Multiple sequence alignment - TraesCS1A01G314000

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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 TraesCS1A01G314000 chr1A 100.000 3918 0 0 1 3918 505536676 505540593 0.000000e+00 7236.0
1 TraesCS1A01G314000 chr1A 100.000 1164 0 0 4197 5360 505540872 505542035 0.000000e+00 2150.0
2 TraesCS1A01G314000 chr1A 80.576 695 90 29 16 702 547253699 547254356 1.340000e-135 494.0
3 TraesCS1A01G314000 chr1A 97.183 71 2 0 206 276 505536847 505536917 2.620000e-23 121.0
4 TraesCS1A01G314000 chr1A 97.183 71 2 0 172 242 505536881 505536951 2.620000e-23 121.0
5 TraesCS1A01G314000 chr1D 93.381 3792 147 34 206 3918 409535036 409538802 0.000000e+00 5517.0
6 TraesCS1A01G314000 chr1D 92.154 599 21 6 4197 4794 409538826 409539399 0.000000e+00 822.0
7 TraesCS1A01G314000 chr1D 88.859 368 21 7 554 903 110519783 110519418 8.240000e-118 435.0
8 TraesCS1A01G314000 chr1D 87.263 369 25 1 4847 5193 409539398 409539766 8.360000e-108 401.0
9 TraesCS1A01G314000 chr1D 95.041 242 11 1 1 242 409534866 409535106 3.920000e-101 379.0
10 TraesCS1A01G314000 chr1D 93.220 118 7 1 5229 5345 409539949 409540066 7.140000e-39 172.0
11 TraesCS1A01G314000 chr1B 93.375 3698 153 36 279 3918 551720803 551724466 0.000000e+00 5387.0
12 TraesCS1A01G314000 chr1B 90.339 1180 60 10 4197 5345 551724489 551725645 0.000000e+00 1498.0
13 TraesCS1A01G314000 chr1B 83.369 463 55 12 326 769 546686363 546685904 5.000000e-110 409.0
14 TraesCS1A01G314000 chr1B 86.224 196 15 7 16 209 627744745 627744560 9.100000e-48 202.0
15 TraesCS1A01G314000 chr1B 83.920 199 21 6 16 209 77805729 77805921 4.270000e-41 180.0
16 TraesCS1A01G314000 chr5B 85.704 1364 132 32 2578 3917 582834178 582835502 0.000000e+00 1380.0
17 TraesCS1A01G314000 chr5B 81.745 997 116 38 1610 2559 582833213 582834190 0.000000e+00 773.0
18 TraesCS1A01G314000 chr5B 83.965 792 69 23 279 1025 692786412 692785634 0.000000e+00 706.0
19 TraesCS1A01G314000 chr5B 88.307 573 54 10 1053 1613 582832611 582833182 0.000000e+00 675.0
20 TraesCS1A01G314000 chr5B 82.192 511 63 16 202 702 472745860 472745368 1.070000e-111 414.0
21 TraesCS1A01G314000 chr5A 85.507 1242 116 27 2693 3918 594954759 594955952 0.000000e+00 1238.0
22 TraesCS1A01G314000 chr5A 81.106 995 125 38 1610 2563 594953722 594954694 0.000000e+00 737.0
23 TraesCS1A01G314000 chr5A 87.958 573 56 5 1053 1613 594953120 594953691 0.000000e+00 664.0
24 TraesCS1A01G314000 chr5A 87.338 308 30 6 4204 4508 594955980 594956281 1.430000e-90 344.0
25 TraesCS1A01G314000 chr5A 89.051 137 8 4 16 146 175564057 175564192 4.300000e-36 163.0
26 TraesCS1A01G314000 chr5A 77.049 183 33 7 2232 2410 594978178 594978355 4.420000e-16 97.1
27 TraesCS1A01G314000 chr5D 91.162 792 50 9 3122 3913 475501802 475502573 0.000000e+00 1057.0
28 TraesCS1A01G314000 chr5D 81.994 1244 148 44 1893 3093 475500594 475501804 0.000000e+00 987.0
29 TraesCS1A01G314000 chr5D 87.698 569 51 5 1053 1613 475499757 475500314 0.000000e+00 645.0
30 TraesCS1A01G314000 chr5D 84.816 652 71 12 279 903 12992590 12991940 9.800000e-177 630.0
31 TraesCS1A01G314000 chr5D 79.669 905 118 28 16 902 114628218 114627362 4.620000e-165 592.0
32 TraesCS1A01G314000 chr5D 86.613 493 47 11 428 903 486900292 486899802 1.320000e-145 527.0
33 TraesCS1A01G314000 chr5D 81.849 595 65 21 202 769 391983398 391982820 1.360000e-125 460.0
34 TraesCS1A01G314000 chr5D 88.197 305 33 2 4206 4508 475502609 475502912 1.420000e-95 361.0
35 TraesCS1A01G314000 chr2A 86.751 634 54 10 279 903 691231101 691230489 0.000000e+00 678.0
36 TraesCS1A01G314000 chr2A 100.000 28 0 0 1 28 691231409 691231382 1.000000e-02 52.8
37 TraesCS1A01G314000 chr6D 80.143 982 103 45 96 1033 389609280 389608347 0.000000e+00 649.0
38 TraesCS1A01G314000 chr2D 84.085 710 72 18 202 900 547676046 547676725 0.000000e+00 647.0
39 TraesCS1A01G314000 chr7D 81.170 786 76 22 279 1019 79530166 79530924 2.800000e-157 566.0
40 TraesCS1A01G314000 chr6B 88.208 424 42 4 281 702 656034188 656033771 2.880000e-137 499.0
41 TraesCS1A01G314000 chr6B 85.494 324 24 11 603 903 712258020 712258343 3.120000e-82 316.0
42 TraesCS1A01G314000 chr3A 84.163 221 20 9 1 209 94426824 94427041 3.270000e-47 200.0
43 TraesCS1A01G314000 chr3A 84.737 190 19 8 24 209 51280234 51280417 1.190000e-41 182.0
44 TraesCS1A01G314000 chr6A 84.500 200 21 9 16 209 579956472 579956277 7.090000e-44 189.0
45 TraesCS1A01G314000 chr6A 89.051 137 8 4 16 146 118962692 118962557 4.300000e-36 163.0
46 TraesCS1A01G314000 chr3D 85.890 163 19 4 49 209 414650509 414650349 2.570000e-38 171.0


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 TraesCS1A01G314000 chr1A 505536676 505542035 5359 False 2407.000000 7236 98.59150 1 5360 4 chr1A.!!$F2 5359
1 TraesCS1A01G314000 chr1A 547253699 547254356 657 False 494.000000 494 80.57600 16 702 1 chr1A.!!$F1 686
2 TraesCS1A01G314000 chr1D 409534866 409540066 5200 False 1458.200000 5517 92.21180 1 5345 5 chr1D.!!$F1 5344
3 TraesCS1A01G314000 chr1B 551720803 551725645 4842 False 3442.500000 5387 91.85700 279 5345 2 chr1B.!!$F2 5066
4 TraesCS1A01G314000 chr5B 582832611 582835502 2891 False 942.666667 1380 85.25200 1053 3917 3 chr5B.!!$F1 2864
5 TraesCS1A01G314000 chr5B 692785634 692786412 778 True 706.000000 706 83.96500 279 1025 1 chr5B.!!$R2 746
6 TraesCS1A01G314000 chr5A 594953120 594956281 3161 False 745.750000 1238 85.47725 1053 4508 4 chr5A.!!$F3 3455
7 TraesCS1A01G314000 chr5D 475499757 475502912 3155 False 762.500000 1057 87.26275 1053 4508 4 chr5D.!!$F1 3455
8 TraesCS1A01G314000 chr5D 12991940 12992590 650 True 630.000000 630 84.81600 279 903 1 chr5D.!!$R1 624
9 TraesCS1A01G314000 chr5D 114627362 114628218 856 True 592.000000 592 79.66900 16 902 1 chr5D.!!$R2 886
10 TraesCS1A01G314000 chr5D 391982820 391983398 578 True 460.000000 460 81.84900 202 769 1 chr5D.!!$R3 567
11 TraesCS1A01G314000 chr2A 691230489 691231409 920 True 365.400000 678 93.37550 1 903 2 chr2A.!!$R1 902
12 TraesCS1A01G314000 chr6D 389608347 389609280 933 True 649.000000 649 80.14300 96 1033 1 chr6D.!!$R1 937
13 TraesCS1A01G314000 chr2D 547676046 547676725 679 False 647.000000 647 84.08500 202 900 1 chr2D.!!$F1 698
14 TraesCS1A01G314000 chr7D 79530166 79530924 758 False 566.000000 566 81.17000 279 1019 1 chr7D.!!$F1 740

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
905 1099 2.238144 CAATTGGAGAGGCTTGGAGAGA 59.762 50.000 0.00 0.0 0.00 3.10 F
1969 2261 0.032540 CACAAGGCAAAAGCCTCACC 59.967 55.000 9.77 0.0 39.63 4.02 F
2088 2381 0.839946 CCATCCAACCCGAAGATCCT 59.160 55.000 0.00 0.0 0.00 3.24 F
3227 3617 4.437390 GCTGATTTGCACTTGCGTAGTATT 60.437 41.667 0.00 0.0 45.83 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2682 3045 2.225091 ACATGCATTCCCACTCTTCCAA 60.225 45.455 0.00 0.0 0.00 3.53 R
3278 3668 2.582052 AGCTCCTCAGTAATCTCGAGG 58.418 52.381 13.56 0.0 46.49 4.63 R
4213 4614 6.857437 TTCATACTCTCAACTTCATCTCCA 57.143 37.500 0.00 0.0 0.00 3.86 R
5136 5568 0.031178 CAAGGCACCTGCAAGACAAC 59.969 55.000 0.00 0.0 44.36 3.32 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
86 143 2.363680 CAGTCCATAGGCAGGTAGACAG 59.636 54.545 0.00 0.00 0.00 3.51
192 280 5.957842 TTTGTATCGGATGAAAACTTGCT 57.042 34.783 0.00 0.00 0.00 3.91
193 281 4.944962 TGTATCGGATGAAAACTTGCTG 57.055 40.909 0.00 0.00 0.00 4.41
194 282 4.323417 TGTATCGGATGAAAACTTGCTGT 58.677 39.130 0.00 0.00 0.00 4.40
195 283 5.483811 TGTATCGGATGAAAACTTGCTGTA 58.516 37.500 0.00 0.00 0.00 2.74
196 284 5.580691 TGTATCGGATGAAAACTTGCTGTAG 59.419 40.000 0.00 0.00 0.00 2.74
197 285 4.265904 TCGGATGAAAACTTGCTGTAGA 57.734 40.909 0.00 0.00 0.00 2.59
198 286 4.832248 TCGGATGAAAACTTGCTGTAGAT 58.168 39.130 0.00 0.00 0.00 1.98
199 287 5.245531 TCGGATGAAAACTTGCTGTAGATT 58.754 37.500 0.00 0.00 0.00 2.40
200 288 5.122239 TCGGATGAAAACTTGCTGTAGATTG 59.878 40.000 0.00 0.00 0.00 2.67
201 289 5.644644 GGATGAAAACTTGCTGTAGATTGG 58.355 41.667 0.00 0.00 0.00 3.16
202 290 5.415701 GGATGAAAACTTGCTGTAGATTGGA 59.584 40.000 0.00 0.00 0.00 3.53
203 291 6.096001 GGATGAAAACTTGCTGTAGATTGGAT 59.904 38.462 0.00 0.00 0.00 3.41
204 292 7.283127 GGATGAAAACTTGCTGTAGATTGGATA 59.717 37.037 0.00 0.00 0.00 2.59
255 352 9.823647 AGATTGGATATTGTATCGGATGAATAC 57.176 33.333 0.00 0.00 0.00 1.89
266 363 5.592104 TCGGATGAATACTTGCTGTAGAA 57.408 39.130 0.00 0.00 34.24 2.10
337 442 6.959639 TTATATGTGGAAGGATTTTGCCTC 57.040 37.500 0.00 0.00 37.26 4.70
438 554 7.795431 ATGTTGTTATTTGAACATGTTAGCG 57.205 32.000 11.95 0.00 40.49 4.26
442 558 3.848272 ATTTGAACATGTTAGCGGTGG 57.152 42.857 11.95 0.00 0.00 4.61
468 584 2.743664 TGCAATGACTGGCGATATATGC 59.256 45.455 0.00 0.00 0.00 3.14
471 587 4.142534 GCAATGACTGGCGATATATGCAAT 60.143 41.667 0.00 0.00 0.00 3.56
478 594 3.191162 TGGCGATATATGCAATGGAAAGC 59.809 43.478 0.00 0.00 0.00 3.51
505 624 5.302360 AGTTGTTTTATCTGCACCGTCTTA 58.698 37.500 0.00 0.00 0.00 2.10
531 652 5.335191 CCTGAAACCAAAGCTTAGCAGTAAG 60.335 44.000 7.07 0.00 39.04 2.34
628 763 5.106948 GGTATTGTTGGCATGATAGATGTCG 60.107 44.000 0.00 0.00 0.00 4.35
654 789 7.706607 GCAAATCTTGTTTAGGATTGGGAATAC 59.293 37.037 0.00 0.00 33.19 1.89
704 870 8.974060 TGATTTTAACAGTCAGACCTAAAGTT 57.026 30.769 0.00 0.00 0.00 2.66
777 945 8.479313 TTTCGTATTATGCCATGATAGATGTC 57.521 34.615 0.00 0.00 0.00 3.06
863 1036 7.086685 TCTATACCTTTGGAACTTGGAGTTT 57.913 36.000 0.00 0.00 38.80 2.66
905 1099 2.238144 CAATTGGAGAGGCTTGGAGAGA 59.762 50.000 0.00 0.00 0.00 3.10
913 1107 2.816672 GAGGCTTGGAGAGAAAACAAGG 59.183 50.000 0.00 0.00 41.33 3.61
925 1119 4.336280 AGAAAACAAGGAGGTAATCTGCC 58.664 43.478 0.00 0.00 33.99 4.85
937 1131 2.789409 AATCTGCCGTTCCTAGCTTT 57.211 45.000 0.00 0.00 0.00 3.51
947 1144 6.037830 TGCCGTTCCTAGCTTTTATACATTTC 59.962 38.462 0.00 0.00 0.00 2.17
953 1150 9.855021 TTCCTAGCTTTTATACATTTCTTTTGC 57.145 29.630 0.00 0.00 0.00 3.68
957 1154 8.227731 AGCTTTTATACATTTCTTTTGCGAAC 57.772 30.769 0.00 0.00 0.00 3.95
962 1159 9.906660 TTTATACATTTCTTTTGCGAACTGAAT 57.093 25.926 0.00 0.00 30.74 2.57
969 1167 9.612620 ATTTCTTTTGCGAACTGAATAAAGTAG 57.387 29.630 0.00 0.00 0.00 2.57
1019 1217 6.540914 TCTGAAATGGTGAATTTACGTATCCC 59.459 38.462 0.00 0.00 38.64 3.85
1025 1223 5.302568 TGGTGAATTTACGTATCCCTATCGT 59.697 40.000 0.00 0.00 40.78 3.73
1080 1282 2.124403 GTCGTCCTCGCCCCTCTA 60.124 66.667 0.00 0.00 36.96 2.43
1216 1418 0.958822 CCCCCGAACCTTCAAACTTG 59.041 55.000 0.00 0.00 0.00 3.16
1227 1436 3.259123 CCTTCAAACTTGGATTTCCCCAG 59.741 47.826 0.00 0.00 37.53 4.45
1241 1451 5.843019 TTTCCCCAGAATACTTCAACTCT 57.157 39.130 0.00 0.00 0.00 3.24
1255 1465 5.046014 ACTTCAACTCTGATGGAGCTAACAT 60.046 40.000 3.21 3.21 45.48 2.71
1560 1775 3.557264 CCTTTCCTGCCGTCTTACTTTCT 60.557 47.826 0.00 0.00 0.00 2.52
1569 1784 0.249398 TCTTACTTTCTCCCAGCCGC 59.751 55.000 0.00 0.00 0.00 6.53
1662 1914 2.361610 CGCCCCACAGAAATGCCT 60.362 61.111 0.00 0.00 0.00 4.75
1697 1950 6.059787 AGAGGACTTTGTCTAGCATTTCAT 57.940 37.500 0.00 0.00 32.47 2.57
1726 1979 8.999431 GTGAAGTATTTACTTTGATTGAGGTCA 58.001 33.333 4.57 0.00 45.84 4.02
1740 1998 5.488262 TTGAGGTCATGTGAGAAGATCAA 57.512 39.130 0.00 0.00 40.43 2.57
1937 2229 7.967908 TGAAGAACTTCTTAAGAACTCCAGAT 58.032 34.615 13.99 0.00 36.73 2.90
1969 2261 0.032540 CACAAGGCAAAAGCCTCACC 59.967 55.000 9.77 0.00 39.63 4.02
1978 2271 1.068352 AAAGCCTCACCCACCCTCTT 61.068 55.000 0.00 0.00 0.00 2.85
1996 2289 4.572389 CCTCTTTCATAAACGATGGAGTGG 59.428 45.833 0.00 0.00 36.08 4.00
2048 2341 3.260380 CCCATCTCAAGAGTGACACTTCT 59.740 47.826 10.01 5.71 0.00 2.85
2088 2381 0.839946 CCATCCAACCCGAAGATCCT 59.160 55.000 0.00 0.00 0.00 3.24
2257 2555 5.843673 TTGTTGTGCTGGATTTTCTGTTA 57.156 34.783 0.00 0.00 0.00 2.41
2376 2674 5.682212 GCCGGAAAATTTGCTCCTTGATATT 60.682 40.000 5.05 0.00 0.00 1.28
2428 2736 5.657470 CACCCAATGTGTTATCGTATCAG 57.343 43.478 0.00 0.00 40.26 2.90
2446 2760 7.817478 TCGTATCAGAGTGCTTATTTTGAGAAA 59.183 33.333 0.00 0.00 0.00 2.52
2493 2807 9.845740 ATATGCCAGTGATAAATGTACTGTTTA 57.154 29.630 0.00 0.69 40.04 2.01
2556 2916 8.397906 TCAACTACATCATTGCTGTAAATTAGC 58.602 33.333 2.34 0.00 41.49 3.09
2558 2918 7.056635 ACTACATCATTGCTGTAAATTAGCCT 58.943 34.615 2.34 0.00 40.42 4.58
2559 2919 8.210946 ACTACATCATTGCTGTAAATTAGCCTA 58.789 33.333 2.34 0.00 40.42 3.93
2560 2920 7.264373 ACATCATTGCTGTAAATTAGCCTAC 57.736 36.000 0.00 0.00 40.42 3.18
2682 3045 8.133627 GCTCTAATGAAATGCATGTATGTTTCT 58.866 33.333 0.00 0.00 37.28 2.52
2849 3219 8.688747 ATCAAGATATCCTTTTAGGCTGAAAG 57.311 34.615 21.26 21.26 34.61 2.62
2921 3296 4.492570 GCACTATACATCTCGTGTGTTTGC 60.493 45.833 0.00 0.00 42.24 3.68
3030 3412 5.836821 ACAGAGACGAAATAGCAGATACA 57.163 39.130 0.00 0.00 0.00 2.29
3227 3617 4.437390 GCTGATTTGCACTTGCGTAGTATT 60.437 41.667 0.00 0.00 45.83 1.89
3278 3668 5.220710 AGATGCATGTCCTGTATACCTTC 57.779 43.478 2.46 0.00 29.38 3.46
4422 4823 4.843220 AAGGCTAACTGAATATGCATGC 57.157 40.909 11.82 11.82 0.00 4.06
4448 4849 4.944962 TTGCAATCGAATTACTGGTCAG 57.055 40.909 0.00 0.00 0.00 3.51
4525 4927 9.444600 TCAAGATAAGTTTAAGCGGTAAATTCT 57.555 29.630 0.00 0.00 34.23 2.40
4526 4928 9.490663 CAAGATAAGTTTAAGCGGTAAATTCTG 57.509 33.333 0.00 0.00 34.23 3.02
4527 4929 8.788325 AGATAAGTTTAAGCGGTAAATTCTGT 57.212 30.769 0.00 0.00 34.23 3.41
4528 4930 9.227777 AGATAAGTTTAAGCGGTAAATTCTGTT 57.772 29.630 0.00 0.00 34.23 3.16
4529 4931 9.274065 GATAAGTTTAAGCGGTAAATTCTGTTG 57.726 33.333 0.00 0.00 34.23 3.33
4530 4932 6.870971 AGTTTAAGCGGTAAATTCTGTTGA 57.129 33.333 0.00 0.00 34.23 3.18
4531 4933 7.266922 AGTTTAAGCGGTAAATTCTGTTGAA 57.733 32.000 0.00 0.00 34.23 2.69
4532 4934 7.136772 AGTTTAAGCGGTAAATTCTGTTGAAC 58.863 34.615 0.00 0.00 34.23 3.18
4533 4935 6.621316 TTAAGCGGTAAATTCTGTTGAACA 57.379 33.333 0.00 0.00 34.71 3.18
4534 4936 4.483476 AGCGGTAAATTCTGTTGAACAC 57.517 40.909 0.00 0.00 34.71 3.32
4535 4937 4.134563 AGCGGTAAATTCTGTTGAACACT 58.865 39.130 0.00 0.00 34.71 3.55
4536 4938 4.578928 AGCGGTAAATTCTGTTGAACACTT 59.421 37.500 0.00 0.00 34.71 3.16
4537 4939 4.909880 GCGGTAAATTCTGTTGAACACTTC 59.090 41.667 0.00 0.00 34.71 3.01
4538 4940 5.504994 GCGGTAAATTCTGTTGAACACTTCA 60.505 40.000 0.00 0.00 38.04 3.02
4539 4941 6.491394 CGGTAAATTCTGTTGAACACTTCAA 58.509 36.000 0.00 0.00 46.68 2.69
4666 5069 6.701340 TCAAGAGTGTATCAGCAAGTATGTT 58.299 36.000 0.00 0.00 0.00 2.71
4706 5109 2.054799 AGCTTGGTTACCCTGTCTGAA 58.945 47.619 0.00 0.00 0.00 3.02
4708 5111 3.074538 AGCTTGGTTACCCTGTCTGAAAT 59.925 43.478 0.00 0.00 0.00 2.17
4790 5195 7.041721 TCATACTGCAGATTTCTTGATAACGT 58.958 34.615 23.35 0.00 0.00 3.99
4792 5197 5.482908 ACTGCAGATTTCTTGATAACGTCT 58.517 37.500 23.35 0.00 0.00 4.18
4793 5198 5.349817 ACTGCAGATTTCTTGATAACGTCTG 59.650 40.000 23.35 0.00 35.82 3.51
4796 5201 5.419542 CAGATTTCTTGATAACGTCTGGGA 58.580 41.667 0.00 0.00 0.00 4.37
4797 5202 5.521735 CAGATTTCTTGATAACGTCTGGGAG 59.478 44.000 0.00 0.00 0.00 4.30
4811 5220 0.895100 TGGGAGCAATGTTCCTGTGC 60.895 55.000 15.61 0.00 38.59 4.57
4849 5258 2.353269 TGTTACTGTGTGGTCTTTTGCG 59.647 45.455 0.00 0.00 0.00 4.85
4877 5286 8.359642 CCTCCTCTTATTTGTTGTTTGAATTCA 58.640 33.333 3.38 3.38 0.00 2.57
4914 5323 5.683876 TTACAAAGGAGATTGGGAGAGAG 57.316 43.478 0.00 0.00 34.56 3.20
4935 5344 2.820197 GTTGAATCTTGTCCCAACTCCC 59.180 50.000 0.00 0.00 36.78 4.30
4946 5355 0.178992 CCAACTCCCAACCTTGCTGA 60.179 55.000 0.00 0.00 0.00 4.26
4953 5362 1.410648 CCCAACCTTGCTGATATGGCT 60.411 52.381 0.00 0.00 0.00 4.75
4971 5380 1.065854 GCTAGTCATGTTCTGCCCAGT 60.066 52.381 0.00 0.00 0.00 4.00
5052 5484 5.221048 GGCGTATAATGAGTGGCAAGAATTT 60.221 40.000 0.00 0.00 0.00 1.82
5063 5495 6.393171 AGTGGCAAGAATTTTCTTCATAAGC 58.607 36.000 2.59 3.74 45.23 3.09
5071 5503 9.538508 AAGAATTTTCTTCATAAGCAATATGCC 57.461 29.630 0.00 0.00 43.36 4.40
5073 5505 5.437289 TTTCTTCATAAGCAATATGCCGG 57.563 39.130 0.00 0.00 46.52 6.13
5075 5507 4.065088 TCTTCATAAGCAATATGCCGGAC 58.935 43.478 5.05 0.00 46.52 4.79
5090 5522 2.548480 GCCGGACATTTTGATAGGTAGC 59.452 50.000 5.05 0.00 0.00 3.58
5136 5568 4.371855 TGTAGTCTTCCATGCGTTAGAG 57.628 45.455 0.00 0.00 0.00 2.43
5141 5573 3.368236 GTCTTCCATGCGTTAGAGTTGTC 59.632 47.826 0.00 0.00 0.00 3.18
5247 5845 1.188863 ATTTCAGCAATGGGTCAGGC 58.811 50.000 0.00 0.00 0.00 4.85
5248 5846 1.243342 TTTCAGCAATGGGTCAGGCG 61.243 55.000 0.00 0.00 0.00 5.52
5294 5892 3.260380 TCTTCTCTTTGCTCCTCTTCCTG 59.740 47.826 0.00 0.00 0.00 3.86
5298 5896 2.238144 TCTTTGCTCCTCTTCCTGGATG 59.762 50.000 0.00 0.00 32.56 3.51
5345 5943 6.514947 TGTGAATGAATCTTTTTCCAACCAG 58.485 36.000 0.00 0.00 0.00 4.00
5346 5944 5.928264 GTGAATGAATCTTTTTCCAACCAGG 59.072 40.000 0.00 0.00 39.47 4.45
5356 5954 0.682852 TCCAACCAGGACAAGTACCG 59.317 55.000 0.00 0.00 43.07 4.02
5357 5955 0.682852 CCAACCAGGACAAGTACCGA 59.317 55.000 0.00 0.00 41.22 4.69
5358 5956 1.278127 CCAACCAGGACAAGTACCGAT 59.722 52.381 0.00 0.00 41.22 4.18
5359 5957 2.346803 CAACCAGGACAAGTACCGATG 58.653 52.381 0.00 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 143 0.539518 GAGGGAGGAAGAAGGAGTGC 59.460 60.000 0.00 0.00 0.00 4.40
171 259 4.759693 ACAGCAAGTTTTCATCCGATACAA 59.240 37.500 0.00 0.00 0.00 2.41
172 260 4.323417 ACAGCAAGTTTTCATCCGATACA 58.677 39.130 0.00 0.00 0.00 2.29
173 261 4.946784 ACAGCAAGTTTTCATCCGATAC 57.053 40.909 0.00 0.00 0.00 2.24
174 262 5.972935 TCTACAGCAAGTTTTCATCCGATA 58.027 37.500 0.00 0.00 0.00 2.92
175 263 4.832248 TCTACAGCAAGTTTTCATCCGAT 58.168 39.130 0.00 0.00 0.00 4.18
176 264 4.265904 TCTACAGCAAGTTTTCATCCGA 57.734 40.909 0.00 0.00 0.00 4.55
177 265 5.327091 CAATCTACAGCAAGTTTTCATCCG 58.673 41.667 0.00 0.00 0.00 4.18
178 266 5.415701 TCCAATCTACAGCAAGTTTTCATCC 59.584 40.000 0.00 0.00 0.00 3.51
179 267 6.500684 TCCAATCTACAGCAAGTTTTCATC 57.499 37.500 0.00 0.00 0.00 2.92
180 268 8.757982 ATATCCAATCTACAGCAAGTTTTCAT 57.242 30.769 0.00 0.00 0.00 2.57
181 269 8.461222 CAATATCCAATCTACAGCAAGTTTTCA 58.539 33.333 0.00 0.00 0.00 2.69
182 270 8.462016 ACAATATCCAATCTACAGCAAGTTTTC 58.538 33.333 0.00 0.00 0.00 2.29
183 271 8.353423 ACAATATCCAATCTACAGCAAGTTTT 57.647 30.769 0.00 0.00 0.00 2.43
184 272 7.944729 ACAATATCCAATCTACAGCAAGTTT 57.055 32.000 0.00 0.00 0.00 2.66
185 273 9.277783 GATACAATATCCAATCTACAGCAAGTT 57.722 33.333 0.00 0.00 0.00 2.66
186 274 7.600375 CGATACAATATCCAATCTACAGCAAGT 59.400 37.037 0.00 0.00 0.00 3.16
187 275 7.063898 CCGATACAATATCCAATCTACAGCAAG 59.936 40.741 0.00 0.00 0.00 4.01
188 276 6.873605 CCGATACAATATCCAATCTACAGCAA 59.126 38.462 0.00 0.00 0.00 3.91
189 277 6.210584 TCCGATACAATATCCAATCTACAGCA 59.789 38.462 0.00 0.00 0.00 4.41
190 278 6.631016 TCCGATACAATATCCAATCTACAGC 58.369 40.000 0.00 0.00 0.00 4.40
191 279 8.470002 TCATCCGATACAATATCCAATCTACAG 58.530 37.037 0.00 0.00 0.00 2.74
192 280 8.361169 TCATCCGATACAATATCCAATCTACA 57.639 34.615 0.00 0.00 0.00 2.74
193 281 9.823647 ATTCATCCGATACAATATCCAATCTAC 57.176 33.333 0.00 0.00 0.00 2.59
195 283 9.823647 GTATTCATCCGATACAATATCCAATCT 57.176 33.333 0.00 0.00 0.00 2.40
196 284 9.823647 AGTATTCATCCGATACAATATCCAATC 57.176 33.333 0.00 0.00 0.00 2.67
198 286 9.435688 CAAGTATTCATCCGATACAATATCCAA 57.564 33.333 0.00 0.00 0.00 3.53
199 287 7.549134 GCAAGTATTCATCCGATACAATATCCA 59.451 37.037 0.00 0.00 0.00 3.41
200 288 7.766278 AGCAAGTATTCATCCGATACAATATCC 59.234 37.037 0.00 0.00 0.00 2.59
201 289 8.598924 CAGCAAGTATTCATCCGATACAATATC 58.401 37.037 0.00 0.00 0.00 1.63
202 290 8.097038 ACAGCAAGTATTCATCCGATACAATAT 58.903 33.333 0.00 0.00 0.00 1.28
203 291 7.441836 ACAGCAAGTATTCATCCGATACAATA 58.558 34.615 0.00 0.00 0.00 1.90
204 292 6.291377 ACAGCAAGTATTCATCCGATACAAT 58.709 36.000 0.00 0.00 0.00 2.71
243 332 5.791336 TCTACAGCAAGTATTCATCCGAT 57.209 39.130 0.00 0.00 30.93 4.18
255 352 8.099537 AGTATCCAATATCCATTCTACAGCAAG 58.900 37.037 0.00 0.00 0.00 4.01
266 363 4.989277 TGCAGCAAGTATCCAATATCCAT 58.011 39.130 0.00 0.00 0.00 3.41
307 408 8.408601 CAAAATCCTTCCACATATAAACCTGAG 58.591 37.037 0.00 0.00 0.00 3.35
337 442 4.771590 AGCATTATCACAAACACCTGTG 57.228 40.909 0.00 0.00 46.70 3.66
422 538 3.417101 TCCACCGCTAACATGTTCAAAT 58.583 40.909 15.85 0.00 0.00 2.32
438 554 0.238289 CAGTCATTGCACGTTCCACC 59.762 55.000 0.00 0.00 0.00 4.61
442 558 1.154413 CGCCAGTCATTGCACGTTC 60.154 57.895 0.00 0.00 0.00 3.95
468 584 9.696917 AGATAAAACAACTTAAGCTTTCCATTG 57.303 29.630 3.20 7.52 0.00 2.82
471 587 7.145323 GCAGATAAAACAACTTAAGCTTTCCA 58.855 34.615 3.20 0.00 0.00 3.53
478 594 5.997385 ACGGTGCAGATAAAACAACTTAAG 58.003 37.500 0.00 0.00 0.00 1.85
505 624 3.295973 TGCTAAGCTTTGGTTTCAGGTT 58.704 40.909 3.20 0.00 35.04 3.50
531 652 3.693085 TCCTGCTCTCTCAAAATTGCATC 59.307 43.478 0.00 0.00 0.00 3.91
538 659 1.356124 AGGCTCCTGCTCTCTCAAAA 58.644 50.000 0.00 0.00 39.59 2.44
628 763 5.659440 TCCCAATCCTAAACAAGATTTGC 57.341 39.130 0.00 0.00 30.29 3.68
704 870 5.559148 AACATGCAAAAGGGGAAACAATA 57.441 34.783 0.00 0.00 0.00 1.90
777 945 9.241317 CAGCAAATCAAATAATTAGTTAGCTGG 57.759 33.333 18.20 2.70 39.44 4.85
863 1036 2.557924 GACAATGTTGATGCCCTGTTCA 59.442 45.455 0.00 0.00 0.00 3.18
905 1099 3.081804 CGGCAGATTACCTCCTTGTTTT 58.918 45.455 0.00 0.00 0.00 2.43
913 1107 2.546162 GCTAGGAACGGCAGATTACCTC 60.546 54.545 0.00 0.00 32.95 3.85
947 1144 9.055248 CATTCTACTTTATTCAGTTCGCAAAAG 57.945 33.333 0.00 0.00 0.00 2.27
953 1150 8.979574 GGGATACATTCTACTTTATTCAGTTCG 58.020 37.037 0.00 0.00 39.74 3.95
1025 1223 3.071479 GGTGGAGAGACGTTAAATGCAA 58.929 45.455 0.00 0.00 0.00 4.08
1080 1282 4.473520 CACTCCGGCCGCTCCATT 62.474 66.667 22.85 0.00 34.01 3.16
1181 1383 1.506907 GGGGCTAGGGTTTCAAGGGT 61.507 60.000 0.00 0.00 0.00 4.34
1227 1436 5.669477 AGCTCCATCAGAGTTGAAGTATTC 58.331 41.667 0.00 0.00 44.88 1.75
1241 1451 0.179048 CCGCCATGTTAGCTCCATCA 60.179 55.000 0.00 0.00 0.00 3.07
1255 1465 3.350612 CGCCGAAGTTTTCCGCCA 61.351 61.111 0.00 0.00 31.50 5.69
1569 1784 0.299300 TCGAATCAATAAACGCCGCG 59.701 50.000 12.14 12.14 0.00 6.46
1616 1866 3.665871 GCTCAAAACGTTCAAGCTTCATC 59.334 43.478 17.41 0.00 0.00 2.92
1684 1937 5.886960 ACTTCACCAATGAAATGCTAGAC 57.113 39.130 0.00 0.00 44.28 2.59
1697 1950 8.792633 CCTCAATCAAAGTAAATACTTCACCAA 58.207 33.333 6.31 0.00 45.17 3.67
1726 1979 6.251471 ACCCTTTTCATTGATCTTCTCACAT 58.749 36.000 0.00 0.00 32.17 3.21
1879 2171 5.183904 TGATGTACAGAGATCCATCATACCG 59.816 44.000 0.33 0.00 38.90 4.02
1937 2229 6.707440 TTTGCCTTGTGTTTCTAAAGATGA 57.293 33.333 0.00 0.00 0.00 2.92
1969 2261 3.627577 CCATCGTTTATGAAAGAGGGTGG 59.372 47.826 8.36 0.48 39.38 4.61
1978 2271 5.414789 TTCTCCACTCCATCGTTTATGAA 57.585 39.130 0.00 0.00 37.86 2.57
2048 2341 5.338632 TGGTTTAGATCTCAGACTGGGTTA 58.661 41.667 0.00 0.00 0.00 2.85
2376 2674 2.507484 CATGCAGAAGAACCAACCTCA 58.493 47.619 0.00 0.00 0.00 3.86
2411 2709 5.907207 AGCACTCTGATACGATAACACATT 58.093 37.500 0.00 0.00 0.00 2.71
2571 2933 6.948886 TGTTGGTAGGCATAATTTACTTTCCA 59.051 34.615 0.00 0.00 0.00 3.53
2682 3045 2.225091 ACATGCATTCCCACTCTTCCAA 60.225 45.455 0.00 0.00 0.00 3.53
2742 3111 8.771920 TCTCACAAGTAATTTTCACATATCGT 57.228 30.769 0.00 0.00 0.00 3.73
3061 3443 7.806690 TGTCAAATATTACACTGCACTCTTTC 58.193 34.615 0.00 0.00 0.00 2.62
3065 3447 6.238484 GGGATGTCAAATATTACACTGCACTC 60.238 42.308 0.00 0.00 0.00 3.51
3227 3617 8.927675 AAGTAACCAGGTGTTTACAATCATAA 57.072 30.769 0.00 0.00 38.42 1.90
3278 3668 2.582052 AGCTCCTCAGTAATCTCGAGG 58.418 52.381 13.56 0.00 46.49 4.63
4213 4614 6.857437 TTCATACTCTCAACTTCATCTCCA 57.143 37.500 0.00 0.00 0.00 3.86
4272 4673 8.792830 TCAAAATATCGTCAAGAGAAATCCTT 57.207 30.769 0.00 0.00 0.00 3.36
4353 4754 3.526534 CAAGGAGCTTAGGCACTAGTTC 58.473 50.000 0.00 0.00 44.25 3.01
4422 4823 7.471721 TGACCAGTAATTCGATTGCAAAATAG 58.528 34.615 1.71 0.00 0.00 1.73
4448 4849 6.715718 TCTGAGTACAGTACAGGATTATAGGC 59.284 42.308 13.37 0.00 43.81 3.93
4515 4917 6.055231 TGAAGTGTTCAACAGAATTTACCG 57.945 37.500 0.00 0.00 36.59 4.02
4527 4929 6.153067 ACGTTGAATTTGTTGAAGTGTTCAA 58.847 32.000 0.00 0.00 46.68 2.69
4528 4930 5.704888 ACGTTGAATTTGTTGAAGTGTTCA 58.295 33.333 0.00 0.00 38.04 3.18
4529 4931 6.526674 AGAACGTTGAATTTGTTGAAGTGTTC 59.473 34.615 5.00 0.00 0.00 3.18
4530 4932 6.307800 CAGAACGTTGAATTTGTTGAAGTGTT 59.692 34.615 5.00 0.00 0.00 3.32
4531 4933 5.799936 CAGAACGTTGAATTTGTTGAAGTGT 59.200 36.000 5.00 0.00 0.00 3.55
4532 4934 5.229887 CCAGAACGTTGAATTTGTTGAAGTG 59.770 40.000 5.00 0.00 0.00 3.16
4533 4935 5.339990 CCAGAACGTTGAATTTGTTGAAGT 58.660 37.500 5.00 0.00 0.00 3.01
4534 4936 4.739716 CCCAGAACGTTGAATTTGTTGAAG 59.260 41.667 5.00 0.00 0.00 3.02
4535 4937 4.399618 TCCCAGAACGTTGAATTTGTTGAA 59.600 37.500 5.00 0.00 0.00 2.69
4536 4938 3.948473 TCCCAGAACGTTGAATTTGTTGA 59.052 39.130 5.00 0.00 0.00 3.18
4537 4939 4.300189 TCCCAGAACGTTGAATTTGTTG 57.700 40.909 5.00 0.00 0.00 3.33
4538 4940 4.582656 TGATCCCAGAACGTTGAATTTGTT 59.417 37.500 5.00 0.00 0.00 2.83
4539 4941 4.141287 TGATCCCAGAACGTTGAATTTGT 58.859 39.130 5.00 0.00 0.00 2.83
4540 4942 4.764679 TGATCCCAGAACGTTGAATTTG 57.235 40.909 5.00 0.00 0.00 2.32
4541 4943 5.982890 ATTGATCCCAGAACGTTGAATTT 57.017 34.783 5.00 0.00 0.00 1.82
4542 4944 5.982890 AATTGATCCCAGAACGTTGAATT 57.017 34.783 5.00 0.00 0.00 2.17
4543 4945 5.711976 AGAAATTGATCCCAGAACGTTGAAT 59.288 36.000 5.00 0.00 0.00 2.57
4544 4946 5.070001 AGAAATTGATCCCAGAACGTTGAA 58.930 37.500 5.00 0.00 0.00 2.69
4545 4947 4.651778 AGAAATTGATCCCAGAACGTTGA 58.348 39.130 5.00 0.00 0.00 3.18
4586 4989 6.373779 GCAAAACATATGCTACGCTATCAAT 58.626 36.000 1.58 0.00 40.64 2.57
4666 5069 5.439721 AGCTGGATATGAAAATGTACTGCA 58.560 37.500 0.00 0.00 0.00 4.41
4739 5144 1.561076 AGGTGGCATCAGAGCATGTTA 59.439 47.619 0.00 0.00 35.83 2.41
4740 5145 0.330604 AGGTGGCATCAGAGCATGTT 59.669 50.000 0.00 0.00 35.83 2.71
4750 5155 5.067674 TGCAGTATGAATTTAAGGTGGCATC 59.932 40.000 0.00 0.00 39.69 3.91
4786 5191 1.523758 GAACATTGCTCCCAGACGTT 58.476 50.000 0.00 0.00 0.00 3.99
4790 5195 1.067295 ACAGGAACATTGCTCCCAGA 58.933 50.000 2.41 0.00 32.95 3.86
4792 5197 0.895100 GCACAGGAACATTGCTCCCA 60.895 55.000 2.41 0.00 35.77 4.37
4793 5198 0.895100 TGCACAGGAACATTGCTCCC 60.895 55.000 2.41 0.00 38.87 4.30
4811 5220 8.340443 CACAGTAACATCAAATGACATATCCTG 58.660 37.037 0.00 0.00 0.00 3.86
4816 5225 6.939730 ACCACACAGTAACATCAAATGACATA 59.060 34.615 0.00 0.00 0.00 2.29
4849 5258 4.522789 TCAAACAACAAATAAGAGGAGGCC 59.477 41.667 0.00 0.00 0.00 5.19
4884 5293 8.893563 TCCCAATCTCCTTTGTAATTGTATTT 57.106 30.769 0.00 0.00 0.00 1.40
4902 5311 5.495640 ACAAGATTCAACTCTCTCCCAATC 58.504 41.667 0.00 0.00 0.00 2.67
4935 5344 3.812053 GACTAGCCATATCAGCAAGGTTG 59.188 47.826 0.00 0.00 0.00 3.77
4946 5355 3.244700 GGGCAGAACATGACTAGCCATAT 60.245 47.826 23.07 0.00 43.72 1.78
4953 5362 2.371841 ACAACTGGGCAGAACATGACTA 59.628 45.455 0.00 0.00 36.99 2.59
4971 5380 8.990163 AAGAAAATGACTAGGGAGTTTTACAA 57.010 30.769 0.00 0.00 35.45 2.41
5052 5484 4.515191 GTCCGGCATATTGCTTATGAAGAA 59.485 41.667 0.00 0.00 44.28 2.52
5063 5495 5.241506 ACCTATCAAAATGTCCGGCATATTG 59.758 40.000 11.07 6.23 36.67 1.90
5071 5503 3.804036 TGGCTACCTATCAAAATGTCCG 58.196 45.455 0.00 0.00 0.00 4.79
5073 5505 4.781934 ACCTGGCTACCTATCAAAATGTC 58.218 43.478 0.00 0.00 0.00 3.06
5075 5507 6.601613 TGTTAACCTGGCTACCTATCAAAATG 59.398 38.462 2.48 0.00 0.00 2.32
5090 5522 3.634448 TGTCCACAACATTGTTAACCTGG 59.366 43.478 2.48 5.29 39.91 4.45
5136 5568 0.031178 CAAGGCACCTGCAAGACAAC 59.969 55.000 0.00 0.00 44.36 3.32
5141 5573 0.245539 CAATCCAAGGCACCTGCAAG 59.754 55.000 0.00 0.00 44.36 4.01
5247 5845 2.203800 TTCGCTGGCAACTATAGTCG 57.796 50.000 5.70 4.50 37.61 4.18
5248 5846 3.259064 TGTTTCGCTGGCAACTATAGTC 58.741 45.455 5.70 0.00 37.61 2.59
5294 5892 4.775236 ACAATACAGCTCTTCCTTCATCC 58.225 43.478 0.00 0.00 0.00 3.51
5298 5896 4.161377 AGAGGACAATACAGCTCTTCCTTC 59.839 45.833 0.00 0.00 33.48 3.46


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

AutoCloner maintained by Alex Coulton.