Multiple sequence alignment - TraesCS3A01G064600

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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 TraesCS3A01G064600 chr3A 100.000 3354 0 0 1 3354 38282924 38279571 0.000000e+00 6194.0
1 TraesCS3A01G064600 chr3A 96.397 1249 37 2 1302 2546 38300575 38301819 0.000000e+00 2050.0
2 TraesCS3A01G064600 chr3A 87.295 244 20 4 3103 3339 38303091 38303330 5.520000e-68 268.0
3 TraesCS3A01G064600 chr3D 91.364 1378 78 17 1207 2554 28547917 28546551 0.000000e+00 1847.0
4 TraesCS3A01G064600 chr3D 90.328 1251 93 10 1263 2499 28944485 28945721 0.000000e+00 1615.0
5 TraesCS3A01G064600 chr3D 89.521 1231 70 22 1232 2437 28592230 28591034 0.000000e+00 1504.0
6 TraesCS3A01G064600 chr3D 87.417 755 57 14 102 841 28549045 28548314 0.000000e+00 833.0
7 TraesCS3A01G064600 chr3D 86.183 731 54 14 2655 3354 28520625 28519911 0.000000e+00 747.0
8 TraesCS3A01G064600 chr3D 87.130 676 49 18 173 837 28869192 28868544 0.000000e+00 732.0
9 TraesCS3A01G064600 chr3D 91.245 514 45 0 1338 1851 28864700 28864187 0.000000e+00 701.0
10 TraesCS3A01G064600 chr3D 86.522 460 28 11 2889 3319 28519224 28518770 3.030000e-130 475.0
11 TraesCS3A01G064600 chr3D 85.350 314 31 9 230 531 28593020 28592710 9.040000e-81 311.0
12 TraesCS3A01G064600 chr3D 86.640 247 19 4 3108 3354 28584575 28584343 9.230000e-66 261.0
13 TraesCS3A01G064600 chr3D 84.058 207 18 7 844 1042 28548263 28548064 5.710000e-43 185.0
14 TraesCS3A01G064600 chr3D 82.627 236 16 12 932 1158 28867066 28866847 5.710000e-43 185.0
15 TraesCS3A01G064600 chr3D 83.938 193 17 8 848 1028 28592476 28592286 4.450000e-39 172.0
16 TraesCS3A01G064600 chr3D 80.749 187 21 10 848 1028 28944215 28944392 7.550000e-27 132.0
17 TraesCS3A01G064600 chr3D 97.059 68 1 1 603 669 28736303 28736236 2.740000e-21 113.0
18 TraesCS3A01G064600 chr3D 96.364 55 2 0 29 83 28584148 28584202 1.280000e-14 91.6
19 TraesCS3A01G064600 chr3B 89.485 1398 87 27 1197 2554 49152003 49153380 0.000000e+00 1712.0
20 TraesCS3A01G064600 chr3B 88.691 1291 111 15 1611 2872 47476655 47475371 0.000000e+00 1543.0
21 TraesCS3A01G064600 chr3B 89.173 859 55 13 1677 2502 47742097 47741244 0.000000e+00 1037.0
22 TraesCS3A01G064600 chr3B 88.359 859 62 13 1677 2502 48079293 48078440 0.000000e+00 998.0
23 TraesCS3A01G064600 chr3B 84.191 1088 74 48 3 1018 47544097 47543036 0.000000e+00 966.0
24 TraesCS3A01G064600 chr3B 86.826 797 71 13 2589 3354 48071834 48071041 0.000000e+00 859.0
25 TraesCS3A01G064600 chr3B 86.700 797 72 13 2589 3354 47802391 47801598 0.000000e+00 854.0
26 TraesCS3A01G064600 chr3B 86.683 796 74 13 2589 3354 47855972 47855179 0.000000e+00 854.0
27 TraesCS3A01G064600 chr3B 86.700 797 72 10 2589 3354 48134288 48133495 0.000000e+00 854.0
28 TraesCS3A01G064600 chr3B 86.575 797 73 13 2589 3354 47734840 47734047 0.000000e+00 848.0
29 TraesCS3A01G064600 chr3B 86.430 759 57 23 102 846 49151109 49151835 0.000000e+00 789.0
30 TraesCS3A01G064600 chr3B 87.736 424 40 8 1258 1675 47864523 47864106 5.030000e-133 484.0
31 TraesCS3A01G064600 chr3B 87.736 424 40 8 1258 1675 48080101 48079684 5.030000e-133 484.0
32 TraesCS3A01G064600 chr3B 87.500 424 41 8 1258 1675 47742878 47742461 2.340000e-131 479.0
33 TraesCS3A01G064600 chr3B 83.551 383 48 11 102 473 47745844 47745466 8.910000e-91 344.0
34 TraesCS3A01G064600 chr3B 83.551 383 48 11 102 473 47867177 47866799 8.910000e-91 344.0
35 TraesCS3A01G064600 chr3B 83.029 383 50 11 102 473 47813599 47813221 1.930000e-87 333.0
36 TraesCS3A01G064600 chr3B 82.507 383 52 11 102 473 48083113 48082735 4.170000e-84 322.0
37 TraesCS3A01G064600 chr3B 84.375 256 29 3 102 350 47605795 47605544 1.200000e-59 241.0
38 TraesCS3A01G064600 chr3B 87.500 200 18 5 468 663 47812745 47812549 1.210000e-54 224.0
39 TraesCS3A01G064600 chr3B 82.397 267 25 5 3110 3354 49154581 49154847 2.620000e-51 213.0
40 TraesCS3A01G064600 chr3B 86.432 199 20 5 469 663 47866638 47866443 9.430000e-51 211.0
41 TraesCS3A01G064600 chr3B 92.771 83 5 1 1 83 49155067 49154986 5.880000e-23 119.0
42 TraesCS3A01G064600 chr6B 92.105 1064 61 8 1302 2364 131693925 131694966 0.000000e+00 1478.0
43 TraesCS3A01G064600 chr6B 87.908 306 30 5 230 531 131691834 131692136 1.480000e-93 353.0
44 TraesCS3A01G064600 chr6B 86.053 337 23 4 2237 2551 131719616 131719950 1.150000e-89 340.0
45 TraesCS3A01G064600 chr5B 80.263 152 24 5 2889 3037 45641587 45641735 3.540000e-20 110.0
46 TraesCS3A01G064600 chr7D 81.618 136 15 7 2881 3012 120272819 120272690 1.650000e-18 104.0


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 TraesCS3A01G064600 chr3A 38279571 38282924 3353 True 6194.000000 6194 100.000000 1 3354 1 chr3A.!!$R1 3353
1 TraesCS3A01G064600 chr3A 38300575 38303330 2755 False 1159.000000 2050 91.846000 1302 3339 2 chr3A.!!$F1 2037
2 TraesCS3A01G064600 chr3D 28546551 28549045 2494 True 955.000000 1847 87.613000 102 2554 3 chr3D.!!$R4 2452
3 TraesCS3A01G064600 chr3D 28944215 28945721 1506 False 873.500000 1615 85.538500 848 2499 2 chr3D.!!$F2 1651
4 TraesCS3A01G064600 chr3D 28591034 28593020 1986 True 662.333333 1504 86.269667 230 2437 3 chr3D.!!$R5 2207
5 TraesCS3A01G064600 chr3D 28518770 28520625 1855 True 611.000000 747 86.352500 2655 3354 2 chr3D.!!$R3 699
6 TraesCS3A01G064600 chr3D 28864187 28869192 5005 True 539.333333 732 87.000667 173 1851 3 chr3D.!!$R6 1678
7 TraesCS3A01G064600 chr3B 47475371 47476655 1284 True 1543.000000 1543 88.691000 1611 2872 1 chr3B.!!$R1 1261
8 TraesCS3A01G064600 chr3B 47543036 47544097 1061 True 966.000000 966 84.191000 3 1018 1 chr3B.!!$R2 1015
9 TraesCS3A01G064600 chr3B 49151109 49154847 3738 False 904.666667 1712 86.104000 102 3354 3 chr3B.!!$F1 3252
10 TraesCS3A01G064600 chr3B 48071041 48071834 793 True 859.000000 859 86.826000 2589 3354 1 chr3B.!!$R7 765
11 TraesCS3A01G064600 chr3B 47801598 47802391 793 True 854.000000 854 86.700000 2589 3354 1 chr3B.!!$R5 765
12 TraesCS3A01G064600 chr3B 47855179 47855972 793 True 854.000000 854 86.683000 2589 3354 1 chr3B.!!$R6 765
13 TraesCS3A01G064600 chr3B 48133495 48134288 793 True 854.000000 854 86.700000 2589 3354 1 chr3B.!!$R8 765
14 TraesCS3A01G064600 chr3B 47734047 47734840 793 True 848.000000 848 86.575000 2589 3354 1 chr3B.!!$R4 765
15 TraesCS3A01G064600 chr3B 47741244 47745844 4600 True 620.000000 1037 86.741333 102 2502 3 chr3B.!!$R10 2400
16 TraesCS3A01G064600 chr3B 48078440 48083113 4673 True 601.333333 998 86.200667 102 2502 3 chr3B.!!$R13 2400
17 TraesCS3A01G064600 chr3B 47864106 47867177 3071 True 346.333333 484 85.906333 102 1675 3 chr3B.!!$R12 1573
18 TraesCS3A01G064600 chr3B 47812549 47813599 1050 True 278.500000 333 85.264500 102 663 2 chr3B.!!$R11 561
19 TraesCS3A01G064600 chr6B 131691834 131694966 3132 False 915.500000 1478 90.006500 230 2364 2 chr6B.!!$F2 2134

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
99 100 0.036105 TCACATGCCAATCAGAGCGT 60.036 50.0 0.0 0.0 0.0 5.07 F
929 4373 0.392595 CTCCGTTTCTTACAGCCCCC 60.393 60.0 0.0 0.0 0.0 5.40 F
1251 6350 0.790495 CACATTGCACGATCACACGC 60.790 55.0 0.0 0.0 36.7 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 9387 1.069765 CTTCATCAGCGGCGGGTAT 59.930 57.895 9.78 0.0 0.0 2.73 R
2122 9486 0.034767 AGTCGTCGTAGGGGTGATGA 60.035 55.000 0.00 0.0 0.0 2.92 R
2635 10552 0.393402 TAACTCGTCTCCGCCAGCTA 60.393 55.000 0.00 0.0 0.0 3.32 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.442513 AGCATAACATAAAGCTCAGTTTCC 57.557 37.500 0.00 0.00 30.05 3.13
38 39 2.423185 TCAGTTTCCAGTTGTTGTGCTG 59.577 45.455 0.00 0.00 0.00 4.41
49 50 4.644685 AGTTGTTGTGCTGGACTGTAAAAT 59.355 37.500 0.00 0.00 0.00 1.82
57 58 4.404073 TGCTGGACTGTAAAATTGTGGTTT 59.596 37.500 0.00 0.00 0.00 3.27
89 90 7.289549 TGGGATCAATAATAATTTCACATGCCA 59.710 33.333 0.00 0.00 0.00 4.92
90 91 8.149647 GGGATCAATAATAATTTCACATGCCAA 58.850 33.333 0.00 0.00 0.00 4.52
91 92 9.715121 GGATCAATAATAATTTCACATGCCAAT 57.285 29.630 0.00 0.00 0.00 3.16
94 95 9.752961 TCAATAATAATTTCACATGCCAATCAG 57.247 29.630 0.00 0.00 0.00 2.90
95 96 9.752961 CAATAATAATTTCACATGCCAATCAGA 57.247 29.630 0.00 0.00 0.00 3.27
96 97 9.976511 AATAATAATTTCACATGCCAATCAGAG 57.023 29.630 0.00 0.00 0.00 3.35
97 98 3.795623 ATTTCACATGCCAATCAGAGC 57.204 42.857 0.00 0.00 0.00 4.09
98 99 1.089112 TTCACATGCCAATCAGAGCG 58.911 50.000 0.00 0.00 0.00 5.03
99 100 0.036105 TCACATGCCAATCAGAGCGT 60.036 50.000 0.00 0.00 0.00 5.07
100 101 0.806868 CACATGCCAATCAGAGCGTT 59.193 50.000 0.00 0.00 0.00 4.84
132 133 2.496899 ATTTTCTCCATCGTGCACCT 57.503 45.000 12.15 0.00 0.00 4.00
138 139 0.901827 TCCATCGTGCACCTGTATGT 59.098 50.000 12.15 0.00 0.00 2.29
145 146 2.404215 GTGCACCTGTATGTATAGGCG 58.596 52.381 5.22 0.00 38.04 5.52
150 151 4.799586 GCACCTGTATGTATAGGCGAATGT 60.800 45.833 3.06 0.00 38.04 2.71
151 152 5.297547 CACCTGTATGTATAGGCGAATGTT 58.702 41.667 3.06 0.00 38.04 2.71
152 153 5.758296 CACCTGTATGTATAGGCGAATGTTT 59.242 40.000 3.06 0.00 38.04 2.83
153 154 6.260050 CACCTGTATGTATAGGCGAATGTTTT 59.740 38.462 3.06 0.00 38.04 2.43
206 232 2.438763 AGCTTTGGAGAGATCCATCCAG 59.561 50.000 14.36 7.38 46.01 3.86
304 341 1.002544 CAGAACCAGGACCAGGAGAAC 59.997 57.143 10.44 0.00 0.00 3.01
331 372 1.075536 AGGACATCTCCCAACCCAAAC 59.924 52.381 0.00 0.00 37.25 2.93
391 439 3.536917 CCATCACCCGGCGCTCTA 61.537 66.667 7.64 0.00 0.00 2.43
523 1375 4.104183 TCCGGCCGGAATCCCAAC 62.104 66.667 43.93 0.00 42.05 3.77
596 1455 4.448537 TGCCTTTTCAAACCGGATATTG 57.551 40.909 9.46 10.80 0.00 1.90
748 4119 7.559335 AGTATCCTGAACCATGAATATGCTA 57.441 36.000 0.00 0.00 32.79 3.49
749 4120 7.619050 AGTATCCTGAACCATGAATATGCTAG 58.381 38.462 0.00 0.00 32.79 3.42
750 4121 4.645535 TCCTGAACCATGAATATGCTAGC 58.354 43.478 8.10 8.10 32.79 3.42
751 4122 4.349048 TCCTGAACCATGAATATGCTAGCT 59.651 41.667 17.23 4.07 32.79 3.32
881 4308 1.876156 GTCAGGAATCGAATGCCATCC 59.124 52.381 0.00 0.00 0.00 3.51
882 4309 0.870393 CAGGAATCGAATGCCATCCG 59.130 55.000 0.00 0.00 35.31 4.18
883 4310 0.469917 AGGAATCGAATGCCATCCGT 59.530 50.000 0.00 0.00 35.31 4.69
884 4311 1.134098 AGGAATCGAATGCCATCCGTT 60.134 47.619 0.00 0.00 35.31 4.44
885 4312 1.676006 GGAATCGAATGCCATCCGTTT 59.324 47.619 0.00 0.00 0.00 3.60
929 4373 0.392595 CTCCGTTTCTTACAGCCCCC 60.393 60.000 0.00 0.00 0.00 5.40
930 4374 1.743995 CCGTTTCTTACAGCCCCCG 60.744 63.158 0.00 0.00 0.00 5.73
931 4375 2.396157 CGTTTCTTACAGCCCCCGC 61.396 63.158 0.00 0.00 0.00 6.13
942 5735 4.924187 CCCCCGCCAACCAACCAA 62.924 66.667 0.00 0.00 0.00 3.67
946 5739 2.027460 CGCCAACCAACCAAGCAC 59.973 61.111 0.00 0.00 0.00 4.40
947 5740 2.780094 CGCCAACCAACCAAGCACA 61.780 57.895 0.00 0.00 0.00 4.57
948 5741 1.519719 GCCAACCAACCAAGCACAA 59.480 52.632 0.00 0.00 0.00 3.33
949 5742 0.809636 GCCAACCAACCAAGCACAAC 60.810 55.000 0.00 0.00 0.00 3.32
954 5767 2.577700 ACCAACCAAGCACAACGATTA 58.422 42.857 0.00 0.00 0.00 1.75
960 5773 2.235536 AAGCACAACGATTACCGCGC 62.236 55.000 0.00 0.00 43.32 6.86
985 5802 2.636830 GCACTTGCATAGGTGACTCAT 58.363 47.619 15.84 0.00 40.88 2.90
986 5803 3.797039 GCACTTGCATAGGTGACTCATA 58.203 45.455 15.84 0.00 40.88 2.15
987 5804 4.384056 GCACTTGCATAGGTGACTCATAT 58.616 43.478 15.84 0.00 40.88 1.78
988 5805 5.541845 GCACTTGCATAGGTGACTCATATA 58.458 41.667 15.84 0.00 40.88 0.86
994 5811 8.650143 TTGCATAGGTGACTCATATATACTGA 57.350 34.615 0.00 0.00 43.67 3.41
999 5816 6.296803 AGGTGACTCATATATACTGACGACA 58.703 40.000 0.00 0.00 32.90 4.35
1045 5869 4.783621 GCATGCCCACTGCTCCGA 62.784 66.667 6.36 0.00 42.00 4.55
1046 5870 2.191375 CATGCCCACTGCTCCGAT 59.809 61.111 0.00 0.00 42.00 4.18
1082 5908 4.886247 CCATGCTTGGCCATTTTTAATG 57.114 40.909 6.09 5.36 35.85 1.90
1083 5909 3.065648 CCATGCTTGGCCATTTTTAATGC 59.934 43.478 6.09 1.98 35.85 3.56
1084 5910 3.413846 TGCTTGGCCATTTTTAATGCA 57.586 38.095 6.09 4.73 0.00 3.96
1085 5911 3.952931 TGCTTGGCCATTTTTAATGCAT 58.047 36.364 6.09 0.00 0.00 3.96
1086 5912 3.690139 TGCTTGGCCATTTTTAATGCATG 59.310 39.130 6.09 0.00 0.00 4.06
1089 5915 5.335819 GCTTGGCCATTTTTAATGCATGTTT 60.336 36.000 6.09 0.00 0.00 2.83
1090 5916 6.645790 TTGGCCATTTTTAATGCATGTTTT 57.354 29.167 6.09 0.00 0.00 2.43
1091 5917 6.251655 TGGCCATTTTTAATGCATGTTTTC 57.748 33.333 0.00 0.00 0.00 2.29
1158 5984 3.853671 GTGCGTTTCTATGAAATGGCAAG 59.146 43.478 16.95 0.00 0.00 4.01
1159 5985 3.505680 TGCGTTTCTATGAAATGGCAAGT 59.494 39.130 14.59 0.00 0.00 3.16
1163 5989 6.148948 CGTTTCTATGAAATGGCAAGTTGAA 58.851 36.000 7.16 0.00 0.00 2.69
1166 5992 8.992073 GTTTCTATGAAATGGCAAGTTGAAAAT 58.008 29.630 7.16 0.00 0.00 1.82
1170 5996 6.998968 TGAAATGGCAAGTTGAAAATTTGT 57.001 29.167 7.16 0.00 44.33 2.83
1172 6049 6.373774 TGAAATGGCAAGTTGAAAATTTGTGT 59.626 30.769 7.16 0.00 44.33 3.72
1177 6054 4.259770 GCAAGTTGAAAATTTGTGTGTCCG 60.260 41.667 7.16 0.00 44.33 4.79
1179 6056 5.821516 AGTTGAAAATTTGTGTGTCCGTA 57.178 34.783 0.00 0.00 0.00 4.02
1251 6350 0.790495 CACATTGCACGATCACACGC 60.790 55.000 0.00 0.00 36.70 5.34
1260 6370 3.547413 GCACGATCACACGCACTACTATA 60.547 47.826 0.00 0.00 36.70 1.31
1279 6393 6.220930 ACTATACGTTTTCTTCTTGCTGACA 58.779 36.000 0.00 0.00 0.00 3.58
1298 6422 2.290896 ACAATCGAGGAATTCTTGGGCA 60.291 45.455 5.23 0.00 0.00 5.36
1299 6423 2.754552 CAATCGAGGAATTCTTGGGCAA 59.245 45.455 5.23 0.00 0.00 4.52
2122 9486 3.161450 ATACAGACCGGCGGCCAT 61.161 61.111 28.71 10.34 0.00 4.40
2464 9871 5.121105 GGATAGTTGCCGTACCTTACAATT 58.879 41.667 0.00 0.00 0.00 2.32
2471 9880 2.093152 CCGTACCTTACAATTGACGTGC 59.907 50.000 13.59 4.95 0.00 5.34
2489 9898 3.124466 CGTGCTGGTCGAATAAATCACAA 59.876 43.478 0.00 0.00 0.00 3.33
2559 10476 1.339610 CGATTTTGTTTGGGAGGCACA 59.660 47.619 0.00 0.00 0.00 4.57
2635 10552 2.288886 GCTTCGGCTAGGAATAATCCGT 60.289 50.000 3.19 0.00 43.55 4.69
2673 10699 5.079643 AGTTAGAAGGTTAACGGGTGTAGA 58.920 41.667 0.00 0.00 38.32 2.59
2675 10701 6.891908 AGTTAGAAGGTTAACGGGTGTAGATA 59.108 38.462 0.00 0.00 38.32 1.98
2709 11525 1.617947 ATCAGAACTGGAGGTCGGCC 61.618 60.000 0.00 0.00 0.00 6.13
2799 11616 8.539770 TTGAACTTTTAAAAATCAGTGTGCAA 57.460 26.923 12.99 9.40 0.00 4.08
2815 11638 8.367911 TCAGTGTGCAATATATTACCCTAAGAG 58.632 37.037 0.00 0.00 0.00 2.85
2816 11639 7.118390 CAGTGTGCAATATATTACCCTAAGAGC 59.882 40.741 0.00 0.00 0.00 4.09
2817 11640 6.371825 GTGTGCAATATATTACCCTAAGAGCC 59.628 42.308 0.00 0.00 0.00 4.70
2818 11641 5.880887 GTGCAATATATTACCCTAAGAGCCC 59.119 44.000 0.00 0.00 0.00 5.19
2865 11702 4.495422 TCTTTTAGCTTCGACATGTCTCC 58.505 43.478 22.95 8.69 0.00 3.71
2967 11804 7.348274 TCTGGGTCATTAGATTAAGATCCAACT 59.652 37.037 0.00 0.00 40.51 3.16
3038 11879 4.894784 TCTTCTGCAAAATCGACTTACCT 58.105 39.130 0.00 0.00 0.00 3.08
3043 11884 7.072177 TCTGCAAAATCGACTTACCTAAATG 57.928 36.000 0.00 0.00 0.00 2.32
3048 11889 7.968405 GCAAAATCGACTTACCTAAATGACAAT 59.032 33.333 0.00 0.00 0.00 2.71
3052 11893 9.449719 AATCGACTTACCTAAATGACAATTTCT 57.550 29.630 0.00 0.00 37.23 2.52
3162 12241 0.249197 TCCGAGAGATCTGCATTGCG 60.249 55.000 0.00 0.00 0.00 4.85
3292 12384 5.734720 TCATCATCCACCTTCTTGTAAGAC 58.265 41.667 0.00 0.00 34.13 3.01
3294 12386 3.263425 TCATCCACCTTCTTGTAAGACCC 59.737 47.826 0.00 0.00 34.13 4.46
3342 12442 7.171678 GGAGCTGATGTAATATTGTAACCTGAC 59.828 40.741 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.749118 GGAAACTGAGCTTTATGTTATGCTTG 59.251 38.462 0.00 0.00 35.76 4.01
1 2 6.434028 TGGAAACTGAGCTTTATGTTATGCTT 59.566 34.615 0.00 0.00 35.76 3.91
10 11 5.594317 ACAACAACTGGAAACTGAGCTTTAT 59.406 36.000 0.00 0.00 0.00 1.40
25 26 1.382522 ACAGTCCAGCACAACAACTG 58.617 50.000 0.00 0.00 42.33 3.16
38 39 9.139174 CATAATCAAACCACAATTTTACAGTCC 57.861 33.333 0.00 0.00 0.00 3.85
49 50 8.601047 TTATTGATCCCATAATCAAACCACAA 57.399 30.769 3.66 0.00 45.91 3.33
80 81 0.036105 ACGCTCTGATTGGCATGTGA 60.036 50.000 0.00 0.00 0.00 3.58
83 84 0.027194 CGAACGCTCTGATTGGCATG 59.973 55.000 0.00 0.00 0.00 4.06
84 85 0.108186 TCGAACGCTCTGATTGGCAT 60.108 50.000 0.00 0.00 0.00 4.40
85 86 0.320334 TTCGAACGCTCTGATTGGCA 60.320 50.000 0.00 0.00 0.00 4.92
86 87 0.371645 CTTCGAACGCTCTGATTGGC 59.628 55.000 0.00 0.00 0.00 4.52
87 88 1.996292 TCTTCGAACGCTCTGATTGG 58.004 50.000 0.00 0.00 0.00 3.16
89 90 2.926200 CACATCTTCGAACGCTCTGATT 59.074 45.455 0.00 0.00 0.00 2.57
90 91 2.534298 CACATCTTCGAACGCTCTGAT 58.466 47.619 0.00 0.00 0.00 2.90
91 92 1.982612 CACATCTTCGAACGCTCTGA 58.017 50.000 0.00 0.00 0.00 3.27
92 93 0.368227 GCACATCTTCGAACGCTCTG 59.632 55.000 0.00 0.00 0.00 3.35
93 94 0.244994 AGCACATCTTCGAACGCTCT 59.755 50.000 0.00 0.00 0.00 4.09
94 95 1.909376 TAGCACATCTTCGAACGCTC 58.091 50.000 0.00 0.00 0.00 5.03
95 96 2.586258 ATAGCACATCTTCGAACGCT 57.414 45.000 0.00 0.22 0.00 5.07
96 97 3.658351 AAATAGCACATCTTCGAACGC 57.342 42.857 0.00 0.00 0.00 4.84
97 98 5.456192 AGAAAATAGCACATCTTCGAACG 57.544 39.130 0.00 0.00 0.00 3.95
98 99 5.351465 TGGAGAAAATAGCACATCTTCGAAC 59.649 40.000 0.00 0.00 0.00 3.95
99 100 5.487433 TGGAGAAAATAGCACATCTTCGAA 58.513 37.500 0.00 0.00 0.00 3.71
100 101 5.084818 TGGAGAAAATAGCACATCTTCGA 57.915 39.130 0.00 0.00 0.00 3.71
168 194 5.953183 CAAAGCTAAGTTTGGCATATCACA 58.047 37.500 3.06 0.00 37.10 3.58
193 219 1.898472 CGGCATACTGGATGGATCTCT 59.102 52.381 1.35 0.00 35.91 3.10
206 232 3.546002 TTTGTGCTACAAACGGCATAC 57.454 42.857 9.46 0.00 42.55 2.39
331 372 7.204290 TGGGAACATACCATCTCTAGATGAGG 61.204 46.154 19.30 7.93 44.80 3.86
411 459 5.050972 CGTCTTATATTGGCTCCGTCTTTTC 60.051 44.000 0.00 0.00 0.00 2.29
523 1375 2.461110 CGCGGACGGAAAGATTGGG 61.461 63.158 0.00 0.00 34.97 4.12
596 1455 7.517614 TGATGAGAATAGATACTCTGGTCAC 57.482 40.000 0.00 0.00 34.65 3.67
748 4119 0.038744 ATGCAAAGGTGGTAGCAGCT 59.961 50.000 20.35 20.35 40.71 4.24
749 4120 0.453390 GATGCAAAGGTGGTAGCAGC 59.547 55.000 16.07 16.07 40.71 5.25
750 4121 1.098050 GGATGCAAAGGTGGTAGCAG 58.902 55.000 0.00 0.00 40.71 4.24
751 4122 0.698238 AGGATGCAAAGGTGGTAGCA 59.302 50.000 0.00 0.00 41.73 3.49
881 4308 6.503616 TTTATGTAGCTGCAAAACAAAACG 57.496 33.333 9.07 0.00 0.00 3.60
882 4309 8.162245 GCTATTTATGTAGCTGCAAAACAAAAC 58.838 33.333 9.07 0.00 42.93 2.43
883 4310 7.330700 GGCTATTTATGTAGCTGCAAAACAAAA 59.669 33.333 9.07 5.49 45.03 2.44
884 4311 6.811170 GGCTATTTATGTAGCTGCAAAACAAA 59.189 34.615 9.07 7.53 45.03 2.83
885 4312 6.329496 GGCTATTTATGTAGCTGCAAAACAA 58.671 36.000 9.07 0.00 45.03 2.83
910 4344 0.392595 GGGGGCTGTAAGAAACGGAG 60.393 60.000 0.00 0.00 36.47 4.63
929 4373 2.027460 GTGCTTGGTTGGTTGGCG 59.973 61.111 0.00 0.00 0.00 5.69
930 4374 0.809636 GTTGTGCTTGGTTGGTTGGC 60.810 55.000 0.00 0.00 0.00 4.52
931 4375 0.527385 CGTTGTGCTTGGTTGGTTGG 60.527 55.000 0.00 0.00 0.00 3.77
942 5735 2.736682 GCGCGGTAATCGTTGTGCT 61.737 57.895 8.83 0.00 41.72 4.40
946 5739 1.518572 AGAGGCGCGGTAATCGTTG 60.519 57.895 8.83 0.00 41.72 4.10
947 5740 1.518572 CAGAGGCGCGGTAATCGTT 60.519 57.895 8.83 0.00 41.72 3.85
948 5741 2.104331 CAGAGGCGCGGTAATCGT 59.896 61.111 8.83 0.00 41.72 3.73
949 5742 3.330853 GCAGAGGCGCGGTAATCG 61.331 66.667 8.83 0.00 42.76 3.34
973 5786 8.101419 TGTCGTCAGTATATATGAGTCACCTAT 58.899 37.037 0.00 0.00 0.00 2.57
985 5802 7.284716 AGAGTTGTCCATTGTCGTCAGTATATA 59.715 37.037 0.00 0.00 0.00 0.86
986 5803 6.096987 AGAGTTGTCCATTGTCGTCAGTATAT 59.903 38.462 0.00 0.00 0.00 0.86
987 5804 5.417894 AGAGTTGTCCATTGTCGTCAGTATA 59.582 40.000 0.00 0.00 0.00 1.47
988 5805 4.220821 AGAGTTGTCCATTGTCGTCAGTAT 59.779 41.667 0.00 0.00 0.00 2.12
994 5811 3.069586 TCTGAAGAGTTGTCCATTGTCGT 59.930 43.478 0.00 0.00 0.00 4.34
999 5816 4.260170 GAGCATCTGAAGAGTTGTCCATT 58.740 43.478 0.00 0.00 0.00 3.16
1044 5868 4.002316 GCATGGCAGAGGAGAAGATTATC 58.998 47.826 0.00 0.00 0.00 1.75
1045 5869 3.651904 AGCATGGCAGAGGAGAAGATTAT 59.348 43.478 0.00 0.00 0.00 1.28
1046 5870 3.044156 AGCATGGCAGAGGAGAAGATTA 58.956 45.455 0.00 0.00 0.00 1.75
1082 5908 9.195411 TCTGACAAATTAAAGATGAAAACATGC 57.805 29.630 0.00 0.00 0.00 4.06
1110 5936 5.999205 ATGTGCTGAAATTTGGTGGAATA 57.001 34.783 0.00 0.00 0.00 1.75
1150 5976 5.647225 ACACACAAATTTTCAACTTGCCATT 59.353 32.000 0.00 0.00 0.00 3.16
1158 5984 6.259638 TCTTACGGACACACAAATTTTCAAC 58.740 36.000 0.00 0.00 0.00 3.18
1159 5985 6.438259 TCTTACGGACACACAAATTTTCAA 57.562 33.333 0.00 0.00 0.00 2.69
1163 5989 7.499321 TGTAATCTTACGGACACACAAATTT 57.501 32.000 0.00 0.00 36.45 1.82
1166 5992 6.566942 GCAATGTAATCTTACGGACACACAAA 60.567 38.462 0.00 0.00 36.45 2.83
1170 5996 4.827692 AGCAATGTAATCTTACGGACACA 58.172 39.130 0.00 0.00 36.45 3.72
1172 6049 6.578944 ACATAGCAATGTAATCTTACGGACA 58.421 36.000 0.00 0.00 44.66 4.02
1251 6350 7.541091 TCAGCAAGAAGAAAACGTATAGTAGTG 59.459 37.037 0.00 0.00 0.00 2.74
1260 6370 4.552767 CGATTGTCAGCAAGAAGAAAACGT 60.553 41.667 0.00 0.00 38.10 3.99
1279 6393 2.806945 TGCCCAAGAATTCCTCGATT 57.193 45.000 0.65 0.00 0.00 3.34
1298 6422 1.228245 ACCTGTGACGGCTGCATTT 60.228 52.632 0.50 0.00 0.00 2.32
1299 6423 1.968017 CACCTGTGACGGCTGCATT 60.968 57.895 0.50 0.00 0.00 3.56
2023 9387 1.069765 CTTCATCAGCGGCGGGTAT 59.930 57.895 9.78 0.00 0.00 2.73
2122 9486 0.034767 AGTCGTCGTAGGGGTGATGA 60.035 55.000 0.00 0.00 0.00 2.92
2217 9581 2.240500 GCCGTGGACTCATCATCGC 61.241 63.158 0.00 0.00 0.00 4.58
2306 9670 0.806102 CAACATCGGTAGTCGGGCTG 60.806 60.000 0.00 0.00 39.77 4.85
2464 9871 2.442212 TTTATTCGACCAGCACGTCA 57.558 45.000 4.34 0.00 32.74 4.35
2471 9880 8.519492 AACAAAATTGTGATTTATTCGACCAG 57.481 30.769 1.62 0.00 41.31 4.00
2489 9898 8.233868 GCAACTTACTTTCCAACAAAACAAAAT 58.766 29.630 0.00 0.00 0.00 1.82
2609 10526 0.912486 ATTCCTAGCCGAAGCCTTGT 59.088 50.000 0.00 0.00 41.25 3.16
2616 10533 3.057033 GCTACGGATTATTCCTAGCCGAA 60.057 47.826 6.54 0.00 44.43 4.30
2635 10552 0.393402 TAACTCGTCTCCGCCAGCTA 60.393 55.000 0.00 0.00 0.00 3.32
2639 10556 0.809385 CTTCTAACTCGTCTCCGCCA 59.191 55.000 0.00 0.00 0.00 5.69
2673 10699 1.745320 GATGCCGACAGTCCCCGTAT 61.745 60.000 0.00 0.00 0.00 3.06
2675 10701 3.771160 GATGCCGACAGTCCCCGT 61.771 66.667 0.00 0.00 0.00 5.28
2685 11501 0.904865 ACCTCCAGTTCTGATGCCGA 60.905 55.000 1.00 0.00 0.00 5.54
2709 11525 3.788333 ATTCATCAATTGTCAAGCCCG 57.212 42.857 5.13 0.00 0.00 6.13
2799 11616 5.586877 TGACGGGCTCTTAGGGTAATATAT 58.413 41.667 0.00 0.00 0.00 0.86
2882 11719 1.684734 TGTAGCCGGTCCCTTCTCC 60.685 63.158 1.90 0.00 0.00 3.71
2919 11756 8.720562 CCAGAAAATTAACTTGCCCAAAAATAG 58.279 33.333 0.00 0.00 0.00 1.73
2967 11804 5.192522 AGAGGAAGAAGAAATAAGGATGGCA 59.807 40.000 0.00 0.00 0.00 4.92
3292 12384 2.289945 CCTTCAGAGTTCAGACCAAGGG 60.290 54.545 0.00 0.00 0.00 3.95
3294 12386 4.314121 CTTCCTTCAGAGTTCAGACCAAG 58.686 47.826 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.