Multiple sequence alignment - TraesCS1D01G269300

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G269300 chr1D 100.000 4345 0 0 1 4345 364774219 364769875 0.000000e+00 8024.0
1 TraesCS1D01G269300 chr1B 93.899 2557 99 24 1803 4345 488217536 488215023 0.000000e+00 3805.0
2 TraesCS1D01G269300 chr1B 92.034 954 46 14 848 1788 488218454 488217518 0.000000e+00 1314.0
3 TraesCS1D01G269300 chr1B 90.164 366 35 1 69 433 488219135 488218770 3.930000e-130 475.0
4 TraesCS1D01G269300 chr1B 94.048 84 5 0 464 547 488218766 488218683 1.270000e-25 128.0
5 TraesCS1D01G269300 chr1B 75.746 268 55 9 276 537 357910160 357910423 4.560000e-25 126.0
6 TraesCS1D01G269300 chr1A 93.702 2588 86 24 1803 4345 463829428 463826873 0.000000e+00 3805.0
7 TraesCS1D01G269300 chr1A 92.265 1086 55 11 706 1788 463830469 463829410 0.000000e+00 1513.0
8 TraesCS1D01G269300 chr1A 89.644 618 61 3 1 616 463855171 463854555 0.000000e+00 784.0
9 TraesCS1D01G269300 chr1A 94.444 36 1 1 429 463 590688924 590688959 2.000000e-03 54.7
10 TraesCS1D01G269300 chr5D 84.086 509 52 11 2363 2843 142542095 142542602 8.510000e-127 464.0
11 TraesCS1D01G269300 chr2D 83.300 503 55 18 2369 2843 321610038 321609537 1.860000e-118 436.0
12 TraesCS1D01G269300 chr7A 81.925 509 53 19 2363 2843 616160027 616160524 1.130000e-105 394.0
13 TraesCS1D01G269300 chr6D 84.899 298 35 9 2038 2333 384363757 384364046 4.250000e-75 292.0
14 TraesCS1D01G269300 chr6D 84.281 299 35 9 2038 2333 384368795 384369084 9.200000e-72 281.0
15 TraesCS1D01G269300 chr6D 82.235 349 38 16 1990 2333 384366899 384367228 3.310000e-71 279.0
16 TraesCS1D01G269300 chr6B 91.279 172 15 0 1975 2146 383821979 383821808 7.260000e-58 235.0
17 TraesCS1D01G269300 chrUn 89.773 176 18 0 1971 2146 300810628 300810803 4.370000e-55 226.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G269300 chr1D 364769875 364774219 4344 True 8024.0 8024 100.00000 1 4345 1 chr1D.!!$R1 4344
1 TraesCS1D01G269300 chr1B 488215023 488219135 4112 True 1430.5 3805 92.53625 69 4345 4 chr1B.!!$R1 4276
2 TraesCS1D01G269300 chr1A 463826873 463830469 3596 True 2659.0 3805 92.98350 706 4345 2 chr1A.!!$R2 3639
3 TraesCS1D01G269300 chr1A 463854555 463855171 616 True 784.0 784 89.64400 1 616 1 chr1A.!!$R1 615
4 TraesCS1D01G269300 chr5D 142542095 142542602 507 False 464.0 464 84.08600 2363 2843 1 chr5D.!!$F1 480
5 TraesCS1D01G269300 chr2D 321609537 321610038 501 True 436.0 436 83.30000 2369 2843 1 chr2D.!!$R1 474
6 TraesCS1D01G269300 chr6D 384363757 384369084 5327 False 284.0 292 83.80500 1990 2333 3 chr6D.!!$F1 343

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
704 733 0.101399 CTGATCACGGAGGAACGGAG 59.899 60.000 0.00 0.00 38.39 4.63 F
752 781 0.742505 TTCCTATGTGTACGGAGCCG 59.257 55.000 7.48 7.48 46.03 5.52 F
911 942 1.224120 AGCCATAATCCCTCTCCCTCA 59.776 52.381 0.00 0.00 0.00 3.86 F
1769 1813 1.418373 CGTTCGATTGTGCTGAGACA 58.582 50.000 0.00 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 1925 0.391661 ATGCATTTCTGTCGTCGGCT 60.392 50.0 0.00 0.0 0.00 5.52 R
2256 5700 5.350365 TCCACGCAAACATTACTTCTATGAC 59.650 40.0 0.00 0.0 0.00 3.06 R
2279 5723 6.000840 AGTTTTTCAGAGTTCAGAAGGGATC 58.999 40.0 0.00 0.0 0.00 3.36 R
3389 6882 0.652071 GACATTGCGATCGATGTGCA 59.348 50.0 22.67 15.8 45.08 4.57 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
48 49 1.675116 GCCAACCTAGGAAAGACGGAC 60.675 57.143 17.98 0.00 0.00 4.79
54 55 2.093447 CCTAGGAAAGACGGACTGCATT 60.093 50.000 1.05 0.00 0.00 3.56
75 76 5.751243 TTTGTCACTAGAACCAAAAGAGC 57.249 39.130 0.00 0.00 0.00 4.09
82 83 2.062636 AGAACCAAAAGAGCCCACCTA 58.937 47.619 0.00 0.00 0.00 3.08
120 121 5.634118 AGAACATGAGACTCCAAAATCCAA 58.366 37.500 0.00 0.00 0.00 3.53
136 137 4.473520 AATCACGCTCGGGGGCTG 62.474 66.667 0.00 0.00 0.00 4.85
279 281 2.290577 GGAAGCATCTTGGAGAGTTGGT 60.291 50.000 0.00 0.00 37.39 3.67
288 290 1.337728 TGGAGAGTTGGTGTACATGCG 60.338 52.381 0.00 0.00 0.00 4.73
304 306 0.974010 TGCGAAGGAACCCTCGGTAT 60.974 55.000 12.71 0.00 33.12 2.73
316 318 3.118519 ACCCTCGGTATGATGTTGGTTAC 60.119 47.826 0.00 0.00 32.11 2.50
323 325 2.489938 TGATGTTGGTTACAGAGCCC 57.510 50.000 0.00 0.00 40.83 5.19
375 377 2.679059 GCGAGGTTAGGGGTAGTTTTCC 60.679 54.545 0.00 0.00 0.00 3.13
387 389 3.132467 GGTAGTTTTCCGCCATCTACTCT 59.868 47.826 0.00 0.00 33.69 3.24
394 396 1.609555 CCGCCATCTACTCTGTAGACC 59.390 57.143 9.27 2.06 0.00 3.85
435 437 5.779241 TCATCATCCCTTTTGTAACCTCT 57.221 39.130 0.00 0.00 0.00 3.69
436 438 5.745227 TCATCATCCCTTTTGTAACCTCTC 58.255 41.667 0.00 0.00 0.00 3.20
550 553 0.247736 CTCCCTTCTGTCACTTCCGG 59.752 60.000 0.00 0.00 0.00 5.14
568 571 2.877974 GACGCGTTCGCCACTTGTT 61.878 57.895 15.53 0.00 39.84 2.83
578 581 2.041244 CGCCACTTGTTAGTTTTTCGC 58.959 47.619 0.00 0.00 30.26 4.70
582 585 3.181495 CCACTTGTTAGTTTTTCGCACCA 60.181 43.478 0.00 0.00 30.26 4.17
584 587 5.278071 CCACTTGTTAGTTTTTCGCACCATA 60.278 40.000 0.00 0.00 30.26 2.74
616 619 1.115467 ATCTCGGAGATCAAACGCCT 58.885 50.000 14.68 0.00 33.89 5.52
617 620 0.895530 TCTCGGAGATCAAACGCCTT 59.104 50.000 2.97 0.00 33.89 4.35
619 622 2.076863 CTCGGAGATCAAACGCCTTTT 58.923 47.619 0.00 0.00 33.89 2.27
620 623 3.056393 TCTCGGAGATCAAACGCCTTTTA 60.056 43.478 2.97 0.00 33.89 1.52
621 624 3.666274 TCGGAGATCAAACGCCTTTTAA 58.334 40.909 0.00 0.00 0.00 1.52
623 626 4.515944 TCGGAGATCAAACGCCTTTTAAAA 59.484 37.500 0.00 0.00 0.00 1.52
627 630 5.769367 AGATCAAACGCCTTTTAAAACTCC 58.231 37.500 0.00 0.00 0.00 3.85
628 631 3.954999 TCAAACGCCTTTTAAAACTCCG 58.045 40.909 0.00 3.00 0.00 4.63
630 633 0.236449 ACGCCTTTTAAAACTCCGCG 59.764 50.000 18.13 18.13 43.45 6.46
631 634 0.513820 CGCCTTTTAAAACTCCGCGA 59.486 50.000 8.23 0.00 40.50 5.87
632 635 1.069771 CGCCTTTTAAAACTCCGCGAA 60.070 47.619 8.23 0.00 40.50 4.70
634 637 2.031420 GCCTTTTAAAACTCCGCGAACT 60.031 45.455 8.23 0.00 0.00 3.01
635 638 3.549423 GCCTTTTAAAACTCCGCGAACTT 60.549 43.478 8.23 0.00 0.00 2.66
652 655 7.958567 CCGCGAACTTTTGTTATGTAAGATTAA 59.041 33.333 8.23 0.00 43.66 1.40
673 702 9.659830 GATTAATTGTGAACATAATCGGGTTAC 57.340 33.333 0.00 0.00 0.00 2.50
684 713 1.214589 CGGGTTACGGACTGTCTGG 59.785 63.158 20.03 9.31 39.42 3.86
689 718 1.204941 GTTACGGACTGTCTGGCTGAT 59.795 52.381 20.03 2.07 33.22 2.90
696 725 0.179116 CTGTCTGGCTGATCACGGAG 60.179 60.000 0.00 0.00 0.00 4.63
699 728 0.614697 TCTGGCTGATCACGGAGGAA 60.615 55.000 0.00 0.00 0.00 3.36
700 729 0.460987 CTGGCTGATCACGGAGGAAC 60.461 60.000 0.00 0.00 0.00 3.62
701 730 1.519455 GGCTGATCACGGAGGAACG 60.519 63.158 0.00 0.00 40.31 3.95
702 731 1.519455 GCTGATCACGGAGGAACGG 60.519 63.158 0.00 0.00 38.39 4.44
703 732 1.945354 GCTGATCACGGAGGAACGGA 61.945 60.000 0.00 0.00 38.39 4.69
704 733 0.101399 CTGATCACGGAGGAACGGAG 59.899 60.000 0.00 0.00 38.39 4.63
729 758 3.878778 AGGACTGCTTGTTGGATATGTC 58.121 45.455 0.00 0.00 0.00 3.06
738 767 6.889177 TGCTTGTTGGATATGTCAATTTCCTA 59.111 34.615 0.00 0.00 35.53 2.94
746 775 7.655732 TGGATATGTCAATTTCCTATGTGTACG 59.344 37.037 0.00 0.00 35.53 3.67
752 781 0.742505 TTCCTATGTGTACGGAGCCG 59.257 55.000 7.48 7.48 46.03 5.52
774 805 3.623510 GCTAGTTCCAGCTGATTGTAACC 59.376 47.826 17.39 0.00 38.57 2.85
814 845 8.785329 AAAACAATTGTGGTGACTGTAAAATT 57.215 26.923 12.82 0.00 0.00 1.82
815 846 8.785329 AAACAATTGTGGTGACTGTAAAATTT 57.215 26.923 12.82 0.00 0.00 1.82
817 848 8.865590 ACAATTGTGGTGACTGTAAAATTTAC 57.134 30.769 11.07 8.82 0.00 2.01
821 852 7.867305 TGTGGTGACTGTAAAATTTACAGAA 57.133 32.000 37.58 26.53 45.69 3.02
822 853 8.282455 TGTGGTGACTGTAAAATTTACAGAAA 57.718 30.769 37.58 26.26 45.69 2.52
823 854 8.402472 TGTGGTGACTGTAAAATTTACAGAAAG 58.598 33.333 37.58 21.21 45.69 2.62
825 856 9.179909 TGGTGACTGTAAAATTTACAGAAAGAA 57.820 29.630 37.58 22.87 45.69 2.52
831 862 9.393249 CTGTAAAATTTACAGAAAGAATTCGCA 57.607 29.630 31.39 2.29 45.69 5.10
833 864 9.607285 GTAAAATTTACAGAAAGAATTCGCAGA 57.393 29.630 10.70 0.00 40.63 4.26
835 866 9.528018 AAAATTTACAGAAAGAATTCGCAGAAA 57.472 25.926 0.00 0.00 45.90 2.52
836 867 9.528018 AAATTTACAGAAAGAATTCGCAGAAAA 57.472 25.926 0.00 0.00 45.90 2.29
837 868 9.528018 AATTTACAGAAAGAATTCGCAGAAAAA 57.472 25.926 0.00 0.00 45.90 1.94
911 942 1.224120 AGCCATAATCCCTCTCCCTCA 59.776 52.381 0.00 0.00 0.00 3.86
1196 1235 5.586243 GCTTCCTGTAGATAATCAAACAGCA 59.414 40.000 5.84 0.00 38.39 4.41
1214 1253 6.377327 ACAGCAAATTAGGGTATCGAATTG 57.623 37.500 0.00 0.00 32.35 2.32
1227 1266 2.917933 TCGAATTGGGGATACTGCTTG 58.082 47.619 0.00 0.00 0.00 4.01
1278 1320 6.594788 ATGGTGAAAATTGTATTGCTCTGT 57.405 33.333 0.00 0.00 0.00 3.41
1314 1356 6.619232 GCTTTGCTTCAAATGATTAGTTTGGC 60.619 38.462 0.00 0.00 37.22 4.52
1576 1620 7.066284 AGTGTGTTCATTTACTCATTGCTATCC 59.934 37.037 0.00 0.00 0.00 2.59
1662 1706 5.363562 AGCTCATGGATGTTGTCATAGAA 57.636 39.130 0.00 0.00 34.06 2.10
1769 1813 1.418373 CGTTCGATTGTGCTGAGACA 58.582 50.000 0.00 0.00 0.00 3.41
1770 1814 1.995484 CGTTCGATTGTGCTGAGACAT 59.005 47.619 0.00 0.00 0.00 3.06
1771 1815 2.222663 CGTTCGATTGTGCTGAGACATG 60.223 50.000 0.00 0.00 0.00 3.21
1772 1816 2.738846 GTTCGATTGTGCTGAGACATGT 59.261 45.455 0.00 0.00 0.00 3.21
1773 1817 3.044235 TCGATTGTGCTGAGACATGTT 57.956 42.857 0.00 0.00 0.00 2.71
1774 1818 3.402110 TCGATTGTGCTGAGACATGTTT 58.598 40.909 0.00 0.00 0.00 2.83
1775 1819 3.814842 TCGATTGTGCTGAGACATGTTTT 59.185 39.130 0.00 0.00 0.00 2.43
1776 1820 3.910170 CGATTGTGCTGAGACATGTTTTG 59.090 43.478 0.00 0.00 0.00 2.44
1777 1821 4.319694 CGATTGTGCTGAGACATGTTTTGA 60.320 41.667 0.00 0.00 0.00 2.69
1778 1822 4.979943 TTGTGCTGAGACATGTTTTGAA 57.020 36.364 0.00 0.00 0.00 2.69
1779 1823 5.518848 TTGTGCTGAGACATGTTTTGAAT 57.481 34.783 0.00 0.00 0.00 2.57
1780 1824 4.862350 TGTGCTGAGACATGTTTTGAATG 58.138 39.130 0.00 0.00 0.00 2.67
1781 1825 4.579753 TGTGCTGAGACATGTTTTGAATGA 59.420 37.500 0.00 0.00 0.00 2.57
1782 1826 4.913924 GTGCTGAGACATGTTTTGAATGAC 59.086 41.667 0.00 0.00 0.00 3.06
1783 1827 4.022935 TGCTGAGACATGTTTTGAATGACC 60.023 41.667 0.00 0.00 0.00 4.02
1784 1828 4.022935 GCTGAGACATGTTTTGAATGACCA 60.023 41.667 0.00 0.00 0.00 4.02
1785 1829 5.694231 TGAGACATGTTTTGAATGACCAG 57.306 39.130 0.00 0.00 0.00 4.00
1786 1830 5.375773 TGAGACATGTTTTGAATGACCAGA 58.624 37.500 0.00 0.00 0.00 3.86
1787 1831 6.005823 TGAGACATGTTTTGAATGACCAGAT 58.994 36.000 0.00 0.00 0.00 2.90
1788 1832 6.149973 TGAGACATGTTTTGAATGACCAGATC 59.850 38.462 0.00 0.00 0.00 2.75
1789 1833 5.416952 AGACATGTTTTGAATGACCAGATCC 59.583 40.000 0.00 0.00 0.00 3.36
1790 1834 5.078949 ACATGTTTTGAATGACCAGATCCA 58.921 37.500 0.00 0.00 0.00 3.41
1791 1835 5.718130 ACATGTTTTGAATGACCAGATCCAT 59.282 36.000 0.00 0.00 0.00 3.41
1792 1836 6.211986 ACATGTTTTGAATGACCAGATCCATT 59.788 34.615 0.00 0.00 35.87 3.16
1793 1837 6.669125 TGTTTTGAATGACCAGATCCATTT 57.331 33.333 0.00 0.00 33.57 2.32
1794 1838 6.690530 TGTTTTGAATGACCAGATCCATTTC 58.309 36.000 0.00 0.00 33.57 2.17
1795 1839 6.494491 TGTTTTGAATGACCAGATCCATTTCT 59.506 34.615 0.00 0.00 33.57 2.52
1796 1840 7.669304 TGTTTTGAATGACCAGATCCATTTCTA 59.331 33.333 0.00 0.00 33.57 2.10
1797 1841 8.522830 GTTTTGAATGACCAGATCCATTTCTAA 58.477 33.333 0.00 0.00 33.57 2.10
1798 1842 8.648698 TTTGAATGACCAGATCCATTTCTAAA 57.351 30.769 0.00 0.00 33.57 1.85
1799 1843 8.648698 TTGAATGACCAGATCCATTTCTAAAA 57.351 30.769 0.00 0.00 33.57 1.52
1800 1844 8.648698 TGAATGACCAGATCCATTTCTAAAAA 57.351 30.769 0.00 0.00 33.57 1.94
1842 1886 1.562672 ATTCCTGGCTAGGCAACCGT 61.563 55.000 20.64 4.38 44.22 4.83
1869 1913 2.951457 TCATAGTGATGAACCGCGAA 57.049 45.000 8.23 0.00 39.20 4.70
1973 2017 1.886222 GCTGGGCATGGTAAGACAACA 60.886 52.381 0.00 0.00 0.00 3.33
2256 5700 2.548057 ACTGTGCAACTTGGTTACGATG 59.452 45.455 0.00 0.00 38.04 3.84
2279 5723 5.121611 TGTCATAGAAGTAATGTTTGCGTGG 59.878 40.000 0.00 0.00 0.00 4.94
2404 5849 0.881796 GGCAGACTTGTGTAAAGGCC 59.118 55.000 0.00 0.00 0.00 5.19
2418 5864 6.038161 TGTGTAAAGGCCATATTTCTTGATCG 59.962 38.462 5.01 0.00 0.00 3.69
2941 6423 2.520536 GCTGTGGGTGAGTGGTCCT 61.521 63.158 0.00 0.00 0.00 3.85
2945 6427 0.608640 GTGGGTGAGTGGTCCTACAG 59.391 60.000 0.00 0.00 35.69 2.74
2955 6437 5.958380 TGAGTGGTCCTACAGTCTAATGATT 59.042 40.000 0.00 0.00 40.61 2.57
2995 6479 1.375098 GCATGCTCTCTCCAGTTGCC 61.375 60.000 11.37 0.00 0.00 4.52
3027 6517 7.623999 AGATCTACATACCATTCCATCAAGT 57.376 36.000 0.00 0.00 0.00 3.16
3038 6528 0.036388 CCATCAAGTAGTGCGGGTGT 60.036 55.000 0.00 0.00 0.00 4.16
3154 6647 5.929415 TGTATGTTTCGATCAACTGCAGTTA 59.071 36.000 30.67 19.01 36.32 2.24
3290 6783 2.158842 AGCAGCTTTCCGCATCTTATCT 60.159 45.455 0.00 0.00 42.61 1.98
3347 6840 2.232452 AGAGAGACCTCCAACATGAACG 59.768 50.000 0.00 0.00 40.30 3.95
3353 6846 3.338249 ACCTCCAACATGAACGATGAAG 58.662 45.455 0.00 0.00 35.80 3.02
3380 6873 6.137794 ACACTTTACCAGAGATCATACTCG 57.862 41.667 0.00 0.00 41.25 4.18
3386 6879 2.095668 CCAGAGATCATACTCGCCGTAC 60.096 54.545 0.00 0.00 41.25 3.67
3388 6881 0.237761 AGATCATACTCGCCGTACGC 59.762 55.000 10.49 4.62 43.23 4.42
3389 6882 0.237761 GATCATACTCGCCGTACGCT 59.762 55.000 10.49 0.00 43.23 5.07
3397 6890 3.913573 GCCGTACGCTGCACATCG 61.914 66.667 10.49 0.00 0.00 3.84
3401 6894 1.840061 GTACGCTGCACATCGATCG 59.160 57.895 9.36 9.36 0.00 3.69
3442 6935 5.688500 GCCATCATAGGACAATTTCTCTGGA 60.689 44.000 0.00 0.00 0.00 3.86
3443 6936 5.762218 CCATCATAGGACAATTTCTCTGGAC 59.238 44.000 0.00 0.00 0.00 4.02
3444 6937 5.359194 TCATAGGACAATTTCTCTGGACC 57.641 43.478 0.00 0.00 0.00 4.46
3445 6938 5.032846 TCATAGGACAATTTCTCTGGACCT 58.967 41.667 0.00 0.00 0.00 3.85
3446 6939 5.488919 TCATAGGACAATTTCTCTGGACCTT 59.511 40.000 0.00 0.00 0.00 3.50
3447 6940 6.672218 TCATAGGACAATTTCTCTGGACCTTA 59.328 38.462 0.00 0.00 0.00 2.69
3474 6973 7.102346 CCTATGTGTGGAATGAGGAATCTATC 58.898 42.308 0.00 0.00 0.00 2.08
3696 7205 2.682563 GCATTTTCCGGACTACCCATGA 60.683 50.000 1.83 0.00 34.14 3.07
3724 7233 2.230992 TGGTGAAATTTGATCGGCCTTG 59.769 45.455 0.00 0.00 0.00 3.61
3753 7275 8.530311 TCCACATTTGAAATGTTATGCTGTTAT 58.470 29.630 20.00 0.00 0.00 1.89
3754 7276 9.800433 CCACATTTGAAATGTTATGCTGTTATA 57.200 29.630 20.00 0.00 0.00 0.98
3766 7288 8.839343 TGTTATGCTGTTATACAATTCATCAGG 58.161 33.333 0.00 0.00 0.00 3.86
3767 7289 5.756195 TGCTGTTATACAATTCATCAGGC 57.244 39.130 0.00 0.00 0.00 4.85
3768 7290 5.192176 TGCTGTTATACAATTCATCAGGCA 58.808 37.500 0.00 0.00 0.00 4.75
3769 7291 5.066375 TGCTGTTATACAATTCATCAGGCAC 59.934 40.000 0.00 0.00 0.00 5.01
3770 7292 5.297776 GCTGTTATACAATTCATCAGGCACT 59.702 40.000 0.00 0.00 43.88 4.40
3771 7293 6.483307 GCTGTTATACAATTCATCAGGCACTA 59.517 38.462 0.00 0.00 36.02 2.74
3784 7306 1.176527 GGCACTAGAATTTGCAGGCA 58.823 50.000 0.00 0.00 40.75 4.75
3786 7308 2.599659 GCACTAGAATTTGCAGGCAAC 58.400 47.619 6.14 0.00 38.68 4.17
3947 7469 7.547370 AGTTACTCTCAAATTGACATACTGCTC 59.453 37.037 0.00 0.00 0.00 4.26
4013 7553 2.923121 TGCCAGAGCTATGGATTTCAC 58.077 47.619 31.31 12.28 43.57 3.18
4014 7554 2.239402 TGCCAGAGCTATGGATTTCACA 59.761 45.455 31.31 14.84 43.57 3.58
4054 7594 5.649395 ACAGTATCCAGGTTCATTCACATTG 59.351 40.000 0.00 0.00 0.00 2.82
4133 7673 5.441718 AAGCCTTTGTCCTATCAATCTCA 57.558 39.130 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.721142 CTTCTTGAAGCTTTTGAGCTAGC 58.279 43.478 6.62 6.62 45.54 3.42
14 15 3.033909 AGGTTGGCTTCTTGAAGCTTTT 58.966 40.909 27.48 11.74 44.86 2.27
33 34 0.895530 TGCAGTCCGTCTTTCCTAGG 59.104 55.000 0.82 0.82 0.00 3.02
48 49 5.437289 TTTGGTTCTAGTGACAAATGCAG 57.563 39.130 0.00 0.00 0.00 4.41
54 55 4.134563 GGCTCTTTTGGTTCTAGTGACAA 58.865 43.478 0.00 0.00 0.00 3.18
75 76 0.468648 GGGGACGAAATCTAGGTGGG 59.531 60.000 0.00 0.00 0.00 4.61
82 83 3.502123 TGTTCTTTGGGGACGAAATCT 57.498 42.857 0.00 0.00 31.93 2.40
136 137 1.356624 GGTGTATTGCATCGCCAGC 59.643 57.895 10.41 1.91 34.73 4.85
255 257 4.077822 CAACTCTCCAAGATGCTTCCTTT 58.922 43.478 0.00 0.00 0.00 3.11
258 260 2.290577 ACCAACTCTCCAAGATGCTTCC 60.291 50.000 0.00 0.00 0.00 3.46
279 281 0.981183 AGGGTTCCTTCGCATGTACA 59.019 50.000 0.00 0.00 0.00 2.90
288 290 2.434702 ACATCATACCGAGGGTTCCTTC 59.565 50.000 0.00 0.00 37.09 3.46
304 306 1.338674 CGGGCTCTGTAACCAACATCA 60.339 52.381 0.00 0.00 37.50 3.07
316 318 1.078426 CCAGGGTTTACGGGCTCTG 60.078 63.158 0.00 0.00 0.00 3.35
323 325 0.037605 AGCGAGAACCAGGGTTTACG 60.038 55.000 19.06 19.06 38.60 3.18
375 377 2.577700 AGGTCTACAGAGTAGATGGCG 58.422 52.381 9.80 0.00 0.00 5.69
476 479 2.615912 ACGGTGAGGTAATACTCTACGC 59.384 50.000 0.00 0.00 39.28 4.42
550 553 1.550659 TAACAAGTGGCGAACGCGTC 61.551 55.000 14.44 5.31 43.78 5.19
582 585 2.304180 CCGAGATGAGGAGGCCATTTAT 59.696 50.000 5.01 0.00 0.00 1.40
584 587 0.471617 CCGAGATGAGGAGGCCATTT 59.528 55.000 5.01 0.00 0.00 2.32
596 599 1.202463 AGGCGTTTGATCTCCGAGATG 60.202 52.381 15.85 2.23 34.53 2.90
616 619 5.400703 ACAAAAGTTCGCGGAGTTTTAAAA 58.599 33.333 27.91 0.00 32.44 1.52
617 620 4.984205 ACAAAAGTTCGCGGAGTTTTAAA 58.016 34.783 27.91 0.35 32.44 1.52
619 622 4.619437 AACAAAAGTTCGCGGAGTTTTA 57.381 36.364 27.91 0.00 32.44 1.52
620 623 3.497297 AACAAAAGTTCGCGGAGTTTT 57.503 38.095 24.12 24.12 33.58 2.43
621 624 4.035909 ACATAACAAAAGTTCGCGGAGTTT 59.964 37.500 14.56 14.56 0.00 2.66
623 626 3.135994 ACATAACAAAAGTTCGCGGAGT 58.864 40.909 6.13 0.00 0.00 3.85
627 630 8.868744 TTAATCTTACATAACAAAAGTTCGCG 57.131 30.769 0.00 0.00 0.00 5.87
652 655 4.573201 CCGTAACCCGATTATGTTCACAAT 59.427 41.667 0.00 0.00 39.56 2.71
662 691 2.424601 CAGACAGTCCGTAACCCGATTA 59.575 50.000 0.00 0.00 39.56 1.75
664 693 0.815734 CAGACAGTCCGTAACCCGAT 59.184 55.000 0.00 0.00 39.56 4.18
666 695 1.214589 CCAGACAGTCCGTAACCCG 59.785 63.158 0.00 0.00 0.00 5.28
673 702 0.459237 GTGATCAGCCAGACAGTCCG 60.459 60.000 0.00 0.00 0.00 4.79
684 713 1.519455 CCGTTCCTCCGTGATCAGC 60.519 63.158 0.00 0.00 0.00 4.26
689 718 2.141011 TACCCTCCGTTCCTCCGTGA 62.141 60.000 0.00 0.00 0.00 4.35
696 725 1.957765 GCAGTCCTACCCTCCGTTCC 61.958 65.000 0.00 0.00 0.00 3.62
699 728 1.078710 AAGCAGTCCTACCCTCCGT 59.921 57.895 0.00 0.00 0.00 4.69
700 729 1.258445 ACAAGCAGTCCTACCCTCCG 61.258 60.000 0.00 0.00 0.00 4.63
701 730 0.984995 AACAAGCAGTCCTACCCTCC 59.015 55.000 0.00 0.00 0.00 4.30
702 731 1.339151 CCAACAAGCAGTCCTACCCTC 60.339 57.143 0.00 0.00 0.00 4.30
703 732 0.693049 CCAACAAGCAGTCCTACCCT 59.307 55.000 0.00 0.00 0.00 4.34
704 733 0.690762 TCCAACAAGCAGTCCTACCC 59.309 55.000 0.00 0.00 0.00 3.69
729 758 3.560068 GGCTCCGTACACATAGGAAATTG 59.440 47.826 0.00 0.00 33.10 2.32
738 767 1.035932 ACTAGCGGCTCCGTACACAT 61.036 55.000 5.39 0.00 42.09 3.21
746 775 2.202946 GCTGGAACTAGCGGCTCC 60.203 66.667 5.39 1.76 33.46 4.70
752 781 3.623510 GGTTACAATCAGCTGGAACTAGC 59.376 47.826 15.13 2.01 39.68 3.42
793 824 8.864069 TGTAAATTTTACAGTCACCACAATTG 57.136 30.769 16.17 3.24 0.00 2.32
838 869 9.958234 GCTTTCTTTTCTCTTTCTTTCTGTATT 57.042 29.630 0.00 0.00 0.00 1.89
839 870 8.286097 CGCTTTCTTTTCTCTTTCTTTCTGTAT 58.714 33.333 0.00 0.00 0.00 2.29
840 871 7.494625 TCGCTTTCTTTTCTCTTTCTTTCTGTA 59.505 33.333 0.00 0.00 0.00 2.74
841 872 6.316390 TCGCTTTCTTTTCTCTTTCTTTCTGT 59.684 34.615 0.00 0.00 0.00 3.41
842 873 6.719365 TCGCTTTCTTTTCTCTTTCTTTCTG 58.281 36.000 0.00 0.00 0.00 3.02
843 874 6.763610 TCTCGCTTTCTTTTCTCTTTCTTTCT 59.236 34.615 0.00 0.00 0.00 2.52
844 875 6.949449 TCTCGCTTTCTTTTCTCTTTCTTTC 58.051 36.000 0.00 0.00 0.00 2.62
845 876 6.927294 TCTCGCTTTCTTTTCTCTTTCTTT 57.073 33.333 0.00 0.00 0.00 2.52
942 973 4.824515 AGAGGGAGGGGTCGAGCG 62.825 72.222 8.77 0.00 0.00 5.03
953 984 1.064611 CCGAAGTAGGTCTGAGAGGGA 60.065 57.143 0.00 0.00 0.00 4.20
1049 1087 2.106332 GGGAGATGTACGGGTGCG 59.894 66.667 0.00 0.00 0.00 5.34
1196 1235 5.656549 TCCCCAATTCGATACCCTAATTT 57.343 39.130 0.00 0.00 0.00 1.82
1214 1253 2.128771 TTTCTGCAAGCAGTATCCCC 57.871 50.000 20.34 0.00 43.96 4.81
1227 1266 9.294030 CCAACTGATAAAGTCATAATTTTCTGC 57.706 33.333 0.00 0.00 38.56 4.26
1278 1320 6.974932 TTTGAAGCAAAGCAATGTAAACAA 57.025 29.167 0.00 0.00 0.00 2.83
1314 1356 1.665916 CAGACCCAGCAGTGTGTCG 60.666 63.158 0.00 0.00 33.04 4.35
1549 1593 6.246420 AGCAATGAGTAAATGAACACACTC 57.754 37.500 0.00 0.00 38.30 3.51
1576 1620 0.462047 GGATACCACTGCAAGGTCCG 60.462 60.000 13.35 0.00 40.54 4.79
1636 1680 7.337938 TCTATGACAACATCCATGAGCTTTAA 58.662 34.615 0.00 0.00 37.87 1.52
1662 1706 1.694696 GGAATTCTAGCATCCCGGACT 59.305 52.381 0.73 0.00 0.00 3.85
1692 1736 3.113043 GACCACTACCTTAGGATGGGTT 58.887 50.000 19.43 5.34 37.07 4.11
1769 1813 6.862469 AATGGATCTGGTCATTCAAAACAT 57.138 33.333 0.00 0.00 0.00 2.71
1770 1814 6.494491 AGAAATGGATCTGGTCATTCAAAACA 59.506 34.615 0.00 0.00 33.03 2.83
1771 1815 6.928520 AGAAATGGATCTGGTCATTCAAAAC 58.071 36.000 0.00 0.00 33.03 2.43
1772 1816 8.648698 TTAGAAATGGATCTGGTCATTCAAAA 57.351 30.769 0.00 0.00 33.03 2.44
1773 1817 8.648698 TTTAGAAATGGATCTGGTCATTCAAA 57.351 30.769 0.00 0.00 33.03 2.69
1774 1818 8.648698 TTTTAGAAATGGATCTGGTCATTCAA 57.351 30.769 0.00 0.00 33.03 2.69
1775 1819 8.648698 TTTTTAGAAATGGATCTGGTCATTCA 57.351 30.769 0.00 0.00 33.03 2.57
1798 1842 7.507829 TCCATCTGGTCATTCAAAACATTTTT 58.492 30.769 0.00 0.00 36.34 1.94
1799 1843 7.065120 TCCATCTGGTCATTCAAAACATTTT 57.935 32.000 0.00 0.00 36.34 1.82
1800 1844 6.669125 TCCATCTGGTCATTCAAAACATTT 57.331 33.333 0.00 0.00 36.34 2.32
1801 1845 6.862469 ATCCATCTGGTCATTCAAAACATT 57.138 33.333 0.00 0.00 36.34 2.71
1842 1886 5.279006 GCGGTTCATCACTATGATCCTTCTA 60.279 44.000 11.68 0.00 44.71 2.10
1881 1925 0.391661 ATGCATTTCTGTCGTCGGCT 60.392 50.000 0.00 0.00 0.00 5.52
2211 5655 8.218488 AGTGTACCTCTTCTTATGGAAAAGTTT 58.782 33.333 0.00 0.00 33.07 2.66
2256 5700 5.350365 TCCACGCAAACATTACTTCTATGAC 59.650 40.000 0.00 0.00 0.00 3.06
2279 5723 6.000840 AGTTTTTCAGAGTTCAGAAGGGATC 58.999 40.000 0.00 0.00 0.00 3.36
2945 6427 8.289618 TGCACTACTCAAAACAAATCATTAGAC 58.710 33.333 0.00 0.00 0.00 2.59
2980 6464 1.609208 TTTTGGCAACTGGAGAGAGC 58.391 50.000 0.00 0.00 37.61 4.09
3002 6486 8.727100 ACTTGATGGAATGGTATGTAGATCTA 57.273 34.615 0.00 0.00 0.00 1.98
3004 6488 8.589338 ACTACTTGATGGAATGGTATGTAGATC 58.411 37.037 0.00 0.00 32.06 2.75
3025 6515 2.335316 TTTTTCACACCCGCACTACT 57.665 45.000 0.00 0.00 0.00 2.57
3026 6516 2.412325 CGATTTTTCACACCCGCACTAC 60.412 50.000 0.00 0.00 0.00 2.73
3027 6517 1.801771 CGATTTTTCACACCCGCACTA 59.198 47.619 0.00 0.00 0.00 2.74
3038 6528 6.094325 ACAAACCTGTCAGTAACGATTTTTCA 59.906 34.615 0.00 0.00 0.00 2.69
3347 6840 9.255304 GATCTCTGGTAAAGTGTTATCTTCATC 57.745 37.037 0.00 0.00 0.00 2.92
3353 6846 9.685828 GAGTATGATCTCTGGTAAAGTGTTATC 57.314 37.037 0.00 0.00 0.00 1.75
3380 6873 3.913573 CGATGTGCAGCGTACGGC 61.914 66.667 18.39 13.37 44.05 5.68
3386 6879 2.097661 ATTGCGATCGATGTGCAGCG 62.098 55.000 21.57 9.26 40.15 5.18
3388 6881 0.654160 ACATTGCGATCGATGTGCAG 59.346 50.000 21.57 12.26 43.80 4.41
3389 6882 0.652071 GACATTGCGATCGATGTGCA 59.348 50.000 22.67 15.80 45.08 4.57
3394 6887 4.319046 GCTACAAATGACATTGCGATCGAT 60.319 41.667 21.57 0.00 33.52 3.59
3397 6890 3.283256 CGCTACAAATGACATTGCGATC 58.717 45.455 20.07 3.31 43.81 3.69
3401 6894 1.135431 TGGCGCTACAAATGACATTGC 60.135 47.619 7.64 0.00 33.52 3.56
3442 6935 5.339200 CCTCATTCCACACATAGGTTAAGGT 60.339 44.000 0.00 0.00 0.00 3.50
3443 6936 5.104527 TCCTCATTCCACACATAGGTTAAGG 60.105 44.000 0.00 0.00 0.00 2.69
3444 6937 5.989477 TCCTCATTCCACACATAGGTTAAG 58.011 41.667 0.00 0.00 0.00 1.85
3445 6938 6.381498 TTCCTCATTCCACACATAGGTTAA 57.619 37.500 0.00 0.00 0.00 2.01
3446 6939 6.386927 AGATTCCTCATTCCACACATAGGTTA 59.613 38.462 0.00 0.00 0.00 2.85
3447 6940 4.927267 TTCCTCATTCCACACATAGGTT 57.073 40.909 0.00 0.00 0.00 3.50
3474 6973 2.959707 GGATATAGCCACCCTATCCTCG 59.040 54.545 1.04 0.00 38.47 4.63
3545 7045 1.556911 CAGCTCAGACCCCTACACAAT 59.443 52.381 0.00 0.00 0.00 2.71
3550 7050 1.686052 CAGATCAGCTCAGACCCCTAC 59.314 57.143 0.00 0.00 0.00 3.18
3621 7129 9.574516 GAACCAGTTCCATTTATCCATACTTAT 57.425 33.333 0.00 0.00 33.64 1.73
3696 7205 5.335661 GCCGATCAAATTTCACCAAAGTAGT 60.336 40.000 0.00 0.00 0.00 2.73
3724 7233 5.813672 AGCATAACATTTCAAATGTGGATGC 59.186 36.000 32.71 32.71 44.27 3.91
3753 7275 7.415541 GCAAATTCTAGTGCCTGATGAATTGTA 60.416 37.037 0.00 0.00 37.40 2.41
3754 7276 6.626623 GCAAATTCTAGTGCCTGATGAATTGT 60.627 38.462 0.00 0.00 37.40 2.71
3755 7277 5.747197 GCAAATTCTAGTGCCTGATGAATTG 59.253 40.000 0.00 0.00 37.40 2.32
3756 7278 5.419788 TGCAAATTCTAGTGCCTGATGAATT 59.580 36.000 1.03 0.00 40.14 2.17
3757 7279 4.951715 TGCAAATTCTAGTGCCTGATGAAT 59.048 37.500 1.03 0.00 40.14 2.57
3758 7280 4.334552 TGCAAATTCTAGTGCCTGATGAA 58.665 39.130 1.03 0.00 40.14 2.57
3759 7281 3.943381 CTGCAAATTCTAGTGCCTGATGA 59.057 43.478 1.03 0.00 40.14 2.92
3760 7282 3.066342 CCTGCAAATTCTAGTGCCTGATG 59.934 47.826 1.03 0.00 40.14 3.07
3761 7283 3.285484 CCTGCAAATTCTAGTGCCTGAT 58.715 45.455 1.03 0.00 40.14 2.90
3762 7284 2.715046 CCTGCAAATTCTAGTGCCTGA 58.285 47.619 1.03 0.00 40.14 3.86
3763 7285 1.133790 GCCTGCAAATTCTAGTGCCTG 59.866 52.381 1.03 0.00 40.14 4.85
3764 7286 1.272092 TGCCTGCAAATTCTAGTGCCT 60.272 47.619 1.03 0.00 40.14 4.75
3765 7287 1.176527 TGCCTGCAAATTCTAGTGCC 58.823 50.000 1.03 0.00 40.14 5.01
3766 7288 2.599659 GTTGCCTGCAAATTCTAGTGC 58.400 47.619 6.07 0.00 41.29 4.40
3767 7289 2.226437 ACGTTGCCTGCAAATTCTAGTG 59.774 45.455 6.07 0.00 37.70 2.74
3768 7290 2.504367 ACGTTGCCTGCAAATTCTAGT 58.496 42.857 6.07 0.00 37.70 2.57
3769 7291 4.882671 ATACGTTGCCTGCAAATTCTAG 57.117 40.909 6.07 0.00 37.70 2.43
3770 7292 6.540551 TGAATATACGTTGCCTGCAAATTCTA 59.459 34.615 19.13 9.22 37.70 2.10
3771 7293 5.356751 TGAATATACGTTGCCTGCAAATTCT 59.643 36.000 19.13 5.95 37.70 2.40
3784 7306 8.421784 AGGATATCTGTGTTGTGAATATACGTT 58.578 33.333 2.05 0.00 0.00 3.99
3970 7492 5.733620 AGGATGTAAAAAGTCGGTGTAGA 57.266 39.130 0.00 0.00 0.00 2.59
4013 7553 8.633561 TGGATACTGTGTAGTCATCTTCTATTG 58.366 37.037 0.00 0.00 38.36 1.90
4014 7554 8.768501 TGGATACTGTGTAGTCATCTTCTATT 57.231 34.615 0.00 0.00 38.36 1.73
4054 7594 4.067896 TCAGTCAGGAATCAACTGAAAGC 58.932 43.478 9.06 0.00 45.66 3.51
4133 7673 3.118112 CCATGCTCCCTGTCATAGACTTT 60.118 47.826 0.00 0.00 33.15 2.66


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

AutoCloner maintained by Alex Coulton.