Multiple sequence alignment - TraesCS2D01G353200

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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 TraesCS2D01G353200 chr2D 100.000 3838 0 0 1 3838 451462270 451458433 0.000000e+00 7088.0
1 TraesCS2D01G353200 chr2D 83.857 669 72 20 7 669 120986967 120986329 4.240000e-169 604.0
2 TraesCS2D01G353200 chr2D 82.192 657 76 27 6 641 166942084 166941448 9.440000e-146 527.0
3 TraesCS2D01G353200 chr2D 84.821 112 14 3 558 667 53374759 53374869 4.050000e-20 110.0
4 TraesCS2D01G353200 chr2B 93.941 1799 84 12 1227 3023 531720324 531718549 0.000000e+00 2695.0
5 TraesCS2D01G353200 chr2B 96.463 820 19 5 3022 3838 531718485 531717673 0.000000e+00 1345.0
6 TraesCS2D01G353200 chr2B 88.393 672 45 15 1 657 75343655 75344308 0.000000e+00 778.0
7 TraesCS2D01G353200 chr2B 84.541 414 32 8 751 1146 531720723 531720324 7.780000e-102 381.0
8 TraesCS2D01G353200 chr2A 92.820 1713 109 9 1227 2931 597845431 597847137 0.000000e+00 2470.0
9 TraesCS2D01G353200 chr2A 94.715 719 30 6 3123 3838 597848853 597849566 0.000000e+00 1110.0
10 TraesCS2D01G353200 chr2A 86.874 419 27 12 751 1146 597845018 597845431 9.780000e-121 444.0
11 TraesCS2D01G353200 chr2A 89.535 86 7 2 583 667 184649372 184649456 1.460000e-19 108.0
12 TraesCS2D01G353200 chr2A 85.000 100 11 4 587 683 822761 822663 8.770000e-17 99.0
13 TraesCS2D01G353200 chr7D 90.347 663 52 4 17 668 359150746 359151407 0.000000e+00 859.0
14 TraesCS2D01G353200 chr6A 89.003 682 53 8 1 669 539722007 539722679 0.000000e+00 824.0
15 TraesCS2D01G353200 chr6B 86.784 681 67 11 4 668 205348376 205347703 0.000000e+00 737.0
16 TraesCS2D01G353200 chr7A 83.731 670 84 18 18 672 137918247 137918906 9.120000e-171 610.0
17 TraesCS2D01G353200 chr7A 88.991 109 12 0 2723 2831 40256795 40256687 6.690000e-28 135.0
18 TraesCS2D01G353200 chr1D 91.542 402 25 5 1 400 411693897 411694291 2.610000e-151 545.0
19 TraesCS2D01G353200 chr1D 92.268 388 21 5 15 400 411718401 411718781 3.370000e-150 542.0
20 TraesCS2D01G353200 chr1D 85.507 207 17 6 475 669 411694275 411694480 1.810000e-48 204.0
21 TraesCS2D01G353200 chr1D 82.805 221 16 8 475 674 411718765 411718984 1.100000e-40 178.0
22 TraesCS2D01G353200 chr1B 82.569 109 14 4 561 667 611686126 611686021 1.470000e-14 91.6


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 TraesCS2D01G353200 chr2D 451458433 451462270 3837 True 7088.000000 7088 100.000000 1 3838 1 chr2D.!!$R3 3837
1 TraesCS2D01G353200 chr2D 120986329 120986967 638 True 604.000000 604 83.857000 7 669 1 chr2D.!!$R1 662
2 TraesCS2D01G353200 chr2D 166941448 166942084 636 True 527.000000 527 82.192000 6 641 1 chr2D.!!$R2 635
3 TraesCS2D01G353200 chr2B 531717673 531720723 3050 True 1473.666667 2695 91.648333 751 3838 3 chr2B.!!$R1 3087
4 TraesCS2D01G353200 chr2B 75343655 75344308 653 False 778.000000 778 88.393000 1 657 1 chr2B.!!$F1 656
5 TraesCS2D01G353200 chr2A 597845018 597849566 4548 False 1341.333333 2470 91.469667 751 3838 3 chr2A.!!$F2 3087
6 TraesCS2D01G353200 chr7D 359150746 359151407 661 False 859.000000 859 90.347000 17 668 1 chr7D.!!$F1 651
7 TraesCS2D01G353200 chr6A 539722007 539722679 672 False 824.000000 824 89.003000 1 669 1 chr6A.!!$F1 668
8 TraesCS2D01G353200 chr6B 205347703 205348376 673 True 737.000000 737 86.784000 4 668 1 chr6B.!!$R1 664
9 TraesCS2D01G353200 chr7A 137918247 137918906 659 False 610.000000 610 83.731000 18 672 1 chr7A.!!$F1 654
10 TraesCS2D01G353200 chr1D 411693897 411694480 583 False 374.500000 545 88.524500 1 669 2 chr1D.!!$F1 668
11 TraesCS2D01G353200 chr1D 411718401 411718984 583 False 360.000000 542 87.536500 15 674 2 chr1D.!!$F2 659

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
877 918 1.278985 TCTCATCAGCACCGTCCATTT 59.721 47.619 0.0 0.0 0.0 2.32 F
1657 1717 0.042131 TGGTTATGAGGTCCGAGGGT 59.958 55.000 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2780 2845 0.175760 TCTTGCAGTAGGTCGATGCC 59.824 55.000 5.55 0.0 39.22 4.40 R
3102 4732 1.663135 GAGAATTCAAGCGACTCTGGC 59.337 52.381 8.44 0.0 0.00 4.85 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
281 290 4.361451 CGGAGCTGCAATTTTTAGACAT 57.639 40.909 5.91 0.00 0.00 3.06
303 312 6.488006 ACATCAAATTGAAGAACTACACTGCT 59.512 34.615 5.15 0.00 0.00 4.24
345 355 2.159841 CGCTAGGTGTTGTGTTCGATTG 60.160 50.000 0.00 0.00 0.00 2.67
354 365 4.572795 TGTTGTGTTCGATTGCACTTTAGA 59.427 37.500 13.72 0.00 36.63 2.10
426 437 5.239744 TCTTTTAATTAAAGGTCACGCAGCA 59.760 36.000 16.85 0.00 42.88 4.41
433 444 3.559238 AAGGTCACGCAGCAATTTTAG 57.441 42.857 0.00 0.00 0.00 1.85
434 445 2.504367 AGGTCACGCAGCAATTTTAGT 58.496 42.857 0.00 0.00 0.00 2.24
436 447 3.435671 AGGTCACGCAGCAATTTTAGTAC 59.564 43.478 0.00 0.00 0.00 2.73
510 522 1.611261 AGGTTCGATTCCCACCCGA 60.611 57.895 0.00 0.00 0.00 5.14
553 583 3.729965 CTCAGCGCGAGGCCAGATT 62.730 63.158 12.10 0.00 45.17 2.40
555 585 1.301244 CAGCGCGAGGCCAGATTAT 60.301 57.895 12.10 0.00 45.17 1.28
575 605 8.293867 AGATTATTTTTGGACGAACGAAAATCA 58.706 29.630 18.45 12.27 41.31 2.57
791 832 3.434167 CCCGAATCCCACATCTTCATCTT 60.434 47.826 0.00 0.00 0.00 2.40
821 862 2.124278 GACGGCCTTCCCATTCCC 60.124 66.667 0.00 0.00 0.00 3.97
877 918 1.278985 TCTCATCAGCACCGTCCATTT 59.721 47.619 0.00 0.00 0.00 2.32
971 1028 4.596585 CCCCACCCACCCACACAC 62.597 72.222 0.00 0.00 0.00 3.82
972 1029 3.814906 CCCACCCACCCACACACA 61.815 66.667 0.00 0.00 0.00 3.72
973 1030 2.518349 CCACCCACCCACACACAC 60.518 66.667 0.00 0.00 0.00 3.82
974 1031 2.273776 CACCCACCCACACACACA 59.726 61.111 0.00 0.00 0.00 3.72
975 1032 2.118404 CACCCACCCACACACACAC 61.118 63.158 0.00 0.00 0.00 3.82
977 1034 2.118404 CCCACCCACACACACACAC 61.118 63.158 0.00 0.00 0.00 3.82
980 1037 1.377987 ACCCACACACACACACACC 60.378 57.895 0.00 0.00 0.00 4.16
981 1038 2.118404 CCCACACACACACACACCC 61.118 63.158 0.00 0.00 0.00 4.61
982 1039 2.118404 CCACACACACACACACCCC 61.118 63.158 0.00 0.00 0.00 4.95
983 1040 2.118404 CACACACACACACACCCCC 61.118 63.158 0.00 0.00 0.00 5.40
1086 1146 0.836400 TCTCCTTCCCCGCTTGAAGT 60.836 55.000 0.00 0.00 38.00 3.01
1090 1150 1.005394 TTCCCCGCTTGAAGTCGAC 60.005 57.895 7.70 7.70 0.00 4.20
1094 1154 2.027625 CCGCTTGAAGTCGACCACC 61.028 63.158 13.01 2.04 0.00 4.61
1104 1164 3.740397 CGACCACCGCTCGTACCA 61.740 66.667 0.00 0.00 0.00 3.25
1105 1165 2.126189 GACCACCGCTCGTACCAC 60.126 66.667 0.00 0.00 0.00 4.16
1121 1181 1.419922 CACAAATCTCGCCGGTTCG 59.580 57.895 1.90 0.00 0.00 3.95
1133 1193 2.722201 CGGTTCGGAGCCTAGCCTT 61.722 63.158 9.30 0.00 0.00 4.35
1146 1206 3.004106 GCCTAGCCTTACAATTGATGCAG 59.996 47.826 13.59 8.44 0.00 4.41
1147 1207 4.454678 CCTAGCCTTACAATTGATGCAGA 58.545 43.478 13.59 1.14 0.00 4.26
1148 1208 4.883585 CCTAGCCTTACAATTGATGCAGAA 59.116 41.667 13.59 0.00 0.00 3.02
1149 1209 5.533903 CCTAGCCTTACAATTGATGCAGAAT 59.466 40.000 13.59 0.00 0.00 2.40
1150 1210 5.927281 AGCCTTACAATTGATGCAGAATT 57.073 34.783 13.59 0.00 0.00 2.17
1151 1211 7.229306 CCTAGCCTTACAATTGATGCAGAATTA 59.771 37.037 13.59 0.00 0.00 1.40
1152 1212 6.799512 AGCCTTACAATTGATGCAGAATTAC 58.200 36.000 13.59 0.00 0.00 1.89
1153 1213 5.979517 GCCTTACAATTGATGCAGAATTACC 59.020 40.000 13.59 0.00 0.00 2.85
1154 1214 6.507023 CCTTACAATTGATGCAGAATTACCC 58.493 40.000 13.59 0.00 0.00 3.69
1155 1215 6.461509 CCTTACAATTGATGCAGAATTACCCC 60.462 42.308 13.59 0.00 0.00 4.95
1156 1216 3.706086 ACAATTGATGCAGAATTACCCCC 59.294 43.478 13.59 0.00 0.00 5.40
1170 1230 3.270000 CCCCCGACGCGAAATTTT 58.730 55.556 15.93 0.00 0.00 1.82
1171 1231 1.154112 CCCCCGACGCGAAATTTTG 60.154 57.895 15.93 0.59 0.00 2.44
1172 1232 1.579084 CCCCCGACGCGAAATTTTGA 61.579 55.000 15.93 0.00 0.00 2.69
1173 1233 0.453782 CCCCGACGCGAAATTTTGAC 60.454 55.000 15.93 0.27 0.00 3.18
1174 1234 0.453782 CCCGACGCGAAATTTTGACC 60.454 55.000 15.93 0.00 0.00 4.02
1175 1235 0.515564 CCGACGCGAAATTTTGACCT 59.484 50.000 15.93 0.00 0.00 3.85
1176 1236 1.591248 CGACGCGAAATTTTGACCTG 58.409 50.000 15.93 0.00 0.00 4.00
1177 1237 1.070175 CGACGCGAAATTTTGACCTGT 60.070 47.619 15.93 1.72 0.00 4.00
1178 1238 2.307049 GACGCGAAATTTTGACCTGTG 58.693 47.619 15.93 0.00 0.00 3.66
1179 1239 1.673920 ACGCGAAATTTTGACCTGTGT 59.326 42.857 15.93 0.00 0.00 3.72
1180 1240 2.098443 ACGCGAAATTTTGACCTGTGTT 59.902 40.909 15.93 0.00 0.00 3.32
1181 1241 2.719046 CGCGAAATTTTGACCTGTGTTC 59.281 45.455 9.75 0.00 0.00 3.18
1182 1242 2.719046 GCGAAATTTTGACCTGTGTTCG 59.281 45.455 9.75 0.00 39.38 3.95
1183 1243 3.790789 GCGAAATTTTGACCTGTGTTCGT 60.791 43.478 9.75 0.00 38.79 3.85
1184 1244 4.347813 CGAAATTTTGACCTGTGTTCGTT 58.652 39.130 0.00 0.00 33.55 3.85
1185 1245 4.436523 CGAAATTTTGACCTGTGTTCGTTC 59.563 41.667 0.00 0.00 33.55 3.95
1186 1246 5.576447 AAATTTTGACCTGTGTTCGTTCT 57.424 34.783 0.00 0.00 0.00 3.01
1187 1247 4.813296 ATTTTGACCTGTGTTCGTTCTC 57.187 40.909 0.00 0.00 0.00 2.87
1188 1248 2.971660 TTGACCTGTGTTCGTTCTCA 57.028 45.000 0.00 0.00 0.00 3.27
1189 1249 3.469008 TTGACCTGTGTTCGTTCTCAT 57.531 42.857 0.00 0.00 0.00 2.90
1190 1250 3.469008 TGACCTGTGTTCGTTCTCATT 57.531 42.857 0.00 0.00 0.00 2.57
1191 1251 3.804036 TGACCTGTGTTCGTTCTCATTT 58.196 40.909 0.00 0.00 0.00 2.32
1192 1252 3.807622 TGACCTGTGTTCGTTCTCATTTC 59.192 43.478 0.00 0.00 0.00 2.17
1193 1253 3.139077 ACCTGTGTTCGTTCTCATTTCC 58.861 45.455 0.00 0.00 0.00 3.13
1194 1254 3.181454 ACCTGTGTTCGTTCTCATTTCCT 60.181 43.478 0.00 0.00 0.00 3.36
1195 1255 3.815401 CCTGTGTTCGTTCTCATTTCCTT 59.185 43.478 0.00 0.00 0.00 3.36
1196 1256 4.083802 CCTGTGTTCGTTCTCATTTCCTTC 60.084 45.833 0.00 0.00 0.00 3.46
1197 1257 3.813166 TGTGTTCGTTCTCATTTCCTTCC 59.187 43.478 0.00 0.00 0.00 3.46
1198 1258 3.813166 GTGTTCGTTCTCATTTCCTTCCA 59.187 43.478 0.00 0.00 0.00 3.53
1199 1259 4.274950 GTGTTCGTTCTCATTTCCTTCCAA 59.725 41.667 0.00 0.00 0.00 3.53
1200 1260 4.515191 TGTTCGTTCTCATTTCCTTCCAAG 59.485 41.667 0.00 0.00 0.00 3.61
1201 1261 4.351874 TCGTTCTCATTTCCTTCCAAGT 57.648 40.909 0.00 0.00 0.00 3.16
1202 1262 4.065088 TCGTTCTCATTTCCTTCCAAGTG 58.935 43.478 0.00 0.00 0.00 3.16
1203 1263 3.189287 CGTTCTCATTTCCTTCCAAGTGG 59.811 47.826 0.00 0.00 0.00 4.00
1204 1264 4.398319 GTTCTCATTTCCTTCCAAGTGGA 58.602 43.478 0.00 0.00 43.73 4.02
1205 1265 4.292186 TCTCATTTCCTTCCAAGTGGAG 57.708 45.455 0.00 0.00 46.36 3.86
1206 1266 3.009473 TCTCATTTCCTTCCAAGTGGAGG 59.991 47.826 2.51 2.51 46.36 4.30
1211 1271 2.155065 CTTCCAAGTGGAGGGGTGT 58.845 57.895 1.53 0.00 46.36 4.16
1212 1272 0.478507 CTTCCAAGTGGAGGGGTGTT 59.521 55.000 1.53 0.00 46.36 3.32
1213 1273 0.930726 TTCCAAGTGGAGGGGTGTTT 59.069 50.000 0.00 0.00 46.36 2.83
1214 1274 0.184933 TCCAAGTGGAGGGGTGTTTG 59.815 55.000 0.00 0.00 39.78 2.93
1215 1275 0.184933 CCAAGTGGAGGGGTGTTTGA 59.815 55.000 0.00 0.00 37.39 2.69
1216 1276 1.203050 CCAAGTGGAGGGGTGTTTGAT 60.203 52.381 0.00 0.00 37.39 2.57
1217 1277 1.888512 CAAGTGGAGGGGTGTTTGATG 59.111 52.381 0.00 0.00 0.00 3.07
1218 1278 0.251341 AGTGGAGGGGTGTTTGATGC 60.251 55.000 0.00 0.00 0.00 3.91
1219 1279 0.251341 GTGGAGGGGTGTTTGATGCT 60.251 55.000 0.00 0.00 0.00 3.79
1220 1280 0.482446 TGGAGGGGTGTTTGATGCTT 59.518 50.000 0.00 0.00 0.00 3.91
1221 1281 1.177401 GGAGGGGTGTTTGATGCTTC 58.823 55.000 0.00 0.00 0.00 3.86
1222 1282 1.177401 GAGGGGTGTTTGATGCTTCC 58.823 55.000 0.00 0.00 0.00 3.46
1223 1283 0.482446 AGGGGTGTTTGATGCTTCCA 59.518 50.000 0.00 0.00 0.00 3.53
1224 1284 1.133199 AGGGGTGTTTGATGCTTCCAA 60.133 47.619 0.00 0.00 0.00 3.53
1225 1285 1.691434 GGGGTGTTTGATGCTTCCAAA 59.309 47.619 0.00 0.00 0.00 3.28
1226 1286 2.103941 GGGGTGTTTGATGCTTCCAAAA 59.896 45.455 0.00 0.00 35.57 2.44
1271 1331 0.329596 GGTGCCTTCCAGATTCACCT 59.670 55.000 0.00 0.00 42.77 4.00
1494 1554 1.488705 CCACAGGGCCTACCACAAGA 61.489 60.000 5.28 0.00 43.89 3.02
1560 1620 5.321959 TGTTCTTTTGTGAATTGCAGTGA 57.678 34.783 0.00 0.00 0.00 3.41
1572 1632 1.180456 TGCAGTGACATTGCCCTTGG 61.180 55.000 18.99 0.00 40.81 3.61
1576 1636 0.603065 GTGACATTGCCCTTGGTTCC 59.397 55.000 0.00 0.00 0.00 3.62
1590 1650 4.398319 CTTGGTTCCTGTGTTTCTATGGT 58.602 43.478 0.00 0.00 0.00 3.55
1605 1665 6.627087 TTCTATGGTTGGAGAGTTTCTGAT 57.373 37.500 0.00 0.00 0.00 2.90
1612 1672 2.420372 TGGAGAGTTTCTGATCGACGAG 59.580 50.000 3.01 0.00 0.00 4.18
1613 1673 2.420722 GGAGAGTTTCTGATCGACGAGT 59.579 50.000 3.01 0.00 0.00 4.18
1657 1717 0.042131 TGGTTATGAGGTCCGAGGGT 59.958 55.000 0.00 0.00 0.00 4.34
1696 1756 1.689959 CAAGCGGTGAAAACTCATGC 58.310 50.000 0.00 0.00 0.00 4.06
1737 1797 6.421377 AATTTTTGCCAAACTCACTTTGTC 57.579 33.333 0.00 0.00 38.08 3.18
1765 1826 6.313411 GTCAGATCCATGACTTTCTGAAGAAG 59.687 42.308 14.35 0.00 44.39 2.85
1847 1908 2.664402 AGCCTGAACCACTTCACAAT 57.336 45.000 0.00 0.00 32.68 2.71
1921 1983 8.537728 TGAGATTTAGGATGCAACCATTTAAT 57.462 30.769 16.21 8.41 0.00 1.40
2036 2101 6.847421 AGGTAAGTTACAGTCGTAATTCCT 57.153 37.500 14.81 0.00 39.72 3.36
2087 2152 9.539825 AATGCAATATGTTTTGTGTTACTGAAA 57.460 25.926 0.00 0.00 0.00 2.69
2179 2244 0.796312 ACCGATAAAAGCAGCACACG 59.204 50.000 0.00 0.00 0.00 4.49
2253 2318 1.884579 ACTGAATCAGCACAGGCAAAG 59.115 47.619 10.62 0.00 44.61 2.77
2361 2426 1.915078 GCCCTGGTGCCATAGTCTGT 61.915 60.000 0.00 0.00 0.00 3.41
2442 2507 3.198872 CAGAAGAAAGGGAATAGCGTCC 58.801 50.000 0.00 0.00 36.90 4.79
2461 2526 2.203195 AGCTTGTGGACGCTGCAA 60.203 55.556 0.00 0.00 34.69 4.08
2467 2532 1.301401 GTGGACGCTGCAAGGTACA 60.301 57.895 0.00 0.00 0.00 2.90
2470 2535 1.276705 TGGACGCTGCAAGGTACATTA 59.723 47.619 0.00 0.00 0.00 1.90
2519 2584 5.559770 TCATGCCTTGAAAACTCATCACTA 58.440 37.500 0.00 0.00 0.00 2.74
2521 2586 5.885230 TGCCTTGAAAACTCATCACTATG 57.115 39.130 0.00 0.00 0.00 2.23
2524 2589 6.149973 TGCCTTGAAAACTCATCACTATGAAG 59.850 38.462 0.00 0.00 41.57 3.02
2541 2606 2.833943 TGAAGCATGCACTCTTCTCCTA 59.166 45.455 21.98 7.16 39.41 2.94
2563 2628 3.498774 ACAAGGGGACATGATAGCATC 57.501 47.619 0.00 0.00 30.68 3.91
2640 2705 7.083062 TGATATCACCCTGCAAAGATAGATT 57.917 36.000 0.00 0.00 0.00 2.40
2725 2790 2.970974 GCTTCTGTGAAGGCGGCAC 61.971 63.158 13.08 5.41 36.81 5.01
2756 2821 0.311790 CACAATGTGCTTTCACGCCT 59.688 50.000 0.00 0.00 46.01 5.52
2780 2845 0.540923 CCTCTGAAGGGAAGGAGCTG 59.459 60.000 0.00 0.00 39.21 4.24
2970 3036 5.048083 TCAATGCACATAAAGTTCCTGTTCC 60.048 40.000 0.00 0.00 0.00 3.62
3059 4689 1.148310 CAATATAGCCAAGGCCGTCG 58.852 55.000 7.62 0.00 43.17 5.12
3129 4759 7.343691 CAGAGTCGCTTGAATTCTCATATTTC 58.656 38.462 7.05 0.00 0.00 2.17
3132 4805 8.218338 AGTCGCTTGAATTCTCATATTTCATT 57.782 30.769 7.05 0.00 29.90 2.57
3206 4879 2.725221 ATCCAAGGCTTGACTGATCC 57.275 50.000 28.18 0.00 0.00 3.36
3250 4923 7.269937 CGAACTTGAACAAAAGCTCAATAGATG 59.730 37.037 0.00 0.00 31.40 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
281 290 6.942532 AAGCAGTGTAGTTCTTCAATTTGA 57.057 33.333 0.00 0.00 0.00 2.69
303 312 1.338011 CGAGTTAACCACGCCCCTAAA 60.338 52.381 0.88 0.00 0.00 1.85
327 337 2.546368 GTGCAATCGAACACAACACCTA 59.454 45.455 10.64 0.00 36.77 3.08
345 355 6.487689 AGCAAAAGTCTATGTCTAAAGTGC 57.512 37.500 0.00 0.00 0.00 4.40
433 444 4.062293 TGCGGCCATATATGTTTCAGTAC 58.938 43.478 11.73 0.00 0.00 2.73
434 445 4.062293 GTGCGGCCATATATGTTTCAGTA 58.938 43.478 11.73 0.00 0.00 2.74
436 447 3.058708 CAGTGCGGCCATATATGTTTCAG 60.059 47.826 11.73 3.07 0.00 3.02
473 485 1.154035 GCAACCGGCAGCATGTAAC 60.154 57.895 13.33 0.00 43.97 2.50
553 583 7.327275 CCAATGATTTTCGTTCGTCCAAAAATA 59.673 33.333 0.00 0.00 32.90 1.40
555 585 5.460419 CCAATGATTTTCGTTCGTCCAAAAA 59.540 36.000 0.00 0.00 0.00 1.94
575 605 1.187974 TCGTCCGTCATGGTACCAAT 58.812 50.000 20.76 4.78 39.52 3.16
742 783 0.458260 ACAACCGCGAAAGGCTTTTT 59.542 45.000 14.66 0.72 40.44 1.94
743 784 0.458260 AACAACCGCGAAAGGCTTTT 59.542 45.000 14.66 0.00 40.44 2.27
744 785 0.458260 AAACAACCGCGAAAGGCTTT 59.542 45.000 13.25 13.25 40.44 3.51
745 786 0.458260 AAAACAACCGCGAAAGGCTT 59.542 45.000 8.23 0.00 40.44 4.35
746 787 0.248866 CAAAACAACCGCGAAAGGCT 60.249 50.000 8.23 0.00 40.44 4.58
747 788 1.212455 CCAAAACAACCGCGAAAGGC 61.212 55.000 8.23 0.00 38.69 4.35
748 789 1.212455 GCCAAAACAACCGCGAAAGG 61.212 55.000 8.23 0.00 37.30 3.11
749 790 2.212579 GCCAAAACAACCGCGAAAG 58.787 52.632 8.23 0.00 0.00 2.62
750 791 4.403976 GCCAAAACAACCGCGAAA 57.596 50.000 8.23 0.00 0.00 3.46
821 862 2.835431 AGGAGATCGGACGGGCAG 60.835 66.667 0.00 0.00 0.00 4.85
954 1011 4.596585 GTGTGTGGGTGGGTGGGG 62.597 72.222 0.00 0.00 0.00 4.96
955 1012 3.814906 TGTGTGTGGGTGGGTGGG 61.815 66.667 0.00 0.00 0.00 4.61
958 1015 2.274104 GTGTGTGTGTGGGTGGGT 59.726 61.111 0.00 0.00 0.00 4.51
962 1019 1.377987 GGTGTGTGTGTGTGTGGGT 60.378 57.895 0.00 0.00 0.00 4.51
966 1023 2.274104 GGGGGTGTGTGTGTGTGT 59.726 61.111 0.00 0.00 0.00 3.72
982 1039 4.560856 CTTCTCGCGCTCTCGGGG 62.561 72.222 5.56 0.00 46.85 5.73
984 1041 1.656875 CATCTTCTCGCGCTCTCGG 60.657 63.158 5.56 0.00 35.95 4.63
985 1042 2.292206 GCATCTTCTCGCGCTCTCG 61.292 63.158 5.56 0.00 39.07 4.04
997 1057 2.097825 GTTGATCTTGGGCTGCATCTT 58.902 47.619 0.50 0.00 0.00 2.40
1090 1150 0.672401 ATTTGTGGTACGAGCGGTGG 60.672 55.000 0.00 0.00 0.00 4.61
1094 1154 0.914551 CGAGATTTGTGGTACGAGCG 59.085 55.000 0.00 0.00 0.00 5.03
1104 1164 1.740296 CCGAACCGGCGAGATTTGT 60.740 57.895 9.30 0.00 41.17 2.83
1105 1165 3.089784 CCGAACCGGCGAGATTTG 58.910 61.111 9.30 3.56 41.17 2.32
1121 1181 3.560636 TCAATTGTAAGGCTAGGCTCC 57.439 47.619 20.50 13.55 0.00 4.70
1133 1193 4.892934 GGGGGTAATTCTGCATCAATTGTA 59.107 41.667 5.13 0.00 0.00 2.41
1153 1213 1.154112 CAAAATTTCGCGTCGGGGG 60.154 57.895 5.77 0.00 0.00 5.40
1154 1214 0.453782 GTCAAAATTTCGCGTCGGGG 60.454 55.000 5.77 0.00 0.00 5.73
1155 1215 0.453782 GGTCAAAATTTCGCGTCGGG 60.454 55.000 5.77 2.31 0.00 5.14
1156 1216 0.515564 AGGTCAAAATTTCGCGTCGG 59.484 50.000 5.77 0.00 0.00 4.79
1157 1217 1.070175 ACAGGTCAAAATTTCGCGTCG 60.070 47.619 5.77 0.00 0.00 5.12
1158 1218 2.286772 ACACAGGTCAAAATTTCGCGTC 60.287 45.455 5.77 0.00 0.00 5.19
1159 1219 1.673920 ACACAGGTCAAAATTTCGCGT 59.326 42.857 5.77 0.00 0.00 6.01
1160 1220 2.399396 ACACAGGTCAAAATTTCGCG 57.601 45.000 0.00 0.00 0.00 5.87
1161 1221 2.719046 CGAACACAGGTCAAAATTTCGC 59.281 45.455 0.00 0.00 0.00 4.70
1162 1222 3.947626 ACGAACACAGGTCAAAATTTCG 58.052 40.909 0.00 0.00 40.07 3.46
1163 1223 5.578776 AGAACGAACACAGGTCAAAATTTC 58.421 37.500 0.00 0.00 0.00 2.17
1164 1224 5.124776 TGAGAACGAACACAGGTCAAAATTT 59.875 36.000 0.00 0.00 0.00 1.82
1165 1225 4.638421 TGAGAACGAACACAGGTCAAAATT 59.362 37.500 0.00 0.00 0.00 1.82
1166 1226 4.196193 TGAGAACGAACACAGGTCAAAAT 58.804 39.130 0.00 0.00 0.00 1.82
1167 1227 3.601435 TGAGAACGAACACAGGTCAAAA 58.399 40.909 0.00 0.00 0.00 2.44
1168 1228 3.254470 TGAGAACGAACACAGGTCAAA 57.746 42.857 0.00 0.00 0.00 2.69
1169 1229 2.971660 TGAGAACGAACACAGGTCAA 57.028 45.000 0.00 0.00 0.00 3.18
1170 1230 3.469008 AATGAGAACGAACACAGGTCA 57.531 42.857 0.00 0.00 0.00 4.02
1171 1231 3.186613 GGAAATGAGAACGAACACAGGTC 59.813 47.826 0.00 0.00 0.00 3.85
1172 1232 3.139077 GGAAATGAGAACGAACACAGGT 58.861 45.455 0.00 0.00 0.00 4.00
1173 1233 3.403038 AGGAAATGAGAACGAACACAGG 58.597 45.455 0.00 0.00 0.00 4.00
1174 1234 4.083802 GGAAGGAAATGAGAACGAACACAG 60.084 45.833 0.00 0.00 0.00 3.66
1175 1235 3.813166 GGAAGGAAATGAGAACGAACACA 59.187 43.478 0.00 0.00 0.00 3.72
1176 1236 3.813166 TGGAAGGAAATGAGAACGAACAC 59.187 43.478 0.00 0.00 0.00 3.32
1177 1237 4.079980 TGGAAGGAAATGAGAACGAACA 57.920 40.909 0.00 0.00 0.00 3.18
1178 1238 4.515567 ACTTGGAAGGAAATGAGAACGAAC 59.484 41.667 0.00 0.00 0.00 3.95
1179 1239 4.515191 CACTTGGAAGGAAATGAGAACGAA 59.485 41.667 0.00 0.00 0.00 3.85
1180 1240 4.065088 CACTTGGAAGGAAATGAGAACGA 58.935 43.478 0.00 0.00 0.00 3.85
1181 1241 3.189287 CCACTTGGAAGGAAATGAGAACG 59.811 47.826 0.00 0.00 37.39 3.95
1182 1242 4.398319 TCCACTTGGAAGGAAATGAGAAC 58.602 43.478 0.00 0.00 42.18 3.01
1183 1243 4.507335 CCTCCACTTGGAAGGAAATGAGAA 60.507 45.833 0.00 0.00 44.91 2.87
1184 1244 3.009473 CCTCCACTTGGAAGGAAATGAGA 59.991 47.826 0.00 0.00 44.91 3.27
1185 1245 3.350833 CCTCCACTTGGAAGGAAATGAG 58.649 50.000 0.00 0.00 44.91 2.90
1186 1246 2.041620 CCCTCCACTTGGAAGGAAATGA 59.958 50.000 7.07 0.00 46.61 2.57
1187 1247 2.450476 CCCTCCACTTGGAAGGAAATG 58.550 52.381 7.07 0.00 46.61 2.32
1188 1248 1.359130 CCCCTCCACTTGGAAGGAAAT 59.641 52.381 13.80 0.00 46.61 2.17
1189 1249 0.777446 CCCCTCCACTTGGAAGGAAA 59.223 55.000 13.80 0.00 46.61 3.13
1190 1250 0.402861 ACCCCTCCACTTGGAAGGAA 60.403 55.000 13.80 0.00 46.61 3.36
1191 1251 1.133809 CACCCCTCCACTTGGAAGGA 61.134 60.000 13.80 0.00 46.61 3.36
1192 1252 1.380302 CACCCCTCCACTTGGAAGG 59.620 63.158 5.97 5.97 44.91 3.46
1193 1253 0.478507 AACACCCCTCCACTTGGAAG 59.521 55.000 0.00 0.00 44.91 3.46
1194 1254 0.930726 AAACACCCCTCCACTTGGAA 59.069 50.000 0.00 0.00 44.91 3.53
1195 1255 0.184933 CAAACACCCCTCCACTTGGA 59.815 55.000 0.00 0.00 43.08 3.53
1196 1256 0.184933 TCAAACACCCCTCCACTTGG 59.815 55.000 0.00 0.00 0.00 3.61
1197 1257 1.888512 CATCAAACACCCCTCCACTTG 59.111 52.381 0.00 0.00 0.00 3.16
1198 1258 1.823250 GCATCAAACACCCCTCCACTT 60.823 52.381 0.00 0.00 0.00 3.16
1199 1259 0.251341 GCATCAAACACCCCTCCACT 60.251 55.000 0.00 0.00 0.00 4.00
1200 1260 0.251341 AGCATCAAACACCCCTCCAC 60.251 55.000 0.00 0.00 0.00 4.02
1201 1261 0.482446 AAGCATCAAACACCCCTCCA 59.518 50.000 0.00 0.00 0.00 3.86
1202 1262 1.177401 GAAGCATCAAACACCCCTCC 58.823 55.000 0.00 0.00 0.00 4.30
1203 1263 1.177401 GGAAGCATCAAACACCCCTC 58.823 55.000 0.00 0.00 0.00 4.30
1204 1264 0.482446 TGGAAGCATCAAACACCCCT 59.518 50.000 0.00 0.00 0.00 4.79
1205 1265 1.337118 TTGGAAGCATCAAACACCCC 58.663 50.000 0.00 0.00 0.00 4.95
1206 1266 3.467374 TTTTGGAAGCATCAAACACCC 57.533 42.857 0.00 0.00 34.34 4.61
1207 1267 4.886579 AGATTTTGGAAGCATCAAACACC 58.113 39.130 0.00 0.00 34.34 4.16
1208 1268 6.219302 CAAGATTTTGGAAGCATCAAACAC 57.781 37.500 0.00 0.00 34.34 3.32
1222 1282 7.333423 TCGGTGTAGAATACTTCCAAGATTTTG 59.667 37.037 0.00 0.00 43.54 2.44
1223 1283 7.391620 TCGGTGTAGAATACTTCCAAGATTTT 58.608 34.615 0.00 0.00 43.54 1.82
1224 1284 6.942976 TCGGTGTAGAATACTTCCAAGATTT 58.057 36.000 0.00 0.00 43.54 2.17
1225 1285 6.540438 TCGGTGTAGAATACTTCCAAGATT 57.460 37.500 0.00 0.00 43.54 2.40
1226 1286 6.540438 TTCGGTGTAGAATACTTCCAAGAT 57.460 37.500 0.00 0.00 43.54 2.40
1271 1331 0.963225 TCGACACGGATCAGTCCAAA 59.037 50.000 0.00 0.00 45.37 3.28
1311 1371 3.453679 GAGCCTCTTCGCCTCCGT 61.454 66.667 0.00 0.00 35.54 4.69
1494 1554 2.829458 GACGCCCTCGAGGTAGCT 60.829 66.667 29.25 15.51 39.41 3.32
1560 1620 0.188342 ACAGGAACCAAGGGCAATGT 59.812 50.000 0.00 0.00 0.00 2.71
1572 1632 4.394729 TCCAACCATAGAAACACAGGAAC 58.605 43.478 0.00 0.00 0.00 3.62
1576 1636 4.899502 ACTCTCCAACCATAGAAACACAG 58.100 43.478 0.00 0.00 0.00 3.66
1590 1650 2.817844 TCGTCGATCAGAAACTCTCCAA 59.182 45.455 0.00 0.00 0.00 3.53
1605 1665 1.300620 CAACCCTGCAACTCGTCGA 60.301 57.895 0.00 0.00 0.00 4.20
1657 1717 3.035363 TGCTAGAATTATCCGGTCACCA 58.965 45.455 0.00 0.00 0.00 4.17
1696 1756 5.560966 AAATTACCTTGCTGTTCCGTATG 57.439 39.130 0.00 0.00 0.00 2.39
1737 1797 5.425630 TCAGAAAGTCATGGATCTGACATG 58.574 41.667 15.28 10.09 46.45 3.21
1765 1826 4.377897 ACCAGTTAACTTACAGTCTGCAC 58.622 43.478 5.07 0.00 0.00 4.57
1781 1842 4.040461 ACACACAGATTACAGCTACCAGTT 59.960 41.667 0.00 0.00 0.00 3.16
1786 1847 4.207224 CGCATACACACAGATTACAGCTAC 59.793 45.833 0.00 0.00 0.00 3.58
1847 1908 7.807433 CGTTTCTAATGTCAAAATGTGGATTGA 59.193 33.333 0.00 0.00 33.37 2.57
1894 1955 6.855763 AATGGTTGCATCCTAAATCTCAAA 57.144 33.333 14.81 0.00 0.00 2.69
1921 1983 8.933653 TCCTGAACCTGAAATATGTACATGATA 58.066 33.333 18.81 0.00 0.00 2.15
2087 2152 6.006449 ACCTATGCAACAGAGATGTTCTTTT 58.994 36.000 0.00 0.00 32.41 2.27
2179 2244 4.260538 CGATGCAGAGCTTGGAATAACTTC 60.261 45.833 0.00 0.00 0.00 3.01
2253 2318 4.799564 TTTCCCAAACTCCAATGTATGC 57.200 40.909 0.00 0.00 0.00 3.14
2361 2426 0.603707 CGGGCACAGCTTCTTCTTCA 60.604 55.000 0.00 0.00 0.00 3.02
2461 2526 2.514726 AGGGCCTGGATAATGTACCT 57.485 50.000 4.50 0.00 0.00 3.08
2467 2532 2.690936 GCAAGGAAAGGGCCTGGATAAT 60.691 50.000 6.92 0.00 38.58 1.28
2470 2535 1.000866 GCAAGGAAAGGGCCTGGAT 59.999 57.895 6.92 0.00 38.58 3.41
2519 2584 2.239150 AGGAGAAGAGTGCATGCTTCAT 59.761 45.455 24.41 9.60 42.21 2.57
2521 2586 2.399916 AGGAGAAGAGTGCATGCTTC 57.600 50.000 20.33 18.48 40.54 3.86
2524 2589 3.338249 TGTTTAGGAGAAGAGTGCATGC 58.662 45.455 11.82 11.82 0.00 4.06
2541 2606 3.737559 TGCTATCATGTCCCCTTGTTT 57.262 42.857 0.00 0.00 0.00 2.83
2563 2628 6.347079 GCAATCTGGTGAAAAATTGACACATG 60.347 38.462 0.00 0.00 36.42 3.21
2573 2638 7.230849 AGAATGTATGCAATCTGGTGAAAAA 57.769 32.000 0.02 0.00 33.88 1.94
2640 2705 1.086696 GCAAGCTCGATAAACCAGCA 58.913 50.000 0.00 0.00 35.46 4.41
2725 2790 1.739466 CACATTGTGAGATCCCCAACG 59.261 52.381 11.45 0.00 35.23 4.10
2756 2821 1.132527 TCCTTCCCTTCAGAGGTTGGA 60.133 52.381 0.00 0.00 41.85 3.53
2780 2845 0.175760 TCTTGCAGTAGGTCGATGCC 59.824 55.000 5.55 0.00 39.22 4.40
3059 4689 6.833342 TTTTCTCTACAACCGTCTAAACAC 57.167 37.500 0.00 0.00 0.00 3.32
3102 4732 1.663135 GAGAATTCAAGCGACTCTGGC 59.337 52.381 8.44 0.00 0.00 4.85
3139 4812 5.822519 TGATATATTTGTGCGGCTCTCTTTT 59.177 36.000 0.00 0.00 0.00 2.27
3140 4813 5.368145 TGATATATTTGTGCGGCTCTCTTT 58.632 37.500 0.00 0.00 0.00 2.52
3141 4814 4.960938 TGATATATTTGTGCGGCTCTCTT 58.039 39.130 0.00 0.00 0.00 2.85
3142 4815 4.607293 TGATATATTTGTGCGGCTCTCT 57.393 40.909 0.00 0.00 0.00 3.10
3143 4816 5.869753 AATGATATATTTGTGCGGCTCTC 57.130 39.130 0.00 0.00 0.00 3.20
3144 4817 7.744087 TTAAATGATATATTTGTGCGGCTCT 57.256 32.000 0.00 0.00 0.00 4.09
3145 4818 8.236586 TGATTAAATGATATATTTGTGCGGCTC 58.763 33.333 0.00 0.00 0.00 4.70
3206 4879 5.034152 AGTTCGTGTTACACAAGCATTTTG 58.966 37.500 16.09 0.00 33.40 2.44
3301 4977 4.094294 TGACAAAAACAGAAGTTGACGAGG 59.906 41.667 0.00 0.00 38.17 4.63


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

AutoCloner maintained by Alex Coulton.