Multiple sequence alignment - TraesCS4A01G091600

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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 TraesCS4A01G091600 chr4A 100.000 2348 0 0 1 2348 98557788 98560135 0.000000e+00 4337.0
1 TraesCS4A01G091600 chr4B 91.142 779 25 11 1589 2348 451490322 451489569 0.000000e+00 1016.0
2 TraesCS4A01G091600 chr4B 89.474 760 47 16 4 740 451491976 451491227 0.000000e+00 929.0
3 TraesCS4A01G091600 chr4B 90.162 742 32 18 790 1507 451491050 451490326 0.000000e+00 928.0
4 TraesCS4A01G091600 chr4B 90.000 80 5 3 1488 1565 30370081 30370003 1.480000e-17 100.0
5 TraesCS4A01G091600 chr4B 92.754 69 3 2 1498 1565 32904998 32904931 5.340000e-17 99.0
6 TraesCS4A01G091600 chr4B 92.647 68 5 0 1498 1565 624868549 624868482 5.340000e-17 99.0
7 TraesCS4A01G091600 chr4D 89.987 779 34 20 1590 2348 366691636 366690882 0.000000e+00 966.0
8 TraesCS4A01G091600 chr4D 90.713 743 40 10 4 740 366693169 366692450 0.000000e+00 963.0
9 TraesCS4A01G091600 chr4D 87.912 637 40 21 790 1417 366692352 366691744 0.000000e+00 715.0
10 TraesCS4A01G091600 chr7D 94.030 67 4 0 1499 1565 339780287 339780221 4.130000e-18 102.0
11 TraesCS4A01G091600 chr7D 91.549 71 6 0 1495 1565 613432766 613432696 5.340000e-17 99.0
12 TraesCS4A01G091600 chr7A 94.030 67 4 0 1499 1565 78824048 78824114 4.130000e-18 102.0
13 TraesCS4A01G091600 chr3D 94.030 67 2 2 1500 1565 31774580 31774515 1.480000e-17 100.0
14 TraesCS4A01G091600 chr5A 92.647 68 5 0 1498 1565 678663651 678663584 5.340000e-17 99.0
15 TraesCS4A01G091600 chr2D 91.429 70 6 0 1496 1565 178776549 178776480 1.920000e-16 97.1


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 TraesCS4A01G091600 chr4A 98557788 98560135 2347 False 4337.000000 4337 100.000000 1 2348 1 chr4A.!!$F1 2347
1 TraesCS4A01G091600 chr4B 451489569 451491976 2407 True 957.666667 1016 90.259333 4 2348 3 chr4B.!!$R4 2344
2 TraesCS4A01G091600 chr4D 366690882 366693169 2287 True 881.333333 966 89.537333 4 2348 3 chr4D.!!$R1 2344

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
965 1136 0.04087 CAACACACCGCAATACGCAA 60.041 50.0 0.0 0.0 42.6 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1997 2266 0.326264 TCTCCCTCTTCTTTGCTGGC 59.674 55.0 0.0 0.0 0.0 4.85 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
51 52 2.105993 AGGTCTGGTCCCTGTTTTGTAC 59.894 50.000 0.00 0.00 0.00 2.90
99 100 6.405286 CCTTGTGACATACTACTCTGAAGAGG 60.405 46.154 11.87 0.00 46.13 3.69
133 141 1.004277 TGGGCCTAAGAATGAAACGCT 59.996 47.619 4.53 0.00 0.00 5.07
185 193 1.344763 GGACATATCCAACCCTCTCCG 59.655 57.143 0.00 0.00 45.47 4.63
186 194 2.040178 GACATATCCAACCCTCTCCGT 58.960 52.381 0.00 0.00 0.00 4.69
194 202 1.335132 AACCCTCTCCGTGTGTGTGT 61.335 55.000 0.00 0.00 0.00 3.72
210 218 4.079748 GTTTGTACGGTGCGGCGG 62.080 66.667 9.78 0.00 0.00 6.13
323 331 2.618816 GGACACTCCATTCCATCTTGCA 60.619 50.000 0.00 0.00 36.28 4.08
363 371 2.159572 CGGTTATGCTTGGAAGGTTTCG 60.160 50.000 0.00 0.00 0.00 3.46
369 377 2.223745 GCTTGGAAGGTTTCGGTTACA 58.776 47.619 0.00 0.00 0.00 2.41
377 385 1.597578 TTTCGGTTACACCCCGTGC 60.598 57.895 0.00 0.00 45.63 5.34
505 515 7.186804 CCACGATTCTTTTGGTATTGTGTATC 58.813 38.462 0.00 0.00 33.65 2.24
635 647 2.143876 AGTGAAAACAACAGGCACCT 57.856 45.000 0.00 0.00 0.00 4.00
637 649 1.748493 GTGAAAACAACAGGCACCTGA 59.252 47.619 23.30 0.00 46.30 3.86
639 651 3.568007 GTGAAAACAACAGGCACCTGATA 59.432 43.478 23.30 0.00 46.30 2.15
644 656 6.909550 AAACAACAGGCACCTGATATTTTA 57.090 33.333 23.30 0.00 46.30 1.52
645 657 5.897377 ACAACAGGCACCTGATATTTTAC 57.103 39.130 23.30 0.00 46.30 2.01
647 659 5.648092 ACAACAGGCACCTGATATTTTACTC 59.352 40.000 23.30 0.00 46.30 2.59
648 660 5.435686 ACAGGCACCTGATATTTTACTCA 57.564 39.130 23.30 0.00 46.30 3.41
655 667 7.010460 GGCACCTGATATTTTACTCATTTTTGC 59.990 37.037 0.00 0.00 0.00 3.68
656 668 7.010460 GCACCTGATATTTTACTCATTTTTGCC 59.990 37.037 0.00 0.00 0.00 4.52
657 669 8.253113 CACCTGATATTTTACTCATTTTTGCCT 58.747 33.333 0.00 0.00 0.00 4.75
658 670 8.815912 ACCTGATATTTTACTCATTTTTGCCTT 58.184 29.630 0.00 0.00 0.00 4.35
660 672 9.305925 CTGATATTTTACTCATTTTTGCCTTCC 57.694 33.333 0.00 0.00 0.00 3.46
661 673 8.257306 TGATATTTTACTCATTTTTGCCTTCCC 58.743 33.333 0.00 0.00 0.00 3.97
662 674 6.686484 ATTTTACTCATTTTTGCCTTCCCT 57.314 33.333 0.00 0.00 0.00 4.20
663 675 7.790782 ATTTTACTCATTTTTGCCTTCCCTA 57.209 32.000 0.00 0.00 0.00 3.53
679 705 6.520272 CCTTCCCTATGTTCTGATCAGTTAG 58.480 44.000 21.92 16.53 0.00 2.34
740 766 1.198637 GTCTGCAGCAATGTTGAGGTC 59.801 52.381 9.47 0.00 0.00 3.85
741 767 1.202794 TCTGCAGCAATGTTGAGGTCA 60.203 47.619 9.47 0.00 0.00 4.02
750 914 1.496060 TGTTGAGGTCATATCGCCCT 58.504 50.000 0.00 0.00 0.00 5.19
755 919 0.755698 AGGTCATATCGCCCTGTCGT 60.756 55.000 0.00 0.00 0.00 4.34
778 942 0.239879 CACGCCGCCTAAATTGTGTT 59.760 50.000 0.00 0.00 0.00 3.32
779 943 0.239879 ACGCCGCCTAAATTGTGTTG 59.760 50.000 0.00 0.00 0.00 3.33
780 944 0.455972 CGCCGCCTAAATTGTGTTGG 60.456 55.000 0.00 0.00 0.00 3.77
781 945 0.735978 GCCGCCTAAATTGTGTTGGC 60.736 55.000 0.00 0.00 40.14 4.52
782 946 0.108851 CCGCCTAAATTGTGTTGGCC 60.109 55.000 0.00 0.00 40.40 5.36
783 947 0.600557 CGCCTAAATTGTGTTGGCCA 59.399 50.000 0.00 0.00 40.40 5.36
784 948 1.000283 CGCCTAAATTGTGTTGGCCAA 60.000 47.619 16.05 16.05 40.40 4.52
785 949 2.546795 CGCCTAAATTGTGTTGGCCAAA 60.547 45.455 22.47 4.55 40.40 3.28
786 950 3.066380 GCCTAAATTGTGTTGGCCAAAG 58.934 45.455 22.47 11.24 37.81 2.77
787 951 3.066380 CCTAAATTGTGTTGGCCAAAGC 58.934 45.455 22.47 16.32 38.76 3.51
788 952 2.706339 AAATTGTGTTGGCCAAAGCA 57.294 40.000 22.47 18.86 42.56 3.91
826 990 2.945080 ATGCATCAGATTCACCGGAT 57.055 45.000 9.46 0.00 0.00 4.18
874 1038 0.447801 AAAATAGGCAGCGCAAGTCG 59.552 50.000 11.47 0.00 42.12 4.18
910 1081 1.133761 GCCTCCTTATCTTGAACCCCC 60.134 57.143 0.00 0.00 0.00 5.40
911 1082 2.205342 CCTCCTTATCTTGAACCCCCA 58.795 52.381 0.00 0.00 0.00 4.96
912 1083 2.092375 CCTCCTTATCTTGAACCCCCAC 60.092 54.545 0.00 0.00 0.00 4.61
913 1084 2.576191 CTCCTTATCTTGAACCCCCACA 59.424 50.000 0.00 0.00 0.00 4.17
914 1085 2.576191 TCCTTATCTTGAACCCCCACAG 59.424 50.000 0.00 0.00 0.00 3.66
915 1086 2.576191 CCTTATCTTGAACCCCCACAGA 59.424 50.000 0.00 0.00 0.00 3.41
916 1087 3.370953 CCTTATCTTGAACCCCCACAGAG 60.371 52.174 0.00 0.00 0.00 3.35
919 1090 2.131854 TCTTGAACCCCCACAGAGAAA 58.868 47.619 0.00 0.00 0.00 2.52
920 1091 2.106511 TCTTGAACCCCCACAGAGAAAG 59.893 50.000 0.00 0.00 0.00 2.62
921 1092 0.110486 TGAACCCCCACAGAGAAAGC 59.890 55.000 0.00 0.00 0.00 3.51
922 1093 0.110486 GAACCCCCACAGAGAAAGCA 59.890 55.000 0.00 0.00 0.00 3.91
930 1101 3.452627 CCCACAGAGAAAGCAGTAGGTAT 59.547 47.826 0.00 0.00 0.00 2.73
943 1114 4.758674 GCAGTAGGTATACGGACACATCTA 59.241 45.833 8.11 0.00 36.97 1.98
953 1124 2.076863 GGACACATCTAGCCAACACAC 58.923 52.381 0.00 0.00 0.00 3.82
960 1131 1.276705 TCTAGCCAACACACCGCAATA 59.723 47.619 0.00 0.00 0.00 1.90
962 1133 1.154301 GCCAACACACCGCAATACG 60.154 57.895 0.00 0.00 43.15 3.06
963 1134 1.154301 CCAACACACCGCAATACGC 60.154 57.895 0.00 0.00 41.76 4.42
964 1135 1.571953 CAACACACCGCAATACGCA 59.428 52.632 0.00 0.00 42.60 5.24
965 1136 0.040870 CAACACACCGCAATACGCAA 60.041 50.000 0.00 0.00 42.60 4.85
966 1137 0.237235 AACACACCGCAATACGCAAG 59.763 50.000 0.00 0.00 42.60 4.01
967 1138 1.511887 CACACCGCAATACGCAAGC 60.512 57.895 0.00 0.00 42.60 4.01
968 1139 1.963855 ACACCGCAATACGCAAGCA 60.964 52.632 0.00 0.00 42.60 3.91
973 1144 1.212490 GCAATACGCAAGCAGGCAA 59.788 52.632 0.50 0.00 45.62 4.52
1401 1607 0.179156 CCGTGCCAGCATCAATCAAC 60.179 55.000 0.00 0.00 0.00 3.18
1409 1619 4.807304 GCCAGCATCAATCAACCAATAAAG 59.193 41.667 0.00 0.00 0.00 1.85
1433 1667 2.633657 CGCACTTGCAGGTGTGTC 59.366 61.111 28.61 13.35 41.22 3.67
1437 1671 1.069765 ACTTGCAGGTGTGTCGGAG 59.930 57.895 0.00 0.00 0.00 4.63
1438 1672 2.280797 TTGCAGGTGTGTCGGAGC 60.281 61.111 0.00 0.00 0.00 4.70
1441 1675 1.672356 GCAGGTGTGTCGGAGCATT 60.672 57.895 0.00 0.00 0.00 3.56
1496 1743 3.858040 CGCATTTCTCTACGCACAC 57.142 52.632 0.00 0.00 0.00 3.82
1507 1754 6.939551 TCTCTACGCACACAAAAATACTAC 57.060 37.500 0.00 0.00 0.00 2.73
1509 1756 6.805271 TCTCTACGCACACAAAAATACTACTC 59.195 38.462 0.00 0.00 0.00 2.59
1510 1757 5.865552 TCTACGCACACAAAAATACTACTCC 59.134 40.000 0.00 0.00 0.00 3.85
1511 1758 3.749609 ACGCACACAAAAATACTACTCCC 59.250 43.478 0.00 0.00 0.00 4.30
1512 1759 4.000988 CGCACACAAAAATACTACTCCCT 58.999 43.478 0.00 0.00 0.00 4.20
1513 1760 4.092968 CGCACACAAAAATACTACTCCCTC 59.907 45.833 0.00 0.00 0.00 4.30
1514 1761 4.395231 GCACACAAAAATACTACTCCCTCC 59.605 45.833 0.00 0.00 0.00 4.30
1515 1762 5.803470 GCACACAAAAATACTACTCCCTCCT 60.803 44.000 0.00 0.00 0.00 3.69
1516 1763 6.238648 CACACAAAAATACTACTCCCTCCTT 58.761 40.000 0.00 0.00 0.00 3.36
1517 1764 6.715264 CACACAAAAATACTACTCCCTCCTTT 59.285 38.462 0.00 0.00 0.00 3.11
1518 1765 6.940867 ACACAAAAATACTACTCCCTCCTTTC 59.059 38.462 0.00 0.00 0.00 2.62
1519 1766 6.374613 CACAAAAATACTACTCCCTCCTTTCC 59.625 42.308 0.00 0.00 0.00 3.13
1520 1767 6.045106 ACAAAAATACTACTCCCTCCTTTCCA 59.955 38.462 0.00 0.00 0.00 3.53
1521 1768 6.713731 AAAATACTACTCCCTCCTTTCCAA 57.286 37.500 0.00 0.00 0.00 3.53
1522 1769 6.713731 AAATACTACTCCCTCCTTTCCAAA 57.286 37.500 0.00 0.00 0.00 3.28
1523 1770 6.713731 AATACTACTCCCTCCTTTCCAAAA 57.286 37.500 0.00 0.00 0.00 2.44
1524 1771 6.910259 ATACTACTCCCTCCTTTCCAAAAT 57.090 37.500 0.00 0.00 0.00 1.82
1525 1772 8.401955 AATACTACTCCCTCCTTTCCAAAATA 57.598 34.615 0.00 0.00 0.00 1.40
1526 1773 6.910259 ACTACTCCCTCCTTTCCAAAATAT 57.090 37.500 0.00 0.00 0.00 1.28
1527 1774 9.684702 ATACTACTCCCTCCTTTCCAAAATATA 57.315 33.333 0.00 0.00 0.00 0.86
1528 1775 8.401955 ACTACTCCCTCCTTTCCAAAATATAA 57.598 34.615 0.00 0.00 0.00 0.98
1529 1776 8.495260 ACTACTCCCTCCTTTCCAAAATATAAG 58.505 37.037 0.00 0.00 0.00 1.73
1530 1777 7.525158 ACTCCCTCCTTTCCAAAATATAAGA 57.475 36.000 0.00 0.00 0.00 2.10
1531 1778 7.939781 ACTCCCTCCTTTCCAAAATATAAGAA 58.060 34.615 0.00 0.00 0.00 2.52
1532 1779 7.834681 ACTCCCTCCTTTCCAAAATATAAGAAC 59.165 37.037 0.00 0.00 0.00 3.01
1533 1780 6.826741 TCCCTCCTTTCCAAAATATAAGAACG 59.173 38.462 0.00 0.00 0.00 3.95
1534 1781 6.602009 CCCTCCTTTCCAAAATATAAGAACGT 59.398 38.462 0.00 0.00 0.00 3.99
1535 1782 7.122204 CCCTCCTTTCCAAAATATAAGAACGTT 59.878 37.037 0.00 0.00 0.00 3.99
1536 1783 8.520351 CCTCCTTTCCAAAATATAAGAACGTTT 58.480 33.333 0.46 0.00 0.00 3.60
1537 1784 9.908152 CTCCTTTCCAAAATATAAGAACGTTTT 57.092 29.630 0.46 0.00 0.00 2.43
1566 1813 7.311364 ACTACATTAGTGTCAAAAACGTTGT 57.689 32.000 0.00 0.00 39.77 3.32
1567 1814 7.184106 ACTACATTAGTGTCAAAAACGTTGTG 58.816 34.615 0.00 3.48 39.77 3.33
1568 1815 5.336744 ACATTAGTGTCAAAAACGTTGTGG 58.663 37.500 0.00 0.00 31.41 4.17
1569 1816 2.931512 AGTGTCAAAAACGTTGTGGG 57.068 45.000 0.00 0.00 0.00 4.61
1570 1817 2.438411 AGTGTCAAAAACGTTGTGGGA 58.562 42.857 0.00 0.00 0.00 4.37
1571 1818 2.162809 AGTGTCAAAAACGTTGTGGGAC 59.837 45.455 13.81 13.81 0.00 4.46
1572 1819 2.095161 GTGTCAAAAACGTTGTGGGACA 60.095 45.455 17.64 17.64 0.00 4.02
1573 1820 2.162608 TGTCAAAAACGTTGTGGGACAG 59.837 45.455 17.64 0.00 41.80 3.51
1574 1821 2.420722 GTCAAAAACGTTGTGGGACAGA 59.579 45.455 15.17 0.00 41.80 3.41
1575 1822 2.680841 TCAAAAACGTTGTGGGACAGAG 59.319 45.455 0.00 0.00 41.80 3.35
1576 1823 1.675552 AAAACGTTGTGGGACAGAGG 58.324 50.000 0.00 0.00 41.80 3.69
1577 1824 0.544697 AAACGTTGTGGGACAGAGGT 59.455 50.000 0.00 0.00 41.80 3.85
1578 1825 1.416243 AACGTTGTGGGACAGAGGTA 58.584 50.000 0.00 0.00 41.80 3.08
1579 1826 0.966920 ACGTTGTGGGACAGAGGTAG 59.033 55.000 0.00 0.00 41.80 3.18
1580 1827 0.966920 CGTTGTGGGACAGAGGTAGT 59.033 55.000 0.00 0.00 41.80 2.73
1581 1828 2.165167 CGTTGTGGGACAGAGGTAGTA 58.835 52.381 0.00 0.00 41.80 1.82
1582 1829 2.163815 CGTTGTGGGACAGAGGTAGTAG 59.836 54.545 0.00 0.00 41.80 2.57
1583 1830 3.163467 GTTGTGGGACAGAGGTAGTAGT 58.837 50.000 0.00 0.00 41.80 2.73
1584 1831 4.338879 GTTGTGGGACAGAGGTAGTAGTA 58.661 47.826 0.00 0.00 41.80 1.82
1585 1832 4.232188 TGTGGGACAGAGGTAGTAGTAG 57.768 50.000 0.00 0.00 41.80 2.57
1586 1833 3.590630 TGTGGGACAGAGGTAGTAGTAGT 59.409 47.826 0.00 0.00 41.80 2.73
1587 1834 4.043812 TGTGGGACAGAGGTAGTAGTAGTT 59.956 45.833 0.00 0.00 41.80 2.24
1620 1867 4.631813 GTCTTTGCCTCTCGTGAATTATGT 59.368 41.667 0.00 0.00 0.00 2.29
1629 1876 6.019479 CCTCTCGTGAATTATGTTTGCTCTAC 60.019 42.308 0.00 0.00 0.00 2.59
1630 1877 6.631016 TCTCGTGAATTATGTTTGCTCTACT 58.369 36.000 0.00 0.00 0.00 2.57
1631 1878 6.752351 TCTCGTGAATTATGTTTGCTCTACTC 59.248 38.462 0.00 0.00 0.00 2.59
1632 1879 6.631016 TCGTGAATTATGTTTGCTCTACTCT 58.369 36.000 0.00 0.00 0.00 3.24
1633 1880 7.768240 TCGTGAATTATGTTTGCTCTACTCTA 58.232 34.615 0.00 0.00 0.00 2.43
1675 1937 0.035439 ATGGGGGCAGTTCTAACACG 60.035 55.000 0.00 0.00 0.00 4.49
1698 1960 7.492669 CACGAACTGGACATACTTCTGATTTAT 59.507 37.037 0.00 0.00 0.00 1.40
1706 1968 8.131731 GGACATACTTCTGATTTATTTTCCTGC 58.868 37.037 0.00 0.00 0.00 4.85
1786 2050 7.033530 AGTAGATAGAACCTCACAAGAATCG 57.966 40.000 0.00 0.00 0.00 3.34
1796 2060 5.240623 ACCTCACAAGAATCGCAATAACAAA 59.759 36.000 0.00 0.00 0.00 2.83
1797 2061 6.071952 ACCTCACAAGAATCGCAATAACAAAT 60.072 34.615 0.00 0.00 0.00 2.32
1798 2062 6.252015 CCTCACAAGAATCGCAATAACAAATG 59.748 38.462 0.00 0.00 0.00 2.32
1799 2063 6.092092 TCACAAGAATCGCAATAACAAATGG 58.908 36.000 0.00 0.00 0.00 3.16
1800 2064 4.864247 ACAAGAATCGCAATAACAAATGGC 59.136 37.500 0.00 0.00 0.00 4.40
1801 2065 4.717233 AGAATCGCAATAACAAATGGCA 57.283 36.364 0.00 0.00 0.00 4.92
1802 2066 4.675510 AGAATCGCAATAACAAATGGCAG 58.324 39.130 0.00 0.00 0.00 4.85
1803 2067 4.398988 AGAATCGCAATAACAAATGGCAGA 59.601 37.500 0.00 0.00 0.00 4.26
1804 2068 4.924305 ATCGCAATAACAAATGGCAGAT 57.076 36.364 0.00 0.00 0.00 2.90
1870 2134 1.565305 GAGGTCACACGCATCTGATC 58.435 55.000 0.00 0.00 0.00 2.92
1871 2135 0.897621 AGGTCACACGCATCTGATCA 59.102 50.000 0.00 0.00 0.00 2.92
1872 2136 1.483827 AGGTCACACGCATCTGATCAT 59.516 47.619 0.00 0.00 0.00 2.45
1884 2153 4.700700 CATCTGATCATGTTGGCTGTAGA 58.299 43.478 0.00 0.00 0.00 2.59
1885 2154 4.397481 TCTGATCATGTTGGCTGTAGAG 57.603 45.455 0.00 0.00 0.00 2.43
1962 2231 2.805671 TGATACACCTGAAACAAGCACG 59.194 45.455 0.00 0.00 0.00 5.34
1997 2266 2.223203 GCCGATGAGAACTGCAGAAATG 60.223 50.000 23.35 0.00 0.00 2.32
1998 2267 2.223203 CCGATGAGAACTGCAGAAATGC 60.223 50.000 23.35 6.08 0.00 3.56
1999 2268 2.223203 CGATGAGAACTGCAGAAATGCC 60.223 50.000 23.35 4.76 0.00 4.40
2000 2269 2.275134 TGAGAACTGCAGAAATGCCA 57.725 45.000 23.35 7.41 0.00 4.92
2001 2270 2.156917 TGAGAACTGCAGAAATGCCAG 58.843 47.619 23.35 0.00 0.00 4.85
2002 2271 0.886563 AGAACTGCAGAAATGCCAGC 59.113 50.000 23.35 0.00 0.00 4.85
2003 2272 0.599558 GAACTGCAGAAATGCCAGCA 59.400 50.000 23.35 0.00 35.43 4.41
2004 2273 1.000060 GAACTGCAGAAATGCCAGCAA 60.000 47.619 23.35 0.00 36.44 3.91
2019 2288 2.093553 CCAGCAAAGAAGAGGGAGAGAG 60.094 54.545 0.00 0.00 0.00 3.20
2048 2317 0.402887 TCTGTCCTCCTACCGTGTCA 59.597 55.000 0.00 0.00 0.00 3.58
2238 2507 7.446625 AGCGGCTCATATAATTCAGAGAAAAAT 59.553 33.333 0.00 0.00 0.00 1.82
2248 2529 5.954296 TTCAGAGAAAAATTGCAGAGGAG 57.046 39.130 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.905357 CATCCCTTCCTGGTCTCGTT 59.095 55.000 0.00 0.00 0.00 3.85
1 2 0.978146 CCATCCCTTCCTGGTCTCGT 60.978 60.000 0.00 0.00 0.00 4.18
2 3 1.690219 CCCATCCCTTCCTGGTCTCG 61.690 65.000 0.00 0.00 0.00 4.04
51 52 1.520174 CATTGCTATCACGAGCTCACG 59.480 52.381 15.40 3.56 43.27 4.35
99 100 2.649129 GCCCATTTGCTCCACCCAC 61.649 63.158 0.00 0.00 0.00 4.61
133 141 3.820467 CAGGACAGCATCAAAACTAACCA 59.180 43.478 0.00 0.00 0.00 3.67
183 191 0.302288 CCGTACAAACACACACACGG 59.698 55.000 0.00 0.00 42.41 4.94
184 192 1.000884 ACCGTACAAACACACACACG 58.999 50.000 0.00 0.00 0.00 4.49
185 193 1.530236 GCACCGTACAAACACACACAC 60.530 52.381 0.00 0.00 0.00 3.82
186 194 0.727970 GCACCGTACAAACACACACA 59.272 50.000 0.00 0.00 0.00 3.72
194 202 2.504163 ATACCGCCGCACCGTACAAA 62.504 55.000 0.00 0.00 0.00 2.83
210 218 3.187227 CACACAGAGACCAGCAACAATAC 59.813 47.826 0.00 0.00 0.00 1.89
337 345 0.322997 TTCCAAGCATAACCGGTGGG 60.323 55.000 8.52 1.11 40.11 4.61
369 377 3.175710 AAGAACTGGGCACGGGGT 61.176 61.111 0.00 0.00 0.00 4.95
377 385 0.745845 CAGCCGATGGAAGAACTGGG 60.746 60.000 0.00 0.00 0.00 4.45
505 515 2.749776 TCACACAGTTCACACCATACG 58.250 47.619 0.00 0.00 0.00 3.06
623 635 5.570320 AGTAAAATATCAGGTGCCTGTTGT 58.430 37.500 16.85 5.56 43.96 3.32
635 647 8.257306 GGGAAGGCAAAAATGAGTAAAATATCA 58.743 33.333 0.00 0.00 0.00 2.15
637 649 8.379428 AGGGAAGGCAAAAATGAGTAAAATAT 57.621 30.769 0.00 0.00 0.00 1.28
639 651 6.686484 AGGGAAGGCAAAAATGAGTAAAAT 57.314 33.333 0.00 0.00 0.00 1.82
644 656 4.677182 ACATAGGGAAGGCAAAAATGAGT 58.323 39.130 0.00 0.00 0.00 3.41
645 657 5.420104 AGAACATAGGGAAGGCAAAAATGAG 59.580 40.000 0.00 0.00 0.00 2.90
647 659 5.185635 TCAGAACATAGGGAAGGCAAAAATG 59.814 40.000 0.00 0.00 0.00 2.32
648 660 5.332743 TCAGAACATAGGGAAGGCAAAAAT 58.667 37.500 0.00 0.00 0.00 1.82
655 667 5.365021 AACTGATCAGAACATAGGGAAGG 57.635 43.478 29.27 0.00 0.00 3.46
656 668 7.118496 ACTAACTGATCAGAACATAGGGAAG 57.882 40.000 29.27 11.69 0.00 3.46
657 669 7.038302 ACAACTAACTGATCAGAACATAGGGAA 60.038 37.037 29.27 1.35 0.00 3.97
658 670 6.440647 ACAACTAACTGATCAGAACATAGGGA 59.559 38.462 29.27 2.58 0.00 4.20
660 672 7.065085 CCAACAACTAACTGATCAGAACATAGG 59.935 40.741 29.27 14.17 0.00 2.57
661 673 7.413438 GCCAACAACTAACTGATCAGAACATAG 60.413 40.741 29.27 22.68 0.00 2.23
662 674 6.371548 GCCAACAACTAACTGATCAGAACATA 59.628 38.462 29.27 14.07 0.00 2.29
663 675 5.182001 GCCAACAACTAACTGATCAGAACAT 59.818 40.000 29.27 13.71 0.00 2.71
679 705 3.059166 CAGCCAAACTATTGCCAACAAC 58.941 45.455 0.00 0.00 38.99 3.32
740 766 1.209128 GAACACGACAGGGCGATATG 58.791 55.000 0.00 0.00 34.83 1.78
741 767 0.821517 TGAACACGACAGGGCGATAT 59.178 50.000 0.00 0.00 34.83 1.63
755 919 0.519519 CAATTTAGGCGGCGTGAACA 59.480 50.000 9.37 0.00 0.00 3.18
778 942 1.186267 TGATGCACATGCTTTGGCCA 61.186 50.000 0.00 0.00 42.66 5.36
779 943 0.459585 CTGATGCACATGCTTTGGCC 60.460 55.000 5.31 0.00 42.66 5.36
780 944 0.528924 TCTGATGCACATGCTTTGGC 59.471 50.000 5.31 0.00 42.66 4.52
781 945 1.135199 GGTCTGATGCACATGCTTTGG 60.135 52.381 5.31 0.00 42.66 3.28
782 946 1.466866 CGGTCTGATGCACATGCTTTG 60.467 52.381 5.31 0.00 42.66 2.77
783 947 0.806868 CGGTCTGATGCACATGCTTT 59.193 50.000 5.31 0.00 42.66 3.51
784 948 0.036105 TCGGTCTGATGCACATGCTT 60.036 50.000 5.31 0.00 42.66 3.91
785 949 0.742281 GTCGGTCTGATGCACATGCT 60.742 55.000 5.31 0.00 42.66 3.79
786 950 1.020861 TGTCGGTCTGATGCACATGC 61.021 55.000 0.00 0.00 42.50 4.06
787 951 1.441738 TTGTCGGTCTGATGCACATG 58.558 50.000 0.00 0.00 0.00 3.21
788 952 2.183478 TTTGTCGGTCTGATGCACAT 57.817 45.000 0.00 0.00 0.00 3.21
874 1038 2.820037 GCTGGCTAGCGACCAACC 60.820 66.667 6.22 0.00 40.67 3.77
910 1081 5.274718 CGTATACCTACTGCTTTCTCTGTG 58.725 45.833 0.00 0.00 0.00 3.66
911 1082 4.338682 CCGTATACCTACTGCTTTCTCTGT 59.661 45.833 0.00 0.00 0.00 3.41
912 1083 4.579340 TCCGTATACCTACTGCTTTCTCTG 59.421 45.833 0.00 0.00 0.00 3.35
913 1084 4.579753 GTCCGTATACCTACTGCTTTCTCT 59.420 45.833 0.00 0.00 0.00 3.10
914 1085 4.337555 TGTCCGTATACCTACTGCTTTCTC 59.662 45.833 0.00 0.00 0.00 2.87
915 1086 4.097589 GTGTCCGTATACCTACTGCTTTCT 59.902 45.833 0.00 0.00 0.00 2.52
916 1087 4.142315 TGTGTCCGTATACCTACTGCTTTC 60.142 45.833 0.00 0.00 0.00 2.62
919 1090 3.008835 TGTGTCCGTATACCTACTGCT 57.991 47.619 0.00 0.00 0.00 4.24
920 1091 3.568853 AGATGTGTCCGTATACCTACTGC 59.431 47.826 0.00 0.00 0.00 4.40
921 1092 5.106634 GCTAGATGTGTCCGTATACCTACTG 60.107 48.000 0.00 0.00 0.00 2.74
922 1093 5.002516 GCTAGATGTGTCCGTATACCTACT 58.997 45.833 0.00 0.00 0.00 2.57
930 1101 2.094390 GTGTTGGCTAGATGTGTCCGTA 60.094 50.000 0.00 0.00 0.00 4.02
943 1114 1.573829 CGTATTGCGGTGTGTTGGCT 61.574 55.000 0.00 0.00 36.85 4.75
960 1131 2.412937 GTTGTTGCCTGCTTGCGT 59.587 55.556 0.00 0.00 0.00 5.24
962 1133 2.355009 CGGTTGTTGCCTGCTTGC 60.355 61.111 0.00 0.00 0.00 4.01
963 1134 2.355009 GCGGTTGTTGCCTGCTTG 60.355 61.111 0.00 0.00 0.00 4.01
964 1135 2.832661 TGCGGTTGTTGCCTGCTT 60.833 55.556 0.00 0.00 0.00 3.91
965 1136 3.289834 CTGCGGTTGTTGCCTGCT 61.290 61.111 0.00 0.00 0.00 4.24
967 1138 4.347453 GGCTGCGGTTGTTGCCTG 62.347 66.667 0.00 0.00 41.92 4.85
986 1157 0.527565 CCCCATCTTCGGTTTGCTTG 59.472 55.000 0.00 0.00 0.00 4.01
995 1166 1.471676 CGAACTCCTTCCCCATCTTCG 60.472 57.143 0.00 0.00 0.00 3.79
1164 1361 3.770040 ATGCCGTAGCCGAGCACA 61.770 61.111 0.00 0.00 38.69 4.57
1233 1430 1.911766 GAAGGACCAGACGGGGTGA 60.912 63.158 0.08 0.00 42.53 4.02
1390 1596 6.418819 CGGAATCTTTATTGGTTGATTGATGC 59.581 38.462 0.00 0.00 30.41 3.91
1401 1607 1.670811 AGTGCGCGGAATCTTTATTGG 59.329 47.619 8.83 0.00 0.00 3.16
1409 1619 2.099062 CTGCAAGTGCGCGGAATC 59.901 61.111 8.83 0.00 45.83 2.52
1433 1667 2.093973 ACCTCAGTAGACAAATGCTCCG 60.094 50.000 0.00 0.00 0.00 4.63
1437 1671 3.686726 CAGGAACCTCAGTAGACAAATGC 59.313 47.826 0.00 0.00 0.00 3.56
1438 1672 4.256920 CCAGGAACCTCAGTAGACAAATG 58.743 47.826 0.00 0.00 0.00 2.32
1441 1675 2.632996 CACCAGGAACCTCAGTAGACAA 59.367 50.000 0.00 0.00 0.00 3.18
1496 1743 6.481643 TGGAAAGGAGGGAGTAGTATTTTTG 58.518 40.000 0.00 0.00 0.00 2.44
1507 1754 7.012421 CGTTCTTATATTTTGGAAAGGAGGGAG 59.988 40.741 0.00 0.00 0.00 4.30
1509 1756 6.602009 ACGTTCTTATATTTTGGAAAGGAGGG 59.398 38.462 0.00 0.00 0.00 4.30
1510 1757 7.625828 ACGTTCTTATATTTTGGAAAGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
1511 1758 9.908152 AAAACGTTCTTATATTTTGGAAAGGAG 57.092 29.630 0.00 0.00 0.00 3.69
1542 1789 7.184106 CACAACGTTTTTGACACTAATGTAGT 58.816 34.615 0.00 0.00 39.95 2.73
1543 1790 6.631238 CCACAACGTTTTTGACACTAATGTAG 59.369 38.462 0.00 0.00 39.95 2.74
1544 1791 6.458478 CCCACAACGTTTTTGACACTAATGTA 60.458 38.462 0.00 0.00 39.95 2.29
1545 1792 5.336744 CCACAACGTTTTTGACACTAATGT 58.663 37.500 0.00 0.00 43.71 2.71
1546 1793 4.737765 CCCACAACGTTTTTGACACTAATG 59.262 41.667 0.00 0.00 0.00 1.90
1547 1794 4.641094 TCCCACAACGTTTTTGACACTAAT 59.359 37.500 0.00 0.00 0.00 1.73
1548 1795 4.008330 TCCCACAACGTTTTTGACACTAA 58.992 39.130 0.00 0.00 0.00 2.24
1549 1796 3.374678 GTCCCACAACGTTTTTGACACTA 59.625 43.478 0.00 0.00 0.00 2.74
1550 1797 2.162809 GTCCCACAACGTTTTTGACACT 59.837 45.455 0.00 0.00 0.00 3.55
1551 1798 2.095161 TGTCCCACAACGTTTTTGACAC 60.095 45.455 12.89 7.74 0.00 3.67
1552 1799 2.160205 TGTCCCACAACGTTTTTGACA 58.840 42.857 12.89 12.89 0.00 3.58
1553 1800 2.420722 TCTGTCCCACAACGTTTTTGAC 59.579 45.455 0.00 4.12 0.00 3.18
1554 1801 2.680841 CTCTGTCCCACAACGTTTTTGA 59.319 45.455 0.00 0.00 0.00 2.69
1555 1802 2.223479 CCTCTGTCCCACAACGTTTTTG 60.223 50.000 0.00 0.00 0.00 2.44
1556 1803 2.021457 CCTCTGTCCCACAACGTTTTT 58.979 47.619 0.00 0.00 0.00 1.94
1557 1804 1.064979 ACCTCTGTCCCACAACGTTTT 60.065 47.619 0.00 0.00 0.00 2.43
1558 1805 0.544697 ACCTCTGTCCCACAACGTTT 59.455 50.000 0.00 0.00 0.00 3.60
1559 1806 1.343465 CTACCTCTGTCCCACAACGTT 59.657 52.381 0.00 0.00 0.00 3.99
1560 1807 0.966920 CTACCTCTGTCCCACAACGT 59.033 55.000 0.00 0.00 0.00 3.99
1561 1808 0.966920 ACTACCTCTGTCCCACAACG 59.033 55.000 0.00 0.00 0.00 4.10
1562 1809 3.163467 ACTACTACCTCTGTCCCACAAC 58.837 50.000 0.00 0.00 0.00 3.32
1563 1810 3.537795 ACTACTACCTCTGTCCCACAA 57.462 47.619 0.00 0.00 0.00 3.33
1564 1811 3.590630 ACTACTACTACCTCTGTCCCACA 59.409 47.826 0.00 0.00 0.00 4.17
1565 1812 4.233632 ACTACTACTACCTCTGTCCCAC 57.766 50.000 0.00 0.00 0.00 4.61
1566 1813 4.539293 AGAACTACTACTACCTCTGTCCCA 59.461 45.833 0.00 0.00 0.00 4.37
1567 1814 5.114764 AGAACTACTACTACCTCTGTCCC 57.885 47.826 0.00 0.00 0.00 4.46
1580 1827 6.395629 GCAAAGACACATGGTAGAACTACTA 58.604 40.000 11.04 6.27 36.36 1.82
1581 1828 5.238583 GCAAAGACACATGGTAGAACTACT 58.761 41.667 11.04 0.00 36.36 2.57
1582 1829 4.392138 GGCAAAGACACATGGTAGAACTAC 59.608 45.833 0.00 3.66 35.40 2.73
1583 1830 4.286032 AGGCAAAGACACATGGTAGAACTA 59.714 41.667 0.00 0.00 0.00 2.24
1584 1831 3.073062 AGGCAAAGACACATGGTAGAACT 59.927 43.478 0.00 0.00 0.00 3.01
1585 1832 3.412386 AGGCAAAGACACATGGTAGAAC 58.588 45.455 0.00 0.00 0.00 3.01
1586 1833 3.327757 AGAGGCAAAGACACATGGTAGAA 59.672 43.478 0.00 0.00 0.00 2.10
1587 1834 2.906389 AGAGGCAAAGACACATGGTAGA 59.094 45.455 0.00 0.00 0.00 2.59
1620 1867 4.532521 AGAAAGGCCTTAGAGTAGAGCAAA 59.467 41.667 20.84 0.00 0.00 3.68
1629 1876 4.030216 AGGAGAAGAGAAAGGCCTTAGAG 58.970 47.826 20.84 0.00 0.00 2.43
1630 1877 4.067944 AGGAGAAGAGAAAGGCCTTAGA 57.932 45.455 20.84 0.00 0.00 2.10
1631 1878 4.512484 CAAGGAGAAGAGAAAGGCCTTAG 58.488 47.826 20.84 0.00 34.21 2.18
1632 1879 3.264450 CCAAGGAGAAGAGAAAGGCCTTA 59.736 47.826 20.84 0.00 34.21 2.69
1633 1880 2.040947 CCAAGGAGAAGAGAAAGGCCTT 59.959 50.000 13.78 13.78 36.24 4.35
1681 1943 8.677300 TGCAGGAAAATAAATCAGAAGTATGTC 58.323 33.333 0.00 0.00 0.00 3.06
1698 1960 4.037923 GGAACTGAATGAAGTGCAGGAAAA 59.962 41.667 0.00 0.00 34.05 2.29
1706 1968 4.096231 TGTGTTGTGGAACTGAATGAAGTG 59.904 41.667 0.00 0.00 38.04 3.16
1786 2050 6.578545 CGTGTATATCTGCCATTTGTTATTGC 59.421 38.462 0.00 0.00 0.00 3.56
1796 2060 4.174009 GCGTATTCGTGTATATCTGCCAT 58.826 43.478 0.00 0.00 39.49 4.40
1797 2061 3.571571 GCGTATTCGTGTATATCTGCCA 58.428 45.455 0.00 0.00 39.49 4.92
1798 2062 2.592897 CGCGTATTCGTGTATATCTGCC 59.407 50.000 0.00 0.00 41.80 4.85
1799 2063 3.865428 CGCGTATTCGTGTATATCTGC 57.135 47.619 0.00 0.00 41.80 4.26
1833 2097 3.642848 ACCTCCGGTTAAATCGGCTATTA 59.357 43.478 0.00 0.00 46.43 0.98
1853 2117 1.596260 CATGATCAGATGCGTGTGACC 59.404 52.381 8.09 0.00 29.51 4.02
1870 2134 4.177026 GTCTACACTCTACAGCCAACATG 58.823 47.826 0.00 0.00 0.00 3.21
1871 2135 3.195825 GGTCTACACTCTACAGCCAACAT 59.804 47.826 0.00 0.00 0.00 2.71
1872 2136 2.561419 GGTCTACACTCTACAGCCAACA 59.439 50.000 0.00 0.00 0.00 3.33
1884 2153 1.602237 CCGGGCAATGGTCTACACT 59.398 57.895 0.00 0.00 0.00 3.55
1885 2154 2.112815 GCCGGGCAATGGTCTACAC 61.113 63.158 15.62 0.00 0.00 2.90
1977 2246 3.670311 CATTTCTGCAGTTCTCATCGG 57.330 47.619 14.67 0.00 0.00 4.18
1997 2266 0.326264 TCTCCCTCTTCTTTGCTGGC 59.674 55.000 0.00 0.00 0.00 4.85
1998 2267 1.905215 TCTCTCCCTCTTCTTTGCTGG 59.095 52.381 0.00 0.00 0.00 4.85
1999 2268 2.093553 CCTCTCTCCCTCTTCTTTGCTG 60.094 54.545 0.00 0.00 0.00 4.41
2000 2269 2.187100 CCTCTCTCCCTCTTCTTTGCT 58.813 52.381 0.00 0.00 0.00 3.91
2001 2270 1.209261 CCCTCTCTCCCTCTTCTTTGC 59.791 57.143 0.00 0.00 0.00 3.68
2002 2271 1.836802 CCCCTCTCTCCCTCTTCTTTG 59.163 57.143 0.00 0.00 0.00 2.77
2003 2272 1.274126 CCCCCTCTCTCCCTCTTCTTT 60.274 57.143 0.00 0.00 0.00 2.52
2004 2273 0.341609 CCCCCTCTCTCCCTCTTCTT 59.658 60.000 0.00 0.00 0.00 2.52
2019 2288 1.411651 GGAGGACAGATACTGCCCCC 61.412 65.000 0.00 0.00 34.47 5.40
2048 2317 2.418910 CGAGTGGATCCCGTCAGCT 61.419 63.158 9.90 0.00 0.00 4.24
2120 2389 1.350319 CTCGTTCGAGCTCTCCGAG 59.650 63.158 23.06 23.06 39.02 4.63
2209 2478 4.814147 TCTGAATTATATGAGCCGCTGAG 58.186 43.478 0.00 0.00 0.00 3.35
2238 2507 1.681666 CTGCCTTCCTCCTCTGCAA 59.318 57.895 0.00 0.00 0.00 4.08
2248 2529 4.681978 ACACGGTCGCTGCCTTCC 62.682 66.667 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.