Multiple sequence alignment - TraesCS2D01G049900

Loading Multiple Alignment...

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 TraesCS2D01G049900 chr2D 100.000 4329 0 0 1 4329 18301957 18306285 0.000000e+00 7995.0
1 TraesCS2D01G049900 chr2D 91.370 1518 94 15 1180 2677 487360888 487362388 0.000000e+00 2043.0
2 TraesCS2D01G049900 chr2D 95.701 442 19 0 1 442 513950102 513950543 0.000000e+00 712.0
3 TraesCS2D01G049900 chr2D 82.974 417 41 14 2181 2573 43463166 43463576 2.480000e-92 350.0
4 TraesCS2D01G049900 chr2D 85.000 80 12 0 3879 3958 234530068 234530147 9.980000e-12 82.4
5 TraesCS2D01G049900 chr2A 90.966 2236 123 24 816 3012 19446578 19448773 0.000000e+00 2937.0
6 TraesCS2D01G049900 chr2A 90.408 1324 76 19 3047 4329 19448773 19450086 0.000000e+00 1694.0
7 TraesCS2D01G049900 chr2A 94.796 442 20 1 1 442 166853749 166853311 0.000000e+00 686.0
8 TraesCS2D01G049900 chr2A 90.169 356 27 5 471 819 41626298 41626652 1.420000e-124 457.0
9 TraesCS2D01G049900 chr2A 86.861 411 25 11 3359 3745 732561151 732561556 2.390000e-117 433.0
10 TraesCS2D01G049900 chr2A 96.875 32 0 1 3331 3361 630289088 630289057 8.000000e-03 52.8
11 TraesCS2D01G049900 chr2A 96.875 32 0 1 3331 3361 638681441 638681410 8.000000e-03 52.8
12 TraesCS2D01G049900 chr2B 88.391 2524 166 56 886 3361 30429409 30431853 0.000000e+00 2920.0
13 TraesCS2D01G049900 chr2B 94.796 442 23 0 1 442 210706187 210705746 0.000000e+00 689.0
14 TraesCS2D01G049900 chr2B 91.908 346 27 1 471 815 210704243 210703898 2.340000e-132 483.0
15 TraesCS2D01G049900 chr2B 89.362 329 31 3 495 819 65430094 65430422 1.120000e-110 411.0
16 TraesCS2D01G049900 chr2B 100.000 30 0 0 3929 3958 456031671 456031642 6.050000e-04 56.5
17 TraesCS2D01G049900 chr6D 95.701 442 19 0 1 442 126849623 126849182 0.000000e+00 712.0
18 TraesCS2D01G049900 chr6D 95.475 442 18 2 1 442 452834916 452835355 0.000000e+00 704.0
19 TraesCS2D01G049900 chr6D 89.385 358 34 2 471 824 87469188 87468831 8.540000e-122 448.0
20 TraesCS2D01G049900 chr6D 85.401 411 30 16 3362 3746 55900199 55900605 2.430000e-107 399.0
21 TraesCS2D01G049900 chr6D 85.158 411 29 17 3359 3742 452840626 452841031 4.060000e-105 392.0
22 TraesCS2D01G049900 chr6D 96.875 32 0 1 3331 3361 32658560 32658591 8.000000e-03 52.8
23 TraesCS2D01G049900 chr1B 95.249 442 21 0 1 442 597078344 597077903 0.000000e+00 701.0
24 TraesCS2D01G049900 chr1B 80.653 429 50 15 2139 2543 635816995 635816576 7.040000e-78 302.0
25 TraesCS2D01G049900 chr1B 87.013 77 9 1 3882 3958 367592390 367592465 7.710000e-13 86.1
26 TraesCS2D01G049900 chrUn 95.023 442 22 0 1 442 295917942 295918383 0.000000e+00 695.0
27 TraesCS2D01G049900 chrUn 95.023 442 22 0 1 442 326795376 326794935 0.000000e+00 695.0
28 TraesCS2D01G049900 chrUn 83.602 744 103 11 1070 1811 16338390 16337664 0.000000e+00 680.0
29 TraesCS2D01G049900 chrUn 87.123 365 22 9 3411 3751 28729203 28728840 1.460000e-104 390.0
30 TraesCS2D01G049900 chrUn 86.026 229 29 1 1816 2041 16379526 16379754 4.330000e-60 243.0
31 TraesCS2D01G049900 chrUn 85.526 228 30 1 1816 2040 16337093 16336866 7.240000e-58 235.0
32 TraesCS2D01G049900 chr4D 94.796 442 23 0 1 442 293372473 293372914 0.000000e+00 689.0
33 TraesCS2D01G049900 chr4D 89.275 345 30 2 471 815 41722064 41722401 4.000000e-115 425.0
34 TraesCS2D01G049900 chr4D 85.542 415 31 10 3353 3745 56312651 56313058 1.450000e-109 407.0
35 TraesCS2D01G049900 chr4D 83.063 431 43 14 2167 2573 478731751 478732175 8.850000e-97 364.0
36 TraesCS2D01G049900 chr5A 81.995 772 94 22 1844 2578 119031162 119031925 7.960000e-172 614.0
37 TraesCS2D01G049900 chr5A 82.787 122 13 8 3839 3956 149405473 149405356 7.660000e-18 102.0
38 TraesCS2D01G049900 chr4B 81.995 772 94 19 1844 2578 334214433 334213670 7.960000e-172 614.0
39 TraesCS2D01G049900 chr7D 89.595 346 35 1 471 815 83807475 83807820 5.140000e-119 438.0
40 TraesCS2D01G049900 chr7D 86.341 410 26 11 3359 3744 48707156 48707559 1.860000e-113 420.0
41 TraesCS2D01G049900 chr7D 96.875 32 0 1 3331 3361 57715050 57715081 8.000000e-03 52.8
42 TraesCS2D01G049900 chr7D 96.875 32 0 1 3331 3361 538141724 538141693 8.000000e-03 52.8
43 TraesCS2D01G049900 chr7B 89.235 353 32 3 471 817 196377523 196377875 1.850000e-118 436.0
44 TraesCS2D01G049900 chr7B 96.875 32 0 1 3331 3361 87167551 87167520 8.000000e-03 52.8
45 TraesCS2D01G049900 chr5D 86.861 411 28 8 3359 3745 362192525 362192933 1.850000e-118 436.0
46 TraesCS2D01G049900 chr5D 85.610 410 28 14 3362 3745 550182586 550182182 6.740000e-108 401.0
47 TraesCS2D01G049900 chr5D 85.185 81 10 2 3879 3958 459011681 459011602 9.980000e-12 82.4
48 TraesCS2D01G049900 chr4A 90.090 333 33 0 471 803 173472970 173473302 2.390000e-117 433.0
49 TraesCS2D01G049900 chr4A 84.127 63 7 2 3897 3958 454401074 454401014 1.680000e-04 58.4
50 TraesCS2D01G049900 chr7A 85.612 417 28 10 3358 3747 85029184 85028773 4.030000e-110 409.0
51 TraesCS2D01G049900 chr7A 83.413 416 37 16 3357 3745 541459474 541459884 1.480000e-94 357.0
52 TraesCS2D01G049900 chr7A 84.127 63 7 2 3897 3958 281326788 281326728 1.680000e-04 58.4
53 TraesCS2D01G049900 chr3D 88.184 347 30 4 473 815 522087838 522087499 1.870000e-108 403.0
54 TraesCS2D01G049900 chr3D 85.024 414 27 19 3362 3746 606568393 606567986 5.250000e-104 388.0
55 TraesCS2D01G049900 chr3D 86.555 119 13 2 3842 3958 41255408 41255291 1.260000e-25 128.0
56 TraesCS2D01G049900 chr1A 84.878 410 31 10 3362 3745 546957161 546956757 6.790000e-103 385.0
57 TraesCS2D01G049900 chr1A 96.875 32 0 1 3331 3361 542765906 542765937 8.000000e-03 52.8
58 TraesCS2D01G049900 chr3B 86.441 354 24 5 3415 3745 765028269 765028621 2.460000e-97 366.0
59 TraesCS2D01G049900 chr3A 85.387 349 22 9 3434 3756 57206045 57205700 6.940000e-88 335.0
60 TraesCS2D01G049900 chr3A 84.375 352 27 12 3362 3690 32281298 32280952 1.940000e-83 320.0


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 TraesCS2D01G049900 chr2D 18301957 18306285 4328 False 7995.0 7995 100.000 1 4329 1 chr2D.!!$F1 4328
1 TraesCS2D01G049900 chr2D 487360888 487362388 1500 False 2043.0 2043 91.370 1180 2677 1 chr2D.!!$F4 1497
2 TraesCS2D01G049900 chr2A 19446578 19450086 3508 False 2315.5 2937 90.687 816 4329 2 chr2A.!!$F3 3513
3 TraesCS2D01G049900 chr2B 30429409 30431853 2444 False 2920.0 2920 88.391 886 3361 1 chr2B.!!$F1 2475
4 TraesCS2D01G049900 chr2B 210703898 210706187 2289 True 586.0 689 93.352 1 815 2 chr2B.!!$R2 814
5 TraesCS2D01G049900 chrUn 16336866 16338390 1524 True 457.5 680 84.564 1070 2040 2 chrUn.!!$R3 970
6 TraesCS2D01G049900 chr5A 119031162 119031925 763 False 614.0 614 81.995 1844 2578 1 chr5A.!!$F1 734
7 TraesCS2D01G049900 chr4B 334213670 334214433 763 True 614.0 614 81.995 1844 2578 1 chr4B.!!$R1 734

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
856 2332 0.179215 CCTTGACGAAATGTGCTCGC 60.179 55.0 0.00 0.00 39.97 5.03 F
1720 3222 0.036306 TGAAGAAGGCTCCGGAAACC 59.964 55.0 14.18 14.18 0.00 3.27 F
3018 5153 0.249447 GGCCTGTTTGGTTTGTGCTC 60.249 55.0 0.00 0.00 38.35 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2687 4819 0.530744 TCCTCCTCGTCAACGGATTG 59.469 55.0 2.31 0.00 40.29 2.67 R
3100 5239 0.110486 GAGGAGCAAGACCACCCAAA 59.890 55.0 0.00 0.00 0.00 3.28 R
3997 6169 0.388659 ATTATTGCGCCGGTACCGTA 59.611 50.0 31.24 14.22 37.81 4.02 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
250 251 1.597854 CGCAGCAGGAGTTCACCAA 60.598 57.895 0.00 0.00 0.00 3.67
315 316 0.326927 GGTAAACCCTAGCCAGCACA 59.673 55.000 0.00 0.00 0.00 4.57
330 331 3.241530 ACAGCCTCGTCCAAGCCA 61.242 61.111 0.00 0.00 0.00 4.75
413 414 3.372730 GCATCGGCTTGCAACCCA 61.373 61.111 11.32 0.18 42.31 4.51
459 460 5.784177 CGCAGGTTTGATACTATATCCTGT 58.216 41.667 9.50 0.00 41.77 4.00
462 463 6.814146 GCAGGTTTGATACTATATCCTGTAGC 59.186 42.308 9.50 0.00 41.77 3.58
463 464 7.310113 GCAGGTTTGATACTATATCCTGTAGCT 60.310 40.741 9.50 0.00 41.77 3.32
464 465 8.589338 CAGGTTTGATACTATATCCTGTAGCTT 58.411 37.037 0.00 0.00 37.00 3.74
465 466 9.824216 AGGTTTGATACTATATCCTGTAGCTTA 57.176 33.333 0.00 0.00 0.00 3.09
475 1950 1.471676 CCTGTAGCTTAGTCTTGCCGG 60.472 57.143 0.00 0.00 0.00 6.13
584 2059 0.183492 ACCAGCATGAACTGTGGTGT 59.817 50.000 0.00 0.00 42.02 4.16
592 2067 4.439974 GCATGAACTGTGGTGTTTTCTGAA 60.440 41.667 0.00 0.00 0.00 3.02
627 2102 1.227645 GGCGCTGGCATGAGACATA 60.228 57.895 7.64 0.00 42.47 2.29
680 2156 8.873215 TTTTTATTAAAAGTTGAATGCGGACA 57.127 26.923 2.12 0.00 0.00 4.02
702 2178 1.366111 AAATGGATCGACGCGTTGGG 61.366 55.000 25.66 12.67 0.00 4.12
769 2245 2.619646 GGCTGACCTAAACGGACAAAAA 59.380 45.455 0.00 0.00 37.01 1.94
770 2246 3.304458 GGCTGACCTAAACGGACAAAAAG 60.304 47.826 0.00 0.00 37.01 2.27
793 2269 1.229315 ACAAATGCGCCGTCCGTTTA 61.229 50.000 4.18 0.00 39.71 2.01
805 2281 1.523032 CCGTTTAGGTCGGCCCATC 60.523 63.158 0.08 0.00 41.48 3.51
806 2282 1.219664 CGTTTAGGTCGGCCCATCA 59.780 57.895 0.08 0.00 34.66 3.07
824 2300 3.746045 TCAGAGTTGCTTTTACCGACT 57.254 42.857 0.00 0.00 0.00 4.18
850 2326 0.953960 GGACGCCCTTGACGAAATGT 60.954 55.000 0.00 0.00 0.00 2.71
856 2332 0.179215 CCTTGACGAAATGTGCTCGC 60.179 55.000 0.00 0.00 39.97 5.03
924 2400 0.602638 GACCAACCATGTCAGCGTCA 60.603 55.000 0.00 0.00 32.91 4.35
1060 2556 3.897122 GACAAGCCCCACCCACCA 61.897 66.667 0.00 0.00 0.00 4.17
1061 2557 3.434179 ACAAGCCCCACCCACCAA 61.434 61.111 0.00 0.00 0.00 3.67
1062 2558 2.601367 CAAGCCCCACCCACCAAG 60.601 66.667 0.00 0.00 0.00 3.61
1063 2559 4.621087 AAGCCCCACCCACCAAGC 62.621 66.667 0.00 0.00 0.00 4.01
1066 2562 4.722700 CCCCACCCACCAAGCGAG 62.723 72.222 0.00 0.00 0.00 5.03
1068 2564 4.641645 CCACCCACCAAGCGAGCA 62.642 66.667 0.00 0.00 0.00 4.26
1075 2571 2.818714 CCAAGCGAGCAGAGCAGG 60.819 66.667 0.00 0.00 37.01 4.85
1104 2600 2.363795 AGGGCGGTGGAGATCGAA 60.364 61.111 0.00 0.00 0.00 3.71
1368 2867 2.184579 GTACCTCGGCAGCACCTC 59.815 66.667 0.00 0.00 35.61 3.85
1652 3154 8.181904 TGGGGAATTTTATGAAGAAGATATGC 57.818 34.615 0.00 0.00 0.00 3.14
1653 3155 7.233348 TGGGGAATTTTATGAAGAAGATATGCC 59.767 37.037 0.00 0.00 0.00 4.40
1718 3220 1.348064 TCTGAAGAAGGCTCCGGAAA 58.652 50.000 5.23 0.00 0.00 3.13
1720 3222 0.036306 TGAAGAAGGCTCCGGAAACC 59.964 55.000 14.18 14.18 0.00 3.27
1850 3933 2.279741 GATTCAGCAGTGATGCGGTTA 58.720 47.619 2.75 0.00 40.27 2.85
1903 3986 0.955428 TGTCAGCAATGGAGGCGAAC 60.955 55.000 0.00 0.00 36.08 3.95
1905 3988 0.955428 TCAGCAATGGAGGCGAACAC 60.955 55.000 0.00 0.00 36.08 3.32
2057 4150 1.073199 AAGGGTGTGAAGGAAGCCG 59.927 57.895 0.00 0.00 39.00 5.52
2066 4159 0.960364 GAAGGAAGCCGTGCCATTGA 60.960 55.000 0.00 0.00 0.00 2.57
2136 4230 2.911484 AGAATCTGACCGGAAGCAATC 58.089 47.619 9.46 4.61 0.00 2.67
2178 4280 1.879380 TGTCAAGGAAGAATTGGTGCG 59.121 47.619 0.00 0.00 0.00 5.34
2245 4350 1.116308 TCGCCTCCATTATCGGTGAA 58.884 50.000 0.00 0.00 34.64 3.18
2278 4383 1.743252 GCCGCAAGAACAGAGGAGG 60.743 63.158 0.00 0.00 43.02 4.30
2593 4725 2.373707 GGACATGCTCTGGGAGGCT 61.374 63.158 0.00 0.00 0.00 4.58
2662 4794 3.637273 GACACCAAGCCCCGAGGT 61.637 66.667 0.00 0.00 35.65 3.85
2687 4819 2.127232 GCAGCAAGGCGAACGAAC 60.127 61.111 0.00 0.00 0.00 3.95
2885 5020 0.870307 GTCGCGCCGTAAGTGATGAT 60.870 55.000 0.00 0.00 0.00 2.45
2894 5029 2.472861 CGTAAGTGATGATGATCGGCAC 59.527 50.000 8.78 8.78 0.00 5.01
2987 5122 9.639601 AGTTTGTGTATACGTATATGATGATGG 57.360 33.333 17.86 0.00 0.00 3.51
3015 5150 0.758123 ATGGGCCTGTTTGGTTTGTG 59.242 50.000 4.53 0.00 38.35 3.33
3018 5153 0.249447 GGCCTGTTTGGTTTGTGCTC 60.249 55.000 0.00 0.00 38.35 4.26
3019 5154 0.746659 GCCTGTTTGGTTTGTGCTCT 59.253 50.000 0.00 0.00 38.35 4.09
3020 5155 1.269257 GCCTGTTTGGTTTGTGCTCTC 60.269 52.381 0.00 0.00 38.35 3.20
3021 5156 2.023673 CCTGTTTGGTTTGTGCTCTCA 58.976 47.619 0.00 0.00 0.00 3.27
3022 5157 2.223572 CCTGTTTGGTTTGTGCTCTCAC 60.224 50.000 0.00 0.00 43.40 3.51
3023 5158 2.684881 CTGTTTGGTTTGTGCTCTCACT 59.315 45.455 0.00 0.00 43.49 3.41
3024 5159 2.682856 TGTTTGGTTTGTGCTCTCACTC 59.317 45.455 0.00 0.00 43.49 3.51
3025 5160 2.945668 GTTTGGTTTGTGCTCTCACTCT 59.054 45.455 0.00 0.00 43.49 3.24
3026 5161 2.533266 TGGTTTGTGCTCTCACTCTC 57.467 50.000 0.00 0.00 43.49 3.20
3027 5162 1.762370 TGGTTTGTGCTCTCACTCTCA 59.238 47.619 0.00 0.00 43.49 3.27
3028 5163 2.224137 TGGTTTGTGCTCTCACTCTCAG 60.224 50.000 0.00 0.00 43.49 3.35
3029 5164 1.797635 GTTTGTGCTCTCACTCTCAGC 59.202 52.381 0.00 0.00 43.49 4.26
3030 5165 1.336131 TTGTGCTCTCACTCTCAGCT 58.664 50.000 0.00 0.00 43.49 4.24
3031 5166 0.887247 TGTGCTCTCACTCTCAGCTC 59.113 55.000 0.00 0.00 43.49 4.09
3032 5167 0.887247 GTGCTCTCACTCTCAGCTCA 59.113 55.000 0.00 0.00 40.03 4.26
3033 5168 1.135315 GTGCTCTCACTCTCAGCTCAG 60.135 57.143 0.00 0.00 40.03 3.35
3100 5239 7.768807 TGGTTTGTTGCCAAATACTTATACT 57.231 32.000 0.00 0.00 42.26 2.12
3103 5242 8.921670 GGTTTGTTGCCAAATACTTATACTTTG 58.078 33.333 0.00 0.00 42.26 2.77
3107 5246 6.767524 TGCCAAATACTTATACTTTGGGTG 57.232 37.500 13.46 0.00 45.82 4.61
3108 5247 5.654650 TGCCAAATACTTATACTTTGGGTGG 59.345 40.000 13.46 0.00 45.82 4.61
3109 5248 5.655090 GCCAAATACTTATACTTTGGGTGGT 59.345 40.000 13.46 0.00 45.82 4.16
3111 5250 7.116736 CCAAATACTTATACTTTGGGTGGTCT 58.883 38.462 5.56 0.00 43.30 3.85
3113 5252 8.458843 CAAATACTTATACTTTGGGTGGTCTTG 58.541 37.037 0.00 0.00 0.00 3.02
3120 5264 1.779061 TTGGGTGGTCTTGCTCCTCC 61.779 60.000 0.00 0.00 37.74 4.30
3132 5277 0.603975 GCTCCTCCGCATGTAATCCC 60.604 60.000 0.00 0.00 0.00 3.85
3161 5307 6.876789 AGCATCTCAAATTGCAATGATTCAAA 59.123 30.769 13.82 0.00 41.35 2.69
3318 5464 0.175989 CGAAGAGAGTGGTAAGGGCC 59.824 60.000 0.00 0.00 0.00 5.80
3320 5466 1.483004 GAAGAGAGTGGTAAGGGCCTC 59.517 57.143 6.46 0.00 0.00 4.70
3390 5537 5.046448 ACGTTTGGTTCCTGGTACATATGTA 60.046 40.000 11.62 11.62 38.20 2.29
3398 5545 8.693625 GGTTCCTGGTACATATGTATCCTATAC 58.306 40.741 20.88 13.97 38.20 1.47
3399 5546 8.404000 GTTCCTGGTACATATGTATCCTATACG 58.596 40.741 20.88 10.11 38.20 3.06
3445 5592 9.877137 ACAACAAAAAGTCAAAAATTTCTGAAC 57.123 25.926 0.00 0.00 0.00 3.18
3489 5636 8.208224 TGACCTTTCATTGTACTAGTGAGAAAA 58.792 33.333 5.39 0.00 0.00 2.29
3507 5654 7.327518 GTGAGAAAAGTTCCACGAAAAGAAAAA 59.672 33.333 0.00 0.00 0.00 1.94
3592 5763 7.336931 ACCTATAATTTTCGCTGTGAAGTCAAT 59.663 33.333 3.65 0.00 37.99 2.57
3791 5963 5.894298 TGCCATGTTATATGGAGAGAGTT 57.106 39.130 12.25 0.00 41.64 3.01
3792 5964 6.252599 TGCCATGTTATATGGAGAGAGTTT 57.747 37.500 12.25 0.00 41.64 2.66
3793 5965 6.662755 TGCCATGTTATATGGAGAGAGTTTT 58.337 36.000 12.25 0.00 41.64 2.43
3886 6058 2.092323 AGCCCTCAGCCGTTATTTTTC 58.908 47.619 0.00 0.00 45.47 2.29
3891 6063 4.082245 CCCTCAGCCGTTATTTTTCAATGT 60.082 41.667 0.00 0.00 0.00 2.71
3901 6073 7.959651 CCGTTATTTTTCAATGTCTCTCTCTTG 59.040 37.037 0.00 0.00 0.00 3.02
3904 6076 5.679734 TTTTCAATGTCTCTCTCTTGCAC 57.320 39.130 0.00 0.00 0.00 4.57
3924 6096 5.184671 TGCACATAGGCAAAAATGACATGTA 59.815 36.000 0.00 0.00 41.65 2.29
3927 6099 5.951747 ACATAGGCAAAAATGACATGTAGGT 59.048 36.000 0.00 0.00 0.00 3.08
3980 6152 4.828072 ACCCATCTCCAGAACTTAACTC 57.172 45.455 0.00 0.00 0.00 3.01
3997 6169 3.080300 ACTCTCCGACTTGTCAGATCT 57.920 47.619 0.00 0.00 0.00 2.75
4004 6176 3.242673 CCGACTTGTCAGATCTACGGTAC 60.243 52.174 0.00 0.00 35.40 3.34
4096 6268 1.402968 CTGCCCTCAATTTCATCGTGG 59.597 52.381 0.00 0.00 0.00 4.94
4151 6324 7.793888 CACAGTATTACACATCATCATTTACGC 59.206 37.037 0.00 0.00 0.00 4.42
4197 6370 1.063166 GCAGCATTGCTCGCCTTAC 59.937 57.895 8.54 0.00 46.95 2.34
4199 6372 1.815421 AGCATTGCTCGCCTTACCG 60.815 57.895 5.03 0.00 30.62 4.02
4210 6383 2.073816 CGCCTTACCGTCATTTTCTGT 58.926 47.619 0.00 0.00 0.00 3.41
4212 6385 3.071479 GCCTTACCGTCATTTTCTGTGA 58.929 45.455 0.00 0.00 0.00 3.58
4215 6388 4.935205 CCTTACCGTCATTTTCTGTGATGA 59.065 41.667 0.00 0.00 35.16 2.92
4219 6392 4.821805 ACCGTCATTTTCTGTGATGAAAGT 59.178 37.500 0.00 0.00 37.27 2.66
4223 6396 6.896613 CGTCATTTTCTGTGATGAAAGTATCG 59.103 38.462 0.00 0.00 37.27 2.92
4239 6412 5.767816 AGTATCGTTTTGGATATTTGGCC 57.232 39.130 0.00 0.00 31.96 5.36
4262 6435 0.178903 AGACTGGAGCACCTGGGTTA 60.179 55.000 11.55 0.00 39.06 2.85
4279 6452 4.038763 TGGGTTATCGTGATATGACTGGTC 59.961 45.833 0.00 0.00 0.00 4.02
4290 6463 0.681733 TGACTGGTCAGGAGAGTTGC 59.318 55.000 0.00 0.00 34.14 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
232 233 1.597854 TTGGTGAACTCCTGCTGCG 60.598 57.895 0.00 0.00 0.00 5.18
315 316 4.021925 GGTGGCTTGGACGAGGCT 62.022 66.667 13.47 0.00 42.29 4.58
358 359 2.890474 CCATCCGAGGAAACGCCG 60.890 66.667 0.00 0.00 43.43 6.46
361 362 1.290203 CATCACCATCCGAGGAAACG 58.710 55.000 0.00 0.00 0.00 3.60
413 414 2.845795 ACGTGGAAACCGGGGACT 60.846 61.111 6.32 0.00 0.00 3.85
422 423 1.290955 CTGCGGGTAGACGTGGAAA 59.709 57.895 0.00 0.00 35.98 3.13
446 447 8.962679 GCAAGACTAAGCTACAGGATATAGTAT 58.037 37.037 0.00 0.00 0.00 2.12
447 448 7.393796 GGCAAGACTAAGCTACAGGATATAGTA 59.606 40.741 0.00 0.00 0.00 1.82
448 449 6.209788 GGCAAGACTAAGCTACAGGATATAGT 59.790 42.308 0.00 0.00 0.00 2.12
450 451 5.183331 CGGCAAGACTAAGCTACAGGATATA 59.817 44.000 0.00 0.00 0.00 0.86
451 452 4.021894 CGGCAAGACTAAGCTACAGGATAT 60.022 45.833 0.00 0.00 0.00 1.63
452 453 3.318275 CGGCAAGACTAAGCTACAGGATA 59.682 47.826 0.00 0.00 0.00 2.59
453 454 2.101582 CGGCAAGACTAAGCTACAGGAT 59.898 50.000 0.00 0.00 0.00 3.24
454 455 1.476891 CGGCAAGACTAAGCTACAGGA 59.523 52.381 0.00 0.00 0.00 3.86
456 457 1.927895 CCGGCAAGACTAAGCTACAG 58.072 55.000 0.00 0.00 0.00 2.74
457 458 0.108329 GCCGGCAAGACTAAGCTACA 60.108 55.000 24.80 0.00 0.00 2.74
459 460 0.830648 ATGCCGGCAAGACTAAGCTA 59.169 50.000 36.33 4.88 0.00 3.32
462 463 1.009829 GTCATGCCGGCAAGACTAAG 58.990 55.000 42.41 23.61 40.30 2.18
463 464 0.392461 GGTCATGCCGGCAAGACTAA 60.392 55.000 44.98 22.55 42.27 2.24
464 465 1.220749 GGTCATGCCGGCAAGACTA 59.779 57.895 44.98 22.88 42.27 2.59
465 466 2.045926 GGTCATGCCGGCAAGACT 60.046 61.111 44.98 26.49 42.27 3.24
466 467 2.359850 TGGTCATGCCGGCAAGAC 60.360 61.111 42.37 42.37 42.01 3.01
467 468 2.359850 GTGGTCATGCCGGCAAGA 60.360 61.111 36.33 32.55 41.21 3.02
565 2040 0.183492 ACACCACAGTTCATGCTGGT 59.817 50.000 5.48 0.45 41.26 4.00
584 2059 1.327303 ACAATGCCGGCTTCAGAAAA 58.673 45.000 29.70 4.25 0.00 2.29
610 2085 1.016627 TTTATGTCTCATGCCAGCGC 58.983 50.000 0.00 0.00 0.00 5.92
627 2102 2.764314 GCCGATCATGCCAGCGTTT 61.764 57.895 0.00 0.00 0.00 3.60
680 2156 1.327460 CAACGCGTCGATCCATTTCAT 59.673 47.619 14.44 0.00 0.00 2.57
702 2178 0.248458 CATTTGGGTCGGCAATACGC 60.248 55.000 0.00 0.00 41.28 4.42
705 2181 1.550327 TTGCATTTGGGTCGGCAATA 58.450 45.000 0.00 0.00 40.94 1.90
745 2221 3.186047 CCGTTTAGGTCAGCCGCG 61.186 66.667 0.00 0.00 40.50 6.46
751 2227 2.288458 CGCTTTTTGTCCGTTTAGGTCA 59.712 45.455 0.00 0.00 41.99 4.02
754 2230 1.874872 TCCGCTTTTTGTCCGTTTAGG 59.125 47.619 0.00 0.00 42.97 2.69
756 2232 2.286872 TGTCCGCTTTTTGTCCGTTTA 58.713 42.857 0.00 0.00 0.00 2.01
770 2246 4.811761 GACGGCGCATTTGTCCGC 62.812 66.667 10.83 0.00 46.49 5.54
793 2269 1.613630 AACTCTGATGGGCCGACCT 60.614 57.895 0.00 0.00 41.11 3.85
799 2275 2.164422 GGTAAAAGCAACTCTGATGGGC 59.836 50.000 0.00 0.00 0.00 5.36
805 2281 3.120991 CGAAGTCGGTAAAAGCAACTCTG 60.121 47.826 0.00 0.00 35.37 3.35
806 2282 3.057734 CGAAGTCGGTAAAAGCAACTCT 58.942 45.455 0.00 0.00 35.37 3.24
835 2311 0.169009 GAGCACATTTCGTCAAGGGC 59.831 55.000 0.00 0.00 0.00 5.19
856 2332 3.481903 CACCTACGCGCTGCAGTG 61.482 66.667 23.02 23.02 0.00 3.66
1035 2527 1.077805 TGGGGCTTGTCGTCTCCTA 59.922 57.895 0.00 0.00 0.00 2.94
1060 2556 4.774503 GGCCTGCTCTGCTCGCTT 62.775 66.667 0.00 0.00 0.00 4.68
1094 2590 2.017782 CGTCTTCCTCTTCGATCTCCA 58.982 52.381 0.00 0.00 0.00 3.86
1104 2600 0.108615 CGCCATTGTCGTCTTCCTCT 60.109 55.000 0.00 0.00 0.00 3.69
1427 2926 3.859414 GGAGCAGAGCTGGCCGAT 61.859 66.667 0.00 0.00 39.88 4.18
1718 3220 2.289133 GCTCCGAAGAAGAAGACAAGGT 60.289 50.000 0.00 0.00 0.00 3.50
1720 3222 3.032017 TGCTCCGAAGAAGAAGACAAG 57.968 47.619 0.00 0.00 0.00 3.16
1850 3933 5.066593 GTCACACTCCAATCTCTTTTCCTT 58.933 41.667 0.00 0.00 0.00 3.36
1903 3986 2.047844 CTGACCCGCTCAGGTGTG 60.048 66.667 0.00 0.00 42.69 3.82
1905 3988 3.535629 TTGCTGACCCGCTCAGGTG 62.536 63.158 9.62 0.00 46.08 4.00
1929 4012 1.914634 TCGCTGAGAAATCGAAGAGC 58.085 50.000 0.00 0.00 43.63 4.09
1930 4013 5.174761 CCTTATTCGCTGAGAAATCGAAGAG 59.825 44.000 0.00 0.00 43.96 2.85
2057 4150 4.730657 CAAGATTCAGTCTTCAATGGCAC 58.269 43.478 0.00 0.00 45.35 5.01
2136 4230 0.895530 TACAAGTTCCTCCTCTGGCG 59.104 55.000 0.00 0.00 0.00 5.69
2178 4280 1.512156 TTTTTCCGCCACCTTCGAGC 61.512 55.000 0.00 0.00 0.00 5.03
2214 4316 1.294857 GGAGGCGATTTCTTCAGCTC 58.705 55.000 0.00 0.00 0.00 4.09
2253 4358 3.423154 GTTCTTGCGGCGGGTCTG 61.423 66.667 9.78 0.00 0.00 3.51
2312 4417 3.071023 TCTTCTTGATGGTCTTGTCCGTT 59.929 43.478 0.00 0.00 0.00 4.44
2494 4626 3.059472 CTCGTACAGCTTGCACGCG 62.059 63.158 9.78 3.53 37.08 6.01
2683 4815 0.713883 CCTCGTCAACGGATTGTTCG 59.286 55.000 2.31 0.00 39.29 3.95
2687 4819 0.530744 TCCTCCTCGTCAACGGATTG 59.469 55.000 2.31 0.00 40.29 2.67
2875 5010 3.493176 CCAGTGCCGATCATCATCACTTA 60.493 47.826 6.15 0.00 36.01 2.24
2987 5122 7.539034 AACCAAACAGGCCCATATATATTTC 57.461 36.000 0.00 0.00 43.14 2.17
3001 5136 2.023673 TGAGAGCACAAACCAAACAGG 58.976 47.619 0.00 0.00 45.67 4.00
3015 5150 0.457035 CCTGAGCTGAGAGTGAGAGC 59.543 60.000 0.01 0.00 0.00 4.09
3028 5163 1.398390 CGACATTTTGGTAGCCTGAGC 59.602 52.381 0.00 0.00 40.32 4.26
3029 5164 2.009774 CCGACATTTTGGTAGCCTGAG 58.990 52.381 0.00 0.00 0.00 3.35
3030 5165 1.948611 GCCGACATTTTGGTAGCCTGA 60.949 52.381 0.00 0.00 0.00 3.86
3031 5166 0.451783 GCCGACATTTTGGTAGCCTG 59.548 55.000 0.00 0.00 0.00 4.85
3032 5167 0.679960 GGCCGACATTTTGGTAGCCT 60.680 55.000 0.00 0.00 37.34 4.58
3033 5168 0.963355 TGGCCGACATTTTGGTAGCC 60.963 55.000 0.00 0.00 39.54 3.93
3095 5234 3.054655 GGAGCAAGACCACCCAAAGTATA 60.055 47.826 0.00 0.00 0.00 1.47
3096 5235 2.290960 GGAGCAAGACCACCCAAAGTAT 60.291 50.000 0.00 0.00 0.00 2.12
3097 5236 1.073284 GGAGCAAGACCACCCAAAGTA 59.927 52.381 0.00 0.00 0.00 2.24
3100 5239 0.110486 GAGGAGCAAGACCACCCAAA 59.890 55.000 0.00 0.00 0.00 3.28
3103 5242 2.671682 GGAGGAGCAAGACCACCC 59.328 66.667 0.00 0.00 33.19 4.61
3104 5243 2.266055 CGGAGGAGCAAGACCACC 59.734 66.667 0.00 0.00 35.37 4.61
3113 5252 0.603975 GGGATTACATGCGGAGGAGC 60.604 60.000 0.00 0.00 37.71 4.70
3120 5264 1.961277 GCTCCGGGGATTACATGCG 60.961 63.158 4.80 0.00 0.00 4.73
3132 5277 1.097232 TGCAATTTGAGATGCTCCGG 58.903 50.000 0.00 0.00 42.97 5.14
3161 5307 1.077985 ATGCCCTCTTTTGCTGCCT 59.922 52.632 0.00 0.00 0.00 4.75
3290 5436 0.600557 CACTCTCTTCGTGGCTGTCT 59.399 55.000 0.00 0.00 0.00 3.41
3318 5464 1.680735 ACCATGCTCGCTCTTAGAGAG 59.319 52.381 14.14 10.26 43.73 3.20
3320 5466 2.593346 AACCATGCTCGCTCTTAGAG 57.407 50.000 4.63 4.63 38.68 2.43
3371 5518 5.473273 AGGATACATATGTACCAGGAACCA 58.527 41.667 24.31 4.34 41.41 3.67
3373 5520 8.404000 CGTATAGGATACATATGTACCAGGAAC 58.596 40.741 24.31 16.08 41.41 3.62
3419 5566 9.877137 GTTCAGAAATTTTTGACTTTTTGTTGT 57.123 25.926 10.73 0.00 0.00 3.32
3462 5609 7.297936 TCTCACTAGTACAATGAAAGGTCAA 57.702 36.000 0.00 0.00 37.30 3.18
3540 5688 7.335673 TCACTATTCATGCTATTTTGACCGAAA 59.664 33.333 0.00 0.00 0.00 3.46
3800 5972 7.164230 TGAAGGAAGTGTTAGAGAGAAGATC 57.836 40.000 0.00 0.00 0.00 2.75
3834 6006 9.293404 ACAAGAACCTAGTTATATGCGTAGATA 57.707 33.333 0.00 0.00 0.00 1.98
3886 6058 4.809958 CCTATGTGCAAGAGAGAGACATTG 59.190 45.833 0.00 0.00 0.00 2.82
3891 6063 2.460669 TGCCTATGTGCAAGAGAGAGA 58.539 47.619 0.00 0.00 38.56 3.10
3901 6073 4.497300 ACATGTCATTTTTGCCTATGTGC 58.503 39.130 0.00 0.00 0.00 4.57
3904 6076 6.267817 CACCTACATGTCATTTTTGCCTATG 58.732 40.000 0.00 0.00 0.00 2.23
3927 6099 5.839063 AGTACAATAGTGAGCTTATAGCCCA 59.161 40.000 0.00 0.00 43.77 5.36
3942 6114 6.821388 AGATGGGTTAGAGCAAGTACAATAG 58.179 40.000 0.00 0.00 0.00 1.73
3980 6152 2.032302 CCGTAGATCTGACAAGTCGGAG 59.968 54.545 16.06 3.67 46.93 4.63
3997 6169 0.388659 ATTATTGCGCCGGTACCGTA 59.611 50.000 31.24 14.22 37.81 4.02
4004 6176 1.796459 GGTGTAGTATTATTGCGCCGG 59.204 52.381 4.18 0.00 0.00 6.13
4038 6210 3.517901 TGGAAGGTTACATAGGTGTCCAG 59.482 47.826 0.00 0.00 39.77 3.86
4096 6268 4.176752 GGAGACGATGGGCCCCAC 62.177 72.222 22.27 12.56 35.80 4.61
4108 6280 2.370189 CTGTGATTGGGGATAGGGAGAC 59.630 54.545 0.00 0.00 0.00 3.36
4151 6324 5.303165 ACGAAAGGTTAGGTAAGGAGTTTG 58.697 41.667 0.00 0.00 0.00 2.93
4180 6353 1.723870 GGTAAGGCGAGCAATGCTG 59.276 57.895 14.48 6.39 39.88 4.41
4183 6356 0.739462 TGACGGTAAGGCGAGCAATG 60.739 55.000 0.00 0.00 0.00 2.82
4191 6364 3.071479 TCACAGAAAATGACGGTAAGGC 58.929 45.455 0.00 0.00 0.00 4.35
4197 6370 5.362556 ACTTTCATCACAGAAAATGACGG 57.637 39.130 0.00 0.00 37.09 4.79
4199 6372 7.743104 ACGATACTTTCATCACAGAAAATGAC 58.257 34.615 0.00 0.00 37.09 3.06
4212 6385 7.920682 GCCAAATATCCAAAACGATACTTTCAT 59.079 33.333 0.00 0.00 0.00 2.57
4215 6388 6.379988 AGGCCAAATATCCAAAACGATACTTT 59.620 34.615 5.01 0.00 0.00 2.66
4219 6392 5.690865 AGAGGCCAAATATCCAAAACGATA 58.309 37.500 5.01 0.00 0.00 2.92
4223 6396 6.038714 CAGTCTAGAGGCCAAATATCCAAAAC 59.961 42.308 5.01 0.00 0.00 2.43
4239 6412 1.110442 CCAGGTGCTCCAGTCTAGAG 58.890 60.000 7.70 0.00 35.89 2.43
4262 6435 3.566351 TCCTGACCAGTCATATCACGAT 58.434 45.455 0.04 0.00 39.13 3.73
4279 6452 2.046892 CCACCGGCAACTCTCCTG 60.047 66.667 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.