Multiple sequence alignment - TraesCS1B01G181600

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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 TraesCS1B01G181600 chr1B 100.000 5679 0 0 1 5679 328647170 328641492 0.000000e+00 10488.0
1 TraesCS1B01G181600 chr1B 100.000 55 0 0 5207 5261 328641910 328641856 1.010000e-17 102.0
2 TraesCS1B01G181600 chr1B 100.000 55 0 0 5261 5315 328641964 328641910 1.010000e-17 102.0
3 TraesCS1B01G181600 chr1A 93.871 3671 136 31 129 3757 297701591 297697968 0.000000e+00 5450.0
4 TraesCS1B01G181600 chr1A 91.344 1756 75 35 3770 5472 297697984 297696253 0.000000e+00 2329.0
5 TraesCS1B01G181600 chr1A 84.004 1019 142 14 2135 3146 342865448 342866452 0.000000e+00 959.0
6 TraesCS1B01G181600 chr1A 90.526 95 7 2 1 94 31842287 31842380 2.150000e-24 124.0
7 TraesCS1B01G181600 chr1A 94.340 53 1 1 5209 5261 297696445 297696395 4.720000e-11 80.5
8 TraesCS1B01G181600 chr1A 96.875 32 1 0 5540 5571 297695957 297695926 3.000000e-03 54.7
9 TraesCS1B01G181600 chr1D 96.267 1259 22 5 713 1948 229324736 229323480 0.000000e+00 2041.0
10 TraesCS1B01G181600 chr1D 96.161 1120 38 4 4054 5172 229322396 229321281 0.000000e+00 1825.0
11 TraesCS1B01G181600 chr1D 84.540 1022 144 9 2137 3153 120019642 120020654 0.000000e+00 1000.0
12 TraesCS1B01G181600 chr1D 86.196 920 117 7 2138 3052 484433228 484432314 0.000000e+00 987.0
13 TraesCS1B01G181600 chr1D 95.758 495 20 1 5169 5662 229320977 229320483 0.000000e+00 797.0
14 TraesCS1B01G181600 chr1D 94.538 238 12 1 3498 3734 229323027 229322790 3.230000e-97 366.0
15 TraesCS1B01G181600 chr1D 83.688 282 36 6 3773 4054 229322789 229322518 2.030000e-64 257.0
16 TraesCS1B01G181600 chr1D 98.182 55 1 0 5207 5261 229320885 229320831 4.680000e-16 97.1
17 TraesCS1B01G181600 chr1D 98.182 55 1 0 5261 5315 229320939 229320885 4.680000e-16 97.1
18 TraesCS1B01G181600 chr1D 88.406 69 8 0 3019 3087 418764156 418764088 3.650000e-12 84.2
19 TraesCS1B01G181600 chr1D 97.143 35 1 0 5541 5575 229320574 229320540 6.140000e-05 60.2
20 TraesCS1B01G181600 chr7D 86.579 909 111 7 2136 3039 621300067 621300969 0.000000e+00 992.0
21 TraesCS1B01G181600 chr7D 90.506 158 13 2 3341 3498 34756866 34757021 2.070000e-49 207.0
22 TraesCS1B01G181600 chr7B 86.075 912 119 5 2133 3039 580662425 580663333 0.000000e+00 974.0
23 TraesCS1B01G181600 chr5D 85.667 914 115 12 2129 3034 72905282 72904377 0.000000e+00 948.0
24 TraesCS1B01G181600 chr5D 90.526 95 7 2 1 94 359002458 359002551 2.150000e-24 124.0
25 TraesCS1B01G181600 chr5D 92.941 85 5 1 10 94 487920730 487920647 7.730000e-24 122.0
26 TraesCS1B01G181600 chr5D 89.474 95 8 2 1 94 10759940 10759847 1.000000e-22 119.0
27 TraesCS1B01G181600 chr5D 91.765 85 7 0 1 85 324352466 324352550 1.000000e-22 119.0
28 TraesCS1B01G181600 chr5D 89.474 95 8 2 1 94 434423782 434423875 1.000000e-22 119.0
29 TraesCS1B01G181600 chr2D 85.385 910 123 7 2135 3039 551154861 551153957 0.000000e+00 935.0
30 TraesCS1B01G181600 chr2D 90.526 95 7 2 1 94 629532863 629532770 2.150000e-24 124.0
31 TraesCS1B01G181600 chr6D 84.494 948 130 12 2134 3072 417771411 417772350 0.000000e+00 920.0
32 TraesCS1B01G181600 chr6D 80.254 709 104 18 2451 3152 47319841 47320520 8.490000e-138 501.0
33 TraesCS1B01G181600 chr6D 82.402 483 67 7 2653 3132 17237416 17237883 6.850000e-109 405.0
34 TraesCS1B01G181600 chr6D 90.385 156 14 1 3341 3496 392273226 392273072 2.680000e-48 204.0
35 TraesCS1B01G181600 chr4B 91.558 154 12 1 3341 3494 106227561 106227409 1.600000e-50 211.0
36 TraesCS1B01G181600 chr4B 90.566 159 13 2 3340 3498 438375334 438375178 5.770000e-50 209.0
37 TraesCS1B01G181600 chr4A 91.139 158 11 3 3341 3498 690411441 690411287 1.600000e-50 211.0
38 TraesCS1B01G181600 chr5A 90.446 157 13 2 3339 3494 295076273 295076428 7.460000e-49 206.0
39 TraesCS1B01G181600 chr3A 88.304 171 16 3 3341 3510 582283367 582283200 9.650000e-48 202.0
40 TraesCS1B01G181600 chr2A 90.323 155 14 1 3341 3495 141506318 141506471 9.650000e-48 202.0
41 TraesCS1B01G181600 chr4D 91.209 91 7 1 1 90 415291887 415291977 7.730000e-24 122.0
42 TraesCS1B01G181600 chr4D 89.474 95 8 2 1 94 14434877 14434784 1.000000e-22 119.0


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 TraesCS1B01G181600 chr1B 328641492 328647170 5678 True 10488.00 10488 100.000000 1 5679 1 chr1B.!!$R1 5678
1 TraesCS1B01G181600 chr1A 297695926 297701591 5665 True 1978.55 5450 94.107500 129 5571 4 chr1A.!!$R1 5442
2 TraesCS1B01G181600 chr1A 342865448 342866452 1004 False 959.00 959 84.004000 2135 3146 1 chr1A.!!$F2 1011
3 TraesCS1B01G181600 chr1D 120019642 120020654 1012 False 1000.00 1000 84.540000 2137 3153 1 chr1D.!!$F1 1016
4 TraesCS1B01G181600 chr1D 484432314 484433228 914 True 987.00 987 86.196000 2138 3052 1 chr1D.!!$R2 914
5 TraesCS1B01G181600 chr1D 229320483 229324736 4253 True 692.55 2041 94.989875 713 5662 8 chr1D.!!$R3 4949
6 TraesCS1B01G181600 chr7D 621300067 621300969 902 False 992.00 992 86.579000 2136 3039 1 chr7D.!!$F2 903
7 TraesCS1B01G181600 chr7B 580662425 580663333 908 False 974.00 974 86.075000 2133 3039 1 chr7B.!!$F1 906
8 TraesCS1B01G181600 chr5D 72904377 72905282 905 True 948.00 948 85.667000 2129 3034 1 chr5D.!!$R2 905
9 TraesCS1B01G181600 chr2D 551153957 551154861 904 True 935.00 935 85.385000 2135 3039 1 chr2D.!!$R1 904
10 TraesCS1B01G181600 chr6D 417771411 417772350 939 False 920.00 920 84.494000 2134 3072 1 chr6D.!!$F3 938
11 TraesCS1B01G181600 chr6D 47319841 47320520 679 False 501.00 501 80.254000 2451 3152 1 chr6D.!!$F2 701

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
87 88 0.036732 AATTGAAGCGGACCTCAGCA 59.963 50.0 0.21 0.00 39.54 4.41 F
88 89 0.254178 ATTGAAGCGGACCTCAGCAT 59.746 50.0 0.21 0.00 39.54 3.79 F
95 96 0.597568 CGGACCTCAGCATGCAAAAA 59.402 50.0 21.98 0.57 34.76 1.94 F
1791 1828 1.026182 CGGTTGCTATCCTTGCAGCA 61.026 55.0 0.00 0.00 45.72 4.41 F
2690 2859 0.037326 TGACTTGACATCTCCACCGC 60.037 55.0 0.00 0.00 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1791 1828 4.998672 CCGATAGACTCTCCGAAGAATAGT 59.001 45.833 3.17 0.00 39.76 2.12 R
2072 2234 5.240403 GGTCTTCCGGGTTGTACTATACTAG 59.760 48.000 0.00 0.00 0.00 2.57 R
2271 2434 4.572389 GCAAGAACACTCCACATTATCGAT 59.428 41.667 2.16 2.16 0.00 3.59 R
3760 3943 1.073763 CCATCTTATCATTCCCCCGCA 59.926 52.381 0.00 0.00 0.00 5.69 R
4720 5026 0.107263 TGTGCTCCAGTGAAGTGCAA 60.107 50.000 0.00 0.00 35.69 4.08 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
20 21 1.452110 TCATGCATTGTTCTGACCCG 58.548 50.000 0.00 0.00 0.00 5.28
21 22 1.003003 TCATGCATTGTTCTGACCCGA 59.997 47.619 0.00 0.00 0.00 5.14
22 23 2.019249 CATGCATTGTTCTGACCCGAT 58.981 47.619 0.00 0.00 0.00 4.18
23 24 2.198827 TGCATTGTTCTGACCCGATT 57.801 45.000 0.00 0.00 0.00 3.34
24 25 2.513753 TGCATTGTTCTGACCCGATTT 58.486 42.857 0.00 0.00 0.00 2.17
25 26 2.228582 TGCATTGTTCTGACCCGATTTG 59.771 45.455 0.00 0.00 0.00 2.32
26 27 2.228822 GCATTGTTCTGACCCGATTTGT 59.771 45.455 0.00 0.00 0.00 2.83
27 28 3.670627 GCATTGTTCTGACCCGATTTGTC 60.671 47.826 0.00 0.00 0.00 3.18
28 29 3.485463 TTGTTCTGACCCGATTTGTCT 57.515 42.857 0.00 0.00 33.83 3.41
29 30 3.485463 TGTTCTGACCCGATTTGTCTT 57.515 42.857 0.00 0.00 33.83 3.01
30 31 3.815809 TGTTCTGACCCGATTTGTCTTT 58.184 40.909 0.00 0.00 33.83 2.52
31 32 4.204012 TGTTCTGACCCGATTTGTCTTTT 58.796 39.130 0.00 0.00 33.83 2.27
32 33 4.642885 TGTTCTGACCCGATTTGTCTTTTT 59.357 37.500 0.00 0.00 33.83 1.94
46 47 4.481195 TTTTTGCCGAGAGCTGCT 57.519 50.000 0.00 0.00 44.23 4.24
47 48 2.247790 TTTTTGCCGAGAGCTGCTC 58.752 52.632 21.72 21.72 44.23 4.26
48 49 0.534877 TTTTTGCCGAGAGCTGCTCA 60.535 50.000 29.49 8.15 44.15 4.26
49 50 0.952497 TTTTGCCGAGAGCTGCTCAG 60.952 55.000 29.49 21.79 44.15 3.35
50 51 1.820010 TTTGCCGAGAGCTGCTCAGA 61.820 55.000 29.49 7.15 44.15 3.27
51 52 1.611474 TTGCCGAGAGCTGCTCAGAT 61.611 55.000 29.49 10.97 44.15 2.90
52 53 0.753111 TGCCGAGAGCTGCTCAGATA 60.753 55.000 29.49 12.91 44.15 1.98
53 54 0.602562 GCCGAGAGCTGCTCAGATAT 59.397 55.000 29.49 10.20 44.15 1.63
54 55 1.402720 GCCGAGAGCTGCTCAGATATC 60.403 57.143 29.49 17.18 44.15 1.63
55 56 1.202114 CCGAGAGCTGCTCAGATATCC 59.798 57.143 29.49 9.58 44.15 2.59
56 57 1.885233 CGAGAGCTGCTCAGATATCCA 59.115 52.381 29.49 0.00 44.15 3.41
57 58 2.295629 CGAGAGCTGCTCAGATATCCAA 59.704 50.000 29.49 0.00 44.15 3.53
58 59 3.243670 CGAGAGCTGCTCAGATATCCAAA 60.244 47.826 29.49 0.00 44.15 3.28
59 60 4.561123 CGAGAGCTGCTCAGATATCCAAAT 60.561 45.833 29.49 5.90 44.15 2.32
60 61 4.643463 AGAGCTGCTCAGATATCCAAATG 58.357 43.478 29.49 0.00 32.06 2.32
61 62 4.347292 AGAGCTGCTCAGATATCCAAATGA 59.653 41.667 29.49 0.00 32.06 2.57
62 63 5.013287 AGAGCTGCTCAGATATCCAAATGAT 59.987 40.000 29.49 1.88 33.50 2.45
63 64 5.632118 AGCTGCTCAGATATCCAAATGATT 58.368 37.500 0.00 0.00 34.76 2.57
64 65 6.069331 AGCTGCTCAGATATCCAAATGATTT 58.931 36.000 0.00 0.00 34.76 2.17
65 66 6.550108 AGCTGCTCAGATATCCAAATGATTTT 59.450 34.615 0.00 0.00 34.76 1.82
66 67 7.722728 AGCTGCTCAGATATCCAAATGATTTTA 59.277 33.333 0.00 0.00 34.76 1.52
67 68 8.355169 GCTGCTCAGATATCCAAATGATTTTAA 58.645 33.333 0.00 0.00 34.76 1.52
78 79 8.027440 TCCAAATGATTTTAAAATTGAAGCGG 57.973 30.769 14.45 10.99 0.00 5.52
79 80 7.875041 TCCAAATGATTTTAAAATTGAAGCGGA 59.125 29.630 14.45 12.77 0.00 5.54
80 81 7.956943 CCAAATGATTTTAAAATTGAAGCGGAC 59.043 33.333 14.45 0.06 0.00 4.79
81 82 7.595311 AATGATTTTAAAATTGAAGCGGACC 57.405 32.000 14.45 0.00 0.00 4.46
82 83 6.339587 TGATTTTAAAATTGAAGCGGACCT 57.660 33.333 14.45 0.00 0.00 3.85
83 84 6.386654 TGATTTTAAAATTGAAGCGGACCTC 58.613 36.000 14.45 0.00 0.00 3.85
84 85 5.776173 TTTTAAAATTGAAGCGGACCTCA 57.224 34.783 0.00 0.00 0.00 3.86
85 86 5.371115 TTTAAAATTGAAGCGGACCTCAG 57.629 39.130 0.00 0.00 0.00 3.35
86 87 1.168714 AAATTGAAGCGGACCTCAGC 58.831 50.000 0.00 0.00 37.32 4.26
87 88 0.036732 AATTGAAGCGGACCTCAGCA 59.963 50.000 0.21 0.00 39.54 4.41
88 89 0.254178 ATTGAAGCGGACCTCAGCAT 59.746 50.000 0.21 0.00 39.54 3.79
89 90 0.674581 TTGAAGCGGACCTCAGCATG 60.675 55.000 0.21 0.00 39.54 4.06
90 91 2.437359 AAGCGGACCTCAGCATGC 60.437 61.111 10.51 10.51 39.54 4.06
91 92 3.258228 AAGCGGACCTCAGCATGCA 62.258 57.895 21.98 0.00 39.54 3.96
92 93 2.747460 GCGGACCTCAGCATGCAA 60.747 61.111 21.98 6.54 37.03 4.08
93 94 2.334946 GCGGACCTCAGCATGCAAA 61.335 57.895 21.98 6.13 37.03 3.68
94 95 1.865788 GCGGACCTCAGCATGCAAAA 61.866 55.000 21.98 3.33 37.03 2.44
95 96 0.597568 CGGACCTCAGCATGCAAAAA 59.402 50.000 21.98 0.57 34.76 1.94
141 142 2.216898 GTGCAGATAAGACTGGGCATC 58.783 52.381 0.00 0.00 38.22 3.91
142 143 1.839354 TGCAGATAAGACTGGGCATCA 59.161 47.619 0.00 0.00 38.22 3.07
146 147 4.340381 GCAGATAAGACTGGGCATCAAAAT 59.660 41.667 0.00 0.00 38.22 1.82
147 148 5.735354 GCAGATAAGACTGGGCATCAAAATG 60.735 44.000 0.00 0.00 38.22 2.32
162 163 6.373779 CATCAAAATGCTACACTCGTTTCTT 58.626 36.000 0.00 0.00 0.00 2.52
163 164 5.747565 TCAAAATGCTACACTCGTTTCTTG 58.252 37.500 0.00 0.00 0.00 3.02
172 173 4.909894 ACACTCGTTTCTTGCTTCTTTTC 58.090 39.130 0.00 0.00 0.00 2.29
177 178 3.384668 GTTTCTTGCTTCTTTTCTGGCC 58.615 45.455 0.00 0.00 0.00 5.36
180 181 3.233507 TCTTGCTTCTTTTCTGGCCATT 58.766 40.909 5.51 0.00 0.00 3.16
241 243 4.720649 TCTAGACCAATTCCGAGTTCAG 57.279 45.455 0.00 0.00 0.00 3.02
247 249 5.875359 AGACCAATTCCGAGTTCAGTAATTC 59.125 40.000 0.00 0.00 0.00 2.17
248 250 5.556915 ACCAATTCCGAGTTCAGTAATTCA 58.443 37.500 0.00 0.00 0.00 2.57
353 355 4.445699 GCAGATCGCCTAACCCAG 57.554 61.111 0.00 0.00 32.94 4.45
362 364 1.339631 CGCCTAACCCAGTTGATTGGA 60.340 52.381 0.00 0.00 40.87 3.53
368 370 5.590259 CCTAACCCAGTTGATTGGATACTTG 59.410 44.000 0.00 0.00 40.87 3.16
369 371 3.968265 ACCCAGTTGATTGGATACTTGG 58.032 45.455 0.00 0.00 40.87 3.61
370 372 3.333680 ACCCAGTTGATTGGATACTTGGT 59.666 43.478 0.00 0.00 40.87 3.67
421 427 2.307768 CTCAATGAGAAGCCCATGCAT 58.692 47.619 3.77 0.00 41.13 3.96
479 485 2.278857 CGTAGCTAGCTGCACGGG 60.279 66.667 28.85 11.63 45.94 5.28
501 507 2.220824 TCTTCGACACACAAGCATTTCG 59.779 45.455 0.00 0.00 0.00 3.46
582 588 6.917477 CACATTAGAGCTAGAAGTCATCTGTC 59.083 42.308 0.00 0.00 39.30 3.51
602 608 5.593010 TGTCTTTTAATTTTGGGTCCGTTG 58.407 37.500 0.00 0.00 0.00 4.10
679 687 6.732896 AGGGAGATCGTGTATATCTTGTTT 57.267 37.500 0.00 0.00 33.82 2.83
681 689 7.565680 AGGGAGATCGTGTATATCTTGTTTTT 58.434 34.615 0.00 0.00 33.82 1.94
1138 1163 4.100084 TCCGCCTCCGTCTCCGTA 62.100 66.667 0.00 0.00 0.00 4.02
1791 1828 1.026182 CGGTTGCTATCCTTGCAGCA 61.026 55.000 0.00 0.00 45.72 4.41
2118 2280 3.120546 CGCAACAGTTTCGATGACTCAAT 60.121 43.478 0.00 0.00 0.00 2.57
2126 2289 7.095187 ACAGTTTCGATGACTCAATTTAGGTTC 60.095 37.037 0.00 0.00 0.00 3.62
2270 2433 2.814097 GCCACCACTCACACCTACAAAT 60.814 50.000 0.00 0.00 0.00 2.32
2271 2434 3.558321 GCCACCACTCACACCTACAAATA 60.558 47.826 0.00 0.00 0.00 1.40
2339 2502 2.875933 GTCGCCGATCCATCCAAATAAA 59.124 45.455 0.00 0.00 0.00 1.40
2458 2622 4.100653 TCAAGAAAGAGATCCGCATCATCT 59.899 41.667 0.00 0.00 33.01 2.90
2651 2820 2.139917 GAACAGGCATGACACAACGTA 58.860 47.619 4.84 0.00 0.00 3.57
2690 2859 0.037326 TGACTTGACATCTCCACCGC 60.037 55.000 0.00 0.00 0.00 5.68
2693 2862 0.247460 CTTGACATCTCCACCGCAGA 59.753 55.000 0.00 0.00 0.00 4.26
2703 2872 1.154413 CACCGCAGATTCGTGCAAC 60.154 57.895 0.00 0.00 44.21 4.17
2758 2928 1.568612 CGCTGCTCCACAAACGATGT 61.569 55.000 0.00 0.00 45.34 3.06
2760 2930 1.664016 GCTGCTCCACAAACGATGTTG 60.664 52.381 0.00 0.00 41.46 3.33
2761 2931 1.603802 CTGCTCCACAAACGATGTTGT 59.396 47.619 0.00 0.00 41.46 3.32
3109 3281 1.909781 AGACCCTCCACGCCGTTTA 60.910 57.895 0.00 0.00 0.00 2.01
3110 3282 1.219935 GACCCTCCACGCCGTTTAT 59.780 57.895 0.00 0.00 0.00 1.40
3315 3498 6.374613 GGTGAGAAGTTCCTTTATGGGTAAAG 59.625 42.308 0.00 1.85 44.12 1.85
3350 3533 4.120589 GCTCTTTGTTTATACTCCCTCCG 58.879 47.826 0.00 0.00 0.00 4.63
3429 3612 7.678194 ATGAGTGAACAAACACATTAAAACG 57.322 32.000 0.00 0.00 42.45 3.60
3437 3620 8.555166 AACAAACACATTAAAACGTGTCTATG 57.445 30.769 8.57 10.07 45.37 2.23
3440 3623 9.098746 CAAACACATTAAAACGTGTCTATGTAC 57.901 33.333 8.57 0.00 45.37 2.90
3777 3960 3.374042 TTTTGCGGGGGAATGATAAGA 57.626 42.857 0.00 0.00 0.00 2.10
3778 3961 3.593442 TTTGCGGGGGAATGATAAGAT 57.407 42.857 0.00 0.00 0.00 2.40
3779 3962 2.566833 TGCGGGGGAATGATAAGATG 57.433 50.000 0.00 0.00 0.00 2.90
3780 3963 1.073763 TGCGGGGGAATGATAAGATGG 59.926 52.381 0.00 0.00 0.00 3.51
3786 3969 4.202673 GGGGGAATGATAAGATGGCCTTTA 60.203 45.833 3.32 0.49 36.34 1.85
3978 4161 2.065899 TATGGTGGGGCTTAATGCAC 57.934 50.000 0.00 0.00 46.31 4.57
4004 4187 3.989167 GCAACTGCTTATGAATTGCAACA 59.011 39.130 0.00 0.00 44.01 3.33
4148 4453 2.093216 GCTCTGCAGCACATGGTAC 58.907 57.895 9.47 0.00 46.06 3.34
4477 4783 3.023832 CGCCTCCATTTTTGGGTAAGAT 58.976 45.455 0.00 0.00 0.00 2.40
4480 4786 4.711846 GCCTCCATTTTTGGGTAAGATTCT 59.288 41.667 0.00 0.00 0.00 2.40
4486 4792 6.369615 CCATTTTTGGGTAAGATTCTTTGCAG 59.630 38.462 3.86 0.00 0.00 4.41
4684 4990 6.515200 GCATTATAGGCGAGAAGTAAGAGACA 60.515 42.308 0.00 0.00 0.00 3.41
4720 5026 1.139058 GATTCTGTGCCAGACGGGTAT 59.861 52.381 4.59 0.00 40.46 2.73
4763 5069 2.983791 GGCGCTGTACAGGGGTTA 59.016 61.111 33.27 0.00 41.16 2.85
4769 5075 2.431057 CGCTGTACAGGGGTTAGAAGAT 59.569 50.000 27.60 0.00 37.68 2.40
4826 5132 1.884579 CACAGCTTGAAGAGGCATGTT 59.115 47.619 0.00 0.00 0.00 2.71
4959 5265 5.127845 ACACTGATGAAGTTGTCGAGGATAT 59.872 40.000 0.00 0.00 36.83 1.63
4968 5274 4.830046 AGTTGTCGAGGATATAGTCATGCT 59.170 41.667 0.00 0.00 0.00 3.79
5029 5335 4.880886 AAGTGCAAAGAAAACCAATTGC 57.119 36.364 0.00 2.58 46.29 3.56
5042 5348 3.902218 ACCAATTGCATGGCTACATAGT 58.098 40.909 6.24 0.00 44.75 2.12
5055 5361 5.186198 GGCTACATAGTTCAGATGGTTTGT 58.814 41.667 0.00 0.00 0.00 2.83
5056 5362 5.065218 GGCTACATAGTTCAGATGGTTTGTG 59.935 44.000 0.00 0.00 0.00 3.33
5091 5397 5.414454 TGTGTTGTACAAATATGGGAGAAGC 59.586 40.000 10.51 0.00 36.06 3.86
5124 5453 2.816087 ACAAGTAGTTGCAAGCATGGAG 59.184 45.455 10.30 0.00 37.14 3.86
5127 5456 3.276857 AGTAGTTGCAAGCATGGAGATG 58.723 45.455 0.00 0.00 0.00 2.90
5172 5502 4.750021 TTCTGGTGAGATCTGATCCTTG 57.250 45.455 13.83 0.32 0.00 3.61
5184 5821 4.361783 TCTGATCCTTGGTCTGTATTCCA 58.638 43.478 0.00 0.00 0.00 3.53
5244 5881 7.928908 TCAAGAGAACAAAATGCACATAAAC 57.071 32.000 0.00 0.00 0.00 2.01
5341 6005 2.367202 GCTGCTACAGGGGCCTACA 61.367 63.158 0.84 0.00 31.21 2.74
5428 6092 0.527565 GTTAGGTGAAGACGCGGGTA 59.472 55.000 12.47 0.00 0.00 3.69
5508 6263 2.310233 CGGTGTGACAAGACAGGCG 61.310 63.158 0.00 0.00 0.00 5.52
5519 6274 2.925170 ACAGGCGTCTTGCTCCCT 60.925 61.111 0.00 0.00 45.43 4.20
5533 6288 1.617536 TCCCTGGCAAGAGCTCCAT 60.618 57.895 10.93 0.00 41.70 3.41
5621 6377 4.157817 GCATGCACCTTGCTTTCG 57.842 55.556 14.21 0.00 45.31 3.46
5662 6418 3.430453 CCATACCCCCGCATTTAATGAT 58.570 45.455 9.36 0.00 0.00 2.45
5663 6419 3.193267 CCATACCCCCGCATTTAATGATG 59.807 47.826 9.36 1.84 0.00 3.07
5664 6420 2.452600 ACCCCCGCATTTAATGATGT 57.547 45.000 9.36 0.00 0.00 3.06
5665 6421 3.586470 ACCCCCGCATTTAATGATGTA 57.414 42.857 9.36 0.00 0.00 2.29
5666 6422 3.904717 ACCCCCGCATTTAATGATGTAA 58.095 40.909 9.36 0.00 0.00 2.41
5667 6423 3.888930 ACCCCCGCATTTAATGATGTAAG 59.111 43.478 9.36 0.00 0.00 2.34
5668 6424 3.888930 CCCCCGCATTTAATGATGTAAGT 59.111 43.478 9.36 0.00 0.00 2.24
5669 6425 4.261572 CCCCCGCATTTAATGATGTAAGTG 60.262 45.833 9.36 0.00 0.00 3.16
5671 6427 5.163561 CCCCGCATTTAATGATGTAAGTGTT 60.164 40.000 9.36 0.00 0.00 3.32
5672 6428 5.971202 CCCGCATTTAATGATGTAAGTGTTC 59.029 40.000 9.36 0.00 0.00 3.18
5673 6429 6.183360 CCCGCATTTAATGATGTAAGTGTTCT 60.183 38.462 9.36 0.00 0.00 3.01
5674 6430 7.250569 CCGCATTTAATGATGTAAGTGTTCTT 58.749 34.615 9.36 0.00 37.65 2.52
5675 6431 7.429340 CCGCATTTAATGATGTAAGTGTTCTTC 59.571 37.037 9.36 0.00 35.36 2.87
5676 6432 8.177663 CGCATTTAATGATGTAAGTGTTCTTCT 58.822 33.333 9.36 0.00 35.36 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.452110 TCGGGTCAGAACAATGCATG 58.548 50.000 0.00 0.00 0.00 4.06
3 4 2.425143 ATCGGGTCAGAACAATGCAT 57.575 45.000 0.00 0.00 0.00 3.96
4 5 2.198827 AATCGGGTCAGAACAATGCA 57.801 45.000 0.00 0.00 0.00 3.96
5 6 2.228822 ACAAATCGGGTCAGAACAATGC 59.771 45.455 0.00 0.00 0.00 3.56
6 7 3.753272 AGACAAATCGGGTCAGAACAATG 59.247 43.478 0.00 0.00 37.74 2.82
7 8 4.021102 AGACAAATCGGGTCAGAACAAT 57.979 40.909 0.00 0.00 37.74 2.71
8 9 3.485463 AGACAAATCGGGTCAGAACAA 57.515 42.857 0.00 0.00 37.74 2.83
9 10 3.485463 AAGACAAATCGGGTCAGAACA 57.515 42.857 0.00 0.00 37.74 3.18
10 11 4.830826 AAAAGACAAATCGGGTCAGAAC 57.169 40.909 0.00 0.00 37.74 3.01
29 30 0.534877 TGAGCAGCTCTCGGCAAAAA 60.535 50.000 23.15 0.00 44.86 1.94
30 31 0.952497 CTGAGCAGCTCTCGGCAAAA 60.952 55.000 23.15 0.00 44.86 2.44
31 32 1.375140 CTGAGCAGCTCTCGGCAAA 60.375 57.895 23.15 0.00 44.86 3.68
32 33 1.611474 ATCTGAGCAGCTCTCGGCAA 61.611 55.000 23.15 0.68 45.76 4.52
33 34 0.753111 TATCTGAGCAGCTCTCGGCA 60.753 55.000 23.15 2.15 45.76 5.69
34 35 0.602562 ATATCTGAGCAGCTCTCGGC 59.397 55.000 23.15 0.00 45.76 5.54
36 37 1.885233 TGGATATCTGAGCAGCTCTCG 59.115 52.381 23.15 13.93 44.86 4.04
37 38 4.333913 TTTGGATATCTGAGCAGCTCTC 57.666 45.455 23.15 11.57 42.23 3.20
38 39 4.347292 TCATTTGGATATCTGAGCAGCTCT 59.653 41.667 23.15 5.93 0.00 4.09
39 40 4.639334 TCATTTGGATATCTGAGCAGCTC 58.361 43.478 16.21 16.21 0.00 4.09
40 41 4.701651 TCATTTGGATATCTGAGCAGCT 57.298 40.909 0.00 0.00 0.00 4.24
41 42 5.961396 AATCATTTGGATATCTGAGCAGC 57.039 39.130 2.05 0.00 34.28 5.25
52 53 8.667463 CCGCTTCAATTTTAAAATCATTTGGAT 58.333 29.630 13.68 0.00 38.05 3.41
53 54 7.875041 TCCGCTTCAATTTTAAAATCATTTGGA 59.125 29.630 13.68 13.13 0.00 3.53
54 55 7.956943 GTCCGCTTCAATTTTAAAATCATTTGG 59.043 33.333 13.68 11.35 0.00 3.28
55 56 7.956943 GGTCCGCTTCAATTTTAAAATCATTTG 59.043 33.333 13.68 9.32 0.00 2.32
56 57 7.877612 AGGTCCGCTTCAATTTTAAAATCATTT 59.122 29.630 13.68 0.00 0.00 2.32
57 58 7.386059 AGGTCCGCTTCAATTTTAAAATCATT 58.614 30.769 13.68 0.00 0.00 2.57
58 59 6.935167 AGGTCCGCTTCAATTTTAAAATCAT 58.065 32.000 13.68 0.00 0.00 2.45
59 60 6.015856 TGAGGTCCGCTTCAATTTTAAAATCA 60.016 34.615 13.68 1.60 0.00 2.57
60 61 6.386654 TGAGGTCCGCTTCAATTTTAAAATC 58.613 36.000 13.68 0.78 0.00 2.17
61 62 6.339587 TGAGGTCCGCTTCAATTTTAAAAT 57.660 33.333 7.64 7.64 0.00 1.82
62 63 5.768317 CTGAGGTCCGCTTCAATTTTAAAA 58.232 37.500 2.51 2.51 30.12 1.52
63 64 4.320935 GCTGAGGTCCGCTTCAATTTTAAA 60.321 41.667 0.00 0.00 30.12 1.52
64 65 3.190535 GCTGAGGTCCGCTTCAATTTTAA 59.809 43.478 0.00 0.00 30.12 1.52
65 66 2.747446 GCTGAGGTCCGCTTCAATTTTA 59.253 45.455 0.00 0.00 30.12 1.52
66 67 1.541588 GCTGAGGTCCGCTTCAATTTT 59.458 47.619 0.00 0.00 30.12 1.82
67 68 1.168714 GCTGAGGTCCGCTTCAATTT 58.831 50.000 0.00 0.00 30.12 1.82
68 69 0.036732 TGCTGAGGTCCGCTTCAATT 59.963 50.000 0.00 0.00 30.12 2.32
69 70 0.254178 ATGCTGAGGTCCGCTTCAAT 59.746 50.000 0.00 0.00 30.12 2.57
70 71 0.674581 CATGCTGAGGTCCGCTTCAA 60.675 55.000 0.00 0.00 30.12 2.69
71 72 1.078918 CATGCTGAGGTCCGCTTCA 60.079 57.895 0.00 0.00 0.00 3.02
72 73 2.467826 GCATGCTGAGGTCCGCTTC 61.468 63.158 11.37 0.00 0.00 3.86
73 74 2.437359 GCATGCTGAGGTCCGCTT 60.437 61.111 11.37 0.00 0.00 4.68
74 75 2.753009 TTTGCATGCTGAGGTCCGCT 62.753 55.000 20.33 0.00 0.00 5.52
75 76 1.865788 TTTTGCATGCTGAGGTCCGC 61.866 55.000 20.33 0.00 0.00 5.54
76 77 0.597568 TTTTTGCATGCTGAGGTCCG 59.402 50.000 20.33 0.00 0.00 4.79
107 108 4.640771 ATCTGCACCTAGTCAGGAAAAA 57.359 40.909 0.00 0.00 45.91 1.94
108 109 5.483937 TCTTATCTGCACCTAGTCAGGAAAA 59.516 40.000 0.00 0.00 45.91 2.29
109 110 5.023452 TCTTATCTGCACCTAGTCAGGAAA 58.977 41.667 0.00 0.77 45.91 3.13
110 111 4.402793 GTCTTATCTGCACCTAGTCAGGAA 59.597 45.833 0.00 0.85 45.91 3.36
111 112 3.954904 GTCTTATCTGCACCTAGTCAGGA 59.045 47.826 0.00 0.00 45.91 3.86
112 113 7.183276 CCAGTCTTATCTGCACCTAGTCAGG 62.183 52.000 0.00 0.00 39.66 3.86
113 114 4.202101 CCAGTCTTATCTGCACCTAGTCAG 60.202 50.000 0.00 0.00 34.47 3.51
114 115 3.701542 CCAGTCTTATCTGCACCTAGTCA 59.298 47.826 0.00 0.00 34.47 3.41
115 116 3.068873 CCCAGTCTTATCTGCACCTAGTC 59.931 52.174 0.00 0.00 34.47 2.59
116 117 3.034635 CCCAGTCTTATCTGCACCTAGT 58.965 50.000 0.00 0.00 34.47 2.57
117 118 2.224161 GCCCAGTCTTATCTGCACCTAG 60.224 54.545 0.00 0.00 34.47 3.02
118 119 1.762957 GCCCAGTCTTATCTGCACCTA 59.237 52.381 0.00 0.00 34.47 3.08
119 120 0.543749 GCCCAGTCTTATCTGCACCT 59.456 55.000 0.00 0.00 34.47 4.00
120 121 0.253044 TGCCCAGTCTTATCTGCACC 59.747 55.000 0.00 0.00 34.47 5.01
121 122 2.216898 GATGCCCAGTCTTATCTGCAC 58.783 52.381 0.00 0.00 34.47 4.57
122 123 1.839354 TGATGCCCAGTCTTATCTGCA 59.161 47.619 0.00 0.00 34.47 4.41
123 124 2.627515 TGATGCCCAGTCTTATCTGC 57.372 50.000 0.00 0.00 34.47 4.26
124 125 5.735354 GCATTTTGATGCCCAGTCTTATCTG 60.735 44.000 0.00 0.00 41.47 2.90
125 126 4.340381 GCATTTTGATGCCCAGTCTTATCT 59.660 41.667 0.00 0.00 41.47 1.98
126 127 4.614946 GCATTTTGATGCCCAGTCTTATC 58.385 43.478 0.00 0.00 41.47 1.75
127 128 4.660789 GCATTTTGATGCCCAGTCTTAT 57.339 40.909 0.00 0.00 41.47 1.73
141 142 4.379793 GCAAGAAACGAGTGTAGCATTTTG 59.620 41.667 0.00 0.00 0.00 2.44
142 143 4.275936 AGCAAGAAACGAGTGTAGCATTTT 59.724 37.500 0.00 0.00 0.00 1.82
146 147 2.526304 AGCAAGAAACGAGTGTAGCA 57.474 45.000 0.00 0.00 0.00 3.49
147 148 3.060602 AGAAGCAAGAAACGAGTGTAGC 58.939 45.455 0.00 0.00 0.00 3.58
162 163 3.134442 ACAAAATGGCCAGAAAAGAAGCA 59.866 39.130 13.05 0.00 0.00 3.91
163 164 3.732212 ACAAAATGGCCAGAAAAGAAGC 58.268 40.909 13.05 0.00 0.00 3.86
190 192 5.587388 ATGAAGCAACAAGTTCCCATATG 57.413 39.130 0.00 0.00 0.00 1.78
204 206 8.806429 TTGGTCTAGATGAATAAATGAAGCAA 57.194 30.769 0.00 0.00 0.00 3.91
241 243 6.782150 CCTTCGGGTTGTATTTCTGAATTAC 58.218 40.000 13.01 13.01 0.00 1.89
303 305 5.476091 GCTCATAAGTTAGCTAGGGATGT 57.524 43.478 0.00 0.00 35.80 3.06
353 355 3.088532 TGCCACCAAGTATCCAATCAAC 58.911 45.455 0.00 0.00 0.00 3.18
362 364 6.825610 TCTTGAAATTTTTGCCACCAAGTAT 58.174 32.000 11.21 0.00 33.39 2.12
368 370 5.817296 AGAGTTTCTTGAAATTTTTGCCACC 59.183 36.000 0.00 0.00 0.00 4.61
369 371 6.908870 AGAGTTTCTTGAAATTTTTGCCAC 57.091 33.333 0.00 0.00 0.00 5.01
370 372 7.605691 TCAAAGAGTTTCTTGAAATTTTTGCCA 59.394 29.630 16.16 0.00 37.35 4.92
501 507 0.897621 CCCCCAAAAGCAAGATCACC 59.102 55.000 0.00 0.00 0.00 4.02
582 588 7.151976 AGAATCAACGGACCCAAAATTAAAAG 58.848 34.615 0.00 0.00 0.00 2.27
602 608 3.128415 GCTGCTTCCTTCCTTTGAGAATC 59.872 47.826 0.00 0.00 0.00 2.52
1791 1828 4.998672 CCGATAGACTCTCCGAAGAATAGT 59.001 45.833 3.17 0.00 39.76 2.12
2071 2233 5.825151 GTCTTCCGGGTTGTACTATACTAGT 59.175 44.000 0.00 0.00 42.68 2.57
2072 2234 5.240403 GGTCTTCCGGGTTGTACTATACTAG 59.760 48.000 0.00 0.00 0.00 2.57
2270 2433 5.753438 GCAAGAACACTCCACATTATCGATA 59.247 40.000 0.00 0.00 0.00 2.92
2271 2434 4.572389 GCAAGAACACTCCACATTATCGAT 59.428 41.667 2.16 2.16 0.00 3.59
2339 2502 1.874345 CGGCTGTAGGTTCCGACACT 61.874 60.000 0.86 0.00 45.53 3.55
2703 2872 1.739562 GAGGTGGAGCAGCTTCGTG 60.740 63.158 0.00 0.00 42.53 4.35
2758 2928 4.112634 CAGTGTCGTTTCTCTCTTGACAA 58.887 43.478 0.00 0.00 40.84 3.18
2760 2930 2.473235 GCAGTGTCGTTTCTCTCTTGAC 59.527 50.000 0.00 0.00 0.00 3.18
2761 2931 2.100749 TGCAGTGTCGTTTCTCTCTTGA 59.899 45.455 0.00 0.00 0.00 3.02
3109 3281 4.609018 CGGGCTTCGGATCGGCAT 62.609 66.667 0.00 0.00 34.75 4.40
3146 3321 4.212425 CCATTTAAACTTTTTGGCCGGTTC 59.788 41.667 1.90 0.00 0.00 3.62
3190 3373 5.095490 CGTTGGCAGAAGGAAATTATTGTC 58.905 41.667 0.00 0.00 0.00 3.18
3315 3498 4.045636 ACAAAGAGCAACATTTCACCAC 57.954 40.909 0.00 0.00 0.00 4.16
3386 3569 9.337396 TCACTCATTTCAGTTTGTATGTAGTTT 57.663 29.630 0.00 0.00 0.00 2.66
3398 3581 6.266168 TGTGTTTGTTCACTCATTTCAGTT 57.734 33.333 0.00 0.00 38.90 3.16
3429 3612 8.932945 TTTCTGAATCAGATGTACATAGACAC 57.067 34.615 14.31 8.27 40.39 3.67
3756 3939 3.702792 TCTTATCATTCCCCCGCAAAAA 58.297 40.909 0.00 0.00 0.00 1.94
3757 3940 3.374042 TCTTATCATTCCCCCGCAAAA 57.626 42.857 0.00 0.00 0.00 2.44
3758 3941 3.221771 CATCTTATCATTCCCCCGCAAA 58.778 45.455 0.00 0.00 0.00 3.68
3759 3942 2.488891 CCATCTTATCATTCCCCCGCAA 60.489 50.000 0.00 0.00 0.00 4.85
3760 3943 1.073763 CCATCTTATCATTCCCCCGCA 59.926 52.381 0.00 0.00 0.00 5.69
3761 3944 1.826385 CCATCTTATCATTCCCCCGC 58.174 55.000 0.00 0.00 0.00 6.13
3762 3945 1.614317 GGCCATCTTATCATTCCCCCG 60.614 57.143 0.00 0.00 0.00 5.73
3763 3946 1.713078 AGGCCATCTTATCATTCCCCC 59.287 52.381 5.01 0.00 0.00 5.40
3764 3947 3.532641 AAGGCCATCTTATCATTCCCC 57.467 47.619 5.01 0.00 33.14 4.81
3765 3948 5.420104 CCATAAAGGCCATCTTATCATTCCC 59.580 44.000 5.01 0.00 34.78 3.97
3766 3949 6.521151 CCATAAAGGCCATCTTATCATTCC 57.479 41.667 5.01 0.00 34.78 3.01
3786 3969 4.727507 TGGTATTTTAAACGCATGCCAT 57.272 36.364 13.15 0.00 28.67 4.40
3861 4044 3.012518 CAGAATCAACTGGCCCAAGTAG 58.987 50.000 0.00 0.00 34.64 2.57
3943 4126 6.205784 CCCACCATAACATTAGCATTTTACG 58.794 40.000 0.00 0.00 0.00 3.18
3978 4161 3.777478 CAATTCATAAGCAGTTGCCCTG 58.223 45.455 0.00 0.00 44.53 4.45
3986 4169 6.954616 TTTGATGTTGCAATTCATAAGCAG 57.045 33.333 13.74 0.00 39.72 4.24
4004 4187 3.573967 AGGCGGTTCAAGTTTCATTTGAT 59.426 39.130 0.00 0.00 34.76 2.57
4045 4228 9.824216 AGGAACATATCTAATACTGCTAGGTTA 57.176 33.333 0.00 0.00 0.00 2.85
4148 4453 3.245264 ACCAACAAAGGAATCCCACCTAG 60.245 47.826 0.00 0.00 36.67 3.02
4486 4792 9.632807 TTGTGTAAATTTTATTGTCCAGCATAC 57.367 29.630 0.00 0.00 0.00 2.39
4720 5026 0.107263 TGTGCTCCAGTGAAGTGCAA 60.107 50.000 0.00 0.00 35.69 4.08
4959 5265 5.124457 GCTGAAATGGAGAAAAGCATGACTA 59.876 40.000 0.00 0.00 0.00 2.59
4968 5274 5.596836 AAGTTGTGCTGAAATGGAGAAAA 57.403 34.783 0.00 0.00 0.00 2.29
5029 5335 4.965814 ACCATCTGAACTATGTAGCCATG 58.034 43.478 0.00 0.00 32.29 3.66
5042 5348 6.472016 TCAGCTATTACACAAACCATCTGAA 58.528 36.000 0.00 0.00 0.00 3.02
5055 5361 7.971183 TTTGTACAACACATCAGCTATTACA 57.029 32.000 8.07 0.00 36.90 2.41
5091 5397 4.442706 CAACTACTTGTACATAGGGGCTG 58.557 47.826 0.00 0.00 0.00 4.85
5124 5453 4.864916 TGCTTTTCGCTCATTAGACATC 57.135 40.909 0.00 0.00 40.11 3.06
5127 5456 5.393962 ACAATTGCTTTTCGCTCATTAGAC 58.606 37.500 5.05 0.00 40.11 2.59
5184 5821 5.745227 TCTGTGAGGAAAACAAAGACTTCT 58.255 37.500 0.00 0.00 28.14 2.85
5244 5881 4.021102 ACTATCCCAAAAGTGACACCAG 57.979 45.455 0.84 0.00 0.00 4.00
5341 6005 2.599139 TATGGACTAGGGCCACCGCT 62.599 60.000 6.18 0.00 43.47 5.52
5385 6049 3.044305 GTGGCAGTGTCTCCGCAC 61.044 66.667 0.00 0.00 39.51 5.34
5450 6115 2.661537 CGCGAGGTGTTGAGTGCA 60.662 61.111 0.00 0.00 0.00 4.57
5519 6274 0.547553 TATGCATGGAGCTCTTGCCA 59.452 50.000 27.77 19.87 45.94 4.92
5533 6288 1.688942 CCATGGGCCTCCTTTTATGCA 60.689 52.381 2.85 0.00 0.00 3.96
5588 6343 2.171870 GCATGCTTAACCCCCTACTGTA 59.828 50.000 11.37 0.00 0.00 2.74
5590 6345 1.064758 TGCATGCTTAACCCCCTACTG 60.065 52.381 20.33 0.00 0.00 2.74
5641 6397 2.870175 TCATTAAATGCGGGGGTATGG 58.130 47.619 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.