Multiple sequence alignment - TraesCS5A01G154600

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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 TraesCS5A01G154600 chr5A 100.000 3076 0 0 1 3076 331890869 331887794 0.000000e+00 5681.0
1 TraesCS5A01G154600 chr5D 94.229 1161 35 14 327 1476 249088258 249087119 0.000000e+00 1744.0
2 TraesCS5A01G154600 chr5D 93.408 804 30 13 1611 2402 249087051 249086259 0.000000e+00 1170.0
3 TraesCS5A01G154600 chr5D 89.759 332 24 6 1 326 249088660 249088333 1.710000e-112 416.0
4 TraesCS5A01G154600 chr5D 100.000 37 0 0 1465 1501 249087101 249087065 5.500000e-08 69.4
5 TraesCS5A01G154600 chr5B 93.021 1003 35 14 518 1501 282012684 282011698 0.000000e+00 1432.0
6 TraesCS5A01G154600 chr5B 92.000 575 27 9 1807 2362 282011314 282010740 0.000000e+00 789.0
7 TraesCS5A01G154600 chr5B 90.964 332 23 5 1 326 282013427 282013097 1.010000e-119 440.0
8 TraesCS5A01G154600 chr5B 96.602 206 3 3 327 530 282013022 282012819 3.800000e-89 339.0
9 TraesCS5A01G154600 chr5B 97.175 177 5 0 1611 1787 282011683 282011507 1.790000e-77 300.0
10 TraesCS5A01G154600 chr1A 96.855 636 20 0 2441 3076 155144503 155143868 0.000000e+00 1064.0
11 TraesCS5A01G154600 chr2A 89.508 305 32 0 2442 2746 771550634 771550330 1.340000e-103 387.0
12 TraesCS5A01G154600 chr2A 86.147 231 32 0 1847 2077 750581233 750581003 1.830000e-62 250.0
13 TraesCS5A01G154600 chr2A 86.147 231 32 0 1847 2077 750617278 750617048 1.830000e-62 250.0
14 TraesCS5A01G154600 chr6B 90.071 282 28 0 2444 2725 567602840 567602559 1.740000e-97 366.0
15 TraesCS5A01G154600 chr7A 88.197 305 36 0 2442 2746 624884118 624883814 6.270000e-97 364.0
16 TraesCS5A01G154600 chr2B 88.745 231 26 0 1847 2077 758389858 758389628 1.810000e-72 283.0
17 TraesCS5A01G154600 chr2B 88.312 231 27 0 1847 2077 758147492 758147262 8.400000e-71 278.0
18 TraesCS5A01G154600 chr2D 87.069 232 30 0 1847 2078 585861020 585861251 2.350000e-66 263.0
19 TraesCS5A01G154600 chr2D 87.013 231 30 0 1847 2077 619426466 619426236 8.460000e-66 261.0
20 TraesCS5A01G154600 chr2D 86.147 231 32 0 1847 2077 619436523 619436293 1.830000e-62 250.0


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 TraesCS5A01G154600 chr5A 331887794 331890869 3075 True 5681.00 5681 100.0000 1 3076 1 chr5A.!!$R1 3075
1 TraesCS5A01G154600 chr5D 249086259 249088660 2401 True 849.85 1744 94.3490 1 2402 4 chr5D.!!$R1 2401
2 TraesCS5A01G154600 chr5B 282010740 282013427 2687 True 660.00 1432 93.9524 1 2362 5 chr5B.!!$R1 2361
3 TraesCS5A01G154600 chr1A 155143868 155144503 635 True 1064.00 1064 96.8550 2441 3076 1 chr1A.!!$R1 635

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
697 936 0.537653 CTTCCTTTCTCCGTCTCCCC 59.462 60.0 0.0 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2584 3066 0.179062 CAGTCCTGGGATGCTACTGC 60.179 60.0 0.0 0.0 40.2 4.4 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
42 44 6.041637 TGAACTACTAACTCAATGTGTCAGGT 59.958 38.462 0.00 0.00 0.00 4.00
57 60 5.525745 TGTGTCAGGTGTTGTACTTAATGTG 59.474 40.000 0.00 0.00 0.00 3.21
118 126 5.826601 TTGTATTGTCAAAGTTGCACTGA 57.173 34.783 0.00 0.00 0.00 3.41
127 135 9.979578 TTGTCAAAGTTGCACTGAAATATAAAT 57.020 25.926 0.00 0.00 0.00 1.40
156 164 8.487313 AAACAAAACAAGTTAAACTCATTCCC 57.513 30.769 0.00 0.00 0.00 3.97
157 165 6.270064 ACAAAACAAGTTAAACTCATTCCCG 58.730 36.000 0.00 0.00 0.00 5.14
209 217 3.004839 CAGGAGAAGTGACTTCGAGTTGA 59.995 47.826 18.62 0.00 44.34 3.18
221 229 6.984474 TGACTTCGAGTTGAACTATCTTGTTT 59.016 34.615 0.00 0.00 31.87 2.83
222 230 7.494625 TGACTTCGAGTTGAACTATCTTGTTTT 59.505 33.333 0.00 0.00 31.87 2.43
223 231 8.882415 ACTTCGAGTTGAACTATCTTGTTTTA 57.118 30.769 0.00 0.00 31.87 1.52
244 252 6.627395 TTATCGTAGGGTGCATTATTTTGG 57.373 37.500 0.00 0.00 0.00 3.28
262 270 2.919971 GCACGGGAGCCATAAGATC 58.080 57.895 0.00 0.00 0.00 2.75
266 274 2.103094 CACGGGAGCCATAAGATCTTCA 59.897 50.000 12.24 0.00 0.00 3.02
272 280 4.502950 GGAGCCATAAGATCTTCAGTGAGG 60.503 50.000 12.24 7.23 0.00 3.86
309 317 1.930251 CTAGGCCTAGGCAGCTGATA 58.070 55.000 34.09 15.06 44.11 2.15
332 414 3.788227 ATCAAACAGGCTCTGGTACAA 57.212 42.857 7.06 0.00 38.70 2.41
472 556 3.521796 GCCTTTGCCTCCGCATCC 61.522 66.667 0.00 0.00 46.67 3.51
525 756 5.893500 TGGATTCACCTAGCTAGCTAGTAT 58.106 41.667 37.50 27.25 43.22 2.12
619 858 6.921857 TCGTGCCTGAAAACTAAGTATATAGC 59.078 38.462 0.00 0.00 0.00 2.97
647 886 2.094675 GAGTTGTCATCACATTGGGGG 58.905 52.381 0.00 0.00 30.55 5.40
648 887 1.428912 AGTTGTCATCACATTGGGGGT 59.571 47.619 0.00 0.00 30.55 4.95
649 888 1.818674 GTTGTCATCACATTGGGGGTC 59.181 52.381 0.00 0.00 30.55 4.46
652 891 2.158400 TGTCATCACATTGGGGGTCAAA 60.158 45.455 0.00 0.00 39.05 2.69
653 892 2.493278 GTCATCACATTGGGGGTCAAAG 59.507 50.000 0.00 0.00 39.05 2.77
654 893 2.378208 TCATCACATTGGGGGTCAAAGA 59.622 45.455 0.00 0.00 39.05 2.52
655 894 2.584835 TCACATTGGGGGTCAAAGAG 57.415 50.000 0.00 0.00 39.05 2.85
656 895 0.890683 CACATTGGGGGTCAAAGAGC 59.109 55.000 0.00 0.00 39.05 4.09
657 896 0.779997 ACATTGGGGGTCAAAGAGCT 59.220 50.000 0.00 0.00 39.05 4.09
658 897 1.147817 ACATTGGGGGTCAAAGAGCTT 59.852 47.619 0.00 0.00 39.05 3.74
659 898 1.821136 CATTGGGGGTCAAAGAGCTTC 59.179 52.381 0.00 0.00 39.05 3.86
697 936 0.537653 CTTCCTTTCTCCGTCTCCCC 59.462 60.000 0.00 0.00 0.00 4.81
738 977 2.491693 CGTAACTGGATTTGGCATGGTT 59.508 45.455 0.00 0.00 0.00 3.67
892 1131 6.591750 AGCATATAAATACGTAGCTCACCT 57.408 37.500 0.08 0.00 0.00 4.00
1058 1303 1.202256 CGTCGGAGAAATCATCGACCA 60.202 52.381 16.79 0.00 46.11 4.02
1223 1468 2.351276 GGTGAGTCACCGGCCAAT 59.649 61.111 26.12 0.00 44.95 3.16
1256 1501 2.418692 TGCTTATTGCGTCCTTTTCGA 58.581 42.857 0.00 0.00 46.63 3.71
1289 1534 1.677518 AACACTTGTCGTGGTTGCTGA 60.678 47.619 0.00 0.00 41.99 4.26
1300 1545 1.093159 GGTTGCTGATGCTCCTTCTG 58.907 55.000 0.00 0.00 40.48 3.02
1308 1553 2.092592 TGATGCTCCTTCTGATGCATGT 60.093 45.455 2.46 0.00 44.80 3.21
1309 1554 3.135167 TGATGCTCCTTCTGATGCATGTA 59.865 43.478 2.46 0.00 44.80 2.29
1327 1572 6.320926 TGCATGTATATGTTACTGCCATGTTT 59.679 34.615 1.14 0.00 36.65 2.83
1408 1662 1.549203 ACCTCCATTGGTACGTACGT 58.451 50.000 25.98 25.98 38.79 3.57
1414 1668 3.056962 TCCATTGGTACGTACGTGCTAAA 60.057 43.478 31.46 25.49 35.32 1.85
1417 1671 4.757799 TTGGTACGTACGTGCTAAACTA 57.242 40.909 30.65 16.62 29.75 2.24
1432 1686 8.480853 CGTGCTAAACTAGAGCTAATCATTAAC 58.519 37.037 0.00 0.00 40.76 2.01
1502 1785 6.676990 TGATGCATCATCATACTCCTAAGT 57.323 37.500 25.42 0.00 44.60 2.24
1503 1786 6.695429 TGATGCATCATCATACTCCTAAGTC 58.305 40.000 25.42 0.00 44.60 3.01
1504 1787 5.474578 TGCATCATCATACTCCTAAGTCC 57.525 43.478 0.00 0.00 36.92 3.85
1505 1788 5.150715 TGCATCATCATACTCCTAAGTCCT 58.849 41.667 0.00 0.00 36.92 3.85
1506 1789 6.314917 TGCATCATCATACTCCTAAGTCCTA 58.685 40.000 0.00 0.00 36.92 2.94
1507 1790 6.782494 TGCATCATCATACTCCTAAGTCCTAA 59.218 38.462 0.00 0.00 36.92 2.69
1521 1804 6.483640 CCTAAGTCCTAACACAAATATGCCTC 59.516 42.308 0.00 0.00 0.00 4.70
1522 1805 4.781934 AGTCCTAACACAAATATGCCTCC 58.218 43.478 0.00 0.00 0.00 4.30
1523 1806 4.227300 AGTCCTAACACAAATATGCCTCCA 59.773 41.667 0.00 0.00 0.00 3.86
1524 1807 4.947388 GTCCTAACACAAATATGCCTCCAA 59.053 41.667 0.00 0.00 0.00 3.53
1525 1808 5.066505 GTCCTAACACAAATATGCCTCCAAG 59.933 44.000 0.00 0.00 0.00 3.61
1526 1809 4.339247 CCTAACACAAATATGCCTCCAAGG 59.661 45.833 0.00 0.00 38.80 3.61
1537 1820 2.757894 CCTCCAAGGCTAGTCTAGGA 57.242 55.000 5.83 1.54 0.00 2.94
1538 1821 3.252554 CCTCCAAGGCTAGTCTAGGAT 57.747 52.381 5.83 0.00 0.00 3.24
1539 1822 2.896685 CCTCCAAGGCTAGTCTAGGATG 59.103 54.545 5.83 0.00 0.00 3.51
1540 1823 2.896685 CTCCAAGGCTAGTCTAGGATGG 59.103 54.545 6.47 6.47 0.00 3.51
1541 1824 2.247635 TCCAAGGCTAGTCTAGGATGGT 59.752 50.000 11.63 0.00 0.00 3.55
1542 1825 2.630580 CCAAGGCTAGTCTAGGATGGTC 59.369 54.545 8.97 0.00 0.00 4.02
1543 1826 3.571590 CAAGGCTAGTCTAGGATGGTCT 58.428 50.000 8.97 0.00 0.00 3.85
1544 1827 3.518992 AGGCTAGTCTAGGATGGTCTC 57.481 52.381 8.97 0.00 0.00 3.36
1545 1828 2.156098 GGCTAGTCTAGGATGGTCTCG 58.844 57.143 8.97 0.00 0.00 4.04
1546 1829 2.487625 GGCTAGTCTAGGATGGTCTCGT 60.488 54.545 8.97 0.00 0.00 4.18
1547 1830 3.215975 GCTAGTCTAGGATGGTCTCGTT 58.784 50.000 8.97 0.00 0.00 3.85
1548 1831 3.633065 GCTAGTCTAGGATGGTCTCGTTT 59.367 47.826 8.97 0.00 0.00 3.60
1549 1832 4.261280 GCTAGTCTAGGATGGTCTCGTTTC 60.261 50.000 8.97 0.00 0.00 2.78
1550 1833 3.970842 AGTCTAGGATGGTCTCGTTTCT 58.029 45.455 0.00 0.00 0.00 2.52
1551 1834 4.345854 AGTCTAGGATGGTCTCGTTTCTT 58.654 43.478 0.00 0.00 0.00 2.52
1552 1835 4.773149 AGTCTAGGATGGTCTCGTTTCTTT 59.227 41.667 0.00 0.00 0.00 2.52
1553 1836 5.246429 AGTCTAGGATGGTCTCGTTTCTTTT 59.754 40.000 0.00 0.00 0.00 2.27
1554 1837 6.436532 AGTCTAGGATGGTCTCGTTTCTTTTA 59.563 38.462 0.00 0.00 0.00 1.52
1555 1838 7.124448 AGTCTAGGATGGTCTCGTTTCTTTTAT 59.876 37.037 0.00 0.00 0.00 1.40
1556 1839 8.411683 GTCTAGGATGGTCTCGTTTCTTTTATA 58.588 37.037 0.00 0.00 0.00 0.98
1557 1840 8.411683 TCTAGGATGGTCTCGTTTCTTTTATAC 58.588 37.037 0.00 0.00 0.00 1.47
1558 1841 7.184067 AGGATGGTCTCGTTTCTTTTATACT 57.816 36.000 0.00 0.00 0.00 2.12
1559 1842 7.266400 AGGATGGTCTCGTTTCTTTTATACTC 58.734 38.462 0.00 0.00 0.00 2.59
1560 1843 6.479331 GGATGGTCTCGTTTCTTTTATACTCC 59.521 42.308 0.00 0.00 0.00 3.85
1561 1844 6.600882 TGGTCTCGTTTCTTTTATACTCCT 57.399 37.500 0.00 0.00 0.00 3.69
1562 1845 7.707624 TGGTCTCGTTTCTTTTATACTCCTA 57.292 36.000 0.00 0.00 0.00 2.94
1563 1846 7.542025 TGGTCTCGTTTCTTTTATACTCCTAC 58.458 38.462 0.00 0.00 0.00 3.18
1564 1847 6.977502 GGTCTCGTTTCTTTTATACTCCTACC 59.022 42.308 0.00 0.00 0.00 3.18
1565 1848 7.363268 GGTCTCGTTTCTTTTATACTCCTACCA 60.363 40.741 0.00 0.00 0.00 3.25
1566 1849 7.487509 GTCTCGTTTCTTTTATACTCCTACCAC 59.512 40.741 0.00 0.00 0.00 4.16
1567 1850 7.177216 TCTCGTTTCTTTTATACTCCTACCACA 59.823 37.037 0.00 0.00 0.00 4.17
1568 1851 7.318141 TCGTTTCTTTTATACTCCTACCACAG 58.682 38.462 0.00 0.00 0.00 3.66
1569 1852 7.177216 TCGTTTCTTTTATACTCCTACCACAGA 59.823 37.037 0.00 0.00 0.00 3.41
1570 1853 7.275123 CGTTTCTTTTATACTCCTACCACAGAC 59.725 40.741 0.00 0.00 0.00 3.51
1571 1854 8.312564 GTTTCTTTTATACTCCTACCACAGACT 58.687 37.037 0.00 0.00 0.00 3.24
1572 1855 7.642082 TCTTTTATACTCCTACCACAGACTC 57.358 40.000 0.00 0.00 0.00 3.36
1573 1856 6.606395 TCTTTTATACTCCTACCACAGACTCC 59.394 42.308 0.00 0.00 0.00 3.85
1574 1857 2.414994 TACTCCTACCACAGACTCCG 57.585 55.000 0.00 0.00 0.00 4.63
1575 1858 0.404812 ACTCCTACCACAGACTCCGT 59.595 55.000 0.00 0.00 0.00 4.69
1576 1859 0.811915 CTCCTACCACAGACTCCGTG 59.188 60.000 0.00 0.00 0.00 4.94
1577 1860 1.215647 CCTACCACAGACTCCGTGC 59.784 63.158 0.00 0.00 32.85 5.34
1578 1861 1.251527 CCTACCACAGACTCCGTGCT 61.252 60.000 0.00 0.00 32.85 4.40
1579 1862 0.603569 CTACCACAGACTCCGTGCTT 59.396 55.000 0.00 0.00 32.85 3.91
1580 1863 0.317160 TACCACAGACTCCGTGCTTG 59.683 55.000 0.00 0.00 32.85 4.01
1581 1864 1.069765 CCACAGACTCCGTGCTTGT 59.930 57.895 0.00 0.00 32.85 3.16
1582 1865 0.532862 CCACAGACTCCGTGCTTGTT 60.533 55.000 0.00 0.00 32.85 2.83
1583 1866 1.299541 CACAGACTCCGTGCTTGTTT 58.700 50.000 0.00 0.00 0.00 2.83
1584 1867 2.479837 CACAGACTCCGTGCTTGTTTA 58.520 47.619 0.00 0.00 0.00 2.01
1585 1868 3.067106 CACAGACTCCGTGCTTGTTTAT 58.933 45.455 0.00 0.00 0.00 1.40
1586 1869 3.123621 CACAGACTCCGTGCTTGTTTATC 59.876 47.826 0.00 0.00 0.00 1.75
1587 1870 3.244078 ACAGACTCCGTGCTTGTTTATCA 60.244 43.478 0.00 0.00 0.00 2.15
1588 1871 3.745975 CAGACTCCGTGCTTGTTTATCAA 59.254 43.478 0.00 0.00 34.61 2.57
1614 1897 9.736023 AGAATAAATTATTCATGCGTCCTTTTC 57.264 29.630 23.00 0.00 45.41 2.29
1646 1929 3.717707 CAGGTTAGTGATGGACATACCG 58.282 50.000 0.00 0.00 42.61 4.02
1707 1990 7.333528 TGGCAGAAATTAATATGGACAAGTC 57.666 36.000 0.00 0.00 0.00 3.01
1789 2072 6.117911 TGTGGATTTCGCATTGTACTATTG 57.882 37.500 0.00 0.00 0.00 1.90
1791 2074 4.637977 TGGATTTCGCATTGTACTATTGCA 59.362 37.500 13.18 0.00 35.84 4.08
1792 2075 5.207768 GGATTTCGCATTGTACTATTGCAG 58.792 41.667 13.18 7.78 35.84 4.41
1830 2288 9.431887 TCATGCGTTAAGTTTTCTTATTACTCT 57.568 29.630 0.00 0.00 41.33 3.24
2008 2467 2.358737 GTGCTACTGCCTTGGCGT 60.359 61.111 7.18 10.11 38.71 5.68
2079 2538 1.739562 CGGAGGTGCAGCTGAAGTC 60.740 63.158 25.60 8.44 0.00 3.01
2216 2693 0.671472 TGCCGTGCATTGTGAGAGAG 60.671 55.000 0.00 0.00 31.71 3.20
2243 2720 5.106948 CGTGCGATTGCCAAGATAGAATATT 60.107 40.000 1.50 0.00 41.78 1.28
2373 2855 4.021894 GCTCACATGTTCGGTATATCTCCT 60.022 45.833 0.00 0.00 0.00 3.69
2387 2869 1.018148 TCTCCTTTGCACGCGAAAAA 58.982 45.000 15.93 9.25 0.00 1.94
2402 2884 5.410439 ACGCGAAAAAGTGTTCCATATAAGT 59.590 36.000 15.93 0.00 0.00 2.24
2403 2885 6.591062 ACGCGAAAAAGTGTTCCATATAAGTA 59.409 34.615 15.93 0.00 0.00 2.24
2404 2886 7.279313 ACGCGAAAAAGTGTTCCATATAAGTAT 59.721 33.333 15.93 0.00 0.00 2.12
2405 2887 7.792508 CGCGAAAAAGTGTTCCATATAAGTATC 59.207 37.037 0.00 0.00 0.00 2.24
2406 2888 8.827677 GCGAAAAAGTGTTCCATATAAGTATCT 58.172 33.333 0.00 0.00 0.00 1.98
2413 2895 9.830186 AGTGTTCCATATAAGTATCTCATACCT 57.170 33.333 0.00 0.00 36.40 3.08
2468 2950 2.048127 GTTTGGCGGACGAGCTCT 60.048 61.111 12.85 0.00 37.29 4.09
2494 2976 2.632028 AGCTCGGTATCCTAGTCGTCTA 59.368 50.000 0.00 0.00 0.00 2.59
2521 3003 0.325933 ATCTAGCAGCTGCACCAACA 59.674 50.000 38.24 17.05 45.16 3.33
2541 3023 7.967854 ACCAACACATTTAATGACATGTATTCG 59.032 33.333 12.28 0.00 32.16 3.34
2546 3028 7.585210 CACATTTAATGACATGTATTCGAGCTG 59.415 37.037 12.28 0.00 32.16 4.24
2574 3056 5.955959 AGGATATATGCCACACCGTATTCTA 59.044 40.000 0.00 0.00 0.00 2.10
2584 3066 6.563381 GCCACACCGTATTCTATATTTTCGTG 60.563 42.308 0.00 0.00 0.00 4.35
2624 3106 0.740149 CGAAAATGCATGGCAGGCTA 59.260 50.000 25.44 11.95 43.65 3.93
2719 3201 1.078848 AGCTCACGCTCCCATGTTC 60.079 57.895 0.00 0.00 45.15 3.18
2740 3222 4.145052 TCAGAGATAAGCCGATGAGCTAA 58.855 43.478 0.00 0.00 44.11 3.09
2741 3223 4.769488 TCAGAGATAAGCCGATGAGCTAAT 59.231 41.667 0.00 0.00 44.11 1.73
2825 3307 1.293924 CGGAGAACAGCAGCCTAATG 58.706 55.000 0.00 0.00 0.00 1.90
2866 3348 6.244552 TCTCATCAGTGAATAGCTTGGAAT 57.755 37.500 0.00 0.00 33.05 3.01
2978 3460 1.168714 GGGTGGAGACAAACATCTGC 58.831 55.000 0.00 0.00 46.06 4.26
3018 3500 1.597461 GGGAGGCGCTTCTACAAGT 59.403 57.895 19.65 0.00 31.45 3.16
3026 3508 1.739067 GCTTCTACAAGTGCCCGATT 58.261 50.000 0.00 0.00 31.45 3.34
3046 3528 6.073276 CCGATTGACAGTGTAAGTTTTCATCA 60.073 38.462 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 44 7.913297 GCAAGAAAACTCACATTAAGTACAACA 59.087 33.333 0.00 0.00 0.00 3.33
156 164 5.425577 AGCAGCGTCCTATACATATATCG 57.574 43.478 0.00 0.00 0.00 2.92
157 165 9.021863 GTTTTAGCAGCGTCCTATACATATATC 57.978 37.037 0.00 0.00 0.00 1.63
168 176 1.071699 TGAAGGTTTTAGCAGCGTCCT 59.928 47.619 0.00 0.00 0.00 3.85
197 205 7.409465 AAACAAGATAGTTCAACTCGAAGTC 57.591 36.000 0.00 0.00 38.31 3.01
209 217 6.537660 GCACCCTACGATAAAACAAGATAGTT 59.462 38.462 0.00 0.00 0.00 2.24
221 229 5.009210 GCCAAAATAATGCACCCTACGATAA 59.991 40.000 0.00 0.00 0.00 1.75
222 230 4.517453 GCCAAAATAATGCACCCTACGATA 59.483 41.667 0.00 0.00 0.00 2.92
223 231 3.317993 GCCAAAATAATGCACCCTACGAT 59.682 43.478 0.00 0.00 0.00 3.73
244 252 0.394565 AGATCTTATGGCTCCCGTGC 59.605 55.000 0.00 0.00 0.00 5.34
248 256 3.389329 TCACTGAAGATCTTATGGCTCCC 59.611 47.826 8.25 0.00 0.00 4.30
309 317 4.469657 TGTACCAGAGCCTGTTTGATTTT 58.530 39.130 0.00 0.00 0.00 1.82
332 414 7.861629 TCAAGTATCATCCAGGTATGTTCTTT 58.138 34.615 0.00 0.00 0.00 2.52
525 756 7.957002 TCTGCTTTCTCTCTTTTCTCTCTTAA 58.043 34.615 0.00 0.00 0.00 1.85
619 858 4.257267 TGTGATGACAACTCACAGGTAG 57.743 45.455 7.63 0.00 45.97 3.18
697 936 3.369756 ACGGATGCAATGTACAAGTAACG 59.630 43.478 0.00 7.50 0.00 3.18
738 977 7.177832 TCGGAGTGAATAAAATCTTGAGGTA 57.822 36.000 0.00 0.00 0.00 3.08
835 1074 4.831741 GATACGATCGATTCCTTGCATC 57.168 45.455 24.34 6.01 0.00 3.91
864 1103 8.761497 GTGAGCTACGTATTTATATGCTTGAAA 58.239 33.333 0.00 0.00 0.00 2.69
1011 1256 1.218316 GACGACCAGCGGATTCCTT 59.782 57.895 0.30 0.00 46.49 3.36
1058 1303 1.302511 ACCGCCGAAGCATCAAAGT 60.303 52.632 0.00 0.00 39.83 2.66
1160 1405 2.819284 CCCCGGGAGCCAGTTATCC 61.819 68.421 26.32 0.00 34.64 2.59
1271 1516 4.808119 GCATCAGCAACCACGACAAGTG 62.808 54.545 0.00 0.00 44.90 3.16
1272 1517 1.229428 CATCAGCAACCACGACAAGT 58.771 50.000 0.00 0.00 0.00 3.16
1273 1518 0.110056 GCATCAGCAACCACGACAAG 60.110 55.000 0.00 0.00 41.58 3.16
1274 1519 0.534877 AGCATCAGCAACCACGACAA 60.535 50.000 0.00 0.00 45.49 3.18
1278 1523 0.957395 AAGGAGCATCAGCAACCACG 60.957 55.000 0.00 0.00 45.49 4.94
1281 1526 1.093159 CAGAAGGAGCATCAGCAACC 58.907 55.000 0.00 0.00 45.49 3.77
1284 1529 1.746171 GCATCAGAAGGAGCATCAGCA 60.746 52.381 0.00 0.00 45.49 4.41
1286 1531 2.327200 TGCATCAGAAGGAGCATCAG 57.673 50.000 0.00 0.00 36.25 2.90
1300 1545 6.149973 ACATGGCAGTAACATATACATGCATC 59.850 38.462 0.00 0.00 38.14 3.91
1306 1551 7.695480 ACAAAACATGGCAGTAACATATACA 57.305 32.000 0.00 0.00 0.00 2.29
1308 1553 9.456147 AGTAACAAAACATGGCAGTAACATATA 57.544 29.630 0.00 0.00 0.00 0.86
1309 1554 8.348285 AGTAACAAAACATGGCAGTAACATAT 57.652 30.769 0.00 0.00 0.00 1.78
1327 1572 4.163458 GGATCCACCATCACCTAGTAACAA 59.837 45.833 6.95 0.00 38.79 2.83
1405 1659 5.578005 TGATTAGCTCTAGTTTAGCACGT 57.422 39.130 4.87 0.00 42.62 4.49
1406 1660 8.480853 GTTAATGATTAGCTCTAGTTTAGCACG 58.519 37.037 4.87 0.00 42.62 5.34
1407 1661 8.766151 GGTTAATGATTAGCTCTAGTTTAGCAC 58.234 37.037 4.87 0.00 42.62 4.40
1408 1662 8.482943 TGGTTAATGATTAGCTCTAGTTTAGCA 58.517 33.333 4.87 0.00 42.62 3.49
1414 1668 7.195374 TGGTTGGTTAATGATTAGCTCTAGT 57.805 36.000 0.00 0.00 0.00 2.57
1417 1671 7.118723 TGAATGGTTGGTTAATGATTAGCTCT 58.881 34.615 0.00 0.00 0.00 4.09
1449 1703 4.772100 ACAAGAAATTAGGGTTGACATGGG 59.228 41.667 0.00 0.00 0.00 4.00
1450 1704 5.982890 ACAAGAAATTAGGGTTGACATGG 57.017 39.130 0.00 0.00 0.00 3.66
1501 1784 4.523083 TGGAGGCATATTTGTGTTAGGAC 58.477 43.478 0.00 0.00 0.00 3.85
1502 1785 4.853468 TGGAGGCATATTTGTGTTAGGA 57.147 40.909 0.00 0.00 0.00 2.94
1503 1786 4.339247 CCTTGGAGGCATATTTGTGTTAGG 59.661 45.833 0.00 0.00 0.00 2.69
1504 1787 5.505173 CCTTGGAGGCATATTTGTGTTAG 57.495 43.478 0.00 0.00 0.00 2.34
1521 1804 2.630580 GACCATCCTAGACTAGCCTTGG 59.369 54.545 16.24 16.24 0.00 3.61
1522 1805 3.571590 AGACCATCCTAGACTAGCCTTG 58.428 50.000 3.76 1.56 0.00 3.61
1523 1806 3.749310 CGAGACCATCCTAGACTAGCCTT 60.749 52.174 3.76 0.00 0.00 4.35
1524 1807 2.224670 CGAGACCATCCTAGACTAGCCT 60.225 54.545 3.76 0.00 0.00 4.58
1525 1808 2.156098 CGAGACCATCCTAGACTAGCC 58.844 57.143 3.76 0.00 0.00 3.93
1526 1809 2.853705 ACGAGACCATCCTAGACTAGC 58.146 52.381 3.76 0.00 0.00 3.42
1527 1810 5.127491 AGAAACGAGACCATCCTAGACTAG 58.873 45.833 2.18 2.18 0.00 2.57
1528 1811 5.113446 AGAAACGAGACCATCCTAGACTA 57.887 43.478 0.00 0.00 0.00 2.59
1529 1812 3.970842 AGAAACGAGACCATCCTAGACT 58.029 45.455 0.00 0.00 0.00 3.24
1530 1813 4.722361 AAGAAACGAGACCATCCTAGAC 57.278 45.455 0.00 0.00 0.00 2.59
1531 1814 5.740290 AAAAGAAACGAGACCATCCTAGA 57.260 39.130 0.00 0.00 0.00 2.43
1532 1815 8.414778 AGTATAAAAGAAACGAGACCATCCTAG 58.585 37.037 0.00 0.00 0.00 3.02
1533 1816 8.302515 AGTATAAAAGAAACGAGACCATCCTA 57.697 34.615 0.00 0.00 0.00 2.94
1534 1817 7.184067 AGTATAAAAGAAACGAGACCATCCT 57.816 36.000 0.00 0.00 0.00 3.24
1535 1818 6.479331 GGAGTATAAAAGAAACGAGACCATCC 59.521 42.308 0.00 0.00 0.00 3.51
1536 1819 7.266400 AGGAGTATAAAAGAAACGAGACCATC 58.734 38.462 0.00 0.00 0.00 3.51
1537 1820 7.184067 AGGAGTATAAAAGAAACGAGACCAT 57.816 36.000 0.00 0.00 0.00 3.55
1538 1821 6.600882 AGGAGTATAAAAGAAACGAGACCA 57.399 37.500 0.00 0.00 0.00 4.02
1539 1822 6.977502 GGTAGGAGTATAAAAGAAACGAGACC 59.022 42.308 0.00 0.00 0.00 3.85
1540 1823 7.487509 GTGGTAGGAGTATAAAAGAAACGAGAC 59.512 40.741 0.00 0.00 0.00 3.36
1541 1824 7.177216 TGTGGTAGGAGTATAAAAGAAACGAGA 59.823 37.037 0.00 0.00 0.00 4.04
1542 1825 7.318141 TGTGGTAGGAGTATAAAAGAAACGAG 58.682 38.462 0.00 0.00 0.00 4.18
1543 1826 7.177216 TCTGTGGTAGGAGTATAAAAGAAACGA 59.823 37.037 0.00 0.00 0.00 3.85
1544 1827 7.275123 GTCTGTGGTAGGAGTATAAAAGAAACG 59.725 40.741 0.00 0.00 0.00 3.60
1545 1828 8.312564 AGTCTGTGGTAGGAGTATAAAAGAAAC 58.687 37.037 0.00 0.00 0.00 2.78
1546 1829 8.431910 AGTCTGTGGTAGGAGTATAAAAGAAA 57.568 34.615 0.00 0.00 0.00 2.52
1547 1830 7.123847 GGAGTCTGTGGTAGGAGTATAAAAGAA 59.876 40.741 0.00 0.00 0.00 2.52
1548 1831 6.606395 GGAGTCTGTGGTAGGAGTATAAAAGA 59.394 42.308 0.00 0.00 0.00 2.52
1549 1832 6.459848 CGGAGTCTGTGGTAGGAGTATAAAAG 60.460 46.154 0.00 0.00 0.00 2.27
1550 1833 5.359009 CGGAGTCTGTGGTAGGAGTATAAAA 59.641 44.000 0.00 0.00 0.00 1.52
1551 1834 4.885907 CGGAGTCTGTGGTAGGAGTATAAA 59.114 45.833 0.00 0.00 0.00 1.40
1552 1835 4.080129 ACGGAGTCTGTGGTAGGAGTATAA 60.080 45.833 3.08 0.00 29.74 0.98
1553 1836 3.457380 ACGGAGTCTGTGGTAGGAGTATA 59.543 47.826 3.08 0.00 29.74 1.47
1554 1837 2.241685 ACGGAGTCTGTGGTAGGAGTAT 59.758 50.000 3.08 0.00 29.74 2.12
1555 1838 1.632409 ACGGAGTCTGTGGTAGGAGTA 59.368 52.381 3.08 0.00 29.74 2.59
1556 1839 0.404812 ACGGAGTCTGTGGTAGGAGT 59.595 55.000 3.08 0.00 29.74 3.85
1557 1840 0.811915 CACGGAGTCTGTGGTAGGAG 59.188 60.000 22.38 0.00 41.61 3.69
1558 1841 1.248785 GCACGGAGTCTGTGGTAGGA 61.249 60.000 28.99 0.00 41.61 2.94
1559 1842 1.215647 GCACGGAGTCTGTGGTAGG 59.784 63.158 28.99 7.98 41.61 3.18
1560 1843 0.603569 AAGCACGGAGTCTGTGGTAG 59.396 55.000 31.39 9.69 46.43 3.18
1561 1844 0.317160 CAAGCACGGAGTCTGTGGTA 59.683 55.000 31.39 0.00 46.43 3.25
1563 1846 0.532862 AACAAGCACGGAGTCTGTGG 60.533 55.000 28.99 17.17 41.61 4.17
1564 1847 1.299541 AAACAAGCACGGAGTCTGTG 58.700 50.000 25.15 25.15 41.61 3.66
1565 1848 2.902705 TAAACAAGCACGGAGTCTGT 57.097 45.000 0.00 0.00 41.61 3.41
1566 1849 3.325870 TGATAAACAAGCACGGAGTCTG 58.674 45.455 0.00 0.00 41.61 3.51
1567 1850 3.678056 TGATAAACAAGCACGGAGTCT 57.322 42.857 0.00 0.00 41.61 3.24
1584 1867 9.071276 AGGACGCATGAATAATTTATTCTTGAT 57.929 29.630 30.30 22.58 45.66 2.57
1585 1868 8.450578 AGGACGCATGAATAATTTATTCTTGA 57.549 30.769 30.30 15.16 45.66 3.02
1586 1869 9.520204 AAAGGACGCATGAATAATTTATTCTTG 57.480 29.630 25.90 25.90 45.61 3.02
1588 1871 9.736023 GAAAAGGACGCATGAATAATTTATTCT 57.264 29.630 23.10 10.99 43.79 2.40
1589 1872 9.515020 TGAAAAGGACGCATGAATAATTTATTC 57.485 29.630 18.29 18.29 43.73 1.75
1592 1875 9.868277 AAATGAAAAGGACGCATGAATAATTTA 57.132 25.926 0.00 0.00 0.00 1.40
1593 1876 8.658609 CAAATGAAAAGGACGCATGAATAATTT 58.341 29.630 0.00 0.00 0.00 1.82
1594 1877 7.201548 GCAAATGAAAAGGACGCATGAATAATT 60.202 33.333 0.00 0.00 0.00 1.40
1595 1878 6.256321 GCAAATGAAAAGGACGCATGAATAAT 59.744 34.615 0.00 0.00 0.00 1.28
1596 1879 5.576384 GCAAATGAAAAGGACGCATGAATAA 59.424 36.000 0.00 0.00 0.00 1.40
1597 1880 5.101628 GCAAATGAAAAGGACGCATGAATA 58.898 37.500 0.00 0.00 0.00 1.75
1598 1881 3.928375 GCAAATGAAAAGGACGCATGAAT 59.072 39.130 0.00 0.00 0.00 2.57
1599 1882 3.005684 AGCAAATGAAAAGGACGCATGAA 59.994 39.130 0.00 0.00 0.00 2.57
1600 1883 2.557924 AGCAAATGAAAAGGACGCATGA 59.442 40.909 0.00 0.00 0.00 3.07
1601 1884 2.664568 CAGCAAATGAAAAGGACGCATG 59.335 45.455 0.00 0.00 0.00 4.06
1602 1885 2.297033 ACAGCAAATGAAAAGGACGCAT 59.703 40.909 0.00 0.00 0.00 4.73
1603 1886 1.680735 ACAGCAAATGAAAAGGACGCA 59.319 42.857 0.00 0.00 0.00 5.24
1604 1887 2.053627 CACAGCAAATGAAAAGGACGC 58.946 47.619 0.00 0.00 0.00 5.19
1605 1888 2.053627 GCACAGCAAATGAAAAGGACG 58.946 47.619 0.00 0.00 0.00 4.79
1606 1889 3.054878 CTGCACAGCAAATGAAAAGGAC 58.945 45.455 0.00 0.00 38.41 3.85
1607 1890 2.036217 CCTGCACAGCAAATGAAAAGGA 59.964 45.455 0.00 0.00 38.41 3.36
1608 1891 2.224113 ACCTGCACAGCAAATGAAAAGG 60.224 45.455 0.00 0.00 38.41 3.11
1609 1892 3.102052 ACCTGCACAGCAAATGAAAAG 57.898 42.857 0.00 0.00 38.41 2.27
1614 1897 2.553602 TCACTAACCTGCACAGCAAATG 59.446 45.455 0.00 0.00 38.41 2.32
1646 1929 1.902508 TGACTGACATCACCTCCTTCC 59.097 52.381 0.00 0.00 0.00 3.46
1707 1990 0.742505 CTGGTTAGTGCATGCATGGG 59.257 55.000 25.64 4.09 0.00 4.00
1789 2072 9.318041 CTTAACGCATGATTAAACATATACTGC 57.682 33.333 0.00 0.00 0.00 4.40
1809 2267 8.922676 TCAGCAGAGTAATAAGAAAACTTAACG 58.077 33.333 0.00 0.00 0.00 3.18
1830 2288 1.069978 TCCTGACACGTTTCATCAGCA 59.930 47.619 4.61 0.00 38.84 4.41
1837 2296 2.135933 CCTCAGTTCCTGACACGTTTC 58.864 52.381 0.00 0.00 35.39 2.78
2079 2538 4.988598 ACAGCCTTGTCGCCGTGG 62.989 66.667 0.00 0.00 29.46 4.94
2107 2566 1.656652 GTCCTGTTGTCGATGATGGG 58.343 55.000 0.00 0.00 0.00 4.00
2133 2592 6.677781 TCTTTGCCTTCAATAATTAGGTCG 57.322 37.500 0.00 0.00 31.33 4.79
2216 2693 2.257286 ATCTTGGCAATCGCACGCAC 62.257 55.000 0.00 0.00 41.24 5.34
2243 2720 8.840833 AACACACAGATACAAATACATACACA 57.159 30.769 0.00 0.00 0.00 3.72
2273 2750 6.109359 AGTACTTGTCATGTTGATAAGCTCC 58.891 40.000 12.23 3.29 45.69 4.70
2322 2804 3.938963 CACCTCAGTGTACCGCAAATATT 59.061 43.478 0.00 0.00 39.30 1.28
2323 2805 3.196901 TCACCTCAGTGTACCGCAAATAT 59.803 43.478 0.00 0.00 44.83 1.28
2324 2806 2.563620 TCACCTCAGTGTACCGCAAATA 59.436 45.455 0.00 0.00 44.83 1.40
2325 2807 1.346395 TCACCTCAGTGTACCGCAAAT 59.654 47.619 0.00 0.00 44.83 2.32
2326 2808 0.753867 TCACCTCAGTGTACCGCAAA 59.246 50.000 0.00 0.00 44.83 3.68
2373 2855 1.914700 GAACACTTTTTCGCGTGCAAA 59.085 42.857 5.77 1.06 34.58 3.68
2387 2869 9.830186 AGGTATGAGATACTTATATGGAACACT 57.170 33.333 0.00 0.00 37.21 3.55
2419 2901 8.983702 TTCGGTTATGGGCTAACTATTTAAAT 57.016 30.769 5.89 5.89 39.78 1.40
2420 2902 8.804912 TTTCGGTTATGGGCTAACTATTTAAA 57.195 30.769 0.00 0.00 39.78 1.52
2421 2903 8.804912 TTTTCGGTTATGGGCTAACTATTTAA 57.195 30.769 0.00 0.00 39.78 1.52
2422 2904 8.842280 CATTTTCGGTTATGGGCTAACTATTTA 58.158 33.333 0.00 0.00 39.78 1.40
2423 2905 7.683463 GCATTTTCGGTTATGGGCTAACTATTT 60.683 37.037 0.00 0.00 39.78 1.40
2424 2906 6.238925 GCATTTTCGGTTATGGGCTAACTATT 60.239 38.462 0.00 0.00 39.78 1.73
2425 2907 5.240844 GCATTTTCGGTTATGGGCTAACTAT 59.759 40.000 0.00 0.00 39.78 2.12
2426 2908 4.577283 GCATTTTCGGTTATGGGCTAACTA 59.423 41.667 0.00 0.00 39.78 2.24
2427 2909 3.380320 GCATTTTCGGTTATGGGCTAACT 59.620 43.478 0.00 0.00 39.78 2.24
2428 2910 3.490249 GGCATTTTCGGTTATGGGCTAAC 60.490 47.826 0.00 0.00 39.25 2.34
2429 2911 2.691011 GGCATTTTCGGTTATGGGCTAA 59.309 45.455 0.00 0.00 0.00 3.09
2430 2912 2.303175 GGCATTTTCGGTTATGGGCTA 58.697 47.619 0.00 0.00 0.00 3.93
2431 2913 1.111277 GGCATTTTCGGTTATGGGCT 58.889 50.000 0.00 0.00 0.00 5.19
2432 2914 0.248866 CGGCATTTTCGGTTATGGGC 60.249 55.000 0.00 0.00 0.00 5.36
2433 2915 1.099689 ACGGCATTTTCGGTTATGGG 58.900 50.000 0.00 0.00 0.00 4.00
2434 2916 2.920490 CAAACGGCATTTTCGGTTATGG 59.080 45.455 0.00 0.00 35.15 2.74
2435 2917 2.920490 CCAAACGGCATTTTCGGTTATG 59.080 45.455 0.00 0.00 35.15 1.90
2436 2918 3.224884 CCAAACGGCATTTTCGGTTAT 57.775 42.857 0.00 0.00 35.15 1.89
2437 2919 2.708386 CCAAACGGCATTTTCGGTTA 57.292 45.000 0.00 0.00 35.15 2.85
2438 2920 3.579066 CCAAACGGCATTTTCGGTT 57.421 47.368 0.00 0.00 38.12 4.44
2468 2950 3.082548 GACTAGGATACCGAGCTGCATA 58.917 50.000 1.02 0.00 29.11 3.14
2521 3003 7.254898 CCAGCTCGAATACATGTCATTAAATGT 60.255 37.037 0.00 0.00 40.13 2.71
2584 3066 0.179062 CAGTCCTGGGATGCTACTGC 60.179 60.000 0.00 0.00 40.20 4.40
2594 3076 0.804989 GCATTTTCGTCAGTCCTGGG 59.195 55.000 0.00 0.00 0.00 4.45
2596 3078 2.159476 CCATGCATTTTCGTCAGTCCTG 60.159 50.000 0.00 0.00 0.00 3.86
2624 3106 1.067212 GGATCGATGGCACGTCTAACT 59.933 52.381 0.54 0.00 34.70 2.24
2719 3201 4.511617 TTAGCTCATCGGCTTATCTCTG 57.488 45.455 0.00 0.00 42.97 3.35
2740 3222 2.088950 ACGTTCGGATTCCAAACGAT 57.911 45.000 30.13 14.77 46.42 3.73
2741 3223 1.527736 CAACGTTCGGATTCCAAACGA 59.472 47.619 30.13 7.23 46.42 3.85
2825 3307 0.746659 GAGCTGAGAGGAGGAGAAGC 59.253 60.000 0.00 0.00 0.00 3.86
2831 3313 1.958579 CTGATGAGAGCTGAGAGGAGG 59.041 57.143 0.00 0.00 0.00 4.30
2978 3460 1.581447 GTTCGGCCCTTCTTTGCTG 59.419 57.895 0.00 0.00 35.14 4.41
3018 3500 1.346395 ACTTACACTGTCAATCGGGCA 59.654 47.619 0.00 0.00 0.00 5.36
3026 3508 7.255104 GGACATTGATGAAAACTTACACTGTCA 60.255 37.037 1.65 0.00 40.38 3.58
3046 3528 3.828451 CCATGGAACTTCTTGTGGACATT 59.172 43.478 5.56 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.