Multiple sequence alignment - TraesCS5D01G382900

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G382900 chr5D 100.000 4919 0 0 1 4919 452495087 452500005 0.000000e+00 9084.0
1 TraesCS5D01G382900 chr5D 91.667 84 7 0 1219 1302 546858322 546858405 3.110000e-22 117.0
2 TraesCS5D01G382900 chr5A 92.940 4051 192 41 855 4858 571427755 571431758 0.000000e+00 5810.0
3 TraesCS5D01G382900 chr5A 92.500 120 6 3 4795 4914 571431740 571431856 8.470000e-38 169.0
4 TraesCS5D01G382900 chr5B 92.911 2243 89 18 716 2914 552840068 552842284 0.000000e+00 3197.0
5 TraesCS5D01G382900 chr5B 95.003 1741 56 14 3063 4790 552842706 552844428 0.000000e+00 2704.0
6 TraesCS5D01G382900 chr5B 87.563 394 23 8 313 696 552839116 552839493 2.720000e-117 433.0
7 TraesCS5D01G382900 chr5B 83.172 309 13 11 2 310 552838682 552838951 3.800000e-61 246.0
8 TraesCS5D01G382900 chr5B 96.552 87 3 0 2897 2983 552842626 552842712 1.430000e-30 145.0
9 TraesCS5D01G382900 chr5B 86.207 58 7 1 1219 1275 690024980 690025037 1.480000e-05 62.1


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 TraesCS5D01G382900 chr5D 452495087 452500005 4918 False 9084.0 9084 100.0000 1 4919 1 chr5D.!!$F1 4918
1 TraesCS5D01G382900 chr5A 571427755 571431856 4101 False 2989.5 5810 92.7200 855 4914 2 chr5A.!!$F1 4059
2 TraesCS5D01G382900 chr5B 552838682 552844428 5746 False 1345.0 3197 91.0402 2 4790 5 chr5B.!!$F2 4788

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
709 882 0.165295 GAAAGGCCGACAAGTAACGC 59.835 55.0 0.00 0.0 0.00 4.84 F
1342 2109 0.108472 GCCTTCTTCCATGCTTTGGC 60.108 55.0 1.73 0.0 46.01 4.52 F
2313 3093 0.530650 ACTTCAGCGACACCACACTG 60.531 55.0 0.00 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2691 3476 0.260230 TTCCCACTGCTGGAAACCAA 59.740 50.0 0.0 0.0 40.55 3.67 R
2981 4126 0.546267 AGAGGTGGCTGATGGAGTGT 60.546 55.0 0.0 0.0 0.00 3.55 R
3928 5079 0.110486 ACAAACGGTCATTCCAGCCT 59.890 50.0 0.0 0.0 35.57 4.58 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
17 18 2.888863 GGAGACCTCTGACTGCGG 59.111 66.667 0.00 0.00 0.00 5.69
33 34 2.181021 GGGAACGACGACGATGCT 59.819 61.111 15.32 0.00 42.66 3.79
41 42 2.815211 CGACGATGCTGGTGGTGG 60.815 66.667 0.00 0.00 0.00 4.61
61 62 2.622436 GCATGAACTGGACACCTACTC 58.378 52.381 0.00 0.00 0.00 2.59
74 75 4.430441 ACACCTACTCTGGGAAAAGAGAT 58.570 43.478 8.16 0.00 45.59 2.75
78 79 5.659079 ACCTACTCTGGGAAAAGAGATAGTG 59.341 44.000 8.16 4.20 45.59 2.74
79 80 5.659079 CCTACTCTGGGAAAAGAGATAGTGT 59.341 44.000 8.16 0.00 45.59 3.55
80 81 5.669164 ACTCTGGGAAAAGAGATAGTGTC 57.331 43.478 8.16 0.00 45.59 3.67
81 82 5.087323 ACTCTGGGAAAAGAGATAGTGTCA 58.913 41.667 8.16 0.00 45.59 3.58
82 83 5.544176 ACTCTGGGAAAAGAGATAGTGTCAA 59.456 40.000 8.16 0.00 45.59 3.18
83 84 5.794894 TCTGGGAAAAGAGATAGTGTCAAC 58.205 41.667 0.00 0.00 0.00 3.18
84 85 4.566004 TGGGAAAAGAGATAGTGTCAACG 58.434 43.478 0.00 0.00 0.00 4.10
85 86 4.039973 TGGGAAAAGAGATAGTGTCAACGT 59.960 41.667 0.00 0.00 0.00 3.99
86 87 4.626172 GGGAAAAGAGATAGTGTCAACGTC 59.374 45.833 0.00 0.00 0.00 4.34
87 88 4.626172 GGAAAAGAGATAGTGTCAACGTCC 59.374 45.833 0.00 0.00 0.00 4.79
88 89 5.470047 AAAAGAGATAGTGTCAACGTCCT 57.530 39.130 0.00 0.00 0.00 3.85
89 90 6.349944 GGAAAAGAGATAGTGTCAACGTCCTA 60.350 42.308 0.00 0.00 0.00 2.94
90 91 6.585695 AAAGAGATAGTGTCAACGTCCTAA 57.414 37.500 0.00 0.00 0.00 2.69
91 92 6.585695 AAGAGATAGTGTCAACGTCCTAAA 57.414 37.500 0.00 0.00 0.00 1.85
92 93 5.952033 AGAGATAGTGTCAACGTCCTAAAC 58.048 41.667 0.00 0.00 0.00 2.01
93 94 5.475909 AGAGATAGTGTCAACGTCCTAAACA 59.524 40.000 0.00 0.00 0.00 2.83
94 95 5.710984 AGATAGTGTCAACGTCCTAAACAG 58.289 41.667 0.00 0.00 0.00 3.16
95 96 3.814005 AGTGTCAACGTCCTAAACAGT 57.186 42.857 0.00 0.00 0.00 3.55
96 97 3.454375 AGTGTCAACGTCCTAAACAGTG 58.546 45.455 0.00 0.00 0.00 3.66
97 98 2.542595 GTGTCAACGTCCTAAACAGTGG 59.457 50.000 0.00 0.00 0.00 4.00
98 99 1.529865 GTCAACGTCCTAAACAGTGGC 59.470 52.381 0.00 0.00 0.00 5.01
99 100 0.872388 CAACGTCCTAAACAGTGGCC 59.128 55.000 0.00 0.00 0.00 5.36
100 101 0.470766 AACGTCCTAAACAGTGGCCA 59.529 50.000 0.00 0.00 0.00 5.36
118 119 3.243602 GGCCAAAACCGTCTAACATTTGT 60.244 43.478 0.00 0.00 30.89 2.83
150 151 2.176798 TCAAAACCACTCAAGGGGATGT 59.823 45.455 5.03 0.00 0.00 3.06
157 158 5.506708 ACCACTCAAGGGGATGTTTTATAC 58.493 41.667 5.03 0.00 0.00 1.47
166 167 7.576861 AGGGGATGTTTTATACGGTTTTATG 57.423 36.000 0.00 0.00 0.00 1.90
212 213 6.183360 GCAAAATTGCGTTTAGGAGATTTCAG 60.183 38.462 1.90 0.00 45.11 3.02
219 220 5.582665 GCGTTTAGGAGATTTCAGAGTGATT 59.417 40.000 0.00 0.00 0.00 2.57
220 221 6.092807 GCGTTTAGGAGATTTCAGAGTGATTT 59.907 38.462 0.00 0.00 0.00 2.17
221 222 7.459486 CGTTTAGGAGATTTCAGAGTGATTTG 58.541 38.462 0.00 0.00 0.00 2.32
222 223 7.118390 CGTTTAGGAGATTTCAGAGTGATTTGT 59.882 37.037 0.00 0.00 0.00 2.83
223 224 9.436957 GTTTAGGAGATTTCAGAGTGATTTGTA 57.563 33.333 0.00 0.00 0.00 2.41
227 228 8.986991 AGGAGATTTCAGAGTGATTTGTATACT 58.013 33.333 4.17 0.00 0.00 2.12
228 229 9.606631 GGAGATTTCAGAGTGATTTGTATACTT 57.393 33.333 4.17 0.00 0.00 2.24
246 247 3.733337 ACTTCTTTCTTCTGACATGCGT 58.267 40.909 0.00 0.00 0.00 5.24
310 311 3.618351 CCAATTATTGCCCATGCCAAAA 58.382 40.909 0.00 0.27 36.33 2.44
338 501 0.322648 GCCCATGCAAAAAGAAGGCT 59.677 50.000 0.00 0.00 36.00 4.58
339 502 1.673923 GCCCATGCAAAAAGAAGGCTC 60.674 52.381 0.00 0.00 36.00 4.70
343 506 2.995466 TGCAAAAAGAAGGCTCATCG 57.005 45.000 0.00 0.00 0.00 3.84
352 515 1.943340 GAAGGCTCATCGATCCCAAAC 59.057 52.381 0.00 0.00 0.00 2.93
353 516 0.181350 AGGCTCATCGATCCCAAACC 59.819 55.000 0.00 0.00 0.00 3.27
355 518 1.416401 GGCTCATCGATCCCAAACCTA 59.584 52.381 0.00 0.00 0.00 3.08
356 519 2.548920 GGCTCATCGATCCCAAACCTAG 60.549 54.545 0.00 0.00 0.00 3.02
357 520 2.760374 CTCATCGATCCCAAACCTAGC 58.240 52.381 0.00 0.00 0.00 3.42
376 539 1.284715 CATATGGCCATGCTGCACG 59.715 57.895 29.04 0.00 0.00 5.34
377 540 1.152902 ATATGGCCATGCTGCACGT 60.153 52.632 29.04 0.99 0.00 4.49
406 569 4.889427 GGCACGAAATTTCAGCCC 57.111 55.556 28.55 17.01 40.27 5.19
408 571 0.316841 GGCACGAAATTTCAGCCCAA 59.683 50.000 28.55 0.00 40.27 4.12
417 580 0.469705 TTTCAGCCCAACACATGCCT 60.470 50.000 0.00 0.00 0.00 4.75
456 619 4.501285 GGCCTTACCCGCCCTTCC 62.501 72.222 0.00 0.00 40.78 3.46
457 620 4.501285 GCCTTACCCGCCCTTCCC 62.501 72.222 0.00 0.00 0.00 3.97
489 652 4.717313 AAGGCCGACCCCGAAAGC 62.717 66.667 0.00 0.00 38.22 3.51
529 692 0.739462 GGCACGCCCCTTTTTATTGC 60.739 55.000 0.00 0.00 0.00 3.56
530 693 0.246360 GCACGCCCCTTTTTATTGCT 59.754 50.000 0.00 0.00 0.00 3.91
536 699 1.627834 CCCCTTTTTATTGCTGGCCAA 59.372 47.619 7.01 0.00 37.94 4.52
537 700 2.615240 CCCCTTTTTATTGCTGGCCAAC 60.615 50.000 7.01 1.82 35.99 3.77
538 701 2.038295 CCCTTTTTATTGCTGGCCAACA 59.962 45.455 7.01 5.56 35.99 3.33
539 702 3.066380 CCTTTTTATTGCTGGCCAACAC 58.934 45.455 8.74 0.06 35.99 3.32
540 703 2.430546 TTTTATTGCTGGCCAACACG 57.569 45.000 8.74 0.00 35.99 4.49
541 704 0.600557 TTTATTGCTGGCCAACACGG 59.399 50.000 8.74 0.00 35.99 4.94
542 705 0.250945 TTATTGCTGGCCAACACGGA 60.251 50.000 8.74 0.00 35.99 4.69
543 706 0.250945 TATTGCTGGCCAACACGGAA 60.251 50.000 8.74 3.42 35.99 4.30
544 707 1.805428 ATTGCTGGCCAACACGGAAC 61.805 55.000 8.74 0.00 35.99 3.62
545 708 2.904866 GCTGGCCAACACGGAACA 60.905 61.111 7.01 0.00 36.56 3.18
546 709 2.485795 GCTGGCCAACACGGAACAA 61.486 57.895 7.01 0.00 36.56 2.83
550 713 1.658686 GGCCAACACGGAACAACACA 61.659 55.000 0.00 0.00 36.56 3.72
708 881 0.437295 CGAAAGGCCGACAAGTAACG 59.563 55.000 0.00 0.00 0.00 3.18
709 882 0.165295 GAAAGGCCGACAAGTAACGC 59.835 55.000 0.00 0.00 0.00 4.84
710 883 1.562575 AAAGGCCGACAAGTAACGCG 61.563 55.000 3.53 3.53 0.00 6.01
711 884 3.484547 GGCCGACAAGTAACGCGG 61.485 66.667 12.47 0.00 46.14 6.46
712 885 3.484547 GCCGACAAGTAACGCGGG 61.485 66.667 12.47 0.00 43.73 6.13
713 886 3.484547 CCGACAAGTAACGCGGGC 61.485 66.667 12.47 0.00 40.08 6.13
714 887 3.484547 CGACAAGTAACGCGGGCC 61.485 66.667 12.47 0.00 0.00 5.80
1095 1852 4.107051 AACCGCGTCTACGACCCG 62.107 66.667 4.92 0.41 43.02 5.28
1221 1978 4.504916 CGCCTCACCCAGCTCTCG 62.505 72.222 0.00 0.00 0.00 4.04
1310 2067 2.106332 CCCCGTAAGCGCGATCTT 59.894 61.111 12.10 7.34 36.67 2.40
1311 2068 1.520787 CCCCGTAAGCGCGATCTTT 60.521 57.895 12.10 0.00 36.67 2.52
1332 2099 4.404098 TTCCCCGCGCCTTCTTCC 62.404 66.667 0.00 0.00 0.00 3.46
1342 2109 0.108472 GCCTTCTTCCATGCTTTGGC 60.108 55.000 1.73 0.00 46.01 4.52
1354 2122 1.965643 TGCTTTGGCTCTCTGCATTTT 59.034 42.857 0.00 0.00 45.15 1.82
1357 2125 3.305881 GCTTTGGCTCTCTGCATTTTCTT 60.306 43.478 0.00 0.00 45.15 2.52
1384 2152 6.963322 AGTAACTTGGATTTGCTAGATCCTT 58.037 36.000 9.66 0.73 42.88 3.36
1392 2160 1.301322 GCTAGATCCTTCCTGCGCC 60.301 63.158 4.18 0.00 0.00 6.53
1458 2226 1.373748 GTTGCCAATGCTGCTGTGG 60.374 57.895 15.21 15.21 38.71 4.17
1524 2292 3.078837 GTTGGTTGGTATGATCCGTGTT 58.921 45.455 0.00 0.00 0.00 3.32
1533 2301 5.186215 TGGTATGATCCGTGTTCTTTCTGTA 59.814 40.000 0.00 0.00 0.00 2.74
1556 2324 6.446781 ACAATTCATTGATCTAGTTGCAGG 57.553 37.500 6.53 0.00 40.14 4.85
1557 2325 5.163581 ACAATTCATTGATCTAGTTGCAGGC 60.164 40.000 6.53 0.00 40.14 4.85
1558 2326 3.920231 TCATTGATCTAGTTGCAGGCT 57.080 42.857 0.00 0.00 0.00 4.58
1559 2327 4.226427 TCATTGATCTAGTTGCAGGCTT 57.774 40.909 0.00 0.00 0.00 4.35
1560 2328 3.943381 TCATTGATCTAGTTGCAGGCTTG 59.057 43.478 0.00 0.00 0.00 4.01
1611 2379 3.925453 TTGCCTGTACGCAAGATCA 57.075 47.368 4.30 0.00 43.65 2.92
1645 2413 2.364970 TGCATTGTGACAAAGGGAAAGG 59.635 45.455 0.62 0.00 0.00 3.11
1713 2481 4.202727 TGGGGGATTGGAAAATAGTTGTCA 60.203 41.667 0.00 0.00 0.00 3.58
1777 2545 3.841845 ACAATGGTAGGGTTAGCACTGTA 59.158 43.478 0.00 0.00 43.46 2.74
1819 2587 6.127423 GCTCGAATAGTAGCCTTATATGGGAA 60.127 42.308 6.78 0.00 32.40 3.97
1839 2607 4.953579 GGAACATATAAGGTGAAAGCCCAA 59.046 41.667 0.00 0.00 32.25 4.12
1841 2609 6.098266 GGAACATATAAGGTGAAAGCCCAATT 59.902 38.462 0.00 0.00 32.25 2.32
1849 2617 3.260632 GGTGAAAGCCCAATTGTGGTAAT 59.739 43.478 4.43 0.00 44.30 1.89
1850 2618 4.262851 GGTGAAAGCCCAATTGTGGTAATT 60.263 41.667 4.43 3.04 44.30 1.40
1851 2619 5.304778 GTGAAAGCCCAATTGTGGTAATTT 58.695 37.500 4.43 8.17 44.30 1.82
1852 2620 5.762711 GTGAAAGCCCAATTGTGGTAATTTT 59.237 36.000 4.43 5.89 44.30 1.82
1853 2621 6.262049 GTGAAAGCCCAATTGTGGTAATTTTT 59.738 34.615 4.43 3.92 44.30 1.94
1901 2680 3.058016 AGCACCAAGTCAACATGAATTCG 60.058 43.478 0.00 0.00 31.77 3.34
1922 2701 6.539649 TCGTGAAAGGTTCTAACATTTGAG 57.460 37.500 9.92 2.55 42.21 3.02
1945 2724 7.338196 TGAGGCGGTAATTCTTATTTCATCAAA 59.662 33.333 0.00 0.00 0.00 2.69
2016 2795 6.878389 AGAAATGAGAAACCTCTGTCATCTTC 59.122 38.462 0.00 0.00 29.54 2.87
2313 3093 0.530650 ACTTCAGCGACACCACACTG 60.531 55.000 0.00 0.00 0.00 3.66
2424 3204 9.750125 GAGTTTTGAAGGACTATTTTGTGATTT 57.250 29.630 0.00 0.00 0.00 2.17
2434 3214 7.986889 GGACTATTTTGTGATTTATTGGCCAAT 59.013 33.333 32.59 32.59 34.93 3.16
2442 3222 6.161381 GTGATTTATTGGCCAATCATCCATC 58.839 40.000 33.89 24.56 40.62 3.51
2587 3367 5.905913 ACTAGGTATATCAAAGAGCAAGGGT 59.094 40.000 0.00 0.00 0.00 4.34
2661 3446 7.604657 AGTTTGGTATGGTTAAATTTGGTCA 57.395 32.000 0.00 0.00 0.00 4.02
2687 3472 4.708177 ACCAGACATGTGCCAGTATTATC 58.292 43.478 1.15 0.00 0.00 1.75
2691 3476 5.819379 CAGACATGTGCCAGTATTATCTTGT 59.181 40.000 1.15 0.00 0.00 3.16
2758 3543 3.882888 GAGGGTGTCAAGTGTCAAATTGA 59.117 43.478 0.00 0.00 33.16 2.57
2782 3567 4.996788 AAGGTTTCTGGATGATGCAATC 57.003 40.909 0.00 0.00 45.83 2.67
3002 4147 1.004044 CACTCCATCAGCCACCTCTTT 59.996 52.381 0.00 0.00 0.00 2.52
3132 4278 9.052759 GTTGTTTAGTTTCCTTCTCAACTATGA 57.947 33.333 0.00 0.00 35.80 2.15
3142 4288 4.552883 TCTCAACTATGACTATCCCCCA 57.447 45.455 0.00 0.00 0.00 4.96
3242 4388 2.645297 TGTCCCAACTTACAATAGGGCA 59.355 45.455 0.00 0.00 39.42 5.36
3245 4391 4.080751 GTCCCAACTTACAATAGGGCAGTA 60.081 45.833 0.00 0.00 39.42 2.74
3351 4497 3.952535 AGTGTTCAGTCATTTTTGTCGC 58.047 40.909 0.00 0.00 0.00 5.19
3509 4655 0.749454 CAGCTTCACCCTGGTATGGC 60.749 60.000 0.00 0.00 0.00 4.40
3549 4697 6.761242 TGTACTGTTGTTGCCATCATCTATAC 59.239 38.462 0.00 0.00 0.00 1.47
3923 5074 4.273148 TCAACAAGTTCTTCTAGGCTCC 57.727 45.455 0.00 0.00 0.00 4.70
3924 5075 3.904339 TCAACAAGTTCTTCTAGGCTCCT 59.096 43.478 0.00 0.00 0.00 3.69
3925 5076 3.971245 ACAAGTTCTTCTAGGCTCCTG 57.029 47.619 0.00 0.00 0.00 3.86
3926 5077 2.569404 ACAAGTTCTTCTAGGCTCCTGG 59.431 50.000 0.00 0.00 0.00 4.45
3927 5078 2.834549 CAAGTTCTTCTAGGCTCCTGGA 59.165 50.000 0.00 0.00 0.00 3.86
3928 5079 3.191888 AGTTCTTCTAGGCTCCTGGAA 57.808 47.619 13.07 13.07 40.41 3.53
4076 5234 3.187842 TCAAAGCTCATCGATATGCATGC 59.812 43.478 11.82 11.82 32.76 4.06
4114 5275 9.140286 GCGAGTCATTTTATGCTGAGTATATTA 57.860 33.333 0.00 0.00 0.00 0.98
4260 5422 5.118990 ACAGCTCGTGCATCTTTGTATATT 58.881 37.500 12.58 0.00 42.74 1.28
4289 5451 4.091549 TCACCTGGGTACGACTATTTCTT 58.908 43.478 0.00 0.00 0.00 2.52
4330 5492 3.437049 GTCTGCTGGGTTGTTTATGTCTC 59.563 47.826 0.00 0.00 0.00 3.36
4391 5556 5.998981 TCGCAGGTCCACTCTTTTATTTTAA 59.001 36.000 0.00 0.00 0.00 1.52
4395 5560 9.489084 GCAGGTCCACTCTTTTATTTTAATTTT 57.511 29.630 0.00 0.00 0.00 1.82
4398 5563 9.431887 GGTCCACTCTTTTATTTTAATTTTCCC 57.568 33.333 0.00 0.00 0.00 3.97
4399 5564 9.990360 GTCCACTCTTTTATTTTAATTTTCCCA 57.010 29.630 0.00 0.00 0.00 4.37
4401 5566 8.935844 CCACTCTTTTATTTTAATTTTCCCAGC 58.064 33.333 0.00 0.00 0.00 4.85
4402 5567 9.487790 CACTCTTTTATTTTAATTTTCCCAGCA 57.512 29.630 0.00 0.00 0.00 4.41
4403 5568 9.710900 ACTCTTTTATTTTAATTTTCCCAGCAG 57.289 29.630 0.00 0.00 0.00 4.24
4404 5569 9.927668 CTCTTTTATTTTAATTTTCCCAGCAGA 57.072 29.630 0.00 0.00 0.00 4.26
4587 5753 4.036734 GTCCATTACCATTACCATGTGCAG 59.963 45.833 0.00 0.00 0.00 4.41
4588 5754 3.243501 CCATTACCATTACCATGTGCAGC 60.244 47.826 0.00 0.00 0.00 5.25
4589 5755 1.662517 TACCATTACCATGTGCAGCG 58.337 50.000 0.00 0.00 0.00 5.18
4681 5851 0.855349 GGACGTTAGCTGATGCATCG 59.145 55.000 21.34 16.36 42.74 3.84
4796 5966 3.365969 CGCACCAATAAAGAAACCACCTC 60.366 47.826 0.00 0.00 0.00 3.85
4884 6095 2.083774 TGGAAAAAGATGTGCCTAGCG 58.916 47.619 0.00 0.00 0.00 4.26
4885 6096 1.202188 GGAAAAAGATGTGCCTAGCGC 60.202 52.381 0.00 0.00 39.75 5.92
4914 6125 2.158885 GCTCACTAAAGCTCTAAGGGGG 60.159 54.545 0.00 0.00 39.27 5.40
4915 6126 3.108376 CTCACTAAAGCTCTAAGGGGGT 58.892 50.000 0.00 0.00 0.00 4.95
4916 6127 3.519913 CTCACTAAAGCTCTAAGGGGGTT 59.480 47.826 0.00 0.00 0.00 4.11
4917 6128 3.914435 TCACTAAAGCTCTAAGGGGGTTT 59.086 43.478 0.00 0.00 37.07 3.27
4918 6129 4.019591 TCACTAAAGCTCTAAGGGGGTTTC 60.020 45.833 0.00 0.00 35.31 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.716017 CCCGCAGTCAGAGGTCTCC 61.716 68.421 0.00 0.00 35.04 3.71
17 18 2.158959 CCAGCATCGTCGTCGTTCC 61.159 63.158 1.33 0.00 38.33 3.62
33 34 1.228521 CCAGTTCATGCCACCACCA 60.229 57.895 0.00 0.00 0.00 4.17
41 42 2.234908 AGAGTAGGTGTCCAGTTCATGC 59.765 50.000 0.00 0.00 0.00 4.06
61 62 4.627467 CGTTGACACTATCTCTTTTCCCAG 59.373 45.833 0.00 0.00 0.00 4.45
74 75 4.500205 CCACTGTTTAGGACGTTGACACTA 60.500 45.833 0.00 0.00 0.00 2.74
78 79 1.529865 GCCACTGTTTAGGACGTTGAC 59.470 52.381 0.00 0.00 0.00 3.18
79 80 1.541670 GGCCACTGTTTAGGACGTTGA 60.542 52.381 0.00 0.00 0.00 3.18
80 81 0.872388 GGCCACTGTTTAGGACGTTG 59.128 55.000 0.00 0.00 0.00 4.10
81 82 0.470766 TGGCCACTGTTTAGGACGTT 59.529 50.000 0.00 0.00 34.89 3.99
82 83 0.470766 TTGGCCACTGTTTAGGACGT 59.529 50.000 3.88 0.00 34.89 4.34
83 84 1.600023 TTTGGCCACTGTTTAGGACG 58.400 50.000 3.88 0.00 34.89 4.79
84 85 2.035449 GGTTTTGGCCACTGTTTAGGAC 59.965 50.000 3.88 0.00 0.00 3.85
85 86 2.312390 GGTTTTGGCCACTGTTTAGGA 58.688 47.619 3.88 0.00 0.00 2.94
86 87 1.000717 CGGTTTTGGCCACTGTTTAGG 60.001 52.381 3.88 0.00 0.00 2.69
87 88 1.679153 ACGGTTTTGGCCACTGTTTAG 59.321 47.619 3.88 0.00 28.71 1.85
88 89 1.677052 GACGGTTTTGGCCACTGTTTA 59.323 47.619 3.88 0.00 33.68 2.01
89 90 0.458260 GACGGTTTTGGCCACTGTTT 59.542 50.000 3.88 0.00 33.68 2.83
90 91 0.395173 AGACGGTTTTGGCCACTGTT 60.395 50.000 3.88 0.00 33.68 3.16
91 92 0.470766 TAGACGGTTTTGGCCACTGT 59.529 50.000 3.88 5.21 36.40 3.55
92 93 1.265905 GTTAGACGGTTTTGGCCACTG 59.734 52.381 3.88 0.94 0.00 3.66
93 94 1.134037 TGTTAGACGGTTTTGGCCACT 60.134 47.619 3.88 0.00 0.00 4.00
94 95 1.310904 TGTTAGACGGTTTTGGCCAC 58.689 50.000 3.88 0.00 0.00 5.01
95 96 2.279935 ATGTTAGACGGTTTTGGCCA 57.720 45.000 0.00 0.00 0.00 5.36
96 97 3.243602 ACAAATGTTAGACGGTTTTGGCC 60.244 43.478 0.00 0.00 32.85 5.36
97 98 3.972403 ACAAATGTTAGACGGTTTTGGC 58.028 40.909 5.89 0.00 32.85 4.52
98 99 5.176407 TGACAAATGTTAGACGGTTTTGG 57.824 39.130 5.89 0.00 32.85 3.28
99 100 5.116983 GCATGACAAATGTTAGACGGTTTTG 59.883 40.000 0.00 0.51 34.34 2.44
100 101 5.219633 GCATGACAAATGTTAGACGGTTTT 58.780 37.500 0.00 0.00 0.00 2.43
118 119 1.340889 GTGGTTTTGAAGCTGGCATGA 59.659 47.619 0.00 0.00 0.00 3.07
196 197 7.118390 ACAAATCACTCTGAAATCTCCTAAACG 59.882 37.037 0.00 0.00 0.00 3.60
197 198 8.329203 ACAAATCACTCTGAAATCTCCTAAAC 57.671 34.615 0.00 0.00 0.00 2.01
219 220 7.063426 CGCATGTCAGAAGAAAGAAGTATACAA 59.937 37.037 5.50 0.00 0.00 2.41
220 221 6.531594 CGCATGTCAGAAGAAAGAAGTATACA 59.468 38.462 5.50 0.00 0.00 2.29
221 222 6.531948 ACGCATGTCAGAAGAAAGAAGTATAC 59.468 38.462 0.00 0.00 0.00 1.47
222 223 6.631016 ACGCATGTCAGAAGAAAGAAGTATA 58.369 36.000 0.00 0.00 0.00 1.47
223 224 5.482908 ACGCATGTCAGAAGAAAGAAGTAT 58.517 37.500 0.00 0.00 0.00 2.12
224 225 4.883083 ACGCATGTCAGAAGAAAGAAGTA 58.117 39.130 0.00 0.00 0.00 2.24
225 226 3.733337 ACGCATGTCAGAAGAAAGAAGT 58.267 40.909 0.00 0.00 0.00 3.01
226 227 3.181536 CGACGCATGTCAGAAGAAAGAAG 60.182 47.826 0.00 0.00 45.80 2.85
227 228 2.731451 CGACGCATGTCAGAAGAAAGAA 59.269 45.455 0.00 0.00 45.80 2.52
228 229 2.328473 CGACGCATGTCAGAAGAAAGA 58.672 47.619 0.00 0.00 45.80 2.52
229 230 1.391485 CCGACGCATGTCAGAAGAAAG 59.609 52.381 0.00 0.00 45.80 2.62
230 231 1.428448 CCGACGCATGTCAGAAGAAA 58.572 50.000 0.00 0.00 45.80 2.52
231 232 0.389817 CCCGACGCATGTCAGAAGAA 60.390 55.000 0.00 0.00 45.80 2.52
232 233 1.215382 CCCGACGCATGTCAGAAGA 59.785 57.895 0.00 0.00 45.80 2.87
233 234 2.456119 GCCCGACGCATGTCAGAAG 61.456 63.158 0.00 0.00 45.80 2.85
234 235 2.434185 GCCCGACGCATGTCAGAA 60.434 61.111 0.00 0.00 45.80 3.02
246 247 5.061721 TGAGCCATATATATAGAGCCCGA 57.938 43.478 11.35 0.00 0.00 5.14
310 311 5.131784 TCTTTTTGCATGGGCTTTGAAATT 58.868 33.333 0.00 0.00 41.91 1.82
338 501 1.416401 GGCTAGGTTTGGGATCGATGA 59.584 52.381 0.54 0.00 0.00 2.92
339 502 1.140852 TGGCTAGGTTTGGGATCGATG 59.859 52.381 0.54 0.00 0.00 3.84
343 506 3.690460 CCATATGGCTAGGTTTGGGATC 58.310 50.000 9.29 0.00 0.00 3.36
357 520 1.663739 GTGCAGCATGGCCATATGG 59.336 57.895 20.30 18.07 35.86 2.74
406 569 1.404748 TGTTGTGTCAGGCATGTGTTG 59.595 47.619 0.00 0.00 0.00 3.33
408 571 1.024271 GTGTTGTGTCAGGCATGTGT 58.976 50.000 0.00 0.00 0.00 3.72
417 580 5.655488 CCCTTTTAATTGTGTGTTGTGTCA 58.345 37.500 0.00 0.00 0.00 3.58
489 652 1.823899 GCCCGACATTAAGGCCTGG 60.824 63.158 5.69 0.40 41.00 4.45
529 692 1.358759 GTTGTTCCGTGTTGGCCAG 59.641 57.895 5.11 0.00 37.80 4.85
530 693 1.378646 TGTTGTTCCGTGTTGGCCA 60.379 52.632 0.00 0.00 37.80 5.36
536 699 1.091537 CAGGTTGTGTTGTTCCGTGT 58.908 50.000 0.00 0.00 0.00 4.49
537 700 0.380378 CCAGGTTGTGTTGTTCCGTG 59.620 55.000 0.00 0.00 0.00 4.94
538 701 0.034863 ACCAGGTTGTGTTGTTCCGT 60.035 50.000 0.00 0.00 0.00 4.69
539 702 0.380378 CACCAGGTTGTGTTGTTCCG 59.620 55.000 0.00 0.00 0.00 4.30
540 703 0.102300 GCACCAGGTTGTGTTGTTCC 59.898 55.000 0.00 0.00 38.52 3.62
541 704 0.248458 CGCACCAGGTTGTGTTGTTC 60.248 55.000 0.00 0.00 38.52 3.18
542 705 1.662438 CCGCACCAGGTTGTGTTGTT 61.662 55.000 0.00 0.00 38.52 2.83
543 706 2.118404 CCGCACCAGGTTGTGTTGT 61.118 57.895 0.00 0.00 38.52 3.32
544 707 2.721231 CCGCACCAGGTTGTGTTG 59.279 61.111 0.00 0.00 38.52 3.33
545 708 3.216292 GCCGCACCAGGTTGTGTT 61.216 61.111 0.00 0.00 38.52 3.32
667 840 4.876679 CGGCCCTTTTGTTTTTAGGAAAAA 59.123 37.500 0.00 0.00 36.56 1.94
672 845 3.737032 TTCGGCCCTTTTGTTTTTAGG 57.263 42.857 0.00 0.00 0.00 2.69
696 869 3.484547 GCCCGCGTTACTTGTCGG 61.485 66.667 4.92 0.00 41.41 4.79
697 870 3.484547 GGCCCGCGTTACTTGTCG 61.485 66.667 4.92 0.00 0.00 4.35
700 873 2.510691 ATCGGCCCGCGTTACTTG 60.511 61.111 4.92 0.00 0.00 3.16
701 874 2.202837 GATCGGCCCGCGTTACTT 60.203 61.111 4.92 0.00 0.00 2.24
738 1466 1.525442 GCCAGTTATACAGGCCGGT 59.475 57.895 14.55 14.55 44.02 5.28
779 1507 1.877576 GCTGTAAAAGGGCCTGGCAC 61.878 60.000 22.05 18.62 0.00 5.01
843 1571 3.118884 GCGGGGAACAGTTCAGTTCTATA 60.119 47.826 15.36 0.00 45.52 1.31
1095 1852 1.298859 GGATCTTGGTGTCGGTGCAC 61.299 60.000 8.80 8.80 38.56 4.57
1221 1978 2.498726 CGGAAGAGGGAGAGCTGC 59.501 66.667 0.00 0.00 0.00 5.25
1332 2099 1.103803 ATGCAGAGAGCCAAAGCATG 58.896 50.000 0.00 0.00 43.60 4.06
1342 2109 5.936956 AGTTACTCCAAGAAAATGCAGAGAG 59.063 40.000 2.69 0.00 0.00 3.20
1354 2122 4.985538 AGCAAATCCAAGTTACTCCAAGA 58.014 39.130 0.00 0.00 0.00 3.02
1357 2125 5.755409 TCTAGCAAATCCAAGTTACTCCA 57.245 39.130 0.00 0.00 0.00 3.86
1392 2160 1.135689 GCATTTCCACAAGCACGTAGG 60.136 52.381 0.00 0.00 0.00 3.18
1533 2301 5.163581 GCCTGCAACTAGATCAATGAATTGT 60.164 40.000 0.00 0.00 38.84 2.71
1557 2325 1.091771 CGTCACCCTATGGCTGCAAG 61.092 60.000 0.50 0.00 33.59 4.01
1558 2326 1.078497 CGTCACCCTATGGCTGCAA 60.078 57.895 0.50 0.00 33.59 4.08
1559 2327 1.337384 ATCGTCACCCTATGGCTGCA 61.337 55.000 0.50 0.00 33.59 4.41
1560 2328 0.882042 CATCGTCACCCTATGGCTGC 60.882 60.000 0.00 0.00 33.59 5.25
1611 2379 5.181748 GTCACAATGCAGAGTTAGGAAGAT 58.818 41.667 0.00 0.00 0.00 2.40
1645 2413 4.982295 GCATTGGTCCTTGTTAGTTTCAAC 59.018 41.667 0.00 0.00 0.00 3.18
1713 2481 4.141914 GGATTATCTCAACTTCCCTCACGT 60.142 45.833 0.00 0.00 0.00 4.49
1797 2565 6.931838 TGTTCCCATATAAGGCTACTATTCG 58.068 40.000 0.00 0.00 0.00 3.34
1819 2587 5.957774 ACAATTGGGCTTTCACCTTATATGT 59.042 36.000 10.83 0.00 0.00 2.29
1826 2594 1.341080 CCACAATTGGGCTTTCACCT 58.659 50.000 10.83 0.00 39.57 4.00
1853 2621 8.415950 TGAGGCTCTAACATTATTTCCAAAAA 57.584 30.769 16.72 0.00 0.00 1.94
1854 2622 8.415950 TTGAGGCTCTAACATTATTTCCAAAA 57.584 30.769 16.72 0.00 0.00 2.44
1856 2624 6.095440 GCTTGAGGCTCTAACATTATTTCCAA 59.905 38.462 16.72 0.00 38.06 3.53
1857 2625 5.590259 GCTTGAGGCTCTAACATTATTTCCA 59.410 40.000 16.72 0.00 38.06 3.53
1858 2626 5.590259 TGCTTGAGGCTCTAACATTATTTCC 59.410 40.000 16.72 0.00 42.39 3.13
1859 2627 6.458888 GGTGCTTGAGGCTCTAACATTATTTC 60.459 42.308 16.72 0.00 42.39 2.17
1861 2629 4.884164 GGTGCTTGAGGCTCTAACATTATT 59.116 41.667 16.72 0.00 42.39 1.40
1863 2631 3.263170 TGGTGCTTGAGGCTCTAACATTA 59.737 43.478 16.72 0.79 42.39 1.90
1864 2632 2.040278 TGGTGCTTGAGGCTCTAACATT 59.960 45.455 16.72 0.00 42.39 2.71
1865 2633 1.630369 TGGTGCTTGAGGCTCTAACAT 59.370 47.619 16.72 0.00 42.39 2.71
1867 2635 2.079925 CTTGGTGCTTGAGGCTCTAAC 58.920 52.381 16.72 4.10 42.39 2.34
1868 2636 1.699634 ACTTGGTGCTTGAGGCTCTAA 59.300 47.619 16.72 7.55 42.39 2.10
1869 2637 1.276421 GACTTGGTGCTTGAGGCTCTA 59.724 52.381 16.72 7.33 42.39 2.43
1877 2656 3.713858 TTCATGTTGACTTGGTGCTTG 57.286 42.857 0.00 0.00 0.00 4.01
1901 2680 5.461526 GCCTCAAATGTTAGAACCTTTCAC 58.538 41.667 0.00 0.00 0.00 3.18
1922 2701 7.254852 TGTTTGATGAAATAAGAATTACCGCC 58.745 34.615 0.00 0.00 30.46 6.13
2162 2942 7.621832 TTAAGCAACGATTCAACATGAAAAG 57.378 32.000 0.00 0.00 40.12 2.27
2424 3204 6.452757 TTCTAGATGGATGATTGGCCAATA 57.547 37.500 30.73 18.51 37.78 1.90
2429 3209 4.333690 AGCATTCTAGATGGATGATTGGC 58.666 43.478 7.02 0.00 0.00 4.52
2442 3222 6.042777 TGATGGTTCGTTTCTAGCATTCTAG 58.957 40.000 0.00 0.00 42.87 2.43
2493 3273 2.567615 GAGTTCAGGAGGCAGGAAGTTA 59.432 50.000 0.00 0.00 0.00 2.24
2587 3367 4.666253 GCACCAAGCCAGCCAGGA 62.666 66.667 5.10 0.00 41.22 3.86
2661 3446 1.074405 ACTGGCACATGTCTGGTTCAT 59.926 47.619 0.00 0.00 38.20 2.57
2687 3472 1.067516 CCACTGCTGGAAACCAACAAG 59.932 52.381 0.00 0.00 40.55 3.16
2691 3476 0.260230 TTCCCACTGCTGGAAACCAA 59.740 50.000 0.00 0.00 40.55 3.67
2758 3543 3.499338 TGCATCATCCAGAAACCTTTGT 58.501 40.909 0.00 0.00 0.00 2.83
2813 3598 6.048509 CAGTAATGCCCAAACAAAGAAAACT 58.951 36.000 0.00 0.00 0.00 2.66
2981 4126 0.546267 AGAGGTGGCTGATGGAGTGT 60.546 55.000 0.00 0.00 0.00 3.55
3002 4147 4.162320 GGCTACCATATTCCATAGCTGCTA 59.838 45.833 12.40 12.40 39.98 3.49
3050 4196 6.266103 ACAGATGGTGAAACAGTCATGAAAAT 59.734 34.615 0.00 0.00 39.98 1.82
3132 4278 5.903923 AGTTTTCAGAATTTGGGGGATAGT 58.096 37.500 0.00 0.00 0.00 2.12
3142 4288 5.953571 ACTACCCTGGAGTTTTCAGAATTT 58.046 37.500 0.00 0.00 34.36 1.82
3242 4388 6.648192 AGCAGCATTTCTCAGAGTTATTACT 58.352 36.000 0.00 0.00 37.31 2.24
3245 4391 5.743117 AGAGCAGCATTTCTCAGAGTTATT 58.257 37.500 0.00 0.00 0.00 1.40
3509 4655 1.902508 AGTACATCTGTGGTCCCACTG 59.097 52.381 16.91 15.95 46.30 3.66
3549 4697 5.757886 TCAGAATTCGCTTGGTTAAAAGTG 58.242 37.500 0.00 0.00 38.71 3.16
3795 4946 1.286260 GACCGACTCGTGCTTGTCT 59.714 57.895 0.00 0.00 0.00 3.41
3923 5074 0.745845 CGGTCATTCCAGCCTTCCAG 60.746 60.000 0.00 0.00 35.57 3.86
3924 5075 1.299648 CGGTCATTCCAGCCTTCCA 59.700 57.895 0.00 0.00 35.57 3.53
3925 5076 0.322546 AACGGTCATTCCAGCCTTCC 60.323 55.000 0.00 0.00 35.57 3.46
3926 5077 1.200020 CAAACGGTCATTCCAGCCTTC 59.800 52.381 0.00 0.00 35.57 3.46
3927 5078 1.247567 CAAACGGTCATTCCAGCCTT 58.752 50.000 0.00 0.00 35.57 4.35
3928 5079 0.110486 ACAAACGGTCATTCCAGCCT 59.890 50.000 0.00 0.00 35.57 4.58
3929 5080 0.521735 GACAAACGGTCATTCCAGCC 59.478 55.000 0.00 0.00 46.19 4.85
4076 5234 5.991328 AAATGACTCGCAATAGGTACATG 57.009 39.130 0.00 0.00 0.00 3.21
4260 5422 1.141254 TCGTACCCAGGTGAGCAAAAA 59.859 47.619 0.00 0.00 0.00 1.94
4270 5432 4.730949 TCAAGAAATAGTCGTACCCAGG 57.269 45.455 0.00 0.00 0.00 4.45
4289 5451 6.660521 AGCAGACCAATTTTTCTGTATCATCA 59.339 34.615 12.58 0.00 41.24 3.07
4330 5492 4.159879 AGGACGTGAACTACCCTGAAATAG 59.840 45.833 0.00 0.00 0.00 1.73
4398 5563 1.523258 CATTCGCCTCCCTCTGCTG 60.523 63.158 0.00 0.00 0.00 4.41
4399 5564 1.684386 CTCATTCGCCTCCCTCTGCT 61.684 60.000 0.00 0.00 0.00 4.24
4400 5565 1.227497 CTCATTCGCCTCCCTCTGC 60.227 63.158 0.00 0.00 0.00 4.26
4401 5566 1.333636 ACCTCATTCGCCTCCCTCTG 61.334 60.000 0.00 0.00 0.00 3.35
4402 5567 1.002274 ACCTCATTCGCCTCCCTCT 59.998 57.895 0.00 0.00 0.00 3.69
4403 5568 1.144936 CACCTCATTCGCCTCCCTC 59.855 63.158 0.00 0.00 0.00 4.30
4404 5569 1.306141 TCACCTCATTCGCCTCCCT 60.306 57.895 0.00 0.00 0.00 4.20
4532 5698 6.006449 ACAAGAATATTCAGGTCAACAGCTT 58.994 36.000 17.56 0.00 0.00 3.74
4589 5755 4.805581 AGGTAACGACTGCTTCCTGCAC 62.806 54.545 0.00 0.00 45.61 4.57
4699 5869 1.668419 CCTGTTTCTTATCAGGCCGG 58.332 55.000 0.00 0.00 43.45 6.13
4819 5989 3.849145 CAGTTTTTCTGTTTTCGCGACAA 59.151 39.130 9.15 5.74 39.17 3.18
4820 5990 3.421741 CAGTTTTTCTGTTTTCGCGACA 58.578 40.909 9.15 0.00 39.17 4.35
4822 5992 2.159503 TGCAGTTTTTCTGTTTTCGCGA 60.160 40.909 3.71 3.71 45.23 5.87
4823 5993 2.181205 TGCAGTTTTTCTGTTTTCGCG 58.819 42.857 0.00 0.00 45.23 5.87
4852 6063 5.829924 ACATCTTTTTCCATGTCACAAGAGT 59.170 36.000 0.00 0.00 0.00 3.24
4884 6095 2.554365 CTTTAGTGAGCTGTGCGCGC 62.554 60.000 27.26 27.26 45.59 6.86
4885 6096 1.417592 CTTTAGTGAGCTGTGCGCG 59.582 57.895 0.00 0.00 45.59 6.86


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

AutoCloner maintained by Alex Coulton.