Multiple sequence alignment - TraesCS3B01G395100

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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 TraesCS3B01G395100 chr3B 100.000 7439 0 0 1 7439 622479863 622472425 0.000000e+00 13738.0
1 TraesCS3B01G395100 chr3B 94.438 863 38 4 1 856 492743003 492742144 0.000000e+00 1319.0
2 TraesCS3B01G395100 chr3B 85.271 516 52 14 335 839 245923346 245923848 1.850000e-140 510.0
3 TraesCS3B01G395100 chr3B 83.265 245 34 4 623 862 240266525 240266767 1.260000e-52 219.0
4 TraesCS3B01G395100 chr3B 96.875 64 2 0 262 325 245923296 245923359 2.840000e-19 108.0
5 TraesCS3B01G395100 chr3D 95.238 3990 119 25 877 4841 468773811 468769868 0.000000e+00 6250.0
6 TraesCS3B01G395100 chr3D 92.609 2652 98 46 4840 7439 468769838 468767233 0.000000e+00 3722.0
7 TraesCS3B01G395100 chr3D 88.034 468 36 8 262 719 284206569 284207026 3.050000e-148 536.0
8 TraesCS3B01G395100 chr3A 94.955 2240 63 24 2843 5033 610555005 610552767 0.000000e+00 3465.0
9 TraesCS3B01G395100 chr3A 93.996 1982 73 17 895 2855 610557021 610555065 0.000000e+00 2959.0
10 TraesCS3B01G395100 chr3A 92.562 1815 62 12 5058 6847 610552772 610551006 0.000000e+00 2536.0
11 TraesCS3B01G395100 chr3A 93.471 291 14 3 7150 7439 610550730 610550444 1.920000e-115 427.0
12 TraesCS3B01G395100 chr3A 88.235 187 15 5 6994 7179 610550914 610550734 4.520000e-52 217.0
13 TraesCS3B01G395100 chr3A 88.000 75 8 1 2918 2991 699997971 699998045 3.700000e-13 87.9
14 TraesCS3B01G395100 chr6D 92.722 1113 75 6 2462 3568 224668959 224667847 0.000000e+00 1602.0
15 TraesCS3B01G395100 chr7B 95.139 864 39 3 1 862 221892620 221893482 0.000000e+00 1360.0
16 TraesCS3B01G395100 chr7B 82.529 601 64 19 265 862 29687410 29686848 2.410000e-134 490.0
17 TraesCS3B01G395100 chr7B 88.095 168 20 0 695 862 246618192 246618359 4.550000e-47 200.0
18 TraesCS3B01G395100 chr2B 94.554 863 43 2 1 862 113193933 113193074 0.000000e+00 1330.0
19 TraesCS3B01G395100 chr6B 90.137 659 57 8 2928 3581 343374382 343375037 0.000000e+00 850.0
20 TraesCS3B01G395100 chr6B 84.897 629 67 11 1614 2235 343112983 343113590 1.770000e-170 610.0
21 TraesCS3B01G395100 chr6B 80.000 140 17 10 2053 2184 88453629 88453493 7.950000e-15 93.5
22 TraesCS3B01G395100 chr2A 86.314 548 54 10 331 862 476213957 476214499 1.800000e-160 577.0
23 TraesCS3B01G395100 chr1A 92.778 360 16 2 265 615 444122748 444122390 5.150000e-141 512.0
24 TraesCS3B01G395100 chr1A 82.474 582 65 13 2090 2664 261372571 261372020 6.750000e-130 475.0
25 TraesCS3B01G395100 chr1A 83.775 302 28 11 3723 4011 474179400 474179693 4.420000e-67 267.0
26 TraesCS3B01G395100 chr1A 80.269 223 32 12 2956 3175 261371799 261371586 2.780000e-34 158.0
27 TraesCS3B01G395100 chr1A 83.636 165 21 6 2956 3119 474179159 474179318 4.650000e-32 150.0
28 TraesCS3B01G395100 chr1A 88.596 114 7 2 2090 2198 474173985 474174097 4.680000e-27 134.0
29 TraesCS3B01G395100 chr1D 92.500 360 17 2 265 615 344590986 344590628 2.390000e-139 507.0
30 TraesCS3B01G395100 chr1B 92.287 363 18 2 262 615 466093906 466094267 2.390000e-139 507.0
31 TraesCS3B01G395100 chr1B 89.444 360 28 2 265 615 682437622 682437264 5.300000e-121 446.0
32 TraesCS3B01G395100 chr4A 82.990 582 62 13 2090 2664 605127821 605128372 6.710000e-135 492.0
33 TraesCS3B01G395100 chr4A 87.336 229 27 2 635 862 130499273 130499500 2.060000e-65 261.0
34 TraesCS3B01G395100 chr4A 80.269 223 32 12 2956 3175 605128593 605128806 2.780000e-34 158.0
35 TraesCS3B01G395100 chr4A 79.167 144 18 10 2050 2184 377610487 377610347 1.030000e-13 89.8
36 TraesCS3B01G395100 chr7D 86.777 242 30 2 621 862 430991384 430991145 1.230000e-67 268.0
37 TraesCS3B01G395100 chr5B 96.429 84 3 0 1 84 577345703 577345620 1.010000e-28 139.0
38 TraesCS3B01G395100 chr5B 82.051 156 6 11 84 239 577334697 577334564 6.100000e-21 113.0
39 TraesCS3B01G395100 chr5B 80.000 145 15 13 2050 2184 211736280 211736140 2.210000e-15 95.3


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 TraesCS3B01G395100 chr3B 622472425 622479863 7438 True 13738.0 13738 100.0000 1 7439 1 chr3B.!!$R2 7438
1 TraesCS3B01G395100 chr3B 492742144 492743003 859 True 1319.0 1319 94.4380 1 856 1 chr3B.!!$R1 855
2 TraesCS3B01G395100 chr3B 245923296 245923848 552 False 309.0 510 91.0730 262 839 2 chr3B.!!$F2 577
3 TraesCS3B01G395100 chr3D 468767233 468773811 6578 True 4986.0 6250 93.9235 877 7439 2 chr3D.!!$R1 6562
4 TraesCS3B01G395100 chr3A 610550444 610557021 6577 True 1920.8 3465 92.6438 895 7439 5 chr3A.!!$R1 6544
5 TraesCS3B01G395100 chr6D 224667847 224668959 1112 True 1602.0 1602 92.7220 2462 3568 1 chr6D.!!$R1 1106
6 TraesCS3B01G395100 chr7B 221892620 221893482 862 False 1360.0 1360 95.1390 1 862 1 chr7B.!!$F1 861
7 TraesCS3B01G395100 chr7B 29686848 29687410 562 True 490.0 490 82.5290 265 862 1 chr7B.!!$R1 597
8 TraesCS3B01G395100 chr2B 113193074 113193933 859 True 1330.0 1330 94.5540 1 862 1 chr2B.!!$R1 861
9 TraesCS3B01G395100 chr6B 343374382 343375037 655 False 850.0 850 90.1370 2928 3581 1 chr6B.!!$F2 653
10 TraesCS3B01G395100 chr6B 343112983 343113590 607 False 610.0 610 84.8970 1614 2235 1 chr6B.!!$F1 621
11 TraesCS3B01G395100 chr2A 476213957 476214499 542 False 577.0 577 86.3140 331 862 1 chr2A.!!$F1 531
12 TraesCS3B01G395100 chr1A 261371586 261372571 985 True 316.5 475 81.3715 2090 3175 2 chr1A.!!$R2 1085
13 TraesCS3B01G395100 chr1A 474179159 474179693 534 False 208.5 267 83.7055 2956 4011 2 chr1A.!!$F2 1055
14 TraesCS3B01G395100 chr4A 605127821 605128806 985 False 325.0 492 81.6295 2090 3175 2 chr4A.!!$F2 1085

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
829 897 0.107081 TGGTACCAAAGTGTCACCCG 59.893 55.000 13.60 0.0 0.0 5.28 F
843 911 0.742505 CACCCGGCTCGAGTTATGTA 59.257 55.000 15.13 0.0 0.0 2.29 F
2628 2731 0.478072 TTCTGGATGTTGGCTGTGGT 59.522 50.000 0.00 0.0 0.0 4.16 F
3512 3747 0.034477 CCTATTTGGCTGTTCCCGGT 60.034 55.000 0.00 0.0 0.0 5.28 F
4128 4376 2.624838 ACTGGCCACATTGTTTTCTCTG 59.375 45.455 0.00 0.0 0.0 3.35 F
5075 5368 3.380142 CAATTTTGCGTGTAGGTTTGCT 58.620 40.909 0.00 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2628 2731 0.958091 ATGCGCCAAAACTTGCTACA 59.042 45.000 4.18 0.0 0.00 2.74 R
2685 2788 4.951715 TGATTCTCATGAACATCTTTGGGG 59.048 41.667 12.75 0.0 34.71 4.96 R
3700 3935 4.415596 ACATCCCAAGGATTTGCAGTTTA 58.584 39.130 0.00 0.0 39.79 2.01 R
4954 5246 0.911769 TCAGGACAACCCATAGCCTG 59.088 55.000 0.00 0.0 45.77 4.85 R
5201 5494 1.210722 TGCCAGGCAACGAATATACCA 59.789 47.619 13.33 0.0 46.39 3.25 R
6587 6920 0.107831 ACGCAAAGGAGCAACCACTA 59.892 50.000 2.96 0.0 42.04 2.74 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
133 134 2.510012 CGCGGAGAGAGCAATGCA 60.510 61.111 8.35 0.00 34.19 3.96
242 248 1.581934 CGCCGGCTGAATAAAGATCA 58.418 50.000 26.68 0.00 0.00 2.92
386 416 1.899437 GCTTGACGTCCATCCCCTGA 61.899 60.000 14.12 0.00 0.00 3.86
529 571 0.394352 GGGACCATGTTCTTGCGGAT 60.394 55.000 0.00 0.00 0.00 4.18
531 573 1.453155 GACCATGTTCTTGCGGATGT 58.547 50.000 0.00 0.00 0.00 3.06
605 653 1.372997 GCGAAGGAACTCAGACGCA 60.373 57.895 0.00 0.00 42.35 5.24
682 749 1.272313 ACCTTAGGCACGACTAGGTGA 60.272 52.381 0.00 0.00 40.38 4.02
829 897 0.107081 TGGTACCAAAGTGTCACCCG 59.893 55.000 13.60 0.00 0.00 5.28
834 902 2.030562 AAAGTGTCACCCGGCTCG 59.969 61.111 0.00 0.00 0.00 5.03
843 911 0.742505 CACCCGGCTCGAGTTATGTA 59.257 55.000 15.13 0.00 0.00 2.29
869 937 9.936759 AACCTACAGTGAATTTTTCAAAAAGAA 57.063 25.926 1.08 0.00 42.15 2.52
870 938 9.936759 ACCTACAGTGAATTTTTCAAAAAGAAA 57.063 25.926 1.08 0.00 44.21 2.52
1236 1311 3.444417 TCCCCCTCCTCCCGCATA 61.444 66.667 0.00 0.00 0.00 3.14
1338 1413 4.867599 CCGCCCGCTTCGTCTACC 62.868 72.222 0.00 0.00 0.00 3.18
1348 1423 1.917336 TTCGTCTACCCCCAATGCCC 61.917 60.000 0.00 0.00 0.00 5.36
1374 1449 2.503061 CCTCCAGTGGCATCTCCG 59.497 66.667 3.51 0.00 37.80 4.63
1375 1450 2.202987 CTCCAGTGGCATCTCCGC 60.203 66.667 3.51 0.00 45.76 5.54
1384 1459 4.161295 CATCTCCGCCGCCTCCAA 62.161 66.667 0.00 0.00 0.00 3.53
1425 1506 3.411351 CCAACGCCAACTCCGTCG 61.411 66.667 0.00 0.00 38.06 5.12
1426 1507 4.072088 CAACGCCAACTCCGTCGC 62.072 66.667 0.00 0.00 38.06 5.19
1830 1917 0.963355 GGAGCAGAGACGAGGTGAGT 60.963 60.000 0.00 0.00 0.00 3.41
1837 1924 4.443621 CAGAGACGAGGTGAGTATCTGTA 58.556 47.826 11.44 0.00 46.72 2.74
1971 2060 4.616953 CACACAGGGTTTATTGTTTCACC 58.383 43.478 0.00 0.00 0.00 4.02
2048 2138 6.926826 ACATTTGATGTATGCCATTATTGCTG 59.073 34.615 0.00 0.00 42.78 4.41
2071 2161 4.726416 CAGAATCGAATTGAACCAACTGG 58.274 43.478 0.00 0.00 42.17 4.00
2085 2182 1.112916 AACTGGGTTGGCTTTTCCCG 61.113 55.000 0.00 0.00 43.75 5.14
2176 2278 1.732259 CCTCATACACGCTTGGTTGAC 59.268 52.381 0.00 0.00 0.00 3.18
2336 2439 9.594478 AAATTACTCAAATCTTTTTGGAAACGT 57.406 25.926 0.00 0.00 42.10 3.99
2440 2543 4.940046 CACATATGGGTTCTAGATGCATCC 59.060 45.833 23.06 7.20 0.00 3.51
2474 2577 6.146021 CAGGAACATGCAAAAGACAAATAACC 59.854 38.462 0.00 0.00 0.00 2.85
2628 2731 0.478072 TTCTGGATGTTGGCTGTGGT 59.522 50.000 0.00 0.00 0.00 4.16
2685 2788 2.676076 GTGTTGACATTGTCCATTGCC 58.324 47.619 14.05 0.00 0.00 4.52
2919 3105 7.881232 ACCTACTTTATTCCTTCGATTGACAAA 59.119 33.333 0.00 0.00 0.00 2.83
3195 3422 8.306761 AGTTGTCCATTTGTTGATTTTAGGATC 58.693 33.333 0.00 0.00 0.00 3.36
3256 3486 3.150767 CCCGTTGACTGGTAATGGAAAA 58.849 45.455 0.00 0.00 36.51 2.29
3257 3487 3.190535 CCCGTTGACTGGTAATGGAAAAG 59.809 47.826 0.00 0.00 36.51 2.27
3512 3747 0.034477 CCTATTTGGCTGTTCCCGGT 60.034 55.000 0.00 0.00 0.00 5.28
3656 3891 8.874156 TGATTAAATCTACAGTATGCCAGAGAT 58.126 33.333 0.00 0.00 42.53 2.75
3669 3904 6.879276 ATGCCAGAGATATTCTTTCATGTG 57.121 37.500 0.00 0.00 32.41 3.21
3678 3913 8.674263 AGATATTCTTTCATGTGAAGGATGAC 57.326 34.615 8.16 8.25 39.40 3.06
3684 3919 6.430925 TCTTTCATGTGAAGGATGACGAAAAT 59.569 34.615 3.74 0.00 35.60 1.82
3700 3935 6.084326 ACGAAAATTGGAAGTGCATAGTTT 57.916 33.333 0.00 0.00 0.00 2.66
3926 4173 4.120589 GGAGGAAGCCTGTAAATAACTCG 58.879 47.826 0.00 0.00 31.76 4.18
4128 4376 2.624838 ACTGGCCACATTGTTTTCTCTG 59.375 45.455 0.00 0.00 0.00 3.35
4178 4426 6.209361 GGCCTTAAAATAGCACTTTAGATGC 58.791 40.000 0.00 0.00 43.74 3.91
4513 4762 4.602006 CATGTATCAGTCGACTACCTGTG 58.398 47.826 19.57 5.77 0.00 3.66
4860 5152 5.163405 TGTTAGCAAAGCTACTAGATGGAGG 60.163 44.000 0.00 0.00 41.12 4.30
4869 5161 4.586841 GCTACTAGATGGAGGACTCACATT 59.413 45.833 0.00 0.00 0.00 2.71
4884 5176 7.029563 GGACTCACATTTGTTTGGATGAATAC 58.970 38.462 0.00 0.00 0.00 1.89
4887 5179 7.448161 ACTCACATTTGTTTGGATGAATACAGA 59.552 33.333 0.00 0.00 0.00 3.41
4954 5246 5.472137 TGTCACAACCTTTTGCTCTAATACC 59.528 40.000 0.00 0.00 36.00 2.73
5034 5327 6.841443 TGTGGAATATTGTTTGTTTTGCTG 57.159 33.333 0.00 0.00 0.00 4.41
5037 5330 7.010923 TGTGGAATATTGTTTGTTTTGCTGAAC 59.989 33.333 0.00 0.00 0.00 3.18
5075 5368 3.380142 CAATTTTGCGTGTAGGTTTGCT 58.620 40.909 0.00 0.00 0.00 3.91
5201 5494 2.897326 GGCCCATGACTGGTAAGTTTTT 59.103 45.455 0.00 0.00 41.37 1.94
5300 5593 3.497103 AAGCATAGCATATCAGCCACA 57.503 42.857 0.00 0.00 34.23 4.17
5302 5595 4.030314 AGCATAGCATATCAGCCACATT 57.970 40.909 0.00 0.00 34.23 2.71
5304 5597 4.831155 AGCATAGCATATCAGCCACATTTT 59.169 37.500 0.00 0.00 34.23 1.82
5305 5598 5.048224 AGCATAGCATATCAGCCACATTTTC 60.048 40.000 0.00 0.00 34.23 2.29
5438 5735 7.562454 TTCCTATATTTTCCGGACATCAAAC 57.438 36.000 1.83 0.00 0.00 2.93
5478 5775 3.261580 TGGTAGATGCTTGACGTGAATG 58.738 45.455 0.00 0.00 0.00 2.67
5489 5786 0.036105 ACGTGAATGAGCTCATGGCA 60.036 50.000 29.34 25.06 44.79 4.92
5726 6023 9.956720 CATGTTAGTTCTTTGTTCAGATTTCTT 57.043 29.630 0.00 0.00 0.00 2.52
5857 6154 6.380095 AAACAATTGAGGTGCTTACGTTAA 57.620 33.333 13.59 0.00 0.00 2.01
5894 6191 1.064003 ATGGATGCCCGGCTATGTAA 58.936 50.000 11.61 0.00 34.29 2.41
5898 6195 2.038033 GGATGCCCGGCTATGTAACTAA 59.962 50.000 11.61 0.00 0.00 2.24
5907 6205 4.032900 CGGCTATGTAACTAAGTTGCACTG 59.967 45.833 0.00 0.00 40.49 3.66
5984 6282 5.011635 TCTGTGGTAGTTGTAATGCAGAAGA 59.988 40.000 0.00 0.00 0.00 2.87
5994 6292 1.813513 ATGCAGAAGAACCGACCTTG 58.186 50.000 0.00 0.00 0.00 3.61
5996 6294 1.901650 GCAGAAGAACCGACCTTGCG 61.902 60.000 0.00 0.00 0.00 4.85
6001 6299 0.034896 AGAACCGACCTTGCGTCATT 59.965 50.000 0.00 0.00 42.07 2.57
6024 6322 7.905604 TTCATCGGATATACCTTATTTGCAG 57.094 36.000 0.00 0.00 36.31 4.41
6025 6323 7.004555 TCATCGGATATACCTTATTTGCAGT 57.995 36.000 0.00 0.00 36.31 4.40
6029 6327 6.704493 TCGGATATACCTTATTTGCAGTTCAC 59.296 38.462 0.00 0.00 36.31 3.18
6064 6362 1.340088 TACCAGGTGTAACGCCTCAA 58.660 50.000 0.76 0.00 43.13 3.02
6087 6385 2.609427 TCTTGCTTGAGATGGATCGG 57.391 50.000 0.00 0.00 0.00 4.18
6140 6438 7.046033 ATCCGTGATAAAAAGGAAACGATAGT 58.954 34.615 0.00 0.00 43.08 2.12
6334 6652 4.629523 TCCGGCACCGTTGGAACC 62.630 66.667 8.49 0.00 37.81 3.62
6518 6837 2.745968 AGACTTGGCAAAGGTTTTGGA 58.254 42.857 5.66 0.00 37.76 3.53
6519 6838 3.308401 AGACTTGGCAAAGGTTTTGGAT 58.692 40.909 5.66 0.00 37.76 3.41
6520 6839 3.070015 AGACTTGGCAAAGGTTTTGGATG 59.930 43.478 5.66 0.00 37.76 3.51
6522 6841 3.070015 ACTTGGCAAAGGTTTTGGATGAG 59.930 43.478 5.66 0.00 37.76 2.90
6523 6842 2.676748 TGGCAAAGGTTTTGGATGAGT 58.323 42.857 3.97 0.00 0.00 3.41
6524 6843 3.037549 TGGCAAAGGTTTTGGATGAGTT 58.962 40.909 3.97 0.00 0.00 3.01
6525 6844 3.069443 TGGCAAAGGTTTTGGATGAGTTC 59.931 43.478 3.97 0.00 0.00 3.01
6526 6845 3.321968 GGCAAAGGTTTTGGATGAGTTCT 59.678 43.478 3.97 0.00 0.00 3.01
6560 6893 7.681259 TCAAGGAAAGAGAATGGATGAGATA 57.319 36.000 0.00 0.00 0.00 1.98
6562 6895 8.373981 TCAAGGAAAGAGAATGGATGAGATATC 58.626 37.037 0.00 0.00 0.00 1.63
6587 6920 4.032960 TGTACTGGGCTGTGATGAAAAT 57.967 40.909 0.00 0.00 0.00 1.82
6653 6986 7.094975 TGACCGAGGTTTACAAATGTTCTATTG 60.095 37.037 0.00 0.00 0.00 1.90
6659 6992 9.073475 AGGTTTACAAATGTTCTATTGCTGTTA 57.927 29.630 0.00 0.00 0.00 2.41
6732 7065 7.517614 TTTCCATGTCAACTTTTATGTAGCA 57.482 32.000 0.00 0.00 0.00 3.49
6809 7143 1.970640 GGGGGTGAAAAATGACAAGCT 59.029 47.619 0.00 0.00 0.00 3.74
6862 7196 2.961526 TAAGACGGACAGGAGCATTC 57.038 50.000 0.00 0.00 0.00 2.67
6864 7198 0.534412 AGACGGACAGGAGCATTCTG 59.466 55.000 0.00 0.00 0.00 3.02
6926 7265 6.855763 TTTGGAAATGAGCAATAGGATTGT 57.144 33.333 1.47 0.00 0.00 2.71
6936 7275 8.177119 TGAGCAATAGGATTGTAACACTTTTT 57.823 30.769 1.47 0.00 0.00 1.94
7143 7485 3.382048 CGGAGCCCTAAACTATACCAC 57.618 52.381 0.00 0.00 0.00 4.16
7147 7518 5.392125 GGAGCCCTAAACTATACCACTCTA 58.608 45.833 0.00 0.00 0.00 2.43
7148 7519 5.837438 GGAGCCCTAAACTATACCACTCTAA 59.163 44.000 0.00 0.00 0.00 2.10
7258 7632 1.134753 TGCGGGCAAAGCTCAATTATG 59.865 47.619 0.00 0.00 35.28 1.90
7301 7699 8.083828 ACTATCTTCTCCACATACACAAGAAT 57.916 34.615 0.00 0.00 0.00 2.40
7337 7735 2.497675 TGAGTACAGTTCATGAGCTCCC 59.502 50.000 12.15 0.69 34.59 4.30
7375 7773 5.486775 CAGTCCATGAGGGGAGTATATCATT 59.513 44.000 0.00 0.00 38.57 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 7.703621 CCATGCATGCTAAATTATTATAGGCAC 59.296 37.037 21.69 0.00 31.91 5.01
133 134 2.654877 CGGCACAAGTCCGGTAGT 59.345 61.111 0.00 0.00 42.99 2.73
171 177 2.434884 CCACTGAACCGAGCGCAT 60.435 61.111 11.47 0.00 0.00 4.73
242 248 1.667191 CGCTGAGCTGCTCACAAGT 60.667 57.895 27.35 0.00 35.39 3.16
278 284 2.499685 GCCTACCTCGTCGGCATT 59.500 61.111 2.68 0.00 42.82 3.56
386 416 0.109132 CGCCCGTCGTTAAGTACCTT 60.109 55.000 0.00 0.00 0.00 3.50
417 457 3.503363 GCTCCACGCCAGCATCAC 61.503 66.667 0.00 0.00 36.82 3.06
485 527 1.405821 CTCGACTACCTCGGCAAGATT 59.594 52.381 0.00 0.00 43.16 2.40
641 708 4.831710 GGTGAATACTAGTCTATTCGGGGT 59.168 45.833 0.00 0.00 36.33 4.95
642 709 5.078256 AGGTGAATACTAGTCTATTCGGGG 58.922 45.833 0.00 0.00 36.33 5.73
643 710 6.651975 AAGGTGAATACTAGTCTATTCGGG 57.348 41.667 0.00 0.00 36.33 5.14
650 717 4.338682 CGTGCCTAAGGTGAATACTAGTCT 59.661 45.833 0.00 0.00 0.00 3.24
682 749 2.555547 GCCAGCTTGCTTTGACCGT 61.556 57.895 1.78 0.00 0.00 4.83
709 777 1.589716 ATTTGCTGACTTGGCCGAGC 61.590 55.000 20.81 13.15 0.00 5.03
753 821 1.367471 GCAAGGGGTTCACTTTGGC 59.633 57.895 0.00 0.00 0.00 4.52
803 871 5.121105 GTGACACTTTGGTACCACTACTTT 58.879 41.667 16.04 0.00 0.00 2.66
829 897 4.097589 ACTGTAGGTTACATAACTCGAGCC 59.902 45.833 13.61 2.57 38.15 4.70
843 911 9.936759 TTCTTTTTGAAAAATTCACTGTAGGTT 57.063 25.926 3.28 0.00 39.87 3.50
871 939 8.857098 GGAGTATGTACAGTGGTTGATAGAATA 58.143 37.037 0.33 0.00 0.00 1.75
872 940 7.565398 AGGAGTATGTACAGTGGTTGATAGAAT 59.435 37.037 0.33 0.00 0.00 2.40
873 941 6.895756 AGGAGTATGTACAGTGGTTGATAGAA 59.104 38.462 0.33 0.00 0.00 2.10
874 942 6.432581 AGGAGTATGTACAGTGGTTGATAGA 58.567 40.000 0.33 0.00 0.00 1.98
875 943 6.239064 GGAGGAGTATGTACAGTGGTTGATAG 60.239 46.154 0.33 0.00 0.00 2.08
1117 1192 2.048127 GGCGAAGAAGAGCACGGT 60.048 61.111 0.00 0.00 34.54 4.83
1236 1311 2.128507 GGAAGGGGAGCGAGACGAT 61.129 63.158 0.00 0.00 0.00 3.73
1269 1344 3.194968 GGTCGAAGGAGATGTTGGAGTTA 59.805 47.826 0.00 0.00 0.00 2.24
1367 1442 3.466791 ATTGGAGGCGGCGGAGATG 62.467 63.158 9.78 0.00 0.00 2.90
1368 1443 3.164269 ATTGGAGGCGGCGGAGAT 61.164 61.111 9.78 0.00 0.00 2.75
1369 1444 4.161295 CATTGGAGGCGGCGGAGA 62.161 66.667 9.78 0.00 0.00 3.71
1374 1449 4.133796 GTTGGCATTGGAGGCGGC 62.134 66.667 0.00 0.00 36.77 6.53
1375 1450 2.361610 AGTTGGCATTGGAGGCGG 60.362 61.111 0.00 0.00 36.77 6.13
1376 1451 2.409870 GGAGTTGGCATTGGAGGCG 61.410 63.158 0.00 0.00 36.77 5.52
1377 1452 2.409870 CGGAGTTGGCATTGGAGGC 61.410 63.158 0.00 0.00 0.00 4.70
1378 1453 1.002134 ACGGAGTTGGCATTGGAGG 60.002 57.895 0.00 0.00 37.78 4.30
1379 1454 4.722193 ACGGAGTTGGCATTGGAG 57.278 55.556 0.00 0.00 37.78 3.86
1570 1657 2.747855 GTTGCCAAGCTCCTCCGG 60.748 66.667 0.00 0.00 0.00 5.14
1573 1660 3.793144 CGCGTTGCCAAGCTCCTC 61.793 66.667 0.00 0.00 0.00 3.71
1830 1917 5.290493 ACCGGCAAGAATCAATACAGATA 57.710 39.130 0.00 0.00 0.00 1.98
1837 1924 3.057315 CAGTTGAACCGGCAAGAATCAAT 60.057 43.478 0.00 0.00 33.12 2.57
1971 2060 5.400485 GCTAAAACTTTGAGTGCTGTGATTG 59.600 40.000 0.00 0.00 0.00 2.67
2048 2138 4.161333 CAGTTGGTTCAATTCGATTCTGC 58.839 43.478 0.00 0.00 0.00 4.26
2071 2161 1.460273 TTCTGCGGGAAAAGCCAACC 61.460 55.000 0.00 0.00 38.95 3.77
2117 2214 4.456911 CACCTGCAATTCACAGAAGTACAT 59.543 41.667 6.58 0.00 37.32 2.29
2122 2219 2.030540 CCACACCTGCAATTCACAGAAG 60.031 50.000 6.58 2.21 37.32 2.85
2176 2278 1.470098 CAATTCTGCCCTCCTTTGTCG 59.530 52.381 0.00 0.00 0.00 4.35
2336 2439 9.877178 TTTTAAGCAATTTGAAGTTACCTTTCA 57.123 25.926 0.00 0.00 33.00 2.69
2407 2510 9.429109 TCTAGAACCCATATGTGTTATGTTCTA 57.571 33.333 8.25 13.18 36.15 2.10
2413 2516 7.078249 TGCATCTAGAACCCATATGTGTTAT 57.922 36.000 3.38 3.56 0.00 1.89
2440 2543 1.535028 TGCATGTTCCTGTTAAGCACG 59.465 47.619 0.00 0.00 0.00 5.34
2474 2577 2.483877 TGCAGTCCATGAAACTTTAGCG 59.516 45.455 0.00 0.00 0.00 4.26
2528 2631 4.192429 TGTGCTTCGAATGAGATTCAGA 57.808 40.909 0.00 0.00 39.22 3.27
2628 2731 0.958091 ATGCGCCAAAACTTGCTACA 59.042 45.000 4.18 0.00 0.00 2.74
2685 2788 4.951715 TGATTCTCATGAACATCTTTGGGG 59.048 41.667 12.75 0.00 34.71 4.96
2919 3105 8.650143 AATTATGACAACAGGAATTAAGTGGT 57.350 30.769 0.00 0.00 0.00 4.16
3195 3422 9.535878 AACAAAAGAAGACTTTACTCTGACTAG 57.464 33.333 0.00 0.00 44.32 2.57
3256 3486 5.043281 TCCCTCTAGTCCTAATGAACTTCCT 60.043 44.000 0.00 0.00 0.00 3.36
3257 3487 5.209659 TCCCTCTAGTCCTAATGAACTTCC 58.790 45.833 0.00 0.00 0.00 3.46
3335 3567 4.012374 AGCACGATCAAAAACAGATCCAT 58.988 39.130 0.00 0.00 38.90 3.41
3512 3747 5.164954 GTGCAATTTAACTTATGCGGGAAA 58.835 37.500 0.00 0.00 41.61 3.13
3656 3891 6.639563 TCGTCATCCTTCACATGAAAGAATA 58.360 36.000 0.00 0.00 31.98 1.75
3669 3904 5.393962 CACTTCCAATTTTCGTCATCCTTC 58.606 41.667 0.00 0.00 0.00 3.46
3678 3913 8.424731 GTTTAAACTATGCACTTCCAATTTTCG 58.575 33.333 11.18 0.00 0.00 3.46
3684 3919 5.300539 TGCAGTTTAAACTATGCACTTCCAA 59.699 36.000 23.79 6.74 37.08 3.53
3700 3935 4.415596 ACATCCCAAGGATTTGCAGTTTA 58.584 39.130 0.00 0.00 39.79 2.01
4128 4376 9.922305 CCGACAAGAATTAAAGATCTTAATGAC 57.078 33.333 8.75 1.44 34.24 3.06
4152 4400 4.879545 TCTAAAGTGCTATTTTAAGGCCCG 59.120 41.667 0.00 0.00 0.00 6.13
4178 4426 5.469373 TGATGGAAATGAAAGATCGTTCG 57.531 39.130 15.26 0.00 33.63 3.95
4417 4666 7.801716 AGTTTGTGTCAAATAAGCTCAGTAA 57.198 32.000 0.00 0.00 0.00 2.24
4418 4667 7.801716 AAGTTTGTGTCAAATAAGCTCAGTA 57.198 32.000 0.00 0.00 0.00 2.74
4630 4879 7.384115 TCGAGTATATCATCCCAAAATTTCGTC 59.616 37.037 0.00 0.00 0.00 4.20
4860 5152 7.592938 TGTATTCATCCAAACAAATGTGAGTC 58.407 34.615 0.00 0.00 0.00 3.36
4869 5161 4.900684 TCGGTCTGTATTCATCCAAACAA 58.099 39.130 0.00 0.00 0.00 2.83
4884 5176 6.422100 CAGTATTTCCATGTATTCTCGGTCTG 59.578 42.308 0.00 0.00 0.00 3.51
4887 5179 5.057149 GCAGTATTTCCATGTATTCTCGGT 58.943 41.667 0.00 0.00 0.00 4.69
4954 5246 0.911769 TCAGGACAACCCATAGCCTG 59.088 55.000 0.00 0.00 45.77 4.85
5037 5330 8.961092 CGCAAAATTGGTAATAGAAATGAGATG 58.039 33.333 0.00 0.00 0.00 2.90
5075 5368 2.463620 GCGACCGATCAATGCAGCA 61.464 57.895 0.00 0.00 0.00 4.41
5201 5494 1.210722 TGCCAGGCAACGAATATACCA 59.789 47.619 13.33 0.00 46.39 3.25
5300 5593 7.463961 AGACAAGATGCAATGAGAAGAAAAT 57.536 32.000 0.00 0.00 0.00 1.82
5302 5595 6.072286 GGAAGACAAGATGCAATGAGAAGAAA 60.072 38.462 0.00 0.00 0.00 2.52
5304 5597 4.940046 GGAAGACAAGATGCAATGAGAAGA 59.060 41.667 0.00 0.00 0.00 2.87
5305 5598 4.942483 AGGAAGACAAGATGCAATGAGAAG 59.058 41.667 0.00 0.00 0.00 2.85
5405 5702 5.273944 CGGAAAATATAGGAAGCAAAGCAC 58.726 41.667 0.00 0.00 0.00 4.40
5478 5775 2.615912 GTGGAAACTATGCCATGAGCTC 59.384 50.000 6.82 6.82 44.23 4.09
5489 5786 8.533569 TTCTTCAAGAAAAAGGTGGAAACTAT 57.466 30.769 0.00 0.00 29.99 2.12
5857 6154 6.491403 GCATCCATGTAATAAACCATCTCCTT 59.509 38.462 0.00 0.00 0.00 3.36
5907 6205 1.310904 TGTCAACCGGGTGCTTAAAC 58.689 50.000 16.88 8.12 0.00 2.01
5994 6292 4.111375 AGGTATATCCGATGAATGACGC 57.889 45.455 0.00 0.00 41.99 5.19
5996 6294 8.391106 GCAAATAAGGTATATCCGATGAATGAC 58.609 37.037 0.00 0.00 41.99 3.06
6001 6299 7.004555 ACTGCAAATAAGGTATATCCGATGA 57.995 36.000 0.00 0.00 41.99 2.92
6024 6322 8.506168 TGGTAATGAGAGAAAATATGGTGAAC 57.494 34.615 0.00 0.00 0.00 3.18
6025 6323 7.775093 CCTGGTAATGAGAGAAAATATGGTGAA 59.225 37.037 0.00 0.00 0.00 3.18
6029 6327 7.056635 ACACCTGGTAATGAGAGAAAATATGG 58.943 38.462 0.00 0.00 0.00 2.74
6064 6362 5.012458 TCCGATCCATCTCAAGCAAGATAAT 59.988 40.000 0.00 0.00 34.21 1.28
6140 6438 5.419542 CGTCTGTTATTTCCTTGATCTCCA 58.580 41.667 0.00 0.00 0.00 3.86
6269 6587 0.526954 CATTGCTTGCCGGAGAATGC 60.527 55.000 5.05 4.30 0.00 3.56
6534 6867 6.413052 TCTCATCCATTCTCTTTCCTTGAAG 58.587 40.000 0.00 0.00 0.00 3.02
6537 6870 8.377034 AGATATCTCATCCATTCTCTTTCCTTG 58.623 37.037 0.00 0.00 0.00 3.61
6538 6871 8.377034 CAGATATCTCATCCATTCTCTTTCCTT 58.623 37.037 1.03 0.00 0.00 3.36
6560 6893 1.977854 TCACAGCCCAGTACAACAGAT 59.022 47.619 0.00 0.00 0.00 2.90
6562 6895 2.079158 CATCACAGCCCAGTACAACAG 58.921 52.381 0.00 0.00 0.00 3.16
6587 6920 0.107831 ACGCAAAGGAGCAACCACTA 59.892 50.000 2.96 0.00 42.04 2.74
6653 6986 2.351350 CCAATGGACCAACGTTAACAGC 60.351 50.000 0.00 0.00 0.00 4.40
6659 6992 2.039746 TGAGATCCAATGGACCAACGTT 59.960 45.455 3.09 0.00 32.98 3.99
6732 7065 7.722728 ACATACAGCATGGAAGAACATATCAAT 59.277 33.333 0.00 0.00 43.62 2.57
6830 7164 6.017605 CCTGTCCGTCTTATAGTTGTATACGT 60.018 42.308 0.00 0.00 0.00 3.57
6862 7196 4.188247 TCCTACAGACCGATCAAAACAG 57.812 45.455 0.00 0.00 0.00 3.16
6864 7198 6.496338 AAAATCCTACAGACCGATCAAAAC 57.504 37.500 0.00 0.00 0.00 2.43
6893 7227 4.332268 TGCTCATTTCCAAAACAAACAAGC 59.668 37.500 0.00 0.00 0.00 4.01
6979 7318 9.936759 AACAAAAATCCTAGTTTGTCTCAAAAA 57.063 25.926 9.00 0.00 44.96 1.94
7009 7348 6.415573 CAACCCCTACTTGCTCTAATTAAGT 58.584 40.000 0.00 0.00 38.19 2.24
7013 7352 3.850173 TCCAACCCCTACTTGCTCTAATT 59.150 43.478 0.00 0.00 0.00 1.40
7026 7365 4.044065 TCAGAATACAATGTTCCAACCCCT 59.956 41.667 0.00 0.00 0.00 4.79
7067 7408 1.671979 CATGGTCAGTGATGCCGATT 58.328 50.000 0.00 0.00 0.00 3.34
7204 7578 2.422597 TGTTTGGCATTAGGTGAGACG 58.577 47.619 0.00 0.00 0.00 4.18
7279 7653 7.170965 ACAATTCTTGTGTATGTGGAGAAGAT 58.829 34.615 0.00 0.00 43.48 2.40
7305 7703 0.968901 CTGTACTCAGGCCGGTGGTA 60.969 60.000 1.90 8.30 37.97 3.25
7307 7705 1.827399 AACTGTACTCAGGCCGGTGG 61.827 60.000 1.90 3.80 45.14 4.61
7337 7735 1.336795 TGGACTGTACTCACATGTGCG 60.337 52.381 21.38 17.70 33.14 5.34
7375 7773 3.261643 AGCACTTGAGTCATGGTATCACA 59.738 43.478 10.49 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.