Multiple sequence alignment - TraesCS5D01G179000

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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 TraesCS5D01G179000 chr5D 100.000 5253 0 0 1 5253 278278465 278283717 0.000000e+00 9701.0
1 TraesCS5D01G179000 chr5D 90.385 260 23 1 1854 2113 278280187 278280444 1.810000e-89 340.0
2 TraesCS5D01G179000 chr5D 90.385 260 23 1 1723 1980 278280318 278280577 1.810000e-89 340.0
3 TraesCS5D01G179000 chr5D 87.786 131 13 2 1983 2113 278280184 278280311 3.280000e-32 150.0
4 TraesCS5D01G179000 chr5D 87.786 131 13 2 1720 1847 278280447 278280577 3.280000e-32 150.0
5 TraesCS5D01G179000 chr5B 95.285 5133 160 35 1 5088 316368123 316373218 0.000000e+00 8063.0
6 TraesCS5D01G179000 chr5B 88.593 263 23 2 1851 2113 316369842 316370097 3.950000e-81 313.0
7 TraesCS5D01G179000 chr5B 87.266 267 23 4 1720 1980 316369972 316370233 1.430000e-75 294.0
8 TraesCS5D01G179000 chr5B 88.618 123 12 1 1982 2104 316369840 316369960 1.180000e-31 148.0
9 TraesCS5D01G179000 chr5B 83.544 158 24 2 5091 5247 340615302 340615458 4.240000e-31 147.0
10 TraesCS5D01G179000 chr5A 94.611 5066 156 57 1 4997 367598046 367603063 0.000000e+00 7734.0
11 TraesCS5D01G179000 chr5A 90.875 263 22 1 1851 2113 367599760 367600020 8.370000e-93 351.0
12 TraesCS5D01G179000 chr5A 90.698 258 22 1 1725 1980 367599896 367600153 5.040000e-90 342.0
13 TraesCS5D01G179000 chr5A 87.879 132 14 1 1982 2113 367599758 367599887 2.530000e-33 154.0
14 TraesCS5D01G179000 chr5A 87.786 131 13 2 1720 1847 367600023 367600153 3.280000e-32 150.0
15 TraesCS5D01G179000 chr7D 86.986 146 18 1 5091 5236 155265112 155265256 4.210000e-36 163.0
16 TraesCS5D01G179000 chr7D 82.822 163 25 2 5091 5253 540626757 540626598 5.480000e-30 143.0
17 TraesCS5D01G179000 chr7D 81.875 160 26 3 5091 5249 11679942 11680099 1.190000e-26 132.0
18 TraesCS5D01G179000 chr4B 81.731 208 25 8 4688 4882 237949932 237949725 1.510000e-35 161.0
19 TraesCS5D01G179000 chr4D 84.049 163 25 1 5091 5253 327379518 327379679 7.040000e-34 156.0
20 TraesCS5D01G179000 chr2A 78.099 242 39 9 4688 4915 161631232 161631473 1.970000e-29 141.0
21 TraesCS5D01G179000 chr2A 78.099 242 37 10 4688 4914 379152244 379152484 7.090000e-29 139.0
22 TraesCS5D01G179000 chr2A 76.613 248 43 10 4683 4916 660500108 660499862 7.140000e-24 122.0
23 TraesCS5D01G179000 chr3B 82.609 161 20 7 5093 5248 616887695 616887538 9.180000e-28 135.0
24 TraesCS5D01G179000 chr1D 83.007 153 23 3 5091 5242 475955264 475955114 9.180000e-28 135.0
25 TraesCS5D01G179000 chr1D 87.356 87 10 1 4808 4893 7983522 7983436 1.200000e-16 99.0
26 TraesCS5D01G179000 chr4A 81.595 163 29 1 5091 5253 143701499 143701338 3.300000e-27 134.0
27 TraesCS5D01G179000 chr2D 81.707 164 27 3 5091 5253 134636438 134636599 3.300000e-27 134.0
28 TraesCS5D01G179000 chr2B 77.778 225 36 9 4704 4915 755063241 755063018 5.520000e-25 126.0
29 TraesCS5D01G179000 chr2B 80.672 119 22 1 4797 4914 357919814 357919932 2.010000e-14 91.6


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 TraesCS5D01G179000 chr5D 278278465 278283717 5252 False 2136.2 9701 91.2684 1 5253 5 chr5D.!!$F1 5252
1 TraesCS5D01G179000 chr5B 316368123 316373218 5095 False 2204.5 8063 89.9405 1 5088 4 chr5B.!!$F2 5087
2 TraesCS5D01G179000 chr5A 367598046 367603063 5017 False 1746.2 7734 90.3698 1 4997 5 chr5A.!!$F1 4996


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
429 432 0.040692 GTCGGTTTCGGTTTGCTTCC 60.041 55.000 0.00 0.00 36.95 3.46 F
481 485 0.324645 CCTGCCTACAAATTGGGCCT 60.325 55.000 4.53 0.00 44.71 5.19 F
482 486 0.819582 CTGCCTACAAATTGGGCCTG 59.180 55.000 4.53 0.00 44.71 4.85 F
1892 1925 1.134250 TGCACAGCACCAGTGAAACTA 60.134 47.619 0.99 0.00 38.58 2.24 F
2432 2469 0.937304 CCATTCAAGTATGACGGCCG 59.063 55.000 26.86 26.86 34.61 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1329 1356 0.314935 CAATGGACTTGTGCCGCTTT 59.685 50.000 0.00 0.0 0.0 3.51 R
1892 1925 2.658285 TGCATAGCTAGGCAAAAGCAT 58.342 42.857 29.27 0.0 40.3 3.79 R
2376 2413 3.004419 TCTTCTGGCGTGTAATATCCTCG 59.996 47.826 0.00 0.0 0.0 4.63 R
2964 3007 1.089112 GTAACATGCGTACCCAACCC 58.911 55.000 0.00 0.0 0.0 4.11 R
4271 4328 1.273759 GGTTTCTTACGTCTCCCCCT 58.726 55.000 0.00 0.0 0.0 4.79 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
61 62 2.591715 GGCCGGCAGCGTGATAAT 60.592 61.111 30.85 0.00 45.17 1.28
76 77 5.123344 GCGTGATAATGGAAAACCTAGTGTT 59.877 40.000 0.00 0.00 39.43 3.32
94 95 3.057946 GTGTTGGAAGGAAGATTCACAGC 60.058 47.826 0.00 0.00 0.00 4.40
127 128 4.773149 ACCGACTTCTCCAATCTAAGACTT 59.227 41.667 0.00 0.00 0.00 3.01
137 138 7.836685 TCTCCAATCTAAGACTTCTCAGTGTAT 59.163 37.037 0.00 0.00 31.22 2.29
145 146 6.287589 AGACTTCTCAGTGTATAACCCAAG 57.712 41.667 0.00 0.00 31.22 3.61
155 156 1.477553 ATAACCCAAGTACCTCGCGA 58.522 50.000 9.26 9.26 0.00 5.87
166 167 4.521062 CTCGCGAGCAAGAGGGGG 62.521 72.222 25.07 0.00 0.00 5.40
171 172 2.959484 CGAGCAAGAGGGGGCTTCA 61.959 63.158 0.00 0.00 41.22 3.02
227 228 3.427425 CGACCAAATTCGGCGGCA 61.427 61.111 10.53 0.00 35.26 5.69
229 230 1.154035 GACCAAATTCGGCGGCAAG 60.154 57.895 10.53 0.00 0.00 4.01
256 257 1.466186 AAGGCTGAAGGAAGGGGGT 60.466 57.895 0.00 0.00 0.00 4.95
259 261 3.090765 CTGAAGGAAGGGGGTGGG 58.909 66.667 0.00 0.00 0.00 4.61
429 432 0.040692 GTCGGTTTCGGTTTGCTTCC 60.041 55.000 0.00 0.00 36.95 3.46
444 447 3.881019 TTCCAGACGAGGCGAGGGT 62.881 63.158 0.00 0.00 0.00 4.34
480 484 1.960040 GCCTGCCTACAAATTGGGCC 61.960 60.000 10.08 0.00 44.71 5.80
481 485 0.324645 CCTGCCTACAAATTGGGCCT 60.325 55.000 4.53 0.00 44.71 5.19
482 486 0.819582 CTGCCTACAAATTGGGCCTG 59.180 55.000 4.53 0.00 44.71 4.85
886 910 7.606456 GGAAGTAAATAAATAGGGATGATCGCA 59.394 37.037 12.18 0.00 0.00 5.10
930 954 8.013378 GGTTTATTTCGGTGGATTATATGTTCG 58.987 37.037 0.00 0.00 0.00 3.95
1088 1112 1.536662 AGGACAAGGAGAAGCCCGT 60.537 57.895 0.00 0.00 37.37 5.28
1089 1113 1.376037 GGACAAGGAGAAGCCCGTG 60.376 63.158 0.00 0.00 40.74 4.94
1152 1179 2.397413 CTGTCAACCCCAAGACGCCT 62.397 60.000 0.00 0.00 37.58 5.52
1173 1200 2.159184 TCTTGTCATTGCGGCAAACAAA 60.159 40.909 24.79 16.56 28.21 2.83
1215 1242 3.692406 GGCTCGGTCTTGTCGGGT 61.692 66.667 0.00 0.00 0.00 5.28
1281 1308 1.611673 CCTGTCAAGTTTGGAGCCGAT 60.612 52.381 0.00 0.00 0.00 4.18
1293 1320 1.989966 GAGCCGATGAGGACGACGAA 61.990 60.000 0.00 0.00 45.00 3.85
1305 1332 4.223514 GACGAAGACGACGTTGCT 57.776 55.556 0.13 0.00 43.97 3.91
1485 1512 4.563782 TGGGTAGTAGCTATAAGGGCTTT 58.436 43.478 0.00 0.00 40.74 3.51
1666 1694 8.840833 TTGCAATACTTACAAAGATACACTGA 57.159 30.769 0.00 0.00 0.00 3.41
1880 1913 8.774890 ATAAAATCAATTTACATTGCACAGCA 57.225 26.923 0.00 0.00 39.90 4.41
1881 1914 6.470557 AAATCAATTTACATTGCACAGCAC 57.529 33.333 0.00 0.00 39.90 4.40
1892 1925 1.134250 TGCACAGCACCAGTGAAACTA 60.134 47.619 0.99 0.00 38.58 2.24
2049 2085 3.825328 CTTTTGCCTAGCCATCCATACT 58.175 45.455 0.00 0.00 0.00 2.12
2376 2413 2.627699 TGCCAAAAATGGGAGACAGTTC 59.372 45.455 0.00 0.00 36.16 3.01
2432 2469 0.937304 CCATTCAAGTATGACGGCCG 59.063 55.000 26.86 26.86 34.61 6.13
2622 2659 1.888512 GAGGAAAAGGTGCATGCTCAA 59.111 47.619 20.33 0.00 32.47 3.02
2658 2695 2.220824 GGCTTCAAAAATTGGTTCGTGC 59.779 45.455 0.00 0.00 0.00 5.34
2799 2840 5.009410 ACAGAGAAGCTCATTTGAACAAAGG 59.991 40.000 5.73 5.73 33.32 3.11
2823 2864 6.166982 GTCTAACTATCAAACACCTGCTTCT 58.833 40.000 0.00 0.00 0.00 2.85
2910 2953 2.300152 TGAGGTGTCTGTGGATCACTTC 59.700 50.000 0.00 0.00 38.22 3.01
2934 2977 4.398247 CTTTTCTTAAGCTTGCGTGCTAG 58.602 43.478 9.86 0.00 43.24 3.42
2964 3007 4.264253 TGATTGCTTCCACACTATTCCAG 58.736 43.478 0.00 0.00 0.00 3.86
3033 3076 2.276201 TCCGCCAGTTAATTGTCATCG 58.724 47.619 0.00 0.00 0.00 3.84
3116 3160 9.743581 TGCATAGAATGGACATATTATGATGTT 57.256 29.630 10.62 0.59 40.18 2.71
3137 3181 7.581213 TGTTCCTTTATGTGAACAACTGAAT 57.419 32.000 2.82 0.00 45.64 2.57
3141 3185 7.874940 TCCTTTATGTGAACAACTGAATTCTG 58.125 34.615 10.51 10.51 0.00 3.02
3151 3195 6.808008 ACAACTGAATTCTGTATCCTGTTG 57.192 37.500 17.16 12.32 36.25 3.33
3527 3578 1.005805 CACATGGGGGACTTCATTCCA 59.994 52.381 0.00 0.00 37.40 3.53
3700 3751 7.969314 TCAAATTGAAAACTAAACACCAAAGC 58.031 30.769 0.00 0.00 0.00 3.51
3858 3910 2.401583 TTACGTCTGCATGCATTCCT 57.598 45.000 22.97 7.06 0.00 3.36
3912 3964 6.876257 GCTCAGTGACCTAATTAATCCTATGG 59.124 42.308 0.00 0.00 0.00 2.74
3914 3966 9.090103 CTCAGTGACCTAATTAATCCTATGGTA 57.910 37.037 0.00 0.00 0.00 3.25
4183 4238 7.343833 AGCCATGACCTTCTTTAATGAATGATT 59.656 33.333 11.60 0.00 0.00 2.57
4254 4311 6.180472 ACCCAAGGAAACAATACTACTGATG 58.820 40.000 0.00 0.00 0.00 3.07
4271 4328 3.650950 GCAAGGGGAGGTCAGCCA 61.651 66.667 0.00 0.00 37.19 4.75
4472 4529 5.072040 AGCTTTGCTGTTTTAGTGTTTGT 57.928 34.783 0.00 0.00 37.57 2.83
4513 4570 0.390124 TGTGTCCTACGGTGGTGTTC 59.610 55.000 0.00 0.00 0.00 3.18
4722 4781 3.014623 GTGGTTTATTAGGCACCCTCAC 58.985 50.000 0.00 0.00 34.61 3.51
4791 4853 5.182487 ACTGTGTCACAAACATTACACTGA 58.818 37.500 7.18 0.00 41.54 3.41
4792 4854 5.822519 ACTGTGTCACAAACATTACACTGAT 59.177 36.000 7.18 1.47 41.54 2.90
4917 5004 2.755655 ACTCAGACGGATGGAGTAACTG 59.244 50.000 0.00 0.00 39.95 3.16
4988 5079 2.355197 TGGGCACTACGATGAATTGTG 58.645 47.619 0.00 0.00 0.00 3.33
4999 5090 7.817478 ACTACGATGAATTGTGTTGATGACTTA 59.183 33.333 0.00 0.00 0.00 2.24
5017 5108 7.055667 TGACTTACTGAAGAGACAAGTCATT 57.944 36.000 10.51 0.00 42.84 2.57
5025 5116 2.307098 AGAGACAAGTCATTTGAGGGGG 59.693 50.000 2.72 0.00 39.21 5.40
5088 5179 5.129815 TGTTACCTTAACCAGCCTATAGTGG 59.870 44.000 7.66 7.66 37.88 4.00
5090 5181 4.887367 ACCTTAACCAGCCTATAGTGGTA 58.113 43.478 13.83 1.38 46.82 3.25
5091 5182 4.900054 ACCTTAACCAGCCTATAGTGGTAG 59.100 45.833 13.83 9.40 46.82 3.18
5092 5183 4.283722 CCTTAACCAGCCTATAGTGGTAGG 59.716 50.000 13.83 13.51 46.82 3.18
5093 5184 3.700863 AACCAGCCTATAGTGGTAGGA 57.299 47.619 13.83 0.00 46.82 2.94
5094 5185 3.246416 ACCAGCCTATAGTGGTAGGAG 57.754 52.381 12.24 0.00 45.62 3.69
5095 5186 1.896465 CCAGCCTATAGTGGTAGGAGC 59.104 57.143 4.21 0.00 43.27 4.70
5096 5187 2.491825 CCAGCCTATAGTGGTAGGAGCT 60.492 54.545 4.21 0.00 43.27 4.09
5097 5188 2.823154 CAGCCTATAGTGGTAGGAGCTC 59.177 54.545 4.71 4.71 43.27 4.09
5098 5189 2.719705 AGCCTATAGTGGTAGGAGCTCT 59.280 50.000 14.64 2.18 43.27 4.09
5099 5190 3.141272 AGCCTATAGTGGTAGGAGCTCTT 59.859 47.826 14.64 8.96 43.27 2.85
5100 5191 3.257127 GCCTATAGTGGTAGGAGCTCTTG 59.743 52.174 14.64 0.00 43.27 3.02
5101 5192 3.829601 CCTATAGTGGTAGGAGCTCTTGG 59.170 52.174 14.64 0.00 43.27 3.61
5102 5193 2.160721 TAGTGGTAGGAGCTCTTGGG 57.839 55.000 14.64 0.00 0.00 4.12
5103 5194 0.117340 AGTGGTAGGAGCTCTTGGGT 59.883 55.000 14.64 0.00 0.00 4.51
5104 5195 0.250513 GTGGTAGGAGCTCTTGGGTG 59.749 60.000 14.64 0.00 0.00 4.61
5105 5196 1.222113 GGTAGGAGCTCTTGGGTGC 59.778 63.158 14.64 0.00 0.00 5.01
5106 5197 1.268283 GGTAGGAGCTCTTGGGTGCT 61.268 60.000 14.64 2.54 45.61 4.40
5109 5200 3.072476 GAGCTCTTGGGTGCTCCA 58.928 61.111 6.43 0.85 46.93 3.86
5121 5212 2.550830 GTGCTCCACACCCCTATATG 57.449 55.000 0.00 0.00 44.02 1.78
5122 5213 2.047061 GTGCTCCACACCCCTATATGA 58.953 52.381 0.00 0.00 44.02 2.15
5123 5214 2.438021 GTGCTCCACACCCCTATATGAA 59.562 50.000 0.00 0.00 44.02 2.57
5124 5215 3.073062 GTGCTCCACACCCCTATATGAAT 59.927 47.826 0.00 0.00 44.02 2.57
5125 5216 4.286032 GTGCTCCACACCCCTATATGAATA 59.714 45.833 0.00 0.00 44.02 1.75
5126 5217 5.045578 GTGCTCCACACCCCTATATGAATAT 60.046 44.000 0.00 0.00 44.02 1.28
5127 5218 5.551583 TGCTCCACACCCCTATATGAATATT 59.448 40.000 0.00 0.00 0.00 1.28
5128 5219 6.733334 TGCTCCACACCCCTATATGAATATTA 59.267 38.462 0.00 0.00 0.00 0.98
5129 5220 7.238723 TGCTCCACACCCCTATATGAATATTAA 59.761 37.037 0.00 0.00 0.00 1.40
5130 5221 8.107095 GCTCCACACCCCTATATGAATATTAAA 58.893 37.037 0.00 0.00 0.00 1.52
5132 5223 9.973661 TCCACACCCCTATATGAATATTAAATG 57.026 33.333 0.00 0.00 0.00 2.32
5133 5224 9.753674 CCACACCCCTATATGAATATTAAATGT 57.246 33.333 0.00 0.00 0.00 2.71
5194 5285 6.834168 TGAAGATATCAAACCTGGGTTTTC 57.166 37.500 14.27 9.95 44.84 2.29
5195 5286 6.310941 TGAAGATATCAAACCTGGGTTTTCA 58.689 36.000 14.27 10.99 44.84 2.69
5196 5287 6.780031 TGAAGATATCAAACCTGGGTTTTCAA 59.220 34.615 14.27 4.96 44.84 2.69
5197 5288 7.454380 TGAAGATATCAAACCTGGGTTTTCAAT 59.546 33.333 14.27 10.86 44.84 2.57
5198 5289 7.174107 AGATATCAAACCTGGGTTTTCAATG 57.826 36.000 14.27 5.14 44.84 2.82
5199 5290 6.725834 AGATATCAAACCTGGGTTTTCAATGT 59.274 34.615 14.27 7.66 44.84 2.71
5200 5291 7.893302 AGATATCAAACCTGGGTTTTCAATGTA 59.107 33.333 14.27 3.73 44.84 2.29
5201 5292 6.933514 ATCAAACCTGGGTTTTCAATGTAT 57.066 33.333 14.27 0.00 44.84 2.29
5202 5293 6.739331 TCAAACCTGGGTTTTCAATGTATT 57.261 33.333 14.27 0.00 44.84 1.89
5203 5294 6.754193 TCAAACCTGGGTTTTCAATGTATTC 58.246 36.000 14.27 0.00 44.84 1.75
5204 5295 5.738619 AACCTGGGTTTTCAATGTATTCC 57.261 39.130 0.00 0.00 34.22 3.01
5205 5296 4.093743 ACCTGGGTTTTCAATGTATTCCC 58.906 43.478 0.00 0.00 0.00 3.97
5206 5297 4.093011 CCTGGGTTTTCAATGTATTCCCA 58.907 43.478 0.00 0.00 40.70 4.37
5207 5298 4.716287 CCTGGGTTTTCAATGTATTCCCAT 59.284 41.667 0.00 0.00 41.82 4.00
5208 5299 5.395546 CCTGGGTTTTCAATGTATTCCCATG 60.396 44.000 0.00 0.00 41.82 3.66
5209 5300 5.090139 TGGGTTTTCAATGTATTCCCATGT 58.910 37.500 0.00 0.00 38.51 3.21
5210 5301 5.046735 TGGGTTTTCAATGTATTCCCATGTG 60.047 40.000 0.00 0.00 38.51 3.21
5211 5302 5.186797 GGGTTTTCAATGTATTCCCATGTGA 59.813 40.000 0.00 0.00 34.20 3.58
5212 5303 6.295575 GGGTTTTCAATGTATTCCCATGTGAA 60.296 38.462 0.00 0.00 34.20 3.18
5213 5304 7.158021 GGTTTTCAATGTATTCCCATGTGAAA 58.842 34.615 0.00 0.00 34.21 2.69
5214 5305 7.823799 GGTTTTCAATGTATTCCCATGTGAAAT 59.176 33.333 0.00 0.00 35.00 2.17
5215 5306 9.218440 GTTTTCAATGTATTCCCATGTGAAATT 57.782 29.630 0.00 0.00 35.00 1.82
5216 5307 9.790344 TTTTCAATGTATTCCCATGTGAAATTT 57.210 25.926 0.00 0.00 35.00 1.82
5217 5308 9.790344 TTTCAATGTATTCCCATGTGAAATTTT 57.210 25.926 0.00 0.00 32.86 1.82
5218 5309 8.774890 TCAATGTATTCCCATGTGAAATTTTG 57.225 30.769 0.00 0.00 0.00 2.44
5219 5310 8.373981 TCAATGTATTCCCATGTGAAATTTTGT 58.626 29.630 0.00 0.00 0.00 2.83
5220 5311 8.444715 CAATGTATTCCCATGTGAAATTTTGTG 58.555 33.333 0.00 0.00 0.00 3.33
5221 5312 7.060383 TGTATTCCCATGTGAAATTTTGTGT 57.940 32.000 0.00 0.00 0.00 3.72
5222 5313 8.183104 TGTATTCCCATGTGAAATTTTGTGTA 57.817 30.769 0.00 0.00 0.00 2.90
5223 5314 8.642432 TGTATTCCCATGTGAAATTTTGTGTAA 58.358 29.630 0.00 0.00 0.00 2.41
5224 5315 9.482627 GTATTCCCATGTGAAATTTTGTGTAAA 57.517 29.630 0.00 0.00 0.00 2.01
5225 5316 8.970859 ATTCCCATGTGAAATTTTGTGTAAAA 57.029 26.923 0.00 0.00 39.86 1.52
5226 5317 8.792830 TTCCCATGTGAAATTTTGTGTAAAAA 57.207 26.923 0.00 0.00 39.09 1.94
5227 5318 8.970859 TCCCATGTGAAATTTTGTGTAAAAAT 57.029 26.923 0.00 0.00 39.09 1.82
5248 5339 6.560253 AATATCAGAAAACATATCGGTGGC 57.440 37.500 0.00 0.00 0.00 5.01
5249 5340 3.342377 TCAGAAAACATATCGGTGGCA 57.658 42.857 0.00 0.00 0.00 4.92
5250 5341 3.680490 TCAGAAAACATATCGGTGGCAA 58.320 40.909 0.00 0.00 0.00 4.52
5251 5342 4.075682 TCAGAAAACATATCGGTGGCAAA 58.924 39.130 0.00 0.00 0.00 3.68
5252 5343 4.155826 TCAGAAAACATATCGGTGGCAAAG 59.844 41.667 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 2.896801 GCTGCCGGCCATCGTATTG 61.897 63.158 26.77 3.67 37.11 1.90
61 62 3.460340 TCCTTCCAACACTAGGTTTTCCA 59.540 43.478 0.00 0.00 43.73 3.53
76 77 1.004745 GGGCTGTGAATCTTCCTTCCA 59.995 52.381 0.00 0.00 0.00 3.53
94 95 2.537401 GAGAAGTCGGTACATTTCGGG 58.463 52.381 0.00 0.00 0.00 5.14
127 128 5.586877 AGGTACTTGGGTTATACACTGAGA 58.413 41.667 0.00 0.00 27.25 3.27
145 146 1.226717 CCTCTTGCTCGCGAGGTAC 60.227 63.158 35.10 20.30 41.49 3.34
155 156 1.430369 AAGTGAAGCCCCCTCTTGCT 61.430 55.000 0.00 0.00 40.17 3.91
201 202 3.521765 AATTTGGTCGGGGCAGCCA 62.522 57.895 15.19 0.00 0.00 4.75
227 228 3.289834 CAGCCTTGCGCACCACTT 61.290 61.111 11.12 0.00 41.38 3.16
229 230 3.259425 CTTCAGCCTTGCGCACCAC 62.259 63.158 11.12 1.16 41.38 4.16
256 257 0.481128 GGTGAGTTCCTTTTCCCCCA 59.519 55.000 0.00 0.00 0.00 4.96
259 261 2.171003 CCATGGTGAGTTCCTTTTCCC 58.829 52.381 2.57 0.00 0.00 3.97
429 432 4.803426 GCACCCTCGCCTCGTCTG 62.803 72.222 0.00 0.00 0.00 3.51
444 447 4.958897 CCGGGGGTCCAAAACGCA 62.959 66.667 0.00 0.00 42.43 5.24
470 474 2.983791 CCCAGCAGGCCCAATTTG 59.016 61.111 0.00 0.00 0.00 2.32
518 522 0.679505 CAGAGACAAGTCGGGTTCCA 59.320 55.000 0.00 0.00 34.09 3.53
828 852 0.189822 ATCTAGCCTCCCCCTCAGAC 59.810 60.000 0.00 0.00 0.00 3.51
930 954 4.213482 CACACAAAAGCTAACAGGTCTACC 59.787 45.833 0.00 0.00 0.00 3.18
1152 1179 1.028130 TGTTTGCCGCAATGACAAGA 58.972 45.000 6.64 0.00 0.00 3.02
1173 1200 3.302347 CTTCACCTCGAGCGGCCTT 62.302 63.158 6.99 0.00 0.00 4.35
1215 1242 1.000896 GCTAAAGGCCAGCTTCCCA 60.001 57.895 5.01 0.00 36.07 4.37
1281 1308 1.864862 GTCGTCTTCGTCGTCCTCA 59.135 57.895 0.00 0.00 38.33 3.86
1293 1320 1.591594 CACACCAGCAACGTCGTCT 60.592 57.895 0.00 0.00 0.00 4.18
1329 1356 0.314935 CAATGGACTTGTGCCGCTTT 59.685 50.000 0.00 0.00 0.00 3.51
1877 1910 2.867109 AGCATAGTTTCACTGGTGCT 57.133 45.000 10.92 10.92 42.56 4.40
1878 1911 3.923017 AAAGCATAGTTTCACTGGTGC 57.077 42.857 7.60 7.60 39.71 5.01
1879 1912 3.983344 GCAAAAGCATAGTTTCACTGGTG 59.017 43.478 0.00 0.00 0.00 4.17
1880 1913 3.005791 GGCAAAAGCATAGTTTCACTGGT 59.994 43.478 0.00 0.00 0.00 4.00
1881 1914 3.256631 AGGCAAAAGCATAGTTTCACTGG 59.743 43.478 0.00 0.00 0.00 4.00
1892 1925 2.658285 TGCATAGCTAGGCAAAAGCAT 58.342 42.857 29.27 0.00 40.30 3.79
2049 2085 9.982651 GATGTCCATATTAGACAAGCTACTAAA 57.017 33.333 8.93 3.85 46.67 1.85
2376 2413 3.004419 TCTTCTGGCGTGTAATATCCTCG 59.996 47.826 0.00 0.00 0.00 4.63
2583 2620 1.075425 CTTCAGCAAGCCGAGTCTCG 61.075 60.000 15.53 15.53 40.07 4.04
2622 2659 2.165998 GAAGCCTGAGCATCCTTTGTT 58.834 47.619 0.00 0.00 43.56 2.83
2799 2840 6.091441 CAGAAGCAGGTGTTTGATAGTTAGAC 59.909 42.308 0.00 0.00 0.00 2.59
2823 2864 6.306199 ACCTTCATATGCACCATATAAAGCA 58.694 36.000 0.00 0.00 33.17 3.91
2910 2953 2.922335 GCACGCAAGCTTAAGAAAAGGG 60.922 50.000 6.67 3.68 45.62 3.95
2934 2977 2.622942 TGTGGAAGCAATCAAACCAGAC 59.377 45.455 0.00 0.00 0.00 3.51
2964 3007 1.089112 GTAACATGCGTACCCAACCC 58.911 55.000 0.00 0.00 0.00 4.11
3033 3076 5.923114 GCCAAAAACTCAGAGAAGAAAATCC 59.077 40.000 3.79 0.00 0.00 3.01
3116 3160 7.502226 ACAGAATTCAGTTGTTCACATAAAGGA 59.498 33.333 8.44 0.00 0.00 3.36
3137 3181 5.719563 TGTAGGATGACAACAGGATACAGAA 59.280 40.000 0.00 0.00 41.41 3.02
3141 3185 9.862371 CTATAATGTAGGATGACAACAGGATAC 57.138 37.037 0.00 0.00 31.83 2.24
3700 3751 5.091261 ACAGGCATTTACTAGAACTGGAG 57.909 43.478 0.00 0.00 0.00 3.86
3775 3826 9.859427 GAATACAGGATTCATTGTTTCATTTGA 57.141 29.630 0.00 0.00 43.16 2.69
3820 3872 5.529800 ACGTAAACTTAACAATTCACCAGCT 59.470 36.000 0.00 0.00 0.00 4.24
3886 3938 5.957771 AGGATTAATTAGGTCACTGAGCA 57.042 39.130 10.78 0.00 31.89 4.26
4254 4311 3.635268 CTGGCTGACCTCCCCTTGC 62.635 68.421 0.00 0.00 36.63 4.01
4271 4328 1.273759 GGTTTCTTACGTCTCCCCCT 58.726 55.000 0.00 0.00 0.00 4.79
4513 4570 7.148540 CCATTTGAAACATCAACTTTGGCATAG 60.149 37.037 3.24 3.24 0.00 2.23
4629 4688 1.678627 TCGCTTTGCACTAGCCAAAAA 59.321 42.857 12.95 0.00 41.13 1.94
4722 4781 8.364142 TCTATGGTCAAACTTTAACCCAAAATG 58.636 33.333 0.00 0.00 31.78 2.32
4882 4969 4.389077 CCGTCTGAGTTTATTGTGTCTTCC 59.611 45.833 0.00 0.00 0.00 3.46
4988 5079 6.926272 ACTTGTCTCTTCAGTAAGTCATCAAC 59.074 38.462 0.00 0.00 34.13 3.18
4999 5090 5.303971 CCTCAAATGACTTGTCTCTTCAGT 58.696 41.667 2.35 0.00 36.34 3.41
5025 5116 4.830826 AAAGAAAAACCTCGACATCACC 57.169 40.909 0.00 0.00 0.00 4.02
5033 5124 9.900264 CAAGTTTCATTAAAAAGAAAAACCTCG 57.100 29.630 0.00 0.00 35.71 4.63
5070 5161 5.145564 TCCTACCACTATAGGCTGGTTAAG 58.854 45.833 17.57 11.15 41.51 1.85
5078 5169 3.163616 AGAGCTCCTACCACTATAGGC 57.836 52.381 10.93 0.00 41.51 3.93
5088 5179 2.291856 AGCACCCAAGAGCTCCTAC 58.708 57.895 10.93 0.00 34.53 3.18
5089 5180 4.896979 AGCACCCAAGAGCTCCTA 57.103 55.556 10.93 0.00 34.53 2.94
5102 5193 2.047061 TCATATAGGGGTGTGGAGCAC 58.953 52.381 0.00 0.00 46.97 4.40
5103 5194 2.487746 TCATATAGGGGTGTGGAGCA 57.512 50.000 0.00 0.00 0.00 4.26
5104 5195 5.700402 ATATTCATATAGGGGTGTGGAGC 57.300 43.478 0.00 0.00 0.00 4.70
5106 5197 9.973661 CATTTAATATTCATATAGGGGTGTGGA 57.026 33.333 0.00 0.00 0.00 4.02
5107 5198 9.753674 ACATTTAATATTCATATAGGGGTGTGG 57.246 33.333 0.00 0.00 0.00 4.17
5170 5261 6.780031 TGAAAACCCAGGTTTGATATCTTCAA 59.220 34.615 15.33 0.00 46.22 2.69
5171 5262 6.310941 TGAAAACCCAGGTTTGATATCTTCA 58.689 36.000 15.33 10.31 46.22 3.02
5172 5263 6.834168 TGAAAACCCAGGTTTGATATCTTC 57.166 37.500 15.33 8.01 46.22 2.87
5173 5264 7.235399 ACATTGAAAACCCAGGTTTGATATCTT 59.765 33.333 15.33 0.00 46.22 2.40
5174 5265 6.725834 ACATTGAAAACCCAGGTTTGATATCT 59.274 34.615 15.33 0.00 46.22 1.98
5175 5266 6.935167 ACATTGAAAACCCAGGTTTGATATC 58.065 36.000 15.33 9.64 46.22 1.63
5176 5267 6.933514 ACATTGAAAACCCAGGTTTGATAT 57.066 33.333 15.33 6.54 46.22 1.63
5177 5268 8.429237 AATACATTGAAAACCCAGGTTTGATA 57.571 30.769 15.33 4.59 46.22 2.15
5178 5269 6.933514 ATACATTGAAAACCCAGGTTTGAT 57.066 33.333 15.33 7.68 46.22 2.57
5179 5270 6.239458 GGAATACATTGAAAACCCAGGTTTGA 60.239 38.462 15.33 5.79 46.22 2.69
5180 5271 5.931724 GGAATACATTGAAAACCCAGGTTTG 59.068 40.000 15.33 6.15 46.22 2.93
5182 5273 4.530553 GGGAATACATTGAAAACCCAGGTT 59.469 41.667 0.00 0.00 40.45 3.50
5183 5274 4.093743 GGGAATACATTGAAAACCCAGGT 58.906 43.478 0.00 0.00 36.27 4.00
5184 5275 4.093011 TGGGAATACATTGAAAACCCAGG 58.907 43.478 0.00 0.00 40.52 4.45
5185 5276 5.187576 ACATGGGAATACATTGAAAACCCAG 59.812 40.000 0.00 0.00 46.86 4.45
5187 5278 5.186797 TCACATGGGAATACATTGAAAACCC 59.813 40.000 0.00 0.00 36.72 4.11
5188 5279 6.279513 TCACATGGGAATACATTGAAAACC 57.720 37.500 0.00 0.00 0.00 3.27
5189 5280 8.776376 ATTTCACATGGGAATACATTGAAAAC 57.224 30.769 12.06 0.00 39.00 2.43
5190 5281 9.790344 AAATTTCACATGGGAATACATTGAAAA 57.210 25.926 12.06 0.00 39.00 2.29
5191 5282 9.790344 AAAATTTCACATGGGAATACATTGAAA 57.210 25.926 12.06 7.91 39.36 2.69
5192 5283 9.217278 CAAAATTTCACATGGGAATACATTGAA 57.783 29.630 12.06 0.00 31.94 2.69
5193 5284 8.373981 ACAAAATTTCACATGGGAATACATTGA 58.626 29.630 22.33 5.92 0.00 2.57
5194 5285 8.444715 CACAAAATTTCACATGGGAATACATTG 58.555 33.333 12.06 15.62 0.00 2.82
5195 5286 8.156165 ACACAAAATTTCACATGGGAATACATT 58.844 29.630 12.06 5.74 0.00 2.71
5196 5287 7.678837 ACACAAAATTTCACATGGGAATACAT 58.321 30.769 12.06 0.00 0.00 2.29
5197 5288 7.060383 ACACAAAATTTCACATGGGAATACA 57.940 32.000 12.06 0.00 0.00 2.29
5198 5289 9.482627 TTTACACAAAATTTCACATGGGAATAC 57.517 29.630 12.06 0.00 0.00 1.89
5200 5291 8.970859 TTTTACACAAAATTTCACATGGGAAT 57.029 26.923 12.06 0.00 0.00 3.01
5201 5292 8.792830 TTTTTACACAAAATTTCACATGGGAA 57.207 26.923 6.21 6.21 33.72 3.97
5202 5293 8.970859 ATTTTTACACAAAATTTCACATGGGA 57.029 26.923 0.00 0.00 33.72 4.37
5222 5313 7.920682 GCCACCGATATGTTTTCTGATATTTTT 59.079 33.333 0.00 0.00 0.00 1.94
5223 5314 7.068103 TGCCACCGATATGTTTTCTGATATTTT 59.932 33.333 0.00 0.00 0.00 1.82
5224 5315 6.545666 TGCCACCGATATGTTTTCTGATATTT 59.454 34.615 0.00 0.00 0.00 1.40
5225 5316 6.061441 TGCCACCGATATGTTTTCTGATATT 58.939 36.000 0.00 0.00 0.00 1.28
5226 5317 5.620206 TGCCACCGATATGTTTTCTGATAT 58.380 37.500 0.00 0.00 0.00 1.63
5227 5318 5.029807 TGCCACCGATATGTTTTCTGATA 57.970 39.130 0.00 0.00 0.00 2.15
5228 5319 3.884895 TGCCACCGATATGTTTTCTGAT 58.115 40.909 0.00 0.00 0.00 2.90
5229 5320 3.342377 TGCCACCGATATGTTTTCTGA 57.658 42.857 0.00 0.00 0.00 3.27
5230 5321 4.414852 CTTTGCCACCGATATGTTTTCTG 58.585 43.478 0.00 0.00 0.00 3.02
5231 5322 4.701956 CTTTGCCACCGATATGTTTTCT 57.298 40.909 0.00 0.00 0.00 2.52



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

AutoCloner maintained by Alex Coulton.