Multiple sequence alignment - TraesCS7D01G168100

Loading Multiple Alignment...

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 TraesCS7D01G168100 chr7D 100.000 2294 0 0 1 2294 118160549 118162842 0.000000e+00 4237
1 TraesCS7D01G168100 chr7D 82.849 344 24 9 1665 1979 118160577 118160240 2.240000e-70 276
2 TraesCS7D01G168100 chr7A 86.964 1864 111 56 2 1781 122682324 122684139 0.000000e+00 1975
3 TraesCS7D01G168100 chr7A 88.095 378 41 4 1917 2292 122684616 122684991 1.620000e-121 446
4 TraesCS7D01G168100 chr7A 90.860 186 13 4 1661 1846 122682355 122682174 1.760000e-61 246
5 TraesCS7D01G168100 chr7B 91.965 809 45 9 734 1539 79315562 79316353 0.000000e+00 1116
6 TraesCS7D01G168100 chr7B 87.925 530 29 10 49 571 79313008 79313509 1.960000e-165 592
7 TraesCS7D01G168100 chr7B 89.855 345 26 4 1871 2208 79316896 79317238 3.500000e-118 435
8 TraesCS7D01G168100 chr7B 94.375 160 6 3 1630 1787 79316350 79316508 2.280000e-60 243
9 TraesCS7D01G168100 chr7B 94.079 152 6 2 568 719 79315356 79315504 6.380000e-56 228
10 TraesCS7D01G168100 chr7B 93.525 139 4 4 1668 1806 79313006 79312873 3.860000e-48 202
11 TraesCS7D01G168100 chr6A 97.030 101 1 2 1682 1781 55551265 55551364 3.920000e-38 169
12 TraesCS7D01G168100 chrUn 96.117 103 2 2 1681 1782 21199035 21198934 1.410000e-37 167
13 TraesCS7D01G168100 chr2D 93.519 108 7 0 1676 1783 122055658 122055551 6.560000e-36 161
14 TraesCS7D01G168100 chr4B 91.818 110 6 3 1686 1794 559287198 559287091 1.420000e-32 150
15 TraesCS7D01G168100 chr3A 87.619 105 9 4 2159 2261 40849397 40849295 4.000000e-23 119


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 TraesCS7D01G168100 chr7D 118160549 118162842 2293 False 4237.0 4237 100.0000 1 2294 1 chr7D.!!$F1 2293
1 TraesCS7D01G168100 chr7A 122682324 122684991 2667 False 1210.5 1975 87.5295 2 2292 2 chr7A.!!$F1 2290
2 TraesCS7D01G168100 chr7B 79313008 79317238 4230 False 522.8 1116 91.6398 49 2208 5 chr7B.!!$F1 2159

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
202 210 0.0293 CACAAACTGACCACCTTGCG 59.971 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2060 4687 0.323725 GAAGGGGAGGCTGCATTTCA 60.324 55.0 8.68 0.0 0.0 2.69 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
25 26 5.677178 GTCGTTGTTGAAAAGATTCTCACAC 59.323 40.000 0.00 0.00 36.48 3.82
29 30 7.855409 CGTTGTTGAAAAGATTCTCACACAATA 59.145 33.333 0.00 0.00 36.48 1.90
30 31 9.683069 GTTGTTGAAAAGATTCTCACACAATAT 57.317 29.630 0.00 0.00 36.48 1.28
39 40 9.725019 AAGATTCTCACACAATATTACTCAACA 57.275 29.630 0.00 0.00 0.00 3.33
40 41 9.376075 AGATTCTCACACAATATTACTCAACAG 57.624 33.333 0.00 0.00 0.00 3.16
42 43 5.874810 TCTCACACAATATTACTCAACAGGC 59.125 40.000 0.00 0.00 0.00 4.85
43 44 5.555966 TCACACAATATTACTCAACAGGCA 58.444 37.500 0.00 0.00 0.00 4.75
44 45 5.411361 TCACACAATATTACTCAACAGGCAC 59.589 40.000 0.00 0.00 0.00 5.01
45 46 4.391830 ACACAATATTACTCAACAGGCACG 59.608 41.667 0.00 0.00 0.00 5.34
90 92 2.161410 TGGCCGTCAATTGATTTTCGAG 59.839 45.455 12.12 5.98 0.00 4.04
95 100 5.003778 GCCGTCAATTGATTTTCGAGAATTG 59.996 40.000 12.12 6.22 37.21 2.32
115 120 1.994779 GCAATTCATTTTGCCTCCACG 59.005 47.619 0.00 0.00 44.94 4.94
118 123 0.958091 TTCATTTTGCCTCCACGTGG 59.042 50.000 29.26 29.26 0.00 4.94
125 130 2.665000 CCTCCACGTGGCATGTCT 59.335 61.111 30.25 0.00 34.44 3.41
126 131 1.448540 CCTCCACGTGGCATGTCTC 60.449 63.158 30.25 0.00 34.44 3.36
127 132 1.293179 CTCCACGTGGCATGTCTCA 59.707 57.895 30.25 9.01 34.44 3.27
128 133 1.005037 TCCACGTGGCATGTCTCAC 60.005 57.895 30.25 2.55 34.44 3.51
160 168 3.130160 GGCTGAGGAGGCAAAGCG 61.130 66.667 0.00 0.00 44.34 4.68
185 193 1.993370 CTTTCCTCGGACGATTGACAC 59.007 52.381 0.00 0.00 0.00 3.67
197 205 2.032030 CGATTGACACAAACTGACCACC 60.032 50.000 0.00 0.00 0.00 4.61
198 206 2.799126 TTGACACAAACTGACCACCT 57.201 45.000 0.00 0.00 0.00 4.00
199 207 2.799126 TGACACAAACTGACCACCTT 57.201 45.000 0.00 0.00 0.00 3.50
200 208 2.364632 TGACACAAACTGACCACCTTG 58.635 47.619 0.00 0.00 0.00 3.61
201 209 1.065551 GACACAAACTGACCACCTTGC 59.934 52.381 0.00 0.00 0.00 4.01
202 210 0.029300 CACAAACTGACCACCTTGCG 59.971 55.000 0.00 0.00 0.00 4.85
203 211 1.008538 CAAACTGACCACCTTGCGC 60.009 57.895 0.00 0.00 0.00 6.09
204 212 2.542907 AAACTGACCACCTTGCGCG 61.543 57.895 0.00 0.00 0.00 6.86
205 213 4.988598 ACTGACCACCTTGCGCGG 62.989 66.667 8.83 0.14 0.00 6.46
206 214 4.988598 CTGACCACCTTGCGCGGT 62.989 66.667 8.83 2.54 37.93 5.68
207 215 4.555709 TGACCACCTTGCGCGGTT 62.556 61.111 8.83 0.00 34.29 4.44
208 216 3.284449 GACCACCTTGCGCGGTTT 61.284 61.111 8.83 0.00 34.29 3.27
209 217 3.249973 GACCACCTTGCGCGGTTTC 62.250 63.158 8.83 1.20 34.29 2.78
210 218 4.038080 CCACCTTGCGCGGTTTCC 62.038 66.667 8.83 0.00 34.29 3.13
211 219 4.038080 CACCTTGCGCGGTTTCCC 62.038 66.667 8.83 0.00 34.29 3.97
212 220 4.572571 ACCTTGCGCGGTTTCCCA 62.573 61.111 8.83 0.00 31.94 4.37
213 221 4.038080 CCTTGCGCGGTTTCCCAC 62.038 66.667 8.83 0.00 0.00 4.61
214 222 4.383602 CTTGCGCGGTTTCCCACG 62.384 66.667 8.83 0.00 39.31 4.94
215 223 4.912485 TTGCGCGGTTTCCCACGA 62.912 61.111 8.83 0.00 38.58 4.35
219 227 3.423154 GCGGTTTCCCACGAGCAG 61.423 66.667 0.00 0.00 31.93 4.24
220 228 3.423154 CGGTTTCCCACGAGCAGC 61.423 66.667 0.00 0.00 0.00 5.25
221 229 2.032681 GGTTTCCCACGAGCAGCT 59.967 61.111 0.00 0.00 0.00 4.24
222 230 2.035442 GGTTTCCCACGAGCAGCTC 61.035 63.158 12.94 12.94 0.00 4.09
238 250 2.755876 TCGCATCGCCTGACTCCT 60.756 61.111 0.00 0.00 0.00 3.69
282 294 0.738975 AATCGCAGACGCTACAGCTA 59.261 50.000 0.00 0.00 42.51 3.32
492 512 3.319122 CCTGTTAATTCCAGCCATTAGCC 59.681 47.826 0.56 0.00 45.47 3.93
534 554 0.525455 GCCCGAAAATGGTCGATTGC 60.525 55.000 0.00 0.00 43.86 3.56
561 581 4.666908 GCCTTTTTCTCATTTCGAGTCGAC 60.667 45.833 16.28 7.70 42.88 4.20
641 2528 2.046988 CTCATGCGTGCCACCTCA 60.047 61.111 0.00 0.00 0.00 3.86
660 2547 0.457851 AGAGACGATCGCTTCCCAAG 59.542 55.000 16.60 0.00 0.00 3.61
673 2560 1.078848 CCCAAGGCGGAGTTCAGAG 60.079 63.158 0.00 0.00 36.56 3.35
674 2561 1.743252 CCAAGGCGGAGTTCAGAGC 60.743 63.158 0.00 0.00 36.56 4.09
776 2705 1.538876 AGGCTTGCACCACCTCCTA 60.539 57.895 0.00 0.00 0.00 2.94
800 2730 2.515757 TTGCGTGCAAGCCTCACA 60.516 55.556 22.00 0.00 34.27 3.58
826 2756 1.852280 GGAAAAGCAACTTGACGCAAC 59.148 47.619 0.00 0.00 0.00 4.17
846 2776 4.175337 GCATGCCGGCCACCTCTA 62.175 66.667 26.77 2.60 0.00 2.43
847 2777 2.203070 CATGCCGGCCACCTCTAC 60.203 66.667 26.77 0.00 0.00 2.59
848 2778 2.687200 ATGCCGGCCACCTCTACA 60.687 61.111 26.77 0.73 0.00 2.74
890 2820 1.419374 GTACACAGGACACAGAAGCG 58.581 55.000 0.00 0.00 0.00 4.68
956 2887 1.630244 CCGGTTCGTAGTCTCGTCGT 61.630 60.000 0.00 0.00 0.00 4.34
957 2888 0.517946 CGGTTCGTAGTCTCGTCGTG 60.518 60.000 0.00 0.00 0.00 4.35
958 2889 0.792640 GGTTCGTAGTCTCGTCGTGA 59.207 55.000 0.00 0.00 0.00 4.35
998 2939 0.966179 GCTGGTTTAGTTGTTGGGGG 59.034 55.000 0.00 0.00 0.00 5.40
1018 2959 3.567579 ATGGGCAACGTGGTGGAGG 62.568 63.158 0.00 0.00 37.60 4.30
1302 3249 1.784525 GCGCAGACTAGTTGAAGTGT 58.215 50.000 0.30 0.00 0.00 3.55
1306 3253 4.762809 CGCAGACTAGTTGAAGTGTTTTC 58.237 43.478 0.00 0.00 0.00 2.29
1307 3254 4.508124 CGCAGACTAGTTGAAGTGTTTTCT 59.492 41.667 0.00 0.00 0.00 2.52
1318 3265 4.094887 TGAAGTGTTTTCTGTGTTGAGCTC 59.905 41.667 6.82 6.82 0.00 4.09
1335 3282 1.914634 CTCATGTACGAGTCAGTGGC 58.085 55.000 0.00 0.00 0.00 5.01
1380 3327 2.983907 TCGTTGGTAGTGGTTGTTCA 57.016 45.000 0.00 0.00 0.00 3.18
1396 3343 8.021396 GTGGTTGTTCATAAGAAAGGATTGTAC 58.979 37.037 0.00 0.00 35.08 2.90
1402 3349 8.879759 GTTCATAAGAAAGGATTGTACGATGAA 58.120 33.333 0.00 0.00 35.08 2.57
1408 3355 8.425577 AGAAAGGATTGTACGATGAACATAAG 57.574 34.615 0.00 0.00 0.00 1.73
1413 3360 8.041323 AGGATTGTACGATGAACATAAGAAAGT 58.959 33.333 0.00 0.00 0.00 2.66
1420 3367 8.373048 ACGATGAACATAAGAAAGTTTGTGTA 57.627 30.769 0.00 0.00 32.20 2.90
1449 3396 4.813161 AGTAGATTGAACTGCAATGGATCG 59.187 41.667 0.00 0.00 46.90 3.69
1460 3407 5.155509 TGCAATGGATCGTTCGATTTTAG 57.844 39.130 9.05 1.48 28.89 1.85
1499 3446 2.621338 CTGTTTCTGGCTGCTTATCGA 58.379 47.619 0.00 0.00 0.00 3.59
1503 3450 1.596477 CTGGCTGCTTATCGAGGCC 60.596 63.158 0.00 0.00 42.73 5.19
1516 3466 2.202932 AGGCCGATAGCTGTTGCG 60.203 61.111 0.00 0.00 45.42 4.85
1542 3492 4.919754 GTGTTCAGCATGGTTTCAATCTTC 59.080 41.667 0.00 0.00 36.16 2.87
1570 3521 3.160269 CAGACTCCCCTTTTGCAAGATT 58.840 45.455 0.00 0.00 30.57 2.40
1611 3562 1.260544 ATGCAGCCTCCCTTTGTTTC 58.739 50.000 0.00 0.00 0.00 2.78
1617 3581 1.344438 GCCTCCCTTTGTTTCTTTGGG 59.656 52.381 0.00 0.00 39.22 4.12
1620 3584 2.957474 TCCCTTTGTTTCTTTGGGAGG 58.043 47.619 0.00 0.00 41.57 4.30
1627 3591 2.512056 TGTTTCTTTGGGAGGGAGACAA 59.488 45.455 0.00 0.00 0.00 3.18
1663 3628 8.388103 CGTGAATTTTTGTATAGGACACTTAGG 58.612 37.037 0.00 0.00 37.96 2.69
1664 3629 9.444600 GTGAATTTTTGTATAGGACACTTAGGA 57.555 33.333 0.00 0.00 37.96 2.94
1774 3739 2.160615 CGAATCTCTCAGGCGTCGATAT 59.839 50.000 0.00 0.00 0.00 1.63
1811 3776 9.762933 ATATATTTTGCCGAATTATTGTTGCTT 57.237 25.926 0.00 0.00 0.00 3.91
1813 3778 7.897575 ATTTTGCCGAATTATTGTTGCTTAA 57.102 28.000 0.00 0.00 0.00 1.85
1814 3779 7.715265 TTTTGCCGAATTATTGTTGCTTAAA 57.285 28.000 0.00 0.00 0.00 1.52
1815 3780 7.897575 TTTGCCGAATTATTGTTGCTTAAAT 57.102 28.000 0.00 0.00 0.00 1.40
1817 3782 7.288317 TGCCGAATTATTGTTGCTTAAATTG 57.712 32.000 0.00 0.00 0.00 2.32
1830 3977 6.343226 TGCTTAAATTGAAAGTTGCAACAC 57.657 33.333 30.11 20.14 0.00 3.32
1838 3985 2.331019 AAGTTGCAACACGAACCGGC 62.331 55.000 30.11 0.04 0.00 6.13
1849 3996 0.438445 CGAACCGGCATATATGTGCG 59.562 55.000 17.01 12.32 45.97 5.34
1852 3999 0.602638 ACCGGCATATATGTGCGTGG 60.603 55.000 23.77 23.77 45.97 4.94
1856 4003 2.601979 CGGCATATATGTGCGTGGTTTG 60.602 50.000 17.01 0.00 45.97 2.93
1858 4005 3.562141 GGCATATATGTGCGTGGTTTGTA 59.438 43.478 17.01 0.00 45.97 2.41
1859 4006 4.523813 GCATATATGTGCGTGGTTTGTAC 58.476 43.478 14.14 0.00 35.10 2.90
1864 4011 0.952010 GTGCGTGGTTTGTACGGGAT 60.952 55.000 0.00 0.00 41.56 3.85
1867 4014 1.595794 GCGTGGTTTGTACGGGATATG 59.404 52.381 0.00 0.00 41.56 1.78
1868 4015 2.206750 CGTGGTTTGTACGGGATATGG 58.793 52.381 0.00 0.00 37.86 2.74
1875 4495 4.974368 TTGTACGGGATATGGCTTTTTG 57.026 40.909 0.00 0.00 0.00 2.44
1881 4501 3.383185 CGGGATATGGCTTTTTGGCTAAA 59.617 43.478 0.00 0.00 42.34 1.85
1889 4509 5.062528 TGGCTTTTTGGCTAAATTTTGGAG 58.937 37.500 0.00 0.00 42.34 3.86
1893 4513 7.151976 GCTTTTTGGCTAAATTTTGGAGAGTA 58.848 34.615 0.00 0.00 0.00 2.59
1899 4519 6.214819 TGGCTAAATTTTGGAGAGTAGGTACT 59.785 38.462 0.00 0.00 46.37 2.73
1942 4567 8.645730 CACAATATGCATAGAGATGGATCTAC 57.354 38.462 12.79 0.00 42.61 2.59
1965 4590 6.993079 ACTATCCCGCAAAGAAAAGAAAATT 58.007 32.000 0.00 0.00 0.00 1.82
2035 4660 4.411869 TCTCACATAATATTGGCTGTCCCA 59.588 41.667 0.00 0.00 43.51 4.37
2054 4679 4.462483 TCCCATACCAAAATTGCTTCACTC 59.538 41.667 0.00 0.00 0.00 3.51
2060 4687 2.298163 CAAAATTGCTTCACTCTGGCCT 59.702 45.455 3.32 0.00 0.00 5.19
2076 4703 1.755783 CCTGAAATGCAGCCTCCCC 60.756 63.158 0.00 0.00 43.50 4.81
2079 4706 0.323725 TGAAATGCAGCCTCCCCTTC 60.324 55.000 0.00 0.00 0.00 3.46
2083 4710 0.411058 ATGCAGCCTCCCCTTCTTTT 59.589 50.000 0.00 0.00 0.00 2.27
2084 4711 0.540365 TGCAGCCTCCCCTTCTTTTG 60.540 55.000 0.00 0.00 0.00 2.44
2096 4724 3.368531 CCCTTCTTTTGGGTAGAGAGACG 60.369 52.174 0.00 0.00 39.82 4.18
2148 4776 0.533755 GAGGCCGAGCAATGCTACAT 60.534 55.000 8.12 0.00 39.88 2.29
2192 4821 4.641094 ACTTAGTCTTACGGAGAGTGATGG 59.359 45.833 8.24 0.83 38.51 3.51
2225 4854 3.023735 GGGAATGGGCCCCACTCT 61.024 66.667 22.27 0.00 42.62 3.24
2226 4855 1.696314 GGGAATGGGCCCCACTCTA 60.696 63.158 22.27 0.00 42.62 2.43
2233 4862 1.010294 TGGGCCCCACTCTAGGAATTA 59.990 52.381 22.27 0.00 0.00 1.40
2237 4866 2.696158 GCCCCACTCTAGGAATTAGGGA 60.696 54.545 0.00 0.00 36.96 4.20
2241 4870 4.946478 CACTCTAGGAATTAGGGAGTGG 57.054 50.000 16.12 4.99 45.61 4.00
2252 4881 7.018650 AGGAATTAGGGAGTGGGATAAATTAGG 59.981 40.741 0.00 0.00 0.00 2.69
2258 4887 3.555966 AGTGGGATAAATTAGGTGCTGC 58.444 45.455 0.00 0.00 0.00 5.25
2266 4895 2.563013 ATTAGGTGCTGCCAGCCCTG 62.563 60.000 27.11 0.41 41.51 4.45
2272 4901 2.421399 GCTGCCAGCCCTGAATTCC 61.421 63.158 5.06 0.00 34.48 3.01
2275 4904 1.755783 GCCAGCCCTGAATTCCCAG 60.756 63.158 2.27 0.00 0.00 4.45
2276 4905 2.001803 CCAGCCCTGAATTCCCAGA 58.998 57.895 2.27 0.00 36.29 3.86
2281 4910 0.995024 CCCTGAATTCCCAGAGTGGT 59.005 55.000 2.27 0.00 35.17 4.16
2283 4912 2.780010 CCCTGAATTCCCAGAGTGGTAT 59.220 50.000 2.27 0.00 35.17 2.73
2292 4921 4.684724 TCCCAGAGTGGTATCAACTAAGT 58.315 43.478 0.00 0.00 35.17 2.24
2293 4922 4.710375 TCCCAGAGTGGTATCAACTAAGTC 59.290 45.833 0.00 0.00 35.17 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.205565 GTGAGAATCTTTTCAACAACGACC 58.794 41.667 0.00 0.00 34.08 4.79
25 26 3.373748 TGCGTGCCTGTTGAGTAATATTG 59.626 43.478 0.00 0.00 0.00 1.90
29 30 1.890876 TTGCGTGCCTGTTGAGTAAT 58.109 45.000 0.00 0.00 0.00 1.89
30 31 1.601903 CTTTGCGTGCCTGTTGAGTAA 59.398 47.619 0.00 0.00 0.00 2.24
36 37 1.007038 CATGCTTTGCGTGCCTGTT 60.007 52.632 0.00 0.00 38.74 3.16
43 44 2.223782 ACACAAATGACATGCTTTGCGT 60.224 40.909 13.11 8.89 36.12 5.24
44 45 2.396601 ACACAAATGACATGCTTTGCG 58.603 42.857 13.11 8.41 36.12 4.85
45 46 4.053295 AGAACACAAATGACATGCTTTGC 58.947 39.130 13.11 0.00 36.12 3.68
115 120 2.034879 CACGGGTGAGACATGCCAC 61.035 63.158 0.00 0.00 0.00 5.01
118 123 0.037697 TGTACACGGGTGAGACATGC 60.038 55.000 0.00 0.00 0.00 4.06
160 168 0.105039 ATCGTCCGAGGAAAGCCATC 59.895 55.000 0.00 0.00 36.29 3.51
172 180 2.096909 GTCAGTTTGTGTCAATCGTCCG 60.097 50.000 0.00 0.00 0.00 4.79
185 193 1.008538 GCGCAAGGTGGTCAGTTTG 60.009 57.895 0.30 0.00 38.28 2.93
205 213 3.567473 GAGCTGCTCGTGGGAAAC 58.433 61.111 14.68 0.00 0.00 2.78
214 222 4.887987 AGGCGATGCGAGCTGCTC 62.888 66.667 19.53 19.53 46.63 4.26
217 225 3.260483 GTCAGGCGATGCGAGCTG 61.260 66.667 0.00 0.00 34.52 4.24
218 226 3.423162 GAGTCAGGCGATGCGAGCT 62.423 63.158 0.00 0.00 34.52 4.09
219 227 2.959071 GAGTCAGGCGATGCGAGC 60.959 66.667 0.00 0.00 0.00 5.03
220 228 2.279120 GGAGTCAGGCGATGCGAG 60.279 66.667 0.00 0.00 0.00 5.03
221 229 2.755876 AGGAGTCAGGCGATGCGA 60.756 61.111 0.00 0.00 0.00 5.10
222 230 2.584418 CAGGAGTCAGGCGATGCG 60.584 66.667 0.00 0.00 0.00 4.73
238 250 4.357947 GCGAGTGGCGAGTCACCA 62.358 66.667 4.01 0.00 44.57 4.17
377 393 1.896660 GTGGCCGGTTCTTGCAAGA 60.897 57.895 25.16 25.16 0.00 3.02
561 581 3.195698 GCTTGCGGCTAACCTCGG 61.196 66.667 0.00 0.00 38.06 4.63
641 2528 0.457851 CTTGGGAAGCGATCGTCTCT 59.542 55.000 17.81 2.08 0.00 3.10
673 2560 3.764049 GTGTCTGGACGAACGCGC 61.764 66.667 5.73 0.00 42.48 6.86
674 2561 2.354188 TGTGTCTGGACGAACGCG 60.354 61.111 3.53 3.53 44.79 6.01
794 2724 2.281208 TTTTCCGGCGGTGTGAGG 60.281 61.111 27.32 0.00 0.00 3.86
800 2730 1.826487 AAGTTGCTTTTCCGGCGGT 60.826 52.632 27.32 0.00 0.00 5.68
890 2820 2.266554 CAGTCGAAGAGAATGTGCTCC 58.733 52.381 0.00 0.00 39.84 4.70
998 2939 1.586154 CTCCACCACGTTGCCCATTC 61.586 60.000 0.00 0.00 0.00 2.67
1083 3024 3.009115 TAGACCAGCCCCTGCACC 61.009 66.667 0.00 0.00 41.13 5.01
1284 3231 4.508124 AGAAAACACTTCAACTAGTCTGCG 59.492 41.667 0.00 0.00 0.00 5.18
1302 3249 4.211164 CGTACATGAGCTCAACACAGAAAA 59.789 41.667 22.50 0.00 0.00 2.29
1306 3253 2.919859 CTCGTACATGAGCTCAACACAG 59.080 50.000 22.50 12.53 0.00 3.66
1307 3254 2.296190 ACTCGTACATGAGCTCAACACA 59.704 45.455 22.50 3.43 39.68 3.72
1318 3265 1.413767 GCGCCACTGACTCGTACATG 61.414 60.000 0.00 0.00 0.00 3.21
1335 3282 1.191647 ACGAAACTAAGAAAGCACGCG 59.808 47.619 3.53 3.53 0.00 6.01
1380 3327 8.964476 ATGTTCATCGTACAATCCTTTCTTAT 57.036 30.769 0.00 0.00 0.00 1.73
1396 3343 9.265938 CATACACAAACTTTCTTATGTTCATCG 57.734 33.333 0.00 0.00 0.00 3.84
1402 3349 9.555727 ACTGTACATACACAAACTTTCTTATGT 57.444 29.630 0.00 0.00 35.08 2.29
1413 3360 9.203421 CAGTTCAATCTACTGTACATACACAAA 57.797 33.333 0.00 0.00 38.51 2.83
1420 3367 6.317140 CCATTGCAGTTCAATCTACTGTACAT 59.683 38.462 0.00 0.00 43.21 2.29
1460 3407 4.537015 ACAGCAGCAGATTTCGTTTAAAC 58.463 39.130 8.35 8.35 0.00 2.01
1499 3446 2.202932 CGCAACAGCTATCGGCCT 60.203 61.111 0.00 0.00 43.05 5.19
1503 3450 0.790207 ACACAACGCAACAGCTATCG 59.210 50.000 0.00 0.00 0.00 2.92
1516 3466 3.435105 TGAAACCATGCTGAACACAAC 57.565 42.857 0.00 0.00 0.00 3.32
1542 3492 0.695347 AAAGGGGAGTCTGCCTTCTG 59.305 55.000 10.60 0.00 0.00 3.02
1611 3562 0.771127 TGGTTGTCTCCCTCCCAAAG 59.229 55.000 0.00 0.00 0.00 2.77
1617 3581 4.809426 CACGTAATATTGGTTGTCTCCCTC 59.191 45.833 0.00 0.00 0.00 4.30
1620 3584 6.920569 ATTCACGTAATATTGGTTGTCTCC 57.079 37.500 0.00 0.00 0.00 3.71
1651 3615 8.783660 ATTCTCACATAATCCTAAGTGTCCTA 57.216 34.615 0.00 0.00 33.84 2.94
1663 3628 9.055248 CGTTGTTGAAAAGATTCTCACATAATC 57.945 33.333 0.00 0.00 36.48 1.75
1664 3629 8.783093 TCGTTGTTGAAAAGATTCTCACATAAT 58.217 29.630 0.00 0.00 36.48 1.28
1785 3750 9.762933 AAGCAACAATAATTCGGCAAAATATAT 57.237 25.926 0.00 0.00 0.00 0.86
1787 3752 9.593134 TTAAGCAACAATAATTCGGCAAAATAT 57.407 25.926 0.00 0.00 0.00 1.28
1802 3767 7.551035 TGCAACTTTCAATTTAAGCAACAAT 57.449 28.000 0.00 0.00 0.00 2.71
1803 3768 6.974932 TGCAACTTTCAATTTAAGCAACAA 57.025 29.167 0.00 0.00 0.00 2.83
1806 3771 6.454848 CGTGTTGCAACTTTCAATTTAAGCAA 60.455 34.615 28.61 1.09 38.28 3.91
1807 3772 5.005203 CGTGTTGCAACTTTCAATTTAAGCA 59.995 36.000 28.61 1.83 0.00 3.91
1808 3773 5.231147 TCGTGTTGCAACTTTCAATTTAAGC 59.769 36.000 28.61 0.00 0.00 3.09
1809 3774 6.804534 TCGTGTTGCAACTTTCAATTTAAG 57.195 33.333 28.61 8.93 0.00 1.85
1810 3775 6.035112 GGTTCGTGTTGCAACTTTCAATTTAA 59.965 34.615 28.61 2.96 0.00 1.52
1811 3776 5.517054 GGTTCGTGTTGCAACTTTCAATTTA 59.483 36.000 28.61 3.73 0.00 1.40
1812 3777 4.328712 GGTTCGTGTTGCAACTTTCAATTT 59.671 37.500 28.61 0.00 0.00 1.82
1813 3778 3.862845 GGTTCGTGTTGCAACTTTCAATT 59.137 39.130 28.61 0.00 0.00 2.32
1814 3779 3.443976 GGTTCGTGTTGCAACTTTCAAT 58.556 40.909 28.61 0.00 0.00 2.57
1815 3780 2.729467 CGGTTCGTGTTGCAACTTTCAA 60.729 45.455 28.61 13.92 0.00 2.69
1817 3782 1.462791 CGGTTCGTGTTGCAACTTTC 58.537 50.000 28.61 17.62 0.00 2.62
1830 3977 0.438445 CGCACATATATGCCGGTTCG 59.562 55.000 12.79 4.04 42.99 3.95
1838 3985 4.318475 CCGTACAAACCACGCACATATATG 60.318 45.833 11.29 11.29 38.07 1.78
1849 3996 1.944709 GCCATATCCCGTACAAACCAC 59.055 52.381 0.00 0.00 0.00 4.16
1852 3999 4.976224 AAAAGCCATATCCCGTACAAAC 57.024 40.909 0.00 0.00 0.00 2.93
1856 4003 2.034179 GCCAAAAAGCCATATCCCGTAC 59.966 50.000 0.00 0.00 0.00 3.67
1858 4005 1.111277 GCCAAAAAGCCATATCCCGT 58.889 50.000 0.00 0.00 0.00 5.28
1859 4006 1.402787 AGCCAAAAAGCCATATCCCG 58.597 50.000 0.00 0.00 0.00 5.14
1864 4011 6.773638 TCCAAAATTTAGCCAAAAAGCCATA 58.226 32.000 0.00 0.00 0.00 2.74
1867 4014 5.304778 TCTCCAAAATTTAGCCAAAAAGCC 58.695 37.500 0.00 0.00 0.00 4.35
1868 4015 5.991606 ACTCTCCAAAATTTAGCCAAAAAGC 59.008 36.000 0.00 0.00 0.00 3.51
1875 4495 6.651086 AGTACCTACTCTCCAAAATTTAGCC 58.349 40.000 0.00 0.00 0.00 3.93
1899 4519 4.741928 TGTGCTATAGGATAGGTCTGGA 57.258 45.455 1.04 0.00 0.00 3.86
1942 4567 7.384932 ACAAATTTTCTTTTCTTTGCGGGATAG 59.615 33.333 0.00 0.00 33.03 2.08
1965 4590 1.121378 CCATGCCCATATGCCAACAA 58.879 50.000 0.00 0.00 0.00 2.83
2035 4660 4.082026 GCCAGAGTGAAGCAATTTTGGTAT 60.082 41.667 0.00 0.00 38.04 2.73
2060 4687 0.323725 GAAGGGGAGGCTGCATTTCA 60.324 55.000 8.68 0.00 0.00 2.69
2076 4703 3.851098 CCGTCTCTCTACCCAAAAGAAG 58.149 50.000 0.00 0.00 0.00 2.85
2079 4706 1.405661 GGCCGTCTCTCTACCCAAAAG 60.406 57.143 0.00 0.00 0.00 2.27
2083 4710 0.325296 ATTGGCCGTCTCTCTACCCA 60.325 55.000 0.00 0.00 0.00 4.51
2084 4711 1.700955 TATTGGCCGTCTCTCTACCC 58.299 55.000 0.00 0.00 0.00 3.69
2134 4762 3.970610 GCATGTAAATGTAGCATTGCTCG 59.029 43.478 15.81 0.00 40.44 5.03
2148 4776 9.944663 CTAAGTCTGTAAAAAGTTGCATGTAAA 57.055 29.630 0.00 0.00 0.00 2.01
2192 4821 4.461781 CCATTCCCTCCAATCTGATAATGC 59.538 45.833 0.00 0.00 0.00 3.56
2222 4851 4.200447 TCCCACTCCCTAATTCCTAGAG 57.800 50.000 0.00 0.00 0.00 2.43
2223 4852 4.852991 ATCCCACTCCCTAATTCCTAGA 57.147 45.455 0.00 0.00 0.00 2.43
2225 4854 7.964730 AATTTATCCCACTCCCTAATTCCTA 57.035 36.000 0.00 0.00 0.00 2.94
2226 4855 6.865651 AATTTATCCCACTCCCTAATTCCT 57.134 37.500 0.00 0.00 0.00 3.36
2233 4862 3.138468 GCACCTAATTTATCCCACTCCCT 59.862 47.826 0.00 0.00 0.00 4.20
2237 4866 3.555966 GCAGCACCTAATTTATCCCACT 58.444 45.455 0.00 0.00 0.00 4.00
2241 4870 2.294512 GCTGGCAGCACCTAATTTATCC 59.705 50.000 33.33 0.00 41.89 2.59
2258 4887 0.106819 CTCTGGGAATTCAGGGCTGG 60.107 60.000 7.93 0.00 35.58 4.85
2266 4895 5.104259 AGTTGATACCACTCTGGGAATTC 57.896 43.478 0.00 0.00 43.37 2.17


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

AutoCloner maintained by Alex Coulton.