Multiple sequence alignment - TraesCS5D01G097300

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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 TraesCS5D01G097300 chr5D 100.000 3049 0 0 1 3049 108085442 108088490 0.000000e+00 5631.0
1 TraesCS5D01G097300 chr5B 91.259 2128 119 34 1 2101 118419372 118421459 0.000000e+00 2837.0
2 TraesCS5D01G097300 chr5B 91.741 787 37 10 2271 3049 118421471 118422237 0.000000e+00 1068.0
3 TraesCS5D01G097300 chr5B 75.546 458 92 13 189 629 306420012 306419558 1.110000e-49 207.0
4 TraesCS5D01G097300 chr5B 75.546 458 92 13 189 629 306420750 306420296 1.110000e-49 207.0
5 TraesCS5D01G097300 chr5B 75.546 458 92 13 189 629 306421488 306421034 1.110000e-49 207.0
6 TraesCS5D01G097300 chr5B 75.546 458 92 13 189 629 306422226 306421772 1.110000e-49 207.0
7 TraesCS5D01G097300 chr5B 75.556 315 62 12 283 590 510495015 510495321 1.140000e-29 141.0
8 TraesCS5D01G097300 chr5A 92.226 1325 58 17 801 2111 111553753 111555046 0.000000e+00 1834.0
9 TraesCS5D01G097300 chr5A 89.933 745 39 13 2334 3049 111555060 111555797 0.000000e+00 928.0
10 TraesCS5D01G097300 chr5A 85.221 724 78 8 93 788 111552872 111553594 0.000000e+00 717.0
11 TraesCS5D01G097300 chr5A 95.187 187 4 5 2089 2272 703668177 703668361 1.070000e-74 291.0
12 TraesCS5D01G097300 chr5A 76.718 451 87 13 197 629 359018059 359017609 5.080000e-58 235.0
13 TraesCS5D01G097300 chr5A 95.522 67 3 0 1 67 111552809 111552875 1.160000e-19 108.0
14 TraesCS5D01G097300 chr4D 98.266 173 3 0 2102 2274 211346689 211346861 1.370000e-78 303.0
15 TraesCS5D01G097300 chr4D 98.817 169 2 0 2104 2272 22027381 22027549 4.940000e-78 302.0
16 TraesCS5D01G097300 chr3D 99.401 167 1 0 2109 2275 513620196 513620362 1.370000e-78 303.0
17 TraesCS5D01G097300 chr7D 97.701 174 4 0 2108 2281 612142832 612142659 1.780000e-77 300.0
18 TraesCS5D01G097300 chr6D 97.714 175 3 1 2099 2273 141130966 141130793 1.780000e-77 300.0
19 TraesCS5D01G097300 chr4B 95.676 185 6 2 2090 2272 143897964 143898148 2.300000e-76 296.0
20 TraesCS5D01G097300 chr4A 96.111 180 6 1 2099 2278 570473039 570473217 2.970000e-75 292.0
21 TraesCS5D01G097300 chr2A 93.299 194 9 4 2096 2287 770140145 770139954 1.790000e-72 283.0
22 TraesCS5D01G097300 chr2B 74.232 423 79 18 197 590 460820742 460821163 1.890000e-32 150.0
23 TraesCS5D01G097300 chr3A 75.373 268 49 5 150 401 116517112 116517378 2.480000e-21 113.0
24 TraesCS5D01G097300 chr7A 74.729 277 52 13 336 596 697129085 697128811 1.160000e-19 108.0
25 TraesCS5D01G097300 chr1D 90.909 44 3 1 2588 2630 478981250 478981293 1.180000e-04 58.4


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 TraesCS5D01G097300 chr5D 108085442 108088490 3048 False 5631.00 5631 100.0000 1 3049 1 chr5D.!!$F1 3048
1 TraesCS5D01G097300 chr5B 118419372 118422237 2865 False 1952.50 2837 91.5000 1 3049 2 chr5B.!!$F2 3048
2 TraesCS5D01G097300 chr5B 306419558 306422226 2668 True 207.00 207 75.5460 189 629 4 chr5B.!!$R1 440
3 TraesCS5D01G097300 chr5A 111552809 111555797 2988 False 896.75 1834 90.7255 1 3049 4 chr5A.!!$F2 3048

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
586 2117 0.257039 GGGACTACGTCTACCCTCCA 59.743 60.0 14.09 0.0 39.28 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2257 4248 0.108945 CGTTGTACTCCCTCCGTTCC 60.109 60.0 0.0 0.0 0.0 3.62 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
77 90 4.671569 CCGCCGCTAGCTCATCCC 62.672 72.222 13.93 0.00 40.39 3.85
122 135 3.247056 TTCTCATTGGTGCCGCGGA 62.247 57.895 33.48 11.82 0.00 5.54
263 1024 4.783621 TCCTGGTGCCAGCGATGC 62.784 66.667 12.54 0.00 42.35 3.91
483 2008 3.695606 GCCACACTCGAGGAGGCA 61.696 66.667 28.84 0.00 44.59 4.75
563 2093 2.355837 GCGCTCCAGTTGTCGACA 60.356 61.111 15.76 15.76 0.00 4.35
574 2105 0.314935 TTGTCGACAACGGGGACTAC 59.685 55.000 26.53 0.00 40.21 2.73
586 2117 0.257039 GGGACTACGTCTACCCTCCA 59.743 60.000 14.09 0.00 39.28 3.86
593 2124 1.035932 CGTCTACCCTCCACCATCGT 61.036 60.000 0.00 0.00 0.00 3.73
609 2140 1.007271 CGTCGACACTGCCTGAACT 60.007 57.895 17.16 0.00 0.00 3.01
622 2154 2.214181 CTGAACTAGCGTCGGCCACT 62.214 60.000 2.24 0.00 41.24 4.00
711 2243 4.056125 CTGCGCGACTGGGTGAGA 62.056 66.667 12.10 0.00 0.00 3.27
810 2602 3.149648 GGGGAGCGGCAAATGCAT 61.150 61.111 7.80 0.00 44.36 3.96
821 2613 3.983343 GCAAATGCATGCAGAGTGCGT 62.983 52.381 27.11 9.19 44.68 5.24
832 2624 2.100252 GCAGAGTGCGTGGGTAGTATTA 59.900 50.000 0.00 0.00 31.71 0.98
1326 3297 2.434884 CATGGCTTCGACGCTGGT 60.435 61.111 14.02 0.00 0.00 4.00
1407 3378 4.223032 TCACCTCCTAGAAAATGTCTGTCC 59.777 45.833 0.00 0.00 37.12 4.02
1410 3381 4.425520 CTCCTAGAAAATGTCTGTCCGTC 58.574 47.826 0.00 0.00 37.12 4.79
1416 3387 4.281182 AGAAAATGTCTGTCCGTCAGTACT 59.719 41.667 0.00 0.00 43.97 2.73
1417 3388 5.475909 AGAAAATGTCTGTCCGTCAGTACTA 59.524 40.000 0.00 0.00 43.97 1.82
1418 3389 5.916661 AAATGTCTGTCCGTCAGTACTAT 57.083 39.130 0.00 0.00 43.97 2.12
1638 3611 7.527796 TCTAGTGGAGTTAGCTATAATCACCT 58.472 38.462 0.00 0.00 0.00 4.00
1733 3709 9.971922 AACTTTTTCAACTTGATAGAGAAATGG 57.028 29.630 6.73 0.00 32.94 3.16
1741 3717 1.070758 GATAGAGAAATGGGAGGCGCA 59.929 52.381 10.83 0.00 0.00 6.09
1743 3719 0.393537 AGAGAAATGGGAGGCGCAAG 60.394 55.000 10.83 0.00 43.44 4.01
1794 3781 4.361451 AGTGTGACAAAAGCTCTGTTTG 57.639 40.909 7.64 7.64 40.95 2.93
1798 3785 3.128589 GTGACAAAAGCTCTGTTTGGTGA 59.871 43.478 12.69 0.00 39.74 4.02
1806 3793 4.573900 AGCTCTGTTTGGTGATTACTGAG 58.426 43.478 0.00 0.00 39.45 3.35
1807 3794 4.040952 AGCTCTGTTTGGTGATTACTGAGT 59.959 41.667 0.00 0.00 38.99 3.41
1808 3795 5.246203 AGCTCTGTTTGGTGATTACTGAGTA 59.754 40.000 0.00 0.00 38.99 2.59
1809 3796 5.348997 GCTCTGTTTGGTGATTACTGAGTAC 59.651 44.000 0.00 0.00 38.99 2.73
1810 3797 6.665992 TCTGTTTGGTGATTACTGAGTACT 57.334 37.500 0.00 0.00 0.00 2.73
1934 3921 2.298446 AGTGCATGAGGTAGATGGATCG 59.702 50.000 0.00 0.00 0.00 3.69
2053 4040 1.472376 CGGATCTCAAGACTGAAGGCC 60.472 57.143 0.00 0.00 0.00 5.19
2065 4052 2.040412 ACTGAAGGCCTTTTCCTCGAAT 59.960 45.455 21.54 0.00 34.82 3.34
2119 4110 9.931698 TTTGTATATATGATATACTCCCTCCGT 57.068 33.333 14.60 0.00 32.98 4.69
2120 4111 9.931698 TTGTATATATGATATACTCCCTCCGTT 57.068 33.333 14.60 0.00 32.98 4.44
2121 4112 9.570468 TGTATATATGATATACTCCCTCCGTTC 57.430 37.037 14.60 0.00 32.98 3.95
2122 4113 9.012161 GTATATATGATATACTCCCTCCGTTCC 57.988 40.741 8.69 0.00 0.00 3.62
2123 4114 3.897657 TGATATACTCCCTCCGTTCCT 57.102 47.619 0.00 0.00 0.00 3.36
2124 4115 5.531753 ATGATATACTCCCTCCGTTCCTA 57.468 43.478 0.00 0.00 0.00 2.94
2125 4116 5.329191 TGATATACTCCCTCCGTTCCTAA 57.671 43.478 0.00 0.00 0.00 2.69
2126 4117 5.708544 TGATATACTCCCTCCGTTCCTAAA 58.291 41.667 0.00 0.00 0.00 1.85
2127 4118 6.320518 TGATATACTCCCTCCGTTCCTAAAT 58.679 40.000 0.00 0.00 0.00 1.40
2128 4119 7.472741 TGATATACTCCCTCCGTTCCTAAATA 58.527 38.462 0.00 0.00 0.00 1.40
2129 4120 8.120538 TGATATACTCCCTCCGTTCCTAAATAT 58.879 37.037 0.00 0.00 0.00 1.28
2130 4121 8.912614 ATATACTCCCTCCGTTCCTAAATATT 57.087 34.615 0.00 0.00 0.00 1.28
2131 4122 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2132 4123 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2133 4124 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2134 4125 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2135 4126 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2136 4127 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2137 4128 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2138 4129 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
2139 4130 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2140 4131 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2141 4132 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2142 4133 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2159 4150 9.436957 TCTTTCTAGACATTTCAAATGACTACC 57.563 33.333 17.30 1.06 0.00 3.18
2160 4151 9.219603 CTTTCTAGACATTTCAAATGACTACCA 57.780 33.333 17.30 5.07 0.00 3.25
2161 4152 8.547967 TTCTAGACATTTCAAATGACTACCAC 57.452 34.615 17.30 0.12 0.00 4.16
2162 4153 7.676004 TCTAGACATTTCAAATGACTACCACA 58.324 34.615 17.30 0.05 0.00 4.17
2163 4154 8.321353 TCTAGACATTTCAAATGACTACCACAT 58.679 33.333 17.30 0.00 0.00 3.21
2164 4155 9.599866 CTAGACATTTCAAATGACTACCACATA 57.400 33.333 17.30 0.00 0.00 2.29
2165 4156 8.268850 AGACATTTCAAATGACTACCACATAC 57.731 34.615 17.30 0.00 0.00 2.39
2166 4157 7.882791 AGACATTTCAAATGACTACCACATACA 59.117 33.333 17.30 0.00 0.00 2.29
2167 4158 8.044060 ACATTTCAAATGACTACCACATACAG 57.956 34.615 17.30 0.00 0.00 2.74
2168 4159 7.882791 ACATTTCAAATGACTACCACATACAGA 59.117 33.333 17.30 0.00 0.00 3.41
2169 4160 8.896744 CATTTCAAATGACTACCACATACAGAT 58.103 33.333 3.82 0.00 0.00 2.90
2170 4161 7.848223 TTCAAATGACTACCACATACAGATG 57.152 36.000 0.00 0.00 39.16 2.90
2172 4163 8.073467 TCAAATGACTACCACATACAGATGTA 57.927 34.615 0.00 0.00 44.82 2.29
2173 4164 8.704668 TCAAATGACTACCACATACAGATGTAT 58.295 33.333 0.00 0.00 44.82 2.29
2211 4202 5.220710 AGTGTAGATTCACTCAGTTTGCT 57.779 39.130 0.00 0.00 44.07 3.91
2212 4203 5.233988 AGTGTAGATTCACTCAGTTTGCTC 58.766 41.667 0.00 0.00 44.07 4.26
2213 4204 4.390297 GTGTAGATTCACTCAGTTTGCTCC 59.610 45.833 0.00 0.00 35.68 4.70
2214 4205 2.693069 AGATTCACTCAGTTTGCTCCG 58.307 47.619 0.00 0.00 0.00 4.63
2215 4206 2.037772 AGATTCACTCAGTTTGCTCCGT 59.962 45.455 0.00 0.00 0.00 4.69
2216 4207 3.258372 AGATTCACTCAGTTTGCTCCGTA 59.742 43.478 0.00 0.00 0.00 4.02
2217 4208 3.678056 TTCACTCAGTTTGCTCCGTAT 57.322 42.857 0.00 0.00 0.00 3.06
2218 4209 2.959516 TCACTCAGTTTGCTCCGTATG 58.040 47.619 0.00 0.00 0.00 2.39
2219 4210 2.299013 TCACTCAGTTTGCTCCGTATGT 59.701 45.455 0.00 0.00 0.00 2.29
2220 4211 3.508402 TCACTCAGTTTGCTCCGTATGTA 59.492 43.478 0.00 0.00 0.00 2.29
2221 4212 3.859961 CACTCAGTTTGCTCCGTATGTAG 59.140 47.826 0.00 0.00 0.00 2.74
2222 4213 3.510360 ACTCAGTTTGCTCCGTATGTAGT 59.490 43.478 0.00 0.00 0.00 2.73
2223 4214 4.106029 TCAGTTTGCTCCGTATGTAGTC 57.894 45.455 0.00 0.00 0.00 2.59
2224 4215 3.508402 TCAGTTTGCTCCGTATGTAGTCA 59.492 43.478 0.00 0.00 0.00 3.41
2225 4216 3.612860 CAGTTTGCTCCGTATGTAGTCAC 59.387 47.826 0.00 0.00 0.00 3.67
2226 4217 3.510360 AGTTTGCTCCGTATGTAGTCACT 59.490 43.478 0.00 0.00 0.00 3.41
2227 4218 4.021368 AGTTTGCTCCGTATGTAGTCACTT 60.021 41.667 0.00 0.00 0.00 3.16
2228 4219 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
2229 4220 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
2230 4221 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
2231 4222 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
2232 4223 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
2233 4224 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
2234 4225 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
2235 4226 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
2236 4227 6.367695 TCCGTATGTAGTCACTTGTTGAAATG 59.632 38.462 0.00 0.00 35.39 2.32
2237 4228 6.015504 CGTATGTAGTCACTTGTTGAAATGC 58.984 40.000 0.00 0.00 35.39 3.56
2238 4229 4.829064 TGTAGTCACTTGTTGAAATGCC 57.171 40.909 0.00 0.00 35.39 4.40
2239 4230 4.460263 TGTAGTCACTTGTTGAAATGCCT 58.540 39.130 0.00 0.00 35.39 4.75
2240 4231 5.616270 TGTAGTCACTTGTTGAAATGCCTA 58.384 37.500 0.00 0.00 35.39 3.93
2241 4232 5.700832 TGTAGTCACTTGTTGAAATGCCTAG 59.299 40.000 0.00 0.00 35.39 3.02
2242 4233 4.973168 AGTCACTTGTTGAAATGCCTAGA 58.027 39.130 0.00 0.00 35.39 2.43
2243 4234 5.376625 AGTCACTTGTTGAAATGCCTAGAA 58.623 37.500 0.00 0.00 35.39 2.10
2244 4235 5.827797 AGTCACTTGTTGAAATGCCTAGAAA 59.172 36.000 0.00 0.00 35.39 2.52
2245 4236 6.016777 AGTCACTTGTTGAAATGCCTAGAAAG 60.017 38.462 0.00 0.00 35.39 2.62
2246 4237 6.017109 GTCACTTGTTGAAATGCCTAGAAAGA 60.017 38.462 0.00 0.00 35.39 2.52
2247 4238 6.017109 TCACTTGTTGAAATGCCTAGAAAGAC 60.017 38.462 0.00 0.00 0.00 3.01
2248 4239 5.827797 ACTTGTTGAAATGCCTAGAAAGACA 59.172 36.000 0.00 0.00 0.00 3.41
2249 4240 6.321181 ACTTGTTGAAATGCCTAGAAAGACAA 59.679 34.615 0.00 0.00 0.00 3.18
2250 4241 6.317789 TGTTGAAATGCCTAGAAAGACAAG 57.682 37.500 0.00 0.00 0.00 3.16
2251 4242 5.827797 TGTTGAAATGCCTAGAAAGACAAGT 59.172 36.000 0.00 0.00 0.00 3.16
2252 4243 6.995686 TGTTGAAATGCCTAGAAAGACAAGTA 59.004 34.615 0.00 0.00 0.00 2.24
2253 4244 7.665559 TGTTGAAATGCCTAGAAAGACAAGTAT 59.334 33.333 0.00 0.00 0.00 2.12
2254 4245 8.515414 GTTGAAATGCCTAGAAAGACAAGTATT 58.485 33.333 0.00 0.00 0.00 1.89
2255 4246 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
2256 4247 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
2258 4249 8.738645 AATGCCTAGAAAGACAAGTATTTAGG 57.261 34.615 5.26 5.26 0.00 2.69
2259 4250 7.490657 TGCCTAGAAAGACAAGTATTTAGGA 57.509 36.000 11.40 0.00 26.70 2.94
2260 4251 7.913789 TGCCTAGAAAGACAAGTATTTAGGAA 58.086 34.615 11.40 1.02 26.70 3.36
2261 4252 7.822822 TGCCTAGAAAGACAAGTATTTAGGAAC 59.177 37.037 11.40 0.00 26.70 3.62
2262 4253 7.010275 GCCTAGAAAGACAAGTATTTAGGAACG 59.990 40.741 11.40 0.00 26.70 3.95
2263 4254 7.491696 CCTAGAAAGACAAGTATTTAGGAACGG 59.508 40.741 4.01 0.00 26.70 4.44
2264 4255 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
2265 4256 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
2266 4257 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
2267 4258 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
2268 4259 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
2269 4260 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
2270 4261 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
2275 4266 1.264295 AGGAACGGAGGGAGTACAAC 58.736 55.000 0.00 0.00 0.00 3.32
2277 4268 0.108945 GAACGGAGGGAGTACAACGG 60.109 60.000 0.00 0.00 0.00 4.44
2331 4322 4.142609 TCATTGCCCACATACTCTCTTC 57.857 45.455 0.00 0.00 0.00 2.87
2341 4332 5.879223 CCACATACTCTCTTCTTGCTTTGAT 59.121 40.000 0.00 0.00 0.00 2.57
2343 4334 7.550551 CCACATACTCTCTTCTTGCTTTGATTA 59.449 37.037 0.00 0.00 0.00 1.75
2385 4383 4.142988 TGCTAGCTTGTGTTTATGTAACGC 60.143 41.667 17.23 0.00 45.43 4.84
2409 4407 0.802222 GCGATTGTGCAGCGAGAGTA 60.802 55.000 0.00 0.00 34.15 2.59
2501 4500 6.952773 TCATATTTTGGGGCTTATGTGTAC 57.047 37.500 0.00 0.00 0.00 2.90
2652 4651 6.380095 TTGGTTCGCTAACAAGTTTACAAT 57.620 33.333 3.30 0.00 37.34 2.71
2668 4667 5.885230 TTACAATGTTCCATCTTCAGCAG 57.115 39.130 0.00 0.00 0.00 4.24
2701 4700 3.565307 AGAAACAAATGGCCAGACAGAA 58.435 40.909 13.05 0.00 0.00 3.02
2707 4714 8.995027 AAACAAATGGCCAGACAGAATATATA 57.005 30.769 13.05 0.00 0.00 0.86
2708 4715 9.592196 AAACAAATGGCCAGACAGAATATATAT 57.408 29.630 13.05 0.00 0.00 0.86
2709 4716 9.592196 AACAAATGGCCAGACAGAATATATATT 57.408 29.630 13.05 7.72 0.00 1.28
2710 4717 9.592196 ACAAATGGCCAGACAGAATATATATTT 57.408 29.630 13.05 0.00 0.00 1.40
2757 4764 0.109132 GGGCAAGAAAATGGCGACTG 60.109 55.000 0.00 0.00 46.12 3.51
2763 4770 2.069273 AGAAAATGGCGACTGAACTCG 58.931 47.619 0.00 0.00 36.70 4.18
2788 4795 3.111265 AGGGCCTTCACTTCCTGAT 57.889 52.632 0.00 0.00 0.00 2.90
2794 4801 3.526534 GCCTTCACTTCCTGATAGACAC 58.473 50.000 0.00 0.00 0.00 3.67
2850 4857 3.708631 AGAAATCTCCATGATCCGTCACT 59.291 43.478 0.00 0.00 37.14 3.41
2851 4858 3.742433 AATCTCCATGATCCGTCACTC 57.258 47.619 0.00 0.00 37.14 3.51
2852 4859 2.143876 TCTCCATGATCCGTCACTCA 57.856 50.000 0.00 0.00 37.14 3.41
2853 4860 2.027385 TCTCCATGATCCGTCACTCAG 58.973 52.381 0.00 0.00 37.14 3.35
2871 4878 2.486592 TCAGTCTCTGCGACAACGAATA 59.513 45.455 0.17 0.00 45.32 1.75
2882 4889 6.156519 TGCGACAACGAATATTAGCATCTAT 58.843 36.000 0.00 0.00 42.66 1.98
2960 4994 5.931146 TCAAATGGCATGACAAAATGTTACC 59.069 36.000 4.70 0.00 0.00 2.85
3035 5070 3.464907 CAATTTGTGTTGGCAATCCACA 58.535 40.909 16.85 16.85 43.33 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 135 3.764466 CCGGCGAGCTCTCCTTGT 61.764 66.667 20.16 0.00 0.00 3.16
256 1017 4.148825 GGAGACCACGGCATCGCT 62.149 66.667 0.00 0.00 40.63 4.93
483 2008 1.608717 CCTCAAGGGCGCACTAGAGT 61.609 60.000 15.36 0.00 0.00 3.24
527 2057 2.940467 TCCTCCATGCCTGGCCAA 60.940 61.111 17.53 0.00 42.80 4.52
574 2105 1.035932 ACGATGGTGGAGGGTAGACG 61.036 60.000 0.00 0.00 0.00 4.18
586 2117 2.261671 GGCAGTGTCGACGATGGT 59.738 61.111 18.17 0.00 0.00 3.55
593 2124 0.243907 GCTAGTTCAGGCAGTGTCGA 59.756 55.000 0.00 0.00 0.00 4.20
639 2171 0.392461 GTAATTCCAGCGTGGCCTCA 60.392 55.000 3.32 0.00 37.47 3.86
711 2243 3.092511 ATCCAGATGGCCGGTGCT 61.093 61.111 1.90 0.00 37.74 4.40
746 2278 2.240162 CTCAAGGTACACCGCCTCCC 62.240 65.000 0.00 0.00 42.08 4.30
755 2287 1.270625 CCTTTCACCGCTCAAGGTACA 60.271 52.381 0.00 0.00 43.89 2.90
793 2441 3.149648 ATGCATTTGCCGCTCCCC 61.150 61.111 0.00 0.00 41.18 4.81
794 2442 2.105528 CATGCATTTGCCGCTCCC 59.894 61.111 0.00 0.00 41.18 4.30
810 2602 0.896479 TACTACCCACGCACTCTGCA 60.896 55.000 0.00 0.00 45.36 4.41
813 2605 3.129988 GTGTAATACTACCCACGCACTCT 59.870 47.826 0.00 0.00 0.00 3.24
1269 3240 1.227674 GAAGATGCCGAGGCCGAAT 60.228 57.895 12.05 0.00 41.09 3.34
1416 3387 6.150976 GCCAGCAGCCACAACATTATTATATA 59.849 38.462 0.00 0.00 34.35 0.86
1417 3388 5.047802 GCCAGCAGCCACAACATTATTATAT 60.048 40.000 0.00 0.00 34.35 0.86
1418 3389 4.278170 GCCAGCAGCCACAACATTATTATA 59.722 41.667 0.00 0.00 34.35 0.98
1497 3468 8.187480 TGAATGTTTCCAAATATCATTACGGTG 58.813 33.333 0.00 0.00 0.00 4.94
1733 3709 2.768492 CCATGCTTCTTGCGCCTCC 61.768 63.158 4.18 0.00 46.63 4.30
1741 3717 6.610075 ATCCATTGTAAAACCATGCTTCTT 57.390 33.333 0.00 0.00 0.00 2.52
1743 3719 7.411804 CGAAAATCCATTGTAAAACCATGCTTC 60.412 37.037 0.00 0.00 0.00 3.86
1934 3921 6.430308 ACATATGAGCAAGATCCATCATTGAC 59.570 38.462 10.38 0.00 34.38 3.18
2053 4040 2.669391 GCAACTGCCATTCGAGGAAAAG 60.669 50.000 0.00 0.00 34.31 2.27
2096 4083 9.012161 GGAACGGAGGGAGTATATCATATATAC 57.988 40.741 8.42 8.42 0.00 1.47
2109 4100 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
2110 4101 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2111 4102 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2112 4103 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2113 4104 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2114 4105 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2115 4106 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2116 4107 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2133 4124 9.436957 GGTAGTCATTTGAAATGTCTAGAAAGA 57.563 33.333 19.92 3.04 0.00 2.52
2134 4125 9.219603 TGGTAGTCATTTGAAATGTCTAGAAAG 57.780 33.333 19.92 0.00 0.00 2.62
2135 4126 8.999431 GTGGTAGTCATTTGAAATGTCTAGAAA 58.001 33.333 19.92 9.72 0.00 2.52
2136 4127 8.154203 TGTGGTAGTCATTTGAAATGTCTAGAA 58.846 33.333 19.92 11.56 0.00 2.10
2137 4128 7.676004 TGTGGTAGTCATTTGAAATGTCTAGA 58.324 34.615 19.92 10.61 0.00 2.43
2138 4129 7.905604 TGTGGTAGTCATTTGAAATGTCTAG 57.094 36.000 19.92 0.00 0.00 2.43
2139 4130 9.378551 GTATGTGGTAGTCATTTGAAATGTCTA 57.621 33.333 16.93 16.93 0.00 2.59
2140 4131 7.882791 TGTATGTGGTAGTCATTTGAAATGTCT 59.117 33.333 18.62 18.62 0.00 3.41
2141 4132 8.039603 TGTATGTGGTAGTCATTTGAAATGTC 57.960 34.615 16.62 11.74 0.00 3.06
2142 4133 7.882791 TCTGTATGTGGTAGTCATTTGAAATGT 59.117 33.333 16.62 2.38 0.00 2.71
2143 4134 8.267620 TCTGTATGTGGTAGTCATTTGAAATG 57.732 34.615 11.54 11.54 0.00 2.32
2144 4135 8.896744 CATCTGTATGTGGTAGTCATTTGAAAT 58.103 33.333 0.00 0.00 0.00 2.17
2145 4136 7.882791 ACATCTGTATGTGGTAGTCATTTGAAA 59.117 33.333 0.00 0.00 44.79 2.69
2146 4137 7.394016 ACATCTGTATGTGGTAGTCATTTGAA 58.606 34.615 0.00 0.00 44.79 2.69
2147 4138 6.946340 ACATCTGTATGTGGTAGTCATTTGA 58.054 36.000 0.00 0.00 44.79 2.69
2148 4139 8.893219 ATACATCTGTATGTGGTAGTCATTTG 57.107 34.615 2.10 0.00 45.99 2.32
2190 4181 4.390297 GGAGCAAACTGAGTGAATCTACAC 59.610 45.833 0.00 0.00 40.60 2.90
2191 4182 4.569943 GGAGCAAACTGAGTGAATCTACA 58.430 43.478 0.00 0.00 0.00 2.74
2192 4183 3.614616 CGGAGCAAACTGAGTGAATCTAC 59.385 47.826 0.00 0.00 0.00 2.59
2193 4184 3.258372 ACGGAGCAAACTGAGTGAATCTA 59.742 43.478 0.00 0.00 0.00 1.98
2194 4185 2.037772 ACGGAGCAAACTGAGTGAATCT 59.962 45.455 0.00 0.00 0.00 2.40
2195 4186 2.417719 ACGGAGCAAACTGAGTGAATC 58.582 47.619 0.00 0.00 0.00 2.52
2196 4187 2.550830 ACGGAGCAAACTGAGTGAAT 57.449 45.000 0.00 0.00 0.00 2.57
2197 4188 3.244078 ACATACGGAGCAAACTGAGTGAA 60.244 43.478 0.00 0.00 0.00 3.18
2198 4189 2.299013 ACATACGGAGCAAACTGAGTGA 59.701 45.455 0.00 0.00 0.00 3.41
2199 4190 2.688507 ACATACGGAGCAAACTGAGTG 58.311 47.619 0.00 0.00 0.00 3.51
2200 4191 3.510360 ACTACATACGGAGCAAACTGAGT 59.490 43.478 0.00 0.00 0.00 3.41
2201 4192 4.106197 GACTACATACGGAGCAAACTGAG 58.894 47.826 0.00 0.00 0.00 3.35
2202 4193 3.508402 TGACTACATACGGAGCAAACTGA 59.492 43.478 0.00 0.00 0.00 3.41
2203 4194 3.612860 GTGACTACATACGGAGCAAACTG 59.387 47.826 0.00 0.00 0.00 3.16
2204 4195 3.510360 AGTGACTACATACGGAGCAAACT 59.490 43.478 0.00 0.00 0.00 2.66
2205 4196 3.846360 AGTGACTACATACGGAGCAAAC 58.154 45.455 0.00 0.00 0.00 2.93
2206 4197 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2207 4198 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
2208 4199 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
2209 4200 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
2210 4201 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2211 4202 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
2212 4203 6.534059 CATTTCAACAAGTGACTACATACGG 58.466 40.000 0.00 0.00 35.39 4.02
2213 4204 6.015504 GCATTTCAACAAGTGACTACATACG 58.984 40.000 0.00 0.00 35.39 3.06
2214 4205 6.149474 AGGCATTTCAACAAGTGACTACATAC 59.851 38.462 0.00 0.00 35.84 2.39
2215 4206 6.237901 AGGCATTTCAACAAGTGACTACATA 58.762 36.000 0.00 0.00 35.84 2.29
2216 4207 5.072741 AGGCATTTCAACAAGTGACTACAT 58.927 37.500 0.00 0.00 35.84 2.29
2217 4208 4.460263 AGGCATTTCAACAAGTGACTACA 58.540 39.130 0.00 0.00 35.84 2.74
2218 4209 5.932303 TCTAGGCATTTCAACAAGTGACTAC 59.068 40.000 0.00 0.00 38.51 2.73
2219 4210 6.109156 TCTAGGCATTTCAACAAGTGACTA 57.891 37.500 0.00 0.00 38.51 2.59
2220 4211 4.973168 TCTAGGCATTTCAACAAGTGACT 58.027 39.130 0.00 0.00 40.60 3.41
2221 4212 5.689383 TTCTAGGCATTTCAACAAGTGAC 57.311 39.130 0.00 0.00 35.39 3.67
2222 4213 6.017109 GTCTTTCTAGGCATTTCAACAAGTGA 60.017 38.462 0.00 0.00 0.00 3.41
2223 4214 6.145535 GTCTTTCTAGGCATTTCAACAAGTG 58.854 40.000 0.00 0.00 0.00 3.16
2224 4215 5.827797 TGTCTTTCTAGGCATTTCAACAAGT 59.172 36.000 0.00 0.00 29.10 3.16
2225 4216 6.317789 TGTCTTTCTAGGCATTTCAACAAG 57.682 37.500 0.00 0.00 29.10 3.16
2226 4217 6.321181 ACTTGTCTTTCTAGGCATTTCAACAA 59.679 34.615 0.00 0.00 35.56 2.83
2227 4218 5.827797 ACTTGTCTTTCTAGGCATTTCAACA 59.172 36.000 0.00 0.00 35.56 3.33
2228 4219 6.319141 ACTTGTCTTTCTAGGCATTTCAAC 57.681 37.500 0.00 0.00 35.56 3.18
2229 4220 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
2230 4221 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
2232 4223 9.178758 CCTAAATACTTGTCTTTCTAGGCATTT 57.821 33.333 0.00 0.00 35.56 2.32
2233 4224 8.548877 TCCTAAATACTTGTCTTTCTAGGCATT 58.451 33.333 0.00 0.00 35.56 3.56
2234 4225 8.090788 TCCTAAATACTTGTCTTTCTAGGCAT 57.909 34.615 0.00 0.00 35.56 4.40
2235 4226 7.490657 TCCTAAATACTTGTCTTTCTAGGCA 57.509 36.000 0.00 0.00 33.22 4.75
2236 4227 7.010275 CGTTCCTAAATACTTGTCTTTCTAGGC 59.990 40.741 0.00 0.00 0.00 3.93
2237 4228 7.491696 CCGTTCCTAAATACTTGTCTTTCTAGG 59.508 40.741 0.00 0.00 0.00 3.02
2238 4229 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
2239 4230 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
2240 4231 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
2241 4232 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
2242 4233 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
2243 4234 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
2244 4235 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
2245 4236 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
2246 4237 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
2247 4238 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
2248 4239 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
2249 4240 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
2250 4241 4.646492 TGTACTCCCTCCGTTCCTAAATAC 59.354 45.833 0.00 0.00 0.00 1.89
2251 4242 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
2252 4243 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
2253 4244 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
2254 4245 2.827921 GTTGTACTCCCTCCGTTCCTAA 59.172 50.000 0.00 0.00 0.00 2.69
2255 4246 2.450476 GTTGTACTCCCTCCGTTCCTA 58.550 52.381 0.00 0.00 0.00 2.94
2256 4247 1.264295 GTTGTACTCCCTCCGTTCCT 58.736 55.000 0.00 0.00 0.00 3.36
2257 4248 0.108945 CGTTGTACTCCCTCCGTTCC 60.109 60.000 0.00 0.00 0.00 3.62
2258 4249 0.108945 CCGTTGTACTCCCTCCGTTC 60.109 60.000 0.00 0.00 0.00 3.95
2259 4250 0.540365 TCCGTTGTACTCCCTCCGTT 60.540 55.000 0.00 0.00 0.00 4.44
2260 4251 0.540365 TTCCGTTGTACTCCCTCCGT 60.540 55.000 0.00 0.00 0.00 4.69
2261 4252 0.604578 TTTCCGTTGTACTCCCTCCG 59.395 55.000 0.00 0.00 0.00 4.63
2262 4253 2.038164 AGTTTTCCGTTGTACTCCCTCC 59.962 50.000 0.00 0.00 0.00 4.30
2263 4254 3.397849 AGTTTTCCGTTGTACTCCCTC 57.602 47.619 0.00 0.00 0.00 4.30
2264 4255 3.899980 AGTAGTTTTCCGTTGTACTCCCT 59.100 43.478 0.00 0.00 0.00 4.20
2265 4256 3.992427 CAGTAGTTTTCCGTTGTACTCCC 59.008 47.826 0.00 0.00 0.00 4.30
2266 4257 3.992427 CCAGTAGTTTTCCGTTGTACTCC 59.008 47.826 0.00 0.00 0.00 3.85
2267 4258 4.625028 ACCAGTAGTTTTCCGTTGTACTC 58.375 43.478 0.00 0.00 0.00 2.59
2268 4259 4.502087 GGACCAGTAGTTTTCCGTTGTACT 60.502 45.833 0.00 0.00 0.00 2.73
2269 4260 3.742882 GGACCAGTAGTTTTCCGTTGTAC 59.257 47.826 0.00 0.00 0.00 2.90
2270 4261 3.387374 TGGACCAGTAGTTTTCCGTTGTA 59.613 43.478 0.00 0.00 0.00 2.41
2275 4266 6.259387 GGTAATATTGGACCAGTAGTTTTCCG 59.741 42.308 2.09 0.00 35.65 4.30
2302 4293 4.641989 AGTATGTGGGCAATGAAATGAGTC 59.358 41.667 0.00 0.00 0.00 3.36
2331 4322 9.801714 CACTAAAGCAAAAATAATCAAAGCAAG 57.198 29.630 0.00 0.00 0.00 4.01
2341 4332 9.677567 CTAGCAAGTTCACTAAAGCAAAAATAA 57.322 29.630 0.00 0.00 0.00 1.40
2343 4334 6.642540 GCTAGCAAGTTCACTAAAGCAAAAAT 59.357 34.615 10.63 0.00 0.00 1.82
2385 4383 2.528743 CGCTGCACAATCGCCCTAG 61.529 63.158 0.00 0.00 0.00 3.02
2409 4407 3.009033 TGCCATTGAGCCTAACACTAACT 59.991 43.478 0.00 0.00 0.00 2.24
2479 4477 6.735694 GCAGTACACATAAGCCCCAAAATATG 60.736 42.308 0.00 0.00 33.12 1.78
2501 4500 3.937706 CTGAACTAGTCCAATCCAAGCAG 59.062 47.826 0.00 0.00 0.00 4.24
2718 4725 3.473625 CCCCTTACATTCGGTTATCACC 58.526 50.000 0.00 0.00 40.16 4.02
2719 4726 3.473625 CCCCCTTACATTCGGTTATCAC 58.526 50.000 0.00 0.00 0.00 3.06
2720 4727 2.158726 GCCCCCTTACATTCGGTTATCA 60.159 50.000 0.00 0.00 0.00 2.15
2721 4728 2.158726 TGCCCCCTTACATTCGGTTATC 60.159 50.000 0.00 0.00 0.00 1.75
2722 4729 1.847737 TGCCCCCTTACATTCGGTTAT 59.152 47.619 0.00 0.00 0.00 1.89
2723 4730 1.287217 TGCCCCCTTACATTCGGTTA 58.713 50.000 0.00 0.00 0.00 2.85
2757 4764 0.827368 AGGCCCTGAAGATCGAGTTC 59.173 55.000 0.00 3.81 0.00 3.01
2763 4770 2.637947 GAAGTGAAGGCCCTGAAGATC 58.362 52.381 0.00 0.00 0.00 2.75
2788 4795 5.163405 ACAGTTGAAAGAGCTTGAGTGTCTA 60.163 40.000 0.00 0.00 0.00 2.59
2794 4801 4.636249 ACCTACAGTTGAAAGAGCTTGAG 58.364 43.478 0.00 0.00 0.00 3.02
2960 4994 5.868801 ACGGGATTTTAAAAGTGCATGAATG 59.131 36.000 6.79 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.