Multiple sequence alignment - TraesCS2A01G371200

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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 TraesCS2A01G371200 chr2A 100.000 3417 0 0 1 3417 613701800 613698384 0.000000e+00 6311.0
1 TraesCS2A01G371200 chr2A 84.977 872 66 29 1382 2234 613876399 613875574 0.000000e+00 824.0
2 TraesCS2A01G371200 chr2A 82.615 673 73 27 741 1382 613877313 613876654 3.850000e-154 555.0
3 TraesCS2A01G371200 chr2A 79.732 745 131 16 1692 2428 613689359 613688627 3.910000e-144 521.0
4 TraesCS2A01G371200 chr2A 83.065 372 59 4 2048 2417 613476663 613476294 5.460000e-88 335.0
5 TraesCS2A01G371200 chr2A 76.145 415 74 17 1111 1523 613689773 613689382 9.680000e-46 195.0
6 TraesCS2A01G371200 chr2D 87.518 2796 160 58 765 3417 472230435 472227686 0.000000e+00 3055.0
7 TraesCS2A01G371200 chr2D 87.524 1058 64 31 1389 2425 472442585 472441575 0.000000e+00 1160.0
8 TraesCS2A01G371200 chr2D 91.412 687 57 2 1 687 82192772 82193456 0.000000e+00 941.0
9 TraesCS2A01G371200 chr2D 89.237 734 76 2 1 734 387226155 387225425 0.000000e+00 915.0
10 TraesCS2A01G371200 chr2D 82.976 699 57 24 741 1384 472443943 472443252 2.960000e-160 575.0
11 TraesCS2A01G371200 chr2D 84.000 375 54 6 2046 2417 472130409 472130038 4.190000e-94 355.0
12 TraesCS2A01G371200 chr2D 92.683 41 1 2 2492 2531 472441214 472441175 1.320000e-04 58.4
13 TraesCS2A01G371200 chr2B 92.234 734 49 5 1714 2442 551564953 551564223 0.000000e+00 1033.0
14 TraesCS2A01G371200 chr2B 82.477 856 66 40 741 1531 551566053 551565217 0.000000e+00 673.0
15 TraesCS2A01G371200 chr2B 81.525 682 107 15 1752 2426 551399072 551398403 8.340000e-151 544.0
16 TraesCS2A01G371200 chr2B 80.501 559 93 14 1874 2428 551481174 551480628 6.820000e-112 414.0
17 TraesCS2A01G371200 chr2B 83.378 373 60 2 2046 2417 551448884 551448513 9.080000e-91 344.0
18 TraesCS2A01G371200 chr2B 76.607 389 73 13 998 1372 551399667 551399283 7.480000e-47 198.0
19 TraesCS2A01G371200 chr3D 89.730 740 73 2 1 740 319046685 319047421 0.000000e+00 942.0
20 TraesCS2A01G371200 chr3D 81.034 348 35 11 2679 3015 186608691 186609018 7.320000e-62 248.0
21 TraesCS2A01G371200 chr7D 89.782 734 71 3 1 734 438722816 438723545 0.000000e+00 937.0
22 TraesCS2A01G371200 chr7D 89.218 742 68 5 1 741 607928750 607929480 0.000000e+00 917.0
23 TraesCS2A01G371200 chr3B 89.782 734 72 2 1 734 325854712 325855442 0.000000e+00 937.0
24 TraesCS2A01G371200 chr3B 87.845 181 14 3 2836 3015 672763794 672763621 4.470000e-49 206.0
25 TraesCS2A01G371200 chrUn 89.779 724 73 1 1 724 24022607 24023329 0.000000e+00 926.0
26 TraesCS2A01G371200 chr1D 89.510 734 62 8 1 734 222729468 222728750 0.000000e+00 915.0
27 TraesCS2A01G371200 chr1D 89.252 735 73 5 1 734 435048961 435049690 0.000000e+00 915.0
28 TraesCS2A01G371200 chr5D 85.470 351 30 11 2679 3015 335223714 335224057 2.520000e-91 346.0
29 TraesCS2A01G371200 chr7A 79.301 372 54 15 998 1359 68211336 68211694 4.410000e-59 239.0
30 TraesCS2A01G371200 chr7A 80.524 267 47 3 1096 1359 70182815 70183079 2.080000e-47 200.0
31 TraesCS2A01G371200 chr1B 77.591 357 40 22 2725 3070 606491549 606491876 2.710000e-41 180.0
32 TraesCS2A01G371200 chr7B 78.521 284 50 5 1085 1359 5942793 5943074 3.500000e-40 176.0
33 TraesCS2A01G371200 chr6A 84.091 176 23 2 2728 2903 349889511 349889341 7.590000e-37 165.0
34 TraesCS2A01G371200 chr5B 81.679 131 11 8 2679 2797 600185890 600186019 2.810000e-16 97.1
35 TraesCS2A01G371200 chr5B 95.556 45 2 0 2887 2931 600186045 600186089 4.730000e-09 73.1
36 TraesCS2A01G371200 chr5B 77.778 117 11 8 2812 2923 600186009 600186115 1.320000e-04 58.4


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 TraesCS2A01G371200 chr2A 613698384 613701800 3416 True 6311.0 6311 100.000000 1 3417 1 chr2A.!!$R2 3416
1 TraesCS2A01G371200 chr2A 613875574 613877313 1739 True 689.5 824 83.796000 741 2234 2 chr2A.!!$R4 1493
2 TraesCS2A01G371200 chr2A 613688627 613689773 1146 True 358.0 521 77.938500 1111 2428 2 chr2A.!!$R3 1317
3 TraesCS2A01G371200 chr2D 472227686 472230435 2749 True 3055.0 3055 87.518000 765 3417 1 chr2D.!!$R3 2652
4 TraesCS2A01G371200 chr2D 82192772 82193456 684 False 941.0 941 91.412000 1 687 1 chr2D.!!$F1 686
5 TraesCS2A01G371200 chr2D 387225425 387226155 730 True 915.0 915 89.237000 1 734 1 chr2D.!!$R1 733
6 TraesCS2A01G371200 chr2D 472441175 472443943 2768 True 597.8 1160 87.727667 741 2531 3 chr2D.!!$R4 1790
7 TraesCS2A01G371200 chr2B 551564223 551566053 1830 True 853.0 1033 87.355500 741 2442 2 chr2B.!!$R4 1701
8 TraesCS2A01G371200 chr2B 551480628 551481174 546 True 414.0 414 80.501000 1874 2428 1 chr2B.!!$R2 554
9 TraesCS2A01G371200 chr2B 551398403 551399667 1264 True 371.0 544 79.066000 998 2426 2 chr2B.!!$R3 1428
10 TraesCS2A01G371200 chr3D 319046685 319047421 736 False 942.0 942 89.730000 1 740 1 chr3D.!!$F2 739
11 TraesCS2A01G371200 chr7D 438722816 438723545 729 False 937.0 937 89.782000 1 734 1 chr7D.!!$F1 733
12 TraesCS2A01G371200 chr7D 607928750 607929480 730 False 917.0 917 89.218000 1 741 1 chr7D.!!$F2 740
13 TraesCS2A01G371200 chr3B 325854712 325855442 730 False 937.0 937 89.782000 1 734 1 chr3B.!!$F1 733
14 TraesCS2A01G371200 chrUn 24022607 24023329 722 False 926.0 926 89.779000 1 724 1 chrUn.!!$F1 723
15 TraesCS2A01G371200 chr1D 222728750 222729468 718 True 915.0 915 89.510000 1 734 1 chr1D.!!$R1 733
16 TraesCS2A01G371200 chr1D 435048961 435049690 729 False 915.0 915 89.252000 1 734 1 chr1D.!!$F1 733

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
444 445 0.103390 TTCTTGAAGGTGTCGTCGCA 59.897 50.0 0.0 0.0 0.0 5.10 F
1428 2238 0.107703 GAAGCACCGGTGATGGATGA 60.108 55.0 38.3 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1439 2249 0.379669 CCTGCAAATCATCCGAGTGC 59.620 55.0 0.00 0.00 36.89 4.40 R
3201 4561 0.036732 GGTGGGACTGTTCATGAGCA 59.963 55.0 12.02 12.02 0.00 4.26 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
72 73 3.764466 CAGGACCGAGCTCGCCTT 61.764 66.667 30.49 16.95 38.18 4.35
144 145 1.482748 GGGTCTCAACGTTGGGGGTA 61.483 60.000 27.19 6.11 0.00 3.69
210 211 2.415608 GGGTGCGACAGATCTCGGA 61.416 63.158 6.51 0.77 34.06 4.55
235 236 1.822990 GTGGTGTCGAGGTCTTGGATA 59.177 52.381 0.00 0.00 0.00 2.59
422 423 2.442188 GCGACGGCGAAGATCGTTT 61.442 57.895 18.90 0.00 42.81 3.60
435 436 4.625607 AGATCGTTTCCTTCTTGAAGGT 57.374 40.909 23.78 8.14 40.81 3.50
444 445 0.103390 TTCTTGAAGGTGTCGTCGCA 59.897 50.000 0.00 0.00 0.00 5.10
481 482 2.983791 CGGCTTCGGGGGAAACTA 59.016 61.111 0.00 0.00 0.00 2.24
540 541 2.358737 CCTTTCTGAAGGCGCCGT 60.359 61.111 23.20 20.21 45.59 5.68
587 588 0.390340 GCTTCATCTCTGCGTGGTGA 60.390 55.000 0.00 0.00 0.00 4.02
602 603 1.007842 TGGTGATAGTGCTAGGGGTGA 59.992 52.381 0.00 0.00 0.00 4.02
638 639 2.891580 GCGTCTATGTATCTTCCCCTGA 59.108 50.000 0.00 0.00 0.00 3.86
639 640 3.321111 GCGTCTATGTATCTTCCCCTGAA 59.679 47.826 0.00 0.00 0.00 3.02
641 642 5.185249 GCGTCTATGTATCTTCCCCTGAATA 59.815 44.000 0.00 0.00 0.00 1.75
647 648 4.411869 TGTATCTTCCCCTGAATATGTGCA 59.588 41.667 0.00 0.00 0.00 4.57
699 700 4.032960 ACTGGGTGCTTGTTGATTGATA 57.967 40.909 0.00 0.00 0.00 2.15
703 704 4.458989 TGGGTGCTTGTTGATTGATACTTC 59.541 41.667 0.00 0.00 0.00 3.01
818 823 2.548904 GAGAGGCTGCTAAATCATGCTG 59.451 50.000 0.00 0.00 0.00 4.41
855 863 0.179094 AAGACGACGAGCACCACAAA 60.179 50.000 0.00 0.00 0.00 2.83
866 874 2.342279 CCACAAAGGCGACCGAGA 59.658 61.111 0.00 0.00 0.00 4.04
867 875 1.079127 CCACAAAGGCGACCGAGAT 60.079 57.895 0.00 0.00 0.00 2.75
868 876 0.174845 CCACAAAGGCGACCGAGATA 59.825 55.000 0.00 0.00 0.00 1.98
869 877 1.278238 CACAAAGGCGACCGAGATAC 58.722 55.000 0.00 0.00 0.00 2.24
870 878 0.179145 ACAAAGGCGACCGAGATACG 60.179 55.000 0.00 0.00 42.18 3.06
927 953 5.163034 CCTCCCATAACCATAACCATAACCA 60.163 44.000 0.00 0.00 0.00 3.67
931 957 7.010160 CCCATAACCATAACCATAACCATCTT 58.990 38.462 0.00 0.00 0.00 2.40
956 1008 3.620785 GAGGAGCGGCCCATCGAT 61.621 66.667 0.00 0.00 37.37 3.59
962 1014 3.133014 CGGCCCATCGATCTCTGT 58.867 61.111 0.00 0.00 0.00 3.41
985 1047 1.862806 GCACTTGTTGGAGCTCGTC 59.137 57.895 7.83 1.06 0.00 4.20
1056 1156 3.406764 GTTAGCCTATGCATGCTTAGCT 58.593 45.455 27.17 26.33 41.13 3.32
1057 1157 2.181954 AGCCTATGCATGCTTAGCTC 57.818 50.000 27.17 21.30 41.13 4.09
1059 1159 2.158711 AGCCTATGCATGCTTAGCTCAA 60.159 45.455 27.17 3.98 41.13 3.02
1060 1160 2.620115 GCCTATGCATGCTTAGCTCAAA 59.380 45.455 27.17 3.27 37.47 2.69
1061 1161 3.549625 GCCTATGCATGCTTAGCTCAAAC 60.550 47.826 27.17 12.67 37.47 2.93
1062 1162 2.838386 ATGCATGCTTAGCTCAAACG 57.162 45.000 20.33 0.00 0.00 3.60
1079 1200 1.726853 ACGTCTATGGAACTTGCAGC 58.273 50.000 0.00 0.00 0.00 5.25
1083 1204 3.871006 CGTCTATGGAACTTGCAGCAATA 59.129 43.478 8.67 0.00 0.00 1.90
1085 1206 5.008019 CGTCTATGGAACTTGCAGCAATATT 59.992 40.000 8.67 6.38 0.00 1.28
1102 1223 2.882927 ATTATCGACTGCGGTTGCTA 57.117 45.000 8.17 0.00 43.34 3.49
1103 1224 2.882927 TTATCGACTGCGGTTGCTAT 57.117 45.000 8.17 0.29 43.34 2.97
1115 1236 0.874607 GTTGCTATAGGGTCGCCGTG 60.875 60.000 1.04 0.00 0.00 4.94
1271 1392 0.243907 CTGGTGTCGTCTTCCATCGT 59.756 55.000 0.00 0.00 0.00 3.73
1320 1441 2.186076 CTACGCTAGCTGGTTTTCTCG 58.814 52.381 13.93 0.00 0.00 4.04
1428 2238 0.107703 GAAGCACCGGTGATGGATGA 60.108 55.000 38.30 0.00 0.00 2.92
1432 2242 1.311859 CACCGGTGATGGATGAATGG 58.688 55.000 31.31 0.00 0.00 3.16
1433 2243 1.134128 CACCGGTGATGGATGAATGGA 60.134 52.381 31.31 0.00 0.00 3.41
1434 2244 1.776667 ACCGGTGATGGATGAATGGAT 59.223 47.619 6.12 0.00 0.00 3.41
1435 2245 2.156917 CCGGTGATGGATGAATGGATG 58.843 52.381 0.00 0.00 0.00 3.51
1436 2246 2.156917 CGGTGATGGATGAATGGATGG 58.843 52.381 0.00 0.00 0.00 3.51
1437 2247 2.224597 CGGTGATGGATGAATGGATGGA 60.225 50.000 0.00 0.00 0.00 3.41
1438 2248 3.560668 CGGTGATGGATGAATGGATGGAT 60.561 47.826 0.00 0.00 0.00 3.41
1439 2249 3.762288 GGTGATGGATGAATGGATGGATG 59.238 47.826 0.00 0.00 0.00 3.51
1440 2250 3.192844 GTGATGGATGAATGGATGGATGC 59.807 47.826 0.00 0.00 0.00 3.91
1466 2276 4.335315 TCGGATGATTTGCAGGTGAATAAC 59.665 41.667 0.00 0.00 0.00 1.89
1489 2299 2.029743 CGGTTTGTGGGGTTGAGTG 58.970 57.895 0.00 0.00 0.00 3.51
1561 2371 4.464069 TTTGTCCTTTTCTGTTGTTGGG 57.536 40.909 0.00 0.00 0.00 4.12
1654 2476 4.485163 GCAGCGACCAATTTTACTTGATT 58.515 39.130 0.00 0.00 0.00 2.57
1656 2478 6.090129 GCAGCGACCAATTTTACTTGATTAA 58.910 36.000 0.00 0.00 0.00 1.40
1815 2760 0.035439 GTTGAAGAATGCCCGGGAGA 60.035 55.000 29.31 10.55 0.00 3.71
1922 2867 3.565764 TCGTCCGAGGGAAGAATAGTA 57.434 47.619 0.00 0.00 37.28 1.82
1958 2903 4.417426 TTATGGACTGCTAAGGGTAAGC 57.583 45.455 0.00 0.00 40.50 3.09
2216 3186 2.125310 CCGCCATGAACGCCTACA 60.125 61.111 0.00 0.00 0.00 2.74
2459 3748 4.254709 TTGCCCTGCTCGTGTGCT 62.255 61.111 0.00 0.00 0.00 4.40
2473 3762 2.946947 GTGCTGCACACTGGGTTAT 58.053 52.632 26.70 0.00 46.41 1.89
2553 3869 4.023107 TCACAAGAAACAGACTACCGAGAG 60.023 45.833 0.00 0.00 0.00 3.20
2608 3924 1.499049 GAGAGCGTCTCAAACCGTTT 58.501 50.000 9.09 0.00 42.90 3.60
2613 3929 2.223377 AGCGTCTCAAACCGTTTTCATC 59.777 45.455 0.00 0.00 0.00 2.92
2684 4000 1.265095 CAGCAGTTTCTGTGAACGCAT 59.735 47.619 0.00 0.00 34.13 4.73
2697 4013 1.138266 GAACGCATTAGTGGGAGCCTA 59.862 52.381 9.34 0.00 40.48 3.93
2716 4032 5.420104 AGCCTATTGGACCAGAAAGAAATTG 59.580 40.000 0.00 0.00 34.57 2.32
2722 4038 5.392995 TGGACCAGAAAGAAATTGAATGGA 58.607 37.500 0.00 0.00 0.00 3.41
2735 4060 1.204146 GAATGGACTAGCCCACTGGA 58.796 55.000 0.00 0.00 39.34 3.86
2736 4061 1.559682 GAATGGACTAGCCCACTGGAA 59.440 52.381 0.00 0.00 39.34 3.53
2737 4062 0.912486 ATGGACTAGCCCACTGGAAC 59.088 55.000 0.00 0.00 39.34 3.62
2738 4063 1.198759 TGGACTAGCCCACTGGAACC 61.199 60.000 0.00 0.00 34.97 3.62
2739 4064 1.602771 GACTAGCCCACTGGAACCC 59.397 63.158 0.00 0.00 0.00 4.11
2740 4065 1.911702 GACTAGCCCACTGGAACCCC 61.912 65.000 0.00 0.00 0.00 4.95
2741 4066 1.923395 CTAGCCCACTGGAACCCCA 60.923 63.158 0.00 0.00 40.95 4.96
2742 4067 2.198304 CTAGCCCACTGGAACCCCAC 62.198 65.000 0.00 0.00 37.58 4.61
2743 4068 2.706341 TAGCCCACTGGAACCCCACT 62.706 60.000 0.00 0.00 37.58 4.00
2744 4069 3.146828 GCCCACTGGAACCCCACTT 62.147 63.158 0.00 0.00 37.58 3.16
2756 4081 4.458397 GAACCCCACTTTACCCTATTAGC 58.542 47.826 0.00 0.00 0.00 3.09
2762 4087 4.351111 CCACTTTACCCTATTAGCCCATCT 59.649 45.833 0.00 0.00 0.00 2.90
2764 4089 6.295916 CCACTTTACCCTATTAGCCCATCTAG 60.296 46.154 0.00 0.00 0.00 2.43
2772 4097 6.183360 CCCTATTAGCCCATCTAGATAGCTTG 60.183 46.154 26.06 16.64 33.39 4.01
2808 4166 3.110178 GCGCCGCAACGTACTTCT 61.110 61.111 3.15 0.00 34.88 2.85
2819 4177 1.584742 GTACTTCTACCGCCGTCGC 60.585 63.158 0.00 0.00 0.00 5.19
2820 4178 2.764314 TACTTCTACCGCCGTCGCC 61.764 63.158 0.00 0.00 0.00 5.54
2873 4231 4.148825 CTTCCTCCTCGCACCCCG 62.149 72.222 0.00 0.00 38.61 5.73
2919 4277 1.439644 CCCTACCTCGCAGCTTCTC 59.560 63.158 0.00 0.00 0.00 2.87
2923 4281 1.323271 TACCTCGCAGCTTCTCCCTG 61.323 60.000 0.00 0.00 0.00 4.45
2964 4322 2.423926 ATCAAGAATCGACGATCCCG 57.576 50.000 11.42 0.74 42.50 5.14
2986 4344 4.260355 CTCGGCCGGACGCGATTA 62.260 66.667 29.18 6.28 38.94 1.75
3025 4383 1.166531 AACCCTGACACTTGCTTCGC 61.167 55.000 0.00 0.00 0.00 4.70
3037 4395 1.080435 TGCTTCGCGATCTGCTCTTG 61.080 55.000 22.87 4.34 43.27 3.02
3133 4491 6.390504 TCCCACTTACTCCCACATAATCTAT 58.609 40.000 0.00 0.00 0.00 1.98
3148 4506 9.183368 CACATAATCTATGCTAGTCTAGATGGA 57.817 37.037 11.27 8.86 39.79 3.41
3194 4554 4.574828 CCGTGTTGGGACTAATGGATTAAG 59.425 45.833 0.00 0.00 0.00 1.85
3195 4555 4.574828 CGTGTTGGGACTAATGGATTAAGG 59.425 45.833 0.00 0.00 0.00 2.69
3196 4556 5.506708 GTGTTGGGACTAATGGATTAAGGT 58.493 41.667 0.00 0.00 0.00 3.50
3197 4557 5.357032 GTGTTGGGACTAATGGATTAAGGTG 59.643 44.000 0.00 0.00 0.00 4.00
3198 4558 4.788925 TGGGACTAATGGATTAAGGTGG 57.211 45.455 0.00 0.00 0.00 4.61
3199 4559 3.461831 TGGGACTAATGGATTAAGGTGGG 59.538 47.826 0.00 0.00 0.00 4.61
3200 4560 3.720002 GGGACTAATGGATTAAGGTGGGA 59.280 47.826 0.00 0.00 0.00 4.37
3201 4561 4.354087 GGGACTAATGGATTAAGGTGGGAT 59.646 45.833 0.00 0.00 0.00 3.85
3202 4562 5.316987 GGACTAATGGATTAAGGTGGGATG 58.683 45.833 0.00 0.00 0.00 3.51
3203 4563 4.729868 ACTAATGGATTAAGGTGGGATGC 58.270 43.478 0.00 0.00 0.00 3.91
3204 4564 3.979501 AATGGATTAAGGTGGGATGCT 57.020 42.857 0.00 0.00 0.00 3.79
3205 4565 3.515602 ATGGATTAAGGTGGGATGCTC 57.484 47.619 0.00 0.00 0.00 4.26
3206 4566 2.204463 TGGATTAAGGTGGGATGCTCA 58.796 47.619 0.00 0.00 0.00 4.26
3207 4567 2.785269 TGGATTAAGGTGGGATGCTCAT 59.215 45.455 0.00 0.00 0.00 2.90
3208 4568 3.152341 GGATTAAGGTGGGATGCTCATG 58.848 50.000 0.00 0.00 0.00 3.07
3209 4569 3.181440 GGATTAAGGTGGGATGCTCATGA 60.181 47.826 0.00 0.00 0.00 3.07
3210 4570 4.464008 GATTAAGGTGGGATGCTCATGAA 58.536 43.478 0.00 0.00 0.00 2.57
3223 4583 2.171448 GCTCATGAACAGTCCCACCTAT 59.829 50.000 0.00 0.00 0.00 2.57
3240 4600 6.402222 CCACCTATAGCCTGATTCTTCATAC 58.598 44.000 0.00 0.00 0.00 2.39
3248 4608 3.941483 CCTGATTCTTCATACACACACCC 59.059 47.826 0.00 0.00 0.00 4.61
3249 4609 3.941483 CTGATTCTTCATACACACACCCC 59.059 47.826 0.00 0.00 0.00 4.95
3251 4611 0.611200 TCTTCATACACACACCCCCG 59.389 55.000 0.00 0.00 0.00 5.73
3267 4627 0.323360 CCCGCCCCTTGAATTTCAGA 60.323 55.000 0.00 0.00 0.00 3.27
3275 4635 2.821969 CCTTGAATTTCAGAGGGTGTGG 59.178 50.000 14.74 1.99 0.00 4.17
3276 4636 2.584835 TGAATTTCAGAGGGTGTGGG 57.415 50.000 0.00 0.00 0.00 4.61
3292 4652 4.532834 GTGTGGGCCCTTAATCTGATTTA 58.467 43.478 25.70 0.00 0.00 1.40
3297 4657 5.534654 TGGGCCCTTAATCTGATTTATTTCG 59.465 40.000 25.70 0.00 0.00 3.46
3298 4658 5.048013 GGGCCCTTAATCTGATTTATTTCGG 60.048 44.000 17.04 2.05 0.00 4.30
3308 4668 7.953158 TCTGATTTATTTCGGTCAGATGATC 57.047 36.000 0.16 0.00 41.40 2.92
3321 4681 5.189180 GTCAGATGATCCCAACTAAGCTTT 58.811 41.667 3.20 0.00 0.00 3.51
3349 4709 4.976224 AAAGTTCGTAAATATGTGCCCC 57.024 40.909 0.00 0.00 0.00 5.80
3352 4712 1.961793 TCGTAAATATGTGCCCCTGC 58.038 50.000 0.00 0.00 38.26 4.85
3360 4720 3.216292 GTGCCCCTGCGTGTGTTT 61.216 61.111 0.00 0.00 41.78 2.83
3361 4721 2.441164 TGCCCCTGCGTGTGTTTT 60.441 55.556 0.00 0.00 41.78 2.43
3375 4735 4.027458 CGTGTGTTTTCTTGTCATTGCTTG 60.027 41.667 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.462678 GAGGGGGACGAGGTCAGC 61.463 72.222 0.00 0.00 33.68 4.26
144 145 4.351054 CTTTCGCACCCCTGGGCT 62.351 66.667 7.39 0.00 39.32 5.19
210 211 0.251832 AGACCTCGACACCACCTCAT 60.252 55.000 0.00 0.00 0.00 2.90
303 304 2.032528 CACACGGCCATGGTGACT 59.967 61.111 14.67 0.00 38.73 3.41
407 408 0.037605 AAGGAAACGATCTTCGCCGT 60.038 50.000 0.00 0.00 45.12 5.68
435 436 0.733909 CAATGAGAGCTGCGACGACA 60.734 55.000 0.00 0.00 0.00 4.35
444 445 0.463295 CATGACGGGCAATGAGAGCT 60.463 55.000 0.00 0.00 0.00 4.09
540 541 2.736144 ACGAACCATACGCTTCAAGA 57.264 45.000 0.00 0.00 0.00 3.02
560 561 5.335976 CCACGCAGAGATGAAGCTACATATA 60.336 44.000 0.00 0.00 0.00 0.86
587 588 2.158755 GCAACATCACCCCTAGCACTAT 60.159 50.000 0.00 0.00 0.00 2.12
632 633 2.019249 CACACTGCACATATTCAGGGG 58.981 52.381 0.00 0.00 38.01 4.79
638 639 1.401409 GCGCAACACACTGCACATATT 60.401 47.619 0.30 0.00 42.77 1.28
639 640 0.168788 GCGCAACACACTGCACATAT 59.831 50.000 0.30 0.00 42.77 1.78
641 642 2.188829 AGCGCAACACACTGCACAT 61.189 52.632 11.47 0.00 42.77 3.21
647 648 1.429021 CACAACAGCGCAACACACT 59.571 52.632 11.47 0.00 0.00 3.55
658 659 3.438781 AGTACAAACACACACCACAACAG 59.561 43.478 0.00 0.00 0.00 3.16
661 662 2.750166 CCAGTACAAACACACACCACAA 59.250 45.455 0.00 0.00 0.00 3.33
703 704 8.345565 AGGCTTTTTCGCTCTGTTTTATATATG 58.654 33.333 0.00 0.00 0.00 1.78
713 714 3.801114 AAAAAGGCTTTTTCGCTCTGT 57.199 38.095 27.63 7.67 38.39 3.41
803 806 4.913335 AACATCCAGCATGATTTAGCAG 57.087 40.909 0.00 0.00 39.69 4.24
818 823 1.231958 TTCGTCCGGCACAAACATCC 61.232 55.000 0.00 0.00 0.00 3.51
871 879 0.179092 ACACTTATAACGGCTCCGGC 60.179 55.000 13.31 0.00 44.69 6.13
927 953 1.883275 CCGCTCCTCACGATCTAAGAT 59.117 52.381 0.00 0.00 0.00 2.40
931 957 2.194212 GGCCGCTCCTCACGATCTA 61.194 63.158 0.00 0.00 0.00 1.98
936 988 4.899239 GATGGGCCGCTCCTCACG 62.899 72.222 0.00 0.00 34.39 4.35
956 1008 2.407090 CAACAAGTGCGATGACAGAGA 58.593 47.619 0.00 0.00 0.00 3.10
962 1014 0.035317 AGCTCCAACAAGTGCGATGA 59.965 50.000 0.00 0.00 0.00 2.92
985 1047 2.174107 CATGAGGTTGCACGCACG 59.826 61.111 0.00 0.00 0.00 5.34
1022 1092 0.605589 GGCTAACCTCGTGTTTGGCT 60.606 55.000 15.89 0.00 46.57 4.75
1048 1148 3.194755 TCCATAGACGTTTGAGCTAAGCA 59.805 43.478 0.00 0.00 0.00 3.91
1056 1156 3.734463 TGCAAGTTCCATAGACGTTTGA 58.266 40.909 0.00 0.00 0.00 2.69
1057 1157 3.667960 GCTGCAAGTTCCATAGACGTTTG 60.668 47.826 0.00 0.00 35.30 2.93
1059 1159 2.076863 GCTGCAAGTTCCATAGACGTT 58.923 47.619 0.00 0.00 35.30 3.99
1060 1160 1.001974 TGCTGCAAGTTCCATAGACGT 59.998 47.619 0.00 0.00 35.30 4.34
1061 1161 1.725641 TGCTGCAAGTTCCATAGACG 58.274 50.000 0.00 0.00 35.30 4.18
1062 1162 6.382869 AATATTGCTGCAAGTTCCATAGAC 57.617 37.500 20.72 0.00 35.30 2.59
1079 1200 3.494626 AGCAACCGCAGTCGATAATATTG 59.505 43.478 0.00 0.00 42.27 1.90
1083 1204 2.882927 TAGCAACCGCAGTCGATAAT 57.117 45.000 0.00 0.00 42.27 1.28
1085 1206 2.228103 CCTATAGCAACCGCAGTCGATA 59.772 50.000 0.00 0.00 42.27 2.92
1102 1223 2.363276 TGACCACGGCGACCCTAT 60.363 61.111 16.62 0.00 0.00 2.57
1103 1224 3.376078 GTGACCACGGCGACCCTA 61.376 66.667 16.62 0.00 0.00 3.53
1115 1236 1.003718 CTTGTTCCCTCCGGTGACC 60.004 63.158 4.76 0.00 0.00 4.02
1225 1346 3.191539 GCGCTTTGAGCCTCTCCG 61.192 66.667 0.00 0.00 38.18 4.63
1271 1392 0.965866 AAGCGTCCGTGATCTCCAGA 60.966 55.000 0.00 0.00 0.00 3.86
1390 1512 0.389426 CAAACCTTGGATGCAGCAGC 60.389 55.000 3.51 0.62 42.57 5.25
1391 1513 1.250328 TCAAACCTTGGATGCAGCAG 58.750 50.000 3.51 0.00 0.00 4.24
1392 1514 1.614903 CTTCAAACCTTGGATGCAGCA 59.385 47.619 3.51 0.00 0.00 4.41
1428 2238 0.839277 TCCGAGTGCATCCATCCATT 59.161 50.000 0.00 0.00 0.00 3.16
1432 2242 2.469274 ATCATCCGAGTGCATCCATC 57.531 50.000 0.00 0.00 0.00 3.51
1433 2243 2.882761 CAAATCATCCGAGTGCATCCAT 59.117 45.455 0.00 0.00 0.00 3.41
1434 2244 2.291365 CAAATCATCCGAGTGCATCCA 58.709 47.619 0.00 0.00 0.00 3.41
1435 2245 1.002033 GCAAATCATCCGAGTGCATCC 60.002 52.381 0.00 0.00 36.55 3.51
1436 2246 1.672363 TGCAAATCATCCGAGTGCATC 59.328 47.619 0.00 0.00 39.78 3.91
1437 2247 1.674441 CTGCAAATCATCCGAGTGCAT 59.326 47.619 0.00 0.00 42.24 3.96
1438 2248 1.089112 CTGCAAATCATCCGAGTGCA 58.911 50.000 0.00 0.00 41.43 4.57
1439 2249 0.379669 CCTGCAAATCATCCGAGTGC 59.620 55.000 0.00 0.00 36.89 4.40
1440 2250 1.399440 CACCTGCAAATCATCCGAGTG 59.601 52.381 0.00 0.00 0.00 3.51
1489 2299 1.140816 GATATCGAACTCTTGGCCGC 58.859 55.000 0.00 0.00 0.00 6.53
1553 2363 6.745159 ACAAATTACAAAAACCCCAACAAC 57.255 33.333 0.00 0.00 0.00 3.32
1556 2366 7.466185 GCAGTAACAAATTACAAAAACCCCAAC 60.466 37.037 0.44 0.00 42.83 3.77
1559 2369 6.285224 AGCAGTAACAAATTACAAAAACCCC 58.715 36.000 0.44 0.00 42.83 4.95
1675 2499 4.603231 AAAAAGTCGCGCCGATTTTATA 57.397 36.364 17.66 0.00 42.96 0.98
1676 2500 3.481112 AAAAAGTCGCGCCGATTTTAT 57.519 38.095 17.66 9.39 42.96 1.40
1815 2760 0.602638 TTCTTTGCGCTGTCGATGGT 60.603 50.000 9.73 0.00 38.10 3.55
1871 2816 2.505982 GGCAGCAGGGCTTCGATA 59.494 61.111 0.00 0.00 36.40 2.92
2216 3186 2.835431 CCTCGCCAGGATCCTCGT 60.835 66.667 12.69 0.00 43.65 4.18
2446 3735 3.720193 GTGCAGCACACGAGCAGG 61.720 66.667 21.22 0.00 40.07 4.85
2459 3748 0.112218 AGCCAATAACCCAGTGTGCA 59.888 50.000 0.00 0.00 0.00 4.57
2461 3750 1.176527 CCAGCCAATAACCCAGTGTG 58.823 55.000 0.00 0.00 0.00 3.82
2473 3762 2.969821 AAGGTAACACATCCAGCCAA 57.030 45.000 0.00 0.00 41.41 4.52
2594 3910 2.806244 AGGATGAAAACGGTTTGAGACG 59.194 45.455 1.45 0.00 0.00 4.18
2595 3911 3.120649 CGAGGATGAAAACGGTTTGAGAC 60.121 47.826 1.45 0.00 0.00 3.36
2603 3919 9.991388 TTATTATTTTTACGAGGATGAAAACGG 57.009 29.630 0.00 0.00 0.00 4.44
2666 3982 2.405892 AATGCGTTCACAGAAACTGC 57.594 45.000 0.00 0.00 34.37 4.40
2673 3989 2.002586 CTCCCACTAATGCGTTCACAG 58.997 52.381 0.00 0.00 0.00 3.66
2674 3990 1.943968 GCTCCCACTAATGCGTTCACA 60.944 52.381 0.00 0.00 0.00 3.58
2675 3991 0.727398 GCTCCCACTAATGCGTTCAC 59.273 55.000 0.00 0.00 0.00 3.18
2676 3992 0.392461 GGCTCCCACTAATGCGTTCA 60.392 55.000 0.00 0.00 0.00 3.18
2677 3993 0.107654 AGGCTCCCACTAATGCGTTC 60.108 55.000 0.00 0.00 0.00 3.95
2684 4000 2.124411 GGTCCAATAGGCTCCCACTAA 58.876 52.381 0.00 0.00 33.74 2.24
2697 4013 6.497954 TCCATTCAATTTCTTTCTGGTCCAAT 59.502 34.615 0.00 0.00 0.00 3.16
2716 4032 1.204146 TCCAGTGGGCTAGTCCATTC 58.796 55.000 21.26 7.71 39.26 2.67
2722 4038 1.923909 GGGGTTCCAGTGGGCTAGT 60.924 63.158 9.92 0.00 0.00 2.57
2735 4060 3.203710 GGCTAATAGGGTAAAGTGGGGTT 59.796 47.826 0.00 0.00 0.00 4.11
2736 4061 2.781757 GGCTAATAGGGTAAAGTGGGGT 59.218 50.000 0.00 0.00 0.00 4.95
2737 4062 2.107726 GGGCTAATAGGGTAAAGTGGGG 59.892 54.545 0.00 0.00 0.00 4.96
2738 4063 2.781174 TGGGCTAATAGGGTAAAGTGGG 59.219 50.000 0.00 0.00 0.00 4.61
2739 4064 4.351111 AGATGGGCTAATAGGGTAAAGTGG 59.649 45.833 0.00 0.00 0.00 4.00
2740 4065 5.568620 AGATGGGCTAATAGGGTAAAGTG 57.431 43.478 0.00 0.00 0.00 3.16
2741 4066 6.631107 TCTAGATGGGCTAATAGGGTAAAGT 58.369 40.000 0.00 0.00 0.00 2.66
2742 4067 7.741554 ATCTAGATGGGCTAATAGGGTAAAG 57.258 40.000 3.89 0.00 0.00 1.85
2743 4068 7.344871 GCTATCTAGATGGGCTAATAGGGTAAA 59.655 40.741 15.79 0.00 0.00 2.01
2744 4069 6.839657 GCTATCTAGATGGGCTAATAGGGTAA 59.160 42.308 15.79 0.00 0.00 2.85
2756 4081 3.556633 CCTGCACAAGCTATCTAGATGGG 60.557 52.174 15.79 9.02 42.74 4.00
2762 4087 1.414181 GCTCCCTGCACAAGCTATCTA 59.586 52.381 0.00 0.00 42.74 1.98
2764 4089 2.700329 GCTCCCTGCACAAGCTATC 58.300 57.895 0.00 0.00 42.74 2.08
2794 4152 1.408474 GCGGTAGAAGTACGTTGCGG 61.408 60.000 0.00 0.00 0.00 5.69
2799 4157 1.796796 GACGGCGGTAGAAGTACGT 59.203 57.895 13.24 0.00 37.26 3.57
2849 4207 2.355193 GCGAGGAGGAAGAGGCAGT 61.355 63.158 0.00 0.00 0.00 4.40
2854 4212 2.726351 GGGGTGCGAGGAGGAAGAG 61.726 68.421 0.00 0.00 0.00 2.85
2926 4284 2.511600 GGAACATCGGTGAGGCGG 60.512 66.667 0.65 0.00 0.00 6.13
2937 4295 4.503910 TCGTCGATTCTTGATTGGAACAT 58.496 39.130 0.00 0.00 39.30 2.71
2973 4331 3.330853 CTGCTAATCGCGTCCGGC 61.331 66.667 5.77 7.94 43.27 6.13
2986 4344 2.362120 GGCTGCCATTGACCTGCT 60.362 61.111 15.17 0.00 0.00 4.24
3025 4383 3.242673 GCCTCAATTTCAAGAGCAGATCG 60.243 47.826 0.00 0.00 0.00 3.69
3037 4395 4.924305 TGCTTATGGATGCCTCAATTTC 57.076 40.909 0.00 0.00 0.00 2.17
3133 4491 4.610333 TGGAAGTTCCATCTAGACTAGCA 58.390 43.478 21.05 0.00 42.67 3.49
3148 4506 3.039252 TGGTGGAAAATGGTGGAAGTT 57.961 42.857 0.00 0.00 0.00 2.66
3156 4514 1.410882 ACACGGTTTGGTGGAAAATGG 59.589 47.619 0.00 0.00 42.23 3.16
3194 4554 1.340405 ACTGTTCATGAGCATCCCACC 60.340 52.381 13.00 0.00 0.00 4.61
3195 4555 2.012673 GACTGTTCATGAGCATCCCAC 58.987 52.381 13.00 0.00 0.00 4.61
3196 4556 1.065199 GGACTGTTCATGAGCATCCCA 60.065 52.381 20.41 0.00 0.00 4.37
3197 4557 1.673168 GGACTGTTCATGAGCATCCC 58.327 55.000 20.41 16.71 0.00 3.85
3198 4558 1.065199 TGGGACTGTTCATGAGCATCC 60.065 52.381 21.77 21.77 0.00 3.51
3199 4559 2.012673 GTGGGACTGTTCATGAGCATC 58.987 52.381 13.00 11.81 0.00 3.91
3200 4560 1.340405 GGTGGGACTGTTCATGAGCAT 60.340 52.381 13.00 3.68 0.00 3.79
3201 4561 0.036732 GGTGGGACTGTTCATGAGCA 59.963 55.000 12.02 12.02 0.00 4.26
3202 4562 0.326264 AGGTGGGACTGTTCATGAGC 59.674 55.000 2.05 2.05 0.00 4.26
3203 4563 4.502259 GCTATAGGTGGGACTGTTCATGAG 60.502 50.000 1.04 0.00 0.00 2.90
3204 4564 3.388024 GCTATAGGTGGGACTGTTCATGA 59.612 47.826 1.04 0.00 0.00 3.07
3205 4565 3.495100 GGCTATAGGTGGGACTGTTCATG 60.495 52.174 1.04 0.00 0.00 3.07
3206 4566 2.706190 GGCTATAGGTGGGACTGTTCAT 59.294 50.000 1.04 0.00 0.00 2.57
3207 4567 2.116238 GGCTATAGGTGGGACTGTTCA 58.884 52.381 1.04 0.00 0.00 3.18
3208 4568 2.103263 CAGGCTATAGGTGGGACTGTTC 59.897 54.545 1.04 0.00 0.00 3.18
3209 4569 2.119495 CAGGCTATAGGTGGGACTGTT 58.881 52.381 1.04 0.00 0.00 3.16
3210 4570 1.291033 TCAGGCTATAGGTGGGACTGT 59.709 52.381 1.04 0.00 0.00 3.55
3223 4583 5.419542 GTGTGTGTATGAAGAATCAGGCTA 58.580 41.667 0.00 0.00 39.39 3.93
3248 4608 0.323360 TCTGAAATTCAAGGGGCGGG 60.323 55.000 0.00 0.00 0.00 6.13
3249 4609 1.098050 CTCTGAAATTCAAGGGGCGG 58.902 55.000 0.00 0.00 0.00 6.13
3251 4611 1.272704 ACCCTCTGAAATTCAAGGGGC 60.273 52.381 29.38 0.00 43.23 5.80
3275 4635 5.535030 ACCGAAATAAATCAGATTAAGGGCC 59.465 40.000 0.00 0.00 0.00 5.80
3276 4636 6.262273 TGACCGAAATAAATCAGATTAAGGGC 59.738 38.462 0.00 0.00 0.00 5.19
3292 4652 3.200825 AGTTGGGATCATCTGACCGAAAT 59.799 43.478 0.00 0.00 0.00 2.17
3297 4657 3.135530 AGCTTAGTTGGGATCATCTGACC 59.864 47.826 0.00 0.00 0.00 4.02
3298 4658 4.414337 AGCTTAGTTGGGATCATCTGAC 57.586 45.455 0.00 0.00 0.00 3.51
3308 4668 7.454260 ACTTTAATGAGAAAGCTTAGTTGGG 57.546 36.000 0.00 0.00 39.60 4.12
3321 4681 8.609176 GGCACATATTTACGAACTTTAATGAGA 58.391 33.333 0.00 0.00 0.00 3.27
3349 4709 2.823196 TGACAAGAAAACACACGCAG 57.177 45.000 0.00 0.00 0.00 5.18
3352 4712 3.694734 AGCAATGACAAGAAAACACACG 58.305 40.909 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.