Multiple sequence alignment - TraesCS4B01G272800

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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 TraesCS4B01G272800 chr4B 100.000 2895 0 0 1 2895 550501807 550504701 0.000000e+00 5347.0
1 TraesCS4B01G272800 chr4B 87.712 1416 134 17 632 2033 550433451 550432062 0.000000e+00 1615.0
2 TraesCS4B01G272800 chr4B 92.803 931 61 3 1189 2113 550487576 550486646 0.000000e+00 1343.0
3 TraesCS4B01G272800 chr4B 85.558 914 125 6 986 1894 547309457 547310368 0.000000e+00 950.0
4 TraesCS4B01G272800 chr4B 89.013 537 46 9 657 1193 550488284 550487761 0.000000e+00 652.0
5 TraesCS4B01G272800 chr4B 82.511 223 21 11 1 221 550433909 550433703 2.290000e-41 180.0
6 TraesCS4B01G272800 chr4B 96.053 76 3 0 221 296 550489237 550489162 1.090000e-24 124.0
7 TraesCS4B01G272800 chr4D 92.578 2048 108 18 99 2120 442395158 442397187 0.000000e+00 2900.0
8 TraesCS4B01G272800 chr4D 91.683 1551 95 21 575 2116 442223441 442221916 0.000000e+00 2119.0
9 TraesCS4B01G272800 chr4D 89.450 1564 117 25 574 2120 442249242 442247710 0.000000e+00 1930.0
10 TraesCS4B01G272800 chr4D 86.361 1591 141 43 473 2033 442215873 442214329 0.000000e+00 1666.0
11 TraesCS4B01G272800 chr4D 85.246 915 127 8 986 1894 441255867 441256779 0.000000e+00 935.0
12 TraesCS4B01G272800 chr4D 82.960 223 20 8 1 221 442216347 442216141 4.930000e-43 185.0
13 TraesCS4B01G272800 chr4D 94.286 105 4 1 1 103 442389722 442389826 2.990000e-35 159.0
14 TraesCS4B01G272800 chr4D 78.802 217 19 12 221 411 442249564 442249349 1.410000e-23 121.0
15 TraesCS4B01G272800 chr4D 96.078 51 2 0 222 272 442224024 442223974 1.850000e-12 84.2
16 TraesCS4B01G272800 chr4D 90.909 44 4 0 1 44 442251102 442251059 3.120000e-05 60.2
17 TraesCS4B01G272800 chr4A 90.866 1675 115 13 462 2123 24919987 24918338 0.000000e+00 2211.0
18 TraesCS4B01G272800 chr4A 90.041 1466 109 18 576 2033 24935155 24936591 0.000000e+00 1864.0
19 TraesCS4B01G272800 chr4A 85.714 560 73 6 2339 2894 131994515 131993959 4.160000e-163 584.0
20 TraesCS4B01G272800 chr4A 92.208 77 6 0 2161 2237 24918338 24918262 3.050000e-20 110.0
21 TraesCS4B01G272800 chr5D 81.123 1282 161 43 657 1894 544798751 544799995 0.000000e+00 952.0
22 TraesCS4B01G272800 chr5D 94.737 38 2 0 230 267 544810929 544810966 3.120000e-05 60.2
23 TraesCS4B01G272800 chr2B 95.722 561 23 1 2335 2894 96227413 96226853 0.000000e+00 902.0
24 TraesCS4B01G272800 chr5B 79.827 1274 186 41 657 1894 687223392 687224630 0.000000e+00 863.0
25 TraesCS4B01G272800 chr5B 83.986 562 81 9 2321 2881 462728457 462729010 5.490000e-147 531.0
26 TraesCS4B01G272800 chr5B 80.606 330 28 15 848 1167 687259492 687259795 3.750000e-54 222.0
27 TraesCS4B01G272800 chr1A 90.374 561 53 1 2335 2894 486760540 486759980 0.000000e+00 736.0
28 TraesCS4B01G272800 chr1A 89.127 561 60 1 2335 2894 486809032 486808472 0.000000e+00 697.0
29 TraesCS4B01G272800 chr1A 79.292 367 40 18 843 1193 569356151 569355805 1.040000e-54 224.0
30 TraesCS4B01G272800 chr7D 94.397 464 25 1 2335 2797 125453050 125453513 0.000000e+00 712.0
31 TraesCS4B01G272800 chr6B 88.434 562 63 2 2335 2894 281634435 281633874 0.000000e+00 676.0
32 TraesCS4B01G272800 chr5A 86.121 562 76 2 2335 2894 604236176 604236737 3.190000e-169 604.0
33 TraesCS4B01G272800 chr7A 85.841 565 77 3 2332 2894 672879463 672880026 5.340000e-167 597.0


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 TraesCS4B01G272800 chr4B 550501807 550504701 2894 False 5347.000000 5347 100.0000 1 2895 1 chr4B.!!$F2 2894
1 TraesCS4B01G272800 chr4B 547309457 547310368 911 False 950.000000 950 85.5580 986 1894 1 chr4B.!!$F1 908
2 TraesCS4B01G272800 chr4B 550432062 550433909 1847 True 897.500000 1615 85.1115 1 2033 2 chr4B.!!$R1 2032
3 TraesCS4B01G272800 chr4B 550486646 550489237 2591 True 706.333333 1343 92.6230 221 2113 3 chr4B.!!$R2 1892
4 TraesCS4B01G272800 chr4D 442395158 442397187 2029 False 2900.000000 2900 92.5780 99 2120 1 chr4D.!!$F3 2021
5 TraesCS4B01G272800 chr4D 442221916 442224024 2108 True 1101.600000 2119 93.8805 222 2116 2 chr4D.!!$R2 1894
6 TraesCS4B01G272800 chr4D 441255867 441256779 912 False 935.000000 935 85.2460 986 1894 1 chr4D.!!$F1 908
7 TraesCS4B01G272800 chr4D 442214329 442216347 2018 True 925.500000 1666 84.6605 1 2033 2 chr4D.!!$R1 2032
8 TraesCS4B01G272800 chr4D 442247710 442251102 3392 True 703.733333 1930 86.3870 1 2120 3 chr4D.!!$R3 2119
9 TraesCS4B01G272800 chr4A 24935155 24936591 1436 False 1864.000000 1864 90.0410 576 2033 1 chr4A.!!$F1 1457
10 TraesCS4B01G272800 chr4A 24918262 24919987 1725 True 1160.500000 2211 91.5370 462 2237 2 chr4A.!!$R2 1775
11 TraesCS4B01G272800 chr4A 131993959 131994515 556 True 584.000000 584 85.7140 2339 2894 1 chr4A.!!$R1 555
12 TraesCS4B01G272800 chr5D 544798751 544799995 1244 False 952.000000 952 81.1230 657 1894 1 chr5D.!!$F1 1237
13 TraesCS4B01G272800 chr2B 96226853 96227413 560 True 902.000000 902 95.7220 2335 2894 1 chr2B.!!$R1 559
14 TraesCS4B01G272800 chr5B 687223392 687224630 1238 False 863.000000 863 79.8270 657 1894 1 chr5B.!!$F2 1237
15 TraesCS4B01G272800 chr5B 462728457 462729010 553 False 531.000000 531 83.9860 2321 2881 1 chr5B.!!$F1 560
16 TraesCS4B01G272800 chr1A 486759980 486760540 560 True 736.000000 736 90.3740 2335 2894 1 chr1A.!!$R1 559
17 TraesCS4B01G272800 chr1A 486808472 486809032 560 True 697.000000 697 89.1270 2335 2894 1 chr1A.!!$R2 559
18 TraesCS4B01G272800 chr6B 281633874 281634435 561 True 676.000000 676 88.4340 2335 2894 1 chr6B.!!$R1 559
19 TraesCS4B01G272800 chr5A 604236176 604236737 561 False 604.000000 604 86.1210 2335 2894 1 chr5A.!!$F1 559
20 TraesCS4B01G272800 chr7A 672879463 672880026 563 False 597.000000 597 85.8410 2332 2894 1 chr7A.!!$F1 562

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
260 1597 1.168714 GTTGGGCTTGCAGTTAGAGG 58.831 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 4482 0.038892 TTTACAGCGACACCTCGTCC 60.039 55.0 0.0 0.0 42.07 4.79 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
48 1134 8.714179 TGAAAAGAATAACCCGCATATAATACG 58.286 33.333 0.00 0.00 0.00 3.06
61 1147 8.182227 CCGCATATAATACGACTATTGAAGAGA 58.818 37.037 0.00 0.00 0.00 3.10
62 1148 9.216087 CGCATATAATACGACTATTGAAGAGAG 57.784 37.037 0.00 0.00 0.00 3.20
114 1200 7.577616 GCATGTTTTCTCTAAACCAATTAGGCT 60.578 37.037 0.00 0.00 44.49 4.58
146 1436 7.262772 CAAGTAATAATCAAGGTCGGTGTAGA 58.737 38.462 0.00 0.00 0.00 2.59
260 1597 1.168714 GTTGGGCTTGCAGTTAGAGG 58.831 55.000 0.00 0.00 0.00 3.69
306 1929 5.011635 AGCGGGAATTCCAAAGTAACAAAAT 59.988 36.000 25.67 0.00 37.91 1.82
317 1940 5.523438 AAGTAACAAAATTCCGGCTTTCA 57.477 34.783 0.00 0.00 0.00 2.69
344 1967 4.816385 TCAGCTACTTGTTCTTGTCTTTGG 59.184 41.667 0.00 0.00 0.00 3.28
380 2005 6.430000 GTCTGAATGTAGGTAGCCAAGAAAAA 59.570 38.462 0.00 0.00 0.00 1.94
421 2054 4.702612 TCTGGTGCGAAATGCCTTTAATTA 59.297 37.500 0.00 0.00 45.60 1.40
448 2082 1.954382 TGCATCTACTCGACGCCTTAT 59.046 47.619 0.00 0.00 27.50 1.73
494 2160 8.677300 TCTAATTAGCCAAGCAGAAAACATAAG 58.323 33.333 7.67 0.00 0.00 1.73
509 2176 8.495949 AGAAAACATAAGACATCACAAACGTAG 58.504 33.333 0.00 0.00 0.00 3.51
551 2218 6.173339 CAGTTCAGTATTAAAGGCCTCTTGA 58.827 40.000 5.23 0.00 32.75 3.02
591 2807 4.024809 ACTCAACAAAAGCGAGCTAGTTTC 60.025 41.667 0.00 0.00 0.00 2.78
711 2948 8.511748 AATTAAGGAAAGCTCTATAGATCCCA 57.488 34.615 14.09 3.27 0.00 4.37
712 2949 8.692682 ATTAAGGAAAGCTCTATAGATCCCAT 57.307 34.615 14.09 8.21 0.00 4.00
713 2950 9.790297 ATTAAGGAAAGCTCTATAGATCCCATA 57.210 33.333 14.09 7.46 0.00 2.74
714 2951 7.489239 AAGGAAAGCTCTATAGATCCCATAC 57.511 40.000 14.09 0.00 0.00 2.39
715 2952 5.654650 AGGAAAGCTCTATAGATCCCATACG 59.345 44.000 14.09 0.00 0.00 3.06
716 2953 5.419471 GGAAAGCTCTATAGATCCCATACGT 59.581 44.000 2.11 0.00 0.00 3.57
792 3050 3.453424 CATCCATACGATCGTTGGAACA 58.547 45.455 34.56 22.83 38.12 3.18
841 3101 4.208047 CACGACAATCATTTCTCTCGATCC 59.792 45.833 0.00 0.00 0.00 3.36
891 3171 2.443387 CACCATTGTCGCAATCATTCG 58.557 47.619 2.65 0.00 0.00 3.34
1032 3327 2.912624 GCGCTTCCTGCAGCTGTTT 61.913 57.895 16.64 0.00 43.06 2.83
1054 3349 3.016474 GCAGTTCTCGCGTTCTGCC 62.016 63.158 24.31 13.77 44.84 4.85
1369 3895 3.094062 ATCGTGCGGGCAGTGCTAT 62.094 57.895 16.11 0.00 0.00 2.97
1375 3901 1.097547 GCGGGCAGTGCTATGTCATT 61.098 55.000 16.11 0.00 0.00 2.57
1711 4237 0.464735 CGGTGAAAGGGACCAACACA 60.465 55.000 0.00 0.00 32.45 3.72
1956 4482 9.914131 ACATATATGCACACTACTAGTATTGTG 57.086 33.333 33.08 33.08 44.51 3.33
2051 4579 2.045926 GCCTCGGTCAAGTGGCAT 60.046 61.111 5.34 0.00 46.64 4.40
2070 4598 7.989826 GTGGCATTACACTAAAGATTGAAGAT 58.010 34.615 0.00 0.00 38.32 2.40
2116 4644 4.082245 CCACATGTTCAAGGATTTACCACC 60.082 45.833 0.00 0.00 42.04 4.61
2120 4648 2.745821 GTTCAAGGATTTACCACCGGAC 59.254 50.000 9.46 0.00 42.04 4.79
2122 4650 2.372504 TCAAGGATTTACCACCGGACAA 59.627 45.455 9.46 0.00 42.04 3.18
2123 4651 2.747446 CAAGGATTTACCACCGGACAAG 59.253 50.000 9.46 0.00 42.04 3.16
2124 4652 2.262637 AGGATTTACCACCGGACAAGA 58.737 47.619 9.46 0.00 42.04 3.02
2125 4653 2.236395 AGGATTTACCACCGGACAAGAG 59.764 50.000 9.46 0.00 42.04 2.85
2126 4654 2.007608 GATTTACCACCGGACAAGAGC 58.992 52.381 9.46 0.00 0.00 4.09
2127 4655 0.759959 TTTACCACCGGACAAGAGCA 59.240 50.000 9.46 0.00 0.00 4.26
2128 4656 0.034337 TTACCACCGGACAAGAGCAC 59.966 55.000 9.46 0.00 0.00 4.40
2129 4657 2.149803 TACCACCGGACAAGAGCACG 62.150 60.000 9.46 0.00 0.00 5.34
2130 4658 2.029073 CACCGGACAAGAGCACGT 59.971 61.111 9.46 0.00 0.00 4.49
2131 4659 2.022129 CACCGGACAAGAGCACGTC 61.022 63.158 9.46 0.00 0.00 4.34
2132 4660 2.805353 CCGGACAAGAGCACGTCG 60.805 66.667 0.00 0.00 32.74 5.12
2133 4661 2.805353 CGGACAAGAGCACGTCGG 60.805 66.667 0.00 0.00 32.74 4.79
2134 4662 2.649034 GGACAAGAGCACGTCGGA 59.351 61.111 0.00 0.00 32.74 4.55
2135 4663 1.444553 GGACAAGAGCACGTCGGAG 60.445 63.158 0.00 0.00 32.74 4.63
2136 4664 1.286260 GACAAGAGCACGTCGGAGT 59.714 57.895 0.00 0.00 0.00 3.85
2137 4665 1.004277 GACAAGAGCACGTCGGAGTG 61.004 60.000 0.00 6.78 44.47 3.51
2138 4666 1.007271 CAAGAGCACGTCGGAGTGT 60.007 57.895 11.60 1.16 43.61 3.55
2139 4667 0.597637 CAAGAGCACGTCGGAGTGTT 60.598 55.000 11.60 6.64 43.61 3.32
2140 4668 0.104304 AAGAGCACGTCGGAGTGTTT 59.896 50.000 11.60 2.73 43.61 2.83
2141 4669 0.597637 AGAGCACGTCGGAGTGTTTG 60.598 55.000 11.60 0.00 43.61 2.93
2142 4670 0.874607 GAGCACGTCGGAGTGTTTGT 60.875 55.000 11.60 0.00 43.61 2.83
2143 4671 0.874607 AGCACGTCGGAGTGTTTGTC 60.875 55.000 11.60 0.00 43.61 3.18
2144 4672 1.844003 CACGTCGGAGTGTTTGTCG 59.156 57.895 0.00 0.00 37.35 4.35
2145 4673 1.947642 ACGTCGGAGTGTTTGTCGC 60.948 57.895 0.00 0.00 0.00 5.19
2146 4674 1.660575 CGTCGGAGTGTTTGTCGCT 60.661 57.895 0.00 0.00 39.84 4.93
2147 4675 1.853319 GTCGGAGTGTTTGTCGCTG 59.147 57.895 0.00 0.00 36.99 5.18
2148 4676 1.300620 TCGGAGTGTTTGTCGCTGG 60.301 57.895 0.00 0.00 36.99 4.85
2149 4677 2.946762 GGAGTGTTTGTCGCTGGC 59.053 61.111 0.00 0.00 36.99 4.85
2150 4678 1.891919 GGAGTGTTTGTCGCTGGCA 60.892 57.895 0.00 0.00 36.99 4.92
2151 4679 1.444119 GGAGTGTTTGTCGCTGGCAA 61.444 55.000 0.00 0.00 36.99 4.52
2152 4680 0.317020 GAGTGTTTGTCGCTGGCAAC 60.317 55.000 0.00 0.00 36.99 4.17
2154 4682 0.865639 GTGTTTGTCGCTGGCAACAC 60.866 55.000 9.63 9.63 46.17 3.32
2155 4683 1.029408 TGTTTGTCGCTGGCAACACT 61.029 50.000 0.00 0.00 46.17 3.55
2156 4684 0.100503 GTTTGTCGCTGGCAACACTT 59.899 50.000 0.00 0.00 46.17 3.16
2157 4685 0.100325 TTTGTCGCTGGCAACACTTG 59.900 50.000 0.00 0.00 46.17 3.16
2158 4686 0.746204 TTGTCGCTGGCAACACTTGA 60.746 50.000 0.00 0.00 46.17 3.02
2159 4687 1.279840 GTCGCTGGCAACACTTGAC 59.720 57.895 0.00 0.00 46.17 3.18
2177 4705 4.926860 TGACATGCTTCTTTATGTGTCG 57.073 40.909 0.00 0.00 38.94 4.35
2178 4706 3.684305 TGACATGCTTCTTTATGTGTCGG 59.316 43.478 0.00 0.00 38.94 4.79
2190 4718 1.934589 TGTGTCGGAGTGTTTGTCAG 58.065 50.000 0.00 0.00 0.00 3.51
2228 4756 6.371825 GGGAAATCGACAAATAGAGTCTTTGT 59.628 38.462 9.49 9.49 46.55 2.83
2237 4765 5.899120 AATAGAGTCTTTGTCGAGTGCTA 57.101 39.130 0.00 0.00 0.00 3.49
2238 4766 6.458232 AATAGAGTCTTTGTCGAGTGCTAT 57.542 37.500 0.00 0.00 0.00 2.97
2239 4767 7.569639 AATAGAGTCTTTGTCGAGTGCTATA 57.430 36.000 0.00 0.00 0.00 1.31
2240 4768 5.899120 AGAGTCTTTGTCGAGTGCTATAA 57.101 39.130 0.00 0.00 0.00 0.98
2241 4769 6.268825 AGAGTCTTTGTCGAGTGCTATAAA 57.731 37.500 0.00 0.00 0.00 1.40
2242 4770 6.688578 AGAGTCTTTGTCGAGTGCTATAAAA 58.311 36.000 0.00 0.00 0.00 1.52
2243 4771 6.586844 AGAGTCTTTGTCGAGTGCTATAAAAC 59.413 38.462 0.00 0.00 0.00 2.43
2244 4772 6.456501 AGTCTTTGTCGAGTGCTATAAAACT 58.543 36.000 0.00 0.00 0.00 2.66
2245 4773 6.366332 AGTCTTTGTCGAGTGCTATAAAACTG 59.634 38.462 0.00 0.00 0.00 3.16
2246 4774 6.365247 GTCTTTGTCGAGTGCTATAAAACTGA 59.635 38.462 0.00 0.00 0.00 3.41
2247 4775 6.586463 TCTTTGTCGAGTGCTATAAAACTGAG 59.414 38.462 0.00 0.00 0.00 3.35
2248 4776 4.174009 TGTCGAGTGCTATAAAACTGAGC 58.826 43.478 0.00 0.00 36.72 4.26
2249 4777 4.174009 GTCGAGTGCTATAAAACTGAGCA 58.826 43.478 0.00 0.00 43.74 4.26
2272 4800 8.579863 AGCAATTTTAATATGCTCCTTGATACC 58.420 33.333 4.78 0.00 46.98 2.73
2273 4801 8.579863 GCAATTTTAATATGCTCCTTGATACCT 58.420 33.333 0.00 0.00 37.12 3.08
2277 4805 9.561069 TTTTAATATGCTCCTTGATACCTTCTC 57.439 33.333 0.00 0.00 0.00 2.87
2278 4806 8.497910 TTAATATGCTCCTTGATACCTTCTCT 57.502 34.615 0.00 0.00 0.00 3.10
2279 4807 7.385894 AATATGCTCCTTGATACCTTCTCTT 57.614 36.000 0.00 0.00 0.00 2.85
2280 4808 5.707066 ATGCTCCTTGATACCTTCTCTTT 57.293 39.130 0.00 0.00 0.00 2.52
2281 4809 5.505181 TGCTCCTTGATACCTTCTCTTTT 57.495 39.130 0.00 0.00 0.00 2.27
2282 4810 5.491982 TGCTCCTTGATACCTTCTCTTTTC 58.508 41.667 0.00 0.00 0.00 2.29
2283 4811 5.013079 TGCTCCTTGATACCTTCTCTTTTCA 59.987 40.000 0.00 0.00 0.00 2.69
2284 4812 5.352846 GCTCCTTGATACCTTCTCTTTTCAC 59.647 44.000 0.00 0.00 0.00 3.18
2285 4813 6.433847 TCCTTGATACCTTCTCTTTTCACA 57.566 37.500 0.00 0.00 0.00 3.58
2286 4814 7.020827 TCCTTGATACCTTCTCTTTTCACAT 57.979 36.000 0.00 0.00 0.00 3.21
2287 4815 6.881065 TCCTTGATACCTTCTCTTTTCACATG 59.119 38.462 0.00 0.00 0.00 3.21
2288 4816 6.881065 CCTTGATACCTTCTCTTTTCACATGA 59.119 38.462 0.00 0.00 0.00 3.07
2289 4817 7.065563 CCTTGATACCTTCTCTTTTCACATGAG 59.934 40.741 0.00 0.00 0.00 2.90
2290 4818 7.009179 TGATACCTTCTCTTTTCACATGAGT 57.991 36.000 0.00 0.00 0.00 3.41
2291 4819 8.134202 TGATACCTTCTCTTTTCACATGAGTA 57.866 34.615 0.00 0.00 0.00 2.59
2292 4820 8.253810 TGATACCTTCTCTTTTCACATGAGTAG 58.746 37.037 0.00 0.00 0.00 2.57
2293 4821 5.241662 ACCTTCTCTTTTCACATGAGTAGC 58.758 41.667 0.00 0.00 0.00 3.58
2294 4822 5.221722 ACCTTCTCTTTTCACATGAGTAGCA 60.222 40.000 0.00 0.00 0.00 3.49
2295 4823 5.121454 CCTTCTCTTTTCACATGAGTAGCAC 59.879 44.000 0.00 0.00 0.00 4.40
2296 4824 4.237724 TCTCTTTTCACATGAGTAGCACG 58.762 43.478 0.00 0.00 0.00 5.34
2297 4825 3.325870 TCTTTTCACATGAGTAGCACGG 58.674 45.455 0.00 0.00 0.00 4.94
2298 4826 1.438651 TTTCACATGAGTAGCACGGC 58.561 50.000 0.00 0.00 0.00 5.68
2299 4827 0.608130 TTCACATGAGTAGCACGGCT 59.392 50.000 0.00 3.87 43.41 5.52
2300 4828 0.108662 TCACATGAGTAGCACGGCTG 60.109 55.000 0.00 0.00 40.10 4.85
2301 4829 1.448540 ACATGAGTAGCACGGCTGC 60.449 57.895 0.00 7.18 44.63 5.25
2302 4830 1.448365 CATGAGTAGCACGGCTGCA 60.448 57.895 14.27 8.01 46.97 4.41
2303 4831 0.812811 CATGAGTAGCACGGCTGCAT 60.813 55.000 14.27 9.50 46.97 3.96
2304 4832 0.812811 ATGAGTAGCACGGCTGCATG 60.813 55.000 14.27 0.00 46.97 4.06
2305 4833 1.448540 GAGTAGCACGGCTGCATGT 60.449 57.895 14.27 0.00 46.97 3.21
2306 4834 1.003355 AGTAGCACGGCTGCATGTT 60.003 52.632 14.27 0.00 46.97 2.71
2307 4835 0.606401 AGTAGCACGGCTGCATGTTT 60.606 50.000 14.27 0.00 46.97 2.83
2308 4836 1.083489 GTAGCACGGCTGCATGTTTA 58.917 50.000 0.50 0.00 46.97 2.01
2309 4837 1.083489 TAGCACGGCTGCATGTTTAC 58.917 50.000 0.50 0.00 46.97 2.01
2310 4838 0.888736 AGCACGGCTGCATGTTTACA 60.889 50.000 0.50 0.00 46.97 2.41
2311 4839 0.171007 GCACGGCTGCATGTTTACAT 59.829 50.000 0.50 0.00 43.62 2.29
2312 4840 5.023116 TAGCACGGCTGCATGTTTACATG 62.023 47.826 16.57 16.57 46.97 3.21
2325 4853 6.712241 ATGTTTACATGAGTCTTTGTCGAG 57.288 37.500 0.00 0.00 34.83 4.04
2326 4854 4.988540 TGTTTACATGAGTCTTTGTCGAGG 59.011 41.667 0.00 0.00 0.00 4.63
2327 4855 2.751166 ACATGAGTCTTTGTCGAGGG 57.249 50.000 0.00 0.00 0.00 4.30
2328 4856 2.248248 ACATGAGTCTTTGTCGAGGGA 58.752 47.619 0.00 0.00 0.00 4.20
2329 4857 2.232452 ACATGAGTCTTTGTCGAGGGAG 59.768 50.000 0.00 0.00 0.00 4.30
2330 4858 0.603569 TGAGTCTTTGTCGAGGGAGC 59.396 55.000 0.00 0.00 0.00 4.70
2331 4859 0.603569 GAGTCTTTGTCGAGGGAGCA 59.396 55.000 0.00 0.00 0.00 4.26
2332 4860 1.205893 GAGTCTTTGTCGAGGGAGCAT 59.794 52.381 0.00 0.00 0.00 3.79
2333 4861 1.066573 AGTCTTTGTCGAGGGAGCATG 60.067 52.381 0.00 0.00 0.00 4.06
2709 5240 0.721154 TCGATCATTGCAGCAACGAC 59.279 50.000 10.85 1.99 0.00 4.34
2768 5299 1.476471 GGAGTGAGCTGCAGCCATATT 60.476 52.381 34.39 16.62 43.38 1.28
2882 5413 5.361857 CAGAAATACTCATTTGGCCATCCTT 59.638 40.000 6.09 0.00 34.44 3.36
2894 5425 3.205056 TGGCCATCCTTTATGTTGGAGAT 59.795 43.478 0.00 0.00 35.63 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 6.177610 TGCGGGTTATTCTTTTCAGTTATCT 58.822 36.000 0.00 0.00 0.00 1.98
114 1200 6.819649 CGACCTTGATTATTACTTGGTAACCA 59.180 38.462 0.00 0.00 30.49 3.67
117 1203 6.819649 CACCGACCTTGATTATTACTTGGTAA 59.180 38.462 0.00 0.00 32.36 2.85
146 1436 4.402155 TGCTTCTTGTTCAAGGTCAAATGT 59.598 37.500 11.82 0.00 0.00 2.71
260 1597 4.830826 AGCCACAACTAACTAAAACTGC 57.169 40.909 0.00 0.00 0.00 4.40
306 1929 0.951558 GCTGAAAGTGAAAGCCGGAA 59.048 50.000 5.05 0.00 35.30 4.30
317 1940 5.675538 AGACAAGAACAAGTAGCTGAAAGT 58.324 37.500 0.00 0.00 35.30 2.66
344 1967 5.873164 ACCTACATTCAGACCGTACAATTTC 59.127 40.000 0.00 0.00 0.00 2.17
380 2005 3.952323 CCAGAGAAGATGCAACCATTCAT 59.048 43.478 0.00 0.00 0.00 2.57
421 2054 2.334838 GTCGAGTAGATGCAACCGTTT 58.665 47.619 0.00 0.00 0.00 3.60
494 2160 2.660236 GTCGACCTACGTTTGTGATGTC 59.340 50.000 3.51 0.00 43.13 3.06
509 2176 1.607148 CTGGTTTGAAAAGGGTCGACC 59.393 52.381 27.04 27.04 40.67 4.79
551 2218 2.098934 TGAGTGCGCACAAATGTTTCTT 59.901 40.909 39.21 17.06 0.00 2.52
591 2807 4.582701 AAGTCTATAGCAGTAGCAGCTG 57.417 45.455 10.11 10.11 45.49 4.24
654 2877 9.793252 CATTCAAAATGATAGGTTAACTGAAGG 57.207 33.333 5.42 2.59 0.00 3.46
709 2946 3.123804 GCAGGTCTGAATGTACGTATGG 58.876 50.000 0.00 0.00 0.00 2.74
710 2947 2.789339 CGCAGGTCTGAATGTACGTATG 59.211 50.000 0.00 0.00 0.00 2.39
711 2948 2.426024 ACGCAGGTCTGAATGTACGTAT 59.574 45.455 0.00 0.00 0.00 3.06
712 2949 1.814394 ACGCAGGTCTGAATGTACGTA 59.186 47.619 1.65 0.00 0.00 3.57
713 2950 0.601558 ACGCAGGTCTGAATGTACGT 59.398 50.000 1.65 0.00 0.00 3.57
714 2951 1.654105 GAACGCAGGTCTGAATGTACG 59.346 52.381 1.65 0.00 0.00 3.67
715 2952 2.683968 TGAACGCAGGTCTGAATGTAC 58.316 47.619 1.65 0.00 0.00 2.90
716 2953 3.394674 TTGAACGCAGGTCTGAATGTA 57.605 42.857 1.65 0.00 0.00 2.29
841 3101 9.979578 CTTAAATAGGATCTAGCTAGCATATGG 57.020 37.037 18.83 0.00 0.00 2.74
891 3171 2.675317 CGAGAGTGGATTTGGAGGTGAC 60.675 54.545 0.00 0.00 0.00 3.67
948 3228 3.388676 AGGGAGAGATGATTGAGCTTCTG 59.611 47.826 0.00 0.00 0.00 3.02
1054 3349 3.564027 GGAATTGACCGGCGCGAG 61.564 66.667 12.10 1.76 0.00 5.03
1223 3734 1.532437 ACACATTCAGACATGCACACG 59.468 47.619 0.00 0.00 0.00 4.49
1303 3829 1.963855 CGCCACGTTGTTGATCCCA 60.964 57.895 0.00 0.00 0.00 4.37
1336 3862 1.398041 CACGATGCACCGTCATTGAAT 59.602 47.619 1.08 0.00 41.29 2.57
1369 3895 2.892374 CTGGTGTCGCAGATAATGACA 58.108 47.619 0.00 0.00 40.67 3.58
1375 3901 0.608130 ACTTGCTGGTGTCGCAGATA 59.392 50.000 0.00 0.00 40.67 1.98
1906 4432 9.513906 TGTCTGAAAATGAGTTGATAATACCAA 57.486 29.630 0.00 0.00 0.00 3.67
1926 4452 9.740710 ATACTAGTAGTGTGCATATATGTCTGA 57.259 33.333 13.29 0.00 0.00 3.27
1956 4482 0.038892 TTTACAGCGACACCTCGTCC 60.039 55.000 0.00 0.00 42.07 4.79
2070 4598 6.782988 TGGGGTTCCATATTTTTACAGTTCAA 59.217 34.615 0.00 0.00 38.32 2.69
2088 4616 2.286365 TCCTTGAACATGTGGGGTTC 57.714 50.000 0.00 0.00 43.78 3.62
2116 4644 2.805353 CCGACGTGCTCTTGTCCG 60.805 66.667 0.00 0.00 0.00 4.79
2120 4648 0.597637 AACACTCCGACGTGCTCTTG 60.598 55.000 0.00 0.00 38.45 3.02
2122 4650 0.597637 CAAACACTCCGACGTGCTCT 60.598 55.000 0.00 0.00 38.45 4.09
2123 4651 0.874607 ACAAACACTCCGACGTGCTC 60.875 55.000 0.00 0.00 38.45 4.26
2124 4652 0.874607 GACAAACACTCCGACGTGCT 60.875 55.000 0.00 0.00 38.45 4.40
2125 4653 1.563173 GACAAACACTCCGACGTGC 59.437 57.895 0.00 0.00 38.45 5.34
2126 4654 1.844003 CGACAAACACTCCGACGTG 59.156 57.895 0.00 3.02 40.67 4.49
2127 4655 1.947642 GCGACAAACACTCCGACGT 60.948 57.895 0.00 0.00 0.00 4.34
2128 4656 1.660575 AGCGACAAACACTCCGACG 60.661 57.895 0.00 0.00 0.00 5.12
2129 4657 1.557443 CCAGCGACAAACACTCCGAC 61.557 60.000 0.00 0.00 0.00 4.79
2130 4658 1.300620 CCAGCGACAAACACTCCGA 60.301 57.895 0.00 0.00 0.00 4.55
2131 4659 2.954753 GCCAGCGACAAACACTCCG 61.955 63.158 0.00 0.00 0.00 4.63
2132 4660 1.444119 TTGCCAGCGACAAACACTCC 61.444 55.000 0.00 0.00 0.00 3.85
2133 4661 0.317020 GTTGCCAGCGACAAACACTC 60.317 55.000 5.11 0.00 0.00 3.51
2134 4662 1.029408 TGTTGCCAGCGACAAACACT 61.029 50.000 10.29 0.00 37.39 3.55
2135 4663 0.865639 GTGTTGCCAGCGACAAACAC 60.866 55.000 14.17 10.49 41.46 3.32
2136 4664 1.029408 AGTGTTGCCAGCGACAAACA 61.029 50.000 14.17 1.89 41.46 2.83
2137 4665 0.100503 AAGTGTTGCCAGCGACAAAC 59.899 50.000 14.17 3.64 41.46 2.93
2138 4666 0.100325 CAAGTGTTGCCAGCGACAAA 59.900 50.000 14.17 0.00 41.46 2.83
2139 4667 0.746204 TCAAGTGTTGCCAGCGACAA 60.746 50.000 14.17 0.00 41.46 3.18
2140 4668 1.153269 TCAAGTGTTGCCAGCGACA 60.153 52.632 8.66 8.66 37.95 4.35
2141 4669 1.279840 GTCAAGTGTTGCCAGCGAC 59.720 57.895 2.90 2.90 0.00 5.19
2142 4670 0.534877 ATGTCAAGTGTTGCCAGCGA 60.535 50.000 0.00 0.00 0.00 4.93
2143 4671 0.386352 CATGTCAAGTGTTGCCAGCG 60.386 55.000 0.00 0.00 0.00 5.18
2144 4672 0.665369 GCATGTCAAGTGTTGCCAGC 60.665 55.000 0.00 0.00 0.00 4.85
2145 4673 0.956633 AGCATGTCAAGTGTTGCCAG 59.043 50.000 0.00 0.00 35.71 4.85
2146 4674 1.337703 GAAGCATGTCAAGTGTTGCCA 59.662 47.619 0.00 0.00 35.71 4.92
2147 4675 1.610522 AGAAGCATGTCAAGTGTTGCC 59.389 47.619 0.00 0.00 35.71 4.52
2148 4676 3.360249 AAGAAGCATGTCAAGTGTTGC 57.640 42.857 0.00 0.00 35.34 4.17
2149 4677 6.361481 CACATAAAGAAGCATGTCAAGTGTTG 59.639 38.462 0.00 0.00 33.12 3.33
2150 4678 6.039717 ACACATAAAGAAGCATGTCAAGTGTT 59.960 34.615 0.00 0.00 33.12 3.32
2151 4679 5.532406 ACACATAAAGAAGCATGTCAAGTGT 59.468 36.000 0.00 0.00 33.12 3.55
2152 4680 6.005583 ACACATAAAGAAGCATGTCAAGTG 57.994 37.500 0.00 0.00 33.12 3.16
2153 4681 5.106948 CGACACATAAAGAAGCATGTCAAGT 60.107 40.000 0.00 0.00 36.99 3.16
2154 4682 5.319139 CGACACATAAAGAAGCATGTCAAG 58.681 41.667 0.00 0.00 36.99 3.02
2155 4683 4.154015 CCGACACATAAAGAAGCATGTCAA 59.846 41.667 0.00 0.00 36.99 3.18
2156 4684 3.684305 CCGACACATAAAGAAGCATGTCA 59.316 43.478 0.00 0.00 36.99 3.58
2157 4685 3.932710 TCCGACACATAAAGAAGCATGTC 59.067 43.478 0.00 0.00 33.12 3.06
2158 4686 3.935203 CTCCGACACATAAAGAAGCATGT 59.065 43.478 0.00 0.00 35.79 3.21
2159 4687 3.935203 ACTCCGACACATAAAGAAGCATG 59.065 43.478 0.00 0.00 0.00 4.06
2163 4691 5.236478 ACAAACACTCCGACACATAAAGAAG 59.764 40.000 0.00 0.00 0.00 2.85
2177 4705 3.181490 GGAAAACACCTGACAAACACTCC 60.181 47.826 0.00 0.00 0.00 3.85
2178 4706 3.442273 TGGAAAACACCTGACAAACACTC 59.558 43.478 0.00 0.00 0.00 3.51
2228 4756 4.450082 TGCTCAGTTTTATAGCACTCGA 57.550 40.909 0.00 0.00 41.15 4.04
2230 4758 9.840427 TTAAAATTGCTCAGTTTTATAGCACTC 57.160 29.630 9.91 0.00 45.41 3.51
2247 4775 8.579863 AGGTATCAAGGAGCATATTAAAATTGC 58.420 33.333 0.00 0.73 36.63 3.56
2251 4779 9.561069 GAGAAGGTATCAAGGAGCATATTAAAA 57.439 33.333 0.00 0.00 0.00 1.52
2252 4780 8.938883 AGAGAAGGTATCAAGGAGCATATTAAA 58.061 33.333 0.00 0.00 0.00 1.52
2253 4781 8.497910 AGAGAAGGTATCAAGGAGCATATTAA 57.502 34.615 0.00 0.00 0.00 1.40
2254 4782 8.497910 AAGAGAAGGTATCAAGGAGCATATTA 57.502 34.615 0.00 0.00 0.00 0.98
2255 4783 7.385894 AAGAGAAGGTATCAAGGAGCATATT 57.614 36.000 0.00 0.00 0.00 1.28
2256 4784 7.385894 AAAGAGAAGGTATCAAGGAGCATAT 57.614 36.000 0.00 0.00 0.00 1.78
2257 4785 6.814954 AAAGAGAAGGTATCAAGGAGCATA 57.185 37.500 0.00 0.00 0.00 3.14
2258 4786 5.707066 AAAGAGAAGGTATCAAGGAGCAT 57.293 39.130 0.00 0.00 0.00 3.79
2259 4787 5.013079 TGAAAAGAGAAGGTATCAAGGAGCA 59.987 40.000 0.00 0.00 0.00 4.26
2260 4788 5.352846 GTGAAAAGAGAAGGTATCAAGGAGC 59.647 44.000 0.00 0.00 0.00 4.70
2261 4789 6.467677 TGTGAAAAGAGAAGGTATCAAGGAG 58.532 40.000 0.00 0.00 0.00 3.69
2262 4790 6.433847 TGTGAAAAGAGAAGGTATCAAGGA 57.566 37.500 0.00 0.00 0.00 3.36
2263 4791 6.881065 TCATGTGAAAAGAGAAGGTATCAAGG 59.119 38.462 0.00 0.00 0.00 3.61
2264 4792 7.605691 ACTCATGTGAAAAGAGAAGGTATCAAG 59.394 37.037 0.94 0.00 33.69 3.02
2265 4793 7.453393 ACTCATGTGAAAAGAGAAGGTATCAA 58.547 34.615 0.94 0.00 33.69 2.57
2266 4794 7.009179 ACTCATGTGAAAAGAGAAGGTATCA 57.991 36.000 0.94 0.00 33.69 2.15
2267 4795 7.223777 GCTACTCATGTGAAAAGAGAAGGTATC 59.776 40.741 0.94 0.00 33.69 2.24
2268 4796 7.044798 GCTACTCATGTGAAAAGAGAAGGTAT 58.955 38.462 0.94 0.00 33.69 2.73
2269 4797 6.014584 TGCTACTCATGTGAAAAGAGAAGGTA 60.015 38.462 0.94 0.00 33.69 3.08
2270 4798 5.221722 TGCTACTCATGTGAAAAGAGAAGGT 60.222 40.000 0.94 0.00 33.69 3.50
2271 4799 5.121454 GTGCTACTCATGTGAAAAGAGAAGG 59.879 44.000 0.94 0.00 33.69 3.46
2272 4800 5.164012 CGTGCTACTCATGTGAAAAGAGAAG 60.164 44.000 0.94 0.00 33.69 2.85
2273 4801 4.686091 CGTGCTACTCATGTGAAAAGAGAA 59.314 41.667 0.94 0.00 33.69 2.87
2274 4802 4.237724 CGTGCTACTCATGTGAAAAGAGA 58.762 43.478 0.94 0.00 33.69 3.10
2275 4803 3.369147 CCGTGCTACTCATGTGAAAAGAG 59.631 47.826 0.94 0.00 35.56 2.85
2276 4804 3.325870 CCGTGCTACTCATGTGAAAAGA 58.674 45.455 0.94 0.00 0.00 2.52
2277 4805 2.159653 GCCGTGCTACTCATGTGAAAAG 60.160 50.000 0.94 0.00 0.00 2.27
2278 4806 1.804151 GCCGTGCTACTCATGTGAAAA 59.196 47.619 0.94 0.00 0.00 2.29
2279 4807 1.001974 AGCCGTGCTACTCATGTGAAA 59.998 47.619 0.94 0.00 36.99 2.69
2280 4808 0.608130 AGCCGTGCTACTCATGTGAA 59.392 50.000 0.94 0.00 36.99 3.18
2281 4809 0.108662 CAGCCGTGCTACTCATGTGA 60.109 55.000 0.94 0.00 36.40 3.58
2282 4810 2.377004 CAGCCGTGCTACTCATGTG 58.623 57.895 0.00 0.00 36.40 3.21
2283 4811 4.919653 CAGCCGTGCTACTCATGT 57.080 55.556 0.00 0.00 36.40 3.21
2293 4821 1.898938 CATGTAAACATGCAGCCGTG 58.101 50.000 9.98 0.00 45.92 4.94
2302 4830 5.639506 CCTCGACAAAGACTCATGTAAACAT 59.360 40.000 0.00 0.00 36.96 2.71
2303 4831 4.988540 CCTCGACAAAGACTCATGTAAACA 59.011 41.667 0.00 0.00 0.00 2.83
2304 4832 4.389077 CCCTCGACAAAGACTCATGTAAAC 59.611 45.833 0.00 0.00 0.00 2.01
2305 4833 4.282449 TCCCTCGACAAAGACTCATGTAAA 59.718 41.667 0.00 0.00 0.00 2.01
2306 4834 3.830178 TCCCTCGACAAAGACTCATGTAA 59.170 43.478 0.00 0.00 0.00 2.41
2307 4835 3.427573 TCCCTCGACAAAGACTCATGTA 58.572 45.455 0.00 0.00 0.00 2.29
2308 4836 2.232452 CTCCCTCGACAAAGACTCATGT 59.768 50.000 0.00 0.00 0.00 3.21
2309 4837 2.886081 CTCCCTCGACAAAGACTCATG 58.114 52.381 0.00 0.00 0.00 3.07
2310 4838 1.205893 GCTCCCTCGACAAAGACTCAT 59.794 52.381 0.00 0.00 0.00 2.90
2311 4839 0.603569 GCTCCCTCGACAAAGACTCA 59.396 55.000 0.00 0.00 0.00 3.41
2312 4840 0.603569 TGCTCCCTCGACAAAGACTC 59.396 55.000 0.00 0.00 0.00 3.36
2313 4841 1.066573 CATGCTCCCTCGACAAAGACT 60.067 52.381 0.00 0.00 0.00 3.24
2314 4842 1.338200 ACATGCTCCCTCGACAAAGAC 60.338 52.381 0.00 0.00 0.00 3.01
2315 4843 0.976641 ACATGCTCCCTCGACAAAGA 59.023 50.000 0.00 0.00 0.00 2.52
2316 4844 1.813513 AACATGCTCCCTCGACAAAG 58.186 50.000 0.00 0.00 0.00 2.77
2317 4845 2.270352 AAACATGCTCCCTCGACAAA 57.730 45.000 0.00 0.00 0.00 2.83
2318 4846 2.270352 AAAACATGCTCCCTCGACAA 57.730 45.000 0.00 0.00 0.00 3.18
2319 4847 2.270352 AAAAACATGCTCCCTCGACA 57.730 45.000 0.00 0.00 0.00 4.35
2389 4917 5.385198 ACCCACACTTGATGTTTTATCACT 58.615 37.500 0.00 0.00 40.64 3.41
2743 5274 3.947132 CTGCAGCTCACTCCACCCG 62.947 68.421 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.