Multiple sequence alignment - TraesCS2D01G176300

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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 TraesCS2D01G176300 chr2D 100.000 2525 0 0 1 2525 119822926 119820402 0.000000e+00 4663
1 TraesCS2D01G176300 chr2D 92.793 111 7 1 463 572 470676054 470676164 2.600000e-35 159
2 TraesCS2D01G176300 chr2D 88.430 121 14 0 452 572 12692237 12692357 2.020000e-31 147
3 TraesCS2D01G176300 chr2A 92.421 1227 64 9 611 1814 122134077 122132857 0.000000e+00 1724
4 TraesCS2D01G176300 chr2A 86.975 238 14 12 169 403 122134678 122134455 4.170000e-63 252
5 TraesCS2D01G176300 chr2A 77.778 288 48 13 98 383 707556532 707556259 2.010000e-36 163
6 TraesCS2D01G176300 chr2A 92.174 115 8 1 459 572 539014584 539014698 7.230000e-36 161
7 TraesCS2D01G176300 chr2B 92.432 740 46 7 1085 1815 172175706 172174968 0.000000e+00 1048
8 TraesCS2D01G176300 chr2B 93.404 470 30 1 611 1080 172176224 172175756 0.000000e+00 695
9 TraesCS2D01G176300 chr2B 89.607 433 32 8 1 426 172178156 172177730 2.860000e-149 538
10 TraesCS2D01G176300 chr2B 93.043 115 7 1 459 572 575148100 575147986 1.550000e-37 167
11 TraesCS2D01G176300 chr2B 90.435 115 10 1 459 572 518048328 518048442 1.560000e-32 150
12 TraesCS2D01G176300 chr1B 92.500 720 31 6 1810 2525 29584244 29583544 0.000000e+00 1009
13 TraesCS2D01G176300 chr3A 83.401 735 86 18 1811 2516 54349321 54350048 0.000000e+00 649
14 TraesCS2D01G176300 chr3A 83.220 733 90 19 1811 2516 54362428 54363154 2.120000e-180 641
15 TraesCS2D01G176300 chr3A 82.585 735 83 22 1811 2516 54327550 54328268 7.720000e-170 606
16 TraesCS2D01G176300 chr3A 78.992 238 34 11 75 305 747768611 747768839 5.630000e-32 148
17 TraesCS2D01G176300 chr3A 82.558 172 25 3 2191 2361 14070515 14070348 2.020000e-31 147
18 TraesCS2D01G176300 chr1A 83.564 724 86 19 1814 2510 586701127 586701844 0.000000e+00 647
19 TraesCS2D01G176300 chr1A 82.806 727 88 23 1814 2516 518054160 518053447 1.280000e-172 616
20 TraesCS2D01G176300 chr7A 88.427 337 29 4 2194 2525 571272054 571272385 5.060000e-107 398
21 TraesCS2D01G176300 chr3B 88.650 326 19 4 2200 2520 809221334 809221022 5.100000e-102 381
22 TraesCS2D01G176300 chr3B 84.709 327 32 8 1815 2134 809221660 809221345 6.780000e-81 311
23 TraesCS2D01G176300 chr7D 74.000 700 134 22 1814 2500 523432893 523433557 9.030000e-60 241
24 TraesCS2D01G176300 chr6B 73.287 715 120 35 1814 2520 551971826 551971175 1.980000e-46 196
25 TraesCS2D01G176300 chr7B 74.590 488 74 25 1814 2294 545989735 545989291 4.320000e-38 169
26 TraesCS2D01G176300 chr3D 90.517 116 10 1 459 573 14846785 14846670 4.350000e-33 152
27 TraesCS2D01G176300 chr3D 88.983 118 13 0 455 572 581983589 581983706 2.020000e-31 147
28 TraesCS2D01G176300 chrUn 78.992 238 35 10 75 305 33732737 33732966 5.630000e-32 148
29 TraesCS2D01G176300 chrUn 78.992 238 34 11 75 305 397470245 397470017 5.630000e-32 148
30 TraesCS2D01G176300 chr6D 90.265 113 11 0 460 572 367751319 367751207 5.630000e-32 148
31 TraesCS2D01G176300 chr5A 92.233 103 8 0 470 572 464481730 464481628 2.020000e-31 147
32 TraesCS2D01G176300 chr5B 92.222 90 6 1 2435 2524 595295142 595295054 2.640000e-25 126


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 TraesCS2D01G176300 chr2D 119820402 119822926 2524 True 4663.000000 4663 100.000000 1 2525 1 chr2D.!!$R1 2524
1 TraesCS2D01G176300 chr2A 122132857 122134678 1821 True 988.000000 1724 89.698000 169 1814 2 chr2A.!!$R2 1645
2 TraesCS2D01G176300 chr2B 172174968 172178156 3188 True 760.333333 1048 91.814333 1 1815 3 chr2B.!!$R2 1814
3 TraesCS2D01G176300 chr1B 29583544 29584244 700 True 1009.000000 1009 92.500000 1810 2525 1 chr1B.!!$R1 715
4 TraesCS2D01G176300 chr3A 54349321 54350048 727 False 649.000000 649 83.401000 1811 2516 1 chr3A.!!$F2 705
5 TraesCS2D01G176300 chr3A 54362428 54363154 726 False 641.000000 641 83.220000 1811 2516 1 chr3A.!!$F3 705
6 TraesCS2D01G176300 chr3A 54327550 54328268 718 False 606.000000 606 82.585000 1811 2516 1 chr3A.!!$F1 705
7 TraesCS2D01G176300 chr1A 586701127 586701844 717 False 647.000000 647 83.564000 1814 2510 1 chr1A.!!$F1 696
8 TraesCS2D01G176300 chr1A 518053447 518054160 713 True 616.000000 616 82.806000 1814 2516 1 chr1A.!!$R1 702
9 TraesCS2D01G176300 chr3B 809221022 809221660 638 True 346.000000 381 86.679500 1815 2520 2 chr3B.!!$R1 705
10 TraesCS2D01G176300 chr7D 523432893 523433557 664 False 241.000000 241 74.000000 1814 2500 1 chr7D.!!$F1 686

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
560 2064 0.036306 GAGGGACAAGCTTTTCCGGA 59.964 55.0 22.30 0.00 32.00 5.14 F
1300 2990 0.036388 GAAGGCTGATGGACCGTCAA 60.036 55.0 17.16 2.26 34.92 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1413 3106 0.037697 CATGGTTGCATTGCAGCAGT 60.038 50.0 24.07 11.03 46.54 4.40 R
2332 4101 1.480219 GCGCGTCTTCGGATCGAATT 61.480 55.0 8.43 0.00 44.85 2.17 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
26 27 8.373981 AGCGTAGAAAGACTATATAGTACTCCA 58.626 37.037 15.42 0.00 36.50 3.86
54 60 4.340950 TCCGGAGAAATGGATAAAAATGGC 59.659 41.667 0.00 0.00 0.00 4.40
61 67 5.514274 AATGGATAAAAATGGCCGTACTG 57.486 39.130 0.00 0.00 0.00 2.74
66 72 3.428413 AAAAATGGCCGTACTGTAGGT 57.572 42.857 0.00 0.00 0.00 3.08
151 157 4.506802 GGGGTATGGGTAGAATAAGGCAAG 60.507 50.000 0.00 0.00 0.00 4.01
152 158 4.506802 GGGTATGGGTAGAATAAGGCAAGG 60.507 50.000 0.00 0.00 0.00 3.61
162 168 5.541845 AGAATAAGGCAAGGAAAGTTTTGC 58.458 37.500 2.70 2.70 46.76 3.68
211 218 8.920509 TGATTCAGTTGATTGATTTAATGCAG 57.079 30.769 0.00 0.00 0.00 4.41
214 221 7.649533 TCAGTTGATTGATTTAATGCAGGAT 57.350 32.000 0.00 0.00 0.00 3.24
293 300 6.670077 ATGTTTGTTTTTATTTTGTGCGGT 57.330 29.167 0.00 0.00 0.00 5.68
309 316 2.508716 TGCGGTATTGGTTGGGGTTATA 59.491 45.455 0.00 0.00 0.00 0.98
314 321 6.566141 CGGTATTGGTTGGGGTTATAAAAAG 58.434 40.000 0.00 0.00 0.00 2.27
322 329 7.616542 TGGTTGGGGTTATAAAAAGAACCTATC 59.383 37.037 14.28 0.00 43.94 2.08
323 330 7.837689 GGTTGGGGTTATAAAAAGAACCTATCT 59.162 37.037 3.96 0.00 43.94 1.98
338 345 2.580783 CCTATCTGGGAAACAAAGGGGA 59.419 50.000 0.00 0.00 0.00 4.81
341 348 2.957474 TCTGGGAAACAAAGGGGAAAG 58.043 47.619 0.00 0.00 0.00 2.62
357 364 1.489560 AAAGGGGAACGTGGGAGGAG 61.490 60.000 0.00 0.00 0.00 3.69
362 369 1.202842 GGGAACGTGGGAGGAGAAAAA 60.203 52.381 0.00 0.00 0.00 1.94
363 370 1.878088 GGAACGTGGGAGGAGAAAAAC 59.122 52.381 0.00 0.00 0.00 2.43
384 391 0.755698 GATAGGAGGTGGAGGCGACA 60.756 60.000 0.00 0.00 0.00 4.35
407 448 8.779354 ACAAAATCAACTCAGTAGAGATTACC 57.221 34.615 0.00 0.00 44.98 2.85
428 1932 3.127548 CCTCGATGATTTCACAACTTGGG 59.872 47.826 0.00 0.00 0.00 4.12
432 1936 4.096231 CGATGATTTCACAACTTGGGCATA 59.904 41.667 0.00 0.00 0.00 3.14
456 1960 4.490899 TGCGGTTTAGTTACCCATGTAT 57.509 40.909 0.00 0.00 34.56 2.29
458 1962 5.254901 TGCGGTTTAGTTACCCATGTATTT 58.745 37.500 0.00 0.00 34.56 1.40
459 1963 5.354792 TGCGGTTTAGTTACCCATGTATTTC 59.645 40.000 0.00 0.00 34.56 2.17
460 1964 5.220912 GCGGTTTAGTTACCCATGTATTTCC 60.221 44.000 0.00 0.00 34.56 3.13
463 1967 7.201670 CGGTTTAGTTACCCATGTATTTCCTTC 60.202 40.741 0.00 0.00 34.56 3.46
467 1971 3.953542 ACCCATGTATTTCCTTCCTCC 57.046 47.619 0.00 0.00 0.00 4.30
469 1973 2.438021 CCCATGTATTTCCTTCCTCCGA 59.562 50.000 0.00 0.00 0.00 4.55
470 1974 3.118038 CCCATGTATTTCCTTCCTCCGAA 60.118 47.826 0.00 0.00 0.00 4.30
471 1975 4.523083 CCATGTATTTCCTTCCTCCGAAA 58.477 43.478 0.00 0.00 32.82 3.46
473 1977 5.417580 CCATGTATTTCCTTCCTCCGAAAAA 59.582 40.000 0.00 0.00 32.08 1.94
475 1979 4.457949 TGTATTTCCTTCCTCCGAAAAAGC 59.542 41.667 0.00 0.00 32.08 3.51
476 1980 2.951229 TTCCTTCCTCCGAAAAAGCT 57.049 45.000 0.00 0.00 0.00 3.74
477 1981 2.951229 TCCTTCCTCCGAAAAAGCTT 57.049 45.000 0.00 0.00 0.00 3.74
478 1982 2.504367 TCCTTCCTCCGAAAAAGCTTG 58.496 47.619 0.00 0.00 0.00 4.01
479 1983 2.158667 TCCTTCCTCCGAAAAAGCTTGT 60.159 45.455 0.00 0.00 0.00 3.16
480 1984 2.226674 CCTTCCTCCGAAAAAGCTTGTC 59.773 50.000 0.00 0.00 0.00 3.18
482 1986 2.218603 TCCTCCGAAAAAGCTTGTCAC 58.781 47.619 0.00 0.00 0.00 3.67
483 1987 1.946768 CCTCCGAAAAAGCTTGTCACA 59.053 47.619 0.00 0.00 0.00 3.58
484 1988 2.357637 CCTCCGAAAAAGCTTGTCACAA 59.642 45.455 0.00 0.00 0.00 3.33
485 1989 3.548818 CCTCCGAAAAAGCTTGTCACAAG 60.549 47.826 13.67 13.67 0.00 3.16
486 1990 2.119457 CCGAAAAAGCTTGTCACAAGC 58.881 47.619 31.68 31.68 43.31 4.01
495 1999 4.348198 GCTTGTCACAAGCTTATTCCTC 57.652 45.455 31.50 2.91 40.01 3.71
496 2000 3.753272 GCTTGTCACAAGCTTATTCCTCA 59.247 43.478 31.50 0.00 40.01 3.86
497 2001 4.216257 GCTTGTCACAAGCTTATTCCTCAA 59.784 41.667 31.50 0.18 40.01 3.02
498 2002 5.278463 GCTTGTCACAAGCTTATTCCTCAAA 60.278 40.000 31.50 0.00 40.01 2.69
499 2003 6.571150 GCTTGTCACAAGCTTATTCCTCAAAT 60.571 38.462 31.50 0.00 40.01 2.32
500 2004 6.258230 TGTCACAAGCTTATTCCTCAAATG 57.742 37.500 0.00 0.00 0.00 2.32
502 2006 6.489700 TGTCACAAGCTTATTCCTCAAATGAA 59.510 34.615 0.00 0.00 0.00 2.57
503 2007 7.177216 TGTCACAAGCTTATTCCTCAAATGAAT 59.823 33.333 0.00 0.00 36.46 2.57
504 2008 7.487189 GTCACAAGCTTATTCCTCAAATGAATG 59.513 37.037 0.00 0.00 34.43 2.67
505 2009 7.177216 TCACAAGCTTATTCCTCAAATGAATGT 59.823 33.333 0.00 0.00 34.43 2.71
506 2010 8.461222 CACAAGCTTATTCCTCAAATGAATGTA 58.539 33.333 0.00 0.00 34.43 2.29
507 2011 9.193806 ACAAGCTTATTCCTCAAATGAATGTAT 57.806 29.630 0.00 0.00 34.43 2.29
508 2012 9.674824 CAAGCTTATTCCTCAAATGAATGTATC 57.325 33.333 0.00 0.00 34.43 2.24
524 2028 9.770097 ATGAATGTATCTATCACTAACTTGGTG 57.230 33.333 0.00 0.00 36.17 4.17
525 2029 7.710907 TGAATGTATCTATCACTAACTTGGTGC 59.289 37.037 0.44 0.00 34.97 5.01
526 2030 6.791867 TGTATCTATCACTAACTTGGTGCT 57.208 37.500 0.44 0.00 34.97 4.40
528 2032 7.941919 TGTATCTATCACTAACTTGGTGCTAG 58.058 38.462 8.95 8.95 35.80 3.42
530 2034 7.847711 ATCTATCACTAACTTGGTGCTAGAT 57.152 36.000 18.71 18.71 42.50 1.98
532 2036 8.167605 TCTATCACTAACTTGGTGCTAGATAC 57.832 38.462 12.39 0.00 37.44 2.24
534 2038 6.791867 TCACTAACTTGGTGCTAGATACAT 57.208 37.500 0.00 0.00 34.97 2.29
535 2039 7.182817 TCACTAACTTGGTGCTAGATACATT 57.817 36.000 0.00 0.00 34.97 2.71
537 2041 8.755028 TCACTAACTTGGTGCTAGATACATTTA 58.245 33.333 0.00 0.00 34.97 1.40
538 2042 9.547753 CACTAACTTGGTGCTAGATACATTTAT 57.452 33.333 0.00 0.00 0.00 1.40
543 2047 9.113838 ACTTGGTGCTAGATACATTTATTTGAG 57.886 33.333 0.00 0.00 0.00 3.02
545 2049 6.998074 TGGTGCTAGATACATTTATTTGAGGG 59.002 38.462 0.00 0.00 0.00 4.30
547 2051 7.173390 GGTGCTAGATACATTTATTTGAGGGAC 59.827 40.741 0.00 0.00 0.00 4.46
548 2052 7.715249 GTGCTAGATACATTTATTTGAGGGACA 59.285 37.037 0.00 0.00 0.00 4.02
549 2053 8.271458 TGCTAGATACATTTATTTGAGGGACAA 58.729 33.333 0.00 0.00 36.65 3.18
550 2054 8.778358 GCTAGATACATTTATTTGAGGGACAAG 58.222 37.037 0.00 0.00 39.77 3.16
551 2055 7.573968 AGATACATTTATTTGAGGGACAAGC 57.426 36.000 0.00 0.00 39.77 4.01
552 2056 7.349598 AGATACATTTATTTGAGGGACAAGCT 58.650 34.615 0.00 0.00 39.77 3.74
554 2058 6.670695 ACATTTATTTGAGGGACAAGCTTT 57.329 33.333 0.00 0.00 39.77 3.51
556 2060 7.154656 ACATTTATTTGAGGGACAAGCTTTTC 58.845 34.615 3.91 3.91 39.77 2.29
557 2061 5.722021 TTATTTGAGGGACAAGCTTTTCC 57.278 39.130 21.34 21.34 39.77 3.13
558 2062 1.604604 TTGAGGGACAAGCTTTTCCG 58.395 50.000 22.30 2.85 34.20 4.30
559 2063 0.250727 TGAGGGACAAGCTTTTCCGG 60.251 55.000 22.30 0.00 32.00 5.14
560 2064 0.036306 GAGGGACAAGCTTTTCCGGA 59.964 55.000 22.30 0.00 32.00 5.14
561 2065 0.250770 AGGGACAAGCTTTTCCGGAC 60.251 55.000 22.30 11.02 32.00 4.79
562 2066 1.574702 GGGACAAGCTTTTCCGGACG 61.575 60.000 22.30 0.00 32.00 4.79
563 2067 1.574702 GGACAAGCTTTTCCGGACGG 61.575 60.000 15.65 3.96 0.00 4.79
564 2068 0.601841 GACAAGCTTTTCCGGACGGA 60.602 55.000 1.83 9.76 43.52 4.69
574 2078 0.038744 TCCGGACGGAAGGAGTAGTT 59.961 55.000 11.57 0.00 42.05 2.24
584 2088 4.095782 CGGAAGGAGTAGTTCTCTCAGAAG 59.904 50.000 0.00 0.00 42.40 2.85
587 2091 4.258543 AGGAGTAGTTCTCTCAGAAGTCG 58.741 47.826 0.00 0.00 42.40 4.18
588 2092 4.004982 GGAGTAGTTCTCTCAGAAGTCGT 58.995 47.826 0.00 0.00 42.40 4.34
590 2094 5.365403 AGTAGTTCTCTCAGAAGTCGTTG 57.635 43.478 0.00 0.00 38.68 4.10
591 2095 4.822896 AGTAGTTCTCTCAGAAGTCGTTGT 59.177 41.667 0.00 0.00 38.68 3.32
592 2096 5.996513 AGTAGTTCTCTCAGAAGTCGTTGTA 59.003 40.000 0.00 0.00 38.68 2.41
594 2098 4.822896 AGTTCTCTCAGAAGTCGTTGTACT 59.177 41.667 0.00 0.00 32.70 2.73
595 2099 4.750952 TCTCTCAGAAGTCGTTGTACTG 57.249 45.455 0.00 0.00 0.00 2.74
597 2101 5.004448 TCTCTCAGAAGTCGTTGTACTGAT 58.996 41.667 0.00 0.00 37.07 2.90
599 2103 5.700846 TCTCAGAAGTCGTTGTACTGATTC 58.299 41.667 0.00 0.00 37.07 2.52
601 2105 6.653740 TCTCAGAAGTCGTTGTACTGATTCTA 59.346 38.462 0.00 0.00 37.07 2.10
602 2106 7.174426 TCTCAGAAGTCGTTGTACTGATTCTAA 59.826 37.037 0.00 0.00 37.07 2.10
603 2107 7.654568 TCAGAAGTCGTTGTACTGATTCTAAA 58.345 34.615 0.00 0.00 33.57 1.85
604 2108 8.139350 TCAGAAGTCGTTGTACTGATTCTAAAA 58.861 33.333 0.00 0.00 33.57 1.52
605 2109 8.761497 CAGAAGTCGTTGTACTGATTCTAAAAA 58.239 33.333 0.00 0.00 0.00 1.94
632 2273 1.134640 TGTTGTACTGTGCGTTCCAGT 60.135 47.619 8.43 8.43 44.90 4.00
666 2307 1.480954 ACGTCGGATATGGTCTTGCTT 59.519 47.619 0.00 0.00 0.00 3.91
675 2316 7.668469 TCGGATATGGTCTTGCTTAGTCTATAA 59.332 37.037 0.00 0.00 0.00 0.98
685 2326 8.721478 TCTTGCTTAGTCTATAACTTTGCAAAG 58.279 33.333 32.53 32.53 45.51 2.77
703 2344 4.398319 CAAAGGACACCTTGGACTATTGT 58.602 43.478 3.73 0.00 43.92 2.71
733 2374 0.599060 GATAGTCCTCGTGCTAGCCC 59.401 60.000 13.29 0.00 0.00 5.19
813 2454 4.376225 AAGGAACCTAAACCGGATTCAA 57.624 40.909 9.46 0.00 0.00 2.69
861 2502 1.535462 GATAAATTGCCACCGATCGGG 59.465 52.381 35.87 24.12 43.62 5.14
923 2564 4.208746 AGTCCGAGGATAGGTTGAACTAG 58.791 47.826 0.00 0.00 30.33 2.57
947 2588 1.408340 GAACTCTAGAAGGCCCGTACC 59.592 57.143 0.00 0.00 0.00 3.34
1024 2669 2.226315 TCCATCCTGTGCTGCCTGT 61.226 57.895 0.00 0.00 0.00 4.00
1211 2901 2.456577 TGATCCTCGGTTCAGACATCA 58.543 47.619 0.00 0.00 0.00 3.07
1299 2989 0.904865 AGAAGGCTGATGGACCGTCA 60.905 55.000 15.71 15.71 36.96 4.35
1300 2990 0.036388 GAAGGCTGATGGACCGTCAA 60.036 55.000 17.16 2.26 34.92 3.18
1310 3003 0.036388 GGACCGTCAATGGAAGCTCA 60.036 55.000 0.00 0.00 0.00 4.26
1383 3076 0.767375 ATGACTGCCCGATATGCCTT 59.233 50.000 0.00 0.00 0.00 4.35
1386 3079 0.107456 ACTGCCCGATATGCCTTGAG 59.893 55.000 0.00 0.00 0.00 3.02
1413 3106 7.160049 AGTATGACTACGAGAATCCGAAGATA 58.840 38.462 0.00 0.00 32.82 1.98
1504 3197 1.082117 GGTCTGTGCCGTCGTAATGG 61.082 60.000 0.00 0.00 34.35 3.16
1684 3392 5.349817 CAGCAGAGTAATGACCTTGTTGTAG 59.650 44.000 0.00 0.00 0.00 2.74
1685 3393 5.012148 AGCAGAGTAATGACCTTGTTGTAGT 59.988 40.000 0.00 0.00 0.00 2.73
1686 3394 5.348997 GCAGAGTAATGACCTTGTTGTAGTC 59.651 44.000 0.00 0.00 0.00 2.59
1801 3515 3.632189 AGATTGTTTGCTGAAACTTCGC 58.368 40.909 0.00 1.12 41.87 4.70
1858 3574 5.246203 GGTAGCATCTGGACATGTTATCCTA 59.754 44.000 0.00 0.00 37.13 2.94
1920 3637 4.647853 AGTCTCAGCATATACGGGTGTAAA 59.352 41.667 5.61 0.00 35.38 2.01
2142 3871 1.661341 GATGAAGTGTAGGGCAGCAG 58.339 55.000 0.00 0.00 0.00 4.24
2168 3930 1.286849 TCTCGGTCCCCATCTACTCAA 59.713 52.381 0.00 0.00 0.00 3.02
2388 4157 5.835819 TCAATGGGTGGTCTTTGATTTGTTA 59.164 36.000 0.00 0.00 0.00 2.41
2416 4190 3.312890 CCATAGGTTCCAGAGAGGTCAT 58.687 50.000 0.00 0.00 39.02 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.523188 CGGACGGATGGAGTACTATATAGTC 59.477 48.000 18.68 10.64 37.73 2.59
15 16 2.639347 TCCGGACGGATGGAGTACTATA 59.361 50.000 9.76 0.00 39.76 1.31
26 27 1.424638 ATCCATTTCTCCGGACGGAT 58.575 50.000 14.50 4.39 44.24 4.18
29 30 5.505654 CCATTTTTATCCATTTCTCCGGACG 60.506 44.000 0.00 0.00 33.05 4.79
151 157 5.767816 TCTCAACTAAGGCAAAACTTTCC 57.232 39.130 0.00 0.00 32.02 3.13
152 158 8.542953 CAAAATCTCAACTAAGGCAAAACTTTC 58.457 33.333 0.00 0.00 32.02 2.62
193 200 7.259882 TCACATCCTGCATTAAATCAATCAAC 58.740 34.615 0.00 0.00 0.00 3.18
290 297 6.377712 TCTTTTTATAACCCCAACCAATACCG 59.622 38.462 0.00 0.00 0.00 4.02
293 300 7.956881 AGGTTCTTTTTATAACCCCAACCAATA 59.043 33.333 13.96 0.00 45.23 1.90
309 316 7.202001 CCTTTGTTTCCCAGATAGGTTCTTTTT 60.202 37.037 0.00 0.00 34.66 1.94
314 321 4.017126 CCCTTTGTTTCCCAGATAGGTTC 58.983 47.826 0.00 0.00 34.66 3.62
322 329 1.970640 CCTTTCCCCTTTGTTTCCCAG 59.029 52.381 0.00 0.00 0.00 4.45
323 330 1.413808 CCCTTTCCCCTTTGTTTCCCA 60.414 52.381 0.00 0.00 0.00 4.37
338 345 1.462627 TCCTCCCACGTTCCCCTTT 60.463 57.895 0.00 0.00 0.00 3.11
341 348 1.486145 TTTCTCCTCCCACGTTCCCC 61.486 60.000 0.00 0.00 0.00 4.81
357 364 3.532542 CTCCACCTCCTATCCGTTTTTC 58.467 50.000 0.00 0.00 0.00 2.29
362 369 1.457831 GCCTCCACCTCCTATCCGT 60.458 63.158 0.00 0.00 0.00 4.69
363 370 2.565645 CGCCTCCACCTCCTATCCG 61.566 68.421 0.00 0.00 0.00 4.18
384 391 7.976734 CGAGGTAATCTCTACTGAGTTGATTTT 59.023 37.037 11.33 5.59 40.30 1.82
407 448 3.426695 GCCCAAGTTGTGAAATCATCGAG 60.427 47.826 1.45 0.00 0.00 4.04
432 1936 2.863132 TGGGTAACTAAACCGCATGT 57.137 45.000 0.00 0.00 40.73 3.21
448 1952 2.438021 TCGGAGGAAGGAAATACATGGG 59.562 50.000 0.00 0.00 0.00 4.00
456 1960 3.223674 AGCTTTTTCGGAGGAAGGAAA 57.776 42.857 5.10 0.00 32.80 3.13
458 1962 2.158667 ACAAGCTTTTTCGGAGGAAGGA 60.159 45.455 0.00 0.00 32.80 3.36
459 1963 2.226674 GACAAGCTTTTTCGGAGGAAGG 59.773 50.000 0.00 0.00 32.80 3.46
460 1964 2.878406 TGACAAGCTTTTTCGGAGGAAG 59.122 45.455 0.00 0.00 32.80 3.46
463 1967 1.946768 TGTGACAAGCTTTTTCGGAGG 59.053 47.619 0.00 0.00 0.00 4.30
475 1979 5.947228 TTGAGGAATAAGCTTGTGACAAG 57.053 39.130 20.42 20.42 0.00 3.16
476 1980 6.489700 TCATTTGAGGAATAAGCTTGTGACAA 59.510 34.615 9.86 0.00 0.00 3.18
477 1981 6.003326 TCATTTGAGGAATAAGCTTGTGACA 58.997 36.000 9.86 0.00 0.00 3.58
478 1982 6.500684 TCATTTGAGGAATAAGCTTGTGAC 57.499 37.500 9.86 0.00 0.00 3.67
479 1983 7.177216 ACATTCATTTGAGGAATAAGCTTGTGA 59.823 33.333 9.86 0.00 33.40 3.58
480 1984 7.318141 ACATTCATTTGAGGAATAAGCTTGTG 58.682 34.615 9.86 0.00 33.40 3.33
482 1986 9.674824 GATACATTCATTTGAGGAATAAGCTTG 57.325 33.333 9.86 0.00 33.40 4.01
483 1987 9.638176 AGATACATTCATTTGAGGAATAAGCTT 57.362 29.630 3.48 3.48 33.40 3.74
498 2002 9.770097 CACCAAGTTAGTGATAGATACATTCAT 57.230 33.333 0.00 0.00 37.42 2.57
499 2003 7.710907 GCACCAAGTTAGTGATAGATACATTCA 59.289 37.037 5.56 0.00 37.42 2.57
500 2004 7.928706 AGCACCAAGTTAGTGATAGATACATTC 59.071 37.037 5.56 0.00 37.42 2.67
502 2006 7.366847 AGCACCAAGTTAGTGATAGATACAT 57.633 36.000 5.56 0.00 37.42 2.29
503 2007 6.791867 AGCACCAAGTTAGTGATAGATACA 57.208 37.500 5.56 0.00 37.42 2.29
511 2015 6.791867 ATGTATCTAGCACCAAGTTAGTGA 57.208 37.500 5.56 0.00 37.42 3.41
512 2016 7.849804 AAATGTATCTAGCACCAAGTTAGTG 57.150 36.000 0.00 0.00 38.30 2.74
516 2020 9.461312 TCAAATAAATGTATCTAGCACCAAGTT 57.539 29.630 0.00 0.00 0.00 2.66
517 2021 9.113838 CTCAAATAAATGTATCTAGCACCAAGT 57.886 33.333 0.00 0.00 0.00 3.16
518 2022 8.562892 CCTCAAATAAATGTATCTAGCACCAAG 58.437 37.037 0.00 0.00 0.00 3.61
519 2023 7.502226 CCCTCAAATAAATGTATCTAGCACCAA 59.498 37.037 0.00 0.00 0.00 3.67
520 2024 6.998074 CCCTCAAATAAATGTATCTAGCACCA 59.002 38.462 0.00 0.00 0.00 4.17
521 2025 7.173390 GTCCCTCAAATAAATGTATCTAGCACC 59.827 40.741 0.00 0.00 0.00 5.01
523 2027 7.801104 TGTCCCTCAAATAAATGTATCTAGCA 58.199 34.615 0.00 0.00 0.00 3.49
524 2028 8.677148 TTGTCCCTCAAATAAATGTATCTAGC 57.323 34.615 0.00 0.00 32.64 3.42
525 2029 8.778358 GCTTGTCCCTCAAATAAATGTATCTAG 58.222 37.037 0.00 0.00 35.48 2.43
526 2030 8.494433 AGCTTGTCCCTCAAATAAATGTATCTA 58.506 33.333 0.00 0.00 35.48 1.98
528 2032 7.573968 AGCTTGTCCCTCAAATAAATGTATC 57.426 36.000 0.00 0.00 35.48 2.24
530 2034 7.775053 AAAGCTTGTCCCTCAAATAAATGTA 57.225 32.000 0.00 0.00 35.48 2.29
532 2036 6.591448 GGAAAAGCTTGTCCCTCAAATAAATG 59.409 38.462 23.49 0.00 35.48 2.32
534 2038 5.278758 CGGAAAAGCTTGTCCCTCAAATAAA 60.279 40.000 26.94 0.00 35.48 1.40
535 2039 4.217550 CGGAAAAGCTTGTCCCTCAAATAA 59.782 41.667 26.94 0.00 35.48 1.40
537 2041 2.558359 CGGAAAAGCTTGTCCCTCAAAT 59.442 45.455 26.94 0.00 35.48 2.32
538 2042 1.953686 CGGAAAAGCTTGTCCCTCAAA 59.046 47.619 26.94 0.00 35.48 2.69
540 2044 0.250727 CCGGAAAAGCTTGTCCCTCA 60.251 55.000 26.94 0.00 0.00 3.86
541 2045 0.036306 TCCGGAAAAGCTTGTCCCTC 59.964 55.000 26.94 5.77 0.00 4.30
543 2047 1.574702 CGTCCGGAAAAGCTTGTCCC 61.575 60.000 26.94 13.97 0.00 4.46
545 2049 0.601841 TCCGTCCGGAAAAGCTTGTC 60.602 55.000 5.23 8.23 42.05 3.18
547 2051 4.371975 TCCGTCCGGAAAAGCTTG 57.628 55.556 5.23 0.00 42.05 4.01
556 2060 0.455005 GAACTACTCCTTCCGTCCGG 59.545 60.000 0.00 0.00 0.00 5.14
557 2061 1.401199 GAGAACTACTCCTTCCGTCCG 59.599 57.143 0.00 0.00 39.53 4.79
558 2062 2.684374 GAGAGAACTACTCCTTCCGTCC 59.316 54.545 0.00 0.00 45.96 4.79
559 2063 3.345414 TGAGAGAACTACTCCTTCCGTC 58.655 50.000 0.00 0.00 45.96 4.79
560 2064 3.009253 TCTGAGAGAACTACTCCTTCCGT 59.991 47.826 0.00 0.00 45.96 4.69
561 2065 3.611970 TCTGAGAGAACTACTCCTTCCG 58.388 50.000 0.00 0.00 45.96 4.30
562 2066 5.014202 ACTTCTGAGAGAACTACTCCTTCC 58.986 45.833 0.00 0.00 45.96 3.46
563 2067 5.163794 CGACTTCTGAGAGAACTACTCCTTC 60.164 48.000 0.00 0.00 45.96 3.46
564 2068 4.698304 CGACTTCTGAGAGAACTACTCCTT 59.302 45.833 0.00 0.00 45.96 3.36
565 2069 4.258543 CGACTTCTGAGAGAACTACTCCT 58.741 47.826 0.00 0.00 45.96 3.69
566 2070 4.004982 ACGACTTCTGAGAGAACTACTCC 58.995 47.826 0.00 0.00 45.96 3.85
567 2071 5.049267 ACAACGACTTCTGAGAGAACTACTC 60.049 44.000 0.00 0.00 45.22 2.59
568 2072 4.822896 ACAACGACTTCTGAGAGAACTACT 59.177 41.667 0.00 0.00 29.89 2.57
569 2073 5.110940 ACAACGACTTCTGAGAGAACTAC 57.889 43.478 0.00 0.00 29.89 2.73
570 2074 5.996513 AGTACAACGACTTCTGAGAGAACTA 59.003 40.000 0.00 0.00 29.89 2.24
574 2078 4.386711 TCAGTACAACGACTTCTGAGAGA 58.613 43.478 0.00 0.00 32.49 3.10
603 2107 4.109050 CGCACAGTACAACAACCATTTTT 58.891 39.130 0.00 0.00 0.00 1.94
604 2108 3.129638 ACGCACAGTACAACAACCATTTT 59.870 39.130 0.00 0.00 0.00 1.82
605 2109 2.685897 ACGCACAGTACAACAACCATTT 59.314 40.909 0.00 0.00 0.00 2.32
607 2111 1.961793 ACGCACAGTACAACAACCAT 58.038 45.000 0.00 0.00 0.00 3.55
608 2112 1.666700 GAACGCACAGTACAACAACCA 59.333 47.619 0.00 0.00 0.00 3.67
609 2113 1.003223 GGAACGCACAGTACAACAACC 60.003 52.381 0.00 0.00 0.00 3.77
632 2273 1.403647 CCGACGTGGACTATCTTTGCA 60.404 52.381 0.00 0.00 42.00 4.08
666 2307 6.877322 GGTGTCCTTTGCAAAGTTATAGACTA 59.123 38.462 31.67 19.30 37.72 2.59
675 2316 1.756538 CCAAGGTGTCCTTTGCAAAGT 59.243 47.619 31.67 14.03 41.69 2.66
685 2326 2.039879 ACCACAATAGTCCAAGGTGTCC 59.960 50.000 0.00 0.00 0.00 4.02
703 2344 4.398358 CACGAGGACTATCTAGTGAAACCA 59.602 45.833 0.00 0.00 41.02 3.67
733 2374 0.863799 CCTTGGTCGATCATCATGCG 59.136 55.000 0.00 0.00 0.00 4.73
783 2424 3.308259 GGTTTAGGTTCCTTTCCTCCCTC 60.308 52.174 0.00 0.00 36.60 4.30
813 2454 0.815615 GGAATCCGATTCTGGCGCTT 60.816 55.000 18.46 0.00 39.24 4.68
861 2502 1.006922 GCACAAGCACTTGGAAGGC 60.007 57.895 14.51 8.60 44.45 4.35
923 2564 1.338655 CGGGCCTTCTAGAGTTCTAGC 59.661 57.143 0.84 1.40 44.24 3.42
947 2588 2.125912 CAGACGGAGGAACCAGCG 60.126 66.667 0.00 0.00 38.90 5.18
1029 2674 2.434709 TCGTCATCGTCGTCGGGA 60.435 61.111 1.55 0.00 38.33 5.14
1177 2867 3.120130 CGAGGATCATCGTAAGGTAGAGC 60.120 52.174 20.95 0.00 37.91 4.09
1180 2870 3.147629 ACCGAGGATCATCGTAAGGTAG 58.852 50.000 26.06 12.68 41.12 3.18
1182 2872 2.068834 ACCGAGGATCATCGTAAGGT 57.931 50.000 26.06 14.97 41.12 3.50
1211 2901 4.688021 GAGCAGAATAGATTTCTCCGTGT 58.312 43.478 0.00 0.00 0.00 4.49
1299 2989 2.262774 CTCCCGGCTGAGCTTCCATT 62.263 60.000 3.72 0.00 0.00 3.16
1300 2990 2.688666 TCCCGGCTGAGCTTCCAT 60.689 61.111 3.72 0.00 0.00 3.41
1330 3023 1.807814 ACACAGACTTGAGTTCCCCT 58.192 50.000 0.00 0.00 0.00 4.79
1383 3076 5.064558 GGATTCTCGTAGTCATACTCCTCA 58.935 45.833 0.00 0.00 0.00 3.86
1386 3079 4.063689 TCGGATTCTCGTAGTCATACTCC 58.936 47.826 0.00 0.00 0.00 3.85
1413 3106 0.037697 CATGGTTGCATTGCAGCAGT 60.038 50.000 24.07 11.03 46.54 4.40
1497 3190 3.435671 GGTCCTCTTTGAACACCATTACG 59.564 47.826 0.00 0.00 0.00 3.18
1504 3197 3.253432 GGTCATTGGTCCTCTTTGAACAC 59.747 47.826 0.00 0.00 29.99 3.32
1588 3290 1.665169 TGATTTCATCGACGCCATGTG 59.335 47.619 0.00 0.00 0.00 3.21
1732 3442 5.345202 CAGATGCAAAAGCTTTGTCTCATTC 59.655 40.000 13.54 4.32 0.00 2.67
1801 3515 1.764851 CCGCTCTCGAATCTTAGCAG 58.235 55.000 0.00 0.00 38.10 4.24
1920 3637 2.816087 AGCGTCAGATCACTGCATTTTT 59.184 40.909 0.00 0.00 43.17 1.94
1931 3648 5.943706 TCCTTACAGTATAGCGTCAGATC 57.056 43.478 0.00 0.00 0.00 2.75
1993 3710 1.404315 GGCTCGTCACCTTAACCTGAG 60.404 57.143 0.00 0.00 0.00 3.35
2083 3801 0.872388 ACCTTGACGGCGATGTTTTC 59.128 50.000 16.62 0.00 35.61 2.29
2168 3930 1.773653 GATGGAGGAGAAGGGCTCAAT 59.226 52.381 0.00 0.00 45.81 2.57
2325 4094 4.976731 CGTCTTCGGATCGAATTGAATACT 59.023 41.667 3.18 0.00 44.85 2.12
2332 4101 1.480219 GCGCGTCTTCGGATCGAATT 61.480 55.000 8.43 0.00 44.85 2.17
2370 4139 6.073819 GCATGTTTAACAAATCAAAGACCACC 60.074 38.462 0.66 0.00 0.00 4.61
2371 4140 6.073819 GGCATGTTTAACAAATCAAAGACCAC 60.074 38.462 0.66 0.00 0.00 4.16
2388 4157 3.266772 TCTCTGGAACCTATGGCATGTTT 59.733 43.478 10.98 0.00 0.00 2.83
2416 4190 2.334946 GGCTGCTCAACATCCGCAA 61.335 57.895 0.00 0.00 32.66 4.85


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

AutoCloner maintained by Alex Coulton.