Multiple sequence alignment - TraesCS5B01G339200

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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 TraesCS5B01G339200 chr5B 100.000 3569 0 0 928 4496 523213361 523216929 0.000000e+00 6591
1 TraesCS5B01G339200 chr5B 100.000 517 0 0 1 517 523212434 523212950 0.000000e+00 955
2 TraesCS5B01G339200 chr5A 92.443 2726 135 35 959 3644 547332422 547329728 0.000000e+00 3827
3 TraesCS5B01G339200 chr5A 91.534 567 44 3 3927 4492 547327017 547326454 0.000000e+00 778
4 TraesCS5B01G339200 chr5A 87.452 263 15 8 3672 3932 547327295 547327049 2.050000e-73 287
5 TraesCS5B01G339200 chr5A 79.677 310 22 24 1 305 547333048 547332775 7.680000e-43 185
6 TraesCS5B01G339200 chr5D 92.175 2722 139 30 959 3659 432514691 432512023 0.000000e+00 3779
7 TraesCS5B01G339200 chr5D 92.580 566 33 4 3927 4492 432508982 432508426 0.000000e+00 804
8 TraesCS5B01G339200 chr5D 80.832 553 42 27 1 500 432515565 432515024 4.250000e-100 375
9 TraesCS5B01G339200 chr2B 86.207 580 39 16 3383 3948 53599778 53600330 1.390000e-164 590
10 TraesCS5B01G339200 chr2B 89.474 190 11 3 3137 3326 53590616 53590796 9.730000e-57 231
11 TraesCS5B01G339200 chr3B 94.902 255 13 0 4238 4492 783678604 783678350 2.520000e-107 399
12 TraesCS5B01G339200 chr3B 91.057 123 11 0 1004 1126 625336935 625336813 2.780000e-37 167
13 TraesCS5B01G339200 chr2A 86.772 378 20 9 3164 3541 746066169 746066516 1.170000e-105 394
14 TraesCS5B01G339200 chr1A 90.230 174 17 0 1614 1787 533697552 533697725 1.260000e-55 228
15 TraesCS5B01G339200 chr1A 91.870 123 10 0 1004 1126 478567440 478567562 5.980000e-39 172
16 TraesCS5B01G339200 chr1D 92.683 123 9 0 1004 1126 377973954 377974076 1.290000e-40 178
17 TraesCS5B01G339200 chr1B 91.057 123 11 0 1004 1126 505626343 505626465 2.780000e-37 167
18 TraesCS5B01G339200 chr3D 89.431 123 13 0 1004 1126 470894837 470894715 6.020000e-34 156


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 TraesCS5B01G339200 chr5B 523212434 523216929 4495 False 3773.000000 6591 100.0000 1 4496 2 chr5B.!!$F1 4495
1 TraesCS5B01G339200 chr5A 547326454 547333048 6594 True 1269.250000 3827 87.7765 1 4492 4 chr5A.!!$R1 4491
2 TraesCS5B01G339200 chr5D 432508426 432515565 7139 True 1652.666667 3779 88.5290 1 4492 3 chr5D.!!$R1 4491
3 TraesCS5B01G339200 chr2B 53599778 53600330 552 False 590.000000 590 86.2070 3383 3948 1 chr2B.!!$F2 565

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
988 1320 0.036306 TGACGGGAGGGCTTTTTCTC 59.964 55.0 0.00 0.0 0.00 2.87 F
1711 2046 0.108138 ACTGCGCCAACCAGATACTC 60.108 55.0 4.18 0.0 34.47 2.59 F
2956 3300 0.107654 GCTATGCCGGAAACCTGAGT 60.108 55.0 5.05 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2937 3281 0.107654 ACTCAGGTTTCCGGCATAGC 60.108 55.0 0.00 0.0 0.0 2.97 R
3177 3540 0.034059 AGACGGCACCAAGAGTTCAG 59.966 55.0 0.00 0.0 0.0 3.02 R
3861 8255 0.322816 GCATGCCTCCAACTCCAAGA 60.323 55.0 6.36 0.0 0.0 3.02 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
42 43 5.348451 TCCATTCATGATTCATATACACGCG 59.652 40.000 3.53 3.53 0.00 6.01
49 50 8.856247 TCATGATTCATATACACGCGTTATAAC 58.144 33.333 10.22 5.47 0.00 1.89
94 98 6.205464 CGAGGCTATCAATGTGAACCATATTT 59.795 38.462 0.00 0.00 31.97 1.40
96 100 7.719483 AGGCTATCAATGTGAACCATATTTTG 58.281 34.615 0.00 0.00 31.97 2.44
98 102 7.864379 GGCTATCAATGTGAACCATATTTTGAG 59.136 37.037 0.00 0.00 31.97 3.02
106 110 6.313658 TGTGAACCATATTTTGAGAGTCGATG 59.686 38.462 0.00 0.00 0.00 3.84
108 112 6.313658 TGAACCATATTTTGAGAGTCGATGTG 59.686 38.462 0.00 0.00 0.00 3.21
148 153 7.227512 CCTCATCCGAAATCTATTTACAAGCTT 59.772 37.037 0.00 0.00 0.00 3.74
175 180 2.344441 CGTTACCATCATCGTCACACAC 59.656 50.000 0.00 0.00 0.00 3.82
176 181 3.322369 GTTACCATCATCGTCACACACA 58.678 45.455 0.00 0.00 0.00 3.72
178 183 2.844946 ACCATCATCGTCACACACAAA 58.155 42.857 0.00 0.00 0.00 2.83
179 184 2.548057 ACCATCATCGTCACACACAAAC 59.452 45.455 0.00 0.00 0.00 2.93
180 185 2.411418 CCATCATCGTCACACACAAACG 60.411 50.000 0.00 0.00 37.74 3.60
238 249 9.664332 CATAGAAAAAGATCTGAAAAGAGGAGA 57.336 33.333 0.00 0.00 0.00 3.71
239 250 9.889128 ATAGAAAAAGATCTGAAAAGAGGAGAG 57.111 33.333 0.00 0.00 0.00 3.20
241 252 6.694445 AAAAGATCTGAAAAGAGGAGAGGA 57.306 37.500 0.00 0.00 0.00 3.71
242 253 5.937975 AAGATCTGAAAAGAGGAGAGGAG 57.062 43.478 0.00 0.00 0.00 3.69
263 274 2.592308 GGCCACATCAGTCCCTCC 59.408 66.667 0.00 0.00 0.00 4.30
264 275 2.592308 GCCACATCAGTCCCTCCC 59.408 66.667 0.00 0.00 0.00 4.30
266 277 1.307343 CCACATCAGTCCCTCCCCT 60.307 63.158 0.00 0.00 0.00 4.79
267 278 1.341156 CCACATCAGTCCCTCCCCTC 61.341 65.000 0.00 0.00 0.00 4.30
268 279 1.003573 ACATCAGTCCCTCCCCTCC 59.996 63.158 0.00 0.00 0.00 4.30
330 642 2.421314 CGCCTCCGCATCCACATA 59.579 61.111 0.00 0.00 34.03 2.29
349 661 4.603535 CGCCCCCATTCCCATCCC 62.604 72.222 0.00 0.00 0.00 3.85
350 662 4.239568 GCCCCCATTCCCATCCCC 62.240 72.222 0.00 0.00 0.00 4.81
355 677 1.701024 CCATTCCCATCCCCTCCCA 60.701 63.158 0.00 0.00 0.00 4.37
502 831 4.838486 GACGTCAGCGGCTCCGAG 62.838 72.222 21.23 3.73 44.12 4.63
504 833 4.838486 CGTCAGCGGCTCCGAGAC 62.838 72.222 13.11 16.28 42.83 3.36
505 834 4.500116 GTCAGCGGCTCCGAGACC 62.500 72.222 13.11 0.00 42.83 3.85
506 835 4.742649 TCAGCGGCTCCGAGACCT 62.743 66.667 13.11 0.00 42.83 3.85
507 836 4.200283 CAGCGGCTCCGAGACCTC 62.200 72.222 13.11 0.00 42.83 3.85
510 839 3.522731 CGGCTCCGAGACCTCCAG 61.523 72.222 1.35 0.00 42.83 3.86
511 840 3.844090 GGCTCCGAGACCTCCAGC 61.844 72.222 0.00 6.95 33.49 4.85
512 841 4.200283 GCTCCGAGACCTCCAGCG 62.200 72.222 0.00 0.00 0.00 5.18
513 842 2.438614 CTCCGAGACCTCCAGCGA 60.439 66.667 0.00 0.00 0.00 4.93
514 843 2.750637 TCCGAGACCTCCAGCGAC 60.751 66.667 0.00 0.00 0.00 5.19
515 844 2.752238 CCGAGACCTCCAGCGACT 60.752 66.667 0.00 0.00 0.00 4.18
516 845 2.487428 CGAGACCTCCAGCGACTG 59.513 66.667 0.00 0.00 0.00 3.51
988 1320 0.036306 TGACGGGAGGGCTTTTTCTC 59.964 55.000 0.00 0.00 0.00 2.87
1009 1341 3.197790 CGTTCGCCATGGCAGAGG 61.198 66.667 34.93 22.87 42.06 3.69
1204 1538 2.097160 GCTGAATGTGCGCGTCTG 59.903 61.111 8.43 1.82 0.00 3.51
1206 1540 1.417592 CTGAATGTGCGCGTCTGTC 59.582 57.895 8.43 0.00 0.00 3.51
1220 1555 3.542310 GCGTCTGTCTGTTTGTTTGTTTC 59.458 43.478 0.00 0.00 0.00 2.78
1221 1556 4.095610 CGTCTGTCTGTTTGTTTGTTTCC 58.904 43.478 0.00 0.00 0.00 3.13
1360 1695 1.371022 CATCGTCGAGCTCATCCCG 60.371 63.158 15.40 9.54 0.00 5.14
1363 1698 2.413765 GTCGAGCTCATCCCGTCC 59.586 66.667 15.40 0.00 0.00 4.79
1364 1699 3.209812 TCGAGCTCATCCCGTCCG 61.210 66.667 15.40 0.00 0.00 4.79
1708 2043 1.220749 GGACTGCGCCAACCAGATA 59.779 57.895 4.18 0.00 34.47 1.98
1711 2046 0.108138 ACTGCGCCAACCAGATACTC 60.108 55.000 4.18 0.00 34.47 2.59
1812 2147 9.797556 AAAGGTAAAACACTTCAAATTCAGTAC 57.202 29.630 0.00 0.00 0.00 2.73
1815 2150 9.874215 GGTAAAACACTTCAAATTCAGTACTAC 57.126 33.333 0.00 0.00 0.00 2.73
1816 2151 9.577003 GTAAAACACTTCAAATTCAGTACTACG 57.423 33.333 0.00 0.00 0.00 3.51
1817 2152 8.428186 AAAACACTTCAAATTCAGTACTACGA 57.572 30.769 0.00 0.00 0.00 3.43
1818 2153 8.603242 AAACACTTCAAATTCAGTACTACGAT 57.397 30.769 0.00 0.00 0.00 3.73
1819 2154 8.603242 AACACTTCAAATTCAGTACTACGATT 57.397 30.769 0.00 0.00 0.00 3.34
1820 2155 8.240883 ACACTTCAAATTCAGTACTACGATTC 57.759 34.615 0.00 0.00 0.00 2.52
1821 2156 7.870954 ACACTTCAAATTCAGTACTACGATTCA 59.129 33.333 0.00 0.00 0.00 2.57
1822 2157 8.162880 CACTTCAAATTCAGTACTACGATTCAC 58.837 37.037 0.00 0.00 0.00 3.18
1824 2159 7.812309 TCAAATTCAGTACTACGATTCACTG 57.188 36.000 0.00 0.00 39.79 3.66
1847 2182 1.688735 ACTAACTGTCACTGAGCTGCA 59.311 47.619 1.02 0.00 0.00 4.41
1862 2197 2.227388 AGCTGCAATGCACACTTAAGTC 59.773 45.455 2.72 0.00 33.79 3.01
1864 2199 2.217750 TGCAATGCACACTTAAGTCGT 58.782 42.857 2.72 5.08 31.71 4.34
1867 2202 3.548014 GCAATGCACACTTAAGTCGTTGT 60.548 43.478 20.37 9.22 0.00 3.32
1882 2217 4.056050 GTCGTTGTGAAGAGTGTACCAAT 58.944 43.478 0.00 0.00 0.00 3.16
1886 2221 3.146066 TGTGAAGAGTGTACCAATTGCC 58.854 45.455 0.00 0.00 0.00 4.52
1891 2226 4.098914 AGAGTGTACCAATTGCCTGAAA 57.901 40.909 0.00 0.00 0.00 2.69
1897 2232 6.493458 AGTGTACCAATTGCCTGAAATACTTT 59.507 34.615 0.00 0.00 0.00 2.66
1898 2233 6.586082 GTGTACCAATTGCCTGAAATACTTTG 59.414 38.462 0.00 0.00 0.00 2.77
1902 2237 6.705825 ACCAATTGCCTGAAATACTTTGTTTC 59.294 34.615 0.00 0.00 36.39 2.78
1904 2239 5.759506 TTGCCTGAAATACTTTGTTTCGA 57.240 34.783 0.00 0.00 38.18 3.71
1919 2254 8.400947 ACTTTGTTTCGATCATGGATATTTCTG 58.599 33.333 0.00 0.00 0.00 3.02
1921 2256 7.864108 TGTTTCGATCATGGATATTTCTGTT 57.136 32.000 0.00 0.00 0.00 3.16
1974 2311 8.184192 GTGTGGACATTTCTATCAATAGGTTTG 58.816 37.037 0.00 0.00 0.00 2.93
2046 2383 5.930569 GGGTGAGATAATTTACCGGTACATC 59.069 44.000 15.53 14.01 34.01 3.06
2169 2506 1.208293 GTCTGGAGACTAAAGGGCCAG 59.792 57.143 6.18 0.00 45.77 4.85
2214 2551 2.562738 GTCAAAGAAATCTTGGGGTGGG 59.437 50.000 0.00 0.00 36.12 4.61
2280 2617 2.771763 AAAGAGCCGACGGTCTGCTG 62.772 60.000 28.02 2.92 46.12 4.41
2358 2695 9.975218 AACAAGATCCAGTATAACAAGGTTAAT 57.025 29.630 0.00 0.00 0.00 1.40
2414 2752 3.054878 CCTTGAAAGTGATTGCTTGCAC 58.945 45.455 0.00 0.00 34.00 4.57
2432 2770 5.885230 TGCACTTCTATTTGTCCATTCAG 57.115 39.130 0.00 0.00 0.00 3.02
2435 2773 6.660521 TGCACTTCTATTTGTCCATTCAGAAT 59.339 34.615 0.00 0.00 0.00 2.40
2464 2802 8.506168 TTCTTAATAAACCTGGAGCATACAAG 57.494 34.615 0.00 0.00 0.00 3.16
2465 2803 7.630082 TCTTAATAAACCTGGAGCATACAAGT 58.370 34.615 0.00 0.00 0.00 3.16
2466 2804 8.764558 TCTTAATAAACCTGGAGCATACAAGTA 58.235 33.333 0.00 0.00 0.00 2.24
2467 2805 8.726870 TTAATAAACCTGGAGCATACAAGTAC 57.273 34.615 0.00 0.00 0.00 2.73
2503 2841 5.931441 AACTTGCTCTGTTAACATCACTC 57.069 39.130 9.13 0.00 0.00 3.51
2545 2886 5.872617 GCTTAAACAAAGTTTCACCCTGTTT 59.127 36.000 6.40 6.40 41.65 2.83
2548 2889 6.844097 AAACAAAGTTTCACCCTGTTTCTA 57.156 33.333 0.00 0.00 35.82 2.10
2559 2900 3.458487 ACCCTGTTTCTACCTTGTCTTGT 59.542 43.478 0.00 0.00 0.00 3.16
2572 2913 0.608640 GTCTTGTCCAGGATGTCGGT 59.391 55.000 0.00 0.00 0.00 4.69
2602 2943 3.991367 ACTTGAAAGTTACTCGAGGGTG 58.009 45.455 18.41 0.00 35.21 4.61
2635 2976 1.333702 GCGTTCAACACAATTGCGAGA 60.334 47.619 5.05 0.00 0.00 4.04
2770 3111 1.134580 CCATTCTCGATCCAGCACACT 60.135 52.381 0.00 0.00 0.00 3.55
2788 3129 1.307517 TCCATACGCCTCCCCCTTT 60.308 57.895 0.00 0.00 0.00 3.11
2874 3215 1.515521 CCGCCGAGCAAAAAGAACCT 61.516 55.000 0.00 0.00 0.00 3.50
2937 3281 3.118956 GGTGATGTAGAGAAGGTGTGGAG 60.119 52.174 0.00 0.00 0.00 3.86
2956 3300 0.107654 GCTATGCCGGAAACCTGAGT 60.108 55.000 5.05 0.00 0.00 3.41
3092 3455 4.322725 CCCTGTACAGAAGCAACATCAGTA 60.323 45.833 24.68 0.00 0.00 2.74
3117 3480 2.663826 TTTTTGTGCTTTCTTGGCGT 57.336 40.000 0.00 0.00 0.00 5.68
3144 3507 1.620413 CCGCGGACCGTGTACTTTTC 61.620 60.000 24.07 0.00 35.46 2.29
3156 3519 1.709115 GTACTTTTCACCCCCTCCCTT 59.291 52.381 0.00 0.00 0.00 3.95
3177 3540 6.183360 CCCTTCTCACCTAGTAATGGAGTAAC 60.183 46.154 0.00 0.00 0.00 2.50
3188 3551 6.702329 AGTAATGGAGTAACTGAACTCTTGG 58.298 40.000 12.31 0.00 44.42 3.61
3203 3566 1.001633 TCTTGGTGCCGTCTAGTTTCC 59.998 52.381 0.00 0.00 0.00 3.13
3289 3652 4.659172 TCGGGTTGGGCAGCAAGG 62.659 66.667 0.00 0.00 0.00 3.61
3294 3657 4.918278 TTGGGCAGCAAGGCAGCA 62.918 61.111 7.86 0.00 42.80 4.41
3317 3683 5.368256 AGTGATTGAACTTGAGATGTTGC 57.632 39.130 0.00 0.00 0.00 4.17
3416 3783 3.004315 CAGTGGGATGTTTGTTGTGGTAC 59.996 47.826 0.00 0.00 0.00 3.34
3417 3784 2.031508 GTGGGATGTTTGTTGTGGTACG 60.032 50.000 0.00 0.00 0.00 3.67
3418 3785 1.068816 GGGATGTTTGTTGTGGTACGC 60.069 52.381 0.00 0.00 40.62 4.42
3419 3786 1.877443 GGATGTTTGTTGTGGTACGCT 59.123 47.619 0.00 0.00 40.97 5.07
3481 3852 7.994911 ACTTACATGCTCCTTGATGAATTGATA 59.005 33.333 0.00 0.00 0.00 2.15
3651 4033 6.797033 GCTGTGTGCAAATTAGTTACAGTTAG 59.203 38.462 0.00 0.00 42.31 2.34
3655 4037 7.797123 GTGTGCAAATTAGTTACAGTTAGTGTC 59.203 37.037 0.00 0.00 40.94 3.67
3665 8058 7.208080 AGTTACAGTTAGTGTCTTAACCAGTG 58.792 38.462 0.00 0.00 40.94 3.66
3666 8059 4.377897 ACAGTTAGTGTCTTAACCAGTGC 58.622 43.478 0.00 0.00 31.90 4.40
3670 8063 5.303589 AGTTAGTGTCTTAACCAGTGCAGTA 59.696 40.000 0.00 0.00 34.75 2.74
3681 8074 3.006323 ACCAGTGCAGTAGTTTCTCTCTG 59.994 47.826 0.00 0.00 0.00 3.35
3716 8110 1.919600 GCTTGGCCTCTCCATGGAGT 61.920 60.000 35.34 0.00 46.04 3.85
3724 8118 3.873801 GCCTCTCCATGGAGTAAGCAAAA 60.874 47.826 35.34 16.76 42.49 2.44
3726 8120 3.944015 CTCTCCATGGAGTAAGCAAAAGG 59.056 47.826 35.34 11.72 42.49 3.11
3727 8121 3.587061 TCTCCATGGAGTAAGCAAAAGGA 59.413 43.478 35.34 13.81 42.49 3.36
3728 8122 3.686016 TCCATGGAGTAAGCAAAAGGAC 58.314 45.455 11.44 0.00 0.00 3.85
3729 8123 3.073798 TCCATGGAGTAAGCAAAAGGACA 59.926 43.478 11.44 0.00 0.00 4.02
3770 8164 1.474077 GCAAAGCCATCGAAACCTCAT 59.526 47.619 0.00 0.00 0.00 2.90
3771 8165 2.733227 GCAAAGCCATCGAAACCTCATG 60.733 50.000 0.00 0.00 0.00 3.07
3772 8166 1.098050 AAGCCATCGAAACCTCATGC 58.902 50.000 0.00 0.00 0.00 4.06
3773 8167 0.254178 AGCCATCGAAACCTCATGCT 59.746 50.000 0.00 0.00 0.00 3.79
3774 8168 0.659957 GCCATCGAAACCTCATGCTC 59.340 55.000 0.00 0.00 0.00 4.26
3775 8169 2.013563 GCCATCGAAACCTCATGCTCA 61.014 52.381 0.00 0.00 0.00 4.26
3834 8228 1.684049 CGTGGCCTTCCTCTCCTCT 60.684 63.158 3.32 0.00 0.00 3.69
3835 8229 1.671901 CGTGGCCTTCCTCTCCTCTC 61.672 65.000 3.32 0.00 0.00 3.20
3861 8255 1.749063 TCATCTGATCGTACGCCTTGT 59.251 47.619 11.24 0.00 0.00 3.16
3958 8389 2.548904 CGTGCTCGTATAAGTAGAGGCT 59.451 50.000 0.00 0.00 32.96 4.58
3960 8391 2.293677 TGCTCGTATAAGTAGAGGCTGC 59.706 50.000 0.00 0.00 32.96 5.25
4004 8436 2.954318 TCTGCAAGCTGCTTCTTTCTTT 59.046 40.909 12.82 0.00 45.31 2.52
4008 8440 3.306818 CAAGCTGCTTCTTTCTTTCTGC 58.693 45.455 12.82 0.00 0.00 4.26
4010 8442 1.885233 GCTGCTTCTTTCTTTCTGCCT 59.115 47.619 0.00 0.00 0.00 4.75
4026 8458 3.238241 CTGCGTAGTTCGACGGCG 61.238 66.667 2.87 2.87 43.13 6.46
4057 8489 0.525761 GCGACAGACAGAGAGAAGCT 59.474 55.000 0.00 0.00 0.00 3.74
4060 8492 1.271934 GACAGACAGAGAGAAGCTGCA 59.728 52.381 1.02 0.00 36.86 4.41
4061 8493 1.690893 ACAGACAGAGAGAAGCTGCAA 59.309 47.619 1.02 0.00 36.86 4.08
4062 8494 2.067766 CAGACAGAGAGAAGCTGCAAC 58.932 52.381 1.02 0.00 36.86 4.17
4068 8500 1.001860 GAGAGAAGCTGCAACTCACCT 59.998 52.381 21.32 8.90 33.69 4.00
4071 8503 2.180131 GAAGCTGCAACTCACCTGCG 62.180 60.000 1.02 0.00 42.97 5.18
4432 8864 4.593864 GACGCGATCCTCTGCCCC 62.594 72.222 15.93 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 8.748582 TCTTCTTTGTTATAACGCGTGTATATG 58.251 33.333 14.98 0.00 0.00 1.78
32 33 8.861033 TCTTCTTTGTTATAACGCGTGTATAT 57.139 30.769 14.98 10.07 0.00 0.86
49 50 5.046910 TCGCATTAAGGCTTTCTTCTTTG 57.953 39.130 10.75 0.00 36.93 2.77
94 98 0.969149 ACAGGCACATCGACTCTCAA 59.031 50.000 0.00 0.00 0.00 3.02
96 100 1.535015 GCTACAGGCACATCGACTCTC 60.535 57.143 0.00 0.00 41.35 3.20
98 102 0.867753 CGCTACAGGCACATCGACTC 60.868 60.000 0.00 0.00 41.91 3.36
106 110 0.031449 GAGGAGATCGCTACAGGCAC 59.969 60.000 0.00 0.00 41.91 5.01
108 112 0.965439 ATGAGGAGATCGCTACAGGC 59.035 55.000 0.00 0.00 37.64 4.85
117 121 8.307483 TGTAAATAGATTTCGGATGAGGAGATC 58.693 37.037 0.00 0.00 0.00 2.75
148 153 2.100252 GACGATGATGGTAACGGAAGGA 59.900 50.000 0.00 0.00 42.51 3.36
175 180 2.311701 TACCGGCGTGCTTCGTTTG 61.312 57.895 6.01 0.00 42.13 2.93
176 181 2.029369 TACCGGCGTGCTTCGTTT 59.971 55.556 6.01 0.00 42.13 3.60
178 183 3.909258 CTGTACCGGCGTGCTTCGT 62.909 63.158 6.01 0.00 42.13 3.85
179 184 3.179265 CTGTACCGGCGTGCTTCG 61.179 66.667 6.01 0.00 43.12 3.79
180 185 2.813908 CCTGTACCGGCGTGCTTC 60.814 66.667 6.01 0.00 0.00 3.86
330 642 2.845345 GGATGGGAATGGGGGCGAT 61.845 63.158 0.00 0.00 0.00 4.58
349 661 4.864334 GCATCTGGCGGTGGGAGG 62.864 72.222 0.00 0.00 0.00 4.30
959 1288 2.303175 CCCTCCCGTCAGAAACAAAAA 58.697 47.619 0.00 0.00 0.00 1.94
960 1289 1.975660 CCCTCCCGTCAGAAACAAAA 58.024 50.000 0.00 0.00 0.00 2.44
961 1290 0.536460 GCCCTCCCGTCAGAAACAAA 60.536 55.000 0.00 0.00 0.00 2.83
962 1291 1.072505 GCCCTCCCGTCAGAAACAA 59.927 57.895 0.00 0.00 0.00 2.83
963 1292 1.415672 AAGCCCTCCCGTCAGAAACA 61.416 55.000 0.00 0.00 0.00 2.83
964 1293 0.250770 AAAGCCCTCCCGTCAGAAAC 60.251 55.000 0.00 0.00 0.00 2.78
978 1307 0.110192 CGAACGCAGGAGAAAAAGCC 60.110 55.000 0.00 0.00 0.00 4.35
1009 1341 1.203928 CGCTCCTTCATCATGTCGAC 58.796 55.000 9.11 9.11 0.00 4.20
1131 1463 2.028112 TGAAGTGATTGACCGAGGGAAG 60.028 50.000 0.00 0.00 0.00 3.46
1204 1538 5.324784 AGGAAGGAAACAAACAAACAGAC 57.675 39.130 0.00 0.00 0.00 3.51
1206 1540 5.109210 GGAAGGAAGGAAACAAACAAACAG 58.891 41.667 0.00 0.00 0.00 3.16
1220 1555 1.079336 GACGGGTTCGGAAGGAAGG 60.079 63.158 0.00 0.00 41.39 3.46
1221 1556 1.079336 GGACGGGTTCGGAAGGAAG 60.079 63.158 0.00 0.00 41.39 3.46
1306 1641 2.765807 AGCCAGTCCATCTCCCGG 60.766 66.667 0.00 0.00 0.00 5.73
1360 1695 3.462678 GGGAGCTCCTGGACGGAC 61.463 72.222 31.36 9.17 36.69 4.79
1364 1699 3.462678 GTCGGGGAGCTCCTGGAC 61.463 72.222 31.36 29.68 42.31 4.02
1667 2002 1.901654 CTCTGCTGCAGCTTCCTCCT 61.902 60.000 36.61 0.00 42.66 3.69
1812 2147 5.881447 ACAGTTAGTAGCAGTGAATCGTAG 58.119 41.667 0.00 0.00 0.00 3.51
1815 2150 4.559251 GTGACAGTTAGTAGCAGTGAATCG 59.441 45.833 0.00 0.00 0.00 3.34
1816 2151 5.574830 CAGTGACAGTTAGTAGCAGTGAATC 59.425 44.000 0.00 0.00 32.99 2.52
1817 2152 5.243954 TCAGTGACAGTTAGTAGCAGTGAAT 59.756 40.000 0.00 0.00 36.36 2.57
1818 2153 4.583073 TCAGTGACAGTTAGTAGCAGTGAA 59.417 41.667 0.00 0.00 36.36 3.18
1819 2154 4.142038 TCAGTGACAGTTAGTAGCAGTGA 58.858 43.478 0.00 0.00 36.79 3.41
1820 2155 4.480541 CTCAGTGACAGTTAGTAGCAGTG 58.519 47.826 0.00 0.00 0.00 3.66
1821 2156 3.057174 GCTCAGTGACAGTTAGTAGCAGT 60.057 47.826 0.00 0.00 0.00 4.40
1822 2157 3.192422 AGCTCAGTGACAGTTAGTAGCAG 59.808 47.826 0.00 0.00 0.00 4.24
1824 2159 3.506810 CAGCTCAGTGACAGTTAGTAGC 58.493 50.000 0.00 0.00 0.00 3.58
1847 2182 3.874543 TCACAACGACTTAAGTGTGCATT 59.125 39.130 14.14 0.00 33.84 3.56
1862 2197 4.772434 CAATTGGTACACTCTTCACAACG 58.228 43.478 0.00 0.00 39.29 4.10
1864 2199 3.568007 GGCAATTGGTACACTCTTCACAA 59.432 43.478 7.72 0.00 39.29 3.33
1867 2202 3.072330 TCAGGCAATTGGTACACTCTTCA 59.928 43.478 7.72 0.00 39.29 3.02
1882 2217 5.759506 TCGAAACAAAGTATTTCAGGCAA 57.240 34.783 0.00 0.00 35.03 4.52
1886 2221 7.751732 TCCATGATCGAAACAAAGTATTTCAG 58.248 34.615 0.00 0.00 35.03 3.02
1897 2232 7.864108 AACAGAAATATCCATGATCGAAACA 57.136 32.000 0.00 0.00 0.00 2.83
1902 2237 9.603298 CACAATTAACAGAAATATCCATGATCG 57.397 33.333 0.00 0.00 0.00 3.69
1944 2279 8.739039 CCTATTGATAGAAATGTCCACACAAAA 58.261 33.333 0.00 0.00 32.14 2.44
1945 2280 7.888021 ACCTATTGATAGAAATGTCCACACAAA 59.112 33.333 0.00 0.00 32.14 2.83
1946 2281 7.402054 ACCTATTGATAGAAATGTCCACACAA 58.598 34.615 0.00 0.00 32.14 3.33
1948 2283 7.865706 AACCTATTGATAGAAATGTCCACAC 57.134 36.000 0.00 0.00 32.05 3.82
1949 2284 7.888021 ACAAACCTATTGATAGAAATGTCCACA 59.112 33.333 0.00 0.00 32.05 4.17
1950 2285 8.281212 ACAAACCTATTGATAGAAATGTCCAC 57.719 34.615 0.00 0.00 32.05 4.02
1951 2286 8.106462 TGACAAACCTATTGATAGAAATGTCCA 58.894 33.333 17.44 9.76 36.31 4.02
1952 2287 8.506168 TGACAAACCTATTGATAGAAATGTCC 57.494 34.615 17.44 8.37 36.31 4.02
2046 2383 1.197721 GGTGAGAATTGTTCAGCCGTG 59.802 52.381 7.26 0.00 37.15 4.94
2169 2506 1.497722 CTGAGGCGCCGTTTTCTTC 59.502 57.895 23.20 12.00 0.00 2.87
2214 2551 3.551846 TCCAACAAGACCCTTCACTTTC 58.448 45.455 0.00 0.00 0.00 2.62
2280 2617 2.002586 TGTCGCAATCTTAAGCTCTGC 58.997 47.619 11.21 11.21 0.00 4.26
2358 2695 6.269077 TCAAACTGAGTAGGTGTGAAGGATTA 59.731 38.462 0.00 0.00 0.00 1.75
2362 2699 4.336889 TCAAACTGAGTAGGTGTGAAGG 57.663 45.455 0.00 0.00 0.00 3.46
2432 2770 8.686334 TGCTCCAGGTTTATTAAGAATCAATTC 58.314 33.333 0.00 0.00 37.06 2.17
2435 2773 9.120538 GTATGCTCCAGGTTTATTAAGAATCAA 57.879 33.333 0.00 0.00 0.00 2.57
2443 2781 8.086143 AGTACTTGTATGCTCCAGGTTTATTA 57.914 34.615 0.00 0.00 0.00 0.98
2444 2782 6.958767 AGTACTTGTATGCTCCAGGTTTATT 58.041 36.000 0.00 0.00 0.00 1.40
2445 2783 6.561519 AGTACTTGTATGCTCCAGGTTTAT 57.438 37.500 0.00 0.00 0.00 1.40
2448 2786 4.910458 AAGTACTTGTATGCTCCAGGTT 57.090 40.909 7.48 0.00 0.00 3.50
2464 2802 8.940952 AGAGCAAGTTTCTGATGATAAAAGTAC 58.059 33.333 0.00 0.00 0.00 2.73
2465 2803 8.939929 CAGAGCAAGTTTCTGATGATAAAAGTA 58.060 33.333 0.00 0.00 43.75 2.24
2466 2804 7.446625 ACAGAGCAAGTTTCTGATGATAAAAGT 59.553 33.333 10.83 0.00 43.75 2.66
2467 2805 7.814642 ACAGAGCAAGTTTCTGATGATAAAAG 58.185 34.615 10.83 0.00 43.75 2.27
2503 2841 7.700234 TGTTTAAGCAAGTCATGTACAAAGTTG 59.300 33.333 18.22 18.22 0.00 3.16
2545 2886 3.254093 TCCTGGACAAGACAAGGTAGA 57.746 47.619 0.00 0.00 0.00 2.59
2548 2889 2.039084 GACATCCTGGACAAGACAAGGT 59.961 50.000 0.00 0.00 0.00 3.50
2559 2900 0.970937 GGACTGACCGACATCCTGGA 60.971 60.000 0.00 0.00 0.00 3.86
2572 2913 6.208007 TCGAGTAACTTTCAAGTATGGACTGA 59.792 38.462 0.00 0.00 38.57 3.41
2635 2976 2.364243 CGTAGATCACGTCGTCGATT 57.636 50.000 9.47 0.00 45.82 3.34
2770 3111 1.307517 AAAGGGGGAGGCGTATGGA 60.308 57.895 0.00 0.00 0.00 3.41
2788 3129 2.515398 CAGAAGGTGGGTGTGGCA 59.485 61.111 0.00 0.00 0.00 4.92
2874 3215 2.852495 GATCTCGGGTTTCGCTGGCA 62.852 60.000 0.00 0.00 39.05 4.92
2937 3281 0.107654 ACTCAGGTTTCCGGCATAGC 60.108 55.000 0.00 0.00 0.00 2.97
2974 3318 4.735132 TCCCTTTCAGGCGCGTCG 62.735 66.667 8.43 1.39 32.73 5.12
2980 3324 2.278332 AAACTCAGTCCCTTTCAGGC 57.722 50.000 0.00 0.00 32.73 4.85
3144 3507 2.301738 GGTGAGAAGGGAGGGGGTG 61.302 68.421 0.00 0.00 0.00 4.61
3156 3519 6.728411 TCAGTTACTCCATTACTAGGTGAGA 58.272 40.000 0.00 0.00 0.00 3.27
3177 3540 0.034059 AGACGGCACCAAGAGTTCAG 59.966 55.000 0.00 0.00 0.00 3.02
3188 3551 1.270147 ACACAGGAAACTAGACGGCAC 60.270 52.381 0.00 0.00 40.21 5.01
3203 3566 2.861750 GCTGACTGACTGACTGACACAG 60.862 54.545 0.00 0.00 40.68 3.66
3294 3657 5.533903 AGCAACATCTCAAGTTCAATCACTT 59.466 36.000 0.00 0.00 37.49 3.16
3317 3683 2.107292 CCTACAGCAGCAGCAGCAG 61.107 63.158 12.92 6.60 45.49 4.24
3352 3718 2.034687 CCACTGGTGGCTTCAGGG 59.965 66.667 6.84 7.54 44.73 4.45
3416 3783 4.465512 GAATGCACGGCCACAGCG 62.466 66.667 2.24 0.00 41.24 5.18
3417 3784 3.044059 GAGAATGCACGGCCACAGC 62.044 63.158 2.24 3.43 38.76 4.40
3418 3785 1.028330 ATGAGAATGCACGGCCACAG 61.028 55.000 2.24 0.00 0.00 3.66
3419 3786 1.002257 ATGAGAATGCACGGCCACA 60.002 52.632 2.24 0.00 0.00 4.17
3481 3852 7.301054 CAAAGAAATGAAGAAACTAGCGTCAT 58.699 34.615 0.00 0.00 36.31 3.06
3651 4033 3.991367 ACTACTGCACTGGTTAAGACAC 58.009 45.455 0.00 0.00 0.00 3.67
3655 4037 5.542779 AGAGAAACTACTGCACTGGTTAAG 58.457 41.667 0.00 0.00 0.00 1.85
3659 4041 3.006323 CAGAGAGAAACTACTGCACTGGT 59.994 47.826 0.00 0.00 0.00 4.00
3660 4042 3.006323 ACAGAGAGAAACTACTGCACTGG 59.994 47.826 0.00 0.00 34.25 4.00
3665 8058 2.342179 GCCACAGAGAGAAACTACTGC 58.658 52.381 0.00 0.00 34.25 4.40
3666 8059 2.564947 AGGCCACAGAGAGAAACTACTG 59.435 50.000 5.01 0.00 36.58 2.74
3670 8063 1.071385 CACAGGCCACAGAGAGAAACT 59.929 52.381 5.01 0.00 0.00 2.66
3681 8074 2.439156 GCAGATCCCACAGGCCAC 60.439 66.667 5.01 0.00 0.00 5.01
3716 8110 5.298276 CAGTAACAAGGTGTCCTTTTGCTTA 59.702 40.000 0.00 0.00 41.69 3.09
3724 8118 2.775384 TGGTTCAGTAACAAGGTGTCCT 59.225 45.455 0.00 0.00 37.34 3.85
3726 8120 3.311596 GTGTGGTTCAGTAACAAGGTGTC 59.688 47.826 0.00 0.00 37.34 3.67
3727 8121 3.275999 GTGTGGTTCAGTAACAAGGTGT 58.724 45.455 0.00 0.00 37.34 4.16
3728 8122 2.286833 CGTGTGGTTCAGTAACAAGGTG 59.713 50.000 0.00 0.00 37.34 4.00
3729 8123 2.557317 CGTGTGGTTCAGTAACAAGGT 58.443 47.619 0.00 0.00 37.34 3.50
3790 8184 8.070171 GCTTGGTATATTTGTAGTGCAAGTATG 58.930 37.037 15.95 3.81 39.38 2.39
3802 8196 2.021457 GGCCACGCTTGGTATATTTGT 58.979 47.619 11.38 0.00 45.98 2.83
3861 8255 0.322816 GCATGCCTCCAACTCCAAGA 60.323 55.000 6.36 0.00 0.00 3.02
3960 8391 4.899239 GAGGACCATGGCCTCGCG 62.899 72.222 28.34 0.00 42.22 5.87
4004 8436 1.211969 GTCGAACTACGCAGGCAGA 59.788 57.895 0.00 0.00 42.26 4.26
4008 8440 2.879462 GCCGTCGAACTACGCAGG 60.879 66.667 0.00 0.00 41.51 4.85
4010 8442 4.764336 CCGCCGTCGAACTACGCA 62.764 66.667 0.00 0.00 41.51 5.24
4039 8471 1.732077 GCAGCTTCTCTCTGTCTGTCG 60.732 57.143 0.00 0.00 34.21 4.35
4121 8553 4.452733 CACCGCCGTCCCCTTCTC 62.453 72.222 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.