Multiple sequence alignment - TraesCS2A01G363000

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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 TraesCS2A01G363000 chr2A 100.000 4493 0 0 1 4493 607510719 607515211 0.000000e+00 8298.0
1 TraesCS2A01G363000 chr2A 94.732 2050 61 4 1755 3784 610176435 610178457 0.000000e+00 3144.0
2 TraesCS2A01G363000 chr2A 93.199 397 21 3 1389 1785 610176138 610176528 3.010000e-161 579.0
3 TraesCS2A01G363000 chr2A 91.084 415 19 8 823 1222 610175174 610175585 3.060000e-151 545.0
4 TraesCS2A01G363000 chr2A 89.928 139 8 1 1623 1761 610176453 610176585 1.660000e-39 174.0
5 TraesCS2A01G363000 chr2A 86.408 103 9 4 3839 3938 610124534 610124634 1.710000e-19 108.0
6 TraesCS2A01G363000 chr2A 84.259 108 11 2 1755 1856 607512404 607512511 2.860000e-17 100.0
7 TraesCS2A01G363000 chr2A 84.259 108 11 2 1686 1793 607512473 607512574 2.860000e-17 100.0
8 TraesCS2A01G363000 chr2A 88.710 62 7 0 4008 4069 81088559 81088620 4.820000e-10 76.8
9 TraesCS2A01G363000 chr2B 95.572 2123 61 6 1599 3697 545152021 545154134 0.000000e+00 3369.0
10 TraesCS2A01G363000 chr2B 90.292 958 38 17 3558 4493 545154372 545155296 0.000000e+00 1203.0
11 TraesCS2A01G363000 chr2B 81.726 1286 196 26 2252 3522 186403263 186404524 0.000000e+00 1037.0
12 TraesCS2A01G363000 chr2B 91.040 346 14 5 889 1225 545151015 545151352 6.850000e-123 451.0
13 TraesCS2A01G363000 chr2B 79.581 573 98 16 239 801 557047742 557047179 4.210000e-105 392.0
14 TraesCS2A01G363000 chr2B 78.674 347 59 12 932 1272 185763885 185763548 2.720000e-52 217.0
15 TraesCS2A01G363000 chr2B 90.625 160 15 0 674 833 644557914 644557755 3.520000e-51 213.0
16 TraesCS2A01G363000 chr2B 83.197 244 14 17 1274 1490 545151780 545152023 9.860000e-47 198.0
17 TraesCS2A01G363000 chr2B 90.196 102 10 0 1755 1856 545152108 545152209 2.820000e-27 134.0
18 TraesCS2A01G363000 chr2B 80.117 171 10 9 1623 1793 545152126 545152272 6.150000e-19 106.0
19 TraesCS2A01G363000 chr2B 87.097 93 10 2 3718 3808 724550923 724551015 2.210000e-18 104.0
20 TraesCS2A01G363000 chr2B 85.437 103 10 4 3839 3938 544999234 544999334 7.950000e-18 102.0
21 TraesCS2A01G363000 chr2D 92.909 1777 71 21 2757 4493 462240872 462242633 0.000000e+00 2532.0
22 TraesCS2A01G363000 chr2D 82.248 1290 183 31 2252 3520 131642937 131641673 0.000000e+00 1072.0
23 TraesCS2A01G363000 chr2D 98.905 548 6 0 2213 2760 462240245 462240792 0.000000e+00 979.0
24 TraesCS2A01G363000 chr2D 88.194 847 51 25 856 1663 462228686 462229522 0.000000e+00 965.0
25 TraesCS2A01G363000 chr2D 97.917 192 4 0 1810 2001 462239992 462240183 2.590000e-87 333.0
26 TraesCS2A01G363000 chr2D 89.103 156 11 2 1670 1825 462238092 462238241 5.930000e-44 189.0
27 TraesCS2A01G363000 chr2D 93.814 97 6 0 1763 1859 462238116 462238212 3.620000e-31 147.0
28 TraesCS2A01G363000 chr2D 80.829 193 31 6 613 802 616012894 616013083 3.620000e-31 147.0
29 TraesCS2A01G363000 chr2D 98.039 51 1 0 2170 2220 462240184 462240234 6.190000e-14 89.8
30 TraesCS2A01G363000 chr2D 95.238 42 1 1 1878 1918 462229481 462229522 1.040000e-06 65.8
31 TraesCS2A01G363000 chr1B 82.420 1587 203 31 1968 3528 275553324 275554860 0.000000e+00 1315.0
32 TraesCS2A01G363000 chr1B 82.168 1587 204 34 1970 3528 275671947 275673482 0.000000e+00 1290.0
33 TraesCS2A01G363000 chr1B 83.825 1323 161 28 2212 3528 275358641 275359916 0.000000e+00 1208.0
34 TraesCS2A01G363000 chr1B 83.737 1322 164 27 2212 3528 275458631 275459906 0.000000e+00 1203.0
35 TraesCS2A01G363000 chr1B 96.639 238 8 0 1 238 550223419 550223656 3.260000e-106 396.0
36 TraesCS2A01G363000 chr1B 84.559 272 34 7 1003 1272 275357268 275357533 3.450000e-66 263.0
37 TraesCS2A01G363000 chr1B 84.559 272 34 7 1003 1272 275457258 275457523 3.450000e-66 263.0
38 TraesCS2A01G363000 chr1B 84.559 272 34 7 1003 1272 275552225 275552490 3.450000e-66 263.0
39 TraesCS2A01G363000 chr1B 84.559 272 34 7 1003 1272 275670481 275670746 3.450000e-66 263.0
40 TraesCS2A01G363000 chr1B 96.591 88 3 0 1 88 643258872 643258959 3.620000e-31 147.0
41 TraesCS2A01G363000 chr1B 91.011 89 6 1 3715 3801 480973023 480972935 7.900000e-23 119.0
42 TraesCS2A01G363000 chr1A 82.116 1588 206 33 1968 3528 246129303 246127767 0.000000e+00 1288.0
43 TraesCS2A01G363000 chr1A 81.186 388 49 19 902 1272 246130533 246130153 1.580000e-74 291.0
44 TraesCS2A01G363000 chr1A 86.735 98 11 1 3717 3812 587861308 587861405 1.710000e-19 108.0
45 TraesCS2A01G363000 chr5A 95.833 600 23 1 236 833 568570436 568569837 0.000000e+00 968.0
46 TraesCS2A01G363000 chr5A 98.739 238 3 0 1 238 568573541 568573304 1.490000e-114 424.0
47 TraesCS2A01G363000 chr7D 81.513 595 80 19 239 824 620704531 620703958 3.170000e-126 462.0
48 TraesCS2A01G363000 chr7D 86.316 285 36 3 475 758 402555210 402555492 1.570000e-79 307.0
49 TraesCS2A01G363000 chr6B 96.639 238 8 0 1 238 648197924 648198161 3.260000e-106 396.0
50 TraesCS2A01G363000 chr6B 95.798 238 10 0 1 238 563864629 563864866 7.050000e-103 385.0
51 TraesCS2A01G363000 chr6B 95.378 238 9 2 1 238 563911998 563912233 1.180000e-100 377.0
52 TraesCS2A01G363000 chr6B 98.020 101 2 0 1 101 196073075 196072975 4.620000e-40 176.0
53 TraesCS2A01G363000 chr3B 79.159 571 100 15 242 801 104503396 104503958 1.180000e-100 377.0
54 TraesCS2A01G363000 chr3B 88.764 89 8 2 3718 3804 135685089 135685001 1.710000e-19 108.0
55 TraesCS2A01G363000 chr6D 81.699 459 66 15 236 684 292716398 292716848 2.550000e-97 366.0
56 TraesCS2A01G363000 chrUn 86.728 324 38 3 236 555 69827716 69828038 5.530000e-94 355.0
57 TraesCS2A01G363000 chr3A 94.211 190 9 1 51 238 31816546 31816357 5.690000e-74 289.0
58 TraesCS2A01G363000 chr3A 77.193 342 60 17 470 802 699785646 699785314 2.760000e-42 183.0
59 TraesCS2A01G363000 chr3D 80.833 360 67 2 475 833 11398621 11398263 9.520000e-72 281.0
60 TraesCS2A01G363000 chr3D 89.888 89 7 2 3718 3804 85447128 85447040 3.670000e-21 113.0
61 TraesCS2A01G363000 chr4A 82.609 299 32 9 239 533 652201391 652201109 3.470000e-61 246.0
62 TraesCS2A01G363000 chr4A 85.714 217 8 4 370 582 733606760 733606563 1.640000e-49 207.0
63 TraesCS2A01G363000 chr7A 80.339 295 32 13 245 532 43530602 43530327 2.740000e-47 200.0
64 TraesCS2A01G363000 chr5B 90.066 151 15 0 674 824 606712496 606712646 3.550000e-46 196.0
65 TraesCS2A01G363000 chr5B 90.066 151 15 0 674 824 606732489 606732639 3.550000e-46 196.0
66 TraesCS2A01G363000 chr6A 76.316 342 63 17 470 802 420591937 420592269 2.780000e-37 167.0
67 TraesCS2A01G363000 chr7B 90.179 112 7 2 69 176 686810681 686810570 4.690000e-30 143.0
68 TraesCS2A01G363000 chr1D 91.954 87 5 1 3717 3801 358222551 358222637 2.200000e-23 121.0
69 TraesCS2A01G363000 chr4B 100.000 28 0 0 149 176 558585459 558585486 8.000000e-03 52.8


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 TraesCS2A01G363000 chr2A 607510719 607515211 4492 False 2832.666667 8298 89.506000 1 4493 3 chr2A.!!$F3 4492
1 TraesCS2A01G363000 chr2A 610175174 610178457 3283 False 1110.500000 3144 92.235750 823 3784 4 chr2A.!!$F4 2961
2 TraesCS2A01G363000 chr2B 186403263 186404524 1261 False 1037.000000 1037 81.726000 2252 3522 1 chr2B.!!$F1 1270
3 TraesCS2A01G363000 chr2B 545151015 545155296 4281 False 910.166667 3369 88.402333 889 4493 6 chr2B.!!$F4 3604
4 TraesCS2A01G363000 chr2B 557047179 557047742 563 True 392.000000 392 79.581000 239 801 1 chr2B.!!$R2 562
5 TraesCS2A01G363000 chr2D 131641673 131642937 1264 True 1072.000000 1072 82.248000 2252 3520 1 chr2D.!!$R1 1268
6 TraesCS2A01G363000 chr2D 462238092 462242633 4541 False 711.633333 2532 95.114500 1670 4493 6 chr2D.!!$F3 2823
7 TraesCS2A01G363000 chr2D 462228686 462229522 836 False 515.400000 965 91.716000 856 1918 2 chr2D.!!$F2 1062
8 TraesCS2A01G363000 chr1B 275552225 275554860 2635 False 789.000000 1315 83.489500 1003 3528 2 chr1B.!!$F5 2525
9 TraesCS2A01G363000 chr1B 275670481 275673482 3001 False 776.500000 1290 83.363500 1003 3528 2 chr1B.!!$F6 2525
10 TraesCS2A01G363000 chr1B 275357268 275359916 2648 False 735.500000 1208 84.192000 1003 3528 2 chr1B.!!$F3 2525
11 TraesCS2A01G363000 chr1B 275457258 275459906 2648 False 733.000000 1203 84.148000 1003 3528 2 chr1B.!!$F4 2525
12 TraesCS2A01G363000 chr1A 246127767 246130533 2766 True 789.500000 1288 81.651000 902 3528 2 chr1A.!!$R1 2626
13 TraesCS2A01G363000 chr5A 568569837 568573541 3704 True 696.000000 968 97.286000 1 833 2 chr5A.!!$R1 832
14 TraesCS2A01G363000 chr7D 620703958 620704531 573 True 462.000000 462 81.513000 239 824 1 chr7D.!!$R1 585
15 TraesCS2A01G363000 chr3B 104503396 104503958 562 False 377.000000 377 79.159000 242 801 1 chr3B.!!$F1 559

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
932 3811 0.096454 CTAACTTAAAGTGCGGCGGC 59.904 55.0 9.78 9.68 40.52 6.53 F
1592 5032 0.107456 AACCAGAGTGCTGTGGAGTG 59.893 55.0 20.26 0.00 46.01 3.51 F
1604 5044 0.107945 GTGGAGTGCCTGGAGATGAC 60.108 60.0 0.00 0.00 34.31 3.06 F
1851 5291 0.109597 GTGAAGGCCAATCAAGCACG 60.110 55.0 12.33 0.00 0.00 5.34 F
1857 5297 0.379669 GCCAATCAAGCACGGAGATG 59.620 55.0 0.00 0.00 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1843 5283 0.035317 ACTTGCATCTCCGTGCTTGA 59.965 50.000 0.0 0.0 45.27 3.02 R
3208 8773 0.178767 TCTCCGCCACCATCAGAATG 59.821 55.000 0.0 0.0 37.54 2.67 R
3209 8774 0.911769 TTCTCCGCCACCATCAGAAT 59.088 50.000 0.0 0.0 0.00 2.40 R
3221 8786 1.438814 CCCATTGGCATTTCTCCGC 59.561 57.895 0.0 0.0 0.00 5.54 R
3828 9787 1.872952 TGCATTCAGTTCGGTTCTGTG 59.127 47.619 0.0 0.0 34.86 3.66 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
47 48 2.125552 CCGAGATTGCCACGCTCA 60.126 61.111 0.00 0.00 0.00 4.26
223 224 8.130469 GGAAAATCTTTAAAACTGAACCGTACA 58.870 33.333 0.00 0.00 0.00 2.90
313 3184 2.439104 GGGAGGCGCAGAGGAGAAT 61.439 63.158 10.83 0.00 0.00 2.40
544 3420 3.433598 CGGGATATTTTGCCTCTGGAGAA 60.434 47.826 0.00 0.00 32.55 2.87
610 3486 3.569210 TGGGCCCACCAGTGACAG 61.569 66.667 24.45 0.00 46.80 3.51
661 3539 0.602905 AGCGGAGTAAGCAAAAGCGT 60.603 50.000 0.00 0.00 37.01 5.07
685 3563 4.636206 GTGGGAAGCGAAACTATTCATTCT 59.364 41.667 0.00 0.00 35.15 2.40
793 3671 1.309950 CCGGATTCGTCTGAGCTCTA 58.690 55.000 16.19 0.00 33.95 2.43
814 3692 2.839228 AGGAGGCTTGTAGGAACATCT 58.161 47.619 0.00 0.00 34.97 2.90
824 3702 7.225734 GGCTTGTAGGAACATCTTTCTCTTATC 59.774 40.741 0.00 0.00 34.97 1.75
826 3704 9.883142 CTTGTAGGAACATCTTTCTCTTATCTT 57.117 33.333 0.00 0.00 34.97 2.40
839 3717 9.784680 CTTTCTCTTATCTTTTGATGGAATGTG 57.215 33.333 0.00 0.00 39.88 3.21
932 3811 0.096454 CTAACTTAAAGTGCGGCGGC 59.904 55.000 9.78 9.68 40.52 6.53
933 3812 1.628447 TAACTTAAAGTGCGGCGGCG 61.628 55.000 28.70 28.70 44.10 6.46
934 3813 4.160635 CTTAAAGTGCGGCGGCGG 62.161 66.667 33.02 14.77 44.10 6.13
978 3865 1.211457 AGGCCTGGTTAGCAATCTCAG 59.789 52.381 3.11 0.00 0.00 3.35
979 3866 1.673168 GCCTGGTTAGCAATCTCAGG 58.327 55.000 0.00 0.00 45.59 3.86
1065 3977 2.031768 GAGATGGATCCGCAGCCC 59.968 66.667 7.39 0.00 0.00 5.19
1118 4030 0.460987 GAGATTGCGTCCCTGGTGAG 60.461 60.000 0.00 0.00 0.00 3.51
1155 4067 1.453524 CAGTCTGACGTTCTTTCGCTG 59.546 52.381 1.52 0.00 0.00 5.18
1190 4102 0.680061 AGGAAACTCACGTCCCTGAC 59.320 55.000 0.00 0.00 32.90 3.51
1200 4112 1.064946 GTCCCTGACGAGCGAGATG 59.935 63.158 0.00 0.00 0.00 2.90
1262 4175 2.946762 GGAGGTCAAACGCACAGC 59.053 61.111 0.00 0.00 0.00 4.40
1298 4610 7.873719 AGATCTCCAGGAGTATATACGATTG 57.126 40.000 16.65 6.85 0.00 2.67
1361 4674 0.610687 GACCAGAGGACCAAGGAGTG 59.389 60.000 0.00 0.00 0.00 3.51
1375 4688 2.175202 AGGAGTGTGTGGAGATGACTC 58.825 52.381 0.00 0.00 41.94 3.36
1386 4699 2.364970 GGAGATGACTCATCAGGTGGAG 59.635 54.545 19.21 0.00 42.72 3.86
1387 4700 1.761784 AGATGACTCATCAGGTGGAGC 59.238 52.381 19.21 0.00 42.72 4.70
1409 4752 0.107752 CAGAGGAGCAAGGAAGAGGC 60.108 60.000 0.00 0.00 0.00 4.70
1422 4765 2.208431 GAAGAGGCGGATGAATCTGTG 58.792 52.381 1.27 0.00 35.60 3.66
1446 4886 2.027837 AGATTTGGCAATGGACCTTTGC 60.028 45.455 28.54 28.54 46.82 3.68
1470 4910 0.238289 CAAACATGGAGACGCACCAC 59.762 55.000 0.00 0.00 40.36 4.16
1506 4946 3.249091 CCAGACGACAGATGACAAAGAG 58.751 50.000 0.00 0.00 0.00 2.85
1562 5002 1.807165 CCGACCAGATGACTGTGCG 60.807 63.158 0.00 0.00 42.05 5.34
1592 5032 0.107456 AACCAGAGTGCTGTGGAGTG 59.893 55.000 20.26 0.00 46.01 3.51
1604 5044 0.107945 GTGGAGTGCCTGGAGATGAC 60.108 60.000 0.00 0.00 34.31 3.06
1818 5258 2.172505 TGCGTTTAGGATGATGGACCAT 59.827 45.455 6.71 6.71 0.00 3.55
1839 5279 5.393461 CCATGGAAAATCAAGTAGTGAAGGC 60.393 44.000 5.56 0.00 40.50 4.35
1840 5280 4.079253 TGGAAAATCAAGTAGTGAAGGCC 58.921 43.478 0.00 0.00 40.50 5.19
1841 5281 4.079253 GGAAAATCAAGTAGTGAAGGCCA 58.921 43.478 5.01 0.00 40.50 5.36
1842 5282 4.522789 GGAAAATCAAGTAGTGAAGGCCAA 59.477 41.667 5.01 0.00 40.50 4.52
1843 5283 5.185828 GGAAAATCAAGTAGTGAAGGCCAAT 59.814 40.000 5.01 0.00 40.50 3.16
1844 5284 5.904362 AAATCAAGTAGTGAAGGCCAATC 57.096 39.130 5.01 3.05 40.50 2.67
1845 5285 4.574674 ATCAAGTAGTGAAGGCCAATCA 57.425 40.909 5.01 6.30 40.50 2.57
1846 5286 4.365514 TCAAGTAGTGAAGGCCAATCAA 57.634 40.909 12.33 0.00 31.51 2.57
1847 5287 4.326826 TCAAGTAGTGAAGGCCAATCAAG 58.673 43.478 12.33 1.06 31.51 3.02
1848 5288 2.716217 AGTAGTGAAGGCCAATCAAGC 58.284 47.619 12.33 6.52 0.00 4.01
1849 5289 2.040278 AGTAGTGAAGGCCAATCAAGCA 59.960 45.455 12.33 0.00 0.00 3.91
1850 5290 1.251251 AGTGAAGGCCAATCAAGCAC 58.749 50.000 12.33 5.81 0.00 4.40
1851 5291 0.109597 GTGAAGGCCAATCAAGCACG 60.110 55.000 12.33 0.00 0.00 5.34
1852 5292 1.243342 TGAAGGCCAATCAAGCACGG 61.243 55.000 5.01 0.00 0.00 4.94
1853 5293 0.960364 GAAGGCCAATCAAGCACGGA 60.960 55.000 5.01 0.00 0.00 4.69
1854 5294 0.962356 AAGGCCAATCAAGCACGGAG 60.962 55.000 5.01 0.00 0.00 4.63
1855 5295 1.377202 GGCCAATCAAGCACGGAGA 60.377 57.895 0.00 0.00 0.00 3.71
1856 5296 0.749454 GGCCAATCAAGCACGGAGAT 60.749 55.000 0.00 0.00 0.00 2.75
1857 5297 0.379669 GCCAATCAAGCACGGAGATG 59.620 55.000 0.00 0.00 0.00 2.90
1858 5298 0.379669 CCAATCAAGCACGGAGATGC 59.620 55.000 0.00 0.00 46.50 3.91
2018 7443 2.433604 AGATGCTCGAATGTGAGGATGT 59.566 45.455 6.25 0.43 45.62 3.06
2121 7546 1.294138 CTTACGCAAGGACCGGGAA 59.706 57.895 6.32 0.00 46.39 3.97
2343 7801 0.714439 GCGGTAACTTCGAAGACAGC 59.286 55.000 31.08 24.87 34.32 4.40
2354 7812 5.921408 ACTTCGAAGACAGCAGTAAGTAAAG 59.079 40.000 31.08 0.00 34.32 1.85
2846 8408 3.073356 TGATTATGATGCCTGCAGGATCA 59.927 43.478 37.21 33.94 36.72 2.92
3009 8571 2.556622 CCATGAAGGTTTACACACCACC 59.443 50.000 0.00 0.00 39.62 4.61
3208 8773 3.560068 AGTTGTGTTGGTTGATTCTCGTC 59.440 43.478 0.00 0.00 0.00 4.20
3209 8774 3.186702 TGTGTTGGTTGATTCTCGTCA 57.813 42.857 0.00 0.00 0.00 4.35
3220 8785 4.436332 TGATTCTCGTCATTCTGATGGTG 58.564 43.478 0.00 0.00 34.27 4.17
3221 8786 2.967599 TCTCGTCATTCTGATGGTGG 57.032 50.000 0.00 0.00 34.27 4.61
3222 8787 1.134699 TCTCGTCATTCTGATGGTGGC 60.135 52.381 0.00 0.00 34.27 5.01
3304 8869 2.645838 ACTTGAAGAAAGCCTGCAGA 57.354 45.000 17.39 0.00 39.76 4.26
3310 8875 1.446907 AGAAAGCCTGCAGATTGTCG 58.553 50.000 17.39 0.00 0.00 4.35
3318 8883 2.068519 CTGCAGATTGTCGTACAAGCA 58.931 47.619 8.42 12.54 46.06 3.91
3465 9030 3.141398 CCAACTTGCTAAGCACAAGAGA 58.859 45.455 10.26 0.00 45.99 3.10
3585 9155 5.997129 CCTGTTGCCCAATTTTATCTGTTTT 59.003 36.000 0.00 0.00 0.00 2.43
3628 9572 7.596248 TGCAAAACTGCAGAATTATTTCTCTTC 59.404 33.333 23.35 0.00 40.28 2.87
3634 9578 9.039870 ACTGCAGAATTATTTCTCTTCGATTAG 57.960 33.333 23.35 0.00 40.28 1.73
3635 9579 8.948631 TGCAGAATTATTTCTCTTCGATTAGT 57.051 30.769 0.00 0.00 40.28 2.24
3636 9580 9.383519 TGCAGAATTATTTCTCTTCGATTAGTT 57.616 29.630 0.00 0.00 40.28 2.24
3653 9597 9.529325 TCGATTAGTTATTAATCTGTCCAACTG 57.471 33.333 8.62 0.00 43.61 3.16
3658 9602 8.691661 AGTTATTAATCTGTCCAACTGTTTGT 57.308 30.769 0.00 0.00 0.00 2.83
3736 9682 6.094061 GTGAAGTACTGCCTCTGTAAACTAG 58.906 44.000 0.00 0.00 0.00 2.57
3823 9782 0.963355 TCTAAAATGCCGCCGCCTTT 60.963 50.000 0.00 0.00 34.71 3.11
3824 9783 0.736053 CTAAAATGCCGCCGCCTTTA 59.264 50.000 1.27 2.21 32.42 1.85
3828 9787 0.102300 AATGCCGCCGCCTTTAAATC 59.898 50.000 0.00 0.00 0.00 2.17
3830 9789 1.226575 GCCGCCGCCTTTAAATCAC 60.227 57.895 0.00 0.00 0.00 3.06
3831 9790 1.928706 GCCGCCGCCTTTAAATCACA 61.929 55.000 0.00 0.00 0.00 3.58
3832 9791 0.098728 CCGCCGCCTTTAAATCACAG 59.901 55.000 0.00 0.00 0.00 3.66
3833 9792 1.083489 CGCCGCCTTTAAATCACAGA 58.917 50.000 0.00 0.00 0.00 3.41
3834 9793 1.466950 CGCCGCCTTTAAATCACAGAA 59.533 47.619 0.00 0.00 0.00 3.02
3835 9794 2.727916 CGCCGCCTTTAAATCACAGAAC 60.728 50.000 0.00 0.00 0.00 3.01
3836 9795 2.415491 GCCGCCTTTAAATCACAGAACC 60.415 50.000 0.00 0.00 0.00 3.62
3837 9796 2.159572 CCGCCTTTAAATCACAGAACCG 60.160 50.000 0.00 0.00 0.00 4.44
3859 9836 3.795623 ACTGAATGCATGATTTCCTGC 57.204 42.857 0.00 1.41 38.87 4.85
3894 9871 5.221661 ACCTCTAATCACAGAACCGAACTTT 60.222 40.000 0.00 0.00 0.00 2.66
3910 9887 5.176958 CCGAACTTTGTGAACTACCTGTAAG 59.823 44.000 0.00 0.00 0.00 2.34
3926 9903 4.519730 CCTGTAAGTCTTATCTACCCCTCG 59.480 50.000 0.00 0.00 0.00 4.63
3943 9921 4.137543 CCCTCGCAAGCTATAAAAAGGAT 58.862 43.478 0.00 0.00 37.18 3.24
3982 9961 4.358310 ACCATCCTATCATAGTCTCCAGGA 59.642 45.833 0.00 0.00 36.66 3.86
4028 10007 1.332997 GCATACAGCAGCTCATTCCAC 59.667 52.381 0.00 0.00 44.79 4.02
4198 10177 0.833287 ATCACAGGGGTCTTCATCCG 59.167 55.000 0.00 0.00 0.00 4.18
4219 10198 2.159028 GGCTCATGACCTTCTCCAGTAC 60.159 54.545 0.00 0.00 0.00 2.73
4253 10232 0.449388 GGTACTCGGTGAGGTACGTG 59.551 60.000 0.00 0.00 39.13 4.49
4280 10259 0.697079 ATATCGGCTCGGTCTCCCTA 59.303 55.000 0.00 0.00 0.00 3.53
4295 10274 1.204113 CCCTATGGCATCTCCCTCCC 61.204 65.000 1.65 0.00 0.00 4.30
4352 10331 9.868277 GGATCGATCATGAGAGTAAGATTAATT 57.132 33.333 25.93 0.00 0.00 1.40
4362 10341 8.141909 TGAGAGTAAGATTAATTGTACCGATGG 58.858 37.037 0.00 0.00 0.00 3.51
4364 10343 5.995897 AGTAAGATTAATTGTACCGATGGCC 59.004 40.000 0.00 0.00 0.00 5.36
4367 10346 6.182507 AGATTAATTGTACCGATGGCCTAA 57.817 37.500 3.32 0.00 0.00 2.69
4476 10458 4.935205 TCTATGTTCTTGTCGACCCATTTG 59.065 41.667 14.12 4.90 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 8.301252 TGGATCAAAATGATTCACAAGATGAT 57.699 30.769 0.00 0.00 37.45 2.45
194 195 7.147966 ACGGTTCAGTTTTAAAGATTTTCCAGT 60.148 33.333 0.00 0.00 0.00 4.00
223 224 4.809426 CGGAGGAGCTATATTCGTTTGTTT 59.191 41.667 0.00 0.00 0.00 2.83
334 3208 3.453679 GTCGCTCTCGCTCCCCTT 61.454 66.667 0.00 0.00 35.26 3.95
473 3349 3.727726 CCGAGGGCATTTTTGACTTTTT 58.272 40.909 0.00 0.00 0.00 1.94
610 3486 4.436998 CCGCTGACGAGTGGGGTC 62.437 72.222 0.00 0.00 45.06 4.46
638 3515 3.181510 CGCTTTTGCTTACTCCGCTATTT 60.182 43.478 0.00 0.00 44.80 1.40
641 3518 1.337447 ACGCTTTTGCTTACTCCGCTA 60.337 47.619 0.00 0.00 44.80 4.26
661 3539 3.410631 TGAATAGTTTCGCTTCCCACA 57.589 42.857 0.00 0.00 34.39 4.17
685 3563 4.079970 CGGATCTGGGAGTAGCACTATAA 58.920 47.826 0.00 0.00 0.00 0.98
793 3671 3.185455 AGATGTTCCTACAAGCCTCCTT 58.815 45.455 0.00 0.00 37.91 3.36
814 3692 9.300681 ACACATTCCATCAAAAGATAAGAGAAA 57.699 29.630 0.00 0.00 0.00 2.52
824 3702 6.018832 GGAACACAAACACATTCCATCAAAAG 60.019 38.462 0.00 0.00 40.38 2.27
826 3704 5.128499 AGGAACACAAACACATTCCATCAAA 59.872 36.000 4.78 0.00 42.66 2.69
828 3706 4.214310 AGGAACACAAACACATTCCATCA 58.786 39.130 4.78 0.00 42.66 3.07
978 3865 0.336392 ATCTCTCCTTTTTGGGGGCC 59.664 55.000 0.00 0.00 36.78 5.80
979 3866 1.769026 GATCTCTCCTTTTTGGGGGC 58.231 55.000 0.00 0.00 36.78 5.80
1032 3944 1.298713 CTCTTCCATCGCCGACTCG 60.299 63.158 0.00 0.00 0.00 4.18
1037 3949 0.319728 ATCCATCTCTTCCATCGCCG 59.680 55.000 0.00 0.00 0.00 6.46
1118 4030 1.002868 TGCTTCTCCCTGAGCAAGC 60.003 57.895 15.30 15.30 40.11 4.01
1155 4067 0.395862 TCCTCACGGTCTCAGGATCC 60.396 60.000 2.48 2.48 30.92 3.36
1235 4148 1.346479 TTTGACCTCCGGAACCACCA 61.346 55.000 5.23 0.00 38.90 4.17
1236 4149 0.887836 GTTTGACCTCCGGAACCACC 60.888 60.000 5.23 0.00 0.00 4.61
1237 4150 1.226030 CGTTTGACCTCCGGAACCAC 61.226 60.000 5.23 0.00 0.00 4.16
1262 4175 4.880537 AGATCTTGCTCCGCGGCG 62.881 66.667 23.51 17.52 34.52 6.46
1313 4625 1.544724 TTGGCCAGCCATCTGTTTAC 58.455 50.000 13.10 0.00 46.64 2.01
1361 4674 2.499289 ACCTGATGAGTCATCTCCACAC 59.501 50.000 28.73 6.71 41.06 3.82
1386 4699 0.676151 CTTCCTTGCTCCTCTGGTGC 60.676 60.000 3.96 3.96 41.88 5.01
1387 4700 0.979665 TCTTCCTTGCTCCTCTGGTG 59.020 55.000 0.00 0.00 0.00 4.17
1422 4765 2.450476 AGGTCCATTGCCAAATCTGTC 58.550 47.619 0.00 0.00 0.00 3.51
1446 4886 3.236816 GTGCGTCTCCATGTTTGATTTG 58.763 45.455 0.00 0.00 0.00 2.32
1490 4930 3.653344 TGTTCCTCTTTGTCATCTGTCG 58.347 45.455 0.00 0.00 0.00 4.35
1506 4946 1.340889 TCTGCTGCCACAAAATGTTCC 59.659 47.619 0.00 0.00 0.00 3.62
1562 5002 2.675348 GCACTCTGGTTCTCATAACAGC 59.325 50.000 0.00 0.00 0.00 4.40
1604 5044 0.321564 TTTGCCCACCGTGAGATCAG 60.322 55.000 0.00 0.00 0.00 2.90
1646 5086 1.293924 GTCCATCATCCTCAACGCAG 58.706 55.000 0.00 0.00 0.00 5.18
1729 5169 4.899239 CATCCTCGACGCCAGGGC 62.899 72.222 0.00 0.00 37.85 5.19
1730 5170 2.502492 ATCATCCTCGACGCCAGGG 61.502 63.158 3.01 0.00 0.00 4.45
1731 5171 1.300465 CATCATCCTCGACGCCAGG 60.300 63.158 0.00 0.00 0.00 4.45
1732 5172 1.300465 CCATCATCCTCGACGCCAG 60.300 63.158 0.00 0.00 0.00 4.85
1733 5173 1.756561 TCCATCATCCTCGACGCCA 60.757 57.895 0.00 0.00 0.00 5.69
1734 5174 1.300233 GTCCATCATCCTCGACGCC 60.300 63.158 0.00 0.00 0.00 5.68
1818 5258 4.079253 GGCCTTCACTACTTGATTTTCCA 58.921 43.478 0.00 0.00 32.84 3.53
1839 5279 0.379669 GCATCTCCGTGCTTGATTGG 59.620 55.000 0.00 0.00 41.82 3.16
1840 5280 1.089112 TGCATCTCCGTGCTTGATTG 58.911 50.000 0.34 0.00 45.27 2.67
1841 5281 1.741706 CTTGCATCTCCGTGCTTGATT 59.258 47.619 0.00 0.00 45.27 2.57
1842 5282 1.339438 ACTTGCATCTCCGTGCTTGAT 60.339 47.619 0.00 0.00 45.27 2.57
1843 5283 0.035317 ACTTGCATCTCCGTGCTTGA 59.965 50.000 0.00 0.00 45.27 3.02
1844 5284 0.445436 GACTTGCATCTCCGTGCTTG 59.555 55.000 0.00 0.00 45.27 4.01
1845 5285 0.674895 GGACTTGCATCTCCGTGCTT 60.675 55.000 0.00 0.00 45.27 3.91
1846 5286 1.078848 GGACTTGCATCTCCGTGCT 60.079 57.895 0.00 0.00 45.27 4.40
1847 5287 0.955428 TTGGACTTGCATCTCCGTGC 60.955 55.000 5.85 0.00 45.25 5.34
1848 5288 1.667724 GATTGGACTTGCATCTCCGTG 59.332 52.381 5.85 0.00 0.00 4.94
1849 5289 1.278985 TGATTGGACTTGCATCTCCGT 59.721 47.619 5.85 0.00 0.00 4.69
1850 5290 2.028420 TGATTGGACTTGCATCTCCG 57.972 50.000 5.85 0.00 0.00 4.63
1851 5291 3.350833 ACTTGATTGGACTTGCATCTCC 58.649 45.455 3.61 3.61 0.00 3.71
1852 5292 5.446473 CGTTACTTGATTGGACTTGCATCTC 60.446 44.000 0.00 0.00 0.00 2.75
1853 5293 4.393062 CGTTACTTGATTGGACTTGCATCT 59.607 41.667 0.00 0.00 0.00 2.90
1854 5294 4.391830 TCGTTACTTGATTGGACTTGCATC 59.608 41.667 0.00 0.00 0.00 3.91
1855 5295 4.323417 TCGTTACTTGATTGGACTTGCAT 58.677 39.130 0.00 0.00 0.00 3.96
1856 5296 3.734463 TCGTTACTTGATTGGACTTGCA 58.266 40.909 0.00 0.00 0.00 4.08
1857 5297 4.742438 TTCGTTACTTGATTGGACTTGC 57.258 40.909 0.00 0.00 0.00 4.01
1858 5298 5.147162 GCTTTCGTTACTTGATTGGACTTG 58.853 41.667 0.00 0.00 0.00 3.16
1859 5299 4.819630 TGCTTTCGTTACTTGATTGGACTT 59.180 37.500 0.00 0.00 0.00 3.01
1860 5300 4.385825 TGCTTTCGTTACTTGATTGGACT 58.614 39.130 0.00 0.00 0.00 3.85
1861 5301 4.742438 TGCTTTCGTTACTTGATTGGAC 57.258 40.909 0.00 0.00 0.00 4.02
1862 5302 5.759506 TTTGCTTTCGTTACTTGATTGGA 57.240 34.783 0.00 0.00 0.00 3.53
1982 7407 5.023551 GAGCATCTCGTAATATTTGCACC 57.976 43.478 9.55 0.00 32.66 5.01
2018 7443 1.933051 TCTCCTCATCTTCCTCCTCCA 59.067 52.381 0.00 0.00 0.00 3.86
2121 7546 1.298859 GCGCGTCCTTTTGATCCTGT 61.299 55.000 8.43 0.00 0.00 4.00
2153 7578 2.420022 CTCGGTGTGTCAATTTGATCCC 59.580 50.000 1.78 0.38 0.00 3.85
2354 7812 7.969536 TGAGAAGGAATCGATGGATTTTATC 57.030 36.000 0.00 3.99 42.86 1.75
2751 8221 9.067986 GGGGGAAATTAAGAGAAATACTATGTG 57.932 37.037 0.00 0.00 0.00 3.21
3003 8565 0.179020 TGTTGCTGGAGAAGGTGGTG 60.179 55.000 0.00 0.00 0.00 4.17
3158 8720 3.069300 GGATAGGGAGTCCGTAACTTTCC 59.931 52.174 15.28 13.20 38.74 3.13
3160 8722 3.705072 CTGGATAGGGAGTCCGTAACTTT 59.295 47.826 15.28 0.00 38.74 2.66
3208 8773 0.178767 TCTCCGCCACCATCAGAATG 59.821 55.000 0.00 0.00 37.54 2.67
3209 8774 0.911769 TTCTCCGCCACCATCAGAAT 59.088 50.000 0.00 0.00 0.00 2.40
3221 8786 1.438814 CCCATTGGCATTTCTCCGC 59.561 57.895 0.00 0.00 0.00 5.54
3304 8869 4.816392 TGTGAGTATGCTTGTACGACAAT 58.184 39.130 0.00 0.00 37.48 2.71
3310 8875 4.177026 CCAGACTGTGAGTATGCTTGTAC 58.823 47.826 0.93 0.00 36.19 2.90
3465 9030 8.428063 CAAACATGTCCTTCTAAGAGGATATCT 58.572 37.037 0.00 0.00 46.94 1.98
3555 9125 7.068103 CAGATAAAATTGGGCAACAGGTACATA 59.932 37.037 0.00 0.00 39.74 2.29
3585 9155 2.222007 GCAAACCACATGCAAGACAA 57.778 45.000 0.00 0.00 43.29 3.18
3634 9578 8.564574 TCACAAACAGTTGGACAGATTAATAAC 58.435 33.333 0.00 0.00 39.22 1.89
3635 9579 8.684386 TCACAAACAGTTGGACAGATTAATAA 57.316 30.769 0.00 0.00 39.22 1.40
3636 9580 8.684386 TTCACAAACAGTTGGACAGATTAATA 57.316 30.769 0.00 0.00 39.22 0.98
3653 9597 7.009815 TCGGATAACATTAGTCGATTCACAAAC 59.990 37.037 0.00 0.00 0.00 2.93
3658 9602 6.387041 AGTCGGATAACATTAGTCGATTCA 57.613 37.500 0.00 0.00 0.00 2.57
3698 9642 7.118390 GGCAGTACTTCACATAGCATAATAAGG 59.882 40.741 0.00 0.00 0.00 2.69
3796 9755 4.056050 CGGCGGCATTTTAGATACTACTT 58.944 43.478 10.53 0.00 0.00 2.24
3823 9782 5.106712 GCATTCAGTTCGGTTCTGTGATTTA 60.107 40.000 0.00 0.00 34.86 1.40
3824 9783 4.320494 GCATTCAGTTCGGTTCTGTGATTT 60.320 41.667 0.00 0.00 34.86 2.17
3828 9787 1.872952 TGCATTCAGTTCGGTTCTGTG 59.127 47.619 0.00 0.00 34.86 3.66
3830 9789 2.743664 TCATGCATTCAGTTCGGTTCTG 59.256 45.455 0.00 0.00 0.00 3.02
3831 9790 3.057969 TCATGCATTCAGTTCGGTTCT 57.942 42.857 0.00 0.00 0.00 3.01
3832 9791 4.361451 AATCATGCATTCAGTTCGGTTC 57.639 40.909 0.00 0.00 0.00 3.62
3833 9792 4.380867 GGAAATCATGCATTCAGTTCGGTT 60.381 41.667 0.00 0.00 0.00 4.44
3834 9793 3.129287 GGAAATCATGCATTCAGTTCGGT 59.871 43.478 0.00 0.00 0.00 4.69
3835 9794 3.379372 AGGAAATCATGCATTCAGTTCGG 59.621 43.478 0.00 0.00 0.00 4.30
3836 9795 4.348656 CAGGAAATCATGCATTCAGTTCG 58.651 43.478 0.00 0.00 0.00 3.95
3859 9836 7.331026 TCTGTGATTAGAGGTGGATAAACTTG 58.669 38.462 0.00 0.00 0.00 3.16
3894 9871 8.954350 GTAGATAAGACTTACAGGTAGTTCACA 58.046 37.037 0.00 0.00 0.00 3.58
3910 9887 2.546162 GCTTGCGAGGGGTAGATAAGAC 60.546 54.545 2.37 0.00 0.00 3.01
3982 9961 1.228675 CTCCAGGCAGGCAAAGGTT 60.229 57.895 0.00 0.00 37.29 3.50
4198 10177 0.908198 ACTGGAGAAGGTCATGAGCC 59.092 55.000 20.92 12.97 0.00 4.70
4253 10232 1.217882 CCGAGCCGATATTCAACCAC 58.782 55.000 0.00 0.00 0.00 4.16
4280 10259 1.840650 CTCGGGAGGGAGATGCCAT 60.841 63.158 0.00 0.00 38.95 4.40
4352 10331 5.027460 ACCATATATTAGGCCATCGGTACA 58.973 41.667 5.01 0.00 0.00 2.90
4362 10341 3.506067 GCCACCACAACCATATATTAGGC 59.494 47.826 0.00 0.00 0.00 3.93
4364 10343 3.751175 CCGCCACCACAACCATATATTAG 59.249 47.826 0.00 0.00 0.00 1.73
4367 10346 1.493022 ACCGCCACCACAACCATATAT 59.507 47.619 0.00 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.