Multiple sequence alignment - TraesCS1D01G002100

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 TraesCS1D01G002100 chr1D 100.000 2930 0 0 1 2930 508821 511750 0.000000e+00 5411.0
1 TraesCS1D01G002100 chr1B 90.595 2435 117 61 476 2826 4219442 4221848 0.000000e+00 3125.0
2 TraesCS1D01G002100 chr1B 88.889 135 5 8 999 1124 42308156 42308023 1.090000e-34 158.0
3 TraesCS1D01G002100 chr1B 89.412 85 6 1 637 718 4216003 4216087 1.440000e-18 104.0
4 TraesCS1D01G002100 chr1A 86.153 2542 173 83 487 2930 3116764 3119224 0.000000e+00 2579.0
5 TraesCS1D01G002100 chr1A 93.036 359 21 2 1179 1533 497899436 497899078 3.350000e-144 521.0
6 TraesCS1D01G002100 chr1A 80.052 386 42 17 1 379 3116399 3116756 1.350000e-63 254.0
7 TraesCS1D01G002100 chr1A 89.051 137 5 8 997 1124 398810905 398810770 8.400000e-36 161.0
8 TraesCS1D01G002100 chr2A 90.103 677 32 15 888 1533 174025401 174024729 0.000000e+00 846.0
9 TraesCS1D01G002100 chr6A 89.365 677 37 16 888 1533 531810051 531810723 0.000000e+00 819.0
10 TraesCS1D01G002100 chr4A 89.466 674 36 14 888 1533 130525325 130525991 0.000000e+00 819.0
11 TraesCS1D01G002100 chr7B 91.304 437 32 4 1864 2300 600816223 600815793 2.510000e-165 592.0
12 TraesCS1D01G002100 chr7B 90.435 345 21 7 2234 2574 637934047 637933711 7.450000e-121 444.0
13 TraesCS1D01G002100 chr7B 90.654 107 7 3 386 490 522717197 522717302 3.940000e-29 139.0
14 TraesCS1D01G002100 chr7B 97.436 39 1 0 2703 2741 637932987 637932949 1.880000e-07 67.6
15 TraesCS1D01G002100 chr2B 91.304 437 32 4 1864 2300 692992108 692992538 2.510000e-165 592.0
16 TraesCS1D01G002100 chr2B 89.051 137 5 8 997 1124 69375264 69375129 8.400000e-36 161.0
17 TraesCS1D01G002100 chr2B 92.079 101 8 0 395 495 670987885 670987985 3.040000e-30 143.0
18 TraesCS1D01G002100 chr3B 91.284 436 32 4 1865 2300 557930182 557930611 9.040000e-165 590.0
19 TraesCS1D01G002100 chr3B 91.076 437 33 4 1864 2300 44082694 44083124 1.170000e-163 586.0
20 TraesCS1D01G002100 chr3B 90.826 436 32 6 1865 2300 82507955 82507528 7.040000e-161 577.0
21 TraesCS1D01G002100 chr3B 91.594 345 23 5 2233 2573 782533261 782532919 3.420000e-129 472.0
22 TraesCS1D01G002100 chr3B 100.000 30 0 0 574 603 8802223 8802194 4.080000e-04 56.5
23 TraesCS1D01G002100 chr6B 91.076 437 33 4 1864 2300 387961427 387960997 1.170000e-163 586.0
24 TraesCS1D01G002100 chr6B 91.908 346 22 5 2233 2574 700077913 700078256 2.040000e-131 479.0
25 TraesCS1D01G002100 chr5B 91.076 437 33 4 1864 2300 58980002 58979572 1.170000e-163 586.0
26 TraesCS1D01G002100 chr5B 91.034 435 33 5 1864 2298 27043566 27043138 1.510000e-162 582.0
27 TraesCS1D01G002100 chr5B 89.781 137 4 9 997 1124 480409932 480410067 1.810000e-37 167.0
28 TraesCS1D01G002100 chr7A 85.279 394 26 13 890 1255 703520838 703520449 7.670000e-101 377.0
29 TraesCS1D01G002100 chr7A 84.858 317 16 14 888 1176 268850306 268849994 1.030000e-74 291.0
30 TraesCS1D01G002100 chr5D 90.500 200 15 3 2233 2429 438252993 438253191 8.050000e-66 261.0
31 TraesCS1D01G002100 chr5D 92.157 102 6 2 384 485 495161374 495161473 3.040000e-30 143.0
32 TraesCS1D01G002100 chr5D 97.436 39 1 0 2703 2741 438253681 438253719 1.880000e-07 67.6
33 TraesCS1D01G002100 chr2D 89.904 208 14 4 2233 2435 525670292 525670087 8.050000e-66 261.0
34 TraesCS1D01G002100 chr2D 90.099 202 13 4 2233 2429 60275290 60275489 3.750000e-64 255.0
35 TraesCS1D01G002100 chr2D 97.436 39 1 0 2703 2741 525669603 525669565 1.880000e-07 67.6
36 TraesCS1D01G002100 chr4B 89.423 208 15 4 2233 2435 277740523 277740318 3.750000e-64 255.0
37 TraesCS1D01G002100 chr4B 87.500 64 2 1 2678 2741 277739854 277739797 5.240000e-08 69.4
38 TraesCS1D01G002100 chr3A 78.679 333 48 11 1056 1366 13075122 13075453 1.780000e-47 200.0
39 TraesCS1D01G002100 chr3A 93.750 96 6 0 390 485 83731731 83731826 8.460000e-31 145.0
40 TraesCS1D01G002100 chr3A 87.395 119 11 4 374 492 709066778 709066664 1.830000e-27 134.0
41 TraesCS1D01G002100 chr3D 78.313 332 51 9 1056 1366 7186668 7186337 8.290000e-46 195.0
42 TraesCS1D01G002100 chr5A 89.781 137 4 8 997 1124 664782985 664783120 1.810000e-37 167.0
43 TraesCS1D01G002100 chr4D 98.901 91 1 0 400 490 191234886 191234796 2.340000e-36 163.0
44 TraesCS1D01G002100 chr7D 97.753 89 2 0 401 489 4902285 4902197 1.410000e-33 154.0
45 TraesCS1D01G002100 chr7D 97.753 89 2 0 399 487 621487680 621487592 1.410000e-33 154.0
46 TraesCS1D01G002100 chr7D 93.069 101 7 0 385 485 34845541 34845641 6.540000e-32 148.0


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 TraesCS1D01G002100 chr1D 508821 511750 2929 False 5411.0 5411 100.0000 1 2930 1 chr1D.!!$F1 2929
1 TraesCS1D01G002100 chr1B 4216003 4221848 5845 False 1614.5 3125 90.0035 476 2826 2 chr1B.!!$F1 2350
2 TraesCS1D01G002100 chr1A 3116399 3119224 2825 False 1416.5 2579 83.1025 1 2930 2 chr1A.!!$F1 2929
3 TraesCS1D01G002100 chr2A 174024729 174025401 672 True 846.0 846 90.1030 888 1533 1 chr2A.!!$R1 645
4 TraesCS1D01G002100 chr6A 531810051 531810723 672 False 819.0 819 89.3650 888 1533 1 chr6A.!!$F1 645
5 TraesCS1D01G002100 chr4A 130525325 130525991 666 False 819.0 819 89.4660 888 1533 1 chr4A.!!$F1 645
6 TraesCS1D01G002100 chr7B 637932949 637934047 1098 True 255.8 444 93.9355 2234 2741 2 chr7B.!!$R2 507

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
68 69 0.035317 ACAAGGCTGCTTGATCGTGA 59.965 50.0 15.41 0.0 37.72 4.35 F
358 359 0.100682 ATTCCGGTCGATGTCTCGTG 59.899 55.0 0.00 0.0 45.25 4.35 F
1007 4055 0.178975 AAACCTCCACCAATGGCGAA 60.179 50.0 0.00 0.0 46.80 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 4712 0.040958 CTTCTCCAGCGTGTTGTTGC 60.041 55.0 0.00 0.00 0.0 4.17 R
1795 4873 0.182537 TTCTTCACCACCACCACCTG 59.817 55.0 0.00 0.00 0.0 4.00 R
2196 5309 1.689243 GGCAAATTGAGGGCCCCATC 61.689 60.0 21.43 11.77 41.9 3.51 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
68 69 0.035317 ACAAGGCTGCTTGATCGTGA 59.965 50.000 15.41 0.00 37.72 4.35
100 101 8.149647 TGAAAAGCATTTCCATAACACATTTCT 58.850 29.630 11.60 0.00 43.54 2.52
113 114 8.783093 CATAACACATTTCTTTGTTACCTCTCA 58.217 33.333 0.00 0.00 40.19 3.27
120 121 8.680903 CATTTCTTTGTTACCTCTCAAGCATAT 58.319 33.333 0.00 0.00 0.00 1.78
142 143 3.980646 TGTAGCACACACCAATGTTTC 57.019 42.857 0.00 0.00 36.72 2.78
143 144 3.282885 TGTAGCACACACCAATGTTTCA 58.717 40.909 0.00 0.00 36.72 2.69
150 151 4.206814 CACACACCAATGTTTCAAATGTCG 59.793 41.667 0.00 0.00 36.72 4.35
152 153 3.243704 ACACCAATGTTTCAAATGTCGGG 60.244 43.478 0.00 0.00 34.46 5.14
172 173 2.224670 GGAACATACATATTCCCGGCCA 60.225 50.000 2.24 0.00 38.81 5.36
174 175 3.140325 ACATACATATTCCCGGCCAAG 57.860 47.619 2.24 0.00 0.00 3.61
175 176 1.812571 CATACATATTCCCGGCCAAGC 59.187 52.381 2.24 0.00 0.00 4.01
176 177 1.136828 TACATATTCCCGGCCAAGCT 58.863 50.000 2.24 0.00 0.00 3.74
178 179 1.529244 ATATTCCCGGCCAAGCTGC 60.529 57.895 2.24 0.00 32.89 5.25
179 180 2.283143 ATATTCCCGGCCAAGCTGCA 62.283 55.000 2.24 0.00 32.89 4.41
180 181 2.491770 TATTCCCGGCCAAGCTGCAA 62.492 55.000 2.24 0.00 32.89 4.08
182 183 3.384532 CCCGGCCAAGCTGCAAAT 61.385 61.111 2.24 0.00 32.89 2.32
183 184 2.051518 CCCGGCCAAGCTGCAAATA 61.052 57.895 2.24 0.00 32.89 1.40
184 185 1.603236 CCCGGCCAAGCTGCAAATAA 61.603 55.000 2.24 0.00 32.89 1.40
187 188 2.195922 CGGCCAAGCTGCAAATAATTC 58.804 47.619 2.24 0.00 0.00 2.17
190 191 3.192466 GCCAAGCTGCAAATAATTCCAG 58.808 45.455 1.02 0.00 0.00 3.86
196 197 7.201582 CCAAGCTGCAAATAATTCCAGATTTTC 60.202 37.037 1.02 0.00 32.27 2.29
198 199 7.618137 AGCTGCAAATAATTCCAGATTTTCTT 58.382 30.769 1.02 0.00 0.00 2.52
200 201 8.724229 GCTGCAAATAATTCCAGATTTTCTTTT 58.276 29.630 0.00 0.00 0.00 2.27
249 250 7.775120 TCTCTAAATTTCAATGAGATTTGGGC 58.225 34.615 18.38 0.00 30.78 5.36
250 251 7.616935 TCTCTAAATTTCAATGAGATTTGGGCT 59.383 33.333 18.38 0.00 30.78 5.19
251 252 8.821686 TCTAAATTTCAATGAGATTTGGGCTA 57.178 30.769 18.38 1.55 30.78 3.93
252 253 9.253832 TCTAAATTTCAATGAGATTTGGGCTAA 57.746 29.630 18.38 1.26 30.78 3.09
255 256 9.743581 AAATTTCAATGAGATTTGGGCTAATTT 57.256 25.926 10.42 1.14 27.70 1.82
258 259 9.820725 TTTCAATGAGATTTGGGCTAATTTATG 57.179 29.630 0.00 0.00 0.00 1.90
259 260 7.436118 TCAATGAGATTTGGGCTAATTTATGC 58.564 34.615 0.00 0.00 0.00 3.14
262 263 7.422465 TGAGATTTGGGCTAATTTATGCTTT 57.578 32.000 0.00 0.00 0.00 3.51
263 264 7.267128 TGAGATTTGGGCTAATTTATGCTTTG 58.733 34.615 0.00 0.00 0.00 2.77
264 265 6.051074 AGATTTGGGCTAATTTATGCTTTGC 58.949 36.000 0.00 0.00 0.00 3.68
265 266 5.419239 TTTGGGCTAATTTATGCTTTGCT 57.581 34.783 0.00 0.00 0.00 3.91
266 267 5.419239 TTGGGCTAATTTATGCTTTGCTT 57.581 34.783 0.00 0.00 0.00 3.91
272 273 7.404203 GGCTAATTTATGCTTTGCTTGAATTG 58.596 34.615 14.01 8.32 34.60 2.32
278 279 0.390209 CTTTGCTTGAATTGGGCCGG 60.390 55.000 0.00 0.00 0.00 6.13
281 282 1.321805 TGCTTGAATTGGGCCGGATG 61.322 55.000 5.05 0.00 0.00 3.51
290 291 2.196245 GGGCCGGATGATTCAAGGC 61.196 63.158 5.05 17.58 42.83 4.35
293 294 1.230324 GCCGGATGATTCAAGGCTAC 58.770 55.000 5.05 0.00 41.34 3.58
295 296 2.487934 CCGGATGATTCAAGGCTACAG 58.512 52.381 0.00 0.00 0.00 2.74
355 356 1.852895 CGAAATTCCGGTCGATGTCTC 59.147 52.381 6.34 0.00 39.64 3.36
356 357 1.852895 GAAATTCCGGTCGATGTCTCG 59.147 52.381 0.00 0.00 46.41 4.04
358 359 0.100682 ATTCCGGTCGATGTCTCGTG 59.899 55.000 0.00 0.00 45.25 4.35
359 360 2.537792 TTCCGGTCGATGTCTCGTGC 62.538 60.000 0.00 0.00 45.25 5.34
365 372 2.112522 GTCGATGTCTCGTGCATACAG 58.887 52.381 0.00 0.00 45.25 2.74
379 386 1.094073 ATACAGACGGACGGACGGAG 61.094 60.000 6.00 0.00 38.39 4.63
386 393 0.305922 CGGACGGACGGAGTACATAC 59.694 60.000 0.00 0.00 45.67 2.39
387 394 1.382522 GGACGGACGGAGTACATACA 58.617 55.000 0.00 0.00 45.67 2.29
388 395 1.952296 GGACGGACGGAGTACATACAT 59.048 52.381 0.00 0.00 45.67 2.29
391 398 4.937620 GGACGGACGGAGTACATACATATA 59.062 45.833 0.00 0.00 45.67 0.86
393 400 6.763135 GGACGGACGGAGTACATACATATATA 59.237 42.308 0.00 0.00 45.67 0.86
394 401 7.254590 GGACGGACGGAGTACATACATATATAC 60.255 44.444 0.00 0.00 45.67 1.47
396 403 7.065085 ACGGACGGAGTACATACATATATACAC 59.935 40.741 0.00 0.00 45.67 2.90
400 407 9.239551 ACGGAGTACATACATATATACACACAT 57.760 33.333 0.00 0.00 41.94 3.21
410 417 8.354711 ACATATATACACACATACTCCCTCTG 57.645 38.462 0.00 0.00 0.00 3.35
411 418 7.950684 ACATATATACACACATACTCCCTCTGT 59.049 37.037 0.00 0.00 0.00 3.41
412 419 9.462606 CATATATACACACATACTCCCTCTGTA 57.537 37.037 0.00 0.00 0.00 2.74
415 422 5.148651 ACACACATACTCCCTCTGTAAAC 57.851 43.478 0.00 0.00 0.00 2.01
416 423 4.838986 ACACACATACTCCCTCTGTAAACT 59.161 41.667 0.00 0.00 0.00 2.66
417 424 6.014647 ACACACATACTCCCTCTGTAAACTA 58.985 40.000 0.00 0.00 0.00 2.24
418 425 6.495872 ACACACATACTCCCTCTGTAAACTAA 59.504 38.462 0.00 0.00 0.00 2.24
419 426 7.180408 ACACACATACTCCCTCTGTAAACTAAT 59.820 37.037 0.00 0.00 0.00 1.73
427 434 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
479 486 9.490379 AAATGCTCTTATATTAGTTTACGGAGG 57.510 33.333 0.00 0.00 0.00 4.30
480 487 6.989659 TGCTCTTATATTAGTTTACGGAGGG 58.010 40.000 0.00 0.00 0.00 4.30
481 488 6.779049 TGCTCTTATATTAGTTTACGGAGGGA 59.221 38.462 0.00 0.00 0.00 4.20
496 3461 4.021280 ACGGAGGGAGTAGAAAAGAAGAAC 60.021 45.833 0.00 0.00 0.00 3.01
523 3488 5.334724 CCATTTGATGGGAAGAAGAAAGG 57.665 43.478 0.00 0.00 46.86 3.11
604 3577 4.935702 TGCTTGTGAAACTTGGAATCTTG 58.064 39.130 0.00 0.00 38.04 3.02
605 3578 3.737774 GCTTGTGAAACTTGGAATCTTGC 59.262 43.478 0.00 0.00 38.04 4.01
607 3580 4.305989 TGTGAAACTTGGAATCTTGCAC 57.694 40.909 0.00 0.00 38.04 4.57
610 3583 1.632589 AACTTGGAATCTTGCACCCC 58.367 50.000 0.00 0.00 0.00 4.95
730 3710 2.065899 CACTGTTGGAAGTCCCCAAA 57.934 50.000 0.00 0.00 46.68 3.28
733 3713 2.091333 ACTGTTGGAAGTCCCCAAACAT 60.091 45.455 0.00 0.00 46.68 2.71
772 3756 2.356667 CCAAGCAACCCCTCTCCC 59.643 66.667 0.00 0.00 0.00 4.30
776 3760 2.285743 GCAACCCCTCTCCCCTCT 60.286 66.667 0.00 0.00 0.00 3.69
777 3761 2.371259 GCAACCCCTCTCCCCTCTC 61.371 68.421 0.00 0.00 0.00 3.20
781 3765 2.018086 CCCCTCTCCCCTCTCCTCT 61.018 68.421 0.00 0.00 0.00 3.69
813 3797 6.887002 AGGAGTTCAACCAGAAGAAATATTCC 59.113 38.462 0.00 0.00 36.78 3.01
816 3809 7.461749 AGTTCAACCAGAAGAAATATTCCTCA 58.538 34.615 0.00 0.00 36.78 3.86
828 3821 7.744733 AGAAATATTCCTCATCTTCTTCTCCC 58.255 38.462 0.00 0.00 0.00 4.30
830 3823 6.933514 ATATTCCTCATCTTCTTCTCCCTC 57.066 41.667 0.00 0.00 0.00 4.30
841 3834 1.216678 CTTCTCCCTCCCTCTCAGCTA 59.783 57.143 0.00 0.00 0.00 3.32
843 3836 1.063567 TCTCCCTCCCTCTCAGCTAAC 60.064 57.143 0.00 0.00 0.00 2.34
886 3897 8.683550 TTGATCGTCAAAGCTTATATATACCG 57.316 34.615 0.00 0.00 32.71 4.02
927 3946 0.682292 GATCGTCCCTTCTCCCATCC 59.318 60.000 0.00 0.00 0.00 3.51
928 3947 0.764752 ATCGTCCCTTCTCCCATCCC 60.765 60.000 0.00 0.00 0.00 3.85
929 3948 1.383248 CGTCCCTTCTCCCATCCCT 60.383 63.158 0.00 0.00 0.00 4.20
1007 4055 0.178975 AAACCTCCACCAATGGCGAA 60.179 50.000 0.00 0.00 46.80 4.70
1634 4703 4.875713 GGCGACGCCCAATCCCAT 62.876 66.667 28.74 0.00 44.06 4.00
1637 4712 1.889105 CGACGCCCAATCCCATCAG 60.889 63.158 0.00 0.00 0.00 2.90
1648 4723 1.081242 CCCATCAGCAACAACACGC 60.081 57.895 0.00 0.00 0.00 5.34
1818 4899 1.603739 GGTGGTGGTGAAGAAGGGC 60.604 63.158 0.00 0.00 0.00 5.19
1950 5031 6.295719 TGAGATGATCGATGATGATCCAAT 57.704 37.500 0.54 0.00 43.34 3.16
1951 5032 6.338937 TGAGATGATCGATGATGATCCAATC 58.661 40.000 0.54 0.00 43.34 2.67
1952 5033 6.070995 TGAGATGATCGATGATGATCCAATCA 60.071 38.462 0.54 7.15 43.34 2.57
1997 5078 7.195646 TGATTATTGCACAGCTTAATTGTAGC 58.804 34.615 6.34 6.34 38.93 3.58
2014 5095 8.985315 AATTGTAGCTCTGATCCATTAATTCA 57.015 30.769 0.00 0.00 0.00 2.57
2056 5138 7.887996 TGCATTCCTTCATTCATTTGTAAAC 57.112 32.000 0.00 0.00 0.00 2.01
2119 5226 6.072508 ACAGCAATGTTTAGTGTAACCATCAG 60.073 38.462 0.00 0.00 37.80 2.90
2139 5249 7.009815 CCATCAGCATCATCATGTTGTAAAAAC 59.990 37.037 3.76 0.00 40.99 2.43
2144 5254 6.400303 GCATCATCATGTTGTAAAAACACAGC 60.400 38.462 3.76 0.00 32.37 4.40
2163 5273 6.427547 ACACAGCCCATTTCATTTTATTTGTG 59.572 34.615 0.00 0.00 37.59 3.33
2196 5309 7.223582 TGCAATTTGTAACCAATTGTTGTACAG 59.776 33.333 4.43 0.39 37.83 2.74
2198 5311 9.474920 CAATTTGTAACCAATTGTTGTACAGAT 57.525 29.630 4.43 7.45 37.83 2.90
2200 5313 6.567687 TGTAACCAATTGTTGTACAGATGG 57.432 37.500 4.43 4.50 39.84 3.51
2208 5321 0.548926 TTGTACAGATGGGGCCCTCA 60.549 55.000 25.93 18.75 0.00 3.86
2301 5415 3.784511 AGATCAGGCTATTCACATGGG 57.215 47.619 0.00 0.00 0.00 4.00
2310 5424 5.606749 AGGCTATTCACATGGGTTGTATCTA 59.393 40.000 0.00 0.00 36.57 1.98
2311 5425 5.701290 GGCTATTCACATGGGTTGTATCTAC 59.299 44.000 0.00 0.00 36.57 2.59
2312 5426 6.464465 GGCTATTCACATGGGTTGTATCTACT 60.464 42.308 0.00 0.00 36.57 2.57
2313 5427 6.992715 GCTATTCACATGGGTTGTATCTACTT 59.007 38.462 0.00 0.00 36.57 2.24
2314 5428 7.041780 GCTATTCACATGGGTTGTATCTACTTG 60.042 40.741 0.00 0.00 36.57 3.16
2315 5429 6.367374 TTCACATGGGTTGTATCTACTTGA 57.633 37.500 0.00 0.00 36.57 3.02
2341 5463 7.298374 AGAGTATTTTATCCCCTTTGATTCCC 58.702 38.462 0.00 0.00 0.00 3.97
2387 5512 6.466308 AAAAACAAGCAAGAACAAGAACAC 57.534 33.333 0.00 0.00 0.00 3.32
2388 5513 4.782019 AACAAGCAAGAACAAGAACACA 57.218 36.364 0.00 0.00 0.00 3.72
2401 5526 5.111293 ACAAGAACACAAAATTTGAGGCAG 58.889 37.500 13.19 0.00 0.00 4.85
2404 5529 5.733676 AGAACACAAAATTTGAGGCAGTTT 58.266 33.333 13.19 0.00 0.00 2.66
2469 5594 4.142116 TGGAGCATCACCAATTTGCTAATG 60.142 41.667 1.63 0.00 46.21 1.90
2533 5658 7.276658 TGTACAGGAGTGACAAGAATAACAAA 58.723 34.615 0.00 0.00 0.00 2.83
2574 5699 8.925338 TGGGTTATGTTTTGTTAGGTTTATTGT 58.075 29.630 0.00 0.00 0.00 2.71
2582 5707 9.589111 GTTTTGTTAGGTTTATTGTTTCCTTCA 57.411 29.630 0.00 0.00 0.00 3.02
2585 5732 8.472007 TGTTAGGTTTATTGTTTCCTTCATGT 57.528 30.769 0.00 0.00 0.00 3.21
2624 5771 8.496534 TTTATCTGATGATGATTCCTAGGACA 57.503 34.615 12.22 7.86 34.32 4.02
2655 5803 6.706295 AGATTGAACCCAGACAAAACAAAAA 58.294 32.000 0.00 0.00 0.00 1.94
2656 5804 6.818142 AGATTGAACCCAGACAAAACAAAAAG 59.182 34.615 0.00 0.00 0.00 2.27
2657 5805 4.249661 TGAACCCAGACAAAACAAAAAGC 58.750 39.130 0.00 0.00 0.00 3.51
2658 5806 3.971245 ACCCAGACAAAACAAAAAGCA 57.029 38.095 0.00 0.00 0.00 3.91
2659 5807 4.278975 ACCCAGACAAAACAAAAAGCAA 57.721 36.364 0.00 0.00 0.00 3.91
2660 5808 4.252878 ACCCAGACAAAACAAAAAGCAAG 58.747 39.130 0.00 0.00 0.00 4.01
2731 6474 3.786368 TCAGATTCATCCACACCAACA 57.214 42.857 0.00 0.00 0.00 3.33
2817 6565 0.180171 GCTTGGGGCCAAACAAAACT 59.820 50.000 4.39 0.00 35.33 2.66
2826 6574 3.490249 GGCCAAACAAAACTACACTCCAC 60.490 47.826 0.00 0.00 0.00 4.02
2828 6576 4.668289 CCAAACAAAACTACACTCCACAC 58.332 43.478 0.00 0.00 0.00 3.82
2831 6579 2.933906 ACAAAACTACACTCCACACACG 59.066 45.455 0.00 0.00 0.00 4.49
2835 6583 3.570926 ACTACACTCCACACACGTATG 57.429 47.619 0.00 0.00 0.00 2.39
2882 6630 2.803956 GCATCAGCTTTGCAACAAACAT 59.196 40.909 12.45 0.00 39.90 2.71
2888 6636 2.867647 GCTTTGCAACAAACATCCTCCC 60.868 50.000 0.00 0.00 0.00 4.30
2889 6637 1.337118 TTGCAACAAACATCCTCCCC 58.663 50.000 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.039856 TGCTGGCCTTGAGTTTTTCC 58.960 50.000 3.32 0.00 0.00 3.13
68 69 7.977853 GTGTTATGGAAATGCTTTTCATGATCT 59.022 33.333 22.27 6.50 42.55 2.75
100 101 6.237901 ACACATATGCTTGAGAGGTAACAAA 58.762 36.000 1.58 0.00 41.41 2.83
137 138 4.822350 TGTATGTTCCCGACATTTGAAACA 59.178 37.500 0.00 0.00 46.80 2.83
142 143 6.668323 GGAATATGTATGTTCCCGACATTTG 58.332 40.000 8.68 0.00 46.80 2.32
143 144 6.877611 GGAATATGTATGTTCCCGACATTT 57.122 37.500 8.68 0.00 46.80 2.32
152 153 3.134574 TGGCCGGGAATATGTATGTTC 57.865 47.619 2.18 0.00 0.00 3.18
158 159 0.466189 CAGCTTGGCCGGGAATATGT 60.466 55.000 2.18 0.00 0.00 2.29
161 162 2.124320 GCAGCTTGGCCGGGAATA 60.124 61.111 2.18 0.00 0.00 1.75
165 166 1.603236 TTATTTGCAGCTTGGCCGGG 61.603 55.000 2.18 0.00 0.00 5.73
240 241 6.051074 GCAAAGCATAAATTAGCCCAAATCT 58.949 36.000 0.00 0.00 0.00 2.40
241 242 6.051074 AGCAAAGCATAAATTAGCCCAAATC 58.949 36.000 0.00 0.00 0.00 2.17
242 243 5.993055 AGCAAAGCATAAATTAGCCCAAAT 58.007 33.333 0.00 0.00 0.00 2.32
245 246 4.465660 TCAAGCAAAGCATAAATTAGCCCA 59.534 37.500 0.00 0.00 0.00 5.36
246 247 5.009854 TCAAGCAAAGCATAAATTAGCCC 57.990 39.130 0.00 0.00 0.00 5.19
247 248 7.404203 CAATTCAAGCAAAGCATAAATTAGCC 58.596 34.615 0.00 0.00 0.00 3.93
249 250 7.466320 GCCCAATTCAAGCAAAGCATAAATTAG 60.466 37.037 0.00 0.00 0.00 1.73
250 251 6.315891 GCCCAATTCAAGCAAAGCATAAATTA 59.684 34.615 0.00 0.00 0.00 1.40
251 252 5.124297 GCCCAATTCAAGCAAAGCATAAATT 59.876 36.000 0.00 0.00 0.00 1.82
252 253 4.637091 GCCCAATTCAAGCAAAGCATAAAT 59.363 37.500 0.00 0.00 0.00 1.40
254 255 3.598299 GCCCAATTCAAGCAAAGCATAA 58.402 40.909 0.00 0.00 0.00 1.90
255 256 2.093553 GGCCCAATTCAAGCAAAGCATA 60.094 45.455 0.00 0.00 0.00 3.14
256 257 1.339342 GGCCCAATTCAAGCAAAGCAT 60.339 47.619 0.00 0.00 0.00 3.79
257 258 0.035176 GGCCCAATTCAAGCAAAGCA 59.965 50.000 0.00 0.00 0.00 3.91
258 259 1.015607 CGGCCCAATTCAAGCAAAGC 61.016 55.000 0.00 0.00 0.00 3.51
259 260 0.390209 CCGGCCCAATTCAAGCAAAG 60.390 55.000 0.00 0.00 0.00 2.77
262 263 1.000233 ATCCGGCCCAATTCAAGCA 60.000 52.632 0.00 0.00 0.00 3.91
263 264 1.037030 TCATCCGGCCCAATTCAAGC 61.037 55.000 0.00 0.00 0.00 4.01
264 265 1.696063 ATCATCCGGCCCAATTCAAG 58.304 50.000 0.00 0.00 0.00 3.02
265 266 2.031120 GAATCATCCGGCCCAATTCAA 58.969 47.619 0.00 0.00 0.00 2.69
266 267 1.064091 TGAATCATCCGGCCCAATTCA 60.064 47.619 13.78 13.78 34.80 2.57
272 273 2.196245 GCCTTGAATCATCCGGCCC 61.196 63.158 0.00 0.00 35.96 5.80
278 279 6.312426 CGGAATATCTGTAGCCTTGAATCATC 59.688 42.308 0.00 0.00 0.00 2.92
281 282 4.932200 CCGGAATATCTGTAGCCTTGAATC 59.068 45.833 0.00 0.00 0.00 2.52
290 291 0.389948 GGGCGCCGGAATATCTGTAG 60.390 60.000 22.54 0.00 0.00 2.74
293 294 2.738521 CGGGCGCCGGAATATCTG 60.739 66.667 28.59 0.00 44.15 2.90
310 311 4.548346 CGAAATTCGAGTAGATTCGTTGCC 60.548 45.833 10.18 0.00 43.74 4.52
311 312 4.031426 ACGAAATTCGAGTAGATTCGTTGC 59.969 41.667 22.92 0.00 46.31 4.17
315 316 4.269312 TCGACGAAATTCGAGTAGATTCG 58.731 43.478 22.92 17.41 43.74 3.34
355 356 1.872234 CCGTCCGTCTGTATGCACG 60.872 63.158 0.00 0.00 35.72 5.34
356 357 0.801067 GTCCGTCCGTCTGTATGCAC 60.801 60.000 0.00 0.00 0.00 4.57
358 359 1.585521 CGTCCGTCCGTCTGTATGC 60.586 63.158 0.00 0.00 0.00 3.14
359 360 1.063649 CCGTCCGTCCGTCTGTATG 59.936 63.158 0.00 0.00 0.00 2.39
365 372 1.372087 ATGTACTCCGTCCGTCCGTC 61.372 60.000 0.00 0.00 0.00 4.79
386 393 8.354711 ACAGAGGGAGTATGTGTGTATATATG 57.645 38.462 0.00 0.00 0.00 1.78
388 395 9.871175 TTTACAGAGGGAGTATGTGTGTATATA 57.129 33.333 0.00 0.00 31.40 0.86
391 398 6.668283 AGTTTACAGAGGGAGTATGTGTGTAT 59.332 38.462 0.00 0.00 31.40 2.29
393 400 4.838986 AGTTTACAGAGGGAGTATGTGTGT 59.161 41.667 0.00 0.00 31.40 3.72
394 401 5.407407 AGTTTACAGAGGGAGTATGTGTG 57.593 43.478 0.00 0.00 31.40 3.82
402 409 8.861086 TGCTCTTATATTAGTTTACAGAGGGAG 58.139 37.037 0.00 0.00 0.00 4.30
453 460 9.490379 CCTCCGTAAACTAATATAAGAGCATTT 57.510 33.333 0.00 0.00 0.00 2.32
455 462 7.453752 TCCCTCCGTAAACTAATATAAGAGCAT 59.546 37.037 0.00 0.00 0.00 3.79
456 463 6.779049 TCCCTCCGTAAACTAATATAAGAGCA 59.221 38.462 0.00 0.00 0.00 4.26
457 464 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
458 465 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
460 467 9.512588 TCTACTCCCTCCGTAAACTAATATAAG 57.487 37.037 0.00 0.00 0.00 1.73
461 468 9.866655 TTCTACTCCCTCCGTAAACTAATATAA 57.133 33.333 0.00 0.00 0.00 0.98
462 469 9.866655 TTTCTACTCCCTCCGTAAACTAATATA 57.133 33.333 0.00 0.00 0.00 0.86
463 470 8.773033 TTTCTACTCCCTCCGTAAACTAATAT 57.227 34.615 0.00 0.00 0.00 1.28
464 471 8.593945 TTTTCTACTCCCTCCGTAAACTAATA 57.406 34.615 0.00 0.00 0.00 0.98
466 473 6.721208 TCTTTTCTACTCCCTCCGTAAACTAA 59.279 38.462 0.00 0.00 0.00 2.24
467 474 6.248433 TCTTTTCTACTCCCTCCGTAAACTA 58.752 40.000 0.00 0.00 0.00 2.24
468 475 5.082425 TCTTTTCTACTCCCTCCGTAAACT 58.918 41.667 0.00 0.00 0.00 2.66
474 481 4.221041 AGTTCTTCTTTTCTACTCCCTCCG 59.779 45.833 0.00 0.00 0.00 4.63
475 482 5.483811 CAGTTCTTCTTTTCTACTCCCTCC 58.516 45.833 0.00 0.00 0.00 4.30
477 484 4.908481 ACCAGTTCTTCTTTTCTACTCCCT 59.092 41.667 0.00 0.00 0.00 4.20
479 486 5.221661 TGGACCAGTTCTTCTTTTCTACTCC 60.222 44.000 0.00 0.00 0.00 3.85
480 487 5.855045 TGGACCAGTTCTTCTTTTCTACTC 58.145 41.667 0.00 0.00 0.00 2.59
481 488 5.888982 TGGACCAGTTCTTCTTTTCTACT 57.111 39.130 0.00 0.00 0.00 2.57
521 3486 4.681484 AGCCCATTTCATTTTCTCTTCCT 58.319 39.130 0.00 0.00 0.00 3.36
522 3487 4.708909 AGAGCCCATTTCATTTTCTCTTCC 59.291 41.667 0.00 0.00 0.00 3.46
523 3488 5.911378 AGAGCCCATTTCATTTTCTCTTC 57.089 39.130 0.00 0.00 0.00 2.87
604 3577 0.034186 TCTCATGTTGATGGGGGTGC 60.034 55.000 0.00 0.00 29.98 5.01
605 3578 1.561076 TCTCTCATGTTGATGGGGGTG 59.439 52.381 0.00 0.00 31.54 4.61
607 3580 1.842562 ACTCTCTCATGTTGATGGGGG 59.157 52.381 0.00 0.00 30.64 5.40
610 3583 3.947868 ACCAACTCTCTCATGTTGATGG 58.052 45.455 7.33 0.67 44.29 3.51
730 3710 2.747446 GGACGGTGCATGAGTTTTATGT 59.253 45.455 0.00 0.00 0.00 2.29
733 3713 2.147958 GTGGACGGTGCATGAGTTTTA 58.852 47.619 5.42 0.00 0.00 1.52
781 3765 1.630369 CTGGTTGAACTCCTCCATGGA 59.370 52.381 15.27 15.27 43.86 3.41
813 3797 2.965147 GAGGGAGGGAGAAGAAGATGAG 59.035 54.545 0.00 0.00 0.00 2.90
816 3809 2.589664 TGAGAGGGAGGGAGAAGAAGAT 59.410 50.000 0.00 0.00 0.00 2.40
826 3819 0.031616 AGGTTAGCTGAGAGGGAGGG 60.032 60.000 0.00 0.00 0.00 4.30
828 3821 2.091885 AGAGAGGTTAGCTGAGAGGGAG 60.092 54.545 0.00 0.00 0.00 4.30
830 3823 2.452600 AGAGAGGTTAGCTGAGAGGG 57.547 55.000 0.00 0.00 0.00 4.30
886 3897 2.125350 CTTGTCGGAGGAGCCTGC 60.125 66.667 0.00 0.00 0.00 4.85
927 3946 1.977129 GGATCAATGGAGGAGAGGAGG 59.023 57.143 0.00 0.00 0.00 4.30
928 3947 2.687297 TGGATCAATGGAGGAGAGGAG 58.313 52.381 0.00 0.00 0.00 3.69
929 3948 2.875102 TGGATCAATGGAGGAGAGGA 57.125 50.000 0.00 0.00 0.00 3.71
1007 4055 1.912043 CCATCTCCCTCTTCTTGGTGT 59.088 52.381 0.00 0.00 0.00 4.16
1623 4692 0.971959 TGTTGCTGATGGGATTGGGC 60.972 55.000 0.00 0.00 0.00 5.36
1628 4697 1.167851 CGTGTTGTTGCTGATGGGAT 58.832 50.000 0.00 0.00 0.00 3.85
1630 4699 1.081242 GCGTGTTGTTGCTGATGGG 60.081 57.895 0.00 0.00 0.00 4.00
1631 4700 1.951510 AGCGTGTTGTTGCTGATGG 59.048 52.632 0.00 0.00 40.62 3.51
1637 4712 0.040958 CTTCTCCAGCGTGTTGTTGC 60.041 55.000 0.00 0.00 0.00 4.17
1648 4723 3.267974 GGCAAACGCCTTCTCCAG 58.732 61.111 0.00 0.00 46.85 3.86
1721 4796 1.744741 GAAGCAGCAGCAGGAGACC 60.745 63.158 3.17 0.00 45.49 3.85
1795 4873 0.182537 TTCTTCACCACCACCACCTG 59.817 55.000 0.00 0.00 0.00 4.00
1950 5031 4.341520 CAGTGGTGAGATGAGATGAGATGA 59.658 45.833 0.00 0.00 0.00 2.92
1951 5032 4.341520 TCAGTGGTGAGATGAGATGAGATG 59.658 45.833 0.00 0.00 0.00 2.90
1952 5033 4.544683 TCAGTGGTGAGATGAGATGAGAT 58.455 43.478 0.00 0.00 0.00 2.75
1953 5034 3.973425 TCAGTGGTGAGATGAGATGAGA 58.027 45.455 0.00 0.00 0.00 3.27
1954 5035 4.940905 ATCAGTGGTGAGATGAGATGAG 57.059 45.455 0.00 0.00 35.66 2.90
1997 5078 7.286087 TGAATTGGGTGAATTAATGGATCAGAG 59.714 37.037 0.00 0.00 34.18 3.35
2014 5095 6.993902 GGAATGCAAATATGAATGAATTGGGT 59.006 34.615 0.00 0.00 0.00 4.51
2056 5138 8.251026 TGAGTCAAGGTTAACTATGATGTACAG 58.749 37.037 14.13 0.00 0.00 2.74
2119 5226 6.400303 GCTGTGTTTTTACAACATGATGATGC 60.400 38.462 10.29 0.00 32.14 3.91
2139 5249 6.649973 TCACAAATAAAATGAAATGGGCTGTG 59.350 34.615 0.00 0.00 0.00 3.66
2183 5293 2.166254 GGCCCCATCTGTACAACAATTG 59.834 50.000 3.24 3.24 0.00 2.32
2196 5309 1.689243 GGCAAATTGAGGGCCCCATC 61.689 60.000 21.43 11.77 41.90 3.51
2198 5311 2.284552 GGCAAATTGAGGGCCCCA 60.285 61.111 21.43 14.13 41.90 4.96
2310 5424 8.390921 TCAAAGGGGATAAAATACTCTTCAAGT 58.609 33.333 0.00 0.00 42.33 3.16
2311 5425 8.807948 TCAAAGGGGATAAAATACTCTTCAAG 57.192 34.615 0.00 0.00 0.00 3.02
2312 5426 9.768215 AATCAAAGGGGATAAAATACTCTTCAA 57.232 29.630 0.00 0.00 0.00 2.69
2313 5427 9.408648 GAATCAAAGGGGATAAAATACTCTTCA 57.591 33.333 0.00 0.00 0.00 3.02
2314 5428 8.851145 GGAATCAAAGGGGATAAAATACTCTTC 58.149 37.037 0.00 0.00 0.00 2.87
2315 5429 7.785028 GGGAATCAAAGGGGATAAAATACTCTT 59.215 37.037 0.00 0.00 0.00 2.85
2341 5463 3.889815 TCTGGGCTCAATTCTTATGGTG 58.110 45.455 0.00 0.00 0.00 4.17
2382 5507 6.421377 AAAACTGCCTCAAATTTTGTGTTC 57.579 33.333 8.89 2.48 0.00 3.18
2383 5508 6.816134 AAAAACTGCCTCAAATTTTGTGTT 57.184 29.167 8.89 5.59 0.00 3.32
2385 5510 8.397148 ACAATAAAAACTGCCTCAAATTTTGTG 58.603 29.630 8.89 6.62 0.00 3.33
2386 5511 8.504812 ACAATAAAAACTGCCTCAAATTTTGT 57.495 26.923 8.89 0.00 0.00 2.83
2499 5624 2.104111 TCACTCCTGTACAACAACTGGG 59.896 50.000 0.00 0.00 38.60 4.45
2624 5771 6.790232 TTGTCTGGGTTCAATCTTTTCTTT 57.210 33.333 0.00 0.00 0.00 2.52
2655 5803 3.282021 TGTTCTTGTTCTTGCTCTTGCT 58.718 40.909 0.00 0.00 40.48 3.91
2656 5804 3.698029 TGTTCTTGTTCTTGCTCTTGC 57.302 42.857 0.00 0.00 40.20 4.01
2657 5805 4.496895 CGTTTGTTCTTGTTCTTGCTCTTG 59.503 41.667 0.00 0.00 0.00 3.02
2658 5806 4.156008 ACGTTTGTTCTTGTTCTTGCTCTT 59.844 37.500 0.00 0.00 0.00 2.85
2659 5807 3.689649 ACGTTTGTTCTTGTTCTTGCTCT 59.310 39.130 0.00 0.00 0.00 4.09
2660 5808 4.016113 ACGTTTGTTCTTGTTCTTGCTC 57.984 40.909 0.00 0.00 0.00 4.26
2731 6474 2.827921 GTTGATGGGGTGCTCAATTCTT 59.172 45.455 0.00 0.00 34.18 2.52
2743 6486 2.530460 TCCTTTGGATGTTGATGGGG 57.470 50.000 0.00 0.00 0.00 4.96
2805 6553 3.129638 TGTGGAGTGTAGTTTTGTTTGGC 59.870 43.478 0.00 0.00 0.00 4.52
2817 6565 5.009911 ACTTTACATACGTGTGTGGAGTGTA 59.990 40.000 25.95 3.00 39.39 2.90
2826 6574 8.067784 AGTGAAATGAAACTTTACATACGTGTG 58.932 33.333 11.09 11.09 39.39 3.82
2828 6576 9.525007 GTAGTGAAATGAAACTTTACATACGTG 57.475 33.333 0.00 0.00 0.00 4.49
2835 6583 9.599322 CTGATGTGTAGTGAAATGAAACTTTAC 57.401 33.333 0.00 0.00 0.00 2.01
2888 6636 3.749665 TCAATTCTTGTTGCCCTTTGG 57.250 42.857 0.00 0.00 0.00 3.28
2889 6637 6.029346 ACTATCAATTCTTGTTGCCCTTTG 57.971 37.500 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.