Multiple sequence alignment - TraesCS1A01G089400

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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 TraesCS1A01G089400 chr1A 100.000 5281 0 0 1 5281 78951858 78957138 0.000000e+00 9753.0
1 TraesCS1A01G089400 chr1A 91.403 1105 66 10 3147 4240 78547259 78548345 0.000000e+00 1487.0
2 TraesCS1A01G089400 chr1A 91.404 919 61 10 3193 4107 78338531 78339435 0.000000e+00 1243.0
3 TraesCS1A01G089400 chr1A 90.530 623 47 9 4588 5210 78339431 78340041 0.000000e+00 813.0
4 TraesCS1A01G089400 chr1A 84.286 770 82 26 4517 5270 78548639 78549385 0.000000e+00 715.0
5 TraesCS1A01G089400 chr1A 86.667 525 40 16 2098 2594 78546744 78547266 5.980000e-154 555.0
6 TraesCS1A01G089400 chr1A 82.913 515 55 22 2098 2594 78338004 78338503 2.920000e-117 433.0
7 TraesCS1A01G089400 chr1A 80.065 617 50 24 1443 2039 78543191 78543754 1.780000e-104 390.0
8 TraesCS1A01G089400 chr1A 82.734 278 38 4 5005 5281 79117008 79116740 6.840000e-59 239.0
9 TraesCS1A01G089400 chr1A 96.491 114 3 1 1543 1656 78335442 78335554 2.510000e-43 187.0
10 TraesCS1A01G089400 chr1A 86.957 161 14 6 2984 3138 115367914 115367755 1.950000e-39 174.0
11 TraesCS1A01G089400 chr1A 95.294 85 3 1 1648 1732 78335884 78335967 3.320000e-27 134.0
12 TraesCS1A01G089400 chr1A 93.103 58 4 0 1469 1526 78335392 78335449 9.420000e-13 86.1
13 TraesCS1A01G089400 chr1D 93.923 4130 132 34 1237 5281 84722653 84726748 0.000000e+00 6126.0
14 TraesCS1A01G089400 chr1D 91.603 1048 65 14 3147 4190 84569413 84570441 0.000000e+00 1426.0
15 TraesCS1A01G089400 chr1D 87.268 1131 92 19 3147 4243 84612086 84613198 0.000000e+00 1243.0
16 TraesCS1A01G089400 chr1D 87.879 858 68 14 4443 5279 84613343 84614185 0.000000e+00 976.0
17 TraesCS1A01G089400 chr1D 87.572 692 48 19 4524 5210 84570972 84571630 0.000000e+00 767.0
18 TraesCS1A01G089400 chr1D 85.958 527 41 14 2098 2594 84611570 84612093 2.800000e-147 532.0
19 TraesCS1A01G089400 chr1D 84.121 529 46 21 1549 2043 84565758 84566282 1.330000e-130 477.0
20 TraesCS1A01G089400 chr1D 81.644 523 47 20 1543 2030 84610795 84611303 6.410000e-104 388.0
21 TraesCS1A01G089400 chr1D 90.169 295 28 1 2098 2391 84566392 84566686 2.980000e-102 383.0
22 TraesCS1A01G089400 chr1D 82.818 291 19 17 4176 4435 84570467 84570757 1.140000e-56 231.0
23 TraesCS1A01G089400 chr1D 78.730 315 35 19 4971 5281 84893352 84893066 1.170000e-41 182.0
24 TraesCS1A01G089400 chr1D 96.970 33 1 0 4245 4277 411567726 411567694 7.390000e-04 56.5
25 TraesCS1A01G089400 chr1B 94.517 2134 76 12 2097 4206 137445959 137448075 0.000000e+00 3254.0
26 TraesCS1A01G089400 chr1B 93.425 2190 83 16 2090 4240 137177893 137180060 0.000000e+00 3190.0
27 TraesCS1A01G089400 chr1B 88.666 1394 83 31 3148 4504 137153075 137154430 0.000000e+00 1629.0
28 TraesCS1A01G089400 chr1B 88.540 1082 84 19 3193 4240 137174670 137175745 0.000000e+00 1275.0
29 TraesCS1A01G089400 chr1B 87.296 858 66 18 4274 5106 137448144 137448983 0.000000e+00 941.0
30 TraesCS1A01G089400 chr1B 90.805 609 27 3 1443 2051 137445277 137445856 0.000000e+00 787.0
31 TraesCS1A01G089400 chr1B 90.613 522 28 3 1543 2063 137177413 137177914 0.000000e+00 673.0
32 TraesCS1A01G089400 chr1B 85.824 522 46 9 2098 2593 137174123 137174642 3.620000e-146 529.0
33 TraesCS1A01G089400 chr1B 91.445 339 27 2 4944 5281 137180436 137180773 1.040000e-126 464.0
34 TraesCS1A01G089400 chr1B 90.030 331 27 5 4726 5056 137154861 137155185 1.760000e-114 424.0
35 TraesCS1A01G089400 chr1B 87.297 370 26 7 2098 2448 137152505 137152872 2.290000e-108 403.0
36 TraesCS1A01G089400 chr1B 96.739 184 6 0 1549 1732 137151856 137152039 1.850000e-79 307.0
37 TraesCS1A01G089400 chr1B 94.898 196 8 2 4524 4717 137154526 137154721 6.640000e-79 305.0
38 TraesCS1A01G089400 chr1B 91.429 210 8 8 1237 1442 137445033 137445236 4.030000e-71 279.0
39 TraesCS1A01G089400 chr1B 91.525 177 15 0 5105 5281 137449227 137449403 1.470000e-60 244.0
40 TraesCS1A01G089400 chr1B 92.073 164 10 1 5047 5210 137162262 137162422 1.480000e-55 228.0
41 TraesCS1A01G089400 chr1B 95.161 62 2 1 1463 1523 137177356 137177417 4.350000e-16 97.1
42 TraesCS1A01G089400 chr1B 94.643 56 3 0 1471 1526 137151808 137151863 2.620000e-13 87.9
43 TraesCS1A01G089400 chr3B 94.075 827 39 2 326 1142 441467227 441468053 0.000000e+00 1247.0
44 TraesCS1A01G089400 chr3B 94.937 316 16 0 10 325 441466867 441467182 3.670000e-136 496.0
45 TraesCS1A01G089400 chr7D 94.289 823 32 4 329 1142 6785839 6785023 0.000000e+00 1245.0
46 TraesCS1A01G089400 chr7D 94.427 323 18 0 3 325 6786209 6785887 1.020000e-136 497.0
47 TraesCS1A01G089400 chr6B 93.185 631 33 2 521 1141 692009988 692010618 0.000000e+00 918.0
48 TraesCS1A01G089400 chr6B 95.283 318 15 0 8 325 692009346 692009663 6.100000e-139 505.0
49 TraesCS1A01G089400 chr6B 95.074 203 9 1 326 527 692009708 692009910 8.530000e-83 318.0
50 TraesCS1A01G089400 chr6B 91.667 84 5 2 3061 3142 60628638 60628721 1.200000e-21 115.0
51 TraesCS1A01G089400 chr3A 90.551 127 11 1 3016 3141 383695626 383695500 3.270000e-37 167.0
52 TraesCS1A01G089400 chr3A 100.000 32 0 0 2628 2659 550440208 550440239 5.710000e-05 60.2
53 TraesCS1A01G089400 chr7B 90.435 115 7 3 3030 3142 119289062 119289174 1.180000e-31 148.0
54 TraesCS1A01G089400 chr7A 92.771 83 5 1 3061 3142 186536994 186537076 9.290000e-23 119.0
55 TraesCS1A01G089400 chr2A 93.103 58 3 1 1184 1240 35838688 35838631 3.390000e-12 84.2
56 TraesCS1A01G089400 chr2A 100.000 32 0 0 5088 5119 686036191 686036160 5.710000e-05 60.2
57 TraesCS1A01G089400 chr2B 93.478 46 2 1 2906 2951 777673437 777673481 3.410000e-07 67.6
58 TraesCS1A01G089400 chr4A 97.059 34 1 0 4245 4278 651626651 651626684 2.050000e-04 58.4


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 TraesCS1A01G089400 chr1A 78951858 78957138 5280 False 9753.000000 9753 100.000000 1 5281 1 chr1A.!!$F1 5280
1 TraesCS1A01G089400 chr1A 78543191 78549385 6194 False 786.750000 1487 85.605250 1443 5270 4 chr1A.!!$F3 3827
2 TraesCS1A01G089400 chr1A 78335392 78340041 4649 False 482.683333 1243 91.622500 1469 5210 6 chr1A.!!$F2 3741
3 TraesCS1A01G089400 chr1D 84722653 84726748 4095 False 6126.000000 6126 93.923000 1237 5281 1 chr1D.!!$F1 4044
4 TraesCS1A01G089400 chr1D 84610795 84614185 3390 False 784.750000 1243 85.687250 1543 5279 4 chr1D.!!$F3 3736
5 TraesCS1A01G089400 chr1D 84565758 84571630 5872 False 656.800000 1426 87.256600 1549 5210 5 chr1D.!!$F2 3661
6 TraesCS1A01G089400 chr1B 137445033 137449403 4370 False 1101.000000 3254 91.114400 1237 5281 5 chr1B.!!$F4 4044
7 TraesCS1A01G089400 chr1B 137174123 137180773 6650 False 1038.016667 3190 90.834667 1463 5281 6 chr1B.!!$F3 3818
8 TraesCS1A01G089400 chr1B 137151808 137155185 3377 False 525.983333 1629 92.045500 1471 5056 6 chr1B.!!$F2 3585
9 TraesCS1A01G089400 chr3B 441466867 441468053 1186 False 871.500000 1247 94.506000 10 1142 2 chr3B.!!$F1 1132
10 TraesCS1A01G089400 chr7D 6785023 6786209 1186 True 871.000000 1245 94.358000 3 1142 2 chr7D.!!$R1 1139
11 TraesCS1A01G089400 chr6B 692009346 692010618 1272 False 580.333333 918 94.514000 8 1141 3 chr6B.!!$F2 1133

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
327 372 0.320374 CTTCGTGCCAGTGTCCCTAA 59.680 55.000 0.00 0.0 0.00 2.69 F
1156 1296 1.002624 GGAACGGCAGGTGATGGAA 60.003 57.895 0.00 0.0 0.00 3.53 F
1213 1353 0.248012 TGAGAAGCCGCGTATTGGAA 59.752 50.000 4.92 0.0 0.00 3.53 F
1221 1361 0.519519 CGCGTATTGGAAGTGGCAAA 59.480 50.000 0.00 0.0 0.00 3.68 F
1703 3822 0.534203 GCAAACTCGACCTGGACCAA 60.534 55.000 0.00 0.0 0.00 3.67 F
2682 12116 0.692756 TCCGATACTCCCCCAATGCA 60.693 55.000 0.00 0.0 0.00 3.96 F
3816 13278 0.944311 AAGTGAGTGGTGCGCTAACG 60.944 55.000 9.73 0.0 44.07 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1193 1333 0.248012 TCCAATACGCGGCTTCTCAA 59.752 50.000 12.47 0.0 0.00 3.02 R
2807 12242 0.252375 TCGGGGTACTAGGGTTGCTT 60.252 55.000 0.00 0.0 0.00 3.91 R
2941 12386 2.882876 GCCTGAGCGAGGACGTTA 59.117 61.111 8.90 0.0 46.33 3.18 R
3085 12530 5.708230 GGGCCAATATGGATACGTAAATTCA 59.292 40.000 4.39 0.0 40.96 2.57 R
3523 12984 0.700564 ACAGTCCTCCCATGCACATT 59.299 50.000 0.00 0.0 0.00 2.71 R
3981 13443 0.392461 GCATCTTGTACTCCCCGCAA 60.392 55.000 0.00 0.0 0.00 4.85 R
4830 14854 3.010472 TGGGAATGATGTTCATCCAGTGT 59.990 43.478 9.83 0.0 35.76 3.55 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
37 38 3.834231 AGCCACAATTTCTAAACCTGCAT 59.166 39.130 0.00 0.00 0.00 3.96
113 114 3.344535 TGGATCAATAGGGTGGCTCTA 57.655 47.619 0.00 0.00 0.00 2.43
215 216 1.139734 GACGATCGCCTGAGCTTCA 59.860 57.895 16.60 0.00 36.60 3.02
327 372 0.320374 CTTCGTGCCAGTGTCCCTAA 59.680 55.000 0.00 0.00 0.00 2.69
359 404 2.143925 CTGTTTCTCCACCCTTCGTTC 58.856 52.381 0.00 0.00 0.00 3.95
612 742 4.584874 TCATACTCGGCCAAAATCAAAGA 58.415 39.130 2.24 0.00 0.00 2.52
786 916 4.275936 GCTTTGACTAAAGTTCTTGCCTGA 59.724 41.667 0.00 0.00 44.11 3.86
876 1015 5.434408 CAGATCATCATCCTCAAGGTTCAA 58.566 41.667 0.00 0.00 36.34 2.69
924 1063 2.922234 GGCCAGCCCTGCTAATCT 59.078 61.111 0.00 0.00 36.40 2.40
1038 1177 4.051932 GGGGGAGGTCGTGAGATT 57.948 61.111 0.00 0.00 45.19 2.40
1053 1192 3.260884 GTGAGATTGGGGAACAGAGTACA 59.739 47.826 0.00 0.00 0.00 2.90
1142 1282 1.684734 TCGCCAGACCTAGGGGAAC 60.685 63.158 14.81 1.59 44.03 3.62
1143 1283 2.901042 GCCAGACCTAGGGGAACG 59.099 66.667 14.81 0.00 36.25 3.95
1144 1284 2.732619 GCCAGACCTAGGGGAACGG 61.733 68.421 14.81 7.14 36.25 4.44
1145 1285 2.732619 CCAGACCTAGGGGAACGGC 61.733 68.421 14.81 0.00 36.25 5.68
1146 1286 1.987855 CAGACCTAGGGGAACGGCA 60.988 63.158 14.81 0.00 36.25 5.69
1147 1287 1.686110 AGACCTAGGGGAACGGCAG 60.686 63.158 14.81 0.00 36.25 4.85
1149 1289 2.687566 CCTAGGGGAACGGCAGGT 60.688 66.667 0.00 0.00 33.58 4.00
1150 1290 2.584608 CTAGGGGAACGGCAGGTG 59.415 66.667 0.00 0.00 0.00 4.00
1152 1292 1.306654 TAGGGGAACGGCAGGTGAT 60.307 57.895 0.00 0.00 0.00 3.06
1153 1293 1.622607 TAGGGGAACGGCAGGTGATG 61.623 60.000 0.00 0.00 0.00 3.07
1155 1295 2.668632 GGAACGGCAGGTGATGGA 59.331 61.111 0.00 0.00 0.00 3.41
1156 1296 1.002624 GGAACGGCAGGTGATGGAA 60.003 57.895 0.00 0.00 0.00 3.53
1157 1297 1.305930 GGAACGGCAGGTGATGGAAC 61.306 60.000 0.00 0.00 0.00 3.62
1158 1298 1.303317 AACGGCAGGTGATGGAACC 60.303 57.895 0.00 0.00 40.85 3.62
1176 1316 3.864789 ACCTTCTGGTGTGAAGTCAAT 57.135 42.857 0.00 0.00 46.51 2.57
1177 1317 3.744660 ACCTTCTGGTGTGAAGTCAATC 58.255 45.455 0.00 0.00 46.51 2.67
1178 1318 3.392616 ACCTTCTGGTGTGAAGTCAATCT 59.607 43.478 0.00 0.00 46.51 2.40
1179 1319 4.141390 ACCTTCTGGTGTGAAGTCAATCTT 60.141 41.667 0.00 0.00 46.51 2.40
1180 1320 4.214971 CCTTCTGGTGTGAAGTCAATCTTG 59.785 45.833 0.00 0.00 41.17 3.02
1181 1321 4.687901 TCTGGTGTGAAGTCAATCTTGA 57.312 40.909 0.00 0.00 36.40 3.02
1183 1323 5.436175 TCTGGTGTGAAGTCAATCTTGAAA 58.564 37.500 0.00 0.00 39.21 2.69
1185 1325 5.192927 TGGTGTGAAGTCAATCTTGAAAGT 58.807 37.500 0.00 0.00 39.21 2.66
1186 1326 5.066375 TGGTGTGAAGTCAATCTTGAAAGTG 59.934 40.000 0.00 0.00 39.21 3.16
1188 1328 5.066505 GTGTGAAGTCAATCTTGAAAGTGGT 59.933 40.000 0.00 0.00 39.21 4.16
1189 1329 6.260050 GTGTGAAGTCAATCTTGAAAGTGGTA 59.740 38.462 0.00 0.00 39.21 3.25
1190 1330 6.826231 TGTGAAGTCAATCTTGAAAGTGGTAA 59.174 34.615 0.00 0.00 39.21 2.85
1191 1331 7.502226 TGTGAAGTCAATCTTGAAAGTGGTAAT 59.498 33.333 0.00 0.00 39.21 1.89
1192 1332 8.352942 GTGAAGTCAATCTTGAAAGTGGTAATT 58.647 33.333 0.00 0.00 39.21 1.40
1193 1333 8.912988 TGAAGTCAATCTTGAAAGTGGTAATTT 58.087 29.630 0.00 0.00 39.21 1.82
1195 1335 9.533253 AAGTCAATCTTGAAAGTGGTAATTTTG 57.467 29.630 0.00 0.00 39.21 2.44
1197 1337 9.185192 GTCAATCTTGAAAGTGGTAATTTTGAG 57.815 33.333 0.00 0.00 39.21 3.02
1198 1338 9.130661 TCAATCTTGAAAGTGGTAATTTTGAGA 57.869 29.630 0.00 0.00 33.55 3.27
1200 1340 9.971922 AATCTTGAAAGTGGTAATTTTGAGAAG 57.028 29.630 0.00 0.00 0.00 2.85
1201 1341 7.425606 TCTTGAAAGTGGTAATTTTGAGAAGC 58.574 34.615 0.00 0.00 0.00 3.86
1202 1342 6.084326 TGAAAGTGGTAATTTTGAGAAGCC 57.916 37.500 0.00 0.00 0.00 4.35
1206 1346 1.467342 GGTAATTTTGAGAAGCCGCGT 59.533 47.619 4.92 0.00 0.00 6.01
1207 1347 2.674357 GGTAATTTTGAGAAGCCGCGTA 59.326 45.455 4.92 0.00 0.00 4.42
1208 1348 3.311596 GGTAATTTTGAGAAGCCGCGTAT 59.688 43.478 4.92 0.00 0.00 3.06
1209 1349 4.201881 GGTAATTTTGAGAAGCCGCGTATT 60.202 41.667 4.92 0.00 0.00 1.89
1210 1350 2.892373 TTTTGAGAAGCCGCGTATTG 57.108 45.000 4.92 0.00 0.00 1.90
1211 1351 1.083489 TTTGAGAAGCCGCGTATTGG 58.917 50.000 4.92 0.00 0.00 3.16
1213 1353 0.248012 TGAGAAGCCGCGTATTGGAA 59.752 50.000 4.92 0.00 0.00 3.53
1214 1354 0.931005 GAGAAGCCGCGTATTGGAAG 59.069 55.000 4.92 0.00 0.00 3.46
1217 1357 1.024579 AAGCCGCGTATTGGAAGTGG 61.025 55.000 4.92 0.00 39.94 4.00
1218 1358 3.098555 CCGCGTATTGGAAGTGGC 58.901 61.111 4.92 0.00 30.09 5.01
1219 1359 1.743623 CCGCGTATTGGAAGTGGCA 60.744 57.895 4.92 0.00 30.09 4.92
1220 1360 1.302383 CCGCGTATTGGAAGTGGCAA 61.302 55.000 4.92 0.00 30.09 4.52
1221 1361 0.519519 CGCGTATTGGAAGTGGCAAA 59.480 50.000 0.00 0.00 0.00 3.68
1223 1363 2.353269 CGCGTATTGGAAGTGGCAAATA 59.647 45.455 0.00 0.00 0.00 1.40
1225 1365 4.497340 CGCGTATTGGAAGTGGCAAATATT 60.497 41.667 0.00 0.00 0.00 1.28
1226 1366 4.976116 GCGTATTGGAAGTGGCAAATATTC 59.024 41.667 0.00 0.00 0.00 1.75
1228 1368 6.559810 CGTATTGGAAGTGGCAAATATTCAA 58.440 36.000 0.00 0.00 0.00 2.69
1229 1369 7.202526 CGTATTGGAAGTGGCAAATATTCAAT 58.797 34.615 0.00 0.00 0.00 2.57
1231 1371 9.382275 GTATTGGAAGTGGCAAATATTCAATTT 57.618 29.630 0.00 0.00 0.00 1.82
1232 1372 8.866970 ATTGGAAGTGGCAAATATTCAATTTT 57.133 26.923 0.00 0.00 0.00 1.82
1235 1375 7.818930 TGGAAGTGGCAAATATTCAATTTTCTC 59.181 33.333 0.00 0.00 0.00 2.87
1592 3365 2.758979 GTGGGACCAAGAAGAGTATCGA 59.241 50.000 0.00 0.00 42.67 3.59
1668 3781 1.210478 AGGGCTGTTTCATATGCGTCT 59.790 47.619 0.00 0.00 0.00 4.18
1703 3822 0.534203 GCAAACTCGACCTGGACCAA 60.534 55.000 0.00 0.00 0.00 3.67
1718 3837 2.609737 GGACCAAGAGTGTACGTTCCAG 60.610 54.545 0.00 0.00 0.00 3.86
1719 3838 2.035576 GACCAAGAGTGTACGTTCCAGT 59.964 50.000 0.00 0.00 0.00 4.00
1720 3839 2.035576 ACCAAGAGTGTACGTTCCAGTC 59.964 50.000 12.44 12.44 33.36 3.51
1721 3840 2.609737 CCAAGAGTGTACGTTCCAGTCC 60.610 54.545 15.31 3.19 33.60 3.85
1722 3841 1.991121 AGAGTGTACGTTCCAGTCCA 58.009 50.000 15.31 0.00 33.60 4.02
1771 3901 5.163933 GCATCTCGTTATGTTCGGTTAAACA 60.164 40.000 0.00 0.00 42.92 2.83
1777 3907 8.531622 TCGTTATGTTCGGTTAAACATCTTTA 57.468 30.769 5.59 0.00 44.53 1.85
1842 4019 3.053693 CCACTCAAATCCCCTTCATACCA 60.054 47.826 0.00 0.00 0.00 3.25
2412 9245 7.938490 TGCCACAGACACATACAATATATCAAT 59.062 33.333 0.00 0.00 0.00 2.57
2449 9285 3.924918 CTGGTACCTCATATCAGTCGG 57.075 52.381 14.36 0.00 37.26 4.79
2450 9286 3.223435 CTGGTACCTCATATCAGTCGGT 58.777 50.000 14.36 0.00 37.26 4.69
2462 11856 3.981071 TCAGTCGGTTGATTTCCTGAT 57.019 42.857 0.00 0.00 0.00 2.90
2598 12032 6.106673 AGTTTTGTATCTGTTCCATACTCGG 58.893 40.000 0.00 0.00 0.00 4.63
2677 12111 2.122989 GCCTCCGATACTCCCCCA 60.123 66.667 0.00 0.00 0.00 4.96
2682 12116 0.692756 TCCGATACTCCCCCAATGCA 60.693 55.000 0.00 0.00 0.00 3.96
2736 12170 8.722622 TTTAAAACAAGTACAATATTCCCCCA 57.277 30.769 0.00 0.00 0.00 4.96
2807 12242 3.882888 CTCAACCCAGTAAAGAAGCAACA 59.117 43.478 0.00 0.00 0.00 3.33
2941 12386 2.040278 CTGCCCCTCCTCCTCACT 59.960 66.667 0.00 0.00 0.00 3.41
3022 12467 9.819267 AAGTAATATGCTGTTCCTAACTTCTAC 57.181 33.333 0.00 0.00 0.00 2.59
3085 12530 5.465056 CGTATTGGCACTTTTTCAAAATGGT 59.535 36.000 1.21 0.00 0.00 3.55
3115 12560 3.132289 CGTATCCATATTGGCCCGATACT 59.868 47.826 0.00 0.00 37.47 2.12
3338 12798 5.867716 TCTGAGTCTAATTACCTTGTTTCGC 59.132 40.000 0.00 0.00 0.00 4.70
3502 12963 8.477256 TCATGGTATGCGATGATATATTCTTCA 58.523 33.333 4.41 0.00 35.41 3.02
3523 12984 7.720957 TCTTCAAAATCAATCTGAAGGTGAAGA 59.279 33.333 16.92 16.92 44.04 2.87
3691 13152 2.213499 CATTCATTAGGAGGTCGGTGC 58.787 52.381 0.00 0.00 0.00 5.01
3816 13278 0.944311 AAGTGAGTGGTGCGCTAACG 60.944 55.000 9.73 0.00 44.07 3.18
3835 13297 1.021390 GGCAGGTGACAATGGAGTCG 61.021 60.000 0.00 0.00 41.41 4.18
3981 13443 5.828328 TGGTTACGATGATGAGAGTATCACT 59.172 40.000 0.00 0.00 41.91 3.41
3990 13452 1.067821 GAGAGTATCACTTGCGGGGAG 59.932 57.143 0.00 0.00 37.82 4.30
4009 13471 4.323104 GGGAGTACAAGATGCTTCTGAAGT 60.323 45.833 17.97 5.55 30.72 3.01
4257 13792 1.572415 AGAGTTATACCCCCTCCGTCA 59.428 52.381 0.00 0.00 0.00 4.35
4392 14097 4.622740 GCCTTGTTGAATTGCAAGATGTAC 59.377 41.667 4.94 0.09 43.29 2.90
4431 14142 6.494893 TGTCTATGCCTTGTTGAATTACAC 57.505 37.500 0.00 0.00 0.00 2.90
4830 14854 2.083774 CGCCCATCAAAAGAACTGCTA 58.916 47.619 0.00 0.00 0.00 3.49
4924 14952 6.890979 AGAAGAAGAAAATTCTGGTTGAGG 57.109 37.500 0.00 0.00 37.65 3.86
5028 15079 4.730949 ATGCTTGGTTTGATCAATGGAG 57.269 40.909 9.40 6.62 0.00 3.86
5174 15473 2.385803 TCCATCTCCGTTTCCTAGGAC 58.614 52.381 12.22 0.00 32.33 3.85
5230 15529 1.546476 CAGCTTCTTCTACGTCCAGGT 59.454 52.381 0.00 0.00 0.00 4.00
5239 15538 4.774660 TCTACGTCCAGGTAGAGATCTT 57.225 45.455 0.00 0.00 42.88 2.40
5270 15569 5.850128 GCAATGTCGAAAGATGAAGATATGC 59.150 40.000 0.00 0.00 45.19 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.447714 GGCTGGAGGGGGATCTGAC 61.448 68.421 0.00 0.00 0.00 3.51
1 2 2.040464 GGCTGGAGGGGGATCTGA 60.040 66.667 0.00 0.00 0.00 3.27
37 38 6.828273 AGGCATAACTCTGTACATAATGCAAA 59.172 34.615 20.20 0.00 34.54 3.68
113 114 6.992123 TCGAGAACATGCAAATAATATGGACT 59.008 34.615 0.00 0.00 0.00 3.85
172 173 5.602978 AGAGAAGTGGAAAAGAGGACTACAA 59.397 40.000 0.00 0.00 0.00 2.41
327 372 6.325286 GGGTGGAGAAACAGAGAAGTATCTAT 59.675 42.308 0.00 0.00 35.54 1.98
391 436 3.897141 AGGGCTAGAGTTAAGCTTGAC 57.103 47.619 13.22 13.22 39.97 3.18
612 742 1.064825 ATGGGACTTCCGTGGAGTTT 58.935 50.000 0.00 0.00 38.76 2.66
766 896 4.776349 TGTCAGGCAAGAACTTTAGTCAA 58.224 39.130 0.00 0.00 0.00 3.18
772 902 2.487986 CCTCCTGTCAGGCAAGAACTTT 60.488 50.000 14.64 0.00 34.61 2.66
786 916 3.322466 CCCTTGGTCGCCTCCTGT 61.322 66.667 0.00 0.00 0.00 4.00
876 1015 1.074566 CTGGAAAGCTCCTGGAAAGGT 59.925 52.381 0.00 0.00 42.94 3.50
924 1063 2.964310 GCTTCAGGAGAGGGCAGCA 61.964 63.158 0.00 0.00 0.00 4.41
1038 1177 2.232941 GTCGATTGTACTCTGTTCCCCA 59.767 50.000 0.00 0.00 0.00 4.96
1053 1192 1.743623 TCCGGCAATTGCGTCGATT 60.744 52.632 24.67 0.00 43.26 3.34
1142 1282 2.671070 AGGTTCCATCACCTGCCG 59.329 61.111 0.00 0.00 46.22 5.69
1159 1299 5.034852 TCAAGATTGACTTCACACCAGAA 57.965 39.130 0.00 0.00 36.61 3.02
1161 1301 5.297776 ACTTTCAAGATTGACTTCACACCAG 59.702 40.000 0.00 0.00 36.83 4.00
1163 1303 5.506317 CCACTTTCAAGATTGACTTCACACC 60.506 44.000 0.00 0.00 36.83 4.16
1164 1304 5.066505 ACCACTTTCAAGATTGACTTCACAC 59.933 40.000 0.00 0.00 36.83 3.82
1166 1306 5.757850 ACCACTTTCAAGATTGACTTCAC 57.242 39.130 0.00 0.00 36.83 3.18
1167 1307 8.463930 AATTACCACTTTCAAGATTGACTTCA 57.536 30.769 0.00 0.00 36.83 3.02
1168 1308 9.750125 AAAATTACCACTTTCAAGATTGACTTC 57.250 29.630 0.00 0.00 36.83 3.01
1170 1310 8.912988 TCAAAATTACCACTTTCAAGATTGACT 58.087 29.630 0.00 0.00 36.83 3.41
1172 1312 9.130661 TCTCAAAATTACCACTTTCAAGATTGA 57.869 29.630 0.00 0.00 34.92 2.57
1173 1313 9.748708 TTCTCAAAATTACCACTTTCAAGATTG 57.251 29.630 0.00 0.00 0.00 2.67
1174 1314 9.971922 CTTCTCAAAATTACCACTTTCAAGATT 57.028 29.630 0.00 0.00 0.00 2.40
1176 1316 7.425606 GCTTCTCAAAATTACCACTTTCAAGA 58.574 34.615 0.00 0.00 0.00 3.02
1177 1317 6.642540 GGCTTCTCAAAATTACCACTTTCAAG 59.357 38.462 0.00 0.00 0.00 3.02
1178 1318 6.512297 GGCTTCTCAAAATTACCACTTTCAA 58.488 36.000 0.00 0.00 0.00 2.69
1179 1319 5.278266 CGGCTTCTCAAAATTACCACTTTCA 60.278 40.000 0.00 0.00 0.00 2.69
1180 1320 5.154222 CGGCTTCTCAAAATTACCACTTTC 58.846 41.667 0.00 0.00 0.00 2.62
1181 1321 4.558697 GCGGCTTCTCAAAATTACCACTTT 60.559 41.667 0.00 0.00 0.00 2.66
1183 1323 2.488153 GCGGCTTCTCAAAATTACCACT 59.512 45.455 0.00 0.00 0.00 4.00
1185 1325 1.466950 CGCGGCTTCTCAAAATTACCA 59.533 47.619 0.00 0.00 0.00 3.25
1186 1326 1.467342 ACGCGGCTTCTCAAAATTACC 59.533 47.619 12.47 0.00 0.00 2.85
1188 1328 4.201871 CCAATACGCGGCTTCTCAAAATTA 60.202 41.667 12.47 0.00 0.00 1.40
1189 1329 3.427503 CCAATACGCGGCTTCTCAAAATT 60.428 43.478 12.47 0.00 0.00 1.82
1190 1330 2.097466 CCAATACGCGGCTTCTCAAAAT 59.903 45.455 12.47 0.00 0.00 1.82
1191 1331 1.466950 CCAATACGCGGCTTCTCAAAA 59.533 47.619 12.47 0.00 0.00 2.44
1192 1332 1.083489 CCAATACGCGGCTTCTCAAA 58.917 50.000 12.47 0.00 0.00 2.69
1193 1333 0.248012 TCCAATACGCGGCTTCTCAA 59.752 50.000 12.47 0.00 0.00 3.02
1195 1335 0.931005 CTTCCAATACGCGGCTTCTC 59.069 55.000 12.47 0.00 0.00 2.87
1197 1337 0.373716 CACTTCCAATACGCGGCTTC 59.626 55.000 12.47 0.00 0.00 3.86
1198 1338 1.024579 CCACTTCCAATACGCGGCTT 61.025 55.000 12.47 0.00 0.00 4.35
1200 1340 3.098555 CCACTTCCAATACGCGGC 58.901 61.111 12.47 0.00 0.00 6.53
1201 1341 1.302383 TTGCCACTTCCAATACGCGG 61.302 55.000 12.47 0.00 0.00 6.46
1202 1342 0.519519 TTTGCCACTTCCAATACGCG 59.480 50.000 3.53 3.53 0.00 6.01
1206 1346 9.956640 AAAATTGAATATTTGCCACTTCCAATA 57.043 25.926 0.00 0.00 0.00 1.90
1207 1347 8.866970 AAAATTGAATATTTGCCACTTCCAAT 57.133 26.923 0.00 0.00 0.00 3.16
1208 1348 8.156165 AGAAAATTGAATATTTGCCACTTCCAA 58.844 29.630 0.00 0.00 0.00 3.53
1209 1349 7.678837 AGAAAATTGAATATTTGCCACTTCCA 58.321 30.769 0.00 0.00 0.00 3.53
1210 1350 7.278646 GGAGAAAATTGAATATTTGCCACTTCC 59.721 37.037 0.00 0.00 0.00 3.46
1211 1351 8.037166 AGGAGAAAATTGAATATTTGCCACTTC 58.963 33.333 0.00 0.00 0.00 3.01
1213 1353 7.486407 AGGAGAAAATTGAATATTTGCCACT 57.514 32.000 0.00 0.00 0.00 4.00
1214 1354 7.603784 ACAAGGAGAAAATTGAATATTTGCCAC 59.396 33.333 0.00 0.00 0.00 5.01
1217 1357 8.037166 AGGACAAGGAGAAAATTGAATATTTGC 58.963 33.333 0.00 0.00 0.00 3.68
1218 1358 9.933723 AAGGACAAGGAGAAAATTGAATATTTG 57.066 29.630 0.00 0.00 0.00 2.32
1219 1359 9.933723 CAAGGACAAGGAGAAAATTGAATATTT 57.066 29.630 0.00 0.00 0.00 1.40
1220 1360 8.534496 CCAAGGACAAGGAGAAAATTGAATATT 58.466 33.333 0.00 0.00 0.00 1.28
1221 1361 7.675619 ACCAAGGACAAGGAGAAAATTGAATAT 59.324 33.333 0.00 0.00 0.00 1.28
1223 1363 5.840693 ACCAAGGACAAGGAGAAAATTGAAT 59.159 36.000 0.00 0.00 0.00 2.57
1225 1365 4.803452 ACCAAGGACAAGGAGAAAATTGA 58.197 39.130 0.00 0.00 0.00 2.57
1226 1366 5.291971 CAACCAAGGACAAGGAGAAAATTG 58.708 41.667 0.00 0.00 0.00 2.32
1228 1368 3.897505 CCAACCAAGGACAAGGAGAAAAT 59.102 43.478 0.00 0.00 0.00 1.82
1229 1369 3.295973 CCAACCAAGGACAAGGAGAAAA 58.704 45.455 0.00 0.00 0.00 2.29
1231 1371 1.144913 CCCAACCAAGGACAAGGAGAA 59.855 52.381 0.00 0.00 0.00 2.87
1232 1372 0.771127 CCCAACCAAGGACAAGGAGA 59.229 55.000 0.00 0.00 0.00 3.71
1235 1375 1.228862 CCCCCAACCAAGGACAAGG 60.229 63.158 0.00 0.00 0.00 3.61
1668 3781 0.315886 TTGCCGTCGAAGAAGTAGCA 59.684 50.000 0.00 0.00 39.69 3.49
1703 3822 1.991121 TGGACTGGAACGTACACTCT 58.009 50.000 0.00 0.00 0.00 3.24
1718 3837 2.319844 GGGGATTGGATTGGATTGGAC 58.680 52.381 0.00 0.00 0.00 4.02
1719 3838 1.220236 GGGGGATTGGATTGGATTGGA 59.780 52.381 0.00 0.00 0.00 3.53
1720 3839 1.221265 AGGGGGATTGGATTGGATTGG 59.779 52.381 0.00 0.00 0.00 3.16
1721 3840 2.781403 AGGGGGATTGGATTGGATTG 57.219 50.000 0.00 0.00 0.00 2.67
1722 3841 4.916963 TTAAGGGGGATTGGATTGGATT 57.083 40.909 0.00 0.00 0.00 3.01
1771 3901 7.413446 TGAATCAAAATCCACCTCCTAAAGAT 58.587 34.615 0.00 0.00 0.00 2.40
1777 3907 5.136105 GCTATGAATCAAAATCCACCTCCT 58.864 41.667 0.00 0.00 0.00 3.69
1842 4019 0.550914 TGTTCTGTTGCAAGGGGAGT 59.449 50.000 0.00 0.00 0.00 3.85
1952 4193 6.511929 GCAGAAAGTGAAAGTAACCTTCAGAC 60.512 42.308 0.00 0.00 0.00 3.51
2065 7136 9.097257 TGTATGTATGTATGTATGTATGCATGC 57.903 33.333 11.82 11.82 36.70 4.06
2412 9245 5.354792 GGTACCAGTACAAGAAAACACACAA 59.645 40.000 7.15 0.00 37.78 3.33
2448 9284 6.535963 AATTTCTCCATCAGGAAATCAACC 57.464 37.500 0.00 0.00 45.19 3.77
2449 9285 8.090214 TCAAAATTTCTCCATCAGGAAATCAAC 58.910 33.333 0.00 0.00 45.19 3.18
2450 9286 8.192743 TCAAAATTTCTCCATCAGGAAATCAA 57.807 30.769 0.00 0.00 45.19 2.57
2462 11856 6.978080 GCACAACTTAACTCAAAATTTCTCCA 59.022 34.615 0.00 0.00 0.00 3.86
2598 12032 4.811557 GGTTGGCTCAAGTATCTGTACATC 59.188 45.833 0.00 0.00 33.09 3.06
2778 12213 1.276622 TTACTGGGTTGAGAGGGCTC 58.723 55.000 0.00 0.00 41.67 4.70
2807 12242 0.252375 TCGGGGTACTAGGGTTGCTT 60.252 55.000 0.00 0.00 0.00 3.91
2941 12386 2.882876 GCCTGAGCGAGGACGTTA 59.117 61.111 8.90 0.00 46.33 3.18
2981 12426 7.337689 AGCATATTACTTTCATGTTTGCTCTCA 59.662 33.333 0.00 0.00 32.86 3.27
3085 12530 5.708230 GGGCCAATATGGATACGTAAATTCA 59.292 40.000 4.39 0.00 40.96 2.57
3380 12841 7.218614 TGCTTGTTTCTGGAATTGATTGAATT 58.781 30.769 0.00 0.00 36.94 2.17
3424 12885 4.400251 TGAATCATCCTGCAAGACCAATTC 59.600 41.667 8.28 8.28 34.07 2.17
3502 12963 8.086522 CACATTCTTCACCTTCAGATTGATTTT 58.913 33.333 0.00 0.00 0.00 1.82
3523 12984 0.700564 ACAGTCCTCCCATGCACATT 59.299 50.000 0.00 0.00 0.00 2.71
3691 13152 2.082231 CTTGATCTCAACAGTGCCCTG 58.918 52.381 0.00 0.00 44.68 4.45
3816 13278 1.021390 CGACTCCATTGTCACCTGCC 61.021 60.000 0.00 0.00 36.82 4.85
3981 13443 0.392461 GCATCTTGTACTCCCCGCAA 60.392 55.000 0.00 0.00 0.00 4.85
3990 13452 5.698545 AGTGAACTTCAGAAGCATCTTGTAC 59.301 40.000 10.33 3.96 32.03 2.90
4009 13471 5.995282 AGAAATACACAATCGACCAAGTGAA 59.005 36.000 13.22 0.00 35.97 3.18
4157 13648 9.906660 CAGAAGAGTCAGAATAGATACAATACC 57.093 37.037 0.00 0.00 0.00 2.73
4312 13896 5.839063 CAGTAAATACTACTCCCTCCATCCA 59.161 44.000 0.00 0.00 34.13 3.41
4558 14436 6.489361 ACTGAGCTCTTGATTCTGACAAAAAT 59.511 34.615 16.19 0.00 0.00 1.82
4830 14854 3.010472 TGGGAATGATGTTCATCCAGTGT 59.990 43.478 9.83 0.00 35.76 3.55
5028 15079 4.142534 TGCTCTGAAGTGCATATTGCTTTC 60.143 41.667 3.05 5.88 45.31 2.62


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

AutoCloner maintained by Alex Coulton.