Multiple sequence alignment - TraesCS4D01G297200

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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 TraesCS4D01G297200 chr4D 100.000 4774 0 0 1 4774 466291512 466296285 0.000000e+00 8817.0
1 TraesCS4D01G297200 chr4D 90.220 1769 123 30 2506 4249 466335876 466337619 0.000000e+00 2263.0
2 TraesCS4D01G297200 chr4D 86.724 1853 115 61 707 2481 466334087 466335886 0.000000e+00 1938.0
3 TraesCS4D01G297200 chr4D 89.519 1393 96 29 904 2269 466730916 466729547 0.000000e+00 1718.0
4 TraesCS4D01G297200 chr4D 88.073 1484 109 45 2348 3795 466405058 466406509 0.000000e+00 1698.0
5 TraesCS4D01G297200 chr4D 85.429 1551 95 51 701 2176 466403088 466404582 0.000000e+00 1491.0
6 TraesCS4D01G297200 chr4D 92.735 234 17 0 2602 2835 466728702 466728469 5.920000e-89 339.0
7 TraesCS4D01G297200 chr4D 87.425 167 10 6 2182 2348 466404849 466405004 1.060000e-41 182.0
8 TraesCS4D01G297200 chr4D 88.652 141 5 9 2333 2470 466729030 466728898 1.370000e-35 161.0
9 TraesCS4D01G297200 chr4B 87.046 3219 202 106 707 3795 584125610 584128743 0.000000e+00 3435.0
10 TraesCS4D01G297200 chr4B 87.979 2504 153 69 15 2440 583764629 583767062 0.000000e+00 2820.0
11 TraesCS4D01G297200 chr4B 91.246 1782 123 16 2600 4356 583767406 583769179 0.000000e+00 2396.0
12 TraesCS4D01G297200 chr4B 86.344 1860 111 64 707 2481 584054245 584056046 0.000000e+00 1895.0
13 TraesCS4D01G297200 chr4B 90.352 1306 82 27 2558 3829 584056123 584057418 0.000000e+00 1674.0
14 TraesCS4D01G297200 chr4B 91.340 843 66 3 2946 3781 584527788 584526946 0.000000e+00 1146.0
15 TraesCS4D01G297200 chr4B 90.656 610 41 9 904 1510 584529935 584529339 0.000000e+00 797.0
16 TraesCS4D01G297200 chr4B 88.015 534 58 4 3831 4358 584057697 584058230 1.130000e-175 627.0
17 TraesCS4D01G297200 chr4B 85.302 381 48 6 4363 4737 583769226 583769604 2.080000e-103 387.0
18 TraesCS4D01G297200 chr4B 89.062 64 2 5 2875 2938 584527907 584527849 1.840000e-09 75.0
19 TraesCS4D01G297200 chr4A 91.326 2179 115 31 15 2160 4476184 4474047 0.000000e+00 2909.0
20 TraesCS4D01G297200 chr4A 89.748 2146 125 44 15 2100 4242416 4240306 0.000000e+00 2656.0
21 TraesCS4D01G297200 chr4A 92.025 1793 103 19 2600 4356 4239470 4237682 0.000000e+00 2483.0
22 TraesCS4D01G297200 chr4A 90.197 1775 133 25 2600 4358 4473169 4471420 0.000000e+00 2276.0
23 TraesCS4D01G297200 chr4A 88.991 1408 88 33 787 2154 4157676 4159056 0.000000e+00 1679.0
24 TraesCS4D01G297200 chr4A 91.847 1202 77 16 2606 3795 4194494 4193302 0.000000e+00 1657.0
25 TraesCS4D01G297200 chr4A 90.336 1221 58 23 903 2073 4196461 4195251 0.000000e+00 1546.0
26 TraesCS4D01G297200 chr4A 91.885 838 56 4 2946 3781 4160357 4161184 0.000000e+00 1160.0
27 TraesCS4D01G297200 chr4A 96.947 262 8 0 1547 1808 4005000 4004739 1.580000e-119 440.0
28 TraesCS4D01G297200 chr4A 93.617 235 15 0 2602 2836 4159928 4160162 7.600000e-93 351.0
29 TraesCS4D01G297200 chr4A 83.273 275 14 16 2227 2499 4474021 4473777 1.730000e-54 224.0
30 TraesCS4D01G297200 chr4A 90.446 157 12 1 2386 2542 4194790 4194637 2.250000e-48 204.0
31 TraesCS4D01G297200 chr4A 83.429 175 15 7 707 874 4196744 4196577 2.980000e-32 150.0
32 TraesCS4D01G297200 chrUn 90.814 381 20 6 1573 1938 479224296 479223916 3.320000e-136 496.0
33 TraesCS4D01G297200 chr3D 85.194 412 57 1 4363 4774 592522314 592521907 2.050000e-113 420.0
34 TraesCS4D01G297200 chr1D 85.024 414 55 6 4363 4774 344617394 344616986 9.560000e-112 414.0
35 TraesCS4D01G297200 chr1D 85.946 370 47 2 4405 4774 204049639 204049275 1.610000e-104 390.0
36 TraesCS4D01G297200 chr5B 84.951 412 57 4 4363 4774 531631142 531631548 3.440000e-111 412.0
37 TraesCS4D01G297200 chr5B 80.120 166 30 3 502 665 64426350 64426186 2.330000e-23 121.0
38 TraesCS4D01G297200 chr2D 83.698 411 62 3 4363 4773 80420464 80420059 2.700000e-102 383.0
39 TraesCS4D01G297200 chr1A 83.005 406 61 4 4369 4774 259067538 259067141 1.260000e-95 361.0
40 TraesCS4D01G297200 chr1A 73.362 229 53 6 300 525 9088264 9088041 1.420000e-10 78.7
41 TraesCS4D01G297200 chr1B 82.039 412 69 4 4363 4774 447307015 447306609 3.540000e-91 346.0
42 TraesCS4D01G297200 chr2A 82.082 413 65 5 4363 4774 502270551 502270147 1.270000e-90 344.0
43 TraesCS4D01G297200 chr2A 75.897 390 68 14 300 674 367684600 367684978 4.910000e-40 176.0
44 TraesCS4D01G297200 chr5D 75.904 415 91 7 252 662 66611382 66611791 2.250000e-48 204.0
45 TraesCS4D01G297200 chr5D 78.261 207 27 7 482 673 99417939 99417736 3.020000e-22 117.0
46 TraesCS4D01G297200 chr5A 74.638 414 92 9 258 665 57649398 57648992 2.280000e-38 171.0
47 TraesCS4D01G297200 chr5A 79.808 208 26 7 482 673 103569897 103570104 2.320000e-28 137.0
48 TraesCS4D01G297200 chr2B 84.337 83 8 4 3751 3833 692624959 692624882 5.120000e-10 76.8


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 TraesCS4D01G297200 chr4D 466291512 466296285 4773 False 8817.000000 8817 100.000000 1 4774 1 chr4D.!!$F1 4773
1 TraesCS4D01G297200 chr4D 466334087 466337619 3532 False 2100.500000 2263 88.472000 707 4249 2 chr4D.!!$F2 3542
2 TraesCS4D01G297200 chr4D 466403088 466406509 3421 False 1123.666667 1698 86.975667 701 3795 3 chr4D.!!$F3 3094
3 TraesCS4D01G297200 chr4D 466728469 466730916 2447 True 739.333333 1718 90.302000 904 2835 3 chr4D.!!$R1 1931
4 TraesCS4D01G297200 chr4B 584125610 584128743 3133 False 3435.000000 3435 87.046000 707 3795 1 chr4B.!!$F1 3088
5 TraesCS4D01G297200 chr4B 583764629 583769604 4975 False 1867.666667 2820 88.175667 15 4737 3 chr4B.!!$F2 4722
6 TraesCS4D01G297200 chr4B 584054245 584058230 3985 False 1398.666667 1895 88.237000 707 4358 3 chr4B.!!$F3 3651
7 TraesCS4D01G297200 chr4B 584526946 584529935 2989 True 672.666667 1146 90.352667 904 3781 3 chr4B.!!$R1 2877
8 TraesCS4D01G297200 chr4A 4237682 4242416 4734 True 2569.500000 2656 90.886500 15 4356 2 chr4A.!!$R3 4341
9 TraesCS4D01G297200 chr4A 4471420 4476184 4764 True 1803.000000 2909 88.265333 15 4358 3 chr4A.!!$R4 4343
10 TraesCS4D01G297200 chr4A 4157676 4161184 3508 False 1063.333333 1679 91.497667 787 3781 3 chr4A.!!$F1 2994
11 TraesCS4D01G297200 chr4A 4193302 4196744 3442 True 889.250000 1657 89.014500 707 3795 4 chr4A.!!$R2 3088

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
951 1111 0.108186 GCACACATCCCTCGATCACA 60.108 55.000 0.00 0.00 0.00 3.58 F
2305 3823 2.158726 ACCGCCTTGACTTTTCAACCTA 60.159 45.455 0.00 0.00 36.79 3.08 F
2889 5187 1.660607 TCGTAGAAGCGTACGTTCGAT 59.339 47.619 19.16 9.49 44.94 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2869 5153 1.067693 TCGAACGTACGCTTCTACGA 58.932 50.0 16.72 13.83 41.75 3.43 R
3716 6109 0.321653 AAAGCTCGGCGATCCAGTTT 60.322 50.0 11.27 0.00 0.00 2.66 R
4744 7487 0.104304 ACATTAGTAGGAAGCGGCCG 59.896 55.0 24.05 24.05 0.00 6.13 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
34 35 9.550406 ACATTGAAATAGCCCATGATTAATTTG 57.450 29.630 0.00 0.00 0.00 2.32
82 83 5.412904 TGCATGTGTGATTTTATACGGACAA 59.587 36.000 0.00 0.00 0.00 3.18
159 163 4.141287 CCCCAACTTGAAGTGTCAACATA 58.859 43.478 0.00 0.00 38.88 2.29
185 189 5.440207 AATTTTATAGGGGTACACACCGT 57.560 39.130 0.00 0.00 46.41 4.83
247 252 2.882876 GCACCTGCATGCTGGAAG 59.117 61.111 40.39 31.83 42.62 3.46
256 261 2.042831 ATGCTGGAAGTTCGCTGGC 61.043 57.895 4.67 3.52 35.30 4.85
327 333 2.798148 AAGTCGTTGGATCCCGCACC 62.798 60.000 9.90 0.00 0.00 5.01
348 354 4.407296 ACCAGGGCACATCAAGTTTAAAAA 59.593 37.500 0.00 0.00 0.00 1.94
352 358 7.307930 CCAGGGCACATCAAGTTTAAAAATTTC 60.308 37.037 0.00 0.00 0.00 2.17
393 400 9.191995 GATTTTGTCCGTCATAGTTTTTGAAAT 57.808 29.630 0.00 0.00 0.00 2.17
399 406 9.106070 GTCCGTCATAGTTTTTGAAATATAGGT 57.894 33.333 0.00 0.00 0.00 3.08
414 421 2.243602 TAGGTTTTTGTCGGTCGCTT 57.756 45.000 0.00 0.00 0.00 4.68
429 436 3.187842 GGTCGCTTGTACCAAGTTTTAGG 59.812 47.826 5.92 0.00 36.96 2.69
470 477 0.457851 TTTTGTTGGCCACTGGTTCG 59.542 50.000 3.88 0.00 0.00 3.95
512 519 3.607209 GTCGCTCGTACCAAGTTCTAAAG 59.393 47.826 0.00 0.00 0.00 1.85
595 602 6.386654 GTCACCGGAAACACAAATATGAAAT 58.613 36.000 9.46 0.00 0.00 2.17
712 744 1.369091 CGACCTAGCTGCGGCATTTT 61.369 55.000 21.93 0.35 41.70 1.82
759 791 6.036735 CGTTTTCTAAGAGACACAGTGGAAAA 59.963 38.462 5.31 6.53 31.80 2.29
890 1050 1.038130 TCTCTCGCAGCCTTCCTACC 61.038 60.000 0.00 0.00 0.00 3.18
951 1111 0.108186 GCACACATCCCTCGATCACA 60.108 55.000 0.00 0.00 0.00 3.58
1784 2049 4.377841 GCTATTGATCTAGCCAACGAATGC 60.378 45.833 3.17 0.00 38.54 3.56
1931 2224 3.372206 AGCTATCGTACTCGTGTAAACGT 59.628 43.478 5.14 0.00 38.33 3.99
1950 2243 5.291293 ACGTGTGTATACAAGGAAATTGC 57.709 39.130 7.25 0.00 43.15 3.56
1953 2246 5.095490 GTGTGTATACAAGGAAATTGCAGC 58.905 41.667 7.25 0.00 43.15 5.25
1991 2284 5.551233 AGCAAGTTCACACAGAGCTTATAA 58.449 37.500 0.00 0.00 44.72 0.98
2002 2295 9.248291 CACACAGAGCTTATAACAAAACAAAAT 57.752 29.630 0.00 0.00 0.00 1.82
2088 2644 5.437289 AATACATGCCATATTTGGTGACG 57.563 39.130 4.00 0.00 45.57 4.35
2120 2950 2.885894 AGATTTCGGAGAGTCGGATACC 59.114 50.000 0.00 0.00 38.43 2.73
2218 3316 5.778750 AGTTTAGCTAACCTAGACCAGACAA 59.221 40.000 5.45 0.00 37.46 3.18
2246 3344 3.493524 GCCTAGGTAGGTCTCTTGCATTC 60.494 52.174 11.31 0.00 45.42 2.67
2305 3823 2.158726 ACCGCCTTGACTTTTCAACCTA 60.159 45.455 0.00 0.00 36.79 3.08
2309 3827 3.502595 GCCTTGACTTTTCAACCTACCTC 59.497 47.826 0.00 0.00 36.79 3.85
2311 3829 4.445735 CCTTGACTTTTCAACCTACCTCCA 60.446 45.833 0.00 0.00 36.79 3.86
2312 3830 4.781775 TGACTTTTCAACCTACCTCCAA 57.218 40.909 0.00 0.00 0.00 3.53
2331 3916 6.015688 CCTCCAAGCATGAGCAATTTATATGT 60.016 38.462 0.00 0.00 45.49 2.29
2574 4808 2.947127 AGAGAAGCATATGGAAGGGC 57.053 50.000 4.56 0.00 0.00 5.19
2869 5153 8.677300 AGAATTCATGCACGTATACAGAAAATT 58.323 29.630 8.44 0.06 0.00 1.82
2886 5184 4.812862 AAATTCGTAGAAGCGTACGTTC 57.187 40.909 17.90 17.56 45.90 3.95
2889 5187 1.660607 TCGTAGAAGCGTACGTTCGAT 59.339 47.619 19.16 9.49 44.94 3.59
2890 5188 2.857748 TCGTAGAAGCGTACGTTCGATA 59.142 45.455 19.16 6.36 44.94 2.92
2891 5189 2.954529 CGTAGAAGCGTACGTTCGATAC 59.045 50.000 19.16 15.02 40.75 2.24
2895 5193 2.635141 AGCGTACGTTCGATACTACG 57.365 50.000 19.16 8.81 43.08 3.51
3030 5400 2.288825 GGTGTCCAAGTTCATCGAGTCA 60.289 50.000 0.00 0.00 0.00 3.41
3385 5756 2.357009 AGCCTGCGATTATCTTTTGCTG 59.643 45.455 0.00 0.00 0.00 4.41
3387 5758 2.357009 CCTGCGATTATCTTTTGCTGCT 59.643 45.455 0.00 0.00 0.00 4.24
3388 5759 3.360533 CTGCGATTATCTTTTGCTGCTG 58.639 45.455 0.00 0.00 0.00 4.41
3424 5812 4.155950 TGCTGACGTGCATTGGTT 57.844 50.000 0.00 0.00 38.12 3.67
3441 5834 3.849064 TTTTTGGCAGTGGGACGG 58.151 55.556 0.00 0.00 0.00 4.79
3797 6190 2.182904 TACGTACGCATAGCACAGTG 57.817 50.000 16.72 0.00 0.00 3.66
3869 6555 1.364626 CCGAGTCTGTACGTACGCCT 61.365 60.000 20.18 14.82 0.00 5.52
3877 6563 3.312421 TCTGTACGTACGCCTGGTATAAC 59.688 47.826 20.18 0.80 32.74 1.89
3927 6616 1.176527 CGTGATTCCATTGGTGGCTT 58.823 50.000 1.86 0.00 45.63 4.35
4079 6768 0.106708 CTCCGCATTGGGCTAGCTTA 59.893 55.000 15.72 0.55 41.67 3.09
4148 6840 2.093764 CCTTTGTTGTTGGCACCTTTGA 60.094 45.455 0.00 0.00 0.00 2.69
4150 6842 2.957491 TGTTGTTGGCACCTTTGAAG 57.043 45.000 0.00 0.00 0.00 3.02
4183 6878 1.611673 CGTTGTCTTCAGAAGGGCCAT 60.612 52.381 6.18 0.00 0.00 4.40
4211 6906 1.492133 TTGCTGCTACCCTCAAGGCT 61.492 55.000 0.00 0.00 40.58 4.58
4221 6916 0.321653 CCTCAAGGCTTGCCGTAACT 60.322 55.000 22.31 0.00 0.00 2.24
4283 6979 1.452110 TCACATCGATGTTTGGCTGG 58.548 50.000 28.04 14.98 39.39 4.85
4314 7011 2.412591 CCCCATCTCAACCCTATGACT 58.587 52.381 0.00 0.00 0.00 3.41
4358 7055 0.950836 CATTGGTCGCCAACAACTGA 59.049 50.000 12.53 0.00 46.95 3.41
4360 7057 0.107410 TTGGTCGCCAACAACTGAGT 60.107 50.000 7.15 0.00 38.75 3.41
4365 7102 3.547413 GGTCGCCAACAACTGAGTTAAAC 60.547 47.826 0.00 0.00 0.00 2.01
4377 7114 3.386486 TGAGTTAAACACTGCTACCACG 58.614 45.455 0.00 0.00 35.01 4.94
4378 7115 2.140717 AGTTAAACACTGCTACCACGC 58.859 47.619 0.00 0.00 32.83 5.34
4386 7123 3.127533 GCTACCACGCCCTTGCAG 61.128 66.667 0.00 0.00 37.32 4.41
4390 7127 0.037590 TACCACGCCCTTGCAGAATT 59.962 50.000 0.00 0.00 37.32 2.17
4400 7137 3.119029 CCCTTGCAGAATTTGTACATGGG 60.119 47.826 0.00 4.03 38.78 4.00
4403 7140 3.505386 TGCAGAATTTGTACATGGGGTT 58.495 40.909 0.00 0.00 0.00 4.11
4410 7147 3.748645 TTGTACATGGGGTTTAGGCAT 57.251 42.857 0.00 0.00 0.00 4.40
4411 7148 3.011566 TGTACATGGGGTTTAGGCATG 57.988 47.619 0.00 0.00 0.00 4.06
4418 7155 1.272480 GGGGTTTAGGCATGTGGACTT 60.272 52.381 0.00 0.00 35.43 3.01
4420 7157 2.514803 GGTTTAGGCATGTGGACTTGT 58.485 47.619 0.00 0.00 35.43 3.16
4428 7165 2.414559 GCATGTGGACTTGTTCATTCGG 60.415 50.000 0.00 0.00 0.00 4.30
4440 7177 5.598416 TGTTCATTCGGACATACTCATCT 57.402 39.130 0.00 0.00 0.00 2.90
4443 7180 7.371159 TGTTCATTCGGACATACTCATCTATC 58.629 38.462 0.00 0.00 0.00 2.08
4453 7190 5.417266 ACATACTCATCTATCAGATCACCGG 59.583 44.000 0.00 0.00 31.32 5.28
4459 7196 4.180377 TCTATCAGATCACCGGGTACTT 57.820 45.455 6.32 0.00 0.00 2.24
4489 7226 1.945387 CATCCGAATAGCTGCAGTGT 58.055 50.000 16.64 5.74 0.00 3.55
4508 7245 7.093333 TGCAGTGTATTTCTGATAAGAGGAGAA 60.093 37.037 0.00 0.00 35.20 2.87
4509 7246 7.766278 GCAGTGTATTTCTGATAAGAGGAGAAA 59.234 37.037 0.00 0.00 39.42 2.52
4520 7257 7.689299 TGATAAGAGGAGAAACCAATCTTTCA 58.311 34.615 0.00 0.00 42.04 2.69
4522 7259 5.310409 AGAGGAGAAACCAATCTTTCACA 57.690 39.130 0.00 0.00 42.04 3.58
4523 7260 5.694995 AGAGGAGAAACCAATCTTTCACAA 58.305 37.500 0.00 0.00 42.04 3.33
4525 7262 4.829492 AGGAGAAACCAATCTTTCACAAGG 59.171 41.667 0.00 0.00 42.04 3.61
4526 7263 4.550422 GAGAAACCAATCTTTCACAAGGC 58.450 43.478 0.00 0.00 33.26 4.35
4552 7289 2.742053 TCCTTGCACTCGAAATAGTTGC 59.258 45.455 0.00 0.00 0.00 4.17
4554 7291 1.075542 TGCACTCGAAATAGTTGCCG 58.924 50.000 0.00 0.00 0.00 5.69
4556 7293 2.264813 GCACTCGAAATAGTTGCCGTA 58.735 47.619 0.00 0.00 0.00 4.02
4579 7316 2.854032 CCACCCCCGGCTGGATAT 60.854 66.667 15.09 0.00 37.49 1.63
4582 7319 4.351054 CCCCCGGCTGGATATGGC 62.351 72.222 15.09 0.00 37.49 4.40
4599 7336 1.373570 GGCTGAACACATGTCTAGCC 58.626 55.000 18.20 18.20 44.20 3.93
4600 7337 1.002366 GCTGAACACATGTCTAGCCG 58.998 55.000 0.00 0.00 33.53 5.52
4602 7339 2.688507 CTGAACACATGTCTAGCCGTT 58.311 47.619 0.00 0.00 0.00 4.44
4607 7344 0.892755 ACATGTCTAGCCGTTCGGAA 59.107 50.000 15.69 1.24 0.00 4.30
4632 7369 1.538075 CGCCGGAATAGGTTGTGTTTT 59.462 47.619 5.05 0.00 0.00 2.43
4633 7370 2.030628 CGCCGGAATAGGTTGTGTTTTT 60.031 45.455 5.05 0.00 0.00 1.94
4646 7383 1.197036 GTGTTTTTAGAGCGGGTCAGC 59.803 52.381 10.15 0.00 37.41 4.26
4652 7389 4.500116 GAGCGGGTCAGCGGACTC 62.500 72.222 16.66 12.08 43.77 3.36
4662 7399 2.229302 GTCAGCGGACTCAAAGTAGTCT 59.771 50.000 9.95 0.00 44.42 3.24
4666 7403 2.338500 CGGACTCAAAGTAGTCTTGCC 58.662 52.381 4.20 0.00 44.42 4.52
4692 7429 3.383092 GCAATGGCCTCTCTCTCTG 57.617 57.895 3.32 0.00 0.00 3.35
4694 7431 1.743091 GCAATGGCCTCTCTCTCTGTG 60.743 57.143 3.32 0.00 0.00 3.66
4696 7433 1.949799 ATGGCCTCTCTCTCTGTGTT 58.050 50.000 3.32 0.00 0.00 3.32
4701 7444 2.064762 CCTCTCTCTCTGTGTTTTGCG 58.935 52.381 0.00 0.00 0.00 4.85
4708 7451 4.756642 TCTCTCTGTGTTTTGCGATTCAAT 59.243 37.500 0.00 0.00 34.12 2.57
4709 7452 4.786507 TCTCTGTGTTTTGCGATTCAATG 58.213 39.130 0.00 0.00 34.12 2.82
4710 7453 3.307674 TCTGTGTTTTGCGATTCAATGC 58.692 40.909 0.00 0.00 34.12 3.56
4712 7455 2.223900 TGTGTTTTGCGATTCAATGCCA 60.224 40.909 0.00 0.00 34.12 4.92
4722 7465 2.057137 TTCAATGCCAGAGTATGCCC 57.943 50.000 0.00 0.00 0.00 5.36
4741 7484 4.237207 GGGATCGAGCCCCCGAAC 62.237 72.222 28.96 0.78 42.62 3.95
4742 7485 3.467226 GGATCGAGCCCCCGAACA 61.467 66.667 9.02 0.00 42.22 3.18
4743 7486 2.808206 GGATCGAGCCCCCGAACAT 61.808 63.158 9.02 0.00 42.22 2.71
4744 7487 1.301009 GATCGAGCCCCCGAACATC 60.301 63.158 0.00 0.00 42.22 3.06
4745 7488 3.151958 ATCGAGCCCCCGAACATCG 62.152 63.158 0.00 0.00 42.22 3.84
4754 7497 3.564027 CGAACATCGGCCGCTTCC 61.564 66.667 23.51 7.30 36.00 3.46
4755 7498 2.125106 GAACATCGGCCGCTTCCT 60.125 61.111 23.51 2.81 0.00 3.36
4756 7499 1.143183 GAACATCGGCCGCTTCCTA 59.857 57.895 23.51 1.11 0.00 2.94
4757 7500 1.152383 GAACATCGGCCGCTTCCTAC 61.152 60.000 23.51 4.52 0.00 3.18
4758 7501 1.614241 AACATCGGCCGCTTCCTACT 61.614 55.000 23.51 0.00 0.00 2.57
4759 7502 0.754217 ACATCGGCCGCTTCCTACTA 60.754 55.000 23.51 0.00 0.00 1.82
4760 7503 0.387929 CATCGGCCGCTTCCTACTAA 59.612 55.000 23.51 0.00 0.00 2.24
4761 7504 1.000955 CATCGGCCGCTTCCTACTAAT 59.999 52.381 23.51 0.61 0.00 1.73
4762 7505 0.387929 TCGGCCGCTTCCTACTAATG 59.612 55.000 23.51 0.00 0.00 1.90
4763 7506 0.104304 CGGCCGCTTCCTACTAATGT 59.896 55.000 14.67 0.00 0.00 2.71
4764 7507 1.583054 GGCCGCTTCCTACTAATGTG 58.417 55.000 0.00 0.00 0.00 3.21
4765 7508 1.583054 GCCGCTTCCTACTAATGTGG 58.417 55.000 0.00 0.00 0.00 4.17
4766 7509 1.134491 GCCGCTTCCTACTAATGTGGT 60.134 52.381 0.00 0.00 0.00 4.16
4767 7510 2.822764 CCGCTTCCTACTAATGTGGTC 58.177 52.381 0.00 0.00 0.00 4.02
4768 7511 2.167693 CCGCTTCCTACTAATGTGGTCA 59.832 50.000 0.00 0.00 0.00 4.02
4769 7512 3.181465 CCGCTTCCTACTAATGTGGTCAT 60.181 47.826 0.00 0.00 35.59 3.06
4770 7513 3.804325 CGCTTCCTACTAATGTGGTCATG 59.196 47.826 0.00 0.00 34.19 3.07
4771 7514 4.130118 GCTTCCTACTAATGTGGTCATGG 58.870 47.826 0.00 0.00 34.19 3.66
4772 7515 4.141711 GCTTCCTACTAATGTGGTCATGGA 60.142 45.833 0.00 0.00 34.19 3.41
4773 7516 5.353394 TTCCTACTAATGTGGTCATGGAC 57.647 43.478 0.00 0.00 34.19 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.520874 TGGGCTATTTCAATGTTTTGTCGA 59.479 37.500 0.00 0.00 34.32 4.20
2 3 6.397272 TCATGGGCTATTTCAATGTTTTGTC 58.603 36.000 0.00 0.00 34.32 3.18
3 4 6.357579 TCATGGGCTATTTCAATGTTTTGT 57.642 33.333 0.00 0.00 34.32 2.83
8 9 9.550406 CAAATTAATCATGGGCTATTTCAATGT 57.450 29.630 0.00 0.00 0.00 2.71
9 10 9.550406 ACAAATTAATCATGGGCTATTTCAATG 57.450 29.630 0.00 0.00 0.00 2.82
34 35 2.140717 CACTTCGAGTTGGGGTGTTAC 58.859 52.381 0.00 0.00 0.00 2.50
82 83 6.597832 TCAAATAAAACGATTTGGACCCAT 57.402 33.333 0.28 0.00 43.87 4.00
159 163 6.993902 CGGTGTGTACCCCTATAAAATTACAT 59.006 38.462 0.00 0.00 44.53 2.29
185 189 4.610605 TCCACCTAGAACGAAAATGACA 57.389 40.909 0.00 0.00 0.00 3.58
327 333 7.226325 TGAAATTTTTAAACTTGATGTGCCCTG 59.774 33.333 0.00 0.00 0.00 4.45
352 358 6.785164 CGGACAAAATCGCAAGTTTAAAAATG 59.215 34.615 0.00 0.00 39.48 2.32
393 400 3.598019 AGCGACCGACAAAAACCTATA 57.402 42.857 0.00 0.00 0.00 1.31
399 406 1.598601 GGTACAAGCGACCGACAAAAA 59.401 47.619 0.00 0.00 0.00 1.94
414 421 7.663043 AATTTCAACCCTAAAACTTGGTACA 57.337 32.000 0.00 0.00 0.00 2.90
533 540 6.908825 TGAGATCCGTTTTAATGAGTTTTGG 58.091 36.000 0.00 0.00 0.00 3.28
544 551 6.940298 AGGTCTTTCAAATGAGATCCGTTTTA 59.060 34.615 0.00 0.00 31.92 1.52
549 556 3.624861 CCAGGTCTTTCAAATGAGATCCG 59.375 47.826 0.00 0.00 0.00 4.18
643 651 5.774498 TCCTCTTTTTCTCTTGGCTTTTC 57.226 39.130 0.00 0.00 0.00 2.29
951 1111 1.941209 GCTGTGTGTGTGGTGATCGAT 60.941 52.381 0.00 0.00 0.00 3.59
1236 1421 2.049802 TCGTCGCGGTTCTTCCAC 60.050 61.111 6.13 0.00 35.57 4.02
1784 2049 3.683937 CCTTGGTTTGCCTGGGCG 61.684 66.667 7.14 0.00 45.51 6.13
1931 2224 4.764308 TGCTGCAATTTCCTTGTATACACA 59.236 37.500 4.68 0.00 37.18 3.72
1950 2243 3.852286 TGCTTGGCATATTCTTTTGCTG 58.148 40.909 0.00 0.00 38.88 4.41
1953 2246 5.927689 TGAACTTGCTTGGCATATTCTTTTG 59.072 36.000 13.48 0.00 38.76 2.44
2088 2644 3.119101 TCTCCGAAATCTCTAAGGCACAC 60.119 47.826 0.00 0.00 0.00 3.82
2179 3277 9.777575 GTTAGCTAAACTGTCTACTCTAGAAAG 57.222 37.037 7.99 0.00 44.21 2.62
2180 3278 8.738106 GGTTAGCTAAACTGTCTACTCTAGAAA 58.262 37.037 14.49 0.00 38.23 2.52
2188 3286 6.376581 TGGTCTAGGTTAGCTAAACTGTCTAC 59.623 42.308 30.27 21.01 38.23 2.59
2246 3344 5.332355 GCGTCTAGTGTACTTTGAACTTGTG 60.332 44.000 0.00 0.00 0.00 3.33
2305 3823 2.226962 AATTGCTCATGCTTGGAGGT 57.773 45.000 0.00 0.00 40.48 3.85
2309 3827 6.509656 ACACATATAAATTGCTCATGCTTGG 58.490 36.000 0.00 0.00 40.48 3.61
2311 3829 7.067859 AGTGACACATATAAATTGCTCATGCTT 59.932 33.333 8.59 0.00 40.48 3.91
2312 3830 6.544931 AGTGACACATATAAATTGCTCATGCT 59.455 34.615 8.59 0.00 40.48 3.79
2356 4057 9.912634 ACTAATGGTCAAACATGAAATACTTTG 57.087 29.630 0.00 0.00 0.00 2.77
2359 4060 8.879759 CGTACTAATGGTCAAACATGAAATACT 58.120 33.333 0.00 0.00 0.00 2.12
2360 4061 8.662141 ACGTACTAATGGTCAAACATGAAATAC 58.338 33.333 0.00 0.00 0.00 1.89
2361 4062 8.780846 ACGTACTAATGGTCAAACATGAAATA 57.219 30.769 0.00 0.00 0.00 1.40
2362 4063 7.681939 ACGTACTAATGGTCAAACATGAAAT 57.318 32.000 0.00 0.00 0.00 2.17
2365 4066 5.808540 GCTACGTACTAATGGTCAAACATGA 59.191 40.000 0.00 0.00 0.00 3.07
2543 4367 3.526931 TGCTTCTCTAAATCAGGGACG 57.473 47.619 0.00 0.00 31.63 4.79
2869 5153 1.067693 TCGAACGTACGCTTCTACGA 58.932 50.000 16.72 13.83 41.75 3.43
2889 5187 3.541996 TGAGTCCCGATGTACGTAGTA 57.458 47.619 0.00 0.00 45.11 1.82
2891 5189 2.941064 TCTTGAGTCCCGATGTACGTAG 59.059 50.000 0.00 0.00 40.78 3.51
2895 5193 3.587797 TGTTCTTGAGTCCCGATGTAC 57.412 47.619 0.00 0.00 0.00 2.90
3030 5400 1.133976 GGCAGCTTCCATGACAGGTAT 60.134 52.381 0.00 0.00 0.00 2.73
3361 5731 4.214971 AGCAAAAGATAATCGCAGGCTATG 59.785 41.667 0.00 0.00 0.00 2.23
3424 5812 1.076632 ACCGTCCCACTGCCAAAAA 60.077 52.632 0.00 0.00 0.00 1.94
3441 5834 4.176752 GGGGATCAGCGGGTGGAC 62.177 72.222 7.42 2.04 0.00 4.02
3566 5959 1.456331 CCCCATCATGGCCTTCACC 60.456 63.158 3.32 0.00 35.79 4.02
3626 6019 2.186903 CAGTGGCGGCGGTAGAAT 59.813 61.111 9.78 0.00 0.00 2.40
3716 6109 0.321653 AAAGCTCGGCGATCCAGTTT 60.322 50.000 11.27 0.00 0.00 2.66
3797 6190 1.542544 GTACGTAGGACGATGTGTGC 58.457 55.000 5.94 0.00 46.05 4.57
4021 6710 5.437191 AAACTAGCCAGCCTAAAGTACAT 57.563 39.130 0.00 0.00 0.00 2.29
4064 6753 9.143631 CAAATAATAAATAAGCTAGCCCAATGC 57.856 33.333 12.13 0.00 41.71 3.56
4183 6878 1.002134 GTAGCAGCAAAGGAGGGCA 60.002 57.895 0.00 0.00 0.00 5.36
4191 6886 0.609131 GCCTTGAGGGTAGCAGCAAA 60.609 55.000 0.00 0.00 37.43 3.68
4301 6998 2.554344 GGGCAAACAGTCATAGGGTTGA 60.554 50.000 0.00 0.00 0.00 3.18
4314 7011 2.915137 GGGCTTTCCGGGCAAACA 60.915 61.111 0.00 0.00 0.00 2.83
4358 7055 2.140717 GCGTGGTAGCAGTGTTTAACT 58.859 47.619 0.00 0.00 40.93 2.24
4360 7057 1.515081 GGCGTGGTAGCAGTGTTTAA 58.485 50.000 0.00 0.00 39.27 1.52
4365 7102 2.034879 CAAGGGCGTGGTAGCAGTG 61.035 63.158 0.00 0.00 39.27 3.66
4377 7114 3.514645 CATGTACAAATTCTGCAAGGGC 58.485 45.455 0.00 0.00 41.68 5.19
4378 7115 3.119029 CCCATGTACAAATTCTGCAAGGG 60.119 47.826 0.00 1.67 32.78 3.95
4386 7123 4.464597 TGCCTAAACCCCATGTACAAATTC 59.535 41.667 0.00 0.00 0.00 2.17
4390 7127 3.245443 ACATGCCTAAACCCCATGTACAA 60.245 43.478 0.00 0.00 45.43 2.41
4400 7137 2.514803 ACAAGTCCACATGCCTAAACC 58.485 47.619 0.00 0.00 0.00 3.27
4403 7140 3.500448 TGAACAAGTCCACATGCCTAA 57.500 42.857 0.00 0.00 0.00 2.69
4410 7147 2.158885 TGTCCGAATGAACAAGTCCACA 60.159 45.455 0.00 0.00 0.00 4.17
4411 7148 2.489971 TGTCCGAATGAACAAGTCCAC 58.510 47.619 0.00 0.00 0.00 4.02
4418 7155 5.598416 AGATGAGTATGTCCGAATGAACA 57.402 39.130 0.00 0.00 0.00 3.18
4420 7157 7.448469 TCTGATAGATGAGTATGTCCGAATGAA 59.552 37.037 0.00 0.00 0.00 2.57
4428 7165 6.404184 CCGGTGATCTGATAGATGAGTATGTC 60.404 46.154 0.00 0.00 34.53 3.06
4440 7177 2.882761 CGAAGTACCCGGTGATCTGATA 59.117 50.000 0.00 0.00 0.00 2.15
4443 7180 0.815734 ACGAAGTACCCGGTGATCTG 59.184 55.000 0.00 0.00 41.94 2.90
4459 7196 2.238942 ATTCGGATGCTTGCATACGA 57.761 45.000 31.28 31.28 45.13 3.43
4489 7226 9.838339 GATTGGTTTCTCCTCTTATCAGAAATA 57.162 33.333 0.00 0.00 38.19 1.40
4508 7245 3.259123 GGATGCCTTGTGAAAGATTGGTT 59.741 43.478 0.00 0.00 0.00 3.67
4509 7246 2.827921 GGATGCCTTGTGAAAGATTGGT 59.172 45.455 0.00 0.00 0.00 3.67
4523 7260 1.606531 GAGTGCAAGGAGGATGCCT 59.393 57.895 0.00 0.00 43.16 4.75
4525 7262 0.391661 TTCGAGTGCAAGGAGGATGC 60.392 55.000 0.00 0.00 44.08 3.91
4526 7263 2.099141 TTTCGAGTGCAAGGAGGATG 57.901 50.000 0.00 0.00 0.00 3.51
4570 7307 1.312815 GTGTTCAGCCATATCCAGCC 58.687 55.000 0.00 0.00 0.00 4.85
4571 7308 2.042686 TGTGTTCAGCCATATCCAGC 57.957 50.000 0.00 0.00 0.00 4.85
4573 7310 3.200605 AGACATGTGTTCAGCCATATCCA 59.799 43.478 1.15 0.00 0.00 3.41
4579 7316 1.339055 GGCTAGACATGTGTTCAGCCA 60.339 52.381 24.77 0.00 46.19 4.75
4582 7319 2.370281 ACGGCTAGACATGTGTTCAG 57.630 50.000 1.15 0.00 0.00 3.02
4614 7351 5.391629 GCTCTAAAAACACAACCTATTCCGG 60.392 44.000 0.00 0.00 0.00 5.14
4616 7353 5.391629 CCGCTCTAAAAACACAACCTATTCC 60.392 44.000 0.00 0.00 0.00 3.01
4632 7369 2.361992 TCCGCTGACCCGCTCTAA 60.362 61.111 0.00 0.00 0.00 2.10
4633 7370 3.138798 GTCCGCTGACCCGCTCTA 61.139 66.667 0.00 0.00 35.34 2.43
4646 7383 2.288825 TGGCAAGACTACTTTGAGTCCG 60.289 50.000 0.02 0.00 45.97 4.79
4652 7389 4.499183 CCTACTCTGGCAAGACTACTTTG 58.501 47.826 0.00 0.00 33.70 2.77
4653 7390 4.810191 CCTACTCTGGCAAGACTACTTT 57.190 45.455 0.00 0.00 33.70 2.66
4691 7428 2.223900 TGGCATTGAATCGCAAAACACA 60.224 40.909 0.00 0.00 40.48 3.72
4692 7429 2.402305 TGGCATTGAATCGCAAAACAC 58.598 42.857 0.00 0.00 40.48 3.32
4694 7431 2.919229 CTCTGGCATTGAATCGCAAAAC 59.081 45.455 0.00 0.00 40.48 2.43
4696 7433 2.161855 ACTCTGGCATTGAATCGCAAA 58.838 42.857 0.00 0.00 40.48 3.68
4710 7453 1.831652 GATCCCGGGGCATACTCTGG 61.832 65.000 23.50 0.00 0.00 3.86
4712 7455 1.908793 CGATCCCGGGGCATACTCT 60.909 63.158 23.50 0.00 0.00 3.24
4737 7480 2.622903 TAGGAAGCGGCCGATGTTCG 62.623 60.000 33.48 0.00 40.07 3.95
4738 7481 1.143183 TAGGAAGCGGCCGATGTTC 59.857 57.895 33.48 25.66 0.00 3.18
4739 7482 1.153429 GTAGGAAGCGGCCGATGTT 60.153 57.895 33.48 18.92 0.00 2.71
4740 7483 0.754217 TAGTAGGAAGCGGCCGATGT 60.754 55.000 33.48 14.20 0.00 3.06
4741 7484 0.387929 TTAGTAGGAAGCGGCCGATG 59.612 55.000 33.48 0.00 0.00 3.84
4742 7485 1.000955 CATTAGTAGGAAGCGGCCGAT 59.999 52.381 33.48 23.90 0.00 4.18
4743 7486 0.387929 CATTAGTAGGAAGCGGCCGA 59.612 55.000 33.48 2.66 0.00 5.54
4744 7487 0.104304 ACATTAGTAGGAAGCGGCCG 59.896 55.000 24.05 24.05 0.00 6.13
4745 7488 1.583054 CACATTAGTAGGAAGCGGCC 58.417 55.000 0.00 0.00 0.00 6.13
4746 7489 1.134491 ACCACATTAGTAGGAAGCGGC 60.134 52.381 0.00 0.00 0.00 6.53
4747 7490 2.167693 TGACCACATTAGTAGGAAGCGG 59.832 50.000 0.00 0.00 0.00 5.52
4748 7491 3.520290 TGACCACATTAGTAGGAAGCG 57.480 47.619 0.00 0.00 0.00 4.68
4749 7492 4.130118 CCATGACCACATTAGTAGGAAGC 58.870 47.826 0.00 0.00 34.15 3.86
4750 7493 5.360591 GTCCATGACCACATTAGTAGGAAG 58.639 45.833 0.00 0.00 34.15 3.46
4751 7494 5.353394 GTCCATGACCACATTAGTAGGAA 57.647 43.478 0.00 0.00 34.15 3.36


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

AutoCloner maintained by Alex Coulton.