Multiple sequence alignment - TraesCS3B01G267600

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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 TraesCS3B01G267600 chr3B 100.000 4981 0 0 1 4981 430521461 430526441 0.000000e+00 9199.0
1 TraesCS3B01G267600 chr3B 84.783 92 10 3 2023 2114 381754759 381754846 6.870000e-14 89.8
2 TraesCS3B01G267600 chr3D 95.513 3878 139 18 1 3853 331190930 331194797 0.000000e+00 6165.0
3 TraesCS3B01G267600 chr3D 93.460 1208 21 13 3747 4902 331194800 331196001 0.000000e+00 1740.0
4 TraesCS3B01G267600 chr3A 95.238 2079 84 8 2076 4153 448308133 448310197 0.000000e+00 3277.0
5 TraesCS3B01G267600 chr3A 93.120 1279 52 12 813 2060 448306666 448307939 0.000000e+00 1842.0
6 TraesCS3B01G267600 chr3A 91.667 684 28 11 4154 4835 448310227 448310883 0.000000e+00 920.0
7 TraesCS3B01G267600 chr3A 84.981 799 98 10 24 813 448255227 448256012 0.000000e+00 791.0
8 TraesCS3B01G267600 chr3A 86.047 86 8 3 2031 2116 672085903 672085984 6.870000e-14 89.8
9 TraesCS3B01G267600 chr3A 93.220 59 1 1 4833 4888 448311189 448311247 3.200000e-12 84.2
10 TraesCS3B01G267600 chr3A 80.583 103 13 5 2013 2114 243663451 243663355 6.920000e-09 73.1
11 TraesCS3B01G267600 chr4B 83.286 353 43 10 453 790 80001630 80001279 1.350000e-80 311.0
12 TraesCS3B01G267600 chr1B 83.776 339 42 11 454 781 658742317 658741981 4.840000e-80 309.0
13 TraesCS3B01G267600 chr1B 91.954 87 7 0 4894 4980 649320196 649320282 6.770000e-24 122.0
14 TraesCS3B01G267600 chr6D 82.133 347 31 17 450 777 362873265 362872931 8.220000e-68 268.0
15 TraesCS3B01G267600 chr5A 81.818 308 39 15 454 747 69224501 69224805 4.980000e-60 243.0
16 TraesCS3B01G267600 chr5D 78.814 354 58 13 454 791 391195257 391194905 6.490000e-54 222.0
17 TraesCS3B01G267600 chr4A 80.756 291 39 13 518 791 725367354 725367064 1.400000e-50 211.0
18 TraesCS3B01G267600 chr4A 93.902 82 5 0 4898 4979 319197878 319197959 1.880000e-24 124.0
19 TraesCS3B01G267600 chr4A 94.937 79 4 0 4901 4979 497880383 497880305 1.880000e-24 124.0
20 TraesCS3B01G267600 chr7D 80.198 303 40 16 508 791 617656738 617657039 5.050000e-50 209.0
21 TraesCS3B01G267600 chr7D 80.180 111 11 8 2017 2118 419411891 419411783 6.920000e-09 73.1
22 TraesCS3B01G267600 chr2A 79.348 276 47 8 472 738 10236394 10236668 8.520000e-43 185.0
23 TraesCS3B01G267600 chr2A 81.553 103 12 5 2013 2114 606237560 606237656 1.490000e-10 78.7
24 TraesCS3B01G267600 chrUn 75.563 311 58 15 454 753 11854769 11854466 2.420000e-28 137.0
25 TraesCS3B01G267600 chr7B 95.062 81 4 0 4899 4979 413999920 413999840 1.460000e-25 128.0
26 TraesCS3B01G267600 chr2B 93.976 83 5 0 4897 4979 541082033 541081951 5.230000e-25 126.0
27 TraesCS3B01G267600 chr2B 93.902 82 5 0 4896 4977 180328259 180328340 1.880000e-24 124.0
28 TraesCS3B01G267600 chr2B 93.902 82 5 0 4898 4979 783882817 783882898 1.880000e-24 124.0
29 TraesCS3B01G267600 chr6B 94.937 79 4 0 4901 4979 25272808 25272730 1.880000e-24 124.0
30 TraesCS3B01G267600 chr1A 93.902 82 5 0 4898 4979 376474606 376474687 1.880000e-24 124.0
31 TraesCS3B01G267600 chr7A 81.553 103 12 5 2013 2114 623742091 623742187 1.490000e-10 78.7
32 TraesCS3B01G267600 chr7A 80.000 105 13 4 2018 2115 678142728 678142625 2.490000e-08 71.3
33 TraesCS3B01G267600 chr7A 80.000 100 14 4 2016 2114 84015600 84015506 8.950000e-08 69.4
34 TraesCS3B01G267600 chr2D 82.796 93 8 5 2024 2115 124801051 124800966 5.350000e-10 76.8
35 TraesCS3B01G267600 chr2D 88.679 53 6 0 2069 2121 519898894 519898946 1.160000e-06 65.8
36 TraesCS3B01G267600 chr2D 83.607 61 6 4 2056 2116 591303894 591303950 3.000000e-03 54.7
37 TraesCS3B01G267600 chr1D 91.489 47 2 2 2071 2116 239811087 239811042 4.160000e-06 63.9


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 TraesCS3B01G267600 chr3B 430521461 430526441 4980 False 9199.0 9199 100.00000 1 4981 1 chr3B.!!$F2 4980
1 TraesCS3B01G267600 chr3D 331190930 331196001 5071 False 3952.5 6165 94.48650 1 4902 2 chr3D.!!$F1 4901
2 TraesCS3B01G267600 chr3A 448306666 448311247 4581 False 1530.8 3277 93.31125 813 4888 4 chr3A.!!$F3 4075
3 TraesCS3B01G267600 chr3A 448255227 448256012 785 False 791.0 791 84.98100 24 813 1 chr3A.!!$F1 789

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
718 728 0.108804 GTCGTCGCCTGATCCAAGAA 60.109 55.0 0.00 0.0 0.0 2.52 F
1280 1308 0.752658 TGATGCCGATCTGATCCGTT 59.247 50.0 11.84 0.0 0.0 4.44 F
1839 1867 0.447801 CTGGGGCTTCGATTCAAACG 59.552 55.0 0.00 0.0 0.0 3.60 F
3249 3478 0.385390 CCACAGGTGTTCTTGGCAAC 59.615 55.0 0.00 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 1744 1.226945 AACAACTTGTTGCGCCTGC 60.227 52.632 4.18 0.00 39.45 4.85 R
2864 3093 0.037790 AGAGACGAAACAGCTGCTCC 60.038 55.000 15.27 1.38 0.00 4.70 R
3333 3562 0.445436 CGCAAGTGAGAGAACATGGC 59.555 55.000 0.00 0.00 0.00 4.40 R
4916 5648 0.108756 GCCGAATAGGATAGGGTCGC 60.109 60.000 0.00 0.00 45.00 5.19 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
76 77 2.435069 CCTCTCATCTTCATGCACCTCT 59.565 50.000 0.00 0.00 0.00 3.69
77 78 3.118334 CCTCTCATCTTCATGCACCTCTT 60.118 47.826 0.00 0.00 0.00 2.85
119 120 0.174389 AGGCATGTAGACAGAGCACG 59.826 55.000 10.76 0.00 33.99 5.34
123 124 3.448686 GCATGTAGACAGAGCACGTAAT 58.551 45.455 0.00 0.00 33.00 1.89
142 143 1.068083 CAGCGGCATGACTATCGGT 59.932 57.895 1.45 0.00 0.00 4.69
172 173 0.742281 ATGACGTGCTGGTGATGCTC 60.742 55.000 0.00 0.00 0.00 4.26
237 238 1.889545 GCAAGGAGCATCTATGGGAC 58.110 55.000 0.00 0.00 44.79 4.46
336 337 2.044806 GCCTAGGATGATGTGCCGGT 62.045 60.000 14.75 0.00 0.00 5.28
351 352 1.657822 CCGGTTGGTTTTGGTTTTGG 58.342 50.000 0.00 0.00 0.00 3.28
361 362 4.141597 GGTTTTGGTTTTGGAAGGGAATCA 60.142 41.667 0.00 0.00 0.00 2.57
394 395 0.545787 ACATACGTGGTGGGAGGGAA 60.546 55.000 0.00 0.00 0.00 3.97
402 403 3.708451 GTGGTGGGAGGGAATTAAACAT 58.292 45.455 0.00 0.00 0.00 2.71
415 416 4.881157 ATTAAACATAGGGAGGCAAGGT 57.119 40.909 0.00 0.00 0.00 3.50
441 442 1.975680 GGTAGAAGGTGAGGTGAACCA 59.024 52.381 1.62 0.00 40.40 3.67
502 505 3.450578 TCGCGAAGATACCAATTACACC 58.549 45.455 6.20 0.00 0.00 4.16
516 522 0.178932 TACACCTGGTCTCTGCACCT 60.179 55.000 0.00 0.00 37.34 4.00
522 528 1.895798 CTGGTCTCTGCACCTACAAGA 59.104 52.381 0.00 0.00 37.34 3.02
523 529 2.300152 CTGGTCTCTGCACCTACAAGAA 59.700 50.000 0.00 0.00 37.34 2.52
524 530 2.300152 TGGTCTCTGCACCTACAAGAAG 59.700 50.000 0.00 0.00 37.34 2.85
552 558 3.693807 AGACATCCAGAATGCACACAAT 58.306 40.909 0.00 0.00 39.12 2.71
602 612 2.875672 GCCTTGCCACAGTGATCAACTA 60.876 50.000 0.62 0.00 36.83 2.24
603 613 3.614092 CCTTGCCACAGTGATCAACTAT 58.386 45.455 0.62 0.00 36.83 2.12
631 641 1.822371 ACACAAACCACCACCAAAGAC 59.178 47.619 0.00 0.00 0.00 3.01
634 644 3.103742 ACAAACCACCACCAAAGACAAT 58.896 40.909 0.00 0.00 0.00 2.71
663 673 7.492994 CCGAAAAACATAAAAGGTCTCCAAAAA 59.507 33.333 0.00 0.00 0.00 1.94
669 679 2.320745 AAGGTCTCCAAAAACGACGT 57.679 45.000 0.00 0.00 0.00 4.34
677 687 2.031191 TCCAAAAACGACGTCTTCAAGC 59.969 45.455 14.70 0.00 0.00 4.01
679 689 3.421741 CAAAAACGACGTCTTCAAGCAA 58.578 40.909 14.70 0.00 0.00 3.91
718 728 0.108804 GTCGTCGCCTGATCCAAGAA 60.109 55.000 0.00 0.00 0.00 2.52
729 739 5.885912 GCCTGATCCAAGAACATAGGTTTTA 59.114 40.000 0.00 0.00 37.36 1.52
730 740 6.183360 GCCTGATCCAAGAACATAGGTTTTAC 60.183 42.308 0.00 0.00 37.36 2.01
733 743 4.581868 TCCAAGAACATAGGTTTTACCCG 58.418 43.478 0.00 0.00 39.75 5.28
736 750 4.482952 AGAACATAGGTTTTACCCGGAG 57.517 45.455 0.73 0.00 39.75 4.63
893 908 4.935352 TCCAATCCAACCAAACTTTCTG 57.065 40.909 0.00 0.00 0.00 3.02
1280 1308 0.752658 TGATGCCGATCTGATCCGTT 59.247 50.000 11.84 0.00 0.00 4.44
1379 1407 4.407365 CTGGTTGGGGGATGATATTTACC 58.593 47.826 0.00 0.00 0.00 2.85
1716 1744 4.263435 GGAGACACCGATACTAGGATAGG 58.737 52.174 12.35 12.35 44.97 2.57
1839 1867 0.447801 CTGGGGCTTCGATTCAAACG 59.552 55.000 0.00 0.00 0.00 3.60
1916 1966 9.620660 GTAACAAAATGTCTCCAAATATTTCGT 57.379 29.630 0.00 0.00 0.00 3.85
1970 2021 3.713858 TCTTGTTCAGTGTTTGCCATG 57.286 42.857 0.00 0.00 0.00 3.66
1983 2034 4.405036 TGTTTGCCATGGTATGCATAACAT 59.595 37.500 27.96 27.96 41.15 2.71
2078 2307 9.330063 CTGATTTATAAGCTGGAGTTTCATACA 57.670 33.333 0.00 0.00 0.00 2.29
2086 2315 6.006449 AGCTGGAGTTTCATACAAAATCAGT 58.994 36.000 0.00 0.00 0.00 3.41
2553 2782 1.382522 TTGAGCGCATCAGAATTCCC 58.617 50.000 11.47 0.00 39.68 3.97
2864 3093 6.932356 TTTAGAGCTTCAAGGCATTGATAG 57.068 37.500 15.42 14.98 44.75 2.08
3006 3235 4.463891 CCAGGTGCAAAGTTTCCAGATTAT 59.536 41.667 0.00 0.00 0.00 1.28
3249 3478 0.385390 CCACAGGTGTTCTTGGCAAC 59.615 55.000 0.00 0.00 0.00 4.17
3267 3496 2.741092 GTTGAGCCCCGTCACAGA 59.259 61.111 0.00 0.00 0.00 3.41
3291 3520 4.847198 TCATCATGTATGACCTTGTTGCT 58.153 39.130 0.00 0.00 39.77 3.91
3302 3531 0.595095 CTTGTTGCTGGACCTTCTGC 59.405 55.000 0.00 0.00 0.00 4.26
3309 3538 1.151668 CTGGACCTTCTGCAACTTCG 58.848 55.000 0.00 0.00 0.00 3.79
3310 3539 0.468226 TGGACCTTCTGCAACTTCGT 59.532 50.000 0.00 0.00 0.00 3.85
3312 3541 1.264288 GGACCTTCTGCAACTTCGTTG 59.736 52.381 2.51 2.51 45.24 4.10
3333 3562 0.374758 CGCAATCGTCAATCCCAGTG 59.625 55.000 0.00 0.00 0.00 3.66
3336 3565 0.327924 AATCGTCAATCCCAGTGCCA 59.672 50.000 0.00 0.00 0.00 4.92
3339 3568 0.677731 CGTCAATCCCAGTGCCATGT 60.678 55.000 0.00 0.00 0.00 3.21
3348 3577 1.002888 CCAGTGCCATGTTCTCTCACT 59.997 52.381 0.00 0.00 38.40 3.41
3363 3592 2.094659 CACTTGCGGGCGTCTACTG 61.095 63.158 0.00 0.00 0.00 2.74
3716 3947 8.565416 GCTGGATATTACCACTTAATTTGTACC 58.435 37.037 0.00 0.00 35.91 3.34
3719 3950 7.933033 GGATATTACCACTTAATTTGTACCCGA 59.067 37.037 0.00 0.00 32.31 5.14
3737 3968 2.352421 CCGATCTGTACCGTTGACTTGT 60.352 50.000 0.00 0.00 0.00 3.16
3760 4101 2.100584 TGGCATCAACAAAACCAGTGAC 59.899 45.455 0.00 0.00 0.00 3.67
3819 4162 7.052248 TCCCTCTCTTAATTTATTTTCCCGTC 58.948 38.462 0.00 0.00 0.00 4.79
3838 4181 4.142534 CCGTCATTGATGCAATTGTCTCTT 60.143 41.667 7.40 0.00 31.05 2.85
3839 4182 4.791676 CGTCATTGATGCAATTGTCTCTTG 59.208 41.667 7.40 6.86 31.05 3.02
3840 4183 5.618418 CGTCATTGATGCAATTGTCTCTTGT 60.618 40.000 7.40 0.00 31.05 3.16
3841 4184 5.571741 GTCATTGATGCAATTGTCTCTTGTG 59.428 40.000 7.40 5.48 31.05 3.33
3842 4185 5.474189 TCATTGATGCAATTGTCTCTTGTGA 59.526 36.000 7.40 7.32 31.05 3.58
3843 4186 5.970317 TTGATGCAATTGTCTCTTGTGAT 57.030 34.783 7.40 0.00 0.00 3.06
3844 4187 7.337436 TCATTGATGCAATTGTCTCTTGTGATA 59.663 33.333 7.40 0.00 31.05 2.15
3940 4329 5.224888 GTTTCACATGATGCACATTTCTGT 58.775 37.500 0.00 0.00 37.07 3.41
4017 4407 0.524862 GGGCGTCGAGAGAAACTGTA 59.475 55.000 0.00 0.00 45.01 2.74
4056 4446 1.136419 CGATGCTGTCTATCAATGCGC 60.136 52.381 0.00 0.00 0.00 6.09
4156 4575 4.741239 GTGCCTCCCTCCCTCCCA 62.741 72.222 0.00 0.00 0.00 4.37
4332 4751 1.429825 CATCTGCTCTGCTGCTTGC 59.570 57.895 0.00 3.23 43.25 4.01
4457 4876 0.927537 GCTGGTTTTGTGCCGTTTTC 59.072 50.000 0.00 0.00 0.00 2.29
4507 4926 4.473199 GTTTTGCATACTCCTTTTCGTCC 58.527 43.478 0.00 0.00 0.00 4.79
4521 4940 1.358152 TCGTCCCAAACCTGAGGATT 58.642 50.000 4.99 0.00 30.92 3.01
4611 5031 0.098728 CGGATGATGAAACGTTGGCC 59.901 55.000 0.00 0.00 0.00 5.36
4896 5628 7.177041 AGGTAATAGGTAGGAATGATTCTCGAC 59.823 40.741 5.03 2.44 0.00 4.20
4902 5634 4.946478 AGGAATGATTCTCGACCTAAGG 57.054 45.455 5.03 0.00 0.00 2.69
4903 5635 3.070302 AGGAATGATTCTCGACCTAAGGC 59.930 47.826 5.03 0.00 0.00 4.35
4904 5636 3.394719 GAATGATTCTCGACCTAAGGCC 58.605 50.000 0.00 0.00 0.00 5.19
4905 5637 1.860641 TGATTCTCGACCTAAGGCCA 58.139 50.000 5.01 0.00 0.00 5.36
4906 5638 2.184533 TGATTCTCGACCTAAGGCCAA 58.815 47.619 5.01 0.00 0.00 4.52
4907 5639 2.093658 TGATTCTCGACCTAAGGCCAAC 60.094 50.000 5.01 0.00 0.00 3.77
4908 5640 1.640917 TTCTCGACCTAAGGCCAACT 58.359 50.000 5.01 0.00 0.00 3.16
4909 5641 1.183549 TCTCGACCTAAGGCCAACTC 58.816 55.000 5.01 0.00 0.00 3.01
4910 5642 0.175989 CTCGACCTAAGGCCAACTCC 59.824 60.000 5.01 0.00 0.00 3.85
4911 5643 0.543410 TCGACCTAAGGCCAACTCCA 60.543 55.000 5.01 0.00 0.00 3.86
4912 5644 0.391263 CGACCTAAGGCCAACTCCAC 60.391 60.000 5.01 0.00 0.00 4.02
4913 5645 0.035343 GACCTAAGGCCAACTCCACC 60.035 60.000 5.01 0.00 0.00 4.61
4914 5646 1.078426 CCTAAGGCCAACTCCACCG 60.078 63.158 5.01 0.00 0.00 4.94
4915 5647 1.745489 CTAAGGCCAACTCCACCGC 60.745 63.158 5.01 0.00 0.00 5.68
4916 5648 3.599285 TAAGGCCAACTCCACCGCG 62.599 63.158 5.01 0.00 0.00 6.46
4926 5658 4.944372 CCACCGCGCGACCCTATC 62.944 72.222 34.63 0.00 0.00 2.08
4927 5659 4.944372 CACCGCGCGACCCTATCC 62.944 72.222 34.63 0.00 0.00 2.59
4929 5661 2.981909 CCGCGCGACCCTATCCTA 60.982 66.667 34.63 0.00 0.00 2.94
4930 5662 2.341101 CCGCGCGACCCTATCCTAT 61.341 63.158 34.63 0.00 0.00 2.57
4931 5663 1.585006 CGCGCGACCCTATCCTATT 59.415 57.895 28.94 0.00 0.00 1.73
4932 5664 0.456312 CGCGCGACCCTATCCTATTC 60.456 60.000 28.94 0.00 0.00 1.75
4933 5665 0.456312 GCGCGACCCTATCCTATTCG 60.456 60.000 12.10 0.00 0.00 3.34
4934 5666 0.170561 CGCGACCCTATCCTATTCGG 59.829 60.000 0.00 0.00 0.00 4.30
4935 5667 0.108756 GCGACCCTATCCTATTCGGC 60.109 60.000 0.00 0.00 0.00 5.54
4936 5668 1.546961 CGACCCTATCCTATTCGGCT 58.453 55.000 0.00 0.00 0.00 5.52
4937 5669 1.473278 CGACCCTATCCTATTCGGCTC 59.527 57.143 0.00 0.00 0.00 4.70
4938 5670 1.826096 GACCCTATCCTATTCGGCTCC 59.174 57.143 0.00 0.00 0.00 4.70
4939 5671 0.818296 CCCTATCCTATTCGGCTCCG 59.182 60.000 1.14 1.14 41.35 4.63
4940 5672 1.546961 CCTATCCTATTCGGCTCCGT 58.453 55.000 8.28 0.00 40.74 4.69
4941 5673 1.893801 CCTATCCTATTCGGCTCCGTT 59.106 52.381 8.28 0.47 40.74 4.44
4942 5674 2.094649 CCTATCCTATTCGGCTCCGTTC 60.095 54.545 8.28 0.00 40.74 3.95
4943 5675 0.314302 ATCCTATTCGGCTCCGTTCG 59.686 55.000 8.28 0.00 40.74 3.95
4944 5676 1.033746 TCCTATTCGGCTCCGTTCGT 61.034 55.000 8.28 0.00 40.74 3.85
4945 5677 0.179119 CCTATTCGGCTCCGTTCGTT 60.179 55.000 8.28 0.00 40.74 3.85
4946 5678 1.636988 CTATTCGGCTCCGTTCGTTT 58.363 50.000 8.28 0.00 40.74 3.60
4947 5679 1.323534 CTATTCGGCTCCGTTCGTTTG 59.676 52.381 8.28 0.00 40.74 2.93
4948 5680 1.296056 ATTCGGCTCCGTTCGTTTGG 61.296 55.000 8.28 0.00 40.74 3.28
4949 5681 3.419759 CGGCTCCGTTCGTTTGGG 61.420 66.667 0.00 0.00 34.35 4.12
4950 5682 3.053896 GGCTCCGTTCGTTTGGGG 61.054 66.667 0.00 0.00 0.00 4.96
4951 5683 2.281276 GCTCCGTTCGTTTGGGGT 60.281 61.111 0.00 0.00 0.00 4.95
4952 5684 1.004679 GCTCCGTTCGTTTGGGGTA 60.005 57.895 0.00 0.00 0.00 3.69
4953 5685 0.603439 GCTCCGTTCGTTTGGGGTAA 60.603 55.000 0.00 0.00 0.00 2.85
4954 5686 1.881591 CTCCGTTCGTTTGGGGTAAA 58.118 50.000 0.00 0.00 0.00 2.01
4955 5687 2.220313 CTCCGTTCGTTTGGGGTAAAA 58.780 47.619 0.00 0.00 0.00 1.52
4956 5688 2.617774 CTCCGTTCGTTTGGGGTAAAAA 59.382 45.455 0.00 0.00 0.00 1.94
4957 5689 2.617774 TCCGTTCGTTTGGGGTAAAAAG 59.382 45.455 0.00 0.00 0.00 2.27
4958 5690 2.287728 CCGTTCGTTTGGGGTAAAAAGG 60.288 50.000 0.00 0.00 0.00 3.11
4959 5691 2.617774 CGTTCGTTTGGGGTAAAAAGGA 59.382 45.455 0.00 0.00 31.54 3.36
4960 5692 3.548616 CGTTCGTTTGGGGTAAAAAGGAC 60.549 47.826 0.00 0.00 32.76 3.85
4961 5693 3.294038 TCGTTTGGGGTAAAAAGGACA 57.706 42.857 0.00 0.00 0.00 4.02
4962 5694 3.629087 TCGTTTGGGGTAAAAAGGACAA 58.371 40.909 0.00 0.00 0.00 3.18
4963 5695 4.021916 TCGTTTGGGGTAAAAAGGACAAA 58.978 39.130 0.00 0.00 0.00 2.83
4964 5696 4.465305 TCGTTTGGGGTAAAAAGGACAAAA 59.535 37.500 0.00 0.00 30.73 2.44
4965 5697 4.806775 CGTTTGGGGTAAAAAGGACAAAAG 59.193 41.667 0.00 0.00 30.73 2.27
4966 5698 5.394333 CGTTTGGGGTAAAAAGGACAAAAGA 60.394 40.000 0.00 0.00 31.95 2.52
4967 5699 5.862678 TTGGGGTAAAAAGGACAAAAGAG 57.137 39.130 0.00 0.00 0.00 2.85
4968 5700 4.219919 TGGGGTAAAAAGGACAAAAGAGG 58.780 43.478 0.00 0.00 0.00 3.69
4969 5701 3.006537 GGGGTAAAAAGGACAAAAGAGGC 59.993 47.826 0.00 0.00 0.00 4.70
4970 5702 3.305131 GGGTAAAAAGGACAAAAGAGGCG 60.305 47.826 0.00 0.00 0.00 5.52
4971 5703 3.305131 GGTAAAAAGGACAAAAGAGGCGG 60.305 47.826 0.00 0.00 0.00 6.13
4972 5704 0.673985 AAAAGGACAAAAGAGGCGGC 59.326 50.000 0.00 0.00 0.00 6.53
4973 5705 1.179174 AAAGGACAAAAGAGGCGGCC 61.179 55.000 12.11 12.11 0.00 6.13
4974 5706 3.062466 GGACAAAAGAGGCGGCCC 61.062 66.667 17.02 7.43 0.00 5.80
4975 5707 2.282180 GACAAAAGAGGCGGCCCA 60.282 61.111 17.02 0.00 0.00 5.36
4976 5708 2.282462 ACAAAAGAGGCGGCCCAG 60.282 61.111 17.02 1.90 0.00 4.45
4977 5709 3.752339 CAAAAGAGGCGGCCCAGC 61.752 66.667 17.02 5.66 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.593006 GAACAACGATGTCCGCATAGG 59.407 52.381 0.00 0.00 39.40 2.57
43 44 1.203441 ATGAGAGGAAGCTGGTGCCA 61.203 55.000 6.65 0.00 40.80 4.92
76 77 5.068067 TCACGGTATCGATTTCATCCACTAA 59.932 40.000 1.71 0.00 40.11 2.24
77 78 4.581409 TCACGGTATCGATTTCATCCACTA 59.419 41.667 1.71 0.00 40.11 2.74
107 108 2.223272 CGCTGATTACGTGCTCTGTCTA 60.223 50.000 0.00 0.00 0.00 2.59
119 120 2.663602 CGATAGTCATGCCGCTGATTAC 59.336 50.000 0.00 0.00 0.00 1.89
123 124 1.363807 CCGATAGTCATGCCGCTGA 59.636 57.895 0.00 0.00 0.00 4.26
142 143 1.215382 CACGTCATCTTCCTCGGCA 59.785 57.895 0.00 0.00 0.00 5.69
152 153 0.742281 AGCATCACCAGCACGTCATC 60.742 55.000 0.00 0.00 0.00 2.92
172 173 4.409588 CGACCTCACGCGCAAACG 62.410 66.667 5.73 0.82 44.07 3.60
230 231 8.651589 ATCTACTTCGATTCTTATGTCCCATA 57.348 34.615 0.00 0.00 0.00 2.74
237 238 7.008176 CGATGCTGATCTACTTCGATTCTTATG 59.992 40.741 14.40 0.00 36.02 1.90
281 282 0.179009 ATGCCATGATAGTTGCCGCT 60.179 50.000 0.00 0.00 0.00 5.52
285 286 2.730090 GCGCATATGCCATGATAGTTGC 60.730 50.000 21.77 11.13 37.91 4.17
336 337 3.182152 TCCCTTCCAAAACCAAAACCAA 58.818 40.909 0.00 0.00 0.00 3.67
369 370 3.021695 CTCCCACCACGTATGTCTCTTA 58.978 50.000 0.00 0.00 0.00 2.10
370 371 1.825474 CTCCCACCACGTATGTCTCTT 59.175 52.381 0.00 0.00 0.00 2.85
371 372 1.475403 CTCCCACCACGTATGTCTCT 58.525 55.000 0.00 0.00 0.00 3.10
394 395 4.536765 CACCTTGCCTCCCTATGTTTAAT 58.463 43.478 0.00 0.00 0.00 1.40
402 403 3.015145 GCCCACCTTGCCTCCCTA 61.015 66.667 0.00 0.00 0.00 3.53
415 416 1.987855 CTCACCTTCTACCCGCCCA 60.988 63.158 0.00 0.00 0.00 5.36
423 424 3.773119 GGTATGGTTCACCTCACCTTCTA 59.227 47.826 10.68 0.00 37.49 2.10
502 505 1.895798 TCTTGTAGGTGCAGAGACCAG 59.104 52.381 0.00 0.00 38.63 4.00
516 522 5.924356 TGGATGTCTTTGTGACTTCTTGTA 58.076 37.500 10.15 0.00 44.48 2.41
522 528 4.217118 GCATTCTGGATGTCTTTGTGACTT 59.783 41.667 0.00 0.00 45.54 3.01
523 529 3.755378 GCATTCTGGATGTCTTTGTGACT 59.245 43.478 0.00 0.00 45.54 3.41
524 530 3.503363 TGCATTCTGGATGTCTTTGTGAC 59.497 43.478 0.00 0.00 45.54 3.67
541 547 7.763172 TTTTTCTTTTCGTATTGTGTGCATT 57.237 28.000 0.00 0.00 0.00 3.56
585 595 4.020307 TCTCAATAGTTGATCACTGTGGCA 60.020 41.667 8.11 4.15 39.30 4.92
602 612 1.956477 GGTGGTTTGTGTGCTCTCAAT 59.044 47.619 4.31 0.00 0.00 2.57
603 613 1.340502 TGGTGGTTTGTGTGCTCTCAA 60.341 47.619 0.00 0.00 0.00 3.02
631 641 7.599171 AGACCTTTTATGTTTTTCGGGTATTG 58.401 34.615 0.00 0.00 0.00 1.90
634 644 5.706833 GGAGACCTTTTATGTTTTTCGGGTA 59.293 40.000 0.00 0.00 0.00 3.69
679 689 1.665735 CGGCGCTTGTGCACTATTTTT 60.666 47.619 19.41 0.00 39.64 1.94
708 718 6.184789 GGGTAAAACCTATGTTCTTGGATCA 58.815 40.000 0.00 0.00 38.64 2.92
718 728 3.450096 GTCTCTCCGGGTAAAACCTATGT 59.550 47.826 0.00 0.00 38.64 2.29
1018 1035 2.982130 GGAGAGATGTGGTGCCGT 59.018 61.111 0.00 0.00 0.00 5.68
1248 1276 1.301558 GCATCAGCTGCCTATCGCT 60.302 57.895 9.47 0.00 45.66 4.93
1280 1308 2.895404 GGCGGTACATACCTAGAATCCA 59.105 50.000 6.52 0.00 44.25 3.41
1487 1515 1.405105 CAATCAAATCCGGCCATTCGT 59.595 47.619 2.24 0.00 0.00 3.85
1496 1524 1.447317 CGCCCCTCCAATCAAATCCG 61.447 60.000 0.00 0.00 0.00 4.18
1716 1744 1.226945 AACAACTTGTTGCGCCTGC 60.227 52.632 4.18 0.00 39.45 4.85
1839 1867 3.069443 TGCCCCTTCAGATCAAAACAAAC 59.931 43.478 0.00 0.00 0.00 2.93
2013 2064 8.014263 TGGGACAGAGGGAGTATATGTTAATAA 58.986 37.037 0.00 0.00 0.00 1.40
2078 2307 7.598493 CGTCCCAAAATAAATGTCACTGATTTT 59.402 33.333 0.00 0.00 31.55 1.82
2086 2315 4.013728 CCTCCGTCCCAAAATAAATGTCA 58.986 43.478 0.00 0.00 0.00 3.58
2328 2557 9.686683 ATTCTTTATAAGCAAAGAGAGCCTAAA 57.313 29.630 0.00 0.00 43.49 1.85
2553 2782 6.077197 TGAAATAACTCGAAAGTTGAATGCG 58.923 36.000 0.59 0.00 45.37 4.73
2864 3093 0.037790 AGAGACGAAACAGCTGCTCC 60.038 55.000 15.27 1.38 0.00 4.70
2953 3182 4.104383 ACAGCCTCTTCCAATCTTTTGA 57.896 40.909 0.00 0.00 34.60 2.69
3019 3248 5.958380 TGTGAGTCACCTGATCTACCTTTAT 59.042 40.000 20.43 0.00 32.73 1.40
3102 3331 9.569167 CATGAGTCGTACTTGTATAAAGAGAAA 57.431 33.333 0.00 0.00 0.00 2.52
3249 3478 2.738521 CTGTGACGGGGCTCAACG 60.739 66.667 0.00 0.00 0.00 4.10
3267 3496 4.637534 GCAACAAGGTCATACATGATGAGT 59.362 41.667 0.00 0.00 45.46 3.41
3291 3520 0.468226 ACGAAGTTGCAGAAGGTCCA 59.532 50.000 0.00 0.00 37.78 4.02
3330 3559 2.775890 CAAGTGAGAGAACATGGCACT 58.224 47.619 0.00 0.00 41.19 4.40
3333 3562 0.445436 CGCAAGTGAGAGAACATGGC 59.555 55.000 0.00 0.00 0.00 4.40
3336 3565 0.674895 GCCCGCAAGTGAGAGAACAT 60.675 55.000 0.00 0.00 0.00 2.71
3339 3568 2.048222 CGCCCGCAAGTGAGAGAA 60.048 61.111 0.00 0.00 0.00 2.87
3348 3577 1.373748 GTTCAGTAGACGCCCGCAA 60.374 57.895 0.00 0.00 0.00 4.85
3363 3592 1.899142 ACCAGCTTCTCTCTCAGGTTC 59.101 52.381 0.00 0.00 0.00 3.62
3537 3766 3.509137 GACAAGGTCGTCGGCACCA 62.509 63.158 10.54 0.00 36.23 4.17
3716 3947 2.259618 CAAGTCAACGGTACAGATCGG 58.740 52.381 0.00 0.00 31.62 4.18
3719 3950 3.813166 CCAAACAAGTCAACGGTACAGAT 59.187 43.478 0.00 0.00 0.00 2.90
3737 3968 3.196469 TCACTGGTTTTGTTGATGCCAAA 59.804 39.130 0.00 0.00 33.49 3.28
3760 4101 2.543777 TCTTCCACAAAAGACGAGGG 57.456 50.000 0.00 0.00 30.38 4.30
3819 4162 5.705902 TCACAAGAGACAATTGCATCAATG 58.294 37.500 5.05 9.40 34.04 2.82
3940 4329 3.492337 AGGCACTTGAAATTTTACCCGA 58.508 40.909 0.00 0.00 27.25 5.14
4156 4575 1.077501 CTGGACGTTGGCCCATCAT 60.078 57.895 0.00 0.00 0.00 2.45
4332 4751 1.605500 CACGTGAACAATGAATGCCG 58.394 50.000 10.90 0.00 0.00 5.69
4507 4926 2.679837 CACATCGAATCCTCAGGTTTGG 59.320 50.000 0.00 0.00 0.00 3.28
4611 5031 1.542492 AAGTTCAGCAAGGGCATCAG 58.458 50.000 0.00 0.00 44.61 2.90
4896 5628 1.078426 CGGTGGAGTTGGCCTTAGG 60.078 63.158 3.32 0.00 0.00 2.69
4909 5641 4.944372 GATAGGGTCGCGCGGTGG 62.944 72.222 31.69 0.71 0.00 4.61
4910 5642 4.944372 GGATAGGGTCGCGCGGTG 62.944 72.222 31.69 1.17 0.00 4.94
4911 5643 3.779850 TAGGATAGGGTCGCGCGGT 62.780 63.158 31.69 14.72 0.00 5.68
4912 5644 1.874345 AATAGGATAGGGTCGCGCGG 61.874 60.000 31.69 11.75 0.00 6.46
4913 5645 0.456312 GAATAGGATAGGGTCGCGCG 60.456 60.000 26.76 26.76 0.00 6.86
4914 5646 0.456312 CGAATAGGATAGGGTCGCGC 60.456 60.000 0.00 0.00 0.00 6.86
4915 5647 0.170561 CCGAATAGGATAGGGTCGCG 59.829 60.000 0.00 0.00 45.00 5.87
4916 5648 0.108756 GCCGAATAGGATAGGGTCGC 60.109 60.000 0.00 0.00 45.00 5.19
4917 5649 1.473278 GAGCCGAATAGGATAGGGTCG 59.527 57.143 0.00 0.00 39.82 4.79
4918 5650 1.826096 GGAGCCGAATAGGATAGGGTC 59.174 57.143 4.16 4.16 46.96 4.46
4919 5651 1.891450 CGGAGCCGAATAGGATAGGGT 60.891 57.143 2.00 0.00 39.82 4.34
4920 5652 0.818296 CGGAGCCGAATAGGATAGGG 59.182 60.000 2.00 0.00 39.82 3.53
4921 5653 1.546961 ACGGAGCCGAATAGGATAGG 58.453 55.000 16.83 0.00 39.82 2.57
4922 5654 2.414293 CGAACGGAGCCGAATAGGATAG 60.414 54.545 16.83 0.00 39.82 2.08
4923 5655 1.538512 CGAACGGAGCCGAATAGGATA 59.461 52.381 16.83 0.00 39.82 2.59
4924 5656 0.314302 CGAACGGAGCCGAATAGGAT 59.686 55.000 16.83 0.00 44.48 3.24
4925 5657 1.033746 ACGAACGGAGCCGAATAGGA 61.034 55.000 16.83 0.00 45.00 2.94
4926 5658 0.179119 AACGAACGGAGCCGAATAGG 60.179 55.000 16.83 2.71 42.83 2.57
4927 5659 1.323534 CAAACGAACGGAGCCGAATAG 59.676 52.381 16.83 6.94 42.83 1.73
4928 5660 1.352114 CAAACGAACGGAGCCGAATA 58.648 50.000 16.83 0.00 42.83 1.75
4929 5661 1.296056 CCAAACGAACGGAGCCGAAT 61.296 55.000 16.83 3.75 42.83 3.34
4930 5662 1.957186 CCAAACGAACGGAGCCGAA 60.957 57.895 16.83 0.00 42.83 4.30
4931 5663 2.356553 CCAAACGAACGGAGCCGA 60.357 61.111 16.83 0.00 42.83 5.54
4932 5664 3.419759 CCCAAACGAACGGAGCCG 61.420 66.667 7.48 7.48 46.03 5.52
4933 5665 2.453379 TACCCCAAACGAACGGAGCC 62.453 60.000 0.00 0.00 0.00 4.70
4934 5666 0.603439 TTACCCCAAACGAACGGAGC 60.603 55.000 0.00 0.00 0.00 4.70
4935 5667 1.881591 TTTACCCCAAACGAACGGAG 58.118 50.000 0.00 0.00 0.00 4.63
4936 5668 2.338577 TTTTACCCCAAACGAACGGA 57.661 45.000 0.00 0.00 0.00 4.69
4937 5669 2.287728 CCTTTTTACCCCAAACGAACGG 60.288 50.000 0.00 0.00 0.00 4.44
4938 5670 2.617774 TCCTTTTTACCCCAAACGAACG 59.382 45.455 0.00 0.00 0.00 3.95
4939 5671 3.380954 TGTCCTTTTTACCCCAAACGAAC 59.619 43.478 0.00 0.00 0.00 3.95
4940 5672 3.629087 TGTCCTTTTTACCCCAAACGAA 58.371 40.909 0.00 0.00 0.00 3.85
4941 5673 3.294038 TGTCCTTTTTACCCCAAACGA 57.706 42.857 0.00 0.00 0.00 3.85
4942 5674 4.388378 TTTGTCCTTTTTACCCCAAACG 57.612 40.909 0.00 0.00 0.00 3.60
4943 5675 5.979993 TCTTTTGTCCTTTTTACCCCAAAC 58.020 37.500 0.00 0.00 0.00 2.93
4944 5676 5.129650 CCTCTTTTGTCCTTTTTACCCCAAA 59.870 40.000 0.00 0.00 0.00 3.28
4945 5677 4.651962 CCTCTTTTGTCCTTTTTACCCCAA 59.348 41.667 0.00 0.00 0.00 4.12
4946 5678 4.219919 CCTCTTTTGTCCTTTTTACCCCA 58.780 43.478 0.00 0.00 0.00 4.96
4947 5679 3.006537 GCCTCTTTTGTCCTTTTTACCCC 59.993 47.826 0.00 0.00 0.00 4.95
4948 5680 3.305131 CGCCTCTTTTGTCCTTTTTACCC 60.305 47.826 0.00 0.00 0.00 3.69
4949 5681 3.305131 CCGCCTCTTTTGTCCTTTTTACC 60.305 47.826 0.00 0.00 0.00 2.85
4950 5682 3.855895 GCCGCCTCTTTTGTCCTTTTTAC 60.856 47.826 0.00 0.00 0.00 2.01
4951 5683 2.295070 GCCGCCTCTTTTGTCCTTTTTA 59.705 45.455 0.00 0.00 0.00 1.52
4952 5684 1.068588 GCCGCCTCTTTTGTCCTTTTT 59.931 47.619 0.00 0.00 0.00 1.94
4953 5685 0.673985 GCCGCCTCTTTTGTCCTTTT 59.326 50.000 0.00 0.00 0.00 2.27
4954 5686 1.179174 GGCCGCCTCTTTTGTCCTTT 61.179 55.000 0.71 0.00 0.00 3.11
4955 5687 1.603739 GGCCGCCTCTTTTGTCCTT 60.604 57.895 0.71 0.00 0.00 3.36
4956 5688 2.034221 GGCCGCCTCTTTTGTCCT 59.966 61.111 0.71 0.00 0.00 3.85
4957 5689 3.062466 GGGCCGCCTCTTTTGTCC 61.062 66.667 9.86 0.00 0.00 4.02
4958 5690 2.282180 TGGGCCGCCTCTTTTGTC 60.282 61.111 9.86 0.00 0.00 3.18
4959 5691 2.282462 CTGGGCCGCCTCTTTTGT 60.282 61.111 9.86 0.00 0.00 2.83
4960 5692 3.752339 GCTGGGCCGCCTCTTTTG 61.752 66.667 9.86 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.