Multiple sequence alignment - TraesCS5D01G421100

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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 TraesCS5D01G421100 chr5D 100.000 3409 0 0 1 3409 481424510 481427918 0.000000e+00 6296.0
1 TraesCS5D01G421100 chr5D 88.287 1016 66 21 1419 2411 481303228 481304213 0.000000e+00 1168.0
2 TraesCS5D01G421100 chr5D 87.548 1044 68 22 1419 2411 481183941 481184973 0.000000e+00 1151.0
3 TraesCS5D01G421100 chr5D 79.753 647 62 39 642 1258 481183325 481183932 4.100000e-109 405.0
4 TraesCS5D01G421100 chr5D 89.818 275 18 3 999 1264 481302940 481303213 9.060000e-91 344.0
5 TraesCS5D01G421100 chr5D 82.857 105 14 4 466 568 481180600 481180702 1.300000e-14 91.6
6 TraesCS5D01G421100 chr5B 90.517 1856 96 27 1472 3280 589998696 590000518 0.000000e+00 2379.0
7 TraesCS5D01G421100 chr5B 88.476 1319 72 44 1 1280 589997349 589998626 0.000000e+00 1520.0
8 TraesCS5D01G421100 chr5B 87.894 1016 72 21 1419 2411 589894575 589895562 0.000000e+00 1147.0
9 TraesCS5D01G421100 chr5B 84.608 981 80 25 1482 2411 589677264 589678224 0.000000e+00 909.0
10 TraesCS5D01G421100 chr5B 93.625 251 13 1 1000 1250 589676850 589677097 4.150000e-99 372.0
11 TraesCS5D01G421100 chr5B 90.909 275 15 5 999 1264 589894271 589894544 8.990000e-96 361.0
12 TraesCS5D01G421100 chr5B 82.174 230 13 8 665 891 589676517 589676721 4.520000e-39 172.0
13 TraesCS5D01G421100 chr5B 96.939 98 3 0 2597 2694 166379086 166379183 7.570000e-37 165.0
14 TraesCS5D01G421100 chr5B 82.877 146 20 4 71 215 589996547 589996688 3.570000e-25 126.0
15 TraesCS5D01G421100 chr5A 91.125 1431 78 20 1883 3285 600439045 600440454 0.000000e+00 1893.0
16 TraesCS5D01G421100 chr5A 91.597 1309 63 23 1 1279 600437323 600438614 0.000000e+00 1764.0
17 TraesCS5D01G421100 chr5A 88.025 977 65 16 1469 2411 600361809 600362767 0.000000e+00 1109.0
18 TraesCS5D01G421100 chr5A 96.296 378 12 2 1472 1848 600438664 600439040 1.340000e-173 619.0
19 TraesCS5D01G421100 chr5A 89.189 444 32 6 1419 1848 600237182 600237623 1.080000e-149 540.0
20 TraesCS5D01G421100 chr5A 82.187 567 53 15 1883 2411 600237628 600238184 8.680000e-121 444.0
21 TraesCS5D01G421100 chr5A 93.382 272 11 2 999 1264 600361473 600361743 2.470000e-106 396.0
22 TraesCS5D01G421100 chr5A 92.164 268 14 4 1000 1264 600236884 600237147 4.150000e-99 372.0
23 TraesCS5D01G421100 chr5A 97.080 137 4 0 3272 3408 600440479 600440615 7.360000e-57 231.0
24 TraesCS5D01G421100 chr5A 81.022 274 15 13 77 332 600433092 600433346 2.090000e-42 183.0
25 TraesCS5D01G421100 chr5A 88.489 139 13 3 71 207 600436422 600436559 7.570000e-37 165.0
26 TraesCS5D01G421100 chr5A 79.339 242 18 12 642 882 600236536 600236746 1.280000e-29 141.0
27 TraesCS5D01G421100 chr4B 84.783 552 66 4 1856 2392 663941389 663940841 3.870000e-149 538.0
28 TraesCS5D01G421100 chr4B 83.614 415 52 9 1424 1825 663941894 663941483 3.210000e-100 375.0
29 TraesCS5D01G421100 chr4B 95.918 98 4 0 2596 2693 511163806 511163709 3.520000e-35 159.0
30 TraesCS5D01G421100 chr4D 81.111 450 59 9 1972 2397 506482766 506483213 1.520000e-88 337.0
31 TraesCS5D01G421100 chr4D 88.976 254 25 1 1004 1254 506470753 506471006 9.190000e-81 311.0
32 TraesCS5D01G421100 chr4D 94.118 119 7 0 1856 1974 506471114 506471232 7.510000e-42 182.0
33 TraesCS5D01G421100 chr4D 95.960 99 3 1 2596 2693 414999660 414999562 3.520000e-35 159.0
34 TraesCS5D01G421100 chr7B 95.238 105 3 2 2589 2693 162120914 162120812 7.570000e-37 165.0
35 TraesCS5D01G421100 chr3A 96.907 97 3 0 2597 2693 470095682 470095778 2.720000e-36 163.0
36 TraesCS5D01G421100 chr1A 95.960 99 2 2 2597 2695 460934476 460934572 3.520000e-35 159.0
37 TraesCS5D01G421100 chr7D 91.150 113 8 2 2582 2693 580850194 580850083 5.890000e-33 152.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G421100 chr5D 481424510 481427918 3408 False 6296.000000 6296 100.000000 1 3409 1 chr5D.!!$F1 3408
1 TraesCS5D01G421100 chr5D 481302940 481304213 1273 False 756.000000 1168 89.052500 999 2411 2 chr5D.!!$F3 1412
2 TraesCS5D01G421100 chr5D 481180600 481184973 4373 False 549.200000 1151 83.386000 466 2411 3 chr5D.!!$F2 1945
3 TraesCS5D01G421100 chr5B 589996547 590000518 3971 False 1341.666667 2379 87.290000 1 3280 3 chr5B.!!$F4 3279
4 TraesCS5D01G421100 chr5B 589894271 589895562 1291 False 754.000000 1147 89.401500 999 2411 2 chr5B.!!$F3 1412
5 TraesCS5D01G421100 chr5B 589676517 589678224 1707 False 484.333333 909 86.802333 665 2411 3 chr5B.!!$F2 1746
6 TraesCS5D01G421100 chr5A 600433092 600440615 7523 False 809.166667 1893 90.934833 1 3408 6 chr5A.!!$F3 3407
7 TraesCS5D01G421100 chr5A 600361473 600362767 1294 False 752.500000 1109 90.703500 999 2411 2 chr5A.!!$F2 1412
8 TraesCS5D01G421100 chr5A 600236536 600238184 1648 False 374.250000 540 85.719750 642 2411 4 chr5A.!!$F1 1769
9 TraesCS5D01G421100 chr4B 663940841 663941894 1053 True 456.500000 538 84.198500 1424 2392 2 chr4B.!!$R2 968

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
526 4850 1.059913 CAAAGGACCCAGTCAGAGGT 58.94 55.0 0.0 0.0 39.75 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2417 9621 0.039074 ACTCTGAAGACGTGCGAAGG 60.039 55.0 0.0 0.0 0.0 3.46 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
173 4471 7.227873 TCATCCATGGTTCTTTTTAGTGTGTA 58.772 34.615 12.58 0.00 0.00 2.90
214 4512 5.784578 ACAACCCACTTTACTTTTGATCC 57.215 39.130 0.00 0.00 0.00 3.36
526 4850 1.059913 CAAAGGACCCAGTCAGAGGT 58.940 55.000 0.00 0.00 39.75 3.85
536 4863 6.270231 GGACCCAGTCAGAGGTTATATATGTT 59.730 42.308 0.00 0.00 36.17 2.71
625 5068 4.447724 TCGCACAGACAAATTAACACTCTC 59.552 41.667 0.00 0.00 0.00 3.20
626 5069 4.449068 CGCACAGACAAATTAACACTCTCT 59.551 41.667 0.00 0.00 0.00 3.10
629 5072 7.513968 GCACAGACAAATTAACACTCTCTTAG 58.486 38.462 0.00 0.00 0.00 2.18
630 5073 7.513968 CACAGACAAATTAACACTCTCTTAGC 58.486 38.462 0.00 0.00 0.00 3.09
631 5074 7.386299 CACAGACAAATTAACACTCTCTTAGCT 59.614 37.037 0.00 0.00 0.00 3.32
632 5075 7.600752 ACAGACAAATTAACACTCTCTTAGCTC 59.399 37.037 0.00 0.00 0.00 4.09
634 5077 6.769512 ACAAATTAACACTCTCTTAGCTCCA 58.230 36.000 0.00 0.00 0.00 3.86
638 5081 1.552792 ACACTCTCTTAGCTCCAAGGC 59.447 52.381 0.00 0.00 0.00 4.35
804 7688 2.751816 GCCCGCCTCATTTATAAACCCT 60.752 50.000 0.00 0.00 0.00 4.34
846 7733 3.132289 TCATCTACTTAACTCCAAGGCCG 59.868 47.826 0.00 0.00 0.00 6.13
931 7824 1.403249 GGTCCGTAGAACTAAGCGCAA 60.403 52.381 11.47 0.00 0.00 4.85
972 7865 2.157863 GCAAGAAGTACAAACGAGAGCC 59.842 50.000 0.00 0.00 0.00 4.70
973 7866 3.654414 CAAGAAGTACAAACGAGAGCCT 58.346 45.455 0.00 0.00 0.00 4.58
974 7867 4.058817 CAAGAAGTACAAACGAGAGCCTT 58.941 43.478 0.00 0.00 0.00 4.35
984 7903 1.825474 ACGAGAGCCTTGCTAGCTAAA 59.175 47.619 17.23 1.40 41.75 1.85
994 7913 6.484977 AGCCTTGCTAGCTAAAATTGATAGAC 59.515 38.462 17.23 0.00 39.29 2.59
1188 8154 1.613630 GGCCAGGAAGTCCCTCAGA 60.614 63.158 0.00 0.00 45.60 3.27
1255 8221 2.118403 TCTCCCCAGTGAGTTCCTTT 57.882 50.000 0.00 0.00 33.93 3.11
1256 8222 1.978580 TCTCCCCAGTGAGTTCCTTTC 59.021 52.381 0.00 0.00 33.93 2.62
1257 8223 1.981495 CTCCCCAGTGAGTTCCTTTCT 59.019 52.381 0.00 0.00 0.00 2.52
1258 8224 1.978580 TCCCCAGTGAGTTCCTTTCTC 59.021 52.381 0.00 0.00 0.00 2.87
1259 8225 1.981495 CCCCAGTGAGTTCCTTTCTCT 59.019 52.381 0.00 0.00 33.59 3.10
1260 8226 2.027653 CCCCAGTGAGTTCCTTTCTCTC 60.028 54.545 0.00 0.00 33.59 3.20
1261 8227 2.027653 CCCAGTGAGTTCCTTTCTCTCC 60.028 54.545 0.00 0.00 33.59 3.71
1262 8228 2.634940 CCAGTGAGTTCCTTTCTCTCCA 59.365 50.000 0.00 0.00 33.59 3.86
1263 8229 3.262915 CCAGTGAGTTCCTTTCTCTCCAT 59.737 47.826 0.00 0.00 33.59 3.41
1264 8230 4.467795 CCAGTGAGTTCCTTTCTCTCCATA 59.532 45.833 0.00 0.00 33.59 2.74
1265 8231 5.130145 CCAGTGAGTTCCTTTCTCTCCATAT 59.870 44.000 0.00 0.00 33.59 1.78
1266 8232 6.325028 CCAGTGAGTTCCTTTCTCTCCATATA 59.675 42.308 0.00 0.00 33.59 0.86
1270 8236 7.286775 GTGAGTTCCTTTCTCTCCATATACTCT 59.713 40.741 0.00 0.00 33.59 3.24
1280 8252 8.235359 TCTCTCCATATACTCTATGCATCATG 57.765 38.462 0.19 0.00 0.00 3.07
1281 8253 7.838193 TCTCTCCATATACTCTATGCATCATGT 59.162 37.037 0.19 2.92 0.00 3.21
1282 8254 8.005192 TCTCCATATACTCTATGCATCATGTC 57.995 38.462 0.19 0.00 0.00 3.06
1283 8255 7.069208 TCTCCATATACTCTATGCATCATGTCC 59.931 40.741 0.19 0.00 0.00 4.02
1284 8256 6.899631 TCCATATACTCTATGCATCATGTCCT 59.100 38.462 0.19 0.00 0.00 3.85
1286 8258 7.147776 CCATATACTCTATGCATCATGTCCTGA 60.148 40.741 0.19 0.00 38.53 3.86
1287 8259 6.870895 ATACTCTATGCATCATGTCCTGAT 57.129 37.500 0.19 0.00 45.78 2.90
1289 8261 4.591924 ACTCTATGCATCATGTCCTGATCA 59.408 41.667 0.19 0.00 42.91 2.92
1290 8262 5.248705 ACTCTATGCATCATGTCCTGATCAT 59.751 40.000 0.19 7.59 42.91 2.45
1291 8263 5.488341 TCTATGCATCATGTCCTGATCATG 58.512 41.667 0.19 0.00 42.91 3.07
1292 8264 2.227194 TGCATCATGTCCTGATCATGC 58.773 47.619 6.70 6.70 42.91 4.06
1294 8266 2.484651 GCATCATGTCCTGATCATGCTC 59.515 50.000 0.00 0.00 42.91 4.26
1297 8269 2.158856 TCATGTCCTGATCATGCTCACC 60.159 50.000 0.00 0.00 41.40 4.02
1300 8272 0.179702 TCCTGATCATGCTCACCTGC 59.820 55.000 0.00 0.00 0.00 4.85
1306 8278 0.746923 TCATGCTCACCTGCTCATGC 60.747 55.000 0.00 0.00 36.99 4.06
1307 8279 1.453379 ATGCTCACCTGCTCATGCC 60.453 57.895 0.00 0.00 38.71 4.40
1310 8282 1.748122 CTCACCTGCTCATGCCCAC 60.748 63.158 0.00 0.00 38.71 4.61
1311 8283 3.129502 CACCTGCTCATGCCCACG 61.130 66.667 0.00 0.00 38.71 4.94
1312 8284 3.640407 ACCTGCTCATGCCCACGT 61.640 61.111 0.00 0.00 38.71 4.49
1317 8289 2.672651 CTCATGCCCACGTTGCCA 60.673 61.111 4.50 0.00 0.00 4.92
1320 8292 3.762247 ATGCCCACGTTGCCATGC 61.762 61.111 4.50 0.00 0.00 4.06
1330 8302 4.419280 CACGTTGCCATGCATGTTAATTA 58.581 39.130 24.58 2.25 38.76 1.40
1331 8303 4.861462 CACGTTGCCATGCATGTTAATTAA 59.139 37.500 24.58 7.92 38.76 1.40
1334 8306 5.747675 CGTTGCCATGCATGTTAATTAATCA 59.252 36.000 24.58 5.99 38.76 2.57
1335 8307 6.255237 CGTTGCCATGCATGTTAATTAATCAA 59.745 34.615 24.58 10.83 38.76 2.57
1336 8308 7.401080 GTTGCCATGCATGTTAATTAATCAAC 58.599 34.615 24.58 16.93 38.76 3.18
1338 8310 6.047870 GCCATGCATGTTAATTAATCAACCA 58.952 36.000 24.58 0.00 0.00 3.67
1339 8311 6.538021 GCCATGCATGTTAATTAATCAACCAA 59.462 34.615 24.58 0.00 0.00 3.67
1340 8312 7.065563 GCCATGCATGTTAATTAATCAACCAAA 59.934 33.333 24.58 0.00 0.00 3.28
1341 8313 8.389603 CCATGCATGTTAATTAATCAACCAAAC 58.610 33.333 24.58 0.00 0.00 2.93
1342 8314 9.153721 CATGCATGTTAATTAATCAACCAAACT 57.846 29.630 18.91 0.00 0.00 2.66
1343 8315 9.723601 ATGCATGTTAATTAATCAACCAAACTT 57.276 25.926 0.00 0.00 0.00 2.66
1344 8316 8.986847 TGCATGTTAATTAATCAACCAAACTTG 58.013 29.630 0.31 0.00 0.00 3.16
1345 8317 8.987890 GCATGTTAATTAATCAACCAAACTTGT 58.012 29.630 0.31 0.00 0.00 3.16
1348 8320 9.535878 TGTTAATTAATCAACCAAACTTGTTCC 57.464 29.630 0.31 0.00 0.00 3.62
1349 8321 9.758651 GTTAATTAATCAACCAAACTTGTTCCT 57.241 29.630 0.31 0.00 0.00 3.36
1355 8327 5.258051 TCAACCAAACTTGTTCCTAACTGT 58.742 37.500 0.00 0.00 0.00 3.55
1356 8328 6.416415 TCAACCAAACTTGTTCCTAACTGTA 58.584 36.000 0.00 0.00 0.00 2.74
1359 8331 6.362248 ACCAAACTTGTTCCTAACTGTATGT 58.638 36.000 0.00 0.00 0.00 2.29
1363 8335 9.701098 CAAACTTGTTCCTAACTGTATGTAGTA 57.299 33.333 0.00 0.00 0.00 1.82
1364 8336 9.702494 AAACTTGTTCCTAACTGTATGTAGTAC 57.298 33.333 0.00 0.00 0.00 2.73
1365 8337 7.533426 ACTTGTTCCTAACTGTATGTAGTACG 58.467 38.462 0.00 0.00 36.01 3.67
1366 8338 7.175641 ACTTGTTCCTAACTGTATGTAGTACGT 59.824 37.037 0.00 0.00 36.01 3.57
1367 8339 8.560355 TTGTTCCTAACTGTATGTAGTACGTA 57.440 34.615 0.00 0.00 36.01 3.57
1368 8340 7.974675 TGTTCCTAACTGTATGTAGTACGTAC 58.025 38.462 21.13 21.13 40.18 3.67
1369 8341 7.824289 TGTTCCTAACTGTATGTAGTACGTACT 59.176 37.037 29.62 29.62 40.36 2.73
1370 8342 8.669243 GTTCCTAACTGTATGTAGTACGTACTT 58.331 37.037 31.58 17.41 40.36 2.24
1371 8343 8.201554 TCCTAACTGTATGTAGTACGTACTTG 57.798 38.462 31.58 21.01 40.36 3.16
1372 8344 7.824289 TCCTAACTGTATGTAGTACGTACTTGT 59.176 37.037 31.58 21.48 40.36 3.16
1373 8345 8.119226 CCTAACTGTATGTAGTACGTACTTGTC 58.881 40.741 31.58 21.32 40.36 3.18
1374 8346 7.439157 AACTGTATGTAGTACGTACTTGTCA 57.561 36.000 31.58 25.30 40.36 3.58
1375 8347 7.621428 ACTGTATGTAGTACGTACTTGTCAT 57.379 36.000 31.58 28.73 40.36 3.06
1376 8348 7.692088 ACTGTATGTAGTACGTACTTGTCATC 58.308 38.462 31.58 22.05 40.36 2.92
1377 8349 7.335171 ACTGTATGTAGTACGTACTTGTCATCA 59.665 37.037 31.58 24.21 40.36 3.07
1378 8350 8.217131 TGTATGTAGTACGTACTTGTCATCAT 57.783 34.615 31.58 23.59 40.36 2.45
1379 8351 8.680001 TGTATGTAGTACGTACTTGTCATCATT 58.320 33.333 31.58 15.43 40.36 2.57
1380 8352 9.512435 GTATGTAGTACGTACTTGTCATCATTT 57.488 33.333 31.58 15.14 37.55 2.32
1381 8353 8.630278 ATGTAGTACGTACTTGTCATCATTTC 57.370 34.615 31.58 4.04 37.73 2.17
1382 8354 7.595604 TGTAGTACGTACTTGTCATCATTTCA 58.404 34.615 31.58 7.67 37.73 2.69
1383 8355 6.946229 AGTACGTACTTGTCATCATTTCAC 57.054 37.500 22.45 0.00 31.13 3.18
1384 8356 6.688578 AGTACGTACTTGTCATCATTTCACT 58.311 36.000 22.45 0.00 31.13 3.41
1386 8358 4.690748 ACGTACTTGTCATCATTTCACTGG 59.309 41.667 0.00 0.00 0.00 4.00
1390 8362 6.469782 ACTTGTCATCATTTCACTGGTTTT 57.530 33.333 0.00 0.00 0.00 2.43
1401 8373 9.796120 TCATTTCACTGGTTTTAACTTTTACTG 57.204 29.630 0.00 0.00 0.00 2.74
1409 8381 8.190888 TGGTTTTAACTTTTACTGCACAAATG 57.809 30.769 0.00 0.00 0.00 2.32
1410 8382 7.278868 TGGTTTTAACTTTTACTGCACAAATGG 59.721 33.333 0.00 0.00 0.00 3.16
1411 8383 6.836577 TTTAACTTTTACTGCACAAATGGC 57.163 33.333 0.00 0.00 0.00 4.40
1412 8384 4.670896 AACTTTTACTGCACAAATGGCT 57.329 36.364 0.00 0.00 0.00 4.75
1415 8387 3.658757 TTTACTGCACAAATGGCTTCC 57.341 42.857 0.00 0.00 0.00 3.46
1416 8388 2.284754 TACTGCACAAATGGCTTCCA 57.715 45.000 0.00 0.00 38.19 3.53
1417 8389 1.412079 ACTGCACAAATGGCTTCCAA 58.588 45.000 0.00 0.00 36.95 3.53
1473 8476 2.422479 CAGAGTGCAATCATCCACTTGG 59.578 50.000 17.53 0.00 42.01 3.61
1519 8522 2.197465 GGTGGGGAGAAAGAGTGGTAT 58.803 52.381 0.00 0.00 0.00 2.73
1681 8693 1.347817 GGCTGAAGAAGTCGCTCGTG 61.348 60.000 0.00 0.00 0.00 4.35
1783 8807 3.008517 TCCTCCCCGAGCATGCAA 61.009 61.111 21.98 0.00 0.00 4.08
2264 9453 2.290323 ACTACAGAGCCCATTGTCAACC 60.290 50.000 0.00 0.00 0.00 3.77
2324 9513 1.198178 GCCGCCAACGATTTCTACAAA 59.802 47.619 0.00 0.00 43.93 2.83
2333 9531 3.508793 ACGATTTCTACAAAGTCGAGGGA 59.491 43.478 9.23 0.00 36.28 4.20
2460 9664 5.305585 TGTTCAGGGTAGACAAACAGAATC 58.694 41.667 0.00 0.00 0.00 2.52
2468 9672 1.289109 ACAAACAGAATCCGCCGACG 61.289 55.000 0.00 0.00 39.67 5.12
2482 9686 1.202973 CCGACGCGCTAGAACAGATG 61.203 60.000 5.73 0.00 0.00 2.90
2498 9702 3.001414 CAGATGCTGTCAAGTGAGGAAG 58.999 50.000 0.00 0.00 0.00 3.46
2556 9760 0.898320 TAGTCAGCAGAGCTTCACCC 59.102 55.000 0.00 0.00 36.40 4.61
2642 9846 4.201871 TGTCGCAGTTTTGAACTAAGGTTG 60.202 41.667 0.00 0.00 40.46 3.77
2643 9847 4.034742 GTCGCAGTTTTGAACTAAGGTTGA 59.965 41.667 0.00 0.00 40.46 3.18
2644 9848 4.636648 TCGCAGTTTTGAACTAAGGTTGAA 59.363 37.500 0.00 0.00 40.46 2.69
2645 9849 4.733405 CGCAGTTTTGAACTAAGGTTGAAC 59.267 41.667 0.00 0.00 40.46 3.18
2646 9850 5.448632 CGCAGTTTTGAACTAAGGTTGAACT 60.449 40.000 0.00 0.00 40.46 3.01
2649 9853 7.971722 GCAGTTTTGAACTAAGGTTGAACTAAA 59.028 33.333 0.00 0.00 40.46 1.85
2670 9874 5.751243 AACTTAGTTCAAAACTGCGACAT 57.249 34.783 2.65 0.00 42.84 3.06
2684 9888 4.201910 ACTGCGACATTTATTTTGGATCGG 60.202 41.667 0.00 0.00 0.00 4.18
2713 9918 7.064253 GGAGTAGTGTATAAACCATGTGTGTTC 59.936 40.741 0.00 0.00 0.00 3.18
2803 10008 8.589629 GCATGTTTTAATTCAATCAGTCATGTC 58.410 33.333 0.00 0.00 33.78 3.06
2807 10012 9.897744 GTTTTAATTCAATCAGTCATGTCTGAA 57.102 29.630 23.35 10.00 45.65 3.02
2809 10014 5.791367 ATTCAATCAGTCATGTCTGAACG 57.209 39.130 23.35 17.40 45.65 3.95
2879 10084 6.701145 TGTTGCTGGTTGAACAGTAAAATA 57.299 33.333 1.08 0.00 43.09 1.40
2963 10169 5.890334 AGTGTTTGATGTGTTCGTGAAAAT 58.110 33.333 0.00 0.00 0.00 1.82
2968 10174 9.140286 TGTTTGATGTGTTCGTGAAAATTTTTA 57.860 25.926 4.63 0.00 0.00 1.52
3144 10350 2.713877 TGGCACCCGTAAAAGTATTCC 58.286 47.619 0.00 0.00 0.00 3.01
3146 10352 2.941064 GGCACCCGTAAAAGTATTCCTC 59.059 50.000 0.00 0.00 0.00 3.71
3147 10353 3.602483 GCACCCGTAAAAGTATTCCTCA 58.398 45.455 0.00 0.00 0.00 3.86
3154 10360 5.180492 CCGTAAAAGTATTCCTCACAAGCAA 59.820 40.000 0.00 0.00 0.00 3.91
3181 10387 9.515226 GAGCATATATACCAAGGAACCAAATAA 57.485 33.333 0.00 0.00 0.00 1.40
3189 10411 6.314917 ACCAAGGAACCAAATAATCAGTTCT 58.685 36.000 0.00 0.00 38.87 3.01
3216 10438 7.389053 ACACCAGATTTCTTATCACTTTCAGAC 59.611 37.037 0.00 0.00 0.00 3.51
3246 10468 9.236006 AGTGAGCAAAAATAATCAGTTCTACAT 57.764 29.630 0.00 0.00 0.00 2.29
3280 10502 2.109128 TCGCTCCTAGATTGATCTCCCT 59.891 50.000 0.00 0.00 38.32 4.20
3285 10507 2.630098 CCTAGATTGATCTCCCTTCGCA 59.370 50.000 0.00 0.00 38.32 5.10
3286 10508 3.260380 CCTAGATTGATCTCCCTTCGCAT 59.740 47.826 0.00 0.00 38.32 4.73
3287 10509 3.123157 AGATTGATCTCCCTTCGCATG 57.877 47.619 0.00 0.00 29.30 4.06
3289 10511 0.811219 TTGATCTCCCTTCGCATGCG 60.811 55.000 33.61 33.61 41.35 4.73
3297 10557 0.234106 CCTTCGCATGCGCAATCTAG 59.766 55.000 34.45 20.95 38.40 2.43
3408 10668 1.067354 CAAGATTTCTTGTGCTGGCCC 60.067 52.381 11.37 0.00 46.11 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.039879 ACACCGGTTCTGGCTTTCTTAT 59.960 45.455 2.97 0.00 0.00 1.73
1 2 1.418637 ACACCGGTTCTGGCTTTCTTA 59.581 47.619 2.97 0.00 0.00 2.10
2 3 0.182775 ACACCGGTTCTGGCTTTCTT 59.817 50.000 2.97 0.00 0.00 2.52
3 4 0.182775 AACACCGGTTCTGGCTTTCT 59.817 50.000 2.97 0.00 29.00 2.52
4 5 1.886886 TAACACCGGTTCTGGCTTTC 58.113 50.000 2.97 0.00 38.45 2.62
18 4313 0.517316 CCAGAAGGTGCGCTTAACAC 59.483 55.000 9.73 0.00 37.31 3.32
173 4471 5.329493 GTTGTTGAAGTAAGTCGTTTTGCT 58.671 37.500 0.00 0.00 0.00 3.91
227 4525 4.591498 TCTGGTGGAGCAAAGTAAAGTAGA 59.409 41.667 0.00 0.00 0.00 2.59
314 4626 3.115554 GTTCAGTTTGTGCATGTCAACC 58.884 45.455 0.00 0.00 0.00 3.77
536 4863 4.694760 AAGGCATGAGCTCATACATACA 57.305 40.909 28.27 0.00 41.70 2.29
583 4916 3.003378 GCGAATGGGAAAGCATAGGTTAC 59.997 47.826 0.00 0.00 0.00 2.50
629 5072 0.453390 GCATGTGTTAGCCTTGGAGC 59.547 55.000 0.00 0.00 0.00 4.70
630 5073 1.825090 TGCATGTGTTAGCCTTGGAG 58.175 50.000 0.00 0.00 0.00 3.86
631 5074 2.161855 CTTGCATGTGTTAGCCTTGGA 58.838 47.619 0.00 0.00 0.00 3.53
632 5075 1.403249 GCTTGCATGTGTTAGCCTTGG 60.403 52.381 1.14 0.00 0.00 3.61
634 5077 1.270550 GTGCTTGCATGTGTTAGCCTT 59.729 47.619 3.48 0.00 32.73 4.35
638 5081 1.538512 AGCTGTGCTTGCATGTGTTAG 59.461 47.619 0.00 0.00 33.89 2.34
846 7733 2.918712 TAGGATAGCAAGCTCTTGGC 57.081 50.000 11.15 4.36 40.74 4.52
886 7779 7.136119 CCTCTCGATGTAATCTCTTAAGTGTC 58.864 42.308 1.63 0.00 42.58 3.67
931 7824 3.982241 GCTGGTTGCCGCTGCTTT 61.982 61.111 0.70 0.00 38.71 3.51
940 7833 1.208614 CTTCTTGCTCGCTGGTTGC 59.791 57.895 0.00 0.00 38.57 4.17
972 7865 6.073548 CGGGTCTATCAATTTTAGCTAGCAAG 60.074 42.308 18.83 0.00 0.00 4.01
973 7866 5.758296 CGGGTCTATCAATTTTAGCTAGCAA 59.242 40.000 18.83 6.50 0.00 3.91
974 7867 5.297547 CGGGTCTATCAATTTTAGCTAGCA 58.702 41.667 18.83 0.00 0.00 3.49
984 7903 1.416401 ACCATCGCGGGTCTATCAATT 59.584 47.619 6.13 0.00 35.96 2.32
1014 7956 1.047596 ACTCCATGGCGCTCATCTCT 61.048 55.000 6.96 0.00 32.92 3.10
1188 8154 0.106167 TCTCCCGGATGACCTCGATT 60.106 55.000 0.73 0.00 0.00 3.34
1246 8212 7.833285 AGAGTATATGGAGAGAAAGGAACTC 57.167 40.000 0.00 0.00 38.49 3.01
1255 8221 7.838193 ACATGATGCATAGAGTATATGGAGAGA 59.162 37.037 0.00 0.00 0.00 3.10
1256 8222 8.009622 ACATGATGCATAGAGTATATGGAGAG 57.990 38.462 0.00 0.00 0.00 3.20
1257 8223 7.069208 GGACATGATGCATAGAGTATATGGAGA 59.931 40.741 0.00 0.00 0.00 3.71
1258 8224 7.069702 AGGACATGATGCATAGAGTATATGGAG 59.930 40.741 0.00 0.00 0.00 3.86
1259 8225 6.899631 AGGACATGATGCATAGAGTATATGGA 59.100 38.462 0.00 4.19 0.00 3.41
1260 8226 6.985059 CAGGACATGATGCATAGAGTATATGG 59.015 42.308 0.00 0.00 0.00 2.74
1261 8227 7.779073 TCAGGACATGATGCATAGAGTATATG 58.221 38.462 0.00 0.15 31.12 1.78
1262 8228 7.968014 TCAGGACATGATGCATAGAGTATAT 57.032 36.000 0.00 0.00 31.12 0.86
1280 8252 1.950828 CAGGTGAGCATGATCAGGAC 58.049 55.000 15.20 7.97 0.00 3.85
1281 8253 0.179702 GCAGGTGAGCATGATCAGGA 59.820 55.000 15.20 0.00 0.00 3.86
1282 8254 0.180642 AGCAGGTGAGCATGATCAGG 59.819 55.000 15.20 8.31 36.85 3.86
1283 8255 1.134491 TGAGCAGGTGAGCATGATCAG 60.134 52.381 15.20 3.97 36.85 2.90
1284 8256 0.906775 TGAGCAGGTGAGCATGATCA 59.093 50.000 10.16 10.16 36.85 2.92
1286 8258 1.968704 CATGAGCAGGTGAGCATGAT 58.031 50.000 0.00 0.00 40.29 2.45
1287 8259 0.746923 GCATGAGCAGGTGAGCATGA 60.747 55.000 13.49 0.00 40.29 3.07
1289 8261 1.453379 GGCATGAGCAGGTGAGCAT 60.453 57.895 0.00 0.00 44.61 3.79
1290 8262 2.045634 GGCATGAGCAGGTGAGCA 60.046 61.111 0.00 0.00 44.61 4.26
1291 8263 2.827642 GGGCATGAGCAGGTGAGC 60.828 66.667 0.00 0.00 44.61 4.26
1292 8264 1.748122 GTGGGCATGAGCAGGTGAG 60.748 63.158 0.00 0.00 44.61 3.51
1294 8266 3.129502 CGTGGGCATGAGCAGGTG 61.130 66.667 0.00 0.00 44.61 4.00
1297 8269 2.872557 CAACGTGGGCATGAGCAG 59.127 61.111 0.00 0.00 44.61 4.24
1300 8272 2.672651 TGGCAACGTGGGCATGAG 60.673 61.111 16.40 0.00 38.55 2.90
1310 8282 5.747675 TGATTAATTAACATGCATGGCAACG 59.252 36.000 29.41 4.72 43.62 4.10
1311 8283 7.401080 GTTGATTAATTAACATGCATGGCAAC 58.599 34.615 29.41 20.67 43.62 4.17
1312 8284 6.538021 GGTTGATTAATTAACATGCATGGCAA 59.462 34.615 29.41 21.62 43.62 4.52
1317 8289 9.723601 AAGTTTGGTTGATTAATTAACATGCAT 57.276 25.926 20.78 0.00 0.00 3.96
1330 8302 6.379988 ACAGTTAGGAACAAGTTTGGTTGATT 59.620 34.615 0.00 0.00 0.00 2.57
1331 8303 5.891551 ACAGTTAGGAACAAGTTTGGTTGAT 59.108 36.000 0.00 0.00 0.00 2.57
1334 8306 6.831868 ACATACAGTTAGGAACAAGTTTGGTT 59.168 34.615 0.00 0.00 30.79 3.67
1335 8307 6.362248 ACATACAGTTAGGAACAAGTTTGGT 58.638 36.000 0.00 0.00 30.79 3.67
1336 8308 6.877611 ACATACAGTTAGGAACAAGTTTGG 57.122 37.500 0.00 0.00 30.79 3.28
1338 8310 9.702494 GTACTACATACAGTTAGGAACAAGTTT 57.298 33.333 0.00 0.00 33.54 2.66
1339 8311 8.025445 CGTACTACATACAGTTAGGAACAAGTT 58.975 37.037 0.00 0.00 32.79 2.66
1340 8312 7.175641 ACGTACTACATACAGTTAGGAACAAGT 59.824 37.037 0.00 0.00 32.79 3.16
1341 8313 7.533426 ACGTACTACATACAGTTAGGAACAAG 58.467 38.462 0.00 0.00 32.79 3.16
1342 8314 7.452880 ACGTACTACATACAGTTAGGAACAA 57.547 36.000 0.00 0.00 32.79 2.83
1343 8315 7.824289 AGTACGTACTACATACAGTTAGGAACA 59.176 37.037 26.36 0.00 34.13 3.18
1344 8316 8.202745 AGTACGTACTACATACAGTTAGGAAC 57.797 38.462 26.36 0.00 34.13 3.62
1345 8317 8.668353 CAAGTACGTACTACATACAGTTAGGAA 58.332 37.037 27.59 0.00 34.99 3.36
1346 8318 7.824289 ACAAGTACGTACTACATACAGTTAGGA 59.176 37.037 27.59 0.00 34.99 2.94
1347 8319 7.978982 ACAAGTACGTACTACATACAGTTAGG 58.021 38.462 27.59 7.40 34.99 2.69
1348 8320 8.659491 TGACAAGTACGTACTACATACAGTTAG 58.341 37.037 27.59 8.92 34.99 2.34
1349 8321 8.546597 TGACAAGTACGTACTACATACAGTTA 57.453 34.615 27.59 11.67 34.99 2.24
1350 8322 7.439157 TGACAAGTACGTACTACATACAGTT 57.561 36.000 27.59 6.80 34.99 3.16
1355 8327 9.726232 GAAATGATGACAAGTACGTACTACATA 57.274 33.333 27.59 15.21 34.99 2.29
1356 8328 8.248253 TGAAATGATGACAAGTACGTACTACAT 58.752 33.333 27.59 27.35 34.99 2.29
1359 8331 7.753580 CAGTGAAATGATGACAAGTACGTACTA 59.246 37.037 27.59 13.23 34.99 1.82
1363 8335 4.690748 CCAGTGAAATGATGACAAGTACGT 59.309 41.667 0.00 0.00 0.00 3.57
1364 8336 4.690748 ACCAGTGAAATGATGACAAGTACG 59.309 41.667 0.00 0.00 0.00 3.67
1365 8337 6.560253 AACCAGTGAAATGATGACAAGTAC 57.440 37.500 0.00 0.00 0.00 2.73
1366 8338 7.581213 AAAACCAGTGAAATGATGACAAGTA 57.419 32.000 0.00 0.00 0.00 2.24
1367 8339 6.469782 AAAACCAGTGAAATGATGACAAGT 57.530 33.333 0.00 0.00 0.00 3.16
1368 8340 8.137437 AGTTAAAACCAGTGAAATGATGACAAG 58.863 33.333 0.00 0.00 0.00 3.16
1369 8341 8.006298 AGTTAAAACCAGTGAAATGATGACAA 57.994 30.769 0.00 0.00 0.00 3.18
1370 8342 7.581213 AGTTAAAACCAGTGAAATGATGACA 57.419 32.000 0.00 0.00 0.00 3.58
1371 8343 8.871686 AAAGTTAAAACCAGTGAAATGATGAC 57.128 30.769 0.00 0.00 0.00 3.06
1375 8347 9.796120 CAGTAAAAGTTAAAACCAGTGAAATGA 57.204 29.630 0.00 0.00 0.00 2.57
1376 8348 8.539674 GCAGTAAAAGTTAAAACCAGTGAAATG 58.460 33.333 0.00 0.00 0.00 2.32
1377 8349 8.254508 TGCAGTAAAAGTTAAAACCAGTGAAAT 58.745 29.630 0.00 0.00 0.00 2.17
1378 8350 7.542824 GTGCAGTAAAAGTTAAAACCAGTGAAA 59.457 33.333 0.00 0.00 0.00 2.69
1379 8351 7.030768 GTGCAGTAAAAGTTAAAACCAGTGAA 58.969 34.615 0.00 0.00 0.00 3.18
1380 8352 6.151312 TGTGCAGTAAAAGTTAAAACCAGTGA 59.849 34.615 0.00 0.00 0.00 3.41
1381 8353 6.326375 TGTGCAGTAAAAGTTAAAACCAGTG 58.674 36.000 0.00 0.00 0.00 3.66
1382 8354 6.518208 TGTGCAGTAAAAGTTAAAACCAGT 57.482 33.333 0.00 0.00 0.00 4.00
1383 8355 7.820044 TTTGTGCAGTAAAAGTTAAAACCAG 57.180 32.000 0.00 0.00 0.00 4.00
1384 8356 7.278868 CCATTTGTGCAGTAAAAGTTAAAACCA 59.721 33.333 0.00 0.00 0.00 3.67
1386 8358 7.011016 AGCCATTTGTGCAGTAAAAGTTAAAAC 59.989 33.333 0.00 0.00 0.00 2.43
1390 8362 5.782893 AGCCATTTGTGCAGTAAAAGTTA 57.217 34.783 0.00 0.00 0.00 2.24
1398 8370 1.342174 CTTGGAAGCCATTTGTGCAGT 59.658 47.619 0.00 0.00 31.53 4.40
1399 8371 1.938016 GCTTGGAAGCCATTTGTGCAG 60.938 52.381 0.00 0.00 46.20 4.41
1401 8373 2.831597 GCTTGGAAGCCATTTGTGC 58.168 52.632 0.00 0.00 46.20 4.57
1409 8381 4.450080 CAGAAAAGAATTTGCTTGGAAGCC 59.550 41.667 8.87 0.00 42.80 4.35
1410 8382 4.450080 CCAGAAAAGAATTTGCTTGGAAGC 59.550 41.667 4.33 4.33 42.80 3.86
1411 8383 5.846203 TCCAGAAAAGAATTTGCTTGGAAG 58.154 37.500 0.00 0.00 42.80 3.46
1412 8384 5.867903 TCCAGAAAAGAATTTGCTTGGAA 57.132 34.783 0.00 0.00 42.80 3.53
1415 8387 6.757947 TCTTGTTCCAGAAAAGAATTTGCTTG 59.242 34.615 0.00 0.00 42.80 4.01
1416 8388 6.877236 TCTTGTTCCAGAAAAGAATTTGCTT 58.123 32.000 0.00 0.00 42.80 3.91
1447 8434 2.286872 GGATGATTGCACTCTGTCAGG 58.713 52.381 5.59 0.00 0.00 3.86
1473 8476 1.942657 TGCTCGCCTCTGCATAATTTC 59.057 47.619 0.00 0.00 37.32 2.17
1783 8807 0.320697 GTGGACCACTTACGGCTTCT 59.679 55.000 17.84 0.00 0.00 2.85
1865 8957 0.812014 CTTGCACCACACCACACGTA 60.812 55.000 0.00 0.00 0.00 3.57
2264 9453 3.649277 CTGGTGGAAGGAGACGGCG 62.649 68.421 4.80 4.80 0.00 6.46
2324 9513 1.569548 TCCTCCAAGTATCCCTCGACT 59.430 52.381 0.00 0.00 0.00 4.18
2333 9531 1.883275 CTCGCGATCTCCTCCAAGTAT 59.117 52.381 10.36 0.00 0.00 2.12
2417 9621 0.039074 ACTCTGAAGACGTGCGAAGG 60.039 55.000 0.00 0.00 0.00 3.46
2468 9672 0.926846 GACAGCATCTGTTCTAGCGC 59.073 55.000 0.00 0.00 45.44 5.92
2482 9686 2.139118 GTCACTTCCTCACTTGACAGC 58.861 52.381 0.00 0.00 38.60 4.40
2644 9848 6.314400 TGTCGCAGTTTTGAACTAAGTTTAGT 59.686 34.615 0.00 0.00 45.43 2.24
2645 9849 6.711579 TGTCGCAGTTTTGAACTAAGTTTAG 58.288 36.000 0.00 0.00 40.46 1.85
2646 9850 6.665474 TGTCGCAGTTTTGAACTAAGTTTA 57.335 33.333 0.00 0.00 40.46 2.01
2649 9853 5.751243 AATGTCGCAGTTTTGAACTAAGT 57.249 34.783 0.00 0.00 40.46 2.24
2670 9874 4.855298 ACTCCCTCCGATCCAAAATAAA 57.145 40.909 0.00 0.00 0.00 1.40
2684 9888 6.127140 ACACATGGTTTATACACTACTCCCTC 60.127 42.308 0.00 0.00 0.00 4.30
2713 9918 6.972901 ACACACAAGTCATACTATGTATCACG 59.027 38.462 0.00 0.00 0.00 4.35
2772 9977 6.211184 ACTGATTGAATTAAAACATGCCTGGA 59.789 34.615 0.00 0.00 0.00 3.86
2781 9986 9.897744 TTCAGACATGACTGATTGAATTAAAAC 57.102 29.630 24.90 0.00 44.67 2.43
2803 10008 4.809426 AGAACAAGGTACAAGAACGTTCAG 59.191 41.667 28.78 22.00 35.00 3.02
2807 10012 3.118519 ACCAGAACAAGGTACAAGAACGT 60.119 43.478 0.00 0.00 37.67 3.99
2809 10014 4.272748 GTGACCAGAACAAGGTACAAGAAC 59.727 45.833 0.00 0.00 40.09 3.01
2879 10084 8.506168 TTCTACTCTGTTGTTCATTTGTTTCT 57.494 30.769 0.00 0.00 0.00 2.52
2910 10115 7.781693 AGGAGGAACATGCACATAATAAAAGAT 59.218 33.333 0.00 0.00 0.00 2.40
2912 10117 7.148018 ACAGGAGGAACATGCACATAATAAAAG 60.148 37.037 0.00 0.00 33.22 2.27
2968 10174 8.238631 GGAAGCATAATTGTTCATTTTTGCATT 58.761 29.630 17.58 11.95 36.17 3.56
3079 10285 8.164070 AGACATATACAGGTTCTTGTCCTTTTT 58.836 33.333 0.00 0.00 35.27 1.94
3144 10350 6.226052 TGGTATATATGCTCTTGCTTGTGAG 58.774 40.000 0.62 0.00 40.48 3.51
3146 10352 6.072838 CCTTGGTATATATGCTCTTGCTTGTG 60.073 42.308 0.62 0.00 40.48 3.33
3147 10353 6.000219 CCTTGGTATATATGCTCTTGCTTGT 59.000 40.000 0.62 0.00 40.48 3.16
3154 10360 6.763715 TTGGTTCCTTGGTATATATGCTCT 57.236 37.500 0.62 0.00 0.00 4.09
3181 10387 8.762645 TGATAAGAAATCTGGTGTAGAACTGAT 58.237 33.333 0.00 0.00 39.30 2.90
3182 10388 8.035394 GTGATAAGAAATCTGGTGTAGAACTGA 58.965 37.037 0.00 0.00 39.30 3.41
3183 10389 8.037758 AGTGATAAGAAATCTGGTGTAGAACTG 58.962 37.037 0.00 0.00 39.30 3.16
3184 10390 8.140112 AGTGATAAGAAATCTGGTGTAGAACT 57.860 34.615 0.00 0.00 39.30 3.01
3189 10411 8.593679 TCTGAAAGTGATAAGAAATCTGGTGTA 58.406 33.333 0.00 0.00 33.76 2.90
3246 10468 0.955428 GGAGCGACAAACTGGATGCA 60.955 55.000 0.00 0.00 0.00 3.96
3285 10507 5.506815 CCAATCAAATGTCTAGATTGCGCAT 60.507 40.000 12.75 0.40 44.40 4.73
3286 10508 4.201940 CCAATCAAATGTCTAGATTGCGCA 60.202 41.667 5.66 5.66 44.40 6.09
3287 10509 4.285292 CCAATCAAATGTCTAGATTGCGC 58.715 43.478 0.00 0.00 44.40 6.09
3289 10511 5.841957 ACCCAATCAAATGTCTAGATTGC 57.158 39.130 0.00 0.00 44.40 3.56
3297 10557 7.151308 TGACAAAATGTACCCAATCAAATGTC 58.849 34.615 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.