Multiple sequence alignment - TraesCS7A01G437300

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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 TraesCS7A01G437300 chr7A 100.000 3431 0 0 1 3431 631983743 631987173 0.000000e+00 6336.0
1 TraesCS7A01G437300 chr7A 93.642 173 11 0 2773 2945 115807694 115807522 3.400000e-65 259.0
2 TraesCS7A01G437300 chr7D 94.959 2797 88 17 1 2761 548230384 548233163 0.000000e+00 4335.0
3 TraesCS7A01G437300 chr7D 97.342 489 13 0 2943 3431 548233190 548233678 0.000000e+00 832.0
4 TraesCS7A01G437300 chr7D 96.728 489 16 0 2943 3431 548235387 548235875 0.000000e+00 815.0
5 TraesCS7A01G437300 chr7D 95.192 312 13 1 2452 2761 548235049 548235360 3.080000e-135 492.0
6 TraesCS7A01G437300 chr7B 95.101 2776 90 17 2 2747 591460939 591463698 0.000000e+00 4331.0
7 TraesCS7A01G437300 chr7B 94.632 503 12 5 2943 3431 591463729 591464230 0.000000e+00 765.0
8 TraesCS7A01G437300 chr7B 95.758 165 7 0 2780 2944 412800478 412800314 2.030000e-67 267.0
9 TraesCS7A01G437300 chr7B 93.642 173 11 0 2777 2949 92045855 92046027 3.400000e-65 259.0
10 TraesCS7A01G437300 chr6D 86.639 2642 209 69 21 2588 51342280 51344851 0.000000e+00 2791.0
11 TraesCS7A01G437300 chr6D 85.989 2648 214 69 1 2588 51067577 51070127 0.000000e+00 2689.0
12 TraesCS7A01G437300 chr6D 86.726 2471 204 49 160 2580 53176500 53174104 0.000000e+00 2632.0
13 TraesCS7A01G437300 chr6D 85.992 2520 222 56 122 2587 50955828 50958270 0.000000e+00 2577.0
14 TraesCS7A01G437300 chr6D 88.088 2082 173 30 618 2649 51348748 51350804 0.000000e+00 2401.0
15 TraesCS7A01G437300 chr6D 87.800 2082 182 29 618 2649 51073966 51076025 0.000000e+00 2372.0
16 TraesCS7A01G437300 chr6D 84.770 499 45 14 2943 3431 53173859 53173382 4.010000e-129 472.0
17 TraesCS7A01G437300 chr6D 89.041 365 19 11 2966 3318 50958572 50958927 1.890000e-117 433.0
18 TraesCS7A01G437300 chr6D 83.918 342 27 14 3093 3419 51345348 51345676 5.560000e-78 302.0
19 TraesCS7A01G437300 chr6D 83.333 342 29 14 3093 3419 51070624 51070952 1.200000e-74 291.0
20 TraesCS7A01G437300 chr6D 93.678 174 10 1 2773 2946 302057015 302057187 3.400000e-65 259.0
21 TraesCS7A01G437300 chr6D 87.162 148 11 4 2944 3086 51345091 51345235 9.850000e-36 161.0
22 TraesCS7A01G437300 chr6D 85.811 148 13 4 2944 3086 51070367 51070511 2.130000e-32 150.0
23 TraesCS7A01G437300 chr6B 86.830 2536 209 54 114 2588 120595968 120593497 0.000000e+00 2717.0
24 TraesCS7A01G437300 chr6B 88.277 2269 183 32 345 2580 120355401 120353183 0.000000e+00 2639.0
25 TraesCS7A01G437300 chr6B 88.023 2054 175 38 580 2588 120132997 120130970 0.000000e+00 2364.0
26 TraesCS7A01G437300 chr6B 88.229 1971 149 35 654 2588 120317474 120315551 0.000000e+00 2278.0
27 TraesCS7A01G437300 chr6B 83.034 501 55 21 2943 3431 120315318 120314836 8.800000e-116 427.0
28 TraesCS7A01G437300 chr6B 84.802 329 21 13 3103 3419 120352696 120352385 1.550000e-78 303.0
29 TraesCS7A01G437300 chr6B 79.946 369 41 18 2 352 120355855 120355502 1.230000e-59 241.0
30 TraesCS7A01G437300 chr6B 89.583 144 12 2 2943 3086 120352929 120352789 2.720000e-41 180.0
31 TraesCS7A01G437300 chr6B 76.435 331 32 28 74 399 120318146 120317857 1.660000e-28 137.0
32 TraesCS7A01G437300 chr6B 77.670 206 20 18 1 198 120133877 120133690 6.060000e-18 102.0
33 TraesCS7A01G437300 chr5D 88.109 2279 168 45 374 2568 57819200 57821459 0.000000e+00 2612.0
34 TraesCS7A01G437300 chr5B 87.717 2304 172 49 376 2588 60826329 60824046 0.000000e+00 2584.0
35 TraesCS7A01G437300 chr3D 87.060 2357 217 40 289 2588 560025269 560022944 0.000000e+00 2582.0
36 TraesCS7A01G437300 chr1B 86.938 2358 217 41 289 2588 4519380 4517056 0.000000e+00 2564.0
37 TraesCS7A01G437300 chr1B 88.622 1960 149 32 691 2588 70232797 70234744 0.000000e+00 2316.0
38 TraesCS7A01G437300 chr1B 91.304 184 14 2 2766 2949 619401633 619401452 2.040000e-62 250.0
39 TraesCS7A01G437300 chr1B 100.000 39 0 0 244 282 3935790 3935828 4.750000e-09 73.1
40 TraesCS7A01G437300 chr1B 100.000 38 0 0 244 281 4543455 4543418 1.710000e-08 71.3
41 TraesCS7A01G437300 chr1B 75.862 174 17 13 188 338 4955373 4955202 7.950000e-07 65.8
42 TraesCS7A01G437300 chr6A 87.376 2313 182 43 321 2588 64168187 64165940 0.000000e+00 2553.0
43 TraesCS7A01G437300 chr6A 85.177 479 45 17 2949 3416 64165698 64165235 5.180000e-128 468.0
44 TraesCS7A01G437300 chr6A 76.884 796 82 50 21 773 64175761 64175025 1.170000e-94 357.0
45 TraesCS7A01G437300 chr6A 80.623 289 33 15 3 285 64168675 64168404 5.810000e-48 202.0
46 TraesCS7A01G437300 chr2D 95.783 166 7 0 2779 2944 32474469 32474304 5.640000e-68 268.0
47 TraesCS7A01G437300 chr2D 91.803 183 13 2 2777 2958 161906849 161907030 1.580000e-63 254.0
48 TraesCS7A01G437300 chrUn 93.785 177 10 1 2779 2954 74119450 74119626 7.300000e-67 265.0
49 TraesCS7A01G437300 chr4A 94.186 172 9 1 2777 2947 346686828 346686999 9.440000e-66 261.0
50 TraesCS7A01G437300 chr3B 82.308 260 33 8 286 536 318290228 318290483 2.680000e-51 213.0
51 TraesCS7A01G437300 chr1A 78.495 186 11 15 181 340 32545121 32545303 1.010000e-15 95.3


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 TraesCS7A01G437300 chr7A 631983743 631987173 3430 False 6336.000000 6336 100.00000 1 3431 1 chr7A.!!$F1 3430
1 TraesCS7A01G437300 chr7D 548230384 548235875 5491 False 1618.500000 4335 96.05525 1 3431 4 chr7D.!!$F1 3430
2 TraesCS7A01G437300 chr7B 591460939 591464230 3291 False 2548.000000 4331 94.86650 2 3431 2 chr7B.!!$F2 3429
3 TraesCS7A01G437300 chr6D 53173382 53176500 3118 True 1552.000000 2632 85.74800 160 3431 2 chr6D.!!$R1 3271
4 TraesCS7A01G437300 chr6D 50955828 50958927 3099 False 1505.000000 2577 87.51650 122 3318 2 chr6D.!!$F2 3196
5 TraesCS7A01G437300 chr6D 51342280 51350804 8524 False 1413.750000 2791 86.45175 21 3419 4 chr6D.!!$F4 3398
6 TraesCS7A01G437300 chr6D 51067577 51076025 8448 False 1375.500000 2689 85.73325 1 3419 4 chr6D.!!$F3 3418
7 TraesCS7A01G437300 chr6B 120593497 120595968 2471 True 2717.000000 2717 86.83000 114 2588 1 chr6B.!!$R1 2474
8 TraesCS7A01G437300 chr6B 120130970 120133877 2907 True 1233.000000 2364 82.84650 1 2588 2 chr6B.!!$R2 2587
9 TraesCS7A01G437300 chr6B 120314836 120318146 3310 True 947.333333 2278 82.56600 74 3431 3 chr6B.!!$R3 3357
10 TraesCS7A01G437300 chr6B 120352385 120355855 3470 True 840.750000 2639 85.65200 2 3419 4 chr6B.!!$R4 3417
11 TraesCS7A01G437300 chr5D 57819200 57821459 2259 False 2612.000000 2612 88.10900 374 2568 1 chr5D.!!$F1 2194
12 TraesCS7A01G437300 chr5B 60824046 60826329 2283 True 2584.000000 2584 87.71700 376 2588 1 chr5B.!!$R1 2212
13 TraesCS7A01G437300 chr3D 560022944 560025269 2325 True 2582.000000 2582 87.06000 289 2588 1 chr3D.!!$R1 2299
14 TraesCS7A01G437300 chr1B 4517056 4519380 2324 True 2564.000000 2564 86.93800 289 2588 1 chr1B.!!$R1 2299
15 TraesCS7A01G437300 chr1B 70232797 70234744 1947 False 2316.000000 2316 88.62200 691 2588 1 chr1B.!!$F2 1897
16 TraesCS7A01G437300 chr6A 64165235 64168675 3440 True 1074.333333 2553 84.39200 3 3416 3 chr6A.!!$R2 3413
17 TraesCS7A01G437300 chr6A 64175025 64175761 736 True 357.000000 357 76.88400 21 773 1 chr6A.!!$R1 752

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
182 221 0.615850 CTTCTCCTGACCCCTGTTCC 59.384 60.0 0.0 0.0 0.00 3.62 F
500 1166 1.076332 CCAAGCACGCTACAAGTACC 58.924 55.0 0.0 0.0 0.00 3.34 F
1983 2965 2.103263 CCTTTACGCTCTAGCCCTCAAT 59.897 50.0 0.0 0.0 37.91 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 2909 1.595093 GGCGTCCTGGTTTCCCAATG 61.595 60.000 0.00 0.0 41.27 2.82 R
2308 3291 4.579454 AAGACTCTAACTTACGTGCACA 57.421 40.909 18.64 0.0 0.00 4.57 R
2932 4012 0.108329 CACGCAAATACTCCCTCCGT 60.108 55.000 0.00 0.0 0.00 4.69 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
41 53 3.027412 CTCCTCTCCTCCGAATCAAAGA 58.973 50.000 0.00 0.00 0.00 2.52
47 59 1.009829 CTCCGAATCAAAGAAGCGGG 58.990 55.000 0.00 0.00 42.10 6.13
135 173 1.731433 CCGCCGTTTCTATCTCCCGA 61.731 60.000 0.00 0.00 0.00 5.14
182 221 0.615850 CTTCTCCTGACCCCTGTTCC 59.384 60.000 0.00 0.00 0.00 3.62
183 222 1.192146 TTCTCCTGACCCCTGTTCCG 61.192 60.000 0.00 0.00 0.00 4.30
184 223 3.316573 CTCCTGACCCCTGTTCCGC 62.317 68.421 0.00 0.00 0.00 5.54
185 224 3.322466 CCTGACCCCTGTTCCGCT 61.322 66.667 0.00 0.00 0.00 5.52
186 225 2.046892 CTGACCCCTGTTCCGCTG 60.047 66.667 0.00 0.00 0.00 5.18
187 226 2.847234 TGACCCCTGTTCCGCTGT 60.847 61.111 0.00 0.00 0.00 4.40
188 227 2.397413 CTGACCCCTGTTCCGCTGTT 62.397 60.000 0.00 0.00 0.00 3.16
189 228 1.671379 GACCCCTGTTCCGCTGTTC 60.671 63.158 0.00 0.00 0.00 3.18
291 525 8.840200 ACCGGTAGTATCATCCATAGATTTAT 57.160 34.615 4.49 0.00 0.00 1.40
312 548 8.574251 TTTATTGCTGTAAAGCCATTCTTCTA 57.426 30.769 1.45 0.00 32.88 2.10
313 549 6.690194 ATTGCTGTAAAGCCATTCTTCTAG 57.310 37.500 1.45 0.00 32.88 2.43
314 550 5.165961 TGCTGTAAAGCCATTCTTCTAGT 57.834 39.130 1.45 0.00 32.88 2.57
315 551 5.560724 TGCTGTAAAGCCATTCTTCTAGTT 58.439 37.500 1.45 0.00 32.88 2.24
316 552 5.643777 TGCTGTAAAGCCATTCTTCTAGTTC 59.356 40.000 1.45 0.00 32.88 3.01
317 553 5.877564 GCTGTAAAGCCATTCTTCTAGTTCT 59.122 40.000 0.00 0.00 32.88 3.01
406 1059 8.150945 TCTAGTTGAACAGATATTAGATTGGCC 58.849 37.037 0.00 0.00 0.00 5.36
453 1109 1.078848 GAACTCATCGGCTGTGGCT 60.079 57.895 0.00 0.00 38.73 4.75
500 1166 1.076332 CCAAGCACGCTACAAGTACC 58.924 55.000 0.00 0.00 0.00 3.34
506 1177 3.194968 AGCACGCTACAAGTACCAACTAT 59.805 43.478 0.00 0.00 33.75 2.12
650 1469 5.179368 TGGCTCGTTTCTTTGTATTCTCTTG 59.821 40.000 0.00 0.00 0.00 3.02
685 1596 6.106673 TGTTCAGGCTCTGCTACTTAATTAC 58.893 40.000 0.00 0.00 0.00 1.89
805 1739 5.122239 TCTCCATGCTTATGAAGAACAAACG 59.878 40.000 0.00 0.00 0.00 3.60
863 1807 9.594478 TTCATCAGTATTTTCTTCGTAGCAATA 57.406 29.630 0.00 0.00 0.00 1.90
1578 2550 8.501070 AGAGGAATCAATCATTATGACTTCCTT 58.499 33.333 20.85 13.30 40.66 3.36
1686 2668 2.620585 CTCCTCATACGATGCTCACAGA 59.379 50.000 0.00 0.00 0.00 3.41
1759 2741 4.260784 CGCATATTAGAACTTGGCCAGAAC 60.261 45.833 5.11 0.00 0.00 3.01
1863 2845 4.965814 ACATGATTGCATTATCTCGGAGT 58.034 39.130 0.00 0.00 30.68 3.85
1927 2909 3.312828 CGCTACTCTATTGATGTCAGCC 58.687 50.000 0.00 0.00 0.00 4.85
1983 2965 2.103263 CCTTTACGCTCTAGCCCTCAAT 59.897 50.000 0.00 0.00 37.91 2.57
2308 3291 1.002069 TGGATTGGCTGAACTGGGAT 58.998 50.000 0.00 0.00 0.00 3.85
2438 3445 8.717717 AGATTCCCTTATGTATTGATGAAGTGA 58.282 33.333 0.00 0.00 0.00 3.41
2612 3669 4.708421 ACTTTTATAGTAGGCACCACTCGA 59.292 41.667 0.00 0.00 34.56 4.04
2779 3859 1.273269 AAGATCTGCCTCTGCCTGCT 61.273 55.000 0.00 0.00 36.33 4.24
2780 3860 0.398239 AGATCTGCCTCTGCCTGCTA 60.398 55.000 0.00 0.00 36.33 3.49
2781 3861 0.249826 GATCTGCCTCTGCCTGCTAC 60.250 60.000 0.00 0.00 36.33 3.58
2782 3862 0.690411 ATCTGCCTCTGCCTGCTACT 60.690 55.000 0.00 0.00 36.33 2.57
2783 3863 1.143620 CTGCCTCTGCCTGCTACTC 59.856 63.158 0.00 0.00 36.33 2.59
2784 3864 2.308968 CTGCCTCTGCCTGCTACTCC 62.309 65.000 0.00 0.00 36.33 3.85
2785 3865 3.100503 GCCTCTGCCTGCTACTCCC 62.101 68.421 0.00 0.00 0.00 4.30
2786 3866 1.382420 CCTCTGCCTGCTACTCCCT 60.382 63.158 0.00 0.00 0.00 4.20
2787 3867 1.398958 CCTCTGCCTGCTACTCCCTC 61.399 65.000 0.00 0.00 0.00 4.30
2788 3868 1.381872 TCTGCCTGCTACTCCCTCC 60.382 63.158 0.00 0.00 0.00 4.30
2789 3869 2.759973 TGCCTGCTACTCCCTCCG 60.760 66.667 0.00 0.00 0.00 4.63
2790 3870 2.760385 GCCTGCTACTCCCTCCGT 60.760 66.667 0.00 0.00 0.00 4.69
2791 3871 2.359967 GCCTGCTACTCCCTCCGTT 61.360 63.158 0.00 0.00 0.00 4.44
2792 3872 1.900545 GCCTGCTACTCCCTCCGTTT 61.901 60.000 0.00 0.00 0.00 3.60
2793 3873 0.175989 CCTGCTACTCCCTCCGTTTC 59.824 60.000 0.00 0.00 0.00 2.78
2794 3874 1.187087 CTGCTACTCCCTCCGTTTCT 58.813 55.000 0.00 0.00 0.00 2.52
2795 3875 2.376109 CTGCTACTCCCTCCGTTTCTA 58.624 52.381 0.00 0.00 0.00 2.10
2796 3876 2.758979 CTGCTACTCCCTCCGTTTCTAA 59.241 50.000 0.00 0.00 0.00 2.10
2797 3877 3.167485 TGCTACTCCCTCCGTTTCTAAA 58.833 45.455 0.00 0.00 0.00 1.85
2798 3878 3.773119 TGCTACTCCCTCCGTTTCTAAAT 59.227 43.478 0.00 0.00 0.00 1.40
2799 3879 4.957954 TGCTACTCCCTCCGTTTCTAAATA 59.042 41.667 0.00 0.00 0.00 1.40
2800 3880 5.601313 TGCTACTCCCTCCGTTTCTAAATAT 59.399 40.000 0.00 0.00 0.00 1.28
2801 3881 6.099269 TGCTACTCCCTCCGTTTCTAAATATT 59.901 38.462 0.00 0.00 0.00 1.28
2802 3882 6.990939 GCTACTCCCTCCGTTTCTAAATATTT 59.009 38.462 5.89 5.89 0.00 1.40
2803 3883 7.041984 GCTACTCCCTCCGTTTCTAAATATTTG 60.042 40.741 11.05 1.65 0.00 2.32
2804 3884 6.718294 ACTCCCTCCGTTTCTAAATATTTGT 58.282 36.000 11.05 0.00 0.00 2.83
2805 3885 6.822170 ACTCCCTCCGTTTCTAAATATTTGTC 59.178 38.462 11.05 0.00 0.00 3.18
2806 3886 6.954232 TCCCTCCGTTTCTAAATATTTGTCT 58.046 36.000 11.05 0.00 0.00 3.41
2807 3887 7.399634 TCCCTCCGTTTCTAAATATTTGTCTT 58.600 34.615 11.05 0.00 0.00 3.01
2808 3888 7.886446 TCCCTCCGTTTCTAAATATTTGTCTTT 59.114 33.333 11.05 0.00 0.00 2.52
2809 3889 8.182227 CCCTCCGTTTCTAAATATTTGTCTTTC 58.818 37.037 11.05 0.00 0.00 2.62
2810 3890 8.947115 CCTCCGTTTCTAAATATTTGTCTTTCT 58.053 33.333 11.05 0.00 0.00 2.52
2825 3905 7.979115 TTGTCTTTCTAAACGTTTCAAATGG 57.021 32.000 18.42 7.39 0.00 3.16
2826 3906 7.323049 TGTCTTTCTAAACGTTTCAAATGGA 57.677 32.000 18.42 9.38 0.00 3.41
2827 3907 7.190871 TGTCTTTCTAAACGTTTCAAATGGAC 58.809 34.615 18.42 18.78 0.00 4.02
2828 3908 7.066525 TGTCTTTCTAAACGTTTCAAATGGACT 59.933 33.333 18.42 0.00 0.00 3.85
2829 3909 8.553696 GTCTTTCTAAACGTTTCAAATGGACTA 58.446 33.333 18.42 0.00 0.00 2.59
2830 3910 8.553696 TCTTTCTAAACGTTTCAAATGGACTAC 58.446 33.333 18.42 0.00 0.00 2.73
2831 3911 7.789273 TTCTAAACGTTTCAAATGGACTACA 57.211 32.000 18.42 0.00 0.00 2.74
2832 3912 7.789273 TCTAAACGTTTCAAATGGACTACAA 57.211 32.000 18.42 0.00 0.00 2.41
2833 3913 7.632721 TCTAAACGTTTCAAATGGACTACAAC 58.367 34.615 18.42 0.00 0.00 3.32
2834 3914 5.821516 AACGTTTCAAATGGACTACAACA 57.178 34.783 0.00 0.00 0.00 3.33
2835 3915 6.385649 AACGTTTCAAATGGACTACAACAT 57.614 33.333 0.00 0.00 0.00 2.71
2836 3916 7.499321 AACGTTTCAAATGGACTACAACATA 57.501 32.000 0.00 0.00 0.00 2.29
2837 3917 6.894828 ACGTTTCAAATGGACTACAACATAC 58.105 36.000 0.00 0.00 0.00 2.39
2838 3918 6.013085 CGTTTCAAATGGACTACAACATACG 58.987 40.000 0.00 0.00 0.00 3.06
2839 3919 6.311723 GTTTCAAATGGACTACAACATACGG 58.688 40.000 0.00 0.00 0.00 4.02
2840 3920 5.408880 TCAAATGGACTACAACATACGGA 57.591 39.130 0.00 0.00 0.00 4.69
2841 3921 5.984725 TCAAATGGACTACAACATACGGAT 58.015 37.500 0.00 0.00 0.00 4.18
2842 3922 5.815222 TCAAATGGACTACAACATACGGATG 59.185 40.000 5.94 5.94 39.16 3.51
2844 3924 6.474140 AATGGACTACAACATACGGATGTA 57.526 37.500 15.10 0.00 45.93 2.29
2845 3925 6.665992 ATGGACTACAACATACGGATGTAT 57.334 37.500 15.10 8.21 45.93 2.29
2846 3926 6.474140 TGGACTACAACATACGGATGTATT 57.526 37.500 15.10 6.48 45.93 1.89
2847 3927 6.880484 TGGACTACAACATACGGATGTATTT 58.120 36.000 15.10 3.78 45.93 1.40
2848 3928 8.009622 TGGACTACAACATACGGATGTATTTA 57.990 34.615 15.10 4.80 45.93 1.40
2849 3929 8.139350 TGGACTACAACATACGGATGTATTTAG 58.861 37.037 15.10 15.91 45.93 1.85
2850 3930 8.355169 GGACTACAACATACGGATGTATTTAGA 58.645 37.037 15.10 0.00 45.93 2.10
2851 3931 9.178427 GACTACAACATACGGATGTATTTAGAC 57.822 37.037 15.10 10.93 45.93 2.59
2852 3932 8.689061 ACTACAACATACGGATGTATTTAGACA 58.311 33.333 15.10 0.00 45.93 3.41
2853 3933 9.692749 CTACAACATACGGATGTATTTAGACAT 57.307 33.333 15.10 0.00 45.93 3.06
2885 3965 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
2886 3966 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
2887 3967 5.700832 TGTAGATTCACTCATTTTGCTTCGT 59.299 36.000 0.00 0.00 0.00 3.85
2888 3968 6.871492 TGTAGATTCACTCATTTTGCTTCGTA 59.129 34.615 0.00 0.00 0.00 3.43
2889 3969 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
2890 3970 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
2891 3971 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
2892 3972 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
2893 3973 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
2894 3974 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
2895 3975 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
2896 3976 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
2897 3977 6.818644 ACTCATTTTGCTTCGTATGTAGTCAT 59.181 34.615 0.00 0.00 38.00 3.06
2898 3978 7.334421 ACTCATTTTGCTTCGTATGTAGTCATT 59.666 33.333 0.00 0.00 35.70 2.57
2899 3979 8.039603 TCATTTTGCTTCGTATGTAGTCATTT 57.960 30.769 0.00 0.00 35.70 2.32
2900 3980 7.962373 TCATTTTGCTTCGTATGTAGTCATTTG 59.038 33.333 0.00 0.00 35.70 2.32
2901 3981 6.795098 TTTGCTTCGTATGTAGTCATTTGT 57.205 33.333 0.00 0.00 35.70 2.83
2902 3982 6.795098 TTGCTTCGTATGTAGTCATTTGTT 57.205 33.333 0.00 0.00 35.70 2.83
2903 3983 6.795098 TGCTTCGTATGTAGTCATTTGTTT 57.205 33.333 0.00 0.00 35.70 2.83
2904 3984 7.892778 TGCTTCGTATGTAGTCATTTGTTTA 57.107 32.000 0.00 0.00 35.70 2.01
2905 3985 8.312896 TGCTTCGTATGTAGTCATTTGTTTAA 57.687 30.769 0.00 0.00 35.70 1.52
2906 3986 8.775527 TGCTTCGTATGTAGTCATTTGTTTAAA 58.224 29.630 0.00 0.00 35.70 1.52
2907 3987 9.769093 GCTTCGTATGTAGTCATTTGTTTAAAT 57.231 29.630 0.00 0.00 36.97 1.40
2935 4015 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2936 4016 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2937 4017 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2938 4018 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2939 4019 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2940 4020 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2941 4021 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3243 4505 5.368816 GGCTTCTAGAAATTTAGAGGGGGTA 59.631 44.000 6.63 0.00 31.68 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 53 3.645268 GAGGACAATGCCCCCGCTT 62.645 63.158 0.00 0.00 35.36 4.68
47 59 2.825836 CAGCGGAGGACAATGCCC 60.826 66.667 0.00 0.00 0.00 5.36
135 173 1.153628 GCGGTACCTTGAGCACGAT 60.154 57.895 10.90 0.00 0.00 3.73
183 222 0.928451 GAACCAACGCAACGAACAGC 60.928 55.000 0.00 0.00 0.00 4.40
184 223 0.316689 GGAACCAACGCAACGAACAG 60.317 55.000 0.00 0.00 0.00 3.16
185 224 1.722677 GGAACCAACGCAACGAACA 59.277 52.632 0.00 0.00 0.00 3.18
186 225 4.601315 GGAACCAACGCAACGAAC 57.399 55.556 0.00 0.00 0.00 3.95
312 548 9.274206 CAAAAAGCTTACTTTCTACCTAGAACT 57.726 33.333 0.00 0.00 45.48 3.01
313 549 8.016229 GCAAAAAGCTTACTTTCTACCTAGAAC 58.984 37.037 0.00 0.00 45.48 3.01
314 550 7.717875 TGCAAAAAGCTTACTTTCTACCTAGAA 59.282 33.333 0.00 0.00 45.48 2.10
315 551 7.221450 TGCAAAAAGCTTACTTTCTACCTAGA 58.779 34.615 0.00 0.00 45.48 2.43
316 552 7.435068 TGCAAAAAGCTTACTTTCTACCTAG 57.565 36.000 0.00 0.00 45.48 3.02
317 553 6.072673 GCTGCAAAAAGCTTACTTTCTACCTA 60.073 38.462 0.00 0.00 45.48 3.08
357 887 7.172342 AGAAATACTAGTATTTGTTGCCACCA 58.828 34.615 34.72 0.32 43.52 4.17
406 1059 8.099537 AGGGTGCAGTGATTATCAATAGATAAG 58.900 37.037 0.00 0.00 46.69 1.73
422 1078 0.179048 TGAGTTCACAGGGTGCAGTG 60.179 55.000 0.00 0.00 37.10 3.66
453 1109 9.243105 CAAGAAAGGAAGTAGGGAAATCATTTA 57.757 33.333 0.00 0.00 0.00 1.40
488 1152 5.106869 TGCAAAATAGTTGGTACTTGTAGCG 60.107 40.000 5.66 0.00 35.78 4.26
627 1443 5.390991 CCAAGAGAATACAAAGAAACGAGCC 60.391 44.000 0.00 0.00 0.00 4.70
650 1469 4.154918 CAGAGCCTGAACAATGAACTAACC 59.845 45.833 0.00 0.00 32.44 2.85
685 1596 7.910162 CCACATCATTGAATTAAACTAGAACCG 59.090 37.037 0.00 0.00 0.00 4.44
805 1739 5.934935 TTTTCTGTATCCGTCCAAAACTC 57.065 39.130 0.00 0.00 0.00 3.01
863 1807 2.498167 GAGATCACACTGGCAACACTT 58.502 47.619 0.00 0.00 46.17 3.16
1485 2457 4.475016 AGGTATTCCAGCCATTCTACACTT 59.525 41.667 0.00 0.00 35.89 3.16
1578 2550 5.512942 TCATCCATCCTGAACCAAACTTA 57.487 39.130 0.00 0.00 0.00 2.24
1863 2845 3.069300 TGATGCTTTTAAGGTTGCTGCAA 59.931 39.130 11.69 11.69 32.66 4.08
1927 2909 1.595093 GGCGTCCTGGTTTCCCAATG 61.595 60.000 0.00 0.00 41.27 2.82
1945 2927 6.715464 CGTAAAGGCTGTTATCAGTAAATGG 58.285 40.000 2.85 0.00 43.05 3.16
2308 3291 4.579454 AAGACTCTAACTTACGTGCACA 57.421 40.909 18.64 0.00 0.00 4.57
2779 3859 7.854337 ACAAATATTTAGAAACGGAGGGAGTA 58.146 34.615 0.00 0.00 0.00 2.59
2780 3860 6.718294 ACAAATATTTAGAAACGGAGGGAGT 58.282 36.000 0.00 0.00 0.00 3.85
2781 3861 7.048512 AGACAAATATTTAGAAACGGAGGGAG 58.951 38.462 0.00 0.00 0.00 4.30
2782 3862 6.954232 AGACAAATATTTAGAAACGGAGGGA 58.046 36.000 0.00 0.00 0.00 4.20
2783 3863 7.625828 AAGACAAATATTTAGAAACGGAGGG 57.374 36.000 0.00 0.00 0.00 4.30
2784 3864 8.947115 AGAAAGACAAATATTTAGAAACGGAGG 58.053 33.333 0.00 0.00 0.00 4.30
2799 3879 9.030301 CCATTTGAAACGTTTAGAAAGACAAAT 57.970 29.630 20.19 20.19 36.38 2.32
2800 3880 8.244802 TCCATTTGAAACGTTTAGAAAGACAAA 58.755 29.630 14.65 16.94 0.00 2.83
2801 3881 7.698970 GTCCATTTGAAACGTTTAGAAAGACAA 59.301 33.333 14.65 9.09 0.00 3.18
2802 3882 7.066525 AGTCCATTTGAAACGTTTAGAAAGACA 59.933 33.333 24.70 14.17 0.00 3.41
2803 3883 7.415229 AGTCCATTTGAAACGTTTAGAAAGAC 58.585 34.615 14.65 18.74 0.00 3.01
2804 3884 7.562454 AGTCCATTTGAAACGTTTAGAAAGA 57.438 32.000 14.65 9.85 0.00 2.52
2805 3885 8.339714 TGTAGTCCATTTGAAACGTTTAGAAAG 58.660 33.333 14.65 8.53 0.00 2.62
2806 3886 8.211116 TGTAGTCCATTTGAAACGTTTAGAAA 57.789 30.769 14.65 15.52 0.00 2.52
2807 3887 7.789273 TGTAGTCCATTTGAAACGTTTAGAA 57.211 32.000 14.65 11.83 0.00 2.10
2808 3888 7.280428 TGTTGTAGTCCATTTGAAACGTTTAGA 59.720 33.333 14.65 2.42 0.00 2.10
2809 3889 7.411274 TGTTGTAGTCCATTTGAAACGTTTAG 58.589 34.615 14.65 2.03 0.00 1.85
2810 3890 7.317842 TGTTGTAGTCCATTTGAAACGTTTA 57.682 32.000 14.65 0.00 0.00 2.01
2811 3891 6.197364 TGTTGTAGTCCATTTGAAACGTTT 57.803 33.333 14.57 14.57 0.00 3.60
2812 3892 5.821516 TGTTGTAGTCCATTTGAAACGTT 57.178 34.783 0.00 0.00 0.00 3.99
2813 3893 6.347079 CGTATGTTGTAGTCCATTTGAAACGT 60.347 38.462 0.00 0.00 0.00 3.99
2814 3894 6.013085 CGTATGTTGTAGTCCATTTGAAACG 58.987 40.000 0.00 0.00 0.00 3.60
2815 3895 6.148150 TCCGTATGTTGTAGTCCATTTGAAAC 59.852 38.462 0.00 0.00 0.00 2.78
2816 3896 6.231951 TCCGTATGTTGTAGTCCATTTGAAA 58.768 36.000 0.00 0.00 0.00 2.69
2817 3897 5.795972 TCCGTATGTTGTAGTCCATTTGAA 58.204 37.500 0.00 0.00 0.00 2.69
2818 3898 5.408880 TCCGTATGTTGTAGTCCATTTGA 57.591 39.130 0.00 0.00 0.00 2.69
2819 3899 5.584649 ACATCCGTATGTTGTAGTCCATTTG 59.415 40.000 0.00 0.00 44.07 2.32
2820 3900 5.741011 ACATCCGTATGTTGTAGTCCATTT 58.259 37.500 0.00 0.00 44.07 2.32
2821 3901 5.353394 ACATCCGTATGTTGTAGTCCATT 57.647 39.130 0.00 0.00 44.07 3.16
2822 3902 6.665992 ATACATCCGTATGTTGTAGTCCAT 57.334 37.500 0.00 0.00 44.07 3.41
2823 3903 6.474140 AATACATCCGTATGTTGTAGTCCA 57.526 37.500 0.00 0.00 44.07 4.02
2824 3904 8.355169 TCTAAATACATCCGTATGTTGTAGTCC 58.645 37.037 0.00 0.00 44.07 3.85
2825 3905 9.178427 GTCTAAATACATCCGTATGTTGTAGTC 57.822 37.037 0.00 0.00 44.07 2.59
2826 3906 8.689061 TGTCTAAATACATCCGTATGTTGTAGT 58.311 33.333 0.00 0.00 44.07 2.73
2827 3907 9.692749 ATGTCTAAATACATCCGTATGTTGTAG 57.307 33.333 0.00 0.00 44.07 2.74
2862 3942 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
2863 3943 5.700832 ACGAAGCAAAATGAGTGAATCTACA 59.299 36.000 0.00 0.00 0.00 2.74
2864 3944 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
2865 3945 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
2866 3946 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
2867 3947 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
2868 3948 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
2869 3949 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
2870 3950 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
2871 3951 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
2872 3952 6.163476 TGACTACATACGAAGCAAAATGAGT 58.837 36.000 0.00 0.00 0.00 3.41
2873 3953 6.647212 TGACTACATACGAAGCAAAATGAG 57.353 37.500 0.00 0.00 0.00 2.90
2874 3954 7.609760 AATGACTACATACGAAGCAAAATGA 57.390 32.000 0.00 0.00 35.50 2.57
2875 3955 7.750458 ACAAATGACTACATACGAAGCAAAATG 59.250 33.333 0.00 0.00 35.50 2.32
2876 3956 7.816640 ACAAATGACTACATACGAAGCAAAAT 58.183 30.769 0.00 0.00 35.50 1.82
2877 3957 7.197071 ACAAATGACTACATACGAAGCAAAA 57.803 32.000 0.00 0.00 35.50 2.44
2878 3958 6.795098 ACAAATGACTACATACGAAGCAAA 57.205 33.333 0.00 0.00 35.50 3.68
2879 3959 6.795098 AACAAATGACTACATACGAAGCAA 57.205 33.333 0.00 0.00 35.50 3.91
2880 3960 6.795098 AAACAAATGACTACATACGAAGCA 57.205 33.333 0.00 0.00 35.50 3.91
2881 3961 9.769093 ATTTAAACAAATGACTACATACGAAGC 57.231 29.630 0.00 0.00 35.50 3.86
2909 3989 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2910 3990 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2911 3991 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2912 3992 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2913 3993 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
2914 3994 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2915 3995 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2916 3996 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2917 3997 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2918 3998 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2919 3999 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2920 4000 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2921 4001 7.628501 AATACTCCCTCCGTTCCTAAATATT 57.371 36.000 0.00 0.00 0.00 1.28
2922 4002 7.450903 CAAATACTCCCTCCGTTCCTAAATAT 58.549 38.462 0.00 0.00 0.00 1.28
2923 4003 6.687139 GCAAATACTCCCTCCGTTCCTAAATA 60.687 42.308 0.00 0.00 0.00 1.40
2924 4004 5.681639 CAAATACTCCCTCCGTTCCTAAAT 58.318 41.667 0.00 0.00 0.00 1.40
2925 4005 4.624604 GCAAATACTCCCTCCGTTCCTAAA 60.625 45.833 0.00 0.00 0.00 1.85
2926 4006 3.118519 GCAAATACTCCCTCCGTTCCTAA 60.119 47.826 0.00 0.00 0.00 2.69
2927 4007 2.433239 GCAAATACTCCCTCCGTTCCTA 59.567 50.000 0.00 0.00 0.00 2.94
2928 4008 1.209747 GCAAATACTCCCTCCGTTCCT 59.790 52.381 0.00 0.00 0.00 3.36
2929 4009 1.664873 GCAAATACTCCCTCCGTTCC 58.335 55.000 0.00 0.00 0.00 3.62
2930 4010 1.287425 CGCAAATACTCCCTCCGTTC 58.713 55.000 0.00 0.00 0.00 3.95
2931 4011 0.611714 ACGCAAATACTCCCTCCGTT 59.388 50.000 0.00 0.00 0.00 4.44
2932 4012 0.108329 CACGCAAATACTCCCTCCGT 60.108 55.000 0.00 0.00 0.00 4.69
2933 4013 0.108329 ACACGCAAATACTCCCTCCG 60.108 55.000 0.00 0.00 0.00 4.63
2934 4014 1.369625 CACACGCAAATACTCCCTCC 58.630 55.000 0.00 0.00 0.00 4.30
2935 4015 1.369625 CCACACGCAAATACTCCCTC 58.630 55.000 0.00 0.00 0.00 4.30
2936 4016 0.676782 GCCACACGCAAATACTCCCT 60.677 55.000 0.00 0.00 37.47 4.20
2937 4017 1.800681 GCCACACGCAAATACTCCC 59.199 57.895 0.00 0.00 37.47 4.30
3243 4505 8.198109 ACTCTTGTGATATGTATAAGAAACGCT 58.802 33.333 0.00 0.00 0.00 5.07
3341 6804 5.070770 ACAATCACAACAAAAGTTCAGCA 57.929 34.783 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.