Multiple sequence alignment - TraesCS2A01G436000

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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 TraesCS2A01G436000 chr2A 100.000 2303 0 0 1 2303 688238571 688236269 0.000000e+00 4253.0
1 TraesCS2A01G436000 chr2D 93.435 1965 97 14 145 2099 545034817 545036759 0.000000e+00 2885.0
2 TraesCS2A01G436000 chr2D 90.299 134 12 1 2115 2247 545036745 545036878 8.460000e-40 174.0
3 TraesCS2A01G436000 chr2D 84.667 150 15 5 146 291 545034928 545034783 2.390000e-30 143.0
4 TraesCS2A01G436000 chr2D 94.737 57 3 0 2247 2303 545036906 545036962 3.150000e-14 89.8
5 TraesCS2A01G436000 chr2B 94.198 1310 66 7 328 1632 651926424 651927728 0.000000e+00 1989.0
6 TraesCS2A01G436000 chr2B 87.762 286 14 9 1608 1893 651928586 651928850 4.780000e-82 315.0
7 TraesCS2A01G436000 chr2B 90.323 186 17 1 1890 2075 651929083 651929267 2.290000e-60 243.0
8 TraesCS2A01G436000 chr2B 89.683 126 12 1 2123 2247 651929270 651929395 2.370000e-35 159.0
9 TraesCS2A01G436000 chr6A 99.310 145 1 0 1 145 602356652 602356508 1.750000e-66 263.0
10 TraesCS2A01G436000 chr5A 99.310 145 1 0 1 145 450435767 450435623 1.750000e-66 263.0
11 TraesCS2A01G436000 chr3B 99.310 145 1 0 1 145 176924093 176923949 1.750000e-66 263.0
12 TraesCS2A01G436000 chr7A 99.306 144 1 0 1 144 439630325 439630468 6.310000e-66 261.0
13 TraesCS2A01G436000 chr1B 99.306 144 1 0 1 144 317556855 317556998 6.310000e-66 261.0
14 TraesCS2A01G436000 chr1B 97.973 148 2 1 1 148 626586125 626586271 2.940000e-64 255.0
15 TraesCS2A01G436000 chr1A 99.306 144 1 0 1 144 37618961 37618818 6.310000e-66 261.0
16 TraesCS2A01G436000 chr1A 98.621 145 1 1 1 145 147684940 147685083 2.940000e-64 255.0
17 TraesCS2A01G436000 chr4A 96.753 154 3 2 1 153 737301832 737301680 2.940000e-64 255.0


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 TraesCS2A01G436000 chr2A 688236269 688238571 2302 True 4253.0 4253 100.000000 1 2303 1 chr2A.!!$R1 2302
1 TraesCS2A01G436000 chr2D 545034817 545036962 2145 False 1049.6 2885 92.823667 145 2303 3 chr2D.!!$F1 2158
2 TraesCS2A01G436000 chr2B 651926424 651929395 2971 False 676.5 1989 90.491500 328 2247 4 chr2B.!!$F1 1919

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
27 28 0.466543 ACGTGTGTGTTAGGCCTTCA 59.533 50.0 12.58 8.6 0.0 3.02 F
138 139 0.678048 GCTCGGCCTCCAAAGACAAT 60.678 55.0 0.00 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1239 1252 0.531753 GCGAATCCCTCTTCTGAGCC 60.532 60.0 0.0 0.0 38.93 4.70 R
1943 3075 0.542333 GAGGAGGCCCTAACTGAACC 59.458 60.0 0.0 0.0 44.53 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
24 25 4.771127 CACGTGTGTGTTAGGCCT 57.229 55.556 11.78 11.78 41.34 5.19
25 26 3.000815 CACGTGTGTGTTAGGCCTT 57.999 52.632 12.58 0.00 41.34 4.35
26 27 0.865769 CACGTGTGTGTTAGGCCTTC 59.134 55.000 12.58 5.51 41.34 3.46
27 28 0.466543 ACGTGTGTGTTAGGCCTTCA 59.533 50.000 12.58 8.60 0.00 3.02
28 29 1.071699 ACGTGTGTGTTAGGCCTTCAT 59.928 47.619 12.58 0.00 0.00 2.57
29 30 2.300723 ACGTGTGTGTTAGGCCTTCATA 59.699 45.455 12.58 6.79 0.00 2.15
30 31 3.055385 ACGTGTGTGTTAGGCCTTCATAT 60.055 43.478 12.58 0.00 0.00 1.78
31 32 4.160814 ACGTGTGTGTTAGGCCTTCATATA 59.839 41.667 12.58 5.14 0.00 0.86
32 33 5.163343 ACGTGTGTGTTAGGCCTTCATATAT 60.163 40.000 12.58 0.00 0.00 0.86
33 34 6.041182 ACGTGTGTGTTAGGCCTTCATATATA 59.959 38.462 12.58 0.00 0.00 0.86
34 35 7.097192 CGTGTGTGTTAGGCCTTCATATATAT 58.903 38.462 12.58 0.00 0.00 0.86
35 36 7.063426 CGTGTGTGTTAGGCCTTCATATATATG 59.937 40.741 12.58 15.47 35.04 1.78
36 37 7.878127 GTGTGTGTTAGGCCTTCATATATATGT 59.122 37.037 12.58 4.89 35.26 2.29
37 38 7.877612 TGTGTGTTAGGCCTTCATATATATGTG 59.122 37.037 12.58 14.19 35.26 3.21
38 39 7.878127 GTGTGTTAGGCCTTCATATATATGTGT 59.122 37.037 12.58 5.08 35.26 3.72
39 40 7.877612 TGTGTTAGGCCTTCATATATATGTGTG 59.122 37.037 12.58 11.45 35.26 3.82
40 41 7.878127 GTGTTAGGCCTTCATATATATGTGTGT 59.122 37.037 12.58 6.50 35.26 3.72
41 42 8.436778 TGTTAGGCCTTCATATATATGTGTGTT 58.563 33.333 12.58 7.71 35.26 3.32
42 43 9.284968 GTTAGGCCTTCATATATATGTGTGTTT 57.715 33.333 12.58 8.12 35.26 2.83
43 44 9.860650 TTAGGCCTTCATATATATGTGTGTTTT 57.139 29.630 12.58 6.94 35.26 2.43
44 45 8.766994 AGGCCTTCATATATATGTGTGTTTTT 57.233 30.769 19.78 1.57 35.26 1.94
107 108 9.934641 CAACAAAATTCAAATTTTTCAAAACCG 57.065 25.926 10.05 1.52 43.91 4.44
108 109 9.899226 AACAAAATTCAAATTTTTCAAAACCGA 57.101 22.222 10.05 0.00 43.91 4.69
109 110 9.553418 ACAAAATTCAAATTTTTCAAAACCGAG 57.447 25.926 10.05 0.38 43.91 4.63
110 111 8.522661 CAAAATTCAAATTTTTCAAAACCGAGC 58.477 29.630 10.05 0.00 43.91 5.03
111 112 7.552458 AATTCAAATTTTTCAAAACCGAGCT 57.448 28.000 0.00 0.00 0.00 4.09
112 113 6.582437 TTCAAATTTTTCAAAACCGAGCTC 57.418 33.333 2.73 2.73 0.00 4.09
113 114 5.047188 TCAAATTTTTCAAAACCGAGCTCC 58.953 37.500 8.47 0.00 0.00 4.70
114 115 4.664150 AATTTTTCAAAACCGAGCTCCA 57.336 36.364 8.47 0.00 0.00 3.86
115 116 4.871933 ATTTTTCAAAACCGAGCTCCAT 57.128 36.364 8.47 0.00 0.00 3.41
116 117 3.641437 TTTTCAAAACCGAGCTCCATG 57.359 42.857 8.47 0.00 0.00 3.66
117 118 1.533625 TTCAAAACCGAGCTCCATGG 58.466 50.000 4.97 4.97 0.00 3.66
118 119 0.690192 TCAAAACCGAGCTCCATGGA 59.310 50.000 15.27 15.27 0.00 3.41
119 120 1.089920 CAAAACCGAGCTCCATGGAG 58.910 55.000 33.73 33.73 44.56 3.86
127 128 3.160047 CTCCATGGAGCTCGGCCT 61.160 66.667 28.45 0.00 35.31 5.19
128 129 3.157252 TCCATGGAGCTCGGCCTC 61.157 66.667 11.44 0.00 0.00 4.70
134 135 2.982130 GAGCTCGGCCTCCAAAGA 59.018 61.111 0.00 0.00 0.00 2.52
135 136 1.448717 GAGCTCGGCCTCCAAAGAC 60.449 63.158 0.00 0.00 0.00 3.01
136 137 2.172483 GAGCTCGGCCTCCAAAGACA 62.172 60.000 0.00 0.00 0.00 3.41
137 138 1.302511 GCTCGGCCTCCAAAGACAA 60.303 57.895 0.00 0.00 0.00 3.18
138 139 0.678048 GCTCGGCCTCCAAAGACAAT 60.678 55.000 0.00 0.00 0.00 2.71
139 140 1.406887 GCTCGGCCTCCAAAGACAATA 60.407 52.381 0.00 0.00 0.00 1.90
140 141 2.746472 GCTCGGCCTCCAAAGACAATAT 60.746 50.000 0.00 0.00 0.00 1.28
141 142 3.134458 CTCGGCCTCCAAAGACAATATC 58.866 50.000 0.00 0.00 0.00 1.63
142 143 2.158813 TCGGCCTCCAAAGACAATATCC 60.159 50.000 0.00 0.00 0.00 2.59
143 144 2.222027 GGCCTCCAAAGACAATATCCG 58.778 52.381 0.00 0.00 0.00 4.18
181 182 9.937175 GCTATAAAGTTTTAAAGTGGAGCATAG 57.063 33.333 0.00 0.00 0.00 2.23
202 203 7.413328 GCATAGAAATTTTGACATTTTGAGCCC 60.413 37.037 0.00 0.00 0.00 5.19
226 227 9.586435 CCCCTTTAAAATGTGACAATTTCTATC 57.414 33.333 1.32 0.00 0.00 2.08
228 229 9.289303 CCTTTAAAATGTGACAATTTCTATCCG 57.711 33.333 1.32 0.00 0.00 4.18
273 274 6.633500 AACTAGTGCTGTTCAAAATAAGCA 57.367 33.333 0.00 0.00 43.10 3.91
276 277 8.335532 ACTAGTGCTGTTCAAAATAAGCAATA 57.664 30.769 0.00 0.84 46.48 1.90
320 321 1.615384 GGCATCTCAGGCAAAAGGAGT 60.615 52.381 0.00 0.00 0.00 3.85
330 331 4.761739 CAGGCAAAAGGAGTATGAAGTTGA 59.238 41.667 0.00 0.00 0.00 3.18
398 399 7.569599 AGGTTTATTGAGAAAGAACTAGGGA 57.430 36.000 0.00 0.00 0.00 4.20
439 447 7.657761 CAGGGGATAGACATGTACTACATTTTC 59.342 40.741 0.00 0.19 36.53 2.29
461 469 6.639632 TCTTCAGAGGAGGTTTGAAATTTG 57.360 37.500 0.00 0.00 31.11 2.32
468 476 5.683681 AGGAGGTTTGAAATTTGCATGTTT 58.316 33.333 0.00 0.00 0.00 2.83
470 478 5.526846 GGAGGTTTGAAATTTGCATGTTTGA 59.473 36.000 0.00 0.00 0.00 2.69
482 490 9.491675 AATTTGCATGTTTGATTTAGAATGACA 57.508 25.926 0.00 0.00 0.00 3.58
538 547 8.829612 CAATTTCAAGCTTTCAGGTAAAAATGT 58.170 29.630 0.00 0.00 0.00 2.71
575 584 7.174253 TGTTCCTACAATGTGTCACCTAATTTC 59.826 37.037 0.00 0.00 0.00 2.17
580 589 6.668323 ACAATGTGTCACCTAATTTCTTTCG 58.332 36.000 0.00 0.00 0.00 3.46
610 620 3.489813 TCGTGACGACATTCCACTG 57.510 52.632 2.39 0.00 0.00 3.66
703 716 4.974368 TCATTGTTTAGTTTATGGGGCG 57.026 40.909 0.00 0.00 0.00 6.13
752 765 6.349694 GGGAAAGAAACATCTGATCCAGAAAC 60.350 42.308 0.43 0.00 44.04 2.78
756 769 1.303309 CATCTGATCCAGAAACCGGC 58.697 55.000 0.00 0.00 44.04 6.13
809 822 3.728076 AGTCTTCACTGAACGTGCTAA 57.272 42.857 0.00 0.00 43.46 3.09
887 900 3.755628 GCGACCTAGCGGTGACCA 61.756 66.667 1.11 0.00 45.73 4.02
909 922 2.364970 GTCATCTGGGGAGTCTGATGAG 59.635 54.545 12.44 0.00 45.80 2.90
1018 1031 1.202348 GAATGGCGGAAAACTCAAGGG 59.798 52.381 0.00 0.00 0.00 3.95
1047 1060 4.398358 AGTTCAAGCATCCATGATCTGTTG 59.602 41.667 0.00 0.00 0.00 3.33
1239 1252 1.563410 AGGATGAGGGAAGAAGCAAGG 59.437 52.381 0.00 0.00 0.00 3.61
1324 1337 5.349824 GAAGACGAAGCTTCTTTGTCAAT 57.650 39.130 25.30 17.41 40.80 2.57
1345 1358 8.305317 GTCAATGGGTAGATAATGTACTAGACC 58.695 40.741 0.00 0.00 0.00 3.85
1542 1555 8.584157 AGGTGATCTACTGATCTATGTGATTTC 58.416 37.037 7.42 0.00 46.84 2.17
1544 1557 7.540400 GTGATCTACTGATCTATGTGATTTCCG 59.460 40.741 7.42 0.00 46.84 4.30
1580 1593 2.397252 GCATCAGTCGTCTTGCGC 59.603 61.111 0.00 0.00 41.07 6.09
1619 2514 2.865670 GCATTTTCACGGCATTGTTCCA 60.866 45.455 0.00 0.00 0.00 3.53
1659 2555 9.599866 TGTAATGTAGACTGGATTTATGTTCTG 57.400 33.333 0.00 0.00 0.00 3.02
1707 2603 3.130340 GTGCCATGTAAACCGATTGGAAT 59.870 43.478 5.81 0.00 39.21 3.01
1715 2611 5.463724 TGTAAACCGATTGGAATTTGTTTGC 59.536 36.000 5.81 0.00 39.21 3.68
1772 2668 1.457455 CCCAAAACCAGGGCACTGT 60.457 57.895 16.38 0.00 43.36 3.55
1785 2681 0.110056 GCACTGTCAAGATTGTGGCG 60.110 55.000 0.00 0.00 0.00 5.69
1843 2739 0.957888 GGCACTCCCTTTCAGCAGAC 60.958 60.000 0.00 0.00 0.00 3.51
1950 3082 6.923199 ATTTCAAATGAAGGATGGTTCAGT 57.077 33.333 0.00 0.00 39.78 3.41
2027 3164 1.009829 AATGAGAGCCGTTCAATCGC 58.990 50.000 0.00 0.00 0.00 4.58
2028 3165 0.108186 ATGAGAGCCGTTCAATCGCA 60.108 50.000 0.00 0.00 0.00 5.10
2029 3166 0.108186 TGAGAGCCGTTCAATCGCAT 60.108 50.000 0.00 0.00 0.00 4.73
2030 3167 0.579156 GAGAGCCGTTCAATCGCATC 59.421 55.000 0.00 0.00 0.00 3.91
2031 3168 1.148157 AGAGCCGTTCAATCGCATCG 61.148 55.000 0.00 0.00 0.00 3.84
2047 3184 2.671070 GCATCGTGGTTGTCAAATTCCC 60.671 50.000 0.00 0.00 0.00 3.97
2056 3193 8.792633 CGTGGTTGTCAAATTCCCATATAATAT 58.207 33.333 0.00 0.00 0.00 1.28
2057 3194 9.912634 GTGGTTGTCAAATTCCCATATAATATG 57.087 33.333 0.00 0.00 0.00 1.78
2078 3215 5.041951 TGTTCCTTTGATTTCGATTTCCG 57.958 39.130 0.00 0.00 40.25 4.30
2079 3216 4.517453 TGTTCCTTTGATTTCGATTTCCGT 59.483 37.500 0.00 0.00 39.75 4.69
2080 3217 5.701750 TGTTCCTTTGATTTCGATTTCCGTA 59.298 36.000 0.00 0.00 39.75 4.02
2081 3218 6.373216 TGTTCCTTTGATTTCGATTTCCGTAT 59.627 34.615 0.00 0.00 39.75 3.06
2082 3219 6.995511 TCCTTTGATTTCGATTTCCGTATT 57.004 33.333 0.00 0.00 39.75 1.89
2083 3220 7.385778 TCCTTTGATTTCGATTTCCGTATTT 57.614 32.000 0.00 0.00 39.75 1.40
2084 3221 8.495361 TCCTTTGATTTCGATTTCCGTATTTA 57.505 30.769 0.00 0.00 39.75 1.40
2085 3222 8.392612 TCCTTTGATTTCGATTTCCGTATTTAC 58.607 33.333 0.00 0.00 39.75 2.01
2086 3223 7.642586 CCTTTGATTTCGATTTCCGTATTTACC 59.357 37.037 0.00 0.00 39.75 2.85
2087 3224 7.852971 TTGATTTCGATTTCCGTATTTACCT 57.147 32.000 0.00 0.00 39.75 3.08
2088 3225 8.945481 TTGATTTCGATTTCCGTATTTACCTA 57.055 30.769 0.00 0.00 39.75 3.08
2089 3226 8.583810 TGATTTCGATTTCCGTATTTACCTAG 57.416 34.615 0.00 0.00 39.75 3.02
2090 3227 8.415553 TGATTTCGATTTCCGTATTTACCTAGA 58.584 33.333 0.00 0.00 39.75 2.43
2091 3228 9.420551 GATTTCGATTTCCGTATTTACCTAGAT 57.579 33.333 0.00 0.00 39.75 1.98
2092 3229 8.807667 TTTCGATTTCCGTATTTACCTAGATC 57.192 34.615 0.00 0.00 39.75 2.75
2093 3230 6.917533 TCGATTTCCGTATTTACCTAGATCC 58.082 40.000 0.00 0.00 39.75 3.36
2094 3231 6.718454 TCGATTTCCGTATTTACCTAGATCCT 59.282 38.462 0.00 0.00 39.75 3.24
2095 3232 7.028361 CGATTTCCGTATTTACCTAGATCCTC 58.972 42.308 0.00 0.00 0.00 3.71
2096 3233 7.094291 CGATTTCCGTATTTACCTAGATCCTCT 60.094 40.741 0.00 0.00 0.00 3.69
2097 3234 7.909485 TTTCCGTATTTACCTAGATCCTCTT 57.091 36.000 0.00 0.00 0.00 2.85
2098 3235 7.909485 TTCCGTATTTACCTAGATCCTCTTT 57.091 36.000 0.00 0.00 0.00 2.52
2099 3236 7.909485 TCCGTATTTACCTAGATCCTCTTTT 57.091 36.000 0.00 0.00 0.00 2.27
2100 3237 8.315220 TCCGTATTTACCTAGATCCTCTTTTT 57.685 34.615 0.00 0.00 0.00 1.94
2133 3270 4.034410 GGGACCTAGATCCTCTTTGACTT 58.966 47.826 2.23 0.00 38.95 3.01
2151 3289 7.692460 TTGACTTAAAGATCATCACAATGCT 57.308 32.000 0.00 0.00 32.58 3.79
2167 3305 5.694910 CACAATGCTCTGAAAGAAAGCAAAT 59.305 36.000 0.00 0.00 45.52 2.32
2190 3328 2.660552 AAGTGGCACGTCCGTTCG 60.661 61.111 12.71 0.00 37.80 3.95
2197 3335 1.082117 GCACGTCCGTTCGAATCCAT 61.082 55.000 0.00 0.00 34.70 3.41
2200 3338 2.280708 CACGTCCGTTCGAATCCATTAC 59.719 50.000 0.00 0.00 34.70 1.89
2258 3424 2.411748 TGTAGCAAGAAAATCGAGTGCG 59.588 45.455 0.00 0.00 40.17 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.466543 TGAAGGCCTAACACACACGT 59.533 50.000 5.16 0.00 0.00 4.49
9 10 1.808411 ATGAAGGCCTAACACACACG 58.192 50.000 5.16 0.00 0.00 4.49
10 11 7.878127 ACATATATATGAAGGCCTAACACACAC 59.122 37.037 26.05 0.00 37.15 3.82
11 12 7.877612 CACATATATATGAAGGCCTAACACACA 59.122 37.037 26.05 0.08 37.15 3.72
12 13 7.878127 ACACATATATATGAAGGCCTAACACAC 59.122 37.037 26.05 0.00 37.15 3.82
13 14 7.877612 CACACATATATATGAAGGCCTAACACA 59.122 37.037 26.05 4.89 37.15 3.72
14 15 7.878127 ACACACATATATATGAAGGCCTAACAC 59.122 37.037 26.05 0.00 37.15 3.32
15 16 7.973402 ACACACATATATATGAAGGCCTAACA 58.027 34.615 26.05 10.71 37.15 2.41
16 17 8.848474 AACACACATATATATGAAGGCCTAAC 57.152 34.615 26.05 3.96 37.15 2.34
17 18 9.860650 AAAACACACATATATATGAAGGCCTAA 57.139 29.630 26.05 0.00 37.15 2.69
18 19 9.860650 AAAAACACACATATATATGAAGGCCTA 57.139 29.630 26.05 0.00 37.15 3.93
19 20 8.766994 AAAAACACACATATATATGAAGGCCT 57.233 30.769 26.05 0.00 37.15 5.19
81 82 9.934641 CGGTTTTGAAAAATTTGAATTTTGTTG 57.065 25.926 13.45 0.00 45.16 3.33
82 83 9.899226 TCGGTTTTGAAAAATTTGAATTTTGTT 57.101 22.222 13.45 1.62 45.16 2.83
83 84 9.553418 CTCGGTTTTGAAAAATTTGAATTTTGT 57.447 25.926 13.45 6.00 45.16 2.83
84 85 8.522661 GCTCGGTTTTGAAAAATTTGAATTTTG 58.477 29.630 13.45 1.84 45.16 2.44
86 87 7.984391 AGCTCGGTTTTGAAAAATTTGAATTT 58.016 26.923 0.00 0.00 40.15 1.82
87 88 7.254761 GGAGCTCGGTTTTGAAAAATTTGAATT 60.255 33.333 7.83 0.00 0.00 2.17
88 89 6.202762 GGAGCTCGGTTTTGAAAAATTTGAAT 59.797 34.615 7.83 0.00 0.00 2.57
89 90 5.522097 GGAGCTCGGTTTTGAAAAATTTGAA 59.478 36.000 7.83 0.00 0.00 2.69
90 91 5.047188 GGAGCTCGGTTTTGAAAAATTTGA 58.953 37.500 7.83 0.00 0.00 2.69
91 92 4.808364 TGGAGCTCGGTTTTGAAAAATTTG 59.192 37.500 7.83 0.00 0.00 2.32
92 93 5.017294 TGGAGCTCGGTTTTGAAAAATTT 57.983 34.783 7.83 0.00 0.00 1.82
93 94 4.664150 TGGAGCTCGGTTTTGAAAAATT 57.336 36.364 7.83 0.00 0.00 1.82
94 95 4.559153 CATGGAGCTCGGTTTTGAAAAAT 58.441 39.130 7.83 0.00 0.00 1.82
95 96 3.243704 CCATGGAGCTCGGTTTTGAAAAA 60.244 43.478 5.56 0.00 0.00 1.94
96 97 2.295909 CCATGGAGCTCGGTTTTGAAAA 59.704 45.455 5.56 0.00 0.00 2.29
97 98 1.885887 CCATGGAGCTCGGTTTTGAAA 59.114 47.619 5.56 0.00 0.00 2.69
98 99 1.073125 TCCATGGAGCTCGGTTTTGAA 59.927 47.619 11.44 0.00 0.00 2.69
99 100 0.690192 TCCATGGAGCTCGGTTTTGA 59.310 50.000 11.44 0.00 0.00 2.69
100 101 1.089920 CTCCATGGAGCTCGGTTTTG 58.910 55.000 28.45 2.18 35.31 2.44
101 102 3.558674 CTCCATGGAGCTCGGTTTT 57.441 52.632 28.45 0.00 35.31 2.43
110 111 3.160047 AGGCCGAGCTCCATGGAG 61.160 66.667 33.73 33.73 44.56 3.86
111 112 3.157252 GAGGCCGAGCTCCATGGA 61.157 66.667 15.27 15.27 0.00 3.41
112 113 4.247380 GGAGGCCGAGCTCCATGG 62.247 72.222 4.97 4.97 39.45 3.66
113 114 3.473647 TGGAGGCCGAGCTCCATG 61.474 66.667 8.47 0.00 44.02 3.66
115 116 2.927856 TTTGGAGGCCGAGCTCCA 60.928 61.111 8.47 7.35 46.84 3.86
116 117 2.124942 CTTTGGAGGCCGAGCTCC 60.125 66.667 8.47 0.00 40.05 4.70
117 118 1.448717 GTCTTTGGAGGCCGAGCTC 60.449 63.158 2.73 2.73 0.00 4.09
118 119 1.768684 TTGTCTTTGGAGGCCGAGCT 61.769 55.000 0.00 0.00 0.00 4.09
119 120 0.678048 ATTGTCTTTGGAGGCCGAGC 60.678 55.000 0.00 0.00 0.00 5.03
120 121 2.691409 TATTGTCTTTGGAGGCCGAG 57.309 50.000 0.00 0.00 0.00 4.63
121 122 2.158813 GGATATTGTCTTTGGAGGCCGA 60.159 50.000 0.00 0.00 0.00 5.54
122 123 2.222027 GGATATTGTCTTTGGAGGCCG 58.778 52.381 0.00 0.00 0.00 6.13
123 124 2.222027 CGGATATTGTCTTTGGAGGCC 58.778 52.381 0.00 0.00 0.00 5.19
124 125 1.604278 GCGGATATTGTCTTTGGAGGC 59.396 52.381 0.00 0.00 0.00 4.70
125 126 2.158755 AGGCGGATATTGTCTTTGGAGG 60.159 50.000 0.00 0.00 0.00 4.30
126 127 3.199880 AGGCGGATATTGTCTTTGGAG 57.800 47.619 0.00 0.00 0.00 3.86
127 128 3.709653 ACTAGGCGGATATTGTCTTTGGA 59.290 43.478 0.00 0.00 0.00 3.53
128 129 4.073293 ACTAGGCGGATATTGTCTTTGG 57.927 45.455 0.00 0.00 0.00 3.28
129 130 6.761714 AGTAAACTAGGCGGATATTGTCTTTG 59.238 38.462 0.00 0.00 0.00 2.77
130 131 6.761714 CAGTAAACTAGGCGGATATTGTCTTT 59.238 38.462 0.00 0.00 0.00 2.52
131 132 6.281405 CAGTAAACTAGGCGGATATTGTCTT 58.719 40.000 0.00 0.00 0.00 3.01
132 133 5.739358 GCAGTAAACTAGGCGGATATTGTCT 60.739 44.000 0.00 0.00 0.00 3.41
133 134 4.448060 GCAGTAAACTAGGCGGATATTGTC 59.552 45.833 0.00 0.00 0.00 3.18
134 135 4.101119 AGCAGTAAACTAGGCGGATATTGT 59.899 41.667 0.00 0.00 0.00 2.71
135 136 4.632153 AGCAGTAAACTAGGCGGATATTG 58.368 43.478 0.00 0.00 0.00 1.90
136 137 4.957684 AGCAGTAAACTAGGCGGATATT 57.042 40.909 0.00 0.00 0.00 1.28
137 138 7.713734 TTATAGCAGTAAACTAGGCGGATAT 57.286 36.000 0.00 0.00 0.00 1.63
138 139 7.232127 ACTTTATAGCAGTAAACTAGGCGGATA 59.768 37.037 0.00 0.00 0.00 2.59
139 140 6.041751 ACTTTATAGCAGTAAACTAGGCGGAT 59.958 38.462 0.00 0.00 0.00 4.18
140 141 5.361857 ACTTTATAGCAGTAAACTAGGCGGA 59.638 40.000 0.00 0.00 0.00 5.54
141 142 5.598769 ACTTTATAGCAGTAAACTAGGCGG 58.401 41.667 0.00 0.00 0.00 6.13
142 143 7.535489 AAACTTTATAGCAGTAAACTAGGCG 57.465 36.000 0.00 0.00 0.00 5.52
181 182 5.308014 AGGGGCTCAAAATGTCAAAATTTC 58.692 37.500 0.00 0.00 0.00 2.17
202 203 9.289303 CGGATAGAAATTGTCACATTTTAAAGG 57.711 33.333 0.00 0.00 0.00 3.11
226 227 9.058424 GTTTACTGCTATAAAGTTTTAAAGCGG 57.942 33.333 17.27 17.27 0.00 5.52
276 277 8.537016 GCCCCTACTTTTTGTTATCCTAATTTT 58.463 33.333 0.00 0.00 0.00 1.82
294 295 0.621571 TTGCCTGAGATGCCCCTACT 60.622 55.000 0.00 0.00 0.00 2.57
320 321 3.056107 CCTCCGGAGTGTTCAACTTCATA 60.056 47.826 29.25 0.00 40.07 2.15
330 331 2.107552 TCCATTTTTCCTCCGGAGTGTT 59.892 45.455 29.25 5.80 31.21 3.32
393 394 6.013812 CCCCTGAAATTTCAACATTTTCCCTA 60.014 38.462 20.82 0.00 36.64 3.53
398 399 8.314021 GTCTATCCCCTGAAATTTCAACATTTT 58.686 33.333 20.82 8.02 36.64 1.82
403 404 6.378280 ACATGTCTATCCCCTGAAATTTCAAC 59.622 38.462 20.82 13.74 36.64 3.18
439 447 5.221303 TGCAAATTTCAAACCTCCTCTGAAG 60.221 40.000 0.00 0.00 31.11 3.02
461 469 7.307694 TCAGTGTCATTCTAAATCAAACATGC 58.692 34.615 0.00 0.00 0.00 4.06
468 476 6.377996 CCCCAAATCAGTGTCATTCTAAATCA 59.622 38.462 0.00 0.00 0.00 2.57
470 478 6.256053 ACCCCAAATCAGTGTCATTCTAAAT 58.744 36.000 0.00 0.00 0.00 1.40
482 490 2.046292 CCCAACAAACCCCAAATCAGT 58.954 47.619 0.00 0.00 0.00 3.41
575 584 5.052567 CGTCACGACAAGATAATACCGAAAG 60.053 44.000 0.00 0.00 0.00 2.62
610 620 0.467290 TGTCCAAACAAGAGGGGTGC 60.467 55.000 0.00 0.00 30.70 5.01
680 690 5.124776 TCGCCCCATAAACTAAACAATGAAG 59.875 40.000 0.00 0.00 0.00 3.02
752 765 1.002134 AAGGGACATTGTCTGCCGG 60.002 57.895 16.02 0.00 32.47 6.13
756 769 5.065914 TCTTCAAAGAAGGGACATTGTCTG 58.934 41.667 16.02 5.36 30.23 3.51
809 822 5.240623 TGAAGGAGTTGACGTTGCATATTTT 59.759 36.000 0.00 0.00 0.00 1.82
887 900 2.023598 TCATCAGACTCCCCAGATGACT 60.024 50.000 0.00 0.00 41.21 3.41
909 922 3.369756 TGACTTCAACGCCATATTCGTTC 59.630 43.478 8.95 1.05 46.81 3.95
1018 1031 2.486966 GATGCTTGAACTGCCGGC 59.513 61.111 22.73 22.73 0.00 6.13
1239 1252 0.531753 GCGAATCCCTCTTCTGAGCC 60.532 60.000 0.00 0.00 38.93 4.70
1306 1319 2.554032 CCCATTGACAAAGAAGCTTCGT 59.446 45.455 20.43 15.11 0.00 3.85
1318 1331 8.857098 GTCTAGTACATTATCTACCCATTGACA 58.143 37.037 0.00 0.00 0.00 3.58
1324 1337 7.157947 TGAGGTCTAGTACATTATCTACCCA 57.842 40.000 0.00 0.00 0.00 4.51
1345 1358 8.236586 TCGATGAAACATGGTAAGAAAAATGAG 58.763 33.333 0.00 0.00 0.00 2.90
1441 1454 4.157656 CCGGTAAAGAATTGGAAATGAGCA 59.842 41.667 0.00 0.00 0.00 4.26
1542 1555 2.555199 CTGAAAGCCTAATGTCTCCGG 58.445 52.381 0.00 0.00 0.00 5.14
1544 1557 2.293170 GCCTGAAAGCCTAATGTCTCC 58.707 52.381 0.00 0.00 0.00 3.71
1619 2514 9.944376 AGTCTACATTACAAGTTCACAACATAT 57.056 29.630 0.00 0.00 0.00 1.78
1659 2555 4.563976 GCATCACAAATTCACCATTGTAGC 59.436 41.667 0.00 0.00 37.66 3.58
1707 2603 1.552337 TGTGGGCTCAAAGCAAACAAA 59.448 42.857 0.00 0.00 44.75 2.83
1715 2611 1.072965 AGGTCTCTTGTGGGCTCAAAG 59.927 52.381 0.00 0.00 0.00 2.77
1800 2696 7.875554 GCCCAGACCAATGAATTTAACTTTTTA 59.124 33.333 0.00 0.00 0.00 1.52
1868 2764 6.959361 AGTAATGTGTTTCAACAGTCACATC 58.041 36.000 9.49 0.53 46.33 3.06
1935 3067 2.026262 GCCCTAACTGAACCATCCTTCA 60.026 50.000 0.00 0.00 0.00 3.02
1943 3075 0.542333 GAGGAGGCCCTAACTGAACC 59.458 60.000 0.00 0.00 44.53 3.62
1950 3082 2.270434 ACATCAAGAGGAGGCCCTAA 57.730 50.000 0.00 0.00 44.53 2.69
2007 3139 1.267732 GCGATTGAACGGCTCTCATTG 60.268 52.381 0.00 0.00 0.00 2.82
2008 3140 1.009829 GCGATTGAACGGCTCTCATT 58.990 50.000 0.00 0.00 0.00 2.57
2027 3164 2.556189 TGGGAATTTGACAACCACGATG 59.444 45.455 0.00 0.00 0.00 3.84
2028 3165 2.870175 TGGGAATTTGACAACCACGAT 58.130 42.857 0.00 0.00 0.00 3.73
2029 3166 2.350057 TGGGAATTTGACAACCACGA 57.650 45.000 0.00 0.00 0.00 4.35
2030 3167 4.981806 ATATGGGAATTTGACAACCACG 57.018 40.909 0.00 0.00 33.42 4.94
2031 3168 9.912634 CATATTATATGGGAATTTGACAACCAC 57.087 33.333 4.38 0.00 33.42 4.16
2056 3193 4.517453 ACGGAAATCGAAATCAAAGGAACA 59.483 37.500 0.00 0.00 42.43 3.18
2057 3194 5.043189 ACGGAAATCGAAATCAAAGGAAC 57.957 39.130 0.00 0.00 42.43 3.62
2068 3205 7.232127 AGGATCTAGGTAAATACGGAAATCGAA 59.768 37.037 0.00 0.00 42.43 3.71
2102 3239 0.996583 ATCTAGGTCCCCCGCAAAAA 59.003 50.000 0.00 0.00 35.12 1.94
2103 3240 0.544697 GATCTAGGTCCCCCGCAAAA 59.455 55.000 0.00 0.00 35.12 2.44
2104 3241 1.342672 GGATCTAGGTCCCCCGCAAA 61.343 60.000 11.38 0.00 35.12 3.68
2105 3242 1.764854 GGATCTAGGTCCCCCGCAA 60.765 63.158 11.38 0.00 35.12 4.85
2106 3243 2.122989 GGATCTAGGTCCCCCGCA 60.123 66.667 11.38 0.00 35.12 5.69
2107 3244 1.909287 GAGGATCTAGGTCCCCCGC 60.909 68.421 18.95 2.34 39.17 6.13
2108 3245 4.523512 GAGGATCTAGGTCCCCCG 57.476 66.667 18.95 0.00 39.17 5.73
2140 3278 4.857588 GCTTTCTTTCAGAGCATTGTGATG 59.142 41.667 0.00 0.00 36.45 3.07
2150 3288 7.866393 ACTTGATTCATTTGCTTTCTTTCAGAG 59.134 33.333 0.00 0.00 0.00 3.35
2151 3289 7.650504 CACTTGATTCATTTGCTTTCTTTCAGA 59.349 33.333 0.00 0.00 0.00 3.27
2167 3305 0.948623 CGGACGTGCCACTTGATTCA 60.949 55.000 0.00 0.00 35.94 2.57


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

AutoCloner maintained by Alex Coulton.