Multiple sequence alignment - TraesCS1D01G171000

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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 TraesCS1D01G171000 chr1D 100.000 2199 0 0 1 2199 244445201 244447399 0.000000e+00 4061
1 TraesCS1D01G171000 chr1D 95.543 1234 44 7 1 1224 394180070 394181302 0.000000e+00 1964
2 TraesCS1D01G171000 chr1D 95.130 1232 51 6 1 1224 483921805 483920575 0.000000e+00 1934
3 TraesCS1D01G171000 chr1D 95.743 1104 39 7 128 1224 254490942 254492044 0.000000e+00 1772
4 TraesCS1D01G171000 chr1D 96.774 837 25 2 1365 2199 72632690 72633526 0.000000e+00 1395
5 TraesCS1D01G171000 chr1D 96.992 831 23 2 1370 2199 282985308 282986137 0.000000e+00 1395
6 TraesCS1D01G171000 chr1D 96.871 831 25 1 1370 2199 41818704 41817874 0.000000e+00 1389
7 TraesCS1D01G171000 chr1D 97.241 145 3 1 1226 1369 206075135 206075279 6.060000e-61 244
8 TraesCS1D01G171000 chr1D 97.241 145 3 1 1226 1369 254500228 254500084 6.060000e-61 244
9 TraesCS1D01G171000 chrUn 95.211 1232 50 6 1 1224 317472033 317470803 0.000000e+00 1940
10 TraesCS1D01G171000 chrUn 97.931 145 2 1 1226 1369 439558990 439559134 1.300000e-62 250
11 TraesCS1D01G171000 chr6D 95.462 1212 46 7 1 1204 431404060 431405270 0.000000e+00 1925
12 TraesCS1D01G171000 chr6D 96.407 835 28 2 1366 2199 382785246 382784413 0.000000e+00 1375
13 TraesCS1D01G171000 chr5D 94.886 1232 54 6 1 1224 6206670 6205440 0.000000e+00 1917
14 TraesCS1D01G171000 chr5D 96.751 831 26 1 1370 2199 343174718 343175548 0.000000e+00 1384
15 TraesCS1D01G171000 chr5D 97.931 145 2 1 1226 1369 329164404 329164260 1.300000e-62 250
16 TraesCS1D01G171000 chr5D 97.931 145 2 1 1226 1369 560874698 560874554 1.300000e-62 250
17 TraesCS1D01G171000 chr3B 94.720 1231 57 6 1 1224 201507731 201508960 0.000000e+00 1906
18 TraesCS1D01G171000 chr3B 98.621 145 1 1 1226 1369 201516909 201516765 2.800000e-64 255
19 TraesCS1D01G171000 chr3D 94.314 1231 45 7 1 1224 21898709 21899921 0.000000e+00 1862
20 TraesCS1D01G171000 chr2D 94.084 1234 60 9 1 1224 334227069 334228299 0.000000e+00 1862
21 TraesCS1D01G171000 chr2D 97.112 831 22 2 1370 2199 112397753 112398582 0.000000e+00 1400
22 TraesCS1D01G171000 chr2D 97.931 145 2 1 1226 1369 362297226 362297082 1.300000e-62 250
23 TraesCS1D01G171000 chr7D 97.112 831 22 2 1370 2199 111627536 111628365 0.000000e+00 1400
24 TraesCS1D01G171000 chr7D 97.205 823 21 2 1370 2191 248750246 248749425 0.000000e+00 1391
25 TraesCS1D01G171000 chr7D 98.592 142 1 1 1226 1366 231532141 231532282 1.300000e-62 250
26 TraesCS1D01G171000 chr4D 96.751 831 25 2 1370 2199 374579861 374579032 0.000000e+00 1384
27 TraesCS1D01G171000 chr7B 97.917 144 3 0 1226 1369 102631401 102631544 1.300000e-62 250


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 TraesCS1D01G171000 chr1D 244445201 244447399 2198 False 4061 4061 100.000 1 2199 1 chr1D.!!$F3 2198
1 TraesCS1D01G171000 chr1D 394180070 394181302 1232 False 1964 1964 95.543 1 1224 1 chr1D.!!$F6 1223
2 TraesCS1D01G171000 chr1D 483920575 483921805 1230 True 1934 1934 95.130 1 1224 1 chr1D.!!$R3 1223
3 TraesCS1D01G171000 chr1D 254490942 254492044 1102 False 1772 1772 95.743 128 1224 1 chr1D.!!$F4 1096
4 TraesCS1D01G171000 chr1D 72632690 72633526 836 False 1395 1395 96.774 1365 2199 1 chr1D.!!$F1 834
5 TraesCS1D01G171000 chr1D 282985308 282986137 829 False 1395 1395 96.992 1370 2199 1 chr1D.!!$F5 829
6 TraesCS1D01G171000 chr1D 41817874 41818704 830 True 1389 1389 96.871 1370 2199 1 chr1D.!!$R1 829
7 TraesCS1D01G171000 chrUn 317470803 317472033 1230 True 1940 1940 95.211 1 1224 1 chrUn.!!$R1 1223
8 TraesCS1D01G171000 chr6D 431404060 431405270 1210 False 1925 1925 95.462 1 1204 1 chr6D.!!$F1 1203
9 TraesCS1D01G171000 chr6D 382784413 382785246 833 True 1375 1375 96.407 1366 2199 1 chr6D.!!$R1 833
10 TraesCS1D01G171000 chr5D 6205440 6206670 1230 True 1917 1917 94.886 1 1224 1 chr5D.!!$R1 1223
11 TraesCS1D01G171000 chr5D 343174718 343175548 830 False 1384 1384 96.751 1370 2199 1 chr5D.!!$F1 829
12 TraesCS1D01G171000 chr3B 201507731 201508960 1229 False 1906 1906 94.720 1 1224 1 chr3B.!!$F1 1223
13 TraesCS1D01G171000 chr3D 21898709 21899921 1212 False 1862 1862 94.314 1 1224 1 chr3D.!!$F1 1223
14 TraesCS1D01G171000 chr2D 334227069 334228299 1230 False 1862 1862 94.084 1 1224 1 chr2D.!!$F2 1223
15 TraesCS1D01G171000 chr2D 112397753 112398582 829 False 1400 1400 97.112 1370 2199 1 chr2D.!!$F1 829
16 TraesCS1D01G171000 chr7D 111627536 111628365 829 False 1400 1400 97.112 1370 2199 1 chr7D.!!$F1 829
17 TraesCS1D01G171000 chr7D 248749425 248750246 821 True 1391 1391 97.205 1370 2191 1 chr7D.!!$R1 821
18 TraesCS1D01G171000 chr4D 374579032 374579861 829 True 1384 1384 96.751 1370 2199 1 chr4D.!!$R1 829

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
790 813 1.97266 GAGCATAGAACAGGCGGGGT 61.973 60.0 0.0 0.0 39.49 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 1839 0.039618 TTTCACAGGAATGGGCCTCC 59.96 55.0 4.53 4.01 35.66 4.3 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
56 57 3.428316 CCAAAACAAACACGCTACCAAGT 60.428 43.478 0.00 0.00 0.00 3.16
79 80 2.415491 GCGCTACATCCCTTTTCCAAAC 60.415 50.000 0.00 0.00 0.00 2.93
80 81 2.163613 CGCTACATCCCTTTTCCAAACC 59.836 50.000 0.00 0.00 0.00 3.27
86 87 5.620206 ACATCCCTTTTCCAAACCAAATTC 58.380 37.500 0.00 0.00 0.00 2.17
134 135 6.505044 TCATGTCTTCTTTTCCACATCATG 57.495 37.500 0.00 0.00 33.74 3.07
150 151 8.301720 TCCACATCATGATTTTCTTCTTCTTTG 58.698 33.333 5.16 0.00 0.00 2.77
219 237 7.257722 GTGTCATTTCTTCTTTTTGGTCTCAA 58.742 34.615 0.00 0.00 0.00 3.02
322 340 5.860648 AGGAAGAAGGGGTCATCTTTTTA 57.139 39.130 0.00 0.00 36.08 1.52
323 341 6.408770 AGGAAGAAGGGGTCATCTTTTTAT 57.591 37.500 0.00 0.00 36.08 1.40
438 458 4.774200 ACAAGGAAGGAGGATTTTCAATGG 59.226 41.667 0.00 0.00 0.00 3.16
441 461 3.309848 GGAAGGAGGATTTTCAATGGGGA 60.310 47.826 0.00 0.00 0.00 4.81
679 702 4.218417 AGAAAAGATGGATTGGGTTGAACG 59.782 41.667 0.00 0.00 0.00 3.95
686 709 2.289444 GGATTGGGTTGAACGTCAGAGA 60.289 50.000 0.00 0.00 0.00 3.10
763 786 2.222027 CCCAAGCTAAATAAGGCCTCG 58.778 52.381 5.23 0.00 0.00 4.63
781 804 4.054671 CCTCGGAAATCAGAGCATAGAAC 58.945 47.826 5.21 0.00 36.95 3.01
790 813 1.972660 GAGCATAGAACAGGCGGGGT 61.973 60.000 0.00 0.00 39.49 4.95
799 822 2.120909 CAGGCGGGGTTGGCTAATG 61.121 63.158 0.00 0.00 43.82 1.90
940 970 8.848474 TTCTTCTTCTTCGGATTCAAAATAGT 57.152 30.769 0.00 0.00 0.00 2.12
1007 1037 1.342374 GGAAAGGAGGTTCATGGCCAT 60.342 52.381 14.09 14.09 0.00 4.40
1184 1216 2.270923 GCAAGCATACGACTCATCACA 58.729 47.619 0.00 0.00 0.00 3.58
1192 1224 8.213518 AGCATACGACTCATCACAAAATAAAT 57.786 30.769 0.00 0.00 0.00 1.40
1224 1256 3.313012 TCGTGTGTTCGATCTTTCCAT 57.687 42.857 0.00 0.00 34.85 3.41
1225 1257 4.443913 TCGTGTGTTCGATCTTTCCATA 57.556 40.909 0.00 0.00 34.85 2.74
1226 1258 4.811908 TCGTGTGTTCGATCTTTCCATAA 58.188 39.130 0.00 0.00 34.85 1.90
1227 1259 5.231702 TCGTGTGTTCGATCTTTCCATAAA 58.768 37.500 0.00 0.00 34.85 1.40
1228 1260 5.697178 TCGTGTGTTCGATCTTTCCATAAAA 59.303 36.000 0.00 0.00 34.85 1.52
1229 1261 6.370442 TCGTGTGTTCGATCTTTCCATAAAAT 59.630 34.615 0.00 0.00 34.85 1.82
1230 1262 6.682863 CGTGTGTTCGATCTTTCCATAAAATC 59.317 38.462 0.00 0.00 0.00 2.17
1231 1263 6.967199 GTGTGTTCGATCTTTCCATAAAATCC 59.033 38.462 0.00 0.00 0.00 3.01
1232 1264 6.183360 TGTGTTCGATCTTTCCATAAAATCCG 60.183 38.462 0.00 0.00 0.00 4.18
1233 1265 5.295787 TGTTCGATCTTTCCATAAAATCCGG 59.704 40.000 0.00 0.00 0.00 5.14
1234 1266 5.284861 TCGATCTTTCCATAAAATCCGGA 57.715 39.130 6.61 6.61 0.00 5.14
1235 1267 5.676552 TCGATCTTTCCATAAAATCCGGAA 58.323 37.500 9.01 0.00 37.03 4.30
1236 1268 6.296026 TCGATCTTTCCATAAAATCCGGAAT 58.704 36.000 9.01 0.00 38.56 3.01
1237 1269 7.446769 TCGATCTTTCCATAAAATCCGGAATA 58.553 34.615 9.01 2.39 38.56 1.75
1238 1270 8.100791 TCGATCTTTCCATAAAATCCGGAATAT 58.899 33.333 9.01 5.02 38.56 1.28
1239 1271 8.391106 CGATCTTTCCATAAAATCCGGAATATC 58.609 37.037 9.01 0.00 38.56 1.63
1240 1272 9.454859 GATCTTTCCATAAAATCCGGAATATCT 57.545 33.333 9.01 0.00 38.56 1.98
1241 1273 9.813826 ATCTTTCCATAAAATCCGGAATATCTT 57.186 29.630 9.01 0.00 38.56 2.40
1242 1274 9.284968 TCTTTCCATAAAATCCGGAATATCTTC 57.715 33.333 9.01 0.00 38.56 2.87
1243 1275 9.289782 CTTTCCATAAAATCCGGAATATCTTCT 57.710 33.333 9.01 0.00 38.56 2.85
1244 1276 9.640952 TTTCCATAAAATCCGGAATATCTTCTT 57.359 29.630 9.01 0.00 38.56 2.52
1245 1277 9.640952 TTCCATAAAATCCGGAATATCTTCTTT 57.359 29.630 9.01 0.00 33.88 2.52
1246 1278 9.066892 TCCATAAAATCCGGAATATCTTCTTTG 57.933 33.333 9.01 0.00 0.00 2.77
1247 1279 8.850156 CCATAAAATCCGGAATATCTTCTTTGT 58.150 33.333 9.01 0.00 0.00 2.83
1248 1280 9.669353 CATAAAATCCGGAATATCTTCTTTGTG 57.331 33.333 9.01 1.58 0.00 3.33
1249 1281 7.938140 AAAATCCGGAATATCTTCTTTGTGA 57.062 32.000 9.01 0.00 0.00 3.58
1250 1282 8.525290 AAAATCCGGAATATCTTCTTTGTGAT 57.475 30.769 9.01 0.00 0.00 3.06
1251 1283 7.502120 AATCCGGAATATCTTCTTTGTGATG 57.498 36.000 9.01 0.00 0.00 3.07
1252 1284 6.233905 TCCGGAATATCTTCTTTGTGATGA 57.766 37.500 0.00 0.00 34.09 2.92
1253 1285 6.830912 TCCGGAATATCTTCTTTGTGATGAT 58.169 36.000 0.00 0.00 40.94 2.45
1254 1286 7.962441 TCCGGAATATCTTCTTTGTGATGATA 58.038 34.615 0.00 0.00 42.30 2.15
1255 1287 8.428852 TCCGGAATATCTTCTTTGTGATGATAA 58.571 33.333 0.00 0.00 41.80 1.75
1256 1288 9.224267 CCGGAATATCTTCTTTGTGATGATAAT 57.776 33.333 0.00 0.00 41.80 1.28
1258 1290 9.837525 GGAATATCTTCTTTGTGATGATAATGC 57.162 33.333 0.00 0.00 41.80 3.56
1259 1291 9.837525 GAATATCTTCTTTGTGATGATAATGCC 57.162 33.333 0.00 0.00 41.80 4.40
1260 1292 8.929260 ATATCTTCTTTGTGATGATAATGCCA 57.071 30.769 0.00 0.00 41.80 4.92
1261 1293 7.649533 ATCTTCTTTGTGATGATAATGCCAA 57.350 32.000 0.00 0.00 37.67 4.52
1262 1294 7.465353 TCTTCTTTGTGATGATAATGCCAAA 57.535 32.000 0.00 0.00 0.00 3.28
1263 1295 7.894708 TCTTCTTTGTGATGATAATGCCAAAA 58.105 30.769 0.00 0.00 0.00 2.44
1264 1296 8.366401 TCTTCTTTGTGATGATAATGCCAAAAA 58.634 29.630 0.00 0.00 0.00 1.94
1280 1312 2.050477 AAAAATCTCAAGTTGGCGCG 57.950 45.000 0.00 0.00 0.00 6.86
1281 1313 0.951558 AAAATCTCAAGTTGGCGCGT 59.048 45.000 8.43 0.00 0.00 6.01
1282 1314 0.517316 AAATCTCAAGTTGGCGCGTC 59.483 50.000 2.29 2.29 0.00 5.19
1283 1315 0.320771 AATCTCAAGTTGGCGCGTCT 60.321 50.000 13.81 0.50 0.00 4.18
1284 1316 0.320771 ATCTCAAGTTGGCGCGTCTT 60.321 50.000 13.81 7.19 0.00 3.01
1285 1317 0.531974 TCTCAAGTTGGCGCGTCTTT 60.532 50.000 13.81 0.45 0.00 2.52
1286 1318 0.110644 CTCAAGTTGGCGCGTCTTTC 60.111 55.000 13.81 1.92 0.00 2.62
1287 1319 0.531974 TCAAGTTGGCGCGTCTTTCT 60.532 50.000 13.81 4.55 0.00 2.52
1288 1320 0.307760 CAAGTTGGCGCGTCTTTCTT 59.692 50.000 13.81 10.83 0.00 2.52
1289 1321 1.021968 AAGTTGGCGCGTCTTTCTTT 58.978 45.000 13.81 0.00 0.00 2.52
1290 1322 0.586802 AGTTGGCGCGTCTTTCTTTC 59.413 50.000 13.81 0.00 0.00 2.62
1291 1323 0.586802 GTTGGCGCGTCTTTCTTTCT 59.413 50.000 13.81 0.00 0.00 2.52
1292 1324 1.002792 GTTGGCGCGTCTTTCTTTCTT 60.003 47.619 13.81 0.00 0.00 2.52
1293 1325 0.865769 TGGCGCGTCTTTCTTTCTTC 59.134 50.000 13.81 0.00 0.00 2.87
1294 1326 0.166161 GGCGCGTCTTTCTTTCTTCC 59.834 55.000 8.43 0.00 0.00 3.46
1295 1327 1.149148 GCGCGTCTTTCTTTCTTCCT 58.851 50.000 8.43 0.00 0.00 3.36
1296 1328 1.531578 GCGCGTCTTTCTTTCTTCCTT 59.468 47.619 8.43 0.00 0.00 3.36
1297 1329 2.031944 GCGCGTCTTTCTTTCTTCCTTT 60.032 45.455 8.43 0.00 0.00 3.11
1298 1330 3.800163 CGCGTCTTTCTTTCTTCCTTTC 58.200 45.455 0.00 0.00 0.00 2.62
1299 1331 3.364068 CGCGTCTTTCTTTCTTCCTTTCC 60.364 47.826 0.00 0.00 0.00 3.13
1300 1332 3.058155 GCGTCTTTCTTTCTTCCTTTCCC 60.058 47.826 0.00 0.00 0.00 3.97
1301 1333 4.390264 CGTCTTTCTTTCTTCCTTTCCCT 58.610 43.478 0.00 0.00 0.00 4.20
1302 1334 4.822350 CGTCTTTCTTTCTTCCTTTCCCTT 59.178 41.667 0.00 0.00 0.00 3.95
1303 1335 5.995897 CGTCTTTCTTTCTTCCTTTCCCTTA 59.004 40.000 0.00 0.00 0.00 2.69
1304 1336 6.655425 CGTCTTTCTTTCTTCCTTTCCCTTAT 59.345 38.462 0.00 0.00 0.00 1.73
1305 1337 7.361286 CGTCTTTCTTTCTTCCTTTCCCTTATG 60.361 40.741 0.00 0.00 0.00 1.90
1306 1338 7.448777 GTCTTTCTTTCTTCCTTTCCCTTATGT 59.551 37.037 0.00 0.00 0.00 2.29
1307 1339 8.004801 TCTTTCTTTCTTCCTTTCCCTTATGTT 58.995 33.333 0.00 0.00 0.00 2.71
1308 1340 7.524717 TTCTTTCTTCCTTTCCCTTATGTTG 57.475 36.000 0.00 0.00 0.00 3.33
1309 1341 6.010219 TCTTTCTTCCTTTCCCTTATGTTGG 58.990 40.000 0.00 0.00 0.00 3.77
1310 1342 5.333566 TTCTTCCTTTCCCTTATGTTGGT 57.666 39.130 0.00 0.00 0.00 3.67
1311 1343 4.918588 TCTTCCTTTCCCTTATGTTGGTC 58.081 43.478 0.00 0.00 0.00 4.02
1312 1344 4.352595 TCTTCCTTTCCCTTATGTTGGTCA 59.647 41.667 0.00 0.00 0.00 4.02
1313 1345 4.946160 TCCTTTCCCTTATGTTGGTCAT 57.054 40.909 0.00 0.00 40.25 3.06
1314 1346 5.269554 TCCTTTCCCTTATGTTGGTCATT 57.730 39.130 0.00 0.00 37.91 2.57
1315 1347 6.395780 TCCTTTCCCTTATGTTGGTCATTA 57.604 37.500 0.00 0.00 37.91 1.90
1316 1348 6.423182 TCCTTTCCCTTATGTTGGTCATTAG 58.577 40.000 0.00 0.00 37.91 1.73
1317 1349 6.216662 TCCTTTCCCTTATGTTGGTCATTAGA 59.783 38.462 0.00 0.00 35.85 2.10
1318 1350 6.543831 CCTTTCCCTTATGTTGGTCATTAGAG 59.456 42.308 0.00 0.00 35.85 2.43
1319 1351 5.630415 TCCCTTATGTTGGTCATTAGAGG 57.370 43.478 0.00 0.00 35.85 3.69
1320 1352 4.137543 CCCTTATGTTGGTCATTAGAGGC 58.862 47.826 0.00 0.00 35.85 4.70
1321 1353 4.137543 CCTTATGTTGGTCATTAGAGGCC 58.862 47.826 0.00 0.00 35.85 5.19
1322 1354 4.141390 CCTTATGTTGGTCATTAGAGGCCT 60.141 45.833 3.86 3.86 35.85 5.19
1323 1355 3.567478 ATGTTGGTCATTAGAGGCCTC 57.433 47.619 26.22 26.22 32.08 4.70
1324 1356 2.551270 TGTTGGTCATTAGAGGCCTCT 58.449 47.619 36.62 36.62 43.40 3.69
1325 1357 2.912956 TGTTGGTCATTAGAGGCCTCTT 59.087 45.455 39.23 21.08 40.93 2.85
1326 1358 3.274288 GTTGGTCATTAGAGGCCTCTTG 58.726 50.000 39.23 30.54 40.93 3.02
1327 1359 2.832838 TGGTCATTAGAGGCCTCTTGA 58.167 47.619 39.23 32.20 40.93 3.02
1328 1360 2.501723 TGGTCATTAGAGGCCTCTTGAC 59.498 50.000 38.08 38.08 42.44 3.18
1329 1361 2.769095 GGTCATTAGAGGCCTCTTGACT 59.231 50.000 40.59 24.98 42.62 3.41
1330 1362 3.198853 GGTCATTAGAGGCCTCTTGACTT 59.801 47.826 40.59 24.40 42.62 3.01
1331 1363 4.323868 GGTCATTAGAGGCCTCTTGACTTT 60.324 45.833 40.59 23.82 42.62 2.66
1332 1364 5.249420 GTCATTAGAGGCCTCTTGACTTTT 58.751 41.667 38.20 21.14 41.11 2.27
1333 1365 5.352846 GTCATTAGAGGCCTCTTGACTTTTC 59.647 44.000 38.20 23.74 41.11 2.29
1334 1366 5.249393 TCATTAGAGGCCTCTTGACTTTTCT 59.751 40.000 39.23 14.61 40.93 2.52
1335 1367 3.694043 AGAGGCCTCTTGACTTTTCTC 57.306 47.619 30.40 0.00 36.31 2.87
1336 1368 3.247162 AGAGGCCTCTTGACTTTTCTCT 58.753 45.455 30.40 2.58 36.31 3.10
1337 1369 3.650461 AGAGGCCTCTTGACTTTTCTCTT 59.350 43.478 30.40 2.08 36.31 2.85
1338 1370 4.000325 GAGGCCTCTTGACTTTTCTCTTC 59.000 47.826 26.25 0.00 0.00 2.87
1339 1371 3.078097 GGCCTCTTGACTTTTCTCTTCC 58.922 50.000 0.00 0.00 0.00 3.46
1340 1372 3.078097 GCCTCTTGACTTTTCTCTTCCC 58.922 50.000 0.00 0.00 0.00 3.97
1341 1373 3.244735 GCCTCTTGACTTTTCTCTTCCCT 60.245 47.826 0.00 0.00 0.00 4.20
1342 1374 4.020128 GCCTCTTGACTTTTCTCTTCCCTA 60.020 45.833 0.00 0.00 0.00 3.53
1343 1375 5.338789 GCCTCTTGACTTTTCTCTTCCCTAT 60.339 44.000 0.00 0.00 0.00 2.57
1344 1376 6.127026 GCCTCTTGACTTTTCTCTTCCCTATA 60.127 42.308 0.00 0.00 0.00 1.31
1345 1377 7.581658 GCCTCTTGACTTTTCTCTTCCCTATAA 60.582 40.741 0.00 0.00 0.00 0.98
1346 1378 8.322091 CCTCTTGACTTTTCTCTTCCCTATAAA 58.678 37.037 0.00 0.00 0.00 1.40
1347 1379 9.377312 CTCTTGACTTTTCTCTTCCCTATAAAG 57.623 37.037 0.00 0.00 0.00 1.85
1348 1380 8.322091 TCTTGACTTTTCTCTTCCCTATAAAGG 58.678 37.037 0.00 0.00 43.25 3.11
1421 1453 2.166870 ACGTGTTTGTCACAGTAGGTCA 59.833 45.455 0.00 0.00 46.44 4.02
1562 1594 4.212004 CACTTCCATGATGATAAATCGCGT 59.788 41.667 5.77 0.00 0.00 6.01
1564 1596 2.480037 TCCATGATGATAAATCGCGTGC 59.520 45.455 5.77 0.00 0.00 5.34
1688 1720 2.445682 CCCGACCAATGGGGATTTAA 57.554 50.000 3.55 0.00 46.95 1.52
1734 1766 1.155424 GGAAACACGTGTCGGCTCAA 61.155 55.000 23.61 0.00 0.00 3.02
1736 1768 0.741574 AAACACGTGTCGGCTCAACA 60.742 50.000 23.61 0.00 0.00 3.33
1846 1878 2.358984 GCCGGCCCGTTTGACTTA 60.359 61.111 18.11 0.00 0.00 2.24
1912 1944 5.163622 GCATGTTCGCATATAGCCCATTTAT 60.164 40.000 0.00 0.00 41.38 1.40
2106 2138 2.279935 AACTGGCCCGTAATGAACAA 57.720 45.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.505625 GGGTACAAAATGTCGTAAGTTCAAATA 58.494 33.333 0.00 0.00 39.48 1.40
56 57 1.271652 TGGAAAAGGGATGTAGCGCAA 60.272 47.619 11.47 0.00 0.00 4.85
79 80 6.411630 CAATGGCATTGTACAAGAATTTGG 57.588 37.500 27.93 1.43 35.78 3.28
113 114 7.713734 AATCATGATGTGGAAAAGAAGACAT 57.286 32.000 9.46 0.00 0.00 3.06
192 210 4.932146 ACCAAAAAGAAGAAATGACACGG 58.068 39.130 0.00 0.00 0.00 4.94
477 497 6.294286 GCTAAAGCACCAAACCATAAAGTACA 60.294 38.462 0.00 0.00 41.59 2.90
561 582 6.013379 TCCCTCCCATAGCAATAACTAGAATG 60.013 42.308 0.00 0.00 0.00 2.67
686 709 9.647918 AAATGGGGTTTACCAAATTTTTAATGT 57.352 25.926 0.69 0.00 45.13 2.71
763 786 3.563390 GCCTGTTCTATGCTCTGATTTCC 59.437 47.826 0.00 0.00 0.00 3.13
781 804 2.120909 CATTAGCCAACCCCGCCTG 61.121 63.158 0.00 0.00 0.00 4.85
790 813 7.035004 CGAAATCCTTTCATTTCATTAGCCAA 58.965 34.615 6.70 0.00 41.19 4.52
799 822 7.617533 TTTTCGTTCGAAATCCTTTCATTTC 57.382 32.000 18.55 0.00 39.63 2.17
819 842 7.305474 TCCTTGTCGAATTAGCAAAGATTTTC 58.695 34.615 0.00 0.00 0.00 2.29
988 1018 1.753073 CATGGCCATGAACCTCCTTTC 59.247 52.381 37.84 0.00 41.20 2.62
1007 1037 7.020827 ACTCTGATTCTAACATCTTTTCCCA 57.979 36.000 0.00 0.00 0.00 4.37
1149 1181 2.482336 TGCTTGCGACAATAACGACAAT 59.518 40.909 0.00 0.00 0.00 2.71
1224 1256 9.627123 ATCACAAAGAAGATATTCCGGATTTTA 57.373 29.630 4.15 0.00 0.00 1.52
1225 1257 7.938140 TCACAAAGAAGATATTCCGGATTTT 57.062 32.000 4.15 0.00 0.00 1.82
1226 1258 7.775093 TCATCACAAAGAAGATATTCCGGATTT 59.225 33.333 4.15 0.00 0.00 2.17
1227 1259 7.282585 TCATCACAAAGAAGATATTCCGGATT 58.717 34.615 4.15 4.05 0.00 3.01
1228 1260 6.830912 TCATCACAAAGAAGATATTCCGGAT 58.169 36.000 4.15 0.00 0.00 4.18
1229 1261 6.233905 TCATCACAAAGAAGATATTCCGGA 57.766 37.500 0.00 0.00 0.00 5.14
1230 1262 8.607441 TTATCATCACAAAGAAGATATTCCGG 57.393 34.615 0.00 0.00 36.95 5.14
1232 1264 9.837525 GCATTATCATCACAAAGAAGATATTCC 57.162 33.333 0.00 0.00 36.95 3.01
1233 1265 9.837525 GGCATTATCATCACAAAGAAGATATTC 57.162 33.333 0.00 0.00 36.95 1.75
1234 1266 9.358406 TGGCATTATCATCACAAAGAAGATATT 57.642 29.630 0.00 0.00 36.95 1.28
1235 1267 8.929260 TGGCATTATCATCACAAAGAAGATAT 57.071 30.769 0.00 0.00 36.95 1.63
1236 1268 8.750515 TTGGCATTATCATCACAAAGAAGATA 57.249 30.769 0.00 0.00 36.23 1.98
1237 1269 7.649533 TTGGCATTATCATCACAAAGAAGAT 57.350 32.000 0.00 0.00 38.21 2.40
1238 1270 7.465353 TTTGGCATTATCATCACAAAGAAGA 57.535 32.000 0.00 0.00 0.00 2.87
1239 1271 8.537049 TTTTTGGCATTATCATCACAAAGAAG 57.463 30.769 0.00 0.00 0.00 2.85
1261 1293 1.336755 ACGCGCCAACTTGAGATTTTT 59.663 42.857 5.73 0.00 0.00 1.94
1262 1294 0.951558 ACGCGCCAACTTGAGATTTT 59.048 45.000 5.73 0.00 0.00 1.82
1263 1295 0.517316 GACGCGCCAACTTGAGATTT 59.483 50.000 5.73 0.00 0.00 2.17
1264 1296 0.320771 AGACGCGCCAACTTGAGATT 60.321 50.000 5.73 0.00 0.00 2.40
1265 1297 0.320771 AAGACGCGCCAACTTGAGAT 60.321 50.000 5.73 0.00 0.00 2.75
1266 1298 0.531974 AAAGACGCGCCAACTTGAGA 60.532 50.000 5.73 0.00 0.00 3.27
1267 1299 0.110644 GAAAGACGCGCCAACTTGAG 60.111 55.000 5.73 0.00 0.00 3.02
1268 1300 0.531974 AGAAAGACGCGCCAACTTGA 60.532 50.000 5.73 0.00 0.00 3.02
1269 1301 0.307760 AAGAAAGACGCGCCAACTTG 59.692 50.000 5.73 0.00 0.00 3.16
1270 1302 1.002792 GAAAGAAAGACGCGCCAACTT 60.003 47.619 5.73 4.20 0.00 2.66
1271 1303 0.586802 GAAAGAAAGACGCGCCAACT 59.413 50.000 5.73 0.00 0.00 3.16
1272 1304 0.586802 AGAAAGAAAGACGCGCCAAC 59.413 50.000 5.73 0.00 0.00 3.77
1273 1305 1.263217 GAAGAAAGAAAGACGCGCCAA 59.737 47.619 5.73 0.00 0.00 4.52
1274 1306 0.865769 GAAGAAAGAAAGACGCGCCA 59.134 50.000 5.73 0.00 0.00 5.69
1275 1307 0.166161 GGAAGAAAGAAAGACGCGCC 59.834 55.000 5.73 0.00 0.00 6.53
1276 1308 1.149148 AGGAAGAAAGAAAGACGCGC 58.851 50.000 5.73 0.00 0.00 6.86
1277 1309 3.364068 GGAAAGGAAGAAAGAAAGACGCG 60.364 47.826 3.53 3.53 0.00 6.01
1278 1310 3.058155 GGGAAAGGAAGAAAGAAAGACGC 60.058 47.826 0.00 0.00 0.00 5.19
1279 1311 4.390264 AGGGAAAGGAAGAAAGAAAGACG 58.610 43.478 0.00 0.00 0.00 4.18
1280 1312 7.448777 ACATAAGGGAAAGGAAGAAAGAAAGAC 59.551 37.037 0.00 0.00 0.00 3.01
1281 1313 7.526918 ACATAAGGGAAAGGAAGAAAGAAAGA 58.473 34.615 0.00 0.00 0.00 2.52
1282 1314 7.767250 ACATAAGGGAAAGGAAGAAAGAAAG 57.233 36.000 0.00 0.00 0.00 2.62
1283 1315 7.015195 CCAACATAAGGGAAAGGAAGAAAGAAA 59.985 37.037 0.00 0.00 0.00 2.52
1284 1316 6.493458 CCAACATAAGGGAAAGGAAGAAAGAA 59.507 38.462 0.00 0.00 0.00 2.52
1285 1317 6.010219 CCAACATAAGGGAAAGGAAGAAAGA 58.990 40.000 0.00 0.00 0.00 2.52
1286 1318 5.775195 ACCAACATAAGGGAAAGGAAGAAAG 59.225 40.000 0.00 0.00 0.00 2.62
1287 1319 5.711698 ACCAACATAAGGGAAAGGAAGAAA 58.288 37.500 0.00 0.00 0.00 2.52
1288 1320 5.163034 TGACCAACATAAGGGAAAGGAAGAA 60.163 40.000 0.00 0.00 0.00 2.52
1289 1321 4.352595 TGACCAACATAAGGGAAAGGAAGA 59.647 41.667 0.00 0.00 0.00 2.87
1290 1322 4.662278 TGACCAACATAAGGGAAAGGAAG 58.338 43.478 0.00 0.00 0.00 3.46
1291 1323 4.733077 TGACCAACATAAGGGAAAGGAA 57.267 40.909 0.00 0.00 0.00 3.36
1292 1324 4.946160 ATGACCAACATAAGGGAAAGGA 57.054 40.909 0.00 0.00 37.46 3.36
1293 1325 6.423182 TCTAATGACCAACATAAGGGAAAGG 58.577 40.000 0.00 0.00 38.38 3.11
1294 1326 6.543831 CCTCTAATGACCAACATAAGGGAAAG 59.456 42.308 0.00 0.00 38.38 2.62
1295 1327 6.423182 CCTCTAATGACCAACATAAGGGAAA 58.577 40.000 0.00 0.00 38.38 3.13
1296 1328 5.631481 GCCTCTAATGACCAACATAAGGGAA 60.631 44.000 0.00 0.00 38.38 3.97
1297 1329 4.141482 GCCTCTAATGACCAACATAAGGGA 60.141 45.833 0.00 0.00 38.38 4.20
1298 1330 4.137543 GCCTCTAATGACCAACATAAGGG 58.862 47.826 0.00 0.00 38.38 3.95
1299 1331 4.137543 GGCCTCTAATGACCAACATAAGG 58.862 47.826 0.00 0.00 38.38 2.69
1300 1332 5.041191 AGGCCTCTAATGACCAACATAAG 57.959 43.478 0.00 0.00 38.38 1.73
1301 1333 4.721776 AGAGGCCTCTAATGACCAACATAA 59.278 41.667 34.40 0.00 38.35 1.90
1302 1334 4.298626 AGAGGCCTCTAATGACCAACATA 58.701 43.478 34.40 0.00 38.35 2.29
1303 1335 3.118531 AGAGGCCTCTAATGACCAACAT 58.881 45.455 34.40 4.82 38.35 2.71
1304 1336 2.551270 AGAGGCCTCTAATGACCAACA 58.449 47.619 34.40 0.00 38.35 3.33
1305 1337 3.055094 TCAAGAGGCCTCTAATGACCAAC 60.055 47.826 35.31 3.32 39.39 3.77
1306 1338 3.055094 GTCAAGAGGCCTCTAATGACCAA 60.055 47.826 36.99 18.26 39.64 3.67
1307 1339 2.501723 GTCAAGAGGCCTCTAATGACCA 59.498 50.000 36.99 18.54 39.64 4.02
1308 1340 2.769095 AGTCAAGAGGCCTCTAATGACC 59.231 50.000 39.94 29.45 43.39 4.02
1309 1341 4.479786 AAGTCAAGAGGCCTCTAATGAC 57.520 45.455 38.49 38.49 43.02 3.06
1310 1342 5.249393 AGAAAAGTCAAGAGGCCTCTAATGA 59.751 40.000 35.31 30.41 39.39 2.57
1311 1343 5.495640 AGAAAAGTCAAGAGGCCTCTAATG 58.504 41.667 35.31 28.70 39.39 1.90
1312 1344 5.487131 AGAGAAAAGTCAAGAGGCCTCTAAT 59.513 40.000 35.31 18.77 39.39 1.73
1313 1345 4.841246 AGAGAAAAGTCAAGAGGCCTCTAA 59.159 41.667 35.31 23.14 39.39 2.10
1314 1346 4.421131 AGAGAAAAGTCAAGAGGCCTCTA 58.579 43.478 35.31 18.77 39.39 2.43
1315 1347 3.247162 AGAGAAAAGTCAAGAGGCCTCT 58.753 45.455 30.40 30.40 42.75 3.69
1316 1348 3.694043 AGAGAAAAGTCAAGAGGCCTC 57.306 47.619 26.22 26.22 0.00 4.70
1317 1349 3.244735 GGAAGAGAAAAGTCAAGAGGCCT 60.245 47.826 3.86 3.86 0.00 5.19
1318 1350 3.078097 GGAAGAGAAAAGTCAAGAGGCC 58.922 50.000 0.00 0.00 0.00 5.19
1319 1351 3.078097 GGGAAGAGAAAAGTCAAGAGGC 58.922 50.000 0.00 0.00 0.00 4.70
1320 1352 4.632327 AGGGAAGAGAAAAGTCAAGAGG 57.368 45.455 0.00 0.00 0.00 3.69
1321 1353 9.377312 CTTTATAGGGAAGAGAAAAGTCAAGAG 57.623 37.037 0.00 0.00 0.00 2.85
1322 1354 8.322091 CCTTTATAGGGAAGAGAAAAGTCAAGA 58.678 37.037 0.00 0.00 37.94 3.02
1323 1355 8.322091 TCCTTTATAGGGAAGAGAAAAGTCAAG 58.678 37.037 0.00 0.00 42.26 3.02
1324 1356 8.214721 TCCTTTATAGGGAAGAGAAAAGTCAA 57.785 34.615 0.00 0.00 42.26 3.18
1325 1357 7.808279 TCCTTTATAGGGAAGAGAAAAGTCA 57.192 36.000 0.00 0.00 42.26 3.41
1326 1358 9.688091 AAATCCTTTATAGGGAAGAGAAAAGTC 57.312 33.333 0.00 0.00 42.26 3.01
1327 1359 9.467796 CAAATCCTTTATAGGGAAGAGAAAAGT 57.532 33.333 0.00 0.00 42.26 2.66
1328 1360 9.467796 ACAAATCCTTTATAGGGAAGAGAAAAG 57.532 33.333 0.00 0.00 42.26 2.27
1329 1361 9.822727 AACAAATCCTTTATAGGGAAGAGAAAA 57.177 29.630 0.00 0.00 42.26 2.29
1330 1362 9.822727 AAACAAATCCTTTATAGGGAAGAGAAA 57.177 29.630 0.00 0.00 42.26 2.52
1331 1363 9.822727 AAAACAAATCCTTTATAGGGAAGAGAA 57.177 29.630 0.00 0.00 42.26 2.87
1332 1364 9.822727 AAAAACAAATCCTTTATAGGGAAGAGA 57.177 29.630 0.00 0.00 42.26 3.10
1421 1453 3.812609 TGTACATGCATGACAGAAAACGT 59.187 39.130 32.75 8.94 0.00 3.99
1550 1582 1.006086 CTGTGGCACGCGATTTATCA 58.994 50.000 15.93 3.78 45.01 2.15
1562 1594 0.463654 ACGAAAGCACTTCTGTGGCA 60.464 50.000 0.00 0.00 43.97 4.92
1564 1596 1.581934 TGACGAAAGCACTTCTGTGG 58.418 50.000 0.00 0.00 43.97 4.17
1619 1651 0.103572 GACCCGATAGCTTAACGGCA 59.896 55.000 16.64 0.00 44.45 5.69
1687 1719 5.048083 AGCCAATGATGATTTTACACGTGTT 60.048 36.000 28.55 8.70 0.00 3.32
1688 1720 4.458989 AGCCAATGATGATTTTACACGTGT 59.541 37.500 26.52 26.52 0.00 4.49
1734 1766 2.577563 TGGATGACATCTGTCCCAATGT 59.422 45.455 14.95 0.00 44.15 2.71
1736 1768 2.848694 AGTGGATGACATCTGTCCCAAT 59.151 45.455 14.95 5.51 44.15 3.16
1807 1839 0.039618 TTTCACAGGAATGGGCCTCC 59.960 55.000 4.53 4.01 35.66 4.30
1846 1878 0.673644 CGACCCGCCATCTTTTGACT 60.674 55.000 0.00 0.00 0.00 3.41
1912 1944 3.038945 GCCTTGGGTTAGCGGGCTA 62.039 63.158 0.00 0.00 39.68 3.93
2106 2138 6.037830 GCCGTTAATGGTGTAAAGTGATACAT 59.962 38.462 15.21 0.00 38.03 2.29


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

AutoCloner maintained by Alex Coulton.