Multiple sequence alignment - TraesCS6B01G142200

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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 TraesCS6B01G142200 chr6B 100.000 3121 0 0 1 3121 142100094 142096974 0.000000e+00 5764.0
1 TraesCS6B01G142200 chr6B 82.097 944 141 20 1075 2007 665161710 665160784 0.000000e+00 782.0
2 TraesCS6B01G142200 chr6B 81.667 960 155 17 1071 2024 95237021 95236077 0.000000e+00 778.0
3 TraesCS6B01G142200 chr6B 94.485 272 2 2 2181 2439 142092836 142092565 1.040000e-109 407.0
4 TraesCS6B01G142200 chr6D 93.060 1124 60 4 1071 2180 67326166 67325047 0.000000e+00 1628.0
5 TraesCS6B01G142200 chr6D 93.562 963 40 3 2181 3121 12199142 12200104 0.000000e+00 1415.0
6 TraesCS6B01G142200 chr6D 87.005 1085 118 14 1075 2144 466527829 466526753 0.000000e+00 1201.0
7 TraesCS6B01G142200 chr6D 86.859 1073 118 12 1075 2141 466551244 466550189 0.000000e+00 1179.0
8 TraesCS6B01G142200 chr6D 82.309 944 139 19 1075 2007 439921486 439920560 0.000000e+00 793.0
9 TraesCS6B01G142200 chr6D 81.722 941 146 17 1075 2007 440014675 440013753 0.000000e+00 761.0
10 TraesCS6B01G142200 chr5B 96.458 960 19 4 2176 3121 461831837 461832795 0.000000e+00 1570.0
11 TraesCS6B01G142200 chr5B 94.444 270 4 1 2181 2439 461860767 461861036 3.750000e-109 405.0
12 TraesCS6B01G142200 chr4A 95.213 961 29 9 2177 3121 703714594 703713635 0.000000e+00 1504.0
13 TraesCS6B01G142200 chr4A 95.099 959 32 4 2177 3121 703612778 703611821 0.000000e+00 1496.0
14 TraesCS6B01G142200 chr4A 94.161 274 3 7 2181 2441 703709466 703709193 3.750000e-109 405.0
15 TraesCS6B01G142200 chr4A 91.786 280 4 7 2181 2441 703607649 703607370 3.800000e-99 372.0
16 TraesCS6B01G142200 chr7A 94.974 955 34 7 2181 3121 80586911 80587865 0.000000e+00 1485.0
17 TraesCS6B01G142200 chr7A 81.965 926 150 11 1071 1992 219397514 219398426 0.000000e+00 769.0
18 TraesCS6B01G142200 chr7A 86.054 294 6 4 2181 2439 80591977 80592270 1.830000e-72 283.0
19 TraesCS6B01G142200 chr6A 90.099 1111 78 11 1071 2180 84699249 84698170 0.000000e+00 1413.0
20 TraesCS6B01G142200 chr6A 81.289 962 150 19 1071 2021 101354725 101355667 0.000000e+00 752.0
21 TraesCS6B01G142200 chr6A 92.157 408 28 2 1 408 84701340 84700937 9.710000e-160 573.0
22 TraesCS6B01G142200 chr6A 89.714 350 26 7 679 1023 84700542 84700198 3.700000e-119 438.0
23 TraesCS6B01G142200 chr6A 84.783 230 14 5 452 679 84700791 84700581 8.770000e-51 211.0
24 TraesCS6B01G142200 chr4D 81.688 628 115 0 2494 3121 128713503 128712876 9.920000e-145 523.0
25 TraesCS6B01G142200 chr3A 78.649 740 140 15 2396 3121 150000041 150000776 2.820000e-130 475.0
26 TraesCS6B01G142200 chrUn 80.317 630 114 10 2497 3121 69777108 69776484 4.710000e-128 468.0
27 TraesCS6B01G142200 chr1B 79.872 626 124 2 2497 3121 639489869 639489245 1.020000e-124 457.0
28 TraesCS6B01G142200 chr2D 86.022 279 23 10 2181 2444 649033084 649033361 5.090000e-73 285.0
29 TraesCS6B01G142200 chr2A 90.476 63 3 3 2414 2474 44710554 44710615 2.580000e-11 80.5


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 TraesCS6B01G142200 chr6B 142096974 142100094 3120 True 5764.00 5764 100.00000 1 3121 1 chr6B.!!$R3 3120
1 TraesCS6B01G142200 chr6B 665160784 665161710 926 True 782.00 782 82.09700 1075 2007 1 chr6B.!!$R4 932
2 TraesCS6B01G142200 chr6B 95236077 95237021 944 True 778.00 778 81.66700 1071 2024 1 chr6B.!!$R1 953
3 TraesCS6B01G142200 chr6D 67325047 67326166 1119 True 1628.00 1628 93.06000 1071 2180 1 chr6D.!!$R1 1109
4 TraesCS6B01G142200 chr6D 12199142 12200104 962 False 1415.00 1415 93.56200 2181 3121 1 chr6D.!!$F1 940
5 TraesCS6B01G142200 chr6D 466526753 466527829 1076 True 1201.00 1201 87.00500 1075 2144 1 chr6D.!!$R4 1069
6 TraesCS6B01G142200 chr6D 466550189 466551244 1055 True 1179.00 1179 86.85900 1075 2141 1 chr6D.!!$R5 1066
7 TraesCS6B01G142200 chr6D 439920560 439921486 926 True 793.00 793 82.30900 1075 2007 1 chr6D.!!$R2 932
8 TraesCS6B01G142200 chr6D 440013753 440014675 922 True 761.00 761 81.72200 1075 2007 1 chr6D.!!$R3 932
9 TraesCS6B01G142200 chr5B 461831837 461832795 958 False 1570.00 1570 96.45800 2176 3121 1 chr5B.!!$F1 945
10 TraesCS6B01G142200 chr4A 703713635 703714594 959 True 1504.00 1504 95.21300 2177 3121 1 chr4A.!!$R4 944
11 TraesCS6B01G142200 chr4A 703611821 703612778 957 True 1496.00 1496 95.09900 2177 3121 1 chr4A.!!$R2 944
12 TraesCS6B01G142200 chr7A 80586911 80587865 954 False 1485.00 1485 94.97400 2181 3121 1 chr7A.!!$F1 940
13 TraesCS6B01G142200 chr7A 219397514 219398426 912 False 769.00 769 81.96500 1071 1992 1 chr7A.!!$F3 921
14 TraesCS6B01G142200 chr6A 101354725 101355667 942 False 752.00 752 81.28900 1071 2021 1 chr6A.!!$F1 950
15 TraesCS6B01G142200 chr6A 84698170 84701340 3170 True 658.75 1413 89.18825 1 2180 4 chr6A.!!$R1 2179
16 TraesCS6B01G142200 chr4D 128712876 128713503 627 True 523.00 523 81.68800 2494 3121 1 chr4D.!!$R1 627
17 TraesCS6B01G142200 chr3A 150000041 150000776 735 False 475.00 475 78.64900 2396 3121 1 chr3A.!!$F1 725
18 TraesCS6B01G142200 chrUn 69776484 69777108 624 True 468.00 468 80.31700 2497 3121 1 chrUn.!!$R1 624
19 TraesCS6B01G142200 chr1B 639489245 639489869 624 True 457.00 457 79.87200 2497 3121 1 chr1B.!!$R1 624

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
689 832 0.033699 AAGCAAGGAGGATGGAAGGC 60.034 55.0 0.00 0.0 0.00 4.35 F
2008 3100 0.104855 TGTCTGCACTGTGGTGACTC 59.895 55.0 10.21 0.0 45.61 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 3170 0.758685 CAGGCAAAGACACCCCCAAA 60.759 55.0 0.00 0.0 0.00 3.28 R
3053 4180 0.038983 TCGACGCGAACATCAAGGAA 60.039 50.0 15.93 0.0 31.06 3.36 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
31 32 7.309867 CCTCTTTCCACTAAAGCTAGTTGTCTA 60.310 40.741 0.00 0.00 43.70 2.59
78 79 2.553028 GGATGCAGAGAAAGGACCACAA 60.553 50.000 0.00 0.00 0.00 3.33
166 167 0.603065 AAGCGGCTTTGGAAACATCC 59.397 50.000 9.94 0.00 42.32 3.51
171 172 2.287909 CGGCTTTGGAAACATCCGAAAA 60.288 45.455 0.00 0.00 45.16 2.29
183 184 1.674359 TCCGAAAAGCTGCAAAGTGA 58.326 45.000 1.02 0.00 0.00 3.41
244 245 7.539034 TGATTTCCTCATCGGTAAGATCATA 57.461 36.000 0.00 0.00 37.52 2.15
245 246 8.138928 TGATTTCCTCATCGGTAAGATCATAT 57.861 34.615 0.00 0.00 37.52 1.78
251 252 6.091849 CCTCATCGGTAAGATCATATGCTTTG 59.908 42.308 0.00 0.00 37.52 2.77
292 293 3.198068 TCACTCAGACACAAGTTGCTTC 58.802 45.455 1.81 0.00 0.00 3.86
327 328 3.058432 CACTGCTTCAAACCATCAGACAG 60.058 47.826 0.00 0.00 0.00 3.51
341 342 8.408043 ACCATCAGACAGTCATCAAAATTTAA 57.592 30.769 2.66 0.00 0.00 1.52
344 345 9.552114 CATCAGACAGTCATCAAAATTTAAGTC 57.448 33.333 2.66 0.00 0.00 3.01
354 355 9.844790 TCATCAAAATTTAAGTCAGCATACAAG 57.155 29.630 0.00 0.00 0.00 3.16
358 359 9.462174 CAAAATTTAAGTCAGCATACAAGACAA 57.538 29.630 0.00 0.00 34.80 3.18
361 362 4.357918 AAGTCAGCATACAAGACAACCT 57.642 40.909 0.00 0.00 34.80 3.50
370 371 8.230486 CAGCATACAAGACAACCTAAGTAAAAG 58.770 37.037 0.00 0.00 0.00 2.27
390 391 6.763715 AAAGTTATATGGGAGCAGGATGTA 57.236 37.500 0.00 0.00 39.31 2.29
397 398 2.092429 TGGGAGCAGGATGTAATTGGTC 60.092 50.000 0.00 0.00 39.31 4.02
400 401 2.866762 GAGCAGGATGTAATTGGTCGTC 59.133 50.000 0.00 0.00 39.31 4.20
408 409 5.293569 GGATGTAATTGGTCGTCTGGTAAAG 59.706 44.000 0.00 0.00 0.00 1.85
410 411 4.283978 TGTAATTGGTCGTCTGGTAAAGGA 59.716 41.667 0.00 0.00 0.00 3.36
411 412 4.360951 AATTGGTCGTCTGGTAAAGGAA 57.639 40.909 0.00 0.00 0.00 3.36
412 413 3.396260 TTGGTCGTCTGGTAAAGGAAG 57.604 47.619 0.00 0.00 0.00 3.46
413 414 1.621814 TGGTCGTCTGGTAAAGGAAGG 59.378 52.381 0.00 0.00 0.00 3.46
414 415 1.066358 GGTCGTCTGGTAAAGGAAGGG 60.066 57.143 0.00 0.00 0.00 3.95
415 416 1.066358 GTCGTCTGGTAAAGGAAGGGG 60.066 57.143 0.00 0.00 0.00 4.79
416 417 0.252197 CGTCTGGTAAAGGAAGGGGG 59.748 60.000 0.00 0.00 0.00 5.40
417 418 1.665137 GTCTGGTAAAGGAAGGGGGA 58.335 55.000 0.00 0.00 0.00 4.81
418 419 1.560146 GTCTGGTAAAGGAAGGGGGAG 59.440 57.143 0.00 0.00 0.00 4.30
419 420 0.919710 CTGGTAAAGGAAGGGGGAGG 59.080 60.000 0.00 0.00 0.00 4.30
420 421 0.197661 TGGTAAAGGAAGGGGGAGGT 59.802 55.000 0.00 0.00 0.00 3.85
421 422 1.379776 GGTAAAGGAAGGGGGAGGTT 58.620 55.000 0.00 0.00 0.00 3.50
422 423 1.714787 GGTAAAGGAAGGGGGAGGTTT 59.285 52.381 0.00 0.00 0.00 3.27
423 424 2.921612 GGTAAAGGAAGGGGGAGGTTTA 59.078 50.000 0.00 0.00 0.00 2.01
424 425 3.308688 GGTAAAGGAAGGGGGAGGTTTAC 60.309 52.174 0.00 0.00 32.18 2.01
425 426 2.452923 AAGGAAGGGGGAGGTTTACT 57.547 50.000 0.00 0.00 0.00 2.24
426 427 1.670059 AGGAAGGGGGAGGTTTACTG 58.330 55.000 0.00 0.00 0.00 2.74
427 428 1.153565 AGGAAGGGGGAGGTTTACTGA 59.846 52.381 0.00 0.00 0.00 3.41
428 429 1.281287 GGAAGGGGGAGGTTTACTGAC 59.719 57.143 0.00 0.00 0.00 3.51
429 430 1.982958 GAAGGGGGAGGTTTACTGACA 59.017 52.381 0.00 0.00 0.00 3.58
430 431 1.657804 AGGGGGAGGTTTACTGACAG 58.342 55.000 0.00 0.00 0.00 3.51
431 432 1.132495 AGGGGGAGGTTTACTGACAGT 60.132 52.381 13.68 13.68 0.00 3.55
432 433 1.278413 GGGGGAGGTTTACTGACAGTC 59.722 57.143 12.39 0.00 0.00 3.51
433 434 2.258109 GGGGAGGTTTACTGACAGTCT 58.742 52.381 12.39 2.47 0.00 3.24
434 435 2.234168 GGGGAGGTTTACTGACAGTCTC 59.766 54.545 12.39 11.97 0.00 3.36
435 436 2.897969 GGGAGGTTTACTGACAGTCTCA 59.102 50.000 12.39 0.00 0.00 3.27
443 444 2.634982 CTGACAGTCTCAGTGAGAGC 57.365 55.000 23.27 16.78 44.35 4.09
444 445 1.885233 CTGACAGTCTCAGTGAGAGCA 59.115 52.381 23.27 16.38 44.35 4.26
445 446 1.885233 TGACAGTCTCAGTGAGAGCAG 59.115 52.381 23.27 16.93 44.35 4.24
446 447 0.602562 ACAGTCTCAGTGAGAGCAGC 59.397 55.000 23.27 11.40 44.35 5.25
447 448 0.889994 CAGTCTCAGTGAGAGCAGCT 59.110 55.000 23.27 13.52 44.35 4.24
448 449 2.090760 CAGTCTCAGTGAGAGCAGCTA 58.909 52.381 23.27 0.00 44.35 3.32
449 450 2.689471 CAGTCTCAGTGAGAGCAGCTAT 59.311 50.000 23.27 0.00 44.35 2.97
450 451 2.689471 AGTCTCAGTGAGAGCAGCTATG 59.311 50.000 23.27 0.00 44.35 2.23
462 463 1.747709 CAGCTATGCTTCCAACTGCT 58.252 50.000 0.00 0.00 36.40 4.24
489 592 0.659427 TGCGACGGTTATACTCCTCG 59.341 55.000 0.00 0.00 0.00 4.63
510 615 3.499157 CGAGGTAGGTGCTATAGTCAGAC 59.501 52.174 0.84 0.00 0.00 3.51
514 619 2.025155 AGGTGCTATAGTCAGACCACG 58.975 52.381 0.84 0.00 0.00 4.94
518 623 3.858238 GTGCTATAGTCAGACCACGAAAC 59.142 47.826 0.84 0.00 0.00 2.78
540 645 2.223135 GGAACGATCTTTTGCTAGCAGC 60.223 50.000 18.45 0.00 42.82 5.25
550 655 1.225704 GCTAGCAGCCTGTCCCATT 59.774 57.895 10.63 0.00 34.48 3.16
570 675 6.041296 CCCATTCCCATAATTTCTCCAAGAAG 59.959 42.308 0.00 0.00 35.37 2.85
572 677 7.508296 CCATTCCCATAATTTCTCCAAGAAGAT 59.492 37.037 0.00 0.00 35.37 2.40
577 682 7.917505 CCCATAATTTCTCCAAGAAGATTTTCG 59.082 37.037 0.00 0.00 35.37 3.46
578 683 8.677300 CCATAATTTCTCCAAGAAGATTTTCGA 58.323 33.333 0.00 0.00 35.37 3.71
579 684 9.713740 CATAATTTCTCCAAGAAGATTTTCGAG 57.286 33.333 0.00 0.00 35.37 4.04
580 685 7.986085 AATTTCTCCAAGAAGATTTTCGAGA 57.014 32.000 0.00 0.00 35.37 4.04
581 686 6.787085 TTTCTCCAAGAAGATTTTCGAGAC 57.213 37.500 2.78 0.00 35.37 3.36
582 687 5.468540 TCTCCAAGAAGATTTTCGAGACA 57.531 39.130 0.00 0.00 38.38 3.41
583 688 5.853936 TCTCCAAGAAGATTTTCGAGACAA 58.146 37.500 0.00 0.00 38.38 3.18
584 689 5.928839 TCTCCAAGAAGATTTTCGAGACAAG 59.071 40.000 0.00 0.00 38.38 3.16
585 690 5.611374 TCCAAGAAGATTTTCGAGACAAGT 58.389 37.500 0.00 0.00 38.38 3.16
586 691 5.466728 TCCAAGAAGATTTTCGAGACAAGTG 59.533 40.000 0.00 0.00 38.38 3.16
587 692 5.466728 CCAAGAAGATTTTCGAGACAAGTGA 59.533 40.000 0.00 0.00 38.38 3.41
588 693 6.148480 CCAAGAAGATTTTCGAGACAAGTGAT 59.852 38.462 0.00 0.00 38.38 3.06
589 694 7.331934 CCAAGAAGATTTTCGAGACAAGTGATA 59.668 37.037 0.00 0.00 38.38 2.15
590 695 8.712363 CAAGAAGATTTTCGAGACAAGTGATAA 58.288 33.333 0.00 0.00 38.38 1.75
591 696 9.442047 AAGAAGATTTTCGAGACAAGTGATAAT 57.558 29.630 0.00 0.00 38.38 1.28
594 699 9.653287 AAGATTTTCGAGACAAGTGATAATACA 57.347 29.630 0.00 0.00 0.00 2.29
595 700 9.088512 AGATTTTCGAGACAAGTGATAATACAC 57.911 33.333 0.00 0.00 40.60 2.90
596 701 8.771920 ATTTTCGAGACAAGTGATAATACACA 57.228 30.769 0.00 0.00 42.45 3.72
597 702 8.596271 TTTTCGAGACAAGTGATAATACACAA 57.404 30.769 0.00 0.00 42.45 3.33
598 703 8.596271 TTTCGAGACAAGTGATAATACACAAA 57.404 30.769 0.00 0.00 42.45 2.83
599 704 8.596271 TTCGAGACAAGTGATAATACACAAAA 57.404 30.769 0.00 0.00 42.45 2.44
622 727 8.480643 AAAAAGAAGAAATCGTCGTCAGATAT 57.519 30.769 0.00 0.00 37.22 1.63
673 778 6.357240 GTCGAACAGATGAAAAAGTAACAAGC 59.643 38.462 0.00 0.00 0.00 4.01
679 784 6.860023 CAGATGAAAAAGTAACAAGCAAGGAG 59.140 38.462 0.00 0.00 0.00 3.69
680 785 5.514274 TGAAAAAGTAACAAGCAAGGAGG 57.486 39.130 0.00 0.00 0.00 4.30
681 786 5.197451 TGAAAAAGTAACAAGCAAGGAGGA 58.803 37.500 0.00 0.00 0.00 3.71
689 832 0.033699 AAGCAAGGAGGATGGAAGGC 60.034 55.000 0.00 0.00 0.00 4.35
695 838 0.822532 GGAGGATGGAAGGCATGCTG 60.823 60.000 18.92 0.00 30.84 4.41
703 846 1.471684 GGAAGGCATGCTGAACTTCAG 59.528 52.381 25.77 13.68 46.90 3.02
721 864 6.966884 AACTTCAGTTACCATGGTACTTGACC 60.967 42.308 26.11 12.29 41.89 4.02
737 880 1.078072 ACCATATTTGACGGCGGCA 60.078 52.632 13.60 13.60 0.00 5.69
745 888 2.892425 GACGGCGGCATCTCCTTG 60.892 66.667 8.47 0.00 0.00 3.61
746 889 4.473520 ACGGCGGCATCTCCTTGG 62.474 66.667 13.24 0.00 0.00 3.61
759 902 4.508551 TCTCCTTGGTGTATCTACCGTA 57.491 45.455 0.00 0.00 43.87 4.02
792 935 4.819610 TCCTCCATCTCCTTGATCATACA 58.180 43.478 0.00 0.00 32.05 2.29
822 965 2.230266 AGTTCGTCTCTGCCTCTTCTTC 59.770 50.000 0.00 0.00 0.00 2.87
877 1020 3.353836 TCCAAACGCCTGCGCTTC 61.354 61.111 9.73 0.00 44.19 3.86
890 1033 2.899339 GCTTCGCCTCCATCTGCC 60.899 66.667 0.00 0.00 0.00 4.85
893 1036 2.967929 CTTCGCCTCCATCTGCCTCG 62.968 65.000 0.00 0.00 0.00 4.63
896 1039 3.160047 CCTCCATCTGCCTCGCCT 61.160 66.667 0.00 0.00 0.00 5.52
897 1040 2.420890 CTCCATCTGCCTCGCCTC 59.579 66.667 0.00 0.00 0.00 4.70
898 1041 3.157252 TCCATCTGCCTCGCCTCC 61.157 66.667 0.00 0.00 0.00 4.30
899 1042 3.473647 CCATCTGCCTCGCCTCCA 61.474 66.667 0.00 0.00 0.00 3.86
920 1063 4.354155 CGTCCAAACGCAAGGAGA 57.646 55.556 0.00 0.00 42.82 3.71
922 1065 0.319555 CGTCCAAACGCAAGGAGAGA 60.320 55.000 0.00 0.00 42.82 3.10
941 1084 2.081425 ATCTGATCGTGCCTCGGCTC 62.081 60.000 9.65 4.68 42.51 4.70
983 1130 2.104963 GCCCGATCTGATCTAGGGTTTT 59.895 50.000 23.38 0.00 43.82 2.43
986 1133 4.833380 CCCGATCTGATCTAGGGTTTTCTA 59.167 45.833 17.73 0.00 37.36 2.10
1012 1159 3.696548 GTCAACAGGGATGGAAAAGGATC 59.303 47.826 0.00 0.00 0.00 3.36
1016 1163 0.178990 GGGATGGAAAAGGATCGGGG 60.179 60.000 0.00 0.00 0.00 5.73
1017 1164 0.843984 GGATGGAAAAGGATCGGGGA 59.156 55.000 0.00 0.00 0.00 4.81
1023 1170 2.158885 GGAAAAGGATCGGGGAGAAGAG 60.159 54.545 0.00 0.00 0.00 2.85
1025 1172 0.399233 AAGGATCGGGGAGAAGAGGG 60.399 60.000 0.00 0.00 0.00 4.30
1027 1174 1.233369 GATCGGGGAGAAGAGGGGA 59.767 63.158 0.00 0.00 0.00 4.81
1028 1175 0.830023 GATCGGGGAGAAGAGGGGAG 60.830 65.000 0.00 0.00 0.00 4.30
1029 1176 2.319410 ATCGGGGAGAAGAGGGGAGG 62.319 65.000 0.00 0.00 0.00 4.30
1030 1177 3.010226 CGGGGAGAAGAGGGGAGGA 62.010 68.421 0.00 0.00 0.00 3.71
1032 1179 0.983905 GGGGAGAAGAGGGGAGGAAC 60.984 65.000 0.00 0.00 0.00 3.62
1034 1181 1.199615 GGAGAAGAGGGGAGGAACAG 58.800 60.000 0.00 0.00 0.00 3.16
1035 1182 1.273324 GGAGAAGAGGGGAGGAACAGA 60.273 57.143 0.00 0.00 0.00 3.41
1041 1664 2.573915 AGAGGGGAGGAACAGAAACATC 59.426 50.000 0.00 0.00 0.00 3.06
1042 1665 1.279271 AGGGGAGGAACAGAAACATCG 59.721 52.381 0.00 0.00 0.00 3.84
1048 1671 1.464997 GGAACAGAAACATCGTGGAGC 59.535 52.381 0.00 0.00 0.00 4.70
1049 1672 1.464997 GAACAGAAACATCGTGGAGCC 59.535 52.381 0.00 0.00 0.00 4.70
1050 1673 0.687354 ACAGAAACATCGTGGAGCCT 59.313 50.000 0.00 0.00 0.00 4.58
1059 1682 4.329545 GTGGAGCCTGCGGGTTCA 62.330 66.667 27.45 15.89 43.44 3.18
1060 1683 4.020617 TGGAGCCTGCGGGTTCAG 62.021 66.667 27.45 0.00 43.44 3.02
1068 1691 1.941325 CTGCGGGTTCAGGAAGATAC 58.059 55.000 0.00 0.00 0.00 2.24
1069 1692 1.207089 CTGCGGGTTCAGGAAGATACA 59.793 52.381 0.00 0.00 0.00 2.29
1221 2269 2.159627 CGAGGTTGGGAAATTTGAGACG 59.840 50.000 0.00 0.00 0.00 4.18
1281 2332 4.219033 GCTACAACAATTGGTTCAACTCG 58.781 43.478 10.83 0.00 37.72 4.18
1298 2349 2.158900 ACTCGCATAAAGATCCCCTGTG 60.159 50.000 0.00 0.00 0.00 3.66
1344 2395 3.496898 GCTGTGGCTTGCTAAAACC 57.503 52.632 0.00 0.00 35.22 3.27
1350 2401 1.241315 GGCTTGCTAAAACCGGCAGA 61.241 55.000 0.00 0.00 39.68 4.26
1402 2453 3.270877 CTCCTTGGTAATGTTCCTTCCG 58.729 50.000 0.00 0.00 0.00 4.30
1404 2455 2.747446 CCTTGGTAATGTTCCTTCCGTG 59.253 50.000 0.00 0.00 0.00 4.94
1477 2531 7.797038 TTGAATCATACATGTCCATTCTCAG 57.203 36.000 18.24 0.00 0.00 3.35
1536 2623 2.035442 GTTGGTCTTCTCCGCCAGC 61.035 63.158 0.00 0.00 33.41 4.85
1562 2651 6.071784 TGAGAATGTGATTTATGCAACTTGCT 60.072 34.615 14.78 3.57 45.31 3.91
1679 2768 2.604914 CGTGAATCTGGACAATCTTCCG 59.395 50.000 0.00 0.00 38.69 4.30
1755 2844 5.424121 AAAAGAGTTGTGCATCACAGTAC 57.576 39.130 0.00 0.00 45.39 2.73
1856 2948 2.036256 AAGCCACATGCCCCTGAC 59.964 61.111 0.00 0.00 42.71 3.51
2008 3100 0.104855 TGTCTGCACTGTGGTGACTC 59.895 55.000 10.21 0.00 45.61 3.36
2048 3140 3.681034 GCCCATCGAGATATCCATGGAAG 60.681 52.174 20.67 6.46 38.52 3.46
2071 3163 0.235144 GATGAGCGCATGCAGATCAC 59.765 55.000 24.92 17.33 46.23 3.06
2074 3166 1.773054 GAGCGCATGCAGATCACTGG 61.773 60.000 19.57 0.00 46.23 4.00
2078 3170 1.540580 CGCATGCAGATCACTGGAGAT 60.541 52.381 19.57 0.00 46.67 2.75
2085 3177 1.849039 AGATCACTGGAGATTTGGGGG 59.151 52.381 0.00 0.00 0.00 5.40
2113 3205 1.675310 CTGCCATGGTTCGCTTCCA 60.675 57.895 14.67 0.00 39.41 3.53
2211 3304 9.905713 AACATGATTATGTAATGGTCTTGTAGT 57.094 29.630 3.20 0.00 46.54 2.73
2272 3376 8.874744 AGGCGTATAGGATAGATTAGTTGTAA 57.125 34.615 0.00 0.00 0.00 2.41
2536 3663 1.265454 CCGTTCCTACCTCTGGCCTT 61.265 60.000 3.32 0.00 0.00 4.35
3053 4180 3.456277 GGAATACCAACCACTCATCTCCT 59.544 47.826 0.00 0.00 35.97 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 7.667557 TGTTACTGACATAGACAACTAGCTTT 58.332 34.615 0.00 0.00 32.00 3.51
54 55 3.055094 GTGGTCCTTTCTCTGCATCCTAA 60.055 47.826 0.00 0.00 0.00 2.69
55 56 2.501723 GTGGTCCTTTCTCTGCATCCTA 59.498 50.000 0.00 0.00 0.00 2.94
56 57 1.280421 GTGGTCCTTTCTCTGCATCCT 59.720 52.381 0.00 0.00 0.00 3.24
78 79 5.049267 GCTTGCATTTGACCATGAAATGTTT 60.049 36.000 15.74 0.00 44.81 2.83
118 119 3.557903 TTCCTCACCTGGCAGCAGC 62.558 63.158 9.56 0.00 41.10 5.25
119 120 1.673665 GTTCCTCACCTGGCAGCAG 60.674 63.158 9.56 3.33 0.00 4.24
151 152 3.317150 CTTTTCGGATGTTTCCAAAGCC 58.683 45.455 0.00 0.00 42.74 4.35
166 167 2.223340 ACACTCACTTTGCAGCTTTTCG 60.223 45.455 0.00 0.00 0.00 3.46
171 172 0.749091 TGCACACTCACTTTGCAGCT 60.749 50.000 0.00 0.00 41.29 4.24
183 184 1.227943 ATCCACAAGCGTGCACACT 60.228 52.632 18.64 10.08 42.17 3.55
222 223 6.820656 GCATATGATCTTACCGATGAGGAAAT 59.179 38.462 6.97 0.00 45.00 2.17
230 231 6.014242 TCTCCAAAGCATATGATCTTACCGAT 60.014 38.462 6.97 0.00 34.25 4.18
244 245 2.009774 CGGACGAAATCTCCAAAGCAT 58.990 47.619 0.00 0.00 0.00 3.79
245 246 1.438651 CGGACGAAATCTCCAAAGCA 58.561 50.000 0.00 0.00 0.00 3.91
271 272 2.988010 AGCAACTTGTGTCTGAGTGA 57.012 45.000 0.00 0.00 0.00 3.41
292 293 2.687700 AGCAGTGTATCAGCAAGGAG 57.312 50.000 0.00 0.00 0.00 3.69
327 328 9.624697 TTGTATGCTGACTTAAATTTTGATGAC 57.375 29.630 0.00 0.00 0.00 3.06
341 342 5.012148 ACTTAGGTTGTCTTGTATGCTGACT 59.988 40.000 8.36 0.00 0.00 3.41
344 345 7.667043 TTTACTTAGGTTGTCTTGTATGCTG 57.333 36.000 0.00 0.00 0.00 4.41
354 355 9.895138 TCCCATATAACTTTTACTTAGGTTGTC 57.105 33.333 0.00 0.00 0.00 3.18
358 359 8.097791 TGCTCCCATATAACTTTTACTTAGGT 57.902 34.615 0.00 0.00 0.00 3.08
361 362 8.326765 TCCTGCTCCCATATAACTTTTACTTA 57.673 34.615 0.00 0.00 0.00 2.24
370 371 6.375455 CCAATTACATCCTGCTCCCATATAAC 59.625 42.308 0.00 0.00 0.00 1.89
374 375 3.721575 ACCAATTACATCCTGCTCCCATA 59.278 43.478 0.00 0.00 0.00 2.74
376 377 1.922447 ACCAATTACATCCTGCTCCCA 59.078 47.619 0.00 0.00 0.00 4.37
377 378 2.576615 GACCAATTACATCCTGCTCCC 58.423 52.381 0.00 0.00 0.00 4.30
390 391 4.324267 CTTCCTTTACCAGACGACCAATT 58.676 43.478 0.00 0.00 0.00 2.32
397 398 0.252197 CCCCCTTCCTTTACCAGACG 59.748 60.000 0.00 0.00 0.00 4.18
400 401 0.919710 CCTCCCCCTTCCTTTACCAG 59.080 60.000 0.00 0.00 0.00 4.00
408 409 1.281287 GTCAGTAAACCTCCCCCTTCC 59.719 57.143 0.00 0.00 0.00 3.46
410 411 1.985895 CTGTCAGTAAACCTCCCCCTT 59.014 52.381 0.00 0.00 0.00 3.95
411 412 1.132495 ACTGTCAGTAAACCTCCCCCT 60.132 52.381 2.87 0.00 0.00 4.79
412 413 1.278413 GACTGTCAGTAAACCTCCCCC 59.722 57.143 5.21 0.00 0.00 5.40
413 414 2.234168 GAGACTGTCAGTAAACCTCCCC 59.766 54.545 5.21 0.00 0.00 4.81
414 415 2.897969 TGAGACTGTCAGTAAACCTCCC 59.102 50.000 5.21 0.00 0.00 4.30
415 416 4.181309 CTGAGACTGTCAGTAAACCTCC 57.819 50.000 5.21 0.00 46.89 4.30
425 426 1.885233 CTGCTCTCACTGAGACTGTCA 59.115 52.381 10.88 1.16 45.39 3.58
426 427 1.402720 GCTGCTCTCACTGAGACTGTC 60.403 57.143 4.50 0.00 45.39 3.51
427 428 0.602562 GCTGCTCTCACTGAGACTGT 59.397 55.000 4.50 0.00 45.39 3.55
428 429 0.889994 AGCTGCTCTCACTGAGACTG 59.110 55.000 4.50 7.60 45.39 3.51
429 430 2.505650 TAGCTGCTCTCACTGAGACT 57.494 50.000 4.91 3.74 45.39 3.24
430 431 2.799207 GCATAGCTGCTCTCACTGAGAC 60.799 54.545 4.91 3.66 45.39 3.36
431 432 1.408340 GCATAGCTGCTCTCACTGAGA 59.592 52.381 4.91 8.50 45.39 3.27
432 433 1.855513 GCATAGCTGCTCTCACTGAG 58.144 55.000 4.91 0.00 45.32 3.35
443 444 1.400846 CAGCAGTTGGAAGCATAGCTG 59.599 52.381 0.00 0.00 39.62 4.24
444 445 1.747709 CAGCAGTTGGAAGCATAGCT 58.252 50.000 0.00 0.00 42.56 3.32
445 446 0.100146 GCAGCAGTTGGAAGCATAGC 59.900 55.000 0.00 0.00 0.00 2.97
446 447 1.456296 TGCAGCAGTTGGAAGCATAG 58.544 50.000 0.00 0.00 0.00 2.23
447 448 1.908344 TTGCAGCAGTTGGAAGCATA 58.092 45.000 0.00 0.00 34.87 3.14
448 449 1.067142 CATTGCAGCAGTTGGAAGCAT 60.067 47.619 0.00 0.00 40.65 3.79
449 450 0.315886 CATTGCAGCAGTTGGAAGCA 59.684 50.000 0.00 0.00 40.65 3.91
450 451 0.316204 ACATTGCAGCAGTTGGAAGC 59.684 50.000 11.06 0.00 40.65 3.86
451 452 2.400399 CAACATTGCAGCAGTTGGAAG 58.600 47.619 16.36 0.00 40.65 3.46
452 453 2.512485 CAACATTGCAGCAGTTGGAA 57.488 45.000 16.36 0.00 41.61 3.53
489 592 3.822167 GGTCTGACTATAGCACCTACCTC 59.178 52.174 7.85 0.00 0.00 3.85
510 615 1.425412 AAGATCGTTCCGTTTCGTGG 58.575 50.000 0.00 0.00 0.00 4.94
514 619 3.537793 AGCAAAAGATCGTTCCGTTTC 57.462 42.857 0.00 0.00 0.00 2.78
518 623 1.999735 TGCTAGCAAAAGATCGTTCCG 59.000 47.619 16.84 0.00 0.00 4.30
550 655 8.899887 AAAATCTTCTTGGAGAAATTATGGGA 57.100 30.769 0.00 0.00 33.19 4.37
570 675 8.869897 TGTGTATTATCACTTGTCTCGAAAATC 58.130 33.333 0.00 0.00 38.90 2.17
572 677 8.596271 TTGTGTATTATCACTTGTCTCGAAAA 57.404 30.769 0.00 0.00 38.90 2.29
597 702 6.787085 ATCTGACGACGATTTCTTCTTTTT 57.213 33.333 0.00 0.00 0.00 1.94
598 703 7.010552 CCATATCTGACGACGATTTCTTCTTTT 59.989 37.037 0.00 0.00 0.00 2.27
599 704 6.477033 CCATATCTGACGACGATTTCTTCTTT 59.523 38.462 0.00 0.00 0.00 2.52
603 708 5.043903 CACCATATCTGACGACGATTTCTT 58.956 41.667 0.00 0.00 0.00 2.52
611 716 2.533266 ATGCCACCATATCTGACGAC 57.467 50.000 0.00 0.00 0.00 4.34
665 770 3.350219 TCCATCCTCCTTGCTTGTTAC 57.650 47.619 0.00 0.00 0.00 2.50
673 778 1.688772 CATGCCTTCCATCCTCCTTG 58.311 55.000 0.00 0.00 29.71 3.61
679 784 0.743097 GTTCAGCATGCCTTCCATCC 59.257 55.000 15.66 0.00 34.76 3.51
680 785 1.760192 AGTTCAGCATGCCTTCCATC 58.240 50.000 15.66 0.00 34.76 3.51
681 786 2.097825 GAAGTTCAGCATGCCTTCCAT 58.902 47.619 15.66 0.00 37.63 3.41
695 838 6.147328 GTCAAGTACCATGGTAACTGAAGTTC 59.853 42.308 27.14 16.84 39.31 3.01
721 864 1.195448 GAGATGCCGCCGTCAAATATG 59.805 52.381 0.00 0.00 0.00 1.78
725 868 2.435938 GGAGATGCCGCCGTCAAA 60.436 61.111 0.00 0.00 0.00 2.69
737 880 3.912248 ACGGTAGATACACCAAGGAGAT 58.088 45.455 0.00 0.00 38.61 2.75
745 888 6.714356 AGGATAAGAAGTACGGTAGATACACC 59.286 42.308 0.00 0.00 35.04 4.16
746 889 7.094848 GGAGGATAAGAAGTACGGTAGATACAC 60.095 44.444 0.00 0.00 0.00 2.90
759 902 4.171841 AGGAGATGGAGGAGGATAAGAAGT 59.828 45.833 0.00 0.00 0.00 3.01
792 935 6.038997 AGGCAGAGACGAACTATTTTACTT 57.961 37.500 0.00 0.00 0.00 2.24
808 951 0.107752 GCAGGGAAGAAGAGGCAGAG 60.108 60.000 0.00 0.00 0.00 3.35
893 1036 2.171635 GTTTGGACGACATGGAGGC 58.828 57.895 0.00 0.00 0.00 4.70
920 1063 2.037053 CCGAGGCACGATCAGATCT 58.963 57.895 5.74 0.00 45.77 2.75
922 1065 2.081425 GAGCCGAGGCACGATCAGAT 62.081 60.000 17.18 0.00 45.77 2.90
956 1099 1.265236 AGATCAGATCGGGCTCATCC 58.735 55.000 4.67 0.00 0.00 3.51
962 1105 1.343069 AACCCTAGATCAGATCGGGC 58.657 55.000 18.87 0.00 34.39 6.13
983 1130 1.191535 CATCCCTGTTGACGGGTAGA 58.808 55.000 8.14 0.03 42.56 2.59
986 1133 1.131303 TTCCATCCCTGTTGACGGGT 61.131 55.000 8.14 0.00 42.56 5.28
992 1139 2.684881 CGATCCTTTTCCATCCCTGTTG 59.315 50.000 0.00 0.00 0.00 3.33
993 1140 2.357154 CCGATCCTTTTCCATCCCTGTT 60.357 50.000 0.00 0.00 0.00 3.16
1012 1159 2.444895 CCTCCCCTCTTCTCCCCG 60.445 72.222 0.00 0.00 0.00 5.73
1016 1163 2.239681 TCTGTTCCTCCCCTCTTCTC 57.760 55.000 0.00 0.00 0.00 2.87
1017 1164 2.640332 GTTTCTGTTCCTCCCCTCTTCT 59.360 50.000 0.00 0.00 0.00 2.85
1023 1170 1.003233 ACGATGTTTCTGTTCCTCCCC 59.997 52.381 0.00 0.00 0.00 4.81
1025 1172 2.076863 CCACGATGTTTCTGTTCCTCC 58.923 52.381 0.00 0.00 0.00 4.30
1027 1174 2.872038 GCTCCACGATGTTTCTGTTCCT 60.872 50.000 0.00 0.00 0.00 3.36
1028 1175 1.464997 GCTCCACGATGTTTCTGTTCC 59.535 52.381 0.00 0.00 0.00 3.62
1029 1176 1.464997 GGCTCCACGATGTTTCTGTTC 59.535 52.381 0.00 0.00 0.00 3.18
1030 1177 1.072331 AGGCTCCACGATGTTTCTGTT 59.928 47.619 0.00 0.00 0.00 3.16
1032 1179 1.081892 CAGGCTCCACGATGTTTCTG 58.918 55.000 0.00 0.00 0.00 3.02
1034 1181 1.796796 GCAGGCTCCACGATGTTTC 59.203 57.895 0.00 0.00 0.00 2.78
1035 1182 2.034879 CGCAGGCTCCACGATGTTT 61.035 57.895 0.00 0.00 0.00 2.83
1049 1672 1.207089 TGTATCTTCCTGAACCCGCAG 59.793 52.381 0.00 0.00 35.66 5.18
1050 1673 1.271856 TGTATCTTCCTGAACCCGCA 58.728 50.000 0.00 0.00 0.00 5.69
1055 1678 5.873732 GTTCAGCAATGTATCTTCCTGAAC 58.126 41.667 13.40 13.40 46.40 3.18
1056 1679 4.943705 GGTTCAGCAATGTATCTTCCTGAA 59.056 41.667 0.00 0.00 37.08 3.02
1057 1680 4.517285 GGTTCAGCAATGTATCTTCCTGA 58.483 43.478 0.00 0.00 0.00 3.86
1059 1682 3.535561 CGGTTCAGCAATGTATCTTCCT 58.464 45.455 0.00 0.00 0.00 3.36
1060 1683 2.614057 CCGGTTCAGCAATGTATCTTCC 59.386 50.000 0.00 0.00 0.00 3.46
1061 1684 3.309954 GTCCGGTTCAGCAATGTATCTTC 59.690 47.826 0.00 0.00 0.00 2.87
1062 1685 3.270877 GTCCGGTTCAGCAATGTATCTT 58.729 45.455 0.00 0.00 0.00 2.40
1063 1686 2.236146 TGTCCGGTTCAGCAATGTATCT 59.764 45.455 0.00 0.00 0.00 1.98
1064 1687 2.627945 TGTCCGGTTCAGCAATGTATC 58.372 47.619 0.00 0.00 0.00 2.24
1065 1688 2.779755 TGTCCGGTTCAGCAATGTAT 57.220 45.000 0.00 0.00 0.00 2.29
1066 1689 2.779755 ATGTCCGGTTCAGCAATGTA 57.220 45.000 0.00 0.00 0.00 2.29
1067 1690 2.356135 GTATGTCCGGTTCAGCAATGT 58.644 47.619 0.00 0.00 0.00 2.71
1068 1691 1.670811 GGTATGTCCGGTTCAGCAATG 59.329 52.381 0.00 0.00 0.00 2.82
1069 1692 1.408266 GGGTATGTCCGGTTCAGCAAT 60.408 52.381 0.00 0.00 37.00 3.56
1221 2269 1.373570 GTAGACATGCCAGCTCAACC 58.626 55.000 0.00 0.00 0.00 3.77
1263 2311 3.077229 TGCGAGTTGAACCAATTGTTG 57.923 42.857 4.43 0.00 37.29 3.33
1281 2332 4.381932 CCAAAACACAGGGGATCTTTATGC 60.382 45.833 0.00 0.00 0.00 3.14
1344 2395 2.403987 CTAGTCGACCGTCTGCCG 59.596 66.667 13.01 0.00 0.00 5.69
1350 2401 3.269178 CTTAAGAGTCCTAGTCGACCGT 58.731 50.000 13.01 0.00 32.91 4.83
1353 2404 7.118971 TGACTTAACTTAAGAGTCCTAGTCGAC 59.881 40.741 10.09 7.70 38.71 4.20
1402 2453 0.103755 TCCAGATGCAGATCGCTCAC 59.896 55.000 10.16 3.41 43.06 3.51
1404 2455 2.166821 AATCCAGATGCAGATCGCTC 57.833 50.000 10.16 6.18 43.06 5.03
1448 2502 8.847196 AGAATGGACATGTATGATTCAAATGAG 58.153 33.333 18.90 0.00 0.00 2.90
1505 2582 7.013083 CGGAGAAGACCAACTTAAGCTACTATA 59.987 40.741 1.29 0.00 39.13 1.31
1536 2623 6.252869 GCAAGTTGCATAAATCACATTCTCAG 59.747 38.462 22.90 0.00 44.26 3.35
1643 2732 1.530323 TCACGTGCTGTAGTCTGCTA 58.470 50.000 11.67 0.00 38.91 3.49
1648 2737 2.094700 TCCAGATTCACGTGCTGTAGTC 60.095 50.000 11.67 0.00 0.00 2.59
1679 2768 4.336713 GTCCAAGCTAAATCACATCCTTCC 59.663 45.833 0.00 0.00 0.00 3.46
1755 2844 3.148412 TCATATTGCACCAATGATCCCG 58.852 45.455 0.00 0.00 35.54 5.14
1856 2948 2.301346 ACCAGGTTCTTGTGCTTGAAG 58.699 47.619 0.00 0.00 0.00 3.02
1977 3069 2.639839 AGTGCAGACATACCTTCCTGTT 59.360 45.455 0.00 0.00 0.00 3.16
2024 3116 3.555527 CATGGATATCTCGATGGGCAT 57.444 47.619 2.05 0.00 34.85 4.40
2048 3140 3.182472 CTGCATGCGCTCATCAGCC 62.182 63.158 14.09 0.00 43.56 4.85
2071 3163 0.995024 AGACACCCCCAAATCTCCAG 59.005 55.000 0.00 0.00 0.00 3.86
2074 3166 1.546029 GCAAAGACACCCCCAAATCTC 59.454 52.381 0.00 0.00 0.00 2.75
2078 3170 0.758685 CAGGCAAAGACACCCCCAAA 60.759 55.000 0.00 0.00 0.00 3.28
2085 3177 1.181098 ACCATGGCAGGCAAAGACAC 61.181 55.000 13.04 0.00 0.00 3.67
2137 3229 5.368145 TGAGTTCAGAGTGCTTACAAACAT 58.632 37.500 0.00 0.00 0.00 2.71
2211 3304 1.112113 GAGATCGCTACAACCAGGGA 58.888 55.000 0.00 0.00 41.19 4.20
2378 3494 1.732259 GGCCGCGTGATCTTATATTGG 59.268 52.381 4.92 0.00 0.00 3.16
2536 3663 4.772624 AGAGGCTCAGATGTGTTGTAGTTA 59.227 41.667 18.26 0.00 0.00 2.24
3053 4180 0.038983 TCGACGCGAACATCAAGGAA 60.039 50.000 15.93 0.00 31.06 3.36


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

AutoCloner maintained by Alex Coulton.