Multiple sequence alignment - TraesCS7A01G210500

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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 TraesCS7A01G210500 chr7A 100.000 3221 0 0 1 3221 173494523 173491303 0.000000e+00 5949
1 TraesCS7A01G210500 chr7B 91.394 1650 86 21 595 2222 136889163 136887548 0.000000e+00 2209
2 TraesCS7A01G210500 chr7B 83.474 593 81 15 1 584 150194834 150195418 1.320000e-148 536
3 TraesCS7A01G210500 chr7D 90.735 1673 81 20 598 2245 170608488 170606865 0.000000e+00 2163
4 TraesCS7A01G210500 chr7D 78.832 548 101 14 2669 3208 106618094 106617554 3.950000e-94 355
5 TraesCS7A01G210500 chr7D 77.491 271 56 4 1190 1456 170730877 170730608 1.200000e-34 158
6 TraesCS7A01G210500 chr3B 92.266 918 51 10 2314 3221 749723438 749722531 0.000000e+00 1284
7 TraesCS7A01G210500 chr3B 77.803 892 170 18 2333 3209 141828776 141827898 2.850000e-145 525
8 TraesCS7A01G210500 chr1A 85.235 596 78 8 1 591 260717953 260717363 3.550000e-169 604
9 TraesCS7A01G210500 chr3D 84.848 594 80 8 1 588 329014913 329015502 9.950000e-165 590
10 TraesCS7A01G210500 chr3D 83.446 592 86 9 1 587 338495450 338496034 1.020000e-149 540
11 TraesCS7A01G210500 chr4B 78.603 902 166 17 2333 3220 671797011 671796123 3.600000e-159 571
12 TraesCS7A01G210500 chr5A 77.989 895 170 18 2330 3211 445547250 445548130 1.320000e-148 536
13 TraesCS7A01G210500 chr5A 83.165 594 82 16 1 584 62971290 62971875 7.910000e-146 527
14 TraesCS7A01G210500 chr2B 83.305 593 82 15 1 584 752859479 752858895 6.120000e-147 531
15 TraesCS7A01G210500 chr2B 94.152 171 9 1 2314 2483 670598497 670598667 3.190000e-65 259
16 TraesCS7A01G210500 chr5B 83.137 593 83 15 1 584 129724788 129724204 2.850000e-145 525
17 TraesCS7A01G210500 chr3A 83.193 595 79 18 1 584 550525578 550524994 2.850000e-145 525
18 TraesCS7A01G210500 chr6B 82.968 593 84 14 1 584 4544017 4544601 1.320000e-143 520
19 TraesCS7A01G210500 chrUn 77.318 895 178 18 2330 3211 15347835 15348717 3.710000e-139 505
20 TraesCS7A01G210500 chrUn 77.248 901 180 18 2333 3220 272741828 272740940 3.710000e-139 505
21 TraesCS7A01G210500 chr1D 75.604 910 180 33 2315 3202 432364587 432363698 2.310000e-111 412
22 TraesCS7A01G210500 chr5D 79.158 499 99 5 2644 3139 399907857 399908353 1.110000e-89 340


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 TraesCS7A01G210500 chr7A 173491303 173494523 3220 True 5949 5949 100.000 1 3221 1 chr7A.!!$R1 3220
1 TraesCS7A01G210500 chr7B 136887548 136889163 1615 True 2209 2209 91.394 595 2222 1 chr7B.!!$R1 1627
2 TraesCS7A01G210500 chr7B 150194834 150195418 584 False 536 536 83.474 1 584 1 chr7B.!!$F1 583
3 TraesCS7A01G210500 chr7D 170606865 170608488 1623 True 2163 2163 90.735 598 2245 1 chr7D.!!$R2 1647
4 TraesCS7A01G210500 chr7D 106617554 106618094 540 True 355 355 78.832 2669 3208 1 chr7D.!!$R1 539
5 TraesCS7A01G210500 chr3B 749722531 749723438 907 True 1284 1284 92.266 2314 3221 1 chr3B.!!$R2 907
6 TraesCS7A01G210500 chr3B 141827898 141828776 878 True 525 525 77.803 2333 3209 1 chr3B.!!$R1 876
7 TraesCS7A01G210500 chr1A 260717363 260717953 590 True 604 604 85.235 1 591 1 chr1A.!!$R1 590
8 TraesCS7A01G210500 chr3D 329014913 329015502 589 False 590 590 84.848 1 588 1 chr3D.!!$F1 587
9 TraesCS7A01G210500 chr3D 338495450 338496034 584 False 540 540 83.446 1 587 1 chr3D.!!$F2 586
10 TraesCS7A01G210500 chr4B 671796123 671797011 888 True 571 571 78.603 2333 3220 1 chr4B.!!$R1 887
11 TraesCS7A01G210500 chr5A 445547250 445548130 880 False 536 536 77.989 2330 3211 1 chr5A.!!$F2 881
12 TraesCS7A01G210500 chr5A 62971290 62971875 585 False 527 527 83.165 1 584 1 chr5A.!!$F1 583
13 TraesCS7A01G210500 chr2B 752858895 752859479 584 True 531 531 83.305 1 584 1 chr2B.!!$R1 583
14 TraesCS7A01G210500 chr5B 129724204 129724788 584 True 525 525 83.137 1 584 1 chr5B.!!$R1 583
15 TraesCS7A01G210500 chr3A 550524994 550525578 584 True 525 525 83.193 1 584 1 chr3A.!!$R1 583
16 TraesCS7A01G210500 chr6B 4544017 4544601 584 False 520 520 82.968 1 584 1 chr6B.!!$F1 583
17 TraesCS7A01G210500 chrUn 15347835 15348717 882 False 505 505 77.318 2330 3211 1 chrUn.!!$F1 881
18 TraesCS7A01G210500 chrUn 272740940 272741828 888 True 505 505 77.248 2333 3220 1 chrUn.!!$R1 887
19 TraesCS7A01G210500 chr1D 432363698 432364587 889 True 412 412 75.604 2315 3202 1 chr1D.!!$R1 887

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
728 744 0.107831 TTTACAGTTCGGCCAGTGCT 59.892 50.0 2.24 0.0 37.74 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2301 2338 0.179084 TAGCATGCGCCTTAGTGTCC 60.179 55.0 13.01 0.0 39.83 4.02 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
25 26 3.387947 GTCGGTGATGTCCCGGGT 61.388 66.667 22.86 0.00 45.51 5.28
30 31 1.153168 GTGATGTCCCGGGTGATGG 60.153 63.158 22.86 0.00 0.00 3.51
45 46 2.537792 GATGGCGACGAAGACGGACA 62.538 60.000 0.00 0.00 46.96 4.02
57 58 0.108804 GACGGACAGGCGATGAAGAA 60.109 55.000 0.00 0.00 0.00 2.52
60 61 0.389948 GGACAGGCGATGAAGAACGT 60.390 55.000 0.00 0.00 0.00 3.99
93 94 1.001641 GGCAGTGAGGCATGAAGGT 60.002 57.895 0.00 0.00 43.51 3.50
157 158 4.203076 GCGGCCGGTGTAGTCGAT 62.203 66.667 29.38 0.00 0.00 3.59
161 162 1.731433 GGCCGGTGTAGTCGATGCTA 61.731 60.000 1.90 0.00 0.00 3.49
253 254 2.393764 AGCAAAAAGAAAACGCCGATG 58.606 42.857 0.00 0.00 0.00 3.84
275 277 4.116328 CGACCGGCGAGAGAGCAA 62.116 66.667 9.30 0.00 44.57 3.91
389 395 1.003355 CGGCAACAGTCATGGAGGT 60.003 57.895 0.00 0.00 0.00 3.85
392 398 1.021390 GCAACAGTCATGGAGGTCGG 61.021 60.000 0.00 0.00 0.00 4.79
399 405 2.040464 ATGGAGGTCGGCCATCCT 60.040 61.111 20.57 14.59 42.31 3.24
401 407 2.764128 GGAGGTCGGCCATCCTGA 60.764 66.667 18.80 0.00 37.19 3.86
471 485 5.363005 GGTTAGCCTGATACTGTTAGAAGGA 59.637 44.000 0.00 0.00 0.00 3.36
475 489 5.721960 AGCCTGATACTGTTAGAAGGAAGAA 59.278 40.000 0.00 0.00 0.00 2.52
512 526 9.898152 TTGCGGAATATGATGGATGTATTATTA 57.102 29.630 0.00 0.00 0.00 0.98
525 539 8.271458 TGGATGTATTATTAAGTCTTCAAGGCA 58.729 33.333 0.00 0.00 0.00 4.75
556 570 8.762481 ATATTAAATACAAGGTTTGGAGGACC 57.238 34.615 0.00 0.00 37.44 4.46
592 607 8.810990 CCTAAAGATAGGTAGGAGACGAATAT 57.189 38.462 0.00 0.00 43.32 1.28
593 608 8.679100 CCTAAAGATAGGTAGGAGACGAATATG 58.321 40.741 0.00 0.00 43.32 1.78
606 621 3.375642 ACGAATATGCGTGACAGATCTG 58.624 45.455 21.37 21.37 43.79 2.90
643 658 3.251479 TCTCGAATGTCTGGAATGGTG 57.749 47.619 0.00 0.00 0.00 4.17
646 661 1.106285 GAATGTCTGGAATGGTGGGC 58.894 55.000 0.00 0.00 0.00 5.36
661 677 1.153686 GGGCGACTTCCGTTCCTAC 60.154 63.158 0.00 0.00 41.15 3.18
686 702 1.329292 CGACACGCCAGTCAAAAAGAA 59.671 47.619 4.34 0.00 38.43 2.52
715 731 2.656560 ACCGCTAGCTCAGTTTACAG 57.343 50.000 13.93 0.00 0.00 2.74
716 732 1.893801 ACCGCTAGCTCAGTTTACAGT 59.106 47.619 13.93 0.00 0.00 3.55
717 733 2.299297 ACCGCTAGCTCAGTTTACAGTT 59.701 45.455 13.93 0.00 0.00 3.16
718 734 2.924290 CCGCTAGCTCAGTTTACAGTTC 59.076 50.000 13.93 0.00 0.00 3.01
719 735 2.594654 CGCTAGCTCAGTTTACAGTTCG 59.405 50.000 13.93 0.00 0.00 3.95
720 736 2.924290 GCTAGCTCAGTTTACAGTTCGG 59.076 50.000 7.70 0.00 0.00 4.30
721 737 1.797025 AGCTCAGTTTACAGTTCGGC 58.203 50.000 0.00 0.00 0.00 5.54
722 738 0.796927 GCTCAGTTTACAGTTCGGCC 59.203 55.000 0.00 0.00 0.00 6.13
723 739 1.876416 GCTCAGTTTACAGTTCGGCCA 60.876 52.381 2.24 0.00 0.00 5.36
724 740 2.069273 CTCAGTTTACAGTTCGGCCAG 58.931 52.381 2.24 0.00 0.00 4.85
725 741 1.414919 TCAGTTTACAGTTCGGCCAGT 59.585 47.619 2.24 0.00 0.00 4.00
726 742 1.531149 CAGTTTACAGTTCGGCCAGTG 59.469 52.381 2.24 0.00 0.00 3.66
727 743 0.237498 GTTTACAGTTCGGCCAGTGC 59.763 55.000 2.24 0.00 0.00 4.40
728 744 0.107831 TTTACAGTTCGGCCAGTGCT 59.892 50.000 2.24 0.00 37.74 4.40
729 745 0.320421 TTACAGTTCGGCCAGTGCTC 60.320 55.000 2.24 0.00 37.74 4.26
730 746 1.468506 TACAGTTCGGCCAGTGCTCA 61.469 55.000 2.24 0.00 37.74 4.26
731 747 1.376424 CAGTTCGGCCAGTGCTCAT 60.376 57.895 2.24 0.00 37.74 2.90
732 748 1.376424 AGTTCGGCCAGTGCTCATG 60.376 57.895 2.24 0.00 37.74 3.07
733 749 2.046023 TTCGGCCAGTGCTCATGG 60.046 61.111 2.24 0.00 41.04 3.66
738 754 2.513204 CCAGTGCTCATGGCCTCG 60.513 66.667 3.32 0.00 40.92 4.63
739 755 2.267006 CAGTGCTCATGGCCTCGT 59.733 61.111 3.32 0.00 40.92 4.18
740 756 1.517361 CAGTGCTCATGGCCTCGTA 59.483 57.895 3.32 0.00 40.92 3.43
741 757 0.807667 CAGTGCTCATGGCCTCGTAC 60.808 60.000 3.32 0.00 40.92 3.67
742 758 1.218047 GTGCTCATGGCCTCGTACA 59.782 57.895 3.32 0.00 40.92 2.90
743 759 0.807667 GTGCTCATGGCCTCGTACAG 60.808 60.000 3.32 0.00 40.92 2.74
763 779 1.781555 CGCACCTGTTTAGCACTCG 59.218 57.895 0.00 0.00 0.00 4.18
798 814 2.371841 TCCACCATCACAAGTGTAAGCT 59.628 45.455 0.00 0.00 31.88 3.74
803 819 3.427098 CCATCACAAGTGTAAGCTGCATG 60.427 47.826 1.02 0.00 0.00 4.06
805 821 0.883833 ACAAGTGTAAGCTGCATGCC 59.116 50.000 16.68 0.00 44.23 4.40
822 838 0.372334 GCCAATTACGTACCGTGCAG 59.628 55.000 0.00 0.00 41.39 4.41
842 858 0.801067 CGCTAACTAGTCACCACCGC 60.801 60.000 0.00 0.00 0.00 5.68
849 865 1.466025 TAGTCACCACCGCCTTCGTT 61.466 55.000 0.00 0.00 0.00 3.85
857 873 1.234615 ACCGCCTTCGTTGTCAATGG 61.235 55.000 4.95 0.00 0.00 3.16
860 876 2.006888 CGCCTTCGTTGTCAATGGTAT 58.993 47.619 4.95 0.00 0.00 2.73
870 886 1.452025 GTCAATGGTATCGCATCGACG 59.548 52.381 0.00 0.00 39.18 5.12
882 898 1.374252 ATCGACGTGCCACTTCCAC 60.374 57.895 0.00 0.00 0.00 4.02
891 912 0.886490 GCCACTTCCACCTGACACTG 60.886 60.000 0.00 0.00 0.00 3.66
897 918 3.328931 ACTTCCACCTGACACTGATGAAT 59.671 43.478 0.00 0.00 0.00 2.57
918 939 3.708890 TGTTCATGAAGCAGCACAAAAG 58.291 40.909 8.80 0.00 0.00 2.27
926 947 3.930634 AGCAGCACAAAAGAAGAATCC 57.069 42.857 0.00 0.00 0.00 3.01
932 953 6.403200 GCAGCACAAAAGAAGAATCCGTATAA 60.403 38.462 0.00 0.00 0.00 0.98
977 998 8.071967 CACATCATAAACATAACGCTCATGATT 58.928 33.333 0.00 0.00 31.14 2.57
988 1009 2.214244 CGCTCATGATTCGTAGTTCGTG 59.786 50.000 0.00 0.00 40.80 4.35
1017 1054 2.093447 ACCGATGGAGTTTCATGGAGTC 60.093 50.000 0.00 0.00 0.00 3.36
1150 1187 2.435938 TGATGCCGCCGTTTCTCC 60.436 61.111 0.00 0.00 0.00 3.71
1157 1194 2.125106 GCCGTTTCTCCCGAGCAT 60.125 61.111 0.00 0.00 0.00 3.79
1672 1709 2.514013 GCCGGCATGTTCGACTACG 61.514 63.158 24.80 0.00 41.26 3.51
1792 1829 2.034532 TCACGCTCCGGTACTCCA 59.965 61.111 0.00 0.00 0.00 3.86
1970 2007 0.684479 CAGTGGGAGATGGACGAGGA 60.684 60.000 0.00 0.00 0.00 3.71
2134 2171 1.229209 TGGGAGCCGGAGAAGTTCT 60.229 57.895 5.05 4.68 0.00 3.01
2224 2261 4.682787 TCACATGCTGATCGGTTAACTAG 58.317 43.478 5.42 0.49 0.00 2.57
2225 2262 4.159693 TCACATGCTGATCGGTTAACTAGT 59.840 41.667 5.42 0.00 0.00 2.57
2227 2264 5.459107 CACATGCTGATCGGTTAACTAGTAC 59.541 44.000 5.42 0.00 0.00 2.73
2229 2266 5.496133 TGCTGATCGGTTAACTAGTACTC 57.504 43.478 0.00 0.00 0.00 2.59
2231 2268 4.337555 GCTGATCGGTTAACTAGTACTCCA 59.662 45.833 0.00 0.00 0.00 3.86
2232 2269 5.163581 GCTGATCGGTTAACTAGTACTCCAA 60.164 44.000 0.00 0.00 0.00 3.53
2233 2270 6.461231 GCTGATCGGTTAACTAGTACTCCAAT 60.461 42.308 0.00 0.00 0.00 3.16
2234 2271 7.414222 TGATCGGTTAACTAGTACTCCAATT 57.586 36.000 0.00 0.00 0.00 2.32
2235 2272 8.523915 TGATCGGTTAACTAGTACTCCAATTA 57.476 34.615 0.00 0.00 0.00 1.40
2236 2273 8.408601 TGATCGGTTAACTAGTACTCCAATTAC 58.591 37.037 0.00 0.00 0.00 1.89
2237 2274 7.100458 TCGGTTAACTAGTACTCCAATTACC 57.900 40.000 0.00 0.89 0.00 2.85
2238 2275 6.663093 TCGGTTAACTAGTACTCCAATTACCA 59.337 38.462 0.00 0.00 0.00 3.25
2239 2276 7.342799 TCGGTTAACTAGTACTCCAATTACCAT 59.657 37.037 0.00 0.00 0.00 3.55
2240 2277 7.983484 CGGTTAACTAGTACTCCAATTACCATT 59.017 37.037 0.00 0.00 0.00 3.16
2241 2278 9.676861 GGTTAACTAGTACTCCAATTACCATTT 57.323 33.333 0.00 0.00 0.00 2.32
2249 2286 9.762381 AGTACTCCAATTACCATTTTTATGGAA 57.238 29.630 10.96 2.27 44.39 3.53
2260 2297 8.980481 ACCATTTTTATGGAATAGTACTCCAG 57.020 34.615 6.49 0.00 46.04 3.86
2261 2298 8.557450 ACCATTTTTATGGAATAGTACTCCAGT 58.443 33.333 6.49 0.00 46.04 4.00
2284 2321 8.379457 AGTAACTTACTGCTCTGTTAAAAAGG 57.621 34.615 0.33 0.00 37.69 3.11
2285 2322 5.690997 ACTTACTGCTCTGTTAAAAAGGC 57.309 39.130 0.00 0.00 0.00 4.35
2286 2323 5.377478 ACTTACTGCTCTGTTAAAAAGGCT 58.623 37.500 0.00 0.00 0.00 4.58
2287 2324 5.470437 ACTTACTGCTCTGTTAAAAAGGCTC 59.530 40.000 0.00 0.00 0.00 4.70
2288 2325 4.092116 ACTGCTCTGTTAAAAAGGCTCT 57.908 40.909 0.00 0.00 0.00 4.09
2289 2326 3.817647 ACTGCTCTGTTAAAAAGGCTCTG 59.182 43.478 0.00 0.00 0.00 3.35
2290 2327 3.817647 CTGCTCTGTTAAAAAGGCTCTGT 59.182 43.478 0.00 0.00 0.00 3.41
2291 2328 4.207165 TGCTCTGTTAAAAAGGCTCTGTT 58.793 39.130 0.00 0.00 0.00 3.16
2292 2329 4.275936 TGCTCTGTTAAAAAGGCTCTGTTC 59.724 41.667 0.00 0.00 0.00 3.18
2293 2330 4.517075 GCTCTGTTAAAAAGGCTCTGTTCT 59.483 41.667 0.00 0.00 0.00 3.01
2294 2331 5.334491 GCTCTGTTAAAAAGGCTCTGTTCTC 60.334 44.000 0.00 0.00 0.00 2.87
2295 2332 5.063880 TCTGTTAAAAAGGCTCTGTTCTCC 58.936 41.667 0.00 0.00 0.00 3.71
2296 2333 4.787551 TGTTAAAAAGGCTCTGTTCTCCA 58.212 39.130 0.00 0.00 0.00 3.86
2297 2334 5.385198 TGTTAAAAAGGCTCTGTTCTCCAT 58.615 37.500 0.00 0.00 0.00 3.41
2298 2335 5.833131 TGTTAAAAAGGCTCTGTTCTCCATT 59.167 36.000 0.00 0.00 0.00 3.16
2299 2336 4.861102 AAAAAGGCTCTGTTCTCCATTG 57.139 40.909 0.00 0.00 0.00 2.82
2300 2337 2.503895 AAGGCTCTGTTCTCCATTGG 57.496 50.000 0.00 0.00 0.00 3.16
2301 2338 0.622665 AGGCTCTGTTCTCCATTGGG 59.377 55.000 2.09 0.00 0.00 4.12
2302 2339 0.394899 GGCTCTGTTCTCCATTGGGG 60.395 60.000 2.09 0.00 38.37 4.96
2303 2340 0.620556 GCTCTGTTCTCCATTGGGGA 59.379 55.000 0.00 0.00 45.89 4.81
2304 2341 1.680249 GCTCTGTTCTCCATTGGGGAC 60.680 57.143 4.25 1.55 42.15 4.46
2305 2342 1.630369 CTCTGTTCTCCATTGGGGACA 59.370 52.381 4.25 6.25 42.15 4.02
2306 2343 1.351017 TCTGTTCTCCATTGGGGACAC 59.649 52.381 4.25 7.73 42.15 3.67
2307 2344 1.352352 CTGTTCTCCATTGGGGACACT 59.648 52.381 4.25 0.00 42.15 3.55
2308 2345 2.571653 CTGTTCTCCATTGGGGACACTA 59.428 50.000 4.25 0.00 42.15 2.74
2309 2346 2.983192 TGTTCTCCATTGGGGACACTAA 59.017 45.455 4.25 0.00 42.15 2.24
2310 2347 3.009033 TGTTCTCCATTGGGGACACTAAG 59.991 47.826 4.25 0.00 42.15 2.18
2311 2348 2.196595 TCTCCATTGGGGACACTAAGG 58.803 52.381 0.00 0.00 42.15 2.69
2312 2349 0.623723 TCCATTGGGGACACTAAGGC 59.376 55.000 2.09 0.00 42.15 4.35
2373 2410 7.171630 AGGTGATATTCTTACGTCTGAAGTT 57.828 36.000 0.75 0.00 0.00 2.66
2384 2421 4.916870 ACGTCTGAAGTTTTAAAGGCAAC 58.083 39.130 0.00 0.00 0.00 4.17
2422 2459 3.459227 TCCAGCTGGATGGAATGATACAA 59.541 43.478 32.00 3.90 46.45 2.41
2453 2490 6.014156 GTGCTCATACCTAAGGTGGATAATCT 60.014 42.308 0.00 0.00 36.19 2.40
2483 2520 7.969850 ATATATCCCAATATAGGCCCATCAA 57.030 36.000 0.00 0.00 34.56 2.57
2534 2572 3.125146 TCAAAGATGATTGCCTTTCGACG 59.875 43.478 0.00 0.00 30.89 5.12
2537 2575 2.932614 AGATGATTGCCTTTCGACGAAG 59.067 45.455 10.61 1.37 0.00 3.79
2540 2586 2.288825 TGATTGCCTTTCGACGAAGAGT 60.289 45.455 10.61 0.00 0.00 3.24
2567 2613 4.870123 ATTATTGCACCTGTTCAAAGCA 57.130 36.364 0.00 0.00 0.00 3.91
2593 2639 2.093500 TGTTCCTGGGAGATCAATCACG 60.093 50.000 0.00 0.00 0.00 4.35
2621 2667 8.439971 ACAATATTCTTATTGCCTATGAGTCCA 58.560 33.333 5.80 0.00 45.75 4.02
2622 2668 9.458727 CAATATTCTTATTGCCTATGAGTCCAT 57.541 33.333 0.00 0.00 38.58 3.41
2623 2669 9.458727 AATATTCTTATTGCCTATGAGTCCATG 57.541 33.333 0.00 0.00 34.31 3.66
2624 2670 5.894298 TCTTATTGCCTATGAGTCCATGT 57.106 39.130 0.00 0.00 34.31 3.21
2625 2671 6.994421 TCTTATTGCCTATGAGTCCATGTA 57.006 37.500 0.00 0.00 34.31 2.29
2626 2672 7.373617 TCTTATTGCCTATGAGTCCATGTAA 57.626 36.000 0.00 0.00 34.31 2.41
2627 2673 7.217200 TCTTATTGCCTATGAGTCCATGTAAC 58.783 38.462 0.00 0.00 34.31 2.50
2631 2677 4.164030 TGCCTATGAGTCCATGTAACATGT 59.836 41.667 0.00 0.00 34.31 3.21
2698 2747 4.163078 AGTGAAGCTAGATATGCACAAGGT 59.837 41.667 10.05 0.00 0.00 3.50
2734 2783 4.218635 GGAATGGGTCTTTCTGGAGAAAAC 59.781 45.833 3.52 5.11 42.72 2.43
2740 2789 5.278512 GGGTCTTTCTGGAGAAAACAATGAC 60.279 44.000 3.52 6.60 42.72 3.06
2748 2797 8.190326 TCTGGAGAAAACAATGACTAGACTTA 57.810 34.615 0.00 0.00 0.00 2.24
2832 2881 5.256474 CCAGGTTTAATGACCAAGAGACAT 58.744 41.667 0.00 0.00 42.35 3.06
2851 2900 5.418524 AGACATATATGTTTGTGCCAAGCAA 59.581 36.000 19.19 0.00 40.04 3.91
2868 2917 2.208349 AGGGACTTCAGCAGGGGT 59.792 61.111 0.00 0.00 27.25 4.95
2869 2918 1.464198 AGGGACTTCAGCAGGGGTT 60.464 57.895 0.00 0.00 27.25 4.11
2957 3007 1.349688 AGGTTCGTGGCATTGAAGGTA 59.650 47.619 5.51 0.00 0.00 3.08
3006 3056 8.050778 TCAGTGTCTCATTTACTTTTTGTTGT 57.949 30.769 0.00 0.00 0.00 3.32
3033 3083 5.296151 TCCCTTATACTCATGAAAGCTGG 57.704 43.478 0.00 0.00 0.00 4.85
3087 3138 6.893958 ACTAGAGATTACTGTGCAAATTCG 57.106 37.500 0.00 0.00 0.00 3.34
3182 3233 7.811236 CACAGATTTGCACTGAACTGAATATTT 59.189 33.333 9.59 0.00 38.55 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.180769 CCGTCTTCGTCGCCATCA 59.819 61.111 0.00 0.00 35.01 3.07
30 31 2.504244 CCTGTCCGTCTTCGTCGC 60.504 66.667 0.00 0.00 35.01 5.19
45 46 2.094659 CGCACGTTCTTCATCGCCT 61.095 57.895 0.00 0.00 0.00 5.52
80 81 1.685224 GGGACACCTTCATGCCTCA 59.315 57.895 0.00 0.00 0.00 3.86
124 125 1.368345 CCGCTTCATCATCAACCGCA 61.368 55.000 0.00 0.00 0.00 5.69
157 158 1.681793 GCCTCTACTCCGACATTAGCA 59.318 52.381 0.00 0.00 0.00 3.49
161 162 1.437986 GCGCCTCTACTCCGACATT 59.562 57.895 0.00 0.00 0.00 2.71
203 204 0.881118 ATGCTTGATCGGTTTGCGTT 59.119 45.000 0.00 0.00 0.00 4.84
230 231 2.600867 TCGGCGTTTTCTTTTTGCTTTG 59.399 40.909 6.85 0.00 0.00 2.77
234 235 2.389998 TCATCGGCGTTTTCTTTTTGC 58.610 42.857 6.85 0.00 0.00 3.68
253 254 1.071567 CTCTCTCGCCGGTCGTTTTC 61.072 60.000 16.00 0.00 39.67 2.29
317 322 4.379174 GTCATGTTGACCGGCTGT 57.621 55.556 0.00 0.00 41.37 4.40
365 370 2.840753 ATGACTGTTGCCGGGGGTT 61.841 57.895 2.18 0.00 0.00 4.11
378 384 1.690219 GATGGCCGACCTCCATGACT 61.690 60.000 0.00 0.00 43.90 3.41
471 485 2.162681 CCGCAACAATCCCTCTTTCTT 58.837 47.619 0.00 0.00 0.00 2.52
475 489 2.514458 ATTCCGCAACAATCCCTCTT 57.486 45.000 0.00 0.00 0.00 2.85
536 550 4.105697 TCTGGTCCTCCAAACCTTGTATTT 59.894 41.667 0.00 0.00 43.81 1.40
538 552 3.256704 TCTGGTCCTCCAAACCTTGTAT 58.743 45.455 0.00 0.00 43.81 2.29
546 560 1.827399 GACGCCTCTGGTCCTCCAAA 61.827 60.000 0.00 0.00 43.81 3.28
556 570 3.254657 CCTATCTTTAGGAGACGCCTCTG 59.745 52.174 0.00 0.00 46.97 3.35
588 603 4.406648 TTCCAGATCTGTCACGCATATT 57.593 40.909 21.11 0.00 0.00 1.28
591 606 2.768253 TTTCCAGATCTGTCACGCAT 57.232 45.000 21.11 0.00 0.00 4.73
592 607 2.768253 ATTTCCAGATCTGTCACGCA 57.232 45.000 21.11 0.00 0.00 5.24
593 608 5.545658 TTTTATTTCCAGATCTGTCACGC 57.454 39.130 21.11 0.00 0.00 5.34
661 677 0.388520 TTGACTGGCGTGTCGAGATG 60.389 55.000 0.00 0.00 39.64 2.90
686 702 0.178975 AGCTAGCGGTAGAGCTCCAT 60.179 55.000 25.15 0.00 46.08 3.41
715 731 2.401766 CCATGAGCACTGGCCGAAC 61.402 63.158 0.00 0.00 42.56 3.95
716 732 2.046023 CCATGAGCACTGGCCGAA 60.046 61.111 0.00 0.00 42.56 4.30
721 737 1.960040 TACGAGGCCATGAGCACTGG 61.960 60.000 5.01 0.56 46.50 4.00
722 738 0.807667 GTACGAGGCCATGAGCACTG 60.808 60.000 5.01 0.00 46.50 3.66
723 739 1.257750 TGTACGAGGCCATGAGCACT 61.258 55.000 5.01 0.00 46.50 4.40
724 740 0.807667 CTGTACGAGGCCATGAGCAC 60.808 60.000 5.01 0.00 46.50 4.40
725 741 1.517361 CTGTACGAGGCCATGAGCA 59.483 57.895 5.01 0.00 46.50 4.26
726 742 1.227380 CCTGTACGAGGCCATGAGC 60.227 63.158 5.01 0.00 42.60 4.26
734 750 3.760035 AGGTGCGCCTGTACGAGG 61.760 66.667 20.48 6.91 45.05 4.63
743 759 1.912371 GAGTGCTAAACAGGTGCGCC 61.912 60.000 8.71 8.71 37.87 6.53
763 779 3.139029 GTGGATTCCACGTGACCTC 57.861 57.895 19.65 9.74 44.95 3.85
822 838 0.801067 CGGTGGTGACTAGTTAGCGC 60.801 60.000 18.95 18.95 0.00 5.92
842 858 2.030457 GCGATACCATTGACAACGAAGG 59.970 50.000 0.00 0.00 0.00 3.46
849 865 2.880963 TCGATGCGATACCATTGACA 57.119 45.000 0.00 0.00 32.11 3.58
870 886 1.148273 TGTCAGGTGGAAGTGGCAC 59.852 57.895 10.29 10.29 0.00 5.01
882 898 4.939439 TCATGAACATTCATCAGTGTCAGG 59.061 41.667 4.08 0.00 45.62 3.86
891 912 4.103357 GTGCTGCTTCATGAACATTCATC 58.897 43.478 3.38 0.00 45.62 2.92
897 918 3.380954 TCTTTTGTGCTGCTTCATGAACA 59.619 39.130 3.38 7.23 0.00 3.18
950 971 6.538381 TCATGAGCGTTATGTTTATGATGTGT 59.462 34.615 0.00 0.00 30.55 3.72
951 972 6.947258 TCATGAGCGTTATGTTTATGATGTG 58.053 36.000 0.00 0.00 30.55 3.21
952 973 7.734924 ATCATGAGCGTTATGTTTATGATGT 57.265 32.000 7.51 0.00 41.07 3.06
953 974 7.476492 CGAATCATGAGCGTTATGTTTATGATG 59.524 37.037 8.72 0.00 41.53 3.07
967 988 2.214244 CACGAACTACGAATCATGAGCG 59.786 50.000 16.42 16.42 45.77 5.03
988 1009 3.810941 TGAAACTCCATCGGTGTTAACAC 59.189 43.478 27.20 27.20 45.72 3.32
997 1034 2.093500 TGACTCCATGAAACTCCATCGG 60.093 50.000 0.00 0.00 0.00 4.18
1017 1054 3.880846 GCAATCGCCGGGAGCTTG 61.881 66.667 2.18 9.59 40.39 4.01
1027 1064 2.410469 GCTGTGATGGGCAATCGC 59.590 61.111 8.52 8.52 44.66 4.58
1146 1183 3.147595 CCGGTCATGCTCGGGAGA 61.148 66.667 15.72 0.00 42.32 3.71
1157 1194 3.770040 CTCGTCCATGGCCGGTCA 61.770 66.667 13.22 13.22 0.00 4.02
1368 1405 2.587194 CTCATGGCGCCGAGGAAG 60.587 66.667 23.90 10.75 0.00 3.46
1494 1531 0.231790 GCTCGTAGCGGTAGACGTAG 59.768 60.000 9.48 7.22 46.52 3.51
1950 1987 0.684479 CCTCGTCCATCTCCCACTGA 60.684 60.000 0.00 0.00 0.00 3.41
1951 1988 0.684479 TCCTCGTCCATCTCCCACTG 60.684 60.000 0.00 0.00 0.00 3.66
1970 2007 2.188994 GGCGCATCTCCTTCTGCT 59.811 61.111 10.83 0.00 36.23 4.24
2134 2171 3.936203 GCAGTCACGGGACACCCA 61.936 66.667 22.01 0.00 45.83 4.51
2235 2272 8.557450 ACTGGAGTACTATTCCATAAAAATGGT 58.443 33.333 0.00 0.00 43.46 3.55
2236 2273 8.980481 ACTGGAGTACTATTCCATAAAAATGG 57.020 34.615 0.00 0.00 43.46 3.16
2259 2296 7.041303 GCCTTTTTAACAGAGCAGTAAGTTACT 60.041 37.037 9.85 9.85 40.28 2.24
2260 2297 7.041303 AGCCTTTTTAACAGAGCAGTAAGTTAC 60.041 37.037 4.78 4.78 0.00 2.50
2261 2298 6.996282 AGCCTTTTTAACAGAGCAGTAAGTTA 59.004 34.615 0.00 0.00 0.00 2.24
2262 2299 5.828328 AGCCTTTTTAACAGAGCAGTAAGTT 59.172 36.000 0.00 0.00 0.00 2.66
2263 2300 5.377478 AGCCTTTTTAACAGAGCAGTAAGT 58.623 37.500 0.00 0.00 0.00 2.24
2264 2301 5.703130 AGAGCCTTTTTAACAGAGCAGTAAG 59.297 40.000 0.00 0.00 0.00 2.34
2265 2302 5.470098 CAGAGCCTTTTTAACAGAGCAGTAA 59.530 40.000 0.00 0.00 0.00 2.24
2266 2303 4.997395 CAGAGCCTTTTTAACAGAGCAGTA 59.003 41.667 0.00 0.00 0.00 2.74
2267 2304 3.817647 CAGAGCCTTTTTAACAGAGCAGT 59.182 43.478 0.00 0.00 0.00 4.40
2268 2305 3.817647 ACAGAGCCTTTTTAACAGAGCAG 59.182 43.478 0.00 0.00 0.00 4.24
2269 2306 3.820557 ACAGAGCCTTTTTAACAGAGCA 58.179 40.909 0.00 0.00 0.00 4.26
2270 2307 4.517075 AGAACAGAGCCTTTTTAACAGAGC 59.483 41.667 0.00 0.00 0.00 4.09
2271 2308 5.180304 GGAGAACAGAGCCTTTTTAACAGAG 59.820 44.000 0.00 0.00 0.00 3.35
2272 2309 5.063880 GGAGAACAGAGCCTTTTTAACAGA 58.936 41.667 0.00 0.00 0.00 3.41
2273 2310 4.821805 TGGAGAACAGAGCCTTTTTAACAG 59.178 41.667 0.00 0.00 0.00 3.16
2274 2311 4.787551 TGGAGAACAGAGCCTTTTTAACA 58.212 39.130 0.00 0.00 0.00 2.41
2275 2312 5.966742 ATGGAGAACAGAGCCTTTTTAAC 57.033 39.130 0.00 0.00 0.00 2.01
2276 2313 5.243730 CCAATGGAGAACAGAGCCTTTTTAA 59.756 40.000 0.00 0.00 0.00 1.52
2277 2314 4.766891 CCAATGGAGAACAGAGCCTTTTTA 59.233 41.667 0.00 0.00 0.00 1.52
2278 2315 3.575687 CCAATGGAGAACAGAGCCTTTTT 59.424 43.478 0.00 0.00 0.00 1.94
2279 2316 3.160269 CCAATGGAGAACAGAGCCTTTT 58.840 45.455 0.00 0.00 0.00 2.27
2280 2317 2.556114 CCCAATGGAGAACAGAGCCTTT 60.556 50.000 0.00 0.00 0.00 3.11
2281 2318 1.005215 CCCAATGGAGAACAGAGCCTT 59.995 52.381 0.00 0.00 0.00 4.35
2282 2319 0.622665 CCCAATGGAGAACAGAGCCT 59.377 55.000 0.00 0.00 0.00 4.58
2283 2320 0.394899 CCCCAATGGAGAACAGAGCC 60.395 60.000 0.00 0.00 35.39 4.70
2284 2321 0.620556 TCCCCAATGGAGAACAGAGC 59.379 55.000 0.00 0.00 38.61 4.09
2285 2322 1.630369 TGTCCCCAATGGAGAACAGAG 59.370 52.381 0.00 0.00 46.38 3.35
2286 2323 1.351017 GTGTCCCCAATGGAGAACAGA 59.649 52.381 0.00 0.00 46.38 3.41
2287 2324 1.352352 AGTGTCCCCAATGGAGAACAG 59.648 52.381 0.00 0.00 46.38 3.16
2288 2325 1.444933 AGTGTCCCCAATGGAGAACA 58.555 50.000 0.00 0.00 46.38 3.18
2289 2326 3.610911 CTTAGTGTCCCCAATGGAGAAC 58.389 50.000 0.00 0.00 46.38 3.01
2290 2327 2.576191 CCTTAGTGTCCCCAATGGAGAA 59.424 50.000 0.00 0.00 46.38 2.87
2291 2328 2.196595 CCTTAGTGTCCCCAATGGAGA 58.803 52.381 0.00 0.00 46.38 3.71
2292 2329 1.408822 GCCTTAGTGTCCCCAATGGAG 60.409 57.143 0.00 0.00 46.38 3.86
2293 2330 0.623723 GCCTTAGTGTCCCCAATGGA 59.376 55.000 0.00 0.00 42.41 3.41
2294 2331 0.748005 CGCCTTAGTGTCCCCAATGG 60.748 60.000 0.00 0.00 0.00 3.16
2295 2332 1.376609 GCGCCTTAGTGTCCCCAATG 61.377 60.000 0.00 0.00 0.00 2.82
2296 2333 1.077716 GCGCCTTAGTGTCCCCAAT 60.078 57.895 0.00 0.00 0.00 3.16
2297 2334 1.847798 ATGCGCCTTAGTGTCCCCAA 61.848 55.000 4.18 0.00 0.00 4.12
2298 2335 2.297895 ATGCGCCTTAGTGTCCCCA 61.298 57.895 4.18 0.00 0.00 4.96
2299 2336 1.819632 CATGCGCCTTAGTGTCCCC 60.820 63.158 4.18 0.00 0.00 4.81
2300 2337 2.472909 GCATGCGCCTTAGTGTCCC 61.473 63.158 4.18 0.00 0.00 4.46
2301 2338 0.179084 TAGCATGCGCCTTAGTGTCC 60.179 55.000 13.01 0.00 39.83 4.02
2302 2339 1.871080 ATAGCATGCGCCTTAGTGTC 58.129 50.000 13.01 0.00 39.83 3.67
2303 2340 2.332063 AATAGCATGCGCCTTAGTGT 57.668 45.000 13.01 0.00 39.83 3.55
2304 2341 3.698029 AAAATAGCATGCGCCTTAGTG 57.302 42.857 13.01 0.00 39.83 2.74
2327 2364 6.127366 ACCTACAATATGCCAACATTTCTTGG 60.127 38.462 0.00 0.00 43.36 3.61
2384 2421 7.549839 TCCAGCTGGAATATTCTTTTCATTTG 58.450 34.615 33.41 0.00 42.18 2.32
2422 2459 5.775701 CCACCTTAGGTATGAGCACTATAGT 59.224 44.000 2.52 0.00 32.11 2.12
2453 2490 7.187336 TGGGCCTATATTGGGATATATTTTCCA 59.813 37.037 4.53 0.00 34.77 3.53
2514 2551 3.334691 TCGTCGAAAGGCAATCATCTTT 58.665 40.909 0.00 0.00 36.09 2.52
2534 2572 7.989826 ACAGGTGCAATAATTTCATACTCTTC 58.010 34.615 0.00 0.00 0.00 2.87
2537 2575 7.761409 TGAACAGGTGCAATAATTTCATACTC 58.239 34.615 0.00 0.00 0.00 2.59
2540 2586 7.545265 GCTTTGAACAGGTGCAATAATTTCATA 59.455 33.333 0.00 0.00 0.00 2.15
2567 2613 4.453480 TTGATCTCCCAGGAACAAAAGT 57.547 40.909 0.00 0.00 0.00 2.66
2698 2747 1.484653 CCCATTCCACACGGTCATAGA 59.515 52.381 0.00 0.00 0.00 1.98
2708 2757 2.040278 CTCCAGAAAGACCCATTCCACA 59.960 50.000 0.00 0.00 0.00 4.17
2740 2789 9.698309 TGAACTCTTCATGAAAACTAAGTCTAG 57.302 33.333 9.88 0.00 34.08 2.43
2809 2858 4.651778 TGTCTCTTGGTCATTAAACCTGG 58.348 43.478 0.00 0.00 40.20 4.45
2851 2900 1.464198 AACCCCTGCTGAAGTCCCT 60.464 57.895 0.00 0.00 0.00 4.20
2868 2917 7.654022 AGAAACAAATAAGGTGAAACAGGAA 57.346 32.000 0.00 0.00 39.98 3.36
2869 2918 7.559897 AGAAGAAACAAATAAGGTGAAACAGGA 59.440 33.333 0.00 0.00 39.98 3.86
3006 3056 7.500227 CAGCTTTCATGAGTATAAGGGAATCAA 59.500 37.037 6.93 0.00 0.00 2.57
3087 3138 2.354821 CGCTTCACTAATTAGTTGGCCC 59.645 50.000 15.60 3.27 33.46 5.80
3182 3233 5.717178 ACCTCTCAGAAATAGCTTCAGTGTA 59.283 40.000 0.00 0.00 36.40 2.90


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

AutoCloner maintained by Alex Coulton.