Multiple sequence alignment - TraesCS5B01G058300

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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 TraesCS5B01G058300 chr5B 100.000 6383 0 0 1 6383 64252396 64258778 0.000000e+00 11788.0
1 TraesCS5B01G058300 chr5B 77.733 247 52 2 4030 4276 559997319 559997076 1.430000e-31 148.0
2 TraesCS5B01G058300 chr5B 97.368 38 1 0 1 38 657803823 657803860 1.490000e-06 65.8
3 TraesCS5B01G058300 chr5D 96.996 4993 112 19 417 5395 66770175 66765207 0.000000e+00 8355.0
4 TraesCS5B01G058300 chr5D 88.904 730 37 11 5387 6102 66765024 66764325 0.000000e+00 859.0
5 TraesCS5B01G058300 chr5D 94.755 286 12 2 6098 6383 66764193 66763911 5.870000e-120 442.0
6 TraesCS5B01G058300 chr5D 87.762 286 33 2 31 315 66772754 66772470 3.690000e-87 333.0
7 TraesCS5B01G058300 chr5D 77.043 257 56 2 4020 4276 457782189 457781936 1.850000e-30 145.0
8 TraesCS5B01G058300 chr5D 89.873 79 7 1 1899 1976 66768623 66768545 4.070000e-17 100.0
9 TraesCS5B01G058300 chr5A 90.798 3271 202 44 2881 6102 57364744 57367964 0.000000e+00 4281.0
10 TraesCS5B01G058300 chr5A 92.870 1655 79 17 417 2053 57362041 57363674 0.000000e+00 2366.0
11 TraesCS5B01G058300 chr5A 90.164 549 40 6 2475 3010 57364196 57364743 0.000000e+00 702.0
12 TraesCS5B01G058300 chr5A 85.832 607 49 15 1899 2479 57363559 57364154 1.520000e-170 610.0
13 TraesCS5B01G058300 chr5A 92.657 286 21 0 6098 6383 57368146 57368431 4.600000e-111 412.0
14 TraesCS5B01G058300 chr5A 88.608 79 8 1 1899 1976 57363635 57363713 1.890000e-15 95.3
15 TraesCS5B01G058300 chr4D 96.466 1132 32 4 1934 3061 55363191 55364318 0.000000e+00 1862.0
16 TraesCS5B01G058300 chr3B 100.000 36 0 0 1 36 53068019 53067984 4.130000e-07 67.6
17 TraesCS5B01G058300 chr3B 89.362 47 3 2 1 45 509637622 509637576 2.490000e-04 58.4
18 TraesCS5B01G058300 chrUn 97.368 38 1 0 1 38 166021940 166021903 1.490000e-06 65.8
19 TraesCS5B01G058300 chr7A 100.000 35 0 0 1 35 349983282 349983316 1.490000e-06 65.8
20 TraesCS5B01G058300 chr7A 97.368 38 0 1 1 38 150127815 150127779 5.340000e-06 63.9
21 TraesCS5B01G058300 chr7A 97.368 38 0 1 3 40 563335668 563335704 5.340000e-06 63.9
22 TraesCS5B01G058300 chr7A 92.857 42 3 0 1 42 419599986 419599945 1.920000e-05 62.1
23 TraesCS5B01G058300 chr4A 97.436 39 0 1 1 39 112422300 112422337 1.490000e-06 65.8


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 TraesCS5B01G058300 chr5B 64252396 64258778 6382 False 11788.00 11788 100.000000 1 6383 1 chr5B.!!$F1 6382
1 TraesCS5B01G058300 chr5D 66763911 66772754 8843 True 2017.80 8355 91.658000 31 6383 5 chr5D.!!$R2 6352
2 TraesCS5B01G058300 chr5A 57362041 57368431 6390 False 1411.05 4281 90.154833 417 6383 6 chr5A.!!$F1 5966
3 TraesCS5B01G058300 chr4D 55363191 55364318 1127 False 1862.00 1862 96.466000 1934 3061 1 chr4D.!!$F1 1127

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
21 22 0.396435 AGGACATCTGCCGTGACAAA 59.604 50.000 0.0 0.0 0.00 2.83 F
214 216 0.462047 GAGACACCCCGCCTAACATG 60.462 60.000 0.0 0.0 0.00 3.21 F
369 371 0.672401 TCTGGACGGATGAAAACGCC 60.672 55.000 0.0 0.0 0.00 5.68 F
1999 4276 0.322816 ATGGACTTGCTGTGGCGAAT 60.323 50.000 0.0 0.0 42.25 3.34 F
2245 4523 1.605710 CAAGTGGGCACAAGTCTCTTG 59.394 52.381 0.0 0.0 0.00 3.02 F
3191 5688 3.244596 ACTCTACAAGCCTTTCAACCCTC 60.245 47.826 0.0 0.0 0.00 4.30 F
3962 6472 2.485814 GCTTGTGCTCCTTTGTTCTAGG 59.514 50.000 0.0 0.0 36.03 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 4044 0.539438 TCAAGGGTCCACAATGGTGC 60.539 55.000 0.00 0.00 43.88 5.01 R
1811 4049 0.991920 ACCGATCAAGGGTCCACAAT 59.008 50.000 0.00 0.00 29.94 2.71 R
2116 4394 1.059098 ACAGATCAAGTCAGGCACCA 58.941 50.000 0.00 0.00 0.00 4.17 R
3191 5688 3.007831 GGGAGGAAAGATCTGATAGCCAG 59.992 52.174 0.00 0.00 44.27 4.85 R
3962 6472 6.183360 TGGGCAATGTGATATTTCTGAAATCC 60.183 38.462 18.22 12.23 32.38 3.01 R
4657 7168 2.100197 TCTCATCACACGGGAGGTTAG 58.900 52.381 0.00 0.00 0.00 2.34 R
5629 8359 0.370273 CGGTTCCGATTCAGAAAGCG 59.630 55.000 5.19 2.63 43.65 4.68 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
18 19 3.650409 CTAGGACATCTGCCGTGAC 57.350 57.895 0.00 0.00 0.00 3.67
19 20 0.817654 CTAGGACATCTGCCGTGACA 59.182 55.000 0.00 0.00 0.00 3.58
20 21 1.204704 CTAGGACATCTGCCGTGACAA 59.795 52.381 0.00 0.00 0.00 3.18
21 22 0.396435 AGGACATCTGCCGTGACAAA 59.604 50.000 0.00 0.00 0.00 2.83
22 23 1.003580 AGGACATCTGCCGTGACAAAT 59.996 47.619 0.00 0.00 0.00 2.32
23 24 1.398390 GGACATCTGCCGTGACAAATC 59.602 52.381 0.00 0.00 0.00 2.17
24 25 1.398390 GACATCTGCCGTGACAAATCC 59.602 52.381 0.00 0.00 0.00 3.01
25 26 1.271325 ACATCTGCCGTGACAAATCCA 60.271 47.619 0.00 0.00 0.00 3.41
26 27 1.131126 CATCTGCCGTGACAAATCCAC 59.869 52.381 0.00 0.00 0.00 4.02
64 65 1.840741 CGTGACGTCGAATGATCTCAC 59.159 52.381 11.62 0.00 33.34 3.51
65 66 2.727916 CGTGACGTCGAATGATCTCACA 60.728 50.000 11.62 0.00 35.02 3.58
94 95 1.134438 AGTTCCCCCTTGGAGGTCAC 61.134 60.000 0.00 0.00 46.24 3.67
95 96 1.850755 TTCCCCCTTGGAGGTCACC 60.851 63.158 0.00 0.00 46.24 4.02
111 112 1.050988 CACCGACCCCTCATCCTCAT 61.051 60.000 0.00 0.00 0.00 2.90
112 113 0.760945 ACCGACCCCTCATCCTCATC 60.761 60.000 0.00 0.00 0.00 2.92
142 143 2.589157 CGACCTAGGCCCACAACCA 61.589 63.158 9.30 0.00 0.00 3.67
157 158 3.322466 CCAGACCCCGACAAGCCT 61.322 66.667 0.00 0.00 0.00 4.58
158 159 2.266055 CAGACCCCGACAAGCCTC 59.734 66.667 0.00 0.00 0.00 4.70
159 160 3.382832 AGACCCCGACAAGCCTCG 61.383 66.667 0.00 0.00 0.00 4.63
177 179 2.577059 CTAGACGAGGGCCGCAAA 59.423 61.111 8.33 0.00 43.32 3.68
194 196 2.592459 GCAAAGACAACGACAACAACAC 59.408 45.455 0.00 0.00 0.00 3.32
200 202 1.656594 CAACGACAACAACACGAGACA 59.343 47.619 0.00 0.00 0.00 3.41
201 203 1.274596 ACGACAACAACACGAGACAC 58.725 50.000 0.00 0.00 0.00 3.67
203 205 0.935196 GACAACAACACGAGACACCC 59.065 55.000 0.00 0.00 0.00 4.61
204 206 0.463116 ACAACAACACGAGACACCCC 60.463 55.000 0.00 0.00 0.00 4.95
205 207 1.227438 AACAACACGAGACACCCCG 60.227 57.895 0.00 0.00 0.00 5.73
209 211 3.066190 CACGAGACACCCCGCCTA 61.066 66.667 0.00 0.00 0.00 3.93
210 212 2.283388 ACGAGACACCCCGCCTAA 60.283 61.111 0.00 0.00 0.00 2.69
214 216 0.462047 GAGACACCCCGCCTAACATG 60.462 60.000 0.00 0.00 0.00 3.21
223 225 1.705337 CGCCTAACATGGTTGCCTCG 61.705 60.000 0.00 0.00 0.00 4.63
245 247 3.791973 AATCACTCAAGGAGACGCTAG 57.208 47.619 0.00 0.00 33.32 3.42
247 249 2.360844 TCACTCAAGGAGACGCTAGAG 58.639 52.381 0.00 0.00 33.32 2.43
253 255 1.034838 AGGAGACGCTAGAGCACCTG 61.035 60.000 1.89 0.00 42.21 4.00
274 276 2.657237 GTCATATCGCCCCTCCCG 59.343 66.667 0.00 0.00 0.00 5.14
292 294 3.142951 CCCGTTTTCTACCATGTTCACA 58.857 45.455 0.00 0.00 0.00 3.58
315 317 9.778993 CACATGTGGATCTTTTAAAGTGAATAG 57.221 33.333 18.51 0.00 0.00 1.73
333 335 8.993121 AGTGAATAGATCTTTTATTACCATGCG 58.007 33.333 0.00 0.00 0.00 4.73
334 336 8.774586 GTGAATAGATCTTTTATTACCATGCGT 58.225 33.333 0.00 0.00 0.00 5.24
335 337 9.337396 TGAATAGATCTTTTATTACCATGCGTT 57.663 29.630 0.00 0.00 0.00 4.84
337 339 5.821204 AGATCTTTTATTACCATGCGTTGC 58.179 37.500 0.00 0.00 0.00 4.17
342 344 2.057137 ATTACCATGCGTTGCTCCAT 57.943 45.000 0.00 0.00 0.00 3.41
343 345 1.093972 TTACCATGCGTTGCTCCATG 58.906 50.000 0.00 0.00 38.78 3.66
345 347 3.594568 CATGCGTTGCTCCATGGT 58.405 55.556 12.58 0.00 36.16 3.55
347 349 1.093972 CATGCGTTGCTCCATGGTTA 58.906 50.000 12.58 0.00 36.16 2.85
348 350 1.677576 CATGCGTTGCTCCATGGTTAT 59.322 47.619 12.58 0.00 36.16 1.89
349 351 1.832883 TGCGTTGCTCCATGGTTATT 58.167 45.000 12.58 0.00 0.00 1.40
350 352 2.166829 TGCGTTGCTCCATGGTTATTT 58.833 42.857 12.58 0.00 0.00 1.40
351 353 2.163412 TGCGTTGCTCCATGGTTATTTC 59.837 45.455 12.58 0.00 0.00 2.17
352 354 2.423538 GCGTTGCTCCATGGTTATTTCT 59.576 45.455 12.58 0.00 0.00 2.52
353 355 3.731867 GCGTTGCTCCATGGTTATTTCTG 60.732 47.826 12.58 0.00 0.00 3.02
354 356 3.181497 CGTTGCTCCATGGTTATTTCTGG 60.181 47.826 12.58 0.00 0.00 3.86
355 357 4.016444 GTTGCTCCATGGTTATTTCTGGA 58.984 43.478 12.58 0.00 36.40 3.86
356 358 3.620488 TGCTCCATGGTTATTTCTGGAC 58.380 45.455 12.58 0.00 34.21 4.02
357 359 2.614057 GCTCCATGGTTATTTCTGGACG 59.386 50.000 12.58 0.00 34.21 4.79
358 360 3.206150 CTCCATGGTTATTTCTGGACGG 58.794 50.000 12.58 0.00 34.21 4.79
359 361 2.841266 TCCATGGTTATTTCTGGACGGA 59.159 45.455 12.58 0.00 32.92 4.69
360 362 3.458118 TCCATGGTTATTTCTGGACGGAT 59.542 43.478 12.58 0.00 32.92 4.18
361 363 3.565482 CCATGGTTATTTCTGGACGGATG 59.435 47.826 2.57 0.00 0.00 3.51
362 364 4.450976 CATGGTTATTTCTGGACGGATGA 58.549 43.478 0.00 0.00 0.00 2.92
363 365 4.561500 TGGTTATTTCTGGACGGATGAA 57.438 40.909 0.00 0.00 0.00 2.57
364 366 4.912586 TGGTTATTTCTGGACGGATGAAA 58.087 39.130 0.00 0.00 34.75 2.69
365 367 5.317808 TGGTTATTTCTGGACGGATGAAAA 58.682 37.500 0.00 0.00 34.09 2.29
366 368 5.182380 TGGTTATTTCTGGACGGATGAAAAC 59.818 40.000 0.00 0.00 34.09 2.43
367 369 5.321516 GTTATTTCTGGACGGATGAAAACG 58.678 41.667 0.00 0.00 34.09 3.60
368 370 1.153353 TTCTGGACGGATGAAAACGC 58.847 50.000 0.00 0.00 0.00 4.84
369 371 0.672401 TCTGGACGGATGAAAACGCC 60.672 55.000 0.00 0.00 0.00 5.68
413 415 2.249309 CAGCGAAACACTGGTGCG 59.751 61.111 0.17 0.00 0.00 5.34
414 416 2.972505 AGCGAAACACTGGTGCGG 60.973 61.111 0.00 0.00 0.00 5.69
415 417 3.276846 GCGAAACACTGGTGCGGT 61.277 61.111 0.00 0.00 0.00 5.68
484 2702 1.555477 CCAACGCTTGTGTGAAAACC 58.445 50.000 0.00 0.00 0.00 3.27
522 2740 2.363788 TGCTCAATACTCACCACGTC 57.636 50.000 0.00 0.00 0.00 4.34
556 2774 7.728847 TTGCGTAATCTGCACTCATAAATAT 57.271 32.000 0.00 0.00 43.10 1.28
584 2802 2.202878 CACCACCCAGTATCGGCG 60.203 66.667 0.00 0.00 0.00 6.46
664 2882 2.348998 CAGCCAAAGACCGAGCCT 59.651 61.111 0.00 0.00 0.00 4.58
747 2975 3.759910 AACCACCCAAAACCCCCGG 62.760 63.158 0.00 0.00 0.00 5.73
1338 3576 1.595382 CGTGGATGATTCGGAGCCC 60.595 63.158 0.00 0.00 0.00 5.19
1355 3593 4.039357 CGAGTCGGGTGCTGTCGT 62.039 66.667 4.10 0.00 0.00 4.34
1661 3899 1.334870 CGATCCACGAGCAGATCTCTG 60.335 57.143 2.75 2.75 45.77 3.35
1761 3999 0.821517 ATGAACACGCCCGATCTACA 59.178 50.000 0.00 0.00 0.00 2.74
1804 4042 3.157217 ATCTGGCGCCGTGAGATCC 62.157 63.158 23.90 0.00 0.00 3.36
1811 4049 3.770040 CCGTGAGATCCCGCACCA 61.770 66.667 5.65 0.00 39.50 4.17
1830 4068 0.991920 ATTGTGGACCCTTGATCGGT 59.008 50.000 0.00 0.00 35.88 4.69
1852 4090 2.230508 GCCCGATCGGAATCTATACACA 59.769 50.000 35.42 0.00 37.50 3.72
1853 4091 3.305813 GCCCGATCGGAATCTATACACAA 60.306 47.826 35.42 0.00 37.50 3.33
1854 4092 4.486090 CCCGATCGGAATCTATACACAAG 58.514 47.826 35.42 9.28 37.50 3.16
1855 4093 4.022242 CCCGATCGGAATCTATACACAAGT 60.022 45.833 35.42 0.00 37.50 3.16
1927 4165 1.893808 CTTGCTGTGGCGAACCTGT 60.894 57.895 0.00 0.00 42.25 4.00
1999 4276 0.322816 ATGGACTTGCTGTGGCGAAT 60.323 50.000 0.00 0.00 42.25 3.34
2116 4394 4.742012 AGGTCGTTATATGATCCCTGACT 58.258 43.478 0.00 0.00 0.00 3.41
2245 4523 1.605710 CAAGTGGGCACAAGTCTCTTG 59.394 52.381 0.00 0.00 0.00 3.02
2324 4622 8.691661 ATAATTCTGGTTAGTTTTGTCACAGT 57.308 30.769 0.00 0.00 0.00 3.55
2548 4900 8.861086 TCTATGGGACTTTAGTCATGATTAGAC 58.139 37.037 11.67 0.00 46.47 2.59
2783 5136 4.829492 CCTCATCCCTAAATCACAAATCCC 59.171 45.833 0.00 0.00 0.00 3.85
2786 5139 4.310022 TCCCTAAATCACAAATCCCGTT 57.690 40.909 0.00 0.00 0.00 4.44
2897 5390 4.391140 GCACTAGCAAACTGTTCAGTAC 57.609 45.455 5.87 0.09 41.58 2.73
3191 5688 3.244596 ACTCTACAAGCCTTTCAACCCTC 60.245 47.826 0.00 0.00 0.00 4.30
3377 5874 9.388506 CAACAAGATAATGATTCTACTGACCTT 57.611 33.333 0.00 0.00 0.00 3.50
3529 6026 7.041635 TGCTATTGTTCATATGGATTGTTGG 57.958 36.000 2.13 0.00 0.00 3.77
3561 6060 5.468072 TCAGAAATTGAGCTGACTGAACTTC 59.532 40.000 0.00 0.00 36.31 3.01
3962 6472 2.485814 GCTTGTGCTCCTTTGTTCTAGG 59.514 50.000 0.00 0.00 36.03 3.02
4285 6795 7.882791 TCTGGAATAGATGTAAGTGCTCAAAAA 59.117 33.333 0.00 0.00 0.00 1.94
4706 7217 1.616865 AGCTGCTGCAACATCAATTGT 59.383 42.857 18.42 0.00 42.74 2.71
4744 7255 7.723109 AATCTTAGGTTGAAATATAGGGGGT 57.277 36.000 0.00 0.00 0.00 4.95
4753 7265 6.979018 TGAAATATAGGGGGTATTGCCATA 57.021 37.500 0.00 0.00 39.65 2.74
4826 7338 1.081840 GAACGAGTTTGCAGCAGCC 60.082 57.895 0.00 0.00 41.13 4.85
5143 7665 0.845102 AGTCCCAACAACCTAGGGGG 60.845 60.000 14.81 13.60 43.03 5.40
5224 7748 3.236047 TCTGAGCCTACTGGTGTTGTAA 58.764 45.455 0.00 0.00 35.27 2.41
5225 7749 3.258372 TCTGAGCCTACTGGTGTTGTAAG 59.742 47.826 0.00 0.00 35.27 2.34
5226 7750 2.289444 TGAGCCTACTGGTGTTGTAAGC 60.289 50.000 0.00 0.00 35.27 3.09
5227 7751 1.978580 AGCCTACTGGTGTTGTAAGCT 59.021 47.619 0.00 0.00 34.12 3.74
5228 7752 2.028020 AGCCTACTGGTGTTGTAAGCTC 60.028 50.000 0.00 0.00 33.85 4.09
5229 7753 2.028020 GCCTACTGGTGTTGTAAGCTCT 60.028 50.000 0.00 0.00 35.27 4.09
5230 7754 3.194968 GCCTACTGGTGTTGTAAGCTCTA 59.805 47.826 0.00 0.00 35.27 2.43
5316 7843 1.651737 AGGGCATGGTGTAGTGTGTA 58.348 50.000 0.00 0.00 0.00 2.90
5335 7862 1.745489 GCCTAGCACCCTTGGTTCG 60.745 63.158 0.00 0.00 36.49 3.95
5415 8133 3.342377 TGTCATGTTCCTGCCGATTTA 57.658 42.857 0.00 0.00 0.00 1.40
5420 8138 6.038161 TGTCATGTTCCTGCCGATTTATTTAG 59.962 38.462 0.00 0.00 0.00 1.85
5458 8176 3.260632 TGGATGCTGCTGTAACTGTAAGA 59.739 43.478 0.00 0.00 37.43 2.10
5466 8184 3.120511 GCTGTAACTGTAAGACTGCAAGC 60.121 47.826 11.66 0.00 36.23 4.01
5470 8188 2.673833 ACTGTAAGACTGCAAGCGTAC 58.326 47.619 0.00 0.00 34.81 3.67
5570 8295 3.016613 TACGAGGGGCCCAGATGGA 62.017 63.158 27.72 4.53 37.39 3.41
5631 8361 3.074412 TGAAAGAAATTCAGTCCCTCGC 58.926 45.455 0.00 0.00 43.08 5.03
5632 8362 3.244561 TGAAAGAAATTCAGTCCCTCGCT 60.245 43.478 0.00 0.00 43.08 4.93
5752 8482 5.440685 CGTTTTTGTCGCTTAATCTCACTT 58.559 37.500 0.00 0.00 0.00 3.16
5798 8528 1.446791 CAGAGAGGAGCCATGGAGC 59.553 63.158 18.40 5.75 0.00 4.70
5896 8626 3.365465 CCTCGCCTCGTAAGTGATCTATG 60.365 52.174 0.00 0.00 39.48 2.23
5897 8627 3.473625 TCGCCTCGTAAGTGATCTATGA 58.526 45.455 0.00 0.00 39.48 2.15
5898 8628 3.250280 TCGCCTCGTAAGTGATCTATGAC 59.750 47.826 0.00 0.00 39.48 3.06
5899 8629 3.609644 CGCCTCGTAAGTGATCTATGACC 60.610 52.174 0.00 0.00 39.48 4.02
5900 8630 3.318275 GCCTCGTAAGTGATCTATGACCA 59.682 47.826 0.00 0.00 39.48 4.02
5901 8631 4.021894 GCCTCGTAAGTGATCTATGACCAT 60.022 45.833 0.00 0.00 39.48 3.55
5902 8632 5.704888 CCTCGTAAGTGATCTATGACCATC 58.295 45.833 0.00 0.00 39.48 3.51
5948 8678 1.278127 GCTAGCAAGTAGGGTGGTTCA 59.722 52.381 10.63 0.00 0.00 3.18
5967 8697 2.534903 GCCCCGCGATTTACTGCTC 61.535 63.158 8.23 0.00 0.00 4.26
5992 8722 2.202837 GGCGCCGGTTTCGACTAT 60.203 61.111 12.58 0.00 39.00 2.12
6036 8779 4.157958 GCGAGGCTTTGCTCTGCG 62.158 66.667 0.00 0.00 0.00 5.18
6048 8791 0.645868 GCTCTGCGTACGGTTGATTC 59.354 55.000 18.39 0.00 0.00 2.52
6269 9198 2.168521 TCGGGCTACATGGAAGAAGAAG 59.831 50.000 0.00 0.00 0.00 2.85
6283 9213 0.877071 AAGAAGCACAATGTGAGCGG 59.123 50.000 18.66 0.00 38.98 5.52
6311 9241 5.330455 TCTTCTCACGCAGTTCTATCATT 57.670 39.130 0.00 0.00 41.61 2.57
6312 9242 5.344066 TCTTCTCACGCAGTTCTATCATTC 58.656 41.667 0.00 0.00 41.61 2.67
6341 9273 3.624326 TTTTGCGATGTTTGACTCCAG 57.376 42.857 0.00 0.00 0.00 3.86
6345 9277 1.470098 GCGATGTTTGACTCCAGCATT 59.530 47.619 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.817654 TGTCACGGCAGATGTCCTAG 59.182 55.000 0.00 0.00 0.00 3.02
1 2 1.262417 TTGTCACGGCAGATGTCCTA 58.738 50.000 0.00 0.00 0.00 2.94
2 3 0.396435 TTTGTCACGGCAGATGTCCT 59.604 50.000 0.00 0.00 0.00 3.85
3 4 1.398390 GATTTGTCACGGCAGATGTCC 59.602 52.381 0.00 0.00 0.00 4.02
4 5 1.398390 GGATTTGTCACGGCAGATGTC 59.602 52.381 0.00 0.00 0.00 3.06
5 6 1.271325 TGGATTTGTCACGGCAGATGT 60.271 47.619 0.00 0.00 0.00 3.06
6 7 1.131126 GTGGATTTGTCACGGCAGATG 59.869 52.381 0.00 0.00 0.00 2.90
7 8 1.453155 GTGGATTTGTCACGGCAGAT 58.547 50.000 0.00 0.00 0.00 2.90
8 9 2.927004 GTGGATTTGTCACGGCAGA 58.073 52.632 0.00 0.00 0.00 4.26
14 15 3.064820 ACTTTGTGTCGTGGATTTGTCAC 59.935 43.478 0.00 0.00 0.00 3.67
15 16 3.064682 CACTTTGTGTCGTGGATTTGTCA 59.935 43.478 0.00 0.00 0.00 3.58
16 17 3.617669 CACTTTGTGTCGTGGATTTGTC 58.382 45.455 0.00 0.00 0.00 3.18
17 18 3.691049 CACTTTGTGTCGTGGATTTGT 57.309 42.857 0.00 0.00 0.00 2.83
24 25 1.831389 CTCGGCCACTTTGTGTCGTG 61.831 60.000 2.24 0.00 32.99 4.35
25 26 1.594293 CTCGGCCACTTTGTGTCGT 60.594 57.895 2.24 0.00 32.99 4.34
26 27 2.954753 GCTCGGCCACTTTGTGTCG 61.955 63.158 2.24 0.00 32.66 4.35
27 28 2.946762 GCTCGGCCACTTTGTGTC 59.053 61.111 2.24 0.00 0.00 3.67
28 29 2.972505 CGCTCGGCCACTTTGTGT 60.973 61.111 2.24 0.00 0.00 3.72
29 30 2.972505 ACGCTCGGCCACTTTGTG 60.973 61.111 2.24 0.00 0.00 3.33
39 40 2.202440 ATTCGACGTCACGCTCGG 60.202 61.111 17.16 0.00 33.77 4.63
50 51 4.052159 ACCTCATGTGAGATCATTCGAC 57.948 45.455 11.47 0.00 44.74 4.20
64 65 0.543749 GGGGGAACTCTCACCTCATG 59.456 60.000 0.00 0.00 45.60 3.07
65 66 0.419459 AGGGGGAACTCTCACCTCAT 59.581 55.000 0.00 0.00 34.38 2.90
79 80 3.717294 CGGTGACCTCCAAGGGGG 61.717 72.222 2.68 2.68 40.58 5.40
94 95 1.810606 CGATGAGGATGAGGGGTCGG 61.811 65.000 0.00 0.00 0.00 4.79
95 96 1.662608 CGATGAGGATGAGGGGTCG 59.337 63.158 0.00 0.00 0.00 4.79
111 112 0.107361 TAGGTCGATGTCTGCTCCGA 60.107 55.000 0.00 0.00 0.00 4.55
112 113 0.309302 CTAGGTCGATGTCTGCTCCG 59.691 60.000 0.00 0.00 0.00 4.63
142 143 3.382832 CGAGGCTTGTCGGGGTCT 61.383 66.667 0.00 0.00 36.26 3.85
149 150 1.801332 TCGTCTAGCGAGGCTTGTC 59.199 57.895 3.19 0.00 45.68 3.18
159 160 3.659089 TTTGCGGCCCTCGTCTAGC 62.659 63.158 0.00 0.00 41.72 3.42
168 170 2.975799 TCGTTGTCTTTGCGGCCC 60.976 61.111 0.00 0.00 0.00 5.80
170 172 0.928451 GTTGTCGTTGTCTTTGCGGC 60.928 55.000 0.00 0.00 0.00 6.53
177 179 1.924524 CTCGTGTTGTTGTCGTTGTCT 59.075 47.619 0.00 0.00 0.00 3.41
194 196 1.956629 ATGTTAGGCGGGGTGTCTCG 61.957 60.000 0.00 0.00 32.27 4.04
200 202 1.001393 CAACCATGTTAGGCGGGGT 60.001 57.895 0.00 0.00 0.00 4.95
201 203 2.414785 GCAACCATGTTAGGCGGGG 61.415 63.158 0.00 0.00 0.00 5.73
203 205 1.376609 GAGGCAACCATGTTAGGCGG 61.377 60.000 0.00 0.00 37.17 6.13
204 206 1.705337 CGAGGCAACCATGTTAGGCG 61.705 60.000 0.00 0.00 37.17 5.52
205 207 0.392461 TCGAGGCAACCATGTTAGGC 60.392 55.000 0.00 0.00 37.17 3.93
208 210 3.438781 GTGATTTCGAGGCAACCATGTTA 59.561 43.478 0.00 0.00 37.17 2.41
209 211 2.228822 GTGATTTCGAGGCAACCATGTT 59.771 45.455 0.00 0.00 37.17 2.71
210 212 1.812571 GTGATTTCGAGGCAACCATGT 59.187 47.619 0.00 0.00 37.17 3.21
214 216 1.808411 TGAGTGATTTCGAGGCAACC 58.192 50.000 0.00 0.00 37.17 3.77
223 225 2.966050 AGCGTCTCCTTGAGTGATTTC 58.034 47.619 0.00 0.00 0.00 2.17
315 317 5.821204 AGCAACGCATGGTAATAAAAGATC 58.179 37.500 0.00 0.00 38.18 2.75
317 319 4.095782 GGAGCAACGCATGGTAATAAAAGA 59.904 41.667 0.00 0.00 40.59 2.52
318 320 4.142491 TGGAGCAACGCATGGTAATAAAAG 60.142 41.667 0.00 0.00 40.59 2.27
319 321 3.759086 TGGAGCAACGCATGGTAATAAAA 59.241 39.130 0.00 0.00 40.59 1.52
321 323 2.992593 TGGAGCAACGCATGGTAATAA 58.007 42.857 0.00 0.00 40.59 1.40
322 324 2.700722 TGGAGCAACGCATGGTAATA 57.299 45.000 0.00 0.00 40.59 0.98
326 328 2.048023 CCATGGAGCAACGCATGGT 61.048 57.895 5.56 1.64 43.97 3.55
327 329 1.597797 AACCATGGAGCAACGCATGG 61.598 55.000 21.47 13.84 44.83 3.66
329 331 2.057137 ATAACCATGGAGCAACGCAT 57.943 45.000 21.47 0.00 0.00 4.73
331 333 2.423538 AGAAATAACCATGGAGCAACGC 59.576 45.455 21.47 1.86 0.00 4.84
332 334 3.181497 CCAGAAATAACCATGGAGCAACG 60.181 47.826 21.47 0.00 34.60 4.10
333 335 4.016444 TCCAGAAATAACCATGGAGCAAC 58.984 43.478 21.47 5.17 36.92 4.17
334 336 4.016444 GTCCAGAAATAACCATGGAGCAA 58.984 43.478 21.47 0.16 42.35 3.91
335 337 3.620488 GTCCAGAAATAACCATGGAGCA 58.380 45.455 21.47 2.60 42.35 4.26
337 339 3.118408 TCCGTCCAGAAATAACCATGGAG 60.118 47.826 21.47 0.00 42.35 3.86
342 344 4.561500 TTCATCCGTCCAGAAATAACCA 57.438 40.909 0.00 0.00 0.00 3.67
343 345 5.637809 GTTTTCATCCGTCCAGAAATAACC 58.362 41.667 0.00 0.00 32.00 2.85
344 346 5.321516 CGTTTTCATCCGTCCAGAAATAAC 58.678 41.667 0.00 0.00 32.00 1.89
345 347 4.142773 GCGTTTTCATCCGTCCAGAAATAA 60.143 41.667 0.00 0.00 32.00 1.40
347 349 2.161609 GCGTTTTCATCCGTCCAGAAAT 59.838 45.455 0.00 0.00 32.00 2.17
348 350 1.533731 GCGTTTTCATCCGTCCAGAAA 59.466 47.619 0.00 0.00 0.00 2.52
349 351 1.153353 GCGTTTTCATCCGTCCAGAA 58.847 50.000 0.00 0.00 0.00 3.02
350 352 0.672401 GGCGTTTTCATCCGTCCAGA 60.672 55.000 0.00 0.00 0.00 3.86
351 353 1.794222 GGCGTTTTCATCCGTCCAG 59.206 57.895 0.00 0.00 0.00 3.86
352 354 2.030401 CGGCGTTTTCATCCGTCCA 61.030 57.895 0.00 0.00 38.47 4.02
353 355 2.746803 CCGGCGTTTTCATCCGTCC 61.747 63.158 6.01 0.00 41.46 4.79
354 356 0.737019 TACCGGCGTTTTCATCCGTC 60.737 55.000 6.01 0.00 41.46 4.79
355 357 0.108041 ATACCGGCGTTTTCATCCGT 60.108 50.000 6.01 0.00 41.46 4.69
356 358 1.855513 TATACCGGCGTTTTCATCCG 58.144 50.000 6.01 0.00 42.58 4.18
357 359 2.033492 CGTTATACCGGCGTTTTCATCC 60.033 50.000 6.01 0.00 0.00 3.51
358 360 2.859538 TCGTTATACCGGCGTTTTCATC 59.140 45.455 6.01 0.00 0.00 2.92
359 361 2.861935 CTCGTTATACCGGCGTTTTCAT 59.138 45.455 6.01 0.00 0.00 2.57
360 362 2.261345 CTCGTTATACCGGCGTTTTCA 58.739 47.619 6.01 0.00 0.00 2.69
361 363 1.005662 GCTCGTTATACCGGCGTTTTC 60.006 52.381 6.01 0.00 0.00 2.29
362 364 1.001624 GCTCGTTATACCGGCGTTTT 58.998 50.000 6.01 0.00 0.00 2.43
363 365 0.108709 TGCTCGTTATACCGGCGTTT 60.109 50.000 6.01 0.00 0.00 3.60
364 366 0.103572 ATGCTCGTTATACCGGCGTT 59.896 50.000 6.01 0.00 0.00 4.84
365 367 0.103572 AATGCTCGTTATACCGGCGT 59.896 50.000 6.01 0.00 0.00 5.68
366 368 1.070843 CAAATGCTCGTTATACCGGCG 60.071 52.381 0.00 0.00 0.00 6.46
367 369 2.033151 GTCAAATGCTCGTTATACCGGC 60.033 50.000 0.00 0.00 0.00 6.13
368 370 2.217847 CGTCAAATGCTCGTTATACCGG 59.782 50.000 0.00 0.00 0.00 5.28
369 371 2.347292 GCGTCAAATGCTCGTTATACCG 60.347 50.000 0.00 0.00 0.00 4.02
370 372 2.605818 TGCGTCAAATGCTCGTTATACC 59.394 45.455 0.00 0.00 0.00 2.73
371 373 3.918258 TGCGTCAAATGCTCGTTATAC 57.082 42.857 0.00 0.00 0.00 1.47
372 374 3.930229 ACTTGCGTCAAATGCTCGTTATA 59.070 39.130 0.00 0.00 0.00 0.98
396 398 2.249309 CGCACCAGTGTTTCGCTG 59.751 61.111 0.00 3.68 41.13 5.18
412 414 2.861462 AACCAACATTGAACACACCG 57.139 45.000 0.00 0.00 0.00 4.94
413 415 4.116747 TGAAACCAACATTGAACACACC 57.883 40.909 0.00 0.00 0.00 4.16
414 416 4.031201 CGTTGAAACCAACATTGAACACAC 59.969 41.667 8.71 0.00 42.97 3.82
415 417 4.082733 TCGTTGAAACCAACATTGAACACA 60.083 37.500 8.71 0.00 42.97 3.72
420 2638 4.703645 TTGTCGTTGAAACCAACATTGA 57.296 36.364 8.71 0.00 42.97 2.57
484 2702 2.350772 GCATTTATGGGGAGATTTCGCG 60.351 50.000 0.00 0.00 37.15 5.87
522 2740 3.780801 GCAGATTACGCAATTTCACGAAG 59.219 43.478 0.00 0.00 0.00 3.79
556 2774 3.189606 ACTGGGTGGTGAATATCTTCCA 58.810 45.455 0.00 0.00 0.00 3.53
1338 3576 4.039357 ACGACAGCACCCGACTCG 62.039 66.667 0.00 0.00 0.00 4.18
1355 3593 3.579302 CCACCAACCCCTGCCTCA 61.579 66.667 0.00 0.00 0.00 3.86
1761 3999 2.045524 TCACACATTGGCAAATTGGGT 58.954 42.857 3.01 2.96 0.00 4.51
1804 4042 3.061848 GGGTCCACAATGGTGCGG 61.062 66.667 0.00 0.00 43.88 5.69
1806 4044 0.539438 TCAAGGGTCCACAATGGTGC 60.539 55.000 0.00 0.00 43.88 5.01
1811 4049 0.991920 ACCGATCAAGGGTCCACAAT 59.008 50.000 0.00 0.00 29.94 2.71
1830 4068 2.230508 GTGTATAGATTCCGATCGGGCA 59.769 50.000 32.79 20.60 37.37 5.36
1852 4090 5.505181 TCTTCCTGGAGAATTGCTTACTT 57.495 39.130 0.00 0.00 32.82 2.24
1853 4091 5.505181 TTCTTCCTGGAGAATTGCTTACT 57.495 39.130 0.00 0.00 32.82 2.24
1854 4092 5.124617 CCTTTCTTCCTGGAGAATTGCTTAC 59.875 44.000 0.00 0.00 35.70 2.34
1855 4093 5.222130 ACCTTTCTTCCTGGAGAATTGCTTA 60.222 40.000 0.00 0.00 35.70 3.09
1999 4276 9.520515 AAGTCCATTTCTAAAAAGCAGATAAGA 57.479 29.630 0.00 0.00 0.00 2.10
2092 4369 3.756963 TCAGGGATCATATAACGACCTCG 59.243 47.826 0.00 0.00 46.33 4.63
2116 4394 1.059098 ACAGATCAAGTCAGGCACCA 58.941 50.000 0.00 0.00 0.00 4.17
2245 4523 2.828520 TGAGCTAGGCAGGCATATCTAC 59.171 50.000 0.00 0.00 0.00 2.59
2548 4900 5.467035 AAAATAGGTTGGAACATGTGTGG 57.533 39.130 0.00 0.00 39.30 4.17
2897 5390 5.245531 TCAGTAAGCACCTTCAACCAATAG 58.754 41.667 0.00 0.00 0.00 1.73
3191 5688 3.007831 GGGAGGAAAGATCTGATAGCCAG 59.992 52.174 0.00 0.00 44.27 4.85
3377 5874 6.611642 GGCCCAGACTATCCATCATACTAATA 59.388 42.308 0.00 0.00 0.00 0.98
3529 6026 7.114529 CAGTCAGCTCAATTTCTGAAATTTGAC 59.885 37.037 29.42 29.42 41.10 3.18
3962 6472 6.183360 TGGGCAATGTGATATTTCTGAAATCC 60.183 38.462 18.22 12.23 32.38 3.01
4319 6830 8.656849 AGTAAGAACATAGCTTCATTTTGTACG 58.343 33.333 0.00 0.00 0.00 3.67
4482 6993 3.578282 TGGACACTGAAGAAGCATCTACA 59.422 43.478 0.00 0.00 33.77 2.74
4657 7168 2.100197 TCTCATCACACGGGAGGTTAG 58.900 52.381 0.00 0.00 0.00 2.34
4706 7217 8.145767 TCAACCTAAGATTAAGACGAAACTTGA 58.854 33.333 0.00 0.00 0.00 3.02
4742 7253 8.299570 CAGGAACATAAGATTTATGGCAATACC 58.700 37.037 12.07 6.81 39.84 2.73
4744 7255 8.995027 ACAGGAACATAAGATTTATGGCAATA 57.005 30.769 12.07 0.00 0.00 1.90
4753 7265 7.444183 TCGTTCAGAAACAGGAACATAAGATTT 59.556 33.333 0.00 0.00 42.67 2.17
4826 7338 3.570638 CAAGGCATGCGAGGCTCG 61.571 66.667 31.40 31.40 44.47 5.03
5143 7665 3.956744 ACTAATCTTCCTTTCCTGTGCC 58.043 45.455 0.00 0.00 0.00 5.01
5224 7748 5.537188 CAGAGAAACAAGAACAGTAGAGCT 58.463 41.667 0.00 0.00 0.00 4.09
5225 7749 4.151512 GCAGAGAAACAAGAACAGTAGAGC 59.848 45.833 0.00 0.00 0.00 4.09
5226 7750 5.292765 TGCAGAGAAACAAGAACAGTAGAG 58.707 41.667 0.00 0.00 0.00 2.43
5227 7751 5.276461 TGCAGAGAAACAAGAACAGTAGA 57.724 39.130 0.00 0.00 0.00 2.59
5228 7752 5.991328 TTGCAGAGAAACAAGAACAGTAG 57.009 39.130 0.00 0.00 0.00 2.57
5229 7753 6.751514 TTTTGCAGAGAAACAAGAACAGTA 57.248 33.333 0.00 0.00 0.00 2.74
5230 7754 5.643379 TTTTGCAGAGAAACAAGAACAGT 57.357 34.783 0.00 0.00 0.00 3.55
5316 7843 1.685820 GAACCAAGGGTGCTAGGCT 59.314 57.895 0.00 0.00 35.34 4.58
5407 8125 7.148306 TGGAAACAAGAGACTAAATAAATCGGC 60.148 37.037 0.00 0.00 37.44 5.54
5458 8176 0.389391 AGACAGTGTACGCTTGCAGT 59.611 50.000 6.11 1.12 0.00 4.40
5470 8188 2.154462 GGAAATCCACACCAGACAGTG 58.846 52.381 0.00 0.00 43.65 3.66
5483 8201 1.457346 CAGCTCACACTGGGAAATCC 58.543 55.000 0.00 0.00 33.85 3.01
5543 8268 1.700955 GGCCCCTCGTACTAATCTCA 58.299 55.000 0.00 0.00 0.00 3.27
5554 8279 2.615227 CTTTCCATCTGGGCCCCTCG 62.615 65.000 22.27 8.04 36.21 4.63
5570 8295 5.738619 AACAAAAGAACAGGTGGAACTTT 57.261 34.783 0.00 0.00 36.74 2.66
5629 8359 0.370273 CGGTTCCGATTCAGAAAGCG 59.630 55.000 5.19 2.63 43.65 4.68
5630 8360 1.661112 CTCGGTTCCGATTCAGAAAGC 59.339 52.381 14.34 0.00 37.83 3.51
5631 8361 2.668457 CACTCGGTTCCGATTCAGAAAG 59.332 50.000 14.34 3.23 37.83 2.62
5632 8362 2.611971 CCACTCGGTTCCGATTCAGAAA 60.612 50.000 14.34 0.00 37.83 2.52
5652 8382 5.215252 TCATTCCTATCCGATTCAACTCC 57.785 43.478 0.00 0.00 0.00 3.85
5752 8482 2.892334 GCGCGTGCTGTTCTTCCAA 61.892 57.895 15.02 0.00 38.39 3.53
5948 8678 2.513897 GCAGTAAATCGCGGGGCT 60.514 61.111 6.13 0.00 0.00 5.19
5989 8719 1.726322 GCCGCAGCTCGTCGTATAG 60.726 63.158 0.00 0.00 36.19 1.31
6036 8779 1.194495 CGCCTACGAATCAACCGTAC 58.806 55.000 0.00 0.00 43.93 3.67
6048 8791 4.891727 AATCAGCCGCCGCCTACG 62.892 66.667 0.00 0.00 39.67 3.51
6154 9083 1.927174 CGGCGAAACTCCTACAAGATG 59.073 52.381 0.00 0.00 0.00 2.90
6269 9198 2.146073 AAAGGCCGCTCACATTGTGC 62.146 55.000 12.04 0.43 32.98 4.57
6283 9213 1.230324 ACTGCGTGAGAAGAAAAGGC 58.770 50.000 0.00 0.00 40.08 4.35
6341 9273 3.181514 GCATGCAATCTGGAAAACAATGC 60.182 43.478 14.21 0.00 35.19 3.56
6345 9277 4.705991 TGATAGCATGCAATCTGGAAAACA 59.294 37.500 21.98 1.14 0.00 2.83


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

AutoCloner maintained by Alex Coulton.