Multiple sequence alignment - TraesCS2D01G030900

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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 TraesCS2D01G030900 chr2D 100.000 3028 0 0 1 3028 12553270 12556297 0.000000e+00 5592.0
1 TraesCS2D01G030900 chr2D 89.159 535 58 0 1498 2032 13191949 13191415 0.000000e+00 667.0
2 TraesCS2D01G030900 chr2D 84.561 421 62 2 1011 1431 13193093 13192676 6.040000e-112 414.0
3 TraesCS2D01G030900 chr2D 81.679 131 20 4 2611 2739 54073919 54073791 4.130000e-19 106.0
4 TraesCS2D01G030900 chr2B 91.626 1636 95 19 456 2068 18952634 18951018 0.000000e+00 2224.0
5 TraesCS2D01G030900 chr2B 92.243 838 48 12 140 967 18846250 18847080 0.000000e+00 1171.0
6 TraesCS2D01G030900 chr2B 91.172 725 56 5 45 768 18980847 18980130 0.000000e+00 977.0
7 TraesCS2D01G030900 chr2B 88.411 535 62 0 1498 2032 23716155 23715621 0.000000e+00 645.0
8 TraesCS2D01G030900 chr2B 93.472 337 21 1 1 337 18952960 18952625 1.620000e-137 499.0
9 TraesCS2D01G030900 chr2B 83.645 428 65 4 1011 1437 23717268 23716845 6.080000e-107 398.0
10 TraesCS2D01G030900 chr2B 90.347 259 15 5 759 1010 18978425 18978170 6.260000e-87 331.0
11 TraesCS2D01G030900 chr2B 86.592 179 24 0 522 700 540973130 540972952 6.620000e-47 198.0
12 TraesCS2D01G030900 chr2B 80.769 208 30 9 2398 2596 18978123 18977917 1.450000e-33 154.0
13 TraesCS2D01G030900 chr2A 87.528 1756 116 40 900 2596 13010610 13012321 0.000000e+00 1934.0
14 TraesCS2D01G030900 chr2A 88.972 535 59 0 1498 2032 15227828 15227294 0.000000e+00 662.0
15 TraesCS2D01G030900 chr2A 89.709 515 32 9 761 1273 13009827 13010322 3.290000e-179 638.0
16 TraesCS2D01G030900 chr2A 87.191 445 39 8 2590 3028 13012397 13012829 9.760000e-135 490.0
17 TraesCS2D01G030900 chr2A 83.645 428 65 4 1011 1437 15228992 15228569 6.080000e-107 398.0
18 TraesCS2D01G030900 chr2A 93.333 60 4 0 761 820 13010518 13010577 4.160000e-14 89.8
19 TraesCS2D01G030900 chr2A 80.899 89 14 3 2635 2722 429279401 429279487 1.950000e-07 67.6
20 TraesCS2D01G030900 chr7A 93.988 499 28 2 1516 2014 308637299 308636803 0.000000e+00 754.0
21 TraesCS2D01G030900 chr3B 92.268 194 14 1 511 704 168973607 168973415 1.070000e-69 274.0
22 TraesCS2D01G030900 chr1A 92.105 190 15 0 511 700 38722714 38722903 4.980000e-68 268.0
23 TraesCS2D01G030900 chr6B 84.472 161 19 4 2747 2905 257239912 257239756 1.450000e-33 154.0
24 TraesCS2D01G030900 chr7D 95.652 69 3 0 1835 1903 61751536 61751468 8.870000e-21 111.0
25 TraesCS2D01G030900 chr5D 83.333 78 12 1 2657 2733 453821200 453821123 1.510000e-08 71.3
26 TraesCS2D01G030900 chr4B 95.556 45 1 1 2693 2736 612922136 612922092 1.510000e-08 71.3
27 TraesCS2D01G030900 chr3A 92.308 39 3 0 555 593 731216088 731216126 4.220000e-04 56.5
28 TraesCS2D01G030900 chr5A 100.000 29 0 0 2694 2722 332327771 332327799 2.000000e-03 54.7


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 TraesCS2D01G030900 chr2D 12553270 12556297 3027 False 5592.000000 5592 100.000000 1 3028 1 chr2D.!!$F1 3027
1 TraesCS2D01G030900 chr2D 13191415 13193093 1678 True 540.500000 667 86.860000 1011 2032 2 chr2D.!!$R2 1021
2 TraesCS2D01G030900 chr2B 18951018 18952960 1942 True 1361.500000 2224 92.549000 1 2068 2 chr2B.!!$R2 2067
3 TraesCS2D01G030900 chr2B 18846250 18847080 830 False 1171.000000 1171 92.243000 140 967 1 chr2B.!!$F1 827
4 TraesCS2D01G030900 chr2B 23715621 23717268 1647 True 521.500000 645 86.028000 1011 2032 2 chr2B.!!$R4 1021
5 TraesCS2D01G030900 chr2B 18977917 18980847 2930 True 487.333333 977 87.429333 45 2596 3 chr2B.!!$R3 2551
6 TraesCS2D01G030900 chr2A 13009827 13012829 3002 False 787.950000 1934 89.440250 761 3028 4 chr2A.!!$F2 2267
7 TraesCS2D01G030900 chr2A 15227294 15228992 1698 True 530.000000 662 86.308500 1011 2032 2 chr2A.!!$R1 1021

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
959 2693 0.036388 TTGTCCCTCCGAAGCATCAC 60.036 55.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2473 5621 0.30776 CTGTGTCAGCGGTTGGTTTC 59.692 55.0 0.0 0.0 0.0 2.78 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 1.855213 GCCACTGCATGCGACAAGAA 61.855 55.000 14.09 0.00 37.47 2.52
26 27 1.002576 CACTGCATGCGACAAGAAACA 60.003 47.619 14.09 0.00 0.00 2.83
29 30 1.044725 GCATGCGACAAGAAACAACG 58.955 50.000 0.00 0.00 0.00 4.10
39 40 5.379732 ACAAGAAACAACGGAAGAAACAA 57.620 34.783 0.00 0.00 0.00 2.83
93 94 2.351544 GCCGATACGAAGGAGTACCATC 60.352 54.545 0.00 0.00 38.94 3.51
96 97 4.288531 CGATACGAAGGAGTACCATCAAC 58.711 47.826 0.00 0.00 38.94 3.18
104 105 5.241403 AGGAGTACCATCAACATTTGTGA 57.759 39.130 0.00 0.00 38.94 3.58
168 169 3.299503 AGTGAAAGGAACTGGCACAAAT 58.700 40.909 0.00 0.00 43.01 2.32
206 207 2.819595 GGAAGCGATGCGAGGCAA 60.820 61.111 0.00 0.00 43.62 4.52
207 208 2.398554 GGAAGCGATGCGAGGCAAA 61.399 57.895 0.00 0.00 43.62 3.68
289 290 0.643822 TACCCCTTTCCCCGGTCTAT 59.356 55.000 0.00 0.00 0.00 1.98
290 291 0.643822 ACCCCTTTCCCCGGTCTATA 59.356 55.000 0.00 0.00 0.00 1.31
340 341 1.002033 GCGATAAAATGCAGAGGCCAG 60.002 52.381 5.01 0.00 40.13 4.85
341 342 1.002033 CGATAAAATGCAGAGGCCAGC 60.002 52.381 5.01 6.72 40.13 4.85
397 398 1.807742 TCGACCACCGGCTAAAAATTG 59.192 47.619 0.00 0.00 39.14 2.32
439 440 1.734465 GCCCAAAGTGAAGACATCTCG 59.266 52.381 0.00 0.00 0.00 4.04
440 441 1.734465 CCCAAAGTGAAGACATCTCGC 59.266 52.381 0.00 0.00 0.00 5.03
443 444 2.807967 CAAAGTGAAGACATCTCGCCAA 59.192 45.455 0.00 0.00 0.00 4.52
462 463 2.559668 CAATTCCTGCACACAATCCAGT 59.440 45.455 0.00 0.00 0.00 4.00
531 532 5.652014 TCAATAGATCCGCCTTTGTCAATTT 59.348 36.000 0.00 0.00 0.00 1.82
592 594 4.700213 GCTGATAGGTTAGCCAAGTTTTCA 59.300 41.667 0.00 0.00 37.19 2.69
595 597 7.467403 GCTGATAGGTTAGCCAAGTTTTCATAC 60.467 40.741 0.00 0.00 37.19 2.39
605 607 7.955918 AGCCAAGTTTTCATACTTTCTTGATT 58.044 30.769 0.00 0.00 36.24 2.57
637 639 2.685897 TGTTTGGTTGCTACAACCTCAC 59.314 45.455 25.33 21.08 40.88 3.51
740 742 6.406961 GGCCTTTAAAACTTTAGGCAGCATAT 60.407 38.462 14.07 0.00 43.60 1.78
779 2495 5.577945 GTGCATTTTCTATTGGGTCACATTG 59.422 40.000 0.00 0.00 0.00 2.82
831 2548 0.249911 AACAGTGTTCACCTCCGAGC 60.250 55.000 1.64 0.00 0.00 5.03
851 2572 3.074538 AGCCTTAGGTGGTGTCATTTTCT 59.925 43.478 0.00 0.00 0.00 2.52
891 2613 0.539051 AGCAGGTTCGGGAGATTCAG 59.461 55.000 0.00 0.00 39.57 3.02
922 2650 3.307480 GCTTGGCTTCTAGTCACCCTAAA 60.307 47.826 0.00 0.00 24.00 1.85
959 2693 0.036388 TTGTCCCTCCGAAGCATCAC 60.036 55.000 0.00 0.00 0.00 3.06
983 2717 2.060275 CTGATTCCATCCTCATCCCCA 58.940 52.381 0.00 0.00 0.00 4.96
989 2723 1.353694 CCATCCTCATCCCCATCTTCC 59.646 57.143 0.00 0.00 0.00 3.46
992 2726 1.846439 TCCTCATCCCCATCTTCCAAC 59.154 52.381 0.00 0.00 0.00 3.77
1454 4494 3.508012 AGTACCTACTGCTCACTCTGTTG 59.492 47.826 0.00 0.00 34.72 3.33
1474 4522 3.985410 TGGCCATCCCAAAGAAGAG 57.015 52.632 0.00 0.00 41.82 2.85
1700 4816 4.426112 CTCTCCTGCGCGCTGACA 62.426 66.667 35.37 21.31 0.00 3.58
1910 5026 1.626654 CCATGGACAACGTCGTGCTC 61.627 60.000 5.56 0.00 32.65 4.26
2033 5149 2.022195 CCCATGGAGCTCTGAAACATG 58.978 52.381 15.22 16.70 38.82 3.21
2034 5150 2.356432 CCCATGGAGCTCTGAAACATGA 60.356 50.000 23.51 0.00 40.92 3.07
2035 5151 3.349927 CCATGGAGCTCTGAAACATGAA 58.650 45.455 23.51 0.00 40.92 2.57
2036 5152 3.952323 CCATGGAGCTCTGAAACATGAAT 59.048 43.478 23.51 0.00 40.92 2.57
2068 5184 7.884877 TCACTCACTGGTTAGATGAAATTGATT 59.115 33.333 0.00 0.00 0.00 2.57
2069 5185 8.180267 CACTCACTGGTTAGATGAAATTGATTC 58.820 37.037 0.00 0.00 38.60 2.52
2075 5191 7.919690 TGGTTAGATGAAATTGATTCGATGTC 58.080 34.615 0.00 0.00 41.18 3.06
2078 5194 6.040962 AGATGAAATTGATTCGATGTCGTG 57.959 37.500 3.83 0.00 41.18 4.35
2087 5203 4.747605 TGATTCGATGTCGTGTGAAGAAAA 59.252 37.500 2.04 0.00 40.80 2.29
2114 5230 8.870116 TGTATTCTGCAACAGTATATATGGAGT 58.130 33.333 0.00 0.00 33.55 3.85
2115 5231 9.144747 GTATTCTGCAACAGTATATATGGAGTG 57.855 37.037 0.00 0.00 33.55 3.51
2116 5232 6.976934 TCTGCAACAGTATATATGGAGTGA 57.023 37.500 0.00 0.00 33.55 3.41
2117 5233 7.544804 TCTGCAACAGTATATATGGAGTGAT 57.455 36.000 0.00 0.00 33.55 3.06
2118 5234 7.966812 TCTGCAACAGTATATATGGAGTGATT 58.033 34.615 0.00 0.00 33.55 2.57
2119 5235 9.088987 TCTGCAACAGTATATATGGAGTGATTA 57.911 33.333 0.00 0.00 33.55 1.75
2120 5236 9.881649 CTGCAACAGTATATATGGAGTGATTAT 57.118 33.333 0.00 0.00 0.00 1.28
2121 5237 9.875691 TGCAACAGTATATATGGAGTGATTATC 57.124 33.333 0.00 0.00 0.00 1.75
2122 5238 9.875691 GCAACAGTATATATGGAGTGATTATCA 57.124 33.333 0.00 0.00 0.00 2.15
2133 5249 3.825498 GTGATTATCACTTCGTGCTCG 57.175 47.619 17.19 0.81 43.73 5.03
2137 5253 3.291809 TTATCACTTCGTGCTCGACAA 57.708 42.857 10.88 0.00 46.03 3.18
2141 5257 1.388093 CACTTCGTGCTCGACAAGATG 59.612 52.381 10.88 4.66 46.03 2.90
2144 5260 1.982612 TCGTGCTCGACAAGATGAAG 58.017 50.000 6.80 0.00 41.35 3.02
2157 5273 9.430623 TCGACAAGATGAAGTTGATTAAATACA 57.569 29.630 0.00 0.00 0.00 2.29
2208 5324 6.527423 ACACTTCAATGCAATCCAATTTCTT 58.473 32.000 0.00 0.00 0.00 2.52
2209 5325 6.993902 ACACTTCAATGCAATCCAATTTCTTT 59.006 30.769 0.00 0.00 0.00 2.52
2216 5332 5.775686 TGCAATCCAATTTCTTTGAGTGAG 58.224 37.500 0.00 0.00 37.53 3.51
2223 5339 7.940571 CCAATTTCTTTGAGTGAGCGCACAA 62.941 44.000 22.91 7.62 40.07 3.33
2312 5432 9.696917 ATGGTCAAGTTGATTAAAGATTTGTTC 57.303 29.630 9.18 0.00 0.00 3.18
2354 5474 9.647797 AGTTAATCATTTTTAAATCGGGGTTTC 57.352 29.630 0.00 0.00 0.00 2.78
2359 5479 3.710209 TTTAAATCGGGGTTTCGGGTA 57.290 42.857 0.00 0.00 0.00 3.69
2364 5484 0.691904 TCGGGGTTTCGGGTATTGTT 59.308 50.000 0.00 0.00 0.00 2.83
2365 5485 1.089112 CGGGGTTTCGGGTATTGTTC 58.911 55.000 0.00 0.00 0.00 3.18
2366 5486 1.466856 GGGGTTTCGGGTATTGTTCC 58.533 55.000 0.00 0.00 0.00 3.62
2367 5487 1.005097 GGGGTTTCGGGTATTGTTCCT 59.995 52.381 0.00 0.00 0.00 3.36
2368 5488 2.362736 GGGTTTCGGGTATTGTTCCTC 58.637 52.381 0.00 0.00 0.00 3.71
2369 5489 2.290450 GGGTTTCGGGTATTGTTCCTCA 60.290 50.000 0.00 0.00 0.00 3.86
2370 5490 3.414269 GGTTTCGGGTATTGTTCCTCAA 58.586 45.455 0.00 0.00 40.53 3.02
2372 5492 4.082949 GGTTTCGGGTATTGTTCCTCAAAG 60.083 45.833 0.00 0.00 39.62 2.77
2373 5493 3.343941 TCGGGTATTGTTCCTCAAAGG 57.656 47.619 0.00 0.00 39.62 3.11
2376 5496 4.081309 TCGGGTATTGTTCCTCAAAGGTAG 60.081 45.833 0.00 0.00 39.62 3.18
2377 5497 4.524053 GGGTATTGTTCCTCAAAGGTAGG 58.476 47.826 0.00 0.00 39.62 3.18
2379 5499 4.941873 GGTATTGTTCCTCAAAGGTAGGTG 59.058 45.833 0.00 0.00 39.62 4.00
2380 5500 4.993705 ATTGTTCCTCAAAGGTAGGTGA 57.006 40.909 0.00 0.00 39.62 4.02
2381 5501 4.781775 TTGTTCCTCAAAGGTAGGTGAA 57.218 40.909 0.00 0.00 36.53 3.18
2382 5502 4.781775 TGTTCCTCAAAGGTAGGTGAAA 57.218 40.909 0.00 0.00 36.53 2.69
2384 5504 4.080243 TGTTCCTCAAAGGTAGGTGAAACA 60.080 41.667 0.00 0.00 35.79 2.83
2386 5506 4.651778 TCCTCAAAGGTAGGTGAAACATG 58.348 43.478 0.00 0.00 35.79 3.21
2387 5507 4.349636 TCCTCAAAGGTAGGTGAAACATGA 59.650 41.667 0.00 0.00 35.79 3.07
2388 5508 5.070001 CCTCAAAGGTAGGTGAAACATGAA 58.930 41.667 0.00 0.00 39.98 2.57
2389 5509 5.711976 CCTCAAAGGTAGGTGAAACATGAAT 59.288 40.000 0.00 0.00 39.98 2.57
2390 5510 6.884295 CCTCAAAGGTAGGTGAAACATGAATA 59.116 38.462 0.00 0.00 39.98 1.75
2391 5511 7.557719 CCTCAAAGGTAGGTGAAACATGAATAT 59.442 37.037 0.00 0.00 39.98 1.28
2392 5512 8.877864 TCAAAGGTAGGTGAAACATGAATATT 57.122 30.769 0.00 0.00 39.98 1.28
2393 5513 9.967451 TCAAAGGTAGGTGAAACATGAATATTA 57.033 29.630 0.00 0.00 39.98 0.98
2395 5515 9.975218 AAAGGTAGGTGAAACATGAATATTACT 57.025 29.630 0.00 0.00 39.98 2.24
2435 5583 2.332063 ATATGACTTGGCCACTTCGG 57.668 50.000 3.88 0.00 38.11 4.30
2438 5586 2.032681 ACTTGGCCACTTCGGAGC 59.967 61.111 3.88 0.00 36.56 4.70
2459 5607 4.814294 CTAGGCCACCGTGACCGC 62.814 72.222 5.01 0.00 0.00 5.68
2484 5632 2.561037 CCACCCAGAAACCAACCGC 61.561 63.158 0.00 0.00 0.00 5.68
2491 5639 0.107410 AGAAACCAACCGCTGACACA 60.107 50.000 0.00 0.00 0.00 3.72
2497 5645 0.602638 CAACCGCTGACACAGGCTTA 60.603 55.000 0.00 0.00 31.21 3.09
2498 5646 0.107831 AACCGCTGACACAGGCTTAA 59.892 50.000 0.00 0.00 31.21 1.85
2499 5647 0.324943 ACCGCTGACACAGGCTTAAT 59.675 50.000 0.00 0.00 31.21 1.40
2537 5693 4.620723 TCTTCCCCTCTCATTTAGCTACA 58.379 43.478 0.00 0.00 0.00 2.74
2545 5701 5.277857 TCTCATTTAGCTACAGGGCTTAC 57.722 43.478 0.00 0.00 42.97 2.34
2546 5702 4.101119 TCTCATTTAGCTACAGGGCTTACC 59.899 45.833 0.00 0.00 42.97 2.85
2547 5703 2.973694 TTTAGCTACAGGGCTTACCG 57.026 50.000 0.00 0.00 46.96 4.02
2548 5704 1.856629 TTAGCTACAGGGCTTACCGT 58.143 50.000 0.00 0.00 46.96 4.83
2655 5893 4.634199 AGTTTGCATGAATTCTGTTTGGG 58.366 39.130 7.05 0.00 0.00 4.12
2667 5905 7.713073 TGAATTCTGTTTGGGTTGTTAAAATCC 59.287 33.333 7.05 0.00 0.00 3.01
2675 5913 3.119955 GGGTTGTTAAAATCCGCTCTGAC 60.120 47.826 0.00 0.00 0.00 3.51
2685 5923 0.110056 CCGCTCTGACATGTTTGTGC 60.110 55.000 0.00 7.79 35.79 4.57
2686 5924 0.587768 CGCTCTGACATGTTTGTGCA 59.412 50.000 18.87 5.71 35.79 4.57
2716 5954 4.479993 GCCGGCTCCTGCATCAGT 62.480 66.667 22.15 0.00 41.91 3.41
2717 5955 2.513204 CCGGCTCCTGCATCAGTG 60.513 66.667 0.00 0.00 41.91 3.66
2718 5956 2.267006 CGGCTCCTGCATCAGTGT 59.733 61.111 0.00 0.00 41.91 3.55
2719 5957 1.812922 CGGCTCCTGCATCAGTGTC 60.813 63.158 0.00 0.00 41.91 3.67
2720 5958 1.451028 GGCTCCTGCATCAGTGTCC 60.451 63.158 0.00 0.00 41.91 4.02
2721 5959 1.812922 GCTCCTGCATCAGTGTCCG 60.813 63.158 0.00 0.00 39.41 4.79
2722 5960 1.593787 CTCCTGCATCAGTGTCCGT 59.406 57.895 0.00 0.00 0.00 4.69
2723 5961 0.738762 CTCCTGCATCAGTGTCCGTG 60.739 60.000 0.00 0.00 0.00 4.94
2729 5967 1.016130 CATCAGTGTCCGTGGACTGC 61.016 60.000 19.17 12.10 44.80 4.40
2739 5977 2.204136 TGGACTGCTCCCCACCAT 60.204 61.111 0.00 0.00 35.34 3.55
2743 5981 1.691482 GGACTGCTCCCCACCATAGTA 60.691 57.143 0.00 0.00 0.00 1.82
2745 5983 2.706190 GACTGCTCCCCACCATAGTAAT 59.294 50.000 0.00 0.00 0.00 1.89
2795 6033 6.016527 GGGCCTAATAGTAAAACAATGCTACC 60.017 42.308 0.84 0.00 0.00 3.18
2842 6080 5.221843 TGTGGGCTAGACTTCATGTAAAACT 60.222 40.000 0.00 0.00 0.00 2.66
2843 6081 5.705905 GTGGGCTAGACTTCATGTAAAACTT 59.294 40.000 0.00 0.00 0.00 2.66
2947 6187 6.164176 GGATACGATGTTCGATTTAGGGATT 58.836 40.000 3.62 0.00 43.74 3.01
2967 6207 5.833131 GGATTAACATTGGAGATGCCCTTAA 59.167 40.000 0.00 0.00 34.97 1.85
2979 6219 7.939039 TGGAGATGCCCTTAATCAGTTATAAAG 59.061 37.037 0.00 0.00 34.97 1.85
2994 6234 6.094186 CAGTTATAAAGTGAAGCTTCCCCTTC 59.906 42.308 23.42 12.06 41.21 3.46
2997 6237 1.000771 GTGAAGCTTCCCCTTCCCC 60.001 63.158 23.42 0.00 40.34 4.81
3004 6247 0.614697 CTTCCCCTTCCCCGCAAAAT 60.615 55.000 0.00 0.00 0.00 1.82
3005 6248 0.178918 TTCCCCTTCCCCGCAAAATT 60.179 50.000 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.976987 TGTTTCTTCCGTTGTTTCTTGTC 58.023 39.130 0.00 0.00 0.00 3.18
23 24 5.278604 GTGCTAATTGTTTCTTCCGTTGTT 58.721 37.500 0.00 0.00 0.00 2.83
26 27 3.886505 TGGTGCTAATTGTTTCTTCCGTT 59.113 39.130 0.00 0.00 0.00 4.44
29 30 5.652452 AGGTATGGTGCTAATTGTTTCTTCC 59.348 40.000 0.00 0.00 0.00 3.46
39 40 3.134081 ACGCTACAAGGTATGGTGCTAAT 59.866 43.478 0.00 0.00 31.84 1.73
168 169 5.205821 TCCTCCCTATGATTAGTTTCACGA 58.794 41.667 0.00 0.00 0.00 4.35
289 290 1.003959 TGGCATTGTCAGCGCACTA 60.004 52.632 11.47 0.00 0.00 2.74
290 291 2.281692 TGGCATTGTCAGCGCACT 60.282 55.556 11.47 0.00 0.00 4.40
340 341 1.611006 GGGCCTACTTACTAGTACGGC 59.389 57.143 17.23 17.23 43.27 5.68
341 342 2.883386 CTGGGCCTACTTACTAGTACGG 59.117 54.545 4.53 6.80 35.78 4.02
397 398 0.690762 TAAGGGTTGAGTGGGACTGC 59.309 55.000 0.00 0.00 0.00 4.40
439 440 1.404583 GGATTGTGTGCAGGAATTGGC 60.405 52.381 0.00 0.00 0.00 4.52
440 441 1.894466 TGGATTGTGTGCAGGAATTGG 59.106 47.619 0.00 0.00 0.00 3.16
462 463 3.527533 CAACGATTTTATCCGGGTCTCA 58.472 45.455 0.00 0.00 0.00 3.27
503 504 3.392616 ACAAAGGCGGATCTATTGAGGAT 59.607 43.478 0.00 0.00 0.00 3.24
592 594 8.993424 ACATGTCTACCCTAATCAAGAAAGTAT 58.007 33.333 0.00 0.00 0.00 2.12
595 597 8.454106 CAAACATGTCTACCCTAATCAAGAAAG 58.546 37.037 0.00 0.00 0.00 2.62
605 607 3.329520 AGCAACCAAACATGTCTACCCTA 59.670 43.478 0.00 0.00 0.00 3.53
637 639 3.257127 GGAGAGGAATACAGAAGGGATCG 59.743 52.174 0.00 0.00 0.00 3.69
779 2495 4.023365 GCCATATTTTGAGGCTCATGTCTC 60.023 45.833 19.50 1.40 44.92 3.36
831 2548 6.238648 ACTTAGAAAATGACACCACCTAAGG 58.761 40.000 0.00 0.00 37.18 2.69
875 2597 0.539051 CTGCTGAATCTCCCGAACCT 59.461 55.000 0.00 0.00 0.00 3.50
878 2600 0.324614 TTGCTGCTGAATCTCCCGAA 59.675 50.000 0.00 0.00 0.00 4.30
922 2650 0.541764 AATGGATGCGGTTGGTGGTT 60.542 50.000 0.00 0.00 0.00 3.67
983 2717 3.350833 GCCATGTTCTCTGTTGGAAGAT 58.649 45.455 0.00 0.00 0.00 2.40
989 2723 1.503542 GCGGCCATGTTCTCTGTTG 59.496 57.895 2.24 0.00 0.00 3.33
992 2726 3.869272 GCGCGGCCATGTTCTCTG 61.869 66.667 8.83 0.00 0.00 3.35
1236 3634 1.301479 GTCAAGGTCCACGTGGTCC 60.301 63.158 35.07 35.07 42.66 4.46
1437 3835 3.062763 CCAACAACAGAGTGAGCAGTAG 58.937 50.000 0.00 0.00 0.00 2.57
1442 3840 0.819259 TGGCCAACAACAGAGTGAGC 60.819 55.000 0.61 0.00 0.00 4.26
1443 3841 1.808945 GATGGCCAACAACAGAGTGAG 59.191 52.381 10.96 0.00 0.00 3.51
1444 3842 1.545428 GGATGGCCAACAACAGAGTGA 60.545 52.381 10.96 0.00 0.00 3.41
1445 3843 0.883833 GGATGGCCAACAACAGAGTG 59.116 55.000 10.96 0.00 0.00 3.51
1454 4494 1.821136 CTCTTCTTTGGGATGGCCAAC 59.179 52.381 10.96 7.12 35.15 3.77
1521 4637 2.354729 CAGCCCCACGATTCCCAA 59.645 61.111 0.00 0.00 0.00 4.12
1526 4642 3.978193 TTGCCCAGCCCCACGATT 61.978 61.111 0.00 0.00 0.00 3.34
1700 4816 0.036952 CCATGTGCTTGGTCTCGTCT 60.037 55.000 0.00 0.00 31.74 4.18
2016 5132 4.851843 TCATTCATGTTTCAGAGCTCCAT 58.148 39.130 10.93 3.14 0.00 3.41
2033 5149 6.166279 TCTAACCAGTGAGTGATGTTCATTC 58.834 40.000 0.00 0.00 34.21 2.67
2034 5150 6.114187 TCTAACCAGTGAGTGATGTTCATT 57.886 37.500 0.00 0.00 0.00 2.57
2035 5151 5.745312 TCTAACCAGTGAGTGATGTTCAT 57.255 39.130 0.00 0.00 0.00 2.57
2036 5152 5.245977 TCATCTAACCAGTGAGTGATGTTCA 59.754 40.000 0.00 0.00 34.63 3.18
2068 5184 4.055360 ACATTTTCTTCACACGACATCGA 58.945 39.130 8.54 0.00 43.02 3.59
2069 5185 4.389664 ACATTTTCTTCACACGACATCG 57.610 40.909 0.00 0.00 46.33 3.84
2075 5191 5.688823 TGCAGAATACATTTTCTTCACACG 58.311 37.500 0.00 0.00 33.69 4.49
2078 5194 7.141363 ACTGTTGCAGAATACATTTTCTTCAC 58.859 34.615 2.91 0.00 33.69 3.18
2087 5203 9.881649 CTCCATATATACTGTTGCAGAATACAT 57.118 33.333 2.91 0.00 35.18 2.29
2125 5241 1.269723 ACTTCATCTTGTCGAGCACGA 59.730 47.619 0.88 0.88 46.56 4.35
2126 5242 1.702886 ACTTCATCTTGTCGAGCACG 58.297 50.000 0.00 0.00 41.26 5.34
2127 5243 3.059884 TCAACTTCATCTTGTCGAGCAC 58.940 45.455 0.00 0.00 0.00 4.40
2128 5244 3.385193 TCAACTTCATCTTGTCGAGCA 57.615 42.857 0.00 0.00 0.00 4.26
2129 5245 4.935885 AATCAACTTCATCTTGTCGAGC 57.064 40.909 0.00 0.00 0.00 5.03
2130 5246 9.907576 GTATTTAATCAACTTCATCTTGTCGAG 57.092 33.333 0.00 0.00 0.00 4.04
2131 5247 9.430623 TGTATTTAATCAACTTCATCTTGTCGA 57.569 29.630 0.00 0.00 0.00 4.20
2132 5248 9.478019 GTGTATTTAATCAACTTCATCTTGTCG 57.522 33.333 0.00 0.00 0.00 4.35
2137 5253 9.520515 ACCAAGTGTATTTAATCAACTTCATCT 57.479 29.630 3.22 0.00 0.00 2.90
2157 5273 8.741603 AATATACGCCAATAAAGTAACCAAGT 57.258 30.769 0.00 0.00 0.00 3.16
2208 5324 2.031769 CAGATTTTGTGCGCTCACTCAA 60.032 45.455 12.40 6.05 43.49 3.02
2209 5325 1.532437 CAGATTTTGTGCGCTCACTCA 59.468 47.619 12.40 0.00 43.49 3.41
2216 5332 0.313672 TTCACCCAGATTTTGTGCGC 59.686 50.000 0.00 0.00 0.00 6.09
2223 5339 6.855763 TGCAGATTTTATTCACCCAGATTT 57.144 33.333 0.00 0.00 0.00 2.17
2287 5407 8.141268 GGAACAAATCTTTAATCAACTTGACCA 58.859 33.333 0.00 0.00 0.00 4.02
2354 5474 3.067684 ACCTTTGAGGAACAATACCCG 57.932 47.619 0.07 0.00 37.67 5.28
2359 5479 4.993705 TCACCTACCTTTGAGGAACAAT 57.006 40.909 0.07 0.00 37.67 2.71
2364 5484 4.349636 TCATGTTTCACCTACCTTTGAGGA 59.650 41.667 0.07 0.00 37.67 3.71
2365 5485 4.651778 TCATGTTTCACCTACCTTTGAGG 58.348 43.478 0.00 0.00 42.49 3.86
2366 5486 6.824305 ATTCATGTTTCACCTACCTTTGAG 57.176 37.500 0.00 0.00 0.00 3.02
2367 5487 8.877864 AATATTCATGTTTCACCTACCTTTGA 57.122 30.769 0.00 0.00 0.00 2.69
2369 5489 9.975218 AGTAATATTCATGTTTCACCTACCTTT 57.025 29.630 0.00 0.00 0.00 3.11
2389 5509 9.877222 TCATGTTCCACCTATCTTCTAGTAATA 57.123 33.333 0.00 0.00 0.00 0.98
2390 5510 8.783660 TCATGTTCCACCTATCTTCTAGTAAT 57.216 34.615 0.00 0.00 0.00 1.89
2391 5511 8.603898 TTCATGTTCCACCTATCTTCTAGTAA 57.396 34.615 0.00 0.00 0.00 2.24
2392 5512 8.783660 ATTCATGTTCCACCTATCTTCTAGTA 57.216 34.615 0.00 0.00 0.00 1.82
2393 5513 7.682787 ATTCATGTTCCACCTATCTTCTAGT 57.317 36.000 0.00 0.00 0.00 2.57
2394 5514 9.650539 CATATTCATGTTCCACCTATCTTCTAG 57.349 37.037 0.00 0.00 0.00 2.43
2395 5515 9.379770 TCATATTCATGTTCCACCTATCTTCTA 57.620 33.333 0.00 0.00 33.57 2.10
2396 5516 8.153550 GTCATATTCATGTTCCACCTATCTTCT 58.846 37.037 0.00 0.00 33.57 2.85
2401 5521 7.000472 CCAAGTCATATTCATGTTCCACCTAT 59.000 38.462 0.00 0.00 33.57 2.57
2442 5590 4.814294 GCGGTCACGGTGGCCTAG 62.814 72.222 27.54 15.26 40.79 3.02
2452 5600 4.717313 GTGGGGGAAGGCGGTCAC 62.717 72.222 0.00 0.00 0.00 3.67
2459 5607 1.076727 GTTTCTGGGTGGGGGAAGG 59.923 63.158 0.00 0.00 0.00 3.46
2473 5621 0.307760 CTGTGTCAGCGGTTGGTTTC 59.692 55.000 0.00 0.00 0.00 2.78
2484 5632 2.636830 CCTCCATTAAGCCTGTGTCAG 58.363 52.381 0.00 0.00 0.00 3.51
2491 5639 1.700042 CCTCCGCCTCCATTAAGCCT 61.700 60.000 0.00 0.00 0.00 4.58
2497 5645 0.398318 GAATAGCCTCCGCCTCCATT 59.602 55.000 0.00 0.00 34.57 3.16
2498 5646 0.472734 AGAATAGCCTCCGCCTCCAT 60.473 55.000 0.00 0.00 34.57 3.41
2499 5647 0.691078 AAGAATAGCCTCCGCCTCCA 60.691 55.000 0.00 0.00 34.57 3.86
2545 5701 2.954684 TAAGCTCACAGGGCCACGG 61.955 63.158 6.18 0.00 0.00 4.94
2546 5702 1.741770 GTAAGCTCACAGGGCCACG 60.742 63.158 6.18 0.00 0.00 4.94
2547 5703 0.674895 CAGTAAGCTCACAGGGCCAC 60.675 60.000 6.18 0.00 0.00 5.01
2548 5704 1.679311 CAGTAAGCTCACAGGGCCA 59.321 57.895 6.18 0.00 0.00 5.36
2577 5733 8.991243 ATTTACATTTCCAATGACATGTCTTG 57.009 30.769 25.55 23.10 40.25 3.02
2633 5871 4.101430 ACCCAAACAGAATTCATGCAAACT 59.899 37.500 8.44 0.00 0.00 2.66
2655 5893 4.742438 TGTCAGAGCGGATTTTAACAAC 57.258 40.909 0.00 0.00 0.00 3.32
2667 5905 0.587768 TGCACAAACATGTCAGAGCG 59.412 50.000 0.00 0.00 0.00 5.03
2675 5913 1.198767 CAACCGTGTGCACAAACATG 58.801 50.000 23.59 14.66 36.92 3.21
2685 5923 3.430862 CGGCCATCCAACCGTGTG 61.431 66.667 2.24 0.00 44.46 3.82
2702 5940 1.451028 GGACACTGATGCAGGAGCC 60.451 63.158 0.00 0.00 41.13 4.70
2715 5953 2.048127 GGAGCAGTCCACGGACAC 60.048 66.667 18.21 9.69 46.76 3.67
2716 5954 3.311110 GGGAGCAGTCCACGGACA 61.311 66.667 18.21 0.00 46.07 4.02
2717 5955 4.083862 GGGGAGCAGTCCACGGAC 62.084 72.222 8.23 8.23 46.07 4.79
2722 5960 0.982852 CTATGGTGGGGAGCAGTCCA 60.983 60.000 0.00 0.00 46.07 4.02
2723 5961 0.983378 ACTATGGTGGGGAGCAGTCC 60.983 60.000 0.00 0.00 43.05 3.85
2761 5999 6.691255 TTTACTATTAGGCCCACCGAATAT 57.309 37.500 0.00 0.00 41.14 1.28
2766 6004 3.876341 TGTTTTACTATTAGGCCCACCG 58.124 45.455 0.00 0.00 42.76 4.94
2911 6151 2.767445 CGTATCCGTCCGCTGACCA 61.767 63.158 2.40 0.00 38.32 4.02
2929 6169 8.076178 CCAATGTTAATCCCTAAATCGAACATC 58.924 37.037 0.00 0.00 35.56 3.06
2930 6170 7.777910 TCCAATGTTAATCCCTAAATCGAACAT 59.222 33.333 0.00 0.00 37.58 2.71
2934 6174 7.131907 TCTCCAATGTTAATCCCTAAATCGA 57.868 36.000 0.00 0.00 0.00 3.59
2941 6181 3.437052 GGGCATCTCCAATGTTAATCCCT 60.437 47.826 0.00 0.00 36.21 4.20
2943 6183 3.837355 AGGGCATCTCCAATGTTAATCC 58.163 45.455 0.00 0.00 36.21 3.01
2944 6184 6.959639 TTAAGGGCATCTCCAATGTTAATC 57.040 37.500 0.00 0.00 36.21 1.75
2947 6187 6.012337 TGATTAAGGGCATCTCCAATGTTA 57.988 37.500 0.00 0.00 36.21 2.41
2967 6207 6.069381 AGGGGAAGCTTCACTTTATAACTGAT 60.069 38.462 27.18 0.00 39.29 2.90
2979 6219 1.000771 GGGGAAGGGGAAGCTTCAC 60.001 63.158 27.02 24.20 32.60 3.18


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

AutoCloner maintained by Alex Coulton.