Multiple sequence alignment - TraesCS1D01G364200

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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 TraesCS1D01G364200 chr1D 100.000 2634 0 0 1 2634 445316507 445319140 0.000000e+00 4865.0
1 TraesCS1D01G364200 chr1D 89.426 889 50 16 810 1658 445387272 445386388 0.000000e+00 1081.0
2 TraesCS1D01G364200 chr1D 84.827 1127 99 35 789 1847 446558169 446559291 0.000000e+00 1068.0
3 TraesCS1D01G364200 chr1D 88.760 605 59 6 5 602 378109455 378108853 0.000000e+00 732.0
4 TraesCS1D01G364200 chr1D 83.333 336 38 10 1894 2216 446559273 446559603 7.130000e-76 294.0
5 TraesCS1D01G364200 chr1D 87.425 167 16 4 800 965 355824978 355825140 1.240000e-43 187.0
6 TraesCS1D01G364200 chr1D 92.593 81 2 4 708 786 446558048 446558126 2.140000e-21 113.0
7 TraesCS1D01G364200 chr1B 87.424 1646 103 48 642 2248 606839503 606841083 0.000000e+00 1797.0
8 TraesCS1D01G364200 chr1B 95.540 695 29 2 794 1487 607429808 607429115 0.000000e+00 1110.0
9 TraesCS1D01G364200 chr1B 87.872 940 84 16 950 1864 611131355 611132289 0.000000e+00 1077.0
10 TraesCS1D01G364200 chr1B 90.222 767 45 16 792 1539 610965287 610966042 0.000000e+00 974.0
11 TraesCS1D01G364200 chr1B 82.070 937 82 39 1556 2435 610966021 610966928 0.000000e+00 721.0
12 TraesCS1D01G364200 chr1B 85.784 408 30 8 2248 2634 608461675 608461275 8.780000e-110 407.0
13 TraesCS1D01G364200 chr1B 95.652 253 7 2 2383 2634 606841316 606841565 1.140000e-108 403.0
14 TraesCS1D01G364200 chr1B 92.623 244 10 1 1811 2046 587848578 587848821 6.980000e-91 344.0
15 TraesCS1D01G364200 chr1B 84.122 296 22 12 1964 2248 608462054 608461773 2.010000e-66 263.0
16 TraesCS1D01G364200 chr1B 82.569 218 25 4 1916 2124 611132300 611132513 2.080000e-41 180.0
17 TraesCS1D01G364200 chr1B 94.231 52 1 2 2335 2384 606841104 606841155 7.820000e-11 78.7
18 TraesCS1D01G364200 chr1B 91.837 49 3 1 748 795 610965201 610965249 1.690000e-07 67.6
19 TraesCS1D01G364200 chr1A 90.043 1165 61 30 337 1488 541318627 541319749 0.000000e+00 1458.0
20 TraesCS1D01G364200 chr1A 84.897 1119 100 36 795 1864 542358183 542359281 0.000000e+00 1066.0
21 TraesCS1D01G364200 chr1A 90.608 724 32 15 963 1652 542170255 542170976 0.000000e+00 928.0
22 TraesCS1D01G364200 chr1A 95.971 273 9 2 2359 2631 541382565 541382835 2.410000e-120 442.0
23 TraesCS1D01G364200 chr1A 79.056 339 28 19 1913 2249 510579232 510578935 2.680000e-45 193.0
24 TraesCS1D01G364200 chr1A 87.425 167 15 5 800 965 456650702 456650863 1.240000e-43 187.0
25 TraesCS1D01G364200 chr1A 84.672 137 11 3 1910 2046 552506896 552507022 7.650000e-26 128.0
26 TraesCS1D01G364200 chr1A 84.848 132 10 2 1913 2044 154791418 154791297 9.900000e-25 124.0
27 TraesCS1D01G364200 chr1A 83.212 137 13 3 1910 2046 531920130 531920256 1.660000e-22 117.0
28 TraesCS1D01G364200 chr1A 93.548 62 3 1 1803 1864 154791501 154791441 1.000000e-14 91.6
29 TraesCS1D01G364200 chr6A 90.000 670 49 12 837 1491 67142335 67141669 0.000000e+00 850.0
30 TraesCS1D01G364200 chr6A 87.869 610 61 9 2 602 550622115 550622720 0.000000e+00 704.0
31 TraesCS1D01G364200 chr6A 85.401 137 10 3 1910 2046 595963841 595963967 1.640000e-27 134.0
32 TraesCS1D01G364200 chr6A 91.935 62 4 1 1803 1864 595963761 595963821 4.670000e-13 86.1
33 TraesCS1D01G364200 chr6D 87.849 716 67 12 785 1484 47812082 47812793 0.000000e+00 822.0
34 TraesCS1D01G364200 chr6B 90.333 600 45 5 2 600 514658802 514658215 0.000000e+00 774.0
35 TraesCS1D01G364200 chr6B 90.881 318 17 8 1811 2117 66894742 66894426 1.460000e-112 416.0
36 TraesCS1D01G364200 chr4D 89.867 602 50 7 3 600 152885948 152885354 0.000000e+00 763.0
37 TraesCS1D01G364200 chr3D 89.438 587 56 4 3 585 446704638 446705222 0.000000e+00 736.0
38 TraesCS1D01G364200 chr3D 87.356 609 62 8 3 604 518739014 518738414 0.000000e+00 684.0
39 TraesCS1D01G364200 chr7B 88.119 606 61 8 3 600 68533272 68533874 0.000000e+00 710.0
40 TraesCS1D01G364200 chr7B 82.508 606 59 26 1450 2046 425856988 425856421 3.050000e-134 488.0
41 TraesCS1D01G364200 chr7B 91.798 317 16 6 1811 2117 469017871 469018187 1.450000e-117 433.0
42 TraesCS1D01G364200 chr7B 91.167 317 18 6 1811 2117 603522265 603521949 3.130000e-114 422.0
43 TraesCS1D01G364200 chr7B 87.952 166 17 3 2085 2248 691515807 691515643 2.680000e-45 193.0
44 TraesCS1D01G364200 chr7B 84.328 134 10 3 1913 2046 691515938 691515816 1.280000e-23 121.0
45 TraesCS1D01G364200 chr5B 87.624 606 67 7 3 602 425175937 425176540 0.000000e+00 697.0
46 TraesCS1D01G364200 chr5B 81.894 602 61 23 1450 2046 667131414 667130856 5.140000e-127 464.0
47 TraesCS1D01G364200 chr5B 91.798 317 16 6 1811 2117 10091180 10090864 1.450000e-117 433.0
48 TraesCS1D01G364200 chr5B 94.068 236 14 0 1811 2046 204689483 204689718 2.490000e-95 359.0
49 TraesCS1D01G364200 chr2B 87.107 605 67 8 5 603 157035846 157036445 0.000000e+00 675.0
50 TraesCS1D01G364200 chr2B 92.429 317 14 6 1811 2117 726406949 726407265 6.690000e-121 444.0
51 TraesCS1D01G364200 chr2B 90.909 319 18 7 1809 2117 38675882 38675565 4.050000e-113 418.0
52 TraesCS1D01G364200 chr2B 89.157 166 15 3 2085 2248 710353738 710353902 1.240000e-48 204.0
53 TraesCS1D01G364200 chr7D 84.718 602 49 20 1450 2046 16676085 16676648 1.770000e-156 562.0
54 TraesCS1D01G364200 chr3A 83.003 606 62 23 1450 2046 722492543 722491970 6.500000e-141 510.0
55 TraesCS1D01G364200 chr3A 90.373 322 13 7 1811 2114 8917901 8918222 8.780000e-110 407.0
56 TraesCS1D01G364200 chr5A 93.691 317 10 6 1811 2117 131654356 131654672 1.430000e-127 466.0
57 TraesCS1D01G364200 chr5A 95.339 236 11 0 1811 2046 9732957 9733192 2.480000e-100 375.0
58 TraesCS1D01G364200 chr2A 92.114 317 15 4 1811 2117 24792546 24792230 3.110000e-119 438.0
59 TraesCS1D01G364200 chr2A 91.824 318 15 2 1811 2117 484064619 484064936 1.450000e-117 433.0
60 TraesCS1D01G364200 chr3B 91.798 317 16 6 1811 2117 775129283 775128967 1.450000e-117 433.0
61 TraesCS1D01G364200 chr3B 91.167 317 18 6 1811 2117 164255693 164255377 3.130000e-114 422.0
62 TraesCS1D01G364200 chr7A 90.221 317 21 6 1811 2117 631783263 631783579 3.160000e-109 405.0
63 TraesCS1D01G364200 chr4B 84.672 137 11 3 1910 2046 317668688 317668814 7.650000e-26 128.0
64 TraesCS1D01G364200 chr4B 93.548 62 3 1 1803 1864 317668608 317668668 1.000000e-14 91.6


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 TraesCS1D01G364200 chr1D 445316507 445319140 2633 False 4865.000000 4865 100.000000 1 2634 1 chr1D.!!$F2 2633
1 TraesCS1D01G364200 chr1D 445386388 445387272 884 True 1081.000000 1081 89.426000 810 1658 1 chr1D.!!$R2 848
2 TraesCS1D01G364200 chr1D 378108853 378109455 602 True 732.000000 732 88.760000 5 602 1 chr1D.!!$R1 597
3 TraesCS1D01G364200 chr1D 446558048 446559603 1555 False 491.666667 1068 86.917667 708 2216 3 chr1D.!!$F3 1508
4 TraesCS1D01G364200 chr1B 607429115 607429808 693 True 1110.000000 1110 95.540000 794 1487 1 chr1B.!!$R1 693
5 TraesCS1D01G364200 chr1B 606839503 606841565 2062 False 759.566667 1797 92.435667 642 2634 3 chr1B.!!$F2 1992
6 TraesCS1D01G364200 chr1B 611131355 611132513 1158 False 628.500000 1077 85.220500 950 2124 2 chr1B.!!$F4 1174
7 TraesCS1D01G364200 chr1B 610965201 610966928 1727 False 587.533333 974 88.043000 748 2435 3 chr1B.!!$F3 1687
8 TraesCS1D01G364200 chr1B 608461275 608462054 779 True 335.000000 407 84.953000 1964 2634 2 chr1B.!!$R2 670
9 TraesCS1D01G364200 chr1A 541318627 541319749 1122 False 1458.000000 1458 90.043000 337 1488 1 chr1A.!!$F3 1151
10 TraesCS1D01G364200 chr1A 542358183 542359281 1098 False 1066.000000 1066 84.897000 795 1864 1 chr1A.!!$F6 1069
11 TraesCS1D01G364200 chr1A 542170255 542170976 721 False 928.000000 928 90.608000 963 1652 1 chr1A.!!$F5 689
12 TraesCS1D01G364200 chr6A 67141669 67142335 666 True 850.000000 850 90.000000 837 1491 1 chr6A.!!$R1 654
13 TraesCS1D01G364200 chr6A 550622115 550622720 605 False 704.000000 704 87.869000 2 602 1 chr6A.!!$F1 600
14 TraesCS1D01G364200 chr6D 47812082 47812793 711 False 822.000000 822 87.849000 785 1484 1 chr6D.!!$F1 699
15 TraesCS1D01G364200 chr6B 514658215 514658802 587 True 774.000000 774 90.333000 2 600 1 chr6B.!!$R2 598
16 TraesCS1D01G364200 chr4D 152885354 152885948 594 True 763.000000 763 89.867000 3 600 1 chr4D.!!$R1 597
17 TraesCS1D01G364200 chr3D 446704638 446705222 584 False 736.000000 736 89.438000 3 585 1 chr3D.!!$F1 582
18 TraesCS1D01G364200 chr3D 518738414 518739014 600 True 684.000000 684 87.356000 3 604 1 chr3D.!!$R1 601
19 TraesCS1D01G364200 chr7B 68533272 68533874 602 False 710.000000 710 88.119000 3 600 1 chr7B.!!$F1 597
20 TraesCS1D01G364200 chr7B 425856421 425856988 567 True 488.000000 488 82.508000 1450 2046 1 chr7B.!!$R1 596
21 TraesCS1D01G364200 chr5B 425175937 425176540 603 False 697.000000 697 87.624000 3 602 1 chr5B.!!$F2 599
22 TraesCS1D01G364200 chr5B 667130856 667131414 558 True 464.000000 464 81.894000 1450 2046 1 chr5B.!!$R2 596
23 TraesCS1D01G364200 chr2B 157035846 157036445 599 False 675.000000 675 87.107000 5 603 1 chr2B.!!$F1 598
24 TraesCS1D01G364200 chr7D 16676085 16676648 563 False 562.000000 562 84.718000 1450 2046 1 chr7D.!!$F1 596
25 TraesCS1D01G364200 chr3A 722491970 722492543 573 True 510.000000 510 83.003000 1450 2046 1 chr3A.!!$R1 596

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
25 26 1.142748 CCTGCTAGGACTTGGAGCG 59.857 63.158 0.0 0.0 37.67 5.03 F
1534 1814 0.099436 GCTCATCGGTGGAAATGTGC 59.901 55.000 0.0 0.0 35.87 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1544 1824 0.109532 TCCACCATGGCAAGAACGAA 59.890 50.000 13.04 0.0 37.47 3.85 R
2465 3066 1.341209 CTTGAAACCCTTTGGCTCACC 59.659 52.381 0.00 0.0 33.59 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.142748 CCTGCTAGGACTTGGAGCG 59.857 63.158 0.00 0.00 37.67 5.03
26 27 1.608717 CCTGCTAGGACTTGGAGCGT 61.609 60.000 0.00 0.00 37.67 5.07
40 41 1.583054 GAGCGTGAAGAAACTGTGGT 58.417 50.000 0.00 0.00 0.00 4.16
60 61 2.175878 AGGTGATGACTGCTTGTGTC 57.824 50.000 0.00 0.00 35.21 3.67
93 94 6.072452 ACAATATGATCGTAGAAGATGAGCGA 60.072 38.462 0.41 0.00 43.58 4.93
95 96 3.206964 TGATCGTAGAAGATGAGCGACT 58.793 45.455 0.00 0.00 43.58 4.18
161 162 1.614525 TGCCTGAGCATGGAGGAGT 60.615 57.895 0.00 0.00 46.52 3.85
207 208 3.745332 TTTCATCATGACATGCGTGAC 57.255 42.857 14.17 7.25 44.84 3.67
208 209 1.655484 TCATCATGACATGCGTGACC 58.345 50.000 14.17 4.54 44.84 4.02
212 213 3.680620 ATGACATGCGTGACCGGGG 62.681 63.158 14.17 0.00 33.68 5.73
605 643 2.157863 GCGTTGGAGTTGCTCTTAGTTC 59.842 50.000 0.00 0.00 0.00 3.01
704 748 1.244019 GGATGTTGGCGGCAAAGAGT 61.244 55.000 27.23 12.22 0.00 3.24
777 822 1.326213 CCAACAGCCCAACACCACAA 61.326 55.000 0.00 0.00 0.00 3.33
851 947 1.840630 CGAACCAATCACAGCACGCA 61.841 55.000 0.00 0.00 0.00 5.24
948 1055 4.187694 CTCATCTTCTCTCCCGAAAAAGG 58.812 47.826 0.00 0.00 0.00 3.11
949 1056 2.474410 TCTTCTCTCCCGAAAAAGGC 57.526 50.000 0.00 0.00 0.00 4.35
953 1060 2.938838 TCTCTCCCGAAAAAGGCAAAA 58.061 42.857 0.00 0.00 0.00 2.44
957 1086 2.360801 CTCCCGAAAAAGGCAAAACTCA 59.639 45.455 0.00 0.00 0.00 3.41
959 1088 2.116366 CCGAAAAAGGCAAAACTCACG 58.884 47.619 0.00 0.00 0.00 4.35
961 1090 2.535331 GAAAAAGGCAAAACTCACGCA 58.465 42.857 0.00 0.00 0.00 5.24
1516 1757 1.281899 GTCGTCTTAGCCAGATGTGC 58.718 55.000 3.29 0.00 39.36 4.57
1533 1813 1.131126 GTGCTCATCGGTGGAAATGTG 59.869 52.381 0.00 0.00 0.00 3.21
1534 1814 0.099436 GCTCATCGGTGGAAATGTGC 59.901 55.000 0.00 0.00 35.87 4.57
1535 1815 0.374758 CTCATCGGTGGAAATGTGCG 59.625 55.000 0.00 0.00 0.00 5.34
1536 1816 0.321210 TCATCGGTGGAAATGTGCGT 60.321 50.000 0.00 0.00 0.00 5.24
1537 1817 0.179192 CATCGGTGGAAATGTGCGTG 60.179 55.000 0.00 0.00 0.00 5.34
1538 1818 1.922135 ATCGGTGGAAATGTGCGTGC 61.922 55.000 0.00 0.00 0.00 5.34
1539 1819 2.616330 CGGTGGAAATGTGCGTGCT 61.616 57.895 0.00 0.00 0.00 4.40
1540 1820 1.295357 CGGTGGAAATGTGCGTGCTA 61.295 55.000 0.00 0.00 0.00 3.49
1541 1821 0.447801 GGTGGAAATGTGCGTGCTAG 59.552 55.000 0.00 0.00 0.00 3.42
1542 1822 1.156736 GTGGAAATGTGCGTGCTAGT 58.843 50.000 0.00 0.00 0.00 2.57
1543 1823 1.135972 GTGGAAATGTGCGTGCTAGTG 60.136 52.381 0.00 0.00 0.00 2.74
1544 1824 1.156736 GGAAATGTGCGTGCTAGTGT 58.843 50.000 0.00 0.00 0.00 3.55
1545 1825 1.535462 GGAAATGTGCGTGCTAGTGTT 59.465 47.619 0.00 0.00 0.00 3.32
1546 1826 2.412847 GGAAATGTGCGTGCTAGTGTTC 60.413 50.000 0.00 0.00 0.00 3.18
1547 1827 0.790207 AATGTGCGTGCTAGTGTTCG 59.210 50.000 0.00 0.00 0.00 3.95
1548 1828 0.319555 ATGTGCGTGCTAGTGTTCGT 60.320 50.000 0.00 0.00 0.00 3.85
1549 1829 0.528901 TGTGCGTGCTAGTGTTCGTT 60.529 50.000 0.00 0.00 0.00 3.85
1550 1830 0.161024 GTGCGTGCTAGTGTTCGTTC 59.839 55.000 0.00 0.00 0.00 3.95
1551 1831 0.031585 TGCGTGCTAGTGTTCGTTCT 59.968 50.000 0.00 0.00 0.00 3.01
1552 1832 1.137513 GCGTGCTAGTGTTCGTTCTT 58.862 50.000 0.00 0.00 0.00 2.52
1553 1833 1.136611 GCGTGCTAGTGTTCGTTCTTG 60.137 52.381 0.00 0.00 0.00 3.02
1554 1834 1.136611 CGTGCTAGTGTTCGTTCTTGC 60.137 52.381 0.00 0.00 34.23 4.01
1555 1835 1.194772 GTGCTAGTGTTCGTTCTTGCC 59.805 52.381 0.00 0.00 33.09 4.52
1556 1836 1.202592 TGCTAGTGTTCGTTCTTGCCA 60.203 47.619 0.00 0.00 33.09 4.92
1557 1837 2.076863 GCTAGTGTTCGTTCTTGCCAT 58.923 47.619 0.00 0.00 0.00 4.40
1558 1838 2.159653 GCTAGTGTTCGTTCTTGCCATG 60.160 50.000 0.00 0.00 0.00 3.66
1559 1839 1.238439 AGTGTTCGTTCTTGCCATGG 58.762 50.000 7.63 7.63 0.00 3.66
1560 1840 0.951558 GTGTTCGTTCTTGCCATGGT 59.048 50.000 14.67 0.00 0.00 3.55
1561 1841 0.950836 TGTTCGTTCTTGCCATGGTG 59.049 50.000 14.67 4.40 0.00 4.17
1562 1842 0.240945 GTTCGTTCTTGCCATGGTGG 59.759 55.000 14.67 4.03 41.55 4.61
1563 1843 0.109532 TTCGTTCTTGCCATGGTGGA 59.890 50.000 14.67 6.48 40.96 4.02
1564 1844 0.327924 TCGTTCTTGCCATGGTGGAT 59.672 50.000 14.67 0.00 40.96 3.41
1565 1845 0.452987 CGTTCTTGCCATGGTGGATG 59.547 55.000 14.67 0.76 40.96 3.51
1566 1846 1.549203 GTTCTTGCCATGGTGGATGT 58.451 50.000 14.67 0.00 40.96 3.06
1567 1847 2.722094 GTTCTTGCCATGGTGGATGTA 58.278 47.619 14.67 0.00 40.96 2.29
1568 1848 2.684881 GTTCTTGCCATGGTGGATGTAG 59.315 50.000 14.67 1.05 40.96 2.74
1569 1849 1.915489 TCTTGCCATGGTGGATGTAGT 59.085 47.619 14.67 0.00 40.96 2.73
1717 2017 3.431922 TGATTATCCCGACTCGTGAAC 57.568 47.619 0.00 0.00 0.00 3.18
1790 2097 5.766222 CTTAAATGATGCCTTGGCTGTATC 58.234 41.667 13.18 8.14 0.00 2.24
1801 2108 5.730568 GCCTTGGCTGTATCAAATTTCGTAG 60.731 44.000 4.11 0.00 0.00 3.51
1806 2114 5.350365 GGCTGTATCAAATTTCGTAGTCACA 59.650 40.000 0.00 0.00 0.00 3.58
1810 2118 8.014322 TGTATCAAATTTCGTAGTCACAAGTC 57.986 34.615 0.00 0.00 0.00 3.01
1864 2172 1.337823 GCCTTGGCTCGTTCAGTTCTA 60.338 52.381 4.11 0.00 0.00 2.10
1866 2174 3.430374 GCCTTGGCTCGTTCAGTTCTATA 60.430 47.826 4.11 0.00 0.00 1.31
1867 2175 4.755411 CCTTGGCTCGTTCAGTTCTATAA 58.245 43.478 0.00 0.00 0.00 0.98
1868 2176 5.360591 CCTTGGCTCGTTCAGTTCTATAAT 58.639 41.667 0.00 0.00 0.00 1.28
1869 2177 5.463724 CCTTGGCTCGTTCAGTTCTATAATC 59.536 44.000 0.00 0.00 0.00 1.75
1870 2178 5.592104 TGGCTCGTTCAGTTCTATAATCA 57.408 39.130 0.00 0.00 0.00 2.57
1872 2180 5.127194 TGGCTCGTTCAGTTCTATAATCACT 59.873 40.000 0.00 0.00 0.00 3.41
1874 2182 6.858993 GGCTCGTTCAGTTCTATAATCACTAG 59.141 42.308 0.00 0.00 0.00 2.57
1888 2196 9.416794 CTATAATCACTAGTATGTTCAGCCTTG 57.583 37.037 0.00 0.00 0.00 3.61
1890 2198 5.073311 TCACTAGTATGTTCAGCCTTGAC 57.927 43.478 0.00 0.00 31.71 3.18
1891 2199 4.526650 TCACTAGTATGTTCAGCCTTGACA 59.473 41.667 0.00 0.00 31.71 3.58
1892 2200 5.187772 TCACTAGTATGTTCAGCCTTGACAT 59.812 40.000 0.00 0.00 31.71 3.06
1893 2201 5.877012 CACTAGTATGTTCAGCCTTGACATT 59.123 40.000 0.00 0.00 31.71 2.71
1894 2202 5.877012 ACTAGTATGTTCAGCCTTGACATTG 59.123 40.000 0.00 0.00 31.71 2.82
1895 2203 4.910195 AGTATGTTCAGCCTTGACATTGA 58.090 39.130 0.00 0.00 31.71 2.57
1896 2204 5.316167 AGTATGTTCAGCCTTGACATTGAA 58.684 37.500 0.00 0.00 31.71 2.69
1897 2205 5.948162 AGTATGTTCAGCCTTGACATTGAAT 59.052 36.000 0.00 0.00 32.76 2.57
1898 2206 4.771590 TGTTCAGCCTTGACATTGAATC 57.228 40.909 0.00 0.00 32.76 2.52
1899 2207 4.401022 TGTTCAGCCTTGACATTGAATCT 58.599 39.130 0.00 0.00 32.76 2.40
1900 2208 4.216902 TGTTCAGCCTTGACATTGAATCTG 59.783 41.667 0.00 0.00 32.76 2.90
1901 2209 4.290711 TCAGCCTTGACATTGAATCTGA 57.709 40.909 0.00 0.00 0.00 3.27
1902 2210 4.654915 TCAGCCTTGACATTGAATCTGAA 58.345 39.130 0.00 0.00 0.00 3.02
1903 2211 5.258841 TCAGCCTTGACATTGAATCTGAAT 58.741 37.500 0.00 0.00 0.00 2.57
1904 2212 5.124936 TCAGCCTTGACATTGAATCTGAATG 59.875 40.000 0.00 0.00 36.94 2.67
1905 2213 5.124936 CAGCCTTGACATTGAATCTGAATGA 59.875 40.000 0.00 0.00 35.23 2.57
1906 2214 5.713389 AGCCTTGACATTGAATCTGAATGAA 59.287 36.000 0.00 0.00 35.23 2.57
1907 2215 5.803967 GCCTTGACATTGAATCTGAATGAAC 59.196 40.000 0.00 0.00 35.23 3.18
1908 2216 6.570957 GCCTTGACATTGAATCTGAATGAACA 60.571 38.462 0.00 0.00 35.23 3.18
1911 2230 5.106038 TGACATTGAATCTGAATGAACAGCC 60.106 40.000 0.00 0.00 37.75 4.85
1958 2282 1.002868 ATCCCTGTGACTGCTGCAC 60.003 57.895 0.00 9.92 36.81 4.57
1960 2284 0.831711 TCCCTGTGACTGCTGCACTA 60.832 55.000 0.00 0.00 37.18 2.74
1980 2304 3.703001 AAACTCTCACCTGTACCATGG 57.297 47.619 11.19 11.19 0.00 3.66
1987 2311 3.066291 CACCTGTACCATGGTGCTAAA 57.934 47.619 29.82 12.23 45.68 1.85
2046 2370 4.691860 ATTTTGCACTGCTCATACTGTC 57.308 40.909 1.98 0.00 0.00 3.51
2049 2381 2.964740 TGCACTGCTCATACTGTCTTC 58.035 47.619 1.98 0.00 0.00 2.87
2205 2541 2.679059 GCTGCTGCAGATCAGAAAGGTA 60.679 50.000 32.30 0.00 45.72 3.08
2217 2553 6.998074 AGATCAGAAAGGTAAACACATGTTCA 59.002 34.615 0.00 0.00 37.25 3.18
2286 2721 1.679305 GAGGGCGTGAGGAGACTGA 60.679 63.158 0.00 0.00 44.43 3.41
2322 2757 3.576550 AGAAGGTCCTTCTCTGAACTGTC 59.423 47.826 25.96 0.00 46.42 3.51
2402 3003 9.931210 GGCATCTAGTTTATTGTTTACATGTAC 57.069 33.333 4.68 0.00 0.00 2.90
2412 3013 4.963373 TGTTTACATGTACCCATATCCGG 58.037 43.478 4.68 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.067972 TCACCTACCACAGTTTCTTCAC 57.932 45.455 0.00 0.00 0.00 3.18
26 27 4.346709 TCATCACCTACCACAGTTTCTTCA 59.653 41.667 0.00 0.00 0.00 3.02
40 41 2.632512 TGACACAAGCAGTCATCACCTA 59.367 45.455 0.00 0.00 40.80 3.08
60 61 6.956299 TCTACGATCATATTGTGCATGATG 57.044 37.500 4.51 0.00 41.96 3.07
161 162 3.120130 GGTGAACTGTTCAAACGTTGTCA 60.120 43.478 23.55 0.00 42.15 3.58
207 208 1.303236 TTGCATGTGAGTTCCCCGG 60.303 57.895 0.00 0.00 0.00 5.73
208 209 0.606401 AGTTGCATGTGAGTTCCCCG 60.606 55.000 0.00 0.00 0.00 5.73
430 458 1.456705 TGGCCGCCCTTTTTCAACT 60.457 52.632 7.03 0.00 0.00 3.16
496 524 4.065088 TCCGTCTTGTTTGAGATTTGAGG 58.935 43.478 0.00 0.00 0.00 3.86
661 704 8.333235 TCCCAAGCAAAAATCTACTCCTTATTA 58.667 33.333 0.00 0.00 0.00 0.98
662 705 7.182060 TCCCAAGCAAAAATCTACTCCTTATT 58.818 34.615 0.00 0.00 0.00 1.40
663 706 6.731467 TCCCAAGCAAAAATCTACTCCTTAT 58.269 36.000 0.00 0.00 0.00 1.73
704 748 1.570813 CGCGGATCATGTTTGCTCTA 58.429 50.000 0.00 0.00 0.00 2.43
777 822 2.267006 CTGGTGCCACTGATCGCT 59.733 61.111 0.00 0.00 0.00 4.93
808 904 2.202756 GTGAGGCGGATCGTGGAC 60.203 66.667 0.00 0.00 0.00 4.02
851 947 0.034477 GATCCGTGGGATGGTGGTTT 60.034 55.000 1.07 0.00 43.27 3.27
948 1055 2.051345 CGGGTGCGTGAGTTTTGC 60.051 61.111 0.00 0.00 0.00 3.68
949 1056 2.051345 GCGGGTGCGTGAGTTTTG 60.051 61.111 0.00 0.00 0.00 2.44
974 1129 0.250166 CGGCGTTAAATAGGAGGGGG 60.250 60.000 0.00 0.00 0.00 5.40
1178 1369 2.359975 CGGTGGGGCTTCTTCACC 60.360 66.667 0.00 0.00 45.36 4.02
1493 1693 1.402259 CATCTGGCTAAGACGACGACT 59.598 52.381 0.00 0.00 37.88 4.18
1516 1757 0.374758 CGCACATTTCCACCGATGAG 59.625 55.000 0.00 0.00 0.00 2.90
1533 1813 1.136611 CAAGAACGAACACTAGCACGC 60.137 52.381 0.00 0.00 0.00 5.34
1534 1814 1.136611 GCAAGAACGAACACTAGCACG 60.137 52.381 0.00 0.00 0.00 5.34
1535 1815 1.194772 GGCAAGAACGAACACTAGCAC 59.805 52.381 0.00 0.00 0.00 4.40
1536 1816 1.202592 TGGCAAGAACGAACACTAGCA 60.203 47.619 0.00 0.00 0.00 3.49
1537 1817 1.508632 TGGCAAGAACGAACACTAGC 58.491 50.000 0.00 0.00 0.00 3.42
1538 1818 2.416547 CCATGGCAAGAACGAACACTAG 59.583 50.000 0.00 0.00 0.00 2.57
1539 1819 2.224426 ACCATGGCAAGAACGAACACTA 60.224 45.455 13.04 0.00 0.00 2.74
1540 1820 1.238439 CCATGGCAAGAACGAACACT 58.762 50.000 0.00 0.00 0.00 3.55
1541 1821 0.951558 ACCATGGCAAGAACGAACAC 59.048 50.000 13.04 0.00 0.00 3.32
1542 1822 0.950836 CACCATGGCAAGAACGAACA 59.049 50.000 13.04 0.00 0.00 3.18
1543 1823 0.240945 CCACCATGGCAAGAACGAAC 59.759 55.000 13.04 0.00 0.00 3.95
1544 1824 0.109532 TCCACCATGGCAAGAACGAA 59.890 50.000 13.04 0.00 37.47 3.85
1545 1825 0.327924 ATCCACCATGGCAAGAACGA 59.672 50.000 13.04 0.00 37.47 3.85
1546 1826 0.452987 CATCCACCATGGCAAGAACG 59.547 55.000 13.04 0.00 37.47 3.95
1547 1827 1.549203 ACATCCACCATGGCAAGAAC 58.451 50.000 13.04 0.00 37.47 3.01
1548 1828 2.308570 ACTACATCCACCATGGCAAGAA 59.691 45.455 13.04 0.00 37.47 2.52
1549 1829 1.915489 ACTACATCCACCATGGCAAGA 59.085 47.619 13.04 6.53 37.47 3.02
1550 1830 2.424601 CAACTACATCCACCATGGCAAG 59.575 50.000 13.04 1.56 37.47 4.01
1551 1831 2.224992 ACAACTACATCCACCATGGCAA 60.225 45.455 13.04 0.00 37.47 4.52
1552 1832 1.354031 ACAACTACATCCACCATGGCA 59.646 47.619 13.04 0.00 37.47 4.92
1553 1833 1.745087 CACAACTACATCCACCATGGC 59.255 52.381 13.04 0.00 37.47 4.40
1554 1834 3.009723 GACACAACTACATCCACCATGG 58.990 50.000 11.19 11.19 39.43 3.66
1555 1835 3.686241 CAGACACAACTACATCCACCATG 59.314 47.826 0.00 0.00 38.64 3.66
1556 1836 3.327757 ACAGACACAACTACATCCACCAT 59.672 43.478 0.00 0.00 0.00 3.55
1557 1837 2.703536 ACAGACACAACTACATCCACCA 59.296 45.455 0.00 0.00 0.00 4.17
1558 1838 3.402628 ACAGACACAACTACATCCACC 57.597 47.619 0.00 0.00 0.00 4.61
1559 1839 4.449068 CAGAACAGACACAACTACATCCAC 59.551 45.833 0.00 0.00 0.00 4.02
1560 1840 4.343814 TCAGAACAGACACAACTACATCCA 59.656 41.667 0.00 0.00 0.00 3.41
1561 1841 4.883083 TCAGAACAGACACAACTACATCC 58.117 43.478 0.00 0.00 0.00 3.51
1562 1842 5.928839 ACATCAGAACAGACACAACTACATC 59.071 40.000 0.00 0.00 0.00 3.06
1563 1843 5.858381 ACATCAGAACAGACACAACTACAT 58.142 37.500 0.00 0.00 0.00 2.29
1564 1844 5.163457 TGACATCAGAACAGACACAACTACA 60.163 40.000 0.00 0.00 0.00 2.74
1565 1845 5.175856 GTGACATCAGAACAGACACAACTAC 59.824 44.000 0.00 0.00 0.00 2.73
1566 1846 5.289595 GTGACATCAGAACAGACACAACTA 58.710 41.667 0.00 0.00 0.00 2.24
1567 1847 4.122776 GTGACATCAGAACAGACACAACT 58.877 43.478 0.00 0.00 0.00 3.16
1568 1848 3.248602 GGTGACATCAGAACAGACACAAC 59.751 47.826 0.00 0.00 0.00 3.32
1569 1849 3.118445 TGGTGACATCAGAACAGACACAA 60.118 43.478 0.00 0.00 33.40 3.33
1717 2017 5.948992 AGTAGCTAAAACTGGCAGAAAAG 57.051 39.130 23.66 13.19 0.00 2.27
1790 2097 7.121974 AGATGACTTGTGACTACGAAATTTG 57.878 36.000 0.00 0.00 0.00 2.32
1806 2114 4.458295 CAGAGGCAATCAACAAGATGACTT 59.542 41.667 0.00 0.00 36.96 3.01
1810 2118 4.380233 GGTTCAGAGGCAATCAACAAGATG 60.380 45.833 0.00 0.00 36.96 2.90
1864 2172 7.928706 GTCAAGGCTGAACATACTAGTGATTAT 59.071 37.037 5.39 0.00 31.88 1.28
1866 2174 6.109359 GTCAAGGCTGAACATACTAGTGATT 58.891 40.000 5.39 0.00 31.88 2.57
1867 2175 5.187772 TGTCAAGGCTGAACATACTAGTGAT 59.812 40.000 5.39 0.00 31.88 3.06
1868 2176 4.526650 TGTCAAGGCTGAACATACTAGTGA 59.473 41.667 5.39 0.00 31.88 3.41
1869 2177 4.820897 TGTCAAGGCTGAACATACTAGTG 58.179 43.478 5.39 0.00 31.88 2.74
1870 2178 5.683876 ATGTCAAGGCTGAACATACTAGT 57.316 39.130 11.99 0.00 31.88 2.57
1872 2180 6.048732 TCAATGTCAAGGCTGAACATACTA 57.951 37.500 13.53 2.76 31.88 1.82
1874 2182 5.627499 TTCAATGTCAAGGCTGAACATAC 57.373 39.130 13.53 0.00 31.88 2.39
1878 2186 4.456911 TCAGATTCAATGTCAAGGCTGAAC 59.543 41.667 0.00 0.00 31.88 3.18
1879 2187 4.654915 TCAGATTCAATGTCAAGGCTGAA 58.345 39.130 0.00 0.00 31.88 3.02
1880 2188 4.290711 TCAGATTCAATGTCAAGGCTGA 57.709 40.909 0.00 0.00 0.00 4.26
1881 2189 5.124936 TCATTCAGATTCAATGTCAAGGCTG 59.875 40.000 0.00 0.00 33.61 4.85
1883 2191 5.571784 TCATTCAGATTCAATGTCAAGGC 57.428 39.130 0.00 0.00 33.61 4.35
1884 2192 6.916440 TGTTCATTCAGATTCAATGTCAAGG 58.084 36.000 0.00 0.00 33.61 3.61
1888 2196 5.125097 AGGCTGTTCATTCAGATTCAATGTC 59.875 40.000 0.00 0.00 37.61 3.06
1890 2198 5.578005 AGGCTGTTCATTCAGATTCAATG 57.422 39.130 0.00 0.00 37.61 2.82
1891 2199 5.623824 GCAAGGCTGTTCATTCAGATTCAAT 60.624 40.000 0.00 0.00 37.61 2.57
1892 2200 4.321452 GCAAGGCTGTTCATTCAGATTCAA 60.321 41.667 0.00 0.00 37.61 2.69
1893 2201 3.192001 GCAAGGCTGTTCATTCAGATTCA 59.808 43.478 0.00 0.00 37.61 2.57
1894 2202 3.442977 AGCAAGGCTGTTCATTCAGATTC 59.557 43.478 0.00 0.00 37.57 2.52
1895 2203 3.428532 AGCAAGGCTGTTCATTCAGATT 58.571 40.909 0.00 0.00 37.57 2.40
1896 2204 3.083122 AGCAAGGCTGTTCATTCAGAT 57.917 42.857 0.00 0.00 37.57 2.90
1897 2205 2.574006 AGCAAGGCTGTTCATTCAGA 57.426 45.000 0.00 0.00 37.57 3.27
1908 2216 6.840780 ATTACAGAATAAAACAGCAAGGCT 57.159 33.333 0.00 0.00 40.77 4.58
1911 2230 9.696917 AAAGGAATTACAGAATAAAACAGCAAG 57.303 29.630 0.00 0.00 0.00 4.01
1980 2304 7.443259 TCCTAATTTACCAGTTGTTTAGCAC 57.557 36.000 0.00 0.00 0.00 4.40
2013 2337 5.098211 GCAGTGCAAAATAGAAACATCTCC 58.902 41.667 11.09 0.00 0.00 3.71
2217 2553 8.974060 TCTACTGAAAAGATTTTAACACAGGT 57.026 30.769 0.00 0.00 0.00 4.00
2286 2721 4.162131 AGGACCTTCTGTTGCAAAAACATT 59.838 37.500 0.00 0.00 0.00 2.71
2322 2757 3.930618 TGTTAGAGCAAAAACACGTTCG 58.069 40.909 0.00 0.00 30.88 3.95
2402 3003 1.623811 CTTGTCCCTACCGGATATGGG 59.376 57.143 9.46 13.85 44.66 4.00
2406 3007 2.674420 CTTCCTTGTCCCTACCGGATA 58.326 52.381 9.46 0.00 44.66 2.59
2412 3013 4.223255 ACTTTAGAGCTTCCTTGTCCCTAC 59.777 45.833 0.00 0.00 0.00 3.18
2450 3051 6.882610 TGGCTCACCAATTATGTATCATTC 57.117 37.500 0.00 0.00 45.37 2.67
2465 3066 1.341209 CTTGAAACCCTTTGGCTCACC 59.659 52.381 0.00 0.00 33.59 4.02


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

AutoCloner maintained by Alex Coulton.