Multiple sequence alignment - TraesCS1B01G387700

Loading Multiple Alignment...

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 TraesCS1B01G387700 chr1B 100.000 4442 0 0 1 4442 621957992 621953551 0.000000e+00 8203.0
1 TraesCS1B01G387700 chr1D 92.174 2466 137 28 1 2423 451958805 451956353 0.000000e+00 3434.0
2 TraesCS1B01G387700 chr1D 92.744 1640 82 15 2418 4040 451956322 451954703 0.000000e+00 2335.0
3 TraesCS1B01G387700 chr1D 87.725 334 32 5 4028 4357 451954630 451954302 9.020000e-102 381.0
4 TraesCS1B01G387700 chr1D 89.706 68 7 0 4375 4442 451954308 451954241 2.200000e-13 87.9
5 TraesCS1B01G387700 chr1D 100.000 29 0 0 2301 2329 223162010 223162038 2.000000e-03 54.7
6 TraesCS1B01G387700 chr1D 100.000 29 0 0 2301 2329 254483923 254483895 2.000000e-03 54.7
7 TraesCS1B01G387700 chr1A 93.849 1577 72 14 782 2342 546516904 546515337 0.000000e+00 2351.0
8 TraesCS1B01G387700 chr1A 92.472 704 37 11 2377 3075 546515338 546514646 0.000000e+00 992.0
9 TraesCS1B01G387700 chr1A 94.131 443 23 2 3267 3709 546514647 546514208 0.000000e+00 671.0
10 TraesCS1B01G387700 chr1A 96.073 331 12 1 3711 4040 546514173 546513843 5.060000e-149 538.0
11 TraesCS1B01G387700 chr1A 82.779 331 25 10 4029 4357 546513772 546513472 2.630000e-67 267.0
12 TraesCS1B01G387700 chr1A 91.176 68 6 0 4375 4442 546513478 546513411 4.730000e-15 93.5
13 TraesCS1B01G387700 chr6A 84.615 117 15 3 3781 3897 556975386 556975499 3.630000e-21 113.0
14 TraesCS1B01G387700 chr6B 82.906 117 17 3 3781 3897 620180645 620180758 7.860000e-18 102.0
15 TraesCS1B01G387700 chrUn 100.000 29 0 0 2301 2329 443804162 443804190 2.000000e-03 54.7
16 TraesCS1B01G387700 chrUn 100.000 29 0 0 2301 2329 445362362 445362334 2.000000e-03 54.7
17 TraesCS1B01G387700 chr6D 100.000 29 0 0 2301 2329 336543397 336543369 2.000000e-03 54.7
18 TraesCS1B01G387700 chr6D 100.000 29 0 0 2301 2329 427829904 427829876 2.000000e-03 54.7
19 TraesCS1B01G387700 chr6D 100.000 29 0 0 2301 2329 431396952 431396980 2.000000e-03 54.7


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 TraesCS1B01G387700 chr1B 621953551 621957992 4441 True 8203.000 8203 100.000000 1 4442 1 chr1B.!!$R1 4441
1 TraesCS1B01G387700 chr1D 451954241 451958805 4564 True 1559.475 3434 90.587250 1 4442 4 chr1D.!!$R2 4441
2 TraesCS1B01G387700 chr1A 546513411 546516904 3493 True 818.750 2351 91.746667 782 4442 6 chr1A.!!$R1 3660

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
75 76 0.109597 CGGCAAGCCAATCTCACAAC 60.110 55.000 12.19 0.00 35.37 3.32 F
227 234 0.179062 CATGTACCTGCCTCCTCAGC 60.179 60.000 0.00 0.00 32.87 4.26 F
1356 1387 0.250252 TGTGATGTGGAAGCAAGCGA 60.250 50.000 0.00 0.00 0.00 4.93 F
1545 1580 0.687920 TGGAAAGCCCACACGTGATA 59.312 50.000 25.01 0.00 40.82 2.15 F
3194 3296 1.152860 TTTCCTTCAGGCGGCACAA 60.153 52.632 13.08 1.63 34.44 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1255 1283 0.526524 GACACCCTGAAGAGATCGCG 60.527 60.000 0.00 0.0 0.00 5.87 R
1418 1453 1.257743 GCACACAGTCCTCCTACAGA 58.742 55.000 0.00 0.0 0.00 3.41 R
3184 3286 2.036992 TCAATTTCATTTTGTGCCGCCT 59.963 40.909 0.00 0.0 0.00 5.52 R
3229 3331 2.094026 GGAATGCAAAGGGGCTGTTAAG 60.094 50.000 0.00 0.0 34.04 1.85 R
4361 4585 0.250553 TGCGTTTGTCACCTTAGGGG 60.251 55.000 2.32 0.0 41.89 4.79 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
57 58 5.391312 AAGAAGGGAAACAATTGGAATCG 57.609 39.130 10.83 0.00 0.00 3.34
58 59 3.763897 AGAAGGGAAACAATTGGAATCGG 59.236 43.478 10.83 0.00 0.00 4.18
75 76 0.109597 CGGCAAGCCAATCTCACAAC 60.110 55.000 12.19 0.00 35.37 3.32
82 83 1.081892 CCAATCTCACAACGAGCTGG 58.918 55.000 0.00 0.00 41.98 4.85
91 92 1.670811 ACAACGAGCTGGACAACTTTG 59.329 47.619 1.44 0.00 0.00 2.77
92 93 1.670811 CAACGAGCTGGACAACTTTGT 59.329 47.619 1.44 0.00 45.65 2.83
114 120 2.224450 CGTTATTTCCGCCCCTTCCTAT 60.224 50.000 0.00 0.00 0.00 2.57
131 137 0.643822 TATCCTTACCCCTTCCCCGT 59.356 55.000 0.00 0.00 0.00 5.28
139 145 2.365105 CCTTCCCCGTCAGCCCTA 60.365 66.667 0.00 0.00 0.00 3.53
145 151 1.418908 CCCCGTCAGCCCTATCCATT 61.419 60.000 0.00 0.00 0.00 3.16
153 160 5.506317 CGTCAGCCCTATCCATTCATTTTTC 60.506 44.000 0.00 0.00 0.00 2.29
188 195 2.597455 CCATCTCTCTCCCTCTCTTCC 58.403 57.143 0.00 0.00 0.00 3.46
197 204 3.203487 TCTCCCTCTCTTCCTCTACCTTC 59.797 52.174 0.00 0.00 0.00 3.46
199 206 2.023888 CCCTCTCTTCCTCTACCTTCCA 60.024 54.545 0.00 0.00 0.00 3.53
202 209 2.655407 TCTCTTCCTCTACCTTCCACCT 59.345 50.000 0.00 0.00 0.00 4.00
207 214 1.888436 CTCTACCTTCCACCTGCGCA 61.888 60.000 10.98 10.98 0.00 6.09
217 224 1.375908 ACCTGCGCACATGTACCTG 60.376 57.895 5.66 0.00 0.00 4.00
224 231 0.462759 GCACATGTACCTGCCTCCTC 60.463 60.000 0.00 0.00 0.00 3.71
227 234 0.179062 CATGTACCTGCCTCCTCAGC 60.179 60.000 0.00 0.00 32.87 4.26
229 236 1.990060 GTACCTGCCTCCTCAGCCA 60.990 63.158 0.00 0.00 32.87 4.75
247 254 1.662686 CACTCCTTCTCCCTCCCTTT 58.337 55.000 0.00 0.00 0.00 3.11
260 267 1.007387 CCCTTTTCGCAGCAACCAC 60.007 57.895 0.00 0.00 0.00 4.16
262 269 1.370414 CTTTTCGCAGCAACCACCG 60.370 57.895 0.00 0.00 0.00 4.94
263 270 2.058829 CTTTTCGCAGCAACCACCGT 62.059 55.000 0.00 0.00 0.00 4.83
264 271 1.658686 TTTTCGCAGCAACCACCGTT 61.659 50.000 0.00 0.00 0.00 4.44
299 307 1.092921 TTTTCTCGTGCGCAACCACT 61.093 50.000 14.00 0.00 33.60 4.00
310 318 2.203788 AACCACTGCGAGGAGGGA 60.204 61.111 0.00 0.00 0.00 4.20
312 320 1.903877 AACCACTGCGAGGAGGGATG 61.904 60.000 0.00 0.00 0.00 3.51
353 361 3.748048 TGTTGTCAATCTACTGAAGCTGC 59.252 43.478 0.00 0.00 0.00 5.25
373 381 2.113139 CACGGGGTGCTCCAAACT 59.887 61.111 7.20 0.00 37.22 2.66
377 385 0.821711 CGGGGTGCTCCAAACTGAAA 60.822 55.000 7.20 0.00 37.22 2.69
378 386 1.632589 GGGGTGCTCCAAACTGAAAT 58.367 50.000 7.20 0.00 37.22 2.17
383 391 4.441792 GGTGCTCCAAACTGAAATTGTTT 58.558 39.130 0.00 0.00 38.04 2.83
385 393 5.351458 GTGCTCCAAACTGAAATTGTTTCT 58.649 37.500 4.32 0.00 40.32 2.52
393 401 7.323656 CCAAACTGAAATTGTTTCTAGTTAGCG 59.676 37.037 14.54 9.76 38.66 4.26
394 402 5.928153 ACTGAAATTGTTTCTAGTTAGCGC 58.072 37.500 0.00 0.00 40.32 5.92
396 404 3.385079 AATTGTTTCTAGTTAGCGCGC 57.615 42.857 26.66 26.66 0.00 6.86
583 592 7.009174 GCAACCGACAATGATAAATTTTTCGAT 59.991 33.333 0.00 0.00 0.00 3.59
603 612 0.943835 CGATGAACTGACGGTGTGCA 60.944 55.000 0.00 0.00 0.00 4.57
679 689 3.081061 CGGTTCACATTCCCATTTCTCA 58.919 45.455 0.00 0.00 0.00 3.27
778 797 5.411781 ACGTCATGAAAGATTCAGACCTAC 58.588 41.667 0.00 2.49 43.98 3.18
779 798 5.186021 ACGTCATGAAAGATTCAGACCTACT 59.814 40.000 0.00 0.00 43.98 2.57
780 799 5.518128 CGTCATGAAAGATTCAGACCTACTG 59.482 44.000 0.00 0.00 43.98 2.74
892 914 1.226688 GAGTGAGCAGCATACGCGA 60.227 57.895 15.93 0.00 45.49 5.87
1202 1226 2.270205 CATCTGGTGCGCCCTTCT 59.730 61.111 15.15 0.00 0.00 2.85
1294 1322 2.017559 GCTCCTGCGATCCGGTAGTT 62.018 60.000 0.00 0.00 0.00 2.24
1356 1387 0.250252 TGTGATGTGGAAGCAAGCGA 60.250 50.000 0.00 0.00 0.00 4.93
1357 1388 1.089920 GTGATGTGGAAGCAAGCGAT 58.910 50.000 0.00 0.00 0.00 4.58
1359 1390 1.739466 TGATGTGGAAGCAAGCGATTC 59.261 47.619 0.00 0.00 36.79 2.52
1418 1453 4.530161 AGAGTACAGAGATGAACTTGGCTT 59.470 41.667 0.00 0.00 0.00 4.35
1420 1455 4.530161 AGTACAGAGATGAACTTGGCTTCT 59.470 41.667 0.00 0.00 0.00 2.85
1430 1465 1.903183 ACTTGGCTTCTGTAGGAGGAC 59.097 52.381 0.00 0.00 0.00 3.85
1436 1471 2.353208 GCTTCTGTAGGAGGACTGTGTG 60.353 54.545 0.00 0.00 0.00 3.82
1485 1520 3.780902 CACGCCTATGTGATCTGTGTTA 58.219 45.455 0.00 0.00 42.55 2.41
1532 1567 8.585018 AGTAACATGGTTTTATTCCTTGGAAAG 58.415 33.333 6.16 0.00 45.69 2.62
1537 1572 4.562757 GGTTTTATTCCTTGGAAAGCCCAC 60.563 45.833 6.16 0.98 46.62 4.61
1538 1573 3.534357 TTATTCCTTGGAAAGCCCACA 57.466 42.857 6.16 0.00 46.62 4.17
1541 1576 1.528309 CCTTGGAAAGCCCACACGT 60.528 57.895 0.00 0.00 46.62 4.49
1545 1580 0.687920 TGGAAAGCCCACACGTGATA 59.312 50.000 25.01 0.00 40.82 2.15
1560 1595 3.181465 ACGTGATAGGTTAATCAGGCTGG 60.181 47.826 15.73 0.00 42.68 4.85
1588 1623 1.792367 GTTGCATTTTCCCGTTTGCTC 59.208 47.619 0.00 0.00 36.10 4.26
1639 1674 3.447742 CTTTTCCAAAACCACTCAGTGC 58.552 45.455 0.00 0.00 31.34 4.40
1642 1677 2.665165 TCCAAAACCACTCAGTGCAAT 58.335 42.857 0.00 0.00 31.34 3.56
1653 1688 5.163784 CCACTCAGTGCAATCAGAACTATTG 60.164 44.000 0.00 0.00 32.01 1.90
1672 1707 1.968017 CTGCTGCACAACCGGACAT 60.968 57.895 9.46 0.00 0.00 3.06
1676 1711 1.915614 CTGCACAACCGGACATCAGC 61.916 60.000 9.46 4.83 0.00 4.26
1687 1722 2.856557 CGGACATCAGCATCGCATATAG 59.143 50.000 0.00 0.00 0.00 1.31
1688 1723 3.428045 CGGACATCAGCATCGCATATAGA 60.428 47.826 0.00 0.00 0.00 1.98
1689 1724 4.691175 GGACATCAGCATCGCATATAGAT 58.309 43.478 0.00 0.00 0.00 1.98
1798 1836 4.460263 TGAATAGCAAGTTGGACAGTTGT 58.540 39.130 4.75 0.00 38.03 3.32
1895 1933 5.230323 AGTTTCTTACTTCTTCTGGGGTC 57.770 43.478 0.00 0.00 31.29 4.46
2077 2115 4.044426 GTCGCAATCAAGAAAGTGCTTTT 58.956 39.130 0.00 0.00 34.79 2.27
2119 2157 2.164422 CTCGTGACTAGTTGCATCTCCA 59.836 50.000 0.00 0.00 0.00 3.86
2120 2158 2.094700 TCGTGACTAGTTGCATCTCCAC 60.095 50.000 0.00 7.49 0.00 4.02
2138 2185 4.655963 TCCACAAAGAATTCTCTTCCCTG 58.344 43.478 8.78 2.79 41.23 4.45
2160 2207 7.443879 CCCTGTTGGTATTATTTGTTGCTTTTT 59.556 33.333 0.00 0.00 0.00 1.94
2269 2319 6.360370 AAGACACCTTGCTGAAAGATAGTA 57.640 37.500 0.00 0.00 38.24 1.82
2400 2450 7.504924 TTCATGAGGTGGTTAACTACTTTTG 57.495 36.000 19.90 14.24 0.00 2.44
2458 2544 3.691118 GTGCACATCTTCATCCTAAAGCA 59.309 43.478 13.17 0.00 0.00 3.91
2642 2735 7.900352 GTCTGTCAGTTTAGCTTCATATTTTCG 59.100 37.037 0.00 0.00 0.00 3.46
2710 2803 9.494271 TGTATTCATATCCACATAAGCTCTTTC 57.506 33.333 0.00 0.00 0.00 2.62
2733 2826 4.337555 CCTCAGAATGGGTTTCTAAGCATG 59.662 45.833 0.00 0.00 42.98 4.06
2943 3044 7.651027 ATTGTTTCCTTTCCATCCTCTAATG 57.349 36.000 0.00 0.00 0.00 1.90
3003 3104 5.411669 AGTTTCTGATTTATCACCGGAACAC 59.588 40.000 9.46 0.00 32.50 3.32
3076 3177 6.100279 TCCATTTCAGGTAGCTCTATTCATGT 59.900 38.462 0.00 0.00 0.00 3.21
3077 3178 6.426328 CCATTTCAGGTAGCTCTATTCATGTC 59.574 42.308 0.00 0.00 0.00 3.06
3087 3188 7.275888 AGCTCTATTCATGTCTCTTCTGTAG 57.724 40.000 0.00 0.00 0.00 2.74
3110 3211 7.534723 AGATATATTACACGCCCTCAAGTTA 57.465 36.000 0.00 0.00 0.00 2.24
3148 3249 6.128795 CGAAAAGAATATCGGAGTAATCAGCC 60.129 42.308 0.00 0.00 35.49 4.85
3166 3268 4.674281 AGCCAACTATAGCTGGAGTTAC 57.326 45.455 23.65 7.37 38.11 2.50
3183 3285 9.626045 CTGGAGTTACATTATTTTGTTTCCTTC 57.374 33.333 0.00 0.00 30.74 3.46
3184 3286 9.137459 TGGAGTTACATTATTTTGTTTCCTTCA 57.863 29.630 0.00 0.00 30.74 3.02
3186 3288 9.626045 GAGTTACATTATTTTGTTTCCTTCAGG 57.374 33.333 0.00 0.00 0.00 3.86
3187 3289 8.088365 AGTTACATTATTTTGTTTCCTTCAGGC 58.912 33.333 0.00 0.00 34.44 4.85
3194 3296 1.152860 TTTCCTTCAGGCGGCACAA 60.153 52.632 13.08 1.63 34.44 3.33
3216 3318 7.492020 CACAAAATGAAATTGACTTCCACTTGA 59.508 33.333 0.00 0.00 36.10 3.02
3227 3329 5.827267 TGACTTCCACTTGAATCAAATGTGA 59.173 36.000 14.49 4.72 38.41 3.58
3229 3331 6.917533 ACTTCCACTTGAATCAAATGTGATC 58.082 36.000 14.49 0.00 44.02 2.92
3255 3357 0.462789 GCCCCTTTGCATTCCATGAG 59.537 55.000 0.00 0.00 0.00 2.90
3284 3386 6.472163 GTGTGGAATATTTCACGCCAATTTAG 59.528 38.462 24.37 0.00 38.15 1.85
3322 3424 3.013276 TCAGACTTGTTACACTCGCAG 57.987 47.619 0.00 0.00 0.00 5.18
3367 3469 1.473258 TTGTGCTGACTTGTGCCTTT 58.527 45.000 0.00 0.00 0.00 3.11
3368 3470 1.473258 TGTGCTGACTTGTGCCTTTT 58.527 45.000 0.00 0.00 0.00 2.27
3434 3536 9.802039 AATAGCGTATTTAATGGGGAAATCTTA 57.198 29.630 0.00 0.00 0.00 2.10
3486 3588 8.668510 ATTTGCCTTATACTCAGATTACACTG 57.331 34.615 0.00 0.00 39.02 3.66
3557 3659 3.565902 GCCATATAAAGTGCCCTTCTGTC 59.434 47.826 0.00 0.00 0.00 3.51
3564 3666 0.249911 GTGCCCTTCTGTCGAACTGT 60.250 55.000 0.00 0.00 0.00 3.55
3617 3719 5.234329 GCATATTTTGCGCTAGTAGACAGAA 59.766 40.000 9.73 0.53 42.54 3.02
3779 3914 3.081061 TCAAAACGCCATTCAGTAGCAT 58.919 40.909 0.00 0.00 0.00 3.79
3849 3984 1.906105 TTGGGCTATGACCACCCGTC 61.906 60.000 0.00 0.00 42.46 4.79
3993 4129 4.500716 CCCTCGCATTGTTAAGGTTTTTGT 60.501 41.667 0.00 0.00 0.00 2.83
4035 4172 6.915300 CACGTAAACTGAATCAATGGTTTTCA 59.085 34.615 4.77 0.00 34.40 2.69
4040 4177 7.642071 AACTGAATCAATGGTTTTCAATTCG 57.358 32.000 0.00 0.00 0.00 3.34
4041 4178 6.158598 ACTGAATCAATGGTTTTCAATTCGG 58.841 36.000 0.00 0.00 36.20 4.30
4042 4179 6.095432 TGAATCAATGGTTTTCAATTCGGT 57.905 33.333 0.00 0.00 0.00 4.69
4043 4180 6.520272 TGAATCAATGGTTTTCAATTCGGTT 58.480 32.000 0.00 0.00 0.00 4.44
4044 4181 6.989169 TGAATCAATGGTTTTCAATTCGGTTT 59.011 30.769 0.00 0.00 0.00 3.27
4045 4182 7.170658 TGAATCAATGGTTTTCAATTCGGTTTC 59.829 33.333 0.00 0.00 0.00 2.78
4046 4183 6.155475 TCAATGGTTTTCAATTCGGTTTCT 57.845 33.333 0.00 0.00 0.00 2.52
4047 4184 6.212955 TCAATGGTTTTCAATTCGGTTTCTC 58.787 36.000 0.00 0.00 0.00 2.87
4077 4299 4.096984 ACCGGATCATTCTTTCTGAAATGC 59.903 41.667 9.46 0.00 38.29 3.56
4096 4320 1.067846 GCGATCGATATACAGGTGGCA 60.068 52.381 21.57 0.00 0.00 4.92
4098 4322 2.987149 CGATCGATATACAGGTGGCAAC 59.013 50.000 10.26 0.00 0.00 4.17
4119 4343 1.291637 TCCTCCCCCGGTGACTATTTA 59.708 52.381 0.00 0.00 0.00 1.40
4153 4377 3.674997 GGCAGTTCTCAAAGTGGTATGA 58.325 45.455 0.00 0.00 36.49 2.15
4197 4421 8.718734 ACACAGATTTCTAACTCGAAATAAACC 58.281 33.333 0.00 0.00 42.09 3.27
4211 4435 5.343058 CGAAATAAACCGACGAACTTCAGTA 59.657 40.000 0.00 0.00 0.00 2.74
4246 4470 4.406972 TGAGCTATCACTTCCAGCAGTAAT 59.593 41.667 0.00 0.00 37.78 1.89
4273 4497 7.826252 ACTCGCATCTTTTATCTGCCATTATAT 59.174 33.333 0.00 0.00 32.24 0.86
4282 4506 3.524826 TCTGCCATTATATCCAGGAGCT 58.475 45.455 0.00 0.00 0.00 4.09
4306 4530 0.587768 GCATTTTGCCTTGCACAACC 59.412 50.000 0.00 0.00 38.71 3.77
4309 4533 2.021355 TTTTGCCTTGCACAACCAAG 57.979 45.000 0.00 0.00 38.71 3.61
4318 4542 3.100545 CACAACCAAGTGCTCCTGT 57.899 52.632 0.00 0.00 32.04 4.00
4332 4556 2.739379 GCTCCTGTAACTGAAGCAAGAC 59.261 50.000 0.00 0.00 0.00 3.01
4341 4565 6.597672 TGTAACTGAAGCAAGACAAAGAGAAA 59.402 34.615 0.00 0.00 0.00 2.52
4343 4567 6.515272 ACTGAAGCAAGACAAAGAGAAAAA 57.485 33.333 0.00 0.00 0.00 1.94
4344 4568 6.325596 ACTGAAGCAAGACAAAGAGAAAAAC 58.674 36.000 0.00 0.00 0.00 2.43
4345 4569 6.071952 ACTGAAGCAAGACAAAGAGAAAAACA 60.072 34.615 0.00 0.00 0.00 2.83
4347 4571 7.322664 TGAAGCAAGACAAAGAGAAAAACAAT 58.677 30.769 0.00 0.00 0.00 2.71
4348 4572 7.276218 TGAAGCAAGACAAAGAGAAAAACAATG 59.724 33.333 0.00 0.00 0.00 2.82
4349 4573 6.044682 AGCAAGACAAAGAGAAAAACAATGG 58.955 36.000 0.00 0.00 0.00 3.16
4350 4574 6.042143 GCAAGACAAAGAGAAAAACAATGGA 58.958 36.000 0.00 0.00 0.00 3.41
4351 4575 6.534793 GCAAGACAAAGAGAAAAACAATGGAA 59.465 34.615 0.00 0.00 0.00 3.53
4352 4576 7.064490 GCAAGACAAAGAGAAAAACAATGGAAA 59.936 33.333 0.00 0.00 0.00 3.13
4353 4577 8.382875 CAAGACAAAGAGAAAAACAATGGAAAC 58.617 33.333 0.00 0.00 0.00 2.78
4354 4578 6.751888 AGACAAAGAGAAAAACAATGGAAACG 59.248 34.615 0.00 0.00 0.00 3.60
4355 4579 5.290885 ACAAAGAGAAAAACAATGGAAACGC 59.709 36.000 0.00 0.00 0.00 4.84
4356 4580 3.977427 AGAGAAAAACAATGGAAACGCC 58.023 40.909 0.00 0.00 37.10 5.68
4357 4581 2.724174 GAGAAAAACAATGGAAACGCCG 59.276 45.455 0.00 0.00 40.66 6.46
4358 4582 2.359531 AGAAAAACAATGGAAACGCCGA 59.640 40.909 0.00 0.00 40.66 5.54
4359 4583 2.128367 AAAACAATGGAAACGCCGAC 57.872 45.000 0.00 0.00 40.66 4.79
4360 4584 0.312729 AAACAATGGAAACGCCGACC 59.687 50.000 0.00 0.00 40.66 4.79
4361 4585 1.520600 AACAATGGAAACGCCGACCC 61.521 55.000 0.00 0.00 40.66 4.46
4362 4586 2.360726 AATGGAAACGCCGACCCC 60.361 61.111 0.00 0.00 40.66 4.95
4363 4587 3.931190 AATGGAAACGCCGACCCCC 62.931 63.158 0.00 0.00 40.66 5.40
4380 4604 0.250553 CCCCTAAGGTGACAAACGCA 60.251 55.000 0.00 0.00 0.00 5.24
4383 4607 1.070175 CCTAAGGTGACAAACGCAACG 60.070 52.381 0.00 0.00 0.00 4.10
4389 4613 1.082756 GACAAACGCAACGGCTGAG 60.083 57.895 0.00 0.00 38.10 3.35
4391 4615 3.660111 AAACGCAACGGCTGAGGC 61.660 61.111 0.00 0.00 38.10 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.165030 CAGCCAGTTTAGCCTCAAATGG 59.835 50.000 0.82 0.82 0.00 3.16
40 41 1.548269 TGCCGATTCCAATTGTTTCCC 59.452 47.619 4.43 0.00 0.00 3.97
47 48 1.265236 TTGGCTTGCCGATTCCAATT 58.735 45.000 7.18 0.00 34.01 2.32
57 58 0.109597 CGTTGTGAGATTGGCTTGCC 60.110 55.000 4.43 4.43 0.00 4.52
58 59 0.874390 TCGTTGTGAGATTGGCTTGC 59.126 50.000 0.00 0.00 0.00 4.01
91 92 1.012086 GAAGGGGCGGAAATAACGAC 58.988 55.000 0.00 0.00 39.02 4.34
92 93 0.107557 GGAAGGGGCGGAAATAACGA 60.108 55.000 0.00 0.00 0.00 3.85
93 94 0.107361 AGGAAGGGGCGGAAATAACG 60.107 55.000 0.00 0.00 0.00 3.18
94 95 3.409570 GATAGGAAGGGGCGGAAATAAC 58.590 50.000 0.00 0.00 0.00 1.89
95 96 2.374170 GGATAGGAAGGGGCGGAAATAA 59.626 50.000 0.00 0.00 0.00 1.40
96 97 1.982958 GGATAGGAAGGGGCGGAAATA 59.017 52.381 0.00 0.00 0.00 1.40
97 98 0.771755 GGATAGGAAGGGGCGGAAAT 59.228 55.000 0.00 0.00 0.00 2.17
99 100 0.327191 AAGGATAGGAAGGGGCGGAA 60.327 55.000 0.00 0.00 0.00 4.30
100 101 0.564171 TAAGGATAGGAAGGGGCGGA 59.436 55.000 0.00 0.00 0.00 5.54
101 102 0.685660 GTAAGGATAGGAAGGGGCGG 59.314 60.000 0.00 0.00 0.00 6.13
102 103 0.685660 GGTAAGGATAGGAAGGGGCG 59.314 60.000 0.00 0.00 0.00 6.13
103 104 1.065647 GGGTAAGGATAGGAAGGGGC 58.934 60.000 0.00 0.00 0.00 5.80
114 120 1.306397 GACGGGGAAGGGGTAAGGA 60.306 63.158 0.00 0.00 0.00 3.36
131 137 5.769835 AGAAAAATGAATGGATAGGGCTGA 58.230 37.500 0.00 0.00 0.00 4.26
139 145 5.050769 CGTCGATCGAGAAAAATGAATGGAT 60.051 40.000 20.09 0.00 42.86 3.41
188 195 1.153549 GCGCAGGTGGAAGGTAGAG 60.154 63.158 0.30 0.00 0.00 2.43
197 204 2.398554 GGTACATGTGCGCAGGTGG 61.399 63.158 26.39 8.48 40.12 4.61
199 206 1.375908 CAGGTACATGTGCGCAGGT 60.376 57.895 22.15 22.15 42.66 4.00
202 209 2.745884 GGCAGGTACATGTGCGCA 60.746 61.111 5.66 5.66 40.82 6.09
207 214 1.198713 CTGAGGAGGCAGGTACATGT 58.801 55.000 9.57 2.69 32.26 3.21
217 224 2.250741 GAAGGAGTGGCTGAGGAGGC 62.251 65.000 0.00 0.00 45.19 4.70
224 231 1.621672 GGAGGGAGAAGGAGTGGCTG 61.622 65.000 0.00 0.00 0.00 4.85
227 234 0.252927 AAGGGAGGGAGAAGGAGTGG 60.253 60.000 0.00 0.00 0.00 4.00
229 236 2.270858 GAAAAGGGAGGGAGAAGGAGT 58.729 52.381 0.00 0.00 0.00 3.85
247 254 2.515057 AACGGTGGTTGCTGCGAA 60.515 55.556 0.00 0.00 34.37 4.70
282 290 2.108157 AGTGGTTGCGCACGAGAA 59.892 55.556 11.12 0.00 0.00 2.87
283 291 2.661537 CAGTGGTTGCGCACGAGA 60.662 61.111 11.12 0.00 0.00 4.04
299 307 0.975556 TTGTAGCATCCCTCCTCGCA 60.976 55.000 0.00 0.00 0.00 5.10
310 318 2.305928 TGTGTGTGCCTTTTGTAGCAT 58.694 42.857 0.00 0.00 41.86 3.79
312 320 2.034558 ACATGTGTGTGCCTTTTGTAGC 59.965 45.455 0.00 0.00 37.14 3.58
363 371 5.596836 AGAAACAATTTCAGTTTGGAGCA 57.403 34.783 4.25 0.00 42.10 4.26
373 381 4.668177 GCGCGCTAACTAGAAACAATTTCA 60.668 41.667 26.67 0.00 42.10 2.69
377 385 1.323534 CGCGCGCTAACTAGAAACAAT 59.676 47.619 30.48 0.00 0.00 2.71
378 386 0.711670 CGCGCGCTAACTAGAAACAA 59.288 50.000 30.48 0.00 0.00 2.83
436 444 4.671549 CACTGCTTGTGGCGCACG 62.672 66.667 10.83 0.00 45.43 5.34
457 465 2.341101 CCCTTGCAGCAGCCTCAAG 61.341 63.158 14.33 14.33 41.13 3.02
539 548 4.025858 AGCCATCGTGCTGCCACT 62.026 61.111 0.00 0.00 40.90 4.00
546 555 4.465512 CGGTTGCAGCCATCGTGC 62.466 66.667 20.42 0.00 41.59 5.34
583 592 0.666274 GCACACCGTCAGTTCATCGA 60.666 55.000 0.00 0.00 0.00 3.59
629 638 1.196104 CGGAGGGTTAGGTTGGGTGA 61.196 60.000 0.00 0.00 0.00 4.02
754 773 4.499183 AGGTCTGAATCTTTCATGACGTC 58.501 43.478 9.11 9.11 39.30 4.34
756 775 5.518128 CAGTAGGTCTGAATCTTTCATGACG 59.482 44.000 0.00 0.00 46.27 4.35
808 827 1.299089 GCACGGTGCACCTGTTTTC 60.299 57.895 32.28 17.61 44.26 2.29
892 914 1.321074 GGGTTCGGGATCGTCTGTCT 61.321 60.000 0.00 0.00 37.69 3.41
954 978 0.183492 TGTTCACTCTGGCTGGCTTT 59.817 50.000 2.00 0.00 0.00 3.51
1255 1283 0.526524 GACACCCTGAAGAGATCGCG 60.527 60.000 0.00 0.00 0.00 5.87
1364 1395 4.454504 GGAACCTAAGATTTCTGAAACGCA 59.545 41.667 4.73 0.00 0.00 5.24
1398 1433 4.629200 CAGAAGCCAAGTTCATCTCTGTAC 59.371 45.833 0.00 0.00 0.00 2.90
1418 1453 1.257743 GCACACAGTCCTCCTACAGA 58.742 55.000 0.00 0.00 0.00 3.41
1420 1455 1.964448 CGCACACAGTCCTCCTACA 59.036 57.895 0.00 0.00 0.00 2.74
1445 1480 3.362014 CGTGCATCGAACTGATAAATCCG 60.362 47.826 0.00 0.00 42.86 4.18
1532 1567 2.389962 TTAACCTATCACGTGTGGGC 57.610 50.000 16.51 0.00 0.00 5.36
1537 1572 3.804325 CAGCCTGATTAACCTATCACGTG 59.196 47.826 9.94 9.94 31.51 4.49
1538 1573 3.181465 CCAGCCTGATTAACCTATCACGT 60.181 47.826 0.00 0.00 31.51 4.49
1541 1576 3.393687 ACCCAGCCTGATTAACCTATCA 58.606 45.455 0.00 0.00 33.66 2.15
1545 1580 2.092375 GCTAACCCAGCCTGATTAACCT 60.092 50.000 0.00 0.00 45.23 3.50
1560 1595 2.671070 CGGGAAAATGCAACAGCTAACC 60.671 50.000 0.00 0.00 0.00 2.85
1588 1623 4.701956 ATCTCGTGCAAGTTATTTTGGG 57.298 40.909 0.00 0.00 0.00 4.12
1639 1674 3.692576 GCAGCAGCAATAGTTCTGATTG 58.307 45.455 0.00 0.00 41.58 2.67
1653 1688 4.030452 GTCCGGTTGTGCAGCAGC 62.030 66.667 0.00 0.00 42.57 5.25
1655 1690 1.965930 GATGTCCGGTTGTGCAGCA 60.966 57.895 0.00 0.00 0.00 4.41
1672 1707 5.904362 AGTACATCTATATGCGATGCTGA 57.096 39.130 13.62 1.83 41.45 4.26
1676 1711 8.323854 GCAACATAAGTACATCTATATGCGATG 58.676 37.037 12.62 12.62 42.97 3.84
1687 1722 6.880822 TCAGTAACGCAACATAAGTACATC 57.119 37.500 0.00 0.00 0.00 3.06
1688 1723 8.814235 GTTATCAGTAACGCAACATAAGTACAT 58.186 33.333 0.00 0.00 31.67 2.29
1689 1724 8.030692 AGTTATCAGTAACGCAACATAAGTACA 58.969 33.333 0.00 0.00 43.92 2.90
1798 1836 1.264020 CAGCTTAACGAAACAGCAGCA 59.736 47.619 0.00 0.00 35.88 4.41
1892 1930 3.064545 CCGCAGAAAGAGATGAAATGACC 59.935 47.826 0.00 0.00 0.00 4.02
1895 1933 2.223433 GGCCGCAGAAAGAGATGAAATG 60.223 50.000 0.00 0.00 0.00 2.32
2077 2115 8.184848 CACGAGTATATCAAGTTCTGAGAGAAA 58.815 37.037 0.00 0.00 35.75 2.52
2119 2157 4.829492 CCAACAGGGAAGAGAATTCTTTGT 59.171 41.667 9.87 5.36 43.63 2.83
2120 2158 4.829492 ACCAACAGGGAAGAGAATTCTTTG 59.171 41.667 9.87 7.28 43.63 2.77
2160 2207 8.061920 TGGGGTATTGATAAACATGTCCATTTA 58.938 33.333 0.00 0.00 0.00 1.40
2166 2213 8.006298 TGAATTGGGGTATTGATAAACATGTC 57.994 34.615 0.00 0.00 0.00 3.06
2733 2826 8.355169 TCATACATTACCTGTAACGAGGAATAC 58.645 37.037 0.00 0.00 43.42 1.89
2905 3006 7.775053 AAGGAAACAATAGACCATTAGCAAA 57.225 32.000 0.00 0.00 0.00 3.68
2943 3044 6.127897 ACAACTGCAGCAGAATTTAATAGACC 60.128 38.462 29.70 0.00 35.18 3.85
3076 3177 7.120873 GGGCGTGTAATATATCTACAGAAGAGA 59.879 40.741 7.56 0.00 37.74 3.10
3077 3178 7.121463 AGGGCGTGTAATATATCTACAGAAGAG 59.879 40.741 7.56 0.00 37.74 2.85
3087 3188 8.656849 CAATAACTTGAGGGCGTGTAATATATC 58.343 37.037 0.00 0.00 34.04 1.63
3098 3199 4.035208 GGTGATTACAATAACTTGAGGGCG 59.965 45.833 0.00 0.00 36.20 6.13
3110 3211 8.335356 CGATATTCTTTTCGTGGTGATTACAAT 58.665 33.333 0.00 0.00 0.00 2.71
3166 3268 4.864247 CCGCCTGAAGGAAACAAAATAATG 59.136 41.667 0.00 0.00 37.39 1.90
3183 3285 2.083167 ATTTCATTTTGTGCCGCCTG 57.917 45.000 0.00 0.00 0.00 4.85
3184 3286 2.036992 TCAATTTCATTTTGTGCCGCCT 59.963 40.909 0.00 0.00 0.00 5.52
3186 3288 3.059166 AGTCAATTTCATTTTGTGCCGC 58.941 40.909 0.00 0.00 0.00 6.53
3187 3289 4.150451 GGAAGTCAATTTCATTTTGTGCCG 59.850 41.667 0.00 0.00 0.00 5.69
3194 3296 8.423349 TGATTCAAGTGGAAGTCAATTTCATTT 58.577 29.630 0.00 0.00 39.30 2.32
3216 3318 5.127682 GGGGCTGTTAAGATCACATTTGATT 59.872 40.000 0.00 0.00 42.95 2.57
3227 3329 2.603075 TGCAAAGGGGCTGTTAAGAT 57.397 45.000 0.00 0.00 34.04 2.40
3229 3331 2.094026 GGAATGCAAAGGGGCTGTTAAG 60.094 50.000 0.00 0.00 34.04 1.85
3255 3357 4.814234 TGGCGTGAAATATTCCACACTATC 59.186 41.667 5.62 3.10 33.13 2.08
3322 3424 2.678336 ACACCTAAAAATAGCTGCGAGC 59.322 45.455 0.00 0.47 42.84 5.03
3368 3470 2.746362 CCAGCAAAAACCTGCACAAAAA 59.254 40.909 0.00 0.00 45.18 1.94
3434 3536 6.708054 GCCAACTAGCAGTATTTCTCATACAT 59.292 38.462 0.00 0.00 0.00 2.29
3557 3659 1.179332 CAACACACGCAAACAGTTCG 58.821 50.000 0.00 0.00 0.00 3.95
3564 3666 1.989165 GCAAAGAACAACACACGCAAA 59.011 42.857 0.00 0.00 0.00 3.68
3617 3719 3.770263 TCGTAAATTCGACGACCATCT 57.230 42.857 10.55 0.00 43.99 2.90
3779 3914 4.163427 ACAGGGAGAGAGATGACAAGAAA 58.837 43.478 0.00 0.00 0.00 2.52
3993 4129 1.593933 CGTGAGAAACCGAAACCGAAA 59.406 47.619 0.00 0.00 0.00 3.46
4041 4178 6.316390 AGAATGATCCGGTTTATGTGAGAAAC 59.684 38.462 0.00 0.00 36.29 2.78
4042 4179 6.414732 AGAATGATCCGGTTTATGTGAGAAA 58.585 36.000 0.00 0.00 0.00 2.52
4043 4180 5.989477 AGAATGATCCGGTTTATGTGAGAA 58.011 37.500 0.00 0.00 0.00 2.87
4044 4181 5.614324 AGAATGATCCGGTTTATGTGAGA 57.386 39.130 0.00 0.00 0.00 3.27
4045 4182 6.540189 AGAAAGAATGATCCGGTTTATGTGAG 59.460 38.462 0.00 0.00 0.00 3.51
4046 4183 6.316140 CAGAAAGAATGATCCGGTTTATGTGA 59.684 38.462 0.00 0.00 0.00 3.58
4047 4184 6.316140 TCAGAAAGAATGATCCGGTTTATGTG 59.684 38.462 0.00 0.00 0.00 3.21
4077 4299 2.987149 GTTGCCACCTGTATATCGATCG 59.013 50.000 9.36 9.36 0.00 3.69
4096 4320 1.807771 TAGTCACCGGGGGAGGAGTT 61.808 60.000 2.42 0.00 34.73 3.01
4098 4322 0.398664 AATAGTCACCGGGGGAGGAG 60.399 60.000 2.42 0.00 34.73 3.69
4133 4357 5.689383 TTTCATACCACTTTGAGAACTGC 57.311 39.130 0.00 0.00 0.00 4.40
4153 4377 7.275888 TCTGTGTGCAGTTTATCAATCTTTT 57.724 32.000 0.00 0.00 43.05 2.27
4187 4411 4.149396 ACTGAAGTTCGTCGGTTTATTTCG 59.851 41.667 0.00 0.00 33.09 3.46
4197 4421 2.657372 GCTTCTGTACTGAAGTTCGTCG 59.343 50.000 31.13 14.53 43.74 5.12
4236 4460 3.377346 AGATGCGAGTATTACTGCTGG 57.623 47.619 0.00 0.00 0.00 4.85
4246 4470 4.400529 TGGCAGATAAAAGATGCGAGTA 57.599 40.909 0.00 0.00 40.90 2.59
4273 4497 3.119029 GCAAAATGCATAAAGCTCCTGGA 60.119 43.478 0.00 0.00 44.26 3.86
4306 4530 2.481952 GCTTCAGTTACAGGAGCACTTG 59.518 50.000 3.03 0.00 0.00 3.16
4309 4533 2.169832 TGCTTCAGTTACAGGAGCAC 57.830 50.000 6.64 0.00 0.00 4.40
4314 4538 4.816385 TCTTTGTCTTGCTTCAGTTACAGG 59.184 41.667 0.00 0.00 0.00 4.00
4318 4542 7.624360 TTTTCTCTTTGTCTTGCTTCAGTTA 57.376 32.000 0.00 0.00 0.00 2.24
4332 4556 5.276820 GGCGTTTCCATTGTTTTTCTCTTTG 60.277 40.000 0.00 0.00 34.01 2.77
4341 4565 0.312729 GGTCGGCGTTTCCATTGTTT 59.687 50.000 6.85 0.00 34.01 2.83
4343 4567 1.969589 GGGTCGGCGTTTCCATTGT 60.970 57.895 6.85 0.00 34.01 2.71
4344 4568 2.696759 GGGGTCGGCGTTTCCATTG 61.697 63.158 6.85 0.00 34.01 2.82
4345 4569 2.360726 GGGGTCGGCGTTTCCATT 60.361 61.111 6.85 0.00 34.01 3.16
4360 4584 0.958876 GCGTTTGTCACCTTAGGGGG 60.959 60.000 0.00 0.00 40.03 5.40
4361 4585 0.250553 TGCGTTTGTCACCTTAGGGG 60.251 55.000 2.32 0.00 41.89 4.79
4362 4586 1.265905 GTTGCGTTTGTCACCTTAGGG 59.734 52.381 2.32 0.00 38.88 3.53
4363 4587 1.070175 CGTTGCGTTTGTCACCTTAGG 60.070 52.381 0.00 0.00 0.00 2.69
4364 4588 1.070175 CCGTTGCGTTTGTCACCTTAG 60.070 52.381 0.00 0.00 0.00 2.18
4365 4589 0.938713 CCGTTGCGTTTGTCACCTTA 59.061 50.000 0.00 0.00 0.00 2.69
4366 4590 1.725066 CCGTTGCGTTTGTCACCTT 59.275 52.632 0.00 0.00 0.00 3.50
4367 4591 2.830285 GCCGTTGCGTTTGTCACCT 61.830 57.895 0.00 0.00 0.00 4.00
4368 4592 2.353030 GCCGTTGCGTTTGTCACC 60.353 61.111 0.00 0.00 0.00 4.02
4369 4593 1.654137 CAGCCGTTGCGTTTGTCAC 60.654 57.895 0.00 0.00 44.33 3.67
4370 4594 1.771073 CTCAGCCGTTGCGTTTGTCA 61.771 55.000 0.00 0.00 44.33 3.58
4371 4595 1.082756 CTCAGCCGTTGCGTTTGTC 60.083 57.895 0.00 0.00 44.33 3.18
4372 4596 2.542907 CCTCAGCCGTTGCGTTTGT 61.543 57.895 0.00 0.00 44.33 2.83
4373 4597 2.252260 CCTCAGCCGTTGCGTTTG 59.748 61.111 0.00 0.00 44.33 2.93
4389 4613 1.270550 CATGTGAGGTTTTGACAGGCC 59.729 52.381 0.00 0.00 0.00 5.19
4391 4615 2.554032 GTCCATGTGAGGTTTTGACAGG 59.446 50.000 0.00 0.00 0.00 4.00
4400 4624 2.376518 ACATTTCCAGTCCATGTGAGGT 59.623 45.455 0.00 0.00 29.74 3.85


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

AutoCloner maintained by Alex Coulton.