Multiple sequence alignment - TraesCS1D01G087200

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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 TraesCS1D01G087200 chr1D 100.000 3681 0 0 1 3681 72460633 72456953 0.000000e+00 6798
1 TraesCS1D01G087200 chr1D 98.802 2837 29 2 846 3681 72443381 72440549 0.000000e+00 5046
2 TraesCS1D01G087200 chr1D 81.392 1580 229 40 1004 2531 72435177 72433611 0.000000e+00 1229
3 TraesCS1D01G087200 chr1D 84.367 1209 155 24 1043 2233 71769580 71768388 0.000000e+00 1155
4 TraesCS1D01G087200 chr1D 84.840 343 28 15 2266 2605 71768388 71768067 1.280000e-84 324
5 TraesCS1D01G087200 chr1B 84.690 2358 286 48 1035 3358 113516201 113513885 0.000000e+00 2285
6 TraesCS1D01G087200 chr1B 80.662 1872 272 51 1004 2831 113498640 113496815 0.000000e+00 1369
7 TraesCS1D01G087200 chr1B 80.609 1872 276 49 1004 2831 113315852 113314024 0.000000e+00 1365
8 TraesCS1D01G087200 chr1B 80.556 1872 277 49 1004 2831 113213491 113211663 0.000000e+00 1360
9 TraesCS1D01G087200 chr1B 85.998 1107 115 19 1026 2102 50992772 50993868 0.000000e+00 1149
10 TraesCS1D01G087200 chr1B 83.719 1210 150 33 1055 2233 113025832 113024639 0.000000e+00 1099
11 TraesCS1D01G087200 chr1B 82.143 812 101 27 2748 3552 51003270 51004044 0.000000e+00 656
12 TraesCS1D01G087200 chr1B 85.651 453 43 14 2087 2526 51002720 51003163 1.200000e-124 457
13 TraesCS1D01G087200 chr1B 77.945 730 92 38 2132 2831 113407749 113407059 3.450000e-105 392
14 TraesCS1D01G087200 chr1B 82.303 469 48 17 3241 3680 113023931 113023469 1.250000e-99 374
15 TraesCS1D01G087200 chr1B 90.385 260 25 0 3422 3681 113509999 113509740 3.520000e-90 342
16 TraesCS1D01G087200 chr1A 86.109 1375 154 20 1033 2387 32191446 32192803 0.000000e+00 1447
17 TraesCS1D01G087200 chr1A 88.889 252 19 7 678 927 405523323 405523079 5.970000e-78 302
18 TraesCS1D01G087200 chrUn 82.718 1273 201 13 1004 2262 372932933 372934200 0.000000e+00 1114
19 TraesCS1D01G087200 chr3B 92.683 656 47 1 19 673 644146446 644145791 0.000000e+00 944
20 TraesCS1D01G087200 chr3B 91.921 656 51 2 19 673 519054824 519054170 0.000000e+00 917
21 TraesCS1D01G087200 chr2D 92.133 661 46 3 16 671 632084591 632083932 0.000000e+00 928
22 TraesCS1D01G087200 chr4B 91.945 658 52 1 16 672 580798920 580799577 0.000000e+00 920
23 TraesCS1D01G087200 chr4B 92.656 640 44 2 37 673 2487670 2487031 0.000000e+00 918
24 TraesCS1D01G087200 chr7D 91.704 663 49 4 16 673 6791497 6792158 0.000000e+00 915
25 TraesCS1D01G087200 chr2B 91.768 656 53 1 19 673 655521982 655521327 0.000000e+00 911
26 TraesCS1D01G087200 chr7B 91.590 654 51 1 25 674 680192425 680193078 0.000000e+00 900
27 TraesCS1D01G087200 chr3D 91.101 663 54 2 16 673 37987190 37986528 0.000000e+00 893
28 TraesCS1D01G087200 chr4D 85.870 276 27 7 678 951 73405449 73405184 2.160000e-72 283


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 TraesCS1D01G087200 chr1D 72456953 72460633 3680 True 6798.0 6798 100.0000 1 3681 1 chr1D.!!$R3 3680
1 TraesCS1D01G087200 chr1D 72440549 72443381 2832 True 5046.0 5046 98.8020 846 3681 1 chr1D.!!$R2 2835
2 TraesCS1D01G087200 chr1D 72433611 72435177 1566 True 1229.0 1229 81.3920 1004 2531 1 chr1D.!!$R1 1527
3 TraesCS1D01G087200 chr1D 71768067 71769580 1513 True 739.5 1155 84.6035 1043 2605 2 chr1D.!!$R4 1562
4 TraesCS1D01G087200 chr1B 113496815 113498640 1825 True 1369.0 1369 80.6620 1004 2831 1 chr1B.!!$R4 1827
5 TraesCS1D01G087200 chr1B 113314024 113315852 1828 True 1365.0 1365 80.6090 1004 2831 1 chr1B.!!$R2 1827
6 TraesCS1D01G087200 chr1B 113211663 113213491 1828 True 1360.0 1360 80.5560 1004 2831 1 chr1B.!!$R1 1827
7 TraesCS1D01G087200 chr1B 113509740 113516201 6461 True 1313.5 2285 87.5375 1035 3681 2 chr1B.!!$R6 2646
8 TraesCS1D01G087200 chr1B 50992772 50993868 1096 False 1149.0 1149 85.9980 1026 2102 1 chr1B.!!$F1 1076
9 TraesCS1D01G087200 chr1B 113023469 113025832 2363 True 736.5 1099 83.0110 1055 3680 2 chr1B.!!$R5 2625
10 TraesCS1D01G087200 chr1B 51002720 51004044 1324 False 556.5 656 83.8970 2087 3552 2 chr1B.!!$F2 1465
11 TraesCS1D01G087200 chr1B 113407059 113407749 690 True 392.0 392 77.9450 2132 2831 1 chr1B.!!$R3 699
12 TraesCS1D01G087200 chr1A 32191446 32192803 1357 False 1447.0 1447 86.1090 1033 2387 1 chr1A.!!$F1 1354
13 TraesCS1D01G087200 chrUn 372932933 372934200 1267 False 1114.0 1114 82.7180 1004 2262 1 chrUn.!!$F1 1258
14 TraesCS1D01G087200 chr3B 644145791 644146446 655 True 944.0 944 92.6830 19 673 1 chr3B.!!$R2 654
15 TraesCS1D01G087200 chr3B 519054170 519054824 654 True 917.0 917 91.9210 19 673 1 chr3B.!!$R1 654
16 TraesCS1D01G087200 chr2D 632083932 632084591 659 True 928.0 928 92.1330 16 671 1 chr2D.!!$R1 655
17 TraesCS1D01G087200 chr4B 580798920 580799577 657 False 920.0 920 91.9450 16 672 1 chr4B.!!$F1 656
18 TraesCS1D01G087200 chr4B 2487031 2487670 639 True 918.0 918 92.6560 37 673 1 chr4B.!!$R1 636
19 TraesCS1D01G087200 chr7D 6791497 6792158 661 False 915.0 915 91.7040 16 673 1 chr7D.!!$F1 657
20 TraesCS1D01G087200 chr2B 655521327 655521982 655 True 911.0 911 91.7680 19 673 1 chr2B.!!$R1 654
21 TraesCS1D01G087200 chr7B 680192425 680193078 653 False 900.0 900 91.5900 25 674 1 chr7B.!!$F1 649
22 TraesCS1D01G087200 chr3D 37986528 37987190 662 True 893.0 893 91.1010 16 673 1 chr3D.!!$R1 657

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
812 816 0.101399 CCGTGGGATCTGACGAAGAG 59.899 60.0 15.73 0.0 38.67 2.85 F
816 820 0.248702 GGGATCTGACGAAGAGCGAC 60.249 60.0 0.00 0.0 42.55 5.19 F
817 821 0.248702 GGATCTGACGAAGAGCGACC 60.249 60.0 0.00 0.0 42.55 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2084 2172 1.201181 TCCAAATTTCAATCGGGCGTG 59.799 47.619 0.0 0.0 0.00 5.34 R
2406 2514 9.768215 TCTGGGTGAAAAAGAAAGGATAATTAT 57.232 29.630 0.0 0.0 0.00 1.28 R
2885 3037 5.407995 GCAATATCTTGTGACTCATCCTAGC 59.592 44.000 0.0 0.0 34.69 3.42 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
20 21 2.433664 CGGTCACCGGCAACTACC 60.434 66.667 8.94 0.77 44.15 3.18
21 22 2.745037 GGTCACCGGCAACTACCA 59.255 61.111 0.00 0.00 0.00 3.25
22 23 1.670083 GGTCACCGGCAACTACCAC 60.670 63.158 0.00 0.00 0.00 4.16
23 24 1.070105 GTCACCGGCAACTACCACA 59.930 57.895 0.00 0.00 0.00 4.17
24 25 0.533308 GTCACCGGCAACTACCACAA 60.533 55.000 0.00 0.00 0.00 3.33
25 26 0.533308 TCACCGGCAACTACCACAAC 60.533 55.000 0.00 0.00 0.00 3.32
26 27 1.228033 ACCGGCAACTACCACAACC 60.228 57.895 0.00 0.00 0.00 3.77
27 28 2.322081 CCGGCAACTACCACAACCG 61.322 63.158 0.00 0.00 40.30 4.44
28 29 2.951458 GGCAACTACCACAACCGC 59.049 61.111 0.00 0.00 0.00 5.68
29 30 1.599797 GGCAACTACCACAACCGCT 60.600 57.895 0.00 0.00 0.00 5.52
105 107 4.435970 TCCGCCTCGCCTCTGGTA 62.436 66.667 0.00 0.00 0.00 3.25
137 139 3.224324 GAGGCGCGGTGGATCCTA 61.224 66.667 14.23 0.00 0.00 2.94
138 140 2.762459 AGGCGCGGTGGATCCTAA 60.762 61.111 14.23 0.00 0.00 2.69
219 223 7.406031 TGTATTCTACTCAGGAAGACGAAAT 57.594 36.000 0.00 0.00 37.62 2.17
222 226 4.087182 TCTACTCAGGAAGACGAAATGGT 58.913 43.478 0.00 0.00 0.00 3.55
263 267 2.242882 TAAAGGTCTTCCCGCCTAGT 57.757 50.000 0.00 0.00 38.74 2.57
303 307 1.605971 TAGCATCGTTGGTGGGCGTA 61.606 55.000 8.40 0.00 34.79 4.42
384 388 2.600556 CGTCTACGTTCGTGTGTCTTCA 60.601 50.000 8.14 0.00 34.11 3.02
390 394 3.049912 CGTTCGTGTGTCTTCAGATTGA 58.950 45.455 0.00 0.00 0.00 2.57
429 433 6.345298 TGTTATTCTTCATCTGTGGCGATTA 58.655 36.000 0.00 0.00 0.00 1.75
442 446 1.438651 GCGATTACTGTTCTGGTGCA 58.561 50.000 0.00 0.00 0.00 4.57
483 487 0.603707 ACGACGACTTCCCGACTGTA 60.604 55.000 0.00 0.00 0.00 2.74
488 492 2.681848 ACGACTTCCCGACTGTATACTG 59.318 50.000 8.11 8.11 0.00 2.74
495 499 3.007074 TCCCGACTGTATACTGCAACAAA 59.993 43.478 9.48 0.00 0.00 2.83
564 568 1.066573 AGCTCGCTTCAGTGCTTGTAT 60.067 47.619 0.00 0.00 37.66 2.29
589 593 2.108425 TCGCTAGGTGGTCTATGGATCT 59.892 50.000 0.00 0.00 0.00 2.75
590 594 2.230025 CGCTAGGTGGTCTATGGATCTG 59.770 54.545 0.00 0.00 0.00 2.90
591 595 2.564947 GCTAGGTGGTCTATGGATCTGG 59.435 54.545 0.00 0.00 0.00 3.86
592 596 3.755483 GCTAGGTGGTCTATGGATCTGGA 60.755 52.174 0.00 0.00 0.00 3.86
593 597 3.645053 AGGTGGTCTATGGATCTGGAT 57.355 47.619 0.00 0.00 0.00 3.41
594 598 3.246301 AGGTGGTCTATGGATCTGGATG 58.754 50.000 0.00 0.00 0.00 3.51
595 599 2.975489 GGTGGTCTATGGATCTGGATGT 59.025 50.000 0.00 0.00 0.00 3.06
596 600 4.140686 AGGTGGTCTATGGATCTGGATGTA 60.141 45.833 0.00 0.00 0.00 2.29
597 601 4.593206 GGTGGTCTATGGATCTGGATGTAA 59.407 45.833 0.00 0.00 0.00 2.41
598 602 5.249393 GGTGGTCTATGGATCTGGATGTAAT 59.751 44.000 0.00 0.00 0.00 1.89
599 603 6.240002 GGTGGTCTATGGATCTGGATGTAATT 60.240 42.308 0.00 0.00 0.00 1.40
600 604 7.227156 GTGGTCTATGGATCTGGATGTAATTT 58.773 38.462 0.00 0.00 0.00 1.82
601 605 7.721399 GTGGTCTATGGATCTGGATGTAATTTT 59.279 37.037 0.00 0.00 0.00 1.82
602 606 8.281531 TGGTCTATGGATCTGGATGTAATTTTT 58.718 33.333 0.00 0.00 0.00 1.94
603 607 9.793259 GGTCTATGGATCTGGATGTAATTTTTA 57.207 33.333 0.00 0.00 0.00 1.52
629 633 8.819643 TTATTTTTGGTATTTGTTGTACTGCC 57.180 30.769 0.00 0.00 0.00 4.85
630 634 5.854010 TTTTGGTATTTGTTGTACTGCCA 57.146 34.783 0.00 0.00 0.00 4.92
631 635 6.412362 TTTTGGTATTTGTTGTACTGCCAT 57.588 33.333 0.00 0.00 0.00 4.40
632 636 5.384063 TTGGTATTTGTTGTACTGCCATG 57.616 39.130 0.00 0.00 0.00 3.66
633 637 4.657013 TGGTATTTGTTGTACTGCCATGA 58.343 39.130 0.00 0.00 0.00 3.07
634 638 5.260424 TGGTATTTGTTGTACTGCCATGAT 58.740 37.500 0.00 0.00 0.00 2.45
635 639 5.714333 TGGTATTTGTTGTACTGCCATGATT 59.286 36.000 0.00 0.00 0.00 2.57
636 640 6.035843 GGTATTTGTTGTACTGCCATGATTG 58.964 40.000 0.00 0.00 0.00 2.67
637 641 5.981088 ATTTGTTGTACTGCCATGATTGA 57.019 34.783 0.00 0.00 0.00 2.57
638 642 5.781210 TTTGTTGTACTGCCATGATTGAA 57.219 34.783 0.00 0.00 0.00 2.69
639 643 5.375417 TTGTTGTACTGCCATGATTGAAG 57.625 39.130 0.00 0.00 0.00 3.02
640 644 4.650734 TGTTGTACTGCCATGATTGAAGA 58.349 39.130 0.00 0.00 0.00 2.87
641 645 5.255687 TGTTGTACTGCCATGATTGAAGAT 58.744 37.500 0.00 0.00 0.00 2.40
642 646 5.124297 TGTTGTACTGCCATGATTGAAGATG 59.876 40.000 0.00 0.00 0.00 2.90
643 647 5.101648 TGTACTGCCATGATTGAAGATGA 57.898 39.130 0.00 0.00 0.00 2.92
644 648 5.499313 TGTACTGCCATGATTGAAGATGAA 58.501 37.500 0.00 0.00 0.00 2.57
645 649 6.124340 TGTACTGCCATGATTGAAGATGAAT 58.876 36.000 0.00 0.00 0.00 2.57
646 650 6.604396 TGTACTGCCATGATTGAAGATGAATT 59.396 34.615 0.00 0.00 0.00 2.17
647 651 5.902681 ACTGCCATGATTGAAGATGAATTG 58.097 37.500 0.00 0.00 0.00 2.32
648 652 5.655090 ACTGCCATGATTGAAGATGAATTGA 59.345 36.000 0.00 0.00 0.00 2.57
649 653 6.323996 ACTGCCATGATTGAAGATGAATTGAT 59.676 34.615 0.00 0.00 0.00 2.57
650 654 6.745116 TGCCATGATTGAAGATGAATTGATC 58.255 36.000 0.00 0.00 0.00 2.92
651 655 5.856986 GCCATGATTGAAGATGAATTGATCG 59.143 40.000 0.00 0.00 0.00 3.69
652 656 6.379386 CCATGATTGAAGATGAATTGATCGG 58.621 40.000 0.00 0.00 0.00 4.18
653 657 6.206048 CCATGATTGAAGATGAATTGATCGGA 59.794 38.462 0.00 0.00 0.00 4.55
654 658 7.255346 CCATGATTGAAGATGAATTGATCGGAA 60.255 37.037 0.00 0.00 0.00 4.30
655 659 7.255491 TGATTGAAGATGAATTGATCGGAAG 57.745 36.000 0.00 0.00 0.00 3.46
688 692 1.530323 AAAACTATGACACCGGCACC 58.470 50.000 0.00 0.00 0.00 5.01
689 693 0.672401 AAACTATGACACCGGCACCG 60.672 55.000 0.00 1.02 39.44 4.94
759 763 3.721706 CGCCCTTGCTCCCCTTCT 61.722 66.667 0.00 0.00 34.43 2.85
760 764 2.273776 GCCCTTGCTCCCCTTCTC 59.726 66.667 0.00 0.00 33.53 2.87
761 765 2.586792 CCCTTGCTCCCCTTCTCG 59.413 66.667 0.00 0.00 0.00 4.04
762 766 2.124942 CCTTGCTCCCCTTCTCGC 60.125 66.667 0.00 0.00 0.00 5.03
763 767 2.665000 CTTGCTCCCCTTCTCGCA 59.335 61.111 0.00 0.00 0.00 5.10
764 768 1.743252 CTTGCTCCCCTTCTCGCAC 60.743 63.158 0.00 0.00 31.24 5.34
765 769 3.589654 TTGCTCCCCTTCTCGCACG 62.590 63.158 0.00 0.00 31.24 5.34
767 771 4.821589 CTCCCCTTCTCGCACGCC 62.822 72.222 0.00 0.00 0.00 5.68
778 782 4.101448 GCACGCCCCACCATCTCT 62.101 66.667 0.00 0.00 0.00 3.10
779 783 2.671070 CACGCCCCACCATCTCTT 59.329 61.111 0.00 0.00 0.00 2.85
780 784 1.002134 CACGCCCCACCATCTCTTT 60.002 57.895 0.00 0.00 0.00 2.52
781 785 1.026718 CACGCCCCACCATCTCTTTC 61.027 60.000 0.00 0.00 0.00 2.62
782 786 1.815421 CGCCCCACCATCTCTTTCG 60.815 63.158 0.00 0.00 0.00 3.46
783 787 2.115291 GCCCCACCATCTCTTTCGC 61.115 63.158 0.00 0.00 0.00 4.70
784 788 1.604378 CCCCACCATCTCTTTCGCT 59.396 57.895 0.00 0.00 0.00 4.93
785 789 0.462759 CCCCACCATCTCTTTCGCTC 60.463 60.000 0.00 0.00 0.00 5.03
786 790 0.807667 CCCACCATCTCTTTCGCTCG 60.808 60.000 0.00 0.00 0.00 5.03
787 791 0.173481 CCACCATCTCTTTCGCTCGA 59.827 55.000 0.00 0.00 0.00 4.04
788 792 1.272781 CACCATCTCTTTCGCTCGAC 58.727 55.000 0.00 0.00 0.00 4.20
789 793 1.135257 CACCATCTCTTTCGCTCGACT 60.135 52.381 0.00 0.00 0.00 4.18
790 794 1.135257 ACCATCTCTTTCGCTCGACTG 60.135 52.381 0.00 0.00 0.00 3.51
791 795 1.554392 CATCTCTTTCGCTCGACTGG 58.446 55.000 0.00 0.00 0.00 4.00
792 796 0.457851 ATCTCTTTCGCTCGACTGGG 59.542 55.000 0.00 0.00 0.00 4.45
793 797 1.807573 CTCTTTCGCTCGACTGGGC 60.808 63.158 0.00 0.00 0.00 5.36
794 798 2.815647 CTTTCGCTCGACTGGGCC 60.816 66.667 0.00 0.00 0.00 5.80
795 799 4.735132 TTTCGCTCGACTGGGCCG 62.735 66.667 0.00 0.00 0.00 6.13
802 806 4.530857 CGACTGGGCCGTGGGATC 62.531 72.222 5.76 0.00 0.00 3.36
803 807 3.083997 GACTGGGCCGTGGGATCT 61.084 66.667 5.76 0.00 0.00 2.75
804 808 3.391665 GACTGGGCCGTGGGATCTG 62.392 68.421 5.76 0.00 0.00 2.90
805 809 3.083349 CTGGGCCGTGGGATCTGA 61.083 66.667 0.00 0.00 0.00 3.27
806 810 3.391665 CTGGGCCGTGGGATCTGAC 62.392 68.421 0.00 0.00 0.00 3.51
807 811 4.530857 GGGCCGTGGGATCTGACG 62.531 72.222 0.00 9.31 35.31 4.35
808 812 3.458163 GGCCGTGGGATCTGACGA 61.458 66.667 15.73 0.00 37.81 4.20
809 813 2.577059 GCCGTGGGATCTGACGAA 59.423 61.111 15.73 0.00 37.81 3.85
810 814 1.519455 GCCGTGGGATCTGACGAAG 60.519 63.158 15.73 4.52 37.81 3.79
811 815 1.945354 GCCGTGGGATCTGACGAAGA 61.945 60.000 15.73 0.00 37.81 2.87
812 816 0.101399 CCGTGGGATCTGACGAAGAG 59.899 60.000 15.73 0.00 38.67 2.85
813 817 0.526524 CGTGGGATCTGACGAAGAGC 60.527 60.000 10.41 0.00 40.80 4.09
814 818 0.526524 GTGGGATCTGACGAAGAGCG 60.527 60.000 0.00 0.00 42.55 5.03
815 819 0.679960 TGGGATCTGACGAAGAGCGA 60.680 55.000 0.00 0.00 42.55 4.93
816 820 0.248702 GGGATCTGACGAAGAGCGAC 60.249 60.000 0.00 0.00 42.55 5.19
817 821 0.248702 GGATCTGACGAAGAGCGACC 60.249 60.000 0.00 0.00 42.55 4.79
818 822 0.590230 GATCTGACGAAGAGCGACCG 60.590 60.000 0.00 0.00 44.57 4.79
819 823 2.600122 ATCTGACGAAGAGCGACCGC 62.600 60.000 6.25 6.25 44.57 5.68
820 824 4.415332 TGACGAAGAGCGACCGCC 62.415 66.667 11.03 2.97 44.57 6.13
821 825 4.415332 GACGAAGAGCGACCGCCA 62.415 66.667 11.03 0.00 44.57 5.69
822 826 4.421479 ACGAAGAGCGACCGCCAG 62.421 66.667 11.03 1.29 44.57 4.85
824 828 4.821589 GAAGAGCGACCGCCAGGG 62.822 72.222 11.03 0.00 43.47 4.45
836 840 2.851102 CCAGGGGAGGGATGCGAT 60.851 66.667 0.00 0.00 0.00 4.58
837 841 2.429058 CAGGGGAGGGATGCGATG 59.571 66.667 0.00 0.00 0.00 3.84
838 842 2.851102 AGGGGAGGGATGCGATGG 60.851 66.667 0.00 0.00 0.00 3.51
839 843 3.958860 GGGGAGGGATGCGATGGG 61.959 72.222 0.00 0.00 0.00 4.00
840 844 3.958860 GGGAGGGATGCGATGGGG 61.959 72.222 0.00 0.00 0.00 4.96
841 845 4.650377 GGAGGGATGCGATGGGGC 62.650 72.222 0.00 0.00 0.00 5.80
842 846 4.996434 GAGGGATGCGATGGGGCG 62.996 72.222 0.00 0.00 35.06 6.13
1032 1036 7.865889 CAGCTCTTGGAATATACGTATGTACAA 59.134 37.037 18.37 16.09 32.26 2.41
1925 2013 6.903883 AAGTACTGGTGCTGATAAATTACG 57.096 37.500 0.00 0.00 0.00 3.18
2084 2172 3.935828 AGCGGAAAATAGAGCTTCTCAAC 59.064 43.478 0.00 0.00 36.41 3.18
2406 2514 4.672542 GCGCTTCATGCTTGTATTGAAGAA 60.673 41.667 14.28 0.00 45.88 2.52
2630 2760 4.418392 GTTTGATCTCACACATGAATGCC 58.582 43.478 0.00 0.00 33.30 4.40
2772 2924 2.107204 CAAGGGATGGGGATCTTACCAG 59.893 54.545 9.53 0.00 40.67 4.00
2885 3037 8.442632 TCATCAATAACTATTCTGGAAGCAAG 57.557 34.615 0.00 0.00 0.00 4.01
2913 3065 5.407995 GGATGAGTCACAAGATATTGCTAGC 59.592 44.000 8.10 8.10 0.00 3.42
3358 3530 6.478344 CACTGCTTTATAACTCTAGAAGCCTG 59.522 42.308 7.65 4.22 41.40 4.85
3359 3531 5.360591 TGCTTTATAACTCTAGAAGCCTGC 58.639 41.667 7.65 0.43 41.40 4.85
3360 3532 4.752604 GCTTTATAACTCTAGAAGCCTGCC 59.247 45.833 0.00 0.00 37.37 4.85
3361 3533 5.454045 GCTTTATAACTCTAGAAGCCTGCCT 60.454 44.000 0.00 0.00 37.37 4.75
3456 7454 7.726216 TCTAACTCAACTTTGATGTCAGAAGA 58.274 34.615 10.03 0.00 36.46 2.87
3631 7655 2.812011 GGGAGAAACAACATAAGCACGT 59.188 45.455 0.00 0.00 0.00 4.49
3649 7673 1.149627 TTACACACCACACCAGGGC 59.850 57.895 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.533308 TTGTGGTAGTTGCCGGTGAC 60.533 55.000 1.90 1.72 0.00 3.67
7 8 1.512156 GGTTGTGGTAGTTGCCGGTG 61.512 60.000 1.90 0.00 0.00 4.94
8 9 1.228033 GGTTGTGGTAGTTGCCGGT 60.228 57.895 1.90 0.00 0.00 5.28
9 10 2.322081 CGGTTGTGGTAGTTGCCGG 61.322 63.158 0.00 0.00 36.05 6.13
10 11 2.961669 GCGGTTGTGGTAGTTGCCG 61.962 63.158 0.00 0.00 41.79 5.69
11 12 1.599797 AGCGGTTGTGGTAGTTGCC 60.600 57.895 0.00 0.00 0.00 4.52
12 13 1.574428 CAGCGGTTGTGGTAGTTGC 59.426 57.895 0.00 0.00 0.00 4.17
13 14 1.574428 GCAGCGGTTGTGGTAGTTG 59.426 57.895 0.00 0.00 0.00 3.16
14 15 1.599797 GGCAGCGGTTGTGGTAGTT 60.600 57.895 0.00 0.00 0.00 2.24
16 17 1.741770 GAGGCAGCGGTTGTGGTAG 60.742 63.158 0.00 0.00 0.00 3.18
17 18 1.764571 AAGAGGCAGCGGTTGTGGTA 61.765 55.000 0.00 0.00 0.00 3.25
18 19 3.120086 AAGAGGCAGCGGTTGTGGT 62.120 57.895 0.00 0.00 0.00 4.16
19 20 2.281761 AAGAGGCAGCGGTTGTGG 60.282 61.111 0.00 0.00 0.00 4.17
20 21 2.328099 GGAAGAGGCAGCGGTTGTG 61.328 63.158 0.00 0.00 0.00 3.33
21 22 2.032681 GGAAGAGGCAGCGGTTGT 59.967 61.111 0.00 0.00 0.00 3.32
22 23 1.743252 GAGGAAGAGGCAGCGGTTG 60.743 63.158 0.00 0.00 0.00 3.77
23 24 2.665603 GAGGAAGAGGCAGCGGTT 59.334 61.111 0.00 0.00 0.00 4.44
24 25 2.516048 TAGGAGGAAGAGGCAGCGGT 62.516 60.000 0.00 0.00 0.00 5.68
25 26 1.330655 TTAGGAGGAAGAGGCAGCGG 61.331 60.000 0.00 0.00 0.00 5.52
26 27 0.537188 TTTAGGAGGAAGAGGCAGCG 59.463 55.000 0.00 0.00 0.00 5.18
27 28 2.789409 TTTTAGGAGGAAGAGGCAGC 57.211 50.000 0.00 0.00 0.00 5.25
97 99 4.629442 CCCTAGGGCTACCAGAGG 57.371 66.667 16.90 0.00 40.27 3.69
198 200 5.187967 ACCATTTCGTCTTCCTGAGTAGAAT 59.812 40.000 0.00 0.00 0.00 2.40
203 207 2.289694 CCACCATTTCGTCTTCCTGAGT 60.290 50.000 0.00 0.00 0.00 3.41
219 223 1.600636 CTTCAGAAAGCCGCCACCA 60.601 57.895 0.00 0.00 0.00 4.17
222 226 0.677731 CCATCTTCAGAAAGCCGCCA 60.678 55.000 0.00 0.00 32.18 5.69
263 267 3.948719 GCACCACTGGAACGGGGA 61.949 66.667 0.71 0.00 44.03 4.81
421 425 1.943968 GCACCAGAACAGTAATCGCCA 60.944 52.381 0.00 0.00 0.00 5.69
429 433 0.179045 GACCAGTGCACCAGAACAGT 60.179 55.000 14.63 0.24 0.00 3.55
461 465 3.289062 TCGGGAAGTCGTCGTGCA 61.289 61.111 0.00 0.00 0.00 4.57
483 487 2.352617 CGGGCACAATTTGTTGCAGTAT 60.353 45.455 18.83 0.00 0.00 2.12
488 492 0.031994 AGTCGGGCACAATTTGTTGC 59.968 50.000 0.00 7.27 0.00 4.17
495 499 1.079819 CGTCAGAGTCGGGCACAAT 60.080 57.895 0.00 0.00 0.00 2.71
564 568 1.674441 CATAGACCACCTAGCGACGAA 59.326 52.381 0.00 0.00 0.00 3.85
603 607 9.430623 GGCAGTACAACAAATACCAAAAATAAT 57.569 29.630 0.00 0.00 0.00 1.28
604 608 8.421784 TGGCAGTACAACAAATACCAAAAATAA 58.578 29.630 0.00 0.00 0.00 1.40
605 609 7.952671 TGGCAGTACAACAAATACCAAAAATA 58.047 30.769 0.00 0.00 0.00 1.40
606 610 6.821388 TGGCAGTACAACAAATACCAAAAAT 58.179 32.000 0.00 0.00 0.00 1.82
607 611 6.222038 TGGCAGTACAACAAATACCAAAAA 57.778 33.333 0.00 0.00 0.00 1.94
608 612 5.854010 TGGCAGTACAACAAATACCAAAA 57.146 34.783 0.00 0.00 0.00 2.44
609 613 5.536538 TCATGGCAGTACAACAAATACCAAA 59.463 36.000 0.00 0.00 0.00 3.28
610 614 5.073428 TCATGGCAGTACAACAAATACCAA 58.927 37.500 0.00 0.00 0.00 3.67
611 615 4.657013 TCATGGCAGTACAACAAATACCA 58.343 39.130 0.00 0.00 0.00 3.25
612 616 5.835113 ATCATGGCAGTACAACAAATACC 57.165 39.130 0.00 0.00 0.00 2.73
613 617 6.851609 TCAATCATGGCAGTACAACAAATAC 58.148 36.000 0.00 0.00 0.00 1.89
614 618 7.392953 TCTTCAATCATGGCAGTACAACAAATA 59.607 33.333 0.00 0.00 0.00 1.40
615 619 5.981088 TCAATCATGGCAGTACAACAAAT 57.019 34.783 0.00 0.00 0.00 2.32
616 620 5.534278 TCTTCAATCATGGCAGTACAACAAA 59.466 36.000 0.00 0.00 0.00 2.83
617 621 5.069318 TCTTCAATCATGGCAGTACAACAA 58.931 37.500 0.00 0.00 0.00 2.83
618 622 4.650734 TCTTCAATCATGGCAGTACAACA 58.349 39.130 0.00 0.00 0.00 3.33
619 623 5.355071 TCATCTTCAATCATGGCAGTACAAC 59.645 40.000 0.00 0.00 0.00 3.32
620 624 5.499313 TCATCTTCAATCATGGCAGTACAA 58.501 37.500 0.00 0.00 0.00 2.41
621 625 5.101648 TCATCTTCAATCATGGCAGTACA 57.898 39.130 0.00 0.00 0.00 2.90
622 626 6.630444 ATTCATCTTCAATCATGGCAGTAC 57.370 37.500 0.00 0.00 0.00 2.73
623 627 6.829811 TCAATTCATCTTCAATCATGGCAGTA 59.170 34.615 0.00 0.00 0.00 2.74
624 628 5.655090 TCAATTCATCTTCAATCATGGCAGT 59.345 36.000 0.00 0.00 0.00 4.40
625 629 6.144078 TCAATTCATCTTCAATCATGGCAG 57.856 37.500 0.00 0.00 0.00 4.85
626 630 6.514376 CGATCAATTCATCTTCAATCATGGCA 60.514 38.462 0.00 0.00 0.00 4.92
627 631 5.856986 CGATCAATTCATCTTCAATCATGGC 59.143 40.000 0.00 0.00 0.00 4.40
628 632 6.206048 TCCGATCAATTCATCTTCAATCATGG 59.794 38.462 0.00 0.00 0.00 3.66
629 633 7.198306 TCCGATCAATTCATCTTCAATCATG 57.802 36.000 0.00 0.00 0.00 3.07
630 634 7.718314 TCTTCCGATCAATTCATCTTCAATCAT 59.282 33.333 0.00 0.00 0.00 2.45
631 635 7.049754 TCTTCCGATCAATTCATCTTCAATCA 58.950 34.615 0.00 0.00 0.00 2.57
632 636 7.488187 TCTTCCGATCAATTCATCTTCAATC 57.512 36.000 0.00 0.00 0.00 2.67
633 637 8.461249 AATCTTCCGATCAATTCATCTTCAAT 57.539 30.769 0.00 0.00 0.00 2.57
634 638 7.870509 AATCTTCCGATCAATTCATCTTCAA 57.129 32.000 0.00 0.00 0.00 2.69
635 639 7.012704 GGAAATCTTCCGATCAATTCATCTTCA 59.987 37.037 0.00 0.00 40.59 3.02
636 640 7.358830 GGAAATCTTCCGATCAATTCATCTTC 58.641 38.462 0.00 0.00 40.59 2.87
637 641 7.269477 GGAAATCTTCCGATCAATTCATCTT 57.731 36.000 0.00 0.00 40.59 2.40
638 642 6.874288 GGAAATCTTCCGATCAATTCATCT 57.126 37.500 0.00 0.00 40.59 2.90
668 672 1.883926 GGTGCCGGTGTCATAGTTTTT 59.116 47.619 1.90 0.00 0.00 1.94
669 673 1.530323 GGTGCCGGTGTCATAGTTTT 58.470 50.000 1.90 0.00 0.00 2.43
670 674 0.672401 CGGTGCCGGTGTCATAGTTT 60.672 55.000 1.90 0.00 35.56 2.66
671 675 1.079405 CGGTGCCGGTGTCATAGTT 60.079 57.895 1.90 0.00 35.56 2.24
672 676 2.577059 CGGTGCCGGTGTCATAGT 59.423 61.111 1.90 0.00 35.56 2.12
711 715 4.704833 CCAGTCACCAGGTGGCGG 62.705 72.222 18.81 17.80 43.57 6.13
712 716 4.704833 CCCAGTCACCAGGTGGCG 62.705 72.222 18.81 13.04 43.57 5.69
713 717 4.351054 CCCCAGTCACCAGGTGGC 62.351 72.222 17.25 17.25 38.58 5.01
714 718 4.351054 GCCCCAGTCACCAGGTGG 62.351 72.222 20.14 3.07 42.17 4.61
715 719 4.704833 CGCCCCAGTCACCAGGTG 62.705 72.222 14.19 14.19 34.45 4.00
743 747 2.273776 GAGAAGGGGAGCAAGGGC 59.726 66.667 0.00 0.00 41.61 5.19
744 748 2.586792 CGAGAAGGGGAGCAAGGG 59.413 66.667 0.00 0.00 0.00 3.95
745 749 2.124942 GCGAGAAGGGGAGCAAGG 60.125 66.667 0.00 0.00 0.00 3.61
746 750 1.743252 GTGCGAGAAGGGGAGCAAG 60.743 63.158 0.00 0.00 41.56 4.01
747 751 2.347490 GTGCGAGAAGGGGAGCAA 59.653 61.111 0.00 0.00 41.56 3.91
748 752 4.069232 CGTGCGAGAAGGGGAGCA 62.069 66.667 0.00 0.00 37.26 4.26
750 754 4.821589 GGCGTGCGAGAAGGGGAG 62.822 72.222 0.00 0.00 0.00 4.30
761 765 3.628646 AAGAGATGGTGGGGCGTGC 62.629 63.158 0.00 0.00 0.00 5.34
762 766 1.002134 AAAGAGATGGTGGGGCGTG 60.002 57.895 0.00 0.00 0.00 5.34
763 767 1.299976 GAAAGAGATGGTGGGGCGT 59.700 57.895 0.00 0.00 0.00 5.68
764 768 1.815421 CGAAAGAGATGGTGGGGCG 60.815 63.158 0.00 0.00 0.00 6.13
765 769 2.115291 GCGAAAGAGATGGTGGGGC 61.115 63.158 0.00 0.00 0.00 5.80
766 770 0.462759 GAGCGAAAGAGATGGTGGGG 60.463 60.000 0.00 0.00 0.00 4.96
767 771 0.807667 CGAGCGAAAGAGATGGTGGG 60.808 60.000 0.00 0.00 0.00 4.61
768 772 0.173481 TCGAGCGAAAGAGATGGTGG 59.827 55.000 0.00 0.00 0.00 4.61
769 773 1.135257 AGTCGAGCGAAAGAGATGGTG 60.135 52.381 0.00 0.00 0.00 4.17
770 774 1.135257 CAGTCGAGCGAAAGAGATGGT 60.135 52.381 0.00 0.00 0.00 3.55
771 775 1.554392 CAGTCGAGCGAAAGAGATGG 58.446 55.000 0.00 0.00 0.00 3.51
772 776 1.554392 CCAGTCGAGCGAAAGAGATG 58.446 55.000 0.00 0.00 0.00 2.90
773 777 0.457851 CCCAGTCGAGCGAAAGAGAT 59.542 55.000 0.00 0.00 0.00 2.75
774 778 1.883732 CCCAGTCGAGCGAAAGAGA 59.116 57.895 0.00 0.00 0.00 3.10
775 779 1.807573 GCCCAGTCGAGCGAAAGAG 60.808 63.158 0.00 0.00 0.00 2.85
776 780 2.261671 GCCCAGTCGAGCGAAAGA 59.738 61.111 0.00 0.00 0.00 2.52
777 781 2.815647 GGCCCAGTCGAGCGAAAG 60.816 66.667 0.00 0.00 0.00 2.62
778 782 4.735132 CGGCCCAGTCGAGCGAAA 62.735 66.667 0.00 0.00 29.41 3.46
785 789 4.530857 GATCCCACGGCCCAGTCG 62.531 72.222 0.00 0.00 36.42 4.18
786 790 3.083997 AGATCCCACGGCCCAGTC 61.084 66.667 0.00 0.00 0.00 3.51
787 791 3.402681 CAGATCCCACGGCCCAGT 61.403 66.667 0.00 0.00 0.00 4.00
788 792 3.083349 TCAGATCCCACGGCCCAG 61.083 66.667 0.00 0.00 0.00 4.45
789 793 3.399181 GTCAGATCCCACGGCCCA 61.399 66.667 0.00 0.00 0.00 5.36
790 794 4.530857 CGTCAGATCCCACGGCCC 62.531 72.222 0.00 0.00 32.19 5.80
791 795 2.907897 CTTCGTCAGATCCCACGGCC 62.908 65.000 12.71 0.00 36.64 6.13
792 796 1.519455 CTTCGTCAGATCCCACGGC 60.519 63.158 12.71 0.00 36.64 5.68
793 797 0.101399 CTCTTCGTCAGATCCCACGG 59.899 60.000 12.71 0.54 36.64 4.94
794 798 0.526524 GCTCTTCGTCAGATCCCACG 60.527 60.000 7.56 7.56 37.36 4.94
795 799 0.526524 CGCTCTTCGTCAGATCCCAC 60.527 60.000 0.00 0.00 0.00 4.61
796 800 0.679960 TCGCTCTTCGTCAGATCCCA 60.680 55.000 0.00 0.00 39.67 4.37
797 801 0.248702 GTCGCTCTTCGTCAGATCCC 60.249 60.000 0.00 0.00 39.67 3.85
798 802 0.248702 GGTCGCTCTTCGTCAGATCC 60.249 60.000 0.00 0.00 39.67 3.36
799 803 0.590230 CGGTCGCTCTTCGTCAGATC 60.590 60.000 0.00 0.00 39.67 2.75
800 804 1.429825 CGGTCGCTCTTCGTCAGAT 59.570 57.895 0.00 0.00 39.67 2.90
801 805 2.868196 CGGTCGCTCTTCGTCAGA 59.132 61.111 0.00 0.00 39.67 3.27
802 806 2.876645 GCGGTCGCTCTTCGTCAG 60.877 66.667 8.20 0.00 39.67 3.51
803 807 4.415332 GGCGGTCGCTCTTCGTCA 62.415 66.667 15.04 0.00 41.60 4.35
804 808 4.415332 TGGCGGTCGCTCTTCGTC 62.415 66.667 15.04 0.00 41.60 4.20
805 809 4.421479 CTGGCGGTCGCTCTTCGT 62.421 66.667 15.04 0.00 41.60 3.85
807 811 4.821589 CCCTGGCGGTCGCTCTTC 62.822 72.222 15.04 0.00 41.60 2.87
819 823 2.851102 ATCGCATCCCTCCCCTGG 60.851 66.667 0.00 0.00 0.00 4.45
820 824 2.429058 CATCGCATCCCTCCCCTG 59.571 66.667 0.00 0.00 0.00 4.45
821 825 2.851102 CCATCGCATCCCTCCCCT 60.851 66.667 0.00 0.00 0.00 4.79
822 826 3.958860 CCCATCGCATCCCTCCCC 61.959 72.222 0.00 0.00 0.00 4.81
823 827 3.958860 CCCCATCGCATCCCTCCC 61.959 72.222 0.00 0.00 0.00 4.30
824 828 4.650377 GCCCCATCGCATCCCTCC 62.650 72.222 0.00 0.00 0.00 4.30
825 829 4.996434 CGCCCCATCGCATCCCTC 62.996 72.222 0.00 0.00 0.00 4.30
840 844 4.426313 CTTCCCTTCCCACCCCGC 62.426 72.222 0.00 0.00 0.00 6.13
841 845 3.728373 CCTTCCCTTCCCACCCCG 61.728 72.222 0.00 0.00 0.00 5.73
842 846 3.347590 CCCTTCCCTTCCCACCCC 61.348 72.222 0.00 0.00 0.00 4.95
843 847 2.204244 TCCCTTCCCTTCCCACCC 60.204 66.667 0.00 0.00 0.00 4.61
844 848 2.309504 CCTCCCTTCCCTTCCCACC 61.310 68.421 0.00 0.00 0.00 4.61
1032 1036 0.902516 AGCGCTTCTCCTTCTCAGGT 60.903 55.000 2.64 0.00 41.69 4.00
1925 2013 3.077359 CAACATCTTCCTCACCACCTTC 58.923 50.000 0.00 0.00 0.00 3.46
2084 2172 1.201181 TCCAAATTTCAATCGGGCGTG 59.799 47.619 0.00 0.00 0.00 5.34
2406 2514 9.768215 TCTGGGTGAAAAAGAAAGGATAATTAT 57.232 29.630 0.00 0.00 0.00 1.28
2885 3037 5.407995 GCAATATCTTGTGACTCATCCTAGC 59.592 44.000 0.00 0.00 34.69 3.42
2913 3065 6.761099 ATATATACTTACCAGCAGAGACGG 57.239 41.667 0.00 0.00 0.00 4.79
3456 7454 6.092122 TGCGACGAAAATCAGAGTTTATCATT 59.908 34.615 0.00 0.00 0.00 2.57
3545 7543 8.153550 ACACTGTTCAGAAGTTCTTATTCTCAT 58.846 33.333 1.56 0.00 34.80 2.90
3631 7655 1.149627 GCCCTGGTGTGGTGTGTAA 59.850 57.895 0.00 0.00 0.00 2.41
3649 7673 3.939066 ACCCTATTTCTCAGTTTCCACG 58.061 45.455 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.