Multiple sequence alignment - TraesCS6A01G294900

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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 TraesCS6A01G294900 chr6A 100.000 2537 0 0 1 2537 528947892 528950428 0.000000e+00 4686.0
1 TraesCS6A01G294900 chr6A 93.914 723 40 3 1 721 23491588 23490868 0.000000e+00 1088.0
2 TraesCS6A01G294900 chr6A 93.680 712 44 1 1 712 415096239 415096949 0.000000e+00 1064.0
3 TraesCS6A01G294900 chr6A 87.629 97 9 2 1673 1767 528949509 528949604 2.670000e-20 110.0
4 TraesCS6A01G294900 chr6A 87.629 97 9 2 1618 1713 528949564 528949658 2.670000e-20 110.0
5 TraesCS6A01G294900 chr6D 92.596 959 43 13 722 1665 384300586 384301531 0.000000e+00 1352.0
6 TraesCS6A01G294900 chr6D 80.503 159 16 11 1671 1825 384301482 384301629 9.600000e-20 108.0
7 TraesCS6A01G294900 chr6B 90.557 1006 63 17 722 1713 574521052 574522039 0.000000e+00 1303.0
8 TraesCS6A01G294900 chr6B 90.714 700 62 1 1838 2537 45761750 45761054 0.000000e+00 929.0
9 TraesCS6A01G294900 chr6B 81.022 137 14 9 1672 1803 574521946 574522075 5.780000e-17 99.0
10 TraesCS6A01G294900 chr7A 93.961 712 43 0 1 712 276128379 276127668 0.000000e+00 1077.0
11 TraesCS6A01G294900 chr7A 93.499 723 45 1 1 721 594889217 594889939 0.000000e+00 1074.0
12 TraesCS6A01G294900 chr7A 93.829 713 43 1 1 713 41434349 41435060 0.000000e+00 1072.0
13 TraesCS6A01G294900 chr7A 85.401 274 36 4 2258 2528 567387982 567388254 5.340000e-72 281.0
14 TraesCS6A01G294900 chr7A 87.500 56 7 0 2369 2424 64128613 64128668 5.860000e-07 65.8
15 TraesCS6A01G294900 chr1A 93.935 709 43 0 1 709 562897154 562897862 0.000000e+00 1072.0
16 TraesCS6A01G294900 chr1A 90.483 704 63 1 1838 2537 384289648 384290351 0.000000e+00 926.0
17 TraesCS6A01G294900 chr4A 93.379 725 44 3 1 722 146694138 146693415 0.000000e+00 1070.0
18 TraesCS6A01G294900 chr4A 93.689 713 43 2 1 713 565696695 565697405 0.000000e+00 1066.0
19 TraesCS6A01G294900 chr4A 94.539 531 29 0 1838 2368 712380915 712380385 0.000000e+00 821.0
20 TraesCS6A01G294900 chr4A 93.843 536 32 1 1835 2370 712207362 712207896 0.000000e+00 806.0
21 TraesCS6A01G294900 chr4A 89.085 284 29 2 2254 2537 712207725 712208006 4.020000e-93 351.0
22 TraesCS6A01G294900 chr4A 89.085 284 30 1 2254 2537 712380555 712380273 4.020000e-93 351.0
23 TraesCS6A01G294900 chr4A 76.364 385 80 11 1855 2231 407608599 407608980 1.990000e-46 196.0
24 TraesCS6A01G294900 chr3A 93.794 709 42 2 1 709 32995760 32996466 0.000000e+00 1064.0
25 TraesCS6A01G294900 chr3D 91.114 709 53 3 1838 2537 432501988 432502695 0.000000e+00 952.0
26 TraesCS6A01G294900 chr3D 93.856 472 29 0 2066 2537 596437344 596436873 0.000000e+00 712.0
27 TraesCS6A01G294900 chr3D 93.617 188 12 0 1838 2025 596437531 596437344 5.340000e-72 281.0
28 TraesCS6A01G294900 chr4D 93.609 532 34 0 1839 2370 327906260 327906791 0.000000e+00 795.0
29 TraesCS6A01G294900 chr4D 89.437 284 29 1 2254 2537 327906619 327906901 8.630000e-95 357.0
30 TraesCS6A01G294900 chr5A 75.871 402 78 17 1838 2228 592987714 592987321 1.200000e-43 187.0
31 TraesCS6A01G294900 chr1B 85.000 100 8 6 2433 2528 434642934 434643030 7.470000e-16 95.3


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 TraesCS6A01G294900 chr6A 528947892 528950428 2536 False 1635.333333 4686 91.752667 1 2537 3 chr6A.!!$F2 2536
1 TraesCS6A01G294900 chr6A 23490868 23491588 720 True 1088.000000 1088 93.914000 1 721 1 chr6A.!!$R1 720
2 TraesCS6A01G294900 chr6A 415096239 415096949 710 False 1064.000000 1064 93.680000 1 712 1 chr6A.!!$F1 711
3 TraesCS6A01G294900 chr6D 384300586 384301629 1043 False 730.000000 1352 86.549500 722 1825 2 chr6D.!!$F1 1103
4 TraesCS6A01G294900 chr6B 45761054 45761750 696 True 929.000000 929 90.714000 1838 2537 1 chr6B.!!$R1 699
5 TraesCS6A01G294900 chr6B 574521052 574522075 1023 False 701.000000 1303 85.789500 722 1803 2 chr6B.!!$F1 1081
6 TraesCS6A01G294900 chr7A 276127668 276128379 711 True 1077.000000 1077 93.961000 1 712 1 chr7A.!!$R1 711
7 TraesCS6A01G294900 chr7A 594889217 594889939 722 False 1074.000000 1074 93.499000 1 721 1 chr7A.!!$F4 720
8 TraesCS6A01G294900 chr7A 41434349 41435060 711 False 1072.000000 1072 93.829000 1 713 1 chr7A.!!$F1 712
9 TraesCS6A01G294900 chr1A 562897154 562897862 708 False 1072.000000 1072 93.935000 1 709 1 chr1A.!!$F2 708
10 TraesCS6A01G294900 chr1A 384289648 384290351 703 False 926.000000 926 90.483000 1838 2537 1 chr1A.!!$F1 699
11 TraesCS6A01G294900 chr4A 146693415 146694138 723 True 1070.000000 1070 93.379000 1 722 1 chr4A.!!$R1 721
12 TraesCS6A01G294900 chr4A 565696695 565697405 710 False 1066.000000 1066 93.689000 1 713 1 chr4A.!!$F2 712
13 TraesCS6A01G294900 chr4A 712380273 712380915 642 True 586.000000 821 91.812000 1838 2537 2 chr4A.!!$R2 699
14 TraesCS6A01G294900 chr4A 712207362 712208006 644 False 578.500000 806 91.464000 1835 2537 2 chr4A.!!$F3 702
15 TraesCS6A01G294900 chr3A 32995760 32996466 706 False 1064.000000 1064 93.794000 1 709 1 chr3A.!!$F1 708
16 TraesCS6A01G294900 chr3D 432501988 432502695 707 False 952.000000 952 91.114000 1838 2537 1 chr3D.!!$F1 699
17 TraesCS6A01G294900 chr3D 596436873 596437531 658 True 496.500000 712 93.736500 1838 2537 2 chr3D.!!$R1 699
18 TraesCS6A01G294900 chr4D 327906260 327906901 641 False 576.000000 795 91.523000 1839 2537 2 chr4D.!!$F1 698

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
719 720 0.037303 AGTGGCCTGAGGACATGTTG 59.963 55.0 11.8 0.0 45.49 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1670 1694 0.105224 AACCACGACCGACATGACAA 59.895 50.0 0.0 0.0 0.0 3.18 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
205 206 3.682155 GCACCATGAGATGCTCTTCTTCT 60.682 47.826 8.74 0.00 38.84 2.85
264 265 1.068921 GCTCTTCCTCCTCATCCGC 59.931 63.158 0.00 0.00 0.00 5.54
306 307 3.660111 GCCGAACACCTTGCGCTT 61.660 61.111 9.73 0.00 0.00 4.68
713 714 0.875059 CGAAAAAGTGGCCTGAGGAC 59.125 55.000 0.65 0.00 0.00 3.85
715 716 2.519013 GAAAAAGTGGCCTGAGGACAT 58.481 47.619 11.80 0.00 45.49 3.06
716 717 1.915141 AAAAGTGGCCTGAGGACATG 58.085 50.000 11.80 0.00 45.49 3.21
718 719 0.773644 AAGTGGCCTGAGGACATGTT 59.226 50.000 11.80 4.41 45.49 2.71
719 720 0.037303 AGTGGCCTGAGGACATGTTG 59.963 55.000 11.80 0.00 45.49 3.33
720 721 0.962356 GTGGCCTGAGGACATGTTGG 60.962 60.000 11.80 0.00 45.49 3.77
740 741 3.834799 GCATGCAGCAGCCTTCCC 61.835 66.667 14.21 0.00 44.79 3.97
741 742 2.044252 CATGCAGCAGCCTTCCCT 60.044 61.111 0.00 0.00 41.13 4.20
742 743 2.119655 CATGCAGCAGCCTTCCCTC 61.120 63.158 0.00 0.00 41.13 4.30
765 768 0.677098 TCGACCGTGAAGGAGAGAGG 60.677 60.000 0.00 0.00 45.00 3.69
818 821 8.272866 TGATATAAACGTGCGACTAATGAATTG 58.727 33.333 0.00 0.00 0.00 2.32
870 874 1.082117 CGCCGGCCGCCTATAAATAG 61.082 60.000 22.85 2.44 0.00 1.73
933 937 1.078848 ACACGCCTCCATTGCTCTC 60.079 57.895 0.00 0.00 0.00 3.20
935 939 1.992277 ACGCCTCCATTGCTCTCCT 60.992 57.895 0.00 0.00 0.00 3.69
988 993 4.233408 GCGACTTGCAAGCTTTGG 57.767 55.556 26.27 9.60 45.45 3.28
994 999 0.319297 CTTGCAAGCTTTGGTCCTGC 60.319 55.000 14.65 0.00 0.00 4.85
1013 1018 3.995506 GACCAATGGCCTCCACCGG 62.996 68.421 3.32 0.00 35.80 5.28
1262 1270 4.803426 GTCGCGGGAGAGTGGCAG 62.803 72.222 6.13 0.00 0.00 4.85
1268 1276 2.348998 GGAGAGTGGCAGGTGTGG 59.651 66.667 0.00 0.00 0.00 4.17
1314 1322 1.301401 CGTGAAGAAGTGCGGGGAA 60.301 57.895 0.00 0.00 0.00 3.97
1368 1376 3.849951 ATGTACTGCGAGCCGGGG 61.850 66.667 2.18 0.00 0.00 5.73
1464 1472 2.601266 CGTTAACAAGTGCAGGGAAACG 60.601 50.000 6.39 0.00 33.51 3.60
1512 1520 1.290324 GCTCCAAGACTGCGAGACA 59.710 57.895 3.73 0.00 0.00 3.41
1585 1605 4.457496 CCGAGGCACACGCTCCAT 62.457 66.667 0.00 0.00 42.01 3.41
1616 1637 4.984161 CCTTTGTTGGTTTCATGTCATGTC 59.016 41.667 12.54 5.11 0.00 3.06
1656 1680 6.515340 CGTTGTTGTTTTAGATTTCGTCTAGC 59.485 38.462 0.00 0.00 40.42 3.42
1657 1681 6.476243 TGTTGTTTTAGATTTCGTCTAGCC 57.524 37.500 0.00 0.00 40.42 3.93
1658 1682 6.228258 TGTTGTTTTAGATTTCGTCTAGCCT 58.772 36.000 0.00 0.00 40.42 4.58
1659 1683 6.708949 TGTTGTTTTAGATTTCGTCTAGCCTT 59.291 34.615 0.00 0.00 40.42 4.35
1660 1684 6.721571 TGTTTTAGATTTCGTCTAGCCTTG 57.278 37.500 0.00 0.00 40.42 3.61
1661 1685 6.228258 TGTTTTAGATTTCGTCTAGCCTTGT 58.772 36.000 0.00 0.00 40.42 3.16
1662 1686 6.367969 TGTTTTAGATTTCGTCTAGCCTTGTC 59.632 38.462 0.00 0.00 40.42 3.18
1663 1687 5.654603 TTAGATTTCGTCTAGCCTTGTCA 57.345 39.130 0.00 0.00 40.42 3.58
1664 1688 4.744795 AGATTTCGTCTAGCCTTGTCAT 57.255 40.909 0.00 0.00 34.69 3.06
1665 1689 4.688021 AGATTTCGTCTAGCCTTGTCATC 58.312 43.478 0.00 0.00 34.69 2.92
1666 1690 3.953712 TTTCGTCTAGCCTTGTCATCA 57.046 42.857 0.00 0.00 0.00 3.07
1667 1691 2.941453 TCGTCTAGCCTTGTCATCAC 57.059 50.000 0.00 0.00 0.00 3.06
1668 1692 2.167662 TCGTCTAGCCTTGTCATCACA 58.832 47.619 0.00 0.00 0.00 3.58
1669 1693 2.094700 TCGTCTAGCCTTGTCATCACAC 60.095 50.000 0.00 0.00 29.76 3.82
1670 1694 2.094494 CGTCTAGCCTTGTCATCACACT 60.094 50.000 0.00 0.00 29.76 3.55
1671 1695 3.615110 CGTCTAGCCTTGTCATCACACTT 60.615 47.826 0.00 0.00 29.76 3.16
1672 1696 3.681897 GTCTAGCCTTGTCATCACACTTG 59.318 47.826 0.00 0.00 29.76 3.16
1673 1697 2.645838 AGCCTTGTCATCACACTTGT 57.354 45.000 0.00 0.00 29.76 3.16
1674 1698 2.498167 AGCCTTGTCATCACACTTGTC 58.502 47.619 0.00 0.00 29.76 3.18
1675 1699 2.158769 AGCCTTGTCATCACACTTGTCA 60.159 45.455 0.00 0.00 29.76 3.58
1676 1700 2.816087 GCCTTGTCATCACACTTGTCAT 59.184 45.455 0.00 0.00 29.76 3.06
1677 1701 3.365666 GCCTTGTCATCACACTTGTCATG 60.366 47.826 0.00 0.00 29.76 3.07
1678 1702 3.817084 CCTTGTCATCACACTTGTCATGT 59.183 43.478 0.00 0.00 29.76 3.21
1679 1703 4.083643 CCTTGTCATCACACTTGTCATGTC 60.084 45.833 0.00 0.00 29.76 3.06
1680 1704 3.059166 TGTCATCACACTTGTCATGTCG 58.941 45.455 0.00 0.00 0.00 4.35
1681 1705 2.413112 GTCATCACACTTGTCATGTCGG 59.587 50.000 0.00 0.00 0.00 4.79
1682 1706 2.037121 TCATCACACTTGTCATGTCGGT 59.963 45.455 0.00 0.00 0.00 4.69
1683 1707 2.148916 TCACACTTGTCATGTCGGTC 57.851 50.000 0.00 0.00 0.00 4.79
1684 1708 0.784178 CACACTTGTCATGTCGGTCG 59.216 55.000 0.00 0.00 0.00 4.79
1685 1709 0.387929 ACACTTGTCATGTCGGTCGT 59.612 50.000 0.00 0.00 0.00 4.34
1686 1710 0.784178 CACTTGTCATGTCGGTCGTG 59.216 55.000 0.00 0.00 34.61 4.35
1687 1711 0.319555 ACTTGTCATGTCGGTCGTGG 60.320 55.000 0.00 0.00 34.14 4.94
1688 1712 0.319555 CTTGTCATGTCGGTCGTGGT 60.320 55.000 0.00 0.00 34.14 4.16
1689 1713 0.105224 TTGTCATGTCGGTCGTGGTT 59.895 50.000 0.00 0.00 34.14 3.67
1690 1714 0.598942 TGTCATGTCGGTCGTGGTTG 60.599 55.000 0.00 0.00 34.14 3.77
1691 1715 0.599204 GTCATGTCGGTCGTGGTTGT 60.599 55.000 0.00 0.00 34.14 3.32
1692 1716 0.105224 TCATGTCGGTCGTGGTTGTT 59.895 50.000 0.00 0.00 34.14 2.83
1693 1717 0.234625 CATGTCGGTCGTGGTTGTTG 59.765 55.000 0.00 0.00 0.00 3.33
1694 1718 0.179067 ATGTCGGTCGTGGTTGTTGT 60.179 50.000 0.00 0.00 0.00 3.32
1695 1719 0.391395 TGTCGGTCGTGGTTGTTGTT 60.391 50.000 0.00 0.00 0.00 2.83
1696 1720 1.134877 TGTCGGTCGTGGTTGTTGTTA 60.135 47.619 0.00 0.00 0.00 2.41
1697 1721 1.523934 GTCGGTCGTGGTTGTTGTTAG 59.476 52.381 0.00 0.00 0.00 2.34
1698 1722 1.408340 TCGGTCGTGGTTGTTGTTAGA 59.592 47.619 0.00 0.00 0.00 2.10
1699 1723 2.036217 TCGGTCGTGGTTGTTGTTAGAT 59.964 45.455 0.00 0.00 0.00 1.98
1700 1724 2.803956 CGGTCGTGGTTGTTGTTAGATT 59.196 45.455 0.00 0.00 0.00 2.40
1701 1725 3.249080 CGGTCGTGGTTGTTGTTAGATTT 59.751 43.478 0.00 0.00 0.00 2.17
1702 1726 4.609783 CGGTCGTGGTTGTTGTTAGATTTC 60.610 45.833 0.00 0.00 0.00 2.17
1703 1727 4.273969 GGTCGTGGTTGTTGTTAGATTTCA 59.726 41.667 0.00 0.00 0.00 2.69
1704 1728 5.048991 GGTCGTGGTTGTTGTTAGATTTCAT 60.049 40.000 0.00 0.00 0.00 2.57
1705 1729 6.077838 GTCGTGGTTGTTGTTAGATTTCATC 58.922 40.000 0.00 0.00 0.00 2.92
1706 1730 5.995282 TCGTGGTTGTTGTTAGATTTCATCT 59.005 36.000 0.00 0.00 43.33 2.90
1707 1731 7.117236 GTCGTGGTTGTTGTTAGATTTCATCTA 59.883 37.037 0.00 0.00 40.76 1.98
1708 1732 7.330946 TCGTGGTTGTTGTTAGATTTCATCTAG 59.669 37.037 0.00 0.00 42.40 2.43
1709 1733 7.413000 CGTGGTTGTTGTTAGATTTCATCTAGG 60.413 40.741 0.00 0.00 42.40 3.02
1710 1734 6.374333 TGGTTGTTGTTAGATTTCATCTAGGC 59.626 38.462 0.00 0.00 42.40 3.93
1711 1735 6.599638 GGTTGTTGTTAGATTTCATCTAGGCT 59.400 38.462 0.00 0.00 42.40 4.58
1712 1736 7.121315 GGTTGTTGTTAGATTTCATCTAGGCTT 59.879 37.037 0.00 0.00 42.40 4.35
1713 1737 7.615582 TGTTGTTAGATTTCATCTAGGCTTG 57.384 36.000 0.00 0.00 42.40 4.01
1714 1738 7.168219 TGTTGTTAGATTTCATCTAGGCTTGT 58.832 34.615 0.00 0.00 42.40 3.16
1715 1739 7.334421 TGTTGTTAGATTTCATCTAGGCTTGTC 59.666 37.037 0.00 0.00 42.40 3.18
1716 1740 6.946340 TGTTAGATTTCATCTAGGCTTGTCA 58.054 36.000 0.00 0.00 42.40 3.58
1717 1741 7.568349 TGTTAGATTTCATCTAGGCTTGTCAT 58.432 34.615 0.00 0.00 42.40 3.06
1718 1742 7.712639 TGTTAGATTTCATCTAGGCTTGTCATC 59.287 37.037 0.00 0.00 42.40 2.92
1719 1743 6.244552 AGATTTCATCTAGGCTTGTCATCA 57.755 37.500 0.00 0.00 38.00 3.07
1720 1744 6.054295 AGATTTCATCTAGGCTTGTCATCAC 58.946 40.000 0.00 0.00 38.00 3.06
1721 1745 4.824479 TTCATCTAGGCTTGTCATCACA 57.176 40.909 0.00 0.00 0.00 3.58
1722 1746 4.128925 TCATCTAGGCTTGTCATCACAC 57.871 45.455 0.00 0.00 29.76 3.82
1739 1763 1.202486 ACACTTGTCATGTCGGTCGTT 60.202 47.619 0.00 0.00 0.00 3.85
1750 1774 2.170770 GTCGGTCGTTGTTGTTGTTTG 58.829 47.619 0.00 0.00 0.00 2.93
1754 1778 3.425858 CGGTCGTTGTTGTTGTTTGTTTT 59.574 39.130 0.00 0.00 0.00 2.43
1755 1779 4.615961 CGGTCGTTGTTGTTGTTTGTTTTA 59.384 37.500 0.00 0.00 0.00 1.52
1803 1833 6.073447 TGCTTCAAAATAAGGGACTGGATA 57.927 37.500 0.00 0.00 40.86 2.59
1808 1838 7.937700 TCAAAATAAGGGACTGGATAGATCT 57.062 36.000 0.00 0.00 40.86 2.75
1813 1843 3.696045 AGGGACTGGATAGATCTCATCG 58.304 50.000 0.00 0.00 37.18 3.84
1825 1855 1.068083 CTCATCGATCACCCGTGGG 59.932 63.158 2.58 2.58 42.03 4.61
1843 1873 5.106237 CCGTGGGTATCTAAGATGTACTAGC 60.106 48.000 0.00 0.00 0.00 3.42
1916 1954 6.591935 ACAAGTGATTAAGGTTGTCTTCAGA 58.408 36.000 0.00 0.00 36.93 3.27
1934 1972 4.887748 TCAGAGTCGAAGCTCATTTCTTT 58.112 39.130 5.90 0.00 37.94 2.52
1938 1976 3.923461 AGTCGAAGCTCATTTCTTTCTCG 59.077 43.478 0.00 0.00 0.00 4.04
2027 2065 1.074167 AGGCTCCCCGAATCCAGAT 60.074 57.895 0.00 0.00 35.76 2.90
2041 2079 6.323482 CCGAATCCAGATCATATGTAGAGGAT 59.677 42.308 13.15 13.15 36.25 3.24
2064 2102 9.614792 GGATAAATGTGGTTGTCTAGACTATTT 57.385 33.333 23.01 18.31 0.00 1.40
2089 2127 1.270412 TGTTATCTCAAACACGCGGGT 60.270 47.619 9.01 9.01 34.50 5.28
2152 2190 1.920835 GCCACACTCTCCCCTTCCT 60.921 63.158 0.00 0.00 0.00 3.36
2211 2249 2.092807 GCCCTGTCCTTTAAACCGGATA 60.093 50.000 9.46 0.00 0.00 2.59
2326 2364 2.797786 TCACCCTTTAAAACGGGATGG 58.202 47.619 17.28 7.92 43.44 3.51
2376 2414 6.571731 GCCCTATGTTCTTCACCCTTTAAAAC 60.572 42.308 0.00 0.00 0.00 2.43
2381 2419 4.376225 TCTTCACCCTTTAAAACGGGAT 57.624 40.909 17.28 1.83 43.44 3.85
2383 2421 3.791953 TCACCCTTTAAAACGGGATGA 57.208 42.857 17.28 13.55 43.44 2.92
2384 2422 4.310022 TCACCCTTTAAAACGGGATGAT 57.690 40.909 17.28 0.00 43.44 2.45
2385 2423 4.013728 TCACCCTTTAAAACGGGATGATG 58.986 43.478 17.28 6.93 43.44 3.07
2401 2439 1.598701 GATGCCCACCTCACCTTTGC 61.599 60.000 0.00 0.00 0.00 3.68
2407 2445 1.607467 ACCTCACCTTTGCCATGGC 60.607 57.895 30.54 30.54 42.35 4.40
2417 2455 4.684623 GCCATGGCACCCTATGTT 57.315 55.556 32.08 0.00 41.49 2.71
2418 2456 2.419057 GCCATGGCACCCTATGTTC 58.581 57.895 32.08 0.00 41.49 3.18
2419 2457 0.106519 GCCATGGCACCCTATGTTCT 60.107 55.000 32.08 0.00 41.49 3.01
2420 2458 1.686115 GCCATGGCACCCTATGTTCTT 60.686 52.381 32.08 0.00 41.49 2.52
2421 2459 2.301346 CCATGGCACCCTATGTTCTTC 58.699 52.381 0.00 0.00 0.00 2.87
2422 2460 2.357050 CCATGGCACCCTATGTTCTTCA 60.357 50.000 0.00 0.00 0.00 3.02
2423 2461 2.489938 TGGCACCCTATGTTCTTCAC 57.510 50.000 0.00 0.00 0.00 3.18
2424 2462 1.004277 TGGCACCCTATGTTCTTCACC 59.996 52.381 0.00 0.00 0.00 4.02
2429 2528 1.561542 CCCTATGTTCTTCACCCTGCT 59.438 52.381 0.00 0.00 0.00 4.24
2446 2545 4.392166 TAGCCGCCCCACTCTCCA 62.392 66.667 0.00 0.00 0.00 3.86
2484 2584 1.888512 GTGTTTGTGCTGATCCACCAT 59.111 47.619 0.38 0.00 34.85 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.456000 GCGAGAGAACATTTCGGCA 58.544 52.632 0.00 0.00 35.05 5.69
58 59 2.556189 CTGCATGCTCTACTCCGACTAT 59.444 50.000 20.33 0.00 0.00 2.12
142 143 1.586028 GGCGAGCAATGAAAAGCCA 59.414 52.632 0.00 0.00 43.65 4.75
323 324 1.373246 CGGAGGCACGGTTTAACGA 60.373 57.895 0.00 0.00 37.61 3.85
375 376 4.020617 CGGCAGCCTCTCCCACAA 62.021 66.667 10.54 0.00 0.00 3.33
504 505 3.154710 GTCAAGGTTTTCTTTCCCCGAT 58.845 45.455 0.00 0.00 32.41 4.18
511 512 5.030147 AGGGGAAAAGTCAAGGTTTTCTTT 58.970 37.500 7.92 0.00 41.63 2.52
577 578 2.669569 GCGCTGGGAAGCAGTTGA 60.670 61.111 0.00 0.00 34.41 3.18
641 642 2.921754 CTCTTAAGACGCCGAAAATCGT 59.078 45.455 0.00 0.00 38.40 3.73
713 714 2.971997 GCTGCATGCATCCAACATG 58.028 52.632 22.97 7.95 46.19 3.21
739 740 0.388649 CCTTCACGGTCGAACAGAGG 60.389 60.000 0.00 0.00 0.00 3.69
740 741 0.596577 TCCTTCACGGTCGAACAGAG 59.403 55.000 0.00 0.00 0.00 3.35
741 742 0.596577 CTCCTTCACGGTCGAACAGA 59.403 55.000 0.00 0.00 0.00 3.41
742 743 0.596577 TCTCCTTCACGGTCGAACAG 59.403 55.000 0.00 0.00 0.00 3.16
765 768 2.513897 GTGGTATGTCGGCAGGCC 60.514 66.667 0.00 0.00 0.00 5.19
818 821 6.983890 GGAGATCTCAGATGGTAAGAGAAAAC 59.016 42.308 23.85 0.00 41.30 2.43
870 874 1.909302 TGAGAGTGGAAATGAGGGTCC 59.091 52.381 0.00 0.00 0.00 4.46
988 993 3.134127 GGCCATTGGTCGCAGGAC 61.134 66.667 4.26 0.00 42.66 3.85
994 999 2.438434 GGTGGAGGCCATTGGTCG 60.438 66.667 5.01 0.00 35.28 4.79
1245 1253 4.803426 CTGCCACTCTCCCGCGAC 62.803 72.222 8.23 0.00 0.00 5.19
1268 1276 3.284449 ACTTTGCGTTGGTCGGGC 61.284 61.111 0.00 0.00 40.26 6.13
1272 1280 1.008538 CTGGCACTTTGCGTTGGTC 60.009 57.895 0.00 0.00 46.21 4.02
1368 1376 3.617538 GCCGTCTGTATCGCGCAC 61.618 66.667 8.75 1.84 0.00 5.34
1430 1438 1.302192 TTAACGCAGGACAGGCACC 60.302 57.895 0.00 0.00 0.00 5.01
1475 1483 2.469516 CCGCCACAACTAATCGGGC 61.470 63.158 0.00 0.00 41.20 6.13
1482 1490 2.463589 CTTGGAGCCCGCCACAACTA 62.464 60.000 0.00 0.00 37.75 2.24
1512 1520 1.376424 CTTCTGGTGCGTGCATCCT 60.376 57.895 2.12 0.00 0.00 3.24
1519 1527 1.374758 GCTACTGCTTCTGGTGCGT 60.375 57.895 0.00 0.00 36.03 5.24
1585 1605 1.859302 AACCAACAAAGGGAAGTGCA 58.141 45.000 0.00 0.00 0.00 4.57
1616 1637 1.441515 AACGATGACCGACACGACG 60.442 57.895 0.00 0.00 41.76 5.12
1656 1680 3.817084 ACATGACAAGTGTGATGACAAGG 59.183 43.478 16.34 0.00 41.24 3.61
1657 1681 4.376717 CGACATGACAAGTGTGATGACAAG 60.377 45.833 16.34 2.74 41.24 3.16
1658 1682 3.494251 CGACATGACAAGTGTGATGACAA 59.506 43.478 16.34 0.00 41.24 3.18
1659 1683 3.059166 CGACATGACAAGTGTGATGACA 58.941 45.455 16.34 0.00 41.24 3.58
1660 1684 2.413112 CCGACATGACAAGTGTGATGAC 59.587 50.000 16.34 9.91 41.24 3.06
1661 1685 2.037121 ACCGACATGACAAGTGTGATGA 59.963 45.455 16.34 0.00 41.24 2.92
1662 1686 2.413112 GACCGACATGACAAGTGTGATG 59.587 50.000 9.03 9.03 43.71 3.07
1663 1687 2.688507 GACCGACATGACAAGTGTGAT 58.311 47.619 0.00 0.00 0.00 3.06
1664 1688 1.601914 CGACCGACATGACAAGTGTGA 60.602 52.381 0.00 0.00 0.00 3.58
1665 1689 0.784178 CGACCGACATGACAAGTGTG 59.216 55.000 0.00 0.00 0.00 3.82
1666 1690 0.387929 ACGACCGACATGACAAGTGT 59.612 50.000 0.00 0.00 0.00 3.55
1667 1691 0.784178 CACGACCGACATGACAAGTG 59.216 55.000 0.00 0.00 0.00 3.16
1668 1692 0.319555 CCACGACCGACATGACAAGT 60.320 55.000 0.00 0.00 0.00 3.16
1669 1693 0.319555 ACCACGACCGACATGACAAG 60.320 55.000 0.00 0.00 0.00 3.16
1670 1694 0.105224 AACCACGACCGACATGACAA 59.895 50.000 0.00 0.00 0.00 3.18
1671 1695 0.598942 CAACCACGACCGACATGACA 60.599 55.000 0.00 0.00 0.00 3.58
1672 1696 0.599204 ACAACCACGACCGACATGAC 60.599 55.000 0.00 0.00 0.00 3.06
1673 1697 0.105224 AACAACCACGACCGACATGA 59.895 50.000 0.00 0.00 0.00 3.07
1674 1698 0.234625 CAACAACCACGACCGACATG 59.765 55.000 0.00 0.00 0.00 3.21
1675 1699 0.179067 ACAACAACCACGACCGACAT 60.179 50.000 0.00 0.00 0.00 3.06
1676 1700 0.391395 AACAACAACCACGACCGACA 60.391 50.000 0.00 0.00 0.00 4.35
1677 1701 1.523934 CTAACAACAACCACGACCGAC 59.476 52.381 0.00 0.00 0.00 4.79
1678 1702 1.408340 TCTAACAACAACCACGACCGA 59.592 47.619 0.00 0.00 0.00 4.69
1679 1703 1.855513 TCTAACAACAACCACGACCG 58.144 50.000 0.00 0.00 0.00 4.79
1680 1704 4.273969 TGAAATCTAACAACAACCACGACC 59.726 41.667 0.00 0.00 0.00 4.79
1681 1705 5.412526 TGAAATCTAACAACAACCACGAC 57.587 39.130 0.00 0.00 0.00 4.34
1682 1706 6.236017 GATGAAATCTAACAACAACCACGA 57.764 37.500 0.00 0.00 41.17 4.35
1696 1720 8.328517 GTGTGATGACAAGCCTAGATGAAATCT 61.329 40.741 0.00 0.00 45.32 2.40
1697 1721 5.819379 TGTGATGACAAGCCTAGATGAAATC 59.181 40.000 0.00 0.00 46.04 2.17
1698 1722 5.587844 GTGTGATGACAAGCCTAGATGAAAT 59.412 40.000 0.00 0.00 32.49 2.17
1699 1723 4.937620 GTGTGATGACAAGCCTAGATGAAA 59.062 41.667 0.00 0.00 32.49 2.69
1700 1724 4.223700 AGTGTGATGACAAGCCTAGATGAA 59.776 41.667 0.00 0.00 32.49 2.57
1701 1725 3.771479 AGTGTGATGACAAGCCTAGATGA 59.229 43.478 0.00 0.00 32.49 2.92
1702 1726 4.134379 AGTGTGATGACAAGCCTAGATG 57.866 45.455 0.00 0.00 32.49 2.90
1703 1727 4.019860 ACAAGTGTGATGACAAGCCTAGAT 60.020 41.667 0.00 0.00 32.49 1.98
1704 1728 3.324846 ACAAGTGTGATGACAAGCCTAGA 59.675 43.478 0.00 0.00 32.49 2.43
1705 1729 3.668447 ACAAGTGTGATGACAAGCCTAG 58.332 45.455 0.00 0.00 32.49 3.02
1706 1730 3.070878 TGACAAGTGTGATGACAAGCCTA 59.929 43.478 0.00 0.00 32.49 3.93
1707 1731 2.158769 TGACAAGTGTGATGACAAGCCT 60.159 45.455 0.00 0.00 32.49 4.58
1708 1732 2.221169 TGACAAGTGTGATGACAAGCC 58.779 47.619 0.00 0.00 32.49 4.35
1709 1733 3.251729 ACATGACAAGTGTGATGACAAGC 59.748 43.478 16.34 0.00 41.24 4.01
1710 1734 4.376717 CGACATGACAAGTGTGATGACAAG 60.377 45.833 16.34 2.74 41.24 3.16
1711 1735 3.494251 CGACATGACAAGTGTGATGACAA 59.506 43.478 16.34 0.00 41.24 3.18
1712 1736 3.059166 CGACATGACAAGTGTGATGACA 58.941 45.455 16.34 0.00 41.24 3.58
1713 1737 2.413112 CCGACATGACAAGTGTGATGAC 59.587 50.000 16.34 9.91 41.24 3.06
1714 1738 2.037121 ACCGACATGACAAGTGTGATGA 59.963 45.455 16.34 0.00 41.24 2.92
1715 1739 2.413112 GACCGACATGACAAGTGTGATG 59.587 50.000 9.03 9.03 43.71 3.07
1716 1740 2.688507 GACCGACATGACAAGTGTGAT 58.311 47.619 0.00 0.00 0.00 3.06
1717 1741 1.601914 CGACCGACATGACAAGTGTGA 60.602 52.381 0.00 0.00 0.00 3.58
1718 1742 0.784178 CGACCGACATGACAAGTGTG 59.216 55.000 0.00 0.00 0.00 3.82
1719 1743 0.387929 ACGACCGACATGACAAGTGT 59.612 50.000 0.00 0.00 0.00 3.55
1720 1744 1.192312 CAACGACCGACATGACAAGTG 59.808 52.381 0.00 0.00 0.00 3.16
1721 1745 1.202486 ACAACGACCGACATGACAAGT 60.202 47.619 0.00 0.00 0.00 3.16
1722 1746 1.497991 ACAACGACCGACATGACAAG 58.502 50.000 0.00 0.00 0.00 3.16
1739 1763 6.544622 CCTAGACGTAAAACAAACAACAACA 58.455 36.000 0.00 0.00 0.00 3.33
1750 1774 4.377124 GCAACAGAAGCCTAGACGTAAAAC 60.377 45.833 0.00 0.00 0.00 2.43
1754 1778 1.890489 TGCAACAGAAGCCTAGACGTA 59.110 47.619 0.00 0.00 0.00 3.57
1755 1779 0.679505 TGCAACAGAAGCCTAGACGT 59.320 50.000 0.00 0.00 0.00 4.34
1808 1838 3.216237 CCCACGGGTGATCGATGA 58.784 61.111 0.54 0.00 0.00 2.92
1818 1848 4.150359 AGTACATCTTAGATACCCACGGG 58.850 47.826 0.00 0.00 42.03 5.28
1821 1851 6.715718 TCTGCTAGTACATCTTAGATACCCAC 59.284 42.308 0.00 0.00 0.00 4.61
1825 1855 6.797995 GCGTTCTGCTAGTACATCTTAGATAC 59.202 42.308 0.00 0.00 41.73 2.24
1826 1856 6.072618 GGCGTTCTGCTAGTACATCTTAGATA 60.073 42.308 0.00 0.00 45.43 1.98
1827 1857 5.278561 GGCGTTCTGCTAGTACATCTTAGAT 60.279 44.000 0.00 0.00 45.43 1.98
1828 1858 4.036498 GGCGTTCTGCTAGTACATCTTAGA 59.964 45.833 0.00 0.00 45.43 2.10
1829 1859 4.036971 AGGCGTTCTGCTAGTACATCTTAG 59.963 45.833 0.00 0.00 45.43 2.18
1830 1860 3.952323 AGGCGTTCTGCTAGTACATCTTA 59.048 43.478 0.00 0.00 45.43 2.10
1831 1861 2.761208 AGGCGTTCTGCTAGTACATCTT 59.239 45.455 0.00 0.00 45.43 2.40
1832 1862 2.099921 CAGGCGTTCTGCTAGTACATCT 59.900 50.000 0.00 0.00 45.43 2.90
1833 1863 2.464865 CAGGCGTTCTGCTAGTACATC 58.535 52.381 0.00 0.00 45.43 3.06
1889 1927 8.062065 TGAAGACAACCTTAATCACTTGTTTT 57.938 30.769 0.00 0.00 34.68 2.43
1896 1934 5.346281 CGACTCTGAAGACAACCTTAATCAC 59.654 44.000 0.00 0.00 34.68 3.06
1916 1954 3.923461 CGAGAAAGAAATGAGCTTCGACT 59.077 43.478 0.00 0.00 0.00 4.18
1934 1972 1.372004 CACGCCCAAACGTACGAGA 60.372 57.895 24.41 0.00 46.34 4.04
1938 1976 2.660612 CGGACACGCCCAAACGTAC 61.661 63.158 0.00 0.00 46.34 3.67
1972 2010 1.886542 GAATTTTGGGAGCCTGTTCGT 59.113 47.619 0.00 0.00 0.00 3.85
2027 2065 8.713971 ACAACCACATTTATCCTCTACATATGA 58.286 33.333 10.38 0.00 0.00 2.15
2041 2079 9.880157 GGTAAATAGTCTAGACAACCACATTTA 57.120 33.333 24.44 17.28 0.00 1.40
2064 2102 3.615056 CGCGTGTTTGAGATAACATGGTA 59.385 43.478 0.00 0.00 42.55 3.25
2089 2127 3.093057 CGGATGGGGTTTTTGTATTGGA 58.907 45.455 0.00 0.00 0.00 3.53
2152 2190 8.596271 TGTTTCACTATGACGAAAATCAAGTA 57.404 30.769 0.00 0.00 33.17 2.24
2326 2364 1.150536 TTGAAGGTGAGGTGGGCAC 59.849 57.895 0.00 0.00 35.56 5.01
2381 2419 0.251297 CAAAGGTGAGGTGGGCATCA 60.251 55.000 0.00 0.00 32.55 3.07
2383 2421 1.607467 GCAAAGGTGAGGTGGGCAT 60.607 57.895 0.00 0.00 0.00 4.40
2384 2422 2.203480 GCAAAGGTGAGGTGGGCA 60.203 61.111 0.00 0.00 0.00 5.36
2385 2423 2.991540 GGCAAAGGTGAGGTGGGC 60.992 66.667 0.00 0.00 0.00 5.36
2401 2439 2.301346 GAAGAACATAGGGTGCCATGG 58.699 52.381 7.63 7.63 0.00 3.66
2407 2445 2.941415 GCAGGGTGAAGAACATAGGGTG 60.941 54.545 0.00 0.00 0.00 4.61
2408 2446 1.282157 GCAGGGTGAAGAACATAGGGT 59.718 52.381 0.00 0.00 0.00 4.34
2412 2450 2.170607 GGCTAGCAGGGTGAAGAACATA 59.829 50.000 18.24 0.00 0.00 2.29
2413 2451 1.065126 GGCTAGCAGGGTGAAGAACAT 60.065 52.381 18.24 0.00 0.00 2.71
2414 2452 0.324943 GGCTAGCAGGGTGAAGAACA 59.675 55.000 18.24 0.00 0.00 3.18
2415 2453 0.741221 CGGCTAGCAGGGTGAAGAAC 60.741 60.000 18.24 0.00 0.00 3.01
2416 2454 1.596934 CGGCTAGCAGGGTGAAGAA 59.403 57.895 18.24 0.00 0.00 2.52
2417 2455 3.298958 CGGCTAGCAGGGTGAAGA 58.701 61.111 18.24 0.00 0.00 2.87
2429 2528 4.392166 TGGAGAGTGGGGCGGCTA 62.392 66.667 9.56 0.00 0.00 3.93
2439 2538 1.014804 AGAGGATCAGGGTGGAGAGT 58.985 55.000 0.00 0.00 37.82 3.24
2446 2545 1.231641 CGGGAGAGAGGATCAGGGT 59.768 63.158 0.00 0.00 37.82 4.34
2484 2584 1.459539 CTCCTCCCCCTTATGGCGA 60.460 63.158 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.