Multiple sequence alignment - TraesCS5D01G098900

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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 TraesCS5D01G098900 chr5D 100.000 9295 0 0 1 9295 110370124 110379418 0.000000e+00 17165.0
1 TraesCS5D01G098900 chr5D 88.827 358 33 5 2621 2971 9118203 9117846 5.160000e-117 433.0
2 TraesCS5D01G098900 chr5D 87.465 359 36 6 2621 2973 9072732 9072377 1.120000e-108 405.0
3 TraesCS5D01G098900 chr5D 95.455 66 3 0 6547 6612 110376607 110376672 1.280000e-18 106.0
4 TraesCS5D01G098900 chr5D 95.455 66 3 0 6484 6549 110376670 110376735 1.280000e-18 106.0
5 TraesCS5D01G098900 chr5D 100.000 28 0 0 372 399 461621618 461621591 1.700000e-02 52.8
6 TraesCS5D01G098900 chr5B 96.821 4026 76 17 4652 8645 122427941 122423936 0.000000e+00 6678.0
7 TraesCS5D01G098900 chr5B 98.514 2220 25 3 2440 4652 122430202 122427984 0.000000e+00 3910.0
8 TraesCS5D01G098900 chr5B 96.936 1730 41 8 719 2441 122432050 122430326 0.000000e+00 2891.0
9 TraesCS5D01G098900 chr5B 95.804 572 18 3 8727 9295 122423937 122423369 0.000000e+00 918.0
10 TraesCS5D01G098900 chr5B 90.148 406 28 4 15 420 122434800 122434407 1.380000e-142 518.0
11 TraesCS5D01G098900 chr5B 95.556 135 5 1 539 672 122434073 122433939 2.030000e-51 215.0
12 TraesCS5D01G098900 chr5B 97.600 125 2 1 417 541 122434356 122434233 7.310000e-51 213.0
13 TraesCS5D01G098900 chr5B 94.382 89 5 0 8640 8728 86069387 86069475 4.530000e-28 137.0
14 TraesCS5D01G098900 chr5B 95.455 66 3 0 6547 6612 122426084 122426019 1.280000e-18 106.0
15 TraesCS5D01G098900 chr5A 96.355 3951 102 18 719 4652 116582270 116578345 0.000000e+00 6460.0
16 TraesCS5D01G098900 chr5A 96.589 3049 71 13 5617 8645 116576927 116573892 0.000000e+00 5024.0
17 TraesCS5D01G098900 chr5A 96.534 981 18 6 4652 5617 116578302 116577323 0.000000e+00 1609.0
18 TraesCS5D01G098900 chr5A 93.509 570 30 3 8727 9295 116573893 116573330 0.000000e+00 841.0
19 TraesCS5D01G098900 chr5A 92.089 316 23 2 1 315 116583397 116583083 2.380000e-120 444.0
20 TraesCS5D01G098900 chr5A 83.444 151 12 6 444 582 116582884 116582735 2.720000e-25 128.0
21 TraesCS5D01G098900 chr5A 96.970 66 2 0 6547 6612 116576043 116575978 2.740000e-20 111.0
22 TraesCS5D01G098900 chr5A 100.000 38 0 0 628 665 116582297 116582260 4.660000e-08 71.3
23 TraesCS5D01G098900 chr7B 88.837 215 22 2 2669 2882 743851759 743851972 7.160000e-66 263.0
24 TraesCS5D01G098900 chr7B 87.442 215 25 2 2669 2882 744191765 744191552 7.210000e-61 246.0
25 TraesCS5D01G098900 chr7A 96.629 89 3 0 8641 8729 73734931 73734843 2.090000e-31 148.0
26 TraesCS5D01G098900 chr4D 95.699 93 3 1 8640 8731 259840212 259840304 2.090000e-31 148.0
27 TraesCS5D01G098900 chr4D 95.455 88 4 0 8641 8728 478668927 478669014 3.500000e-29 141.0
28 TraesCS5D01G098900 chr4D 93.548 93 6 0 8636 8728 182067331 182067423 1.260000e-28 139.0
29 TraesCS5D01G098900 chr1B 96.552 87 3 0 8644 8730 28500504 28500418 2.710000e-30 145.0
30 TraesCS5D01G098900 chr1B 92.857 98 5 2 8632 8728 447815460 447815364 3.500000e-29 141.0
31 TraesCS5D01G098900 chr6B 92.929 99 5 2 8636 8732 628895851 628895949 9.730000e-30 143.0
32 TraesCS5D01G098900 chr1A 93.684 95 6 0 8644 8738 90811235 90811141 9.730000e-30 143.0
33 TraesCS5D01G098900 chr3A 88.333 60 5 2 369 426 41615101 41615160 4.660000e-08 71.3
34 TraesCS5D01G098900 chr3D 100.000 28 0 0 372 399 477826650 477826623 1.700000e-02 52.8


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 TraesCS5D01G098900 chr5D 110370124 110379418 9294 False 5792.333333 17165 96.97000 1 9295 3 chr5D.!!$F1 9294
1 TraesCS5D01G098900 chr5B 122423369 122434800 11431 True 1931.125000 6678 95.85425 15 9295 8 chr5B.!!$R1 9280
2 TraesCS5D01G098900 chr5A 116573330 116583397 10067 True 1836.037500 6460 94.43625 1 9295 8 chr5A.!!$R1 9294

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
205 207 0.994263 GCGAAACAGAAATGGCATGC 59.006 50.000 9.90 9.9 0.00 4.06 F
1638 4277 1.003718 GTTGGGAGGCACGCTTAGT 60.004 57.895 0.24 0.0 0.00 2.24 F
1962 4603 0.874175 TGCTGACTGTCGTGTTTCGG 60.874 55.000 2.98 0.0 40.32 4.30 F
3519 6291 1.084018 TTTCTGGCCAAAGGATCCCT 58.916 50.000 7.01 0.0 33.87 4.20 F
4561 7334 3.498397 ACTTGTGTTAGCGTTCCATTGAG 59.502 43.478 0.00 0.0 0.00 3.02 F
5086 7913 0.885879 CATGCTGCATGTGACCTTGT 59.114 50.000 29.59 0.0 37.12 3.16 F
6713 9972 1.134007 CAAGCAGGGATCATACTGGCA 60.134 52.381 11.65 0.0 35.30 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1843 4483 0.467290 TCCAACAGAAGGCAACCACC 60.467 55.000 0.00 0.0 37.17 4.61 R
3519 6291 2.700371 CTGCATGAGTATGTACCCCTCA 59.300 50.000 0.00 8.2 39.38 3.86 R
4226 6998 1.269723 GGGTTTCCAGCCTTTTTCTCG 59.730 52.381 0.00 0.0 37.61 4.04 R
4645 7418 1.236628 GGCAGCTCTCCATATTGCAG 58.763 55.000 0.00 0.0 36.53 4.41 R
6755 10014 0.250793 TTGTCGGCGGTATCCACATT 59.749 50.000 7.21 0.0 0.00 2.71 R
6910 10169 0.947244 AACTTGAAAGACTGCTGGCG 59.053 50.000 0.00 0.0 0.00 5.69 R
8322 11581 2.096069 CAGACAGCAGTGGATCAAAACG 60.096 50.000 0.00 0.0 0.00 3.60 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 1.789078 CGCAGGTGCCATGATTAGCC 61.789 60.000 0.00 0.00 37.91 3.93
58 59 2.143925 GTGTGGACTGCTCTTACCAAC 58.856 52.381 0.00 0.00 34.11 3.77
140 142 2.014068 GCTCGAAGACCCCATTTGGAG 61.014 57.143 0.00 0.00 37.39 3.86
141 143 1.279271 CTCGAAGACCCCATTTGGAGT 59.721 52.381 0.00 0.00 37.39 3.85
159 161 3.008049 GGAGTTCTGGAAGTTGCTCCTAA 59.992 47.826 9.20 0.00 40.84 2.69
205 207 0.994263 GCGAAACAGAAATGGCATGC 59.006 50.000 9.90 9.90 0.00 4.06
258 260 1.486211 TGGCGGAAACCCTTTTCAAA 58.514 45.000 0.00 0.00 42.72 2.69
279 281 4.900635 ATTGCCAGTTCCATTTCGTATC 57.099 40.909 0.00 0.00 0.00 2.24
317 319 1.745232 TGTTTAACGCATGCTAGGGG 58.255 50.000 17.13 1.61 0.00 4.79
318 320 1.279558 TGTTTAACGCATGCTAGGGGA 59.720 47.619 17.13 0.00 0.00 4.81
340 426 6.463331 GGGATTGAACATGATAACATTGGCAT 60.463 38.462 0.00 0.00 34.15 4.40
387 473 3.870419 CACTAGTGACTACTACCTCCGTC 59.130 52.174 18.45 0.00 38.36 4.79
665 3292 6.463995 TTCAAACTGTAATTTCAGTGGCTT 57.536 33.333 17.24 6.64 46.25 4.35
666 3293 6.463995 TCAAACTGTAATTTCAGTGGCTTT 57.536 33.333 17.24 6.32 46.25 3.51
667 3294 6.872920 TCAAACTGTAATTTCAGTGGCTTTT 58.127 32.000 17.24 5.99 46.25 2.27
668 3295 7.327214 TCAAACTGTAATTTCAGTGGCTTTTT 58.673 30.769 17.24 5.35 46.25 1.94
693 3320 5.766150 TTGAGTGGTTGTAATTTCAGTGG 57.234 39.130 0.00 0.00 0.00 4.00
694 3321 3.568007 TGAGTGGTTGTAATTTCAGTGGC 59.432 43.478 0.00 0.00 0.00 5.01
695 3322 3.821033 GAGTGGTTGTAATTTCAGTGGCT 59.179 43.478 0.00 0.00 0.00 4.75
696 3323 4.980573 AGTGGTTGTAATTTCAGTGGCTA 58.019 39.130 0.00 0.00 0.00 3.93
697 3324 5.003804 AGTGGTTGTAATTTCAGTGGCTAG 58.996 41.667 0.00 0.00 0.00 3.42
698 3325 5.001232 GTGGTTGTAATTTCAGTGGCTAGA 58.999 41.667 0.00 0.00 0.00 2.43
699 3326 5.648092 GTGGTTGTAATTTCAGTGGCTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
700 3327 6.151144 GTGGTTGTAATTTCAGTGGCTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
701 3328 6.719370 TGGTTGTAATTTCAGTGGCTAGATTT 59.281 34.615 0.00 0.00 0.00 2.17
702 3329 7.232534 TGGTTGTAATTTCAGTGGCTAGATTTT 59.767 33.333 0.00 0.00 0.00 1.82
703 3330 8.088365 GGTTGTAATTTCAGTGGCTAGATTTTT 58.912 33.333 0.00 0.00 0.00 1.94
727 3354 4.900635 TCTTGAGAAACTTTTCAGTGGC 57.099 40.909 4.58 0.00 39.61 5.01
728 3355 4.526970 TCTTGAGAAACTTTTCAGTGGCT 58.473 39.130 4.58 0.00 39.61 4.75
729 3356 5.680619 TCTTGAGAAACTTTTCAGTGGCTA 58.319 37.500 4.58 0.00 39.61 3.93
730 3357 6.299141 TCTTGAGAAACTTTTCAGTGGCTAT 58.701 36.000 4.58 0.00 39.61 2.97
790 3417 2.301870 ACCCAACGAGACAGAAGCATAA 59.698 45.455 0.00 0.00 0.00 1.90
948 3586 1.662686 AAGGGAGAAGAGAACCCCAG 58.337 55.000 0.00 0.00 44.21 4.45
950 3588 1.152271 AGGGAGAAGAGAACCCCAGAA 59.848 52.381 0.00 0.00 44.21 3.02
951 3589 1.557371 GGGAGAAGAGAACCCCAGAAG 59.443 57.143 0.00 0.00 38.69 2.85
1056 3694 3.060866 GAGGTCAAGTGCCTCCGT 58.939 61.111 9.40 0.00 45.05 4.69
1156 3794 3.157949 CCTTCCTCTCCCCGCTCC 61.158 72.222 0.00 0.00 0.00 4.70
1159 3797 2.863019 CTTCCTCTCCCCGCTCCTCA 62.863 65.000 0.00 0.00 0.00 3.86
1224 3862 4.835891 CCCGGGGAGGCGAGTAGT 62.836 72.222 14.71 0.00 39.21 2.73
1236 3874 4.657824 AGTAGTTGCGGCGCACGT 62.658 61.111 36.57 26.03 46.52 4.49
1353 3991 6.206829 GGAAGGCTTTGTGTAGTTCACTTTAT 59.793 38.462 0.00 0.00 46.27 1.40
1604 4243 1.133761 AGGCGAGTAGAGGTAGATGCA 60.134 52.381 0.00 0.00 0.00 3.96
1630 4269 1.899437 GACGATCAGGTTGGGAGGCA 61.899 60.000 0.00 0.00 0.00 4.75
1631 4270 1.450312 CGATCAGGTTGGGAGGCAC 60.450 63.158 0.00 0.00 0.00 5.01
1634 4273 4.335647 CAGGTTGGGAGGCACGCT 62.336 66.667 0.24 0.00 0.00 5.07
1638 4277 1.003718 GTTGGGAGGCACGCTTAGT 60.004 57.895 0.24 0.00 0.00 2.24
1796 4436 8.160765 TCTATTTAGAAAGGAAATGGACACACA 58.839 33.333 0.00 0.00 31.25 3.72
1843 4483 2.320587 GGTTCCGCAGTGCTGTGAG 61.321 63.158 14.33 0.00 43.32 3.51
1844 4484 2.031012 TTCCGCAGTGCTGTGAGG 59.969 61.111 14.33 6.60 43.32 3.86
1845 4485 2.807107 TTCCGCAGTGCTGTGAGGT 61.807 57.895 14.33 0.00 43.32 3.85
1855 4495 1.518903 GCTGTGAGGTGGTTGCCTTC 61.519 60.000 0.00 0.00 39.34 3.46
1913 4554 8.925700 GTCTCTGAAAGTTTTGTTGTGAAAATT 58.074 29.630 0.00 0.00 33.76 1.82
1959 4600 1.732941 TTGTGCTGACTGTCGTGTTT 58.267 45.000 2.98 0.00 0.00 2.83
1962 4603 0.874175 TGCTGACTGTCGTGTTTCGG 60.874 55.000 2.98 0.00 40.32 4.30
2919 5691 5.311016 CGTCGATTATACGTTTGCAATCT 57.689 39.130 0.00 0.00 35.66 2.40
3294 6066 4.122776 CAGATGCTAAAGCGAGTAATGGT 58.877 43.478 0.00 0.00 45.83 3.55
3519 6291 1.084018 TTTCTGGCCAAAGGATCCCT 58.916 50.000 7.01 0.00 33.87 4.20
4226 6998 4.784710 GCTCTTGCTCGCATGATTAAAGAC 60.785 45.833 7.77 0.00 36.03 3.01
4406 7178 7.209471 TGTTACATAAACATTTCCTGTGTCC 57.791 36.000 3.83 0.00 43.22 4.02
4561 7334 3.498397 ACTTGTGTTAGCGTTCCATTGAG 59.502 43.478 0.00 0.00 0.00 3.02
4645 7418 5.227908 TGAATGACGTGAAGTTTCTAGTCC 58.772 41.667 0.00 4.40 35.24 3.85
5086 7913 0.885879 CATGCTGCATGTGACCTTGT 59.114 50.000 29.59 0.00 37.12 3.16
5150 7978 4.872691 CACTATCGCTTTCTCCATGTTTCT 59.127 41.667 0.00 0.00 0.00 2.52
5162 7990 9.912634 TTTCTCCATGTTTCTGATTTTCATAAC 57.087 29.630 0.00 0.00 0.00 1.89
5346 8181 1.888215 TCAGCTTGCTCAGGTTTCTG 58.112 50.000 0.00 0.00 42.21 3.02
5487 8323 3.339436 ACCAGCCTCATCCTATATCCTCT 59.661 47.826 0.00 0.00 0.00 3.69
5489 8325 4.161942 CCAGCCTCATCCTATATCCTCTTG 59.838 50.000 0.00 0.00 0.00 3.02
5490 8326 5.022122 CAGCCTCATCCTATATCCTCTTGA 58.978 45.833 0.00 0.00 0.00 3.02
5491 8327 5.483231 CAGCCTCATCCTATATCCTCTTGAA 59.517 44.000 0.00 0.00 0.00 2.69
5492 8328 6.156602 CAGCCTCATCCTATATCCTCTTGAAT 59.843 42.308 0.00 0.00 0.00 2.57
5493 8329 6.156602 AGCCTCATCCTATATCCTCTTGAATG 59.843 42.308 0.00 0.00 0.00 2.67
5769 9021 6.815142 AGAAATTCAATTGGTTTATCAGCAGC 59.185 34.615 5.42 0.00 33.34 5.25
6214 9466 3.599343 GCAGTGTGTCATGGACTTATGA 58.401 45.455 0.00 0.00 34.83 2.15
6238 9497 5.210715 CAATGCTTTTGAAGAGTGAGTGTC 58.789 41.667 0.00 0.00 0.00 3.67
6490 9749 2.366533 AGTTGCTTGGCATCTCATCTG 58.633 47.619 0.00 0.00 38.76 2.90
6574 9833 5.976870 TCTAAATGAAAGGAGGATTAGGGGT 59.023 40.000 0.00 0.00 0.00 4.95
6584 9843 1.981495 GGATTAGGGGTGAGGATGAGG 59.019 57.143 0.00 0.00 0.00 3.86
6621 9880 1.500844 CAGAGCCTCAAAAGCAGCG 59.499 57.895 0.00 0.00 0.00 5.18
6635 9894 2.622436 AGCAGCGAAGTAATCCTGAAC 58.378 47.619 0.00 0.00 31.64 3.18
6658 9917 3.369147 CGGATGACAAACTTGCTACTGAG 59.631 47.826 0.00 0.00 0.00 3.35
6713 9972 1.134007 CAAGCAGGGATCATACTGGCA 60.134 52.381 11.65 0.00 35.30 4.92
6753 10012 8.097038 TGATACCAATCATTCTAATCTGCCTAC 58.903 37.037 0.00 0.00 37.20 3.18
6754 10013 6.506538 ACCAATCATTCTAATCTGCCTACT 57.493 37.500 0.00 0.00 0.00 2.57
6755 10014 7.618019 ACCAATCATTCTAATCTGCCTACTA 57.382 36.000 0.00 0.00 0.00 1.82
7048 10307 5.893824 TGAGAATGCCTGTGAATCTACTAGA 59.106 40.000 0.00 0.00 0.00 2.43
7569 10828 7.227873 TCATGTTGTTCCCAAATACTGAACTA 58.772 34.615 0.00 0.00 39.24 2.24
7599 10858 3.254411 TGGCGTGAATTGCAATCTGTTAA 59.746 39.130 13.38 0.00 0.00 2.01
7649 10908 5.073965 TGTTATTCCTTTTACCCTGTCAGGT 59.926 40.000 17.85 8.44 44.37 4.00
7826 11085 4.579340 AGCATTGTCATGGATGAAGATGAC 59.421 41.667 13.63 0.00 45.87 3.06
7947 11206 0.655733 ATGTGCACCTTATAACGCGC 59.344 50.000 15.69 0.00 35.48 6.86
8054 11313 5.116983 GGAAGTAACAACATTTTGTGCATCG 59.883 40.000 0.00 0.00 45.69 3.84
8081 11340 2.765689 TTTTGGGGGTGTTCTGATGT 57.234 45.000 0.00 0.00 0.00 3.06
8105 11364 1.007387 CTTGTTGGTTTCAGCCGCC 60.007 57.895 0.00 0.00 0.00 6.13
8153 11412 3.499737 CCTGATGCCACGAACCGC 61.500 66.667 0.00 0.00 0.00 5.68
8322 11581 1.200716 CCACCATGACAATGCACTGAC 59.799 52.381 0.26 0.00 31.93 3.51
8381 11640 2.169144 CCTGTGGTATGATCTGTCTGCA 59.831 50.000 0.00 0.00 0.00 4.41
8404 11663 7.823799 TGCACTCTGTAGAAATCATGTAAATCA 59.176 33.333 0.00 0.00 0.00 2.57
8434 11699 3.943381 TGATCAGTTGAGGCAGCAAATAG 59.057 43.478 0.00 0.00 0.00 1.73
8435 11700 3.423539 TCAGTTGAGGCAGCAAATAGT 57.576 42.857 0.00 0.00 0.00 2.12
8436 11701 4.551702 TCAGTTGAGGCAGCAAATAGTA 57.448 40.909 0.00 0.00 0.00 1.82
8533 11798 6.292919 CGGCCTAAAAGAGCAAATATACACTC 60.293 42.308 0.00 0.00 0.00 3.51
8572 11837 5.629125 AGAAATCTCTGCCTCAGAAAACTT 58.371 37.500 0.00 0.00 40.18 2.66
8601 11866 3.982475 TCATCTCGATGTTGCATACTCC 58.018 45.455 6.78 0.00 39.72 3.85
8646 11911 6.995511 TTTGACACTACTTTTGCAACTACT 57.004 33.333 0.00 0.00 0.00 2.57
8647 11912 6.598753 TTGACACTACTTTTGCAACTACTC 57.401 37.500 0.00 0.00 0.00 2.59
8648 11913 5.054477 TGACACTACTTTTGCAACTACTCC 58.946 41.667 0.00 0.00 0.00 3.85
8649 11914 4.386711 ACACTACTTTTGCAACTACTCCC 58.613 43.478 0.00 0.00 0.00 4.30
8650 11915 4.102681 ACACTACTTTTGCAACTACTCCCT 59.897 41.667 0.00 0.00 0.00 4.20
8651 11916 4.691216 CACTACTTTTGCAACTACTCCCTC 59.309 45.833 0.00 0.00 0.00 4.30
8652 11917 3.141767 ACTTTTGCAACTACTCCCTCC 57.858 47.619 0.00 0.00 0.00 4.30
8653 11918 2.076863 CTTTTGCAACTACTCCCTCCG 58.923 52.381 0.00 0.00 0.00 4.63
8654 11919 1.053424 TTTGCAACTACTCCCTCCGT 58.947 50.000 0.00 0.00 0.00 4.69
8655 11920 1.927487 TTGCAACTACTCCCTCCGTA 58.073 50.000 0.00 0.00 0.00 4.02
8656 11921 1.927487 TGCAACTACTCCCTCCGTAA 58.073 50.000 0.00 0.00 0.00 3.18
8657 11922 2.250031 TGCAACTACTCCCTCCGTAAA 58.750 47.619 0.00 0.00 0.00 2.01
8658 11923 2.835764 TGCAACTACTCCCTCCGTAAAT 59.164 45.455 0.00 0.00 0.00 1.40
8659 11924 3.262405 TGCAACTACTCCCTCCGTAAATT 59.738 43.478 0.00 0.00 0.00 1.82
8660 11925 4.467082 TGCAACTACTCCCTCCGTAAATTA 59.533 41.667 0.00 0.00 0.00 1.40
8661 11926 5.046448 TGCAACTACTCCCTCCGTAAATTAA 60.046 40.000 0.00 0.00 0.00 1.40
8662 11927 6.053650 GCAACTACTCCCTCCGTAAATTAAT 58.946 40.000 0.00 0.00 0.00 1.40
8663 11928 7.147689 TGCAACTACTCCCTCCGTAAATTAATA 60.148 37.037 0.00 0.00 0.00 0.98
8664 11929 7.876582 GCAACTACTCCCTCCGTAAATTAATAT 59.123 37.037 0.00 0.00 0.00 1.28
8670 11935 9.377238 ACTCCCTCCGTAAATTAATATAAGAGT 57.623 33.333 0.00 0.00 0.00 3.24
8671 11936 9.640963 CTCCCTCCGTAAATTAATATAAGAGTG 57.359 37.037 0.00 0.00 0.00 3.51
8672 11937 9.151177 TCCCTCCGTAAATTAATATAAGAGTGT 57.849 33.333 0.00 0.00 0.00 3.55
8673 11938 9.774413 CCCTCCGTAAATTAATATAAGAGTGTT 57.226 33.333 0.00 0.00 0.00 3.32
8751 12016 0.670546 ACAGCACACGAGGTACATGC 60.671 55.000 0.00 0.00 36.52 4.06
8986 12251 2.099638 CGTAGCGCGTACAGCTGA 59.900 61.111 23.35 0.48 45.60 4.26
9132 12397 7.433425 GCAGAAACACCTTAATAATTCTCATGC 59.567 37.037 0.00 0.00 0.00 4.06
9136 12401 7.559590 ACACCTTAATAATTCTCATGCTGAC 57.440 36.000 0.00 0.00 0.00 3.51
9184 12452 6.238759 CCAGCAAACAGGGTAGAAATATAAGC 60.239 42.308 0.00 0.00 0.00 3.09
9191 12459 7.004691 ACAGGGTAGAAATATAAGCCAAATCC 58.995 38.462 0.00 0.00 33.14 3.01
9202 12470 8.773033 ATATAAGCCAAATCCACTTCTTGATT 57.227 30.769 0.00 0.00 32.72 2.57
9207 12475 5.183904 GCCAAATCCACTTCTTGATTACAGT 59.816 40.000 0.00 0.00 31.20 3.55
9208 12476 6.294731 GCCAAATCCACTTCTTGATTACAGTT 60.295 38.462 0.00 0.00 31.20 3.16
9209 12477 7.308435 CCAAATCCACTTCTTGATTACAGTTC 58.692 38.462 0.00 0.00 31.20 3.01
9227 12495 7.300556 ACAGTTCACTATGATATCTGCATCT 57.699 36.000 3.98 0.00 0.00 2.90
9236 12504 9.814899 ACTATGATATCTGCATCTACTATTTGC 57.185 33.333 3.98 0.00 36.91 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.789078 CGGCTAATCATGGCACCTGC 61.789 60.000 0.00 0.00 41.14 4.85
6 7 0.107456 CTCGGCTAATCATGGCACCT 59.893 55.000 0.00 0.00 34.13 4.00
58 59 8.889849 ATCTTCAACGACCAAAATATAAAACG 57.110 30.769 0.00 0.00 0.00 3.60
140 142 5.123027 CAGATTTAGGAGCAACTTCCAGAAC 59.877 44.000 0.00 0.00 39.84 3.01
141 143 5.248640 CAGATTTAGGAGCAACTTCCAGAA 58.751 41.667 0.00 0.00 39.84 3.02
159 161 1.272425 TGGTCCATTTTCCCGCAGATT 60.272 47.619 0.00 0.00 0.00 2.40
205 207 4.275936 ACCAAAAGAACAGAACTGGAATCG 59.724 41.667 6.76 0.00 34.19 3.34
258 260 4.526970 AGATACGAAATGGAACTGGCAAT 58.473 39.130 0.00 0.00 0.00 3.56
300 302 2.948979 CAATCCCCTAGCATGCGTTAAA 59.051 45.455 13.01 0.00 0.00 1.52
317 319 8.332464 CAAATGCCAATGTTATCATGTTCAATC 58.668 33.333 0.00 0.00 34.19 2.67
318 320 7.825270 ACAAATGCCAATGTTATCATGTTCAAT 59.175 29.630 0.00 0.00 34.19 2.57
340 426 5.184096 TCAGAAACAACAAGGCTGTTACAAA 59.816 36.000 0.00 0.00 44.15 2.83
387 473 8.846607 GCCTACAAAAACGTGTTATATTTTGAG 58.153 33.333 21.46 15.15 42.48 3.02
536 704 5.163963 GCAATTGTTTTGCTATGGTTGTAGC 60.164 40.000 7.40 0.00 45.71 3.58
537 705 5.348451 GGCAATTGTTTTGCTATGGTTGTAG 59.652 40.000 7.40 0.00 44.36 2.74
668 3295 7.038659 CCACTGAAATTACAACCACTCAAAAA 58.961 34.615 0.00 0.00 0.00 1.94
669 3296 6.568869 CCACTGAAATTACAACCACTCAAAA 58.431 36.000 0.00 0.00 0.00 2.44
670 3297 5.451242 GCCACTGAAATTACAACCACTCAAA 60.451 40.000 0.00 0.00 0.00 2.69
671 3298 4.037446 GCCACTGAAATTACAACCACTCAA 59.963 41.667 0.00 0.00 0.00 3.02
672 3299 3.568007 GCCACTGAAATTACAACCACTCA 59.432 43.478 0.00 0.00 0.00 3.41
673 3300 3.821033 AGCCACTGAAATTACAACCACTC 59.179 43.478 0.00 0.00 0.00 3.51
674 3301 3.832527 AGCCACTGAAATTACAACCACT 58.167 40.909 0.00 0.00 0.00 4.00
675 3302 5.001232 TCTAGCCACTGAAATTACAACCAC 58.999 41.667 0.00 0.00 0.00 4.16
676 3303 5.235850 TCTAGCCACTGAAATTACAACCA 57.764 39.130 0.00 0.00 0.00 3.67
677 3304 6.759497 AATCTAGCCACTGAAATTACAACC 57.241 37.500 0.00 0.00 0.00 3.77
702 3329 6.589907 GCCACTGAAAAGTTTCTCAAGAAAAA 59.410 34.615 6.76 0.00 44.58 1.94
703 3330 6.071391 AGCCACTGAAAAGTTTCTCAAGAAAA 60.071 34.615 6.76 0.00 44.58 2.29
704 3331 5.418840 AGCCACTGAAAAGTTTCTCAAGAAA 59.581 36.000 1.06 1.06 41.29 2.52
705 3332 4.949856 AGCCACTGAAAAGTTTCTCAAGAA 59.050 37.500 5.45 0.00 38.02 2.52
706 3333 4.526970 AGCCACTGAAAAGTTTCTCAAGA 58.473 39.130 5.45 0.00 38.02 3.02
707 3334 4.907879 AGCCACTGAAAAGTTTCTCAAG 57.092 40.909 5.45 0.00 38.02 3.02
708 3335 8.635765 AATATAGCCACTGAAAAGTTTCTCAA 57.364 30.769 5.45 0.00 38.02 3.02
709 3336 8.514594 CAAATATAGCCACTGAAAAGTTTCTCA 58.485 33.333 5.45 0.00 38.02 3.27
710 3337 7.486232 GCAAATATAGCCACTGAAAAGTTTCTC 59.514 37.037 5.45 0.00 38.02 2.87
711 3338 7.039784 TGCAAATATAGCCACTGAAAAGTTTCT 60.040 33.333 5.45 0.00 38.02 2.52
712 3339 7.090173 TGCAAATATAGCCACTGAAAAGTTTC 58.910 34.615 0.00 0.00 37.69 2.78
713 3340 6.991938 TGCAAATATAGCCACTGAAAAGTTT 58.008 32.000 0.00 0.00 0.00 2.66
714 3341 6.588719 TGCAAATATAGCCACTGAAAAGTT 57.411 33.333 0.00 0.00 0.00 2.66
715 3342 6.588719 TTGCAAATATAGCCACTGAAAAGT 57.411 33.333 0.00 0.00 0.00 2.66
716 3343 6.477688 CCATTGCAAATATAGCCACTGAAAAG 59.522 38.462 1.71 0.00 0.00 2.27
717 3344 6.070881 ACCATTGCAAATATAGCCACTGAAAA 60.071 34.615 1.71 0.00 0.00 2.29
718 3345 5.421693 ACCATTGCAAATATAGCCACTGAAA 59.578 36.000 1.71 0.00 0.00 2.69
719 3346 4.955450 ACCATTGCAAATATAGCCACTGAA 59.045 37.500 1.71 0.00 0.00 3.02
720 3347 4.535781 ACCATTGCAAATATAGCCACTGA 58.464 39.130 1.71 0.00 0.00 3.41
721 3348 4.924305 ACCATTGCAAATATAGCCACTG 57.076 40.909 1.71 0.00 0.00 3.66
722 3349 5.010012 GCTTACCATTGCAAATATAGCCACT 59.990 40.000 1.71 0.00 0.00 4.00
723 3350 5.221224 TGCTTACCATTGCAAATATAGCCAC 60.221 40.000 1.71 0.00 36.15 5.01
724 3351 4.892345 TGCTTACCATTGCAAATATAGCCA 59.108 37.500 1.71 0.00 36.15 4.75
725 3352 5.452078 TGCTTACCATTGCAAATATAGCC 57.548 39.130 1.71 0.00 36.15 3.93
948 3586 4.760047 TCCTTGCGGCCGAGCTTC 62.760 66.667 33.48 11.67 38.13 3.86
950 3588 4.767255 CTTCCTTGCGGCCGAGCT 62.767 66.667 33.48 0.00 38.13 4.09
1156 3794 3.423154 GGTTTGACGCGGGCTGAG 61.423 66.667 12.47 0.00 0.00 3.35
1159 3797 3.310860 CTAGGGTTTGACGCGGGCT 62.311 63.158 12.47 0.00 36.04 5.19
1236 3874 1.306141 AGCCTCCCAACCTGATCGA 60.306 57.895 0.00 0.00 0.00 3.59
1353 3991 1.004277 GGAACCTAGTGCCACCAATGA 59.996 52.381 0.00 0.00 29.85 2.57
1604 4243 3.282745 AACCTGATCGTCGTGCGCT 62.283 57.895 9.73 0.00 41.07 5.92
1630 4269 2.064014 GCCACGTAGAAAACTAAGCGT 58.936 47.619 0.00 0.00 0.00 5.07
1631 4270 2.334838 AGCCACGTAGAAAACTAAGCG 58.665 47.619 0.00 0.00 0.00 4.68
1634 4273 4.563061 GGAGAAGCCACGTAGAAAACTAA 58.437 43.478 0.00 0.00 36.34 2.24
1638 4277 1.337447 CCGGAGAAGCCACGTAGAAAA 60.337 52.381 0.00 0.00 35.94 2.29
1796 4436 0.989602 GTAGCAACCCTACCCCAACT 59.010 55.000 0.00 0.00 40.47 3.16
1824 4464 2.591429 CACAGCACTGCGGAACCA 60.591 61.111 8.26 0.00 0.00 3.67
1826 4466 2.320587 CCTCACAGCACTGCGGAAC 61.321 63.158 8.26 0.00 0.00 3.62
1843 4483 0.467290 TCCAACAGAAGGCAACCACC 60.467 55.000 0.00 0.00 37.17 4.61
1844 4484 1.620822 ATCCAACAGAAGGCAACCAC 58.379 50.000 0.00 0.00 37.17 4.16
1845 4485 1.962807 CAATCCAACAGAAGGCAACCA 59.037 47.619 0.00 0.00 37.17 3.67
1913 4554 4.776837 ACCATGAATCTAACCAATTTGGCA 59.223 37.500 15.49 3.91 42.67 4.92
1962 4603 3.638592 AATGTGTACCGGCAGCCCC 62.639 63.158 5.63 0.00 0.00 5.80
2489 5255 8.897752 GTGCTCTTATCACTGAAAAATAAGGAT 58.102 33.333 0.00 0.00 34.94 3.24
2493 5259 7.446931 TGTGGTGCTCTTATCACTGAAAAATAA 59.553 33.333 0.00 0.00 34.97 1.40
2638 5404 3.058224 GCAAGTACAATTCCGCTGACTTT 60.058 43.478 0.00 0.00 0.00 2.66
3122 5894 6.940867 AGGTGTAACTTGGGAAGATTCTTTAC 59.059 38.462 0.00 0.00 36.74 2.01
3519 6291 2.700371 CTGCATGAGTATGTACCCCTCA 59.300 50.000 0.00 8.20 39.38 3.86
4226 6998 1.269723 GGGTTTCCAGCCTTTTTCTCG 59.730 52.381 0.00 0.00 37.61 4.04
4561 7334 3.123621 CAGCATGGAGAACGTAAACTGAC 59.876 47.826 0.00 0.00 0.00 3.51
4645 7418 1.236628 GGCAGCTCTCCATATTGCAG 58.763 55.000 0.00 0.00 36.53 4.41
4787 7611 9.814899 TTTGTCATCAAAATAGTTTCACAACAT 57.185 25.926 0.00 0.00 40.08 2.71
5086 7913 6.245408 AGTAAATCCAGGTACAATCTGCAAA 58.755 36.000 0.00 0.00 0.00 3.68
5150 7978 9.645059 TGAAACAAAAGTGTGTTATGAAAATCA 57.355 25.926 0.00 0.00 40.86 2.57
5162 7990 9.150348 ACCTAAAAGAAATGAAACAAAAGTGTG 57.850 29.630 0.00 0.00 38.27 3.82
5346 8181 2.719426 ACACAGTACAGCGGTAAGTC 57.281 50.000 0.00 0.00 0.00 3.01
5487 8323 6.017440 CACTAAGAAGAAAACCCGTCATTCAA 60.017 38.462 0.00 0.00 0.00 2.69
5489 8325 5.106673 CCACTAAGAAGAAAACCCGTCATTC 60.107 44.000 0.00 0.00 0.00 2.67
5490 8326 4.760204 CCACTAAGAAGAAAACCCGTCATT 59.240 41.667 0.00 0.00 0.00 2.57
5491 8327 4.041198 TCCACTAAGAAGAAAACCCGTCAT 59.959 41.667 0.00 0.00 0.00 3.06
5492 8328 3.388676 TCCACTAAGAAGAAAACCCGTCA 59.611 43.478 0.00 0.00 0.00 4.35
5493 8329 3.999046 TCCACTAAGAAGAAAACCCGTC 58.001 45.455 0.00 0.00 0.00 4.79
5547 8386 6.127925 ACGTACACGAATGAGTGGTTTAGATA 60.128 38.462 9.04 0.00 45.80 1.98
6202 9454 6.623486 TCAAAAGCATTGTCATAAGTCCATG 58.377 36.000 2.69 0.00 0.00 3.66
6214 9466 4.641989 ACACTCACTCTTCAAAAGCATTGT 59.358 37.500 2.69 0.00 0.00 2.71
6238 9497 7.537596 TGGTCAATTGGCCTAATTTATATGG 57.462 36.000 28.49 0.00 41.34 2.74
6490 9749 4.166144 TCACCCCTAATCCTCCTTTCATTC 59.834 45.833 0.00 0.00 0.00 2.67
6574 9833 0.984961 CTGGAAGGGCCTCATCCTCA 60.985 60.000 21.96 5.21 37.63 3.86
6584 9843 1.587043 GCTTCGGTTTCTGGAAGGGC 61.587 60.000 3.31 0.00 39.96 5.19
6635 9894 2.416547 CAGTAGCAAGTTTGTCATCCGG 59.583 50.000 0.00 0.00 0.00 5.14
6658 9917 4.940046 TGAGTTCCTTTGCTCATCTCATTC 59.060 41.667 0.00 0.00 36.89 2.67
6713 9972 7.292319 TGATTGGTATCATCATTCTGGTGAAT 58.708 34.615 0.00 0.00 41.38 2.57
6736 9995 7.290014 TCCACATTAGTAGGCAGATTAGAATGA 59.710 37.037 0.00 0.00 0.00 2.57
6753 10012 1.067974 TGTCGGCGGTATCCACATTAG 59.932 52.381 7.21 0.00 0.00 1.73
6754 10013 1.112950 TGTCGGCGGTATCCACATTA 58.887 50.000 7.21 0.00 0.00 1.90
6755 10014 0.250793 TTGTCGGCGGTATCCACATT 59.749 50.000 7.21 0.00 0.00 2.71
6910 10169 0.947244 AACTTGAAAGACTGCTGGCG 59.053 50.000 0.00 0.00 0.00 5.69
6912 10171 4.389374 TCCTAAACTTGAAAGACTGCTGG 58.611 43.478 0.00 0.00 0.00 4.85
7048 10307 6.238869 GCTTTTTGACAACTTTCTGAGGATCT 60.239 38.462 0.00 0.00 34.92 2.75
7250 10509 7.346751 AGGAAAGAGTGCAACAGAAATTAAA 57.653 32.000 0.00 0.00 41.43 1.52
7251 10510 6.016276 GGAGGAAAGAGTGCAACAGAAATTAA 60.016 38.462 0.00 0.00 41.43 1.40
7252 10511 5.473504 GGAGGAAAGAGTGCAACAGAAATTA 59.526 40.000 0.00 0.00 41.43 1.40
7253 10512 4.279420 GGAGGAAAGAGTGCAACAGAAATT 59.721 41.667 0.00 0.00 41.43 1.82
7254 10513 3.823304 GGAGGAAAGAGTGCAACAGAAAT 59.177 43.478 0.00 0.00 41.43 2.17
7259 10518 3.297134 AAAGGAGGAAAGAGTGCAACA 57.703 42.857 0.00 0.00 41.43 3.33
7480 10739 2.730094 GGCAGTTTGGCACAGGTG 59.270 61.111 0.00 0.00 43.14 4.00
7569 10828 3.661944 TGCAATTCACGCCAATCATTTT 58.338 36.364 0.00 0.00 0.00 1.82
7599 10858 2.836981 AGCTGAGACAAGAATAGCCACT 59.163 45.455 0.00 0.00 35.05 4.00
7649 10908 6.053005 ACAAACCTTTAATGAGTCGTCTTCA 58.947 36.000 0.00 0.00 0.00 3.02
7826 11085 4.945543 TCTTCATCACCAAGTTCATGGATG 59.054 41.667 0.00 0.00 43.54 3.51
7829 11088 4.582869 TCTCTTCATCACCAAGTTCATGG 58.417 43.478 0.00 0.00 46.38 3.66
7830 11089 6.429078 TCTTTCTCTTCATCACCAAGTTCATG 59.571 38.462 0.00 0.00 0.00 3.07
8066 11325 2.162681 CAAAGACATCAGAACACCCCC 58.837 52.381 0.00 0.00 0.00 5.40
8080 11339 2.860136 GCTGAAACCAACAAGCAAAGAC 59.140 45.455 0.00 0.00 0.00 3.01
8081 11340 2.159114 GGCTGAAACCAACAAGCAAAGA 60.159 45.455 0.00 0.00 0.00 2.52
8105 11364 6.417044 GCATGAATAAGCTCATAGCAGTTTTG 59.583 38.462 0.00 0.00 45.56 2.44
8153 11412 3.861840 TGCCTTCATTAGTTCCTTCTCG 58.138 45.455 0.00 0.00 0.00 4.04
8322 11581 2.096069 CAGACAGCAGTGGATCAAAACG 60.096 50.000 0.00 0.00 0.00 3.60
8381 11640 8.035394 ACGTGATTTACATGATTTCTACAGAGT 58.965 33.333 0.00 0.00 38.72 3.24
8404 11663 2.932622 GCCTCAACTGATCACATCACGT 60.933 50.000 0.00 0.00 35.06 4.49
8447 11712 7.343574 TGCCAGAGGTGTAGAATACTTTACATA 59.656 37.037 0.00 0.00 43.54 2.29
8457 11722 4.225942 TCTCAAATGCCAGAGGTGTAGAAT 59.774 41.667 0.00 0.00 32.76 2.40
8533 11798 7.493971 CAGAGATTTCTCAAGGTAATACCACAG 59.506 40.741 12.54 4.29 45.21 3.66
8572 11837 6.011476 TGCAACATCGAGATGAAATTTGAA 57.989 33.333 18.76 5.59 41.20 2.69
8644 11909 9.377238 ACTCTTATATTAATTTACGGAGGGAGT 57.623 33.333 13.95 0.00 0.00 3.85
8645 11910 9.640963 CACTCTTATATTAATTTACGGAGGGAG 57.359 37.037 13.95 0.00 0.00 4.30
8646 11911 9.151177 ACACTCTTATATTAATTTACGGAGGGA 57.849 33.333 16.65 0.00 0.00 4.20
8647 11912 9.774413 AACACTCTTATATTAATTTACGGAGGG 57.226 33.333 11.91 11.91 0.00 4.30
8711 11976 8.924303 TGCTGTATTATACTCCATCTGTAAACT 58.076 33.333 3.92 0.00 0.00 2.66
8712 11977 8.979574 GTGCTGTATTATACTCCATCTGTAAAC 58.020 37.037 3.92 0.00 0.00 2.01
8713 11978 8.700973 TGTGCTGTATTATACTCCATCTGTAAA 58.299 33.333 3.92 0.00 0.00 2.01
8714 11979 8.141909 GTGTGCTGTATTATACTCCATCTGTAA 58.858 37.037 3.92 0.00 0.00 2.41
8715 11980 7.521585 CGTGTGCTGTATTATACTCCATCTGTA 60.522 40.741 3.92 0.00 0.00 2.74
8716 11981 6.516718 GTGTGCTGTATTATACTCCATCTGT 58.483 40.000 3.92 0.00 0.00 3.41
8717 11982 5.631096 CGTGTGCTGTATTATACTCCATCTG 59.369 44.000 3.92 0.00 0.00 2.90
8718 11983 5.535030 TCGTGTGCTGTATTATACTCCATCT 59.465 40.000 3.92 0.00 0.00 2.90
8719 11984 5.769367 TCGTGTGCTGTATTATACTCCATC 58.231 41.667 3.92 0.00 0.00 3.51
8720 11985 5.279006 CCTCGTGTGCTGTATTATACTCCAT 60.279 44.000 3.92 0.00 0.00 3.41
8721 11986 4.037565 CCTCGTGTGCTGTATTATACTCCA 59.962 45.833 3.92 0.00 0.00 3.86
8722 11987 4.037684 ACCTCGTGTGCTGTATTATACTCC 59.962 45.833 3.92 0.00 0.00 3.85
8723 11988 5.184340 ACCTCGTGTGCTGTATTATACTC 57.816 43.478 3.92 0.00 0.00 2.59
8724 11989 5.591472 TGTACCTCGTGTGCTGTATTATACT 59.409 40.000 3.92 0.00 0.00 2.12
8725 11990 5.824429 TGTACCTCGTGTGCTGTATTATAC 58.176 41.667 0.00 0.00 0.00 1.47
9136 12401 2.352421 CCCTGCTTCTGAATTGCACAAG 60.352 50.000 0.70 0.00 32.91 3.16
9184 12452 6.824305 ACTGTAATCAAGAAGTGGATTTGG 57.176 37.500 0.00 0.00 35.49 3.28
9191 12459 8.763049 TCATAGTGAACTGTAATCAAGAAGTG 57.237 34.615 0.00 0.00 0.00 3.16
9202 12470 8.414629 AGATGCAGATATCATAGTGAACTGTA 57.585 34.615 5.32 0.00 32.78 2.74
9227 12495 6.032094 CGAAGTCGAGGTAAAGCAAATAGTA 58.968 40.000 0.00 0.00 43.02 1.82
9236 12504 5.502220 GCTCTACTACGAAGTCGAGGTAAAG 60.502 48.000 7.87 7.13 42.83 1.85


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

AutoCloner maintained by Alex Coulton.