Multiple sequence alignment - TraesCS5B01G512700

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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 TraesCS5B01G512700 chr5B 100.000 3470 0 0 1 3470 677811039 677814508 0.000000e+00 6408
1 TraesCS5B01G512700 chr5B 89.810 1423 96 16 1509 2908 677751024 677749628 0.000000e+00 1779
2 TraesCS5B01G512700 chr5B 81.197 1755 262 40 1562 3302 699437470 699439170 0.000000e+00 1351
3 TraesCS5B01G512700 chr5B 79.421 1623 270 41 976 2569 699415077 699416664 0.000000e+00 1088
4 TraesCS5B01G512700 chr5B 80.280 1359 237 21 1022 2370 703634128 703635465 0.000000e+00 996
5 TraesCS5B01G512700 chr5B 79.012 1477 234 38 967 2420 685257229 685255806 0.000000e+00 941
6 TraesCS5B01G512700 chr5B 80.389 1285 197 25 1311 2569 703523257 703524512 0.000000e+00 926
7 TraesCS5B01G512700 chr5B 80.431 1160 190 22 1310 2450 699998180 699999321 0.000000e+00 850
8 TraesCS5B01G512700 chr5B 75.962 1560 323 31 957 2500 685499442 685500965 0.000000e+00 756
9 TraesCS5B01G512700 chr5B 83.655 777 79 18 2568 3327 699274790 699275535 0.000000e+00 688
10 TraesCS5B01G512700 chr5B 79.850 933 108 35 2568 3470 699999332 700000214 2.960000e-170 608
11 TraesCS5B01G512700 chr5B 91.691 349 20 6 3127 3470 677749479 677749135 3.130000e-130 475
12 TraesCS5B01G512700 chr5B 76.966 890 165 28 1693 2570 699433036 699433897 4.050000e-129 472
13 TraesCS5B01G512700 chr5B 76.911 628 101 26 1018 1627 685543835 685544436 2.010000e-82 316
14 TraesCS5B01G512700 chr5B 83.860 285 37 9 2568 2851 703524449 703524725 2.660000e-66 263
15 TraesCS5B01G512700 chr5B 89.032 155 9 4 2938 3092 677749630 677749484 5.910000e-43 185
16 TraesCS5B01G512700 chr5B 79.352 247 33 14 2572 2817 699433837 699434066 1.290000e-34 158
17 TraesCS5B01G512700 chr5B 98.438 64 1 0 2568 2631 677750046 677749983 2.830000e-21 113
18 TraesCS5B01G512700 chr4A 91.993 1711 89 18 874 2569 632939182 632940859 0.000000e+00 2357
19 TraesCS5B01G512700 chr4A 81.227 1598 247 28 1003 2569 616618706 616617131 0.000000e+00 1240
20 TraesCS5B01G512700 chr4A 79.878 1476 235 32 967 2419 625542252 625543688 0.000000e+00 1024
21 TraesCS5B01G512700 chr4A 82.272 942 146 15 1640 2569 616840051 616839119 0.000000e+00 795
22 TraesCS5B01G512700 chr4A 79.299 1198 199 30 1388 2573 616791310 616790150 0.000000e+00 793
23 TraesCS5B01G512700 chr4A 84.062 778 75 20 2568 3327 616236593 616235847 0.000000e+00 704
24 TraesCS5B01G512700 chr4A 82.496 697 48 27 2568 3251 632940796 632941431 8.470000e-151 544
25 TraesCS5B01G512700 chr4A 85.230 413 44 8 3069 3470 616789800 616789394 3.220000e-110 409
26 TraesCS5B01G512700 chr4A 79.525 547 101 5 997 1533 616840676 616840131 2.530000e-101 379
27 TraesCS5B01G512700 chr4A 93.220 236 13 2 3237 3469 632941486 632941721 9.220000e-91 344
28 TraesCS5B01G512700 chr4A 77.734 503 89 13 1026 1524 616871852 616871369 1.580000e-73 287
29 TraesCS5B01G512700 chr4A 80.353 397 41 20 3069 3461 625544895 625545258 2.050000e-67 267
30 TraesCS5B01G512700 chr4A 76.471 238 39 11 3206 3436 616883870 616883643 2.830000e-21 113
31 TraesCS5B01G512700 chr5D 97.188 1067 19 5 1866 2927 537216838 537217898 0.000000e+00 1794
32 TraesCS5B01G512700 chr5D 91.037 781 63 5 2 779 380087931 380088707 0.000000e+00 1048
33 TraesCS5B01G512700 chr5D 91.744 751 53 7 5 751 512220997 512221742 0.000000e+00 1035
34 TraesCS5B01G512700 chr5D 78.721 1626 280 42 976 2569 551119822 551121413 0.000000e+00 1026
35 TraesCS5B01G512700 chr5D 80.473 1352 209 36 1242 2569 551114355 551115675 0.000000e+00 983
36 TraesCS5B01G512700 chr5D 79.897 1363 219 29 967 2316 543465677 543464357 0.000000e+00 948
37 TraesCS5B01G512700 chr5D 76.463 1623 332 38 957 2556 543508842 543507247 0.000000e+00 835
38 TraesCS5B01G512700 chr5D 97.500 440 8 1 3031 3470 537217898 537218334 0.000000e+00 749
39 TraesCS5B01G512700 chr5D 84.041 777 76 20 2568 3327 552049879 552049134 0.000000e+00 704
40 TraesCS5B01G512700 chr5D 77.471 1194 229 29 993 2172 552422802 552421635 0.000000e+00 678
41 TraesCS5B01G512700 chr5D 80.242 744 84 32 2568 3302 551115612 551116301 5.170000e-138 501
42 TraesCS5B01G512700 chr5D 79.787 658 117 11 966 1619 551611437 551612082 6.780000e-127 464
43 TraesCS5B01G512700 chr5D 84.178 493 56 10 2964 3455 543463950 543463479 3.160000e-125 459
44 TraesCS5B01G512700 chr5D 83.990 381 59 2 977 1356 552405546 552405167 7.080000e-97 364
45 TraesCS5B01G512700 chr5D 75.794 252 39 14 3206 3443 551075957 551076200 1.320000e-19 108
46 TraesCS5B01G512700 chr2D 93.245 755 45 3 5 757 539155722 539154972 0.000000e+00 1107
47 TraesCS5B01G512700 chr2D 92.185 755 51 5 5 757 176586891 176587639 0.000000e+00 1061
48 TraesCS5B01G512700 chr7D 92.084 758 52 5 2 757 504249156 504248405 0.000000e+00 1061
49 TraesCS5B01G512700 chr6D 92.185 755 49 6 5 757 441785551 441784805 0.000000e+00 1059
50 TraesCS5B01G512700 chr4D 91.842 760 53 5 2 759 464369985 464370737 0.000000e+00 1051
51 TraesCS5B01G512700 chr1A 91.899 753 56 3 5 757 561525304 561526051 0.000000e+00 1048
52 TraesCS5B01G512700 chr3D 91.799 756 54 6 5 757 517006900 517006150 0.000000e+00 1046


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 TraesCS5B01G512700 chr5B 677811039 677814508 3469 False 6408.000000 6408 100.000000 1 3470 1 chr5B.!!$F1 3469
1 TraesCS5B01G512700 chr5B 699415077 699416664 1587 False 1088.000000 1088 79.421000 976 2569 1 chr5B.!!$F5 1593
2 TraesCS5B01G512700 chr5B 703634128 703635465 1337 False 996.000000 996 80.280000 1022 2370 1 chr5B.!!$F6 1348
3 TraesCS5B01G512700 chr5B 685255806 685257229 1423 True 941.000000 941 79.012000 967 2420 1 chr5B.!!$R1 1453
4 TraesCS5B01G512700 chr5B 685499442 685500965 1523 False 756.000000 756 75.962000 957 2500 1 chr5B.!!$F2 1543
5 TraesCS5B01G512700 chr5B 699998180 700000214 2034 False 729.000000 850 80.140500 1310 3470 2 chr5B.!!$F8 2160
6 TraesCS5B01G512700 chr5B 699274790 699275535 745 False 688.000000 688 83.655000 2568 3327 1 chr5B.!!$F4 759
7 TraesCS5B01G512700 chr5B 699433036 699439170 6134 False 660.333333 1351 79.171667 1562 3302 3 chr5B.!!$F7 1740
8 TraesCS5B01G512700 chr5B 677749135 677751024 1889 True 638.000000 1779 92.242750 1509 3470 4 chr5B.!!$R2 1961
9 TraesCS5B01G512700 chr5B 703523257 703524725 1468 False 594.500000 926 82.124500 1311 2851 2 chr5B.!!$F9 1540
10 TraesCS5B01G512700 chr5B 685543835 685544436 601 False 316.000000 316 76.911000 1018 1627 1 chr5B.!!$F3 609
11 TraesCS5B01G512700 chr4A 616617131 616618706 1575 True 1240.000000 1240 81.227000 1003 2569 1 chr4A.!!$R2 1566
12 TraesCS5B01G512700 chr4A 632939182 632941721 2539 False 1081.666667 2357 89.236333 874 3469 3 chr4A.!!$F2 2595
13 TraesCS5B01G512700 chr4A 616235847 616236593 746 True 704.000000 704 84.062000 2568 3327 1 chr4A.!!$R1 759
14 TraesCS5B01G512700 chr4A 625542252 625545258 3006 False 645.500000 1024 80.115500 967 3461 2 chr4A.!!$F1 2494
15 TraesCS5B01G512700 chr4A 616789394 616791310 1916 True 601.000000 793 82.264500 1388 3470 2 chr4A.!!$R5 2082
16 TraesCS5B01G512700 chr4A 616839119 616840676 1557 True 587.000000 795 80.898500 997 2569 2 chr4A.!!$R6 1572
17 TraesCS5B01G512700 chr5D 537216838 537218334 1496 False 1271.500000 1794 97.344000 1866 3470 2 chr5D.!!$F5 1604
18 TraesCS5B01G512700 chr5D 380087931 380088707 776 False 1048.000000 1048 91.037000 2 779 1 chr5D.!!$F1 777
19 TraesCS5B01G512700 chr5D 512220997 512221742 745 False 1035.000000 1035 91.744000 5 751 1 chr5D.!!$F2 746
20 TraesCS5B01G512700 chr5D 551114355 551121413 7058 False 836.666667 1026 79.812000 976 3302 3 chr5D.!!$F6 2326
21 TraesCS5B01G512700 chr5D 543507247 543508842 1595 True 835.000000 835 76.463000 957 2556 1 chr5D.!!$R1 1599
22 TraesCS5B01G512700 chr5D 552049134 552049879 745 True 704.000000 704 84.041000 2568 3327 1 chr5D.!!$R2 759
23 TraesCS5B01G512700 chr5D 543463479 543465677 2198 True 703.500000 948 82.037500 967 3455 2 chr5D.!!$R5 2488
24 TraesCS5B01G512700 chr5D 552421635 552422802 1167 True 678.000000 678 77.471000 993 2172 1 chr5D.!!$R4 1179
25 TraesCS5B01G512700 chr5D 551611437 551612082 645 False 464.000000 464 79.787000 966 1619 1 chr5D.!!$F4 653
26 TraesCS5B01G512700 chr2D 539154972 539155722 750 True 1107.000000 1107 93.245000 5 757 1 chr2D.!!$R1 752
27 TraesCS5B01G512700 chr2D 176586891 176587639 748 False 1061.000000 1061 92.185000 5 757 1 chr2D.!!$F1 752
28 TraesCS5B01G512700 chr7D 504248405 504249156 751 True 1061.000000 1061 92.084000 2 757 1 chr7D.!!$R1 755
29 TraesCS5B01G512700 chr6D 441784805 441785551 746 True 1059.000000 1059 92.185000 5 757 1 chr6D.!!$R1 752
30 TraesCS5B01G512700 chr4D 464369985 464370737 752 False 1051.000000 1051 91.842000 2 759 1 chr4D.!!$F1 757
31 TraesCS5B01G512700 chr1A 561525304 561526051 747 False 1048.000000 1048 91.899000 5 757 1 chr1A.!!$F1 752
32 TraesCS5B01G512700 chr3D 517006150 517006900 750 True 1046.000000 1046 91.799000 5 757 1 chr3D.!!$R1 752

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
787 799 0.035725 TGGCTGTTGGAGATGCTCTG 60.036 55.0 0.0 0.0 0.0 3.35 F
803 815 0.041238 TCTGAGGGACGGTTGGAGAT 59.959 55.0 0.0 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 7855 0.542702 AACCCCAAACTGCCATCCTG 60.543 55.0 0.0 0.0 0.00 3.86 R
2564 8653 0.603707 CTTGTCGCCTCCAAGCTGAA 60.604 55.0 0.0 0.0 33.55 3.02 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
142 143 1.852965 CTCCTTCCTCCTCTCCTCTCT 59.147 57.143 0.00 0.00 0.00 3.10
186 187 4.482386 CGAAGAACTGTTCCTCGTTGATA 58.518 43.478 25.60 0.00 38.47 2.15
213 214 2.044946 GGGAAGCGTTGCCTCCAT 60.045 61.111 8.57 0.00 40.65 3.41
687 695 4.676951 CTGCCGCCTTTTCCCCCA 62.677 66.667 0.00 0.00 0.00 4.96
688 696 4.676951 TGCCGCCTTTTCCCCCAG 62.677 66.667 0.00 0.00 0.00 4.45
713 723 3.993376 AATCGTTTCCCGCGCGCTA 62.993 57.895 30.48 11.81 36.19 4.26
714 724 3.993376 ATCGTTTCCCGCGCGCTAA 62.993 57.895 30.48 17.74 36.19 3.09
715 725 4.494400 CGTTTCCCGCGCGCTAAC 62.494 66.667 30.48 23.84 0.00 2.34
718 730 1.962306 TTTCCCGCGCGCTAACTTT 60.962 52.632 30.48 0.00 0.00 2.66
778 790 1.464734 TTTTTGACGTGGCTGTTGGA 58.535 45.000 0.00 0.00 0.00 3.53
783 795 1.639298 GACGTGGCTGTTGGAGATGC 61.639 60.000 0.00 0.00 0.00 3.91
784 796 1.376424 CGTGGCTGTTGGAGATGCT 60.376 57.895 0.00 0.00 0.00 3.79
785 797 1.364626 CGTGGCTGTTGGAGATGCTC 61.365 60.000 0.00 0.00 0.00 4.26
787 799 0.035725 TGGCTGTTGGAGATGCTCTG 60.036 55.000 0.00 0.00 0.00 3.35
788 800 0.251354 GGCTGTTGGAGATGCTCTGA 59.749 55.000 0.00 0.00 0.00 3.27
792 804 1.198713 GTTGGAGATGCTCTGAGGGA 58.801 55.000 6.83 0.00 0.00 4.20
793 805 1.134551 GTTGGAGATGCTCTGAGGGAC 60.135 57.143 6.83 0.00 0.00 4.46
795 807 1.739049 GAGATGCTCTGAGGGACGG 59.261 63.158 6.83 0.00 0.00 4.79
796 808 1.000993 AGATGCTCTGAGGGACGGT 59.999 57.895 6.83 0.00 0.00 4.83
799 811 1.903877 ATGCTCTGAGGGACGGTTGG 61.904 60.000 6.83 0.00 0.00 3.77
800 812 2.283529 GCTCTGAGGGACGGTTGGA 61.284 63.158 6.83 0.00 0.00 3.53
803 815 0.041238 TCTGAGGGACGGTTGGAGAT 59.959 55.000 0.00 0.00 0.00 2.75
805 817 1.153349 GAGGGACGGTTGGAGATGC 60.153 63.158 0.00 0.00 0.00 3.91
806 818 1.613630 AGGGACGGTTGGAGATGCT 60.614 57.895 0.00 0.00 0.00 3.79
808 820 1.617947 GGGACGGTTGGAGATGCTCT 61.618 60.000 0.00 0.00 0.00 4.09
810 822 1.480954 GGACGGTTGGAGATGCTCTAA 59.519 52.381 0.00 0.00 0.00 2.10
811 823 2.541556 GACGGTTGGAGATGCTCTAAC 58.458 52.381 13.26 13.26 46.44 2.34
817 829 3.247006 TGGAGATGCTCTAACGAAACC 57.753 47.619 0.00 0.00 0.00 3.27
818 830 2.093658 TGGAGATGCTCTAACGAAACCC 60.094 50.000 0.00 0.00 0.00 4.11
820 832 3.596214 GAGATGCTCTAACGAAACCCAA 58.404 45.455 0.00 0.00 0.00 4.12
822 834 1.519408 TGCTCTAACGAAACCCAAGC 58.481 50.000 0.00 0.00 0.00 4.01
826 838 2.678336 CTCTAACGAAACCCAAGCATCC 59.322 50.000 0.00 0.00 0.00 3.51
828 840 1.698506 AACGAAACCCAAGCATCCAA 58.301 45.000 0.00 0.00 0.00 3.53
833 845 1.538687 AACCCAAGCATCCAAGCAGC 61.539 55.000 0.00 0.00 36.85 5.25
835 847 1.214589 CCAAGCATCCAAGCAGCAC 59.785 57.895 0.00 0.00 36.85 4.40
836 848 1.529152 CCAAGCATCCAAGCAGCACA 61.529 55.000 0.00 0.00 36.85 4.57
837 849 0.315886 CAAGCATCCAAGCAGCACAA 59.684 50.000 0.00 0.00 36.85 3.33
838 850 1.042229 AAGCATCCAAGCAGCACAAA 58.958 45.000 0.00 0.00 36.85 2.83
841 853 2.827322 AGCATCCAAGCAGCACAAATTA 59.173 40.909 0.00 0.00 36.85 1.40
843 855 3.184541 CATCCAAGCAGCACAAATTAGC 58.815 45.455 0.00 0.00 0.00 3.09
844 856 1.545582 TCCAAGCAGCACAAATTAGCC 59.454 47.619 0.00 0.00 0.00 3.93
846 858 0.109132 AAGCAGCACAAATTAGCCGC 60.109 50.000 0.00 0.00 34.48 6.53
848 860 1.226379 CAGCACAAATTAGCCGCCG 60.226 57.895 0.00 0.00 0.00 6.46
904 916 4.629523 TGTCGGAAACCCCACGCC 62.630 66.667 0.00 0.00 34.14 5.68
989 5482 4.530857 CCCGAAATCCTCGCCGCT 62.531 66.667 0.00 0.00 46.71 5.52
1031 5527 4.530857 GCCGGTACCATCGCTGCT 62.531 66.667 13.54 0.00 0.00 4.24
1256 5763 3.048602 CGTCCCGGACTTCACACT 58.951 61.111 15.70 0.00 0.00 3.55
1370 5892 1.305930 GGGGACGAGAACATGTTGCC 61.306 60.000 17.58 6.11 0.00 4.52
1372 5894 0.605319 GGACGAGAACATGTTGCCCA 60.605 55.000 17.58 0.00 0.00 5.36
1376 5898 0.099436 GAGAACATGTTGCCCATCGC 59.901 55.000 17.58 0.00 38.31 4.58
1380 5902 2.824041 ATGTTGCCCATCGCGGTC 60.824 61.111 6.13 0.00 42.08 4.79
1389 5911 4.175489 ATCGCGGTCGTCGTCTGG 62.175 66.667 6.13 0.00 41.72 3.86
1393 5915 4.112341 CGGTCGTCGTCTGGGACC 62.112 72.222 0.00 0.00 45.34 4.46
1426 5948 4.475135 GGAAGGACCTGCCGGAGC 62.475 72.222 5.05 0.00 43.43 4.70
1427 5949 4.475135 GAAGGACCTGCCGGAGCC 62.475 72.222 5.05 1.77 43.43 4.70
1440 5962 1.516423 GGAGCCCGACCTAGTGAAC 59.484 63.158 0.00 0.00 0.00 3.18
1441 5963 1.139095 GAGCCCGACCTAGTGAACG 59.861 63.158 0.00 0.00 0.00 3.95
1447 5969 0.522180 CGACCTAGTGAACGACAGCT 59.478 55.000 0.00 0.00 0.00 4.24
1448 5970 1.736126 CGACCTAGTGAACGACAGCTA 59.264 52.381 0.00 0.00 0.00 3.32
1449 5971 2.355132 CGACCTAGTGAACGACAGCTAT 59.645 50.000 0.00 0.00 0.00 2.97
1451 5973 2.427453 ACCTAGTGAACGACAGCTATGG 59.573 50.000 0.00 0.00 0.00 2.74
1455 5977 1.523938 GAACGACAGCTATGGGGCC 60.524 63.158 0.00 0.00 0.00 5.80
1456 5978 3.385749 AACGACAGCTATGGGGCCG 62.386 63.158 0.00 0.00 0.00 6.13
1522 6044 3.069318 GCCCCTTCGAGGTCGTCT 61.069 66.667 0.00 0.00 40.80 4.18
1523 6045 2.647158 GCCCCTTCGAGGTCGTCTT 61.647 63.158 0.00 0.00 40.80 3.01
1526 6048 0.317479 CCCTTCGAGGTCGTCTTTGT 59.683 55.000 0.00 0.00 40.80 2.83
1529 6051 1.792949 CTTCGAGGTCGTCTTTGTTGG 59.207 52.381 0.00 0.00 40.80 3.77
1531 6053 1.566018 CGAGGTCGTCTTTGTTGGCC 61.566 60.000 0.00 0.00 34.11 5.36
1532 6054 0.250338 GAGGTCGTCTTTGTTGGCCT 60.250 55.000 3.32 0.00 0.00 5.19
1533 6055 0.535102 AGGTCGTCTTTGTTGGCCTG 60.535 55.000 3.32 0.00 0.00 4.85
1534 6056 1.515521 GGTCGTCTTTGTTGGCCTGG 61.516 60.000 3.32 0.00 0.00 4.45
1535 6057 1.228124 TCGTCTTTGTTGGCCTGGG 60.228 57.895 3.32 0.00 0.00 4.45
1537 6059 1.832167 GTCTTTGTTGGCCTGGGCA 60.832 57.895 20.19 20.19 44.11 5.36
1540 6062 2.791501 CTTTGTTGGCCTGGGCATGC 62.792 60.000 24.56 19.06 44.11 4.06
1546 6068 3.818787 GCCTGGGCATGCGTGAAG 61.819 66.667 12.44 6.11 41.49 3.02
1547 6069 2.046023 CCTGGGCATGCGTGAAGA 60.046 61.111 12.44 0.00 0.00 2.87
1558 6080 3.474806 GTGAAGACGATGGTGCCG 58.525 61.111 0.00 0.00 0.00 5.69
1560 6082 2.279810 TGAAGACGATGGTGCCGGA 61.280 57.895 5.05 0.00 0.00 5.14
1561 6083 1.144057 GAAGACGATGGTGCCGGAT 59.856 57.895 5.05 0.00 0.00 4.18
1562 6084 1.153369 AAGACGATGGTGCCGGATG 60.153 57.895 5.05 0.00 0.00 3.51
1634 7619 3.495983 CCGTGCCCTATATTTGATCACCA 60.496 47.826 0.00 0.00 0.00 4.17
1858 7855 2.464682 GCTATCCTCATGGCGATGC 58.535 57.895 3.45 0.00 0.00 3.91
1951 7948 0.107800 CAGAGCTGGGTCATGGAGTG 60.108 60.000 0.00 0.00 0.00 3.51
2535 8624 1.021390 GCGACAGGGGTCTTGTGATG 61.021 60.000 0.00 0.00 42.05 3.07
2536 8625 0.608130 CGACAGGGGTCTTGTGATGA 59.392 55.000 0.00 0.00 42.05 2.92
2537 8626 1.001974 CGACAGGGGTCTTGTGATGAA 59.998 52.381 0.00 0.00 42.05 2.57
2538 8627 2.355108 CGACAGGGGTCTTGTGATGAAT 60.355 50.000 0.00 0.00 42.05 2.57
2539 8628 3.690460 GACAGGGGTCTTGTGATGAATT 58.310 45.455 0.00 0.00 40.99 2.17
2540 8629 4.622933 CGACAGGGGTCTTGTGATGAATTA 60.623 45.833 0.00 0.00 42.05 1.40
2541 8630 5.440610 GACAGGGGTCTTGTGATGAATTAT 58.559 41.667 0.00 0.00 40.99 1.28
2542 8631 5.195940 ACAGGGGTCTTGTGATGAATTATG 58.804 41.667 0.00 0.00 0.00 1.90
2543 8632 5.195940 CAGGGGTCTTGTGATGAATTATGT 58.804 41.667 0.00 0.00 0.00 2.29
2544 8633 5.297776 CAGGGGTCTTGTGATGAATTATGTC 59.702 44.000 0.00 0.00 0.00 3.06
2545 8634 5.192522 AGGGGTCTTGTGATGAATTATGTCT 59.807 40.000 0.00 0.00 0.00 3.41
2546 8635 6.386927 AGGGGTCTTGTGATGAATTATGTCTA 59.613 38.462 0.00 0.00 0.00 2.59
2547 8636 7.072961 AGGGGTCTTGTGATGAATTATGTCTAT 59.927 37.037 0.00 0.00 0.00 1.98
2548 8637 7.721399 GGGGTCTTGTGATGAATTATGTCTATT 59.279 37.037 0.00 0.00 0.00 1.73
2549 8638 8.778358 GGGTCTTGTGATGAATTATGTCTATTC 58.222 37.037 0.00 0.00 33.58 1.75
2550 8639 9.330063 GGTCTTGTGATGAATTATGTCTATTCA 57.670 33.333 0.00 0.00 43.80 2.57
2555 8644 9.481340 TGTGATGAATTATGTCTATTCAGTAGC 57.519 33.333 0.00 0.00 43.15 3.58
2556 8645 9.481340 GTGATGAATTATGTCTATTCAGTAGCA 57.519 33.333 0.00 0.00 43.15 3.49
2557 8646 9.481340 TGATGAATTATGTCTATTCAGTAGCAC 57.519 33.333 0.00 0.00 43.15 4.40
2558 8647 9.703892 GATGAATTATGTCTATTCAGTAGCACT 57.296 33.333 0.00 0.00 43.15 4.40
2560 8649 9.890629 TGAATTATGTCTATTCAGTAGCACTTT 57.109 29.630 0.00 0.00 37.15 2.66
2563 8652 6.992063 ATGTCTATTCAGTAGCACTTTTGG 57.008 37.500 0.00 0.00 0.00 3.28
2564 8653 5.865085 TGTCTATTCAGTAGCACTTTTGGT 58.135 37.500 0.00 0.00 37.24 3.67
2565 8654 6.296026 TGTCTATTCAGTAGCACTTTTGGTT 58.704 36.000 0.00 0.00 34.50 3.67
2566 8655 6.426937 TGTCTATTCAGTAGCACTTTTGGTTC 59.573 38.462 0.00 0.00 34.50 3.62
2704 8971 0.768622 AGTTTCCCCATGTCGTTGGA 59.231 50.000 3.83 0.00 39.25 3.53
2727 8994 4.021368 AGTGCGTAAGTTAGTGAATGGAGT 60.021 41.667 0.00 0.00 41.68 3.85
2728 8995 5.184479 AGTGCGTAAGTTAGTGAATGGAGTA 59.816 40.000 0.00 0.00 41.68 2.59
2729 8996 6.040878 GTGCGTAAGTTAGTGAATGGAGTAT 58.959 40.000 0.00 0.00 41.68 2.12
2730 8997 7.067859 AGTGCGTAAGTTAGTGAATGGAGTATA 59.932 37.037 0.00 0.00 41.68 1.47
2824 9109 2.687842 GCATCTGCAGACAGTAGCC 58.312 57.895 20.97 0.00 44.77 3.93
2829 9114 4.507710 CATCTGCAGACAGTAGCCTTTTA 58.492 43.478 20.97 0.00 44.77 1.52
2830 9115 4.617253 TCTGCAGACAGTAGCCTTTTAA 57.383 40.909 13.74 0.00 44.77 1.52
2968 9268 6.128553 CGCTCTAGAGAAGTAGAGATGATGAC 60.129 46.154 24.24 0.00 46.32 3.06
3047 9360 6.630071 AGTGTTCTCTTTTTAGCAAAGCAAA 58.370 32.000 0.00 0.00 0.00 3.68
3057 9370 6.693315 TTTAGCAAAGCAAAGTTACTGACT 57.307 33.333 0.00 0.00 41.47 3.41
3067 9380 2.584236 AGTTACTGACTGAGTGACGGT 58.416 47.619 0.00 0.00 44.20 4.83
3204 9522 4.610333 TGCAGGGAAGATCTTGAGTAGTA 58.390 43.478 14.00 0.00 0.00 1.82
3205 9523 4.646945 TGCAGGGAAGATCTTGAGTAGTAG 59.353 45.833 14.00 0.00 0.00 2.57
3206 9524 4.647399 GCAGGGAAGATCTTGAGTAGTAGT 59.353 45.833 14.00 0.00 0.00 2.73
3241 10412 0.168788 CATGTTTGGCCTACAGTGCG 59.831 55.000 15.00 2.86 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 143 1.990160 GAGAGGAGGGCGGAGAGAGA 61.990 65.000 0.00 0.00 0.00 3.10
186 187 1.670811 CAACGCTTCCCGCAAGATATT 59.329 47.619 0.00 0.00 41.76 1.28
213 214 1.367471 CGAGGAATCCATGGCGCTA 59.633 57.895 6.96 0.00 0.00 4.26
224 225 1.742768 GCCGAGATGGACGAGGAAT 59.257 57.895 0.00 0.00 42.00 3.01
344 345 1.270625 GGGACATGAACTTCACCGACA 60.271 52.381 0.00 0.00 0.00 4.35
687 695 3.799755 GGAAACGATTGCGCGCCT 61.800 61.111 30.77 16.71 42.48 5.52
688 696 4.829518 GGGAAACGATTGCGCGCC 62.830 66.667 30.77 12.70 42.48 6.53
713 723 2.978010 CAGCGGTGGCGGAAAGTT 60.978 61.111 6.74 0.00 46.35 2.66
715 725 4.697756 TCCAGCGGTGGCGGAAAG 62.698 66.667 28.72 3.47 44.60 2.62
759 771 1.403679 CTCCAACAGCCACGTCAAAAA 59.596 47.619 0.00 0.00 0.00 1.94
760 772 1.021202 CTCCAACAGCCACGTCAAAA 58.979 50.000 0.00 0.00 0.00 2.44
762 774 0.396435 ATCTCCAACAGCCACGTCAA 59.604 50.000 0.00 0.00 0.00 3.18
763 775 0.320683 CATCTCCAACAGCCACGTCA 60.321 55.000 0.00 0.00 0.00 4.35
764 776 1.639298 GCATCTCCAACAGCCACGTC 61.639 60.000 0.00 0.00 0.00 4.34
765 777 1.672356 GCATCTCCAACAGCCACGT 60.672 57.895 0.00 0.00 0.00 4.49
766 778 1.364626 GAGCATCTCCAACAGCCACG 61.365 60.000 0.00 0.00 0.00 4.94
783 795 0.612174 TCTCCAACCGTCCCTCAGAG 60.612 60.000 0.00 0.00 0.00 3.35
784 796 0.041238 ATCTCCAACCGTCCCTCAGA 59.959 55.000 0.00 0.00 0.00 3.27
785 797 0.176680 CATCTCCAACCGTCCCTCAG 59.823 60.000 0.00 0.00 0.00 3.35
787 799 1.153349 GCATCTCCAACCGTCCCTC 60.153 63.158 0.00 0.00 0.00 4.30
788 800 1.613630 AGCATCTCCAACCGTCCCT 60.614 57.895 0.00 0.00 0.00 4.20
803 815 1.202710 TGCTTGGGTTTCGTTAGAGCA 60.203 47.619 0.00 0.00 36.43 4.26
805 817 2.678336 GGATGCTTGGGTTTCGTTAGAG 59.322 50.000 0.00 0.00 0.00 2.43
806 818 2.039216 TGGATGCTTGGGTTTCGTTAGA 59.961 45.455 0.00 0.00 0.00 2.10
808 820 2.570415 TGGATGCTTGGGTTTCGTTA 57.430 45.000 0.00 0.00 0.00 3.18
810 822 1.247567 CTTGGATGCTTGGGTTTCGT 58.752 50.000 0.00 0.00 0.00 3.85
811 823 0.109132 GCTTGGATGCTTGGGTTTCG 60.109 55.000 0.00 0.00 0.00 3.46
817 829 1.214589 GTGCTGCTTGGATGCTTGG 59.785 57.895 0.00 0.00 0.00 3.61
818 830 0.315886 TTGTGCTGCTTGGATGCTTG 59.684 50.000 0.00 0.00 0.00 4.01
820 832 1.263356 ATTTGTGCTGCTTGGATGCT 58.737 45.000 0.00 0.00 0.00 3.79
822 834 3.184541 GCTAATTTGTGCTGCTTGGATG 58.815 45.455 0.00 0.00 0.00 3.51
826 838 1.621107 CGGCTAATTTGTGCTGCTTG 58.379 50.000 0.00 0.00 0.00 4.01
833 845 2.102161 GCCGGCGGCTAATTTGTG 59.898 61.111 41.44 5.82 46.69 3.33
860 872 1.340399 CCAGGAGAGTGGCTGCCATA 61.340 60.000 26.22 0.00 35.28 2.74
861 873 2.677289 CCAGGAGAGTGGCTGCCAT 61.677 63.158 26.22 13.77 35.28 4.40
862 874 3.324930 CCAGGAGAGTGGCTGCCA 61.325 66.667 19.30 19.30 35.18 4.92
868 880 3.721706 GTGGGGCCAGGAGAGTGG 61.722 72.222 4.39 0.00 41.01 4.00
871 883 3.406200 CAGGTGGGGCCAGGAGAG 61.406 72.222 4.39 0.00 40.61 3.20
904 916 1.566018 GGTTCGGTTCAACCAGCTCG 61.566 60.000 7.52 0.00 44.79 5.03
912 924 1.070105 CTCCCACGGTTCGGTTCAA 59.930 57.895 0.00 0.00 0.00 2.69
943 955 0.817634 TTTGAGCCGTGTTGTGAGGG 60.818 55.000 0.00 0.00 0.00 4.30
1246 5753 2.218953 TTCGTGGTGAGTGTGAAGTC 57.781 50.000 0.00 0.00 0.00 3.01
1256 5763 2.673114 GCGCCGAATTTCGTGGTGA 61.673 57.895 16.89 0.00 38.40 4.02
1290 5797 2.598099 TGGTACCCGCAGTCGTCA 60.598 61.111 10.07 0.00 0.00 4.35
1370 5892 4.175489 AGACGACGACCGCGATGG 62.175 66.667 8.23 0.00 43.32 3.51
1372 5894 4.175489 CCAGACGACGACCGCGAT 62.175 66.667 8.23 0.00 43.32 4.58
1376 5898 4.112341 GGTCCCAGACGACGACCG 62.112 72.222 0.00 0.00 45.44 4.79
1409 5931 4.475135 GCTCCGGCAGGTCCTTCC 62.475 72.222 1.81 0.00 39.05 3.46
1410 5932 4.475135 GGCTCCGGCAGGTCCTTC 62.475 72.222 1.81 0.00 40.87 3.46
1422 5944 1.516423 GTTCACTAGGTCGGGCTCC 59.484 63.158 0.00 0.00 0.00 4.70
1423 5945 1.139095 CGTTCACTAGGTCGGGCTC 59.861 63.158 0.00 0.00 0.00 4.70
1424 5946 1.303888 TCGTTCACTAGGTCGGGCT 60.304 57.895 0.00 0.00 0.00 5.19
1425 5947 1.153881 GTCGTTCACTAGGTCGGGC 60.154 63.158 0.00 0.00 0.00 6.13
1426 5948 0.170561 CTGTCGTTCACTAGGTCGGG 59.829 60.000 0.00 0.00 0.00 5.14
1427 5949 0.456312 GCTGTCGTTCACTAGGTCGG 60.456 60.000 0.00 0.00 0.00 4.79
1429 5951 3.489398 CCATAGCTGTCGTTCACTAGGTC 60.489 52.174 0.00 0.00 0.00 3.85
1430 5952 2.427453 CCATAGCTGTCGTTCACTAGGT 59.573 50.000 0.00 0.00 0.00 3.08
1431 5953 2.223829 CCCATAGCTGTCGTTCACTAGG 60.224 54.545 0.00 0.00 0.00 3.02
1432 5954 2.223829 CCCCATAGCTGTCGTTCACTAG 60.224 54.545 0.00 0.00 0.00 2.57
1433 5955 1.754803 CCCCATAGCTGTCGTTCACTA 59.245 52.381 0.00 0.00 0.00 2.74
1434 5956 0.537188 CCCCATAGCTGTCGTTCACT 59.463 55.000 0.00 0.00 0.00 3.41
1435 5957 1.090052 GCCCCATAGCTGTCGTTCAC 61.090 60.000 0.00 0.00 0.00 3.18
1436 5958 1.220749 GCCCCATAGCTGTCGTTCA 59.779 57.895 0.00 0.00 0.00 3.18
1437 5959 1.523938 GGCCCCATAGCTGTCGTTC 60.524 63.158 0.00 0.00 0.00 3.95
1438 5960 2.590092 GGCCCCATAGCTGTCGTT 59.410 61.111 0.00 0.00 0.00 3.85
1505 6027 2.168666 AAAGACGACCTCGAAGGGGC 62.169 60.000 0.78 0.00 40.58 5.80
1511 6033 0.599204 GCCAACAAAGACGACCTCGA 60.599 55.000 0.78 0.00 43.02 4.04
1515 6037 1.515521 CCAGGCCAACAAAGACGACC 61.516 60.000 5.01 0.00 0.00 4.79
1516 6038 1.515521 CCCAGGCCAACAAAGACGAC 61.516 60.000 5.01 0.00 0.00 4.34
1517 6039 1.228124 CCCAGGCCAACAAAGACGA 60.228 57.895 5.01 0.00 0.00 4.20
1520 6042 1.155859 ATGCCCAGGCCAACAAAGA 59.844 52.632 5.01 0.00 41.09 2.52
1522 6044 2.881528 GCATGCCCAGGCCAACAAA 61.882 57.895 6.36 0.00 41.09 2.83
1523 6045 3.312718 GCATGCCCAGGCCAACAA 61.313 61.111 6.36 0.00 41.09 2.83
1529 6051 3.818787 CTTCACGCATGCCCAGGC 61.819 66.667 13.15 0.38 42.35 4.85
1531 6053 2.743752 CGTCTTCACGCATGCCCAG 61.744 63.158 13.15 0.00 39.69 4.45
1532 6054 2.520465 ATCGTCTTCACGCATGCCCA 62.520 55.000 13.15 0.00 46.28 5.36
1533 6055 1.815421 ATCGTCTTCACGCATGCCC 60.815 57.895 13.15 0.00 46.28 5.36
1534 6056 1.349627 CATCGTCTTCACGCATGCC 59.650 57.895 13.15 0.00 46.28 4.40
1535 6057 1.349627 CCATCGTCTTCACGCATGC 59.650 57.895 7.91 7.91 46.28 4.06
1537 6059 1.361668 GCACCATCGTCTTCACGCAT 61.362 55.000 0.00 0.00 46.28 4.73
1543 6065 1.144057 ATCCGGCACCATCGTCTTC 59.856 57.895 0.00 0.00 0.00 2.87
1544 6066 1.153369 CATCCGGCACCATCGTCTT 60.153 57.895 0.00 0.00 0.00 3.01
1545 6067 2.501128 CATCCGGCACCATCGTCT 59.499 61.111 0.00 0.00 0.00 4.18
1546 6068 3.272334 GCATCCGGCACCATCGTC 61.272 66.667 0.00 0.00 43.97 4.20
1593 7548 1.742880 CATGCTCCAGTCACCGGTG 60.743 63.158 29.26 29.26 0.00 4.94
1621 7585 4.733165 CCCCAGTGATGGTGATCAAATAT 58.267 43.478 0.00 0.00 40.39 1.28
1684 7669 3.782443 AGGGGGCATTCGGTCGAC 61.782 66.667 7.13 7.13 0.00 4.20
1858 7855 0.542702 AACCCCAAACTGCCATCCTG 60.543 55.000 0.00 0.00 0.00 3.86
1951 7948 6.436261 TCCTGAGATCGATAATTGTACGTTC 58.564 40.000 0.00 0.00 0.00 3.95
2537 8626 9.113838 CCAAAAGTGCTACTGAATAGACATAAT 57.886 33.333 0.00 0.00 31.83 1.28
2538 8627 8.100791 ACCAAAAGTGCTACTGAATAGACATAA 58.899 33.333 0.00 0.00 31.83 1.90
2539 8628 7.620880 ACCAAAAGTGCTACTGAATAGACATA 58.379 34.615 0.00 0.00 31.83 2.29
2540 8629 6.476378 ACCAAAAGTGCTACTGAATAGACAT 58.524 36.000 0.00 0.00 31.83 3.06
2541 8630 5.865085 ACCAAAAGTGCTACTGAATAGACA 58.135 37.500 0.00 0.00 31.83 3.41
2542 8631 6.426937 TGAACCAAAAGTGCTACTGAATAGAC 59.573 38.462 0.00 0.00 31.83 2.59
2543 8632 6.530120 TGAACCAAAAGTGCTACTGAATAGA 58.470 36.000 0.00 0.00 31.83 1.98
2544 8633 6.621596 GCTGAACCAAAAGTGCTACTGAATAG 60.622 42.308 0.00 0.00 0.00 1.73
2545 8634 5.181245 GCTGAACCAAAAGTGCTACTGAATA 59.819 40.000 0.00 0.00 0.00 1.75
2546 8635 4.022849 GCTGAACCAAAAGTGCTACTGAAT 60.023 41.667 0.00 0.00 0.00 2.57
2547 8636 3.315191 GCTGAACCAAAAGTGCTACTGAA 59.685 43.478 0.00 0.00 0.00 3.02
2548 8637 2.878406 GCTGAACCAAAAGTGCTACTGA 59.122 45.455 0.00 0.00 0.00 3.41
2549 8638 2.880890 AGCTGAACCAAAAGTGCTACTG 59.119 45.455 0.00 0.00 0.00 2.74
2550 8639 3.214696 AGCTGAACCAAAAGTGCTACT 57.785 42.857 0.00 0.00 0.00 2.57
2551 8640 3.550842 CCAAGCTGAACCAAAAGTGCTAC 60.551 47.826 0.00 0.00 0.00 3.58
2552 8641 2.622942 CCAAGCTGAACCAAAAGTGCTA 59.377 45.455 0.00 0.00 0.00 3.49
2553 8642 1.410153 CCAAGCTGAACCAAAAGTGCT 59.590 47.619 0.00 0.00 0.00 4.40
2554 8643 1.408702 TCCAAGCTGAACCAAAAGTGC 59.591 47.619 0.00 0.00 0.00 4.40
2555 8644 2.035066 CCTCCAAGCTGAACCAAAAGTG 59.965 50.000 0.00 0.00 0.00 3.16
2556 8645 2.310538 CCTCCAAGCTGAACCAAAAGT 58.689 47.619 0.00 0.00 0.00 2.66
2557 8646 1.000171 GCCTCCAAGCTGAACCAAAAG 60.000 52.381 0.00 0.00 0.00 2.27
2558 8647 1.039856 GCCTCCAAGCTGAACCAAAA 58.960 50.000 0.00 0.00 0.00 2.44
2559 8648 1.172180 CGCCTCCAAGCTGAACCAAA 61.172 55.000 0.00 0.00 0.00 3.28
2560 8649 1.600636 CGCCTCCAAGCTGAACCAA 60.601 57.895 0.00 0.00 0.00 3.67
2561 8650 2.032528 CGCCTCCAAGCTGAACCA 59.967 61.111 0.00 0.00 0.00 3.67
2562 8651 2.035442 GTCGCCTCCAAGCTGAACC 61.035 63.158 0.00 0.00 0.00 3.62
2563 8652 0.884704 TTGTCGCCTCCAAGCTGAAC 60.885 55.000 0.00 0.00 0.00 3.18
2564 8653 0.603707 CTTGTCGCCTCCAAGCTGAA 60.604 55.000 0.00 0.00 33.55 3.02
2565 8654 1.004560 CTTGTCGCCTCCAAGCTGA 60.005 57.895 0.00 0.00 33.55 4.26
2566 8655 2.037136 CCTTGTCGCCTCCAAGCTG 61.037 63.158 0.00 0.00 38.36 4.24
2663 8930 6.888430 ACTATCAAACTTACTGACAAAAGCG 58.112 36.000 0.00 0.00 0.00 4.68
2704 8971 4.021368 ACTCCATTCACTAACTTACGCACT 60.021 41.667 0.00 0.00 0.00 4.40
2728 8995 9.877178 GAATCGGAGGTTCATTACAAGATATAT 57.123 33.333 0.00 0.00 0.00 0.86
2729 8996 9.090103 AGAATCGGAGGTTCATTACAAGATATA 57.910 33.333 0.00 0.00 0.00 0.86
2730 8997 7.967908 AGAATCGGAGGTTCATTACAAGATAT 58.032 34.615 0.00 0.00 0.00 1.63
2824 9109 7.492344 AGCAAACTGTCAAAATGGACTTAAAAG 59.508 33.333 0.00 0.00 38.61 2.27
2829 9114 5.343307 AAGCAAACTGTCAAAATGGACTT 57.657 34.783 0.00 0.00 38.61 3.01
2830 9115 5.343307 AAAGCAAACTGTCAAAATGGACT 57.657 34.783 0.00 0.00 38.61 3.85
2898 9198 7.118825 AGACATGCCATTATTATCAACTCATCG 59.881 37.037 0.00 0.00 0.00 3.84
2968 9268 2.180017 GCCAGCATGCAGAAACCG 59.820 61.111 21.98 0.00 31.97 4.44
3047 9360 2.584236 ACCGTCACTCAGTCAGTAACT 58.416 47.619 0.00 0.00 39.44 2.24
3057 9370 7.758076 CAGTTTACATCTTATAACCGTCACTCA 59.242 37.037 0.00 0.00 0.00 3.41
3241 10412 5.584649 TGGACATTGCAGTTTACTAGTATGC 59.415 40.000 16.64 16.64 37.40 3.14


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

AutoCloner maintained by Alex Coulton.