Multiple sequence alignment - TraesCS4D01G143400

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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 TraesCS4D01G143400 chr4D 100.000 7181 0 0 1 7181 130576480 130569300 0.000000e+00 13261.0
1 TraesCS4D01G143400 chr4D 85.308 633 93 0 4779 5411 164881771 164882403 0.000000e+00 654.0
2 TraesCS4D01G143400 chr4D 93.478 46 1 2 767 812 3300016 3299973 4.650000e-07 67.6
3 TraesCS4D01G143400 chr4A 97.385 4704 96 15 787 5471 436379656 436384351 0.000000e+00 7980.0
4 TraesCS4D01G143400 chr4A 96.950 787 24 0 5736 6522 436384677 436385463 0.000000e+00 1321.0
5 TraesCS4D01G143400 chr4A 84.472 805 91 12 1 795 436378696 436379476 0.000000e+00 763.0
6 TraesCS4D01G143400 chr4A 85.466 633 92 0 4779 5411 385772745 385773377 0.000000e+00 660.0
7 TraesCS4D01G143400 chr4A 95.897 390 15 1 6715 7104 436385973 436386361 1.310000e-176 630.0
8 TraesCS4D01G143400 chr4A 97.285 221 2 2 5469 5686 436384459 436384678 8.800000e-99 372.0
9 TraesCS4D01G143400 chr4A 72.596 624 135 29 1 602 21519345 21519954 9.580000e-39 172.0
10 TraesCS4D01G143400 chr4A 96.078 51 1 1 6565 6614 436385532 436385582 1.660000e-11 82.4
11 TraesCS4D01G143400 chr4A 97.143 35 1 0 6522 6556 436385548 436385582 7.780000e-05 60.2
12 TraesCS4D01G143400 chrUn 97.688 4411 82 14 2092 6491 55739235 55734834 0.000000e+00 7563.0
13 TraesCS4D01G143400 chrUn 97.869 1361 23 4 722 2077 55741411 55740052 0.000000e+00 2348.0
14 TraesCS4D01G143400 chrUn 91.477 704 51 9 28 723 55742192 55741490 0.000000e+00 959.0
15 TraesCS4D01G143400 chrUn 90.909 297 18 2 6722 7018 55732382 55732095 2.430000e-104 390.0
16 TraesCS4D01G143400 chrUn 86.207 203 16 9 6522 6719 55734717 55734522 7.300000e-50 209.0
17 TraesCS4D01G143400 chrUn 93.519 108 7 0 6543 6650 55734754 55734647 2.070000e-35 161.0
18 TraesCS4D01G143400 chrUn 95.745 94 4 0 7011 7104 55730692 55730599 1.250000e-32 152.0
19 TraesCS4D01G143400 chr4B 85.466 633 92 0 4779 5411 207102378 207103010 0.000000e+00 660.0
20 TraesCS4D01G143400 chr4B 73.121 439 94 21 3 425 399296593 399297023 1.260000e-27 135.0
21 TraesCS4D01G143400 chr5D 83.146 623 102 1 4779 5401 447875136 447874517 3.760000e-157 566.0
22 TraesCS4D01G143400 chr5D 86.957 92 9 3 1 91 269151547 269151636 4.580000e-17 100.0
23 TraesCS4D01G143400 chr5D 90.411 73 4 3 4574 4645 447875286 447875216 7.670000e-15 93.5
24 TraesCS4D01G143400 chr5D 93.617 47 1 1 767 813 531233536 531233580 1.290000e-07 69.4
25 TraesCS4D01G143400 chr5A 82.825 623 104 1 4779 5401 565743480 565742861 8.140000e-154 555.0
26 TraesCS4D01G143400 chr5A 87.671 73 6 3 4574 4645 654417026 654416956 1.660000e-11 82.4
27 TraesCS4D01G143400 chr5B 81.862 623 110 1 4779 5401 546810247 546809628 8.260000e-144 521.0
28 TraesCS4D01G143400 chr5B 90.000 50 1 3 767 816 364121296 364121251 2.160000e-05 62.1
29 TraesCS4D01G143400 chr7B 77.572 486 80 23 2 468 52295356 52295831 4.270000e-67 267.0
30 TraesCS4D01G143400 chr7B 70.717 642 146 37 1 617 666713562 666714186 9.850000e-19 106.0
31 TraesCS4D01G143400 chr3B 74.883 641 130 24 1 617 588487645 588487012 5.520000e-66 263.0
32 TraesCS4D01G143400 chr3B 81.369 263 47 2 4802 5063 570068718 570068457 5.640000e-51 213.0
33 TraesCS4D01G143400 chr3A 72.799 636 132 39 6 617 553018414 553019032 2.060000e-40 178.0
34 TraesCS4D01G143400 chr3A 85.882 85 11 1 7 91 554426590 554426507 9.920000e-14 89.8
35 TraesCS4D01G143400 chr2A 73.150 473 107 17 2 460 641937521 641937055 1.250000e-32 152.0
36 TraesCS4D01G143400 chr2A 89.041 73 5 3 4574 4645 611734591 611734521 3.570000e-13 87.9
37 TraesCS4D01G143400 chr1B 88.889 72 6 2 4575 4645 141681397 141681467 3.570000e-13 87.9
38 TraesCS4D01G143400 chr2B 87.671 73 6 3 4574 4645 62787031 62787101 1.660000e-11 82.4
39 TraesCS4D01G143400 chr2B 93.333 45 1 2 767 811 28212942 28212900 1.670000e-06 65.8
40 TraesCS4D01G143400 chr1A 93.478 46 1 1 767 812 124018848 124018891 4.650000e-07 67.6
41 TraesCS4D01G143400 chr1A 92.500 40 2 1 1009 1047 180468014 180467975 1.000000e-03 56.5
42 TraesCS4D01G143400 chr6D 91.489 47 2 2 767 813 468348633 468348677 6.010000e-06 63.9


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 TraesCS4D01G143400 chr4D 130569300 130576480 7180 True 13261.000000 13261 100.000000 1 7181 1 chr4D.!!$R2 7180
1 TraesCS4D01G143400 chr4D 164881771 164882403 632 False 654.000000 654 85.308000 4779 5411 1 chr4D.!!$F1 632
2 TraesCS4D01G143400 chr4A 436378696 436386361 7665 False 1601.228571 7980 95.030000 1 7104 7 chr4A.!!$F3 7103
3 TraesCS4D01G143400 chr4A 385772745 385773377 632 False 660.000000 660 85.466000 4779 5411 1 chr4A.!!$F2 632
4 TraesCS4D01G143400 chrUn 55730599 55742192 11593 True 1683.142857 7563 93.344857 28 7104 7 chrUn.!!$R1 7076
5 TraesCS4D01G143400 chr4B 207102378 207103010 632 False 660.000000 660 85.466000 4779 5411 1 chr4B.!!$F1 632
6 TraesCS4D01G143400 chr5D 447874517 447875286 769 True 329.750000 566 86.778500 4574 5401 2 chr5D.!!$R1 827
7 TraesCS4D01G143400 chr5A 565742861 565743480 619 True 555.000000 555 82.825000 4779 5401 1 chr5A.!!$R1 622
8 TraesCS4D01G143400 chr5B 546809628 546810247 619 True 521.000000 521 81.862000 4779 5401 1 chr5B.!!$R2 622
9 TraesCS4D01G143400 chr3B 588487012 588487645 633 True 263.000000 263 74.883000 1 617 1 chr3B.!!$R2 616

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
748 860 1.025041 GGGAAAAGCATCACCCGATC 58.975 55.000 0.00 0.00 32.73 3.69 F
1086 1391 1.129917 CCTGATCTCCCTGCTGTCAT 58.870 55.000 0.00 0.00 0.00 3.06 F
2040 2349 1.611006 CGAGACCGTCCTGATGATCAT 59.389 52.381 8.25 8.25 0.00 2.45 F
2718 3831 0.244721 AAGAAGCGGCAAATCCAAGC 59.755 50.000 1.45 0.00 34.01 4.01 F
3180 4298 1.204941 CCGTACTTCCTCAGTTCCCTG 59.795 57.143 0.00 0.00 40.25 4.45 F
4056 5180 0.582005 GTGCTCCGGTTTGATATCGC 59.418 55.000 0.00 0.00 0.00 4.58 F
5739 6976 1.207570 CTGATCTGCTGCTGGACTCTT 59.792 52.381 6.69 0.00 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 2349 0.388520 CACGGCTTCTGTGACGATCA 60.389 55.000 5.79 0.0 39.73 2.92 R
2331 3443 1.287191 GAGAGCGATGCCTGCGATA 59.713 57.895 0.00 0.0 37.44 2.92 R
3180 4298 1.756538 CATACTTGGGGTTGGAATGGC 59.243 52.381 0.00 0.0 0.00 4.40 R
4056 5180 2.093288 TGCTAGCTGAAGATGGACAAGG 60.093 50.000 17.23 0.0 0.00 3.61 R
5504 6741 9.744468 ACAAGTTTCTATACAAAAACCACATTC 57.256 29.630 0.00 0.0 36.29 2.67 R
6020 7257 1.452651 ACCTGCAATGGGATGCTCG 60.453 57.895 0.00 0.0 46.54 5.03 R
7123 12260 0.107410 TTAAGGGGGCTGCGTACATG 60.107 55.000 0.00 0.0 0.00 3.21 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
94 96 4.065321 AGAATATCTCTCCCAAGCAACG 57.935 45.455 0.00 0.00 0.00 4.10
111 113 3.724374 CAACGTACAAACTCTCTCCCAA 58.276 45.455 0.00 0.00 0.00 4.12
165 167 5.297029 GGAGCTTCGTAATCTTAAAGCCAAT 59.703 40.000 2.56 0.00 44.01 3.16
211 232 4.944619 TGCACACATTTTCCAATTGGTA 57.055 36.364 23.76 12.33 36.34 3.25
229 250 2.796593 GGTATGTTATACGACAACCGGC 59.203 50.000 0.00 0.00 43.93 6.13
259 280 6.600822 CCATTCTTCTGCCTTATCTTTCAGAA 59.399 38.462 0.00 0.00 41.57 3.02
290 313 8.519799 TTGAAGTCTCACTAAAACAAATTCCT 57.480 30.769 0.00 0.00 0.00 3.36
322 345 8.360390 ACATCTTTGATTTTAAAAGTCCCAGAC 58.640 33.333 6.79 0.00 36.29 3.51
323 346 6.966021 TCTTTGATTTTAAAAGTCCCAGACG 58.034 36.000 6.79 0.00 37.67 4.18
524 552 6.499172 TCTGATGTCTGAGTAATCGACATTC 58.501 40.000 22.11 17.34 45.47 2.67
658 689 2.076863 CCGACTCCGCTTCATTTTCTT 58.923 47.619 0.00 0.00 0.00 2.52
660 691 3.058224 CCGACTCCGCTTCATTTTCTTTT 60.058 43.478 0.00 0.00 0.00 2.27
662 693 4.319477 CGACTCCGCTTCATTTTCTTTTCA 60.319 41.667 0.00 0.00 0.00 2.69
690 721 8.044060 ACAATCCATATACAAATTATCCGCTG 57.956 34.615 0.00 0.00 0.00 5.18
748 860 1.025041 GGGAAAAGCATCACCCGATC 58.975 55.000 0.00 0.00 32.73 3.69
749 861 1.025041 GGAAAAGCATCACCCGATCC 58.975 55.000 0.00 0.00 0.00 3.36
974 1276 2.275418 CCGGATCCCCAAACCCTG 59.725 66.667 6.06 0.00 0.00 4.45
1086 1391 1.129917 CCTGATCTCCCTGCTGTCAT 58.870 55.000 0.00 0.00 0.00 3.06
1149 1454 3.528370 CCTCCGTCCCGCTCGATT 61.528 66.667 0.00 0.00 0.00 3.34
1221 1526 1.795768 TGTGCTCGTTTGATCTGGTC 58.204 50.000 0.00 0.00 0.00 4.02
1579 1886 7.425224 AGGTGTGCATCTATAGAGTTACTTT 57.575 36.000 8.70 0.00 0.00 2.66
1628 1935 5.159209 CCGTCCAATATAGGTTAGCGTTAG 58.841 45.833 0.00 0.00 0.00 2.34
1730 2037 6.013379 TCTGGATGTCTTGTTTATGTTCTCCT 60.013 38.462 0.00 0.00 0.00 3.69
1731 2038 6.542821 TGGATGTCTTGTTTATGTTCTCCTT 58.457 36.000 0.00 0.00 0.00 3.36
1745 2052 5.728471 TGTTCTCCTTTTCAGATGCTCTAG 58.272 41.667 0.00 0.00 0.00 2.43
1858 2167 4.482025 AGGGATTGTCAAAATCCAGGGATA 59.518 41.667 8.99 0.00 46.22 2.59
2040 2349 1.611006 CGAGACCGTCCTGATGATCAT 59.389 52.381 8.25 8.25 0.00 2.45
2078 3011 5.509163 GCCGTGATTCTGAAAGGTATAGCTA 60.509 44.000 4.57 0.00 0.00 3.32
2135 3246 3.391965 TGTTTTGTTGCAATGATGGCTC 58.608 40.909 0.59 0.00 0.00 4.70
2226 3337 7.716998 ACCTAACATGTCTTATTCATGGTGATC 59.283 37.037 0.00 0.00 42.23 2.92
2227 3338 6.609237 AACATGTCTTATTCATGGTGATCG 57.391 37.500 0.00 0.00 44.57 3.69
2228 3339 5.674525 ACATGTCTTATTCATGGTGATCGT 58.325 37.500 10.01 0.00 44.57 3.73
2331 3443 1.175983 GGACCGCGAGAGAGATGGAT 61.176 60.000 8.23 0.00 0.00 3.41
2715 3828 1.922135 GCGAAGAAGCGGCAAATCCA 61.922 55.000 1.45 0.00 34.01 3.41
2718 3831 0.244721 AAGAAGCGGCAAATCCAAGC 59.755 50.000 1.45 0.00 34.01 4.01
2791 3904 7.040892 ACACCGCGTCTATAGATCTTTATGTAA 60.041 37.037 5.57 0.00 0.00 2.41
3024 4142 2.614779 CATGTACCACTCAGCACTCAG 58.385 52.381 0.00 0.00 0.00 3.35
3180 4298 1.204941 CCGTACTTCCTCAGTTCCCTG 59.795 57.143 0.00 0.00 40.25 4.45
3207 4325 2.092212 CCAACCCCAAGTATGCTCTCAT 60.092 50.000 0.00 0.00 36.73 2.90
3230 4348 5.646606 TCAACCAAGTTTTTCTTCTTTCCG 58.353 37.500 0.00 0.00 33.63 4.30
3253 4371 6.529829 CCGTTCTTCAGTTTTGTTGATTTCAA 59.470 34.615 0.00 0.00 0.00 2.69
3266 4384 8.830201 TTGTTGATTTCAATTGGGACTTATTG 57.170 30.769 5.42 0.00 38.24 1.90
3387 4505 3.260380 CCAGCCATTTATTTCCACCACAA 59.740 43.478 0.00 0.00 0.00 3.33
3400 4518 2.742053 CCACCACAATGTACTACTGCAC 59.258 50.000 0.00 0.00 0.00 4.57
3510 4628 4.277672 GTGCTGTTGGATATCATTGAGCAT 59.722 41.667 16.88 0.00 35.28 3.79
3620 4738 8.169268 GCATCTGTAACTACAATACAAACACTC 58.831 37.037 0.00 0.00 35.50 3.51
3720 4838 6.210584 TGTTCTAGTGACAACACCATATGAGA 59.789 38.462 3.65 0.00 46.99 3.27
3732 4852 6.060136 ACACCATATGAGATGTTGGAAGATG 58.940 40.000 3.65 0.00 33.36 2.90
3825 4948 3.572642 TCCAGTCGAGATGGCCTTATAA 58.427 45.455 3.32 0.00 37.76 0.98
3867 4990 7.026562 TGATGCAAATAAGTTGTATGTTTCCG 58.973 34.615 0.00 0.00 42.00 4.30
3884 5007 8.920509 ATGTTTCCGTTTTATTATTACTTGGC 57.079 30.769 0.00 0.00 0.00 4.52
4056 5180 0.582005 GTGCTCCGGTTTGATATCGC 59.418 55.000 0.00 0.00 0.00 4.58
5445 6569 3.922171 AATTGTTTTCCTGTGGCCAAA 57.078 38.095 7.24 0.00 0.00 3.28
5504 6741 3.683822 GCTGTTCTTGGATTCTGACTCAG 59.316 47.826 0.00 0.00 0.00 3.35
5687 6924 2.093973 CCGTCAACTTCTCACCTGCTAT 60.094 50.000 0.00 0.00 0.00 2.97
5712 6949 5.431765 TCCTCCTCTTTGAAGCATACATTC 58.568 41.667 0.00 0.00 0.00 2.67
5739 6976 1.207570 CTGATCTGCTGCTGGACTCTT 59.792 52.381 6.69 0.00 0.00 2.85
5772 7009 9.123709 TCTTTTTGTTATGCGTATGTTTTCATC 57.876 29.630 0.00 0.00 41.25 2.92
5829 7066 7.281999 GCCTTGATCTATACTTCTGCTTTTCTT 59.718 37.037 0.00 0.00 0.00 2.52
5910 7147 3.221771 CTTGGTGAAAGTTGTCATCCCA 58.778 45.455 0.00 0.00 0.00 4.37
5913 7150 2.218603 GTGAAAGTTGTCATCCCACGT 58.781 47.619 0.00 0.00 0.00 4.49
6012 7249 9.339492 GAATAATTCTGTCAGAGAAAAGCTTTG 57.661 33.333 13.54 0.00 44.11 2.77
6020 7257 3.979495 CAGAGAAAAGCTTTGTGATGCAC 59.021 43.478 13.54 0.00 34.56 4.57
6229 7466 4.034048 AGTGCTTTGTGTAGTTTGTTCGAG 59.966 41.667 0.00 0.00 0.00 4.04
6444 7681 7.389884 GCCAGTAACTTTACCTTTAGCTTTACT 59.610 37.037 0.00 0.00 34.19 2.24
6491 7728 4.278170 TCTTGAACAACTTGGCATGGTAAG 59.722 41.667 5.31 0.00 0.00 2.34
6501 7738 5.665812 ACTTGGCATGGTAAGTAAGATCCTA 59.334 40.000 5.31 0.00 35.50 2.94
6503 7740 7.512746 ACTTGGCATGGTAAGTAAGATCCTATA 59.487 37.037 5.31 0.00 35.50 1.31
6540 7811 7.287810 ACAGAAGTAGAAACCCAATAAGTTGT 58.712 34.615 0.00 0.00 33.36 3.32
6541 7812 7.228706 ACAGAAGTAGAAACCCAATAAGTTGTG 59.771 37.037 0.00 0.00 33.36 3.33
6542 7813 6.715264 AGAAGTAGAAACCCAATAAGTTGTGG 59.285 38.462 1.29 1.29 33.36 4.17
6544 7815 6.370453 AGTAGAAACCCAATAAGTTGTGGTT 58.630 36.000 6.66 7.69 44.05 3.67
6545 7816 5.529581 AGAAACCCAATAAGTTGTGGTTG 57.470 39.130 11.89 0.00 42.71 3.77
6608 7906 7.790782 ATCCCAATAAGTTGTGGTTGTTATT 57.209 32.000 6.66 0.00 33.36 1.40
6678 8148 7.022384 CGGACGGAGAGTATTTCTTATATCAC 58.978 42.308 0.00 0.00 35.87 3.06
6848 10575 1.887854 CATGCACACCCAACAATGAGA 59.112 47.619 0.00 0.00 0.00 3.27
6925 10652 3.153919 TCCAATTGGACTGGCTTAACAC 58.846 45.455 23.63 0.00 39.78 3.32
6929 10656 0.400213 TGGACTGGCTTAACACTGGG 59.600 55.000 0.00 0.00 0.00 4.45
6964 10691 1.971167 TCAAACATCCACTGGGCGC 60.971 57.895 0.00 0.00 0.00 6.53
7104 12241 9.967346 CTCGATCTTCTTAATGTAAACCTCATA 57.033 33.333 0.00 0.00 0.00 2.15
7116 12253 9.747898 AATGTAAACCTCATAATGTAAACCTCA 57.252 29.630 0.00 0.00 0.00 3.86
7117 12254 9.920946 ATGTAAACCTCATAATGTAAACCTCAT 57.079 29.630 0.00 0.00 0.00 2.90
7118 12255 9.747898 TGTAAACCTCATAATGTAAACCTCATT 57.252 29.630 0.00 0.00 38.72 2.57
7121 12258 8.650143 AACCTCATAATGTAAACCTCATTTGT 57.350 30.769 0.00 0.00 36.92 2.83
7122 12259 8.650143 ACCTCATAATGTAAACCTCATTTGTT 57.350 30.769 0.00 0.00 36.92 2.83
7123 12260 8.739972 ACCTCATAATGTAAACCTCATTTGTTC 58.260 33.333 0.00 0.00 36.92 3.18
7124 12261 8.739039 CCTCATAATGTAAACCTCATTTGTTCA 58.261 33.333 0.00 0.00 36.92 3.18
7127 12264 9.859427 CATAATGTAAACCTCATTTGTTCATGT 57.141 29.630 0.00 0.00 36.92 3.21
7130 12267 6.893759 TGTAAACCTCATTTGTTCATGTACG 58.106 36.000 0.00 0.00 0.00 3.67
7131 12268 4.419522 AACCTCATTTGTTCATGTACGC 57.580 40.909 0.00 0.00 0.00 4.42
7132 12269 3.407698 ACCTCATTTGTTCATGTACGCA 58.592 40.909 0.00 0.00 0.00 5.24
7133 12270 3.436704 ACCTCATTTGTTCATGTACGCAG 59.563 43.478 0.00 0.00 0.00 5.18
7134 12271 3.419915 CTCATTTGTTCATGTACGCAGC 58.580 45.455 0.00 0.00 0.00 5.25
7135 12272 2.161410 TCATTTGTTCATGTACGCAGCC 59.839 45.455 0.00 0.00 0.00 4.85
7136 12273 0.878416 TTTGTTCATGTACGCAGCCC 59.122 50.000 0.00 0.00 0.00 5.19
7137 12274 0.958382 TTGTTCATGTACGCAGCCCC 60.958 55.000 0.00 0.00 0.00 5.80
7138 12275 2.112815 GTTCATGTACGCAGCCCCC 61.113 63.158 0.00 0.00 0.00 5.40
7139 12276 2.297895 TTCATGTACGCAGCCCCCT 61.298 57.895 0.00 0.00 0.00 4.79
7140 12277 1.847798 TTCATGTACGCAGCCCCCTT 61.848 55.000 0.00 0.00 0.00 3.95
7141 12278 0.978667 TCATGTACGCAGCCCCCTTA 60.979 55.000 0.00 0.00 0.00 2.69
7142 12279 0.107410 CATGTACGCAGCCCCCTTAA 60.107 55.000 0.00 0.00 0.00 1.85
7143 12280 0.621609 ATGTACGCAGCCCCCTTAAA 59.378 50.000 0.00 0.00 0.00 1.52
7144 12281 0.621609 TGTACGCAGCCCCCTTAAAT 59.378 50.000 0.00 0.00 0.00 1.40
7145 12282 1.306148 GTACGCAGCCCCCTTAAATC 58.694 55.000 0.00 0.00 0.00 2.17
7146 12283 0.181824 TACGCAGCCCCCTTAAATCC 59.818 55.000 0.00 0.00 0.00 3.01
7147 12284 1.077068 CGCAGCCCCCTTAAATCCA 60.077 57.895 0.00 0.00 0.00 3.41
7148 12285 1.384222 CGCAGCCCCCTTAAATCCAC 61.384 60.000 0.00 0.00 0.00 4.02
7149 12286 0.324275 GCAGCCCCCTTAAATCCACA 60.324 55.000 0.00 0.00 0.00 4.17
7150 12287 1.689258 GCAGCCCCCTTAAATCCACAT 60.689 52.381 0.00 0.00 0.00 3.21
7151 12288 2.310538 CAGCCCCCTTAAATCCACATC 58.689 52.381 0.00 0.00 0.00 3.06
7152 12289 2.091665 CAGCCCCCTTAAATCCACATCT 60.092 50.000 0.00 0.00 0.00 2.90
7153 12290 2.091665 AGCCCCCTTAAATCCACATCTG 60.092 50.000 0.00 0.00 0.00 2.90
7154 12291 2.310538 CCCCCTTAAATCCACATCTGC 58.689 52.381 0.00 0.00 0.00 4.26
7155 12292 2.358090 CCCCCTTAAATCCACATCTGCA 60.358 50.000 0.00 0.00 0.00 4.41
7156 12293 3.569491 CCCCTTAAATCCACATCTGCAT 58.431 45.455 0.00 0.00 0.00 3.96
7157 12294 3.571401 CCCCTTAAATCCACATCTGCATC 59.429 47.826 0.00 0.00 0.00 3.91
7158 12295 3.251729 CCCTTAAATCCACATCTGCATCG 59.748 47.826 0.00 0.00 0.00 3.84
7159 12296 3.304257 CCTTAAATCCACATCTGCATCGC 60.304 47.826 0.00 0.00 0.00 4.58
7160 12297 1.027357 AAATCCACATCTGCATCGCC 58.973 50.000 0.00 0.00 0.00 5.54
7161 12298 0.820891 AATCCACATCTGCATCGCCC 60.821 55.000 0.00 0.00 0.00 6.13
7162 12299 1.703014 ATCCACATCTGCATCGCCCT 61.703 55.000 0.00 0.00 0.00 5.19
7163 12300 1.452651 CCACATCTGCATCGCCCTT 60.453 57.895 0.00 0.00 0.00 3.95
7164 12301 0.179048 CCACATCTGCATCGCCCTTA 60.179 55.000 0.00 0.00 0.00 2.69
7165 12302 1.667236 CACATCTGCATCGCCCTTAA 58.333 50.000 0.00 0.00 0.00 1.85
7166 12303 2.016318 CACATCTGCATCGCCCTTAAA 58.984 47.619 0.00 0.00 0.00 1.52
7167 12304 2.620115 CACATCTGCATCGCCCTTAAAT 59.380 45.455 0.00 0.00 0.00 1.40
7168 12305 2.880890 ACATCTGCATCGCCCTTAAATC 59.119 45.455 0.00 0.00 0.00 2.17
7169 12306 3.144506 CATCTGCATCGCCCTTAAATCT 58.855 45.455 0.00 0.00 0.00 2.40
7170 12307 4.202357 ACATCTGCATCGCCCTTAAATCTA 60.202 41.667 0.00 0.00 0.00 1.98
7171 12308 4.623932 TCTGCATCGCCCTTAAATCTAT 57.376 40.909 0.00 0.00 0.00 1.98
7172 12309 5.738619 TCTGCATCGCCCTTAAATCTATA 57.261 39.130 0.00 0.00 0.00 1.31
7173 12310 6.299805 TCTGCATCGCCCTTAAATCTATAT 57.700 37.500 0.00 0.00 0.00 0.86
7174 12311 7.418337 TCTGCATCGCCCTTAAATCTATATA 57.582 36.000 0.00 0.00 0.00 0.86
7175 12312 7.265673 TCTGCATCGCCCTTAAATCTATATAC 58.734 38.462 0.00 0.00 0.00 1.47
7176 12313 6.941857 TGCATCGCCCTTAAATCTATATACA 58.058 36.000 0.00 0.00 0.00 2.29
7177 12314 7.390823 TGCATCGCCCTTAAATCTATATACAA 58.609 34.615 0.00 0.00 0.00 2.41
7178 12315 7.880713 TGCATCGCCCTTAAATCTATATACAAA 59.119 33.333 0.00 0.00 0.00 2.83
7179 12316 8.726988 GCATCGCCCTTAAATCTATATACAAAA 58.273 33.333 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 37 4.782019 TGCCCTAACTACATTTTTGCTG 57.218 40.909 0.00 0.00 0.00 4.41
43 45 9.474313 TTTATGAAATCTTTGCCCTAACTACAT 57.526 29.630 0.00 0.00 0.00 2.29
94 96 6.487689 CAAGAATTGGGAGAGAGTTTGTAC 57.512 41.667 0.00 0.00 43.94 2.90
165 167 8.906867 CAAAGAGATTTATGGCTAAATTCCTCA 58.093 33.333 13.81 0.00 37.61 3.86
211 232 2.973694 AGCCGGTTGTCGTATAACAT 57.026 45.000 1.90 0.00 37.11 2.71
229 250 8.688747 AAAGATAAGGCAGAAGAATGGAATAG 57.311 34.615 0.00 0.00 0.00 1.73
259 280 9.974980 TTTGTTTTAGTGAGACTTCAAGTTTTT 57.025 25.926 0.00 0.00 34.49 1.94
290 313 9.950680 GACTTTTAAAATCAAAGATGTGTCTCA 57.049 29.630 0.09 0.00 35.54 3.27
352 377 9.192642 GTCTTTATAGACTAAAGAGGAAGACCT 57.807 37.037 6.12 0.00 46.76 3.85
603 633 6.018994 GGACTTTGACGCGATTATATTTCACT 60.019 38.462 15.93 0.00 0.00 3.41
662 693 9.691362 GCGGATAATTTGTATATGGATTGTTTT 57.309 29.630 0.00 0.00 0.00 2.43
748 860 7.095695 ACCAATTGTAAACGAATTAGATGGG 57.904 36.000 4.43 0.00 0.00 4.00
749 861 9.878599 GATACCAATTGTAAACGAATTAGATGG 57.121 33.333 4.43 0.00 31.94 3.51
811 1112 4.765856 AGTACGGATGTAAGCGGATTAGAT 59.234 41.667 0.00 0.00 30.33 1.98
812 1113 4.139786 AGTACGGATGTAAGCGGATTAGA 58.860 43.478 0.00 0.00 30.94 2.10
813 1114 4.500603 AGTACGGATGTAAGCGGATTAG 57.499 45.455 0.00 0.00 30.94 1.73
1149 1454 2.187958 AGTACTGCTAAGCACCCATGA 58.812 47.619 0.00 0.00 33.79 3.07
1221 1526 2.030457 CGGGCTGTTGAATTAACGCTAG 59.970 50.000 0.00 0.00 42.34 3.42
1579 1886 4.260985 CATCAACCAACAGGTGTATGCTA 58.739 43.478 0.00 0.00 35.32 3.49
1628 1935 0.681175 ATGACCAGGTTGCTTTTGGC 59.319 50.000 0.00 0.00 42.22 4.52
1730 2037 7.147655 AGGCACTATAACTAGAGCATCTGAAAA 60.148 37.037 0.00 0.00 43.01 2.29
1731 2038 6.325028 AGGCACTATAACTAGAGCATCTGAAA 59.675 38.462 0.00 0.00 43.01 2.69
1745 2052 2.678336 GACACAAGCCAGGCACTATAAC 59.322 50.000 15.80 0.00 36.02 1.89
1858 2167 5.878406 TCCTTGTCTTTTTCTCTGTCTCT 57.122 39.130 0.00 0.00 0.00 3.10
2040 2349 0.388520 CACGGCTTCTGTGACGATCA 60.389 55.000 5.79 0.00 39.73 2.92
2135 3246 5.947228 AACACAAGTCACATGACCATAAG 57.053 39.130 8.41 0.00 45.85 1.73
2169 3280 5.252969 GCACTGGCAATCATATTCAAAGA 57.747 39.130 0.00 0.00 40.72 2.52
2226 3337 5.594724 AAATGTGCATTTTGGAAATCACG 57.405 34.783 4.48 0.00 37.74 4.35
2331 3443 1.287191 GAGAGCGATGCCTGCGATA 59.713 57.895 0.00 0.00 37.44 2.92
2639 3752 6.909909 TGGTAGTGCAGATATAGATGTAACG 58.090 40.000 0.00 0.00 0.00 3.18
2791 3904 4.740268 CAAGCATTGCACTGTATTGACAT 58.260 39.130 11.91 0.00 40.39 3.06
3103 4221 2.476821 GCTTGCTGCTTCAACACAATT 58.523 42.857 0.00 0.00 38.95 2.32
3180 4298 1.756538 CATACTTGGGGTTGGAATGGC 59.243 52.381 0.00 0.00 0.00 4.40
3207 4325 5.184287 ACGGAAAGAAGAAAAACTTGGTTGA 59.816 36.000 0.00 0.00 39.13 3.18
3230 4348 9.693157 CAATTGAAATCAACAAAACTGAAGAAC 57.307 29.630 0.00 0.00 38.86 3.01
3253 4371 9.747898 TGTTCTGTAATTACAATAAGTCCCAAT 57.252 29.630 18.55 0.00 35.50 3.16
3387 4505 6.106673 GGTTGTTCATAGTGCAGTAGTACAT 58.893 40.000 7.45 0.00 32.20 2.29
3400 4518 2.985896 ACCACATCCGGTTGTTCATAG 58.014 47.619 15.58 4.37 34.91 2.23
3510 4628 9.770097 CTAGACAAAGGATATAAAAGCATCAGA 57.230 33.333 0.00 0.00 0.00 3.27
3620 4738 5.163913 CCACGAAGCATCTTCAACTCTTTAG 60.164 44.000 7.27 0.00 0.00 1.85
3696 4814 6.631016 TCTCATATGGTGTTGTCACTAGAAC 58.369 40.000 2.13 0.00 43.41 3.01
3720 4838 6.252599 TCTAATACCAGCATCTTCCAACAT 57.747 37.500 0.00 0.00 0.00 2.71
3732 4852 2.679082 TCTCCCACCTCTAATACCAGC 58.321 52.381 0.00 0.00 0.00 4.85
3825 4948 6.721704 TGCATCAGAAGATACTATCACACT 57.278 37.500 0.00 0.00 31.88 3.55
3884 5007 6.587608 AGAAAGTTTTGCTCAGTTTTCAGTTG 59.412 34.615 0.00 0.00 0.00 3.16
4056 5180 2.093288 TGCTAGCTGAAGATGGACAAGG 60.093 50.000 17.23 0.00 0.00 3.61
5504 6741 9.744468 ACAAGTTTCTATACAAAAACCACATTC 57.256 29.630 0.00 0.00 36.29 2.67
5687 6924 5.241403 TGTATGCTTCAAAGAGGAGGAAA 57.759 39.130 0.00 0.00 0.00 3.13
5739 6976 5.508200 ACGCATAACAAAAAGAAACCTCA 57.492 34.783 0.00 0.00 0.00 3.86
5829 7066 7.624549 AGGAATGACTAACAGAATCAGCTAAA 58.375 34.615 0.00 0.00 0.00 1.85
5869 7106 2.092267 AGTTACCTGATGGATGCATGCA 60.092 45.455 25.04 25.04 37.04 3.96
5998 7235 3.979495 GTGCATCACAAAGCTTTTCTCTG 59.021 43.478 9.53 6.59 34.08 3.35
5999 7236 3.304257 CGTGCATCACAAAGCTTTTCTCT 60.304 43.478 9.53 0.00 33.40 3.10
6020 7257 1.452651 ACCTGCAATGGGATGCTCG 60.453 57.895 0.00 0.00 46.54 5.03
6229 7466 3.314357 AGAAGGGAAAACGTTGCTGTAAC 59.686 43.478 0.00 0.00 35.90 2.50
6444 7681 3.928727 CTCTTTTGAGCCATTTGCAGA 57.071 42.857 0.00 0.00 44.83 4.26
6527 7798 6.311735 AGATAACAACCACAACTTATTGGGT 58.688 36.000 0.00 0.00 37.55 4.51
6540 7811 4.603131 ACGGAGGTAGTAGATAACAACCA 58.397 43.478 0.00 0.00 0.00 3.67
6541 7812 4.886489 AGACGGAGGTAGTAGATAACAACC 59.114 45.833 0.00 0.00 0.00 3.77
6542 7813 6.989169 TCTAGACGGAGGTAGTAGATAACAAC 59.011 42.308 0.00 0.00 0.00 3.32
6544 7815 6.737720 TCTAGACGGAGGTAGTAGATAACA 57.262 41.667 0.00 0.00 0.00 2.41
6545 7816 7.385267 TGATCTAGACGGAGGTAGTAGATAAC 58.615 42.308 0.00 0.00 34.75 1.89
6557 7828 8.951243 TCTACAAATGATATGATCTAGACGGAG 58.049 37.037 0.00 0.00 0.00 4.63
6608 7906 6.159928 TGAGTGAATCTAGAGGGAGGTAGTAA 59.840 42.308 0.00 0.00 0.00 2.24
6773 10500 6.381481 TCTTACAATGCAAGCATCATAAGG 57.619 37.500 23.76 13.74 36.04 2.69
6838 10565 5.010922 TGGTCCCAGATTTTTCTCATTGTTG 59.989 40.000 0.00 0.00 0.00 3.33
6848 10575 8.112183 GGATGATATAGATGGTCCCAGATTTTT 58.888 37.037 0.00 0.00 0.00 1.94
6925 10652 0.107703 TAGCCAATCTTCACGCCCAG 60.108 55.000 0.00 0.00 0.00 4.45
6929 10656 2.010145 TGACTAGCCAATCTTCACGC 57.990 50.000 0.00 0.00 0.00 5.34
6933 10660 4.943705 TGGATGTTTGACTAGCCAATCTTC 59.056 41.667 0.00 0.40 0.00 2.87
7104 12241 8.020819 CGTACATGAACAAATGAGGTTTACATT 58.979 33.333 0.00 0.00 39.25 2.71
7105 12242 7.526608 CGTACATGAACAAATGAGGTTTACAT 58.473 34.615 0.00 0.00 0.00 2.29
7106 12243 6.566942 GCGTACATGAACAAATGAGGTTTACA 60.567 38.462 0.00 0.00 0.00 2.41
7107 12244 5.793457 GCGTACATGAACAAATGAGGTTTAC 59.207 40.000 0.00 0.00 0.00 2.01
7108 12245 5.470437 TGCGTACATGAACAAATGAGGTTTA 59.530 36.000 0.00 0.00 0.00 2.01
7109 12246 4.277174 TGCGTACATGAACAAATGAGGTTT 59.723 37.500 0.00 0.00 0.00 3.27
7110 12247 3.818210 TGCGTACATGAACAAATGAGGTT 59.182 39.130 0.00 0.00 0.00 3.50
7111 12248 3.407698 TGCGTACATGAACAAATGAGGT 58.592 40.909 0.00 0.00 0.00 3.85
7112 12249 3.728864 GCTGCGTACATGAACAAATGAGG 60.729 47.826 0.00 0.00 0.00 3.86
7113 12250 3.419915 GCTGCGTACATGAACAAATGAG 58.580 45.455 0.00 0.00 0.00 2.90
7114 12251 2.161410 GGCTGCGTACATGAACAAATGA 59.839 45.455 0.00 0.00 0.00 2.57
7115 12252 2.518949 GGCTGCGTACATGAACAAATG 58.481 47.619 0.00 0.00 0.00 2.32
7116 12253 1.472480 GGGCTGCGTACATGAACAAAT 59.528 47.619 0.00 0.00 0.00 2.32
7117 12254 0.878416 GGGCTGCGTACATGAACAAA 59.122 50.000 0.00 0.00 0.00 2.83
7118 12255 0.958382 GGGGCTGCGTACATGAACAA 60.958 55.000 0.00 0.00 0.00 2.83
7119 12256 1.376683 GGGGCTGCGTACATGAACA 60.377 57.895 0.00 0.00 0.00 3.18
7120 12257 2.112815 GGGGGCTGCGTACATGAAC 61.113 63.158 0.00 0.00 0.00 3.18
7121 12258 1.847798 AAGGGGGCTGCGTACATGAA 61.848 55.000 0.00 0.00 0.00 2.57
7122 12259 0.978667 TAAGGGGGCTGCGTACATGA 60.979 55.000 0.00 0.00 0.00 3.07
7123 12260 0.107410 TTAAGGGGGCTGCGTACATG 60.107 55.000 0.00 0.00 0.00 3.21
7124 12261 0.621609 TTTAAGGGGGCTGCGTACAT 59.378 50.000 0.00 0.00 0.00 2.29
7125 12262 0.621609 ATTTAAGGGGGCTGCGTACA 59.378 50.000 0.00 0.00 0.00 2.90
7126 12263 1.306148 GATTTAAGGGGGCTGCGTAC 58.694 55.000 0.00 0.00 0.00 3.67
7127 12264 0.181824 GGATTTAAGGGGGCTGCGTA 59.818 55.000 0.00 0.00 0.00 4.42
7128 12265 1.076995 GGATTTAAGGGGGCTGCGT 60.077 57.895 0.00 0.00 0.00 5.24
7129 12266 1.077068 TGGATTTAAGGGGGCTGCG 60.077 57.895 0.00 0.00 0.00 5.18
7130 12267 0.324275 TGTGGATTTAAGGGGGCTGC 60.324 55.000 0.00 0.00 0.00 5.25
7131 12268 2.091665 AGATGTGGATTTAAGGGGGCTG 60.092 50.000 0.00 0.00 0.00 4.85
7132 12269 2.091665 CAGATGTGGATTTAAGGGGGCT 60.092 50.000 0.00 0.00 0.00 5.19
7133 12270 2.310538 CAGATGTGGATTTAAGGGGGC 58.689 52.381 0.00 0.00 0.00 5.80
7134 12271 2.310538 GCAGATGTGGATTTAAGGGGG 58.689 52.381 0.00 0.00 0.00 5.40
7135 12272 3.017048 TGCAGATGTGGATTTAAGGGG 57.983 47.619 0.00 0.00 0.00 4.79
7136 12273 3.251729 CGATGCAGATGTGGATTTAAGGG 59.748 47.826 0.00 0.00 34.30 3.95
7137 12274 3.304257 GCGATGCAGATGTGGATTTAAGG 60.304 47.826 0.00 0.00 34.30 2.69
7138 12275 3.304257 GGCGATGCAGATGTGGATTTAAG 60.304 47.826 0.00 0.00 34.30 1.85
7139 12276 2.618241 GGCGATGCAGATGTGGATTTAA 59.382 45.455 0.00 0.00 34.30 1.52
7140 12277 2.221169 GGCGATGCAGATGTGGATTTA 58.779 47.619 0.00 0.00 34.30 1.40
7141 12278 1.027357 GGCGATGCAGATGTGGATTT 58.973 50.000 0.00 0.00 34.30 2.17
7142 12279 0.820891 GGGCGATGCAGATGTGGATT 60.821 55.000 0.00 0.00 34.30 3.01
7143 12280 1.228063 GGGCGATGCAGATGTGGAT 60.228 57.895 0.00 0.00 37.46 3.41
7144 12281 1.913951 AAGGGCGATGCAGATGTGGA 61.914 55.000 0.00 0.00 0.00 4.02
7145 12282 0.179048 TAAGGGCGATGCAGATGTGG 60.179 55.000 0.00 0.00 0.00 4.17
7146 12283 1.667236 TTAAGGGCGATGCAGATGTG 58.333 50.000 0.00 0.00 0.00 3.21
7147 12284 2.418368 TTTAAGGGCGATGCAGATGT 57.582 45.000 0.00 0.00 0.00 3.06
7148 12285 3.144506 AGATTTAAGGGCGATGCAGATG 58.855 45.455 0.00 0.00 0.00 2.90
7149 12286 3.498774 AGATTTAAGGGCGATGCAGAT 57.501 42.857 0.00 0.00 0.00 2.90
7150 12287 4.623932 ATAGATTTAAGGGCGATGCAGA 57.376 40.909 0.00 0.00 0.00 4.26
7151 12288 7.041721 TGTATATAGATTTAAGGGCGATGCAG 58.958 38.462 0.00 0.00 0.00 4.41
7152 12289 6.941857 TGTATATAGATTTAAGGGCGATGCA 58.058 36.000 0.00 0.00 0.00 3.96
7153 12290 7.843490 TTGTATATAGATTTAAGGGCGATGC 57.157 36.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.