Multiple sequence alignment - TraesCS4A01G249800

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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 TraesCS4A01G249800 chr4A 100.000 2294 0 0 1 2294 560963956 560966249 0.000000e+00 4237.0
1 TraesCS4A01G249800 chr4A 82.985 670 64 30 743 1374 560951388 560952045 5.530000e-156 560.0
2 TraesCS4A01G249800 chr4A 85.401 137 14 6 1007 1141 46561065 46561197 1.110000e-28 137.0
3 TraesCS4A01G249800 chr4D 90.153 782 42 14 779 1553 39353554 39354307 0.000000e+00 985.0
4 TraesCS4A01G249800 chr4D 91.339 635 39 13 14 644 39352809 39353431 0.000000e+00 854.0
5 TraesCS4A01G249800 chr4D 91.850 319 18 6 996 1313 39394541 39394230 2.710000e-119 438.0
6 TraesCS4A01G249800 chr4D 93.684 95 2 1 646 736 39353463 39353557 3.070000e-29 139.0
7 TraesCS4A01G249800 chr4D 84.962 133 17 3 1007 1139 418358168 418358039 5.140000e-27 132.0
8 TraesCS4A01G249800 chr4D 80.451 133 6 3 743 874 39394833 39394720 1.460000e-12 84.2
9 TraesCS4A01G249800 chr4D 93.478 46 2 1 150 194 394189167 394189122 1.470000e-07 67.6
10 TraesCS4A01G249800 chr4B 86.842 912 61 17 650 1555 57801960 57801102 0.000000e+00 965.0
11 TraesCS4A01G249800 chr4B 92.929 594 37 5 1705 2294 408180099 408179507 0.000000e+00 859.0
12 TraesCS4A01G249800 chr4B 92.542 590 41 3 1707 2294 641810447 641809859 0.000000e+00 843.0
13 TraesCS4A01G249800 chr4B 84.983 586 47 22 743 1301 57806634 57806063 7.160000e-155 556.0
14 TraesCS4A01G249800 chr4B 86.452 465 44 9 1 456 57803818 57803364 2.050000e-135 492.0
15 TraesCS4A01G249800 chr4B 85.714 126 11 3 529 654 57802110 57801992 2.390000e-25 126.0
16 TraesCS4A01G249800 chr4B 91.489 47 2 2 150 194 483905209 483905163 1.900000e-06 63.9
17 TraesCS4A01G249800 chr7D 93.434 594 35 4 1703 2294 46530616 46531207 0.000000e+00 878.0
18 TraesCS4A01G249800 chr5A 93.390 590 36 3 1707 2294 1193189 1193777 0.000000e+00 870.0
19 TraesCS4A01G249800 chr5A 93.098 594 37 4 1703 2294 434132930 434132339 0.000000e+00 867.0
20 TraesCS4A01G249800 chr6D 92.881 590 40 2 1707 2294 16183148 16182559 0.000000e+00 856.0
21 TraesCS4A01G249800 chr6D 88.732 71 6 1 263 333 36659844 36659912 4.060000e-13 86.1
22 TraesCS4A01G249800 chr6D 87.324 71 7 1 263 333 36634937 36635005 1.890000e-11 80.5
23 TraesCS4A01G249800 chr6D 93.023 43 2 1 291 332 365442660 365442618 6.840000e-06 62.1
24 TraesCS4A01G249800 chr5D 92.724 591 36 5 1707 2294 549659958 549659372 0.000000e+00 846.0
25 TraesCS4A01G249800 chr5D 92.411 593 42 3 1705 2294 483565078 483565670 0.000000e+00 843.0
26 TraesCS4A01G249800 chr1B 92.230 592 44 2 1705 2294 205993681 205993090 0.000000e+00 837.0
27 TraesCS4A01G249800 chr7B 92.771 83 6 0 1007 1089 469742207 469742289 1.110000e-23 121.0
28 TraesCS4A01G249800 chr2B 80.576 139 24 3 201 338 156918817 156918953 1.120000e-18 104.0
29 TraesCS4A01G249800 chr1D 91.045 67 5 1 273 338 60323573 60323507 3.140000e-14 89.8
30 TraesCS4A01G249800 chr1D 89.286 56 4 2 279 333 414741484 414741430 4.090000e-08 69.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G249800 chr4A 560963956 560966249 2293 False 4237.000000 4237 100.000000 1 2294 1 chr4A.!!$F3 2293
1 TraesCS4A01G249800 chr4A 560951388 560952045 657 False 560.000000 560 82.985000 743 1374 1 chr4A.!!$F2 631
2 TraesCS4A01G249800 chr4D 39352809 39354307 1498 False 659.333333 985 91.725333 14 1553 3 chr4D.!!$F1 1539
3 TraesCS4A01G249800 chr4D 39394230 39394833 603 True 261.100000 438 86.150500 743 1313 2 chr4D.!!$R3 570
4 TraesCS4A01G249800 chr4B 408179507 408180099 592 True 859.000000 859 92.929000 1705 2294 1 chr4B.!!$R1 589
5 TraesCS4A01G249800 chr4B 641809859 641810447 588 True 843.000000 843 92.542000 1707 2294 1 chr4B.!!$R3 587
6 TraesCS4A01G249800 chr4B 57801102 57806634 5532 True 534.750000 965 85.997750 1 1555 4 chr4B.!!$R4 1554
7 TraesCS4A01G249800 chr7D 46530616 46531207 591 False 878.000000 878 93.434000 1703 2294 1 chr7D.!!$F1 591
8 TraesCS4A01G249800 chr5A 1193189 1193777 588 False 870.000000 870 93.390000 1707 2294 1 chr5A.!!$F1 587
9 TraesCS4A01G249800 chr5A 434132339 434132930 591 True 867.000000 867 93.098000 1703 2294 1 chr5A.!!$R1 591
10 TraesCS4A01G249800 chr6D 16182559 16183148 589 True 856.000000 856 92.881000 1707 2294 1 chr6D.!!$R1 587
11 TraesCS4A01G249800 chr5D 549659372 549659958 586 True 846.000000 846 92.724000 1707 2294 1 chr5D.!!$R1 587
12 TraesCS4A01G249800 chr5D 483565078 483565670 592 False 843.000000 843 92.411000 1705 2294 1 chr5D.!!$F1 589
13 TraesCS4A01G249800 chr1B 205993090 205993681 591 True 837.000000 837 92.230000 1705 2294 1 chr1B.!!$R1 589

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
654 4725 1.207329 CCCCACTAGTAGTTCACAGCC 59.793 57.143 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1663 5823 0.03582 TCTTTTTCCGGCCGTGCTAT 60.036 50.0 26.12 0.0 0.0 2.97 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
81 2898 7.714500 AGGCACTCCTCTAGGTATATATTTCT 58.286 38.462 0.00 0.00 38.72 2.52
82 2899 8.847816 AGGCACTCCTCTAGGTATATATTTCTA 58.152 37.037 0.00 0.00 38.72 2.10
172 2990 8.455682 CAGATTTTTAAGCATGGCAAATTGAAT 58.544 29.630 0.00 0.00 0.00 2.57
201 3020 4.837896 TGTCAATTTATGTTGGTGCGAA 57.162 36.364 0.00 0.00 0.00 4.70
219 3043 6.128391 GGTGCGAAGATGACACATTTAGTTTA 60.128 38.462 0.00 0.00 36.00 2.01
223 3047 7.801315 GCGAAGATGACACATTTAGTTTACAAA 59.199 33.333 0.00 0.00 0.00 2.83
289 3113 3.573967 CCATGCTTCCCAACTAAACTTGT 59.426 43.478 0.00 0.00 0.00 3.16
303 3127 2.270352 ACTTGTCATCCTCGGCAAAA 57.730 45.000 0.00 0.00 0.00 2.44
316 3140 6.098679 TCCTCGGCAAAAATAAATTGTCATG 58.901 36.000 0.00 0.00 31.96 3.07
339 3163 6.607689 TGAAAAACGTTCGATTTGCTATGAT 58.392 32.000 0.00 0.00 0.00 2.45
340 3164 7.081349 TGAAAAACGTTCGATTTGCTATGATT 58.919 30.769 0.00 0.00 0.00 2.57
341 3165 8.231161 TGAAAAACGTTCGATTTGCTATGATTA 58.769 29.630 0.00 0.00 0.00 1.75
342 3166 9.221775 GAAAAACGTTCGATTTGCTATGATTAT 57.778 29.630 0.00 0.00 0.00 1.28
343 3167 9.567848 AAAAACGTTCGATTTGCTATGATTATT 57.432 25.926 0.00 0.00 0.00 1.40
344 3168 8.767944 AAACGTTCGATTTGCTATGATTATTC 57.232 30.769 0.00 0.00 0.00 1.75
429 3253 7.593273 CGAAATAACATTGTTGTAACACCACAT 59.407 33.333 12.30 0.00 38.92 3.21
498 4387 2.977405 AGCGTGAGTTGCTTTGATTC 57.023 45.000 0.00 0.00 40.48 2.52
610 4616 4.320456 CAGTCCACACTGCGGCCT 62.320 66.667 0.00 0.00 43.77 5.19
644 4650 1.568504 CACCTCAAGCCCCACTAGTA 58.431 55.000 0.00 0.00 0.00 1.82
654 4725 1.207329 CCCCACTAGTAGTTCACAGCC 59.793 57.143 0.00 0.00 0.00 4.85
828 4909 2.556287 CAGAAGCCACCGCGAAAC 59.444 61.111 8.23 0.00 41.18 2.78
829 4910 2.668550 AGAAGCCACCGCGAAACC 60.669 61.111 8.23 0.00 41.18 3.27
830 4911 3.733960 GAAGCCACCGCGAAACCC 61.734 66.667 8.23 0.00 41.18 4.11
831 4912 4.572571 AAGCCACCGCGAAACCCA 62.573 61.111 8.23 0.00 41.18 4.51
834 4915 4.973055 CCACCGCGAAACCCACGA 62.973 66.667 8.23 0.00 0.00 4.35
835 4916 3.411351 CACCGCGAAACCCACGAG 61.411 66.667 8.23 0.00 0.00 4.18
963 5072 4.753662 ACGAGCTCCCCGTAGCCA 62.754 66.667 8.47 0.00 43.86 4.75
1114 5256 3.374402 CGCAGTCCACCTCCTCGT 61.374 66.667 0.00 0.00 0.00 4.18
1115 5257 2.574399 GCAGTCCACCTCCTCGTC 59.426 66.667 0.00 0.00 0.00 4.20
1116 5258 2.878429 CAGTCCACCTCCTCGTCG 59.122 66.667 0.00 0.00 0.00 5.12
1117 5259 1.972223 CAGTCCACCTCCTCGTCGT 60.972 63.158 0.00 0.00 0.00 4.34
1118 5260 1.674980 AGTCCACCTCCTCGTCGTC 60.675 63.158 0.00 0.00 0.00 4.20
1119 5261 1.970114 GTCCACCTCCTCGTCGTCA 60.970 63.158 0.00 0.00 0.00 4.35
1343 5500 3.891366 CTCTTCTGGGGAGAGATCTCTTC 59.109 52.174 25.81 23.55 42.48 2.87
1381 5538 1.824852 GGCCAAGGAATTGGTCGATTT 59.175 47.619 0.00 0.00 43.90 2.17
1382 5539 3.020984 GGCCAAGGAATTGGTCGATTTA 58.979 45.455 0.00 0.00 43.90 1.40
1383 5540 3.636764 GGCCAAGGAATTGGTCGATTTAT 59.363 43.478 0.00 0.00 43.90 1.40
1384 5541 4.499696 GGCCAAGGAATTGGTCGATTTATG 60.500 45.833 0.00 0.00 43.90 1.90
1475 5634 6.712241 ACTCGCATTTGTGCATATATACTC 57.288 37.500 0.00 0.00 34.41 2.59
1498 5657 3.865745 GGACGACAATGATGAATCTCGTT 59.134 43.478 6.73 0.00 33.76 3.85
1500 5659 3.865745 ACGACAATGATGAATCTCGTTCC 59.134 43.478 0.00 0.00 35.91 3.62
1502 5661 2.609459 ACAATGATGAATCTCGTTCCGC 59.391 45.455 0.00 0.00 35.91 5.54
1512 5671 0.517316 CTCGTTCCGCTTTTCCCTTG 59.483 55.000 0.00 0.00 0.00 3.61
1524 5683 4.809007 GCTTTTCCCTTGAGAGGAATCACT 60.809 45.833 0.00 0.00 46.74 3.41
1526 5686 5.422214 TTTCCCTTGAGAGGAATCACTAC 57.578 43.478 0.00 0.00 46.74 2.73
1529 5689 4.223032 TCCCTTGAGAGGAATCACTACAAC 59.777 45.833 0.00 0.00 46.74 3.32
1531 5691 3.232213 TGAGAGGAATCACTACAACGC 57.768 47.619 0.00 0.00 0.00 4.84
1555 5715 7.851472 CGCCCGTTAAACAAACAAATTTTAATT 59.149 29.630 0.00 0.00 38.03 1.40
1556 5716 9.504710 GCCCGTTAAACAAACAAATTTTAATTT 57.495 25.926 0.00 0.00 39.07 1.82
1597 5757 2.444281 TTTTTCGGACCGAGGGAGT 58.556 52.632 17.51 0.00 37.14 3.85
1598 5758 1.631405 TTTTTCGGACCGAGGGAGTA 58.369 50.000 17.51 0.00 37.14 2.59
1599 5759 0.890683 TTTTCGGACCGAGGGAGTAC 59.109 55.000 17.51 0.00 37.14 2.73
1600 5760 1.308069 TTTCGGACCGAGGGAGTACG 61.308 60.000 17.51 0.00 43.10 3.67
1601 5761 2.124983 CGGACCGAGGGAGTACGA 60.125 66.667 8.64 0.00 44.55 3.43
1602 5762 2.178890 CGGACCGAGGGAGTACGAG 61.179 68.421 8.64 0.00 44.55 4.18
1603 5763 1.823041 GGACCGAGGGAGTACGAGG 60.823 68.421 0.00 0.00 0.00 4.63
1604 5764 1.077858 GACCGAGGGAGTACGAGGT 60.078 63.158 0.00 0.00 34.27 3.85
1605 5765 1.077858 ACCGAGGGAGTACGAGGTC 60.078 63.158 0.00 0.00 0.00 3.85
1606 5766 2.178890 CCGAGGGAGTACGAGGTCG 61.179 68.421 0.00 0.00 46.33 4.79
1607 5767 1.153489 CGAGGGAGTACGAGGTCGA 60.153 63.158 6.35 0.00 43.02 4.20
1608 5768 0.742281 CGAGGGAGTACGAGGTCGAA 60.742 60.000 6.35 0.00 43.02 3.71
1609 5769 1.015868 GAGGGAGTACGAGGTCGAAG 58.984 60.000 6.35 0.00 43.02 3.79
1610 5770 0.394080 AGGGAGTACGAGGTCGAAGG 60.394 60.000 6.35 0.00 43.02 3.46
1611 5771 1.382692 GGGAGTACGAGGTCGAAGGG 61.383 65.000 6.35 0.00 43.02 3.95
1612 5772 1.432657 GAGTACGAGGTCGAAGGGC 59.567 63.158 6.35 0.00 43.02 5.19
1613 5773 1.303888 AGTACGAGGTCGAAGGGCA 60.304 57.895 6.35 0.00 43.02 5.36
1614 5774 0.896940 AGTACGAGGTCGAAGGGCAA 60.897 55.000 6.35 0.00 43.02 4.52
1615 5775 0.458025 GTACGAGGTCGAAGGGCAAG 60.458 60.000 6.35 0.00 43.02 4.01
1616 5776 0.609957 TACGAGGTCGAAGGGCAAGA 60.610 55.000 6.35 0.00 43.02 3.02
1617 5777 1.258445 ACGAGGTCGAAGGGCAAGAT 61.258 55.000 6.35 0.00 43.02 2.40
1618 5778 0.528684 CGAGGTCGAAGGGCAAGATC 60.529 60.000 0.00 0.00 43.02 2.75
1619 5779 0.827368 GAGGTCGAAGGGCAAGATCT 59.173 55.000 0.00 0.00 0.00 2.75
1620 5780 1.208293 GAGGTCGAAGGGCAAGATCTT 59.792 52.381 0.88 0.88 0.00 2.40
1621 5781 1.208293 AGGTCGAAGGGCAAGATCTTC 59.792 52.381 4.57 0.75 36.84 2.87
1622 5782 1.066143 GGTCGAAGGGCAAGATCTTCA 60.066 52.381 4.57 0.00 39.30 3.02
1623 5783 2.615493 GGTCGAAGGGCAAGATCTTCAA 60.615 50.000 4.57 0.00 39.30 2.69
1624 5784 2.416893 GTCGAAGGGCAAGATCTTCAAC 59.583 50.000 4.57 0.00 39.30 3.18
1625 5785 1.740025 CGAAGGGCAAGATCTTCAACC 59.260 52.381 4.57 8.15 39.30 3.77
1626 5786 2.616510 CGAAGGGCAAGATCTTCAACCT 60.617 50.000 4.57 10.35 39.30 3.50
1627 5787 3.369471 CGAAGGGCAAGATCTTCAACCTA 60.369 47.826 17.82 0.00 39.30 3.08
1628 5788 4.589908 GAAGGGCAAGATCTTCAACCTAA 58.410 43.478 17.82 0.00 39.19 2.69
1629 5789 4.870021 AGGGCAAGATCTTCAACCTAAT 57.130 40.909 16.59 4.11 0.00 1.73
1630 5790 5.198602 AGGGCAAGATCTTCAACCTAATT 57.801 39.130 16.59 0.00 0.00 1.40
1631 5791 4.952335 AGGGCAAGATCTTCAACCTAATTG 59.048 41.667 16.59 0.83 39.94 2.32
1632 5792 4.706962 GGGCAAGATCTTCAACCTAATTGT 59.293 41.667 4.57 0.00 39.54 2.71
1633 5793 5.163612 GGGCAAGATCTTCAACCTAATTGTC 60.164 44.000 4.57 0.00 39.54 3.18
1634 5794 5.649831 GGCAAGATCTTCAACCTAATTGTCT 59.350 40.000 4.57 0.00 39.54 3.41
1635 5795 6.183360 GGCAAGATCTTCAACCTAATTGTCTC 60.183 42.308 4.57 0.00 39.54 3.36
1636 5796 6.597280 GCAAGATCTTCAACCTAATTGTCTCT 59.403 38.462 4.57 0.00 39.54 3.10
1637 5797 7.413877 GCAAGATCTTCAACCTAATTGTCTCTG 60.414 40.741 4.57 0.00 39.54 3.35
1638 5798 6.112058 AGATCTTCAACCTAATTGTCTCTGC 58.888 40.000 0.00 0.00 39.54 4.26
1639 5799 4.579869 TCTTCAACCTAATTGTCTCTGCC 58.420 43.478 0.00 0.00 39.54 4.85
1640 5800 3.350219 TCAACCTAATTGTCTCTGCCC 57.650 47.619 0.00 0.00 39.54 5.36
1641 5801 2.642311 TCAACCTAATTGTCTCTGCCCA 59.358 45.455 0.00 0.00 39.54 5.36
1642 5802 3.266772 TCAACCTAATTGTCTCTGCCCAT 59.733 43.478 0.00 0.00 39.54 4.00
1643 5803 3.567478 ACCTAATTGTCTCTGCCCATC 57.433 47.619 0.00 0.00 0.00 3.51
1644 5804 2.158900 ACCTAATTGTCTCTGCCCATCG 60.159 50.000 0.00 0.00 0.00 3.84
1645 5805 2.158900 CCTAATTGTCTCTGCCCATCGT 60.159 50.000 0.00 0.00 0.00 3.73
1646 5806 2.029838 AATTGTCTCTGCCCATCGTC 57.970 50.000 0.00 0.00 0.00 4.20
1647 5807 0.179100 ATTGTCTCTGCCCATCGTCG 60.179 55.000 0.00 0.00 0.00 5.12
1648 5808 1.248101 TTGTCTCTGCCCATCGTCGA 61.248 55.000 0.00 0.00 0.00 4.20
1649 5809 1.037579 TGTCTCTGCCCATCGTCGAT 61.038 55.000 0.75 0.75 0.00 3.59
1650 5810 0.318275 GTCTCTGCCCATCGTCGATC 60.318 60.000 4.34 0.00 0.00 3.69
1651 5811 1.006805 CTCTGCCCATCGTCGATCC 60.007 63.158 4.34 0.00 0.00 3.36
1652 5812 2.029666 CTGCCCATCGTCGATCCC 59.970 66.667 4.34 0.00 0.00 3.85
1653 5813 3.521529 CTGCCCATCGTCGATCCCC 62.522 68.421 4.34 0.00 0.00 4.81
1654 5814 4.664677 GCCCATCGTCGATCCCCG 62.665 72.222 4.34 0.00 40.25 5.73
1655 5815 4.664677 CCCATCGTCGATCCCCGC 62.665 72.222 4.34 0.00 38.37 6.13
1656 5816 3.606662 CCATCGTCGATCCCCGCT 61.607 66.667 4.34 0.00 38.37 5.52
1657 5817 2.355126 CATCGTCGATCCCCGCTG 60.355 66.667 4.34 0.00 38.37 5.18
1658 5818 4.286320 ATCGTCGATCCCCGCTGC 62.286 66.667 0.75 0.00 38.37 5.25
1664 5824 4.195334 GATCCCCGCTGCCACCAT 62.195 66.667 0.00 0.00 0.00 3.55
1665 5825 2.772191 ATCCCCGCTGCCACCATA 60.772 61.111 0.00 0.00 0.00 2.74
1666 5826 2.738213 GATCCCCGCTGCCACCATAG 62.738 65.000 0.00 0.00 0.00 2.23
1668 5828 4.488136 CCCGCTGCCACCATAGCA 62.488 66.667 0.00 0.00 39.87 3.49
1669 5829 3.204827 CCGCTGCCACCATAGCAC 61.205 66.667 0.00 0.00 39.87 4.40
1670 5830 3.566853 CGCTGCCACCATAGCACG 61.567 66.667 0.00 0.00 39.87 5.34
1671 5831 3.204827 GCTGCCACCATAGCACGG 61.205 66.667 0.00 0.00 39.67 4.94
1672 5832 3.204827 CTGCCACCATAGCACGGC 61.205 66.667 0.00 0.00 45.11 5.68
1673 5833 4.794648 TGCCACCATAGCACGGCC 62.795 66.667 0.00 0.00 44.22 6.13
1676 5836 4.155733 CACCATAGCACGGCCGGA 62.156 66.667 31.76 12.19 0.00 5.14
1677 5837 3.395702 ACCATAGCACGGCCGGAA 61.396 61.111 31.76 11.97 0.00 4.30
1678 5838 2.124901 CCATAGCACGGCCGGAAA 60.125 61.111 31.76 12.37 0.00 3.13
1679 5839 1.747367 CCATAGCACGGCCGGAAAA 60.747 57.895 31.76 12.78 0.00 2.29
1680 5840 1.309499 CCATAGCACGGCCGGAAAAA 61.309 55.000 31.76 11.17 0.00 1.94
1681 5841 0.098728 CATAGCACGGCCGGAAAAAG 59.901 55.000 31.76 11.37 0.00 2.27
1682 5842 0.035820 ATAGCACGGCCGGAAAAAGA 60.036 50.000 31.76 7.98 0.00 2.52
1683 5843 0.952010 TAGCACGGCCGGAAAAAGAC 60.952 55.000 31.76 8.92 0.00 3.01
1684 5844 2.258726 GCACGGCCGGAAAAAGACT 61.259 57.895 31.76 0.57 0.00 3.24
1685 5845 1.866925 CACGGCCGGAAAAAGACTC 59.133 57.895 31.76 0.00 0.00 3.36
1686 5846 1.666872 ACGGCCGGAAAAAGACTCG 60.667 57.895 31.76 0.00 0.00 4.18
1687 5847 1.373748 CGGCCGGAAAAAGACTCGA 60.374 57.895 20.10 0.00 0.00 4.04
1688 5848 1.352156 CGGCCGGAAAAAGACTCGAG 61.352 60.000 20.10 11.84 0.00 4.04
1689 5849 1.636570 GGCCGGAAAAAGACTCGAGC 61.637 60.000 13.61 5.49 0.00 5.03
1690 5850 0.949105 GCCGGAAAAAGACTCGAGCA 60.949 55.000 13.61 0.00 0.00 4.26
1691 5851 1.071605 CCGGAAAAAGACTCGAGCAG 58.928 55.000 13.61 0.00 0.00 4.24
1692 5852 0.440371 CGGAAAAAGACTCGAGCAGC 59.560 55.000 13.61 2.04 0.00 5.25
1693 5853 0.799393 GGAAAAAGACTCGAGCAGCC 59.201 55.000 13.61 0.80 0.00 4.85
1694 5854 1.609320 GGAAAAAGACTCGAGCAGCCT 60.609 52.381 13.61 1.71 0.00 4.58
1695 5855 2.147150 GAAAAAGACTCGAGCAGCCTT 58.853 47.619 13.61 8.15 0.00 4.35
1696 5856 1.802069 AAAAGACTCGAGCAGCCTTC 58.198 50.000 13.61 0.81 0.00 3.46
1697 5857 0.681733 AAAGACTCGAGCAGCCTTCA 59.318 50.000 13.61 0.00 0.00 3.02
1698 5858 0.037790 AAGACTCGAGCAGCCTTCAC 60.038 55.000 13.61 0.00 0.00 3.18
1699 5859 1.181741 AGACTCGAGCAGCCTTCACA 61.182 55.000 13.61 0.00 0.00 3.58
1700 5860 0.108424 GACTCGAGCAGCCTTCACAT 60.108 55.000 13.61 0.00 0.00 3.21
1701 5861 0.108424 ACTCGAGCAGCCTTCACATC 60.108 55.000 13.61 0.00 0.00 3.06
1702 5862 0.809241 CTCGAGCAGCCTTCACATCC 60.809 60.000 0.00 0.00 0.00 3.51
1703 5863 1.078918 CGAGCAGCCTTCACATCCA 60.079 57.895 0.00 0.00 0.00 3.41
1751 5911 2.993008 GGCCTCTGCATCTGGACA 59.007 61.111 0.00 0.00 40.13 4.02
1764 5924 0.930310 CTGGACAATGCATACGACCG 59.070 55.000 0.00 0.00 0.00 4.79
1818 5978 9.477484 ACAAAGTGATACAACAGTAAGACTAAG 57.523 33.333 0.00 0.00 0.00 2.18
1819 5979 9.477484 CAAAGTGATACAACAGTAAGACTAAGT 57.523 33.333 0.00 0.00 0.00 2.24
1914 6075 0.250467 ACAGACATCGCAGCCAAACT 60.250 50.000 0.00 0.00 0.00 2.66
1923 6084 3.896122 TCGCAGCCAAACTTAAACATTC 58.104 40.909 0.00 0.00 0.00 2.67
1986 6147 3.989698 CTACCAGTCCGGCGCACTG 62.990 68.421 23.56 23.56 40.96 3.66
2067 6230 0.532862 GTGTGTACTGCTGCACCACT 60.533 55.000 17.75 0.00 34.94 4.00
2081 6244 0.834687 ACCACTTTGTCCGGCCTCTA 60.835 55.000 0.00 0.00 0.00 2.43
2099 6262 2.038814 TATGCCATCGACGCCACCAT 62.039 55.000 4.01 0.00 0.00 3.55
2113 6276 1.674359 CACCATGGCGCCTAATAACA 58.326 50.000 29.70 5.17 0.00 2.41
2149 6312 1.609210 TCCCTCGCCACACATCAGA 60.609 57.895 0.00 0.00 0.00 3.27
2229 6392 1.476488 GCACCGCTCCACCAATTATTT 59.524 47.619 0.00 0.00 0.00 1.40
2262 6425 1.874345 CTCGAGCCCGTGTACACCTT 61.874 60.000 20.11 3.32 37.05 3.50
2279 6442 1.466167 CCTTCAAGAATGACGCCACAG 59.534 52.381 0.00 0.00 34.61 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.543735 AGCCACTATAAAAGAAGGACAAACT 58.456 36.000 0.00 0.00 0.00 2.66
172 2990 8.768955 GCACCAACATAAATTGACATAAAAACA 58.231 29.630 0.00 0.00 0.00 2.83
201 3020 9.897744 CATGTTTGTAAACTAAATGTGTCATCT 57.102 29.630 8.74 0.00 39.59 2.90
223 3047 4.669206 TTTTGCCAGAACATTGTCATGT 57.331 36.364 0.00 0.00 46.34 3.21
246 3070 3.570975 GGTAAATTCGTCCCAGTTTGGTT 59.429 43.478 0.00 0.00 35.17 3.67
247 3071 3.151554 GGTAAATTCGTCCCAGTTTGGT 58.848 45.455 0.00 0.00 35.17 3.67
248 3072 3.150767 TGGTAAATTCGTCCCAGTTTGG 58.849 45.455 0.00 0.00 37.25 3.28
249 3073 4.732784 CATGGTAAATTCGTCCCAGTTTG 58.267 43.478 0.00 0.00 0.00 2.93
258 3082 3.080300 TGGGAAGCATGGTAAATTCGT 57.920 42.857 0.00 0.00 0.00 3.85
289 3113 6.071672 TGACAATTTATTTTTGCCGAGGATGA 60.072 34.615 0.00 0.00 0.00 2.92
303 3127 8.789881 TCGAACGTTTTTCATGACAATTTATT 57.210 26.923 0.46 0.00 0.00 1.40
316 3140 7.492614 AATCATAGCAAATCGAACGTTTTTC 57.507 32.000 0.46 0.00 0.00 2.29
364 3188 9.965902 ATTTTAGGACTCAACTACAAATCTGAT 57.034 29.630 0.00 0.00 0.00 2.90
627 4633 1.867363 ACTACTAGTGGGGCTTGAGG 58.133 55.000 11.30 0.00 0.00 3.86
644 4650 2.356313 CGCACTCGGCTGTGAACT 60.356 61.111 10.86 0.00 41.67 3.01
942 5049 2.821366 TACGGGGAGCTCGTCGTC 60.821 66.667 27.84 7.23 41.38 4.20
944 5051 4.253257 GCTACGGGGAGCTCGTCG 62.253 72.222 20.70 20.70 41.38 5.12
945 5052 3.902086 GGCTACGGGGAGCTCGTC 61.902 72.222 7.83 2.20 42.43 4.20
946 5053 4.753662 TGGCTACGGGGAGCTCGT 62.754 66.667 7.83 5.86 42.43 4.18
948 5055 2.760385 AGTGGCTACGGGGAGCTC 60.760 66.667 4.71 4.71 42.43 4.09
955 5064 1.258445 ACAAGGAGGAGTGGCTACGG 61.258 60.000 0.00 0.00 0.00 4.02
963 5072 2.943978 CGCCGGAACAAGGAGGAGT 61.944 63.158 5.05 0.00 0.00 3.85
992 5106 2.120232 CGTACTTGGACATCTCGATGC 58.880 52.381 6.81 0.79 42.39 3.91
1296 5447 1.289066 CTCGTTGTTCGGAGCCTCA 59.711 57.895 0.00 0.00 40.32 3.86
1343 5500 5.756195 TGGCCTCAAAAATATTCTCATCG 57.244 39.130 3.32 0.00 0.00 3.84
1382 5539 9.912634 CACAAACTAATTAAAGAATGGTGTCAT 57.087 29.630 0.00 0.00 34.56 3.06
1383 5540 8.908903 ACACAAACTAATTAAAGAATGGTGTCA 58.091 29.630 0.00 0.00 0.00 3.58
1475 5634 2.469147 CGAGATTCATCATTGTCGTCCG 59.531 50.000 0.00 0.00 0.00 4.79
1498 5657 0.324943 CCTCTCAAGGGAAAAGCGGA 59.675 55.000 0.00 0.00 39.21 5.54
1500 5659 2.185004 TTCCTCTCAAGGGAAAAGCG 57.815 50.000 0.00 0.00 43.56 4.68
1502 5661 4.916183 AGTGATTCCTCTCAAGGGAAAAG 58.084 43.478 0.00 0.00 44.64 2.27
1512 5671 2.541556 GGCGTTGTAGTGATTCCTCTC 58.458 52.381 0.00 0.00 0.00 3.20
1524 5683 2.679837 TGTTTGTTTAACGGGCGTTGTA 59.320 40.909 0.00 0.00 39.72 2.41
1526 5686 2.190325 TGTTTGTTTAACGGGCGTTG 57.810 45.000 0.00 0.00 39.72 4.10
1529 5689 4.780546 AAATTTGTTTGTTTAACGGGCG 57.219 36.364 0.00 0.00 39.72 6.13
1579 5739 1.273327 GTACTCCCTCGGTCCGAAAAA 59.727 52.381 16.23 2.29 34.74 1.94
1580 5740 0.890683 GTACTCCCTCGGTCCGAAAA 59.109 55.000 16.23 2.66 34.74 2.29
1581 5741 1.308069 CGTACTCCCTCGGTCCGAAA 61.308 60.000 16.23 3.03 34.74 3.46
1582 5742 1.746615 CGTACTCCCTCGGTCCGAA 60.747 63.158 16.23 0.00 34.74 4.30
1583 5743 2.124983 CGTACTCCCTCGGTCCGA 60.125 66.667 14.54 14.54 0.00 4.55
1584 5744 2.124983 TCGTACTCCCTCGGTCCG 60.125 66.667 4.39 4.39 0.00 4.79
1585 5745 1.823041 CCTCGTACTCCCTCGGTCC 60.823 68.421 0.00 0.00 0.00 4.46
1586 5746 1.077858 ACCTCGTACTCCCTCGGTC 60.078 63.158 0.00 0.00 0.00 4.79
1587 5747 1.077858 GACCTCGTACTCCCTCGGT 60.078 63.158 0.00 0.00 0.00 4.69
1588 5748 2.178890 CGACCTCGTACTCCCTCGG 61.179 68.421 0.00 0.00 34.11 4.63
1589 5749 0.742281 TTCGACCTCGTACTCCCTCG 60.742 60.000 0.00 0.00 40.80 4.63
1590 5750 1.015868 CTTCGACCTCGTACTCCCTC 58.984 60.000 0.00 0.00 40.80 4.30
1591 5751 0.394080 CCTTCGACCTCGTACTCCCT 60.394 60.000 0.00 0.00 40.80 4.20
1592 5752 1.382692 CCCTTCGACCTCGTACTCCC 61.383 65.000 0.00 0.00 40.80 4.30
1593 5753 2.002509 GCCCTTCGACCTCGTACTCC 62.003 65.000 0.00 0.00 40.80 3.85
1594 5754 1.310933 TGCCCTTCGACCTCGTACTC 61.311 60.000 0.00 0.00 40.80 2.59
1595 5755 0.896940 TTGCCCTTCGACCTCGTACT 60.897 55.000 0.00 0.00 40.80 2.73
1596 5756 0.458025 CTTGCCCTTCGACCTCGTAC 60.458 60.000 0.00 0.00 40.80 3.67
1597 5757 0.609957 TCTTGCCCTTCGACCTCGTA 60.610 55.000 0.00 0.00 40.80 3.43
1598 5758 1.258445 ATCTTGCCCTTCGACCTCGT 61.258 55.000 0.00 0.00 40.80 4.18
1599 5759 0.528684 GATCTTGCCCTTCGACCTCG 60.529 60.000 0.00 0.00 41.45 4.63
1600 5760 0.827368 AGATCTTGCCCTTCGACCTC 59.173 55.000 0.00 0.00 0.00 3.85
1601 5761 1.208293 GAAGATCTTGCCCTTCGACCT 59.792 52.381 14.00 0.00 30.88 3.85
1602 5762 1.066143 TGAAGATCTTGCCCTTCGACC 60.066 52.381 14.00 0.00 41.10 4.79
1603 5763 2.386661 TGAAGATCTTGCCCTTCGAC 57.613 50.000 14.00 0.00 41.10 4.20
1604 5764 2.615493 GGTTGAAGATCTTGCCCTTCGA 60.615 50.000 14.00 0.00 41.10 3.71
1605 5765 1.740025 GGTTGAAGATCTTGCCCTTCG 59.260 52.381 14.00 0.00 41.10 3.79
1606 5766 3.078891 AGGTTGAAGATCTTGCCCTTC 57.921 47.619 14.00 0.00 39.26 3.46
1607 5767 4.657814 TTAGGTTGAAGATCTTGCCCTT 57.342 40.909 14.00 0.00 0.00 3.95
1608 5768 4.870021 ATTAGGTTGAAGATCTTGCCCT 57.130 40.909 14.00 15.95 0.00 5.19
1609 5769 4.706962 ACAATTAGGTTGAAGATCTTGCCC 59.293 41.667 14.00 9.43 40.37 5.36
1610 5770 5.649831 AGACAATTAGGTTGAAGATCTTGCC 59.350 40.000 14.00 11.92 40.37 4.52
1611 5771 6.597280 AGAGACAATTAGGTTGAAGATCTTGC 59.403 38.462 14.00 5.38 40.37 4.01
1612 5772 7.413877 GCAGAGACAATTAGGTTGAAGATCTTG 60.414 40.741 14.00 0.00 40.37 3.02
1613 5773 6.597280 GCAGAGACAATTAGGTTGAAGATCTT 59.403 38.462 7.95 7.95 40.37 2.40
1614 5774 6.112058 GCAGAGACAATTAGGTTGAAGATCT 58.888 40.000 0.00 0.00 40.37 2.75
1615 5775 5.295540 GGCAGAGACAATTAGGTTGAAGATC 59.704 44.000 0.00 0.00 40.37 2.75
1616 5776 5.189180 GGCAGAGACAATTAGGTTGAAGAT 58.811 41.667 0.00 0.00 40.37 2.40
1617 5777 4.565652 GGGCAGAGACAATTAGGTTGAAGA 60.566 45.833 0.00 0.00 40.37 2.87
1618 5778 3.691609 GGGCAGAGACAATTAGGTTGAAG 59.308 47.826 0.00 0.00 40.37 3.02
1619 5779 3.073798 TGGGCAGAGACAATTAGGTTGAA 59.926 43.478 0.00 0.00 40.37 2.69
1620 5780 2.642311 TGGGCAGAGACAATTAGGTTGA 59.358 45.455 0.00 0.00 40.37 3.18
1621 5781 3.071874 TGGGCAGAGACAATTAGGTTG 57.928 47.619 0.00 0.00 43.64 3.77
1622 5782 3.682718 CGATGGGCAGAGACAATTAGGTT 60.683 47.826 0.00 0.00 0.00 3.50
1623 5783 2.158900 CGATGGGCAGAGACAATTAGGT 60.159 50.000 0.00 0.00 0.00 3.08
1624 5784 2.158900 ACGATGGGCAGAGACAATTAGG 60.159 50.000 0.00 0.00 0.00 2.69
1625 5785 3.126831 GACGATGGGCAGAGACAATTAG 58.873 50.000 0.00 0.00 0.00 1.73
1626 5786 2.481276 CGACGATGGGCAGAGACAATTA 60.481 50.000 0.00 0.00 0.00 1.40
1627 5787 1.740380 CGACGATGGGCAGAGACAATT 60.740 52.381 0.00 0.00 0.00 2.32
1628 5788 0.179100 CGACGATGGGCAGAGACAAT 60.179 55.000 0.00 0.00 0.00 2.71
1629 5789 1.215382 CGACGATGGGCAGAGACAA 59.785 57.895 0.00 0.00 0.00 3.18
1630 5790 1.037579 ATCGACGATGGGCAGAGACA 61.038 55.000 10.09 0.00 0.00 3.41
1631 5791 0.318275 GATCGACGATGGGCAGAGAC 60.318 60.000 16.49 0.00 0.00 3.36
1632 5792 1.456196 GGATCGACGATGGGCAGAGA 61.456 60.000 16.49 0.00 0.00 3.10
1633 5793 1.006805 GGATCGACGATGGGCAGAG 60.007 63.158 16.49 0.00 0.00 3.35
1634 5794 2.498941 GGGATCGACGATGGGCAGA 61.499 63.158 16.49 0.00 0.00 4.26
1635 5795 2.029666 GGGATCGACGATGGGCAG 59.970 66.667 16.49 0.00 0.00 4.85
1636 5796 3.546543 GGGGATCGACGATGGGCA 61.547 66.667 16.49 0.00 0.00 5.36
1637 5797 4.664677 CGGGGATCGACGATGGGC 62.665 72.222 16.49 0.31 42.43 5.36
1638 5798 4.664677 GCGGGGATCGACGATGGG 62.665 72.222 16.49 2.56 42.43 4.00
1639 5799 3.606662 AGCGGGGATCGACGATGG 61.607 66.667 16.49 2.92 42.43 3.51
1640 5800 2.355126 CAGCGGGGATCGACGATG 60.355 66.667 16.49 10.68 42.43 3.84
1641 5801 4.286320 GCAGCGGGGATCGACGAT 62.286 66.667 10.78 10.78 42.43 3.73
1647 5807 2.738213 CTATGGTGGCAGCGGGGATC 62.738 65.000 12.58 0.00 0.00 3.36
1648 5808 2.772191 TATGGTGGCAGCGGGGAT 60.772 61.111 12.58 2.32 0.00 3.85
1649 5809 3.479203 CTATGGTGGCAGCGGGGA 61.479 66.667 12.58 0.00 0.00 4.81
1651 5811 4.488136 TGCTATGGTGGCAGCGGG 62.488 66.667 12.58 5.67 40.79 6.13
1652 5812 3.204827 GTGCTATGGTGGCAGCGG 61.205 66.667 12.58 6.02 40.79 5.52
1653 5813 3.566853 CGTGCTATGGTGGCAGCG 61.567 66.667 12.58 0.00 40.79 5.18
1654 5814 3.204827 CCGTGCTATGGTGGCAGC 61.205 66.667 10.30 10.30 40.54 5.25
1655 5815 3.204827 GCCGTGCTATGGTGGCAG 61.205 66.667 0.00 0.00 46.76 4.85
1659 5819 3.673956 TTCCGGCCGTGCTATGGTG 62.674 63.158 26.12 5.01 0.00 4.17
1660 5820 2.472414 TTTTCCGGCCGTGCTATGGT 62.472 55.000 26.12 0.00 0.00 3.55
1661 5821 1.309499 TTTTTCCGGCCGTGCTATGG 61.309 55.000 26.12 6.69 0.00 2.74
1662 5822 0.098728 CTTTTTCCGGCCGTGCTATG 59.901 55.000 26.12 7.54 0.00 2.23
1663 5823 0.035820 TCTTTTTCCGGCCGTGCTAT 60.036 50.000 26.12 0.00 0.00 2.97
1664 5824 0.952010 GTCTTTTTCCGGCCGTGCTA 60.952 55.000 26.12 3.18 0.00 3.49
1665 5825 2.112297 TCTTTTTCCGGCCGTGCT 59.888 55.556 26.12 0.00 0.00 4.40
1666 5826 2.183858 GAGTCTTTTTCCGGCCGTGC 62.184 60.000 26.12 4.48 0.00 5.34
1667 5827 1.866925 GAGTCTTTTTCCGGCCGTG 59.133 57.895 26.12 15.93 0.00 4.94
1668 5828 1.666872 CGAGTCTTTTTCCGGCCGT 60.667 57.895 26.12 0.43 0.00 5.68
1669 5829 1.352156 CTCGAGTCTTTTTCCGGCCG 61.352 60.000 21.04 21.04 0.00 6.13
1670 5830 1.636570 GCTCGAGTCTTTTTCCGGCC 61.637 60.000 15.13 0.00 0.00 6.13
1671 5831 0.949105 TGCTCGAGTCTTTTTCCGGC 60.949 55.000 15.13 0.00 0.00 6.13
1672 5832 1.071605 CTGCTCGAGTCTTTTTCCGG 58.928 55.000 15.13 0.00 0.00 5.14
1673 5833 0.440371 GCTGCTCGAGTCTTTTTCCG 59.560 55.000 15.13 0.00 0.00 4.30
1674 5834 0.799393 GGCTGCTCGAGTCTTTTTCC 59.201 55.000 15.13 2.61 0.00 3.13
1675 5835 1.802069 AGGCTGCTCGAGTCTTTTTC 58.198 50.000 15.13 0.00 29.69 2.29
1676 5836 2.262423 AAGGCTGCTCGAGTCTTTTT 57.738 45.000 15.13 1.21 44.74 1.94
1680 5840 1.181741 TGTGAAGGCTGCTCGAGTCT 61.182 55.000 15.13 4.23 38.77 3.24
1681 5841 0.108424 ATGTGAAGGCTGCTCGAGTC 60.108 55.000 15.13 7.10 0.00 3.36
1682 5842 0.108424 GATGTGAAGGCTGCTCGAGT 60.108 55.000 15.13 0.00 0.00 4.18
1683 5843 0.809241 GGATGTGAAGGCTGCTCGAG 60.809 60.000 8.45 8.45 0.00 4.04
1684 5844 1.219124 GGATGTGAAGGCTGCTCGA 59.781 57.895 0.00 0.00 0.00 4.04
1685 5845 0.463295 ATGGATGTGAAGGCTGCTCG 60.463 55.000 0.00 0.00 0.00 5.03
1686 5846 2.627515 TATGGATGTGAAGGCTGCTC 57.372 50.000 0.00 0.00 0.00 4.26
1687 5847 3.589951 AATATGGATGTGAAGGCTGCT 57.410 42.857 0.00 0.00 0.00 4.24
1688 5848 4.660789 AAAATATGGATGTGAAGGCTGC 57.339 40.909 0.00 0.00 0.00 5.25
1751 5911 5.994887 TTAATAAAGCGGTCGTATGCATT 57.005 34.783 3.54 0.00 0.00 3.56
1818 5978 2.157668 CAGTTGTTGCATAGACGGTGAC 59.842 50.000 0.00 0.00 0.00 3.67
1819 5979 2.224185 ACAGTTGTTGCATAGACGGTGA 60.224 45.455 0.00 0.00 0.00 4.02
1986 6147 1.448013 GTAGGCGTCCTGGTTGAGC 60.448 63.158 8.44 0.00 34.61 4.26
2031 6192 3.072915 ACACACTGAAGATGGATTGGTGA 59.927 43.478 0.00 0.00 0.00 4.02
2067 6230 1.223487 GGCATAGAGGCCGGACAAA 59.777 57.895 11.69 0.00 45.40 2.83
2081 6244 3.405093 ATGGTGGCGTCGATGGCAT 62.405 57.895 33.02 17.44 46.76 4.40
2099 6262 2.775351 GTGCTGTTATTAGGCGCCA 58.225 52.632 31.54 9.64 0.00 5.69
2107 6270 0.392998 CGCAGGAGGGTGCTGTTATT 60.393 55.000 0.00 0.00 41.62 1.40
2149 6312 3.681835 GTGGTGGAGACTCGGCGT 61.682 66.667 6.85 0.00 0.00 5.68
2188 6351 3.797865 GCTTCATCCTGCACATTAATGGC 60.798 47.826 19.37 18.11 0.00 4.40
2229 6392 1.152419 TCGAGGGACCAGTGGACAA 60.152 57.895 18.40 0.00 0.00 3.18
2262 6425 0.684535 TCCTGTGGCGTCATTCTTGA 59.315 50.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.