Multiple sequence alignment - TraesCS1B01G306000

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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 TraesCS1B01G306000 chr1B 100.000 2861 0 0 1 2861 529441327 529438467 0.000000e+00 5284.0
1 TraesCS1B01G306000 chr1B 93.668 1595 81 10 1070 2651 529544686 529543099 0.000000e+00 2368.0
2 TraesCS1B01G306000 chr1B 86.641 771 59 16 1920 2647 529573103 529572334 0.000000e+00 813.0
3 TraesCS1B01G306000 chr1B 96.296 486 17 1 599 1083 529552943 529552458 0.000000e+00 797.0
4 TraesCS1B01G306000 chr1B 90.313 351 24 4 1920 2261 529502456 529502107 4.350000e-123 451.0
5 TraesCS1B01G306000 chr1B 95.714 70 2 1 599 667 529541459 529541390 8.380000e-21 111.0
6 TraesCS1B01G306000 chr1B 92.500 40 3 0 488 527 529440788 529440749 1.110000e-04 58.4
7 TraesCS1B01G306000 chr1B 92.500 40 3 0 540 579 529440840 529440801 1.110000e-04 58.4
8 TraesCS1B01G306000 chr1A 94.723 2217 76 6 540 2755 492194503 492192327 0.000000e+00 3408.0
9 TraesCS1B01G306000 chr1A 86.842 760 72 13 1920 2670 492196636 492195896 0.000000e+00 824.0
10 TraesCS1B01G306000 chr1A 94.206 535 14 6 1 527 492194989 492194464 0.000000e+00 800.0
11 TraesCS1B01G306000 chr1A 87.671 73 7 2 266 337 44366668 44366597 1.830000e-12 84.2
12 TraesCS1B01G306000 chr1A 94.231 52 3 0 650 701 492192039 492192090 2.360000e-11 80.5
13 TraesCS1B01G306000 chr1D 93.886 1832 77 8 662 2489 393475599 393477399 0.000000e+00 2730.0
14 TraesCS1B01G306000 chr1D 90.070 574 50 3 1920 2489 393694636 393695206 0.000000e+00 737.0
15 TraesCS1B01G306000 chr1D 89.863 582 43 8 1920 2489 393443627 393444204 0.000000e+00 734.0
16 TraesCS1B01G306000 chr1D 85.047 107 13 2 2492 2595 393444243 393444349 3.900000e-19 106.0
17 TraesCS1B01G306000 chr1D 85.047 107 13 2 2492 2595 393695245 393695351 3.900000e-19 106.0
18 TraesCS1B01G306000 chr1D 94.231 52 3 0 650 701 393697057 393697006 2.360000e-11 80.5
19 TraesCS1B01G306000 chr2A 92.573 929 55 5 987 1915 612772118 612773032 0.000000e+00 1321.0
20 TraesCS1B01G306000 chr2A 90.550 963 52 23 1 953 612763003 612763936 0.000000e+00 1238.0
21 TraesCS1B01G306000 chr2A 88.753 818 65 15 1920 2731 612761523 612762319 0.000000e+00 976.0
22 TraesCS1B01G306000 chr2A 95.327 107 5 0 2755 2861 531097884 531097990 1.360000e-38 171.0
23 TraesCS1B01G306000 chr2A 95.455 66 3 0 540 605 612763492 612763557 3.900000e-19 106.0
24 TraesCS1B01G306000 chr4D 92.157 510 14 8 16 524 349002446 349002930 0.000000e+00 697.0
25 TraesCS1B01G306000 chr4D 96.970 66 2 0 540 605 349002894 349002959 8.380000e-21 111.0
26 TraesCS1B01G306000 chr5A 91.132 530 15 11 6 524 663371194 663371702 0.000000e+00 689.0
27 TraesCS1B01G306000 chr5A 88.158 76 9 0 2758 2833 30203302 30203227 1.090000e-14 91.6
28 TraesCS1B01G306000 chr2B 93.146 321 16 3 1592 1912 545186924 545187238 1.550000e-127 466.0
29 TraesCS1B01G306000 chr2B 93.312 314 21 0 1295 1608 545183933 545184246 5.580000e-127 464.0
30 TraesCS1B01G306000 chr2B 94.828 232 12 0 870 1101 545173532 545173763 2.100000e-96 363.0
31 TraesCS1B01G306000 chr2B 96.410 195 7 0 1104 1298 545181134 545181328 3.560000e-84 322.0
32 TraesCS1B01G306000 chr2B 94.040 151 9 0 709 859 545171241 545171391 2.220000e-56 230.0
33 TraesCS1B01G306000 chr2D 95.633 229 10 0 873 1101 465971550 465971322 4.500000e-98 368.0
34 TraesCS1B01G306000 chr2D 95.897 195 8 0 1104 1298 465967695 465967501 1.650000e-82 316.0
35 TraesCS1B01G306000 chr2D 94.702 151 8 0 709 859 465972186 465972036 4.770000e-58 235.0
36 TraesCS1B01G306000 chr2D 100.000 32 0 0 602 633 465972205 465972236 3.080000e-05 60.2
37 TraesCS1B01G306000 chr7D 86.154 195 16 8 331 522 565217028 565216842 1.740000e-47 200.0
38 TraesCS1B01G306000 chr4B 87.059 170 13 6 331 498 483768682 483768844 1.750000e-42 183.0
39 TraesCS1B01G306000 chr4B 96.154 104 4 0 2758 2861 495393859 495393962 1.360000e-38 171.0
40 TraesCS1B01G306000 chr7A 87.273 165 12 6 336 498 27223569 27223726 2.260000e-41 180.0
41 TraesCS1B01G306000 chr6B 86.905 168 13 6 331 496 387165694 387165854 2.260000e-41 180.0
42 TraesCS1B01G306000 chr6B 89.062 128 5 6 203 321 599410571 599410444 1.780000e-32 150.0
43 TraesCS1B01G306000 chr3D 86.905 168 13 6 331 496 357440911 357440751 2.260000e-41 180.0
44 TraesCS1B01G306000 chr6A 84.962 133 4 9 203 319 546481318 546481186 1.390000e-23 121.0
45 TraesCS1B01G306000 chr5D 76.974 152 33 2 1141 1291 37047790 37047940 5.080000e-13 86.1
46 TraesCS1B01G306000 chr5D 76.552 145 28 5 1145 1286 33048023 33047882 1.100000e-09 75.0


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 TraesCS1B01G306000 chr1B 529438467 529441327 2860 True 1800.266667 5284 95.000000 1 2861 3 chr1B.!!$R4 2860
1 TraesCS1B01G306000 chr1B 529541390 529544686 3296 True 1239.500000 2368 94.691000 599 2651 2 chr1B.!!$R5 2052
2 TraesCS1B01G306000 chr1B 529572334 529573103 769 True 813.000000 813 86.641000 1920 2647 1 chr1B.!!$R3 727
3 TraesCS1B01G306000 chr1A 492192327 492196636 4309 True 1677.333333 3408 91.923667 1 2755 3 chr1A.!!$R2 2754
4 TraesCS1B01G306000 chr1D 393475599 393477399 1800 False 2730.000000 2730 93.886000 662 2489 1 chr1D.!!$F1 1827
5 TraesCS1B01G306000 chr1D 393694636 393695351 715 False 421.500000 737 87.558500 1920 2595 2 chr1D.!!$F3 675
6 TraesCS1B01G306000 chr1D 393443627 393444349 722 False 420.000000 734 87.455000 1920 2595 2 chr1D.!!$F2 675
7 TraesCS1B01G306000 chr2A 612772118 612773032 914 False 1321.000000 1321 92.573000 987 1915 1 chr2A.!!$F2 928
8 TraesCS1B01G306000 chr2A 612761523 612763936 2413 False 773.333333 1238 91.586000 1 2731 3 chr2A.!!$F3 2730
9 TraesCS1B01G306000 chr4D 349002446 349002959 513 False 404.000000 697 94.563500 16 605 2 chr4D.!!$F1 589
10 TraesCS1B01G306000 chr5A 663371194 663371702 508 False 689.000000 689 91.132000 6 524 1 chr5A.!!$F1 518
11 TraesCS1B01G306000 chr2B 545181134 545187238 6104 False 417.333333 466 94.289333 1104 1912 3 chr2B.!!$F2 808
12 TraesCS1B01G306000 chr2B 545171241 545173763 2522 False 296.500000 363 94.434000 709 1101 2 chr2B.!!$F1 392
13 TraesCS1B01G306000 chr2D 465967501 465972186 4685 True 306.333333 368 95.410667 709 1298 3 chr2D.!!$R1 589

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
748 2404 0.029567 CCTCTCGCGCTCGATTACTT 59.97 55.0 5.56 0.0 44.56 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2558 15383 0.611896 GCCACAGCCCACAGGTTATT 60.612 55.0 0.0 0.0 34.57 1.4 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
245 1894 4.583489 TCTTGTTCGTCTCTGTTCCTAGTT 59.417 41.667 0.00 0.00 0.00 2.24
246 1895 4.500603 TGTTCGTCTCTGTTCCTAGTTC 57.499 45.455 0.00 0.00 0.00 3.01
247 1896 4.142790 TGTTCGTCTCTGTTCCTAGTTCT 58.857 43.478 0.00 0.00 0.00 3.01
248 1897 4.583489 TGTTCGTCTCTGTTCCTAGTTCTT 59.417 41.667 0.00 0.00 0.00 2.52
249 1898 5.155643 GTTCGTCTCTGTTCCTAGTTCTTC 58.844 45.833 0.00 0.00 0.00 2.87
250 1899 4.653868 TCGTCTCTGTTCCTAGTTCTTCT 58.346 43.478 0.00 0.00 0.00 2.85
251 1900 4.696402 TCGTCTCTGTTCCTAGTTCTTCTC 59.304 45.833 0.00 0.00 0.00 2.87
252 1901 4.698304 CGTCTCTGTTCCTAGTTCTTCTCT 59.302 45.833 0.00 0.00 0.00 3.10
261 1910 4.956700 TCCTAGTTCTTCTCTGTACATGGG 59.043 45.833 0.00 0.00 0.00 4.00
354 2003 5.005682 TCGTTTTCATGCTCATATTCGACAG 59.994 40.000 0.00 0.00 0.00 3.51
382 2031 6.913873 TGTCCAAAACAACTACTGTAAGTC 57.086 37.500 0.00 0.00 40.49 3.01
427 2082 6.620877 TTAGTTCAGGGACATTACAGACAT 57.379 37.500 0.00 0.00 0.00 3.06
478 2134 7.735917 TCTCAGACCACAATCTTAGAAAAGAA 58.264 34.615 0.00 0.00 44.75 2.52
493 2149 4.688413 AGAAAAGAACTCGACAGCTGATTC 59.312 41.667 23.35 14.58 0.00 2.52
494 2150 3.951775 AAGAACTCGACAGCTGATTCT 57.048 42.857 23.35 16.44 0.00 2.40
495 2151 3.229276 AGAACTCGACAGCTGATTCTG 57.771 47.619 23.35 8.69 39.86 3.02
496 2152 2.094286 AGAACTCGACAGCTGATTCTGG 60.094 50.000 23.35 7.59 38.36 3.86
497 2153 0.534412 ACTCGACAGCTGATTCTGGG 59.466 55.000 23.35 7.22 38.36 4.45
498 2154 0.534412 CTCGACAGCTGATTCTGGGT 59.466 55.000 23.35 0.00 38.36 4.51
499 2155 0.247460 TCGACAGCTGATTCTGGGTG 59.753 55.000 23.35 0.00 38.36 4.61
500 2156 0.247460 CGACAGCTGATTCTGGGTGA 59.753 55.000 23.35 0.00 38.36 4.02
501 2157 1.134580 CGACAGCTGATTCTGGGTGAT 60.135 52.381 23.35 0.00 38.36 3.06
502 2158 2.679059 CGACAGCTGATTCTGGGTGATT 60.679 50.000 23.35 0.00 38.36 2.57
503 2159 2.941720 GACAGCTGATTCTGGGTGATTC 59.058 50.000 23.35 0.00 38.36 2.52
504 2160 2.575279 ACAGCTGATTCTGGGTGATTCT 59.425 45.455 23.35 0.00 38.36 2.40
505 2161 2.943690 CAGCTGATTCTGGGTGATTCTG 59.056 50.000 8.42 0.00 33.41 3.02
506 2162 1.674962 GCTGATTCTGGGTGATTCTGC 59.325 52.381 0.00 0.00 40.25 4.26
507 2163 2.942752 GCTGATTCTGGGTGATTCTGCA 60.943 50.000 11.60 0.00 43.32 4.41
508 2164 2.943690 CTGATTCTGGGTGATTCTGCAG 59.056 50.000 7.63 7.63 0.00 4.41
509 2165 2.295885 GATTCTGGGTGATTCTGCAGG 58.704 52.381 15.13 0.00 0.00 4.85
510 2166 1.361204 TTCTGGGTGATTCTGCAGGA 58.639 50.000 15.13 5.14 0.00 3.86
511 2167 1.361204 TCTGGGTGATTCTGCAGGAA 58.639 50.000 15.13 7.46 38.41 3.36
512 2168 1.704628 TCTGGGTGATTCTGCAGGAAA 59.295 47.619 15.13 1.43 37.49 3.13
513 2169 1.815003 CTGGGTGATTCTGCAGGAAAC 59.185 52.381 15.13 8.28 37.49 2.78
514 2170 1.425066 TGGGTGATTCTGCAGGAAACT 59.575 47.619 15.13 0.00 46.44 2.66
528 2184 4.664688 AGGAAACTGATTCTGGGTGATT 57.335 40.909 0.00 0.00 41.13 2.57
529 2185 4.593956 AGGAAACTGATTCTGGGTGATTC 58.406 43.478 0.00 0.00 41.13 2.52
530 2186 4.290722 AGGAAACTGATTCTGGGTGATTCT 59.709 41.667 0.00 0.00 41.13 2.40
531 2187 4.397417 GGAAACTGATTCTGGGTGATTCTG 59.603 45.833 0.00 0.00 38.18 3.02
532 2188 2.996631 ACTGATTCTGGGTGATTCTGC 58.003 47.619 0.00 0.00 31.51 4.26
533 2189 2.306805 ACTGATTCTGGGTGATTCTGCA 59.693 45.455 0.00 0.00 31.51 4.41
534 2190 2.943690 CTGATTCTGGGTGATTCTGCAG 59.056 50.000 7.63 7.63 0.00 4.41
535 2191 2.295885 GATTCTGGGTGATTCTGCAGG 58.704 52.381 15.13 0.00 0.00 4.85
536 2192 1.361204 TTCTGGGTGATTCTGCAGGA 58.639 50.000 15.13 5.14 0.00 3.86
537 2193 1.361204 TCTGGGTGATTCTGCAGGAA 58.639 50.000 15.13 7.46 38.41 3.36
538 2194 1.704628 TCTGGGTGATTCTGCAGGAAA 59.295 47.619 15.13 1.43 37.49 3.13
539 2195 1.815003 CTGGGTGATTCTGCAGGAAAC 59.185 52.381 15.13 8.28 37.49 2.78
540 2196 1.425066 TGGGTGATTCTGCAGGAAACT 59.575 47.619 15.13 0.00 46.44 2.66
562 2218 1.361204 TTCTGGGTGATTCTGCAGGA 58.639 50.000 15.13 5.14 0.00 3.86
613 2269 2.583685 GATTTTGGAGACTGCGCGGC 62.584 60.000 18.15 9.47 0.00 6.53
642 2298 2.446036 GGCGGAGGAGGGGTATGT 60.446 66.667 0.00 0.00 0.00 2.29
748 2404 0.029567 CCTCTCGCGCTCGATTACTT 59.970 55.000 5.56 0.00 44.56 2.24
836 2492 1.822990 TCCACTCCAGGCTTTAGTACG 59.177 52.381 0.00 0.00 0.00 3.67
842 2498 4.534401 GGCTTTAGTACGGGCCTG 57.466 61.111 11.02 11.02 41.20 4.85
1057 4872 3.191581 TGCTATATACAAGAGAGCGGCTC 59.808 47.826 22.13 22.13 44.29 4.70
1059 4874 3.651803 ATATACAAGAGAGCGGCTCAC 57.348 47.619 29.88 24.02 46.45 3.51
1065 4880 3.073735 AGAGCGGCTCACTGGGAG 61.074 66.667 29.88 1.60 46.93 4.30
1209 8648 6.816640 TCAACAGTGGCTCAATACAGTTATAC 59.183 38.462 0.00 0.00 0.00 1.47
1248 8687 7.465647 GCACATGATGAAGTTGATCTAAGACTG 60.466 40.741 0.00 0.00 0.00 3.51
1407 11454 6.354938 TGGAGAGAATGAAGAGGATGATTTG 58.645 40.000 0.00 0.00 0.00 2.32
1435 11482 7.342284 AGCTGATTGATGGAATCTCAGAATTTT 59.658 33.333 9.49 0.00 44.16 1.82
1497 11549 1.000274 GGTGGAAATTGTGGTGCAGTC 60.000 52.381 0.00 0.00 0.00 3.51
1701 14447 1.743772 GCTGTCACATGGGATACGCTT 60.744 52.381 0.00 0.00 37.60 4.68
1729 14475 7.684187 TGAATTTGAAGTTCAAGGTTGATCACC 60.684 37.037 17.36 0.02 37.70 4.02
2101 14855 2.887152 CACCAAAGGAGAAGTTGAAGGG 59.113 50.000 0.00 0.00 0.00 3.95
2169 14924 4.058817 CGAGCCTGTTAGACTCTGTTTTT 58.941 43.478 0.00 0.00 0.00 1.94
2198 14953 0.918983 TTGCCCAGATGAACCCCTAG 59.081 55.000 0.00 0.00 0.00 3.02
2206 14963 4.944317 CCAGATGAACCCCTAGAGTTTTTC 59.056 45.833 0.00 0.00 0.00 2.29
2207 14964 5.280727 CCAGATGAACCCCTAGAGTTTTTCT 60.281 44.000 0.00 0.00 40.06 2.52
2558 15383 0.890542 ATTGCAGCGCTGAGGAAACA 60.891 50.000 40.21 23.85 0.00 2.83
2647 15473 3.319198 GTGGGAAGGACTCCGGCA 61.319 66.667 0.00 0.00 46.51 5.69
2726 16774 5.163652 GGTGCTGTTATTAAACACCCTCATC 60.164 44.000 11.04 0.00 44.04 2.92
2755 16803 1.915614 AATCGTCGCCGTCGTGTACT 61.916 55.000 3.41 0.00 36.96 2.73
2756 16804 2.301902 ATCGTCGCCGTCGTGTACTC 62.302 60.000 3.41 0.00 36.96 2.59
2757 16805 2.572647 GTCGCCGTCGTGTACTCG 60.573 66.667 10.97 10.97 36.96 4.18
2758 16806 3.792047 TCGCCGTCGTGTACTCGG 61.792 66.667 16.50 14.15 45.94 4.63
2759 16807 3.792047 CGCCGTCGTGTACTCGGA 61.792 66.667 16.50 2.02 46.05 4.55
2760 16808 2.099831 GCCGTCGTGTACTCGGAG 59.900 66.667 16.50 2.83 46.05 4.63
2771 17803 3.246936 GTGTACTCGGAGGTGTTTGTTTC 59.753 47.826 10.23 0.00 0.00 2.78
2772 17804 1.578583 ACTCGGAGGTGTTTGTTTCG 58.421 50.000 10.23 0.00 0.00 3.46
2773 17805 0.234884 CTCGGAGGTGTTTGTTTCGC 59.765 55.000 0.00 0.00 0.00 4.70
2774 17806 1.083015 CGGAGGTGTTTGTTTCGCG 60.083 57.895 0.00 0.00 0.00 5.87
2775 17807 1.768112 CGGAGGTGTTTGTTTCGCGT 61.768 55.000 5.77 0.00 0.00 6.01
2776 17808 0.041576 GGAGGTGTTTGTTTCGCGTC 60.042 55.000 5.77 0.00 0.00 5.19
2777 17809 0.935196 GAGGTGTTTGTTTCGCGTCT 59.065 50.000 5.77 0.00 0.00 4.18
2778 17810 2.129607 GAGGTGTTTGTTTCGCGTCTA 58.870 47.619 5.77 0.00 0.00 2.59
2779 17811 2.735134 GAGGTGTTTGTTTCGCGTCTAT 59.265 45.455 5.77 0.00 0.00 1.98
2780 17812 3.135994 AGGTGTTTGTTTCGCGTCTATT 58.864 40.909 5.77 0.00 0.00 1.73
2781 17813 3.562557 AGGTGTTTGTTTCGCGTCTATTT 59.437 39.130 5.77 0.00 0.00 1.40
2782 17814 3.662186 GGTGTTTGTTTCGCGTCTATTTG 59.338 43.478 5.77 0.00 0.00 2.32
2783 17815 4.276460 GTGTTTGTTTCGCGTCTATTTGT 58.724 39.130 5.77 0.00 0.00 2.83
2784 17816 4.374828 GTGTTTGTTTCGCGTCTATTTGTC 59.625 41.667 5.77 0.00 0.00 3.18
2785 17817 3.799137 TTGTTTCGCGTCTATTTGTCC 57.201 42.857 5.77 0.00 0.00 4.02
2786 17818 1.722464 TGTTTCGCGTCTATTTGTCCG 59.278 47.619 5.77 0.00 0.00 4.79
2787 17819 1.723003 GTTTCGCGTCTATTTGTCCGT 59.277 47.619 5.77 0.00 0.00 4.69
2788 17820 2.068837 TTCGCGTCTATTTGTCCGTT 57.931 45.000 5.77 0.00 0.00 4.44
2789 17821 2.917701 TCGCGTCTATTTGTCCGTTA 57.082 45.000 5.77 0.00 0.00 3.18
2790 17822 3.425577 TCGCGTCTATTTGTCCGTTAT 57.574 42.857 5.77 0.00 0.00 1.89
2791 17823 3.365832 TCGCGTCTATTTGTCCGTTATC 58.634 45.455 5.77 0.00 0.00 1.75
2792 17824 2.470257 CGCGTCTATTTGTCCGTTATCC 59.530 50.000 0.00 0.00 0.00 2.59
2793 17825 2.470257 GCGTCTATTTGTCCGTTATCCG 59.530 50.000 0.00 0.00 0.00 4.18
2794 17826 3.793129 GCGTCTATTTGTCCGTTATCCGA 60.793 47.826 0.00 0.00 39.56 4.55
2795 17827 4.543692 CGTCTATTTGTCCGTTATCCGAT 58.456 43.478 0.00 0.00 39.56 4.18
2796 17828 4.980434 CGTCTATTTGTCCGTTATCCGATT 59.020 41.667 0.00 0.00 39.56 3.34
2797 17829 6.144854 CGTCTATTTGTCCGTTATCCGATTA 58.855 40.000 0.00 0.00 39.56 1.75
2798 17830 6.087291 CGTCTATTTGTCCGTTATCCGATTAC 59.913 42.308 0.00 0.00 39.56 1.89
2799 17831 6.919662 GTCTATTTGTCCGTTATCCGATTACA 59.080 38.462 0.00 0.00 39.56 2.41
2800 17832 7.114529 GTCTATTTGTCCGTTATCCGATTACAG 59.885 40.741 0.00 0.00 39.56 2.74
2801 17833 3.088194 TGTCCGTTATCCGATTACAGC 57.912 47.619 0.00 0.00 39.56 4.40
2802 17834 2.049228 GTCCGTTATCCGATTACAGCG 58.951 52.381 0.00 0.00 39.56 5.18
2811 17843 3.594603 CCGATTACAGCGGGATCTAAT 57.405 47.619 0.00 0.00 44.87 1.73
2812 17844 4.713824 CCGATTACAGCGGGATCTAATA 57.286 45.455 0.00 0.00 44.87 0.98
2813 17845 4.421948 CCGATTACAGCGGGATCTAATAC 58.578 47.826 0.00 0.00 44.87 1.89
2814 17846 4.421948 CGATTACAGCGGGATCTAATACC 58.578 47.826 0.00 0.00 0.00 2.73
2831 17863 8.393671 TCTAATACCGTTAAACATGTTTGGTT 57.606 30.769 29.72 17.50 36.52 3.67
2832 17864 8.848182 TCTAATACCGTTAAACATGTTTGGTTT 58.152 29.630 29.72 22.89 41.11 3.27
2834 17866 8.800231 AATACCGTTAAACATGTTTGGTTTAC 57.200 30.769 29.72 18.22 39.63 2.01
2835 17867 6.453926 ACCGTTAAACATGTTTGGTTTACT 57.546 33.333 29.72 7.19 39.63 2.24
2837 17869 6.752815 ACCGTTAAACATGTTTGGTTTACTTG 59.247 34.615 29.72 15.49 39.63 3.16
2839 17871 6.291902 CGTTAAACATGTTTGGTTTACTTGGC 60.292 38.462 29.72 8.03 39.63 4.52
2840 17872 3.744238 ACATGTTTGGTTTACTTGGCC 57.256 42.857 0.00 0.00 0.00 5.36
2841 17873 3.304829 ACATGTTTGGTTTACTTGGCCT 58.695 40.909 3.32 0.00 0.00 5.19
2842 17874 3.069443 ACATGTTTGGTTTACTTGGCCTG 59.931 43.478 3.32 0.00 0.00 4.85
2844 17876 3.899726 TGTTTGGTTTACTTGGCCTGTA 58.100 40.909 3.32 4.56 0.00 2.74
2845 17877 4.279145 TGTTTGGTTTACTTGGCCTGTAA 58.721 39.130 14.84 14.84 0.00 2.41
2846 17878 4.098196 TGTTTGGTTTACTTGGCCTGTAAC 59.902 41.667 17.37 13.33 30.70 2.50
2848 17880 1.808343 GGTTTACTTGGCCTGTAACCG 59.192 52.381 17.37 0.00 30.70 4.44
2849 17881 2.550639 GGTTTACTTGGCCTGTAACCGA 60.551 50.000 17.37 5.21 30.70 4.69
2850 17882 3.340928 GTTTACTTGGCCTGTAACCGAT 58.659 45.455 17.37 0.00 30.70 4.18
2851 17883 3.706600 TTACTTGGCCTGTAACCGATT 57.293 42.857 14.84 0.00 0.00 3.34
2852 17884 4.822685 TTACTTGGCCTGTAACCGATTA 57.177 40.909 14.84 0.00 0.00 1.75
2853 17885 2.981898 ACTTGGCCTGTAACCGATTAC 58.018 47.619 3.32 0.00 41.07 1.89
2854 17886 2.285977 CTTGGCCTGTAACCGATTACC 58.714 52.381 3.32 0.00 40.12 2.85
2858 17890 1.474498 GCCTGTAACCGATTACCCTGG 60.474 57.143 0.00 0.00 40.12 4.45
2860 17892 2.502538 CCTGTAACCGATTACCCTGGAA 59.497 50.000 0.00 0.00 40.12 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
245 1894 5.250543 TCCATTTTCCCATGTACAGAGAAGA 59.749 40.000 0.33 0.19 0.00 2.87
246 1895 5.500234 TCCATTTTCCCATGTACAGAGAAG 58.500 41.667 0.33 0.00 0.00 2.85
247 1896 5.512942 TCCATTTTCCCATGTACAGAGAA 57.487 39.130 0.33 1.30 0.00 2.87
248 1897 5.439721 CATCCATTTTCCCATGTACAGAGA 58.560 41.667 0.33 0.00 0.00 3.10
249 1898 4.581824 CCATCCATTTTCCCATGTACAGAG 59.418 45.833 0.33 0.00 0.00 3.35
250 1899 4.229353 TCCATCCATTTTCCCATGTACAGA 59.771 41.667 0.33 0.00 0.00 3.41
251 1900 4.535781 TCCATCCATTTTCCCATGTACAG 58.464 43.478 0.33 0.00 0.00 2.74
252 1901 4.599720 TCCATCCATTTTCCCATGTACA 57.400 40.909 0.00 0.00 0.00 2.90
261 1910 7.495135 AACAAACAAACATCCATCCATTTTC 57.505 32.000 0.00 0.00 0.00 2.29
374 2023 7.072030 GTGTGTTGAATTGCTAAGACTTACAG 58.928 38.462 0.00 0.00 0.00 2.74
376 2025 6.954944 TGTGTGTTGAATTGCTAAGACTTAC 58.045 36.000 0.00 0.00 0.00 2.34
377 2026 6.765989 ACTGTGTGTTGAATTGCTAAGACTTA 59.234 34.615 0.00 0.00 0.00 2.24
378 2027 5.590259 ACTGTGTGTTGAATTGCTAAGACTT 59.410 36.000 0.00 0.00 0.00 3.01
382 2031 7.915397 ACTAAAACTGTGTGTTGAATTGCTAAG 59.085 33.333 0.00 0.00 39.13 2.18
427 2082 4.211125 TGGGATGAGTTGTGTGCTAAAAA 58.789 39.130 0.00 0.00 0.00 1.94
478 2134 0.534412 CCCAGAATCAGCTGTCGAGT 59.466 55.000 14.67 0.00 34.06 4.18
493 2149 1.815003 GTTTCCTGCAGAATCACCCAG 59.185 52.381 17.39 0.00 33.44 4.45
494 2150 1.425066 AGTTTCCTGCAGAATCACCCA 59.575 47.619 17.39 0.00 33.44 4.51
495 2151 1.815003 CAGTTTCCTGCAGAATCACCC 59.185 52.381 17.39 0.00 33.44 4.61
496 2152 2.783135 TCAGTTTCCTGCAGAATCACC 58.217 47.619 17.39 0.00 38.66 4.02
497 2153 4.699257 AGAATCAGTTTCCTGCAGAATCAC 59.301 41.667 17.39 6.24 38.66 3.06
498 2154 4.698780 CAGAATCAGTTTCCTGCAGAATCA 59.301 41.667 17.39 0.00 38.66 2.57
499 2155 4.096081 CCAGAATCAGTTTCCTGCAGAATC 59.904 45.833 17.39 7.03 38.66 2.52
500 2156 4.015084 CCAGAATCAGTTTCCTGCAGAAT 58.985 43.478 17.39 0.00 38.66 2.40
501 2157 3.415212 CCAGAATCAGTTTCCTGCAGAA 58.585 45.455 17.39 4.81 38.66 3.02
502 2158 2.290514 CCCAGAATCAGTTTCCTGCAGA 60.291 50.000 17.39 0.00 38.66 4.26
503 2159 2.089980 CCCAGAATCAGTTTCCTGCAG 58.910 52.381 6.78 6.78 38.66 4.41
504 2160 1.425066 ACCCAGAATCAGTTTCCTGCA 59.575 47.619 0.00 0.00 38.66 4.41
505 2161 1.815003 CACCCAGAATCAGTTTCCTGC 59.185 52.381 0.00 0.00 38.66 4.85
506 2162 3.423539 TCACCCAGAATCAGTTTCCTG 57.576 47.619 0.00 0.00 40.25 3.86
507 2163 4.290722 AGAATCACCCAGAATCAGTTTCCT 59.709 41.667 0.00 0.00 34.67 3.36
508 2164 4.397417 CAGAATCACCCAGAATCAGTTTCC 59.603 45.833 0.00 0.00 34.67 3.13
509 2165 4.142513 GCAGAATCACCCAGAATCAGTTTC 60.143 45.833 0.00 0.00 34.31 2.78
510 2166 3.760684 GCAGAATCACCCAGAATCAGTTT 59.239 43.478 0.00 0.00 0.00 2.66
511 2167 3.245016 TGCAGAATCACCCAGAATCAGTT 60.245 43.478 0.00 0.00 0.00 3.16
512 2168 2.306805 TGCAGAATCACCCAGAATCAGT 59.693 45.455 0.00 0.00 0.00 3.41
513 2169 2.943690 CTGCAGAATCACCCAGAATCAG 59.056 50.000 8.42 0.00 0.00 2.90
514 2170 2.356432 CCTGCAGAATCACCCAGAATCA 60.356 50.000 17.39 0.00 0.00 2.57
515 2171 2.092753 TCCTGCAGAATCACCCAGAATC 60.093 50.000 17.39 0.00 0.00 2.52
516 2172 1.918262 TCCTGCAGAATCACCCAGAAT 59.082 47.619 17.39 0.00 0.00 2.40
517 2173 1.361204 TCCTGCAGAATCACCCAGAA 58.639 50.000 17.39 0.00 0.00 3.02
518 2174 1.361204 TTCCTGCAGAATCACCCAGA 58.639 50.000 17.39 0.00 0.00 3.86
519 2175 1.815003 GTTTCCTGCAGAATCACCCAG 59.185 52.381 17.39 0.00 33.44 4.45
520 2176 1.425066 AGTTTCCTGCAGAATCACCCA 59.575 47.619 17.39 0.00 33.44 4.51
521 2177 1.815003 CAGTTTCCTGCAGAATCACCC 59.185 52.381 17.39 0.00 33.44 4.61
522 2178 2.783135 TCAGTTTCCTGCAGAATCACC 58.217 47.619 17.39 0.00 38.66 4.02
523 2179 4.699257 AGAATCAGTTTCCTGCAGAATCAC 59.301 41.667 17.39 6.24 38.66 3.06
524 2180 4.698780 CAGAATCAGTTTCCTGCAGAATCA 59.301 41.667 17.39 0.00 38.66 2.57
525 2181 4.096081 CCAGAATCAGTTTCCTGCAGAATC 59.904 45.833 17.39 7.03 38.66 2.52
526 2182 4.015084 CCAGAATCAGTTTCCTGCAGAAT 58.985 43.478 17.39 0.00 38.66 2.40
527 2183 3.415212 CCAGAATCAGTTTCCTGCAGAA 58.585 45.455 17.39 4.81 38.66 3.02
528 2184 2.290514 CCCAGAATCAGTTTCCTGCAGA 60.291 50.000 17.39 0.00 38.66 4.26
529 2185 2.089980 CCCAGAATCAGTTTCCTGCAG 58.910 52.381 6.78 6.78 38.66 4.41
530 2186 1.425066 ACCCAGAATCAGTTTCCTGCA 59.575 47.619 0.00 0.00 38.66 4.41
531 2187 1.815003 CACCCAGAATCAGTTTCCTGC 59.185 52.381 0.00 0.00 38.66 4.85
532 2188 3.423539 TCACCCAGAATCAGTTTCCTG 57.576 47.619 0.00 0.00 40.25 3.86
533 2189 4.290722 AGAATCACCCAGAATCAGTTTCCT 59.709 41.667 0.00 0.00 34.67 3.36
534 2190 4.397417 CAGAATCACCCAGAATCAGTTTCC 59.603 45.833 0.00 0.00 34.67 3.13
535 2191 4.142513 GCAGAATCACCCAGAATCAGTTTC 60.143 45.833 0.00 0.00 34.31 2.78
536 2192 3.760684 GCAGAATCACCCAGAATCAGTTT 59.239 43.478 0.00 0.00 0.00 2.66
537 2193 3.245016 TGCAGAATCACCCAGAATCAGTT 60.245 43.478 0.00 0.00 0.00 3.16
538 2194 2.306805 TGCAGAATCACCCAGAATCAGT 59.693 45.455 0.00 0.00 0.00 3.41
539 2195 2.943690 CTGCAGAATCACCCAGAATCAG 59.056 50.000 8.42 0.00 0.00 2.90
540 2196 2.356432 CCTGCAGAATCACCCAGAATCA 60.356 50.000 17.39 0.00 0.00 2.57
541 2197 2.092753 TCCTGCAGAATCACCCAGAATC 60.093 50.000 17.39 0.00 0.00 2.52
542 2198 1.918262 TCCTGCAGAATCACCCAGAAT 59.082 47.619 17.39 0.00 0.00 2.40
543 2199 1.361204 TCCTGCAGAATCACCCAGAA 58.639 50.000 17.39 0.00 0.00 3.02
544 2200 1.361204 TTCCTGCAGAATCACCCAGA 58.639 50.000 17.39 0.00 0.00 3.86
545 2201 1.815003 GTTTCCTGCAGAATCACCCAG 59.185 52.381 17.39 0.00 33.44 4.45
562 2218 3.398318 AACTTCCCCCAAACTCAGTTT 57.602 42.857 0.00 0.00 36.05 2.66
569 2225 4.693283 CTTTTGAGAAACTTCCCCCAAAC 58.307 43.478 0.00 0.00 0.00 2.93
613 2269 3.168237 CTCCGCCGCAAAATAGCCG 62.168 63.158 0.00 0.00 0.00 5.52
642 2298 7.254898 GCTACTATGCAGAGACAAAATAATGCA 60.255 37.037 16.75 0.00 46.50 3.96
748 2404 1.597854 CAACCCTGCTGACGCTTCA 60.598 57.895 0.00 0.00 36.97 3.02
823 2479 4.534401 GGCCCGTACTAAAGCCTG 57.466 61.111 0.00 0.00 42.34 4.85
836 2492 1.401905 GATGTTGATTTCGACAGGCCC 59.598 52.381 0.00 0.00 42.95 5.80
1209 8648 5.594926 TCATCATGTGCTGCTATATATCCG 58.405 41.667 0.00 0.00 0.00 4.18
1248 8687 6.912591 CCCTGCTACGATTGAAAACATAATTC 59.087 38.462 0.00 0.00 0.00 2.17
1386 11433 5.752650 TGCAAATCATCCTCTTCATTCTCT 58.247 37.500 0.00 0.00 0.00 3.10
1407 11454 3.211865 TGAGATTCCATCAATCAGCTGC 58.788 45.455 9.47 0.00 43.27 5.25
1497 11549 3.788434 ACAAGTGCAAAAGACGTATCG 57.212 42.857 0.00 0.00 0.00 2.92
1701 14447 9.076781 TGATCAACCTTGAACTTCAAATTCATA 57.923 29.630 5.72 0.00 41.13 2.15
1729 14475 6.631238 CGTTCAATATTATTGTTACGGCCTTG 59.369 38.462 23.52 0.00 0.00 3.61
1735 14481 9.005180 ACAATTGCGTTCAATATTATTGTTACG 57.995 29.630 25.14 25.14 41.77 3.18
1859 14605 6.055588 ACACAATACTGTTAACTGCTCAACT 58.944 36.000 11.98 0.00 31.64 3.16
1959 14713 6.946340 TCTTAGAAAGCAATCACATCAGGTA 58.054 36.000 0.00 0.00 0.00 3.08
2101 14855 3.797546 GCTGCAGACGCTGGCTTC 61.798 66.667 20.43 0.00 39.64 3.86
2169 14924 3.153130 TCATCTGGGCAAAATTCGTCAA 58.847 40.909 0.00 0.00 0.00 3.18
2174 14929 2.093500 GGGGTTCATCTGGGCAAAATTC 60.093 50.000 0.00 0.00 0.00 2.17
2226 14983 8.717717 TGAAGGGATAGACTGATGTTAATCAAT 58.282 33.333 0.00 0.00 42.28 2.57
2236 14993 5.643421 AAGCAATGAAGGGATAGACTGAT 57.357 39.130 0.00 0.00 0.00 2.90
2447 15224 4.379499 GCCAGTAACATAAACCTCAACTGC 60.379 45.833 0.00 0.00 33.26 4.40
2558 15383 0.611896 GCCACAGCCCACAGGTTATT 60.612 55.000 0.00 0.00 34.57 1.40
2647 15473 2.507102 CGCAGCGTCGTCTTCCAT 60.507 61.111 6.65 0.00 0.00 3.41
2726 16774 2.726691 GCGACGATTCACACACCGG 61.727 63.158 0.00 0.00 0.00 5.28
2755 16803 1.492319 CGCGAAACAAACACCTCCGA 61.492 55.000 0.00 0.00 0.00 4.55
2756 16804 1.083015 CGCGAAACAAACACCTCCG 60.083 57.895 0.00 0.00 0.00 4.63
2757 16805 0.041576 GACGCGAAACAAACACCTCC 60.042 55.000 15.93 0.00 0.00 4.30
2758 16806 0.935196 AGACGCGAAACAAACACCTC 59.065 50.000 15.93 0.00 0.00 3.85
2759 16807 2.228138 TAGACGCGAAACAAACACCT 57.772 45.000 15.93 0.00 0.00 4.00
2760 16808 3.531262 AATAGACGCGAAACAAACACC 57.469 42.857 15.93 0.00 0.00 4.16
2771 17803 2.470257 GGATAACGGACAAATAGACGCG 59.530 50.000 3.53 3.53 0.00 6.01
2772 17804 2.470257 CGGATAACGGACAAATAGACGC 59.530 50.000 0.00 0.00 39.42 5.19
2773 17805 3.956233 TCGGATAACGGACAAATAGACG 58.044 45.455 0.00 0.00 44.45 4.18
2774 17806 6.919662 TGTAATCGGATAACGGACAAATAGAC 59.080 38.462 0.00 0.00 44.45 2.59
2775 17807 7.041635 TGTAATCGGATAACGGACAAATAGA 57.958 36.000 0.00 0.00 44.45 1.98
2776 17808 6.128902 GCTGTAATCGGATAACGGACAAATAG 60.129 42.308 0.00 0.00 44.45 1.73
2777 17809 5.693104 GCTGTAATCGGATAACGGACAAATA 59.307 40.000 0.00 0.00 44.45 1.40
2778 17810 4.510340 GCTGTAATCGGATAACGGACAAAT 59.490 41.667 0.00 0.00 44.45 2.32
2779 17811 3.866910 GCTGTAATCGGATAACGGACAAA 59.133 43.478 0.00 0.00 44.45 2.83
2780 17812 3.450578 GCTGTAATCGGATAACGGACAA 58.549 45.455 0.00 0.00 44.45 3.18
2781 17813 2.542205 CGCTGTAATCGGATAACGGACA 60.542 50.000 0.00 0.00 44.45 4.02
2782 17814 2.049228 CGCTGTAATCGGATAACGGAC 58.951 52.381 0.00 0.00 44.45 4.79
2783 17815 2.410785 CGCTGTAATCGGATAACGGA 57.589 50.000 0.00 0.00 44.45 4.69
2791 17823 3.594603 ATTAGATCCCGCTGTAATCGG 57.405 47.619 0.00 0.00 46.05 4.18
2792 17824 4.421948 GGTATTAGATCCCGCTGTAATCG 58.578 47.826 0.00 0.00 0.00 3.34
2793 17825 4.082354 ACGGTATTAGATCCCGCTGTAATC 60.082 45.833 7.20 0.00 45.49 1.75
2794 17826 3.830755 ACGGTATTAGATCCCGCTGTAAT 59.169 43.478 7.20 0.00 45.49 1.89
2795 17827 3.225104 ACGGTATTAGATCCCGCTGTAA 58.775 45.455 7.20 0.00 45.49 2.41
2796 17828 2.867624 ACGGTATTAGATCCCGCTGTA 58.132 47.619 7.20 0.00 45.49 2.74
2797 17829 1.700955 ACGGTATTAGATCCCGCTGT 58.299 50.000 7.20 0.00 45.49 4.40
2798 17830 2.814280 AACGGTATTAGATCCCGCTG 57.186 50.000 7.20 0.00 45.49 5.18
2799 17831 4.099881 TGTTTAACGGTATTAGATCCCGCT 59.900 41.667 7.20 0.00 45.49 5.52
2800 17832 4.370917 TGTTTAACGGTATTAGATCCCGC 58.629 43.478 7.20 0.00 45.49 6.13
2801 17833 5.987347 ACATGTTTAACGGTATTAGATCCCG 59.013 40.000 5.88 5.88 46.93 5.14
2802 17834 7.797038 AACATGTTTAACGGTATTAGATCCC 57.203 36.000 4.92 0.00 0.00 3.85
2803 17835 8.126700 CCAAACATGTTTAACGGTATTAGATCC 58.873 37.037 22.87 0.00 0.00 3.36
2804 17836 8.671028 ACCAAACATGTTTAACGGTATTAGATC 58.329 33.333 23.37 0.00 28.43 2.75
2805 17837 8.570068 ACCAAACATGTTTAACGGTATTAGAT 57.430 30.769 23.37 4.41 28.43 1.98
2806 17838 7.982761 ACCAAACATGTTTAACGGTATTAGA 57.017 32.000 23.37 0.00 28.43 2.10
2808 17840 9.890352 GTAAACCAAACATGTTTAACGGTATTA 57.110 29.630 24.36 20.50 39.23 0.98
2809 17841 8.631797 AGTAAACCAAACATGTTTAACGGTATT 58.368 29.630 24.36 21.18 39.23 1.89
2810 17842 8.168790 AGTAAACCAAACATGTTTAACGGTAT 57.831 30.769 24.36 15.28 39.23 2.73
2811 17843 7.565323 AGTAAACCAAACATGTTTAACGGTA 57.435 32.000 24.36 12.57 39.23 4.02
2812 17844 6.453926 AGTAAACCAAACATGTTTAACGGT 57.546 33.333 22.87 21.54 39.23 4.83
2813 17845 6.199342 CCAAGTAAACCAAACATGTTTAACGG 59.801 38.462 22.87 20.93 39.23 4.44
2814 17846 6.291902 GCCAAGTAAACCAAACATGTTTAACG 60.292 38.462 22.87 15.18 39.23 3.18
2815 17847 6.018588 GGCCAAGTAAACCAAACATGTTTAAC 60.019 38.462 22.87 15.02 39.23 2.01
2816 17848 6.049790 GGCCAAGTAAACCAAACATGTTTAA 58.950 36.000 22.87 4.72 39.23 1.52
2817 17849 5.364157 AGGCCAAGTAAACCAAACATGTTTA 59.636 36.000 22.87 5.07 37.18 2.01
2818 17850 4.163268 AGGCCAAGTAAACCAAACATGTTT 59.837 37.500 18.13 18.13 39.19 2.83
2819 17851 3.709141 AGGCCAAGTAAACCAAACATGTT 59.291 39.130 5.01 4.92 0.00 2.71
2820 17852 3.069443 CAGGCCAAGTAAACCAAACATGT 59.931 43.478 5.01 0.00 0.00 3.21
2821 17853 3.069443 ACAGGCCAAGTAAACCAAACATG 59.931 43.478 5.01 0.00 0.00 3.21
2822 17854 3.304829 ACAGGCCAAGTAAACCAAACAT 58.695 40.909 5.01 0.00 0.00 2.71
2831 17863 3.706600 AATCGGTTACAGGCCAAGTAA 57.293 42.857 14.65 14.65 0.00 2.24
2832 17864 3.118665 GGTAATCGGTTACAGGCCAAGTA 60.119 47.826 19.72 4.47 41.59 2.24
2833 17865 2.355412 GGTAATCGGTTACAGGCCAAGT 60.355 50.000 19.72 5.68 41.59 3.16
2834 17866 2.285977 GGTAATCGGTTACAGGCCAAG 58.714 52.381 19.72 0.00 41.59 3.61
2835 17867 1.065272 GGGTAATCGGTTACAGGCCAA 60.065 52.381 19.72 0.00 41.59 4.52
2837 17869 0.835276 AGGGTAATCGGTTACAGGCC 59.165 55.000 19.72 11.80 41.59 5.19
2839 17871 2.112998 TCCAGGGTAATCGGTTACAGG 58.887 52.381 19.72 16.70 41.59 4.00
2840 17872 3.899052 TTCCAGGGTAATCGGTTACAG 57.101 47.619 19.72 9.00 41.59 2.74


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

AutoCloner maintained by Alex Coulton.