Multiple sequence alignment - TraesCS6B01G386900

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 TraesCS6B01G386900 chr6B 100.000 3722 0 0 1 3722 661840116 661843837 0.000000e+00 6874.0
1 TraesCS6B01G386900 chr6B 90.945 1535 123 5 516 2050 661709776 661711294 0.000000e+00 2050.0
2 TraesCS6B01G386900 chr6B 90.691 1128 105 0 923 2050 661569098 661570225 0.000000e+00 1502.0
3 TraesCS6B01G386900 chr6B 87.736 212 22 3 3511 3720 720648770 720648979 1.030000e-60 244.0
4 TraesCS6B01G386900 chr6D 96.028 1284 47 2 919 2200 437267763 437269044 0.000000e+00 2085.0
5 TraesCS6B01G386900 chr6D 93.794 854 35 6 2873 3722 437270107 437270946 0.000000e+00 1267.0
6 TraesCS6B01G386900 chr6D 89.803 912 82 10 1 904 421890209 421891117 0.000000e+00 1158.0
7 TraesCS6B01G386900 chr6D 94.939 494 18 5 2386 2873 437269045 437269537 0.000000e+00 767.0
8 TraesCS6B01G386900 chr6D 79.753 973 179 13 1084 2050 437187212 437188172 0.000000e+00 689.0
9 TraesCS6B01G386900 chr6D 89.252 214 19 3 3511 3722 470519489 470519278 7.930000e-67 265.0
10 TraesCS6B01G386900 chr1D 90.044 914 84 7 6 915 27990483 27989573 0.000000e+00 1177.0
11 TraesCS6B01G386900 chr1D 80.463 389 53 12 3353 3722 130295381 130295765 3.660000e-70 276.0
12 TraesCS6B01G386900 chr1D 86.806 144 16 3 3356 3497 148662397 148662539 1.380000e-34 158.0
13 TraesCS6B01G386900 chr1A 89.783 920 83 9 1 915 583589296 583588383 0.000000e+00 1168.0
14 TraesCS6B01G386900 chr1A 92.268 194 15 0 2200 2393 309178231 309178424 3.660000e-70 276.0
15 TraesCS6B01G386900 chr1A 77.807 374 70 13 3356 3722 202182041 202182408 6.260000e-53 219.0
16 TraesCS6B01G386900 chr1B 89.142 921 94 6 2 918 31355199 31356117 0.000000e+00 1142.0
17 TraesCS6B01G386900 chr2D 89.427 908 89 7 15 918 320485632 320484728 0.000000e+00 1138.0
18 TraesCS6B01G386900 chr2D 88.829 922 93 9 1 917 13992325 13991409 0.000000e+00 1123.0
19 TraesCS6B01G386900 chr2D 89.796 49 3 2 2874 2921 73590941 73590894 1.120000e-05 62.1
20 TraesCS6B01G386900 chr7B 89.480 903 89 6 6 903 467711601 467712502 0.000000e+00 1136.0
21 TraesCS6B01G386900 chrUn 89.192 916 89 9 10 918 9919917 9920829 0.000000e+00 1134.0
22 TraesCS6B01G386900 chr4D 88.357 919 95 12 1 916 85178793 85177884 0.000000e+00 1094.0
23 TraesCS6B01G386900 chr4D 80.214 374 63 8 3356 3722 122691987 122691618 1.700000e-68 270.0
24 TraesCS6B01G386900 chr4D 84.211 152 21 3 3347 3497 498629521 498629372 1.080000e-30 145.0
25 TraesCS6B01G386900 chr5D 84.334 383 42 8 3353 3722 472747083 472747460 3.530000e-95 359.0
26 TraesCS6B01G386900 chr5D 91.837 196 14 2 2200 2394 488352505 488352311 4.740000e-69 272.0
27 TraesCS6B01G386900 chr5D 80.392 153 25 5 3356 3505 342230188 342230338 1.090000e-20 111.0
28 TraesCS6B01G386900 chr5D 95.000 40 2 0 2882 2921 449275977 449275938 3.100000e-06 63.9
29 TraesCS6B01G386900 chr5B 82.723 382 44 13 3360 3722 428145419 428145797 1.670000e-83 320.0
30 TraesCS6B01G386900 chr5B 93.023 43 3 0 2879 2921 548724271 548724313 3.100000e-06 63.9
31 TraesCS6B01G386900 chr5A 88.797 241 24 2 3485 3722 269283241 269283481 3.640000e-75 292.0
32 TraesCS6B01G386900 chr5A 87.190 242 29 2 3479 3720 644019187 644018948 1.320000e-69 274.0
33 TraesCS6B01G386900 chr5A 91.795 195 16 0 2200 2394 32064401 32064207 4.740000e-69 272.0
34 TraesCS6B01G386900 chr5A 95.000 40 2 0 2882 2921 568160853 568160814 3.100000e-06 63.9
35 TraesCS6B01G386900 chr7A 94.086 186 9 2 2200 2384 723356043 723355859 7.870000e-72 281.0
36 TraesCS6B01G386900 chr7A 91.878 197 13 3 2201 2396 493517878 493517684 4.740000e-69 272.0
37 TraesCS6B01G386900 chr3A 94.086 186 9 2 2200 2384 323103774 323103958 7.870000e-72 281.0
38 TraesCS6B01G386900 chr3A 91.414 198 13 4 2200 2396 401557376 401557570 6.130000e-68 268.0
39 TraesCS6B01G386900 chr3A 91.667 48 4 0 2874 2921 712154898 712154851 2.400000e-07 67.6
40 TraesCS6B01G386900 chr6A 91.667 204 14 3 2201 2402 7988459 7988661 2.830000e-71 279.0
41 TraesCS6B01G386900 chr2A 92.708 192 13 1 2201 2392 774010393 774010583 3.660000e-70 276.0
42 TraesCS6B01G386900 chr4A 78.175 252 42 11 3352 3596 718244783 718245028 8.330000e-32 148.0
43 TraesCS6B01G386900 chr4A 91.667 48 4 0 2874 2921 576057480 576057433 2.400000e-07 67.6
44 TraesCS6B01G386900 chr3D 85.816 141 19 1 3356 3495 373321365 373321225 8.330000e-32 148.0
45 TraesCS6B01G386900 chr3D 91.667 48 4 0 2874 2921 576773296 576773249 2.400000e-07 67.6
46 TraesCS6B01G386900 chr7D 91.667 48 4 0 2874 2921 63724498 63724545 2.400000e-07 67.6


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 TraesCS6B01G386900 chr6B 661840116 661843837 3721 False 6874 6874 100.000000 1 3722 1 chr6B.!!$F3 3721
1 TraesCS6B01G386900 chr6B 661709776 661711294 1518 False 2050 2050 90.945000 516 2050 1 chr6B.!!$F2 1534
2 TraesCS6B01G386900 chr6B 661569098 661570225 1127 False 1502 1502 90.691000 923 2050 1 chr6B.!!$F1 1127
3 TraesCS6B01G386900 chr6D 437267763 437270946 3183 False 1373 2085 94.920333 919 3722 3 chr6D.!!$F3 2803
4 TraesCS6B01G386900 chr6D 421890209 421891117 908 False 1158 1158 89.803000 1 904 1 chr6D.!!$F1 903
5 TraesCS6B01G386900 chr6D 437187212 437188172 960 False 689 689 79.753000 1084 2050 1 chr6D.!!$F2 966
6 TraesCS6B01G386900 chr1D 27989573 27990483 910 True 1177 1177 90.044000 6 915 1 chr1D.!!$R1 909
7 TraesCS6B01G386900 chr1A 583588383 583589296 913 True 1168 1168 89.783000 1 915 1 chr1A.!!$R1 914
8 TraesCS6B01G386900 chr1B 31355199 31356117 918 False 1142 1142 89.142000 2 918 1 chr1B.!!$F1 916
9 TraesCS6B01G386900 chr2D 320484728 320485632 904 True 1138 1138 89.427000 15 918 1 chr2D.!!$R3 903
10 TraesCS6B01G386900 chr2D 13991409 13992325 916 True 1123 1123 88.829000 1 917 1 chr2D.!!$R1 916
11 TraesCS6B01G386900 chr7B 467711601 467712502 901 False 1136 1136 89.480000 6 903 1 chr7B.!!$F1 897
12 TraesCS6B01G386900 chrUn 9919917 9920829 912 False 1134 1134 89.192000 10 918 1 chrUn.!!$F1 908
13 TraesCS6B01G386900 chr4D 85177884 85178793 909 True 1094 1094 88.357000 1 916 1 chr4D.!!$R1 915

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
848 867 0.602638 TTGATCGTGCTGCTTCCGTT 60.603 50.0 0.0 0.0 0.0 4.44 F
1487 1511 0.538287 GTATGATCTTGGGGGCAGGC 60.538 60.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1743 1767 0.251634 TGTGTGCATATCGAAGCCCA 59.748 50.0 0.00 0.0 0.0 5.36 R
2950 3550 0.038166 GGAAGCTGACCATCCAACCA 59.962 55.0 5.47 0.0 33.3 3.67 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
136 138 1.338136 CCATCTGGGTTCTAGCGGGT 61.338 60.000 0.00 0.00 0.00 5.28
141 144 3.766691 GGTTCTAGCGGGTCGGCA 61.767 66.667 0.00 0.00 34.64 5.69
258 262 2.263540 GGAGCTTTACGGGCGTGA 59.736 61.111 0.00 0.00 34.52 4.35
318 322 2.699954 CTCCTGCTATTGTGTTCGGTT 58.300 47.619 0.00 0.00 0.00 4.44
382 387 4.029809 GGTGTTGCGGCCCCTAGT 62.030 66.667 0.00 0.00 0.00 2.57
385 390 3.400054 GTTGCGGCCCCTAGTCCT 61.400 66.667 0.00 0.00 0.00 3.85
425 430 4.373116 GGCCTCACTTCGCGGTGA 62.373 66.667 15.79 15.79 42.96 4.02
774 782 3.486875 CGTGAAGCTTCTTTGTTTCCGTT 60.487 43.478 26.09 0.00 0.00 4.44
848 867 0.602638 TTGATCGTGCTGCTTCCGTT 60.603 50.000 0.00 0.00 0.00 4.44
853 872 1.598130 GTGCTGCTTCCGTTCCAGT 60.598 57.895 0.00 0.00 0.00 4.00
885 904 6.870971 TTGACTGTATTGGTTGGTTACTTC 57.129 37.500 0.00 0.00 0.00 3.01
927 946 9.770503 GAAAACCCTATTTCGAAGATTTAGAAC 57.229 33.333 0.00 0.00 35.04 3.01
1059 1078 2.677875 CCCTGCCAGGTCTTTGCC 60.678 66.667 10.47 0.00 31.93 4.52
1198 1219 1.297967 CGAGATCGACGTGCTCCTG 60.298 63.158 0.00 0.00 43.02 3.86
1258 1279 4.415332 CGTGACCCGGACACCTCG 62.415 72.222 20.23 9.72 35.17 4.63
1315 1336 4.493747 CGGGTCGCTCTTCCGTCC 62.494 72.222 0.00 0.00 39.04 4.79
1316 1337 3.069318 GGGTCGCTCTTCCGTCCT 61.069 66.667 0.00 0.00 36.79 3.85
1485 1509 1.270518 CGAGTATGATCTTGGGGGCAG 60.271 57.143 0.00 0.00 0.00 4.85
1487 1511 0.538287 GTATGATCTTGGGGGCAGGC 60.538 60.000 0.00 0.00 0.00 4.85
1510 1534 3.081804 GGTGGTGATCAAAGAATTCCGT 58.918 45.455 0.00 0.00 0.00 4.69
1597 1621 2.346803 CATAGCAAGTACGGTGTGCTT 58.653 47.619 17.20 2.96 46.25 3.91
1617 1641 4.856607 GTTCTCGCCGGAGCCGAG 62.857 72.222 20.06 20.06 42.83 4.63
1680 1704 0.716108 CCGAACGATGAAGACTGTGC 59.284 55.000 0.00 0.00 0.00 4.57
1717 1741 2.108075 TCTCTTGGACCTTGATGGCAAA 59.892 45.455 0.00 0.00 40.22 3.68
1743 1767 7.721399 ACTTCACATGGTGTCTATCTTCTTTTT 59.279 33.333 0.00 0.00 34.79 1.94
1896 1920 0.462225 TGTCCGGCGAACAAGTTCAA 60.462 50.000 9.30 0.00 39.46 2.69
1965 1989 6.401688 CGTTTACACGTGTATGACATTGGATT 60.402 38.462 27.82 0.00 41.84 3.01
2050 2074 1.024046 TGGTTTCCGCACATCATCCG 61.024 55.000 0.00 0.00 0.00 4.18
2072 2096 5.825679 CCGGGACCAATTGAATAAGATTGTA 59.174 40.000 7.12 0.00 32.65 2.41
2170 2194 8.552034 GTTAGCTTGATCATGAGTATGTTTACC 58.448 37.037 12.54 0.00 35.73 2.85
2172 2196 5.559035 GCTTGATCATGAGTATGTTTACCGC 60.559 44.000 12.54 0.00 35.73 5.68
2200 2224 2.819608 ACATAATTGTCCAGTGCCACAC 59.180 45.455 0.00 0.00 34.10 3.82
2201 2225 2.647683 TAATTGTCCAGTGCCACACA 57.352 45.000 0.00 0.00 36.74 3.72
2202 2226 1.321474 AATTGTCCAGTGCCACACAG 58.679 50.000 0.00 0.00 36.74 3.66
2203 2227 0.183492 ATTGTCCAGTGCCACACAGT 59.817 50.000 0.00 0.00 36.74 3.55
2204 2228 0.034574 TTGTCCAGTGCCACACAGTT 60.035 50.000 0.00 0.00 36.74 3.16
2205 2229 0.034574 TGTCCAGTGCCACACAGTTT 60.035 50.000 0.00 0.00 36.74 2.66
2206 2230 1.102978 GTCCAGTGCCACACAGTTTT 58.897 50.000 0.00 0.00 36.74 2.43
2207 2231 1.102154 TCCAGTGCCACACAGTTTTG 58.898 50.000 0.00 0.00 36.74 2.44
2208 2232 0.528249 CCAGTGCCACACAGTTTTGC 60.528 55.000 0.00 0.00 36.74 3.68
2209 2233 0.457035 CAGTGCCACACAGTTTTGCT 59.543 50.000 0.00 0.00 36.74 3.91
2210 2234 1.675483 CAGTGCCACACAGTTTTGCTA 59.325 47.619 0.00 0.00 36.74 3.49
2211 2235 2.098934 CAGTGCCACACAGTTTTGCTAA 59.901 45.455 0.00 0.00 36.74 3.09
2212 2236 2.757868 AGTGCCACACAGTTTTGCTAAA 59.242 40.909 0.00 0.00 36.74 1.85
2213 2237 3.115554 GTGCCACACAGTTTTGCTAAAG 58.884 45.455 0.00 0.00 34.08 1.85
2214 2238 2.127251 GCCACACAGTTTTGCTAAAGC 58.873 47.619 0.00 0.00 42.50 3.51
2215 2239 6.977821 GTGCCACACAGTTTTGCTAAAGCA 62.978 45.833 0.00 0.00 40.87 3.91
2240 2264 7.069852 CATCTAGATGTGCCATAAGTATTGC 57.930 40.000 22.42 0.00 34.23 3.56
2241 2265 6.173427 TCTAGATGTGCCATAAGTATTGCA 57.827 37.500 0.00 0.00 32.69 4.08
2250 2274 7.403312 TGCCATAAGTATTGCACATTTAAGT 57.597 32.000 0.00 0.00 30.49 2.24
2251 2275 7.835822 TGCCATAAGTATTGCACATTTAAGTT 58.164 30.769 0.00 0.00 30.49 2.66
2252 2276 7.973388 TGCCATAAGTATTGCACATTTAAGTTC 59.027 33.333 0.00 0.00 30.49 3.01
2253 2277 8.190784 GCCATAAGTATTGCACATTTAAGTTCT 58.809 33.333 0.00 0.00 0.00 3.01
2280 2304 9.995957 ATATCATTGATCTTACGTAGAGATTCG 57.004 33.333 16.29 9.16 36.02 3.34
2281 2305 7.260558 TCATTGATCTTACGTAGAGATTCGT 57.739 36.000 16.29 0.00 42.82 3.85
2282 2306 7.353497 TCATTGATCTTACGTAGAGATTCGTC 58.647 38.462 16.29 9.00 40.70 4.20
2283 2307 6.922247 TTGATCTTACGTAGAGATTCGTCT 57.078 37.500 16.29 1.19 40.70 4.18
2284 2308 6.288426 TGATCTTACGTAGAGATTCGTCTG 57.712 41.667 16.29 0.00 40.70 3.51
2285 2309 5.236695 TGATCTTACGTAGAGATTCGTCTGG 59.763 44.000 16.29 0.00 40.70 3.86
2286 2310 4.763073 TCTTACGTAGAGATTCGTCTGGA 58.237 43.478 0.00 0.00 40.70 3.86
2287 2311 5.366460 TCTTACGTAGAGATTCGTCTGGAT 58.634 41.667 0.00 0.00 40.70 3.41
2288 2312 6.519382 TCTTACGTAGAGATTCGTCTGGATA 58.481 40.000 0.00 0.00 40.70 2.59
2289 2313 7.160049 TCTTACGTAGAGATTCGTCTGGATAT 58.840 38.462 0.00 0.00 40.70 1.63
2290 2314 7.660617 TCTTACGTAGAGATTCGTCTGGATATT 59.339 37.037 0.00 0.00 40.70 1.28
2291 2315 6.636562 ACGTAGAGATTCGTCTGGATATTT 57.363 37.500 0.00 0.00 35.30 1.40
2292 2316 7.040473 ACGTAGAGATTCGTCTGGATATTTT 57.960 36.000 0.00 0.00 35.30 1.82
2293 2317 7.140048 ACGTAGAGATTCGTCTGGATATTTTC 58.860 38.462 0.00 0.00 35.30 2.29
2294 2318 7.013464 ACGTAGAGATTCGTCTGGATATTTTCT 59.987 37.037 0.00 0.00 35.30 2.52
2295 2319 7.863375 CGTAGAGATTCGTCTGGATATTTTCTT 59.137 37.037 0.00 0.00 0.00 2.52
2296 2320 9.535878 GTAGAGATTCGTCTGGATATTTTCTTT 57.464 33.333 0.00 0.00 0.00 2.52
2298 2322 9.454859 AGAGATTCGTCTGGATATTTTCTTTTT 57.545 29.630 0.00 0.00 0.00 1.94
2299 2323 9.709600 GAGATTCGTCTGGATATTTTCTTTTTC 57.290 33.333 0.00 0.00 0.00 2.29
2300 2324 9.454859 AGATTCGTCTGGATATTTTCTTTTTCT 57.545 29.630 0.00 0.00 0.00 2.52
2335 2359 9.436957 TTTCCTCTTTATACTTGATTCACTCAC 57.563 33.333 0.00 0.00 32.17 3.51
2336 2360 8.367660 TCCTCTTTATACTTGATTCACTCACT 57.632 34.615 0.00 0.00 32.17 3.41
2337 2361 8.816894 TCCTCTTTATACTTGATTCACTCACTT 58.183 33.333 0.00 0.00 32.17 3.16
2344 2368 8.939201 ATACTTGATTCACTCACTTAGATGTG 57.061 34.615 0.00 0.00 39.15 3.21
2345 2369 5.641209 ACTTGATTCACTCACTTAGATGTGC 59.359 40.000 0.00 0.00 37.81 4.57
2346 2370 5.151297 TGATTCACTCACTTAGATGTGCA 57.849 39.130 0.00 0.00 37.81 4.57
2347 2371 5.550290 TGATTCACTCACTTAGATGTGCAA 58.450 37.500 0.00 0.00 37.81 4.08
2348 2372 6.175471 TGATTCACTCACTTAGATGTGCAAT 58.825 36.000 0.00 0.00 37.81 3.56
2349 2373 7.330262 TGATTCACTCACTTAGATGTGCAATA 58.670 34.615 0.00 0.00 37.81 1.90
2350 2374 7.823799 TGATTCACTCACTTAGATGTGCAATAA 59.176 33.333 0.00 0.00 37.81 1.40
2351 2375 6.968131 TCACTCACTTAGATGTGCAATAAC 57.032 37.500 0.00 0.00 37.81 1.89
2352 2376 6.701340 TCACTCACTTAGATGTGCAATAACT 58.299 36.000 0.00 0.00 37.81 2.24
2353 2377 7.836842 TCACTCACTTAGATGTGCAATAACTA 58.163 34.615 0.00 0.00 37.81 2.24
2354 2378 7.976175 TCACTCACTTAGATGTGCAATAACTAG 59.024 37.037 0.00 0.00 37.81 2.57
2355 2379 7.976175 CACTCACTTAGATGTGCAATAACTAGA 59.024 37.037 0.00 0.00 37.81 2.43
2356 2380 8.194104 ACTCACTTAGATGTGCAATAACTAGAG 58.806 37.037 0.00 0.00 37.81 2.43
2357 2381 6.980978 TCACTTAGATGTGCAATAACTAGAGC 59.019 38.462 0.00 0.00 37.81 4.09
2358 2382 6.758416 CACTTAGATGTGCAATAACTAGAGCA 59.242 38.462 0.00 0.00 34.10 4.26
2483 2507 5.948992 ATGTTTGCAAGAGAACTAGGTTC 57.051 39.130 0.00 2.57 42.25 3.62
2553 2580 1.691976 TCGATCTCCGCCAATATGGTT 59.308 47.619 0.00 0.00 40.46 3.67
2555 2582 2.289072 CGATCTCCGCCAATATGGTTCT 60.289 50.000 0.00 0.00 40.46 3.01
2621 2650 4.525949 GGTCCTTACGGAGGCGGC 62.526 72.222 0.00 0.00 45.87 6.53
2661 2690 3.494048 GCATCCTCATCGAGATGGTCTTT 60.494 47.826 12.54 0.00 39.24 2.52
2664 2693 2.359214 CCTCATCGAGATGGTCTTTCGA 59.641 50.000 12.54 0.00 45.96 3.71
2671 2700 3.377485 CGAGATGGTCTTTCGAGGACTTA 59.623 47.826 16.36 9.25 36.49 2.24
2676 2705 4.341487 TGGTCTTTCGAGGACTTATCTCA 58.659 43.478 16.36 6.00 34.47 3.27
2710 2739 2.233922 GAGATGGAGAGGACGAAACCAA 59.766 50.000 0.00 0.00 34.28 3.67
2761 2791 0.748005 CCAACGCCATCCCTCGAAAT 60.748 55.000 0.00 0.00 0.00 2.17
2771 2801 1.626321 TCCCTCGAAATGTGTGCCTAA 59.374 47.619 0.00 0.00 0.00 2.69
2851 2881 1.017177 TCCGCTTGTTCGAATTCCCG 61.017 55.000 0.00 2.76 0.00 5.14
2880 3480 4.139786 GGACCTCCGCCACGATATATATA 58.860 47.826 0.00 0.00 0.00 0.86
2935 3535 5.827797 TGAGTGTTGCTTCAGAAAAATAGGT 59.172 36.000 0.00 0.00 0.00 3.08
2950 3550 1.477553 TAGGTCGCGTGTTTAGGGAT 58.522 50.000 5.77 0.00 33.22 3.85
2975 3578 4.524802 TGGATGGTCAGCTTCCATATTT 57.475 40.909 17.12 0.32 44.52 1.40
2983 3586 4.641989 GTCAGCTTCCATATTTGTGTCCAT 59.358 41.667 0.00 0.00 0.00 3.41
3025 3628 4.472286 CGCGGACAAATTTTGTATCTGTT 58.528 39.130 14.49 0.00 45.52 3.16
3055 3658 7.684619 AGGGTAATGTTAGAGATGCCCTTATAT 59.315 37.037 0.00 0.00 42.09 0.86
3056 3659 8.989131 GGGTAATGTTAGAGATGCCCTTATATA 58.011 37.037 0.00 0.00 32.47 0.86
3157 3760 5.392380 GGTTCATGACTAATTCTGCCACAAG 60.392 44.000 0.00 0.00 0.00 3.16
3162 3765 7.611467 TCATGACTAATTCTGCCACAAGTAAAT 59.389 33.333 0.00 0.00 0.00 1.40
3167 3770 9.515226 ACTAATTCTGCCACAAGTAAATCTTAA 57.485 29.630 0.00 0.00 34.66 1.85
3179 3782 7.068226 ACAAGTAAATCTTAAGCAAAGTGTGGT 59.932 33.333 0.00 0.00 35.07 4.16
3235 3838 7.866898 CCATAACAAATGTGACAAGATTTGACA 59.133 33.333 20.40 11.73 45.43 3.58
3237 3840 9.814899 ATAACAAATGTGACAAGATTTGACAAA 57.185 25.926 20.40 2.48 45.43 2.83
3238 3841 8.545229 AACAAATGTGACAAGATTTGACAAAA 57.455 26.923 20.40 0.00 45.43 2.44
3316 3920 0.534203 AACCGCAAATGTGACGAGGT 60.534 50.000 0.00 0.00 0.00 3.85
3382 3986 2.330041 CAACGCACGACCCCAAAC 59.670 61.111 0.00 0.00 0.00 2.93
3385 3989 2.280524 CGCACGACCCCAAACAGA 60.281 61.111 0.00 0.00 0.00 3.41
3448 4052 2.169146 CGGCGTCCACCCGTATTTC 61.169 63.158 0.00 0.00 40.84 2.17
3461 4065 2.289444 CCGTATTTCTGGATATGCCGGT 60.289 50.000 1.90 0.00 44.00 5.28
3469 4073 4.221422 ATATGCCGGTCGTGCGCT 62.221 61.111 9.73 0.00 0.00 5.92
3477 4081 2.658707 GGTCGTGCGCTCAACACTC 61.659 63.158 9.73 0.00 35.84 3.51
3478 4082 2.729491 TCGTGCGCTCAACACTCG 60.729 61.111 9.73 1.02 35.84 4.18
3479 4083 3.767230 CGTGCGCTCAACACTCGG 61.767 66.667 9.73 0.00 35.84 4.63
3480 4084 4.077188 GTGCGCTCAACACTCGGC 62.077 66.667 9.73 0.00 35.12 5.54
3481 4085 4.299547 TGCGCTCAACACTCGGCT 62.300 61.111 9.73 0.00 0.00 5.52
3482 4086 3.782244 GCGCTCAACACTCGGCTG 61.782 66.667 0.00 0.00 0.00 4.85
3483 4087 3.782244 CGCTCAACACTCGGCTGC 61.782 66.667 0.00 0.00 0.00 5.25
3484 4088 2.666190 GCTCAACACTCGGCTGCA 60.666 61.111 0.50 0.00 0.00 4.41
3485 4089 2.037136 GCTCAACACTCGGCTGCAT 61.037 57.895 0.50 0.00 0.00 3.96
3486 4090 1.975363 GCTCAACACTCGGCTGCATC 61.975 60.000 0.50 0.00 0.00 3.91
3487 4091 0.390866 CTCAACACTCGGCTGCATCT 60.391 55.000 0.50 0.00 0.00 2.90
3490 4094 2.159819 AACACTCGGCTGCATCTCGT 62.160 55.000 0.50 0.00 0.00 4.18
3528 4132 5.201910 TCGCCGCATTTCTTATTATTTTCG 58.798 37.500 0.00 0.00 0.00 3.46
3534 4138 6.686679 CGCATTTCTTATTATTTTCGTCAGCA 59.313 34.615 0.00 0.00 0.00 4.41
3583 4187 9.605275 CATTCACCAAATCTTGACTAGAATAGA 57.395 33.333 0.00 0.00 42.77 1.98
3671 4275 5.053145 CGCAAGCTGGATTAGTATCTTCTT 58.947 41.667 0.00 0.00 0.00 2.52
3675 4279 7.875041 GCAAGCTGGATTAGTATCTTCTTGATA 59.125 37.037 0.00 0.00 35.67 2.15
3708 4312 3.821033 TGATCTGCGGATTCTCGATCTTA 59.179 43.478 9.98 0.00 35.02 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 151 2.126071 ACGACGATGAAGCCACGG 60.126 61.111 0.00 0.00 0.00 4.94
369 373 3.399181 CAGGACTAGGGGCCGCAA 61.399 66.667 23.39 0.00 0.00 4.85
382 387 0.271927 ATGGGGAATAGGAGCCAGGA 59.728 55.000 0.00 0.00 0.00 3.86
385 390 1.215173 CACAATGGGGAATAGGAGCCA 59.785 52.381 0.00 0.00 0.00 4.75
425 430 4.640855 CACGCCGTCTCACCACGT 62.641 66.667 0.00 0.00 38.14 4.49
464 469 1.811965 CAAACCGACCATCATCTTGCA 59.188 47.619 0.00 0.00 0.00 4.08
508 513 1.831736 CCTACGATCCCAACCTTCACT 59.168 52.381 0.00 0.00 0.00 3.41
825 844 0.955428 GAAGCAGCACGATCAACCCA 60.955 55.000 0.00 0.00 0.00 4.51
848 867 7.202001 CCAATACAGTCAATGATAGGTACTGGA 60.202 40.741 11.34 0.54 41.43 3.86
853 872 7.092623 ACCAACCAATACAGTCAATGATAGGTA 60.093 37.037 0.00 0.00 0.00 3.08
885 904 3.743911 GGTTTTCCCCGCTTTGTATTTTG 59.256 43.478 0.00 0.00 0.00 2.44
927 946 2.125673 CGTAGCACCTGGGTTCGG 60.126 66.667 0.00 0.00 34.66 4.30
1017 1036 6.677675 GCTGATTGATATCTCTCGATCGATGT 60.678 42.308 19.78 1.30 38.43 3.06
1177 1198 1.936880 GAGCACGTCGATCTCGCAG 60.937 63.158 0.00 2.73 39.60 5.18
1258 1279 1.603739 GTCCCACAGGAAGGTTGCC 60.604 63.158 0.00 0.00 46.38 4.52
1309 1330 2.281484 GCTTGTGCCAAGGACGGA 60.281 61.111 14.32 0.00 0.00 4.69
1315 1336 3.741476 GCCGGAGCTTGTGCCAAG 61.741 66.667 5.05 9.75 40.80 3.61
1316 1337 4.577677 TGCCGGAGCTTGTGCCAA 62.578 61.111 5.05 0.00 40.80 4.52
1458 1482 0.595053 AAGATCATACTCGTGCCGCG 60.595 55.000 0.00 0.00 43.01 6.46
1485 1509 1.909700 TTCTTTGATCACCACCAGCC 58.090 50.000 0.00 0.00 0.00 4.85
1487 1511 3.127548 CGGAATTCTTTGATCACCACCAG 59.872 47.826 5.23 0.00 0.00 4.00
1510 1534 2.445464 TGCCCCTTTTGCCAGCAA 60.445 55.556 0.00 0.00 0.00 3.91
1597 1621 3.760035 GGCTCCGGCGAGAACTCA 61.760 66.667 9.30 0.00 38.52 3.41
1617 1641 1.668751 TCGTTTTCACAGTGCTCAACC 59.331 47.619 0.00 0.00 0.00 3.77
1680 1704 5.518847 TCCAAGAGAAAGTAATACGAATGCG 59.481 40.000 0.00 0.00 44.79 4.73
1717 1741 6.365970 AAGAAGATAGACACCATGTGAAGT 57.634 37.500 0.49 0.00 36.96 3.01
1743 1767 0.251634 TGTGTGCATATCGAAGCCCA 59.748 50.000 0.00 0.00 0.00 5.36
1885 1909 3.049912 GGGACGCAATTTGAACTTGTTC 58.950 45.455 0.00 6.56 0.00 3.18
1896 1920 0.673437 CAAGGTGTTGGGACGCAATT 59.327 50.000 8.31 0.00 38.03 2.32
1949 1973 8.050778 TCCTTGTTTAATCCAATGTCATACAC 57.949 34.615 0.00 0.00 0.00 2.90
1965 1989 2.629137 TCGTGCACTACCTCCTTGTTTA 59.371 45.455 16.19 0.00 0.00 2.01
2050 2074 7.287696 ACCATACAATCTTATTCAATTGGTCCC 59.712 37.037 5.42 0.00 37.23 4.46
2172 2196 9.632416 GTGGCACTGGACAATTATGTGTAACAG 62.632 44.444 11.13 7.54 43.32 3.16
2226 2250 7.403312 ACTTAAATGTGCAATACTTATGGCA 57.597 32.000 0.00 0.00 40.19 4.92
2227 2251 8.190784 AGAACTTAAATGTGCAATACTTATGGC 58.809 33.333 0.00 0.00 33.16 4.40
2254 2278 9.995957 CGAATCTCTACGTAAGATCAATGATAT 57.004 33.333 15.80 0.00 43.62 1.63
2255 2279 9.000486 ACGAATCTCTACGTAAGATCAATGATA 58.000 33.333 15.80 0.00 40.92 2.15
2256 2280 7.877003 ACGAATCTCTACGTAAGATCAATGAT 58.123 34.615 15.80 0.00 40.92 2.45
2257 2281 7.226918 AGACGAATCTCTACGTAAGATCAATGA 59.773 37.037 15.80 0.00 42.74 2.57
2258 2282 7.322461 CAGACGAATCTCTACGTAAGATCAATG 59.678 40.741 15.80 10.75 42.74 2.82
2259 2283 7.356540 CAGACGAATCTCTACGTAAGATCAAT 58.643 38.462 15.80 5.83 42.74 2.57
2260 2284 6.238402 CCAGACGAATCTCTACGTAAGATCAA 60.238 42.308 15.80 0.44 42.74 2.57
2261 2285 5.236695 CCAGACGAATCTCTACGTAAGATCA 59.763 44.000 15.80 0.97 42.74 2.92
2262 2286 5.466058 TCCAGACGAATCTCTACGTAAGATC 59.534 44.000 15.80 8.36 42.74 2.75
2263 2287 5.366460 TCCAGACGAATCTCTACGTAAGAT 58.634 41.667 11.91 11.91 42.74 2.40
2264 2288 4.763073 TCCAGACGAATCTCTACGTAAGA 58.237 43.478 0.00 3.49 42.74 2.10
2265 2289 5.676532 ATCCAGACGAATCTCTACGTAAG 57.323 43.478 0.00 0.00 42.74 2.34
2266 2290 7.741027 AATATCCAGACGAATCTCTACGTAA 57.259 36.000 0.00 0.00 42.74 3.18
2267 2291 7.741027 AAATATCCAGACGAATCTCTACGTA 57.259 36.000 0.00 0.00 42.74 3.57
2268 2292 6.636562 AAATATCCAGACGAATCTCTACGT 57.363 37.500 0.00 0.00 45.32 3.57
2269 2293 7.364200 AGAAAATATCCAGACGAATCTCTACG 58.636 38.462 0.00 0.00 30.42 3.51
2270 2294 9.535878 AAAGAAAATATCCAGACGAATCTCTAC 57.464 33.333 0.00 0.00 30.42 2.59
2272 2296 9.454859 AAAAAGAAAATATCCAGACGAATCTCT 57.545 29.630 0.00 0.00 30.42 3.10
2273 2297 9.709600 GAAAAAGAAAATATCCAGACGAATCTC 57.290 33.333 0.00 0.00 30.42 2.75
2274 2298 9.454859 AGAAAAAGAAAATATCCAGACGAATCT 57.545 29.630 0.00 0.00 34.57 2.40
2309 2333 9.436957 GTGAGTGAATCAAGTATAAAGAGGAAA 57.563 33.333 0.00 0.00 40.43 3.13
2310 2334 8.816894 AGTGAGTGAATCAAGTATAAAGAGGAA 58.183 33.333 0.00 0.00 40.43 3.36
2311 2335 8.367660 AGTGAGTGAATCAAGTATAAAGAGGA 57.632 34.615 0.00 0.00 40.43 3.71
2319 2343 7.493971 GCACATCTAAGTGAGTGAATCAAGTAT 59.506 37.037 0.00 0.00 42.05 2.12
2320 2344 6.813649 GCACATCTAAGTGAGTGAATCAAGTA 59.186 38.462 0.00 0.00 42.05 2.24
2321 2345 5.641209 GCACATCTAAGTGAGTGAATCAAGT 59.359 40.000 0.00 0.00 42.05 3.16
2322 2346 5.640783 TGCACATCTAAGTGAGTGAATCAAG 59.359 40.000 0.00 0.00 42.05 3.02
2323 2347 5.550290 TGCACATCTAAGTGAGTGAATCAA 58.450 37.500 0.00 0.00 42.05 2.57
2324 2348 5.151297 TGCACATCTAAGTGAGTGAATCA 57.849 39.130 0.00 0.00 42.05 2.57
2325 2349 6.674694 ATTGCACATCTAAGTGAGTGAATC 57.325 37.500 0.00 0.00 42.05 2.52
2326 2350 7.826252 AGTTATTGCACATCTAAGTGAGTGAAT 59.174 33.333 0.00 0.00 42.05 2.57
2327 2351 7.161404 AGTTATTGCACATCTAAGTGAGTGAA 58.839 34.615 0.00 0.00 42.05 3.18
2328 2352 6.701340 AGTTATTGCACATCTAAGTGAGTGA 58.299 36.000 0.00 0.00 42.05 3.41
2329 2353 6.974932 AGTTATTGCACATCTAAGTGAGTG 57.025 37.500 0.00 0.00 42.05 3.51
2330 2354 8.067751 TCTAGTTATTGCACATCTAAGTGAGT 57.932 34.615 0.00 0.00 42.05 3.41
2331 2355 7.168972 GCTCTAGTTATTGCACATCTAAGTGAG 59.831 40.741 0.00 0.00 42.05 3.51
2332 2356 6.980978 GCTCTAGTTATTGCACATCTAAGTGA 59.019 38.462 0.00 0.00 42.05 3.41
2333 2357 6.758416 TGCTCTAGTTATTGCACATCTAAGTG 59.242 38.462 0.00 0.00 42.37 3.16
2334 2358 6.878317 TGCTCTAGTTATTGCACATCTAAGT 58.122 36.000 0.00 0.00 0.00 2.24
2359 2383 5.065218 GGTGTGTTTAAGGCACATCTAGATG 59.935 44.000 27.63 27.63 46.66 2.90
2360 2384 5.186198 GGTGTGTTTAAGGCACATCTAGAT 58.814 41.667 14.97 0.00 46.66 1.98
2361 2385 4.575885 GGTGTGTTTAAGGCACATCTAGA 58.424 43.478 14.97 0.00 46.66 2.43
2362 2386 4.946784 GGTGTGTTTAAGGCACATCTAG 57.053 45.455 14.97 0.00 46.66 2.43
2365 2389 4.584327 AAAGGTGTGTTTAAGGCACATC 57.416 40.909 14.97 14.53 46.66 3.06
2366 2390 5.351948 AAAAAGGTGTGTTTAAGGCACAT 57.648 34.783 14.97 3.67 46.66 3.21
2367 2391 4.810191 AAAAAGGTGTGTTTAAGGCACA 57.190 36.364 9.85 9.85 43.60 4.57
2368 2392 9.483916 AATATTAAAAAGGTGTGTTTAAGGCAC 57.516 29.630 5.59 5.59 33.84 5.01
2439 2463 4.322080 TGAAGGACATACATCCATCGTC 57.678 45.455 0.00 0.00 38.98 4.20
2440 2464 4.753516 TTGAAGGACATACATCCATCGT 57.246 40.909 0.00 0.00 38.98 3.73
2527 2552 1.956629 TTGGCGGAGATCGAAGGGAC 61.957 60.000 0.00 0.00 42.43 4.46
2553 2580 0.976641 ATTCACTGGCTGTCGGAAGA 59.023 50.000 0.00 0.00 38.16 2.87
2555 2582 1.207089 CCTATTCACTGGCTGTCGGAA 59.793 52.381 0.00 0.00 0.00 4.30
2621 2650 4.557942 GTTGCCATCAACCAAGCG 57.442 55.556 0.00 0.00 45.15 4.68
2628 2657 0.322366 TGAGGATGCGTTGCCATCAA 60.322 50.000 4.75 0.00 42.63 2.57
2661 2690 4.360563 GCGAATTTGAGATAAGTCCTCGA 58.639 43.478 0.00 0.00 33.51 4.04
2664 2693 3.458189 CGGCGAATTTGAGATAAGTCCT 58.542 45.455 0.00 0.00 0.00 3.85
2671 2700 2.009774 CTCAACCGGCGAATTTGAGAT 58.990 47.619 27.44 0.00 46.16 2.75
2676 2705 1.094785 CCATCTCAACCGGCGAATTT 58.905 50.000 9.30 0.00 0.00 1.82
2710 2739 6.208599 CCTAGTGTGTTTATTGGACAACCATT 59.791 38.462 0.00 0.00 46.34 3.16
2761 2791 1.270094 CGGTCTGAACTTAGGCACACA 60.270 52.381 0.00 0.00 0.00 3.72
2851 2881 4.554036 GGCGGAGGTCCAGATGCC 62.554 72.222 0.00 0.00 35.14 4.40
2913 3513 5.049405 CGACCTATTTTTCTGAAGCAACACT 60.049 40.000 0.00 0.00 0.00 3.55
2935 3535 0.322322 AACCATCCCTAAACACGCGA 59.678 50.000 15.93 0.00 0.00 5.87
2950 3550 0.038166 GGAAGCTGACCATCCAACCA 59.962 55.000 5.47 0.00 33.30 3.67
2975 3578 1.899142 TCAGATTCGTCCATGGACACA 59.101 47.619 37.42 26.04 44.77 3.72
2983 3586 2.422479 CGGACTAGTTCAGATTCGTCCA 59.578 50.000 1.17 0.00 40.62 4.02
3017 3620 9.099454 CTCTAACATTACCCTCAAAACAGATAC 57.901 37.037 0.00 0.00 0.00 2.24
3025 3628 5.437060 GGCATCTCTAACATTACCCTCAAA 58.563 41.667 0.00 0.00 0.00 2.69
3157 3760 6.143919 GCAACCACACTTTGCTTAAGATTTAC 59.856 38.462 6.67 0.00 44.96 2.01
3162 3765 3.708563 GCAACCACACTTTGCTTAAGA 57.291 42.857 6.67 0.00 44.96 2.10
3199 3802 7.651304 TGTCACATTTGTTATGGTCATTTTGTC 59.349 33.333 0.00 0.00 0.00 3.18
3238 3841 3.440173 CCACGTGTCATAGGCTCATTTTT 59.560 43.478 15.65 0.00 0.00 1.94
3252 3855 0.246635 AGCTACATGGTCCACGTGTC 59.753 55.000 15.65 7.11 46.14 3.67
3316 3920 6.164876 CACAACATTTTAGGGATTGATTGCA 58.835 36.000 0.00 0.00 0.00 4.08
3382 3986 1.442184 CGGACAGAACGGACGTCTG 60.442 63.158 22.81 22.81 37.50 3.51
3407 4011 1.270550 CCATTGCCACTCCAAACAGAC 59.729 52.381 0.00 0.00 0.00 3.51
3448 4052 1.956170 GCACGACCGGCATATCCAG 60.956 63.158 0.00 0.00 34.01 3.86
3461 4065 2.729491 CGAGTGTTGAGCGCACGA 60.729 61.111 11.47 0.00 42.68 4.35
3469 4073 0.390340 GAGATGCAGCCGAGTGTTGA 60.390 55.000 0.00 0.00 0.00 3.18
3478 4082 2.699576 TATGCGGACGAGATGCAGCC 62.700 60.000 0.00 0.00 42.65 4.85
3479 4083 1.300156 TATGCGGACGAGATGCAGC 60.300 57.895 0.00 0.00 42.65 5.25
3480 4084 0.249031 TGTATGCGGACGAGATGCAG 60.249 55.000 0.00 0.00 42.65 4.41
3481 4085 0.389025 ATGTATGCGGACGAGATGCA 59.611 50.000 0.00 0.00 43.67 3.96
3482 4086 1.502231 AATGTATGCGGACGAGATGC 58.498 50.000 0.00 0.00 0.00 3.91
3483 4087 4.536364 AAAAATGTATGCGGACGAGATG 57.464 40.909 0.00 0.00 0.00 2.90
3506 4110 4.967575 ACGAAAATAATAAGAAATGCGGCG 59.032 37.500 0.51 0.51 0.00 6.46
3671 4275 4.371786 GCAGATCAACGATGAAGGTATCA 58.628 43.478 0.00 0.00 43.67 2.15
3675 4279 1.645034 CGCAGATCAACGATGAAGGT 58.355 50.000 0.00 0.00 39.49 3.50
3683 4287 0.848942 CGAGAATCCGCAGATCAACG 59.151 55.000 0.00 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.