Multiple sequence alignment - TraesCS2A01G543600

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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 TraesCS2A01G543600 chr2A 100.000 2807 0 0 1 2807 753435297 753432491 0.000000e+00 5184.0
1 TraesCS2A01G543600 chr2A 82.321 1120 150 27 928 2016 753405169 753404067 0.000000e+00 928.0
2 TraesCS2A01G543600 chr2A 79.111 900 150 18 1104 1981 753464740 753463857 1.120000e-163 586.0
3 TraesCS2A01G543600 chr2A 78.240 409 84 5 1541 1946 734798843 734799249 9.980000e-65 257.0
4 TraesCS2A01G543600 chr2A 96.774 31 1 0 2485 2515 753422815 753422785 5.000000e-03 52.8
5 TraesCS2A01G543600 chr2B 97.502 2042 36 7 133 2171 763494204 763492175 0.000000e+00 3474.0
6 TraesCS2A01G543600 chr2B 97.076 513 12 1 2295 2807 763492176 763491667 0.000000e+00 861.0
7 TraesCS2A01G543600 chr2B 80.891 1010 154 25 998 1989 763506318 763505330 0.000000e+00 760.0
8 TraesCS2A01G543600 chr2B 80.471 1019 158 23 1030 2024 763449630 763448629 0.000000e+00 741.0
9 TraesCS2A01G543600 chr2B 84.733 393 49 6 959 1351 763334933 763334552 1.580000e-102 383.0
10 TraesCS2A01G543600 chr2B 84.314 255 32 5 949 1198 762811782 762811531 2.790000e-60 243.0
11 TraesCS2A01G543600 chr2B 98.529 136 2 0 1 136 763494417 763494282 1.000000e-59 241.0
12 TraesCS2A01G543600 chr2B 96.377 138 4 1 2159 2296 517436873 517437009 2.810000e-55 226.0
13 TraesCS2A01G543600 chr2B 93.919 148 8 1 2152 2299 245013908 245013762 3.640000e-54 222.0
14 TraesCS2A01G543600 chr2B 87.500 184 17 2 1223 1400 762806163 762805980 1.020000e-49 207.0
15 TraesCS2A01G543600 chr2B 96.774 31 1 0 2485 2515 763477155 763477125 5.000000e-03 52.8
16 TraesCS2A01G543600 chr2D 87.193 1140 129 9 973 2104 621671450 621670320 0.000000e+00 1280.0
17 TraesCS2A01G543600 chr2D 80.702 1083 170 17 949 2005 621590103 621589034 0.000000e+00 806.0
18 TraesCS2A01G543600 chr2D 80.241 997 161 21 1030 2008 621610181 621609203 0.000000e+00 717.0
19 TraesCS2A01G543600 chr2D 89.423 520 39 11 2295 2807 621670280 621669770 2.360000e-180 641.0
20 TraesCS2A01G543600 chr2D 77.389 429 94 3 1541 1967 601427419 601427846 4.640000e-63 252.0
21 TraesCS2A01G543600 chr2D 100.000 30 0 0 705 734 621671737 621671708 3.910000e-04 56.5
22 TraesCS2A01G543600 chr2D 100.000 30 0 0 705 734 621672633 621672604 3.910000e-04 56.5
23 TraesCS2A01G543600 chr7B 77.556 401 83 5 1587 1982 692377152 692376754 4.670000e-58 235.0
24 TraesCS2A01G543600 chr7B 99.213 127 1 0 2170 2296 493212415 493212541 2.170000e-56 230.0
25 TraesCS2A01G543600 chr7B 75.616 406 85 8 1587 1982 692339845 692339444 3.690000e-44 189.0
26 TraesCS2A01G543600 chr7B 75.192 391 85 10 1600 1984 690905063 690905447 1.030000e-39 174.0
27 TraesCS2A01G543600 chr5B 99.219 128 1 0 2169 2296 345346858 345346731 6.050000e-57 231.0
28 TraesCS2A01G543600 chr5A 97.037 135 4 0 2162 2296 9840963 9840829 7.820000e-56 228.0
29 TraesCS2A01G543600 chr6B 97.710 131 3 0 2166 2296 618224322 618224192 2.810000e-55 226.0
30 TraesCS2A01G543600 chr6B 94.444 144 8 0 2167 2310 678328940 678328797 3.640000e-54 222.0
31 TraesCS2A01G543600 chr3A 96.324 136 5 0 2161 2296 372191259 372191124 1.010000e-54 224.0
32 TraesCS2A01G543600 chr6A 95.683 139 4 2 2159 2296 168123624 168123761 3.640000e-54 222.0
33 TraesCS2A01G543600 chr5D 81.481 270 46 4 1695 1962 45874033 45874300 4.710000e-53 219.0
34 TraesCS2A01G543600 chr7D 76.546 388 81 8 1600 1982 607109878 607110260 1.320000e-48 204.0
35 TraesCS2A01G543600 chr3B 74.269 171 27 10 2129 2296 201343418 201343574 3.910000e-04 56.5


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 TraesCS2A01G543600 chr2A 753432491 753435297 2806 True 5184.000000 5184 100.000000 1 2807 1 chr2A.!!$R3 2806
1 TraesCS2A01G543600 chr2A 753404067 753405169 1102 True 928.000000 928 82.321000 928 2016 1 chr2A.!!$R1 1088
2 TraesCS2A01G543600 chr2A 753463857 753464740 883 True 586.000000 586 79.111000 1104 1981 1 chr2A.!!$R4 877
3 TraesCS2A01G543600 chr2B 763491667 763494417 2750 True 1525.333333 3474 97.702333 1 2807 3 chr2B.!!$R8 2806
4 TraesCS2A01G543600 chr2B 763505330 763506318 988 True 760.000000 760 80.891000 998 1989 1 chr2B.!!$R7 991
5 TraesCS2A01G543600 chr2B 763448629 763449630 1001 True 741.000000 741 80.471000 1030 2024 1 chr2B.!!$R5 994
6 TraesCS2A01G543600 chr2D 621589034 621590103 1069 True 806.000000 806 80.702000 949 2005 1 chr2D.!!$R1 1056
7 TraesCS2A01G543600 chr2D 621609203 621610181 978 True 717.000000 717 80.241000 1030 2008 1 chr2D.!!$R2 978
8 TraesCS2A01G543600 chr2D 621669770 621672633 2863 True 508.500000 1280 94.154000 705 2807 4 chr2D.!!$R3 2102

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
512 594 0.035056 ATGCCCAAGGACTGTGCTAC 60.035 55.000 1.14 0.0 0.0 3.58 F
855 959 1.146263 GGTAAGCCCATCGTCCAGG 59.854 63.158 0.00 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1672 2749 0.036010 CTGTTTCTCGCTGTCCCCAT 60.036 55.0 0.0 0.0 0.0 4.0 R
2279 3374 0.251297 TGTTACTCCCTCCGTCCGAA 60.251 55.0 0.0 0.0 0.0 4.3 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
151 233 1.909700 CTGGAAAGCAAGTGGCCTTA 58.090 50.000 3.32 0.00 46.50 2.69
162 244 0.454600 GTGGCCTTATCGTCTCGTCA 59.545 55.000 3.32 0.00 0.00 4.35
194 276 1.805945 GCGGAGTTAGGCTGTGTCG 60.806 63.158 0.00 0.00 0.00 4.35
214 296 1.227002 CTCCCGTTCGGCTAGCTTC 60.227 63.158 15.72 0.00 0.00 3.86
215 297 1.945354 CTCCCGTTCGGCTAGCTTCA 61.945 60.000 15.72 0.00 0.00 3.02
218 300 1.080093 CGTTCGGCTAGCTTCACCA 60.080 57.895 15.72 0.00 0.00 4.17
278 360 4.552365 AGCGGGATGTGCGGATGG 62.552 66.667 0.00 0.00 37.44 3.51
305 387 1.755179 CGGCAACATCCATTTCTCCT 58.245 50.000 0.00 0.00 0.00 3.69
385 467 2.094906 CCGTCATACCACAAAGACTCGA 60.095 50.000 0.00 0.00 0.00 4.04
414 496 1.869342 GCAGCTTTGTTTGCGATGGTT 60.869 47.619 0.00 0.00 35.28 3.67
419 501 2.804931 GTTTGCGATGGTTGCGGC 60.805 61.111 0.00 0.00 34.24 6.53
458 540 3.879351 GAAGCAACAACGGCGGCAG 62.879 63.158 13.24 0.00 36.08 4.85
512 594 0.035056 ATGCCCAAGGACTGTGCTAC 60.035 55.000 1.14 0.00 0.00 3.58
592 674 6.291585 CGTTTTGTGAGGTTGCTTTTACAATC 60.292 38.462 0.00 0.00 0.00 2.67
672 754 5.507315 CCAAGTTTGTTCCATGAAGTACACC 60.507 44.000 0.00 0.00 0.00 4.16
825 909 3.331150 ACAATAGCCAATCGTTCGTTCA 58.669 40.909 0.00 0.00 0.00 3.18
853 957 2.727392 CCGGTAAGCCCATCGTCCA 61.727 63.158 0.00 0.00 0.00 4.02
854 958 1.227263 CGGTAAGCCCATCGTCCAG 60.227 63.158 0.00 0.00 0.00 3.86
855 959 1.146263 GGTAAGCCCATCGTCCAGG 59.854 63.158 0.00 0.00 0.00 4.45
896 1000 3.092511 ATCGTCCAGGCCAGCCAT 61.093 61.111 12.03 0.00 38.92 4.40
897 1001 1.766059 ATCGTCCAGGCCAGCCATA 60.766 57.895 12.03 0.00 38.92 2.74
970 1107 3.376464 CTATTCGCCGTCGTCGCG 61.376 66.667 0.00 0.00 37.70 5.87
1086 2108 4.307908 GGCACGCACGTGTTCACC 62.308 66.667 22.66 12.45 46.90 4.02
1548 2618 2.476619 AGACTTGTCGAACAATCTTGCG 59.523 45.455 0.00 0.00 37.48 4.85
1560 2630 1.896220 ATCTTGCGAAACTGCTGGAA 58.104 45.000 0.00 0.00 35.36 3.53
1670 2747 4.577246 CGCTCAGCTCTACGGGCC 62.577 72.222 0.00 0.00 0.00 5.80
1672 2749 3.019003 GCTCAGCTCTACGGGCCAA 62.019 63.158 4.39 0.00 0.00 4.52
1673 2750 1.826024 CTCAGCTCTACGGGCCAAT 59.174 57.895 4.39 0.00 0.00 3.16
2017 3112 5.955488 ACAGAGGATATATGTACGTGATGC 58.045 41.667 0.00 0.00 29.54 3.91
2112 3207 4.868314 AGTTTCGCTAGGTTTAGAGTGT 57.132 40.909 0.00 0.00 0.00 3.55
2160 3255 6.559810 TGTGAACATTTAGTTTGTTGGTCAG 58.440 36.000 0.00 0.00 41.51 3.51
2171 3266 3.980646 TGTTGGTCAGTTGCAACATAC 57.019 42.857 30.11 24.56 33.30 2.39
2172 3267 3.550820 TGTTGGTCAGTTGCAACATACT 58.449 40.909 30.11 7.72 33.30 2.12
2173 3268 3.563808 TGTTGGTCAGTTGCAACATACTC 59.436 43.478 30.11 19.06 33.30 2.59
2174 3269 2.778299 TGGTCAGTTGCAACATACTCC 58.222 47.619 30.11 22.09 0.00 3.85
2175 3270 2.084546 GGTCAGTTGCAACATACTCCC 58.915 52.381 30.11 16.41 0.00 4.30
2176 3271 2.290323 GGTCAGTTGCAACATACTCCCT 60.290 50.000 30.11 5.09 0.00 4.20
2177 3272 3.003480 GTCAGTTGCAACATACTCCCTC 58.997 50.000 30.11 7.19 0.00 4.30
2178 3273 2.027192 TCAGTTGCAACATACTCCCTCC 60.027 50.000 30.11 0.00 0.00 4.30
2179 3274 1.066143 AGTTGCAACATACTCCCTCCG 60.066 52.381 30.11 0.00 0.00 4.63
2180 3275 0.981183 TTGCAACATACTCCCTCCGT 59.019 50.000 0.00 0.00 0.00 4.69
2181 3276 0.535335 TGCAACATACTCCCTCCGTC 59.465 55.000 0.00 0.00 0.00 4.79
2182 3277 0.179081 GCAACATACTCCCTCCGTCC 60.179 60.000 0.00 0.00 0.00 4.79
2183 3278 0.102481 CAACATACTCCCTCCGTCCG 59.898 60.000 0.00 0.00 0.00 4.79
2184 3279 0.033796 AACATACTCCCTCCGTCCGA 60.034 55.000 0.00 0.00 0.00 4.55
2185 3280 0.033796 ACATACTCCCTCCGTCCGAA 60.034 55.000 0.00 0.00 0.00 4.30
2186 3281 1.108776 CATACTCCCTCCGTCCGAAA 58.891 55.000 0.00 0.00 0.00 3.46
2187 3282 1.479323 CATACTCCCTCCGTCCGAAAA 59.521 52.381 0.00 0.00 0.00 2.29
2188 3283 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
2189 3284 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2190 3285 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2191 3286 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2192 3287 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2193 3288 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2194 3289 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2195 3290 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2196 3291 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
2197 3292 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2198 3293 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
2199 3294 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
2200 3295 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
2201 3296 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
2202 3297 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
2203 3298 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
2204 3299 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
2205 3300 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
2206 3301 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
2207 3302 7.273381 CCGAAAATACTTGTCATCAAAATGGAC 59.727 37.037 0.00 0.00 33.42 4.02
2208 3303 7.807433 CGAAAATACTTGTCATCAAAATGGACA 59.193 33.333 0.00 0.00 33.42 4.02
2209 3304 9.474920 GAAAATACTTGTCATCAAAATGGACAA 57.525 29.630 0.00 0.00 34.59 3.18
2210 3305 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
2211 3306 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
2212 3307 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
2213 3308 7.775397 ACTTGTCATCAAAATGGACAAAAAG 57.225 32.000 7.70 0.11 34.98 2.27
2214 3309 6.762661 ACTTGTCATCAAAATGGACAAAAAGG 59.237 34.615 7.70 0.11 34.98 3.11
2215 3310 5.609423 TGTCATCAAAATGGACAAAAAGGG 58.391 37.500 0.00 0.00 33.42 3.95
2216 3311 5.365025 TGTCATCAAAATGGACAAAAAGGGA 59.635 36.000 0.00 0.00 33.42 4.20
2217 3312 6.043012 TGTCATCAAAATGGACAAAAAGGGAT 59.957 34.615 0.00 0.00 33.42 3.85
2218 3313 6.369615 GTCATCAAAATGGACAAAAAGGGATG 59.630 38.462 0.00 0.00 33.42 3.51
2219 3314 5.885449 TCAAAATGGACAAAAAGGGATGT 57.115 34.783 0.00 0.00 0.00 3.06
2220 3315 6.985653 TCAAAATGGACAAAAAGGGATGTA 57.014 33.333 0.00 0.00 0.00 2.29
2221 3316 7.552050 TCAAAATGGACAAAAAGGGATGTAT 57.448 32.000 0.00 0.00 0.00 2.29
2222 3317 7.385267 TCAAAATGGACAAAAAGGGATGTATG 58.615 34.615 0.00 0.00 0.00 2.39
2223 3318 6.933514 AAATGGACAAAAAGGGATGTATGT 57.066 33.333 0.00 0.00 0.00 2.29
2224 3319 8.310382 CAAAATGGACAAAAAGGGATGTATGTA 58.690 33.333 0.00 0.00 0.00 2.29
2225 3320 7.645058 AATGGACAAAAAGGGATGTATGTAG 57.355 36.000 0.00 0.00 0.00 2.74
2226 3321 6.381498 TGGACAAAAAGGGATGTATGTAGA 57.619 37.500 0.00 0.00 0.00 2.59
2227 3322 6.785076 TGGACAAAAAGGGATGTATGTAGAA 58.215 36.000 0.00 0.00 0.00 2.10
2228 3323 6.657541 TGGACAAAAAGGGATGTATGTAGAAC 59.342 38.462 0.00 0.00 0.00 3.01
2229 3324 6.884836 GGACAAAAAGGGATGTATGTAGAACT 59.115 38.462 0.00 0.00 0.00 3.01
2230 3325 8.044908 GGACAAAAAGGGATGTATGTAGAACTA 58.955 37.037 0.00 0.00 0.00 2.24
2231 3326 9.444600 GACAAAAAGGGATGTATGTAGAACTAA 57.555 33.333 0.00 0.00 0.00 2.24
2232 3327 9.802039 ACAAAAAGGGATGTATGTAGAACTAAA 57.198 29.630 0.00 0.00 0.00 1.85
2253 3348 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
2261 3356 9.170890 ACATCTAGATACATCCCCTTTTATTCA 57.829 33.333 4.54 0.00 0.00 2.57
2267 3362 9.713684 AGATACATCCCCTTTTATTCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
2270 3365 8.378115 ACATCCCCTTTTATTCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
2271 3366 8.260114 ACATCCCCTTTTATTCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
2272 3367 7.789202 TCCCCTTTTATTCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
2273 3368 8.200024 TCCCCTTTTATTCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
2274 3369 8.313292 TCCCCTTTTATTCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
2275 3370 8.096414 CCCCTTTTATTCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
2283 3378 8.741101 TTCATTTTGATGACAAGTATTTTCGG 57.259 30.769 0.00 0.00 37.32 4.30
2284 3379 8.105097 TCATTTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
2285 3380 8.020819 TCATTTTGATGACAAGTATTTTCGGAC 58.979 33.333 0.00 0.00 37.32 4.79
2286 3381 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
2287 3382 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
2288 3383 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
2289 3384 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2290 3385 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2291 3386 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2292 3387 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
2293 3388 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
2294 3389 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
2295 3390 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
2325 3420 3.133542 TGATCATGTTGCCTAGTCCTGAG 59.866 47.826 0.00 0.00 0.00 3.35
2414 3511 7.607991 AGGTTGTCTTGTCATATTTAGTCCTTG 59.392 37.037 0.00 0.00 0.00 3.61
2431 3529 4.941873 GTCCTTGTAGAGGTATTTTGGTGG 59.058 45.833 0.00 0.00 46.39 4.61
2432 3530 4.847512 TCCTTGTAGAGGTATTTTGGTGGA 59.152 41.667 0.00 0.00 46.39 4.02
2433 3531 4.941873 CCTTGTAGAGGTATTTTGGTGGAC 59.058 45.833 0.00 0.00 40.95 4.02
2744 3848 4.944048 ACCTCACCAAAAATAGTGCAAAC 58.056 39.130 0.00 0.00 33.90 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 0.175760 TCAGAGTAGCAATGTCGGGC 59.824 55.000 0.00 0.00 0.00 6.13
151 233 1.356979 CGATGCCTGACGAGACGAT 59.643 57.895 0.00 0.00 0.00 3.73
162 244 2.516930 CCGCCAAATCCGATGCCT 60.517 61.111 0.00 0.00 0.00 4.75
194 276 4.893601 GCTAGCCGAACGGGAGCC 62.894 72.222 15.01 0.00 38.47 4.70
246 328 1.448922 CCGCTTCGAAAACCCCACAA 61.449 55.000 0.00 0.00 0.00 3.33
278 360 2.126734 GATGTTGCCGCACACTGC 60.127 61.111 0.00 0.00 40.69 4.40
284 366 0.810648 GAGAAATGGATGTTGCCGCA 59.189 50.000 0.00 0.00 0.00 5.69
305 387 2.927477 GTCGACTTCAACCAATGCGATA 59.073 45.455 8.70 0.00 0.00 2.92
365 447 2.915463 GTCGAGTCTTTGTGGTATGACG 59.085 50.000 0.00 0.00 34.92 4.35
385 467 3.524541 CAAACAAAGCTGCCTTTTCTGT 58.475 40.909 0.00 0.00 39.20 3.41
414 496 1.002430 AGAGAAATGAGAACTGCCGCA 59.998 47.619 0.00 0.00 0.00 5.69
458 540 2.484264 CCCTCGTCACAAAATTGGACTC 59.516 50.000 10.76 0.00 0.00 3.36
512 594 9.667989 GGAATGATCCAAAAACAAGAAATTTTG 57.332 29.630 0.00 4.45 45.79 2.44
567 649 4.416620 TGTAAAAGCAACCTCACAAAACG 58.583 39.130 0.00 0.00 0.00 3.60
592 674 2.306341 ACAGATGCCGAGACATGAAG 57.694 50.000 0.00 0.00 0.00 3.02
812 896 1.791555 GCTGCCATGAACGAACGATTG 60.792 52.381 0.00 0.00 0.00 2.67
855 959 2.044946 CTACCACTGGGCCTTGGC 60.045 66.667 20.88 2.49 36.20 4.52
856 960 2.044946 GCTACCACTGGGCCTTGG 60.045 66.667 19.74 19.74 37.90 3.61
857 961 1.377725 CTGCTACCACTGGGCCTTG 60.378 63.158 4.53 1.35 37.90 3.61
858 962 3.081554 CTGCTACCACTGGGCCTT 58.918 61.111 4.53 0.00 37.90 4.35
896 1000 2.454336 TGAAATCTCCTCGGCCTCTA 57.546 50.000 0.00 0.00 0.00 2.43
897 1001 1.691434 GATGAAATCTCCTCGGCCTCT 59.309 52.381 0.00 0.00 41.17 3.69
970 1107 0.393808 TGTGCGGAGGGGAAATTAGC 60.394 55.000 0.00 0.00 0.00 3.09
1308 2333 0.181350 ATGGCCGGGAGAAGATCAAC 59.819 55.000 2.18 0.00 0.00 3.18
1548 2618 1.981256 TGTTCCCTTCCAGCAGTTTC 58.019 50.000 0.00 0.00 0.00 2.78
1560 2630 1.375326 GTCCGCTCCTTTGTTCCCT 59.625 57.895 0.00 0.00 0.00 4.20
1670 2747 0.804989 GTTTCTCGCTGTCCCCATTG 59.195 55.000 0.00 0.00 0.00 2.82
1672 2749 0.036010 CTGTTTCTCGCTGTCCCCAT 60.036 55.000 0.00 0.00 0.00 4.00
1673 2750 1.371183 CTGTTTCTCGCTGTCCCCA 59.629 57.895 0.00 0.00 0.00 4.96
2017 3112 1.396301 GCGATCAGACTCTTTGCTTGG 59.604 52.381 0.00 0.00 0.00 3.61
2112 3207 1.378882 AACTAGTACGCGCGGATCCA 61.379 55.000 35.22 13.86 0.00 3.41
2160 3255 1.338769 ACGGAGGGAGTATGTTGCAAC 60.339 52.381 22.83 22.83 0.00 4.17
2171 3266 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
2172 3267 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
2173 3268 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2174 3269 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2175 3270 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2176 3271 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
2177 3272 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
2178 3273 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
2179 3274 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
2180 3275 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
2181 3276 7.273381 GTCCATTTTGATGACAAGTATTTTCGG 59.727 37.037 0.00 0.00 37.32 4.30
2182 3277 7.807433 TGTCCATTTTGATGACAAGTATTTTCG 59.193 33.333 0.00 0.00 37.32 3.46
2183 3278 9.474920 TTGTCCATTTTGATGACAAGTATTTTC 57.525 29.630 0.00 0.00 37.32 2.29
2184 3279 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
2185 3280 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
2186 3281 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
2187 3282 9.480053 CTTTTTGTCCATTTTGATGACAAGTAT 57.520 29.630 0.00 0.00 37.13 2.12
2188 3283 7.925483 CCTTTTTGTCCATTTTGATGACAAGTA 59.075 33.333 0.00 0.00 37.13 2.24
2189 3284 6.762661 CCTTTTTGTCCATTTTGATGACAAGT 59.237 34.615 0.00 0.00 37.13 3.16
2190 3285 6.203338 CCCTTTTTGTCCATTTTGATGACAAG 59.797 38.462 0.00 0.00 37.13 3.16
2191 3286 6.054295 CCCTTTTTGTCCATTTTGATGACAA 58.946 36.000 0.00 0.00 34.47 3.18
2192 3287 5.365025 TCCCTTTTTGTCCATTTTGATGACA 59.635 36.000 0.00 0.00 0.00 3.58
2193 3288 5.852827 TCCCTTTTTGTCCATTTTGATGAC 58.147 37.500 0.00 0.00 0.00 3.06
2194 3289 6.043012 ACATCCCTTTTTGTCCATTTTGATGA 59.957 34.615 0.00 0.00 32.39 2.92
2195 3290 6.232692 ACATCCCTTTTTGTCCATTTTGATG 58.767 36.000 0.00 0.00 33.80 3.07
2196 3291 6.438186 ACATCCCTTTTTGTCCATTTTGAT 57.562 33.333 0.00 0.00 0.00 2.57
2197 3292 5.885449 ACATCCCTTTTTGTCCATTTTGA 57.115 34.783 0.00 0.00 0.00 2.69
2198 3293 7.160726 ACATACATCCCTTTTTGTCCATTTTG 58.839 34.615 0.00 0.00 0.00 2.44
2199 3294 7.315066 ACATACATCCCTTTTTGTCCATTTT 57.685 32.000 0.00 0.00 0.00 1.82
2200 3295 6.933514 ACATACATCCCTTTTTGTCCATTT 57.066 33.333 0.00 0.00 0.00 2.32
2201 3296 7.410174 TCTACATACATCCCTTTTTGTCCATT 58.590 34.615 0.00 0.00 0.00 3.16
2202 3297 6.969043 TCTACATACATCCCTTTTTGTCCAT 58.031 36.000 0.00 0.00 0.00 3.41
2203 3298 6.381498 TCTACATACATCCCTTTTTGTCCA 57.619 37.500 0.00 0.00 0.00 4.02
2204 3299 6.884836 AGTTCTACATACATCCCTTTTTGTCC 59.115 38.462 0.00 0.00 0.00 4.02
2205 3300 7.923414 AGTTCTACATACATCCCTTTTTGTC 57.077 36.000 0.00 0.00 0.00 3.18
2206 3301 9.802039 TTTAGTTCTACATACATCCCTTTTTGT 57.198 29.630 0.00 0.00 0.00 2.83
2227 3322 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
2235 3330 9.170890 TGAATAAAAGGGGATGTATCTAGATGT 57.829 33.333 15.79 1.25 0.00 3.06
2241 3336 9.713684 TCAAAATGAATAAAAGGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
2244 3339 9.486123 TCATCAAAATGAATAAAAGGGGATGTA 57.514 29.630 0.00 0.00 38.97 2.29
2245 3340 8.260114 GTCATCAAAATGAATAAAAGGGGATGT 58.740 33.333 0.00 0.00 43.42 3.06
2246 3341 8.259411 TGTCATCAAAATGAATAAAAGGGGATG 58.741 33.333 0.00 0.00 43.42 3.51
2247 3342 8.378115 TGTCATCAAAATGAATAAAAGGGGAT 57.622 30.769 0.00 0.00 43.42 3.85
2248 3343 7.789202 TGTCATCAAAATGAATAAAAGGGGA 57.211 32.000 0.00 0.00 43.42 4.81
2249 3344 8.096414 ACTTGTCATCAAAATGAATAAAAGGGG 58.904 33.333 0.00 0.00 43.42 4.79
2257 3352 9.357652 CCGAAAATACTTGTCATCAAAATGAAT 57.642 29.630 0.00 0.00 43.42 2.57
2258 3353 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
2259 3354 8.020819 GTCCGAAAATACTTGTCATCAAAATGA 58.979 33.333 0.00 0.00 39.63 2.57
2260 3355 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
2261 3356 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
2262 3357 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
2263 3358 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
2264 3359 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
2265 3360 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
2266 3361 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
2267 3362 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2268 3363 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
2269 3364 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2270 3365 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2271 3366 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2272 3367 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2273 3368 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2274 3369 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2275 3370 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2276 3371 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
2277 3372 1.273327 GTTACTCCCTCCGTCCGAAAA 59.727 52.381 0.00 0.00 0.00 2.29
2278 3373 0.890683 GTTACTCCCTCCGTCCGAAA 59.109 55.000 0.00 0.00 0.00 3.46
2279 3374 0.251297 TGTTACTCCCTCCGTCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
2280 3375 0.962356 GTGTTACTCCCTCCGTCCGA 60.962 60.000 0.00 0.00 0.00 4.55
2281 3376 1.509923 GTGTTACTCCCTCCGTCCG 59.490 63.158 0.00 0.00 0.00 4.79
2282 3377 0.614134 AGGTGTTACTCCCTCCGTCC 60.614 60.000 0.00 0.00 0.00 4.79
2283 3378 1.264295 AAGGTGTTACTCCCTCCGTC 58.736 55.000 0.00 0.00 0.00 4.79
2284 3379 1.346722 CAAAGGTGTTACTCCCTCCGT 59.653 52.381 0.00 0.00 0.00 4.69
2285 3380 1.621814 TCAAAGGTGTTACTCCCTCCG 59.378 52.381 0.00 0.00 0.00 4.63
2286 3381 3.263425 TGATCAAAGGTGTTACTCCCTCC 59.737 47.826 0.00 0.00 0.00 4.30
2287 3382 4.553330 TGATCAAAGGTGTTACTCCCTC 57.447 45.455 0.00 0.00 0.00 4.30
2288 3383 4.289672 ACATGATCAAAGGTGTTACTCCCT 59.710 41.667 0.00 0.00 0.00 4.20
2289 3384 4.589908 ACATGATCAAAGGTGTTACTCCC 58.410 43.478 0.00 0.00 0.00 4.30
2290 3385 5.619981 GCAACATGATCAAAGGTGTTACTCC 60.620 44.000 15.42 0.00 33.79 3.85
2291 3386 5.393962 GCAACATGATCAAAGGTGTTACTC 58.606 41.667 15.42 5.01 33.79 2.59
2292 3387 4.218417 GGCAACATGATCAAAGGTGTTACT 59.782 41.667 15.42 0.00 33.79 2.24
2293 3388 4.218417 AGGCAACATGATCAAAGGTGTTAC 59.782 41.667 15.42 9.20 41.41 2.50
2294 3389 4.406456 AGGCAACATGATCAAAGGTGTTA 58.594 39.130 15.42 0.00 41.41 2.41
2295 3390 3.233507 AGGCAACATGATCAAAGGTGTT 58.766 40.909 15.42 11.32 41.41 3.32
2325 3420 4.398044 TCCTTCCAATTATCTGCGAAAACC 59.602 41.667 0.00 0.00 0.00 3.27
2414 3511 5.414765 CCAAAGTCCACCAAAATACCTCTAC 59.585 44.000 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.