Multiple sequence alignment - TraesCS2D01G100600

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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 TraesCS2D01G100600 chr2D 100.000 3244 0 0 548 3791 52646415 52649658 0.000000e+00 5991.0
1 TraesCS2D01G100600 chr2D 93.801 1855 83 15 1037 2863 52851972 52853822 0.000000e+00 2760.0
2 TraesCS2D01G100600 chr2D 90.285 597 49 4 1081 1672 53649011 53649603 0.000000e+00 773.0
3 TraesCS2D01G100600 chr2D 79.931 1156 146 35 1039 2152 52959456 52960567 0.000000e+00 771.0
4 TraesCS2D01G100600 chr2D 80.209 955 112 40 1978 2880 53649918 53650847 0.000000e+00 645.0
5 TraesCS2D01G100600 chr2D 86.929 482 44 10 548 1016 52851437 52851912 1.210000e-144 523.0
6 TraesCS2D01G100600 chr2D 100.000 154 0 0 1 154 52645868 52646021 6.200000e-73 285.0
7 TraesCS2D01G100600 chr2D 90.909 154 11 1 1 154 52851161 52851311 1.790000e-48 204.0
8 TraesCS2D01G100600 chr2D 93.860 114 7 0 2896 3009 133612932 133612819 5.030000e-39 172.0
9 TraesCS2D01G100600 chr2D 78.431 255 39 6 1359 1611 417544108 417544348 6.560000e-33 152.0
10 TraesCS2D01G100600 chr2D 75.000 312 50 18 2523 2814 53086731 53086428 6.650000e-23 119.0
11 TraesCS2D01G100600 chr2A 88.458 2192 114 32 548 2659 54011765 54013897 0.000000e+00 2518.0
12 TraesCS2D01G100600 chr2A 85.744 2392 200 61 548 2878 54111333 54113644 0.000000e+00 2398.0
13 TraesCS2D01G100600 chr2A 79.613 1241 158 40 962 2152 54139796 54140991 0.000000e+00 802.0
14 TraesCS2D01G100600 chr2A 88.310 633 59 9 1053 1672 54474145 54473515 0.000000e+00 745.0
15 TraesCS2D01G100600 chr2A 81.345 788 89 27 2000 2743 54473180 54472407 4.220000e-164 588.0
16 TraesCS2D01G100600 chr2A 88.312 154 17 1 1 154 54011396 54011548 2.330000e-42 183.0
17 TraesCS2D01G100600 chr2B 90.774 1485 91 16 1185 2651 82714081 82715537 0.000000e+00 1941.0
18 TraesCS2D01G100600 chr2B 87.045 1814 111 40 1036 2810 82851627 82853355 0.000000e+00 1934.0
19 TraesCS2D01G100600 chr2B 81.625 1932 194 71 1050 2879 83955434 83953562 0.000000e+00 1452.0
20 TraesCS2D01G100600 chr2B 92.832 865 52 6 1084 1945 82361285 82362142 0.000000e+00 1245.0
21 TraesCS2D01G100600 chr2B 89.675 891 61 17 1976 2862 82362137 82363000 0.000000e+00 1107.0
22 TraesCS2D01G100600 chr2B 83.192 827 93 26 2938 3737 759515846 759515039 0.000000e+00 715.0
23 TraesCS2D01G100600 chr2B 81.316 942 109 31 1059 1973 83211160 83212061 0.000000e+00 702.0
24 TraesCS2D01G100600 chr2B 93.668 379 21 3 548 923 82712815 82713193 7.110000e-157 564.0
25 TraesCS2D01G100600 chr2B 86.667 495 36 13 551 1024 82360712 82361197 4.340000e-144 521.0
26 TraesCS2D01G100600 chr2B 86.458 480 45 11 548 1016 82851098 82851568 3.380000e-140 508.0
27 TraesCS2D01G100600 chr2B 92.241 232 9 3 2649 2880 82717655 82717877 1.700000e-83 320.0
28 TraesCS2D01G100600 chr2B 92.073 164 8 3 1031 1192 82713727 82713887 3.810000e-55 226.0
29 TraesCS2D01G100600 chr2B 90.909 154 11 1 1 154 82850820 82850970 1.790000e-48 204.0
30 TraesCS2D01G100600 chr2B 92.424 132 10 0 2883 3014 4084372 4084503 5.000000e-44 189.0
31 TraesCS2D01G100600 chr2B 87.662 154 16 1 1 154 82712546 82712696 3.890000e-40 176.0
32 TraesCS2D01G100600 chr2B 85.714 105 11 3 556 657 83210593 83210696 1.440000e-19 108.0
33 TraesCS2D01G100600 chr5B 88.014 851 85 14 2896 3736 685695970 685696813 0.000000e+00 990.0
34 TraesCS2D01G100600 chr5B 89.583 48 5 0 1147 1194 267779274 267779227 1.140000e-05 62.1
35 TraesCS2D01G100600 chr7D 87.010 816 81 15 2935 3737 580843325 580844128 0.000000e+00 896.0
36 TraesCS2D01G100600 chr7D 87.746 710 75 11 3036 3738 624778473 624777769 0.000000e+00 819.0
37 TraesCS2D01G100600 chr7D 88.525 671 68 9 3046 3712 24939569 24940234 0.000000e+00 804.0
38 TraesCS2D01G100600 chr7D 90.226 133 12 1 2882 3014 24939357 24939488 5.030000e-39 172.0
39 TraesCS2D01G100600 chr7D 80.097 206 35 2 1413 1618 438368682 438368881 8.480000e-32 148.0
40 TraesCS2D01G100600 chr7D 72.441 254 64 4 1365 1618 143975585 143975338 4.060000e-10 76.8
41 TraesCS2D01G100600 chr5D 88.089 722 74 10 3019 3732 322573077 322573794 0.000000e+00 846.0
42 TraesCS2D01G100600 chr5D 85.965 57 8 0 1138 1194 238066212 238066268 1.140000e-05 62.1
43 TraesCS2D01G100600 chr3D 87.775 728 74 13 3017 3735 14383877 14384598 0.000000e+00 837.0
44 TraesCS2D01G100600 chr6A 88.646 687 69 7 3050 3734 8733091 8733770 0.000000e+00 828.0
45 TraesCS2D01G100600 chr6A 93.277 119 8 0 2896 3014 34557983 34558101 3.890000e-40 176.0
46 TraesCS2D01G100600 chr7B 87.432 732 69 16 3019 3741 427403900 427404617 0.000000e+00 821.0
47 TraesCS2D01G100600 chr7B 79.612 206 36 2 1413 1618 455271989 455271790 3.950000e-30 143.0
48 TraesCS2D01G100600 chr6B 84.350 869 97 17 2882 3741 508186382 508187220 0.000000e+00 815.0
49 TraesCS2D01G100600 chr6B 93.277 119 8 0 2896 3014 143631476 143631594 3.890000e-40 176.0
50 TraesCS2D01G100600 chrUn 89.107 661 62 10 3040 3696 23301555 23300901 0.000000e+00 813.0
51 TraesCS2D01G100600 chr4A 92.481 133 10 0 2882 3014 725675248 725675116 1.390000e-44 191.0
52 TraesCS2D01G100600 chr4A 75.319 235 46 8 1382 1613 691247059 691247284 6.700000e-18 102.0
53 TraesCS2D01G100600 chr3A 91.729 133 11 0 2882 3014 19792669 19792537 6.470000e-43 185.0
54 TraesCS2D01G100600 chr1D 88.550 131 15 0 2881 3011 493900218 493900348 3.920000e-35 159.0
55 TraesCS2D01G100600 chr7A 80.193 207 33 4 1413 1618 489163267 489163466 8.480000e-32 148.0
56 TraesCS2D01G100600 chr7A 87.500 64 8 0 681 744 579618941 579618878 1.460000e-09 75.0
57 TraesCS2D01G100600 chr6D 84.091 88 14 0 1524 1611 465213446 465213359 6.750000e-13 86.1
58 TraesCS2D01G100600 chr5A 89.583 48 5 0 1147 1194 317248162 317248115 1.140000e-05 62.1


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 TraesCS2D01G100600 chr2D 52645868 52649658 3790 False 3138.000000 5991 100.000000 1 3791 2 chr2D.!!$F3 3790
1 TraesCS2D01G100600 chr2D 52851161 52853822 2661 False 1162.333333 2760 90.546333 1 2863 3 chr2D.!!$F4 2862
2 TraesCS2D01G100600 chr2D 52959456 52960567 1111 False 771.000000 771 79.931000 1039 2152 1 chr2D.!!$F1 1113
3 TraesCS2D01G100600 chr2D 53649011 53650847 1836 False 709.000000 773 85.247000 1081 2880 2 chr2D.!!$F5 1799
4 TraesCS2D01G100600 chr2A 54111333 54113644 2311 False 2398.000000 2398 85.744000 548 2878 1 chr2A.!!$F1 2330
5 TraesCS2D01G100600 chr2A 54011396 54013897 2501 False 1350.500000 2518 88.385000 1 2659 2 chr2A.!!$F3 2658
6 TraesCS2D01G100600 chr2A 54139796 54140991 1195 False 802.000000 802 79.613000 962 2152 1 chr2A.!!$F2 1190
7 TraesCS2D01G100600 chr2A 54472407 54474145 1738 True 666.500000 745 84.827500 1053 2743 2 chr2A.!!$R1 1690
8 TraesCS2D01G100600 chr2B 83953562 83955434 1872 True 1452.000000 1452 81.625000 1050 2879 1 chr2B.!!$R1 1829
9 TraesCS2D01G100600 chr2B 82360712 82363000 2288 False 957.666667 1245 89.724667 551 2862 3 chr2B.!!$F2 2311
10 TraesCS2D01G100600 chr2B 82850820 82853355 2535 False 882.000000 1934 88.137333 1 2810 3 chr2B.!!$F4 2809
11 TraesCS2D01G100600 chr2B 759515039 759515846 807 True 715.000000 715 83.192000 2938 3737 1 chr2B.!!$R2 799
12 TraesCS2D01G100600 chr2B 82712546 82717877 5331 False 645.400000 1941 91.283600 1 2880 5 chr2B.!!$F3 2879
13 TraesCS2D01G100600 chr2B 83210593 83212061 1468 False 405.000000 702 83.515000 556 1973 2 chr2B.!!$F5 1417
14 TraesCS2D01G100600 chr5B 685695970 685696813 843 False 990.000000 990 88.014000 2896 3736 1 chr5B.!!$F1 840
15 TraesCS2D01G100600 chr7D 580843325 580844128 803 False 896.000000 896 87.010000 2935 3737 1 chr7D.!!$F2 802
16 TraesCS2D01G100600 chr7D 624777769 624778473 704 True 819.000000 819 87.746000 3036 3738 1 chr7D.!!$R2 702
17 TraesCS2D01G100600 chr7D 24939357 24940234 877 False 488.000000 804 89.375500 2882 3712 2 chr7D.!!$F3 830
18 TraesCS2D01G100600 chr5D 322573077 322573794 717 False 846.000000 846 88.089000 3019 3732 1 chr5D.!!$F2 713
19 TraesCS2D01G100600 chr3D 14383877 14384598 721 False 837.000000 837 87.775000 3017 3735 1 chr3D.!!$F1 718
20 TraesCS2D01G100600 chr6A 8733091 8733770 679 False 828.000000 828 88.646000 3050 3734 1 chr6A.!!$F1 684
21 TraesCS2D01G100600 chr7B 427403900 427404617 717 False 821.000000 821 87.432000 3019 3741 1 chr7B.!!$F1 722
22 TraesCS2D01G100600 chr6B 508186382 508187220 838 False 815.000000 815 84.350000 2882 3741 1 chr6B.!!$F2 859
23 TraesCS2D01G100600 chrUn 23300901 23301555 654 True 813.000000 813 89.107000 3040 3696 1 chrUn.!!$R1 656

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
27 28 0.314302 CACTCCCGAACTCGTTGTCT 59.686 55.000 0.00 0.00 37.74 3.41 F
88 91 1.400846 CCGCTAGAAACAGCTAGACGA 59.599 52.381 0.26 0.00 40.20 4.20 F
1045 1543 5.594725 TCTCCACATATCTAGTCTTCCACAC 59.405 44.000 0.00 0.00 0.00 3.82 F
2181 3088 0.033504 ATACTACTTCATGCCGGCGG 59.966 55.000 24.35 24.35 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1045 1543 1.269831 GGATCTACTGCCTTGCTACGG 60.270 57.143 0.0 0.0 0.00 4.02 R
1108 1620 1.462731 CGGCTCCTCCATCTCCAGAG 61.463 65.000 0.0 0.0 34.01 3.35 R
2578 3553 0.243907 AACACACGACGATCCTCCTG 59.756 55.000 0.0 0.0 0.00 3.86 R
3505 6731 1.227853 AGCACGAAAAGCCCGTTCT 60.228 52.632 0.0 0.0 38.29 3.01 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
23 24 1.872653 GCTTTCACTCCCGAACTCGTT 60.873 52.381 0.00 0.00 37.74 3.85
27 28 0.314302 CACTCCCGAACTCGTTGTCT 59.686 55.000 0.00 0.00 37.74 3.41
68 71 1.598130 GGCTGCATATGGACGACCC 60.598 63.158 4.56 0.00 34.81 4.46
88 91 1.400846 CCGCTAGAAACAGCTAGACGA 59.599 52.381 0.26 0.00 40.20 4.20
572 575 7.444629 AGCACATATCATTAGCAGGTTAATG 57.555 36.000 8.93 8.93 40.67 1.90
647 660 6.633234 GGATTAAAATCGCGGAAGAAAGAATC 59.367 38.462 6.13 5.88 36.27 2.52
853 908 9.050601 CCTATTAACTCTTGATGATTCCAGTTC 57.949 37.037 0.00 0.00 0.00 3.01
1045 1543 5.594725 TCTCCACATATCTAGTCTTCCACAC 59.405 44.000 0.00 0.00 0.00 3.82
1116 1649 2.725312 GCGGTGATGGCTCTGGAGA 61.725 63.158 1.35 0.00 0.00 3.71
1292 2028 2.437281 TCTCCCCGGTGAGTACTACTAG 59.563 54.545 13.98 0.00 33.93 2.57
1938 2812 1.298713 CTCGCCTTCCTCGATGACG 60.299 63.158 0.00 0.00 41.26 4.35
1973 2853 1.205064 CTTGCTCAACAACGCCGAG 59.795 57.895 0.00 0.00 33.68 4.63
2107 3005 1.594293 CGCTTGAACCGGACACAGT 60.594 57.895 9.46 0.00 0.00 3.55
2181 3088 0.033504 ATACTACTTCATGCCGGCGG 59.966 55.000 24.35 24.35 0.00 6.13
2305 3212 4.656117 TTCGTCGGCGCTGCTGAA 62.656 61.111 12.58 14.71 46.01 3.02
2329 3236 4.643387 GCTGGGCTTGGACACGGT 62.643 66.667 0.00 0.00 0.00 4.83
2506 3449 6.925165 GCAATAGATGGTTATTTGGTTGATGG 59.075 38.462 0.00 0.00 0.00 3.51
2514 3457 5.297029 GGTTATTTGGTTGATGGTAGCTCTC 59.703 44.000 0.00 0.00 0.00 3.20
2515 3458 4.851639 ATTTGGTTGATGGTAGCTCTCT 57.148 40.909 0.00 0.00 0.00 3.10
2519 3462 3.133542 TGGTTGATGGTAGCTCTCTGATG 59.866 47.826 0.00 0.00 0.00 3.07
2578 3553 2.052782 AATTAGGCGGTGGTGATTCC 57.947 50.000 0.00 0.00 0.00 3.01
2702 5816 6.327626 AGGAGGCATCTGTAGTTTGTACATAT 59.672 38.462 0.00 0.00 0.00 1.78
2703 5817 7.509318 AGGAGGCATCTGTAGTTTGTACATATA 59.491 37.037 0.00 0.00 0.00 0.86
2770 5905 5.888982 ACCCTATCGAGTTGGTTGATAAT 57.111 39.130 0.00 0.00 31.98 1.28
2771 5906 5.611374 ACCCTATCGAGTTGGTTGATAATG 58.389 41.667 0.00 0.00 31.98 1.90
2775 5910 8.094548 CCCTATCGAGTTGGTTGATAATGATAA 58.905 37.037 0.00 0.00 31.98 1.75
2799 5934 2.161855 TGATTGTGTGTTGATGGAGCC 58.838 47.619 0.00 0.00 0.00 4.70
2829 5964 7.650834 ATTCCCGTTGTAAATGTTCAATTTG 57.349 32.000 0.00 0.00 0.00 2.32
2865 6007 4.126437 CGTACATGCCATGGTTGATTCTA 58.874 43.478 19.78 3.30 33.60 2.10
2880 6022 7.183112 TGGTTGATTCTAGGGTCTTGGTTATTA 59.817 37.037 0.00 0.00 0.00 0.98
2908 6050 1.703513 AGAAAACGGGCCTTTAGTCCT 59.296 47.619 0.84 0.00 0.00 3.85
2936 6078 0.178533 AACCGGGACAAGACAAACGA 59.821 50.000 6.32 0.00 0.00 3.85
2974 6116 1.648116 TTAGTCCCGGTTGGCTTACT 58.352 50.000 0.00 0.00 0.00 2.24
2978 6120 1.277273 GTCCCGGTTGGCTTACTAACT 59.723 52.381 0.00 0.00 0.00 2.24
3014 6156 4.680237 CGTGGCCGCTGTCTGGAA 62.680 66.667 15.69 0.00 0.00 3.53
3015 6157 2.743928 GTGGCCGCTGTCTGGAAG 60.744 66.667 9.68 0.00 0.00 3.46
3157 6357 5.902613 TTCTAAATCGTCTAACTTCCCGA 57.097 39.130 0.00 0.00 0.00 5.14
3166 6366 1.616865 CTAACTTCCCGACTGGTCACA 59.383 52.381 1.63 0.00 34.77 3.58
3191 6392 2.451490 CTCTCACTACTCCAGCCTGAA 58.549 52.381 0.00 0.00 0.00 3.02
3222 6425 2.083628 TCCGAGTTCTATTCCCCCTC 57.916 55.000 0.00 0.00 0.00 4.30
3236 6439 2.028876 CCCCCTCGTTTTCAAGTTTGT 58.971 47.619 0.00 0.00 0.00 2.83
3320 6523 3.141398 AGCATGAAGTCACACGTTTCAT 58.859 40.909 6.59 6.59 41.01 2.57
3408 6614 4.150897 AGTAGCTTGACCACAGTTTGAA 57.849 40.909 0.00 0.00 0.00 2.69
3410 6616 5.133221 AGTAGCTTGACCACAGTTTGAAAT 58.867 37.500 0.00 0.00 0.00 2.17
3411 6617 5.594317 AGTAGCTTGACCACAGTTTGAAATT 59.406 36.000 0.00 0.00 0.00 1.82
3412 6618 5.343307 AGCTTGACCACAGTTTGAAATTT 57.657 34.783 0.00 0.00 0.00 1.82
3413 6619 5.733676 AGCTTGACCACAGTTTGAAATTTT 58.266 33.333 0.00 0.00 0.00 1.82
3488 6714 4.329462 TCTAAAAATTGGCAAAACGGCT 57.671 36.364 3.01 0.00 41.89 5.52
3505 6731 1.295792 GCTTATGGCCGTCGAAATCA 58.704 50.000 0.00 0.00 34.27 2.57
3510 6736 1.011968 TGGCCGTCGAAATCAGAACG 61.012 55.000 0.00 0.00 0.00 3.95
3578 6808 7.170828 CAGTATCGTATGCAAAAGTTATAGCCA 59.829 37.037 0.00 0.00 0.00 4.75
3738 6978 4.647424 TTTGAAAACTGAAATGGCGAGT 57.353 36.364 0.00 0.00 0.00 4.18
3739 6979 5.759506 TTTGAAAACTGAAATGGCGAGTA 57.240 34.783 0.00 0.00 0.00 2.59
3740 6980 5.356882 TTGAAAACTGAAATGGCGAGTAG 57.643 39.130 0.00 0.00 0.00 2.57
3741 6981 4.385825 TGAAAACTGAAATGGCGAGTAGT 58.614 39.130 0.00 0.00 0.00 2.73
3742 6982 4.819630 TGAAAACTGAAATGGCGAGTAGTT 59.180 37.500 0.00 0.00 0.00 2.24
3743 6983 5.049680 TGAAAACTGAAATGGCGAGTAGTTC 60.050 40.000 0.00 0.00 0.00 3.01
3744 6984 2.973945 ACTGAAATGGCGAGTAGTTCC 58.026 47.619 0.00 0.00 0.00 3.62
3745 6985 1.927174 CTGAAATGGCGAGTAGTTCCG 59.073 52.381 0.00 0.00 0.00 4.30
3746 6986 1.274167 TGAAATGGCGAGTAGTTCCGT 59.726 47.619 0.00 0.00 0.00 4.69
3747 6987 1.659098 GAAATGGCGAGTAGTTCCGTG 59.341 52.381 0.00 0.00 0.00 4.94
3748 6988 0.739813 AATGGCGAGTAGTTCCGTGC 60.740 55.000 0.00 0.00 0.00 5.34
3749 6989 1.605058 ATGGCGAGTAGTTCCGTGCT 61.605 55.000 0.00 0.00 0.00 4.40
3750 6990 1.080025 GGCGAGTAGTTCCGTGCTT 60.080 57.895 0.00 0.00 0.00 3.91
3751 6991 0.669625 GGCGAGTAGTTCCGTGCTTT 60.670 55.000 0.00 0.00 0.00 3.51
3752 6992 0.714439 GCGAGTAGTTCCGTGCTTTC 59.286 55.000 0.00 0.00 0.00 2.62
3753 6993 1.347320 CGAGTAGTTCCGTGCTTTCC 58.653 55.000 0.00 0.00 0.00 3.13
3754 6994 1.067776 CGAGTAGTTCCGTGCTTTCCT 60.068 52.381 0.00 0.00 0.00 3.36
3755 6995 2.608268 GAGTAGTTCCGTGCTTTCCTC 58.392 52.381 0.00 0.00 0.00 3.71
3756 6996 1.968493 AGTAGTTCCGTGCTTTCCTCA 59.032 47.619 0.00 0.00 0.00 3.86
3757 6997 2.567615 AGTAGTTCCGTGCTTTCCTCAT 59.432 45.455 0.00 0.00 0.00 2.90
3758 6998 3.767673 AGTAGTTCCGTGCTTTCCTCATA 59.232 43.478 0.00 0.00 0.00 2.15
3759 6999 3.252974 AGTTCCGTGCTTTCCTCATAG 57.747 47.619 0.00 0.00 0.00 2.23
3760 7000 2.832129 AGTTCCGTGCTTTCCTCATAGA 59.168 45.455 0.00 0.00 0.00 1.98
3761 7001 3.118956 AGTTCCGTGCTTTCCTCATAGAG 60.119 47.826 0.00 0.00 0.00 2.43
3770 7010 2.814023 CCTCATAGAGGTCGCCTGT 58.186 57.895 4.89 2.18 44.25 4.00
3771 7011 1.115467 CCTCATAGAGGTCGCCTGTT 58.885 55.000 4.89 0.00 44.25 3.16
3772 7012 1.482593 CCTCATAGAGGTCGCCTGTTT 59.517 52.381 4.89 0.00 44.25 2.83
3773 7013 2.693591 CCTCATAGAGGTCGCCTGTTTA 59.306 50.000 4.89 0.00 44.25 2.01
3774 7014 3.132289 CCTCATAGAGGTCGCCTGTTTAA 59.868 47.826 4.89 0.00 44.25 1.52
3775 7015 4.202264 CCTCATAGAGGTCGCCTGTTTAAT 60.202 45.833 4.89 0.00 44.25 1.40
3776 7016 5.353394 TCATAGAGGTCGCCTGTTTAATT 57.647 39.130 2.98 0.00 31.76 1.40
3777 7017 5.741011 TCATAGAGGTCGCCTGTTTAATTT 58.259 37.500 2.98 0.00 31.76 1.82
3778 7018 6.880484 TCATAGAGGTCGCCTGTTTAATTTA 58.120 36.000 2.98 0.00 31.76 1.40
3779 7019 7.506114 TCATAGAGGTCGCCTGTTTAATTTAT 58.494 34.615 2.98 0.00 31.76 1.40
3780 7020 7.656137 TCATAGAGGTCGCCTGTTTAATTTATC 59.344 37.037 2.98 0.00 31.76 1.75
3781 7021 5.990668 AGAGGTCGCCTGTTTAATTTATCT 58.009 37.500 2.98 0.00 31.76 1.98
3782 7022 7.120923 AGAGGTCGCCTGTTTAATTTATCTA 57.879 36.000 2.98 0.00 31.76 1.98
3783 7023 6.985059 AGAGGTCGCCTGTTTAATTTATCTAC 59.015 38.462 2.98 0.00 31.76 2.59
3784 7024 6.053650 AGGTCGCCTGTTTAATTTATCTACC 58.946 40.000 0.00 0.00 29.57 3.18
3785 7025 5.818857 GGTCGCCTGTTTAATTTATCTACCA 59.181 40.000 0.00 0.00 0.00 3.25
3786 7026 6.316890 GGTCGCCTGTTTAATTTATCTACCAA 59.683 38.462 0.00 0.00 0.00 3.67
3787 7027 7.012989 GGTCGCCTGTTTAATTTATCTACCAAT 59.987 37.037 0.00 0.00 0.00 3.16
3788 7028 8.403236 GTCGCCTGTTTAATTTATCTACCAATT 58.597 33.333 0.00 0.00 0.00 2.32
3789 7029 8.962679 TCGCCTGTTTAATTTATCTACCAATTT 58.037 29.630 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 37 8.719648 CATATGCAGCCACAGAAAATTTAAAAA 58.280 29.630 0.00 0.00 0.00 1.94
36 39 6.817641 CCATATGCAGCCACAGAAAATTTAAA 59.182 34.615 0.00 0.00 0.00 1.52
37 40 6.154192 TCCATATGCAGCCACAGAAAATTTAA 59.846 34.615 0.00 0.00 0.00 1.52
38 41 5.655974 TCCATATGCAGCCACAGAAAATTTA 59.344 36.000 0.00 0.00 0.00 1.40
39 42 4.467082 TCCATATGCAGCCACAGAAAATTT 59.533 37.500 0.00 0.00 0.00 1.82
88 91 3.308438 ACCAGTAACAACGAGCGTTAT 57.692 42.857 8.03 3.54 36.46 1.89
571 574 1.879380 GCACTGTGTAATCACCAAGCA 59.121 47.619 9.86 0.00 43.26 3.91
572 575 2.154462 AGCACTGTGTAATCACCAAGC 58.846 47.619 9.86 0.00 43.26 4.01
853 908 5.579904 CGCTCATGATAACATCCTGGATAAG 59.420 44.000 9.27 0.31 34.15 1.73
981 1117 2.282180 GGTTTGGAAGAGCGGCCA 60.282 61.111 2.24 0.00 0.00 5.36
1045 1543 1.269831 GGATCTACTGCCTTGCTACGG 60.270 57.143 0.00 0.00 0.00 4.02
1108 1620 1.462731 CGGCTCCTCCATCTCCAGAG 61.463 65.000 0.00 0.00 34.01 3.35
1135 1668 4.344865 GGAAGCCCGGTGGAAGCA 62.345 66.667 0.00 0.00 0.00 3.91
1938 2812 3.057736 AGCAAGTCATCATTGTTGAGCAC 60.058 43.478 9.01 0.00 34.73 4.40
2105 3003 3.525537 CGTCTTTATGGTCAGATGCACT 58.474 45.455 0.00 0.00 0.00 4.40
2107 3005 2.499693 TCCGTCTTTATGGTCAGATGCA 59.500 45.455 0.00 0.00 33.06 3.96
2186 3093 2.403378 GCCGCCAAGATTGCCGTTA 61.403 57.895 0.00 0.00 0.00 3.18
2277 3184 1.226323 CCGACGAAGACGCTACCTG 60.226 63.158 0.00 0.00 45.37 4.00
2345 3252 0.458543 CCATCAGGAACGAGGTGTCG 60.459 60.000 0.00 0.00 44.89 4.35
2506 3449 4.987912 GCAACTAATCCATCAGAGAGCTAC 59.012 45.833 0.00 0.00 0.00 3.58
2514 3457 8.218338 AGTTAATGAAGCAACTAATCCATCAG 57.782 34.615 0.00 0.00 33.29 2.90
2515 3458 8.579850 AAGTTAATGAAGCAACTAATCCATCA 57.420 30.769 0.00 0.00 33.92 3.07
2519 3462 7.748847 TCGAAAGTTAATGAAGCAACTAATCC 58.251 34.615 0.00 0.00 33.92 3.01
2578 3553 0.243907 AACACACGACGATCCTCCTG 59.756 55.000 0.00 0.00 0.00 3.86
2770 5905 8.583296 TCCATCAACACACAATCAAATTTATCA 58.417 29.630 0.00 0.00 0.00 2.15
2771 5906 8.984891 TCCATCAACACACAATCAAATTTATC 57.015 30.769 0.00 0.00 0.00 1.75
2775 5910 5.232463 GCTCCATCAACACACAATCAAATT 58.768 37.500 0.00 0.00 0.00 1.82
2799 5934 7.244898 TGAACATTTACAACGGGAATAATTCG 58.755 34.615 0.00 0.00 0.00 3.34
2865 6007 7.416731 TCTACTAGTGTAATAACCAAGACCCT 58.583 38.462 5.39 0.00 0.00 4.34
2880 6022 2.254508 AGGCCCGTTTTCTACTAGTGT 58.745 47.619 5.39 0.00 0.00 3.55
2928 6070 2.695359 TGGGCATTAGTCTCGTTTGTC 58.305 47.619 0.00 0.00 0.00 3.18
2936 6078 5.641155 ACTAAAGGTTTTGGGCATTAGTCT 58.359 37.500 0.00 0.00 30.07 3.24
2974 6116 3.105283 GGAGCTCCTTTAGTCCCAGTTA 58.895 50.000 26.25 0.00 0.00 2.24
2978 6120 1.276622 GTGGAGCTCCTTTAGTCCCA 58.723 55.000 32.28 7.65 36.82 4.37
3138 6338 4.142315 CCAGTCGGGAAGTTAGACGATTTA 60.142 45.833 0.00 0.00 40.01 1.40
3157 6357 1.620819 GTGAGAGGATGTGTGACCAGT 59.379 52.381 0.00 0.00 0.00 4.00
3166 6366 2.383855 GCTGGAGTAGTGAGAGGATGT 58.616 52.381 0.00 0.00 0.00 3.06
3191 6392 2.035576 AGAACTCGGAAGTTAAGCGTGT 59.964 45.455 0.00 0.00 45.80 4.49
3236 6439 9.616156 TTACTATTGTCAGGAAAACAACAAGTA 57.384 29.630 8.07 8.07 39.29 2.24
3454 6677 8.319881 TGCCAATTTTTAGAATCATCAATTCCA 58.680 29.630 0.00 0.00 44.20 3.53
3455 6678 8.721019 TGCCAATTTTTAGAATCATCAATTCC 57.279 30.769 0.00 0.00 44.20 3.01
3463 6687 5.178438 GCCGTTTTGCCAATTTTTAGAATCA 59.822 36.000 0.00 0.00 0.00 2.57
3477 6701 4.494811 GCCATAAGCCGTTTTGCC 57.505 55.556 0.00 0.00 34.35 4.52
3488 6714 2.933906 GTTCTGATTTCGACGGCCATAA 59.066 45.455 2.24 0.00 0.00 1.90
3505 6731 1.227853 AGCACGAAAAGCCCGTTCT 60.228 52.632 0.00 0.00 38.29 3.01
3510 6736 3.782889 AATATTCAGCACGAAAAGCCC 57.217 42.857 0.00 0.00 37.12 5.19
3552 6780 7.170828 TGGCTATAACTTTTGCATACGATACTG 59.829 37.037 0.00 0.00 0.00 2.74
3553 6781 7.214381 TGGCTATAACTTTTGCATACGATACT 58.786 34.615 0.00 0.00 0.00 2.12
3554 6782 7.416154 TGGCTATAACTTTTGCATACGATAC 57.584 36.000 0.00 0.00 0.00 2.24
3555 6783 8.615878 AATGGCTATAACTTTTGCATACGATA 57.384 30.769 0.00 0.00 0.00 2.92
3714 6954 5.290885 ACTCGCCATTTCAGTTTTCAAAAAC 59.709 36.000 9.77 9.77 46.54 2.43
3720 6960 5.358298 AACTACTCGCCATTTCAGTTTTC 57.642 39.130 0.00 0.00 0.00 2.29
3738 6978 4.021229 TCTATGAGGAAAGCACGGAACTA 58.979 43.478 0.00 0.00 0.00 2.24
3739 6979 2.832129 TCTATGAGGAAAGCACGGAACT 59.168 45.455 0.00 0.00 0.00 3.01
3740 6980 3.190874 CTCTATGAGGAAAGCACGGAAC 58.809 50.000 0.00 0.00 0.00 3.62
3741 6981 3.526931 CTCTATGAGGAAAGCACGGAA 57.473 47.619 0.00 0.00 0.00 4.30
3753 6993 2.969628 AAACAGGCGACCTCTATGAG 57.030 50.000 0.00 0.00 0.00 2.90
3754 6994 5.353394 AATTAAACAGGCGACCTCTATGA 57.647 39.130 0.00 0.00 0.00 2.15
3755 6995 7.657761 AGATAAATTAAACAGGCGACCTCTATG 59.342 37.037 0.00 0.00 0.00 2.23
3756 6996 7.736893 AGATAAATTAAACAGGCGACCTCTAT 58.263 34.615 0.00 0.00 0.00 1.98
3757 6997 7.120923 AGATAAATTAAACAGGCGACCTCTA 57.879 36.000 0.00 0.00 0.00 2.43
3758 6998 5.990668 AGATAAATTAAACAGGCGACCTCT 58.009 37.500 0.00 0.00 0.00 3.69
3759 6999 6.202379 GGTAGATAAATTAAACAGGCGACCTC 59.798 42.308 0.00 0.00 0.00 3.85
3760 7000 6.053650 GGTAGATAAATTAAACAGGCGACCT 58.946 40.000 0.00 0.00 0.00 3.85
3761 7001 5.818857 TGGTAGATAAATTAAACAGGCGACC 59.181 40.000 0.00 0.00 0.00 4.79
3762 7002 6.913873 TGGTAGATAAATTAAACAGGCGAC 57.086 37.500 0.00 0.00 0.00 5.19
3763 7003 8.514330 AATTGGTAGATAAATTAAACAGGCGA 57.486 30.769 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.