Multiple sequence alignment - TraesCS1A01G379500

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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 TraesCS1A01G379500 chr1A 100.000 5029 0 0 1 5029 551529397 551534425 0.000000e+00 9287.0
1 TraesCS1A01G379500 chr1A 85.182 2065 218 44 2034 4033 551788380 551786339 0.000000e+00 2037.0
2 TraesCS1A01G379500 chr1A 78.104 749 150 13 2366 3105 552892057 552891314 3.550000e-126 462.0
3 TraesCS1A01G379500 chr1A 84.011 369 42 7 4232 4593 551747576 551747218 6.240000e-89 339.0
4 TraesCS1A01G379500 chr1A 78.916 332 57 10 31 353 536970725 536970398 3.940000e-51 213.0
5 TraesCS1A01G379500 chr1B 91.649 4227 131 49 883 5029 631715128 631719212 0.000000e+00 5646.0
6 TraesCS1A01G379500 chr1B 81.148 2090 298 62 2007 4032 637952595 637954652 0.000000e+00 1589.0
7 TraesCS1A01G379500 chr1B 88.914 893 76 17 1 873 631714178 631715067 0.000000e+00 1079.0
8 TraesCS1A01G379500 chr1B 74.028 720 119 32 25 722 598875450 598876123 1.090000e-56 231.0
9 TraesCS1A01G379500 chr1B 90.286 175 17 0 3858 4032 632721361 632721187 3.920000e-56 230.0
10 TraesCS1A01G379500 chr1D 96.309 2601 69 11 1784 4376 459520969 459523550 0.000000e+00 4246.0
11 TraesCS1A01G379500 chr1D 90.370 2191 160 29 2212 4376 459626678 459624513 0.000000e+00 2830.0
12 TraesCS1A01G379500 chr1D 86.985 1552 88 34 1 1489 459518103 459519603 0.000000e+00 1642.0
13 TraesCS1A01G379500 chr1D 81.310 2076 287 51 2007 4032 463007230 463009254 0.000000e+00 1591.0
14 TraesCS1A01G379500 chr1D 85.924 817 83 13 2063 2855 460196798 460195990 0.000000e+00 843.0
15 TraesCS1A01G379500 chr1D 92.969 384 9 5 4646 5029 459523831 459524196 1.230000e-150 544.0
16 TraesCS1A01G379500 chr1D 92.969 384 9 5 4646 5029 459624232 459623867 1.230000e-150 544.0
17 TraesCS1A01G379500 chr1D 78.533 750 145 15 2366 3105 461398261 461397518 3.520000e-131 479.0
18 TraesCS1A01G379500 chr1D 85.829 374 42 5 4232 4597 460194598 460194228 2.200000e-103 387.0
19 TraesCS1A01G379500 chr1D 95.516 223 8 2 1581 1802 459519930 459520151 6.190000e-94 355.0
20 TraesCS1A01G379500 chr1D 86.878 221 13 9 4403 4613 459523542 459523756 3.030000e-57 233.0
21 TraesCS1A01G379500 chr1D 87.736 212 10 9 4412 4613 459624512 459624307 3.030000e-57 233.0
22 TraesCS1A01G379500 chr1D 80.851 235 40 3 26 256 441066068 441066301 4.000000e-41 180.0
23 TraesCS1A01G379500 chr1D 74.807 389 62 16 379 748 441066414 441066785 5.250000e-30 143.0
24 TraesCS1A01G379500 chr3D 76.173 1662 331 39 2406 4015 575598181 575596533 0.000000e+00 815.0
25 TraesCS1A01G379500 chr3A 75.444 1690 337 51 2406 4039 711079604 711077937 0.000000e+00 750.0
26 TraesCS1A01G379500 chr3B 75.249 1709 347 50 2356 4018 766377660 766379338 0.000000e+00 743.0
27 TraesCS1A01G379500 chr5D 75.716 733 142 18 32 746 267757724 267758438 8.070000e-88 335.0
28 TraesCS1A01G379500 chr5D 86.614 127 12 5 29 152 484945035 484944911 8.780000e-28 135.0
29 TraesCS1A01G379500 chr2A 74.699 747 165 17 2373 3109 759577438 759576706 1.360000e-80 311.0
30 TraesCS1A01G379500 chr2B 73.829 726 167 17 2395 3109 775763665 775762952 2.980000e-67 267.0
31 TraesCS1A01G379500 chrUn 73.816 718 167 16 2401 3109 349736311 349737016 1.070000e-66 265.0
32 TraesCS1A01G379500 chrUn 87.013 77 7 3 653 728 46252837 46252763 3.230000e-12 84.2
33 TraesCS1A01G379500 chr6D 84.103 195 26 3 32 225 462684998 462684808 3.090000e-42 183.0
34 TraesCS1A01G379500 chr7B 84.270 178 17 6 30 196 668224416 668224239 4.030000e-36 163.0
35 TraesCS1A01G379500 chr7B 85.897 78 7 4 653 728 642755414 642755339 4.170000e-11 80.5
36 TraesCS1A01G379500 chr5A 84.615 130 15 5 29 156 606273880 606273754 1.900000e-24 124.0
37 TraesCS1A01G379500 chr7D 88.889 72 4 4 653 722 111093014 111092945 8.970000e-13 86.1
38 TraesCS1A01G379500 chr4B 92.453 53 2 2 671 722 164901916 164901865 1.940000e-09 75.0
39 TraesCS1A01G379500 chr4B 90.566 53 3 2 671 722 164879420 164879369 9.030000e-08 69.4
40 TraesCS1A01G379500 chr6A 93.617 47 3 0 4037 4083 30556288 30556334 2.510000e-08 71.3


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 TraesCS1A01G379500 chr1A 551529397 551534425 5028 False 9287.000000 9287 100.000000 1 5029 1 chr1A.!!$F1 5028
1 TraesCS1A01G379500 chr1A 551786339 551788380 2041 True 2037.000000 2037 85.182000 2034 4033 1 chr1A.!!$R3 1999
2 TraesCS1A01G379500 chr1A 552891314 552892057 743 True 462.000000 462 78.104000 2366 3105 1 chr1A.!!$R4 739
3 TraesCS1A01G379500 chr1B 631714178 631719212 5034 False 3362.500000 5646 90.281500 1 5029 2 chr1B.!!$F3 5028
4 TraesCS1A01G379500 chr1B 637952595 637954652 2057 False 1589.000000 1589 81.148000 2007 4032 1 chr1B.!!$F2 2025
5 TraesCS1A01G379500 chr1B 598875450 598876123 673 False 231.000000 231 74.028000 25 722 1 chr1B.!!$F1 697
6 TraesCS1A01G379500 chr1D 463007230 463009254 2024 False 1591.000000 1591 81.310000 2007 4032 1 chr1D.!!$F1 2025
7 TraesCS1A01G379500 chr1D 459518103 459524196 6093 False 1404.000000 4246 91.731400 1 5029 5 chr1D.!!$F3 5028
8 TraesCS1A01G379500 chr1D 459623867 459626678 2811 True 1202.333333 2830 90.358333 2212 5029 3 chr1D.!!$R2 2817
9 TraesCS1A01G379500 chr1D 460194228 460196798 2570 True 615.000000 843 85.876500 2063 4597 2 chr1D.!!$R3 2534
10 TraesCS1A01G379500 chr1D 461397518 461398261 743 True 479.000000 479 78.533000 2366 3105 1 chr1D.!!$R1 739
11 TraesCS1A01G379500 chr3D 575596533 575598181 1648 True 815.000000 815 76.173000 2406 4015 1 chr3D.!!$R1 1609
12 TraesCS1A01G379500 chr3A 711077937 711079604 1667 True 750.000000 750 75.444000 2406 4039 1 chr3A.!!$R1 1633
13 TraesCS1A01G379500 chr3B 766377660 766379338 1678 False 743.000000 743 75.249000 2356 4018 1 chr3B.!!$F1 1662
14 TraesCS1A01G379500 chr5D 267757724 267758438 714 False 335.000000 335 75.716000 32 746 1 chr5D.!!$F1 714
15 TraesCS1A01G379500 chr2A 759576706 759577438 732 True 311.000000 311 74.699000 2373 3109 1 chr2A.!!$R1 736
16 TraesCS1A01G379500 chr2B 775762952 775763665 713 True 267.000000 267 73.829000 2395 3109 1 chr2B.!!$R1 714
17 TraesCS1A01G379500 chrUn 349736311 349737016 705 False 265.000000 265 73.816000 2401 3109 1 chrUn.!!$F1 708

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
371 392 0.655733 CAACTGCCGTTTCAAGACGT 59.344 50.000 0.00 0.00 41.26 4.34 F
1431 1615 0.698818 ACCAAGTTCAGATCCCACCC 59.301 55.000 0.00 0.00 0.00 4.61 F
1511 1695 0.169009 GCAACCATCGCTTCCTTCAC 59.831 55.000 0.00 0.00 0.00 3.18 F
1557 1741 0.541764 TGCCAGTTTCAACCATCCCC 60.542 55.000 0.00 0.00 0.00 4.81 F
1609 2067 2.557924 TCCAGCTGTGCTACAAATTTGG 59.442 45.455 21.74 6.60 36.40 3.28 F
1711 2169 3.490933 GGGACAAAAAGAAGTGCTCCAAC 60.491 47.826 0.00 0.00 0.00 3.77 F
3549 5436 3.558829 TCCTACGCGTAAGTCTCTATGTG 59.441 47.826 20.97 3.65 41.68 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1492 1676 0.169009 GTGAAGGAAGCGATGGTTGC 59.831 55.000 0.00 0.00 0.00 4.17 R
2301 3644 1.349627 GCCGAGATGCATGTGTTCG 59.650 57.895 2.46 8.16 0.00 3.95 R
2913 4290 4.101119 CCCTAATCCATCCTCAGTAACGTT 59.899 45.833 5.88 5.88 0.00 3.99 R
3549 5436 6.520272 ACATTAATACCACTCTGAGAGATGC 58.480 40.000 17.71 0.00 33.32 3.91 R
3687 5588 2.386661 TTCCGGCACTCAAGATTCTC 57.613 50.000 0.00 0.00 0.00 2.87 R
3695 5596 1.899814 AGACTGTTATTCCGGCACTCA 59.100 47.619 0.00 0.00 0.00 3.41 R
4856 6885 0.035056 GTACATTCTGGCCCTGCACT 60.035 55.000 0.00 0.00 0.00 4.40 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
159 162 6.038603 TCCAGTGATGATGCAAAAATAGCTAC 59.961 38.462 0.00 0.00 0.00 3.58
223 226 5.005682 GGTTGCTTCACATTTTTGTTGTCTC 59.994 40.000 0.00 0.00 0.00 3.36
224 227 4.681744 TGCTTCACATTTTTGTTGTCTCC 58.318 39.130 0.00 0.00 0.00 3.71
226 229 4.497340 GCTTCACATTTTTGTTGTCTCCGA 60.497 41.667 0.00 0.00 0.00 4.55
259 271 4.319766 CGAAAAAGCTAGTGCACATGAAGT 60.320 41.667 21.04 0.00 42.74 3.01
356 377 4.988598 CGGCAGGGTCACGCAACT 62.989 66.667 0.00 0.00 0.00 3.16
371 392 0.655733 CAACTGCCGTTTCAAGACGT 59.344 50.000 0.00 0.00 41.26 4.34
482 503 2.037144 GCAATTTGGAGGAGGCATCAT 58.963 47.619 0.00 0.00 0.00 2.45
772 825 2.093306 TTAGGAGCACACCAACATCG 57.907 50.000 0.00 0.00 0.00 3.84
816 869 3.242518 GCCTTCGTGGTTTAAAATCAGC 58.757 45.455 0.00 0.00 38.35 4.26
824 877 8.325421 TCGTGGTTTAAAATCAGCTATTTGTA 57.675 30.769 0.00 0.00 37.85 2.41
875 955 2.363680 CACGGGAGATGCTCTAATGAGT 59.636 50.000 0.00 0.00 42.13 3.41
1051 1157 4.832608 GACCCCGATTCGCCGCTT 62.833 66.667 0.00 0.00 0.00 4.68
1160 1290 2.423926 CCTGCTGCAGGTACGTATAG 57.576 55.000 35.03 10.97 45.82 1.31
1241 1371 2.673893 GCACCCCAATTCATTTCGGAAC 60.674 50.000 0.00 0.00 0.00 3.62
1327 1497 1.078848 CTCCGGCCAACTCCTTCAG 60.079 63.158 2.24 0.00 0.00 3.02
1343 1513 3.304123 CCTTCAGATCGTCAGACCGTATC 60.304 52.174 0.00 0.00 0.00 2.24
1428 1612 3.557054 CGAGAAACCAAGTTCAGATCCCA 60.557 47.826 0.00 0.00 0.00 4.37
1429 1613 3.753797 GAGAAACCAAGTTCAGATCCCAC 59.246 47.826 0.00 0.00 0.00 4.61
1430 1614 2.586648 AACCAAGTTCAGATCCCACC 57.413 50.000 0.00 0.00 0.00 4.61
1431 1615 0.698818 ACCAAGTTCAGATCCCACCC 59.301 55.000 0.00 0.00 0.00 4.61
1432 1616 0.995024 CCAAGTTCAGATCCCACCCT 59.005 55.000 0.00 0.00 0.00 4.34
1433 1617 1.065126 CCAAGTTCAGATCCCACCCTC 60.065 57.143 0.00 0.00 0.00 4.30
1434 1618 1.912043 CAAGTTCAGATCCCACCCTCT 59.088 52.381 0.00 0.00 0.00 3.69
1435 1619 1.872773 AGTTCAGATCCCACCCTCTC 58.127 55.000 0.00 0.00 0.00 3.20
1489 1673 1.652563 GACCACCGACCAAAAGCAC 59.347 57.895 0.00 0.00 0.00 4.40
1490 1674 1.077357 ACCACCGACCAAAAGCACA 60.077 52.632 0.00 0.00 0.00 4.57
1491 1675 1.101049 ACCACCGACCAAAAGCACAG 61.101 55.000 0.00 0.00 0.00 3.66
1492 1676 1.654220 CACCGACCAAAAGCACAGG 59.346 57.895 0.00 0.00 0.00 4.00
1493 1677 2.193536 ACCGACCAAAAGCACAGGC 61.194 57.895 0.00 0.00 41.61 4.85
1494 1678 2.192861 CCGACCAAAAGCACAGGCA 61.193 57.895 0.00 0.00 44.61 4.75
1495 1679 1.732917 CGACCAAAAGCACAGGCAA 59.267 52.632 0.00 0.00 44.61 4.52
1496 1680 0.594796 CGACCAAAAGCACAGGCAAC 60.595 55.000 0.00 0.00 44.61 4.17
1497 1681 0.249447 GACCAAAAGCACAGGCAACC 60.249 55.000 0.00 0.00 44.61 3.77
1498 1682 0.975040 ACCAAAAGCACAGGCAACCA 60.975 50.000 0.00 0.00 44.61 3.67
1499 1683 0.393820 CCAAAAGCACAGGCAACCAT 59.606 50.000 0.00 0.00 44.61 3.55
1500 1684 1.606224 CCAAAAGCACAGGCAACCATC 60.606 52.381 0.00 0.00 44.61 3.51
1501 1685 0.314935 AAAAGCACAGGCAACCATCG 59.685 50.000 0.00 0.00 44.61 3.84
1502 1686 2.146073 AAAGCACAGGCAACCATCGC 62.146 55.000 0.00 0.00 44.61 4.58
1503 1687 3.058160 GCACAGGCAACCATCGCT 61.058 61.111 0.00 0.00 40.72 4.93
1504 1688 2.629656 GCACAGGCAACCATCGCTT 61.630 57.895 0.00 0.00 40.72 4.68
1505 1689 1.503542 CACAGGCAACCATCGCTTC 59.496 57.895 0.00 0.00 37.17 3.86
1506 1690 1.675641 ACAGGCAACCATCGCTTCC 60.676 57.895 0.00 0.00 37.17 3.46
1507 1691 1.377725 CAGGCAACCATCGCTTCCT 60.378 57.895 0.00 0.00 37.17 3.36
1508 1692 0.962356 CAGGCAACCATCGCTTCCTT 60.962 55.000 0.00 0.00 37.17 3.36
1509 1693 0.678048 AGGCAACCATCGCTTCCTTC 60.678 55.000 0.00 0.00 37.17 3.46
1510 1694 0.960364 GGCAACCATCGCTTCCTTCA 60.960 55.000 0.00 0.00 0.00 3.02
1511 1695 0.169009 GCAACCATCGCTTCCTTCAC 59.831 55.000 0.00 0.00 0.00 3.18
1512 1696 1.522668 CAACCATCGCTTCCTTCACA 58.477 50.000 0.00 0.00 0.00 3.58
1513 1697 2.086869 CAACCATCGCTTCCTTCACAT 58.913 47.619 0.00 0.00 0.00 3.21
1514 1698 2.029838 ACCATCGCTTCCTTCACATC 57.970 50.000 0.00 0.00 0.00 3.06
1547 1731 1.338579 CCTCTGTCCTCTGCCAGTTTC 60.339 57.143 0.00 0.00 0.00 2.78
1557 1741 0.541764 TGCCAGTTTCAACCATCCCC 60.542 55.000 0.00 0.00 0.00 4.81
1609 2067 2.557924 TCCAGCTGTGCTACAAATTTGG 59.442 45.455 21.74 6.60 36.40 3.28
1711 2169 3.490933 GGGACAAAAAGAAGTGCTCCAAC 60.491 47.826 0.00 0.00 0.00 3.77
1723 2181 4.074970 AGTGCTCCAACAGTTCCATTAAG 58.925 43.478 0.00 0.00 0.00 1.85
2067 3370 6.817641 CAGAGTTCATAGTTCTCTCTTGCAAT 59.182 38.462 0.00 0.00 36.57 3.56
2070 3373 8.885494 AGTTCATAGTTCTCTCTTGCAATATC 57.115 34.615 0.00 0.00 0.00 1.63
2100 3407 7.451501 TTCATGAGCAAAATTGAGACATACA 57.548 32.000 0.00 0.00 0.00 2.29
2101 3408 7.080353 TCATGAGCAAAATTGAGACATACAG 57.920 36.000 0.00 0.00 0.00 2.74
2102 3409 6.656270 TCATGAGCAAAATTGAGACATACAGT 59.344 34.615 0.00 0.00 0.00 3.55
2913 4290 4.019792 AGTTTACATCTGTGCCATGTCA 57.980 40.909 0.00 0.00 35.95 3.58
3284 5000 6.628919 AGTGAGGTATGTGTTGGTTTTAAC 57.371 37.500 0.00 0.00 0.00 2.01
3549 5436 3.558829 TCCTACGCGTAAGTCTCTATGTG 59.441 47.826 20.97 3.65 41.68 3.21
3838 5739 7.182817 TGGACATAACCTATGGCTATGATAC 57.817 40.000 12.32 4.64 43.84 2.24
3862 5772 4.309099 AGAACTTGTAACGTCGCCAAATA 58.691 39.130 0.00 0.00 0.00 1.40
4057 5967 1.154338 GCTGTGTGCATCGCTTGAC 60.154 57.895 0.00 0.00 42.31 3.18
4085 5995 1.286849 CCCGGGGTAATCCTCCTTTTT 59.713 52.381 14.71 0.00 35.33 1.94
4123 6033 2.158827 TGGATCATTGACGTGGTATGGG 60.159 50.000 0.00 0.00 0.00 4.00
4218 6176 1.600413 GCCAGGCTTTTGTTCAACTCG 60.600 52.381 3.29 0.00 0.00 4.18
4230 6188 1.003718 CAACTCGGGAAGTGGGACC 60.004 63.158 0.00 0.00 38.58 4.46
4376 6344 7.516155 GCAAATGATGTTTCATCCAATCATTCG 60.516 37.037 9.47 1.57 41.83 3.34
4377 6345 5.503662 TGATGTTTCATCCAATCATTCGG 57.496 39.130 7.18 0.00 0.00 4.30
4379 6347 2.097304 TGTTTCATCCAATCATTCGGCG 59.903 45.455 0.00 0.00 0.00 6.46
4380 6348 2.323968 TTCATCCAATCATTCGGCGA 57.676 45.000 4.99 4.99 0.00 5.54
4382 6350 2.849942 TCATCCAATCATTCGGCGATT 58.150 42.857 11.76 3.93 33.33 3.34
4486 6464 8.037166 GGGCAGTTTATCTTTGATCTTGATTTT 58.963 33.333 0.00 0.00 0.00 1.82
4522 6501 8.505625 GCAACATGTTTATTTCATTTTGGATGT 58.494 29.630 8.77 0.00 35.11 3.06
4676 6701 3.673338 GGTCTGCCAAATTAAAAAGCGTC 59.327 43.478 0.00 0.00 34.09 5.19
4685 6710 8.162245 GCCAAATTAAAAAGCGTCAGAAATTAG 58.838 33.333 0.00 0.00 0.00 1.73
4686 6711 9.191995 CCAAATTAAAAAGCGTCAGAAATTAGT 57.808 29.630 0.00 0.00 0.00 2.24
4820 6849 1.573932 CGAGCATTTGCAACGGACA 59.426 52.632 0.00 0.00 45.16 4.02
4842 6871 2.686816 CGGATTGTGAACCGGCACC 61.687 63.158 0.00 0.00 44.59 5.01
4846 6875 4.858680 TGTGAACCGGCACCGCAA 62.859 61.111 0.00 0.00 37.99 4.85
4847 6876 3.361977 GTGAACCGGCACCGCAAT 61.362 61.111 0.00 0.00 38.24 3.56
4848 6877 3.361158 TGAACCGGCACCGCAATG 61.361 61.111 0.00 0.00 38.24 2.82
4849 6878 4.776647 GAACCGGCACCGCAATGC 62.777 66.667 0.00 0.00 45.34 3.56
4855 6884 2.126346 GCACCGCAATGCAGAACC 60.126 61.111 5.91 0.00 45.39 3.62
4856 6885 2.918345 GCACCGCAATGCAGAACCA 61.918 57.895 5.91 0.00 45.39 3.67
4877 6906 0.403655 TGCAGGGCCAGAATGTACAA 59.596 50.000 6.18 0.00 0.00 2.41
4921 6950 4.224818 AGAGTTAGGCTGAGCATTCTTCTT 59.775 41.667 6.82 0.00 0.00 2.52
4922 6951 4.916183 AGTTAGGCTGAGCATTCTTCTTT 58.084 39.130 6.82 0.00 0.00 2.52
4924 6953 3.430042 AGGCTGAGCATTCTTCTTTCA 57.570 42.857 6.82 0.00 0.00 2.69
4925 6954 3.345414 AGGCTGAGCATTCTTCTTTCAG 58.655 45.455 6.82 0.00 38.57 3.02
4928 6957 4.880696 GGCTGAGCATTCTTCTTTCAGTAT 59.119 41.667 6.82 0.00 38.00 2.12
4929 6958 6.051717 GGCTGAGCATTCTTCTTTCAGTATA 58.948 40.000 6.82 0.00 38.00 1.47
4930 6959 6.018343 GGCTGAGCATTCTTCTTTCAGTATAC 60.018 42.308 6.82 0.00 38.00 1.47
4931 6960 6.536582 GCTGAGCATTCTTCTTTCAGTATACA 59.463 38.462 5.50 0.00 38.00 2.29
4974 7003 5.562113 GCAACCAAAAACGCAGAAGTACTAT 60.562 40.000 0.00 0.00 0.00 2.12
4977 7006 4.403453 CAAAAACGCAGAAGTACTATGCC 58.597 43.478 21.18 8.87 36.60 4.40
4978 7007 1.922570 AACGCAGAAGTACTATGCCG 58.077 50.000 21.18 18.39 36.60 5.69
4979 7008 1.100510 ACGCAGAAGTACTATGCCGA 58.899 50.000 21.18 0.00 36.60 5.54
4980 7009 1.475280 ACGCAGAAGTACTATGCCGAA 59.525 47.619 21.18 0.00 36.60 4.30
5008 7041 5.718146 TGCAACAGAACAGATTTTGAAACA 58.282 33.333 0.00 0.00 0.00 2.83
5020 7053 8.133627 ACAGATTTTGAAACATCAACAAGAGAG 58.866 33.333 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.051334 TAGTGTGGTTTGCTTGCTGT 57.949 45.000 0.00 0.00 0.00 4.40
159 162 7.310052 TGTATCCTACATAAGCTATTGGAGCAG 60.310 40.741 3.04 0.00 43.23 4.24
179 182 0.178068 ACCGTGTGGCTGATGTATCC 59.822 55.000 0.00 0.00 39.70 2.59
180 183 1.290203 CACCGTGTGGCTGATGTATC 58.710 55.000 0.00 0.00 39.70 2.24
224 227 2.474842 CTTTTTCGCCGGTGTCGTCG 62.475 60.000 16.01 2.25 39.22 5.12
226 229 2.888998 GCTTTTTCGCCGGTGTCGT 61.889 57.895 16.01 0.00 33.95 4.34
343 364 4.988598 CGGCAGTTGCGTGACCCT 62.989 66.667 0.00 0.00 43.26 4.34
361 382 1.537348 CCACGAGGTGACGTCTTGAAA 60.537 52.381 17.92 0.00 44.76 2.69
395 416 2.142220 TGCCGACAAGGAAGAAGGT 58.858 52.632 0.00 0.00 45.00 3.50
435 456 0.546122 ATTTGCAGCCCCTCGTATCA 59.454 50.000 0.00 0.00 0.00 2.15
438 459 0.107703 CAGATTTGCAGCCCCTCGTA 60.108 55.000 0.00 0.00 0.00 3.43
535 572 2.603776 ACGCCTTCTTCGACCCCT 60.604 61.111 0.00 0.00 0.00 4.79
740 779 6.183360 GGTGTGCTCCTAAAAAGTATGATGTC 60.183 42.308 0.00 0.00 0.00 3.06
748 787 3.626930 TGTTGGTGTGCTCCTAAAAAGT 58.373 40.909 0.00 0.00 0.00 2.66
749 788 4.613622 CGATGTTGGTGTGCTCCTAAAAAG 60.614 45.833 0.00 0.00 0.00 2.27
772 825 5.733373 GCCCAAAAACGATGATCCAATAGAC 60.733 44.000 0.00 0.00 0.00 2.59
875 955 6.823689 ACCGATTCCTAGTAAAACTCGTACTA 59.176 38.462 0.00 0.00 33.80 1.82
946 1050 8.447053 CGCTAGCTTCTTTTCTCTTCTTTATTT 58.553 33.333 13.93 0.00 0.00 1.40
947 1051 7.065204 CCGCTAGCTTCTTTTCTCTTCTTTATT 59.935 37.037 13.93 0.00 0.00 1.40
948 1052 6.536941 CCGCTAGCTTCTTTTCTCTTCTTTAT 59.463 38.462 13.93 0.00 0.00 1.40
949 1053 5.869888 CCGCTAGCTTCTTTTCTCTTCTTTA 59.130 40.000 13.93 0.00 0.00 1.85
981 1085 0.620556 TGGTGAAAGAGATCCCCTGC 59.379 55.000 0.00 0.00 0.00 4.85
1100 1230 3.730761 GATGCCGATGCCGATGCC 61.731 66.667 0.00 0.00 38.22 4.40
1101 1231 4.081030 CGATGCCGATGCCGATGC 62.081 66.667 0.00 0.00 38.22 3.91
1102 1232 3.417224 CCGATGCCGATGCCGATG 61.417 66.667 0.00 0.00 38.22 3.84
1114 1244 0.392193 AGAGGTTTCAGCAGCCGATG 60.392 55.000 0.00 0.00 0.00 3.84
1160 1290 2.202623 AGATGCGGCGTTCGAGAC 60.203 61.111 9.37 0.00 42.43 3.36
1186 1316 1.919240 TCGCCTAACACAGAAGAGGA 58.081 50.000 0.00 0.00 0.00 3.71
1188 1318 4.058817 AGTTTTCGCCTAACACAGAAGAG 58.941 43.478 0.00 0.00 0.00 2.85
1241 1371 7.472543 CGAGGAATTTTGGTATTGAAAGTAGG 58.527 38.462 0.00 0.00 0.00 3.18
1322 1492 3.304123 GGATACGGTCTGACGATCTGAAG 60.304 52.174 1.07 0.00 37.61 3.02
1327 1497 1.267261 CCAGGATACGGTCTGACGATC 59.733 57.143 1.07 4.83 46.39 3.69
1343 1513 0.394352 CAGGTCCCCGAAAATCCAGG 60.394 60.000 0.00 0.00 0.00 4.45
1428 1612 1.229984 CAAAGGGAGGGGAGAGGGT 60.230 63.158 0.00 0.00 0.00 4.34
1429 1613 1.082954 TCAAAGGGAGGGGAGAGGG 59.917 63.158 0.00 0.00 0.00 4.30
1430 1614 1.617947 CGTCAAAGGGAGGGGAGAGG 61.618 65.000 0.00 0.00 0.00 3.69
1431 1615 0.614979 TCGTCAAAGGGAGGGGAGAG 60.615 60.000 0.00 0.00 32.28 3.20
1432 1616 0.614979 CTCGTCAAAGGGAGGGGAGA 60.615 60.000 0.00 0.00 33.62 3.71
1433 1617 0.614979 TCTCGTCAAAGGGAGGGGAG 60.615 60.000 0.00 0.00 36.02 4.30
1434 1618 0.178915 TTCTCGTCAAAGGGAGGGGA 60.179 55.000 0.00 0.00 39.06 4.81
1435 1619 0.690762 TTTCTCGTCAAAGGGAGGGG 59.309 55.000 0.00 0.00 33.06 4.79
1489 1673 0.962356 AAGGAAGCGATGGTTGCCTG 60.962 55.000 0.00 0.00 32.00 4.85
1490 1674 0.678048 GAAGGAAGCGATGGTTGCCT 60.678 55.000 0.00 0.00 32.00 4.75
1491 1675 0.960364 TGAAGGAAGCGATGGTTGCC 60.960 55.000 0.00 0.00 32.00 4.52
1492 1676 0.169009 GTGAAGGAAGCGATGGTTGC 59.831 55.000 0.00 0.00 0.00 4.17
1493 1677 1.522668 TGTGAAGGAAGCGATGGTTG 58.477 50.000 0.00 0.00 0.00 3.77
1494 1678 2.026822 AGATGTGAAGGAAGCGATGGTT 60.027 45.455 0.00 0.00 0.00 3.67
1495 1679 1.556911 AGATGTGAAGGAAGCGATGGT 59.443 47.619 0.00 0.00 0.00 3.55
1496 1680 2.322355 AGATGTGAAGGAAGCGATGG 57.678 50.000 0.00 0.00 0.00 3.51
1497 1681 4.149571 CGATTAGATGTGAAGGAAGCGATG 59.850 45.833 0.00 0.00 30.97 3.84
1498 1682 4.202161 ACGATTAGATGTGAAGGAAGCGAT 60.202 41.667 0.00 0.00 33.48 4.58
1499 1683 3.130516 ACGATTAGATGTGAAGGAAGCGA 59.869 43.478 0.00 0.00 33.48 4.93
1500 1684 3.448686 ACGATTAGATGTGAAGGAAGCG 58.551 45.455 0.00 0.00 35.23 4.68
1501 1685 4.688021 AGACGATTAGATGTGAAGGAAGC 58.312 43.478 0.00 0.00 0.00 3.86
1502 1686 5.163509 TGGAGACGATTAGATGTGAAGGAAG 60.164 44.000 0.00 0.00 0.00 3.46
1503 1687 4.709886 TGGAGACGATTAGATGTGAAGGAA 59.290 41.667 0.00 0.00 0.00 3.36
1504 1688 4.098044 GTGGAGACGATTAGATGTGAAGGA 59.902 45.833 0.00 0.00 0.00 3.36
1505 1689 4.363999 GTGGAGACGATTAGATGTGAAGG 58.636 47.826 0.00 0.00 0.00 3.46
1506 1690 4.098654 AGGTGGAGACGATTAGATGTGAAG 59.901 45.833 0.00 0.00 0.00 3.02
1507 1691 4.023980 AGGTGGAGACGATTAGATGTGAA 58.976 43.478 0.00 0.00 0.00 3.18
1508 1692 3.632333 AGGTGGAGACGATTAGATGTGA 58.368 45.455 0.00 0.00 0.00 3.58
1509 1693 3.634448 AGAGGTGGAGACGATTAGATGTG 59.366 47.826 0.00 0.00 0.00 3.21
1510 1694 3.634448 CAGAGGTGGAGACGATTAGATGT 59.366 47.826 0.00 0.00 0.00 3.06
1511 1695 3.634448 ACAGAGGTGGAGACGATTAGATG 59.366 47.826 0.00 0.00 0.00 2.90
1512 1696 3.886505 GACAGAGGTGGAGACGATTAGAT 59.113 47.826 0.00 0.00 0.00 1.98
1513 1697 3.280295 GACAGAGGTGGAGACGATTAGA 58.720 50.000 0.00 0.00 0.00 2.10
1514 1698 2.359531 GGACAGAGGTGGAGACGATTAG 59.640 54.545 0.00 0.00 0.00 1.73
1547 1731 1.315257 CCGAAGCTTGGGGATGGTTG 61.315 60.000 19.17 0.00 0.00 3.77
1557 1741 2.815647 GGCTCGACCCGAAGCTTG 60.816 66.667 2.10 0.00 34.74 4.01
1578 1762 1.457346 CACAGCTGGAATCCCAAGTC 58.543 55.000 19.93 0.00 42.98 3.01
1609 2067 0.387929 TCATCCCGCGATCTAACACC 59.612 55.000 8.23 0.00 0.00 4.16
1669 2127 2.425102 CCAACTTCCCCTAACCCACAAA 60.425 50.000 0.00 0.00 0.00 2.83
1711 2169 5.567138 AATTTCCGAGCTTAATGGAACTG 57.433 39.130 9.39 0.00 41.28 3.16
1723 2181 5.462068 GGTGCCAATATAAAAATTTCCGAGC 59.538 40.000 0.00 0.00 0.00 5.03
1741 2199 0.553819 AGTGGTTTTACAGGGTGCCA 59.446 50.000 0.00 0.00 0.00 4.92
2067 3370 8.339344 TCAATTTTGCTCATGAAACTCAGATA 57.661 30.769 0.00 0.00 0.00 1.98
2070 3373 6.581542 GTCTCAATTTTGCTCATGAAACTCAG 59.418 38.462 0.00 0.00 0.00 3.35
2100 3407 6.228995 GCAGTGGGAGTTTTTAAGTACTACT 58.771 40.000 0.00 0.00 36.98 2.57
2101 3408 5.119743 CGCAGTGGGAGTTTTTAAGTACTAC 59.880 44.000 0.00 0.00 0.00 2.73
2102 3409 5.221501 ACGCAGTGGGAGTTTTTAAGTACTA 60.222 40.000 14.98 0.00 42.51 1.82
2112 3419 1.447317 CTGCAACGCAGTGGGAGTTT 61.447 55.000 14.98 0.00 45.38 2.66
2287 3624 4.310357 TGTGTTCGTGTGCTAGAAGTTA 57.690 40.909 0.00 0.00 0.00 2.24
2288 3625 3.173668 TGTGTTCGTGTGCTAGAAGTT 57.826 42.857 0.00 0.00 0.00 2.66
2289 3626 2.882927 TGTGTTCGTGTGCTAGAAGT 57.117 45.000 0.00 0.00 0.00 3.01
2301 3644 1.349627 GCCGAGATGCATGTGTTCG 59.650 57.895 2.46 8.16 0.00 3.95
2382 3746 4.518970 TGACAAGTTCAACCATTAGCTTCC 59.481 41.667 0.00 0.00 0.00 3.46
2913 4290 4.101119 CCCTAATCCATCCTCAGTAACGTT 59.899 45.833 5.88 5.88 0.00 3.99
3549 5436 6.520272 ACATTAATACCACTCTGAGAGATGC 58.480 40.000 17.71 0.00 33.32 3.91
3687 5588 2.386661 TTCCGGCACTCAAGATTCTC 57.613 50.000 0.00 0.00 0.00 2.87
3695 5596 1.899814 AGACTGTTATTCCGGCACTCA 59.100 47.619 0.00 0.00 0.00 3.41
3838 5739 0.706729 GGCGACGTTACAAGTTCTCG 59.293 55.000 0.00 0.00 0.00 4.04
3862 5772 2.086869 CAATCATTCTCGCAGTTGGGT 58.913 47.619 0.00 0.00 0.00 4.51
4085 5995 4.349636 TGATCCACTGGTACCTTTTTCTCA 59.650 41.667 14.36 7.01 0.00 3.27
4123 6033 2.526432 TCTATTGCTACCGAGATCCCC 58.474 52.381 0.00 0.00 0.00 4.81
4184 6136 3.294214 AGCCTGGCCAATAAATCTCTTG 58.706 45.455 16.57 0.00 0.00 3.02
4218 6176 0.771755 AACTCAAGGTCCCACTTCCC 59.228 55.000 0.00 0.00 0.00 3.97
4291 6259 2.238521 TCTCCAATTCAAACAGCCACC 58.761 47.619 0.00 0.00 0.00 4.61
4376 6344 2.554032 CCCTCATCAACCATTAATCGCC 59.446 50.000 0.00 0.00 0.00 5.54
4377 6345 3.214328 ACCCTCATCAACCATTAATCGC 58.786 45.455 0.00 0.00 0.00 4.58
4379 6347 4.202151 GCCAACCCTCATCAACCATTAATC 60.202 45.833 0.00 0.00 0.00 1.75
4380 6348 3.706086 GCCAACCCTCATCAACCATTAAT 59.294 43.478 0.00 0.00 0.00 1.40
4382 6350 2.042297 TGCCAACCCTCATCAACCATTA 59.958 45.455 0.00 0.00 0.00 1.90
4486 6464 7.921214 TGAAATAAACATGTTGCTACGGAAAAA 59.079 29.630 12.82 0.00 0.00 1.94
4491 6470 7.810766 AAATGAAATAAACATGTTGCTACGG 57.189 32.000 12.82 0.00 0.00 4.02
4492 6471 8.161610 CCAAAATGAAATAAACATGTTGCTACG 58.838 33.333 12.82 0.00 39.94 3.51
4496 6475 8.505625 ACATCCAAAATGAAATAAACATGTTGC 58.494 29.630 12.82 0.63 39.94 4.17
4522 6501 6.126565 TGTCCTAGACCATCTAAGCTACTGTA 60.127 42.308 0.00 0.00 0.00 2.74
4523 6502 5.134661 GTCCTAGACCATCTAAGCTACTGT 58.865 45.833 0.00 0.00 0.00 3.55
4524 6503 5.009210 GTGTCCTAGACCATCTAAGCTACTG 59.991 48.000 0.00 0.00 0.00 2.74
4525 6504 5.103855 AGTGTCCTAGACCATCTAAGCTACT 60.104 44.000 0.00 0.00 0.00 2.57
4526 6505 5.134661 AGTGTCCTAGACCATCTAAGCTAC 58.865 45.833 0.00 0.00 0.00 3.58
4626 6625 0.817634 CCGTTTCACCCTGCTCAACA 60.818 55.000 0.00 0.00 0.00 3.33
4676 6701 6.687081 TTGGCCGGTAATAACTAATTTCTG 57.313 37.500 1.90 0.00 0.00 3.02
4685 6710 3.482436 TGATGGATTGGCCGGTAATAAC 58.518 45.455 1.90 2.51 40.66 1.89
4686 6711 3.866703 TGATGGATTGGCCGGTAATAA 57.133 42.857 1.90 0.00 40.66 1.40
4687 6712 3.073798 ACATGATGGATTGGCCGGTAATA 59.926 43.478 1.90 0.00 40.66 0.98
4688 6713 2.158475 ACATGATGGATTGGCCGGTAAT 60.158 45.455 1.90 4.35 40.66 1.89
4820 6849 0.953960 GCCGGTTCACAATCCGTTCT 60.954 55.000 1.90 0.00 44.51 3.01
4842 6871 1.443194 GCACTGGTTCTGCATTGCG 60.443 57.895 3.84 0.00 34.56 4.85
4846 6875 1.303888 CCCTGCACTGGTTCTGCAT 60.304 57.895 0.00 0.00 43.61 3.96
4847 6876 2.113774 CCCTGCACTGGTTCTGCA 59.886 61.111 0.00 0.00 42.42 4.41
4848 6877 3.368571 GCCCTGCACTGGTTCTGC 61.369 66.667 0.00 0.00 35.03 4.26
4849 6878 2.674380 GGCCCTGCACTGGTTCTG 60.674 66.667 0.00 0.00 0.00 3.02
4850 6879 3.177884 TGGCCCTGCACTGGTTCT 61.178 61.111 0.00 0.00 0.00 3.01
4851 6880 2.674380 CTGGCCCTGCACTGGTTC 60.674 66.667 0.00 0.00 0.00 3.62
4852 6881 2.085343 ATTCTGGCCCTGCACTGGTT 62.085 55.000 0.00 0.00 0.00 3.67
4853 6882 2.541907 ATTCTGGCCCTGCACTGGT 61.542 57.895 0.00 0.00 0.00 4.00
4854 6883 2.050350 CATTCTGGCCCTGCACTGG 61.050 63.158 0.00 0.00 0.00 4.00
4855 6884 0.035152 TACATTCTGGCCCTGCACTG 60.035 55.000 0.00 0.00 0.00 3.66
4856 6885 0.035056 GTACATTCTGGCCCTGCACT 60.035 55.000 0.00 0.00 0.00 4.40
4877 6906 2.632996 TGAACCGTCCATTTCTCTCTGT 59.367 45.455 0.00 0.00 0.00 3.41
4925 6954 9.968743 GCAAATACAGTAGTTGACTTTGTATAC 57.031 33.333 22.08 0.00 35.64 1.47
4928 6957 8.339714 GTTGCAAATACAGTAGTTGACTTTGTA 58.660 33.333 22.08 6.81 35.64 2.41
4929 6958 6.935741 TGCAAATACAGTAGTTGACTTTGT 57.064 33.333 22.08 0.00 35.64 2.83
4930 6959 6.636850 GGTTGCAAATACAGTAGTTGACTTTG 59.363 38.462 22.08 10.43 35.64 2.77
4931 6960 6.320164 TGGTTGCAAATACAGTAGTTGACTTT 59.680 34.615 22.08 0.00 35.64 2.66
4974 7003 1.028130 TCTGTTGCAAATGTTCGGCA 58.972 45.000 0.00 0.00 35.41 5.69
4977 7006 3.951306 TCTGTTCTGTTGCAAATGTTCG 58.049 40.909 0.00 0.00 0.00 3.95
4978 7007 6.833342 AAATCTGTTCTGTTGCAAATGTTC 57.167 33.333 0.00 0.00 0.00 3.18
4979 7008 6.817641 TCAAAATCTGTTCTGTTGCAAATGTT 59.182 30.769 0.00 0.00 0.00 2.71
4980 7009 6.339730 TCAAAATCTGTTCTGTTGCAAATGT 58.660 32.000 0.00 0.00 0.00 2.71
5008 7041 1.677217 GCTTCCCGCTCTCTTGTTGAT 60.677 52.381 0.00 0.00 35.14 2.57


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

AutoCloner maintained by Alex Coulton.