Multiple sequence alignment - TraesCS4D01G198000

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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 TraesCS4D01G198000 chr4D 100.000 3194 0 0 837 4030 344109715 344112908 0.000000e+00 5899.0
1 TraesCS4D01G198000 chr4D 100.000 553 0 0 1 553 344108879 344109431 0.000000e+00 1022.0
2 TraesCS4D01G198000 chr4D 89.062 192 18 3 3649 3838 3847390 3847580 6.730000e-58 235.0
3 TraesCS4D01G198000 chr4D 100.000 61 0 0 2720 2780 344111549 344111609 3.290000e-21 113.0
4 TraesCS4D01G198000 chr4D 100.000 61 0 0 2671 2731 344111598 344111658 3.290000e-21 113.0
5 TraesCS4D01G198000 chr4D 97.222 36 1 0 3545 3580 344112388 344112423 1.210000e-05 62.1
6 TraesCS4D01G198000 chr4D 97.222 36 1 0 3510 3545 344112423 344112458 1.210000e-05 62.1
7 TraesCS4D01G198000 chr4A 94.150 1812 60 22 942 2721 121506215 121504418 0.000000e+00 2717.0
8 TraesCS4D01G198000 chr4A 89.062 704 33 24 2720 3404 121504468 121503790 0.000000e+00 833.0
9 TraesCS4D01G198000 chr4A 92.219 347 15 6 2 338 121507055 121506711 7.830000e-132 481.0
10 TraesCS4D01G198000 chr4A 87.466 367 38 5 3547 3909 121503611 121503249 2.240000e-112 416.0
11 TraesCS4D01G198000 chr4A 96.089 179 6 1 373 551 121506713 121506536 1.420000e-74 291.0
12 TraesCS4D01G198000 chr4A 92.727 110 7 1 3436 3545 121503686 121503578 1.500000e-34 158.0
13 TraesCS4D01G198000 chr4B 94.276 1415 40 17 837 2242 426104584 426105966 0.000000e+00 2126.0
14 TraesCS4D01G198000 chr4B 91.987 1198 43 27 2234 3394 426108410 426109591 0.000000e+00 1631.0
15 TraesCS4D01G198000 chr4B 95.039 383 18 1 150 531 426104072 426104454 5.760000e-168 601.0
16 TraesCS4D01G198000 chr4B 92.045 176 13 1 3853 4028 426109963 426110137 3.110000e-61 246.0
17 TraesCS4D01G198000 chr4B 95.588 68 3 0 2720 2787 426108855 426108922 4.260000e-20 110.0
18 TraesCS4D01G198000 chr3D 90.000 260 22 2 3594 3851 336825920 336826177 2.320000e-87 333.0
19 TraesCS4D01G198000 chr3D 89.831 177 16 1 3594 3768 383591468 383591644 4.050000e-55 226.0
20 TraesCS4D01G198000 chr3D 84.516 155 21 3 1039 1191 496733042 496733195 2.510000e-32 150.0
21 TraesCS4D01G198000 chr2A 91.358 243 21 0 3602 3844 32775341 32775099 2.320000e-87 333.0
22 TraesCS4D01G198000 chr2A 89.641 251 25 1 3602 3852 81461832 81461583 6.500000e-83 318.0
23 TraesCS4D01G198000 chr2A 83.333 66 10 1 3922 3987 14279838 14279774 4.350000e-05 60.2
24 TraesCS4D01G198000 chr7A 90.157 254 23 1 3594 3845 701288247 701288500 3.000000e-86 329.0
25 TraesCS4D01G198000 chr7A 90.123 243 24 0 3602 3844 445605545 445605787 2.340000e-82 316.0
26 TraesCS4D01G198000 chr7A 83.951 162 26 0 1042 1203 133058859 133058698 5.390000e-34 156.0
27 TraesCS4D01G198000 chr3A 88.845 251 24 4 3602 3851 678509178 678508931 5.060000e-79 305.0
28 TraesCS4D01G198000 chr3A 84.756 164 22 3 1039 1200 638074547 638074385 1.160000e-35 161.0
29 TraesCS4D01G198000 chr7D 84.568 162 25 0 1042 1203 134178575 134178414 1.160000e-35 161.0
30 TraesCS4D01G198000 chr7B 84.568 162 25 0 1042 1203 96281871 96281710 1.160000e-35 161.0
31 TraesCS4D01G198000 chr2B 89.908 109 11 0 3736 3844 784978357 784978249 1.510000e-29 141.0
32 TraesCS4D01G198000 chr2B 84.848 66 9 1 3922 3987 21539492 21539556 9.350000e-07 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G198000 chr4D 344108879 344112908 4029 False 1211.866667 5899 99.074000 1 4030 6 chr4D.!!$F2 4029
1 TraesCS4D01G198000 chr4A 121503249 121507055 3806 True 816.000000 2717 91.952167 2 3909 6 chr4A.!!$R1 3907
2 TraesCS4D01G198000 chr4B 426104072 426110137 6065 False 942.800000 2126 93.787000 150 4028 5 chr4B.!!$F1 3878

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
108 115 0.108424 AGACAGTGCAAGAGGATCGC 60.108 55.000 0.00 0.0 42.67 4.58 F
551 563 1.408702 GTGAGTGGCATCTCTCTCTCC 59.591 57.143 14.98 0.0 35.28 3.71 F
1293 1311 1.070786 GGTGACGTTCAAGGAGGCA 59.929 57.895 0.00 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1211 1227 1.351080 ATGGCAGTGGAGGGAGATGG 61.351 60.0 0.0 0.0 0.0 3.51 R
2404 4907 0.662619 CGGAAGCAGCAAAGTGACAA 59.337 50.0 0.0 0.0 0.0 3.18 R
3276 5874 0.248661 CAGCGATGGGACTACAGACG 60.249 60.0 0.0 0.0 0.0 4.18 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
22 23 2.433970 CTGAAAAGCCACCTTTGGGAAA 59.566 45.455 0.00 0.00 44.15 3.13
26 27 0.261696 AGCCACCTTTGGGAAACACT 59.738 50.000 0.00 0.00 44.15 3.55
28 29 1.611977 GCCACCTTTGGGAAACACTAC 59.388 52.381 0.00 0.00 44.15 2.73
42 44 7.668052 TGGGAAACACTACTGTAAAAATGCTAT 59.332 33.333 0.00 0.00 0.00 2.97
108 115 0.108424 AGACAGTGCAAGAGGATCGC 60.108 55.000 0.00 0.00 42.67 4.58
141 152 1.482593 GAGCTAGCTAGTTGGCCAAGA 59.517 52.381 21.21 9.31 0.00 3.02
250 261 3.056678 TCCATCCGTTTTACTACTGCGAA 60.057 43.478 0.00 0.00 0.00 4.70
307 318 9.484806 AATGAATCCTCAGAGAATACCAAAAAT 57.515 29.630 0.00 0.00 34.23 1.82
315 326 6.881065 TCAGAGAATACCAAAAATGAGACTGG 59.119 38.462 0.00 0.00 34.95 4.00
389 401 3.119137 GGCCAGTTCATTCCCACATAAAC 60.119 47.826 0.00 0.00 0.00 2.01
455 467 2.614057 CAACCTTCATCGCCCTCAATAC 59.386 50.000 0.00 0.00 0.00 1.89
551 563 1.408702 GTGAGTGGCATCTCTCTCTCC 59.591 57.143 14.98 0.00 35.28 3.71
915 931 1.820906 GCATCGCCATTCAGCTCCA 60.821 57.895 0.00 0.00 0.00 3.86
1009 1025 4.856801 GGCCGGCCATGACGATGT 62.857 66.667 40.73 0.00 35.20 3.06
1208 1224 4.452733 CGGCTTCGTCAGTCCCCC 62.453 72.222 0.00 0.00 0.00 5.40
1224 1241 1.768077 CCCCTCCATCTCCCTCCAC 60.768 68.421 0.00 0.00 0.00 4.02
1293 1311 1.070786 GGTGACGTTCAAGGAGGCA 59.929 57.895 0.00 0.00 0.00 4.75
1365 1383 2.980233 GCCAACTGCAACCTCGCT 60.980 61.111 0.00 0.00 40.77 4.93
1712 1734 2.357034 CAGCAGTACCACGGCGTT 60.357 61.111 11.19 0.00 44.04 4.84
1770 1792 2.105128 GCACGTCGCATCCTAGCT 59.895 61.111 0.00 0.00 41.79 3.32
1782 1807 2.188994 CTAGCTGCACCTCCTGCC 59.811 66.667 1.02 0.00 46.51 4.85
1787 1812 3.947132 CTGCACCTCCTGCCTCACG 62.947 68.421 0.00 0.00 46.51 4.35
1788 1813 4.008933 GCACCTCCTGCCTCACGT 62.009 66.667 0.00 0.00 40.42 4.49
1789 1814 2.646175 GCACCTCCTGCCTCACGTA 61.646 63.158 0.00 0.00 40.42 3.57
1859 1884 3.775065 TCGCGAGAGTTCTCTGTTG 57.225 52.632 3.71 0.00 40.75 3.33
2182 2228 8.857694 AAAAGAAAACTAATTACCCGATCTGA 57.142 30.769 0.00 0.00 0.00 3.27
2208 2254 4.469657 TCCTTGTCCTGTTTTTACAGCAT 58.530 39.130 0.00 0.00 36.46 3.79
2209 2255 4.518970 TCCTTGTCCTGTTTTTACAGCATC 59.481 41.667 0.00 0.00 36.46 3.91
2210 2256 4.278170 CCTTGTCCTGTTTTTACAGCATCA 59.722 41.667 0.00 0.00 36.46 3.07
2211 2257 5.221224 CCTTGTCCTGTTTTTACAGCATCAA 60.221 40.000 0.00 0.00 36.46 2.57
2277 4773 3.551454 CCACTGATTTGTCTGCTTTGTGG 60.551 47.826 0.00 0.00 36.85 4.17
2698 5210 2.361610 CCCACAGTCATGGTGCCC 60.362 66.667 0.00 0.00 38.16 5.36
2718 5230 1.967779 CCCCAAAGGTAACCAACTTGG 59.032 52.381 6.24 6.24 45.02 3.61
2730 5242 3.565905 CCAACTTGGTCATCTCAAAGC 57.434 47.619 0.00 0.00 31.35 3.51
2731 5243 2.229784 CCAACTTGGTCATCTCAAAGCC 59.770 50.000 0.00 0.00 31.35 4.35
2732 5244 2.206576 ACTTGGTCATCTCAAAGCCC 57.793 50.000 0.00 0.00 0.00 5.19
2733 5245 1.425066 ACTTGGTCATCTCAAAGCCCA 59.575 47.619 0.00 0.00 0.00 5.36
2734 5246 1.815003 CTTGGTCATCTCAAAGCCCAC 59.185 52.381 0.00 0.00 0.00 4.61
2735 5247 0.770499 TGGTCATCTCAAAGCCCACA 59.230 50.000 0.00 0.00 0.00 4.17
2736 5248 1.271543 TGGTCATCTCAAAGCCCACAG 60.272 52.381 0.00 0.00 0.00 3.66
2737 5249 1.271597 GGTCATCTCAAAGCCCACAGT 60.272 52.381 0.00 0.00 0.00 3.55
2738 5250 2.079925 GTCATCTCAAAGCCCACAGTC 58.920 52.381 0.00 0.00 0.00 3.51
2739 5251 1.699083 TCATCTCAAAGCCCACAGTCA 59.301 47.619 0.00 0.00 0.00 3.41
2740 5252 2.306805 TCATCTCAAAGCCCACAGTCAT 59.693 45.455 0.00 0.00 0.00 3.06
2741 5253 2.189594 TCTCAAAGCCCACAGTCATG 57.810 50.000 0.00 0.00 0.00 3.07
2742 5254 1.171308 CTCAAAGCCCACAGTCATGG 58.829 55.000 0.00 0.00 39.71 3.66
2743 5255 0.478072 TCAAAGCCCACAGTCATGGT 59.522 50.000 0.00 0.00 38.16 3.55
2744 5256 0.599558 CAAAGCCCACAGTCATGGTG 59.400 55.000 0.00 0.00 38.16 4.17
2745 5257 1.181098 AAAGCCCACAGTCATGGTGC 61.181 55.000 0.00 0.00 38.16 5.01
2746 5258 3.064324 GCCCACAGTCATGGTGCC 61.064 66.667 0.00 0.00 38.16 5.01
2747 5259 2.361610 CCCACAGTCATGGTGCCC 60.362 66.667 0.00 0.00 38.16 5.36
2748 5260 2.361610 CCACAGTCATGGTGCCCC 60.362 66.667 0.00 0.00 34.77 5.80
2749 5261 2.361610 CACAGTCATGGTGCCCCC 60.362 66.667 0.00 0.00 0.00 5.40
2765 5277 2.391926 CCCCCAAAGGTAACCAACTT 57.608 50.000 0.00 0.00 37.17 2.66
2766 5278 1.967779 CCCCCAAAGGTAACCAACTTG 59.032 52.381 0.00 0.00 37.17 3.16
2787 5299 4.194640 TGGTCATCTCAAAGCTAGATTGC 58.805 43.478 0.00 0.00 31.22 3.56
2788 5300 4.080695 TGGTCATCTCAAAGCTAGATTGCT 60.081 41.667 0.00 0.00 46.40 3.91
2789 5301 5.129320 TGGTCATCTCAAAGCTAGATTGCTA 59.871 40.000 0.00 0.00 43.24 3.49
2790 5302 5.695816 GGTCATCTCAAAGCTAGATTGCTAG 59.304 44.000 0.00 0.00 45.63 3.42
2900 5482 0.179166 ACGTGCAACACAGCTTTGTG 60.179 50.000 6.22 5.34 44.74 3.33
2909 5493 5.761003 CAACACAGCTTTGTGATTGTATGA 58.239 37.500 6.22 0.00 42.02 2.15
2910 5494 6.207928 CAACACAGCTTTGTGATTGTATGAA 58.792 36.000 6.22 0.00 42.02 2.57
2911 5495 6.389830 ACACAGCTTTGTGATTGTATGAAA 57.610 33.333 12.62 0.00 42.02 2.69
2912 5496 6.985117 ACACAGCTTTGTGATTGTATGAAAT 58.015 32.000 12.62 0.00 42.02 2.17
2913 5497 7.436118 ACACAGCTTTGTGATTGTATGAAATT 58.564 30.769 12.62 0.00 42.02 1.82
2914 5498 7.383029 ACACAGCTTTGTGATTGTATGAAATTG 59.617 33.333 12.62 0.00 42.02 2.32
2915 5499 7.383029 CACAGCTTTGTGATTGTATGAAATTGT 59.617 33.333 0.00 0.00 42.02 2.71
2916 5500 8.575589 ACAGCTTTGTGATTGTATGAAATTGTA 58.424 29.630 0.00 0.00 0.00 2.41
2917 5501 9.577110 CAGCTTTGTGATTGTATGAAATTGTAT 57.423 29.630 0.00 0.00 0.00 2.29
3215 5809 6.206634 CCCAGCAAAGTCTGTAACAAAGATTA 59.793 38.462 0.00 0.00 32.32 1.75
3216 5810 7.094205 CCCAGCAAAGTCTGTAACAAAGATTAT 60.094 37.037 0.00 0.00 32.32 1.28
3218 5812 9.334693 CAGCAAAGTCTGTAACAAAGATTATTC 57.665 33.333 0.00 0.00 0.00 1.75
3220 5814 7.481798 GCAAAGTCTGTAACAAAGATTATTCCG 59.518 37.037 0.00 0.00 0.00 4.30
3221 5815 8.504005 CAAAGTCTGTAACAAAGATTATTCCGT 58.496 33.333 0.00 0.00 0.00 4.69
3223 5817 7.612677 AGTCTGTAACAAAGATTATTCCGTCT 58.387 34.615 0.00 0.00 0.00 4.18
3224 5818 7.760340 AGTCTGTAACAAAGATTATTCCGTCTC 59.240 37.037 0.00 0.00 0.00 3.36
3225 5819 7.760340 GTCTGTAACAAAGATTATTCCGTCTCT 59.240 37.037 0.00 0.00 0.00 3.10
3226 5820 7.974501 TCTGTAACAAAGATTATTCCGTCTCTC 59.025 37.037 0.00 0.00 0.00 3.20
3227 5821 7.837863 TGTAACAAAGATTATTCCGTCTCTCT 58.162 34.615 0.00 0.00 0.00 3.10
3323 5921 3.354397 GCAGCGAACCTGAATAAAATCG 58.646 45.455 0.00 0.00 44.64 3.34
3366 5964 2.126734 GCTCGCAATGGTGTGTGC 60.127 61.111 0.00 0.00 44.61 4.57
3386 5984 0.528017 CTGAGCTCGCTGAGTTGGTA 59.472 55.000 9.64 0.00 31.39 3.25
3394 5992 4.557205 CTCGCTGAGTTGGTAAACTTAGT 58.443 43.478 10.81 0.00 46.84 2.24
3395 5993 5.706916 CTCGCTGAGTTGGTAAACTTAGTA 58.293 41.667 10.81 1.78 46.84 1.82
3399 6255 6.034683 CGCTGAGTTGGTAAACTTAGTATCAC 59.965 42.308 10.81 0.00 46.84 3.06
3400 6256 6.872020 GCTGAGTTGGTAAACTTAGTATCACA 59.128 38.462 10.81 0.00 46.84 3.58
3404 6260 8.040716 AGTTGGTAAACTTAGTATCACATTGC 57.959 34.615 0.00 0.00 44.47 3.56
3410 6266 5.584253 ACTTAGTATCACATTGCGTCTCT 57.416 39.130 0.00 0.00 0.00 3.10
3415 6271 5.583495 AGTATCACATTGCGTCTCTACTTC 58.417 41.667 0.00 0.00 0.00 3.01
3467 6364 2.627945 TGTCGGTAATGCAAGACCATC 58.372 47.619 17.82 11.17 35.26 3.51
3472 6369 5.353123 GTCGGTAATGCAAGACCATCTTAAA 59.647 40.000 17.82 0.00 33.78 1.52
3506 6403 0.093026 CGGCTCTCACGCGTAAAAAG 59.907 55.000 13.44 8.61 0.00 2.27
3508 6405 1.796459 GGCTCTCACGCGTAAAAAGAA 59.204 47.619 13.44 0.00 0.00 2.52
3509 6406 2.411160 GGCTCTCACGCGTAAAAAGAAC 60.411 50.000 13.44 8.10 0.00 3.01
3510 6407 2.717893 GCTCTCACGCGTAAAAAGAACG 60.718 50.000 13.44 3.52 43.12 3.95
3518 6415 3.444618 CGTAAAAAGAACGCAGGGTAC 57.555 47.619 0.00 0.00 33.04 3.34
3519 6416 2.158254 CGTAAAAAGAACGCAGGGTACC 59.842 50.000 2.17 2.17 40.91 3.34
3520 6417 4.352596 CGTAAAAAGAACGCAGGGTACCA 61.353 47.826 15.35 0.00 42.41 3.25
3521 6418 6.133660 CGTAAAAAGAACGCAGGGTACCAG 62.134 50.000 15.35 6.74 42.41 4.00
3539 6436 8.561738 GGTACCAGATTTCTATCACAAAGAAA 57.438 34.615 7.15 1.15 44.64 2.52
3545 6442 4.857871 TTCTATCACAAAGAAATCGGCG 57.142 40.909 0.00 0.00 30.15 6.46
3561 6458 1.230324 GGCGCAGGATACCAGATTTC 58.770 55.000 10.83 0.00 37.17 2.17
3583 6480 1.438651 TCACAAAGAAATCGGCTCCG 58.561 50.000 1.14 1.14 41.35 4.63
3597 6494 1.517832 CTCCGAAACCGGCTCTCAT 59.482 57.895 0.00 0.00 46.35 2.90
3635 6532 2.183478 TTTGGAGCGAGAGAAATGCA 57.817 45.000 0.00 0.00 0.00 3.96
3637 6534 0.737367 TGGAGCGAGAGAAATGCACG 60.737 55.000 0.00 0.00 0.00 5.34
3639 6536 3.168271 GCGAGAGAAATGCACGCA 58.832 55.556 10.30 0.00 46.75 5.24
3643 6540 1.129251 CGAGAGAAATGCACGCATGTT 59.871 47.619 5.06 2.57 36.68 2.71
3650 6547 1.378531 ATGCACGCATGTTCCGTAAT 58.621 45.000 3.17 0.00 37.12 1.89
3653 6550 1.004292 GCACGCATGTTCCGTAATACC 60.004 52.381 0.00 0.00 37.12 2.73
3654 6551 1.256895 CACGCATGTTCCGTAATACCG 59.743 52.381 0.00 0.00 37.12 4.02
3655 6552 0.231279 CGCATGTTCCGTAATACCGC 59.769 55.000 0.00 0.00 0.00 5.68
3681 6578 1.000717 CGGTAGGGGTTTTTGTTGCTG 60.001 52.381 0.00 0.00 0.00 4.41
3682 6579 1.343142 GGTAGGGGTTTTTGTTGCTGG 59.657 52.381 0.00 0.00 0.00 4.85
3693 6590 6.928492 GGTTTTTGTTGCTGGAATCAAAGATA 59.072 34.615 8.62 0.00 32.67 1.98
3701 6598 8.632679 GTTGCTGGAATCAAAGATATATCCAAA 58.367 33.333 9.18 0.00 36.59 3.28
3805 6704 8.350722 CAAAAACCTCTAACCCTTCTTCTTAAC 58.649 37.037 0.00 0.00 0.00 2.01
3807 6706 5.160386 ACCTCTAACCCTTCTTCTTAACCA 58.840 41.667 0.00 0.00 0.00 3.67
3837 6736 2.905075 GCAAGTCTTTTGCCCAGTTTT 58.095 42.857 0.54 0.00 39.38 2.43
3842 6742 6.128145 GCAAGTCTTTTGCCCAGTTTTAAAAA 60.128 34.615 1.31 0.00 39.38 1.94
3873 6773 0.601311 GAGAACGACAGTTGCTGGCT 60.601 55.000 0.25 0.00 41.34 4.75
3874 6774 0.882042 AGAACGACAGTTGCTGGCTG 60.882 55.000 0.25 0.00 41.34 4.85
3921 6821 2.819608 GGTGCTATCCACTTTTGCTCAA 59.180 45.455 0.00 0.00 44.08 3.02
3955 6855 0.027716 GATGTGCTGCATCGCTTCAG 59.972 55.000 5.27 0.00 43.75 3.02
3960 6860 2.352651 GTGCTGCATCGCTTCAGAAATA 59.647 45.455 5.27 0.00 32.26 1.40
3963 6863 3.064545 GCTGCATCGCTTCAGAAATAGTT 59.935 43.478 0.00 0.00 32.26 2.24
3967 6867 4.260538 GCATCGCTTCAGAAATAGTTCAGG 60.261 45.833 5.62 0.00 36.09 3.86
3999 6899 1.348594 GTAGCAGCGTTCAATCGGC 59.651 57.895 0.00 0.00 0.00 5.54
4007 6907 1.714794 CGTTCAATCGGCTCAACTCT 58.285 50.000 0.00 0.00 0.00 3.24
4014 6914 5.592054 TCAATCGGCTCAACTCTACTATTG 58.408 41.667 0.00 0.00 0.00 1.90
4017 6917 4.014406 TCGGCTCAACTCTACTATTGTCA 58.986 43.478 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.681175 CCCAAAGGTGGCTTTTCAGG 59.319 55.000 0.00 0.00 44.46 3.86
17 18 6.327279 AGCATTTTTACAGTAGTGTTTCCC 57.673 37.500 8.85 0.00 38.19 3.97
22 23 7.438459 GGATCGATAGCATTTTTACAGTAGTGT 59.562 37.037 8.55 8.55 41.06 3.55
26 27 7.722363 TCAGGATCGATAGCATTTTTACAGTA 58.278 34.615 0.00 0.00 0.00 2.74
28 29 7.482654 TTCAGGATCGATAGCATTTTTACAG 57.517 36.000 0.00 0.00 0.00 2.74
42 44 8.651389 AGGAGATTAATTAACATTCAGGATCGA 58.349 33.333 0.00 0.00 0.00 3.59
70 77 2.161855 CTTGCTGTAATCTTGTGCCCA 58.838 47.619 0.00 0.00 0.00 5.36
108 115 1.068610 GCTAGCTCGCTCTACATGGAG 60.069 57.143 7.70 0.00 36.50 3.86
141 152 2.830285 AACGTGCTCGCGCCTTTTT 61.830 52.632 8.29 0.00 41.18 1.94
180 191 2.753029 GTGGAGACAGCTGGCCTT 59.247 61.111 18.28 0.00 44.46 4.35
324 335 8.934023 AAAATGGAAAACAACTGATCTAGGTA 57.066 30.769 0.00 0.00 0.00 3.08
355 366 7.038799 GGGAATGAACTGGCCATCATTATTATT 60.039 37.037 27.02 11.24 44.15 1.40
364 375 1.106285 GTGGGAATGAACTGGCCATC 58.894 55.000 5.51 1.61 0.00 3.51
371 383 4.295141 TCCGTTTATGTGGGAATGAACT 57.705 40.909 0.00 0.00 0.00 3.01
455 467 1.732259 GCTGTGTAGATCCGGTGTTTG 59.268 52.381 0.00 0.00 0.00 2.93
866 878 2.665603 GACTGGTGAGGAGGCCAC 59.334 66.667 5.01 0.00 0.00 5.01
867 879 2.997315 CGACTGGTGAGGAGGCCA 60.997 66.667 5.01 0.00 0.00 5.36
963 979 2.679639 CGCTCTGCCACCCAACTAATTA 60.680 50.000 0.00 0.00 0.00 1.40
1053 1069 1.557443 CGAACACCTTGGTCAGCGTC 61.557 60.000 0.00 0.00 32.48 5.19
1208 1224 1.694133 GCAGTGGAGGGAGATGGAGG 61.694 65.000 0.00 0.00 0.00 4.30
1211 1227 1.351080 ATGGCAGTGGAGGGAGATGG 61.351 60.000 0.00 0.00 0.00 3.51
1213 1229 1.992519 GCATGGCAGTGGAGGGAGAT 61.993 60.000 0.00 0.00 0.00 2.75
1712 1734 2.757099 GCGGGGTAGAACGGGAGA 60.757 66.667 0.00 0.00 0.00 3.71
1763 1785 4.040645 CAGGAGGTGCAGCTAGGA 57.959 61.111 20.22 0.00 0.00 2.94
1782 1807 7.446013 AGGAGGAAGAAGAATATACTACGTGAG 59.554 40.741 0.00 0.00 0.00 3.51
1787 1812 6.614160 GCGAGGAGGAAGAAGAATATACTAC 58.386 44.000 0.00 0.00 0.00 2.73
1788 1813 5.411977 CGCGAGGAGGAAGAAGAATATACTA 59.588 44.000 0.00 0.00 0.00 1.82
1789 1814 4.216687 CGCGAGGAGGAAGAAGAATATACT 59.783 45.833 0.00 0.00 0.00 2.12
1857 1882 2.463553 CGAATCCTCGTACTACGCAA 57.536 50.000 3.57 0.00 42.21 4.85
2166 2212 6.163135 AGGAAAGTCAGATCGGGTAATTAG 57.837 41.667 0.00 0.00 0.00 1.73
2182 2228 5.163550 GCTGTAAAAACAGGACAAGGAAAGT 60.164 40.000 7.57 0.00 38.14 2.66
2208 2254 9.399797 AGATGCAGTCAGTTTAATATTGATTGA 57.600 29.630 0.00 0.00 32.30 2.57
2209 2255 9.661187 GAGATGCAGTCAGTTTAATATTGATTG 57.339 33.333 0.00 0.00 33.34 2.67
2210 2256 9.399797 TGAGATGCAGTCAGTTTAATATTGATT 57.600 29.630 0.00 0.00 0.00 2.57
2211 2257 8.969260 TGAGATGCAGTCAGTTTAATATTGAT 57.031 30.769 0.00 0.00 0.00 2.57
2243 4739 8.950210 CAGACAAATCAGTGGTCAGTTTAATAT 58.050 33.333 0.00 0.00 34.04 1.28
2277 4773 1.559682 TGGGGAGTAGCTGAATGAACC 59.440 52.381 0.00 0.00 0.00 3.62
2404 4907 0.662619 CGGAAGCAGCAAAGTGACAA 59.337 50.000 0.00 0.00 0.00 3.18
2698 5210 1.967779 CCAAGTTGGTTACCTTTGGGG 59.032 52.381 14.21 6.37 35.71 4.96
2718 5230 2.079925 GACTGTGGGCTTTGAGATGAC 58.920 52.381 0.00 0.00 0.00 3.06
2721 5233 2.619849 CCATGACTGTGGGCTTTGAGAT 60.620 50.000 0.00 0.00 35.55 2.75
2722 5234 1.271543 CCATGACTGTGGGCTTTGAGA 60.272 52.381 0.00 0.00 35.55 3.27
2724 5236 0.478072 ACCATGACTGTGGGCTTTGA 59.522 50.000 0.00 0.00 43.77 2.69
2725 5237 0.599558 CACCATGACTGTGGGCTTTG 59.400 55.000 0.00 0.00 43.77 2.77
2726 5238 1.181098 GCACCATGACTGTGGGCTTT 61.181 55.000 0.00 0.00 43.77 3.51
2727 5239 1.604593 GCACCATGACTGTGGGCTT 60.605 57.895 0.00 0.00 43.77 4.35
2728 5240 2.034687 GCACCATGACTGTGGGCT 59.965 61.111 0.00 0.00 43.77 5.19
2729 5241 3.064324 GGCACCATGACTGTGGGC 61.064 66.667 0.00 0.00 43.77 5.36
2746 5258 1.967779 CAAGTTGGTTACCTTTGGGGG 59.032 52.381 2.07 0.00 40.03 5.40
2747 5259 1.967779 CCAAGTTGGTTACCTTTGGGG 59.032 52.381 14.21 6.37 35.71 4.96
2759 5271 3.152341 AGCTTTGAGATGACCAAGTTGG 58.848 45.455 20.76 20.76 45.02 3.77
2760 5272 5.240891 TCTAGCTTTGAGATGACCAAGTTG 58.759 41.667 0.00 0.00 0.00 3.16
2761 5273 5.489792 TCTAGCTTTGAGATGACCAAGTT 57.510 39.130 0.00 0.00 0.00 2.66
2762 5274 5.690464 ATCTAGCTTTGAGATGACCAAGT 57.310 39.130 0.00 0.00 32.30 3.16
2763 5275 5.220815 GCAATCTAGCTTTGAGATGACCAAG 60.221 44.000 0.00 0.00 33.85 3.61
2764 5276 4.637534 GCAATCTAGCTTTGAGATGACCAA 59.362 41.667 0.00 0.00 33.85 3.67
2765 5277 4.080695 AGCAATCTAGCTTTGAGATGACCA 60.081 41.667 0.00 0.00 43.70 4.02
2766 5278 4.450053 AGCAATCTAGCTTTGAGATGACC 58.550 43.478 0.00 0.00 43.70 4.02
2824 5403 2.132762 ACTGCTACTGGTTTTCGTTCG 58.867 47.619 0.00 0.00 0.00 3.95
2900 5482 6.072728 TGGCGCCTATACAATTTCATACAATC 60.073 38.462 29.70 0.00 0.00 2.67
2909 5493 8.807948 ATATTAAGATGGCGCCTATACAATTT 57.192 30.769 29.70 13.19 0.00 1.82
2910 5494 8.807948 AATATTAAGATGGCGCCTATACAATT 57.192 30.769 29.70 14.22 0.00 2.32
2911 5495 8.677300 CAAATATTAAGATGGCGCCTATACAAT 58.323 33.333 29.70 21.53 0.00 2.71
2912 5496 7.361713 GCAAATATTAAGATGGCGCCTATACAA 60.362 37.037 29.70 16.23 0.00 2.41
2913 5497 6.093495 GCAAATATTAAGATGGCGCCTATACA 59.907 38.462 29.70 7.00 0.00 2.29
2914 5498 6.458342 GGCAAATATTAAGATGGCGCCTATAC 60.458 42.308 29.70 15.55 34.17 1.47
2915 5499 5.588648 GGCAAATATTAAGATGGCGCCTATA 59.411 40.000 29.70 7.94 34.17 1.31
2916 5500 4.399303 GGCAAATATTAAGATGGCGCCTAT 59.601 41.667 29.70 19.23 34.17 2.57
2917 5501 3.756434 GGCAAATATTAAGATGGCGCCTA 59.244 43.478 29.70 14.84 34.17 3.93
2918 5502 2.558359 GGCAAATATTAAGATGGCGCCT 59.442 45.455 29.70 13.55 34.17 5.52
3215 5809 2.169769 ACGAGAGAGAGAGAGACGGAAT 59.830 50.000 0.00 0.00 0.00 3.01
3216 5810 1.551430 ACGAGAGAGAGAGAGACGGAA 59.449 52.381 0.00 0.00 0.00 4.30
3218 5812 2.018542 AACGAGAGAGAGAGAGACGG 57.981 55.000 0.00 0.00 0.00 4.79
3220 5814 4.255301 TGGTAAACGAGAGAGAGAGAGAC 58.745 47.826 0.00 0.00 0.00 3.36
3221 5815 4.554960 TGGTAAACGAGAGAGAGAGAGA 57.445 45.455 0.00 0.00 0.00 3.10
3276 5874 0.248661 CAGCGATGGGACTACAGACG 60.249 60.000 0.00 0.00 0.00 4.18
3306 5904 4.835199 ACGACGATTTTATTCAGGTTCG 57.165 40.909 0.00 0.00 0.00 3.95
3323 5921 4.922719 AGAGAATGACCGAAGATTACGAC 58.077 43.478 0.00 0.00 0.00 4.34
3366 5964 1.447489 CCAACTCAGCGAGCTCAGG 60.447 63.158 15.40 2.02 32.04 3.86
3386 5984 6.398918 AGAGACGCAATGTGATACTAAGTTT 58.601 36.000 0.00 0.00 0.00 2.66
3394 5992 4.334481 TCGAAGTAGAGACGCAATGTGATA 59.666 41.667 0.00 0.00 0.00 2.15
3395 5993 3.128764 TCGAAGTAGAGACGCAATGTGAT 59.871 43.478 0.00 0.00 0.00 3.06
3399 6255 4.149922 TGTTTTCGAAGTAGAGACGCAATG 59.850 41.667 0.00 0.00 0.00 2.82
3400 6256 4.304110 TGTTTTCGAAGTAGAGACGCAAT 58.696 39.130 0.00 0.00 0.00 3.56
3404 6260 5.213675 AGTTCTGTTTTCGAAGTAGAGACG 58.786 41.667 8.20 0.00 0.00 4.18
3410 6266 7.222224 GTCTCTCAAAGTTCTGTTTTCGAAGTA 59.778 37.037 0.00 0.00 0.00 2.24
3415 6271 5.718649 TGTCTCTCAAAGTTCTGTTTTCG 57.281 39.130 0.00 0.00 0.00 3.46
3467 6364 3.306166 CCGGTAATGACGCTCACTTTAAG 59.694 47.826 0.00 0.00 0.00 1.85
3472 6369 1.153628 GCCGGTAATGACGCTCACT 60.154 57.895 1.90 0.00 0.00 3.41
3506 6403 2.007608 GAAATCTGGTACCCTGCGTTC 58.992 52.381 10.07 3.23 0.00 3.95
3508 6405 1.276622 AGAAATCTGGTACCCTGCGT 58.723 50.000 10.07 0.00 0.00 5.24
3509 6406 3.069586 TGATAGAAATCTGGTACCCTGCG 59.930 47.826 10.07 0.00 32.93 5.18
3510 6407 4.141711 TGTGATAGAAATCTGGTACCCTGC 60.142 45.833 10.07 0.00 32.93 4.85
3511 6408 5.614324 TGTGATAGAAATCTGGTACCCTG 57.386 43.478 10.07 2.26 32.93 4.45
3512 6409 6.443849 TCTTTGTGATAGAAATCTGGTACCCT 59.556 38.462 10.07 0.00 32.93 4.34
3513 6410 6.650120 TCTTTGTGATAGAAATCTGGTACCC 58.350 40.000 10.07 0.00 32.93 3.69
3514 6411 8.561738 TTTCTTTGTGATAGAAATCTGGTACC 57.438 34.615 4.43 4.43 36.86 3.34
3523 6420 4.436852 GCGCCGATTTCTTTGTGATAGAAA 60.437 41.667 0.00 0.00 43.52 2.52
3524 6421 3.063452 GCGCCGATTTCTTTGTGATAGAA 59.937 43.478 0.00 0.00 0.00 2.10
3525 6422 2.607635 GCGCCGATTTCTTTGTGATAGA 59.392 45.455 0.00 0.00 0.00 1.98
3526 6423 2.351418 TGCGCCGATTTCTTTGTGATAG 59.649 45.455 4.18 0.00 0.00 2.08
3527 6424 2.351418 CTGCGCCGATTTCTTTGTGATA 59.649 45.455 4.18 0.00 0.00 2.15
3528 6425 1.131126 CTGCGCCGATTTCTTTGTGAT 59.869 47.619 4.18 0.00 0.00 3.06
3529 6426 0.516877 CTGCGCCGATTTCTTTGTGA 59.483 50.000 4.18 0.00 0.00 3.58
3530 6427 0.454957 CCTGCGCCGATTTCTTTGTG 60.455 55.000 4.18 0.00 0.00 3.33
3531 6428 0.605319 TCCTGCGCCGATTTCTTTGT 60.605 50.000 4.18 0.00 0.00 2.83
3532 6429 0.734889 ATCCTGCGCCGATTTCTTTG 59.265 50.000 4.18 0.00 0.00 2.77
3533 6430 1.940613 GTATCCTGCGCCGATTTCTTT 59.059 47.619 4.18 0.00 0.00 2.52
3534 6431 1.583054 GTATCCTGCGCCGATTTCTT 58.417 50.000 4.18 0.00 0.00 2.52
3535 6432 0.249911 GGTATCCTGCGCCGATTTCT 60.250 55.000 4.18 0.00 0.00 2.52
3536 6433 0.531974 TGGTATCCTGCGCCGATTTC 60.532 55.000 4.18 3.30 0.00 2.17
3537 6434 0.532862 CTGGTATCCTGCGCCGATTT 60.533 55.000 4.18 0.00 0.00 2.17
3538 6435 1.069765 CTGGTATCCTGCGCCGATT 59.930 57.895 4.18 0.00 0.00 3.34
3539 6436 1.188219 ATCTGGTATCCTGCGCCGAT 61.188 55.000 4.18 8.74 0.00 4.18
3540 6437 1.399744 AATCTGGTATCCTGCGCCGA 61.400 55.000 4.18 0.00 0.00 5.54
3541 6438 0.532862 AAATCTGGTATCCTGCGCCG 60.533 55.000 4.18 0.00 0.00 6.46
3542 6439 1.202698 AGAAATCTGGTATCCTGCGCC 60.203 52.381 4.18 0.00 0.00 6.53
3543 6440 2.246719 AGAAATCTGGTATCCTGCGC 57.753 50.000 0.00 0.00 0.00 6.09
3544 6441 4.926238 GTGATAGAAATCTGGTATCCTGCG 59.074 45.833 0.00 0.00 32.93 5.18
3545 6442 5.858381 TGTGATAGAAATCTGGTATCCTGC 58.142 41.667 0.00 0.00 32.93 4.85
3561 6458 3.246226 CGGAGCCGATTTCTTTGTGATAG 59.754 47.826 2.00 0.00 42.83 2.08
3583 6480 5.059833 AGATAAATCATGAGAGCCGGTTTC 58.940 41.667 1.90 0.98 0.00 2.78
3597 6494 6.184068 TCCAAATTTCCCACGAGATAAATCA 58.816 36.000 0.00 0.00 0.00 2.57
3637 6534 0.231279 CGCGGTATTACGGAACATGC 59.769 55.000 0.00 0.00 0.00 4.06
3655 6552 3.556298 AAAACCCCTACCGGCACCG 62.556 63.158 0.00 1.02 39.44 4.94
3660 6557 0.315886 GCAACAAAAACCCCTACCGG 59.684 55.000 0.00 0.00 0.00 5.28
3693 6590 5.824624 CTGCAAGACACCATAGTTTGGATAT 59.175 40.000 6.62 0.00 42.81 1.63
3701 6598 0.620556 CCCCTGCAAGACACCATAGT 59.379 55.000 0.00 0.00 34.07 2.12
3716 6613 7.201911 GCTACATTATTCAAATACTTTGCCCCT 60.202 37.037 0.00 0.00 40.43 4.79
3724 6621 4.084013 GCGGCGCTACATTATTCAAATACT 60.084 41.667 26.86 0.00 0.00 2.12
3725 6622 4.148891 GCGGCGCTACATTATTCAAATAC 58.851 43.478 26.86 0.00 0.00 1.89
3729 6626 0.579630 CGCGGCGCTACATTATTCAA 59.420 50.000 30.54 0.00 0.00 2.69
3733 6630 0.387367 CTCTCGCGGCGCTACATTAT 60.387 55.000 30.54 0.00 0.00 1.28
3742 6639 4.214383 CACATTGCTCTCGCGGCG 62.214 66.667 17.70 17.70 39.65 6.46
3744 6641 1.133253 CAACACATTGCTCTCGCGG 59.867 57.895 6.13 0.00 39.65 6.46
3753 6650 6.237542 GCAAATAGCCGAATTACAACACATTG 60.238 38.462 0.00 0.00 38.46 2.82
3785 6682 5.757099 TGGTTAAGAAGAAGGGTTAGAGG 57.243 43.478 0.00 0.00 0.00 3.69
3786 6683 7.394816 TCATTGGTTAAGAAGAAGGGTTAGAG 58.605 38.462 0.00 0.00 0.00 2.43
3787 6684 7.324388 TCATTGGTTAAGAAGAAGGGTTAGA 57.676 36.000 0.00 0.00 0.00 2.10
3790 6687 6.839134 ACTTTCATTGGTTAAGAAGAAGGGTT 59.161 34.615 0.00 0.00 0.00 4.11
3805 6704 4.326504 AAAGACTTGCCACTTTCATTGG 57.673 40.909 0.00 0.00 37.17 3.16
3807 6706 4.122046 GCAAAAGACTTGCCACTTTCATT 58.878 39.130 0.00 0.00 39.38 2.57
3850 6750 3.525537 CCAGCAACTGTCGTTCTCATAT 58.474 45.455 0.00 0.00 0.00 1.78
3855 6755 0.882042 CAGCCAGCAACTGTCGTTCT 60.882 55.000 0.00 0.00 0.00 3.01
3921 6821 1.536766 CACATCAAGCCGTTCATGTGT 59.463 47.619 3.25 0.00 40.77 3.72
3955 6855 3.123621 CACGACACAGCCTGAACTATTTC 59.876 47.826 0.00 0.00 0.00 2.17
3960 6860 0.530650 CACACGACACAGCCTGAACT 60.531 55.000 0.00 0.00 0.00 3.01
3963 6863 1.227234 CACACACGACACAGCCTGA 60.227 57.895 0.00 0.00 0.00 3.86
3967 6867 0.874175 TGCTACACACACGACACAGC 60.874 55.000 0.00 0.00 0.00 4.40
3999 6899 9.814899 ATCTCATTTGACAATAGTAGAGTTGAG 57.185 33.333 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.