Multiple sequence alignment - TraesCS6A01G372700

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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 TraesCS6A01G372700 chr6A 100.000 9764 0 0 1 9764 596431236 596421473 0.000000e+00 18031.0
1 TraesCS6A01G372700 chr6A 88.477 512 37 8 8581 9082 554453604 554454103 5.050000e-167 599.0
2 TraesCS6A01G372700 chr6A 86.792 477 43 6 9153 9629 554454108 554454564 1.880000e-141 514.0
3 TraesCS6A01G372700 chr6A 91.826 367 27 2 5070 5435 596322484 596322120 8.750000e-140 508.0
4 TraesCS6A01G372700 chr6A 93.040 273 19 0 4787 5059 596334925 596334653 5.490000e-107 399.0
5 TraesCS6A01G372700 chr6A 85.409 281 21 8 7751 8015 554453146 554453422 3.470000e-69 274.0
6 TraesCS6A01G372700 chr6A 75.895 419 67 22 168 569 592867435 592867836 6.020000e-42 183.0
7 TraesCS6A01G372700 chr6A 87.705 122 12 2 8010 8130 554453483 554453602 1.320000e-28 139.0
8 TraesCS6A01G372700 chr6D 97.739 4953 70 17 2809 7736 450833927 450828992 0.000000e+00 8488.0
9 TraesCS6A01G372700 chr6D 92.860 2885 119 26 1 2822 450836825 450833965 0.000000e+00 4106.0
10 TraesCS6A01G372700 chr6D 86.143 1934 141 41 7751 9641 408643221 408645070 0.000000e+00 1969.0
11 TraesCS6A01G372700 chr6D 95.629 1144 32 5 7736 8865 450828955 450827816 0.000000e+00 1820.0
12 TraesCS6A01G372700 chr6D 87.673 868 73 16 8906 9764 450827808 450826966 0.000000e+00 979.0
13 TraesCS6A01G372700 chr6B 92.136 3357 146 34 1344 4620 684512299 684508981 0.000000e+00 4628.0
14 TraesCS6A01G372700 chr6B 95.425 2339 86 11 4784 7119 684508990 684506670 0.000000e+00 3707.0
15 TraesCS6A01G372700 chr6B 91.725 1861 85 25 7736 9575 684506026 684504214 0.000000e+00 2519.0
16 TraesCS6A01G372700 chr6B 91.472 727 40 8 8108 8816 613104601 613105323 0.000000e+00 979.0
17 TraesCS6A01G372700 chr6B 93.750 608 20 8 7146 7736 684506671 684506065 0.000000e+00 896.0
18 TraesCS6A01G372700 chr6B 89.139 755 34 16 684 1401 684513021 684512278 0.000000e+00 896.0
19 TraesCS6A01G372700 chr6B 88.119 606 39 16 6 596 684531212 684530625 0.000000e+00 689.0
20 TraesCS6A01G372700 chr6B 87.624 606 42 16 6 596 684514353 684513766 0.000000e+00 673.0
21 TraesCS6A01G372700 chr6B 87.291 299 17 11 684 972 684529881 684529594 1.220000e-83 322.0
22 TraesCS6A01G372700 chr6B 84.774 243 20 5 8848 9082 613105322 613105555 2.740000e-55 228.0
23 TraesCS6A01G372700 chr6B 89.167 120 11 1 8002 8121 613104246 613104363 2.200000e-31 148.0
24 TraesCS6A01G372700 chrUn 100.000 397 0 0 4799 5195 479090844 479091240 0.000000e+00 734.0
25 TraesCS6A01G372700 chr2A 78.089 429 69 17 173 582 195310211 195310633 2.110000e-61 248.0
26 TraesCS6A01G372700 chr2A 80.451 133 18 6 1344 1474 232452323 232452449 2.900000e-15 95.3
27 TraesCS6A01G372700 chr2B 77.907 430 70 17 172 582 237344501 237344924 2.720000e-60 244.0
28 TraesCS6A01G372700 chr7D 96.825 126 4 0 4617 4742 617790592 617790717 2.760000e-50 211.0
29 TraesCS6A01G372700 chr7D 76.852 216 35 10 1261 1474 83969868 83970070 3.730000e-19 108.0
30 TraesCS6A01G372700 chr3D 96.825 126 4 0 4617 4742 26165695 26165820 2.760000e-50 211.0
31 TraesCS6A01G372700 chr2D 94.853 136 5 1 4617 4750 215831967 215831832 2.760000e-50 211.0
32 TraesCS6A01G372700 chr2D 77.778 216 33 10 1261 1474 41230934 41231136 1.720000e-22 119.0
33 TraesCS6A01G372700 chr5B 93.617 141 7 1 4612 4750 291787011 291786871 9.940000e-50 209.0
34 TraesCS6A01G372700 chr5A 96.094 128 5 0 4615 4742 643242134 643242007 9.940000e-50 209.0
35 TraesCS6A01G372700 chr5A 90.667 150 13 1 4617 4766 455084716 455084568 2.150000e-46 198.0
36 TraesCS6A01G372700 chr5A 90.000 60 4 2 1 59 419678550 419678608 1.050000e-09 76.8
37 TraesCS6A01G372700 chr1A 94.776 134 7 0 4609 4742 545919628 545919761 9.940000e-50 209.0
38 TraesCS6A01G372700 chr1A 83.333 72 10 2 4 74 325116332 325116262 2.280000e-06 65.8
39 TraesCS6A01G372700 chr5D 92.908 141 8 1 4612 4750 257502293 257502153 4.620000e-48 204.0
40 TraesCS6A01G372700 chr5D 100.000 31 0 0 1261 1291 481216978 481217008 3.810000e-04 58.4
41 TraesCS6A01G372700 chr4D 86.667 120 3 4 9652 9764 20108886 20108773 4.790000e-23 121.0
42 TraesCS6A01G372700 chr3B 76.852 216 35 10 1261 1474 651955081 651954879 3.730000e-19 108.0
43 TraesCS6A01G372700 chr1B 76.682 223 22 14 1261 1474 46568921 46569122 8.070000e-16 97.1
44 TraesCS6A01G372700 chr1D 87.324 71 9 0 4 74 5246700 5246630 2.260000e-11 82.4
45 TraesCS6A01G372700 chr4A 90.000 60 4 2 4 62 173854972 173855030 1.050000e-09 76.8


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 TraesCS6A01G372700 chr6A 596421473 596431236 9763 True 18031.000000 18031 100.000000 1 9764 1 chr6A.!!$R3 9763
1 TraesCS6A01G372700 chr6A 554453146 554454564 1418 False 381.500000 599 87.095750 7751 9629 4 chr6A.!!$F2 1878
2 TraesCS6A01G372700 chr6D 450826966 450836825 9859 True 3848.250000 8488 93.475250 1 9764 4 chr6D.!!$R1 9763
3 TraesCS6A01G372700 chr6D 408643221 408645070 1849 False 1969.000000 1969 86.143000 7751 9641 1 chr6D.!!$F1 1890
4 TraesCS6A01G372700 chr6B 684504214 684514353 10139 True 2219.833333 4628 91.633167 6 9575 6 chr6B.!!$R1 9569
5 TraesCS6A01G372700 chr6B 684529594 684531212 1618 True 505.500000 689 87.705000 6 972 2 chr6B.!!$R2 966
6 TraesCS6A01G372700 chr6B 613104246 613105555 1309 False 451.666667 979 88.471000 8002 9082 3 chr6B.!!$F1 1080

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
464 496 0.521867 CGAATCCTCGCGTGTCGTTA 60.522 55.000 5.77 0.00 38.45 3.18 F
1377 2104 0.250234 TAGTGCCATCAGCCTGTCAC 59.750 55.000 0.00 0.00 42.71 3.67 F
2088 2877 0.171903 CCATTGCTAGTTGCTGCCAC 59.828 55.000 0.00 0.00 43.37 5.01 F
2213 3004 1.007387 CGTTGGAGTTGGCTTTGGC 60.007 57.895 0.00 0.00 37.82 4.52 F
2238 3029 2.061061 GGAGGGGGATCAGATGACATT 58.939 52.381 0.00 0.00 0.00 2.71 F
2289 3080 2.575532 CAAAGGTCCTTCTGCTTCACA 58.424 47.619 4.10 0.00 0.00 3.58 F
2830 3704 3.053095 AGGCCCTCAATGTCTTGATTCAT 60.053 43.478 0.00 0.00 40.52 2.57 F
4070 4963 3.315470 CGCTGGAGCTTATACAGTACTGA 59.685 47.826 29.30 13.09 39.32 3.41 F
5978 6881 1.149288 TGTGTAGGAGAGGGTGAGGTT 59.851 52.381 0.00 0.00 0.00 3.50 F
7455 8370 1.447838 GATCTTGACTCGGCGCCAA 60.448 57.895 28.98 7.25 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 2761 0.167470 CTGTCAACATTGCTGGAGCG 59.833 55.000 0.00 0.0 45.83 5.03 R
2935 3810 0.681733 TCTGTGAGTGCCTCTGTTCC 59.318 55.000 4.21 0.0 0.00 3.62 R
3361 4245 0.743345 CTTACCAGGGCGGCAAGTAC 60.743 60.000 12.47 0.0 39.03 2.73 R
3792 4679 2.554032 AGGTTGAATTGTAGCACACAGC 59.446 45.455 0.00 0.0 46.19 4.40 R
3841 4734 9.838339 ACAAATTAACTCATTACTCAGATAGGG 57.162 33.333 0.00 0.0 0.00 3.53 R
4668 5561 3.472652 CGGGCATATTTGTAAGGCACTA 58.527 45.455 0.00 0.0 38.49 2.74 R
4671 5564 1.028905 GCGGGCATATTTGTAAGGCA 58.971 50.000 0.00 0.0 0.00 4.75 R
6378 7281 1.142748 CTTCCACTCGCCTAGCAGG 59.857 63.158 0.00 0.0 38.80 4.85 R
7464 8379 1.753930 ATGTGGCATCAGATTCGCAA 58.246 45.000 0.00 0.0 0.00 4.85 R
9302 10694 0.806102 TGCAATTCGAGACGCCTAGC 60.806 55.000 0.00 0.0 0.00 3.42 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
50 51 8.697507 AAAATCCCTACATGATTCAATCCTAC 57.302 34.615 0.00 0.00 31.39 3.18
203 233 3.378911 TTTGCTATCTGTCGTGTCACA 57.621 42.857 3.42 0.00 0.00 3.58
265 295 3.680490 TGCCATCATTTTGTTCGGTCTA 58.320 40.909 0.00 0.00 0.00 2.59
327 357 3.252554 AGGCCATTGACAAGGGTAAAA 57.747 42.857 19.42 0.00 34.09 1.52
343 373 7.703058 AGGGTAAAATGACCAAAATACTCTG 57.297 36.000 0.00 0.00 41.73 3.35
344 374 6.663523 AGGGTAAAATGACCAAAATACTCTGG 59.336 38.462 0.00 0.00 41.73 3.86
345 375 6.661805 GGGTAAAATGACCAAAATACTCTGGA 59.338 38.462 0.00 0.00 41.73 3.86
346 376 7.362660 GGGTAAAATGACCAAAATACTCTGGAC 60.363 40.741 0.00 0.00 41.73 4.02
348 378 5.520748 AATGACCAAAATACTCTGGACCT 57.479 39.130 0.00 0.00 36.49 3.85
393 424 5.190925 ACAACTTGCTATAACCTATGGGTCA 59.809 40.000 0.00 0.00 46.67 4.02
439 470 3.670625 AGGTAAAATAGCTTCACGTGCA 58.329 40.909 11.67 0.00 31.36 4.57
455 487 2.520904 GCAGTGCTCGAATCCTCGC 61.521 63.158 8.18 0.00 45.04 5.03
460 492 2.224885 GCTCGAATCCTCGCGTGTC 61.225 63.158 5.77 0.00 45.04 3.67
464 496 0.521867 CGAATCCTCGCGTGTCGTTA 60.522 55.000 5.77 0.00 38.45 3.18
565 597 5.491078 TCCTAGGGTATTTTGGTCACTTCAT 59.509 40.000 9.46 0.00 0.00 2.57
585 617 2.551270 TCCTGGTCAGTAGCCTTCAAT 58.449 47.619 0.00 0.00 0.00 2.57
596 628 1.066143 AGCCTTCAATCGGACGACAAT 60.066 47.619 0.00 0.00 0.00 2.71
597 629 1.737793 GCCTTCAATCGGACGACAATT 59.262 47.619 0.00 0.00 0.00 2.32
598 630 2.933906 GCCTTCAATCGGACGACAATTA 59.066 45.455 0.00 0.00 0.00 1.40
599 631 3.001330 GCCTTCAATCGGACGACAATTAG 59.999 47.826 0.00 0.00 0.00 1.73
600 632 3.555956 CCTTCAATCGGACGACAATTAGG 59.444 47.826 0.00 0.00 0.00 2.69
602 634 3.777478 TCAATCGGACGACAATTAGGAC 58.223 45.455 0.00 0.00 0.00 3.85
603 635 2.864343 CAATCGGACGACAATTAGGACC 59.136 50.000 0.00 0.00 0.00 4.46
604 636 0.819582 TCGGACGACAATTAGGACCC 59.180 55.000 0.00 0.00 0.00 4.46
606 638 1.138266 CGGACGACAATTAGGACCCAT 59.862 52.381 0.00 0.00 0.00 4.00
607 639 2.363038 CGGACGACAATTAGGACCCATA 59.637 50.000 0.00 0.00 0.00 2.74
608 640 3.006537 CGGACGACAATTAGGACCCATAT 59.993 47.826 0.00 0.00 0.00 1.78
654 686 5.975988 TTGAGATAGCTCCCCACTTATTT 57.024 39.130 5.36 0.00 40.55 1.40
658 690 5.934781 AGATAGCTCCCCACTTATTTCAAG 58.065 41.667 0.00 0.00 0.00 3.02
670 702 4.999311 ACTTATTTCAAGTGGTAACCGGAC 59.001 41.667 9.46 0.00 0.00 4.79
726 1418 9.769093 ACACGCTTAATAAAATGATTACAGTTC 57.231 29.630 0.00 0.00 33.12 3.01
742 1434 9.599322 GATTACAGTTCATGTAGTTGAAGTTTG 57.401 33.333 0.00 0.00 45.05 2.93
783 1476 2.433604 TGTGACACAACCATGGCAAAAT 59.566 40.909 13.04 0.00 40.05 1.82
790 1483 6.474630 ACACAACCATGGCAAAATTGATAAT 58.525 32.000 13.04 0.00 0.00 1.28
862 1555 3.834799 GCCCACCCTACTCGTCCG 61.835 72.222 0.00 0.00 0.00 4.79
899 1598 1.376424 ATCCCAACTGCAGCTCACG 60.376 57.895 15.27 0.00 0.00 4.35
1377 2104 0.250234 TAGTGCCATCAGCCTGTCAC 59.750 55.000 0.00 0.00 42.71 3.67
1378 2105 1.302752 GTGCCATCAGCCTGTCACA 60.303 57.895 0.00 0.00 42.71 3.58
1381 2108 1.303799 GCCATCAGCCTGTCACACTG 61.304 60.000 0.00 0.00 34.35 3.66
1416 2177 5.934625 AGTAGTTCCTTGAATCACACATGAC 59.065 40.000 0.00 0.00 37.79 3.06
1492 2255 2.119495 ACCCTAGCAGTGTTATCCTGG 58.881 52.381 0.00 0.00 0.00 4.45
1553 2316 8.500753 TGTAAATTGTGACCCATATTAGTGTC 57.499 34.615 0.00 0.00 0.00 3.67
1554 2317 7.554835 TGTAAATTGTGACCCATATTAGTGTCC 59.445 37.037 0.00 0.00 0.00 4.02
1563 2326 6.698380 ACCCATATTAGTGTCCGTGAATATC 58.302 40.000 0.00 0.00 0.00 1.63
1636 2421 2.031157 GCCGCAACTCACAATGTAACTT 60.031 45.455 0.00 0.00 0.00 2.66
1669 2454 5.613329 TCTTTGCTGGCTCAATTTGATTTT 58.387 33.333 0.00 0.00 0.00 1.82
1670 2455 5.467399 TCTTTGCTGGCTCAATTTGATTTTG 59.533 36.000 0.00 0.00 0.00 2.44
1671 2456 3.068560 TGCTGGCTCAATTTGATTTTGC 58.931 40.909 0.00 0.00 0.00 3.68
1673 2458 3.370061 GCTGGCTCAATTTGATTTTGCTC 59.630 43.478 0.00 0.00 0.00 4.26
1714 2502 5.342259 GGAGTGTTGAATGTTTCGCAATAAC 59.658 40.000 0.00 0.00 0.00 1.89
1745 2533 7.970614 CCCTACTTTCTATTTTTGTGCATCTTC 59.029 37.037 0.00 0.00 0.00 2.87
1875 2664 3.936372 TTTAGAGGTTGAGTCCTGACG 57.064 47.619 0.00 0.00 38.02 4.35
1899 2688 6.625740 CGCCATTTAGAGGAATTTTGTGTGAT 60.626 38.462 0.00 0.00 0.00 3.06
1926 2715 3.326297 TCACAGTTACATCCACATGACCA 59.674 43.478 0.00 0.00 33.72 4.02
2088 2877 0.171903 CCATTGCTAGTTGCTGCCAC 59.828 55.000 0.00 0.00 43.37 5.01
2115 2904 3.496130 GGAGCCTGAATCACGTATTGATG 59.504 47.826 0.00 0.00 44.86 3.07
2166 2957 5.047021 TCCAACATTTTTGTCTTCAACCACA 60.047 36.000 0.00 0.00 32.93 4.17
2194 2985 6.705825 CCATTTACAATAGCTATTTTTGGGGC 59.294 38.462 16.46 0.00 0.00 5.80
2213 3004 1.007387 CGTTGGAGTTGGCTTTGGC 60.007 57.895 0.00 0.00 37.82 4.52
2238 3029 2.061061 GGAGGGGGATCAGATGACATT 58.939 52.381 0.00 0.00 0.00 2.71
2265 3056 6.618811 TCGTGAGTTGAGAATAAAGGTAGAC 58.381 40.000 0.00 0.00 0.00 2.59
2268 3059 5.189145 TGAGTTGAGAATAAAGGTAGACCCC 59.811 44.000 0.00 0.00 36.42 4.95
2289 3080 2.575532 CAAAGGTCCTTCTGCTTCACA 58.424 47.619 4.10 0.00 0.00 3.58
2392 3189 8.621532 TGATCTTGTATTGGGATTATAACAGC 57.378 34.615 0.00 0.00 0.00 4.40
2440 3238 9.710900 GGTTTGAAAAATCTTCATTCATACCTT 57.289 29.630 15.50 0.00 44.65 3.50
2724 3546 8.605746 CATAAATATTTTGGCTCCATGTGTTTG 58.394 33.333 5.91 0.00 0.00 2.93
2764 3586 9.253832 CTCCTGACTATTCTGAGGATATGTTAT 57.746 37.037 0.00 0.00 34.07 1.89
2771 3593 9.539825 CTATTCTGAGGATATGTTATGTATGGC 57.460 37.037 0.00 0.00 0.00 4.40
2789 3611 3.234353 TGGCCCATTGTGAAAATGTACA 58.766 40.909 0.00 0.00 0.00 2.90
2830 3704 3.053095 AGGCCCTCAATGTCTTGATTCAT 60.053 43.478 0.00 0.00 40.52 2.57
3155 4034 9.937175 GTCATTTTATCTACCTTAGAAACATGC 57.063 33.333 0.00 0.00 38.50 4.06
3361 4245 5.765182 ACTTTGTCAATGTCTACTTTGGAGG 59.235 40.000 8.38 1.14 33.42 4.30
3523 4409 3.379057 GGCGCTTAGGCAAGGTTAATTTA 59.621 43.478 7.64 0.00 45.92 1.40
3688 4575 7.784633 ATTTCTTCTCAGTCTTAAGCTATGC 57.215 36.000 0.00 0.00 0.00 3.14
3792 4679 9.944663 AGTAATTTGTGTGTATTGTACAAAGTG 57.055 29.630 13.23 0.00 44.51 3.16
3841 4734 5.667466 AGGAATCAATTTGGATGACATTGC 58.333 37.500 0.00 0.00 0.00 3.56
4070 4963 3.315470 CGCTGGAGCTTATACAGTACTGA 59.685 47.826 29.30 13.09 39.32 3.41
4671 5564 1.745320 CGATAAGGCGCCCTGGTAGT 61.745 60.000 26.15 0.00 32.13 2.73
5252 6155 9.816354 GTAACCATGGAGCATAAATGTTAAAAT 57.184 29.630 21.47 0.00 0.00 1.82
5286 6189 8.908786 TCATTATTCCAGATCTTAACCATGAC 57.091 34.615 0.00 0.00 0.00 3.06
5581 6484 1.676967 GAGCAAGAACAGGGGGCTG 60.677 63.158 0.00 0.00 34.44 4.85
5850 6753 5.614324 TGCTAGTTGGTGCTGAGTTATAT 57.386 39.130 0.00 0.00 0.00 0.86
5863 6766 8.763356 GTGCTGAGTTATATTGATTCTCTCTTG 58.237 37.037 0.00 0.00 0.00 3.02
5978 6881 1.149288 TGTGTAGGAGAGGGTGAGGTT 59.851 52.381 0.00 0.00 0.00 3.50
6220 7123 7.761249 GGTCTTGGAAATTATGTGGATCTTTTG 59.239 37.037 0.00 0.00 0.00 2.44
6272 7175 7.112779 AGTTTACTTGTAGCCTATCTTGCATT 58.887 34.615 0.00 0.00 0.00 3.56
6378 7281 7.436080 TCATTCTTGAATTGCTTTGTTGTCTTC 59.564 33.333 0.00 0.00 0.00 2.87
6691 7595 5.483231 TCCAAATAAATCCATGCTGAAACCA 59.517 36.000 0.00 0.00 0.00 3.67
6721 7625 2.677848 GGAAACAGAGGGCCTCCC 59.322 66.667 29.62 19.05 45.90 4.30
7059 7964 7.529880 AATAGCTTTATTGCAGTTTTGATGC 57.470 32.000 0.00 0.00 44.11 3.91
7074 7979 4.686191 TTGATGCAACCACCAAATTTCT 57.314 36.364 0.00 0.00 0.00 2.52
7217 8122 7.386025 TGACTCACAGTAATCATCAAACAGAAG 59.614 37.037 0.00 0.00 0.00 2.85
7455 8370 1.447838 GATCTTGACTCGGCGCCAA 60.448 57.895 28.98 7.25 0.00 4.52
7613 8529 2.434336 TGTTATGCGAGGCCTAGTCAAT 59.566 45.455 14.88 8.58 0.00 2.57
7626 8543 5.106118 GGCCTAGTCAATTCTGTTTTCCTTC 60.106 44.000 0.00 0.00 0.00 3.46
7732 8654 8.796475 AGTATGATGGCAATATTGTAATGGTTC 58.204 33.333 16.61 5.76 0.00 3.62
7894 8899 1.522668 CGAAGCAAGGTGTTCCATCA 58.477 50.000 0.00 0.00 35.89 3.07
7997 9011 3.968265 TCCCCTCTTGAGCCTTTTTATG 58.032 45.455 0.00 0.00 0.00 1.90
7998 9012 3.591527 TCCCCTCTTGAGCCTTTTTATGA 59.408 43.478 0.00 0.00 0.00 2.15
8209 9554 5.529430 TCTTGTCAGCGGAAAGTTCATTTTA 59.471 36.000 0.00 0.00 0.00 1.52
8245 9599 1.875963 CGGAACATTGCTGTGTCCC 59.124 57.895 0.00 0.00 35.22 4.46
8428 9782 2.453983 TTGCTGGGTAAAAATGCTGC 57.546 45.000 0.00 0.00 0.00 5.25
8523 9891 9.810545 GCCTTATATCCTTCAGTATATTCTCAC 57.189 37.037 0.00 0.00 0.00 3.51
8542 9910 9.842775 ATTCTCACTGATCATATGTTGTTACAT 57.157 29.630 1.90 0.00 46.49 2.29
8543 9911 8.652810 TCTCACTGATCATATGTTGTTACATG 57.347 34.615 1.90 0.00 44.56 3.21
8544 9912 8.260114 TCTCACTGATCATATGTTGTTACATGT 58.740 33.333 2.69 2.69 44.56 3.21
8580 9948 8.607459 AGATTTGTCGATGTAGAAATTCATGTC 58.393 33.333 0.00 0.00 0.00 3.06
8587 9955 6.536582 CGATGTAGAAATTCATGTCCAGTTCT 59.463 38.462 0.00 9.03 0.00 3.01
8700 10069 3.118075 TGTCCTCATGTTGACCAAGTTGA 60.118 43.478 3.87 0.00 0.00 3.18
8839 10210 9.638239 GTTAACCAATCTGCAATTCTTCAATTA 57.362 29.630 0.00 0.00 30.51 1.40
8900 10271 3.260884 TGAAGAGGCTCATCTTTTACGGT 59.739 43.478 19.32 0.00 39.63 4.83
9016 10390 3.563808 TGAATTTTGCTGTAGTCGCACTT 59.436 39.130 0.00 0.00 37.07 3.16
9082 10467 8.893219 ATTGAAATCGATGAAGCTACATTCTA 57.107 30.769 0.00 0.00 0.00 2.10
9088 10473 9.764363 AATCGATGAAGCTACATTCTATGTAAA 57.236 29.630 0.00 0.00 44.44 2.01
9089 10474 9.935241 ATCGATGAAGCTACATTCTATGTAAAT 57.065 29.630 0.00 0.00 44.44 1.40
9254 10646 3.149196 AGAACACAAGATTTGCGGACAT 58.851 40.909 0.00 0.00 0.00 3.06
9257 10649 4.419522 ACACAAGATTTGCGGACATAAC 57.580 40.909 0.00 0.00 0.00 1.89
9302 10694 6.017933 GCATATTCTGTTCTTGTTCGTCTTG 58.982 40.000 0.00 0.00 0.00 3.02
9304 10696 3.179443 TCTGTTCTTGTTCGTCTTGCT 57.821 42.857 0.00 0.00 0.00 3.91
9313 10705 4.386245 CGTCTTGCTAGGCGTCTC 57.614 61.111 14.09 0.00 44.27 3.36
9316 10708 0.170561 GTCTTGCTAGGCGTCTCGAA 59.829 55.000 0.00 0.00 0.00 3.71
9327 10719 1.913403 GCGTCTCGAATTGCAAAATGG 59.087 47.619 1.71 0.00 0.00 3.16
9330 10722 3.603770 CGTCTCGAATTGCAAAATGGAAC 59.396 43.478 1.71 0.00 28.29 3.62
9331 10723 3.920412 GTCTCGAATTGCAAAATGGAACC 59.080 43.478 1.71 0.00 28.29 3.62
9335 10727 3.738282 CGAATTGCAAAATGGAACCGAAA 59.262 39.130 1.71 0.00 32.17 3.46
9368 10761 5.005740 TGATGTCATCTGAACTTTGAAGGG 58.994 41.667 13.90 0.00 0.00 3.95
9377 10773 4.204012 TGAACTTTGAAGGGTGTACAAGG 58.796 43.478 0.00 0.00 0.00 3.61
9463 10865 4.827087 ACCATGAGCAGCGCCTCG 62.827 66.667 2.29 0.00 34.56 4.63
9484 10886 1.522806 GATGTTGGGCCGCGTGATA 60.523 57.895 4.92 0.00 0.00 2.15
9587 10989 3.569701 GTCATCCTGGTTGAACAACACAT 59.430 43.478 17.43 3.10 42.85 3.21
9607 11011 2.235016 TGTGAACCAAAGGGAAATCGG 58.765 47.619 0.00 0.00 38.05 4.18
9637 11041 9.077885 AGAAACCAAGCAAATTTCAGTTATAGA 57.922 29.630 0.00 0.00 35.26 1.98
9691 11098 0.036388 GGAATGACTGCCGAACCTGA 60.036 55.000 0.00 0.00 0.00 3.86
9692 11099 1.610624 GGAATGACTGCCGAACCTGAA 60.611 52.381 0.00 0.00 0.00 3.02
9693 11100 1.734465 GAATGACTGCCGAACCTGAAG 59.266 52.381 0.00 0.00 0.00 3.02
9694 11101 0.976641 ATGACTGCCGAACCTGAAGA 59.023 50.000 0.00 0.00 0.00 2.87
9695 11102 0.976641 TGACTGCCGAACCTGAAGAT 59.023 50.000 0.00 0.00 0.00 2.40
9696 11103 2.176045 TGACTGCCGAACCTGAAGATA 58.824 47.619 0.00 0.00 0.00 1.98
9710 11117 6.347696 ACCTGAAGATAAAGATTCTGAGCAG 58.652 40.000 0.00 0.00 0.00 4.24
9725 11132 4.211164 TCTGAGCAGAACACATTTGTTACG 59.789 41.667 0.00 0.00 46.43 3.18
9731 11138 3.003275 AGAACACATTTGTTACGGCAGTG 59.997 43.478 0.00 0.00 46.43 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 116 8.284693 GGGACACTTTGATTCATTTGAATTTTG 58.715 33.333 7.20 4.04 44.14 2.44
179 181 3.987868 TGACACGACAGATAGCAAAACTC 59.012 43.478 0.00 0.00 0.00 3.01
203 233 6.998673 ACCTTCTAGTTGCAAAATTGAGTAGT 59.001 34.615 0.00 0.00 26.28 2.73
265 295 4.836125 CCGAGTGGCATTTATTTAGCAT 57.164 40.909 0.00 0.00 0.00 3.79
327 357 4.536090 TGAGGTCCAGAGTATTTTGGTCAT 59.464 41.667 0.00 0.00 35.89 3.06
343 373 7.740805 AGAGGAAATATTGATAAGTGAGGTCC 58.259 38.462 0.00 0.00 0.00 4.46
344 374 9.699703 GTAGAGGAAATATTGATAAGTGAGGTC 57.300 37.037 0.00 0.00 0.00 3.85
345 375 9.213777 TGTAGAGGAAATATTGATAAGTGAGGT 57.786 33.333 0.00 0.00 0.00 3.85
436 467 4.919653 GAGGATTCGAGCACTGCA 57.080 55.556 3.30 0.00 0.00 4.41
487 519 4.202514 TGGGTCCTAATTGTCAACACATGA 60.203 41.667 0.00 0.00 35.05 3.07
565 597 2.024176 TTGAAGGCTACTGACCAGGA 57.976 50.000 0.00 0.00 0.00 3.86
585 617 0.819582 GGGTCCTAATTGTCGTCCGA 59.180 55.000 0.00 0.00 0.00 4.55
596 628 9.762381 ACAAACTCAAAAATATATGGGTCCTAA 57.238 29.630 0.00 0.00 27.80 2.69
597 629 9.762381 AACAAACTCAAAAATATATGGGTCCTA 57.238 29.630 0.00 0.00 27.80 2.94
598 630 8.531146 CAACAAACTCAAAAATATATGGGTCCT 58.469 33.333 0.00 0.00 27.80 3.85
599 631 8.527810 TCAACAAACTCAAAAATATATGGGTCC 58.472 33.333 0.00 0.00 27.80 4.46
654 686 0.314935 GTCGTCCGGTTACCACTTGA 59.685 55.000 0.00 0.00 0.00 3.02
658 690 0.249405 TGTTGTCGTCCGGTTACCAC 60.249 55.000 0.00 1.22 0.00 4.16
670 702 1.497991 ACCACTCGTCAATGTTGTCG 58.502 50.000 6.13 6.13 40.22 4.35
747 1439 8.349983 GGTTGTGTCACACTACTCAATTTTATT 58.650 33.333 19.86 0.00 39.34 1.40
801 1494 7.013655 GCTGGAATACATTGATCATTGGTACTT 59.986 37.037 19.02 8.50 0.00 2.24
802 1495 6.488006 GCTGGAATACATTGATCATTGGTACT 59.512 38.462 19.02 3.22 0.00 2.73
803 1496 6.566564 CGCTGGAATACATTGATCATTGGTAC 60.567 42.308 19.02 7.66 0.00 3.34
804 1497 5.469760 CGCTGGAATACATTGATCATTGGTA 59.530 40.000 19.02 11.79 0.00 3.25
805 1498 4.276678 CGCTGGAATACATTGATCATTGGT 59.723 41.667 19.02 10.19 0.00 3.67
806 1499 4.320714 CCGCTGGAATACATTGATCATTGG 60.321 45.833 19.02 5.14 0.00 3.16
807 1500 4.516321 TCCGCTGGAATACATTGATCATTG 59.484 41.667 14.54 14.54 0.00 2.82
862 1555 3.082055 GGAGGGGAAGGGGACGAC 61.082 72.222 0.00 0.00 0.00 4.34
969 1668 4.778143 CCGGCGGGTTTCTCTGGG 62.778 72.222 20.56 0.00 0.00 4.45
1416 2177 6.019156 ACACTTTATCCAAACAAAACAATGCG 60.019 34.615 0.00 0.00 0.00 4.73
1492 2255 4.324267 AGTTGGTCCATTGTAGCAAGTAC 58.676 43.478 0.24 0.00 36.50 2.73
1553 2316 3.924918 ATGAGACTCGGATATTCACGG 57.075 47.619 0.00 0.00 0.00 4.94
1554 2317 6.036083 ACAAAAATGAGACTCGGATATTCACG 59.964 38.462 0.00 0.00 0.00 4.35
1563 2326 9.529325 TGATAGTATAACAAAAATGAGACTCGG 57.471 33.333 0.00 0.00 0.00 4.63
1636 2421 2.573462 AGCCAGCAAAGAGATTGGACTA 59.427 45.455 0.00 0.00 39.54 2.59
1669 2454 2.543777 AAACGCAAAGACCTAGAGCA 57.456 45.000 0.00 0.00 0.00 4.26
1670 2455 2.095718 CCAAAACGCAAAGACCTAGAGC 60.096 50.000 0.00 0.00 0.00 4.09
1671 2456 3.399330 TCCAAAACGCAAAGACCTAGAG 58.601 45.455 0.00 0.00 0.00 2.43
1673 2458 3.058914 CACTCCAAAACGCAAAGACCTAG 60.059 47.826 0.00 0.00 0.00 3.02
1714 2502 6.349363 GCACAAAAATAGAAAGTAGGGAGTGG 60.349 42.308 0.00 0.00 0.00 4.00
1745 2533 1.290203 AGCGAACCTGTGCAATATCG 58.710 50.000 0.00 0.00 0.00 2.92
1755 2543 7.432252 GGATTTTCATGTATAAAAGCGAACCTG 59.568 37.037 0.00 0.00 34.01 4.00
1875 2664 6.024552 TCACACAAAATTCCTCTAAATGGC 57.975 37.500 0.00 0.00 0.00 4.40
1899 2688 7.041721 GTCATGTGGATGTAACTGTGAAGATA 58.958 38.462 0.00 0.00 0.00 1.98
1926 2715 8.181904 AGAAAGTTAATGAAACACCATGATGT 57.818 30.769 0.00 0.00 40.83 3.06
1953 2742 6.826231 TGGAGCGGTGAGAAAAATTATAATGA 59.174 34.615 0.00 0.00 0.00 2.57
1972 2761 0.167470 CTGTCAACATTGCTGGAGCG 59.833 55.000 0.00 0.00 45.83 5.03
2088 2877 0.596083 CGTGATTCAGGCTCCTAGCG 60.596 60.000 0.00 0.00 43.62 4.26
2166 2957 7.933033 CCCAAAAATAGCTATTGTAAATGGCAT 59.067 33.333 19.53 0.00 0.00 4.40
2194 2985 1.659794 CCAAAGCCAACTCCAACGG 59.340 57.895 0.00 0.00 0.00 4.44
2213 3004 2.194859 CATCTGATCCCCCTCCTATGG 58.805 57.143 0.00 0.00 0.00 2.74
2238 3029 4.245660 CCTTTATTCTCAACTCACGAGCA 58.754 43.478 0.00 0.00 0.00 4.26
2265 3056 1.304464 GCAGAAGGACCTTTGGGGG 60.304 63.158 8.49 0.00 40.03 5.40
2268 3059 1.882623 GTGAAGCAGAAGGACCTTTGG 59.117 52.381 8.49 4.99 0.00 3.28
2289 3080 1.409802 CCCTTGCTCAGCCAGATTCAT 60.410 52.381 0.00 0.00 0.00 2.57
2392 3189 0.991920 TCAAGGAGGGTGCTTTAGGG 59.008 55.000 0.00 0.00 0.00 3.53
2631 3453 1.371558 GTCGGTTGCTCCAGGTTCT 59.628 57.895 0.00 0.00 35.57 3.01
2724 3546 3.194542 AGTCAGGAGTCAGAACAGCATAC 59.805 47.826 0.00 0.00 0.00 2.39
2764 3586 3.837146 ACATTTTCACAATGGGCCATACA 59.163 39.130 21.54 0.60 32.14 2.29
2771 3593 8.824159 TGTTTTATGTACATTTTCACAATGGG 57.176 30.769 14.77 0.00 32.14 4.00
2789 3611 4.386424 GGCCTGTTAGGAGGGATGTTTTAT 60.386 45.833 0.00 0.00 37.67 1.40
2830 3704 9.826574 TGAACTCTTAACAAAGAAAGCTAGTTA 57.173 29.630 0.00 0.00 0.00 2.24
2928 3803 5.189736 TGTGAGTGCCTCTGTTCCTAAATAT 59.810 40.000 4.21 0.00 0.00 1.28
2935 3810 0.681733 TCTGTGAGTGCCTCTGTTCC 59.318 55.000 4.21 0.00 0.00 3.62
3022 3899 4.999950 AGTGGAAGTGCAAGTTTAGATGAG 59.000 41.667 0.00 0.00 0.00 2.90
3361 4245 0.743345 CTTACCAGGGCGGCAAGTAC 60.743 60.000 12.47 0.00 39.03 2.73
3431 4315 3.045601 ACCAAGGTTCTCAAGATCACG 57.954 47.619 0.00 0.00 0.00 4.35
3523 4409 6.962311 TCCAAGTCATATAGCCTAATCTGGAT 59.038 38.462 0.00 0.00 0.00 3.41
3792 4679 2.554032 AGGTTGAATTGTAGCACACAGC 59.446 45.455 0.00 0.00 46.19 4.40
3841 4734 9.838339 ACAAATTAACTCATTACTCAGATAGGG 57.162 33.333 0.00 0.00 0.00 3.53
4668 5561 3.472652 CGGGCATATTTGTAAGGCACTA 58.527 45.455 0.00 0.00 38.49 2.74
4671 5564 1.028905 GCGGGCATATTTGTAAGGCA 58.971 50.000 0.00 0.00 0.00 4.75
5286 6189 1.198408 CACACAGTTGCCAGTATGCAG 59.802 52.381 0.00 0.00 43.21 4.41
5439 6342 8.774586 CCAGTGTATAGTGCAAGTATATTTTCC 58.225 37.037 0.00 0.00 37.09 3.13
5581 6484 6.691388 GGTGCATTCCGAAGTAAATATGTTTC 59.309 38.462 0.00 0.00 0.00 2.78
5732 6635 3.490439 TGTCATCTTCTGGCTGTTTCA 57.510 42.857 0.00 0.00 0.00 2.69
5850 6753 6.721668 TGAACTAGAGTCCAAGAGAGAATCAA 59.278 38.462 0.00 0.00 37.82 2.57
6153 7056 7.307337 GCGATTGTTTCAAAATGTTTGAGGAAT 60.307 33.333 3.83 4.38 0.00 3.01
6378 7281 1.142748 CTTCCACTCGCCTAGCAGG 59.857 63.158 0.00 0.00 38.80 4.85
6543 7446 9.354673 TCTGAACATTTCCTGAAAGTTATTCTT 57.645 29.630 0.00 0.00 38.10 2.52
6544 7447 8.924511 TCTGAACATTTCCTGAAAGTTATTCT 57.075 30.769 0.00 0.00 33.32 2.40
6721 7625 2.704572 AGGCAGACAAAAAGATCTCCG 58.295 47.619 0.00 0.00 0.00 4.63
7059 7964 4.218417 CCTCCACTAGAAATTTGGTGGTTG 59.782 45.833 22.74 18.41 46.42 3.77
7074 7979 4.775253 TGATCAACACATACACCTCCACTA 59.225 41.667 0.00 0.00 0.00 2.74
7127 8032 3.651206 CCAAATACATGCAACAGCAACA 58.349 40.909 0.00 0.00 42.37 3.33
7346 8261 6.643388 AGAGTGAAAAACCTTGCTTTCATTT 58.357 32.000 1.02 0.00 42.01 2.32
7464 8379 1.753930 ATGTGGCATCAGATTCGCAA 58.246 45.000 0.00 0.00 0.00 4.85
7465 8380 1.753930 AATGTGGCATCAGATTCGCA 58.246 45.000 0.00 0.68 32.24 5.10
7613 8529 8.966868 ACTTAAATCAGTTGAAGGAAAACAGAA 58.033 29.630 0.00 0.00 0.00 3.02
7626 8543 6.076981 AGGCACAAAGACTTAAATCAGTTG 57.923 37.500 0.00 0.46 20.59 3.16
7754 8752 5.351465 GGAATGACTACACAACACCATACTG 59.649 44.000 0.00 0.00 0.00 2.74
7894 8899 4.433615 CGCGTATAGATGGCCTATTCAAT 58.566 43.478 3.32 0.00 38.87 2.57
8209 9554 2.014128 CCGCTGGTAACGATCCAAATT 58.986 47.619 0.00 0.00 42.51 1.82
8245 9599 2.032550 CCCTTATCAAGCAGCAACGATG 59.967 50.000 0.00 0.00 0.00 3.84
8428 9782 6.195244 GCATTGCAGTATAACGAAATCAAGTG 59.805 38.462 3.15 0.00 0.00 3.16
8523 9891 8.886719 AGACAACATGTAACAACATATGATCAG 58.113 33.333 10.38 0.00 0.00 2.90
8542 9910 6.038161 ACATCGACAAATCTTTTCAGACAACA 59.962 34.615 0.00 0.00 0.00 3.33
8543 9911 6.430451 ACATCGACAAATCTTTTCAGACAAC 58.570 36.000 0.00 0.00 0.00 3.32
8544 9912 6.618287 ACATCGACAAATCTTTTCAGACAA 57.382 33.333 0.00 0.00 0.00 3.18
8634 10003 2.523015 CAATTGATTGCAGAACCGAGC 58.477 47.619 0.00 0.00 0.00 5.03
8817 10188 7.703621 CGATTAATTGAAGAATTGCAGATTGGT 59.296 33.333 0.00 0.00 33.63 3.67
8900 10271 1.451504 CCACTTCACAGCCCACAGA 59.548 57.895 0.00 0.00 0.00 3.41
9016 10390 7.182817 ACTGTTACATGCTCTAGGAAATACA 57.817 36.000 0.00 0.00 0.00 2.29
9110 10497 5.989477 TGTGAGATGATCTACCGGAAAAAT 58.011 37.500 9.46 0.00 0.00 1.82
9130 10517 2.481568 CACAGCCTGATGTTGTACTGTG 59.518 50.000 0.00 6.56 46.10 3.66
9131 10518 2.771089 CACAGCCTGATGTTGTACTGT 58.229 47.619 0.00 0.00 38.84 3.55
9226 10617 4.916831 CGCAAATCTTGTGTTCTATTGCAA 59.083 37.500 0.00 0.00 41.15 4.08
9273 10665 7.199766 ACGAACAAGAACAGAATATGCAAAAA 58.800 30.769 0.00 0.00 0.00 1.94
9302 10694 0.806102 TGCAATTCGAGACGCCTAGC 60.806 55.000 0.00 0.00 0.00 3.42
9304 10696 2.087501 TTTGCAATTCGAGACGCCTA 57.912 45.000 0.00 0.00 0.00 3.93
9313 10705 2.940147 TCGGTTCCATTTTGCAATTCG 58.060 42.857 0.00 0.00 0.00 3.34
9349 10741 4.137543 ACACCCTTCAAAGTTCAGATGAC 58.862 43.478 0.00 0.00 0.00 3.06
9360 10752 1.497286 AGGCCTTGTACACCCTTCAAA 59.503 47.619 0.00 0.00 0.00 2.69
9368 10761 1.900486 ACAGGACTAGGCCTTGTACAC 59.100 52.381 28.30 17.40 35.66 2.90
9445 10847 2.894387 GAGGCGCTGCTCATGGTC 60.894 66.667 7.64 0.00 0.00 4.02
9587 10989 2.235016 CCGATTTCCCTTTGGTTCACA 58.765 47.619 0.00 0.00 0.00 3.58
9607 11011 5.812127 ACTGAAATTTGCTTGGTTTCTGAAC 59.188 36.000 0.00 0.00 35.82 3.18
9637 11041 6.763135 CACTGGTAGCACTACATTCACATAAT 59.237 38.462 9.87 0.00 37.78 1.28
9642 11046 3.926616 ACACTGGTAGCACTACATTCAC 58.073 45.455 9.87 0.00 37.78 3.18
9643 11047 4.562757 GGAACACTGGTAGCACTACATTCA 60.563 45.833 9.87 0.00 37.78 2.57
9644 11048 3.933332 GGAACACTGGTAGCACTACATTC 59.067 47.826 9.87 5.27 37.78 2.67
9678 11085 3.260884 TCTTTATCTTCAGGTTCGGCAGT 59.739 43.478 0.00 0.00 0.00 4.40
9696 11103 7.417116 AACAAATGTGTTCTGCTCAGAATCTTT 60.417 33.333 14.54 11.81 45.00 2.52
9710 11117 3.242936 ACACTGCCGTAACAAATGTGTTC 60.243 43.478 4.02 0.00 45.00 3.18
9725 11132 3.721706 CCTCCTCCCCACACTGCC 61.722 72.222 0.00 0.00 0.00 4.85
9731 11138 2.284995 AGTGCTCCTCCTCCCCAC 60.285 66.667 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.