Multiple sequence alignment - TraesCS7D01G328000

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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 TraesCS7D01G328000 chr7D 100.000 6848 0 0 1 6848 419373128 419366281 0.000000e+00 12646.0
1 TraesCS7D01G328000 chr7D 87.273 220 23 4 1 215 1140726 1140945 5.300000e-61 246.0
2 TraesCS7D01G328000 chr7D 84.404 218 31 3 6391 6606 547271404 547271188 1.940000e-50 211.0
3 TraesCS7D01G328000 chr7A 94.995 2198 93 13 509 2700 514017278 514019464 0.000000e+00 3434.0
4 TraesCS7D01G328000 chr7A 93.360 1777 75 14 5094 6832 514023678 514025449 0.000000e+00 2588.0
5 TraesCS7D01G328000 chr7A 92.852 1385 63 12 2692 4045 514020380 514021759 0.000000e+00 1977.0
6 TraesCS7D01G328000 chr7A 96.641 1042 31 4 4064 5102 514022271 514023311 0.000000e+00 1727.0
7 TraesCS7D01G328000 chr7A 86.364 66 9 0 3033 3098 63110119 63110184 9.530000e-09 73.1
8 TraesCS7D01G328000 chr7B 85.523 1720 167 43 647 2313 435118739 435117049 0.000000e+00 1722.0
9 TraesCS7D01G328000 chr7B 86.588 932 103 12 3452 4378 435115617 435114703 0.000000e+00 1009.0
10 TraesCS7D01G328000 chr7B 88.904 748 60 15 4380 5108 435114641 435113898 0.000000e+00 900.0
11 TraesCS7D01G328000 chr7B 89.086 733 63 10 5553 6278 435112927 435112205 0.000000e+00 894.0
12 TraesCS7D01G328000 chr7B 85.123 894 98 15 2317 3195 435117010 435116137 0.000000e+00 881.0
13 TraesCS7D01G328000 chr7B 88.484 521 40 16 1 505 598900444 598900960 4.540000e-171 612.0
14 TraesCS7D01G328000 chr7B 86.486 407 34 14 1 390 204062953 204062551 1.770000e-115 427.0
15 TraesCS7D01G328000 chr7B 81.000 600 61 23 5101 5666 435113528 435112948 1.770000e-115 427.0
16 TraesCS7D01G328000 chr7B 87.085 271 31 3 6391 6660 469067951 469067684 3.100000e-78 303.0
17 TraesCS7D01G328000 chr7B 91.406 128 11 0 6270 6397 435112185 435112058 7.060000e-40 176.0
18 TraesCS7D01G328000 chr4D 92.368 511 23 9 1 505 109915978 109915478 0.000000e+00 713.0
19 TraesCS7D01G328000 chr4D 83.406 458 41 16 6402 6826 417989673 417990128 6.440000e-105 392.0
20 TraesCS7D01G328000 chr4D 81.124 445 54 8 6397 6812 191296085 191296528 5.120000e-86 329.0
21 TraesCS7D01G328000 chr4D 77.778 243 39 13 6395 6629 230920326 230920561 1.200000e-27 135.0
22 TraesCS7D01G328000 chrUn 86.732 407 33 14 1 390 391493848 391493446 3.790000e-117 433.0
23 TraesCS7D01G328000 chrUn 86.486 407 34 14 1 390 391404011 391403609 1.770000e-115 427.0
24 TraesCS7D01G328000 chrUn 96.386 83 1 2 424 505 391403608 391403527 1.200000e-27 135.0
25 TraesCS7D01G328000 chrUn 96.386 83 1 2 424 505 391493445 391493364 1.200000e-27 135.0
26 TraesCS7D01G328000 chr1A 80.934 514 74 17 1 503 318507596 318507096 1.080000e-102 385.0
27 TraesCS7D01G328000 chr4A 80.658 517 77 21 1 503 39586190 39585683 5.010000e-101 379.0
28 TraesCS7D01G328000 chr4A 81.412 425 49 15 6419 6814 212757469 212757892 3.080000e-83 320.0
29 TraesCS7D01G328000 chr4B 80.984 447 51 18 6397 6814 212090722 212091163 2.380000e-84 324.0
30 TraesCS7D01G328000 chr4B 78.782 509 81 23 17 511 624514958 624515453 3.990000e-82 316.0
31 TraesCS7D01G328000 chr4B 80.313 447 58 17 6397 6814 212148516 212148961 1.850000e-80 311.0
32 TraesCS7D01G328000 chr6B 77.778 513 85 21 1 500 714259085 714259581 8.690000e-74 289.0
33 TraesCS7D01G328000 chr2B 84.252 254 36 4 6395 6646 258697106 258696855 1.910000e-60 244.0
34 TraesCS7D01G328000 chr2B 87.500 64 6 2 3030 3092 108160361 108160299 9.530000e-09 73.1
35 TraesCS7D01G328000 chr2D 77.313 454 67 16 6395 6814 360552480 360552931 1.150000e-57 235.0
36 TraesCS7D01G328000 chr2D 77.865 384 46 17 6395 6744 293174205 293174583 1.160000e-47 202.0
37 TraesCS7D01G328000 chr3D 84.956 226 34 0 6435 6660 217557195 217557420 5.340000e-56 230.0
38 TraesCS7D01G328000 chr2A 77.042 453 68 18 6397 6814 431104731 431105182 1.920000e-55 228.0
39 TraesCS7D01G328000 chr2A 81.457 151 19 5 6673 6817 620663793 620663646 1.560000e-21 115.0
40 TraesCS7D01G328000 chr1D 77.243 457 60 23 6395 6811 96481051 96481503 1.920000e-55 228.0
41 TraesCS7D01G328000 chr3A 83.019 159 16 9 340 496 553323438 553323587 4.310000e-27 134.0
42 TraesCS7D01G328000 chr5A 100.000 29 0 0 4242 4270 692170246 692170218 3.000000e-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 TraesCS7D01G328000 chr7D 419366281 419373128 6847 True 12646.000000 12646 100.000000 1 6848 1 chr7D.!!$R1 6847
1 TraesCS7D01G328000 chr7A 514017278 514025449 8171 False 2431.500000 3434 94.462000 509 6832 4 chr7A.!!$F2 6323
2 TraesCS7D01G328000 chr7B 435112058 435118739 6681 True 858.428571 1722 86.804286 647 6397 7 chr7B.!!$R3 5750
3 TraesCS7D01G328000 chr7B 598900444 598900960 516 False 612.000000 612 88.484000 1 505 1 chr7B.!!$F1 504
4 TraesCS7D01G328000 chr4D 109915478 109915978 500 True 713.000000 713 92.368000 1 505 1 chr4D.!!$R1 504
5 TraesCS7D01G328000 chr1A 318507096 318507596 500 True 385.000000 385 80.934000 1 503 1 chr1A.!!$R1 502
6 TraesCS7D01G328000 chr4A 39585683 39586190 507 True 379.000000 379 80.658000 1 503 1 chr4A.!!$R1 502

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
534 619 0.458716 GCGCCAGGACTTCTAGTCAC 60.459 60.000 0.00 0.00 46.79 3.67 F
1633 1762 0.249155 GGTTCGCATCATGCAATGGG 60.249 55.000 11.00 8.71 46.73 4.00 F
1713 1842 1.402720 GCCATGGTGTTGGACAAATCG 60.403 52.381 14.67 0.00 39.25 3.34 F
2582 2764 2.870175 ACAATTTCAACGTCCCATCCA 58.130 42.857 0.00 0.00 0.00 3.41 F
3768 5272 0.179018 AGTCACAAGTGCCCCTTCAC 60.179 55.000 0.00 0.00 37.24 3.18 F
4023 5531 2.166870 TGCCAGCCTCTAAATTGCATTG 59.833 45.455 0.00 0.00 0.00 2.82 F
4209 6211 2.543777 AGTACACATTTGCGACACCT 57.456 45.000 0.00 0.00 0.00 4.00 F
5214 7696 5.507149 CGTCCAAGACATCTCTATCAAGGAG 60.507 48.000 0.00 0.00 32.09 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2315 2485 0.388907 ATGTGCTCGCATTGGTTTGC 60.389 50.000 0.00 0.0 39.29 3.68 R
2604 2786 1.542030 ACTACTCTCTCTGGTTGTGCG 59.458 52.381 0.00 0.0 0.00 5.34 R
3633 5137 0.039035 TCCTTGTTATGTGGGTGGCC 59.961 55.000 0.00 0.0 0.00 5.36 R
4071 6072 0.664761 GCCATGGGTTCATGTCATCG 59.335 55.000 15.13 0.0 46.96 3.84 R
4729 6805 2.772568 TGAACACGCAAAAGGACATG 57.227 45.000 0.00 0.0 0.00 3.21 R
5191 7673 5.596361 TCTCCTTGATAGAGATGTCTTGGAC 59.404 44.000 0.00 0.0 35.46 4.02 R
5348 7831 7.039270 ACCAACATTTTTCTAAAAGTGTCCAC 58.961 34.615 14.28 0.0 44.62 4.02 R
6264 8929 1.299014 CATTGGTTTGTGTGCGCGT 60.299 52.632 8.43 0.0 0.00 6.01 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
85 128 9.883142 AGTTCATCAAATTTGGTAAAAAGTTCA 57.117 25.926 17.90 0.00 0.00 3.18
148 211 6.362686 TCATCGATTTGAAAAAGTTCGTCAG 58.637 36.000 0.00 0.00 36.46 3.51
255 332 9.894439 AAAAATGAAAATAGAAAAACGAACACG 57.106 25.926 0.00 0.00 0.00 4.49
315 398 4.470334 AAGTTTGCATGTCAGTTTTGGT 57.530 36.364 0.00 0.00 0.00 3.67
365 448 0.525029 GGACGTCCCGAGTTCGATTC 60.525 60.000 24.75 0.00 43.02 2.52
505 590 0.534203 GGGCGCCGAATAGGATTCAA 60.534 55.000 22.54 0.00 45.00 2.69
506 591 0.586802 GGCGCCGAATAGGATTCAAC 59.413 55.000 12.58 0.00 45.00 3.18
507 592 1.295792 GCGCCGAATAGGATTCAACA 58.704 50.000 0.00 0.00 45.00 3.33
531 616 2.359967 GGGCGCCAGGACTTCTAGT 61.360 63.158 30.85 0.00 0.00 2.57
533 618 1.605058 GGCGCCAGGACTTCTAGTCA 61.605 60.000 24.80 0.00 46.79 3.41
534 619 0.458716 GCGCCAGGACTTCTAGTCAC 60.459 60.000 0.00 0.00 46.79 3.67
541 626 2.952978 AGGACTTCTAGTCACCGCATAG 59.047 50.000 8.89 0.00 46.79 2.23
580 665 1.318576 CGGTGGGCTCTTTTGTCTTT 58.681 50.000 0.00 0.00 0.00 2.52
582 667 1.341209 GGTGGGCTCTTTTGTCTTTGG 59.659 52.381 0.00 0.00 0.00 3.28
583 668 1.341209 GTGGGCTCTTTTGTCTTTGGG 59.659 52.381 0.00 0.00 0.00 4.12
584 669 1.063266 TGGGCTCTTTTGTCTTTGGGT 60.063 47.619 0.00 0.00 0.00 4.51
589 674 3.490933 GCTCTTTTGTCTTTGGGTTGACC 60.491 47.826 0.00 0.00 40.81 4.02
592 677 1.104577 TTGTCTTTGGGTTGACCGCC 61.105 55.000 0.00 0.00 44.64 6.13
619 704 4.209307 TGGTAGATCAACACGGCAATTA 57.791 40.909 0.00 0.00 0.00 1.40
623 708 6.183360 TGGTAGATCAACACGGCAATTATTTC 60.183 38.462 0.00 0.00 0.00 2.17
644 729 5.917541 TCCGTCTCTGTAAACATTTGAAC 57.082 39.130 0.00 0.00 0.00 3.18
735 824 6.037098 AGCTAATTAGACTCTTGCTTACACG 58.963 40.000 16.85 0.00 0.00 4.49
746 835 4.560136 TTGCTTACACGCAATCAAAAGA 57.440 36.364 0.00 0.00 44.30 2.52
781 870 3.315470 AGAGCGTCGCTACTGATATTCAA 59.685 43.478 21.77 0.00 39.88 2.69
953 1046 3.973425 AGGGCACAATTTCTAGCTCATT 58.027 40.909 0.00 0.00 0.00 2.57
1344 1442 1.377725 AGGCGGATGCACTTTGAGG 60.378 57.895 0.00 0.00 45.35 3.86
1417 1519 9.502145 GTTTTGTTTTCTCCATTCAAAATTTCC 57.498 29.630 0.00 0.00 39.18 3.13
1492 1594 8.608844 AAATTATAGGAACCGATGATTCTGTC 57.391 34.615 4.95 0.00 0.00 3.51
1510 1612 5.590818 TCTGTCCAATCCCTAAGTTAGACT 58.409 41.667 11.66 0.00 0.00 3.24
1582 1711 9.855021 TTAAGAAAGAAGAAAACAAAGGTCTTG 57.145 29.630 0.00 0.00 31.80 3.02
1633 1762 0.249155 GGTTCGCATCATGCAATGGG 60.249 55.000 11.00 8.71 46.73 4.00
1677 1806 1.494960 GAAGGGAGATGAGGTCAGCT 58.505 55.000 0.00 0.00 46.40 4.24
1713 1842 1.402720 GCCATGGTGTTGGACAAATCG 60.403 52.381 14.67 0.00 39.25 3.34
1743 1872 3.543626 TGTGGTAGGGGTGGGGGA 61.544 66.667 0.00 0.00 0.00 4.81
1768 1897 6.112058 AGGAGTTAGCAAAGATGATGAACTC 58.888 40.000 0.00 0.00 36.25 3.01
1944 2074 5.437191 AGTTATAGGGTATATGCAAGGGC 57.563 43.478 0.00 0.00 41.68 5.19
2005 2135 5.009510 TGGATCATTTTCATTGTTCACACGT 59.990 36.000 0.00 0.00 0.00 4.49
2012 2142 8.750416 CATTTTCATTGTTCACACGTGATTTAA 58.250 29.630 25.01 10.65 39.64 1.52
2073 2204 3.889520 TTGGTTTGGCTTACGGTTTTT 57.110 38.095 0.00 0.00 0.00 1.94
2315 2485 7.826252 CCCATGTACTAAGGAAATGATCTATGG 59.174 40.741 0.00 0.00 0.00 2.74
2358 2528 7.837202 TCATACACCACTAAATAAGGAAACG 57.163 36.000 0.00 0.00 0.00 3.60
2382 2552 6.606768 GCTATGGCAAGAAGACAATATTAGC 58.393 40.000 0.00 0.00 39.98 3.09
2413 2583 9.740710 AAATAGTTATTGCCAGAAAAGAGTAGT 57.259 29.630 0.00 0.00 0.00 2.73
2582 2764 2.870175 ACAATTTCAACGTCCCATCCA 58.130 42.857 0.00 0.00 0.00 3.41
2604 2786 6.665680 TCCATAGCTAAGAGGGTTGATATCTC 59.334 42.308 3.98 0.00 0.00 2.75
2617 2799 3.023832 TGATATCTCGCACAACCAGAGA 58.976 45.455 3.98 0.00 44.00 3.10
2712 3818 8.793592 CATAAAATAAGGAAATACCCTAGCCAC 58.206 37.037 0.00 0.00 40.05 5.01
2830 3936 5.148651 TGAACTAAGGAAACACTCTAGCC 57.851 43.478 0.00 0.00 0.00 3.93
2915 4023 8.496916 ACTTAACTTAAGAAGGAAACACCCTAA 58.503 33.333 10.09 0.00 39.09 2.69
2927 4035 5.068591 GGAAACACCCTAACAACAAGACAAT 59.931 40.000 0.00 0.00 0.00 2.71
3068 4177 8.112016 TGTACTATCTTAGTGATGCCTCATAC 57.888 38.462 0.00 0.00 39.81 2.39
3098 4207 3.517500 GGTGAGGTGGAAGAGAGAGAAAT 59.482 47.826 0.00 0.00 0.00 2.17
3126 4241 3.513515 AGAGGTGTTTCTCTTAGCTCAGG 59.486 47.826 0.00 0.00 40.93 3.86
3179 4294 4.307443 TGCCTACAATCTACGAGATGTG 57.693 45.455 0.00 0.00 34.65 3.21
3372 4505 6.704289 ACATTCAAGTCACCATGATAATGG 57.296 37.500 7.65 7.65 46.92 3.16
3386 4519 6.344500 CATGATAATGGCTCTATAGGACACC 58.656 44.000 0.00 0.00 0.00 4.16
3479 4983 6.530913 CATACATGATGGAGTAAGGAAACG 57.469 41.667 0.00 0.00 31.20 3.60
3481 4985 3.270027 CATGATGGAGTAAGGAAACGCA 58.730 45.455 0.00 0.00 0.00 5.24
3501 5005 5.163385 ACGCAAATAGCCACCTACATAACTA 60.163 40.000 0.00 0.00 41.38 2.24
3547 5051 7.961283 GCAAATAGTTGTACAAAGCTAGTTACC 59.039 37.037 10.51 5.50 37.06 2.85
3572 5076 6.480285 GTTGTTCGTCAAAAAGCTAGTTACA 58.520 36.000 0.00 0.00 37.81 2.41
3592 5096 9.871238 AGTTACAGTTAGAACAATATGGTGTAG 57.129 33.333 0.00 0.00 0.00 2.74
3611 5115 6.051717 GTGTAGAACTAATGATGAGGCACAT 58.948 40.000 0.00 0.00 42.47 3.21
3629 5133 4.276926 GCACATCATGGAATAAGGGAACTC 59.723 45.833 0.00 0.00 42.68 3.01
3633 5137 5.116084 TCATGGAATAAGGGAACTCTTGG 57.884 43.478 0.00 0.00 42.68 3.61
3768 5272 0.179018 AGTCACAAGTGCCCCTTCAC 60.179 55.000 0.00 0.00 37.24 3.18
3990 5498 6.313658 GGGAACATAAATCTTCAAATGGCAAC 59.686 38.462 0.00 0.00 0.00 4.17
4003 5511 6.148948 TCAAATGGCAACGAACTTTTCTATG 58.851 36.000 0.00 0.00 42.51 2.23
4023 5531 2.166870 TGCCAGCCTCTAAATTGCATTG 59.833 45.455 0.00 0.00 0.00 2.82
4113 6114 9.585099 TGGCTCATTTGACAAATAAATTGATAC 57.415 29.630 12.98 4.87 41.85 2.24
4209 6211 2.543777 AGTACACATTTGCGACACCT 57.456 45.000 0.00 0.00 0.00 4.00
4628 6703 7.431249 ACATGAAGCATTTTATGTGGATGATC 58.569 34.615 0.00 0.00 40.69 2.92
4729 6805 9.424319 TGGAGCTTACTAATATCGATTCAATTC 57.576 33.333 1.71 0.00 0.00 2.17
4984 7063 6.018994 GTGATCATCCGTTGAAGGTATGTAAC 60.019 42.308 0.00 0.00 38.03 2.50
5061 7141 6.259167 GCCGTTCTACCAACAAATATGTATCA 59.741 38.462 0.00 0.00 39.40 2.15
5214 7696 5.507149 CGTCCAAGACATCTCTATCAAGGAG 60.507 48.000 0.00 0.00 32.09 3.69
5245 7727 7.764141 TCATTTCTCATTTGAAGTCAATGGA 57.236 32.000 0.00 0.00 35.55 3.41
5534 8034 3.810310 TGTGTATGTGTGTGTGAGTGA 57.190 42.857 0.00 0.00 0.00 3.41
5535 8035 4.130286 TGTGTATGTGTGTGTGAGTGAA 57.870 40.909 0.00 0.00 0.00 3.18
5536 8036 4.119136 TGTGTATGTGTGTGTGAGTGAAG 58.881 43.478 0.00 0.00 0.00 3.02
5537 8037 4.119862 GTGTATGTGTGTGTGAGTGAAGT 58.880 43.478 0.00 0.00 0.00 3.01
5772 8432 8.477419 AAAATGAGATCTTTTACCTTGTTGGA 57.523 30.769 0.00 0.00 39.71 3.53
5933 8593 0.981183 AATTGACCGAGTGCCCTACA 59.019 50.000 0.00 0.00 0.00 2.74
6199 8864 5.442391 GCTAATGGGTGTGGGTCTATAAAA 58.558 41.667 0.00 0.00 0.00 1.52
6277 8970 0.305313 TAAAGGACGCGCACACAAAC 59.695 50.000 5.73 0.00 0.00 2.93
6403 9096 5.465724 AGTTGATACTTCTTTTGTCACGACC 59.534 40.000 0.00 0.00 0.00 4.79
6406 9099 0.865769 CTTCTTTTGTCACGACCCGG 59.134 55.000 0.00 0.00 0.00 5.73
6412 9105 4.065281 GTCACGACCCGGTCCCTG 62.065 72.222 12.16 7.66 0.00 4.45
6449 9142 0.319555 TGCGCTTACTGTGTCAGTCC 60.320 55.000 9.73 0.00 41.21 3.85
6457 9150 0.174389 CTGTGTCAGTCCCTGGATCG 59.826 60.000 0.00 0.00 31.51 3.69
6460 9153 2.307768 GTGTCAGTCCCTGGATCGATA 58.692 52.381 0.00 0.00 31.51 2.92
6472 9165 2.102925 TGGATCGATAGCTGACATGCAA 59.897 45.455 0.00 0.00 34.99 4.08
6474 9167 3.186001 GGATCGATAGCTGACATGCAAAG 59.814 47.826 0.00 0.00 34.99 2.77
6479 9172 2.211250 AGCTGACATGCAAAGTGGAT 57.789 45.000 0.00 0.00 34.99 3.41
6523 9216 8.668353 ACATCATGTGTCAAGTATTACATTGTC 58.332 33.333 0.00 0.00 35.77 3.18
6528 9221 6.533723 TGTGTCAAGTATTACATTGTCGATCC 59.466 38.462 0.00 0.00 0.00 3.36
6537 9230 3.149196 ACATTGTCGATCCAGTGCTTTT 58.851 40.909 0.00 0.00 0.00 2.27
6538 9231 3.569701 ACATTGTCGATCCAGTGCTTTTT 59.430 39.130 0.00 0.00 0.00 1.94
6579 9272 5.386958 TCGTGGGCTAGCTTACAATATAG 57.613 43.478 15.72 1.09 0.00 1.31
6587 9280 6.820656 GGCTAGCTTACAATATAGTCATGCAT 59.179 38.462 15.72 0.00 0.00 3.96
6589 9282 6.957984 AGCTTACAATATAGTCATGCATCG 57.042 37.500 0.00 0.00 0.00 3.84
6631 9324 0.957395 GTGTCCATGCACTCACAGGG 60.957 60.000 0.00 0.00 42.89 4.45
6648 9341 3.381908 ACAGGGAGAAGTTGAGTATAGCG 59.618 47.826 0.00 0.00 0.00 4.26
6660 9353 6.323225 AGTTGAGTATAGCGTTGTAACCCTAT 59.677 38.462 7.02 7.02 35.06 2.57
6670 9363 3.627395 TGTAACCCTATGTCCTGCAAG 57.373 47.619 0.00 0.00 0.00 4.01
6702 9395 2.086869 CAGCCACAAGGGTCAATACAG 58.913 52.381 0.00 0.00 45.83 2.74
6723 9416 4.157289 CAGAATGTATTGGCAAGCTTCACT 59.843 41.667 5.96 0.00 0.00 3.41
6789 9482 0.919981 TTTTGCTTTGCGCGAAACAG 59.080 45.000 12.10 7.50 44.94 3.16
6814 9507 7.513781 AGTTTCCCTACCTTTTTAGTAGTGGTA 59.486 37.037 0.00 0.00 36.30 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
505 590 3.706373 CCTGGCGCCCACTAGTGT 61.706 66.667 26.77 0.00 0.00 3.55
506 591 3.390521 TCCTGGCGCCCACTAGTG 61.391 66.667 26.77 16.34 0.00 2.74
507 592 3.391382 GTCCTGGCGCCCACTAGT 61.391 66.667 26.77 0.00 0.00 2.57
580 665 3.505790 AAGCATGGCGGTCAACCCA 62.506 57.895 0.00 0.00 35.21 4.51
582 667 2.568090 CAAGCATGGCGGTCAACC 59.432 61.111 0.00 0.00 0.00 3.77
583 668 2.568090 CCAAGCATGGCGGTCAAC 59.432 61.111 0.00 0.00 40.58 3.18
592 677 2.352651 CCGTGTTGATCTACCAAGCATG 59.647 50.000 4.82 0.00 0.00 4.06
619 704 7.360361 GTTCAAATGTTTACAGAGACGGAAAT 58.640 34.615 0.00 0.00 0.00 2.17
623 708 4.446385 TCGTTCAAATGTTTACAGAGACGG 59.554 41.667 0.00 0.00 0.00 4.79
644 729 7.579450 GCAATCTCGTAAAGCTTTATTAAGTCG 59.421 37.037 21.28 17.64 33.74 4.18
688 774 0.951558 TTCCGTTGAGGCAAAAGAGC 59.048 50.000 0.00 0.00 40.77 4.09
735 824 4.051237 GTGGAGGTTTGTCTTTTGATTGC 58.949 43.478 0.00 0.00 0.00 3.56
746 835 1.006102 CGCTCTCGTGGAGGTTTGT 60.006 57.895 9.39 0.00 42.08 2.83
781 870 3.065925 GGTTGCGAGTCCGTTACTACTAT 59.934 47.826 0.00 0.00 39.07 2.12
953 1046 7.456902 ACAGTACTCTTAACTAGGGGATTGAAA 59.543 37.037 0.00 0.00 0.00 2.69
1029 1122 1.138863 ATGGCCTCCAGATCCCATCC 61.139 60.000 3.32 0.00 36.75 3.51
1074 1167 1.394618 GCACGTACTCCATCTCCTCT 58.605 55.000 0.00 0.00 0.00 3.69
1259 1352 3.832615 ACCGACAACTACCAAGAACTT 57.167 42.857 0.00 0.00 0.00 2.66
1260 1353 3.832615 AACCGACAACTACCAAGAACT 57.167 42.857 0.00 0.00 0.00 3.01
1327 1425 3.056313 GCCTCAAAGTGCATCCGCC 62.056 63.158 0.00 0.00 37.32 6.13
1344 1442 3.767673 TCACCCCATATAGGTCGATTAGC 59.232 47.826 0.00 0.00 34.56 3.09
1492 1594 7.764901 GTCACTTTAGTCTAACTTAGGGATTGG 59.235 40.741 0.00 0.00 28.48 3.16
1677 1806 2.502142 TGGCACTCTCGACCTAAGTA 57.498 50.000 0.00 0.00 0.00 2.24
1743 1872 6.479884 AGTTCATCATCTTTGCTAACTCCTT 58.520 36.000 0.00 0.00 0.00 3.36
1768 1897 1.625616 CTAAAGTCCTACCGTGCACG 58.374 55.000 31.77 31.77 39.44 5.34
1944 2074 4.344104 ACCAAATACATCCAACTTCCCAG 58.656 43.478 0.00 0.00 0.00 4.45
2012 2142 9.791801 AGGTTAATTCATTTTTATTTTGGTGCT 57.208 25.926 0.00 0.00 0.00 4.40
2062 2192 8.188139 ACAATGGATAAGCATAAAAACCGTAAG 58.812 33.333 0.00 0.00 0.00 2.34
2073 2204 6.003950 GCCCTCTTAACAATGGATAAGCATA 58.996 40.000 4.00 0.00 31.48 3.14
2285 2420 4.538490 TCATTTCCTTAGTACATGGGTGGT 59.462 41.667 0.00 0.00 0.00 4.16
2315 2485 0.388907 ATGTGCTCGCATTGGTTTGC 60.389 50.000 0.00 0.00 39.29 3.68
2327 2497 7.041780 CCTTATTTAGTGGTGTATGATGTGCTC 60.042 40.741 0.00 0.00 0.00 4.26
2358 2528 6.205464 TGCTAATATTGTCTTCTTGCCATAGC 59.795 38.462 0.00 0.00 40.48 2.97
2382 2552 9.912634 TCTTTTCTGGCAATAACTATTTTTCTG 57.087 29.630 0.00 0.00 0.00 3.02
2413 2583 2.296792 CACACCACCATCAGTTTGTCA 58.703 47.619 0.00 0.00 0.00 3.58
2552 2734 6.313164 GGGACGTTGAAATTGTAAACCAAAAA 59.687 34.615 0.00 0.00 36.44 1.94
2582 2764 5.126384 GCGAGATATCAACCCTCTTAGCTAT 59.874 44.000 5.32 0.00 0.00 2.97
2604 2786 1.542030 ACTACTCTCTCTGGTTGTGCG 59.458 52.381 0.00 0.00 0.00 5.34
2617 2799 1.763968 TCCACATGCGCTACTACTCT 58.236 50.000 9.73 0.00 0.00 3.24
2712 3818 3.044235 TGCATGCACCTATTATCTCGG 57.956 47.619 18.46 0.00 0.00 4.63
3056 4165 4.996758 CACCAATTATCGTATGAGGCATCA 59.003 41.667 2.36 2.36 40.50 3.07
3068 4177 4.122776 CTCTTCCACCTCACCAATTATCG 58.877 47.826 0.00 0.00 0.00 2.92
3238 4353 8.924511 AGTGCTATGGTGCTATTAATGTTTAT 57.075 30.769 0.00 0.00 0.00 1.40
3243 4358 7.657354 TGTCTTAGTGCTATGGTGCTATTAATG 59.343 37.037 0.00 0.00 0.00 1.90
3372 4505 2.596904 TTTGCGGTGTCCTATAGAGC 57.403 50.000 0.00 0.00 0.00 4.09
3427 4566 6.093633 GGGACTGTCACTTTACCATAACATTC 59.906 42.308 10.38 0.00 0.00 2.67
3429 4568 5.250774 AGGGACTGTCACTTTACCATAACAT 59.749 40.000 6.77 0.00 37.18 2.71
3430 4569 4.595781 AGGGACTGTCACTTTACCATAACA 59.404 41.667 6.77 0.00 37.18 2.41
3479 4983 6.289064 ACTAGTTATGTAGGTGGCTATTTGC 58.711 40.000 0.00 0.00 41.94 3.68
3481 4985 9.998106 CATTACTAGTTATGTAGGTGGCTATTT 57.002 33.333 12.68 0.00 0.00 1.40
3501 5005 2.089980 CTTGGCAGCAAGAGCATTACT 58.910 47.619 0.00 0.00 45.49 2.24
3611 5115 4.079787 CCCAAGAGTTCCCTTATTCCATGA 60.080 45.833 0.00 0.00 0.00 3.07
3633 5137 0.039035 TCCTTGTTATGTGGGTGGCC 59.961 55.000 0.00 0.00 0.00 5.36
3736 5240 3.579151 ACTTGTGACTAGGAGAGAAACCC 59.421 47.826 0.00 0.00 0.00 4.11
3768 5272 5.286558 TCAAAACAAAGAACGCCTAAAAACG 59.713 36.000 0.00 0.00 0.00 3.60
3840 5345 5.669164 ACTAACAACCAAACCACACAAAT 57.331 34.783 0.00 0.00 0.00 2.32
3990 5498 2.352960 GAGGCTGGCATAGAAAAGTTCG 59.647 50.000 3.38 0.00 34.02 3.95
4003 5511 2.428171 TCAATGCAATTTAGAGGCTGGC 59.572 45.455 0.00 0.00 31.22 4.85
4060 6061 6.094325 GGGTTCATGTCATCGTGGTAAAAATA 59.906 38.462 0.00 0.00 0.00 1.40
4062 6063 4.216687 GGGTTCATGTCATCGTGGTAAAAA 59.783 41.667 0.00 0.00 0.00 1.94
4071 6072 0.664761 GCCATGGGTTCATGTCATCG 59.335 55.000 15.13 0.00 46.96 3.84
4178 6180 7.589587 TCGCAAATGTGTACTAATCAAAACAAG 59.410 33.333 0.00 0.00 0.00 3.16
4324 6326 5.935789 CCAATCCAAATGAGAGTGCAATTTT 59.064 36.000 0.00 0.00 0.00 1.82
4338 6340 6.608405 TCATATGAGAAGTTGCCAATCCAAAT 59.392 34.615 0.00 0.00 0.00 2.32
4729 6805 2.772568 TGAACACGCAAAAGGACATG 57.227 45.000 0.00 0.00 0.00 3.21
4970 7049 8.736244 GGCTCAAAATTAGTTACATACCTTCAA 58.264 33.333 0.00 0.00 0.00 2.69
4984 7063 7.338800 ACATACATTGGAGGCTCAAAATTAG 57.661 36.000 17.69 6.08 0.00 1.73
5040 7120 9.337396 GGTGATGATACATATTTGTTGGTAGAA 57.663 33.333 0.00 0.00 37.28 2.10
5081 7161 6.828785 ACTAAGTTTATAAGGCCCAAGATGTG 59.171 38.462 0.00 0.00 0.00 3.21
5191 7673 5.596361 TCTCCTTGATAGAGATGTCTTGGAC 59.404 44.000 0.00 0.00 35.46 4.02
5233 7715 7.864108 ATCGAATTGTATTCCATTGACTTCA 57.136 32.000 0.00 0.00 0.00 3.02
5348 7831 7.039270 ACCAACATTTTTCTAAAAGTGTCCAC 58.961 34.615 14.28 0.00 44.62 4.02
5519 8019 7.877612 TGATAAATACTTCACTCACACACACAT 59.122 33.333 0.00 0.00 0.00 3.21
5530 8030 7.913789 TGTGGGTACTTGATAAATACTTCACT 58.086 34.615 0.00 0.00 31.11 3.41
5535 8035 9.793259 CCAATATGTGGGTACTTGATAAATACT 57.207 33.333 0.00 0.00 44.64 2.12
5746 8406 8.923270 TCCAACAAGGTAAAAGATCTCATTTTT 58.077 29.630 0.00 0.00 39.02 1.94
6243 8908 7.675637 GCGCGTCCTTTAGTTTCTTACATAAAT 60.676 37.037 8.43 0.00 0.00 1.40
6264 8929 1.299014 CATTGGTTTGTGTGCGCGT 60.299 52.632 8.43 0.00 0.00 6.01
6277 8970 9.466497 AGTATTGTAGCATATTAATCCCATTGG 57.534 33.333 0.00 0.00 0.00 3.16
6412 9105 1.406903 CAGAGATTTGGGCCCCATTC 58.593 55.000 22.27 14.69 31.53 2.67
6449 9142 2.930023 GCATGTCAGCTATCGATCCAGG 60.930 54.545 0.00 0.00 0.00 4.45
6457 9150 3.273434 TCCACTTTGCATGTCAGCTATC 58.727 45.455 0.00 0.00 34.99 2.08
6460 9153 1.816835 CATCCACTTTGCATGTCAGCT 59.183 47.619 0.00 0.00 34.99 4.24
6472 9165 4.023980 TCTCGGTACTTCATCATCCACTT 58.976 43.478 0.00 0.00 0.00 3.16
6474 9167 4.386867 TTCTCGGTACTTCATCATCCAC 57.613 45.455 0.00 0.00 0.00 4.02
6479 9172 6.709018 TGATGTATTCTCGGTACTTCATCA 57.291 37.500 0.00 0.00 38.27 3.07
6486 9179 5.588240 TGACACATGATGTATTCTCGGTAC 58.412 41.667 0.00 0.00 43.56 3.34
6523 9216 6.021596 GTGTGTATTAAAAAGCACTGGATCG 58.978 40.000 0.00 0.00 33.44 3.69
6528 9221 7.435068 AGTAGGTGTGTATTAAAAAGCACTG 57.565 36.000 0.00 0.00 33.44 3.66
6537 9230 6.405065 CCACGAGCTAAGTAGGTGTGTATTAA 60.405 42.308 13.79 0.00 34.31 1.40
6538 9231 5.066893 CCACGAGCTAAGTAGGTGTGTATTA 59.933 44.000 13.79 0.00 34.31 0.98
6579 9272 5.417811 AGAATGATATCTCCGATGCATGAC 58.582 41.667 2.46 0.00 0.00 3.06
6587 9280 6.207614 CCACAAGACTAGAATGATATCTCCGA 59.792 42.308 3.98 0.00 0.00 4.55
6589 9282 7.151308 CACCACAAGACTAGAATGATATCTCC 58.849 42.308 3.98 0.00 0.00 3.71
6631 9324 6.253083 GGTTACAACGCTATACTCAACTTCTC 59.747 42.308 0.00 0.00 0.00 2.87
6646 9339 2.277084 CAGGACATAGGGTTACAACGC 58.723 52.381 1.17 1.17 41.65 4.84
6648 9341 3.343941 TGCAGGACATAGGGTTACAAC 57.656 47.619 0.00 0.00 0.00 3.32
6660 9353 3.261580 CAACGTATCATCTTGCAGGACA 58.738 45.455 0.00 0.00 0.00 4.02
6670 9363 1.368641 TGTGGCTGCAACGTATCATC 58.631 50.000 2.19 0.00 0.00 2.92
6702 9395 4.708726 AGTGAAGCTTGCCAATACATTC 57.291 40.909 2.10 0.00 0.00 2.67
6723 9416 3.386402 CCTTTTCCAACAAGCCAAACCTA 59.614 43.478 0.00 0.00 0.00 3.08
6789 9482 6.537355 ACCACTACTAAAAAGGTAGGGAAAC 58.463 40.000 4.90 0.00 41.66 2.78


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

AutoCloner maintained by Alex Coulton.