Multiple sequence alignment - TraesCS1D01G370200

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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 TraesCS1D01G370200 chr1D 100.000 3276 0 0 1 3276 448753466 448756741 0.000000e+00 6050.0
1 TraesCS1D01G370200 chr1D 89.424 1371 111 24 1924 3276 448792586 448793940 0.000000e+00 1698.0
2 TraesCS1D01G370200 chr1D 88.862 1221 93 16 1924 3135 448789750 448790936 0.000000e+00 1461.0
3 TraesCS1D01G370200 chr1D 87.024 1287 63 27 674 1926 448786277 448787493 0.000000e+00 1356.0
4 TraesCS1D01G370200 chr1D 85.360 444 50 10 58 500 448785829 448786258 2.320000e-121 446.0
5 TraesCS1D01G370200 chr1D 93.827 81 5 0 1268 1348 449281872 449281952 4.440000e-24 122.0
6 TraesCS1D01G370200 chr1A 95.280 1356 54 10 1924 3276 544392600 544393948 0.000000e+00 2141.0
7 TraesCS1D01G370200 chr1A 89.866 1194 53 27 770 1926 544389000 544390162 0.000000e+00 1472.0
8 TraesCS1D01G370200 chr1A 91.667 84 6 1 1266 1348 544487077 544487160 7.430000e-22 115.0
9 TraesCS1D01G370200 chr1B 88.038 1371 117 32 1924 3276 614507920 614509261 0.000000e+00 1580.0
10 TraesCS1D01G370200 chr1B 88.061 1181 64 28 770 1926 614499517 614500644 0.000000e+00 1328.0
11 TraesCS1D01G370200 chr1B 88.489 834 71 19 2455 3276 614503610 614504430 0.000000e+00 985.0
12 TraesCS1D01G370200 chr1B 89.425 539 44 7 1924 2458 614502825 614503354 0.000000e+00 667.0
13 TraesCS1D01G370200 chr1B 92.593 81 6 0 1268 1348 614942675 614942755 2.070000e-22 117.0
14 TraesCS1D01G370200 chr1B 90.476 42 3 1 20 61 486776093 486776133 2.000000e-03 54.7
15 TraesCS1D01G370200 chr4A 95.312 128 6 0 542 669 519575607 519575480 1.540000e-48 204.0
16 TraesCS1D01G370200 chr4A 93.750 128 7 1 542 668 11366139 11366012 1.200000e-44 191.0
17 TraesCS1D01G370200 chr2D 96.667 120 3 1 543 661 470212096 470212215 7.170000e-47 198.0
18 TraesCS1D01G370200 chr7A 93.284 134 7 2 542 673 563500544 563500411 2.580000e-46 196.0
19 TraesCS1D01G370200 chr7A 97.619 42 1 0 1950 1991 200512562 200512521 4.530000e-09 73.1
20 TraesCS1D01G370200 chr5A 94.574 129 4 2 542 669 244431653 244431527 2.580000e-46 196.0
21 TraesCS1D01G370200 chr5A 93.750 128 6 2 542 668 643571092 643571218 1.200000e-44 191.0
22 TraesCS1D01G370200 chr3A 94.531 128 6 1 542 668 686515117 686514990 2.580000e-46 196.0
23 TraesCS1D01G370200 chr3A 93.846 130 5 3 541 669 9970216 9970343 3.340000e-45 193.0
24 TraesCS1D01G370200 chr3B 93.798 129 5 3 541 668 696703814 696703688 1.200000e-44 191.0
25 TraesCS1D01G370200 chr3D 100.000 35 0 0 33 67 85820305 85820271 7.590000e-07 65.8
26 TraesCS1D01G370200 chr3D 97.368 38 1 0 1950 1987 532172001 532172038 7.590000e-07 65.8
27 TraesCS1D01G370200 chr3D 95.000 40 2 0 33 72 552918070 552918031 2.730000e-06 63.9
28 TraesCS1D01G370200 chr7D 88.462 52 6 0 1950 2001 46993653 46993602 2.730000e-06 63.9
29 TraesCS1D01G370200 chr6D 91.489 47 2 2 1960 2005 464009962 464009917 2.730000e-06 63.9
30 TraesCS1D01G370200 chr5D 94.737 38 2 0 35 72 378950078 378950115 3.530000e-05 60.2
31 TraesCS1D01G370200 chr2B 100.000 29 0 0 47 75 75754201 75754173 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 TraesCS1D01G370200 chr1D 448753466 448756741 3275 False 6050.00 6050 100.00000 1 3276 1 chr1D.!!$F1 3275
1 TraesCS1D01G370200 chr1D 448785829 448793940 8111 False 1240.25 1698 87.66750 58 3276 4 chr1D.!!$F3 3218
2 TraesCS1D01G370200 chr1A 544389000 544393948 4948 False 1806.50 2141 92.57300 770 3276 2 chr1A.!!$F2 2506
3 TraesCS1D01G370200 chr1B 614499517 614509261 9744 False 1140.00 1580 88.50325 770 3276 4 chr1B.!!$F3 2506

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
51 52 0.108756 GGTGAGGCGAGACTACCAAC 60.109 60.0 0.0 0.0 0.0 3.77 F
938 940 0.173255 GCAATGTGTTCCCAATCCGG 59.827 55.0 0.0 0.0 0.0 5.14 F
1078 1082 0.250467 AGGTGTCGTGCAAGCAATCT 60.250 50.0 0.0 0.0 0.0 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1386 1440 0.249155 TTAACCACGGCGATCGATCC 60.249 55.0 21.57 10.69 42.43 3.36 R
1850 1917 0.400594 AGGTTGGGTTGACTGGTAGC 59.599 55.0 0.00 0.00 0.00 3.58 R
2594 5492 1.866853 CTCCCCAAGCAAAGTTCGCC 61.867 60.0 0.00 0.00 0.00 5.54 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
22 23 1.728323 AAAAACCAACATGGAGGGGG 58.272 50.000 2.85 0.60 40.96 5.40
23 24 0.565674 AAAACCAACATGGAGGGGGT 59.434 50.000 2.85 1.18 40.96 4.95
24 25 0.565674 AAACCAACATGGAGGGGGTT 59.434 50.000 2.85 6.75 40.96 4.11
25 26 0.178935 AACCAACATGGAGGGGGTTG 60.179 55.000 2.85 0.00 40.96 3.77
26 27 1.071314 ACCAACATGGAGGGGGTTGA 61.071 55.000 2.85 0.00 43.41 3.18
27 28 0.336048 CCAACATGGAGGGGGTTGAT 59.664 55.000 5.40 0.00 43.41 2.57
28 29 1.477553 CAACATGGAGGGGGTTGATG 58.522 55.000 0.00 0.00 43.41 3.07
29 30 0.336048 AACATGGAGGGGGTTGATGG 59.664 55.000 0.00 0.00 0.00 3.51
30 31 1.231068 CATGGAGGGGGTTGATGGG 59.769 63.158 0.00 0.00 0.00 4.00
31 32 1.230616 ATGGAGGGGGTTGATGGGT 60.231 57.895 0.00 0.00 0.00 4.51
32 33 1.583784 ATGGAGGGGGTTGATGGGTG 61.584 60.000 0.00 0.00 0.00 4.61
33 34 2.683475 GAGGGGGTTGATGGGTGG 59.317 66.667 0.00 0.00 0.00 4.61
34 35 2.121042 AGGGGGTTGATGGGTGGT 60.121 61.111 0.00 0.00 0.00 4.16
35 36 2.037208 GGGGGTTGATGGGTGGTG 59.963 66.667 0.00 0.00 0.00 4.17
36 37 2.543797 GGGGGTTGATGGGTGGTGA 61.544 63.158 0.00 0.00 0.00 4.02
37 38 1.000896 GGGGTTGATGGGTGGTGAG 60.001 63.158 0.00 0.00 0.00 3.51
38 39 1.000896 GGGTTGATGGGTGGTGAGG 60.001 63.158 0.00 0.00 0.00 3.86
39 40 1.678970 GGTTGATGGGTGGTGAGGC 60.679 63.158 0.00 0.00 0.00 4.70
40 41 2.040544 GTTGATGGGTGGTGAGGCG 61.041 63.158 0.00 0.00 0.00 5.52
41 42 2.220586 TTGATGGGTGGTGAGGCGA 61.221 57.895 0.00 0.00 0.00 5.54
42 43 2.184020 TTGATGGGTGGTGAGGCGAG 62.184 60.000 0.00 0.00 0.00 5.03
43 44 2.284625 ATGGGTGGTGAGGCGAGA 60.285 61.111 0.00 0.00 0.00 4.04
44 45 2.579684 GATGGGTGGTGAGGCGAGAC 62.580 65.000 0.00 0.00 0.00 3.36
45 46 2.997897 GGGTGGTGAGGCGAGACT 60.998 66.667 0.00 0.00 0.00 3.24
46 47 1.681327 GGGTGGTGAGGCGAGACTA 60.681 63.158 0.00 0.00 0.00 2.59
47 48 1.511768 GGTGGTGAGGCGAGACTAC 59.488 63.158 0.00 0.00 0.00 2.73
48 49 1.511768 GTGGTGAGGCGAGACTACC 59.488 63.158 0.00 0.00 0.00 3.18
49 50 1.076014 TGGTGAGGCGAGACTACCA 59.924 57.895 0.00 0.00 38.98 3.25
50 51 0.541063 TGGTGAGGCGAGACTACCAA 60.541 55.000 0.00 0.00 38.39 3.67
51 52 0.108756 GGTGAGGCGAGACTACCAAC 60.109 60.000 0.00 0.00 0.00 3.77
52 53 0.889306 GTGAGGCGAGACTACCAACT 59.111 55.000 0.00 0.00 0.00 3.16
53 54 1.135344 GTGAGGCGAGACTACCAACTC 60.135 57.143 0.00 0.00 0.00 3.01
54 55 0.456628 GAGGCGAGACTACCAACTCC 59.543 60.000 0.00 0.00 0.00 3.85
55 56 0.971447 AGGCGAGACTACCAACTCCC 60.971 60.000 0.00 0.00 0.00 4.30
56 57 1.516423 GCGAGACTACCAACTCCCC 59.484 63.158 0.00 0.00 0.00 4.81
61 62 3.512724 CGAGACTACCAACTCCCCTTTAA 59.487 47.826 0.00 0.00 0.00 1.52
67 68 9.287818 AGACTACCAACTCCCCTTTAATAATAA 57.712 33.333 0.00 0.00 0.00 1.40
89 90 9.469807 AATAAAGATTTAACGCATCACAAAACA 57.530 25.926 0.00 0.00 0.00 2.83
91 92 6.747659 AGATTTAACGCATCACAAAACAAC 57.252 33.333 0.00 0.00 0.00 3.32
92 93 6.503524 AGATTTAACGCATCACAAAACAACT 58.496 32.000 0.00 0.00 0.00 3.16
93 94 7.644490 AGATTTAACGCATCACAAAACAACTA 58.356 30.769 0.00 0.00 0.00 2.24
94 95 8.296713 AGATTTAACGCATCACAAAACAACTAT 58.703 29.630 0.00 0.00 0.00 2.12
95 96 8.810652 ATTTAACGCATCACAAAACAACTATT 57.189 26.923 0.00 0.00 0.00 1.73
96 97 8.635877 TTTAACGCATCACAAAACAACTATTT 57.364 26.923 0.00 0.00 0.00 1.40
97 98 8.635877 TTAACGCATCACAAAACAACTATTTT 57.364 26.923 0.00 0.00 31.87 1.82
98 99 9.731819 TTAACGCATCACAAAACAACTATTTTA 57.268 25.926 0.00 0.00 30.57 1.52
99 100 8.810652 AACGCATCACAAAACAACTATTTTAT 57.189 26.923 0.00 0.00 30.57 1.40
100 101 8.226543 ACGCATCACAAAACAACTATTTTATG 57.773 30.769 0.00 0.00 30.57 1.90
101 102 7.328249 ACGCATCACAAAACAACTATTTTATGG 59.672 33.333 0.00 0.00 28.94 2.74
102 103 7.328249 CGCATCACAAAACAACTATTTTATGGT 59.672 33.333 0.00 0.00 28.94 3.55
106 107 7.436673 TCACAAAACAACTATTTTATGGTGTGC 59.563 33.333 0.00 0.00 28.94 4.57
107 108 6.704050 ACAAAACAACTATTTTATGGTGTGCC 59.296 34.615 0.00 0.00 30.57 5.01
126 127 7.387948 GGTGTGCCACTATGATAAAATACCTAG 59.612 40.741 0.00 0.00 34.40 3.02
128 129 8.148351 TGTGCCACTATGATAAAATACCTAGTC 58.852 37.037 0.00 0.00 0.00 2.59
146 147 6.331042 ACCTAGTCTAACCAAAAACTTACCCT 59.669 38.462 0.00 0.00 0.00 4.34
149 150 6.665695 AGTCTAACCAAAAACTTACCCTGAA 58.334 36.000 0.00 0.00 0.00 3.02
155 156 4.808895 CCAAAAACTTACCCTGAAAGCAAC 59.191 41.667 0.00 0.00 0.00 4.17
179 180 3.270433 AGTGGTTGAATGATTGGGAGGAT 59.730 43.478 0.00 0.00 0.00 3.24
200 201 2.916269 TGATGGTATCCCAGGTTTGACA 59.084 45.455 0.00 0.00 46.15 3.58
201 202 2.871096 TGGTATCCCAGGTTTGACAC 57.129 50.000 0.00 0.00 35.17 3.67
206 207 0.472471 TCCCAGGTTTGACACTGTCC 59.528 55.000 6.72 0.00 32.90 4.02
214 215 0.673985 TTGACACTGTCCGGTCTCAG 59.326 55.000 17.39 17.39 35.11 3.35
266 267 3.557595 CACATTCCCTTGATAGCGACTTC 59.442 47.826 0.00 0.00 0.00 3.01
288 289 3.300009 GCAACTTCGACCATGTTTTCAG 58.700 45.455 0.00 0.00 0.00 3.02
297 298 6.954944 TCGACCATGTTTTCAGTTTTCTTAG 58.045 36.000 0.00 0.00 0.00 2.18
370 371 6.587990 AGACGACATCTCTGTTGATAACAAAG 59.412 38.462 0.00 0.00 41.61 2.77
373 374 4.142816 ACATCTCTGTTGATAACAAAGCGC 60.143 41.667 0.00 0.00 41.61 5.92
376 377 4.625742 TCTCTGTTGATAACAAAGCGCTAC 59.374 41.667 12.05 1.49 41.61 3.58
379 380 3.682858 TGTTGATAACAAAGCGCTACTCC 59.317 43.478 12.05 0.00 38.72 3.85
402 403 6.051074 CCGACCCGGTCTTAAATACTTAAAT 58.949 40.000 15.70 0.00 42.73 1.40
405 406 9.097257 CGACCCGGTCTTAAATACTTAAATAAA 57.903 33.333 15.70 0.00 0.00 1.40
452 453 2.370281 TCAGTGAGAGGCGACATTTC 57.630 50.000 0.00 0.00 0.00 2.17
456 457 0.320374 TGAGAGGCGACATTTCCGTT 59.680 50.000 0.00 0.00 0.00 4.44
462 463 1.597663 GGCGACATTTCCGTTGATAGG 59.402 52.381 0.00 0.00 0.00 2.57
465 466 3.123804 CGACATTTCCGTTGATAGGGAG 58.876 50.000 0.00 0.00 39.36 4.30
466 467 3.181479 CGACATTTCCGTTGATAGGGAGA 60.181 47.826 0.00 0.00 39.36 3.71
467 468 4.372656 GACATTTCCGTTGATAGGGAGAG 58.627 47.826 0.00 0.00 39.36 3.20
468 469 4.030913 ACATTTCCGTTGATAGGGAGAGA 58.969 43.478 0.00 0.00 39.36 3.10
473 474 5.063017 TCCGTTGATAGGGAGAGATAACT 57.937 43.478 0.00 0.00 33.51 2.24
492 493 3.851098 ACTTTGACCTAGTCTTCATCGC 58.149 45.455 0.00 0.00 33.15 4.58
500 501 6.376299 TGACCTAGTCTTCATCGCTACTTAAA 59.624 38.462 0.00 0.00 33.15 1.52
501 502 7.094075 TGACCTAGTCTTCATCGCTACTTAAAA 60.094 37.037 0.00 0.00 33.15 1.52
502 503 7.259161 ACCTAGTCTTCATCGCTACTTAAAAG 58.741 38.462 0.00 0.00 0.00 2.27
503 504 6.697892 CCTAGTCTTCATCGCTACTTAAAAGG 59.302 42.308 0.00 0.00 0.00 3.11
504 505 6.282199 AGTCTTCATCGCTACTTAAAAGGA 57.718 37.500 0.00 0.00 0.00 3.36
505 506 6.698380 AGTCTTCATCGCTACTTAAAAGGAA 58.302 36.000 0.00 0.00 0.00 3.36
506 507 7.159372 AGTCTTCATCGCTACTTAAAAGGAAA 58.841 34.615 0.00 0.00 0.00 3.13
508 509 8.451748 GTCTTCATCGCTACTTAAAAGGAAAAT 58.548 33.333 0.00 0.00 0.00 1.82
531 532 9.762381 AAATAATAAACCTCTAAATCACCCACA 57.238 29.630 0.00 0.00 0.00 4.17
532 533 9.936329 AATAATAAACCTCTAAATCACCCACAT 57.064 29.630 0.00 0.00 0.00 3.21
538 539 9.762381 AAACCTCTAAATCACCCACATATAAAA 57.238 29.630 0.00 0.00 0.00 1.52
539 540 9.762381 AACCTCTAAATCACCCACATATAAAAA 57.238 29.630 0.00 0.00 0.00 1.94
540 541 9.408648 ACCTCTAAATCACCCACATATAAAAAG 57.591 33.333 0.00 0.00 0.00 2.27
541 542 9.627123 CCTCTAAATCACCCACATATAAAAAGA 57.373 33.333 0.00 0.00 0.00 2.52
546 547 8.893563 AATCACCCACATATAAAAAGAAAGGA 57.106 30.769 0.00 0.00 0.00 3.36
547 548 8.893563 ATCACCCACATATAAAAAGAAAGGAA 57.106 30.769 0.00 0.00 0.00 3.36
548 549 8.713708 TCACCCACATATAAAAAGAAAGGAAA 57.286 30.769 0.00 0.00 0.00 3.13
549 550 9.148879 TCACCCACATATAAAAAGAAAGGAAAA 57.851 29.630 0.00 0.00 0.00 2.29
550 551 9.771534 CACCCACATATAAAAAGAAAGGAAAAA 57.228 29.630 0.00 0.00 0.00 1.94
551 552 9.996554 ACCCACATATAAAAAGAAAGGAAAAAG 57.003 29.630 0.00 0.00 0.00 2.27
552 553 9.435688 CCCACATATAAAAAGAAAGGAAAAAGG 57.564 33.333 0.00 0.00 0.00 3.11
564 565 9.658799 AAGAAAGGAAAAAGGAAAAAGAGAAAG 57.341 29.630 0.00 0.00 0.00 2.62
565 566 9.035890 AGAAAGGAAAAAGGAAAAAGAGAAAGA 57.964 29.630 0.00 0.00 0.00 2.52
566 567 9.653287 GAAAGGAAAAAGGAAAAAGAGAAAGAA 57.347 29.630 0.00 0.00 0.00 2.52
583 584 9.883142 AGAGAAAGAAAATATTCACTCGAATCT 57.117 29.630 0.00 0.00 41.09 2.40
585 586 9.658799 AGAAAGAAAATATTCACTCGAATCTCA 57.341 29.630 0.00 0.00 41.09 3.27
589 590 9.388506 AGAAAATATTCACTCGAATCTCAATGT 57.611 29.630 0.00 0.00 41.09 2.71
595 596 7.993821 TTCACTCGAATCTCAATGTAAGATC 57.006 36.000 0.00 0.00 32.29 2.75
596 597 7.100458 TCACTCGAATCTCAATGTAAGATCA 57.900 36.000 0.00 0.00 32.29 2.92
597 598 7.547227 TCACTCGAATCTCAATGTAAGATCAA 58.453 34.615 0.00 0.00 32.29 2.57
598 599 8.200120 TCACTCGAATCTCAATGTAAGATCAAT 58.800 33.333 0.00 0.00 32.29 2.57
599 600 8.274248 CACTCGAATCTCAATGTAAGATCAATG 58.726 37.037 0.00 0.00 32.29 2.82
600 601 8.200120 ACTCGAATCTCAATGTAAGATCAATGA 58.800 33.333 0.00 0.00 32.29 2.57
601 602 9.205719 CTCGAATCTCAATGTAAGATCAATGAT 57.794 33.333 0.00 0.00 32.29 2.45
629 630 8.613060 ATGACTTAGATGTGCAATACTTATGG 57.387 34.615 0.00 0.00 0.00 2.74
630 631 6.483307 TGACTTAGATGTGCAATACTTATGGC 59.517 38.462 0.00 0.00 33.16 4.40
631 632 6.356556 ACTTAGATGTGCAATACTTATGGCA 58.643 36.000 0.00 0.00 40.19 4.92
696 697 9.228636 GAACTCTAAATCAATCTTAGACGACTC 57.771 37.037 0.00 0.00 33.04 3.36
704 705 1.135139 TCTTAGACGACTCATGCAGCC 59.865 52.381 0.00 0.00 0.00 4.85
730 731 1.005924 ACAAAATTCCCCTGATCGGCT 59.994 47.619 0.00 0.00 0.00 5.52
748 749 1.134250 GCTGATCCCCTTCCACTCTTC 60.134 57.143 0.00 0.00 0.00 2.87
766 767 3.997021 TCTTCAGAAACTCTTGCCGATTC 59.003 43.478 0.00 0.00 0.00 2.52
767 768 3.685139 TCAGAAACTCTTGCCGATTCT 57.315 42.857 0.00 0.00 0.00 2.40
778 779 2.840974 CCGATTCTGTGGCTCGTTT 58.159 52.632 0.00 0.00 0.00 3.60
798 799 5.820947 CGTTTTACCATCCTATAACTTGCCT 59.179 40.000 0.00 0.00 0.00 4.75
829 830 7.480760 AAAGCACTTGTCCAATTATACCAAT 57.519 32.000 0.00 0.00 0.00 3.16
938 940 0.173255 GCAATGTGTTCCCAATCCGG 59.827 55.000 0.00 0.00 0.00 5.14
1033 1037 1.969589 GCTTCCCGGGAAAAAGCGA 60.970 57.895 34.78 13.09 36.41 4.93
1046 1050 0.685097 AAAGCGAGCCAGGTACAAGA 59.315 50.000 0.00 0.00 0.00 3.02
1078 1082 0.250467 AGGTGTCGTGCAAGCAATCT 60.250 50.000 0.00 0.00 0.00 2.40
1125 1167 4.529219 TATGCCGCTCGGTGCCAG 62.529 66.667 10.24 0.00 38.78 4.85
1347 1397 2.356553 GCCAACGACACGCAGGTA 60.357 61.111 0.00 0.00 0.00 3.08
1385 1439 3.845178 TCTCAGATTGATTGTTACGCGT 58.155 40.909 19.17 19.17 0.00 6.01
1386 1440 3.612423 TCTCAGATTGATTGTTACGCGTG 59.388 43.478 24.59 0.00 0.00 5.34
1387 1441 2.670905 TCAGATTGATTGTTACGCGTGG 59.329 45.455 24.59 0.00 0.00 4.94
1388 1442 2.670905 CAGATTGATTGTTACGCGTGGA 59.329 45.455 24.59 7.64 0.00 4.02
1430 1491 3.414700 CTCGGCGCGCTCTGTTTT 61.415 61.111 32.29 0.00 0.00 2.43
1441 1503 2.489329 CGCTCTGTTTTGATGGATGGTT 59.511 45.455 0.00 0.00 0.00 3.67
1850 1917 4.569966 CAGGTACCACGTCACTAGTAGTAG 59.430 50.000 15.94 2.87 0.00 2.57
1865 1932 2.320681 AGTAGCTACCAGTCAACCCA 57.679 50.000 20.31 0.00 0.00 4.51
1884 1962 0.252193 AACCTGCCTCTCAGCTCTCT 60.252 55.000 0.00 0.00 41.50 3.10
1906 1984 7.614192 TCTCTAAGTGACACATGTATCTTGGTA 59.386 37.037 8.59 0.00 0.00 3.25
1908 1986 8.758829 TCTAAGTGACACATGTATCTTGGTATT 58.241 33.333 8.59 0.00 0.00 1.89
1909 1987 9.383519 CTAAGTGACACATGTATCTTGGTATTT 57.616 33.333 8.59 0.00 0.00 1.40
1944 4577 6.201425 GCAACACAATGTGAATCTTGATTTGT 59.799 34.615 21.34 0.00 36.96 2.83
1946 4579 6.144854 ACACAATGTGAATCTTGATTTGTCG 58.855 36.000 21.34 0.00 36.96 4.35
1993 4626 9.829507 ATAAATTTGGTCAAAGTTTGTGAATCA 57.170 25.926 15.08 0.24 39.07 2.57
2002 4636 6.476380 TCAAAGTTTGTGAATCATGACTTTGC 59.524 34.615 26.17 0.00 46.14 3.68
2092 4726 6.875726 GCAAGGAAATAAAAGGCAAAAGAGAT 59.124 34.615 0.00 0.00 0.00 2.75
2115 4749 9.860898 AGATTAAACCAATTTATCTTGAACTGC 57.139 29.630 0.00 0.00 30.33 4.40
2218 4852 6.790232 TTGAAATGAGGAGAAACACCTTTT 57.210 33.333 0.00 0.00 37.93 2.27
2557 5455 5.126222 TGTCAATAGTTTTGTGCCTTTGTCA 59.874 36.000 0.00 0.00 0.00 3.58
2594 5492 0.327924 TATTGGACCACAGTGGCAGG 59.672 55.000 20.48 0.00 42.67 4.85
2628 5526 1.203001 GGGGAGGTTTTGTGATGACCA 60.203 52.381 0.00 0.00 35.89 4.02
2705 5604 2.432628 CGACCTGCTTCGTCCCAC 60.433 66.667 0.00 0.00 34.16 4.61
2875 10603 5.694006 GGATTGTTCTAGAGAATCATGGACG 59.306 44.000 20.17 0.00 37.82 4.79
2980 13555 4.217983 ACACTAGGACTTTACACTTCTCCG 59.782 45.833 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.061735 ACCCCCTCCATGTTGGTTTTT 60.062 47.619 0.00 0.00 39.03 1.94
4 5 0.565674 ACCCCCTCCATGTTGGTTTT 59.434 50.000 0.00 0.00 39.03 2.43
5 6 0.565674 AACCCCCTCCATGTTGGTTT 59.434 50.000 0.00 0.00 39.03 3.27
6 7 0.178935 CAACCCCCTCCATGTTGGTT 60.179 55.000 0.00 0.00 39.82 3.67
7 8 1.071314 TCAACCCCCTCCATGTTGGT 61.071 55.000 0.00 0.00 39.77 3.67
8 9 0.336048 ATCAACCCCCTCCATGTTGG 59.664 55.000 0.00 0.00 39.77 3.77
9 10 1.477553 CATCAACCCCCTCCATGTTG 58.522 55.000 0.00 0.00 40.48 3.33
10 11 0.336048 CCATCAACCCCCTCCATGTT 59.664 55.000 0.00 0.00 0.00 2.71
11 12 1.583784 CCCATCAACCCCCTCCATGT 61.584 60.000 0.00 0.00 0.00 3.21
12 13 1.231068 CCCATCAACCCCCTCCATG 59.769 63.158 0.00 0.00 0.00 3.66
13 14 1.230616 ACCCATCAACCCCCTCCAT 60.231 57.895 0.00 0.00 0.00 3.41
14 15 2.212761 ACCCATCAACCCCCTCCA 59.787 61.111 0.00 0.00 0.00 3.86
15 16 2.683475 CACCCATCAACCCCCTCC 59.317 66.667 0.00 0.00 0.00 4.30
16 17 2.238701 ACCACCCATCAACCCCCTC 61.239 63.158 0.00 0.00 0.00 4.30
17 18 2.121042 ACCACCCATCAACCCCCT 60.121 61.111 0.00 0.00 0.00 4.79
18 19 2.037208 CACCACCCATCAACCCCC 59.963 66.667 0.00 0.00 0.00 5.40
19 20 1.000896 CTCACCACCCATCAACCCC 60.001 63.158 0.00 0.00 0.00 4.95
20 21 1.000896 CCTCACCACCCATCAACCC 60.001 63.158 0.00 0.00 0.00 4.11
21 22 1.678970 GCCTCACCACCCATCAACC 60.679 63.158 0.00 0.00 0.00 3.77
22 23 2.040544 CGCCTCACCACCCATCAAC 61.041 63.158 0.00 0.00 0.00 3.18
23 24 2.184020 CTCGCCTCACCACCCATCAA 62.184 60.000 0.00 0.00 0.00 2.57
24 25 2.606213 TCGCCTCACCACCCATCA 60.606 61.111 0.00 0.00 0.00 3.07
25 26 2.187946 CTCGCCTCACCACCCATC 59.812 66.667 0.00 0.00 0.00 3.51
26 27 2.284625 TCTCGCCTCACCACCCAT 60.285 61.111 0.00 0.00 0.00 4.00
27 28 2.435120 TAGTCTCGCCTCACCACCCA 62.435 60.000 0.00 0.00 0.00 4.51
28 29 1.681327 TAGTCTCGCCTCACCACCC 60.681 63.158 0.00 0.00 0.00 4.61
29 30 1.511768 GTAGTCTCGCCTCACCACC 59.488 63.158 0.00 0.00 0.00 4.61
30 31 1.248785 TGGTAGTCTCGCCTCACCAC 61.249 60.000 0.00 0.00 34.40 4.16
31 32 0.541063 TTGGTAGTCTCGCCTCACCA 60.541 55.000 0.00 0.00 37.50 4.17
32 33 0.108756 GTTGGTAGTCTCGCCTCACC 60.109 60.000 0.00 0.00 0.00 4.02
33 34 0.889306 AGTTGGTAGTCTCGCCTCAC 59.111 55.000 0.00 0.00 0.00 3.51
34 35 1.174783 GAGTTGGTAGTCTCGCCTCA 58.825 55.000 0.00 0.00 0.00 3.86
35 36 0.456628 GGAGTTGGTAGTCTCGCCTC 59.543 60.000 0.00 0.00 0.00 4.70
36 37 0.971447 GGGAGTTGGTAGTCTCGCCT 60.971 60.000 0.00 0.00 37.57 5.52
37 38 1.516423 GGGAGTTGGTAGTCTCGCC 59.484 63.158 0.00 0.00 37.57 5.54
38 39 0.971447 AGGGGAGTTGGTAGTCTCGC 60.971 60.000 0.00 0.00 41.02 5.03
39 40 1.558233 AAGGGGAGTTGGTAGTCTCG 58.442 55.000 0.00 0.00 0.00 4.04
40 41 5.695424 ATTAAAGGGGAGTTGGTAGTCTC 57.305 43.478 0.00 0.00 0.00 3.36
41 42 7.766736 ATTATTAAAGGGGAGTTGGTAGTCT 57.233 36.000 0.00 0.00 0.00 3.24
42 43 9.910267 TTTATTATTAAAGGGGAGTTGGTAGTC 57.090 33.333 0.00 0.00 0.00 2.59
43 44 9.916360 CTTTATTATTAAAGGGGAGTTGGTAGT 57.084 33.333 8.61 0.00 40.35 2.73
67 68 6.978080 AGTTGTTTTGTGATGCGTTAAATCTT 59.022 30.769 0.00 0.00 0.00 2.40
80 81 7.436673 GCACACCATAAAATAGTTGTTTTGTGA 59.563 33.333 10.74 0.00 40.47 3.58
84 85 6.821388 TGGCACACCATAAAATAGTTGTTTT 58.179 32.000 0.00 0.00 42.67 2.43
102 103 8.029782 ACTAGGTATTTTATCATAGTGGCACA 57.970 34.615 21.41 6.31 31.51 4.57
126 127 6.947644 TTCAGGGTAAGTTTTTGGTTAGAC 57.052 37.500 0.00 0.00 0.00 2.59
128 129 6.183360 TGCTTTCAGGGTAAGTTTTTGGTTAG 60.183 38.462 0.00 0.00 0.00 2.34
132 133 4.664150 TGCTTTCAGGGTAAGTTTTTGG 57.336 40.909 0.00 0.00 0.00 3.28
134 135 5.669164 TGTTGCTTTCAGGGTAAGTTTTT 57.331 34.783 0.00 0.00 0.00 1.94
135 136 5.186992 ACTTGTTGCTTTCAGGGTAAGTTTT 59.813 36.000 0.00 0.00 0.00 2.43
155 156 3.194116 CCTCCCAATCATTCAACCACTTG 59.806 47.826 0.00 0.00 0.00 3.16
200 201 2.681848 CGTATTACTGAGACCGGACAGT 59.318 50.000 26.09 26.09 46.81 3.55
201 202 2.033049 CCGTATTACTGAGACCGGACAG 59.967 54.545 9.46 16.75 37.66 3.51
206 207 8.675504 AGATATTAATCCGTATTACTGAGACCG 58.324 37.037 0.00 0.00 31.98 4.79
238 239 2.514458 ATCAAGGGAATGTGGTGTCC 57.486 50.000 0.00 0.00 0.00 4.02
244 245 3.185246 AGTCGCTATCAAGGGAATGTG 57.815 47.619 0.00 0.00 45.31 3.21
266 267 2.286713 TGAAAACATGGTCGAAGTTGCG 60.287 45.455 0.00 0.00 0.00 4.85
275 276 8.154649 TCTCTAAGAAAACTGAAAACATGGTC 57.845 34.615 0.00 0.00 0.00 4.02
366 367 1.810030 GGGTCGGAGTAGCGCTTTG 60.810 63.158 18.68 0.92 0.00 2.77
376 377 6.627953 TTTAAGTATTTAAGACCGGGTCGGAG 60.628 42.308 20.87 0.00 38.39 4.63
379 380 8.647143 TTATTTAAGTATTTAAGACCGGGTCG 57.353 34.615 20.87 0.00 37.67 4.79
409 410 9.163894 TGAAAGAATATCCTCATAGATTGGTCT 57.836 33.333 0.00 0.00 38.52 3.85
410 411 9.434420 CTGAAAGAATATCCTCATAGATTGGTC 57.566 37.037 0.00 0.00 34.07 4.02
411 412 8.943085 ACTGAAAGAATATCCTCATAGATTGGT 58.057 33.333 0.00 0.00 37.43 3.67
413 414 9.993454 TCACTGAAAGAATATCCTCATAGATTG 57.007 33.333 0.00 0.00 37.43 2.67
415 416 9.599056 TCTCACTGAAAGAATATCCTCATAGAT 57.401 33.333 0.00 0.00 37.43 1.98
417 418 8.306038 CCTCTCACTGAAAGAATATCCTCATAG 58.694 40.741 0.00 0.00 37.43 2.23
418 419 7.256119 GCCTCTCACTGAAAGAATATCCTCATA 60.256 40.741 0.00 0.00 37.43 2.15
419 420 6.464180 GCCTCTCACTGAAAGAATATCCTCAT 60.464 42.308 0.00 0.00 37.43 2.90
420 421 5.163364 GCCTCTCACTGAAAGAATATCCTCA 60.163 44.000 0.00 0.00 37.43 3.86
421 422 5.296748 GCCTCTCACTGAAAGAATATCCTC 58.703 45.833 0.00 0.00 37.43 3.71
422 423 4.202202 CGCCTCTCACTGAAAGAATATCCT 60.202 45.833 0.00 0.00 37.43 3.24
424 425 4.742659 GTCGCCTCTCACTGAAAGAATATC 59.257 45.833 0.00 0.00 37.43 1.63
425 426 4.160439 TGTCGCCTCTCACTGAAAGAATAT 59.840 41.667 0.00 0.00 37.43 1.28
433 434 1.066858 GGAAATGTCGCCTCTCACTGA 60.067 52.381 0.00 0.00 0.00 3.41
452 453 5.793030 AAGTTATCTCTCCCTATCAACGG 57.207 43.478 0.00 0.00 0.00 4.44
456 457 6.444704 AGGTCAAAGTTATCTCTCCCTATCA 58.555 40.000 0.00 0.00 0.00 2.15
462 463 7.122948 TGAAGACTAGGTCAAAGTTATCTCTCC 59.877 40.741 0.00 0.00 34.60 3.71
465 466 7.646130 CGATGAAGACTAGGTCAAAGTTATCTC 59.354 40.741 0.00 0.00 34.60 2.75
466 467 7.484975 CGATGAAGACTAGGTCAAAGTTATCT 58.515 38.462 0.00 0.00 34.60 1.98
467 468 6.199342 GCGATGAAGACTAGGTCAAAGTTATC 59.801 42.308 0.00 0.00 34.60 1.75
468 469 6.043411 GCGATGAAGACTAGGTCAAAGTTAT 58.957 40.000 0.00 0.00 34.60 1.89
473 474 4.705507 AGTAGCGATGAAGACTAGGTCAAA 59.294 41.667 0.00 0.00 34.60 2.69
505 506 9.762381 TGTGGGTGATTTAGAGGTTTATTATTT 57.238 29.630 0.00 0.00 0.00 1.40
506 507 9.936329 ATGTGGGTGATTTAGAGGTTTATTATT 57.064 29.630 0.00 0.00 0.00 1.40
514 515 9.408648 CTTTTTATATGTGGGTGATTTAGAGGT 57.591 33.333 0.00 0.00 0.00 3.85
520 521 9.320295 TCCTTTCTTTTTATATGTGGGTGATTT 57.680 29.630 0.00 0.00 0.00 2.17
521 522 8.893563 TCCTTTCTTTTTATATGTGGGTGATT 57.106 30.769 0.00 0.00 0.00 2.57
522 523 8.893563 TTCCTTTCTTTTTATATGTGGGTGAT 57.106 30.769 0.00 0.00 0.00 3.06
523 524 8.713708 TTTCCTTTCTTTTTATATGTGGGTGA 57.286 30.769 0.00 0.00 0.00 4.02
524 525 9.771534 TTTTTCCTTTCTTTTTATATGTGGGTG 57.228 29.630 0.00 0.00 0.00 4.61
525 526 9.996554 CTTTTTCCTTTCTTTTTATATGTGGGT 57.003 29.630 0.00 0.00 0.00 4.51
526 527 9.435688 CCTTTTTCCTTTCTTTTTATATGTGGG 57.564 33.333 0.00 0.00 0.00 4.61
538 539 9.658799 CTTTCTCTTTTTCCTTTTTCCTTTCTT 57.341 29.630 0.00 0.00 0.00 2.52
539 540 9.035890 TCTTTCTCTTTTTCCTTTTTCCTTTCT 57.964 29.630 0.00 0.00 0.00 2.52
540 541 9.653287 TTCTTTCTCTTTTTCCTTTTTCCTTTC 57.347 29.630 0.00 0.00 0.00 2.62
557 558 9.883142 AGATTCGAGTGAATATTTTCTTTCTCT 57.117 29.630 0.00 0.00 44.79 3.10
559 560 9.658799 TGAGATTCGAGTGAATATTTTCTTTCT 57.341 29.630 0.00 0.00 44.79 2.52
563 564 9.388506 ACATTGAGATTCGAGTGAATATTTTCT 57.611 29.630 0.00 0.00 44.79 2.52
569 570 9.684448 GATCTTACATTGAGATTCGAGTGAATA 57.316 33.333 0.00 0.00 44.79 1.75
571 572 7.547227 TGATCTTACATTGAGATTCGAGTGAA 58.453 34.615 0.00 0.00 38.76 3.18
572 573 7.100458 TGATCTTACATTGAGATTCGAGTGA 57.900 36.000 0.00 0.00 34.13 3.41
573 574 7.761651 TTGATCTTACATTGAGATTCGAGTG 57.238 36.000 0.00 0.00 34.13 3.51
574 575 8.200120 TCATTGATCTTACATTGAGATTCGAGT 58.800 33.333 0.00 0.00 34.13 4.18
575 576 8.585189 TCATTGATCTTACATTGAGATTCGAG 57.415 34.615 0.00 0.00 34.13 4.04
603 604 9.710900 CCATAAGTATTGCACATCTAAGTCATA 57.289 33.333 0.00 0.00 0.00 2.15
604 605 7.173907 GCCATAAGTATTGCACATCTAAGTCAT 59.826 37.037 0.00 0.00 0.00 3.06
605 606 6.483307 GCCATAAGTATTGCACATCTAAGTCA 59.517 38.462 0.00 0.00 0.00 3.41
606 607 6.483307 TGCCATAAGTATTGCACATCTAAGTC 59.517 38.462 0.00 0.00 30.49 3.01
607 608 6.356556 TGCCATAAGTATTGCACATCTAAGT 58.643 36.000 0.00 0.00 30.49 2.24
608 609 6.866010 TGCCATAAGTATTGCACATCTAAG 57.134 37.500 0.00 0.00 30.49 2.18
616 617 6.173427 TCTAGATGTGCCATAAGTATTGCA 57.827 37.500 0.00 0.00 32.69 4.08
617 618 7.069852 CATCTAGATGTGCCATAAGTATTGC 57.930 40.000 22.42 0.00 34.23 3.56
668 669 9.575783 GTCGTCTAAGATTGATTTAGAGTTCTT 57.424 33.333 0.00 0.00 37.70 2.52
669 670 8.962679 AGTCGTCTAAGATTGATTTAGAGTTCT 58.037 33.333 0.00 0.00 37.70 3.01
670 671 9.228636 GAGTCGTCTAAGATTGATTTAGAGTTC 57.771 37.037 0.00 0.00 37.70 3.01
671 672 8.740906 TGAGTCGTCTAAGATTGATTTAGAGTT 58.259 33.333 0.00 0.00 37.70 3.01
672 673 8.282455 TGAGTCGTCTAAGATTGATTTAGAGT 57.718 34.615 0.00 0.00 37.70 3.24
704 705 3.749665 TCAGGGGAATTTTGTGCAAAG 57.250 42.857 0.00 0.00 0.00 2.77
730 731 2.191400 CTGAAGAGTGGAAGGGGATCA 58.809 52.381 0.00 0.00 0.00 2.92
748 749 3.070018 ACAGAATCGGCAAGAGTTTCTG 58.930 45.455 16.54 16.54 44.59 3.02
766 767 1.737793 GGATGGTAAAACGAGCCACAG 59.262 52.381 0.00 0.00 32.38 3.66
767 768 1.349688 AGGATGGTAAAACGAGCCACA 59.650 47.619 0.00 0.00 34.68 4.17
778 779 6.763715 ATGAGGCAAGTTATAGGATGGTAA 57.236 37.500 0.00 0.00 0.00 2.85
852 853 8.621286 GCACTGTATATTGCTTTATGTAGGTTT 58.379 33.333 0.00 0.00 35.74 3.27
853 854 7.773224 TGCACTGTATATTGCTTTATGTAGGTT 59.227 33.333 3.58 0.00 39.62 3.50
854 855 7.279615 TGCACTGTATATTGCTTTATGTAGGT 58.720 34.615 3.58 0.00 39.62 3.08
855 856 7.728847 TGCACTGTATATTGCTTTATGTAGG 57.271 36.000 3.58 0.00 39.62 3.18
883 884 9.459640 GTTTGATTCATATCCATGTCTTGATTG 57.540 33.333 0.00 0.00 33.57 2.67
938 940 1.235281 GGGGTCGTTTGAGTTGCCTC 61.235 60.000 0.00 0.00 38.27 4.70
951 953 2.993471 GCATGTGGCAAAGGGGTCG 61.993 63.158 0.00 0.00 43.97 4.79
1003 1007 1.135689 CCGGGAAGCAAGTGAATTTCG 60.136 52.381 0.00 0.00 0.00 3.46
1005 1009 1.203001 TCCCGGGAAGCAAGTGAATTT 60.203 47.619 24.50 0.00 0.00 1.82
1033 1037 2.982130 CCGCTCTTGTACCTGGCT 59.018 61.111 0.00 0.00 0.00 4.75
1046 1050 2.124983 CACCTAGCATGTGCCGCT 60.125 61.111 0.57 0.00 43.38 5.52
1362 1412 4.105486 CGCGTAACAATCAATCTGAGAGA 58.895 43.478 0.00 0.00 0.00 3.10
1368 1418 2.967362 TCCACGCGTAACAATCAATCT 58.033 42.857 13.44 0.00 0.00 2.40
1371 1421 1.656594 CGATCCACGCGTAACAATCAA 59.343 47.619 13.44 0.00 34.51 2.57
1372 1422 1.135344 TCGATCCACGCGTAACAATCA 60.135 47.619 13.44 1.63 42.26 2.57
1385 1439 1.385756 TAACCACGGCGATCGATCCA 61.386 55.000 21.57 0.00 42.43 3.41
1386 1440 0.249155 TTAACCACGGCGATCGATCC 60.249 55.000 21.57 10.69 42.43 3.36
1387 1441 1.779569 ATTAACCACGGCGATCGATC 58.220 50.000 21.57 15.68 42.43 3.69
1388 1442 2.234300 AATTAACCACGGCGATCGAT 57.766 45.000 21.57 0.00 42.43 3.59
1430 1491 1.472552 CGAACGCCTAACCATCCATCA 60.473 52.381 0.00 0.00 0.00 3.07
1584 1651 2.357517 AACCTGTTCGCAGCGGAG 60.358 61.111 16.42 8.61 43.67 4.63
1605 1672 2.677979 GCGAGAAACAAGGGACCGC 61.678 63.158 0.00 0.00 0.00 5.68
1850 1917 0.400594 AGGTTGGGTTGACTGGTAGC 59.599 55.000 0.00 0.00 0.00 3.58
1884 1962 9.378551 GAAATACCAAGATACATGTGTCACTTA 57.621 33.333 22.66 9.69 0.00 2.24
2023 4657 3.857093 AGAACGACAAATTGCAACACAAC 59.143 39.130 0.00 0.00 42.27 3.32
2092 4726 8.637986 ACAGCAGTTCAAGATAAATTGGTTTAA 58.362 29.630 0.00 0.00 33.76 1.52
2150 4784 6.304683 GCTTTGCGTATTGTGTTTAAACTAGG 59.695 38.462 18.72 9.54 0.00 3.02
2218 4852 3.084039 CAAGAGCCATTTTGCTAGTCCA 58.916 45.455 0.00 0.00 42.95 4.02
2400 5036 6.823286 TCCAACTATCATTACCTGGAATGA 57.177 37.500 17.76 17.76 46.93 2.57
2474 5372 5.660460 ACTTCAAACTTTTAACCTTGCCAG 58.340 37.500 0.00 0.00 0.00 4.85
2557 5455 8.211629 GGTCCAATATAGTAAGTTCCATGAGTT 58.788 37.037 0.00 0.00 0.00 3.01
2594 5492 1.866853 CTCCCCAAGCAAAGTTCGCC 61.867 60.000 0.00 0.00 0.00 5.54
2628 5526 1.976898 CCTGCACATTGCCATGGTT 59.023 52.632 14.67 0.00 44.23 3.67
2764 5663 4.204012 GCTACTGGGCAACACCATAATAA 58.796 43.478 0.00 0.00 40.36 1.40
2966 13541 4.755411 TCTAATGGCGGAGAAGTGTAAAG 58.245 43.478 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.