Multiple sequence alignment - TraesCS2B01G236400

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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 TraesCS2B01G236400 chr2B 100.000 4874 0 0 1 4874 236778825 236773952 0.000000e+00 9001.0
1 TraesCS2B01G236400 chr2B 87.743 1648 181 13 2233 3873 798318257 798316624 0.000000e+00 1905.0
2 TraesCS2B01G236400 chr2B 86.341 1640 220 4 2233 3870 798614319 798612682 0.000000e+00 1784.0
3 TraesCS2B01G236400 chr2B 84.980 739 106 3 1340 2077 798615175 798614441 0.000000e+00 745.0
4 TraesCS2B01G236400 chr2B 84.595 740 109 5 1336 2074 798723291 798724026 0.000000e+00 730.0
5 TraesCS2B01G236400 chr2B 74.170 542 124 14 1543 2074 236527939 236527404 1.370000e-50 211.0
6 TraesCS2B01G236400 chr2B 82.036 167 19 8 4200 4364 11325078 11324921 1.100000e-26 132.0
7 TraesCS2B01G236400 chr2D 94.735 3875 139 29 266 4087 180089359 180085497 0.000000e+00 5965.0
8 TraesCS2B01G236400 chr2D 88.608 1580 176 4 2233 3810 639396713 639398290 0.000000e+00 1917.0
9 TraesCS2B01G236400 chr2D 86.402 1640 219 4 2233 3870 639667251 639668888 0.000000e+00 1790.0
10 TraesCS2B01G236400 chr2D 88.889 585 61 3 4290 4874 180074965 180074385 0.000000e+00 717.0
11 TraesCS2B01G236400 chr2D 83.266 741 110 8 1339 2078 639666404 639667131 0.000000e+00 669.0
12 TraesCS2B01G236400 chr2D 86.275 204 16 8 1 193 180090331 180090129 1.370000e-50 211.0
13 TraesCS2B01G236400 chr2D 77.866 253 26 17 996 1248 639393581 639393803 3.960000e-26 130.0
14 TraesCS2B01G236400 chr2A 95.917 1984 57 8 2112 4094 194423379 194421419 0.000000e+00 3193.0
15 TraesCS2B01G236400 chr2A 93.448 1862 70 23 266 2101 194425262 194423427 0.000000e+00 2715.0
16 TraesCS2B01G236400 chr2A 87.614 1639 201 2 2233 3870 765040534 765042171 0.000000e+00 1901.0
17 TraesCS2B01G236400 chr2A 86.849 768 77 8 4119 4874 194419004 194418249 0.000000e+00 837.0
18 TraesCS2B01G236400 chr2A 85.210 737 104 5 1339 2074 765039668 765040400 0.000000e+00 752.0
19 TraesCS2B01G236400 chr2A 89.286 196 12 6 4 193 194437640 194437448 2.270000e-58 237.0
20 TraesCS2B01G236400 chr7A 88.853 1561 171 2 2233 3790 727431545 727429985 0.000000e+00 1916.0
21 TraesCS2B01G236400 chr7A 85.054 736 102 5 1339 2073 727433897 727433169 0.000000e+00 743.0
22 TraesCS2B01G236400 chr7A 80.303 132 14 6 1124 1255 727434223 727434104 6.720000e-14 89.8
23 TraesCS2B01G236400 chr7D 88.725 1561 173 2 2233 3790 638473426 638474986 0.000000e+00 1905.0
24 TraesCS2B01G236400 chr7D 84.501 742 103 9 1339 2077 638470777 638471509 0.000000e+00 723.0
25 TraesCS2B01G236400 chr7D 78.381 1013 155 35 1117 2077 638558638 638559638 2.510000e-167 599.0
26 TraesCS2B01G236400 chr7D 80.952 168 22 7 4200 4364 52240882 52240722 1.840000e-24 124.0
27 TraesCS2B01G236400 chr7D 80.723 166 24 5 4200 4364 100762151 100762309 6.630000e-24 122.0
28 TraesCS2B01G236400 chr7D 83.594 128 12 5 1121 1248 638470229 638470347 1.430000e-20 111.0
29 TraesCS2B01G236400 chr4D 83.004 506 76 10 4373 4874 120066951 120067450 2.680000e-122 449.0
30 TraesCS2B01G236400 chr4A 83.071 508 73 13 4373 4874 555797593 555797093 2.680000e-122 449.0
31 TraesCS2B01G236400 chr4A 83.071 508 73 13 4373 4874 702638151 702638651 2.680000e-122 449.0
32 TraesCS2B01G236400 chr6A 82.874 508 74 13 4373 4874 7713453 7712953 1.240000e-120 444.0
33 TraesCS2B01G236400 chr5A 82.738 504 81 6 4373 4874 670003323 670003822 1.240000e-120 444.0
34 TraesCS2B01G236400 chr3D 82.903 503 76 10 4373 4871 441020604 441021100 1.240000e-120 444.0
35 TraesCS2B01G236400 chr3D 86.029 136 10 3 14 140 554765852 554765717 2.370000e-28 137.0
36 TraesCS2B01G236400 chr1A 82.677 508 78 9 4373 4874 543948271 543947768 4.480000e-120 442.0
37 TraesCS2B01G236400 chrUn 86.957 138 16 2 1119 1255 88119324 88119188 2.350000e-33 154.0
38 TraesCS2B01G236400 chrUn 86.957 138 16 2 1119 1255 88974600 88974464 2.350000e-33 154.0
39 TraesCS2B01G236400 chrUn 86.029 136 10 3 14 140 335611004 335611139 2.370000e-28 137.0
40 TraesCS2B01G236400 chrUn 86.029 136 10 3 14 140 406195323 406195458 2.370000e-28 137.0
41 TraesCS2B01G236400 chrUn 80.838 167 23 6 4200 4364 91230819 91230660 6.630000e-24 122.0
42 TraesCS2B01G236400 chr1B 81.928 166 22 5 4201 4364 226479577 226479736 3.060000e-27 134.0
43 TraesCS2B01G236400 chr1B 81.437 167 23 5 4200 4364 226476765 226476925 3.960000e-26 130.0
44 TraesCS2B01G236400 chr5D 80.838 167 23 6 4200 4364 276732303 276732144 6.630000e-24 122.0
45 TraesCS2B01G236400 chr5D 80.838 167 22 7 4200 4364 564461820 564461662 6.630000e-24 122.0
46 TraesCS2B01G236400 chr7B 80.124 161 20 7 1110 1270 734252892 734252744 5.160000e-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 TraesCS2B01G236400 chr2B 236773952 236778825 4873 True 9001.000000 9001 100.000000 1 4874 1 chr2B.!!$R3 4873
1 TraesCS2B01G236400 chr2B 798316624 798318257 1633 True 1905.000000 1905 87.743000 2233 3873 1 chr2B.!!$R4 1640
2 TraesCS2B01G236400 chr2B 798612682 798615175 2493 True 1264.500000 1784 85.660500 1340 3870 2 chr2B.!!$R5 2530
3 TraesCS2B01G236400 chr2B 798723291 798724026 735 False 730.000000 730 84.595000 1336 2074 1 chr2B.!!$F1 738
4 TraesCS2B01G236400 chr2B 236527404 236527939 535 True 211.000000 211 74.170000 1543 2074 1 chr2B.!!$R2 531
5 TraesCS2B01G236400 chr2D 180085497 180090331 4834 True 3088.000000 5965 90.505000 1 4087 2 chr2D.!!$R2 4086
6 TraesCS2B01G236400 chr2D 639666404 639668888 2484 False 1229.500000 1790 84.834000 1339 3870 2 chr2D.!!$F2 2531
7 TraesCS2B01G236400 chr2D 639393581 639398290 4709 False 1023.500000 1917 83.237000 996 3810 2 chr2D.!!$F1 2814
8 TraesCS2B01G236400 chr2D 180074385 180074965 580 True 717.000000 717 88.889000 4290 4874 1 chr2D.!!$R1 584
9 TraesCS2B01G236400 chr2A 194418249 194425262 7013 True 2248.333333 3193 92.071333 266 4874 3 chr2A.!!$R2 4608
10 TraesCS2B01G236400 chr2A 765039668 765042171 2503 False 1326.500000 1901 86.412000 1339 3870 2 chr2A.!!$F1 2531
11 TraesCS2B01G236400 chr7A 727429985 727434223 4238 True 916.266667 1916 84.736667 1124 3790 3 chr7A.!!$R1 2666
12 TraesCS2B01G236400 chr7D 638470229 638474986 4757 False 913.000000 1905 85.606667 1121 3790 3 chr7D.!!$F3 2669
13 TraesCS2B01G236400 chr7D 638558638 638559638 1000 False 599.000000 599 78.381000 1117 2077 1 chr7D.!!$F2 960
14 TraesCS2B01G236400 chr4A 555797093 555797593 500 True 449.000000 449 83.071000 4373 4874 1 chr4A.!!$R1 501
15 TraesCS2B01G236400 chr4A 702638151 702638651 500 False 449.000000 449 83.071000 4373 4874 1 chr4A.!!$F1 501
16 TraesCS2B01G236400 chr6A 7712953 7713453 500 True 444.000000 444 82.874000 4373 4874 1 chr6A.!!$R1 501
17 TraesCS2B01G236400 chr1A 543947768 543948271 503 True 442.000000 442 82.677000 4373 4874 1 chr1A.!!$R1 501

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
62 63 0.183731 CATGGCTACTTTCCCCTCCC 59.816 60.0 0.00 0.00 0.0 4.30 F
1305 2412 0.166597 TGCTGTTCTCGTACGTACCG 59.833 55.0 19.67 14.34 0.0 4.02 F
1977 3187 1.267121 AAGGAGATGGTGTACGTGCT 58.733 50.0 4.97 0.00 0.0 4.40 F
3516 7926 0.034896 ATGACAAGTTCGCCGACCTT 59.965 50.0 0.00 0.00 0.0 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1977 3187 0.030195 TCCCATCAGCCATCCAGGTA 60.030 55.0 0.00 0.00 40.61 3.08 R
3299 7709 0.041839 GCCGATCACGTGAATCATGC 60.042 55.0 24.13 18.81 37.88 4.06 R
3771 8181 0.456221 CGACATACAAGAGCCCGACT 59.544 55.0 0.00 0.00 0.00 4.18 R
4801 11622 0.759346 GGAGTGCTATAGGTGTGGGG 59.241 60.0 1.04 0.00 0.00 4.96 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
23 24 1.361993 CGAGAGGAAGGAGGCATCG 59.638 63.158 0.00 0.00 0.00 3.84
37 38 3.201290 AGGCATCGATGATGAACTGAAC 58.799 45.455 29.20 6.68 42.09 3.18
41 42 4.493708 GCATCGATGATGAACTGAACTGTG 60.494 45.833 29.20 0.00 42.09 3.66
60 61 0.466372 GGCATGGCTACTTTCCCCTC 60.466 60.000 12.86 0.00 0.00 4.30
62 63 0.183731 CATGGCTACTTTCCCCTCCC 59.816 60.000 0.00 0.00 0.00 4.30
100 101 7.361885 CCTCCTTGATTTCTCTTCTGATTTGTG 60.362 40.741 0.00 0.00 0.00 3.33
125 126 4.039124 CCCCATTGTAGCCAAATTATGACC 59.961 45.833 0.00 0.00 33.44 4.02
128 129 5.221303 CCATTGTAGCCAAATTATGACCTGG 60.221 44.000 0.00 0.00 33.44 4.45
132 133 4.803329 AGCCAAATTATGACCTGGATCT 57.197 40.909 0.00 0.00 0.00 2.75
133 134 4.723309 AGCCAAATTATGACCTGGATCTC 58.277 43.478 0.00 0.00 0.00 2.75
134 135 4.414846 AGCCAAATTATGACCTGGATCTCT 59.585 41.667 0.00 0.00 0.00 3.10
135 136 4.518211 GCCAAATTATGACCTGGATCTCTG 59.482 45.833 0.00 0.00 0.00 3.35
136 137 5.688807 CCAAATTATGACCTGGATCTCTGT 58.311 41.667 0.00 0.00 0.00 3.41
137 138 5.530171 CCAAATTATGACCTGGATCTCTGTG 59.470 44.000 0.00 0.00 0.00 3.66
138 139 3.827008 TTATGACCTGGATCTCTGTGC 57.173 47.619 0.00 0.00 0.00 4.57
139 140 0.463204 ATGACCTGGATCTCTGTGCG 59.537 55.000 0.00 0.00 0.00 5.34
144 156 2.268920 GGATCTCTGTGCGGGCAA 59.731 61.111 0.00 0.00 0.00 4.52
156 168 1.014352 GCGGGCAAAGATCGTAACAT 58.986 50.000 0.00 0.00 0.00 2.71
163 175 4.508971 GCAAAGATCGTAACATCATCACG 58.491 43.478 0.00 0.00 37.03 4.35
166 178 3.982475 AGATCGTAACATCATCACGCAT 58.018 40.909 0.00 0.00 35.70 4.73
175 187 4.478699 ACATCATCACGCATGTTTCTTTG 58.521 39.130 0.00 0.00 33.66 2.77
177 189 4.145876 TCATCACGCATGTTTCTTTGTC 57.854 40.909 0.00 0.00 33.66 3.18
193 205 6.214191 TCTTTGTCTGGCACATTGTTTTTA 57.786 33.333 0.00 0.00 38.20 1.52
194 206 6.039616 TCTTTGTCTGGCACATTGTTTTTAC 58.960 36.000 0.00 0.00 38.20 2.01
195 207 5.590530 TTGTCTGGCACATTGTTTTTACT 57.409 34.783 0.00 0.00 38.20 2.24
196 208 5.590530 TGTCTGGCACATTGTTTTTACTT 57.409 34.783 0.00 0.00 38.20 2.24
197 209 5.971763 TGTCTGGCACATTGTTTTTACTTT 58.028 33.333 0.00 0.00 38.20 2.66
198 210 6.402222 TGTCTGGCACATTGTTTTTACTTTT 58.598 32.000 0.00 0.00 38.20 2.27
199 211 6.876257 TGTCTGGCACATTGTTTTTACTTTTT 59.124 30.769 0.00 0.00 38.20 1.94
200 212 8.035394 TGTCTGGCACATTGTTTTTACTTTTTA 58.965 29.630 0.00 0.00 38.20 1.52
201 213 9.040939 GTCTGGCACATTGTTTTTACTTTTTAT 57.959 29.630 0.00 0.00 38.20 1.40
202 214 9.606631 TCTGGCACATTGTTTTTACTTTTTATT 57.393 25.926 0.00 0.00 38.20 1.40
224 236 7.886629 ATTATCCTTTTAGCATGTGTGATGT 57.113 32.000 0.00 0.00 0.00 3.06
226 238 4.650734 TCCTTTTAGCATGTGTGATGTCA 58.349 39.130 0.00 0.00 0.00 3.58
243 933 2.666022 TGTCATTATCGCACACAGTTCG 59.334 45.455 0.00 0.00 0.00 3.95
251 941 0.386858 GCACACAGTTCGACGCTAGA 60.387 55.000 0.00 0.00 0.00 2.43
270 996 4.046938 AGAGTGTATGTTAGATGTGCGG 57.953 45.455 0.00 0.00 0.00 5.69
277 1003 1.003118 TGTTAGATGTGCGGCTCCTTT 59.997 47.619 0.00 0.00 0.00 3.11
386 1115 5.727434 GGTTATCTGGAAACCGACTTTAGA 58.273 41.667 0.00 0.00 37.26 2.10
509 1242 4.764823 ACTGAGGAGAGTAAAGTGAGAGTG 59.235 45.833 0.00 0.00 0.00 3.51
546 1279 2.480610 CGCACACACCTTGGCAACT 61.481 57.895 0.00 0.00 37.61 3.16
547 1280 1.163420 CGCACACACCTTGGCAACTA 61.163 55.000 0.00 0.00 37.61 2.24
549 1282 1.613437 GCACACACCTTGGCAACTATT 59.387 47.619 0.00 0.00 37.61 1.73
551 1284 3.443681 GCACACACCTTGGCAACTATTAT 59.556 43.478 0.00 0.00 37.61 1.28
676 1413 7.050970 TGTCACTCCATACCAATACAGATAC 57.949 40.000 0.00 0.00 0.00 2.24
677 1414 6.839134 TGTCACTCCATACCAATACAGATACT 59.161 38.462 0.00 0.00 0.00 2.12
678 1415 7.148641 GTCACTCCATACCAATACAGATACTG 58.851 42.308 0.00 0.00 37.52 2.74
735 1491 3.725490 AGTAGGTGAGTTTTTGTCGGTC 58.275 45.455 0.00 0.00 0.00 4.79
902 1663 2.354072 GCGACTAGCTAGCGCCTG 60.354 66.667 33.37 17.58 44.04 4.85
903 1664 2.835705 GCGACTAGCTAGCGCCTGA 61.836 63.158 33.37 0.41 44.04 3.86
957 1718 2.034939 TCTGGTCGACACGAAAAAGCTA 59.965 45.455 18.91 0.00 37.72 3.32
1159 1920 4.194720 CCGCGGACGAGGGAGAAG 62.195 72.222 24.07 0.00 43.93 2.85
1168 1929 2.042843 AGGGAGAAGCGTCGGGAT 60.043 61.111 0.00 0.00 0.00 3.85
1273 2034 2.587194 CTGCGCGCCATTCTAGCT 60.587 61.111 30.77 0.00 0.00 3.32
1276 2037 2.464459 GCGCGCCATTCTAGCTTGT 61.464 57.895 23.24 0.00 0.00 3.16
1304 2411 2.182825 CATGCTGTTCTCGTACGTACC 58.817 52.381 19.67 6.08 0.00 3.34
1305 2412 0.166597 TGCTGTTCTCGTACGTACCG 59.833 55.000 19.67 14.34 0.00 4.02
1308 2415 1.660607 CTGTTCTCGTACGTACCGCTA 59.339 52.381 19.67 2.72 0.00 4.26
1323 2446 1.335597 CCGCTACAGTTCTGAACACGA 60.336 52.381 21.50 5.83 0.00 4.35
1755 2953 2.034221 GCTGTCTTGTGGGTCCCC 59.966 66.667 5.13 0.00 0.00 4.81
1890 3088 3.632145 TGCGCAGAGAGTATGATGAGTTA 59.368 43.478 5.66 0.00 0.00 2.24
1977 3187 1.267121 AAGGAGATGGTGTACGTGCT 58.733 50.000 4.97 0.00 0.00 4.40
2117 3410 6.704050 CGATTAGTCTAGTGAGAGATCAGTCA 59.296 42.308 0.00 0.00 30.20 3.41
2228 6635 7.671827 ACAAGCTTTGAATTAACGTGTTTTTC 58.328 30.769 0.00 0.00 0.00 2.29
2487 6894 2.352503 ACATCAACAATTCGCAAGCC 57.647 45.000 0.00 0.00 37.18 4.35
2491 6898 1.686052 TCAACAATTCGCAAGCCCTTT 59.314 42.857 0.00 0.00 37.18 3.11
2592 6999 2.256591 CGACCCGACGGACCGATAT 61.257 63.158 23.38 0.00 32.95 1.63
2787 7194 3.146618 AGCTCGACGTCGTTCATAAAT 57.853 42.857 34.40 12.43 40.80 1.40
2802 7209 2.631160 TAAATTCGATGCCGGATGGT 57.369 45.000 5.05 0.00 33.52 3.55
3198 7605 1.346365 CGATCGTCACGGTGTTCATT 58.654 50.000 7.03 0.00 0.00 2.57
3299 7709 1.162181 TACCTCGTCGCCGTCATAGG 61.162 60.000 0.00 0.00 35.01 2.57
3378 7788 2.899838 TGCCGCAACGAGCAGTTT 60.900 55.556 0.00 0.00 46.13 2.66
3516 7926 0.034896 ATGACAAGTTCGCCGACCTT 59.965 50.000 0.00 0.00 0.00 3.50
3879 8289 1.614241 GGCCATCTGGGTAGACACGT 61.614 60.000 0.00 0.00 39.65 4.49
3880 8290 1.108776 GCCATCTGGGTAGACACGTA 58.891 55.000 0.00 0.00 39.65 3.57
3951 8361 7.509141 AATTTGAGTGTGTGTATTCATGTCA 57.491 32.000 0.00 0.00 0.00 3.58
3995 8405 2.826128 TGTGTGCCACTCCTCTACTTAG 59.174 50.000 0.00 0.00 35.11 2.18
4100 8515 8.506168 TGAGACCATCAGTATAATTTTTCACC 57.494 34.615 0.00 0.00 32.77 4.02
4103 8518 9.533831 AGACCATCAGTATAATTTTTCACCTTT 57.466 29.630 0.00 0.00 0.00 3.11
4145 10950 5.957842 TTTCATCGCTGGAATGTTAAAGT 57.042 34.783 0.00 0.00 0.00 2.66
4175 10980 1.450905 GCGCGTAATCAATCTACCGAC 59.549 52.381 8.43 0.00 0.00 4.79
4176 10981 2.723209 CGCGTAATCAATCTACCGACA 58.277 47.619 0.00 0.00 0.00 4.35
4182 10987 5.005394 CGTAATCAATCTACCGACAACCAAG 59.995 44.000 0.00 0.00 0.00 3.61
4192 10997 1.333308 CGACAACCAAGCAATCACACA 59.667 47.619 0.00 0.00 0.00 3.72
4215 11030 4.666512 AGGCACTTGTTAATGAGGTTCAT 58.333 39.130 0.00 0.00 34.06 2.57
4231 11046 3.316308 GGTTCATCAACATGGCTACATCC 59.684 47.826 0.00 0.00 34.35 3.51
4233 11048 2.158623 TCATCAACATGGCTACATCCCC 60.159 50.000 0.00 0.00 34.35 4.81
4240 11055 1.152398 GGCTACATCCCCGGGTCTA 60.152 63.158 21.85 4.56 0.00 2.59
4241 11056 0.761702 GGCTACATCCCCGGGTCTAA 60.762 60.000 21.85 1.60 0.00 2.10
4242 11057 0.391966 GCTACATCCCCGGGTCTAAC 59.608 60.000 21.85 0.00 0.00 2.34
4243 11058 2.033208 GCTACATCCCCGGGTCTAACT 61.033 57.143 21.85 0.00 0.00 2.24
4244 11059 2.754186 GCTACATCCCCGGGTCTAACTA 60.754 54.545 21.85 0.00 0.00 2.24
4245 11060 2.789323 ACATCCCCGGGTCTAACTAT 57.211 50.000 21.85 0.00 0.00 2.12
4246 11061 2.326428 ACATCCCCGGGTCTAACTATG 58.674 52.381 21.85 12.76 0.00 2.23
4247 11062 2.090943 ACATCCCCGGGTCTAACTATGA 60.091 50.000 21.85 6.21 0.00 2.15
4257 11072 5.562307 CGGGTCTAACTATGAACTATGGACG 60.562 48.000 0.00 0.00 0.00 4.79
4274 11089 1.122019 ACGCTCCTCCCCATGATACC 61.122 60.000 0.00 0.00 0.00 2.73
4283 11098 3.512496 TCCCCATGATACCGCTACAATA 58.488 45.455 0.00 0.00 0.00 1.90
4285 11100 3.260884 CCCCATGATACCGCTACAATACT 59.739 47.826 0.00 0.00 0.00 2.12
4286 11101 4.245660 CCCATGATACCGCTACAATACTG 58.754 47.826 0.00 0.00 0.00 2.74
4287 11102 3.679980 CCATGATACCGCTACAATACTGC 59.320 47.826 0.00 0.00 0.00 4.40
4288 11103 3.380479 TGATACCGCTACAATACTGCC 57.620 47.619 0.00 0.00 0.00 4.85
4304 11119 3.569210 CCCACCAGCACCCAGACA 61.569 66.667 0.00 0.00 0.00 3.41
4313 11128 2.034879 CACCCAGACATCGGCACAC 61.035 63.158 0.00 0.00 0.00 3.82
4315 11130 2.048222 CCAGACATCGGCACACGT 60.048 61.111 0.00 0.00 44.69 4.49
4319 11134 2.019951 GACATCGGCACACGTCGTT 61.020 57.895 0.00 0.00 42.21 3.85
4328 11144 4.003788 CACGTCGTTGGCTCCCCT 62.004 66.667 0.00 0.00 0.00 4.79
4386 11202 5.665916 AAAATATTCTCCACCTTGGCAAG 57.334 39.130 20.31 20.31 37.47 4.01
4388 11204 1.915141 ATTCTCCACCTTGGCAAGTG 58.085 50.000 24.57 20.47 37.47 3.16
4399 11215 1.729586 TGGCAAGTGTTCTCTACCCT 58.270 50.000 0.00 0.00 0.00 4.34
4430 11246 1.154205 CCATGCGTCGAACCTCCATC 61.154 60.000 0.00 0.00 0.00 3.51
4486 11302 2.034799 GCTACTCCCAGGCTCCACATA 61.035 57.143 0.00 0.00 0.00 2.29
4552 11370 6.895040 GTCAATACTCGAGCAAAATTAAGTCG 59.105 38.462 13.61 0.00 0.00 4.18
4563 11381 7.649057 AGCAAAATTAAGTCGCTTCTTTACTT 58.351 30.769 0.00 0.00 37.27 2.24
4575 11393 6.088616 TCGCTTCTTTACTTTAGTTTACGCTC 59.911 38.462 0.00 0.00 0.00 5.03
4577 11395 6.368243 GCTTCTTTACTTTAGTTTACGCTCCT 59.632 38.462 0.00 0.00 0.00 3.69
4609 11427 6.266203 GAGTATCTGTTCAATGACATCACG 57.734 41.667 0.00 0.00 0.00 4.35
4623 11441 2.230508 ACATCACGTACCGATCACTGTT 59.769 45.455 0.00 0.00 0.00 3.16
4639 11458 3.845775 CACTGTTTGTGTGAAAGTGAACG 59.154 43.478 0.00 0.00 40.54 3.95
4704 11523 9.137459 CTCAATATCCTAACTCTTTCCTGACTA 57.863 37.037 0.00 0.00 0.00 2.59
4747 11567 4.680237 CCGTCGCCCAGCTGTCAA 62.680 66.667 13.81 0.00 0.00 3.18
4801 11622 2.941453 TCGGACAGTCTCTTACATGC 57.059 50.000 0.00 0.00 0.00 4.06
4830 11651 3.321111 CCTATAGCACTCCGCCTTCTTAA 59.679 47.826 0.00 0.00 44.04 1.85
4838 11659 2.930682 CTCCGCCTTCTTAAGTACTTGC 59.069 50.000 18.56 10.48 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.043816 TCATCGATGCCTCCTTCCTC 58.956 55.000 20.81 0.00 0.00 3.71
9 10 1.347050 CATCATCGATGCCTCCTTCCT 59.653 52.381 20.81 0.00 33.17 3.36
10 11 1.345741 TCATCATCGATGCCTCCTTCC 59.654 52.381 20.81 0.00 39.63 3.46
23 24 3.076621 TGCCACAGTTCAGTTCATCATC 58.923 45.455 0.00 0.00 0.00 2.92
37 38 1.098050 GGAAAGTAGCCATGCCACAG 58.902 55.000 0.00 0.00 0.00 3.66
41 42 0.466372 GAGGGGAAAGTAGCCATGCC 60.466 60.000 0.00 0.00 0.00 4.40
60 61 2.674220 GGAGGAAGAGCACTGGGGG 61.674 68.421 0.00 0.00 0.00 5.40
62 63 0.035630 CAAGGAGGAAGAGCACTGGG 60.036 60.000 0.00 0.00 0.00 4.45
100 101 4.892934 TCATAATTTGGCTACAATGGGGAC 59.107 41.667 0.00 0.00 36.29 4.46
125 126 2.202987 GCCCGCACAGAGATCCAG 60.203 66.667 0.00 0.00 0.00 3.86
128 129 0.391661 TCTTTGCCCGCACAGAGATC 60.392 55.000 1.44 0.00 30.37 2.75
132 133 1.741401 CGATCTTTGCCCGCACAGA 60.741 57.895 7.92 7.92 37.20 3.41
133 134 0.739462 TACGATCTTTGCCCGCACAG 60.739 55.000 0.00 0.00 0.00 3.66
134 135 0.320858 TTACGATCTTTGCCCGCACA 60.321 50.000 0.00 0.00 0.00 4.57
135 136 0.096454 GTTACGATCTTTGCCCGCAC 59.904 55.000 0.00 0.00 0.00 5.34
136 137 0.320858 TGTTACGATCTTTGCCCGCA 60.321 50.000 0.00 0.00 0.00 5.69
137 138 1.003866 GATGTTACGATCTTTGCCCGC 60.004 52.381 0.00 0.00 0.00 6.13
138 139 2.276201 TGATGTTACGATCTTTGCCCG 58.724 47.619 0.00 0.00 0.00 6.13
139 140 3.876914 TGATGATGTTACGATCTTTGCCC 59.123 43.478 0.00 0.00 0.00 5.36
144 156 3.780902 TGCGTGATGATGTTACGATCTT 58.219 40.909 0.00 0.00 41.86 2.40
156 168 3.814842 AGACAAAGAAACATGCGTGATGA 59.185 39.130 14.17 0.00 35.80 2.92
163 175 2.223782 TGTGCCAGACAAAGAAACATGC 60.224 45.455 0.00 0.00 0.00 4.06
166 178 3.446873 ACAATGTGCCAGACAAAGAAACA 59.553 39.130 0.00 0.00 38.36 2.83
175 187 6.902224 AAAAGTAAAAACAATGTGCCAGAC 57.098 33.333 0.00 0.00 0.00 3.51
198 210 9.407380 ACATCACACATGCTAAAAGGATAATAA 57.593 29.630 0.00 0.00 0.00 1.40
199 211 8.978874 ACATCACACATGCTAAAAGGATAATA 57.021 30.769 0.00 0.00 0.00 0.98
200 212 7.557358 TGACATCACACATGCTAAAAGGATAAT 59.443 33.333 0.00 0.00 0.00 1.28
201 213 6.883756 TGACATCACACATGCTAAAAGGATAA 59.116 34.615 0.00 0.00 0.00 1.75
202 214 6.413892 TGACATCACACATGCTAAAAGGATA 58.586 36.000 0.00 0.00 0.00 2.59
203 215 5.255687 TGACATCACACATGCTAAAAGGAT 58.744 37.500 0.00 0.00 0.00 3.24
204 216 4.650734 TGACATCACACATGCTAAAAGGA 58.349 39.130 0.00 0.00 0.00 3.36
205 217 5.571784 ATGACATCACACATGCTAAAAGG 57.428 39.130 0.00 0.00 0.00 3.11
206 218 7.585210 CGATAATGACATCACACATGCTAAAAG 59.415 37.037 0.00 0.00 0.00 2.27
207 219 7.408910 CGATAATGACATCACACATGCTAAAA 58.591 34.615 0.00 0.00 0.00 1.52
208 220 6.511605 GCGATAATGACATCACACATGCTAAA 60.512 38.462 0.00 0.00 0.00 1.85
213 225 4.034279 TGTGCGATAATGACATCACACATG 59.966 41.667 3.46 0.00 40.97 3.21
224 236 2.921121 GTCGAACTGTGTGCGATAATGA 59.079 45.455 4.01 0.00 45.75 2.57
226 238 1.917955 CGTCGAACTGTGTGCGATAAT 59.082 47.619 4.01 0.00 45.75 1.28
243 933 5.910166 CACATCTAACATACACTCTAGCGTC 59.090 44.000 0.00 0.00 0.00 5.19
251 941 2.168521 AGCCGCACATCTAACATACACT 59.831 45.455 0.00 0.00 0.00 3.55
277 1003 8.716646 TGAGAGCTGTTATATTCATCGAAAAA 57.283 30.769 0.00 0.00 0.00 1.94
332 1058 2.476241 CCTCAATGGCGTTTTCAAAAGC 59.524 45.455 1.97 1.97 41.65 3.51
333 1059 3.976169 TCCTCAATGGCGTTTTCAAAAG 58.024 40.909 0.00 0.00 35.26 2.27
338 1064 3.643159 AAGTTCCTCAATGGCGTTTTC 57.357 42.857 0.00 0.00 35.26 2.29
371 1100 3.672767 TCACCTCTAAAGTCGGTTTCC 57.327 47.619 0.00 0.00 0.00 3.13
386 1115 0.251653 TACTCCGGAGCACTTCACCT 60.252 55.000 31.56 11.00 0.00 4.00
509 1242 1.007734 CATGAATCAGCATGCCCGC 60.008 57.895 15.66 0.11 39.19 6.13
716 1472 2.101249 ACGACCGACAAAAACTCACCTA 59.899 45.455 0.00 0.00 0.00 3.08
735 1491 2.599082 GAGTTCTGACGGAGCAAATACG 59.401 50.000 0.64 0.00 42.79 3.06
957 1718 0.690411 CCCTGACAGCTGATCTCCCT 60.690 60.000 23.35 0.00 0.00 4.20
1158 1919 4.286320 GCGATGGATCCCGACGCT 62.286 66.667 27.62 2.80 43.13 5.07
1304 2411 1.714460 GTCGTGTTCAGAACTGTAGCG 59.286 52.381 14.51 10.47 0.00 4.26
1305 2412 2.726760 CAGTCGTGTTCAGAACTGTAGC 59.273 50.000 14.51 1.92 0.00 3.58
1308 2415 2.794981 CGACAGTCGTGTTCAGAACTGT 60.795 50.000 15.21 9.47 40.57 3.55
1755 2953 5.526115 TCTACACAGTACTTCCGACAAAAG 58.474 41.667 0.00 0.00 0.00 2.27
1890 3088 1.954035 GGGAGTCTACCCTCACCTTT 58.046 55.000 0.00 0.00 45.90 3.11
1977 3187 0.030195 TCCCATCAGCCATCCAGGTA 60.030 55.000 0.00 0.00 40.61 3.08
2038 3248 0.617413 CCAGCATGTTGTCCTCTCCT 59.383 55.000 8.84 0.00 0.00 3.69
2195 6584 9.744468 ACGTTAATTCAAAGCTTGTTTTAATCT 57.256 25.926 0.00 0.00 0.00 2.40
2196 6585 9.777843 CACGTTAATTCAAAGCTTGTTTTAATC 57.222 29.630 0.00 0.00 0.00 1.75
2228 6635 1.689273 GGCCTAGTATGACCTGTGAGG 59.311 57.143 0.00 0.00 42.49 3.86
2288 6695 2.143122 TGAAGTCAAGTGGATTGTCGC 58.857 47.619 0.00 0.00 40.05 5.19
2487 6894 0.323725 AGCACATAGGGGCACAAAGG 60.324 55.000 3.65 0.00 0.00 3.11
2491 6898 0.625316 ATGAAGCACATAGGGGCACA 59.375 50.000 3.65 4.01 37.46 4.57
2547 6954 4.314440 AAGCGCTGCGGGAACTGA 62.314 61.111 24.61 0.00 36.31 3.41
2589 6996 1.173043 CACGGTTGTGGTTGGCATAT 58.827 50.000 0.00 0.00 42.59 1.78
2658 7065 2.281900 GTGCCGGTGCCAAGGTAA 60.282 61.111 1.90 0.00 36.33 2.85
2787 7194 2.513666 GCACCATCCGGCATCGAA 60.514 61.111 0.00 0.00 39.00 3.71
2802 7209 0.975556 TAGACCGCTCCTGGATTGCA 60.976 55.000 8.44 0.00 0.00 4.08
3198 7605 1.276622 GGAAGAGGTTGTAGGCCAGA 58.723 55.000 5.01 0.00 0.00 3.86
3299 7709 0.041839 GCCGATCACGTGAATCATGC 60.042 55.000 24.13 18.81 37.88 4.06
3378 7788 1.145156 CGTGGCCCCGATCATGTAA 59.855 57.895 0.00 0.00 0.00 2.41
3771 8181 0.456221 CGACATACAAGAGCCCGACT 59.544 55.000 0.00 0.00 0.00 4.18
3951 8361 7.228108 CACAATGACCAGTTCTCATGCTATATT 59.772 37.037 0.00 0.00 0.00 1.28
3995 8405 9.877178 TTTGAAGAAAAGATAGGTACATCTCTC 57.123 33.333 0.00 0.00 34.08 3.20
4049 8463 4.795268 TGCTAGAGTTGTTCTTACACGAG 58.205 43.478 0.00 0.00 37.36 4.18
4129 10934 5.064198 TCGGATTAACTTTAACATTCCAGCG 59.936 40.000 0.00 0.00 0.00 5.18
4142 10947 0.457035 TACGCGCCTCGGATTAACTT 59.543 50.000 5.73 0.00 43.86 2.66
4144 10949 1.454653 GATTACGCGCCTCGGATTAAC 59.545 52.381 5.73 0.00 43.86 2.01
4145 10950 1.067364 TGATTACGCGCCTCGGATTAA 59.933 47.619 5.73 0.00 43.86 1.40
4175 10980 2.746269 CCTTGTGTGATTGCTTGGTTG 58.254 47.619 0.00 0.00 0.00 3.77
4176 10981 1.069049 GCCTTGTGTGATTGCTTGGTT 59.931 47.619 0.00 0.00 0.00 3.67
4182 10987 1.774639 CAAGTGCCTTGTGTGATTGC 58.225 50.000 6.74 0.00 36.79 3.56
4192 10997 4.469657 TGAACCTCATTAACAAGTGCCTT 58.530 39.130 0.00 0.00 0.00 4.35
4210 11025 3.316308 GGGATGTAGCCATGTTGATGAAC 59.684 47.826 0.00 0.00 0.00 3.18
4215 11030 0.180171 CGGGGATGTAGCCATGTTGA 59.820 55.000 0.00 0.00 0.00 3.18
4231 11046 4.021368 CCATAGTTCATAGTTAGACCCGGG 60.021 50.000 22.25 22.25 0.00 5.73
4233 11048 5.562307 CGTCCATAGTTCATAGTTAGACCCG 60.562 48.000 0.00 0.00 0.00 5.28
4240 11055 3.961408 AGGAGCGTCCATAGTTCATAGTT 59.039 43.478 6.78 0.00 39.61 2.24
4241 11056 3.567397 AGGAGCGTCCATAGTTCATAGT 58.433 45.455 6.78 0.00 39.61 2.12
4242 11057 3.057174 GGAGGAGCGTCCATAGTTCATAG 60.057 52.174 4.45 0.00 39.61 2.23
4243 11058 2.891580 GGAGGAGCGTCCATAGTTCATA 59.108 50.000 4.45 0.00 39.61 2.15
4244 11059 1.689273 GGAGGAGCGTCCATAGTTCAT 59.311 52.381 4.45 0.00 39.61 2.57
4245 11060 1.112113 GGAGGAGCGTCCATAGTTCA 58.888 55.000 4.45 0.00 39.61 3.18
4246 11061 0.389757 GGGAGGAGCGTCCATAGTTC 59.610 60.000 10.95 0.00 39.61 3.01
4247 11062 1.049289 GGGGAGGAGCGTCCATAGTT 61.049 60.000 10.95 0.00 39.61 2.24
4257 11072 1.674057 CGGTATCATGGGGAGGAGC 59.326 63.158 0.00 0.00 0.00 4.70
4274 11089 0.107897 TGGTGGGCAGTATTGTAGCG 60.108 55.000 0.00 0.00 0.00 4.26
4287 11102 2.826777 GATGTCTGGGTGCTGGTGGG 62.827 65.000 0.00 0.00 0.00 4.61
4288 11103 1.377725 GATGTCTGGGTGCTGGTGG 60.378 63.158 0.00 0.00 0.00 4.61
4304 11119 2.736995 CCAACGACGTGTGCCGAT 60.737 61.111 0.00 0.00 40.70 4.18
4313 11128 2.742372 CAAGGGGAGCCAACGACG 60.742 66.667 0.00 0.00 0.00 5.12
4315 11130 4.697756 CGCAAGGGGAGCCAACGA 62.698 66.667 0.00 0.00 0.00 3.85
4319 11134 2.297895 ATGTACGCAAGGGGAGCCA 61.298 57.895 0.00 0.00 46.39 4.75
4328 11144 5.352846 ACAACATAATAGCACATGTACGCAA 59.647 36.000 10.46 0.00 34.32 4.85
4366 11182 4.019174 CACTTGCCAAGGTGGAGAATATT 58.981 43.478 9.64 0.00 40.96 1.28
4386 11202 7.932491 GGATAAATCCTAAAGGGTAGAGAACAC 59.068 40.741 1.52 0.00 43.73 3.32
4430 11246 9.133627 CATCGTATAATCTCAAGTCCAATGTAG 57.866 37.037 0.00 0.00 0.00 2.74
4552 11370 6.368243 AGGAGCGTAAACTAAAGTAAAGAAGC 59.632 38.462 0.00 0.00 0.00 3.86
4563 11381 5.477984 TCTGGAAGTTAGGAGCGTAAACTAA 59.522 40.000 0.00 0.00 33.24 2.24
4570 11388 1.926108 ACTCTGGAAGTTAGGAGCGT 58.074 50.000 0.00 0.00 33.03 5.07
4623 11441 1.668751 GAGCCGTTCACTTTCACACAA 59.331 47.619 0.00 0.00 0.00 3.33
4639 11458 1.065551 GTGGCGTCCAATATTTGAGCC 59.934 52.381 16.46 16.46 42.00 4.70
4747 11567 5.930135 AGACACCTGTGAATTTGACTAAGT 58.070 37.500 3.94 0.00 0.00 2.24
4787 11608 1.278985 TGTGGGGCATGTAAGAGACTG 59.721 52.381 0.00 0.00 0.00 3.51
4801 11622 0.759346 GGAGTGCTATAGGTGTGGGG 59.241 60.000 1.04 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.