Multiple sequence alignment - TraesCS6A01G118400

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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 TraesCS6A01G118400 chr6A 100.000 6856 0 0 1 6856 89586684 89593539 0.000000e+00 12661
1 TraesCS6A01G118400 chr6A 92.419 277 16 5 5119 5394 182314900 182315172 2.320000e-104 390
2 TraesCS6A01G118400 chr6D 98.617 5135 71 0 1 5135 73062644 73067778 0.000000e+00 9090
3 TraesCS6A01G118400 chr6D 97.365 1366 23 4 5501 6856 73067830 73069192 0.000000e+00 2311
4 TraesCS6A01G118400 chr6D 82.133 375 60 6 6207 6575 192631053 192630680 1.440000e-81 315
5 TraesCS6A01G118400 chr6D 100.000 56 0 0 5391 5446 73067775 73067830 3.380000e-18 104
6 TraesCS6A01G118400 chr6B 98.014 5135 99 1 1 5135 147576486 147581617 0.000000e+00 8914
7 TraesCS6A01G118400 chr6B 97.819 1467 31 1 5391 6856 147581614 147583080 0.000000e+00 2531
8 TraesCS6A01G118400 chr5A 83.513 558 79 12 6163 6710 55328550 55329104 6.130000e-140 508
9 TraesCS6A01G118400 chr2A 83.513 558 79 12 6163 6710 461726643 461727197 6.130000e-140 508
10 TraesCS6A01G118400 chr2A 92.989 271 18 1 5129 5399 625011944 625011675 1.790000e-105 394
11 TraesCS6A01G118400 chr7A 83.333 558 80 12 6163 6710 332925892 332926446 2.850000e-138 503
12 TraesCS6A01G118400 chr7A 95.094 265 13 0 5130 5394 578444758 578444494 1.060000e-112 418
13 TraesCS6A01G118400 chr7A 95.402 261 12 0 5134 5394 527996822 527996562 3.830000e-112 416
14 TraesCS6A01G118400 chr4A 94.636 261 14 0 5134 5394 62950252 62950512 8.280000e-109 405
15 TraesCS6A01G118400 chr4A 91.986 287 19 4 5109 5394 112854693 112854410 3.850000e-107 399
16 TraesCS6A01G118400 chr4A 93.309 269 17 1 5129 5397 574544940 574544673 4.980000e-106 396
17 TraesCS6A01G118400 chr3D 94.636 261 14 0 5134 5394 91831627 91831887 8.280000e-109 405
18 TraesCS6A01G118400 chr1A 93.939 264 16 0 5131 5394 147365692 147365955 3.850000e-107 399
19 TraesCS6A01G118400 chr1B 81.684 475 74 5 6207 6669 511483908 511484381 3.880000e-102 383
20 TraesCS6A01G118400 chr7D 85.276 163 21 3 6562 6723 370399865 370399705 1.530000e-36 165


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 TraesCS6A01G118400 chr6A 89586684 89593539 6855 False 12661.0 12661 100.000000 1 6856 1 chr6A.!!$F1 6855
1 TraesCS6A01G118400 chr6D 73062644 73069192 6548 False 3835.0 9090 98.660667 1 6856 3 chr6D.!!$F1 6855
2 TraesCS6A01G118400 chr6B 147576486 147583080 6594 False 5722.5 8914 97.916500 1 6856 2 chr6B.!!$F1 6855
3 TraesCS6A01G118400 chr5A 55328550 55329104 554 False 508.0 508 83.513000 6163 6710 1 chr5A.!!$F1 547
4 TraesCS6A01G118400 chr2A 461726643 461727197 554 False 508.0 508 83.513000 6163 6710 1 chr2A.!!$F1 547
5 TraesCS6A01G118400 chr7A 332925892 332926446 554 False 503.0 503 83.333000 6163 6710 1 chr7A.!!$F1 547

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
394 395 2.802816 CTGTGTTCCTTCAAGGAGAACG 59.197 50.000 6.17 2.88 46.73 3.95 F
1014 1015 0.553819 AGCGGATGTCCTCTAGGTCT 59.446 55.000 0.00 0.00 36.34 3.85 F
1269 1270 0.815213 AAGCAGAAAGACAGCGCACA 60.815 50.000 11.47 0.00 36.14 4.57 F
2114 2115 1.277557 GGTTCACCACTCTGCAGATCT 59.722 52.381 18.63 2.13 35.64 2.75 F
2628 2629 1.611673 GGCCTTAAGCAGTCTCTTGCA 60.612 52.381 0.00 0.00 46.47 4.08 F
3185 3186 0.919710 GGTCAGGTTAGCATTCCCCT 59.080 55.000 0.00 0.00 0.00 4.79 F
4765 4766 2.005451 CCGCACTTTCTGAATCCTCTG 58.995 52.381 0.00 0.00 0.00 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 1270 2.071778 TTCTGGCCTCAAAAACTGCT 57.928 45.000 3.32 0.0 0.00 4.24 R
2607 2608 1.611673 GCAAGAGACTGCTTAAGGCCA 60.612 52.381 5.01 0.0 39.34 5.36 R
2628 2629 2.562298 CTCAAGCTCACCAGACTTCTCT 59.438 50.000 0.00 0.0 0.00 3.10 R
3185 3186 4.713553 TGGTTCTAACATTCTGAACTGCA 58.286 39.130 0.00 0.0 39.73 4.41 R
4535 4536 1.335182 CTCGAGCGATGTCCACTGTAT 59.665 52.381 0.00 0.0 0.00 2.29 R
5140 5141 0.037160 GCAGGGTAAAAAGGACCGGA 59.963 55.000 9.46 0.0 37.90 5.14 R
6200 6211 1.340991 GCCCAACAGAATAGCTCCCAA 60.341 52.381 0.00 0.0 0.00 4.12 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
150 151 6.240894 ACAAATCTTGAGTGAATTAGCTGGA 58.759 36.000 0.00 0.00 0.00 3.86
342 343 4.702131 GTGAAAGAGGTAATGAATGCTGGT 59.298 41.667 0.00 0.00 0.00 4.00
394 395 2.802816 CTGTGTTCCTTCAAGGAGAACG 59.197 50.000 6.17 2.88 46.73 3.95
792 793 5.777802 ACAGTTGTGTGTCAAAAACATGAA 58.222 33.333 0.00 0.00 40.80 2.57
796 797 7.487509 CAGTTGTGTGTCAAAAACATGAACATA 59.512 33.333 0.00 0.00 40.80 2.29
893 894 3.818180 ACAATCAGCATTCTCATCCTCC 58.182 45.455 0.00 0.00 0.00 4.30
1014 1015 0.553819 AGCGGATGTCCTCTAGGTCT 59.446 55.000 0.00 0.00 36.34 3.85
1269 1270 0.815213 AAGCAGAAAGACAGCGCACA 60.815 50.000 11.47 0.00 36.14 4.57
1549 1550 2.496871 CCTAATGATTTGGGTGCAAGCA 59.503 45.455 0.00 0.00 34.77 3.91
1588 1589 5.723887 AGTATTTTGGACTCTGTGGATCTCT 59.276 40.000 0.00 0.00 0.00 3.10
1650 1651 4.509230 TCTGCTCAAAGCGATAATGCTAAG 59.491 41.667 0.00 0.00 46.60 2.18
1749 1750 8.279970 TGGTTAAGAACATGTATGATTCCTTG 57.720 34.615 0.00 0.00 0.00 3.61
1983 1984 6.746364 GCTTGAGATGCAGTTCTTTAATGAAG 59.254 38.462 4.14 0.00 36.67 3.02
2032 2033 8.308931 TGAACGAGGAGCTTAAATTAGTTTCTA 58.691 33.333 0.00 0.00 0.00 2.10
2033 2034 9.148104 GAACGAGGAGCTTAAATTAGTTTCTAA 57.852 33.333 0.00 0.00 0.00 2.10
2114 2115 1.277557 GGTTCACCACTCTGCAGATCT 59.722 52.381 18.63 2.13 35.64 2.75
2607 2608 2.009774 GCCTTGATAGTGCAACGTGAT 58.990 47.619 0.00 0.00 45.86 3.06
2628 2629 1.611673 GGCCTTAAGCAGTCTCTTGCA 60.612 52.381 0.00 0.00 46.47 4.08
2859 2860 9.243105 GAAGTCTTAGAAGATCTAGATATGCCT 57.757 37.037 4.89 6.50 37.39 4.75
3185 3186 0.919710 GGTCAGGTTAGCATTCCCCT 59.080 55.000 0.00 0.00 0.00 4.79
3800 3801 4.159506 AGAGACTGGTAGAGATGACAAAGC 59.840 45.833 0.00 0.00 0.00 3.51
3984 3985 4.973168 AGCAGACTCAAAAATACCAGTCA 58.027 39.130 0.00 0.00 38.20 3.41
4076 4077 2.166459 AGTTAGAGCATGCTCGCAGTAA 59.834 45.455 35.50 26.28 46.90 2.24
4314 4315 5.461737 CACTTCACTGAGAGAGAAACTGAAC 59.538 44.000 0.00 0.00 0.00 3.18
4359 4360 3.005791 GCCTGGTGCAACAAAAAGATAGT 59.994 43.478 5.64 0.00 39.98 2.12
4535 4536 9.897744 CTTGAGTAGATTGTTAAATGCTTTGAA 57.102 29.630 0.00 0.00 0.00 2.69
4765 4766 2.005451 CCGCACTTTCTGAATCCTCTG 58.995 52.381 0.00 0.00 0.00 3.35
4773 4774 6.147492 CACTTTCTGAATCCTCTGAACAGAAG 59.853 42.308 0.00 0.39 42.76 2.85
4915 4916 5.047235 GGTCAACTAAGAGAGGTCTGCTTTA 60.047 44.000 0.00 0.00 31.37 1.85
5037 5038 6.072508 GCACAAATATGGTGGACATACCTATG 60.073 42.308 9.17 0.00 44.41 2.23
5140 5141 3.268023 GCACTTTGCATAGTACTCCCT 57.732 47.619 9.60 0.00 44.26 4.20
5141 5142 3.198872 GCACTTTGCATAGTACTCCCTC 58.801 50.000 9.60 0.00 44.26 4.30
5142 5143 3.798202 CACTTTGCATAGTACTCCCTCC 58.202 50.000 9.60 0.00 0.00 4.30
5143 5144 2.431057 ACTTTGCATAGTACTCCCTCCG 59.569 50.000 8.15 0.00 0.00 4.63
5144 5145 1.410004 TTGCATAGTACTCCCTCCGG 58.590 55.000 0.00 0.00 0.00 5.14
5145 5146 0.260816 TGCATAGTACTCCCTCCGGT 59.739 55.000 0.00 0.00 0.00 5.28
5146 5147 0.960286 GCATAGTACTCCCTCCGGTC 59.040 60.000 0.00 0.00 0.00 4.79
5147 5148 1.618487 CATAGTACTCCCTCCGGTCC 58.382 60.000 0.00 0.00 0.00 4.46
5148 5149 1.145325 CATAGTACTCCCTCCGGTCCT 59.855 57.143 0.00 0.00 0.00 3.85
5149 5150 1.302907 TAGTACTCCCTCCGGTCCTT 58.697 55.000 0.00 0.00 0.00 3.36
5150 5151 0.412640 AGTACTCCCTCCGGTCCTTT 59.587 55.000 0.00 0.00 0.00 3.11
5151 5152 1.203275 AGTACTCCCTCCGGTCCTTTT 60.203 52.381 0.00 0.00 0.00 2.27
5152 5153 1.627329 GTACTCCCTCCGGTCCTTTTT 59.373 52.381 0.00 0.00 0.00 1.94
5153 5154 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
5154 5155 1.627329 ACTCCCTCCGGTCCTTTTTAC 59.373 52.381 0.00 0.00 0.00 2.01
5155 5156 0.986527 TCCCTCCGGTCCTTTTTACC 59.013 55.000 0.00 0.00 0.00 2.85
5156 5157 0.034767 CCCTCCGGTCCTTTTTACCC 60.035 60.000 0.00 0.00 33.10 3.69
5157 5158 0.989602 CCTCCGGTCCTTTTTACCCT 59.010 55.000 0.00 0.00 33.10 4.34
5158 5159 1.339727 CCTCCGGTCCTTTTTACCCTG 60.340 57.143 0.00 0.00 33.10 4.45
5159 5160 0.037160 TCCGGTCCTTTTTACCCTGC 59.963 55.000 0.00 0.00 33.10 4.85
5160 5161 0.250989 CCGGTCCTTTTTACCCTGCA 60.251 55.000 0.00 0.00 33.10 4.41
5161 5162 1.615919 CCGGTCCTTTTTACCCTGCAT 60.616 52.381 0.00 0.00 33.10 3.96
5162 5163 2.356330 CCGGTCCTTTTTACCCTGCATA 60.356 50.000 0.00 0.00 33.10 3.14
5163 5164 3.551846 CGGTCCTTTTTACCCTGCATAT 58.448 45.455 0.00 0.00 33.10 1.78
5164 5165 4.445162 CCGGTCCTTTTTACCCTGCATATA 60.445 45.833 0.00 0.00 33.10 0.86
5165 5166 5.127491 CGGTCCTTTTTACCCTGCATATAA 58.873 41.667 0.00 0.00 33.10 0.98
5166 5167 5.238650 CGGTCCTTTTTACCCTGCATATAAG 59.761 44.000 0.00 0.00 33.10 1.73
5167 5168 6.362248 GGTCCTTTTTACCCTGCATATAAGA 58.638 40.000 0.00 0.00 0.00 2.10
5168 5169 6.831868 GGTCCTTTTTACCCTGCATATAAGAA 59.168 38.462 0.00 0.00 0.00 2.52
5169 5170 7.505923 GGTCCTTTTTACCCTGCATATAAGAAT 59.494 37.037 0.00 0.00 0.00 2.40
5170 5171 8.914011 GTCCTTTTTACCCTGCATATAAGAATT 58.086 33.333 0.00 0.00 0.00 2.17
5171 5172 8.912988 TCCTTTTTACCCTGCATATAAGAATTG 58.087 33.333 0.00 0.00 0.00 2.32
5172 5173 8.695456 CCTTTTTACCCTGCATATAAGAATTGT 58.305 33.333 0.00 0.00 0.00 2.71
5173 5174 9.736023 CTTTTTACCCTGCATATAAGAATTGTC 57.264 33.333 0.00 0.00 0.00 3.18
5174 5175 9.474313 TTTTTACCCTGCATATAAGAATTGTCT 57.526 29.630 0.00 0.00 34.72 3.41
5175 5176 8.450578 TTTACCCTGCATATAAGAATTGTCTG 57.549 34.615 0.00 0.00 33.05 3.51
5176 5177 6.252599 ACCCTGCATATAAGAATTGTCTGA 57.747 37.500 0.00 0.00 33.05 3.27
5177 5178 6.662755 ACCCTGCATATAAGAATTGTCTGAA 58.337 36.000 0.00 0.00 33.05 3.02
5178 5179 6.769822 ACCCTGCATATAAGAATTGTCTGAAG 59.230 38.462 0.00 0.00 33.05 3.02
5179 5180 6.769822 CCCTGCATATAAGAATTGTCTGAAGT 59.230 38.462 0.00 0.00 33.05 3.01
5180 5181 7.041508 CCCTGCATATAAGAATTGTCTGAAGTC 60.042 40.741 0.00 0.00 33.05 3.01
5181 5182 7.496920 CCTGCATATAAGAATTGTCTGAAGTCA 59.503 37.037 0.00 0.00 33.05 3.41
5182 5183 8.791327 TGCATATAAGAATTGTCTGAAGTCAA 57.209 30.769 0.00 0.00 33.05 3.18
5183 5184 9.230122 TGCATATAAGAATTGTCTGAAGTCAAA 57.770 29.630 0.00 0.00 33.05 2.69
5184 5185 9.495754 GCATATAAGAATTGTCTGAAGTCAAAC 57.504 33.333 0.00 0.00 33.05 2.93
5270 5271 7.138736 ACCATTTGAAAACTAAAGTCATGACG 58.861 34.615 19.85 8.45 36.20 4.35
5271 5272 6.088085 CCATTTGAAAACTAAAGTCATGACGC 59.912 38.462 19.85 0.00 36.20 5.19
5272 5273 5.743026 TTGAAAACTAAAGTCATGACGCA 57.257 34.783 19.85 8.35 36.20 5.24
5273 5274 5.940192 TGAAAACTAAAGTCATGACGCAT 57.060 34.783 19.85 12.36 36.20 4.73
5274 5275 5.927030 TGAAAACTAAAGTCATGACGCATC 58.073 37.500 19.85 11.06 36.20 3.91
5275 5276 5.700832 TGAAAACTAAAGTCATGACGCATCT 59.299 36.000 19.85 6.79 36.20 2.90
5276 5277 6.871492 TGAAAACTAAAGTCATGACGCATCTA 59.129 34.615 19.85 7.52 36.20 1.98
5277 5278 7.386573 TGAAAACTAAAGTCATGACGCATCTAA 59.613 33.333 19.85 2.63 36.20 2.10
5278 5279 7.849804 AAACTAAAGTCATGACGCATCTAAT 57.150 32.000 19.85 2.37 36.20 1.73
5279 5280 6.834959 ACTAAAGTCATGACGCATCTAATG 57.165 37.500 19.85 7.39 36.20 1.90
5280 5281 6.341316 ACTAAAGTCATGACGCATCTAATGT 58.659 36.000 19.85 7.94 36.20 2.71
5281 5282 6.818644 ACTAAAGTCATGACGCATCTAATGTT 59.181 34.615 19.85 2.19 36.20 2.71
5282 5283 5.475273 AAGTCATGACGCATCTAATGTTG 57.525 39.130 19.85 0.00 36.20 3.33
5283 5284 4.507710 AGTCATGACGCATCTAATGTTGT 58.492 39.130 19.85 0.00 36.20 3.32
5284 5285 4.937620 AGTCATGACGCATCTAATGTTGTT 59.062 37.500 19.85 0.00 36.20 2.83
5285 5286 5.023920 GTCATGACGCATCTAATGTTGTTG 58.976 41.667 10.69 0.00 0.00 3.33
5286 5287 4.934602 TCATGACGCATCTAATGTTGTTGA 59.065 37.500 0.00 0.00 0.00 3.18
5287 5288 5.585844 TCATGACGCATCTAATGTTGTTGAT 59.414 36.000 0.00 0.00 0.00 2.57
5288 5289 5.878332 TGACGCATCTAATGTTGTTGATT 57.122 34.783 0.00 0.00 0.00 2.57
5289 5290 6.252967 TGACGCATCTAATGTTGTTGATTT 57.747 33.333 0.00 0.00 0.00 2.17
5290 5291 6.314018 TGACGCATCTAATGTTGTTGATTTC 58.686 36.000 0.00 0.00 0.00 2.17
5291 5292 6.072783 TGACGCATCTAATGTTGTTGATTTCA 60.073 34.615 0.00 0.00 0.00 2.69
5292 5293 6.086222 ACGCATCTAATGTTGTTGATTTCAC 58.914 36.000 0.00 0.00 0.00 3.18
5293 5294 6.085573 CGCATCTAATGTTGTTGATTTCACA 58.914 36.000 0.00 0.00 0.00 3.58
5294 5295 6.748658 CGCATCTAATGTTGTTGATTTCACAT 59.251 34.615 0.00 0.00 0.00 3.21
5295 5296 7.274033 CGCATCTAATGTTGTTGATTTCACATT 59.726 33.333 0.00 0.00 0.00 2.71
5296 5297 8.589629 GCATCTAATGTTGTTGATTTCACATTC 58.410 33.333 0.00 0.00 0.00 2.67
5297 5298 9.850628 CATCTAATGTTGTTGATTTCACATTCT 57.149 29.630 0.00 0.00 0.00 2.40
5298 5299 9.850628 ATCTAATGTTGTTGATTTCACATTCTG 57.149 29.630 0.00 0.00 0.00 3.02
5299 5300 9.065798 TCTAATGTTGTTGATTTCACATTCTGA 57.934 29.630 0.00 0.00 0.00 3.27
5300 5301 9.681692 CTAATGTTGTTGATTTCACATTCTGAA 57.318 29.630 0.00 0.00 37.08 3.02
5302 5303 7.933728 TGTTGTTGATTTCACATTCTGAATG 57.066 32.000 24.79 24.79 44.48 2.67
5344 5345 4.625972 CTTGGTCAAAGTTTACGTGGTT 57.374 40.909 0.00 0.00 0.00 3.67
5345 5346 4.989044 CTTGGTCAAAGTTTACGTGGTTT 58.011 39.130 0.00 0.00 0.00 3.27
5346 5347 4.358494 TGGTCAAAGTTTACGTGGTTTG 57.642 40.909 0.00 2.96 0.00 2.93
5347 5348 4.008330 TGGTCAAAGTTTACGTGGTTTGA 58.992 39.130 0.00 5.39 36.74 2.69
5350 5351 5.883503 TCAAAGTTTACGTGGTTTGACTT 57.116 34.783 0.00 0.00 34.72 3.01
5351 5352 5.871539 TCAAAGTTTACGTGGTTTGACTTC 58.128 37.500 0.00 0.00 34.72 3.01
5352 5353 5.411977 TCAAAGTTTACGTGGTTTGACTTCA 59.588 36.000 0.00 0.00 34.72 3.02
5353 5354 5.883503 AAGTTTACGTGGTTTGACTTCAA 57.116 34.783 0.00 0.00 0.00 2.69
5354 5355 5.883503 AGTTTACGTGGTTTGACTTCAAA 57.116 34.783 0.00 0.07 42.90 2.69
5388 5389 4.004196 ACGAACTAAAAAGGACCAGAGG 57.996 45.455 0.00 0.00 0.00 3.69
5389 5390 3.244457 ACGAACTAAAAAGGACCAGAGGG 60.244 47.826 0.00 0.00 41.29 4.30
5390 5391 3.007614 CGAACTAAAAAGGACCAGAGGGA 59.992 47.826 0.00 0.00 38.05 4.20
5391 5392 4.580868 GAACTAAAAAGGACCAGAGGGAG 58.419 47.826 0.00 0.00 38.05 4.30
5392 5393 3.599348 ACTAAAAAGGACCAGAGGGAGT 58.401 45.455 0.00 0.00 38.05 3.85
5393 5394 4.759953 ACTAAAAAGGACCAGAGGGAGTA 58.240 43.478 0.00 0.00 38.05 2.59
5464 5465 3.046968 TGCACTTACCGCAGAAATGTA 57.953 42.857 0.00 0.00 33.55 2.29
5573 5574 4.261801 TGGAAATGAGGCTTGTACTAAGC 58.738 43.478 16.84 16.84 42.30 3.09
5587 5588 3.059352 ACTAAGCTTCCACCATGTCAC 57.941 47.619 0.00 0.00 0.00 3.67
5623 5624 6.097915 TCGTCTCCTTTATTCTTGTTCACT 57.902 37.500 0.00 0.00 0.00 3.41
5693 5694 6.410942 AACGAATCTCAGATGACCATGATA 57.589 37.500 0.00 0.00 0.00 2.15
5847 5858 0.035152 ATGCTCCGCTGGAATTCACA 60.035 50.000 7.93 2.28 0.00 3.58
6039 6050 8.526147 CAGAACAGATTCACTTCCCAAAATAAT 58.474 33.333 0.00 0.00 37.29 1.28
6052 6063 7.789202 TCCCAAAATAATGAGTTGGAATCAA 57.211 32.000 3.24 0.00 43.82 2.57
6060 6071 8.905660 ATAATGAGTTGGAATCAATGAGAGAG 57.094 34.615 0.00 0.00 35.10 3.20
6200 6211 3.731431 TGACTGGTATGGGTTCTGGTAT 58.269 45.455 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 151 1.138266 GCTTCCAGCAATGATTGGCAT 59.862 47.619 7.35 0.00 41.89 4.40
342 343 3.064207 CAAACTTTCGCACCTGCTACTA 58.936 45.455 0.00 0.00 39.32 1.82
394 395 1.956170 CAGTCCACGTGTGCTCCAC 60.956 63.158 15.65 1.19 40.89 4.02
684 685 1.202440 TCGGAACTGTTAGTTGCACGT 60.202 47.619 12.53 0.00 45.33 4.49
792 793 1.750930 CGATGAGGCCAGGCTATGT 59.249 57.895 12.43 0.00 0.00 2.29
796 797 1.639635 ATTTCCGATGAGGCCAGGCT 61.640 55.000 12.43 1.67 40.77 4.58
893 894 8.499162 AGTTACTTGAATCTTTCTCGTCAAATG 58.501 33.333 0.00 0.00 30.03 2.32
1014 1015 1.066752 CACGAGAACACGTCCACCA 59.933 57.895 0.00 0.00 44.76 4.17
1269 1270 2.071778 TTCTGGCCTCAAAAACTGCT 57.928 45.000 3.32 0.00 0.00 4.24
1508 1509 5.846528 AGGGTACATAGTACCAACCAAAA 57.153 39.130 23.40 0.00 39.31 2.44
1515 1516 7.202149 CCCAAATCATTAGGGTACATAGTACCA 60.202 40.741 23.40 7.75 39.31 3.25
1549 1550 7.175119 GTCCAAAATACTAAAGCTGAGACCTTT 59.825 37.037 2.97 0.00 36.55 3.11
1588 1589 6.942005 TGAAGACTTTGGATTGATTTAGCAGA 59.058 34.615 0.00 0.00 0.00 4.26
1650 1651 3.765026 CTCCGAAAGAGAAGTACTGAGC 58.235 50.000 0.00 0.00 46.50 4.26
1983 1984 4.277672 AGCAAGCACATGTCATCCATATTC 59.722 41.667 0.00 0.00 30.71 1.75
2032 2033 5.570234 TCCAACGCTTCACTTTTACTTTT 57.430 34.783 0.00 0.00 0.00 2.27
2033 2034 5.298276 TCATCCAACGCTTCACTTTTACTTT 59.702 36.000 0.00 0.00 0.00 2.66
2239 2240 6.479660 TGGATTTCTTCAACTGCATTTTCAAC 59.520 34.615 0.00 0.00 0.00 3.18
2607 2608 1.611673 GCAAGAGACTGCTTAAGGCCA 60.612 52.381 5.01 0.00 39.34 5.36
2628 2629 2.562298 CTCAAGCTCACCAGACTTCTCT 59.438 50.000 0.00 0.00 0.00 3.10
2859 2860 5.134202 TGTCTCTAGAATGAAAACGCTCA 57.866 39.130 0.00 0.00 0.00 4.26
3185 3186 4.713553 TGGTTCTAACATTCTGAACTGCA 58.286 39.130 0.00 0.00 39.73 4.41
3800 3801 8.799091 CATTACTCAAAGTATTCAGTACACTCG 58.201 37.037 0.00 0.00 35.67 4.18
3984 3985 5.009010 CACTAATTCCAGTTCAAGCACAAGT 59.991 40.000 0.00 0.00 0.00 3.16
4314 4315 2.099141 TCCCTTTTCTGACAGCGATG 57.901 50.000 0.00 0.00 0.00 3.84
4359 4360 9.725019 TTCATCTCTTCTATAGTTTGCTTCAAA 57.275 29.630 0.00 0.00 0.00 2.69
4535 4536 1.335182 CTCGAGCGATGTCCACTGTAT 59.665 52.381 0.00 0.00 0.00 2.29
4765 4766 7.761704 TGCAGACTCTATAACATTCTTCTGTTC 59.238 37.037 0.00 0.00 39.88 3.18
4773 4774 5.174761 CGCTCTTGCAGACTCTATAACATTC 59.825 44.000 0.00 0.00 39.64 2.67
4915 4916 0.598065 GCAAGGCGATGTGAAAGGTT 59.402 50.000 0.00 0.00 0.00 3.50
5037 5038 4.843728 TGGTCAACATCCCATTAGAAGTC 58.156 43.478 0.00 0.00 0.00 3.01
5139 5140 1.949079 GCAGGGTAAAAAGGACCGGAG 60.949 57.143 9.46 0.00 37.90 4.63
5140 5141 0.037160 GCAGGGTAAAAAGGACCGGA 59.963 55.000 9.46 0.00 37.90 5.14
5141 5142 0.250989 TGCAGGGTAAAAAGGACCGG 60.251 55.000 0.00 0.00 37.90 5.28
5142 5143 1.834188 ATGCAGGGTAAAAAGGACCG 58.166 50.000 0.00 0.00 37.90 4.79
5143 5144 6.362248 TCTTATATGCAGGGTAAAAAGGACC 58.638 40.000 0.00 0.00 36.12 4.46
5144 5145 7.875327 TTCTTATATGCAGGGTAAAAAGGAC 57.125 36.000 0.00 0.00 0.00 3.85
5145 5146 8.912988 CAATTCTTATATGCAGGGTAAAAAGGA 58.087 33.333 0.00 0.00 0.00 3.36
5146 5147 8.695456 ACAATTCTTATATGCAGGGTAAAAAGG 58.305 33.333 0.00 0.00 0.00 3.11
5147 5148 9.736023 GACAATTCTTATATGCAGGGTAAAAAG 57.264 33.333 0.00 0.00 0.00 2.27
5148 5149 9.474313 AGACAATTCTTATATGCAGGGTAAAAA 57.526 29.630 0.00 0.00 0.00 1.94
5149 5150 8.902806 CAGACAATTCTTATATGCAGGGTAAAA 58.097 33.333 0.00 0.00 0.00 1.52
5150 5151 8.271458 TCAGACAATTCTTATATGCAGGGTAAA 58.729 33.333 0.00 0.00 0.00 2.01
5151 5152 7.801104 TCAGACAATTCTTATATGCAGGGTAA 58.199 34.615 0.00 0.00 0.00 2.85
5152 5153 7.373617 TCAGACAATTCTTATATGCAGGGTA 57.626 36.000 0.00 0.00 0.00 3.69
5153 5154 6.252599 TCAGACAATTCTTATATGCAGGGT 57.747 37.500 0.00 0.00 0.00 4.34
5154 5155 6.769822 ACTTCAGACAATTCTTATATGCAGGG 59.230 38.462 0.00 0.00 0.00 4.45
5155 5156 7.496920 TGACTTCAGACAATTCTTATATGCAGG 59.503 37.037 0.00 0.00 0.00 4.85
5156 5157 8.429493 TGACTTCAGACAATTCTTATATGCAG 57.571 34.615 0.00 0.00 0.00 4.41
5157 5158 8.791327 TTGACTTCAGACAATTCTTATATGCA 57.209 30.769 0.00 0.00 0.00 3.96
5158 5159 9.495754 GTTTGACTTCAGACAATTCTTATATGC 57.504 33.333 0.00 0.00 31.96 3.14
5244 5245 8.286800 CGTCATGACTTTAGTTTTCAAATGGTA 58.713 33.333 22.95 0.00 0.00 3.25
5245 5246 7.138736 CGTCATGACTTTAGTTTTCAAATGGT 58.861 34.615 22.95 0.00 0.00 3.55
5246 5247 6.088085 GCGTCATGACTTTAGTTTTCAAATGG 59.912 38.462 22.95 3.02 0.00 3.16
5247 5248 6.636447 TGCGTCATGACTTTAGTTTTCAAATG 59.364 34.615 22.95 3.38 0.00 2.32
5248 5249 6.734137 TGCGTCATGACTTTAGTTTTCAAAT 58.266 32.000 22.95 0.00 0.00 2.32
5249 5250 6.125327 TGCGTCATGACTTTAGTTTTCAAA 57.875 33.333 22.95 0.00 0.00 2.69
5250 5251 5.743026 TGCGTCATGACTTTAGTTTTCAA 57.257 34.783 22.95 0.00 0.00 2.69
5251 5252 5.700832 AGATGCGTCATGACTTTAGTTTTCA 59.299 36.000 22.95 7.45 0.00 2.69
5252 5253 6.170675 AGATGCGTCATGACTTTAGTTTTC 57.829 37.500 22.95 8.71 0.00 2.29
5253 5254 7.667043 TTAGATGCGTCATGACTTTAGTTTT 57.333 32.000 22.95 4.61 0.00 2.43
5254 5255 7.334421 ACATTAGATGCGTCATGACTTTAGTTT 59.666 33.333 22.95 5.95 0.00 2.66
5255 5256 6.818644 ACATTAGATGCGTCATGACTTTAGTT 59.181 34.615 22.95 7.42 0.00 2.24
5256 5257 6.341316 ACATTAGATGCGTCATGACTTTAGT 58.659 36.000 22.95 8.00 0.00 2.24
5257 5258 6.834959 ACATTAGATGCGTCATGACTTTAG 57.165 37.500 22.95 9.02 0.00 1.85
5258 5259 6.593770 ACAACATTAGATGCGTCATGACTTTA 59.406 34.615 22.95 9.76 0.00 1.85
5259 5260 5.412594 ACAACATTAGATGCGTCATGACTTT 59.587 36.000 22.95 7.92 0.00 2.66
5260 5261 4.937620 ACAACATTAGATGCGTCATGACTT 59.062 37.500 22.95 8.27 0.00 3.01
5261 5262 4.507710 ACAACATTAGATGCGTCATGACT 58.492 39.130 22.95 4.97 0.00 3.41
5262 5263 4.864916 ACAACATTAGATGCGTCATGAC 57.135 40.909 16.21 16.21 0.00 3.06
5263 5264 4.934602 TCAACAACATTAGATGCGTCATGA 59.065 37.500 8.99 0.00 0.00 3.07
5264 5265 5.220557 TCAACAACATTAGATGCGTCATG 57.779 39.130 8.99 6.69 0.00 3.07
5265 5266 6.441093 AATCAACAACATTAGATGCGTCAT 57.559 33.333 8.99 0.00 0.00 3.06
5266 5267 5.878332 AATCAACAACATTAGATGCGTCA 57.122 34.783 8.99 0.00 0.00 4.35
5267 5268 6.249260 GTGAAATCAACAACATTAGATGCGTC 59.751 38.462 0.00 0.00 0.00 5.19
5268 5269 6.086222 GTGAAATCAACAACATTAGATGCGT 58.914 36.000 0.00 0.00 0.00 5.24
5269 5270 6.085573 TGTGAAATCAACAACATTAGATGCG 58.914 36.000 0.00 0.00 0.00 4.73
5270 5271 8.470040 AATGTGAAATCAACAACATTAGATGC 57.530 30.769 0.00 0.00 0.00 3.91
5271 5272 9.850628 AGAATGTGAAATCAACAACATTAGATG 57.149 29.630 0.23 0.00 0.00 2.90
5272 5273 9.850628 CAGAATGTGAAATCAACAACATTAGAT 57.149 29.630 0.23 0.00 0.00 1.98
5273 5274 9.065798 TCAGAATGTGAAATCAACAACATTAGA 57.934 29.630 0.23 0.43 37.40 2.10
5274 5275 9.681692 TTCAGAATGTGAAATCAACAACATTAG 57.318 29.630 0.23 0.00 42.49 1.73
5323 5324 4.625972 AACCACGTAAACTTTGACCAAG 57.374 40.909 0.00 0.00 38.64 3.61
5324 5325 4.458295 TCAAACCACGTAAACTTTGACCAA 59.542 37.500 0.00 0.00 29.66 3.67
5325 5326 4.008330 TCAAACCACGTAAACTTTGACCA 58.992 39.130 0.00 0.00 29.66 4.02
5326 5327 4.345288 GTCAAACCACGTAAACTTTGACC 58.655 43.478 19.18 8.99 43.35 4.02
5327 5328 5.225899 AGTCAAACCACGTAAACTTTGAC 57.774 39.130 20.83 20.83 46.84 3.18
5328 5329 5.411977 TGAAGTCAAACCACGTAAACTTTGA 59.588 36.000 0.00 0.00 31.68 2.69
5329 5330 5.632959 TGAAGTCAAACCACGTAAACTTTG 58.367 37.500 0.00 0.00 0.00 2.77
5330 5331 5.883503 TGAAGTCAAACCACGTAAACTTT 57.116 34.783 0.00 0.00 0.00 2.66
5331 5332 5.883503 TTGAAGTCAAACCACGTAAACTT 57.116 34.783 0.00 0.00 32.11 2.66
5332 5333 5.883503 TTTGAAGTCAAACCACGTAAACT 57.116 34.783 2.32 0.00 40.55 2.66
5362 5363 8.636213 CCTCTGGTCCTTTTTAGTTCGTATATA 58.364 37.037 0.00 0.00 0.00 0.86
5363 5364 7.418712 CCCTCTGGTCCTTTTTAGTTCGTATAT 60.419 40.741 0.00 0.00 0.00 0.86
5364 5365 6.127253 CCCTCTGGTCCTTTTTAGTTCGTATA 60.127 42.308 0.00 0.00 0.00 1.47
5365 5366 5.338137 CCCTCTGGTCCTTTTTAGTTCGTAT 60.338 44.000 0.00 0.00 0.00 3.06
5366 5367 4.020839 CCCTCTGGTCCTTTTTAGTTCGTA 60.021 45.833 0.00 0.00 0.00 3.43
5367 5368 3.244457 CCCTCTGGTCCTTTTTAGTTCGT 60.244 47.826 0.00 0.00 0.00 3.85
5368 5369 3.007614 TCCCTCTGGTCCTTTTTAGTTCG 59.992 47.826 0.00 0.00 0.00 3.95
5369 5370 4.041815 ACTCCCTCTGGTCCTTTTTAGTTC 59.958 45.833 0.00 0.00 0.00 3.01
5370 5371 3.981375 ACTCCCTCTGGTCCTTTTTAGTT 59.019 43.478 0.00 0.00 0.00 2.24
5371 5372 3.599348 ACTCCCTCTGGTCCTTTTTAGT 58.401 45.455 0.00 0.00 0.00 2.24
5372 5373 4.778427 ACTACTCCCTCTGGTCCTTTTTAG 59.222 45.833 0.00 0.00 0.00 1.85
5373 5374 4.759953 ACTACTCCCTCTGGTCCTTTTTA 58.240 43.478 0.00 0.00 0.00 1.52
5374 5375 3.599348 ACTACTCCCTCTGGTCCTTTTT 58.401 45.455 0.00 0.00 0.00 1.94
5375 5376 3.277416 ACTACTCCCTCTGGTCCTTTT 57.723 47.619 0.00 0.00 0.00 2.27
5376 5377 3.277416 AACTACTCCCTCTGGTCCTTT 57.723 47.619 0.00 0.00 0.00 3.11
5377 5378 3.277416 AAACTACTCCCTCTGGTCCTT 57.723 47.619 0.00 0.00 0.00 3.36
5378 5379 3.596956 TCTAAACTACTCCCTCTGGTCCT 59.403 47.826 0.00 0.00 0.00 3.85
5379 5380 3.978610 TCTAAACTACTCCCTCTGGTCC 58.021 50.000 0.00 0.00 0.00 4.46
5380 5381 5.997384 TTTCTAAACTACTCCCTCTGGTC 57.003 43.478 0.00 0.00 0.00 4.02
5381 5382 6.082707 TCTTTTCTAAACTACTCCCTCTGGT 58.917 40.000 0.00 0.00 0.00 4.00
5382 5383 6.607004 TCTTTTCTAAACTACTCCCTCTGG 57.393 41.667 0.00 0.00 0.00 3.86
5383 5384 7.550906 CCAATCTTTTCTAAACTACTCCCTCTG 59.449 40.741 0.00 0.00 0.00 3.35
5384 5385 7.458170 TCCAATCTTTTCTAAACTACTCCCTCT 59.542 37.037 0.00 0.00 0.00 3.69
5385 5386 7.549842 GTCCAATCTTTTCTAAACTACTCCCTC 59.450 40.741 0.00 0.00 0.00 4.30
5386 5387 7.237887 AGTCCAATCTTTTCTAAACTACTCCCT 59.762 37.037 0.00 0.00 0.00 4.20
5387 5388 7.334671 CAGTCCAATCTTTTCTAAACTACTCCC 59.665 40.741 0.00 0.00 0.00 4.30
5388 5389 8.095169 TCAGTCCAATCTTTTCTAAACTACTCC 58.905 37.037 0.00 0.00 0.00 3.85
5389 5390 9.660180 ATCAGTCCAATCTTTTCTAAACTACTC 57.340 33.333 0.00 0.00 0.00 2.59
5390 5391 9.442047 CATCAGTCCAATCTTTTCTAAACTACT 57.558 33.333 0.00 0.00 0.00 2.57
5391 5392 9.220767 ACATCAGTCCAATCTTTTCTAAACTAC 57.779 33.333 0.00 0.00 0.00 2.73
5392 5393 9.793259 AACATCAGTCCAATCTTTTCTAAACTA 57.207 29.630 0.00 0.00 0.00 2.24
5393 5394 8.571336 CAACATCAGTCCAATCTTTTCTAAACT 58.429 33.333 0.00 0.00 0.00 2.66
5573 5574 5.458041 AAAGAAATGTGACATGGTGGAAG 57.542 39.130 0.00 0.00 0.00 3.46
5847 5858 6.382282 TCTGAGTTCCATCAGTATCATTCACT 59.618 38.462 3.84 0.00 45.70 3.41
6039 6050 6.169094 GTTCTCTCTCATTGATTCCAACTCA 58.831 40.000 0.00 0.00 34.72 3.41
6052 6063 7.901029 TGTAGTTCAAGAATGTTCTCTCTCAT 58.099 34.615 0.00 0.00 36.28 2.90
6060 6071 8.539770 TCTCTGATTGTAGTTCAAGAATGTTC 57.460 34.615 0.00 0.00 39.55 3.18
6151 6162 7.233553 TCCTTCAATCTCAGAAACTGAACTAGA 59.766 37.037 0.00 0.00 40.18 2.43
6200 6211 1.340991 GCCCAACAGAATAGCTCCCAA 60.341 52.381 0.00 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.