Multiple sequence alignment - TraesCS6D01G336100

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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 TraesCS6D01G336100 chr6D 100.000 4926 0 0 1 4926 437170101 437165176 0.000000e+00 9097.0
1 TraesCS6D01G336100 chr6D 94.975 398 19 1 176 572 468915591 468915194 1.510000e-174 623.0
2 TraesCS6D01G336100 chr6D 86.517 89 7 3 1615 1700 437168404 437168318 5.250000e-15 93.5
3 TraesCS6D01G336100 chr6D 86.517 89 7 3 1698 1784 437168487 437168402 5.250000e-15 93.5
4 TraesCS6D01G336100 chr6A 92.796 3276 151 34 1696 4926 585431920 585428685 0.000000e+00 4663.0
5 TraesCS6D01G336100 chr6A 90.863 996 42 28 750 1700 585432824 585431833 0.000000e+00 1290.0
6 TraesCS6D01G336100 chr6A 83.886 211 19 3 960 1170 391629152 391628957 2.340000e-43 187.0
7 TraesCS6D01G336100 chr6B 92.468 3266 145 48 1696 4926 661342876 661339677 0.000000e+00 4575.0
8 TraesCS6D01G336100 chr6B 88.821 1145 65 38 589 1700 661343904 661342790 0.000000e+00 1347.0
9 TraesCS6D01G336100 chr3D 97.033 573 16 1 3 574 560881996 560881424 0.000000e+00 963.0
10 TraesCS6D01G336100 chr3D 96.491 399 11 3 176 571 613132677 613133075 0.000000e+00 656.0
11 TraesCS6D01G336100 chr7D 97.481 397 8 2 176 571 614369551 614369156 0.000000e+00 676.0
12 TraesCS6D01G336100 chr7D 98.864 176 2 0 3 178 548206717 548206542 1.030000e-81 315.0
13 TraesCS6D01G336100 chr7B 93.719 398 18 4 178 571 717355673 717355279 1.530000e-164 590.0
14 TraesCS6D01G336100 chr3A 94.010 384 23 0 188 571 205708165 205707782 2.560000e-162 582.0
15 TraesCS6D01G336100 chr3A 92.683 287 15 4 4640 4926 681626852 681626572 4.590000e-110 409.0
16 TraesCS6D01G336100 chr1A 94.010 384 21 2 188 571 416581554 416581173 9.190000e-162 580.0
17 TraesCS6D01G336100 chr1A 91.599 369 24 3 179 540 587932209 587932577 2.050000e-138 503.0
18 TraesCS6D01G336100 chr5A 91.192 386 28 4 192 571 603505007 603504622 2.030000e-143 520.0
19 TraesCS6D01G336100 chr5A 93.893 131 8 0 1040 1170 522676973 522676843 1.080000e-46 198.0
20 TraesCS6D01G336100 chr5A 83.886 211 19 7 960 1170 149695589 149695394 2.340000e-43 187.0
21 TraesCS6D01G336100 chr4B 96.516 287 10 0 4640 4926 429270121 429269835 4.460000e-130 475.0
22 TraesCS6D01G336100 chr4B 93.836 146 9 0 33 178 14623637 14623492 2.310000e-53 220.0
23 TraesCS6D01G336100 chr4A 94.366 284 16 0 4643 4926 589150554 589150271 2.110000e-118 436.0
24 TraesCS6D01G336100 chr7A 96.714 213 7 0 4714 4926 130190248 130190036 6.060000e-94 355.0
25 TraesCS6D01G336100 chr7A 96.023 176 6 1 3 178 10531911 10532085 8.070000e-73 285.0
26 TraesCS6D01G336100 chr7A 92.994 157 8 1 4714 4870 130190548 130190395 4.960000e-55 226.0
27 TraesCS6D01G336100 chr5D 97.727 176 4 0 3 178 217295707 217295882 2.230000e-78 303.0
28 TraesCS6D01G336100 chrUn 95.402 174 8 0 5 178 71415438 71415265 1.350000e-70 278.0
29 TraesCS6D01G336100 chrUn 94.828 174 9 0 5 178 331456972 331457145 6.280000e-69 272.0
30 TraesCS6D01G336100 chrUn 94.737 171 9 0 7 177 71474483 71474313 2.920000e-67 267.0
31 TraesCS6D01G336100 chr5B 94.521 146 8 0 33 178 481956106 481956251 4.960000e-55 226.0
32 TraesCS6D01G336100 chr2A 87.931 58 4 3 525 580 57968653 57968597 1.140000e-06 65.8


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 TraesCS6D01G336100 chr6D 437165176 437170101 4925 True 3094.666667 9097 91.011333 1 4926 3 chr6D.!!$R2 4925
1 TraesCS6D01G336100 chr6A 585428685 585432824 4139 True 2976.500000 4663 91.829500 750 4926 2 chr6A.!!$R2 4176
2 TraesCS6D01G336100 chr6B 661339677 661343904 4227 True 2961.000000 4575 90.644500 589 4926 2 chr6B.!!$R1 4337
3 TraesCS6D01G336100 chr3D 560881424 560881996 572 True 963.000000 963 97.033000 3 574 1 chr3D.!!$R1 571
4 TraesCS6D01G336100 chr7A 130190036 130190548 512 True 290.500000 355 94.854000 4714 4926 2 chr7A.!!$R1 212

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
903 934 0.037590 CCCACAAATTCTCCCACCGA 59.962 55.0 0.0 0.0 0.00 4.69 F
1254 1302 0.524414 TTTTCGCTCGATCTGACCGA 59.476 50.0 0.0 0.0 33.03 4.69 F
1814 1884 1.076438 CCCCTTCCCTCAAAACTCCT 58.924 55.0 0.0 0.0 0.00 3.69 F
3542 3640 1.048160 TCAGCACCAGACTCACCACA 61.048 55.0 0.0 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1790 1860 0.560688 TTTTGAGGGAAGGGGCAACT 59.439 50.000 0.00 0.0 0.00 3.16 R
2864 2961 1.210478 ACAACTGAGACAACCAGCAGT 59.790 47.619 0.00 0.0 42.91 4.40 R
3621 3725 0.035739 GGAACCTACAGGAAACGCCA 59.964 55.000 1.29 0.0 40.02 5.69 R
4566 4697 1.153823 GTCGTATGCGTGTGGCTCT 60.154 57.895 2.37 0.0 44.05 4.09 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
147 148 3.655810 CTCTTCCTCGCGCTGGCTT 62.656 63.158 5.56 0.00 36.88 4.35
168 169 3.695606 GTGGGTGGAGCAGCTCGA 61.696 66.667 16.47 9.95 31.98 4.04
431 433 3.197766 GTGGACCTGACCTGTCATAATCA 59.802 47.826 0.00 0.00 39.13 2.57
442 444 6.892485 ACCTGTCATAATCATGATCAGTTGA 58.108 36.000 9.06 7.13 43.03 3.18
450 452 9.000486 CATAATCATGATCAGTTGATAAGCACT 58.000 33.333 9.06 0.00 34.37 4.40
452 454 5.981174 TCATGATCAGTTGATAAGCACTCA 58.019 37.500 0.09 0.00 34.37 3.41
483 485 2.570442 TTTTTGAAACAGCCGACCAC 57.430 45.000 0.00 0.00 0.00 4.16
509 511 8.971073 CCCATTTGGTAGTTATCTGAGAAAAAT 58.029 33.333 0.00 0.00 0.00 1.82
575 577 9.819267 AGTAGTTTTATGCTATTTACTCCTCAC 57.181 33.333 0.00 0.00 0.00 3.51
576 578 9.819267 GTAGTTTTATGCTATTTACTCCTCACT 57.181 33.333 0.00 0.00 0.00 3.41
578 580 9.167311 AGTTTTATGCTATTTACTCCTCACTTG 57.833 33.333 0.00 0.00 0.00 3.16
579 581 7.553881 TTTATGCTATTTACTCCTCACTTGC 57.446 36.000 0.00 0.00 0.00 4.01
580 582 3.873910 TGCTATTTACTCCTCACTTGCC 58.126 45.455 0.00 0.00 0.00 4.52
581 583 3.519510 TGCTATTTACTCCTCACTTGCCT 59.480 43.478 0.00 0.00 0.00 4.75
582 584 3.873952 GCTATTTACTCCTCACTTGCCTG 59.126 47.826 0.00 0.00 0.00 4.85
583 585 2.859165 TTTACTCCTCACTTGCCTGG 57.141 50.000 0.00 0.00 0.00 4.45
584 586 0.324943 TTACTCCTCACTTGCCTGGC 59.675 55.000 12.87 12.87 0.00 4.85
585 587 1.888436 TACTCCTCACTTGCCTGGCG 61.888 60.000 14.98 2.80 0.00 5.69
586 588 3.241530 TCCTCACTTGCCTGGCGT 61.242 61.111 14.98 3.53 0.00 5.68
587 589 3.052082 CCTCACTTGCCTGGCGTG 61.052 66.667 17.43 17.43 0.00 5.34
600 602 1.670811 CTGGCGTGTGTGAAACTTCTT 59.329 47.619 0.00 0.00 38.04 2.52
602 604 2.096819 TGGCGTGTGTGAAACTTCTTTC 59.903 45.455 0.00 0.00 38.04 2.62
606 608 4.033587 GCGTGTGTGAAACTTCTTTCTACA 59.966 41.667 0.00 0.00 37.30 2.74
612 614 7.148086 TGTGTGAAACTTCTTTCTACATGCTTT 60.148 33.333 0.00 0.00 37.30 3.51
624 626 7.466746 TTCTACATGCTTTGCTCCTTTTATT 57.533 32.000 0.00 0.00 0.00 1.40
625 627 8.574251 TTCTACATGCTTTGCTCCTTTTATTA 57.426 30.769 0.00 0.00 0.00 0.98
626 628 8.752005 TCTACATGCTTTGCTCCTTTTATTAT 57.248 30.769 0.00 0.00 0.00 1.28
667 669 4.832823 AGGTAGCACAAAATAAACTTGGCT 59.167 37.500 0.00 0.00 35.69 4.75
693 695 4.431416 TTATCTGGGTCGCATATGGTTT 57.569 40.909 4.56 0.00 0.00 3.27
708 710 6.459024 GCATATGGTTTGCTCGGTAACAATAA 60.459 38.462 4.56 0.00 37.14 1.40
709 711 4.752661 TGGTTTGCTCGGTAACAATAAC 57.247 40.909 0.00 0.00 0.00 1.89
725 727 9.209297 GTAACAATAACAACGACGTTAAACTTT 57.791 29.630 13.77 4.71 35.12 2.66
729 731 2.223317 ACAACGACGTTAAACTTTGGCC 60.223 45.455 13.77 0.00 0.00 5.36
730 732 1.666054 ACGACGTTAAACTTTGGCCA 58.334 45.000 0.00 0.00 0.00 5.36
733 735 2.349155 CGACGTTAAACTTTGGCCAGAC 60.349 50.000 5.11 0.00 0.00 3.51
895 926 0.536460 ACGCGTTCCCCACAAATTCT 60.536 50.000 5.58 0.00 0.00 2.40
898 929 1.173913 CGTTCCCCACAAATTCTCCC 58.826 55.000 0.00 0.00 0.00 4.30
900 931 1.893137 GTTCCCCACAAATTCTCCCAC 59.107 52.381 0.00 0.00 0.00 4.61
901 932 0.407918 TCCCCACAAATTCTCCCACC 59.592 55.000 0.00 0.00 0.00 4.61
902 933 0.965363 CCCCACAAATTCTCCCACCG 60.965 60.000 0.00 0.00 0.00 4.94
903 934 0.037590 CCCACAAATTCTCCCACCGA 59.962 55.000 0.00 0.00 0.00 4.69
905 936 2.446435 CCACAAATTCTCCCACCGAAT 58.554 47.619 0.00 0.00 32.75 3.34
911 942 0.842905 TTCTCCCACCGAATCCCCAA 60.843 55.000 0.00 0.00 0.00 4.12
933 972 4.116328 CGCGAGCTCCTCCACGAA 62.116 66.667 8.47 0.00 31.18 3.85
934 973 2.496817 GCGAGCTCCTCCACGAAT 59.503 61.111 8.47 0.00 0.00 3.34
938 977 2.034048 GAGCTCCTCCACGAATCCCC 62.034 65.000 0.87 0.00 0.00 4.81
939 978 3.108288 GCTCCTCCACGAATCCCCC 62.108 68.421 0.00 0.00 0.00 5.40
940 979 1.383248 CTCCTCCACGAATCCCCCT 60.383 63.158 0.00 0.00 0.00 4.79
941 980 1.382695 TCCTCCACGAATCCCCCTC 60.383 63.158 0.00 0.00 0.00 4.30
942 981 2.444256 CCTCCACGAATCCCCCTCC 61.444 68.421 0.00 0.00 0.00 4.30
991 1037 2.127869 CCGCCGGAGAAGAGGATCA 61.128 63.158 5.05 0.00 37.82 2.92
997 1043 1.330655 GGAGAAGAGGATCACCGCCA 61.331 60.000 0.00 0.00 41.83 5.69
1213 1259 1.383525 CCCCTCGCCCTTACCCTAA 60.384 63.158 0.00 0.00 0.00 2.69
1238 1285 3.144657 ACCTAACCCCGAATTCGTTTT 57.855 42.857 25.10 16.56 37.74 2.43
1254 1302 0.524414 TTTTCGCTCGATCTGACCGA 59.476 50.000 0.00 0.00 33.03 4.69
1263 1317 1.707239 GATCTGACCGACGACGCTCT 61.707 60.000 0.64 0.00 38.29 4.09
1543 1606 1.227999 TTTTCCTTCCGCTCACGCAG 61.228 55.000 0.00 0.00 38.22 5.18
1544 1607 4.742201 TCCTTCCGCTCACGCAGC 62.742 66.667 0.00 0.00 45.85 5.25
1552 1615 2.262603 CTCACGCAGCTGGCTGTA 59.737 61.111 21.34 6.66 45.24 2.74
1553 1616 1.808799 CTCACGCAGCTGGCTGTAG 60.809 63.158 21.34 17.65 45.24 2.74
1554 1617 2.047844 CACGCAGCTGGCTGTAGT 60.048 61.111 21.34 18.19 45.24 2.73
1555 1618 1.215382 CACGCAGCTGGCTGTAGTA 59.785 57.895 21.34 0.00 45.24 1.82
1556 1619 1.078759 CACGCAGCTGGCTGTAGTAC 61.079 60.000 21.34 5.90 45.24 2.73
1573 1643 4.368565 AGTACAGTCCGCCTGATATCTA 57.631 45.455 3.98 0.00 44.49 1.98
1574 1644 4.328536 AGTACAGTCCGCCTGATATCTAG 58.671 47.826 3.98 0.14 44.49 2.43
1585 1655 3.249091 CTGATATCTAGCGCACATGGTC 58.751 50.000 11.47 1.16 0.00 4.02
1606 1676 8.002984 TGGTCAACATAATCGTTCAGATACTA 57.997 34.615 0.00 0.00 38.98 1.82
1658 1728 9.391006 TGAATGAAACTACTAATCGCCTAAATT 57.609 29.630 0.00 0.00 0.00 1.82
1665 1735 8.516811 ACTACTAATCGCCTAAATTAATGACG 57.483 34.615 0.00 0.00 0.00 4.35
1675 1745 6.888430 CCTAAATTAATGACGAGGCATACAC 58.112 40.000 0.00 0.00 0.00 2.90
1676 1746 6.706270 CCTAAATTAATGACGAGGCATACACT 59.294 38.462 0.00 0.00 0.00 3.55
1677 1747 7.226720 CCTAAATTAATGACGAGGCATACACTT 59.773 37.037 0.00 0.00 0.00 3.16
1678 1748 9.256477 CTAAATTAATGACGAGGCATACACTTA 57.744 33.333 0.00 0.00 0.00 2.24
1679 1749 8.500753 AAATTAATGACGAGGCATACACTTAA 57.499 30.769 0.00 0.00 0.00 1.85
1680 1750 8.500753 AATTAATGACGAGGCATACACTTAAA 57.499 30.769 0.00 0.00 0.00 1.52
1681 1751 7.908827 TTAATGACGAGGCATACACTTAAAA 57.091 32.000 0.00 0.00 0.00 1.52
1682 1752 6.811253 AATGACGAGGCATACACTTAAAAA 57.189 33.333 0.00 0.00 0.00 1.94
1683 1753 5.600908 TGACGAGGCATACACTTAAAAAC 57.399 39.130 0.00 0.00 0.00 2.43
1684 1754 5.057819 TGACGAGGCATACACTTAAAAACA 58.942 37.500 0.00 0.00 0.00 2.83
1685 1755 5.703592 TGACGAGGCATACACTTAAAAACAT 59.296 36.000 0.00 0.00 0.00 2.71
1686 1756 6.874664 TGACGAGGCATACACTTAAAAACATA 59.125 34.615 0.00 0.00 0.00 2.29
1687 1757 7.388224 TGACGAGGCATACACTTAAAAACATAA 59.612 33.333 0.00 0.00 0.00 1.90
1688 1758 8.101654 ACGAGGCATACACTTAAAAACATAAA 57.898 30.769 0.00 0.00 0.00 1.40
1689 1759 8.569641 ACGAGGCATACACTTAAAAACATAAAA 58.430 29.630 0.00 0.00 0.00 1.52
1690 1760 9.400638 CGAGGCATACACTTAAAAACATAAAAA 57.599 29.630 0.00 0.00 0.00 1.94
1714 1784 9.438163 AAAATCATAGGATGGATAACATTTGGT 57.562 29.630 0.00 0.00 40.72 3.67
1715 1785 9.438163 AAATCATAGGATGGATAACATTTGGTT 57.562 29.630 0.00 0.00 40.72 3.67
1716 1786 7.822161 TCATAGGATGGATAACATTTGGTTG 57.178 36.000 0.00 0.00 40.72 3.77
1717 1787 7.581814 TCATAGGATGGATAACATTTGGTTGA 58.418 34.615 0.00 0.00 40.72 3.18
1718 1788 8.058235 TCATAGGATGGATAACATTTGGTTGAA 58.942 33.333 0.00 0.00 40.72 2.69
1719 1789 8.863086 CATAGGATGGATAACATTTGGTTGAAT 58.137 33.333 0.00 0.00 40.72 2.57
1720 1790 7.116075 AGGATGGATAACATTTGGTTGAATG 57.884 36.000 0.00 0.00 40.72 2.67
1721 1791 6.896860 AGGATGGATAACATTTGGTTGAATGA 59.103 34.615 4.76 0.00 40.72 2.57
1722 1792 7.399765 AGGATGGATAACATTTGGTTGAATGAA 59.600 33.333 4.76 0.00 40.72 2.57
1723 1793 8.040132 GGATGGATAACATTTGGTTGAATGAAA 58.960 33.333 4.76 0.00 40.72 2.69
1724 1794 8.776376 ATGGATAACATTTGGTTGAATGAAAC 57.224 30.769 4.76 0.00 40.73 2.78
1725 1795 7.823799 ATGGATAACATTTGGTTGAATGAAACC 59.176 33.333 4.76 3.34 42.73 3.27
1748 1818 7.009179 CCACTAATGGCCTAGATGAATTAGA 57.991 40.000 18.63 0.00 39.82 2.10
1749 1819 7.453393 CCACTAATGGCCTAGATGAATTAGAA 58.547 38.462 18.63 0.00 39.82 2.10
1750 1820 7.605691 CCACTAATGGCCTAGATGAATTAGAAG 59.394 40.741 18.63 12.14 39.82 2.85
1751 1821 7.605691 CACTAATGGCCTAGATGAATTAGAAGG 59.394 40.741 18.63 7.90 35.39 3.46
1814 1884 1.076438 CCCCTTCCCTCAAAACTCCT 58.924 55.000 0.00 0.00 0.00 3.69
1850 1920 3.702045 CAGGGGGTGACTGTTTTGTTTTA 59.298 43.478 0.00 0.00 0.00 1.52
1884 1954 8.757982 ATTCTACCATGCACTAGAAAATGAAT 57.242 30.769 12.15 2.43 33.67 2.57
1932 2009 8.970020 TGCTTGAACCAAACAATAATATCAGAT 58.030 29.630 0.00 0.00 0.00 2.90
1933 2010 9.241317 GCTTGAACCAAACAATAATATCAGATG 57.759 33.333 0.00 0.00 0.00 2.90
1941 2018 8.742777 CAAACAATAATATCAGATGTATGGGGG 58.257 37.037 0.00 0.00 0.00 5.40
1968 2045 9.958180 TCACTGAATCAAAAGAATAGATGGTAA 57.042 29.630 0.00 0.00 0.00 2.85
2005 2082 4.111375 ACGCAAAACAAATGTTGGTACA 57.889 36.364 0.00 0.00 38.44 2.90
2023 2100 6.635755 TGGTACATCGATTCTGTGTTATCAA 58.364 36.000 0.00 0.00 0.00 2.57
2026 2103 7.653713 GGTACATCGATTCTGTGTTATCAAGAT 59.346 37.037 0.00 0.00 0.00 2.40
2029 2106 9.201127 ACATCGATTCTGTGTTATCAAGATATG 57.799 33.333 0.00 0.00 0.00 1.78
2064 2141 7.953005 TCCTGTTAATGATGGCATAAAGAAA 57.047 32.000 0.00 0.00 33.44 2.52
2065 2142 8.537728 TCCTGTTAATGATGGCATAAAGAAAT 57.462 30.769 0.00 0.00 33.44 2.17
2066 2143 9.639563 TCCTGTTAATGATGGCATAAAGAAATA 57.360 29.630 0.00 0.00 33.44 1.40
2188 2283 4.464951 TGGTTATCGTTGTATGGAGTCTGT 59.535 41.667 0.00 0.00 0.00 3.41
2213 2308 6.148811 TGTTGCAAGGCTGTTCTTACTAATAC 59.851 38.462 0.00 0.00 0.00 1.89
2295 2390 4.340666 TCCTGCTATCAGAGACATCAACTC 59.659 45.833 0.00 0.00 42.95 3.01
2441 2538 6.055588 TGCTGTCTTATGGTTTAATCTAGCC 58.944 40.000 0.00 0.00 0.00 3.93
2466 2563 7.043192 CCGTTCGTTTCTGTACTCTTTCTTTAA 60.043 37.037 0.00 0.00 0.00 1.52
2494 2591 3.627395 AGAACTCATAAACCATCGGCA 57.373 42.857 0.00 0.00 0.00 5.69
2573 2670 2.989166 GCTTTACTGGAAACTGCATTGC 59.011 45.455 0.46 0.46 0.00 3.56
2583 2680 5.104859 TGGAAACTGCATTGCCATCATTATT 60.105 36.000 6.12 0.00 0.00 1.40
2774 2871 3.620488 ACCTTGTCTTTGTCAGCTTCAA 58.380 40.909 0.00 0.00 0.00 2.69
2864 2961 4.769345 TCATCAATGTAGGTACATGGCA 57.231 40.909 3.38 0.00 45.55 4.92
2868 2965 2.332063 ATGTAGGTACATGGCACTGC 57.668 50.000 1.72 0.00 44.66 4.40
2879 2976 1.227943 GGCACTGCTGGTTGTCTCA 60.228 57.895 0.00 0.00 0.00 3.27
2912 3009 2.479566 TTGGCTCATTCGCTTTCTCT 57.520 45.000 0.00 0.00 0.00 3.10
3126 3223 4.607955 CTCACTGCTATGCCATGAAAATG 58.392 43.478 0.00 0.00 0.00 2.32
3177 3274 4.862902 TGCTATGTAGATCTGCTCCTTC 57.137 45.455 12.30 0.00 0.00 3.46
3184 3281 3.467374 AGATCTGCTCCTTCGATTTCC 57.533 47.619 0.00 0.00 0.00 3.13
3190 3287 4.466370 TCTGCTCCTTCGATTTCCTTTAGA 59.534 41.667 0.00 0.00 0.00 2.10
3260 3358 9.967346 TCTATTGTACTGTGCTATGATAGTTTC 57.033 33.333 0.92 0.00 0.00 2.78
3264 3362 7.611770 TGTACTGTGCTATGATAGTTTCTTGT 58.388 34.615 0.92 0.00 0.00 3.16
3345 3443 2.873649 GCCTGCATCAGTTATAGGCCTC 60.874 54.545 9.68 0.00 46.29 4.70
3542 3640 1.048160 TCAGCACCAGACTCACCACA 61.048 55.000 0.00 0.00 0.00 4.17
3579 3677 4.072131 TGTTCTCTGGCCACTGAATTAAC 58.928 43.478 15.98 11.19 0.00 2.01
3590 3688 9.860650 TGGCCACTGAATTAACTAATTATGTAT 57.139 29.630 0.00 0.00 36.13 2.29
3621 3725 3.243367 TGTTGCAACTTGCTAAATTCGCT 60.243 39.130 28.61 0.00 45.31 4.93
3632 3736 0.240945 AAATTCGCTGGCGTTTCCTG 59.759 50.000 14.55 0.00 40.74 3.86
3633 3737 0.889186 AATTCGCTGGCGTTTCCTGT 60.889 50.000 14.55 0.00 40.74 4.00
3638 3742 0.605589 GCTGGCGTTTCCTGTAGGTT 60.606 55.000 0.00 0.00 36.29 3.50
3649 3753 0.391263 CTGTAGGTTCCGACAAGCCC 60.391 60.000 6.29 0.00 0.00 5.19
3748 3852 1.333636 ACCTCATCTTCTCCCTGGCG 61.334 60.000 0.00 0.00 0.00 5.69
4101 4225 0.244721 TGTCGAGTCTGGTCTGCATG 59.755 55.000 0.00 0.00 0.00 4.06
4148 4272 7.112122 TGCCAGTATTTCAACAGTGAAGATAT 58.888 34.615 0.00 0.00 44.49 1.63
4206 4330 1.113788 ACTTGCATTGGTGTGTTGCT 58.886 45.000 0.00 0.00 37.28 3.91
4232 4356 3.861113 GTGCGAATGAATGAAATGCATGT 59.139 39.130 0.00 0.00 43.54 3.21
4251 4375 7.994194 TGCATGTGCTGTATGTTATTTTCATA 58.006 30.769 6.55 0.00 42.66 2.15
4309 4433 9.793252 TTCTTTGATTGCATAGCTATTTTTCTC 57.207 29.630 2.64 0.00 0.00 2.87
4311 4435 9.745880 CTTTGATTGCATAGCTATTTTTCTCAT 57.254 29.630 2.64 0.00 0.00 2.90
4337 4468 4.569564 ACACTACGTGGAAGAAAGTGTTTC 59.430 41.667 5.70 0.00 46.38 2.78
4536 4667 6.808008 ATTTACAATCTTCTGTGTGTCCTG 57.192 37.500 0.00 0.00 0.00 3.86
4566 4697 4.019858 TGGTTGTGATCAAAGAAACCACA 58.980 39.130 21.01 7.62 44.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.717294 GGAGAAGCCCCGCCTTCA 61.717 66.667 10.11 0.00 42.84 3.02
34 35 3.130160 GGCAAGGAGCTTCGCCTG 61.130 66.667 3.75 0.00 44.79 4.85
121 122 1.686110 GCGAGGAAGAGGGAAGGGA 60.686 63.158 0.00 0.00 0.00 4.20
147 148 3.640407 GCTGCTCCACCCACCTCA 61.640 66.667 0.00 0.00 0.00 3.86
431 433 4.815308 GCTGAGTGCTTATCAACTGATCAT 59.185 41.667 0.00 0.00 38.95 2.45
442 444 2.292267 CCCAAATCGCTGAGTGCTTAT 58.708 47.619 0.00 0.00 40.11 1.73
483 485 7.938140 TTTTCTCAGATAACTACCAAATGGG 57.062 36.000 4.17 0.00 44.81 4.00
571 573 2.281070 ACACGCCAGGCAAGTGAG 60.281 61.111 22.39 3.51 39.04 3.51
574 576 2.884997 TTCACACACGCCAGGCAAGT 62.885 55.000 13.30 6.04 0.00 3.16
575 577 1.723608 TTTCACACACGCCAGGCAAG 61.724 55.000 13.30 5.30 0.00 4.01
576 578 1.750780 TTTCACACACGCCAGGCAA 60.751 52.632 13.30 0.00 0.00 4.52
577 579 2.124529 TTTCACACACGCCAGGCA 60.125 55.556 13.30 0.00 0.00 4.75
578 580 1.724582 AAGTTTCACACACGCCAGGC 61.725 55.000 0.00 0.00 0.00 4.85
579 581 0.307760 GAAGTTTCACACACGCCAGG 59.692 55.000 0.00 0.00 0.00 4.45
580 582 1.299541 AGAAGTTTCACACACGCCAG 58.700 50.000 0.00 0.00 0.00 4.85
581 583 1.745232 AAGAAGTTTCACACACGCCA 58.255 45.000 0.00 0.00 0.00 5.69
582 584 2.354821 AGAAAGAAGTTTCACACACGCC 59.645 45.455 1.03 0.00 44.08 5.68
583 585 3.675467 AGAAAGAAGTTTCACACACGC 57.325 42.857 1.03 0.00 44.08 5.34
584 586 5.712217 TGTAGAAAGAAGTTTCACACACG 57.288 39.130 1.03 0.00 44.08 4.49
585 587 5.909610 GCATGTAGAAAGAAGTTTCACACAC 59.090 40.000 0.00 0.00 44.08 3.82
586 588 5.822519 AGCATGTAGAAAGAAGTTTCACACA 59.177 36.000 0.00 4.73 44.08 3.72
587 589 6.305693 AGCATGTAGAAAGAAGTTTCACAC 57.694 37.500 0.00 0.00 44.08 3.82
600 602 7.466746 AATAAAAGGAGCAAAGCATGTAGAA 57.533 32.000 0.00 0.00 0.00 2.10
606 608 8.466798 ACGTTTATAATAAAAGGAGCAAAGCAT 58.533 29.630 0.00 0.00 0.00 3.79
612 614 7.820386 TGACTCACGTTTATAATAAAAGGAGCA 59.180 33.333 0.00 0.00 0.00 4.26
624 626 6.092955 ACCTCAAACTGACTCACGTTTATA 57.907 37.500 0.00 0.78 32.52 0.98
625 627 4.957296 ACCTCAAACTGACTCACGTTTAT 58.043 39.130 0.00 0.00 32.52 1.40
626 628 4.395959 ACCTCAAACTGACTCACGTTTA 57.604 40.909 0.00 0.00 32.52 2.01
667 669 7.432148 ACCATATGCGACCCAGATAATAATA 57.568 36.000 0.00 0.00 0.00 0.98
672 674 4.133820 CAAACCATATGCGACCCAGATAA 58.866 43.478 0.00 0.00 0.00 1.75
674 676 2.575532 CAAACCATATGCGACCCAGAT 58.424 47.619 0.00 0.00 0.00 2.90
675 677 2.016604 GCAAACCATATGCGACCCAGA 61.017 52.381 0.00 0.00 33.57 3.86
676 678 0.381801 GCAAACCATATGCGACCCAG 59.618 55.000 0.00 0.00 33.57 4.45
693 695 3.429543 GTCGTTGTTATTGTTACCGAGCA 59.570 43.478 0.00 0.00 0.00 4.26
708 710 2.223317 GGCCAAAGTTTAACGTCGTTGT 60.223 45.455 20.62 0.00 0.00 3.32
709 711 2.223294 TGGCCAAAGTTTAACGTCGTTG 60.223 45.455 20.62 2.43 0.00 4.10
725 727 2.503765 TCCGATTAATCTTGTCTGGCCA 59.496 45.455 4.71 4.71 0.00 5.36
729 731 3.123804 CGGGTCCGATTAATCTTGTCTG 58.876 50.000 13.45 2.85 42.83 3.51
730 732 2.102588 CCGGGTCCGATTAATCTTGTCT 59.897 50.000 13.45 0.00 42.83 3.41
733 735 2.480845 GTCCGGGTCCGATTAATCTTG 58.519 52.381 13.45 4.92 42.83 3.02
812 823 1.661617 TCGGTCGCGGATTTGTTATTG 59.338 47.619 6.13 0.00 0.00 1.90
895 926 0.257616 GATTTGGGGATTCGGTGGGA 59.742 55.000 0.00 0.00 0.00 4.37
898 929 1.727467 GCGATTTGGGGATTCGGTG 59.273 57.895 0.00 0.00 33.08 4.94
900 931 3.022287 CGCGATTTGGGGATTCGG 58.978 61.111 0.00 0.00 33.08 4.30
901 932 2.327940 GCGCGATTTGGGGATTCG 59.672 61.111 12.10 0.00 34.99 3.34
902 933 2.105960 CTCGCGCGATTTGGGGATTC 62.106 60.000 34.86 0.00 0.00 2.52
903 934 2.124901 TCGCGCGATTTGGGGATT 60.125 55.556 31.40 0.00 0.00 3.01
911 942 4.577246 GGAGGAGCTCGCGCGATT 62.577 66.667 34.86 24.34 42.32 3.34
926 965 2.366435 GGGAGGGGGATTCGTGGA 60.366 66.667 0.00 0.00 0.00 4.02
927 966 3.489513 GGGGAGGGGGATTCGTGG 61.490 72.222 0.00 0.00 0.00 4.94
929 968 3.406113 ATCGGGGAGGGGGATTCGT 62.406 63.158 0.00 0.00 0.00 3.85
931 970 2.584391 CGATCGGGGAGGGGGATTC 61.584 68.421 7.38 0.00 0.00 2.52
932 971 2.402557 ATCGATCGGGGAGGGGGATT 62.403 60.000 16.41 0.00 0.00 3.01
933 972 2.402557 AATCGATCGGGGAGGGGGAT 62.403 60.000 16.41 0.00 0.00 3.85
934 973 3.096089 AATCGATCGGGGAGGGGGA 62.096 63.158 16.41 0.00 0.00 4.81
955 994 2.582498 CGATCAGTCGGGCCGAAC 60.582 66.667 32.91 23.57 44.00 3.95
1213 1259 2.169144 CGAATTCGGGGTTAGGTTAGGT 59.831 50.000 20.16 0.00 35.37 3.08
1254 1302 2.356313 CCTGCAACAGAGCGTCGT 60.356 61.111 0.00 0.00 37.31 4.34
1263 1317 0.478072 AGTGGTTGATCCCTGCAACA 59.522 50.000 0.00 0.00 45.58 3.33
1573 1643 1.819928 TTATGTTGACCATGTGCGCT 58.180 45.000 9.73 0.00 34.86 5.92
1574 1644 2.719798 GATTATGTTGACCATGTGCGC 58.280 47.619 0.00 0.00 34.86 6.09
1606 1676 7.125391 ACCAAATGTTATCCATCCAAGTATGT 58.875 34.615 0.00 0.00 31.75 2.29
1613 1683 6.666980 TCATTCAACCAAATGTTATCCATCCA 59.333 34.615 0.00 0.00 37.77 3.41
1658 1728 7.388224 TGTTTTTAAGTGTATGCCTCGTCATTA 59.612 33.333 0.00 0.00 0.00 1.90
1688 1758 9.438163 ACCAAATGTTATCCATCCTATGATTTT 57.562 29.630 0.00 0.00 31.75 1.82
1689 1759 9.438163 AACCAAATGTTATCCATCCTATGATTT 57.562 29.630 0.00 0.00 34.69 2.17
1690 1760 8.863086 CAACCAAATGTTATCCATCCTATGATT 58.137 33.333 0.00 0.00 34.69 2.57
1691 1761 8.226810 TCAACCAAATGTTATCCATCCTATGAT 58.773 33.333 0.00 0.00 34.69 2.45
1692 1762 7.581814 TCAACCAAATGTTATCCATCCTATGA 58.418 34.615 0.00 0.00 34.69 2.15
1693 1763 7.822161 TCAACCAAATGTTATCCATCCTATG 57.178 36.000 0.00 0.00 34.69 2.23
1694 1764 8.863086 CATTCAACCAAATGTTATCCATCCTAT 58.137 33.333 0.00 0.00 34.69 2.57
1695 1765 8.058235 TCATTCAACCAAATGTTATCCATCCTA 58.942 33.333 0.00 0.00 37.77 2.94
1696 1766 6.896860 TCATTCAACCAAATGTTATCCATCCT 59.103 34.615 0.00 0.00 37.77 3.24
1697 1767 7.111247 TCATTCAACCAAATGTTATCCATCC 57.889 36.000 0.00 0.00 37.77 3.51
1698 1768 8.872845 GTTTCATTCAACCAAATGTTATCCATC 58.127 33.333 0.00 0.00 37.77 3.51
1699 1769 7.823799 GGTTTCATTCAACCAAATGTTATCCAT 59.176 33.333 0.00 0.00 45.12 3.41
1700 1770 7.158021 GGTTTCATTCAACCAAATGTTATCCA 58.842 34.615 0.00 0.00 45.12 3.41
1701 1771 7.595311 GGTTTCATTCAACCAAATGTTATCC 57.405 36.000 0.00 0.00 45.12 2.59
1725 1795 7.605691 CCTTCTAATTCATCTAGGCCATTAGTG 59.394 40.741 5.01 5.73 31.83 2.74
1726 1796 7.684529 CCTTCTAATTCATCTAGGCCATTAGT 58.315 38.462 5.01 0.00 31.83 2.24
1727 1797 6.597280 GCCTTCTAATTCATCTAGGCCATTAG 59.403 42.308 5.01 7.95 41.74 1.73
1728 1798 6.044287 TGCCTTCTAATTCATCTAGGCCATTA 59.956 38.462 5.01 0.00 45.84 1.90
1729 1799 5.163055 TGCCTTCTAATTCATCTAGGCCATT 60.163 40.000 5.01 0.00 45.84 3.16
1730 1800 4.352001 TGCCTTCTAATTCATCTAGGCCAT 59.648 41.667 5.01 0.00 45.84 4.40
1731 1801 3.716353 TGCCTTCTAATTCATCTAGGCCA 59.284 43.478 5.01 0.00 45.84 5.36
1732 1802 4.357918 TGCCTTCTAATTCATCTAGGCC 57.642 45.455 8.32 0.00 45.84 5.19
1733 1803 8.260818 TGTATATGCCTTCTAATTCATCTAGGC 58.739 37.037 0.00 0.00 46.43 3.93
1734 1804 9.593134 GTGTATATGCCTTCTAATTCATCTAGG 57.407 37.037 0.00 0.00 0.00 3.02
1790 1860 0.560688 TTTTGAGGGAAGGGGCAACT 59.439 50.000 0.00 0.00 0.00 3.16
1814 1884 1.146982 CCCCCTGAAGAAACCTTTCCA 59.853 52.381 0.00 0.00 37.92 3.53
1850 1920 5.072741 AGTGCATGGTAGAATCAAAAGTGT 58.927 37.500 0.00 0.00 0.00 3.55
1884 1954 1.148027 TGCCCATACAAACCCTTTCCA 59.852 47.619 0.00 0.00 0.00 3.53
1932 2009 2.556766 TGATTCAGTGACCCCCATACA 58.443 47.619 0.00 0.00 0.00 2.29
1933 2010 3.644966 TTGATTCAGTGACCCCCATAC 57.355 47.619 0.00 0.00 0.00 2.39
1934 2011 4.290985 TCTTTTGATTCAGTGACCCCCATA 59.709 41.667 0.00 0.00 0.00 2.74
1935 2012 3.075882 TCTTTTGATTCAGTGACCCCCAT 59.924 43.478 0.00 0.00 0.00 4.00
1941 2018 8.273780 ACCATCTATTCTTTTGATTCAGTGAC 57.726 34.615 0.00 0.00 0.00 3.67
1985 2062 4.143639 CGATGTACCAACATTTGTTTTGCG 60.144 41.667 0.00 0.00 46.49 4.85
1999 2076 6.215495 TGATAACACAGAATCGATGTACCA 57.785 37.500 0.00 0.00 0.00 3.25
2029 2106 7.982354 GCCATCATTAACAGGATCCTAGTATAC 59.018 40.741 15.67 0.00 0.00 1.47
2064 2141 8.780846 TCCGTGTATTCACAATTGTTTAGTAT 57.219 30.769 8.77 0.27 44.02 2.12
2065 2142 8.780846 ATCCGTGTATTCACAATTGTTTAGTA 57.219 30.769 8.77 0.00 44.02 1.82
2066 2143 7.681939 ATCCGTGTATTCACAATTGTTTAGT 57.318 32.000 8.77 0.00 44.02 2.24
2188 2283 2.930950 AGTAAGAACAGCCTTGCAACA 58.069 42.857 0.00 0.00 32.27 3.33
2213 2308 5.859495 AGTTAAGTCAAGGGAGACAGAAAG 58.141 41.667 0.00 0.00 40.98 2.62
2295 2390 6.471519 GCAAATAAGCAAAGATAGACAGCAAG 59.528 38.462 0.00 0.00 0.00 4.01
2400 2496 5.598417 AGACAGCAAAAGGGTATCAGTTTTT 59.402 36.000 0.00 0.00 0.00 1.94
2441 2538 5.885020 AAGAAAGAGTACAGAAACGAACG 57.115 39.130 0.00 0.00 0.00 3.95
2466 2563 7.604164 CCGATGGTTTATGAGTTCTATATTGCT 59.396 37.037 0.00 0.00 0.00 3.91
2768 2865 5.573337 ATGGAAACTCAGCTAATTGAAGC 57.427 39.130 0.00 0.00 43.11 3.86
2774 2871 7.093771 CCTTAAACCAATGGAAACTCAGCTAAT 60.094 37.037 6.16 0.00 0.00 1.73
2782 2879 5.306678 TGCATTCCTTAAACCAATGGAAACT 59.693 36.000 6.16 0.00 41.22 2.66
2864 2961 1.210478 ACAACTGAGACAACCAGCAGT 59.790 47.619 0.00 0.00 42.91 4.40
2868 2965 4.701956 AACAAACAACTGAGACAACCAG 57.298 40.909 0.00 0.00 37.64 4.00
2879 2976 7.250569 CGAATGAGCCAATATAACAAACAACT 58.749 34.615 0.00 0.00 0.00 3.16
2912 3009 3.964688 TGAACCAGTGAAAGAGTAGACCA 59.035 43.478 0.00 0.00 0.00 4.02
3045 3142 7.674471 ACAAAAGCTAAGTTGTAGGAGAATC 57.326 36.000 8.22 0.00 36.22 2.52
3177 3274 8.722394 AGAAGCTAAAAGTTCTAAAGGAAATCG 58.278 33.333 0.00 0.00 35.51 3.34
3232 3329 8.698973 ACTATCATAGCACAGTACAATAGACT 57.301 34.615 0.00 0.00 0.00 3.24
3542 3640 2.293399 GAGAACAAAATCCAACCAGCGT 59.707 45.455 0.00 0.00 0.00 5.07
3579 3677 8.020244 TGCAACACACACACAATACATAATTAG 58.980 33.333 0.00 0.00 0.00 1.73
3590 3688 2.670479 CAAGTTGCAACACACACACAA 58.330 42.857 30.11 0.00 0.00 3.33
3593 3697 3.415237 GCAAGTTGCAACACACACA 57.585 47.368 30.11 0.00 44.26 3.72
3621 3725 0.035739 GGAACCTACAGGAAACGCCA 59.964 55.000 1.29 0.00 40.02 5.69
3632 3736 1.078637 GGGGCTTGTCGGAACCTAC 60.079 63.158 0.00 0.00 0.00 3.18
3633 3737 1.229400 AGGGGCTTGTCGGAACCTA 60.229 57.895 0.00 0.00 0.00 3.08
3649 3753 1.378250 CTTGCTGAAGGGGAGCAGG 60.378 63.158 0.00 0.00 46.81 4.85
3670 3774 2.305927 GTCCTTGGTTTCCTCCTCATCA 59.694 50.000 0.00 0.00 0.00 3.07
3748 3852 1.552348 GCATCGCCGAGTACATGCTC 61.552 60.000 2.58 0.00 38.89 4.26
3805 3909 0.670546 ACCCGACATCGACAAGCTTG 60.671 55.000 24.84 24.84 43.02 4.01
4101 4225 3.347216 ACAATGCCTTAGGTCACACATC 58.653 45.455 0.00 0.00 0.00 3.06
4187 4311 1.113788 AGCAACACACCAATGCAAGT 58.886 45.000 0.00 0.00 42.45 3.16
4188 4312 2.228138 AAGCAACACACCAATGCAAG 57.772 45.000 0.00 0.00 42.45 4.01
4191 4315 3.052036 CACTTAAGCAACACACCAATGC 58.948 45.455 1.29 0.00 40.34 3.56
4206 4330 5.707931 TGCATTTCATTCATTCGCACTTAA 58.292 33.333 0.00 0.00 0.00 1.85
4232 4356 9.729023 CCGAAATTATGAAAATAACATACAGCA 57.271 29.630 0.00 0.00 31.26 4.41
4251 4375 6.090898 CGAGTCTGTTCAGAAATACCGAAATT 59.909 38.462 3.99 0.00 0.00 1.82
4261 4385 5.392767 AATAGAGCGAGTCTGTTCAGAAA 57.607 39.130 3.99 0.00 31.19 2.52
4262 4386 5.184096 AGAAATAGAGCGAGTCTGTTCAGAA 59.816 40.000 3.99 0.00 35.66 3.02
4311 4435 7.596248 GAAACACTTTCTTCCACGTAGTGTATA 59.404 37.037 16.10 0.00 46.20 1.47
4312 4436 6.423001 GAAACACTTTCTTCCACGTAGTGTAT 59.577 38.462 16.10 6.47 46.20 2.29
4337 4468 7.165812 CCGACACTGAATTTTTAACTTGTCAAG 59.834 37.037 11.17 11.17 33.27 3.02
4342 4473 5.519722 AGCCGACACTGAATTTTTAACTTG 58.480 37.500 0.00 0.00 0.00 3.16
4359 4490 3.424962 GCAAGACAAGTTCATAAGCCGAC 60.425 47.826 0.00 0.00 0.00 4.79
4536 4667 6.317789 TCTTTGATCACAACCAACTTCATC 57.682 37.500 0.00 0.00 35.63 2.92
4566 4697 1.153823 GTCGTATGCGTGTGGCTCT 60.154 57.895 2.37 0.00 44.05 4.09
4608 4739 4.351054 AAGGCCGTCTTGCTGGGG 62.351 66.667 0.00 0.00 33.76 4.96


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

AutoCloner maintained by Alex Coulton.