Multiple sequence alignment - TraesCS3D01G415300

Loading Multiple Alignment...

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 TraesCS3D01G415300 chr3D 100.000 2603 0 0 1 2603 527125682 527128284 0.000000e+00 4807.0
1 TraesCS3D01G415300 chr3D 98.548 551 8 0 1 551 527120228 527120778 0.000000e+00 974.0
2 TraesCS3D01G415300 chr3D 84.977 639 52 29 921 1516 527135789 527136426 2.220000e-170 608.0
3 TraesCS3D01G415300 chr3B 90.472 1039 49 23 544 1548 696777595 696778617 0.000000e+00 1325.0
4 TraesCS3D01G415300 chr3B 82.121 660 70 33 962 1580 696788521 696787869 2.970000e-144 521.0
5 TraesCS3D01G415300 chr3B 93.478 92 6 0 1881 1972 696780335 696780426 1.260000e-28 137.0
6 TraesCS3D01G415300 chr3B 86.726 113 10 3 1995 2107 696779668 696779775 1.270000e-23 121.0
7 TraesCS3D01G415300 chr3B 93.443 61 4 0 1573 1633 696778683 696778743 9.920000e-15 91.6
8 TraesCS3D01G415300 chr3A 87.842 1061 64 33 544 1548 661654724 661655775 0.000000e+00 1184.0
9 TraesCS3D01G415300 chr3A 85.465 516 51 16 921 1417 661787149 661787659 1.380000e-142 516.0
10 TraesCS3D01G415300 chr3A 89.796 49 4 1 1335 1382 661595855 661595903 7.780000e-06 62.1
11 TraesCS3D01G415300 chr3A 90.698 43 3 1 2473 2514 67436610 67436652 3.620000e-04 56.5
12 TraesCS3D01G415300 chr6D 98.725 549 7 0 1 549 58738481 58737933 0.000000e+00 976.0
13 TraesCS3D01G415300 chr6D 98.195 554 10 0 1 554 58743832 58743279 0.000000e+00 968.0
14 TraesCS3D01G415300 chrUn 98.375 554 9 0 1 554 27177531 27176978 0.000000e+00 974.0
15 TraesCS3D01G415300 chrUn 98.367 551 9 0 4 554 27172063 27171513 0.000000e+00 968.0
16 TraesCS3D01G415300 chr7D 98.378 555 8 1 1 555 106381144 106381697 0.000000e+00 974.0
17 TraesCS3D01G415300 chr7D 98.548 551 8 0 1 551 133217690 133218240 0.000000e+00 974.0
18 TraesCS3D01G415300 chr7D 88.028 142 15 2 1620 1760 50726600 50726740 1.600000e-37 167.0
19 TraesCS3D01G415300 chr4D 98.725 549 6 1 1 549 73332316 73331769 0.000000e+00 974.0
20 TraesCS3D01G415300 chr4D 98.375 554 8 1 1 554 73346321 73345769 0.000000e+00 972.0
21 TraesCS3D01G415300 chr7B 95.798 119 3 2 1632 1749 434926024 434925907 9.510000e-45 191.0
22 TraesCS3D01G415300 chr7B 89.333 150 12 4 1602 1749 733479771 733479624 4.420000e-43 185.0
23 TraesCS3D01G415300 chr5D 92.063 126 10 0 1630 1755 240084594 240084469 7.400000e-41 178.0
24 TraesCS3D01G415300 chr4B 92.063 126 8 2 1633 1757 636708196 636708072 2.660000e-40 176.0
25 TraesCS3D01G415300 chr4B 92.063 126 7 3 1625 1749 122562271 122562394 9.580000e-40 174.0
26 TraesCS3D01G415300 chr5B 90.226 133 9 4 1627 1758 41408125 41408254 1.240000e-38 171.0
27 TraesCS3D01G415300 chr2D 90.226 133 10 3 1623 1753 531937961 531938092 1.240000e-38 171.0
28 TraesCS3D01G415300 chr2D 89.130 138 12 3 1627 1763 484362059 484361924 4.460000e-38 169.0


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 TraesCS3D01G415300 chr3D 527125682 527128284 2602 False 4807.00 4807 100.00000 1 2603 1 chr3D.!!$F2 2602
1 TraesCS3D01G415300 chr3D 527120228 527120778 550 False 974.00 974 98.54800 1 551 1 chr3D.!!$F1 550
2 TraesCS3D01G415300 chr3D 527135789 527136426 637 False 608.00 608 84.97700 921 1516 1 chr3D.!!$F3 595
3 TraesCS3D01G415300 chr3B 696787869 696788521 652 True 521.00 521 82.12100 962 1580 1 chr3B.!!$R1 618
4 TraesCS3D01G415300 chr3B 696777595 696780426 2831 False 418.65 1325 91.02975 544 2107 4 chr3B.!!$F1 1563
5 TraesCS3D01G415300 chr3A 661654724 661655775 1051 False 1184.00 1184 87.84200 544 1548 1 chr3A.!!$F3 1004
6 TraesCS3D01G415300 chr3A 661787149 661787659 510 False 516.00 516 85.46500 921 1417 1 chr3A.!!$F4 496
7 TraesCS3D01G415300 chr6D 58737933 58738481 548 True 976.00 976 98.72500 1 549 1 chr6D.!!$R1 548
8 TraesCS3D01G415300 chr6D 58743279 58743832 553 True 968.00 968 98.19500 1 554 1 chr6D.!!$R2 553
9 TraesCS3D01G415300 chrUn 27176978 27177531 553 True 974.00 974 98.37500 1 554 1 chrUn.!!$R2 553
10 TraesCS3D01G415300 chrUn 27171513 27172063 550 True 968.00 968 98.36700 4 554 1 chrUn.!!$R1 550
11 TraesCS3D01G415300 chr7D 106381144 106381697 553 False 974.00 974 98.37800 1 555 1 chr7D.!!$F2 554
12 TraesCS3D01G415300 chr7D 133217690 133218240 550 False 974.00 974 98.54800 1 551 1 chr7D.!!$F3 550
13 TraesCS3D01G415300 chr4D 73331769 73332316 547 True 974.00 974 98.72500 1 549 1 chr4D.!!$R1 548
14 TraesCS3D01G415300 chr4D 73345769 73346321 552 True 972.00 972 98.37500 1 554 1 chr4D.!!$R2 553

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
774 778 0.249398 AGACTCACATGTTACCGGCC 59.751 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1726 1830 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.0 5.23 0.0 44.66 2.24 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
224 226 4.294232 CGATCGTCTACTTCCTCTACGTA 58.706 47.826 7.03 0.00 35.21 3.57
301 303 2.175878 GCTGAAGCTGACAAGAAGGA 57.824 50.000 0.00 0.00 38.21 3.36
355 357 1.910722 CCTCTGCATGGCCTACTGT 59.089 57.895 3.32 0.00 0.00 3.55
594 596 5.357314 GCCAGACCGTGAGCTATATTATCTA 59.643 44.000 0.00 0.00 0.00 1.98
774 778 0.249398 AGACTCACATGTTACCGGCC 59.751 55.000 0.00 0.00 0.00 6.13
775 779 1.079405 ACTCACATGTTACCGGCCG 60.079 57.895 21.04 21.04 0.00 6.13
776 780 1.813753 CTCACATGTTACCGGCCGG 60.814 63.158 42.17 42.17 42.03 6.13
806 810 3.197790 CCATTGGCTCGGTCTGCG 61.198 66.667 0.00 0.00 0.00 5.18
924 929 2.513666 CCTAATGCGGCCAAGCGA 60.514 61.111 2.24 0.00 40.67 4.93
987 992 4.372656 GCTATATAAGCCCTAGCCAATCG 58.627 47.826 0.00 0.00 46.25 3.34
990 995 2.052047 TAAGCCCTAGCCAATCGCCC 62.052 60.000 0.00 0.00 41.25 6.13
991 996 4.189580 GCCCTAGCCAATCGCCCA 62.190 66.667 0.00 0.00 38.78 5.36
1016 1024 2.549754 GTGACACACCCAGACAATCAAG 59.450 50.000 0.00 0.00 0.00 3.02
1020 1028 1.143684 ACACCCAGACAATCAAGTGCT 59.856 47.619 0.00 0.00 0.00 4.40
1021 1029 2.371841 ACACCCAGACAATCAAGTGCTA 59.628 45.455 0.00 0.00 0.00 3.49
1036 1045 2.323968 TGCTACACACACACACACAT 57.676 45.000 0.00 0.00 0.00 3.21
1037 1046 2.637947 TGCTACACACACACACACATT 58.362 42.857 0.00 0.00 0.00 2.71
1038 1047 2.611751 TGCTACACACACACACACATTC 59.388 45.455 0.00 0.00 0.00 2.67
1039 1048 2.611751 GCTACACACACACACACATTCA 59.388 45.455 0.00 0.00 0.00 2.57
1040 1049 3.250762 GCTACACACACACACACATTCAT 59.749 43.478 0.00 0.00 0.00 2.57
1230 1256 2.391389 GCAAGTCCTACTGCACGGC 61.391 63.158 0.00 0.00 0.00 5.68
1516 1575 2.664185 CGGCTGGCTGATCCGATG 60.664 66.667 4.80 0.00 45.53 3.84
1557 1639 4.024048 CACGCTTTGTGTTGTATCCTCTTT 60.024 41.667 0.00 0.00 43.88 2.52
1617 1721 6.097839 TGTTTCCCGTGTTAGCTATCTTCTAT 59.902 38.462 0.00 0.00 0.00 1.98
1619 1723 6.085555 TCCCGTGTTAGCTATCTTCTATTG 57.914 41.667 0.00 0.00 0.00 1.90
1625 1729 9.731819 CGTGTTAGCTATCTTCTATTGTTTCTA 57.268 33.333 0.00 0.00 0.00 2.10
1643 1747 9.986157 TTGTTTCTATATATATACTCCCTCCGT 57.014 33.333 0.00 0.00 0.00 4.69
1644 1748 9.986157 TGTTTCTATATATATACTCCCTCCGTT 57.014 33.333 0.00 0.00 0.00 4.44
1646 1750 8.899427 TTCTATATATATACTCCCTCCGTTCG 57.101 38.462 0.00 0.00 0.00 3.95
1647 1751 7.448420 TCTATATATATACTCCCTCCGTTCGG 58.552 42.308 4.74 4.74 0.00 4.30
1648 1752 2.965671 ATATACTCCCTCCGTTCGGA 57.034 50.000 13.34 13.34 0.00 4.55
1649 1753 2.734755 TATACTCCCTCCGTTCGGAA 57.265 50.000 14.79 0.00 33.41 4.30
1650 1754 1.856629 ATACTCCCTCCGTTCGGAAA 58.143 50.000 14.79 3.49 33.41 3.13
1651 1755 1.856629 TACTCCCTCCGTTCGGAAAT 58.143 50.000 14.79 2.39 33.41 2.17
1652 1756 1.856629 ACTCCCTCCGTTCGGAAATA 58.143 50.000 14.79 2.82 33.41 1.40
1653 1757 1.479730 ACTCCCTCCGTTCGGAAATAC 59.520 52.381 14.79 0.00 33.41 1.89
1654 1758 0.826062 TCCCTCCGTTCGGAAATACC 59.174 55.000 14.79 0.00 33.41 2.73
1655 1759 0.828677 CCCTCCGTTCGGAAATACCT 59.171 55.000 14.79 0.00 36.31 3.08
1656 1760 1.472728 CCCTCCGTTCGGAAATACCTG 60.473 57.143 14.79 1.97 36.31 4.00
1657 1761 1.206371 CCTCCGTTCGGAAATACCTGT 59.794 52.381 14.79 0.00 36.31 4.00
1658 1762 2.537401 CTCCGTTCGGAAATACCTGTC 58.463 52.381 14.79 0.00 36.31 3.51
1659 1763 1.135315 TCCGTTCGGAAATACCTGTCG 60.135 52.381 11.66 0.00 36.31 4.35
1660 1764 1.135315 CCGTTCGGAAATACCTGTCGA 60.135 52.381 5.19 0.00 36.31 4.20
1661 1765 2.182825 CGTTCGGAAATACCTGTCGAG 58.817 52.381 0.00 0.00 36.31 4.04
1662 1766 2.159476 CGTTCGGAAATACCTGTCGAGA 60.159 50.000 0.00 0.00 36.31 4.04
1663 1767 3.671433 CGTTCGGAAATACCTGTCGAGAA 60.671 47.826 0.00 0.00 36.31 2.87
1664 1768 4.240096 GTTCGGAAATACCTGTCGAGAAA 58.760 43.478 0.00 0.00 36.31 2.52
1665 1769 4.524316 TCGGAAATACCTGTCGAGAAAA 57.476 40.909 0.00 0.00 36.31 2.29
1666 1770 5.080969 TCGGAAATACCTGTCGAGAAAAT 57.919 39.130 0.00 0.00 36.31 1.82
1667 1771 4.868171 TCGGAAATACCTGTCGAGAAAATG 59.132 41.667 0.00 0.00 36.31 2.32
1668 1772 4.034048 CGGAAATACCTGTCGAGAAAATGG 59.966 45.833 0.00 0.00 36.31 3.16
1669 1773 5.183228 GGAAATACCTGTCGAGAAAATGGA 58.817 41.667 0.00 0.00 35.41 3.41
1670 1774 5.823045 GGAAATACCTGTCGAGAAAATGGAT 59.177 40.000 0.00 0.00 35.41 3.41
1671 1775 6.238484 GGAAATACCTGTCGAGAAAATGGATG 60.238 42.308 0.00 0.00 35.41 3.51
1672 1776 3.703001 ACCTGTCGAGAAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
1673 1777 4.819105 ACCTGTCGAGAAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
1674 1778 4.504858 ACCTGTCGAGAAAATGGATGTAC 58.495 43.478 0.00 0.00 0.00 2.90
1675 1779 3.871594 CCTGTCGAGAAAATGGATGTACC 59.128 47.826 0.00 0.00 39.54 3.34
1676 1780 4.383118 CCTGTCGAGAAAATGGATGTACCT 60.383 45.833 0.00 0.00 39.86 3.08
1677 1781 5.163447 CCTGTCGAGAAAATGGATGTACCTA 60.163 44.000 0.00 0.00 39.86 3.08
1678 1782 5.902681 TGTCGAGAAAATGGATGTACCTAG 58.097 41.667 0.00 0.00 39.86 3.02
1679 1783 5.655090 TGTCGAGAAAATGGATGTACCTAGA 59.345 40.000 0.00 0.00 39.86 2.43
1680 1784 6.323996 TGTCGAGAAAATGGATGTACCTAGAT 59.676 38.462 0.00 0.00 39.86 1.98
1681 1785 6.642950 GTCGAGAAAATGGATGTACCTAGATG 59.357 42.308 0.00 0.00 39.86 2.90
1682 1786 6.323996 TCGAGAAAATGGATGTACCTAGATGT 59.676 38.462 0.00 0.00 39.86 3.06
1683 1787 7.504574 TCGAGAAAATGGATGTACCTAGATGTA 59.495 37.037 0.00 0.00 39.86 2.29
1684 1788 8.307483 CGAGAAAATGGATGTACCTAGATGTAT 58.693 37.037 0.00 0.00 39.86 2.29
1722 1826 7.306205 ACATCCATTTTTATTCATTTTGGCG 57.694 32.000 0.00 0.00 0.00 5.69
1723 1827 7.102346 ACATCCATTTTTATTCATTTTGGCGA 58.898 30.769 0.00 0.00 0.00 5.54
1724 1828 6.959671 TCCATTTTTATTCATTTTGGCGAC 57.040 33.333 0.00 0.00 0.00 5.19
1725 1829 6.459066 TCCATTTTTATTCATTTTGGCGACA 58.541 32.000 0.00 0.00 39.83 4.35
1736 1840 3.146783 TGGCGACAAGTAATTCCGG 57.853 52.632 0.00 0.00 37.44 5.14
1737 1841 0.609151 TGGCGACAAGTAATTCCGGA 59.391 50.000 0.00 0.00 37.44 5.14
1738 1842 1.004595 GGCGACAAGTAATTCCGGAC 58.995 55.000 1.83 0.00 0.00 4.79
1739 1843 0.643820 GCGACAAGTAATTCCGGACG 59.356 55.000 1.83 1.53 0.00 4.79
1740 1844 1.274596 CGACAAGTAATTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
1741 1845 1.135315 CGACAAGTAATTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
1742 1846 2.537401 GACAAGTAATTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
1743 1847 1.206371 ACAAGTAATTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1744 1848 0.828677 AAGTAATTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1745 1849 0.032813 AGTAATTCCGGACGGAGGGA 60.033 55.000 13.64 0.00 46.06 4.20
1746 1850 0.388294 GTAATTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
1747 1851 0.032813 TAATTCCGGACGGAGGGAGT 60.033 55.000 13.64 1.45 46.06 3.85
1748 1852 0.032813 AATTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
1829 1933 9.520204 AAATCTGACACACATTTCTAAACTTTG 57.480 29.630 0.00 0.00 0.00 2.77
1830 1934 7.026631 TCTGACACACATTTCTAAACTTTGG 57.973 36.000 0.00 0.00 0.00 3.28
1831 1935 6.826231 TCTGACACACATTTCTAAACTTTGGA 59.174 34.615 0.00 0.00 0.00 3.53
1832 1936 7.502226 TCTGACACACATTTCTAAACTTTGGAT 59.498 33.333 0.00 0.00 0.00 3.41
1833 1937 7.648142 TGACACACATTTCTAAACTTTGGATC 58.352 34.615 0.00 0.00 0.00 3.36
1834 1938 7.284261 TGACACACATTTCTAAACTTTGGATCA 59.716 33.333 0.00 0.00 0.00 2.92
1835 1939 7.425606 ACACACATTTCTAAACTTTGGATCAC 58.574 34.615 0.00 0.00 0.00 3.06
1836 1940 7.285401 ACACACATTTCTAAACTTTGGATCACT 59.715 33.333 0.00 0.00 0.00 3.41
1837 1941 8.783093 CACACATTTCTAAACTTTGGATCACTA 58.217 33.333 0.00 0.00 0.00 2.74
1838 1942 8.784043 ACACATTTCTAAACTTTGGATCACTAC 58.216 33.333 0.00 0.00 0.00 2.73
1839 1943 8.783093 CACATTTCTAAACTTTGGATCACTACA 58.217 33.333 0.00 0.00 0.00 2.74
1840 1944 9.349713 ACATTTCTAAACTTTGGATCACTACAA 57.650 29.630 0.00 0.00 0.00 2.41
1841 1945 9.612620 CATTTCTAAACTTTGGATCACTACAAC 57.387 33.333 0.00 0.00 0.00 3.32
1842 1946 8.740123 TTTCTAAACTTTGGATCACTACAACA 57.260 30.769 0.00 0.00 0.00 3.33
1843 1947 8.740123 TTCTAAACTTTGGATCACTACAACAA 57.260 30.769 0.00 0.00 0.00 2.83
1844 1948 8.149973 TCTAAACTTTGGATCACTACAACAAC 57.850 34.615 0.00 0.00 0.00 3.32
1845 1949 5.418310 AACTTTGGATCACTACAACAACG 57.582 39.130 0.00 0.00 0.00 4.10
1846 1950 4.699637 ACTTTGGATCACTACAACAACGA 58.300 39.130 0.00 0.00 0.00 3.85
1847 1951 5.305585 ACTTTGGATCACTACAACAACGAT 58.694 37.500 0.00 0.00 0.00 3.73
1848 1952 5.408604 ACTTTGGATCACTACAACAACGATC 59.591 40.000 0.00 0.00 33.30 3.69
1849 1953 4.529109 TGGATCACTACAACAACGATCA 57.471 40.909 0.00 0.00 35.29 2.92
1850 1954 5.084818 TGGATCACTACAACAACGATCAT 57.915 39.130 0.00 0.00 35.29 2.45
1851 1955 6.215495 TGGATCACTACAACAACGATCATA 57.785 37.500 0.00 0.00 35.29 2.15
1852 1956 6.816136 TGGATCACTACAACAACGATCATAT 58.184 36.000 0.00 0.00 35.29 1.78
1853 1957 6.701400 TGGATCACTACAACAACGATCATATG 59.299 38.462 0.00 0.00 35.29 1.78
1854 1958 6.701841 GGATCACTACAACAACGATCATATGT 59.298 38.462 1.90 0.00 35.29 2.29
1855 1959 7.224753 GGATCACTACAACAACGATCATATGTT 59.775 37.037 1.90 0.00 37.76 2.71
1856 1960 7.520119 TCACTACAACAACGATCATATGTTC 57.480 36.000 1.90 3.09 35.22 3.18
1857 1961 6.533723 TCACTACAACAACGATCATATGTTCC 59.466 38.462 1.90 0.00 35.22 3.62
1858 1962 6.535150 CACTACAACAACGATCATATGTTCCT 59.465 38.462 1.90 0.00 35.22 3.36
1859 1963 7.064609 CACTACAACAACGATCATATGTTCCTT 59.935 37.037 1.90 0.00 35.22 3.36
1860 1964 6.817765 ACAACAACGATCATATGTTCCTTT 57.182 33.333 1.90 0.00 35.22 3.11
1861 1965 7.214467 ACAACAACGATCATATGTTCCTTTT 57.786 32.000 1.90 0.00 35.22 2.27
1862 1966 7.657336 ACAACAACGATCATATGTTCCTTTTT 58.343 30.769 1.90 0.00 35.22 1.94
1882 1986 6.704512 TTTTTATCCGCAAAAAGCAAGATC 57.295 33.333 0.00 0.00 46.13 2.75
1883 1987 5.384063 TTTATCCGCAAAAAGCAAGATCA 57.616 34.783 0.00 0.00 46.13 2.92
1884 1988 5.581126 TTATCCGCAAAAAGCAAGATCAT 57.419 34.783 0.00 0.00 46.13 2.45
1891 1995 5.801444 CGCAAAAAGCAAGATCATATGTTCA 59.199 36.000 14.67 0.00 46.13 3.18
1929 2033 1.427809 TCATAGGCAGAGGGTCATGG 58.572 55.000 0.00 0.00 0.00 3.66
1947 2051 1.340017 TGGGAGAGCCTTCGGAAAATG 60.340 52.381 0.00 0.00 0.00 2.32
2048 2893 1.350351 CCTTATCCATGAGGGCTCCAG 59.650 57.143 0.00 0.00 36.21 3.86
2055 2900 2.747855 GAGGGCTCCAGTTTGGCG 60.748 66.667 0.00 0.00 37.47 5.69
2061 2906 1.576421 CTCCAGTTTGGCGCTTCAC 59.424 57.895 7.64 0.76 37.47 3.18
2080 2925 2.965147 GCACCGAATTGCGAGCACA 61.965 57.895 0.00 0.00 44.57 4.57
2090 2935 0.179127 TGCGAGCACAGCTATGTCTC 60.179 55.000 6.42 6.42 39.88 3.36
2091 2936 0.179127 GCGAGCACAGCTATGTCTCA 60.179 55.000 14.10 0.00 39.88 3.27
2096 2941 2.005451 GCACAGCTATGTCTCACCTTG 58.995 52.381 0.00 0.00 37.65 3.61
2101 2946 1.134965 GCTATGTCTCACCTTGAGCGT 60.135 52.381 0.00 0.00 43.95 5.07
2102 2947 2.099263 GCTATGTCTCACCTTGAGCGTA 59.901 50.000 0.00 0.42 43.95 4.42
2103 2948 2.949451 ATGTCTCACCTTGAGCGTAG 57.051 50.000 0.00 0.00 43.95 3.51
2104 2949 1.905637 TGTCTCACCTTGAGCGTAGA 58.094 50.000 0.00 0.00 43.95 2.59
2143 3014 5.904941 TGCTGACATCACAGAAATGTTTTT 58.095 33.333 0.00 0.00 37.47 1.94
2253 3126 7.915923 TCGCACATTTAAAAACTGTTCATGTAA 59.084 29.630 0.00 0.00 0.00 2.41
2422 3346 6.533367 ACATTTAAAGCAATGTTCACGTGTTT 59.467 30.769 16.51 8.47 43.54 2.83
2432 3356 8.321716 GCAATGTTCACGTGTTTACAAAAATAA 58.678 29.630 16.51 0.00 0.00 1.40
2437 3361 9.544825 GTTCACGTGTTTACAAAAATAATTTCG 57.455 29.630 16.51 0.00 0.00 3.46
2576 3501 9.145865 TCAAAAACTGTTCAAACCTTGTATTTC 57.854 29.630 0.00 0.00 0.00 2.17
2577 3502 8.930760 CAAAAACTGTTCAAACCTTGTATTTCA 58.069 29.630 0.00 0.00 0.00 2.69
2581 3506 8.474006 ACTGTTCAAACCTTGTATTTCAAAAC 57.526 30.769 0.00 0.00 35.48 2.43
2587 3512 8.242053 TCAAACCTTGTATTTCAAAACGTGTTA 58.758 29.630 0.00 0.00 35.48 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.900016 CAGCAGCAGCAAGGGAACA 60.900 57.895 3.17 0.00 45.49 3.18
224 226 1.878522 GATGATGAAGGCGACGCGT 60.879 57.895 13.85 13.85 0.00 6.01
594 596 6.043287 ATAGCATTTGGGGCTAGCTAGCTT 62.043 45.833 37.42 17.38 46.10 3.74
715 719 3.199891 GTATGTTGGGGCGCCGTC 61.200 66.667 22.54 16.01 0.00 4.79
774 778 2.141122 AATGGGCAAGCACGAAACCG 62.141 55.000 0.00 0.00 0.00 4.44
775 779 0.667184 CAATGGGCAAGCACGAAACC 60.667 55.000 0.00 0.00 0.00 3.27
776 780 0.667184 CCAATGGGCAAGCACGAAAC 60.667 55.000 0.00 0.00 0.00 2.78
777 781 1.664873 CCAATGGGCAAGCACGAAA 59.335 52.632 0.00 0.00 0.00 3.46
850 854 2.408333 GGAGCCATCCATTCAACGG 58.592 57.895 0.00 0.00 45.87 4.44
984 989 1.227704 TGTGTCACGTTTGGGCGAT 60.228 52.632 0.00 0.00 35.59 4.58
985 990 2.174969 GTGTGTCACGTTTGGGCGA 61.175 57.895 0.00 0.00 35.59 5.54
986 991 2.326550 GTGTGTCACGTTTGGGCG 59.673 61.111 0.00 0.00 37.94 6.13
987 992 2.719354 GGTGTGTCACGTTTGGGC 59.281 61.111 0.00 0.00 34.83 5.36
990 995 0.655733 GTCTGGGTGTGTCACGTTTG 59.344 55.000 0.00 0.00 34.83 2.93
991 996 0.250793 TGTCTGGGTGTGTCACGTTT 59.749 50.000 0.00 0.00 34.83 3.60
1020 1028 4.272261 GTGATGAATGTGTGTGTGTGTGTA 59.728 41.667 0.00 0.00 0.00 2.90
1021 1029 3.065233 GTGATGAATGTGTGTGTGTGTGT 59.935 43.478 0.00 0.00 0.00 3.72
1031 1040 3.525537 GATCGACTGGTGATGAATGTGT 58.474 45.455 0.00 0.00 0.00 3.72
1036 1045 2.034685 GGATCGATCGACTGGTGATGAA 59.965 50.000 22.06 0.00 0.00 2.57
1037 1046 1.609072 GGATCGATCGACTGGTGATGA 59.391 52.381 22.06 0.00 0.00 2.92
1038 1047 1.664302 CGGATCGATCGACTGGTGATG 60.664 57.143 22.06 0.88 0.00 3.07
1039 1048 0.593618 CGGATCGATCGACTGGTGAT 59.406 55.000 22.06 1.65 0.00 3.06
1040 1049 0.463116 TCGGATCGATCGACTGGTGA 60.463 55.000 22.06 11.26 0.00 4.02
1163 1189 1.485294 TTGCAGACATGGTACCCGGT 61.485 55.000 10.07 7.40 0.00 5.28
1285 1311 1.372683 GCAGAGGCAGTGGAAGTCA 59.627 57.895 0.00 0.00 40.72 3.41
1557 1639 3.363575 GCGACATGACTTACGAAAAGCAA 60.364 43.478 0.00 0.00 0.00 3.91
1617 1721 9.986157 ACGGAGGGAGTATATATATAGAAACAA 57.014 33.333 2.53 0.00 0.00 2.83
1625 1729 6.257994 TCCGAACGGAGGGAGTATATATAT 57.742 41.667 12.04 0.00 39.76 0.86
1627 1731 4.581309 TCCGAACGGAGGGAGTATATAT 57.419 45.455 12.04 0.00 39.76 0.86
1633 1737 1.479730 GTATTTCCGAACGGAGGGAGT 59.520 52.381 15.34 1.96 46.06 3.85
1634 1738 1.202498 GGTATTTCCGAACGGAGGGAG 60.202 57.143 15.34 0.00 46.06 4.30
1635 1739 0.826062 GGTATTTCCGAACGGAGGGA 59.174 55.000 15.34 7.17 46.06 4.20
1636 1740 0.828677 AGGTATTTCCGAACGGAGGG 59.171 55.000 15.34 0.00 46.06 4.30
1637 1741 1.206371 ACAGGTATTTCCGAACGGAGG 59.794 52.381 15.34 4.52 46.06 4.30
1638 1742 2.537401 GACAGGTATTTCCGAACGGAG 58.463 52.381 15.34 5.60 46.06 4.63
1639 1743 1.135315 CGACAGGTATTTCCGAACGGA 60.135 52.381 12.04 12.04 43.52 4.69
1640 1744 1.135315 TCGACAGGTATTTCCGAACGG 60.135 52.381 6.94 6.94 41.99 4.44
1641 1745 2.159476 TCTCGACAGGTATTTCCGAACG 60.159 50.000 0.00 0.00 41.99 3.95
1642 1746 3.498927 TCTCGACAGGTATTTCCGAAC 57.501 47.619 0.00 0.00 41.99 3.95
1643 1747 4.524316 TTTCTCGACAGGTATTTCCGAA 57.476 40.909 0.00 0.00 41.99 4.30
1644 1748 4.524316 TTTTCTCGACAGGTATTTCCGA 57.476 40.909 0.00 0.00 41.99 4.55
1645 1749 4.034048 CCATTTTCTCGACAGGTATTTCCG 59.966 45.833 0.00 0.00 41.99 4.30
1646 1750 5.183228 TCCATTTTCTCGACAGGTATTTCC 58.817 41.667 0.00 0.00 0.00 3.13
1647 1751 6.316390 ACATCCATTTTCTCGACAGGTATTTC 59.684 38.462 0.00 0.00 0.00 2.17
1648 1752 6.180472 ACATCCATTTTCTCGACAGGTATTT 58.820 36.000 0.00 0.00 0.00 1.40
1649 1753 5.745227 ACATCCATTTTCTCGACAGGTATT 58.255 37.500 0.00 0.00 0.00 1.89
1650 1754 5.359194 ACATCCATTTTCTCGACAGGTAT 57.641 39.130 0.00 0.00 0.00 2.73
1651 1755 4.819105 ACATCCATTTTCTCGACAGGTA 57.181 40.909 0.00 0.00 0.00 3.08
1652 1756 3.703001 ACATCCATTTTCTCGACAGGT 57.297 42.857 0.00 0.00 0.00 4.00
1653 1757 3.871594 GGTACATCCATTTTCTCGACAGG 59.128 47.826 0.00 0.00 35.97 4.00
1654 1758 4.759782 AGGTACATCCATTTTCTCGACAG 58.240 43.478 0.00 0.00 39.02 3.51
1655 1759 4.819105 AGGTACATCCATTTTCTCGACA 57.181 40.909 0.00 0.00 39.02 4.35
1656 1760 6.145338 TCTAGGTACATCCATTTTCTCGAC 57.855 41.667 0.00 0.00 39.02 4.20
1657 1761 6.323996 ACATCTAGGTACATCCATTTTCTCGA 59.676 38.462 0.00 0.00 39.02 4.04
1658 1762 6.516718 ACATCTAGGTACATCCATTTTCTCG 58.483 40.000 0.00 0.00 39.02 4.04
1696 1800 9.044150 CGCCAAAATGAATAAAAATGGATGTAT 57.956 29.630 0.00 0.00 0.00 2.29
1697 1801 8.253810 TCGCCAAAATGAATAAAAATGGATGTA 58.746 29.630 0.00 0.00 0.00 2.29
1698 1802 7.064490 GTCGCCAAAATGAATAAAAATGGATGT 59.936 33.333 0.00 0.00 0.00 3.06
1699 1803 7.064371 TGTCGCCAAAATGAATAAAAATGGATG 59.936 33.333 0.00 0.00 0.00 3.51
1700 1804 7.102346 TGTCGCCAAAATGAATAAAAATGGAT 58.898 30.769 0.00 0.00 0.00 3.41
1701 1805 6.459066 TGTCGCCAAAATGAATAAAAATGGA 58.541 32.000 0.00 0.00 0.00 3.41
1702 1806 6.718454 TGTCGCCAAAATGAATAAAAATGG 57.282 33.333 0.00 0.00 0.00 3.16
1703 1807 7.795859 ACTTGTCGCCAAAATGAATAAAAATG 58.204 30.769 0.00 0.00 0.00 2.32
1704 1808 7.961325 ACTTGTCGCCAAAATGAATAAAAAT 57.039 28.000 0.00 0.00 0.00 1.82
1705 1809 8.873215 TTACTTGTCGCCAAAATGAATAAAAA 57.127 26.923 0.00 0.00 0.00 1.94
1706 1810 9.482627 AATTACTTGTCGCCAAAATGAATAAAA 57.517 25.926 0.00 0.00 0.00 1.52
1707 1811 9.134734 GAATTACTTGTCGCCAAAATGAATAAA 57.865 29.630 0.00 0.00 0.00 1.40
1708 1812 7.757624 GGAATTACTTGTCGCCAAAATGAATAA 59.242 33.333 0.00 0.00 0.00 1.40
1709 1813 7.254852 GGAATTACTTGTCGCCAAAATGAATA 58.745 34.615 0.00 0.00 0.00 1.75
1710 1814 6.099341 GGAATTACTTGTCGCCAAAATGAAT 58.901 36.000 0.00 0.00 0.00 2.57
1711 1815 5.465935 GGAATTACTTGTCGCCAAAATGAA 58.534 37.500 0.00 0.00 0.00 2.57
1712 1816 4.378978 CGGAATTACTTGTCGCCAAAATGA 60.379 41.667 0.00 0.00 0.00 2.57
1713 1817 3.851403 CGGAATTACTTGTCGCCAAAATG 59.149 43.478 0.00 0.00 0.00 2.32
1714 1818 3.119637 CCGGAATTACTTGTCGCCAAAAT 60.120 43.478 0.00 0.00 0.00 1.82
1715 1819 2.226912 CCGGAATTACTTGTCGCCAAAA 59.773 45.455 0.00 0.00 0.00 2.44
1716 1820 1.807742 CCGGAATTACTTGTCGCCAAA 59.192 47.619 0.00 0.00 0.00 3.28
1717 1821 1.002201 TCCGGAATTACTTGTCGCCAA 59.998 47.619 0.00 0.00 0.00 4.52
1718 1822 0.609151 TCCGGAATTACTTGTCGCCA 59.391 50.000 0.00 0.00 0.00 5.69
1719 1823 1.004595 GTCCGGAATTACTTGTCGCC 58.995 55.000 5.23 0.00 0.00 5.54
1720 1824 0.643820 CGTCCGGAATTACTTGTCGC 59.356 55.000 5.23 0.00 0.00 5.19
1721 1825 1.135315 TCCGTCCGGAATTACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
1722 1826 2.537401 CTCCGTCCGGAATTACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1723 1827 1.206371 CCTCCGTCCGGAATTACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1724 1828 1.472728 CCCTCCGTCCGGAATTACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1725 1829 0.828677 CCCTCCGTCCGGAATTACTT 59.171 55.000 5.23 0.00 44.66 2.24
1726 1830 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.000 5.23 0.00 44.66 2.24
1727 1831 0.388294 CTCCCTCCGTCCGGAATTAC 59.612 60.000 5.23 0.00 44.66 1.89
1728 1832 0.032813 ACTCCCTCCGTCCGGAATTA 60.033 55.000 5.23 0.00 44.66 1.40
1729 1833 0.032813 TACTCCCTCCGTCCGGAATT 60.033 55.000 5.23 0.00 44.66 2.17
1730 1834 0.467659 CTACTCCCTCCGTCCGGAAT 60.468 60.000 5.23 0.00 44.66 3.01
1731 1835 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
1732 1836 1.856539 AACTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
1733 1837 0.969409 AAACTACTCCCTCCGTCCGG 60.969 60.000 0.00 0.00 0.00 5.14
1734 1838 0.893447 AAAACTACTCCCTCCGTCCG 59.107 55.000 0.00 0.00 0.00 4.79
1766 1870 7.447374 TCACAGAACTTGTTGGTATTATTGG 57.553 36.000 0.00 0.00 38.16 3.16
1767 1871 9.180678 GTTTCACAGAACTTGTTGGTATTATTG 57.819 33.333 0.00 0.00 38.16 1.90
1812 1916 7.823745 AGTGATCCAAAGTTTAGAAATGTGT 57.176 32.000 0.00 0.00 0.00 3.72
1818 1922 8.617809 GTTGTTGTAGTGATCCAAAGTTTAGAA 58.382 33.333 0.00 0.00 0.00 2.10
1819 1923 7.042321 CGTTGTTGTAGTGATCCAAAGTTTAGA 60.042 37.037 0.00 0.00 0.00 2.10
1820 1924 7.042321 TCGTTGTTGTAGTGATCCAAAGTTTAG 60.042 37.037 0.00 0.00 0.00 1.85
1821 1925 6.762187 TCGTTGTTGTAGTGATCCAAAGTTTA 59.238 34.615 0.00 0.00 0.00 2.01
1822 1926 5.587043 TCGTTGTTGTAGTGATCCAAAGTTT 59.413 36.000 0.00 0.00 0.00 2.66
1823 1927 5.120399 TCGTTGTTGTAGTGATCCAAAGTT 58.880 37.500 0.00 0.00 0.00 2.66
1824 1928 4.699637 TCGTTGTTGTAGTGATCCAAAGT 58.300 39.130 0.00 0.00 0.00 2.66
1825 1929 5.408299 TGATCGTTGTTGTAGTGATCCAAAG 59.592 40.000 0.00 0.00 35.67 2.77
1826 1930 5.301555 TGATCGTTGTTGTAGTGATCCAAA 58.698 37.500 0.00 0.00 35.67 3.28
1827 1931 4.888917 TGATCGTTGTTGTAGTGATCCAA 58.111 39.130 0.00 0.00 35.67 3.53
1828 1932 4.529109 TGATCGTTGTTGTAGTGATCCA 57.471 40.909 0.00 0.00 35.67 3.41
1829 1933 6.701841 ACATATGATCGTTGTTGTAGTGATCC 59.298 38.462 10.38 0.00 35.67 3.36
1830 1934 7.700322 ACATATGATCGTTGTTGTAGTGATC 57.300 36.000 10.38 0.00 36.77 2.92
1831 1935 7.224753 GGAACATATGATCGTTGTTGTAGTGAT 59.775 37.037 10.38 0.00 33.92 3.06
1832 1936 6.533723 GGAACATATGATCGTTGTTGTAGTGA 59.466 38.462 10.38 0.00 33.92 3.41
1833 1937 6.535150 AGGAACATATGATCGTTGTTGTAGTG 59.465 38.462 10.38 0.00 33.92 2.74
1834 1938 6.640518 AGGAACATATGATCGTTGTTGTAGT 58.359 36.000 10.38 0.00 33.92 2.73
1835 1939 7.539712 AAGGAACATATGATCGTTGTTGTAG 57.460 36.000 17.03 0.00 33.92 2.74
1836 1940 7.915293 AAAGGAACATATGATCGTTGTTGTA 57.085 32.000 18.07 0.00 33.92 2.41
1837 1941 6.817765 AAAGGAACATATGATCGTTGTTGT 57.182 33.333 18.07 3.86 33.92 3.32
1859 1963 6.219473 TGATCTTGCTTTTTGCGGATAAAAA 58.781 32.000 0.00 0.00 46.63 1.94
1860 1964 5.777802 TGATCTTGCTTTTTGCGGATAAAA 58.222 33.333 0.00 0.00 46.63 1.52
1861 1965 5.384063 TGATCTTGCTTTTTGCGGATAAA 57.616 34.783 0.00 0.00 46.63 1.40
1862 1966 5.581126 ATGATCTTGCTTTTTGCGGATAA 57.419 34.783 0.00 0.00 46.63 1.75
1863 1967 6.262944 ACATATGATCTTGCTTTTTGCGGATA 59.737 34.615 10.38 0.00 46.63 2.59
1864 1968 5.068198 ACATATGATCTTGCTTTTTGCGGAT 59.932 36.000 10.38 0.00 46.63 4.18
1865 1969 4.398988 ACATATGATCTTGCTTTTTGCGGA 59.601 37.500 10.38 0.00 46.63 5.54
1866 1970 4.675510 ACATATGATCTTGCTTTTTGCGG 58.324 39.130 10.38 0.00 46.63 5.69
1867 1971 5.801444 TGAACATATGATCTTGCTTTTTGCG 59.199 36.000 10.38 0.00 46.63 4.85
1868 1972 7.766219 ATGAACATATGATCTTGCTTTTTGC 57.234 32.000 10.38 0.00 43.25 3.68
1873 1977 9.412460 TCCTAAAATGAACATATGATCTTGCTT 57.588 29.630 10.38 5.88 0.00 3.91
1874 1978 8.985315 TCCTAAAATGAACATATGATCTTGCT 57.015 30.769 10.38 0.00 0.00 3.91
1875 1979 9.455847 GTTCCTAAAATGAACATATGATCTTGC 57.544 33.333 10.38 0.00 41.35 4.01
1891 1995 8.416329 GCCTATGATCATTGTTGTTCCTAAAAT 58.584 33.333 14.65 0.00 0.00 1.82
1910 2014 1.427809 CCATGACCCTCTGCCTATGA 58.572 55.000 0.00 0.00 0.00 2.15
1912 2016 0.268869 TCCCATGACCCTCTGCCTAT 59.731 55.000 0.00 0.00 0.00 2.57
1929 2033 7.794203 ATGTTTACATTTTCCGAAGGCTCTCC 61.794 42.308 0.00 0.00 40.21 3.71
2001 2105 9.953697 CCTTTACGGATCTTATATGAGCTATAC 57.046 37.037 4.16 0.00 33.16 1.47
2003 2107 7.418025 GGCCTTTACGGATCTTATATGAGCTAT 60.418 40.741 0.00 0.00 33.16 2.97
2004 2108 6.127423 GGCCTTTACGGATCTTATATGAGCTA 60.127 42.308 0.00 0.00 33.16 3.32
2006 2110 4.870991 GGCCTTTACGGATCTTATATGAGC 59.129 45.833 0.00 0.00 33.16 4.26
2008 2112 6.681729 AAGGCCTTTACGGATCTTATATGA 57.318 37.500 13.78 0.00 33.16 2.15
2010 2114 7.402071 TGGATAAGGCCTTTACGGATCTTATAT 59.598 37.037 26.08 5.71 39.10 0.86
2065 2910 1.083806 TAGCTGTGCTCGCAATTCGG 61.084 55.000 0.00 0.00 40.44 4.30
2070 2915 0.247460 AGACATAGCTGTGCTCGCAA 59.753 50.000 10.79 0.00 40.44 4.85
2090 2935 2.725644 CGTGTCTACGCTCAAGGTG 58.274 57.895 0.00 0.00 44.11 4.00
2206 3078 9.601971 GTGCGATGAACACTTAATAAAACTAAA 57.398 29.630 0.00 0.00 35.12 1.85
2220 3093 6.198216 ACAGTTTTTAAATGTGCGATGAACAC 59.802 34.615 0.00 0.00 38.55 3.32
2228 3101 6.509317 ACATGAACAGTTTTTAAATGTGCG 57.491 33.333 0.00 0.00 0.00 5.34
2411 3327 9.544825 CGAAATTATTTTTGTAAACACGTGAAC 57.455 29.630 25.01 16.84 0.00 3.18
2412 3328 9.286946 ACGAAATTATTTTTGTAAACACGTGAA 57.713 25.926 25.01 1.90 37.62 3.18
2413 3329 8.734933 CACGAAATTATTTTTGTAAACACGTGA 58.265 29.630 25.01 0.00 44.35 4.35
2544 3469 6.859017 AGGTTTGAACAGTTTTTGAATACGT 58.141 32.000 0.00 0.00 0.00 3.57
2546 3471 8.474006 ACAAGGTTTGAACAGTTTTTGAATAC 57.526 30.769 0.00 0.00 0.00 1.89
2553 3478 9.495572 TTTGAAATACAAGGTTTGAACAGTTTT 57.504 25.926 0.00 0.00 39.77 2.43
2555 3480 8.931775 GTTTTGAAATACAAGGTTTGAACAGTT 58.068 29.630 0.00 0.00 39.77 3.16


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

AutoCloner maintained by Alex Coulton.