Multiple sequence alignment - TraesCS7B01G295900

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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 TraesCS7B01G295900 chr7B 100.000 2665 0 0 1 2665 532423803 532426467 0.000000e+00 4922
1 TraesCS7B01G295900 chr7B 90.388 645 55 6 1 644 53096793 53096155 0.000000e+00 841
2 TraesCS7B01G295900 chr7B 80.763 603 91 10 2071 2665 488388380 488387795 5.230000e-122 448
3 TraesCS7B01G295900 chr7D 90.288 1040 52 23 785 1794 504489904 504490924 0.000000e+00 1315
4 TraesCS7B01G295900 chr7D 90.579 605 48 9 1 605 538846216 538845621 0.000000e+00 793
5 TraesCS7B01G295900 chr7D 90.016 611 52 9 1 607 638568334 638568939 0.000000e+00 782
6 TraesCS7B01G295900 chr7D 83.633 556 58 16 1951 2492 504491033 504491569 2.380000e-135 492
7 TraesCS7B01G295900 chr7D 90.000 180 18 0 603 782 580844799 580844978 1.600000e-57 233
8 TraesCS7B01G295900 chr7D 88.587 184 21 0 603 786 163050668 163050851 9.600000e-55 224
9 TraesCS7B01G295900 chr7A 89.474 969 82 15 928 1888 572138095 572139051 0.000000e+00 1206
10 TraesCS7B01G295900 chr7A 82.587 603 80 11 2071 2665 11090301 11089716 2.370000e-140 508
11 TraesCS7B01G295900 chr7A 81.063 602 91 11 2071 2665 643252916 643252331 2.420000e-125 459
12 TraesCS7B01G295900 chr7A 87.402 127 7 2 791 908 572137981 572138107 1.290000e-28 137
13 TraesCS7B01G295900 chr1B 89.507 791 62 16 2 788 622877729 622878502 0.000000e+00 981
14 TraesCS7B01G295900 chr1B 81.008 595 88 10 2079 2665 363451249 363451826 1.460000e-122 449
15 TraesCS7B01G295900 chr4B 87.389 785 72 9 1 782 670862516 670861756 0.000000e+00 876
16 TraesCS7B01G295900 chr4B 81.561 602 88 12 2071 2665 624404890 624404305 2.400000e-130 475
17 TraesCS7B01G295900 chr4B 81.260 603 86 15 2071 2664 120503553 120504137 1.870000e-126 462
18 TraesCS7B01G295900 chr3D 90.572 647 46 14 1 644 591206034 591205400 0.000000e+00 843
19 TraesCS7B01G295900 chr3D 82.155 594 79 14 2079 2665 31098833 31098260 3.990000e-133 484
20 TraesCS7B01G295900 chr3D 81.926 592 84 11 2079 2663 459220910 459220335 1.860000e-131 479
21 TraesCS7B01G295900 chr3D 81.229 602 81 15 2071 2665 465020372 465020948 8.700000e-125 457
22 TraesCS7B01G295900 chr3D 91.477 176 15 0 603 778 565460244 565460419 2.650000e-60 243
23 TraesCS7B01G295900 chr5D 89.645 647 59 8 1 644 23217906 23217265 0.000000e+00 817
24 TraesCS7B01G295900 chr5D 90.507 611 48 10 1 608 437691367 437691970 0.000000e+00 798
25 TraesCS7B01G295900 chr5D 81.894 602 83 13 2071 2665 435968372 435968954 3.990000e-133 484
26 TraesCS7B01G295900 chr5D 89.888 178 18 0 605 782 434651492 434651669 2.060000e-56 230
27 TraesCS7B01G295900 chr5D 86.667 150 18 2 2071 2219 53871517 53871369 5.900000e-37 165
28 TraesCS7B01G295900 chr2D 90.651 599 50 4 1 598 46879908 46880501 0.000000e+00 791
29 TraesCS7B01G295900 chr2D 87.678 211 20 3 572 782 606014347 606014143 9.530000e-60 241
30 TraesCS7B01G295900 chr1A 90.429 606 51 6 1 605 6432470 6433069 0.000000e+00 791
31 TraesCS7B01G295900 chr1A 81.023 606 86 14 2071 2664 133200801 133201389 3.130000e-124 455
32 TraesCS7B01G295900 chr1A 80.565 602 94 12 2071 2665 516078843 516079428 2.430000e-120 442
33 TraesCS7B01G295900 chr1A 89.071 183 19 1 600 782 6433100 6433281 2.670000e-55 226
34 TraesCS7B01G295900 chr1D 82.090 603 83 14 2071 2665 373998984 373998399 2.380000e-135 492
35 TraesCS7B01G295900 chr1D 81.592 603 86 13 2071 2665 334455257 334454672 2.400000e-130 475
36 TraesCS7B01G295900 chr1D 84.000 150 14 5 1796 1944 373999325 373999185 4.630000e-28 135
37 TraesCS7B01G295900 chr6A 81.592 603 86 10 2071 2665 49742812 49743397 2.400000e-130 475
38 TraesCS7B01G295900 chr4A 81.260 603 88 10 2071 2665 677124981 677124396 5.200000e-127 464
39 TraesCS7B01G295900 chr2B 81.229 602 90 12 2071 2665 450767047 450767632 5.200000e-127 464
40 TraesCS7B01G295900 chr3B 80.961 583 89 14 2089 2665 746850863 746850297 2.430000e-120 442
41 TraesCS7B01G295900 chr3B 88.298 188 19 3 597 782 828381346 828381532 3.450000e-54 222
42 TraesCS7B01G295900 chr6B 79.076 368 54 12 2071 2434 478758962 478759310 5.740000e-57 231
43 TraesCS7B01G295900 chrUn 84.615 234 28 5 550 782 100368073 100368299 2.670000e-55 226
44 TraesCS7B01G295900 chrUn 87.143 140 16 2 2071 2209 39500864 39501002 9.880000e-35 158
45 TraesCS7B01G295900 chrUn 87.143 140 16 2 2071 2209 178683736 178683598 9.880000e-35 158
46 TraesCS7B01G295900 chr5A 83.902 205 25 4 2083 2284 668172875 668172676 3.500000e-44 189


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 TraesCS7B01G295900 chr7B 532423803 532426467 2664 False 4922.0 4922 100.0000 1 2665 1 chr7B.!!$F1 2664
1 TraesCS7B01G295900 chr7B 53096155 53096793 638 True 841.0 841 90.3880 1 644 1 chr7B.!!$R1 643
2 TraesCS7B01G295900 chr7B 488387795 488388380 585 True 448.0 448 80.7630 2071 2665 1 chr7B.!!$R2 594
3 TraesCS7B01G295900 chr7D 504489904 504491569 1665 False 903.5 1315 86.9605 785 2492 2 chr7D.!!$F4 1707
4 TraesCS7B01G295900 chr7D 538845621 538846216 595 True 793.0 793 90.5790 1 605 1 chr7D.!!$R1 604
5 TraesCS7B01G295900 chr7D 638568334 638568939 605 False 782.0 782 90.0160 1 607 1 chr7D.!!$F3 606
6 TraesCS7B01G295900 chr7A 572137981 572139051 1070 False 671.5 1206 88.4380 791 1888 2 chr7A.!!$F1 1097
7 TraesCS7B01G295900 chr7A 11089716 11090301 585 True 508.0 508 82.5870 2071 2665 1 chr7A.!!$R1 594
8 TraesCS7B01G295900 chr7A 643252331 643252916 585 True 459.0 459 81.0630 2071 2665 1 chr7A.!!$R2 594
9 TraesCS7B01G295900 chr1B 622877729 622878502 773 False 981.0 981 89.5070 2 788 1 chr1B.!!$F2 786
10 TraesCS7B01G295900 chr1B 363451249 363451826 577 False 449.0 449 81.0080 2079 2665 1 chr1B.!!$F1 586
11 TraesCS7B01G295900 chr4B 670861756 670862516 760 True 876.0 876 87.3890 1 782 1 chr4B.!!$R2 781
12 TraesCS7B01G295900 chr4B 624404305 624404890 585 True 475.0 475 81.5610 2071 2665 1 chr4B.!!$R1 594
13 TraesCS7B01G295900 chr4B 120503553 120504137 584 False 462.0 462 81.2600 2071 2664 1 chr4B.!!$F1 593
14 TraesCS7B01G295900 chr3D 591205400 591206034 634 True 843.0 843 90.5720 1 644 1 chr3D.!!$R3 643
15 TraesCS7B01G295900 chr3D 31098260 31098833 573 True 484.0 484 82.1550 2079 2665 1 chr3D.!!$R1 586
16 TraesCS7B01G295900 chr3D 459220335 459220910 575 True 479.0 479 81.9260 2079 2663 1 chr3D.!!$R2 584
17 TraesCS7B01G295900 chr3D 465020372 465020948 576 False 457.0 457 81.2290 2071 2665 1 chr3D.!!$F1 594
18 TraesCS7B01G295900 chr5D 23217265 23217906 641 True 817.0 817 89.6450 1 644 1 chr5D.!!$R1 643
19 TraesCS7B01G295900 chr5D 437691367 437691970 603 False 798.0 798 90.5070 1 608 1 chr5D.!!$F3 607
20 TraesCS7B01G295900 chr5D 435968372 435968954 582 False 484.0 484 81.8940 2071 2665 1 chr5D.!!$F2 594
21 TraesCS7B01G295900 chr2D 46879908 46880501 593 False 791.0 791 90.6510 1 598 1 chr2D.!!$F1 597
22 TraesCS7B01G295900 chr1A 6432470 6433281 811 False 508.5 791 89.7500 1 782 2 chr1A.!!$F3 781
23 TraesCS7B01G295900 chr1A 133200801 133201389 588 False 455.0 455 81.0230 2071 2664 1 chr1A.!!$F1 593
24 TraesCS7B01G295900 chr1A 516078843 516079428 585 False 442.0 442 80.5650 2071 2665 1 chr1A.!!$F2 594
25 TraesCS7B01G295900 chr1D 334454672 334455257 585 True 475.0 475 81.5920 2071 2665 1 chr1D.!!$R1 594
26 TraesCS7B01G295900 chr1D 373998399 373999325 926 True 313.5 492 83.0450 1796 2665 2 chr1D.!!$R2 869
27 TraesCS7B01G295900 chr6A 49742812 49743397 585 False 475.0 475 81.5920 2071 2665 1 chr6A.!!$F1 594
28 TraesCS7B01G295900 chr4A 677124396 677124981 585 True 464.0 464 81.2600 2071 2665 1 chr4A.!!$R1 594
29 TraesCS7B01G295900 chr2B 450767047 450767632 585 False 464.0 464 81.2290 2071 2665 1 chr2B.!!$F1 594
30 TraesCS7B01G295900 chr3B 746850297 746850863 566 True 442.0 442 80.9610 2089 2665 1 chr3B.!!$R1 576

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
702 746 0.664761 CGCTCGAACCGGGACTAATA 59.335 55.0 6.32 0.0 0.0 0.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2254 2490 0.036732 ACGATGGTTGACATGCAGGT 59.963 50.0 2.33 2.33 40.72 4.0 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
555 564 7.727578 AAAGAAACTTTGAGAACCCCTTTAA 57.272 32.000 0.00 0.00 0.00 1.52
567 576 1.683938 CCCCTTTAATCCCGGTTGGTC 60.684 57.143 0.00 0.00 34.77 4.02
569 578 2.506644 CCCTTTAATCCCGGTTGGTCTA 59.493 50.000 0.00 0.00 34.77 2.59
626 670 0.901580 TAGTCCCGGTTGGTGTCTCC 60.902 60.000 0.00 0.00 34.77 3.71
665 709 4.018233 TCCCATTTAAACCGGGACTAATGT 60.018 41.667 19.08 0.00 44.28 2.71
668 712 5.065988 CCATTTAAACCGGGACTAATGTCTG 59.934 44.000 6.32 0.00 42.54 3.51
702 746 0.664761 CGCTCGAACCGGGACTAATA 59.335 55.000 6.32 0.00 0.00 0.98
732 776 4.207891 AGTCCAGATTCGTAATGCAACT 57.792 40.909 0.00 0.00 0.00 3.16
737 781 3.310774 CAGATTCGTAATGCAACTGGGAG 59.689 47.826 0.00 0.00 0.00 4.30
747 791 3.937814 TGCAACTGGGAGTAATGTGTAG 58.062 45.455 0.00 0.00 0.00 2.74
750 794 4.811557 GCAACTGGGAGTAATGTGTAGATC 59.188 45.833 0.00 0.00 0.00 2.75
753 797 4.954202 ACTGGGAGTAATGTGTAGATCGAA 59.046 41.667 0.00 0.00 0.00 3.71
778 822 3.181423 TGGACCAAAGCCCTGTTTTCTAT 60.181 43.478 0.00 0.00 0.00 1.98
782 826 5.016831 ACCAAAGCCCTGTTTTCTATTAGG 58.983 41.667 0.00 0.00 0.00 2.69
794 838 8.189119 TGTTTTCTATTAGGGAAAGCAAATGT 57.811 30.769 0.00 0.00 39.57 2.71
796 840 7.775053 TTTCTATTAGGGAAAGCAAATGTGT 57.225 32.000 0.00 0.00 0.00 3.72
803 847 3.319122 GGGAAAGCAAATGTGTCAGAAGT 59.681 43.478 0.00 0.00 0.00 3.01
811 855 5.448496 GCAAATGTGTCAGAAGTTGTGTACA 60.448 40.000 12.51 12.51 0.00 2.90
825 869 2.884012 TGTGTACATGTTGAAAGCCCAG 59.116 45.455 2.30 0.00 0.00 4.45
828 872 4.218417 GTGTACATGTTGAAAGCCCAGAAT 59.782 41.667 2.30 0.00 0.00 2.40
909 963 2.494073 TCAACAAGGTCAAAACGGCTTT 59.506 40.909 0.00 0.00 0.00 3.51
910 964 2.577449 ACAAGGTCAAAACGGCTTTG 57.423 45.000 6.03 6.03 45.03 2.77
915 969 1.673920 GGTCAAAACGGCTTTGTCTCA 59.326 47.619 10.81 0.00 44.18 3.27
916 970 2.098443 GGTCAAAACGGCTTTGTCTCAA 59.902 45.455 10.81 0.00 44.18 3.02
917 971 3.428316 GGTCAAAACGGCTTTGTCTCAAA 60.428 43.478 10.81 0.00 44.18 2.69
1111 1180 3.791928 CTCGTCGTCCAGGATCGCG 62.792 68.421 0.00 0.00 0.00 5.87
1156 1225 2.806621 GGTGTCCGTTCGTACGCC 60.807 66.667 11.24 4.94 46.27 5.68
1252 1321 4.404098 GCGGCCCCGAAGAAGGAA 62.404 66.667 11.48 0.00 42.83 3.36
1324 1393 4.651008 GACGTCGTTGACCCCGCA 62.651 66.667 0.00 0.00 0.00 5.69
1370 1444 5.266788 TCTCCAAGAAGTAAGGATCGGTTA 58.733 41.667 0.00 0.00 0.00 2.85
1381 1455 1.200716 GGATCGGTTAGTGTGACGACA 59.799 52.381 0.00 0.00 38.24 4.35
1488 1564 5.138095 GTCGACGGATCTTTCTTGTTTTTC 58.862 41.667 0.00 0.00 0.00 2.29
1489 1565 5.050295 GTCGACGGATCTTTCTTGTTTTTCT 60.050 40.000 0.00 0.00 0.00 2.52
1499 1575 6.690957 TCTTTCTTGTTTTTCTACGCATGTTG 59.309 34.615 0.00 0.00 0.00 3.33
1548 1624 4.188462 CAAGTTGATTGGCATGCATGATT 58.812 39.130 30.64 10.62 35.08 2.57
1628 1704 5.976458 TGCATGATTTAATTTCCTTGGTCC 58.024 37.500 0.00 0.00 0.00 4.46
1654 1730 3.247648 CGTGTTCTTGACCAAATTCGAGT 59.752 43.478 0.00 0.00 0.00 4.18
1663 1739 2.693074 ACCAAATTCGAGTGCACCTTTT 59.307 40.909 14.63 3.86 0.00 2.27
1664 1740 3.243401 ACCAAATTCGAGTGCACCTTTTC 60.243 43.478 14.63 3.20 0.00 2.29
1666 1742 4.549458 CAAATTCGAGTGCACCTTTTCAT 58.451 39.130 14.63 0.00 0.00 2.57
1669 1745 5.957842 ATTCGAGTGCACCTTTTCATAAA 57.042 34.783 14.63 0.01 0.00 1.40
1670 1746 5.759506 TTCGAGTGCACCTTTTCATAAAA 57.240 34.783 14.63 0.00 0.00 1.52
1673 1749 5.049680 TCGAGTGCACCTTTTCATAAAAGTC 60.050 40.000 14.63 0.00 44.96 3.01
1677 1753 7.147976 AGTGCACCTTTTCATAAAAGTCATTC 58.852 34.615 14.63 0.88 44.96 2.67
1707 1784 9.932207 TTTATTCGTTTGTCTATTTCTACTCCA 57.068 29.630 0.00 0.00 0.00 3.86
1742 1819 5.049543 CACACGCCAAATCCAAAATTTGATT 60.050 36.000 7.37 2.91 40.42 2.57
1743 1820 5.530543 ACACGCCAAATCCAAAATTTGATTT 59.469 32.000 7.37 9.54 40.42 2.17
1744 1821 6.708054 ACACGCCAAATCCAAAATTTGATTTA 59.292 30.769 7.37 0.00 40.42 1.40
1745 1822 7.390162 ACACGCCAAATCCAAAATTTGATTTAT 59.610 29.630 7.37 0.00 40.42 1.40
1746 1823 8.235905 CACGCCAAATCCAAAATTTGATTTATT 58.764 29.630 7.37 0.00 40.42 1.40
1747 1824 8.791675 ACGCCAAATCCAAAATTTGATTTATTT 58.208 25.926 7.37 5.21 40.42 1.40
1772 1849 9.689501 TTATATTTTTATCCTTGAAACGGAGGT 57.310 29.630 0.00 0.00 33.29 3.85
1778 1855 4.693042 TCCTTGAAACGGAGGTAAAAGA 57.307 40.909 0.00 0.00 34.57 2.52
1780 1857 5.438833 TCCTTGAAACGGAGGTAAAAGAAA 58.561 37.500 0.00 0.00 34.57 2.52
1783 1860 6.238925 CCTTGAAACGGAGGTAAAAGAAATGT 60.239 38.462 0.00 0.00 0.00 2.71
1791 1891 7.013846 ACGGAGGTAAAAGAAATGTTTCATTGA 59.986 33.333 8.09 0.00 39.61 2.57
1823 1923 6.453926 TTTACGAAAAACCAGGCTAAAACT 57.546 33.333 0.00 0.00 0.00 2.66
1836 1936 7.834181 ACCAGGCTAAAACTGTTACAATCATAT 59.166 33.333 0.00 0.00 34.16 1.78
1881 1981 2.128771 ATAACCCCATGAGCACACAC 57.871 50.000 0.00 0.00 0.00 3.82
1913 2013 2.818751 ACCTTCCCAACACAGAACAA 57.181 45.000 0.00 0.00 0.00 2.83
1914 2014 2.375146 ACCTTCCCAACACAGAACAAC 58.625 47.619 0.00 0.00 0.00 3.32
1915 2015 1.681264 CCTTCCCAACACAGAACAACC 59.319 52.381 0.00 0.00 0.00 3.77
1916 2016 1.333619 CTTCCCAACACAGAACAACCG 59.666 52.381 0.00 0.00 0.00 4.44
1923 2023 3.814005 ACACAGAACAACCGTAACTCT 57.186 42.857 0.00 0.00 0.00 3.24
1924 2024 3.714391 ACACAGAACAACCGTAACTCTC 58.286 45.455 0.00 0.00 0.00 3.20
1925 2025 2.724690 CACAGAACAACCGTAACTCTCG 59.275 50.000 0.00 0.00 0.00 4.04
1927 2027 2.978489 CAGAACAACCGTAACTCTCGAC 59.022 50.000 0.00 0.00 0.00 4.20
1937 2037 2.787601 AACTCTCGACGCTTGTACAA 57.212 45.000 8.28 8.28 0.00 2.41
1944 2044 2.219903 TCGACGCTTGTACAACACAATG 59.780 45.455 3.59 0.00 45.96 2.82
1945 2045 2.219903 CGACGCTTGTACAACACAATGA 59.780 45.455 3.59 0.00 45.96 2.57
1946 2046 3.302805 CGACGCTTGTACAACACAATGAA 60.303 43.478 3.59 0.00 45.96 2.57
1947 2047 4.593157 GACGCTTGTACAACACAATGAAA 58.407 39.130 3.59 0.00 45.96 2.69
1949 2049 4.796312 ACGCTTGTACAACACAATGAAAAC 59.204 37.500 3.59 0.00 45.96 2.43
1950 2050 4.795795 CGCTTGTACAACACAATGAAAACA 59.204 37.500 3.59 0.00 45.96 2.83
1951 2051 5.287274 CGCTTGTACAACACAATGAAAACAA 59.713 36.000 3.59 0.00 45.96 2.83
1952 2052 6.019961 CGCTTGTACAACACAATGAAAACAAT 60.020 34.615 3.59 0.00 45.96 2.71
1956 2056 5.947503 ACAACACAATGAAAACAATGACG 57.052 34.783 0.00 0.00 0.00 4.35
1960 2109 3.426191 CACAATGAAAACAATGACGCCAG 59.574 43.478 0.00 0.00 0.00 4.85
1993 2142 2.900547 CCAAGGGGCCGAAAATCAT 58.099 52.632 0.00 0.00 0.00 2.45
1994 2143 0.746659 CCAAGGGGCCGAAAATCATC 59.253 55.000 0.00 0.00 0.00 2.92
2006 2155 4.037208 CCGAAAATCATCCATTAAGCAGCT 59.963 41.667 0.00 0.00 0.00 4.24
2039 2188 2.434336 ACATATGGCGCCACTCTTCTTA 59.566 45.455 35.50 19.23 0.00 2.10
2048 2197 2.485814 GCCACTCTTCTTACCTTTGCAG 59.514 50.000 0.00 0.00 0.00 4.41
2082 2312 1.567649 TCACTATACCAGTCCGAGGGT 59.432 52.381 0.00 0.00 41.21 4.34
2087 2318 2.307496 TACCAGTCCGAGGGTAACAA 57.693 50.000 0.00 0.00 36.73 2.83
2101 2332 1.476845 TAACAACCTCCTCGCTGGCA 61.477 55.000 0.00 0.00 35.26 4.92
2204 2437 2.743718 CACCCAGGCGAGTTCACT 59.256 61.111 0.00 0.00 0.00 3.41
2219 2452 1.570813 TCACTTCACGCAGTTCACAG 58.429 50.000 0.00 0.00 41.61 3.66
2228 2464 1.609061 CGCAGTTCACAGGAGGTTGAT 60.609 52.381 0.00 0.00 0.00 2.57
2235 2471 7.275183 CAGTTCACAGGAGGTTGATTCATATA 58.725 38.462 0.00 0.00 0.00 0.86
2236 2472 7.935755 CAGTTCACAGGAGGTTGATTCATATAT 59.064 37.037 0.00 0.00 0.00 0.86
2237 2473 7.935755 AGTTCACAGGAGGTTGATTCATATATG 59.064 37.037 6.36 6.36 0.00 1.78
2238 2474 7.616528 TCACAGGAGGTTGATTCATATATGA 57.383 36.000 11.49 11.49 34.44 2.15
2254 2490 1.344065 ATGACCCTCACACGTGGTTA 58.656 50.000 21.57 4.62 30.97 2.85
2260 2496 0.249699 CTCACACGTGGTTACCTGCA 60.250 55.000 21.57 0.00 0.00 4.41
2280 2516 3.197265 CATGTCAACCATCGTATGCTCA 58.803 45.455 0.00 0.00 0.00 4.26
2285 2521 3.002791 CAACCATCGTATGCTCAACTGT 58.997 45.455 0.00 0.00 0.00 3.55
2286 2522 4.081917 TCAACCATCGTATGCTCAACTGTA 60.082 41.667 0.00 0.00 0.00 2.74
2287 2523 4.046938 ACCATCGTATGCTCAACTGTAG 57.953 45.455 0.00 0.00 0.00 2.74
2288 2524 2.797156 CCATCGTATGCTCAACTGTAGC 59.203 50.000 0.00 0.00 40.50 3.58
2292 2528 4.673403 TGCTCAACTGTAGCACCG 57.327 55.556 1.23 0.00 44.78 4.94
2295 2531 0.737715 GCTCAACTGTAGCACCGGAG 60.738 60.000 9.46 0.00 39.83 4.63
2327 2563 1.142748 AGAGCTCGCACATAGCACC 59.857 57.895 8.37 0.00 46.13 5.01
2335 2571 1.457346 GCACATAGCACCTGAAGCTT 58.543 50.000 0.00 0.00 43.25 3.74
2345 2581 1.293924 CCTGAAGCTTAGGCATCACG 58.706 55.000 0.00 0.00 40.56 4.35
2387 2623 3.406595 GACAATGGCCCCTCCCTCG 62.407 68.421 0.00 0.00 0.00 4.63
2407 2643 2.695359 GGCGAAAGACAACATAGTGGA 58.305 47.619 0.00 0.00 40.66 4.02
2415 2651 3.009473 AGACAACATAGTGGACAAGGCAT 59.991 43.478 0.00 0.00 0.00 4.40
2455 2694 2.637872 CCACTCTAGGGGAGAAACAACA 59.362 50.000 0.00 0.00 44.45 3.33
2466 2705 4.565652 GGGAGAAACAACAATAGAGCTCCA 60.566 45.833 10.93 0.00 41.80 3.86
2481 2720 0.036875 CTCCACAACCCTGTTCTCCC 59.963 60.000 0.00 0.00 31.64 4.30
2533 2772 2.478890 GCGGCGTAGGAGCAGACTA 61.479 63.158 9.37 0.00 39.27 2.59
2540 2779 2.488545 CGTAGGAGCAGACTACAACACT 59.511 50.000 11.38 0.00 40.58 3.55
2542 2781 4.335874 CGTAGGAGCAGACTACAACACTAT 59.664 45.833 11.38 0.00 40.58 2.12
2570 2813 0.177836 GAGAGAGCTTTCCCAGAGCC 59.822 60.000 0.00 0.00 41.03 4.70
2594 2837 2.360475 GCCCGCTCCAGAAAGCTT 60.360 61.111 0.00 0.00 40.23 3.74
2607 2850 2.058829 AAAGCTTCCAACACGCACCG 62.059 55.000 0.00 0.00 0.00 4.94
2609 2852 4.025401 CTTCCAACACGCACCGGC 62.025 66.667 0.00 0.00 0.00 6.13
2625 2868 4.096003 GCAGCTCAACCCGGGCTA 62.096 66.667 24.08 4.88 34.71 3.93
2631 2874 1.481871 CTCAACCCGGGCTACTAGAA 58.518 55.000 24.08 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
329 332 9.753674 TTTCTTCAAACCCTAGATTGTGAATAT 57.246 29.630 0.00 0.00 0.00 1.28
378 381 9.033481 TGTCATGAGTTTTCAAATTTGAATGAC 57.967 29.630 32.30 32.30 45.65 3.06
398 401 6.603237 TGTCTAGTTTCTGTTTGTGTCATG 57.397 37.500 0.00 0.00 0.00 3.07
534 542 6.295123 GGGATTAAAGGGGTTCTCAAAGTTTC 60.295 42.308 0.00 0.00 0.00 2.78
535 544 5.542635 GGGATTAAAGGGGTTCTCAAAGTTT 59.457 40.000 0.00 0.00 0.00 2.66
538 547 3.694566 CGGGATTAAAGGGGTTCTCAAAG 59.305 47.826 0.00 0.00 0.00 2.77
542 551 1.562942 ACCGGGATTAAAGGGGTTCTC 59.437 52.381 6.32 0.00 0.00 2.87
555 564 3.646932 TGGATAGACCAACCGGGAT 57.353 52.632 6.32 0.00 46.75 3.85
601 610 1.378119 CCAACCGGGACTAAAGGGC 60.378 63.158 6.32 0.00 40.01 5.19
626 670 4.934989 GACCTTTAGTCCCGGCTG 57.065 61.111 0.00 0.00 39.84 4.85
702 746 6.525578 TTACGAATCTGGACTAATGTGAGT 57.474 37.500 0.00 0.00 0.00 3.41
716 760 3.055094 ACTCCCAGTTGCATTACGAATCT 60.055 43.478 0.00 0.00 0.00 2.40
732 776 4.954202 AGTTCGATCTACACATTACTCCCA 59.046 41.667 0.00 0.00 0.00 4.37
737 781 5.519206 GGTCCAAGTTCGATCTACACATTAC 59.481 44.000 0.00 0.00 0.00 1.89
747 791 1.468914 GGCTTTGGTCCAAGTTCGATC 59.531 52.381 4.09 0.00 0.00 3.69
750 794 0.537371 AGGGCTTTGGTCCAAGTTCG 60.537 55.000 4.09 0.00 40.27 3.95
753 797 0.261696 AACAGGGCTTTGGTCCAAGT 59.738 50.000 4.09 0.00 40.27 3.16
778 822 4.724399 TCTGACACATTTGCTTTCCCTAA 58.276 39.130 0.00 0.00 0.00 2.69
782 826 4.574599 ACTTCTGACACATTTGCTTTCC 57.425 40.909 0.00 0.00 0.00 3.13
784 828 5.104374 CACAACTTCTGACACATTTGCTTT 58.896 37.500 0.00 0.00 0.00 3.51
785 829 4.158394 ACACAACTTCTGACACATTTGCTT 59.842 37.500 0.00 0.00 0.00 3.91
787 831 4.032703 ACACAACTTCTGACACATTTGC 57.967 40.909 0.00 0.00 0.00 3.68
788 832 6.117911 TGTACACAACTTCTGACACATTTG 57.882 37.500 0.00 0.00 0.00 2.32
789 833 6.318648 ACATGTACACAACTTCTGACACATTT 59.681 34.615 0.00 0.00 0.00 2.32
794 838 5.423886 TCAACATGTACACAACTTCTGACA 58.576 37.500 0.00 0.00 0.00 3.58
796 840 6.458206 GCTTTCAACATGTACACAACTTCTGA 60.458 38.462 0.00 0.00 0.00 3.27
803 847 3.291584 TGGGCTTTCAACATGTACACAA 58.708 40.909 0.00 0.00 0.00 3.33
811 855 7.293073 ACATATCTATTCTGGGCTTTCAACAT 58.707 34.615 0.00 0.00 0.00 2.71
828 872 7.950684 GGGCCTCCATCAGTATATACATATCTA 59.049 40.741 15.18 0.00 0.00 1.98
1032 1090 6.063640 ACGTGTTTGTTAGGGTTTTATGAC 57.936 37.500 0.00 0.00 0.00 3.06
1123 1192 3.569690 CCACGGTTATTCGCGGCC 61.570 66.667 6.13 0.00 0.00 6.13
1129 1198 1.728425 GAACGGACACCACGGTTATTC 59.272 52.381 0.00 0.00 34.44 1.75
1135 1204 1.730547 GTACGAACGGACACCACGG 60.731 63.158 4.63 0.00 35.23 4.94
1252 1321 2.131023 GGGTCCCTCATCCAGAAGAAT 58.869 52.381 0.00 0.00 0.00 2.40
1358 1432 3.127548 GTCGTCACACTAACCGATCCTTA 59.872 47.826 0.00 0.00 0.00 2.69
1359 1433 2.094854 GTCGTCACACTAACCGATCCTT 60.095 50.000 0.00 0.00 0.00 3.36
1360 1434 1.471684 GTCGTCACACTAACCGATCCT 59.528 52.381 0.00 0.00 0.00 3.24
1361 1435 1.200716 TGTCGTCACACTAACCGATCC 59.799 52.381 0.00 0.00 0.00 3.36
1370 1444 0.959553 AGTCGGATTGTCGTCACACT 59.040 50.000 0.00 0.00 29.76 3.55
1407 1481 6.553857 ACAGGTCTCCCGTCTAATATAATCT 58.446 40.000 0.00 0.00 35.12 2.40
1488 1564 2.058798 ACTTCGTGACAACATGCGTAG 58.941 47.619 0.00 0.00 33.49 3.51
1489 1565 1.790043 CACTTCGTGACAACATGCGTA 59.210 47.619 0.00 0.00 35.23 4.42
1499 1575 2.996621 CAAATCTCCTCCACTTCGTGAC 59.003 50.000 0.00 0.00 35.23 3.67
1628 1704 4.475944 GAATTTGGTCAAGAACACGGATG 58.524 43.478 0.00 0.00 0.00 3.51
1669 1745 9.003658 AGACAAACGAATAAATCTGAATGACTT 57.996 29.630 0.00 0.00 0.00 3.01
1670 1746 8.553459 AGACAAACGAATAAATCTGAATGACT 57.447 30.769 0.00 0.00 0.00 3.41
1707 1784 0.541392 TGGCGTGTGGATTGCTAGAT 59.459 50.000 0.00 0.00 0.00 1.98
1746 1823 9.689501 ACCTCCGTTTCAAGGATAAAAATATAA 57.310 29.630 0.00 0.00 37.13 0.98
1748 1825 9.689501 TTACCTCCGTTTCAAGGATAAAAATAT 57.310 29.630 0.00 0.00 37.13 1.28
1749 1826 9.517868 TTTACCTCCGTTTCAAGGATAAAAATA 57.482 29.630 0.00 0.00 37.13 1.40
1756 1833 5.237236 TCTTTTACCTCCGTTTCAAGGAT 57.763 39.130 0.00 0.00 37.13 3.24
1761 1838 6.702716 AACATTTCTTTTACCTCCGTTTCA 57.297 33.333 0.00 0.00 0.00 2.69
1791 1891 7.929245 AGCCTGGTTTTTCGTAAATTAACAAAT 59.071 29.630 0.00 0.00 0.00 2.32
1847 1947 6.433847 TGGGGTTATATGATTGGTGAGTAG 57.566 41.667 0.00 0.00 0.00 2.57
1862 1962 1.678728 CGTGTGTGCTCATGGGGTTAT 60.679 52.381 0.00 0.00 0.00 1.89
1863 1963 0.321210 CGTGTGTGCTCATGGGGTTA 60.321 55.000 0.00 0.00 0.00 2.85
1864 1964 1.600636 CGTGTGTGCTCATGGGGTT 60.601 57.895 0.00 0.00 0.00 4.11
1913 2013 3.978272 AGCGTCGAGAGTTACGGT 58.022 55.556 0.00 0.00 44.20 4.83
1914 2014 0.109873 ACAAGCGTCGAGAGTTACGG 60.110 55.000 0.00 0.00 39.46 4.02
1915 2015 2.164427 GTACAAGCGTCGAGAGTTACG 58.836 52.381 0.00 0.00 41.92 3.18
1916 2016 3.193157 TGTACAAGCGTCGAGAGTTAC 57.807 47.619 0.00 0.00 0.00 2.50
1923 2023 1.923899 TTGTGTTGTACAAGCGTCGA 58.076 45.000 8.98 0.00 44.07 4.20
1937 2037 3.181482 TGGCGTCATTGTTTTCATTGTGT 60.181 39.130 0.00 0.00 34.16 3.72
1944 2044 1.399727 CGGTCTGGCGTCATTGTTTTC 60.400 52.381 0.00 0.00 0.00 2.29
1945 2045 0.591170 CGGTCTGGCGTCATTGTTTT 59.409 50.000 0.00 0.00 0.00 2.43
1946 2046 0.534203 ACGGTCTGGCGTCATTGTTT 60.534 50.000 0.00 0.00 0.00 2.83
1947 2047 1.070786 ACGGTCTGGCGTCATTGTT 59.929 52.632 0.00 0.00 0.00 2.83
1949 2049 1.354337 CTCACGGTCTGGCGTCATTG 61.354 60.000 0.00 0.00 0.00 2.82
1950 2050 1.079819 CTCACGGTCTGGCGTCATT 60.080 57.895 0.00 0.00 0.00 2.57
1951 2051 2.573869 CTCACGGTCTGGCGTCAT 59.426 61.111 0.00 0.00 0.00 3.06
1952 2052 3.680786 CCTCACGGTCTGGCGTCA 61.681 66.667 0.00 0.00 0.00 4.35
1956 2056 1.216710 CTCTTCCTCACGGTCTGGC 59.783 63.158 0.00 0.00 0.00 4.85
1960 2109 0.390472 CTTGGCTCTTCCTCACGGTC 60.390 60.000 0.00 0.00 35.26 4.79
1976 2125 0.746659 GGATGATTTTCGGCCCCTTG 59.253 55.000 0.00 0.00 0.00 3.61
1993 2142 1.091771 GCTCGCAGCTGCTTAATGGA 61.092 55.000 34.22 21.83 38.45 3.41
1994 2143 1.354506 GCTCGCAGCTGCTTAATGG 59.645 57.895 34.22 18.83 38.45 3.16
2006 2155 1.592400 CATATGTCAGGCGCTCGCA 60.592 57.895 16.36 1.85 44.11 5.10
2017 2166 1.202580 AGAAGAGTGGCGCCATATGTC 60.203 52.381 35.23 25.73 0.00 3.06
2020 2169 2.224305 GGTAAGAAGAGTGGCGCCATAT 60.224 50.000 35.23 24.91 0.00 1.78
2039 2188 2.938956 AGTCACTAAGCTGCAAAGGT 57.061 45.000 1.02 0.00 0.00 3.50
2082 2312 1.295423 GCCAGCGAGGAGGTTGTTA 59.705 57.895 2.12 0.00 41.22 2.41
2087 2318 3.073735 CTCTGCCAGCGAGGAGGT 61.074 66.667 2.12 0.00 41.22 3.85
2204 2437 0.249868 CCTCCTGTGAACTGCGTGAA 60.250 55.000 0.00 0.00 0.00 3.18
2219 2452 6.013379 TGAGGGTCATATATGAATCAACCTCC 60.013 42.308 27.42 19.05 38.75 4.30
2228 2464 4.202212 CCACGTGTGAGGGTCATATATGAA 60.202 45.833 16.97 0.00 38.75 2.57
2235 2471 1.001633 GTAACCACGTGTGAGGGTCAT 59.998 52.381 15.65 0.00 32.67 3.06
2236 2472 0.390124 GTAACCACGTGTGAGGGTCA 59.610 55.000 15.65 0.00 32.67 4.02
2237 2473 0.320160 GGTAACCACGTGTGAGGGTC 60.320 60.000 15.65 0.00 32.67 4.46
2238 2474 0.761702 AGGTAACCACGTGTGAGGGT 60.762 55.000 15.65 1.04 36.19 4.34
2254 2490 0.036732 ACGATGGTTGACATGCAGGT 59.963 50.000 2.33 2.33 40.72 4.00
2260 2496 3.541996 TGAGCATACGATGGTTGACAT 57.458 42.857 0.00 0.00 41.77 3.06
2280 2516 2.214216 TGCCTCCGGTGCTACAGTT 61.214 57.895 17.33 0.00 0.00 3.16
2285 2521 2.345991 GTTGTGCCTCCGGTGCTA 59.654 61.111 17.33 6.31 0.00 3.49
2286 2522 4.643387 GGTTGTGCCTCCGGTGCT 62.643 66.667 17.33 0.00 0.00 4.40
2287 2523 4.947147 TGGTTGTGCCTCCGGTGC 62.947 66.667 0.00 6.56 38.35 5.01
2288 2524 2.978010 GTGGTTGTGCCTCCGGTG 60.978 66.667 0.00 0.00 38.35 4.94
2290 2526 2.034066 ATGTGGTTGTGCCTCCGG 59.966 61.111 0.00 0.00 38.35 5.14
2291 2527 1.300971 CTGATGTGGTTGTGCCTCCG 61.301 60.000 0.00 0.00 38.35 4.63
2292 2528 0.036732 TCTGATGTGGTTGTGCCTCC 59.963 55.000 0.00 0.00 38.35 4.30
2295 2531 0.607489 AGCTCTGATGTGGTTGTGCC 60.607 55.000 0.00 0.00 37.90 5.01
2296 2532 0.801251 GAGCTCTGATGTGGTTGTGC 59.199 55.000 6.43 0.00 0.00 4.57
2297 2533 1.073964 CGAGCTCTGATGTGGTTGTG 58.926 55.000 12.85 0.00 0.00 3.33
2298 2534 0.671781 GCGAGCTCTGATGTGGTTGT 60.672 55.000 12.85 0.00 0.00 3.32
2299 2535 0.671472 TGCGAGCTCTGATGTGGTTG 60.671 55.000 12.85 0.00 0.00 3.77
2300 2536 0.671781 GTGCGAGCTCTGATGTGGTT 60.672 55.000 12.85 0.00 0.00 3.67
2301 2537 1.079543 GTGCGAGCTCTGATGTGGT 60.080 57.895 12.85 0.00 0.00 4.16
2302 2538 0.461516 ATGTGCGAGCTCTGATGTGG 60.462 55.000 12.85 0.00 0.00 4.17
2303 2539 2.125685 CTATGTGCGAGCTCTGATGTG 58.874 52.381 12.85 0.00 0.00 3.21
2304 2540 1.537776 GCTATGTGCGAGCTCTGATGT 60.538 52.381 12.85 0.00 36.96 3.06
2305 2541 1.138337 GCTATGTGCGAGCTCTGATG 58.862 55.000 12.85 0.00 36.96 3.07
2335 2571 0.174845 GGTGCTACACGTGATGCCTA 59.825 55.000 25.01 7.90 34.83 3.93
2345 2581 2.434359 GTGCCTCCGGTGCTACAC 60.434 66.667 17.33 11.90 0.00 2.90
2387 2623 2.415512 GTCCACTATGTTGTCTTTCGCC 59.584 50.000 0.00 0.00 0.00 5.54
2407 2643 0.810031 GCCATCGTCGTATGCCTTGT 60.810 55.000 0.00 0.00 0.00 3.16
2415 2651 0.179181 GACAACTCGCCATCGTCGTA 60.179 55.000 0.00 0.00 36.96 3.43
2455 2694 2.269940 ACAGGGTTGTGGAGCTCTATT 58.730 47.619 14.64 0.00 35.83 1.73
2466 2705 2.526046 CGGGGGAGAACAGGGTTGT 61.526 63.158 0.00 0.00 39.87 3.32
2481 2720 2.819595 CGATGTTGGTGGCTCGGG 60.820 66.667 0.00 0.00 0.00 5.14
2516 2755 1.355916 GTAGTCTGCTCCTACGCCG 59.644 63.158 0.00 0.00 0.00 6.46
2528 2767 5.472478 TCTTGTGTCGATAGTGTTGTAGTCT 59.528 40.000 0.00 0.00 37.40 3.24
2531 2770 5.939457 TCTCTTGTGTCGATAGTGTTGTAG 58.061 41.667 0.00 0.00 37.40 2.74
2533 2772 4.519350 TCTCTCTTGTGTCGATAGTGTTGT 59.481 41.667 0.00 0.00 37.40 3.32
2540 2779 4.142359 GGAAAGCTCTCTCTTGTGTCGATA 60.142 45.833 0.00 0.00 0.00 2.92
2542 2781 2.029828 GGAAAGCTCTCTCTTGTGTCGA 60.030 50.000 0.00 0.00 0.00 4.20
2609 2852 1.327690 TAGTAGCCCGGGTTGAGCTG 61.328 60.000 24.63 0.00 37.45 4.24
2616 2859 0.263765 TCCATTCTAGTAGCCCGGGT 59.736 55.000 24.63 11.76 0.00 5.28
2619 2862 2.632996 TCCAATCCATTCTAGTAGCCCG 59.367 50.000 0.00 0.00 0.00 6.13
2625 2868 4.716784 TGTACTGCTCCAATCCATTCTAGT 59.283 41.667 0.00 0.00 0.00 2.57
2631 2874 2.224378 CCGATGTACTGCTCCAATCCAT 60.224 50.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.