Multiple sequence alignment - TraesCS7D01G262000

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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 TraesCS7D01G262000 chr7D 100.000 4180 0 0 1 4180 239346500 239350679 0.000000e+00 7720.0
1 TraesCS7D01G262000 chr7D 96.482 1990 54 3 1588 3561 238970804 238972793 0.000000e+00 3273.0
2 TraesCS7D01G262000 chr7D 96.870 671 19 2 53 722 32891402 32892071 0.000000e+00 1122.0
3 TraesCS7D01G262000 chr7D 90.083 847 66 8 722 1558 239165973 239166811 0.000000e+00 1083.0
4 TraesCS7D01G262000 chr7D 92.953 596 37 3 3585 4180 238972773 238973363 0.000000e+00 863.0
5 TraesCS7D01G262000 chr7A 94.397 1856 67 7 1589 3410 254386149 254388001 0.000000e+00 2817.0
6 TraesCS7D01G262000 chr7A 95.152 722 35 0 1 722 67190658 67191379 0.000000e+00 1140.0
7 TraesCS7D01G262000 chr7A 94.321 722 39 2 1 722 67215766 67216485 0.000000e+00 1105.0
8 TraesCS7D01G262000 chr7A 94.306 720 40 1 1 720 67238821 67239539 0.000000e+00 1101.0
9 TraesCS7D01G262000 chr7A 88.795 589 56 7 3593 4180 254388170 254388749 0.000000e+00 713.0
10 TraesCS7D01G262000 chr7A 95.570 158 6 1 3405 3561 254388025 254388182 6.940000e-63 252.0
11 TraesCS7D01G262000 chr7B 93.588 1856 69 9 1589 3410 215928384 215930223 0.000000e+00 2723.0
12 TraesCS7D01G262000 chr7B 88.605 588 65 2 3593 4180 215930392 215930977 0.000000e+00 713.0
13 TraesCS7D01G262000 chr7B 94.937 158 7 1 3405 3561 215930247 215930404 3.230000e-61 246.0
14 TraesCS7D01G262000 chr3D 95.342 730 32 2 1 729 579245733 579245005 0.000000e+00 1158.0
15 TraesCS7D01G262000 chr3D 87.802 828 92 6 733 1558 148108128 148107308 0.000000e+00 961.0
16 TraesCS7D01G262000 chr3D 86.353 850 96 15 722 1559 488229674 488228833 0.000000e+00 909.0
17 TraesCS7D01G262000 chr3D 86.071 840 109 5 722 1558 148114928 148114094 0.000000e+00 896.0
18 TraesCS7D01G262000 chr1D 94.474 742 19 4 1 721 24147245 24146505 0.000000e+00 1123.0
19 TraesCS7D01G262000 chr1D 96.444 675 22 2 53 726 414289477 414288804 0.000000e+00 1112.0
20 TraesCS7D01G262000 chr1D 87.915 844 84 13 722 1559 251677072 251676241 0.000000e+00 977.0
21 TraesCS7D01G262000 chr1D 89.133 773 70 7 792 1559 231034608 231035371 0.000000e+00 950.0
22 TraesCS7D01G262000 chr1D 87.936 746 39 8 1 721 464328731 464328012 0.000000e+00 832.0
23 TraesCS7D01G262000 chr6D 96.716 670 21 1 53 721 462458107 462458776 0.000000e+00 1114.0
24 TraesCS7D01G262000 chr6D 92.359 746 29 8 1 721 472873158 472873900 0.000000e+00 1037.0
25 TraesCS7D01G262000 chr6D 86.391 845 95 16 722 1558 265725338 265726170 0.000000e+00 905.0
26 TraesCS7D01G262000 chr6D 85.758 330 31 9 722 1045 302031094 302031413 6.700000e-88 335.0
27 TraesCS7D01G262000 chr5D 94.583 720 36 3 3 722 514034233 514033517 0.000000e+00 1110.0
28 TraesCS7D01G262000 chr5D 87.635 833 89 12 734 1557 193201523 193200696 0.000000e+00 955.0
29 TraesCS7D01G262000 chr5D 86.337 849 98 17 722 1559 461532683 461531842 0.000000e+00 909.0
30 TraesCS7D01G262000 chr5D 100.000 30 0 0 1557 1586 282217984 282217955 5.840000e-04 56.5
31 TraesCS7D01G262000 chr2D 93.333 750 25 7 1 728 643651734 643652480 0.000000e+00 1085.0
32 TraesCS7D01G262000 chr2D 98.361 61 1 0 1 61 604971139 604971199 1.590000e-19 108.0
33 TraesCS7D01G262000 chr6B 87.013 847 87 18 722 1559 230524298 230525130 0.000000e+00 933.0
34 TraesCS7D01G262000 chr3A 97.059 34 1 0 1557 1590 467649589 467649556 1.620000e-04 58.4
35 TraesCS7D01G262000 chr3A 100.000 30 0 0 1557 1586 244487428 244487457 5.840000e-04 56.5
36 TraesCS7D01G262000 chr2B 96.970 33 1 0 1557 1589 397944002 397944034 5.840000e-04 56.5


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 TraesCS7D01G262000 chr7D 239346500 239350679 4179 False 7720.000000 7720 100.000000 1 4180 1 chr7D.!!$F3 4179
1 TraesCS7D01G262000 chr7D 238970804 238973363 2559 False 2068.000000 3273 94.717500 1588 4180 2 chr7D.!!$F4 2592
2 TraesCS7D01G262000 chr7D 32891402 32892071 669 False 1122.000000 1122 96.870000 53 722 1 chr7D.!!$F1 669
3 TraesCS7D01G262000 chr7D 239165973 239166811 838 False 1083.000000 1083 90.083000 722 1558 1 chr7D.!!$F2 836
4 TraesCS7D01G262000 chr7A 254386149 254388749 2600 False 1260.666667 2817 92.920667 1589 4180 3 chr7A.!!$F4 2591
5 TraesCS7D01G262000 chr7A 67190658 67191379 721 False 1140.000000 1140 95.152000 1 722 1 chr7A.!!$F1 721
6 TraesCS7D01G262000 chr7A 67215766 67216485 719 False 1105.000000 1105 94.321000 1 722 1 chr7A.!!$F2 721
7 TraesCS7D01G262000 chr7A 67238821 67239539 718 False 1101.000000 1101 94.306000 1 720 1 chr7A.!!$F3 719
8 TraesCS7D01G262000 chr7B 215928384 215930977 2593 False 1227.333333 2723 92.376667 1589 4180 3 chr7B.!!$F1 2591
9 TraesCS7D01G262000 chr3D 579245005 579245733 728 True 1158.000000 1158 95.342000 1 729 1 chr3D.!!$R4 728
10 TraesCS7D01G262000 chr3D 148107308 148108128 820 True 961.000000 961 87.802000 733 1558 1 chr3D.!!$R1 825
11 TraesCS7D01G262000 chr3D 488228833 488229674 841 True 909.000000 909 86.353000 722 1559 1 chr3D.!!$R3 837
12 TraesCS7D01G262000 chr3D 148114094 148114928 834 True 896.000000 896 86.071000 722 1558 1 chr3D.!!$R2 836
13 TraesCS7D01G262000 chr1D 24146505 24147245 740 True 1123.000000 1123 94.474000 1 721 1 chr1D.!!$R1 720
14 TraesCS7D01G262000 chr1D 414288804 414289477 673 True 1112.000000 1112 96.444000 53 726 1 chr1D.!!$R3 673
15 TraesCS7D01G262000 chr1D 251676241 251677072 831 True 977.000000 977 87.915000 722 1559 1 chr1D.!!$R2 837
16 TraesCS7D01G262000 chr1D 231034608 231035371 763 False 950.000000 950 89.133000 792 1559 1 chr1D.!!$F1 767
17 TraesCS7D01G262000 chr1D 464328012 464328731 719 True 832.000000 832 87.936000 1 721 1 chr1D.!!$R4 720
18 TraesCS7D01G262000 chr6D 462458107 462458776 669 False 1114.000000 1114 96.716000 53 721 1 chr6D.!!$F3 668
19 TraesCS7D01G262000 chr6D 472873158 472873900 742 False 1037.000000 1037 92.359000 1 721 1 chr6D.!!$F4 720
20 TraesCS7D01G262000 chr6D 265725338 265726170 832 False 905.000000 905 86.391000 722 1558 1 chr6D.!!$F1 836
21 TraesCS7D01G262000 chr5D 514033517 514034233 716 True 1110.000000 1110 94.583000 3 722 1 chr5D.!!$R4 719
22 TraesCS7D01G262000 chr5D 193200696 193201523 827 True 955.000000 955 87.635000 734 1557 1 chr5D.!!$R1 823
23 TraesCS7D01G262000 chr5D 461531842 461532683 841 True 909.000000 909 86.337000 722 1559 1 chr5D.!!$R3 837
24 TraesCS7D01G262000 chr2D 643651734 643652480 746 False 1085.000000 1085 93.333000 1 728 1 chr2D.!!$F2 727
25 TraesCS7D01G262000 chr6B 230524298 230525130 832 False 933.000000 933 87.013000 722 1559 1 chr6B.!!$F1 837

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
486 516 0.328258 CCATCCTTCTGTCCCGGTTT 59.672 55.0 0.0 0.0 0.00 3.27 F
1569 1633 0.321122 CTCTTGAGCACGGCCTCTTT 60.321 55.0 0.0 0.0 33.02 2.52 F
2771 2867 0.034767 CAGGGCATGAGATGTGTGGT 60.035 55.0 0.0 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1583 1647 0.179009 TACTCCCTCCATCCCGTACG 60.179 60.0 8.69 8.69 0.00 3.67 R
2834 2930 0.249868 CGGTGTCACTCTTCTTGGCA 60.250 55.0 2.35 0.00 0.00 4.92 R
3579 3741 0.035317 GACCCCCGTACTTTTTCGGT 59.965 55.0 0.00 0.00 44.51 4.69 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
424 454 2.561419 CGGCGATGGGGTATATATAGGG 59.439 54.545 0.00 0.00 0.00 3.53
450 480 1.756408 TTTGTCCCGGTTCGTGGCTA 61.756 55.000 0.00 0.00 0.00 3.93
486 516 0.328258 CCATCCTTCTGTCCCGGTTT 59.672 55.000 0.00 0.00 0.00 3.27
498 528 1.597027 CCGGTTTCTGCCACGAACT 60.597 57.895 0.00 0.00 0.00 3.01
546 576 1.002624 GCTCATTGGTCCCGGTTCA 60.003 57.895 0.00 0.00 0.00 3.18
557 587 1.377725 CCGGTTCATGCCAAGAGCT 60.378 57.895 0.00 0.00 44.23 4.09
747 780 2.041265 GAGGGGAGGAGAGGGCAA 59.959 66.667 0.00 0.00 0.00 4.52
932 980 6.904498 TGGCCCGTCGATATTAAATTAAATG 58.096 36.000 0.00 0.00 0.00 2.32
1007 1063 9.991906 CTCCGGAAACATTTTCTACCTATATAA 57.008 33.333 5.23 0.00 0.00 0.98
1157 1217 3.321111 ACTCACGTTCCACTAACACTCAT 59.679 43.478 0.00 0.00 38.03 2.90
1227 1289 3.665190 AGACATGAACGAAACTCCTTCC 58.335 45.455 0.00 0.00 0.00 3.46
1305 1367 9.840427 CACGAATAATATTTGAGTGAACCTTTT 57.160 29.630 7.21 0.00 0.00 2.27
1547 1611 0.824109 ATCGTCGGAGGAGCAAATCA 59.176 50.000 6.55 0.00 0.00 2.57
1559 1623 2.810274 GAGCAAATCACACTCTTGAGCA 59.190 45.455 0.00 0.00 0.00 4.26
1560 1624 2.551459 AGCAAATCACACTCTTGAGCAC 59.449 45.455 0.00 0.00 0.00 4.40
1561 1625 2.663879 GCAAATCACACTCTTGAGCACG 60.664 50.000 0.00 0.00 0.00 5.34
1562 1626 1.800805 AATCACACTCTTGAGCACGG 58.199 50.000 0.00 0.00 0.00 4.94
1563 1627 0.671781 ATCACACTCTTGAGCACGGC 60.672 55.000 0.00 0.00 0.00 5.68
1564 1628 2.031163 ACACTCTTGAGCACGGCC 59.969 61.111 0.00 0.00 0.00 6.13
1565 1629 2.345244 CACTCTTGAGCACGGCCT 59.655 61.111 0.00 0.00 0.00 5.19
1566 1630 1.739562 CACTCTTGAGCACGGCCTC 60.740 63.158 0.00 0.00 0.00 4.70
1567 1631 1.910772 ACTCTTGAGCACGGCCTCT 60.911 57.895 0.00 0.00 33.02 3.69
1568 1632 1.294780 CTCTTGAGCACGGCCTCTT 59.705 57.895 0.00 0.00 33.02 2.85
1569 1633 0.321122 CTCTTGAGCACGGCCTCTTT 60.321 55.000 0.00 0.00 33.02 2.52
1570 1634 0.973632 TCTTGAGCACGGCCTCTTTA 59.026 50.000 0.00 0.00 33.02 1.85
1571 1635 1.079503 CTTGAGCACGGCCTCTTTAC 58.920 55.000 0.00 0.00 33.02 2.01
1572 1636 0.685097 TTGAGCACGGCCTCTTTACT 59.315 50.000 0.00 0.00 33.02 2.24
1573 1637 0.685097 TGAGCACGGCCTCTTTACTT 59.315 50.000 0.00 0.00 33.02 2.24
1574 1638 1.079503 GAGCACGGCCTCTTTACTTG 58.920 55.000 0.00 0.00 0.00 3.16
1575 1639 0.321653 AGCACGGCCTCTTTACTTGG 60.322 55.000 0.00 0.00 0.00 3.61
1576 1640 0.605589 GCACGGCCTCTTTACTTGGT 60.606 55.000 0.00 0.00 0.00 3.67
1577 1641 1.892209 CACGGCCTCTTTACTTGGTT 58.108 50.000 0.00 0.00 0.00 3.67
1578 1642 1.535462 CACGGCCTCTTTACTTGGTTG 59.465 52.381 0.00 0.00 0.00 3.77
1579 1643 0.521735 CGGCCTCTTTACTTGGTTGC 59.478 55.000 0.00 0.00 0.00 4.17
1580 1644 1.616159 GGCCTCTTTACTTGGTTGCA 58.384 50.000 0.00 0.00 0.00 4.08
1581 1645 1.960689 GGCCTCTTTACTTGGTTGCAA 59.039 47.619 0.00 0.00 0.00 4.08
1582 1646 2.029918 GGCCTCTTTACTTGGTTGCAAG 60.030 50.000 0.00 0.00 38.11 4.01
1583 1647 2.608016 GCCTCTTTACTTGGTTGCAAGC 60.608 50.000 21.51 21.51 35.70 4.01
1584 1648 2.350772 CCTCTTTACTTGGTTGCAAGCG 60.351 50.000 22.55 12.41 35.70 4.68
1585 1649 2.290641 CTCTTTACTTGGTTGCAAGCGT 59.709 45.455 22.55 17.23 35.70 5.07
1586 1650 3.468770 TCTTTACTTGGTTGCAAGCGTA 58.531 40.909 22.55 16.27 35.70 4.42
1592 1656 1.743995 GGTTGCAAGCGTACGGGAT 60.744 57.895 18.39 0.00 0.00 3.85
1612 1676 6.522459 CGGGATGGAGGGAGTATTTCATAAAT 60.522 42.308 0.00 0.00 34.90 1.40
1637 1701 7.201702 TGTATGGGATGTAATGTTTCTACCA 57.798 36.000 0.00 0.00 0.00 3.25
1688 1767 7.144000 GCCCAGAGTGAATATTTGATGATTTC 58.856 38.462 0.00 0.00 0.00 2.17
1785 1868 9.109393 AGTACATGCGTTATTCATTAGATTGTT 57.891 29.630 0.00 0.00 0.00 2.83
1852 1935 8.697507 AACTTTTGAGGAATCATGAAGTTAGT 57.302 30.769 0.00 0.00 36.01 2.24
1853 1936 8.103948 ACTTTTGAGGAATCATGAAGTTAGTG 57.896 34.615 0.00 0.00 0.00 2.74
1903 1986 5.330455 TCGCAAGATAGAAACTGACTGAT 57.670 39.130 0.00 0.00 45.01 2.90
1914 1997 6.528321 AGAAACTGACTGATCATTCTGAACA 58.472 36.000 21.57 5.85 34.36 3.18
1928 2011 7.592938 TCATTCTGAACAAAATTCAGCGTTAT 58.407 30.769 11.06 1.40 44.08 1.89
1988 2071 7.663493 ACTTATTGAAACTCTGAAGAAGGGAAG 59.337 37.037 0.00 0.00 0.00 3.46
2181 2277 2.099141 TGCAGATTCCTTCCTCGTTG 57.901 50.000 0.00 0.00 0.00 4.10
2195 2291 2.620112 CGTTGAAGCAGGCAGTGGG 61.620 63.158 0.00 0.00 0.00 4.61
2564 2660 2.045340 GGTGCTTATGGTGGGCGT 60.045 61.111 0.00 0.00 0.00 5.68
2687 2783 2.513204 CTGATGGAGCCTGGCACG 60.513 66.667 22.65 0.00 0.00 5.34
2725 2821 1.068417 TCACCGGTGAACTTGTCCG 59.932 57.895 34.60 4.70 43.30 4.79
2771 2867 0.034767 CAGGGCATGAGATGTGTGGT 60.035 55.000 0.00 0.00 0.00 4.16
2792 2888 2.224843 TGGACACATCAGAGGCATGTTT 60.225 45.455 0.00 0.00 31.83 2.83
2834 2930 2.559668 CCCAGTGCACAACTTTGATGAT 59.440 45.455 21.04 0.00 36.83 2.45
2846 2942 4.660168 ACTTTGATGATGCCAAGAAGAGT 58.340 39.130 0.00 0.00 0.00 3.24
2890 2986 2.124570 CCGTGGGATGCTGGAAGG 60.125 66.667 0.00 0.00 0.00 3.46
2900 2999 3.898123 GGATGCTGGAAGGAGTGTATCTA 59.102 47.826 0.00 0.00 38.10 1.98
2999 3098 2.531206 GAGGAAGTTCTTCGACGGATG 58.469 52.381 2.25 0.00 0.00 3.51
3010 3109 4.157105 TCTTCGACGGATGTAGACAATTCA 59.843 41.667 0.00 0.00 28.83 2.57
3021 3120 6.882610 TGTAGACAATTCAGATTGCAAACT 57.117 33.333 1.71 2.40 45.25 2.66
3053 3152 5.989777 GCTTTTCCTTCTGTTGTACTCTGTA 59.010 40.000 0.00 0.00 0.00 2.74
3266 3366 3.626930 TGCACCAAGTAAAGAAACCAGT 58.373 40.909 0.00 0.00 0.00 4.00
3526 3688 4.101119 AGGTCCGTCCAATTGTTAGGATAG 59.899 45.833 13.67 0.61 39.02 2.08
3557 3719 0.623723 GCAAAGGTATGGGGGTCTCA 59.376 55.000 0.00 0.00 0.00 3.27
3561 3723 1.821088 AGGTATGGGGGTCTCATTCC 58.179 55.000 0.00 0.00 33.84 3.01
3562 3724 0.396811 GGTATGGGGGTCTCATTCCG 59.603 60.000 0.00 0.00 0.00 4.30
3563 3725 1.420430 GTATGGGGGTCTCATTCCGA 58.580 55.000 0.00 0.00 0.00 4.55
3564 3726 1.766496 GTATGGGGGTCTCATTCCGAA 59.234 52.381 0.00 0.00 0.00 4.30
3565 3727 1.295020 ATGGGGGTCTCATTCCGAAA 58.705 50.000 0.00 0.00 0.00 3.46
3566 3728 1.068948 TGGGGGTCTCATTCCGAAAA 58.931 50.000 0.00 0.00 0.00 2.29
3567 3729 1.425831 TGGGGGTCTCATTCCGAAAAA 59.574 47.619 0.00 0.00 0.00 1.94
3568 3730 2.092323 GGGGGTCTCATTCCGAAAAAG 58.908 52.381 0.00 0.00 0.00 2.27
3569 3731 2.554564 GGGGGTCTCATTCCGAAAAAGT 60.555 50.000 0.00 0.00 0.00 2.66
3570 3732 3.154710 GGGGTCTCATTCCGAAAAAGTT 58.845 45.455 0.00 0.00 0.00 2.66
3571 3733 3.572682 GGGGTCTCATTCCGAAAAAGTTT 59.427 43.478 0.00 0.00 0.00 2.66
3572 3734 4.038763 GGGGTCTCATTCCGAAAAAGTTTT 59.961 41.667 0.00 0.00 0.00 2.43
3573 3735 5.452776 GGGGTCTCATTCCGAAAAAGTTTTT 60.453 40.000 13.35 13.35 0.00 1.94
3598 3760 2.845019 CCGAAAAAGTACGGGGGTC 58.155 57.895 0.00 0.00 44.59 4.46
3599 3761 0.322648 CCGAAAAAGTACGGGGGTCT 59.677 55.000 0.00 0.00 44.59 3.85
3600 3762 1.673923 CCGAAAAAGTACGGGGGTCTC 60.674 57.143 0.00 0.00 44.59 3.36
3601 3763 1.274447 CGAAAAAGTACGGGGGTCTCT 59.726 52.381 0.00 0.00 0.00 3.10
3602 3764 2.289257 CGAAAAAGTACGGGGGTCTCTT 60.289 50.000 0.00 0.00 0.00 2.85
3603 3765 3.748083 GAAAAAGTACGGGGGTCTCTTT 58.252 45.455 0.00 0.00 0.00 2.52
3604 3766 3.413846 AAAAGTACGGGGGTCTCTTTC 57.586 47.619 0.00 0.00 0.00 2.62
3742 3908 2.226962 AATCTTCATGCAAGTGCCCT 57.773 45.000 0.00 0.00 41.18 5.19
3748 3914 2.161855 TCATGCAAGTGCCCTTAACAG 58.838 47.619 0.00 0.00 41.18 3.16
3772 3938 5.008613 GCCAACATTTTCTCACTTGTAGTCA 59.991 40.000 0.00 0.00 0.00 3.41
3831 3997 2.549754 CACCAAATCTCGTTGTCTTGCT 59.450 45.455 0.00 0.00 0.00 3.91
3866 4032 2.719705 ACCCTAACCTCATTGTCCCAAA 59.280 45.455 0.00 0.00 0.00 3.28
3929 4095 1.475403 GATGGACGAACTGGAGGAGA 58.525 55.000 0.00 0.00 0.00 3.71
3934 4100 1.743958 GACGAACTGGAGGAGAATCGA 59.256 52.381 0.00 0.00 37.71 3.59
3992 4158 4.135153 CCACCTCACCGCTCCGAG 62.135 72.222 0.00 0.00 0.00 4.63
4067 4233 0.887933 AATTGGTTCACGTCCATGGC 59.112 50.000 6.96 0.96 34.75 4.40
4162 4328 1.636148 ACAGAGTAAACCGGCTACCA 58.364 50.000 0.00 0.00 0.00 3.25
4171 4337 6.181908 AGTAAACCGGCTACCAAAATATTGA 58.818 36.000 0.00 0.00 38.94 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 133 9.277783 TCTTGTTCTTATCTTCTTTCTGAAAGG 57.722 33.333 25.32 13.41 39.01 3.11
214 239 3.532542 AGATTTGTCTAGGTTTAGCGGC 58.467 45.455 0.00 0.00 0.00 6.53
385 413 2.047844 GCGAGCAGAGCACTCCAA 60.048 61.111 0.00 0.00 34.19 3.53
424 454 1.463444 CGAACCGGGACAAATGAGTTC 59.537 52.381 6.32 0.00 0.00 3.01
450 480 0.838987 TGGCCTTTAGTCCCGGTTCT 60.839 55.000 3.32 0.15 0.00 3.01
486 516 2.741092 GTCCCAGTTCGTGGCAGA 59.259 61.111 0.00 0.00 46.45 4.26
498 528 1.154921 CCCACAACCATTGGTCCCA 59.845 57.895 9.22 0.00 33.12 4.37
546 576 0.112995 TTTGTCCCAGCTCTTGGCAT 59.887 50.000 0.00 0.00 46.32 4.40
1026 1086 5.990996 GGTTTCGGTGAATATCGGGTAATTA 59.009 40.000 0.00 0.00 0.00 1.40
1027 1087 4.818005 GGTTTCGGTGAATATCGGGTAATT 59.182 41.667 0.00 0.00 0.00 1.40
1157 1217 7.491372 CACAAGCTTAAGGTAATCACGATCTTA 59.509 37.037 7.76 0.00 0.00 2.10
1203 1264 5.875359 GGAAGGAGTTTCGTTCATGTCTATT 59.125 40.000 11.99 0.00 41.54 1.73
1305 1367 5.295787 GCAAAGGGAACGTCATATGATAACA 59.704 40.000 9.02 0.00 0.00 2.41
1314 1376 1.156736 CGAAGCAAAGGGAACGTCAT 58.843 50.000 0.00 0.00 0.00 3.06
1547 1611 2.031163 GGCCGTGCTCAAGAGTGT 59.969 61.111 0.00 0.00 0.00 3.55
1559 1623 1.892209 CAACCAAGTAAAGAGGCCGT 58.108 50.000 0.00 0.00 0.00 5.68
1560 1624 0.521735 GCAACCAAGTAAAGAGGCCG 59.478 55.000 0.00 0.00 0.00 6.13
1561 1625 1.616159 TGCAACCAAGTAAAGAGGCC 58.384 50.000 0.00 0.00 0.00 5.19
1562 1626 3.288809 CTTGCAACCAAGTAAAGAGGC 57.711 47.619 0.00 0.00 42.76 4.70
1572 1636 2.255172 CCCGTACGCTTGCAACCAA 61.255 57.895 10.49 0.00 0.00 3.67
1573 1637 2.457743 ATCCCGTACGCTTGCAACCA 62.458 55.000 10.49 0.00 0.00 3.67
1574 1638 1.743995 ATCCCGTACGCTTGCAACC 60.744 57.895 10.49 0.00 0.00 3.77
1575 1639 1.423845 CATCCCGTACGCTTGCAAC 59.576 57.895 10.49 0.00 0.00 4.17
1576 1640 1.743623 CCATCCCGTACGCTTGCAA 60.744 57.895 10.49 0.00 0.00 4.08
1577 1641 2.125310 CCATCCCGTACGCTTGCA 60.125 61.111 10.49 0.00 0.00 4.08
1578 1642 1.883084 CTCCATCCCGTACGCTTGC 60.883 63.158 10.49 0.00 0.00 4.01
1579 1643 1.227263 CCTCCATCCCGTACGCTTG 60.227 63.158 10.49 6.55 0.00 4.01
1580 1644 2.432300 CCCTCCATCCCGTACGCTT 61.432 63.158 10.49 0.00 0.00 4.68
1581 1645 2.838225 CCCTCCATCCCGTACGCT 60.838 66.667 10.49 0.00 0.00 5.07
1582 1646 2.836360 TCCCTCCATCCCGTACGC 60.836 66.667 10.49 0.00 0.00 4.42
1583 1647 0.179009 TACTCCCTCCATCCCGTACG 60.179 60.000 8.69 8.69 0.00 3.67
1584 1648 2.305858 ATACTCCCTCCATCCCGTAC 57.694 55.000 0.00 0.00 0.00 3.67
1585 1649 3.236896 GAAATACTCCCTCCATCCCGTA 58.763 50.000 0.00 0.00 0.00 4.02
1586 1650 2.047830 GAAATACTCCCTCCATCCCGT 58.952 52.381 0.00 0.00 0.00 5.28
1592 1656 9.573166 CATACAATTTATGAAATACTCCCTCCA 57.427 33.333 3.07 0.00 0.00 3.86
1612 1676 7.634718 TGGTAGAAACATTACATCCCATACAA 58.365 34.615 0.00 0.00 0.00 2.41
1688 1767 3.947910 TCCTACCGAGTACAACAAAGG 57.052 47.619 0.00 0.00 0.00 3.11
1785 1868 2.162208 GCGATTCCAGCAGTTTGATCAA 59.838 45.455 3.38 3.38 34.19 2.57
1876 1959 7.489435 TCAGTCAGTTTCTATCTTGCGATTTAG 59.511 37.037 0.00 0.00 0.00 1.85
1877 1960 7.320399 TCAGTCAGTTTCTATCTTGCGATTTA 58.680 34.615 0.00 0.00 0.00 1.40
1914 1997 8.434661 CACAAGCATTTAATAACGCTGAATTTT 58.565 29.630 0.00 0.00 34.26 1.82
1928 2011 8.417106 TCACCTGAATTAAACACAAGCATTTAA 58.583 29.630 0.00 0.00 35.38 1.52
2181 2277 2.116125 AACCCCACTGCCTGCTTC 59.884 61.111 0.00 0.00 0.00 3.86
2564 2660 5.549228 AGCAACCATCTCCATGATATCCTTA 59.451 40.000 0.00 0.00 33.36 2.69
2613 2709 0.771755 GGGTTTCCACTCAGGGTTCT 59.228 55.000 0.00 0.00 38.24 3.01
2687 2783 5.585047 GGTGACCTTGTCCAAGTATTCATAC 59.415 44.000 6.31 0.00 36.72 2.39
2725 2821 2.040544 CCCGCATCCAATATCCGCC 61.041 63.158 0.00 0.00 0.00 6.13
2727 2823 1.577328 GCACCCGCATCCAATATCCG 61.577 60.000 0.00 0.00 38.36 4.18
2771 2867 0.986527 ACATGCCTCTGATGTGTCCA 59.013 50.000 0.00 0.00 32.68 4.02
2792 2888 1.339055 CCACCTGCGAAGAAGAATCCA 60.339 52.381 0.00 0.00 0.00 3.41
2834 2930 0.249868 CGGTGTCACTCTTCTTGGCA 60.250 55.000 2.35 0.00 0.00 4.92
2846 2942 1.890041 CCCAAACTTCGCGGTGTCA 60.890 57.895 6.13 0.00 0.00 3.58
2890 2986 1.337387 GGGACGGTGCTAGATACACTC 59.663 57.143 0.00 0.00 38.14 3.51
2982 3081 4.097012 GTCTACATCCGTCGAAGAACTTC 58.903 47.826 0.00 4.67 39.69 3.01
2999 3098 8.579682 AAAAGTTTGCAATCTGAATTGTCTAC 57.420 30.769 10.72 0.00 43.54 2.59
3010 3109 4.677673 AGCTCCAAAAAGTTTGCAATCT 57.322 36.364 0.00 1.10 0.00 2.40
3053 3152 2.614829 ACTTCAGCCACGTACAACTT 57.385 45.000 0.00 0.00 0.00 2.66
3266 3366 4.552378 GCAACGACACAACGGTTACATTTA 60.552 41.667 0.00 0.00 37.61 1.40
3574 3736 3.567585 CCCCCGTACTTTTTCGGTAAAAA 59.432 43.478 0.00 0.00 44.51 1.94
3575 3737 3.145286 CCCCCGTACTTTTTCGGTAAAA 58.855 45.455 0.00 0.00 44.51 1.52
3576 3738 2.105649 ACCCCCGTACTTTTTCGGTAAA 59.894 45.455 0.00 0.00 44.51 2.01
3577 3739 1.696884 ACCCCCGTACTTTTTCGGTAA 59.303 47.619 0.00 0.00 44.51 2.85
3578 3740 1.275010 GACCCCCGTACTTTTTCGGTA 59.725 52.381 0.00 0.00 44.51 4.02
3579 3741 0.035317 GACCCCCGTACTTTTTCGGT 59.965 55.000 0.00 0.00 44.51 4.69
3580 3742 0.322648 AGACCCCCGTACTTTTTCGG 59.677 55.000 0.00 0.00 45.42 4.30
3581 3743 1.274447 AGAGACCCCCGTACTTTTTCG 59.726 52.381 0.00 0.00 0.00 3.46
3582 3744 3.413846 AAGAGACCCCCGTACTTTTTC 57.586 47.619 0.00 0.00 0.00 2.29
3583 3745 3.136992 TGAAAGAGACCCCCGTACTTTTT 59.863 43.478 0.00 0.00 32.50 1.94
3584 3746 2.707257 TGAAAGAGACCCCCGTACTTTT 59.293 45.455 0.00 0.00 32.50 2.27
3585 3747 2.332117 TGAAAGAGACCCCCGTACTTT 58.668 47.619 0.00 0.00 33.95 2.66
3586 3748 2.019807 TGAAAGAGACCCCCGTACTT 57.980 50.000 0.00 0.00 0.00 2.24
3587 3749 2.108970 GATGAAAGAGACCCCCGTACT 58.891 52.381 0.00 0.00 0.00 2.73
3588 3750 1.202382 CGATGAAAGAGACCCCCGTAC 60.202 57.143 0.00 0.00 0.00 3.67
3589 3751 1.108776 CGATGAAAGAGACCCCCGTA 58.891 55.000 0.00 0.00 0.00 4.02
3590 3752 0.613853 TCGATGAAAGAGACCCCCGT 60.614 55.000 0.00 0.00 0.00 5.28
3591 3753 0.753262 ATCGATGAAAGAGACCCCCG 59.247 55.000 0.00 0.00 0.00 5.73
3592 3754 1.269831 CGATCGATGAAAGAGACCCCC 60.270 57.143 10.26 0.00 0.00 5.40
3593 3755 1.681793 TCGATCGATGAAAGAGACCCC 59.318 52.381 15.15 0.00 0.00 4.95
3594 3756 3.651803 ATCGATCGATGAAAGAGACCC 57.348 47.619 28.90 0.00 32.98 4.46
3595 3757 3.984633 GGAATCGATCGATGAAAGAGACC 59.015 47.826 29.99 17.65 34.70 3.85
3596 3758 4.611943 TGGAATCGATCGATGAAAGAGAC 58.388 43.478 29.99 14.29 34.70 3.36
3597 3759 4.918810 TGGAATCGATCGATGAAAGAGA 57.081 40.909 29.99 8.45 34.70 3.10
3598 3760 5.760193 GATGGAATCGATCGATGAAAGAG 57.240 43.478 29.99 0.00 34.70 2.85
3667 3833 4.201990 GGAGGCAGCTTGTTCATGATAAAG 60.202 45.833 11.69 11.69 0.00 1.85
3742 3908 6.127479 ACAAGTGAGAAAATGTTGGCTGTTAA 60.127 34.615 0.00 0.00 0.00 2.01
3748 3914 5.008613 TGACTACAAGTGAGAAAATGTTGGC 59.991 40.000 0.00 0.00 0.00 4.52
3772 3938 7.679732 ATCAATTTATGGGTTCATTGGTGAT 57.320 32.000 0.00 0.00 34.96 3.06
3831 3997 1.271856 TAGGGTTTCTCGCCATGTGA 58.728 50.000 0.00 0.00 0.00 3.58
3866 4032 7.692460 TTTGACATAGATTCATGCAGTCTTT 57.308 32.000 0.00 0.00 0.00 2.52
3934 4100 5.300752 TCTTCAAGTTGATCTTTCGAGCTT 58.699 37.500 6.36 0.00 33.63 3.74
4039 4205 1.177401 GTGAACCAATTGCCCTCCTC 58.823 55.000 0.00 0.00 0.00 3.71
4046 4212 1.402720 CCATGGACGTGAACCAATTGC 60.403 52.381 5.56 0.00 40.93 3.56
4105 4271 0.314935 ATCGCTGGTGGCAAAAACTG 59.685 50.000 0.00 0.00 41.91 3.16


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

AutoCloner maintained by Alex Coulton.