Multiple sequence alignment - TraesCS2A01G324300

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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 TraesCS2A01G324300 chr2A 100.000 2626 0 0 1 2626 554513370 554510745 0.000000e+00 4850.0
1 TraesCS2A01G324300 chr2A 84.203 728 80 15 1051 1745 554519550 554518825 0.000000e+00 675.0
2 TraesCS2A01G324300 chr2B 99.533 857 3 1 1 856 359642987 359643843 0.000000e+00 1559.0
3 TraesCS2A01G324300 chr2B 99.297 853 4 2 1 852 776651274 776650423 0.000000e+00 1541.0
4 TraesCS2A01G324300 chr2B 93.764 866 50 2 885 1747 510792583 510793447 0.000000e+00 1297.0
5 TraesCS2A01G324300 chr2B 83.541 723 88 14 1053 1745 510787861 510788582 0.000000e+00 647.0
6 TraesCS2A01G324300 chr3B 99.068 858 1 2 1 851 520466070 520465213 0.000000e+00 1533.0
7 TraesCS2A01G324300 chr4A 99.063 854 6 2 1 852 559061566 559062419 0.000000e+00 1531.0
8 TraesCS2A01G324300 chr1B 99.063 854 6 2 1 852 428730870 428731723 0.000000e+00 1531.0
9 TraesCS2A01G324300 chr7A 98.481 856 7 2 1 855 494194486 494193636 0.000000e+00 1504.0
10 TraesCS2A01G324300 chr7A 94.872 624 27 4 170 788 678601943 678601320 0.000000e+00 970.0
11 TraesCS2A01G324300 chr7A 96.757 185 5 1 1 185 678602836 678602653 9.130000e-80 307.0
12 TraesCS2A01G324300 chr2D 93.823 858 53 0 885 1742 432029645 432030502 0.000000e+00 1291.0
13 TraesCS2A01G324300 chr2D 85.556 720 78 11 1051 1745 432000299 432001017 0.000000e+00 730.0
14 TraesCS2A01G324300 chr2D 100.000 45 0 0 1685 1729 432000914 432000958 1.670000e-12 84.2
15 TraesCS2A01G324300 chr2D 95.349 43 2 0 1687 1729 432030404 432030446 4.690000e-08 69.4
16 TraesCS2A01G324300 chr7D 90.097 828 50 20 46 855 571239618 571238805 0.000000e+00 1046.0
17 TraesCS2A01G324300 chr7D 90.764 563 39 5 296 853 54008898 54009452 0.000000e+00 739.0
18 TraesCS2A01G324300 chr7D 88.148 270 14 11 46 302 53999962 54000226 3.280000e-79 305.0
19 TraesCS2A01G324300 chr3A 88.172 837 46 23 46 851 41432559 41433373 0.000000e+00 948.0
20 TraesCS2A01G324300 chr5D 88.185 821 53 27 46 835 466564534 466563727 0.000000e+00 939.0
21 TraesCS2A01G324300 chr1A 91.049 324 20 8 1743 2063 548459753 548460070 1.870000e-116 429.0
22 TraesCS2A01G324300 chr1A 89.474 323 25 8 1744 2063 555647243 555647559 1.460000e-107 399.0
23 TraesCS2A01G324300 chr1A 85.401 411 22 13 2201 2578 555648466 555648871 2.450000e-105 392.0
24 TraesCS2A01G324300 chr1A 82.641 409 29 12 2200 2575 548462520 548462919 9.070000e-85 324.0
25 TraesCS2A01G324300 chr1A 79.661 413 40 24 2200 2578 17699158 17699560 9.330000e-65 257.0
26 TraesCS2A01G324300 chr5A 80.872 413 34 20 2200 2578 501496395 501495994 1.540000e-72 283.0


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 TraesCS2A01G324300 chr2A 554510745 554513370 2625 True 4850.0 4850 100.0000 1 2626 1 chr2A.!!$R1 2625
1 TraesCS2A01G324300 chr2A 554518825 554519550 725 True 675.0 675 84.2030 1051 1745 1 chr2A.!!$R2 694
2 TraesCS2A01G324300 chr2B 359642987 359643843 856 False 1559.0 1559 99.5330 1 856 1 chr2B.!!$F1 855
3 TraesCS2A01G324300 chr2B 776650423 776651274 851 True 1541.0 1541 99.2970 1 852 1 chr2B.!!$R1 851
4 TraesCS2A01G324300 chr2B 510792583 510793447 864 False 1297.0 1297 93.7640 885 1747 1 chr2B.!!$F3 862
5 TraesCS2A01G324300 chr2B 510787861 510788582 721 False 647.0 647 83.5410 1053 1745 1 chr2B.!!$F2 692
6 TraesCS2A01G324300 chr3B 520465213 520466070 857 True 1533.0 1533 99.0680 1 851 1 chr3B.!!$R1 850
7 TraesCS2A01G324300 chr4A 559061566 559062419 853 False 1531.0 1531 99.0630 1 852 1 chr4A.!!$F1 851
8 TraesCS2A01G324300 chr1B 428730870 428731723 853 False 1531.0 1531 99.0630 1 852 1 chr1B.!!$F1 851
9 TraesCS2A01G324300 chr7A 494193636 494194486 850 True 1504.0 1504 98.4810 1 855 1 chr7A.!!$R1 854
10 TraesCS2A01G324300 chr7A 678601320 678602836 1516 True 638.5 970 95.8145 1 788 2 chr7A.!!$R2 787
11 TraesCS2A01G324300 chr2D 432029645 432030502 857 False 680.2 1291 94.5860 885 1742 2 chr2D.!!$F2 857
12 TraesCS2A01G324300 chr2D 432000299 432001017 718 False 407.1 730 92.7780 1051 1745 2 chr2D.!!$F1 694
13 TraesCS2A01G324300 chr7D 571238805 571239618 813 True 1046.0 1046 90.0970 46 855 1 chr7D.!!$R1 809
14 TraesCS2A01G324300 chr7D 54008898 54009452 554 False 739.0 739 90.7640 296 853 1 chr7D.!!$F2 557
15 TraesCS2A01G324300 chr3A 41432559 41433373 814 False 948.0 948 88.1720 46 851 1 chr3A.!!$F1 805
16 TraesCS2A01G324300 chr5D 466563727 466564534 807 True 939.0 939 88.1850 46 835 1 chr5D.!!$R1 789
17 TraesCS2A01G324300 chr1A 555647243 555648871 1628 False 395.5 399 87.4375 1744 2578 2 chr1A.!!$F3 834
18 TraesCS2A01G324300 chr1A 548459753 548462919 3166 False 376.5 429 86.8450 1743 2575 2 chr1A.!!$F2 832

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
897 1675 0.03213 TCTGCTCTCGCGTGTTTCTT 59.968 50.0 5.77 0.0 39.65 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 2789 0.400525 ATCGATGGACATGGAGGGGT 60.401 55.0 0.0 0.0 0.0 4.95 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
856 1634 6.183360 TGCACTTTTGAGATTTCGGGATAATC 60.183 38.462 0.00 0.00 33.23 1.75
857 1635 6.038714 GCACTTTTGAGATTTCGGGATAATCT 59.961 38.462 0.00 0.00 43.23 2.40
858 1636 7.226720 GCACTTTTGAGATTTCGGGATAATCTA 59.773 37.037 0.00 0.00 41.24 1.98
859 1637 9.109393 CACTTTTGAGATTTCGGGATAATCTAA 57.891 33.333 0.00 0.00 41.24 2.10
860 1638 9.681062 ACTTTTGAGATTTCGGGATAATCTAAA 57.319 29.630 0.00 0.00 41.24 1.85
861 1639 9.937175 CTTTTGAGATTTCGGGATAATCTAAAC 57.063 33.333 0.00 0.00 41.24 2.01
862 1640 8.446599 TTTGAGATTTCGGGATAATCTAAACC 57.553 34.615 0.00 0.00 41.24 3.27
863 1641 7.374975 TGAGATTTCGGGATAATCTAAACCT 57.625 36.000 0.00 0.00 41.24 3.50
864 1642 8.486942 TGAGATTTCGGGATAATCTAAACCTA 57.513 34.615 0.00 0.00 41.24 3.08
865 1643 8.365647 TGAGATTTCGGGATAATCTAAACCTAC 58.634 37.037 0.00 0.00 41.24 3.18
866 1644 7.376615 AGATTTCGGGATAATCTAAACCTACG 58.623 38.462 0.00 0.00 39.82 3.51
867 1645 5.458041 TTCGGGATAATCTAAACCTACGG 57.542 43.478 0.00 0.00 0.00 4.02
868 1646 4.473444 TCGGGATAATCTAAACCTACGGT 58.527 43.478 0.00 0.00 37.65 4.83
869 1647 4.279169 TCGGGATAATCTAAACCTACGGTG 59.721 45.833 0.00 0.00 35.34 4.94
870 1648 4.279169 CGGGATAATCTAAACCTACGGTGA 59.721 45.833 0.00 0.00 35.34 4.02
871 1649 5.564259 CGGGATAATCTAAACCTACGGTGAG 60.564 48.000 0.00 0.00 35.34 3.51
872 1650 5.537674 GGGATAATCTAAACCTACGGTGAGA 59.462 44.000 0.00 0.00 35.34 3.27
873 1651 6.294620 GGGATAATCTAAACCTACGGTGAGAG 60.295 46.154 0.00 0.00 35.34 3.20
874 1652 4.388378 AATCTAAACCTACGGTGAGAGC 57.612 45.455 0.00 0.00 35.34 4.09
875 1653 3.083122 TCTAAACCTACGGTGAGAGCT 57.917 47.619 0.00 0.00 35.34 4.09
876 1654 3.015327 TCTAAACCTACGGTGAGAGCTC 58.985 50.000 5.27 5.27 35.34 4.09
877 1655 0.526662 AAACCTACGGTGAGAGCTCG 59.473 55.000 8.37 0.00 35.34 5.03
878 1656 0.608582 AACCTACGGTGAGAGCTCGT 60.609 55.000 8.37 5.28 35.34 4.18
879 1657 1.025647 ACCTACGGTGAGAGCTCGTC 61.026 60.000 8.37 7.13 38.19 4.20
880 1658 0.745128 CCTACGGTGAGAGCTCGTCT 60.745 60.000 8.37 0.00 38.71 4.18
881 1659 0.375454 CTACGGTGAGAGCTCGTCTG 59.625 60.000 8.37 10.16 34.71 3.51
882 1660 1.645704 TACGGTGAGAGCTCGTCTGC 61.646 60.000 8.37 4.42 34.71 4.26
897 1675 0.032130 TCTGCTCTCGCGTGTTTCTT 59.968 50.000 5.77 0.00 39.65 2.52
906 1684 1.724654 CGCGTGTTTCTTTGGGAATCG 60.725 52.381 0.00 0.00 33.53 3.34
972 1750 3.368843 CGATCATATAAGTCAGCAGGGGG 60.369 52.174 0.00 0.00 0.00 5.40
1005 1783 2.024868 CGTTCGCACCATCGGTTGA 61.025 57.895 0.00 0.00 31.02 3.18
1071 1852 2.508891 CGAGTTGATCAGGACGCGC 61.509 63.158 5.73 0.00 32.80 6.86
1161 1943 1.274416 ACCAAGGGGGCAGAGATTCTA 60.274 52.381 0.00 0.00 42.05 2.10
1461 2243 4.135153 CCGGTCGTGGAGGAGCTG 62.135 72.222 0.00 0.00 32.39 4.24
1523 2305 1.342174 AGTAGAAGGAACCGAACGCAA 59.658 47.619 0.00 0.00 0.00 4.85
1562 2344 1.672854 CCCAACGCCAGATACCTCGA 61.673 60.000 0.00 0.00 0.00 4.04
1610 2416 1.161843 CCGGCCACGTAACAGATTTT 58.838 50.000 2.24 0.00 38.78 1.82
1614 2420 3.302221 CGGCCACGTAACAGATTTTATCG 60.302 47.826 2.24 0.00 34.81 2.92
1665 2479 6.194692 CGTTCTGTTAGTTTTCTGTTCAAAGC 59.805 38.462 0.00 0.00 0.00 3.51
1750 2565 5.182190 TCGGCTTCAGATGATGTATCTCTAC 59.818 44.000 0.00 0.00 44.34 2.59
1775 2590 2.684001 AATAGGGCAATCGAACGTCA 57.316 45.000 0.00 0.00 0.00 4.35
1784 2599 3.673366 CAATCGAACGTCATGATGGTTG 58.327 45.455 18.97 16.17 0.00 3.77
1785 2600 2.734276 TCGAACGTCATGATGGTTGA 57.266 45.000 17.53 17.53 0.00 3.18
1791 2606 1.660607 CGTCATGATGGTTGAACCTCG 59.339 52.381 16.33 5.42 39.58 4.63
1795 2610 1.790755 TGATGGTTGAACCTCGTTCG 58.209 50.000 16.33 0.00 44.55 3.95
1800 2615 1.416373 GTTGAACCTCGTTCGACCTC 58.584 55.000 12.12 0.00 45.86 3.85
1804 2619 2.678934 CCTCGTTCGACCTCCCCA 60.679 66.667 0.00 0.00 0.00 4.96
1813 2628 0.320946 CGACCTCCCCACGCTAAAAA 60.321 55.000 0.00 0.00 0.00 1.94
1818 2634 1.933853 CTCCCCACGCTAAAAAGATCG 59.066 52.381 0.00 0.00 0.00 3.69
1823 2639 3.259064 CCACGCTAAAAAGATCGAAGGA 58.741 45.455 0.00 0.00 0.00 3.36
1830 2646 5.856986 GCTAAAAAGATCGAAGGAAACAACC 59.143 40.000 0.00 0.00 0.00 3.77
1834 2650 2.105821 AGATCGAAGGAAACAACCCACA 59.894 45.455 0.00 0.00 0.00 4.17
1838 2654 2.621055 CGAAGGAAACAACCCACATTCA 59.379 45.455 0.00 0.00 0.00 2.57
1895 2712 1.157751 AACTCCTCCCCGACCTTCA 59.842 57.895 0.00 0.00 0.00 3.02
1918 2735 5.068460 CAGGTTTGTCTTCCGAGATATCTCT 59.932 44.000 26.29 4.15 40.75 3.10
1946 2763 0.909610 ACACGACCCATCCACATCCT 60.910 55.000 0.00 0.00 0.00 3.24
1950 2767 0.181350 GACCCATCCACATCCTCACC 59.819 60.000 0.00 0.00 0.00 4.02
1972 2789 1.537889 ATCTCCCACGACCACCCAA 60.538 57.895 0.00 0.00 0.00 4.12
2031 2848 1.251527 GCTCGACACCTCCTCTTCCA 61.252 60.000 0.00 0.00 0.00 3.53
2035 2852 1.134965 CGACACCTCCTCTTCCATGAC 60.135 57.143 0.00 0.00 0.00 3.06
2037 2854 0.176680 CACCTCCTCTTCCATGACCG 59.823 60.000 0.00 0.00 0.00 4.79
2071 5172 9.249457 CTTTACGCTCATCTATTATCAAGTTCA 57.751 33.333 0.00 0.00 0.00 3.18
2072 5173 8.575565 TTACGCTCATCTATTATCAAGTTCAC 57.424 34.615 0.00 0.00 0.00 3.18
2080 5181 8.759641 CATCTATTATCAAGTTCACAGTACTGC 58.240 37.037 22.90 6.45 0.00 4.40
2081 5182 7.836842 TCTATTATCAAGTTCACAGTACTGCA 58.163 34.615 22.90 6.91 0.00 4.41
2083 5184 7.744087 ATTATCAAGTTCACAGTACTGCAAA 57.256 32.000 22.90 13.88 0.00 3.68
2095 5196 4.324669 CAGTACTGCAAATACTGTCAGACG 59.675 45.833 21.73 3.40 43.03 4.18
2103 5204 5.444745 GCAAATACTGTCAGACGACTAAAGC 60.445 44.000 6.91 0.00 43.06 3.51
2124 5225 3.743396 GCTAGCTGTTATGCATACTGACC 59.257 47.826 7.70 0.00 34.99 4.02
2185 5286 5.415701 GTGAGATTTTGCTTTCATGGGTCTA 59.584 40.000 0.00 0.00 0.00 2.59
2186 5287 6.009589 TGAGATTTTGCTTTCATGGGTCTAA 58.990 36.000 0.00 0.00 0.00 2.10
2190 5291 6.478512 TTTTGCTTTCATGGGTCTAACTTT 57.521 33.333 0.00 0.00 0.00 2.66
2196 5297 6.642540 GCTTTCATGGGTCTAACTTTCTTTTG 59.357 38.462 0.00 0.00 0.00 2.44
2268 5399 6.394809 AGTTAAAATTAATTGGTTGGCCTCG 58.605 36.000 3.32 0.00 35.27 4.63
2273 5404 2.579410 AATTGGTTGGCCTCGTTAGT 57.421 45.000 3.32 0.00 35.27 2.24
2289 5420 7.868415 GCCTCGTTAGTGTTATATCAGAGATTT 59.132 37.037 0.00 0.00 0.00 2.17
2290 5421 9.186323 CCTCGTTAGTGTTATATCAGAGATTTG 57.814 37.037 0.00 0.00 0.00 2.32
2298 5456 2.611225 ATCAGAGATTTGGCGGACTC 57.389 50.000 0.00 0.00 0.00 3.36
2311 5469 2.224572 GGCGGACTCTCTCTACCTATGA 60.225 54.545 0.00 0.00 0.00 2.15
2332 5490 2.766313 TGATTGGGTGTTGACTTCTCG 58.234 47.619 0.00 0.00 0.00 4.04
2334 5492 0.534203 TTGGGTGTTGACTTCTCGCC 60.534 55.000 0.00 0.00 0.00 5.54
2336 5494 2.027625 GGTGTTGACTTCTCGCCCG 61.028 63.158 0.00 0.00 0.00 6.13
2337 5495 2.357034 TGTTGACTTCTCGCCCGC 60.357 61.111 0.00 0.00 0.00 6.13
2338 5496 2.357034 GTTGACTTCTCGCCCGCA 60.357 61.111 0.00 0.00 0.00 5.69
2400 5564 4.082949 TGACCCGAGATGTATATACAAGCG 60.083 45.833 19.11 19.53 39.99 4.68
2447 5611 9.950496 AGACATAAATATCACATCCTATTGTCC 57.050 33.333 0.00 0.00 0.00 4.02
2453 5617 4.927267 TCACATCCTATTGTCCTGGTTT 57.073 40.909 0.00 0.00 0.00 3.27
2457 5621 5.943416 CACATCCTATTGTCCTGGTTTACAA 59.057 40.000 2.38 2.38 39.73 2.41
2472 5636 8.012809 CCTGGTTTACAACTTGTTTTTCAAAAC 58.987 33.333 8.02 8.02 46.40 2.43
2506 5670 6.694411 CAGCATGTCATTAGCCAAATTAGAAC 59.306 38.462 0.00 0.00 0.00 3.01
2587 5751 7.265647 TCAACAGAAAATTGATTTACGTCCA 57.734 32.000 0.00 0.00 31.11 4.02
2588 5752 7.708051 TCAACAGAAAATTGATTTACGTCCAA 58.292 30.769 0.00 0.00 31.11 3.53
2589 5753 7.646130 TCAACAGAAAATTGATTTACGTCCAAC 59.354 33.333 0.00 0.00 31.11 3.77
2590 5754 7.272037 ACAGAAAATTGATTTACGTCCAACT 57.728 32.000 0.00 0.00 0.00 3.16
2591 5755 7.360361 ACAGAAAATTGATTTACGTCCAACTC 58.640 34.615 0.00 0.00 0.00 3.01
2592 5756 7.012894 ACAGAAAATTGATTTACGTCCAACTCA 59.987 33.333 0.00 0.00 0.00 3.41
2593 5757 7.535258 CAGAAAATTGATTTACGTCCAACTCAG 59.465 37.037 0.00 0.00 0.00 3.35
2594 5758 5.880054 AATTGATTTACGTCCAACTCAGG 57.120 39.130 0.00 0.00 0.00 3.86
2595 5759 2.695359 TGATTTACGTCCAACTCAGGC 58.305 47.619 0.00 0.00 0.00 4.85
2596 5760 2.301870 TGATTTACGTCCAACTCAGGCT 59.698 45.455 0.00 0.00 0.00 4.58
2597 5761 2.922740 TTTACGTCCAACTCAGGCTT 57.077 45.000 0.00 0.00 0.00 4.35
2598 5762 2.450609 TTACGTCCAACTCAGGCTTC 57.549 50.000 0.00 0.00 0.00 3.86
2599 5763 1.334160 TACGTCCAACTCAGGCTTCA 58.666 50.000 0.00 0.00 0.00 3.02
2600 5764 0.468226 ACGTCCAACTCAGGCTTCAA 59.532 50.000 0.00 0.00 0.00 2.69
2601 5765 0.868406 CGTCCAACTCAGGCTTCAAC 59.132 55.000 0.00 0.00 0.00 3.18
2602 5766 1.239347 GTCCAACTCAGGCTTCAACC 58.761 55.000 0.00 0.00 0.00 3.77
2603 5767 0.843309 TCCAACTCAGGCTTCAACCA 59.157 50.000 0.00 0.00 0.00 3.67
2604 5768 1.214175 TCCAACTCAGGCTTCAACCAA 59.786 47.619 0.00 0.00 0.00 3.67
2605 5769 2.158475 TCCAACTCAGGCTTCAACCAAT 60.158 45.455 0.00 0.00 0.00 3.16
2606 5770 2.229784 CCAACTCAGGCTTCAACCAATC 59.770 50.000 0.00 0.00 0.00 2.67
2607 5771 2.886523 CAACTCAGGCTTCAACCAATCA 59.113 45.455 0.00 0.00 0.00 2.57
2608 5772 2.508526 ACTCAGGCTTCAACCAATCAC 58.491 47.619 0.00 0.00 0.00 3.06
2609 5773 2.107204 ACTCAGGCTTCAACCAATCACT 59.893 45.455 0.00 0.00 0.00 3.41
2610 5774 2.486982 CTCAGGCTTCAACCAATCACTG 59.513 50.000 0.00 0.00 0.00 3.66
2611 5775 1.068055 CAGGCTTCAACCAATCACTGC 60.068 52.381 0.00 0.00 0.00 4.40
2612 5776 1.202976 AGGCTTCAACCAATCACTGCT 60.203 47.619 0.00 0.00 0.00 4.24
2613 5777 1.200948 GGCTTCAACCAATCACTGCTC 59.799 52.381 0.00 0.00 0.00 4.26
2614 5778 2.157738 GCTTCAACCAATCACTGCTCT 58.842 47.619 0.00 0.00 0.00 4.09
2615 5779 3.338249 GCTTCAACCAATCACTGCTCTA 58.662 45.455 0.00 0.00 0.00 2.43
2616 5780 3.126000 GCTTCAACCAATCACTGCTCTAC 59.874 47.826 0.00 0.00 0.00 2.59
2617 5781 4.573900 CTTCAACCAATCACTGCTCTACT 58.426 43.478 0.00 0.00 0.00 2.57
2618 5782 4.623932 TCAACCAATCACTGCTCTACTT 57.376 40.909 0.00 0.00 0.00 2.24
2619 5783 5.738619 TCAACCAATCACTGCTCTACTTA 57.261 39.130 0.00 0.00 0.00 2.24
2620 5784 6.299805 TCAACCAATCACTGCTCTACTTAT 57.700 37.500 0.00 0.00 0.00 1.73
2621 5785 6.108687 TCAACCAATCACTGCTCTACTTATG 58.891 40.000 0.00 0.00 0.00 1.90
2622 5786 5.683876 ACCAATCACTGCTCTACTTATGT 57.316 39.130 0.00 0.00 0.00 2.29
2623 5787 5.665459 ACCAATCACTGCTCTACTTATGTC 58.335 41.667 0.00 0.00 0.00 3.06
2624 5788 5.053145 CCAATCACTGCTCTACTTATGTCC 58.947 45.833 0.00 0.00 0.00 4.02
2625 5789 5.163364 CCAATCACTGCTCTACTTATGTCCT 60.163 44.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
862 1640 0.375454 CAGACGAGCTCTCACCGTAG 59.625 60.000 12.85 0.00 36.60 3.51
863 1641 1.645704 GCAGACGAGCTCTCACCGTA 61.646 60.000 12.85 0.00 36.60 4.02
864 1642 2.983930 GCAGACGAGCTCTCACCGT 61.984 63.158 12.85 4.39 39.41 4.83
865 1643 2.202544 GCAGACGAGCTCTCACCG 60.203 66.667 12.85 0.49 0.00 4.94
866 1644 3.283303 AGCAGACGAGCTCTCACC 58.717 61.111 12.85 4.08 42.18 4.02
882 1660 0.512952 CCCAAAGAAACACGCGAGAG 59.487 55.000 15.93 4.52 0.00 3.20
883 1661 0.105224 TCCCAAAGAAACACGCGAGA 59.895 50.000 15.93 0.00 0.00 4.04
888 1666 3.496884 TCTTCGATTCCCAAAGAAACACG 59.503 43.478 0.00 0.00 38.21 4.49
906 1684 1.396301 ACCGTGTACGAGTCGATCTTC 59.604 52.381 21.50 5.05 43.02 2.87
1005 1783 2.866726 GCGGTGTTGGGTGGCAATT 61.867 57.895 0.00 0.00 0.00 2.32
1461 2243 2.726351 CCCCAACTCCGAGCTCTCC 61.726 68.421 12.85 0.00 0.00 3.71
1523 2305 2.234143 GCTTCCTTGTTCTTGCTTCCT 58.766 47.619 0.00 0.00 0.00 3.36
1614 2420 6.568869 CATGATCTCTTATTCCGGTAGATCC 58.431 44.000 18.03 8.30 41.12 3.36
1665 2479 6.530534 ACAAACGACCGATAATCTAGTTTGAG 59.469 38.462 20.28 0.99 45.44 3.02
1750 2565 6.422701 TGACGTTCGATTGCCCTATTTAATAG 59.577 38.462 5.06 5.06 0.00 1.73
1757 2572 2.102420 TCATGACGTTCGATTGCCCTAT 59.898 45.455 0.00 0.00 0.00 2.57
1758 2573 1.478916 TCATGACGTTCGATTGCCCTA 59.521 47.619 0.00 0.00 0.00 3.53
1775 2590 2.028476 TCGAACGAGGTTCAACCATCAT 60.028 45.455 9.90 0.00 42.05 2.45
1784 2599 1.214853 GGGAGGTCGAACGAGGTTC 59.785 63.158 0.00 0.00 38.97 3.62
1785 2600 2.281295 GGGGAGGTCGAACGAGGTT 61.281 63.158 0.00 0.00 0.00 3.50
1791 2606 1.880819 TTAGCGTGGGGAGGTCGAAC 61.881 60.000 0.00 0.00 0.00 3.95
1795 2610 1.002773 TCTTTTTAGCGTGGGGAGGTC 59.997 52.381 0.00 0.00 0.00 3.85
1800 2615 2.018542 TCGATCTTTTTAGCGTGGGG 57.981 50.000 0.00 0.00 0.00 4.96
1804 2619 4.753107 TGTTTCCTTCGATCTTTTTAGCGT 59.247 37.500 0.00 0.00 0.00 5.07
1813 2628 2.105821 TGTGGGTTGTTTCCTTCGATCT 59.894 45.455 0.00 0.00 0.00 2.75
1818 2634 4.501400 CCTTGAATGTGGGTTGTTTCCTTC 60.501 45.833 0.00 0.00 0.00 3.46
1823 2639 3.370104 TGTCCTTGAATGTGGGTTGTTT 58.630 40.909 0.00 0.00 0.00 2.83
1830 2646 4.935352 TTTTTCCTGTCCTTGAATGTGG 57.065 40.909 0.00 0.00 0.00 4.17
1895 2712 5.523438 GAGATATCTCGGAAGACAAACCT 57.477 43.478 16.77 0.00 33.32 3.50
1908 2725 4.709250 GTGTTTGGGGGAAGAGATATCTC 58.291 47.826 22.92 22.92 43.17 2.75
1918 2735 1.721093 ATGGGTCGTGTTTGGGGGAA 61.721 55.000 0.00 0.00 0.00 3.97
1946 2763 2.687200 CGTGGGAGATGGGGGTGA 60.687 66.667 0.00 0.00 0.00 4.02
1950 2767 2.687200 TGGTCGTGGGAGATGGGG 60.687 66.667 0.00 0.00 0.00 4.96
1972 2789 0.400525 ATCGATGGACATGGAGGGGT 60.401 55.000 0.00 0.00 0.00 4.95
2031 2848 1.135083 CGTAAAGAGAGGCACGGTCAT 60.135 52.381 0.00 0.00 0.00 3.06
2035 2852 0.802607 GAGCGTAAAGAGAGGCACGG 60.803 60.000 0.00 0.00 35.04 4.94
2037 2854 2.159170 AGATGAGCGTAAAGAGAGGCAC 60.159 50.000 0.00 0.00 32.60 5.01
2095 5196 6.926272 AGTATGCATAACAGCTAGCTTTAGTC 59.074 38.462 16.46 12.23 34.99 2.59
2103 5204 3.983988 CGGTCAGTATGCATAACAGCTAG 59.016 47.826 8.28 0.00 34.76 3.42
2124 5225 2.781681 AAAATAGAGTCCACACCCCG 57.218 50.000 0.00 0.00 0.00 5.73
2151 5252 7.818930 TGAAAGCAAAATCTCACTTGAGTTTTT 59.181 29.630 16.94 16.94 46.56 1.94
2175 5276 5.136828 TGCAAAAGAAAGTTAGACCCATGA 58.863 37.500 0.00 0.00 0.00 3.07
2196 5297 8.638685 ATGCATACACAAAGAGAAATAATTGC 57.361 30.769 0.00 0.00 0.00 3.56
2256 5387 0.470766 ACACTAACGAGGCCAACCAA 59.529 50.000 5.01 0.00 39.06 3.67
2268 5399 7.095607 CCGCCAAATCTCTGATATAACACTAAC 60.096 40.741 0.00 0.00 0.00 2.34
2273 5404 5.070446 AGTCCGCCAAATCTCTGATATAACA 59.930 40.000 0.00 0.00 0.00 2.41
2289 5420 1.210538 TAGGTAGAGAGAGTCCGCCA 58.789 55.000 0.00 0.00 0.00 5.69
2290 5421 2.156098 CATAGGTAGAGAGAGTCCGCC 58.844 57.143 0.00 0.00 0.00 6.13
2298 5456 5.541868 ACACCCAATCATCATAGGTAGAGAG 59.458 44.000 0.00 0.00 0.00 3.20
2311 5469 3.338249 CGAGAAGTCAACACCCAATCAT 58.662 45.455 0.00 0.00 0.00 2.45
2332 5490 0.679960 AAGTAGTTGGGATTGCGGGC 60.680 55.000 0.00 0.00 0.00 6.13
2334 5492 2.403252 AGAAGTAGTTGGGATTGCGG 57.597 50.000 0.00 0.00 0.00 5.69
2336 5494 5.904362 AATGAAGAAGTAGTTGGGATTGC 57.096 39.130 0.00 0.00 0.00 3.56
2365 5523 2.027385 CTCGGGTCAGATGAGTGATGA 58.973 52.381 0.00 0.00 0.00 2.92
2377 5535 4.082949 CGCTTGTATATACATCTCGGGTCA 60.083 45.833 16.16 0.00 35.89 4.02
2447 5611 8.927315 GTTTTGAAAAACAAGTTGTAAACCAG 57.073 30.769 9.37 0.00 46.51 4.00
2453 5617 6.764877 TTGCGTTTTGAAAAACAAGTTGTA 57.235 29.167 9.37 0.00 46.52 2.41
2457 5621 6.073003 TGGAAATTGCGTTTTGAAAAACAAGT 60.073 30.769 16.53 7.37 46.52 3.16
2472 5636 2.572191 ATGACATGCTGGAAATTGCG 57.428 45.000 0.00 0.00 0.00 4.85
2528 5692 9.631257 TGTGATGAACATATCAGATTACCAATT 57.369 29.630 0.00 0.00 42.53 2.32
2529 5693 9.060347 GTGTGATGAACATATCAGATTACCAAT 57.940 33.333 0.00 0.00 42.53 3.16
2530 5694 8.267183 AGTGTGATGAACATATCAGATTACCAA 58.733 33.333 0.00 0.00 42.53 3.67
2578 5742 2.103432 TGAAGCCTGAGTTGGACGTAAA 59.897 45.455 0.00 0.00 0.00 2.01
2579 5743 1.689813 TGAAGCCTGAGTTGGACGTAA 59.310 47.619 0.00 0.00 0.00 3.18
2580 5744 1.334160 TGAAGCCTGAGTTGGACGTA 58.666 50.000 0.00 0.00 0.00 3.57
2581 5745 0.468226 TTGAAGCCTGAGTTGGACGT 59.532 50.000 0.00 0.00 0.00 4.34
2582 5746 0.868406 GTTGAAGCCTGAGTTGGACG 59.132 55.000 0.00 0.00 0.00 4.79
2583 5747 1.239347 GGTTGAAGCCTGAGTTGGAC 58.761 55.000 0.00 0.00 0.00 4.02
2584 5748 0.843309 TGGTTGAAGCCTGAGTTGGA 59.157 50.000 0.00 0.00 0.00 3.53
2585 5749 1.691196 TTGGTTGAAGCCTGAGTTGG 58.309 50.000 0.00 0.00 0.00 3.77
2586 5750 2.886523 TGATTGGTTGAAGCCTGAGTTG 59.113 45.455 0.00 0.00 0.00 3.16
2587 5751 2.887152 GTGATTGGTTGAAGCCTGAGTT 59.113 45.455 0.00 0.00 0.00 3.01
2588 5752 2.107204 AGTGATTGGTTGAAGCCTGAGT 59.893 45.455 0.00 0.00 0.00 3.41
2589 5753 2.486982 CAGTGATTGGTTGAAGCCTGAG 59.513 50.000 0.00 0.00 0.00 3.35
2590 5754 2.507484 CAGTGATTGGTTGAAGCCTGA 58.493 47.619 0.00 0.00 0.00 3.86
2591 5755 1.068055 GCAGTGATTGGTTGAAGCCTG 60.068 52.381 0.00 0.00 0.00 4.85
2592 5756 1.202976 AGCAGTGATTGGTTGAAGCCT 60.203 47.619 0.00 0.00 32.47 4.58
2593 5757 1.200948 GAGCAGTGATTGGTTGAAGCC 59.799 52.381 0.00 0.00 37.72 4.35
2594 5758 2.157738 AGAGCAGTGATTGGTTGAAGC 58.842 47.619 0.00 0.00 37.72 3.86
2595 5759 4.573900 AGTAGAGCAGTGATTGGTTGAAG 58.426 43.478 0.00 0.00 37.72 3.02
2596 5760 4.623932 AGTAGAGCAGTGATTGGTTGAA 57.376 40.909 0.00 0.00 37.72 2.69
2597 5761 4.623932 AAGTAGAGCAGTGATTGGTTGA 57.376 40.909 0.00 0.00 37.72 3.18
2598 5762 5.877012 ACATAAGTAGAGCAGTGATTGGTTG 59.123 40.000 0.00 0.00 37.72 3.77
2599 5763 6.054860 ACATAAGTAGAGCAGTGATTGGTT 57.945 37.500 0.00 0.00 37.72 3.67
2600 5764 5.395768 GGACATAAGTAGAGCAGTGATTGGT 60.396 44.000 0.00 0.00 41.02 3.67
2601 5765 5.053145 GGACATAAGTAGAGCAGTGATTGG 58.947 45.833 0.00 0.00 0.00 3.16
2602 5766 5.911752 AGGACATAAGTAGAGCAGTGATTG 58.088 41.667 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.