Multiple sequence alignment - TraesCS3B01G196800

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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 TraesCS3B01G196800 chr3B 100.000 2999 0 0 1 2999 223678905 223675907 0.000000e+00 5539.0
1 TraesCS3B01G196800 chr3B 90.819 3017 149 59 53 2999 224165381 224162423 0.000000e+00 3919.0
2 TraesCS3B01G196800 chr3B 89.931 3039 160 61 53 2999 224287864 224284880 0.000000e+00 3783.0
3 TraesCS3B01G196800 chr3B 85.860 983 99 17 933 1898 221912414 221913373 0.000000e+00 1009.0
4 TraesCS3B01G196800 chr3B 91.286 700 38 14 781 1473 223558923 223558240 0.000000e+00 933.0
5 TraesCS3B01G196800 chr3B 84.162 985 96 25 932 1898 215572059 215573001 0.000000e+00 900.0
6 TraesCS3B01G196800 chr3B 92.627 434 22 3 1698 2127 223558131 223557704 1.530000e-172 616.0
7 TraesCS3B01G196800 chr3B 93.317 419 21 2 2582 2999 224319054 224318642 1.980000e-171 612.0
8 TraesCS3B01G196800 chr3B 88.416 423 36 12 791 1208 223690763 223690349 5.770000e-137 497.0
9 TraesCS3B01G196800 chr3B 82.014 278 28 11 396 652 704919730 704919454 1.810000e-52 217.0
10 TraesCS3B01G196800 chr3B 83.505 194 17 3 550 729 224191296 224191104 1.850000e-37 167.0
11 TraesCS3B01G196800 chr3B 83.673 196 13 6 550 729 224201688 224201496 1.850000e-37 167.0
12 TraesCS3B01G196800 chr3B 82.857 140 20 4 2190 2326 224319433 224319295 4.060000e-24 122.0
13 TraesCS3B01G196800 chr3B 93.846 65 4 0 2132 2196 223557675 223557611 6.840000e-17 99.0
14 TraesCS3B01G196800 chr3B 93.220 59 4 0 1747 1805 469631876 469631934 1.480000e-13 87.9
15 TraesCS3B01G196800 chr3B 78.095 105 14 2 2445 2547 224319147 224319050 1.160000e-04 58.4
16 TraesCS3B01G196800 chr3D 91.637 2260 122 37 780 2999 152852246 152850014 0.000000e+00 3064.0
17 TraesCS3B01G196800 chr3D 90.681 998 74 11 758 1745 152702666 152701678 0.000000e+00 1310.0
18 TraesCS3B01G196800 chr3D 83.959 1278 131 29 956 2195 149769996 149768755 0.000000e+00 1157.0
19 TraesCS3B01G196800 chr3D 84.099 1132 119 27 965 2078 149205052 149206140 0.000000e+00 1037.0
20 TraesCS3B01G196800 chr3D 83.874 1141 115 31 965 2078 149544213 149545311 0.000000e+00 1024.0
21 TraesCS3B01G196800 chr3D 88.915 839 49 21 2190 2999 153084044 153083221 0.000000e+00 994.0
22 TraesCS3B01G196800 chr3D 86.015 951 95 15 965 1900 147336050 147335123 0.000000e+00 985.0
23 TraesCS3B01G196800 chr3D 87.033 856 73 16 965 1805 141410578 141411410 0.000000e+00 931.0
24 TraesCS3B01G196800 chr3D 81.827 1073 109 33 1040 2078 360691532 360692552 0.000000e+00 822.0
25 TraesCS3B01G196800 chr3D 88.743 533 25 8 1698 2196 152701800 152701269 1.180000e-173 619.0
26 TraesCS3B01G196800 chr3D 87.273 55 7 0 983 1037 360691451 360691505 2.500000e-06 63.9
27 TraesCS3B01G196800 chr3A 92.072 1337 81 13 824 2155 177671314 177672630 0.000000e+00 1858.0
28 TraesCS3B01G196800 chr3A 92.533 1125 68 4 1008 2127 177888055 177889168 0.000000e+00 1598.0
29 TraesCS3B01G196800 chr3A 83.820 1199 106 43 965 2132 159831977 159833118 0.000000e+00 1059.0
30 TraesCS3B01G196800 chr3A 82.428 1252 118 46 1012 2199 181104902 181106115 0.000000e+00 1000.0
31 TraesCS3B01G196800 chr3A 83.651 1101 110 25 932 2016 166923383 166924429 0.000000e+00 972.0
32 TraesCS3B01G196800 chr3A 87.186 835 49 26 2190 2999 177105075 177105876 0.000000e+00 896.0
33 TraesCS3B01G196800 chr3A 84.764 571 63 12 761 1329 177647063 177647611 4.370000e-153 551.0
34 TraesCS3B01G196800 chr3A 94.479 163 7 2 2152 2312 177672706 177672868 1.780000e-62 250.0
35 TraesCS3B01G196800 chr3A 90.769 65 3 1 2132 2196 177889197 177889258 1.920000e-12 84.2
36 TraesCS3B01G196800 chr6A 82.096 1212 122 44 956 2135 146441640 146440492 0.000000e+00 948.0
37 TraesCS3B01G196800 chr5D 86.170 282 18 3 384 644 344690165 344690446 4.890000e-73 285.0
38 TraesCS3B01G196800 chr5D 94.872 39 2 0 663 701 347367715 347367753 8.980000e-06 62.1
39 TraesCS3B01G196800 chr1D 84.733 262 35 4 394 652 484174799 484175058 1.070000e-64 257.0
40 TraesCS3B01G196800 chr1D 94.872 39 2 0 663 701 296278631 296278593 8.980000e-06 62.1
41 TraesCS3B01G196800 chr7D 83.746 283 24 8 384 644 66965760 66965478 6.420000e-62 248.0
42 TraesCS3B01G196800 chr6D 83.746 283 24 7 384 644 302581159 302581441 6.420000e-62 248.0
43 TraesCS3B01G196800 chr6D 90.741 54 4 1 649 701 130208893 130208946 1.490000e-08 71.3
44 TraesCS3B01G196800 chr6D 94.872 39 2 0 663 701 427237707 427237669 8.980000e-06 62.1
45 TraesCS3B01G196800 chr4B 83.696 276 26 13 394 652 619940484 619940757 2.990000e-60 243.0
46 TraesCS3B01G196800 chr4B 81.272 283 30 12 384 646 646530843 646531122 1.090000e-49 207.0
47 TraesCS3B01G196800 chr1B 85.398 226 27 4 395 617 48908285 48908063 2.330000e-56 230.0
48 TraesCS3B01G196800 chr7B 83.150 273 23 5 394 644 2380674 2380945 8.360000e-56 228.0
49 TraesCS3B01G196800 chr5A 81.852 270 46 3 384 652 363919465 363919198 1.080000e-54 224.0
50 TraesCS3B01G196800 chr4D 81.884 276 36 12 384 652 41722377 41722109 1.400000e-53 220.0
51 TraesCS3B01G196800 chr1A 80.831 313 30 13 361 644 249129757 249130068 5.030000e-53 219.0
52 TraesCS3B01G196800 chr1A 86.290 124 17 0 366 489 588155951 588156074 5.210000e-28 135.0
53 TraesCS3B01G196800 chr7A 80.195 308 35 11 384 667 569059477 569059172 1.090000e-49 207.0
54 TraesCS3B01G196800 chr5B 80.784 255 41 6 382 629 546430611 546430358 3.050000e-45 193.0
55 TraesCS3B01G196800 chr2A 87.500 152 18 1 390 540 599777311 599777462 1.110000e-39 174.0
56 TraesCS3B01G196800 chr4A 94.872 39 2 0 663 701 662465039 662465001 8.980000e-06 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 TraesCS3B01G196800 chr3B 223675907 223678905 2998 True 5539.000000 5539 100.000000 1 2999 1 chr3B.!!$R1 2998
1 TraesCS3B01G196800 chr3B 224162423 224165381 2958 True 3919.000000 3919 90.819000 53 2999 1 chr3B.!!$R3 2946
2 TraesCS3B01G196800 chr3B 224284880 224287864 2984 True 3783.000000 3783 89.931000 53 2999 1 chr3B.!!$R6 2946
3 TraesCS3B01G196800 chr3B 221912414 221913373 959 False 1009.000000 1009 85.860000 933 1898 1 chr3B.!!$F2 965
4 TraesCS3B01G196800 chr3B 215572059 215573001 942 False 900.000000 900 84.162000 932 1898 1 chr3B.!!$F1 966
5 TraesCS3B01G196800 chr3B 223557611 223558923 1312 True 549.333333 933 92.586333 781 2196 3 chr3B.!!$R8 1415
6 TraesCS3B01G196800 chr3B 224318642 224319433 791 True 264.133333 612 84.756333 2190 2999 3 chr3B.!!$R9 809
7 TraesCS3B01G196800 chr3D 152850014 152852246 2232 True 3064.000000 3064 91.637000 780 2999 1 chr3D.!!$R3 2219
8 TraesCS3B01G196800 chr3D 149768755 149769996 1241 True 1157.000000 1157 83.959000 956 2195 1 chr3D.!!$R2 1239
9 TraesCS3B01G196800 chr3D 149205052 149206140 1088 False 1037.000000 1037 84.099000 965 2078 1 chr3D.!!$F2 1113
10 TraesCS3B01G196800 chr3D 149544213 149545311 1098 False 1024.000000 1024 83.874000 965 2078 1 chr3D.!!$F3 1113
11 TraesCS3B01G196800 chr3D 153083221 153084044 823 True 994.000000 994 88.915000 2190 2999 1 chr3D.!!$R4 809
12 TraesCS3B01G196800 chr3D 147335123 147336050 927 True 985.000000 985 86.015000 965 1900 1 chr3D.!!$R1 935
13 TraesCS3B01G196800 chr3D 152701269 152702666 1397 True 964.500000 1310 89.712000 758 2196 2 chr3D.!!$R5 1438
14 TraesCS3B01G196800 chr3D 141410578 141411410 832 False 931.000000 931 87.033000 965 1805 1 chr3D.!!$F1 840
15 TraesCS3B01G196800 chr3D 360691451 360692552 1101 False 442.950000 822 84.550000 983 2078 2 chr3D.!!$F4 1095
16 TraesCS3B01G196800 chr3A 159831977 159833118 1141 False 1059.000000 1059 83.820000 965 2132 1 chr3A.!!$F1 1167
17 TraesCS3B01G196800 chr3A 177671314 177672868 1554 False 1054.000000 1858 93.275500 824 2312 2 chr3A.!!$F6 1488
18 TraesCS3B01G196800 chr3A 181104902 181106115 1213 False 1000.000000 1000 82.428000 1012 2199 1 chr3A.!!$F5 1187
19 TraesCS3B01G196800 chr3A 166923383 166924429 1046 False 972.000000 972 83.651000 932 2016 1 chr3A.!!$F2 1084
20 TraesCS3B01G196800 chr3A 177105075 177105876 801 False 896.000000 896 87.186000 2190 2999 1 chr3A.!!$F3 809
21 TraesCS3B01G196800 chr3A 177888055 177889258 1203 False 841.100000 1598 91.651000 1008 2196 2 chr3A.!!$F7 1188
22 TraesCS3B01G196800 chr3A 177647063 177647611 548 False 551.000000 551 84.764000 761 1329 1 chr3A.!!$F4 568
23 TraesCS3B01G196800 chr6A 146440492 146441640 1148 True 948.000000 948 82.096000 956 2135 1 chr6A.!!$R1 1179

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
906 966 0.103208 ATCGCTGCCCTAGTTTCTCG 59.897 55.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2281 2702 0.179111 CGGACACACATATGAGCGGT 60.179 55.0 10.38 3.72 0.0 5.68 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
36 37 4.394712 GGGTGGACCTGGCTGACG 62.395 72.222 0.00 0.00 35.85 4.35
37 38 3.626924 GGTGGACCTGGCTGACGT 61.627 66.667 0.00 0.00 0.00 4.34
38 39 2.357517 GTGGACCTGGCTGACGTG 60.358 66.667 0.00 0.00 0.00 4.49
39 40 3.625897 TGGACCTGGCTGACGTGG 61.626 66.667 0.00 0.00 0.00 4.94
40 41 3.626924 GGACCTGGCTGACGTGGT 61.627 66.667 0.00 0.00 35.23 4.16
41 42 2.357517 GACCTGGCTGACGTGGTG 60.358 66.667 0.00 0.00 32.30 4.17
42 43 3.883744 GACCTGGCTGACGTGGTGG 62.884 68.421 0.00 0.00 32.30 4.61
43 44 3.625897 CCTGGCTGACGTGGTGGA 61.626 66.667 0.00 0.00 0.00 4.02
44 45 2.357517 CTGGCTGACGTGGTGGAC 60.358 66.667 0.00 0.00 0.00 4.02
59 60 1.664965 GGACGCGCCTGGATATGAC 60.665 63.158 5.73 0.00 0.00 3.06
142 143 1.541379 GGTTAATGACCGGGCTGTTT 58.459 50.000 9.82 1.88 39.00 2.83
158 159 3.243704 GCTGTTTGCCCAGACATTTAACA 60.244 43.478 0.00 0.00 34.23 2.41
184 185 1.079336 GGGGTGTTCGGCTGTAGAC 60.079 63.158 0.00 0.00 0.00 2.59
219 220 4.075963 AGAGTAGAGTAGAAGTAGCCCG 57.924 50.000 0.00 0.00 0.00 6.13
252 253 8.352942 AGATACATCAAAAAGAAACTCCAACAC 58.647 33.333 0.00 0.00 0.00 3.32
262 263 4.157840 AGAAACTCCAACACAACCAACTTC 59.842 41.667 0.00 0.00 0.00 3.01
268 269 6.209788 ACTCCAACACAACCAACTTCTTTTTA 59.790 34.615 0.00 0.00 0.00 1.52
301 302 7.279758 CCAACAAAACCAACTAAACATGAACAT 59.720 33.333 0.00 0.00 0.00 2.71
338 339 4.461081 AGAGTCAAACGAGTCTTCTAGCAT 59.539 41.667 0.00 0.00 39.70 3.79
350 351 5.843421 AGTCTTCTAGCATATCCATTGGTCT 59.157 40.000 1.86 0.00 0.00 3.85
354 355 7.716998 TCTTCTAGCATATCCATTGGTCTTTTC 59.283 37.037 1.86 0.00 0.00 2.29
358 359 4.808042 CATATCCATTGGTCTTTTCCCCT 58.192 43.478 1.86 0.00 0.00 4.79
379 380 3.849911 TCTAATCAGAGCAACTCCAACG 58.150 45.455 0.00 0.00 0.00 4.10
380 381 2.839486 AATCAGAGCAACTCCAACGA 57.161 45.000 0.00 0.00 0.00 3.85
381 382 2.839486 ATCAGAGCAACTCCAACGAA 57.161 45.000 0.00 0.00 0.00 3.85
385 394 0.232303 GAGCAACTCCAACGAACACG 59.768 55.000 0.00 0.00 0.00 4.49
388 397 1.508632 CAACTCCAACGAACACGGAT 58.491 50.000 0.00 0.00 0.00 4.18
468 477 3.985019 TTTAGATTTGGGTCGGCAGTA 57.015 42.857 0.00 0.00 0.00 2.74
476 485 1.153628 GGTCGGCAGTACGCTCAAT 60.154 57.895 9.06 0.00 41.91 2.57
503 512 0.734889 CCCATTTCATGTCCGCACTC 59.265 55.000 0.00 0.00 0.00 3.51
506 515 2.228582 CCATTTCATGTCCGCACTCAAA 59.771 45.455 0.00 0.00 0.00 2.69
545 573 1.450848 CATGTCTCATGCCGGCACT 60.451 57.895 35.50 18.64 0.00 4.40
548 577 1.408969 TGTCTCATGCCGGCACTATA 58.591 50.000 35.50 15.74 0.00 1.31
567 596 2.328989 CAGCGCCGGCATACAATG 59.671 61.111 28.98 9.29 43.41 2.82
602 631 1.742761 ATCACCACACAGTATGCTGC 58.257 50.000 11.09 0.00 46.30 5.25
690 732 4.974989 GTCCGTTTGGGTCGGCGT 62.975 66.667 6.85 0.00 46.49 5.68
694 736 4.025401 GTTTGGGTCGGCGTGCTG 62.025 66.667 6.85 0.00 0.00 4.41
728 770 4.828939 TGCTCTCACATCCTTTGATTTGTT 59.171 37.500 0.00 0.00 31.85 2.83
750 792 4.072131 TGATTGGATTAGAAATAGCGCCC 58.928 43.478 2.29 0.00 0.00 6.13
754 796 1.001633 GATTAGAAATAGCGCCCCCGA 59.998 52.381 2.29 0.00 36.29 5.14
778 829 1.381165 AAAAGAGCGCCAACCACGTT 61.381 50.000 2.29 0.00 0.00 3.99
887 947 1.137594 ATCCCAACTTTCCCCGACCA 61.138 55.000 0.00 0.00 0.00 4.02
903 963 0.107654 ACCATCGCTGCCCTAGTTTC 60.108 55.000 0.00 0.00 0.00 2.78
904 964 0.179000 CCATCGCTGCCCTAGTTTCT 59.821 55.000 0.00 0.00 0.00 2.52
905 965 1.576356 CATCGCTGCCCTAGTTTCTC 58.424 55.000 0.00 0.00 0.00 2.87
906 966 0.103208 ATCGCTGCCCTAGTTTCTCG 59.897 55.000 0.00 0.00 0.00 4.04
907 967 0.963856 TCGCTGCCCTAGTTTCTCGA 60.964 55.000 0.00 0.00 0.00 4.04
908 968 0.802607 CGCTGCCCTAGTTTCTCGAC 60.803 60.000 0.00 0.00 0.00 4.20
909 969 0.533032 GCTGCCCTAGTTTCTCGACT 59.467 55.000 0.00 0.00 0.00 4.18
910 970 1.470112 GCTGCCCTAGTTTCTCGACTC 60.470 57.143 0.00 0.00 0.00 3.36
911 971 1.135333 CTGCCCTAGTTTCTCGACTCC 59.865 57.143 0.00 0.00 0.00 3.85
912 972 0.460722 GCCCTAGTTTCTCGACTCCC 59.539 60.000 0.00 0.00 0.00 4.30
913 973 1.848652 CCCTAGTTTCTCGACTCCCA 58.151 55.000 0.00 0.00 0.00 4.37
914 974 2.176889 CCCTAGTTTCTCGACTCCCAA 58.823 52.381 0.00 0.00 0.00 4.12
915 975 2.094130 CCCTAGTTTCTCGACTCCCAAC 60.094 54.545 0.00 0.00 0.00 3.77
916 976 2.826725 CCTAGTTTCTCGACTCCCAACT 59.173 50.000 0.00 0.00 0.00 3.16
917 977 3.258622 CCTAGTTTCTCGACTCCCAACTT 59.741 47.826 0.00 0.00 0.00 2.66
918 978 3.840124 AGTTTCTCGACTCCCAACTTT 57.160 42.857 0.00 0.00 0.00 2.66
919 979 3.729966 AGTTTCTCGACTCCCAACTTTC 58.270 45.455 0.00 0.00 0.00 2.62
924 984 1.268899 TCGACTCCCAACTTTCTCGAC 59.731 52.381 0.00 0.00 0.00 4.20
928 988 0.601558 TCCCAACTTTCTCGACTCCG 59.398 55.000 0.00 0.00 37.07 4.63
930 990 1.542915 CCCAACTTTCTCGACTCCGTA 59.457 52.381 0.00 0.00 37.05 4.02
962 1036 3.723922 GCCGCCCTAGTTTCCCCA 61.724 66.667 0.00 0.00 0.00 4.96
1093 1198 2.582265 GCGACGTGCGTGAAAGACA 61.582 57.895 0.67 0.00 43.41 3.41
1105 1210 2.223377 GTGAAAGACACGCGGATCTTTT 59.777 45.455 29.12 18.49 43.54 2.27
1209 1314 2.107378 TCCAAAACATCACCCTGTGCTA 59.893 45.455 0.00 0.00 32.98 3.49
1221 1326 2.632512 CCCTGTGCTAACCCAATTTTGT 59.367 45.455 0.00 0.00 0.00 2.83
1663 1786 4.722535 AGAAGGAGCAGCCCCCGA 62.723 66.667 0.00 0.00 37.37 5.14
2231 2652 2.032681 GGCACCTTGACGCTCCTT 59.967 61.111 0.00 0.00 0.00 3.36
2278 2699 4.026804 CACGCACCGTTGATTTAGATAGAC 60.027 45.833 0.00 0.00 38.32 2.59
2281 2702 5.506815 CGCACCGTTGATTTAGATAGACCTA 60.507 44.000 0.00 0.00 0.00 3.08
2293 2715 4.924625 AGATAGACCTACCGCTCATATGT 58.075 43.478 1.90 0.00 0.00 2.29
2366 2805 3.468625 AGGATGCCTGGATCCCTATTTTT 59.531 43.478 9.90 0.00 42.81 1.94
2445 2943 7.252130 GCTGTCAAATCAGTCACTGTCTGTG 62.252 48.000 4.28 3.55 40.35 3.66
2446 2944 3.059325 GTCAAATCAGTCACTGTCTGTGC 60.059 47.826 4.28 1.49 45.81 4.57
2447 2945 3.136763 CAAATCAGTCACTGTCTGTGCT 58.863 45.455 4.28 3.58 45.81 4.40
2448 2946 2.452295 ATCAGTCACTGTCTGTGCTG 57.548 50.000 19.07 19.07 45.81 4.41
2449 2947 1.114627 TCAGTCACTGTCTGTGCTGT 58.885 50.000 21.72 4.43 45.81 4.40
2450 2948 1.067669 TCAGTCACTGTCTGTGCTGTC 59.932 52.381 21.72 8.77 45.81 3.51
2451 2949 1.114627 AGTCACTGTCTGTGCTGTCA 58.885 50.000 5.04 0.00 45.81 3.58
2452 2950 1.482182 AGTCACTGTCTGTGCTGTCAA 59.518 47.619 5.04 0.00 45.81 3.18
2453 2951 2.093500 AGTCACTGTCTGTGCTGTCAAA 60.093 45.455 5.04 0.00 45.81 2.69
2454 2952 2.874701 GTCACTGTCTGTGCTGTCAAAT 59.125 45.455 5.04 0.00 45.81 2.32
2455 2953 3.059325 GTCACTGTCTGTGCTGTCAAATC 60.059 47.826 5.04 0.00 45.81 2.17
2456 2954 2.874086 CACTGTCTGTGCTGTCAAATCA 59.126 45.455 0.00 0.00 40.06 2.57
2457 2955 3.059120 CACTGTCTGTGCTGTCAAATCAG 60.059 47.826 0.00 0.00 40.06 2.90
2458 2956 3.136763 CTGTCTGTGCTGTCAAATCAGT 58.863 45.455 0.00 0.00 37.70 3.41
2459 2957 3.133691 TGTCTGTGCTGTCAAATCAGTC 58.866 45.455 0.00 0.00 37.70 3.51
2460 2958 3.133691 GTCTGTGCTGTCAAATCAGTCA 58.866 45.455 0.00 0.00 37.70 3.41
2461 2959 3.059325 GTCTGTGCTGTCAAATCAGTCAC 60.059 47.826 11.29 11.29 39.91 3.67
2462 2960 3.136763 CTGTGCTGTCAAATCAGTCACT 58.863 45.455 15.76 0.00 40.03 3.41
2463 2961 2.874086 TGTGCTGTCAAATCAGTCACTG 59.126 45.455 0.00 0.00 40.03 3.66
2464 2962 2.874701 GTGCTGTCAAATCAGTCACTGT 59.125 45.455 4.28 0.00 38.32 3.55
2465 2963 3.059325 GTGCTGTCAAATCAGTCACTGTC 60.059 47.826 4.28 0.00 38.32 3.51
2466 2964 3.181462 TGCTGTCAAATCAGTCACTGTCT 60.181 43.478 4.28 0.00 37.70 3.41
2467 2965 3.186001 GCTGTCAAATCAGTCACTGTCTG 59.814 47.826 4.28 1.13 37.70 3.51
2470 2968 6.101650 TGTCAAATCAGTCACTGTCTGTAT 57.898 37.500 4.28 0.00 34.86 2.29
2497 2995 6.681777 AGACTCAATTGCGCTTAAGAAATTT 58.318 32.000 9.73 0.00 0.00 1.82
2508 3006 7.027161 GCGCTTAAGAAATTTGGTTAGAATCA 58.973 34.615 6.67 0.00 0.00 2.57
2509 3007 7.540745 GCGCTTAAGAAATTTGGTTAGAATCAA 59.459 33.333 6.67 0.00 0.00 2.57
2510 3008 9.573133 CGCTTAAGAAATTTGGTTAGAATCAAT 57.427 29.630 6.67 0.00 0.00 2.57
2544 3042 0.396139 TCTCTGCCCCATGGAAATGC 60.396 55.000 15.22 10.79 0.00 3.56
2587 3086 3.760684 GAGTCTTGCCTTGGATTGTGATT 59.239 43.478 0.00 0.00 0.00 2.57
2618 3118 6.349973 ACTACTTGATGTGATAATTGCACG 57.650 37.500 8.23 0.00 39.07 5.34
2698 3199 6.904626 AGGTTGTTCATTCATATCCTTAGCT 58.095 36.000 0.00 0.00 0.00 3.32
2825 3327 6.587226 TGAATGCTTCACAAATAAGAACATGC 59.413 34.615 0.00 0.00 34.08 4.06
2908 3410 5.046376 TCTGGACAGCTGTCTCATATCAAAA 60.046 40.000 38.17 18.47 44.20 2.44
2909 3411 5.748402 TGGACAGCTGTCTCATATCAAAAT 58.252 37.500 38.17 5.09 44.20 1.82
2910 3412 5.819379 TGGACAGCTGTCTCATATCAAAATC 59.181 40.000 38.17 21.20 44.20 2.17
2911 3413 5.819379 GGACAGCTGTCTCATATCAAAATCA 59.181 40.000 38.17 0.00 44.20 2.57
2912 3414 6.317140 GGACAGCTGTCTCATATCAAAATCAA 59.683 38.462 38.17 0.00 44.20 2.57
2913 3415 7.148188 GGACAGCTGTCTCATATCAAAATCAAA 60.148 37.037 38.17 0.00 44.20 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.394712 CGTCAGCCAGGTCCACCC 62.395 72.222 0.00 0.00 36.42 4.61
20 21 3.626924 ACGTCAGCCAGGTCCACC 61.627 66.667 0.00 0.00 0.00 4.61
21 22 2.357517 CACGTCAGCCAGGTCCAC 60.358 66.667 0.00 0.00 0.00 4.02
22 23 3.625897 CCACGTCAGCCAGGTCCA 61.626 66.667 0.00 0.00 0.00 4.02
23 24 3.626924 ACCACGTCAGCCAGGTCC 61.627 66.667 0.00 0.00 0.00 4.46
24 25 2.357517 CACCACGTCAGCCAGGTC 60.358 66.667 0.00 0.00 30.44 3.85
25 26 3.941188 CCACCACGTCAGCCAGGT 61.941 66.667 0.00 0.00 33.91 4.00
26 27 3.625897 TCCACCACGTCAGCCAGG 61.626 66.667 0.00 0.00 0.00 4.45
27 28 2.357517 GTCCACCACGTCAGCCAG 60.358 66.667 0.00 0.00 0.00 4.85
28 29 4.293648 CGTCCACCACGTCAGCCA 62.294 66.667 0.00 0.00 44.07 4.75
38 39 3.165160 ATATCCAGGCGCGTCCACC 62.165 63.158 19.30 7.32 37.29 4.61
39 40 1.956170 CATATCCAGGCGCGTCCAC 60.956 63.158 19.30 3.57 37.29 4.02
40 41 2.131067 TCATATCCAGGCGCGTCCA 61.131 57.895 19.30 0.00 37.29 4.02
41 42 1.664965 GTCATATCCAGGCGCGTCC 60.665 63.158 7.31 9.59 0.00 4.79
42 43 2.016704 CGTCATATCCAGGCGCGTC 61.017 63.158 0.21 0.21 0.00 5.19
43 44 2.027605 CGTCATATCCAGGCGCGT 59.972 61.111 8.43 0.00 0.00 6.01
44 45 2.734723 CCGTCATATCCAGGCGCG 60.735 66.667 0.00 0.00 0.00 6.86
45 46 3.044305 GCCGTCATATCCAGGCGC 61.044 66.667 0.00 0.00 40.17 6.53
48 49 1.179174 TCGGAGCCGTCATATCCAGG 61.179 60.000 8.96 0.00 40.74 4.45
49 50 0.673985 TTCGGAGCCGTCATATCCAG 59.326 55.000 8.96 0.00 40.74 3.86
50 51 0.387929 GTTCGGAGCCGTCATATCCA 59.612 55.000 8.96 0.00 40.74 3.41
51 52 0.387929 TGTTCGGAGCCGTCATATCC 59.612 55.000 8.96 0.00 40.74 2.59
59 60 1.079127 ATCAGGTTGTTCGGAGCCG 60.079 57.895 1.74 1.74 41.35 5.52
138 139 3.243234 CGTGTTAAATGTCTGGGCAAACA 60.243 43.478 0.00 0.00 0.00 2.83
142 143 1.529226 CCGTGTTAAATGTCTGGGCA 58.471 50.000 0.00 0.00 0.00 5.36
158 159 2.203238 CGAACACCCCAAACCCGT 60.203 61.111 0.00 0.00 0.00 5.28
184 185 2.143122 CTACTCTAGAGCCTGAGAGCG 58.857 57.143 19.97 0.00 42.56 5.03
219 220 6.903883 TTCTTTTTGATGTATCTCGCTACC 57.096 37.500 0.00 0.00 0.00 3.18
252 253 7.488322 TGGAATGTCTAAAAAGAAGTTGGTTG 58.512 34.615 0.00 0.00 0.00 3.77
262 263 8.387354 GTTGGTTTTGTTGGAATGTCTAAAAAG 58.613 33.333 0.00 0.00 0.00 2.27
268 269 6.783708 TTAGTTGGTTTTGTTGGAATGTCT 57.216 33.333 0.00 0.00 0.00 3.41
301 302 4.753516 TTGACTCTTCTTCACCTTCACA 57.246 40.909 0.00 0.00 0.00 3.58
307 308 3.718815 ACTCGTTTGACTCTTCTTCACC 58.281 45.455 0.00 0.00 0.00 4.02
311 312 5.523438 AGAAGACTCGTTTGACTCTTCTT 57.477 39.130 9.81 0.00 44.84 2.52
338 339 4.119155 AGAGGGGAAAAGACCAATGGATA 58.881 43.478 6.16 0.00 0.00 2.59
358 359 3.509967 TCGTTGGAGTTGCTCTGATTAGA 59.490 43.478 0.00 0.00 0.00 2.10
379 380 3.896648 ACAAATGTGTCATCCGTGTTC 57.103 42.857 0.00 0.00 29.49 3.18
435 444 0.611714 ATCTAAAACAGGGCGGACGT 59.388 50.000 0.00 0.00 0.00 4.34
442 451 2.752903 CCGACCCAAATCTAAAACAGGG 59.247 50.000 0.00 0.00 42.07 4.45
446 455 2.817844 ACTGCCGACCCAAATCTAAAAC 59.182 45.455 0.00 0.00 0.00 2.43
476 485 2.045438 ATGAAATGGGTCGGCGCA 60.045 55.556 9.93 9.93 41.83 6.09
522 531 1.153568 CGGCATGAGACATGACCGT 60.154 57.895 24.37 0.00 35.53 4.83
526 535 1.450134 GTGCCGGCATGAGACATGA 60.450 57.895 35.23 0.86 0.00 3.07
545 573 1.290955 GTATGCCGGCGCTGGTATA 59.709 57.895 34.12 34.12 35.77 1.47
548 577 3.697439 ATTGTATGCCGGCGCTGGT 62.697 57.895 34.76 19.87 35.36 4.00
580 609 3.879295 GCAGCATACTGTGTGGTGATATT 59.121 43.478 31.70 0.00 45.32 1.28
645 675 4.424711 TGCCGACCCATTCCCAGC 62.425 66.667 0.00 0.00 0.00 4.85
647 677 4.424711 GCTGCCGACCCATTCCCA 62.425 66.667 0.00 0.00 0.00 4.37
650 680 4.467084 TCCGCTGCCGACCCATTC 62.467 66.667 0.00 0.00 36.29 2.67
688 730 1.734477 CAACTCTCGACCCAGCACG 60.734 63.158 0.00 0.00 0.00 5.34
690 732 2.159819 GAGCAACTCTCGACCCAGCA 62.160 60.000 0.00 0.00 31.20 4.41
692 734 0.172352 GAGAGCAACTCTCGACCCAG 59.828 60.000 8.74 0.00 45.76 4.45
699 741 5.857540 ATCAAAGGATGTGAGAGCAACTCTC 60.858 44.000 16.04 16.04 43.38 3.20
700 742 3.326006 TCAAAGGATGTGAGAGCAACTCT 59.674 43.478 11.18 0.00 44.28 3.24
728 770 4.072131 GGGCGCTATTTCTAATCCAATCA 58.928 43.478 7.64 0.00 0.00 2.57
887 947 0.103208 CGAGAAACTAGGGCAGCGAT 59.897 55.000 0.00 0.00 0.00 4.58
903 963 1.540267 TCGAGAAAGTTGGGAGTCGAG 59.460 52.381 0.00 0.00 32.92 4.04
904 964 1.268899 GTCGAGAAAGTTGGGAGTCGA 59.731 52.381 0.00 0.00 34.26 4.20
905 965 1.269998 AGTCGAGAAAGTTGGGAGTCG 59.730 52.381 0.00 0.00 0.00 4.18
906 966 2.352912 GGAGTCGAGAAAGTTGGGAGTC 60.353 54.545 0.00 0.00 0.00 3.36
907 967 1.619332 GGAGTCGAGAAAGTTGGGAGT 59.381 52.381 0.00 0.00 0.00 3.85
908 968 1.402984 CGGAGTCGAGAAAGTTGGGAG 60.403 57.143 0.00 0.00 39.00 4.30
909 969 0.601558 CGGAGTCGAGAAAGTTGGGA 59.398 55.000 0.00 0.00 39.00 4.37
910 970 0.317479 ACGGAGTCGAGAAAGTTGGG 59.683 55.000 0.00 0.00 29.74 4.12
911 971 3.505464 ATACGGAGTCGAGAAAGTTGG 57.495 47.619 0.00 0.00 43.93 3.77
912 972 4.326548 GGAAATACGGAGTCGAGAAAGTTG 59.673 45.833 0.00 0.00 43.93 3.16
913 973 4.492611 GGAAATACGGAGTCGAGAAAGTT 58.507 43.478 0.00 0.00 43.93 2.66
914 974 3.119209 GGGAAATACGGAGTCGAGAAAGT 60.119 47.826 0.00 0.00 43.93 2.66
915 975 3.445857 GGGAAATACGGAGTCGAGAAAG 58.554 50.000 0.00 0.00 43.93 2.62
916 976 2.167075 GGGGAAATACGGAGTCGAGAAA 59.833 50.000 0.00 0.00 43.93 2.52
917 977 1.753073 GGGGAAATACGGAGTCGAGAA 59.247 52.381 0.00 0.00 43.93 2.87
918 978 1.396653 GGGGAAATACGGAGTCGAGA 58.603 55.000 0.00 0.00 43.93 4.04
919 979 0.030369 CGGGGAAATACGGAGTCGAG 59.970 60.000 0.00 0.00 43.93 4.04
924 984 2.607282 CGAAGATCGGGGAAATACGGAG 60.607 54.545 0.00 0.00 36.00 4.63
928 988 1.509703 GGCGAAGATCGGGGAAATAC 58.490 55.000 1.64 0.00 40.84 1.89
930 990 1.227556 CGGCGAAGATCGGGGAAAT 60.228 57.895 0.00 0.00 40.84 2.17
962 1036 2.416162 GCAAACTCCGAGAGTCGAGATT 60.416 50.000 1.33 0.00 42.59 2.40
1105 1210 3.009723 GGAACTCAATGATTTCCTGCGA 58.990 45.455 20.82 0.00 38.05 5.10
1209 1314 4.587262 GTGAGTTCCCTACAAAATTGGGTT 59.413 41.667 0.00 0.00 43.52 4.11
1221 1326 1.335132 GGATGCCGGTGAGTTCCCTA 61.335 60.000 1.90 0.00 0.00 3.53
1566 1686 0.392706 TCAGCTCAACAAGAAGCCGA 59.607 50.000 0.00 0.00 0.00 5.54
2231 2652 2.639065 GGAGAAATGGGTGCGATTACA 58.361 47.619 0.00 0.00 0.00 2.41
2265 2686 5.382616 TGAGCGGTAGGTCTATCTAAATCA 58.617 41.667 0.00 0.00 44.65 2.57
2278 2699 2.545952 GGACACACATATGAGCGGTAGG 60.546 54.545 10.38 0.00 0.00 3.18
2281 2702 0.179111 CGGACACACATATGAGCGGT 60.179 55.000 10.38 3.72 0.00 5.68
2293 2715 2.494471 ACGAAATGATCCTACGGACACA 59.506 45.455 0.00 0.00 32.98 3.72
2419 2917 2.874701 ACAGTGACTGATTTGACAGCAC 59.125 45.455 20.97 0.00 41.06 4.40
2445 2943 3.186001 CAGACAGTGACTGATTTGACAGC 59.814 47.826 20.97 0.00 41.06 4.40
2446 2944 4.375272 ACAGACAGTGACTGATTTGACAG 58.625 43.478 25.94 2.76 42.78 3.51
2447 2945 4.406648 ACAGACAGTGACTGATTTGACA 57.593 40.909 25.94 0.00 38.55 3.58
2448 2946 7.539436 TCTATACAGACAGTGACTGATTTGAC 58.461 38.462 25.94 3.49 38.55 3.18
2449 2947 7.611855 TCTCTATACAGACAGTGACTGATTTGA 59.388 37.037 25.94 16.75 38.55 2.69
2450 2948 7.700234 GTCTCTATACAGACAGTGACTGATTTG 59.300 40.741 25.94 15.32 42.25 2.32
2451 2949 7.613801 AGTCTCTATACAGACAGTGACTGATTT 59.386 37.037 25.94 13.44 44.73 2.17
2452 2950 7.116075 AGTCTCTATACAGACAGTGACTGATT 58.884 38.462 25.94 15.50 44.73 2.57
2453 2951 6.658849 AGTCTCTATACAGACAGTGACTGAT 58.341 40.000 25.94 17.05 44.73 2.90
2454 2952 6.056090 AGTCTCTATACAGACAGTGACTGA 57.944 41.667 25.94 12.03 44.73 3.41
2455 2953 5.877564 TGAGTCTCTATACAGACAGTGACTG 59.122 44.000 19.10 19.10 44.73 3.51
2456 2954 6.056090 TGAGTCTCTATACAGACAGTGACT 57.944 41.667 10.35 6.13 44.73 3.41
2457 2955 6.745159 TTGAGTCTCTATACAGACAGTGAC 57.255 41.667 10.35 0.00 44.73 3.67
2458 2956 7.629437 GCAATTGAGTCTCTATACAGACAGTGA 60.629 40.741 10.34 0.00 44.73 3.41
2459 2957 6.475076 GCAATTGAGTCTCTATACAGACAGTG 59.525 42.308 10.34 1.66 44.73 3.66
2460 2958 6.568869 GCAATTGAGTCTCTATACAGACAGT 58.431 40.000 10.34 0.00 44.73 3.55
2461 2959 5.685068 CGCAATTGAGTCTCTATACAGACAG 59.315 44.000 10.34 0.00 44.73 3.51
2462 2960 5.582550 CGCAATTGAGTCTCTATACAGACA 58.417 41.667 10.34 0.00 44.73 3.41
2463 2961 4.442733 GCGCAATTGAGTCTCTATACAGAC 59.557 45.833 10.34 0.13 42.91 3.51
2464 2962 4.339530 AGCGCAATTGAGTCTCTATACAGA 59.660 41.667 11.47 0.00 0.00 3.41
2465 2963 4.615949 AGCGCAATTGAGTCTCTATACAG 58.384 43.478 11.47 0.00 0.00 2.74
2466 2964 4.655762 AGCGCAATTGAGTCTCTATACA 57.344 40.909 11.47 0.00 0.00 2.29
2467 2965 6.918569 TCTTAAGCGCAATTGAGTCTCTATAC 59.081 38.462 11.47 0.00 0.00 1.47
2470 2968 5.324784 TCTTAAGCGCAATTGAGTCTCTA 57.675 39.130 11.47 0.00 0.00 2.43
2508 3006 8.810041 GGGGCAGAGAATGATTTATGATTTATT 58.190 33.333 0.00 0.00 0.00 1.40
2509 3007 7.951806 TGGGGCAGAGAATGATTTATGATTTAT 59.048 33.333 0.00 0.00 0.00 1.40
2510 3008 7.296856 TGGGGCAGAGAATGATTTATGATTTA 58.703 34.615 0.00 0.00 0.00 1.40
2511 3009 6.138263 TGGGGCAGAGAATGATTTATGATTT 58.862 36.000 0.00 0.00 0.00 2.17
2512 3010 5.708544 TGGGGCAGAGAATGATTTATGATT 58.291 37.500 0.00 0.00 0.00 2.57
2513 3011 5.329191 TGGGGCAGAGAATGATTTATGAT 57.671 39.130 0.00 0.00 0.00 2.45
2514 3012 4.794311 TGGGGCAGAGAATGATTTATGA 57.206 40.909 0.00 0.00 0.00 2.15
2515 3013 4.219944 CCATGGGGCAGAGAATGATTTATG 59.780 45.833 2.85 0.00 0.00 1.90
2544 3042 3.185594 TCGCCAACACTTTGATAGTTTCG 59.814 43.478 0.00 0.00 33.85 3.46
2618 3118 0.912486 ACACCAAGGCTCACTATCCC 59.088 55.000 0.00 0.00 0.00 3.85
2698 3199 4.114073 CAAAGCATGCAAGTTGAACAAGA 58.886 39.130 21.98 0.00 0.00 3.02
2851 3353 7.712797 TCTGAAACCCTAAAACATTGAAGAAC 58.287 34.615 0.00 0.00 0.00 3.01
2908 3410 5.892119 AGCTTCATGATGTCCTTCATTTGAT 59.108 36.000 10.05 0.00 36.83 2.57
2909 3411 5.124936 CAGCTTCATGATGTCCTTCATTTGA 59.875 40.000 10.05 0.00 36.83 2.69
2910 3412 5.105877 ACAGCTTCATGATGTCCTTCATTTG 60.106 40.000 10.05 0.00 42.15 2.32
2911 3413 5.014858 ACAGCTTCATGATGTCCTTCATTT 58.985 37.500 10.05 0.00 42.15 2.32
2912 3414 4.597004 ACAGCTTCATGATGTCCTTCATT 58.403 39.130 10.05 0.00 42.15 2.57
2913 3415 4.232188 ACAGCTTCATGATGTCCTTCAT 57.768 40.909 10.05 0.00 42.15 2.57


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

AutoCloner maintained by Alex Coulton.