Multiple sequence alignment - TraesCS2D01G459000

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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 TraesCS2D01G459000 chr2D 100.000 3377 0 0 1 3377 565696865 565693489 0.000000e+00 6237.0
1 TraesCS2D01G459000 chr2D 87.092 1410 106 40 1280 2627 565591442 565590047 0.000000e+00 1526.0
2 TraesCS2D01G459000 chr2D 88.466 789 79 9 1 786 565683114 565682335 0.000000e+00 942.0
3 TraesCS2D01G459000 chr2D 82.196 938 85 39 1799 2688 565759119 565758216 0.000000e+00 732.0
4 TraesCS2D01G459000 chr2D 89.303 402 34 8 387 786 565599622 565599228 2.340000e-136 496.0
5 TraesCS2D01G459000 chr2D 86.105 475 27 7 2634 3083 565758213 565757753 3.050000e-130 475.0
6 TraesCS2D01G459000 chr2D 84.868 456 43 15 2041 2473 642783304 642783756 1.440000e-118 436.0
7 TraesCS2D01G459000 chr2D 87.227 321 39 2 1357 1675 565760594 565760274 6.890000e-97 364.0
8 TraesCS2D01G459000 chr2D 83.846 390 49 10 1366 1749 565862691 565862310 3.200000e-95 359.0
9 TraesCS2D01G459000 chr2D 86.984 315 40 1 1381 1695 642782335 642782648 1.490000e-93 353.0
10 TraesCS2D01G459000 chr2D 87.313 268 28 4 3106 3372 565757671 565757409 5.480000e-78 302.0
11 TraesCS2D01G459000 chr2D 87.083 240 10 7 1060 1278 565598821 565598582 5.590000e-63 252.0
12 TraesCS2D01G459000 chr2D 89.894 188 15 4 1025 1208 565761061 565760874 4.350000e-59 239.0
13 TraesCS2D01G459000 chr2D 96.350 137 5 0 784 920 565682276 565682140 3.390000e-55 226.0
14 TraesCS2D01G459000 chr2D 89.677 155 13 3 1050 1202 565863037 565862884 9.560000e-46 195.0
15 TraesCS2D01G459000 chr2D 82.128 235 28 7 1806 2038 565861987 565861765 4.450000e-44 189.0
16 TraesCS2D01G459000 chr2D 83.553 152 16 4 1894 2039 565861391 565861243 2.110000e-27 134.0
17 TraesCS2D01G459000 chr2D 85.455 110 11 3 1931 2039 565759207 565759102 3.560000e-20 110.0
18 TraesCS2D01G459000 chr2B 83.483 1338 117 46 1802 3080 678088850 678087558 0.000000e+00 1151.0
19 TraesCS2D01G459000 chr2B 90.366 519 25 7 1285 1798 678069779 678069281 0.000000e+00 658.0
20 TraesCS2D01G459000 chr2B 88.716 514 43 11 2098 2604 678068688 678068183 6.190000e-172 614.0
21 TraesCS2D01G459000 chr2B 83.788 660 58 33 1 656 678071293 678070679 6.280000e-162 580.0
22 TraesCS2D01G459000 chr2B 84.413 571 54 15 2041 2604 677955824 677956366 2.310000e-146 529.0
23 TraesCS2D01G459000 chr2B 84.116 554 53 21 2094 2617 678198079 678197531 1.400000e-138 503.0
24 TraesCS2D01G459000 chr2B 80.342 702 87 28 1371 2039 678089519 678088836 5.070000e-133 484.0
25 TraesCS2D01G459000 chr2B 84.793 434 45 12 1371 1788 677954082 677954510 1.870000e-112 416.0
26 TraesCS2D01G459000 chr2B 88.350 309 20 8 3084 3377 678087468 678087161 1.150000e-94 357.0
27 TraesCS2D01G459000 chr2B 93.388 242 8 3 2842 3083 677956610 677956843 5.360000e-93 351.0
28 TraesCS2D01G459000 chr2B 88.213 263 14 5 1062 1309 678070178 678069918 7.080000e-77 298.0
29 TraesCS2D01G459000 chr2B 88.688 221 19 5 2630 2844 677956362 677956582 7.180000e-67 265.0
30 TraesCS2D01G459000 chr2B 89.362 188 15 5 1025 1207 678089973 678089786 7.290000e-57 231.0
31 TraesCS2D01G459000 chr2B 94.853 136 7 0 3089 3224 678067792 678067657 2.640000e-51 213.0
32 TraesCS2D01G459000 chr2B 94.697 132 6 1 3089 3219 677956920 677957051 1.590000e-48 204.0
33 TraesCS2D01G459000 chr2B 86.885 183 18 5 1025 1201 677953632 677953814 2.050000e-47 200.0
34 TraesCS2D01G459000 chr2B 84.390 205 27 4 2416 2617 677952413 677952615 2.660000e-46 196.0
35 TraesCS2D01G459000 chr2B 79.920 249 37 8 1799 2039 678199164 678198921 1.610000e-38 171.0
36 TraesCS2D01G459000 chr2B 96.000 100 3 1 2985 3083 678067968 678067869 9.700000e-36 161.0
37 TraesCS2D01G459000 chr2B 97.701 87 2 0 2842 2928 678068073 678067987 2.100000e-32 150.0
38 TraesCS2D01G459000 chr2B 84.211 133 11 7 2851 2973 678079776 678079644 1.650000e-23 121.0
39 TraesCS2D01G459000 chr2B 75.254 295 43 19 1760 2039 677955284 677955563 2.750000e-21 113.0
40 TraesCS2D01G459000 chr2B 85.263 95 6 4 1913 2007 678199263 678199177 1.290000e-14 91.6
41 TraesCS2D01G459000 chr2B 100.000 33 0 0 3017 3049 678079616 678079584 1.010000e-05 62.1
42 TraesCS2D01G459000 chr2A 83.058 1210 98 34 1843 2985 706001351 706000182 0.000000e+00 1000.0
43 TraesCS2D01G459000 chr2A 90.446 628 36 11 1284 1894 705935847 705935227 0.000000e+00 806.0
44 TraesCS2D01G459000 chr2A 89.924 526 44 8 265 786 705937090 705936570 0.000000e+00 669.0
45 TraesCS2D01G459000 chr2A 81.369 789 67 40 1892 2627 705926995 705926234 1.360000e-158 569.0
46 TraesCS2D01G459000 chr2A 80.142 705 91 31 1371 2039 706002411 706001720 6.550000e-132 481.0
47 TraesCS2D01G459000 chr2A 83.441 465 39 20 2089 2521 706200571 706200113 6.790000e-107 398.0
48 TraesCS2D01G459000 chr2A 92.565 269 18 2 1 268 705940987 705940720 5.290000e-103 385.0
49 TraesCS2D01G459000 chr2A 91.327 196 11 5 1023 1214 705936229 705936036 2.580000e-66 263.0
50 TraesCS2D01G459000 chr2A 88.398 181 16 5 1025 1203 706202729 706202552 2.640000e-51 213.0
51 TraesCS2D01G459000 chr2A 84.753 223 19 6 2754 2969 705926090 705925876 3.410000e-50 209.0
52 TraesCS2D01G459000 chr2A 85.930 199 17 10 1025 1214 706002876 706002680 5.710000e-48 202.0
53 TraesCS2D01G459000 chr2A 91.216 148 11 2 796 941 705936497 705936350 2.050000e-47 200.0
54 TraesCS2D01G459000 chr2A 88.800 125 12 2 2851 2973 705997224 705997100 5.840000e-33 152.0
55 TraesCS2D01G459000 chr2A 94.595 74 3 1 3010 3083 706000190 706000118 2.750000e-21 113.0
56 TraesCS2D01G459000 chr2A 85.417 96 8 4 1913 2007 706201805 706201715 9.980000e-16 95.3
57 TraesCS2D01G459000 chr2A 98.113 53 0 1 962 1013 705936350 705936298 1.290000e-14 91.6
58 TraesCS2D01G459000 chr2A 85.897 78 5 1 3301 3372 705999903 705999826 1.000000e-10 78.7


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 TraesCS2D01G459000 chr2D 565693489 565696865 3376 True 6237.000000 6237 100.000000 1 3377 1 chr2D.!!$R2 3376
1 TraesCS2D01G459000 chr2D 565590047 565591442 1395 True 1526.000000 1526 87.092000 1280 2627 1 chr2D.!!$R1 1347
2 TraesCS2D01G459000 chr2D 565682140 565683114 974 True 584.000000 942 92.408000 1 920 2 chr2D.!!$R4 919
3 TraesCS2D01G459000 chr2D 642782335 642783756 1421 False 394.500000 436 85.926000 1381 2473 2 chr2D.!!$F1 1092
4 TraesCS2D01G459000 chr2D 565598582 565599622 1040 True 374.000000 496 88.193000 387 1278 2 chr2D.!!$R3 891
5 TraesCS2D01G459000 chr2D 565757409 565761061 3652 True 370.333333 732 86.365000 1025 3372 6 chr2D.!!$R5 2347
6 TraesCS2D01G459000 chr2D 565861243 565863037 1794 True 219.250000 359 84.801000 1050 2039 4 chr2D.!!$R6 989
7 TraesCS2D01G459000 chr2B 678087161 678089973 2812 True 555.750000 1151 85.384250 1025 3377 4 chr2B.!!$R3 2352
8 TraesCS2D01G459000 chr2B 678067657 678071293 3636 True 382.000000 658 91.376714 1 3224 7 chr2B.!!$R1 3223
9 TraesCS2D01G459000 chr2B 677952413 677957051 4638 False 284.250000 529 86.563500 1025 3219 8 chr2B.!!$F1 2194
10 TraesCS2D01G459000 chr2B 678197531 678199263 1732 True 255.200000 503 83.099667 1799 2617 3 chr2B.!!$R4 818
11 TraesCS2D01G459000 chr2A 705935227 705940987 5760 True 402.433333 806 92.265167 1 1894 6 chr2A.!!$R2 1893
12 TraesCS2D01G459000 chr2A 705925876 705926995 1119 True 389.000000 569 83.061000 1892 2969 2 chr2A.!!$R1 1077
13 TraesCS2D01G459000 chr2A 705997100 706002876 5776 True 337.783333 1000 86.403667 1025 3372 6 chr2A.!!$R3 2347
14 TraesCS2D01G459000 chr2A 706200113 706202729 2616 True 235.433333 398 85.752000 1025 2521 3 chr2A.!!$R4 1496

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
362 3997 0.179045 AGTGTTGGTCCTGTGCAGTC 60.179 55.0 0.0 0.0 0.0 3.51 F
953 4725 0.179215 CAACGGCAAAGAGTGATCGC 60.179 55.0 0.0 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1499 5691 0.033504 GAAGCGTGGACTCCTTGTGA 59.966 55.0 0.0 0.0 0.00 3.58 R
2777 10121 0.736325 GGTGAACGATGGAGTCACGG 60.736 60.0 0.0 0.0 32.62 4.94 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
34 35 8.222433 CCATTTGGTGCGCATTTATAATTTATG 58.778 33.333 15.91 6.76 0.00 1.90
77 78 7.981142 TCATTGGATAAACGGAATTGAACTAC 58.019 34.615 0.00 0.00 0.00 2.73
116 117 8.659527 ACAAAGGGGAAAATGTGAGATAATTTT 58.340 29.630 0.00 0.00 38.39 1.82
178 179 1.279271 CAAGGTGAGTCTTGGGGTAGG 59.721 57.143 0.00 0.00 40.14 3.18
183 184 1.149288 TGAGTCTTGGGGTAGGACACT 59.851 52.381 0.00 0.00 37.83 3.55
362 3997 0.179045 AGTGTTGGTCCTGTGCAGTC 60.179 55.000 0.00 0.00 0.00 3.51
382 4017 6.308282 GCAGTCATACTCAACTATATTACCGC 59.692 42.308 0.00 0.00 0.00 5.68
399 4034 2.452006 CGCCAACTTAATGCGGTAAG 57.548 50.000 5.00 5.00 44.29 2.34
443 4106 7.786030 TGGTATGAAAATTTTCCTTGACACAA 58.214 30.769 24.51 6.40 36.36 3.33
444 4107 7.708752 TGGTATGAAAATTTTCCTTGACACAAC 59.291 33.333 24.51 10.30 36.36 3.32
445 4108 7.926018 GGTATGAAAATTTTCCTTGACACAACT 59.074 33.333 24.51 0.00 36.36 3.16
446 4109 9.313118 GTATGAAAATTTTCCTTGACACAACTT 57.687 29.630 24.51 1.25 36.36 2.66
448 4111 8.696410 TGAAAATTTTCCTTGACACAACTTAC 57.304 30.769 24.51 0.00 36.36 2.34
449 4112 7.762159 TGAAAATTTTCCTTGACACAACTTACC 59.238 33.333 24.51 0.00 36.36 2.85
450 4113 6.783708 AATTTTCCTTGACACAACTTACCA 57.216 33.333 0.00 0.00 0.00 3.25
451 4114 5.828299 TTTTCCTTGACACAACTTACCAG 57.172 39.130 0.00 0.00 0.00 4.00
452 4115 4.764050 TTCCTTGACACAACTTACCAGA 57.236 40.909 0.00 0.00 0.00 3.86
453 4116 4.974645 TCCTTGACACAACTTACCAGAT 57.025 40.909 0.00 0.00 0.00 2.90
454 4117 5.304686 TCCTTGACACAACTTACCAGATT 57.695 39.130 0.00 0.00 0.00 2.40
455 4118 5.690865 TCCTTGACACAACTTACCAGATTT 58.309 37.500 0.00 0.00 0.00 2.17
456 4119 6.833041 TCCTTGACACAACTTACCAGATTTA 58.167 36.000 0.00 0.00 0.00 1.40
457 4120 7.284074 TCCTTGACACAACTTACCAGATTTAA 58.716 34.615 0.00 0.00 0.00 1.52
458 4121 7.444183 TCCTTGACACAACTTACCAGATTTAAG 59.556 37.037 0.00 0.00 33.46 1.85
459 4122 7.444183 CCTTGACACAACTTACCAGATTTAAGA 59.556 37.037 0.00 0.00 31.92 2.10
460 4123 8.740123 TTGACACAACTTACCAGATTTAAGAA 57.260 30.769 0.00 0.00 31.92 2.52
461 4124 8.740123 TGACACAACTTACCAGATTTAAGAAA 57.260 30.769 0.00 0.00 31.92 2.52
462 4125 9.349713 TGACACAACTTACCAGATTTAAGAAAT 57.650 29.630 0.00 0.00 31.92 2.17
469 4132 9.476202 ACTTACCAGATTTAAGAAATTTTGCAC 57.524 29.630 0.00 0.00 31.92 4.57
470 4133 9.474920 CTTACCAGATTTAAGAAATTTTGCACA 57.525 29.630 0.00 0.00 0.00 4.57
494 4157 5.145564 AGTTACCTTGTCTGACCAGAACTA 58.854 41.667 10.23 0.00 39.48 2.24
510 4173 8.297470 ACCAGAACTATAACACCGTTTATCTA 57.703 34.615 0.00 0.00 0.00 1.98
517 4180 9.798994 ACTATAACACCGTTTATCTAGTCTTTG 57.201 33.333 0.00 0.00 0.00 2.77
520 4183 7.417496 AACACCGTTTATCTAGTCTTTGAAC 57.583 36.000 0.00 0.00 0.00 3.18
523 4186 5.930569 ACCGTTTATCTAGTCTTTGAACCAC 59.069 40.000 0.00 0.00 0.00 4.16
524 4187 5.929992 CCGTTTATCTAGTCTTTGAACCACA 59.070 40.000 0.00 0.00 0.00 4.17
537 4200 8.755018 GTCTTTGAACCACAAAATTATCAGTTG 58.245 33.333 0.00 0.00 45.97 3.16
694 4360 4.499183 ACTCGCATTTGAGAAAGAGGTAG 58.501 43.478 0.00 0.00 39.35 3.18
712 4378 8.522542 AGAGGTAGAAATACTTCTATCGTGTT 57.477 34.615 0.00 0.00 46.12 3.32
726 4393 1.616865 TCGTGTTGAGAGGTTCGGATT 59.383 47.619 0.00 0.00 0.00 3.01
748 4415 3.211045 GACACTTTGCAAGGTTGGACTA 58.789 45.455 12.08 0.00 0.00 2.59
761 4428 8.345565 GCAAGGTTGGACTATTCATATTAGTTG 58.654 37.037 0.00 0.00 0.00 3.16
767 4434 8.319057 TGGACTATTCATATTAGTTGTCAGGT 57.681 34.615 0.00 0.00 0.00 4.00
768 4435 8.768397 TGGACTATTCATATTAGTTGTCAGGTT 58.232 33.333 0.00 0.00 0.00 3.50
885 4646 2.171448 AGACATGGCAGGTCATTAGGTC 59.829 50.000 30.92 5.20 37.74 3.85
949 4721 2.701587 CCACAACGGCAAAGAGTGA 58.298 52.632 0.00 0.00 32.14 3.41
950 4722 1.238439 CCACAACGGCAAAGAGTGAT 58.762 50.000 0.00 0.00 32.14 3.06
951 4723 1.197721 CCACAACGGCAAAGAGTGATC 59.802 52.381 0.00 0.00 32.14 2.92
952 4724 1.136252 CACAACGGCAAAGAGTGATCG 60.136 52.381 0.00 0.00 32.14 3.69
953 4725 0.179215 CAACGGCAAAGAGTGATCGC 60.179 55.000 0.00 0.00 0.00 4.58
954 4726 1.626654 AACGGCAAAGAGTGATCGCG 61.627 55.000 0.00 0.00 0.00 5.87
955 4727 2.401195 GGCAAAGAGTGATCGCGC 59.599 61.111 0.00 0.00 0.00 6.86
956 4728 2.103042 GGCAAAGAGTGATCGCGCT 61.103 57.895 6.71 6.71 37.63 5.92
957 4729 1.059994 GCAAAGAGTGATCGCGCTG 59.940 57.895 13.50 4.22 34.37 5.18
958 4730 1.059994 CAAAGAGTGATCGCGCTGC 59.940 57.895 13.50 0.00 34.37 5.25
959 4731 1.079543 AAAGAGTGATCGCGCTGCT 60.080 52.632 13.50 1.36 34.37 4.24
960 4732 1.080995 AAAGAGTGATCGCGCTGCTC 61.081 55.000 13.50 6.47 34.37 4.26
961 4733 2.897641 AAGAGTGATCGCGCTGCTCC 62.898 60.000 13.50 0.00 34.37 4.70
1009 4781 1.687123 GCCTCGCTTCACTAGGGATTA 59.313 52.381 0.00 0.00 43.95 1.75
1014 4786 2.690840 GCTTCACTAGGGATTAGGGGA 58.309 52.381 0.00 0.00 33.32 4.81
1224 5198 1.670406 CTGTGCCTTCTTGCTCGCT 60.670 57.895 0.00 0.00 0.00 4.93
1278 5256 4.390264 TGTTGGATCGAATGTGGTTGTTA 58.610 39.130 0.00 0.00 0.00 2.41
1328 5498 2.869801 CCTCTGTTTCACAGCGTACAAA 59.130 45.455 0.00 0.00 45.54 2.83
1392 5570 1.962306 GGTGCCAAACTAACCGCGA 60.962 57.895 8.23 0.00 0.00 5.87
1466 5658 2.047274 TTCGCGGGGAAGAAGCTG 60.047 61.111 6.13 0.00 0.00 4.24
1499 5691 1.221840 CCTGGCCGACTACAGCATT 59.778 57.895 0.00 0.00 33.43 3.56
1649 5846 5.579511 GTGTCGCAAGTATGTACACCTTTAT 59.420 40.000 0.00 0.00 38.53 1.40
1675 5879 8.824159 ACTATTTCTTTCACTATCCATCGATG 57.176 34.615 18.76 18.76 0.00 3.84
1729 5949 3.371898 TGTCTATGAGCTTGTGAATTGCG 59.628 43.478 0.00 0.00 0.00 4.85
1730 5950 3.372206 GTCTATGAGCTTGTGAATTGCGT 59.628 43.478 0.00 0.00 0.00 5.24
1832 8515 5.063564 AGCGTACTTTTTATCAAGCACTAGC 59.936 40.000 0.00 0.00 42.56 3.42
1887 8681 8.593492 TCACTATACATTGATATGCTGTTGTC 57.407 34.615 0.00 0.00 35.03 3.18
1948 8756 2.159934 GCTTGTGAATTGCGATGTTTGC 60.160 45.455 0.00 0.00 0.00 3.68
1997 8815 8.906867 TCGATGCATATGTAGATCATATCTCAA 58.093 33.333 0.00 0.00 44.90 3.02
2007 8825 8.485392 TGTAGATCATATCTCAATGTGGTTTGA 58.515 33.333 0.00 0.00 40.76 2.69
2054 9115 5.555017 AGCATACTATAGTTGATGCCTTGG 58.445 41.667 26.40 2.06 44.65 3.61
2055 9116 4.154918 GCATACTATAGTTGATGCCTTGGC 59.845 45.833 22.28 4.43 39.00 4.52
2079 9143 6.318900 GCCTATTTGCCTTATCACAAGTACTT 59.681 38.462 1.12 1.12 0.00 2.24
2123 9292 6.780457 ATCCTAACTTGTCCATGATTTTGG 57.220 37.500 0.00 0.00 38.18 3.28
2170 9339 0.320374 TCAGGTCTACAAACTGCCGG 59.680 55.000 0.00 0.00 32.42 6.13
2253 9426 2.932187 GCATTGGAAACATGACCCAAGC 60.932 50.000 17.86 16.58 42.48 4.01
2286 9459 3.010420 GCTGGATTAACTGGGAGTTCAC 58.990 50.000 0.00 0.00 39.51 3.18
2288 9461 4.848357 CTGGATTAACTGGGAGTTCACAT 58.152 43.478 0.00 0.00 39.51 3.21
2292 9465 6.208599 TGGATTAACTGGGAGTTCACATTTTC 59.791 38.462 0.00 0.00 39.51 2.29
2318 9499 5.907207 TCGAGTCTTTCTTGGATATGAAGG 58.093 41.667 0.00 0.00 0.00 3.46
2375 9578 9.905713 TCTAGAACCATAAAATATGCTCTTGTT 57.094 29.630 0.00 0.00 0.00 2.83
2410 9617 4.201628 CGTAGTACTGTGCAATTTGCTCTC 60.202 45.833 21.19 12.31 45.31 3.20
2465 9685 7.877097 GTCTACTAGCTTGAATGGATGATGAAT 59.123 37.037 1.04 0.00 0.00 2.57
2498 9720 5.819379 TGCTCTTGCTTCCTATATTTCTGTG 59.181 40.000 0.00 0.00 40.48 3.66
2506 9728 6.017605 GCTTCCTATATTTCTGTGATGTGTGG 60.018 42.308 0.00 0.00 0.00 4.17
2528 9750 5.710099 TGGACTATGGTTGAATCAAGTTTCC 59.290 40.000 0.00 0.00 0.00 3.13
2570 9809 7.067008 TGCTAATTACTAGGAATTGCAAGGTTC 59.933 37.037 23.74 4.68 33.70 3.62
2638 9880 2.616634 ATCTGGTGTAGCATGAGCAG 57.383 50.000 0.00 0.35 45.49 4.24
2649 9891 4.494350 AGCATGAGCAGTGTTAAAACAG 57.506 40.909 0.00 0.00 45.49 3.16
2652 9894 4.023707 GCATGAGCAGTGTTAAAACAGAGT 60.024 41.667 0.00 0.00 39.20 3.24
2737 10040 6.515272 AATCACATTACATTCACCTTCACC 57.485 37.500 0.00 0.00 0.00 4.02
2792 10144 1.183030 TCCACCGTGACTCCATCGTT 61.183 55.000 0.00 0.00 0.00 3.85
2947 10337 4.608948 AGCAAGACTAGCTAGTTTGTGT 57.391 40.909 29.13 21.41 41.32 3.72
3005 10395 8.739039 ACAGCATAGCTTATAACTCTATCTCTG 58.261 37.037 0.00 16.13 36.40 3.35
3050 10440 7.247929 TGTCATGTTCAGTACTAGTATCTCG 57.752 40.000 5.75 0.00 0.00 4.04
3160 10673 3.121738 AGACCCACACTTAAGGAAACG 57.878 47.619 7.53 0.00 0.00 3.60
3185 10699 1.339097 AGGTCTTGCTTCGGTACACT 58.661 50.000 0.00 0.00 0.00 3.55
3194 10708 2.547218 GCTTCGGTACACTCCACTTCAA 60.547 50.000 0.00 0.00 0.00 2.69
3220 10734 8.831715 AATTTTGAAATGGGTAAACTCATCAC 57.168 30.769 0.00 0.00 0.00 3.06
3226 10740 9.391006 TGAAATGGGTAAACTCATCACTAATAC 57.609 33.333 0.00 0.00 0.00 1.89
3319 10833 0.751643 GCCAAATCGCCCACCTATGT 60.752 55.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 7.757526 TGTAGTTCAATTCCGTTTATCCAATG 58.242 34.615 0.00 0.00 0.00 2.82
55 56 7.446013 ACTTGTAGTTCAATTCCGTTTATCCAA 59.554 33.333 0.00 0.00 35.35 3.53
77 78 4.148838 TCCCCTTTGTTATGAACCACTTG 58.851 43.478 0.00 0.00 0.00 3.16
93 94 7.237471 ACCAAAATTATCTCACATTTTCCCCTT 59.763 33.333 0.00 0.00 31.54 3.95
116 117 8.956426 CCTTTTTGTTATATTTCAGAGCTACCA 58.044 33.333 0.00 0.00 0.00 3.25
133 134 4.831107 ACTTTGCACATGTCCTTTTTGTT 58.169 34.783 0.00 0.00 0.00 2.83
178 179 3.141767 ACCCTTCTGCCTTTTAGTGTC 57.858 47.619 0.00 0.00 0.00 3.67
183 184 8.333235 TGAATATCTAAACCCTTCTGCCTTTTA 58.667 33.333 0.00 0.00 0.00 1.52
332 3967 6.536582 CACAGGACCAACACTTATCTTAGATG 59.463 42.308 4.78 0.00 0.00 2.90
362 3997 7.152645 AGTTGGCGGTAATATAGTTGAGTATG 58.847 38.462 0.00 0.00 0.00 2.39
382 4017 6.730960 TTTACTCTTACCGCATTAAGTTGG 57.269 37.500 2.18 0.00 31.87 3.77
443 4106 9.476202 GTGCAAAATTTCTTAAATCTGGTAAGT 57.524 29.630 0.00 0.00 31.67 2.24
444 4107 9.474920 TGTGCAAAATTTCTTAAATCTGGTAAG 57.525 29.630 0.00 0.00 0.00 2.34
445 4108 9.823647 TTGTGCAAAATTTCTTAAATCTGGTAA 57.176 25.926 0.00 0.00 0.00 2.85
446 4109 9.474920 CTTGTGCAAAATTTCTTAAATCTGGTA 57.525 29.630 0.00 0.00 0.00 3.25
447 4110 7.986889 ACTTGTGCAAAATTTCTTAAATCTGGT 59.013 29.630 0.00 0.00 0.00 4.00
448 4111 8.369218 ACTTGTGCAAAATTTCTTAAATCTGG 57.631 30.769 0.00 0.00 0.00 3.86
470 4133 4.409247 AGTTCTGGTCAGACAAGGTAACTT 59.591 41.667 5.01 0.00 45.97 2.66
485 4148 7.179076 AGATAAACGGTGTTATAGTTCTGGT 57.821 36.000 0.00 0.00 0.00 4.00
494 4157 9.148104 GTTCAAAGACTAGATAAACGGTGTTAT 57.852 33.333 0.00 0.00 0.00 1.89
510 4173 8.237811 ACTGATAATTTTGTGGTTCAAAGACT 57.762 30.769 0.00 0.00 45.14 3.24
682 4348 9.887406 CGATAGAAGTATTTCTACCTCTTTCTC 57.113 37.037 9.64 1.54 45.93 2.87
694 4360 7.259161 ACCTCTCAACACGATAGAAGTATTTC 58.741 38.462 0.00 0.00 41.38 2.17
712 4378 2.248248 AGTGTCAATCCGAACCTCTCA 58.752 47.619 0.00 0.00 0.00 3.27
726 4393 1.748493 GTCCAACCTTGCAAAGTGTCA 59.252 47.619 0.43 0.00 44.25 3.58
793 4552 5.899631 TTCTAAACGGGGCTCCTATATTT 57.100 39.130 0.00 0.00 0.00 1.40
885 4646 2.989166 GCCGCTTTCATTTTCTTTCCAG 59.011 45.455 0.00 0.00 0.00 3.86
941 4713 1.079543 AGCAGCGCGATCACTCTTT 60.080 52.632 12.10 0.00 0.00 2.52
942 4714 1.518133 GAGCAGCGCGATCACTCTT 60.518 57.895 12.10 0.00 0.00 2.85
943 4715 2.103934 GAGCAGCGCGATCACTCT 59.896 61.111 12.10 0.00 0.00 3.24
944 4716 2.959071 GGAGCAGCGCGATCACTC 60.959 66.667 12.10 13.28 0.00 3.51
945 4717 3.423162 GAGGAGCAGCGCGATCACT 62.423 63.158 12.10 2.19 0.00 3.41
946 4718 2.959071 GAGGAGCAGCGCGATCAC 60.959 66.667 12.10 0.00 0.00 3.06
947 4719 4.212913 GGAGGAGCAGCGCGATCA 62.213 66.667 12.10 0.00 0.00 2.92
948 4720 3.839642 GAGGAGGAGCAGCGCGATC 62.840 68.421 12.10 5.25 0.00 3.69
949 4721 3.910490 GAGGAGGAGCAGCGCGAT 61.910 66.667 12.10 0.00 0.00 4.58
953 4725 4.200283 GTCGGAGGAGGAGCAGCG 62.200 72.222 0.00 0.00 0.00 5.18
954 4726 3.844090 GGTCGGAGGAGGAGCAGC 61.844 72.222 0.00 0.00 32.38 5.25
955 4727 3.522731 CGGTCGGAGGAGGAGCAG 61.523 72.222 0.00 0.00 32.38 4.24
956 4728 4.043100 TCGGTCGGAGGAGGAGCA 62.043 66.667 0.00 0.00 32.38 4.26
957 4729 3.519930 GTCGGTCGGAGGAGGAGC 61.520 72.222 0.00 0.00 0.00 4.70
958 4730 1.378124 GAAGTCGGTCGGAGGAGGAG 61.378 65.000 0.00 0.00 0.00 3.69
959 4731 1.378250 GAAGTCGGTCGGAGGAGGA 60.378 63.158 0.00 0.00 0.00 3.71
960 4732 2.416432 GGAAGTCGGTCGGAGGAGG 61.416 68.421 0.00 0.00 0.00 4.30
961 4733 2.762234 CGGAAGTCGGTCGGAGGAG 61.762 68.421 0.00 0.00 34.75 3.69
1014 4786 0.037160 GGTGGTGGTGAACGGGTAAT 59.963 55.000 0.00 0.00 0.00 1.89
1050 4890 3.710722 CCGGTTGCTGGCTCTCCT 61.711 66.667 0.00 0.00 0.00 3.69
1224 5198 2.837947 ACATGACCAGATTGAGGAGGA 58.162 47.619 0.00 0.00 0.00 3.71
1260 5234 6.932400 TGGTATATAACAACCACATTCGATCC 59.068 38.462 0.00 0.00 40.84 3.36
1278 5256 2.768527 CAGATCCAGGCCGATGGTATAT 59.231 50.000 10.68 0.00 41.43 0.86
1392 5570 1.305201 ATCGAAACCAACACAGCGTT 58.695 45.000 0.00 0.00 38.83 4.84
1499 5691 0.033504 GAAGCGTGGACTCCTTGTGA 59.966 55.000 0.00 0.00 0.00 3.58
1649 5846 9.914131 CATCGATGGATAGTGAAAGAAATAGTA 57.086 33.333 17.96 0.00 0.00 1.82
1675 5879 0.523968 CATGCATGTAACAGCGGCAC 60.524 55.000 18.91 0.00 37.30 5.01
1729 5949 4.394920 TGAACAGAGGACAACAGAAACAAC 59.605 41.667 0.00 0.00 0.00 3.32
1730 5950 4.584874 TGAACAGAGGACAACAGAAACAA 58.415 39.130 0.00 0.00 0.00 2.83
1832 8515 5.843673 AGTCCATCTACACTACACATGAG 57.156 43.478 0.00 0.00 0.00 2.90
1834 8517 8.417106 AGAAATAGTCCATCTACACTACACATG 58.583 37.037 0.00 0.00 0.00 3.21
1836 8519 7.956328 AGAAATAGTCCATCTACACTACACA 57.044 36.000 0.00 0.00 0.00 3.72
1837 8520 9.303537 GAAAGAAATAGTCCATCTACACTACAC 57.696 37.037 0.00 0.00 0.00 2.90
1838 8521 9.031537 TGAAAGAAATAGTCCATCTACACTACA 57.968 33.333 0.00 0.00 0.00 2.74
1839 8522 9.303537 GTGAAAGAAATAGTCCATCTACACTAC 57.696 37.037 0.00 0.00 32.76 2.73
1840 8523 9.256228 AGTGAAAGAAATAGTCCATCTACACTA 57.744 33.333 0.00 0.00 38.22 2.74
1841 8524 8.140112 AGTGAAAGAAATAGTCCATCTACACT 57.860 34.615 0.00 0.00 36.77 3.55
1917 8715 6.048509 TCGCAATTCACAAGCTTCTATCATA 58.951 36.000 0.00 0.00 0.00 2.15
1948 8756 2.297033 CCCCATCAAACAGACCACAAAG 59.703 50.000 0.00 0.00 0.00 2.77
1997 8815 4.482990 AGTTTCCTGGATTCAAACCACAT 58.517 39.130 0.00 0.00 33.57 3.21
2007 8825 8.151596 GCTAATAAGCTAGTAGTTTCCTGGATT 58.848 37.037 2.13 0.63 45.85 3.01
2039 9070 4.459852 AATAGGCCAAGGCATCAACTAT 57.540 40.909 13.87 7.15 44.11 2.12
2054 9115 5.823045 AGTACTTGTGATAAGGCAAATAGGC 59.177 40.000 0.00 0.00 44.61 3.93
2055 9116 7.697691 CAAGTACTTGTGATAAGGCAAATAGG 58.302 38.462 24.70 0.00 35.92 2.57
2123 9292 4.001248 TGCATAGCACCTGCAACC 57.999 55.556 5.51 0.00 46.06 3.77
2146 9315 1.279271 CAGTTTGTAGACCTGAGGGGG 59.721 57.143 2.38 0.00 40.03 5.40
2170 9339 0.884704 TGTGGCCGCACTTCTTCTTC 60.885 55.000 16.89 0.00 0.00 2.87
2286 9459 5.050363 TCCAAGAAAGACTCGAACGAAAATG 60.050 40.000 0.00 0.00 0.00 2.32
2288 9461 4.435425 TCCAAGAAAGACTCGAACGAAAA 58.565 39.130 0.00 0.00 0.00 2.29
2292 9465 5.340803 TCATATCCAAGAAAGACTCGAACG 58.659 41.667 0.00 0.00 0.00 3.95
2318 9499 8.515414 AGAAGCAACATTTTAACTAGGATGAAC 58.485 33.333 0.00 0.00 0.00 3.18
2375 9578 5.916883 GCACAGTACTACGACAGAAACTAAA 59.083 40.000 0.00 0.00 0.00 1.85
2410 9617 4.563337 ACCTGATTTCATCATTCATGCG 57.437 40.909 0.00 0.00 38.85 4.73
2465 9685 4.655963 AGGAAGCAAGAGCATTACTTGAA 58.344 39.130 11.08 0.00 44.92 2.69
2498 9720 5.185454 TGATTCAACCATAGTCCACACATC 58.815 41.667 0.00 0.00 0.00 3.06
2506 9728 5.125578 GGGGAAACTTGATTCAACCATAGTC 59.874 44.000 0.00 0.00 31.77 2.59
2528 9750 2.887360 CAGAAAATGCTGCCCGGG 59.113 61.111 19.09 19.09 0.00 5.73
2555 9781 1.534729 GACGGAACCTTGCAATTCCT 58.465 50.000 23.11 13.72 42.00 3.36
2570 9809 4.035017 GCATATTTTGATTTGGACGACGG 58.965 43.478 0.00 0.00 0.00 4.79
2638 9880 7.974482 AATGGGTACTACTCTGTTTTAACAC 57.026 36.000 0.00 0.00 34.70 3.32
2665 9962 8.627403 CATGCAGATGACATTTAGTTTCCTAAT 58.373 33.333 0.00 0.00 33.27 1.73
2675 9972 5.780984 TGTTTTGCATGCAGATGACATTTA 58.219 33.333 21.50 0.00 0.00 1.40
2777 10121 0.736325 GGTGAACGATGGAGTCACGG 60.736 60.000 0.00 0.00 32.62 4.94
2778 10122 2.738147 GGTGAACGATGGAGTCACG 58.262 57.895 0.00 0.00 32.62 4.35
2792 10144 1.210967 GGGATGAAATGTACCCGGTGA 59.789 52.381 0.00 0.00 32.73 4.02
2947 10337 2.325661 TGGACCTCTGAATCAGGTGA 57.674 50.000 10.71 0.00 44.87 4.02
3005 10395 1.071699 TGGTCCTTGCAGTGTTACTCC 59.928 52.381 0.00 0.00 0.00 3.85
3050 10440 7.885399 AGAAGCTGTTATATAATGTGGATTCCC 59.115 37.037 0.00 0.00 0.00 3.97
3160 10673 2.987232 ACCGAAGCAAGACCTATTTCC 58.013 47.619 0.00 0.00 0.00 3.13
3194 10708 9.271828 GTGATGAGTTTACCCATTTCAAAATTT 57.728 29.630 0.00 0.00 0.00 1.82
3319 10833 1.760875 GGGTCTCGGCCATGTAGGA 60.761 63.158 2.24 0.00 41.22 2.94


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

AutoCloner maintained by Alex Coulton.