Multiple sequence alignment - TraesCS6A01G030300

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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 TraesCS6A01G030300 chr6A 100.000 3155 0 0 1 3155 15693613 15696767 0.000000e+00 5827
1 TraesCS6A01G030300 chr6A 83.745 1255 170 27 917 2163 15894736 15893508 0.000000e+00 1157
2 TraesCS6A01G030300 chr6A 80.286 1471 247 33 949 2391 15647240 15648695 0.000000e+00 1070
3 TraesCS6A01G030300 chr6A 82.724 1094 174 13 1118 2203 15914022 15912936 0.000000e+00 959
4 TraesCS6A01G030300 chr6A 79.616 677 87 31 217 856 15907890 15907228 3.740000e-119 438
5 TraesCS6A01G030300 chr6A 79.442 681 88 35 164 826 15880385 15879739 4.830000e-118 435
6 TraesCS6A01G030300 chr1B 86.576 1989 234 21 973 2941 48062373 48060398 0.000000e+00 2163
7 TraesCS6A01G030300 chr1B 94.318 176 9 1 2958 3133 48060347 48060173 5.190000e-68 268
8 TraesCS6A01G030300 chr6D 86.246 1963 209 34 1007 2941 15344829 15342900 0.000000e+00 2073
9 TraesCS6A01G030300 chr6D 83.918 1567 211 23 990 2547 14792572 14791038 0.000000e+00 1459
10 TraesCS6A01G030300 chr6D 88.613 887 92 8 1821 2703 14441376 14442257 0.000000e+00 1070
11 TraesCS6A01G030300 chr6D 82.100 1095 180 13 1463 2547 14435570 14436658 0.000000e+00 922
12 TraesCS6A01G030300 chr6D 86.415 795 89 15 1756 2547 15349400 15348622 0.000000e+00 852
13 TraesCS6A01G030300 chr6D 85.250 400 54 5 2544 2941 15347599 15347203 1.050000e-109 407
14 TraesCS6A01G030300 chr6D 85.531 311 42 3 183 492 14727817 14727509 3.930000e-84 322
15 TraesCS6A01G030300 chr6D 94.886 176 8 1 2958 3133 15342849 15342675 1.110000e-69 274
16 TraesCS6A01G030300 chr5D 83.423 1490 198 33 917 2387 27985552 27984093 0.000000e+00 1338
17 TraesCS6A01G030300 chr6B 82.958 1467 185 28 971 2417 26794079 26792658 0.000000e+00 1264
18 TraesCS6A01G030300 chr6B 83.576 1236 162 21 917 2142 27058935 27057731 0.000000e+00 1120
19 TraesCS6A01G030300 chr6B 79.860 1430 253 24 984 2396 26500511 26501922 0.000000e+00 1013
20 TraesCS6A01G030300 chr6B 79.288 1376 244 28 1047 2392 26841906 26840542 0.000000e+00 924
21 TraesCS6A01G030300 chr6B 80.772 1191 199 25 973 2148 28471435 28472610 0.000000e+00 904
22 TraesCS6A01G030300 chr6B 75.745 1241 264 29 982 2200 53077161 53075936 9.750000e-165 590
23 TraesCS6A01G030300 chr6B 81.141 403 51 15 2544 2941 26792362 26791980 1.840000e-77 300
24 TraesCS6A01G030300 chr6B 87.209 172 10 7 8 167 27048350 27048179 5.370000e-43 185
25 TraesCS6A01G030300 chr6B 90.909 88 8 0 167 254 27048082 27047995 5.530000e-23 119
26 TraesCS6A01G030300 chr7B 88.870 575 47 6 2190 2750 731306880 731307451 0.000000e+00 691
27 TraesCS6A01G030300 chr7B 88.348 575 50 4 2190 2750 744822400 744822971 0.000000e+00 675
28 TraesCS6A01G030300 chr7B 93.750 176 8 1 2958 3133 744823087 744823259 8.680000e-66 261
29 TraesCS6A01G030300 chrUn 93.182 176 9 1 2958 3133 49478520 49478692 4.040000e-64 255
30 TraesCS6A01G030300 chrUn 93.182 176 9 1 2958 3133 270806331 270806503 4.040000e-64 255
31 TraesCS6A01G030300 chrUn 93.182 176 9 1 2958 3133 275173117 275172945 4.040000e-64 255
32 TraesCS6A01G030300 chrUn 93.182 176 9 1 2958 3133 332747026 332746854 4.040000e-64 255
33 TraesCS6A01G030300 chrUn 93.182 176 9 1 2958 3133 388080477 388080649 4.040000e-64 255
34 TraesCS6A01G030300 chrUn 93.182 176 9 1 2958 3133 417831470 417831298 4.040000e-64 255
35 TraesCS6A01G030300 chrUn 90.850 153 12 1 2598 2750 49478254 49478404 1.480000e-48 204
36 TraesCS6A01G030300 chrUn 90.850 153 12 1 2598 2750 65539754 65539604 1.480000e-48 204
37 TraesCS6A01G030300 chr2B 91.503 153 11 1 2598 2750 100961983 100961833 3.190000e-50 209
38 TraesCS6A01G030300 chr3B 91.860 86 7 0 1968 2053 819481780 819481865 1.540000e-23 121


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 TraesCS6A01G030300 chr6A 15693613 15696767 3154 False 5827.0 5827 100.00000 1 3155 1 chr6A.!!$F2 3154
1 TraesCS6A01G030300 chr6A 15893508 15894736 1228 True 1157.0 1157 83.74500 917 2163 1 chr6A.!!$R2 1246
2 TraesCS6A01G030300 chr6A 15647240 15648695 1455 False 1070.0 1070 80.28600 949 2391 1 chr6A.!!$F1 1442
3 TraesCS6A01G030300 chr6A 15912936 15914022 1086 True 959.0 959 82.72400 1118 2203 1 chr6A.!!$R4 1085
4 TraesCS6A01G030300 chr6A 15907228 15907890 662 True 438.0 438 79.61600 217 856 1 chr6A.!!$R3 639
5 TraesCS6A01G030300 chr6A 15879739 15880385 646 True 435.0 435 79.44200 164 826 1 chr6A.!!$R1 662
6 TraesCS6A01G030300 chr1B 48060173 48062373 2200 True 1215.5 2163 90.44700 973 3133 2 chr1B.!!$R1 2160
7 TraesCS6A01G030300 chr6D 14791038 14792572 1534 True 1459.0 1459 83.91800 990 2547 1 chr6D.!!$R2 1557
8 TraesCS6A01G030300 chr6D 14441376 14442257 881 False 1070.0 1070 88.61300 1821 2703 1 chr6D.!!$F2 882
9 TraesCS6A01G030300 chr6D 14435570 14436658 1088 False 922.0 922 82.10000 1463 2547 1 chr6D.!!$F1 1084
10 TraesCS6A01G030300 chr6D 15342675 15349400 6725 True 901.5 2073 88.19925 1007 3133 4 chr6D.!!$R3 2126
11 TraesCS6A01G030300 chr5D 27984093 27985552 1459 True 1338.0 1338 83.42300 917 2387 1 chr5D.!!$R1 1470
12 TraesCS6A01G030300 chr6B 27057731 27058935 1204 True 1120.0 1120 83.57600 917 2142 1 chr6B.!!$R2 1225
13 TraesCS6A01G030300 chr6B 26500511 26501922 1411 False 1013.0 1013 79.86000 984 2396 1 chr6B.!!$F1 1412
14 TraesCS6A01G030300 chr6B 26840542 26841906 1364 True 924.0 924 79.28800 1047 2392 1 chr6B.!!$R1 1345
15 TraesCS6A01G030300 chr6B 28471435 28472610 1175 False 904.0 904 80.77200 973 2148 1 chr6B.!!$F2 1175
16 TraesCS6A01G030300 chr6B 26791980 26794079 2099 True 782.0 1264 82.04950 971 2941 2 chr6B.!!$R4 1970
17 TraesCS6A01G030300 chr6B 53075936 53077161 1225 True 590.0 590 75.74500 982 2200 1 chr6B.!!$R3 1218
18 TraesCS6A01G030300 chr7B 731306880 731307451 571 False 691.0 691 88.87000 2190 2750 1 chr7B.!!$F1 560
19 TraesCS6A01G030300 chr7B 744822400 744823259 859 False 468.0 675 91.04900 2190 3133 2 chr7B.!!$F2 943

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
913 959 0.464013 CAGAGGGAGAGCTGCCATTG 60.464 60.0 10.75 4.41 44.28 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2798 6675 0.327924 TCAACCCATCTGCGGTCATT 59.672 50.0 0.0 0.0 31.48 2.57 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
61 62 8.782339 AAGCAAAAATAATCAAGAAATGGAGG 57.218 30.769 0.00 0.00 0.00 4.30
63 64 8.255905 AGCAAAAATAATCAAGAAATGGAGGAG 58.744 33.333 0.00 0.00 0.00 3.69
64 65 8.253113 GCAAAAATAATCAAGAAATGGAGGAGA 58.747 33.333 0.00 0.00 0.00 3.71
67 68 8.884124 AAATAATCAAGAAATGGAGGAGAACA 57.116 30.769 0.00 0.00 0.00 3.18
68 69 9.484806 AAATAATCAAGAAATGGAGGAGAACAT 57.515 29.630 0.00 0.00 0.00 2.71
72 73 9.484806 AATCAAGAAATGGAGGAGAACATATTT 57.515 29.630 0.00 0.00 0.00 1.40
73 74 8.884124 TCAAGAAATGGAGGAGAACATATTTT 57.116 30.769 0.00 0.00 0.00 1.82
131 132 2.979678 ACTAGGCAAAACTGGAGAAGGA 59.020 45.455 0.00 0.00 0.00 3.36
132 133 3.589288 ACTAGGCAAAACTGGAGAAGGAT 59.411 43.478 0.00 0.00 0.00 3.24
133 134 4.783227 ACTAGGCAAAACTGGAGAAGGATA 59.217 41.667 0.00 0.00 0.00 2.59
134 135 4.657814 AGGCAAAACTGGAGAAGGATAA 57.342 40.909 0.00 0.00 0.00 1.75
135 136 4.336280 AGGCAAAACTGGAGAAGGATAAC 58.664 43.478 0.00 0.00 0.00 1.89
136 137 3.444034 GGCAAAACTGGAGAAGGATAACC 59.556 47.826 0.00 0.00 0.00 2.85
138 139 4.522789 GCAAAACTGGAGAAGGATAACCAA 59.477 41.667 0.00 0.00 38.94 3.67
139 140 5.335976 GCAAAACTGGAGAAGGATAACCAAG 60.336 44.000 0.00 0.00 38.94 3.61
140 141 5.843019 AAACTGGAGAAGGATAACCAAGA 57.157 39.130 0.00 0.00 38.94 3.02
141 142 5.843019 AACTGGAGAAGGATAACCAAGAA 57.157 39.130 0.00 0.00 38.94 2.52
142 143 5.843019 ACTGGAGAAGGATAACCAAGAAA 57.157 39.130 0.00 0.00 38.94 2.52
143 144 6.200878 ACTGGAGAAGGATAACCAAGAAAA 57.799 37.500 0.00 0.00 38.94 2.29
144 145 6.004574 ACTGGAGAAGGATAACCAAGAAAAC 58.995 40.000 0.00 0.00 38.94 2.43
146 147 6.369629 TGGAGAAGGATAACCAAGAAAACAA 58.630 36.000 0.00 0.00 38.94 2.83
147 148 7.010160 TGGAGAAGGATAACCAAGAAAACAAT 58.990 34.615 0.00 0.00 38.94 2.71
149 150 9.020731 GGAGAAGGATAACCAAGAAAACAATTA 57.979 33.333 0.00 0.00 38.94 1.40
180 181 4.876107 TGAAAAGCAATTCTCGGTCTATCC 59.124 41.667 3.59 0.00 0.00 2.59
234 239 3.255888 ACAACTCAAGCTCATCGTAGTCA 59.744 43.478 0.00 0.00 0.00 3.41
240 245 4.864806 TCAAGCTCATCGTAGTCATCAAAC 59.135 41.667 0.00 0.00 0.00 2.93
248 253 4.055360 TCGTAGTCATCAAACCAACAGTG 58.945 43.478 0.00 0.00 0.00 3.66
345 357 9.541143 CAAACAGGAAATTAACACAAACCTATT 57.459 29.630 0.00 0.00 0.00 1.73
389 402 8.966069 AAGCTAATACCAAGAAGAAAGTATCC 57.034 34.615 0.00 0.00 0.00 2.59
508 533 7.618019 ATGTATATCCTCACTGTGGTTGTAT 57.382 36.000 8.11 5.23 0.00 2.29
510 535 8.541899 TGTATATCCTCACTGTGGTTGTATAA 57.458 34.615 8.11 0.00 0.00 0.98
513 538 8.732746 ATATCCTCACTGTGGTTGTATAAAAC 57.267 34.615 8.11 0.00 0.00 2.43
700 725 7.010923 TGCACATTTGTTTGTAGTGAAAAATCC 59.989 33.333 0.00 0.00 32.14 3.01
707 732 8.430801 TGTTTGTAGTGAAAAATCCAAAATGG 57.569 30.769 0.00 0.00 39.43 3.16
775 821 4.816048 ATGTGGAGGAGACATAGTAGGA 57.184 45.455 0.00 0.00 32.12 2.94
816 862 6.983906 AACCATGAAAAGAGAAGGAAATGT 57.016 33.333 0.00 0.00 0.00 2.71
844 890 6.648879 TGTTTAGGACAAGGGAAGAAAATG 57.351 37.500 0.00 0.00 34.69 2.32
846 892 5.592587 TTAGGACAAGGGAAGAAAATGGA 57.407 39.130 0.00 0.00 0.00 3.41
848 894 4.347607 AGGACAAGGGAAGAAAATGGATG 58.652 43.478 0.00 0.00 0.00 3.51
850 896 4.158579 GGACAAGGGAAGAAAATGGATGAC 59.841 45.833 0.00 0.00 0.00 3.06
851 897 3.758554 ACAAGGGAAGAAAATGGATGACG 59.241 43.478 0.00 0.00 0.00 4.35
852 898 4.009675 CAAGGGAAGAAAATGGATGACGA 58.990 43.478 0.00 0.00 0.00 4.20
853 899 4.301072 AGGGAAGAAAATGGATGACGAA 57.699 40.909 0.00 0.00 0.00 3.85
854 900 4.662278 AGGGAAGAAAATGGATGACGAAA 58.338 39.130 0.00 0.00 0.00 3.46
856 902 5.716703 AGGGAAGAAAATGGATGACGAAAAT 59.283 36.000 0.00 0.00 0.00 1.82
857 903 5.807011 GGGAAGAAAATGGATGACGAAAATG 59.193 40.000 0.00 0.00 0.00 2.32
858 904 5.807011 GGAAGAAAATGGATGACGAAAATGG 59.193 40.000 0.00 0.00 0.00 3.16
860 906 6.199937 AGAAAATGGATGACGAAAATGGAG 57.800 37.500 0.00 0.00 0.00 3.86
861 907 4.376340 AAATGGATGACGAAAATGGAGC 57.624 40.909 0.00 0.00 0.00 4.70
862 908 1.750193 TGGATGACGAAAATGGAGCC 58.250 50.000 0.00 0.00 0.00 4.70
863 909 1.025041 GGATGACGAAAATGGAGCCC 58.975 55.000 0.00 0.00 0.00 5.19
864 910 1.681780 GGATGACGAAAATGGAGCCCA 60.682 52.381 0.00 0.00 38.19 5.36
875 921 3.967467 ATGGAGCCCATTCTGAATTCT 57.033 42.857 7.05 0.00 42.23 2.40
876 922 3.008835 TGGAGCCCATTCTGAATTCTG 57.991 47.619 7.05 6.50 0.00 3.02
877 923 2.577563 TGGAGCCCATTCTGAATTCTGA 59.422 45.455 10.68 10.68 0.00 3.27
880 926 5.103982 TGGAGCCCATTCTGAATTCTGATTA 60.104 40.000 14.89 2.92 0.00 1.75
881 927 5.829924 GGAGCCCATTCTGAATTCTGATTAA 59.170 40.000 14.89 2.24 0.00 1.40
882 928 6.238869 GGAGCCCATTCTGAATTCTGATTAAC 60.239 42.308 14.89 5.61 0.00 2.01
883 929 5.595952 AGCCCATTCTGAATTCTGATTAACC 59.404 40.000 14.89 5.59 0.00 2.85
884 930 5.360714 GCCCATTCTGAATTCTGATTAACCA 59.639 40.000 14.89 0.89 0.00 3.67
885 931 6.681368 GCCCATTCTGAATTCTGATTAACCAC 60.681 42.308 14.89 0.73 0.00 4.16
886 932 6.458751 CCCATTCTGAATTCTGATTAACCACG 60.459 42.308 14.89 1.04 0.00 4.94
888 934 3.616821 TCTGAATTCTGATTAACCACGCG 59.383 43.478 3.53 3.53 0.00 6.01
889 935 3.591023 TGAATTCTGATTAACCACGCGA 58.409 40.909 15.93 0.00 0.00 5.87
890 936 3.369756 TGAATTCTGATTAACCACGCGAC 59.630 43.478 15.93 0.00 0.00 5.19
891 937 1.342555 TTCTGATTAACCACGCGACG 58.657 50.000 15.93 3.98 0.00 5.12
892 938 1.074319 TCTGATTAACCACGCGACGC 61.074 55.000 15.93 10.49 0.00 5.19
904 950 4.544689 CGACGCGCAGAGGGAGAG 62.545 72.222 5.73 0.00 36.53 3.20
905 951 4.863925 GACGCGCAGAGGGAGAGC 62.864 72.222 5.73 0.00 36.53 4.09
907 953 4.869440 CGCGCAGAGGGAGAGCTG 62.869 72.222 8.75 0.00 35.28 4.24
911 957 3.644719 CAGAGGGAGAGCTGCCAT 58.355 61.111 10.75 0.00 44.28 4.40
912 958 1.913722 CAGAGGGAGAGCTGCCATT 59.086 57.895 10.75 0.00 44.28 3.16
913 959 0.464013 CAGAGGGAGAGCTGCCATTG 60.464 60.000 10.75 4.41 44.28 2.82
914 960 1.823041 GAGGGAGAGCTGCCATTGC 60.823 63.158 10.75 0.00 44.28 3.56
932 978 2.582728 GCAAATTGCAATCCATCGGA 57.417 45.000 13.38 0.00 44.26 4.55
933 979 2.466846 GCAAATTGCAATCCATCGGAG 58.533 47.619 13.38 0.00 44.26 4.63
936 982 4.543692 CAAATTGCAATCCATCGGAGATC 58.456 43.478 13.38 0.00 45.12 2.75
937 983 3.784511 ATTGCAATCCATCGGAGATCT 57.215 42.857 5.99 0.00 45.12 2.75
940 986 4.462508 TGCAATCCATCGGAGATCTATC 57.537 45.455 0.00 0.00 45.12 2.08
1035 4601 1.081242 GTGCGTCGTTTCCCGTCTA 60.081 57.895 0.00 0.00 37.94 2.59
1042 4608 2.487372 GTCGTTTCCCGTCTACTCTCTT 59.513 50.000 0.00 0.00 37.94 2.85
1043 4609 2.746362 TCGTTTCCCGTCTACTCTCTTC 59.254 50.000 0.00 0.00 37.94 2.87
1044 4610 2.486982 CGTTTCCCGTCTACTCTCTTCA 59.513 50.000 0.00 0.00 0.00 3.02
1045 4611 3.670091 CGTTTCCCGTCTACTCTCTTCAC 60.670 52.174 0.00 0.00 0.00 3.18
1046 4612 2.125773 TCCCGTCTACTCTCTTCACC 57.874 55.000 0.00 0.00 0.00 4.02
1047 4613 1.104630 CCCGTCTACTCTCTTCACCC 58.895 60.000 0.00 0.00 0.00 4.61
1058 4636 0.545309 TCTTCACCCTCCACCTCCAG 60.545 60.000 0.00 0.00 0.00 3.86
1082 4660 2.669133 CCATCTTCCCACTCCGCCA 61.669 63.158 0.00 0.00 0.00 5.69
1314 4919 2.328099 GCTGTTCCTCCGCACCAAG 61.328 63.158 0.00 0.00 0.00 3.61
1384 4990 1.378646 TCGAGTCCTGACATCGCCT 60.379 57.895 11.64 0.00 34.42 5.52
1622 5232 3.804153 ATGCGCCGAGGATGCTCAG 62.804 63.158 15.10 3.85 0.00 3.35
1712 5325 2.286294 GGATGTTCAGACAAGCGCTATG 59.714 50.000 12.05 14.11 39.66 2.23
1730 5343 0.310543 TGCGCTGTCACATTCCAAAC 59.689 50.000 9.73 0.00 0.00 2.93
1753 5366 0.887933 GGAGAAGATTGCCGCCAAAA 59.112 50.000 0.00 0.00 34.05 2.44
1924 5537 1.808390 GCTTATCGTCCGGCGTTGT 60.808 57.895 16.00 7.98 42.13 3.32
1948 5561 1.347707 CTTATAGCATGGAGGGCCGAA 59.652 52.381 0.00 0.00 36.79 4.30
1949 5562 1.429930 TATAGCATGGAGGGCCGAAA 58.570 50.000 0.00 0.00 36.79 3.46
2149 5762 6.198591 GGAAGTACCGACTAATTTCAGATTCG 59.801 42.308 0.00 0.00 33.58 3.34
2288 5933 7.551617 GGTTGTTTACTGTAGTATGCCTGTTAT 59.448 37.037 0.00 0.00 0.00 1.89
2293 5938 6.672266 ACTGTAGTATGCCTGTTATATGCT 57.328 37.500 0.00 0.00 0.00 3.79
2298 5943 9.304335 TGTAGTATGCCTGTTATATGCTAGTTA 57.696 33.333 0.00 0.00 0.00 2.24
2299 5944 9.790389 GTAGTATGCCTGTTATATGCTAGTTAG 57.210 37.037 0.00 0.00 0.00 2.34
2300 5945 8.423906 AGTATGCCTGTTATATGCTAGTTAGT 57.576 34.615 0.00 0.00 0.00 2.24
2301 5946 8.524487 AGTATGCCTGTTATATGCTAGTTAGTC 58.476 37.037 0.00 0.00 0.00 2.59
2302 5947 6.724893 TGCCTGTTATATGCTAGTTAGTCA 57.275 37.500 0.00 0.00 0.00 3.41
2303 5948 7.303182 TGCCTGTTATATGCTAGTTAGTCAT 57.697 36.000 0.00 0.00 0.00 3.06
2304 5949 7.735917 TGCCTGTTATATGCTAGTTAGTCATT 58.264 34.615 0.00 0.00 0.00 2.57
2314 5959 5.296780 TGCTAGTTAGTCATTGCTAAATGCC 59.703 40.000 9.50 3.89 42.55 4.40
2316 5961 5.824904 AGTTAGTCATTGCTAAATGCCAG 57.175 39.130 3.25 0.00 42.55 4.85
2448 6207 4.730949 CTTCCATTGAAGGTCATGCAAT 57.269 40.909 0.00 0.00 43.57 3.56
2480 6299 3.070734 TGGGTGGATCAATTTTGTGTTGG 59.929 43.478 0.00 0.00 0.00 3.77
2508 6365 2.029649 CACCCATGAAACCAGAAAGCAG 60.030 50.000 0.00 0.00 0.00 4.24
2513 6370 4.320788 CCATGAAACCAGAAAGCAGAAGAC 60.321 45.833 0.00 0.00 0.00 3.01
2518 6375 7.450074 TGAAACCAGAAAGCAGAAGACTAATA 58.550 34.615 0.00 0.00 0.00 0.98
2569 6427 3.065371 CCCTGCTGTTCGGATTCATAAAC 59.935 47.826 0.00 0.00 0.00 2.01
2669 6543 7.389607 TGTTTTACTCATAAGTTCCAGCTAACC 59.610 37.037 0.00 0.00 36.92 2.85
2671 6545 5.700402 ACTCATAAGTTCCAGCTAACCAT 57.300 39.130 0.00 0.00 28.74 3.55
2672 6546 5.675538 ACTCATAAGTTCCAGCTAACCATC 58.324 41.667 0.00 0.00 28.74 3.51
2696 6570 7.112779 TCTCTCAAATAAAAGAAGATGGACCC 58.887 38.462 0.00 0.00 0.00 4.46
2705 6579 4.408182 AGAAGATGGACCCAATTAGTCG 57.592 45.455 0.00 0.00 34.97 4.18
2706 6580 4.030913 AGAAGATGGACCCAATTAGTCGA 58.969 43.478 0.00 0.00 34.97 4.20
2728 6602 8.015658 GTCGAATGTAAATTTTCTACTGCACTT 58.984 33.333 0.00 0.00 0.00 3.16
2729 6603 8.564574 TCGAATGTAAATTTTCTACTGCACTTT 58.435 29.630 0.00 0.00 0.00 2.66
2804 6681 7.129109 TCTTACTTTGAAACGATGAATGACC 57.871 36.000 0.00 0.00 0.00 4.02
2905 6785 7.414429 CGATTGATGTGTCAGGTCAAATATGTT 60.414 37.037 4.45 0.00 35.70 2.71
2907 6787 7.144722 TGATGTGTCAGGTCAAATATGTTTC 57.855 36.000 0.00 0.00 0.00 2.78
2908 6788 5.605564 TGTGTCAGGTCAAATATGTTTCG 57.394 39.130 0.00 0.00 0.00 3.46
2941 6821 2.365617 TGAGAGGTGTGTTTCTCAGGTC 59.634 50.000 0.35 0.00 43.51 3.85
2942 6822 1.694696 AGAGGTGTGTTTCTCAGGTCC 59.305 52.381 0.00 0.00 32.76 4.46
2943 6823 0.393077 AGGTGTGTTTCTCAGGTCCG 59.607 55.000 0.00 0.00 0.00 4.79
2944 6824 1.228657 GGTGTGTTTCTCAGGTCCGC 61.229 60.000 0.00 0.00 0.00 5.54
2945 6825 0.531974 GTGTGTTTCTCAGGTCCGCA 60.532 55.000 0.00 0.00 0.00 5.69
2946 6826 0.396435 TGTGTTTCTCAGGTCCGCAT 59.604 50.000 0.00 0.00 0.00 4.73
2947 6827 0.798776 GTGTTTCTCAGGTCCGCATG 59.201 55.000 0.00 0.00 0.00 4.06
2948 6828 0.684535 TGTTTCTCAGGTCCGCATGA 59.315 50.000 0.00 0.00 34.04 3.07
2949 6829 1.278985 TGTTTCTCAGGTCCGCATGAT 59.721 47.619 0.00 0.00 34.73 2.45
2950 6830 2.290260 TGTTTCTCAGGTCCGCATGATT 60.290 45.455 0.00 0.00 34.73 2.57
2951 6831 2.028420 TTCTCAGGTCCGCATGATTG 57.972 50.000 0.00 0.00 34.73 2.67
2952 6832 0.904649 TCTCAGGTCCGCATGATTGT 59.095 50.000 0.00 0.00 34.73 2.71
2954 6834 1.667724 CTCAGGTCCGCATGATTGTTC 59.332 52.381 0.00 0.00 34.73 3.18
2955 6835 1.278985 TCAGGTCCGCATGATTGTTCT 59.721 47.619 0.00 0.00 29.72 3.01
2992 6907 3.430218 GCTACAGCTGTATGCCTATTTCG 59.570 47.826 26.22 11.84 44.23 3.46
3103 7018 5.642686 AGTAGTAGCGACAATCAGTTCTTC 58.357 41.667 0.00 0.00 0.00 2.87
3119 7034 1.679153 TCTTCGCACAGTGTGTAGTCA 59.321 47.619 23.73 9.35 35.75 3.41
3133 7048 6.210784 AGTGTGTAGTCAGGCTGAATACTAAA 59.789 38.462 38.71 27.14 45.16 1.85
3134 7049 6.872020 GTGTGTAGTCAGGCTGAATACTAAAA 59.128 38.462 38.71 24.93 45.16 1.52
3135 7050 7.063544 GTGTGTAGTCAGGCTGAATACTAAAAG 59.936 40.741 38.71 5.34 45.16 2.27
3136 7051 7.039293 TGTGTAGTCAGGCTGAATACTAAAAGA 60.039 37.037 38.71 24.07 45.16 2.52
3137 7052 7.489757 GTGTAGTCAGGCTGAATACTAAAAGAG 59.510 40.741 38.71 4.73 45.16 2.85
3138 7053 6.613153 AGTCAGGCTGAATACTAAAAGAGT 57.387 37.500 20.62 0.00 42.69 3.24
3139 7054 7.010339 AGTCAGGCTGAATACTAAAAGAGTT 57.990 36.000 20.62 0.00 39.81 3.01
3140 7055 7.454225 AGTCAGGCTGAATACTAAAAGAGTTT 58.546 34.615 20.62 0.00 39.81 2.66
3141 7056 7.389053 AGTCAGGCTGAATACTAAAAGAGTTTG 59.611 37.037 20.62 0.00 39.81 2.93
3142 7057 6.655003 TCAGGCTGAATACTAAAAGAGTTTGG 59.345 38.462 16.28 0.00 39.81 3.28
3143 7058 6.431234 CAGGCTGAATACTAAAAGAGTTTGGT 59.569 38.462 9.42 0.00 40.99 3.67
3144 7059 6.431234 AGGCTGAATACTAAAAGAGTTTGGTG 59.569 38.462 0.00 0.00 38.71 4.17
3145 7060 6.086871 GCTGAATACTAAAAGAGTTTGGTGC 58.913 40.000 0.00 0.00 38.71 5.01
3146 7061 6.072452 GCTGAATACTAAAAGAGTTTGGTGCT 60.072 38.462 0.00 0.00 38.71 4.40
3147 7062 7.119262 GCTGAATACTAAAAGAGTTTGGTGCTA 59.881 37.037 0.00 0.00 38.71 3.49
3148 7063 9.167311 CTGAATACTAAAAGAGTTTGGTGCTAT 57.833 33.333 0.00 0.00 38.71 2.97
3149 7064 8.946085 TGAATACTAAAAGAGTTTGGTGCTATG 58.054 33.333 0.00 0.00 38.71 2.23
3150 7065 9.162764 GAATACTAAAAGAGTTTGGTGCTATGA 57.837 33.333 0.00 0.00 38.71 2.15
3151 7066 8.723942 ATACTAAAAGAGTTTGGTGCTATGAG 57.276 34.615 0.00 0.00 38.71 2.90
3152 7067 5.940470 ACTAAAAGAGTTTGGTGCTATGAGG 59.060 40.000 0.00 0.00 37.09 3.86
3153 7068 4.373156 AAAGAGTTTGGTGCTATGAGGT 57.627 40.909 0.00 0.00 0.00 3.85
3154 7069 3.340814 AGAGTTTGGTGCTATGAGGTG 57.659 47.619 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 9.223099 CCTCCATTTCTTGATTATTTTTGCTTT 57.777 29.630 0.00 0.00 0.00 3.51
36 37 8.596293 TCCTCCATTTCTTGATTATTTTTGCTT 58.404 29.630 0.00 0.00 0.00 3.91
37 38 8.137745 TCCTCCATTTCTTGATTATTTTTGCT 57.862 30.769 0.00 0.00 0.00 3.91
38 39 8.253113 TCTCCTCCATTTCTTGATTATTTTTGC 58.747 33.333 0.00 0.00 0.00 3.68
41 42 9.312904 TGTTCTCCTCCATTTCTTGATTATTTT 57.687 29.630 0.00 0.00 0.00 1.82
42 43 8.884124 TGTTCTCCTCCATTTCTTGATTATTT 57.116 30.769 0.00 0.00 0.00 1.40
47 48 9.484806 AAAATATGTTCTCCTCCATTTCTTGAT 57.515 29.630 0.00 0.00 0.00 2.57
106 107 5.069119 CCTTCTCCAGTTTTGCCTAGTTTTT 59.931 40.000 0.00 0.00 0.00 1.94
107 108 4.584743 CCTTCTCCAGTTTTGCCTAGTTTT 59.415 41.667 0.00 0.00 0.00 2.43
108 109 4.141251 TCCTTCTCCAGTTTTGCCTAGTTT 60.141 41.667 0.00 0.00 0.00 2.66
110 111 2.979678 TCCTTCTCCAGTTTTGCCTAGT 59.020 45.455 0.00 0.00 0.00 2.57
111 112 3.703001 TCCTTCTCCAGTTTTGCCTAG 57.297 47.619 0.00 0.00 0.00 3.02
113 114 4.336280 GTTATCCTTCTCCAGTTTTGCCT 58.664 43.478 0.00 0.00 0.00 4.75
114 115 3.444034 GGTTATCCTTCTCCAGTTTTGCC 59.556 47.826 0.00 0.00 0.00 4.52
115 116 4.079253 TGGTTATCCTTCTCCAGTTTTGC 58.921 43.478 0.00 0.00 34.23 3.68
116 117 6.003950 TCTTGGTTATCCTTCTCCAGTTTTG 58.996 40.000 0.00 0.00 34.23 2.44
117 118 6.200878 TCTTGGTTATCCTTCTCCAGTTTT 57.799 37.500 0.00 0.00 34.23 2.43
118 119 5.843019 TCTTGGTTATCCTTCTCCAGTTT 57.157 39.130 0.00 0.00 34.23 2.66
119 120 5.843019 TTCTTGGTTATCCTTCTCCAGTT 57.157 39.130 0.00 0.00 34.23 3.16
120 121 5.843019 TTTCTTGGTTATCCTTCTCCAGT 57.157 39.130 0.00 0.00 34.23 4.00
121 122 6.003950 TGTTTTCTTGGTTATCCTTCTCCAG 58.996 40.000 0.00 0.00 34.23 3.86
122 123 5.947663 TGTTTTCTTGGTTATCCTTCTCCA 58.052 37.500 0.00 0.00 34.23 3.86
155 156 6.038714 GGATAGACCGAGAATTGCTTTTCAAT 59.961 38.462 0.00 0.00 46.82 2.57
156 157 5.354234 GGATAGACCGAGAATTGCTTTTCAA 59.646 40.000 0.00 0.00 39.32 2.69
157 158 4.876107 GGATAGACCGAGAATTGCTTTTCA 59.124 41.667 0.00 0.00 0.00 2.69
158 159 5.411083 GGATAGACCGAGAATTGCTTTTC 57.589 43.478 0.00 0.00 0.00 2.29
175 176 2.500098 TGTTCTCCTTTGGGTCGGATAG 59.500 50.000 0.00 0.00 0.00 2.08
178 179 1.071699 CTTGTTCTCCTTTGGGTCGGA 59.928 52.381 0.00 0.00 0.00 4.55
180 181 0.875059 GCTTGTTCTCCTTTGGGTCG 59.125 55.000 0.00 0.00 0.00 4.79
181 182 1.981256 TGCTTGTTCTCCTTTGGGTC 58.019 50.000 0.00 0.00 0.00 4.46
212 213 3.255888 TGACTACGATGAGCTTGAGTTGT 59.744 43.478 0.00 0.00 0.00 3.32
234 239 3.495331 TGCCATACACTGTTGGTTTGAT 58.505 40.909 10.33 0.00 35.34 2.57
240 245 7.750229 AATAGATAATGCCATACACTGTTGG 57.250 36.000 6.19 6.19 36.03 3.77
366 378 8.910351 ATGGATACTTTCTTCTTGGTATTAGC 57.090 34.615 0.00 0.00 37.61 3.09
389 402 9.880157 AAAGATGGAGAATATTTTTCACCAATG 57.120 29.630 9.34 0.00 41.28 2.82
480 494 7.769044 ACAACCACAGTGAGGATATACATAAAC 59.231 37.037 14.09 0.00 0.00 2.01
493 508 8.349245 TGAAATGTTTTATACAACCACAGTGAG 58.651 33.333 0.62 0.00 40.89 3.51
495 520 9.474920 AATGAAATGTTTTATACAACCACAGTG 57.525 29.630 0.00 0.00 40.89 3.66
664 689 5.127031 ACAAACAAATGTGCAGTACTTTCCT 59.873 36.000 0.00 0.00 30.82 3.36
792 838 7.365497 ACATTTCCTTCTCTTTTCATGGTTT 57.635 32.000 0.00 0.00 0.00 3.27
805 851 9.362151 TGTCCTAAACAAAATACATTTCCTTCT 57.638 29.630 0.00 0.00 34.03 2.85
816 862 8.770010 TTTCTTCCCTTGTCCTAAACAAAATA 57.230 30.769 0.00 0.00 46.95 1.40
828 874 4.142600 CGTCATCCATTTTCTTCCCTTGTC 60.143 45.833 0.00 0.00 0.00 3.18
843 889 1.681780 GGGCTCCATTTTCGTCATCCA 60.682 52.381 0.00 0.00 0.00 3.41
844 890 1.025041 GGGCTCCATTTTCGTCATCC 58.975 55.000 0.00 0.00 0.00 3.51
846 892 2.442236 ATGGGCTCCATTTTCGTCAT 57.558 45.000 1.21 0.00 42.23 3.06
856 902 2.577563 TCAGAATTCAGAATGGGCTCCA 59.422 45.455 8.44 0.00 38.19 3.86
857 903 3.287867 TCAGAATTCAGAATGGGCTCC 57.712 47.619 8.44 0.00 36.16 4.70
858 904 6.238869 GGTTAATCAGAATTCAGAATGGGCTC 60.239 42.308 8.44 0.00 36.16 4.70
860 906 5.360714 TGGTTAATCAGAATTCAGAATGGGC 59.639 40.000 8.44 0.00 36.16 5.36
861 907 6.458751 CGTGGTTAATCAGAATTCAGAATGGG 60.459 42.308 8.44 0.00 36.16 4.00
862 908 6.489675 CGTGGTTAATCAGAATTCAGAATGG 58.510 40.000 8.44 0.00 36.16 3.16
863 909 5.967674 GCGTGGTTAATCAGAATTCAGAATG 59.032 40.000 8.44 0.00 37.54 2.67
864 910 5.220662 CGCGTGGTTAATCAGAATTCAGAAT 60.221 40.000 8.44 0.61 0.00 2.40
869 915 3.541516 CGTCGCGTGGTTAATCAGAATTC 60.542 47.826 5.77 0.00 0.00 2.17
871 917 1.924524 CGTCGCGTGGTTAATCAGAAT 59.075 47.619 5.77 0.00 0.00 2.40
872 918 1.342555 CGTCGCGTGGTTAATCAGAA 58.657 50.000 5.77 0.00 0.00 3.02
874 920 1.343821 GCGTCGCGTGGTTAATCAG 59.656 57.895 5.77 0.00 0.00 2.90
875 921 3.465753 GCGTCGCGTGGTTAATCA 58.534 55.556 5.77 0.00 0.00 2.57
888 934 4.863925 GCTCTCCCTCTGCGCGTC 62.864 72.222 8.43 0.00 0.00 5.19
890 936 4.869440 CAGCTCTCCCTCTGCGCG 62.869 72.222 0.00 0.00 0.00 6.86
895 941 1.913722 CAATGGCAGCTCTCCCTCT 59.086 57.895 0.00 0.00 0.00 3.69
896 942 1.823041 GCAATGGCAGCTCTCCCTC 60.823 63.158 0.00 0.00 40.72 4.30
897 943 2.274760 GCAATGGCAGCTCTCCCT 59.725 61.111 0.00 0.00 40.72 4.20
913 959 2.099592 TCTCCGATGGATTGCAATTTGC 59.900 45.455 14.33 14.49 45.29 3.68
914 960 4.277672 AGATCTCCGATGGATTGCAATTTG 59.722 41.667 14.33 1.53 0.00 2.32
915 961 4.467769 AGATCTCCGATGGATTGCAATTT 58.532 39.130 14.33 1.65 0.00 1.82
932 978 1.472082 CGGCGATGCAGAGATAGATCT 59.528 52.381 0.00 0.00 40.50 2.75
933 979 1.906757 CGGCGATGCAGAGATAGATC 58.093 55.000 0.00 0.00 0.00 2.75
936 982 1.735920 GGCGGCGATGCAGAGATAG 60.736 63.158 12.98 0.00 36.28 2.08
937 983 2.340078 GGCGGCGATGCAGAGATA 59.660 61.111 12.98 0.00 36.28 1.98
1035 4601 0.489567 AGGTGGAGGGTGAAGAGAGT 59.510 55.000 0.00 0.00 0.00 3.24
1042 4608 2.607750 GCTGGAGGTGGAGGGTGA 60.608 66.667 0.00 0.00 0.00 4.02
1043 4609 2.608988 AGCTGGAGGTGGAGGGTG 60.609 66.667 0.00 0.00 0.00 4.61
1044 4610 2.284995 GAGCTGGAGGTGGAGGGT 60.285 66.667 0.00 0.00 0.00 4.34
1045 4611 2.040278 AGAGCTGGAGGTGGAGGG 59.960 66.667 0.00 0.00 0.00 4.30
1046 4612 3.028921 GCAGAGCTGGAGGTGGAGG 62.029 68.421 0.00 0.00 0.00 4.30
1047 4613 2.583520 GCAGAGCTGGAGGTGGAG 59.416 66.667 0.00 0.00 0.00 3.86
1058 4636 0.463474 GAGTGGGAAGATGGCAGAGC 60.463 60.000 0.00 0.00 0.00 4.09
1184 4789 1.270907 GAGGTGGGAGAGCTTCTTGA 58.729 55.000 0.00 0.00 30.42 3.02
1285 4890 0.693049 AGGAACAGCGGATCTTTGGT 59.307 50.000 0.00 0.00 0.00 3.67
1314 4919 1.745890 GGCCAAGGTTTTGTCCACC 59.254 57.895 0.00 0.00 32.58 4.61
1334 4940 1.139095 GTGAGCCCGACGACCTTAG 59.861 63.158 0.00 0.00 0.00 2.18
1384 4990 2.680352 GGTGAGGGAGACGAGGCA 60.680 66.667 0.00 0.00 0.00 4.75
1662 5272 1.070957 GGGCACGCCTATACCTTCC 59.929 63.158 8.20 0.00 36.10 3.46
1712 5325 0.387239 GGTTTGGAATGTGACAGCGC 60.387 55.000 0.00 0.00 0.00 5.92
1720 5333 4.453480 TCTTCTCCTTGGTTTGGAATGT 57.547 40.909 0.00 0.00 32.61 2.71
1730 5343 1.379642 GGCGGCAATCTTCTCCTTGG 61.380 60.000 3.07 0.00 0.00 3.61
1753 5366 3.521727 AGGTGGTCTTCAAGTACTCCAT 58.478 45.455 0.00 0.00 0.00 3.41
1924 5537 2.639839 GGCCCTCCATGCTATAAGAGAA 59.360 50.000 0.00 0.00 0.00 2.87
1948 5561 5.962031 TGATAACATAGTACCTGGGTCTGTT 59.038 40.000 0.00 5.59 0.00 3.16
1949 5562 5.525484 TGATAACATAGTACCTGGGTCTGT 58.475 41.667 0.00 0.00 0.00 3.41
2149 5762 5.437060 TCCATAGCCCTTCTTTGTTCATAC 58.563 41.667 0.00 0.00 0.00 2.39
2195 5812 2.094675 CAGGCAGGGTGATAACTTTGG 58.905 52.381 0.00 0.00 0.00 3.28
2288 5933 7.173218 GGCATTTAGCAATGACTAACTAGCATA 59.827 37.037 1.12 0.00 44.30 3.14
2314 5959 8.896744 TCAAATTATCAGTTTCATAAGGAGCTG 58.103 33.333 0.00 0.00 34.00 4.24
2439 6198 3.255725 CCACACATCCAAATTGCATGAC 58.744 45.455 3.61 0.00 0.00 3.06
2448 6207 1.426983 TGATCCACCCACACATCCAAA 59.573 47.619 0.00 0.00 0.00 3.28
2480 6299 0.603065 GGTTTCATGGGTGCTGGTTC 59.397 55.000 0.00 0.00 0.00 3.62
2508 6365 9.774742 GTGGAAAATGACACATTATTAGTCTTC 57.225 33.333 0.00 0.00 37.54 2.87
2518 6375 6.819284 ACATTTCAGTGGAAAATGACACATT 58.181 32.000 19.00 0.00 45.52 2.71
2588 6460 9.859427 CATCTTAACCATTAATTTTGCTCAAGA 57.141 29.630 0.00 0.00 0.00 3.02
2669 6543 8.619546 GGTCCATCTTCTTTTATTTGAGAGATG 58.380 37.037 0.00 0.00 32.93 2.90
2671 6545 7.112779 GGGTCCATCTTCTTTTATTTGAGAGA 58.887 38.462 0.00 0.00 0.00 3.10
2672 6546 6.886459 TGGGTCCATCTTCTTTTATTTGAGAG 59.114 38.462 0.00 0.00 0.00 3.20
2798 6675 0.327924 TCAACCCATCTGCGGTCATT 59.672 50.000 0.00 0.00 31.48 2.57
2804 6681 1.608590 ACAAAACTCAACCCATCTGCG 59.391 47.619 0.00 0.00 0.00 5.18
2905 6785 5.421056 ACACCTCTCACCTTAATCATACGAA 59.579 40.000 0.00 0.00 0.00 3.85
2907 6787 5.043903 CACACCTCTCACCTTAATCATACG 58.956 45.833 0.00 0.00 0.00 3.06
2908 6788 5.978814 ACACACCTCTCACCTTAATCATAC 58.021 41.667 0.00 0.00 0.00 2.39
2924 6804 0.393077 CGGACCTGAGAAACACACCT 59.607 55.000 0.00 0.00 0.00 4.00
2941 6821 1.402968 CCAAGGAGAACAATCATGCGG 59.597 52.381 0.00 0.00 0.00 5.69
2942 6822 1.402968 CCCAAGGAGAACAATCATGCG 59.597 52.381 0.00 0.00 0.00 4.73
2943 6823 1.135721 GCCCAAGGAGAACAATCATGC 59.864 52.381 0.00 0.00 0.00 4.06
2944 6824 2.449464 TGCCCAAGGAGAACAATCATG 58.551 47.619 0.00 0.00 0.00 3.07
2945 6825 2.905415 TGCCCAAGGAGAACAATCAT 57.095 45.000 0.00 0.00 0.00 2.45
2946 6826 2.517959 CTTGCCCAAGGAGAACAATCA 58.482 47.619 0.06 0.00 34.87 2.57
3103 7018 1.284982 GCCTGACTACACACTGTGCG 61.285 60.000 9.20 0.04 36.98 5.34
3105 7020 1.341209 TCAGCCTGACTACACACTGTG 59.659 52.381 7.68 7.68 39.75 3.66
3119 7034 6.431234 CACCAAACTCTTTTAGTATTCAGCCT 59.569 38.462 0.00 0.00 37.50 4.58
3133 7048 3.679389 CACCTCATAGCACCAAACTCTT 58.321 45.455 0.00 0.00 0.00 2.85
3134 7049 3.340814 CACCTCATAGCACCAAACTCT 57.659 47.619 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.