Multiple sequence alignment - TraesCS2A01G547400

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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 TraesCS2A01G547400 chr2A 100.000 2628 0 0 1 2628 755694351 755691724 0.000000e+00 4854.0
1 TraesCS2A01G547400 chr2A 96.135 414 15 1 2061 2474 156623187 156623599 0.000000e+00 675.0
2 TraesCS2A01G547400 chr2A 94.946 277 13 1 2062 2338 156628218 156628493 1.440000e-117 433.0
3 TraesCS2A01G547400 chr2A 96.985 199 6 0 2430 2628 156623599 156623797 4.190000e-88 335.0
4 TraesCS2A01G547400 chr2A 79.054 296 52 8 2334 2627 14023052 14022765 7.420000e-46 195.0
5 TraesCS2A01G547400 chr2A 95.726 117 4 1 1198 1314 767808293 767808178 1.240000e-43 187.0
6 TraesCS2A01G547400 chr2A 81.188 101 13 5 1883 1982 640812549 640812454 2.800000e-10 76.8
7 TraesCS2A01G547400 chr2D 93.947 760 35 7 1310 2059 624286539 624285781 0.000000e+00 1138.0
8 TraesCS2A01G547400 chr2D 92.890 661 26 10 543 1197 624287170 624286525 0.000000e+00 941.0
9 TraesCS2A01G547400 chr2D 90.035 572 49 8 2061 2628 58698427 58698994 0.000000e+00 734.0
10 TraesCS2A01G547400 chr2D 90.035 572 38 9 4 559 624294922 624294354 0.000000e+00 723.0
11 TraesCS2A01G547400 chr2D 87.413 572 62 9 2061 2627 568315038 568315604 0.000000e+00 649.0
12 TraesCS2A01G547400 chr2D 87.900 281 27 7 2062 2338 58706452 58706729 9.070000e-85 324.0
13 TraesCS2A01G547400 chr2D 85.374 294 39 4 2336 2628 395301941 395301651 4.250000e-78 302.0
14 TraesCS2A01G547400 chr2B 92.090 670 28 13 532 1197 766184043 766183395 0.000000e+00 920.0
15 TraesCS2A01G547400 chr2B 92.920 565 33 2 1310 1871 766183409 766182849 0.000000e+00 815.0
16 TraesCS2A01G547400 chr2B 95.000 120 6 0 1198 1317 748078054 748077935 3.450000e-44 189.0
17 TraesCS2A01G547400 chr2B 94.262 122 7 0 1856 1977 766182833 766182712 1.240000e-43 187.0
18 TraesCS2A01G547400 chr2B 95.238 105 5 0 1957 2061 766182705 766182601 1.620000e-37 167.0
19 TraesCS2A01G547400 chr7D 89.667 571 54 4 2062 2628 619453538 619454107 0.000000e+00 723.0
20 TraesCS2A01G547400 chr7D 84.615 78 11 1 26 103 569945460 569945536 2.800000e-10 76.8
21 TraesCS2A01G547400 chr7D 97.619 42 1 0 165 206 64377847 64377888 3.630000e-09 73.1
22 TraesCS2A01G547400 chr7D 83.099 71 11 1 129 198 403144888 403144818 2.180000e-06 63.9
23 TraesCS2A01G547400 chr3A 87.344 561 54 13 2076 2628 481432031 481432582 6.170000e-176 627.0
24 TraesCS2A01G547400 chr3A 95.726 117 4 1 1198 1314 439913334 439913219 1.240000e-43 187.0
25 TraesCS2A01G547400 chr1B 86.819 569 60 7 2062 2628 146324319 146324874 2.870000e-174 621.0
26 TraesCS2A01G547400 chr1B 88.608 79 7 2 26 103 638497575 638497652 7.740000e-16 95.3
27 TraesCS2A01G547400 chr5B 86.364 572 66 12 2062 2628 664243820 664243256 4.810000e-172 614.0
28 TraesCS2A01G547400 chrUn 91.520 342 23 2 4 344 232284691 232284355 1.420000e-127 466.0
29 TraesCS2A01G547400 chrUn 96.970 33 1 0 2011 2043 267176857 267176889 3.650000e-04 56.5
30 TraesCS2A01G547400 chr6B 91.724 145 9 3 1191 1335 681374618 681374477 5.740000e-47 198.0
31 TraesCS2A01G547400 chr7A 96.581 117 4 0 1198 1314 573839743 573839627 7.420000e-46 195.0
32 TraesCS2A01G547400 chr7A 96.581 117 4 0 1198 1314 641014203 641014087 7.420000e-46 195.0
33 TraesCS2A01G547400 chr7A 94.048 84 5 0 1231 1314 573129714 573129631 7.630000e-26 128.0
34 TraesCS2A01G547400 chr7A 95.556 45 2 0 165 209 209158452 209158408 3.630000e-09 73.1
35 TraesCS2A01G547400 chr3B 96.552 116 4 0 1198 1313 566393526 566393411 2.670000e-45 193.0
36 TraesCS2A01G547400 chr3B 96.970 33 1 0 2011 2043 45284265 45284233 3.650000e-04 56.5
37 TraesCS2A01G547400 chr3B 96.970 33 1 0 2011 2043 45287599 45287567 3.650000e-04 56.5
38 TraesCS2A01G547400 chr3B 85.185 54 4 1 187 240 761747758 761747709 5.000000e-03 52.8
39 TraesCS2A01G547400 chr5A 95.726 117 5 0 1198 1314 671198659 671198543 3.450000e-44 189.0
40 TraesCS2A01G547400 chr5A 84.034 119 13 2 1927 2045 621477622 621477734 2.770000e-20 110.0
41 TraesCS2A01G547400 chr4B 94.355 124 6 1 1198 1321 10516315 10516437 3.450000e-44 189.0
42 TraesCS2A01G547400 chr4B 86.458 96 13 0 1880 1975 453367364 453367459 3.580000e-19 106.0
43 TraesCS2A01G547400 chr3D 80.690 145 21 3 1900 2043 569531153 569531291 3.580000e-19 106.0
44 TraesCS2A01G547400 chr4A 85.714 84 11 1 1899 1982 171200328 171200246 1.300000e-13 87.9
45 TraesCS2A01G547400 chr4A 97.059 34 1 0 165 198 246002264 246002231 1.020000e-04 58.4
46 TraesCS2A01G547400 chr6D 89.552 67 6 1 1911 1977 346823459 346823524 1.680000e-12 84.2
47 TraesCS2A01G547400 chr6A 89.552 67 6 1 1911 1977 496630848 496630783 1.680000e-12 84.2
48 TraesCS2A01G547400 chr4D 95.238 42 2 0 165 206 82575328 82575369 1.690000e-07 67.6
49 TraesCS2A01G547400 chr1A 96.970 33 1 0 165 197 462392930 462392898 3.650000e-04 56.5
50 TraesCS2A01G547400 chr5D 96.875 32 1 0 4 35 282851824 282851855 1.000000e-03 54.7


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 TraesCS2A01G547400 chr2A 755691724 755694351 2627 True 4854.00 4854 100.0000 1 2628 1 chr2A.!!$R3 2627
1 TraesCS2A01G547400 chr2A 156623187 156623797 610 False 505.00 675 96.5600 2061 2628 2 chr2A.!!$F2 567
2 TraesCS2A01G547400 chr2D 624285781 624287170 1389 True 1039.50 1138 93.4185 543 2059 2 chr2D.!!$R3 1516
3 TraesCS2A01G547400 chr2D 58698427 58698994 567 False 734.00 734 90.0350 2061 2628 1 chr2D.!!$F1 567
4 TraesCS2A01G547400 chr2D 624294354 624294922 568 True 723.00 723 90.0350 4 559 1 chr2D.!!$R2 555
5 TraesCS2A01G547400 chr2D 568315038 568315604 566 False 649.00 649 87.4130 2061 2627 1 chr2D.!!$F3 566
6 TraesCS2A01G547400 chr2B 766182601 766184043 1442 True 522.25 920 93.6275 532 2061 4 chr2B.!!$R2 1529
7 TraesCS2A01G547400 chr7D 619453538 619454107 569 False 723.00 723 89.6670 2062 2628 1 chr7D.!!$F3 566
8 TraesCS2A01G547400 chr3A 481432031 481432582 551 False 627.00 627 87.3440 2076 2628 1 chr3A.!!$F1 552
9 TraesCS2A01G547400 chr1B 146324319 146324874 555 False 621.00 621 86.8190 2062 2628 1 chr1B.!!$F1 566
10 TraesCS2A01G547400 chr5B 664243256 664243820 564 True 614.00 614 86.3640 2062 2628 1 chr5B.!!$R1 566

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
841 870 0.250513 CCCTGACTACAAGCCTCCAC 59.749 60.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2241 2350 0.252103 AGGAGACCCCGCTTACAAGA 60.252 55.0 0.0 0.0 40.87 3.02 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
38 39 0.403271 GAGGGGGTATCATGCATGCT 59.597 55.000 22.25 15.24 0.00 3.79
41 42 2.162681 GGGGGTATCATGCATGCTAAC 58.837 52.381 22.25 18.71 0.00 2.34
42 43 2.488891 GGGGGTATCATGCATGCTAACA 60.489 50.000 23.18 7.61 0.00 2.41
136 137 4.980573 AGTACTACAGGTTTTTCATGGCA 58.019 39.130 0.00 0.00 31.56 4.92
245 250 6.062258 AGTACCCACTACATGCAGTAATTT 57.938 37.500 0.00 0.00 31.45 1.82
336 341 3.728864 CGCAACACTACAGCCAATCAATC 60.729 47.826 0.00 0.00 0.00 2.67
403 408 3.978855 GCCGTAATTCGAAAAGCAAACTT 59.021 39.130 0.00 0.00 42.86 2.66
735 754 2.188161 CCTCCCTCGGCGAGTCTAC 61.188 68.421 32.41 0.00 0.00 2.59
752 771 4.021368 AGTCTACAACGGCAATCACTTACT 60.021 41.667 0.00 0.00 0.00 2.24
754 773 2.423577 ACAACGGCAATCACTTACTCC 58.576 47.619 0.00 0.00 0.00 3.85
755 774 2.038557 ACAACGGCAATCACTTACTCCT 59.961 45.455 0.00 0.00 0.00 3.69
829 858 0.548510 GGAGCTATTTGCCCCTGACT 59.451 55.000 0.00 0.00 44.23 3.41
834 863 2.945668 GCTATTTGCCCCTGACTACAAG 59.054 50.000 0.00 0.00 35.15 3.16
835 864 1.839424 ATTTGCCCCTGACTACAAGC 58.161 50.000 0.00 0.00 0.00 4.01
836 865 0.251165 TTTGCCCCTGACTACAAGCC 60.251 55.000 0.00 0.00 0.00 4.35
837 866 1.133809 TTGCCCCTGACTACAAGCCT 61.134 55.000 0.00 0.00 0.00 4.58
838 867 1.222113 GCCCCTGACTACAAGCCTC 59.778 63.158 0.00 0.00 0.00 4.70
839 868 1.908483 CCCCTGACTACAAGCCTCC 59.092 63.158 0.00 0.00 0.00 4.30
840 869 0.909610 CCCCTGACTACAAGCCTCCA 60.910 60.000 0.00 0.00 0.00 3.86
841 870 0.250513 CCCTGACTACAAGCCTCCAC 59.749 60.000 0.00 0.00 0.00 4.02
842 871 0.976641 CCTGACTACAAGCCTCCACA 59.023 55.000 0.00 0.00 0.00 4.17
843 872 1.347707 CCTGACTACAAGCCTCCACAA 59.652 52.381 0.00 0.00 0.00 3.33
844 873 2.224523 CCTGACTACAAGCCTCCACAAA 60.225 50.000 0.00 0.00 0.00 2.83
845 874 3.560025 CCTGACTACAAGCCTCCACAAAT 60.560 47.826 0.00 0.00 0.00 2.32
846 875 4.074970 CTGACTACAAGCCTCCACAAATT 58.925 43.478 0.00 0.00 0.00 1.82
935 964 6.019881 GCTGCCAAAACAAACTTACACTTTAG 60.020 38.462 0.00 0.00 0.00 1.85
936 965 6.926313 TGCCAAAACAAACTTACACTTTAGT 58.074 32.000 0.00 0.00 0.00 2.24
937 966 7.379750 TGCCAAAACAAACTTACACTTTAGTT 58.620 30.769 0.00 0.00 36.20 2.24
938 967 8.521176 TGCCAAAACAAACTTACACTTTAGTTA 58.479 29.630 0.00 0.00 33.66 2.24
1074 1110 1.267574 TGTCCATCCAGCCTCTCACC 61.268 60.000 0.00 0.00 0.00 4.02
1115 1151 1.140852 CCACCTCATGGCGATTAGGAA 59.859 52.381 15.12 0.00 43.24 3.36
1186 1222 8.742554 AAAACAAGATGTTATGAAATTCGTCC 57.257 30.769 0.00 0.00 40.14 4.79
1187 1223 7.687941 AACAAGATGTTATGAAATTCGTCCT 57.312 32.000 0.00 0.00 39.09 3.85
1188 1224 7.308782 ACAAGATGTTATGAAATTCGTCCTC 57.691 36.000 0.00 0.00 0.00 3.71
1189 1225 6.878923 ACAAGATGTTATGAAATTCGTCCTCA 59.121 34.615 0.00 0.00 0.00 3.86
1190 1226 7.554118 ACAAGATGTTATGAAATTCGTCCTCAT 59.446 33.333 0.00 0.00 34.29 2.90
1191 1227 7.721286 AGATGTTATGAAATTCGTCCTCATC 57.279 36.000 13.77 13.77 32.22 2.92
1192 1228 7.275183 AGATGTTATGAAATTCGTCCTCATCA 58.725 34.615 19.03 0.00 32.22 3.07
1193 1229 7.770433 AGATGTTATGAAATTCGTCCTCATCAA 59.230 33.333 19.03 0.00 32.22 2.57
1194 1230 7.072177 TGTTATGAAATTCGTCCTCATCAAC 57.928 36.000 0.00 0.00 32.22 3.18
1195 1231 6.652900 TGTTATGAAATTCGTCCTCATCAACA 59.347 34.615 0.00 0.00 32.22 3.33
1196 1232 7.336679 TGTTATGAAATTCGTCCTCATCAACAT 59.663 33.333 0.00 0.00 32.22 2.71
1197 1233 5.550232 TGAAATTCGTCCTCATCAACATG 57.450 39.130 0.00 0.00 0.00 3.21
1198 1234 4.142622 TGAAATTCGTCCTCATCAACATGC 60.143 41.667 0.00 0.00 0.00 4.06
1199 1235 2.470983 TTCGTCCTCATCAACATGCA 57.529 45.000 0.00 0.00 0.00 3.96
1200 1236 2.470983 TCGTCCTCATCAACATGCAA 57.529 45.000 0.00 0.00 0.00 4.08
1201 1237 2.777094 TCGTCCTCATCAACATGCAAA 58.223 42.857 0.00 0.00 0.00 3.68
1202 1238 3.145286 TCGTCCTCATCAACATGCAAAA 58.855 40.909 0.00 0.00 0.00 2.44
1203 1239 3.758023 TCGTCCTCATCAACATGCAAAAT 59.242 39.130 0.00 0.00 0.00 1.82
1204 1240 4.940654 TCGTCCTCATCAACATGCAAAATA 59.059 37.500 0.00 0.00 0.00 1.40
1205 1241 5.414144 TCGTCCTCATCAACATGCAAAATAA 59.586 36.000 0.00 0.00 0.00 1.40
1206 1242 6.095300 TCGTCCTCATCAACATGCAAAATAAT 59.905 34.615 0.00 0.00 0.00 1.28
1207 1243 6.415867 CGTCCTCATCAACATGCAAAATAATC 59.584 38.462 0.00 0.00 0.00 1.75
1208 1244 6.698766 GTCCTCATCAACATGCAAAATAATCC 59.301 38.462 0.00 0.00 0.00 3.01
1209 1245 6.608405 TCCTCATCAACATGCAAAATAATCCT 59.392 34.615 0.00 0.00 0.00 3.24
1210 1246 6.700081 CCTCATCAACATGCAAAATAATCCTG 59.300 38.462 0.00 0.00 0.00 3.86
1211 1247 7.172868 TCATCAACATGCAAAATAATCCTGT 57.827 32.000 0.00 0.00 0.00 4.00
1212 1248 8.291191 TCATCAACATGCAAAATAATCCTGTA 57.709 30.769 0.00 0.00 0.00 2.74
1213 1249 8.190122 TCATCAACATGCAAAATAATCCTGTAC 58.810 33.333 0.00 0.00 0.00 2.90
1214 1250 6.550843 TCAACATGCAAAATAATCCTGTACG 58.449 36.000 0.00 0.00 0.00 3.67
1215 1251 6.372937 TCAACATGCAAAATAATCCTGTACGA 59.627 34.615 0.00 0.00 0.00 3.43
1216 1252 6.119144 ACATGCAAAATAATCCTGTACGAC 57.881 37.500 0.00 0.00 0.00 4.34
1217 1253 5.065988 ACATGCAAAATAATCCTGTACGACC 59.934 40.000 0.00 0.00 0.00 4.79
1218 1254 4.580868 TGCAAAATAATCCTGTACGACCA 58.419 39.130 0.00 0.00 0.00 4.02
1219 1255 4.634004 TGCAAAATAATCCTGTACGACCAG 59.366 41.667 0.00 0.00 0.00 4.00
1231 1267 2.503375 GACCAGGTCGTACGTGCG 60.503 66.667 20.49 20.49 33.03 5.34
1232 1268 2.969806 GACCAGGTCGTACGTGCGA 61.970 63.158 24.89 24.89 38.68 5.10
1256 1292 4.020617 CGCAAGGGGAGGCTGTCA 62.021 66.667 0.00 0.00 0.00 3.58
1257 1293 2.045536 GCAAGGGGAGGCTGTCAG 60.046 66.667 0.00 0.00 0.00 3.51
1258 1294 2.673523 CAAGGGGAGGCTGTCAGG 59.326 66.667 1.14 0.00 0.00 3.86
1259 1295 2.208349 AAGGGGAGGCTGTCAGGT 59.792 61.111 1.14 0.00 0.00 4.00
1260 1296 2.227036 AAGGGGAGGCTGTCAGGTG 61.227 63.158 1.14 0.00 0.00 4.00
1261 1297 3.721706 GGGGAGGCTGTCAGGTGG 61.722 72.222 1.14 0.00 0.00 4.61
1262 1298 3.721706 GGGAGGCTGTCAGGTGGG 61.722 72.222 1.14 0.00 0.00 4.61
1263 1299 4.416738 GGAGGCTGTCAGGTGGGC 62.417 72.222 1.14 0.00 0.00 5.36
1264 1300 4.416738 GAGGCTGTCAGGTGGGCC 62.417 72.222 0.00 0.00 44.38 5.80
1281 1317 4.436998 CACCCCCACGACGAGCTC 62.437 72.222 2.73 2.73 0.00 4.09
1282 1318 4.680537 ACCCCCACGACGAGCTCT 62.681 66.667 12.85 0.00 0.00 4.09
1283 1319 3.827898 CCCCCACGACGAGCTCTC 61.828 72.222 12.85 7.57 0.00 3.20
1284 1320 2.752238 CCCCACGACGAGCTCTCT 60.752 66.667 12.85 0.00 0.00 3.10
1285 1321 2.766400 CCCCACGACGAGCTCTCTC 61.766 68.421 12.85 5.21 35.99 3.20
1286 1322 2.041115 CCCACGACGAGCTCTCTCA 61.041 63.158 12.85 0.00 39.30 3.27
1287 1323 1.135731 CCACGACGAGCTCTCTCAC 59.864 63.158 12.85 0.00 39.30 3.51
1288 1324 1.578206 CCACGACGAGCTCTCTCACA 61.578 60.000 12.85 0.00 39.30 3.58
1289 1325 0.238553 CACGACGAGCTCTCTCACAA 59.761 55.000 12.85 0.00 39.30 3.33
1290 1326 0.952280 ACGACGAGCTCTCTCACAAA 59.048 50.000 12.85 0.00 39.30 2.83
1291 1327 1.332178 CGACGAGCTCTCTCACAAAC 58.668 55.000 12.85 0.00 39.30 2.93
1292 1328 1.332178 GACGAGCTCTCTCACAAACG 58.668 55.000 12.85 0.00 39.30 3.60
1293 1329 0.039074 ACGAGCTCTCTCACAAACGG 60.039 55.000 12.85 0.00 39.30 4.44
1294 1330 0.734253 CGAGCTCTCTCACAAACGGG 60.734 60.000 12.85 0.00 39.30 5.28
1295 1331 0.318762 GAGCTCTCTCACAAACGGGT 59.681 55.000 6.43 0.00 39.16 5.28
1296 1332 0.318762 AGCTCTCTCACAAACGGGTC 59.681 55.000 0.00 0.00 0.00 4.46
1297 1333 1.009389 GCTCTCTCACAAACGGGTCG 61.009 60.000 0.00 0.00 0.00 4.79
1298 1334 0.314302 CTCTCTCACAAACGGGTCGT 59.686 55.000 0.00 0.00 43.97 4.34
1299 1335 1.538512 CTCTCTCACAAACGGGTCGTA 59.461 52.381 0.00 0.00 39.99 3.43
1300 1336 1.267806 TCTCTCACAAACGGGTCGTAC 59.732 52.381 0.00 0.00 39.99 3.67
1301 1337 1.001048 CTCTCACAAACGGGTCGTACA 60.001 52.381 0.00 0.00 39.99 2.90
1302 1338 1.001048 TCTCACAAACGGGTCGTACAG 60.001 52.381 0.00 0.00 39.99 2.74
1303 1339 0.032403 TCACAAACGGGTCGTACAGG 59.968 55.000 0.00 0.00 39.99 4.00
1304 1340 0.032403 CACAAACGGGTCGTACAGGA 59.968 55.000 0.00 0.00 39.99 3.86
1305 1341 0.971386 ACAAACGGGTCGTACAGGAT 59.029 50.000 0.00 0.00 39.99 3.24
1306 1342 1.345415 ACAAACGGGTCGTACAGGATT 59.655 47.619 0.00 0.00 39.99 3.01
1307 1343 1.997606 CAAACGGGTCGTACAGGATTC 59.002 52.381 0.00 0.00 39.99 2.52
1308 1344 0.171903 AACGGGTCGTACAGGATTCG 59.828 55.000 0.00 0.00 39.99 3.34
1309 1345 1.588139 CGGGTCGTACAGGATTCGC 60.588 63.158 0.00 0.00 0.00 4.70
1310 1346 1.588139 GGGTCGTACAGGATTCGCG 60.588 63.158 0.00 0.00 0.00 5.87
1311 1347 1.138247 GGTCGTACAGGATTCGCGT 59.862 57.895 5.77 0.00 0.00 6.01
1312 1348 0.864797 GGTCGTACAGGATTCGCGTC 60.865 60.000 5.77 0.00 0.00 5.19
1313 1349 0.864797 GTCGTACAGGATTCGCGTCC 60.865 60.000 5.77 6.86 38.62 4.79
1318 1354 0.537188 ACAGGATTCGCGTCCTCATT 59.463 50.000 14.89 0.94 45.51 2.57
1387 1423 1.813513 CCCTCACATTCTTCTTGCGT 58.186 50.000 0.00 0.00 0.00 5.24
1407 1443 0.616395 TCCATGGGCTACTTCGGTGA 60.616 55.000 13.02 0.00 0.00 4.02
1427 1463 1.655654 CGCTACTCACTCGCCGATG 60.656 63.158 0.00 0.00 0.00 3.84
1516 1552 1.875420 TTGGGTTCACATGCATGGCG 61.875 55.000 29.41 19.88 0.00 5.69
1618 1654 5.292834 CACACTCGTCGTCTACCTTTATCTA 59.707 44.000 0.00 0.00 0.00 1.98
1760 1799 8.698973 ATGTATCTCACAAGTATGTAGTAGCT 57.301 34.615 0.00 0.00 41.55 3.32
1802 1841 6.493802 ACTCACTGTTAGAGAAAGATACCACA 59.506 38.462 2.52 0.00 36.91 4.17
1805 1844 8.375506 TCACTGTTAGAGAAAGATACCACAATT 58.624 33.333 0.00 0.00 0.00 2.32
2002 2103 1.162698 GAACCGCTAAACTGAACCCC 58.837 55.000 0.00 0.00 0.00 4.95
2009 2110 2.169978 GCTAAACTGAACCCCCGATAGT 59.830 50.000 0.00 0.00 0.00 2.12
2058 2164 0.887247 ACTTGCAGCACACACAACAA 59.113 45.000 0.00 0.00 0.00 2.83
2228 2336 2.717639 CTGGCAAATGGCTAGGTAGT 57.282 50.000 8.50 0.00 46.49 2.73
2241 2350 3.243434 GCTAGGTAGTGTGTGCGTGATAT 60.243 47.826 0.00 0.00 0.00 1.63
2267 2378 3.148279 CGGGGTCTCCTTCCTCCG 61.148 72.222 0.00 0.00 34.48 4.63
2268 2379 3.471806 GGGGTCTCCTTCCTCCGC 61.472 72.222 0.00 0.00 0.00 5.54
2294 2406 6.127101 TCTCCGAATATTCTCCTGTAGTTCA 58.873 40.000 13.45 0.00 0.00 3.18
2463 2621 2.580783 TGGAGAAAATTTCCCCCGAGAT 59.419 45.455 3.79 0.00 33.62 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.574607 ACCCCCTCTGTAAAGAAATATAAGTG 58.425 38.462 0.00 0.00 0.00 3.16
2 3 7.766736 ACCCCCTCTGTAAAGAAATATAAGT 57.233 36.000 0.00 0.00 0.00 2.24
12 13 3.136443 TGCATGATACCCCCTCTGTAAAG 59.864 47.826 0.00 0.00 0.00 1.85
18 19 0.403271 GCATGCATGATACCCCCTCT 59.597 55.000 30.64 0.00 0.00 3.69
24 25 5.954296 ATCTTGTTAGCATGCATGATACC 57.046 39.130 30.64 21.04 30.85 2.73
112 113 6.535540 TGCCATGAAAAACCTGTAGTACTAA 58.464 36.000 3.61 0.00 0.00 2.24
115 116 5.009210 TGTTGCCATGAAAAACCTGTAGTAC 59.991 40.000 0.00 0.00 0.00 2.73
121 122 6.705381 TCTTATTTGTTGCCATGAAAAACCTG 59.295 34.615 0.00 0.00 0.00 4.00
129 130 6.778834 ACATGATCTTATTTGTTGCCATGA 57.221 33.333 0.00 0.00 35.47 3.07
168 173 9.239551 TGATACTACCTTCGTAATGCATAGTAT 57.760 33.333 11.08 11.08 37.18 2.12
223 228 5.878116 TCAAATTACTGCATGTAGTGGGTAC 59.122 40.000 24.73 0.00 32.08 3.34
235 240 7.608308 AAAGTTTGCTTTTCAAATTACTGCA 57.392 28.000 0.00 0.00 45.43 4.41
314 319 1.155889 TGATTGGCTGTAGTGTTGCG 58.844 50.000 0.00 0.00 0.00 4.85
375 380 3.303791 GCTTTTCGAATTACGGCCCATAG 60.304 47.826 0.00 0.00 42.82 2.23
378 383 0.806241 GCTTTTCGAATTACGGCCCA 59.194 50.000 0.00 0.00 42.82 5.36
379 384 0.806241 TGCTTTTCGAATTACGGCCC 59.194 50.000 0.00 0.00 42.82 5.80
501 518 5.116882 AGGCAACGTGGAAAGAGATATTAC 58.883 41.667 0.00 0.00 46.39 1.89
592 611 9.729281 AAACGATTAAGAAGTTTCCAGGTAATA 57.271 29.630 0.00 0.00 33.36 0.98
593 612 8.512138 CAAACGATTAAGAAGTTTCCAGGTAAT 58.488 33.333 0.00 0.00 36.12 1.89
594 613 7.520937 GCAAACGATTAAGAAGTTTCCAGGTAA 60.521 37.037 0.00 0.00 36.12 2.85
735 754 2.699954 AGGAGTAAGTGATTGCCGTTG 58.300 47.619 0.00 0.00 0.00 4.10
768 787 4.706962 AGAAGACTTTGGCAAACTTTGAGT 59.293 37.500 8.93 3.96 0.00 3.41
825 844 3.788227 ATTTGTGGAGGCTTGTAGTCA 57.212 42.857 0.00 0.00 0.00 3.41
829 858 4.219725 GGCTAAAATTTGTGGAGGCTTGTA 59.780 41.667 0.00 0.00 0.00 2.41
834 863 3.006859 AGTTGGCTAAAATTTGTGGAGGC 59.993 43.478 0.00 0.66 0.00 4.70
835 864 4.871933 AGTTGGCTAAAATTTGTGGAGG 57.128 40.909 0.00 0.00 0.00 4.30
836 865 7.830739 AGATTAGTTGGCTAAAATTTGTGGAG 58.169 34.615 0.00 0.00 40.22 3.86
837 866 7.775053 AGATTAGTTGGCTAAAATTTGTGGA 57.225 32.000 0.00 0.00 40.22 4.02
838 867 8.519526 TGTAGATTAGTTGGCTAAAATTTGTGG 58.480 33.333 0.00 0.00 40.22 4.17
839 868 9.906660 TTGTAGATTAGTTGGCTAAAATTTGTG 57.093 29.630 0.00 0.00 40.22 3.33
840 869 9.908152 GTTGTAGATTAGTTGGCTAAAATTTGT 57.092 29.630 0.00 0.00 40.22 2.83
841 870 9.353999 GGTTGTAGATTAGTTGGCTAAAATTTG 57.646 33.333 0.00 0.00 40.22 2.32
842 871 9.309224 AGGTTGTAGATTAGTTGGCTAAAATTT 57.691 29.630 0.00 0.00 40.22 1.82
843 872 8.879427 AGGTTGTAGATTAGTTGGCTAAAATT 57.121 30.769 0.00 0.00 40.22 1.82
844 873 8.879427 AAGGTTGTAGATTAGTTGGCTAAAAT 57.121 30.769 0.00 0.00 40.22 1.82
845 874 8.700439 AAAGGTTGTAGATTAGTTGGCTAAAA 57.300 30.769 0.00 0.00 40.22 1.52
846 875 8.161425 AGAAAGGTTGTAGATTAGTTGGCTAAA 58.839 33.333 0.00 0.00 40.22 1.85
905 934 1.070601 AGTTTGTTTTGGCAGCCATCC 59.929 47.619 17.09 6.76 31.53 3.51
906 935 2.531522 AGTTTGTTTTGGCAGCCATC 57.468 45.000 17.09 9.79 31.53 3.51
935 964 7.211573 GGCTCTCTTCTTTATAGGGAAGTAAC 58.788 42.308 13.04 5.65 39.67 2.50
936 965 6.326843 GGGCTCTCTTCTTTATAGGGAAGTAA 59.673 42.308 13.04 5.74 39.67 2.24
937 966 5.839606 GGGCTCTCTTCTTTATAGGGAAGTA 59.160 44.000 13.04 5.96 39.67 2.24
938 967 4.656575 GGGCTCTCTTCTTTATAGGGAAGT 59.343 45.833 13.04 0.00 39.67 3.01
950 980 1.412937 GGAGGATCAGGGCTCTCTTCT 60.413 57.143 0.00 0.00 36.25 2.85
956 986 3.065462 CTAGGGAGGATCAGGGCTC 57.935 63.158 0.00 0.00 36.25 4.70
1110 1146 0.547229 TAAAGGGGCCGGTGTTCCTA 60.547 55.000 1.90 0.00 0.00 2.94
1115 1151 4.404098 CGCTAAAGGGGCCGGTGT 62.404 66.667 1.90 0.00 0.00 4.16
1179 1215 2.989909 TGCATGTTGATGAGGACGAAT 58.010 42.857 0.00 0.00 0.00 3.34
1186 1222 7.262772 ACAGGATTATTTTGCATGTTGATGAG 58.737 34.615 0.00 0.00 0.00 2.90
1187 1223 7.172868 ACAGGATTATTTTGCATGTTGATGA 57.827 32.000 0.00 0.00 0.00 2.92
1188 1224 7.166307 CGTACAGGATTATTTTGCATGTTGATG 59.834 37.037 0.00 0.00 0.00 3.07
1189 1225 7.066887 TCGTACAGGATTATTTTGCATGTTGAT 59.933 33.333 0.00 0.00 0.00 2.57
1190 1226 6.372937 TCGTACAGGATTATTTTGCATGTTGA 59.627 34.615 0.00 0.00 0.00 3.18
1191 1227 6.468956 GTCGTACAGGATTATTTTGCATGTTG 59.531 38.462 0.00 0.00 0.00 3.33
1192 1228 6.404293 GGTCGTACAGGATTATTTTGCATGTT 60.404 38.462 0.00 0.00 0.00 2.71
1193 1229 5.065988 GGTCGTACAGGATTATTTTGCATGT 59.934 40.000 0.00 0.00 0.00 3.21
1194 1230 5.065859 TGGTCGTACAGGATTATTTTGCATG 59.934 40.000 0.00 0.00 0.00 4.06
1195 1231 5.189928 TGGTCGTACAGGATTATTTTGCAT 58.810 37.500 0.00 0.00 0.00 3.96
1196 1232 4.580868 TGGTCGTACAGGATTATTTTGCA 58.419 39.130 0.00 0.00 0.00 4.08
1197 1233 5.156804 CTGGTCGTACAGGATTATTTTGC 57.843 43.478 0.00 0.00 34.84 3.68
1214 1250 2.503375 CGCACGTACGACCTGGTC 60.503 66.667 24.41 16.99 34.06 4.02
1215 1251 2.979676 TCGCACGTACGACCTGGT 60.980 61.111 24.41 0.00 37.09 4.00
1238 1274 4.785453 GACAGCCTCCCCTTGCGG 62.785 72.222 0.00 0.00 0.00 5.69
1239 1275 3.965539 CTGACAGCCTCCCCTTGCG 62.966 68.421 0.00 0.00 0.00 4.85
1240 1276 2.045536 CTGACAGCCTCCCCTTGC 60.046 66.667 0.00 0.00 0.00 4.01
1241 1277 2.227036 ACCTGACAGCCTCCCCTTG 61.227 63.158 0.00 0.00 0.00 3.61
1242 1278 2.208349 ACCTGACAGCCTCCCCTT 59.792 61.111 0.00 0.00 0.00 3.95
1243 1279 2.608988 CACCTGACAGCCTCCCCT 60.609 66.667 0.00 0.00 0.00 4.79
1244 1280 3.721706 CCACCTGACAGCCTCCCC 61.722 72.222 0.00 0.00 0.00 4.81
1245 1281 3.721706 CCCACCTGACAGCCTCCC 61.722 72.222 0.00 0.00 0.00 4.30
1246 1282 4.416738 GCCCACCTGACAGCCTCC 62.417 72.222 0.00 0.00 0.00 4.30
1247 1283 4.416738 GGCCCACCTGACAGCCTC 62.417 72.222 0.00 0.00 42.34 4.70
1264 1300 4.436998 GAGCTCGTCGTGGGGGTG 62.437 72.222 0.00 0.00 0.00 4.61
1265 1301 4.680537 AGAGCTCGTCGTGGGGGT 62.681 66.667 8.37 0.00 0.00 4.95
1266 1302 3.827898 GAGAGCTCGTCGTGGGGG 61.828 72.222 8.37 0.00 0.00 5.40
1267 1303 2.752238 AGAGAGCTCGTCGTGGGG 60.752 66.667 8.37 0.00 34.09 4.96
1268 1304 2.041115 TGAGAGAGCTCGTCGTGGG 61.041 63.158 8.37 0.00 44.33 4.61
1269 1305 1.135731 GTGAGAGAGCTCGTCGTGG 59.864 63.158 8.37 0.00 44.33 4.94
1270 1306 0.238553 TTGTGAGAGAGCTCGTCGTG 59.761 55.000 8.37 0.00 44.33 4.35
1271 1307 0.952280 TTTGTGAGAGAGCTCGTCGT 59.048 50.000 8.37 0.00 44.33 4.34
1272 1308 1.332178 GTTTGTGAGAGAGCTCGTCG 58.668 55.000 8.37 0.00 44.33 5.12
1273 1309 1.332178 CGTTTGTGAGAGAGCTCGTC 58.668 55.000 8.37 10.03 44.33 4.20
1274 1310 0.039074 CCGTTTGTGAGAGAGCTCGT 60.039 55.000 8.37 0.00 44.33 4.18
1275 1311 0.734253 CCCGTTTGTGAGAGAGCTCG 60.734 60.000 8.37 0.00 44.33 5.03
1276 1312 0.318762 ACCCGTTTGTGAGAGAGCTC 59.681 55.000 5.27 5.27 41.67 4.09
1277 1313 0.318762 GACCCGTTTGTGAGAGAGCT 59.681 55.000 0.00 0.00 0.00 4.09
1278 1314 1.009389 CGACCCGTTTGTGAGAGAGC 61.009 60.000 0.00 0.00 0.00 4.09
1279 1315 0.314302 ACGACCCGTTTGTGAGAGAG 59.686 55.000 0.00 0.00 36.35 3.20
1280 1316 1.267806 GTACGACCCGTTTGTGAGAGA 59.732 52.381 0.00 0.00 41.54 3.10
1281 1317 1.001048 TGTACGACCCGTTTGTGAGAG 60.001 52.381 0.00 0.00 41.54 3.20
1282 1318 1.001048 CTGTACGACCCGTTTGTGAGA 60.001 52.381 0.00 0.00 41.54 3.27
1283 1319 1.415374 CTGTACGACCCGTTTGTGAG 58.585 55.000 0.00 0.00 41.54 3.51
1284 1320 0.032403 CCTGTACGACCCGTTTGTGA 59.968 55.000 0.00 0.00 41.54 3.58
1285 1321 0.032403 TCCTGTACGACCCGTTTGTG 59.968 55.000 0.00 0.00 41.54 3.33
1286 1322 0.971386 ATCCTGTACGACCCGTTTGT 59.029 50.000 0.00 0.00 41.54 2.83
1287 1323 1.997606 GAATCCTGTACGACCCGTTTG 59.002 52.381 0.00 0.00 41.54 2.93
1288 1324 1.403249 CGAATCCTGTACGACCCGTTT 60.403 52.381 0.00 0.00 41.54 3.60
1289 1325 0.171903 CGAATCCTGTACGACCCGTT 59.828 55.000 0.00 0.00 41.54 4.44
1290 1326 1.805254 CGAATCCTGTACGACCCGT 59.195 57.895 0.00 0.00 44.35 5.28
1291 1327 1.588139 GCGAATCCTGTACGACCCG 60.588 63.158 0.00 0.00 0.00 5.28
1292 1328 1.588139 CGCGAATCCTGTACGACCC 60.588 63.158 0.00 0.00 0.00 4.46
1293 1329 0.864797 GACGCGAATCCTGTACGACC 60.865 60.000 15.93 0.00 0.00 4.79
1294 1330 0.864797 GGACGCGAATCCTGTACGAC 60.865 60.000 15.93 0.00 35.68 4.34
1295 1331 1.430632 GGACGCGAATCCTGTACGA 59.569 57.895 15.93 0.00 35.68 3.43
1296 1332 3.993103 GGACGCGAATCCTGTACG 58.007 61.111 15.93 0.00 35.68 3.67
1302 1338 2.546778 TGTTAATGAGGACGCGAATCC 58.453 47.619 15.93 11.06 39.28 3.01
1303 1339 3.121328 CGATGTTAATGAGGACGCGAATC 60.121 47.826 15.93 8.15 0.00 2.52
1304 1340 2.794910 CGATGTTAATGAGGACGCGAAT 59.205 45.455 15.93 0.00 0.00 3.34
1305 1341 2.190161 CGATGTTAATGAGGACGCGAA 58.810 47.619 15.93 0.00 0.00 4.70
1306 1342 1.835121 CGATGTTAATGAGGACGCGA 58.165 50.000 15.93 0.00 0.00 5.87
1307 1343 0.229753 GCGATGTTAATGAGGACGCG 59.770 55.000 3.53 3.53 35.78 6.01
1308 1344 0.582005 GGCGATGTTAATGAGGACGC 59.418 55.000 0.00 0.00 43.00 5.19
1309 1345 1.202533 AGGGCGATGTTAATGAGGACG 60.203 52.381 0.00 0.00 0.00 4.79
1310 1346 2.484889 GAGGGCGATGTTAATGAGGAC 58.515 52.381 0.00 0.00 0.00 3.85
1311 1347 1.416401 GGAGGGCGATGTTAATGAGGA 59.584 52.381 0.00 0.00 0.00 3.71
1312 1348 1.417890 AGGAGGGCGATGTTAATGAGG 59.582 52.381 0.00 0.00 0.00 3.86
1313 1349 2.487934 CAGGAGGGCGATGTTAATGAG 58.512 52.381 0.00 0.00 0.00 2.90
1318 1354 1.823295 GAGCAGGAGGGCGATGTTA 59.177 57.895 0.00 0.00 39.27 2.41
1387 1423 0.251916 CACCGAAGTAGCCCATGGAA 59.748 55.000 15.22 0.00 0.00 3.53
1407 1443 1.167155 ATCGGCGAGTGAGTAGCGAT 61.167 55.000 17.22 0.00 0.00 4.58
1427 1463 1.667724 CTTGATCACCTTGCGGATGAC 59.332 52.381 0.00 0.00 0.00 3.06
1450 1486 4.035102 GGGCCCTTCGGACTGCTT 62.035 66.667 17.04 0.00 37.32 3.91
1494 1530 1.067425 CCATGCATGTGAACCCAAGTG 60.067 52.381 24.58 1.51 0.00 3.16
1495 1531 1.259609 CCATGCATGTGAACCCAAGT 58.740 50.000 24.58 0.00 0.00 3.16
1516 1552 1.260544 AAAGCATGGAACCCAGAAGC 58.739 50.000 0.00 0.00 36.75 3.86
1558 1594 4.945645 TCGACAGAGAACACCCCT 57.054 55.556 0.00 0.00 0.00 4.79
1760 1799 6.936335 ACAGTGAGTACATCAACATGAATCAA 59.064 34.615 0.00 0.00 40.43 2.57
1802 1841 7.362920 GCTCACATGTACTTCCCAATTGTAATT 60.363 37.037 0.00 0.00 0.00 1.40
1805 1844 4.941263 GCTCACATGTACTTCCCAATTGTA 59.059 41.667 0.00 0.00 0.00 2.41
1820 1859 0.606401 ACCAAGGAACCGCTCACATG 60.606 55.000 0.00 0.00 0.00 3.21
1977 2078 0.794473 CAGTTTAGCGGTTCCGGTTC 59.206 55.000 20.40 11.65 40.66 3.62
2002 2103 6.149308 TGCATGAGCCAAATATAAACTATCGG 59.851 38.462 0.00 0.00 41.13 4.18
2009 2110 6.804677 ACGAAATGCATGAGCCAAATATAAA 58.195 32.000 0.00 0.00 41.13 1.40
2058 2164 2.030562 CCCGGTTCGCTGACAGTT 59.969 61.111 0.00 0.00 0.00 3.16
2137 2243 2.905996 ATTCTGGGCCGGCAAGTCA 61.906 57.895 30.85 18.60 0.00 3.41
2139 2245 2.361610 CATTCTGGGCCGGCAAGT 60.362 61.111 30.85 7.23 0.00 3.16
2228 2336 3.616821 GCTTACAAGATATCACGCACACA 59.383 43.478 5.32 0.00 0.00 3.72
2241 2350 0.252103 AGGAGACCCCGCTTACAAGA 60.252 55.000 0.00 0.00 40.87 3.02
2267 2378 2.630580 ACAGGAGAATATTCGGAGAGGC 59.369 50.000 9.78 0.00 38.43 4.70
2268 2379 5.074115 ACTACAGGAGAATATTCGGAGAGG 58.926 45.833 9.78 2.34 38.43 3.69
2463 2621 1.210478 GGAGCTTGTAGATGGCCTTCA 59.790 52.381 19.98 4.32 0.00 3.02


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

AutoCloner maintained by Alex Coulton.