Multiple sequence alignment - TraesCS4B01G226700

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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 TraesCS4B01G226700 chr4B 100.000 4000 0 0 1 4000 473865782 473869781 0.000000e+00 7387.0
1 TraesCS4B01G226700 chr4A 93.848 2227 106 14 703 2916 67989023 67991231 0.000000e+00 3325.0
2 TraesCS4B01G226700 chr4A 92.704 699 50 1 3300 3998 157110205 157110902 0.000000e+00 1007.0
3 TraesCS4B01G226700 chr4A 90.625 192 15 3 2929 3119 157110018 157110207 6.640000e-63 252.0
4 TraesCS4B01G226700 chr4A 76.316 114 25 2 1089 1201 737139399 737139511 4.320000e-05 60.2
5 TraesCS4B01G226700 chr4D 94.654 2095 107 4 815 2905 386548927 386551020 0.000000e+00 3243.0
6 TraesCS4B01G226700 chr4D 81.127 710 100 23 1 689 44186694 44185998 4.550000e-149 538.0
7 TraesCS4B01G226700 chr4D 94.231 52 1 2 688 739 386548507 386548556 1.190000e-10 78.7
8 TraesCS4B01G226700 chr7B 95.448 703 28 2 3299 4000 244663112 244662413 0.000000e+00 1118.0
9 TraesCS4B01G226700 chr7B 84.909 497 64 8 1 492 687820574 687821064 3.590000e-135 492.0
10 TraesCS4B01G226700 chr7B 93.229 192 9 3 2929 3119 244663297 244663109 3.040000e-71 279.0
11 TraesCS4B01G226700 chr7B 83.938 193 24 6 2929 3118 541197470 541197282 1.140000e-40 178.0
12 TraesCS4B01G226700 chr1D 93.705 699 43 1 3300 3998 273471170 273471867 0.000000e+00 1046.0
13 TraesCS4B01G226700 chr1D 93.562 699 44 1 3300 3998 376973299 376972602 0.000000e+00 1040.0
14 TraesCS4B01G226700 chr1D 88.571 210 18 6 2906 3114 273470963 273471167 2.390000e-62 250.0
15 TraesCS4B01G226700 chr1D 82.051 195 26 8 2926 3115 493719305 493719495 1.490000e-34 158.0
16 TraesCS4B01G226700 chr7D 93.133 699 47 1 3300 3998 618061127 618061824 0.000000e+00 1024.0
17 TraesCS4B01G226700 chr7D 92.990 699 37 5 3300 3998 29471422 29472108 0.000000e+00 1009.0
18 TraesCS4B01G226700 chr7D 93.717 191 9 3 3111 3299 433896370 433896559 2.350000e-72 283.0
19 TraesCS4B01G226700 chr7D 89.950 199 17 3 2923 3119 618060932 618061129 1.850000e-63 254.0
20 TraesCS4B01G226700 chr7D 84.091 176 24 4 2929 3102 165359760 165359933 2.470000e-37 167.0
21 TraesCS4B01G226700 chr7D 77.193 114 24 2 1089 1201 5352530 5352418 9.280000e-07 65.8
22 TraesCS4B01G226700 chr3A 92.837 698 48 2 3300 3997 714727106 714726411 0.000000e+00 1011.0
23 TraesCS4B01G226700 chr3A 94.505 182 8 2 3119 3299 466062930 466062750 3.040000e-71 279.0
24 TraesCS4B01G226700 chr3A 88.889 207 19 4 2914 3119 487574288 487574491 6.640000e-63 252.0
25 TraesCS4B01G226700 chr1A 92.429 700 50 3 3300 3998 93515886 93516583 0.000000e+00 996.0
26 TraesCS4B01G226700 chr1A 92.418 699 52 1 3300 3998 304191889 304192586 0.000000e+00 996.0
27 TraesCS4B01G226700 chr1A 80.979 715 99 27 1 693 481507520 481508219 2.120000e-147 532.0
28 TraesCS4B01G226700 chr1A 92.000 200 12 4 2922 3119 561130840 561131037 1.090000e-70 278.0
29 TraesCS4B01G226700 chr2B 86.846 707 67 20 1 689 24851583 24852281 0.000000e+00 767.0
30 TraesCS4B01G226700 chr2B 95.628 183 6 2 3118 3299 70184443 70184262 3.910000e-75 292.0
31 TraesCS4B01G226700 chr2B 95.628 183 6 2 3118 3299 458962289 458962470 3.910000e-75 292.0
32 TraesCS4B01G226700 chr2B 87.654 81 8 1 752 832 380259829 380259751 4.260000e-15 93.5
33 TraesCS4B01G226700 chr6B 86.261 706 74 13 1 690 142222693 142223391 0.000000e+00 745.0
34 TraesCS4B01G226700 chr1B 85.299 619 66 11 1 610 16847152 16847754 2.040000e-172 616.0
35 TraesCS4B01G226700 chr1B 84.591 636 67 14 1 623 17348738 17349355 1.590000e-168 603.0
36 TraesCS4B01G226700 chr1B 84.912 570 61 13 1 564 16624842 16625392 1.620000e-153 553.0
37 TraesCS4B01G226700 chr3D 80.993 705 104 19 1 689 63347233 63346543 2.120000e-147 532.0
38 TraesCS4B01G226700 chr3D 81.789 313 34 9 386 689 519945753 519946051 1.440000e-59 241.0
39 TraesCS4B01G226700 chr5A 77.548 628 101 25 9 623 703379479 703380079 3.830000e-90 342.0
40 TraesCS4B01G226700 chr5A 95.109 184 7 2 3117 3299 670102748 670102566 5.060000e-74 289.0
41 TraesCS4B01G226700 chr3B 84.967 306 28 13 394 689 116683614 116683317 1.090000e-75 294.0
42 TraesCS4B01G226700 chr3B 94.149 188 8 3 3112 3299 94759979 94760163 2.350000e-72 283.0
43 TraesCS4B01G226700 chrUn 95.109 184 7 2 3117 3299 175473801 175473983 5.060000e-74 289.0
44 TraesCS4B01G226700 chr5D 95.109 184 7 2 3117 3299 149772392 149772574 5.060000e-74 289.0
45 TraesCS4B01G226700 chr5B 95.580 181 7 1 3119 3299 698642185 698642006 5.060000e-74 289.0
46 TraesCS4B01G226700 chr2D 79.167 120 17 4 577 689 112554481 112554599 4.290000e-10 76.8
47 TraesCS4B01G226700 chr2D 76.119 134 26 6 1085 1215 112927953 112928083 9.280000e-07 65.8
48 TraesCS4B01G226700 chr7A 76.147 109 24 2 1089 1196 6802557 6802664 5.580000e-04 56.5


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 TraesCS4B01G226700 chr4B 473865782 473869781 3999 False 7387.00 7387 100.0000 1 4000 1 chr4B.!!$F1 3999
1 TraesCS4B01G226700 chr4A 67989023 67991231 2208 False 3325.00 3325 93.8480 703 2916 1 chr4A.!!$F1 2213
2 TraesCS4B01G226700 chr4A 157110018 157110902 884 False 629.50 1007 91.6645 2929 3998 2 chr4A.!!$F3 1069
3 TraesCS4B01G226700 chr4D 386548507 386551020 2513 False 1660.85 3243 94.4425 688 2905 2 chr4D.!!$F1 2217
4 TraesCS4B01G226700 chr4D 44185998 44186694 696 True 538.00 538 81.1270 1 689 1 chr4D.!!$R1 688
5 TraesCS4B01G226700 chr7B 244662413 244663297 884 True 698.50 1118 94.3385 2929 4000 2 chr7B.!!$R2 1071
6 TraesCS4B01G226700 chr1D 376972602 376973299 697 True 1040.00 1040 93.5620 3300 3998 1 chr1D.!!$R1 698
7 TraesCS4B01G226700 chr1D 273470963 273471867 904 False 648.00 1046 91.1380 2906 3998 2 chr1D.!!$F2 1092
8 TraesCS4B01G226700 chr7D 29471422 29472108 686 False 1009.00 1009 92.9900 3300 3998 1 chr7D.!!$F1 698
9 TraesCS4B01G226700 chr7D 618060932 618061824 892 False 639.00 1024 91.5415 2923 3998 2 chr7D.!!$F4 1075
10 TraesCS4B01G226700 chr3A 714726411 714727106 695 True 1011.00 1011 92.8370 3300 3997 1 chr3A.!!$R2 697
11 TraesCS4B01G226700 chr1A 93515886 93516583 697 False 996.00 996 92.4290 3300 3998 1 chr1A.!!$F1 698
12 TraesCS4B01G226700 chr1A 304191889 304192586 697 False 996.00 996 92.4180 3300 3998 1 chr1A.!!$F2 698
13 TraesCS4B01G226700 chr1A 481507520 481508219 699 False 532.00 532 80.9790 1 693 1 chr1A.!!$F3 692
14 TraesCS4B01G226700 chr2B 24851583 24852281 698 False 767.00 767 86.8460 1 689 1 chr2B.!!$F1 688
15 TraesCS4B01G226700 chr6B 142222693 142223391 698 False 745.00 745 86.2610 1 690 1 chr6B.!!$F1 689
16 TraesCS4B01G226700 chr1B 16847152 16847754 602 False 616.00 616 85.2990 1 610 1 chr1B.!!$F2 609
17 TraesCS4B01G226700 chr1B 17348738 17349355 617 False 603.00 603 84.5910 1 623 1 chr1B.!!$F3 622
18 TraesCS4B01G226700 chr1B 16624842 16625392 550 False 553.00 553 84.9120 1 564 1 chr1B.!!$F1 563
19 TraesCS4B01G226700 chr3D 63346543 63347233 690 True 532.00 532 80.9930 1 689 1 chr3D.!!$R1 688
20 TraesCS4B01G226700 chr5A 703379479 703380079 600 False 342.00 342 77.5480 9 623 1 chr5A.!!$F1 614

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
567 598 0.098025 TACATTTTAGCGCGCTTGCC 59.902 50.0 41.04 5.55 34.65 4.52 F
1430 1808 0.251341 GGCTGGGAAAGGTGACATGT 60.251 55.0 0.00 0.00 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2534 2914 0.465097 AGTATGGCCAGCACAGCATC 60.465 55.0 13.05 0.0 0.0 3.91 R
3120 3501 0.541764 TCCCTGCAATCAAACACCCC 60.542 55.0 0.00 0.0 0.0 4.95 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.442272 GCCCCTCTGCCTCGTCTA 60.442 66.667 0.00 0.00 0.00 2.59
65 66 3.692406 GAGGACCACCGTCGGCTT 61.692 66.667 12.28 0.00 40.17 4.35
103 104 2.511829 CGAGGAGGACGAGCGAGA 60.512 66.667 0.00 0.00 0.00 4.04
163 164 3.382832 CGAGGACGCCTTCTGGGT 61.383 66.667 0.00 0.00 43.86 4.51
205 206 1.299165 CGGAGCGTGTCGAATAGGG 60.299 63.158 0.00 0.00 0.00 3.53
210 211 1.996786 GCGTGTCGAATAGGGGTCGA 61.997 60.000 0.00 0.00 44.82 4.20
279 280 1.870055 CGTCGTTCTTCTCCCCCGAA 61.870 60.000 0.00 0.00 0.00 4.30
290 291 1.153429 CCCCCGAAGATGACCGTTC 60.153 63.158 0.00 0.00 0.00 3.95
336 337 0.250234 ACACCACCACCGATGATGAG 59.750 55.000 0.00 0.00 0.00 2.90
339 340 0.105593 CCACCACCGATGATGAGGAG 59.894 60.000 0.00 0.00 0.00 3.69
345 352 1.255882 CCGATGATGAGGAGGAGGAG 58.744 60.000 0.00 0.00 0.00 3.69
351 358 0.560688 ATGAGGAGGAGGAGGAGGAC 59.439 60.000 0.00 0.00 0.00 3.85
389 401 6.775708 AGGTTCTAGTTGCACCATAGTTTTA 58.224 36.000 0.00 0.00 34.29 1.52
549 580 2.428960 TTTGTGTGAGAGCGCGGCTA 62.429 55.000 8.83 0.00 39.88 3.93
567 598 0.098025 TACATTTTAGCGCGCTTGCC 59.902 50.000 41.04 5.55 34.65 4.52
569 600 2.395360 ATTTTAGCGCGCTTGCCGA 61.395 52.632 41.04 19.08 40.02 5.54
699 745 3.072038 TGGAGATGCTCTCATGGGTAATG 59.928 47.826 13.06 0.00 45.12 1.90
700 746 3.326006 GGAGATGCTCTCATGGGTAATGA 59.674 47.826 13.06 0.00 45.12 2.57
701 747 4.314121 GAGATGCTCTCATGGGTAATGAC 58.686 47.826 7.93 0.00 42.90 3.06
745 791 1.661341 GAGTAGGAAGCATGCAGGTG 58.339 55.000 21.98 0.00 0.00 4.00
759 805 0.602638 CAGGTGCGCACAGTAGGAAA 60.603 55.000 38.60 0.00 0.00 3.13
762 808 1.226746 GTGCGCACAGTAGGAAACTT 58.773 50.000 34.52 0.00 43.67 2.66
767 813 3.058224 GCGCACAGTAGGAAACTTTTGAT 60.058 43.478 0.30 0.00 43.67 2.57
832 1196 5.117592 GCTGACCGAAAAATGAAAATCAGTG 59.882 40.000 0.00 0.00 35.76 3.66
853 1221 4.650131 GTGAACTTACACCTAGCCTATCCT 59.350 45.833 0.00 0.00 35.07 3.24
859 1227 4.537945 ACACCTAGCCTATCCTCAAGTA 57.462 45.455 0.00 0.00 0.00 2.24
901 1270 1.406539 CCGGCTTGATCTTTTGGATGG 59.593 52.381 0.00 0.00 34.33 3.51
1035 1407 2.715046 ACGGCAGATCATCACACAAAT 58.285 42.857 0.00 0.00 0.00 2.32
1292 1670 2.427905 CGTCTCGTTGCGGTCGAA 60.428 61.111 0.00 0.00 36.89 3.71
1430 1808 0.251341 GGCTGGGAAAGGTGACATGT 60.251 55.000 0.00 0.00 0.00 3.21
1484 1862 3.723348 GTTGTGAAGCGTCGGGGC 61.723 66.667 0.00 0.00 0.00 5.80
1733 2111 6.090628 TGCATTCTGCCGAAAATTATTTCAAC 59.909 34.615 0.00 0.00 44.23 3.18
1734 2112 6.685767 CATTCTGCCGAAAATTATTTCAACG 58.314 36.000 0.00 0.00 44.24 4.10
1759 2138 8.891928 CGTCTACAACAGTTTGAAAATGTTATG 58.108 33.333 21.10 14.31 35.47 1.90
1772 2151 9.932207 TTGAAAATGTTATGAAGAAATGCATCT 57.068 25.926 0.00 0.00 0.00 2.90
1799 2178 4.336993 GTCACCGCCCATTTACAAATCATA 59.663 41.667 0.00 0.00 0.00 2.15
1837 2216 3.624326 TTTCAGGAAGTGCAATCGTTG 57.376 42.857 0.00 0.00 0.00 4.10
1842 2222 0.521735 GAAGTGCAATCGTTGTCCCC 59.478 55.000 0.00 0.00 0.00 4.81
1872 2252 1.730064 GGTTGAGCTTCAAATCGCGTA 59.270 47.619 5.77 0.00 38.22 4.42
1880 2260 4.868171 AGCTTCAAATCGCGTATTAAGTCA 59.132 37.500 5.77 0.00 0.00 3.41
1891 2271 6.303970 TCGCGTATTAAGTCATAATTCTACGC 59.696 38.462 5.77 12.99 46.28 4.42
1947 2327 1.546029 TCCATCTCAACGAGTCCACAG 59.454 52.381 0.00 0.00 0.00 3.66
2063 2443 1.374758 CGCTGAGAAGGCCGACTTT 60.375 57.895 0.00 0.00 40.21 2.66
2078 2458 2.803133 CGACTTTCTCCTCTGCAACACA 60.803 50.000 0.00 0.00 0.00 3.72
2135 2515 2.445845 CCGGCTACCATCCTCCCA 60.446 66.667 0.00 0.00 0.00 4.37
2360 2740 4.742201 CTGTGGGTCGTCAGGCCG 62.742 72.222 0.00 0.00 44.97 6.13
2747 3127 1.464189 GCGGAGAAAAACATGAGCGAC 60.464 52.381 0.00 0.00 0.00 5.19
2776 3156 4.148696 CCAGTCGTTGAACAATTTGAATGC 59.851 41.667 2.79 0.00 0.00 3.56
2793 3173 1.144716 GCGCTGATGGAGTCCATGA 59.855 57.895 29.60 20.32 45.26 3.07
2857 3237 1.797713 CGTTGTGTCGGCTATGATCGT 60.798 52.381 0.00 0.00 0.00 3.73
2866 3246 3.005367 TCGGCTATGATCGTTATTGAGCA 59.995 43.478 8.51 0.00 38.82 4.26
2889 3269 5.947228 TTCTCATTGTTTAGCACTTGGAG 57.053 39.130 0.00 0.00 0.00 3.86
2890 3270 5.227569 TCTCATTGTTTAGCACTTGGAGA 57.772 39.130 0.00 0.00 0.00 3.71
2917 3297 7.859325 ATGGTGCGTACATTCTACTTTTATT 57.141 32.000 5.86 0.00 0.00 1.40
2918 3298 7.675962 TGGTGCGTACATTCTACTTTTATTT 57.324 32.000 5.86 0.00 0.00 1.40
2919 3299 7.745015 TGGTGCGTACATTCTACTTTTATTTC 58.255 34.615 5.86 0.00 0.00 2.17
3031 3412 4.937201 TCTTGTGTGCTAGTCAAGAAGA 57.063 40.909 14.42 11.00 42.61 2.87
3084 3465 8.958043 GTGTGAAATAATCAATCCGCTATTTTC 58.042 33.333 0.00 0.00 40.50 2.29
3115 3496 8.648557 TTATTGATCGAGTGGATTTAAGAGTG 57.351 34.615 0.00 0.00 34.82 3.51
3116 3497 5.661056 TGATCGAGTGGATTTAAGAGTGT 57.339 39.130 0.00 0.00 34.82 3.55
3117 3498 6.037786 TGATCGAGTGGATTTAAGAGTGTT 57.962 37.500 0.00 0.00 34.82 3.32
3118 3499 7.165460 TGATCGAGTGGATTTAAGAGTGTTA 57.835 36.000 0.00 0.00 34.82 2.41
3119 3500 7.258441 TGATCGAGTGGATTTAAGAGTGTTAG 58.742 38.462 0.00 0.00 34.82 2.34
3120 3501 5.962433 TCGAGTGGATTTAAGAGTGTTAGG 58.038 41.667 0.00 0.00 0.00 2.69
3121 3502 5.105473 TCGAGTGGATTTAAGAGTGTTAGGG 60.105 44.000 0.00 0.00 0.00 3.53
3122 3503 5.429130 GAGTGGATTTAAGAGTGTTAGGGG 58.571 45.833 0.00 0.00 0.00 4.79
3123 3504 4.227527 AGTGGATTTAAGAGTGTTAGGGGG 59.772 45.833 0.00 0.00 0.00 5.40
3124 3505 4.018688 GTGGATTTAAGAGTGTTAGGGGGT 60.019 45.833 0.00 0.00 0.00 4.95
3125 3506 4.018779 TGGATTTAAGAGTGTTAGGGGGTG 60.019 45.833 0.00 0.00 0.00 4.61
3126 3507 4.018688 GGATTTAAGAGTGTTAGGGGGTGT 60.019 45.833 0.00 0.00 0.00 4.16
3127 3508 5.516062 GGATTTAAGAGTGTTAGGGGGTGTT 60.516 44.000 0.00 0.00 0.00 3.32
3128 3509 5.391577 TTTAAGAGTGTTAGGGGGTGTTT 57.608 39.130 0.00 0.00 0.00 2.83
3129 3510 2.951229 AGAGTGTTAGGGGGTGTTTG 57.049 50.000 0.00 0.00 0.00 2.93
3130 3511 2.414612 AGAGTGTTAGGGGGTGTTTGA 58.585 47.619 0.00 0.00 0.00 2.69
3131 3512 2.986728 AGAGTGTTAGGGGGTGTTTGAT 59.013 45.455 0.00 0.00 0.00 2.57
3132 3513 3.397955 AGAGTGTTAGGGGGTGTTTGATT 59.602 43.478 0.00 0.00 0.00 2.57
3133 3514 3.496331 AGTGTTAGGGGGTGTTTGATTG 58.504 45.455 0.00 0.00 0.00 2.67
3134 3515 2.029380 GTGTTAGGGGGTGTTTGATTGC 60.029 50.000 0.00 0.00 0.00 3.56
3135 3516 2.243810 GTTAGGGGGTGTTTGATTGCA 58.756 47.619 0.00 0.00 0.00 4.08
3136 3517 2.214376 TAGGGGGTGTTTGATTGCAG 57.786 50.000 0.00 0.00 0.00 4.41
3137 3518 0.542702 AGGGGGTGTTTGATTGCAGG 60.543 55.000 0.00 0.00 0.00 4.85
3138 3519 1.543944 GGGGGTGTTTGATTGCAGGG 61.544 60.000 0.00 0.00 0.00 4.45
3139 3520 0.541764 GGGGTGTTTGATTGCAGGGA 60.542 55.000 0.00 0.00 0.00 4.20
3140 3521 0.603065 GGGTGTTTGATTGCAGGGAC 59.397 55.000 0.00 0.00 0.00 4.46
3141 3522 1.620822 GGTGTTTGATTGCAGGGACT 58.379 50.000 0.00 0.00 43.88 3.85
3142 3523 1.963515 GGTGTTTGATTGCAGGGACTT 59.036 47.619 0.00 0.00 34.60 3.01
3143 3524 2.365293 GGTGTTTGATTGCAGGGACTTT 59.635 45.455 0.00 0.00 34.60 2.66
3144 3525 3.181466 GGTGTTTGATTGCAGGGACTTTT 60.181 43.478 0.00 0.00 34.60 2.27
3145 3526 4.441792 GTGTTTGATTGCAGGGACTTTTT 58.558 39.130 0.00 0.00 34.60 1.94
3182 3563 4.665833 AAAAGTCCCTAGCAAACCAAAC 57.334 40.909 0.00 0.00 0.00 2.93
3183 3564 3.306472 AAGTCCCTAGCAAACCAAACA 57.694 42.857 0.00 0.00 0.00 2.83
3184 3565 2.863809 AGTCCCTAGCAAACCAAACAG 58.136 47.619 0.00 0.00 0.00 3.16
3185 3566 1.886542 GTCCCTAGCAAACCAAACAGG 59.113 52.381 0.00 0.00 45.67 4.00
3186 3567 1.203001 TCCCTAGCAAACCAAACAGGG 60.203 52.381 0.00 0.00 43.52 4.45
3187 3568 1.256812 CCTAGCAAACCAAACAGGGG 58.743 55.000 0.00 0.00 43.89 4.79
3188 3569 1.256812 CTAGCAAACCAAACAGGGGG 58.743 55.000 0.00 0.00 43.89 5.40
3226 3607 7.859613 CTTTTTGCTAAAAGTCCTTAGAAGC 57.140 36.000 20.79 0.00 43.34 3.86
3227 3608 6.952773 TTTTGCTAAAAGTCCTTAGAAGCA 57.047 33.333 6.73 6.73 31.59 3.91
3228 3609 5.941948 TTGCTAAAAGTCCTTAGAAGCAC 57.058 39.130 9.21 0.00 31.59 4.40
3229 3610 4.324267 TGCTAAAAGTCCTTAGAAGCACC 58.676 43.478 6.73 0.00 31.59 5.01
3230 3611 4.041691 TGCTAAAAGTCCTTAGAAGCACCT 59.958 41.667 6.73 0.00 31.59 4.00
3231 3612 4.632251 GCTAAAAGTCCTTAGAAGCACCTC 59.368 45.833 0.00 0.00 31.59 3.85
3232 3613 3.704800 AAAGTCCTTAGAAGCACCTCC 57.295 47.619 0.00 0.00 0.00 4.30
3233 3614 2.632763 AGTCCTTAGAAGCACCTCCT 57.367 50.000 0.00 0.00 0.00 3.69
3234 3615 2.909217 AGTCCTTAGAAGCACCTCCTT 58.091 47.619 0.00 0.00 0.00 3.36
3235 3616 2.569404 AGTCCTTAGAAGCACCTCCTTG 59.431 50.000 0.00 0.00 0.00 3.61
3236 3617 2.567615 GTCCTTAGAAGCACCTCCTTGA 59.432 50.000 0.00 0.00 0.00 3.02
3237 3618 2.834549 TCCTTAGAAGCACCTCCTTGAG 59.165 50.000 0.00 0.00 0.00 3.02
3238 3619 2.834549 CCTTAGAAGCACCTCCTTGAGA 59.165 50.000 0.00 0.00 0.00 3.27
3239 3620 3.118811 CCTTAGAAGCACCTCCTTGAGAG 60.119 52.174 0.00 0.00 42.83 3.20
3240 3621 2.022718 AGAAGCACCTCCTTGAGAGT 57.977 50.000 0.00 0.00 41.47 3.24
3241 3622 2.334023 AGAAGCACCTCCTTGAGAGTT 58.666 47.619 0.00 0.00 41.47 3.01
3242 3623 2.708325 AGAAGCACCTCCTTGAGAGTTT 59.292 45.455 0.00 0.00 41.47 2.66
3243 3624 3.137360 AGAAGCACCTCCTTGAGAGTTTT 59.863 43.478 0.00 0.00 41.47 2.43
3244 3625 3.584733 AGCACCTCCTTGAGAGTTTTT 57.415 42.857 0.00 0.00 41.47 1.94
3294 3675 5.585820 GTCCTAGGACTAGAGAACCAAAG 57.414 47.826 31.12 0.00 41.57 2.77
3295 3676 4.024670 TCCTAGGACTAGAGAACCAAAGC 58.975 47.826 7.62 0.00 35.21 3.51
3296 3677 3.769844 CCTAGGACTAGAGAACCAAAGCA 59.230 47.826 1.05 0.00 35.21 3.91
3297 3678 3.686916 AGGACTAGAGAACCAAAGCAC 57.313 47.619 0.00 0.00 0.00 4.40
3381 3762 1.956477 CGAGGGGATTTTAAGGCATGG 59.044 52.381 0.00 0.00 0.00 3.66
3396 3777 9.639563 TTTAAGGCATGGAGTTCAATAATATGA 57.360 29.630 0.00 0.00 0.00 2.15
3417 3798 0.827368 AATGAGGCGGGTCTTCTCTC 59.173 55.000 0.00 0.00 0.00 3.20
3430 3811 5.172205 GGTCTTCTCTCTTCCATGTACAAC 58.828 45.833 0.00 0.00 0.00 3.32
3432 3813 4.838423 TCTTCTCTCTTCCATGTACAACCA 59.162 41.667 0.00 0.00 0.00 3.67
3730 4112 5.192927 TCCATGCTTCATTCGGTCTAATTT 58.807 37.500 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.093814 TGGTCTGTAATTAGACGAGGCA 58.906 45.455 2.95 0.00 46.29 4.75
29 30 3.200825 CCTCATGGTCCTGGTCTGTAATT 59.799 47.826 0.00 0.00 0.00 1.40
65 66 3.151958 GATGAGGAGGCGGCGCTAA 62.152 63.158 32.30 4.86 0.00 3.09
132 133 4.052229 CTCGGTGGCGACGTCCTT 62.052 66.667 10.58 0.00 0.00 3.36
163 164 2.357034 GCCTTGCCGTCGTCTTCA 60.357 61.111 0.00 0.00 0.00 3.02
200 201 3.090219 GCCTTGCGTCGACCCCTAT 62.090 63.158 10.58 0.00 0.00 2.57
201 202 3.766691 GCCTTGCGTCGACCCCTA 61.767 66.667 10.58 0.00 0.00 3.53
205 206 1.805945 CTAGTGCCTTGCGTCGACC 60.806 63.158 10.58 3.43 0.00 4.79
229 230 2.287849 CCTCGACGATATCACACTGCAT 60.288 50.000 0.00 0.00 0.00 3.96
279 280 1.254026 TGTCTTCCGAACGGTCATCT 58.746 50.000 12.93 0.00 36.47 2.90
290 291 0.387202 ATCGAGCCAGATGTCTTCCG 59.613 55.000 0.00 0.00 0.00 4.30
330 331 0.560193 CCTCCTCCTCCTCCTCATCA 59.440 60.000 0.00 0.00 0.00 3.07
336 337 1.454295 GTCGTCCTCCTCCTCCTCC 60.454 68.421 0.00 0.00 0.00 4.30
339 340 2.114051 GTCGTCGTCCTCCTCCTCC 61.114 68.421 0.00 0.00 0.00 4.30
345 352 2.360852 TCCCAGTCGTCGTCCTCC 60.361 66.667 0.00 0.00 0.00 4.30
351 358 0.450983 GAACCTACTCCCAGTCGTCG 59.549 60.000 0.00 0.00 0.00 5.12
389 401 8.732746 AAAGAACTACGGTGCAATTAGATAAT 57.267 30.769 0.00 0.00 0.00 1.28
397 411 7.727181 AGATAGATAAAGAACTACGGTGCAAT 58.273 34.615 0.00 0.00 0.00 3.56
536 564 0.391130 AAAATGTAGCCGCGCTCTCA 60.391 50.000 5.56 5.78 40.44 3.27
549 580 1.154035 GGCAAGCGCGCTAAAATGT 60.154 52.632 36.73 15.58 39.92 2.71
583 616 0.793104 GCAGACGCGGTAAAATGCAC 60.793 55.000 12.47 0.00 33.92 4.57
668 714 0.674895 GAGCATCTCCAACAGCCGTT 60.675 55.000 0.00 0.00 35.01 4.44
669 715 1.078848 GAGCATCTCCAACAGCCGT 60.079 57.895 0.00 0.00 0.00 5.68
699 745 3.577649 TGTACTAGCTGCTCACTTGTC 57.422 47.619 4.91 0.00 0.00 3.18
700 746 3.654414 GTTGTACTAGCTGCTCACTTGT 58.346 45.455 4.91 1.59 0.00 3.16
701 747 2.663602 CGTTGTACTAGCTGCTCACTTG 59.336 50.000 4.91 0.00 0.00 3.16
745 791 2.289547 TCAAAAGTTTCCTACTGTGCGC 59.710 45.455 0.00 0.00 37.12 6.09
748 794 6.618287 TCACATCAAAAGTTTCCTACTGTG 57.382 37.500 0.00 0.27 37.12 3.66
759 805 1.882912 TCGCTGCTCACATCAAAAGT 58.117 45.000 0.00 0.00 0.00 2.66
761 807 2.159667 CGATTCGCTGCTCACATCAAAA 60.160 45.455 0.00 0.00 0.00 2.44
762 808 1.394572 CGATTCGCTGCTCACATCAAA 59.605 47.619 0.00 0.00 0.00 2.69
767 813 0.733909 CAGTCGATTCGCTGCTCACA 60.734 55.000 14.40 0.00 0.00 3.58
822 1186 6.128254 GGCTAGGTGTAAGTTCACTGATTTTC 60.128 42.308 0.00 0.00 38.28 2.29
832 1196 4.894114 TGAGGATAGGCTAGGTGTAAGTTC 59.106 45.833 0.00 0.00 0.00 3.01
853 1221 2.094906 ACGCAGCGTTCATACTACTTGA 60.095 45.455 16.61 0.00 36.35 3.02
901 1270 4.271291 GGCTACCACGATTCTCTGATTTTC 59.729 45.833 0.00 0.00 0.00 2.29
945 1314 1.791103 CGTGTGCGGGTCAAACCATT 61.791 55.000 0.00 0.00 41.02 3.16
982 1354 2.536928 GCTCGTTGCTGCTTAAATACGG 60.537 50.000 0.00 0.00 38.95 4.02
1035 1407 2.208619 TGCGTGGGAACGGGAAGTA 61.209 57.895 0.00 0.00 0.00 2.24
1239 1617 1.483424 GCTGAAGAGTATGCCGTCGC 61.483 60.000 0.00 0.00 0.00 5.19
1247 1625 2.246067 TCCTCCTCCTGCTGAAGAGTAT 59.754 50.000 0.00 0.00 30.71 2.12
1292 1670 3.823330 GCGTCGTCCATCCCGTCT 61.823 66.667 0.00 0.00 0.00 4.18
1430 1808 3.299977 CCGGAGTCGACCACCACA 61.300 66.667 22.97 0.00 39.00 4.17
1733 2111 8.891928 CATAACATTTTCAAACTGTTGTAGACG 58.108 33.333 14.44 0.00 36.07 4.18
1734 2112 9.944663 TCATAACATTTTCAAACTGTTGTAGAC 57.055 29.630 14.44 0.00 36.07 2.59
1759 2138 4.024556 CGGTGACCATAGATGCATTTCTTC 60.025 45.833 0.00 0.00 0.00 2.87
1761 2140 3.470709 CGGTGACCATAGATGCATTTCT 58.529 45.455 0.00 0.00 0.00 2.52
1808 2187 7.703621 CGATTGCACTTCCTGAAATATCATTTT 59.296 33.333 0.00 0.00 34.37 1.82
1810 2189 6.319658 ACGATTGCACTTCCTGAAATATCATT 59.680 34.615 0.00 0.00 34.37 2.57
1816 2195 3.569701 ACAACGATTGCACTTCCTGAAAT 59.430 39.130 0.00 0.00 0.00 2.17
1826 2205 4.073052 TGGGGACAACGATTGCAC 57.927 55.556 0.00 0.00 37.44 4.57
1837 2216 0.596082 CAACCGAACACAATGGGGAC 59.404 55.000 0.00 0.00 0.00 4.46
1842 2222 2.290367 TGAAGCTCAACCGAACACAATG 59.710 45.455 0.00 0.00 0.00 2.82
1872 2252 6.425114 CCTGCAGCGTAGAATTATGACTTAAT 59.575 38.462 8.66 0.00 31.61 1.40
1880 2260 2.760374 GCTCCTGCAGCGTAGAATTAT 58.240 47.619 8.66 0.00 38.76 1.28
2048 2428 0.608640 GGAGAAAGTCGGCCTTCTCA 59.391 55.000 25.35 0.00 33.02 3.27
2050 2430 0.899019 GAGGAGAAAGTCGGCCTTCT 59.101 55.000 0.00 0.00 31.27 2.85
2063 2443 2.027745 GGAGAATGTGTTGCAGAGGAGA 60.028 50.000 0.00 0.00 0.00 3.71
2078 2458 1.360551 CGGCTCGATGTCGGAGAAT 59.639 57.895 2.25 0.00 40.56 2.40
2159 2539 4.796231 GCATGTCTCGTCGGCCGT 62.796 66.667 27.15 0.00 37.94 5.68
2534 2914 0.465097 AGTATGGCCAGCACAGCATC 60.465 55.000 13.05 0.00 0.00 3.91
2747 3127 0.878523 TGTTCAACGACTGGCCTTCG 60.879 55.000 21.46 21.46 42.36 3.79
2776 3156 0.749049 TCTCATGGACTCCATCAGCG 59.251 55.000 7.69 0.00 43.15 5.18
2793 3173 5.129485 CCATCCTGTACAACATCTACCTTCT 59.871 44.000 0.00 0.00 0.00 2.85
2866 3246 6.240894 TCTCCAAGTGCTAAACAATGAGAAT 58.759 36.000 0.00 0.00 0.00 2.40
2889 3269 5.796350 AGTAGAATGTACGCACCATTTTC 57.204 39.130 0.00 0.00 32.84 2.29
2890 3270 6.569179 AAAGTAGAATGTACGCACCATTTT 57.431 33.333 0.00 0.00 32.84 1.82
3031 3412 4.438148 CGAAACCCAGAACCAAAATGTTT 58.562 39.130 0.00 0.00 0.00 2.83
3115 3496 2.231235 CTGCAATCAAACACCCCCTAAC 59.769 50.000 0.00 0.00 0.00 2.34
3116 3497 2.524306 CTGCAATCAAACACCCCCTAA 58.476 47.619 0.00 0.00 0.00 2.69
3117 3498 1.272425 CCTGCAATCAAACACCCCCTA 60.272 52.381 0.00 0.00 0.00 3.53
3118 3499 0.542702 CCTGCAATCAAACACCCCCT 60.543 55.000 0.00 0.00 0.00 4.79
3119 3500 1.543944 CCCTGCAATCAAACACCCCC 61.544 60.000 0.00 0.00 0.00 5.40
3120 3501 0.541764 TCCCTGCAATCAAACACCCC 60.542 55.000 0.00 0.00 0.00 4.95
3121 3502 0.603065 GTCCCTGCAATCAAACACCC 59.397 55.000 0.00 0.00 0.00 4.61
3122 3503 1.620822 AGTCCCTGCAATCAAACACC 58.379 50.000 0.00 0.00 0.00 4.16
3123 3504 3.733443 AAAGTCCCTGCAATCAAACAC 57.267 42.857 0.00 0.00 0.00 3.32
3124 3505 4.751767 AAAAAGTCCCTGCAATCAAACA 57.248 36.364 0.00 0.00 0.00 2.83
3160 3541 4.468153 TGTTTGGTTTGCTAGGGACTTTTT 59.532 37.500 0.00 0.00 41.75 1.94
3161 3542 4.027437 TGTTTGGTTTGCTAGGGACTTTT 58.973 39.130 0.00 0.00 41.75 2.27
3162 3543 3.636764 CTGTTTGGTTTGCTAGGGACTTT 59.363 43.478 0.00 0.00 41.75 2.66
3163 3544 3.222603 CTGTTTGGTTTGCTAGGGACTT 58.777 45.455 0.00 0.00 41.75 3.01
3164 3545 2.489073 CCTGTTTGGTTTGCTAGGGACT 60.489 50.000 0.00 0.00 46.37 3.85
3165 3546 1.886542 CCTGTTTGGTTTGCTAGGGAC 59.113 52.381 0.00 0.00 0.00 4.46
3166 3547 1.203001 CCCTGTTTGGTTTGCTAGGGA 60.203 52.381 0.00 0.00 46.19 4.20
3167 3548 1.256812 CCCTGTTTGGTTTGCTAGGG 58.743 55.000 0.00 0.00 38.96 3.53
3168 3549 1.256812 CCCCTGTTTGGTTTGCTAGG 58.743 55.000 0.00 0.00 0.00 3.02
3169 3550 1.256812 CCCCCTGTTTGGTTTGCTAG 58.743 55.000 0.00 0.00 0.00 3.42
3170 3551 3.448469 CCCCCTGTTTGGTTTGCTA 57.552 52.632 0.00 0.00 0.00 3.49
3171 3552 4.293610 CCCCCTGTTTGGTTTGCT 57.706 55.556 0.00 0.00 0.00 3.91
3203 3584 7.200455 GTGCTTCTAAGGACTTTTAGCAAAAA 58.800 34.615 7.07 0.00 43.15 1.94
3204 3585 6.238925 GGTGCTTCTAAGGACTTTTAGCAAAA 60.239 38.462 13.12 0.00 45.42 2.44
3205 3586 5.240844 GGTGCTTCTAAGGACTTTTAGCAAA 59.759 40.000 13.12 0.00 45.42 3.68
3206 3587 4.760204 GGTGCTTCTAAGGACTTTTAGCAA 59.240 41.667 13.12 1.75 45.42 3.91
3207 3588 4.041691 AGGTGCTTCTAAGGACTTTTAGCA 59.958 41.667 13.12 9.74 45.42 3.49
3208 3589 4.580868 AGGTGCTTCTAAGGACTTTTAGC 58.419 43.478 13.12 0.00 45.42 3.09
3209 3590 5.046231 AGGAGGTGCTTCTAAGGACTTTTAG 60.046 44.000 13.12 0.00 45.42 1.85
3210 3591 4.844655 AGGAGGTGCTTCTAAGGACTTTTA 59.155 41.667 13.12 0.00 45.42 1.52
3211 3592 3.653352 AGGAGGTGCTTCTAAGGACTTTT 59.347 43.478 13.12 1.47 45.42 2.27
3212 3593 3.252351 AGGAGGTGCTTCTAAGGACTTT 58.748 45.455 13.12 3.63 45.42 2.66
3213 3594 2.909217 AGGAGGTGCTTCTAAGGACTT 58.091 47.619 13.12 6.52 45.42 3.01
3214 3595 2.569404 CAAGGAGGTGCTTCTAAGGACT 59.431 50.000 13.12 1.24 45.42 3.85
3215 3596 2.567615 TCAAGGAGGTGCTTCTAAGGAC 59.432 50.000 5.86 5.86 45.39 3.85
3216 3597 2.834549 CTCAAGGAGGTGCTTCTAAGGA 59.165 50.000 0.00 0.00 0.00 3.36
3217 3598 2.834549 TCTCAAGGAGGTGCTTCTAAGG 59.165 50.000 0.00 0.00 0.00 2.69
3218 3599 3.513515 ACTCTCAAGGAGGTGCTTCTAAG 59.486 47.826 0.00 0.00 45.83 2.18
3219 3600 3.511477 ACTCTCAAGGAGGTGCTTCTAA 58.489 45.455 0.00 0.00 45.83 2.10
3220 3601 3.176924 ACTCTCAAGGAGGTGCTTCTA 57.823 47.619 0.00 0.00 45.83 2.10
3221 3602 2.022718 ACTCTCAAGGAGGTGCTTCT 57.977 50.000 0.00 0.00 45.83 2.85
3222 3603 2.849294 AACTCTCAAGGAGGTGCTTC 57.151 50.000 0.00 0.00 45.83 3.86
3223 3604 3.584733 AAAACTCTCAAGGAGGTGCTT 57.415 42.857 0.00 0.00 41.89 3.91
3224 3605 3.584733 AAAAACTCTCAAGGAGGTGCT 57.415 42.857 0.00 0.00 41.89 4.40
3272 3653 4.142116 GCTTTGGTTCTCTAGTCCTAGGAC 60.142 50.000 31.29 31.29 44.86 3.85
3273 3654 4.024670 GCTTTGGTTCTCTAGTCCTAGGA 58.975 47.826 7.62 7.62 34.06 2.94
3274 3655 3.769844 TGCTTTGGTTCTCTAGTCCTAGG 59.230 47.826 0.82 0.82 34.06 3.02
3275 3656 4.382147 GGTGCTTTGGTTCTCTAGTCCTAG 60.382 50.000 0.00 0.00 34.56 3.02
3276 3657 3.514309 GGTGCTTTGGTTCTCTAGTCCTA 59.486 47.826 0.00 0.00 0.00 2.94
3277 3658 2.303311 GGTGCTTTGGTTCTCTAGTCCT 59.697 50.000 0.00 0.00 0.00 3.85
3278 3659 2.303311 AGGTGCTTTGGTTCTCTAGTCC 59.697 50.000 0.00 0.00 0.00 3.85
3279 3660 3.686916 AGGTGCTTTGGTTCTCTAGTC 57.313 47.619 0.00 0.00 0.00 2.59
3280 3661 5.763876 ATAAGGTGCTTTGGTTCTCTAGT 57.236 39.130 0.00 0.00 0.00 2.57
3281 3662 6.763610 CCTAATAAGGTGCTTTGGTTCTCTAG 59.236 42.308 0.00 0.00 38.19 2.43
3282 3663 6.650120 CCTAATAAGGTGCTTTGGTTCTCTA 58.350 40.000 0.00 0.00 38.19 2.43
3283 3664 5.501156 CCTAATAAGGTGCTTTGGTTCTCT 58.499 41.667 0.00 0.00 38.19 3.10
3284 3665 5.819825 CCTAATAAGGTGCTTTGGTTCTC 57.180 43.478 0.00 0.00 38.19 2.87
3381 3762 7.805071 CCGCCTCATTTTCATATTATTGAACTC 59.195 37.037 0.00 0.00 35.42 3.01
3396 3777 1.630878 AGAGAAGACCCGCCTCATTTT 59.369 47.619 0.00 0.00 0.00 1.82
3417 3798 6.483307 ACATATCGATTGGTTGTACATGGAAG 59.517 38.462 1.71 0.00 0.00 3.46
3430 3811 3.985008 TCCGGTTGTACATATCGATTGG 58.015 45.455 1.71 0.00 0.00 3.16
3432 3813 4.931661 ACTCCGGTTGTACATATCGATT 57.068 40.909 1.71 0.00 0.00 3.34
3603 3985 6.319715 TCTACAAAAGGGCCCTAAATTTCTT 58.680 36.000 28.96 11.36 0.00 2.52
3730 4112 4.225942 AGTGAACTGAATGAAGGCTGGATA 59.774 41.667 0.00 0.00 0.00 2.59
3802 4190 9.592196 AATATGTTCAATAGTCCCATATTGCTT 57.408 29.630 0.00 0.00 41.12 3.91


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

AutoCloner maintained by Alex Coulton.