Multiple sequence alignment - TraesCS7D01G258900

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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 TraesCS7D01G258900 chr7D 100.000 7149 0 0 406 7554 234562293 234555145 0.000000e+00 13202.0
1 TraesCS7D01G258900 chr7D 92.785 4130 253 11 2201 6300 234654574 234650460 0.000000e+00 5934.0
2 TraesCS7D01G258900 chr7D 87.732 701 42 22 782 1463 234356322 234355647 0.000000e+00 778.0
3 TraesCS7D01G258900 chr7D 86.326 724 63 16 1473 2167 234355460 234354744 0.000000e+00 756.0
4 TraesCS7D01G258900 chr7D 82.289 734 79 26 1473 2167 234655398 234654677 8.440000e-164 588.0
5 TraesCS7D01G258900 chr7D 78.371 712 129 15 4409 5102 234352880 234352176 9.000000e-119 438.0
6 TraesCS7D01G258900 chr7D 78.014 564 82 25 914 1463 234656026 234655491 4.400000e-82 316.0
7 TraesCS7D01G258900 chr7D 100.000 155 0 0 1 155 234562698 234562544 3.450000e-73 287.0
8 TraesCS7D01G258900 chr7D 75.850 294 62 7 7086 7371 169371970 169371678 2.840000e-29 141.0
9 TraesCS7D01G258900 chr7B 95.504 6450 176 35 1180 7554 206517052 206510642 0.000000e+00 10200.0
10 TraesCS7D01G258900 chr7B 92.615 4130 261 12 2201 6300 209645902 209641787 0.000000e+00 5897.0
11 TraesCS7D01G258900 chr7B 96.915 3015 68 4 1388 4379 209148668 209145656 0.000000e+00 5029.0
12 TraesCS7D01G258900 chr7B 92.302 2533 153 9 3798 6300 209323942 209321422 0.000000e+00 3559.0
13 TraesCS7D01G258900 chr7B 95.552 1304 41 8 5049 6337 209141575 209140274 0.000000e+00 2071.0
14 TraesCS7D01G258900 chr7B 86.283 729 59 20 1473 2167 206344217 206343496 0.000000e+00 754.0
15 TraesCS7D01G258900 chr7B 84.876 767 56 25 406 1129 206517794 206517045 0.000000e+00 719.0
16 TraesCS7D01G258900 chr7B 84.667 750 51 24 406 1112 209149916 209149188 0.000000e+00 689.0
17 TraesCS7D01G258900 chr7B 88.462 598 22 19 893 1463 206345007 206344430 0.000000e+00 678.0
18 TraesCS7D01G258900 chr7B 83.757 708 73 20 1494 2171 209646696 209646001 3.850000e-177 632.0
19 TraesCS7D01G258900 chr7B 92.264 349 12 6 6352 6697 209140288 209139952 1.470000e-131 481.0
20 TraesCS7D01G258900 chr7B 79.213 712 123 17 4409 5102 206341633 206340929 8.870000e-129 472.0
21 TraesCS7D01G258900 chr7B 92.727 275 17 3 6655 6928 209139967 209139695 1.980000e-105 394.0
22 TraesCS7D01G258900 chr7B 85.523 373 14 17 836 1187 206345883 206345530 3.350000e-93 353.0
23 TraesCS7D01G258900 chr7B 88.629 299 18 7 1165 1463 209148985 209148703 4.340000e-92 350.0
24 TraesCS7D01G258900 chr7B 83.137 255 36 4 5142 5391 209139505 209139253 7.630000e-55 226.0
25 TraesCS7D01G258900 chr7B 91.613 155 13 0 1 155 206529957 206529803 1.650000e-51 215.0
26 TraesCS7D01G258900 chr7B 90.196 153 10 4 1 153 209150153 209150006 2.150000e-45 195.0
27 TraesCS7D01G258900 chr7B 89.510 143 14 1 5624 5766 209139190 209139049 6.020000e-41 180.0
28 TraesCS7D01G258900 chr7A 97.154 4498 82 11 2153 6633 248936706 248941174 0.000000e+00 7555.0
29 TraesCS7D01G258900 chr7A 92.677 3045 196 11 2201 5223 249282447 249279408 0.000000e+00 4362.0
30 TraesCS7D01G258900 chr7A 94.137 2780 111 25 1473 4227 248544445 248541693 0.000000e+00 4183.0
31 TraesCS7D01G258900 chr7A 93.531 1314 68 7 4224 5524 248541596 248540287 0.000000e+00 1940.0
32 TraesCS7D01G258900 chr7A 90.098 1424 64 33 735 2135 248935352 248936721 0.000000e+00 1777.0
33 TraesCS7D01G258900 chr7A 94.505 728 36 2 5542 6265 249278937 249278210 0.000000e+00 1120.0
34 TraesCS7D01G258900 chr7A 89.381 565 31 14 914 1463 247275012 247274462 0.000000e+00 684.0
35 TraesCS7D01G258900 chr7A 88.364 550 54 6 7007 7554 248549126 248548585 0.000000e+00 652.0
36 TraesCS7D01G258900 chr7A 82.283 762 85 26 1480 2201 249283233 249282482 1.390000e-171 614.0
37 TraesCS7D01G258900 chr7A 86.292 569 54 13 1473 2021 247274251 247273687 1.400000e-166 597.0
38 TraesCS7D01G258900 chr7A 90.855 339 25 5 5219 5553 249279317 249278981 4.160000e-122 449.0
39 TraesCS7D01G258900 chr7A 90.493 284 26 1 466 749 248935055 248935337 2.570000e-99 374.0
40 TraesCS7D01G258900 chr7A 90.406 271 16 3 1203 1463 248544928 248544658 1.560000e-91 348.0
41 TraesCS7D01G258900 chr7A 83.794 253 14 11 920 1166 248545159 248544928 1.650000e-51 215.0
42 TraesCS7D01G258900 chr7A 90.323 155 15 0 1 155 248934626 248934780 3.570000e-48 204.0
43 TraesCS7D01G258900 chr7A 76.965 369 52 25 4983 5329 248536234 248535877 6.020000e-41 180.0
44 TraesCS7D01G258900 chr7A 89.109 101 7 3 1362 1462 247274447 247274351 1.030000e-23 122.0
45 TraesCS7D01G258900 chr7A 83.696 92 5 3 6209 6300 248535274 248535193 2.260000e-10 78.7
46 TraesCS7D01G258900 chr3B 85.298 823 84 16 1362 2164 145509174 145508369 0.000000e+00 815.0
47 TraesCS7D01G258900 chr3B 78.333 420 67 16 4703 5102 145506168 145505753 4.530000e-62 250.0
48 TraesCS7D01G258900 chr3B 87.209 172 8 11 953 1117 145509894 145509730 4.660000e-42 183.0
49 TraesCS7D01G258900 chr5D 80.755 265 46 5 7176 7438 514025006 514024745 1.290000e-47 202.0
50 TraesCS7D01G258900 chr3A 76.031 388 77 12 7063 7437 554206356 554206740 3.600000e-43 187.0
51 TraesCS7D01G258900 chr3A 87.209 86 11 0 7348 7433 8160072 8159987 1.730000e-16 99.0
52 TraesCS7D01G258900 chr5B 79.615 260 44 8 7183 7438 644945598 644945344 2.170000e-40 178.0
53 TraesCS7D01G258900 chr5B 85.294 102 14 1 7240 7340 33553660 33553559 3.730000e-18 104.0
54 TraesCS7D01G258900 chrUn 75.802 343 68 15 7060 7395 127035032 127035366 7.850000e-35 159.0
55 TraesCS7D01G258900 chr5A 86.408 103 11 3 7240 7340 28231730 28231831 8.010000e-20 110.0
56 TraesCS7D01G258900 chr2A 81.818 99 16 2 7074 7170 161562566 161562664 1.750000e-11 82.4
57 TraesCS7D01G258900 chr2A 77.236 123 23 5 7055 7174 50148042 50148162 4.890000e-07 67.6
58 TraesCS7D01G258900 chr1A 90.000 60 5 1 7089 7147 495663615 495663556 8.130000e-10 76.8
59 TraesCS7D01G258900 chr2D 82.857 70 10 2 7058 7126 498777328 498777260 2.280000e-05 62.1


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 TraesCS7D01G258900 chr7D 234555145 234562698 7553 True 6744.500000 13202 100.000000 1 7554 2 chr7D.!!$R3 7553
1 TraesCS7D01G258900 chr7D 234650460 234656026 5566 True 2279.333333 5934 84.362667 914 6300 3 chr7D.!!$R4 5386
2 TraesCS7D01G258900 chr7D 234352176 234356322 4146 True 657.333333 778 84.143000 782 5102 3 chr7D.!!$R2 4320
3 TraesCS7D01G258900 chr7B 206510642 206517794 7152 True 5459.500000 10200 90.190000 406 7554 2 chr7B.!!$R4 7148
4 TraesCS7D01G258900 chr7B 209321422 209323942 2520 True 3559.000000 3559 92.302000 3798 6300 1 chr7B.!!$R2 2502
5 TraesCS7D01G258900 chr7B 209641787 209646696 4909 True 3264.500000 5897 88.186000 1494 6300 2 chr7B.!!$R7 4806
6 TraesCS7D01G258900 chr7B 209145656 209150153 4497 True 1565.750000 5029 90.101750 1 4379 4 chr7B.!!$R6 4378
7 TraesCS7D01G258900 chr7B 209139049 209141575 2526 True 670.400000 2071 90.638000 5049 6928 5 chr7B.!!$R5 1879
8 TraesCS7D01G258900 chr7B 206340929 206345883 4954 True 564.250000 754 84.870250 836 5102 4 chr7B.!!$R3 4266
9 TraesCS7D01G258900 chr7A 248934626 248941174 6548 False 2477.500000 7555 92.017000 1 6633 4 chr7A.!!$F1 6632
10 TraesCS7D01G258900 chr7A 249278210 249283233 5023 True 1636.250000 4362 90.080000 1480 6265 4 chr7A.!!$R4 4785
11 TraesCS7D01G258900 chr7A 248540287 248549126 8839 True 1467.600000 4183 90.046400 920 7554 5 chr7A.!!$R3 6634
12 TraesCS7D01G258900 chr7A 247273687 247275012 1325 True 467.666667 684 88.260667 914 2021 3 chr7A.!!$R1 1107
13 TraesCS7D01G258900 chr3B 145505753 145509894 4141 True 416.000000 815 83.613333 953 5102 3 chr3B.!!$R1 4149

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
515 516 0.034863 TACCTCCGCCACCAAATTCC 60.035 55.000 0.00 0.00 0.00 3.01 F
552 553 0.041839 GCCATCGCTATTCACGCTTG 60.042 55.000 0.00 0.00 0.00 4.01 F
892 1754 0.179108 AGAGGATTAGCGCCGTCAAC 60.179 55.000 2.29 0.00 0.00 3.18 F
1465 4854 0.244721 AGGATTTTTGCTTCAGGCGC 59.755 50.000 0.00 0.00 45.43 6.53 F
1466 4855 0.244721 GGATTTTTGCTTCAGGCGCT 59.755 50.000 7.64 0.00 45.43 5.92 F
1468 4857 0.668401 ATTTTTGCTTCAGGCGCTGC 60.668 50.000 7.64 5.16 45.43 5.25 F
1470 4859 0.888736 TTTTGCTTCAGGCGCTGCTA 60.889 50.000 7.64 0.00 45.43 3.49 F
2758 6695 3.561725 CCCGAGAGTTATGCAAAGGATTC 59.438 47.826 0.00 0.00 0.00 2.52 F
3719 7987 3.630312 GCTACGAAAAATTGGGCTGGATA 59.370 43.478 0.00 0.00 0.00 2.59 F
5657 10242 3.228188 TCTTTGAATGGCCTGTTGAGT 57.772 42.857 3.32 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1367 4636 0.599728 GCTAGCGAGGCATCAAGAGG 60.600 60.000 0.00 0.0 0.00 3.69 R
1463 4852 0.733729 ACGGACTAGAGTTAGCAGCG 59.266 55.000 0.00 0.0 0.00 5.18 R
2486 6423 1.604378 CTTCTCCCCGGTGCAGAAT 59.396 57.895 0.00 0.0 0.00 2.40 R
2758 6695 1.813753 CCGGTCACTATTGCCCACG 60.814 63.158 0.00 0.0 0.00 4.94 R
3655 7923 8.930760 GCTGCTACTTCTTTATTCCATATGTAG 58.069 37.037 1.24 0.0 0.00 2.74 R
3719 7987 9.643693 CTTTTGCCATAATAAGACTGTTGAAAT 57.356 29.630 0.00 0.0 0.00 2.17 R
3735 8004 7.279615 ACACTATAGCATACACTTTTGCCATA 58.720 34.615 0.00 0.0 39.72 2.74 R
4336 8713 4.956075 AGTTACCACATTTCCATCCCATTC 59.044 41.667 0.00 0.0 0.00 2.67 R
5768 10356 6.340522 CCTTTCTTCAAACAACAAACTGGAT 58.659 36.000 0.00 0.0 0.00 3.41 R
7047 11689 0.109723 TTAAGGTGTCTGTGTGGGCC 59.890 55.000 0.00 0.0 0.00 5.80 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
38 39 4.213906 CCATTACATGTGATGCGCTATTCA 59.786 41.667 21.89 6.56 0.00 2.57
53 54 1.163420 ATTCACAAAGCGACGCACCA 61.163 50.000 23.70 0.00 0.00 4.17
55 56 1.369209 CACAAAGCGACGCACCAAG 60.369 57.895 23.70 9.25 0.00 3.61
489 490 3.228188 AGCTTTCATTGTGGTTCCTCA 57.772 42.857 0.00 0.00 0.00 3.86
515 516 0.034863 TACCTCCGCCACCAAATTCC 60.035 55.000 0.00 0.00 0.00 3.01
525 526 2.819608 CCACCAAATTCCGATGTCTTGT 59.180 45.455 0.00 0.00 0.00 3.16
552 553 0.041839 GCCATCGCTATTCACGCTTG 60.042 55.000 0.00 0.00 0.00 4.01
558 559 1.324736 CGCTATTCACGCTTGGAGTTC 59.675 52.381 0.00 0.00 0.00 3.01
588 589 2.553028 CGCCTAAATCTATGTGGGGCAT 60.553 50.000 0.00 0.00 41.42 4.40
674 699 7.009631 TCGCTAAATCTCTCGAGAAAGATTTTG 59.990 37.037 31.29 29.39 45.42 2.44
740 794 8.674263 TTTTGTCAAACAATTGGCTCATTATT 57.326 26.923 10.83 0.00 41.79 1.40
892 1754 0.179108 AGAGGATTAGCGCCGTCAAC 60.179 55.000 2.29 0.00 0.00 3.18
893 1755 0.459585 GAGGATTAGCGCCGTCAACA 60.460 55.000 2.29 0.00 0.00 3.33
896 1758 1.465187 GGATTAGCGCCGTCAACAAAC 60.465 52.381 2.29 0.00 0.00 2.93
1019 4098 4.423209 GCTCCTCCCCACCTCCCT 62.423 72.222 0.00 0.00 0.00 4.20
1034 4122 2.641746 CCCTCCTCCTCCTCCACCT 61.642 68.421 0.00 0.00 0.00 4.00
1352 4617 0.941542 CGTTCTCGGTTGCTTTTCCA 59.058 50.000 0.00 0.00 0.00 3.53
1367 4636 1.149987 TTCCACCGTATGTTGCGAAC 58.850 50.000 0.00 0.00 0.00 3.95
1377 4653 0.874390 TGTTGCGAACCTCTTGATGC 59.126 50.000 0.00 0.00 0.00 3.91
1463 4852 3.256631 TCTTCAGGATTTTTGCTTCAGGC 59.743 43.478 0.00 0.00 42.22 4.85
1464 4853 1.541147 TCAGGATTTTTGCTTCAGGCG 59.459 47.619 0.00 0.00 45.43 5.52
1465 4854 0.244721 AGGATTTTTGCTTCAGGCGC 59.755 50.000 0.00 0.00 45.43 6.53
1466 4855 0.244721 GGATTTTTGCTTCAGGCGCT 59.755 50.000 7.64 0.00 45.43 5.92
1467 4856 1.343506 GATTTTTGCTTCAGGCGCTG 58.656 50.000 7.64 3.67 45.43 5.18
1468 4857 0.668401 ATTTTTGCTTCAGGCGCTGC 60.668 50.000 7.64 5.16 45.43 5.25
1469 4858 1.737355 TTTTTGCTTCAGGCGCTGCT 61.737 50.000 7.64 0.00 45.43 4.24
1470 4859 0.888736 TTTTGCTTCAGGCGCTGCTA 60.889 50.000 7.64 0.00 45.43 3.49
1471 4860 0.888736 TTTGCTTCAGGCGCTGCTAA 60.889 50.000 7.64 5.15 45.43 3.09
2486 6423 4.513777 ACGGAGTGCACCTCTACA 57.486 55.556 14.63 0.00 42.51 2.74
2758 6695 3.561725 CCCGAGAGTTATGCAAAGGATTC 59.438 47.826 0.00 0.00 0.00 2.52
3655 7923 5.063060 GCAGAGAAAATTGTTGATGCCATTC 59.937 40.000 0.00 0.00 0.00 2.67
3719 7987 3.630312 GCTACGAAAAATTGGGCTGGATA 59.370 43.478 0.00 0.00 0.00 2.59
3735 8004 6.547510 GGGCTGGATATTTCAACAGTCTTATT 59.452 38.462 0.00 0.00 35.95 1.40
4204 8481 6.166984 TGTTGATATAGAAGCCAAGGAGAG 57.833 41.667 0.00 0.00 0.00 3.20
4336 8713 4.990543 TGACACTTCTTTGCTATTGTCG 57.009 40.909 0.00 0.00 36.89 4.35
4519 8896 8.072567 GCGATCTAATGATTTGAATAGCTTGTT 58.927 33.333 0.00 0.00 32.19 2.83
5657 10242 3.228188 TCTTTGAATGGCCTGTTGAGT 57.772 42.857 3.32 0.00 0.00 3.41
5760 10348 8.709386 TGTTAATCTGATAGAGCTTTCTTGTC 57.291 34.615 0.00 0.00 0.00 3.18
5768 10356 8.846943 TGATAGAGCTTTCTTGTCAACAAATA 57.153 30.769 0.00 0.00 35.15 1.40
6250 10845 5.250235 TCACGTCCAATTTTGTTGCTTTA 57.750 34.783 0.00 0.00 0.00 1.85
6300 10896 1.340308 TGCAGCATGTAGATTGCAGGT 60.340 47.619 0.00 0.00 41.23 4.00
6327 10923 4.377021 TGGTCTGTTCACACTGTTCATAC 58.623 43.478 0.00 0.00 0.00 2.39
6329 10925 4.377021 GTCTGTTCACACTGTTCATACCA 58.623 43.478 0.00 0.00 0.00 3.25
6422 11021 6.619801 AGAACACTGGATCTGTTTTGTTAC 57.380 37.500 0.87 0.00 31.83 2.50
6623 11222 4.385447 GTGTCGGAGTAGCGAGTATAGTAG 59.615 50.000 0.00 0.00 0.00 2.57
6628 11227 5.105957 CGGAGTAGCGAGTATAGTAGGTCTA 60.106 48.000 0.00 0.00 0.00 2.59
6650 11249 5.592104 ATGTCCACGGGAAAATAAAATCC 57.408 39.130 0.00 0.00 31.38 3.01
6652 11251 4.461081 TGTCCACGGGAAAATAAAATCCAG 59.539 41.667 0.00 0.00 37.46 3.86
6657 11286 5.016831 ACGGGAAAATAAAATCCAGCTCTT 58.983 37.500 0.00 0.00 37.46 2.85
6692 11330 0.101399 CGAAGAGATGTCTCCGGTGG 59.899 60.000 0.00 0.00 43.88 4.61
6693 11331 1.187087 GAAGAGATGTCTCCGGTGGT 58.813 55.000 0.00 0.00 43.88 4.16
6694 11332 0.898320 AAGAGATGTCTCCGGTGGTG 59.102 55.000 0.00 0.00 43.88 4.17
6695 11333 0.972983 AGAGATGTCTCCGGTGGTGG 60.973 60.000 0.00 0.00 43.88 4.61
6696 11334 0.970937 GAGATGTCTCCGGTGGTGGA 60.971 60.000 0.00 0.00 37.02 4.02
6697 11335 0.325671 AGATGTCTCCGGTGGTGGAT 60.326 55.000 0.00 0.00 37.41 3.41
6698 11336 0.105039 GATGTCTCCGGTGGTGGATC 59.895 60.000 0.00 0.00 37.41 3.36
6699 11337 1.676678 ATGTCTCCGGTGGTGGATCG 61.677 60.000 0.00 0.00 37.41 3.69
6729 11367 1.068055 GCCGTTAGAAGACCTTGTCGA 60.068 52.381 0.00 0.00 37.67 4.20
6745 11383 0.892755 TCGACCAACATAGGAACGCT 59.107 50.000 0.00 0.00 34.30 5.07
6755 11393 3.129638 ACATAGGAACGCTGTCTCTCTTC 59.870 47.826 0.00 0.00 0.00 2.87
6853 11491 2.566833 TTCCAATGCTACAGTGCTGT 57.433 45.000 9.90 9.90 46.87 4.40
6856 11494 4.220693 TCCAATGCTACAGTGCTGTATT 57.779 40.909 11.86 3.33 44.15 1.89
6876 11514 8.568676 TGTATTAAGGCACAGCAATTTACTTA 57.431 30.769 0.00 0.00 0.00 2.24
6877 11515 8.673711 TGTATTAAGGCACAGCAATTTACTTAG 58.326 33.333 0.00 0.00 0.00 2.18
6958 11599 4.997395 CAGCCTAAACTCTAAGCACTTGAA 59.003 41.667 0.00 0.00 0.00 2.69
6977 11618 3.126514 TGAACTCGAGCTAACCTTCTACG 59.873 47.826 13.61 0.00 0.00 3.51
6978 11619 1.401199 ACTCGAGCTAACCTTCTACGC 59.599 52.381 13.61 0.00 0.00 4.42
7017 11659 0.468226 TCAAGCCGGTCTCAAACACT 59.532 50.000 1.90 0.00 0.00 3.55
7031 11673 0.608582 AACACTAGGACGAGCGACCT 60.609 55.000 17.05 17.05 42.46 3.85
7036 11678 0.251354 TAGGACGAGCGACCTAGTGT 59.749 55.000 15.17 0.00 40.48 3.55
7047 11689 4.446719 AGCGACCTAGTGTAAAAAGAAACG 59.553 41.667 0.00 0.00 0.00 3.60
7054 11697 2.099427 GTGTAAAAAGAAACGGCCCACA 59.901 45.455 0.00 0.00 0.00 4.17
7093 11736 1.740296 CAAACGTAGGGGCTGACCG 60.740 63.158 0.00 0.00 41.60 4.79
7107 11750 2.673610 GCTGACCGGCATCTCTCATATC 60.674 54.545 0.00 0.00 0.00 1.63
7119 11762 6.703319 CATCTCTCATATCCAGCTCAAATCT 58.297 40.000 0.00 0.00 0.00 2.40
7241 11884 2.492088 TCTAGTGAGGATGTGAACACCG 59.508 50.000 2.46 0.00 34.33 4.94
7242 11885 0.320771 AGTGAGGATGTGAACACCGC 60.321 55.000 2.46 0.00 34.33 5.68
7340 11983 0.540830 ATCCGATTCCTCCCTCTCCG 60.541 60.000 0.00 0.00 0.00 4.63
7425 12068 2.490148 CGCCATAGCCCGACAGAGA 61.490 63.158 0.00 0.00 34.57 3.10
7531 12174 4.196193 GGATAAAACATCACCACCATCGA 58.804 43.478 0.00 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 3.022287 CTTGGTGCGTCGCTTTGT 58.978 55.556 19.50 0.00 0.00 2.83
53 54 3.173953 TGATGATTTTGAGGTGGGCTT 57.826 42.857 0.00 0.00 0.00 4.35
55 56 3.091545 TCTTGATGATTTTGAGGTGGGC 58.908 45.455 0.00 0.00 0.00 5.36
410 411 1.269517 CGATCCAGAGCTAGCAGAACC 60.270 57.143 18.83 0.26 0.00 3.62
415 416 1.329913 TTGCCGATCCAGAGCTAGCA 61.330 55.000 18.83 0.00 0.00 3.49
443 444 1.615392 GCAGGAGTGTGCCATCTTTTT 59.385 47.619 0.00 0.00 37.49 1.94
489 490 2.283388 TGGCGGAGGTACGGTTCT 60.283 61.111 0.00 0.00 0.00 3.01
496 497 0.034863 GGAATTTGGTGGCGGAGGTA 60.035 55.000 0.00 0.00 0.00 3.08
515 516 3.638484 TGGCGATATGTACAAGACATCG 58.362 45.455 19.70 19.70 46.33 3.84
537 538 0.530744 ACTCCAAGCGTGAATAGCGA 59.469 50.000 0.00 0.00 40.04 4.93
558 559 0.034059 AGATTTAGGCGCCGGAGATG 59.966 55.000 23.20 0.00 0.00 2.90
566 567 1.523758 CCCCACATAGATTTAGGCGC 58.476 55.000 0.00 0.00 0.00 6.53
588 589 4.557695 GCAACCGACATCACACCATAAAAA 60.558 41.667 0.00 0.00 0.00 1.94
864 920 2.350964 GCGCTAATCCTCTCCTTCTACG 60.351 54.545 0.00 0.00 0.00 3.51
892 1754 1.488390 ATGCTATGCTTGGGGGTTTG 58.512 50.000 0.00 0.00 0.00 2.93
893 1755 2.110578 GAATGCTATGCTTGGGGGTTT 58.889 47.619 0.00 0.00 0.00 3.27
896 1758 1.174712 CCGAATGCTATGCTTGGGGG 61.175 60.000 0.00 0.00 0.00 5.40
1011 4090 1.075600 GAGGAGGAGGAGGGAGGTG 60.076 68.421 0.00 0.00 0.00 4.00
1012 4091 2.329399 GGAGGAGGAGGAGGGAGGT 61.329 68.421 0.00 0.00 0.00 3.85
1014 4093 1.075600 GTGGAGGAGGAGGAGGGAG 60.076 68.421 0.00 0.00 0.00 4.30
1016 4095 2.041405 GGTGGAGGAGGAGGAGGG 60.041 72.222 0.00 0.00 0.00 4.30
1017 4096 0.689412 GAAGGTGGAGGAGGAGGAGG 60.689 65.000 0.00 0.00 0.00 4.30
1018 4097 0.338120 AGAAGGTGGAGGAGGAGGAG 59.662 60.000 0.00 0.00 0.00 3.69
1019 4098 0.336737 GAGAAGGTGGAGGAGGAGGA 59.663 60.000 0.00 0.00 0.00 3.71
1034 4122 3.812019 GCGACGAGGCCGAGAGAA 61.812 66.667 0.00 0.00 39.50 2.87
1258 4521 2.677003 ATTGCGGCGGAGAAACACG 61.677 57.895 9.78 0.00 0.00 4.49
1352 4617 0.606604 AGAGGTTCGCAACATACGGT 59.393 50.000 0.00 0.00 0.00 4.83
1367 4636 0.599728 GCTAGCGAGGCATCAAGAGG 60.600 60.000 0.00 0.00 0.00 3.69
1377 4653 1.154205 CCAACATTCCGCTAGCGAGG 61.154 60.000 37.39 22.53 42.83 4.63
1463 4852 0.733729 ACGGACTAGAGTTAGCAGCG 59.266 55.000 0.00 0.00 0.00 5.18
1464 4853 2.286301 CGTACGGACTAGAGTTAGCAGC 60.286 54.545 7.57 0.00 0.00 5.25
1465 4854 2.287373 CCGTACGGACTAGAGTTAGCAG 59.713 54.545 30.64 0.00 37.50 4.24
1466 4855 2.283298 CCGTACGGACTAGAGTTAGCA 58.717 52.381 30.64 0.00 37.50 3.49
1467 4856 2.284190 ACCGTACGGACTAGAGTTAGC 58.716 52.381 39.52 0.00 38.96 3.09
1468 4857 4.033817 CAGAACCGTACGGACTAGAGTTAG 59.966 50.000 39.52 18.41 38.96 2.34
1469 4858 3.935203 CAGAACCGTACGGACTAGAGTTA 59.065 47.826 39.52 0.00 38.96 2.24
1470 4859 2.746362 CAGAACCGTACGGACTAGAGTT 59.254 50.000 39.52 21.58 38.96 3.01
1471 4860 2.354259 CAGAACCGTACGGACTAGAGT 58.646 52.381 39.52 13.69 38.96 3.24
2279 6208 2.683933 GTCTCCTCCGCTTCCCCA 60.684 66.667 0.00 0.00 0.00 4.96
2486 6423 1.604378 CTTCTCCCCGGTGCAGAAT 59.396 57.895 0.00 0.00 0.00 2.40
2758 6695 1.813753 CCGGTCACTATTGCCCACG 60.814 63.158 0.00 0.00 0.00 4.94
3655 7923 8.930760 GCTGCTACTTCTTTATTCCATATGTAG 58.069 37.037 1.24 0.00 0.00 2.74
3719 7987 9.643693 CTTTTGCCATAATAAGACTGTTGAAAT 57.356 29.630 0.00 0.00 0.00 2.17
3735 8004 7.279615 ACACTATAGCATACACTTTTGCCATA 58.720 34.615 0.00 0.00 39.72 2.74
4204 8481 5.900865 AGTAGGTTCTACTGAGTAAGTGC 57.099 43.478 6.78 0.00 40.26 4.40
4336 8713 4.956075 AGTTACCACATTTCCATCCCATTC 59.044 41.667 0.00 0.00 0.00 2.67
5698 10286 8.129840 GTGTATCTCAAGTGACTGATTACGTAT 58.870 37.037 0.00 0.00 0.00 3.06
5768 10356 6.340522 CCTTTCTTCAAACAACAAACTGGAT 58.659 36.000 0.00 0.00 0.00 3.41
6220 10815 4.151689 ACAAAATTGGACGTGATGACTACG 59.848 41.667 0.00 0.00 46.31 3.51
6250 10845 0.982704 AGTCCTGCAATGACTCAGCT 59.017 50.000 11.72 0.00 37.20 4.24
6300 10896 1.000843 CAGTGTGAACAGACCATCCGA 59.999 52.381 0.00 0.00 0.00 4.55
6422 11021 5.869344 TCTCGATAAGGAGTCAATGTTGTTG 59.131 40.000 0.00 0.00 35.52 3.33
6623 11222 2.773993 TTTTCCCGTGGACATAGACC 57.226 50.000 0.00 0.00 0.00 3.85
6628 11227 5.020132 TGGATTTTATTTTCCCGTGGACAT 58.980 37.500 0.00 0.00 0.00 3.06
6650 11249 1.734477 CCACACGACCGAAGAGCTG 60.734 63.158 0.00 0.00 0.00 4.24
6652 11251 1.444553 CTCCACACGACCGAAGAGC 60.445 63.158 0.00 0.00 0.00 4.09
6657 11286 1.446516 TTCGTTCTCCACACGACCGA 61.447 55.000 0.00 0.00 46.04 4.69
6692 11330 1.064134 GCCGAAAATGCCGATCCAC 59.936 57.895 0.00 0.00 0.00 4.02
6693 11331 2.118404 GGCCGAAAATGCCGATCCA 61.118 57.895 0.00 0.00 39.48 3.41
6694 11332 2.721859 GGCCGAAAATGCCGATCC 59.278 61.111 0.00 0.00 39.48 3.36
6699 11337 0.806241 TTCTAACGGCCGAAAATGCC 59.194 50.000 35.90 0.00 45.70 4.40
6700 11338 1.735571 TCTTCTAACGGCCGAAAATGC 59.264 47.619 35.90 0.00 0.00 3.56
6729 11367 1.623811 AGACAGCGTTCCTATGTTGGT 59.376 47.619 0.00 0.00 0.00 3.67
6745 11383 4.023107 CCACTTGTAGAACGAAGAGAGACA 60.023 45.833 0.00 0.00 0.00 3.41
6755 11393 2.259618 CCATCGTCCACTTGTAGAACG 58.740 52.381 0.00 0.00 0.00 3.95
6834 11472 2.566833 ACAGCACTGTAGCATTGGAA 57.433 45.000 0.35 0.00 42.90 3.53
6853 11491 9.456147 TTCTAAGTAAATTGCTGTGCCTTAATA 57.544 29.630 0.00 0.00 0.00 0.98
6856 11494 6.940298 ACTTCTAAGTAAATTGCTGTGCCTTA 59.060 34.615 0.00 0.00 37.52 2.69
6876 11514 2.042686 TGTGCTGCACAGAAACTTCT 57.957 45.000 29.99 0.00 39.62 2.85
6958 11599 1.401199 GCGTAGAAGGTTAGCTCGAGT 59.599 52.381 15.13 3.51 0.00 4.18
6977 11618 1.502163 GCGTCTGGCCATAGATGTGC 61.502 60.000 5.51 3.51 36.34 4.57
6978 11619 2.609825 GCGTCTGGCCATAGATGTG 58.390 57.895 5.51 0.00 36.34 3.21
7017 11659 0.251354 ACACTAGGTCGCTCGTCCTA 59.749 55.000 13.04 13.04 35.43 2.94
7031 11673 3.565063 GTGGGCCGTTTCTTTTTACACTA 59.435 43.478 0.00 0.00 0.00 2.74
7036 11678 2.359531 CTGTGTGGGCCGTTTCTTTTTA 59.640 45.455 0.00 0.00 0.00 1.52
7047 11689 0.109723 TTAAGGTGTCTGTGTGGGCC 59.890 55.000 0.00 0.00 0.00 5.80
7054 11697 2.036862 GAGACCGGTTTAAGGTGTCTGT 59.963 50.000 9.42 0.00 45.37 3.41
7093 11736 2.566279 TGAGCTGGATATGAGAGATGCC 59.434 50.000 0.00 0.00 0.00 4.40
7119 11762 4.263572 CGCCCCATATTCGCCCCA 62.264 66.667 0.00 0.00 0.00 4.96
7157 11800 1.356527 GGAACCCGGTCGTCAATTCG 61.357 60.000 0.00 0.00 0.00 3.34
7407 12050 2.016393 TTCTCTGTCGGGCTATGGCG 62.016 60.000 0.00 0.00 39.81 5.69
7413 12056 0.832135 TGGTCTTTCTCTGTCGGGCT 60.832 55.000 0.00 0.00 0.00 5.19
7425 12068 4.514401 GGAGATCCAAATACGTGGTCTTT 58.486 43.478 0.00 0.00 39.88 2.52
7531 12174 1.308998 CTTGACGAGGTTGGTGCTTT 58.691 50.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.