Multiple sequence alignment - TraesCS3A01G484000

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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 TraesCS3A01G484000 chr3A 100.000 3570 0 0 1 3570 713964870 713961301 0.000000e+00 6593.0
1 TraesCS3A01G484000 chr3A 85.282 1189 143 13 1464 2648 713947023 713945863 0.000000e+00 1197.0
2 TraesCS3A01G484000 chr3A 92.965 597 29 9 1 594 41172480 41173066 0.000000e+00 857.0
3 TraesCS3A01G484000 chr3A 87.606 355 36 7 1138 1484 713949773 713949419 4.290000e-109 405.0
4 TraesCS3A01G484000 chr3A 79.701 335 38 17 1000 1321 714000498 714000181 7.760000e-52 215.0
5 TraesCS3A01G484000 chr3A 81.659 229 35 5 998 1221 713995886 713995660 2.190000e-42 183.0
6 TraesCS3A01G484000 chr3B 90.116 1983 166 15 866 2839 771666245 771664284 0.000000e+00 2549.0
7 TraesCS3A01G484000 chr3B 87.160 1729 174 21 937 2648 771623802 771622105 0.000000e+00 1919.0
8 TraesCS3A01G484000 chr3B 96.087 1099 31 8 1750 2839 771630705 771629610 0.000000e+00 1781.0
9 TraesCS3A01G484000 chr3B 91.748 824 62 1 942 1759 771634473 771633650 0.000000e+00 1140.0
10 TraesCS3A01G484000 chr3B 94.110 730 39 2 2840 3569 75727193 75727918 0.000000e+00 1107.0
11 TraesCS3A01G484000 chr3B 88.255 596 58 6 1 594 134034483 134033898 0.000000e+00 702.0
12 TraesCS3A01G484000 chr3B 74.742 871 172 27 1000 1835 771794187 771793330 2.640000e-91 346.0
13 TraesCS3A01G484000 chr3B 77.320 291 43 16 1046 1320 771789529 771789246 2.220000e-32 150.0
14 TraesCS3A01G484000 chr3B 97.403 77 1 1 776 852 771666304 771666229 2.890000e-26 130.0
15 TraesCS3A01G484000 chr3B 100.000 28 0 0 823 850 771623910 771623883 6.000000e-03 52.8
16 TraesCS3A01G484000 chr3D 86.857 1750 167 28 920 2648 578270339 578268632 0.000000e+00 1899.0
17 TraesCS3A01G484000 chr3D 80.012 1711 273 40 866 2539 578273671 578271993 0.000000e+00 1201.0
18 TraesCS3A01G484000 chr3D 89.637 193 9 6 671 852 578273847 578273655 5.960000e-58 235.0
19 TraesCS3A01G484000 chr3D 79.586 338 48 17 998 1320 578282738 578282407 4.640000e-54 222.0
20 TraesCS3A01G484000 chr2B 94.528 731 36 2 2840 3570 245114219 245114945 0.000000e+00 1125.0
21 TraesCS3A01G484000 chr2B 93.570 731 43 2 2840 3570 214384445 214383719 0.000000e+00 1086.0
22 TraesCS3A01G484000 chr6B 93.886 736 39 4 2836 3570 651018834 651018104 0.000000e+00 1105.0
23 TraesCS3A01G484000 chr6B 89.833 600 51 7 1 594 2076915 2076320 0.000000e+00 761.0
24 TraesCS3A01G484000 chr6B 78.824 85 15 2 589 673 237063704 237063785 2.000000e-03 54.7
25 TraesCS3A01G484000 chr4B 93.707 731 41 3 2840 3570 567597124 567596399 0.000000e+00 1090.0
26 TraesCS3A01G484000 chr4B 81.013 79 11 2 597 673 643565323 643565247 3.850000e-05 60.2
27 TraesCS3A01G484000 chr4B 88.889 45 5 0 629 673 643572910 643572866 4.980000e-04 56.5
28 TraesCS3A01G484000 chr2A 93.333 735 44 3 2839 3570 174018493 174017761 0.000000e+00 1081.0
29 TraesCS3A01G484000 chr7B 93.179 733 45 3 2839 3570 667166356 667167084 0.000000e+00 1072.0
30 TraesCS3A01G484000 chr7B 91.960 597 36 9 1 594 23257193 23256606 0.000000e+00 826.0
31 TraesCS3A01G484000 chr7D 92.643 734 46 6 2840 3570 629545823 629545095 0.000000e+00 1050.0
32 TraesCS3A01G484000 chr5D 92.643 734 47 4 2840 3570 405528573 405529302 0.000000e+00 1050.0
33 TraesCS3A01G484000 chr6D 96.296 594 16 3 1 592 10057349 10057938 0.000000e+00 970.0
34 TraesCS3A01G484000 chr6D 97.425 233 6 0 363 595 10047320 10047552 7.180000e-107 398.0
35 TraesCS3A01G484000 chr6D 86.301 73 10 0 603 675 383234481 383234553 2.950000e-11 80.5
36 TraesCS3A01G484000 chr6D 92.500 40 3 0 634 673 376951790 376951751 1.380000e-04 58.4
37 TraesCS3A01G484000 chr4A 93.121 596 32 7 1 594 597228877 597229465 0.000000e+00 865.0
38 TraesCS3A01G484000 chr4A 78.899 218 46 0 1001 1218 94823341 94823558 7.990000e-32 148.0
39 TraesCS3A01G484000 chr2D 89.097 587 51 8 1 580 53776917 53777497 0.000000e+00 717.0
40 TraesCS3A01G484000 chr2D 89.041 584 54 9 1 580 620924645 620924068 0.000000e+00 715.0
41 TraesCS3A01G484000 chr2D 95.238 42 2 0 634 675 305933828 305933787 2.300000e-07 67.6
42 TraesCS3A01G484000 chr2D 97.059 34 0 1 640 673 101988500 101988532 4.980000e-04 56.5
43 TraesCS3A01G484000 chr6A 77.183 355 71 9 21 371 593287583 593287235 7.820000e-47 198.0
44 TraesCS3A01G484000 chr6A 80.769 78 11 4 600 675 525033430 525033505 1.380000e-04 58.4
45 TraesCS3A01G484000 chr1B 76.720 378 74 10 1 372 565968401 565968770 7.820000e-47 198.0
46 TraesCS3A01G484000 chrUn 87.500 48 6 0 626 673 60370068 60370115 4.980000e-04 56.5


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 TraesCS3A01G484000 chr3A 713961301 713964870 3569 True 6593.000000 6593 100.0000 1 3570 1 chr3A.!!$R1 3569
1 TraesCS3A01G484000 chr3A 41172480 41173066 586 False 857.000000 857 92.9650 1 594 1 chr3A.!!$F1 593
2 TraesCS3A01G484000 chr3A 713945863 713949773 3910 True 801.000000 1197 86.4440 1138 2648 2 chr3A.!!$R4 1510
3 TraesCS3A01G484000 chr3B 771629610 771634473 4863 True 1460.500000 1781 93.9175 942 2839 2 chr3B.!!$R3 1897
4 TraesCS3A01G484000 chr3B 771664284 771666304 2020 True 1339.500000 2549 93.7595 776 2839 2 chr3B.!!$R4 2063
5 TraesCS3A01G484000 chr3B 75727193 75727918 725 False 1107.000000 1107 94.1100 2840 3569 1 chr3B.!!$F1 729
6 TraesCS3A01G484000 chr3B 771622105 771623910 1805 True 985.900000 1919 93.5800 823 2648 2 chr3B.!!$R2 1825
7 TraesCS3A01G484000 chr3B 134033898 134034483 585 True 702.000000 702 88.2550 1 594 1 chr3B.!!$R1 593
8 TraesCS3A01G484000 chr3B 771789246 771794187 4941 True 248.000000 346 76.0310 1000 1835 2 chr3B.!!$R5 835
9 TraesCS3A01G484000 chr3D 578268632 578273847 5215 True 1111.666667 1899 85.5020 671 2648 3 chr3D.!!$R2 1977
10 TraesCS3A01G484000 chr2B 245114219 245114945 726 False 1125.000000 1125 94.5280 2840 3570 1 chr2B.!!$F1 730
11 TraesCS3A01G484000 chr2B 214383719 214384445 726 True 1086.000000 1086 93.5700 2840 3570 1 chr2B.!!$R1 730
12 TraesCS3A01G484000 chr6B 651018104 651018834 730 True 1105.000000 1105 93.8860 2836 3570 1 chr6B.!!$R2 734
13 TraesCS3A01G484000 chr6B 2076320 2076915 595 True 761.000000 761 89.8330 1 594 1 chr6B.!!$R1 593
14 TraesCS3A01G484000 chr4B 567596399 567597124 725 True 1090.000000 1090 93.7070 2840 3570 1 chr4B.!!$R1 730
15 TraesCS3A01G484000 chr2A 174017761 174018493 732 True 1081.000000 1081 93.3330 2839 3570 1 chr2A.!!$R1 731
16 TraesCS3A01G484000 chr7B 667166356 667167084 728 False 1072.000000 1072 93.1790 2839 3570 1 chr7B.!!$F1 731
17 TraesCS3A01G484000 chr7B 23256606 23257193 587 True 826.000000 826 91.9600 1 594 1 chr7B.!!$R1 593
18 TraesCS3A01G484000 chr7D 629545095 629545823 728 True 1050.000000 1050 92.6430 2840 3570 1 chr7D.!!$R1 730
19 TraesCS3A01G484000 chr5D 405528573 405529302 729 False 1050.000000 1050 92.6430 2840 3570 1 chr5D.!!$F1 730
20 TraesCS3A01G484000 chr6D 10057349 10057938 589 False 970.000000 970 96.2960 1 592 1 chr6D.!!$F2 591
21 TraesCS3A01G484000 chr4A 597228877 597229465 588 False 865.000000 865 93.1210 1 594 1 chr4A.!!$F2 593
22 TraesCS3A01G484000 chr2D 53776917 53777497 580 False 717.000000 717 89.0970 1 580 1 chr2D.!!$F1 579
23 TraesCS3A01G484000 chr2D 620924068 620924645 577 True 715.000000 715 89.0410 1 580 1 chr2D.!!$R2 579

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
626 640 0.107459 GGACTGGTCTCCCTTGATGC 60.107 60.000 0.67 0.0 0.0 3.91 F
667 681 0.179004 TGTGGGTTGCCGTTGAAGAT 60.179 50.000 0.00 0.0 0.0 2.40 F
668 682 0.240945 GTGGGTTGCCGTTGAAGATG 59.759 55.000 0.00 0.0 0.0 2.90 F
1426 4772 1.134788 CCTATCTCGCGTTTGACCCTT 60.135 52.381 5.77 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 10665 1.187974 CCTGCAAAGATTCATGCCCA 58.812 50.000 10.71 0.0 41.87 5.36 R
1927 10666 1.188863 ACCTGCAAAGATTCATGCCC 58.811 50.000 10.71 0.0 41.87 5.36 R
2003 10750 1.892474 GTAATGCTCCCCAACTTTGCA 59.108 47.619 0.00 0.0 38.05 4.08 R
2922 14695 0.464036 ACAAGGCTGAGTTCGTGTCA 59.536 50.000 0.00 0.0 0.00 3.58 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
73 78 5.047802 CACAGCTGAAGTTATTTGGGTTCAT 60.048 40.000 23.35 0.00 0.00 2.57
105 110 6.463995 AAAAGAACTTGGAGTAATGCACAA 57.536 33.333 0.00 0.00 0.00 3.33
144 149 4.264253 TGGTGTGATAATCTTGGAGCAAG 58.736 43.478 0.00 0.00 42.25 4.01
172 178 7.517614 TTTGTTGCTAATCCAGTGTTTCATA 57.482 32.000 0.00 0.00 0.00 2.15
201 207 8.352942 AGAACCAAACACATTGAAATAGACTTC 58.647 33.333 0.00 0.00 41.85 3.01
202 208 6.668323 ACCAAACACATTGAAATAGACTTCG 58.332 36.000 0.00 0.00 41.85 3.79
203 209 6.262273 ACCAAACACATTGAAATAGACTTCGT 59.738 34.615 0.00 0.00 41.85 3.85
206 212 9.019764 CAAACACATTGAAATAGACTTCGTTTT 57.980 29.630 0.00 0.00 41.85 2.43
221 227 9.760077 AGACTTCGTTTTAATTGTTAGAGAGAA 57.240 29.630 0.00 0.00 0.00 2.87
257 263 9.007901 CAAAGAACTTGAGATCAGGTTTATTCT 57.992 33.333 11.11 2.31 44.57 2.40
323 329 6.706270 CCTACTAGAAGCTTTGAAGTGTTTCA 59.294 38.462 15.59 0.00 41.44 2.69
393 399 6.220930 ACATTGTCACGTTACAAGTCTGTAT 58.779 36.000 19.10 0.00 42.33 2.29
394 400 7.372714 ACATTGTCACGTTACAAGTCTGTATA 58.627 34.615 19.10 0.00 42.33 1.47
580 594 0.241481 AGGAGTTGAGACGCTTCGAC 59.759 55.000 0.00 0.06 0.00 4.20
594 608 4.278669 ACGCTTCGACCTATTATCTCACAT 59.721 41.667 0.00 0.00 0.00 3.21
595 609 5.472478 ACGCTTCGACCTATTATCTCACATA 59.528 40.000 0.00 0.00 0.00 2.29
596 610 6.151312 ACGCTTCGACCTATTATCTCACATAT 59.849 38.462 0.00 0.00 0.00 1.78
597 611 6.689241 CGCTTCGACCTATTATCTCACATATC 59.311 42.308 0.00 0.00 0.00 1.63
598 612 6.975772 GCTTCGACCTATTATCTCACATATCC 59.024 42.308 0.00 0.00 0.00 2.59
599 613 6.679327 TCGACCTATTATCTCACATATCCG 57.321 41.667 0.00 0.00 0.00 4.18
600 614 6.178324 TCGACCTATTATCTCACATATCCGT 58.822 40.000 0.00 0.00 0.00 4.69
601 615 6.093633 TCGACCTATTATCTCACATATCCGTG 59.906 42.308 0.00 0.00 38.29 4.94
602 616 6.127980 CGACCTATTATCTCACATATCCGTGT 60.128 42.308 0.00 0.00 38.12 4.49
603 617 7.159322 ACCTATTATCTCACATATCCGTGTC 57.841 40.000 0.00 0.00 38.12 3.67
604 618 6.153000 ACCTATTATCTCACATATCCGTGTCC 59.847 42.308 0.00 0.00 38.12 4.02
605 619 4.499037 TTATCTCACATATCCGTGTCCG 57.501 45.455 0.00 0.00 38.12 4.79
606 620 1.758936 TCTCACATATCCGTGTCCGT 58.241 50.000 0.00 0.00 38.12 4.69
607 621 1.404035 TCTCACATATCCGTGTCCGTG 59.596 52.381 0.00 0.00 38.12 4.94
608 622 0.458260 TCACATATCCGTGTCCGTGG 59.542 55.000 0.00 0.00 38.12 4.94
609 623 0.458260 CACATATCCGTGTCCGTGGA 59.542 55.000 0.00 0.00 38.95 4.02
610 624 0.458669 ACATATCCGTGTCCGTGGAC 59.541 55.000 12.17 12.17 44.77 4.02
611 625 0.744874 CATATCCGTGTCCGTGGACT 59.255 55.000 19.17 2.08 44.80 3.85
612 626 0.744874 ATATCCGTGTCCGTGGACTG 59.255 55.000 19.17 11.70 44.80 3.51
613 627 1.317431 TATCCGTGTCCGTGGACTGG 61.317 60.000 19.17 19.04 44.80 4.00
614 628 3.612681 CCGTGTCCGTGGACTGGT 61.613 66.667 19.17 0.00 44.80 4.00
615 629 2.049433 CGTGTCCGTGGACTGGTC 60.049 66.667 19.17 7.16 44.80 4.02
616 630 2.561956 CGTGTCCGTGGACTGGTCT 61.562 63.158 19.17 0.00 44.80 3.85
617 631 1.289380 GTGTCCGTGGACTGGTCTC 59.711 63.158 19.17 1.18 44.80 3.36
618 632 1.906824 TGTCCGTGGACTGGTCTCC 60.907 63.158 19.17 0.00 44.80 3.71
619 633 2.283676 TCCGTGGACTGGTCTCCC 60.284 66.667 0.67 0.00 0.00 4.30
620 634 2.283966 CCGTGGACTGGTCTCCCT 60.284 66.667 0.67 0.00 0.00 4.20
621 635 1.913762 CCGTGGACTGGTCTCCCTT 60.914 63.158 0.67 0.00 0.00 3.95
622 636 1.293498 CGTGGACTGGTCTCCCTTG 59.707 63.158 0.67 0.00 0.00 3.61
623 637 1.185618 CGTGGACTGGTCTCCCTTGA 61.186 60.000 0.67 0.00 0.00 3.02
624 638 1.280457 GTGGACTGGTCTCCCTTGAT 58.720 55.000 0.67 0.00 0.00 2.57
625 639 1.065854 GTGGACTGGTCTCCCTTGATG 60.066 57.143 0.67 0.00 0.00 3.07
626 640 0.107459 GGACTGGTCTCCCTTGATGC 60.107 60.000 0.67 0.00 0.00 3.91
627 641 0.908198 GACTGGTCTCCCTTGATGCT 59.092 55.000 0.00 0.00 0.00 3.79
628 642 0.617413 ACTGGTCTCCCTTGATGCTG 59.383 55.000 0.00 0.00 0.00 4.41
629 643 0.907486 CTGGTCTCCCTTGATGCTGA 59.093 55.000 0.00 0.00 0.00 4.26
630 644 0.615331 TGGTCTCCCTTGATGCTGAC 59.385 55.000 0.00 0.00 0.00 3.51
631 645 0.615331 GGTCTCCCTTGATGCTGACA 59.385 55.000 0.00 0.00 0.00 3.58
632 646 1.003580 GGTCTCCCTTGATGCTGACAA 59.996 52.381 0.00 0.00 0.00 3.18
633 647 2.553028 GGTCTCCCTTGATGCTGACAAA 60.553 50.000 0.00 0.00 0.00 2.83
634 648 3.350833 GTCTCCCTTGATGCTGACAAAT 58.649 45.455 0.00 0.00 0.00 2.32
635 649 3.128242 GTCTCCCTTGATGCTGACAAATG 59.872 47.826 0.00 0.00 0.00 2.32
636 650 1.820519 TCCCTTGATGCTGACAAATGC 59.179 47.619 0.00 0.00 0.00 3.56
637 651 1.468565 CCCTTGATGCTGACAAATGCG 60.469 52.381 0.00 0.00 0.00 4.73
638 652 1.468565 CCTTGATGCTGACAAATGCGG 60.469 52.381 0.00 0.00 0.00 5.69
639 653 0.527113 TTGATGCTGACAAATGCGGG 59.473 50.000 0.00 0.00 0.00 6.13
640 654 0.322366 TGATGCTGACAAATGCGGGA 60.322 50.000 0.00 0.00 0.00 5.14
641 655 1.027357 GATGCTGACAAATGCGGGAT 58.973 50.000 0.00 0.00 0.00 3.85
642 656 0.742505 ATGCTGACAAATGCGGGATG 59.257 50.000 0.00 0.00 0.00 3.51
643 657 0.608856 TGCTGACAAATGCGGGATGT 60.609 50.000 0.00 0.00 0.00 3.06
644 658 0.527565 GCTGACAAATGCGGGATGTT 59.472 50.000 0.00 0.00 0.00 2.71
645 659 1.067635 GCTGACAAATGCGGGATGTTT 60.068 47.619 0.00 0.00 0.00 2.83
646 660 2.610232 GCTGACAAATGCGGGATGTTTT 60.610 45.455 0.00 0.00 0.00 2.43
647 661 3.652274 CTGACAAATGCGGGATGTTTTT 58.348 40.909 0.00 0.00 0.00 1.94
662 676 3.442996 TTTTTGTGGGTTGCCGTTG 57.557 47.368 0.00 0.00 0.00 4.10
663 677 0.895530 TTTTTGTGGGTTGCCGTTGA 59.104 45.000 0.00 0.00 0.00 3.18
664 678 0.895530 TTTTGTGGGTTGCCGTTGAA 59.104 45.000 0.00 0.00 0.00 2.69
665 679 0.457851 TTTGTGGGTTGCCGTTGAAG 59.542 50.000 0.00 0.00 0.00 3.02
666 680 0.394488 TTGTGGGTTGCCGTTGAAGA 60.394 50.000 0.00 0.00 0.00 2.87
667 681 0.179004 TGTGGGTTGCCGTTGAAGAT 60.179 50.000 0.00 0.00 0.00 2.40
668 682 0.240945 GTGGGTTGCCGTTGAAGATG 59.759 55.000 0.00 0.00 0.00 2.90
669 683 1.212751 GGGTTGCCGTTGAAGATGC 59.787 57.895 0.00 0.00 0.00 3.91
677 691 1.404986 CCGTTGAAGATGCCCTTACGA 60.405 52.381 10.80 0.00 38.47 3.43
694 708 5.007724 CCTTACGACTTTTGAAGTTTCTGCT 59.992 40.000 0.00 0.00 43.03 4.24
724 742 9.703892 TTTTTGTTCAATTTCAATCCATACGAT 57.296 25.926 0.00 0.00 0.00 3.73
727 745 9.949174 TTGTTCAATTTCAATCCATACGATATG 57.051 29.630 0.00 0.00 0.00 1.78
852 910 9.609346 GGTACAAACTCTACCATGTATATGTTT 57.391 33.333 0.00 0.00 34.74 2.83
878 936 7.451731 TTTTGGAGGATTCTACCATGTATCT 57.548 36.000 0.00 0.00 33.56 1.98
879 937 6.425210 TTGGAGGATTCTACCATGTATCTG 57.575 41.667 0.00 0.00 33.56 2.90
880 938 5.467738 TGGAGGATTCTACCATGTATCTGT 58.532 41.667 0.00 0.00 0.00 3.41
881 939 5.905331 TGGAGGATTCTACCATGTATCTGTT 59.095 40.000 0.00 0.00 0.00 3.16
891 949 5.933617 ACCATGTATCTGTTGCATCATACT 58.066 37.500 0.00 0.00 0.00 2.12
892 950 6.359804 ACCATGTATCTGTTGCATCATACTT 58.640 36.000 0.00 0.00 0.00 2.24
899 957 3.802866 TGTTGCATCATACTTGGCGATA 58.197 40.909 0.00 0.00 0.00 2.92
915 973 5.000591 TGGCGATAGTTGTCATCAGAAAAA 58.999 37.500 0.00 0.00 39.35 1.94
916 974 5.122239 TGGCGATAGTTGTCATCAGAAAAAG 59.878 40.000 0.00 0.00 39.35 2.27
917 975 5.122396 GGCGATAGTTGTCATCAGAAAAAGT 59.878 40.000 0.00 0.00 39.35 2.66
995 1062 1.354337 CGTGGTTCACATCAGCGAGG 61.354 60.000 0.00 0.00 33.40 4.63
1426 4772 1.134788 CCTATCTCGCGTTTGACCCTT 60.135 52.381 5.77 0.00 0.00 3.95
1460 4806 4.383552 GCACTATGAGGTGTTCTTGATCCT 60.384 45.833 0.00 0.00 39.21 3.24
1555 7319 6.786103 CGAAGAAAACTTCACGATAAGTTCAC 59.214 38.462 16.35 13.60 46.40 3.18
1565 7329 4.384846 CACGATAAGTTCACGCTACTTGTT 59.615 41.667 7.44 0.00 36.56 2.83
1719 7489 2.658707 GAGAGTGGTCAACGTGCGC 61.659 63.158 0.00 0.00 0.00 6.09
1812 10536 2.473868 CGTGCTGCTTTGTTATGGTACG 60.474 50.000 0.00 0.00 0.00 3.67
2003 10750 2.158957 ACACCGATAGATGCCAACGAAT 60.159 45.455 0.00 0.00 25.70 3.34
2067 10814 6.200854 GGTTTGTACTTTGCAAATCTTCAAGG 59.799 38.462 13.23 0.59 38.00 3.61
2194 10941 1.141858 CCTAAGGGAATCTGCAGACCC 59.858 57.143 27.61 27.61 42.36 4.46
2209 10956 3.434739 GCAGACCCTGGATCTTTGATGAT 60.435 47.826 0.00 0.00 31.21 2.45
2724 14497 7.337942 TCTGCATCCTTATTTCTCCTTTTCTTC 59.662 37.037 0.00 0.00 0.00 2.87
2752 14525 0.466922 GCCCCATGCATGACTAAGCT 60.467 55.000 28.31 0.00 40.77 3.74
2803 14576 9.612066 TGGTATCTTCTTTTCTTTTTGCAATTT 57.388 25.926 0.00 0.00 0.00 1.82
2831 14604 4.409570 GTGGAGTATACACGTACACACAG 58.590 47.826 5.50 0.00 36.05 3.66
2922 14695 8.746530 CCTTGTATAGGTGTCCGTATATTGTAT 58.253 37.037 0.00 0.00 39.39 2.29
2925 14698 8.733458 TGTATAGGTGTCCGTATATTGTATGAC 58.267 37.037 0.00 0.00 0.00 3.06
2934 14707 6.038492 TCCGTATATTGTATGACACGAACTCA 59.962 38.462 0.00 0.00 0.00 3.41
2948 14721 3.514309 ACGAACTCAGCCTTGTAACCTAT 59.486 43.478 0.00 0.00 0.00 2.57
2949 14722 4.708421 ACGAACTCAGCCTTGTAACCTATA 59.292 41.667 0.00 0.00 0.00 1.31
3062 14836 2.510238 CTCCTCTTTCCGCTGCCG 60.510 66.667 0.00 0.00 0.00 5.69
3235 15165 2.448542 CCCCCGATGGATCTGGGT 60.449 66.667 13.43 0.00 46.46 4.51
3264 15194 1.978580 GGGTCTTTCTCCTTGACCTCA 59.021 52.381 10.60 0.00 46.76 3.86
3480 15410 2.111384 GTCTCTTGGCTCTATGGGTCA 58.889 52.381 0.00 0.00 0.00 4.02
3485 15415 2.254152 TGGCTCTATGGGTCAGTCTT 57.746 50.000 0.00 0.00 0.00 3.01
3486 15416 2.551270 TGGCTCTATGGGTCAGTCTTT 58.449 47.619 0.00 0.00 0.00 2.52
3492 15422 4.935578 TCTATGGGTCAGTCTTTCTCAGA 58.064 43.478 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 78 8.871629 TTACTCCAAGTTCTTTTAATATGGCA 57.128 30.769 0.00 0.00 0.00 4.92
105 110 4.823989 CACACCAAAGAAGAGGAGTTTGAT 59.176 41.667 0.00 0.00 33.78 2.57
144 149 7.865385 TGAAACACTGGATTAGCAACAAATAAC 59.135 33.333 0.00 0.00 0.00 1.89
172 178 8.784043 GTCTATTTCAATGTGTTTGGTTCTAGT 58.216 33.333 0.00 0.00 35.92 2.57
201 207 8.892905 GCAACTTTCTCTCTAACAATTAAAACG 58.107 33.333 0.00 0.00 0.00 3.60
202 208 9.730420 TGCAACTTTCTCTCTAACAATTAAAAC 57.270 29.630 0.00 0.00 0.00 2.43
206 212 8.898761 TGTTTGCAACTTTCTCTCTAACAATTA 58.101 29.630 0.00 0.00 0.00 1.40
207 213 7.771183 TGTTTGCAACTTTCTCTCTAACAATT 58.229 30.769 0.00 0.00 0.00 2.32
208 214 7.333528 TGTTTGCAACTTTCTCTCTAACAAT 57.666 32.000 0.00 0.00 0.00 2.71
219 225 6.586082 TCTCAAGTTCTTTGTTTGCAACTTTC 59.414 34.615 0.00 0.00 37.04 2.62
221 227 6.024552 TCTCAAGTTCTTTGTTTGCAACTT 57.975 33.333 0.00 0.00 39.20 2.66
257 263 5.358090 CATCTGCAAGCTGATCTTTAGAGA 58.642 41.667 10.90 0.00 29.90 3.10
580 594 6.565234 GGACACGGATATGTGAGATAATAGG 58.435 44.000 0.24 0.00 42.55 2.57
594 608 1.317431 CCAGTCCACGGACACGGATA 61.317 60.000 18.21 0.00 46.76 2.59
595 609 2.646175 CCAGTCCACGGACACGGAT 61.646 63.158 18.21 0.00 46.76 4.18
596 610 3.299977 CCAGTCCACGGACACGGA 61.300 66.667 18.21 0.00 46.76 4.69
597 611 3.569049 GACCAGTCCACGGACACGG 62.569 68.421 18.21 18.31 46.76 4.94
598 612 2.049433 GACCAGTCCACGGACACG 60.049 66.667 18.21 9.57 46.76 4.49
599 613 1.289380 GAGACCAGTCCACGGACAC 59.711 63.158 18.21 6.77 46.76 3.67
600 614 1.906824 GGAGACCAGTCCACGGACA 60.907 63.158 18.21 0.00 46.76 4.02
601 615 2.971452 GGAGACCAGTCCACGGAC 59.029 66.667 8.23 8.23 44.86 4.79
613 627 2.479566 TTGTCAGCATCAAGGGAGAC 57.520 50.000 0.00 0.00 0.00 3.36
614 628 3.349927 CATTTGTCAGCATCAAGGGAGA 58.650 45.455 0.00 0.00 0.00 3.71
615 629 2.159282 GCATTTGTCAGCATCAAGGGAG 60.159 50.000 0.00 0.00 0.00 4.30
616 630 1.820519 GCATTTGTCAGCATCAAGGGA 59.179 47.619 0.00 0.00 0.00 4.20
617 631 1.468565 CGCATTTGTCAGCATCAAGGG 60.469 52.381 0.00 0.00 0.00 3.95
618 632 1.468565 CCGCATTTGTCAGCATCAAGG 60.469 52.381 0.00 0.00 0.00 3.61
619 633 1.468565 CCCGCATTTGTCAGCATCAAG 60.469 52.381 0.00 0.00 0.00 3.02
620 634 0.527113 CCCGCATTTGTCAGCATCAA 59.473 50.000 0.00 0.00 0.00 2.57
621 635 0.322366 TCCCGCATTTGTCAGCATCA 60.322 50.000 0.00 0.00 0.00 3.07
622 636 1.027357 ATCCCGCATTTGTCAGCATC 58.973 50.000 0.00 0.00 0.00 3.91
623 637 0.742505 CATCCCGCATTTGTCAGCAT 59.257 50.000 0.00 0.00 0.00 3.79
624 638 0.608856 ACATCCCGCATTTGTCAGCA 60.609 50.000 0.00 0.00 0.00 4.41
625 639 0.527565 AACATCCCGCATTTGTCAGC 59.472 50.000 0.00 0.00 0.00 4.26
626 640 3.302365 AAAACATCCCGCATTTGTCAG 57.698 42.857 0.00 0.00 0.00 3.51
627 641 3.742433 AAAAACATCCCGCATTTGTCA 57.258 38.095 0.00 0.00 0.00 3.58
644 658 0.895530 TCAACGGCAACCCACAAAAA 59.104 45.000 0.00 0.00 0.00 1.94
645 659 0.895530 TTCAACGGCAACCCACAAAA 59.104 45.000 0.00 0.00 0.00 2.44
646 660 0.457851 CTTCAACGGCAACCCACAAA 59.542 50.000 0.00 0.00 0.00 2.83
647 661 0.394488 TCTTCAACGGCAACCCACAA 60.394 50.000 0.00 0.00 0.00 3.33
648 662 0.179004 ATCTTCAACGGCAACCCACA 60.179 50.000 0.00 0.00 0.00 4.17
649 663 0.240945 CATCTTCAACGGCAACCCAC 59.759 55.000 0.00 0.00 0.00 4.61
650 664 1.523154 GCATCTTCAACGGCAACCCA 61.523 55.000 0.00 0.00 0.00 4.51
651 665 1.212751 GCATCTTCAACGGCAACCC 59.787 57.895 0.00 0.00 0.00 4.11
652 666 1.212751 GGCATCTTCAACGGCAACC 59.787 57.895 0.00 0.00 0.00 3.77
653 667 1.212751 GGGCATCTTCAACGGCAAC 59.787 57.895 0.00 0.00 0.00 4.17
654 668 0.539438 AAGGGCATCTTCAACGGCAA 60.539 50.000 0.00 0.00 0.00 4.52
655 669 0.326595 TAAGGGCATCTTCAACGGCA 59.673 50.000 0.00 0.00 36.93 5.69
656 670 0.733150 GTAAGGGCATCTTCAACGGC 59.267 55.000 0.00 0.00 36.93 5.68
657 671 1.006832 CGTAAGGGCATCTTCAACGG 58.993 55.000 6.51 0.00 35.15 4.44
658 672 1.659098 GTCGTAAGGGCATCTTCAACG 59.341 52.381 7.57 7.57 38.25 4.10
659 673 2.973945 AGTCGTAAGGGCATCTTCAAC 58.026 47.619 0.00 0.00 36.93 3.18
660 674 3.695830 AAGTCGTAAGGGCATCTTCAA 57.304 42.857 0.00 0.00 36.93 2.69
661 675 3.695830 AAAGTCGTAAGGGCATCTTCA 57.304 42.857 0.00 0.00 36.93 3.02
662 676 4.000988 TCAAAAGTCGTAAGGGCATCTTC 58.999 43.478 0.00 0.00 36.93 2.87
663 677 4.015872 TCAAAAGTCGTAAGGGCATCTT 57.984 40.909 0.00 0.00 39.40 2.40
664 678 3.695830 TCAAAAGTCGTAAGGGCATCT 57.304 42.857 0.00 0.00 38.47 2.90
665 679 3.751698 ACTTCAAAAGTCGTAAGGGCATC 59.248 43.478 0.00 0.00 37.02 3.91
666 680 3.751518 ACTTCAAAAGTCGTAAGGGCAT 58.248 40.909 0.00 0.00 37.02 4.40
667 681 3.202829 ACTTCAAAAGTCGTAAGGGCA 57.797 42.857 0.00 0.00 37.02 5.36
668 682 4.275196 AGAAACTTCAAAAGTCGTAAGGGC 59.725 41.667 0.00 0.00 41.91 5.19
669 683 5.748592 CAGAAACTTCAAAAGTCGTAAGGG 58.251 41.667 0.00 0.00 41.91 3.95
704 722 8.690203 ACCATATCGTATGGATTGAAATTGAA 57.310 30.769 22.74 0.00 41.64 2.69
755 774 1.065358 TCTCGTTCGAAATTCGCACC 58.935 50.000 10.93 0.00 40.21 5.01
853 911 7.775093 CAGATACATGGTAGAATCCTCCAAAAA 59.225 37.037 0.00 0.00 34.80 1.94
854 912 7.092444 ACAGATACATGGTAGAATCCTCCAAAA 60.092 37.037 0.00 0.00 34.80 2.44
855 913 6.386927 ACAGATACATGGTAGAATCCTCCAAA 59.613 38.462 0.00 0.00 34.80 3.28
856 914 5.905331 ACAGATACATGGTAGAATCCTCCAA 59.095 40.000 0.00 0.00 34.80 3.53
857 915 5.467738 ACAGATACATGGTAGAATCCTCCA 58.532 41.667 0.00 0.00 35.64 3.86
858 916 6.226787 CAACAGATACATGGTAGAATCCTCC 58.773 44.000 0.00 0.00 0.00 4.30
859 917 5.698545 GCAACAGATACATGGTAGAATCCTC 59.301 44.000 0.00 0.00 0.00 3.71
860 918 5.130975 TGCAACAGATACATGGTAGAATCCT 59.869 40.000 0.00 0.00 0.00 3.24
861 919 5.368145 TGCAACAGATACATGGTAGAATCC 58.632 41.667 0.00 0.00 0.00 3.01
862 920 6.707608 TGATGCAACAGATACATGGTAGAATC 59.292 38.462 0.00 0.00 0.00 2.52
863 921 6.594744 TGATGCAACAGATACATGGTAGAAT 58.405 36.000 0.00 0.00 0.00 2.40
864 922 5.988287 TGATGCAACAGATACATGGTAGAA 58.012 37.500 0.00 0.00 0.00 2.10
865 923 5.612725 TGATGCAACAGATACATGGTAGA 57.387 39.130 0.00 0.00 0.00 2.59
866 924 7.157347 AGTATGATGCAACAGATACATGGTAG 58.843 38.462 2.25 0.00 0.00 3.18
867 925 7.066307 AGTATGATGCAACAGATACATGGTA 57.934 36.000 2.25 0.00 0.00 3.25
868 926 5.933617 AGTATGATGCAACAGATACATGGT 58.066 37.500 2.25 0.00 0.00 3.55
869 927 6.293790 CCAAGTATGATGCAACAGATACATGG 60.294 42.308 13.93 13.93 30.52 3.66
870 928 6.665465 CCAAGTATGATGCAACAGATACATG 58.335 40.000 2.25 4.69 0.00 3.21
871 929 5.240183 GCCAAGTATGATGCAACAGATACAT 59.760 40.000 2.25 0.00 0.00 2.29
872 930 4.576053 GCCAAGTATGATGCAACAGATACA 59.424 41.667 2.25 0.00 0.00 2.29
873 931 4.319046 CGCCAAGTATGATGCAACAGATAC 60.319 45.833 2.25 1.37 0.00 2.24
874 932 3.809279 CGCCAAGTATGATGCAACAGATA 59.191 43.478 2.25 0.00 0.00 1.98
875 933 2.615447 CGCCAAGTATGATGCAACAGAT 59.385 45.455 2.25 0.00 0.00 2.90
876 934 2.009051 CGCCAAGTATGATGCAACAGA 58.991 47.619 2.25 0.00 0.00 3.41
877 935 2.009051 TCGCCAAGTATGATGCAACAG 58.991 47.619 2.25 0.00 0.00 3.16
878 936 2.106477 TCGCCAAGTATGATGCAACA 57.894 45.000 0.00 0.00 0.00 3.33
879 937 3.809832 ACTATCGCCAAGTATGATGCAAC 59.190 43.478 0.00 0.00 0.00 4.17
880 938 4.071961 ACTATCGCCAAGTATGATGCAA 57.928 40.909 0.00 0.00 0.00 4.08
881 939 3.751479 ACTATCGCCAAGTATGATGCA 57.249 42.857 0.00 0.00 0.00 3.96
891 949 3.885724 TCTGATGACAACTATCGCCAA 57.114 42.857 0.00 0.00 0.00 4.52
892 950 3.885724 TTCTGATGACAACTATCGCCA 57.114 42.857 0.00 0.00 0.00 5.69
915 973 4.945543 ACGTTTCTGTTTGGGAAAAGTACT 59.054 37.500 6.11 0.00 41.10 2.73
916 974 5.163733 TGACGTTTCTGTTTGGGAAAAGTAC 60.164 40.000 7.48 0.00 42.21 2.73
917 975 4.942483 TGACGTTTCTGTTTGGGAAAAGTA 59.058 37.500 7.48 0.00 42.21 2.24
978 1045 0.037326 GACCTCGCTGATGTGAACCA 60.037 55.000 0.00 0.00 31.75 3.67
995 1062 0.249073 CTCCGTGTGATCCATCGGAC 60.249 60.000 14.98 0.00 45.49 4.79
1053 1127 1.970114 GAGGTCACGTGGTCCGAGA 60.970 63.158 17.00 0.00 40.70 4.04
1443 4789 3.251484 AGGAAGGATCAAGAACACCTCA 58.749 45.455 0.00 0.00 31.89 3.86
1460 4806 3.708236 ACAGCCCTAGATCCTTAGGAA 57.292 47.619 4.56 0.00 42.39 3.36
1555 7319 1.270625 TGGAGGTTCCAACAAGTAGCG 60.271 52.381 0.00 0.00 45.00 4.26
1719 7489 1.455786 GTCGTGAACATCAGTGAACCG 59.544 52.381 0.00 0.00 0.00 4.44
1812 10536 5.689383 ATGATGTGTACCTTGTGACAAAC 57.311 39.130 0.00 0.00 0.00 2.93
1918 10657 7.737869 TGCAAAGATTCATGCCCATAAATATT 58.262 30.769 10.71 0.00 41.87 1.28
1926 10665 1.187974 CCTGCAAAGATTCATGCCCA 58.812 50.000 10.71 0.00 41.87 5.36
1927 10666 1.188863 ACCTGCAAAGATTCATGCCC 58.811 50.000 10.71 0.00 41.87 5.36
1934 10681 5.431765 AGACGATGATAACCTGCAAAGATT 58.568 37.500 0.00 0.00 0.00 2.40
2003 10750 1.892474 GTAATGCTCCCCAACTTTGCA 59.108 47.619 0.00 0.00 38.05 4.08
2014 10761 2.293170 GAGCTTCCAAGGTAATGCTCC 58.707 52.381 0.00 0.00 40.44 4.70
2045 10792 6.463995 ACCTTGAAGATTTGCAAAGTACAA 57.536 33.333 18.19 17.25 0.00 2.41
2067 10814 2.676342 AGGTGCCAAATACGAATTCGAC 59.324 45.455 33.05 17.54 43.02 4.20
2194 10941 7.826744 AGATCATGATCATCATCAAAGATCCAG 59.173 37.037 31.99 0.00 45.23 3.86
2209 10956 6.773685 TGCCATATTTGTCAAGATCATGATCA 59.226 34.615 31.99 13.41 40.22 2.92
2676 14449 2.490903 ACACAAACTATCGGCTCGTAGT 59.509 45.455 0.00 0.00 32.75 2.73
2677 14450 3.146618 ACACAAACTATCGGCTCGTAG 57.853 47.619 0.00 0.00 0.00 3.51
2678 14451 3.192001 AGAACACAAACTATCGGCTCGTA 59.808 43.478 0.00 0.00 0.00 3.43
2679 14452 2.029290 AGAACACAAACTATCGGCTCGT 60.029 45.455 0.00 0.00 0.00 4.18
2752 14525 6.174760 ACTATTTACACAACCGAGGCATTAA 58.825 36.000 0.00 0.00 0.00 1.40
2803 14576 4.766373 TGTACGTGTATACTCCACCTTTGA 59.234 41.667 0.00 0.00 0.00 2.69
2831 14604 8.528917 TGGTTATATATTCTAACATGTCGTGC 57.471 34.615 0.00 0.00 31.98 5.34
2922 14695 0.464036 ACAAGGCTGAGTTCGTGTCA 59.536 50.000 0.00 0.00 0.00 3.58
2925 14698 1.798813 GGTTACAAGGCTGAGTTCGTG 59.201 52.381 0.00 0.00 0.00 4.35
3042 14816 2.124942 CAGCGGAAAGAGGAGGGC 60.125 66.667 0.00 0.00 0.00 5.19
3043 14817 2.124942 GCAGCGGAAAGAGGAGGG 60.125 66.667 0.00 0.00 0.00 4.30
3062 14836 4.660938 AAGGGTGGTGGCTTCGGC 62.661 66.667 0.00 0.00 40.88 5.54
3235 15165 1.874345 GAGAAAGACCCCGTGCTCGA 61.874 60.000 10.21 0.00 39.71 4.04
3480 15410 3.127895 CGTCGAGGATTCTGAGAAAGACT 59.872 47.826 0.00 0.00 33.46 3.24
3485 15415 0.456221 GGCGTCGAGGATTCTGAGAA 59.544 55.000 9.75 0.00 0.00 2.87
3486 15416 1.715862 CGGCGTCGAGGATTCTGAGA 61.716 60.000 1.44 0.00 39.00 3.27
3492 15422 1.226974 CATGACGGCGTCGAGGATT 60.227 57.895 31.90 11.73 40.11 3.01


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

AutoCloner maintained by Alex Coulton.