Multiple sequence alignment - TraesCS1D01G081200

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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 TraesCS1D01G081200 chr1D 100.000 2947 0 0 1 2947 63542583 63545529 0.000000e+00 5443.0
1 TraesCS1D01G081200 chr1D 84.967 153 18 4 1 150 470827581 470827431 1.830000e-32 150.0
2 TraesCS1D01G081200 chr1D 80.488 82 13 3 61 140 445055386 445055466 3.170000e-05 60.2
3 TraesCS1D01G081200 chr1B 85.889 1311 90 30 1204 2445 101591503 101590219 0.000000e+00 1308.0
4 TraesCS1D01G081200 chr1B 92.713 741 36 7 1421 2157 101519655 101520381 0.000000e+00 1053.0
5 TraesCS1D01G081200 chr1B 90.030 672 32 21 621 1288 101518891 101519531 0.000000e+00 837.0
6 TraesCS1D01G081200 chr1B 90.256 626 57 3 1 622 101516449 101517074 0.000000e+00 815.0
7 TraesCS1D01G081200 chr1B 89.619 578 34 12 631 1198 101592160 101591599 0.000000e+00 712.0
8 TraesCS1D01G081200 chr1B 87.179 195 23 2 2754 2947 101522140 101522333 1.370000e-53 220.0
9 TraesCS1D01G081200 chr1B 77.922 308 48 12 2140 2444 101522437 101522727 1.090000e-39 174.0
10 TraesCS1D01G081200 chr1B 100.000 92 0 0 2782 2873 101589442 101589351 1.400000e-38 171.0
11 TraesCS1D01G081200 chr1B 78.519 135 26 3 17 150 29928295 29928427 5.230000e-13 86.1
12 TraesCS1D01G081200 chr1A 90.762 801 49 13 1420 2212 61576286 61577069 0.000000e+00 1046.0
13 TraesCS1D01G081200 chr1A 89.987 799 45 14 621 1408 61575471 61576245 0.000000e+00 1000.0
14 TraesCS1D01G081200 chr1A 88.523 819 73 9 1421 2237 61714141 61714940 0.000000e+00 972.0
15 TraesCS1D01G081200 chr1A 83.238 698 72 26 737 1407 61713409 61714088 1.510000e-167 599.0
16 TraesCS1D01G081200 chr1A 76.880 359 62 17 1565 1914 99018974 99019320 1.800000e-42 183.0
17 TraesCS1D01G081200 chr6A 90.954 409 35 2 148 554 466325241 466325649 1.540000e-152 549.0
18 TraesCS1D01G081200 chr7A 89.387 424 42 3 149 569 534403557 534403134 5.590000e-147 531.0
19 TraesCS1D01G081200 chr7A 89.100 422 44 2 149 568 5486261 5486682 9.360000e-145 523.0
20 TraesCS1D01G081200 chr7A 88.810 420 46 1 149 567 35007411 35007830 5.630000e-142 514.0
21 TraesCS1D01G081200 chr7A 76.279 215 40 7 2490 2700 666149433 666149226 1.440000e-18 104.0
22 TraesCS1D01G081200 chr2A 88.836 421 44 3 146 563 350776538 350776958 5.630000e-142 514.0
23 TraesCS1D01G081200 chr2A 89.024 410 44 1 149 557 414294300 414294709 9.420000e-140 507.0
24 TraesCS1D01G081200 chr4A 88.810 420 43 4 149 565 30740587 30741005 2.030000e-141 512.0
25 TraesCS1D01G081200 chr5B 88.471 425 45 4 149 570 611998811 611999234 7.290000e-141 510.0
26 TraesCS1D01G081200 chr5B 80.435 414 61 17 1484 1884 588156413 588156007 6.170000e-77 298.0
27 TraesCS1D01G081200 chr6D 78.598 799 134 25 1435 2225 6982900 6983669 7.340000e-136 494.0
28 TraesCS1D01G081200 chr6D 81.620 321 30 14 989 1288 6982165 6982477 3.800000e-59 239.0
29 TraesCS1D01G081200 chr5D 80.435 414 61 17 1484 1884 480154987 480154581 6.170000e-77 298.0
30 TraesCS1D01G081200 chr5D 87.342 158 17 1 999 1153 371872972 371872815 8.390000e-41 178.0
31 TraesCS1D01G081200 chr5D 95.238 42 2 0 109 150 413447245 413447286 1.900000e-07 67.6
32 TraesCS1D01G081200 chr5A 80.435 414 61 16 1484 1884 598637742 598637336 6.170000e-77 298.0
33 TraesCS1D01G081200 chr5A 87.742 155 19 0 1001 1155 616878691 616878845 6.490000e-42 182.0
34 TraesCS1D01G081200 chr2D 78.657 417 59 21 944 1341 597939475 597939880 1.750000e-62 250.0
35 TraesCS1D01G081200 chr2D 78.657 417 59 21 944 1341 641960740 641961145 1.750000e-62 250.0
36 TraesCS1D01G081200 chr3B 78.832 137 25 4 15 150 33095537 33095670 4.050000e-14 89.8


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 TraesCS1D01G081200 chr1D 63542583 63545529 2946 False 5443.000000 5443 100.0000 1 2947 1 chr1D.!!$F1 2946
1 TraesCS1D01G081200 chr1B 101589351 101592160 2809 True 730.333333 1308 91.8360 631 2873 3 chr1B.!!$R1 2242
2 TraesCS1D01G081200 chr1B 101516449 101522727 6278 False 619.800000 1053 87.6200 1 2947 5 chr1B.!!$F2 2946
3 TraesCS1D01G081200 chr1A 61575471 61577069 1598 False 1023.000000 1046 90.3745 621 2212 2 chr1A.!!$F2 1591
4 TraesCS1D01G081200 chr1A 61713409 61714940 1531 False 785.500000 972 85.8805 737 2237 2 chr1A.!!$F3 1500
5 TraesCS1D01G081200 chr6D 6982165 6983669 1504 False 366.500000 494 80.1090 989 2225 2 chr6D.!!$F1 1236

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
312 316 0.618968 ACAGGGATGGGGTGAGAGTC 60.619 60.0 0.0 0.0 0.0 3.36 F
930 2769 0.941542 GCTACACACCGCTCAAACAA 59.058 50.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1474 3798 0.784778 GCGTGACTCTGAAAACGGAG 59.215 55.0 0.00 0.0 36.57 4.63 R
2725 6357 0.032130 ACAGACGCGAACACTCACAT 59.968 50.0 15.93 0.0 0.00 3.21 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
28 29 4.747529 AAACCCGTCGCCGCCTAC 62.748 66.667 0.00 0.00 0.00 3.18
39 40 4.849329 CGCCTACGCCGACTGGAC 62.849 72.222 0.00 0.00 37.49 4.02
46 47 3.056328 GCCGACTGGACTTTGCCC 61.056 66.667 0.00 0.00 37.49 5.36
177 180 2.508300 TGGTTGGGGGTAATTAGAGCTC 59.492 50.000 5.27 5.27 0.00 4.09
180 183 0.685660 GGGGGTAATTAGAGCTCGGG 59.314 60.000 8.37 0.00 0.00 5.14
201 204 3.877508 GGAATGAGAATTGAAGGGGTACG 59.122 47.826 0.00 0.00 0.00 3.67
215 218 6.155565 TGAAGGGGTACGAGATTTCAAATCTA 59.844 38.462 12.83 0.00 0.00 1.98
218 221 6.992715 AGGGGTACGAGATTTCAAATCTATTG 59.007 38.462 12.83 8.48 0.00 1.90
232 235 7.647827 TCAAATCTATTGTTTGATTAGGGGGA 58.352 34.615 0.00 0.00 39.81 4.81
247 250 3.417010 AGGGGGATTGGGAGTTCATAAT 58.583 45.455 0.00 0.00 0.00 1.28
255 258 7.234355 GGATTGGGAGTTCATAATGGAATAGT 58.766 38.462 0.00 0.00 0.00 2.12
284 287 0.679505 TGAGACTCCAACTCCAACCG 59.320 55.000 0.00 0.00 33.95 4.44
298 302 4.763279 ACTCCAACCGTTTTATTAACAGGG 59.237 41.667 0.83 0.83 0.00 4.45
300 304 5.572252 TCCAACCGTTTTATTAACAGGGAT 58.428 37.500 8.01 0.00 0.00 3.85
307 311 5.265989 GTTTTATTAACAGGGATGGGGTGA 58.734 41.667 0.00 0.00 0.00 4.02
308 312 4.788925 TTATTAACAGGGATGGGGTGAG 57.211 45.455 0.00 0.00 0.00 3.51
312 316 0.618968 ACAGGGATGGGGTGAGAGTC 60.619 60.000 0.00 0.00 0.00 3.36
332 336 6.204882 AGAGTCGGAAGGAAATTGTTTTAGTG 59.795 38.462 0.00 0.00 0.00 2.74
399 403 4.640647 GTCTATTCCCTTGTCAATTCCCAC 59.359 45.833 0.00 0.00 0.00 4.61
409 414 3.118956 TGTCAATTCCCACAACCAAACAC 60.119 43.478 0.00 0.00 0.00 3.32
430 435 5.010719 ACACGAGAATACAGTTTCTCCTCAA 59.989 40.000 14.70 0.00 45.80 3.02
442 447 3.735237 TCTCCTCAAACTCTCACACAC 57.265 47.619 0.00 0.00 0.00 3.82
449 454 5.297776 CCTCAAACTCTCACACACAATTTCT 59.702 40.000 0.00 0.00 0.00 2.52
455 460 8.627208 AACTCTCACACACAATTTCTATCATT 57.373 30.769 0.00 0.00 0.00 2.57
458 463 6.873605 TCTCACACACAATTTCTATCATTCGT 59.126 34.615 0.00 0.00 0.00 3.85
461 466 6.957635 CACACACAATTTCTATCATTCGTCAG 59.042 38.462 0.00 0.00 0.00 3.51
468 473 2.959030 TCTATCATTCGTCAGACAGGGG 59.041 50.000 0.41 0.00 0.00 4.79
472 477 3.371034 TCATTCGTCAGACAGGGGATTA 58.629 45.455 0.41 0.00 0.00 1.75
473 478 3.384789 TCATTCGTCAGACAGGGGATTAG 59.615 47.826 0.41 0.00 0.00 1.73
482 487 7.290813 GTCAGACAGGGGATTAGGAATAAAAT 58.709 38.462 0.00 0.00 0.00 1.82
487 492 8.712228 ACAGGGGATTAGGAATAAAATGATTC 57.288 34.615 0.00 0.00 35.45 2.52
497 502 8.186709 AGGAATAAAATGATTCATCCCATGTC 57.813 34.615 0.00 0.00 37.53 3.06
506 511 7.140522 TGATTCATCCCATGTCTAATCTCAA 57.859 36.000 0.00 0.00 0.00 3.02
515 520 7.345653 TCCCATGTCTAATCTCAATACAACTCT 59.654 37.037 0.00 0.00 0.00 3.24
516 521 7.655328 CCCATGTCTAATCTCAATACAACTCTC 59.345 40.741 0.00 0.00 0.00 3.20
568 573 2.322081 GCCAAACGCGCTGTAAGGA 61.322 57.895 5.73 0.00 0.00 3.36
616 621 1.278637 GACCAACACGAAAGCACGG 59.721 57.895 0.00 0.00 37.61 4.94
658 2484 6.053632 TGAAAAGAATGCTGATCTGGACTA 57.946 37.500 1.46 0.00 0.00 2.59
707 2533 2.227149 GGAAAACTTTAATCGTGGCCGT 59.773 45.455 0.00 0.00 35.01 5.68
744 2570 1.187567 GGAAAGCAATGGCACCCACT 61.188 55.000 0.00 0.00 44.61 4.00
753 2579 3.414700 GCACCCACTTCGCTGACG 61.415 66.667 0.00 0.00 42.01 4.35
861 2698 2.498056 CCACCAAGGCACCAACCAC 61.498 63.158 0.00 0.00 0.00 4.16
914 2753 1.405526 GGAGGAGTTTGCGTCATGCTA 60.406 52.381 0.00 0.00 46.63 3.49
930 2769 0.941542 GCTACACACCGCTCAAACAA 59.058 50.000 0.00 0.00 0.00 2.83
937 2776 1.132262 CACCGCTCAAACAAACACAGT 59.868 47.619 0.00 0.00 0.00 3.55
938 2777 1.400494 ACCGCTCAAACAAACACAGTC 59.600 47.619 0.00 0.00 0.00 3.51
946 2785 3.829886 AACAAACACAGTCACACACAG 57.170 42.857 0.00 0.00 0.00 3.66
962 2818 1.079127 CAGACACACACCCCGATCC 60.079 63.158 0.00 0.00 0.00 3.36
970 2826 2.041819 ACCCCGATCCCTCACTCC 60.042 66.667 0.00 0.00 0.00 3.85
998 2862 3.501062 GTGTACTAGCAACCAAGGGAAAC 59.499 47.826 0.00 0.00 0.00 2.78
1180 3048 1.743996 GACCACTCAAATCCTCTGGC 58.256 55.000 0.00 0.00 0.00 4.85
1213 3189 3.631250 ACTTGTGTTTGGGTTCTGATGT 58.369 40.909 0.00 0.00 0.00 3.06
1216 3192 5.067283 ACTTGTGTTTGGGTTCTGATGTAAC 59.933 40.000 0.00 0.00 0.00 2.50
1288 3264 2.223852 GGGATCTGCTTCTCTTCGGTAC 60.224 54.545 0.00 0.00 0.00 3.34
1289 3265 2.691011 GGATCTGCTTCTCTTCGGTACT 59.309 50.000 0.00 0.00 0.00 2.73
1290 3266 3.884091 GGATCTGCTTCTCTTCGGTACTA 59.116 47.826 0.00 0.00 0.00 1.82
1303 3290 6.688578 TCTTCGGTACTATGATTAATCTGCC 58.311 40.000 16.24 8.00 0.00 4.85
1313 3300 9.247861 ACTATGATTAATCTGCCTTTTTCAGTT 57.752 29.630 16.24 0.00 33.48 3.16
1379 3373 2.618709 GTTTCTCGGCATCTTAATGGGG 59.381 50.000 0.00 0.00 33.19 4.96
1382 3376 1.152777 CGGCATCTTAATGGGGCCA 60.153 57.895 4.39 0.00 44.82 5.36
1398 3392 2.612672 GGGCCAACTAGTAAAGCGAATC 59.387 50.000 4.39 0.00 0.00 2.52
1413 3407 3.008485 AGCGAATCCTTCCTTTCTGTTCT 59.992 43.478 0.00 0.00 0.00 3.01
1432 3470 2.125106 GTGGGTGGATGCTCCGTC 60.125 66.667 0.00 0.00 40.17 4.79
1470 3794 9.086336 TCTCAAATTCTCAAAAACATTGTGTTC 57.914 29.630 0.00 0.00 40.14 3.18
1474 3798 6.645700 TTCTCAAAAACATTGTGTTCTTGC 57.354 33.333 4.46 0.00 40.14 4.01
1477 3801 5.108517 TCAAAAACATTGTGTTCTTGCTCC 58.891 37.500 4.46 0.00 40.14 4.70
1685 4009 4.966787 GGCCTGCCGACCAACCAA 62.967 66.667 0.00 0.00 0.00 3.67
1760 4084 3.414700 CGCCTGTCCAAGCACGAC 61.415 66.667 0.00 0.00 0.00 4.34
1962 4286 1.230324 GTGATTTGCTAGGCGGGATC 58.770 55.000 0.00 0.00 0.00 3.36
2005 4329 0.610174 ATCACTGATCTGTGTGGCGT 59.390 50.000 26.16 10.49 38.90 5.68
2006 4330 0.392706 TCACTGATCTGTGTGGCGTT 59.607 50.000 26.16 0.00 38.90 4.84
2007 4331 1.202639 TCACTGATCTGTGTGGCGTTT 60.203 47.619 26.16 0.00 38.90 3.60
2008 4332 1.603802 CACTGATCTGTGTGGCGTTTT 59.396 47.619 21.12 0.00 33.61 2.43
2009 4333 1.873591 ACTGATCTGTGTGGCGTTTTC 59.126 47.619 4.21 0.00 0.00 2.29
2157 4522 6.738649 GTCTTCGTAATGCTTTCAGATTTGTC 59.261 38.462 0.00 0.00 0.00 3.18
2283 5595 1.165907 TGGGCAAAGCACTGAACGAG 61.166 55.000 0.00 0.00 30.56 4.18
2286 5598 1.334149 GGCAAAGCACTGAACGAGAAC 60.334 52.381 0.00 0.00 0.00 3.01
2292 5604 6.255215 CAAAGCACTGAACGAGAACTAAAAA 58.745 36.000 0.00 0.00 0.00 1.94
2418 5730 4.074627 TCCGATGTAAAAATATGGCGGA 57.925 40.909 0.00 0.00 43.49 5.54
2426 5738 8.603242 ATGTAAAAATATGGCGGAGTACTTAG 57.397 34.615 0.00 0.00 0.00 2.18
2458 5847 3.945981 TGGTGTAGCACGAGTTTGATA 57.054 42.857 0.00 0.00 34.83 2.15
2468 5857 6.851609 AGCACGAGTTTGATAAATGCAAATA 58.148 32.000 0.00 0.00 37.54 1.40
2482 5871 5.646467 ATGCAAATAATTCAAGCAATCGC 57.354 34.783 0.00 0.00 38.85 4.58
2483 5872 4.492611 TGCAAATAATTCAAGCAATCGCA 58.507 34.783 0.00 0.00 42.27 5.10
2484 5873 4.928020 TGCAAATAATTCAAGCAATCGCAA 59.072 33.333 0.00 0.00 42.27 4.85
2485 5874 5.407691 TGCAAATAATTCAAGCAATCGCAAA 59.592 32.000 0.00 0.00 42.27 3.68
2486 5875 5.729424 GCAAATAATTCAAGCAATCGCAAAC 59.271 36.000 0.00 0.00 42.27 2.93
2496 5885 2.157474 GCAATCGCAAACCAAACCAATC 59.843 45.455 0.00 0.00 38.36 2.67
2513 5903 5.964958 CCAATCTGTGGTTGAATGTTAGT 57.035 39.130 0.00 0.00 43.20 2.24
2516 5906 6.094048 CCAATCTGTGGTTGAATGTTAGTAGG 59.906 42.308 0.00 0.00 43.20 3.18
2519 5909 5.305902 TCTGTGGTTGAATGTTAGTAGGACA 59.694 40.000 0.00 0.00 0.00 4.02
2522 5912 6.268158 TGTGGTTGAATGTTAGTAGGACAGTA 59.732 38.462 0.00 0.00 0.00 2.74
2531 5921 9.798994 AATGTTAGTAGGACAGTAGTATTTTCG 57.201 33.333 0.00 0.00 0.00 3.46
2536 5926 2.934553 GGACAGTAGTATTTTCGGCCAC 59.065 50.000 2.24 0.00 0.00 5.01
2537 5927 2.934553 GACAGTAGTATTTTCGGCCACC 59.065 50.000 2.24 0.00 0.00 4.61
2538 5928 2.303600 ACAGTAGTATTTTCGGCCACCA 59.696 45.455 2.24 0.00 0.00 4.17
2539 5929 2.936498 CAGTAGTATTTTCGGCCACCAG 59.064 50.000 2.24 0.00 0.00 4.00
2540 5930 1.669265 GTAGTATTTTCGGCCACCAGC 59.331 52.381 2.24 0.00 42.60 4.85
2564 5954 6.073440 GCGTTCAAGTCCTAAATTTGACACTA 60.073 38.462 10.33 0.00 33.89 2.74
2565 5955 7.519328 GCGTTCAAGTCCTAAATTTGACACTAA 60.519 37.037 10.33 0.72 33.89 2.24
2570 5960 8.299570 CAAGTCCTAAATTTGACACTAATGCTT 58.700 33.333 10.33 0.00 33.89 3.91
2603 6235 7.422465 TGAATTTATTTTATGCCTTCCTGCT 57.578 32.000 0.00 0.00 0.00 4.24
2604 6236 8.532186 TGAATTTATTTTATGCCTTCCTGCTA 57.468 30.769 0.00 0.00 0.00 3.49
2605 6237 8.413229 TGAATTTATTTTATGCCTTCCTGCTAC 58.587 33.333 0.00 0.00 0.00 3.58
2606 6238 8.539117 AATTTATTTTATGCCTTCCTGCTACT 57.461 30.769 0.00 0.00 0.00 2.57
2607 6239 6.942532 TTATTTTATGCCTTCCTGCTACTG 57.057 37.500 0.00 0.00 0.00 2.74
2608 6240 2.332063 TTATGCCTTCCTGCTACTGC 57.668 50.000 0.00 0.00 40.20 4.40
2609 6241 1.500474 TATGCCTTCCTGCTACTGCT 58.500 50.000 0.00 0.00 40.48 4.24
2614 6246 4.416516 TGCCTTCCTGCTACTGCTATATA 58.583 43.478 0.00 0.00 40.48 0.86
2619 6251 5.624344 TCCTGCTACTGCTATATACGTTC 57.376 43.478 0.00 0.00 40.48 3.95
2624 6256 4.617645 GCTACTGCTATATACGTTCAGTGC 59.382 45.833 0.00 0.00 38.33 4.40
2651 6283 5.348997 GGAGACGTTTCCATCAACTAGAAAG 59.651 44.000 19.71 0.00 37.20 2.62
2661 6293 5.278463 CCATCAACTAGAAAGGTGTTTGTGG 60.278 44.000 0.00 0.00 41.53 4.17
2669 6301 2.335316 AGGTGTTTGTGGCGACTTTA 57.665 45.000 0.00 0.00 0.00 1.85
2698 6330 5.009710 TCTCAAAATAGTGTGTCGTCTCAGT 59.990 40.000 0.00 0.00 0.00 3.41
2702 6334 4.848562 ATAGTGTGTCGTCTCAGTCAAA 57.151 40.909 0.00 0.00 0.00 2.69
2707 6339 3.997681 TGTGTCGTCTCAGTCAAACAAAA 59.002 39.130 0.00 0.00 0.00 2.44
2717 6349 7.862372 GTCTCAGTCAAACAAAAATGCTCATAA 59.138 33.333 0.00 0.00 0.00 1.90
2718 6350 8.412456 TCTCAGTCAAACAAAAATGCTCATAAA 58.588 29.630 0.00 0.00 0.00 1.40
2723 6355 9.423061 GTCAAACAAAAATGCTCATAAAGGTAT 57.577 29.630 0.00 0.00 0.00 2.73
2736 6392 8.552034 GCTCATAAAGGTATAATGTGAGTGTTC 58.448 37.037 0.00 0.00 35.32 3.18
2737 6393 8.642908 TCATAAAGGTATAATGTGAGTGTTCG 57.357 34.615 0.00 0.00 0.00 3.95
2751 6407 0.664224 TGTTCGCGTCTGTACTGTGA 59.336 50.000 5.77 0.00 0.00 3.58
2756 6412 4.163458 TCGCGTCTGTACTGTGATAAAA 57.837 40.909 5.77 0.00 0.00 1.52
2758 6414 4.619760 TCGCGTCTGTACTGTGATAAAAAG 59.380 41.667 5.77 0.00 0.00 2.27
2779 6463 6.628644 AAGACTCCAAAATTACTAGCCTCT 57.371 37.500 0.00 0.00 0.00 3.69
2780 6464 7.735326 AAGACTCCAAAATTACTAGCCTCTA 57.265 36.000 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.423154 GGCAAAGTCCAGTCGGCG 61.423 66.667 0.00 0.00 0.00 6.46
30 31 2.742372 CGGGCAAAGTCCAGTCGG 60.742 66.667 0.00 0.00 0.00 4.79
75 76 1.775934 AACTTTCCCCCGTCTCACCC 61.776 60.000 0.00 0.00 0.00 4.61
76 77 0.605589 CAACTTTCCCCCGTCTCACC 60.606 60.000 0.00 0.00 0.00 4.02
78 79 0.765135 TCCAACTTTCCCCCGTCTCA 60.765 55.000 0.00 0.00 0.00 3.27
82 83 3.167414 CCTCCAACTTTCCCCCGT 58.833 61.111 0.00 0.00 0.00 5.28
89 90 0.741221 GATCGAGCGCCTCCAACTTT 60.741 55.000 2.29 0.00 0.00 2.66
90 91 1.153549 GATCGAGCGCCTCCAACTT 60.154 57.895 2.29 0.00 0.00 2.66
177 180 2.301346 CCCCTTCAATTCTCATTCCCG 58.699 52.381 0.00 0.00 0.00 5.14
180 183 4.766375 TCGTACCCCTTCAATTCTCATTC 58.234 43.478 0.00 0.00 0.00 2.67
215 218 4.015730 TCCCAATCCCCCTAATCAAACAAT 60.016 41.667 0.00 0.00 0.00 2.71
218 221 3.052869 ACTCCCAATCCCCCTAATCAAAC 60.053 47.826 0.00 0.00 0.00 2.93
232 235 7.815383 TGACTATTCCATTATGAACTCCCAAT 58.185 34.615 0.00 0.00 0.00 3.16
247 250 5.429762 AGTCTCAAATCCCATGACTATTCCA 59.570 40.000 0.00 0.00 36.39 3.53
255 258 3.588842 AGTTGGAGTCTCAAATCCCATGA 59.411 43.478 1.47 0.00 34.47 3.07
284 287 5.265989 TCACCCCATCCCTGTTAATAAAAC 58.734 41.667 0.00 0.00 0.00 2.43
298 302 0.461961 CTTCCGACTCTCACCCCATC 59.538 60.000 0.00 0.00 0.00 3.51
300 304 1.609501 CCTTCCGACTCTCACCCCA 60.610 63.158 0.00 0.00 0.00 4.96
307 311 6.204882 CACTAAAACAATTTCCTTCCGACTCT 59.795 38.462 0.00 0.00 0.00 3.24
308 312 6.204108 TCACTAAAACAATTTCCTTCCGACTC 59.796 38.462 0.00 0.00 0.00 3.36
312 316 6.017440 TCACTCACTAAAACAATTTCCTTCCG 60.017 38.462 0.00 0.00 0.00 4.30
332 336 8.831550 GTTATGATGAAGGGTTAAGATTCACTC 58.168 37.037 0.40 1.88 35.89 3.51
363 367 9.981460 ACAAGGGAATAGACAAGAGAAATTAAT 57.019 29.630 0.00 0.00 0.00 1.40
372 376 6.180472 GGAATTGACAAGGGAATAGACAAGA 58.820 40.000 0.00 0.00 0.00 3.02
384 388 2.315176 TGGTTGTGGGAATTGACAAGG 58.685 47.619 0.00 0.00 32.81 3.61
388 392 3.453424 GTGTTTGGTTGTGGGAATTGAC 58.547 45.455 0.00 0.00 0.00 3.18
399 403 5.418310 AACTGTATTCTCGTGTTTGGTTG 57.582 39.130 0.00 0.00 0.00 3.77
430 435 8.627208 AATGATAGAAATTGTGTGTGAGAGTT 57.373 30.769 0.00 0.00 0.00 3.01
442 447 6.018425 CCCTGTCTGACGAATGATAGAAATTG 60.018 42.308 2.98 0.00 0.00 2.32
449 454 3.026707 TCCCCTGTCTGACGAATGATA 57.973 47.619 2.98 0.00 0.00 2.15
455 460 1.286849 TCCTAATCCCCTGTCTGACGA 59.713 52.381 2.98 0.00 0.00 4.20
458 463 6.901615 TTTTATTCCTAATCCCCTGTCTGA 57.098 37.500 0.00 0.00 0.00 3.27
461 466 8.712228 AATCATTTTATTCCTAATCCCCTGTC 57.288 34.615 0.00 0.00 0.00 3.51
472 477 8.008922 AGACATGGGATGAATCATTTTATTCCT 58.991 33.333 0.00 0.00 35.40 3.36
473 478 8.186709 AGACATGGGATGAATCATTTTATTCC 57.813 34.615 0.00 0.00 35.40 3.01
482 487 6.752285 TGAGATTAGACATGGGATGAATCA 57.248 37.500 0.00 0.00 0.00 2.57
487 492 7.935755 AGTTGTATTGAGATTAGACATGGGATG 59.064 37.037 0.00 0.00 0.00 3.51
515 520 9.862149 GAAAGGGGAATGGAAGTTTAATATAGA 57.138 33.333 0.00 0.00 0.00 1.98
516 521 9.868160 AGAAAGGGGAATGGAAGTTTAATATAG 57.132 33.333 0.00 0.00 0.00 1.31
528 533 5.045942 GGCAAAATTTAGAAAGGGGAATGGA 60.046 40.000 0.00 0.00 0.00 3.41
529 534 5.185454 GGCAAAATTTAGAAAGGGGAATGG 58.815 41.667 0.00 0.00 0.00 3.16
568 573 0.973632 TCATGTACTCCAACGCTGGT 59.026 50.000 4.46 0.00 43.97 4.00
616 621 5.934935 TTCATCTTCCTACGGTTTTTGTC 57.065 39.130 0.00 0.00 0.00 3.18
658 2484 0.996583 TACCCGGGCATTCCTTCTTT 59.003 50.000 24.08 0.00 0.00 2.52
685 2511 2.486592 CGGCCACGATTAAAGTTTTCCT 59.513 45.455 2.24 0.00 44.60 3.36
686 2512 2.227149 ACGGCCACGATTAAAGTTTTCC 59.773 45.455 2.24 0.00 44.60 3.13
689 2515 2.619646 ACAACGGCCACGATTAAAGTTT 59.380 40.909 2.24 0.00 44.60 2.66
691 2517 1.886886 ACAACGGCCACGATTAAAGT 58.113 45.000 2.24 0.00 44.60 2.66
692 2518 2.482721 AGAACAACGGCCACGATTAAAG 59.517 45.455 2.24 0.00 44.60 1.85
693 2519 2.496111 AGAACAACGGCCACGATTAAA 58.504 42.857 2.24 0.00 44.60 1.52
694 2520 2.172851 AGAACAACGGCCACGATTAA 57.827 45.000 2.24 0.00 44.60 1.40
695 2521 2.492881 TCTAGAACAACGGCCACGATTA 59.507 45.455 2.24 0.00 44.60 1.75
707 2533 5.049680 GCTTTCCGTGATGTTTCTAGAACAA 60.050 40.000 4.18 0.00 33.42 2.83
753 2579 1.154205 ATTAGTGCATCACGGCTCGC 61.154 55.000 0.00 0.00 39.64 5.03
861 2698 1.743394 GCATCAAAGTTTCCGGGTAGG 59.257 52.381 0.00 0.00 42.97 3.18
914 2753 1.135517 GTGTTTGTTTGAGCGGTGTGT 60.136 47.619 0.00 0.00 0.00 3.72
930 2769 2.289382 TGTGTCTGTGTGTGACTGTGTT 60.289 45.455 0.00 0.00 35.63 3.32
937 2776 0.107897 GGGTGTGTGTCTGTGTGTGA 60.108 55.000 0.00 0.00 0.00 3.58
938 2777 1.095228 GGGGTGTGTGTCTGTGTGTG 61.095 60.000 0.00 0.00 0.00 3.82
946 2785 2.240162 GAGGGATCGGGGTGTGTGTC 62.240 65.000 0.00 0.00 0.00 3.67
962 2818 2.044555 TACACGCGAGGGAGTGAGG 61.045 63.158 15.93 0.00 45.54 3.86
970 2826 0.801067 GGTTGCTAGTACACGCGAGG 60.801 60.000 15.93 7.12 0.00 4.63
998 2862 3.814268 CCTTCACCGGCGCCATTG 61.814 66.667 28.98 22.10 0.00 2.82
1157 3025 0.902531 GAGGATTTGAGTGGTCGGGA 59.097 55.000 0.00 0.00 0.00 5.14
1180 3048 5.334105 CCCAAACACAAGTTGATACGAGAAG 60.334 44.000 10.54 0.00 38.17 2.85
1213 3189 4.808364 GCTGCAAGAAACCAAAACATGTTA 59.192 37.500 12.39 0.00 34.07 2.41
1216 3192 2.545106 GGCTGCAAGAAACCAAAACATG 59.455 45.455 0.50 0.00 34.07 3.21
1290 3266 9.247861 AGTAACTGAAAAAGGCAGATTAATCAT 57.752 29.630 17.56 0.32 36.86 2.45
1303 3290 8.674607 ACAAGGACAAAGTAGTAACTGAAAAAG 58.325 33.333 0.00 0.00 35.62 2.27
1314 3301 9.965824 CATTTATTTTGACAAGGACAAAGTAGT 57.034 29.630 0.00 0.00 38.25 2.73
1315 3302 9.965824 ACATTTATTTTGACAAGGACAAAGTAG 57.034 29.630 0.00 0.00 38.25 2.57
1379 3373 3.532542 AGGATTCGCTTTACTAGTTGGC 58.467 45.455 0.00 2.50 0.00 4.52
1398 3392 2.508526 CCACCAGAACAGAAAGGAAGG 58.491 52.381 0.00 0.00 0.00 3.46
1432 3470 5.942236 TGAGAATTTGAGAGGATGTTTGGAG 59.058 40.000 0.00 0.00 0.00 3.86
1470 3794 2.221981 GTGACTCTGAAAACGGAGCAAG 59.778 50.000 0.00 0.00 33.29 4.01
1474 3798 0.784778 GCGTGACTCTGAAAACGGAG 59.215 55.000 0.00 0.00 36.57 4.63
1477 3801 1.154836 GCGCGTGACTCTGAAAACG 60.155 57.895 8.43 0.00 39.00 3.60
1685 4009 3.048602 CTCTCGTCCACCACCGTT 58.951 61.111 0.00 0.00 0.00 4.44
1760 4084 2.758737 AAGTCCCCGGCGAGGTAG 60.759 66.667 9.30 0.00 38.74 3.18
2005 4329 4.170256 GCGACACCAACAAGAAAAGAAAA 58.830 39.130 0.00 0.00 0.00 2.29
2006 4330 3.729462 CGCGACACCAACAAGAAAAGAAA 60.729 43.478 0.00 0.00 0.00 2.52
2007 4331 2.223157 CGCGACACCAACAAGAAAAGAA 60.223 45.455 0.00 0.00 0.00 2.52
2008 4332 1.329292 CGCGACACCAACAAGAAAAGA 59.671 47.619 0.00 0.00 0.00 2.52
2009 4333 1.329292 TCGCGACACCAACAAGAAAAG 59.671 47.619 3.71 0.00 0.00 2.27
2255 5567 4.040217 TCAGTGCTTTGCCCAAATACAAAT 59.960 37.500 9.45 0.00 35.38 2.32
2261 5573 1.269726 CGTTCAGTGCTTTGCCCAAAT 60.270 47.619 0.00 0.00 0.00 2.32
2264 5576 1.153066 TCGTTCAGTGCTTTGCCCA 60.153 52.632 0.00 0.00 0.00 5.36
2265 5577 0.884704 TCTCGTTCAGTGCTTTGCCC 60.885 55.000 0.00 0.00 0.00 5.36
2341 5653 1.975680 AGTTCCTCAAGTTTAGCCGGA 59.024 47.619 5.05 0.00 0.00 5.14
2342 5654 2.474410 AGTTCCTCAAGTTTAGCCGG 57.526 50.000 0.00 0.00 0.00 6.13
2369 5681 6.715347 ACAGGCTTCTTAAGTGATTTGTTT 57.285 33.333 1.63 0.00 0.00 2.83
2370 5682 6.072452 GCTACAGGCTTCTTAAGTGATTTGTT 60.072 38.462 1.63 0.00 38.06 2.83
2371 5683 5.412904 GCTACAGGCTTCTTAAGTGATTTGT 59.587 40.000 1.63 6.22 38.06 2.83
2372 5684 5.873732 GCTACAGGCTTCTTAAGTGATTTG 58.126 41.667 1.63 0.63 38.06 2.32
2418 5730 7.752638 ACACCAAATTACCCTTTCTAAGTACT 58.247 34.615 0.00 0.00 0.00 2.73
2426 5738 4.379082 CGTGCTACACCAAATTACCCTTTC 60.379 45.833 0.00 0.00 0.00 2.62
2458 5847 6.092396 TGCGATTGCTTGAATTATTTGCATTT 59.908 30.769 6.47 0.00 43.34 2.32
2468 5857 3.383620 TGGTTTGCGATTGCTTGAATT 57.616 38.095 6.47 0.00 43.34 2.17
2496 5885 5.547465 TGTCCTACTAACATTCAACCACAG 58.453 41.667 0.00 0.00 0.00 3.66
2505 5894 9.798994 CGAAAATACTACTGTCCTACTAACATT 57.201 33.333 0.00 0.00 0.00 2.71
2513 5903 4.025360 TGGCCGAAAATACTACTGTCCTA 58.975 43.478 0.00 0.00 0.00 2.94
2516 5906 2.934553 GGTGGCCGAAAATACTACTGTC 59.065 50.000 0.00 0.00 0.00 3.51
2519 5909 2.679930 GCTGGTGGCCGAAAATACTACT 60.680 50.000 0.00 0.00 34.27 2.57
2522 5912 1.024579 CGCTGGTGGCCGAAAATACT 61.025 55.000 0.00 0.00 37.74 2.12
2527 5917 2.975799 GAACGCTGGTGGCCGAAA 60.976 61.111 0.00 0.00 37.74 3.46
2529 5919 4.243008 TTGAACGCTGGTGGCCGA 62.243 61.111 0.00 0.00 37.74 5.54
2530 5920 3.726517 CTTGAACGCTGGTGGCCG 61.727 66.667 0.00 0.00 37.74 6.13
2531 5921 2.594592 ACTTGAACGCTGGTGGCC 60.595 61.111 0.00 0.00 37.74 5.36
2536 5926 4.215399 TCAAATTTAGGACTTGAACGCTGG 59.785 41.667 0.00 0.00 0.00 4.85
2537 5927 5.147162 GTCAAATTTAGGACTTGAACGCTG 58.853 41.667 0.00 0.00 31.21 5.18
2538 5928 4.819630 TGTCAAATTTAGGACTTGAACGCT 59.180 37.500 9.35 0.00 35.11 5.07
2539 5929 4.909880 GTGTCAAATTTAGGACTTGAACGC 59.090 41.667 9.35 0.00 35.11 4.84
2540 5930 6.300354 AGTGTCAAATTTAGGACTTGAACG 57.700 37.500 9.35 0.00 35.11 3.95
2580 6211 8.633561 AGTAGCAGGAAGGCATAAAATAAATTC 58.366 33.333 0.00 0.00 35.83 2.17
2590 6222 1.500474 AGCAGTAGCAGGAAGGCATA 58.500 50.000 0.00 0.00 45.49 3.14
2592 6224 1.500474 ATAGCAGTAGCAGGAAGGCA 58.500 50.000 0.00 0.00 45.49 4.75
2603 6235 4.512571 TCGCACTGAACGTATATAGCAGTA 59.487 41.667 0.00 0.00 37.69 2.74
2604 6236 3.314357 TCGCACTGAACGTATATAGCAGT 59.686 43.478 0.00 0.00 40.17 4.40
2605 6237 3.885358 TCGCACTGAACGTATATAGCAG 58.115 45.455 0.00 0.00 0.00 4.24
2606 6238 3.304458 CCTCGCACTGAACGTATATAGCA 60.304 47.826 0.00 0.00 0.00 3.49
2607 6239 3.058432 TCCTCGCACTGAACGTATATAGC 60.058 47.826 0.00 0.00 0.00 2.97
2608 6240 4.451435 TCTCCTCGCACTGAACGTATATAG 59.549 45.833 0.00 0.00 0.00 1.31
2609 6241 4.212847 GTCTCCTCGCACTGAACGTATATA 59.787 45.833 0.00 0.00 0.00 0.86
2614 6246 1.286260 GTCTCCTCGCACTGAACGT 59.714 57.895 0.00 0.00 0.00 3.99
2619 6251 1.009389 GGAAACGTCTCCTCGCACTG 61.009 60.000 0.00 0.00 32.21 3.66
2624 6256 1.993370 GTTGATGGAAACGTCTCCTCG 59.007 52.381 9.80 0.00 46.90 4.63
2651 6283 2.412325 CGATAAAGTCGCCACAAACACC 60.412 50.000 0.00 0.00 44.33 4.16
2669 6301 5.651530 ACGACACACTATTTTGAGATCGAT 58.348 37.500 0.00 0.00 0.00 3.59
2672 6304 6.093404 TGAGACGACACACTATTTTGAGATC 58.907 40.000 0.00 0.00 0.00 2.75
2684 6316 2.536365 TGTTTGACTGAGACGACACAC 58.464 47.619 0.00 0.00 0.00 3.82
2707 6339 9.060347 CACTCACATTATACCTTTATGAGCATT 57.940 33.333 0.00 0.00 36.41 3.56
2717 6349 3.863424 CGCGAACACTCACATTATACCTT 59.137 43.478 0.00 0.00 0.00 3.50
2718 6350 3.119245 ACGCGAACACTCACATTATACCT 60.119 43.478 15.93 0.00 0.00 3.08
2723 6355 2.287970 ACAGACGCGAACACTCACATTA 60.288 45.455 15.93 0.00 0.00 1.90
2725 6357 0.032130 ACAGACGCGAACACTCACAT 59.968 50.000 15.93 0.00 0.00 3.21
2727 6359 1.050767 GTACAGACGCGAACACTCAC 58.949 55.000 15.93 3.44 0.00 3.51
2736 6392 4.619760 TCTTTTTATCACAGTACAGACGCG 59.380 41.667 3.53 3.53 0.00 6.01
2737 6393 5.634020 AGTCTTTTTATCACAGTACAGACGC 59.366 40.000 0.00 0.00 35.57 5.19
2751 6407 9.755122 AGGCTAGTAATTTTGGAGTCTTTTTAT 57.245 29.630 0.00 0.00 0.00 1.40
2756 6412 6.628644 AGAGGCTAGTAATTTTGGAGTCTT 57.371 37.500 0.00 0.00 0.00 3.01
2758 6414 7.147880 TGTCTAGAGGCTAGTAATTTTGGAGTC 60.148 40.741 0.00 0.00 0.00 3.36
2779 6463 3.664107 GAGGTGTGAAGCAACATGTCTA 58.336 45.455 0.00 0.00 37.23 2.59
2780 6464 2.498167 GAGGTGTGAAGCAACATGTCT 58.502 47.619 0.00 0.00 37.23 3.41


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

AutoCloner maintained by Alex Coulton.