Multiple sequence alignment - TraesCS7B01G412800

Loading Multiple Alignment...

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 TraesCS7B01G412800 chr7B 100.000 3233 0 0 1 3233 680351992 680348760 0.000000e+00 5971.0
1 TraesCS7B01G412800 chr7B 85.155 970 117 9 1499 2467 680369914 680368971 0.000000e+00 968.0
2 TraesCS7B01G412800 chr7B 88.199 322 38 0 1180 1501 680382029 680381708 5.060000e-103 385.0
3 TraesCS7B01G412800 chr7B 80.439 547 63 14 2698 3233 680364278 680363765 8.470000e-101 377.0
4 TraesCS7B01G412800 chr7B 72.643 1294 299 39 991 2258 680854467 680853203 8.470000e-101 377.0
5 TraesCS7B01G412800 chr7B 73.588 1098 231 42 1144 2222 600720656 600721713 1.830000e-97 366.0
6 TraesCS7B01G412800 chr7B 92.593 162 12 0 1052 1213 680466382 680466221 1.940000e-57 233.0
7 TraesCS7B01G412800 chr7B 91.358 162 14 0 1052 1213 680437715 680437554 4.200000e-54 222.0
8 TraesCS7B01G412800 chr7B 87.500 88 5 1 281 362 680468227 680468140 2.650000e-16 97.1
9 TraesCS7B01G412800 chr7B 91.304 69 6 0 228 296 680468311 680468243 9.550000e-16 95.3
10 TraesCS7B01G412800 chr7A 93.743 1806 88 12 497 2279 693062277 693060474 0.000000e+00 2686.0
11 TraesCS7B01G412800 chr7A 93.740 1805 88 12 497 2279 693036030 693034229 0.000000e+00 2684.0
12 TraesCS7B01G412800 chr7A 93.570 1804 93 10 497 2279 693088867 693087066 0.000000e+00 2667.0
13 TraesCS7B01G412800 chr7A 91.422 1842 86 27 497 2279 693134359 693132531 0.000000e+00 2460.0
14 TraesCS7B01G412800 chr7A 90.435 920 63 9 2324 3233 693034234 693033330 0.000000e+00 1188.0
15 TraesCS7B01G412800 chr7A 89.902 921 67 10 2324 3233 693060479 693059574 0.000000e+00 1162.0
16 TraesCS7B01G412800 chr7A 89.617 915 71 12 2324 3233 693087071 693086176 0.000000e+00 1142.0
17 TraesCS7B01G412800 chr7A 91.104 607 40 7 2324 2923 693132536 693131937 0.000000e+00 809.0
18 TraesCS7B01G412800 chr7A 91.459 281 22 2 203 482 693036358 693036079 5.060000e-103 385.0
19 TraesCS7B01G412800 chr7A 90.747 281 24 2 203 482 693062605 693062326 1.100000e-99 374.0
20 TraesCS7B01G412800 chr7A 90.391 281 25 2 203 482 693089195 693088916 5.100000e-98 368.0
21 TraesCS7B01G412800 chr7A 87.847 288 26 3 203 482 693134694 693134408 2.400000e-86 329.0
22 TraesCS7B01G412800 chr7D 90.000 2030 121 36 297 2279 601392254 601390260 0.000000e+00 2549.0
23 TraesCS7B01G412800 chr7D 91.459 925 54 11 2324 3233 601390265 601389351 0.000000e+00 1247.0
24 TraesCS7B01G412800 chr7D 73.232 1386 300 44 991 2345 601494375 601493030 3.830000e-119 438.0
25 TraesCS7B01G412800 chr3D 84.940 1162 119 26 2091 3233 11144314 11143190 0.000000e+00 1125.0
26 TraesCS7B01G412800 chr3D 83.919 541 61 16 2673 3208 11077708 11077189 8.060000e-136 494.0
27 TraesCS7B01G412800 chr3A 84.563 1166 125 28 2091 3233 18780551 18779418 0.000000e+00 1105.0
28 TraesCS7B01G412800 chr3A 84.075 1168 121 34 2091 3233 18168365 18167238 0.000000e+00 1066.0
29 TraesCS7B01G412800 chr3A 73.527 1307 290 35 991 2269 53204186 53205464 2.290000e-121 446.0
30 TraesCS7B01G412800 chr3A 72.076 1214 270 40 993 2182 731787401 731786233 1.890000e-77 300.0
31 TraesCS7B01G412800 chr3B 85.803 641 60 13 2091 2718 25619222 25618600 0.000000e+00 651.0
32 TraesCS7B01G412800 chr3B 85.086 637 65 13 2091 2715 15779362 15779980 9.850000e-175 623.0
33 TraesCS7B01G412800 chr3B 86.738 558 53 10 2092 2641 15728171 15728715 4.620000e-168 601.0
34 TraesCS7B01G412800 chr3B 85.475 537 54 15 2094 2620 15761755 15762277 3.670000e-149 538.0
35 TraesCS7B01G412800 chr3B 87.500 64 4 2 14 77 244992882 244992941 1.610000e-08 71.3
36 TraesCS7B01G412800 chr2D 72.610 1391 289 65 991 2342 33544544 33545881 1.100000e-99 374.0
37 TraesCS7B01G412800 chr6D 72.115 1352 281 57 996 2307 1373130 1374425 1.450000e-83 320.0


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 TraesCS7B01G412800 chr7B 680348760 680351992 3232 True 5971.000000 5971 100.000000 1 3233 1 chr7B.!!$R1 3232
1 TraesCS7B01G412800 chr7B 680368971 680369914 943 True 968.000000 968 85.155000 1499 2467 1 chr7B.!!$R3 968
2 TraesCS7B01G412800 chr7B 680363765 680364278 513 True 377.000000 377 80.439000 2698 3233 1 chr7B.!!$R2 535
3 TraesCS7B01G412800 chr7B 680853203 680854467 1264 True 377.000000 377 72.643000 991 2258 1 chr7B.!!$R6 1267
4 TraesCS7B01G412800 chr7B 600720656 600721713 1057 False 366.000000 366 73.588000 1144 2222 1 chr7B.!!$F1 1078
5 TraesCS7B01G412800 chr7A 693033330 693036358 3028 True 1419.000000 2684 91.878000 203 3233 3 chr7A.!!$R1 3030
6 TraesCS7B01G412800 chr7A 693059574 693062605 3031 True 1407.333333 2686 91.464000 203 3233 3 chr7A.!!$R2 3030
7 TraesCS7B01G412800 chr7A 693086176 693089195 3019 True 1392.333333 2667 91.192667 203 3233 3 chr7A.!!$R3 3030
8 TraesCS7B01G412800 chr7A 693131937 693134694 2757 True 1199.333333 2460 90.124333 203 2923 3 chr7A.!!$R4 2720
9 TraesCS7B01G412800 chr7D 601389351 601392254 2903 True 1898.000000 2549 90.729500 297 3233 2 chr7D.!!$R2 2936
10 TraesCS7B01G412800 chr7D 601493030 601494375 1345 True 438.000000 438 73.232000 991 2345 1 chr7D.!!$R1 1354
11 TraesCS7B01G412800 chr3D 11143190 11144314 1124 True 1125.000000 1125 84.940000 2091 3233 1 chr3D.!!$R2 1142
12 TraesCS7B01G412800 chr3D 11077189 11077708 519 True 494.000000 494 83.919000 2673 3208 1 chr3D.!!$R1 535
13 TraesCS7B01G412800 chr3A 18779418 18780551 1133 True 1105.000000 1105 84.563000 2091 3233 1 chr3A.!!$R2 1142
14 TraesCS7B01G412800 chr3A 18167238 18168365 1127 True 1066.000000 1066 84.075000 2091 3233 1 chr3A.!!$R1 1142
15 TraesCS7B01G412800 chr3A 53204186 53205464 1278 False 446.000000 446 73.527000 991 2269 1 chr3A.!!$F1 1278
16 TraesCS7B01G412800 chr3A 731786233 731787401 1168 True 300.000000 300 72.076000 993 2182 1 chr3A.!!$R3 1189
17 TraesCS7B01G412800 chr3B 25618600 25619222 622 True 651.000000 651 85.803000 2091 2718 1 chr3B.!!$R1 627
18 TraesCS7B01G412800 chr3B 15779362 15779980 618 False 623.000000 623 85.086000 2091 2715 1 chr3B.!!$F3 624
19 TraesCS7B01G412800 chr3B 15728171 15728715 544 False 601.000000 601 86.738000 2092 2641 1 chr3B.!!$F1 549
20 TraesCS7B01G412800 chr3B 15761755 15762277 522 False 538.000000 538 85.475000 2094 2620 1 chr3B.!!$F2 526
21 TraesCS7B01G412800 chr2D 33544544 33545881 1337 False 374.000000 374 72.610000 991 2342 1 chr2D.!!$F1 1351
22 TraesCS7B01G412800 chr6D 1373130 1374425 1295 False 320.000000 320 72.115000 996 2307 1 chr6D.!!$F1 1311

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
199 200 0.034337 GTGGTAGACTCACCCGCAAA 59.966 55.0 0.0 0.0 37.84 3.68 F
804 908 0.175760 GCCAACATAGCTCGACCTCA 59.824 55.0 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1531 1701 1.677633 TGACATGTCTCGGCTCGGA 60.678 57.895 25.55 0.0 0.0 4.55 R
2331 2556 0.958822 AAGTCCGCAACCATCCAAAC 59.041 50.000 0.00 0.0 0.0 2.93 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
21 22 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
22 23 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
23 24 5.670485 TCACTCATTTTGCTCCGTATGTAT 58.330 37.500 0.00 0.00 0.00 2.29
24 25 6.811954 TCACTCATTTTGCTCCGTATGTATA 58.188 36.000 0.00 0.00 0.00 1.47
25 26 7.441836 TCACTCATTTTGCTCCGTATGTATAT 58.558 34.615 0.00 0.00 0.00 0.86
26 27 7.931407 TCACTCATTTTGCTCCGTATGTATATT 59.069 33.333 0.00 0.00 0.00 1.28
27 28 8.223769 CACTCATTTTGCTCCGTATGTATATTC 58.776 37.037 0.00 0.00 0.00 1.75
28 29 8.150945 ACTCATTTTGCTCCGTATGTATATTCT 58.849 33.333 0.00 0.00 0.00 2.40
29 30 8.310406 TCATTTTGCTCCGTATGTATATTCTG 57.690 34.615 0.00 0.00 0.00 3.02
30 31 6.539649 TTTTGCTCCGTATGTATATTCTGC 57.460 37.500 0.00 0.00 0.00 4.26
31 32 4.864704 TGCTCCGTATGTATATTCTGCA 57.135 40.909 0.00 0.00 0.00 4.41
32 33 5.208463 TGCTCCGTATGTATATTCTGCAA 57.792 39.130 0.00 0.00 0.00 4.08
33 34 5.793817 TGCTCCGTATGTATATTCTGCAAT 58.206 37.500 0.00 0.00 0.00 3.56
34 35 5.639082 TGCTCCGTATGTATATTCTGCAATG 59.361 40.000 0.00 0.00 0.00 2.82
35 36 5.063944 GCTCCGTATGTATATTCTGCAATGG 59.936 44.000 0.00 0.00 0.00 3.16
36 37 6.353404 TCCGTATGTATATTCTGCAATGGA 57.647 37.500 0.00 0.00 0.00 3.41
37 38 6.764379 TCCGTATGTATATTCTGCAATGGAA 58.236 36.000 0.00 0.00 0.00 3.53
38 39 7.394016 TCCGTATGTATATTCTGCAATGGAAT 58.606 34.615 5.18 5.18 37.24 3.01
39 40 7.549134 TCCGTATGTATATTCTGCAATGGAATC 59.451 37.037 3.16 0.00 35.40 2.52
40 41 7.550551 CCGTATGTATATTCTGCAATGGAATCT 59.449 37.037 3.16 0.00 35.40 2.40
41 42 8.598924 CGTATGTATATTCTGCAATGGAATCTC 58.401 37.037 3.16 0.00 35.40 2.75
42 43 9.664332 GTATGTATATTCTGCAATGGAATCTCT 57.336 33.333 3.16 0.00 35.40 3.10
49 50 7.943079 TTCTGCAATGGAATCTCTAAAATGA 57.057 32.000 0.00 0.00 0.00 2.57
50 51 7.325660 TCTGCAATGGAATCTCTAAAATGAC 57.674 36.000 0.00 0.00 0.00 3.06
51 52 6.885918 TCTGCAATGGAATCTCTAAAATGACA 59.114 34.615 0.00 0.00 0.00 3.58
52 53 7.558807 TCTGCAATGGAATCTCTAAAATGACAT 59.441 33.333 0.00 0.00 0.00 3.06
53 54 8.750515 TGCAATGGAATCTCTAAAATGACATA 57.249 30.769 0.00 0.00 0.00 2.29
54 55 9.358406 TGCAATGGAATCTCTAAAATGACATAT 57.642 29.630 0.00 0.00 0.00 1.78
72 73 9.829507 ATGACATATTTTTAGGAACTGAGAGAG 57.170 33.333 0.00 0.00 41.52 3.20
73 74 8.816894 TGACATATTTTTAGGAACTGAGAGAGT 58.183 33.333 0.00 0.00 41.52 3.24
80 81 7.657023 TTTAGGAACTGAGAGAGTATTACCC 57.343 40.000 0.00 0.00 41.52 3.69
81 82 4.548669 AGGAACTGAGAGAGTATTACCCC 58.451 47.826 0.00 0.00 37.18 4.95
82 83 3.318557 GGAACTGAGAGAGTATTACCCCG 59.681 52.174 0.00 0.00 33.09 5.73
83 84 2.308690 ACTGAGAGAGTATTACCCCGC 58.691 52.381 0.00 0.00 30.86 6.13
84 85 1.614413 CTGAGAGAGTATTACCCCGCC 59.386 57.143 0.00 0.00 0.00 6.13
85 86 1.063492 TGAGAGAGTATTACCCCGCCA 60.063 52.381 0.00 0.00 0.00 5.69
86 87 2.037144 GAGAGAGTATTACCCCGCCAA 58.963 52.381 0.00 0.00 0.00 4.52
87 88 2.433239 GAGAGAGTATTACCCCGCCAAA 59.567 50.000 0.00 0.00 0.00 3.28
88 89 2.841881 AGAGAGTATTACCCCGCCAAAA 59.158 45.455 0.00 0.00 0.00 2.44
89 90 3.264964 AGAGAGTATTACCCCGCCAAAAA 59.735 43.478 0.00 0.00 0.00 1.94
147 148 9.567776 TTTGATATAATTTCTCTTATTCCGGCA 57.432 29.630 0.00 0.00 0.00 5.69
148 149 9.567776 TTGATATAATTTCTCTTATTCCGGCAA 57.432 29.630 0.00 0.00 0.00 4.52
149 150 9.567776 TGATATAATTTCTCTTATTCCGGCAAA 57.432 29.630 0.00 0.00 0.00 3.68
159 160 8.296713 TCTCTTATTCCGGCAAATAATTAATGC 58.703 33.333 14.89 14.89 39.33 3.56
160 161 8.177119 TCTTATTCCGGCAAATAATTAATGCT 57.823 30.769 19.83 7.93 39.94 3.79
161 162 8.296713 TCTTATTCCGGCAAATAATTAATGCTC 58.703 33.333 19.83 12.38 39.94 4.26
162 163 4.481930 TCCGGCAAATAATTAATGCTCG 57.518 40.909 19.83 19.41 39.94 5.03
163 164 3.880490 TCCGGCAAATAATTAATGCTCGT 59.120 39.130 19.83 0.00 39.94 4.18
164 165 4.024387 TCCGGCAAATAATTAATGCTCGTC 60.024 41.667 19.83 7.90 39.94 4.20
165 166 4.219033 CGGCAAATAATTAATGCTCGTCC 58.781 43.478 19.83 7.64 39.94 4.79
166 167 4.260990 CGGCAAATAATTAATGCTCGTCCA 60.261 41.667 19.83 0.00 39.94 4.02
167 168 5.215160 GGCAAATAATTAATGCTCGTCCAG 58.785 41.667 19.83 0.00 39.94 3.86
168 169 5.008613 GGCAAATAATTAATGCTCGTCCAGA 59.991 40.000 19.83 0.00 39.94 3.86
170 171 6.662616 CAAATAATTAATGCTCGTCCAGAGG 58.337 40.000 0.00 0.00 46.91 3.69
174 175 3.686760 TGCTCGTCCAGAGGAGTG 58.313 61.111 16.34 0.00 46.91 3.51
175 176 2.183046 GCTCGTCCAGAGGAGTGC 59.817 66.667 16.34 3.24 46.91 4.40
176 177 2.347322 GCTCGTCCAGAGGAGTGCT 61.347 63.158 16.34 0.00 46.91 4.40
177 178 1.510383 CTCGTCCAGAGGAGTGCTG 59.490 63.158 8.81 0.00 43.20 4.41
183 184 1.595882 CAGAGGAGTGCTGGAGTGG 59.404 63.158 0.00 0.00 0.00 4.00
184 185 1.157276 AGAGGAGTGCTGGAGTGGT 59.843 57.895 0.00 0.00 0.00 4.16
185 186 0.409876 AGAGGAGTGCTGGAGTGGTA 59.590 55.000 0.00 0.00 0.00 3.25
186 187 0.820871 GAGGAGTGCTGGAGTGGTAG 59.179 60.000 0.00 0.00 0.00 3.18
187 188 0.409876 AGGAGTGCTGGAGTGGTAGA 59.590 55.000 0.00 0.00 0.00 2.59
188 189 0.533032 GGAGTGCTGGAGTGGTAGAC 59.467 60.000 0.00 0.00 0.00 2.59
189 190 1.551452 GAGTGCTGGAGTGGTAGACT 58.449 55.000 0.00 0.00 37.76 3.24
196 197 3.696084 AGTGGTAGACTCACCCGC 58.304 61.111 0.00 0.00 37.84 6.13
197 198 1.228769 AGTGGTAGACTCACCCGCA 60.229 57.895 0.00 0.00 37.84 5.69
198 199 0.830444 AGTGGTAGACTCACCCGCAA 60.830 55.000 0.00 0.00 37.84 4.85
199 200 0.034337 GTGGTAGACTCACCCGCAAA 59.966 55.000 0.00 0.00 37.84 3.68
200 201 0.759959 TGGTAGACTCACCCGCAAAA 59.240 50.000 0.00 0.00 37.84 2.44
201 202 1.141254 TGGTAGACTCACCCGCAAAAA 59.859 47.619 0.00 0.00 37.84 1.94
276 277 2.930682 GAGAACACTGCCGAGTTAATCC 59.069 50.000 0.00 0.00 0.00 3.01
278 279 0.252197 ACACTGCCGAGTTAATCCCC 59.748 55.000 0.00 0.00 0.00 4.81
280 281 0.912487 ACTGCCGAGTTAATCCCCCA 60.912 55.000 0.00 0.00 0.00 4.96
290 291 2.956333 GTTAATCCCCCAAGATTTCCCG 59.044 50.000 0.00 0.00 37.62 5.14
332 340 0.533085 GACTGCGGAGGCCCTAATTC 60.533 60.000 9.36 0.00 38.85 2.17
389 397 2.285368 TGTCCGCCTCCCCAAGAT 60.285 61.111 0.00 0.00 0.00 2.40
410 418 1.552792 GAAGACTTCTCCTCCTGGGTG 59.447 57.143 8.00 0.00 36.25 4.61
435 443 4.112341 GTGTCGCCTCCGCTACGT 62.112 66.667 0.00 0.00 33.47 3.57
561 607 2.060383 CCGACCCATCTGCTCCTGA 61.060 63.158 0.00 0.00 0.00 3.86
567 613 0.179089 CCATCTGCTCCTGACTTCCG 60.179 60.000 0.00 0.00 0.00 4.30
642 715 4.918201 GAGCGCCATCTTCCCCGG 62.918 72.222 2.29 0.00 0.00 5.73
737 832 0.727398 CGTTTTTCCCTCATCTCCGC 59.273 55.000 0.00 0.00 0.00 5.54
755 850 1.140589 CTGGCGCTCAGATCTCGTT 59.859 57.895 17.75 0.00 46.18 3.85
802 906 0.833287 ATGCCAACATAGCTCGACCT 59.167 50.000 0.00 0.00 33.67 3.85
804 908 0.175760 GCCAACATAGCTCGACCTCA 59.824 55.000 0.00 0.00 0.00 3.86
806 910 2.271800 CCAACATAGCTCGACCTCAAC 58.728 52.381 0.00 0.00 0.00 3.18
824 939 4.091939 AGCTGCTGGATCTGCGCA 62.092 61.111 10.98 10.98 36.26 6.09
839 954 2.191641 GCATCTCCAGTCCCAGGC 59.808 66.667 0.00 0.00 0.00 4.85
844 959 1.059584 TCTCCAGTCCCAGGCAAACA 61.060 55.000 0.00 0.00 0.00 2.83
847 962 2.113139 AGTCCCAGGCAAACACGG 59.887 61.111 0.00 0.00 0.00 4.94
870 985 3.190874 CTCGCCTTCCTCATGTACTTTC 58.809 50.000 0.00 0.00 0.00 2.62
873 988 3.132289 CGCCTTCCTCATGTACTTTCCTA 59.868 47.826 0.00 0.00 0.00 2.94
875 990 5.119694 GCCTTCCTCATGTACTTTCCTAAG 58.880 45.833 0.00 0.00 37.40 2.18
1225 1350 2.030185 CCTTCGAGTTTCGTCCTCTTCA 60.030 50.000 0.00 0.00 41.35 3.02
1226 1351 3.367498 CCTTCGAGTTTCGTCCTCTTCAT 60.367 47.826 0.00 0.00 41.35 2.57
1272 1421 2.964464 TCAAAAGCTCTGGCCATTCAAA 59.036 40.909 5.51 0.00 39.73 2.69
1287 1436 3.737559 TTCAAACCAGGCACCAGATAT 57.262 42.857 0.00 0.00 0.00 1.63
1531 1701 3.634397 ATGTCATCACGGTTGGATCTT 57.366 42.857 0.00 0.00 0.00 2.40
1653 1829 1.533273 AGTCCAGCACCGTGGTAGT 60.533 57.895 2.23 0.00 38.88 2.73
1736 1912 1.940613 GTTTGACACAGAAGCCGAGTT 59.059 47.619 0.00 0.00 0.00 3.01
1749 1925 3.162666 AGCCGAGTTATTCCGATGGATA 58.837 45.455 0.00 0.00 0.00 2.59
1826 2008 0.969409 GCTTTCTGGGGCAGCAGATT 60.969 55.000 0.00 0.00 33.45 2.40
2043 2247 2.049063 AACGACCGTGAGCTGCTC 60.049 61.111 22.38 22.38 0.00 4.26
2130 2334 5.614324 ACATTGGGAAGAGTCAATATCGA 57.386 39.130 0.00 0.00 32.92 3.59
2151 2357 4.262207 CGAATGATGCTCACCCAGTACTAT 60.262 45.833 0.00 0.00 0.00 2.12
2276 2498 7.552050 TGTTTTATCCTTGGATTTTGGACAT 57.448 32.000 7.52 0.00 32.16 3.06
2308 2530 8.531982 TCATTTGCTCTTAGCTCTTCTTACTTA 58.468 33.333 0.00 0.00 42.97 2.24
2311 2536 6.857956 TGCTCTTAGCTCTTCTTACTTAGTG 58.142 40.000 0.00 0.00 42.97 2.74
2320 2545 6.095160 GCTCTTCTTACTTAGTGCTACCAGTA 59.905 42.308 0.00 0.00 0.00 2.74
2331 2556 2.093500 TGCTACCAGTAGAACATGCCAG 60.093 50.000 9.02 0.00 35.21 4.85
2429 2702 6.798427 TCTTCCTAATGCTCTGAACTATGT 57.202 37.500 0.00 0.00 0.00 2.29
2430 2703 6.577103 TCTTCCTAATGCTCTGAACTATGTG 58.423 40.000 0.00 0.00 0.00 3.21
2441 2714 8.743714 TGCTCTGAACTATGTGGTATCTATATG 58.256 37.037 0.00 0.00 0.00 1.78
2467 2740 9.797556 GTGTTATTGAAACCTTTTCTACTGTTT 57.202 29.630 0.68 0.00 33.87 2.83
2535 2816 6.950545 TCTGTTATTGTGTTTTAGTCGTTGG 58.049 36.000 0.00 0.00 0.00 3.77
2620 2902 0.673437 ATTTGGTGCAAACACTCGGG 59.327 50.000 0.00 0.00 46.57 5.14
2621 2903 0.681564 TTTGGTGCAAACACTCGGGT 60.682 50.000 0.00 0.00 46.57 5.28
2623 2905 2.258726 GGTGCAAACACTCGGGTCC 61.259 63.158 0.00 0.00 46.57 4.46
2624 2906 1.227853 GTGCAAACACTCGGGTCCT 60.228 57.895 0.00 0.00 43.85 3.85
2625 2907 0.034337 GTGCAAACACTCGGGTCCTA 59.966 55.000 0.00 0.00 43.85 2.94
2626 2908 0.034337 TGCAAACACTCGGGTCCTAC 59.966 55.000 0.00 0.00 0.00 3.18
2627 2909 0.320697 GCAAACACTCGGGTCCTACT 59.679 55.000 0.00 0.00 0.00 2.57
2628 2910 1.672145 GCAAACACTCGGGTCCTACTC 60.672 57.143 0.00 0.00 0.00 2.59
2629 2911 1.616865 CAAACACTCGGGTCCTACTCA 59.383 52.381 0.00 0.00 0.00 3.41
2630 2912 1.546961 AACACTCGGGTCCTACTCAG 58.453 55.000 0.00 0.00 0.00 3.35
2660 2950 3.574284 TCGGAATGCAATTTGGTCAAG 57.426 42.857 0.00 0.00 36.07 3.02
2666 2956 5.422145 GAATGCAATTTGGTCAAGGCTATT 58.578 37.500 0.00 0.00 36.07 1.73
2667 2957 4.888326 TGCAATTTGGTCAAGGCTATTT 57.112 36.364 0.00 0.00 0.00 1.40
2668 2958 4.567971 TGCAATTTGGTCAAGGCTATTTG 58.432 39.130 0.00 0.00 0.00 2.32
2707 2997 6.188400 ACTTTCTATGCTTTTGCTTAGCTC 57.812 37.500 5.60 0.00 46.52 4.09
2723 3013 5.569026 GCTTAGCTCTGTACATTATACCCCC 60.569 48.000 0.00 0.00 0.00 5.40
2801 3094 9.671279 TGCTGATATGATTAAAGAGAAACTTGA 57.329 29.630 0.00 0.00 38.98 3.02
2928 3247 2.744202 CAAGACAGGTGTGCTGGTTATC 59.256 50.000 0.00 0.00 0.00 1.75
2970 3293 2.632512 GGATTTTTCCTTGCCCAGTTCA 59.367 45.455 0.00 0.00 0.00 3.18
2986 3309 4.279671 CCAGTTCAGCCGATATAAGACTCT 59.720 45.833 0.00 0.00 0.00 3.24
3058 3381 3.371285 GGAACTCCGCAATTCTACTGTTC 59.629 47.826 0.00 0.00 33.87 3.18
3084 3407 6.748658 CGTCCATGTAACTAAAGTGACGAATA 59.251 38.462 10.99 0.00 31.87 1.75
3085 3408 7.434307 CGTCCATGTAACTAAAGTGACGAATAT 59.566 37.037 10.99 0.00 31.87 1.28
3086 3409 9.740239 GTCCATGTAACTAAAGTGACGAATATA 57.260 33.333 0.00 0.00 31.87 0.86
3136 3459 6.704937 AGTACTAAAACCTTCTCTTGTTTCCG 59.295 38.462 0.00 0.00 33.76 4.30
3200 3524 0.462759 CCAAGATTGTCCCTCTCCGC 60.463 60.000 0.00 0.00 0.00 5.54
3208 3532 3.710722 CCCTCTCCGCTTGCACCT 61.711 66.667 0.00 0.00 0.00 4.00
3230 3558 0.607489 GCTCATCAGTTGTGGCACCT 60.607 55.000 16.26 2.47 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
4 5 7.095229 GCAGAATATACATACGGAGCAAAATGA 60.095 37.037 0.00 0.00 0.00 2.57
5 6 7.017645 GCAGAATATACATACGGAGCAAAATG 58.982 38.462 0.00 0.00 0.00 2.32
6 7 6.710295 TGCAGAATATACATACGGAGCAAAAT 59.290 34.615 0.00 0.00 0.00 1.82
7 8 6.052360 TGCAGAATATACATACGGAGCAAAA 58.948 36.000 0.00 0.00 0.00 2.44
8 9 5.606505 TGCAGAATATACATACGGAGCAAA 58.393 37.500 0.00 0.00 0.00 3.68
10 11 4.864704 TGCAGAATATACATACGGAGCA 57.135 40.909 0.00 0.00 0.00 4.26
11 12 5.063944 CCATTGCAGAATATACATACGGAGC 59.936 44.000 0.00 0.00 0.00 4.70
12 13 6.398095 TCCATTGCAGAATATACATACGGAG 58.602 40.000 0.00 0.00 0.00 4.63
13 14 6.353404 TCCATTGCAGAATATACATACGGA 57.647 37.500 0.00 0.00 0.00 4.69
14 15 7.550551 AGATTCCATTGCAGAATATACATACGG 59.449 37.037 0.05 0.00 34.12 4.02
15 16 8.484641 AGATTCCATTGCAGAATATACATACG 57.515 34.615 0.05 0.00 34.12 3.06
16 17 9.664332 AGAGATTCCATTGCAGAATATACATAC 57.336 33.333 0.05 0.00 34.12 2.39
23 24 9.631257 TCATTTTAGAGATTCCATTGCAGAATA 57.369 29.630 0.05 0.00 34.12 1.75
24 25 8.411683 GTCATTTTAGAGATTCCATTGCAGAAT 58.588 33.333 0.00 0.00 36.66 2.40
25 26 7.394077 TGTCATTTTAGAGATTCCATTGCAGAA 59.606 33.333 0.00 0.00 0.00 3.02
26 27 6.885918 TGTCATTTTAGAGATTCCATTGCAGA 59.114 34.615 0.00 0.00 0.00 4.26
27 28 7.092137 TGTCATTTTAGAGATTCCATTGCAG 57.908 36.000 0.00 0.00 0.00 4.41
28 29 7.649533 ATGTCATTTTAGAGATTCCATTGCA 57.350 32.000 0.00 0.00 0.00 4.08
46 47 9.829507 CTCTCTCAGTTCCTAAAAATATGTCAT 57.170 33.333 0.00 0.00 0.00 3.06
47 48 8.816894 ACTCTCTCAGTTCCTAAAAATATGTCA 58.183 33.333 0.00 0.00 26.56 3.58
54 55 8.537858 GGGTAATACTCTCTCAGTTCCTAAAAA 58.462 37.037 0.00 0.00 36.43 1.94
55 56 7.125356 GGGGTAATACTCTCTCAGTTCCTAAAA 59.875 40.741 0.00 0.00 36.43 1.52
56 57 6.610425 GGGGTAATACTCTCTCAGTTCCTAAA 59.390 42.308 0.00 0.00 36.43 1.85
57 58 6.134754 GGGGTAATACTCTCTCAGTTCCTAA 58.865 44.000 0.00 0.00 36.43 2.69
58 59 5.689564 CGGGGTAATACTCTCTCAGTTCCTA 60.690 48.000 0.00 0.00 36.43 2.94
59 60 4.548669 GGGGTAATACTCTCTCAGTTCCT 58.451 47.826 0.00 0.00 36.43 3.36
60 61 3.318557 CGGGGTAATACTCTCTCAGTTCC 59.681 52.174 0.00 0.00 36.43 3.62
61 62 3.243468 GCGGGGTAATACTCTCTCAGTTC 60.243 52.174 0.00 0.00 36.43 3.01
62 63 2.694109 GCGGGGTAATACTCTCTCAGTT 59.306 50.000 0.00 0.00 36.43 3.16
63 64 2.308690 GCGGGGTAATACTCTCTCAGT 58.691 52.381 0.00 0.00 39.41 3.41
64 65 1.614413 GGCGGGGTAATACTCTCTCAG 59.386 57.143 0.00 0.00 0.00 3.35
65 66 1.063492 TGGCGGGGTAATACTCTCTCA 60.063 52.381 0.00 0.00 0.00 3.27
66 67 1.700955 TGGCGGGGTAATACTCTCTC 58.299 55.000 0.00 0.00 0.00 3.20
67 68 2.170012 TTGGCGGGGTAATACTCTCT 57.830 50.000 0.00 0.00 0.00 3.10
68 69 2.994186 TTTGGCGGGGTAATACTCTC 57.006 50.000 0.00 0.00 0.00 3.20
69 70 3.724732 TTTTTGGCGGGGTAATACTCT 57.275 42.857 0.00 0.00 0.00 3.24
121 122 9.567776 TGCCGGAATAAGAGAAATTATATCAAA 57.432 29.630 5.05 0.00 0.00 2.69
122 123 9.567776 TTGCCGGAATAAGAGAAATTATATCAA 57.432 29.630 5.05 0.00 0.00 2.57
123 124 9.567776 TTTGCCGGAATAAGAGAAATTATATCA 57.432 29.630 5.05 0.00 0.00 2.15
133 134 8.296713 GCATTAATTATTTGCCGGAATAAGAGA 58.703 33.333 5.05 0.00 35.58 3.10
134 135 8.299570 AGCATTAATTATTTGCCGGAATAAGAG 58.700 33.333 5.05 0.00 35.58 2.85
135 136 8.177119 AGCATTAATTATTTGCCGGAATAAGA 57.823 30.769 5.05 0.00 35.58 2.10
136 137 7.271223 CGAGCATTAATTATTTGCCGGAATAAG 59.729 37.037 5.05 0.00 35.58 1.73
137 138 7.081349 CGAGCATTAATTATTTGCCGGAATAA 58.919 34.615 5.05 8.32 37.07 1.40
138 139 6.205853 ACGAGCATTAATTATTTGCCGGAATA 59.794 34.615 5.05 0.00 37.07 1.75
139 140 5.009610 ACGAGCATTAATTATTTGCCGGAAT 59.990 36.000 5.05 0.00 37.07 3.01
140 141 4.336993 ACGAGCATTAATTATTTGCCGGAA 59.663 37.500 5.05 0.00 37.07 4.30
141 142 3.880490 ACGAGCATTAATTATTTGCCGGA 59.120 39.130 5.05 0.00 37.07 5.14
142 143 4.219033 GACGAGCATTAATTATTTGCCGG 58.781 43.478 21.47 0.00 37.07 6.13
143 144 4.219033 GGACGAGCATTAATTATTTGCCG 58.781 43.478 18.84 18.84 37.07 5.69
144 145 5.008613 TCTGGACGAGCATTAATTATTTGCC 59.991 40.000 14.16 7.72 37.07 4.52
145 146 6.060028 TCTGGACGAGCATTAATTATTTGC 57.940 37.500 11.19 11.19 36.63 3.68
146 147 6.483307 TCCTCTGGACGAGCATTAATTATTTG 59.517 38.462 0.00 0.00 38.49 2.32
147 148 6.591935 TCCTCTGGACGAGCATTAATTATTT 58.408 36.000 0.00 0.00 38.49 1.40
148 149 6.174720 TCCTCTGGACGAGCATTAATTATT 57.825 37.500 0.00 0.00 38.49 1.40
149 150 5.305644 ACTCCTCTGGACGAGCATTAATTAT 59.694 40.000 0.00 0.00 38.49 1.28
150 151 4.649674 ACTCCTCTGGACGAGCATTAATTA 59.350 41.667 0.00 0.00 38.49 1.40
151 152 3.452627 ACTCCTCTGGACGAGCATTAATT 59.547 43.478 0.00 0.00 38.49 1.40
152 153 3.034635 ACTCCTCTGGACGAGCATTAAT 58.965 45.455 0.00 0.00 38.49 1.40
153 154 2.166459 CACTCCTCTGGACGAGCATTAA 59.834 50.000 0.00 0.00 38.49 1.40
154 155 1.751351 CACTCCTCTGGACGAGCATTA 59.249 52.381 0.00 0.00 38.49 1.90
155 156 0.534412 CACTCCTCTGGACGAGCATT 59.466 55.000 0.00 0.00 38.49 3.56
156 157 1.954362 GCACTCCTCTGGACGAGCAT 61.954 60.000 0.00 0.00 38.49 3.79
157 158 2.640302 GCACTCCTCTGGACGAGCA 61.640 63.158 0.00 0.00 38.49 4.26
158 159 2.183046 GCACTCCTCTGGACGAGC 59.817 66.667 0.00 0.00 38.49 5.03
159 160 1.510383 CAGCACTCCTCTGGACGAG 59.490 63.158 0.00 0.00 39.57 4.18
160 161 3.686760 CAGCACTCCTCTGGACGA 58.313 61.111 0.00 0.00 0.00 4.20
165 166 1.190833 ACCACTCCAGCACTCCTCTG 61.191 60.000 0.00 0.00 0.00 3.35
166 167 0.409876 TACCACTCCAGCACTCCTCT 59.590 55.000 0.00 0.00 0.00 3.69
167 168 0.820871 CTACCACTCCAGCACTCCTC 59.179 60.000 0.00 0.00 0.00 3.71
168 169 0.409876 TCTACCACTCCAGCACTCCT 59.590 55.000 0.00 0.00 0.00 3.69
169 170 0.533032 GTCTACCACTCCAGCACTCC 59.467 60.000 0.00 0.00 0.00 3.85
170 171 1.474879 GAGTCTACCACTCCAGCACTC 59.525 57.143 0.00 0.00 45.47 3.51
171 172 1.551452 GAGTCTACCACTCCAGCACT 58.449 55.000 0.00 0.00 45.47 4.40
179 180 0.830444 TTGCGGGTGAGTCTACCACT 60.830 55.000 12.09 0.00 42.69 4.00
180 181 0.034337 TTTGCGGGTGAGTCTACCAC 59.966 55.000 12.09 0.00 42.69 4.16
181 182 0.759959 TTTTGCGGGTGAGTCTACCA 59.240 50.000 12.09 0.00 42.69 3.25
182 183 1.886886 TTTTTGCGGGTGAGTCTACC 58.113 50.000 3.83 3.83 40.10 3.18
208 209 1.810959 TTTGCGGGTGTGTATACCAC 58.189 50.000 13.19 13.19 42.69 4.16
237 238 5.708697 TGTTCTCTTATGACGAGTCTACCAA 59.291 40.000 4.78 0.00 0.00 3.67
276 277 0.611896 AGTTGCGGGAAATCTTGGGG 60.612 55.000 0.00 0.00 0.00 4.96
278 279 1.470098 CTCAGTTGCGGGAAATCTTGG 59.530 52.381 0.00 0.00 0.00 3.61
280 281 2.814336 GTTCTCAGTTGCGGGAAATCTT 59.186 45.455 0.00 0.00 0.00 2.40
290 291 0.601311 ACTCGGCAGTTCTCAGTTGC 60.601 55.000 0.00 0.00 37.11 4.17
319 320 3.933861 TGAGAAAGAATTAGGGCCTCC 57.066 47.619 10.74 0.00 0.00 4.30
332 340 3.559242 GGCGAGATCTGGAAATGAGAAAG 59.441 47.826 9.17 0.00 0.00 2.62
362 370 3.245315 GGCGGACACGATTCGACG 61.245 66.667 13.95 11.99 44.60 5.12
367 375 3.782443 GGGGAGGCGGACACGATT 61.782 66.667 0.00 0.00 44.60 3.34
389 397 1.150135 ACCCAGGAGGAGAAGTCTTCA 59.850 52.381 14.97 0.00 39.89 3.02
410 418 4.773117 GAGGCGACACGACCGGAC 62.773 72.222 9.46 0.00 34.11 4.79
435 443 1.077828 TCCCAAGAGGAGAAGCTCTCA 59.922 52.381 13.06 0.00 45.12 3.27
561 607 1.139095 GCGAAGACGATCCGGAAGT 59.861 57.895 9.01 12.57 42.66 3.01
642 715 2.203195 TCACCTGTGTGGCTGTGC 60.203 61.111 0.00 0.00 42.98 4.57
737 832 0.459237 AAACGAGATCTGAGCGCCAG 60.459 55.000 16.84 16.84 44.27 4.85
755 850 1.134699 CGCCTCTCTGCAGGAATACAA 60.135 52.381 15.13 0.00 35.20 2.41
802 906 0.675837 GCAGATCCAGCAGCTGTTGA 60.676 55.000 29.70 16.77 32.39 3.18
804 908 1.744368 CGCAGATCCAGCAGCTGTT 60.744 57.895 21.26 6.37 32.39 3.16
806 910 3.574445 GCGCAGATCCAGCAGCTG 61.574 66.667 16.23 16.23 0.00 4.24
847 962 0.530870 GTACATGAGGAAGGCGAGGC 60.531 60.000 0.00 0.00 0.00 4.70
849 964 2.969628 AAGTACATGAGGAAGGCGAG 57.030 50.000 0.00 0.00 0.00 5.03
861 976 3.518303 AGGAACGCCTTAGGAAAGTACAT 59.482 43.478 0.69 0.00 43.90 2.29
875 990 1.816224 TGGCTTGAATTAAGGAACGCC 59.184 47.619 0.00 0.00 36.87 5.68
983 1108 0.249120 CATGGTGCTCCGTTGGACTA 59.751 55.000 0.00 0.00 36.30 2.59
1139 1264 5.657474 GATGGTGTTCAAGCATGAATTCAT 58.343 37.500 15.36 15.36 46.95 2.57
1272 1421 2.779430 TGAATGATATCTGGTGCCTGGT 59.221 45.455 3.98 0.00 0.00 4.00
1531 1701 1.677633 TGACATGTCTCGGCTCGGA 60.678 57.895 25.55 0.00 0.00 4.55
1736 1912 4.280929 CAGGAGTGTGTATCCATCGGAATA 59.719 45.833 0.00 0.00 39.47 1.75
1749 1925 3.958860 GGCTGGGCAGGAGTGTGT 61.959 66.667 0.00 0.00 0.00 3.72
1826 2008 1.982660 ACCGATATTCGAGCTGGAGA 58.017 50.000 0.00 0.00 43.74 3.71
2043 2247 8.246180 AGCACATGTTCTGAATTAAACCTTATG 58.754 33.333 0.00 0.00 0.00 1.90
2151 2357 5.682234 TTGGAATAATGCTCTCACTGAGA 57.318 39.130 8.50 8.50 45.39 3.27
2276 2498 3.349927 AGCTAAGAGCAAATGACATGCA 58.650 40.909 3.97 0.00 45.56 3.96
2284 2506 8.536175 ACTAAGTAAGAAGAGCTAAGAGCAAAT 58.464 33.333 0.64 0.00 45.56 2.32
2289 2511 7.095695 AGCACTAAGTAAGAAGAGCTAAGAG 57.904 40.000 0.00 0.00 0.00 2.85
2308 2530 2.093447 GGCATGTTCTACTGGTAGCACT 60.093 50.000 10.69 0.00 31.94 4.40
2311 2536 2.093447 ACTGGCATGTTCTACTGGTAGC 60.093 50.000 3.13 0.00 33.32 3.58
2320 2545 2.173519 CCATCCAAACTGGCATGTTCT 58.826 47.619 0.00 0.00 37.47 3.01
2331 2556 0.958822 AAGTCCGCAACCATCCAAAC 59.041 50.000 0.00 0.00 0.00 2.93
2441 2714 9.797556 AAACAGTAGAAAAGGTTTCAATAACAC 57.202 29.630 3.74 0.00 0.00 3.32
2510 2790 7.442969 TCCAACGACTAAAACACAATAACAGAT 59.557 33.333 0.00 0.00 0.00 2.90
2660 2950 4.342665 AGGAGTACTACTCTGCAAATAGCC 59.657 45.833 14.61 0.00 44.46 3.93
2688 2978 4.836825 ACAGAGCTAAGCAAAAGCATAGA 58.163 39.130 4.15 0.00 42.62 1.98
2707 2997 6.013725 TGCTGATTAGGGGGTATAATGTACAG 60.014 42.308 0.33 0.00 0.00 2.74
2723 3013 7.467557 ACAACAAAAATTGTGTGCTGATTAG 57.532 32.000 0.00 0.00 44.59 1.73
2801 3094 4.643334 TGCTACCGAAGTACATGACAGTAT 59.357 41.667 0.00 0.00 0.00 2.12
2853 3172 8.224389 TCTACCTTAAAAGTACCAAAAACACC 57.776 34.615 0.00 0.00 0.00 4.16
2912 3231 0.036388 ACCGATAACCAGCACACCTG 60.036 55.000 0.00 0.00 41.41 4.00
2928 3247 6.268825 TCCTTAGCTAGCTATAATGAACCG 57.731 41.667 24.69 2.58 0.00 4.44
2963 3286 4.279671 AGAGTCTTATATCGGCTGAACTGG 59.720 45.833 0.00 0.00 0.00 4.00
2970 3293 9.646427 GAATTATTGAAGAGTCTTATATCGGCT 57.354 33.333 5.09 0.00 0.00 5.52
3058 3381 3.611113 CGTCACTTTAGTTACATGGACGG 59.389 47.826 0.00 0.00 42.06 4.79
3086 3409 9.614792 CTAAGTTTCCTTTGCTAGGTGTTATAT 57.385 33.333 5.52 0.00 45.03 0.86
3087 3410 8.599792 ACTAAGTTTCCTTTGCTAGGTGTTATA 58.400 33.333 5.52 0.00 45.03 0.98
3118 3441 3.135895 TCTCCGGAAACAAGAGAAGGTTT 59.864 43.478 5.23 0.00 39.74 3.27
3136 3459 2.774809 AGGGGCAGATACTTTTCTCTCC 59.225 50.000 0.00 0.00 0.00 3.71
3200 3524 0.725686 CTGATGAGCGAAGGTGCAAG 59.274 55.000 0.00 0.00 39.88 4.01
3208 3532 0.250252 TGCCACAACTGATGAGCGAA 60.250 50.000 0.00 0.00 35.50 4.70


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

AutoCloner maintained by Alex Coulton.