Multiple sequence alignment - TraesCS7D01G164400

Loading Multiple Alignment...

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 TraesCS7D01G164400 chr7D 100.000 5131 0 0 1 5131 113590707 113585577 0.000000e+00 9476.0
1 TraesCS7D01G164400 chr7A 90.315 2726 158 41 83 2763 619313306 619310642 0.000000e+00 3474.0
2 TraesCS7D01G164400 chr7A 94.237 1631 60 16 2765 4380 118467740 118466129 0.000000e+00 2460.0
3 TraesCS7D01G164400 chr7A 92.321 1693 64 22 1101 2763 118469865 118468209 0.000000e+00 2346.0
4 TraesCS7D01G164400 chr7A 88.578 1287 54 40 3701 4974 619309081 619307875 0.000000e+00 1476.0
5 TraesCS7D01G164400 chr7A 89.924 526 48 4 99 620 118471899 118471375 0.000000e+00 673.0
6 TraesCS7D01G164400 chr7A 85.160 438 37 11 2765 3184 619309978 619309551 1.710000e-114 424.0
7 TraesCS7D01G164400 chr7A 94.891 137 4 3 847 981 118470006 118469871 1.450000e-50 211.0
8 TraesCS7D01G164400 chr7A 85.802 162 10 4 4970 5131 619307846 619307698 5.320000e-35 159.0
9 TraesCS7D01G164400 chr7A 87.850 107 3 5 674 777 118471237 118471138 3.250000e-22 117.0
10 TraesCS7D01G164400 chr7A 98.485 66 1 0 1 66 118471955 118471890 3.250000e-22 117.0
11 TraesCS7D01G164400 chr7B 96.727 1497 43 4 765 2257 73183590 73182096 0.000000e+00 2488.0
12 TraesCS7D01G164400 chr7B 90.170 824 33 20 3707 4509 73179827 73179031 0.000000e+00 1029.0
13 TraesCS7D01G164400 chr6B 88.541 1597 123 30 993 2541 665740423 665738839 0.000000e+00 1881.0
14 TraesCS7D01G164400 chr6B 84.579 856 74 35 3336 4182 665737276 665736470 0.000000e+00 797.0
15 TraesCS7D01G164400 chr6B 90.130 385 33 4 3900 4284 665733531 665733152 3.570000e-136 496.0
16 TraesCS7D01G164400 chr6B 82.895 152 22 4 2611 2761 665738786 665738638 3.220000e-27 134.0
17 TraesCS7D01G164400 chr6B 88.571 105 7 2 4275 4374 665736450 665736346 6.980000e-24 122.0
18 TraesCS7D01G164400 chr6B 78.873 142 14 3 783 924 665741956 665741831 1.180000e-11 82.4
19 TraesCS7D01G164400 chr6A 91.405 605 44 8 3682 4284 588861121 588860523 0.000000e+00 822.0
20 TraesCS7D01G164400 chr6A 91.327 588 51 0 1658 2245 588863358 588862771 0.000000e+00 804.0
21 TraesCS7D01G164400 chr6A 80.919 283 35 14 3333 3613 588861414 588861149 6.730000e-49 206.0
22 TraesCS7D01G164400 chr6D 90.713 603 52 4 3682 4284 440839750 440839152 0.000000e+00 800.0
23 TraesCS7D01G164400 chr3A 83.213 417 38 15 4394 4806 686840098 686839710 2.270000e-93 353.0
24 TraesCS7D01G164400 chr3D 83.175 315 41 7 4389 4703 549628968 549628666 1.410000e-70 278.0
25 TraesCS7D01G164400 chr3B 88.732 71 6 2 4394 4464 729210521 729210453 9.150000e-13 86.1


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 TraesCS7D01G164400 chr7D 113585577 113590707 5130 True 9476.000000 9476 100.000000 1 5131 1 chr7D.!!$R1 5130
1 TraesCS7D01G164400 chr7A 619307698 619313306 5608 True 1383.250000 3474 87.463750 83 5131 4 chr7A.!!$R2 5048
2 TraesCS7D01G164400 chr7A 118466129 118471955 5826 True 987.333333 2460 92.951333 1 4380 6 chr7A.!!$R1 4379
3 TraesCS7D01G164400 chr7B 73179031 73183590 4559 True 1758.500000 2488 93.448500 765 4509 2 chr7B.!!$R1 3744
4 TraesCS7D01G164400 chr6B 665733152 665741956 8804 True 585.400000 1881 85.598167 783 4374 6 chr6B.!!$R1 3591
5 TraesCS7D01G164400 chr6A 588860523 588863358 2835 True 610.666667 822 87.883667 1658 4284 3 chr6A.!!$R1 2626
6 TraesCS7D01G164400 chr6D 440839152 440839750 598 True 800.000000 800 90.713000 3682 4284 1 chr6D.!!$R1 602

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
72 73 0.521291 GCTTGTGTGTGTGTGTGTGT 59.479 50.0 0.0 0.0 0.00 3.72 F
475 480 0.686789 GCCCCAAATCCAAAAGCAGT 59.313 50.0 0.0 0.0 0.00 4.40 F
2211 4783 0.534652 GCAGTCTCCATGATGCCCTC 60.535 60.0 0.0 0.0 32.49 4.30 F
3300 7311 2.223641 CCTCGGTTTGATCAATGCATGG 60.224 50.0 9.4 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 4234 2.094854 GCTGGCCTTCTTGTCAAAGATG 60.095 50.0 3.32 0.0 42.04 2.90 R
2453 5073 4.584325 AGCAGAACACATGTTGGTTTACAT 59.416 37.5 1.07 0.0 38.56 2.29 R
3476 7599 0.271927 ATGAGGCCAGATCCCCCTTA 59.728 55.0 5.01 0.0 0.00 2.69 R
4935 12536 0.094216 CGACGATGCTTTGCTGTGAG 59.906 55.0 0.00 0.0 0.00 3.51 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
61 62 6.564499 GCATCCAACAAATAAAAGCTTGTGTG 60.564 38.462 0.00 0.00 35.95 3.82
66 67 5.719173 ACAAATAAAAGCTTGTGTGTGTGT 58.281 33.333 8.33 0.94 34.52 3.72
68 69 4.981806 ATAAAAGCTTGTGTGTGTGTGT 57.018 36.364 0.00 0.00 0.00 3.72
70 71 1.533625 AAGCTTGTGTGTGTGTGTGT 58.466 45.000 0.00 0.00 0.00 3.72
71 72 0.804364 AGCTTGTGTGTGTGTGTGTG 59.196 50.000 0.00 0.00 0.00 3.82
72 73 0.521291 GCTTGTGTGTGTGTGTGTGT 59.479 50.000 0.00 0.00 0.00 3.72
73 74 1.728825 GCTTGTGTGTGTGTGTGTGTG 60.729 52.381 0.00 0.00 0.00 3.82
74 75 1.535028 CTTGTGTGTGTGTGTGTGTGT 59.465 47.619 0.00 0.00 0.00 3.72
75 76 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
76 77 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
77 78 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
78 79 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
79 80 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
80 81 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
81 82 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
127 128 2.698274 TGTGTGTGAAAGAGAGCACCTA 59.302 45.455 0.00 0.00 34.19 3.08
188 189 4.626604 GTGTGTGGGCAATTTGACATATTG 59.373 41.667 12.68 12.68 36.34 1.90
228 229 3.562182 TGATCTCAAGCGGATACCAGTA 58.438 45.455 0.00 0.00 0.00 2.74
282 283 2.480845 AGGTAATAGATGCGTTTCGGC 58.519 47.619 0.00 0.00 0.00 5.54
289 290 2.712539 TGCGTTTCGGCAACACTG 59.287 55.556 0.00 0.00 40.59 3.66
306 307 4.314121 ACACTGTGCAGAAGAGAAGAATC 58.686 43.478 7.90 0.00 0.00 2.52
321 322 8.980481 AGAGAAGAATCTGAACAACCTTTTTA 57.020 30.769 0.00 0.00 35.54 1.52
324 325 8.414003 AGAAGAATCTGAACAACCTTTTTAACC 58.586 33.333 0.00 0.00 33.59 2.85
378 382 7.408756 AGCATAATCACTAAGCATCCAAAAA 57.591 32.000 0.00 0.00 0.00 1.94
408 413 5.457148 CAGTTCATATCGAAACGAGGAGAAG 59.543 44.000 0.00 0.00 39.91 2.85
464 469 0.971386 CAGCACTTCAAGCCCCAAAT 59.029 50.000 0.00 0.00 0.00 2.32
474 479 0.978907 AGCCCCAAATCCAAAAGCAG 59.021 50.000 0.00 0.00 0.00 4.24
475 480 0.686789 GCCCCAAATCCAAAAGCAGT 59.313 50.000 0.00 0.00 0.00 4.40
516 527 3.684788 AGCTTCCACTACTGCATAAAACG 59.315 43.478 0.00 0.00 0.00 3.60
518 529 4.201724 GCTTCCACTACTGCATAAAACGAG 60.202 45.833 0.00 0.00 0.00 4.18
615 632 1.675714 CGGCCTCACAGCTATTGTCAA 60.676 52.381 0.00 0.00 38.16 3.18
626 748 5.701290 ACAGCTATTGTCAACTACCAAAGAC 59.299 40.000 0.00 0.00 33.87 3.01
636 758 6.017687 GTCAACTACCAAAGACCGTACAAAAT 60.018 38.462 0.00 0.00 0.00 1.82
647 769 7.562454 AGACCGTACAAAATCAGAAAAAGAA 57.438 32.000 0.00 0.00 0.00 2.52
745 869 1.675720 GCCCTTACCGCCTTACCGTA 61.676 60.000 0.00 0.00 0.00 4.02
746 870 0.823460 CCCTTACCGCCTTACCGTAA 59.177 55.000 0.00 0.00 0.00 3.18
747 871 1.413812 CCCTTACCGCCTTACCGTAAT 59.586 52.381 0.00 0.00 0.00 1.89
748 872 2.158914 CCCTTACCGCCTTACCGTAATT 60.159 50.000 0.00 0.00 0.00 1.40
749 873 3.534554 CCTTACCGCCTTACCGTAATTT 58.465 45.455 0.00 0.00 0.00 1.82
792 2011 3.599412 CCGGGTATTATGACGGTGG 57.401 57.895 0.00 0.00 41.34 4.61
821 2040 4.360889 CATCATTCTAGGCCCTAGGAGAT 58.639 47.826 17.73 14.34 35.03 2.75
947 2173 1.229658 CTCCCTCCTCCCACCAAGT 60.230 63.158 0.00 0.00 0.00 3.16
1218 3790 4.554036 GGCGCCACCATCCTCTCC 62.554 72.222 24.80 0.00 38.86 3.71
1530 4102 2.427245 CCAGTACTCCGGCCTCCTG 61.427 68.421 0.00 0.00 0.00 3.86
1545 4117 4.154347 CTGGCCCCTCTCGCTGTC 62.154 72.222 0.00 0.00 0.00 3.51
2139 4711 2.042930 AGGGACATGGGGAGGACC 59.957 66.667 0.00 0.00 39.11 4.46
2211 4783 0.534652 GCAGTCTCCATGATGCCCTC 60.535 60.000 0.00 0.00 32.49 4.30
2281 4871 4.151883 TCAATTGTAGGCCTGCTTTTCTT 58.848 39.130 22.25 5.41 0.00 2.52
2357 4976 9.838975 TGAAGTAACTTAAATATGCACAACATG 57.161 29.630 0.00 0.00 40.06 3.21
2369 4988 3.869832 TGCACAACATGGTTGAACAATTG 59.130 39.130 15.35 3.24 0.00 2.32
2461 5083 8.301002 TCAGTAAATTGTTAAGCCATGTAAACC 58.699 33.333 0.00 0.00 0.00 3.27
2604 5274 6.072508 TGTGTTCCTCATGCTTCAAGTAAATC 60.073 38.462 0.00 0.00 0.00 2.17
2605 5275 6.003326 TGTTCCTCATGCTTCAAGTAAATCA 58.997 36.000 0.00 0.00 0.00 2.57
2608 5278 5.412594 TCCTCATGCTTCAAGTAAATCACAC 59.587 40.000 0.00 0.00 0.00 3.82
2643 5315 5.415389 TGCTTGCACATATACTGTCATGTTT 59.585 36.000 5.48 0.00 35.29 2.83
2668 5340 5.716228 TCTTTCTGCCATTATCAACATGGTT 59.284 36.000 0.00 0.00 43.01 3.67
2742 5417 5.717119 AATAGCTATGTTCCCTTTGACCT 57.283 39.130 7.09 0.00 0.00 3.85
2743 5418 6.824958 AATAGCTATGTTCCCTTTGACCTA 57.175 37.500 7.09 0.00 0.00 3.08
2763 5450 7.282450 TGACCTATATATATGCTGTGGTAGACG 59.718 40.741 5.44 0.00 0.00 4.18
2808 6409 3.717400 TCTAGTTCTAGCAAGATGGCG 57.283 47.619 2.31 0.00 39.27 5.69
2983 6687 5.295787 TGTCAGCTTGGTAAAGTTTGTAGTG 59.704 40.000 0.00 0.00 35.69 2.74
3072 7053 5.360144 TGTAGTGTATAAGCTTCAGACCTCC 59.640 44.000 0.00 0.00 0.00 4.30
3190 7200 6.699642 TGCTTTTTACTGCCTTTTGTAACATC 59.300 34.615 0.00 0.00 0.00 3.06
3300 7311 2.223641 CCTCGGTTTGATCAATGCATGG 60.224 50.000 9.40 0.00 0.00 3.66
3447 7553 6.700520 ACTGAAGTAACAACTGCTTGTAGTAC 59.299 38.462 0.00 0.00 39.88 2.73
3473 7596 5.841237 TGGTTTTCCATGATCTTTTTACCCA 59.159 36.000 0.00 0.00 46.22 4.51
3476 7599 7.882791 GGTTTTCCATGATCTTTTTACCCAAAT 59.117 33.333 0.00 0.00 40.31 2.32
3477 7600 9.936759 GTTTTCCATGATCTTTTTACCCAAATA 57.063 29.630 0.00 0.00 0.00 1.40
3698 7925 7.612677 AGTACAGTACTACTTTTAGCTTGCAT 58.387 34.615 11.84 0.00 37.23 3.96
3992 8342 2.290260 TGAGAAGAACACGGGCATCAAT 60.290 45.455 0.00 0.00 0.00 2.57
4044 8395 3.088500 GAGAATGTCGTGCAGCCGC 62.089 63.158 0.00 0.00 39.24 6.53
4136 11704 2.305052 AGTCACTGTAAGGTAAAGCCCC 59.695 50.000 0.00 0.00 39.30 5.80
4243 11811 1.336517 TGTTACGTAGGTGCACTGAGC 60.337 52.381 17.98 0.00 45.96 4.26
4264 11832 7.081349 TGAGCTACAATTTTATTTGTGAACGG 58.919 34.615 0.00 0.00 40.00 4.44
4382 11953 7.910162 ACAATATGCACAATTAACTCTAAAGCG 59.090 33.333 0.00 0.00 0.00 4.68
4410 11995 4.537135 TCTAGCAGGATTTGTTTCTCGT 57.463 40.909 0.00 0.00 0.00 4.18
4413 11998 2.549754 AGCAGGATTTGTTTCTCGTGTG 59.450 45.455 0.00 0.00 31.60 3.82
4494 12088 3.119708 GGCTATTTGGGATCGATTCATGC 60.120 47.826 5.94 7.26 0.00 4.06
4500 12094 1.541233 GGGATCGATTCATGCCGAGTT 60.541 52.381 5.94 0.00 38.25 3.01
4501 12095 2.288825 GGGATCGATTCATGCCGAGTTA 60.289 50.000 5.94 0.00 38.25 2.24
4502 12096 2.989840 GGATCGATTCATGCCGAGTTAG 59.010 50.000 0.00 0.00 38.25 2.34
4503 12097 3.553096 GGATCGATTCATGCCGAGTTAGT 60.553 47.826 0.00 0.00 38.25 2.24
4504 12098 3.520290 TCGATTCATGCCGAGTTAGTT 57.480 42.857 0.00 0.00 0.00 2.24
4505 12099 3.444916 TCGATTCATGCCGAGTTAGTTC 58.555 45.455 0.00 0.00 0.00 3.01
4506 12100 3.130516 TCGATTCATGCCGAGTTAGTTCT 59.869 43.478 0.00 0.00 0.00 3.01
4507 12101 3.243877 CGATTCATGCCGAGTTAGTTCTG 59.756 47.826 0.00 0.00 0.00 3.02
4510 12104 4.106029 TCATGCCGAGTTAGTTCTGTAC 57.894 45.455 0.00 0.00 0.00 2.90
4521 12115 2.743938 AGTTCTGTACTTCTGTGCACG 58.256 47.619 13.13 7.36 35.10 5.34
4531 12125 3.434641 ACTTCTGTGCACGAATCTGATTG 59.565 43.478 19.40 11.40 0.00 2.67
4532 12126 3.317603 TCTGTGCACGAATCTGATTGA 57.682 42.857 13.13 0.00 0.00 2.57
4535 12129 4.696877 TCTGTGCACGAATCTGATTGATTT 59.303 37.500 13.13 0.00 44.70 2.17
4545 12139 9.186323 ACGAATCTGATTGATTTCTTATACTCG 57.814 33.333 7.78 2.62 44.70 4.18
4565 12159 0.755698 TATCTCACGGTCTCCCCTGC 60.756 60.000 0.00 0.00 0.00 4.85
4594 12191 3.307480 CGGACCTCAAATCAAGTAGGGTT 60.307 47.826 0.00 0.00 33.16 4.11
4597 12194 6.183360 CGGACCTCAAATCAAGTAGGGTTATA 60.183 42.308 0.00 0.00 33.16 0.98
4623 12220 7.294676 AGTTTTTGATTTGTTTGCTGAGAAC 57.705 32.000 0.00 0.00 0.00 3.01
4630 12227 3.713858 TGTTTGCTGAGAACACAATGG 57.286 42.857 0.00 0.00 32.44 3.16
4648 12245 3.564053 TGGCTGATGATAACTGATGCA 57.436 42.857 0.00 0.00 0.00 3.96
4649 12246 3.208594 TGGCTGATGATAACTGATGCAC 58.791 45.455 0.00 0.00 0.00 4.57
4650 12247 3.208594 GGCTGATGATAACTGATGCACA 58.791 45.455 0.00 0.00 0.00 4.57
4651 12248 3.819337 GGCTGATGATAACTGATGCACAT 59.181 43.478 0.00 0.00 0.00 3.21
4652 12249 4.277672 GGCTGATGATAACTGATGCACATT 59.722 41.667 0.00 0.00 0.00 2.71
4653 12250 5.221185 GGCTGATGATAACTGATGCACATTT 60.221 40.000 0.00 0.00 0.00 2.32
4654 12251 6.016860 GGCTGATGATAACTGATGCACATTTA 60.017 38.462 0.00 0.00 0.00 1.40
4655 12252 7.309012 GGCTGATGATAACTGATGCACATTTAT 60.309 37.037 9.82 9.82 37.16 1.40
4656 12253 8.080417 GCTGATGATAACTGATGCACATTTATT 58.920 33.333 0.00 0.00 35.49 1.40
4657 12254 9.961265 CTGATGATAACTGATGCACATTTATTT 57.039 29.630 0.00 0.00 35.49 1.40
4674 12271 8.524487 ACATTTATTTAATACAAACTTCGGCCA 58.476 29.630 2.24 0.00 0.00 5.36
4677 12274 9.575783 TTTATTTAATACAAACTTCGGCCATTC 57.424 29.630 2.24 0.00 0.00 2.67
4686 12283 2.493278 ACTTCGGCCATTCCATTTCTTG 59.507 45.455 2.24 0.00 34.01 3.02
4715 12312 2.033194 GTTGGTGGTGCCGTAGCTC 61.033 63.158 0.00 0.00 41.21 4.09
4728 12325 3.173599 CCGTAGCTCAAATGCACAATTG 58.826 45.455 3.24 3.24 34.99 2.32
4729 12326 3.173599 CGTAGCTCAAATGCACAATTGG 58.826 45.455 10.83 0.00 34.99 3.16
4732 12329 3.656559 AGCTCAAATGCACAATTGGTTC 58.343 40.909 10.83 0.00 34.99 3.62
4733 12330 3.322828 AGCTCAAATGCACAATTGGTTCT 59.677 39.130 10.83 0.00 34.99 3.01
4737 12334 3.683365 AATGCACAATTGGTTCTTCCC 57.317 42.857 10.83 0.00 34.77 3.97
4738 12335 1.337118 TGCACAATTGGTTCTTCCCC 58.663 50.000 10.83 0.00 34.77 4.81
4739 12336 1.133199 TGCACAATTGGTTCTTCCCCT 60.133 47.619 10.83 0.00 34.77 4.79
4751 12348 4.100963 GGTTCTTCCCCTTTTTGTCATGTT 59.899 41.667 0.00 0.00 0.00 2.71
4776 12373 0.674895 AATCTGTTGCCTCGCCTCAC 60.675 55.000 0.00 0.00 0.00 3.51
4785 12383 1.202359 GCCTCGCCTCACAAACAAAAA 60.202 47.619 0.00 0.00 0.00 1.94
4786 12384 2.459934 CCTCGCCTCACAAACAAAAAC 58.540 47.619 0.00 0.00 0.00 2.43
4789 12387 2.098443 TCGCCTCACAAACAAAAACTCC 59.902 45.455 0.00 0.00 0.00 3.85
4810 12408 1.467734 GAAGTGCCAAGTGCTGATCTG 59.532 52.381 0.00 0.00 42.00 2.90
4822 12420 3.449018 GTGCTGATCTGAAGTAGGAGGAA 59.551 47.826 3.42 0.00 0.00 3.36
4905 12506 1.079888 GCCATTTCAACCGCCTTGG 60.080 57.895 0.00 0.00 46.41 3.61
4914 12515 2.511600 CCGCCTTGGTTAGAGCCG 60.512 66.667 0.00 0.00 0.00 5.52
4932 12533 2.436646 CTCGTCCGGCAAAGGCAT 60.437 61.111 0.00 0.00 43.71 4.40
4933 12534 2.745884 TCGTCCGGCAAAGGCATG 60.746 61.111 0.00 0.00 43.71 4.06
4954 12555 0.094216 CTCACAGCAAAGCATCGTCG 59.906 55.000 0.00 0.00 0.00 5.12
4981 12615 3.068165 CCTAGTTGATGCAGTACCGATGA 59.932 47.826 0.00 0.00 0.00 2.92
4985 12619 1.762370 TGATGCAGTACCGATGACCAT 59.238 47.619 0.00 0.00 0.00 3.55
4989 12623 1.961394 GCAGTACCGATGACCATCCTA 59.039 52.381 4.58 0.00 34.40 2.94
5036 12670 2.124695 CAACGCCCTTAGAGCCCC 60.125 66.667 0.00 0.00 0.00 5.80
5042 12676 4.570663 CCTTAGAGCCCCGTCGCG 62.571 72.222 0.00 0.00 0.00 5.87
5058 12692 3.768632 CGGAGTCGCTTGTAGCAC 58.231 61.111 0.00 0.00 42.58 4.40
5059 12693 2.152699 CGGAGTCGCTTGTAGCACG 61.153 63.158 0.00 0.00 42.58 5.34
5060 12694 1.211969 GGAGTCGCTTGTAGCACGA 59.788 57.895 0.00 0.00 42.58 4.35
5062 12696 3.061674 GTCGCTTGTAGCACGACG 58.938 61.111 0.00 0.00 45.52 5.12
5076 12710 2.399611 GACGTTGTAGCATGGCGC 59.600 61.111 0.00 0.00 42.91 6.53
5100 12734 0.232303 CTCCGTCGCAACACAACTTC 59.768 55.000 0.00 0.00 0.00 3.01
5106 12740 0.592247 CGCAACACAACTTCAGCACC 60.592 55.000 0.00 0.00 0.00 5.01
5121 12755 1.970917 GCACCGGAAGCATGTTCTCG 61.971 60.000 9.46 3.90 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
66 67 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
68 69 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
70 71 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
71 72 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
72 73 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
73 74 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
74 75 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
75 76 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
76 77 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
77 78 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
78 79 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
79 80 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
80 81 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
81 82 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
127 128 2.557452 CCCTCTACCCAACCATGCTTTT 60.557 50.000 0.00 0.00 0.00 2.27
264 265 3.062909 TGTTGCCGAAACGCATCTATTAC 59.937 43.478 0.00 0.00 42.10 1.89
270 271 4.130857 GTGTTGCCGAAACGCATC 57.869 55.556 8.93 0.00 46.54 3.91
282 283 3.461061 TCTTCTCTTCTGCACAGTGTTG 58.539 45.455 1.61 0.00 0.00 3.33
287 288 4.818642 TCAGATTCTTCTCTTCTGCACAG 58.181 43.478 0.00 0.00 37.41 3.66
289 290 4.993584 TGTTCAGATTCTTCTCTTCTGCAC 59.006 41.667 0.00 0.00 37.41 4.57
380 384 5.929992 TCCTCGTTTCGATATGAACTGTTTT 59.070 36.000 0.00 0.00 35.97 2.43
393 398 0.386858 CGTGCTTCTCCTCGTTTCGA 60.387 55.000 0.00 0.00 0.00 3.71
464 469 6.530120 TGATTGTAGTTCTACTGCTTTTGGA 58.470 36.000 10.65 0.00 31.77 3.53
474 479 4.116238 GCTGCTCCTGATTGTAGTTCTAC 58.884 47.826 3.33 3.33 0.00 2.59
475 480 4.026744 AGCTGCTCCTGATTGTAGTTCTA 58.973 43.478 0.00 0.00 0.00 2.10
516 527 9.851043 GTTATAATGCGATTTACAAACTCTCTC 57.149 33.333 0.00 0.00 0.00 3.20
518 529 8.609176 TGGTTATAATGCGATTTACAAACTCTC 58.391 33.333 0.00 0.00 0.00 3.20
567 584 7.925043 ACGTTAATTTGGACACCAATGTATA 57.075 32.000 4.03 0.00 43.55 1.47
590 607 2.802816 CAATAGCTGTGAGGCCGAATAC 59.197 50.000 0.00 0.00 0.00 1.89
615 632 5.613329 TGATTTTGTACGGTCTTTGGTAGT 58.387 37.500 0.00 0.00 0.00 2.73
757 881 0.600057 CGGTAAGGCGGTATACCCTC 59.400 60.000 16.47 8.52 38.68 4.30
760 884 1.115326 ACCCGGTAAGGCGGTATACC 61.115 60.000 12.27 12.27 39.21 2.73
781 2000 0.250510 TGCAACTGCCACCGTCATAA 60.251 50.000 0.00 0.00 41.18 1.90
792 2011 1.336125 GGCCTAGAATGATGCAACTGC 59.664 52.381 0.00 0.00 42.50 4.40
821 2040 1.963855 CCGTGGCCGTGAATGTTGA 60.964 57.895 0.00 0.00 0.00 3.18
947 2173 3.010584 AGGCTAGGGCTTTTCAGATTTCA 59.989 43.478 0.00 0.00 33.67 2.69
1218 3790 3.083349 TGGAGGAGGGACATGCGG 61.083 66.667 0.00 0.00 0.00 5.69
1662 4234 2.094854 GCTGGCCTTCTTGTCAAAGATG 60.095 50.000 3.32 0.00 42.04 2.90
2211 4783 6.258727 GGATGTAACATTACCTGATGACACAG 59.741 42.308 0.00 0.00 37.61 3.66
2281 4871 5.241403 AGTCACCATACTCAAATTGACCA 57.759 39.130 0.00 0.00 35.06 4.02
2402 5022 6.587273 ACAGATCCAATAGAAAGTTAGGAGC 58.413 40.000 0.00 0.00 0.00 4.70
2453 5073 4.584325 AGCAGAACACATGTTGGTTTACAT 59.416 37.500 1.07 0.00 38.56 2.29
2553 5200 7.836842 AGGATCCTATAAATTTTGTGCGTTTT 58.163 30.769 14.27 0.00 0.00 2.43
2604 5274 1.095228 AAGCAACGTGACAGGGTGTG 61.095 55.000 14.26 3.72 0.00 3.82
2605 5275 1.095228 CAAGCAACGTGACAGGGTGT 61.095 55.000 14.26 0.00 0.00 4.16
2608 5278 2.186160 TGCAAGCAACGTGACAGGG 61.186 57.895 0.00 0.00 0.00 4.45
2643 5315 6.211587 CCATGTTGATAATGGCAGAAAGAA 57.788 37.500 0.00 0.00 38.32 2.52
2668 5340 4.518970 GTGGAAGCAACATAACAGAAGGAA 59.481 41.667 0.00 0.00 0.00 3.36
2742 5417 6.376018 TGCACGTCTACCACAGCATATATATA 59.624 38.462 0.00 0.00 32.33 0.86
2743 5418 5.185056 TGCACGTCTACCACAGCATATATAT 59.815 40.000 0.00 0.00 32.33 0.86
2763 5450 2.120909 ATAACCTGCCGGCATGCAC 61.121 57.895 32.87 8.88 36.04 4.57
2808 6409 7.548967 ACTAGCCAACTTACATTCTACTTCTC 58.451 38.462 0.00 0.00 0.00 2.87
2983 6687 2.956333 ACTTGCAAACAGACCTAAACCC 59.044 45.455 0.00 0.00 0.00 4.11
3043 6749 7.549488 GGTCTGAAGCTTATACACTACAACAAT 59.451 37.037 0.00 0.00 0.00 2.71
3072 7053 3.035251 CACATAAACACGCACACAACTG 58.965 45.455 0.00 0.00 0.00 3.16
3190 7200 3.804036 ACCATGTTGATATACCACACCG 58.196 45.455 0.00 0.00 0.00 4.94
3300 7311 2.309501 GCGTGCACCCACAAATTGC 61.310 57.895 12.15 1.12 42.17 3.56
3447 7553 6.818142 GGGTAAAAAGATCATGGAAAACCATG 59.182 38.462 19.36 19.36 46.21 3.66
3460 7566 6.199376 TCCCCCTTATTTGGGTAAAAAGATC 58.801 40.000 0.00 0.00 45.70 2.75
3469 7592 1.859574 CCAGATCCCCCTTATTTGGGT 59.140 52.381 0.00 0.00 45.70 4.51
3470 7593 1.481242 GCCAGATCCCCCTTATTTGGG 60.481 57.143 0.00 0.00 46.68 4.12
3473 7596 1.783365 GAGGCCAGATCCCCCTTATTT 59.217 52.381 5.01 0.00 0.00 1.40
3476 7599 0.271927 ATGAGGCCAGATCCCCCTTA 59.728 55.000 5.01 0.00 0.00 2.69
3477 7600 1.006631 ATGAGGCCAGATCCCCCTT 59.993 57.895 5.01 0.00 0.00 3.95
3485 7610 1.588239 ATGAAGACCATGAGGCCAGA 58.412 50.000 5.01 0.00 39.06 3.86
3521 7646 9.071276 CATGGCATGGAACTTATCTTTATACTT 57.929 33.333 19.80 0.00 0.00 2.24
3527 7659 7.667219 CCTATACATGGCATGGAACTTATCTTT 59.333 37.037 29.49 7.13 33.60 2.52
3992 8342 1.003580 GTGATCTGGCCTTTCCTCACA 59.996 52.381 3.32 0.00 37.45 3.58
4136 11704 2.938956 AAAAGGATCATCCGCCCTAG 57.061 50.000 0.00 0.00 42.75 3.02
4243 11811 6.088883 GCCACCGTTCACAAATAAAATTGTAG 59.911 38.462 0.00 0.00 41.44 2.74
4264 11832 5.824904 ATCATAACACATCAAAGAGCCAC 57.175 39.130 0.00 0.00 0.00 5.01
4382 11953 7.501844 AGAAACAAATCCTGCTAGATACCTAC 58.498 38.462 0.00 0.00 0.00 3.18
4410 11995 4.025040 ACATCTCAAGAGGCATTTCACA 57.975 40.909 0.00 0.00 0.00 3.58
4413 11998 5.633830 TCAAACATCTCAAGAGGCATTTC 57.366 39.130 0.00 0.00 0.00 2.17
4453 12041 1.433534 CCACGAAGTTGAGAAGAGGC 58.566 55.000 0.00 0.00 41.61 4.70
4494 12088 5.154932 CACAGAAGTACAGAACTAACTCGG 58.845 45.833 0.00 0.00 37.50 4.63
4500 12094 3.566742 TCGTGCACAGAAGTACAGAACTA 59.433 43.478 18.64 0.00 37.50 2.24
4501 12095 2.361119 TCGTGCACAGAAGTACAGAACT 59.639 45.455 18.64 0.00 41.49 3.01
4502 12096 2.739292 TCGTGCACAGAAGTACAGAAC 58.261 47.619 18.64 0.00 0.00 3.01
4503 12097 3.446310 TTCGTGCACAGAAGTACAGAA 57.554 42.857 18.64 5.81 0.00 3.02
4504 12098 3.255888 AGATTCGTGCACAGAAGTACAGA 59.744 43.478 18.64 0.00 0.00 3.41
4505 12099 3.366121 CAGATTCGTGCACAGAAGTACAG 59.634 47.826 18.64 9.68 0.00 2.74
4506 12100 3.005367 TCAGATTCGTGCACAGAAGTACA 59.995 43.478 18.64 5.09 0.00 2.90
4507 12101 3.575630 TCAGATTCGTGCACAGAAGTAC 58.424 45.455 18.64 14.68 0.00 2.73
4510 12104 3.681417 TCAATCAGATTCGTGCACAGAAG 59.319 43.478 18.64 9.57 0.00 2.85
4565 12159 4.697352 ACTTGATTTGAGGTCCGAAATCAG 59.303 41.667 21.70 18.88 44.99 2.90
4597 12194 7.903995 TCTCAGCAAACAAATCAAAAACTTT 57.096 28.000 0.00 0.00 0.00 2.66
4623 12220 5.758924 CATCAGTTATCATCAGCCATTGTG 58.241 41.667 0.00 0.00 0.00 3.33
4630 12227 5.434352 AATGTGCATCAGTTATCATCAGC 57.566 39.130 0.00 0.00 0.00 4.26
4648 12245 8.524487 TGGCCGAAGTTTGTATTAAATAAATGT 58.476 29.630 0.00 0.00 0.00 2.71
4649 12246 8.918961 TGGCCGAAGTTTGTATTAAATAAATG 57.081 30.769 0.00 0.00 0.00 2.32
4651 12248 9.575783 GAATGGCCGAAGTTTGTATTAAATAAA 57.424 29.630 0.00 0.00 0.00 1.40
4652 12249 8.192110 GGAATGGCCGAAGTTTGTATTAAATAA 58.808 33.333 0.00 0.00 0.00 1.40
4653 12250 7.339721 TGGAATGGCCGAAGTTTGTATTAAATA 59.660 33.333 0.00 0.00 40.66 1.40
4654 12251 6.153680 TGGAATGGCCGAAGTTTGTATTAAAT 59.846 34.615 0.00 0.00 40.66 1.40
4655 12252 5.477291 TGGAATGGCCGAAGTTTGTATTAAA 59.523 36.000 0.00 0.00 40.66 1.52
4656 12253 5.010933 TGGAATGGCCGAAGTTTGTATTAA 58.989 37.500 0.00 0.00 40.66 1.40
4657 12254 4.590918 TGGAATGGCCGAAGTTTGTATTA 58.409 39.130 0.00 0.00 40.66 0.98
4658 12255 3.426615 TGGAATGGCCGAAGTTTGTATT 58.573 40.909 0.00 0.00 40.66 1.89
4659 12256 3.080300 TGGAATGGCCGAAGTTTGTAT 57.920 42.857 0.00 0.00 40.66 2.29
4660 12257 2.570415 TGGAATGGCCGAAGTTTGTA 57.430 45.000 0.00 0.00 40.66 2.41
4661 12258 1.923356 ATGGAATGGCCGAAGTTTGT 58.077 45.000 0.00 0.00 40.66 2.83
4664 12261 2.807676 AGAAATGGAATGGCCGAAGTT 58.192 42.857 0.00 0.00 40.66 2.66
4669 12266 0.531657 TGCAAGAAATGGAATGGCCG 59.468 50.000 0.00 0.00 40.66 6.13
4677 12274 2.030007 ACCGTGTGATTGCAAGAAATGG 60.030 45.455 4.94 6.70 0.00 3.16
4686 12283 1.285641 CCACCAACCGTGTGATTGC 59.714 57.895 0.00 0.00 41.26 3.56
4708 12305 3.173599 CCAATTGTGCATTTGAGCTACG 58.826 45.455 4.43 0.00 34.99 3.51
4715 12312 3.747529 GGGAAGAACCAATTGTGCATTTG 59.252 43.478 4.43 0.00 41.20 2.32
4728 12325 3.641436 ACATGACAAAAAGGGGAAGAACC 59.359 43.478 0.00 0.00 38.08 3.62
4729 12326 4.937201 ACATGACAAAAAGGGGAAGAAC 57.063 40.909 0.00 0.00 0.00 3.01
4732 12329 4.379652 CCAAACATGACAAAAAGGGGAAG 58.620 43.478 0.00 0.00 0.00 3.46
4733 12330 3.432890 GCCAAACATGACAAAAAGGGGAA 60.433 43.478 0.00 0.00 0.00 3.97
4737 12334 5.528320 AGATTTGCCAAACATGACAAAAAGG 59.472 36.000 0.00 0.00 35.79 3.11
4738 12335 6.037391 ACAGATTTGCCAAACATGACAAAAAG 59.963 34.615 0.00 0.50 35.79 2.27
4739 12336 5.879223 ACAGATTTGCCAAACATGACAAAAA 59.121 32.000 0.00 0.00 35.79 1.94
4776 12373 2.857748 GGCACTTCGGAGTTTTTGTTTG 59.142 45.455 0.00 0.00 32.54 2.93
4785 12383 1.598130 GCACTTGGCACTTCGGAGT 60.598 57.895 0.00 0.00 43.97 3.85
4786 12384 3.257933 GCACTTGGCACTTCGGAG 58.742 61.111 0.00 0.00 43.97 4.63
4810 12408 7.106239 TGAATGATTTCACTTCCTCCTACTTC 58.894 38.462 0.00 0.00 36.94 3.01
4905 12506 2.278013 CGGACGAGCGGCTCTAAC 60.278 66.667 25.96 16.36 0.00 2.34
4906 12507 3.515286 CCGGACGAGCGGCTCTAA 61.515 66.667 25.96 0.00 0.00 2.10
4929 12530 1.445582 GCTTTGCTGTGAGGCATGC 60.446 57.895 9.90 9.90 42.09 4.06
4930 12531 0.530744 ATGCTTTGCTGTGAGGCATG 59.469 50.000 0.00 0.00 41.26 4.06
4931 12532 0.815734 GATGCTTTGCTGTGAGGCAT 59.184 50.000 0.00 0.00 44.73 4.40
4932 12533 1.579964 CGATGCTTTGCTGTGAGGCA 61.580 55.000 0.00 0.00 40.74 4.75
4933 12534 1.136147 CGATGCTTTGCTGTGAGGC 59.864 57.895 0.00 0.00 0.00 4.70
4935 12536 0.094216 CGACGATGCTTTGCTGTGAG 59.906 55.000 0.00 0.00 0.00 3.51
4936 12537 0.599991 ACGACGATGCTTTGCTGTGA 60.600 50.000 0.00 0.00 0.00 3.58
4937 12538 0.235665 AACGACGATGCTTTGCTGTG 59.764 50.000 0.00 0.00 0.00 3.66
4938 12539 0.235665 CAACGACGATGCTTTGCTGT 59.764 50.000 0.00 0.00 0.00 4.40
4939 12540 0.235665 ACAACGACGATGCTTTGCTG 59.764 50.000 0.00 0.00 0.00 4.41
4940 12541 0.512952 GACAACGACGATGCTTTGCT 59.487 50.000 0.00 0.00 0.00 3.91
4941 12542 0.452784 GGACAACGACGATGCTTTGC 60.453 55.000 0.00 0.00 0.00 3.68
4944 12545 1.544691 ACTAGGACAACGACGATGCTT 59.455 47.619 0.00 0.00 0.00 3.91
4954 12555 3.933332 GGTACTGCATCAACTAGGACAAC 59.067 47.826 0.00 0.00 0.00 3.32
4985 12619 0.616395 TTGCCACGGACATCCTAGGA 60.616 55.000 15.46 15.46 31.63 2.94
4989 12623 1.302511 GTGTTGCCACGGACATCCT 60.303 57.895 0.00 0.00 0.00 3.24
4998 12632 2.331451 GGTGCTTCGTGTTGCCAC 59.669 61.111 0.00 0.00 38.27 5.01
5042 12676 1.071567 GTCGTGCTACAAGCGACTCC 61.072 60.000 8.75 0.00 46.26 3.85
5050 12684 1.269154 TGCTACAACGTCGTGCTACAA 60.269 47.619 0.00 0.00 0.00 2.41
5051 12685 0.311477 TGCTACAACGTCGTGCTACA 59.689 50.000 0.00 0.00 0.00 2.74
5052 12686 1.320555 CATGCTACAACGTCGTGCTAC 59.679 52.381 0.00 0.00 0.00 3.58
5053 12687 1.624487 CATGCTACAACGTCGTGCTA 58.376 50.000 0.00 0.00 0.00 3.49
5054 12688 1.014044 CCATGCTACAACGTCGTGCT 61.014 55.000 0.00 0.00 0.00 4.40
5055 12689 1.419922 CCATGCTACAACGTCGTGC 59.580 57.895 0.00 0.00 0.00 5.34
5056 12690 1.419922 GCCATGCTACAACGTCGTG 59.580 57.895 0.00 0.00 0.00 4.35
5057 12691 2.092291 CGCCATGCTACAACGTCGT 61.092 57.895 0.00 0.00 0.00 4.34
5058 12692 2.695055 CGCCATGCTACAACGTCG 59.305 61.111 0.00 0.00 0.00 5.12
5059 12693 2.399611 GCGCCATGCTACAACGTC 59.600 61.111 0.00 0.00 41.73 4.34
5060 12694 3.124921 GGCGCCATGCTACAACGT 61.125 61.111 24.80 0.00 45.43 3.99
5061 12695 3.876198 GGGCGCCATGCTACAACG 61.876 66.667 30.85 0.00 45.43 4.10
5062 12696 3.876198 CGGGCGCCATGCTACAAC 61.876 66.667 30.85 6.07 45.43 3.32
5100 12734 0.957395 AGAACATGCTTCCGGTGCTG 60.957 55.000 19.31 16.52 0.00 4.41
5106 12740 2.279582 ACTACGAGAACATGCTTCCG 57.720 50.000 0.00 5.28 0.00 4.30


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

AutoCloner maintained by Alex Coulton.