Multiple sequence alignment - TraesCS1B01G190000

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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 TraesCS1B01G190000 chr1B 100.000 2745 0 0 745 3489 340809733 340812477 0.000000e+00 5070
1 TraesCS1B01G190000 chr1B 100.000 1178 0 0 3682 4859 340812670 340813847 0.000000e+00 2176
2 TraesCS1B01G190000 chr1B 100.000 411 0 0 1 411 340808989 340809399 0.000000e+00 760
3 TraesCS1B01G190000 chr1B 75.229 327 64 10 2153 2476 368566097 368566409 6.560000e-29 139
4 TraesCS1B01G190000 chr1D 93.824 1700 80 11 1259 2955 235577352 235579029 0.000000e+00 2534
5 TraesCS1B01G190000 chr1D 94.430 1185 55 9 3682 4856 235579609 235580792 0.000000e+00 1812
6 TraesCS1B01G190000 chr1D 97.388 536 14 0 2954 3489 235579063 235579598 0.000000e+00 913
7 TraesCS1B01G190000 chr1D 91.188 522 25 8 745 1263 235576511 235577014 0.000000e+00 689
8 TraesCS1B01G190000 chr1D 85.343 423 35 13 1 411 235576020 235576427 3.500000e-111 412
9 TraesCS1B01G190000 chr1A 92.558 954 46 10 1258 2207 311815142 311814210 0.000000e+00 1345
10 TraesCS1B01G190000 chr1A 92.126 762 43 3 2206 2955 311814086 311813330 0.000000e+00 1059
11 TraesCS1B01G190000 chr1A 93.064 519 26 4 2954 3471 311813296 311812787 0.000000e+00 750
12 TraesCS1B01G190000 chr1A 91.045 536 28 10 745 1264 311816633 311816102 0.000000e+00 706
13 TraesCS1B01G190000 chr1A 90.710 183 12 2 3682 3860 311812799 311812618 6.290000e-59 239
14 TraesCS1B01G190000 chr1A 78.571 224 41 6 2209 2428 313729184 313728964 1.820000e-29 141
15 TraesCS1B01G190000 chr3D 91.411 163 10 4 4367 4527 199249855 199250015 2.280000e-53 220
16 TraesCS1B01G190000 chr3D 91.772 158 11 2 4367 4522 324612921 324612764 8.190000e-53 219
17 TraesCS1B01G190000 chr3D 88.608 158 16 2 4367 4522 324611853 324612010 1.790000e-44 191
18 TraesCS1B01G190000 chrUn 91.447 152 11 2 4367 4516 340505383 340505534 1.770000e-49 207
19 TraesCS1B01G190000 chr3A 90.506 158 13 2 4367 4522 743774137 743773980 1.770000e-49 207
20 TraesCS1B01G190000 chr5A 88.535 157 15 3 4367 4520 601349833 601349677 2.310000e-43 187
21 TraesCS1B01G190000 chr2A 88.125 160 15 3 4366 4522 4796013 4796171 2.310000e-43 187
22 TraesCS1B01G190000 chr5D 87.975 158 17 2 4367 4522 168491680 168491523 8.310000e-43 185


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 TraesCS1B01G190000 chr1B 340808989 340813847 4858 False 2668.666667 5070 100.0000 1 4859 3 chr1B.!!$F2 4858
1 TraesCS1B01G190000 chr1D 235576020 235580792 4772 False 1272.000000 2534 92.4346 1 4856 5 chr1D.!!$F1 4855
2 TraesCS1B01G190000 chr1A 311812618 311816633 4015 True 819.800000 1345 91.9006 745 3860 5 chr1A.!!$R2 3115

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
219 221 0.027848 TGATTGCGCGTATGCATGTG 59.972 50.0 10.16 0.80 45.78 3.21 F
332 343 0.321653 CTCAGTTGTACCCCACTGCC 60.322 60.0 10.64 0.00 0.00 4.85 F
1235 1259 0.038709 AGCGTGTCTCTGTTGAGCTC 60.039 55.0 6.82 6.82 40.03 4.09 F
1236 1260 0.038709 GCGTGTCTCTGTTGAGCTCT 60.039 55.0 16.19 0.00 40.03 4.09 F
1368 2362 0.250038 CATGCAGGTAGGGATCCACG 60.250 60.0 15.23 0.00 0.00 4.94 F
2069 3063 0.321298 AACACACCTCGCCATGTACC 60.321 55.0 0.00 0.00 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1216 1240 0.038709 GAGCTCAACAGAGACACGCT 60.039 55.000 9.40 0.0 0.00 5.07 R
2173 3167 0.109919 CTTTTCCCGCAGTAAACGCC 60.110 55.000 0.00 0.0 0.00 5.68 R
2174 3168 0.728129 GCTTTTCCCGCAGTAAACGC 60.728 55.000 0.00 0.0 0.00 4.84 R
2363 3482 0.952280 CCTGCCATCTCATGCATGTC 59.048 55.000 25.43 9.9 36.79 3.06 R
2755 3886 6.152379 GCACTAATGAAAGAAACCTTCCAAG 58.848 40.000 0.00 0.0 0.00 3.61 R
4031 5242 2.367241 TCAGAAGATTGTGGGACGTTCA 59.633 45.455 0.00 0.0 0.00 3.18 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
46 47 3.715628 TTTCTTCAAGAACTTGCCTGC 57.284 42.857 0.00 0.00 40.24 4.85
61 62 5.011943 ACTTGCCTGCAATTTTTCATTCCTA 59.988 36.000 4.84 0.00 35.20 2.94
96 97 9.975218 AATTTTATCTAATATATGGCCTTCGGT 57.025 29.630 3.32 0.00 0.00 4.69
97 98 9.975218 ATTTTATCTAATATATGGCCTTCGGTT 57.025 29.630 3.32 0.00 0.00 4.44
98 99 9.444600 TTTTATCTAATATATGGCCTTCGGTTC 57.555 33.333 3.32 0.00 0.00 3.62
103 104 6.391227 AATATATGGCCTTCGGTTCTTTTG 57.609 37.500 3.32 0.00 0.00 2.44
105 106 2.060050 TGGCCTTCGGTTCTTTTGAA 57.940 45.000 3.32 0.00 35.84 2.69
106 107 2.379972 TGGCCTTCGGTTCTTTTGAAA 58.620 42.857 3.32 0.00 40.53 2.69
138 139 5.221342 ACAACCACTGCAATTTAAATCCGAA 60.221 36.000 0.10 0.00 0.00 4.30
142 143 4.788100 CACTGCAATTTAAATCCGAACTCG 59.212 41.667 0.10 0.00 39.44 4.18
174 175 8.072567 CACCTTGAGAATAGAAAACAAACTCAG 58.927 37.037 0.00 0.00 35.05 3.35
208 210 5.348418 ACTAACACATATCATGATTGCGC 57.652 39.130 14.65 0.00 0.00 6.09
210 212 2.212652 ACACATATCATGATTGCGCGT 58.787 42.857 14.65 7.65 0.00 6.01
219 221 0.027848 TGATTGCGCGTATGCATGTG 59.972 50.000 10.16 0.80 45.78 3.21
220 222 1.264141 GATTGCGCGTATGCATGTGC 61.264 55.000 10.16 12.46 45.78 4.57
266 271 9.503427 CTTATTTTCACCATAAATTTCGGAGTC 57.497 33.333 12.36 0.00 0.00 3.36
280 285 1.808891 CGGAGTCGTTCCCAGTTTTGT 60.809 52.381 3.68 0.00 43.63 2.83
311 322 3.155093 GATGAAGCGCATCCAATGTTT 57.845 42.857 11.47 0.00 46.23 2.83
312 323 3.514645 GATGAAGCGCATCCAATGTTTT 58.485 40.909 11.47 0.00 46.23 2.43
313 324 2.945278 TGAAGCGCATCCAATGTTTTC 58.055 42.857 11.47 0.37 0.00 2.29
314 325 2.557924 TGAAGCGCATCCAATGTTTTCT 59.442 40.909 11.47 0.00 0.00 2.52
315 326 2.927553 AGCGCATCCAATGTTTTCTC 57.072 45.000 11.47 0.00 0.00 2.87
329 340 3.201266 TGTTTTCTCAGTTGTACCCCACT 59.799 43.478 0.00 0.00 0.00 4.00
330 341 3.485463 TTTCTCAGTTGTACCCCACTG 57.515 47.619 9.61 9.61 0.00 3.66
331 342 0.685097 TCTCAGTTGTACCCCACTGC 59.315 55.000 10.64 0.00 0.00 4.40
332 343 0.321653 CTCAGTTGTACCCCACTGCC 60.322 60.000 10.64 0.00 0.00 4.85
333 344 1.303317 CAGTTGTACCCCACTGCCC 60.303 63.158 4.52 0.00 0.00 5.36
334 345 2.359478 GTTGTACCCCACTGCCCG 60.359 66.667 0.00 0.00 0.00 6.13
335 346 3.642503 TTGTACCCCACTGCCCGG 61.643 66.667 0.00 0.00 0.00 5.73
336 347 4.642488 TGTACCCCACTGCCCGGA 62.642 66.667 0.73 0.00 0.00 5.14
358 369 2.770259 GACGGAGCTCGCGAAAAC 59.230 61.111 25.01 2.35 43.89 2.43
362 373 3.488090 GAGCTCGCGAAAACGGGG 61.488 66.667 11.33 0.00 32.90 5.73
376 387 1.300853 CGGGGCCAAACTGCAAAAG 60.301 57.895 4.39 0.00 0.00 2.27
379 390 1.044611 GGGCCAAACTGCAAAAGGTA 58.955 50.000 4.39 0.00 0.00 3.08
388 399 2.622962 GCAAAAGGTACCGCGGCTT 61.623 57.895 28.58 18.20 0.00 4.35
389 400 1.209127 CAAAAGGTACCGCGGCTTG 59.791 57.895 28.58 14.88 0.00 4.01
390 401 2.622962 AAAAGGTACCGCGGCTTGC 61.623 57.895 28.58 10.63 41.47 4.01
394 405 3.131478 GTACCGCGGCTTGCCATT 61.131 61.111 28.58 5.26 42.08 3.16
395 406 2.822255 TACCGCGGCTTGCCATTC 60.822 61.111 28.58 0.00 42.08 2.67
398 409 2.257980 CGCGGCTTGCCATTCAAA 59.742 55.556 12.45 0.00 42.08 2.69
401 412 1.079888 CGGCTTGCCATTCAAACCC 60.080 57.895 12.45 0.00 37.58 4.11
405 416 1.047002 CTTGCCATTCAAACCCACCA 58.953 50.000 0.00 0.00 33.65 4.17
823 834 2.361757 TCAAGCCCACACAAATCAACAG 59.638 45.455 0.00 0.00 0.00 3.16
926 944 2.223745 GTACTCCCAGATCTCGACTCC 58.776 57.143 0.00 0.00 0.00 3.85
929 947 1.075970 CCCAGATCTCGACTCCCCA 60.076 63.158 0.00 0.00 0.00 4.96
933 951 0.923358 AGATCTCGACTCCCCAGTCT 59.077 55.000 0.00 0.00 46.31 3.24
1084 1103 1.687493 CTTCCCTTCCCTCCTCGCT 60.687 63.158 0.00 0.00 0.00 4.93
1114 1133 3.140814 GTTGCTTCCCGATGGCCC 61.141 66.667 0.00 0.00 0.00 5.80
1167 1186 9.675464 AGCACTATTAGATACTACTAGATGGAC 57.325 37.037 0.00 0.00 0.00 4.02
1194 1218 4.202111 CCACTTCTTGATTTGTTCCCGTTT 60.202 41.667 0.00 0.00 0.00 3.60
1198 1222 5.782893 TCTTGATTTGTTCCCGTTTCATT 57.217 34.783 0.00 0.00 0.00 2.57
1203 1227 3.444703 TTGTTCCCGTTTCATTTGGTG 57.555 42.857 0.00 0.00 0.00 4.17
1216 1240 1.761449 TTTGGTGTCTTTGCTCAGCA 58.239 45.000 0.00 0.00 39.69 4.41
1235 1259 0.038709 AGCGTGTCTCTGTTGAGCTC 60.039 55.000 6.82 6.82 40.03 4.09
1236 1260 0.038709 GCGTGTCTCTGTTGAGCTCT 60.039 55.000 16.19 0.00 40.03 4.09
1264 1288 6.213677 TGTACTGCATCGTTATCCAGTTATC 58.786 40.000 0.00 0.00 39.15 1.75
1265 1289 4.632153 ACTGCATCGTTATCCAGTTATCC 58.368 43.478 0.00 0.00 35.14 2.59
1267 1291 3.389656 TGCATCGTTATCCAGTTATCCCA 59.610 43.478 0.00 0.00 0.00 4.37
1269 1293 3.746045 TCGTTATCCAGTTATCCCAGC 57.254 47.619 0.00 0.00 0.00 4.85
1271 1295 3.131396 CGTTATCCAGTTATCCCAGCAC 58.869 50.000 0.00 0.00 0.00 4.40
1272 1296 3.131396 GTTATCCAGTTATCCCAGCACG 58.869 50.000 0.00 0.00 0.00 5.34
1273 1297 1.204146 ATCCAGTTATCCCAGCACGT 58.796 50.000 0.00 0.00 0.00 4.49
1275 1299 1.349688 TCCAGTTATCCCAGCACGTTT 59.650 47.619 0.00 0.00 0.00 3.60
1277 1301 3.199071 TCCAGTTATCCCAGCACGTTTAT 59.801 43.478 0.00 0.00 0.00 1.40
1278 1302 3.312421 CCAGTTATCCCAGCACGTTTATG 59.688 47.826 0.00 0.00 0.00 1.90
1306 2300 6.522054 TCTTCACCGTTCTTAACATCTTTCT 58.478 36.000 0.00 0.00 0.00 2.52
1309 2303 6.954944 TCACCGTTCTTAACATCTTTCTTTG 58.045 36.000 0.00 0.00 0.00 2.77
1320 2314 9.635404 TTAACATCTTTCTTTGGGAACTCTTTA 57.365 29.630 0.00 0.00 33.13 1.85
1326 2320 9.635404 TCTTTCTTTGGGAACTCTTTATTTACA 57.365 29.630 0.00 0.00 33.13 2.41
1327 2321 9.899226 CTTTCTTTGGGAACTCTTTATTTACAG 57.101 33.333 0.00 0.00 33.13 2.74
1328 2322 8.990163 TTCTTTGGGAACTCTTTATTTACAGT 57.010 30.769 0.00 0.00 0.00 3.55
1366 2360 1.708993 GGCATGCAGGTAGGGATCCA 61.709 60.000 21.36 0.00 0.00 3.41
1368 2362 0.250038 CATGCAGGTAGGGATCCACG 60.250 60.000 15.23 0.00 0.00 4.94
1435 2429 1.557371 CTTGTGGTGGGTTTTGGGTTT 59.443 47.619 0.00 0.00 0.00 3.27
1465 2459 2.390599 CCACAATGACGAGTGCCGG 61.391 63.158 0.00 0.00 43.93 6.13
1518 2512 6.373005 TGGAGGAGTCATTTTTCTCATGTA 57.627 37.500 0.00 0.00 32.93 2.29
1519 2513 6.962182 TGGAGGAGTCATTTTTCTCATGTAT 58.038 36.000 0.00 0.00 32.93 2.29
1520 2514 6.825213 TGGAGGAGTCATTTTTCTCATGTATG 59.175 38.462 0.00 0.00 32.93 2.39
1521 2515 6.825721 GGAGGAGTCATTTTTCTCATGTATGT 59.174 38.462 0.00 0.00 32.93 2.29
1562 2556 7.964624 TGTATCATATTATTCCCACCACGTTA 58.035 34.615 0.00 0.00 0.00 3.18
1563 2557 8.092068 TGTATCATATTATTCCCACCACGTTAG 58.908 37.037 0.00 0.00 0.00 2.34
1564 2558 6.488769 TCATATTATTCCCACCACGTTAGT 57.511 37.500 0.00 0.00 0.00 2.24
1565 2559 6.518493 TCATATTATTCCCACCACGTTAGTC 58.482 40.000 0.00 0.00 0.00 2.59
1566 2560 2.945447 TATTCCCACCACGTTAGTCG 57.055 50.000 0.00 0.00 46.00 4.18
1602 2596 2.813754 CCGAATTGACATGGTTCAGTGT 59.186 45.455 0.00 0.00 0.00 3.55
1629 2623 3.717294 AGGTCGCTGGCGGGATTT 61.717 61.111 14.94 0.00 40.25 2.17
1688 2682 3.440173 ACAGTATCCTTTTTGTGGCATCG 59.560 43.478 0.00 0.00 0.00 3.84
1889 2883 3.953612 TGTGATTCATTTGGGATAGCACC 59.046 43.478 0.00 0.00 0.00 5.01
1984 2978 8.765488 TGATTGCTTGATGGAATTAAATCCTA 57.235 30.769 10.89 0.00 40.35 2.94
1988 2982 7.345691 TGCTTGATGGAATTAAATCCTAGTGA 58.654 34.615 10.89 0.00 40.35 3.41
2069 3063 0.321298 AACACACCTCGCCATGTACC 60.321 55.000 0.00 0.00 0.00 3.34
2173 3167 8.537016 TGTTTATATAACTAGATGATTCCCCGG 58.463 37.037 0.00 0.00 0.00 5.73
2174 3168 7.670605 TTATATAACTAGATGATTCCCCGGG 57.329 40.000 15.80 15.80 0.00 5.73
2215 3334 9.790344 AAAGCTCAAAGACATATAGCTATGAAT 57.210 29.630 16.77 0.00 42.49 2.57
2231 3350 6.828273 AGCTATGAATTATTGCTAACACACCA 59.172 34.615 0.00 0.00 44.30 4.17
2242 3361 3.610677 GCTAACACACCACAAACACAAAC 59.389 43.478 0.00 0.00 0.00 2.93
2342 3461 5.162947 ACCAATAATCAATCTGTAGGGCCAT 60.163 40.000 6.18 0.00 0.00 4.40
2363 3482 4.553756 TCTCTAATCGATTCTCCACACG 57.446 45.455 15.25 0.00 0.00 4.49
2457 3578 5.175388 AGGAAAAATAGGTAGTGGGTCAC 57.825 43.478 0.00 0.00 34.10 3.67
2755 3886 1.079612 GCATGCCCCAACTCTTTGC 60.080 57.895 6.36 0.00 0.00 3.68
2762 3893 1.615392 CCCCAACTCTTTGCTTGGAAG 59.385 52.381 1.88 0.00 39.58 3.46
2813 3944 8.432013 TCACAATCATCTATGCTGGTATAACTT 58.568 33.333 0.00 0.00 0.00 2.66
2963 4164 7.416664 GCTCATCCTATTTTATCTTTTGTGGCA 60.417 37.037 0.00 0.00 0.00 4.92
3133 4334 6.888105 TCATCAGAGTTTAACATGGCTATCA 58.112 36.000 0.00 0.00 0.00 2.15
3195 4396 5.726397 TGAATGCTTCCAATTTTGATCTGG 58.274 37.500 0.00 0.00 0.00 3.86
3317 4519 3.322541 TCCTGTCACACCTTCGAAATACA 59.677 43.478 0.00 0.00 0.00 2.29
3467 4669 8.655901 TCATTTTGGTAAGCTTAAAATTCCCTT 58.344 29.630 7.99 0.00 33.18 3.95
3473 4675 8.361889 TGGTAAGCTTAAAATTCCCTTAAACAC 58.638 33.333 7.99 0.00 0.00 3.32
3474 4676 8.361889 GGTAAGCTTAAAATTCCCTTAAACACA 58.638 33.333 7.99 0.00 0.00 3.72
3476 4678 7.354751 AGCTTAAAATTCCCTTAAACACACA 57.645 32.000 0.00 0.00 0.00 3.72
3744 4949 4.796038 AAATTGCTCCATCTTTGTCTGG 57.204 40.909 0.00 0.00 0.00 3.86
3834 5043 0.818296 GTCGACATGCTGGAGGTAGT 59.182 55.000 11.55 0.00 0.00 2.73
3861 5070 6.197364 TCTAAAGTTCCTCGAAGATGACTC 57.803 41.667 0.00 0.00 33.89 3.36
3921 5131 1.817447 AGCGAGAGTTAGCTTTACCGT 59.183 47.619 0.00 0.00 41.52 4.83
3929 5139 3.834231 AGTTAGCTTTACCGTCCCTTGTA 59.166 43.478 0.00 0.00 0.00 2.41
3990 5201 0.538287 AAGGCTTCTGTTCTGTGGGC 60.538 55.000 0.00 0.00 0.00 5.36
4031 5242 9.193806 AGTAGCATTTTGGACATCTATGAAAAT 57.806 29.630 0.00 0.00 0.00 1.82
4040 5251 5.007724 GGACATCTATGAAAATGAACGTCCC 59.992 44.000 0.00 0.00 33.73 4.46
4102 5313 4.577693 GTGTGATGCCAATATCTGACATGT 59.422 41.667 0.00 0.00 0.00 3.21
4208 5419 8.424133 TGAACACAGTATAATGTAGATGCTCAT 58.576 33.333 5.36 0.00 0.00 2.90
4222 5433 7.887495 TGTAGATGCTCATATACACTCATCTCT 59.113 37.037 11.88 0.00 39.66 3.10
4225 5436 8.905850 AGATGCTCATATACACTCATCTCTATG 58.094 37.037 0.00 0.00 36.82 2.23
4232 5443 9.404348 CATATACACTCATCTCTATGAACACAC 57.596 37.037 0.00 0.00 41.57 3.82
4266 5477 6.207221 ACACTATCTCTATGAGCATGTCTGAG 59.793 42.308 0.00 2.09 0.00 3.35
4281 5492 2.685897 GTCTGAGATACGGAGCTGAACT 59.314 50.000 0.00 0.00 34.24 3.01
4317 5528 1.853963 ACGAAGTCACCATAGGCTCT 58.146 50.000 0.00 0.00 29.74 4.09
4380 5591 6.588204 TGAGCTGTTAGTCCTAAAAGTTTCA 58.412 36.000 0.00 7.44 33.83 2.69
4381 5592 6.482308 TGAGCTGTTAGTCCTAAAAGTTTCAC 59.518 38.462 0.00 0.00 33.83 3.18
4383 5594 5.333875 GCTGTTAGTCCTAAAAGTTTCACCG 60.334 44.000 6.21 0.00 33.83 4.94
4400 5611 0.036671 CCGGGGTGTCACTTTAGTCC 60.037 60.000 2.35 0.00 0.00 3.85
4406 5617 3.756963 GGGTGTCACTTTAGTCCCAATTC 59.243 47.826 2.35 0.00 35.43 2.17
4425 5636 8.231837 CCCAATTCTTTCAAAATGCACATTTAG 58.768 33.333 8.92 3.67 39.88 1.85
4454 5665 9.640963 CCTAATTCTATAATAAGAGGTTCACCG 57.359 37.037 0.00 0.00 42.08 4.94
4458 5669 6.371278 TCTATAATAAGAGGTTCACCGAGGT 58.629 40.000 0.00 0.00 42.08 3.85
4490 5703 3.050275 GCTCGTTGACCTGCCCAC 61.050 66.667 0.00 0.00 0.00 4.61
4513 5726 4.101790 GCGTTGACCCATGCCACG 62.102 66.667 0.00 0.00 0.00 4.94
4519 5732 3.583276 GACCCATGCCACGTCGACA 62.583 63.158 17.16 0.00 0.00 4.35
4543 5757 1.712018 GGCACGGCGGTTCCTATTTC 61.712 60.000 13.24 0.00 0.00 2.17
4550 5764 2.159612 GGCGGTTCCTATTTCGTTTCAC 60.160 50.000 0.00 0.00 0.00 3.18
4551 5765 2.159612 GCGGTTCCTATTTCGTTTCACC 60.160 50.000 0.00 0.00 0.00 4.02
4587 5801 1.496429 ACCATCATCCTCACATTCCCC 59.504 52.381 0.00 0.00 0.00 4.81
4588 5802 1.496001 CCATCATCCTCACATTCCCCA 59.504 52.381 0.00 0.00 0.00 4.96
4615 5829 8.221251 GTCCTAGATCTATTTCTTCCCCAAATT 58.779 37.037 2.11 0.00 0.00 1.82
4619 5833 4.878968 TCTATTTCTTCCCCAAATTCCCC 58.121 43.478 0.00 0.00 0.00 4.81
4632 5848 2.956077 ATTCCCCCTCTCTCTCGCCC 62.956 65.000 0.00 0.00 0.00 6.13
4657 5873 4.142609 CTACCATAGCAGTCACACCATT 57.857 45.455 0.00 0.00 0.00 3.16
4662 5878 0.035056 AGCAGTCACACCATTAGGCC 60.035 55.000 0.00 0.00 39.06 5.19
4688 5904 3.235369 GGAGGATCTCCCACTGGC 58.765 66.667 2.65 0.00 44.36 4.85
4693 5909 2.284625 ATCTCCCACTGGCCGTCA 60.285 61.111 0.00 0.00 0.00 4.35
4712 5928 0.609131 ACAAAGGGGGCATCTTCACG 60.609 55.000 0.00 0.00 0.00 4.35
4735 5951 1.000896 CCCACTCGGATTGCCCTTT 60.001 57.895 0.00 0.00 0.00 3.11
4739 5955 2.280628 CACTCGGATTGCCCTTTAGAC 58.719 52.381 0.00 0.00 0.00 2.59
4778 5994 1.519455 CAGAGGGAATCGTCGCCAC 60.519 63.158 0.00 0.00 37.42 5.01
4829 6045 2.029470 AGAGTTGCGTGAAAGAGGAGAG 60.029 50.000 0.00 0.00 0.00 3.20
4841 6057 3.721706 GGAGAGGGGGTGCCACTG 61.722 72.222 0.00 0.00 37.42 3.66
4856 6072 2.708325 GCCACTGAGAGGGGAATAGATT 59.292 50.000 0.00 0.00 43.10 2.40
4857 6073 3.495806 GCCACTGAGAGGGGAATAGATTG 60.496 52.174 0.00 0.00 43.10 2.67
4858 6074 3.072184 CCACTGAGAGGGGAATAGATTGG 59.928 52.174 0.00 0.00 43.10 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 5.059404 AGTTCGGATTTAAATTGCAGTGG 57.941 39.130 1.43 0.00 0.00 4.00
120 121 4.454504 ACGAGTTCGGATTTAAATTGCAGT 59.545 37.500 1.43 0.00 44.95 4.40
134 135 2.030540 TCAAGGTGTAGAACGAGTTCGG 60.031 50.000 9.94 0.00 43.97 4.30
138 139 5.944599 TCTATTCTCAAGGTGTAGAACGAGT 59.055 40.000 0.00 0.00 34.70 4.18
142 143 8.603242 TGTTTTCTATTCTCAAGGTGTAGAAC 57.397 34.615 0.00 0.00 34.70 3.01
181 182 9.715123 CGCAATCATGATATGTGTTAGTTTAAA 57.285 29.630 9.04 0.00 0.00 1.52
183 184 7.351981 GCGCAATCATGATATGTGTTAGTTTA 58.648 34.615 21.63 0.00 0.00 2.01
186 187 4.084380 CGCGCAATCATGATATGTGTTAGT 60.084 41.667 21.63 0.74 0.00 2.24
187 188 4.084380 ACGCGCAATCATGATATGTGTTAG 60.084 41.667 21.63 17.56 0.00 2.34
242 244 7.334921 ACGACTCCGAAATTTATGGTGAAAATA 59.665 33.333 14.56 0.00 39.50 1.40
245 247 4.998672 ACGACTCCGAAATTTATGGTGAAA 59.001 37.500 14.56 0.00 39.50 2.69
248 250 4.201783 GGAACGACTCCGAAATTTATGGTG 60.202 45.833 8.39 8.52 39.50 4.17
298 303 3.837213 ACTGAGAAAACATTGGATGCG 57.163 42.857 0.00 0.00 0.00 4.73
311 322 1.071699 GCAGTGGGGTACAACTGAGAA 59.928 52.381 20.56 0.00 33.08 2.87
312 323 0.685097 GCAGTGGGGTACAACTGAGA 59.315 55.000 20.56 0.00 33.08 3.27
313 324 0.321653 GGCAGTGGGGTACAACTGAG 60.322 60.000 20.56 2.56 33.08 3.35
314 325 1.758592 GGCAGTGGGGTACAACTGA 59.241 57.895 20.56 0.00 33.08 3.41
315 326 1.303317 GGGCAGTGGGGTACAACTG 60.303 63.158 14.83 14.83 33.88 3.16
342 353 3.103911 CGTTTTCGCGAGCTCCGT 61.104 61.111 19.53 0.00 41.15 4.69
358 369 1.300853 CTTTTGCAGTTTGGCCCCG 60.301 57.895 0.00 0.00 0.00 5.73
362 373 1.601914 CGGTACCTTTTGCAGTTTGGC 60.602 52.381 10.90 0.00 0.00 4.52
388 399 1.500474 TTTGGTGGGTTTGAATGGCA 58.500 45.000 0.00 0.00 0.00 4.92
389 400 2.629336 TTTTGGTGGGTTTGAATGGC 57.371 45.000 0.00 0.00 0.00 4.40
823 834 2.032681 GGGAGTGGGAGTGTGTGC 59.967 66.667 0.00 0.00 0.00 4.57
908 926 0.106419 GGGAGTCGAGATCTGGGAGT 60.106 60.000 0.00 0.00 0.00 3.85
926 944 1.896694 GGAGCAGAGACAGACTGGG 59.103 63.158 7.51 0.00 36.09 4.45
1084 1103 0.560688 AAGCAACTGGGAAAAGGGGA 59.439 50.000 0.00 0.00 0.00 4.81
1114 1133 1.332375 TGAAAAGTTTCGAAGCGGGTG 59.668 47.619 6.35 0.00 40.01 4.61
1167 1186 3.300009 GAACAAATCAAGAAGTGGCGTG 58.700 45.455 0.00 0.00 0.00 5.34
1174 1193 5.181690 TGAAACGGGAACAAATCAAGAAG 57.818 39.130 0.00 0.00 0.00 2.85
1194 1218 2.294233 GCTGAGCAAAGACACCAAATGA 59.706 45.455 0.00 0.00 0.00 2.57
1198 1222 1.311859 CTGCTGAGCAAAGACACCAA 58.688 50.000 9.07 0.00 38.41 3.67
1203 1227 1.206072 CACGCTGCTGAGCAAAGAC 59.794 57.895 9.07 0.00 46.62 3.01
1216 1240 0.038709 GAGCTCAACAGAGACACGCT 60.039 55.000 9.40 0.00 0.00 5.07
1218 1242 2.730715 GCTAGAGCTCAACAGAGACACG 60.731 54.545 17.77 0.00 38.21 4.49
1235 1259 4.230657 GGATAACGATGCAGTACAGCTAG 58.769 47.826 11.81 5.40 34.99 3.42
1236 1260 3.634910 TGGATAACGATGCAGTACAGCTA 59.365 43.478 11.81 0.00 34.99 3.32
1245 1269 3.389656 TGGGATAACTGGATAACGATGCA 59.610 43.478 0.00 0.00 31.76 3.96
1265 1289 1.821216 AGAACCCATAAACGTGCTGG 58.179 50.000 0.00 0.00 0.00 4.85
1267 1291 2.812011 GTGAAGAACCCATAAACGTGCT 59.188 45.455 0.00 0.00 0.00 4.40
1269 1293 3.824414 GGTGAAGAACCCATAAACGTG 57.176 47.619 0.00 0.00 44.02 4.49
1290 2284 7.941919 AGTTCCCAAAGAAAGATGTTAAGAAC 58.058 34.615 0.00 0.00 35.85 3.01
1296 2290 8.712228 ATAAAGAGTTCCCAAAGAAAGATGTT 57.288 30.769 0.00 0.00 35.85 2.71
1330 2324 9.979578 CCTGCATGCCTTAACATTAAATTATTA 57.020 29.630 16.68 0.00 0.00 0.98
1331 2325 8.485392 ACCTGCATGCCTTAACATTAAATTATT 58.515 29.630 16.68 0.00 0.00 1.40
1332 2326 8.021898 ACCTGCATGCCTTAACATTAAATTAT 57.978 30.769 16.68 0.00 0.00 1.28
1333 2327 7.416964 ACCTGCATGCCTTAACATTAAATTA 57.583 32.000 16.68 0.00 0.00 1.40
1435 2429 1.075212 TCATTGTGGGTGCTCATCCAA 59.925 47.619 3.01 0.00 44.47 3.53
1465 2459 1.021390 CAGGGATTGTGAGTGACCGC 61.021 60.000 0.00 0.00 0.00 5.68
1518 2512 3.554934 ACAATTCCATGGACGCATACAT 58.445 40.909 15.91 0.00 0.00 2.29
1519 2513 2.997980 ACAATTCCATGGACGCATACA 58.002 42.857 15.91 0.00 0.00 2.29
1520 2514 4.754618 TGATACAATTCCATGGACGCATAC 59.245 41.667 15.91 4.56 0.00 2.39
1521 2515 4.967036 TGATACAATTCCATGGACGCATA 58.033 39.130 15.91 5.69 0.00 3.14
1562 2556 2.355132 CGGAGCATGACTACTAACGACT 59.645 50.000 0.00 0.00 0.00 4.18
1563 2557 2.353889 TCGGAGCATGACTACTAACGAC 59.646 50.000 0.00 0.00 0.00 4.34
1564 2558 2.635714 TCGGAGCATGACTACTAACGA 58.364 47.619 0.00 0.00 0.00 3.85
1565 2559 3.416119 TTCGGAGCATGACTACTAACG 57.584 47.619 0.00 0.00 0.00 3.18
1566 2560 5.232414 GTCAATTCGGAGCATGACTACTAAC 59.768 44.000 0.00 0.00 39.21 2.34
1567 2561 5.105513 TGTCAATTCGGAGCATGACTACTAA 60.106 40.000 15.90 0.00 42.03 2.24
1568 2562 4.401202 TGTCAATTCGGAGCATGACTACTA 59.599 41.667 15.90 0.00 42.03 1.82
1573 2567 2.032550 CCATGTCAATTCGGAGCATGAC 59.967 50.000 0.00 10.92 41.90 3.06
1629 2623 0.257328 TGTTCTTCCAAGCACCCACA 59.743 50.000 0.00 0.00 0.00 4.17
1688 2682 7.801783 GCCGTAAGTTTAATAGTTTATGCATCC 59.198 37.037 0.19 0.00 0.00 3.51
1889 2883 2.554032 CCAACTGGAAAGGTTGTGCTAG 59.446 50.000 0.00 0.00 41.47 3.42
1984 2978 6.998074 TGATGATTAACCACTGAACTTTCACT 59.002 34.615 0.00 0.00 32.90 3.41
1988 2982 8.859090 TCAATTGATGATTAACCACTGAACTTT 58.141 29.630 3.38 0.00 31.50 2.66
2059 3053 1.821216 ACCTGAAAAGGTACATGGCG 58.179 50.000 0.00 0.00 41.04 5.69
2155 3149 1.975680 GCCCGGGGAATCATCTAGTTA 59.024 52.381 25.28 0.00 0.00 2.24
2173 3167 0.109919 CTTTTCCCGCAGTAAACGCC 60.110 55.000 0.00 0.00 0.00 5.68
2174 3168 0.728129 GCTTTTCCCGCAGTAAACGC 60.728 55.000 0.00 0.00 0.00 4.84
2185 3179 5.825151 AGCTATATGTCTTTGAGCTTTTCCC 59.175 40.000 0.00 0.00 40.55 3.97
2215 3334 5.125578 TGTGTTTGTGGTGTGTTAGCAATAA 59.874 36.000 0.00 0.00 38.75 1.40
2221 3340 4.856487 CAGTTTGTGTTTGTGGTGTGTTAG 59.144 41.667 0.00 0.00 0.00 2.34
2226 3345 3.296322 CACAGTTTGTGTTTGTGGTGT 57.704 42.857 1.13 0.00 43.08 4.16
2242 3361 8.261492 AGATACTGAGCTCATTTTTAACACAG 57.739 34.615 18.63 3.13 0.00 3.66
2252 3371 5.012871 ACATGCCATAGATACTGAGCTCATT 59.987 40.000 18.63 14.83 0.00 2.57
2331 3450 3.157881 TCGATTAGAGATGGCCCTACAG 58.842 50.000 0.00 0.00 0.00 2.74
2342 3461 4.035324 GTCGTGTGGAGAATCGATTAGAGA 59.965 45.833 11.38 0.16 34.37 3.10
2363 3482 0.952280 CCTGCCATCTCATGCATGTC 59.048 55.000 25.43 9.90 36.79 3.06
2755 3886 6.152379 GCACTAATGAAAGAAACCTTCCAAG 58.848 40.000 0.00 0.00 0.00 3.61
2762 3893 9.129209 GAATTAACTGCACTAATGAAAGAAACC 57.871 33.333 0.00 0.00 0.00 3.27
3744 4949 8.732746 ACCCATACAAACATAAGTCAAGATAC 57.267 34.615 0.00 0.00 0.00 2.24
3834 5043 7.036220 GTCATCTTCGAGGAACTTTAGAATCA 58.964 38.462 0.00 0.00 41.55 2.57
3861 5070 9.311916 CATAGAGAGGATTCACTTCAAAGTAAG 57.688 37.037 0.00 0.00 37.08 2.34
3921 5131 7.353414 TGAATGAACAATGTTTTACAAGGGA 57.647 32.000 0.00 0.00 0.00 4.20
3929 5139 7.010738 CAGCTGAACTTGAATGAACAATGTTTT 59.989 33.333 8.42 0.00 0.00 2.43
3990 5201 3.122937 GCTACTGGCACAAAGAAATCG 57.877 47.619 0.00 0.00 38.70 3.34
4031 5242 2.367241 TCAGAAGATTGTGGGACGTTCA 59.633 45.455 0.00 0.00 0.00 3.18
4040 5251 5.645067 TCAGGCTGTATTTCAGAAGATTGTG 59.355 40.000 15.27 0.00 46.27 3.33
4092 5303 5.745312 TCCAGTTTACTCACATGTCAGAT 57.255 39.130 2.79 0.00 0.00 2.90
4102 5313 7.662669 GGTTGGTAAGTTATTCCAGTTTACTCA 59.337 37.037 0.00 0.00 32.63 3.41
4208 5419 7.282450 ACGTGTGTTCATAGAGATGAGTGTATA 59.718 37.037 0.00 0.00 43.03 1.47
4222 5433 0.032267 TGTGCGGACGTGTGTTCATA 59.968 50.000 1.60 0.00 0.00 2.15
4225 5436 2.168503 TGTGTGCGGACGTGTGTTC 61.169 57.895 1.60 0.00 0.00 3.18
4232 5443 0.452184 AGAGATAGTGTGTGCGGACG 59.548 55.000 1.60 0.00 0.00 4.79
4266 5477 6.019779 AGATATTGAGTTCAGCTCCGTATC 57.980 41.667 0.00 3.46 43.48 2.24
4281 5492 7.544566 GTGACTTCGTCAACCTTAAGATATTGA 59.455 37.037 3.36 8.18 44.49 2.57
4309 5520 4.667519 AACCGAATACGAAAGAGCCTAT 57.332 40.909 0.00 0.00 42.66 2.57
4310 5521 4.460948 AAACCGAATACGAAAGAGCCTA 57.539 40.909 0.00 0.00 42.66 3.93
4312 5523 4.156182 CAAAAACCGAATACGAAAGAGCC 58.844 43.478 0.00 0.00 42.66 4.70
4317 5528 3.502979 CCCTCCAAAAACCGAATACGAAA 59.497 43.478 0.00 0.00 42.66 3.46
4349 5560 6.659745 TTAGGACTAACAGCTCAACAACTA 57.340 37.500 0.00 0.00 0.00 2.24
4351 5562 6.260271 ACTTTTAGGACTAACAGCTCAACAAC 59.740 38.462 5.42 0.00 0.00 3.32
4356 5567 6.482308 GTGAAACTTTTAGGACTAACAGCTCA 59.518 38.462 5.42 6.07 0.00 4.26
4380 5591 0.683412 GACTAAAGTGACACCCCGGT 59.317 55.000 0.00 0.00 0.00 5.28
4381 5592 0.036671 GGACTAAAGTGACACCCCGG 60.037 60.000 0.84 0.00 0.00 5.73
4383 5594 1.061546 TGGGACTAAAGTGACACCCC 58.938 55.000 0.84 5.20 36.82 4.95
4400 5611 8.231837 CCTAAATGTGCATTTTGAAAGAATTGG 58.768 33.333 14.29 0.00 40.99 3.16
4406 5617 6.458210 AGGACCTAAATGTGCATTTTGAAAG 58.542 36.000 14.29 6.78 40.99 2.62
4468 5681 2.856032 CAGGTCAACGAGCGCTTG 59.144 61.111 23.34 23.34 35.00 4.01
4513 5726 2.430921 CCGTGCCAGTCTGTCGAC 60.431 66.667 9.11 9.11 40.54 4.20
4519 5732 4.681978 GAACCGCCGTGCCAGTCT 62.682 66.667 0.00 0.00 0.00 3.24
4543 5757 2.836479 AAGTGGTTTTCGGTGAAACG 57.164 45.000 0.00 0.00 39.76 3.60
4550 5764 6.503589 TGATGGTTTATAAGTGGTTTTCGG 57.496 37.500 0.00 0.00 0.00 4.30
4551 5765 7.067008 AGGATGATGGTTTATAAGTGGTTTTCG 59.933 37.037 0.00 0.00 0.00 3.46
4587 5801 5.841237 TGGGGAAGAAATAGATCTAGGACTG 59.159 44.000 8.70 0.00 0.00 3.51
4588 5802 6.044411 TGGGGAAGAAATAGATCTAGGACT 57.956 41.667 8.70 4.37 0.00 3.85
4615 5829 4.144727 GGGCGAGAGAGAGGGGGA 62.145 72.222 0.00 0.00 0.00 4.81
4619 5833 3.535962 GCCAGGGCGAGAGAGAGG 61.536 72.222 0.00 0.00 0.00 3.69
4646 5862 0.537188 CGAGGCCTAATGGTGTGACT 59.463 55.000 4.42 0.00 35.27 3.41
4657 5873 1.381327 CCTCCTTCACCGAGGCCTA 60.381 63.158 4.42 0.00 40.55 3.93
4662 5878 1.036707 GGAGATCCTCCTTCACCGAG 58.963 60.000 5.78 0.00 46.41 4.63
4675 5891 2.359169 TGACGGCCAGTGGGAGATC 61.359 63.158 12.15 0.00 35.59 2.75
4688 5904 2.035626 ATGCCCCCTTTGTGACGG 59.964 61.111 0.00 0.00 0.00 4.79
4693 5909 0.609131 CGTGAAGATGCCCCCTTTGT 60.609 55.000 0.00 0.00 0.00 2.83
4712 5928 2.438434 CAATCCGAGTGGGTGCCC 60.438 66.667 0.00 0.00 37.00 5.36
4761 5977 2.722201 GGTGGCGACGATTCCCTCT 61.722 63.158 0.00 0.00 0.00 3.69
4816 6032 0.615850 CACCCCCTCTCCTCTTTCAC 59.384 60.000 0.00 0.00 0.00 3.18
4829 6045 3.721706 CCTCTCAGTGGCACCCCC 61.722 72.222 15.27 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.