Multiple sequence alignment - TraesCS1B01G142500

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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 TraesCS1B01G142500 chr1B 100.000 2669 0 0 1 2669 192223960 192226628 0.000000e+00 4929
1 TraesCS1B01G142500 chr1D 95.787 1543 55 7 987 2524 143177699 143179236 0.000000e+00 2481
2 TraesCS1B01G142500 chr1D 96.660 509 16 1 479 987 143177109 143177616 0.000000e+00 845
3 TraesCS1B01G142500 chr1D 90.717 474 18 12 2 449 143176179 143176652 2.270000e-170 608
4 TraesCS1B01G142500 chr1A 95.567 1015 26 5 987 1999 146959689 146958692 0.000000e+00 1607
5 TraesCS1B01G142500 chr1A 90.605 777 54 8 228 987 146960546 146959772 0.000000e+00 1013
6 TraesCS1B01G142500 chr1A 95.930 172 7 0 2 173 146960930 146960759 2.020000e-71 279
7 TraesCS1B01G142500 chr1A 88.710 124 14 0 2368 2491 146956263 146956140 4.600000e-33 152
8 TraesCS1B01G142500 chr5D 95.000 180 7 2 2489 2666 128489155 128489334 5.630000e-72 281
9 TraesCS1B01G142500 chr6D 94.444 180 8 2 2492 2669 421432900 421432721 2.620000e-70 276
10 TraesCS1B01G142500 chr6D 93.333 180 10 2 2489 2666 306115286 306115465 5.670000e-67 265
11 TraesCS1B01G142500 chr4D 94.915 177 7 2 2492 2666 359733102 359733278 2.620000e-70 276
12 TraesCS1B01G142500 chr4A 93.923 181 6 4 2490 2665 593958241 593958421 4.380000e-68 268
13 TraesCS1B01G142500 chr4A 92.935 184 10 3 2489 2669 178984382 178984199 5.670000e-67 265
14 TraesCS1B01G142500 chr6B 93.407 182 8 3 2492 2669 430186534 430186353 1.580000e-67 267
15 TraesCS1B01G142500 chr7A 92.513 187 10 4 2486 2669 578712436 578712251 5.670000e-67 265
16 TraesCS1B01G142500 chr5A 92.473 186 11 2 2487 2669 140587239 140587054 2.040000e-66 263
17 TraesCS1B01G142500 chr5A 86.260 131 9 7 621 745 86662157 86662030 1.670000e-27 134
18 TraesCS1B01G142500 chr2A 86.047 129 13 5 621 746 329688158 329688032 1.670000e-27 134
19 TraesCS1B01G142500 chr7B 85.185 135 13 5 621 750 155471305 155471173 6.000000e-27 132
20 TraesCS1B01G142500 chr7B 84.615 130 14 5 621 746 211374182 211374055 1.000000e-24 124
21 TraesCS1B01G142500 chr5B 83.221 149 18 7 605 750 665744619 665744475 2.160000e-26 130
22 TraesCS1B01G142500 chr7D 83.108 148 16 4 604 746 156796992 156796849 2.790000e-25 126
23 TraesCS1B01G142500 chr3A 81.761 159 19 9 585 737 251035741 251035895 1.000000e-24 124


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 TraesCS1B01G142500 chr1B 192223960 192226628 2668 False 4929.000000 4929 100.000 1 2669 1 chr1B.!!$F1 2668
1 TraesCS1B01G142500 chr1D 143176179 143179236 3057 False 1311.333333 2481 94.388 2 2524 3 chr1D.!!$F1 2522
2 TraesCS1B01G142500 chr1A 146956140 146960930 4790 True 762.750000 1607 92.703 2 2491 4 chr1A.!!$R1 2489

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
344 507 1.195115 CCCTCTCTCGGACCAATTCA 58.805 55.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2246 2925 0.446616 GGGGATTTGACGCGAGAAAC 59.553 55.0 15.93 2.8 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
82 83 1.734465 GGACGAATTCCTCACTTGCTG 59.266 52.381 0.00 0.00 41.95 4.41
139 140 3.192922 GCACGAAACCGGCGCTAT 61.193 61.111 7.64 0.00 0.00 2.97
181 207 4.164796 AGGATCCATGACAGTTGCTGATTA 59.835 41.667 15.82 0.00 35.18 1.75
234 393 7.983166 TGGGTAGATACCTTGTGTAAGTATT 57.017 36.000 8.87 0.00 45.72 1.89
245 404 6.932400 CCTTGTGTAAGTATTGTGTTCCTGTA 59.068 38.462 0.00 0.00 31.80 2.74
294 453 2.096980 GCTGTACGGGTAAAAGGATTGC 59.903 50.000 3.34 0.00 0.00 3.56
325 488 4.965200 AAGGCCAGTATTGTATCTCCTC 57.035 45.455 5.01 0.00 0.00 3.71
344 507 1.195115 CCCTCTCTCGGACCAATTCA 58.805 55.000 0.00 0.00 0.00 2.57
357 520 5.230182 GGACCAATTCAGAATGTTTGGAAC 58.770 41.667 17.52 11.62 46.22 3.62
382 545 2.293399 ACTTGTCGGTGGATTTTTCTGC 59.707 45.455 0.00 0.00 0.00 4.26
477 1047 5.499004 TTCAATAGTTTGGGCTAGACACT 57.501 39.130 0.00 0.00 33.44 3.55
593 1184 9.258826 CAAACATGTCAATTTCTTTGTATCCAA 57.741 29.630 0.00 0.00 36.65 3.53
784 1375 7.808381 ACAACGATGATGGATATTTCGTACTAG 59.192 37.037 0.00 0.00 41.71 2.57
1230 1905 1.138036 CATGGCGTCGTTCTACGGA 59.862 57.895 0.00 0.00 42.81 4.69
1613 2288 0.526524 GAGGCCGACGACTTCATCAG 60.527 60.000 0.00 0.00 0.00 2.90
1638 2313 2.486951 TTTACGAGCAGCTACGGATC 57.513 50.000 15.67 0.00 0.00 3.36
1841 2517 2.805353 GCGTGCATCGACGTGACT 60.805 61.111 11.94 0.00 41.54 3.41
1928 2604 4.271696 TGGGAGTGTTTCATGTCTACTG 57.728 45.455 0.00 0.00 0.00 2.74
1962 2638 4.638865 ACGGAGTAATCATTGCCCTTTAAC 59.361 41.667 0.00 0.00 41.94 2.01
1963 2639 4.881850 CGGAGTAATCATTGCCCTTTAACT 59.118 41.667 0.00 0.00 0.00 2.24
2028 2704 8.525316 CACATACATTCACCCATATAAATGCAT 58.475 33.333 0.00 0.00 33.42 3.96
2029 2705 8.525316 ACATACATTCACCCATATAAATGCATG 58.475 33.333 0.00 0.00 38.20 4.06
2033 2709 3.252944 TCACCCATATAAATGCATGCACG 59.747 43.478 25.37 5.46 0.00 5.34
2038 2714 6.828273 ACCCATATAAATGCATGCACGTATAT 59.172 34.615 25.37 25.48 0.00 0.86
2039 2715 7.339212 ACCCATATAAATGCATGCACGTATATT 59.661 33.333 27.21 15.84 0.00 1.28
2241 2920 1.439543 AGCCCTCCTTCACAAACTCT 58.560 50.000 0.00 0.00 0.00 3.24
2246 2925 0.319555 TCCTTCACAAACTCTCGCGG 60.320 55.000 6.13 0.00 0.00 6.46
2253 2932 0.435008 CAAACTCTCGCGGTTTCTCG 59.565 55.000 6.13 0.00 35.09 4.04
2330 3009 1.466167 CCATGTCTCTTCTGTTTGCGG 59.534 52.381 0.00 0.00 0.00 5.69
2360 3039 4.327680 GTCCTTCACACTTGGAAGCTTAT 58.672 43.478 0.00 0.00 40.29 1.73
2365 3044 3.055094 TCACACTTGGAAGCTTATCCCTC 60.055 47.826 0.00 0.00 38.82 4.30
2375 5230 2.030045 GCTTATCCCTCGAGGTGGAGT 61.030 57.143 29.25 12.65 36.75 3.85
2383 5238 1.268899 CTCGAGGTGGAGTTGTTACGT 59.731 52.381 3.91 0.00 0.00 3.57
2402 5257 4.708177 ACGTTCAAGCTAGATATGCCATT 58.292 39.130 0.00 0.00 0.00 3.16
2407 5262 7.041780 CGTTCAAGCTAGATATGCCATTAAACT 60.042 37.037 0.00 0.00 0.00 2.66
2416 5271 6.701841 AGATATGCCATTAAACTAGTGTCACG 59.298 38.462 0.00 0.00 0.00 4.35
2456 5311 1.529244 GTCCCTGGCACTGCTTTGT 60.529 57.895 0.00 0.00 0.00 2.83
2465 5320 1.733912 GCACTGCTTTGTCGATCATCA 59.266 47.619 0.00 0.00 0.00 3.07
2479 5334 5.120674 GTCGATCATCATTGACACAACTTCA 59.879 40.000 0.00 0.00 41.60 3.02
2481 5336 5.349543 CGATCATCATTGACACAACTTCAGA 59.650 40.000 0.00 0.00 33.85 3.27
2508 5364 3.634568 TTTTGTTGGGAACGTAGCATG 57.365 42.857 0.00 0.00 0.00 4.06
2509 5365 2.264005 TTGTTGGGAACGTAGCATGT 57.736 45.000 0.00 0.00 0.00 3.21
2541 5397 3.455619 AAAAATCTACGCTCACGCAAG 57.544 42.857 0.00 0.00 45.53 4.01
2542 5398 2.363788 AAATCTACGCTCACGCAAGA 57.636 45.000 0.00 0.00 45.53 3.02
2543 5399 2.586258 AATCTACGCTCACGCAAGAT 57.414 45.000 0.00 0.00 43.38 2.40
2544 5400 2.126914 ATCTACGCTCACGCAAGATC 57.873 50.000 0.00 0.00 45.53 2.75
2545 5401 1.095600 TCTACGCTCACGCAAGATCT 58.904 50.000 0.00 0.00 45.53 2.75
2546 5402 2.285977 TCTACGCTCACGCAAGATCTA 58.714 47.619 0.00 0.00 45.53 1.98
2547 5403 2.879026 TCTACGCTCACGCAAGATCTAT 59.121 45.455 0.00 0.00 45.53 1.98
2548 5404 2.126914 ACGCTCACGCAAGATCTATC 57.873 50.000 0.00 0.00 45.53 2.08
2549 5405 1.678627 ACGCTCACGCAAGATCTATCT 59.321 47.619 0.00 0.00 45.53 1.98
2550 5406 2.879026 ACGCTCACGCAAGATCTATCTA 59.121 45.455 0.00 0.00 45.53 1.98
2551 5407 3.058570 ACGCTCACGCAAGATCTATCTAG 60.059 47.826 0.00 0.00 45.53 2.43
2552 5408 3.669290 CGCTCACGCAAGATCTATCTAGG 60.669 52.174 0.00 0.00 43.62 3.02
2553 5409 3.504134 GCTCACGCAAGATCTATCTAGGA 59.496 47.826 0.00 0.00 43.62 2.94
2554 5410 4.379394 GCTCACGCAAGATCTATCTAGGAG 60.379 50.000 0.00 0.94 43.62 3.69
2555 5411 4.974399 TCACGCAAGATCTATCTAGGAGA 58.026 43.478 0.00 0.00 43.62 3.71
2556 5412 5.565509 TCACGCAAGATCTATCTAGGAGAT 58.434 41.667 0.00 7.55 38.77 2.75
2557 5413 5.414144 TCACGCAAGATCTATCTAGGAGATG 59.586 44.000 11.48 2.82 36.70 2.90
2558 5414 4.157656 ACGCAAGATCTATCTAGGAGATGC 59.842 45.833 11.48 9.81 36.70 3.91
2559 5415 4.157472 CGCAAGATCTATCTAGGAGATGCA 59.843 45.833 11.48 0.00 35.65 3.96
2560 5416 5.163530 CGCAAGATCTATCTAGGAGATGCAT 60.164 44.000 0.00 0.00 35.65 3.96
2561 5417 6.039159 CGCAAGATCTATCTAGGAGATGCATA 59.961 42.308 0.00 0.00 35.65 3.14
2562 5418 7.428020 GCAAGATCTATCTAGGAGATGCATAG 58.572 42.308 0.00 0.00 35.37 2.23
2563 5419 7.428020 CAAGATCTATCTAGGAGATGCATAGC 58.572 42.308 0.00 0.00 35.37 2.97
2564 5420 6.671605 AGATCTATCTAGGAGATGCATAGCA 58.328 40.000 0.00 0.00 38.03 3.49
2565 5421 7.124721 AGATCTATCTAGGAGATGCATAGCAA 58.875 38.462 0.00 0.00 37.47 3.91
2566 5422 6.522625 TCTATCTAGGAGATGCATAGCAAC 57.477 41.667 0.00 0.00 43.62 4.17
2567 5423 3.650070 TCTAGGAGATGCATAGCAACG 57.350 47.619 0.00 0.00 43.62 4.10
2568 5424 3.222603 TCTAGGAGATGCATAGCAACGA 58.777 45.455 0.00 0.00 43.62 3.85
2569 5425 2.522836 AGGAGATGCATAGCAACGAG 57.477 50.000 0.00 0.00 43.62 4.18
2570 5426 1.069823 AGGAGATGCATAGCAACGAGG 59.930 52.381 0.00 0.00 43.62 4.63
2571 5427 1.506493 GAGATGCATAGCAACGAGGG 58.494 55.000 0.00 0.00 43.62 4.30
2572 5428 0.107456 AGATGCATAGCAACGAGGGG 59.893 55.000 0.00 0.00 43.62 4.79
2573 5429 0.886490 GATGCATAGCAACGAGGGGG 60.886 60.000 0.00 0.00 43.62 5.40
2574 5430 1.344953 ATGCATAGCAACGAGGGGGA 61.345 55.000 0.00 0.00 43.62 4.81
2575 5431 1.227674 GCATAGCAACGAGGGGGAG 60.228 63.158 0.00 0.00 0.00 4.30
2576 5432 1.686325 GCATAGCAACGAGGGGGAGA 61.686 60.000 0.00 0.00 0.00 3.71
2577 5433 0.390860 CATAGCAACGAGGGGGAGAG 59.609 60.000 0.00 0.00 0.00 3.20
2578 5434 0.032017 ATAGCAACGAGGGGGAGAGT 60.032 55.000 0.00 0.00 0.00 3.24
2579 5435 0.970937 TAGCAACGAGGGGGAGAGTG 60.971 60.000 0.00 0.00 0.00 3.51
2580 5436 2.584391 GCAACGAGGGGGAGAGTGT 61.584 63.158 0.00 0.00 0.00 3.55
2581 5437 1.293498 CAACGAGGGGGAGAGTGTG 59.707 63.158 0.00 0.00 0.00 3.82
2582 5438 1.152312 AACGAGGGGGAGAGTGTGT 60.152 57.895 0.00 0.00 0.00 3.72
2583 5439 1.186267 AACGAGGGGGAGAGTGTGTC 61.186 60.000 0.00 0.00 0.00 3.67
2584 5440 1.304547 CGAGGGGGAGAGTGTGTCT 60.305 63.158 0.00 0.00 38.71 3.41
2585 5441 0.034380 CGAGGGGGAGAGTGTGTCTA 60.034 60.000 0.00 0.00 34.71 2.59
2586 5442 1.476477 GAGGGGGAGAGTGTGTCTAC 58.524 60.000 0.00 0.00 34.71 2.59
2587 5443 0.323542 AGGGGGAGAGTGTGTCTACG 60.324 60.000 0.00 0.00 36.91 3.51
2588 5444 0.611340 GGGGGAGAGTGTGTCTACGT 60.611 60.000 0.00 0.00 36.91 3.57
2589 5445 1.340405 GGGGGAGAGTGTGTCTACGTA 60.340 57.143 0.00 0.00 36.91 3.57
2590 5446 1.742268 GGGGAGAGTGTGTCTACGTAC 59.258 57.143 0.00 0.00 36.91 3.67
2591 5447 1.742268 GGGAGAGTGTGTCTACGTACC 59.258 57.143 0.00 0.00 36.91 3.34
2592 5448 1.742268 GGAGAGTGTGTCTACGTACCC 59.258 57.143 0.00 0.00 34.71 3.69
2593 5449 2.617532 GGAGAGTGTGTCTACGTACCCT 60.618 54.545 0.00 0.00 34.71 4.34
2594 5450 2.677337 GAGAGTGTGTCTACGTACCCTC 59.323 54.545 0.00 0.00 34.71 4.30
2595 5451 1.396301 GAGTGTGTCTACGTACCCTCG 59.604 57.143 0.00 0.00 0.00 4.63
2596 5452 1.160137 GTGTGTCTACGTACCCTCGT 58.840 55.000 0.00 0.00 45.97 4.18
2597 5453 2.028112 AGTGTGTCTACGTACCCTCGTA 60.028 50.000 0.00 0.00 43.80 3.43
2603 5459 2.779755 TACGTACCCTCGTAGACCAA 57.220 50.000 0.00 0.00 43.80 3.67
2604 5460 1.909700 ACGTACCCTCGTAGACCAAA 58.090 50.000 0.00 0.00 42.35 3.28
2605 5461 2.238521 ACGTACCCTCGTAGACCAAAA 58.761 47.619 0.00 0.00 42.35 2.44
2606 5462 2.229784 ACGTACCCTCGTAGACCAAAAG 59.770 50.000 0.00 0.00 42.35 2.27
2607 5463 2.229784 CGTACCCTCGTAGACCAAAAGT 59.770 50.000 0.00 0.00 0.00 2.66
2608 5464 2.833631 ACCCTCGTAGACCAAAAGTG 57.166 50.000 0.00 0.00 0.00 3.16
2609 5465 2.322658 ACCCTCGTAGACCAAAAGTGA 58.677 47.619 0.00 0.00 0.00 3.41
2610 5466 2.701951 ACCCTCGTAGACCAAAAGTGAA 59.298 45.455 0.00 0.00 0.00 3.18
2611 5467 3.135167 ACCCTCGTAGACCAAAAGTGAAA 59.865 43.478 0.00 0.00 0.00 2.69
2612 5468 3.746492 CCCTCGTAGACCAAAAGTGAAAG 59.254 47.826 0.00 0.00 0.00 2.62
2613 5469 3.186613 CCTCGTAGACCAAAAGTGAAAGC 59.813 47.826 0.00 0.00 0.00 3.51
2614 5470 2.798283 TCGTAGACCAAAAGTGAAAGCG 59.202 45.455 0.00 0.00 0.00 4.68
2615 5471 2.542595 CGTAGACCAAAAGTGAAAGCGT 59.457 45.455 0.00 0.00 0.00 5.07
2616 5472 3.001939 CGTAGACCAAAAGTGAAAGCGTT 59.998 43.478 0.00 0.00 0.00 4.84
2617 5473 4.495184 CGTAGACCAAAAGTGAAAGCGTTT 60.495 41.667 0.00 0.00 0.00 3.60
2618 5474 3.769536 AGACCAAAAGTGAAAGCGTTTG 58.230 40.909 0.00 0.00 37.50 2.93
2619 5475 3.442273 AGACCAAAAGTGAAAGCGTTTGA 59.558 39.130 6.16 0.00 39.16 2.69
2620 5476 3.507786 ACCAAAAGTGAAAGCGTTTGAC 58.492 40.909 6.16 0.00 39.16 3.18
2621 5477 3.057174 ACCAAAAGTGAAAGCGTTTGACA 60.057 39.130 6.16 0.00 39.16 3.58
2622 5478 3.923461 CCAAAAGTGAAAGCGTTTGACAA 59.077 39.130 6.16 0.00 39.16 3.18
2623 5479 4.201580 CCAAAAGTGAAAGCGTTTGACAAC 60.202 41.667 6.16 0.00 39.16 3.32
2634 5490 2.916111 GTTTGACAACGCGATTGATGT 58.084 42.857 15.93 9.56 41.23 3.06
2635 5491 4.060288 GTTTGACAACGCGATTGATGTA 57.940 40.909 15.93 1.11 41.23 2.29
2636 5492 3.989705 TTGACAACGCGATTGATGTAG 57.010 42.857 15.93 0.00 41.23 2.74
2637 5493 2.954316 TGACAACGCGATTGATGTAGT 58.046 42.857 15.93 0.00 41.23 2.73
2638 5494 2.921121 TGACAACGCGATTGATGTAGTC 59.079 45.455 15.93 3.20 41.23 2.59
2639 5495 1.917955 ACAACGCGATTGATGTAGTCG 59.082 47.619 15.93 0.00 41.23 4.18
2640 5496 2.182014 CAACGCGATTGATGTAGTCGA 58.818 47.619 15.93 0.00 40.55 4.20
2641 5497 2.554806 ACGCGATTGATGTAGTCGAA 57.445 45.000 15.93 0.00 40.55 3.71
2642 5498 2.182825 ACGCGATTGATGTAGTCGAAC 58.817 47.619 15.93 0.00 40.55 3.95
2643 5499 2.159421 ACGCGATTGATGTAGTCGAACT 60.159 45.455 15.93 0.00 40.55 3.01
2644 5500 2.852413 CGCGATTGATGTAGTCGAACTT 59.148 45.455 0.00 0.00 40.55 2.66
2645 5501 3.061797 CGCGATTGATGTAGTCGAACTTC 60.062 47.826 0.00 0.00 40.55 3.01
2646 5502 4.106197 GCGATTGATGTAGTCGAACTTCT 58.894 43.478 0.00 0.00 40.55 2.85
2647 5503 4.563184 GCGATTGATGTAGTCGAACTTCTT 59.437 41.667 0.00 0.00 40.55 2.52
2648 5504 5.275974 GCGATTGATGTAGTCGAACTTCTTC 60.276 44.000 0.00 0.00 40.55 2.87
2649 5505 6.030849 CGATTGATGTAGTCGAACTTCTTCT 58.969 40.000 0.00 0.00 40.55 2.85
2650 5506 7.187480 CGATTGATGTAGTCGAACTTCTTCTA 58.813 38.462 0.00 0.00 40.55 2.10
2651 5507 7.374754 CGATTGATGTAGTCGAACTTCTTCTAG 59.625 40.741 0.00 0.00 40.55 2.43
2652 5508 5.881447 TGATGTAGTCGAACTTCTTCTAGC 58.119 41.667 0.00 0.00 0.00 3.42
2653 5509 5.648526 TGATGTAGTCGAACTTCTTCTAGCT 59.351 40.000 0.00 0.00 0.00 3.32
2654 5510 5.548706 TGTAGTCGAACTTCTTCTAGCTC 57.451 43.478 0.00 0.00 0.00 4.09
2655 5511 4.395542 TGTAGTCGAACTTCTTCTAGCTCC 59.604 45.833 0.00 0.00 0.00 4.70
2656 5512 2.420722 AGTCGAACTTCTTCTAGCTCCG 59.579 50.000 0.00 0.00 0.00 4.63
2657 5513 2.419324 GTCGAACTTCTTCTAGCTCCGA 59.581 50.000 0.00 0.00 0.00 4.55
2658 5514 2.419324 TCGAACTTCTTCTAGCTCCGAC 59.581 50.000 0.00 0.00 0.00 4.79
2659 5515 2.478200 CGAACTTCTTCTAGCTCCGACC 60.478 54.545 0.00 0.00 0.00 4.79
2660 5516 1.096416 ACTTCTTCTAGCTCCGACCG 58.904 55.000 0.00 0.00 0.00 4.79
2661 5517 1.339824 ACTTCTTCTAGCTCCGACCGA 60.340 52.381 0.00 0.00 0.00 4.69
2662 5518 1.950909 CTTCTTCTAGCTCCGACCGAT 59.049 52.381 0.00 0.00 0.00 4.18
2663 5519 1.595466 TCTTCTAGCTCCGACCGATC 58.405 55.000 0.00 0.00 0.00 3.69
2664 5520 1.134189 TCTTCTAGCTCCGACCGATCA 60.134 52.381 0.00 0.00 0.00 2.92
2665 5521 1.676529 CTTCTAGCTCCGACCGATCAA 59.323 52.381 0.00 0.00 0.00 2.57
2666 5522 1.758936 TCTAGCTCCGACCGATCAAA 58.241 50.000 0.00 0.00 0.00 2.69
2667 5523 1.404391 TCTAGCTCCGACCGATCAAAC 59.596 52.381 0.00 0.00 0.00 2.93
2668 5524 1.134367 CTAGCTCCGACCGATCAAACA 59.866 52.381 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.630242 TGTATTCTTGATTTCCTAGCTTTGG 57.370 36.000 0.00 0.00 0.00 3.28
139 140 5.560722 TCCTGGTCAAAAGACAAGATACA 57.439 39.130 1.65 0.00 0.00 2.29
159 160 2.408271 TCAGCAACTGTCATGGATCC 57.592 50.000 4.20 4.20 32.61 3.36
181 207 6.709018 ACCAGTATAAACTTGTGCAAACTT 57.291 33.333 0.00 0.00 30.75 2.66
245 404 0.171903 GCAATGATCGCAAACTGGCT 59.828 50.000 0.00 0.00 0.00 4.75
294 453 4.455877 ACAATACTGGCCTTTCTTTCTTCG 59.544 41.667 3.32 0.00 0.00 3.79
325 488 1.137872 CTGAATTGGTCCGAGAGAGGG 59.862 57.143 0.00 0.00 0.00 4.30
344 507 6.238648 CCGACAAGTAAAGTTCCAAACATTCT 60.239 38.462 0.00 0.00 0.00 2.40
357 520 6.142817 CAGAAAAATCCACCGACAAGTAAAG 58.857 40.000 0.00 0.00 0.00 1.85
403 566 7.812306 TCCTATTAAAATCCTTCCAGTTAGGG 58.188 38.462 0.00 0.00 38.24 3.53
663 1254 5.414144 TGTGTTTGTTCACTCATTTCAGTCA 59.586 36.000 0.00 0.00 38.90 3.41
1613 2288 2.269172 GTAGCTGCTCGTAAAACCTCC 58.731 52.381 4.91 0.00 0.00 4.30
1638 2313 1.953138 GATGGCGATCGAGTGCTGG 60.953 63.158 21.57 0.00 0.00 4.85
1928 2604 7.569591 GCAATGATTACTCCGTGAAATAGTAGC 60.570 40.741 0.00 0.00 0.00 3.58
2007 2683 5.304871 TGCATGCATTTATATGGGTGAATGT 59.695 36.000 18.46 0.00 31.56 2.71
2024 2700 6.443934 AAAGGTAAAATATACGTGCATGCA 57.556 33.333 18.46 18.46 0.00 3.96
2025 2701 8.286800 TCATAAAGGTAAAATATACGTGCATGC 58.713 33.333 11.82 11.82 0.00 4.06
2059 2735 5.982890 TGTGATGTTGTCTCAGTATCTCA 57.017 39.130 0.00 0.00 0.00 3.27
2062 2738 7.840342 AAAGATGTGATGTTGTCTCAGTATC 57.160 36.000 0.00 0.00 34.16 2.24
2063 2739 8.627208 AAAAAGATGTGATGTTGTCTCAGTAT 57.373 30.769 0.00 0.00 34.16 2.12
2090 2766 5.121811 CCAGTGAATACAGGATCTTTCAGG 58.878 45.833 0.00 0.00 35.61 3.86
2229 2908 1.217882 AACCGCGAGAGTTTGTGAAG 58.782 50.000 8.23 0.00 0.00 3.02
2246 2925 0.446616 GGGGATTTGACGCGAGAAAC 59.553 55.000 15.93 2.80 0.00 2.78
2253 2932 3.812577 CCTTTTGGGGATTTGACGC 57.187 52.632 0.00 0.00 35.46 5.19
2307 2986 3.668447 GCAAACAGAAGAGACATGGAGA 58.332 45.455 0.00 0.00 0.00 3.71
2310 2989 1.466167 CCGCAAACAGAAGAGACATGG 59.534 52.381 0.00 0.00 0.00 3.66
2330 3009 1.160329 AGTGTGAAGGACGTGCTTGC 61.160 55.000 27.84 18.63 0.00 4.01
2360 3039 0.471211 AACAACTCCACCTCGAGGGA 60.471 55.000 34.04 21.38 40.27 4.20
2365 3044 2.056577 GAACGTAACAACTCCACCTCG 58.943 52.381 0.00 0.00 0.00 4.63
2375 5230 5.522460 GGCATATCTAGCTTGAACGTAACAA 59.478 40.000 0.99 7.64 0.00 2.83
2383 5238 9.494271 CTAGTTTAATGGCATATCTAGCTTGAA 57.506 33.333 0.00 0.00 0.00 2.69
2402 5257 5.618056 AAGACGATCGTGACACTAGTTTA 57.382 39.130 28.12 0.00 0.00 2.01
2407 5262 3.909776 ACAAAGACGATCGTGACACTA 57.090 42.857 28.12 0.00 0.00 2.74
2416 5271 2.747989 GGGAAAGGGAACAAAGACGATC 59.252 50.000 0.00 0.00 0.00 3.69
2456 5311 5.237048 TGAAGTTGTGTCAATGATGATCGA 58.763 37.500 0.00 0.00 38.01 3.59
2465 5320 4.536364 CAACGTCTGAAGTTGTGTCAAT 57.464 40.909 22.76 0.00 42.72 2.57
2479 5334 3.671164 CGTTCCCAACAAAAACAACGTCT 60.671 43.478 0.00 0.00 33.61 4.18
2481 5336 2.030096 ACGTTCCCAACAAAAACAACGT 60.030 40.909 2.00 2.00 43.58 3.99
2488 5343 2.952978 ACATGCTACGTTCCCAACAAAA 59.047 40.909 0.00 0.00 0.00 2.44
2532 5388 5.000591 TCTCCTAGATAGATCTTGCGTGAG 58.999 45.833 0.00 1.23 38.32 3.51
2533 5389 4.974399 TCTCCTAGATAGATCTTGCGTGA 58.026 43.478 0.00 0.00 38.32 4.35
2534 5390 5.639757 CATCTCCTAGATAGATCTTGCGTG 58.360 45.833 0.00 0.00 38.32 5.34
2535 5391 4.157656 GCATCTCCTAGATAGATCTTGCGT 59.842 45.833 0.00 0.00 38.32 5.24
2536 5392 4.157472 TGCATCTCCTAGATAGATCTTGCG 59.843 45.833 0.00 0.00 36.48 4.85
2537 5393 5.657826 TGCATCTCCTAGATAGATCTTGC 57.342 43.478 0.00 0.69 38.32 4.01
2538 5394 7.068470 TGCTATGCATCTCCTAGATAGATCTTG 59.932 40.741 0.19 0.00 32.12 3.02
2539 5395 7.124721 TGCTATGCATCTCCTAGATAGATCTT 58.875 38.462 0.19 0.00 32.12 2.40
2540 5396 6.671605 TGCTATGCATCTCCTAGATAGATCT 58.328 40.000 0.19 0.00 32.12 2.75
2541 5397 6.957920 TGCTATGCATCTCCTAGATAGATC 57.042 41.667 0.19 0.00 32.12 2.75
2542 5398 6.183360 CGTTGCTATGCATCTCCTAGATAGAT 60.183 42.308 0.19 0.00 38.76 1.98
2543 5399 5.124617 CGTTGCTATGCATCTCCTAGATAGA 59.875 44.000 0.19 0.00 38.76 1.98
2544 5400 5.124617 TCGTTGCTATGCATCTCCTAGATAG 59.875 44.000 0.19 0.00 38.76 2.08
2545 5401 5.010282 TCGTTGCTATGCATCTCCTAGATA 58.990 41.667 0.19 0.00 38.76 1.98
2546 5402 3.829026 TCGTTGCTATGCATCTCCTAGAT 59.171 43.478 0.19 0.00 38.76 1.98
2547 5403 3.222603 TCGTTGCTATGCATCTCCTAGA 58.777 45.455 0.19 0.00 38.76 2.43
2548 5404 3.573598 CTCGTTGCTATGCATCTCCTAG 58.426 50.000 0.19 0.00 38.76 3.02
2549 5405 2.297315 CCTCGTTGCTATGCATCTCCTA 59.703 50.000 0.19 0.00 38.76 2.94
2550 5406 1.069823 CCTCGTTGCTATGCATCTCCT 59.930 52.381 0.19 0.00 38.76 3.69
2551 5407 1.506493 CCTCGTTGCTATGCATCTCC 58.494 55.000 0.19 0.00 38.76 3.71
2552 5408 1.506493 CCCTCGTTGCTATGCATCTC 58.494 55.000 0.19 0.00 38.76 2.75
2553 5409 0.107456 CCCCTCGTTGCTATGCATCT 59.893 55.000 0.19 0.00 38.76 2.90
2554 5410 0.886490 CCCCCTCGTTGCTATGCATC 60.886 60.000 0.19 0.00 38.76 3.91
2555 5411 1.149174 CCCCCTCGTTGCTATGCAT 59.851 57.895 3.79 3.79 38.76 3.96
2556 5412 1.971505 CTCCCCCTCGTTGCTATGCA 61.972 60.000 0.00 0.00 36.47 3.96
2557 5413 1.227674 CTCCCCCTCGTTGCTATGC 60.228 63.158 0.00 0.00 0.00 3.14
2558 5414 0.390860 CTCTCCCCCTCGTTGCTATG 59.609 60.000 0.00 0.00 0.00 2.23
2559 5415 0.032017 ACTCTCCCCCTCGTTGCTAT 60.032 55.000 0.00 0.00 0.00 2.97
2560 5416 0.970937 CACTCTCCCCCTCGTTGCTA 60.971 60.000 0.00 0.00 0.00 3.49
2561 5417 2.120718 ACTCTCCCCCTCGTTGCT 59.879 61.111 0.00 0.00 0.00 3.91
2562 5418 2.266055 CACTCTCCCCCTCGTTGC 59.734 66.667 0.00 0.00 0.00 4.17
2563 5419 1.293498 CACACTCTCCCCCTCGTTG 59.707 63.158 0.00 0.00 0.00 4.10
2564 5420 1.152312 ACACACTCTCCCCCTCGTT 60.152 57.895 0.00 0.00 0.00 3.85
2565 5421 1.606889 GACACACTCTCCCCCTCGT 60.607 63.158 0.00 0.00 0.00 4.18
2566 5422 0.034380 TAGACACACTCTCCCCCTCG 60.034 60.000 0.00 0.00 0.00 4.63
2567 5423 1.476477 GTAGACACACTCTCCCCCTC 58.524 60.000 0.00 0.00 0.00 4.30
2568 5424 0.323542 CGTAGACACACTCTCCCCCT 60.324 60.000 0.00 0.00 0.00 4.79
2569 5425 0.611340 ACGTAGACACACTCTCCCCC 60.611 60.000 0.00 0.00 0.00 5.40
2570 5426 1.742268 GTACGTAGACACACTCTCCCC 59.258 57.143 0.00 0.00 0.00 4.81
2571 5427 1.742268 GGTACGTAGACACACTCTCCC 59.258 57.143 0.00 0.00 0.00 4.30
2572 5428 1.742268 GGGTACGTAGACACACTCTCC 59.258 57.143 0.00 0.00 0.00 3.71
2573 5429 2.677337 GAGGGTACGTAGACACACTCTC 59.323 54.545 10.55 4.79 41.06 3.20
2574 5430 2.709213 GAGGGTACGTAGACACACTCT 58.291 52.381 10.55 0.00 41.06 3.24
2575 5431 1.396301 CGAGGGTACGTAGACACACTC 59.604 57.143 8.17 8.17 40.93 3.51
2576 5432 1.271054 ACGAGGGTACGTAGACACACT 60.271 52.381 0.00 0.00 44.72 3.55
2577 5433 1.160137 ACGAGGGTACGTAGACACAC 58.840 55.000 0.00 0.00 44.72 3.82
2578 5434 2.760634 TACGAGGGTACGTAGACACA 57.239 50.000 0.00 0.00 44.72 3.72
2584 5440 2.779755 TTGGTCTACGAGGGTACGTA 57.220 50.000 0.00 0.00 44.72 3.57
2586 5442 2.229784 ACTTTTGGTCTACGAGGGTACG 59.770 50.000 0.00 0.00 39.31 3.67
2587 5443 3.256631 TCACTTTTGGTCTACGAGGGTAC 59.743 47.826 0.00 0.00 0.00 3.34
2588 5444 3.499338 TCACTTTTGGTCTACGAGGGTA 58.501 45.455 0.00 0.00 0.00 3.69
2589 5445 2.322658 TCACTTTTGGTCTACGAGGGT 58.677 47.619 0.00 0.00 0.00 4.34
2590 5446 3.396260 TTCACTTTTGGTCTACGAGGG 57.604 47.619 0.00 0.00 0.00 4.30
2591 5447 3.186613 GCTTTCACTTTTGGTCTACGAGG 59.813 47.826 0.00 0.00 0.00 4.63
2592 5448 3.120991 CGCTTTCACTTTTGGTCTACGAG 60.121 47.826 0.00 0.00 0.00 4.18
2593 5449 2.798283 CGCTTTCACTTTTGGTCTACGA 59.202 45.455 0.00 0.00 0.00 3.43
2594 5450 2.542595 ACGCTTTCACTTTTGGTCTACG 59.457 45.455 0.00 0.00 0.00 3.51
2595 5451 4.547406 AACGCTTTCACTTTTGGTCTAC 57.453 40.909 0.00 0.00 0.00 2.59
2596 5452 4.636648 TCAAACGCTTTCACTTTTGGTCTA 59.363 37.500 0.00 0.00 31.20 2.59
2597 5453 3.442273 TCAAACGCTTTCACTTTTGGTCT 59.558 39.130 0.00 0.00 31.20 3.85
2598 5454 3.546271 GTCAAACGCTTTCACTTTTGGTC 59.454 43.478 0.00 0.00 31.20 4.02
2599 5455 3.057174 TGTCAAACGCTTTCACTTTTGGT 60.057 39.130 0.00 0.00 31.20 3.67
2600 5456 3.506810 TGTCAAACGCTTTCACTTTTGG 58.493 40.909 0.00 0.00 31.20 3.28
2601 5457 4.870106 GTTGTCAAACGCTTTCACTTTTG 58.130 39.130 0.00 0.00 0.00 2.44
2614 5470 2.916111 ACATCAATCGCGTTGTCAAAC 58.084 42.857 5.77 0.00 38.95 2.93
2615 5471 3.743911 ACTACATCAATCGCGTTGTCAAA 59.256 39.130 5.77 0.00 38.95 2.69
2616 5472 3.322369 ACTACATCAATCGCGTTGTCAA 58.678 40.909 5.77 0.00 38.95 3.18
2617 5473 2.921121 GACTACATCAATCGCGTTGTCA 59.079 45.455 5.77 0.00 38.95 3.58
2618 5474 2.035674 CGACTACATCAATCGCGTTGTC 60.036 50.000 5.77 0.36 38.95 3.18
2619 5475 1.917955 CGACTACATCAATCGCGTTGT 59.082 47.619 5.77 6.34 38.95 3.32
2620 5476 2.182014 TCGACTACATCAATCGCGTTG 58.818 47.619 5.77 10.48 39.25 4.10
2621 5477 2.554806 TCGACTACATCAATCGCGTT 57.445 45.000 5.77 0.00 35.82 4.84
2622 5478 2.159421 AGTTCGACTACATCAATCGCGT 60.159 45.455 5.77 0.00 35.82 6.01
2623 5479 2.451132 AGTTCGACTACATCAATCGCG 58.549 47.619 0.00 0.00 35.82 5.87
2624 5480 4.106197 AGAAGTTCGACTACATCAATCGC 58.894 43.478 0.00 0.00 35.82 4.58
2625 5481 6.030849 AGAAGAAGTTCGACTACATCAATCG 58.969 40.000 0.00 0.00 37.79 3.34
2626 5482 7.166804 GCTAGAAGAAGTTCGACTACATCAATC 59.833 40.741 0.00 0.00 37.79 2.67
2627 5483 6.975772 GCTAGAAGAAGTTCGACTACATCAAT 59.024 38.462 0.00 0.00 37.79 2.57
2628 5484 6.151312 AGCTAGAAGAAGTTCGACTACATCAA 59.849 38.462 0.00 0.00 37.79 2.57
2629 5485 5.648526 AGCTAGAAGAAGTTCGACTACATCA 59.351 40.000 0.00 0.00 37.79 3.07
2630 5486 6.126568 AGCTAGAAGAAGTTCGACTACATC 57.873 41.667 0.00 0.00 37.79 3.06
2631 5487 5.066764 GGAGCTAGAAGAAGTTCGACTACAT 59.933 44.000 0.00 0.00 37.79 2.29
2632 5488 4.395542 GGAGCTAGAAGAAGTTCGACTACA 59.604 45.833 0.00 0.00 37.79 2.74
2633 5489 4.494526 CGGAGCTAGAAGAAGTTCGACTAC 60.495 50.000 0.00 0.00 37.79 2.73
2634 5490 3.622163 CGGAGCTAGAAGAAGTTCGACTA 59.378 47.826 0.00 4.84 37.79 2.59
2635 5491 2.420722 CGGAGCTAGAAGAAGTTCGACT 59.579 50.000 0.00 3.92 37.79 4.18
2636 5492 2.419324 TCGGAGCTAGAAGAAGTTCGAC 59.581 50.000 0.00 0.00 37.79 4.20
2637 5493 2.419324 GTCGGAGCTAGAAGAAGTTCGA 59.581 50.000 0.00 0.00 37.79 3.71
2638 5494 2.478200 GGTCGGAGCTAGAAGAAGTTCG 60.478 54.545 0.00 0.00 37.79 3.95
2639 5495 2.478200 CGGTCGGAGCTAGAAGAAGTTC 60.478 54.545 5.58 0.00 0.00 3.01
2640 5496 1.473278 CGGTCGGAGCTAGAAGAAGTT 59.527 52.381 5.58 0.00 0.00 2.66
2641 5497 1.096416 CGGTCGGAGCTAGAAGAAGT 58.904 55.000 5.58 0.00 0.00 3.01
2642 5498 1.380524 TCGGTCGGAGCTAGAAGAAG 58.619 55.000 5.58 0.00 0.00 2.85
2643 5499 1.948145 GATCGGTCGGAGCTAGAAGAA 59.052 52.381 5.58 0.00 0.00 2.52
2644 5500 1.134189 TGATCGGTCGGAGCTAGAAGA 60.134 52.381 5.58 0.00 30.59 2.87
2645 5501 1.309950 TGATCGGTCGGAGCTAGAAG 58.690 55.000 5.58 0.00 30.59 2.85
2646 5502 1.758936 TTGATCGGTCGGAGCTAGAA 58.241 50.000 5.58 0.00 30.59 2.10
2647 5503 1.404391 GTTTGATCGGTCGGAGCTAGA 59.596 52.381 5.58 0.00 30.59 2.43
2648 5504 1.134367 TGTTTGATCGGTCGGAGCTAG 59.866 52.381 5.58 0.00 30.59 3.42
2649 5505 1.179152 TGTTTGATCGGTCGGAGCTA 58.821 50.000 5.58 0.00 30.59 3.32
2650 5506 1.972198 TGTTTGATCGGTCGGAGCT 59.028 52.632 5.58 0.00 30.59 4.09
2651 5507 4.590487 TGTTTGATCGGTCGGAGC 57.410 55.556 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.