Multiple sequence alignment - TraesCS4B01G275000

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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 TraesCS4B01G275000 chr4B 100.000 4299 0 0 1 4299 552843271 552847569 0.000000e+00 7939.0
1 TraesCS4B01G275000 chr4B 84.800 125 17 2 2908 3031 579733583 579733706 1.620000e-24 124.0
2 TraesCS4B01G275000 chr4B 84.416 77 11 1 4165 4240 552857399 552857475 1.660000e-09 75.0
3 TraesCS4B01G275000 chr4D 88.329 2322 133 51 1 2231 443518135 443520409 0.000000e+00 2660.0
4 TraesCS4B01G275000 chr4D 95.141 1276 57 4 2282 3556 443520406 443521677 0.000000e+00 2008.0
5 TraesCS4B01G275000 chr4D 83.847 681 75 22 3640 4299 443524031 443524697 2.200000e-172 616.0
6 TraesCS4B01G275000 chr4D 82.324 611 77 18 3646 4240 443719669 443720264 6.420000e-138 501.0
7 TraesCS4B01G275000 chr4D 84.921 126 17 2 2908 3032 464156696 464156820 4.510000e-25 126.0
8 TraesCS4B01G275000 chr4A 90.298 1546 88 27 596 2108 24218957 24217441 0.000000e+00 1967.0
9 TraesCS4B01G275000 chr4A 93.722 892 43 4 2656 3535 24217065 24216175 0.000000e+00 1325.0
10 TraesCS4B01G275000 chr4A 83.381 698 90 20 3621 4299 24216170 24215480 1.310000e-174 623.0
11 TraesCS4B01G275000 chr4A 85.891 567 34 17 10 549 24219965 24219418 2.900000e-156 562.0
12 TraesCS4B01G275000 chr4A 92.878 337 24 0 2282 2618 24217398 24217062 1.390000e-134 490.0
13 TraesCS4B01G275000 chr4A 90.491 326 30 1 2297 2622 102625689 102626013 3.070000e-116 429.0
14 TraesCS4B01G275000 chr4A 82.278 158 23 2 3689 3841 77095568 77095725 9.700000e-27 132.0
15 TraesCS4B01G275000 chr4A 80.380 158 25 3 3688 3840 96018825 96018669 9.770000e-22 115.0
16 TraesCS4B01G275000 chr5D 85.873 630 72 5 2278 2903 517413652 517413036 0.000000e+00 654.0
17 TraesCS4B01G275000 chr5D 85.177 452 49 8 1833 2284 517415594 517415161 8.480000e-122 448.0
18 TraesCS4B01G275000 chr5D 89.583 96 8 1 1735 1828 517415854 517415759 2.100000e-23 121.0
19 TraesCS4B01G275000 chr5D 88.732 71 5 2 3539 3607 295543565 295543496 2.750000e-12 84.2
20 TraesCS4B01G275000 chr7A 82.031 640 69 13 2277 2910 111959793 111959194 1.780000e-138 503.0
21 TraesCS4B01G275000 chr2D 89.881 336 32 2 2287 2622 557134395 557134062 8.540000e-117 431.0
22 TraesCS4B01G275000 chr2D 89.583 336 33 2 2287 2622 608571227 608570894 3.970000e-115 425.0
23 TraesCS4B01G275000 chr2D 84.247 146 11 3 1008 1146 117194513 117194373 9.700000e-27 132.0
24 TraesCS4B01G275000 chr2D 89.231 65 7 0 2927 2991 468131499 468131563 9.910000e-12 82.4
25 TraesCS4B01G275000 chr2D 91.071 56 5 0 2916 2971 38095021 38095076 4.610000e-10 76.8
26 TraesCS4B01G275000 chr2D 84.615 65 6 4 4090 4151 39495696 39495759 1.290000e-05 62.1
27 TraesCS4B01G275000 chr1D 81.524 525 79 14 2701 3214 171162740 171162223 2.390000e-112 416.0
28 TraesCS4B01G275000 chr1D 83.562 146 19 2 3692 3833 475925213 475925069 9.700000e-27 132.0
29 TraesCS4B01G275000 chr1D 81.250 80 13 1 3541 3618 394488542 394488463 3.590000e-06 63.9
30 TraesCS4B01G275000 chr7D 86.607 336 40 3 2287 2622 1224819 1225149 2.440000e-97 366.0
31 TraesCS4B01G275000 chr1B 86.928 306 40 0 2909 3214 226357576 226357271 1.140000e-90 344.0
32 TraesCS4B01G275000 chr1B 83.951 162 15 3 1009 1163 199671085 199670928 1.250000e-30 145.0
33 TraesCS4B01G275000 chr1B 81.935 155 20 5 3689 3838 152953782 152953933 1.620000e-24 124.0
34 TraesCS4B01G275000 chr2B 91.558 154 12 1 2287 2440 643297826 643297978 1.210000e-50 211.0
35 TraesCS4B01G275000 chr2B 84.615 156 20 1 3689 3840 566624816 566624971 7.450000e-33 152.0
36 TraesCS4B01G275000 chr2B 91.228 57 5 0 2919 2975 3292169 3292225 1.280000e-10 78.7
37 TraesCS4B01G275000 chr2B 90.909 55 5 0 2768 2822 25673686 25673632 1.660000e-09 75.0
38 TraesCS4B01G275000 chr3B 84.713 157 13 3 1010 1159 612305432 612305584 3.460000e-31 147.0
39 TraesCS4B01G275000 chr3B 78.528 163 21 8 3957 4105 434055035 434054873 1.270000e-15 95.3
40 TraesCS4B01G275000 chr6B 84.314 153 19 2 3689 3837 468734617 468734466 1.250000e-30 145.0
41 TraesCS4B01G275000 chr6A 83.766 154 20 4 3689 3837 607453808 607453961 1.610000e-29 141.0
42 TraesCS4B01G275000 chr2A 83.750 160 15 3 1008 1160 240817664 240817819 1.610000e-29 141.0
43 TraesCS4B01G275000 chr2A 81.410 156 25 1 3689 3840 625025660 625025815 1.620000e-24 124.0
44 TraesCS4B01G275000 chr2A 83.077 65 7 4 4090 4151 56938165 56938102 6.010000e-04 56.5
45 TraesCS4B01G275000 chr7B 84.247 146 12 2 1008 1146 381905345 381905486 9.700000e-27 132.0
46 TraesCS4B01G275000 chr3A 84.247 146 12 2 1008 1146 442907367 442907226 9.700000e-27 132.0
47 TraesCS4B01G275000 chr5A 83.333 144 12 3 1010 1146 691995802 691995664 5.840000e-24 122.0
48 TraesCS4B01G275000 chr5A 94.444 36 2 0 3540 3575 370035903 370035868 6.010000e-04 56.5
49 TraesCS4B01G275000 chr5B 78.610 187 24 8 1013 1184 100735716 100735901 4.550000e-20 110.0


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 TraesCS4B01G275000 chr4B 552843271 552847569 4298 False 7939.000000 7939 100.000000 1 4299 1 chr4B.!!$F1 4298
1 TraesCS4B01G275000 chr4D 443518135 443524697 6562 False 1761.333333 2660 89.105667 1 4299 3 chr4D.!!$F3 4298
2 TraesCS4B01G275000 chr4D 443719669 443720264 595 False 501.000000 501 82.324000 3646 4240 1 chr4D.!!$F1 594
3 TraesCS4B01G275000 chr4A 24215480 24219965 4485 True 993.400000 1967 89.234000 10 4299 5 chr4A.!!$R2 4289
4 TraesCS4B01G275000 chr5D 517413036 517415854 2818 True 407.666667 654 86.877667 1735 2903 3 chr5D.!!$R2 1168
5 TraesCS4B01G275000 chr7A 111959194 111959793 599 True 503.000000 503 82.031000 2277 2910 1 chr7A.!!$R1 633
6 TraesCS4B01G275000 chr1D 171162223 171162740 517 True 416.000000 416 81.524000 2701 3214 1 chr1D.!!$R1 513

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
635 1110 0.108019 ATCCCCCGGAAATACTTCGC 59.892 55.0 0.73 0.0 34.34 4.70 F
920 1409 1.237285 CCTTGTCTGGCCTGGTTTCG 61.237 60.0 10.07 0.0 0.00 3.46 F
1992 2695 0.620556 AGGGAGTGTGGAATCGCATT 59.379 50.0 0.00 0.0 35.69 3.56 F
2681 4908 0.399091 TCTCTGAATCCCTCCGGCAT 60.399 55.0 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 2202 0.652592 GCGAAGATCATTGGTGACGG 59.347 55.0 0.0 0.0 37.14 4.79 R
2372 4599 0.659957 GCGATCTTCATTCTGGTGGC 59.340 55.0 0.0 0.0 0.00 5.01 R
3232 5488 0.252421 TCACCTCCATCACCAGCTCT 60.252 55.0 0.0 0.0 0.00 4.09 R
3918 8485 1.337384 ATGTATCCAGCGGCCTGACA 61.337 55.0 0.0 0.0 41.77 3.58 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
59 63 9.581289 TTTTTGTTTGACCTTATAAGATGAGGA 57.419 29.630 14.28 0.00 38.24 3.71
65 69 7.921041 TGACCTTATAAGATGAGGATTGAGT 57.079 36.000 14.28 0.00 38.24 3.41
66 70 8.324191 TGACCTTATAAGATGAGGATTGAGTT 57.676 34.615 14.28 0.00 38.24 3.01
89 109 1.361204 TGGATGCTGGACTTGGAAGA 58.639 50.000 0.00 0.00 0.00 2.87
96 116 0.397941 TGGACTTGGAAGACTGCCAG 59.602 55.000 1.37 0.00 36.64 4.85
118 148 1.481615 GGTCCAGGTATCTCTCCCTCC 60.482 61.905 0.00 0.00 0.00 4.30
129 159 4.715130 TCCCTCCCTCCCACCACG 62.715 72.222 0.00 0.00 0.00 4.94
132 162 4.394712 CTCCCTCCCACCACGCAC 62.395 72.222 0.00 0.00 0.00 5.34
137 167 2.904866 TCCCACCACGCACAAAGC 60.905 61.111 0.00 0.00 40.87 3.51
138 168 3.977244 CCCACCACGCACAAAGCC 61.977 66.667 0.00 0.00 41.38 4.35
283 317 1.002659 CATCACGGTGGTGGAAAGGTA 59.997 52.381 13.61 0.00 44.50 3.08
308 342 2.018515 ACGCGACAAGGAAAAGGAAAA 58.981 42.857 15.93 0.00 0.00 2.29
309 343 2.424246 ACGCGACAAGGAAAAGGAAAAA 59.576 40.909 15.93 0.00 0.00 1.94
310 344 3.067601 ACGCGACAAGGAAAAGGAAAAAT 59.932 39.130 15.93 0.00 0.00 1.82
311 345 4.276431 ACGCGACAAGGAAAAGGAAAAATA 59.724 37.500 15.93 0.00 0.00 1.40
312 346 5.216648 CGCGACAAGGAAAAGGAAAAATAA 58.783 37.500 0.00 0.00 0.00 1.40
313 347 5.688176 CGCGACAAGGAAAAGGAAAAATAAA 59.312 36.000 0.00 0.00 0.00 1.40
314 348 6.199342 CGCGACAAGGAAAAGGAAAAATAAAA 59.801 34.615 0.00 0.00 0.00 1.52
315 349 7.095816 CGCGACAAGGAAAAGGAAAAATAAAAT 60.096 33.333 0.00 0.00 0.00 1.82
366 400 4.776322 CATTCCGCTCCACCGCCA 62.776 66.667 0.00 0.00 0.00 5.69
367 401 4.778143 ATTCCGCTCCACCGCCAC 62.778 66.667 0.00 0.00 0.00 5.01
417 453 3.062466 CCTCGCGAGTCCTCCACA 61.062 66.667 32.41 0.00 0.00 4.17
635 1110 0.108019 ATCCCCCGGAAATACTTCGC 59.892 55.000 0.73 0.00 34.34 4.70
887 1376 4.384940 GGATAGAAATCTGCACCTTCTCC 58.615 47.826 3.98 0.00 31.91 3.71
920 1409 1.237285 CCTTGTCTGGCCTGGTTTCG 61.237 60.000 10.07 0.00 0.00 3.46
1047 1540 1.796459 CCGTACTTCAACAGGGTTTCG 59.204 52.381 0.00 0.00 0.00 3.46
1083 1576 8.688151 ACAAAGTCAGGTACTACTCATATTCTC 58.312 37.037 0.00 0.00 37.50 2.87
1108 1601 4.384056 CTTCCTGGTATGGCTTATGTGAG 58.616 47.826 0.00 0.00 0.00 3.51
1170 1674 9.080097 ACTGTTAGCTTTCTAGGTATATACTGG 57.920 37.037 12.54 3.94 34.54 4.00
1204 1712 5.365403 TTTTAACAATTCGATGGCGTCTT 57.635 34.783 5.00 0.00 38.98 3.01
1243 1751 4.701956 ATCCAAAAAGTGCATACCTTCG 57.298 40.909 0.00 0.00 0.00 3.79
1255 1777 2.226962 TACCTTCGTGCTTCCTAGGT 57.773 50.000 9.08 0.00 41.80 3.08
1256 1778 1.349067 ACCTTCGTGCTTCCTAGGTT 58.651 50.000 9.08 0.00 35.77 3.50
1283 1805 1.482182 TCTGATCCACTCCATTCACCG 59.518 52.381 0.00 0.00 0.00 4.94
1332 1856 6.599244 TCCAATCAAACCAGTGATATGAACTC 59.401 38.462 0.00 0.00 37.25 3.01
1355 1887 6.169094 TCCAGTGATCTGTCAAAGAATTCTC 58.831 40.000 8.78 0.00 38.79 2.87
1382 1914 6.262049 ACCATTTGCAAGTTAATTTTGGAACC 59.738 34.615 0.00 0.00 35.93 3.62
1416 1956 4.811908 TCCATTTGCAATCTTGTGACATG 58.188 39.130 0.00 0.00 0.00 3.21
1440 1980 6.889177 TGCATGACATGACTTTCCCTTTTATA 59.111 34.615 19.76 0.00 0.00 0.98
1443 1983 7.333528 TGACATGACTTTCCCTTTTATATGC 57.666 36.000 0.00 0.00 0.00 3.14
1507 2047 2.280457 GACGATAGCCTGCTGCCC 60.280 66.667 0.97 0.00 42.71 5.36
1627 2167 2.925170 AGGCAGGACTCGGTGCTT 60.925 61.111 0.00 0.00 39.76 3.91
1662 2202 1.078637 GCCGGGTCTACAAAGGGTC 60.079 63.158 2.18 0.00 0.00 4.46
1691 2231 3.753294 ATGATCTTCGCGAAGGGTTAT 57.247 42.857 39.79 28.79 42.82 1.89
1702 2242 3.740141 GCGAAGGGTTATCGATTGAGGAA 60.740 47.826 1.71 0.00 42.76 3.36
1953 2656 1.866015 AGATGATCACCGGGTTCTCA 58.134 50.000 6.32 10.05 0.00 3.27
1962 2665 1.287425 CCGGGTTCTCATTTACGAGC 58.713 55.000 0.00 0.00 32.75 5.03
1992 2695 0.620556 AGGGAGTGTGGAATCGCATT 59.379 50.000 0.00 0.00 35.69 3.56
1994 2697 2.238646 AGGGAGTGTGGAATCGCATTTA 59.761 45.455 0.00 0.00 35.69 1.40
2007 2710 7.279090 TGGAATCGCATTTATTTTCGAGTAAGA 59.721 33.333 0.00 0.00 34.30 2.10
2020 2723 7.884816 TTTCGAGTAAGACACCTATTCTTTG 57.115 36.000 0.00 0.00 34.99 2.77
2021 2724 5.408356 TCGAGTAAGACACCTATTCTTTGC 58.592 41.667 0.00 0.00 34.99 3.68
2022 2725 5.047590 TCGAGTAAGACACCTATTCTTTGCA 60.048 40.000 0.00 0.00 34.99 4.08
2023 2726 5.812642 CGAGTAAGACACCTATTCTTTGCAT 59.187 40.000 0.00 0.00 34.99 3.96
2024 2727 6.313905 CGAGTAAGACACCTATTCTTTGCATT 59.686 38.462 0.00 0.00 34.99 3.56
2025 2728 7.491372 CGAGTAAGACACCTATTCTTTGCATTA 59.509 37.037 0.00 0.00 34.99 1.90
2066 2777 0.861837 GTCTCTTAATCATGGCGCCG 59.138 55.000 23.90 8.74 0.00 6.46
2087 2798 3.126858 CGACCGGTTTCATTCACATGAAT 59.873 43.478 9.42 1.11 46.68 2.57
2090 2801 4.522405 ACCGGTTTCATTCACATGAATCAA 59.478 37.500 0.00 0.00 46.68 2.57
2095 2806 8.800972 CGGTTTCATTCACATGAATCAATTTAG 58.199 33.333 0.00 0.00 46.68 1.85
2117 2828 4.353737 GCATTCAATTATGCGAGCTTTGA 58.646 39.130 0.00 0.00 41.24 2.69
2119 2830 5.051907 GCATTCAATTATGCGAGCTTTGAAG 60.052 40.000 11.80 6.71 41.24 3.02
2136 2847 3.334691 TGAAGCTACCGTGAATTTGGAG 58.665 45.455 0.00 0.00 0.00 3.86
2155 2866 3.056107 GGAGCCAAATTTGTTAACTCCCC 60.056 47.826 23.31 10.33 36.95 4.81
2156 2867 3.832490 GAGCCAAATTTGTTAACTCCCCT 59.168 43.478 16.73 0.00 0.00 4.79
2163 2874 5.977489 ATTTGTTAACTCCCCTAAACTGC 57.023 39.130 7.22 0.00 0.00 4.40
2164 2875 4.440826 TTGTTAACTCCCCTAAACTGCA 57.559 40.909 7.22 0.00 0.00 4.41
2165 2876 3.746940 TGTTAACTCCCCTAAACTGCAC 58.253 45.455 7.22 0.00 0.00 4.57
2184 2895 8.785468 ACTGCACAATAAATTTTTGCAATTTC 57.215 26.923 0.00 0.00 32.64 2.17
2186 2897 6.359087 TGCACAATAAATTTTTGCAATTTCGC 59.641 30.769 0.00 0.00 32.64 4.70
2187 2898 6.578172 GCACAATAAATTTTTGCAATTTCGCT 59.422 30.769 0.00 0.00 32.64 4.93
2188 2899 7.408500 GCACAATAAATTTTTGCAATTTCGCTG 60.408 33.333 0.00 0.02 32.64 5.18
2243 2954 6.695713 GTCAAACTTTTTGCCGTATTTCTTCT 59.304 34.615 0.00 0.00 0.00 2.85
2248 2959 8.965986 ACTTTTTGCCGTATTTCTTCTTAATC 57.034 30.769 0.00 0.00 0.00 1.75
2249 2960 8.573035 ACTTTTTGCCGTATTTCTTCTTAATCA 58.427 29.630 0.00 0.00 0.00 2.57
2258 2969 8.664798 CGTATTTCTTCTTAATCACATGACCAA 58.335 33.333 0.00 0.00 0.00 3.67
2395 4622 3.005554 CACCAGAATGAAGATCGCACTT 58.994 45.455 0.00 0.00 39.69 3.16
2520 4747 3.364864 CGTTGGATCGCTTTGATGTTTGA 60.365 43.478 0.00 0.00 37.47 2.69
2627 4854 4.881850 ACCTATCATTTTTCATGACCGGTC 59.118 41.667 28.17 28.17 32.10 4.79
2681 4908 0.399091 TCTCTGAATCCCTCCGGCAT 60.399 55.000 0.00 0.00 0.00 4.40
2736 4964 2.358247 TTCGGGCTGGCGAAAGAC 60.358 61.111 0.00 0.00 42.12 3.01
2796 5024 3.834799 GGCACCTACGGCTACGCT 61.835 66.667 0.00 0.00 46.04 5.07
3067 5323 1.561542 CATAGGAAGAAGGTGCTGGGT 59.438 52.381 0.00 0.00 0.00 4.51
3151 5407 2.650116 CGCCTACCACTGCCTCAGT 61.650 63.158 0.00 0.00 46.51 3.41
3199 5455 2.264794 GACATCGTCGCCACCCTT 59.735 61.111 0.00 0.00 0.00 3.95
3342 5598 6.985013 CGTGTACGTTCTTTTCTGCATATAA 58.015 36.000 0.00 0.00 34.11 0.98
3408 5665 1.068741 GACAGTGTTCTCTTGGTCGGT 59.931 52.381 0.00 0.00 0.00 4.69
3472 5739 4.204012 TCTTCGGGAATTTCACAACTTGT 58.796 39.130 0.00 0.00 0.00 3.16
3473 5740 4.642885 TCTTCGGGAATTTCACAACTTGTT 59.357 37.500 0.00 0.00 0.00 2.83
3501 5768 3.997021 GAGAGACTCTTGCGGATCAAAAA 59.003 43.478 6.40 0.00 33.65 1.94
3582 5850 8.147244 AGACATTTTAGGTCACTATTAGTGGT 57.853 34.615 20.83 9.41 45.94 4.16
3592 5860 6.870439 GGTCACTATTAGTGGTCTAAAACGTT 59.130 38.462 20.83 0.00 45.94 3.99
3611 5879 9.977762 AAAACGTTTTATATTAGCTTACGGAAG 57.022 29.630 24.13 1.91 35.60 3.46
3619 5893 4.708726 TTAGCTTACGGAAGGAGTACAC 57.291 45.455 10.00 0.00 32.84 2.90
3631 5905 6.473758 GGAAGGAGTACACTACAGGATTTTT 58.526 40.000 0.00 0.00 0.00 1.94
3668 8227 8.829612 TGTATACAGTTATCATGCATGTTTCAG 58.170 33.333 25.43 14.50 0.00 3.02
3669 8228 5.571784 ACAGTTATCATGCATGTTTCAGG 57.428 39.130 25.43 14.67 0.00 3.86
3704 8267 2.305858 AGGTACTCCTTCCGTTCACT 57.694 50.000 0.00 0.00 42.12 3.41
3810 8377 9.133218 CGTTCGATTCAGAAATAAATTAGAACG 57.867 33.333 16.91 16.91 45.76 3.95
3852 8419 3.869832 GGGAGTAACTAGGATGCGTTTTC 59.130 47.826 0.00 0.00 0.00 2.29
3856 8423 6.038997 AGTAACTAGGATGCGTTTTCTTCT 57.961 37.500 0.00 0.00 0.00 2.85
4125 8702 8.696043 AGATATTAGCACATTTTTCTATGGCA 57.304 30.769 0.00 0.00 0.00 4.92
4132 8709 5.813672 GCACATTTTTCTATGGCATGTCAAT 59.186 36.000 10.98 0.00 0.00 2.57
4143 8720 5.902613 TGGCATGTCAATCTTTAGAAAGG 57.097 39.130 0.00 0.00 36.67 3.11
4197 8774 4.411256 TTTGGAACGGAGTGAGTAGTTT 57.589 40.909 0.00 0.00 45.00 2.66
4232 8809 6.110411 AGGCTACTTAGAAACTAAAGCACA 57.890 37.500 13.48 0.00 0.00 4.57
4233 8810 6.712276 AGGCTACTTAGAAACTAAAGCACAT 58.288 36.000 13.48 1.93 0.00 3.21
4234 8811 7.848128 AGGCTACTTAGAAACTAAAGCACATA 58.152 34.615 13.48 0.00 0.00 2.29
4236 8813 8.604890 GGCTACTTAGAAACTAAAGCACATAAG 58.395 37.037 13.48 0.00 0.00 1.73
4237 8814 8.117370 GCTACTTAGAAACTAAAGCACATAAGC 58.883 37.037 0.00 0.00 0.00 3.09
4242 8819 7.617041 AGAAACTAAAGCACATAAGCTAAGG 57.383 36.000 0.00 0.00 45.89 2.69
4248 8825 3.474600 AGCACATAAGCTAAGGATGCAG 58.525 45.455 11.14 1.56 44.50 4.41
4250 8827 3.629398 GCACATAAGCTAAGGATGCAGTT 59.371 43.478 0.00 0.00 0.00 3.16
4251 8828 4.096984 GCACATAAGCTAAGGATGCAGTTT 59.903 41.667 0.00 0.00 0.00 2.66
4252 8829 5.393461 GCACATAAGCTAAGGATGCAGTTTT 60.393 40.000 0.00 0.00 0.00 2.43
4253 8830 6.032094 CACATAAGCTAAGGATGCAGTTTTG 58.968 40.000 0.00 0.00 0.00 2.44
4256 8833 7.557719 ACATAAGCTAAGGATGCAGTTTTGTAT 59.442 33.333 0.00 0.00 31.86 2.29
4257 8834 6.840780 AAGCTAAGGATGCAGTTTTGTATT 57.159 33.333 0.00 0.00 29.11 1.89
4258 8835 7.938140 AAGCTAAGGATGCAGTTTTGTATTA 57.062 32.000 0.00 0.00 29.11 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.681593 TTCTCCCATTGCATTTTGTGG 57.318 42.857 0.00 0.00 0.00 4.17
7 8 3.008266 CCCTTTCTCCCATTGCATTTTGT 59.992 43.478 0.00 0.00 0.00 2.83
14 16 2.165357 ATTCCCCTTTCTCCCATTGC 57.835 50.000 0.00 0.00 0.00 3.56
17 19 4.502415 ACAAAAATTCCCCTTTCTCCCAT 58.498 39.130 0.00 0.00 0.00 4.00
19 21 4.974645 AACAAAAATTCCCCTTTCTCCC 57.025 40.909 0.00 0.00 0.00 4.30
23 25 5.680619 AGGTCAAACAAAAATTCCCCTTTC 58.319 37.500 0.00 0.00 0.00 2.62
59 63 4.018960 AGTCCAGCATCCAACTAACTCAAT 60.019 41.667 0.00 0.00 0.00 2.57
65 69 2.642311 TCCAAGTCCAGCATCCAACTAA 59.358 45.455 0.00 0.00 0.00 2.24
66 70 2.265367 TCCAAGTCCAGCATCCAACTA 58.735 47.619 0.00 0.00 0.00 2.24
89 109 0.547712 ATACCTGGACCACTGGCAGT 60.548 55.000 15.88 15.88 41.59 4.40
96 116 1.062810 AGGGAGAGATACCTGGACCAC 60.063 57.143 0.00 0.00 35.30 4.16
118 148 2.203280 TTTGTGCGTGGTGGGAGG 60.203 61.111 0.00 0.00 0.00 4.30
129 159 2.010817 CGTCGCTTTGGCTTTGTGC 61.011 57.895 0.00 0.00 41.94 4.57
130 160 2.010817 GCGTCGCTTTGGCTTTGTG 61.011 57.895 10.68 0.00 36.09 3.33
132 162 2.639286 AGCGTCGCTTTGGCTTTG 59.361 55.556 15.47 0.00 33.89 2.77
174 207 2.756283 CGGCGACTTCTCCCCTCT 60.756 66.667 0.00 0.00 0.00 3.69
283 317 1.098712 TTTTCCTTGTCGCGTTGGCT 61.099 50.000 5.77 0.00 36.88 4.75
308 342 7.092623 GGTGGAGACCCCCAATTTTATTTTATT 60.093 37.037 0.00 0.00 38.06 1.40
309 343 6.385759 GGTGGAGACCCCCAATTTTATTTTAT 59.614 38.462 0.00 0.00 38.06 1.40
310 344 5.722441 GGTGGAGACCCCCAATTTTATTTTA 59.278 40.000 0.00 0.00 38.06 1.52
311 345 4.534500 GGTGGAGACCCCCAATTTTATTTT 59.466 41.667 0.00 0.00 38.06 1.82
312 346 4.101114 GGTGGAGACCCCCAATTTTATTT 58.899 43.478 0.00 0.00 38.06 1.40
313 347 3.078305 TGGTGGAGACCCCCAATTTTATT 59.922 43.478 0.00 0.00 42.34 1.40
314 348 2.657459 TGGTGGAGACCCCCAATTTTAT 59.343 45.455 0.00 0.00 42.34 1.40
315 349 2.074579 TGGTGGAGACCCCCAATTTTA 58.925 47.619 0.00 0.00 42.34 1.52
366 400 4.552365 CTGGCGCCATGGATCGGT 62.552 66.667 32.87 0.00 0.00 4.69
367 401 3.541950 ATCTGGCGCCATGGATCGG 62.542 63.158 32.87 16.96 0.00 4.18
374 408 0.035036 CTCATCTCATCTGGCGCCAT 59.965 55.000 32.87 14.47 0.00 4.40
417 453 1.203237 TCTCCCCAGACTGCTTTCTCT 60.203 52.381 0.00 0.00 0.00 3.10
481 519 4.757657 GTCTTCTGTCTGTCTGTCTGTCTA 59.242 45.833 0.00 0.00 0.00 2.59
552 594 4.961511 AAACGCAGCGACGAGGCA 62.962 61.111 24.65 0.00 36.70 4.75
558 600 3.723348 GGTGGGAAACGCAGCGAC 61.723 66.667 24.65 7.75 35.37 5.19
566 608 0.031585 GAAAAGGCGTGGTGGGAAAC 59.968 55.000 0.00 0.00 0.00 2.78
772 1261 2.287308 CGCACGTTTCAATCAAAAGGGA 60.287 45.455 0.00 0.00 28.78 4.20
887 1376 1.607467 CAAGGAACAGGCAAGGGGG 60.607 63.158 0.00 0.00 0.00 5.40
896 1385 0.607489 CCAGGCCAGACAAGGAACAG 60.607 60.000 5.01 0.00 0.00 3.16
929 1421 6.184789 TCACCAAGAACAAGAAACCTAGTTT 58.815 36.000 0.00 0.00 38.54 2.66
930 1422 5.751586 TCACCAAGAACAAGAAACCTAGTT 58.248 37.500 0.00 0.00 0.00 2.24
931 1423 5.130477 TCTCACCAAGAACAAGAAACCTAGT 59.870 40.000 0.00 0.00 0.00 2.57
932 1424 5.467063 GTCTCACCAAGAACAAGAAACCTAG 59.533 44.000 0.00 0.00 35.21 3.02
1047 1540 2.362077 ACCTGACTTTGTTGCATTGGAC 59.638 45.455 0.00 0.00 0.00 4.02
1083 1576 1.518367 TAAGCCATACCAGGAAGGGG 58.482 55.000 0.00 0.00 43.89 4.79
1183 1691 4.434989 CGAAGACGCCATCGAATTGTTAAA 60.435 41.667 0.00 0.00 41.43 1.52
1184 1692 3.061563 CGAAGACGCCATCGAATTGTTAA 59.938 43.478 0.00 0.00 41.43 2.01
1200 1708 7.128976 GGATTGAGAATTAATTGCTCGAAGAC 58.871 38.462 5.17 7.88 0.00 3.01
1204 1712 7.389803 TTTGGATTGAGAATTAATTGCTCGA 57.610 32.000 5.17 11.52 0.00 4.04
1243 1751 4.214332 CAGACTGAAAAACCTAGGAAGCAC 59.786 45.833 17.98 4.51 0.00 4.40
1255 1777 4.705110 TGGAGTGGATCAGACTGAAAAA 57.295 40.909 9.70 0.00 0.00 1.94
1256 1778 4.916041 ATGGAGTGGATCAGACTGAAAA 57.084 40.909 9.70 0.00 0.00 2.29
1355 1887 7.256756 TCCAAAATTAACTTGCAAATGGTTG 57.743 32.000 11.62 5.93 37.83 3.77
1416 1956 4.525912 AAAAGGGAAAGTCATGTCATGC 57.474 40.909 8.03 3.79 0.00 4.06
1440 1980 4.755411 CAATTTTGGAGATTCTGCAGCAT 58.245 39.130 9.47 2.81 32.58 3.79
1443 1983 4.182693 TGCAATTTTGGAGATTCTGCAG 57.817 40.909 7.63 7.63 32.58 4.41
1507 2047 3.254629 CACCTCATGTGGGTTGGAG 57.745 57.895 17.76 1.11 41.52 3.86
1531 2071 3.788766 GCCGAATCGTTGCGCAGT 61.789 61.111 11.31 0.00 0.00 4.40
1627 2167 3.589542 CCAAAGCCACCTCCCCCA 61.590 66.667 0.00 0.00 0.00 4.96
1662 2202 0.652592 GCGAAGATCATTGGTGACGG 59.347 55.000 0.00 0.00 37.14 4.79
1691 2231 1.447838 GCAGCGGTTCCTCAATCGA 60.448 57.895 0.00 0.00 38.51 3.59
1953 2656 0.839946 AGGGGCATCAGCTCGTAAAT 59.160 50.000 0.00 0.00 44.30 1.40
1962 2665 0.692419 ACACTCCCTAGGGGCATCAG 60.692 60.000 28.19 18.97 43.94 2.90
1994 2697 8.936864 CAAAGAATAGGTGTCTTACTCGAAAAT 58.063 33.333 0.00 0.00 34.19 1.82
2007 2710 8.806146 ACAAGAAATAATGCAAAGAATAGGTGT 58.194 29.630 0.00 0.00 0.00 4.16
2017 2720 9.195411 CTCTAGCAAAACAAGAAATAATGCAAA 57.805 29.630 0.00 0.00 34.89 3.68
2018 2721 8.575589 TCTCTAGCAAAACAAGAAATAATGCAA 58.424 29.630 0.00 0.00 34.89 4.08
2019 2722 8.109705 TCTCTAGCAAAACAAGAAATAATGCA 57.890 30.769 0.00 0.00 34.89 3.96
2020 2723 9.578439 AATCTCTAGCAAAACAAGAAATAATGC 57.422 29.630 0.00 0.00 0.00 3.56
2024 2727 9.507329 AGACAATCTCTAGCAAAACAAGAAATA 57.493 29.630 0.00 0.00 0.00 1.40
2025 2728 8.401490 AGACAATCTCTAGCAAAACAAGAAAT 57.599 30.769 0.00 0.00 0.00 2.17
2061 2772 3.376914 GAATGAAACCGGTCGGCGC 62.377 63.158 8.04 0.00 39.32 6.53
2066 2777 4.155826 TGATTCATGTGAATGAAACCGGTC 59.844 41.667 8.04 0.00 44.14 4.79
2117 2828 2.084546 GCTCCAAATTCACGGTAGCTT 58.915 47.619 0.00 0.00 0.00 3.74
2119 2830 0.733150 GGCTCCAAATTCACGGTAGC 59.267 55.000 0.00 0.00 0.00 3.58
2136 2847 5.731957 TTAGGGGAGTTAACAAATTTGGC 57.268 39.130 21.74 9.16 0.00 4.52
2152 2863 7.572910 GCAAAAATTTATTGTGCAGTTTAGGGG 60.573 37.037 9.81 0.00 33.93 4.79
2155 2866 9.881529 ATTGCAAAAATTTATTGTGCAGTTTAG 57.118 25.926 1.71 0.00 40.47 1.85
2163 2874 7.587028 ACAGCGAAATTGCAAAAATTTATTGTG 59.413 29.630 1.71 0.00 37.31 3.33
2164 2875 7.638134 ACAGCGAAATTGCAAAAATTTATTGT 58.362 26.923 1.71 3.00 37.31 2.71
2165 2876 9.757859 ATACAGCGAAATTGCAAAAATTTATTG 57.242 25.926 1.71 2.42 37.31 1.90
2184 2895 5.551760 AAAATCACTGAGGAAATACAGCG 57.448 39.130 0.00 0.00 37.61 5.18
2258 2969 4.672587 AATAGTGCATACTCGACCACAT 57.327 40.909 0.00 0.00 38.36 3.21
2314 4541 9.394477 GTAAATCACAAGTACTTGAACAAATCC 57.606 33.333 36.14 16.33 42.93 3.01
2372 4599 0.659957 GCGATCTTCATTCTGGTGGC 59.340 55.000 0.00 0.00 0.00 5.01
2520 4747 7.338800 AGTTCTGAATTTATGCGAATGGAAT 57.661 32.000 0.00 0.00 0.00 3.01
2570 4797 7.776107 TGTTTTCTGAACCATTTATGTGAACA 58.224 30.769 0.00 0.00 0.00 3.18
2627 4854 7.636359 GCAAGCAAGAAGTATTAGTTTCATACG 59.364 37.037 0.00 0.00 33.07 3.06
2681 4908 4.674362 CGTTGTACTCCTGATGATGAACGA 60.674 45.833 0.00 0.00 36.63 3.85
2736 4964 4.308458 TTGTCACCGACAGGCCCG 62.308 66.667 0.00 0.00 43.69 6.13
2742 4970 1.590525 GTGCGACTTGTCACCGACA 60.591 57.895 1.59 0.00 41.09 4.35
2796 5024 0.689412 TCATGATGTACTCCGGGGCA 60.689 55.000 0.00 0.00 0.00 5.36
3049 5305 2.634639 TACCCAGCACCTTCTTCCTA 57.365 50.000 0.00 0.00 0.00 2.94
3067 5323 1.826921 GAGCCTGGGGTCGACGATA 60.827 63.158 9.92 0.00 32.85 2.92
3151 5407 4.659172 CTGGCCTTGGGGTTGCGA 62.659 66.667 3.32 0.00 34.45 5.10
3232 5488 0.252421 TCACCTCCATCACCAGCTCT 60.252 55.000 0.00 0.00 0.00 4.09
3342 5598 5.532406 ACAGTAAATTCACACAAGCATCACT 59.468 36.000 0.00 0.00 0.00 3.41
3408 5665 5.248477 AGAGAAAGACCCTTAGCATTGTGTA 59.752 40.000 0.00 0.00 0.00 2.90
3472 5739 2.416027 CCGCAAGAGTCTCTCGATTCAA 60.416 50.000 11.48 0.00 43.02 2.69
3473 5740 1.133216 CCGCAAGAGTCTCTCGATTCA 59.867 52.381 11.48 0.00 43.02 2.57
3501 5768 5.281314 TCTGTCTCTAAATTCTTAGGCCCT 58.719 41.667 0.00 0.00 36.03 5.19
3592 5860 9.135189 TGTACTCCTTCCGTAAGCTAATATAAA 57.865 33.333 0.00 0.00 0.00 1.40
3602 5870 4.096081 CCTGTAGTGTACTCCTTCCGTAAG 59.904 50.000 0.00 0.00 0.00 2.34
3647 8206 5.255687 TCCTGAAACATGCATGATAACTGT 58.744 37.500 32.75 7.43 0.00 3.55
3686 8249 4.732672 ATTAGTGAACGGAAGGAGTACC 57.267 45.455 0.00 0.00 0.00 3.34
3734 8297 6.090358 CACTCATTTCAGTCCGTACGTATTTT 59.910 38.462 15.21 0.00 0.00 1.82
3741 8304 4.304110 TGTTCACTCATTTCAGTCCGTAC 58.696 43.478 0.00 0.00 0.00 3.67
3785 8352 9.968743 ACGTTCTAATTTATTTCTGAATCGAAC 57.031 29.630 0.00 0.00 0.00 3.95
3787 8354 9.582431 AGACGTTCTAATTTATTTCTGAATCGA 57.418 29.630 0.00 0.00 0.00 3.59
3810 8377 5.667466 TCCCTCCGTTCACAAATATAAGAC 58.333 41.667 0.00 0.00 0.00 3.01
3852 8419 4.213270 TGGCGTGTGACTTTTAATCAGAAG 59.787 41.667 0.00 0.00 0.00 2.85
3856 8423 3.818210 ACATGGCGTGTGACTTTTAATCA 59.182 39.130 12.39 0.00 40.28 2.57
3901 8468 4.242475 CTGACAATGCTTGTTACTCCGTA 58.758 43.478 3.56 0.00 45.52 4.02
3918 8485 1.337384 ATGTATCCAGCGGCCTGACA 61.337 55.000 0.00 0.00 41.77 3.58
3926 8493 5.920312 CATTAGCAAGTAATGTATCCAGCG 58.080 41.667 0.00 0.00 42.22 5.18
4102 8679 8.863086 ACATGCCATAGAAAAATGTGCTAATAT 58.137 29.630 0.00 0.00 30.53 1.28
4132 8709 5.072600 TGCCCTAAGTCAACCTTTCTAAAGA 59.927 40.000 4.01 0.00 38.28 2.52
4143 8720 2.514803 ACATGGTTGCCCTAAGTCAAC 58.485 47.619 0.00 0.00 41.19 3.18
4166 8743 8.852135 ACTCACTCCGTTCCAAAATAATTAAAA 58.148 29.630 0.00 0.00 0.00 1.52
4169 8746 8.316214 ACTACTCACTCCGTTCCAAAATAATTA 58.684 33.333 0.00 0.00 0.00 1.40
4232 8809 8.525290 AATACAAAACTGCATCCTTAGCTTAT 57.475 30.769 0.00 0.00 0.00 1.73
4233 8810 7.938140 AATACAAAACTGCATCCTTAGCTTA 57.062 32.000 0.00 0.00 0.00 3.09
4234 8811 6.840780 AATACAAAACTGCATCCTTAGCTT 57.159 33.333 0.00 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.