Multiple sequence alignment - TraesCS3A01G032100

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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 TraesCS3A01G032100 chr3A 100.000 3654 0 0 1 3654 17607812 17604159 0.000000e+00 6748.0
1 TraesCS3A01G032100 chr3A 95.349 43 2 0 644 686 17623205 17623163 6.550000e-08 69.4
2 TraesCS3A01G032100 chr3D 92.667 2700 124 24 207 2852 10659743 10662422 0.000000e+00 3821.0
3 TraesCS3A01G032100 chr3D 85.457 832 74 22 2850 3654 10662450 10663261 0.000000e+00 822.0
4 TraesCS3A01G032100 chr3D 79.438 1138 171 38 966 2077 10723548 10724648 0.000000e+00 747.0
5 TraesCS3A01G032100 chr3D 88.650 511 53 4 1665 2173 10647252 10647759 5.180000e-173 617.0
6 TraesCS3A01G032100 chr3D 77.108 1079 194 32 1022 2077 10709680 10710728 3.160000e-160 575.0
7 TraesCS3A01G032100 chr3D 80.341 646 81 29 790 1410 10646619 10647243 7.200000e-122 448.0
8 TraesCS3A01G032100 chr3D 88.816 152 14 3 981 1131 10392622 10392473 2.240000e-42 183.0
9 TraesCS3A01G032100 chr3B 92.273 1540 68 12 1335 2837 26532128 26530603 0.000000e+00 2137.0
10 TraesCS3A01G032100 chr3B 89.390 1065 80 15 226 1272 26533177 26532128 0.000000e+00 1310.0
11 TraesCS3A01G032100 chr3B 83.268 1022 141 17 1070 2077 15054503 15055508 0.000000e+00 913.0
12 TraesCS3A01G032100 chr3B 82.016 1101 150 18 979 2069 14402579 14401517 0.000000e+00 893.0
13 TraesCS3A01G032100 chr3B 89.209 556 60 0 1596 2151 26578112 26577557 0.000000e+00 695.0
14 TraesCS3A01G032100 chr3B 88.178 516 41 13 2854 3365 26530551 26530052 6.750000e-167 597.0
15 TraesCS3A01G032100 chr3B 81.386 736 101 20 878 1593 26583965 26583246 5.300000e-158 568.0
16 TraesCS3A01G032100 chr3B 95.349 43 2 0 644 686 15053342 15053384 6.550000e-08 69.4
17 TraesCS3A01G032100 chr1B 79.767 1290 207 38 908 2157 61943833 61942558 0.000000e+00 887.0
18 TraesCS3A01G032100 chr1A 80.130 1233 189 42 933 2127 41759492 41758278 0.000000e+00 869.0
19 TraesCS3A01G032100 chr6A 88.513 679 74 4 850 1527 318019171 318018496 0.000000e+00 819.0
20 TraesCS3A01G032100 chr1D 84.868 793 109 9 1374 2157 41757563 41756773 0.000000e+00 789.0


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 TraesCS3A01G032100 chr3A 17604159 17607812 3653 True 6748.0 6748 100.0000 1 3654 1 chr3A.!!$R1 3653
1 TraesCS3A01G032100 chr3D 10659743 10663261 3518 False 2321.5 3821 89.0620 207 3654 2 chr3D.!!$F4 3447
2 TraesCS3A01G032100 chr3D 10723548 10724648 1100 False 747.0 747 79.4380 966 2077 1 chr3D.!!$F2 1111
3 TraesCS3A01G032100 chr3D 10709680 10710728 1048 False 575.0 575 77.1080 1022 2077 1 chr3D.!!$F1 1055
4 TraesCS3A01G032100 chr3D 10646619 10647759 1140 False 532.5 617 84.4955 790 2173 2 chr3D.!!$F3 1383
5 TraesCS3A01G032100 chr3B 26530052 26533177 3125 True 1348.0 2137 89.9470 226 3365 3 chr3B.!!$R4 3139
6 TraesCS3A01G032100 chr3B 14401517 14402579 1062 True 893.0 893 82.0160 979 2069 1 chr3B.!!$R1 1090
7 TraesCS3A01G032100 chr3B 26577557 26578112 555 True 695.0 695 89.2090 1596 2151 1 chr3B.!!$R2 555
8 TraesCS3A01G032100 chr3B 26583246 26583965 719 True 568.0 568 81.3860 878 1593 1 chr3B.!!$R3 715
9 TraesCS3A01G032100 chr3B 15053342 15055508 2166 False 491.2 913 89.3085 644 2077 2 chr3B.!!$F1 1433
10 TraesCS3A01G032100 chr1B 61942558 61943833 1275 True 887.0 887 79.7670 908 2157 1 chr1B.!!$R1 1249
11 TraesCS3A01G032100 chr1A 41758278 41759492 1214 True 869.0 869 80.1300 933 2127 1 chr1A.!!$R1 1194
12 TraesCS3A01G032100 chr6A 318018496 318019171 675 True 819.0 819 88.5130 850 1527 1 chr6A.!!$R1 677
13 TraesCS3A01G032100 chr1D 41756773 41757563 790 True 789.0 789 84.8680 1374 2157 1 chr1D.!!$R1 783

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
250 251 0.337773 TCATCCAGCCCACTCTCTCT 59.662 55.0 0.0 0.0 0.00 3.10 F
364 372 0.754957 CTCATCTCTCCGGTCAGGCT 60.755 60.0 0.0 0.0 40.77 4.58 F
2223 3197 0.558712 GCTAAGGAGGAGGAGGAGGA 59.441 60.0 0.0 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2223 3197 0.336737 ATTCTCGTCCTCCTCCACCT 59.663 55.0 0.00 0.0 0.00 4.00 R
2356 3345 2.224523 CCTTAGTTGAACAGCAGGGTGA 60.225 50.0 5.37 0.0 0.00 4.02 R
3248 4294 0.036105 TGATCAGCCACTGCACGAAT 60.036 50.0 0.00 0.0 41.13 3.34 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
167 168 7.806409 TTTAGCGGAGGTTTTAAAGTTTAGT 57.194 32.000 0.00 0.00 40.68 2.24
168 169 8.900983 TTTAGCGGAGGTTTTAAAGTTTAGTA 57.099 30.769 0.00 0.00 40.68 1.82
169 170 6.791887 AGCGGAGGTTTTAAAGTTTAGTAC 57.208 37.500 0.00 0.00 27.67 2.73
170 171 5.406477 AGCGGAGGTTTTAAAGTTTAGTACG 59.594 40.000 0.00 0.00 27.67 3.67
171 172 5.405269 GCGGAGGTTTTAAAGTTTAGTACGA 59.595 40.000 0.00 0.00 0.00 3.43
172 173 6.073819 GCGGAGGTTTTAAAGTTTAGTACGAA 60.074 38.462 0.00 0.00 0.00 3.85
173 174 7.504818 CGGAGGTTTTAAAGTTTAGTACGAAG 58.495 38.462 0.00 0.00 0.00 3.79
174 175 7.359514 CGGAGGTTTTAAAGTTTAGTACGAAGG 60.360 40.741 0.00 0.00 0.00 3.46
175 176 7.194607 AGGTTTTAAAGTTTAGTACGAAGGC 57.805 36.000 0.00 0.00 0.00 4.35
176 177 6.767423 AGGTTTTAAAGTTTAGTACGAAGGCA 59.233 34.615 0.00 0.00 0.00 4.75
177 178 7.282901 AGGTTTTAAAGTTTAGTACGAAGGCAA 59.717 33.333 0.00 0.00 0.00 4.52
178 179 7.914871 GGTTTTAAAGTTTAGTACGAAGGCAAA 59.085 33.333 0.00 0.00 0.00 3.68
179 180 9.454585 GTTTTAAAGTTTAGTACGAAGGCAAAT 57.545 29.630 0.00 0.00 0.00 2.32
180 181 9.667989 TTTTAAAGTTTAGTACGAAGGCAAATC 57.332 29.630 0.00 0.00 0.00 2.17
181 182 6.870971 AAAGTTTAGTACGAAGGCAAATCA 57.129 33.333 0.00 0.00 0.00 2.57
182 183 5.857822 AGTTTAGTACGAAGGCAAATCAC 57.142 39.130 0.00 0.00 0.00 3.06
183 184 5.302360 AGTTTAGTACGAAGGCAAATCACA 58.698 37.500 0.00 0.00 0.00 3.58
184 185 5.178809 AGTTTAGTACGAAGGCAAATCACAC 59.821 40.000 0.00 0.00 0.00 3.82
185 186 3.120321 AGTACGAAGGCAAATCACACA 57.880 42.857 0.00 0.00 0.00 3.72
186 187 2.806244 AGTACGAAGGCAAATCACACAC 59.194 45.455 0.00 0.00 0.00 3.82
187 188 1.674359 ACGAAGGCAAATCACACACA 58.326 45.000 0.00 0.00 0.00 3.72
188 189 1.333619 ACGAAGGCAAATCACACACAC 59.666 47.619 0.00 0.00 0.00 3.82
189 190 1.333308 CGAAGGCAAATCACACACACA 59.667 47.619 0.00 0.00 0.00 3.72
190 191 2.223456 CGAAGGCAAATCACACACACAA 60.223 45.455 0.00 0.00 0.00 3.33
191 192 3.733380 CGAAGGCAAATCACACACACAAA 60.733 43.478 0.00 0.00 0.00 2.83
192 193 3.883830 AGGCAAATCACACACACAAAA 57.116 38.095 0.00 0.00 0.00 2.44
193 194 4.199432 AGGCAAATCACACACACAAAAA 57.801 36.364 0.00 0.00 0.00 1.94
194 195 4.183101 AGGCAAATCACACACACAAAAAG 58.817 39.130 0.00 0.00 0.00 2.27
195 196 3.309410 GGCAAATCACACACACAAAAAGG 59.691 43.478 0.00 0.00 0.00 3.11
196 197 4.180057 GCAAATCACACACACAAAAAGGA 58.820 39.130 0.00 0.00 0.00 3.36
197 198 4.629200 GCAAATCACACACACAAAAAGGAA 59.371 37.500 0.00 0.00 0.00 3.36
198 199 5.121454 GCAAATCACACACACAAAAAGGAAA 59.879 36.000 0.00 0.00 0.00 3.13
199 200 6.348050 GCAAATCACACACACAAAAAGGAAAA 60.348 34.615 0.00 0.00 0.00 2.29
200 201 7.579726 CAAATCACACACACAAAAAGGAAAAA 58.420 30.769 0.00 0.00 0.00 1.94
221 222 2.141122 AATGCCCAGAACGCAAACGG 62.141 55.000 0.00 0.00 46.04 4.44
250 251 0.337773 TCATCCAGCCCACTCTCTCT 59.662 55.000 0.00 0.00 0.00 3.10
251 252 1.202330 CATCCAGCCCACTCTCTCTT 58.798 55.000 0.00 0.00 0.00 2.85
252 253 1.138661 CATCCAGCCCACTCTCTCTTC 59.861 57.143 0.00 0.00 0.00 2.87
257 265 1.194781 GCCCACTCTCTCTTCACCCA 61.195 60.000 0.00 0.00 0.00 4.51
335 343 4.880537 CGCGCTCGCATCCTCCTT 62.881 66.667 14.80 0.00 42.06 3.36
345 353 1.852633 CATCCTCCTTTTCCCCAACC 58.147 55.000 0.00 0.00 0.00 3.77
346 354 1.359130 CATCCTCCTTTTCCCCAACCT 59.641 52.381 0.00 0.00 0.00 3.50
347 355 1.073098 TCCTCCTTTTCCCCAACCTC 58.927 55.000 0.00 0.00 0.00 3.85
348 356 0.777446 CCTCCTTTTCCCCAACCTCA 59.223 55.000 0.00 0.00 0.00 3.86
349 357 1.359130 CCTCCTTTTCCCCAACCTCAT 59.641 52.381 0.00 0.00 0.00 2.90
350 358 2.621668 CCTCCTTTTCCCCAACCTCATC 60.622 54.545 0.00 0.00 0.00 2.92
351 359 2.310052 CTCCTTTTCCCCAACCTCATCT 59.690 50.000 0.00 0.00 0.00 2.90
352 360 2.308866 TCCTTTTCCCCAACCTCATCTC 59.691 50.000 0.00 0.00 0.00 2.75
357 365 1.690219 CCCCAACCTCATCTCTCCGG 61.690 65.000 0.00 0.00 0.00 5.14
364 372 0.754957 CTCATCTCTCCGGTCAGGCT 60.755 60.000 0.00 0.00 40.77 4.58
366 374 1.826054 ATCTCTCCGGTCAGGCTCG 60.826 63.158 0.00 0.00 40.77 5.03
374 382 4.131088 GTCAGGCTCGGGTCGACC 62.131 72.222 27.04 27.04 0.00 4.79
480 495 4.323843 CCGCGACCTCGTATCCGG 62.324 72.222 8.23 0.00 42.22 5.14
481 496 3.580193 CGCGACCTCGTATCCGGT 61.580 66.667 0.00 0.00 42.22 5.28
550 565 3.535629 CTTGCAGCGGACAGACCCA 62.536 63.158 0.00 0.00 34.64 4.51
571 587 4.403432 CCATACGGAGAAAACCTAGGTACA 59.597 45.833 16.67 0.00 0.00 2.90
575 591 3.449737 CGGAGAAAACCTAGGTACATCCA 59.550 47.826 24.26 0.00 39.02 3.41
630 646 2.555757 GCAGTGCCAAAACTCTGAATCT 59.444 45.455 2.85 0.00 33.93 2.40
636 653 6.150140 AGTGCCAAAACTCTGAATCTGAATAC 59.850 38.462 0.00 0.00 0.00 1.89
708 739 4.439057 GTCGCTCTGATTACCCAATAACA 58.561 43.478 0.00 0.00 0.00 2.41
712 743 5.408604 CGCTCTGATTACCCAATAACATACC 59.591 44.000 0.00 0.00 0.00 2.73
827 860 2.738846 CAGTCCTCAACCTGTTTGATCG 59.261 50.000 0.00 0.00 43.54 3.69
885 1017 9.990360 TTGTGACTTTTATCTGTGTATCTTGTA 57.010 29.630 0.00 0.00 0.00 2.41
1080 1915 1.615392 GCCAAAAGGCTGAATGTCACT 59.385 47.619 0.00 0.00 0.00 3.41
1247 2121 5.766670 TGATGAATCTATCTTTGGACATGGC 59.233 40.000 0.00 0.00 0.00 4.40
1277 2217 3.304928 GGCAAGGACATGTTTCTTGTGAG 60.305 47.826 27.99 14.23 39.80 3.51
1322 2265 8.028354 TGGCAACTCAAACAATGAACTATAATG 58.972 33.333 0.00 0.00 37.67 1.90
1405 2350 8.624776 GTTAAAATTTATCCTCATGAGACCCAG 58.375 37.037 24.62 6.94 0.00 4.45
1410 2359 4.762289 ATCCTCATGAGACCCAGTTAAC 57.238 45.455 24.62 0.00 0.00 2.01
1445 2394 3.508840 GCTCCGTGGGGCATTTCG 61.509 66.667 5.72 0.00 0.00 3.46
1454 2404 1.279840 GGGCATTTCGTATGCTCGC 59.720 57.895 19.36 7.81 44.02 5.03
1466 2422 2.021931 GCTCGCATTGCTGTACGC 59.978 61.111 7.12 3.22 39.77 4.42
1477 2433 1.066215 TGCTGTACGCATCAACTGGAT 60.066 47.619 8.05 0.00 45.47 3.41
1618 2574 7.087639 CAGTCACCTACTACAAGAAAGAAGAG 58.912 42.308 0.00 0.00 35.76 2.85
1874 2830 2.226674 GTCATCTCAGTCGTCTGTGTCA 59.773 50.000 9.48 0.00 41.91 3.58
2137 3093 2.624838 CCCAACTTCTGCACTTCAACAT 59.375 45.455 0.00 0.00 0.00 2.71
2158 3114 1.414181 AGGCCCGATACTTGTGATGAG 59.586 52.381 0.00 0.00 0.00 2.90
2223 3197 0.558712 GCTAAGGAGGAGGAGGAGGA 59.441 60.000 0.00 0.00 0.00 3.71
2236 3210 1.382009 GGAGGAGGTGGAGGAGGAC 60.382 68.421 0.00 0.00 0.00 3.85
2333 3322 1.062505 AGGAGGAGGAGGAGGATGAAC 60.063 57.143 0.00 0.00 0.00 3.18
2356 3345 5.712917 ACGACCTTTAAGTCTCAGAAGATCT 59.287 40.000 0.00 0.00 34.46 2.75
2729 3728 3.561313 GCCTTTATGTTCCAGACTTCCCA 60.561 47.826 0.00 0.00 0.00 4.37
2855 3859 3.530265 CCATTGTTAAGCATGGCATGT 57.470 42.857 26.94 12.18 0.00 3.21
2857 3861 3.191669 CATTGTTAAGCATGGCATGTGG 58.808 45.455 26.94 4.09 0.00 4.17
3071 4109 6.910536 AGAAAACAGTACTGTATGCTATGC 57.089 37.500 28.13 11.87 44.13 3.14
3097 4135 7.118825 CAGGTACATATCTCTGCATTTACATGG 59.881 40.741 0.00 0.00 0.00 3.66
3114 4156 1.883084 GGCTGCCGAGTATGAACCG 60.883 63.158 1.35 0.00 0.00 4.44
3127 4169 0.736053 TGAACCGTGACCTTTTGCAC 59.264 50.000 0.00 0.00 0.00 4.57
3138 4180 6.348132 CGTGACCTTTTGCACTTATGATGTTA 60.348 38.462 0.00 0.00 32.98 2.41
3189 4234 1.641577 GGTACACGAGATCACAAGGC 58.358 55.000 0.00 0.00 0.00 4.35
3227 4273 5.600069 ACAGTATCTGCAGGTGATAAGATGA 59.400 40.000 15.13 0.00 34.37 2.92
3239 4285 8.954350 CAGGTGATAAGATGAGATGTTTTCTTT 58.046 33.333 0.00 0.00 33.74 2.52
3240 4286 9.171877 AGGTGATAAGATGAGATGTTTTCTTTC 57.828 33.333 0.00 0.00 33.74 2.62
3256 4302 7.971168 TGTTTTCTTTCTTTCTTAATTCGTGCA 59.029 29.630 0.00 0.00 0.00 4.57
3257 4303 8.472236 GTTTTCTTTCTTTCTTAATTCGTGCAG 58.528 33.333 0.00 0.00 0.00 4.41
3260 4306 5.356882 TTCTTTCTTAATTCGTGCAGTGG 57.643 39.130 0.00 0.00 0.00 4.00
3265 4311 2.401583 TAATTCGTGCAGTGGCTGAT 57.598 45.000 0.00 0.00 41.91 2.90
3273 4319 1.297664 GCAGTGGCTGATCAGATGTC 58.702 55.000 27.04 12.27 36.96 3.06
3300 4346 7.926555 TGGTTATCTGAAGATAGGAACGAAATC 59.073 37.037 0.00 0.00 38.18 2.17
3330 4376 8.730680 CATAATTTGTAGCTGGAGTACTTTGTT 58.269 33.333 0.00 0.00 0.00 2.83
3334 4380 3.214696 AGCTGGAGTACTTTGTTGCTT 57.785 42.857 0.00 0.00 0.00 3.91
3349 4395 4.104776 TGTTGCTTTCTGCTTCTTTTTCG 58.895 39.130 0.00 0.00 43.37 3.46
3366 4412 7.189512 TCTTTTTCGGCGAGTTATACTACTAC 58.810 38.462 10.46 0.00 0.00 2.73
3377 4423 8.404000 CGAGTTATACTACTACAGTTGTTGGAT 58.596 37.037 1.91 0.00 38.80 3.41
3380 4426 9.443283 GTTATACTACTACAGTTGTTGGATACG 57.557 37.037 1.91 0.00 38.80 3.06
3416 4462 7.887996 TTGTGGAAGTAATCATGAATTTTGC 57.112 32.000 0.00 0.00 0.00 3.68
3430 4476 5.250200 TGAATTTTGCCGGTGAGTTATACT 58.750 37.500 1.90 0.00 0.00 2.12
3434 4480 4.380841 TTGCCGGTGAGTTATACTACTG 57.619 45.455 1.90 0.00 0.00 2.74
3435 4481 3.359033 TGCCGGTGAGTTATACTACTGT 58.641 45.455 1.90 0.00 0.00 3.55
3436 4482 3.379372 TGCCGGTGAGTTATACTACTGTC 59.621 47.826 1.90 0.00 0.00 3.51
3447 4493 2.023318 CTACTGTCCGTAGCCCTCG 58.977 63.158 0.00 0.00 39.22 4.63
3483 4529 3.056213 CCTTCCAGTGGCATTGGTT 57.944 52.632 25.91 0.00 37.02 3.67
3486 4532 1.000060 CTTCCAGTGGCATTGGTTGTG 60.000 52.381 25.91 12.30 37.02 3.33
3497 4560 3.490761 GCATTGGTTGTGTGTAGCAACTT 60.491 43.478 7.88 0.00 43.93 2.66
3502 4565 4.700692 TGGTTGTGTGTAGCAACTTAAACA 59.299 37.500 7.88 0.00 43.93 2.83
3509 4572 6.141685 GTGTGTAGCAACTTAAACATTTTCCG 59.858 38.462 0.00 0.00 0.00 4.30
3523 4586 3.791973 TTTTCCGCTGTTGTGTGAATT 57.208 38.095 0.00 0.00 0.00 2.17
3529 4592 3.550639 CCGCTGTTGTGTGAATTGTCAAT 60.551 43.478 0.00 0.00 34.87 2.57
3532 4595 5.284079 GCTGTTGTGTGAATTGTCAATTCT 58.716 37.500 29.49 4.83 45.85 2.40
3534 4597 6.360681 GCTGTTGTGTGAATTGTCAATTCTAC 59.639 38.462 29.49 26.55 45.85 2.59
3538 4601 6.912082 TGTGTGAATTGTCAATTCTACATGG 58.088 36.000 29.49 0.00 45.85 3.66
3560 4623 3.325135 GGGATCCCATCTAGTCGAACATT 59.675 47.826 26.95 0.00 35.81 2.71
3570 4633 6.132791 TCTAGTCGAACATTGGTCTACATC 57.867 41.667 8.84 0.00 0.00 3.06
3577 4640 5.640732 GAACATTGGTCTACATCGCAAATT 58.359 37.500 0.00 0.00 0.00 1.82
3579 4642 4.458989 ACATTGGTCTACATCGCAAATTGT 59.541 37.500 0.00 0.00 0.00 2.71
3586 4649 6.142817 GTCTACATCGCAAATTGTCAAAGTT 58.857 36.000 0.00 0.00 0.00 2.66
3594 4657 8.555166 TCGCAAATTGTCAAAGTTAACTTAAG 57.445 30.769 20.83 15.94 34.61 1.85
3616 4679 9.701098 TTAAGAAATGTACAGTCAACTCGTAAT 57.299 29.630 0.33 0.00 0.00 1.89
3617 4680 7.582435 AGAAATGTACAGTCAACTCGTAATG 57.418 36.000 0.33 0.00 0.00 1.90
3628 4691 5.693104 GTCAACTCGTAATGGTCAACAAGTA 59.307 40.000 0.00 0.00 0.00 2.24
3636 4699 6.425721 CGTAATGGTCAACAAGTAAAGGAGAA 59.574 38.462 0.00 0.00 0.00 2.87
3643 4706 7.391833 GGTCAACAAGTAAAGGAGAAGAATGAT 59.608 37.037 0.00 0.00 0.00 2.45
3648 4711 9.660180 ACAAGTAAAGGAGAAGAATGATCTAAC 57.340 33.333 0.00 0.00 33.77 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 142 8.685427 ACTAAACTTTAAAACCTCCGCTAAAAA 58.315 29.630 0.00 0.00 0.00 1.94
142 143 8.224389 ACTAAACTTTAAAACCTCCGCTAAAA 57.776 30.769 0.00 0.00 0.00 1.52
143 144 7.806409 ACTAAACTTTAAAACCTCCGCTAAA 57.194 32.000 0.00 0.00 0.00 1.85
144 145 7.116233 CGTACTAAACTTTAAAACCTCCGCTAA 59.884 37.037 0.00 0.00 0.00 3.09
145 146 6.586082 CGTACTAAACTTTAAAACCTCCGCTA 59.414 38.462 0.00 0.00 0.00 4.26
146 147 5.406477 CGTACTAAACTTTAAAACCTCCGCT 59.594 40.000 0.00 0.00 0.00 5.52
147 148 5.405269 TCGTACTAAACTTTAAAACCTCCGC 59.595 40.000 0.00 0.00 0.00 5.54
148 149 7.359514 CCTTCGTACTAAACTTTAAAACCTCCG 60.360 40.741 0.00 0.00 0.00 4.63
149 150 7.571983 GCCTTCGTACTAAACTTTAAAACCTCC 60.572 40.741 0.00 0.00 0.00 4.30
150 151 7.041848 TGCCTTCGTACTAAACTTTAAAACCTC 60.042 37.037 0.00 0.00 0.00 3.85
151 152 6.767423 TGCCTTCGTACTAAACTTTAAAACCT 59.233 34.615 0.00 0.00 0.00 3.50
152 153 6.958255 TGCCTTCGTACTAAACTTTAAAACC 58.042 36.000 0.00 0.00 0.00 3.27
153 154 8.839947 TTTGCCTTCGTACTAAACTTTAAAAC 57.160 30.769 0.00 0.00 0.00 2.43
154 155 9.667989 GATTTGCCTTCGTACTAAACTTTAAAA 57.332 29.630 0.00 0.00 0.00 1.52
155 156 8.838365 TGATTTGCCTTCGTACTAAACTTTAAA 58.162 29.630 0.00 0.00 0.00 1.52
156 157 8.284693 GTGATTTGCCTTCGTACTAAACTTTAA 58.715 33.333 0.00 0.00 0.00 1.52
157 158 7.441760 TGTGATTTGCCTTCGTACTAAACTTTA 59.558 33.333 0.00 0.00 0.00 1.85
158 159 6.261381 TGTGATTTGCCTTCGTACTAAACTTT 59.739 34.615 0.00 0.00 0.00 2.66
159 160 5.761234 TGTGATTTGCCTTCGTACTAAACTT 59.239 36.000 0.00 0.00 0.00 2.66
160 161 5.178809 GTGTGATTTGCCTTCGTACTAAACT 59.821 40.000 0.00 0.00 0.00 2.66
161 162 5.049954 TGTGTGATTTGCCTTCGTACTAAAC 60.050 40.000 0.00 0.00 0.00 2.01
162 163 5.049954 GTGTGTGATTTGCCTTCGTACTAAA 60.050 40.000 0.00 0.00 0.00 1.85
163 164 4.449743 GTGTGTGATTTGCCTTCGTACTAA 59.550 41.667 0.00 0.00 0.00 2.24
164 165 3.991773 GTGTGTGATTTGCCTTCGTACTA 59.008 43.478 0.00 0.00 0.00 1.82
165 166 2.806244 GTGTGTGATTTGCCTTCGTACT 59.194 45.455 0.00 0.00 0.00 2.73
166 167 2.546368 TGTGTGTGATTTGCCTTCGTAC 59.454 45.455 0.00 0.00 0.00 3.67
167 168 2.546368 GTGTGTGTGATTTGCCTTCGTA 59.454 45.455 0.00 0.00 0.00 3.43
168 169 1.333619 GTGTGTGTGATTTGCCTTCGT 59.666 47.619 0.00 0.00 0.00 3.85
169 170 1.333308 TGTGTGTGTGATTTGCCTTCG 59.667 47.619 0.00 0.00 0.00 3.79
170 171 3.435105 TTGTGTGTGTGATTTGCCTTC 57.565 42.857 0.00 0.00 0.00 3.46
171 172 3.883830 TTTGTGTGTGTGATTTGCCTT 57.116 38.095 0.00 0.00 0.00 4.35
172 173 3.883830 TTTTGTGTGTGTGATTTGCCT 57.116 38.095 0.00 0.00 0.00 4.75
173 174 3.309410 CCTTTTTGTGTGTGTGATTTGCC 59.691 43.478 0.00 0.00 0.00 4.52
174 175 4.180057 TCCTTTTTGTGTGTGTGATTTGC 58.820 39.130 0.00 0.00 0.00 3.68
175 176 6.718454 TTTCCTTTTTGTGTGTGTGATTTG 57.282 33.333 0.00 0.00 0.00 2.32
176 177 7.736447 TTTTTCCTTTTTGTGTGTGTGATTT 57.264 28.000 0.00 0.00 0.00 2.17
199 200 2.209273 GTTTGCGTTCTGGGCATTTTT 58.791 42.857 0.00 0.00 40.62 1.94
200 201 1.864565 GTTTGCGTTCTGGGCATTTT 58.135 45.000 0.00 0.00 40.62 1.82
201 202 0.318614 CGTTTGCGTTCTGGGCATTT 60.319 50.000 0.00 0.00 40.62 2.32
202 203 1.285641 CGTTTGCGTTCTGGGCATT 59.714 52.632 0.00 0.00 40.62 3.56
203 204 2.625823 CCGTTTGCGTTCTGGGCAT 61.626 57.895 0.00 0.00 40.62 4.40
204 205 3.283684 CCGTTTGCGTTCTGGGCA 61.284 61.111 0.00 0.00 38.93 5.36
205 206 4.700365 GCCGTTTGCGTTCTGGGC 62.700 66.667 0.00 0.00 36.15 5.36
206 207 4.038080 GGCCGTTTGCGTTCTGGG 62.038 66.667 0.00 0.00 42.61 4.45
207 208 3.254014 CTGGCCGTTTGCGTTCTGG 62.254 63.158 0.00 0.00 42.61 3.86
208 209 2.252260 CTGGCCGTTTGCGTTCTG 59.748 61.111 0.00 0.00 42.61 3.02
209 210 2.978010 CCTGGCCGTTTGCGTTCT 60.978 61.111 0.00 0.00 42.61 3.01
210 211 4.700365 GCCTGGCCGTTTGCGTTC 62.700 66.667 7.66 0.00 42.61 3.95
221 222 2.203451 CTGGATGATGGGCCTGGC 60.203 66.667 11.05 11.05 0.00 4.85
232 233 1.138661 GAAGAGAGAGTGGGCTGGATG 59.861 57.143 0.00 0.00 0.00 3.51
335 343 1.916181 GGAGAGATGAGGTTGGGGAAA 59.084 52.381 0.00 0.00 0.00 3.13
345 353 0.754957 AGCCTGACCGGAGAGATGAG 60.755 60.000 9.46 0.00 33.16 2.90
346 354 0.753479 GAGCCTGACCGGAGAGATGA 60.753 60.000 9.46 0.00 33.16 2.92
347 355 1.739049 GAGCCTGACCGGAGAGATG 59.261 63.158 9.46 0.00 33.16 2.90
348 356 1.826054 CGAGCCTGACCGGAGAGAT 60.826 63.158 9.46 0.00 33.16 2.75
349 357 2.438614 CGAGCCTGACCGGAGAGA 60.439 66.667 9.46 0.00 33.16 3.10
357 365 4.131088 GGTCGACCCGAGCCTGAC 62.131 72.222 24.75 0.00 46.63 3.51
520 535 0.179070 GCTGCAAGACCTAGTAGCCC 60.179 60.000 0.00 0.00 37.49 5.19
524 539 0.815734 GTCCGCTGCAAGACCTAGTA 59.184 55.000 8.25 0.00 34.07 1.82
527 542 0.898326 TCTGTCCGCTGCAAGACCTA 60.898 55.000 14.89 3.21 34.07 3.08
550 565 5.303845 GGATGTACCTAGGTTTTCTCCGTAT 59.696 44.000 22.11 1.87 35.41 3.06
636 653 9.741647 AGAGAAGCAGTAAAAAGAAGAAATTTG 57.258 29.630 0.00 0.00 0.00 2.32
712 743 1.327988 CGTGCACCGATACGATAGCG 61.328 60.000 12.15 0.00 42.54 4.26
827 860 8.122952 CACTTATTCAAACGGGACTGAATAATC 58.877 37.037 14.37 0.00 46.05 1.75
885 1017 0.107456 CCGCTATGCTCCCATGTTCT 59.893 55.000 0.00 0.00 32.85 3.01
1080 1915 1.852157 AAGGTGCTCCATCCCCACA 60.852 57.895 7.70 0.00 35.89 4.17
1247 2121 0.729116 CATGTCCTTGCCAAGTAGCG 59.271 55.000 3.37 0.00 34.65 4.26
1277 2217 7.277981 AGTTGCCATAGCTATATTATGTTACGC 59.722 37.037 5.77 0.00 40.80 4.42
1333 2277 9.814899 TCAAGAAACATAAAACAACAACATGAT 57.185 25.926 0.00 0.00 0.00 2.45
1405 2350 6.651225 AGCACTGTGGAATAGAAAGAGTTAAC 59.349 38.462 10.21 0.00 0.00 2.01
1410 2359 4.187694 GGAGCACTGTGGAATAGAAAGAG 58.812 47.826 10.21 0.00 0.00 2.85
1445 2394 1.071239 CGTACAGCAATGCGAGCATAC 60.071 52.381 11.25 6.92 35.31 2.39
1618 2574 3.455469 GGGCATGCCTCCTTGTGC 61.455 66.667 34.70 13.03 36.88 4.57
1874 2830 3.827722 TCGATTTCCTCCTGTTTGGTTT 58.172 40.909 0.00 0.00 37.07 3.27
2137 3093 2.628178 CTCATCACAAGTATCGGGCCTA 59.372 50.000 0.84 0.00 0.00 3.93
2223 3197 0.336737 ATTCTCGTCCTCCTCCACCT 59.663 55.000 0.00 0.00 0.00 4.00
2236 3210 4.056740 CCTCATTGTCCTCATCATTCTCG 58.943 47.826 0.00 0.00 0.00 4.04
2333 3322 6.127869 TGAGATCTTCTGAGACTTAAAGGTCG 60.128 42.308 0.00 0.00 40.76 4.79
2356 3345 2.224523 CCTTAGTTGAACAGCAGGGTGA 60.225 50.000 5.37 0.00 0.00 4.02
2536 3534 2.747686 GTTCCTTGGAGACGGGCA 59.252 61.111 0.00 0.00 0.00 5.36
2648 3646 4.345257 TCTTTGAACTGCAGGAGTCTAAGT 59.655 41.667 19.93 0.00 31.73 2.24
2729 3728 2.417586 GCACGGAAAACCTTTAGCGTAT 59.582 45.455 0.00 0.00 0.00 3.06
2852 3856 2.936919 TTCAGACTCTGCAACCACAT 57.063 45.000 0.62 0.00 0.00 3.21
2853 3857 2.497138 CATTCAGACTCTGCAACCACA 58.503 47.619 0.62 0.00 0.00 4.17
2854 3858 1.198637 GCATTCAGACTCTGCAACCAC 59.801 52.381 0.62 0.00 35.96 4.16
2855 3859 1.202794 TGCATTCAGACTCTGCAACCA 60.203 47.619 0.62 0.00 42.53 3.67
2857 3861 1.135746 GCTGCATTCAGACTCTGCAAC 60.136 52.381 0.00 0.00 44.59 4.17
3071 4109 7.118825 CCATGTAAATGCAGAGATATGTACCTG 59.881 40.741 0.00 0.00 0.00 4.00
3097 4135 1.153628 ACGGTTCATACTCGGCAGC 60.154 57.895 0.00 0.00 0.00 5.25
3114 4156 5.376854 ACATCATAAGTGCAAAAGGTCAC 57.623 39.130 0.00 0.00 0.00 3.67
3153 4195 3.632604 TGTACCCATGCAGAAACGAAAAA 59.367 39.130 0.00 0.00 0.00 1.94
3159 4201 1.732259 CTCGTGTACCCATGCAGAAAC 59.268 52.381 0.00 0.00 0.00 2.78
3239 4285 3.188460 GCCACTGCACGAATTAAGAAAGA 59.812 43.478 0.00 0.00 37.47 2.52
3240 4286 3.189287 AGCCACTGCACGAATTAAGAAAG 59.811 43.478 0.00 0.00 41.13 2.62
3242 4288 2.483877 CAGCCACTGCACGAATTAAGAA 59.516 45.455 0.00 0.00 41.13 2.52
3244 4290 2.076100 TCAGCCACTGCACGAATTAAG 58.924 47.619 0.00 0.00 41.13 1.85
3245 4291 2.177394 TCAGCCACTGCACGAATTAA 57.823 45.000 0.00 0.00 41.13 1.40
3246 4292 2.279741 GATCAGCCACTGCACGAATTA 58.720 47.619 0.00 0.00 41.13 1.40
3247 4293 1.089920 GATCAGCCACTGCACGAATT 58.910 50.000 0.00 0.00 41.13 2.17
3248 4294 0.036105 TGATCAGCCACTGCACGAAT 60.036 50.000 0.00 0.00 41.13 3.34
3249 4295 0.671472 CTGATCAGCCACTGCACGAA 60.671 55.000 10.38 0.00 41.13 3.85
3256 4302 1.485480 CCAGACATCTGATCAGCCACT 59.515 52.381 18.36 10.98 46.59 4.00
3257 4303 1.209019 ACCAGACATCTGATCAGCCAC 59.791 52.381 18.36 8.99 46.59 5.01
3260 4306 5.212532 AGATAACCAGACATCTGATCAGC 57.787 43.478 18.36 3.87 46.59 4.26
3273 4319 6.392625 TCGTTCCTATCTTCAGATAACCAG 57.607 41.667 0.00 0.00 36.66 4.00
3290 4336 6.451064 ACAAATTATGGAGGATTTCGTTCC 57.549 37.500 0.00 0.00 35.90 3.62
3304 4350 8.268850 ACAAAGTACTCCAGCTACAAATTATG 57.731 34.615 0.00 0.00 0.00 1.90
3305 4351 8.730680 CAACAAAGTACTCCAGCTACAAATTAT 58.269 33.333 0.00 0.00 0.00 1.28
3307 4353 6.515035 GCAACAAAGTACTCCAGCTACAAATT 60.515 38.462 0.00 0.00 0.00 1.82
3334 4380 1.531149 CTCGCCGAAAAAGAAGCAGAA 59.469 47.619 0.00 0.00 0.00 3.02
3349 4395 6.129053 ACAACTGTAGTAGTATAACTCGCC 57.871 41.667 0.00 0.00 39.18 5.54
3366 4412 2.805671 TGTTCTGCGTATCCAACAACTG 59.194 45.455 0.00 0.00 0.00 3.16
3377 4423 4.902443 TCCACAAAAATTGTTCTGCGTA 57.098 36.364 0.00 0.00 43.23 4.42
3380 4426 7.437862 TGATTACTTCCACAAAAATTGTTCTGC 59.562 33.333 0.00 0.00 43.23 4.26
3416 4462 3.003068 CGGACAGTAGTATAACTCACCGG 59.997 52.174 0.00 0.00 39.47 5.28
3430 4476 2.117156 GCGAGGGCTACGGACAGTA 61.117 63.158 0.00 0.00 35.83 2.74
3434 4480 4.208686 CCTGCGAGGGCTACGGAC 62.209 72.222 0.00 0.00 40.82 4.79
3435 4481 4.435970 TCCTGCGAGGGCTACGGA 62.436 66.667 2.86 2.69 40.82 4.69
3436 4482 3.905678 CTCCTGCGAGGGCTACGG 61.906 72.222 2.86 0.00 40.82 4.02
3447 4493 2.436292 CTCCACAGCTGCTCCTGC 60.436 66.667 15.27 0.00 36.29 4.85
3473 4519 0.958091 GCTACACACAACCAATGCCA 59.042 50.000 0.00 0.00 0.00 4.92
3480 4526 5.238006 TGTTTAAGTTGCTACACACAACC 57.762 39.130 0.13 0.00 46.85 3.77
3483 4529 6.975772 GGAAAATGTTTAAGTTGCTACACACA 59.024 34.615 0.13 0.00 0.00 3.72
3486 4532 5.116528 GCGGAAAATGTTTAAGTTGCTACAC 59.883 40.000 0.13 0.00 0.00 2.90
3497 4560 4.096532 TCACACAACAGCGGAAAATGTTTA 59.903 37.500 0.00 0.00 37.54 2.01
3502 4565 4.050553 CAATTCACACAACAGCGGAAAAT 58.949 39.130 0.00 0.00 0.00 1.82
3509 4572 5.565723 GAATTGACAATTCACACAACAGC 57.434 39.130 28.23 4.97 45.18 4.40
3523 4586 3.138283 GGGATCCCCATGTAGAATTGACA 59.862 47.826 21.42 0.00 44.65 3.58
3538 4601 2.317040 TGTTCGACTAGATGGGATCCC 58.683 52.381 25.22 25.22 0.00 3.85
3551 4614 2.281762 GCGATGTAGACCAATGTTCGAC 59.718 50.000 0.00 0.00 0.00 4.20
3552 4615 2.094442 TGCGATGTAGACCAATGTTCGA 60.094 45.455 0.00 0.00 0.00 3.71
3554 4617 4.678509 TTTGCGATGTAGACCAATGTTC 57.321 40.909 0.00 0.00 0.00 3.18
3560 4623 3.669536 TGACAATTTGCGATGTAGACCA 58.330 40.909 0.00 0.00 0.00 4.02
3570 4633 8.555166 TCTTAAGTTAACTTTGACAATTTGCG 57.445 30.769 25.07 3.02 37.40 4.85
3586 4649 9.188588 CGAGTTGACTGTACATTTCTTAAGTTA 57.811 33.333 1.63 0.00 0.00 2.24
3594 4657 6.367969 ACCATTACGAGTTGACTGTACATTTC 59.632 38.462 0.00 0.00 0.00 2.17
3605 4668 4.699637 ACTTGTTGACCATTACGAGTTGA 58.300 39.130 0.00 0.00 35.90 3.18
3606 4669 6.533819 TTACTTGTTGACCATTACGAGTTG 57.466 37.500 0.00 0.00 39.24 3.16
3616 4679 5.623956 TCTTCTCCTTTACTTGTTGACCA 57.376 39.130 0.00 0.00 0.00 4.02
3617 4680 6.710744 TCATTCTTCTCCTTTACTTGTTGACC 59.289 38.462 0.00 0.00 0.00 4.02
3628 4691 6.445139 TCCCTGTTAGATCATTCTTCTCCTTT 59.555 38.462 0.00 0.00 33.17 3.11


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

AutoCloner maintained by Alex Coulton.