Multiple sequence alignment - TraesCS5B01G145400

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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 TraesCS5B01G145400 chr5B 100.000 3091 0 0 1 3091 272669073 272672163 0.000000e+00 5709.0
1 TraesCS5B01G145400 chr5B 90.057 352 35 0 1 352 671363617 671363266 1.010000e-124 457.0
2 TraesCS5B01G145400 chr5B 89.518 353 36 1 1 352 594277593 594277945 2.190000e-121 446.0
3 TraesCS5B01G145400 chr5D 94.469 1555 60 8 656 2199 232418757 232417218 0.000000e+00 2372.0
4 TraesCS5B01G145400 chr5D 93.973 896 44 4 2196 3091 232415780 232414895 0.000000e+00 1347.0
5 TraesCS5B01G145400 chr5D 97.674 43 1 0 587 629 232418799 232418757 1.190000e-09 75.0
6 TraesCS5B01G145400 chr5A 93.548 1333 46 16 367 1670 323351291 323352612 0.000000e+00 1949.0
7 TraesCS5B01G145400 chr5A 95.060 749 30 2 1664 2411 323352991 323353733 0.000000e+00 1171.0
8 TraesCS5B01G145400 chr5A 93.827 405 20 1 2395 2794 323354177 323354581 3.410000e-169 604.0
9 TraesCS5B01G145400 chr5A 89.711 311 15 3 2789 3091 323359748 323360049 6.250000e-102 381.0
10 TraesCS5B01G145400 chr3B 90.057 352 35 0 1 352 27480064 27479713 1.010000e-124 457.0
11 TraesCS5B01G145400 chr3B 88.352 352 39 2 1 352 768310826 768310477 3.690000e-114 422.0
12 TraesCS5B01G145400 chr3B 88.102 353 41 1 1 352 145413326 145412974 4.770000e-113 418.0
13 TraesCS5B01G145400 chr4A 89.489 352 37 0 1 352 743611866 743612217 2.190000e-121 446.0
14 TraesCS5B01G145400 chr2B 89.489 352 36 1 1 352 756598275 756597925 7.870000e-121 444.0
15 TraesCS5B01G145400 chr6D 89.205 352 38 0 1 352 15587263 15586912 1.020000e-119 440.0
16 TraesCS5B01G145400 chr6B 88.636 352 40 0 1 352 654636945 654636594 2.200000e-116 429.0
17 TraesCS5B01G145400 chr2A 87.903 124 13 2 1519 1641 10217115 10216993 8.930000e-31 145.0
18 TraesCS5B01G145400 chr2A 84.397 141 18 4 1514 1651 20593129 20593268 5.380000e-28 135.0
19 TraesCS5B01G145400 chr2D 82.759 145 21 4 1514 1655 19240443 19240300 3.240000e-25 126.0
20 TraesCS5B01G145400 chr2D 83.333 96 11 4 2996 3091 16143321 16143411 1.980000e-12 84.2
21 TraesCS5B01G145400 chr7D 87.302 63 8 0 3029 3091 11523098 11523036 4.280000e-09 73.1
22 TraesCS5B01G145400 chr6A 83.951 81 8 3 3006 3083 100411093 100411015 4.280000e-09 73.1


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 TraesCS5B01G145400 chr5B 272669073 272672163 3090 False 5709.000000 5709 100.000 1 3091 1 chr5B.!!$F1 3090
1 TraesCS5B01G145400 chr5D 232414895 232418799 3904 True 1264.666667 2372 95.372 587 3091 3 chr5D.!!$R1 2504
2 TraesCS5B01G145400 chr5A 323351291 323354581 3290 False 1241.333333 1949 94.145 367 2794 3 chr5A.!!$F2 2427

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
332 333 0.036306 GCGGAAGAGAGAAAACCCCA 59.964 55.0 0.0 0.0 0.0 4.96 F
676 684 0.108138 GATGGGTCTCTGGTCCAACG 60.108 60.0 0.0 0.0 33.9 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1910 2326 0.719465 CGTTACTGATGTTGTCGCCC 59.281 55.0 0.0 0.0 0.00 6.13 R
2405 4263 0.465705 CCTAGACATGGCACGGATGT 59.534 55.0 0.0 0.0 36.73 3.06 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
22 23 2.052414 CGACCGGCGTAGATCGAC 60.052 66.667 6.01 0.00 45.27 4.20
27 28 4.977126 GGCGTAGATCGACGGGCG 62.977 72.222 26.24 0.00 43.13 6.13
28 29 4.977126 GCGTAGATCGACGGGCGG 62.977 72.222 26.24 2.39 43.13 6.13
29 30 4.323843 CGTAGATCGACGGGCGGG 62.324 72.222 19.23 0.00 42.86 6.13
30 31 4.642542 GTAGATCGACGGGCGGGC 62.643 72.222 2.16 0.00 41.33 6.13
165 166 2.021106 CGTAGACGCGAGGACGAC 59.979 66.667 15.93 6.81 42.66 4.34
166 167 2.021106 GTAGACGCGAGGACGACG 59.979 66.667 15.93 0.00 42.66 5.12
194 195 1.371558 ACCTGGTCGGTGAAGAAGC 59.628 57.895 0.00 0.00 46.80 3.86
195 196 1.376037 CCTGGTCGGTGAAGAAGCC 60.376 63.158 0.00 0.00 0.00 4.35
201 202 2.654877 GGTGAAGAAGCCGACCGA 59.345 61.111 0.00 0.00 0.00 4.69
202 203 1.218316 GGTGAAGAAGCCGACCGAT 59.782 57.895 0.00 0.00 0.00 4.18
203 204 0.806492 GGTGAAGAAGCCGACCGATC 60.806 60.000 0.00 0.00 0.00 3.69
216 217 4.444838 CGATCGTGCCGGGGTTGA 62.445 66.667 7.03 0.00 0.00 3.18
217 218 2.046700 GATCGTGCCGGGGTTGAA 60.047 61.111 2.18 0.00 0.00 2.69
218 219 2.046314 ATCGTGCCGGGGTTGAAG 60.046 61.111 2.18 0.00 0.00 3.02
219 220 2.798148 GATCGTGCCGGGGTTGAAGT 62.798 60.000 2.18 0.00 0.00 3.01
220 221 1.546589 ATCGTGCCGGGGTTGAAGTA 61.547 55.000 2.18 0.00 0.00 2.24
221 222 1.740296 CGTGCCGGGGTTGAAGTAG 60.740 63.158 2.18 0.00 0.00 2.57
222 223 1.675219 GTGCCGGGGTTGAAGTAGA 59.325 57.895 2.18 0.00 0.00 2.59
223 224 0.391263 GTGCCGGGGTTGAAGTAGAG 60.391 60.000 2.18 0.00 0.00 2.43
224 225 1.221021 GCCGGGGTTGAAGTAGAGG 59.779 63.158 2.18 0.00 0.00 3.69
225 226 1.221021 CCGGGGTTGAAGTAGAGGC 59.779 63.158 0.00 0.00 0.00 4.70
226 227 1.153628 CGGGGTTGAAGTAGAGGCG 60.154 63.158 0.00 0.00 0.00 5.52
227 228 1.449778 GGGGTTGAAGTAGAGGCGC 60.450 63.158 0.00 0.00 0.00 6.53
228 229 1.295423 GGGTTGAAGTAGAGGCGCA 59.705 57.895 10.83 0.00 0.00 6.09
229 230 1.019805 GGGTTGAAGTAGAGGCGCAC 61.020 60.000 10.83 2.06 0.00 5.34
230 231 1.352156 GGTTGAAGTAGAGGCGCACG 61.352 60.000 10.83 0.00 0.00 5.34
231 232 1.080093 TTGAAGTAGAGGCGCACGG 60.080 57.895 10.83 0.00 0.00 4.94
232 233 2.202756 GAAGTAGAGGCGCACGGG 60.203 66.667 10.83 0.00 0.00 5.28
233 234 3.718210 GAAGTAGAGGCGCACGGGG 62.718 68.421 10.83 0.00 0.00 5.73
235 236 4.509737 GTAGAGGCGCACGGGGTC 62.510 72.222 10.83 0.00 0.00 4.46
264 265 4.690719 TGGGCGACGCAAACCGAT 62.691 61.111 23.09 0.00 41.02 4.18
265 266 3.861263 GGGCGACGCAAACCGATC 61.861 66.667 23.09 0.62 41.02 3.69
266 267 3.115892 GGCGACGCAAACCGATCA 61.116 61.111 23.09 0.00 41.02 2.92
267 268 2.673114 GGCGACGCAAACCGATCAA 61.673 57.895 23.09 0.00 41.02 2.57
268 269 1.225745 GCGACGCAAACCGATCAAG 60.226 57.895 16.42 0.00 41.02 3.02
269 270 1.623081 GCGACGCAAACCGATCAAGA 61.623 55.000 16.42 0.00 41.02 3.02
270 271 0.999406 CGACGCAAACCGATCAAGAT 59.001 50.000 0.00 0.00 41.02 2.40
271 272 1.393539 CGACGCAAACCGATCAAGATT 59.606 47.619 0.00 0.00 41.02 2.40
272 273 2.601314 CGACGCAAACCGATCAAGATTA 59.399 45.455 0.00 0.00 41.02 1.75
273 274 3.301835 CGACGCAAACCGATCAAGATTAG 60.302 47.826 0.00 0.00 41.02 1.73
274 275 3.857052 ACGCAAACCGATCAAGATTAGA 58.143 40.909 0.00 0.00 41.02 2.10
275 276 4.442706 ACGCAAACCGATCAAGATTAGAT 58.557 39.130 0.00 0.00 41.02 1.98
276 277 4.508124 ACGCAAACCGATCAAGATTAGATC 59.492 41.667 0.00 0.00 41.02 2.75
286 287 7.553881 GATCAAGATTAGATCGGAAAACCAA 57.446 36.000 0.00 0.00 33.32 3.67
287 288 7.938140 ATCAAGATTAGATCGGAAAACCAAA 57.062 32.000 0.00 0.00 0.00 3.28
288 289 7.753309 TCAAGATTAGATCGGAAAACCAAAA 57.247 32.000 0.00 0.00 0.00 2.44
289 290 8.172352 TCAAGATTAGATCGGAAAACCAAAAA 57.828 30.769 0.00 0.00 0.00 1.94
311 312 5.541098 AAAAACCGACGATCAAGATAACC 57.459 39.130 0.00 0.00 0.00 2.85
312 313 3.880047 AACCGACGATCAAGATAACCA 57.120 42.857 0.00 0.00 0.00 3.67
313 314 3.438297 ACCGACGATCAAGATAACCAG 57.562 47.619 0.00 0.00 0.00 4.00
314 315 2.128035 CCGACGATCAAGATAACCAGC 58.872 52.381 0.00 0.00 0.00 4.85
315 316 1.781429 CGACGATCAAGATAACCAGCG 59.219 52.381 0.00 0.00 0.00 5.18
316 317 2.128035 GACGATCAAGATAACCAGCGG 58.872 52.381 0.00 0.00 0.00 5.52
317 318 1.754803 ACGATCAAGATAACCAGCGGA 59.245 47.619 1.50 0.00 0.00 5.54
318 319 2.167693 ACGATCAAGATAACCAGCGGAA 59.832 45.455 1.50 0.00 0.00 4.30
319 320 2.797156 CGATCAAGATAACCAGCGGAAG 59.203 50.000 1.50 0.00 0.00 3.46
320 321 3.490933 CGATCAAGATAACCAGCGGAAGA 60.491 47.826 1.50 0.00 0.00 2.87
321 322 3.526931 TCAAGATAACCAGCGGAAGAG 57.473 47.619 1.50 0.00 0.00 2.85
322 323 3.096852 TCAAGATAACCAGCGGAAGAGA 58.903 45.455 1.50 0.00 0.00 3.10
323 324 3.131223 TCAAGATAACCAGCGGAAGAGAG 59.869 47.826 1.50 0.00 0.00 3.20
324 325 3.019799 AGATAACCAGCGGAAGAGAGA 57.980 47.619 1.50 0.00 0.00 3.10
325 326 3.366396 AGATAACCAGCGGAAGAGAGAA 58.634 45.455 1.50 0.00 0.00 2.87
326 327 3.769844 AGATAACCAGCGGAAGAGAGAAA 59.230 43.478 1.50 0.00 0.00 2.52
327 328 2.930826 AACCAGCGGAAGAGAGAAAA 57.069 45.000 1.50 0.00 0.00 2.29
328 329 2.171341 ACCAGCGGAAGAGAGAAAAC 57.829 50.000 1.50 0.00 0.00 2.43
329 330 1.270893 ACCAGCGGAAGAGAGAAAACC 60.271 52.381 1.50 0.00 0.00 3.27
330 331 1.443802 CAGCGGAAGAGAGAAAACCC 58.556 55.000 0.00 0.00 0.00 4.11
331 332 0.325272 AGCGGAAGAGAGAAAACCCC 59.675 55.000 0.00 0.00 0.00 4.95
332 333 0.036306 GCGGAAGAGAGAAAACCCCA 59.964 55.000 0.00 0.00 0.00 4.96
333 334 1.544759 GCGGAAGAGAGAAAACCCCAA 60.545 52.381 0.00 0.00 0.00 4.12
334 335 2.858745 CGGAAGAGAGAAAACCCCAAA 58.141 47.619 0.00 0.00 0.00 3.28
335 336 3.219281 CGGAAGAGAGAAAACCCCAAAA 58.781 45.455 0.00 0.00 0.00 2.44
336 337 3.253432 CGGAAGAGAGAAAACCCCAAAAG 59.747 47.826 0.00 0.00 0.00 2.27
337 338 4.470602 GGAAGAGAGAAAACCCCAAAAGA 58.529 43.478 0.00 0.00 0.00 2.52
338 339 4.893524 GGAAGAGAGAAAACCCCAAAAGAA 59.106 41.667 0.00 0.00 0.00 2.52
339 340 5.010112 GGAAGAGAGAAAACCCCAAAAGAAG 59.990 44.000 0.00 0.00 0.00 2.85
340 341 5.130705 AGAGAGAAAACCCCAAAAGAAGT 57.869 39.130 0.00 0.00 0.00 3.01
341 342 4.889995 AGAGAGAAAACCCCAAAAGAAGTG 59.110 41.667 0.00 0.00 0.00 3.16
342 343 3.384789 AGAGAAAACCCCAAAAGAAGTGC 59.615 43.478 0.00 0.00 0.00 4.40
343 344 3.374764 AGAAAACCCCAAAAGAAGTGCT 58.625 40.909 0.00 0.00 0.00 4.40
344 345 3.384789 AGAAAACCCCAAAAGAAGTGCTC 59.615 43.478 0.00 0.00 0.00 4.26
345 346 1.318576 AACCCCAAAAGAAGTGCTCG 58.681 50.000 0.00 0.00 0.00 5.03
346 347 0.537371 ACCCCAAAAGAAGTGCTCGG 60.537 55.000 0.00 0.00 0.00 4.63
347 348 1.244019 CCCCAAAAGAAGTGCTCGGG 61.244 60.000 0.00 0.00 0.00 5.14
348 349 1.244019 CCCAAAAGAAGTGCTCGGGG 61.244 60.000 0.00 0.00 0.00 5.73
349 350 0.250727 CCAAAAGAAGTGCTCGGGGA 60.251 55.000 0.00 0.00 0.00 4.81
350 351 1.604604 CAAAAGAAGTGCTCGGGGAA 58.395 50.000 0.00 0.00 0.00 3.97
351 352 1.953686 CAAAAGAAGTGCTCGGGGAAA 59.046 47.619 0.00 0.00 0.00 3.13
352 353 1.605753 AAAGAAGTGCTCGGGGAAAC 58.394 50.000 0.00 0.00 0.00 2.78
353 354 0.472471 AAGAAGTGCTCGGGGAAACA 59.528 50.000 0.00 0.00 0.00 2.83
354 355 0.693049 AGAAGTGCTCGGGGAAACAT 59.307 50.000 0.00 0.00 0.00 2.71
355 356 1.073923 AGAAGTGCTCGGGGAAACATT 59.926 47.619 0.00 0.00 0.00 2.71
356 357 2.304761 AGAAGTGCTCGGGGAAACATTA 59.695 45.455 0.00 0.00 0.00 1.90
357 358 3.054361 AGAAGTGCTCGGGGAAACATTAT 60.054 43.478 0.00 0.00 0.00 1.28
358 359 4.163458 AGAAGTGCTCGGGGAAACATTATA 59.837 41.667 0.00 0.00 0.00 0.98
359 360 3.805207 AGTGCTCGGGGAAACATTATAC 58.195 45.455 0.00 0.00 0.00 1.47
360 361 3.454812 AGTGCTCGGGGAAACATTATACT 59.545 43.478 0.00 0.00 0.00 2.12
361 362 3.808174 GTGCTCGGGGAAACATTATACTC 59.192 47.826 0.00 0.00 0.00 2.59
362 363 3.452990 TGCTCGGGGAAACATTATACTCA 59.547 43.478 0.00 0.00 0.00 3.41
363 364 4.080807 TGCTCGGGGAAACATTATACTCAA 60.081 41.667 0.00 0.00 0.00 3.02
364 365 4.272748 GCTCGGGGAAACATTATACTCAAC 59.727 45.833 0.00 0.00 0.00 3.18
365 366 5.423704 TCGGGGAAACATTATACTCAACA 57.576 39.130 0.00 0.00 0.00 3.33
396 397 8.258708 ACACCTAGTAGTCCATGAAAAATACTC 58.741 37.037 0.00 0.00 0.00 2.59
441 442 0.457337 CGAAGCTGCCAAATTCTGCC 60.457 55.000 0.00 0.00 0.00 4.85
457 458 0.683828 TGCCATTCCGTCCATGCATT 60.684 50.000 0.00 0.00 0.00 3.56
516 522 2.029649 TCTACTACAACGTGCCAGGTTC 60.030 50.000 0.00 0.00 0.00 3.62
571 577 8.192774 CACAAATTAACAATCCATGCATAGAGT 58.807 33.333 0.00 0.00 0.00 3.24
624 630 2.063156 TGGCAATTTTGTGCGCTAAG 57.937 45.000 9.73 0.00 45.91 2.18
675 683 0.984230 TGATGGGTCTCTGGTCCAAC 59.016 55.000 0.00 0.00 33.90 3.77
676 684 0.108138 GATGGGTCTCTGGTCCAACG 60.108 60.000 0.00 0.00 33.90 4.10
985 997 3.260884 CACCCTCACTAGCCTAGAAAACA 59.739 47.826 5.58 0.00 0.00 2.83
1007 1019 4.016444 ACAACGGCAAAACATATGGATCT 58.984 39.130 7.80 0.00 0.00 2.75
1053 1065 2.354539 GAGATCGAGGCGCTGCTC 60.355 66.667 7.64 5.35 0.00 4.26
1080 1092 2.049156 CAGGAGCTCGTGACGCAA 60.049 61.111 28.24 0.00 33.92 4.85
1284 1311 1.066303 AGTACTGCTGCTGCTATCGAC 59.934 52.381 17.00 7.64 40.48 4.20
1307 1334 0.108615 AAGATGGACGAACAGGCGAG 60.109 55.000 0.00 0.00 34.83 5.03
1411 1443 2.159212 GGCTCATGCATGCACACAATAA 60.159 45.455 25.37 0.00 41.91 1.40
1422 1457 4.048504 TGCACACAATAATAGGTCGATCG 58.951 43.478 9.36 9.36 0.00 3.69
1430 1465 5.934402 ATAATAGGTCGATCGGGCTAATT 57.066 39.130 16.41 11.16 0.00 1.40
1434 1469 2.368875 AGGTCGATCGGGCTAATTGATT 59.631 45.455 16.41 0.00 0.00 2.57
1435 1470 2.737252 GGTCGATCGGGCTAATTGATTC 59.263 50.000 16.41 0.00 0.00 2.52
1436 1471 3.555168 GGTCGATCGGGCTAATTGATTCT 60.555 47.826 16.41 0.00 0.00 2.40
1437 1472 4.321750 GGTCGATCGGGCTAATTGATTCTA 60.322 45.833 16.41 0.00 0.00 2.10
1438 1473 5.227908 GTCGATCGGGCTAATTGATTCTAA 58.772 41.667 16.41 0.00 0.00 2.10
1439 1474 5.694910 GTCGATCGGGCTAATTGATTCTAAA 59.305 40.000 16.41 0.00 0.00 1.85
1440 1475 6.202188 GTCGATCGGGCTAATTGATTCTAAAA 59.798 38.462 16.41 0.00 0.00 1.52
1532 1570 4.023980 TCACATCTTGTAGGAGGAACGAT 58.976 43.478 0.00 0.00 0.00 3.73
1533 1571 5.198207 TCACATCTTGTAGGAGGAACGATA 58.802 41.667 0.00 0.00 0.00 2.92
1568 1606 1.414550 TCACTCGTGACCAATGTTCCA 59.585 47.619 0.00 0.00 34.14 3.53
1672 1971 7.918562 ACTAAACAAAACGCACATACATCTTTT 59.081 29.630 0.00 0.00 0.00 2.27
1677 1976 7.865385 ACAAAACGCACATACATCTTTTGTTAT 59.135 29.630 0.00 0.00 38.18 1.89
1699 1998 8.531982 GTTATCAGATGAGTATGGCTGGTTATA 58.468 37.037 0.00 0.00 0.00 0.98
1701 2000 5.481824 TCAGATGAGTATGGCTGGTTATAGG 59.518 44.000 0.00 0.00 0.00 2.57
1717 2016 0.587768 TAGGCAATCAATCATGCGCG 59.412 50.000 0.00 0.00 43.47 6.86
1718 2017 2.297912 GGCAATCAATCATGCGCGC 61.298 57.895 27.26 27.26 43.47 6.86
1734 2150 0.564312 GCGCGCGCTAATTTTAAACC 59.436 50.000 44.38 13.65 38.26 3.27
1910 2326 0.179181 GTGATCACACATGCAAGGCG 60.179 55.000 21.07 0.00 45.32 5.52
1929 2345 0.719465 GGGCGACAACATCAGTAACG 59.281 55.000 0.00 0.00 0.00 3.18
2054 2470 1.103803 CGGCTCTGCTAGAGGTGTTA 58.896 55.000 12.98 0.00 42.54 2.41
2219 4076 5.574055 CAGTACCGACACATACGTTTACAAT 59.426 40.000 0.00 0.00 0.00 2.71
2221 4078 6.968904 AGTACCGACACATACGTTTACAATAG 59.031 38.462 0.00 0.00 0.00 1.73
2258 4115 4.158394 ACCCTATGAATGCACACATGAAAC 59.842 41.667 14.98 0.00 36.36 2.78
2278 4135 7.568349 TGAAACCTGTATTTATGAGCATCTCT 58.432 34.615 0.00 0.00 34.92 3.10
2350 4207 0.102481 ATAGTCGACGGGCATGTCAC 59.898 55.000 10.46 6.72 38.84 3.67
2460 4778 6.375455 CACCACAAGAAAGCTAACCATCTAAT 59.625 38.462 0.00 0.00 0.00 1.73
2616 4939 9.435688 AACCTACTTCAAATTGGCATTTATTTC 57.564 29.630 0.00 0.00 30.90 2.17
2661 4984 8.185505 GTCTCTAGATAGTCATTTGTCGACTTT 58.814 37.037 17.92 0.00 40.89 2.66
2663 4986 7.827701 TCTAGATAGTCATTTGTCGACTTTGT 58.172 34.615 17.92 0.00 40.89 2.83
2738 5061 2.042569 GGGTTTTCCTAGTTCCCATGGT 59.957 50.000 11.73 0.00 40.46 3.55
2761 5084 8.447833 TGGTAATTGTCGCAATAAAAGAAGTAG 58.552 33.333 5.67 0.00 0.00 2.57
2824 5147 6.154877 TCCTACATAAATCGGTTCAACCTACA 59.845 38.462 4.68 0.00 35.66 2.74
2860 5183 8.977412 TCCAGATAATAGATGTAGAACAACACA 58.023 33.333 0.00 0.00 30.75 3.72
2887 5210 6.760770 TTTTAACTTTAAAGTGCAAGCATGCT 59.239 30.769 21.22 16.30 43.25 3.79
2888 5211 7.923344 TTTTAACTTTAAAGTGCAAGCATGCTA 59.077 29.630 23.00 1.69 43.25 3.49
2932 5255 2.570752 TGCAAGATGCTCTCTCCTTCTT 59.429 45.455 3.78 0.00 45.31 2.52
2936 5259 4.470334 AGATGCTCTCTCCTTCTTCAAC 57.530 45.455 0.00 0.00 0.00 3.18
2976 5299 2.234300 TGTTTGGACGAACTGAGGAC 57.766 50.000 4.24 0.00 0.00 3.85
3048 5371 1.163554 GTACCTTCTGTCTCGACCGT 58.836 55.000 0.00 0.00 0.00 4.83
3054 5377 1.254026 TCTGTCTCGACCGTCCATTT 58.746 50.000 0.00 0.00 0.00 2.32
3083 5406 5.900425 TCAAAGTTCATGCAAGCAAACTTA 58.100 33.333 19.41 7.60 36.53 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.052414 GTCGATCTACGCCGGTCG 60.052 66.667 15.25 15.25 45.38 4.79
6 7 2.052414 CGTCGATCTACGCCGGTC 60.052 66.667 6.86 0.00 39.67 4.79
9 10 4.977126 GCCCGTCGATCTACGCCG 62.977 72.222 13.89 7.36 42.94 6.46
10 11 4.977126 CGCCCGTCGATCTACGCC 62.977 72.222 13.89 6.45 41.51 5.68
11 12 4.977126 CCGCCCGTCGATCTACGC 62.977 72.222 13.89 1.15 41.51 4.42
12 13 4.323843 CCCGCCCGTCGATCTACG 62.324 72.222 12.50 12.50 41.67 3.51
13 14 4.642542 GCCCGCCCGTCGATCTAC 62.643 72.222 0.00 0.00 41.67 2.59
148 149 2.021106 GTCGTCCTCGCGTCTACG 59.979 66.667 18.68 18.68 43.27 3.51
149 150 2.021106 CGTCGTCCTCGCGTCTAC 59.979 66.667 5.77 1.44 36.96 2.59
150 151 3.857854 GCGTCGTCCTCGCGTCTA 61.858 66.667 5.77 0.00 43.94 2.59
178 179 4.285851 GGCTTCTTCACCGACCAG 57.714 61.111 0.00 0.00 0.00 4.00
184 185 0.806492 GATCGGTCGGCTTCTTCACC 60.806 60.000 0.00 0.00 0.00 4.02
185 186 1.140407 CGATCGGTCGGCTTCTTCAC 61.140 60.000 11.03 0.00 44.00 3.18
186 187 1.138883 CGATCGGTCGGCTTCTTCA 59.861 57.895 11.03 0.00 44.00 3.02
187 188 3.999051 CGATCGGTCGGCTTCTTC 58.001 61.111 11.03 0.00 44.00 2.87
204 205 0.391263 CTCTACTTCAACCCCGGCAC 60.391 60.000 0.00 0.00 0.00 5.01
205 206 1.550130 CCTCTACTTCAACCCCGGCA 61.550 60.000 0.00 0.00 0.00 5.69
206 207 1.221021 CCTCTACTTCAACCCCGGC 59.779 63.158 0.00 0.00 0.00 6.13
207 208 1.221021 GCCTCTACTTCAACCCCGG 59.779 63.158 0.00 0.00 0.00 5.73
208 209 1.153628 CGCCTCTACTTCAACCCCG 60.154 63.158 0.00 0.00 0.00 5.73
209 210 1.449778 GCGCCTCTACTTCAACCCC 60.450 63.158 0.00 0.00 0.00 4.95
210 211 1.019805 GTGCGCCTCTACTTCAACCC 61.020 60.000 4.18 0.00 0.00 4.11
211 212 1.352156 CGTGCGCCTCTACTTCAACC 61.352 60.000 4.18 0.00 0.00 3.77
212 213 1.352156 CCGTGCGCCTCTACTTCAAC 61.352 60.000 4.18 0.00 0.00 3.18
213 214 1.080093 CCGTGCGCCTCTACTTCAA 60.080 57.895 4.18 0.00 0.00 2.69
214 215 2.571757 CCGTGCGCCTCTACTTCA 59.428 61.111 4.18 0.00 0.00 3.02
215 216 2.202756 CCCGTGCGCCTCTACTTC 60.203 66.667 4.18 0.00 0.00 3.01
216 217 3.771160 CCCCGTGCGCCTCTACTT 61.771 66.667 4.18 0.00 0.00 2.24
218 219 4.509737 GACCCCGTGCGCCTCTAC 62.510 72.222 4.18 0.00 0.00 2.59
247 248 4.690719 ATCGGTTTGCGTCGCCCA 62.691 61.111 15.88 0.00 0.00 5.36
248 249 3.861263 GATCGGTTTGCGTCGCCC 61.861 66.667 15.88 7.88 0.00 6.13
249 250 2.563086 CTTGATCGGTTTGCGTCGCC 62.563 60.000 15.88 0.00 0.00 5.54
250 251 1.225745 CTTGATCGGTTTGCGTCGC 60.226 57.895 11.10 11.10 0.00 5.19
251 252 0.999406 ATCTTGATCGGTTTGCGTCG 59.001 50.000 0.00 0.00 0.00 5.12
252 253 3.863424 TCTAATCTTGATCGGTTTGCGTC 59.137 43.478 0.00 0.00 0.00 5.19
253 254 3.857052 TCTAATCTTGATCGGTTTGCGT 58.143 40.909 0.00 0.00 0.00 5.24
254 255 5.011451 GATCTAATCTTGATCGGTTTGCG 57.989 43.478 0.00 0.00 32.29 4.85
262 263 7.553881 TTGGTTTTCCGATCTAATCTTGATC 57.446 36.000 0.00 0.00 44.36 2.92
263 264 7.938140 TTTGGTTTTCCGATCTAATCTTGAT 57.062 32.000 0.00 0.00 44.36 2.57
264 265 7.753309 TTTTGGTTTTCCGATCTAATCTTGA 57.247 32.000 0.00 0.00 44.36 3.02
289 290 4.998672 TGGTTATCTTGATCGTCGGTTTTT 59.001 37.500 0.00 0.00 0.00 1.94
290 291 4.571919 TGGTTATCTTGATCGTCGGTTTT 58.428 39.130 0.00 0.00 0.00 2.43
291 292 4.181578 CTGGTTATCTTGATCGTCGGTTT 58.818 43.478 0.00 0.00 0.00 3.27
292 293 3.782046 CTGGTTATCTTGATCGTCGGTT 58.218 45.455 0.00 0.00 0.00 4.44
293 294 2.481449 GCTGGTTATCTTGATCGTCGGT 60.481 50.000 0.00 0.00 0.00 4.69
294 295 2.128035 GCTGGTTATCTTGATCGTCGG 58.872 52.381 0.00 0.00 0.00 4.79
295 296 1.781429 CGCTGGTTATCTTGATCGTCG 59.219 52.381 0.00 0.00 0.00 5.12
296 297 2.128035 CCGCTGGTTATCTTGATCGTC 58.872 52.381 0.00 0.00 0.00 4.20
297 298 1.754803 TCCGCTGGTTATCTTGATCGT 59.245 47.619 0.00 0.00 0.00 3.73
298 299 2.509052 TCCGCTGGTTATCTTGATCG 57.491 50.000 0.00 0.00 0.00 3.69
299 300 4.054671 CTCTTCCGCTGGTTATCTTGATC 58.945 47.826 0.00 0.00 0.00 2.92
300 301 3.706594 TCTCTTCCGCTGGTTATCTTGAT 59.293 43.478 0.00 0.00 0.00 2.57
301 302 3.096852 TCTCTTCCGCTGGTTATCTTGA 58.903 45.455 0.00 0.00 0.00 3.02
302 303 3.131223 TCTCTCTTCCGCTGGTTATCTTG 59.869 47.826 0.00 0.00 0.00 3.02
303 304 3.366396 TCTCTCTTCCGCTGGTTATCTT 58.634 45.455 0.00 0.00 0.00 2.40
304 305 3.019799 TCTCTCTTCCGCTGGTTATCT 57.980 47.619 0.00 0.00 0.00 1.98
305 306 3.802948 TTCTCTCTTCCGCTGGTTATC 57.197 47.619 0.00 0.00 0.00 1.75
306 307 4.254492 GTTTTCTCTCTTCCGCTGGTTAT 58.746 43.478 0.00 0.00 0.00 1.89
307 308 3.556423 GGTTTTCTCTCTTCCGCTGGTTA 60.556 47.826 0.00 0.00 0.00 2.85
308 309 2.495084 GTTTTCTCTCTTCCGCTGGTT 58.505 47.619 0.00 0.00 0.00 3.67
309 310 1.270893 GGTTTTCTCTCTTCCGCTGGT 60.271 52.381 0.00 0.00 0.00 4.00
310 311 1.443802 GGTTTTCTCTCTTCCGCTGG 58.556 55.000 0.00 0.00 0.00 4.85
311 312 1.443802 GGGTTTTCTCTCTTCCGCTG 58.556 55.000 0.00 0.00 0.00 5.18
312 313 0.325272 GGGGTTTTCTCTCTTCCGCT 59.675 55.000 0.00 0.00 0.00 5.52
313 314 0.036306 TGGGGTTTTCTCTCTTCCGC 59.964 55.000 0.00 0.00 0.00 5.54
314 315 2.561478 TTGGGGTTTTCTCTCTTCCG 57.439 50.000 0.00 0.00 0.00 4.30
315 316 4.470602 TCTTTTGGGGTTTTCTCTCTTCC 58.529 43.478 0.00 0.00 0.00 3.46
316 317 5.594725 ACTTCTTTTGGGGTTTTCTCTCTTC 59.405 40.000 0.00 0.00 0.00 2.87
317 318 5.360999 CACTTCTTTTGGGGTTTTCTCTCTT 59.639 40.000 0.00 0.00 0.00 2.85
318 319 4.889995 CACTTCTTTTGGGGTTTTCTCTCT 59.110 41.667 0.00 0.00 0.00 3.10
319 320 4.499865 GCACTTCTTTTGGGGTTTTCTCTC 60.500 45.833 0.00 0.00 0.00 3.20
320 321 3.384789 GCACTTCTTTTGGGGTTTTCTCT 59.615 43.478 0.00 0.00 0.00 3.10
321 322 3.384789 AGCACTTCTTTTGGGGTTTTCTC 59.615 43.478 0.00 0.00 0.00 2.87
322 323 3.374764 AGCACTTCTTTTGGGGTTTTCT 58.625 40.909 0.00 0.00 0.00 2.52
323 324 3.717707 GAGCACTTCTTTTGGGGTTTTC 58.282 45.455 0.00 0.00 0.00 2.29
324 325 2.100749 CGAGCACTTCTTTTGGGGTTTT 59.899 45.455 0.00 0.00 0.00 2.43
325 326 1.681264 CGAGCACTTCTTTTGGGGTTT 59.319 47.619 0.00 0.00 0.00 3.27
326 327 1.318576 CGAGCACTTCTTTTGGGGTT 58.681 50.000 0.00 0.00 0.00 4.11
327 328 0.537371 CCGAGCACTTCTTTTGGGGT 60.537 55.000 0.00 0.00 0.00 4.95
328 329 1.244019 CCCGAGCACTTCTTTTGGGG 61.244 60.000 0.00 0.00 31.87 4.96
329 330 1.244019 CCCCGAGCACTTCTTTTGGG 61.244 60.000 0.00 0.00 33.97 4.12
330 331 0.250727 TCCCCGAGCACTTCTTTTGG 60.251 55.000 0.00 0.00 0.00 3.28
331 332 1.604604 TTCCCCGAGCACTTCTTTTG 58.395 50.000 0.00 0.00 0.00 2.44
332 333 1.954382 GTTTCCCCGAGCACTTCTTTT 59.046 47.619 0.00 0.00 0.00 2.27
333 334 1.133915 TGTTTCCCCGAGCACTTCTTT 60.134 47.619 0.00 0.00 0.00 2.52
334 335 0.472471 TGTTTCCCCGAGCACTTCTT 59.528 50.000 0.00 0.00 0.00 2.52
335 336 0.693049 ATGTTTCCCCGAGCACTTCT 59.307 50.000 0.00 0.00 0.00 2.85
336 337 1.534729 AATGTTTCCCCGAGCACTTC 58.465 50.000 0.00 0.00 0.00 3.01
337 338 2.871096 TAATGTTTCCCCGAGCACTT 57.129 45.000 0.00 0.00 0.00 3.16
338 339 3.454812 AGTATAATGTTTCCCCGAGCACT 59.545 43.478 0.00 0.00 0.00 4.40
339 340 3.805207 AGTATAATGTTTCCCCGAGCAC 58.195 45.455 0.00 0.00 0.00 4.40
340 341 3.452990 TGAGTATAATGTTTCCCCGAGCA 59.547 43.478 0.00 0.00 0.00 4.26
341 342 4.067972 TGAGTATAATGTTTCCCCGAGC 57.932 45.455 0.00 0.00 0.00 5.03
342 343 5.424757 TGTTGAGTATAATGTTTCCCCGAG 58.575 41.667 0.00 0.00 0.00 4.63
343 344 5.423704 TGTTGAGTATAATGTTTCCCCGA 57.576 39.130 0.00 0.00 0.00 5.14
344 345 6.693315 ATTGTTGAGTATAATGTTTCCCCG 57.307 37.500 0.00 0.00 0.00 5.73
345 346 8.837389 GTCTATTGTTGAGTATAATGTTTCCCC 58.163 37.037 0.00 0.00 0.00 4.81
346 347 9.391006 TGTCTATTGTTGAGTATAATGTTTCCC 57.609 33.333 0.00 0.00 0.00 3.97
349 350 9.959721 AGGTGTCTATTGTTGAGTATAATGTTT 57.040 29.630 0.00 0.00 0.00 2.83
356 357 9.122779 GACTACTAGGTGTCTATTGTTGAGTAT 57.877 37.037 9.29 0.00 0.00 2.12
357 358 7.555554 GGACTACTAGGTGTCTATTGTTGAGTA 59.444 40.741 14.24 0.00 34.01 2.59
358 359 6.377712 GGACTACTAGGTGTCTATTGTTGAGT 59.622 42.308 14.24 0.00 34.01 3.41
359 360 6.377429 TGGACTACTAGGTGTCTATTGTTGAG 59.623 42.308 14.24 0.00 34.01 3.02
360 361 6.250711 TGGACTACTAGGTGTCTATTGTTGA 58.749 40.000 14.24 0.00 34.01 3.18
361 362 6.525578 TGGACTACTAGGTGTCTATTGTTG 57.474 41.667 14.24 0.00 34.01 3.33
362 363 6.895756 TCATGGACTACTAGGTGTCTATTGTT 59.104 38.462 14.24 0.00 33.21 2.83
363 364 6.432581 TCATGGACTACTAGGTGTCTATTGT 58.567 40.000 14.24 0.00 33.21 2.71
364 365 6.961360 TCATGGACTACTAGGTGTCTATTG 57.039 41.667 14.24 10.50 33.21 1.90
365 366 7.973048 TTTCATGGACTACTAGGTGTCTATT 57.027 36.000 14.24 1.58 33.21 1.73
377 378 7.169982 CCGAGATGAGTATTTTTCATGGACTAC 59.830 40.741 0.00 0.00 35.50 2.73
396 397 2.887568 GTCTGCGGCACCGAGATG 60.888 66.667 14.43 0.00 42.83 2.90
441 442 1.605710 GGAGAATGCATGGACGGAATG 59.394 52.381 0.00 0.00 0.00 2.67
457 458 6.818644 GTCAACATGCTAGTCAATTAAGGAGA 59.181 38.462 0.00 0.00 0.00 3.71
516 522 0.607620 AACACCGCATGGGGAAATTG 59.392 50.000 33.50 22.71 43.62 2.32
571 577 3.649023 TCTTTGTTGTCCTACCTGGCTAA 59.351 43.478 0.00 0.00 35.26 3.09
624 630 2.036604 GAGCTAGAAGGGGTGTCTATGC 59.963 54.545 0.00 0.00 0.00 3.14
675 683 6.487689 AAGAATAAAGAAAGAGCTGGAACG 57.512 37.500 0.00 0.00 0.00 3.95
676 684 7.040409 TGGAAAGAATAAAGAAAGAGCTGGAAC 60.040 37.037 0.00 0.00 0.00 3.62
714 722 5.828328 GGTTTTGTGGCTAGCTAGGAATATT 59.172 40.000 22.10 0.00 0.00 1.28
717 725 3.267031 AGGTTTTGTGGCTAGCTAGGAAT 59.733 43.478 22.10 0.00 0.00 3.01
718 726 2.642807 AGGTTTTGTGGCTAGCTAGGAA 59.357 45.455 22.10 3.29 0.00 3.36
867 879 4.005650 CCTTCTGTGTACTTGATGTGCAT 58.994 43.478 0.00 0.00 42.86 3.96
869 881 3.403038 ACCTTCTGTGTACTTGATGTGC 58.597 45.455 0.00 0.00 0.00 4.57
985 997 4.016444 AGATCCATATGTTTTGCCGTTGT 58.984 39.130 1.24 0.00 0.00 3.32
1035 1047 3.839642 GAGCAGCGCCTCGATCTCC 62.840 68.421 2.29 0.00 0.00 3.71
1284 1311 1.350193 CCTGTTCGTCCATCTTGTCG 58.650 55.000 0.00 0.00 0.00 4.35
1307 1334 2.388232 CCAACGACGCAACTAGGCC 61.388 63.158 0.00 0.00 0.00 5.19
1411 1443 3.162666 TCAATTAGCCCGATCGACCTAT 58.837 45.455 18.66 0.26 0.00 2.57
1532 1570 3.711086 GAGTGATCTTGATCGCTTGCTA 58.289 45.455 22.49 0.00 41.05 3.49
1533 1571 2.548875 GAGTGATCTTGATCGCTTGCT 58.451 47.619 22.49 5.92 41.05 3.91
1568 1606 3.523157 TCCACTGGTGACCATCATAATGT 59.477 43.478 4.03 0.00 30.82 2.71
1658 1696 8.615211 TCATCTGATAACAAAAGATGTATGTGC 58.385 33.333 10.70 0.00 44.95 4.57
1672 1971 4.655649 ACCAGCCATACTCATCTGATAACA 59.344 41.667 0.00 0.00 0.00 2.41
1677 1976 5.481824 CCTATAACCAGCCATACTCATCTGA 59.518 44.000 0.00 0.00 0.00 3.27
1689 1988 4.144297 TGATTGATTGCCTATAACCAGCC 58.856 43.478 0.00 0.00 0.00 4.85
1699 1998 1.357690 CGCGCATGATTGATTGCCT 59.642 52.632 8.75 0.00 35.41 4.75
1701 2000 2.632547 CGCGCGCATGATTGATTGC 61.633 57.895 32.61 0.00 35.50 3.56
1717 2016 2.592459 CACAGGTTTAAAATTAGCGCGC 59.408 45.455 26.66 26.66 0.00 6.86
1718 2017 4.073169 TCACAGGTTTAAAATTAGCGCG 57.927 40.909 0.00 0.00 0.00 6.86
1734 2150 6.631016 TGTAGTAGCTCCTGTTTAATCACAG 58.369 40.000 0.00 0.97 43.46 3.66
1910 2326 0.719465 CGTTACTGATGTTGTCGCCC 59.281 55.000 0.00 0.00 0.00 6.13
1929 2345 3.930336 TGGGCAGATGATCGATAATGTC 58.070 45.455 0.00 0.00 0.00 3.06
2219 4076 1.563879 AGGGTTGTGTATGCATGCCTA 59.436 47.619 16.68 6.96 0.00 3.93
2221 4078 2.051334 TAGGGTTGTGTATGCATGCC 57.949 50.000 16.68 0.00 0.00 4.40
2258 4115 6.990798 TCTCAGAGATGCTCATAAATACAGG 58.009 40.000 0.00 0.00 32.06 4.00
2278 4135 1.377366 GATGTCGGCTCGGTCTCTCA 61.377 60.000 0.00 0.00 0.00 3.27
2403 4261 2.632377 CTAGACATGGCACGGATGTTT 58.368 47.619 0.00 0.00 34.10 2.83
2405 4263 0.465705 CCTAGACATGGCACGGATGT 59.534 55.000 0.00 0.00 36.73 3.06
2460 4778 8.344831 CAATATTCATCAAGAACTCGGCATAAA 58.655 33.333 0.00 0.00 39.49 1.40
2661 4984 4.696899 ATGTAGAAGACACGAATCGACA 57.303 40.909 10.55 0.27 42.17 4.35
2663 4986 6.910972 GTCAATATGTAGAAGACACGAATCGA 59.089 38.462 10.55 0.00 42.17 3.59
2761 5084 8.276325 CACAAAAGGCATAACTCGATCTATTAC 58.724 37.037 0.00 0.00 0.00 1.89
2811 5134 4.703093 ACCCAATTTATGTAGGTTGAACCG 59.297 41.667 8.98 0.00 44.90 4.44
2887 5210 3.683365 TCAAGTGACTGAGCATGCTTA 57.317 42.857 23.61 17.59 0.00 3.09
2888 5211 2.556144 TCAAGTGACTGAGCATGCTT 57.444 45.000 23.61 5.73 0.00 3.91
2889 5212 2.556144 TTCAAGTGACTGAGCATGCT 57.444 45.000 22.92 22.92 0.00 3.79
2890 5213 3.631145 TTTTCAAGTGACTGAGCATGC 57.369 42.857 10.51 10.51 0.00 4.06
2891 5214 3.918591 GCATTTTCAAGTGACTGAGCATG 59.081 43.478 0.00 0.00 0.00 4.06
2892 5215 3.570975 TGCATTTTCAAGTGACTGAGCAT 59.429 39.130 0.00 0.00 0.00 3.79
2893 5216 2.950975 TGCATTTTCAAGTGACTGAGCA 59.049 40.909 0.00 0.00 0.00 4.26
2894 5217 3.631145 TGCATTTTCAAGTGACTGAGC 57.369 42.857 0.00 0.00 0.00 4.26
2895 5218 5.428496 TCTTGCATTTTCAAGTGACTGAG 57.572 39.130 0.00 0.00 42.90 3.35
2932 5255 2.040278 CCTGTCTTTCCCATGGAGTTGA 59.960 50.000 15.22 0.00 31.21 3.18
2936 5259 1.289160 TCCCTGTCTTTCCCATGGAG 58.711 55.000 15.22 2.37 31.21 3.86
2976 5299 9.669353 CTTTCCCATTTGAGTATTATTCATTCG 57.331 33.333 0.00 0.00 0.00 3.34
3048 5371 5.179742 GCATGAACTTTGATGCAAAAATGGA 59.820 36.000 8.33 0.00 45.34 3.41


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

AutoCloner maintained by Alex Coulton.