Multiple sequence alignment - TraesCS3B01G467100

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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 TraesCS3B01G467100 chr3B 100.000 2639 0 0 1 2639 709515952 709518590 0.000000e+00 4874.0
1 TraesCS3B01G467100 chr3B 80.457 875 159 7 777 1644 709449920 709450789 0.000000e+00 658.0
2 TraesCS3B01G467100 chr3B 85.342 614 85 4 1 610 390225731 390225119 4.790000e-177 630.0
3 TraesCS3B01G467100 chr3B 83.459 532 82 4 1979 2510 10720962 10721487 8.490000e-135 490.0
4 TraesCS3B01G467100 chr3B 76.786 504 97 14 2145 2636 693750993 693750498 5.600000e-67 265.0
5 TraesCS3B01G467100 chr3A 91.007 1212 100 7 648 1856 672216063 672217268 0.000000e+00 1626.0
6 TraesCS3B01G467100 chr3A 82.419 893 140 7 764 1641 672210590 672211480 0.000000e+00 763.0
7 TraesCS3B01G467100 chr3A 85.948 612 76 8 3 611 393968558 393967954 0.000000e+00 645.0
8 TraesCS3B01G467100 chr3A 100.000 28 0 0 145 172 157034432 157034405 5.000000e-03 52.8
9 TraesCS3B01G467100 chr6B 94.377 658 37 0 1982 2639 711634254 711634911 0.000000e+00 1011.0
10 TraesCS3B01G467100 chr5B 95.588 612 22 5 1 610 503793762 503793154 0.000000e+00 976.0
11 TraesCS3B01G467100 chr5B 93.103 58 4 0 1922 1979 513808968 513808911 4.680000e-13 86.1
12 TraesCS3B01G467100 chr5B 90.164 61 6 0 1919 1979 2618495 2618555 2.180000e-11 80.5
13 TraesCS3B01G467100 chr3D 88.179 829 61 18 1079 1906 537031278 537032070 0.000000e+00 953.0
14 TraesCS3B01G467100 chr3D 92.621 515 37 1 648 1161 536989283 536989797 0.000000e+00 739.0
15 TraesCS3B01G467100 chr3D 88.418 613 67 4 1 610 295974615 295974004 0.000000e+00 736.0
16 TraesCS3B01G467100 chr3D 86.620 426 29 4 648 1072 537023356 537023754 1.860000e-121 446.0
17 TraesCS3B01G467100 chr2B 92.661 654 48 0 1986 2639 626105281 626104628 0.000000e+00 942.0
18 TraesCS3B01G467100 chr2B 97.500 40 1 0 559 598 553657187 553657226 4.710000e-08 69.4
19 TraesCS3B01G467100 chr2D 87.994 658 79 0 1982 2639 424043890 424043233 0.000000e+00 778.0
20 TraesCS3B01G467100 chr2D 89.744 117 11 1 45 161 326213834 326213719 5.890000e-32 148.0
21 TraesCS3B01G467100 chr1A 87.994 658 78 1 1982 2639 579871882 579871226 0.000000e+00 776.0
22 TraesCS3B01G467100 chr1A 85.955 178 25 0 1982 2159 579877318 579877141 9.640000e-45 191.0
23 TraesCS3B01G467100 chr5D 87.538 658 81 1 1982 2639 461849223 461848567 0.000000e+00 760.0
24 TraesCS3B01G467100 chr7A 83.677 533 75 6 1982 2514 639231849 639231329 2.360000e-135 492.0
25 TraesCS3B01G467100 chr7A 95.745 47 1 1 1923 1968 717919488 717919442 1.010000e-09 75.0
26 TraesCS3B01G467100 chr2A 96.491 57 2 0 1923 1979 699381709 699381765 7.780000e-16 95.3
27 TraesCS3B01G467100 chrUn 93.103 58 4 0 1922 1979 322140977 322140920 4.680000e-13 86.1
28 TraesCS3B01G467100 chr7B 91.379 58 5 0 1922 1979 318416424 318416367 2.180000e-11 80.5
29 TraesCS3B01G467100 chr7B 97.500 40 1 0 559 598 623935404 623935365 4.710000e-08 69.4
30 TraesCS3B01G467100 chr5A 90.164 61 6 0 1919 1979 643565276 643565336 2.180000e-11 80.5
31 TraesCS3B01G467100 chr4D 97.500 40 1 0 558 597 126767472 126767511 4.710000e-08 69.4
32 TraesCS3B01G467100 chr4B 97.500 40 1 0 559 598 364039539 364039578 4.710000e-08 69.4
33 TraesCS3B01G467100 chr1B 97.500 40 1 0 559 598 577918606 577918567 4.710000e-08 69.4


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 TraesCS3B01G467100 chr3B 709515952 709518590 2638 False 4874 4874 100.000 1 2639 1 chr3B.!!$F3 2638
1 TraesCS3B01G467100 chr3B 709449920 709450789 869 False 658 658 80.457 777 1644 1 chr3B.!!$F2 867
2 TraesCS3B01G467100 chr3B 390225119 390225731 612 True 630 630 85.342 1 610 1 chr3B.!!$R1 609
3 TraesCS3B01G467100 chr3B 10720962 10721487 525 False 490 490 83.459 1979 2510 1 chr3B.!!$F1 531
4 TraesCS3B01G467100 chr3A 672216063 672217268 1205 False 1626 1626 91.007 648 1856 1 chr3A.!!$F2 1208
5 TraesCS3B01G467100 chr3A 672210590 672211480 890 False 763 763 82.419 764 1641 1 chr3A.!!$F1 877
6 TraesCS3B01G467100 chr3A 393967954 393968558 604 True 645 645 85.948 3 611 1 chr3A.!!$R2 608
7 TraesCS3B01G467100 chr6B 711634254 711634911 657 False 1011 1011 94.377 1982 2639 1 chr6B.!!$F1 657
8 TraesCS3B01G467100 chr5B 503793154 503793762 608 True 976 976 95.588 1 610 1 chr5B.!!$R1 609
9 TraesCS3B01G467100 chr3D 537031278 537032070 792 False 953 953 88.179 1079 1906 1 chr3D.!!$F3 827
10 TraesCS3B01G467100 chr3D 536989283 536989797 514 False 739 739 92.621 648 1161 1 chr3D.!!$F1 513
11 TraesCS3B01G467100 chr3D 295974004 295974615 611 True 736 736 88.418 1 610 1 chr3D.!!$R1 609
12 TraesCS3B01G467100 chr2B 626104628 626105281 653 True 942 942 92.661 1986 2639 1 chr2B.!!$R1 653
13 TraesCS3B01G467100 chr2D 424043233 424043890 657 True 778 778 87.994 1982 2639 1 chr2D.!!$R2 657
14 TraesCS3B01G467100 chr1A 579871226 579871882 656 True 776 776 87.994 1982 2639 1 chr1A.!!$R1 657
15 TraesCS3B01G467100 chr5D 461848567 461849223 656 True 760 760 87.538 1982 2639 1 chr5D.!!$R1 657
16 TraesCS3B01G467100 chr7A 639231329 639231849 520 True 492 492 83.677 1982 2514 1 chr7A.!!$R1 532

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
646 652 0.10576 AGATCCCTCGACCTGCTCAT 60.106 55.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1941 1962 0.104304 GGATAACATCCTCGCGTGGT 59.896 55.0 25.1 8.69 46.19 4.16 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
258 263 2.561419 ACGAGGAGCTAAGCTGTAAACA 59.439 45.455 0.00 0.00 39.88 2.83
460 466 4.681978 AGTTGCACGTCGCCCTCC 62.682 66.667 7.38 0.00 41.33 4.30
610 616 4.452733 GCGCCCAGTACTCGCCTT 62.453 66.667 14.63 0.00 42.71 4.35
611 617 2.509336 CGCCCAGTACTCGCCTTG 60.509 66.667 0.00 0.00 0.00 3.61
612 618 2.978824 GCCCAGTACTCGCCTTGA 59.021 61.111 0.00 0.00 0.00 3.02
613 619 1.522569 GCCCAGTACTCGCCTTGAT 59.477 57.895 0.00 0.00 0.00 2.57
614 620 0.750850 GCCCAGTACTCGCCTTGATA 59.249 55.000 0.00 0.00 0.00 2.15
615 621 1.138266 GCCCAGTACTCGCCTTGATAA 59.862 52.381 0.00 0.00 0.00 1.75
616 622 2.419574 GCCCAGTACTCGCCTTGATAAA 60.420 50.000 0.00 0.00 0.00 1.40
617 623 3.744530 GCCCAGTACTCGCCTTGATAAAT 60.745 47.826 0.00 0.00 0.00 1.40
618 624 4.502604 GCCCAGTACTCGCCTTGATAAATA 60.503 45.833 0.00 0.00 0.00 1.40
619 625 4.989168 CCCAGTACTCGCCTTGATAAATAC 59.011 45.833 0.00 0.00 0.00 1.89
620 626 4.989168 CCAGTACTCGCCTTGATAAATACC 59.011 45.833 0.00 0.00 0.00 2.73
621 627 4.989168 CAGTACTCGCCTTGATAAATACCC 59.011 45.833 0.00 0.00 0.00 3.69
622 628 4.652421 AGTACTCGCCTTGATAAATACCCA 59.348 41.667 0.00 0.00 0.00 4.51
623 629 4.706842 ACTCGCCTTGATAAATACCCAT 57.293 40.909 0.00 0.00 0.00 4.00
624 630 4.642429 ACTCGCCTTGATAAATACCCATC 58.358 43.478 0.00 0.00 0.00 3.51
625 631 4.003648 CTCGCCTTGATAAATACCCATCC 58.996 47.826 0.00 0.00 0.00 3.51
626 632 3.650942 TCGCCTTGATAAATACCCATCCT 59.349 43.478 0.00 0.00 0.00 3.24
627 633 4.841813 TCGCCTTGATAAATACCCATCCTA 59.158 41.667 0.00 0.00 0.00 2.94
628 634 5.046591 TCGCCTTGATAAATACCCATCCTAG 60.047 44.000 0.00 0.00 0.00 3.02
629 635 5.046591 CGCCTTGATAAATACCCATCCTAGA 60.047 44.000 0.00 0.00 0.00 2.43
630 636 6.352222 CGCCTTGATAAATACCCATCCTAGAT 60.352 42.308 0.00 0.00 0.00 1.98
631 637 7.051000 GCCTTGATAAATACCCATCCTAGATC 58.949 42.308 0.00 0.00 0.00 2.75
632 638 7.569240 CCTTGATAAATACCCATCCTAGATCC 58.431 42.308 0.00 0.00 0.00 3.36
633 639 7.366011 CCTTGATAAATACCCATCCTAGATCCC 60.366 44.444 0.00 0.00 0.00 3.85
634 640 6.826727 TGATAAATACCCATCCTAGATCCCT 58.173 40.000 0.00 0.00 0.00 4.20
635 641 6.903534 TGATAAATACCCATCCTAGATCCCTC 59.096 42.308 0.00 0.00 0.00 4.30
636 642 2.901338 TACCCATCCTAGATCCCTCG 57.099 55.000 0.00 0.00 0.00 4.63
637 643 1.158904 ACCCATCCTAGATCCCTCGA 58.841 55.000 0.00 0.00 0.00 4.04
638 644 1.203075 ACCCATCCTAGATCCCTCGAC 60.203 57.143 0.00 0.00 0.00 4.20
639 645 1.551452 CCATCCTAGATCCCTCGACC 58.449 60.000 0.00 0.00 0.00 4.79
640 646 1.076350 CCATCCTAGATCCCTCGACCT 59.924 57.143 0.00 0.00 0.00 3.85
641 647 2.166829 CATCCTAGATCCCTCGACCTG 58.833 57.143 0.00 0.00 0.00 4.00
642 648 0.178987 TCCTAGATCCCTCGACCTGC 60.179 60.000 0.00 0.00 0.00 4.85
643 649 0.178975 CCTAGATCCCTCGACCTGCT 60.179 60.000 0.00 0.00 0.00 4.24
644 650 1.243902 CTAGATCCCTCGACCTGCTC 58.756 60.000 0.00 0.00 0.00 4.26
645 651 0.551396 TAGATCCCTCGACCTGCTCA 59.449 55.000 0.00 0.00 0.00 4.26
646 652 0.105760 AGATCCCTCGACCTGCTCAT 60.106 55.000 0.00 0.00 0.00 2.90
662 668 2.704065 GCTCATACCCCCAACTTAGCTA 59.296 50.000 0.00 0.00 0.00 3.32
667 673 2.188817 ACCCCCAACTTAGCTAGACAG 58.811 52.381 0.00 0.00 0.00 3.51
671 677 3.260884 CCCCAACTTAGCTAGACAGTTCA 59.739 47.826 6.37 0.00 0.00 3.18
712 718 0.763035 AGAGTAACCACAAAGCCGGT 59.237 50.000 1.90 0.00 36.98 5.28
715 721 1.417145 AGTAACCACAAAGCCGGTGTA 59.583 47.619 1.90 0.00 35.08 2.90
762 769 1.021202 TTCCACAGACGCAAGGTTTG 58.979 50.000 0.00 0.00 46.39 2.93
770 777 2.027460 GCAAGGTTTGTGGGTGCG 59.973 61.111 0.00 0.00 0.00 5.34
1027 1041 1.680651 CGTCAGCTCCACCCTCTCT 60.681 63.158 0.00 0.00 0.00 3.10
1072 1086 0.551131 AAGGCTCCTCTCCACCCATT 60.551 55.000 0.00 0.00 0.00 3.16
1074 1088 0.332972 GGCTCCTCTCCACCCATTTT 59.667 55.000 0.00 0.00 0.00 1.82
1134 1148 3.671008 TGCCGAGTTGTGTACTTATGT 57.329 42.857 0.00 0.00 37.17 2.29
1161 1175 0.036952 CCAAGGATGTGCTCGTGTCT 60.037 55.000 0.00 0.00 0.00 3.41
1233 1253 4.442753 GCATTTGAGTTGTTTTCCAAGGGA 60.443 41.667 0.00 0.00 32.51 4.20
1341 1361 2.881111 ATGATGAGATGATGGCCCAG 57.119 50.000 0.00 0.00 0.00 4.45
1425 1445 1.905215 AGATGTGGAGTTGTGGAGGAG 59.095 52.381 0.00 0.00 0.00 3.69
1426 1446 1.902508 GATGTGGAGTTGTGGAGGAGA 59.097 52.381 0.00 0.00 0.00 3.71
1505 1525 0.105194 TCTGATAGGATTGGCGGGGA 60.105 55.000 0.00 0.00 0.00 4.81
1560 1580 0.188342 AGGTTGGTGACTGGGCAAAT 59.812 50.000 0.00 0.00 0.00 2.32
1561 1581 1.047801 GGTTGGTGACTGGGCAAATT 58.952 50.000 0.00 0.00 0.00 1.82
1588 1608 4.202398 TGACTGAAGAGATGGCAAAGAAGT 60.202 41.667 0.00 0.00 0.00 3.01
1617 1637 3.365767 GCATTGTTGAGGAGAAGTTGAGC 60.366 47.826 0.00 0.00 0.00 4.26
1620 1640 0.321671 TTGAGGAGAAGTTGAGCGGG 59.678 55.000 0.00 0.00 0.00 6.13
1623 1643 0.832135 AGGAGAAGTTGAGCGGGTCA 60.832 55.000 5.66 5.66 0.00 4.02
1670 1690 9.594478 TGATTATTGTCATGATTAAGTACGTGT 57.406 29.630 0.00 0.00 0.00 4.49
1671 1691 9.849607 GATTATTGTCATGATTAAGTACGTGTG 57.150 33.333 0.00 0.00 0.00 3.82
1705 1725 2.377004 CATCACTCGATGCGCAAGT 58.623 52.632 17.11 11.47 42.54 3.16
1708 1728 1.801512 CACTCGATGCGCAAGTCGA 60.802 57.895 28.34 28.34 43.79 4.20
1710 1730 2.874751 TCGATGCGCAAGTCGAGA 59.125 55.556 27.11 10.71 41.44 4.04
1727 1747 2.037251 CGAGAGTGTTCCCCTCTTTTCA 59.963 50.000 0.00 0.00 39.36 2.69
1728 1748 3.669536 GAGAGTGTTCCCCTCTTTTCAG 58.330 50.000 0.00 0.00 39.36 3.02
1732 1752 4.464947 AGTGTTCCCCTCTTTTCAGAAAG 58.535 43.478 0.00 0.00 42.92 2.62
1733 1753 4.166144 AGTGTTCCCCTCTTTTCAGAAAGA 59.834 41.667 0.00 2.08 46.77 2.52
1771 1792 3.005791 GTGCAAGCCAAATGTAAGTCCTT 59.994 43.478 0.00 0.00 0.00 3.36
1774 1795 5.161358 GCAAGCCAAATGTAAGTCCTTAAC 58.839 41.667 0.00 0.00 0.00 2.01
1782 1803 9.801873 CCAAATGTAAGTCCTTAACAATAATGG 57.198 33.333 0.00 0.00 0.00 3.16
1800 1821 8.601476 CAATAATGGGAAAGACTACGTACTTTC 58.399 37.037 21.68 21.68 46.16 2.62
1836 1857 6.196353 AACATTTTGTTTCGTCTTCATTGACG 59.804 34.615 10.30 10.30 44.42 4.35
1837 1858 9.077531 AACATTTTGTTTCGTCTTCATTGACGC 62.078 37.037 11.52 0.32 44.15 5.19
1844 1865 2.072298 GTCTTCATTGACGCTGCTCTT 58.928 47.619 0.00 0.00 0.00 2.85
1864 1885 7.256286 GCTCTTGTTTTGAGATATGAGCAATT 58.744 34.615 0.00 0.00 43.33 2.32
1933 1954 8.621286 AGTAATACTTAGATGCGAATTTTTGGG 58.379 33.333 0.00 0.00 0.00 4.12
1934 1955 7.639113 AATACTTAGATGCGAATTTTTGGGA 57.361 32.000 0.00 0.00 0.00 4.37
1935 1956 5.310720 ACTTAGATGCGAATTTTTGGGAC 57.689 39.130 0.00 0.00 0.00 4.46
1936 1957 4.764823 ACTTAGATGCGAATTTTTGGGACA 59.235 37.500 0.00 0.00 0.00 4.02
1937 1958 5.418840 ACTTAGATGCGAATTTTTGGGACAT 59.581 36.000 0.00 0.00 39.30 3.06
1938 1959 4.114058 AGATGCGAATTTTTGGGACATG 57.886 40.909 0.00 0.00 39.30 3.21
1939 1960 3.763360 AGATGCGAATTTTTGGGACATGA 59.237 39.130 0.00 0.00 39.30 3.07
1940 1961 4.403432 AGATGCGAATTTTTGGGACATGAT 59.597 37.500 0.00 0.00 39.30 2.45
1941 1962 5.593909 AGATGCGAATTTTTGGGACATGATA 59.406 36.000 0.00 0.00 39.30 2.15
1942 1963 4.992688 TGCGAATTTTTGGGACATGATAC 58.007 39.130 0.00 0.00 39.30 2.24
1943 1964 4.142271 TGCGAATTTTTGGGACATGATACC 60.142 41.667 0.00 0.00 39.30 2.73
1944 1965 4.142271 GCGAATTTTTGGGACATGATACCA 60.142 41.667 0.00 1.24 39.30 3.25
1945 1966 5.339990 CGAATTTTTGGGACATGATACCAC 58.660 41.667 0.00 0.00 39.30 4.16
1946 1967 4.981806 ATTTTTGGGACATGATACCACG 57.018 40.909 0.00 0.00 39.30 4.94
1947 1968 1.745232 TTTGGGACATGATACCACGC 58.255 50.000 0.00 0.00 39.30 5.34
1948 1969 0.461163 TTGGGACATGATACCACGCG 60.461 55.000 3.53 3.53 39.30 6.01
1949 1970 1.324005 TGGGACATGATACCACGCGA 61.324 55.000 15.93 0.00 0.00 5.87
1950 1971 0.597637 GGGACATGATACCACGCGAG 60.598 60.000 15.93 4.16 0.00 5.03
1951 1972 0.597637 GGACATGATACCACGCGAGG 60.598 60.000 21.59 21.59 0.00 4.63
1952 1973 0.384309 GACATGATACCACGCGAGGA 59.616 55.000 29.67 12.99 0.00 3.71
1953 1974 1.000163 GACATGATACCACGCGAGGAT 60.000 52.381 29.67 17.09 0.00 3.24
1954 1975 1.269778 ACATGATACCACGCGAGGATG 60.270 52.381 29.67 22.14 0.00 3.51
1955 1976 1.040646 ATGATACCACGCGAGGATGT 58.959 50.000 29.67 13.63 0.00 3.06
1956 1977 0.821517 TGATACCACGCGAGGATGTT 59.178 50.000 29.67 9.17 0.00 2.71
1957 1978 2.025898 TGATACCACGCGAGGATGTTA 58.974 47.619 29.67 11.24 0.00 2.41
1958 1979 2.626266 TGATACCACGCGAGGATGTTAT 59.374 45.455 29.67 15.60 0.00 1.89
1959 1980 2.787601 TACCACGCGAGGATGTTATC 57.212 50.000 29.67 0.00 0.00 1.75
1969 1990 2.528041 GGATGTTATCCTGACCGACC 57.472 55.000 0.61 0.00 46.19 4.79
1970 1991 1.760613 GGATGTTATCCTGACCGACCA 59.239 52.381 0.61 0.00 46.19 4.02
1971 1992 2.368875 GGATGTTATCCTGACCGACCAT 59.631 50.000 0.61 0.00 46.19 3.55
1972 1993 3.181454 GGATGTTATCCTGACCGACCATT 60.181 47.826 0.61 0.00 46.19 3.16
1973 1994 3.260475 TGTTATCCTGACCGACCATTG 57.740 47.619 0.00 0.00 0.00 2.82
1974 1995 2.093181 TGTTATCCTGACCGACCATTGG 60.093 50.000 0.00 0.00 0.00 3.16
1975 1996 1.874129 TATCCTGACCGACCATTGGT 58.126 50.000 8.42 8.42 44.10 3.67
1976 1997 0.253044 ATCCTGACCGACCATTGGTG 59.747 55.000 14.44 1.96 40.63 4.17
1977 1998 2.040544 CCTGACCGACCATTGGTGC 61.041 63.158 14.44 4.22 40.63 5.01
2047 2068 3.684788 GTCCTGTTACAATCAGCACGAAT 59.315 43.478 0.00 0.00 0.00 3.34
2141 2162 2.898705 CAGAGGTCTGCCACACTATTC 58.101 52.381 0.00 0.00 37.15 1.75
2294 2315 1.984424 TCCACTTCCATCACCACATGA 59.016 47.619 0.00 0.00 43.13 3.07
2351 2372 1.078426 GAGGGCTAAAGCTTCGGCA 60.078 57.895 20.15 0.00 44.74 5.69
2459 2480 8.303156 CCTCCAGAGTGATTATCAGTACTAATG 58.697 40.741 2.13 0.00 28.50 1.90
2480 2501 9.308000 CTAATGGCCCCATCAGTATTTATTTTA 57.692 33.333 0.00 0.00 35.31 1.52
2482 2503 7.354751 TGGCCCCATCAGTATTTATTTTAAC 57.645 36.000 0.00 0.00 0.00 2.01
2498 2519 0.331278 TAACCCAGCCAACATCAGGG 59.669 55.000 0.00 0.00 45.20 4.45
2533 2554 2.747177 TCCATCAGGAATACCACGTCT 58.253 47.619 0.00 0.00 42.23 4.18
2585 2606 1.633432 TCCCTGACCATTTTCACCGAT 59.367 47.619 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
258 263 2.051518 CAGCTCTGCCTCGTCCTCT 61.052 63.158 0.00 0.00 0.00 3.69
302 308 2.361610 CCCCTGCGCCACAAGATT 60.362 61.111 4.18 0.00 0.00 2.40
350 356 2.076100 CAATAACCGCAACAGCTCAGA 58.924 47.619 0.00 0.00 0.00 3.27
460 466 1.482593 AGTAAAGCTCCACCTCCATCG 59.517 52.381 0.00 0.00 0.00 3.84
469 475 0.669318 CGACGGCAAGTAAAGCTCCA 60.669 55.000 0.00 0.00 0.00 3.86
610 616 6.826727 AGGGATCTAGGATGGGTATTTATCA 58.173 40.000 0.00 0.00 0.00 2.15
611 617 6.041069 CGAGGGATCTAGGATGGGTATTTATC 59.959 46.154 0.00 0.00 0.00 1.75
612 618 5.900123 CGAGGGATCTAGGATGGGTATTTAT 59.100 44.000 0.00 0.00 0.00 1.40
613 619 5.015924 TCGAGGGATCTAGGATGGGTATTTA 59.984 44.000 0.00 0.00 0.00 1.40
614 620 4.097418 CGAGGGATCTAGGATGGGTATTT 58.903 47.826 0.00 0.00 0.00 1.40
615 621 3.336997 TCGAGGGATCTAGGATGGGTATT 59.663 47.826 0.00 0.00 0.00 1.89
616 622 2.927007 TCGAGGGATCTAGGATGGGTAT 59.073 50.000 0.00 0.00 0.00 2.73
617 623 2.041350 GTCGAGGGATCTAGGATGGGTA 59.959 54.545 0.00 0.00 0.00 3.69
618 624 1.158904 TCGAGGGATCTAGGATGGGT 58.841 55.000 0.00 0.00 0.00 4.51
619 625 1.551452 GTCGAGGGATCTAGGATGGG 58.449 60.000 0.00 0.00 0.00 4.00
620 626 1.076350 AGGTCGAGGGATCTAGGATGG 59.924 57.143 0.00 0.00 29.74 3.51
621 627 2.166829 CAGGTCGAGGGATCTAGGATG 58.833 57.143 0.00 0.00 29.74 3.51
622 628 1.549037 GCAGGTCGAGGGATCTAGGAT 60.549 57.143 0.00 0.00 29.74 3.24
623 629 0.178987 GCAGGTCGAGGGATCTAGGA 60.179 60.000 0.00 0.00 29.74 2.94
624 630 0.178975 AGCAGGTCGAGGGATCTAGG 60.179 60.000 0.00 0.00 29.74 3.02
625 631 1.243902 GAGCAGGTCGAGGGATCTAG 58.756 60.000 0.00 0.00 29.74 2.43
626 632 0.551396 TGAGCAGGTCGAGGGATCTA 59.449 55.000 0.00 0.00 29.74 1.98
627 633 0.105760 ATGAGCAGGTCGAGGGATCT 60.106 55.000 0.00 0.00 32.45 2.75
628 634 1.271102 GTATGAGCAGGTCGAGGGATC 59.729 57.143 0.00 0.00 0.00 3.36
629 635 1.333177 GTATGAGCAGGTCGAGGGAT 58.667 55.000 0.00 0.00 0.00 3.85
630 636 0.755698 GGTATGAGCAGGTCGAGGGA 60.756 60.000 0.00 0.00 0.00 4.20
631 637 1.742768 GGTATGAGCAGGTCGAGGG 59.257 63.158 0.00 0.00 0.00 4.30
632 638 1.742768 GGGTATGAGCAGGTCGAGG 59.257 63.158 0.00 0.00 0.00 4.63
633 639 1.742768 GGGGTATGAGCAGGTCGAG 59.257 63.158 0.00 0.00 0.00 4.04
634 640 1.760875 GGGGGTATGAGCAGGTCGA 60.761 63.158 0.00 0.00 0.00 4.20
635 641 1.622607 TTGGGGGTATGAGCAGGTCG 61.623 60.000 0.00 0.00 0.00 4.79
636 642 0.107165 GTTGGGGGTATGAGCAGGTC 60.107 60.000 0.00 0.00 0.00 3.85
637 643 0.550147 AGTTGGGGGTATGAGCAGGT 60.550 55.000 0.00 0.00 0.00 4.00
638 644 0.625849 AAGTTGGGGGTATGAGCAGG 59.374 55.000 0.00 0.00 0.00 4.85
639 645 2.746472 GCTAAGTTGGGGGTATGAGCAG 60.746 54.545 0.00 0.00 0.00 4.24
640 646 1.211949 GCTAAGTTGGGGGTATGAGCA 59.788 52.381 0.00 0.00 0.00 4.26
641 647 1.490910 AGCTAAGTTGGGGGTATGAGC 59.509 52.381 0.00 0.00 0.00 4.26
642 648 4.039366 GTCTAGCTAAGTTGGGGGTATGAG 59.961 50.000 0.00 0.00 0.00 2.90
643 649 3.965347 GTCTAGCTAAGTTGGGGGTATGA 59.035 47.826 0.00 0.00 0.00 2.15
644 650 3.709653 TGTCTAGCTAAGTTGGGGGTATG 59.290 47.826 0.00 0.00 0.00 2.39
645 651 3.967987 CTGTCTAGCTAAGTTGGGGGTAT 59.032 47.826 0.00 0.00 0.00 2.73
646 652 3.245875 ACTGTCTAGCTAAGTTGGGGGTA 60.246 47.826 0.00 0.00 0.00 3.69
662 668 1.059098 TCTGCCATGGTGAACTGTCT 58.941 50.000 14.67 0.00 0.00 3.41
667 673 0.737219 GAGCATCTGCCATGGTGAAC 59.263 55.000 14.67 8.93 43.38 3.18
671 677 1.180029 GTTTGAGCATCTGCCATGGT 58.820 50.000 14.67 0.00 43.38 3.55
706 712 0.763223 CCCCCTCTAATACACCGGCT 60.763 60.000 0.00 0.00 0.00 5.52
712 718 3.732742 TCATCTCCTCCCCCTCTAATACA 59.267 47.826 0.00 0.00 0.00 2.29
715 721 3.075181 TCTCATCTCCTCCCCCTCTAAT 58.925 50.000 0.00 0.00 0.00 1.73
762 769 2.112815 GCCTTGATACCGCACCCAC 61.113 63.158 0.00 0.00 0.00 4.61
770 777 1.099879 CAGCCAGCAGCCTTGATACC 61.100 60.000 0.00 0.00 45.47 2.73
1027 1041 0.820074 GGGAGCTTCTCGAGATCGGA 60.820 60.000 17.44 0.00 41.75 4.55
1072 1086 2.664851 CAGCAGCGTGACCGGAAA 60.665 61.111 9.46 0.00 33.68 3.13
1103 1117 1.990160 AACTCGGCAACCAAGGGTCA 61.990 55.000 0.00 0.00 33.12 4.02
1134 1148 1.296392 CACATCCTTGGGACTGCGA 59.704 57.895 0.00 0.00 32.98 5.10
1161 1175 5.815581 ACCTTGTAGATGAAGTGCCATAAA 58.184 37.500 0.00 0.00 0.00 1.40
1233 1253 2.696526 TAGGCCCATACGAGGATTCT 57.303 50.000 0.00 0.00 0.00 2.40
1425 1445 1.714794 AGCTACACAAGTGCACGATC 58.285 50.000 12.01 0.00 0.00 3.69
1426 1446 2.069273 GAAGCTACACAAGTGCACGAT 58.931 47.619 12.01 1.15 0.00 3.73
1467 1487 2.431057 AGATACACCGGATGAGTTGACC 59.569 50.000 9.46 0.00 0.00 4.02
1482 1502 2.567169 CCCGCCAATCCTATCAGATACA 59.433 50.000 0.00 0.00 0.00 2.29
1505 1525 4.017683 AGAAGGAAGAATTCTCCATTGGCT 60.018 41.667 19.67 1.76 46.56 4.75
1560 1580 4.890158 TGCCATCTCTTCAGTCAAGTAA 57.110 40.909 0.00 0.00 33.27 2.24
1561 1581 4.890158 TTGCCATCTCTTCAGTCAAGTA 57.110 40.909 0.00 0.00 33.27 2.24
1588 1608 2.041485 TCTCCTCAACAATGCCATCCAA 59.959 45.455 0.00 0.00 0.00 3.53
1617 1637 4.935205 TGTCAAAATGTAAGATCTGACCCG 59.065 41.667 7.81 0.00 33.78 5.28
1620 1640 8.939929 TCAAGATGTCAAAATGTAAGATCTGAC 58.060 33.333 2.87 2.87 34.99 3.51
1663 1683 2.642139 TAGCCTTAGCACACACGTAC 57.358 50.000 0.00 0.00 43.56 3.67
1664 1684 2.494471 ACATAGCCTTAGCACACACGTA 59.506 45.455 0.00 0.00 43.56 3.57
1665 1685 1.275291 ACATAGCCTTAGCACACACGT 59.725 47.619 0.00 0.00 43.56 4.49
1666 1686 1.660607 CACATAGCCTTAGCACACACG 59.339 52.381 0.00 0.00 43.56 4.49
1670 1690 2.093021 TGATGCACATAGCCTTAGCACA 60.093 45.455 0.00 0.00 44.83 4.57
1671 1691 2.289002 GTGATGCACATAGCCTTAGCAC 59.711 50.000 0.00 0.00 44.83 4.40
1700 1720 0.670854 GGGGAACACTCTCGACTTGC 60.671 60.000 0.00 0.00 0.00 4.01
1701 1721 0.969894 AGGGGAACACTCTCGACTTG 59.030 55.000 0.00 0.00 0.00 3.16
1705 1725 2.011122 AAAGAGGGGAACACTCTCGA 57.989 50.000 0.91 0.00 44.17 4.04
1708 1728 3.318313 TCTGAAAAGAGGGGAACACTCT 58.682 45.455 0.00 0.00 46.77 3.24
1710 1730 4.166144 TCTTTCTGAAAAGAGGGGAACACT 59.834 41.667 4.18 0.00 44.63 3.55
1727 1747 7.308435 GCACAAGCAAATACATACTTCTTTCT 58.692 34.615 0.00 0.00 41.58 2.52
1728 1748 7.498070 GCACAAGCAAATACATACTTCTTTC 57.502 36.000 0.00 0.00 41.58 2.62
1755 1776 9.301153 CATTATTGTTAAGGACTTACATTTGGC 57.699 33.333 0.00 0.00 0.00 4.52
1765 1786 7.699878 AGTCTTTCCCATTATTGTTAAGGACT 58.300 34.615 0.00 0.00 32.21 3.85
1771 1792 8.752187 AGTACGTAGTCTTTCCCATTATTGTTA 58.248 33.333 0.00 0.00 43.93 2.41
1774 1795 8.488651 AAAGTACGTAGTCTTTCCCATTATTG 57.511 34.615 2.79 0.00 43.93 1.90
1810 1831 8.555166 GTCAATGAAGACGAAACAAAATGTTA 57.445 30.769 0.00 0.00 40.14 2.41
1826 1847 1.802960 ACAAGAGCAGCGTCAATGAAG 59.197 47.619 0.00 0.00 0.00 3.02
1836 1857 5.730010 GCTCATATCTCAAAACAAGAGCAGC 60.730 44.000 0.00 0.00 44.77 5.25
1837 1858 5.808403 GCTCATATCTCAAAACAAGAGCAG 58.192 41.667 0.00 0.00 44.77 4.24
1838 1859 5.808042 GCTCATATCTCAAAACAAGAGCA 57.192 39.130 0.00 0.00 44.77 4.26
1844 1865 9.187996 TCCAATAATTGCTCATATCTCAAAACA 57.812 29.630 0.00 0.00 0.00 2.83
1864 1885 8.588290 ACAAATATTGTAGTTGCCTTCCAATA 57.412 30.769 0.00 0.00 43.27 1.90
1907 1928 8.621286 CCCAAAAATTCGCATCTAAGTATTACT 58.379 33.333 0.00 0.00 0.00 2.24
1908 1929 8.617809 TCCCAAAAATTCGCATCTAAGTATTAC 58.382 33.333 0.00 0.00 0.00 1.89
1909 1930 8.617809 GTCCCAAAAATTCGCATCTAAGTATTA 58.382 33.333 0.00 0.00 0.00 0.98
1910 1931 7.122055 TGTCCCAAAAATTCGCATCTAAGTATT 59.878 33.333 0.00 0.00 0.00 1.89
1911 1932 6.601613 TGTCCCAAAAATTCGCATCTAAGTAT 59.398 34.615 0.00 0.00 0.00 2.12
1912 1933 5.941058 TGTCCCAAAAATTCGCATCTAAGTA 59.059 36.000 0.00 0.00 0.00 2.24
1913 1934 4.764823 TGTCCCAAAAATTCGCATCTAAGT 59.235 37.500 0.00 0.00 0.00 2.24
1914 1935 5.309323 TGTCCCAAAAATTCGCATCTAAG 57.691 39.130 0.00 0.00 0.00 2.18
1915 1936 5.417266 TCATGTCCCAAAAATTCGCATCTAA 59.583 36.000 0.00 0.00 0.00 2.10
1916 1937 4.946772 TCATGTCCCAAAAATTCGCATCTA 59.053 37.500 0.00 0.00 0.00 1.98
1917 1938 3.763360 TCATGTCCCAAAAATTCGCATCT 59.237 39.130 0.00 0.00 0.00 2.90
1918 1939 4.108699 TCATGTCCCAAAAATTCGCATC 57.891 40.909 0.00 0.00 0.00 3.91
1919 1940 4.741321 ATCATGTCCCAAAAATTCGCAT 57.259 36.364 0.00 0.00 0.00 4.73
1920 1941 4.142271 GGTATCATGTCCCAAAAATTCGCA 60.142 41.667 0.00 0.00 0.00 5.10
1921 1942 4.142271 TGGTATCATGTCCCAAAAATTCGC 60.142 41.667 0.00 0.00 0.00 4.70
1922 1943 5.339990 GTGGTATCATGTCCCAAAAATTCG 58.660 41.667 0.00 0.00 0.00 3.34
1923 1944 5.339990 CGTGGTATCATGTCCCAAAAATTC 58.660 41.667 0.00 0.00 0.00 2.17
1924 1945 4.381505 GCGTGGTATCATGTCCCAAAAATT 60.382 41.667 0.00 0.00 32.65 1.82
1925 1946 3.130340 GCGTGGTATCATGTCCCAAAAAT 59.870 43.478 0.00 0.00 32.65 1.82
1926 1947 2.490115 GCGTGGTATCATGTCCCAAAAA 59.510 45.455 0.00 0.00 32.65 1.94
1927 1948 2.088423 GCGTGGTATCATGTCCCAAAA 58.912 47.619 0.00 0.00 32.65 2.44
1928 1949 1.745232 GCGTGGTATCATGTCCCAAA 58.255 50.000 0.00 0.00 32.65 3.28
1929 1950 0.461163 CGCGTGGTATCATGTCCCAA 60.461 55.000 0.00 0.00 32.65 4.12
1930 1951 1.142965 CGCGTGGTATCATGTCCCA 59.857 57.895 0.00 0.00 32.65 4.37
1931 1952 0.597637 CTCGCGTGGTATCATGTCCC 60.598 60.000 5.77 0.00 32.65 4.46
1932 1953 0.597637 CCTCGCGTGGTATCATGTCC 60.598 60.000 18.86 0.00 32.65 4.02
1933 1954 0.384309 TCCTCGCGTGGTATCATGTC 59.616 55.000 25.10 0.00 32.65 3.06
1934 1955 1.040646 ATCCTCGCGTGGTATCATGT 58.959 50.000 25.10 3.37 32.65 3.21
1935 1956 1.269778 ACATCCTCGCGTGGTATCATG 60.270 52.381 25.10 21.77 0.00 3.07
1936 1957 1.040646 ACATCCTCGCGTGGTATCAT 58.959 50.000 25.10 9.92 0.00 2.45
1937 1958 0.821517 AACATCCTCGCGTGGTATCA 59.178 50.000 25.10 7.91 0.00 2.15
1938 1959 2.787601 TAACATCCTCGCGTGGTATC 57.212 50.000 25.10 0.00 0.00 2.24
1939 1960 2.029290 GGATAACATCCTCGCGTGGTAT 60.029 50.000 25.10 15.14 46.19 2.73
1940 1961 1.338973 GGATAACATCCTCGCGTGGTA 59.661 52.381 25.10 10.78 46.19 3.25
1941 1962 0.104304 GGATAACATCCTCGCGTGGT 59.896 55.000 25.10 8.69 46.19 4.16
1942 1963 2.900528 GGATAACATCCTCGCGTGG 58.099 57.895 20.92 20.92 46.19 4.94
1951 1972 3.753294 ATGGTCGGTCAGGATAACATC 57.247 47.619 0.00 0.00 0.00 3.06
1952 1973 3.433598 CCAATGGTCGGTCAGGATAACAT 60.434 47.826 0.00 0.00 0.00 2.71
1953 1974 2.093181 CCAATGGTCGGTCAGGATAACA 60.093 50.000 0.00 0.00 0.00 2.41
1954 1975 2.093128 ACCAATGGTCGGTCAGGATAAC 60.093 50.000 0.00 0.00 27.30 1.89
1955 1976 2.093181 CACCAATGGTCGGTCAGGATAA 60.093 50.000 0.00 0.00 33.25 1.75
1956 1977 1.484653 CACCAATGGTCGGTCAGGATA 59.515 52.381 0.00 0.00 33.25 2.59
1957 1978 0.253044 CACCAATGGTCGGTCAGGAT 59.747 55.000 0.00 0.00 33.25 3.24
1958 1979 1.676968 CACCAATGGTCGGTCAGGA 59.323 57.895 0.00 0.00 33.25 3.86
1959 1980 2.040544 GCACCAATGGTCGGTCAGG 61.041 63.158 0.00 0.00 33.25 3.86
1960 1981 0.606401 AAGCACCAATGGTCGGTCAG 60.606 55.000 0.00 0.00 34.76 3.51
1961 1982 0.179004 AAAGCACCAATGGTCGGTCA 60.179 50.000 0.00 0.00 34.76 4.02
1962 1983 0.958822 AAAAGCACCAATGGTCGGTC 59.041 50.000 0.00 0.00 34.76 4.79
1963 1984 1.408969 AAAAAGCACCAATGGTCGGT 58.591 45.000 0.00 1.03 34.76 4.69
2047 2068 3.585862 CCGAGTTTTCTAGTTAGCAGCA 58.414 45.455 0.00 0.00 0.00 4.41
2141 2162 1.150081 GCATGTCCTGAGGGATGGG 59.850 63.158 11.73 0.00 44.33 4.00
2258 2279 0.758734 TGGACTGTCTGGAGGTTGTG 59.241 55.000 7.85 0.00 0.00 3.33
2294 2315 2.031870 GCACAACTCTGGGGTTTTTCT 58.968 47.619 0.00 0.00 0.00 2.52
2459 2480 6.239487 GGGTTAAAATAAATACTGATGGGGCC 60.239 42.308 0.00 0.00 0.00 5.80
2480 2501 1.077265 CCCTGATGTTGGCTGGGTT 59.923 57.895 0.00 0.00 39.08 4.11
2482 2503 2.043652 CCCCTGATGTTGGCTGGG 60.044 66.667 0.00 0.00 42.39 4.45
2498 2519 4.416738 GGACAGTGCTGGAGGCCC 62.417 72.222 0.00 0.00 40.92 5.80
2533 2554 2.195727 TGCTTGAGATACCCATGTGGA 58.804 47.619 0.00 0.00 37.39 4.02
2585 2606 3.292460 ACCTGTTTTTGATCCGGTTCAA 58.708 40.909 21.41 21.41 33.89 2.69


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

AutoCloner maintained by Alex Coulton.