Multiple sequence alignment - TraesCS5A01G522900

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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 TraesCS5A01G522900 chr5A 100.000 3494 0 0 1 3494 684196293 684199786 0.000000e+00 6453.0
1 TraesCS5A01G522900 chr5A 81.644 1460 214 33 1043 2490 391755467 391754050 0.000000e+00 1162.0
2 TraesCS5A01G522900 chr5A 94.539 293 14 1 2 292 6759432 6759140 5.320000e-123 451.0
3 TraesCS5A01G522900 chr5A 93.537 294 17 1 2 293 691452583 691452876 1.490000e-118 436.0
4 TraesCS5A01G522900 chr5A 97.516 161 4 0 793 953 681381308 681381468 3.440000e-70 276.0
5 TraesCS5A01G522900 chr4B 94.147 1794 84 9 946 2728 668100556 668102339 0.000000e+00 2712.0
6 TraesCS5A01G522900 chr4B 94.147 1794 84 9 946 2728 668108214 668109997 0.000000e+00 2712.0
7 TraesCS5A01G522900 chr4B 97.383 726 17 2 2771 3494 668102336 668103061 0.000000e+00 1234.0
8 TraesCS5A01G522900 chr4B 97.383 726 17 2 2771 3494 668109994 668110719 0.000000e+00 1234.0
9 TraesCS5A01G522900 chr4B 93.992 799 41 6 1 796 668099748 668100542 0.000000e+00 1203.0
10 TraesCS5A01G522900 chr4B 93.992 799 41 6 1 796 668107406 668108200 0.000000e+00 1203.0
11 TraesCS5A01G522900 chr4B 96.894 161 5 0 793 953 178808593 178808753 1.600000e-68 270.0
12 TraesCS5A01G522900 chr4B 85.256 156 21 2 792 946 57863382 57863228 3.610000e-35 159.0
13 TraesCS5A01G522900 chr4B 84.967 153 22 1 795 946 376866950 376866798 1.680000e-33 154.0
14 TraesCS5A01G522900 chrUn 93.001 1543 91 10 952 2486 29527565 29526032 0.000000e+00 2235.0
15 TraesCS5A01G522900 chrUn 90.020 1503 115 17 995 2487 28787032 28785555 0.000000e+00 1912.0
16 TraesCS5A01G522900 chrUn 90.772 1257 87 12 952 2202 29652607 29651374 0.000000e+00 1652.0
17 TraesCS5A01G522900 chrUn 86.272 1486 176 16 997 2474 29846996 29848461 0.000000e+00 1589.0
18 TraesCS5A01G522900 chrUn 86.098 1453 177 14 994 2435 29852361 29850923 0.000000e+00 1541.0
19 TraesCS5A01G522900 chrUn 96.657 718 19 3 2779 3494 29648989 29648275 0.000000e+00 1188.0
20 TraesCS5A01G522900 chrUn 94.374 551 20 5 2228 2777 29651381 29650841 0.000000e+00 835.0
21 TraesCS5A01G522900 chrUn 81.316 471 44 21 292 744 29653118 29652674 3.340000e-90 342.0
22 TraesCS5A01G522900 chrUn 79.310 290 26 14 486 753 29527924 29527647 4.640000e-39 172.0
23 TraesCS5A01G522900 chr5B 85.850 1477 183 15 973 2435 689315465 689316929 0.000000e+00 1546.0
24 TraesCS5A01G522900 chr5B 85.432 1469 177 25 973 2425 689331798 689330351 0.000000e+00 1493.0
25 TraesCS5A01G522900 chr5B 85.703 1231 129 26 1027 2254 480170801 480171987 0.000000e+00 1254.0
26 TraesCS5A01G522900 chr5B 82.718 515 84 5 2937 3448 441096528 441097040 1.480000e-123 453.0
27 TraesCS5A01G522900 chr5B 93.878 294 16 1 2 293 108842495 108842788 3.200000e-120 442.0
28 TraesCS5A01G522900 chr5D 84.653 1212 129 29 1021 2221 399985756 399986921 0.000000e+00 1155.0
29 TraesCS5A01G522900 chr2D 85.156 512 73 3 2939 3448 602685554 602685044 4.000000e-144 521.0
30 TraesCS5A01G522900 chr6D 85.019 514 70 6 2939 3448 447512299 447512809 1.860000e-142 516.0
31 TraesCS5A01G522900 chr1B 83.301 515 81 5 2937 3448 394065954 394065442 1.470000e-128 470.0
32 TraesCS5A01G522900 chr1B 83.203 512 82 4 2939 3448 683457825 683457316 1.900000e-127 466.0
33 TraesCS5A01G522900 chr1B 83.074 514 83 4 2937 3448 680780005 680780516 6.830000e-127 464.0
34 TraesCS5A01G522900 chr1B 84.106 151 19 4 795 942 172041691 172041839 1.310000e-29 141.0
35 TraesCS5A01G522900 chr3D 93.814 291 18 0 2 292 63718808 63719098 4.140000e-119 438.0
36 TraesCS5A01G522900 chr3A 93.174 293 18 1 2 292 546304497 546304789 2.490000e-116 429.0
37 TraesCS5A01G522900 chr7D 92.784 291 16 3 2 292 535582248 535582533 1.940000e-112 416.0
38 TraesCS5A01G522900 chr1D 88.487 304 29 3 2 299 399566684 399566381 2.560000e-96 363.0
39 TraesCS5A01G522900 chr6B 94.545 165 9 0 793 957 492305497 492305333 4.480000e-64 255.0
40 TraesCS5A01G522900 chr2B 93.827 162 10 0 795 956 167894119 167893958 9.690000e-61 244.0
41 TraesCS5A01G522900 chr2B 83.851 161 25 1 790 950 782549146 782549305 6.040000e-33 152.0
42 TraesCS5A01G522900 chr7B 95.294 85 4 0 795 879 237517712 237517796 6.080000e-28 135.0
43 TraesCS5A01G522900 chr7B 100.000 46 0 0 908 953 237517800 237517845 6.210000e-13 86.1


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 TraesCS5A01G522900 chr5A 684196293 684199786 3493 False 6453.000000 6453 100.00000 1 3494 1 chr5A.!!$F2 3493
1 TraesCS5A01G522900 chr5A 391754050 391755467 1417 True 1162.000000 1162 81.64400 1043 2490 1 chr5A.!!$R2 1447
2 TraesCS5A01G522900 chr4B 668099748 668103061 3313 False 1716.333333 2712 95.17400 1 3494 3 chr4B.!!$F2 3493
3 TraesCS5A01G522900 chr4B 668107406 668110719 3313 False 1716.333333 2712 95.17400 1 3494 3 chr4B.!!$F3 3493
4 TraesCS5A01G522900 chrUn 28785555 28787032 1477 True 1912.000000 1912 90.02000 995 2487 1 chrUn.!!$R1 1492
5 TraesCS5A01G522900 chrUn 29846996 29848461 1465 False 1589.000000 1589 86.27200 997 2474 1 chrUn.!!$F1 1477
6 TraesCS5A01G522900 chrUn 29850923 29852361 1438 True 1541.000000 1541 86.09800 994 2435 1 chrUn.!!$R2 1441
7 TraesCS5A01G522900 chrUn 29526032 29527924 1892 True 1203.500000 2235 86.15550 486 2486 2 chrUn.!!$R3 2000
8 TraesCS5A01G522900 chrUn 29648275 29653118 4843 True 1004.250000 1652 90.77975 292 3494 4 chrUn.!!$R4 3202
9 TraesCS5A01G522900 chr5B 689315465 689316929 1464 False 1546.000000 1546 85.85000 973 2435 1 chr5B.!!$F4 1462
10 TraesCS5A01G522900 chr5B 689330351 689331798 1447 True 1493.000000 1493 85.43200 973 2425 1 chr5B.!!$R1 1452
11 TraesCS5A01G522900 chr5B 480170801 480171987 1186 False 1254.000000 1254 85.70300 1027 2254 1 chr5B.!!$F3 1227
12 TraesCS5A01G522900 chr5B 441096528 441097040 512 False 453.000000 453 82.71800 2937 3448 1 chr5B.!!$F2 511
13 TraesCS5A01G522900 chr5D 399985756 399986921 1165 False 1155.000000 1155 84.65300 1021 2221 1 chr5D.!!$F1 1200
14 TraesCS5A01G522900 chr2D 602685044 602685554 510 True 521.000000 521 85.15600 2939 3448 1 chr2D.!!$R1 509
15 TraesCS5A01G522900 chr6D 447512299 447512809 510 False 516.000000 516 85.01900 2939 3448 1 chr6D.!!$F1 509
16 TraesCS5A01G522900 chr1B 394065442 394065954 512 True 470.000000 470 83.30100 2937 3448 1 chr1B.!!$R1 511
17 TraesCS5A01G522900 chr1B 683457316 683457825 509 True 466.000000 466 83.20300 2939 3448 1 chr1B.!!$R2 509
18 TraesCS5A01G522900 chr1B 680780005 680780516 511 False 464.000000 464 83.07400 2937 3448 1 chr1B.!!$F2 511

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
874 950 0.109342 CCTCCAAACACTGCAGACCT 59.891 55.0 23.35 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2495 2662 0.967887 TCCGCTGAGGAGGACAGAAG 60.968 60.0 0.0 0.0 45.98 2.85 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
78 79 1.631405 TGAGGGGGAAATTGCACAAG 58.369 50.000 0.00 0.00 0.00 3.16
103 104 9.319143 AGAAGAAACTCCGTTTGATCATTATAG 57.681 33.333 0.00 0.00 35.77 1.31
200 201 3.865745 GCACAAGATAGCAACGTACTCAT 59.134 43.478 0.00 0.00 0.00 2.90
274 275 3.267597 AAACATCCCGCAGCAACGC 62.268 57.895 0.00 0.00 0.00 4.84
329 330 7.429920 ACAAACACAAACGACAACATACATAAC 59.570 33.333 0.00 0.00 0.00 1.89
376 377 9.696917 CATTAGATTTTCAAAGTTTAAGCCTGT 57.303 29.630 0.00 0.00 0.00 4.00
378 379 9.744468 TTAGATTTTCAAAGTTTAAGCCTGTTC 57.256 29.630 0.00 0.00 0.00 3.18
399 400 1.590238 GAGAATCACAGCGGTCGATTG 59.410 52.381 15.28 0.00 33.17 2.67
407 408 2.186903 CGGTCGATTGAGGTGGGG 59.813 66.667 0.00 0.00 0.00 4.96
426 430 3.146847 GGGTGTGGGTAGAGAAACTTTG 58.853 50.000 0.00 0.00 0.00 2.77
452 456 2.298610 TGTTGTAACGTGGCCAATTGA 58.701 42.857 7.24 0.00 0.00 2.57
453 457 2.033550 TGTTGTAACGTGGCCAATTGAC 59.966 45.455 7.24 4.38 0.00 3.18
634 642 3.047877 CGTGGGAACGGCACCTTC 61.048 66.667 0.00 0.00 0.00 3.46
635 643 3.047877 GTGGGAACGGCACCTTCG 61.048 66.667 0.00 0.00 0.00 3.79
636 644 3.552384 TGGGAACGGCACCTTCGT 61.552 61.111 0.00 0.00 43.14 3.85
637 645 2.741211 GGGAACGGCACCTTCGTC 60.741 66.667 0.00 0.00 40.18 4.20
638 646 2.029964 GGAACGGCACCTTCGTCA 59.970 61.111 0.00 0.00 40.18 4.35
639 647 2.027625 GGAACGGCACCTTCGTCAG 61.028 63.158 0.00 0.00 40.18 3.51
690 743 8.134895 TGCAGGACTAAATTGTTTTTCAAGTAG 58.865 33.333 0.00 0.00 39.55 2.57
784 860 3.257393 GCAGTCTTGAGTCATTGATCGT 58.743 45.455 0.00 0.00 0.00 3.73
796 872 4.688879 GTCATTGATCGTTGGTGTGTTAGA 59.311 41.667 0.00 0.00 0.00 2.10
797 873 4.929211 TCATTGATCGTTGGTGTGTTAGAG 59.071 41.667 0.00 0.00 0.00 2.43
798 874 2.683968 TGATCGTTGGTGTGTTAGAGC 58.316 47.619 0.00 0.00 0.00 4.09
799 875 2.036604 TGATCGTTGGTGTGTTAGAGCA 59.963 45.455 0.00 0.00 0.00 4.26
800 876 2.831685 TCGTTGGTGTGTTAGAGCAT 57.168 45.000 0.00 0.00 0.00 3.79
801 877 2.683968 TCGTTGGTGTGTTAGAGCATC 58.316 47.619 0.00 0.00 0.00 3.91
802 878 1.732259 CGTTGGTGTGTTAGAGCATCC 59.268 52.381 0.00 0.00 33.66 3.51
803 879 2.778299 GTTGGTGTGTTAGAGCATCCA 58.222 47.619 0.00 0.00 33.66 3.41
805 881 1.696884 TGGTGTGTTAGAGCATCCACA 59.303 47.619 0.00 0.00 33.44 4.17
806 882 2.289631 TGGTGTGTTAGAGCATCCACAG 60.290 50.000 0.00 0.00 35.89 3.66
807 883 2.289694 GGTGTGTTAGAGCATCCACAGT 60.290 50.000 0.00 0.00 35.89 3.55
808 884 2.738846 GTGTGTTAGAGCATCCACAGTG 59.261 50.000 0.00 0.00 35.89 3.66
809 885 2.368548 TGTGTTAGAGCATCCACAGTGT 59.631 45.455 0.00 0.00 31.42 3.55
810 886 3.181455 TGTGTTAGAGCATCCACAGTGTT 60.181 43.478 0.00 0.00 31.42 3.32
811 887 3.187227 GTGTTAGAGCATCCACAGTGTTG 59.813 47.826 0.00 0.00 33.66 3.33
812 888 3.181455 TGTTAGAGCATCCACAGTGTTGT 60.181 43.478 0.00 0.00 38.31 3.32
822 898 2.939460 ACAGTGTTGTGTTTTCCAGC 57.061 45.000 0.00 0.00 35.83 4.85
823 899 2.166829 ACAGTGTTGTGTTTTCCAGCA 58.833 42.857 0.00 0.00 35.83 4.41
824 900 2.760092 ACAGTGTTGTGTTTTCCAGCAT 59.240 40.909 0.00 0.00 35.83 3.79
825 901 3.181487 ACAGTGTTGTGTTTTCCAGCATC 60.181 43.478 0.00 0.00 35.83 3.91
826 902 3.067180 CAGTGTTGTGTTTTCCAGCATCT 59.933 43.478 0.00 0.00 0.00 2.90
827 903 4.275689 CAGTGTTGTGTTTTCCAGCATCTA 59.724 41.667 0.00 0.00 0.00 1.98
828 904 5.048504 CAGTGTTGTGTTTTCCAGCATCTAT 60.049 40.000 0.00 0.00 0.00 1.98
829 905 5.536161 AGTGTTGTGTTTTCCAGCATCTATT 59.464 36.000 0.00 0.00 0.00 1.73
830 906 5.630680 GTGTTGTGTTTTCCAGCATCTATTG 59.369 40.000 0.00 0.00 0.00 1.90
831 907 5.301551 TGTTGTGTTTTCCAGCATCTATTGT 59.698 36.000 0.00 0.00 0.00 2.71
832 908 6.183360 TGTTGTGTTTTCCAGCATCTATTGTT 60.183 34.615 0.00 0.00 0.00 2.83
833 909 5.771469 TGTGTTTTCCAGCATCTATTGTTG 58.229 37.500 0.00 0.00 36.39 3.33
834 910 4.622740 GTGTTTTCCAGCATCTATTGTTGC 59.377 41.667 2.44 2.44 38.73 4.17
835 911 4.176271 GTTTTCCAGCATCTATTGTTGCC 58.824 43.478 6.59 0.00 39.12 4.52
836 912 3.370840 TTCCAGCATCTATTGTTGCCT 57.629 42.857 6.59 0.00 39.12 4.75
837 913 2.923121 TCCAGCATCTATTGTTGCCTC 58.077 47.619 6.59 0.00 39.12 4.70
838 914 2.507058 TCCAGCATCTATTGTTGCCTCT 59.493 45.455 6.59 0.00 39.12 3.69
839 915 3.711190 TCCAGCATCTATTGTTGCCTCTA 59.289 43.478 6.59 0.00 39.12 2.43
840 916 4.164030 TCCAGCATCTATTGTTGCCTCTAA 59.836 41.667 6.59 0.00 39.12 2.10
841 917 4.883585 CCAGCATCTATTGTTGCCTCTAAA 59.116 41.667 6.59 0.00 39.12 1.85
842 918 5.008415 CCAGCATCTATTGTTGCCTCTAAAG 59.992 44.000 6.59 0.00 39.12 1.85
843 919 5.008415 CAGCATCTATTGTTGCCTCTAAAGG 59.992 44.000 6.59 0.00 46.44 3.11
853 929 2.700722 CCTCTAAAGGCTTGGAGACC 57.299 55.000 23.38 0.00 41.47 3.85
854 930 1.134670 CCTCTAAAGGCTTGGAGACCG 60.135 57.143 23.38 10.23 41.47 4.79
855 931 0.249398 TCTAAAGGCTTGGAGACCGC 59.751 55.000 0.00 0.00 0.00 5.68
856 932 0.744771 CTAAAGGCTTGGAGACCGCC 60.745 60.000 0.00 0.00 43.89 6.13
865 941 3.967715 GAGACCGCCTCCAAACAC 58.032 61.111 0.00 0.00 35.87 3.32
866 942 1.371558 GAGACCGCCTCCAAACACT 59.628 57.895 0.00 0.00 35.87 3.55
867 943 0.951040 GAGACCGCCTCCAAACACTG 60.951 60.000 0.00 0.00 35.87 3.66
868 944 2.594592 ACCGCCTCCAAACACTGC 60.595 61.111 0.00 0.00 0.00 4.40
869 945 2.594303 CCGCCTCCAAACACTGCA 60.594 61.111 0.00 0.00 0.00 4.41
870 946 2.620112 CCGCCTCCAAACACTGCAG 61.620 63.158 13.48 13.48 0.00 4.41
871 947 1.597854 CGCCTCCAAACACTGCAGA 60.598 57.895 23.35 0.00 0.00 4.26
872 948 1.845809 CGCCTCCAAACACTGCAGAC 61.846 60.000 23.35 0.00 0.00 3.51
873 949 1.518903 GCCTCCAAACACTGCAGACC 61.519 60.000 23.35 0.00 0.00 3.85
874 950 0.109342 CCTCCAAACACTGCAGACCT 59.891 55.000 23.35 0.00 0.00 3.85
875 951 1.517242 CTCCAAACACTGCAGACCTC 58.483 55.000 23.35 0.00 0.00 3.85
876 952 0.249868 TCCAAACACTGCAGACCTCG 60.250 55.000 23.35 5.47 0.00 4.63
877 953 1.571460 CAAACACTGCAGACCTCGC 59.429 57.895 23.35 0.00 0.00 5.03
878 954 1.598130 AAACACTGCAGACCTCGCC 60.598 57.895 23.35 0.00 0.00 5.54
879 955 2.044806 AAACACTGCAGACCTCGCCT 62.045 55.000 23.35 0.00 0.00 5.52
880 956 2.125753 CACTGCAGACCTCGCCTC 60.126 66.667 23.35 0.00 0.00 4.70
881 957 2.283532 ACTGCAGACCTCGCCTCT 60.284 61.111 23.35 0.00 0.00 3.69
882 958 1.000771 ACTGCAGACCTCGCCTCTA 60.001 57.895 23.35 0.00 0.00 2.43
883 959 0.396417 ACTGCAGACCTCGCCTCTAT 60.396 55.000 23.35 0.00 0.00 1.98
884 960 1.133761 ACTGCAGACCTCGCCTCTATA 60.134 52.381 23.35 0.00 0.00 1.31
885 961 2.166829 CTGCAGACCTCGCCTCTATAT 58.833 52.381 8.42 0.00 0.00 0.86
886 962 2.560542 CTGCAGACCTCGCCTCTATATT 59.439 50.000 8.42 0.00 0.00 1.28
887 963 2.965831 TGCAGACCTCGCCTCTATATTT 59.034 45.455 0.00 0.00 0.00 1.40
888 964 3.388024 TGCAGACCTCGCCTCTATATTTT 59.612 43.478 0.00 0.00 0.00 1.82
889 965 4.141711 TGCAGACCTCGCCTCTATATTTTT 60.142 41.667 0.00 0.00 0.00 1.94
905 981 2.704725 TTTTTGAGCTTGGCATCGAC 57.295 45.000 0.00 0.00 0.00 4.20
906 982 0.881118 TTTTGAGCTTGGCATCGACC 59.119 50.000 0.00 0.00 0.00 4.79
907 983 0.960364 TTTGAGCTTGGCATCGACCC 60.960 55.000 0.00 0.00 0.00 4.46
908 984 1.841302 TTGAGCTTGGCATCGACCCT 61.841 55.000 5.63 0.00 0.00 4.34
909 985 1.078143 GAGCTTGGCATCGACCCTT 60.078 57.895 5.63 0.00 0.00 3.95
910 986 1.372087 GAGCTTGGCATCGACCCTTG 61.372 60.000 5.63 0.00 0.00 3.61
911 987 3.056313 GCTTGGCATCGACCCTTGC 62.056 63.158 0.00 0.00 38.14 4.01
915 991 3.190878 GCATCGACCCTTGCCTTG 58.809 61.111 0.00 0.00 32.66 3.61
916 992 2.409870 GCATCGACCCTTGCCTTGG 61.410 63.158 0.00 0.00 32.66 3.61
917 993 1.299648 CATCGACCCTTGCCTTGGA 59.700 57.895 0.00 0.00 0.00 3.53
918 994 0.745845 CATCGACCCTTGCCTTGGAG 60.746 60.000 0.00 0.00 0.00 3.86
919 995 1.915078 ATCGACCCTTGCCTTGGAGG 61.915 60.000 0.00 0.00 38.80 4.30
933 1009 3.329093 GAGGCTGCCTCCAAGGAT 58.671 61.111 33.62 4.83 44.36 3.24
934 1010 1.611965 GAGGCTGCCTCCAAGGATT 59.388 57.895 33.62 4.02 44.36 3.01
935 1011 0.839946 GAGGCTGCCTCCAAGGATTA 59.160 55.000 33.62 0.00 44.36 1.75
936 1012 1.212935 GAGGCTGCCTCCAAGGATTAA 59.787 52.381 33.62 0.00 44.36 1.40
937 1013 1.640670 AGGCTGCCTCCAAGGATTAAA 59.359 47.619 17.22 0.00 37.67 1.52
938 1014 1.751351 GGCTGCCTCCAAGGATTAAAC 59.249 52.381 12.43 0.00 37.67 2.01
939 1015 2.446435 GCTGCCTCCAAGGATTAAACA 58.554 47.619 0.00 0.00 37.67 2.83
940 1016 2.825532 GCTGCCTCCAAGGATTAAACAA 59.174 45.455 0.00 0.00 37.67 2.83
941 1017 3.367395 GCTGCCTCCAAGGATTAAACAAC 60.367 47.826 0.00 0.00 37.67 3.32
942 1018 3.826157 CTGCCTCCAAGGATTAAACAACA 59.174 43.478 0.00 0.00 37.67 3.33
943 1019 3.572255 TGCCTCCAAGGATTAAACAACAC 59.428 43.478 0.00 0.00 37.67 3.32
944 1020 3.572255 GCCTCCAAGGATTAAACAACACA 59.428 43.478 0.00 0.00 37.67 3.72
948 1024 7.483307 CCTCCAAGGATTAAACAACACATATG 58.517 38.462 0.00 0.00 37.67 1.78
950 1026 6.042143 CCAAGGATTAAACAACACATATGGC 58.958 40.000 7.80 0.00 0.00 4.40
1470 1587 2.989824 CGGTGGACGGTGAGGTCT 60.990 66.667 0.00 0.00 39.42 3.85
1512 1632 1.262417 GACGATGATGATGTTGCGCAT 59.738 47.619 12.75 0.00 41.24 4.73
2425 2582 1.617018 ATGGCTCGACTTGGCTGCTA 61.617 55.000 0.00 0.00 0.00 3.49
2593 2760 5.069318 GGGAAGATTCAATCTCATTCCCTC 58.931 45.833 21.80 6.46 44.92 4.30
2603 2770 2.497675 TCTCATTCCCTCCGAGTTTCAG 59.502 50.000 0.00 0.00 0.00 3.02
2660 2827 5.248870 ACCACAAAAAGTCTGTGTCATTC 57.751 39.130 2.60 0.00 42.18 2.67
2698 2866 9.461760 GATTGTCGAAACGTAGAAATAGAAAAG 57.538 33.333 0.00 0.00 0.00 2.27
2724 2892 5.878406 AACATCGAATTCTCATAGACCCT 57.122 39.130 3.52 0.00 0.00 4.34
2725 2893 5.461032 ACATCGAATTCTCATAGACCCTC 57.539 43.478 3.52 0.00 0.00 4.30
2726 2894 5.144100 ACATCGAATTCTCATAGACCCTCT 58.856 41.667 3.52 0.00 0.00 3.69
2727 2895 5.600484 ACATCGAATTCTCATAGACCCTCTT 59.400 40.000 3.52 0.00 0.00 2.85
2728 2896 5.521906 TCGAATTCTCATAGACCCTCTTG 57.478 43.478 3.52 0.00 0.00 3.02
2729 2897 5.201243 TCGAATTCTCATAGACCCTCTTGA 58.799 41.667 3.52 0.00 0.00 3.02
2730 2898 5.656859 TCGAATTCTCATAGACCCTCTTGAA 59.343 40.000 3.52 0.00 0.00 2.69
2731 2899 6.325028 TCGAATTCTCATAGACCCTCTTGAAT 59.675 38.462 3.52 0.00 0.00 2.57
2732 2900 6.644592 CGAATTCTCATAGACCCTCTTGAATC 59.355 42.308 3.52 0.00 0.00 2.52
2733 2901 5.878406 TTCTCATAGACCCTCTTGAATCC 57.122 43.478 0.00 0.00 0.00 3.01
2734 2902 5.149584 TCTCATAGACCCTCTTGAATCCT 57.850 43.478 0.00 0.00 0.00 3.24
2735 2903 6.281190 TCTCATAGACCCTCTTGAATCCTA 57.719 41.667 0.00 0.00 0.00 2.94
2736 2904 6.868826 TCTCATAGACCCTCTTGAATCCTAT 58.131 40.000 0.00 0.00 0.00 2.57
2737 2905 8.001300 TCTCATAGACCCTCTTGAATCCTATA 57.999 38.462 0.00 0.00 0.00 1.31
2738 2906 8.456940 TCTCATAGACCCTCTTGAATCCTATAA 58.543 37.037 0.00 0.00 0.00 0.98
2739 2907 8.657387 TCATAGACCCTCTTGAATCCTATAAG 57.343 38.462 0.00 0.00 0.00 1.73
2740 2908 8.456940 TCATAGACCCTCTTGAATCCTATAAGA 58.543 37.037 0.00 0.00 0.00 2.10
2741 2909 9.094578 CATAGACCCTCTTGAATCCTATAAGAA 57.905 37.037 0.00 0.00 30.77 2.52
2742 2910 7.996758 AGACCCTCTTGAATCCTATAAGAAA 57.003 36.000 0.00 0.00 30.77 2.52
2743 2911 8.393959 AGACCCTCTTGAATCCTATAAGAAAA 57.606 34.615 0.00 0.00 30.77 2.29
2744 2912 8.836735 AGACCCTCTTGAATCCTATAAGAAAAA 58.163 33.333 0.00 0.00 30.77 1.94
2807 4867 6.942576 ACTTAAGCATGATTTCGGCCTATAAT 59.057 34.615 0.00 0.00 0.00 1.28
2853 4913 4.097741 CGACCTGATTTTGGGCATTCATAA 59.902 41.667 0.00 0.00 31.53 1.90
2889 4949 2.039509 GCGATAAGCGAGGTAGGGT 58.960 57.895 0.00 0.00 44.57 4.34
2891 4951 1.602416 GCGATAAGCGAGGTAGGGTTC 60.602 57.143 0.00 0.00 44.57 3.62
2892 4952 1.679680 CGATAAGCGAGGTAGGGTTCA 59.320 52.381 0.00 0.00 44.57 3.18
2893 4953 2.296471 CGATAAGCGAGGTAGGGTTCAT 59.704 50.000 0.00 0.00 44.57 2.57
2894 4954 3.612004 CGATAAGCGAGGTAGGGTTCATC 60.612 52.174 0.00 0.00 44.57 2.92
2895 4955 1.867363 AAGCGAGGTAGGGTTCATCT 58.133 50.000 0.00 0.00 0.00 2.90
2896 4956 2.750141 AGCGAGGTAGGGTTCATCTA 57.250 50.000 0.00 0.00 0.00 1.98
3155 5218 1.728490 GAAGCCGCCCACATTCATCC 61.728 60.000 0.00 0.00 0.00 3.51
3482 5545 3.102276 GCTGTTAGAGTTGAGATCGACG 58.898 50.000 0.00 0.00 35.42 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 1.923356 TCTTGTGCAATTTCCCCCTC 58.077 50.000 0.00 0.00 0.00 4.30
122 123 8.455598 TCAACAAACTTAGTTGTTTACAAAGC 57.544 30.769 0.00 0.00 46.97 3.51
274 275 4.247267 TGATACTAGATAAAACCCCGCG 57.753 45.455 0.00 0.00 0.00 6.46
329 330 1.270550 AGAAGAGCAAATTTGTGCCCG 59.729 47.619 19.03 0.00 46.14 6.13
376 377 0.456142 CGACCGCTGTGATTCTCGAA 60.456 55.000 0.00 0.00 0.00 3.71
378 379 0.248661 ATCGACCGCTGTGATTCTCG 60.249 55.000 0.00 0.00 0.00 4.04
399 400 1.229400 TCTACCCACACCCCACCTC 60.229 63.158 0.00 0.00 0.00 3.85
407 408 2.552743 GCCAAAGTTTCTCTACCCACAC 59.447 50.000 0.00 0.00 0.00 3.82
497 501 4.844349 ACATTACTAGGACAATGCCTGT 57.156 40.909 11.68 5.66 42.61 4.00
499 503 5.104527 TGCTAACATTACTAGGACAATGCCT 60.105 40.000 11.68 2.15 42.15 4.75
663 705 7.327214 ACTTGAAAAACAATTTAGTCCTGCAA 58.673 30.769 0.00 0.00 37.88 4.08
784 860 2.105649 TGTGGATGCTCTAACACACCAA 59.894 45.455 0.00 0.00 38.76 3.67
803 879 2.166829 TGCTGGAAAACACAACACTGT 58.833 42.857 0.00 0.00 35.63 3.55
805 881 3.290710 AGATGCTGGAAAACACAACACT 58.709 40.909 0.00 0.00 0.00 3.55
806 882 3.715628 AGATGCTGGAAAACACAACAC 57.284 42.857 0.00 0.00 0.00 3.32
807 883 5.301551 ACAATAGATGCTGGAAAACACAACA 59.698 36.000 0.00 0.00 0.00 3.33
808 884 5.772521 ACAATAGATGCTGGAAAACACAAC 58.227 37.500 0.00 0.00 0.00 3.32
809 885 6.215121 CAACAATAGATGCTGGAAAACACAA 58.785 36.000 0.00 0.00 0.00 3.33
810 886 5.771469 CAACAATAGATGCTGGAAAACACA 58.229 37.500 0.00 0.00 0.00 3.72
811 887 4.622740 GCAACAATAGATGCTGGAAAACAC 59.377 41.667 0.00 0.00 40.09 3.32
812 888 4.321899 GGCAACAATAGATGCTGGAAAACA 60.322 41.667 0.00 0.00 42.55 2.83
813 889 4.082026 AGGCAACAATAGATGCTGGAAAAC 60.082 41.667 0.00 0.00 42.55 2.43
814 890 4.088634 AGGCAACAATAGATGCTGGAAAA 58.911 39.130 0.00 0.00 42.55 2.29
815 891 3.696051 GAGGCAACAATAGATGCTGGAAA 59.304 43.478 0.00 0.00 42.55 3.13
816 892 3.054139 AGAGGCAACAATAGATGCTGGAA 60.054 43.478 0.00 0.00 42.55 3.53
817 893 2.507058 AGAGGCAACAATAGATGCTGGA 59.493 45.455 0.00 0.00 42.55 3.86
818 894 2.928334 AGAGGCAACAATAGATGCTGG 58.072 47.619 0.00 0.00 42.55 4.85
819 895 5.008415 CCTTTAGAGGCAACAATAGATGCTG 59.992 44.000 0.00 0.00 42.55 4.41
820 896 5.128919 CCTTTAGAGGCAACAATAGATGCT 58.871 41.667 0.00 0.00 42.55 3.79
821 897 5.429957 CCTTTAGAGGCAACAATAGATGC 57.570 43.478 0.00 0.00 42.25 3.91
834 910 1.134670 CGGTCTCCAAGCCTTTAGAGG 60.135 57.143 0.00 0.00 46.50 3.69
835 911 1.740718 GCGGTCTCCAAGCCTTTAGAG 60.741 57.143 0.00 0.00 0.00 2.43
836 912 0.249398 GCGGTCTCCAAGCCTTTAGA 59.751 55.000 0.00 0.00 0.00 2.10
837 913 0.744771 GGCGGTCTCCAAGCCTTTAG 60.745 60.000 0.00 0.00 46.83 1.85
838 914 1.298667 GGCGGTCTCCAAGCCTTTA 59.701 57.895 0.00 0.00 46.83 1.85
839 915 2.034221 GGCGGTCTCCAAGCCTTT 59.966 61.111 0.00 0.00 46.83 3.11
848 924 0.951040 CAGTGTTTGGAGGCGGTCTC 60.951 60.000 0.00 0.00 41.71 3.36
849 925 1.071471 CAGTGTTTGGAGGCGGTCT 59.929 57.895 0.00 0.00 0.00 3.85
850 926 2.617274 GCAGTGTTTGGAGGCGGTC 61.617 63.158 0.00 0.00 0.00 4.79
851 927 2.594592 GCAGTGTTTGGAGGCGGT 60.595 61.111 0.00 0.00 0.00 5.68
852 928 2.594303 TGCAGTGTTTGGAGGCGG 60.594 61.111 0.00 0.00 0.00 6.13
853 929 1.597854 TCTGCAGTGTTTGGAGGCG 60.598 57.895 14.67 0.00 44.66 5.52
854 930 1.952263 GTCTGCAGTGTTTGGAGGC 59.048 57.895 14.67 0.00 44.66 4.70
855 931 0.109342 AGGTCTGCAGTGTTTGGAGG 59.891 55.000 14.67 0.00 44.66 4.30
856 932 1.517242 GAGGTCTGCAGTGTTTGGAG 58.483 55.000 14.67 0.00 45.81 3.86
857 933 0.249868 CGAGGTCTGCAGTGTTTGGA 60.250 55.000 14.67 0.00 0.00 3.53
858 934 1.845809 GCGAGGTCTGCAGTGTTTGG 61.846 60.000 14.67 1.50 0.00 3.28
859 935 1.571460 GCGAGGTCTGCAGTGTTTG 59.429 57.895 14.67 5.40 0.00 2.93
860 936 1.598130 GGCGAGGTCTGCAGTGTTT 60.598 57.895 14.67 0.00 0.00 2.83
861 937 2.031163 GGCGAGGTCTGCAGTGTT 59.969 61.111 14.67 0.00 0.00 3.32
862 938 2.919856 AGGCGAGGTCTGCAGTGT 60.920 61.111 14.67 0.00 0.00 3.55
863 939 1.315981 TAGAGGCGAGGTCTGCAGTG 61.316 60.000 14.67 1.14 0.00 3.66
864 940 0.396417 ATAGAGGCGAGGTCTGCAGT 60.396 55.000 14.67 0.00 0.00 4.40
865 941 1.610363 TATAGAGGCGAGGTCTGCAG 58.390 55.000 7.63 7.63 0.00 4.41
866 942 2.294449 ATATAGAGGCGAGGTCTGCA 57.706 50.000 0.00 0.00 0.00 4.41
867 943 3.669251 AAATATAGAGGCGAGGTCTGC 57.331 47.619 0.00 0.00 0.00 4.26
886 962 1.269448 GGTCGATGCCAAGCTCAAAAA 59.731 47.619 0.00 0.00 0.00 1.94
887 963 0.881118 GGTCGATGCCAAGCTCAAAA 59.119 50.000 0.00 0.00 0.00 2.44
888 964 0.960364 GGGTCGATGCCAAGCTCAAA 60.960 55.000 0.00 0.00 0.00 2.69
889 965 1.377202 GGGTCGATGCCAAGCTCAA 60.377 57.895 0.00 0.00 0.00 3.02
890 966 1.841302 AAGGGTCGATGCCAAGCTCA 61.841 55.000 0.00 0.00 0.00 4.26
891 967 1.078143 AAGGGTCGATGCCAAGCTC 60.078 57.895 0.00 0.00 0.00 4.09
892 968 1.377725 CAAGGGTCGATGCCAAGCT 60.378 57.895 0.00 0.00 0.00 3.74
893 969 3.056313 GCAAGGGTCGATGCCAAGC 62.056 63.158 0.00 0.00 36.56 4.01
894 970 3.190878 GCAAGGGTCGATGCCAAG 58.809 61.111 0.00 0.00 36.56 3.61
898 974 2.409870 CCAAGGCAAGGGTCGATGC 61.410 63.158 0.00 0.00 41.82 3.91
899 975 0.745845 CTCCAAGGCAAGGGTCGATG 60.746 60.000 0.00 0.00 0.00 3.84
900 976 1.604378 CTCCAAGGCAAGGGTCGAT 59.396 57.895 0.00 0.00 0.00 3.59
901 977 2.592993 CCTCCAAGGCAAGGGTCGA 61.593 63.158 0.00 0.00 0.00 4.20
902 978 2.045926 CCTCCAAGGCAAGGGTCG 60.046 66.667 0.00 0.00 0.00 4.79
917 993 1.298953 TTAATCCTTGGAGGCAGCCT 58.701 50.000 16.12 16.12 34.61 4.58
918 994 1.751351 GTTTAATCCTTGGAGGCAGCC 59.249 52.381 1.84 1.84 34.61 4.85
919 995 2.446435 TGTTTAATCCTTGGAGGCAGC 58.554 47.619 0.00 0.00 34.61 5.25
920 996 3.826157 TGTTGTTTAATCCTTGGAGGCAG 59.174 43.478 0.00 0.00 34.61 4.85
921 997 3.572255 GTGTTGTTTAATCCTTGGAGGCA 59.428 43.478 0.00 0.00 34.61 4.75
922 998 3.572255 TGTGTTGTTTAATCCTTGGAGGC 59.428 43.478 0.00 0.00 34.61 4.70
923 999 5.982890 ATGTGTTGTTTAATCCTTGGAGG 57.017 39.130 0.00 0.00 36.46 4.30
924 1000 7.483307 CCATATGTGTTGTTTAATCCTTGGAG 58.517 38.462 1.24 0.00 0.00 3.86
925 1001 6.127479 GCCATATGTGTTGTTTAATCCTTGGA 60.127 38.462 1.24 0.00 0.00 3.53
926 1002 6.042143 GCCATATGTGTTGTTTAATCCTTGG 58.958 40.000 1.24 0.00 0.00 3.61
927 1003 6.042143 GGCCATATGTGTTGTTTAATCCTTG 58.958 40.000 0.00 0.00 0.00 3.61
928 1004 5.128663 GGGCCATATGTGTTGTTTAATCCTT 59.871 40.000 4.39 0.00 0.00 3.36
929 1005 4.649218 GGGCCATATGTGTTGTTTAATCCT 59.351 41.667 4.39 0.00 0.00 3.24
930 1006 4.202212 GGGGCCATATGTGTTGTTTAATCC 60.202 45.833 4.39 0.00 0.00 3.01
931 1007 4.404073 TGGGGCCATATGTGTTGTTTAATC 59.596 41.667 4.39 0.00 0.00 1.75
932 1008 4.161377 GTGGGGCCATATGTGTTGTTTAAT 59.839 41.667 4.39 0.00 0.00 1.40
933 1009 3.511934 GTGGGGCCATATGTGTTGTTTAA 59.488 43.478 4.39 0.00 0.00 1.52
934 1010 3.093057 GTGGGGCCATATGTGTTGTTTA 58.907 45.455 4.39 0.00 0.00 2.01
935 1011 1.899142 GTGGGGCCATATGTGTTGTTT 59.101 47.619 4.39 0.00 0.00 2.83
936 1012 1.555967 GTGGGGCCATATGTGTTGTT 58.444 50.000 4.39 0.00 0.00 2.83
937 1013 0.324275 GGTGGGGCCATATGTGTTGT 60.324 55.000 4.39 0.00 37.17 3.32
938 1014 0.324183 TGGTGGGGCCATATGTGTTG 60.324 55.000 4.39 0.00 43.61 3.33
939 1015 2.091692 TGGTGGGGCCATATGTGTT 58.908 52.632 4.39 0.00 43.61 3.32
940 1016 3.848558 TGGTGGGGCCATATGTGT 58.151 55.556 4.39 0.00 43.61 3.72
948 1024 2.997315 GCTTTCCTTGGTGGGGCC 60.997 66.667 0.00 0.00 36.20 5.80
950 1026 0.610232 CTCTGCTTTCCTTGGTGGGG 60.610 60.000 0.00 0.00 36.20 4.96
989 1068 3.113745 CAGCCATGCCGATCAACC 58.886 61.111 0.00 0.00 0.00 3.77
1315 1420 4.329545 GTGGACTGGGAAGCGGCA 62.330 66.667 1.45 0.00 0.00 5.69
1512 1632 1.292941 CCTCCTCCTCCTCCTCCTCA 61.293 65.000 0.00 0.00 0.00 3.86
1588 1708 2.969238 CATGCCCTCGATGTCGCC 60.969 66.667 0.00 0.00 39.60 5.54
2196 2338 2.681064 TGCTTCCTTGCCATGCCC 60.681 61.111 0.00 0.00 0.00 5.36
2200 2342 2.629656 GCGTGTGCTTCCTTGCCAT 61.630 57.895 0.00 0.00 38.39 4.40
2425 2582 4.465305 AGCCATAGATTTTGCTTGAGCTTT 59.535 37.500 4.44 0.00 42.66 3.51
2495 2662 0.967887 TCCGCTGAGGAGGACAGAAG 60.968 60.000 0.00 0.00 45.98 2.85
2496 2663 1.076727 TCCGCTGAGGAGGACAGAA 59.923 57.895 0.00 0.00 45.98 3.02
2497 2664 2.763902 TCCGCTGAGGAGGACAGA 59.236 61.111 0.00 0.00 45.98 3.41
2593 2760 6.093495 TGAGGCAATTATTAACTGAAACTCGG 59.907 38.462 0.00 0.00 0.00 4.63
2603 2770 8.477984 TTTTTGCTCATGAGGCAATTATTAAC 57.522 30.769 23.89 3.45 46.81 2.01
2649 2816 8.797350 ATCATACTTGAATTGAATGACACAGA 57.203 30.769 0.00 0.00 34.96 3.41
2660 2827 7.015289 ACGTTTCGACAATCATACTTGAATTG 58.985 34.615 0.00 0.00 34.96 2.32
2698 2866 7.281100 AGGGTCTATGAGAATTCGATGTTTTTC 59.719 37.037 0.00 0.00 0.00 2.29
2769 2937 8.970859 ATCATGCTTAAGTGCTTCTATAAGTT 57.029 30.769 4.02 0.00 34.99 2.66
2786 4846 5.316167 TGATTATAGGCCGAAATCATGCTT 58.684 37.500 20.03 0.00 35.32 3.91
2793 4853 4.168101 TCCCTCTGATTATAGGCCGAAAT 58.832 43.478 0.00 0.00 0.00 2.17
2853 4913 1.523758 GCATGACTGTCGTTTCCCTT 58.476 50.000 0.00 0.00 0.00 3.95
2887 4947 3.031736 TGGCTACTCTGGTAGATGAACC 58.968 50.000 7.28 0.00 46.01 3.62
2889 4949 4.962362 TGAATGGCTACTCTGGTAGATGAA 59.038 41.667 7.28 0.00 46.01 2.57
2891 4951 4.944619 TGAATGGCTACTCTGGTAGATG 57.055 45.455 7.28 0.00 46.01 2.90
2892 4952 4.346418 CCTTGAATGGCTACTCTGGTAGAT 59.654 45.833 7.28 0.00 46.01 1.98
2893 4953 3.706594 CCTTGAATGGCTACTCTGGTAGA 59.293 47.826 7.28 0.00 46.01 2.59
2894 4954 3.706594 TCCTTGAATGGCTACTCTGGTAG 59.293 47.826 0.00 0.00 45.91 3.18
2895 4955 3.706594 CTCCTTGAATGGCTACTCTGGTA 59.293 47.826 0.00 0.00 0.00 3.25
2896 4956 2.503356 CTCCTTGAATGGCTACTCTGGT 59.497 50.000 0.00 0.00 0.00 4.00
3155 5218 5.583854 CAGATTACTTGGAGGTGATCAACAG 59.416 44.000 14.46 3.76 35.52 3.16


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

AutoCloner maintained by Alex Coulton.