Multiple sequence alignment - TraesCS2B01G362900

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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 TraesCS2B01G362900 chr2B 100.000 3887 0 0 1 3887 517377543 517381429 0.000000e+00 7179.0
1 TraesCS2B01G362900 chr2D 90.527 3969 217 70 1 3885 439436053 439439946 0.000000e+00 5099.0
2 TraesCS2B01G362900 chr2A 91.413 3785 170 61 1 3693 549684717 549680996 0.000000e+00 5046.0
3 TraesCS2B01G362900 chr4D 100.000 76 0 0 1190 1265 482965416 482965491 1.460000e-29 141.0
4 TraesCS2B01G362900 chr1D 92.308 65 5 0 3793 3857 243969150 243969214 4.140000e-15 93.5
5 TraesCS2B01G362900 chrUn 93.443 61 4 0 3797 3857 385510914 385510854 1.490000e-14 91.6
6 TraesCS2B01G362900 chrUn 92.188 64 5 0 3794 3857 388893762 388893825 1.490000e-14 91.6
7 TraesCS2B01G362900 chr7A 92.188 64 5 0 3794 3857 537847050 537847113 1.490000e-14 91.6
8 TraesCS2B01G362900 chr6B 93.443 61 4 0 3797 3857 18741618 18741558 1.490000e-14 91.6
9 TraesCS2B01G362900 chr6B 93.443 61 4 0 3797 3857 406602082 406602022 1.490000e-14 91.6
10 TraesCS2B01G362900 chr1B 92.188 64 5 0 3794 3857 633713631 633713694 1.490000e-14 91.6
11 TraesCS2B01G362900 chr1A 92.188 64 5 0 3794 3857 554478903 554478966 1.490000e-14 91.6


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 TraesCS2B01G362900 chr2B 517377543 517381429 3886 False 7179 7179 100.000 1 3887 1 chr2B.!!$F1 3886
1 TraesCS2B01G362900 chr2D 439436053 439439946 3893 False 5099 5099 90.527 1 3885 1 chr2D.!!$F1 3884
2 TraesCS2B01G362900 chr2A 549680996 549684717 3721 True 5046 5046 91.413 1 3693 1 chr2A.!!$R1 3692

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
76 77 0.321564 TGACATAGCACCAGCACCAC 60.322 55.0 0.00 0.0 45.49 4.16 F
78 79 0.329261 ACATAGCACCAGCACCACAT 59.671 50.0 0.00 0.0 45.49 3.21 F
513 534 0.366871 GCGATACTCACACAAGTGCG 59.633 55.0 0.00 0.0 45.49 5.34 F
598 622 0.527600 TCGGCGCAACATGCTAGTAG 60.528 55.0 10.83 0.0 42.25 2.57 F
2367 2435 0.240145 CCGTCGAGCAGTACACAAGA 59.760 55.0 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1417 1479 0.886563 ACCTGAAACTAGACCGGACG 59.113 55.000 9.46 0.0 0.00 4.79 R
1782 1849 3.462982 ACGCATGACAGAGTTTGTGTTA 58.537 40.909 0.00 0.0 41.05 2.41 R
2367 2435 0.321671 CCACTGACCGTCCTGTGATT 59.678 55.000 17.95 0.0 37.96 2.57 R
2472 2540 1.264749 TGACTTCCAGGATCCCACCG 61.265 60.000 8.55 0.0 34.73 4.94 R
3182 3251 0.034896 AACCATTGACGACTTCCGCT 59.965 50.000 0.00 0.0 43.32 5.52 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
17 18 4.065110 GTGTGCTTGTGGGACCTC 57.935 61.111 0.00 0.00 35.29 3.85
20 21 1.053835 TGTGCTTGTGGGACCTCAGA 61.054 55.000 0.00 0.00 35.29 3.27
23 24 1.003580 TGCTTGTGGGACCTCAGATTC 59.996 52.381 0.00 0.00 0.00 2.52
74 75 2.772739 CTGACATAGCACCAGCACC 58.227 57.895 0.00 0.00 45.49 5.01
76 77 0.321564 TGACATAGCACCAGCACCAC 60.322 55.000 0.00 0.00 45.49 4.16
77 78 0.321564 GACATAGCACCAGCACCACA 60.322 55.000 0.00 0.00 45.49 4.17
78 79 0.329261 ACATAGCACCAGCACCACAT 59.671 50.000 0.00 0.00 45.49 3.21
79 80 1.559219 ACATAGCACCAGCACCACATA 59.441 47.619 0.00 0.00 45.49 2.29
80 81 1.942657 CATAGCACCAGCACCACATAC 59.057 52.381 0.00 0.00 45.49 2.39
81 82 0.980423 TAGCACCAGCACCACATACA 59.020 50.000 0.00 0.00 45.49 2.29
82 83 0.606401 AGCACCAGCACCACATACAC 60.606 55.000 0.00 0.00 45.49 2.90
98 108 8.637986 ACCACATACACAATTAACTGAATTTGT 58.362 29.630 0.00 0.00 35.45 2.83
125 135 9.979270 GTACATGTATGATAATCTAAATGCAGC 57.021 33.333 9.18 0.00 0.00 5.25
126 136 8.625786 ACATGTATGATAATCTAAATGCAGCA 57.374 30.769 0.00 0.00 0.00 4.41
127 137 8.727910 ACATGTATGATAATCTAAATGCAGCAG 58.272 33.333 0.00 0.00 0.00 4.24
129 139 9.948964 ATGTATGATAATCTAAATGCAGCAGTA 57.051 29.630 0.00 0.00 0.00 2.74
130 140 9.428097 TGTATGATAATCTAAATGCAGCAGTAG 57.572 33.333 0.00 5.41 0.00 2.57
183 200 6.387465 AGCACTTCTTCATGTGATCAAATTG 58.613 36.000 0.00 0.00 36.38 2.32
186 203 6.527023 CACTTCTTCATGTGATCAAATTGAGC 59.473 38.462 4.04 4.04 36.38 4.26
234 251 1.026718 CAAGAACACCCTCATCCGGC 61.027 60.000 0.00 0.00 0.00 6.13
258 275 7.265673 GCATATAAACAGTACCTGAGAGTCAA 58.734 38.462 0.00 0.00 35.18 3.18
264 281 4.021016 ACAGTACCTGAGAGTCAATGAACC 60.021 45.833 0.00 0.00 35.18 3.62
274 291 6.174720 AGAGTCAATGAACCAACTGTAGAA 57.825 37.500 0.00 0.00 0.00 2.10
275 292 6.773638 AGAGTCAATGAACCAACTGTAGAAT 58.226 36.000 0.00 0.00 0.00 2.40
276 293 6.876257 AGAGTCAATGAACCAACTGTAGAATC 59.124 38.462 0.00 0.00 0.00 2.52
279 296 7.721399 AGTCAATGAACCAACTGTAGAATCTTT 59.279 33.333 0.00 0.00 0.00 2.52
280 297 8.017946 GTCAATGAACCAACTGTAGAATCTTTC 58.982 37.037 0.00 0.00 0.00 2.62
281 298 7.719193 TCAATGAACCAACTGTAGAATCTTTCA 59.281 33.333 0.00 0.00 0.00 2.69
287 304 7.054124 ACCAACTGTAGAATCTTTCAGTTTCA 58.946 34.615 21.52 0.00 45.01 2.69
288 305 7.227512 ACCAACTGTAGAATCTTTCAGTTTCAG 59.772 37.037 21.52 17.25 45.01 3.02
289 306 7.308229 CCAACTGTAGAATCTTTCAGTTTCAGG 60.308 40.741 21.52 17.77 45.01 3.86
292 309 8.091449 ACTGTAGAATCTTTCAGTTTCAGGTAG 58.909 37.037 12.50 0.00 37.81 3.18
293 310 7.963532 TGTAGAATCTTTCAGTTTCAGGTAGT 58.036 34.615 0.00 0.00 0.00 2.73
294 311 9.085645 TGTAGAATCTTTCAGTTTCAGGTAGTA 57.914 33.333 0.00 0.00 0.00 1.82
295 312 9.924650 GTAGAATCTTTCAGTTTCAGGTAGTAA 57.075 33.333 0.00 0.00 0.00 2.24
296 313 8.834749 AGAATCTTTCAGTTTCAGGTAGTAAC 57.165 34.615 0.00 0.00 0.00 2.50
297 314 8.652290 AGAATCTTTCAGTTTCAGGTAGTAACT 58.348 33.333 0.00 0.00 38.23 2.24
298 315 8.834749 AATCTTTCAGTTTCAGGTAGTAACTC 57.165 34.615 0.00 0.00 35.91 3.01
299 316 7.356089 TCTTTCAGTTTCAGGTAGTAACTCA 57.644 36.000 0.00 0.00 35.91 3.41
300 317 7.963532 TCTTTCAGTTTCAGGTAGTAACTCAT 58.036 34.615 0.00 0.00 35.91 2.90
301 318 9.085645 TCTTTCAGTTTCAGGTAGTAACTCATA 57.914 33.333 0.00 0.00 35.91 2.15
302 319 9.877178 CTTTCAGTTTCAGGTAGTAACTCATAT 57.123 33.333 0.00 0.00 35.91 1.78
366 383 9.918630 CTTAACTTCTTCAACATCATGGAATTT 57.081 29.630 0.00 0.00 0.00 1.82
375 392 6.321945 TCAACATCATGGAATTTATGGTCAGG 59.678 38.462 0.00 0.00 0.00 3.86
376 393 5.142639 ACATCATGGAATTTATGGTCAGGG 58.857 41.667 0.00 0.00 0.00 4.45
381 398 6.332635 TCATGGAATTTATGGTCAGGGATACT 59.667 38.462 0.00 0.00 0.00 2.12
392 409 8.980481 ATGGTCAGGGATACTAAAATAACTTG 57.020 34.615 0.00 0.00 0.00 3.16
393 410 7.924541 TGGTCAGGGATACTAAAATAACTTGT 58.075 34.615 0.00 0.00 0.00 3.16
394 411 9.049050 TGGTCAGGGATACTAAAATAACTTGTA 57.951 33.333 0.00 0.00 0.00 2.41
395 412 9.322773 GGTCAGGGATACTAAAATAACTTGTAC 57.677 37.037 0.00 0.00 0.00 2.90
439 457 2.687370 TCACATGGTGAGTTCATGACG 58.313 47.619 10.52 2.57 43.25 4.35
442 460 2.037121 ACATGGTGAGTTCATGACGACA 59.963 45.455 10.52 0.00 43.25 4.35
446 464 3.311322 TGGTGAGTTCATGACGACAAAAC 59.689 43.478 0.00 7.92 0.00 2.43
473 494 1.852942 TCTTGTCACGAGCTCAACAC 58.147 50.000 15.40 6.75 0.00 3.32
477 498 1.866601 TGTCACGAGCTCAACACAATG 59.133 47.619 15.40 0.00 0.00 2.82
480 501 1.002576 CACGAGCTCAACACAATGCAA 60.003 47.619 15.40 0.00 0.00 4.08
495 516 1.207390 TGCAAACACAATCGCAAAGC 58.793 45.000 0.00 0.00 0.00 3.51
513 534 0.366871 GCGATACTCACACAAGTGCG 59.633 55.000 0.00 0.00 45.49 5.34
542 565 4.362279 ACTCTCTACTAAGCTCGTACTCG 58.638 47.826 0.00 0.00 38.55 4.18
547 570 0.592754 CTAAGCTCGTACTCGGCTGC 60.593 60.000 5.18 0.00 40.98 5.25
552 575 1.073216 CTCGTACTCGGCTGCAACAG 61.073 60.000 0.50 0.00 37.69 3.16
596 620 1.153369 ATCGGCGCAACATGCTAGT 60.153 52.632 10.83 0.00 42.25 2.57
598 622 0.527600 TCGGCGCAACATGCTAGTAG 60.528 55.000 10.83 0.00 42.25 2.57
599 623 1.643832 GGCGCAACATGCTAGTAGC 59.356 57.895 15.56 15.56 42.25 3.58
615 659 1.451337 TAGCAAGCAAGCCGCACAAA 61.451 50.000 6.80 0.00 46.13 2.83
800 845 7.431960 CGAAACACAGAAAATTCATCAGAAACA 59.568 33.333 0.00 0.00 37.29 2.83
815 860 5.996644 TCAGAAACAAGTCTAAAACCCTCA 58.003 37.500 0.00 0.00 0.00 3.86
817 862 6.055588 CAGAAACAAGTCTAAAACCCTCAGA 58.944 40.000 0.00 0.00 0.00 3.27
876 921 3.235481 TTGGCGTTCTCCGGGACA 61.235 61.111 0.00 0.00 36.94 4.02
941 987 2.050350 CCGTCCCCACTCTTCGCTA 61.050 63.158 0.00 0.00 0.00 4.26
1043 1101 1.338020 GAAGGAAGGCTGGTTGTGTTG 59.662 52.381 0.00 0.00 0.00 3.33
1334 1396 2.583441 CCTCAACCCTCACGCTCCA 61.583 63.158 0.00 0.00 0.00 3.86
1374 1436 1.726248 TGAACGACGACATGAATGCTG 59.274 47.619 0.00 0.00 0.00 4.41
1417 1479 1.582610 TTTGGGAAATGCTCGCGGTC 61.583 55.000 6.13 0.00 39.86 4.79
1458 1522 7.329226 CAGGTTGTTTTTGGATATTGTAGCTTG 59.671 37.037 0.00 0.00 0.00 4.01
1537 1603 3.173151 TGGAATCTGAGTACAAGGCTCA 58.827 45.455 0.00 0.00 40.28 4.26
1604 1670 4.081406 TGCAGGCTGTCATTTTCAGTTAT 58.919 39.130 17.16 0.00 35.60 1.89
1626 1693 4.734917 TCTAGAGTTTGCTTCGTTCTAGC 58.265 43.478 0.00 0.00 38.03 3.42
1631 1698 3.605013 TGCTTCGTTCTAGCAGCAA 57.395 47.368 0.00 0.00 43.30 3.91
1693 1760 2.125350 GTCTGCTTCCTGGAGCCG 60.125 66.667 13.24 8.68 42.01 5.52
1801 1868 4.083110 AGCATAACACAAACTCTGTCATGC 60.083 41.667 0.00 0.00 41.17 4.06
1835 1902 6.151648 CACAGTCATTCATAGGTTCACCATTT 59.848 38.462 0.00 0.00 38.89 2.32
1839 1906 6.311200 GTCATTCATAGGTTCACCATTTTTGC 59.689 38.462 0.00 0.00 38.89 3.68
1865 1932 4.006319 GCACTTCCTCTGTATGCTTTCTT 58.994 43.478 0.00 0.00 33.44 2.52
2088 2156 1.671979 TCTACACTACCCGGTCATCG 58.328 55.000 0.00 0.00 38.88 3.84
2091 2159 3.152400 ACTACCCGGTCATCGCCC 61.152 66.667 0.00 0.00 37.59 6.13
2106 2174 2.631580 GCCCCTATCTCTCTCGCCG 61.632 68.421 0.00 0.00 0.00 6.46
2274 2342 3.070748 GCTTTGGAGTGAGAAGGTCTTC 58.929 50.000 2.69 2.69 39.78 2.87
2364 2432 2.257371 GCCGTCGAGCAGTACACA 59.743 61.111 0.00 0.00 0.00 3.72
2367 2435 0.240145 CCGTCGAGCAGTACACAAGA 59.760 55.000 0.00 0.00 0.00 3.02
2400 2468 0.895559 CAGTGGGTTCCCTTGGCTTC 60.896 60.000 9.43 0.00 0.00 3.86
2460 2528 2.030562 CCTGACGGCGTTCTTGGT 59.969 61.111 16.19 0.00 0.00 3.67
2472 2540 0.179040 TTCTTGGTTGTGACCCCGAC 60.179 55.000 0.00 0.00 45.92 4.79
2499 2567 1.059584 TCCTGGAAGTCAAGTGCCCA 61.060 55.000 0.00 0.00 0.00 5.36
2610 2678 2.701780 CCGAGACTGGGTCGACCTG 61.702 68.421 32.52 25.90 39.92 4.00
2688 2756 4.079090 GAGCTCATCCACGACGTG 57.921 61.111 21.02 21.02 0.00 4.49
2712 2780 1.002134 CGAGTTCTGGTGGGGCAAT 60.002 57.895 0.00 0.00 0.00 3.56
2725 2793 4.342427 GCAATGTGATGCCCTCCA 57.658 55.556 0.00 0.00 40.49 3.86
2766 2834 2.110006 GAGGCCGAGGCAAGATCC 59.890 66.667 16.65 0.00 44.11 3.36
2865 2933 3.589735 TGTTATGTAGGGATGTTGGTGGT 59.410 43.478 0.00 0.00 0.00 4.16
2885 2953 6.409234 GGTGGTCATGTAGAATTCTTCCCATA 60.409 42.308 14.36 0.00 0.00 2.74
2971 3039 6.507958 TTACTTCCAAATGATTGCATTCGA 57.492 33.333 4.27 0.00 43.71 3.71
2988 3056 5.331756 GCATTCGATGTCACTTGTTTTTGTG 60.332 40.000 0.00 0.00 35.68 3.33
3034 3102 0.034059 GGTGATGTGCCCTAGGATCG 59.966 60.000 11.48 0.00 0.00 3.69
3061 3129 9.567776 TTCCACATGTTCTTCAGATTTACTTAA 57.432 29.630 0.00 0.00 0.00 1.85
3090 3158 6.613755 GTGAAACTAGAAAACAGGTAGCAA 57.386 37.500 0.00 0.00 0.00 3.91
3119 3188 1.893137 GTGGGGGTCATCCAAAGAAAC 59.107 52.381 0.00 0.00 35.86 2.78
3120 3189 1.501170 TGGGGGTCATCCAAAGAAACA 59.499 47.619 0.00 0.00 37.22 2.83
3161 3230 7.361542 GCTTCTTACATATGGAATGTAGCCATG 60.362 40.741 7.80 0.00 45.39 3.66
3179 3248 3.937706 CCATGACGCATCTTTTTCTCTCT 59.062 43.478 0.00 0.00 0.00 3.10
3180 3249 4.033817 CCATGACGCATCTTTTTCTCTCTC 59.966 45.833 0.00 0.00 0.00 3.20
3181 3250 4.527509 TGACGCATCTTTTTCTCTCTCT 57.472 40.909 0.00 0.00 0.00 3.10
3182 3251 5.644977 TGACGCATCTTTTTCTCTCTCTA 57.355 39.130 0.00 0.00 0.00 2.43
3183 3252 5.645624 TGACGCATCTTTTTCTCTCTCTAG 58.354 41.667 0.00 0.00 0.00 2.43
3184 3253 4.429108 ACGCATCTTTTTCTCTCTCTAGC 58.571 43.478 0.00 0.00 0.00 3.42
3185 3254 3.485378 CGCATCTTTTTCTCTCTCTAGCG 59.515 47.826 0.00 0.00 0.00 4.26
3186 3255 3.801594 GCATCTTTTTCTCTCTCTAGCGG 59.198 47.826 0.00 0.00 0.00 5.52
3187 3256 4.440802 GCATCTTTTTCTCTCTCTAGCGGA 60.441 45.833 0.00 0.00 0.00 5.54
3188 3257 5.655488 CATCTTTTTCTCTCTCTAGCGGAA 58.345 41.667 0.00 0.00 0.00 4.30
3189 3258 5.317733 TCTTTTTCTCTCTCTAGCGGAAG 57.682 43.478 0.00 0.00 0.00 3.46
3190 3259 4.767928 TCTTTTTCTCTCTCTAGCGGAAGT 59.232 41.667 0.00 0.00 0.00 3.01
3191 3260 4.705337 TTTTCTCTCTCTAGCGGAAGTC 57.295 45.455 0.00 0.00 0.00 3.01
3194 3263 1.595794 CTCTCTCTAGCGGAAGTCGTC 59.404 57.143 0.00 0.00 41.72 4.20
3202 3271 0.442699 GCGGAAGTCGTCAATGGTTC 59.557 55.000 0.00 0.00 41.72 3.62
3208 3277 4.421948 GAAGTCGTCAATGGTTCGATAGT 58.578 43.478 0.00 0.00 36.08 2.12
3248 3317 2.352388 GTGCGGTAACTGGCAATCTTA 58.648 47.619 0.00 0.00 41.46 2.10
3249 3318 2.351726 GTGCGGTAACTGGCAATCTTAG 59.648 50.000 0.00 0.00 41.46 2.18
3250 3319 2.235155 TGCGGTAACTGGCAATCTTAGA 59.765 45.455 0.00 0.00 35.98 2.10
3251 3320 3.118408 TGCGGTAACTGGCAATCTTAGAT 60.118 43.478 0.00 0.00 35.98 1.98
3252 3321 3.877508 GCGGTAACTGGCAATCTTAGATT 59.122 43.478 0.99 0.99 0.00 2.40
3253 3322 4.260784 GCGGTAACTGGCAATCTTAGATTG 60.261 45.833 25.65 25.65 0.00 2.67
3322 3419 3.806949 TTTCTGGCCAAAGTGGTCTAT 57.193 42.857 7.01 0.00 44.07 1.98
3368 3465 3.010138 TGAAACAAGGGGTTAGAGGGATG 59.990 47.826 0.00 0.00 39.29 3.51
3426 3523 2.167487 GGTGAACTCTGCTTCCCTAGAG 59.833 54.545 0.00 0.00 44.63 2.43
3436 3533 0.624500 TTCCCTAGAGGCATGGGCTT 60.625 55.000 0.00 0.00 38.98 4.35
3450 3547 1.039785 GGGCTTCCTTGCTTGATCCC 61.040 60.000 0.00 0.00 0.00 3.85
3507 3604 2.590291 TCGCACGCAAGGCAAGAA 60.590 55.556 0.00 0.00 46.39 2.52
3567 3664 1.605710 CATGGATTCTTGCCGGATGAC 59.394 52.381 5.05 0.00 0.00 3.06
3693 3792 1.519455 GGAGTCGACATGCTTCCCG 60.519 63.158 19.50 0.00 0.00 5.14
3731 3830 3.366679 CCTCACATTTGTTGCATGACCTC 60.367 47.826 0.00 0.00 0.00 3.85
3737 3836 1.511850 TGTTGCATGACCTCTTCACG 58.488 50.000 0.00 0.00 36.92 4.35
3738 3837 0.798776 GTTGCATGACCTCTTCACGG 59.201 55.000 0.00 0.00 36.92 4.94
3763 3863 5.049129 GCTACGTAACCCATATACTCTCGTT 60.049 44.000 0.00 0.00 0.00 3.85
3765 3865 4.037208 ACGTAACCCATATACTCTCGTTGG 59.963 45.833 0.00 0.00 0.00 3.77
3776 3876 4.592485 ACTCTCGTTGGGTATCATGATC 57.408 45.455 12.53 4.10 0.00 2.92
3778 3878 2.061773 CTCGTTGGGTATCATGATCGC 58.938 52.381 12.53 12.37 0.00 4.58
3783 3883 1.016130 GGGTATCATGATCGCCTGCG 61.016 60.000 12.53 4.92 41.35 5.18
3784 3884 1.630244 GGTATCATGATCGCCTGCGC 61.630 60.000 12.53 0.00 39.59 6.09
3786 3886 0.668401 TATCATGATCGCCTGCGCAG 60.668 55.000 30.52 30.52 39.59 5.18
3803 3903 2.494059 GCAGCGCTTAGATTATTGGGA 58.506 47.619 7.50 0.00 0.00 4.37
3835 3935 0.665298 GGGCGAGCTTTGGATGAATC 59.335 55.000 0.00 0.00 0.00 2.52
3847 3947 8.316946 AGCTTTGGATGAATCGATCTATTATCA 58.683 33.333 0.00 0.00 0.00 2.15
3864 3964 2.205022 TCAGGCAATCTTGACAAGGG 57.795 50.000 15.13 6.70 39.18 3.95
3866 3966 0.407139 AGGCAATCTTGACAAGGGCT 59.593 50.000 15.13 13.12 39.18 5.19
3880 3980 2.186125 GGCTTCCCCGAAGTACCG 59.814 66.667 3.52 0.00 41.27 4.02
3884 3984 1.608801 GCTTCCCCGAAGTACCGAAAA 60.609 52.381 3.52 0.00 41.27 2.29
3885 3985 2.769893 CTTCCCCGAAGTACCGAAAAA 58.230 47.619 0.00 0.00 35.21 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 9.255304 GACCTAGCTATAAGAACTTTGAATCTG 57.745 37.037 0.00 0.00 0.00 2.90
20 21 9.959721 TTTGACCTAGCTATAAGAACTTTGAAT 57.040 29.630 0.00 0.00 0.00 2.57
59 60 0.329261 ATGTGGTGCTGGTGCTATGT 59.671 50.000 0.00 0.00 40.48 2.29
63 64 0.606401 GTGTATGTGGTGCTGGTGCT 60.606 55.000 0.00 0.00 40.48 4.40
64 65 0.888736 TGTGTATGTGGTGCTGGTGC 60.889 55.000 0.00 0.00 40.20 5.01
66 67 2.584835 ATTGTGTATGTGGTGCTGGT 57.415 45.000 0.00 0.00 0.00 4.00
67 68 4.458989 AGTTAATTGTGTATGTGGTGCTGG 59.541 41.667 0.00 0.00 0.00 4.85
68 69 5.181056 TCAGTTAATTGTGTATGTGGTGCTG 59.819 40.000 0.00 0.00 0.00 4.41
69 70 5.312895 TCAGTTAATTGTGTATGTGGTGCT 58.687 37.500 0.00 0.00 0.00 4.40
70 71 5.621197 TCAGTTAATTGTGTATGTGGTGC 57.379 39.130 0.00 0.00 0.00 5.01
71 72 8.914654 CAAATTCAGTTAATTGTGTATGTGGTG 58.085 33.333 0.00 0.00 37.85 4.17
72 73 8.637986 ACAAATTCAGTTAATTGTGTATGTGGT 58.362 29.630 0.00 0.00 37.85 4.16
73 74 8.914654 CACAAATTCAGTTAATTGTGTATGTGG 58.085 33.333 15.06 4.77 37.50 4.17
74 75 9.462174 ACACAAATTCAGTTAATTGTGTATGTG 57.538 29.630 18.34 17.82 42.03 3.21
79 80 9.462174 CATGTACACAAATTCAGTTAATTGTGT 57.538 29.630 21.95 21.95 43.80 3.72
80 81 9.462174 ACATGTACACAAATTCAGTTAATTGTG 57.538 29.630 14.03 14.03 37.85 3.33
111 121 5.630415 ACCCTACTGCTGCATTTAGATTA 57.370 39.130 16.15 0.00 0.00 1.75
125 135 7.803279 AAAAAGTACTTGAAGAACCCTACTG 57.197 36.000 9.34 0.00 0.00 2.74
150 167 6.071165 TCACATGAAGAAGTGCTATCTCAGAA 60.071 38.462 0.00 0.00 35.76 3.02
151 168 5.420104 TCACATGAAGAAGTGCTATCTCAGA 59.580 40.000 0.00 0.00 35.76 3.27
156 173 6.915544 TTGATCACATGAAGAAGTGCTATC 57.084 37.500 0.00 0.00 35.76 2.08
258 275 7.227156 ACTGAAAGATTCTACAGTTGGTTCAT 58.773 34.615 15.87 0.00 40.03 2.57
274 291 7.963532 TGAGTTACTACCTGAAACTGAAAGAT 58.036 34.615 0.00 0.00 37.43 2.40
275 292 7.356089 TGAGTTACTACCTGAAACTGAAAGA 57.644 36.000 0.00 0.00 37.43 2.52
276 293 9.877178 ATATGAGTTACTACCTGAAACTGAAAG 57.123 33.333 0.00 0.00 42.29 2.62
287 304 9.819267 GCACTAGAAAAATATGAGTTACTACCT 57.181 33.333 0.00 0.00 0.00 3.08
288 305 9.595823 TGCACTAGAAAAATATGAGTTACTACC 57.404 33.333 0.00 0.00 0.00 3.18
297 314 9.494271 GGTCTGATATGCACTAGAAAAATATGA 57.506 33.333 0.00 0.00 0.00 2.15
298 315 8.438513 CGGTCTGATATGCACTAGAAAAATATG 58.561 37.037 0.00 0.00 0.00 1.78
299 316 7.118390 GCGGTCTGATATGCACTAGAAAAATAT 59.882 37.037 0.00 0.00 0.00 1.28
300 317 6.423905 GCGGTCTGATATGCACTAGAAAAATA 59.576 38.462 0.00 0.00 0.00 1.40
301 318 5.237344 GCGGTCTGATATGCACTAGAAAAAT 59.763 40.000 0.00 0.00 0.00 1.82
302 319 4.570772 GCGGTCTGATATGCACTAGAAAAA 59.429 41.667 0.00 0.00 0.00 1.94
392 409 6.684555 CGAATTTGCATGCTTTCTCTAAGTAC 59.315 38.462 20.33 0.00 36.19 2.73
393 410 6.675486 GCGAATTTGCATGCTTTCTCTAAGTA 60.675 38.462 20.33 0.00 33.86 2.24
394 411 5.634896 CGAATTTGCATGCTTTCTCTAAGT 58.365 37.500 20.33 0.00 36.19 2.24
395 412 4.498323 GCGAATTTGCATGCTTTCTCTAAG 59.502 41.667 20.33 7.44 34.21 2.18
396 413 4.156556 AGCGAATTTGCATGCTTTCTCTAA 59.843 37.500 20.33 0.00 37.31 2.10
397 414 3.691118 AGCGAATTTGCATGCTTTCTCTA 59.309 39.130 20.33 0.00 37.31 2.43
432 450 5.989168 AGATGTTACAGTTTTGTCGTCATGA 59.011 36.000 0.00 0.00 38.76 3.07
433 451 6.228273 AGATGTTACAGTTTTGTCGTCATG 57.772 37.500 0.00 0.00 38.76 3.07
434 452 6.260050 ACAAGATGTTACAGTTTTGTCGTCAT 59.740 34.615 6.23 0.00 38.76 3.06
439 457 5.901884 CGTGACAAGATGTTACAGTTTTGTC 59.098 40.000 21.54 21.54 42.72 3.18
442 460 5.277345 GCTCGTGACAAGATGTTACAGTTTT 60.277 40.000 6.28 0.00 36.77 2.43
446 464 3.579709 AGCTCGTGACAAGATGTTACAG 58.420 45.455 6.28 4.26 36.77 2.74
473 494 3.790058 CTTTGCGATTGTGTTTGCATTG 58.210 40.909 0.00 0.00 37.17 2.82
495 516 0.992072 CCGCACTTGTGTGAGTATCG 59.008 55.000 14.93 2.48 46.55 2.92
496 517 1.993370 GTCCGCACTTGTGTGAGTATC 59.007 52.381 14.93 0.00 46.55 2.24
500 521 0.603707 ATGGTCCGCACTTGTGTGAG 60.604 55.000 14.93 6.25 46.55 3.51
513 534 4.453136 CGAGCTTAGTAGAGAGTATGGTCC 59.547 50.000 0.00 0.00 33.03 4.46
596 620 1.451337 TTTGTGCGGCTTGCTTGCTA 61.451 50.000 0.00 0.00 46.63 3.49
598 622 2.279385 TTTGTGCGGCTTGCTTGC 60.279 55.556 0.00 4.07 46.63 4.01
599 623 0.038892 ATCTTTGTGCGGCTTGCTTG 60.039 50.000 0.00 0.00 46.63 4.01
600 624 0.242017 GATCTTTGTGCGGCTTGCTT 59.758 50.000 0.00 0.00 46.63 3.91
602 626 0.455633 CTGATCTTTGTGCGGCTTGC 60.456 55.000 0.00 0.00 46.70 4.01
603 627 1.135859 GTCTGATCTTTGTGCGGCTTG 60.136 52.381 0.00 0.00 0.00 4.01
604 628 1.160137 GTCTGATCTTTGTGCGGCTT 58.840 50.000 0.00 0.00 0.00 4.35
605 629 0.322975 AGTCTGATCTTTGTGCGGCT 59.677 50.000 0.00 0.00 0.00 5.52
606 630 0.445436 CAGTCTGATCTTTGTGCGGC 59.555 55.000 0.00 0.00 0.00 6.53
615 659 4.226168 CCTTACTTTTCCCCAGTCTGATCT 59.774 45.833 0.00 0.00 0.00 2.75
800 845 4.409247 ACTGTGTCTGAGGGTTTTAGACTT 59.591 41.667 0.00 0.00 41.01 3.01
815 860 1.045407 TGCGAGGGTTTACTGTGTCT 58.955 50.000 0.00 0.00 0.00 3.41
817 862 1.878953 CTTGCGAGGGTTTACTGTGT 58.121 50.000 0.00 0.00 0.00 3.72
1282 1344 1.993369 GAAACCATAGTGCAGCGGGC 61.993 60.000 0.00 0.00 45.13 6.13
1315 1377 2.266055 GAGCGTGAGGGTTGAGGG 59.734 66.667 0.00 0.00 0.00 4.30
1316 1378 2.266055 GGAGCGTGAGGGTTGAGG 59.734 66.667 0.00 0.00 0.00 3.86
1318 1380 2.741092 GTGGAGCGTGAGGGTTGA 59.259 61.111 0.00 0.00 0.00 3.18
1417 1479 0.886563 ACCTGAAACTAGACCGGACG 59.113 55.000 9.46 0.00 0.00 4.79
1425 1487 9.410556 CAATATCCAAAAACAACCTGAAACTAG 57.589 33.333 0.00 0.00 0.00 2.57
1458 1522 6.564125 CGACCAAATTAGGAACGATAATCAGC 60.564 42.308 0.00 0.00 35.44 4.26
1502 1568 5.482006 TCAGATTCCAACATGTACAGACAG 58.518 41.667 0.00 0.00 39.50 3.51
1604 1670 4.217767 TGCTAGAACGAAGCAAACTCTAGA 59.782 41.667 8.28 0.00 46.57 2.43
1631 1698 4.136796 TCTGACAAGTGCAAAGCTTATGT 58.863 39.130 0.00 0.00 0.00 2.29
1646 1713 5.888724 TGGGACAAGTAAACATTTCTGACAA 59.111 36.000 0.00 0.00 31.92 3.18
1782 1849 3.462982 ACGCATGACAGAGTTTGTGTTA 58.537 40.909 0.00 0.00 41.05 2.41
1814 1881 6.311200 GCAAAAATGGTGAACCTATGAATGAC 59.689 38.462 0.37 0.00 36.82 3.06
1815 1882 6.397272 GCAAAAATGGTGAACCTATGAATGA 58.603 36.000 0.37 0.00 36.82 2.57
1816 1883 5.289193 CGCAAAAATGGTGAACCTATGAATG 59.711 40.000 0.37 0.00 36.82 2.67
1817 1884 5.410067 CGCAAAAATGGTGAACCTATGAAT 58.590 37.500 0.37 0.00 36.82 2.57
1865 1932 7.707893 GGTTTGGATAAGTAATACGAAGTGCTA 59.292 37.037 0.00 0.00 45.73 3.49
1868 1936 6.509039 GCGGTTTGGATAAGTAATACGAAGTG 60.509 42.308 0.00 0.00 45.73 3.16
1870 1938 5.521010 TGCGGTTTGGATAAGTAATACGAAG 59.479 40.000 0.00 0.00 0.00 3.79
1872 1940 5.008619 TGCGGTTTGGATAAGTAATACGA 57.991 39.130 0.00 0.00 0.00 3.43
1877 1945 4.580868 TGTGATGCGGTTTGGATAAGTAA 58.419 39.130 0.00 0.00 0.00 2.24
2088 2156 2.631580 CGGCGAGAGAGATAGGGGC 61.632 68.421 0.00 0.00 0.00 5.80
2091 2159 1.533731 GAAGACGGCGAGAGAGATAGG 59.466 57.143 16.62 0.00 0.00 2.57
2106 2174 0.326264 ACACCATGAGGGCTGAAGAC 59.674 55.000 0.00 0.00 42.05 3.01
2274 2342 4.864916 CAACTTGATATCTGTTGGTCCG 57.135 45.455 22.76 7.59 37.85 4.79
2352 2420 3.317150 TGTGATTCTTGTGTACTGCTCG 58.683 45.455 0.00 0.00 0.00 5.03
2364 2432 1.971357 ACTGACCGTCCTGTGATTCTT 59.029 47.619 0.00 0.00 0.00 2.52
2367 2435 0.321671 CCACTGACCGTCCTGTGATT 59.678 55.000 17.95 0.00 37.96 2.57
2472 2540 1.264749 TGACTTCCAGGATCCCACCG 61.265 60.000 8.55 0.00 34.73 4.94
2610 2678 0.949105 CGTTGGGTGTCCAGCAGTAC 60.949 60.000 0.00 0.00 45.04 2.73
2694 2762 1.002134 ATTGCCCCACCAGAACTCG 60.002 57.895 0.00 0.00 0.00 4.18
2760 2828 1.142748 CTGCGGCTCGAAGGATCTT 59.857 57.895 0.00 0.00 0.00 2.40
2865 2933 7.861629 ACACTTATGGGAAGAATTCTACATGA 58.138 34.615 21.29 15.68 46.56 3.07
2885 2953 0.034896 CCACCGCCAGAACTACACTT 59.965 55.000 0.00 0.00 0.00 3.16
2940 3008 8.479689 TGCAATCATTTGGAAGTAATTCATGAT 58.520 29.630 5.15 8.06 32.47 2.45
2959 3027 3.752747 ACAAGTGACATCGAATGCAATCA 59.247 39.130 2.09 0.00 0.00 2.57
2960 3028 4.346734 ACAAGTGACATCGAATGCAATC 57.653 40.909 0.00 0.00 0.00 2.67
2971 3039 4.799564 ACCACACAAAAACAAGTGACAT 57.200 36.364 0.00 0.00 39.03 3.06
3034 3102 7.440523 AGTAAATCTGAAGAACATGTGGAAC 57.559 36.000 0.00 0.00 37.35 3.62
3061 3129 9.543783 CTACCTGTTTTCTAGTTTCACTAGTTT 57.456 33.333 10.12 0.00 46.31 2.66
3090 3158 1.496429 GATGACCCCCACCTGATTCAT 59.504 52.381 0.00 0.00 0.00 2.57
3119 3188 3.386486 AGAAGCAAATTGTGTGTGCATG 58.614 40.909 2.16 0.00 40.83 4.06
3120 3189 3.738830 AGAAGCAAATTGTGTGTGCAT 57.261 38.095 2.16 0.00 40.83 3.96
3161 3230 4.502645 GCTAGAGAGAGAAAAAGATGCGTC 59.497 45.833 0.00 0.00 0.00 5.19
3179 3248 1.134367 CCATTGACGACTTCCGCTAGA 59.866 52.381 0.00 0.00 43.32 2.43
3180 3249 1.135083 ACCATTGACGACTTCCGCTAG 60.135 52.381 0.00 0.00 43.32 3.42
3181 3250 0.892755 ACCATTGACGACTTCCGCTA 59.107 50.000 0.00 0.00 43.32 4.26
3182 3251 0.034896 AACCATTGACGACTTCCGCT 59.965 50.000 0.00 0.00 43.32 5.52
3183 3252 0.442699 GAACCATTGACGACTTCCGC 59.557 55.000 0.00 0.00 43.32 5.54
3184 3253 0.713883 CGAACCATTGACGACTTCCG 59.286 55.000 0.00 0.00 45.44 4.30
3185 3254 2.074547 TCGAACCATTGACGACTTCC 57.925 50.000 0.00 0.00 0.00 3.46
3186 3255 4.421948 ACTATCGAACCATTGACGACTTC 58.578 43.478 0.00 0.00 38.79 3.01
3187 3256 4.451629 ACTATCGAACCATTGACGACTT 57.548 40.909 0.00 0.00 38.79 3.01
3188 3257 4.451629 AACTATCGAACCATTGACGACT 57.548 40.909 0.00 0.00 38.79 4.18
3189 3258 4.501921 GGTAACTATCGAACCATTGACGAC 59.498 45.833 0.00 0.00 38.79 4.34
3190 3259 4.440525 GGGTAACTATCGAACCATTGACGA 60.441 45.833 5.63 0.00 40.18 4.20
3191 3260 3.800506 GGGTAACTATCGAACCATTGACG 59.199 47.826 5.63 0.00 34.83 4.35
3194 3263 5.018539 TCAGGGTAACTATCGAACCATTG 57.981 43.478 5.63 3.74 34.83 2.82
3202 3271 6.157211 GGTTACATCATCAGGGTAACTATCG 58.843 44.000 12.06 0.00 43.83 2.92
3208 3277 3.109151 ACGGGTTACATCATCAGGGTAA 58.891 45.455 0.00 0.00 0.00 2.85
3248 3317 3.950397 TCCATTTAAGACACGGCAATCT 58.050 40.909 0.00 0.00 0.00 2.40
3249 3318 4.695217 TTCCATTTAAGACACGGCAATC 57.305 40.909 0.00 0.00 0.00 2.67
3250 3319 4.097892 GGATTCCATTTAAGACACGGCAAT 59.902 41.667 0.00 0.00 0.00 3.56
3251 3320 3.442273 GGATTCCATTTAAGACACGGCAA 59.558 43.478 0.00 0.00 0.00 4.52
3252 3321 3.013921 GGATTCCATTTAAGACACGGCA 58.986 45.455 0.00 0.00 0.00 5.69
3253 3322 2.031683 CGGATTCCATTTAAGACACGGC 59.968 50.000 3.09 0.00 0.00 5.68
3299 3368 0.681175 ACCACTTTGGCCAGAAATGC 59.319 50.000 5.11 0.00 42.67 3.56
3341 3438 4.580580 CCTCTAACCCCTTGTTTCATATGC 59.419 45.833 0.00 0.00 38.42 3.14
3368 3465 3.983044 AATCTGGTGGTACCTTGAGTC 57.017 47.619 14.36 0.00 39.58 3.36
3436 3533 0.914644 CCAGAGGGATCAAGCAAGGA 59.085 55.000 0.00 0.00 35.59 3.36
3450 3547 2.280660 CCATAGCAGCGGCCAGAG 60.281 66.667 4.82 0.00 42.56 3.35
3507 3604 1.279840 GTCGCGTTGCTCTGCTTTT 59.720 52.632 5.77 0.00 0.00 2.27
3567 3664 3.785486 TCGAGAGTAGCAATCCACATTG 58.215 45.455 0.00 0.00 42.26 2.82
3693 3792 4.593864 GGCGAGCTCCATCGGTCC 62.594 72.222 8.47 0.00 42.94 4.46
3737 3836 4.085009 AGAGTATATGGGTTACGTAGCCC 58.915 47.826 33.88 33.88 45.98 5.19
3738 3837 4.142730 CGAGAGTATATGGGTTACGTAGCC 60.143 50.000 19.33 19.33 45.01 3.93
3763 3863 0.035317 GCAGGCGATCATGATACCCA 59.965 55.000 19.12 0.00 0.00 4.51
3765 3865 1.630244 GCGCAGGCGATCATGATACC 61.630 60.000 18.96 13.27 42.83 2.73
3766 3866 0.945743 TGCGCAGGCGATCATGATAC 60.946 55.000 18.96 3.85 44.10 2.24
3783 3883 2.481952 CTCCCAATAATCTAAGCGCTGC 59.518 50.000 12.58 0.00 0.00 5.25
3784 3884 2.481952 GCTCCCAATAATCTAAGCGCTG 59.518 50.000 12.58 0.00 0.00 5.18
3786 3886 2.481952 CTGCTCCCAATAATCTAAGCGC 59.518 50.000 0.00 0.00 32.49 5.92
3793 3893 3.696051 TGCTTGTTCTGCTCCCAATAATC 59.304 43.478 0.00 0.00 0.00 1.75
3803 3903 2.670934 CGCCCTGCTTGTTCTGCT 60.671 61.111 0.00 0.00 0.00 4.24
3835 3935 6.870439 TGTCAAGATTGCCTGATAATAGATCG 59.130 38.462 0.00 0.00 0.00 3.69
3847 3947 0.407139 AGCCCTTGTCAAGATTGCCT 59.593 50.000 14.42 0.27 0.00 4.75
3864 3964 0.037046 TTTCGGTACTTCGGGGAAGC 60.037 55.000 5.33 0.00 42.79 3.86
3866 3966 2.926778 TTTTTCGGTACTTCGGGGAA 57.073 45.000 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.