Multiple sequence alignment - TraesCS3A01G229600

Loading Multiple Alignment...

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 TraesCS3A01G229600 chr3A 100.000 3062 0 0 1 3062 429489607 429492668 0.000000e+00 5655.0
1 TraesCS3A01G229600 chr3A 97.598 1041 15 2 1 1031 234975726 234976766 0.000000e+00 1775.0
2 TraesCS3A01G229600 chr3A 93.130 1048 49 9 1 1029 715421502 715420459 0.000000e+00 1515.0
3 TraesCS3A01G229600 chr3A 95.139 144 7 0 2484 2627 706247345 706247488 8.540000e-56 228.0
4 TraesCS3A01G229600 chr3A 89.381 113 12 0 2105 2217 449437632 449437520 3.180000e-30 143.0
5 TraesCS3A01G229600 chr4B 97.601 1042 14 3 1 1031 187624687 187625728 0.000000e+00 1775.0
6 TraesCS3A01G229600 chr4B 83.457 810 68 27 2288 3062 73269950 73270728 0.000000e+00 693.0
7 TraesCS3A01G229600 chr4B 84.941 425 35 16 2288 2696 559226485 559226074 1.320000e-108 403.0
8 TraesCS3A01G229600 chr4B 92.063 189 10 2 2287 2475 651773301 651773484 8.420000e-66 261.0
9 TraesCS3A01G229600 chr3B 94.221 1021 47 8 1069 2089 416565546 416566554 0.000000e+00 1548.0
10 TraesCS3A01G229600 chr3B 93.333 1020 49 6 31 1031 177923382 177922363 0.000000e+00 1489.0
11 TraesCS3A01G229600 chr3B 87.661 389 42 5 2679 3062 411912457 411912844 6.020000e-122 448.0
12 TraesCS3A01G229600 chr3B 90.674 193 13 1 2285 2477 411911393 411911580 5.070000e-63 252.0
13 TraesCS3A01G229600 chr2B 93.530 1051 46 9 1 1031 625443190 625442142 0.000000e+00 1544.0
14 TraesCS3A01G229600 chr2B 91.912 1051 62 8 1 1031 109189881 109188834 0.000000e+00 1448.0
15 TraesCS3A01G229600 chr3D 93.091 1071 43 18 1031 2084 305318230 305317174 0.000000e+00 1539.0
16 TraesCS3A01G229600 chr3D 91.342 1051 63 9 1 1031 610399049 610398007 0.000000e+00 1411.0
17 TraesCS3A01G229600 chr3D 93.750 144 9 0 2484 2627 520325109 520325252 1.850000e-52 217.0
18 TraesCS3A01G229600 chr3D 90.265 113 11 0 2105 2217 238999532 238999420 6.840000e-32 148.0
19 TraesCS3A01G229600 chr4D 91.817 1051 64 7 1 1031 450711548 450712596 0.000000e+00 1445.0
20 TraesCS3A01G229600 chr4D 85.600 625 43 13 2484 3062 461469236 461468613 2.020000e-171 612.0
21 TraesCS3A01G229600 chr4D 91.150 113 10 0 2105 2217 35066963 35067075 1.470000e-33 154.0
22 TraesCS3A01G229600 chr4D 86.719 128 12 5 2093 2219 139465180 139465303 1.480000e-28 137.0
23 TraesCS3A01G229600 chr2A 91.817 1051 62 7 1 1031 682031066 682030020 0.000000e+00 1443.0
24 TraesCS3A01G229600 chr2A 82.324 826 80 26 2288 3062 122049534 122048724 0.000000e+00 656.0
25 TraesCS3A01G229600 chr2A 93.407 182 7 1 2283 2464 2867064 2866888 6.510000e-67 265.0
26 TraesCS3A01G229600 chr2A 86.508 126 14 3 2093 2217 662973514 662973637 5.330000e-28 135.0
27 TraesCS3A01G229600 chr6B 89.320 1030 88 9 4 1023 436729384 436730401 0.000000e+00 1273.0
28 TraesCS3A01G229600 chr6B 87.918 389 41 5 2679 3062 265592943 265592556 1.290000e-123 453.0
29 TraesCS3A01G229600 chr6D 93.054 835 46 4 1 824 103041124 103040291 0.000000e+00 1210.0
30 TraesCS3A01G229600 chr6D 89.381 113 12 0 2105 2217 394588715 394588603 3.180000e-30 143.0
31 TraesCS3A01G229600 chr2D 91.856 835 58 2 1 825 540626181 540625347 0.000000e+00 1157.0
32 TraesCS3A01G229600 chr2D 91.304 46 4 0 2221 2266 27802623 27802578 2.550000e-06 63.9
33 TraesCS3A01G229600 chr1B 90.683 644 44 4 1 634 571826491 571825854 0.000000e+00 843.0
34 TraesCS3A01G229600 chr1B 89.381 113 12 0 2105 2217 684197839 684197727 3.180000e-30 143.0
35 TraesCS3A01G229600 chr7B 84.408 853 53 32 2285 3062 714068659 714069506 0.000000e+00 765.0
36 TraesCS3A01G229600 chr7B 87.719 399 42 6 2669 3062 292368943 292368547 2.780000e-125 459.0
37 TraesCS3A01G229600 chr7B 93.264 193 8 1 2291 2483 292374277 292374090 2.320000e-71 279.0
38 TraesCS3A01G229600 chr6A 85.946 740 68 16 2358 3062 534946529 534947267 0.000000e+00 758.0
39 TraesCS3A01G229600 chr1D 83.824 748 56 29 2364 3062 467027286 467026555 0.000000e+00 651.0
40 TraesCS3A01G229600 chr7D 85.315 572 44 11 2528 3059 369856934 369857505 3.450000e-154 555.0
41 TraesCS3A01G229600 chr5A 89.904 416 28 7 2658 3062 272869422 272869834 9.730000e-145 523.0
42 TraesCS3A01G229600 chr5A 91.111 360 30 2 2703 3062 664546976 664546619 1.280000e-133 486.0
43 TraesCS3A01G229600 chr5A 92.632 190 9 2 2288 2477 272868066 272868250 5.030000e-68 268.0
44 TraesCS3A01G229600 chr5A 92.361 144 11 0 2484 2627 272868813 272868956 4.000000e-49 206.0
45 TraesCS3A01G229600 chr7A 90.463 367 32 3 2698 3062 670550311 670549946 5.940000e-132 481.0
46 TraesCS3A01G229600 chr5B 86.632 389 46 5 2679 3062 84800198 84799811 2.820000e-115 425.0
47 TraesCS3A01G229600 chr5B 89.950 199 15 2 2285 2483 84800904 84800711 5.070000e-63 252.0
48 TraesCS3A01G229600 chr5B 89.381 113 12 0 2105 2217 254154527 254154639 3.180000e-30 143.0
49 TraesCS3A01G229600 chr5D 94.301 193 6 1 2291 2483 372113632 372113445 1.070000e-74 291.0
50 TraesCS3A01G229600 chr5D 86.508 126 12 5 2093 2217 273374394 273374273 1.920000e-27 134.0
51 TraesCS3A01G229600 chr1A 92.632 190 9 1 2288 2477 30807062 30807246 5.030000e-68 268.0
52 TraesCS3A01G229600 chr1A 95.139 144 7 0 2484 2627 360476155 360476298 8.540000e-56 228.0
53 TraesCS3A01G229600 chr1A 93.750 144 9 0 2484 2627 30807810 30807953 1.850000e-52 217.0


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 TraesCS3A01G229600 chr3A 429489607 429492668 3061 False 5655.000000 5655 100.000000 1 3062 1 chr3A.!!$F2 3061
1 TraesCS3A01G229600 chr3A 234975726 234976766 1040 False 1775.000000 1775 97.598000 1 1031 1 chr3A.!!$F1 1030
2 TraesCS3A01G229600 chr3A 715420459 715421502 1043 True 1515.000000 1515 93.130000 1 1029 1 chr3A.!!$R2 1028
3 TraesCS3A01G229600 chr4B 187624687 187625728 1041 False 1775.000000 1775 97.601000 1 1031 1 chr4B.!!$F2 1030
4 TraesCS3A01G229600 chr4B 73269950 73270728 778 False 693.000000 693 83.457000 2288 3062 1 chr4B.!!$F1 774
5 TraesCS3A01G229600 chr3B 416565546 416566554 1008 False 1548.000000 1548 94.221000 1069 2089 1 chr3B.!!$F1 1020
6 TraesCS3A01G229600 chr3B 177922363 177923382 1019 True 1489.000000 1489 93.333000 31 1031 1 chr3B.!!$R1 1000
7 TraesCS3A01G229600 chr3B 411911393 411912844 1451 False 350.000000 448 89.167500 2285 3062 2 chr3B.!!$F2 777
8 TraesCS3A01G229600 chr2B 625442142 625443190 1048 True 1544.000000 1544 93.530000 1 1031 1 chr2B.!!$R2 1030
9 TraesCS3A01G229600 chr2B 109188834 109189881 1047 True 1448.000000 1448 91.912000 1 1031 1 chr2B.!!$R1 1030
10 TraesCS3A01G229600 chr3D 305317174 305318230 1056 True 1539.000000 1539 93.091000 1031 2084 1 chr3D.!!$R2 1053
11 TraesCS3A01G229600 chr3D 610398007 610399049 1042 True 1411.000000 1411 91.342000 1 1031 1 chr3D.!!$R3 1030
12 TraesCS3A01G229600 chr4D 450711548 450712596 1048 False 1445.000000 1445 91.817000 1 1031 1 chr4D.!!$F3 1030
13 TraesCS3A01G229600 chr4D 461468613 461469236 623 True 612.000000 612 85.600000 2484 3062 1 chr4D.!!$R1 578
14 TraesCS3A01G229600 chr2A 682030020 682031066 1046 True 1443.000000 1443 91.817000 1 1031 1 chr2A.!!$R3 1030
15 TraesCS3A01G229600 chr2A 122048724 122049534 810 True 656.000000 656 82.324000 2288 3062 1 chr2A.!!$R2 774
16 TraesCS3A01G229600 chr6B 436729384 436730401 1017 False 1273.000000 1273 89.320000 4 1023 1 chr6B.!!$F1 1019
17 TraesCS3A01G229600 chr6D 103040291 103041124 833 True 1210.000000 1210 93.054000 1 824 1 chr6D.!!$R1 823
18 TraesCS3A01G229600 chr2D 540625347 540626181 834 True 1157.000000 1157 91.856000 1 825 1 chr2D.!!$R2 824
19 TraesCS3A01G229600 chr1B 571825854 571826491 637 True 843.000000 843 90.683000 1 634 1 chr1B.!!$R1 633
20 TraesCS3A01G229600 chr7B 714068659 714069506 847 False 765.000000 765 84.408000 2285 3062 1 chr7B.!!$F1 777
21 TraesCS3A01G229600 chr6A 534946529 534947267 738 False 758.000000 758 85.946000 2358 3062 1 chr6A.!!$F1 704
22 TraesCS3A01G229600 chr1D 467026555 467027286 731 True 651.000000 651 83.824000 2364 3062 1 chr1D.!!$R1 698
23 TraesCS3A01G229600 chr7D 369856934 369857505 571 False 555.000000 555 85.315000 2528 3059 1 chr7D.!!$F1 531
24 TraesCS3A01G229600 chr5A 272868066 272869834 1768 False 332.333333 523 91.632333 2288 3062 3 chr5A.!!$F1 774
25 TraesCS3A01G229600 chr5B 84799811 84800904 1093 True 338.500000 425 88.291000 2285 3062 2 chr5B.!!$R1 777
26 TraesCS3A01G229600 chr1A 30807062 30807953 891 False 242.500000 268 93.191000 2288 2627 2 chr1A.!!$F2 339

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
665 678 3.181468 CCTCGGTTTCAGGGTTAGGTATC 60.181 52.174 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2260 2300 0.039326 ACGGCCTACCACAGTACTCT 59.961 55.0 0.0 0.0 34.57 3.24 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
148 151 5.875224 TGAGAGTCCATGTAAAATTGTCCA 58.125 37.500 0.00 0.00 0.00 4.02
665 678 3.181468 CCTCGGTTTCAGGGTTAGGTATC 60.181 52.174 0.00 0.00 0.00 2.24
1039 1062 6.239487 GCCAACATGGTAGGTGTGTAGATATA 60.239 42.308 0.00 0.00 40.46 0.86
1133 1161 3.839293 CTGTCGTTCAAACCAAAACCAA 58.161 40.909 0.00 0.00 0.00 3.67
1135 1163 2.924926 GTCGTTCAAACCAAAACCAACC 59.075 45.455 0.00 0.00 0.00 3.77
1136 1164 2.561419 TCGTTCAAACCAAAACCAACCA 59.439 40.909 0.00 0.00 0.00 3.67
1137 1165 3.195825 TCGTTCAAACCAAAACCAACCAT 59.804 39.130 0.00 0.00 0.00 3.55
1138 1166 3.308323 CGTTCAAACCAAAACCAACCATG 59.692 43.478 0.00 0.00 0.00 3.66
1139 1167 4.508662 GTTCAAACCAAAACCAACCATGA 58.491 39.130 0.00 0.00 0.00 3.07
1140 1168 4.826274 TCAAACCAAAACCAACCATGAA 57.174 36.364 0.00 0.00 0.00 2.57
1195 1223 6.152831 ACAGACTATAATATCATGCTGGCGTA 59.847 38.462 0.00 0.00 0.00 4.42
1202 1230 0.451383 TCATGCTGGCGTAACATTGC 59.549 50.000 0.00 0.00 0.00 3.56
1224 1262 7.719778 TGCACTACTGAATCATAGCTTAATG 57.280 36.000 0.00 0.00 0.00 1.90
1263 1301 1.705256 TAACGACATTCGCTGACCAC 58.295 50.000 0.00 0.00 45.12 4.16
1276 1314 3.436496 GCTGACCACGTACTACTTCATC 58.564 50.000 0.00 0.00 0.00 2.92
1537 1575 2.992689 TCGTCAAGGCGCCCTACA 60.993 61.111 26.15 0.85 31.13 2.74
1826 1864 1.712977 GAGATGTACGACGTCGGCCT 61.713 60.000 37.89 25.62 44.95 5.19
1857 1895 2.202676 CGGCTGTCCTTCTCGCTC 60.203 66.667 0.00 0.00 0.00 5.03
1917 1955 4.394712 GACGACCCACAGCCCCAG 62.395 72.222 0.00 0.00 0.00 4.45
2084 2124 1.092921 TCGACAAGCACCGCTGTTTT 61.093 50.000 0.00 0.00 39.62 2.43
2085 2125 0.929824 CGACAAGCACCGCTGTTTTG 60.930 55.000 0.00 2.07 39.62 2.44
2087 2127 0.814457 ACAAGCACCGCTGTTTTGAA 59.186 45.000 8.61 0.00 39.62 2.69
2088 2128 1.202290 ACAAGCACCGCTGTTTTGAAG 60.202 47.619 8.61 0.00 39.62 3.02
2089 2129 0.249031 AAGCACCGCTGTTTTGAAGC 60.249 50.000 0.00 0.00 39.62 3.86
2110 2150 7.948278 AAGCGTAGATTCACTTATTATGGAC 57.052 36.000 0.00 0.00 0.00 4.02
2111 2151 7.291411 AGCGTAGATTCACTTATTATGGACT 57.709 36.000 0.00 0.00 0.00 3.85
2112 2152 8.405418 AGCGTAGATTCACTTATTATGGACTA 57.595 34.615 0.00 0.00 0.00 2.59
2113 2153 8.298140 AGCGTAGATTCACTTATTATGGACTAC 58.702 37.037 0.00 0.00 0.00 2.73
2114 2154 8.080417 GCGTAGATTCACTTATTATGGACTACA 58.920 37.037 0.00 0.00 0.00 2.74
2122 2162 8.577296 TCACTTATTATGGACTACATACAGAGC 58.423 37.037 0.00 0.00 41.61 4.09
2123 2163 8.360390 CACTTATTATGGACTACATACAGAGCA 58.640 37.037 0.00 0.00 41.61 4.26
2124 2164 8.924303 ACTTATTATGGACTACATACAGAGCAA 58.076 33.333 0.00 0.00 41.61 3.91
2125 2165 9.764363 CTTATTATGGACTACATACAGAGCAAA 57.236 33.333 0.00 0.00 41.61 3.68
2128 2168 6.932356 ATGGACTACATACAGAGCAAAATG 57.068 37.500 0.00 0.00 38.26 2.32
2129 2169 6.048732 TGGACTACATACAGAGCAAAATGA 57.951 37.500 0.00 0.00 0.00 2.57
2130 2170 6.108687 TGGACTACATACAGAGCAAAATGAG 58.891 40.000 0.00 0.00 0.00 2.90
2131 2171 6.109359 GGACTACATACAGAGCAAAATGAGT 58.891 40.000 0.00 0.00 0.00 3.41
2132 2172 6.036517 GGACTACATACAGAGCAAAATGAGTG 59.963 42.308 0.00 0.00 0.00 3.51
2133 2173 6.701340 ACTACATACAGAGCAAAATGAGTGA 58.299 36.000 0.00 0.00 0.00 3.41
2134 2174 7.161404 ACTACATACAGAGCAAAATGAGTGAA 58.839 34.615 0.00 0.00 0.00 3.18
2135 2175 7.826252 ACTACATACAGAGCAAAATGAGTGAAT 59.174 33.333 0.00 0.00 0.00 2.57
2136 2176 7.458409 ACATACAGAGCAAAATGAGTGAATT 57.542 32.000 0.00 0.00 0.00 2.17
2137 2177 7.889469 ACATACAGAGCAAAATGAGTGAATTT 58.111 30.769 0.00 0.00 0.00 1.82
2138 2178 9.013229 ACATACAGAGCAAAATGAGTGAATTTA 57.987 29.630 0.00 0.00 0.00 1.40
2142 2182 9.236006 ACAGAGCAAAATGAGTGAATTTATACT 57.764 29.630 0.00 0.00 0.00 2.12
2143 2183 9.713740 CAGAGCAAAATGAGTGAATTTATACTC 57.286 33.333 10.00 10.00 42.77 2.59
2144 2184 9.678260 AGAGCAAAATGAGTGAATTTATACTCT 57.322 29.630 15.15 0.00 42.86 3.24
2177 2217 3.396560 ACATGCATCTGTATGTGATCCG 58.603 45.455 12.26 0.00 46.87 4.18
2178 2218 3.181462 ACATGCATCTGTATGTGATCCGT 60.181 43.478 12.26 0.00 46.87 4.69
2179 2219 4.039124 ACATGCATCTGTATGTGATCCGTA 59.961 41.667 12.26 0.00 46.87 4.02
2180 2220 3.977427 TGCATCTGTATGTGATCCGTAC 58.023 45.455 0.00 0.00 35.38 3.67
2181 2221 3.636764 TGCATCTGTATGTGATCCGTACT 59.363 43.478 12.12 0.00 36.64 2.73
2182 2222 3.983988 GCATCTGTATGTGATCCGTACTG 59.016 47.826 12.12 11.60 36.64 2.74
2183 2223 4.261614 GCATCTGTATGTGATCCGTACTGA 60.262 45.833 17.32 17.32 43.43 3.41
2184 2224 5.736207 GCATCTGTATGTGATCCGTACTGAA 60.736 44.000 18.18 9.09 42.90 3.02
2185 2225 5.907866 TCTGTATGTGATCCGTACTGAAA 57.092 39.130 14.80 2.07 39.28 2.69
2186 2226 6.465439 TCTGTATGTGATCCGTACTGAAAT 57.535 37.500 14.80 0.00 39.28 2.17
2187 2227 6.504398 TCTGTATGTGATCCGTACTGAAATC 58.496 40.000 14.80 0.00 39.28 2.17
2188 2228 6.321435 TCTGTATGTGATCCGTACTGAAATCT 59.679 38.462 14.80 0.00 39.28 2.40
2189 2229 6.873997 TGTATGTGATCCGTACTGAAATCTT 58.126 36.000 12.12 0.00 36.64 2.40
2190 2230 7.327975 TGTATGTGATCCGTACTGAAATCTTT 58.672 34.615 12.12 0.00 36.64 2.52
2191 2231 8.471609 TGTATGTGATCCGTACTGAAATCTTTA 58.528 33.333 12.12 0.00 36.64 1.85
2192 2232 7.772332 ATGTGATCCGTACTGAAATCTTTAC 57.228 36.000 0.00 0.00 0.00 2.01
2193 2233 6.693466 TGTGATCCGTACTGAAATCTTTACA 58.307 36.000 0.00 0.00 0.00 2.41
2194 2234 7.156000 TGTGATCCGTACTGAAATCTTTACAA 58.844 34.615 0.00 0.00 0.00 2.41
2195 2235 7.658167 TGTGATCCGTACTGAAATCTTTACAAA 59.342 33.333 0.00 0.00 0.00 2.83
2196 2236 8.169268 GTGATCCGTACTGAAATCTTTACAAAG 58.831 37.037 0.00 0.00 37.36 2.77
2198 2238 7.647907 TCCGTACTGAAATCTTTACAAAGAC 57.352 36.000 6.56 0.00 46.80 3.01
2199 2239 7.439381 TCCGTACTGAAATCTTTACAAAGACT 58.561 34.615 6.56 0.00 46.80 3.24
2200 2240 7.929785 TCCGTACTGAAATCTTTACAAAGACTT 59.070 33.333 6.56 2.45 46.80 3.01
2201 2241 9.199982 CCGTACTGAAATCTTTACAAAGACTTA 57.800 33.333 6.56 0.00 46.80 2.24
2227 2267 6.662865 TTTAGAAATGGAGTTTGCATTGGA 57.337 33.333 0.00 0.00 37.43 3.53
2228 2268 6.662865 TTAGAAATGGAGTTTGCATTGGAA 57.337 33.333 0.00 0.00 37.43 3.53
2229 2269 5.750352 AGAAATGGAGTTTGCATTGGAAT 57.250 34.783 0.00 0.00 37.43 3.01
2230 2270 5.727434 AGAAATGGAGTTTGCATTGGAATC 58.273 37.500 0.00 0.00 37.43 2.52
2231 2271 5.482878 AGAAATGGAGTTTGCATTGGAATCT 59.517 36.000 1.59 1.59 37.43 2.40
2232 2272 4.996788 ATGGAGTTTGCATTGGAATCTC 57.003 40.909 16.41 16.41 0.00 2.75
2233 2273 3.091545 TGGAGTTTGCATTGGAATCTCC 58.908 45.455 28.02 28.02 39.97 3.71
2234 2274 3.091545 GGAGTTTGCATTGGAATCTCCA 58.908 45.455 28.99 0.18 46.61 3.86
2257 2297 9.893634 TCCAAAAAGACATATATTTAGGAACGA 57.106 29.630 0.00 0.00 0.00 3.85
2264 2304 9.357161 AGACATATATTTAGGAACGAAGAGAGT 57.643 33.333 0.00 0.00 0.00 3.24
2269 2309 6.837471 ATTTAGGAACGAAGAGAGTACTGT 57.163 37.500 0.00 0.00 0.00 3.55
2270 2310 5.624344 TTAGGAACGAAGAGAGTACTGTG 57.376 43.478 0.00 0.00 0.00 3.66
2271 2311 2.820787 AGGAACGAAGAGAGTACTGTGG 59.179 50.000 0.00 0.00 0.00 4.17
2272 2312 2.557490 GGAACGAAGAGAGTACTGTGGT 59.443 50.000 0.00 0.00 0.00 4.16
2273 2313 3.755378 GGAACGAAGAGAGTACTGTGGTA 59.245 47.826 0.00 0.00 0.00 3.25
2274 2314 4.142643 GGAACGAAGAGAGTACTGTGGTAG 60.143 50.000 0.00 0.00 0.00 3.18
2275 2315 3.345414 ACGAAGAGAGTACTGTGGTAGG 58.655 50.000 0.00 0.00 0.00 3.18
2276 2316 2.097791 CGAAGAGAGTACTGTGGTAGGC 59.902 54.545 0.00 0.00 0.00 3.93
2277 2317 2.146920 AGAGAGTACTGTGGTAGGCC 57.853 55.000 0.00 0.00 0.00 5.19
2278 2318 0.739561 GAGAGTACTGTGGTAGGCCG 59.260 60.000 0.00 0.00 37.67 6.13
2279 2319 0.039326 AGAGTACTGTGGTAGGCCGT 59.961 55.000 0.00 0.00 37.67 5.68
2280 2320 1.283029 AGAGTACTGTGGTAGGCCGTA 59.717 52.381 0.00 0.00 37.67 4.02
2281 2321 1.403323 GAGTACTGTGGTAGGCCGTAC 59.597 57.143 0.00 1.56 37.67 3.67
2282 2322 1.176527 GTACTGTGGTAGGCCGTACA 58.823 55.000 12.53 8.78 37.67 2.90
2283 2323 1.753073 GTACTGTGGTAGGCCGTACAT 59.247 52.381 12.53 0.00 37.67 2.29
2444 2484 4.986034 TGTGTTGAAATGTCTGTACTACCG 59.014 41.667 0.00 0.00 0.00 4.02
2500 3098 6.362551 CAGATTGTAGCATTATTCAAGCATGC 59.637 38.462 10.51 10.51 43.15 4.06
2564 3164 3.879912 GTCGAACTTTGAGGGACGA 57.120 52.632 0.00 0.00 0.00 4.20
2623 3226 3.647771 GGAGGGAAGTTGGCCGGT 61.648 66.667 1.90 0.00 0.00 5.28
2805 4454 4.025401 GGGTGCGTCCGCTTGTTG 62.025 66.667 13.31 0.00 42.51 3.33
2816 4466 3.074281 CTTGTTGTCGGGGCCCTA 58.926 61.111 24.38 6.92 0.00 3.53
2901 4551 6.683715 ACTTCAAAACGTTTTCTTTTCTGGA 58.316 32.000 22.90 11.92 0.00 3.86
3009 4659 7.013274 TCAGATTTTGGAAGTTCAATCGAGTTT 59.987 33.333 5.01 0.00 31.95 2.66
3011 4661 8.846211 AGATTTTGGAAGTTCAATCGAGTTTTA 58.154 29.630 5.01 0.00 31.95 1.52
3014 4664 9.810545 TTTTGGAAGTTCAATCGAGTTTTATTT 57.189 25.926 5.01 0.00 0.00 1.40
3027 4677 7.213678 TCGAGTTTTATTTGCTTGGGATTTTT 58.786 30.769 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
665 678 2.809446 TCTCCGAAGTGTAATGCATCG 58.191 47.619 0.00 0.00 31.47 3.84
795 808 8.292444 TCTTTTCTTTCCTTTTCAGATTCACA 57.708 30.769 0.00 0.00 0.00 3.58
1079 1107 0.179119 GGATAACCGCGTGTACTGCT 60.179 55.000 4.92 0.00 0.00 4.24
1133 1161 0.815213 CGGTGCGATGGATTCATGGT 60.815 55.000 0.00 0.00 32.98 3.55
1135 1163 1.509644 CCCGGTGCGATGGATTCATG 61.510 60.000 0.00 0.00 32.98 3.07
1136 1164 1.227943 CCCGGTGCGATGGATTCAT 60.228 57.895 0.00 0.00 36.09 2.57
1137 1165 2.189257 CCCGGTGCGATGGATTCA 59.811 61.111 0.00 0.00 0.00 2.57
1138 1166 1.887707 GACCCGGTGCGATGGATTC 60.888 63.158 0.00 0.00 0.00 2.52
1139 1167 2.189521 GACCCGGTGCGATGGATT 59.810 61.111 0.00 0.00 0.00 3.01
1140 1168 2.764128 AGACCCGGTGCGATGGAT 60.764 61.111 0.00 0.00 0.00 3.41
1175 1203 7.776933 ATGTTACGCCAGCATGATATTATAG 57.223 36.000 0.00 0.00 39.69 1.31
1195 1223 6.118170 AGCTATGATTCAGTAGTGCAATGTT 58.882 36.000 0.00 0.00 0.00 2.71
1202 1230 8.976471 CAGTCATTAAGCTATGATTCAGTAGTG 58.024 37.037 2.56 0.00 36.94 2.74
1224 1262 0.895530 TCGATGGGTTGGAGACAGTC 59.104 55.000 0.00 0.00 44.54 3.51
1263 1301 6.330278 TGGAATCAACAGATGAAGTAGTACG 58.670 40.000 0.00 0.00 42.54 3.67
1276 1314 3.152341 ACTTCTTGCCTGGAATCAACAG 58.848 45.455 0.00 0.00 35.74 3.16
1676 1714 3.080121 CCTCCTCCTTGCTCGCCT 61.080 66.667 0.00 0.00 0.00 5.52
1899 1937 4.954118 TGGGGCTGTGGGTCGTCT 62.954 66.667 0.00 0.00 0.00 4.18
1909 1947 4.201122 GCCATCCTCCTGGGGCTG 62.201 72.222 3.93 1.75 43.09 4.85
1917 1955 3.595819 GCAACAGTGCCATCCTCC 58.404 61.111 0.00 0.00 45.68 4.30
1938 1976 2.030562 AAACTCTGTCACCGCCCG 59.969 61.111 0.00 0.00 0.00 6.13
2084 2124 7.652105 GTCCATAATAAGTGAATCTACGCTTCA 59.348 37.037 0.00 0.00 40.39 3.02
2085 2125 7.868415 AGTCCATAATAAGTGAATCTACGCTTC 59.132 37.037 0.00 0.00 40.39 3.86
2087 2127 7.291411 AGTCCATAATAAGTGAATCTACGCT 57.709 36.000 0.00 0.00 0.00 5.07
2088 2128 8.080417 TGTAGTCCATAATAAGTGAATCTACGC 58.920 37.037 0.00 0.00 0.00 4.42
2096 2136 8.577296 GCTCTGTATGTAGTCCATAATAAGTGA 58.423 37.037 0.00 0.00 37.77 3.41
2097 2137 8.360390 TGCTCTGTATGTAGTCCATAATAAGTG 58.640 37.037 0.00 0.00 37.77 3.16
2098 2138 8.478775 TGCTCTGTATGTAGTCCATAATAAGT 57.521 34.615 0.00 0.00 37.77 2.24
2099 2139 9.764363 TTTGCTCTGTATGTAGTCCATAATAAG 57.236 33.333 0.00 0.00 37.77 1.73
2102 2142 9.060347 CATTTTGCTCTGTATGTAGTCCATAAT 57.940 33.333 0.00 0.00 37.77 1.28
2103 2143 8.264347 TCATTTTGCTCTGTATGTAGTCCATAA 58.736 33.333 0.00 0.00 37.77 1.90
2104 2144 7.791029 TCATTTTGCTCTGTATGTAGTCCATA 58.209 34.615 0.00 0.00 34.86 2.74
2105 2145 6.653020 TCATTTTGCTCTGTATGTAGTCCAT 58.347 36.000 0.00 0.00 37.58 3.41
2106 2146 6.048732 TCATTTTGCTCTGTATGTAGTCCA 57.951 37.500 0.00 0.00 0.00 4.02
2107 2147 6.036517 CACTCATTTTGCTCTGTATGTAGTCC 59.963 42.308 0.00 0.00 0.00 3.85
2108 2148 6.813649 TCACTCATTTTGCTCTGTATGTAGTC 59.186 38.462 0.00 0.00 0.00 2.59
2109 2149 6.701340 TCACTCATTTTGCTCTGTATGTAGT 58.299 36.000 0.00 0.00 0.00 2.73
2110 2150 7.601073 TTCACTCATTTTGCTCTGTATGTAG 57.399 36.000 0.00 0.00 0.00 2.74
2111 2151 8.565896 AATTCACTCATTTTGCTCTGTATGTA 57.434 30.769 0.00 0.00 0.00 2.29
2112 2152 7.458409 AATTCACTCATTTTGCTCTGTATGT 57.542 32.000 0.00 0.00 0.00 2.29
2116 2156 9.236006 AGTATAAATTCACTCATTTTGCTCTGT 57.764 29.630 0.00 0.00 0.00 3.41
2117 2157 9.713740 GAGTATAAATTCACTCATTTTGCTCTG 57.286 33.333 8.98 0.00 40.74 3.35
2118 2158 9.678260 AGAGTATAAATTCACTCATTTTGCTCT 57.322 29.630 13.99 0.00 42.99 4.09
2151 2191 6.313164 GGATCACATACAGATGCATGTAGATG 59.687 42.308 2.46 9.65 38.96 2.90
2152 2192 6.404708 GGATCACATACAGATGCATGTAGAT 58.595 40.000 2.46 2.24 38.96 1.98
2153 2193 5.565439 CGGATCACATACAGATGCATGTAGA 60.565 44.000 2.46 0.00 38.96 2.59
2154 2194 4.624452 CGGATCACATACAGATGCATGTAG 59.376 45.833 2.46 0.00 38.96 2.74
2155 2195 4.039124 ACGGATCACATACAGATGCATGTA 59.961 41.667 2.46 2.64 39.85 2.29
2156 2196 3.181462 ACGGATCACATACAGATGCATGT 60.181 43.478 2.46 0.00 36.43 3.21
2157 2197 3.396560 ACGGATCACATACAGATGCATG 58.603 45.455 2.46 0.00 36.43 4.06
2158 2198 3.758755 ACGGATCACATACAGATGCAT 57.241 42.857 0.00 0.00 36.43 3.96
2159 2199 3.636764 AGTACGGATCACATACAGATGCA 59.363 43.478 0.00 0.00 36.43 3.96
2160 2200 3.983988 CAGTACGGATCACATACAGATGC 59.016 47.826 0.00 0.00 36.43 3.91
2161 2201 5.438761 TCAGTACGGATCACATACAGATG 57.561 43.478 0.00 0.00 39.16 2.90
2162 2202 6.465439 TTTCAGTACGGATCACATACAGAT 57.535 37.500 0.00 0.00 0.00 2.90
2163 2203 5.907866 TTTCAGTACGGATCACATACAGA 57.092 39.130 0.00 0.00 0.00 3.41
2164 2204 6.507900 AGATTTCAGTACGGATCACATACAG 58.492 40.000 0.00 0.00 0.00 2.74
2165 2205 6.465439 AGATTTCAGTACGGATCACATACA 57.535 37.500 0.00 0.00 0.00 2.29
2166 2206 7.772332 AAAGATTTCAGTACGGATCACATAC 57.228 36.000 0.00 0.00 0.00 2.39
2167 2207 8.471609 TGTAAAGATTTCAGTACGGATCACATA 58.528 33.333 0.00 0.00 0.00 2.29
2168 2208 7.327975 TGTAAAGATTTCAGTACGGATCACAT 58.672 34.615 0.00 0.00 0.00 3.21
2169 2209 6.693466 TGTAAAGATTTCAGTACGGATCACA 58.307 36.000 0.00 0.00 0.00 3.58
2170 2210 7.591006 TTGTAAAGATTTCAGTACGGATCAC 57.409 36.000 0.00 0.00 0.00 3.06
2171 2211 8.092068 TCTTTGTAAAGATTTCAGTACGGATCA 58.908 33.333 3.05 0.00 39.95 2.92
2172 2212 8.381387 GTCTTTGTAAAGATTTCAGTACGGATC 58.619 37.037 9.98 0.00 45.83 3.36
2173 2213 8.095169 AGTCTTTGTAAAGATTTCAGTACGGAT 58.905 33.333 9.98 0.00 45.83 4.18
2174 2214 7.439381 AGTCTTTGTAAAGATTTCAGTACGGA 58.561 34.615 9.98 0.00 45.83 4.69
2175 2215 7.653767 AGTCTTTGTAAAGATTTCAGTACGG 57.346 36.000 9.98 0.00 45.83 4.02
2201 2241 8.980596 TCCAATGCAAACTCCATTTCTAAATAT 58.019 29.630 0.00 0.00 30.90 1.28
2202 2242 8.359875 TCCAATGCAAACTCCATTTCTAAATA 57.640 30.769 0.00 0.00 30.90 1.40
2203 2243 7.243604 TCCAATGCAAACTCCATTTCTAAAT 57.756 32.000 0.00 0.00 30.90 1.40
2204 2244 6.662865 TCCAATGCAAACTCCATTTCTAAA 57.337 33.333 0.00 0.00 30.90 1.85
2205 2245 6.662865 TTCCAATGCAAACTCCATTTCTAA 57.337 33.333 0.00 0.00 30.90 2.10
2206 2246 6.664816 AGATTCCAATGCAAACTCCATTTCTA 59.335 34.615 0.00 0.00 30.90 2.10
2207 2247 5.482878 AGATTCCAATGCAAACTCCATTTCT 59.517 36.000 0.00 0.00 30.90 2.52
2208 2248 5.727434 AGATTCCAATGCAAACTCCATTTC 58.273 37.500 0.00 0.00 30.90 2.17
2209 2249 5.337813 GGAGATTCCAATGCAAACTCCATTT 60.338 40.000 8.17 0.00 41.12 2.32
2210 2250 4.161001 GGAGATTCCAATGCAAACTCCATT 59.839 41.667 8.17 0.00 41.12 3.16
2211 2251 3.703052 GGAGATTCCAATGCAAACTCCAT 59.297 43.478 8.17 0.00 41.12 3.41
2212 2252 3.091545 GGAGATTCCAATGCAAACTCCA 58.908 45.455 8.17 0.00 41.12 3.86
2213 2253 3.091545 TGGAGATTCCAATGCAAACTCC 58.908 45.455 6.30 6.30 45.00 3.85
2231 2271 9.893634 TCGTTCCTAAATATATGTCTTTTTGGA 57.106 29.630 0.00 0.00 34.13 3.53
2238 2278 9.357161 ACTCTCTTCGTTCCTAAATATATGTCT 57.643 33.333 0.00 0.00 0.00 3.41
2243 2283 9.624373 ACAGTACTCTCTTCGTTCCTAAATATA 57.376 33.333 0.00 0.00 0.00 0.86
2244 2284 8.407064 CACAGTACTCTCTTCGTTCCTAAATAT 58.593 37.037 0.00 0.00 0.00 1.28
2245 2285 7.148120 CCACAGTACTCTCTTCGTTCCTAAATA 60.148 40.741 0.00 0.00 0.00 1.40
2246 2286 6.350277 CCACAGTACTCTCTTCGTTCCTAAAT 60.350 42.308 0.00 0.00 0.00 1.40
2247 2287 5.048224 CCACAGTACTCTCTTCGTTCCTAAA 60.048 44.000 0.00 0.00 0.00 1.85
2248 2288 4.458295 CCACAGTACTCTCTTCGTTCCTAA 59.542 45.833 0.00 0.00 0.00 2.69
2249 2289 4.008330 CCACAGTACTCTCTTCGTTCCTA 58.992 47.826 0.00 0.00 0.00 2.94
2250 2290 2.820787 CCACAGTACTCTCTTCGTTCCT 59.179 50.000 0.00 0.00 0.00 3.36
2251 2291 2.557490 ACCACAGTACTCTCTTCGTTCC 59.443 50.000 0.00 0.00 0.00 3.62
2252 2292 3.919223 ACCACAGTACTCTCTTCGTTC 57.081 47.619 0.00 0.00 0.00 3.95
2253 2293 3.757493 CCTACCACAGTACTCTCTTCGTT 59.243 47.826 0.00 0.00 0.00 3.85
2254 2294 3.345414 CCTACCACAGTACTCTCTTCGT 58.655 50.000 0.00 0.00 0.00 3.85
2255 2295 2.097791 GCCTACCACAGTACTCTCTTCG 59.902 54.545 0.00 0.00 0.00 3.79
2256 2296 2.427812 GGCCTACCACAGTACTCTCTTC 59.572 54.545 0.00 0.00 35.26 2.87
2257 2297 2.458620 GGCCTACCACAGTACTCTCTT 58.541 52.381 0.00 0.00 35.26 2.85
2258 2298 1.682394 CGGCCTACCACAGTACTCTCT 60.682 57.143 0.00 0.00 34.57 3.10
2259 2299 0.739561 CGGCCTACCACAGTACTCTC 59.260 60.000 0.00 0.00 34.57 3.20
2260 2300 0.039326 ACGGCCTACCACAGTACTCT 59.961 55.000 0.00 0.00 34.57 3.24
2261 2301 1.403323 GTACGGCCTACCACAGTACTC 59.597 57.143 0.00 0.00 35.93 2.59
2262 2302 1.272092 TGTACGGCCTACCACAGTACT 60.272 52.381 13.68 0.00 38.63 2.73
2263 2303 1.176527 TGTACGGCCTACCACAGTAC 58.823 55.000 0.00 4.48 38.40 2.73
2264 2304 2.148446 ATGTACGGCCTACCACAGTA 57.852 50.000 0.00 0.00 34.57 2.74
2265 2305 1.272807 AATGTACGGCCTACCACAGT 58.727 50.000 0.00 0.00 34.57 3.55
2266 2306 2.006888 CAAATGTACGGCCTACCACAG 58.993 52.381 0.00 0.00 34.57 3.66
2267 2307 1.339247 CCAAATGTACGGCCTACCACA 60.339 52.381 0.00 0.00 34.57 4.17
2268 2308 1.375551 CCAAATGTACGGCCTACCAC 58.624 55.000 0.00 0.00 34.57 4.16
2269 2309 0.253610 CCCAAATGTACGGCCTACCA 59.746 55.000 0.00 0.00 34.57 3.25
2270 2310 0.464916 CCCCAAATGTACGGCCTACC 60.465 60.000 0.00 0.00 0.00 3.18
2271 2311 1.099295 GCCCCAAATGTACGGCCTAC 61.099 60.000 0.00 3.18 35.23 3.18
2272 2312 1.225148 GCCCCAAATGTACGGCCTA 59.775 57.895 0.00 0.00 35.23 3.93
2273 2313 2.044352 GCCCCAAATGTACGGCCT 60.044 61.111 0.00 0.00 35.23 5.19
2275 2315 2.361865 TGGCCCCAAATGTACGGC 60.362 61.111 0.00 0.00 40.85 5.68
2276 2316 0.610785 AACTGGCCCCAAATGTACGG 60.611 55.000 0.00 0.00 0.00 4.02
2277 2317 0.808755 GAACTGGCCCCAAATGTACG 59.191 55.000 0.00 0.00 0.00 3.67
2278 2318 2.215942 AGAACTGGCCCCAAATGTAC 57.784 50.000 0.00 0.00 0.00 2.90
2279 2319 2.990740 AAGAACTGGCCCCAAATGTA 57.009 45.000 0.00 0.00 0.00 2.29
2280 2320 2.101640 AAAGAACTGGCCCCAAATGT 57.898 45.000 0.00 0.00 0.00 2.71
2281 2321 2.368221 TGAAAAGAACTGGCCCCAAATG 59.632 45.455 0.00 0.00 0.00 2.32
2282 2322 2.634453 CTGAAAAGAACTGGCCCCAAAT 59.366 45.455 0.00 0.00 0.00 2.32
2283 2323 2.038659 CTGAAAAGAACTGGCCCCAAA 58.961 47.619 0.00 0.00 0.00 3.28
2477 2518 6.210796 TGCATGCTTGAATAATGCTACAATC 58.789 36.000 20.33 0.00 45.51 2.67
2500 3098 7.201714 CCTCCTTTTTGCATCTCTCTATTTCTG 60.202 40.741 0.00 0.00 0.00 3.02
2544 3144 0.318445 CGTCCCTCAAAGTTCGACGT 60.318 55.000 0.00 0.00 40.96 4.34
2585 3185 4.851214 GCTCCTCCTCGCCCCTCT 62.851 72.222 0.00 0.00 0.00 3.69
2729 4331 1.377725 CAGCGGACCTTCAAGCCAT 60.378 57.895 0.00 0.00 0.00 4.40
2730 4332 2.032528 CAGCGGACCTTCAAGCCA 59.967 61.111 0.00 0.00 0.00 4.75
2801 4450 3.006728 CCTAGGGCCCCGACAACA 61.007 66.667 21.43 0.00 0.00 3.33
2812 4462 3.854669 CCGCAGTCCAGCCTAGGG 61.855 72.222 11.72 0.00 0.00 3.53
2901 4551 5.879223 CACAATCTCAGAATTCTGGCTAGTT 59.121 40.000 30.33 15.43 43.91 2.24
2984 4634 6.246420 ACTCGATTGAACTTCCAAAATCTG 57.754 37.500 0.00 0.00 0.00 2.90
3009 4659 5.513962 GGTCCCAAAAATCCCAAGCAAATAA 60.514 40.000 0.00 0.00 0.00 1.40
3011 4661 3.244875 GGTCCCAAAAATCCCAAGCAAAT 60.245 43.478 0.00 0.00 0.00 2.32
3014 4664 1.347062 GGTCCCAAAAATCCCAAGCA 58.653 50.000 0.00 0.00 0.00 3.91
3027 4677 2.767644 TATGGAGAATCTCGGTCCCA 57.232 50.000 3.96 0.00 33.73 4.37


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

AutoCloner maintained by Alex Coulton.