Multiple sequence alignment - TraesCS7B01G061600

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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 TraesCS7B01G061600 chr7B 100.000 3710 0 0 859 4568 64068499 64072208 0.000000e+00 6852.0
1 TraesCS7B01G061600 chr7B 100.000 358 0 0 1 358 64067641 64067998 0.000000e+00 662.0
2 TraesCS7B01G061600 chr7A 91.199 3704 198 60 934 4568 110422698 110426342 0.000000e+00 4916.0
3 TraesCS7B01G061600 chr7A 92.857 56 3 1 859 913 50180292 50180347 3.790000e-11 80.5
4 TraesCS7B01G061600 chr7D 92.320 3190 151 46 859 3991 105454622 105457774 0.000000e+00 4447.0
5 TraesCS7B01G061600 chr7D 91.892 259 21 0 1 259 105453328 105453586 3.360000e-96 363.0
6 TraesCS7B01G061600 chr7D 86.943 314 22 11 3982 4295 105459370 105459664 7.320000e-88 335.0
7 TraesCS7B01G061600 chr7D 94.079 152 7 1 4419 4568 105460056 105460207 3.550000e-56 230.0


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 TraesCS7B01G061600 chr7B 64067641 64072208 4567 False 3757.00 6852 100.0000 1 4568 2 chr7B.!!$F1 4567
1 TraesCS7B01G061600 chr7A 110422698 110426342 3644 False 4916.00 4916 91.1990 934 4568 1 chr7A.!!$F2 3634
2 TraesCS7B01G061600 chr7D 105453328 105460207 6879 False 1343.75 4447 91.3085 1 4568 4 chr7D.!!$F1 4567

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
283 1279 0.114560 ACCTCTTCTTCCTCACCCGA 59.885 55.000 0.0 0.0 0.0 5.14 F
1070 2067 0.183731 TCGCCAGCTCTCCTCATCTA 59.816 55.000 0.0 0.0 0.0 1.98 F
1371 2368 0.631753 TCTCCCCGTTCCTCTCATCT 59.368 55.000 0.0 0.0 0.0 2.90 F
2219 3249 1.001746 ACACTGCTGATGTCTGTGGAG 59.998 52.381 0.0 0.0 37.6 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 3010 0.294887 GCGCGATGTTCGTCTTGTAG 59.705 55.000 12.1 0.0 42.81 2.74 R
2333 3367 0.976641 TGCGTCAGACCAGATTCCTT 59.023 50.000 0.0 0.0 0.00 3.36 R
3322 4365 1.305887 CGTAGGGGAAGGAGGTGGT 60.306 63.158 0.0 0.0 0.00 4.16 R
4093 6791 0.548510 GGTGGGGAGATCTGAAAGGG 59.451 60.000 0.0 0.0 0.00 3.95 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
38 39 5.091261 GAGATTTCCTTAAGTCTCAGCCA 57.909 43.478 13.32 0.00 44.05 4.75
56 57 2.795329 CCAACTGAAACCTAGCCACAT 58.205 47.619 0.00 0.00 0.00 3.21
58 59 3.411446 CAACTGAAACCTAGCCACATCA 58.589 45.455 0.00 0.00 0.00 3.07
91 92 4.695455 AGTGGTACCAATTCGTTGAGATTG 59.305 41.667 18.31 0.00 0.00 2.67
114 115 8.995027 TTGCCTCAATTATGGTAAGTATCAAT 57.005 30.769 0.00 0.00 0.00 2.57
116 117 7.040478 TGCCTCAATTATGGTAAGTATCAATGC 60.040 37.037 0.00 0.00 0.00 3.56
118 119 8.292448 CCTCAATTATGGTAAGTATCAATGCAC 58.708 37.037 0.00 0.00 0.00 4.57
166 167 9.997172 AGAAGAAATTTCAGGTATTTTCCCTAT 57.003 29.630 19.99 0.00 0.00 2.57
168 169 8.011844 AGAAATTTCAGGTATTTTCCCTATGC 57.988 34.615 19.99 0.00 0.00 3.14
176 177 5.307196 AGGTATTTTCCCTATGCGTGTCTAT 59.693 40.000 0.00 0.00 0.00 1.98
208 209 4.976116 CGACTGAAAAATTTGAAGTGGTCC 59.024 41.667 5.63 0.00 0.00 4.46
226 227 3.512680 GTCCGTCGATTTCATCTCAACT 58.487 45.455 0.00 0.00 0.00 3.16
228 229 3.056821 TCCGTCGATTTCATCTCAACTGT 60.057 43.478 0.00 0.00 0.00 3.55
259 260 4.279671 AGATCCAACGTCTAGGACATCATC 59.720 45.833 6.50 1.53 36.60 2.92
260 261 3.632333 TCCAACGTCTAGGACATCATCT 58.368 45.455 0.00 0.00 32.09 2.90
261 262 4.023980 TCCAACGTCTAGGACATCATCTT 58.976 43.478 0.00 0.00 32.09 2.40
262 263 4.098044 TCCAACGTCTAGGACATCATCTTC 59.902 45.833 0.00 0.00 32.09 2.87
263 264 4.363999 CAACGTCTAGGACATCATCTTCC 58.636 47.826 0.00 0.00 32.09 3.46
264 265 3.632333 ACGTCTAGGACATCATCTTCCA 58.368 45.455 0.00 0.00 33.92 3.53
265 266 3.381908 ACGTCTAGGACATCATCTTCCAC 59.618 47.826 0.00 0.00 33.92 4.02
266 267 3.243569 CGTCTAGGACATCATCTTCCACC 60.244 52.174 0.00 0.00 33.92 4.61
267 268 3.964031 GTCTAGGACATCATCTTCCACCT 59.036 47.826 0.00 0.00 33.92 4.00
278 1274 3.260269 TCTTCCACCTCTTCTTCCTCA 57.740 47.619 0.00 0.00 0.00 3.86
281 1277 0.615850 CCACCTCTTCTTCCTCACCC 59.384 60.000 0.00 0.00 0.00 4.61
282 1278 0.247736 CACCTCTTCTTCCTCACCCG 59.752 60.000 0.00 0.00 0.00 5.28
283 1279 0.114560 ACCTCTTCTTCCTCACCCGA 59.885 55.000 0.00 0.00 0.00 5.14
284 1280 1.273324 ACCTCTTCTTCCTCACCCGAT 60.273 52.381 0.00 0.00 0.00 4.18
285 1281 1.410882 CCTCTTCTTCCTCACCCGATC 59.589 57.143 0.00 0.00 0.00 3.69
287 1283 0.466124 CTTCTTCCTCACCCGATCCC 59.534 60.000 0.00 0.00 0.00 3.85
288 1284 0.981277 TTCTTCCTCACCCGATCCCC 60.981 60.000 0.00 0.00 0.00 4.81
289 1285 2.366435 TTCCTCACCCGATCCCCC 60.366 66.667 0.00 0.00 0.00 5.40
315 1311 4.025401 CAAGCCGCCACCACGAAC 62.025 66.667 0.00 0.00 34.06 3.95
322 1318 4.244463 CCACCACGAACCACCGGT 62.244 66.667 0.00 0.00 37.65 5.28
323 1319 2.970324 CACCACGAACCACCGGTG 60.970 66.667 28.26 28.26 42.72 4.94
324 1320 4.922026 ACCACGAACCACCGGTGC 62.922 66.667 29.75 14.74 35.34 5.01
325 1321 4.619227 CCACGAACCACCGGTGCT 62.619 66.667 29.75 18.02 35.34 4.40
326 1322 3.041940 CACGAACCACCGGTGCTC 61.042 66.667 29.75 23.90 35.34 4.26
327 1323 4.657824 ACGAACCACCGGTGCTCG 62.658 66.667 36.17 36.17 39.06 5.03
350 1346 3.322466 CTGTCCTCCCCGCTGGTT 61.322 66.667 0.00 0.00 34.77 3.67
351 1347 2.852075 TGTCCTCCCCGCTGGTTT 60.852 61.111 0.00 0.00 34.77 3.27
352 1348 2.411765 CTGTCCTCCCCGCTGGTTTT 62.412 60.000 0.00 0.00 34.77 2.43
353 1349 1.674651 GTCCTCCCCGCTGGTTTTC 60.675 63.158 0.00 0.00 34.77 2.29
354 1350 1.846124 TCCTCCCCGCTGGTTTTCT 60.846 57.895 0.00 0.00 34.77 2.52
355 1351 1.074951 CCTCCCCGCTGGTTTTCTT 59.925 57.895 0.00 0.00 34.77 2.52
356 1352 0.960861 CCTCCCCGCTGGTTTTCTTC 60.961 60.000 0.00 0.00 34.77 2.87
357 1353 0.960861 CTCCCCGCTGGTTTTCTTCC 60.961 60.000 0.00 0.00 34.77 3.46
905 1901 9.611284 CTTCAAAATTCAATCGACTGAAATGTA 57.389 29.630 13.88 6.50 38.75 2.29
912 1908 7.468922 TCAATCGACTGAAATGTAGCTATTG 57.531 36.000 0.00 0.00 0.00 1.90
913 1909 7.041721 TCAATCGACTGAAATGTAGCTATTGT 58.958 34.615 0.00 0.00 0.00 2.71
914 1910 6.834959 ATCGACTGAAATGTAGCTATTGTG 57.165 37.500 0.00 0.00 0.00 3.33
917 1914 6.697455 TCGACTGAAATGTAGCTATTGTGATC 59.303 38.462 0.00 0.00 0.00 2.92
922 1919 6.767902 TGAAATGTAGCTATTGTGATCTTCCC 59.232 38.462 0.00 0.00 0.00 3.97
928 1925 4.100808 AGCTATTGTGATCTTCCCTGACTC 59.899 45.833 0.00 0.00 0.00 3.36
966 1963 3.550842 GCAAGGACAACTCACAAACCATC 60.551 47.826 0.00 0.00 0.00 3.51
1033 2030 2.209064 TACTCGCACACTCTTCCCGC 62.209 60.000 0.00 0.00 0.00 6.13
1070 2067 0.183731 TCGCCAGCTCTCCTCATCTA 59.816 55.000 0.00 0.00 0.00 1.98
1077 2074 3.256383 CAGCTCTCCTCATCTACATCCTG 59.744 52.174 0.00 0.00 0.00 3.86
1095 2092 4.736896 GTGGTCCTCGTCGCCACC 62.737 72.222 8.16 4.72 44.95 4.61
1125 2122 2.117156 CCAATGCCGCCCTCAGAAG 61.117 63.158 0.00 0.00 0.00 2.85
1190 2187 3.057548 CCACGCCATCTGCAGCAA 61.058 61.111 9.47 0.00 41.33 3.91
1197 2194 2.036256 ATCTGCAGCAACACCCCC 59.964 61.111 9.47 0.00 0.00 5.40
1302 2299 1.185618 TCCTCCCGGCGAATATCCTG 61.186 60.000 9.30 0.00 0.00 3.86
1359 2356 2.123640 GTCTCCTCCCTCTCCCCG 60.124 72.222 0.00 0.00 0.00 5.73
1360 2357 2.617538 TCTCCTCCCTCTCCCCGT 60.618 66.667 0.00 0.00 0.00 5.28
1368 2365 1.000486 CCTCTCCCCGTTCCTCTCA 60.000 63.158 0.00 0.00 0.00 3.27
1371 2368 0.631753 TCTCCCCGTTCCTCTCATCT 59.368 55.000 0.00 0.00 0.00 2.90
1644 2641 1.444553 CGAGCACGTCTCCAACTCC 60.445 63.158 0.00 0.00 38.62 3.85
1785 2782 2.667318 CGACGACAACAGCCGCAAT 61.667 57.895 0.00 0.00 0.00 3.56
1786 2783 1.154413 GACGACAACAGCCGCAATG 60.154 57.895 0.00 0.00 0.00 2.82
1787 2784 2.176546 CGACAACAGCCGCAATGG 59.823 61.111 0.00 0.00 42.50 3.16
1819 2816 3.558282 GACGACAACAACAGCCGCG 62.558 63.158 0.00 0.00 0.00 6.46
1841 2856 3.474904 CAACGGCGATGCGAACGA 61.475 61.111 16.62 0.00 34.22 3.85
1953 2968 2.815308 GCGAGGACGGTGATCCAT 59.185 61.111 0.00 0.00 41.73 3.41
2124 3139 7.270793 GTCGGTAATCATCGTCTATCATTACAC 59.729 40.741 0.00 0.00 33.40 2.90
2182 3197 1.079819 ACGCACGCTACATTGCTCT 60.080 52.632 0.00 0.00 36.54 4.09
2190 3205 1.808945 GCTACATTGCTCTGTGTTGCT 59.191 47.619 5.03 0.00 41.59 3.91
2196 3211 2.118313 TGCTCTGTGTTGCTATGCAT 57.882 45.000 3.79 3.79 38.76 3.96
2201 3216 1.200484 CTGTGTTGCTATGCATGCACA 59.800 47.619 25.37 11.52 45.09 4.57
2219 3249 1.001746 ACACTGCTGATGTCTGTGGAG 59.998 52.381 0.00 0.00 37.60 3.86
2220 3250 1.001746 CACTGCTGATGTCTGTGGAGT 59.998 52.381 0.00 0.00 32.14 3.85
2221 3251 1.001746 ACTGCTGATGTCTGTGGAGTG 59.998 52.381 0.00 0.00 0.00 3.51
2222 3252 1.274447 CTGCTGATGTCTGTGGAGTGA 59.726 52.381 0.00 0.00 0.00 3.41
2307 3341 8.018520 CGATAGAATAGTCAAGTGTAGGACATC 58.981 40.741 0.00 0.00 35.54 3.06
2333 3367 1.308047 GCACGGATAATGCATCACCA 58.692 50.000 0.00 0.00 42.88 4.17
2401 3435 1.987807 ATGCGGGTCCAGATTCCAGG 61.988 60.000 0.00 0.00 0.00 4.45
2459 3493 1.440353 GCATGTGTTCGTGTTCGCC 60.440 57.895 0.00 0.00 36.96 5.54
2514 3548 1.580845 GCATGCCTGTCACCTGTCAC 61.581 60.000 6.36 0.00 0.00 3.67
2588 3622 4.023193 ACTCATCGACAAAAACACCATTCC 60.023 41.667 0.00 0.00 0.00 3.01
2590 3624 4.582656 TCATCGACAAAAACACCATTCCTT 59.417 37.500 0.00 0.00 0.00 3.36
2823 3866 4.789075 TACGCGCACTCCTTCCGC 62.789 66.667 5.73 0.00 43.88 5.54
3117 4160 2.369001 GAGTCCTACCTGGGCCCT 59.631 66.667 25.70 5.02 42.71 5.19
3362 4409 2.002586 CCAAGGCATCTGAACTACGTG 58.997 52.381 0.00 0.00 0.00 4.49
3365 4416 1.090052 GGCATCTGAACTACGTGGGC 61.090 60.000 3.26 0.00 0.00 5.36
3378 4429 1.002366 CGTGGGCTCTCAAGAATTCG 58.998 55.000 0.00 0.00 0.00 3.34
3379 4430 1.673033 CGTGGGCTCTCAAGAATTCGT 60.673 52.381 0.00 0.00 0.00 3.85
3383 4434 2.168728 GGGCTCTCAAGAATTCGTAGGT 59.831 50.000 0.00 0.00 0.00 3.08
3394 4445 9.151471 TCAAGAATTCGTAGGTTTAATCTTGAG 57.849 33.333 9.98 0.00 36.14 3.02
3489 4540 7.993101 TGAATCAGATGATTTTTGGATCTGTC 58.007 34.615 9.33 0.00 44.14 3.51
3491 4542 7.949690 ATCAGATGATTTTTGGATCTGTCAA 57.050 32.000 0.00 0.00 42.48 3.18
3500 4551 7.581213 TTTTTGGATCTGTCAAGTGTACAAT 57.419 32.000 0.00 0.00 0.00 2.71
3503 4554 5.482006 TGGATCTGTCAAGTGTACAATCAG 58.518 41.667 0.00 0.19 0.00 2.90
3538 4594 8.985315 TTTACTATTTGGAATGCAGATGATCT 57.015 30.769 0.00 0.00 0.00 2.75
3542 4598 9.412460 ACTATTTGGAATGCAGATGATCTTTTA 57.588 29.630 0.00 0.00 0.00 1.52
3591 4655 0.706433 ATTTGTGATCTGGTGGGGCT 59.294 50.000 0.00 0.00 0.00 5.19
3597 4661 3.177228 GTGATCTGGTGGGGCTAGATAT 58.823 50.000 0.00 0.00 44.09 1.63
3598 4662 3.196685 GTGATCTGGTGGGGCTAGATATC 59.803 52.174 0.00 0.00 44.09 1.63
3773 4844 1.335324 GCACACAACATCCAGCTTCAC 60.335 52.381 0.00 0.00 0.00 3.18
3780 4851 1.003355 ATCCAGCTTCACACCCACG 60.003 57.895 0.00 0.00 0.00 4.94
3781 4852 1.480212 ATCCAGCTTCACACCCACGA 61.480 55.000 0.00 0.00 0.00 4.35
3782 4853 1.669115 CCAGCTTCACACCCACGAG 60.669 63.158 0.00 0.00 0.00 4.18
3783 4854 1.367471 CAGCTTCACACCCACGAGA 59.633 57.895 0.00 0.00 0.00 4.04
3784 4855 0.668706 CAGCTTCACACCCACGAGAG 60.669 60.000 0.00 0.00 0.00 3.20
3785 4856 0.827925 AGCTTCACACCCACGAGAGA 60.828 55.000 0.00 0.00 0.00 3.10
3786 4857 0.389166 GCTTCACACCCACGAGAGAG 60.389 60.000 0.00 0.00 0.00 3.20
3787 4858 1.248486 CTTCACACCCACGAGAGAGA 58.752 55.000 0.00 0.00 0.00 3.10
3788 4859 1.201181 CTTCACACCCACGAGAGAGAG 59.799 57.143 0.00 0.00 0.00 3.20
3789 4860 0.400594 TCACACCCACGAGAGAGAGA 59.599 55.000 0.00 0.00 0.00 3.10
3790 4861 0.808125 CACACCCACGAGAGAGAGAG 59.192 60.000 0.00 0.00 0.00 3.20
3791 4862 0.693622 ACACCCACGAGAGAGAGAGA 59.306 55.000 0.00 0.00 0.00 3.10
3792 4863 1.339631 ACACCCACGAGAGAGAGAGAG 60.340 57.143 0.00 0.00 0.00 3.20
3793 4864 1.065782 CACCCACGAGAGAGAGAGAGA 60.066 57.143 0.00 0.00 0.00 3.10
3851 4922 5.874261 TCAGTGTTGATGATTGATTCGCTAA 59.126 36.000 0.00 0.00 0.00 3.09
3853 4924 6.849811 CAGTGTTGATGATTGATTCGCTAATC 59.150 38.462 4.06 4.06 41.69 1.75
3906 4979 8.225603 AGAGAGAGAGAGATGAACATAGTTTC 57.774 38.462 0.00 0.00 0.00 2.78
3908 4981 8.593945 AGAGAGAGAGATGAACATAGTTTCTT 57.406 34.615 0.00 0.00 0.00 2.52
3913 4986 9.225436 AGAGAGATGAACATAGTTTCTTTTTCC 57.775 33.333 0.00 0.00 0.00 3.13
3914 4987 9.225436 GAGAGATGAACATAGTTTCTTTTTCCT 57.775 33.333 0.00 0.00 0.00 3.36
3915 4988 9.579932 AGAGATGAACATAGTTTCTTTTTCCTT 57.420 29.630 0.00 0.00 0.00 3.36
3918 4991 9.411801 GATGAACATAGTTTCTTTTTCCTTTCC 57.588 33.333 0.00 0.00 0.00 3.13
3919 4992 8.533569 TGAACATAGTTTCTTTTTCCTTTCCT 57.466 30.769 0.00 0.00 0.00 3.36
3920 4993 8.977412 TGAACATAGTTTCTTTTTCCTTTCCTT 58.023 29.630 0.00 0.00 0.00 3.36
3921 4994 9.817809 GAACATAGTTTCTTTTTCCTTTCCTTT 57.182 29.630 0.00 0.00 0.00 3.11
3960 5048 5.703592 TGGTCGACATAATTTTGCTAACTGT 59.296 36.000 18.91 0.00 0.00 3.55
3961 5049 6.205853 TGGTCGACATAATTTTGCTAACTGTT 59.794 34.615 18.91 0.00 0.00 3.16
3962 5050 7.081976 GGTCGACATAATTTTGCTAACTGTTT 58.918 34.615 18.91 0.00 0.00 2.83
3963 5051 7.060633 GGTCGACATAATTTTGCTAACTGTTTG 59.939 37.037 18.91 0.00 0.00 2.93
3964 5052 7.589954 GTCGACATAATTTTGCTAACTGTTTGT 59.410 33.333 11.55 0.00 0.00 2.83
3979 5072 6.234723 ACTGTTTGTTTGCGATTTTGTTTT 57.765 29.167 0.00 0.00 0.00 2.43
3998 6696 7.825627 TGTTTTAACGAAAATCGCTTTCTAC 57.174 32.000 0.00 0.00 45.12 2.59
4014 6712 5.995897 GCTTTCTACAGTTCTTTAACTCCCA 59.004 40.000 0.00 0.00 44.28 4.37
4015 6713 6.073167 GCTTTCTACAGTTCTTTAACTCCCAC 60.073 42.308 0.00 0.00 44.28 4.61
4017 6715 6.742559 TCTACAGTTCTTTAACTCCCACTT 57.257 37.500 0.00 0.00 44.28 3.16
4040 6738 5.514169 TCAGTGAGAACAGAGGATGATACT 58.486 41.667 0.00 0.00 0.00 2.12
4041 6739 5.359292 TCAGTGAGAACAGAGGATGATACTG 59.641 44.000 0.00 0.00 37.62 2.74
4042 6740 5.359292 CAGTGAGAACAGAGGATGATACTGA 59.641 44.000 0.00 0.00 35.15 3.41
4043 6741 6.040729 CAGTGAGAACAGAGGATGATACTGAT 59.959 42.308 0.00 0.00 35.15 2.90
4044 6742 7.230309 CAGTGAGAACAGAGGATGATACTGATA 59.770 40.741 0.00 0.00 35.15 2.15
4045 6743 7.230510 AGTGAGAACAGAGGATGATACTGATAC 59.769 40.741 0.00 0.00 35.85 2.24
4046 6744 6.491745 TGAGAACAGAGGATGATACTGATACC 59.508 42.308 0.00 0.00 35.85 2.73
4047 6745 6.619464 AGAACAGAGGATGATACTGATACCT 58.381 40.000 0.00 0.00 35.85 3.08
4090 6788 2.271497 GGCTGGCTGCAGTGATCT 59.729 61.111 16.64 0.00 45.15 2.75
4091 6789 1.818785 GGCTGGCTGCAGTGATCTC 60.819 63.158 16.64 0.00 45.15 2.75
4093 6791 1.367599 GCTGGCTGCAGTGATCTCAC 61.368 60.000 16.64 2.01 46.77 3.51
4122 6823 4.410228 CAGATCTCCCCACCTATCTTTTCA 59.590 45.833 0.00 0.00 0.00 2.69
4148 6849 6.598064 TCGACACAAGTAGTATCAAGATCTCA 59.402 38.462 0.00 0.00 0.00 3.27
4192 6901 9.915629 CTAACTGTTTCTGTATACAAAGAGTCT 57.084 33.333 16.27 11.11 35.62 3.24
4338 7047 2.432444 CTGTGCTTCCGGTTATTCCAA 58.568 47.619 0.00 0.00 35.57 3.53
4361 7070 6.851222 ATTATTGCTCTTACTTGATCGGTG 57.149 37.500 2.01 0.00 0.00 4.94
4380 7089 3.010144 CCCCCACCCCTTGATCAG 58.990 66.667 0.00 0.00 0.00 2.90
4381 7090 1.930656 CCCCCACCCCTTGATCAGT 60.931 63.158 0.00 0.00 0.00 3.41
4382 7091 1.509548 CCCCCACCCCTTGATCAGTT 61.510 60.000 0.00 0.00 0.00 3.16
4383 7092 0.034089 CCCCACCCCTTGATCAGTTC 60.034 60.000 0.00 0.00 0.00 3.01
4384 7093 0.698238 CCCACCCCTTGATCAGTTCA 59.302 55.000 0.00 0.00 0.00 3.18
4385 7094 1.340405 CCCACCCCTTGATCAGTTCAG 60.340 57.143 0.00 0.00 35.27 3.02
4386 7095 1.630369 CCACCCCTTGATCAGTTCAGA 59.370 52.381 0.00 0.00 35.27 3.27
4417 7394 1.129437 GCCACTTCTGATCGTTCTTGC 59.871 52.381 0.00 0.00 0.00 4.01
4498 7475 1.201429 GGTGACCTGGACTCCCACAT 61.201 60.000 0.00 0.00 37.58 3.21
4504 7481 2.439156 GGACTCCCACATGCCTGC 60.439 66.667 0.00 0.00 0.00 4.85
4525 7502 4.143194 CTCTCACAGCACAAAATGAGTG 57.857 45.455 0.00 0.00 39.68 3.51
4528 7505 2.291465 TCACAGCACAAAATGAGTGAGC 59.709 45.455 0.00 0.00 38.92 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 5.123027 CAGTTGGCTGAGACTTAAGGAAATC 59.877 44.000 7.53 0.00 45.28 2.17
20 21 4.102524 TCAGTTGGCTGAGACTTAAGGAAA 59.897 41.667 7.53 0.00 45.94 3.13
38 39 3.788227 TGATGTGGCTAGGTTTCAGTT 57.212 42.857 0.00 0.00 0.00 3.16
56 57 7.436673 CGAATTGGTACCACTTTTCAAAAATGA 59.563 33.333 16.04 0.00 0.00 2.57
58 59 7.269316 ACGAATTGGTACCACTTTTCAAAAAT 58.731 30.769 16.04 0.00 0.00 1.82
91 92 7.040478 TGCATTGATACTTACCATAATTGAGGC 60.040 37.037 0.00 0.00 0.00 4.70
114 115 7.097192 AGTCTTTAGATCGAGTTAATTGTGCA 58.903 34.615 0.00 0.00 0.00 4.57
148 149 4.638421 CACGCATAGGGAAAATACCTGAAA 59.362 41.667 0.00 0.00 39.12 2.69
161 162 5.784177 ACTGATAAATAGACACGCATAGGG 58.216 41.667 0.00 0.00 0.00 3.53
162 163 5.569441 CGACTGATAAATAGACACGCATAGG 59.431 44.000 0.00 0.00 0.00 2.57
165 166 4.976731 GTCGACTGATAAATAGACACGCAT 59.023 41.667 8.70 0.00 0.00 4.73
166 167 4.095932 AGTCGACTGATAAATAGACACGCA 59.904 41.667 19.30 0.00 0.00 5.24
228 229 2.100197 AGACGTTGGATCTTGATCCGA 58.900 47.619 20.69 17.49 43.62 4.55
248 249 4.271807 AGAGGTGGAAGATGATGTCCTA 57.728 45.455 0.00 0.00 34.77 2.94
259 260 2.027653 GGTGAGGAAGAAGAGGTGGAAG 60.028 54.545 0.00 0.00 0.00 3.46
260 261 1.978580 GGTGAGGAAGAAGAGGTGGAA 59.021 52.381 0.00 0.00 0.00 3.53
261 262 1.645710 GGTGAGGAAGAAGAGGTGGA 58.354 55.000 0.00 0.00 0.00 4.02
262 263 0.615850 GGGTGAGGAAGAAGAGGTGG 59.384 60.000 0.00 0.00 0.00 4.61
263 264 0.247736 CGGGTGAGGAAGAAGAGGTG 59.752 60.000 0.00 0.00 0.00 4.00
264 265 0.114560 TCGGGTGAGGAAGAAGAGGT 59.885 55.000 0.00 0.00 0.00 3.85
265 266 1.410882 GATCGGGTGAGGAAGAAGAGG 59.589 57.143 0.00 0.00 0.00 3.69
266 267 1.410882 GGATCGGGTGAGGAAGAAGAG 59.589 57.143 0.00 0.00 0.00 2.85
267 268 1.486211 GGATCGGGTGAGGAAGAAGA 58.514 55.000 0.00 0.00 0.00 2.87
298 1294 4.025401 GTTCGTGGTGGCGGCTTG 62.025 66.667 11.43 0.00 0.00 4.01
305 1301 4.244463 ACCGGTGGTTCGTGGTGG 62.244 66.667 6.12 0.00 32.33 4.61
306 1302 2.970324 CACCGGTGGTTCGTGGTG 60.970 66.667 27.57 0.00 45.17 4.17
307 1303 4.922026 GCACCGGTGGTTCGTGGT 62.922 66.667 34.58 0.00 31.02 4.16
308 1304 4.619227 AGCACCGGTGGTTCGTGG 62.619 66.667 32.82 6.70 38.24 4.94
309 1305 3.041940 GAGCACCGGTGGTTCGTG 61.042 66.667 37.42 11.31 41.93 4.35
310 1306 4.657824 CGAGCACCGGTGGTTCGT 62.658 66.667 37.42 10.89 41.93 3.85
333 1329 2.411765 AAAACCAGCGGGGAGGACAG 62.412 60.000 8.08 0.00 41.15 3.51
334 1330 2.406002 GAAAACCAGCGGGGAGGACA 62.406 60.000 8.08 0.00 41.15 4.02
335 1331 1.674651 GAAAACCAGCGGGGAGGAC 60.675 63.158 8.08 0.00 41.15 3.85
336 1332 1.423794 AAGAAAACCAGCGGGGAGGA 61.424 55.000 8.08 0.00 41.15 3.71
337 1333 0.960861 GAAGAAAACCAGCGGGGAGG 60.961 60.000 8.08 0.00 41.15 4.30
338 1334 0.960861 GGAAGAAAACCAGCGGGGAG 60.961 60.000 8.08 0.00 41.15 4.30
339 1335 1.074248 GGAAGAAAACCAGCGGGGA 59.926 57.895 8.08 0.00 41.15 4.81
340 1336 3.681473 GGAAGAAAACCAGCGGGG 58.319 61.111 8.08 1.20 44.81 5.73
869 1865 6.646240 CGATTGAATTTTGAAGTTGGGTCATT 59.354 34.615 0.00 0.00 0.00 2.57
872 1868 5.629435 GTCGATTGAATTTTGAAGTTGGGTC 59.371 40.000 0.00 0.00 0.00 4.46
873 1869 5.301805 AGTCGATTGAATTTTGAAGTTGGGT 59.698 36.000 0.00 0.00 0.00 4.51
905 1901 4.036518 AGTCAGGGAAGATCACAATAGCT 58.963 43.478 0.00 0.00 0.00 3.32
912 1908 1.407258 CTCCGAGTCAGGGAAGATCAC 59.593 57.143 0.00 0.00 32.02 3.06
913 1909 1.006043 ACTCCGAGTCAGGGAAGATCA 59.994 52.381 0.00 0.00 32.02 2.92
914 1910 1.770294 ACTCCGAGTCAGGGAAGATC 58.230 55.000 0.00 0.00 32.02 2.75
917 1914 1.135333 GCTAACTCCGAGTCAGGGAAG 59.865 57.143 0.35 0.00 32.02 3.46
922 1919 2.455032 CGAATGCTAACTCCGAGTCAG 58.545 52.381 0.35 0.00 0.00 3.51
928 1925 1.692148 TTGCGCGAATGCTAACTCCG 61.692 55.000 12.10 0.00 39.65 4.63
966 1963 8.247562 GGTAGGCAGAGACATATATAAGTTCTG 58.752 40.741 17.03 17.03 35.03 3.02
1049 2046 2.086251 GATGAGGAGAGCTGGCGAGG 62.086 65.000 0.00 0.00 0.00 4.63
1070 2067 1.229209 ACGAGGACCACCAGGATGT 60.229 57.895 0.00 0.00 38.69 3.06
1077 2074 4.736896 GTGGCGACGAGGACCACC 62.737 72.222 10.28 0.00 46.65 4.61
1296 2293 2.827190 AGCGCGACCGACAGGATA 60.827 61.111 12.10 0.00 41.02 2.59
1332 2329 2.124653 GAGGAGACGGCCGAGAGA 60.125 66.667 35.90 0.00 0.00 3.10
1359 2356 2.032377 CGAGAGCGTAGATGAGAGGAAC 60.032 54.545 0.00 0.00 0.00 3.62
1360 2357 2.214347 CGAGAGCGTAGATGAGAGGAA 58.786 52.381 0.00 0.00 0.00 3.36
1368 2365 2.913060 GGGGCCGAGAGCGTAGAT 60.913 66.667 0.00 0.00 45.17 1.98
1740 2737 1.207085 GTCGCTGTCTTCGTCGTCT 59.793 57.895 0.00 0.00 0.00 4.18
1792 2789 3.456039 GTTGTCGTCGTCGTCGCC 61.456 66.667 7.01 0.00 38.33 5.54
1793 2790 2.287965 TTGTTGTCGTCGTCGTCGC 61.288 57.895 7.01 3.63 38.33 5.19
1798 2795 1.563173 GGCTGTTGTTGTCGTCGTC 59.437 57.895 0.00 0.00 0.00 4.20
1829 2826 4.543736 CGCTGTCGTTCGCATCGC 62.544 66.667 0.00 0.00 0.00 4.58
1830 2827 3.902063 CCGCTGTCGTTCGCATCG 61.902 66.667 0.00 6.14 0.00 3.84
1835 2832 4.753877 TCTCGCCGCTGTCGTTCG 62.754 66.667 0.00 0.00 0.00 3.95
1836 2833 3.173240 GTCTCGCCGCTGTCGTTC 61.173 66.667 0.00 0.00 0.00 3.95
1935 2950 3.138930 ATGGATCACCGTCCTCGCG 62.139 63.158 0.00 0.00 39.12 5.87
1953 2968 2.601067 TACGTCCCGGCCTTCACA 60.601 61.111 0.00 0.00 0.00 3.58
1995 3010 0.294887 GCGCGATGTTCGTCTTGTAG 59.705 55.000 12.10 0.00 42.81 2.74
2124 3139 3.244422 TGTGCAGGTAGAGTTGGTTAAGG 60.244 47.826 0.00 0.00 0.00 2.69
2201 3216 1.001746 CACTCCACAGACATCAGCAGT 59.998 52.381 0.00 0.00 0.00 4.40
2219 3249 2.618241 TGAAGAACAATGCCACAGTCAC 59.382 45.455 0.00 0.00 0.00 3.67
2220 3250 2.618241 GTGAAGAACAATGCCACAGTCA 59.382 45.455 0.00 0.00 0.00 3.41
2221 3251 2.349817 CGTGAAGAACAATGCCACAGTC 60.350 50.000 0.00 0.00 0.00 3.51
2222 3252 1.603802 CGTGAAGAACAATGCCACAGT 59.396 47.619 0.00 0.00 0.00 3.55
2307 3341 1.001158 TGCATTATCCGTGCATGCATG 60.001 47.619 29.36 29.36 46.53 4.06
2333 3367 0.976641 TGCGTCAGACCAGATTCCTT 59.023 50.000 0.00 0.00 0.00 3.36
2401 3435 1.517257 CGACTCGACTCATGCACCC 60.517 63.158 0.00 0.00 0.00 4.61
2459 3493 2.596904 TTCGGATTTTAGCTCGAGGG 57.403 50.000 15.58 0.00 33.11 4.30
2514 3548 1.812571 AGTTAAGAGCGGCCAACATTG 59.187 47.619 2.24 0.00 0.00 2.82
2588 3622 2.809601 CGCTCGTTGGGACCGAAG 60.810 66.667 0.00 0.00 33.34 3.79
2823 3866 1.805945 GCACTCGCGGTAGAACTGG 60.806 63.158 6.13 0.00 0.00 4.00
2964 4007 2.346365 GTGTCCTGGTTCGGGTCC 59.654 66.667 0.00 0.00 0.00 4.46
3322 4365 1.305887 CGTAGGGGAAGGAGGTGGT 60.306 63.158 0.00 0.00 0.00 4.16
3362 4409 2.168728 ACCTACGAATTCTTGAGAGCCC 59.831 50.000 3.52 0.00 0.00 5.19
3365 4416 8.934507 AGATTAAACCTACGAATTCTTGAGAG 57.065 34.615 3.52 0.00 0.00 3.20
3378 4429 7.413109 GCAGTAACAGCTCAAGATTAAACCTAC 60.413 40.741 0.00 0.00 0.00 3.18
3379 4430 6.594159 GCAGTAACAGCTCAAGATTAAACCTA 59.406 38.462 0.00 0.00 0.00 3.08
3383 4434 4.994852 ACGCAGTAACAGCTCAAGATTAAA 59.005 37.500 0.00 0.00 41.94 1.52
3394 4445 3.413558 CCGAAATTAACGCAGTAACAGC 58.586 45.455 0.00 0.00 45.00 4.40
3489 4540 4.060900 ACTGCTGACTGATTGTACACTTG 58.939 43.478 0.00 0.00 0.00 3.16
3491 4542 4.342862 AACTGCTGACTGATTGTACACT 57.657 40.909 0.00 0.00 0.00 3.55
3500 4551 6.995686 TCCAAATAGTAAAAACTGCTGACTGA 59.004 34.615 0.00 0.00 0.00 3.41
3503 4554 7.062255 GCATTCCAAATAGTAAAAACTGCTGAC 59.938 37.037 0.00 0.00 0.00 3.51
3558 4616 8.758715 CCAGATCACAAATTCAAAGAAAAGTTC 58.241 33.333 0.00 0.00 0.00 3.01
3576 4637 1.428869 ATCTAGCCCCACCAGATCAC 58.571 55.000 0.00 0.00 0.00 3.06
3591 4655 7.062749 ACCACTTAGAAAATGGCGATATCTA 57.937 36.000 0.34 1.54 36.96 1.98
3597 4661 2.739913 CGAACCACTTAGAAAATGGCGA 59.260 45.455 0.00 0.00 36.96 5.54
3598 4662 2.482721 ACGAACCACTTAGAAAATGGCG 59.517 45.455 0.00 0.00 36.96 5.69
3704 4774 4.548669 ACAGTAGGATCTCCTTAACCTCC 58.451 47.826 3.64 0.00 46.09 4.30
3773 4844 1.065782 TCTCTCTCTCTCTCGTGGGTG 60.066 57.143 0.00 0.00 0.00 4.61
3780 4851 4.892934 ACTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.00 0.00 3.20
3781 4852 4.877773 ACTCTCTCTCTCTCTCTCTCTCT 58.122 47.826 0.00 0.00 0.00 3.10
3782 4853 5.362430 AGAACTCTCTCTCTCTCTCTCTCTC 59.638 48.000 0.00 0.00 0.00 3.20
3783 4854 5.276440 AGAACTCTCTCTCTCTCTCTCTCT 58.724 45.833 0.00 0.00 0.00 3.10
3784 4855 5.606348 AGAACTCTCTCTCTCTCTCTCTC 57.394 47.826 0.00 0.00 0.00 3.20
3785 4856 5.364157 GGTAGAACTCTCTCTCTCTCTCTCT 59.636 48.000 0.00 0.00 32.70 3.10
3786 4857 5.602628 GGTAGAACTCTCTCTCTCTCTCTC 58.397 50.000 0.00 0.00 32.70 3.20
3787 4858 4.099573 CGGTAGAACTCTCTCTCTCTCTCT 59.900 50.000 0.00 0.00 32.70 3.10
3788 4859 4.098960 TCGGTAGAACTCTCTCTCTCTCTC 59.901 50.000 0.00 0.00 32.70 3.20
3789 4860 4.028131 TCGGTAGAACTCTCTCTCTCTCT 58.972 47.826 0.00 0.00 32.70 3.10
3790 4861 4.117685 GTCGGTAGAACTCTCTCTCTCTC 58.882 52.174 0.00 0.00 32.70 3.20
3791 4862 3.773119 AGTCGGTAGAACTCTCTCTCTCT 59.227 47.826 0.00 0.00 32.70 3.10
3792 4863 4.133013 AGTCGGTAGAACTCTCTCTCTC 57.867 50.000 0.00 0.00 32.70 3.20
3793 4864 4.258543 CAAGTCGGTAGAACTCTCTCTCT 58.741 47.826 0.00 0.00 32.70 3.10
3880 4951 7.807977 AACTATGTTCATCTCTCTCTCTCTC 57.192 40.000 0.00 0.00 0.00 3.20
3906 4979 7.905604 ACAAACAGAAAAGGAAAGGAAAAAG 57.094 32.000 0.00 0.00 0.00 2.27
3908 4981 7.389330 GGAAACAAACAGAAAAGGAAAGGAAAA 59.611 33.333 0.00 0.00 0.00 2.29
3911 4984 5.482175 TGGAAACAAACAGAAAAGGAAAGGA 59.518 36.000 0.00 0.00 37.44 3.36
3912 4985 5.729510 TGGAAACAAACAGAAAAGGAAAGG 58.270 37.500 0.00 0.00 37.44 3.11
3960 5048 7.045725 TCGTTAAAACAAAATCGCAAACAAA 57.954 28.000 0.00 0.00 0.00 2.83
3961 5049 6.627690 TCGTTAAAACAAAATCGCAAACAA 57.372 29.167 0.00 0.00 0.00 2.83
3962 5050 6.627690 TTCGTTAAAACAAAATCGCAAACA 57.372 29.167 0.00 0.00 0.00 2.83
3963 5051 7.918497 TTTTCGTTAAAACAAAATCGCAAAC 57.082 28.000 0.00 0.00 29.59 2.93
3964 5052 7.575894 CGATTTTCGTTAAAACAAAATCGCAAA 59.424 29.630 27.97 7.33 46.54 3.68
3990 6688 5.995897 TGGGAGTTAAAGAACTGTAGAAAGC 59.004 40.000 0.00 0.00 46.23 3.51
3998 6696 5.237344 CACTGAAGTGGGAGTTAAAGAACTG 59.763 44.000 2.35 0.00 42.79 3.16
4014 6712 4.155709 TCATCCTCTGTTCTCACTGAAGT 58.844 43.478 0.00 0.00 35.01 3.01
4015 6713 4.797800 TCATCCTCTGTTCTCACTGAAG 57.202 45.455 0.00 0.00 35.01 3.02
4017 6715 5.359292 CAGTATCATCCTCTGTTCTCACTGA 59.641 44.000 0.00 0.00 33.24 3.41
4046 6744 3.464907 CAATATGTGGCCTCTGACTGAG 58.535 50.000 3.32 2.46 42.30 3.35
4047 6745 2.420547 GCAATATGTGGCCTCTGACTGA 60.421 50.000 3.32 0.00 0.00 3.41
4054 6752 1.342174 CCCATTGCAATATGTGGCCTC 59.658 52.381 12.53 0.00 0.00 4.70
4090 6788 1.203428 TGGGGAGATCTGAAAGGGTGA 60.203 52.381 0.00 0.00 0.00 4.02
4091 6789 1.065126 GTGGGGAGATCTGAAAGGGTG 60.065 57.143 0.00 0.00 0.00 4.61
4093 6791 0.548510 GGTGGGGAGATCTGAAAGGG 59.451 60.000 0.00 0.00 0.00 3.95
4094 6792 1.589414 AGGTGGGGAGATCTGAAAGG 58.411 55.000 0.00 0.00 0.00 3.11
4095 6793 4.230455 AGATAGGTGGGGAGATCTGAAAG 58.770 47.826 0.00 0.00 0.00 2.62
4096 6794 4.286813 AGATAGGTGGGGAGATCTGAAA 57.713 45.455 0.00 0.00 0.00 2.69
4122 6823 7.283354 TGAGATCTTGATACTACTTGTGTCGAT 59.717 37.037 0.00 0.00 39.29 3.59
4148 6849 5.828328 CAGTTAGAAAGGTTTCTGAAAGGGT 59.172 40.000 14.08 0.00 46.34 4.34
4321 7030 5.451242 GCAATAATTGGAATAACCGGAAGCA 60.451 40.000 9.46 0.00 42.61 3.91
4322 7031 4.982295 GCAATAATTGGAATAACCGGAAGC 59.018 41.667 9.46 0.00 42.61 3.86
4324 7033 6.126409 AGAGCAATAATTGGAATAACCGGAA 58.874 36.000 9.46 0.00 42.61 4.30
4338 7047 5.237344 GCACCGATCAAGTAAGAGCAATAAT 59.763 40.000 0.00 0.00 0.00 1.28
4376 7085 3.617045 GCAGCTCTGAAGTCTGAACTGAT 60.617 47.826 17.69 0.00 39.09 2.90
4380 7089 1.270518 TGGCAGCTCTGAAGTCTGAAC 60.271 52.381 0.29 0.22 31.98 3.18
4381 7090 1.051008 TGGCAGCTCTGAAGTCTGAA 58.949 50.000 0.29 0.00 31.98 3.02
4382 7091 0.319728 GTGGCAGCTCTGAAGTCTGA 59.680 55.000 0.29 0.00 31.98 3.27
4383 7092 0.321021 AGTGGCAGCTCTGAAGTCTG 59.679 55.000 0.29 0.00 32.87 3.51
4384 7093 1.001860 GAAGTGGCAGCTCTGAAGTCT 59.998 52.381 0.29 0.00 0.00 3.24
4385 7094 1.001860 AGAAGTGGCAGCTCTGAAGTC 59.998 52.381 0.29 0.00 0.00 3.01
4386 7095 1.055040 AGAAGTGGCAGCTCTGAAGT 58.945 50.000 0.29 0.00 0.00 3.01
4417 7394 2.870161 CGACGACGGTCTTCTGCG 60.870 66.667 12.10 0.00 41.16 5.18
4504 7481 3.811497 TCACTCATTTTGTGCTGTGAGAG 59.189 43.478 8.09 0.92 40.30 3.20
4525 7502 3.870419 GTCTGATGATCAACCTGAAGCTC 59.130 47.826 0.00 0.00 0.00 4.09
4528 7505 5.485620 TCTTGTCTGATGATCAACCTGAAG 58.514 41.667 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.