 50.000 0.00 0.00 38.32 3.07
2868 3086 0.989890 GACCACGCTACGTTCACATC 59.010 55.000 0.00 0.00 38.32 3.06
2869 3087 0.389426 GGACCACGCTACGTTCACAT 60.389 55.000 0.00 0.00 38.32 3.21
2870 3088 1.007038 GGACCACGCTACGTTCACA 60.007 57.895 0.00 0.00 38.32 3.58
2871 3089 0.319297 AAGGACCACGCTACGTTCAC 60.319 55.000 0.00 0.00 38.32 3.18
2872 3090 0.390124 AAAGGACCACGCTACGTTCA 59.610 50.000 0.00 0.00 38.32 3.18
2873 3091 0.788391 CAAAGGACCACGCTACGTTC 59.212 55.000 0.00 0.00 38.32 3.95
2874 3092 0.105408 ACAAAGGACCACGCTACGTT 59.895 50.000 0.00 0.00 38.32 3.99
2875 3093 0.961019 TACAAAGGACCACGCTACGT 59.039 50.000 0.00 0.00 42.36 3.57
2876 3094 1.068055 AGTACAAAGGACCACGCTACG 60.068 52.381 0.00 0.00 0.00 3.51
2922 3143 6.619437 TGGGTATATATGTATGGCAAGGCTAT 59.381 38.462 0.00 0.00 33.54 2.97
2981 3202 4.686972 CTGAAGTGACTTTGAGTGACTGA 58.313 43.478 0.00 0.00 41.80 3.41
2982 3203 3.247173 GCTGAAGTGACTTTGAGTGACTG 59.753 47.826 0.00 0.00 41.80 3.51
3220 3463 0.724453 CAACACATTGCACCGTACGC 60.724 55.000 10.49 0.00 0.00 4.42
3324 3567 2.043652 TAGGGGCGTCGGTAGCTT 60.044 61.111 0.00 0.00 34.52 3.74
3400 3643 0.109458 CTAGTCCTTGTGTACGCGCA 60.109 55.000 5.73 0.00 0.00 6.09
3505 3748 4.933064 GATCTCGCCGCCGTCCTG 62.933 72.222 0.00 0.00 35.54 3.86
3752 3995 2.158959 GCTACGTACGCAGCACAGG 61.159 63.158 30.62 7.60 37.73 4.00
3877 4120 2.361357 AGGACGTCGGAGTGGAGG 60.361 66.667 9.92 0.00 0.00 4.30
3955 4198 3.355378 TGTCATGGATGAATGGGTTCAC 58.645 45.455 0.00 0.00 46.43 3.18
4480 4730 3.309954 GGTTAGCAAGTTCGTGGATCATC 59.690 47.826 0.00 0.00 0.00 2.92
4482 4732 2.301870 AGGTTAGCAAGTTCGTGGATCA 59.698 45.455 0.00 0.00 0.00 2.92
4483 4733 2.973945 AGGTTAGCAAGTTCGTGGATC 58.026 47.619 0.00 0.00 0.00 3.36
4498 4748 2.389962 CGATCAACGGGGAAAGGTTA 57.610 50.000 0.00 0.00 38.46 2.85
4509 4760 0.795698 TGAATGTGCACCGATCAACG 59.204 50.000 15.69 0.00 42.18 4.10
4520 4771 3.063861 TGATCAAGCGTGTATGAATGTGC 59.936 43.478 0.00 0.00 0.00 4.57
4521 4772 4.784394 GCTGATCAAGCGTGTATGAATGTG 60.784 45.833 0.00 0.00 43.45 3.21
4523 4774 3.870007 GCTGATCAAGCGTGTATGAATG 58.130 45.455 0.00 0.00 43.45 2.67
4681 4934 9.621239 ATTATCTCCCTTAATCTATCTCCAACA 57.379 33.333 0.00 0.00 0.00 3.33
4979 5236 4.142622 ACATCCACACGCATAAATTCACAG 60.143 41.667 0.00 0.00 0.00 3.66
5022 5279 2.960384 CCTTGGCCATGCATTTCTATGA 59.040 45.455 6.09 0.00 33.37 2.15
5190 5453 1.539827 CCAAAAATCCTGTCCCGTGAC 59.460 52.381 0.00 0.00 42.12 3.67
5199 5462 6.332630 GTGTGTCCATATTCCAAAAATCCTG 58.667 40.000 0.00 0.00 0.00 3.86
5219 5482 0.250727 ATGAAGTGGGTTCCGGTGTG 60.251 55.000 0.00 0.00 33.75 3.82
5315 5578 2.205022 AGCTAAGCCAAAGACATGCA 57.795 45.000 0.00 0.00 0.00 3.96
5318 5581 4.576330 AGGTAAGCTAAGCCAAAGACAT 57.424 40.909 0.00 0.00 0.00 3.06
5333 5596 6.094603 CACATTGATCCCTGAGAAAAGGTAAG 59.905 42.308 0.00 0.00 35.34 2.34
5429 5693 4.148696 GCAAATCCGTTCACAAATTCAGTG 59.851 41.667 4.97 4.97 38.32 3.66
5461 5725 6.287107 CAACAGATTGTAAAACAGTCGACT 57.713 37.500 13.58 13.58 39.47 4.18
5480 5744 7.360861 GGACGAACATAGATTTGAATGACAACA 60.361 37.037 0.00 0.00 38.29 3.33
5497 5761 1.274596 GCACGATAACGGACGAACAT 58.725 50.000 0.00 0.00 44.46 2.71
5546 5810 1.676006 CGACAAACAGAAAACCAGCCT 59.324 47.619 0.00 0.00 0.00 4.58
5572 5836 1.138859 GCTGGGGCAGAAACAAAAACT 59.861 47.619 0.00 0.00 38.54 2.66
5575 5839 0.398381 AGGCTGGGGCAGAAACAAAA 60.398 50.000 0.00 0.00 40.87 2.44
5637 5901 5.535753 ACACAGAGAAAATTCAAAAGGGG 57.464 39.130 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.