Multiple sequence alignment - TraesCS7A01G558500

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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 TraesCS7A01G558500 chr7A 100.000 2522 0 0 1 2522 730750909 730748388 0.000000e+00 4658
1 TraesCS7A01G558500 chr7A 96.494 542 14 4 31 570 84187981 84187443 0.000000e+00 891
2 TraesCS7A01G558500 chr7A 88.517 209 20 3 2212 2418 676588489 676588283 1.500000e-62 250
3 TraesCS7A01G558500 chr7A 86.957 207 24 2 2213 2418 677228953 677228749 1.950000e-56 230
4 TraesCS7A01G558500 chr7A 88.000 150 16 1 607 756 730750156 730750009 2.580000e-40 176
5 TraesCS7A01G558500 chr7A 88.000 150 16 1 754 901 730750303 730750154 2.580000e-40 176
6 TraesCS7A01G558500 chr7D 92.952 1433 75 7 571 1981 634804663 634806091 0.000000e+00 2063
7 TraesCS7A01G558500 chr7D 89.891 366 26 7 2066 2427 634806096 634806454 6.360000e-126 460
8 TraesCS7A01G558500 chr7D 91.667 156 11 1 754 907 634804702 634804857 5.460000e-52 215
9 TraesCS7A01G558500 chr7D 89.542 153 16 0 604 756 634804860 634805012 7.120000e-46 195
10 TraesCS7A01G558500 chr7B 93.515 1357 62 7 571 1905 741353800 741352448 0.000000e+00 1995
11 TraesCS7A01G558500 chr7B 87.085 271 13 7 2161 2427 741352221 741351969 1.140000e-73 287
12 TraesCS7A01G558500 chr7B 84.859 284 24 10 571 835 741366533 741366250 4.140000e-68 268
13 TraesCS7A01G558500 chr7B 90.566 159 13 1 754 910 741353761 741353603 2.540000e-50 209
14 TraesCS7A01G558500 chr7B 89.610 154 14 2 604 756 741353603 741353451 7.120000e-46 195
15 TraesCS7A01G558500 chr7B 88.750 160 14 3 755 910 741366493 741366334 2.560000e-45 193
16 TraesCS7A01G558500 chr7B 87.611 113 9 4 2064 2175 741352348 741352240 2.630000e-25 126
17 TraesCS7A01G558500 chr1A 96.863 542 12 4 31 570 155354353 155354891 0.000000e+00 902
18 TraesCS7A01G558500 chr4A 95.088 570 22 5 1 568 639228322 639228887 0.000000e+00 893
19 TraesCS7A01G558500 chr4A 96.310 542 15 4 31 570 365506157 365505619 0.000000e+00 885
20 TraesCS7A01G558500 chr6A 96.494 542 14 4 31 570 51621396 51620858 0.000000e+00 891
21 TraesCS7A01G558500 chr6A 95.941 542 17 4 31 570 548766840 548767378 0.000000e+00 874
22 TraesCS7A01G558500 chr5A 96.317 543 14 5 31 570 462913580 462913041 0.000000e+00 887
23 TraesCS7A01G558500 chr5A 96.455 536 14 4 37 570 436656691 436656159 0.000000e+00 880
24 TraesCS7A01G558500 chr3A 96.111 540 16 4 31 568 199056382 199055846 0.000000e+00 876
25 TraesCS7A01G558500 chr3A 89.806 206 19 1 2213 2418 642270946 642271149 1.920000e-66 263
26 TraesCS7A01G558500 chr3A 89.806 206 19 1 2213 2418 644497862 644497659 1.920000e-66 263
27 TraesCS7A01G558500 chr3A 88.406 207 21 2 2213 2418 707238788 707238584 1.940000e-61 246


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 TraesCS7A01G558500 chr7A 730748388 730750909 2521 True 1670.00 4658 92.0000 1 2522 3 chr7A.!!$R4 2521
1 TraesCS7A01G558500 chr7A 84187443 84187981 538 True 891.00 891 96.4940 31 570 1 chr7A.!!$R1 539
2 TraesCS7A01G558500 chr7D 634804663 634806454 1791 False 733.25 2063 91.0130 571 2427 4 chr7D.!!$F1 1856
3 TraesCS7A01G558500 chr7B 741351969 741353800 1831 True 562.40 1995 89.6774 571 2427 5 chr7B.!!$R1 1856
4 TraesCS7A01G558500 chr1A 155354353 155354891 538 False 902.00 902 96.8630 31 570 1 chr1A.!!$F1 539
5 TraesCS7A01G558500 chr4A 639228322 639228887 565 False 893.00 893 95.0880 1 568 1 chr4A.!!$F1 567
6 TraesCS7A01G558500 chr4A 365505619 365506157 538 True 885.00 885 96.3100 31 570 1 chr4A.!!$R1 539
7 TraesCS7A01G558500 chr6A 51620858 51621396 538 True 891.00 891 96.4940 31 570 1 chr6A.!!$R1 539
8 TraesCS7A01G558500 chr6A 548766840 548767378 538 False 874.00 874 95.9410 31 570 1 chr6A.!!$F1 539
9 TraesCS7A01G558500 chr5A 462913041 462913580 539 True 887.00 887 96.3170 31 570 1 chr5A.!!$R2 539
10 TraesCS7A01G558500 chr5A 436656159 436656691 532 True 880.00 880 96.4550 37 570 1 chr5A.!!$R1 533
11 TraesCS7A01G558500 chr3A 199055846 199056382 536 True 876.00 876 96.1110 31 568 1 chr3A.!!$R1 537

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
604 611 0.109179 ATGTGTGCGCGAAATGCAAT 60.109 45.0 12.1 0.0 45.23 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2497 2590 0.036294 GCACTAATATCCGCCTCCCC 60.036 60.0 0.0 0.0 0.0 4.81 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
19 20 1.613836 AGCACCAAAGAAGCAAGAGG 58.386 50.000 0.00 0.00 0.00 3.69
34 35 1.668826 AGAGGTGAAGCATGGGGTTA 58.331 50.000 0.00 0.00 34.25 2.85
40 41 1.066430 TGAAGCATGGGGTTACGAGAC 60.066 52.381 0.00 0.00 34.25 3.36
192 194 1.078918 CTTGGAGCATCGGCACTGA 60.079 57.895 0.00 0.00 44.61 3.41
277 279 1.813178 GGCTCTTGACTTAAACCTGCC 59.187 52.381 0.00 0.00 0.00 4.85
363 365 3.954258 GCCCAGCAAAGTTATTATGGACT 59.046 43.478 0.00 0.00 0.00 3.85
502 504 0.111253 CTTTGGCTCACAGGAACCCT 59.889 55.000 0.00 0.00 0.00 4.34
519 521 9.284968 CAGGAACCCTCGAAATTATTTGTATAT 57.715 33.333 0.00 0.00 0.00 0.86
520 522 9.503399 AGGAACCCTCGAAATTATTTGTATATC 57.497 33.333 0.00 0.00 0.00 1.63
521 523 9.503399 GGAACCCTCGAAATTATTTGTATATCT 57.497 33.333 0.00 0.00 0.00 1.98
589 593 1.207390 CACAACCCGTGCAAAATGTG 58.793 50.000 0.00 0.00 39.19 3.21
593 600 2.015627 CCCGTGCAAAATGTGTGCG 61.016 57.895 0.00 0.00 45.27 5.34
604 611 0.109179 ATGTGTGCGCGAAATGCAAT 60.109 45.000 12.10 0.00 45.23 3.56
616 623 3.304026 CGAAATGCAATGTATTGTGTGGC 59.696 43.478 0.00 0.00 39.88 5.01
670 677 2.417933 CTGCTAGTTTGTCCAGTCATGC 59.582 50.000 0.00 0.00 0.00 4.06
680 687 3.754850 TGTCCAGTCATGCAGAATTTCTG 59.245 43.478 19.92 19.92 46.90 3.02
716 723 8.049117 TGGCAACATCTAGATAATTTCTCAAGT 58.951 33.333 4.54 0.00 46.17 3.16
731 738 4.985538 TCTCAAGTTTAGGCTTCATTGGT 58.014 39.130 0.00 0.00 0.00 3.67
761 782 4.128925 TCTTCTCATCTGCTATTGCGTT 57.871 40.909 0.00 0.00 43.34 4.84
771 792 4.112634 CTGCTATTGCGTTGTTCTAGCTA 58.887 43.478 0.00 0.00 43.34 3.32
1041 1064 1.056660 TCCTCCTCCTCGCTGTTTTT 58.943 50.000 0.00 0.00 0.00 1.94
1466 1489 1.343431 TACCAACACCCCAACGACCA 61.343 55.000 0.00 0.00 0.00 4.02
1467 1490 1.454111 CCAACACCCCAACGACCAA 60.454 57.895 0.00 0.00 0.00 3.67
1541 1564 2.964925 GCTGTTCACGTCGCACCA 60.965 61.111 0.00 0.00 0.00 4.17
1576 1599 1.202076 GCGTACGTAGATATACGGCCC 60.202 57.143 22.57 9.60 46.68 5.80
1590 1613 7.991460 AGATATACGGCCCTATAAATAAAAGGC 59.009 37.037 5.68 0.00 39.73 4.35
1593 1616 3.058501 CGGCCCTATAAATAAAAGGCGTG 60.059 47.826 0.00 0.00 41.41 5.34
1613 1639 5.277297 GCGTGCTGCTTAATACATCACATTA 60.277 40.000 0.00 0.00 41.73 1.90
1631 1657 9.851686 ATCACATTATCATATTACAACCACTGT 57.148 29.630 0.00 0.00 42.47 3.55
1660 1686 5.950544 ACATGTTAGCCCACTACTATGAA 57.049 39.130 0.00 0.00 31.27 2.57
1691 1717 9.936759 TCATTGATATTTGAGTACACAGTACAA 57.063 29.630 9.68 0.22 0.00 2.41
1703 1729 8.404107 AGTACACAGTACAAGGCAATAAAAAT 57.596 30.769 9.68 0.00 0.00 1.82
1743 1770 2.448542 ACAGCACCCTGACCCAGT 60.449 61.111 0.00 0.00 41.77 4.00
1887 1914 5.163519 ACAGCTAGCTTGTTTGTTTCAACAT 60.164 36.000 16.46 0.00 38.95 2.71
1922 1967 5.454471 GGACTATTCTCCTGCATGTTGATCT 60.454 44.000 0.00 0.00 0.00 2.75
1940 1985 5.649557 TGATCTGTGGTGTTTGTTTTGAAG 58.350 37.500 0.00 0.00 0.00 3.02
1944 2000 2.596862 GTGGTGTTTGTTTTGAAGCGAC 59.403 45.455 0.00 0.00 0.00 5.19
1953 2009 4.162812 TGTTTTGAAGCGACTTGTTGTTC 58.837 39.130 0.00 0.00 0.00 3.18
1967 2023 7.698130 CGACTTGTTGTTCTTCTTTTCTTTCAT 59.302 33.333 0.00 0.00 0.00 2.57
1981 2037 9.414295 TCTTTTCTTTCATATTTGCATCTTGTG 57.586 29.630 0.00 0.00 0.00 3.33
1983 2039 9.761504 TTTTCTTTCATATTTGCATCTTGTGAA 57.238 25.926 0.00 0.00 0.00 3.18
1984 2040 9.932207 TTTCTTTCATATTTGCATCTTGTGAAT 57.068 25.926 0.00 0.00 0.00 2.57
1994 2050 9.932207 ATTTGCATCTTGTGAATAAAAATGAGA 57.068 25.926 0.00 0.00 0.00 3.27
1995 2051 8.746922 TTGCATCTTGTGAATAAAAATGAGAC 57.253 30.769 0.00 0.00 0.00 3.36
1996 2052 7.315142 TGCATCTTGTGAATAAAAATGAGACC 58.685 34.615 0.00 0.00 0.00 3.85
1997 2053 7.039853 TGCATCTTGTGAATAAAAATGAGACCA 60.040 33.333 0.00 0.00 0.00 4.02
1998 2054 7.814107 GCATCTTGTGAATAAAAATGAGACCAA 59.186 33.333 0.00 0.00 0.00 3.67
1999 2055 9.865321 CATCTTGTGAATAAAAATGAGACCAAT 57.135 29.630 0.00 0.00 0.00 3.16
2001 2057 9.300681 TCTTGTGAATAAAAATGAGACCAATCT 57.699 29.630 0.00 0.00 38.15 2.40
2006 2062 9.189156 TGAATAAAAATGAGACCAATCTAAGGG 57.811 33.333 0.00 0.00 34.34 3.95
2007 2063 5.921962 AAAAATGAGACCAATCTAAGGGC 57.078 39.130 0.00 0.00 34.34 5.19
2013 2069 2.778270 AGACCAATCTAAGGGCTAACCC 59.222 50.000 0.00 0.00 44.68 4.11
2014 2070 3.829027 AGACCAATCTAAGGGCTAACCCA 60.829 47.826 3.48 0.00 44.68 4.51
2015 2071 5.318918 AGACCAATCTAAGGGCTAACCCAA 61.319 45.833 3.48 0.00 44.68 4.12
2016 2072 6.594934 AGACCAATCTAAGGGCTAACCCAAT 61.595 44.000 3.48 0.00 44.68 3.16
2017 2073 8.017698 AGACCAATCTAAGGGCTAACCCAATT 62.018 42.308 3.48 0.00 44.68 2.32
2018 2074 9.710544 AGACCAATCTAAGGGCTAACCCAATTC 62.711 44.444 3.48 0.00 44.68 2.17
2023 2079 3.596362 GGCTAACCCAATTCCAGCT 57.404 52.632 0.00 0.00 32.78 4.24
2024 2080 1.106285 GGCTAACCCAATTCCAGCTG 58.894 55.000 6.78 6.78 32.78 4.24
2025 2081 1.616994 GGCTAACCCAATTCCAGCTGT 60.617 52.381 13.81 0.00 32.78 4.40
2026 2082 1.745653 GCTAACCCAATTCCAGCTGTC 59.254 52.381 13.81 0.00 0.00 3.51
2027 2083 2.369394 CTAACCCAATTCCAGCTGTCC 58.631 52.381 13.81 0.00 0.00 4.02
2028 2084 0.482446 AACCCAATTCCAGCTGTCCA 59.518 50.000 13.81 0.00 0.00 4.02
2029 2085 0.038744 ACCCAATTCCAGCTGTCCAG 59.961 55.000 13.81 0.00 0.00 3.86
2030 2086 0.038744 CCCAATTCCAGCTGTCCAGT 59.961 55.000 13.81 0.00 0.00 4.00
2031 2087 1.457346 CCAATTCCAGCTGTCCAGTC 58.543 55.000 13.81 0.00 0.00 3.51
2032 2088 1.271543 CCAATTCCAGCTGTCCAGTCA 60.272 52.381 13.81 0.00 0.00 3.41
2033 2089 2.507484 CAATTCCAGCTGTCCAGTCAA 58.493 47.619 13.81 0.00 0.00 3.18
2034 2090 2.191128 ATTCCAGCTGTCCAGTCAAC 57.809 50.000 13.81 0.00 0.00 3.18
2035 2091 0.249868 TTCCAGCTGTCCAGTCAACG 60.250 55.000 13.81 0.00 0.00 4.10
2036 2092 1.669115 CCAGCTGTCCAGTCAACGG 60.669 63.158 13.81 0.00 0.00 4.44
2037 2093 1.669115 CAGCTGTCCAGTCAACGGG 60.669 63.158 5.25 0.00 0.00 5.28
2038 2094 2.140792 AGCTGTCCAGTCAACGGGT 61.141 57.895 0.00 0.00 32.79 5.28
2039 2095 1.668151 GCTGTCCAGTCAACGGGTC 60.668 63.158 0.00 0.00 32.79 4.46
2040 2096 1.372997 CTGTCCAGTCAACGGGTCG 60.373 63.158 0.00 0.00 32.79 4.79
2041 2097 1.802337 CTGTCCAGTCAACGGGTCGA 61.802 60.000 0.00 0.00 32.79 4.20
2042 2098 1.372623 GTCCAGTCAACGGGTCGAC 60.373 63.158 7.13 7.13 32.79 4.20
2043 2099 1.829096 TCCAGTCAACGGGTCGACA 60.829 57.895 18.91 0.00 34.48 4.35
2044 2100 1.663702 CCAGTCAACGGGTCGACAC 60.664 63.158 18.91 13.91 34.48 3.67
2045 2101 1.663702 CAGTCAACGGGTCGACACC 60.664 63.158 18.91 14.79 42.90 4.16
2059 2115 2.457366 GACACCCTGTCGTCAGATTT 57.543 50.000 11.41 0.00 43.76 2.17
2060 2116 2.069273 GACACCCTGTCGTCAGATTTG 58.931 52.381 11.41 7.28 43.76 2.32
2061 2117 1.416401 ACACCCTGTCGTCAGATTTGT 59.584 47.619 11.41 7.86 43.76 2.83
2062 2118 1.800586 CACCCTGTCGTCAGATTTGTG 59.199 52.381 11.41 8.69 43.76 3.33
2063 2119 1.416401 ACCCTGTCGTCAGATTTGTGT 59.584 47.619 11.41 0.00 43.76 3.72
2064 2120 2.069273 CCCTGTCGTCAGATTTGTGTC 58.931 52.381 11.41 0.00 43.76 3.67
2135 2192 1.599797 CCACGGGAGGCGAGTTTTT 60.600 57.895 0.00 0.00 0.00 1.94
2181 2271 2.516906 TGCATCAAGTCAATTGGCTCA 58.483 42.857 14.03 3.51 39.54 4.26
2184 2274 3.119245 GCATCAAGTCAATTGGCTCACAT 60.119 43.478 14.03 2.85 39.54 3.21
2185 2275 4.669318 CATCAAGTCAATTGGCTCACATC 58.331 43.478 14.03 0.00 39.54 3.06
2187 2277 3.087031 CAAGTCAATTGGCTCACATCCT 58.913 45.455 14.03 0.00 35.08 3.24
2195 2286 1.186200 GGCTCACATCCTTTTTCCCC 58.814 55.000 0.00 0.00 0.00 4.81
2196 2287 1.272704 GGCTCACATCCTTTTTCCCCT 60.273 52.381 0.00 0.00 0.00 4.79
2198 2289 2.450476 CTCACATCCTTTTTCCCCTGG 58.550 52.381 0.00 0.00 0.00 4.45
2199 2290 1.786441 TCACATCCTTTTTCCCCTGGT 59.214 47.619 0.00 0.00 0.00 4.00
2231 2324 4.441913 CCAAGGCACCCAACATGAAATATC 60.442 45.833 0.00 0.00 0.00 1.63
2295 2388 3.052262 AGAGAGAGTTCATGATCCAGGGA 60.052 47.826 0.00 0.00 0.00 4.20
2329 2422 2.290896 TGGTTAGCAAGGAATGAGGTGG 60.291 50.000 0.00 0.00 0.00 4.61
2353 2446 7.775093 TGGGAGATGGTAAGAAAATTACAGATG 59.225 37.037 0.72 0.00 0.00 2.90
2371 2464 3.320359 CCCGGGTAGTGGCAGAAT 58.680 61.111 14.18 0.00 0.00 2.40
2390 2483 5.924254 CAGAATGTGTTTTCAATCATGCACT 59.076 36.000 0.00 0.00 0.00 4.40
2439 2532 2.878580 GCAATGATGCGAATGGAAACA 58.121 42.857 0.00 0.00 43.83 2.83
2440 2533 2.855963 GCAATGATGCGAATGGAAACAG 59.144 45.455 0.00 0.00 43.92 3.16
2441 2534 4.817289 GCAATGATGCGAATGGAAACAGC 61.817 47.826 0.00 0.00 43.92 4.40
2444 2537 2.159352 TGATGCGAATGGAAACAGCATG 60.159 45.455 5.94 0.00 46.15 4.06
2445 2538 1.135527 ATGCGAATGGAAACAGCATGG 59.864 47.619 0.14 0.00 44.96 3.66
2446 2539 4.668311 ATGCGAATGGAAACAGCATGGC 62.668 50.000 0.14 0.00 44.96 4.40
2449 2542 4.615170 TGGAAACAGCATGGCCAA 57.385 50.000 10.96 0.00 43.62 4.52
2450 2543 2.353858 TGGAAACAGCATGGCCAAG 58.646 52.632 10.96 6.55 43.62 3.61
2451 2544 1.186917 TGGAAACAGCATGGCCAAGG 61.187 55.000 10.96 6.44 43.62 3.61
2452 2545 0.899717 GGAAACAGCATGGCCAAGGA 60.900 55.000 10.96 0.00 43.62 3.36
2453 2546 1.188863 GAAACAGCATGGCCAAGGAT 58.811 50.000 10.96 0.00 43.62 3.24
2454 2547 0.899720 AAACAGCATGGCCAAGGATG 59.100 50.000 20.56 20.56 43.62 3.51
2455 2548 0.974010 AACAGCATGGCCAAGGATGG 60.974 55.000 24.32 10.12 45.26 3.51
2456 2549 1.866483 ACAGCATGGCCAAGGATGGA 61.866 55.000 24.32 0.00 46.37 3.41
2457 2550 3.166580 ACAGCATGGCCAAGGATGGAT 62.167 52.381 24.32 7.04 46.37 3.41
2458 2551 4.633758 ACAGCATGGCCAAGGATGGATT 62.634 50.000 24.32 6.43 46.37 3.01
2459 2552 5.295984 ACAGCATGGCCAAGGATGGATTA 62.296 47.826 24.32 0.00 46.37 1.75
2460 2553 6.719148 ACAGCATGGCCAAGGATGGATTAA 62.719 45.833 24.32 0.00 46.37 1.40
2478 2571 9.816354 ATGGATTAAAGTTAATACAAATGGTGC 57.184 29.630 11.74 0.00 44.64 5.01
2479 2572 9.030452 TGGATTAAAGTTAATACAAATGGTGCT 57.970 29.630 6.28 0.00 40.16 4.40
2485 2578 7.938140 AGTTAATACAAATGGTGCTATGTGT 57.062 32.000 0.00 0.00 33.26 3.72
2486 2579 7.761409 AGTTAATACAAATGGTGCTATGTGTG 58.239 34.615 2.18 0.00 31.21 3.82
2487 2580 4.637483 ATACAAATGGTGCTATGTGTGC 57.363 40.909 2.18 0.00 31.21 4.57
2488 2581 2.237643 ACAAATGGTGCTATGTGTGCA 58.762 42.857 0.00 0.00 38.19 4.57
2489 2582 2.627221 ACAAATGGTGCTATGTGTGCAA 59.373 40.909 0.00 0.00 42.41 4.08
2500 2593 3.947173 TGTGCAACACAAAGGGGG 58.053 55.556 0.00 0.00 45.67 5.40
2501 2594 1.307986 TGTGCAACACAAAGGGGGA 59.692 52.632 0.00 0.00 45.67 4.81
2502 2595 0.754957 TGTGCAACACAAAGGGGGAG 60.755 55.000 0.00 0.00 45.67 4.30
2503 2596 1.152567 TGCAACACAAAGGGGGAGG 60.153 57.895 0.00 0.00 0.00 4.30
2504 2597 2.574018 GCAACACAAAGGGGGAGGC 61.574 63.158 0.00 0.00 0.00 4.70
2505 2598 2.115266 AACACAAAGGGGGAGGCG 59.885 61.111 0.00 0.00 0.00 5.52
2506 2599 3.507377 AACACAAAGGGGGAGGCGG 62.507 63.158 0.00 0.00 0.00 6.13
2507 2600 3.646715 CACAAAGGGGGAGGCGGA 61.647 66.667 0.00 0.00 0.00 5.54
2508 2601 2.614013 ACAAAGGGGGAGGCGGAT 60.614 61.111 0.00 0.00 0.00 4.18
2509 2602 1.307517 ACAAAGGGGGAGGCGGATA 60.308 57.895 0.00 0.00 0.00 2.59
2510 2603 0.697854 ACAAAGGGGGAGGCGGATAT 60.698 55.000 0.00 0.00 0.00 1.63
2511 2604 0.478507 CAAAGGGGGAGGCGGATATT 59.521 55.000 0.00 0.00 0.00 1.28
2512 2605 1.702957 CAAAGGGGGAGGCGGATATTA 59.297 52.381 0.00 0.00 0.00 0.98
2513 2606 1.657804 AAGGGGGAGGCGGATATTAG 58.342 55.000 0.00 0.00 0.00 1.73
2514 2607 0.492276 AGGGGGAGGCGGATATTAGT 59.508 55.000 0.00 0.00 0.00 2.24
2515 2608 0.613777 GGGGGAGGCGGATATTAGTG 59.386 60.000 0.00 0.00 0.00 2.74
2516 2609 0.036294 GGGGAGGCGGATATTAGTGC 60.036 60.000 0.00 0.00 0.00 4.40
2517 2610 0.977395 GGGAGGCGGATATTAGTGCT 59.023 55.000 0.00 0.00 0.00 4.40
2518 2611 2.176889 GGGAGGCGGATATTAGTGCTA 58.823 52.381 0.00 0.00 0.00 3.49
2519 2612 2.565834 GGGAGGCGGATATTAGTGCTAA 59.434 50.000 0.00 0.00 0.00 3.09
2520 2613 3.197983 GGGAGGCGGATATTAGTGCTAAT 59.802 47.826 9.13 9.13 39.02 1.73
2521 2614 4.434520 GGAGGCGGATATTAGTGCTAATC 58.565 47.826 7.63 0.00 37.07 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.575532 TCACCTCTTGCTTCTTTGGTG 58.424 47.619 0.00 0.00 44.31 4.17
19 20 1.066430 TCTCGTAACCCCATGCTTCAC 60.066 52.381 0.00 0.00 0.00 3.18
34 35 0.956410 ACTGAGCTAGTGCGTCTCGT 60.956 55.000 0.00 0.00 45.42 4.18
60 61 3.474570 GCAGGAGGAGGACGCCAT 61.475 66.667 0.00 0.00 42.23 4.40
192 194 3.684788 GGATCAGTAACACTTTCGCACAT 59.315 43.478 0.00 0.00 0.00 3.21
243 245 0.267356 AGAGCCAGAGATAGCCCCTT 59.733 55.000 0.00 0.00 0.00 3.95
277 279 3.325870 TCGGTGCTAATCTGAACTTGTG 58.674 45.455 0.00 0.00 0.00 3.33
589 593 1.826327 ATACATTGCATTTCGCGCAC 58.174 45.000 8.75 0.00 46.97 5.34
593 600 3.304026 CCACACAATACATTGCATTTCGC 59.696 43.478 1.84 0.00 41.38 4.70
604 611 3.260632 TGAAGCTAGAGCCACACAATACA 59.739 43.478 0.00 0.00 43.38 2.29
616 623 4.569966 CCATTACTTGCAGTGAAGCTAGAG 59.430 45.833 0.00 0.00 39.26 2.43
670 677 3.382546 CCAATAGTGGCCCAGAAATTCTG 59.617 47.826 15.64 15.64 40.15 3.02
716 723 7.669722 AGAAAAGTATGACCAATGAAGCCTAAA 59.330 33.333 0.00 0.00 0.00 1.85
719 726 5.574188 AGAAAAGTATGACCAATGAAGCCT 58.426 37.500 0.00 0.00 0.00 4.58
731 738 9.322773 CAATAGCAGATGAGAAGAAAAGTATGA 57.677 33.333 0.00 0.00 0.00 2.15
1064 1087 4.260743 CGCAGTTGTTCTTGATGTTGAAGA 60.261 41.667 0.00 0.00 0.00 2.87
1466 1489 4.873810 TGCAGGCGTGTGTGGCTT 62.874 61.111 8.40 0.00 43.82 4.35
1524 1547 2.964925 TGGTGCGACGTGAACAGC 60.965 61.111 0.00 0.00 0.00 4.40
1527 1550 2.656007 TCGTGGTGCGACGTGAAC 60.656 61.111 0.00 0.00 45.68 3.18
1541 1564 3.928375 ACGTACGCCTTTTATTGATTCGT 59.072 39.130 16.72 0.00 0.00 3.85
1576 1599 5.424121 AGCAGCACGCCTTTTATTTATAG 57.576 39.130 0.00 0.00 44.04 1.31
1624 1650 5.126707 GGCTAACATGTAGTAGTACAGTGGT 59.873 44.000 15.39 13.63 42.53 4.16
1631 1657 6.666678 AGTAGTGGGCTAACATGTAGTAGTA 58.333 40.000 0.00 0.00 0.00 1.82
1632 1658 5.516984 AGTAGTGGGCTAACATGTAGTAGT 58.483 41.667 0.00 0.00 0.00 2.73
1633 1659 7.447545 TCATAGTAGTGGGCTAACATGTAGTAG 59.552 40.741 0.00 0.00 0.00 2.57
1660 1686 8.317891 TGTGTACTCAAATATCAATGAAACGT 57.682 30.769 0.00 0.00 0.00 3.99
1678 1704 7.811117 TTTTTATTGCCTTGTACTGTGTACT 57.189 32.000 8.94 0.00 0.00 2.73
1691 1717 9.363401 GGGTAGATAGGTAAATTTTTATTGCCT 57.637 33.333 0.00 1.67 43.93 4.75
1703 1729 7.598248 TGTCCAATCTAGGGTAGATAGGTAAA 58.402 38.462 0.00 0.00 44.44 2.01
1743 1770 6.463897 GCAAGTAATAGTAATGGCTGACCCTA 60.464 42.308 0.00 0.00 33.59 3.53
1855 1882 5.639506 ACAAACAAGCTAGCTGTACACATAG 59.360 40.000 20.16 5.21 0.00 2.23
1887 1914 6.467677 CAGGAGAATAGTCCACTTCTTTTGA 58.532 40.000 0.00 0.00 39.34 2.69
1922 1967 2.229062 TCGCTTCAAAACAAACACCACA 59.771 40.909 0.00 0.00 0.00 4.17
1940 1985 4.909894 AGAAAAGAAGAACAACAAGTCGC 58.090 39.130 0.00 0.00 0.00 5.19
1968 2024 9.932207 TCTCATTTTTATTCACAAGATGCAAAT 57.068 25.926 0.00 0.00 0.00 2.32
1981 2037 8.138074 GCCCTTAGATTGGTCTCATTTTTATTC 58.862 37.037 0.00 0.00 35.87 1.75
1983 2039 7.357471 AGCCCTTAGATTGGTCTCATTTTTAT 58.643 34.615 0.00 0.00 35.87 1.40
1984 2040 6.731467 AGCCCTTAGATTGGTCTCATTTTTA 58.269 36.000 0.00 0.00 35.87 1.52
1985 2041 5.583932 AGCCCTTAGATTGGTCTCATTTTT 58.416 37.500 0.00 0.00 35.87 1.94
1986 2042 5.198602 AGCCCTTAGATTGGTCTCATTTT 57.801 39.130 0.00 0.00 35.87 1.82
1987 2043 4.870021 AGCCCTTAGATTGGTCTCATTT 57.130 40.909 0.00 0.00 35.87 2.32
1988 2044 5.398012 GGTTAGCCCTTAGATTGGTCTCATT 60.398 44.000 0.00 0.00 35.87 2.57
1989 2045 4.103311 GGTTAGCCCTTAGATTGGTCTCAT 59.897 45.833 0.00 0.00 35.87 2.90
1990 2046 3.454812 GGTTAGCCCTTAGATTGGTCTCA 59.545 47.826 0.00 0.00 35.87 3.27
1991 2047 4.074627 GGTTAGCCCTTAGATTGGTCTC 57.925 50.000 0.00 0.00 35.87 3.36
2005 2061 1.106285 CAGCTGGAATTGGGTTAGCC 58.894 55.000 5.57 0.00 35.05 3.93
2006 2062 1.745653 GACAGCTGGAATTGGGTTAGC 59.254 52.381 19.93 0.00 34.71 3.09
2007 2063 2.290896 TGGACAGCTGGAATTGGGTTAG 60.291 50.000 19.93 0.00 0.00 2.34
2008 2064 1.707989 TGGACAGCTGGAATTGGGTTA 59.292 47.619 19.93 0.00 0.00 2.85
2009 2065 0.482446 TGGACAGCTGGAATTGGGTT 59.518 50.000 19.93 0.00 0.00 4.11
2010 2066 0.038744 CTGGACAGCTGGAATTGGGT 59.961 55.000 19.93 0.00 0.00 4.51
2011 2067 0.038744 ACTGGACAGCTGGAATTGGG 59.961 55.000 19.93 3.88 0.00 4.12
2012 2068 1.271543 TGACTGGACAGCTGGAATTGG 60.272 52.381 19.93 5.47 0.00 3.16
2013 2069 2.189594 TGACTGGACAGCTGGAATTG 57.810 50.000 19.93 6.56 0.00 2.32
2014 2070 2.508526 GTTGACTGGACAGCTGGAATT 58.491 47.619 19.93 0.00 0.00 2.17
2015 2071 1.609061 CGTTGACTGGACAGCTGGAAT 60.609 52.381 19.93 0.00 0.00 3.01
2016 2072 0.249868 CGTTGACTGGACAGCTGGAA 60.250 55.000 19.93 1.60 0.00 3.53
2017 2073 1.367471 CGTTGACTGGACAGCTGGA 59.633 57.895 19.93 0.00 0.00 3.86
2018 2074 1.669115 CCGTTGACTGGACAGCTGG 60.669 63.158 19.93 1.96 0.00 4.85
2019 2075 1.669115 CCCGTTGACTGGACAGCTG 60.669 63.158 13.48 13.48 0.00 4.24
2020 2076 2.100879 GACCCGTTGACTGGACAGCT 62.101 60.000 0.00 0.00 0.00 4.24
2021 2077 1.668151 GACCCGTTGACTGGACAGC 60.668 63.158 0.00 0.00 0.00 4.40
2022 2078 1.372997 CGACCCGTTGACTGGACAG 60.373 63.158 0.00 0.00 0.00 3.51
2023 2079 1.829096 TCGACCCGTTGACTGGACA 60.829 57.895 0.00 0.00 0.00 4.02
2024 2080 1.372623 GTCGACCCGTTGACTGGAC 60.373 63.158 3.51 0.00 40.13 4.02
2025 2081 1.829096 TGTCGACCCGTTGACTGGA 60.829 57.895 14.12 0.00 42.95 3.86
2026 2082 1.663702 GTGTCGACCCGTTGACTGG 60.664 63.158 14.12 0.00 42.95 4.00
2027 2083 1.663702 GGTGTCGACCCGTTGACTG 60.664 63.158 14.12 0.00 42.95 3.51
2028 2084 2.732658 GGTGTCGACCCGTTGACT 59.267 61.111 14.12 0.00 42.95 3.41
2040 2096 2.069273 CAAATCTGACGACAGGGTGTC 58.931 52.381 14.76 0.00 43.65 3.67
2041 2097 1.416401 ACAAATCTGACGACAGGGTGT 59.584 47.619 14.76 12.59 43.60 4.16
2042 2098 1.800586 CACAAATCTGACGACAGGGTG 59.199 52.381 14.76 13.20 43.60 4.61
2043 2099 1.416401 ACACAAATCTGACGACAGGGT 59.584 47.619 14.76 5.95 43.60 4.34
2044 2100 2.069273 GACACAAATCTGACGACAGGG 58.931 52.381 14.76 5.38 43.60 4.45
2045 2101 2.754472 TGACACAAATCTGACGACAGG 58.246 47.619 14.76 1.50 43.60 4.00
2046 2102 3.742882 ACATGACACAAATCTGACGACAG 59.257 43.478 8.68 8.68 44.66 3.51
2047 2103 3.727726 ACATGACACAAATCTGACGACA 58.272 40.909 0.00 0.00 0.00 4.35
2048 2104 3.740832 TGACATGACACAAATCTGACGAC 59.259 43.478 0.00 0.00 0.00 4.34
2049 2105 3.988819 TGACATGACACAAATCTGACGA 58.011 40.909 0.00 0.00 0.00 4.20
2050 2106 4.730600 TTGACATGACACAAATCTGACG 57.269 40.909 0.00 0.00 0.00 4.35
2051 2107 5.455392 CCTTTGACATGACACAAATCTGAC 58.545 41.667 0.00 0.00 35.84 3.51
2052 2108 4.022935 GCCTTTGACATGACACAAATCTGA 60.023 41.667 0.00 0.00 35.84 3.27
2053 2109 4.232221 GCCTTTGACATGACACAAATCTG 58.768 43.478 0.00 3.18 35.84 2.90
2054 2110 3.256631 GGCCTTTGACATGACACAAATCT 59.743 43.478 0.00 0.00 35.84 2.40
2055 2111 3.256631 AGGCCTTTGACATGACACAAATC 59.743 43.478 0.00 4.70 35.84 2.17
2056 2112 3.233507 AGGCCTTTGACATGACACAAAT 58.766 40.909 0.00 0.00 35.84 2.32
2057 2113 2.665165 AGGCCTTTGACATGACACAAA 58.335 42.857 0.00 8.30 35.26 2.83
2058 2114 2.363306 AGGCCTTTGACATGACACAA 57.637 45.000 0.00 0.00 0.00 3.33
2059 2115 2.363306 AAGGCCTTTGACATGACACA 57.637 45.000 13.78 0.00 0.00 3.72
2060 2116 3.733443 AAAAGGCCTTTGACATGACAC 57.267 42.857 31.02 0.00 32.36 3.67
2061 2117 3.740764 GCAAAAAGGCCTTTGACATGACA 60.741 43.478 31.02 0.00 38.35 3.58
2062 2118 2.802247 GCAAAAAGGCCTTTGACATGAC 59.198 45.455 31.02 17.43 38.35 3.06
2063 2119 2.545532 CGCAAAAAGGCCTTTGACATGA 60.546 45.455 31.02 0.00 38.35 3.07
2064 2120 1.794116 CGCAAAAAGGCCTTTGACATG 59.206 47.619 31.02 24.74 38.35 3.21
2122 2179 1.574702 CGGGTCAAAAACTCGCCTCC 61.575 60.000 0.00 0.00 46.55 4.30
2135 2192 0.836400 AAGGAAGAGGCTTCGGGTCA 60.836 55.000 0.00 0.00 0.00 4.02
2181 2271 1.077169 GGACCAGGGGAAAAAGGATGT 59.923 52.381 0.00 0.00 0.00 3.06
2184 2274 0.703056 TGGGACCAGGGGAAAAAGGA 60.703 55.000 0.00 0.00 0.00 3.36
2185 2275 0.413434 ATGGGACCAGGGGAAAAAGG 59.587 55.000 0.00 0.00 0.00 3.11
2187 2277 1.077005 CTGATGGGACCAGGGGAAAAA 59.923 52.381 0.00 0.00 0.00 1.94
2195 2286 1.077212 CCTTGGCTGATGGGACCAG 60.077 63.158 0.00 0.00 34.28 4.00
2196 2287 3.089838 CCTTGGCTGATGGGACCA 58.910 61.111 0.00 0.00 0.00 4.02
2198 2289 2.048603 GTGCCTTGGCTGATGGGAC 61.049 63.158 13.18 0.00 33.79 4.46
2199 2290 2.356278 GTGCCTTGGCTGATGGGA 59.644 61.111 13.18 0.00 0.00 4.37
2231 2324 2.165167 ACCAACTCTGCATCCATGTTG 58.835 47.619 0.00 0.00 36.22 3.33
2268 2361 3.550639 GGATCATGAACTCTCTCTCAGCG 60.551 52.174 0.00 0.00 0.00 5.18
2295 2388 3.045634 TGCTAACCACAGCCCATATAGT 58.954 45.455 0.00 0.00 41.04 2.12
2329 2422 7.255277 GGCATCTGTAATTTTCTTACCATCTCC 60.255 40.741 0.00 0.00 0.00 3.71
2371 2464 3.635836 TCCAGTGCATGATTGAAAACACA 59.364 39.130 0.00 0.00 0.00 3.72
2390 2483 3.695606 GCACCGAGAGCCACTCCA 61.696 66.667 3.46 0.00 42.18 3.86
2423 2516 1.532523 TGCTGTTTCCATTCGCATCA 58.467 45.000 0.00 0.00 0.00 3.07
2427 2520 0.803380 GCCATGCTGTTTCCATTCGC 60.803 55.000 0.00 0.00 0.00 4.70
2428 2521 0.179129 GGCCATGCTGTTTCCATTCG 60.179 55.000 0.00 0.00 0.00 3.34
2429 2522 0.896923 TGGCCATGCTGTTTCCATTC 59.103 50.000 0.00 0.00 0.00 2.67
2430 2523 1.276989 CTTGGCCATGCTGTTTCCATT 59.723 47.619 6.09 0.00 0.00 3.16
2431 2524 0.899720 CTTGGCCATGCTGTTTCCAT 59.100 50.000 6.09 0.00 0.00 3.41
2432 2525 1.186917 CCTTGGCCATGCTGTTTCCA 61.187 55.000 6.09 0.00 0.00 3.53
2433 2526 0.899717 TCCTTGGCCATGCTGTTTCC 60.900 55.000 6.09 0.00 0.00 3.13
2434 2527 1.134907 CATCCTTGGCCATGCTGTTTC 60.135 52.381 6.09 0.00 0.00 2.78
2435 2528 0.899720 CATCCTTGGCCATGCTGTTT 59.100 50.000 6.09 0.00 0.00 2.83
2436 2529 0.974010 CCATCCTTGGCCATGCTGTT 60.974 55.000 6.09 0.00 35.85 3.16
2437 2530 1.380785 CCATCCTTGGCCATGCTGT 60.381 57.895 6.09 0.00 35.85 4.40
2438 2531 0.469331 ATCCATCCTTGGCCATGCTG 60.469 55.000 6.09 9.24 43.29 4.41
2439 2532 0.263765 AATCCATCCTTGGCCATGCT 59.736 50.000 6.09 0.00 43.29 3.79
2440 2533 1.999648 TAATCCATCCTTGGCCATGC 58.000 50.000 6.09 0.00 43.29 4.06
2441 2534 3.962718 ACTTTAATCCATCCTTGGCCATG 59.037 43.478 6.09 9.47 43.29 3.66
2442 2535 4.270317 ACTTTAATCCATCCTTGGCCAT 57.730 40.909 6.09 0.00 43.29 4.40
2443 2536 3.756082 ACTTTAATCCATCCTTGGCCA 57.244 42.857 0.00 0.00 43.29 5.36
2444 2537 6.731292 ATTAACTTTAATCCATCCTTGGCC 57.269 37.500 0.00 0.00 43.29 5.36
2445 2538 8.232913 TGTATTAACTTTAATCCATCCTTGGC 57.767 34.615 0.00 0.00 43.29 4.52
2452 2545 9.816354 GCACCATTTGTATTAACTTTAATCCAT 57.184 29.630 0.00 0.00 35.20 3.41
2453 2546 9.030452 AGCACCATTTGTATTAACTTTAATCCA 57.970 29.630 0.00 0.00 35.20 3.41
2459 2552 8.802267 ACACATAGCACCATTTGTATTAACTTT 58.198 29.630 0.00 0.00 0.00 2.66
2460 2553 8.243426 CACACATAGCACCATTTGTATTAACTT 58.757 33.333 0.00 0.00 0.00 2.66
2461 2554 7.628366 GCACACATAGCACCATTTGTATTAACT 60.628 37.037 0.00 0.00 0.00 2.24
2462 2555 6.472163 GCACACATAGCACCATTTGTATTAAC 59.528 38.462 0.00 0.00 0.00 2.01
2463 2556 6.151817 TGCACACATAGCACCATTTGTATTAA 59.848 34.615 0.00 0.00 37.02 1.40
2464 2557 5.649831 TGCACACATAGCACCATTTGTATTA 59.350 36.000 0.00 0.00 37.02 0.98
2465 2558 4.462132 TGCACACATAGCACCATTTGTATT 59.538 37.500 0.00 0.00 37.02 1.89
2466 2559 4.015764 TGCACACATAGCACCATTTGTAT 58.984 39.130 0.00 0.00 37.02 2.29
2467 2560 3.416156 TGCACACATAGCACCATTTGTA 58.584 40.909 0.00 0.00 37.02 2.41
2468 2561 2.237643 TGCACACATAGCACCATTTGT 58.762 42.857 0.00 0.00 37.02 2.83
2469 2562 2.988493 GTTGCACACATAGCACCATTTG 59.012 45.455 0.00 0.00 42.54 2.32
2470 2563 2.627221 TGTTGCACACATAGCACCATTT 59.373 40.909 0.00 0.00 42.54 2.32
2471 2564 2.237643 TGTTGCACACATAGCACCATT 58.762 42.857 0.00 0.00 42.54 3.16
2472 2565 1.908344 TGTTGCACACATAGCACCAT 58.092 45.000 0.00 0.00 42.54 3.55
2473 2566 3.410960 TGTTGCACACATAGCACCA 57.589 47.368 0.00 0.00 42.54 4.17
2483 2576 0.754957 CTCCCCCTTTGTGTTGCACA 60.755 55.000 0.00 0.00 43.02 4.57
2484 2577 1.463553 CCTCCCCCTTTGTGTTGCAC 61.464 60.000 0.00 0.00 34.56 4.57
2485 2578 1.152567 CCTCCCCCTTTGTGTTGCA 60.153 57.895 0.00 0.00 0.00 4.08
2486 2579 2.574018 GCCTCCCCCTTTGTGTTGC 61.574 63.158 0.00 0.00 0.00 4.17
2487 2580 2.268076 CGCCTCCCCCTTTGTGTTG 61.268 63.158 0.00 0.00 0.00 3.33
2488 2581 2.115266 CGCCTCCCCCTTTGTGTT 59.885 61.111 0.00 0.00 0.00 3.32
2489 2582 3.966543 CCGCCTCCCCCTTTGTGT 61.967 66.667 0.00 0.00 0.00 3.72
2490 2583 1.632018 TATCCGCCTCCCCCTTTGTG 61.632 60.000 0.00 0.00 0.00 3.33
2491 2584 0.697854 ATATCCGCCTCCCCCTTTGT 60.698 55.000 0.00 0.00 0.00 2.83
2492 2585 0.478507 AATATCCGCCTCCCCCTTTG 59.521 55.000 0.00 0.00 0.00 2.77
2493 2586 1.985895 CTAATATCCGCCTCCCCCTTT 59.014 52.381 0.00 0.00 0.00 3.11
2494 2587 1.132495 ACTAATATCCGCCTCCCCCTT 60.132 52.381 0.00 0.00 0.00 3.95
2495 2588 0.492276 ACTAATATCCGCCTCCCCCT 59.508 55.000 0.00 0.00 0.00 4.79
2496 2589 0.613777 CACTAATATCCGCCTCCCCC 59.386 60.000 0.00 0.00 0.00 5.40
2497 2590 0.036294 GCACTAATATCCGCCTCCCC 60.036 60.000 0.00 0.00 0.00 4.81
2498 2591 0.977395 AGCACTAATATCCGCCTCCC 59.023 55.000 0.00 0.00 0.00 4.30
2499 2592 3.955650 TTAGCACTAATATCCGCCTCC 57.044 47.619 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.