Multiple sequence alignment - TraesCS7A01G178800

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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 TraesCS7A01G178800 chr7A 100.000 2565 0 0 1 2565 133623798 133626362 0.000000e+00 4737.0
1 TraesCS7A01G178800 chr7A 96.040 707 24 1 6 712 174709700 174710402 0.000000e+00 1147.0
2 TraesCS7A01G178800 chr7A 94.693 716 30 5 1 715 89920161 89920869 0.000000e+00 1105.0
3 TraesCS7A01G178800 chr7A 84.211 209 26 4 985 1193 133605773 133605974 2.010000e-46 196.0
4 TraesCS7A01G178800 chr7A 93.103 58 4 0 1717 1774 678972829 678972886 4.550000e-13 86.1
5 TraesCS7A01G178800 chr7A 93.103 58 4 0 1717 1774 678987038 678987095 4.550000e-13 86.1
6 TraesCS7A01G178800 chr5A 95.910 709 25 2 1 708 645983638 645984343 0.000000e+00 1146.0
7 TraesCS7A01G178800 chr5A 95.640 711 30 1 1 711 561182602 561181893 0.000000e+00 1140.0
8 TraesCS7A01G178800 chr3A 95.365 712 32 1 1 712 87967864 87968574 0.000000e+00 1131.0
9 TraesCS7A01G178800 chr3A 95.332 707 33 0 5 711 88192653 88191947 0.000000e+00 1123.0
10 TraesCS7A01G178800 chr3A 95.218 711 30 1 1 711 678321903 678321197 0.000000e+00 1122.0
11 TraesCS7A01G178800 chr6A 95.063 709 34 1 1 708 376508331 376509039 0.000000e+00 1114.0
12 TraesCS7A01G178800 chr6A 94.643 56 1 2 1720 1774 402232960 402233014 4.550000e-13 86.1
13 TraesCS7A01G178800 chr4A 94.663 712 36 2 1 711 466943385 466942675 0.000000e+00 1103.0
14 TraesCS7A01G178800 chr4A 98.039 51 1 0 1724 1774 219956211 219956261 3.520000e-14 89.8
15 TraesCS7A01G178800 chr4A 96.226 53 2 0 1722 1774 584471989 584472041 1.260000e-13 87.9
16 TraesCS7A01G178800 chr7D 90.427 773 40 19 711 1468 134450661 134451414 0.000000e+00 987.0
17 TraesCS7A01G178800 chr7D 91.286 700 51 8 1813 2509 134464428 134465120 0.000000e+00 946.0
18 TraesCS7A01G178800 chr7D 93.478 276 15 3 1454 1728 134464147 134464420 8.540000e-110 407.0
19 TraesCS7A01G178800 chr7D 82.547 212 27 8 985 1193 134443368 134443572 7.290000e-41 178.0
20 TraesCS7A01G178800 chr7D 95.000 60 1 2 2508 2565 134465895 134465954 2.720000e-15 93.5
21 TraesCS7A01G178800 chr7D 96.226 53 2 0 1722 1774 623644438 623644490 1.260000e-13 87.9
22 TraesCS7A01G178800 chr7B 91.551 722 44 12 1796 2509 96600688 96601400 0.000000e+00 979.0
23 TraesCS7A01G178800 chr7B 85.222 1015 71 40 729 1725 96599746 96600699 0.000000e+00 970.0
24 TraesCS7A01G178800 chr7B 85.965 171 17 7 1023 1193 96585610 96585773 2.620000e-40 176.0
25 TraesCS7A01G178800 chr7B 94.545 55 3 0 1720 1774 559142188 559142242 4.550000e-13 86.1
26 TraesCS7A01G178800 chr7B 88.525 61 4 3 2508 2565 96602178 96602238 1.270000e-08 71.3
27 TraesCS7A01G178800 chr1B 96.296 54 2 0 1721 1774 492329967 492329914 3.520000e-14 89.8
28 TraesCS7A01G178800 chr6D 91.803 61 4 1 1726 1785 46439082 46439142 1.640000e-12 84.2
29 TraesCS7A01G178800 chr6B 90.909 44 3 1 1280 1322 686508057 686508100 9.910000e-05 58.4


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 TraesCS7A01G178800 chr7A 133623798 133626362 2564 False 4737.000000 4737 100.000000 1 2565 1 chr7A.!!$F3 2564
1 TraesCS7A01G178800 chr7A 174709700 174710402 702 False 1147.000000 1147 96.040000 6 712 1 chr7A.!!$F4 706
2 TraesCS7A01G178800 chr7A 89920161 89920869 708 False 1105.000000 1105 94.693000 1 715 1 chr7A.!!$F1 714
3 TraesCS7A01G178800 chr5A 645983638 645984343 705 False 1146.000000 1146 95.910000 1 708 1 chr5A.!!$F1 707
4 TraesCS7A01G178800 chr5A 561181893 561182602 709 True 1140.000000 1140 95.640000 1 711 1 chr5A.!!$R1 710
5 TraesCS7A01G178800 chr3A 87967864 87968574 710 False 1131.000000 1131 95.365000 1 712 1 chr3A.!!$F1 711
6 TraesCS7A01G178800 chr3A 88191947 88192653 706 True 1123.000000 1123 95.332000 5 711 1 chr3A.!!$R1 706
7 TraesCS7A01G178800 chr3A 678321197 678321903 706 True 1122.000000 1122 95.218000 1 711 1 chr3A.!!$R2 710
8 TraesCS7A01G178800 chr6A 376508331 376509039 708 False 1114.000000 1114 95.063000 1 708 1 chr6A.!!$F1 707
9 TraesCS7A01G178800 chr4A 466942675 466943385 710 True 1103.000000 1103 94.663000 1 711 1 chr4A.!!$R1 710
10 TraesCS7A01G178800 chr7D 134450661 134451414 753 False 987.000000 987 90.427000 711 1468 1 chr7D.!!$F2 757
11 TraesCS7A01G178800 chr7D 134464147 134465954 1807 False 482.166667 946 93.254667 1454 2565 3 chr7D.!!$F4 1111
12 TraesCS7A01G178800 chr7B 96599746 96602238 2492 False 673.433333 979 88.432667 729 2565 3 chr7B.!!$F3 1836

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
585 588 0.034863 GCAAGTTTGGACCGGGGATA 60.035 55.0 6.32 0.0 0.0 2.59 F
727 731 0.044855 ACTAGCCAACTCCCCTCCAT 59.955 55.0 0.00 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1468 1498 0.035439 GTCCGATTTCTGCCCAAGGA 60.035 55.000 0.0 0.0 0.0 3.36 R
1746 1780 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.0 0.0 0.0 4.18 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
308 309 2.438975 TCCGGCGTGTACTCCGAT 60.439 61.111 14.42 0.00 46.30 4.18
441 444 0.906282 GAGGGACGTGGGAGGGTTTA 60.906 60.000 0.00 0.00 0.00 2.01
558 561 1.303317 GCTGTCCGTTTCACCCCAT 60.303 57.895 0.00 0.00 0.00 4.00
576 579 0.606944 ATAACCGGCGCAAGTTTGGA 60.607 50.000 17.85 2.90 41.68 3.53
585 588 0.034863 GCAAGTTTGGACCGGGGATA 60.035 55.000 6.32 0.00 0.00 2.59
712 716 1.153823 CGCGGTGGAGTTGGACTAG 60.154 63.158 0.00 0.00 0.00 2.57
727 731 0.044855 ACTAGCCAACTCCCCTCCAT 59.955 55.000 0.00 0.00 0.00 3.41
730 734 2.308722 GCCAACTCCCCTCCATCCA 61.309 63.158 0.00 0.00 0.00 3.41
739 743 1.056700 CCCTCCATCCAGAACCCGAT 61.057 60.000 0.00 0.00 0.00 4.18
846 850 3.512516 GGCAGCGCTGTTCATCCC 61.513 66.667 35.80 24.03 0.00 3.85
902 909 2.739379 GCACAACACTCTTAAGCTCTCC 59.261 50.000 0.00 0.00 0.00 3.71
916 923 2.821366 CTCCGCAAATCCGCAGCT 60.821 61.111 0.00 0.00 0.00 4.24
917 924 2.817423 CTCCGCAAATCCGCAGCTC 61.817 63.158 0.00 0.00 0.00 4.09
929 936 2.821366 CAGCTCCCGCTCGCATTT 60.821 61.111 0.00 0.00 45.15 2.32
1224 1231 2.824041 CTTTCCATGGGCCGACGG 60.824 66.667 13.02 10.29 0.00 4.79
1262 1269 0.760945 AGCCGCCTCCAGCTTAGTAT 60.761 55.000 0.00 0.00 40.39 2.12
1270 1277 5.565045 CGCCTCCAGCTTAGTATTTAGTAGG 60.565 48.000 0.00 0.00 40.39 3.18
1336 1360 4.641989 GCCTGAACCTGAATGATGTGTTAT 59.358 41.667 0.00 0.00 0.00 1.89
1347 1371 7.376615 TGAATGATGTGTTATCATTGTTTGCA 58.623 30.769 17.09 7.89 45.59 4.08
1386 1410 1.403647 GGGGCGTTAAATTGTTGCTCC 60.404 52.381 0.00 0.00 39.34 4.70
1414 1438 6.144078 TCTGATTACAGCGTGTACATGTAT 57.856 37.500 16.28 3.26 43.17 2.29
1415 1439 5.977129 TCTGATTACAGCGTGTACATGTATG 59.023 40.000 16.28 16.30 43.17 2.39
1416 1440 5.897050 TGATTACAGCGTGTACATGTATGA 58.103 37.500 21.80 5.93 31.69 2.15
1417 1441 5.977129 TGATTACAGCGTGTACATGTATGAG 59.023 40.000 21.80 4.62 31.69 2.90
1422 1446 6.338146 ACAGCGTGTACATGTATGAGTAATT 58.662 36.000 21.80 3.54 0.00 1.40
1468 1498 6.653020 TCAGTGCCTATGAATTACTTGTGAT 58.347 36.000 0.00 0.00 0.00 3.06
1473 1503 6.543465 TGCCTATGAATTACTTGTGATCCTTG 59.457 38.462 0.00 0.00 0.00 3.61
1479 1509 1.067295 ACTTGTGATCCTTGGGCAGA 58.933 50.000 0.00 0.00 0.00 4.26
1483 1513 2.726821 TGTGATCCTTGGGCAGAAATC 58.273 47.619 0.00 0.00 0.00 2.17
1506 1536 4.023622 CGGACTGTACACTGATCAGATAGG 60.024 50.000 29.27 16.29 33.93 2.57
1619 1651 6.036300 GCCACATCCATAAATCACAAAACATG 59.964 38.462 0.00 0.00 0.00 3.21
1641 1673 3.199289 GGCTACCACTGTGTTACCCTAAT 59.801 47.826 7.08 0.00 0.00 1.73
1650 1682 7.362056 CCACTGTGTTACCCTAATTCAAAGATG 60.362 40.741 7.08 0.00 0.00 2.90
1725 1759 3.934068 ACATCCAACGGTACCAAACTAG 58.066 45.455 13.54 0.00 0.00 2.57
1726 1760 3.325716 ACATCCAACGGTACCAAACTAGT 59.674 43.478 13.54 0.00 0.00 2.57
1727 1761 4.527816 ACATCCAACGGTACCAAACTAGTA 59.472 41.667 13.54 0.00 0.00 1.82
1728 1762 4.519540 TCCAACGGTACCAAACTAGTAC 57.480 45.455 13.54 0.00 39.51 2.73
1729 1763 4.151883 TCCAACGGTACCAAACTAGTACT 58.848 43.478 13.54 0.00 40.01 2.73
1730 1764 4.218417 TCCAACGGTACCAAACTAGTACTC 59.782 45.833 13.54 0.00 40.01 2.59
1731 1765 4.488879 CAACGGTACCAAACTAGTACTCC 58.511 47.826 13.54 0.00 40.01 3.85
1732 1766 3.092301 ACGGTACCAAACTAGTACTCCC 58.908 50.000 13.54 0.00 40.01 4.30
1733 1767 3.245407 ACGGTACCAAACTAGTACTCCCT 60.245 47.826 13.54 0.00 40.01 4.20
1734 1768 3.379688 CGGTACCAAACTAGTACTCCCTC 59.620 52.174 13.54 0.00 40.01 4.30
1735 1769 3.703556 GGTACCAAACTAGTACTCCCTCC 59.296 52.174 7.15 0.00 40.01 4.30
1736 1770 3.555117 ACCAAACTAGTACTCCCTCCA 57.445 47.619 0.00 0.00 0.00 3.86
1737 1771 4.076175 ACCAAACTAGTACTCCCTCCAT 57.924 45.455 0.00 0.00 0.00 3.41
1738 1772 4.436079 ACCAAACTAGTACTCCCTCCATT 58.564 43.478 0.00 0.00 0.00 3.16
1739 1773 4.470304 ACCAAACTAGTACTCCCTCCATTC 59.530 45.833 0.00 0.00 0.00 2.67
1740 1774 4.141688 CCAAACTAGTACTCCCTCCATTCC 60.142 50.000 0.00 0.00 0.00 3.01
1741 1775 4.348020 AACTAGTACTCCCTCCATTCCA 57.652 45.455 0.00 0.00 0.00 3.53
1742 1776 4.348020 ACTAGTACTCCCTCCATTCCAA 57.652 45.455 0.00 0.00 0.00 3.53
1743 1777 4.695606 ACTAGTACTCCCTCCATTCCAAA 58.304 43.478 0.00 0.00 0.00 3.28
1744 1778 5.289510 ACTAGTACTCCCTCCATTCCAAAT 58.710 41.667 0.00 0.00 0.00 2.32
1745 1779 5.731678 ACTAGTACTCCCTCCATTCCAAATT 59.268 40.000 0.00 0.00 0.00 1.82
1746 1780 6.906901 ACTAGTACTCCCTCCATTCCAAATTA 59.093 38.462 0.00 0.00 0.00 1.40
1747 1781 6.002653 AGTACTCCCTCCATTCCAAATTAC 57.997 41.667 0.00 0.00 0.00 1.89
1748 1782 5.731678 AGTACTCCCTCCATTCCAAATTACT 59.268 40.000 0.00 0.00 0.00 2.24
1749 1783 5.117406 ACTCCCTCCATTCCAAATTACTC 57.883 43.478 0.00 0.00 0.00 2.59
1750 1784 4.130118 CTCCCTCCATTCCAAATTACTCG 58.870 47.826 0.00 0.00 0.00 4.18
1751 1785 3.521937 TCCCTCCATTCCAAATTACTCGT 59.478 43.478 0.00 0.00 0.00 4.18
1752 1786 3.877508 CCCTCCATTCCAAATTACTCGTC 59.122 47.826 0.00 0.00 0.00 4.20
1753 1787 3.555956 CCTCCATTCCAAATTACTCGTCG 59.444 47.826 0.00 0.00 0.00 5.12
1754 1788 2.933906 TCCATTCCAAATTACTCGTCGC 59.066 45.455 0.00 0.00 0.00 5.19
1755 1789 2.675844 CCATTCCAAATTACTCGTCGCA 59.324 45.455 0.00 0.00 0.00 5.10
1756 1790 3.242413 CCATTCCAAATTACTCGTCGCAG 60.242 47.826 0.00 0.00 0.00 5.18
1757 1791 3.306917 TTCCAAATTACTCGTCGCAGA 57.693 42.857 0.00 0.00 0.00 4.26
1758 1792 3.306917 TCCAAATTACTCGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
1759 1793 3.655486 TCCAAATTACTCGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
1760 1794 4.250464 TCCAAATTACTCGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
1761 1795 4.092821 TCCAAATTACTCGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
1762 1796 4.334443 CAAATTACTCGTCGCAGAAATGG 58.666 43.478 0.00 0.00 39.69 3.16
1763 1797 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
1764 1798 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
1765 1799 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
1766 1800 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
1767 1801 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
1768 1802 3.186909 CTCGTCGCAGAAATGGATGTAA 58.813 45.455 0.00 0.00 39.69 2.41
1769 1803 2.927477 TCGTCGCAGAAATGGATGTAAC 59.073 45.455 0.00 0.00 39.69 2.50
1770 1804 2.930040 CGTCGCAGAAATGGATGTAACT 59.070 45.455 0.00 0.00 39.69 2.24
1771 1805 4.109766 CGTCGCAGAAATGGATGTAACTA 58.890 43.478 0.00 0.00 39.69 2.24
1772 1806 4.207224 CGTCGCAGAAATGGATGTAACTAG 59.793 45.833 0.00 0.00 39.69 2.57
1773 1807 5.348986 GTCGCAGAAATGGATGTAACTAGA 58.651 41.667 0.00 0.00 39.69 2.43
1774 1808 5.232414 GTCGCAGAAATGGATGTAACTAGAC 59.768 44.000 0.00 0.00 39.69 2.59
1775 1809 4.207224 CGCAGAAATGGATGTAACTAGACG 59.793 45.833 0.00 0.00 0.00 4.18
1776 1810 5.348986 GCAGAAATGGATGTAACTAGACGA 58.651 41.667 0.00 0.00 0.00 4.20
1777 1811 5.810587 GCAGAAATGGATGTAACTAGACGAA 59.189 40.000 0.00 0.00 0.00 3.85
1778 1812 6.019479 GCAGAAATGGATGTAACTAGACGAAG 60.019 42.308 0.00 0.00 0.00 3.79
1779 1813 6.477033 CAGAAATGGATGTAACTAGACGAAGG 59.523 42.308 0.00 0.00 0.00 3.46
1780 1814 4.939052 ATGGATGTAACTAGACGAAGGG 57.061 45.455 0.00 0.00 0.00 3.95
1781 1815 3.972133 TGGATGTAACTAGACGAAGGGA 58.028 45.455 0.00 0.00 0.00 4.20
1782 1816 3.952323 TGGATGTAACTAGACGAAGGGAG 59.048 47.826 0.00 0.00 0.00 4.30
1783 1817 3.952967 GGATGTAACTAGACGAAGGGAGT 59.047 47.826 0.00 0.00 0.00 3.85
1784 1818 5.128919 GGATGTAACTAGACGAAGGGAGTA 58.871 45.833 0.00 0.00 0.00 2.59
1785 1819 5.769162 GGATGTAACTAGACGAAGGGAGTAT 59.231 44.000 0.00 0.00 0.00 2.12
1786 1820 6.294065 GGATGTAACTAGACGAAGGGAGTATG 60.294 46.154 0.00 0.00 0.00 2.39
1787 1821 5.503927 TGTAACTAGACGAAGGGAGTATGT 58.496 41.667 0.00 0.00 0.00 2.29
1788 1822 5.948162 TGTAACTAGACGAAGGGAGTATGTT 59.052 40.000 0.00 0.00 0.00 2.71
1789 1823 5.997384 AACTAGACGAAGGGAGTATGTTT 57.003 39.130 0.00 0.00 0.00 2.83
1790 1824 5.997384 ACTAGACGAAGGGAGTATGTTTT 57.003 39.130 0.00 0.00 0.00 2.43
1791 1825 6.356186 ACTAGACGAAGGGAGTATGTTTTT 57.644 37.500 0.00 0.00 0.00 1.94
1792 1826 6.164176 ACTAGACGAAGGGAGTATGTTTTTG 58.836 40.000 0.00 0.00 0.00 2.44
1793 1827 3.751698 AGACGAAGGGAGTATGTTTTTGC 59.248 43.478 0.00 0.00 0.00 3.68
1794 1828 3.482436 ACGAAGGGAGTATGTTTTTGCA 58.518 40.909 0.00 0.00 0.00 4.08
1795 1829 3.502211 ACGAAGGGAGTATGTTTTTGCAG 59.498 43.478 0.00 0.00 0.00 4.41
1796 1830 3.119849 CGAAGGGAGTATGTTTTTGCAGG 60.120 47.826 0.00 0.00 0.00 4.85
1797 1831 3.525800 AGGGAGTATGTTTTTGCAGGT 57.474 42.857 0.00 0.00 0.00 4.00
1798 1832 4.650972 AGGGAGTATGTTTTTGCAGGTA 57.349 40.909 0.00 0.00 0.00 3.08
1799 1833 4.332828 AGGGAGTATGTTTTTGCAGGTAC 58.667 43.478 0.00 0.00 0.00 3.34
1800 1834 3.442625 GGGAGTATGTTTTTGCAGGTACC 59.557 47.826 2.73 2.73 0.00 3.34
1801 1835 4.076394 GGAGTATGTTTTTGCAGGTACCA 58.924 43.478 15.94 0.00 0.00 3.25
1802 1836 4.521256 GGAGTATGTTTTTGCAGGTACCAA 59.479 41.667 15.94 0.00 0.00 3.67
1803 1837 5.010213 GGAGTATGTTTTTGCAGGTACCAAA 59.990 40.000 15.94 2.99 0.00 3.28
1804 1838 5.838529 AGTATGTTTTTGCAGGTACCAAAC 58.161 37.500 15.94 15.22 32.40 2.93
1805 1839 5.596772 AGTATGTTTTTGCAGGTACCAAACT 59.403 36.000 15.94 7.97 32.40 2.66
1806 1840 6.773685 AGTATGTTTTTGCAGGTACCAAACTA 59.226 34.615 15.94 6.96 32.40 2.24
1817 1856 7.033185 GCAGGTACCAAACTATTAAAACATGG 58.967 38.462 15.94 0.00 0.00 3.66
1857 1896 0.744414 CCAGGGTGCGGAATGTACAG 60.744 60.000 0.33 0.00 34.44 2.74
1864 1903 1.271379 TGCGGAATGTACAGACGAGTT 59.729 47.619 17.36 0.00 0.00 3.01
1884 1923 4.162131 AGTTTGTCAACAAAAGGAAGCCAT 59.838 37.500 9.73 0.00 46.08 4.40
1933 1973 3.815856 ACTGTCCTATGTCATGCTCTG 57.184 47.619 0.00 0.00 0.00 3.35
1951 1991 3.842820 TCTGCTCAAATTCTCTCGTCAG 58.157 45.455 0.00 0.00 0.00 3.51
1955 1995 3.060098 GCTCAAATTCTCTCGTCAGTTCG 59.940 47.826 0.00 0.00 0.00 3.95
1976 2016 3.119352 CGATGTGAGAGAGTGATCCACAA 60.119 47.826 0.00 0.00 40.52 3.33
2015 2060 6.896860 TCCCATATGTCTTTCCATGTTTTCAT 59.103 34.615 1.24 0.00 41.78 2.57
2036 2081 6.434302 TCATGGATGGTATTTTCCTGAACAT 58.566 36.000 0.00 0.00 32.95 2.71
2095 2140 3.616219 TGGTCATAATTTGGAAGGTCCG 58.384 45.455 0.00 0.00 40.17 4.79
2107 2152 3.146847 GGAAGGTCCGTTGAAACTGAAT 58.853 45.455 0.00 0.00 0.00 2.57
2185 2231 7.745594 CGAAAATGGCCAATGTTTTCTTTTATG 59.254 33.333 27.97 15.29 38.85 1.90
2212 2258 3.331150 TGTCATACCTTCAAACGCGAAT 58.669 40.909 15.93 0.00 0.00 3.34
2221 2267 7.599630 ACCTTCAAACGCGAATACTAATTTA 57.400 32.000 15.93 0.00 0.00 1.40
2347 2393 7.703058 CCTCAAGGTAAAGGTACATGAAAAT 57.297 36.000 0.00 0.00 31.23 1.82
2389 2435 7.925483 AGAAACCATCTTCGATTATCTTCTCAG 59.075 37.037 0.00 0.00 33.39 3.35
2452 2498 8.086851 GGCAAAATGGCAAGTATATTAATTGG 57.913 34.615 0.00 0.00 43.14 3.16
2524 3358 3.281341 TGTTTAACAGCGGCATGAAAG 57.719 42.857 1.45 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
227 228 1.590259 GAGAGCGGCCGTCAAGATC 60.590 63.158 28.70 14.72 0.00 2.75
441 444 1.306056 ATTTGGCGCCATTTCCCCT 60.306 52.632 33.25 7.00 0.00 4.79
558 561 1.227883 TCCAAACTTGCGCCGGTTA 60.228 52.632 4.18 0.00 0.00 2.85
576 579 1.683418 GCTTTCGACCTATCCCCGGT 61.683 60.000 0.00 0.00 37.50 5.28
585 588 0.179067 TTTGTGTCCGCTTTCGACCT 60.179 50.000 0.00 0.00 38.10 3.85
650 654 1.711942 TCCGTTTGGGGTAAAAGGGAT 59.288 47.619 6.93 0.00 44.84 3.85
708 712 0.044855 ATGGAGGGGAGTTGGCTAGT 59.955 55.000 0.00 0.00 0.00 2.57
712 716 2.276309 CTGGATGGAGGGGAGTTGGC 62.276 65.000 0.00 0.00 0.00 4.52
727 731 2.367202 GCTGGGATCGGGTTCTGGA 61.367 63.158 0.00 0.00 0.00 3.86
730 734 1.306141 TCTGCTGGGATCGGGTTCT 60.306 57.895 0.00 0.00 0.00 3.01
902 909 3.880846 GGGAGCTGCGGATTTGCG 61.881 66.667 0.00 0.00 37.81 4.85
916 923 1.882625 CGATGAAATGCGAGCGGGA 60.883 57.895 0.00 0.00 0.00 5.14
917 924 2.628106 CGATGAAATGCGAGCGGG 59.372 61.111 0.00 0.00 0.00 6.13
926 933 0.583438 CTTGCGATCGCCGATGAAAT 59.417 50.000 35.12 0.00 41.76 2.17
929 936 2.961721 GCTTGCGATCGCCGATGA 60.962 61.111 35.12 15.41 41.76 2.92
1012 1019 3.154473 TGGCCGGAAGATCTCGGG 61.154 66.667 20.81 15.96 45.75 5.14
1224 1231 2.124778 GCTCCCTGGCTTCTCTGC 60.125 66.667 0.00 0.00 0.00 4.26
1262 1269 6.423604 GCAAAACTAACCACGTACCTACTAAA 59.576 38.462 0.00 0.00 0.00 1.85
1270 1277 3.231160 GCATGCAAAACTAACCACGTAC 58.769 45.455 14.21 0.00 0.00 3.67
1347 1371 2.969262 CCCCGGGCAAAAATATACCATT 59.031 45.455 17.73 0.00 0.00 3.16
1386 1410 1.478510 ACACGCTGTAATCAGAGGAGG 59.521 52.381 0.00 0.00 43.88 4.30
1438 1468 7.129457 AGTAATTCATAGGCACTGATCTCAA 57.871 36.000 0.00 0.00 41.52 3.02
1451 1481 6.016777 GCCCAAGGATCACAAGTAATTCATAG 60.017 42.308 0.00 0.00 0.00 2.23
1468 1498 0.035439 GTCCGATTTCTGCCCAAGGA 60.035 55.000 0.00 0.00 0.00 3.36
1473 1503 1.066430 TGTACAGTCCGATTTCTGCCC 60.066 52.381 0.00 0.00 35.37 5.36
1479 1509 4.462834 TCTGATCAGTGTACAGTCCGATTT 59.537 41.667 21.92 0.00 33.93 2.17
1483 1513 4.023622 CCTATCTGATCAGTGTACAGTCCG 60.024 50.000 21.92 4.67 33.93 4.79
1506 1536 6.146898 TGCTAATTGAACTTAAAGGTTTCGC 58.853 36.000 0.00 0.00 0.00 4.70
1546 1578 1.730064 GGTTTATTCAAGCTCGCGTGA 59.270 47.619 13.13 2.19 32.98 4.35
1641 1673 5.970640 AGGTATAAGAGGGACCATCTTTGAA 59.029 40.000 25.29 9.36 38.05 2.69
1650 1682 5.246429 CCATTAGTGAGGTATAAGAGGGACC 59.754 48.000 0.00 0.00 0.00 4.46
1725 1759 6.002653 AGTAATTTGGAATGGAGGGAGTAC 57.997 41.667 0.00 0.00 0.00 2.73
1726 1760 5.163343 CGAGTAATTTGGAATGGAGGGAGTA 60.163 44.000 0.00 0.00 0.00 2.59
1727 1761 4.384208 CGAGTAATTTGGAATGGAGGGAGT 60.384 45.833 0.00 0.00 0.00 3.85
1728 1762 4.130118 CGAGTAATTTGGAATGGAGGGAG 58.870 47.826 0.00 0.00 0.00 4.30
1729 1763 3.521937 ACGAGTAATTTGGAATGGAGGGA 59.478 43.478 0.00 0.00 0.00 4.20
1730 1764 3.877508 GACGAGTAATTTGGAATGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1731 1765 3.555956 CGACGAGTAATTTGGAATGGAGG 59.444 47.826 0.00 0.00 0.00 4.30
1732 1766 3.001330 GCGACGAGTAATTTGGAATGGAG 59.999 47.826 0.00 0.00 0.00 3.86
1733 1767 2.933906 GCGACGAGTAATTTGGAATGGA 59.066 45.455 0.00 0.00 0.00 3.41
1734 1768 2.675844 TGCGACGAGTAATTTGGAATGG 59.324 45.455 0.00 0.00 0.00 3.16
1735 1769 3.616821 TCTGCGACGAGTAATTTGGAATG 59.383 43.478 0.00 0.00 0.00 2.67
1736 1770 3.857052 TCTGCGACGAGTAATTTGGAAT 58.143 40.909 0.00 0.00 0.00 3.01
1737 1771 3.306917 TCTGCGACGAGTAATTTGGAA 57.693 42.857 0.00 0.00 0.00 3.53
1738 1772 3.306917 TTCTGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
1739 1773 4.334443 CATTTCTGCGACGAGTAATTTGG 58.666 43.478 0.00 0.00 0.00 3.28
1740 1774 4.092821 TCCATTTCTGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
1741 1775 4.250464 TCCATTTCTGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
1742 1776 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
1743 1777 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
1744 1778 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
1745 1779 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
1746 1780 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
1747 1781 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
1748 1782 2.927477 GTTACATCCATTTCTGCGACGA 59.073 45.455 0.00 0.00 0.00 4.20
1749 1783 2.930040 AGTTACATCCATTTCTGCGACG 59.070 45.455 0.00 0.00 0.00 5.12
1750 1784 5.232414 GTCTAGTTACATCCATTTCTGCGAC 59.768 44.000 0.00 0.00 0.00 5.19
1751 1785 5.348986 GTCTAGTTACATCCATTTCTGCGA 58.651 41.667 0.00 0.00 0.00 5.10
1752 1786 4.207224 CGTCTAGTTACATCCATTTCTGCG 59.793 45.833 0.00 0.00 0.00 5.18
1753 1787 5.348986 TCGTCTAGTTACATCCATTTCTGC 58.651 41.667 0.00 0.00 0.00 4.26
1754 1788 6.477033 CCTTCGTCTAGTTACATCCATTTCTG 59.523 42.308 0.00 0.00 0.00 3.02
1755 1789 6.407074 CCCTTCGTCTAGTTACATCCATTTCT 60.407 42.308 0.00 0.00 0.00 2.52
1756 1790 5.753921 CCCTTCGTCTAGTTACATCCATTTC 59.246 44.000 0.00 0.00 0.00 2.17
1757 1791 5.424252 TCCCTTCGTCTAGTTACATCCATTT 59.576 40.000 0.00 0.00 0.00 2.32
1758 1792 4.960469 TCCCTTCGTCTAGTTACATCCATT 59.040 41.667 0.00 0.00 0.00 3.16
1759 1793 4.543689 TCCCTTCGTCTAGTTACATCCAT 58.456 43.478 0.00 0.00 0.00 3.41
1760 1794 3.952323 CTCCCTTCGTCTAGTTACATCCA 59.048 47.826 0.00 0.00 0.00 3.41
1761 1795 3.952967 ACTCCCTTCGTCTAGTTACATCC 59.047 47.826 0.00 0.00 0.00 3.51
1762 1796 6.262720 ACATACTCCCTTCGTCTAGTTACATC 59.737 42.308 0.00 0.00 0.00 3.06
1763 1797 6.127793 ACATACTCCCTTCGTCTAGTTACAT 58.872 40.000 0.00 0.00 0.00 2.29
1764 1798 5.503927 ACATACTCCCTTCGTCTAGTTACA 58.496 41.667 0.00 0.00 0.00 2.41
1765 1799 6.448207 AACATACTCCCTTCGTCTAGTTAC 57.552 41.667 0.00 0.00 0.00 2.50
1766 1800 7.472334 AAAACATACTCCCTTCGTCTAGTTA 57.528 36.000 0.00 0.00 0.00 2.24
1767 1801 5.997384 AAACATACTCCCTTCGTCTAGTT 57.003 39.130 0.00 0.00 0.00 2.24
1768 1802 5.997384 AAAACATACTCCCTTCGTCTAGT 57.003 39.130 0.00 0.00 0.00 2.57
1769 1803 5.063564 GCAAAAACATACTCCCTTCGTCTAG 59.936 44.000 0.00 0.00 0.00 2.43
1770 1804 4.933400 GCAAAAACATACTCCCTTCGTCTA 59.067 41.667 0.00 0.00 0.00 2.59
1771 1805 3.751698 GCAAAAACATACTCCCTTCGTCT 59.248 43.478 0.00 0.00 0.00 4.18
1772 1806 3.500680 TGCAAAAACATACTCCCTTCGTC 59.499 43.478 0.00 0.00 0.00 4.20
1773 1807 3.482436 TGCAAAAACATACTCCCTTCGT 58.518 40.909 0.00 0.00 0.00 3.85
1774 1808 3.119849 CCTGCAAAAACATACTCCCTTCG 60.120 47.826 0.00 0.00 0.00 3.79
1775 1809 3.826729 ACCTGCAAAAACATACTCCCTTC 59.173 43.478 0.00 0.00 0.00 3.46
1776 1810 3.844640 ACCTGCAAAAACATACTCCCTT 58.155 40.909 0.00 0.00 0.00 3.95
1777 1811 3.525800 ACCTGCAAAAACATACTCCCT 57.474 42.857 0.00 0.00 0.00 4.20
1778 1812 3.442625 GGTACCTGCAAAAACATACTCCC 59.557 47.826 4.06 0.00 0.00 4.30
1779 1813 4.076394 TGGTACCTGCAAAAACATACTCC 58.924 43.478 14.36 0.00 0.00 3.85
1780 1814 5.699097 TTGGTACCTGCAAAAACATACTC 57.301 39.130 14.36 0.00 0.00 2.59
1781 1815 5.596772 AGTTTGGTACCTGCAAAAACATACT 59.403 36.000 20.72 4.59 34.05 2.12
1782 1816 5.838529 AGTTTGGTACCTGCAAAAACATAC 58.161 37.500 20.72 2.69 34.05 2.39
1783 1817 7.768807 ATAGTTTGGTACCTGCAAAAACATA 57.231 32.000 20.72 13.04 34.05 2.29
1784 1818 6.664428 ATAGTTTGGTACCTGCAAAAACAT 57.336 33.333 20.72 12.36 34.05 2.71
1785 1819 6.472686 AATAGTTTGGTACCTGCAAAAACA 57.527 33.333 20.72 11.10 34.05 2.83
1786 1820 8.874744 TTTAATAGTTTGGTACCTGCAAAAAC 57.125 30.769 14.36 14.20 0.00 2.43
1787 1821 9.315525 GTTTTAATAGTTTGGTACCTGCAAAAA 57.684 29.630 14.36 1.58 0.00 1.94
1788 1822 8.475639 TGTTTTAATAGTTTGGTACCTGCAAAA 58.524 29.630 14.36 1.99 0.00 2.44
1789 1823 8.008513 TGTTTTAATAGTTTGGTACCTGCAAA 57.991 30.769 14.36 2.38 0.00 3.68
1790 1824 7.584122 TGTTTTAATAGTTTGGTACCTGCAA 57.416 32.000 14.36 0.35 0.00 4.08
1791 1825 7.309499 CCATGTTTTAATAGTTTGGTACCTGCA 60.309 37.037 14.36 0.00 0.00 4.41
1792 1826 7.033185 CCATGTTTTAATAGTTTGGTACCTGC 58.967 38.462 14.36 3.16 0.00 4.85
1793 1827 8.343168 TCCATGTTTTAATAGTTTGGTACCTG 57.657 34.615 14.36 0.00 0.00 4.00
1794 1828 8.943594 TTCCATGTTTTAATAGTTTGGTACCT 57.056 30.769 14.36 0.00 0.00 3.08
1803 1837 9.691362 GTGTGTTGATTTCCATGTTTTAATAGT 57.309 29.630 0.00 0.00 0.00 2.12
1804 1838 9.912634 AGTGTGTTGATTTCCATGTTTTAATAG 57.087 29.630 0.00 0.00 0.00 1.73
1805 1839 9.906660 GAGTGTGTTGATTTCCATGTTTTAATA 57.093 29.630 0.00 0.00 0.00 0.98
1806 1840 8.420222 TGAGTGTGTTGATTTCCATGTTTTAAT 58.580 29.630 0.00 0.00 0.00 1.40
1817 1856 2.814336 GGAGGGTGAGTGTGTTGATTTC 59.186 50.000 0.00 0.00 0.00 2.17
1857 1896 4.609691 TCCTTTTGTTGACAAACTCGTC 57.390 40.909 8.70 0.00 44.56 4.20
1864 1903 5.860941 TTATGGCTTCCTTTTGTTGACAA 57.139 34.783 0.00 0.00 0.00 3.18
1884 1923 2.093869 ACACGCCTCGGCTAGATTTTTA 60.094 45.455 6.35 0.00 39.32 1.52
1933 1973 3.060098 CGAACTGACGAGAGAATTTGAGC 59.940 47.826 0.00 0.00 35.09 4.26
1951 1991 3.129462 TGGATCACTCTCTCACATCGAAC 59.871 47.826 0.00 0.00 0.00 3.95
1955 1995 4.462508 TTGTGGATCACTCTCTCACATC 57.537 45.455 0.00 0.00 38.02 3.06
1989 2034 6.152661 TGAAAACATGGAAAGACATATGGGAC 59.847 38.462 7.80 0.00 0.00 4.46
1992 2037 7.997107 CATGAAAACATGGAAAGACATATGG 57.003 36.000 7.80 0.00 0.00 2.74
2015 2060 5.579047 ACATGTTCAGGAAAATACCATCCA 58.421 37.500 0.00 0.00 38.23 3.41
2036 2081 3.461773 GGCGCTGCTCCTAGGACA 61.462 66.667 7.62 10.37 0.00 4.02
2095 2140 5.406477 GGCATTTGGAAGATTCAGTTTCAAC 59.594 40.000 0.00 0.00 0.00 3.18
2107 2152 4.576053 CGTAGATCAATGGCATTTGGAAGA 59.424 41.667 10.65 4.78 0.00 2.87
2145 2190 6.711645 TGGCCATTTTCGGTAACCTATAATAC 59.288 38.462 0.00 0.00 0.00 1.89
2185 2231 5.324697 GCGTTTGAAGGTATGACAGAATTC 58.675 41.667 0.00 0.00 0.00 2.17
2221 2267 6.882610 TCACTGCTATGTTTCTTGTCAATT 57.117 33.333 0.00 0.00 0.00 2.32
2234 2280 7.840342 AACTAGAGAAAACATCACTGCTATG 57.160 36.000 0.00 0.00 31.03 2.23
2237 2283 7.389053 CCTAAAACTAGAGAAAACATCACTGCT 59.611 37.037 0.00 0.00 31.03 4.24
2238 2284 7.387948 TCCTAAAACTAGAGAAAACATCACTGC 59.612 37.037 0.00 0.00 31.03 4.40
2239 2285 8.833231 TCCTAAAACTAGAGAAAACATCACTG 57.167 34.615 0.00 0.00 31.03 3.66
2290 2336 5.749109 CACTTCTCCGGCTTACAAACTATAG 59.251 44.000 0.00 0.00 0.00 1.31
2292 2338 4.504858 CACTTCTCCGGCTTACAAACTAT 58.495 43.478 0.00 0.00 0.00 2.12
2389 2435 7.271438 GCTAGCTTAGTGTTTTGACTTAATTGC 59.729 37.037 7.70 0.00 0.00 3.56
2452 2498 2.818130 TTTGACTTCCAATGGCAAGC 57.182 45.000 10.11 5.66 34.23 4.01
2506 2552 4.217334 TCATTCTTTCATGCCGCTGTTAAA 59.783 37.500 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.