Multiple sequence alignment - TraesCS5B01G397200

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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 TraesCS5B01G397200 chr5B 100.000 6248 0 0 1 6248 574908191 574914438 0.000000e+00 11538.0
1 TraesCS5B01G397200 chr5D 94.991 2895 90 19 2609 5475 467779587 467782454 0.000000e+00 4492.0
2 TraesCS5B01G397200 chr5D 91.207 2320 112 29 344 2642 467777338 467779586 0.000000e+00 3070.0
3 TraesCS5B01G397200 chr5D 92.456 570 35 4 5677 6246 467854764 467855325 0.000000e+00 808.0
4 TraesCS5B01G397200 chr5D 91.562 320 6 2 1 300 467776918 467777236 7.490000e-114 422.0
5 TraesCS5B01G397200 chr5D 89.735 302 15 7 5182 5475 467845572 467845865 7.650000e-99 372.0
6 TraesCS5B01G397200 chr5D 92.377 223 11 5 5255 5475 467810061 467810279 4.700000e-81 313.0
7 TraesCS5B01G397200 chr5D 88.213 263 23 7 5218 5475 467845129 467845388 2.190000e-79 307.0
8 TraesCS5B01G397200 chr5A 91.425 3137 113 51 2428 5478 588555699 588558765 0.000000e+00 4159.0
9 TraesCS5B01G397200 chr5A 92.571 848 37 4 1580 2426 588554810 588555632 0.000000e+00 1194.0
10 TraesCS5B01G397200 chr5A 84.121 1291 104 41 347 1613 588553589 588554802 0.000000e+00 1155.0
11 TraesCS5B01G397200 chr5A 93.380 574 26 3 5677 6246 588560790 588561355 0.000000e+00 839.0
12 TraesCS5B01G397200 chr5A 85.024 207 23 7 5469 5672 693053270 693053069 2.950000e-48 204.0
13 TraesCS5B01G397200 chr5A 85.128 195 23 6 5469 5660 694011018 694010827 1.780000e-45 195.0
14 TraesCS5B01G397200 chr5A 87.059 170 20 1 2087 2256 170103854 170103687 2.300000e-44 191.0
15 TraesCS5B01G397200 chr5A 88.652 141 15 1 1 141 588552901 588553040 2.990000e-38 171.0
16 TraesCS5B01G397200 chr3D 84.541 207 25 6 5469 5672 587936489 587936691 1.370000e-46 198.0
17 TraesCS5B01G397200 chr3D 81.818 209 30 7 5469 5672 383595685 383595890 1.080000e-37 169.0
18 TraesCS5B01G397200 chr6A 87.283 173 18 3 2087 2258 10032398 10032567 1.780000e-45 195.0
19 TraesCS5B01G397200 chr2B 87.059 170 20 1 2087 2256 160676759 160676926 2.300000e-44 191.0
20 TraesCS5B01G397200 chrUn 86.471 170 21 1 2087 2256 36273960 36273793 1.070000e-42 185.0
21 TraesCS5B01G397200 chrUn 86.471 170 21 1 2087 2256 313736064 313736231 1.070000e-42 185.0
22 TraesCS5B01G397200 chrUn 100.000 28 0 0 4366 4393 45082369 45082396 1.100000e-02 52.8
23 TraesCS5B01G397200 chrUn 100.000 28 0 0 4366 4393 182433994 182433967 1.100000e-02 52.8
24 TraesCS5B01G397200 chrUn 100.000 28 0 0 4366 4393 182463484 182463457 1.100000e-02 52.8
25 TraesCS5B01G397200 chr3B 86.471 170 21 1 2087 2256 5466187 5466020 1.070000e-42 185.0
26 TraesCS5B01G397200 chr3B 83.092 207 25 10 5469 5670 829093837 829093636 4.980000e-41 180.0
27 TraesCS5B01G397200 chr7D 82.710 214 21 12 5469 5675 384818979 384818775 6.440000e-40 176.0
28 TraesCS5B01G397200 chr7D 81.818 209 28 9 5469 5669 579996930 579997136 3.870000e-37 167.0
29 TraesCS5B01G397200 chr7B 81.313 198 31 5 5481 5675 234518433 234518239 8.390000e-34 156.0
30 TraesCS5B01G397200 chr2A 82.199 191 24 9 5474 5660 738832519 738832703 8.390000e-34 156.0
31 TraesCS5B01G397200 chr2D 88.034 117 12 2 358 473 14121005 14121120 3.040000e-28 137.0
32 TraesCS5B01G397200 chr2D 78.182 220 37 8 350 561 45475834 45475618 5.080000e-26 130.0
33 TraesCS5B01G397200 chr6D 100.000 28 0 0 4366 4393 108508384 108508357 1.100000e-02 52.8
34 TraesCS5B01G397200 chr4D 100.000 28 0 0 4366 4393 241390571 241390598 1.100000e-02 52.8
35 TraesCS5B01G397200 chr4D 100.000 28 0 0 4366 4393 428775793 428775820 1.100000e-02 52.8
36 TraesCS5B01G397200 chr4B 100.000 28 0 0 4366 4393 209184221 209184194 1.100000e-02 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G397200 chr5B 574908191 574914438 6247 False 11538.000000 11538 100.000000 1 6248 1 chr5B.!!$F1 6247
1 TraesCS5B01G397200 chr5D 467776918 467782454 5536 False 2661.333333 4492 92.586667 1 5475 3 chr5D.!!$F3 5474
2 TraesCS5B01G397200 chr5D 467854764 467855325 561 False 808.000000 808 92.456000 5677 6246 1 chr5D.!!$F2 569
3 TraesCS5B01G397200 chr5D 467845129 467845865 736 False 339.500000 372 88.974000 5182 5475 2 chr5D.!!$F4 293
4 TraesCS5B01G397200 chr5A 588552901 588561355 8454 False 1503.600000 4159 90.029800 1 6246 5 chr5A.!!$F1 6245

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
234 255 0.512952 CGAACAAGGAGAAGGCAACG 59.487 55.000 0.00 0.0 46.39 4.10 F
345 782 0.981183 TGTGTCAAGGGGCGAGTAAT 59.019 50.000 0.00 0.0 0.00 1.89 F
605 1044 1.271656 GCCAATGCTTCTATGCCCATC 59.728 52.381 0.00 0.0 33.53 3.51 F
1561 2037 0.912486 AGGTGGGCATGGTTCTACTC 59.088 55.000 0.00 0.0 0.00 2.59 F
2560 3149 0.179089 CTGCCTAGTGCCTAGTGCTG 60.179 60.000 16.09 13.6 42.00 4.41 F
3436 4113 1.489481 TCCAGAATCAGACTGCCGAT 58.511 50.000 0.00 0.0 34.47 4.18 F
4337 5038 1.802960 CTGAGCAATGAGGTGTCACAC 59.197 52.381 0.00 0.0 34.75 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1395 1871 0.036010 AATGCCAGAACCACGAGGAG 60.036 55.000 5.68 0.00 38.69 3.69 R
1396 1872 0.400213 AAATGCCAGAACCACGAGGA 59.600 50.000 5.68 0.00 38.69 3.71 R
1773 2293 1.950216 TGCAAAGCGTGTAAATGGTGA 59.050 42.857 0.00 0.00 0.00 4.02 R
2769 3417 1.756538 ACAAACAACAAGGAAGGCAGG 59.243 47.619 0.00 0.00 0.00 4.85 R
3920 4597 0.037326 CGGCACTTGCTAACCTCTCA 60.037 55.000 0.38 0.00 41.70 3.27 R
4729 5430 0.963355 TAACCTGGCACCGGAATTGC 60.963 55.000 9.46 7.95 39.41 3.56 R
5669 6469 0.035317 CTTCTGTGCTGGGCTGTACA 59.965 55.000 0.00 0.00 0.00 2.90 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
63 64 9.272901 GCTAAAATTTGTTTTTCCTTGTCAAAC 57.727 29.630 0.00 0.00 38.47 2.93
161 182 2.947652 ACACATATCATCTTGCCAGTGC 59.052 45.455 0.00 0.00 38.26 4.40
234 255 0.512952 CGAACAAGGAGAAGGCAACG 59.487 55.000 0.00 0.00 46.39 4.10
326 715 6.763135 TGCTGCTTCAACGATTTATAGATCTT 59.237 34.615 0.00 0.00 0.00 2.40
329 718 7.909267 TGCTTCAACGATTTATAGATCTTGTG 58.091 34.615 0.00 0.00 0.00 3.33
345 782 0.981183 TGTGTCAAGGGGCGAGTAAT 59.019 50.000 0.00 0.00 0.00 1.89
355 792 1.644786 GGCGAGTAATGGCGTTTGCT 61.645 55.000 0.00 0.00 42.25 3.91
411 849 2.125552 CAATCTCCGGCGTGCAGA 60.126 61.111 6.01 4.42 0.00 4.26
412 850 1.741401 CAATCTCCGGCGTGCAGAA 60.741 57.895 6.01 0.00 0.00 3.02
605 1044 1.271656 GCCAATGCTTCTATGCCCATC 59.728 52.381 0.00 0.00 33.53 3.51
615 1054 4.897509 TCTATGCCCATCCTAGTTCATG 57.102 45.455 0.00 0.00 0.00 3.07
630 1069 5.886960 AGTTCATGTTTCTAGCCAATGTC 57.113 39.130 0.00 0.00 0.00 3.06
672 1111 6.881017 GCAAAAAGCTCCATCAAAACTTTAG 58.119 36.000 0.00 0.00 41.15 1.85
853 1313 4.634443 GCCCAGATACTGACAACGTATTTT 59.366 41.667 0.00 0.00 32.44 1.82
937 1397 1.544314 GGCAGAGCTTGAGTCCACTTT 60.544 52.381 0.00 0.00 0.00 2.66
986 1462 2.363361 GGAGGGGAGGAAGGTCGA 59.637 66.667 0.00 0.00 0.00 4.20
987 1463 2.059190 GGAGGGGAGGAAGGTCGAC 61.059 68.421 7.13 7.13 0.00 4.20
989 1465 3.459063 GGGGAGGAAGGTCGACGG 61.459 72.222 9.92 0.00 0.00 4.79
990 1466 3.459063 GGGAGGAAGGTCGACGGG 61.459 72.222 9.92 0.00 0.00 5.28
991 1467 3.459063 GGAGGAAGGTCGACGGGG 61.459 72.222 9.92 0.00 0.00 5.73
992 1468 3.459063 GAGGAAGGTCGACGGGGG 61.459 72.222 9.92 0.00 0.00 5.40
1180 1656 4.142315 GCCTCGTCGCCAAGGTATATATAA 60.142 45.833 0.00 0.00 34.96 0.98
1181 1657 5.622914 GCCTCGTCGCCAAGGTATATATAAA 60.623 44.000 0.00 0.00 34.96 1.40
1182 1658 6.570692 CCTCGTCGCCAAGGTATATATAAAT 58.429 40.000 0.00 0.00 0.00 1.40
1183 1659 7.682741 GCCTCGTCGCCAAGGTATATATAAATA 60.683 40.741 0.00 0.00 34.96 1.40
1184 1660 8.358148 CCTCGTCGCCAAGGTATATATAAATAT 58.642 37.037 0.00 0.00 32.87 1.28
1248 1724 4.426112 CTCGCTGCTGTCGGCTCA 62.426 66.667 5.01 0.00 42.40 4.26
1249 1725 3.713205 CTCGCTGCTGTCGGCTCAT 62.713 63.158 5.01 0.00 42.40 2.90
1283 1759 4.851214 GAGCGGGAGGAGGAGGCT 62.851 72.222 0.00 0.00 36.51 4.58
1297 1773 2.119832 GGCTAGGGGAGGCGGATA 59.880 66.667 0.00 0.00 41.55 2.59
1561 2037 0.912486 AGGTGGGCATGGTTCTACTC 59.088 55.000 0.00 0.00 0.00 2.59
1574 2050 3.254892 GTTCTACTCTTCCCTTTGCTCG 58.745 50.000 0.00 0.00 0.00 5.03
1578 2054 1.625818 ACTCTTCCCTTTGCTCGATGT 59.374 47.619 0.00 0.00 0.00 3.06
1586 2104 4.102524 TCCCTTTGCTCGATGTTACCATAT 59.897 41.667 0.00 0.00 0.00 1.78
1680 2200 4.330894 GGAACGGTATTTTCTAAACCCGAG 59.669 45.833 14.98 0.00 35.64 4.63
1684 2204 4.510571 GGTATTTTCTAAACCCGAGCAGA 58.489 43.478 0.00 0.00 0.00 4.26
1700 2220 6.461092 CCCGAGCAGAGATGTTACTTATACAA 60.461 42.308 0.00 0.00 0.00 2.41
1723 2243 6.566197 AGGATATTATAAGCAACAGCAAGC 57.434 37.500 0.00 0.00 0.00 4.01
1757 2277 6.166279 GGCTCACAGATCGAATGGATAATTA 58.834 40.000 6.03 0.00 34.82 1.40
1773 2293 8.846943 TGGATAATTAATCAGCATACAATCGT 57.153 30.769 0.00 0.00 36.20 3.73
1882 2402 4.946157 CAGACCAGTTGGCAAGAAATATCT 59.054 41.667 0.00 0.00 39.32 1.98
2022 2543 7.114754 TCTTTGAGGTGAGCTTGAATTATCAT 58.885 34.615 0.00 0.00 34.96 2.45
2033 2554 4.754372 TGAATTATCATTCCATCGCTGC 57.246 40.909 0.00 0.00 38.50 5.25
2261 2782 9.145865 CTTCCTGTTAAGACTTCTTCTATTCAC 57.854 37.037 0.00 0.00 37.40 3.18
2262 2783 7.612677 TCCTGTTAAGACTTCTTCTATTCACC 58.387 38.462 0.00 0.00 37.40 4.02
2263 2784 7.234782 TCCTGTTAAGACTTCTTCTATTCACCA 59.765 37.037 0.00 0.00 37.40 4.17
2266 2787 9.436957 TGTTAAGACTTCTTCTATTCACCATTC 57.563 33.333 0.00 0.00 37.40 2.67
2309 2830 4.283467 TCTTGTACATAGCACTGACAAGGT 59.717 41.667 18.87 0.00 44.54 3.50
2311 2832 5.324784 TGTACATAGCACTGACAAGGTAG 57.675 43.478 0.00 0.00 0.00 3.18
2312 2833 3.252974 ACATAGCACTGACAAGGTAGC 57.747 47.619 0.00 0.00 0.00 3.58
2313 2834 2.567169 ACATAGCACTGACAAGGTAGCA 59.433 45.455 0.00 0.00 0.00 3.49
2314 2835 2.743636 TAGCACTGACAAGGTAGCAC 57.256 50.000 0.00 0.00 0.00 4.40
2362 2883 9.544579 AACTAGTATTCCAGGTAGTTACTTCTT 57.455 33.333 0.00 0.00 34.64 2.52
2415 2939 6.311735 AGGGTATTGAACATTGTAACTGGTT 58.688 36.000 0.00 0.00 0.00 3.67
2560 3149 0.179089 CTGCCTAGTGCCTAGTGCTG 60.179 60.000 16.09 13.60 42.00 4.41
2564 3153 1.827969 CCTAGTGCCTAGTGCTGAAGT 59.172 52.381 8.01 0.00 42.00 3.01
2644 3258 7.040473 AGATTTGTAGTTCCTCCTATGTACG 57.960 40.000 0.00 0.00 0.00 3.67
2767 3415 7.969536 ACGATAAAGTATGCTTATCATTGCT 57.030 32.000 0.00 0.00 36.63 3.91
2768 3416 8.383318 ACGATAAAGTATGCTTATCATTGCTT 57.617 30.769 0.00 0.00 36.63 3.91
2769 3417 8.499162 ACGATAAAGTATGCTTATCATTGCTTC 58.501 33.333 0.00 0.00 36.63 3.86
2772 3420 6.630444 AAGTATGCTTATCATTGCTTCCTG 57.370 37.500 0.00 0.00 36.63 3.86
2814 3466 4.910195 TGCAGTTTGAGGAGTTCATACAT 58.090 39.130 0.00 0.00 39.40 2.29
2894 3546 4.112634 GTCCTTTGAACTTGAAACTTGCC 58.887 43.478 0.00 0.00 0.00 4.52
3016 3668 7.412891 GCATGTTTGTGGTGCCTAAATAATTTC 60.413 37.037 0.00 0.00 32.88 2.17
3018 3670 7.375053 TGTTTGTGGTGCCTAAATAATTTCTC 58.625 34.615 0.00 0.00 0.00 2.87
3108 3760 7.094762 GGGATTACATTTTAGCAGGTACTATGC 60.095 40.741 13.60 13.60 44.18 3.14
3119 3771 4.624125 GCAGGTACTATGCTCCTTTCTGTT 60.624 45.833 14.03 0.00 40.59 3.16
3319 3996 3.628008 TCATGGTGTCCATACTCTACGT 58.372 45.455 0.74 0.00 43.15 3.57
3331 4008 5.451381 CCATACTCTACGTGGTTGCAGAATA 60.451 44.000 0.00 0.00 0.00 1.75
3334 4011 5.488341 ACTCTACGTGGTTGCAGAATAATT 58.512 37.500 0.00 0.00 0.00 1.40
3436 4113 1.489481 TCCAGAATCAGACTGCCGAT 58.511 50.000 0.00 0.00 34.47 4.18
3458 4135 7.414319 CCGATTTCAATAATTTTTGGCATTGCT 60.414 33.333 8.82 0.00 0.00 3.91
3527 4204 7.614494 GCCCACATTGCCATATTAATCTATTT 58.386 34.615 0.00 0.00 0.00 1.40
3740 4417 3.499338 TCTTCATGAAAGGCACACCATT 58.501 40.909 9.88 0.00 39.06 3.16
3920 4597 4.037923 ACGAGTGCAATTTTCACCAAAGAT 59.962 37.500 0.00 0.00 35.14 2.40
3965 4642 5.359194 TGTGTAAAATGCTTTTGGGGAAA 57.641 34.783 0.00 0.00 34.19 3.13
4073 4773 4.278419 AGGATCAGGTTAACAACAAACTGC 59.722 41.667 8.10 0.00 42.00 4.40
4102 4803 2.287769 CCCAGGTGCAAAAACAAAAGG 58.712 47.619 0.00 0.00 0.00 3.11
4176 4877 4.037089 GTCTGTAACAAACCAACCCGATTT 59.963 41.667 0.00 0.00 0.00 2.17
4255 4956 6.044754 TGCATACAATCCTTAGGGAATCATCT 59.955 38.462 0.00 0.00 45.78 2.90
4270 4971 6.183360 GGGAATCATCTGTTTTAGGCTAAACC 60.183 42.308 18.87 13.06 37.24 3.27
4337 5038 1.802960 CTGAGCAATGAGGTGTCACAC 59.197 52.381 0.00 0.00 34.75 3.82
4461 5162 6.145534 GCAGAAAGGCTTTGTTTTATGGTTAC 59.854 38.462 18.79 0.00 0.00 2.50
4465 5166 7.961325 AAGGCTTTGTTTTATGGTTACAATG 57.039 32.000 0.00 0.00 32.39 2.82
4729 5430 5.334105 GCAATATCCAGGTGCTGTTAATACG 60.334 44.000 0.00 0.00 35.36 3.06
4741 5442 2.096174 TGTTAATACGCAATTCCGGTGC 59.904 45.455 0.00 2.80 38.68 5.01
4755 5456 1.826720 CCGGTGCCAGGTTAGTAGTAA 59.173 52.381 0.00 0.00 0.00 2.24
4766 5467 7.147949 GCCAGGTTAGTAGTAAGATTCTGTACA 60.148 40.741 0.00 0.00 0.00 2.90
4813 5514 8.661257 TGATTTACATACTAACACATTTGGTCG 58.339 33.333 0.00 0.00 0.00 4.79
4818 5519 6.366877 ACATACTAACACATTTGGTCGTACAC 59.633 38.462 0.00 0.00 0.00 2.90
4827 5528 0.240145 TGGTCGTACACGCTCTTCTG 59.760 55.000 0.00 0.00 39.60 3.02
4830 5531 1.080772 CGTACACGCTCTTCTGGCA 60.081 57.895 0.00 0.00 0.00 4.92
4854 5555 5.900123 ACCAATGGTAGCTAAGTATCTCAGT 59.100 40.000 1.52 0.00 32.11 3.41
4856 5557 7.092846 ACCAATGGTAGCTAAGTATCTCAGTTT 60.093 37.037 1.52 0.00 32.11 2.66
4915 5618 7.429636 TGAGCTTGTAACTAATTGTACAACC 57.570 36.000 11.22 3.09 0.00 3.77
5018 5722 4.359706 AGCAAAACAACGAGGTGAATTTC 58.640 39.130 0.00 0.00 0.00 2.17
5058 5762 3.954258 ACCTGTGTTTCAGAAGGGAAAAG 59.046 43.478 0.00 0.00 46.27 2.27
5269 5981 6.515272 AAACGGCATAGATTCAATTCAACT 57.485 33.333 0.00 0.00 0.00 3.16
5275 5987 6.347240 GGCATAGATTCAATTCAACTCTAGCG 60.347 42.308 0.00 0.00 0.00 4.26
5304 6016 8.865978 CAAATCATGAAGTTTGTTGTATCATGG 58.134 33.333 11.91 0.00 44.62 3.66
5311 6023 7.602644 TGAAGTTTGTTGTATCATGGAGTACTC 59.397 37.037 14.87 14.87 0.00 2.59
5373 6091 6.406370 TGTACTTATACATGCTGTTGAAGCT 58.594 36.000 0.00 0.00 43.41 3.74
5456 6179 8.180706 TGATTGTGAAAGAGAAAAATCCATCA 57.819 30.769 0.00 0.00 0.00 3.07
5475 6198 5.504665 CCATCAACAGTCACTGAACTTGTTC 60.505 44.000 13.14 6.56 35.18 3.18
5476 6199 4.574892 TCAACAGTCACTGAACTTGTTCA 58.425 39.130 13.14 14.42 35.18 3.18
5478 6201 4.946784 ACAGTCACTGAACTTGTTCAAC 57.053 40.909 13.14 11.62 35.18 3.18
5480 6203 4.943705 ACAGTCACTGAACTTGTTCAACAT 59.056 37.500 13.14 3.88 35.18 2.71
5481 6204 5.415701 ACAGTCACTGAACTTGTTCAACATT 59.584 36.000 13.14 2.44 35.18 2.71
5483 6206 6.808212 CAGTCACTGAACTTGTTCAACATTTT 59.192 34.615 15.70 0.00 32.44 1.82
5484 6207 7.329226 CAGTCACTGAACTTGTTCAACATTTTT 59.671 33.333 15.70 0.00 32.44 1.94
5486 6209 7.328249 GTCACTGAACTTGTTCAACATTTTTCA 59.672 33.333 15.70 0.20 0.00 2.69
5487 6210 7.869937 TCACTGAACTTGTTCAACATTTTTCAA 59.130 29.630 15.70 0.00 0.00 2.69
5488 6211 8.494347 CACTGAACTTGTTCAACATTTTTCAAA 58.506 29.630 15.70 0.00 0.00 2.69
5757 8311 2.106683 GCCGTGGTCTGAAATCCCG 61.107 63.158 0.00 0.00 0.00 5.14
5758 8312 1.594833 CCGTGGTCTGAAATCCCGA 59.405 57.895 0.00 0.00 0.00 5.14
5759 8313 0.036765 CCGTGGTCTGAAATCCCGAA 60.037 55.000 0.00 0.00 0.00 4.30
5760 8314 1.609580 CCGTGGTCTGAAATCCCGAAA 60.610 52.381 0.00 0.00 0.00 3.46
5761 8315 2.356135 CGTGGTCTGAAATCCCGAAAT 58.644 47.619 0.00 0.00 0.00 2.17
5762 8316 2.351726 CGTGGTCTGAAATCCCGAAATC 59.648 50.000 0.00 0.00 0.00 2.17
5763 8317 2.683362 GTGGTCTGAAATCCCGAAATCC 59.317 50.000 0.00 0.00 0.00 3.01
5764 8318 2.298610 GGTCTGAAATCCCGAAATCCC 58.701 52.381 0.00 0.00 0.00 3.85
5789 8343 1.000283 GACATCCTAGGCCTCGTCATG 60.000 57.143 9.68 10.19 0.00 3.07
5812 8366 2.137528 GCCTCTACTCCTCCCCTGC 61.138 68.421 0.00 0.00 0.00 4.85
5900 8454 2.591715 GGCTTCCAGCACGTGTGT 60.592 61.111 18.38 1.58 44.75 3.72
5988 8542 1.276844 GCTATGCGCCGACATGTTC 59.723 57.895 4.18 0.00 0.00 3.18
5992 8546 3.554692 GCGCCGACATGTTCCGAG 61.555 66.667 15.03 7.60 0.00 4.63
6007 8561 4.083862 GAGGACACCTGGGGCGTC 62.084 72.222 0.00 0.00 31.76 5.19
6046 8600 1.282930 GACGGCTCGTTCTTCACACC 61.283 60.000 1.80 0.00 41.37 4.16
6122 8676 1.098050 GATGCATTGGGTCCACTGAC 58.902 55.000 10.92 3.94 40.98 3.51
6176 8730 6.204688 CAGAAAACATGCACACCTACTTCTTA 59.795 38.462 0.00 0.00 0.00 2.10
6185 8739 4.625742 CACACCTACTTCTTACACAATCCG 59.374 45.833 0.00 0.00 0.00 4.18
6234 8788 1.689273 AGTTGAGCCCTATCATCGGTC 59.311 52.381 0.00 0.00 0.00 4.79
6246 8800 1.406898 TCATCGGTCATGTCTCTGAGC 59.593 52.381 0.00 0.00 39.65 4.26
6247 8801 1.408340 CATCGGTCATGTCTCTGAGCT 59.592 52.381 0.00 0.00 40.62 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 3.744719 AATGCGCTGCTGCCTGTG 61.745 61.111 9.73 0.00 35.36 3.66
107 108 8.561738 ACTATACTTTTATCACACAAACAGGG 57.438 34.615 0.00 0.00 0.00 4.45
161 182 1.019673 CATTTGATGCGAGGACCAGG 58.980 55.000 0.00 0.00 0.00 4.45
234 255 1.886886 TCCAAAAACAGCCCGTAGTC 58.113 50.000 0.00 0.00 0.00 2.59
326 715 0.981183 ATTACTCGCCCCTTGACACA 59.019 50.000 0.00 0.00 0.00 3.72
329 718 1.095807 GCCATTACTCGCCCCTTGAC 61.096 60.000 0.00 0.00 0.00 3.18
345 782 3.276091 CGACACCAGCAAACGCCA 61.276 61.111 0.00 0.00 0.00 5.69
355 792 2.922740 AGTAAAGGAAAGCGACACCA 57.077 45.000 0.00 0.00 0.00 4.17
411 849 4.202245 TCGTCTTCCTCCGATTGAAATT 57.798 40.909 0.00 0.00 0.00 1.82
412 850 3.887621 TCGTCTTCCTCCGATTGAAAT 57.112 42.857 0.00 0.00 0.00 2.17
605 1044 5.882557 ACATTGGCTAGAAACATGAACTAGG 59.117 40.000 18.77 9.97 35.54 3.02
615 1054 2.695359 TGACCGACATTGGCTAGAAAC 58.305 47.619 0.00 0.00 0.00 2.78
630 1069 2.267426 TGCTTGTCGATGTATTGACCG 58.733 47.619 9.22 3.13 39.88 4.79
708 1147 2.431454 CTCTTCTTCTTTGGGCAGACC 58.569 52.381 0.00 0.00 40.81 3.85
710 1149 1.701847 AGCTCTTCTTCTTTGGGCAGA 59.298 47.619 0.00 0.00 0.00 4.26
817 1276 1.073722 CTGGGCAGTGGAAGCAGAA 59.926 57.895 0.00 0.00 0.00 3.02
853 1313 2.432874 TGAACCTCTGAACGAAGGTGAA 59.567 45.455 0.00 0.00 34.49 3.18
878 1338 0.319383 CAGTGTTCTCGCAGCAGAGT 60.319 55.000 12.18 0.00 39.21 3.24
879 1339 0.038801 TCAGTGTTCTCGCAGCAGAG 60.039 55.000 7.66 7.66 39.52 3.35
880 1340 0.389025 TTCAGTGTTCTCGCAGCAGA 59.611 50.000 0.00 0.00 0.00 4.26
881 1341 0.510359 GTTCAGTGTTCTCGCAGCAG 59.490 55.000 0.00 0.00 0.00 4.24
882 1342 0.179086 TGTTCAGTGTTCTCGCAGCA 60.179 50.000 0.00 0.00 0.00 4.41
937 1397 1.547675 GGCCAACTGAAATGGAGTGGA 60.548 52.381 0.00 0.00 40.56 4.02
989 1465 3.917760 CGTCCATCTCTCGGCCCC 61.918 72.222 0.00 0.00 0.00 5.80
990 1466 4.593864 GCGTCCATCTCTCGGCCC 62.594 72.222 0.00 0.00 0.00 5.80
991 1467 4.933064 CGCGTCCATCTCTCGGCC 62.933 72.222 0.00 0.00 0.00 6.13
992 1468 4.933064 CCGCGTCCATCTCTCGGC 62.933 72.222 4.92 0.00 33.36 5.54
993 1469 4.933064 GCCGCGTCCATCTCTCGG 62.933 72.222 4.92 0.00 42.68 4.63
995 1471 4.933064 CCGCCGCGTCCATCTCTC 62.933 72.222 12.58 0.00 0.00 3.20
1139 1615 3.339093 GGAGGAGGTGGTTGGGGG 61.339 72.222 0.00 0.00 0.00 5.40
1180 1656 4.112331 GGCATAGGGAGGGGAGTTATATT 58.888 47.826 0.00 0.00 0.00 1.28
1181 1657 3.571259 GGGCATAGGGAGGGGAGTTATAT 60.571 52.174 0.00 0.00 0.00 0.86
1182 1658 2.225805 GGGCATAGGGAGGGGAGTTATA 60.226 54.545 0.00 0.00 0.00 0.98
1183 1659 1.487137 GGGCATAGGGAGGGGAGTTAT 60.487 57.143 0.00 0.00 0.00 1.89
1184 1660 0.104620 GGGCATAGGGAGGGGAGTTA 60.105 60.000 0.00 0.00 0.00 2.24
1185 1661 1.386057 GGGCATAGGGAGGGGAGTT 60.386 63.158 0.00 0.00 0.00 3.01
1279 1755 1.816477 ATATCCGCCTCCCCTAGCCT 61.816 60.000 0.00 0.00 0.00 4.58
1283 1759 1.390926 GGGATATCCGCCTCCCCTA 59.609 63.158 15.69 0.00 44.68 3.53
1296 1772 2.509786 GTCAAACGCGGCGGGATA 60.510 61.111 31.03 9.38 0.00 2.59
1394 1870 0.904865 ATGCCAGAACCACGAGGAGA 60.905 55.000 5.68 0.00 38.69 3.71
1395 1871 0.036010 AATGCCAGAACCACGAGGAG 60.036 55.000 5.68 0.00 38.69 3.69
1396 1872 0.400213 AAATGCCAGAACCACGAGGA 59.600 50.000 5.68 0.00 38.69 3.71
1397 1873 0.523072 CAAATGCCAGAACCACGAGG 59.477 55.000 0.00 0.00 42.21 4.63
1561 2037 2.678336 GGTAACATCGAGCAAAGGGAAG 59.322 50.000 0.00 0.00 0.00 3.46
1578 2054 9.967451 TGGAGTAAAAGTGAATTCATATGGTAA 57.033 29.630 12.12 0.00 0.00 2.85
1586 2104 7.523709 GCAGGAAATGGAGTAAAAGTGAATTCA 60.524 37.037 3.38 3.38 0.00 2.57
1601 2119 2.885135 ACATCACAGCAGGAAATGGA 57.115 45.000 0.00 0.00 0.00 3.41
1646 2166 6.371825 AGAAAATACCGTTCCTCAGTTGAATC 59.628 38.462 0.00 0.00 0.00 2.52
1700 2220 6.064060 TGCTTGCTGTTGCTTATAATATCCT 58.936 36.000 0.00 0.00 40.48 3.24
1723 2243 3.308053 CGATCTGTGAGCCATGTAAACTG 59.692 47.826 0.00 0.00 0.00 3.16
1757 2277 3.872696 TGGTGACGATTGTATGCTGATT 58.127 40.909 0.00 0.00 0.00 2.57
1773 2293 1.950216 TGCAAAGCGTGTAAATGGTGA 59.050 42.857 0.00 0.00 0.00 4.02
2261 2782 2.285977 GGGTAAGCAACTACCGAATGG 58.714 52.381 4.22 0.00 42.11 3.16
2262 2783 2.980568 TGGGTAAGCAACTACCGAATG 58.019 47.619 4.22 0.00 42.11 2.67
2263 2784 3.008704 AGTTGGGTAAGCAACTACCGAAT 59.991 43.478 0.00 0.00 40.45 3.34
2266 2787 2.467566 AGTTGGGTAAGCAACTACCG 57.532 50.000 0.00 0.00 42.11 4.02
2309 2830 4.537751 AGCTAGATACCTTGTCAGTGCTA 58.462 43.478 0.00 0.00 0.00 3.49
2311 2832 3.810310 AGCTAGATACCTTGTCAGTGC 57.190 47.619 0.00 0.00 0.00 4.40
2312 2833 5.482908 ACAAAGCTAGATACCTTGTCAGTG 58.517 41.667 0.00 0.00 0.00 3.66
2313 2834 5.746990 ACAAAGCTAGATACCTTGTCAGT 57.253 39.130 0.00 0.00 0.00 3.41
2314 2835 7.324178 AGTTACAAAGCTAGATACCTTGTCAG 58.676 38.462 0.03 0.00 0.00 3.51
2360 2881 7.500227 TGGCAATTCAAGATATAGAAGGTGAAG 59.500 37.037 0.00 0.00 0.00 3.02
2361 2882 7.283127 GTGGCAATTCAAGATATAGAAGGTGAA 59.717 37.037 0.00 0.00 0.00 3.18
2362 2883 6.767902 GTGGCAATTCAAGATATAGAAGGTGA 59.232 38.462 0.00 0.00 0.00 4.02
2415 2939 8.856153 TGGAGCAAATGAAACAGTTACTAATA 57.144 30.769 0.00 0.00 0.00 0.98
2426 2950 5.075858 TGGATGAATGGAGCAAATGAAAC 57.924 39.130 0.00 0.00 0.00 2.78
2486 3075 3.766545 ACTTGCTAAAAGAAGGCATGGA 58.233 40.909 0.00 0.00 36.08 3.41
2560 3149 5.705609 ATTCAACCACAACCATGTACTTC 57.294 39.130 0.00 0.00 37.82 3.01
2564 3153 5.047448 CCATGAATTCAACCACAACCATGTA 60.047 40.000 13.09 0.00 37.82 2.29
2766 3414 1.986882 ACAACAAGGAAGGCAGGAAG 58.013 50.000 0.00 0.00 0.00 3.46
2767 3415 2.430332 CAAACAACAAGGAAGGCAGGAA 59.570 45.455 0.00 0.00 0.00 3.36
2768 3416 2.031120 CAAACAACAAGGAAGGCAGGA 58.969 47.619 0.00 0.00 0.00 3.86
2769 3417 1.756538 ACAAACAACAAGGAAGGCAGG 59.243 47.619 0.00 0.00 0.00 4.85
2772 3420 3.740832 GCATAACAAACAACAAGGAAGGC 59.259 43.478 0.00 0.00 0.00 4.35
2894 3546 4.061596 GGAGAAGTCAAAGAACCTGTCAG 58.938 47.826 0.00 0.00 0.00 3.51
2978 3630 5.183140 ACCACAAACATGCCATTTAGAGTAC 59.817 40.000 0.00 0.00 0.00 2.73
3016 3668 7.497249 CCTGTTCAAGTAAATATTGGGAGAGAG 59.503 40.741 0.00 0.00 0.00 3.20
3018 3670 7.338710 TCCTGTTCAAGTAAATATTGGGAGAG 58.661 38.462 0.00 0.00 0.00 3.20
3108 3760 7.687941 TCAAAAGCCTAATAACAGAAAGGAG 57.312 36.000 0.00 0.00 0.00 3.69
3119 3771 9.920946 ATTACAGAAAGGATCAAAAGCCTAATA 57.079 29.630 0.00 0.00 41.63 0.98
3296 3973 3.632604 CGTAGAGTATGGACACCATGAGT 59.367 47.826 12.78 0.00 44.84 3.41
3319 3996 4.513442 AGCGAGTAATTATTCTGCAACCA 58.487 39.130 19.01 0.00 0.00 3.67
3331 4008 6.875076 ACCTAGAACACATTAGCGAGTAATT 58.125 36.000 0.00 0.00 0.00 1.40
3334 4011 6.016527 CCATACCTAGAACACATTAGCGAGTA 60.017 42.308 0.00 0.00 0.00 2.59
3388 4065 2.168521 TCAAATCCTTAGAGGCCAGACG 59.831 50.000 5.01 0.00 34.61 4.18
3458 4135 8.649841 CGAAACTAGTCGGTATTTGACAAATAA 58.350 33.333 19.69 4.75 38.83 1.40
3740 4417 5.013704 CCCACAAAGTATATATAGGGTGGCA 59.986 44.000 18.10 0.00 42.37 4.92
3920 4597 0.037326 CGGCACTTGCTAACCTCTCA 60.037 55.000 0.38 0.00 41.70 3.27
4051 4730 4.037446 TGCAGTTTGTTGTTAACCTGATCC 59.963 41.667 2.48 0.00 0.00 3.36
4053 4732 5.278957 GGATGCAGTTTGTTGTTAACCTGAT 60.279 40.000 2.48 0.00 0.00 2.90
4054 4733 4.037446 GGATGCAGTTTGTTGTTAACCTGA 59.963 41.667 2.48 0.00 0.00 3.86
4055 4734 4.202101 TGGATGCAGTTTGTTGTTAACCTG 60.202 41.667 2.48 3.21 0.00 4.00
4056 4735 3.957497 TGGATGCAGTTTGTTGTTAACCT 59.043 39.130 2.48 0.00 0.00 3.50
4057 4736 4.298332 CTGGATGCAGTTTGTTGTTAACC 58.702 43.478 5.98 0.00 0.00 2.85
4059 4738 3.976169 GCTGGATGCAGTTTGTTGTTAA 58.024 40.909 16.22 0.00 42.31 2.01
4255 4956 4.394729 CTGTCCTGGTTTAGCCTAAAACA 58.605 43.478 13.97 13.97 42.63 2.83
4270 4971 1.303799 GGCACATCACTGCTGTCCTG 61.304 60.000 0.00 0.00 37.33 3.86
4337 5038 2.602456 CGGATTCACCTCACGATAGTCG 60.602 54.545 0.00 0.00 42.29 4.18
4477 5178 9.716507 ATTATTCAATCGTATTTGCAAGTACAC 57.283 29.630 25.87 8.50 0.00 2.90
4729 5430 0.963355 TAACCTGGCACCGGAATTGC 60.963 55.000 9.46 7.95 39.41 3.56
4741 5442 8.289939 TGTACAGAATCTTACTACTAACCTGG 57.710 38.462 0.00 0.00 0.00 4.45
4755 5456 9.981460 AAAGGAAAGGATAATTGTACAGAATCT 57.019 29.630 0.00 0.00 0.00 2.40
4813 5514 1.014564 GGTGCCAGAAGAGCGTGTAC 61.015 60.000 0.00 0.00 0.00 2.90
4818 5519 1.651240 CCATTGGTGCCAGAAGAGCG 61.651 60.000 0.00 0.00 0.00 5.03
4827 5528 2.420058 ACTTAGCTACCATTGGTGCC 57.580 50.000 18.83 8.82 36.19 5.01
4830 5531 5.900123 ACTGAGATACTTAGCTACCATTGGT 59.100 40.000 13.94 13.94 40.16 3.67
4854 5555 5.692115 TTCATATGGACTAGGCTGACAAA 57.308 39.130 2.13 0.00 0.00 2.83
4856 5557 5.894298 ATTTCATATGGACTAGGCTGACA 57.106 39.130 2.13 0.00 0.00 3.58
5018 5722 7.556844 ACACAGGTATTACTAGTCTGAATTGG 58.443 38.462 13.76 3.03 0.00 3.16
5037 5741 3.243535 GCTTTTCCCTTCTGAAACACAGG 60.244 47.826 0.00 0.00 45.76 4.00
5062 5766 2.025969 CAGTGAGGCGTGTGCTGAG 61.026 63.158 0.00 0.00 42.25 3.35
5269 5981 6.204688 ACAAACTTCATGATTTGAACGCTAGA 59.795 34.615 22.57 0.00 39.44 2.43
5275 5987 9.462174 TGATACAACAAACTTCATGATTTGAAC 57.538 29.630 22.57 10.66 39.44 3.18
5304 6016 5.247792 TCCTTTCTTTTACCCTGGAGTACTC 59.752 44.000 14.87 14.87 0.00 2.59
5311 6023 6.719829 ACAAGTATTCCTTTCTTTTACCCTGG 59.280 38.462 0.00 0.00 0.00 4.45
5656 6456 6.716934 TGGGCTGTACAAGTATTTGAAAAA 57.283 33.333 4.81 0.00 37.73 1.94
5657 6457 5.278758 GCTGGGCTGTACAAGTATTTGAAAA 60.279 40.000 4.81 0.00 37.73 2.29
5658 6458 4.217550 GCTGGGCTGTACAAGTATTTGAAA 59.782 41.667 4.81 0.00 37.73 2.69
5659 6459 3.756434 GCTGGGCTGTACAAGTATTTGAA 59.244 43.478 4.81 0.00 37.73 2.69
5662 6462 3.081804 GTGCTGGGCTGTACAAGTATTT 58.918 45.455 0.00 0.00 0.00 1.40
5663 6463 2.039746 TGTGCTGGGCTGTACAAGTATT 59.960 45.455 0.00 0.00 30.07 1.89
5665 6465 1.001974 CTGTGCTGGGCTGTACAAGTA 59.998 52.381 0.00 0.00 32.58 2.24
5666 6466 0.250467 CTGTGCTGGGCTGTACAAGT 60.250 55.000 0.00 0.00 32.58 3.16
5668 6468 0.472044 TTCTGTGCTGGGCTGTACAA 59.528 50.000 0.00 0.00 32.58 2.41
5669 6469 0.035317 CTTCTGTGCTGGGCTGTACA 59.965 55.000 0.00 0.00 0.00 2.90
5670 6470 0.035458 ACTTCTGTGCTGGGCTGTAC 59.965 55.000 0.00 0.00 0.00 2.90
5671 6471 0.764890 AACTTCTGTGCTGGGCTGTA 59.235 50.000 0.00 0.00 0.00 2.74
5672 6472 0.764890 TAACTTCTGTGCTGGGCTGT 59.235 50.000 0.00 0.00 0.00 4.40
5673 6473 1.160137 GTAACTTCTGTGCTGGGCTG 58.840 55.000 0.00 0.00 0.00 4.85
5674 6474 0.320771 CGTAACTTCTGTGCTGGGCT 60.321 55.000 0.00 0.00 0.00 5.19
5675 6475 0.320421 TCGTAACTTCTGTGCTGGGC 60.320 55.000 0.00 0.00 0.00 5.36
5789 8343 1.829096 GGAGGAGTAGAGGCGGTCC 60.829 68.421 0.00 0.00 0.00 4.46
5812 8366 2.125912 CGGAGAAGCGTGTCTGGG 60.126 66.667 0.00 0.00 0.00 4.45
5980 8534 0.608640 AGGTGTCCTCGGAACATGTC 59.391 55.000 0.00 0.00 0.00 3.06
6007 8561 2.229039 GACATGACGATCCATGGCG 58.771 57.895 6.96 8.69 46.06 5.69
6122 8676 2.032528 TCAAGGGCAAGCCACTCG 59.967 61.111 13.87 0.00 37.98 4.18
6176 8730 2.218603 GTGTTGGAGAACGGATTGTGT 58.781 47.619 0.00 0.00 34.49 3.72
6185 8739 1.828331 GCACCGTCGTGTTGGAGAAC 61.828 60.000 0.00 0.00 42.39 3.01


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

AutoCloner maintained by Alex Coulton.