Multiple sequence alignment - TraesCS4D01G024800

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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 TraesCS4D01G024800 chr4D 100.000 2807 0 0 1 2807 10828225 10831031 0.000000e+00 5184.0
1 TraesCS4D01G024800 chr4D 98.041 2603 47 3 208 2807 10810663 10813264 0.000000e+00 4521.0
2 TraesCS4D01G024800 chr4D 91.477 352 28 2 2059 2409 10881872 10881522 1.510000e-132 483.0
3 TraesCS4D01G024800 chr4D 96.789 218 5 2 4 220 426711544 426711328 2.060000e-96 363.0
4 TraesCS4D01G024800 chr4D 91.765 255 16 3 2555 2807 10881502 10881251 1.600000e-92 350.0
5 TraesCS4D01G024800 chr4A 91.349 1572 113 11 365 1931 591674292 591675845 0.000000e+00 2128.0
6 TraesCS4D01G024800 chr4A 91.163 1573 116 11 364 1931 592927989 592926435 0.000000e+00 2113.0
7 TraesCS4D01G024800 chr4A 91.100 1573 117 11 364 1931 591346787 591348341 0.000000e+00 2108.0
8 TraesCS4D01G024800 chr4A 91.036 1573 116 12 364 1931 591416306 591417858 0.000000e+00 2100.0
9 TraesCS4D01G024800 chr4A 90.909 1573 118 13 364 1931 591293021 591294573 0.000000e+00 2089.0
10 TraesCS4D01G024800 chr4A 90.655 1573 123 13 364 1931 592336335 592334782 0.000000e+00 2069.0
11 TraesCS4D01G024800 chr4A 90.464 1573 128 12 364 1931 592362657 592361102 0.000000e+00 2054.0
12 TraesCS4D01G024800 chr4A 90.879 1524 115 12 364 1882 592310378 592308874 0.000000e+00 2023.0
13 TraesCS4D01G024800 chr4A 89.024 164 17 1 2056 2218 591694066 591693903 4.740000e-48 202.0
14 TraesCS4D01G024800 chr4A 92.727 110 8 0 2450 2559 479776357 479776466 2.890000e-35 159.0
15 TraesCS4D01G024800 chr4A 88.148 135 14 2 233 365 591292860 591292994 2.890000e-35 159.0
16 TraesCS4D01G024800 chr4A 88.148 135 14 2 233 365 591346626 591346760 2.890000e-35 159.0
17 TraesCS4D01G024800 chr4A 88.148 135 14 2 233 365 591416145 591416279 2.890000e-35 159.0
18 TraesCS4D01G024800 chr4A 88.148 135 14 2 233 365 591674130 591674264 2.890000e-35 159.0
19 TraesCS4D01G024800 chr4A 88.148 135 14 2 233 365 592310539 592310405 2.890000e-35 159.0
20 TraesCS4D01G024800 chr4A 88.148 135 14 2 233 365 592638766 592638632 2.890000e-35 159.0
21 TraesCS4D01G024800 chr4A 88.148 135 14 2 233 365 592928150 592928016 2.890000e-35 159.0
22 TraesCS4D01G024800 chr4B 95.389 759 29 5 2054 2807 20356031 20356788 0.000000e+00 1203.0
23 TraesCS4D01G024800 chr4B 89.351 385 37 4 2028 2409 20370419 20370036 5.440000e-132 481.0
24 TraesCS4D01G024800 chr4B 90.588 255 19 3 2555 2807 20370016 20369765 1.610000e-87 333.0
25 TraesCS4D01G024800 chr4B 92.105 152 12 0 214 365 20354295 20354446 6.090000e-52 215.0
26 TraesCS4D01G024800 chr4B 96.491 114 4 0 1941 2054 452855079 452854966 3.690000e-44 189.0
27 TraesCS4D01G024800 chr3D 97.248 218 4 2 4 220 337440644 337440428 4.420000e-98 368.0
28 TraesCS4D01G024800 chr3D 96.380 221 6 2 1 220 528167804 528168023 2.060000e-96 363.0
29 TraesCS4D01G024800 chr7D 96.380 221 6 2 1 220 293221819 293222038 2.060000e-96 363.0
30 TraesCS4D01G024800 chr7D 96.380 221 6 2 1 220 477608743 477608962 2.060000e-96 363.0
31 TraesCS4D01G024800 chr7D 94.915 118 6 0 1938 2055 545698742 545698859 4.770000e-43 185.0
32 TraesCS4D01G024800 chr6D 96.380 221 6 2 1 220 37619518 37619737 2.060000e-96 363.0
33 TraesCS4D01G024800 chr6D 92.727 110 8 0 2450 2559 110796015 110796124 2.890000e-35 159.0
34 TraesCS4D01G024800 chr5D 96.380 221 6 2 1 220 450181642 450181861 2.060000e-96 363.0
35 TraesCS4D01G024800 chr2D 96.380 221 6 2 1 220 307817685 307817904 2.060000e-96 363.0
36 TraesCS4D01G024800 chr2D 96.380 221 6 2 1 220 310157636 310157855 2.060000e-96 363.0
37 TraesCS4D01G024800 chr2D 95.798 119 4 1 1938 2056 617397866 617397749 1.030000e-44 191.0
38 TraesCS4D01G024800 chr6B 97.321 112 3 0 1947 2058 460495301 460495412 1.030000e-44 191.0
39 TraesCS4D01G024800 chr2A 97.321 112 3 0 1945 2056 758757136 758757247 1.030000e-44 191.0
40 TraesCS4D01G024800 chr2B 97.297 111 3 0 1946 2056 501608021 501608131 3.690000e-44 189.0
41 TraesCS4D01G024800 chr1B 97.297 111 3 0 1946 2056 476016021 476016131 3.690000e-44 189.0
42 TraesCS4D01G024800 chr1D 96.396 111 4 0 1947 2057 47705840 47705730 1.720000e-42 183.0
43 TraesCS4D01G024800 chr7B 92.727 110 8 0 2450 2559 68489503 68489612 2.890000e-35 159.0
44 TraesCS4D01G024800 chr7B 92.727 110 8 0 2450 2559 163823256 163823147 2.890000e-35 159.0
45 TraesCS4D01G024800 chr5B 92.727 110 8 0 2450 2559 383646690 383646799 2.890000e-35 159.0
46 TraesCS4D01G024800 chr7A 89.431 123 13 0 2450 2572 729073329 729073207 3.740000e-34 156.0
47 TraesCS4D01G024800 chr1A 90.517 116 10 1 2447 2562 384334444 384334558 4.840000e-33 152.0
48 TraesCS4D01G024800 chr3B 90.769 65 5 1 2589 2653 580469793 580469730 4.980000e-13 86.1


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 TraesCS4D01G024800 chr4D 10828225 10831031 2806 False 5184.0 5184 100.0000 1 2807 1 chr4D.!!$F2 2806
1 TraesCS4D01G024800 chr4D 10810663 10813264 2601 False 4521.0 4521 98.0410 208 2807 1 chr4D.!!$F1 2599
2 TraesCS4D01G024800 chr4D 10881251 10881872 621 True 416.5 483 91.6210 2059 2807 2 chr4D.!!$R2 748
3 TraesCS4D01G024800 chr4A 592334782 592336335 1553 True 2069.0 2069 90.6550 364 1931 1 chr4A.!!$R2 1567
4 TraesCS4D01G024800 chr4A 592361102 592362657 1555 True 2054.0 2054 90.4640 364 1931 1 chr4A.!!$R3 1567
5 TraesCS4D01G024800 chr4A 591674130 591675845 1715 False 1143.5 2128 89.7485 233 1931 2 chr4A.!!$F5 1698
6 TraesCS4D01G024800 chr4A 592926435 592928150 1715 True 1136.0 2113 89.6555 233 1931 2 chr4A.!!$R6 1698
7 TraesCS4D01G024800 chr4A 591346626 591348341 1715 False 1133.5 2108 89.6240 233 1931 2 chr4A.!!$F3 1698
8 TraesCS4D01G024800 chr4A 591416145 591417858 1713 False 1129.5 2100 89.5920 233 1931 2 chr4A.!!$F4 1698
9 TraesCS4D01G024800 chr4A 591292860 591294573 1713 False 1124.0 2089 89.5285 233 1931 2 chr4A.!!$F2 1698
10 TraesCS4D01G024800 chr4A 592308874 592310539 1665 True 1091.0 2023 89.5135 233 1882 2 chr4A.!!$R5 1649
11 TraesCS4D01G024800 chr4B 20354295 20356788 2493 False 709.0 1203 93.7470 214 2807 2 chr4B.!!$F1 2593
12 TraesCS4D01G024800 chr4B 20369765 20370419 654 True 407.0 481 89.9695 2028 2807 2 chr4B.!!$R2 779

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
180 181 0.177604 GATCTGAGTCTGGCCACTGG 59.822 60.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1941 1994 2.159324 CCGAACGGAGGGAGTACTTAAC 60.159 54.545 7.53 0.0 37.5 2.01 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
19 20 3.155167 CTCCCGGTAGAGGTGGGC 61.155 72.222 0.00 0.00 42.98 5.36
20 21 4.791069 TCCCGGTAGAGGTGGGCC 62.791 72.222 0.00 0.00 42.98 5.80
29 30 3.590574 AGGTGGGCCTTGGTTCCC 61.591 66.667 4.53 0.00 44.18 3.97
31 32 3.961414 GTGGGCCTTGGTTCCCGA 61.961 66.667 4.53 0.00 45.60 5.14
32 33 3.961414 TGGGCCTTGGTTCCCGAC 61.961 66.667 4.53 0.00 45.60 4.79
54 55 3.226884 CCCCCGACTGTTACTTGTG 57.773 57.895 0.00 0.00 0.00 3.33
55 56 0.321298 CCCCCGACTGTTACTTGTGG 60.321 60.000 0.00 0.00 0.00 4.17
56 57 0.953960 CCCCGACTGTTACTTGTGGC 60.954 60.000 0.00 0.00 0.00 5.01
57 58 1.289109 CCCGACTGTTACTTGTGGCG 61.289 60.000 0.00 0.00 0.00 5.69
58 59 1.289109 CCGACTGTTACTTGTGGCGG 61.289 60.000 0.00 0.00 0.00 6.13
59 60 0.319211 CGACTGTTACTTGTGGCGGA 60.319 55.000 0.00 0.00 0.00 5.54
60 61 1.429463 GACTGTTACTTGTGGCGGAG 58.571 55.000 0.00 0.00 0.00 4.63
74 75 4.021925 GGAGCGACAGGGCAGGTT 62.022 66.667 0.00 0.00 34.64 3.50
75 76 2.743928 GAGCGACAGGGCAGGTTG 60.744 66.667 0.00 0.00 34.64 3.77
76 77 3.240134 GAGCGACAGGGCAGGTTGA 62.240 63.158 0.00 0.00 34.64 3.18
77 78 2.743928 GCGACAGGGCAGGTTGAG 60.744 66.667 0.00 0.00 0.00 3.02
78 79 3.059982 CGACAGGGCAGGTTGAGA 58.940 61.111 0.00 0.00 0.00 3.27
79 80 1.374758 CGACAGGGCAGGTTGAGAC 60.375 63.158 0.00 0.00 0.00 3.36
80 81 1.003233 GACAGGGCAGGTTGAGACC 60.003 63.158 0.00 0.00 46.92 3.85
90 91 2.233305 GGTTGAGACCACCTAGGAGA 57.767 55.000 17.98 0.00 45.77 3.71
91 92 2.104170 GGTTGAGACCACCTAGGAGAG 58.896 57.143 17.98 5.82 45.77 3.20
92 93 2.291670 GGTTGAGACCACCTAGGAGAGA 60.292 54.545 17.98 0.00 45.77 3.10
93 94 3.020984 GTTGAGACCACCTAGGAGAGAG 58.979 54.545 17.98 1.19 41.22 3.20
94 95 1.566703 TGAGACCACCTAGGAGAGAGG 59.433 57.143 17.98 11.16 41.22 3.69
99 100 1.311747 ACCTAGGAGAGAGGTGGGC 59.688 63.158 17.98 0.00 45.90 5.36
100 101 1.458588 CCTAGGAGAGAGGTGGGCC 60.459 68.421 1.05 0.00 0.00 5.80
125 126 4.557605 GGTCGGCGTTCGCGGATA 62.558 66.667 24.65 6.43 41.25 2.59
126 127 3.317795 GTCGGCGTTCGCGGATAC 61.318 66.667 24.65 13.45 41.25 2.24
127 128 3.511595 TCGGCGTTCGCGGATACT 61.512 61.111 19.92 0.00 41.67 2.12
128 129 2.581409 CGGCGTTCGCGGATACTT 60.581 61.111 17.26 0.00 41.67 2.24
129 130 2.574222 CGGCGTTCGCGGATACTTC 61.574 63.158 17.26 0.00 41.67 3.01
130 131 1.517694 GGCGTTCGCGGATACTTCA 60.518 57.895 6.13 0.00 41.67 3.02
131 132 1.079875 GGCGTTCGCGGATACTTCAA 61.080 55.000 6.13 0.00 41.67 2.69
132 133 0.928229 GCGTTCGCGGATACTTCAAT 59.072 50.000 6.13 0.00 41.67 2.57
133 134 1.326548 GCGTTCGCGGATACTTCAATT 59.673 47.619 6.13 0.00 41.67 2.32
134 135 2.536803 GCGTTCGCGGATACTTCAATTA 59.463 45.455 6.13 0.00 41.67 1.40
135 136 3.000523 GCGTTCGCGGATACTTCAATTAA 59.999 43.478 6.13 0.00 41.67 1.40
136 137 4.502558 CGTTCGCGGATACTTCAATTAAC 58.497 43.478 6.13 0.00 36.88 2.01
137 138 4.031991 CGTTCGCGGATACTTCAATTAACA 59.968 41.667 6.13 0.00 36.88 2.41
138 139 5.253335 GTTCGCGGATACTTCAATTAACAC 58.747 41.667 6.13 0.00 0.00 3.32
139 140 3.548668 TCGCGGATACTTCAATTAACACG 59.451 43.478 6.13 0.00 0.00 4.49
140 141 3.604392 GCGGATACTTCAATTAACACGC 58.396 45.455 0.00 0.00 36.46 5.34
141 142 3.308866 GCGGATACTTCAATTAACACGCT 59.691 43.478 0.00 0.00 40.09 5.07
142 143 4.201783 GCGGATACTTCAATTAACACGCTT 60.202 41.667 0.00 0.00 40.09 4.68
143 144 5.005971 GCGGATACTTCAATTAACACGCTTA 59.994 40.000 0.00 0.00 40.09 3.09
144 145 6.455913 GCGGATACTTCAATTAACACGCTTAA 60.456 38.462 0.00 0.00 40.09 1.85
145 146 7.117454 CGGATACTTCAATTAACACGCTTAAG 58.883 38.462 0.00 0.00 0.00 1.85
146 147 7.407337 GGATACTTCAATTAACACGCTTAAGG 58.593 38.462 4.29 0.00 0.00 2.69
147 148 7.279313 GGATACTTCAATTAACACGCTTAAGGA 59.721 37.037 4.29 0.00 0.00 3.36
148 149 6.481954 ACTTCAATTAACACGCTTAAGGAG 57.518 37.500 4.29 0.00 0.00 3.69
149 150 5.995897 ACTTCAATTAACACGCTTAAGGAGT 59.004 36.000 4.29 0.00 0.00 3.85
150 151 6.485648 ACTTCAATTAACACGCTTAAGGAGTT 59.514 34.615 4.29 8.01 0.00 3.01
151 152 6.476243 TCAATTAACACGCTTAAGGAGTTC 57.524 37.500 4.29 0.00 0.00 3.01
152 153 6.228258 TCAATTAACACGCTTAAGGAGTTCT 58.772 36.000 4.29 0.00 0.00 3.01
153 154 6.708949 TCAATTAACACGCTTAAGGAGTTCTT 59.291 34.615 4.29 0.00 39.40 2.52
154 155 5.917541 TTAACACGCTTAAGGAGTTCTTG 57.082 39.130 4.29 0.00 36.93 3.02
155 156 2.767505 ACACGCTTAAGGAGTTCTTGG 58.232 47.619 4.29 0.00 36.93 3.61
156 157 2.104281 ACACGCTTAAGGAGTTCTTGGT 59.896 45.455 4.29 0.00 36.93 3.67
157 158 3.322828 ACACGCTTAAGGAGTTCTTGGTA 59.677 43.478 4.29 0.00 36.93 3.25
158 159 4.020485 ACACGCTTAAGGAGTTCTTGGTAT 60.020 41.667 4.29 0.00 36.93 2.73
159 160 4.935808 CACGCTTAAGGAGTTCTTGGTATT 59.064 41.667 4.29 0.00 36.93 1.89
160 161 5.411669 CACGCTTAAGGAGTTCTTGGTATTT 59.588 40.000 4.29 0.00 36.93 1.40
161 162 5.411669 ACGCTTAAGGAGTTCTTGGTATTTG 59.588 40.000 4.29 0.00 36.93 2.32
162 163 5.642063 CGCTTAAGGAGTTCTTGGTATTTGA 59.358 40.000 4.29 0.00 36.93 2.69
163 164 6.316390 CGCTTAAGGAGTTCTTGGTATTTGAT 59.684 38.462 4.29 0.00 36.93 2.57
164 165 7.466050 CGCTTAAGGAGTTCTTGGTATTTGATC 60.466 40.741 4.29 0.00 36.93 2.92
165 166 7.554476 GCTTAAGGAGTTCTTGGTATTTGATCT 59.446 37.037 4.29 0.00 36.93 2.75
166 167 8.792830 TTAAGGAGTTCTTGGTATTTGATCTG 57.207 34.615 0.00 0.00 36.93 2.90
167 168 6.627087 AGGAGTTCTTGGTATTTGATCTGA 57.373 37.500 0.00 0.00 0.00 3.27
168 169 6.648192 AGGAGTTCTTGGTATTTGATCTGAG 58.352 40.000 0.00 0.00 0.00 3.35
169 170 6.214412 AGGAGTTCTTGGTATTTGATCTGAGT 59.786 38.462 0.00 0.00 0.00 3.41
170 171 6.536941 GGAGTTCTTGGTATTTGATCTGAGTC 59.463 42.308 0.00 0.00 0.00 3.36
171 172 7.251321 AGTTCTTGGTATTTGATCTGAGTCT 57.749 36.000 0.00 0.00 0.00 3.24
172 173 7.102346 AGTTCTTGGTATTTGATCTGAGTCTG 58.898 38.462 0.00 0.00 0.00 3.51
173 174 5.982356 TCTTGGTATTTGATCTGAGTCTGG 58.018 41.667 0.00 0.00 0.00 3.86
174 175 4.142609 TGGTATTTGATCTGAGTCTGGC 57.857 45.455 0.00 0.00 0.00 4.85
175 176 3.118261 TGGTATTTGATCTGAGTCTGGCC 60.118 47.826 0.00 0.00 0.00 5.36
176 177 3.118261 GGTATTTGATCTGAGTCTGGCCA 60.118 47.826 4.71 4.71 0.00 5.36
177 178 2.479566 TTTGATCTGAGTCTGGCCAC 57.520 50.000 0.00 0.00 0.00 5.01
178 179 1.649321 TTGATCTGAGTCTGGCCACT 58.351 50.000 0.00 0.00 0.00 4.00
179 180 0.900421 TGATCTGAGTCTGGCCACTG 59.100 55.000 0.00 0.00 0.00 3.66
180 181 0.177604 GATCTGAGTCTGGCCACTGG 59.822 60.000 0.00 0.00 0.00 4.00
190 191 2.504032 GCCACTGGCCTATACGCA 59.496 61.111 9.13 0.00 44.06 5.24
191 192 1.887707 GCCACTGGCCTATACGCAC 60.888 63.158 9.13 0.00 44.06 5.34
192 193 1.823295 CCACTGGCCTATACGCACT 59.177 57.895 3.32 0.00 0.00 4.40
193 194 1.037493 CCACTGGCCTATACGCACTA 58.963 55.000 3.32 0.00 0.00 2.74
194 195 1.411246 CCACTGGCCTATACGCACTAA 59.589 52.381 3.32 0.00 0.00 2.24
195 196 2.470821 CACTGGCCTATACGCACTAAC 58.529 52.381 3.32 0.00 0.00 2.34
196 197 1.411612 ACTGGCCTATACGCACTAACC 59.588 52.381 3.32 0.00 0.00 2.85
197 198 1.411246 CTGGCCTATACGCACTAACCA 59.589 52.381 3.32 0.00 0.00 3.67
198 199 1.832366 TGGCCTATACGCACTAACCAA 59.168 47.619 3.32 0.00 0.00 3.67
199 200 2.207590 GGCCTATACGCACTAACCAAC 58.792 52.381 0.00 0.00 0.00 3.77
200 201 2.159000 GGCCTATACGCACTAACCAACT 60.159 50.000 0.00 0.00 0.00 3.16
201 202 3.068590 GGCCTATACGCACTAACCAACTA 59.931 47.826 0.00 0.00 0.00 2.24
202 203 4.047142 GCCTATACGCACTAACCAACTAC 58.953 47.826 0.00 0.00 0.00 2.73
203 204 4.285292 CCTATACGCACTAACCAACTACG 58.715 47.826 0.00 0.00 0.00 3.51
204 205 1.981254 TACGCACTAACCAACTACGC 58.019 50.000 0.00 0.00 0.00 4.42
205 206 1.005294 ACGCACTAACCAACTACGCG 61.005 55.000 3.53 3.53 46.14 6.01
206 207 1.680105 CGCACTAACCAACTACGCGG 61.680 60.000 12.47 0.00 37.72 6.46
207 208 1.356527 GCACTAACCAACTACGCGGG 61.357 60.000 12.47 3.45 0.00 6.13
208 209 0.244450 CACTAACCAACTACGCGGGA 59.756 55.000 12.47 0.00 0.00 5.14
209 210 0.968405 ACTAACCAACTACGCGGGAA 59.032 50.000 12.47 0.00 0.00 3.97
210 211 1.337167 ACTAACCAACTACGCGGGAAC 60.337 52.381 12.47 0.00 0.00 3.62
211 212 0.678395 TAACCAACTACGCGGGAACA 59.322 50.000 12.47 0.00 0.00 3.18
212 213 0.601841 AACCAACTACGCGGGAACAG 60.602 55.000 12.47 1.50 0.00 3.16
226 227 1.270678 GGAACAGTTAAGGGACGCACT 60.271 52.381 0.00 0.00 0.00 4.40
229 230 3.314541 ACAGTTAAGGGACGCACTTAG 57.685 47.619 2.60 0.00 32.52 2.18
246 247 4.278170 CACTTAGAATCAGTTTTGGTGGCA 59.722 41.667 0.00 0.00 0.00 4.92
293 294 2.124570 GGCTCGCATGGTGGACAT 60.125 61.111 0.00 0.00 41.57 3.06
309 310 5.465390 GGTGGACATTTTGCTTTCCTAAAAC 59.535 40.000 0.00 0.00 0.00 2.43
332 333 3.113043 GAGGGAGGTAAGGGCTTTAGAA 58.887 50.000 0.00 0.00 0.00 2.10
548 579 5.539193 GGAGAGGATCCTATAAAGTTCGGAA 59.461 44.000 16.16 0.00 45.64 4.30
578 609 6.149142 AGGTTATTACGCCGAAAATGTTACAA 59.851 34.615 0.00 0.00 0.00 2.41
1074 1125 2.279517 CCAGCCATCTCGTACGCC 60.280 66.667 11.24 0.00 0.00 5.68
1547 1598 1.194121 GCTGCCCCCAAAAAGGACAT 61.194 55.000 0.00 0.00 41.22 3.06
1566 1617 1.212229 GTCCACCGTCTTCGACTCC 59.788 63.158 0.00 0.00 39.71 3.85
1941 1994 1.400371 CGGCGATCGATGACCTCTTAG 60.400 57.143 21.57 0.00 42.43 2.18
2302 2358 2.294074 ACAAGCAGCAGTCGGTTTTAA 58.706 42.857 0.00 0.00 0.00 1.52
2304 2360 3.129638 ACAAGCAGCAGTCGGTTTTAAAA 59.870 39.130 0.00 0.00 0.00 1.52
2308 2364 6.079424 AGCAGCAGTCGGTTTTAAAAATAA 57.921 33.333 1.31 0.00 0.00 1.40
2310 2366 7.151976 AGCAGCAGTCGGTTTTAAAAATAATT 58.848 30.769 1.31 0.00 0.00 1.40
2409 2465 1.339929 TGTGTGTCTCTATGTGTGCGT 59.660 47.619 0.00 0.00 0.00 5.24
2441 2497 7.464710 GCTTTTTCATACTGTCTGATTACCTCG 60.465 40.741 0.00 0.00 0.00 4.63
2502 2558 4.922206 TGAAGACATTTTAGGCCATCTGT 58.078 39.130 5.01 0.15 0.00 3.41
2594 2650 3.689649 CCGGCAGTGCTAGTAAGAAAAAT 59.310 43.478 16.11 0.00 0.00 1.82
2675 2732 6.405842 GCCATAACCCTTGTTTTCTTCCTATG 60.406 42.308 0.00 0.00 35.87 2.23
2683 2740 7.029563 CCTTGTTTTCTTCCTATGCATGTTAC 58.970 38.462 10.16 0.00 0.00 2.50
2712 2769 6.101650 TCGTAGAGATGCAACCATAATGAT 57.898 37.500 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.155167 GCCCACCTCTACCGGGAG 61.155 72.222 7.64 7.64 43.21 4.30
3 4 4.791069 GGCCCACCTCTACCGGGA 62.791 72.222 6.32 0.00 43.21 5.14
4 5 4.798682 AGGCCCACCTCTACCGGG 62.799 72.222 6.32 0.00 46.34 5.73
36 37 0.321298 CCACAAGTAACAGTCGGGGG 60.321 60.000 0.00 0.00 0.00 5.40
37 38 0.953960 GCCACAAGTAACAGTCGGGG 60.954 60.000 0.00 0.00 0.00 5.73
38 39 1.289109 CGCCACAAGTAACAGTCGGG 61.289 60.000 0.00 0.00 0.00 5.14
39 40 1.289109 CCGCCACAAGTAACAGTCGG 61.289 60.000 0.00 0.00 0.00 4.79
40 41 0.319211 TCCGCCACAAGTAACAGTCG 60.319 55.000 0.00 0.00 0.00 4.18
41 42 1.429463 CTCCGCCACAAGTAACAGTC 58.571 55.000 0.00 0.00 0.00 3.51
42 43 0.602905 GCTCCGCCACAAGTAACAGT 60.603 55.000 0.00 0.00 0.00 3.55
43 44 1.626654 CGCTCCGCCACAAGTAACAG 61.627 60.000 0.00 0.00 0.00 3.16
44 45 1.666553 CGCTCCGCCACAAGTAACA 60.667 57.895 0.00 0.00 0.00 2.41
45 46 1.373748 TCGCTCCGCCACAAGTAAC 60.374 57.895 0.00 0.00 0.00 2.50
46 47 1.373748 GTCGCTCCGCCACAAGTAA 60.374 57.895 0.00 0.00 0.00 2.24
47 48 2.260434 GTCGCTCCGCCACAAGTA 59.740 61.111 0.00 0.00 0.00 2.24
48 49 3.865929 CTGTCGCTCCGCCACAAGT 62.866 63.158 0.00 0.00 0.00 3.16
49 50 3.114616 CTGTCGCTCCGCCACAAG 61.115 66.667 0.00 0.00 0.00 3.16
50 51 4.680237 CCTGTCGCTCCGCCACAA 62.680 66.667 0.00 0.00 0.00 3.33
57 58 4.021925 AACCTGCCCTGTCGCTCC 62.022 66.667 0.00 0.00 0.00 4.70
58 59 2.743928 CAACCTGCCCTGTCGCTC 60.744 66.667 0.00 0.00 0.00 5.03
59 60 3.241530 TCAACCTGCCCTGTCGCT 61.242 61.111 0.00 0.00 0.00 4.93
60 61 2.743928 CTCAACCTGCCCTGTCGC 60.744 66.667 0.00 0.00 0.00 5.19
61 62 1.374758 GTCTCAACCTGCCCTGTCG 60.375 63.158 0.00 0.00 0.00 4.35
62 63 1.003233 GGTCTCAACCTGCCCTGTC 60.003 63.158 0.00 0.00 42.80 3.51
63 64 1.770110 TGGTCTCAACCTGCCCTGT 60.770 57.895 0.00 0.00 46.60 4.00
64 65 1.302832 GTGGTCTCAACCTGCCCTG 60.303 63.158 0.00 0.00 46.60 4.45
65 66 2.529744 GGTGGTCTCAACCTGCCCT 61.530 63.158 0.00 0.00 46.60 5.19
66 67 1.198759 TAGGTGGTCTCAACCTGCCC 61.199 60.000 6.12 0.00 46.60 5.36
67 68 0.250513 CTAGGTGGTCTCAACCTGCC 59.749 60.000 6.12 0.77 46.60 4.85
68 69 0.250513 CCTAGGTGGTCTCAACCTGC 59.749 60.000 0.00 0.00 46.60 4.85
69 70 1.827969 CTCCTAGGTGGTCTCAACCTG 59.172 57.143 9.08 0.00 46.60 4.00
70 71 1.717077 TCTCCTAGGTGGTCTCAACCT 59.283 52.381 9.08 1.31 46.60 3.50
71 72 2.104170 CTCTCCTAGGTGGTCTCAACC 58.896 57.143 9.08 0.00 46.66 3.77
72 73 3.020984 CTCTCTCCTAGGTGGTCTCAAC 58.979 54.545 9.08 0.00 37.07 3.18
73 74 2.024846 CCTCTCTCCTAGGTGGTCTCAA 60.025 54.545 9.08 0.00 37.07 3.02
74 75 1.566703 CCTCTCTCCTAGGTGGTCTCA 59.433 57.143 9.08 0.00 37.07 3.27
75 76 1.567175 ACCTCTCTCCTAGGTGGTCTC 59.433 57.143 9.08 0.00 45.78 3.36
76 77 1.688750 ACCTCTCTCCTAGGTGGTCT 58.311 55.000 9.08 0.00 45.78 3.85
82 83 1.458588 GGCCCACCTCTCTCCTAGG 60.459 68.421 0.82 0.82 40.20 3.02
83 84 0.758685 CAGGCCCACCTCTCTCCTAG 60.759 65.000 0.00 0.00 46.34 3.02
84 85 1.311403 CAGGCCCACCTCTCTCCTA 59.689 63.158 0.00 0.00 46.34 2.94
85 86 2.040278 CAGGCCCACCTCTCTCCT 59.960 66.667 0.00 0.00 46.34 3.69
86 87 3.086600 CCAGGCCCACCTCTCTCC 61.087 72.222 0.00 0.00 46.34 3.71
87 88 3.791586 GCCAGGCCCACCTCTCTC 61.792 72.222 0.00 0.00 46.34 3.20
108 109 4.557605 TATCCGCGAACGCCGACC 62.558 66.667 8.23 0.00 41.76 4.79
109 110 3.317795 GTATCCGCGAACGCCGAC 61.318 66.667 8.23 3.19 41.76 4.79
110 111 2.924922 GAAGTATCCGCGAACGCCGA 62.925 60.000 8.23 12.49 41.76 5.54
111 112 2.574222 GAAGTATCCGCGAACGCCG 61.574 63.158 8.23 7.36 42.21 6.46
112 113 1.079875 TTGAAGTATCCGCGAACGCC 61.080 55.000 8.23 1.18 38.22 5.68
113 114 0.928229 ATTGAAGTATCCGCGAACGC 59.072 50.000 8.23 9.20 38.22 4.84
114 115 4.031991 TGTTAATTGAAGTATCCGCGAACG 59.968 41.667 8.23 0.00 39.67 3.95
115 116 5.253335 GTGTTAATTGAAGTATCCGCGAAC 58.747 41.667 8.23 2.36 0.00 3.95
116 117 4.031991 CGTGTTAATTGAAGTATCCGCGAA 59.968 41.667 8.23 0.00 0.00 4.70
117 118 3.548668 CGTGTTAATTGAAGTATCCGCGA 59.451 43.478 8.23 0.00 0.00 5.87
118 119 3.839954 GCGTGTTAATTGAAGTATCCGCG 60.840 47.826 0.00 0.00 0.00 6.46
119 120 3.308866 AGCGTGTTAATTGAAGTATCCGC 59.691 43.478 0.00 0.00 37.82 5.54
120 121 5.464965 AAGCGTGTTAATTGAAGTATCCG 57.535 39.130 0.00 0.00 0.00 4.18
121 122 7.279313 TCCTTAAGCGTGTTAATTGAAGTATCC 59.721 37.037 0.00 0.00 0.00 2.59
122 123 8.193250 TCCTTAAGCGTGTTAATTGAAGTATC 57.807 34.615 0.00 0.00 0.00 2.24
123 124 7.822822 ACTCCTTAAGCGTGTTAATTGAAGTAT 59.177 33.333 0.00 0.00 0.00 2.12
124 125 7.156673 ACTCCTTAAGCGTGTTAATTGAAGTA 58.843 34.615 0.00 0.00 0.00 2.24
125 126 5.995897 ACTCCTTAAGCGTGTTAATTGAAGT 59.004 36.000 0.00 0.00 0.00 3.01
126 127 6.481954 ACTCCTTAAGCGTGTTAATTGAAG 57.518 37.500 0.00 0.00 0.00 3.02
127 128 6.708949 AGAACTCCTTAAGCGTGTTAATTGAA 59.291 34.615 0.00 0.00 0.00 2.69
128 129 6.228258 AGAACTCCTTAAGCGTGTTAATTGA 58.772 36.000 0.00 0.00 0.00 2.57
129 130 6.481954 AGAACTCCTTAAGCGTGTTAATTG 57.518 37.500 0.00 0.00 0.00 2.32
130 131 6.072673 CCAAGAACTCCTTAAGCGTGTTAATT 60.073 38.462 0.00 1.54 32.86 1.40
131 132 5.411669 CCAAGAACTCCTTAAGCGTGTTAAT 59.588 40.000 0.00 0.00 32.86 1.40
132 133 4.753107 CCAAGAACTCCTTAAGCGTGTTAA 59.247 41.667 0.00 0.00 32.86 2.01
133 134 4.202284 ACCAAGAACTCCTTAAGCGTGTTA 60.202 41.667 0.00 0.00 32.86 2.41
134 135 3.139077 CCAAGAACTCCTTAAGCGTGTT 58.861 45.455 0.00 4.31 32.86 3.32
135 136 2.104281 ACCAAGAACTCCTTAAGCGTGT 59.896 45.455 0.00 0.00 32.86 4.49
136 137 2.767505 ACCAAGAACTCCTTAAGCGTG 58.232 47.619 0.00 0.00 32.86 5.34
137 138 4.820894 ATACCAAGAACTCCTTAAGCGT 57.179 40.909 0.00 0.00 32.86 5.07
138 139 5.642063 TCAAATACCAAGAACTCCTTAAGCG 59.358 40.000 0.00 0.00 32.86 4.68
139 140 7.554476 AGATCAAATACCAAGAACTCCTTAAGC 59.446 37.037 0.00 0.00 32.86 3.09
140 141 8.887717 CAGATCAAATACCAAGAACTCCTTAAG 58.112 37.037 0.00 0.00 32.86 1.85
141 142 8.602424 TCAGATCAAATACCAAGAACTCCTTAA 58.398 33.333 0.00 0.00 32.86 1.85
142 143 8.146053 TCAGATCAAATACCAAGAACTCCTTA 57.854 34.615 0.00 0.00 32.86 2.69
143 144 7.020827 TCAGATCAAATACCAAGAACTCCTT 57.979 36.000 0.00 0.00 34.91 3.36
144 145 6.214412 ACTCAGATCAAATACCAAGAACTCCT 59.786 38.462 0.00 0.00 0.00 3.69
145 146 6.410540 ACTCAGATCAAATACCAAGAACTCC 58.589 40.000 0.00 0.00 0.00 3.85
146 147 7.277539 CAGACTCAGATCAAATACCAAGAACTC 59.722 40.741 0.00 0.00 0.00 3.01
147 148 7.102346 CAGACTCAGATCAAATACCAAGAACT 58.898 38.462 0.00 0.00 0.00 3.01
148 149 6.314896 CCAGACTCAGATCAAATACCAAGAAC 59.685 42.308 0.00 0.00 0.00 3.01
149 150 6.409704 CCAGACTCAGATCAAATACCAAGAA 58.590 40.000 0.00 0.00 0.00 2.52
150 151 5.627735 GCCAGACTCAGATCAAATACCAAGA 60.628 44.000 0.00 0.00 0.00 3.02
151 152 4.574013 GCCAGACTCAGATCAAATACCAAG 59.426 45.833 0.00 0.00 0.00 3.61
152 153 4.517285 GCCAGACTCAGATCAAATACCAA 58.483 43.478 0.00 0.00 0.00 3.67
153 154 3.118261 GGCCAGACTCAGATCAAATACCA 60.118 47.826 0.00 0.00 0.00 3.25
154 155 3.118261 TGGCCAGACTCAGATCAAATACC 60.118 47.826 0.00 0.00 0.00 2.73
155 156 3.873952 GTGGCCAGACTCAGATCAAATAC 59.126 47.826 5.11 0.00 0.00 1.89
156 157 3.776969 AGTGGCCAGACTCAGATCAAATA 59.223 43.478 5.11 0.00 0.00 1.40
157 158 2.575279 AGTGGCCAGACTCAGATCAAAT 59.425 45.455 5.11 0.00 0.00 2.32
158 159 1.980765 AGTGGCCAGACTCAGATCAAA 59.019 47.619 5.11 0.00 0.00 2.69
159 160 1.277273 CAGTGGCCAGACTCAGATCAA 59.723 52.381 5.11 0.00 0.00 2.57
160 161 0.900421 CAGTGGCCAGACTCAGATCA 59.100 55.000 5.11 0.00 0.00 2.92
161 162 0.177604 CCAGTGGCCAGACTCAGATC 59.822 60.000 5.11 0.00 0.00 2.75
162 163 1.908340 GCCAGTGGCCAGACTCAGAT 61.908 60.000 24.53 0.00 44.06 2.90
163 164 2.587247 GCCAGTGGCCAGACTCAGA 61.587 63.158 24.53 0.00 44.06 3.27
164 165 2.046507 GCCAGTGGCCAGACTCAG 60.047 66.667 24.53 0.00 44.06 3.35
174 175 1.037493 TAGTGCGTATAGGCCAGTGG 58.963 55.000 14.48 4.20 0.00 4.00
175 176 2.470821 GTTAGTGCGTATAGGCCAGTG 58.529 52.381 14.48 0.00 0.00 3.66
176 177 1.411612 GGTTAGTGCGTATAGGCCAGT 59.588 52.381 14.48 8.26 0.00 4.00
177 178 1.411246 TGGTTAGTGCGTATAGGCCAG 59.589 52.381 14.48 0.00 0.00 4.85
178 179 1.487300 TGGTTAGTGCGTATAGGCCA 58.513 50.000 14.48 1.77 0.00 5.36
179 180 2.159000 AGTTGGTTAGTGCGTATAGGCC 60.159 50.000 14.48 0.00 0.00 5.19
180 181 3.175109 AGTTGGTTAGTGCGTATAGGC 57.825 47.619 10.48 10.48 0.00 3.93
181 182 4.285292 CGTAGTTGGTTAGTGCGTATAGG 58.715 47.826 0.00 0.00 31.58 2.57
182 183 3.727723 GCGTAGTTGGTTAGTGCGTATAG 59.272 47.826 0.00 0.00 37.57 1.31
183 184 3.694734 GCGTAGTTGGTTAGTGCGTATA 58.305 45.455 0.00 0.00 37.57 1.47
184 185 2.533266 GCGTAGTTGGTTAGTGCGTAT 58.467 47.619 0.00 0.00 37.57 3.06
185 186 1.728825 CGCGTAGTTGGTTAGTGCGTA 60.729 52.381 0.00 0.00 37.57 4.42
186 187 1.005294 CGCGTAGTTGGTTAGTGCGT 61.005 55.000 0.00 0.00 37.57 5.24
187 188 1.680105 CCGCGTAGTTGGTTAGTGCG 61.680 60.000 4.92 0.00 43.34 5.34
188 189 1.356527 CCCGCGTAGTTGGTTAGTGC 61.357 60.000 4.92 0.00 0.00 4.40
189 190 0.244450 TCCCGCGTAGTTGGTTAGTG 59.756 55.000 4.92 0.00 0.00 2.74
190 191 0.968405 TTCCCGCGTAGTTGGTTAGT 59.032 50.000 4.92 0.00 0.00 2.24
191 192 1.337074 TGTTCCCGCGTAGTTGGTTAG 60.337 52.381 4.92 0.00 0.00 2.34
192 193 0.678395 TGTTCCCGCGTAGTTGGTTA 59.322 50.000 4.92 0.00 0.00 2.85
193 194 0.601841 CTGTTCCCGCGTAGTTGGTT 60.602 55.000 4.92 0.00 0.00 3.67
194 195 1.005394 CTGTTCCCGCGTAGTTGGT 60.005 57.895 4.92 0.00 0.00 3.67
195 196 0.601841 AACTGTTCCCGCGTAGTTGG 60.602 55.000 4.92 0.00 32.56 3.77
196 197 2.068837 TAACTGTTCCCGCGTAGTTG 57.931 50.000 4.92 0.00 35.26 3.16
197 198 2.611224 CCTTAACTGTTCCCGCGTAGTT 60.611 50.000 4.92 9.86 37.21 2.24
198 199 1.067354 CCTTAACTGTTCCCGCGTAGT 60.067 52.381 4.92 0.00 0.00 2.73
199 200 1.636988 CCTTAACTGTTCCCGCGTAG 58.363 55.000 4.92 0.00 0.00 3.51
200 201 0.247185 CCCTTAACTGTTCCCGCGTA 59.753 55.000 4.92 0.00 0.00 4.42
201 202 1.004200 CCCTTAACTGTTCCCGCGT 60.004 57.895 4.92 0.00 0.00 6.01
202 203 1.017701 GTCCCTTAACTGTTCCCGCG 61.018 60.000 0.00 0.00 0.00 6.46
203 204 1.017701 CGTCCCTTAACTGTTCCCGC 61.018 60.000 0.00 0.00 0.00 6.13
204 205 1.017701 GCGTCCCTTAACTGTTCCCG 61.018 60.000 0.00 0.00 0.00 5.14
205 206 0.035739 TGCGTCCCTTAACTGTTCCC 59.964 55.000 0.00 0.00 0.00 3.97
206 207 1.154197 GTGCGTCCCTTAACTGTTCC 58.846 55.000 0.00 0.00 0.00 3.62
207 208 2.165319 AGTGCGTCCCTTAACTGTTC 57.835 50.000 0.00 0.00 0.00 3.18
208 209 2.632987 AAGTGCGTCCCTTAACTGTT 57.367 45.000 0.00 0.00 0.00 3.16
209 210 2.895404 TCTAAGTGCGTCCCTTAACTGT 59.105 45.455 0.00 0.00 0.00 3.55
210 211 3.587797 TCTAAGTGCGTCCCTTAACTG 57.412 47.619 0.00 0.00 0.00 3.16
211 212 4.222145 TGATTCTAAGTGCGTCCCTTAACT 59.778 41.667 0.00 0.00 0.00 2.24
212 213 4.501071 TGATTCTAAGTGCGTCCCTTAAC 58.499 43.478 0.00 0.00 0.00 2.01
226 227 5.136828 TCTTGCCACCAAAACTGATTCTAA 58.863 37.500 0.00 0.00 0.00 2.10
229 230 4.022068 TCATCTTGCCACCAAAACTGATTC 60.022 41.667 0.00 0.00 0.00 2.52
246 247 9.804977 CCATCTTTTTATTATCCTCCTCATCTT 57.195 33.333 0.00 0.00 0.00 2.40
293 294 5.205056 TCCCTCAGTTTTAGGAAAGCAAAA 58.795 37.500 0.00 0.00 36.08 2.44
309 310 1.290134 AAAGCCCTTACCTCCCTCAG 58.710 55.000 0.00 0.00 0.00 3.35
548 579 3.547054 TTCGGCGTAATAACCTTCCAT 57.453 42.857 6.85 0.00 0.00 3.41
578 609 2.283388 TTCGTAGGAGCCCGTGGT 60.283 61.111 0.00 0.00 0.00 4.16
639 674 2.695561 GGCCCACCCCATGAAAATT 58.304 52.632 0.00 0.00 0.00 1.82
1496 1547 2.357881 CTGCAGTGCTGAAGGCGA 60.358 61.111 17.60 0.00 45.43 5.54
1697 1748 2.235650 CTCAGGAAGGACTCAATGAGCA 59.764 50.000 10.62 0.00 34.49 4.26
1941 1994 2.159324 CCGAACGGAGGGAGTACTTAAC 60.159 54.545 7.53 0.00 37.50 2.01
2304 2360 9.603921 CATTCCAAATGGTAGCAAAGAATTATT 57.396 29.630 0.00 0.00 36.34 1.40
2308 2364 5.981174 CCATTCCAAATGGTAGCAAAGAAT 58.019 37.500 10.01 2.79 34.56 2.40
2365 2421 4.259570 CGCAATCTTCGTTGACACTATCTG 60.260 45.833 0.00 0.00 0.00 2.90
2409 2465 4.883083 AGACAGTATGAAAAAGCGTCTGA 58.117 39.130 0.00 0.00 39.69 3.27
2441 2497 9.523168 AGTGAATAGAGGGAGTACTTATGATAC 57.477 37.037 0.00 0.00 0.00 2.24
2491 2547 5.186256 TGGATTGTTTTACAGATGGCCTA 57.814 39.130 3.32 0.00 0.00 3.93
2494 2550 6.873076 TCAAAATGGATTGTTTTACAGATGGC 59.127 34.615 0.00 0.00 0.00 4.40
2502 2558 8.690884 TCAGACAACTCAAAATGGATTGTTTTA 58.309 29.630 0.00 0.00 33.76 1.52
2594 2650 8.567198 TTTGGAGGATTGAAATCTCTAGGATA 57.433 34.615 3.21 0.00 35.73 2.59
2675 2732 6.563010 GCATCTCTACGAATCAAGTAACATGC 60.563 42.308 0.00 0.00 0.00 4.06
2683 2740 4.183865 TGGTTGCATCTCTACGAATCAAG 58.816 43.478 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.