Multiple sequence alignment - TraesCS1A01G314800

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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 TraesCS1A01G314800 chr1A 100.000 2676 0 0 1 2676 506475188 506472513 0.000000e+00 4942.0
1 TraesCS1A01G314800 chr1A 95.278 1207 40 10 709 1904 506493962 506492762 0.000000e+00 1897.0
2 TraesCS1A01G314800 chr1A 89.283 1241 76 27 709 1912 506489627 506488407 0.000000e+00 1502.0
3 TraesCS1A01G314800 chr1A 96.076 790 16 4 1047 1829 506481145 506480364 0.000000e+00 1273.0
4 TraesCS1A01G314800 chr1A 88.908 568 39 8 1200 1749 506288735 506288174 0.000000e+00 678.0
5 TraesCS1A01G314800 chr1A 83.168 404 43 12 730 1126 506294537 506294152 1.970000e-91 346.0
6 TraesCS1A01G314800 chr1D 94.123 1208 41 15 709 1906 410491397 410490210 0.000000e+00 1810.0
7 TraesCS1A01G314800 chr1D 89.286 1064 77 14 866 1912 410483031 410481988 0.000000e+00 1299.0
8 TraesCS1A01G314800 chr1D 87.500 1040 87 20 729 1749 410472538 410471523 0.000000e+00 1160.0
9 TraesCS1A01G314800 chr1D 89.789 568 45 4 1962 2529 483883798 483883244 0.000000e+00 715.0
10 TraesCS1A01G314800 chr1D 90.541 74 7 0 2529 2602 96168186 96168113 6.100000e-17 99.0
11 TraesCS1A01G314800 chr1B 92.155 1211 70 11 718 1912 553136468 553135267 0.000000e+00 1687.0
12 TraesCS1A01G314800 chr1B 88.303 1043 81 20 730 1749 553025525 553024501 0.000000e+00 1212.0
13 TraesCS1A01G314800 chr1B 90.087 686 66 2 1 685 523152536 523151852 0.000000e+00 889.0
14 TraesCS1A01G314800 chr1B 86.166 253 20 7 1962 2204 15458873 15459120 2.640000e-65 259.0
15 TraesCS1A01G314800 chr6D 91.134 688 58 2 1 686 30534361 30533675 0.000000e+00 929.0
16 TraesCS1A01G314800 chr2A 90.462 692 61 5 3 692 732990831 732990143 0.000000e+00 907.0
17 TraesCS1A01G314800 chr2A 90.449 691 58 7 1 687 668223492 668222806 0.000000e+00 904.0
18 TraesCS1A01G314800 chr2A 89.474 570 47 4 1966 2535 25206340 25205784 0.000000e+00 708.0
19 TraesCS1A01G314800 chr2A 88.986 572 50 4 1964 2535 25237436 25236878 0.000000e+00 695.0
20 TraesCS1A01G314800 chr2A 84.386 570 74 9 1962 2529 119299015 119298459 1.810000e-151 545.0
21 TraesCS1A01G314800 chrUn 90.365 685 64 2 1 684 110780141 110779458 0.000000e+00 898.0
22 TraesCS1A01G314800 chrUn 86.796 568 54 7 1962 2529 348957623 348957077 4.900000e-172 614.0
23 TraesCS1A01G314800 chrUn 91.837 49 4 0 1910 1958 33578166 33578214 4.780000e-08 69.4
24 TraesCS1A01G314800 chrUn 91.837 49 4 0 1910 1958 33762930 33762882 4.780000e-08 69.4
25 TraesCS1A01G314800 chrUn 91.837 49 4 0 1910 1958 33884480 33884432 4.780000e-08 69.4
26 TraesCS1A01G314800 chr5D 90.116 688 67 1 1 687 534087286 534087973 0.000000e+00 893.0
27 TraesCS1A01G314800 chr5D 89.985 689 66 3 2 690 376719893 376719208 0.000000e+00 887.0
28 TraesCS1A01G314800 chr5D 89.261 568 48 4 1962 2529 438807512 438806958 0.000000e+00 699.0
29 TraesCS1A01G314800 chr7B 90.029 682 67 1 1 681 634288381 634287700 0.000000e+00 881.0
30 TraesCS1A01G314800 chr6B 89.826 688 69 1 1 687 57716091 57716778 0.000000e+00 881.0
31 TraesCS1A01G314800 chr5A 90.685 569 40 4 1962 2529 436606063 436606619 0.000000e+00 745.0
32 TraesCS1A01G314800 chr5A 89.119 579 46 4 1962 2529 475516012 475516584 0.000000e+00 704.0
33 TraesCS1A01G314800 chr2B 89.983 579 43 2 1962 2529 757275526 757274952 0.000000e+00 734.0
34 TraesCS1A01G314800 chr3A 89.810 579 44 2 1962 2529 42369264 42368690 0.000000e+00 728.0
35 TraesCS1A01G314800 chr3A 89.003 582 46 6 1962 2530 740092170 740092746 0.000000e+00 704.0
36 TraesCS1A01G314800 chr6A 89.138 580 46 5 1962 2529 48087832 48087258 0.000000e+00 706.0
37 TraesCS1A01G314800 chr3B 87.910 579 53 6 1962 2529 730402316 730401744 0.000000e+00 665.0
38 TraesCS1A01G314800 chr3B 82.600 477 47 12 1962 2427 435299377 435298926 3.230000e-104 388.0
39 TraesCS1A01G314800 chr4A 89.474 323 24 5 1995 2314 604005598 604005913 1.490000e-107 399.0
40 TraesCS1A01G314800 chr4A 90.541 148 14 0 2529 2676 614212113 614212260 2.100000e-46 196.0
41 TraesCS1A01G314800 chr5B 83.439 157 14 5 2529 2676 565154490 565154643 4.650000e-28 135.0
42 TraesCS1A01G314800 chr5B 89.011 91 7 2 2529 2619 230238958 230238871 2.820000e-20 110.0
43 TraesCS1A01G314800 chr2D 91.209 91 6 1 2529 2619 87563759 87563847 3.620000e-24 122.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G314800 chr1A 506472513 506475188 2675 True 4942.0 4942 100.0000 1 2676 1 chr1A.!!$R3 2675
1 TraesCS1A01G314800 chr1A 506488407 506493962 5555 True 1699.5 1897 92.2805 709 1912 2 chr1A.!!$R5 1203
2 TraesCS1A01G314800 chr1A 506480364 506481145 781 True 1273.0 1273 96.0760 1047 1829 1 chr1A.!!$R4 782
3 TraesCS1A01G314800 chr1A 506288174 506288735 561 True 678.0 678 88.9080 1200 1749 1 chr1A.!!$R1 549
4 TraesCS1A01G314800 chr1D 410490210 410491397 1187 True 1810.0 1810 94.1230 709 1906 1 chr1D.!!$R4 1197
5 TraesCS1A01G314800 chr1D 410481988 410483031 1043 True 1299.0 1299 89.2860 866 1912 1 chr1D.!!$R3 1046
6 TraesCS1A01G314800 chr1D 410471523 410472538 1015 True 1160.0 1160 87.5000 729 1749 1 chr1D.!!$R2 1020
7 TraesCS1A01G314800 chr1D 483883244 483883798 554 True 715.0 715 89.7890 1962 2529 1 chr1D.!!$R5 567
8 TraesCS1A01G314800 chr1B 553135267 553136468 1201 True 1687.0 1687 92.1550 718 1912 1 chr1B.!!$R3 1194
9 TraesCS1A01G314800 chr1B 553024501 553025525 1024 True 1212.0 1212 88.3030 730 1749 1 chr1B.!!$R2 1019
10 TraesCS1A01G314800 chr1B 523151852 523152536 684 True 889.0 889 90.0870 1 685 1 chr1B.!!$R1 684
11 TraesCS1A01G314800 chr6D 30533675 30534361 686 True 929.0 929 91.1340 1 686 1 chr6D.!!$R1 685
12 TraesCS1A01G314800 chr2A 732990143 732990831 688 True 907.0 907 90.4620 3 692 1 chr2A.!!$R5 689
13 TraesCS1A01G314800 chr2A 668222806 668223492 686 True 904.0 904 90.4490 1 687 1 chr2A.!!$R4 686
14 TraesCS1A01G314800 chr2A 25205784 25206340 556 True 708.0 708 89.4740 1966 2535 1 chr2A.!!$R1 569
15 TraesCS1A01G314800 chr2A 25236878 25237436 558 True 695.0 695 88.9860 1964 2535 1 chr2A.!!$R2 571
16 TraesCS1A01G314800 chr2A 119298459 119299015 556 True 545.0 545 84.3860 1962 2529 1 chr2A.!!$R3 567
17 TraesCS1A01G314800 chrUn 110779458 110780141 683 True 898.0 898 90.3650 1 684 1 chrUn.!!$R3 683
18 TraesCS1A01G314800 chrUn 348957077 348957623 546 True 614.0 614 86.7960 1962 2529 1 chrUn.!!$R4 567
19 TraesCS1A01G314800 chr5D 534087286 534087973 687 False 893.0 893 90.1160 1 687 1 chr5D.!!$F1 686
20 TraesCS1A01G314800 chr5D 376719208 376719893 685 True 887.0 887 89.9850 2 690 1 chr5D.!!$R1 688
21 TraesCS1A01G314800 chr5D 438806958 438807512 554 True 699.0 699 89.2610 1962 2529 1 chr5D.!!$R2 567
22 TraesCS1A01G314800 chr7B 634287700 634288381 681 True 881.0 881 90.0290 1 681 1 chr7B.!!$R1 680
23 TraesCS1A01G314800 chr6B 57716091 57716778 687 False 881.0 881 89.8260 1 687 1 chr6B.!!$F1 686
24 TraesCS1A01G314800 chr5A 436606063 436606619 556 False 745.0 745 90.6850 1962 2529 1 chr5A.!!$F1 567
25 TraesCS1A01G314800 chr5A 475516012 475516584 572 False 704.0 704 89.1190 1962 2529 1 chr5A.!!$F2 567
26 TraesCS1A01G314800 chr2B 757274952 757275526 574 True 734.0 734 89.9830 1962 2529 1 chr2B.!!$R1 567
27 TraesCS1A01G314800 chr3A 42368690 42369264 574 True 728.0 728 89.8100 1962 2529 1 chr3A.!!$R1 567
28 TraesCS1A01G314800 chr3A 740092170 740092746 576 False 704.0 704 89.0030 1962 2530 1 chr3A.!!$F1 568
29 TraesCS1A01G314800 chr6A 48087258 48087832 574 True 706.0 706 89.1380 1962 2529 1 chr6A.!!$R1 567
30 TraesCS1A01G314800 chr3B 730401744 730402316 572 True 665.0 665 87.9100 1962 2529 1 chr3B.!!$R2 567

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
640 646 0.109919 CGACGATTCAGACGTGTGGA 60.11 55.0 13.32 4.04 43.97 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2583 6237 0.031515 TGAGGAAGGGGGCGATAGAA 60.032 55.0 0.0 0.0 39.76 2.1 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
110 112 5.233988 TGGCAAATATGGTTGTAAAAGCAC 58.766 37.500 0.00 0.00 32.55 4.40
111 113 5.221521 TGGCAAATATGGTTGTAAAAGCACA 60.222 36.000 0.00 0.00 32.55 4.57
112 114 5.874261 GGCAAATATGGTTGTAAAAGCACAT 59.126 36.000 0.00 0.00 32.55 3.21
208 210 8.248253 TCATAGTTGTCGTGTGTGATTAACTAT 58.752 33.333 0.00 0.00 39.28 2.12
235 237 6.567687 CCACATGTGGTCAAACAATAGTTA 57.432 37.500 32.94 0.00 45.53 2.24
258 262 4.709250 TCATGTGTGTTTACCTAGTTGCA 58.291 39.130 0.00 0.00 0.00 4.08
283 287 2.621055 TGTGGTTAATCACAGTTGCCAC 59.379 45.455 17.62 8.15 42.05 5.01
310 314 3.786516 TTATCTGATTGCCACGTACGA 57.213 42.857 24.41 0.00 0.00 3.43
320 324 1.218875 CCACGTACGAGCAACTGCAA 61.219 55.000 24.41 0.00 45.16 4.08
353 357 8.194769 TCTAGCAAACGATTCATAGTTGTCATA 58.805 33.333 0.00 0.00 0.00 2.15
496 502 0.756903 AACTAGTTCGCCCACACAGT 59.243 50.000 1.12 0.00 0.00 3.55
500 506 2.124529 TTCGCCCACACAGTGCAA 60.125 55.556 0.00 0.00 31.34 4.08
567 573 1.079127 CACACCGGCCTTGTCCTAG 60.079 63.158 0.00 0.00 0.00 3.02
584 590 0.317799 TAGGTGGCACGCGAAAACTA 59.682 50.000 15.93 4.34 41.51 2.24
588 594 1.463444 GTGGCACGCGAAAACTATCTT 59.537 47.619 15.93 0.00 0.00 2.40
594 600 4.032445 GCACGCGAAAACTATCTTGATGTA 59.968 41.667 15.93 0.00 0.00 2.29
628 634 4.374399 ACAAACTTAACTGGACGACGATT 58.626 39.130 0.00 0.00 0.00 3.34
640 646 0.109919 CGACGATTCAGACGTGTGGA 60.110 55.000 13.32 4.04 43.97 4.02
687 693 3.560896 TGGGTGCTAGTGTTTTCGTAAAC 59.439 43.478 10.38 10.38 43.17 2.01
692 698 7.331687 GGGTGCTAGTGTTTTCGTAAACTTATA 59.668 37.037 17.01 7.66 43.25 0.98
693 699 8.876790 GGTGCTAGTGTTTTCGTAAACTTATAT 58.123 33.333 17.01 3.53 43.25 0.86
836 848 2.279851 CTCGTTCACGTGGCCACA 60.280 61.111 34.16 13.79 40.80 4.17
983 1002 0.457851 TTCTCTTCCTGCGCTAGCTC 59.542 55.000 13.93 5.25 45.42 4.09
1260 1288 1.152839 CGACCTCCTCCTCCTCCTC 60.153 68.421 0.00 0.00 0.00 3.71
1261 1289 1.641552 CGACCTCCTCCTCCTCCTCT 61.642 65.000 0.00 0.00 0.00 3.69
1498 1526 2.847234 TGGTTCCTGGTGACCGCT 60.847 61.111 14.25 0.00 38.81 5.52
1689 1717 6.307318 GTCAACATCTAAGACGACGTAATGTT 59.693 38.462 0.00 9.44 36.57 2.71
1764 1804 4.090786 GCCACGTTGCAATTTTGTATTACC 59.909 41.667 6.76 0.00 0.00 2.85
1912 1960 4.341520 AGGTCCTCTTGCGGTTAACTATAG 59.658 45.833 5.42 0.00 0.00 1.31
1913 1961 4.501058 GGTCCTCTTGCGGTTAACTATAGG 60.501 50.000 5.42 4.91 0.00 2.57
1914 1962 3.640029 TCCTCTTGCGGTTAACTATAGGG 59.360 47.826 5.42 0.00 0.00 3.53
1915 1963 3.391049 CTCTTGCGGTTAACTATAGGGC 58.609 50.000 5.42 1.21 0.00 5.19
1916 1964 2.767394 TCTTGCGGTTAACTATAGGGCA 59.233 45.455 5.42 3.67 0.00 5.36
1917 1965 2.902705 TGCGGTTAACTATAGGGCAG 57.097 50.000 5.42 0.00 0.00 4.85
1918 1966 2.112998 TGCGGTTAACTATAGGGCAGT 58.887 47.619 5.42 0.00 0.00 4.40
1919 1967 2.159014 TGCGGTTAACTATAGGGCAGTG 60.159 50.000 5.42 0.00 0.00 3.66
1920 1968 2.101917 GCGGTTAACTATAGGGCAGTGA 59.898 50.000 5.42 0.00 0.00 3.41
1921 1969 3.244112 GCGGTTAACTATAGGGCAGTGAT 60.244 47.826 5.42 0.00 0.00 3.06
1922 1970 4.557205 CGGTTAACTATAGGGCAGTGATC 58.443 47.826 5.42 0.00 0.00 2.92
1923 1971 4.281182 CGGTTAACTATAGGGCAGTGATCT 59.719 45.833 5.42 0.00 0.00 2.75
1924 1972 5.542779 GGTTAACTATAGGGCAGTGATCTG 58.457 45.833 5.42 0.00 43.87 2.90
1932 1980 3.190849 CAGTGATCTGCGCCGGTG 61.191 66.667 11.67 11.67 34.79 4.94
1946 1994 4.980805 GGTGCACTGGCCGAACGA 62.981 66.667 17.98 0.00 40.13 3.85
1947 1995 2.742372 GTGCACTGGCCGAACGAT 60.742 61.111 10.32 0.00 40.13 3.73
1948 1996 2.031919 TGCACTGGCCGAACGATT 59.968 55.556 0.00 0.00 40.13 3.34
1949 1997 2.032634 TGCACTGGCCGAACGATTC 61.033 57.895 0.00 0.00 40.13 2.52
1958 2006 3.252484 GAACGATTCGGCCGGTCG 61.252 66.667 35.46 35.46 40.91 4.79
1959 2007 4.807039 AACGATTCGGCCGGTCGG 62.807 66.667 37.70 26.58 39.53 4.79
1989 2037 0.370273 CTTCAGAAAGCGCGCGTATT 59.630 50.000 32.35 25.19 0.00 1.89
2013 2080 1.067776 CCGAATACTGCCCCGATACTC 60.068 57.143 0.00 0.00 0.00 2.59
2014 2081 1.401148 CGAATACTGCCCCGATACTCG 60.401 57.143 0.00 0.00 40.07 4.18
2045 2112 9.842775 CTACCCGATATGTATCCTGTAAGTATA 57.157 37.037 0.00 0.00 0.00 1.47
2149 2218 1.463444 CCCTCGTTTGACGTGAAATCC 59.537 52.381 2.88 0.00 43.14 3.01
2150 2219 1.463444 CCTCGTTTGACGTGAAATCCC 59.537 52.381 2.88 0.00 43.14 3.85
2151 2220 1.463444 CTCGTTTGACGTGAAATCCCC 59.537 52.381 2.88 0.00 43.14 4.81
2152 2221 1.071071 TCGTTTGACGTGAAATCCCCT 59.929 47.619 2.88 0.00 43.14 4.79
2167 2236 6.218730 TGAAATCCCCTCCCTCAATAGTAAAA 59.781 38.462 0.00 0.00 0.00 1.52
2218 2287 4.022416 GGTGTGAGTTCATGCCAAAACATA 60.022 41.667 0.00 0.00 0.00 2.29
2228 2297 7.459795 TCATGCCAAAACATAACTGTCAATA 57.540 32.000 0.00 0.00 33.36 1.90
2300 2372 1.321074 AACAAACCCGCGAAAACCCA 61.321 50.000 8.23 0.00 0.00 4.51
2314 2386 6.557110 GCGAAAACCCAACTGCTAATTAATA 58.443 36.000 0.00 0.00 0.00 0.98
2388 2461 6.595716 TGCTTTGACCTAGAAGCTCTATTTTC 59.404 38.462 13.29 0.00 46.39 2.29
2469 4057 5.287674 TCCATGTTTTCAGAAAATTGGCA 57.712 34.783 23.58 13.95 36.88 4.92
2535 6189 1.559814 CGTGCAACATAGCCGATCG 59.440 57.895 8.51 8.51 35.74 3.69
2558 6212 2.125673 CCACCGTCGGATCGCTTT 60.126 61.111 20.51 0.00 0.00 3.51
2559 6213 2.452813 CCACCGTCGGATCGCTTTG 61.453 63.158 20.51 3.31 0.00 2.77
2560 6214 2.813908 ACCGTCGGATCGCTTTGC 60.814 61.111 20.51 0.00 0.00 3.68
2562 6216 3.564027 CGTCGGATCGCTTTGCCC 61.564 66.667 0.00 0.00 0.00 5.36
2563 6217 2.435938 GTCGGATCGCTTTGCCCA 60.436 61.111 0.00 0.00 0.00 5.36
2564 6218 2.125147 TCGGATCGCTTTGCCCAG 60.125 61.111 0.00 0.00 0.00 4.45
2565 6219 2.125147 CGGATCGCTTTGCCCAGA 60.125 61.111 0.00 0.00 0.00 3.86
2567 6221 2.476320 GGATCGCTTTGCCCAGAGC 61.476 63.158 1.05 1.05 44.14 4.09
2571 6225 2.985847 GCTTTGCCCAGAGCCGTT 60.986 61.111 0.00 0.00 42.71 4.44
2572 6226 1.674322 GCTTTGCCCAGAGCCGTTA 60.674 57.895 0.00 0.00 42.71 3.18
2573 6227 1.648467 GCTTTGCCCAGAGCCGTTAG 61.648 60.000 0.00 0.00 42.71 2.34
2574 6228 0.036388 CTTTGCCCAGAGCCGTTAGA 60.036 55.000 0.00 0.00 42.71 2.10
2575 6229 0.618458 TTTGCCCAGAGCCGTTAGAT 59.382 50.000 0.00 0.00 42.71 1.98
2576 6230 0.178068 TTGCCCAGAGCCGTTAGATC 59.822 55.000 0.00 0.00 42.71 2.75
2577 6231 0.975556 TGCCCAGAGCCGTTAGATCA 60.976 55.000 0.00 0.00 42.71 2.92
2578 6232 0.530870 GCCCAGAGCCGTTAGATCAC 60.531 60.000 0.00 0.00 34.35 3.06
2579 6233 0.824109 CCCAGAGCCGTTAGATCACA 59.176 55.000 0.00 0.00 0.00 3.58
2580 6234 1.471676 CCCAGAGCCGTTAGATCACAC 60.472 57.143 0.00 0.00 0.00 3.82
2581 6235 1.471676 CCAGAGCCGTTAGATCACACC 60.472 57.143 0.00 0.00 0.00 4.16
2582 6236 0.824759 AGAGCCGTTAGATCACACCC 59.175 55.000 0.00 0.00 0.00 4.61
2583 6237 0.824759 GAGCCGTTAGATCACACCCT 59.175 55.000 0.00 0.00 0.00 4.34
2584 6238 1.207329 GAGCCGTTAGATCACACCCTT 59.793 52.381 0.00 0.00 0.00 3.95
2585 6239 1.207329 AGCCGTTAGATCACACCCTTC 59.793 52.381 0.00 0.00 0.00 3.46
2586 6240 1.207329 GCCGTTAGATCACACCCTTCT 59.793 52.381 0.00 0.00 0.00 2.85
2587 6241 2.429610 GCCGTTAGATCACACCCTTCTA 59.570 50.000 0.00 0.00 0.00 2.10
2588 6242 3.069729 GCCGTTAGATCACACCCTTCTAT 59.930 47.826 0.00 0.00 0.00 1.98
2589 6243 4.796618 GCCGTTAGATCACACCCTTCTATC 60.797 50.000 0.00 0.00 0.00 2.08
2590 6244 4.537965 CGTTAGATCACACCCTTCTATCG 58.462 47.826 0.00 0.00 32.28 2.92
2591 6245 4.299978 GTTAGATCACACCCTTCTATCGC 58.700 47.826 0.00 0.00 0.00 4.58
2592 6246 1.689273 AGATCACACCCTTCTATCGCC 59.311 52.381 0.00 0.00 0.00 5.54
2593 6247 0.759346 ATCACACCCTTCTATCGCCC 59.241 55.000 0.00 0.00 0.00 6.13
2594 6248 1.146263 CACACCCTTCTATCGCCCC 59.854 63.158 0.00 0.00 0.00 5.80
2595 6249 2.070650 ACACCCTTCTATCGCCCCC 61.071 63.158 0.00 0.00 0.00 5.40
2596 6250 1.766461 CACCCTTCTATCGCCCCCT 60.766 63.158 0.00 0.00 0.00 4.79
2597 6251 1.004361 ACCCTTCTATCGCCCCCTT 59.996 57.895 0.00 0.00 0.00 3.95
2598 6252 1.054978 ACCCTTCTATCGCCCCCTTC 61.055 60.000 0.00 0.00 0.00 3.46
2599 6253 1.755384 CCTTCTATCGCCCCCTTCC 59.245 63.158 0.00 0.00 0.00 3.46
2600 6254 0.764752 CCTTCTATCGCCCCCTTCCT 60.765 60.000 0.00 0.00 0.00 3.36
2601 6255 0.682292 CTTCTATCGCCCCCTTCCTC 59.318 60.000 0.00 0.00 0.00 3.71
2602 6256 0.031515 TTCTATCGCCCCCTTCCTCA 60.032 55.000 0.00 0.00 0.00 3.86
2603 6257 0.759436 TCTATCGCCCCCTTCCTCAC 60.759 60.000 0.00 0.00 0.00 3.51
2604 6258 2.088674 CTATCGCCCCCTTCCTCACG 62.089 65.000 0.00 0.00 0.00 4.35
2619 6273 3.256105 ACGCGCGTGAACGACAAA 61.256 55.556 37.37 0.00 43.02 2.83
2620 6274 2.053811 CGCGCGTGAACGACAAAA 60.054 55.556 24.19 0.00 43.02 2.44
2621 6275 1.648756 CGCGCGTGAACGACAAAAA 60.649 52.632 24.19 0.00 43.02 1.94
2622 6276 0.989805 CGCGCGTGAACGACAAAAAT 60.990 50.000 24.19 0.00 43.02 1.82
2623 6277 0.695410 GCGCGTGAACGACAAAAATC 59.305 50.000 8.43 0.00 43.02 2.17
2624 6278 1.314581 CGCGTGAACGACAAAAATCC 58.685 50.000 7.10 0.00 43.02 3.01
2625 6279 1.681825 GCGTGAACGACAAAAATCCC 58.318 50.000 7.10 0.00 43.02 3.85
2626 6280 1.664874 GCGTGAACGACAAAAATCCCC 60.665 52.381 7.10 0.00 43.02 4.81
2627 6281 1.068816 CGTGAACGACAAAAATCCCCC 60.069 52.381 0.00 0.00 43.02 5.40
2628 6282 1.068816 GTGAACGACAAAAATCCCCCG 60.069 52.381 0.00 0.00 0.00 5.73
2629 6283 0.109458 GAACGACAAAAATCCCCCGC 60.109 55.000 0.00 0.00 0.00 6.13
2630 6284 0.824182 AACGACAAAAATCCCCCGCA 60.824 50.000 0.00 0.00 0.00 5.69
2631 6285 0.824182 ACGACAAAAATCCCCCGCAA 60.824 50.000 0.00 0.00 0.00 4.85
2632 6286 0.388006 CGACAAAAATCCCCCGCAAC 60.388 55.000 0.00 0.00 0.00 4.17
2633 6287 0.388006 GACAAAAATCCCCCGCAACG 60.388 55.000 0.00 0.00 0.00 4.10
2634 6288 1.736282 CAAAAATCCCCCGCAACGC 60.736 57.895 0.00 0.00 0.00 4.84
2635 6289 1.906333 AAAAATCCCCCGCAACGCT 60.906 52.632 0.00 0.00 0.00 5.07
2636 6290 0.609681 AAAAATCCCCCGCAACGCTA 60.610 50.000 0.00 0.00 0.00 4.26
2637 6291 0.395173 AAAATCCCCCGCAACGCTAT 60.395 50.000 0.00 0.00 0.00 2.97
2638 6292 0.395173 AAATCCCCCGCAACGCTATT 60.395 50.000 0.00 0.00 0.00 1.73
2639 6293 0.395173 AATCCCCCGCAACGCTATTT 60.395 50.000 0.00 0.00 0.00 1.40
2640 6294 1.101049 ATCCCCCGCAACGCTATTTG 61.101 55.000 0.00 0.00 0.00 2.32
2641 6295 2.043980 CCCCCGCAACGCTATTTGT 61.044 57.895 0.00 0.00 0.00 2.83
2642 6296 1.136565 CCCCGCAACGCTATTTGTG 59.863 57.895 0.00 0.00 36.84 3.33
2643 6297 1.514014 CCCGCAACGCTATTTGTGC 60.514 57.895 0.00 0.00 35.94 4.57
2644 6298 1.501741 CCGCAACGCTATTTGTGCT 59.498 52.632 0.00 0.00 35.94 4.40
2645 6299 0.794229 CCGCAACGCTATTTGTGCTG 60.794 55.000 0.00 0.00 35.94 4.41
2646 6300 0.794229 CGCAACGCTATTTGTGCTGG 60.794 55.000 0.00 0.00 30.63 4.85
2647 6301 0.521291 GCAACGCTATTTGTGCTGGA 59.479 50.000 0.00 0.00 0.00 3.86
2648 6302 1.729149 GCAACGCTATTTGTGCTGGAC 60.729 52.381 0.00 0.00 0.00 4.02
2649 6303 1.535028 CAACGCTATTTGTGCTGGACA 59.465 47.619 0.00 0.00 0.00 4.02
2660 6314 3.716195 CTGGACACCCGCCATGGA 61.716 66.667 18.40 0.00 42.00 3.41
2661 6315 3.976701 CTGGACACCCGCCATGGAC 62.977 68.421 18.40 5.97 42.00 4.02
2662 6316 4.796495 GGACACCCGCCATGGACC 62.796 72.222 18.40 0.00 42.00 4.46
2669 6323 4.812476 CGCCATGGACCGCTTCGA 62.812 66.667 18.40 0.00 0.00 3.71
2673 6327 4.162690 ATGGACCGCTTCGAGGCC 62.163 66.667 14.49 0.00 0.00 5.19
2675 6329 4.821589 GGACCGCTTCGAGGCCTG 62.822 72.222 12.00 8.01 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 35 0.739813 ACTAAATCGTCACCCTGCGC 60.740 55.000 0.00 0.00 0.00 6.09
40 42 2.030457 CGGATGGCAACTAAATCGTCAC 59.970 50.000 0.00 0.00 37.61 3.67
110 112 7.227512 AGTTAACCAAAACAGAGAGAGTTGATG 59.772 37.037 0.88 0.00 0.00 3.07
111 113 7.283329 AGTTAACCAAAACAGAGAGAGTTGAT 58.717 34.615 0.88 0.00 0.00 2.57
112 114 6.650120 AGTTAACCAAAACAGAGAGAGTTGA 58.350 36.000 0.88 0.00 0.00 3.18
208 210 9.464060 AACTATTGTTTGACCACATGTGGCAAA 62.464 37.037 36.79 36.79 45.35 3.68
235 237 5.312895 TGCAACTAGGTAAACACACATGAT 58.687 37.500 0.00 0.00 0.00 2.45
258 262 3.242936 GCAACTGTGATTAACCACACGTT 60.243 43.478 0.00 5.39 41.63 3.99
283 287 4.270084 ACGTGGCAATCAGATAAACATACG 59.730 41.667 0.00 0.00 0.00 3.06
325 329 6.163476 ACAACTATGAATCGTTTGCTAGACA 58.837 36.000 0.00 0.00 0.00 3.41
415 420 0.749649 AATTGCTTTTCGCCCACACA 59.250 45.000 0.00 0.00 38.05 3.72
448 454 0.547712 ACAGCCACCACCTAGTCCAT 60.548 55.000 0.00 0.00 0.00 3.41
567 573 0.096454 GATAGTTTTCGCGTGCCACC 59.904 55.000 5.77 0.00 0.00 4.61
588 594 8.771920 AAGTTTGTACGAATCTTGATACATCA 57.228 30.769 0.00 0.00 34.44 3.07
594 600 7.876068 TCCAGTTAAGTTTGTACGAATCTTGAT 59.124 33.333 15.38 4.66 0.00 2.57
606 612 3.441496 TCGTCGTCCAGTTAAGTTTGT 57.559 42.857 0.00 0.00 0.00 2.83
624 630 0.109919 TCGTCCACACGTCTGAATCG 60.110 55.000 0.00 0.00 46.76 3.34
628 634 0.030235 CAACTCGTCCACACGTCTGA 59.970 55.000 0.00 0.00 46.76 3.27
699 705 3.258971 AGAGAACCAGCAGAGTAATGC 57.741 47.619 0.00 0.00 46.88 3.56
700 706 5.359576 AGACTAGAGAACCAGCAGAGTAATG 59.640 44.000 0.00 0.00 0.00 1.90
701 707 5.515106 AGACTAGAGAACCAGCAGAGTAAT 58.485 41.667 0.00 0.00 0.00 1.89
702 708 4.924625 AGACTAGAGAACCAGCAGAGTAA 58.075 43.478 0.00 0.00 0.00 2.24
703 709 4.577988 AGACTAGAGAACCAGCAGAGTA 57.422 45.455 0.00 0.00 0.00 2.59
704 710 3.449746 AGACTAGAGAACCAGCAGAGT 57.550 47.619 0.00 0.00 0.00 3.24
705 711 3.509575 ACAAGACTAGAGAACCAGCAGAG 59.490 47.826 0.00 0.00 0.00 3.35
706 712 3.256879 CACAAGACTAGAGAACCAGCAGA 59.743 47.826 0.00 0.00 0.00 4.26
707 713 3.583806 CACAAGACTAGAGAACCAGCAG 58.416 50.000 0.00 0.00 0.00 4.24
716 722 4.555511 GCCAAAAAGTGCACAAGACTAGAG 60.556 45.833 21.04 0.04 0.00 2.43
858 870 1.332375 GCATTTTATAGCGGCCGTGAA 59.668 47.619 28.70 13.05 0.00 3.18
1498 1526 3.948719 GCCACGGAGAACACCCCA 61.949 66.667 0.00 0.00 0.00 4.96
1689 1717 1.536766 CAGAAAAGAATCCACAGCGCA 59.463 47.619 11.47 0.00 0.00 6.09
1764 1804 8.362860 AGATTTACAGAACTCAATCATCGATG 57.637 34.615 19.61 19.61 0.00 3.84
1777 1817 8.784043 ACAACCTTAACATGAGATTTACAGAAC 58.216 33.333 0.00 0.00 0.00 3.01
1890 1938 3.538634 ATAGTTAACCGCAAGAGGACC 57.461 47.619 0.88 0.00 43.02 4.46
1915 1963 3.190849 CACCGGCGCAGATCACTG 61.191 66.667 10.83 0.00 45.91 3.66
1929 1977 4.980805 TCGTTCGGCCAGTGCACC 62.981 66.667 14.63 0.00 40.13 5.01
1930 1978 2.240612 GAATCGTTCGGCCAGTGCAC 62.241 60.000 9.40 9.40 40.13 4.57
1931 1979 2.031919 AATCGTTCGGCCAGTGCA 59.968 55.556 2.24 0.00 40.13 4.57
1932 1980 2.785258 GAATCGTTCGGCCAGTGC 59.215 61.111 2.24 0.00 0.00 4.40
1941 1989 3.252484 CGACCGGCCGAATCGTTC 61.252 66.667 31.52 16.39 0.00 3.95
1942 1990 4.807039 CCGACCGGCCGAATCGTT 62.807 66.667 34.51 13.23 34.02 3.85
1956 2004 4.918129 GAAGTATCCGCGCGCCGA 62.918 66.667 27.36 25.48 40.02 5.54
1958 2006 3.330853 CTGAAGTATCCGCGCGCC 61.331 66.667 27.36 11.30 0.00 6.53
1959 2007 1.418342 TTTCTGAAGTATCCGCGCGC 61.418 55.000 27.36 23.91 0.00 6.86
1960 2008 0.572590 CTTTCTGAAGTATCCGCGCG 59.427 55.000 25.67 25.67 0.00 6.86
1989 2037 2.908015 GGGGCAGTATTCGGCTGA 59.092 61.111 0.00 0.00 36.12 4.26
2015 2082 8.743085 TTACAGGATACATATCGGGTAGTATC 57.257 38.462 0.00 0.00 41.14 2.24
2016 2083 8.334734 ACTTACAGGATACATATCGGGTAGTAT 58.665 37.037 0.00 0.00 41.41 2.12
2017 2084 7.693132 ACTTACAGGATACATATCGGGTAGTA 58.307 38.462 0.00 0.00 41.41 1.82
2018 2085 6.550163 ACTTACAGGATACATATCGGGTAGT 58.450 40.000 0.00 0.00 41.41 2.73
2019 2086 8.749026 ATACTTACAGGATACATATCGGGTAG 57.251 38.462 0.00 0.00 41.41 3.18
2092 2160 6.316390 CCAAAAAGTATCGCAGAAGTATCCTT 59.684 38.462 0.00 0.00 43.58 3.36
2149 2218 4.200092 GTGCTTTTACTATTGAGGGAGGG 58.800 47.826 0.00 0.00 0.00 4.30
2150 2219 4.843728 TGTGCTTTTACTATTGAGGGAGG 58.156 43.478 0.00 0.00 0.00 4.30
2151 2220 6.352516 AGATGTGCTTTTACTATTGAGGGAG 58.647 40.000 0.00 0.00 0.00 4.30
2152 2221 6.313519 AGATGTGCTTTTACTATTGAGGGA 57.686 37.500 0.00 0.00 0.00 4.20
2179 2248 6.721318 ACTCACACCCATATTGTGTATCTTT 58.279 36.000 7.32 0.00 44.77 2.52
2187 2256 3.696051 GCATGAACTCACACCCATATTGT 59.304 43.478 0.00 0.00 0.00 2.71
2228 2297 8.211116 TGCTCACATTTCAATTGAACAAAAAT 57.789 26.923 20.35 8.31 33.13 1.82
2246 2315 1.897560 TCGACTCTCTCTTGCTCACA 58.102 50.000 0.00 0.00 0.00 3.58
2291 2363 8.973835 TTTATTAATTAGCAGTTGGGTTTTCG 57.026 30.769 0.00 0.00 0.00 3.46
2300 2372 8.644374 TGGTCCACTTTTATTAATTAGCAGTT 57.356 30.769 0.00 0.00 0.00 3.16
2314 2386 2.733956 TCTTGCACTTGGTCCACTTTT 58.266 42.857 0.00 0.00 0.00 2.27
2543 6197 2.813908 GCAAAGCGATCCGACGGT 60.814 61.111 14.79 0.67 45.67 4.83
2544 6198 3.564027 GGCAAAGCGATCCGACGG 61.564 66.667 7.84 7.84 0.00 4.79
2547 6201 2.125147 CTGGGCAAAGCGATCCGA 60.125 61.111 0.00 0.00 0.00 4.55
2556 6210 0.618458 ATCTAACGGCTCTGGGCAAA 59.382 50.000 0.21 0.00 44.01 3.68
2558 6212 0.975556 TGATCTAACGGCTCTGGGCA 60.976 55.000 0.21 0.00 44.01 5.36
2559 6213 0.530870 GTGATCTAACGGCTCTGGGC 60.531 60.000 0.00 0.00 40.90 5.36
2560 6214 0.824109 TGTGATCTAACGGCTCTGGG 59.176 55.000 0.00 0.00 0.00 4.45
2562 6216 1.471676 GGGTGTGATCTAACGGCTCTG 60.472 57.143 0.00 0.00 0.00 3.35
2563 6217 0.824759 GGGTGTGATCTAACGGCTCT 59.175 55.000 0.00 0.00 0.00 4.09
2564 6218 0.824759 AGGGTGTGATCTAACGGCTC 59.175 55.000 0.00 0.00 0.00 4.70
2565 6219 1.207329 GAAGGGTGTGATCTAACGGCT 59.793 52.381 0.00 0.00 0.00 5.52
2567 6221 4.556898 CGATAGAAGGGTGTGATCTAACGG 60.557 50.000 0.00 0.00 37.91 4.44
2569 6223 4.299978 GCGATAGAAGGGTGTGATCTAAC 58.700 47.826 0.00 0.00 39.76 2.34
2570 6224 3.321111 GGCGATAGAAGGGTGTGATCTAA 59.679 47.826 0.00 0.00 39.76 2.10
2571 6225 2.891580 GGCGATAGAAGGGTGTGATCTA 59.108 50.000 0.00 0.00 39.76 1.98
2572 6226 1.689273 GGCGATAGAAGGGTGTGATCT 59.311 52.381 0.00 0.00 39.76 2.75
2573 6227 1.270358 GGGCGATAGAAGGGTGTGATC 60.270 57.143 0.00 0.00 39.76 2.92
2574 6228 0.759346 GGGCGATAGAAGGGTGTGAT 59.241 55.000 0.00 0.00 39.76 3.06
2575 6229 1.335132 GGGGCGATAGAAGGGTGTGA 61.335 60.000 0.00 0.00 39.76 3.58
2576 6230 1.146263 GGGGCGATAGAAGGGTGTG 59.854 63.158 0.00 0.00 39.76 3.82
2577 6231 2.070650 GGGGGCGATAGAAGGGTGT 61.071 63.158 0.00 0.00 39.76 4.16
2578 6232 1.345715 AAGGGGGCGATAGAAGGGTG 61.346 60.000 0.00 0.00 39.76 4.61
2579 6233 1.004361 AAGGGGGCGATAGAAGGGT 59.996 57.895 0.00 0.00 39.76 4.34
2580 6234 1.755384 GAAGGGGGCGATAGAAGGG 59.245 63.158 0.00 0.00 39.76 3.95
2581 6235 0.764752 AGGAAGGGGGCGATAGAAGG 60.765 60.000 0.00 0.00 39.76 3.46
2582 6236 0.682292 GAGGAAGGGGGCGATAGAAG 59.318 60.000 0.00 0.00 39.76 2.85
2583 6237 0.031515 TGAGGAAGGGGGCGATAGAA 60.032 55.000 0.00 0.00 39.76 2.10
2584 6238 0.759436 GTGAGGAAGGGGGCGATAGA 60.759 60.000 0.00 0.00 39.76 1.98
2585 6239 1.749033 GTGAGGAAGGGGGCGATAG 59.251 63.158 0.00 0.00 0.00 2.08
2586 6240 2.131709 CGTGAGGAAGGGGGCGATA 61.132 63.158 0.00 0.00 0.00 2.92
2587 6241 3.470888 CGTGAGGAAGGGGGCGAT 61.471 66.667 0.00 0.00 0.00 4.58
2602 6256 2.294097 TTTTTGTCGTTCACGCGCGT 62.294 50.000 32.73 32.73 39.60 6.01
2603 6257 0.989805 ATTTTTGTCGTTCACGCGCG 60.990 50.000 30.96 30.96 39.60 6.86
2604 6258 0.695410 GATTTTTGTCGTTCACGCGC 59.305 50.000 5.73 0.00 39.60 6.86
2605 6259 1.314581 GGATTTTTGTCGTTCACGCG 58.685 50.000 3.53 3.53 39.60 6.01
2606 6260 1.664874 GGGGATTTTTGTCGTTCACGC 60.665 52.381 0.00 0.00 39.60 5.34
2607 6261 1.068816 GGGGGATTTTTGTCGTTCACG 60.069 52.381 0.00 0.00 41.45 4.35
2608 6262 1.068816 CGGGGGATTTTTGTCGTTCAC 60.069 52.381 0.00 0.00 0.00 3.18
2609 6263 1.240256 CGGGGGATTTTTGTCGTTCA 58.760 50.000 0.00 0.00 0.00 3.18
2610 6264 0.109458 GCGGGGGATTTTTGTCGTTC 60.109 55.000 0.00 0.00 0.00 3.95
2611 6265 0.824182 TGCGGGGGATTTTTGTCGTT 60.824 50.000 0.00 0.00 0.00 3.85
2612 6266 0.824182 TTGCGGGGGATTTTTGTCGT 60.824 50.000 0.00 0.00 0.00 4.34
2613 6267 0.388006 GTTGCGGGGGATTTTTGTCG 60.388 55.000 0.00 0.00 0.00 4.35
2614 6268 0.388006 CGTTGCGGGGGATTTTTGTC 60.388 55.000 0.00 0.00 0.00 3.18
2615 6269 1.663173 CGTTGCGGGGGATTTTTGT 59.337 52.632 0.00 0.00 0.00 2.83
2616 6270 1.736282 GCGTTGCGGGGGATTTTTG 60.736 57.895 0.00 0.00 0.00 2.44
2617 6271 0.609681 TAGCGTTGCGGGGGATTTTT 60.610 50.000 0.00 0.00 0.00 1.94
2618 6272 0.395173 ATAGCGTTGCGGGGGATTTT 60.395 50.000 0.00 0.00 0.00 1.82
2619 6273 0.395173 AATAGCGTTGCGGGGGATTT 60.395 50.000 0.00 0.00 0.00 2.17
2620 6274 0.395173 AAATAGCGTTGCGGGGGATT 60.395 50.000 0.00 0.00 0.00 3.01
2621 6275 1.101049 CAAATAGCGTTGCGGGGGAT 61.101 55.000 0.00 0.00 0.00 3.85
2622 6276 1.747367 CAAATAGCGTTGCGGGGGA 60.747 57.895 0.00 0.00 0.00 4.81
2623 6277 2.043980 ACAAATAGCGTTGCGGGGG 61.044 57.895 0.00 0.00 31.29 5.40
2624 6278 1.136565 CACAAATAGCGTTGCGGGG 59.863 57.895 0.00 0.00 31.29 5.73
2625 6279 1.514014 GCACAAATAGCGTTGCGGG 60.514 57.895 0.00 0.00 31.29 6.13
2626 6280 0.794229 CAGCACAAATAGCGTTGCGG 60.794 55.000 0.00 0.00 37.01 5.69
2627 6281 0.794229 CCAGCACAAATAGCGTTGCG 60.794 55.000 0.00 0.00 37.01 4.85
2628 6282 0.521291 TCCAGCACAAATAGCGTTGC 59.479 50.000 0.00 0.00 37.01 4.17
2629 6283 1.535028 TGTCCAGCACAAATAGCGTTG 59.465 47.619 0.00 0.00 37.01 4.10
2630 6284 1.535462 GTGTCCAGCACAAATAGCGTT 59.465 47.619 0.00 0.00 46.91 4.84
2631 6285 1.156736 GTGTCCAGCACAAATAGCGT 58.843 50.000 0.00 0.00 46.91 5.07
2632 6286 3.975992 GTGTCCAGCACAAATAGCG 57.024 52.632 0.00 0.00 46.91 4.26
2640 6294 4.722700 ATGGCGGGTGTCCAGCAC 62.723 66.667 12.25 3.62 46.97 4.40
2641 6295 4.720902 CATGGCGGGTGTCCAGCA 62.721 66.667 12.25 0.66 36.98 4.41
2643 6297 3.716195 TCCATGGCGGGTGTCCAG 61.716 66.667 6.96 0.00 36.98 3.86
2644 6298 4.028490 GTCCATGGCGGGTGTCCA 62.028 66.667 6.96 0.00 38.09 4.02
2645 6299 4.796495 GGTCCATGGCGGGTGTCC 62.796 72.222 6.96 0.00 34.36 4.02
2652 6306 4.812476 TCGAAGCGGTCCATGGCG 62.812 66.667 6.96 7.18 0.00 5.69


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

AutoCloner maintained by Alex Coulton.