Multiple sequence alignment - TraesCS5B01G535300

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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 TraesCS5B01G535300 chr5B 100.000 2975 0 0 1 2975 691450004 691452978 0.000000e+00 5494.0
1 TraesCS5B01G535300 chr5B 84.427 2119 266 41 1 2093 691151276 691153356 0.000000e+00 2026.0
2 TraesCS5B01G535300 chr5B 79.663 2134 340 57 1 2090 691582742 691584825 0.000000e+00 1450.0
3 TraesCS5B01G535300 chr5B 80.854 1499 238 37 1 1494 691002040 691003494 0.000000e+00 1133.0
4 TraesCS5B01G535300 chr5B 84.829 613 73 13 2132 2731 691153486 691154091 1.530000e-167 599.0
5 TraesCS5B01G535300 chr5B 80.791 531 65 21 2194 2699 691584972 691585490 6.020000e-102 381.0
6 TraesCS5B01G535300 chr5B 78.278 511 62 31 2218 2699 691480620 691481110 1.750000e-72 283.0
7 TraesCS5B01G535300 chr5D 88.316 2773 243 34 1 2731 547458168 547460901 0.000000e+00 3251.0
8 TraesCS5B01G535300 chr5D 81.289 2079 307 59 1 2069 547526311 547528317 0.000000e+00 1609.0
9 TraesCS5B01G535300 chr5D 83.462 520 58 16 2203 2697 547528505 547529021 2.700000e-125 459.0
10 TraesCS5B01G535300 chr5D 88.940 217 24 0 1378 1594 547486927 547487143 4.890000e-68 268.0
11 TraesCS5B01G535300 chr4A 86.877 2751 252 59 1 2699 618087173 618089866 0.000000e+00 2979.0
12 TraesCS5B01G535300 chr4A 80.465 2109 345 42 1 2087 618173080 618175143 0.000000e+00 1550.0
13 TraesCS5B01G535300 chr4A 80.384 1509 232 39 1 1492 618227771 618229232 0.000000e+00 1088.0
14 TraesCS5B01G535300 chr4A 87.795 762 93 0 1 762 618122665 618123426 0.000000e+00 893.0
15 TraesCS5B01G535300 chr4A 79.592 1274 191 40 1447 2699 618124180 618125405 0.000000e+00 848.0
16 TraesCS5B01G535300 chr4A 82.447 564 53 19 2203 2731 618232572 618233124 4.520000e-123 451.0
17 TraesCS5B01G535300 chr4A 81.882 287 13 16 2702 2975 618233065 618233325 3.890000e-49 206.0
18 TraesCS5B01G535300 chr4A 75.000 220 34 12 1511 1719 618229308 618229517 6.830000e-12 82.4
19 TraesCS5B01G535300 chr7B 84.138 290 30 12 2400 2681 53284142 53284423 1.760000e-67 267.0
20 TraesCS5B01G535300 chr7D 73.991 446 91 19 1015 1440 588020972 588020532 1.100000e-34 158.0


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 TraesCS5B01G535300 chr5B 691450004 691452978 2974 False 5494.00 5494 100.00000 1 2975 1 chr5B.!!$F2 2974
1 TraesCS5B01G535300 chr5B 691151276 691154091 2815 False 1312.50 2026 84.62800 1 2731 2 chr5B.!!$F4 2730
2 TraesCS5B01G535300 chr5B 691002040 691003494 1454 False 1133.00 1133 80.85400 1 1494 1 chr5B.!!$F1 1493
3 TraesCS5B01G535300 chr5B 691582742 691585490 2748 False 915.50 1450 80.22700 1 2699 2 chr5B.!!$F5 2698
4 TraesCS5B01G535300 chr5D 547458168 547460901 2733 False 3251.00 3251 88.31600 1 2731 1 chr5D.!!$F1 2730
5 TraesCS5B01G535300 chr5D 547526311 547529021 2710 False 1034.00 1609 82.37550 1 2697 2 chr5D.!!$F3 2696
6 TraesCS5B01G535300 chr4A 618087173 618089866 2693 False 2979.00 2979 86.87700 1 2699 1 chr4A.!!$F1 2698
7 TraesCS5B01G535300 chr4A 618173080 618175143 2063 False 1550.00 1550 80.46500 1 2087 1 chr4A.!!$F2 2086
8 TraesCS5B01G535300 chr4A 618122665 618125405 2740 False 870.50 893 83.69350 1 2699 2 chr4A.!!$F3 2698
9 TraesCS5B01G535300 chr4A 618227771 618233325 5554 False 456.85 1088 79.92825 1 2975 4 chr4A.!!$F4 2974

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
919 959 0.03254 GTTTCAGCCACAAAGCCTGG 59.967 55.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2444 5499 0.039527 GACGAAAAACCTGGCGCATT 60.04 50.0 10.83 0.0 0.0 3.56 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
125 126 6.917533 AGGATGATTGTTTCATTGTGAAGAC 58.082 36.000 0.00 0.00 45.29 3.01
202 203 6.108687 TCTAGCAATGACATCGACAATTCTT 58.891 36.000 0.00 0.00 0.00 2.52
208 209 5.530519 TGACATCGACAATTCTTACTTGC 57.469 39.130 0.00 0.00 0.00 4.01
243 244 2.872842 GCACAAAAAGCTCCGTACCCTA 60.873 50.000 0.00 0.00 0.00 3.53
313 314 3.319122 GGAAGATTGGTGCAGTGAACTTT 59.681 43.478 0.06 0.00 0.00 2.66
338 339 4.215201 CGTATGCGTGTCATTGTTTTTGA 58.785 39.130 0.00 0.00 36.63 2.69
348 349 7.061673 CGTGTCATTGTTTTTGAGTCTTTGAAA 59.938 33.333 0.00 0.00 0.00 2.69
360 361 4.390264 AGTCTTTGAAAGAGTTACCAGCC 58.610 43.478 8.06 0.00 37.96 4.85
535 536 5.253330 TGTTGGTCAACCTATGGAGATTTC 58.747 41.667 10.83 0.00 40.46 2.17
540 541 6.069440 TGGTCAACCTATGGAGATTTCAATCT 60.069 38.462 1.47 1.47 41.68 2.40
782 792 0.325296 ACGCTGGGATGGAGTTCCTA 60.325 55.000 0.00 0.00 35.97 2.94
888 928 2.140717 GACTGTTACCCAGGTGTTTCG 58.859 52.381 0.00 0.00 46.06 3.46
894 934 1.971695 CCCAGGTGTTTCGCTTCCC 60.972 63.158 0.00 0.00 0.00 3.97
919 959 0.032540 GTTTCAGCCACAAAGCCTGG 59.967 55.000 0.00 0.00 0.00 4.45
953 993 5.420725 TCTGCTACATTATCTTGGTGTGT 57.579 39.130 0.00 0.00 0.00 3.72
982 1049 3.068165 CGAGATACCTACAGTGCCAATCA 59.932 47.826 0.00 0.00 0.00 2.57
989 1056 3.949754 CCTACAGTGCCAATCAACATCAT 59.050 43.478 0.00 0.00 0.00 2.45
998 1065 4.096833 GCCAATCAACATCATCAGTAGCAA 59.903 41.667 0.00 0.00 0.00 3.91
1046 1113 0.177836 ATCATTCATCGGTGCGACCA 59.822 50.000 0.00 0.00 39.18 4.02
1097 1164 4.822350 TCCGACTTATCTACCAGTCATCAG 59.178 45.833 0.00 0.00 39.64 2.90
1112 1179 6.532657 CCAGTCATCAGGAAAATTGCAATAAC 59.467 38.462 13.39 7.08 0.00 1.89
1153 1220 4.088056 TCAGTACCCACCGAAAAATTCA 57.912 40.909 0.00 0.00 0.00 2.57
1155 1222 4.276431 TCAGTACCCACCGAAAAATTCAAC 59.724 41.667 0.00 0.00 0.00 3.18
1190 1257 1.748493 TGAAATATTCAAGGTGGCGGC 59.252 47.619 0.00 0.00 36.59 6.53
1301 1386 2.364324 CTGCAGCCAATATCCAATGCTT 59.636 45.455 0.00 0.00 34.80 3.91
1406 1491 4.175516 CTGCGCATTTTGGATTGTGTATT 58.824 39.130 12.24 0.00 0.00 1.89
1428 1513 9.391006 GTATTTCTTACATCTATTGGACAACCA 57.609 33.333 0.00 0.00 45.34 3.67
1547 1722 9.276590 TGCCATTGAGAGTATTACAATTATCTG 57.723 33.333 0.00 0.00 32.92 2.90
1554 1729 9.534565 GAGAGTATTACAATTATCTGCTGTGAA 57.465 33.333 0.00 0.00 0.00 3.18
1563 1738 3.885484 ATCTGCTGTGAAAAGTTGTCG 57.115 42.857 0.00 0.00 0.00 4.35
1564 1739 2.899976 TCTGCTGTGAAAAGTTGTCGA 58.100 42.857 0.00 0.00 0.00 4.20
1565 1740 2.607635 TCTGCTGTGAAAAGTTGTCGAC 59.392 45.455 9.11 9.11 0.00 4.20
1589 1773 3.500331 CCATGCATGGCAGAAGGTA 57.500 52.632 31.95 0.00 43.65 3.08
1594 1778 0.183492 GCATGGCAGAAGGTATGGGA 59.817 55.000 0.00 0.00 0.00 4.37
1637 1821 3.450904 TGGAAGTTACTCAGTGCCCTAT 58.549 45.455 0.00 0.00 0.00 2.57
1707 1901 4.889409 CACTTACAAGCATGTGGGGATATT 59.111 41.667 4.51 0.00 40.84 1.28
1714 1908 4.210331 AGCATGTGGGGATATTTCTTCAC 58.790 43.478 0.00 0.00 0.00 3.18
1740 4555 1.026718 CCAGCGGCCTAGAAAACCTG 61.027 60.000 0.00 0.00 0.00 4.00
1781 4603 5.290493 AGATTATTGGACTGTCGGCATAA 57.710 39.130 1.07 4.88 0.00 1.90
1796 4618 4.777366 TCGGCATAAGATATCCATTCCAGA 59.223 41.667 0.00 0.00 0.00 3.86
1883 4705 2.401766 CCGTTGGTGGAGCAGATGC 61.402 63.158 0.00 0.00 42.49 3.91
1912 4734 8.642935 TTCAGAAATACCAAATGTGTGGATTA 57.357 30.769 0.00 0.00 41.65 1.75
1941 4763 7.953493 ACCTGTAGAAAATTGAAGGGGATAAAA 59.047 33.333 0.00 0.00 0.00 1.52
1969 4791 2.620585 GTGAAAAGAGGCAGCTTCTTGT 59.379 45.455 19.81 14.94 35.20 3.16
1970 4792 2.620115 TGAAAAGAGGCAGCTTCTTGTG 59.380 45.455 19.81 0.00 35.20 3.33
1971 4793 1.613836 AAAGAGGCAGCTTCTTGTGG 58.386 50.000 19.81 0.00 35.20 4.17
2024 4846 1.621814 AGGTACGTGTGCTTACACCAT 59.378 47.619 0.00 0.00 46.86 3.55
2025 4847 1.730064 GGTACGTGTGCTTACACCATG 59.270 52.381 0.00 0.00 46.86 3.66
2026 4848 1.127951 GTACGTGTGCTTACACCATGC 59.872 52.381 0.00 0.00 46.86 4.06
2027 4849 0.533978 ACGTGTGCTTACACCATGCA 60.534 50.000 5.11 0.00 46.86 3.96
2069 4891 4.563374 GCCTCATAATTTGTTGCACCCTTT 60.563 41.667 0.00 0.00 0.00 3.11
2097 5005 9.607988 TGTGTAGGATTAAACATGTATACCAAG 57.392 33.333 0.00 0.00 0.00 3.61
2099 5007 9.826574 TGTAGGATTAAACATGTATACCAAGTC 57.173 33.333 0.00 0.00 0.00 3.01
2152 5162 7.466725 CGGCAATAGTTCCAAATAATTCGAAGA 60.467 37.037 3.35 0.00 0.00 2.87
2170 5180 7.364522 TCGAAGAACTAAATGAACATGGAAG 57.635 36.000 0.00 0.00 0.00 3.46
2186 5196 9.167311 GAACATGGAAGTAATATGAAACTGTCT 57.833 33.333 0.00 0.00 0.00 3.41
2191 5201 6.199342 GGAAGTAATATGAAACTGTCTCTCGC 59.801 42.308 0.00 0.00 0.00 5.03
2192 5202 6.208988 AGTAATATGAAACTGTCTCTCGCA 57.791 37.500 0.00 0.00 0.00 5.10
2207 5227 3.947626 TCTCGCAACTAAGTTGTTTTGC 58.052 40.909 0.00 7.50 44.40 3.68
2283 5306 2.481952 GTGCACTTCCTGATCACTGTTC 59.518 50.000 10.32 0.00 0.00 3.18
2293 5322 4.094590 CCTGATCACTGTTCTTTCTCATGC 59.905 45.833 0.00 0.00 0.00 4.06
2304 5333 5.717078 TCTTTCTCATGCAGCTCAAAATT 57.283 34.783 0.00 0.00 0.00 1.82
2306 5335 4.445452 TTCTCATGCAGCTCAAAATTCC 57.555 40.909 0.00 0.00 0.00 3.01
2307 5336 2.421073 TCTCATGCAGCTCAAAATTCCG 59.579 45.455 0.00 0.00 0.00 4.30
2308 5337 2.161855 TCATGCAGCTCAAAATTCCGT 58.838 42.857 0.00 0.00 0.00 4.69
2309 5338 2.162208 TCATGCAGCTCAAAATTCCGTC 59.838 45.455 0.00 0.00 0.00 4.79
2310 5339 1.896220 TGCAGCTCAAAATTCCGTCT 58.104 45.000 0.00 0.00 0.00 4.18
2312 5341 1.135575 GCAGCTCAAAATTCCGTCTGG 60.136 52.381 0.00 0.00 0.00 3.86
2313 5342 2.154462 CAGCTCAAAATTCCGTCTGGT 58.846 47.619 0.00 0.00 36.30 4.00
2314 5343 2.095567 CAGCTCAAAATTCCGTCTGGTG 60.096 50.000 0.00 0.00 36.30 4.17
2315 5344 1.401539 GCTCAAAATTCCGTCTGGTGC 60.402 52.381 0.00 0.00 36.30 5.01
2316 5345 1.879380 CTCAAAATTCCGTCTGGTGCA 59.121 47.619 0.00 0.00 36.30 4.57
2382 5423 2.661399 TGCCTCTCAGCAGCTGTC 59.339 61.111 22.10 7.83 38.00 3.51
2391 5433 2.673862 CTCAGCAGCTGTCATCTTCTTG 59.326 50.000 22.10 0.90 32.61 3.02
2394 5437 2.149578 GCAGCTGTCATCTTCTTGTGT 58.850 47.619 16.64 0.00 0.00 3.72
2397 5440 4.781071 CAGCTGTCATCTTCTTGTGTTTC 58.219 43.478 5.25 0.00 0.00 2.78
2415 5470 8.251750 TGTGTTTCTTGTACTGCTATTATGTC 57.748 34.615 0.00 0.00 0.00 3.06
2444 5499 2.112297 GGCGGGGCGGATTGATTA 59.888 61.111 0.00 0.00 0.00 1.75
2460 5515 3.843999 TGATTAATGCGCCAGGTTTTTC 58.156 40.909 4.18 0.00 0.00 2.29
2467 5522 1.852067 CGCCAGGTTTTTCGTCCCAG 61.852 60.000 0.00 0.00 0.00 4.45
2521 5600 0.400213 TTCCTGGCGGATGTCAAACT 59.600 50.000 0.00 0.00 39.58 2.66
2522 5601 0.036388 TCCTGGCGGATGTCAAACTC 60.036 55.000 0.00 0.00 33.30 3.01
2523 5602 0.321564 CCTGGCGGATGTCAAACTCA 60.322 55.000 0.00 0.00 0.00 3.41
2524 5603 0.798776 CTGGCGGATGTCAAACTCAC 59.201 55.000 0.00 0.00 0.00 3.51
2584 5666 1.269166 CGGTGCTACGTGATTCTGTC 58.731 55.000 0.00 0.00 0.00 3.51
2645 5741 8.879759 ACTTATGTCGGAAGTGTTTTATATGTG 58.120 33.333 0.00 0.00 35.80 3.21
2646 5742 9.093970 CTTATGTCGGAAGTGTTTTATATGTGA 57.906 33.333 0.00 0.00 0.00 3.58
2648 5744 5.350365 TGTCGGAAGTGTTTTATATGTGAGC 59.650 40.000 0.00 0.00 0.00 4.26
2659 5755 9.890629 TGTTTTATATGTGAGCTCTCTTGTTAT 57.109 29.630 16.19 9.86 0.00 1.89
2674 5773 9.706691 CTCTCTTGTTATGTCTACCAGTTTTAA 57.293 33.333 0.00 0.00 0.00 1.52
2703 5802 7.864686 TGAACAACTTGTTGATGTCAGAATAG 58.135 34.615 18.82 0.00 41.28 1.73
2710 5809 6.882610 TGTTGATGTCAGAATAGCAGTTTT 57.117 33.333 0.00 0.00 0.00 2.43
2712 5811 7.806690 TGTTGATGTCAGAATAGCAGTTTTAC 58.193 34.615 0.00 0.00 0.00 2.01
2727 5826 8.451908 AGCAGTTTTACTTCTGAATAACTTGT 57.548 30.769 0.00 0.00 34.02 3.16
2735 5834 7.121974 ACTTCTGAATAACTTGTTGATGTCG 57.878 36.000 0.00 0.00 0.00 4.35
2736 5835 6.147821 ACTTCTGAATAACTTGTTGATGTCGG 59.852 38.462 0.00 0.00 0.00 4.79
2737 5836 5.789521 TCTGAATAACTTGTTGATGTCGGA 58.210 37.500 0.00 0.00 0.00 4.55
2738 5837 6.227522 TCTGAATAACTTGTTGATGTCGGAA 58.772 36.000 0.00 0.00 0.00 4.30
2739 5838 6.878923 TCTGAATAACTTGTTGATGTCGGAAT 59.121 34.615 0.00 0.00 0.00 3.01
2740 5839 8.038351 TCTGAATAACTTGTTGATGTCGGAATA 58.962 33.333 0.00 0.00 0.00 1.75
2741 5840 8.196802 TGAATAACTTGTTGATGTCGGAATAG 57.803 34.615 0.00 0.00 0.00 1.73
2742 5841 4.946784 AACTTGTTGATGTCGGAATAGC 57.053 40.909 0.00 0.00 0.00 2.97
2743 5842 3.937814 ACTTGTTGATGTCGGAATAGCA 58.062 40.909 0.00 0.00 0.00 3.49
2744 5843 3.935203 ACTTGTTGATGTCGGAATAGCAG 59.065 43.478 0.00 0.00 0.00 4.24
2750 5849 6.092122 TGTTGATGTCGGAATAGCAGTTTTAG 59.908 38.462 0.00 0.00 0.00 1.85
2751 5850 5.972935 TGATGTCGGAATAGCAGTTTTAGA 58.027 37.500 0.00 0.00 0.00 2.10
2776 5875 6.751157 TCTGAATAACTTGGTGACTACGAAA 58.249 36.000 0.00 0.00 0.00 3.46
2781 5880 4.877378 ACTTGGTGACTACGAAATGGTA 57.123 40.909 0.00 0.00 0.00 3.25
2782 5881 5.217978 ACTTGGTGACTACGAAATGGTAA 57.782 39.130 0.00 0.00 0.00 2.85
2845 5948 1.517242 GGTTGACCAGAAGACTGCTG 58.483 55.000 3.07 3.07 42.25 4.41
2851 5954 4.569943 TGACCAGAAGACTGCTGTTTATC 58.430 43.478 9.71 2.65 42.25 1.75
2855 5958 5.181009 CCAGAAGACTGCTGTTTATCATGA 58.819 41.667 9.71 0.00 42.25 3.07
2856 5959 5.645067 CCAGAAGACTGCTGTTTATCATGAA 59.355 40.000 9.71 0.00 42.25 2.57
2857 5960 6.318144 CCAGAAGACTGCTGTTTATCATGAAT 59.682 38.462 9.71 0.00 42.25 2.57
2858 5961 7.408123 CAGAAGACTGCTGTTTATCATGAATC 58.592 38.462 0.00 0.00 37.33 2.52
2859 5962 6.541641 AGAAGACTGCTGTTTATCATGAATCC 59.458 38.462 0.00 0.00 0.00 3.01
2860 5963 5.999044 AGACTGCTGTTTATCATGAATCCT 58.001 37.500 0.00 0.00 0.00 3.24
2861 5964 5.821470 AGACTGCTGTTTATCATGAATCCTG 59.179 40.000 0.00 0.00 0.00 3.86
2862 5965 4.337555 ACTGCTGTTTATCATGAATCCTGC 59.662 41.667 0.00 4.90 0.00 4.85
2863 5966 3.633525 TGCTGTTTATCATGAATCCTGCC 59.366 43.478 0.00 0.00 0.00 4.85
2864 5967 3.005155 GCTGTTTATCATGAATCCTGCCC 59.995 47.826 0.00 0.00 0.00 5.36
2865 5968 3.213506 TGTTTATCATGAATCCTGCCCG 58.786 45.455 0.00 0.00 0.00 6.13
2866 5969 3.214328 GTTTATCATGAATCCTGCCCGT 58.786 45.455 0.00 0.00 0.00 5.28
2867 5970 3.576078 TTATCATGAATCCTGCCCGTT 57.424 42.857 0.00 0.00 0.00 4.44
2868 5971 1.972872 ATCATGAATCCTGCCCGTTC 58.027 50.000 0.00 0.00 0.00 3.95
2869 5972 0.911769 TCATGAATCCTGCCCGTTCT 59.088 50.000 0.00 0.00 0.00 3.01
2870 5973 1.134401 TCATGAATCCTGCCCGTTCTC 60.134 52.381 0.00 0.00 0.00 2.87
2907 6010 3.308401 ACAAAATGAAGCCCCTGAGTTT 58.692 40.909 0.00 0.00 0.00 2.66
2926 6029 9.442047 CTGAGTTTAGATATAAATGGATCACCC 57.558 37.037 0.00 0.00 34.81 4.61
2940 6043 4.830600 TGGATCACCCAAGTTTTAAAGGAC 59.169 41.667 0.00 0.00 43.29 3.85
2941 6044 5.077564 GGATCACCCAAGTTTTAAAGGACT 58.922 41.667 0.00 0.00 34.14 3.85
2945 6048 6.665695 TCACCCAAGTTTTAAAGGACTAGTT 58.334 36.000 0.00 0.00 0.00 2.24
2946 6049 6.544564 TCACCCAAGTTTTAAAGGACTAGTTG 59.455 38.462 0.00 0.00 0.00 3.16
2947 6050 5.831525 ACCCAAGTTTTAAAGGACTAGTTGG 59.168 40.000 13.28 13.28 38.47 3.77
2951 6063 9.292195 CCAAGTTTTAAAGGACTAGTTGGAATA 57.708 33.333 14.44 0.00 40.24 1.75
2969 6081 6.778821 TGGAATAGAACTGAATCCTTCACAA 58.221 36.000 0.00 0.00 35.46 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 126 7.044798 AGGAATTCTTCTAAAGTCATCCTTCG 58.955 38.462 5.23 0.00 33.87 3.79
208 209 1.766494 TTGTGCTGGCATAGGATTGG 58.234 50.000 0.00 0.00 0.00 3.16
243 244 1.266989 GCTAAAGGCTTGTCGCAAAGT 59.733 47.619 0.00 0.00 41.67 2.66
313 314 1.152510 ACAATGACACGCATACGCAA 58.847 45.000 0.00 0.00 45.53 4.85
338 339 4.141482 TGGCTGGTAACTCTTTCAAAGACT 60.141 41.667 0.00 0.00 33.12 3.24
348 349 1.340405 CCAATGCTGGCTGGTAACTCT 60.340 52.381 0.00 0.00 35.39 3.24
360 361 2.418692 TGCTTCAATTTGCCAATGCTG 58.581 42.857 0.00 0.00 38.71 4.41
535 536 7.725397 TGGACCATATTTAAATCCCTGAGATTG 59.275 37.037 3.39 0.00 44.75 2.67
770 780 3.366396 TGACTCACCTAGGAACTCCATC 58.634 50.000 17.98 4.14 41.75 3.51
782 792 0.178861 ACCCCCAGATTGACTCACCT 60.179 55.000 0.00 0.00 0.00 4.00
888 928 2.261215 CTGAAACCAGCTGGGAAGC 58.739 57.895 35.42 21.28 41.15 3.86
937 977 4.894784 AGTCGAACACACCAAGATAATGT 58.105 39.130 0.00 0.00 0.00 2.71
942 982 1.611977 TCGAGTCGAACACACCAAGAT 59.388 47.619 13.98 0.00 31.06 2.40
953 993 3.869832 CACTGTAGGTATCTCGAGTCGAA 59.130 47.826 17.27 8.17 34.74 3.71
982 1049 3.949754 CCCATGTTGCTACTGATGATGTT 59.050 43.478 0.00 0.00 0.00 2.71
989 1056 3.674997 GAGAAACCCATGTTGCTACTGA 58.325 45.455 0.00 0.00 40.66 3.41
1046 1113 9.141400 GTAGAAACTGTTCGAGACTTGATAAAT 57.859 33.333 0.00 0.00 38.90 1.40
1112 1179 7.166628 ACTGATATTAAGTTCTCGCAATTCG 57.833 36.000 0.00 0.00 40.15 3.34
1153 1220 9.810231 GAATATTTCAATGCAACAAAATTCGTT 57.190 25.926 8.31 3.77 0.00 3.85
1155 1222 9.808808 TTGAATATTTCAATGCAACAAAATTCG 57.191 25.926 8.31 0.00 44.21 3.34
1187 1254 3.428862 GGAGTTTATTTTCCCACATGCCG 60.429 47.826 0.00 0.00 0.00 5.69
1259 1329 3.629398 AGTGAGATTCCCGCAATCATTTC 59.371 43.478 7.76 0.00 43.27 2.17
1301 1386 5.148502 ACAAGGAAAAGTAGGTGAGAGAGA 58.851 41.667 0.00 0.00 0.00 3.10
1406 1491 6.214615 TCCTGGTTGTCCAATAGATGTAAGAA 59.785 38.462 0.00 0.00 43.81 2.52
1428 1513 2.057922 AGGTTGGTGAAGACATGTCCT 58.942 47.619 22.21 9.80 0.00 3.85
1505 1623 6.763355 TCAATGGCAGGTAGATATTCTTCTC 58.237 40.000 0.00 0.00 0.00 2.87
1547 1722 1.668751 TGGTCGACAACTTTTCACAGC 59.331 47.619 18.91 0.00 0.00 4.40
1554 1729 2.631160 TGGTCATGGTCGACAACTTT 57.369 45.000 18.91 0.00 37.66 2.66
1581 1765 5.188751 AGAAGAGAAACTCCCATACCTTCTG 59.811 44.000 0.00 0.00 38.05 3.02
1589 1773 7.560796 TTCTTAAGAGAAGAGAAACTCCCAT 57.439 36.000 5.12 0.00 36.99 4.00
1594 1778 9.853177 TTCCAAATTCTTAAGAGAAGAGAAACT 57.147 29.630 5.12 0.00 44.65 2.66
1624 1808 4.141620 CCAGTTGATTATAGGGCACTGAGT 60.142 45.833 0.00 0.00 0.00 3.41
1707 1901 1.209504 CCGCTGGGGATAAGTGAAGAA 59.790 52.381 4.46 0.00 38.47 2.52
1714 1908 0.832135 TCTAGGCCGCTGGGGATAAG 60.832 60.000 15.77 7.54 38.47 1.73
1740 4555 3.740115 TCTTAGTGAAACAAGGGACTGC 58.260 45.455 0.00 0.00 40.86 4.40
1781 4603 3.946824 AGGTGGTCTGGAATGGATATCT 58.053 45.455 2.05 0.00 0.00 1.98
1796 4618 0.400594 GGTACTGCTCCAAAGGTGGT 59.599 55.000 0.00 0.00 46.11 4.16
1883 4705 6.591062 CCACACATTTGGTATTTCTGAAATGG 59.409 38.462 22.47 10.33 39.21 3.16
1912 4734 5.074515 TCCCCTTCAATTTTCTACAGGTCTT 59.925 40.000 0.00 0.00 0.00 3.01
1941 4763 1.600916 GCCTCTTTTCACGGGCTGT 60.601 57.895 0.00 0.00 41.20 4.40
1947 4769 1.517242 AGAAGCTGCCTCTTTTCACG 58.483 50.000 0.00 0.00 0.00 4.35
1969 4791 1.276421 GCTCTCACTTCTTGGCTACCA 59.724 52.381 0.00 0.00 0.00 3.25
1970 4792 1.276421 TGCTCTCACTTCTTGGCTACC 59.724 52.381 0.00 0.00 0.00 3.18
1971 4793 2.615869 CTGCTCTCACTTCTTGGCTAC 58.384 52.381 0.00 0.00 0.00 3.58
2045 4867 2.233431 GGGTGCAACAAATTATGAGGCA 59.767 45.455 3.06 0.00 39.98 4.75
2069 4891 9.961264 TGGTATACATGTTTAATCCTACACAAA 57.039 29.630 2.30 0.00 0.00 2.83
2101 5009 8.883731 CGTAGGTTTGACATTCAGAGAAAATAT 58.116 33.333 0.00 0.00 0.00 1.28
2102 5010 8.251750 CGTAGGTTTGACATTCAGAGAAAATA 57.748 34.615 0.00 0.00 0.00 1.40
2159 5169 8.862325 ACAGTTTCATATTACTTCCATGTTCA 57.138 30.769 0.00 0.00 0.00 3.18
2170 5180 6.531948 AGTTGCGAGAGACAGTTTCATATTAC 59.468 38.462 0.00 0.00 0.00 1.89
2175 5185 3.393089 AGTTGCGAGAGACAGTTTCAT 57.607 42.857 0.00 0.00 0.00 2.57
2177 5187 4.299978 ACTTAGTTGCGAGAGACAGTTTC 58.700 43.478 0.00 0.00 0.00 2.78
2186 5196 3.242936 GGCAAAACAACTTAGTTGCGAGA 60.243 43.478 23.20 0.00 46.20 4.04
2192 5202 8.779354 TTAACAATTGGCAAAACAACTTAGTT 57.221 26.923 10.83 0.00 32.39 2.24
2207 5227 5.804473 TGCTGCAACGATAATTAACAATTGG 59.196 36.000 10.83 0.00 32.38 3.16
2270 5291 4.094590 GCATGAGAAAGAACAGTGATCAGG 59.905 45.833 0.00 0.00 0.00 3.86
2283 5306 4.863131 GGAATTTTGAGCTGCATGAGAAAG 59.137 41.667 1.02 0.00 0.00 2.62
2293 5322 2.095567 CACCAGACGGAATTTTGAGCTG 60.096 50.000 0.00 0.00 35.59 4.24
2304 5333 4.408821 GGGCATGCACCAGACGGA 62.409 66.667 21.36 0.00 35.59 4.69
2306 5335 3.434319 GTGGGCATGCACCAGACG 61.434 66.667 23.28 0.00 39.00 4.18
2307 5336 3.434319 CGTGGGCATGCACCAGAC 61.434 66.667 23.28 12.60 39.00 3.51
2308 5337 3.610619 CTCGTGGGCATGCACCAGA 62.611 63.158 23.28 18.22 39.00 3.86
2309 5338 3.129502 CTCGTGGGCATGCACCAG 61.130 66.667 23.28 15.22 39.00 4.00
2310 5339 4.720902 CCTCGTGGGCATGCACCA 62.721 66.667 19.33 19.79 35.14 4.17
2376 5417 4.712476 AGAAACACAAGAAGATGACAGCT 58.288 39.130 0.00 0.00 0.00 4.24
2382 5423 6.017605 AGCAGTACAAGAAACACAAGAAGATG 60.018 38.462 0.00 0.00 0.00 2.90
2391 5433 7.333423 TGGACATAATAGCAGTACAAGAAACAC 59.667 37.037 0.00 0.00 0.00 3.32
2394 5437 8.726988 GTTTGGACATAATAGCAGTACAAGAAA 58.273 33.333 0.00 0.00 37.39 2.52
2397 5440 7.849804 AGTTTGGACATAATAGCAGTACAAG 57.150 36.000 0.00 0.00 37.39 3.16
2430 5485 0.240945 CGCATTAATCAATCCGCCCC 59.759 55.000 0.00 0.00 0.00 5.80
2444 5499 0.039527 GACGAAAAACCTGGCGCATT 60.040 50.000 10.83 0.00 0.00 3.56
2460 5515 3.502979 GCTAGAGTATAACCTCTGGGACG 59.497 52.174 0.00 0.00 41.81 4.79
2521 5600 2.567985 GAAACAGGGAAAGGTTCGTGA 58.432 47.619 0.00 0.00 0.00 4.35
2522 5601 1.607148 GGAAACAGGGAAAGGTTCGTG 59.393 52.381 0.00 0.00 0.00 4.35
2523 5602 1.812708 CGGAAACAGGGAAAGGTTCGT 60.813 52.381 0.00 0.00 0.00 3.85
2524 5603 0.872388 CGGAAACAGGGAAAGGTTCG 59.128 55.000 0.00 0.00 0.00 3.95
2584 5666 7.859377 AGCATGCATATTCTGACTAAATTTTCG 59.141 33.333 21.98 0.00 0.00 3.46
2645 5741 5.126384 ACTGGTAGACATAACAAGAGAGCTC 59.874 44.000 5.27 5.27 0.00 4.09
2646 5742 5.020132 ACTGGTAGACATAACAAGAGAGCT 58.980 41.667 0.00 0.00 0.00 4.09
2648 5744 9.706691 TTAAAACTGGTAGACATAACAAGAGAG 57.293 33.333 0.00 0.00 0.00 3.20
2659 5755 8.617809 GTTGTTCAGAATTAAAACTGGTAGACA 58.382 33.333 10.78 8.67 35.20 3.41
2674 5773 6.543465 TCTGACATCAACAAGTTGTTCAGAAT 59.457 34.615 24.88 12.87 42.17 2.40
2703 5802 8.958043 CAACAAGTTATTCAGAAGTAAAACTGC 58.042 33.333 0.00 0.00 34.57 4.40
2710 5809 7.330946 CCGACATCAACAAGTTATTCAGAAGTA 59.669 37.037 0.00 0.00 0.00 2.24
2712 5811 6.368791 TCCGACATCAACAAGTTATTCAGAAG 59.631 38.462 0.00 0.00 0.00 2.85
2727 5826 6.403049 TCTAAAACTGCTATTCCGACATCAA 58.597 36.000 0.00 0.00 0.00 2.57
2731 5830 6.042777 CAGATCTAAAACTGCTATTCCGACA 58.957 40.000 0.00 0.00 0.00 4.35
2732 5831 6.273825 TCAGATCTAAAACTGCTATTCCGAC 58.726 40.000 0.00 0.00 34.57 4.79
2733 5832 6.465439 TCAGATCTAAAACTGCTATTCCGA 57.535 37.500 0.00 0.00 34.57 4.55
2734 5833 7.721286 ATTCAGATCTAAAACTGCTATTCCG 57.279 36.000 0.00 0.00 34.57 4.30
2739 5838 9.383519 CCAAGTTATTCAGATCTAAAACTGCTA 57.616 33.333 0.00 0.00 34.57 3.49
2740 5839 7.885399 ACCAAGTTATTCAGATCTAAAACTGCT 59.115 33.333 0.00 0.00 34.57 4.24
2741 5840 7.965107 CACCAAGTTATTCAGATCTAAAACTGC 59.035 37.037 0.00 0.00 34.57 4.40
2742 5841 9.219603 TCACCAAGTTATTCAGATCTAAAACTG 57.780 33.333 0.00 0.00 35.72 3.16
2743 5842 9.220767 GTCACCAAGTTATTCAGATCTAAAACT 57.779 33.333 0.00 0.26 0.00 2.66
2744 5843 9.220767 AGTCACCAAGTTATTCAGATCTAAAAC 57.779 33.333 0.00 0.00 0.00 2.43
2750 5849 6.561614 TCGTAGTCACCAAGTTATTCAGATC 58.438 40.000 0.00 0.00 0.00 2.75
2751 5850 6.525578 TCGTAGTCACCAAGTTATTCAGAT 57.474 37.500 0.00 0.00 0.00 2.90
2845 5948 3.214328 ACGGGCAGGATTCATGATAAAC 58.786 45.455 1.83 0.00 0.00 2.01
2851 5954 1.303309 GAGAACGGGCAGGATTCATG 58.697 55.000 0.00 0.00 0.00 3.07
2855 5958 3.054361 AGTTATTGAGAACGGGCAGGATT 60.054 43.478 0.00 0.00 34.36 3.01
2856 5959 2.505819 AGTTATTGAGAACGGGCAGGAT 59.494 45.455 0.00 0.00 34.36 3.24
2857 5960 1.906574 AGTTATTGAGAACGGGCAGGA 59.093 47.619 0.00 0.00 34.36 3.86
2858 5961 2.403252 AGTTATTGAGAACGGGCAGG 57.597 50.000 0.00 0.00 34.36 4.85
2859 5962 3.502211 ACAAAGTTATTGAGAACGGGCAG 59.498 43.478 0.00 0.00 34.36 4.85
2860 5963 3.252215 CACAAAGTTATTGAGAACGGGCA 59.748 43.478 0.00 0.00 34.36 5.36
2861 5964 3.500680 TCACAAAGTTATTGAGAACGGGC 59.499 43.478 0.00 0.00 34.36 6.13
2862 5965 4.755123 AGTCACAAAGTTATTGAGAACGGG 59.245 41.667 0.00 0.00 34.36 5.28
2863 5966 5.924475 AGTCACAAAGTTATTGAGAACGG 57.076 39.130 0.00 0.00 34.36 4.44
2864 5967 7.402811 TGTAGTCACAAAGTTATTGAGAACG 57.597 36.000 0.00 0.00 34.36 3.95
2896 5999 6.779860 TCCATTTATATCTAAACTCAGGGGC 58.220 40.000 0.00 0.00 29.85 5.80
2934 6037 7.554959 TCAGTTCTATTCCAACTAGTCCTTT 57.445 36.000 0.00 0.00 32.61 3.11
2938 6041 7.787028 AGGATTCAGTTCTATTCCAACTAGTC 58.213 38.462 0.00 0.00 32.61 2.59
2940 6043 8.655651 GAAGGATTCAGTTCTATTCCAACTAG 57.344 38.462 0.00 0.00 46.62 2.57


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

AutoCloner maintained by Alex Coulton.