Multiple sequence alignment - TraesCS5B01G335400

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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 TraesCS5B01G335400 chr5B 100.000 3315 0 0 1 3315 518572887 518569573 0.000000e+00 6122.0
1 TraesCS5B01G335400 chr5B 92.308 91 7 0 1215 1305 280157225 280157135 2.680000e-26 130.0
2 TraesCS5B01G335400 chr5A 89.706 1972 133 28 1309 3243 545129931 545127993 0.000000e+00 2453.0
3 TraesCS5B01G335400 chr5A 86.466 798 58 31 424 1214 545130711 545129957 0.000000e+00 830.0
4 TraesCS5B01G335400 chr5A 91.489 94 8 0 1212 1305 567533807 567533900 2.680000e-26 130.0
5 TraesCS5B01G335400 chr1B 90.157 1788 98 37 1311 3059 516122587 516120839 0.000000e+00 2255.0
6 TraesCS5B01G335400 chr1B 90.546 1227 82 21 1 1212 516123826 516122619 0.000000e+00 1592.0
7 TraesCS5B01G335400 chr1B 94.416 197 9 1 3053 3247 516120681 516120485 5.370000e-78 302.0
8 TraesCS5B01G335400 chr1B 92.222 90 7 0 1216 1305 444057227 444057316 9.650000e-26 128.0
9 TraesCS5B01G335400 chr1B 95.890 73 2 1 3240 3312 164770365 164770436 2.090000e-22 117.0
10 TraesCS5B01G335400 chr1B 93.333 75 4 1 3238 3312 213322529 213322602 3.500000e-20 110.0
11 TraesCS5B01G335400 chr5D 92.766 1092 60 12 1311 2392 429305097 429304015 0.000000e+00 1561.0
12 TraesCS5B01G335400 chr5D 92.991 799 30 12 424 1212 429305911 429305129 0.000000e+00 1142.0
13 TraesCS5B01G335400 chr5D 84.136 353 35 12 54 399 389809204 389809542 4.130000e-84 322.0
14 TraesCS5B01G335400 chr2D 83.662 355 41 11 54 402 87428280 87427937 5.340000e-83 318.0
15 TraesCS5B01G335400 chr2D 81.529 157 13 8 1 156 579454150 579454291 7.520000e-22 115.0
16 TraesCS5B01G335400 chr6A 79.088 373 54 12 54 419 553739349 553738994 5.530000e-58 235.0
17 TraesCS5B01G335400 chr6A 79.940 334 46 16 54 375 608338988 608338664 3.330000e-55 226.0
18 TraesCS5B01G335400 chr6A 93.902 82 3 2 3231 3311 158470211 158470291 4.490000e-24 122.0
19 TraesCS5B01G335400 chr7B 93.407 91 6 0 1215 1305 714409229 714409139 5.770000e-28 135.0
20 TraesCS5B01G335400 chr7B 92.308 91 7 0 1215 1305 556825390 556825300 2.680000e-26 130.0
21 TraesCS5B01G335400 chr7B 94.667 75 3 1 3241 3315 654925853 654925780 7.520000e-22 115.0
22 TraesCS5B01G335400 chr4A 91.753 97 8 0 1215 1311 437917114 437917018 5.770000e-28 135.0
23 TraesCS5B01G335400 chr1A 92.308 91 7 0 1215 1305 527692513 527692423 2.680000e-26 130.0
24 TraesCS5B01G335400 chr1A 90.526 95 9 0 1215 1309 32863848 32863754 3.470000e-25 126.0
25 TraesCS5B01G335400 chr1D 89.362 94 10 0 1212 1305 494935276 494935369 5.810000e-23 119.0
26 TraesCS5B01G335400 chr4B 91.765 85 5 2 3228 3312 527370168 527370250 2.090000e-22 117.0
27 TraesCS5B01G335400 chr4B 95.833 72 2 1 3241 3312 179437360 179437430 7.520000e-22 115.0
28 TraesCS5B01G335400 chr4B 94.286 35 2 0 2767 2801 324428096 324428130 2.000000e-03 54.7
29 TraesCS5B01G335400 chr3A 94.521 73 3 1 3240 3312 233696259 233696330 9.720000e-21 111.0
30 TraesCS5B01G335400 chr2B 92.405 79 5 1 3234 3312 720236266 720236343 9.720000e-21 111.0
31 TraesCS5B01G335400 chr3D 93.333 75 4 1 3238 3312 43577841 43577914 3.500000e-20 110.0


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 TraesCS5B01G335400 chr5B 518569573 518572887 3314 True 6122.0 6122 100.000000 1 3315 1 chr5B.!!$R2 3314
1 TraesCS5B01G335400 chr5A 545127993 545130711 2718 True 1641.5 2453 88.086000 424 3243 2 chr5A.!!$R1 2819
2 TraesCS5B01G335400 chr1B 516120485 516123826 3341 True 1383.0 2255 91.706333 1 3247 3 chr1B.!!$R1 3246
3 TraesCS5B01G335400 chr5D 429304015 429305911 1896 True 1351.5 1561 92.878500 424 2392 2 chr5D.!!$R1 1968

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
100 101 0.255033 GCCTCCTTAAATGGTCGGGT 59.745 55.0 0.00 0.0 0.00 5.28 F
783 814 0.256464 AGAGGTCCTCTCCTGTACCG 59.744 60.0 16.28 0.0 43.44 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1024 1057 1.128147 GCACGCACCTACGTACGTAC 61.128 60.0 23.6 15.9 46.34 3.67 R
2400 2466 0.034059 CACTGAGTTGGTTCGCCTCT 59.966 55.0 0.0 0.0 38.36 3.69 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
23 24 2.757077 GGGAACAGGGACCACTGG 59.243 66.667 12.81 0.00 42.75 4.00
49 50 4.394610 GGACATGAGAGAGAAGGAAAAAGC 59.605 45.833 0.00 0.00 0.00 3.51
50 51 3.999663 ACATGAGAGAGAAGGAAAAAGCG 59.000 43.478 0.00 0.00 0.00 4.68
63 64 5.345702 AGGAAAAAGCGGTAAAAAGTTGAC 58.654 37.500 0.00 0.00 0.00 3.18
69 70 2.099427 GCGGTAAAAAGTTGACCAACCA 59.901 45.455 9.07 0.00 42.06 3.67
85 86 1.301293 CCAGACCCCTCAAAGCCTC 59.699 63.158 0.00 0.00 0.00 4.70
96 97 3.696548 CCTCAAAGCCTCCTTAAATGGTC 59.303 47.826 0.00 0.00 0.00 4.02
100 101 0.255033 GCCTCCTTAAATGGTCGGGT 59.745 55.000 0.00 0.00 0.00 5.28
105 106 2.089201 CCTTAAATGGTCGGGTTGTCC 58.911 52.381 0.00 0.00 0.00 4.02
156 157 9.531942 CTCATATATGAAATGAGTATGAGGAGC 57.468 37.037 16.08 0.00 43.50 4.70
158 159 4.679373 ATGAAATGAGTATGAGGAGCGT 57.321 40.909 0.00 0.00 0.00 5.07
159 160 4.046938 TGAAATGAGTATGAGGAGCGTC 57.953 45.455 0.00 0.00 0.00 5.19
160 161 3.181475 TGAAATGAGTATGAGGAGCGTCC 60.181 47.826 0.00 0.00 36.58 4.79
207 208 1.968493 TCCGCCACATAGGATTAGACC 59.032 52.381 0.00 0.00 41.22 3.85
267 275 3.774216 CTCTCTCTCCTTCTCCACCAATT 59.226 47.826 0.00 0.00 0.00 2.32
279 287 2.166050 TCCACCAATTACATGCATGTGC 59.834 45.455 36.72 0.00 41.89 4.57
282 290 1.536496 CCAATTACATGCATGTGCCCG 60.536 52.381 36.72 23.16 41.89 6.13
300 308 6.485313 TGTGCCCGGACATATATAAAGAAAAG 59.515 38.462 0.73 0.00 0.00 2.27
301 309 6.485648 GTGCCCGGACATATATAAAGAAAAGT 59.514 38.462 0.73 0.00 0.00 2.66
302 310 6.485313 TGCCCGGACATATATAAAGAAAAGTG 59.515 38.462 0.73 0.00 0.00 3.16
304 312 7.095187 GCCCGGACATATATAAAGAAAAGTGAG 60.095 40.741 0.73 0.00 0.00 3.51
310 318 9.838339 ACATATATAAAGAAAAGTGAGGGACAG 57.162 33.333 0.00 0.00 0.00 3.51
313 321 4.731313 AAAGAAAAGTGAGGGACAGGAT 57.269 40.909 0.00 0.00 0.00 3.24
316 324 2.206576 AAAGTGAGGGACAGGATTGC 57.793 50.000 0.00 0.00 0.00 3.56
349 357 7.797121 AAAAATAGGGAATCAAAGTGGACAT 57.203 32.000 0.00 0.00 0.00 3.06
352 360 1.478105 GGGAATCAAAGTGGACATGCC 59.522 52.381 0.00 0.00 37.10 4.40
353 361 1.478105 GGAATCAAAGTGGACATGCCC 59.522 52.381 0.00 0.00 34.97 5.36
356 364 1.303236 CAAAGTGGACATGCCCGGA 60.303 57.895 0.73 0.00 34.97 5.14
398 406 1.055849 GGTGTTTGAGGGGCCAAATT 58.944 50.000 4.39 0.00 38.18 1.82
409 417 0.679960 GGCCAAATTAGTCCGGCTGT 60.680 55.000 0.00 0.00 44.27 4.40
410 418 1.407712 GGCCAAATTAGTCCGGCTGTA 60.408 52.381 0.00 0.00 44.27 2.74
411 419 1.940613 GCCAAATTAGTCCGGCTGTAG 59.059 52.381 0.00 0.00 41.50 2.74
412 420 2.419574 GCCAAATTAGTCCGGCTGTAGA 60.420 50.000 0.00 0.00 41.50 2.59
413 421 3.744530 GCCAAATTAGTCCGGCTGTAGAT 60.745 47.826 0.00 0.00 41.50 1.98
414 422 3.809832 CCAAATTAGTCCGGCTGTAGATG 59.190 47.826 0.00 0.00 0.00 2.90
415 423 2.821991 ATTAGTCCGGCTGTAGATGC 57.178 50.000 0.00 0.00 0.00 3.91
416 424 1.776662 TTAGTCCGGCTGTAGATGCT 58.223 50.000 0.00 0.00 0.00 3.79
637 649 1.322936 GCTTCTTCGATTCTCTGTGCG 59.677 52.381 0.00 0.00 0.00 5.34
783 814 0.256464 AGAGGTCCTCTCCTGTACCG 59.744 60.000 16.28 0.00 43.44 4.02
842 873 2.933056 GCTTGCTTCAGTACCCTCAGAC 60.933 54.545 0.00 0.00 0.00 3.51
1024 1057 2.331805 CGCCTCCGTGTCGATAGG 59.668 66.667 0.00 0.00 34.53 2.57
1029 1062 1.293924 CTCCGTGTCGATAGGTACGT 58.706 55.000 0.00 0.00 41.72 3.57
1035 1068 3.121663 CGTGTCGATAGGTACGTACGTAG 60.122 52.174 27.48 14.97 39.65 3.51
1037 1070 3.181479 TGTCGATAGGTACGTACGTAGGT 60.181 47.826 27.48 22.91 31.13 3.08
1056 1091 2.202479 CGTGCGTGCTCGATCTCA 60.202 61.111 13.13 0.00 39.71 3.27
1208 1247 3.620300 CTTCGGCGCAGGTACGTGA 62.620 63.158 19.35 0.00 34.88 4.35
1214 1253 4.436998 GCAGGTACGTGAGGCGCT 62.437 66.667 19.35 0.00 46.11 5.92
1216 1255 1.734137 CAGGTACGTGAGGCGCTAT 59.266 57.895 10.02 0.00 46.11 2.97
1218 1257 1.335810 CAGGTACGTGAGGCGCTATAA 59.664 52.381 10.02 0.00 46.11 0.98
1219 1258 2.030185 CAGGTACGTGAGGCGCTATAAT 60.030 50.000 10.02 0.00 46.11 1.28
1220 1259 2.626743 AGGTACGTGAGGCGCTATAATT 59.373 45.455 7.64 0.00 46.11 1.40
1224 1263 4.273005 ACGTGAGGCGCTATAATTTTTG 57.727 40.909 7.64 0.00 46.11 2.44
1226 1265 4.028383 CGTGAGGCGCTATAATTTTTGTG 58.972 43.478 7.64 0.00 0.00 3.33
1229 1268 6.548171 GTGAGGCGCTATAATTTTTGTGTTA 58.452 36.000 7.64 0.00 0.00 2.41
1230 1269 7.193595 GTGAGGCGCTATAATTTTTGTGTTAT 58.806 34.615 7.64 0.00 0.00 1.89
1231 1270 8.339714 GTGAGGCGCTATAATTTTTGTGTTATA 58.660 33.333 7.64 0.00 0.00 0.98
1232 1271 8.894731 TGAGGCGCTATAATTTTTGTGTTATAA 58.105 29.630 7.64 0.00 0.00 0.98
1233 1272 9.724839 GAGGCGCTATAATTTTTGTGTTATAAA 57.275 29.630 7.64 0.00 0.00 1.40
1234 1273 9.730420 AGGCGCTATAATTTTTGTGTTATAAAG 57.270 29.630 7.64 0.00 0.00 1.85
1235 1274 9.511144 GGCGCTATAATTTTTGTGTTATAAAGT 57.489 29.630 7.64 0.00 0.00 2.66
1279 1318 7.956420 TTGACAATTTAGGTATACGCATAGG 57.044 36.000 0.00 0.00 0.00 2.57
1280 1319 7.292713 TGACAATTTAGGTATACGCATAGGA 57.707 36.000 0.00 0.00 0.00 2.94
1281 1320 7.149973 TGACAATTTAGGTATACGCATAGGAC 58.850 38.462 0.00 0.00 0.00 3.85
1282 1321 7.014905 TGACAATTTAGGTATACGCATAGGACT 59.985 37.037 0.00 0.00 0.00 3.85
1283 1322 7.732996 ACAATTTAGGTATACGCATAGGACTT 58.267 34.615 0.00 0.00 0.00 3.01
1284 1323 7.656137 ACAATTTAGGTATACGCATAGGACTTG 59.344 37.037 0.00 0.00 0.00 3.16
1285 1324 6.720112 TTTAGGTATACGCATAGGACTTGT 57.280 37.500 0.00 0.00 0.00 3.16
1286 1325 7.822161 TTTAGGTATACGCATAGGACTTGTA 57.178 36.000 0.00 0.00 0.00 2.41
1287 1326 7.822161 TTAGGTATACGCATAGGACTTGTAA 57.178 36.000 0.00 0.00 0.00 2.41
1288 1327 6.720112 AGGTATACGCATAGGACTTGTAAA 57.280 37.500 0.00 0.00 0.00 2.01
1289 1328 7.116075 AGGTATACGCATAGGACTTGTAAAA 57.884 36.000 0.00 0.00 0.00 1.52
1290 1329 7.732996 AGGTATACGCATAGGACTTGTAAAAT 58.267 34.615 0.00 0.00 0.00 1.82
1291 1330 7.656137 AGGTATACGCATAGGACTTGTAAAATG 59.344 37.037 0.00 0.00 0.00 2.32
1292 1331 7.654520 GGTATACGCATAGGACTTGTAAAATGA 59.345 37.037 0.00 0.00 0.00 2.57
1293 1332 9.037737 GTATACGCATAGGACTTGTAAAATGAA 57.962 33.333 0.00 0.00 0.00 2.57
1294 1333 6.811253 ACGCATAGGACTTGTAAAATGAAA 57.189 33.333 0.00 0.00 0.00 2.69
1295 1334 7.391148 ACGCATAGGACTTGTAAAATGAAAT 57.609 32.000 0.00 0.00 0.00 2.17
1296 1335 7.250569 ACGCATAGGACTTGTAAAATGAAATG 58.749 34.615 0.00 0.00 0.00 2.32
1297 1336 6.692681 CGCATAGGACTTGTAAAATGAAATGG 59.307 38.462 0.00 0.00 0.00 3.16
1298 1337 7.415095 CGCATAGGACTTGTAAAATGAAATGGA 60.415 37.037 0.00 0.00 0.00 3.41
1299 1338 7.917505 GCATAGGACTTGTAAAATGAAATGGAG 59.082 37.037 0.00 0.00 0.00 3.86
1300 1339 6.840780 AGGACTTGTAAAATGAAATGGAGG 57.159 37.500 0.00 0.00 0.00 4.30
1301 1340 6.314917 AGGACTTGTAAAATGAAATGGAGGT 58.685 36.000 0.00 0.00 0.00 3.85
1302 1341 7.466804 AGGACTTGTAAAATGAAATGGAGGTA 58.533 34.615 0.00 0.00 0.00 3.08
1303 1342 7.611855 AGGACTTGTAAAATGAAATGGAGGTAG 59.388 37.037 0.00 0.00 0.00 3.18
1306 1345 6.509418 TGTAAAATGAAATGGAGGTAGTGC 57.491 37.500 0.00 0.00 0.00 4.40
1307 1346 6.007076 TGTAAAATGAAATGGAGGTAGTGCA 58.993 36.000 0.00 0.00 0.00 4.57
1341 1380 6.403200 CCGCCATAATTAAACGATCTTATGGG 60.403 42.308 21.60 14.89 45.56 4.00
1345 1384 9.899661 CCATAATTAAACGATCTTATGGGGATA 57.100 33.333 16.20 0.00 43.40 2.59
1537 1577 2.887568 CGACTGCTCCATGGACGC 60.888 66.667 22.16 22.16 0.00 5.19
1591 1631 2.893637 CCAAGTTGGAGATTCGATCGT 58.106 47.619 17.60 0.00 40.96 3.73
1749 1790 2.282040 GCAGCAGCACCACTCCTT 60.282 61.111 0.00 0.00 41.58 3.36
1928 1969 0.463204 CTCATCCGAGCCAGTGATGT 59.537 55.000 0.00 0.00 37.67 3.06
2140 2203 1.007849 CCGCCGGGAAACAAACAAG 60.008 57.895 2.18 0.00 34.06 3.16
2187 2250 2.093310 CGTTGCTGCAGATGAAGTGTAG 59.907 50.000 20.43 0.00 0.00 2.74
2188 2251 3.070018 GTTGCTGCAGATGAAGTGTAGT 58.930 45.455 20.43 0.00 30.88 2.73
2189 2252 4.245660 GTTGCTGCAGATGAAGTGTAGTA 58.754 43.478 20.43 0.00 30.88 1.82
2190 2253 3.849911 TGCTGCAGATGAAGTGTAGTAC 58.150 45.455 20.43 0.00 30.88 2.73
2303 2369 6.027131 TGTGTCGTTGAACAGAAAGAAATTG 58.973 36.000 0.00 0.00 0.00 2.32
2386 2452 1.225426 CAGGGCAGCAGCATTCCTA 59.775 57.895 2.65 0.00 44.61 2.94
2392 2458 1.293924 CAGCAGCATTCCTAGAACCG 58.706 55.000 0.00 0.00 0.00 4.44
2394 2460 1.765314 AGCAGCATTCCTAGAACCGAT 59.235 47.619 0.00 0.00 0.00 4.18
2395 2461 1.869767 GCAGCATTCCTAGAACCGATG 59.130 52.381 0.00 0.00 0.00 3.84
2397 2463 1.417890 AGCATTCCTAGAACCGATGGG 59.582 52.381 0.00 0.00 40.11 4.00
2399 2465 0.393077 ATTCCTAGAACCGATGGGCG 59.607 55.000 0.00 0.00 36.48 6.13
2400 2466 0.685131 TTCCTAGAACCGATGGGCGA 60.685 55.000 0.00 0.00 44.57 5.54
2401 2467 1.107538 TCCTAGAACCGATGGGCGAG 61.108 60.000 0.00 0.00 44.57 5.03
2402 2468 1.107538 CCTAGAACCGATGGGCGAGA 61.108 60.000 0.00 0.00 44.57 4.04
2403 2469 0.312416 CTAGAACCGATGGGCGAGAG 59.688 60.000 0.00 0.00 44.57 3.20
2404 2470 1.107538 TAGAACCGATGGGCGAGAGG 61.108 60.000 0.00 0.00 44.57 3.69
2414 2480 2.048127 GCGAGAGGCGAACCAACT 60.048 61.111 0.00 0.00 44.57 3.16
2415 2481 2.095252 GCGAGAGGCGAACCAACTC 61.095 63.158 0.00 0.00 44.57 3.01
2416 2482 1.289066 CGAGAGGCGAACCAACTCA 59.711 57.895 0.00 0.00 44.57 3.41
2498 2564 1.223187 CCGGGTTACATTACATCGCC 58.777 55.000 0.00 0.00 0.00 5.54
2548 2622 2.288273 ACAGCTACAGACTCACGAAACC 60.288 50.000 0.00 0.00 0.00 3.27
2587 2663 1.700042 GCAGGAGGTGGTATCCCCAG 61.700 65.000 0.00 0.00 46.45 4.45
2632 2709 5.473039 ACTTTGGTGCTCATAATTTTCTGC 58.527 37.500 0.00 0.00 0.00 4.26
2669 2746 4.577834 TCTTACGATGTGTGTTCAGTGA 57.422 40.909 0.00 0.00 0.00 3.41
2718 2795 6.985188 AAGCGTATGTGACAACTTCATTAT 57.015 33.333 0.00 0.00 36.32 1.28
2738 2816 8.786898 TCATTATTCTTAAATGATGTGCTAGCC 58.213 33.333 13.29 4.15 39.01 3.93
2791 2869 5.733676 AGTATGCATGTGTGTGTTCATAGA 58.266 37.500 10.16 0.00 0.00 1.98
2817 2895 9.201989 AGATGAGTATATAAGTGTCTTTGTCCA 57.798 33.333 0.00 0.00 0.00 4.02
2852 2930 7.791029 AGAAAAGAAAAAGAAAACTATGGGCA 58.209 30.769 0.00 0.00 0.00 5.36
3004 3100 0.111253 ACCTCCAGCCCACTTGAAAG 59.889 55.000 0.00 0.00 0.00 2.62
3053 3150 2.557920 GCAGACTAATGCATAGGGCT 57.442 50.000 0.00 0.00 45.77 5.19
3067 3328 5.163205 TGCATAGGGCTAGACATACAAACAT 60.163 40.000 0.00 0.00 45.15 2.71
3149 3412 7.814642 TCAAACAGTTTGCACAAAATTTTCAT 58.185 26.923 19.70 0.00 40.43 2.57
3157 3420 4.512198 TGCACAAAATTTTCATGCTCTTGG 59.488 37.500 25.82 6.99 37.20 3.61
3176 3439 6.441274 TCTTGGTCGTGTAGTAAACTACTTG 58.559 40.000 18.44 11.93 46.74 3.16
3228 3491 8.461249 AGATGAGAACAAATCCATATTCCAAG 57.539 34.615 0.00 0.00 0.00 3.61
3247 3510 8.849543 TTCCAAGTACATATTAACTACTCCCT 57.150 34.615 0.00 0.00 0.00 4.20
3248 3511 8.474710 TCCAAGTACATATTAACTACTCCCTC 57.525 38.462 0.00 0.00 0.00 4.30
3249 3512 7.508296 TCCAAGTACATATTAACTACTCCCTCC 59.492 40.741 0.00 0.00 0.00 4.30
3250 3513 7.289317 CCAAGTACATATTAACTACTCCCTCCA 59.711 40.741 0.00 0.00 0.00 3.86
3251 3514 8.871125 CAAGTACATATTAACTACTCCCTCCAT 58.129 37.037 0.00 0.00 0.00 3.41
3252 3515 8.653036 AGTACATATTAACTACTCCCTCCATC 57.347 38.462 0.00 0.00 0.00 3.51
3253 3516 6.936968 ACATATTAACTACTCCCTCCATCC 57.063 41.667 0.00 0.00 0.00 3.51
3254 3517 5.785940 ACATATTAACTACTCCCTCCATCCC 59.214 44.000 0.00 0.00 0.00 3.85
3255 3518 3.788116 TTAACTACTCCCTCCATCCCA 57.212 47.619 0.00 0.00 0.00 4.37
3256 3519 2.897823 AACTACTCCCTCCATCCCAT 57.102 50.000 0.00 0.00 0.00 4.00
3257 3520 5.427857 TTAACTACTCCCTCCATCCCATA 57.572 43.478 0.00 0.00 0.00 2.74
3258 3521 4.295905 AACTACTCCCTCCATCCCATAA 57.704 45.455 0.00 0.00 0.00 1.90
3259 3522 4.510303 ACTACTCCCTCCATCCCATAAT 57.490 45.455 0.00 0.00 0.00 1.28
3260 3523 4.171234 ACTACTCCCTCCATCCCATAATG 58.829 47.826 0.00 0.00 0.00 1.90
3261 3524 3.080660 ACTCCCTCCATCCCATAATGT 57.919 47.619 0.00 0.00 0.00 2.71
3262 3525 4.228237 ACTCCCTCCATCCCATAATGTA 57.772 45.455 0.00 0.00 0.00 2.29
3263 3526 4.577096 ACTCCCTCCATCCCATAATGTAA 58.423 43.478 0.00 0.00 0.00 2.41
3264 3527 4.599241 ACTCCCTCCATCCCATAATGTAAG 59.401 45.833 0.00 0.00 0.00 2.34
3265 3528 4.838403 TCCCTCCATCCCATAATGTAAGA 58.162 43.478 0.00 0.00 0.00 2.10
3266 3529 4.597507 TCCCTCCATCCCATAATGTAAGAC 59.402 45.833 0.00 0.00 0.00 3.01
3267 3530 4.563580 CCCTCCATCCCATAATGTAAGACG 60.564 50.000 0.00 0.00 0.00 4.18
3268 3531 4.040461 CCTCCATCCCATAATGTAAGACGT 59.960 45.833 0.00 0.00 0.00 4.34
3269 3532 5.454755 CCTCCATCCCATAATGTAAGACGTT 60.455 44.000 0.00 0.00 0.00 3.99
3270 3533 5.996644 TCCATCCCATAATGTAAGACGTTT 58.003 37.500 0.00 0.00 0.00 3.60
3271 3534 6.419791 TCCATCCCATAATGTAAGACGTTTT 58.580 36.000 0.00 0.00 0.00 2.43
3272 3535 6.887545 TCCATCCCATAATGTAAGACGTTTTT 59.112 34.615 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.122547 AGTGGTCCCTGTTCCCGT 60.123 61.111 0.00 0.00 0.00 5.28
9 10 3.953775 CGGCCAGTGGTCCCTGTT 61.954 66.667 8.54 0.00 0.00 3.16
16 17 2.927856 TCATGTCCGGCCAGTGGT 60.928 61.111 11.74 0.00 0.00 4.16
23 24 0.103937 CCTTCTCTCTCATGTCCGGC 59.896 60.000 0.00 0.00 0.00 6.13
49 50 3.628487 TCTGGTTGGTCAACTTTTTACCG 59.372 43.478 12.75 0.00 40.94 4.02
50 51 4.202080 GGTCTGGTTGGTCAACTTTTTACC 60.202 45.833 12.75 9.83 40.94 2.85
63 64 0.895559 GCTTTGAGGGGTCTGGTTGG 60.896 60.000 0.00 0.00 0.00 3.77
69 70 0.476611 AAGGAGGCTTTGAGGGGTCT 60.477 55.000 0.00 0.00 0.00 3.85
85 86 2.089201 GGACAACCCGACCATTTAAGG 58.911 52.381 0.00 0.00 0.00 2.69
100 101 1.152922 GGTTGGGGTTGTCGGACAA 60.153 57.895 19.07 19.07 35.42 3.18
105 106 0.616371 TATGAGGGTTGGGGTTGTCG 59.384 55.000 0.00 0.00 0.00 4.35
107 108 2.652348 TGAATATGAGGGTTGGGGTTGT 59.348 45.455 0.00 0.00 0.00 3.32
108 109 3.380471 TGAATATGAGGGTTGGGGTTG 57.620 47.619 0.00 0.00 0.00 3.77
109 110 3.793827 AGATGAATATGAGGGTTGGGGTT 59.206 43.478 0.00 0.00 0.00 4.11
110 111 3.395941 GAGATGAATATGAGGGTTGGGGT 59.604 47.826 0.00 0.00 0.00 4.95
111 112 3.395607 TGAGATGAATATGAGGGTTGGGG 59.604 47.826 0.00 0.00 0.00 4.96
112 113 4.712051 TGAGATGAATATGAGGGTTGGG 57.288 45.455 0.00 0.00 0.00 4.12
113 114 9.557061 CATATATGAGATGAATATGAGGGTTGG 57.443 37.037 6.92 0.00 36.22 3.77
140 141 2.223829 CGGACGCTCCTCATACTCATTT 60.224 50.000 3.15 0.00 33.30 2.32
183 184 2.971428 AATCCTATGTGGCGGACGCG 62.971 60.000 3.53 3.53 43.06 6.01
186 187 2.288886 GGTCTAATCCTATGTGGCGGAC 60.289 54.545 0.00 0.00 35.26 4.79
189 190 1.002087 GGGGTCTAATCCTATGTGGCG 59.998 57.143 0.00 0.00 35.26 5.69
191 192 2.701551 TGGGGGTCTAATCCTATGTGG 58.298 52.381 0.00 0.00 37.10 4.17
192 193 5.342017 TCTATGGGGGTCTAATCCTATGTG 58.658 45.833 0.00 0.00 0.00 3.21
239 247 4.770010 GTGGAGAAGGAGAGAGAGAGAAAA 59.230 45.833 0.00 0.00 0.00 2.29
247 255 4.467795 TGTAATTGGTGGAGAAGGAGAGAG 59.532 45.833 0.00 0.00 0.00 3.20
251 259 3.629398 GCATGTAATTGGTGGAGAAGGAG 59.371 47.826 0.00 0.00 0.00 3.69
252 260 3.010027 TGCATGTAATTGGTGGAGAAGGA 59.990 43.478 0.00 0.00 0.00 3.36
253 261 3.355378 TGCATGTAATTGGTGGAGAAGG 58.645 45.455 0.00 0.00 0.00 3.46
254 262 4.400251 ACATGCATGTAATTGGTGGAGAAG 59.600 41.667 30.50 0.00 39.68 2.85
255 263 4.158209 CACATGCATGTAATTGGTGGAGAA 59.842 41.667 30.92 0.00 39.39 2.87
256 264 3.695556 CACATGCATGTAATTGGTGGAGA 59.304 43.478 30.92 0.00 39.39 3.71
257 265 3.735820 GCACATGCATGTAATTGGTGGAG 60.736 47.826 30.92 15.77 39.39 3.86
267 275 1.451207 GTCCGGGCACATGCATGTA 60.451 57.895 30.92 12.75 44.36 2.29
279 287 7.387948 CCTCACTTTTCTTTATATATGTCCGGG 59.612 40.741 0.00 0.00 0.00 5.73
282 290 9.274206 GTCCCTCACTTTTCTTTATATATGTCC 57.726 37.037 0.00 0.00 0.00 4.02
300 308 1.021390 CACGCAATCCTGTCCCTCAC 61.021 60.000 0.00 0.00 0.00 3.51
301 309 1.191489 TCACGCAATCCTGTCCCTCA 61.191 55.000 0.00 0.00 0.00 3.86
302 310 0.036388 TTCACGCAATCCTGTCCCTC 60.036 55.000 0.00 0.00 0.00 4.30
304 312 1.635663 CGTTCACGCAATCCTGTCCC 61.636 60.000 0.00 0.00 0.00 4.46
330 338 3.620488 GCATGTCCACTTTGATTCCCTA 58.380 45.455 0.00 0.00 0.00 3.53
344 352 4.778143 AGCGTTCCGGGCATGTCC 62.778 66.667 6.17 6.17 0.00 4.02
345 353 3.499737 CAGCGTTCCGGGCATGTC 61.500 66.667 0.00 0.00 0.00 3.06
380 388 2.897326 ACTAATTTGGCCCCTCAAACAC 59.103 45.455 0.00 0.00 39.13 3.32
381 389 3.161866 GACTAATTTGGCCCCTCAAACA 58.838 45.455 0.00 0.00 39.13 2.83
398 406 1.319541 GAGCATCTACAGCCGGACTA 58.680 55.000 5.05 0.00 0.00 2.59
411 419 0.035176 GAGGAGGCCATCAGAGCATC 59.965 60.000 5.01 0.00 40.21 3.91
412 420 1.417288 GGAGGAGGCCATCAGAGCAT 61.417 60.000 5.01 0.00 0.00 3.79
413 421 2.068821 GGAGGAGGCCATCAGAGCA 61.069 63.158 5.01 0.00 0.00 4.26
414 422 1.757423 GAGGAGGAGGCCATCAGAGC 61.757 65.000 5.01 0.00 0.00 4.09
415 423 1.120795 GGAGGAGGAGGCCATCAGAG 61.121 65.000 5.01 0.00 0.00 3.35
416 424 1.074926 GGAGGAGGAGGCCATCAGA 60.075 63.158 5.01 0.00 0.00 3.27
842 873 0.175989 GGAGTTAAGAGGGCGTCTGG 59.824 60.000 10.92 0.00 34.84 3.86
1024 1057 1.128147 GCACGCACCTACGTACGTAC 61.128 60.000 23.60 15.90 46.34 3.67
1029 1062 2.126773 CACGCACGCACCTACGTA 60.127 61.111 0.00 0.00 46.34 3.57
1037 1070 4.419939 AGATCGAGCACGCACGCA 62.420 61.111 2.38 0.00 39.58 5.24
1056 1091 2.124903 GTATTGCGATGGTCGTCGATT 58.875 47.619 15.67 3.02 44.06 3.34
1208 1247 9.730420 CTTTATAACACAAAAATTATAGCGCCT 57.270 29.630 2.29 0.00 0.00 5.52
1253 1292 8.999431 CCTATGCGTATACCTAAATTGTCAATT 58.001 33.333 4.91 4.91 0.00 2.32
1254 1293 8.372459 TCCTATGCGTATACCTAAATTGTCAAT 58.628 33.333 0.00 0.00 0.00 2.57
1255 1294 7.654520 GTCCTATGCGTATACCTAAATTGTCAA 59.345 37.037 0.00 0.00 0.00 3.18
1256 1295 7.014905 AGTCCTATGCGTATACCTAAATTGTCA 59.985 37.037 0.00 0.00 0.00 3.58
1257 1296 7.376615 AGTCCTATGCGTATACCTAAATTGTC 58.623 38.462 0.00 0.00 0.00 3.18
1258 1297 7.299246 AGTCCTATGCGTATACCTAAATTGT 57.701 36.000 0.00 0.00 0.00 2.71
1259 1298 7.656137 ACAAGTCCTATGCGTATACCTAAATTG 59.344 37.037 0.00 0.00 0.00 2.32
1260 1299 7.732996 ACAAGTCCTATGCGTATACCTAAATT 58.267 34.615 0.00 0.00 0.00 1.82
1261 1300 7.299246 ACAAGTCCTATGCGTATACCTAAAT 57.701 36.000 0.00 0.00 0.00 1.40
1262 1301 6.720112 ACAAGTCCTATGCGTATACCTAAA 57.280 37.500 0.00 0.00 0.00 1.85
1263 1302 7.822161 TTACAAGTCCTATGCGTATACCTAA 57.178 36.000 0.00 0.00 0.00 2.69
1264 1303 7.822161 TTTACAAGTCCTATGCGTATACCTA 57.178 36.000 0.00 0.00 0.00 3.08
1265 1304 6.720112 TTTACAAGTCCTATGCGTATACCT 57.280 37.500 0.00 0.00 0.00 3.08
1266 1305 7.654520 TCATTTTACAAGTCCTATGCGTATACC 59.345 37.037 0.00 0.00 0.00 2.73
1267 1306 8.583810 TCATTTTACAAGTCCTATGCGTATAC 57.416 34.615 0.00 0.00 0.00 1.47
1268 1307 9.602568 TTTCATTTTACAAGTCCTATGCGTATA 57.397 29.630 0.00 0.00 0.00 1.47
1269 1308 8.500753 TTTCATTTTACAAGTCCTATGCGTAT 57.499 30.769 0.00 0.00 0.00 3.06
1270 1309 7.908827 TTTCATTTTACAAGTCCTATGCGTA 57.091 32.000 0.00 0.00 0.00 4.42
1271 1310 6.811253 TTTCATTTTACAAGTCCTATGCGT 57.189 33.333 0.00 0.00 0.00 5.24
1272 1311 6.692681 CCATTTCATTTTACAAGTCCTATGCG 59.307 38.462 0.00 0.00 0.00 4.73
1273 1312 7.771183 TCCATTTCATTTTACAAGTCCTATGC 58.229 34.615 0.00 0.00 0.00 3.14
1274 1313 8.408601 CCTCCATTTCATTTTACAAGTCCTATG 58.591 37.037 0.00 0.00 0.00 2.23
1275 1314 8.116026 ACCTCCATTTCATTTTACAAGTCCTAT 58.884 33.333 0.00 0.00 0.00 2.57
1276 1315 7.466804 ACCTCCATTTCATTTTACAAGTCCTA 58.533 34.615 0.00 0.00 0.00 2.94
1277 1316 6.314917 ACCTCCATTTCATTTTACAAGTCCT 58.685 36.000 0.00 0.00 0.00 3.85
1278 1317 6.590234 ACCTCCATTTCATTTTACAAGTCC 57.410 37.500 0.00 0.00 0.00 3.85
1279 1318 8.237267 CACTACCTCCATTTCATTTTACAAGTC 58.763 37.037 0.00 0.00 0.00 3.01
1280 1319 7.309194 GCACTACCTCCATTTCATTTTACAAGT 60.309 37.037 0.00 0.00 0.00 3.16
1281 1320 7.029563 GCACTACCTCCATTTCATTTTACAAG 58.970 38.462 0.00 0.00 0.00 3.16
1282 1321 6.491745 TGCACTACCTCCATTTCATTTTACAA 59.508 34.615 0.00 0.00 0.00 2.41
1283 1322 6.007076 TGCACTACCTCCATTTCATTTTACA 58.993 36.000 0.00 0.00 0.00 2.41
1284 1323 6.509418 TGCACTACCTCCATTTCATTTTAC 57.491 37.500 0.00 0.00 0.00 2.01
1285 1324 7.716799 AATGCACTACCTCCATTTCATTTTA 57.283 32.000 0.00 0.00 0.00 1.52
1286 1325 6.610075 AATGCACTACCTCCATTTCATTTT 57.390 33.333 0.00 0.00 0.00 1.82
1287 1326 6.610075 AAATGCACTACCTCCATTTCATTT 57.390 33.333 0.00 0.00 34.99 2.32
1288 1327 6.610075 AAAATGCACTACCTCCATTTCATT 57.390 33.333 0.00 0.00 37.99 2.57
1289 1328 6.610075 AAAAATGCACTACCTCCATTTCAT 57.390 33.333 0.00 0.00 37.99 2.57
1341 1380 3.746045 TGCACCTCGGTTAATCTATCC 57.254 47.619 0.00 0.00 0.00 2.59
1345 1384 3.009723 CACAATGCACCTCGGTTAATCT 58.990 45.455 0.00 0.00 0.00 2.40
1618 1658 2.423185 CCGCTGCAAAATGAACTCCATA 59.577 45.455 0.00 0.00 34.45 2.74
1685 1726 2.180204 CGCTTATGGCCGGGAACAG 61.180 63.158 2.18 0.00 37.74 3.16
1912 1953 1.781786 ACTACATCACTGGCTCGGAT 58.218 50.000 0.00 0.00 0.00 4.18
1928 1969 2.163818 GGCACATTGGCGCTATACTA 57.836 50.000 7.64 0.00 31.79 1.82
2130 2191 2.494073 TCCTCCGTTTGCTTGTTTGTTT 59.506 40.909 0.00 0.00 0.00 2.83
2132 2193 1.757682 TCCTCCGTTTGCTTGTTTGT 58.242 45.000 0.00 0.00 0.00 2.83
2140 2203 0.664166 TACGTCGTTCCTCCGTTTGC 60.664 55.000 1.78 0.00 36.12 3.68
2187 2250 5.043903 TGAGACCGATGTACTACTACGTAC 58.956 45.833 0.00 0.00 40.06 3.67
2188 2251 5.043903 GTGAGACCGATGTACTACTACGTA 58.956 45.833 0.00 0.00 0.00 3.57
2189 2252 3.868077 GTGAGACCGATGTACTACTACGT 59.132 47.826 0.00 0.00 0.00 3.57
2190 2253 3.060674 CGTGAGACCGATGTACTACTACG 60.061 52.174 0.00 0.00 0.00 3.51
2303 2369 6.132056 CGTATAGTTCAGCATTTGCATCTTC 58.868 40.000 5.20 0.00 45.16 2.87
2386 2452 2.427245 CCTCTCGCCCATCGGTTCT 61.427 63.158 0.00 0.00 39.05 3.01
2392 2458 2.586357 GTTCGCCTCTCGCCCATC 60.586 66.667 0.00 0.00 38.27 3.51
2395 2461 4.388499 TTGGTTCGCCTCTCGCCC 62.388 66.667 0.00 0.00 38.36 6.13
2397 2463 2.048127 AGTTGGTTCGCCTCTCGC 60.048 61.111 0.00 0.00 38.36 5.03
2399 2465 0.318762 ACTGAGTTGGTTCGCCTCTC 59.681 55.000 0.00 0.00 38.44 3.20
2400 2466 0.034059 CACTGAGTTGGTTCGCCTCT 59.966 55.000 0.00 0.00 38.36 3.69
2401 2467 0.249911 ACACTGAGTTGGTTCGCCTC 60.250 55.000 0.00 0.00 38.36 4.70
2402 2468 0.532862 CACACTGAGTTGGTTCGCCT 60.533 55.000 0.00 0.00 38.36 5.52
2403 2469 0.814010 ACACACTGAGTTGGTTCGCC 60.814 55.000 0.00 0.00 37.92 5.54
2404 2470 0.582005 GACACACTGAGTTGGTTCGC 59.418 55.000 0.00 0.00 0.00 4.70
2405 2471 0.852777 CGACACACTGAGTTGGTTCG 59.147 55.000 0.00 0.00 0.00 3.95
2406 2472 0.582005 GCGACACACTGAGTTGGTTC 59.418 55.000 0.00 0.00 0.00 3.62
2407 2473 0.178068 AGCGACACACTGAGTTGGTT 59.822 50.000 0.00 0.00 0.00 3.67
2408 2474 0.530650 CAGCGACACACTGAGTTGGT 60.531 55.000 0.00 0.00 37.32 3.67
2409 2475 0.249447 TCAGCGACACACTGAGTTGG 60.249 55.000 0.00 0.00 39.21 3.77
2410 2476 3.272766 TCAGCGACACACTGAGTTG 57.727 52.632 0.00 0.00 39.21 3.16
2414 2480 0.315251 CCTTCTCAGCGACACACTGA 59.685 55.000 0.00 0.00 41.78 3.41
2415 2481 1.287730 GCCTTCTCAGCGACACACTG 61.288 60.000 0.00 0.00 36.44 3.66
2416 2482 1.005630 GCCTTCTCAGCGACACACT 60.006 57.895 0.00 0.00 0.00 3.55
2587 2663 4.924462 GTCTAGGACTTAAACTCTGTGTGC 59.076 45.833 0.00 0.00 0.00 4.57
2669 2746 6.477688 TCATAGTCAACGAAAACGTCTTCTTT 59.522 34.615 0.00 0.00 0.00 2.52
2718 2795 4.854173 TGGGCTAGCACATCATTTAAGAA 58.146 39.130 17.75 0.00 0.00 2.52
2734 2812 1.819288 CACTTTCGAGAGACTGGGCTA 59.181 52.381 10.37 0.00 41.84 3.93
2738 2816 1.270826 TGAGCACTTTCGAGAGACTGG 59.729 52.381 10.37 0.00 41.84 4.00
2761 2839 3.737774 CACACACATGCATACTCTATCCG 59.262 47.826 0.00 0.00 0.00 4.18
2764 2842 5.733676 TGAACACACACATGCATACTCTAT 58.266 37.500 0.00 0.00 0.00 1.98
2771 2849 4.835678 TCTCTATGAACACACACATGCAT 58.164 39.130 0.00 0.00 0.00 3.96
2791 2869 9.201989 TGGACAAAGACACTTATATACTCATCT 57.798 33.333 0.00 0.00 0.00 2.90
2803 2881 8.812972 TCTAACATAGTATGGACAAAGACACTT 58.187 33.333 14.59 0.00 33.60 3.16
2828 2906 7.042051 GGTGCCCATAGTTTTCTTTTTCTTTTC 60.042 37.037 0.00 0.00 0.00 2.29
2850 2928 2.293399 ACCTCGTTTCAATCAAAGGTGC 59.707 45.455 0.00 0.00 32.59 5.01
2852 2930 4.204012 TGAACCTCGTTTCAATCAAAGGT 58.796 39.130 0.00 0.00 32.42 3.50
3053 3150 9.158233 GCCTACTTGTTTATGTTTGTATGTCTA 57.842 33.333 0.00 0.00 0.00 2.59
3067 3328 6.123651 TGTTTTTCCTCAGCCTACTTGTTTA 58.876 36.000 0.00 0.00 0.00 2.01
3149 3412 3.319972 AGTTTACTACACGACCAAGAGCA 59.680 43.478 0.00 0.00 0.00 4.26
3176 3439 9.553064 AGATGAGAAAATAAGTATGTCACATCC 57.447 33.333 0.00 0.00 37.15 3.51
3228 3491 7.093421 GGGATGGAGGGAGTAGTTAATATGTAC 60.093 44.444 0.00 0.00 0.00 2.90
3236 3499 5.427857 TTATGGGATGGAGGGAGTAGTTA 57.572 43.478 0.00 0.00 0.00 2.24
3247 3510 5.623956 AACGTCTTACATTATGGGATGGA 57.376 39.130 0.00 0.00 0.00 3.41
3248 3511 6.693315 AAAACGTCTTACATTATGGGATGG 57.307 37.500 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.