Multiple sequence alignment - TraesCS2A01G354700

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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 TraesCS2A01G354700 chr2A 100.000 2962 0 0 1 2962 595982763 595979802 0.000000e+00 5470
1 TraesCS2A01G354700 chr5A 88.843 1201 128 3 1766 2961 469655836 469654637 0.000000e+00 1471
2 TraesCS2A01G354700 chr5A 81.047 1203 223 3 1764 2962 609280636 609281837 0.000000e+00 953
3 TraesCS2A01G354700 chr2D 86.967 1220 147 8 1748 2962 473431042 473429830 0.000000e+00 1362
4 TraesCS2A01G354700 chr2D 89.362 1128 44 15 690 1765 454804500 454805603 0.000000e+00 1349
5 TraesCS2A01G354700 chr2B 90.538 930 36 12 870 1765 534397938 534398849 0.000000e+00 1182
6 TraesCS2A01G354700 chr2B 90.395 583 28 14 244 820 534397385 534397945 0.000000e+00 741
7 TraesCS2A01G354700 chr2B 88.417 259 23 2 1 259 534396518 534396769 3.710000e-79 305
8 TraesCS2A01G354700 chr2B 86.345 249 30 4 292 538 534396768 534397014 4.870000e-68 268
9 TraesCS2A01G354700 chr2B 87.500 208 25 1 4 211 534397180 534397386 3.820000e-59 239
10 TraesCS2A01G354700 chr6B 82.490 1205 206 2 1763 2962 583457601 583458805 0.000000e+00 1051
11 TraesCS2A01G354700 chr4A 82.490 1205 205 3 1763 2962 665830263 665829060 0.000000e+00 1051
12 TraesCS2A01G354700 chr5B 82.436 1207 200 11 1764 2962 505772571 505773773 0.000000e+00 1044
13 TraesCS2A01G354700 chr5B 81.509 1206 209 12 1766 2962 382366755 382367955 0.000000e+00 979
14 TraesCS2A01G354700 chr1A 82.187 1207 206 8 1762 2962 15524630 15525833 0.000000e+00 1029
15 TraesCS2A01G354700 chr7B 82.307 1153 196 7 1766 2912 312384902 312386052 0.000000e+00 992
16 TraesCS2A01G354700 chr1D 80.000 195 34 5 396 589 17234061 17234251 3.980000e-29 139


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 TraesCS2A01G354700 chr2A 595979802 595982763 2961 True 5470 5470 100.000 1 2962 1 chr2A.!!$R1 2961
1 TraesCS2A01G354700 chr5A 469654637 469655836 1199 True 1471 1471 88.843 1766 2961 1 chr5A.!!$R1 1195
2 TraesCS2A01G354700 chr5A 609280636 609281837 1201 False 953 953 81.047 1764 2962 1 chr5A.!!$F1 1198
3 TraesCS2A01G354700 chr2D 473429830 473431042 1212 True 1362 1362 86.967 1748 2962 1 chr2D.!!$R1 1214
4 TraesCS2A01G354700 chr2D 454804500 454805603 1103 False 1349 1349 89.362 690 1765 1 chr2D.!!$F1 1075
5 TraesCS2A01G354700 chr2B 534396518 534398849 2331 False 547 1182 88.639 1 1765 5 chr2B.!!$F1 1764
6 TraesCS2A01G354700 chr6B 583457601 583458805 1204 False 1051 1051 82.490 1763 2962 1 chr6B.!!$F1 1199
7 TraesCS2A01G354700 chr4A 665829060 665830263 1203 True 1051 1051 82.490 1763 2962 1 chr4A.!!$R1 1199
8 TraesCS2A01G354700 chr5B 505772571 505773773 1202 False 1044 1044 82.436 1764 2962 1 chr5B.!!$F2 1198
9 TraesCS2A01G354700 chr5B 382366755 382367955 1200 False 979 979 81.509 1766 2962 1 chr5B.!!$F1 1196
10 TraesCS2A01G354700 chr1A 15524630 15525833 1203 False 1029 1029 82.187 1762 2962 1 chr1A.!!$F1 1200
11 TraesCS2A01G354700 chr7B 312384902 312386052 1150 False 992 992 82.307 1766 2912 1 chr7B.!!$F1 1146

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
531 1163 0.475044 TTAGGCCCAAAACACGAGGT 59.525 50.0 0.0 0.0 0.0 3.85 F
1057 1707 0.035915 AGGCGGAGGAAAAAGAGAGC 60.036 55.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1443 2123 0.034767 CCTTGCCCATCTGCTTCAGA 60.035 55.0 0.00 0.0 44.99 3.27 R
2437 3149 0.248621 GACATGGCGCATGGTAAAGC 60.249 55.0 10.83 0.0 45.16 3.51 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
34 35 4.660938 GCAGGCCACCCGTTCCTT 62.661 66.667 5.01 0.00 35.76 3.36
37 38 4.011517 GGCCACCCGTTCCTTCGA 62.012 66.667 0.00 0.00 0.00 3.71
41 42 0.739813 CCACCCGTTCCTTCGATGAC 60.740 60.000 0.00 0.00 0.00 3.06
45 46 1.137086 CCCGTTCCTTCGATGACATCT 59.863 52.381 13.45 0.00 0.00 2.90
63 64 0.758685 CTTCCACCACCCCTTTGCAA 60.759 55.000 0.00 0.00 0.00 4.08
98 99 6.728200 TCAACAAATGAGTGATGTTCAAGTC 58.272 36.000 0.00 0.00 35.22 3.01
101 102 5.824624 ACAAATGAGTGATGTTCAAGTCTGT 59.175 36.000 0.00 0.00 0.00 3.41
109 110 1.332178 GTTCAAGTCTGTCGAGAGCG 58.668 55.000 4.35 0.00 39.35 5.03
117 118 1.347817 CTGTCGAGAGCGCCAAAGAC 61.348 60.000 2.29 10.28 37.46 3.01
120 121 1.080501 CGAGAGCGCCAAAGACTCA 60.081 57.895 2.29 0.00 32.71 3.41
121 122 1.347817 CGAGAGCGCCAAAGACTCAC 61.348 60.000 2.29 0.00 32.71 3.51
165 166 1.671979 CTGCATCAATGACACCCGAT 58.328 50.000 0.00 0.00 0.00 4.18
166 167 2.019249 CTGCATCAATGACACCCGATT 58.981 47.619 0.00 0.00 0.00 3.34
171 172 5.215160 GCATCAATGACACCCGATTTATTC 58.785 41.667 0.00 0.00 0.00 1.75
173 174 6.432936 CATCAATGACACCCGATTTATTCAG 58.567 40.000 0.00 0.00 0.00 3.02
195 196 1.348036 GCCAACGCCCCTAGATAAGAT 59.652 52.381 0.00 0.00 0.00 2.40
197 198 2.900546 CCAACGCCCCTAGATAAGATCT 59.099 50.000 0.00 0.00 43.33 2.75
198 199 4.087182 CCAACGCCCCTAGATAAGATCTA 58.913 47.826 0.00 0.00 40.76 1.98
207 208 7.410174 CCCCTAGATAAGATCTATGTGAGTCT 58.590 42.308 0.00 0.00 40.82 3.24
208 209 7.556275 CCCCTAGATAAGATCTATGTGAGTCTC 59.444 44.444 0.00 0.00 40.82 3.36
209 210 8.328758 CCCTAGATAAGATCTATGTGAGTCTCT 58.671 40.741 0.00 0.00 40.82 3.10
213 214 9.944376 AGATAAGATCTATGTGAGTCTCTAGTC 57.056 37.037 0.00 0.00 38.00 2.59
214 215 9.944376 GATAAGATCTATGTGAGTCTCTAGTCT 57.056 37.037 0.00 0.00 0.00 3.24
225 226 7.124448 TGTGAGTCTCTAGTCTCTACACATAGA 59.876 40.741 0.65 0.00 36.01 1.98
231 232 8.154203 TCTCTAGTCTCTACACATAGAAGATGG 58.846 40.741 0.00 0.00 36.98 3.51
272 904 1.805945 GCAACAGCCTCGTCTACCG 60.806 63.158 0.00 0.00 38.13 4.02
296 928 0.533308 TTGAACAAACCCCGACGGAG 60.533 55.000 17.49 4.05 34.64 4.63
327 959 0.921347 CGTGTACTCGGCATTGTAGC 59.079 55.000 9.41 0.00 0.00 3.58
355 987 4.025401 GGTCGCGCTTGGGTTGTG 62.025 66.667 5.56 0.00 0.00 3.33
374 1006 6.128090 GGTTGTGGGTTTACTTGCTTCTATAC 60.128 42.308 0.00 0.00 0.00 1.47
376 1008 5.013287 TGTGGGTTTACTTGCTTCTATACCA 59.987 40.000 0.00 0.00 0.00 3.25
377 1009 6.120220 GTGGGTTTACTTGCTTCTATACCAT 58.880 40.000 0.00 0.00 0.00 3.55
400 1032 7.415541 CCATCGATGTACCACTTGATGAAAAAT 60.416 37.037 23.27 0.00 36.25 1.82
401 1033 6.841119 TCGATGTACCACTTGATGAAAAATG 58.159 36.000 0.00 0.00 0.00 2.32
432 1064 3.748568 ACAGAAAAAGAGGAAGCATCGTC 59.251 43.478 3.53 3.53 40.07 4.20
446 1078 2.404215 CATCGTCGGCCTATAAACAGG 58.596 52.381 0.00 0.00 38.86 4.00
482 1114 5.329035 GCTTCAGCCCAATAAGAAATTGA 57.671 39.130 0.00 0.00 34.31 2.57
483 1115 5.105063 GCTTCAGCCCAATAAGAAATTGAC 58.895 41.667 0.00 0.00 34.31 3.18
494 1126 8.260114 CCAATAAGAAATTGACTAGCCCAAAAT 58.740 33.333 2.78 0.00 0.00 1.82
531 1163 0.475044 TTAGGCCCAAAACACGAGGT 59.525 50.000 0.00 0.00 0.00 3.85
548 1180 4.521639 ACGAGGTAGTCACAACAGTGATAA 59.478 41.667 0.00 0.00 43.56 1.75
581 1213 1.606224 GGGGCACAAATGTTGAAGCAG 60.606 52.381 0.00 0.00 37.11 4.24
627 1259 9.974980 TCGGCTAAACTAAATTTGATTTTCTTT 57.025 25.926 0.00 0.00 33.82 2.52
658 1296 3.314635 AGCTAAATTGCTATGCTCTGCAC 59.685 43.478 0.00 0.00 42.10 4.57
660 1298 2.028420 AATTGCTATGCTCTGCACGA 57.972 45.000 0.00 0.00 43.04 4.35
684 1322 4.203076 GACGCCGTCCGCCTGTAT 62.203 66.667 5.81 0.00 41.76 2.29
685 1323 4.203076 ACGCCGTCCGCCTGTATC 62.203 66.667 0.00 0.00 41.76 2.24
686 1324 4.944372 CGCCGTCCGCCTGTATCC 62.944 72.222 0.00 0.00 0.00 2.59
687 1325 3.537874 GCCGTCCGCCTGTATCCT 61.538 66.667 0.00 0.00 0.00 3.24
688 1326 3.090219 GCCGTCCGCCTGTATCCTT 62.090 63.158 0.00 0.00 0.00 3.36
742 1380 4.225267 CCTGTATTAGAAACACCCCTGAGT 59.775 45.833 0.00 0.00 0.00 3.41
771 1409 2.404215 CGATTAGTAGCCCATCGTTGG 58.596 52.381 5.47 5.47 43.23 3.77
827 1465 1.145738 ACAAGTTCAACCAGGCTCCAT 59.854 47.619 0.00 0.00 0.00 3.41
885 1533 4.442192 GGAGCTATTCATCGATACCCATCC 60.442 50.000 0.00 0.00 0.00 3.51
899 1547 1.422531 CCATCCCTTCTCCTCTCCTG 58.577 60.000 0.00 0.00 0.00 3.86
915 1563 5.278561 CCTCTCCTGCTACCTAGAATAAACG 60.279 48.000 0.00 0.00 0.00 3.60
968 1616 1.552799 ATCCATCCACGAGCCACACA 61.553 55.000 0.00 0.00 0.00 3.72
1018 1668 3.403276 CGAAGACAGAGTTCGGTCC 57.597 57.895 8.48 0.00 42.47 4.46
1025 1675 0.037232 CAGAGTTCGGTCCTGTTCCC 60.037 60.000 0.00 0.00 0.00 3.97
1049 1699 2.121832 TGGGAGAGGCGGAGGAAA 59.878 61.111 0.00 0.00 0.00 3.13
1051 1701 1.131303 TGGGAGAGGCGGAGGAAAAA 61.131 55.000 0.00 0.00 0.00 1.94
1052 1702 0.393132 GGGAGAGGCGGAGGAAAAAG 60.393 60.000 0.00 0.00 0.00 2.27
1057 1707 0.035915 AGGCGGAGGAAAAAGAGAGC 60.036 55.000 0.00 0.00 0.00 4.09
1060 1710 1.634702 CGGAGGAAAAAGAGAGCGAG 58.365 55.000 0.00 0.00 0.00 5.03
1063 1713 2.494073 GGAGGAAAAAGAGAGCGAGAGA 59.506 50.000 0.00 0.00 0.00 3.10
1064 1714 3.132111 GGAGGAAAAAGAGAGCGAGAGAT 59.868 47.826 0.00 0.00 0.00 2.75
1065 1715 4.382577 GGAGGAAAAAGAGAGCGAGAGATT 60.383 45.833 0.00 0.00 0.00 2.40
1066 1716 4.502962 AGGAAAAAGAGAGCGAGAGATTG 58.497 43.478 0.00 0.00 0.00 2.67
1067 1717 4.221703 AGGAAAAAGAGAGCGAGAGATTGA 59.778 41.667 0.00 0.00 0.00 2.57
1220 1896 2.572290 CCTGGTTTCGTTTTCTCACCT 58.428 47.619 0.00 0.00 0.00 4.00
1468 2148 0.253044 GCAGATGGGCAAGGTACAGA 59.747 55.000 0.00 0.00 0.00 3.41
1523 2203 2.664851 CTGCACGGCGTTCAAGGA 60.665 61.111 11.19 0.00 0.00 3.36
1558 2238 2.047655 GGGCCACGATGAACGACA 60.048 61.111 4.39 0.00 45.77 4.35
1719 2427 4.891727 GCCGGTGCCATCGACGAT 62.892 66.667 4.05 4.05 0.00 3.73
1833 2541 1.321474 TCAAGTGGCAAAAGCTCCTG 58.679 50.000 0.00 0.00 0.00 3.86
1896 2604 6.424509 GTGCTCTCTGTACGACTATACATAGT 59.575 42.308 1.48 1.48 45.73 2.12
1991 2699 6.108687 TGACGAATCTCAGCAACTAAATGAT 58.891 36.000 0.00 0.00 0.00 2.45
2017 2725 0.601558 CCGAACGGGAGAGACTTTCA 59.398 55.000 5.25 0.00 38.47 2.69
2026 2734 2.610727 GGAGAGACTTTCACCCGTCAAG 60.611 54.545 0.00 0.00 30.96 3.02
2058 2766 3.866651 CCTGTGAAGAGTCGGATTGAAT 58.133 45.455 0.00 0.00 0.00 2.57
2062 2770 6.220726 TGTGAAGAGTCGGATTGAATGATA 57.779 37.500 0.00 0.00 0.00 2.15
2128 2836 3.641434 ATTGCATGTAGTTCTGCCTCT 57.359 42.857 0.00 0.00 37.59 3.69
2157 2865 7.821595 CATCATTGCAGTTGAAAATACACAT 57.178 32.000 5.63 0.00 0.00 3.21
2164 2872 5.640732 CAGTTGAAAATACACATGTAGGCC 58.359 41.667 0.00 0.00 33.52 5.19
2177 2885 0.727398 GTAGGCCGCAAAGATGACAC 59.273 55.000 0.00 0.00 0.00 3.67
2199 2907 7.773149 ACACTACCATCATGTCTTCTTAGTAC 58.227 38.462 0.00 0.00 0.00 2.73
2242 2950 1.426041 CCGTAGATGAAAACGCCCCG 61.426 60.000 0.00 0.00 37.78 5.73
2258 2966 1.514657 CCGTCGACCGATAACGCAA 60.515 57.895 10.58 0.00 39.56 4.85
2267 2975 0.096976 CGATAACGCAACTTGGCCAG 59.903 55.000 5.11 2.72 0.00 4.85
2270 2978 2.690653 TAACGCAACTTGGCCAGCCT 62.691 55.000 5.11 0.00 36.94 4.58
2271 2979 2.359850 CGCAACTTGGCCAGCCTA 60.360 61.111 5.11 0.80 36.94 3.93
2331 3039 2.497675 GCCTGACCAGATCTTCACACTA 59.502 50.000 0.00 0.00 0.00 2.74
2336 3044 5.321927 TGACCAGATCTTCACACTACACTA 58.678 41.667 0.00 0.00 0.00 2.74
2346 3054 4.344978 TCACACTACACTAGCATCTTCCT 58.655 43.478 0.00 0.00 0.00 3.36
2391 3099 3.179443 TCTTCTAGCCAAATGTAGCGG 57.821 47.619 0.00 0.00 0.00 5.52
2402 3110 4.458989 CCAAATGTAGCGGGTGCATATAAT 59.541 41.667 11.09 0.00 46.23 1.28
2467 3179 1.079681 GCCATGTCCGACCGTAACA 60.080 57.895 0.00 0.00 0.00 2.41
2471 3183 1.136305 CATGTCCGACCGTAACATCCT 59.864 52.381 0.00 0.00 31.43 3.24
2502 3214 5.824624 CCAGATTAACATTATGGTGCAGTCT 59.175 40.000 0.00 0.00 0.00 3.24
2547 3259 6.885918 TCATCAGAATATTCAAAAGCCACTCA 59.114 34.615 17.56 0.00 0.00 3.41
2579 3291 1.648504 CGCAGCAGTTGATGATCAGA 58.351 50.000 0.09 0.00 32.25 3.27
2589 3301 5.754406 CAGTTGATGATCAGAGAGATTCCAC 59.246 44.000 0.09 0.00 37.00 4.02
2673 3385 2.370849 GGTCTCCCTTTCTGTACCACAA 59.629 50.000 0.00 0.00 0.00 3.33
2777 3489 4.060900 GCCATAATTCTCATCTTGAGCGA 58.939 43.478 0.00 0.00 43.95 4.93
2782 3494 3.685139 TTCTCATCTTGAGCGAAACCT 57.315 42.857 0.00 0.00 43.95 3.50
2787 3499 0.681733 TCTTGAGCGAAACCTGAGCT 59.318 50.000 0.00 0.00 44.80 4.09
2793 3505 0.889186 GCGAAACCTGAGCTTCCCAA 60.889 55.000 0.00 0.00 0.00 4.12
2810 3522 0.745845 CAAACTCGCCTCCAGATGGG 60.746 60.000 0.00 0.00 35.41 4.00
2822 3534 4.408821 GATGGGCCTGTGTCCGCA 62.409 66.667 4.53 0.00 40.01 5.69
2835 3547 2.272146 CCGCATGGGCTGGTACTT 59.728 61.111 3.80 0.00 38.10 2.24
2869 3581 3.282021 GCATCTGCCAATTGGTTCTCTA 58.718 45.455 25.19 6.47 37.57 2.43
2880 3592 5.543507 ATTGGTTCTCTACTGCTAGATGG 57.456 43.478 0.00 0.00 0.00 3.51
2928 3641 1.002544 CTCTTCTCCGGAAACCAAGCT 59.997 52.381 5.23 0.00 0.00 3.74
2958 3671 3.157680 CCCCCTCTTGGTGACGTT 58.842 61.111 0.00 0.00 0.00 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.537560 GGCCTGCACGGAATCATCG 61.538 63.158 0.00 0.00 33.16 3.84
34 35 1.207089 GGTGGTGGAAGATGTCATCGA 59.793 52.381 7.18 0.00 0.00 3.59
37 38 0.625849 GGGGTGGTGGAAGATGTCAT 59.374 55.000 0.00 0.00 0.00 3.06
41 42 1.549203 CAAAGGGGTGGTGGAAGATG 58.451 55.000 0.00 0.00 0.00 2.90
45 46 0.105246 ATTGCAAAGGGGTGGTGGAA 60.105 50.000 1.71 0.00 0.00 3.53
63 64 6.604396 TCACTCATTTGTTGATTGCCTCATAT 59.396 34.615 0.00 0.00 35.54 1.78
101 102 1.213013 GAGTCTTTGGCGCTCTCGA 59.787 57.895 7.64 0.00 38.10 4.04
109 110 4.742438 TTGTTATTCGTGAGTCTTTGGC 57.258 40.909 0.00 0.00 0.00 4.52
117 118 6.662414 TTGGAAGCTATTGTTATTCGTGAG 57.338 37.500 0.00 0.00 0.00 3.51
154 155 4.130118 GCTCTGAATAAATCGGGTGTCAT 58.870 43.478 0.00 0.00 34.95 3.06
165 166 1.459450 GGGCGTTGGCTCTGAATAAA 58.541 50.000 0.00 0.00 36.44 1.40
166 167 0.393808 GGGGCGTTGGCTCTGAATAA 60.394 55.000 0.00 0.00 40.49 1.40
171 172 1.690219 ATCTAGGGGCGTTGGCTCTG 61.690 60.000 2.61 0.00 40.49 3.35
173 174 0.756903 TTATCTAGGGGCGTTGGCTC 59.243 55.000 0.00 0.00 39.66 4.70
195 196 7.124448 TGTGTAGAGACTAGAGACTCACATAGA 59.876 40.741 5.02 0.00 38.87 1.98
197 198 7.184067 TGTGTAGAGACTAGAGACTCACATA 57.816 40.000 5.02 8.47 38.87 2.29
198 199 6.056090 TGTGTAGAGACTAGAGACTCACAT 57.944 41.667 5.02 0.00 38.87 3.21
207 208 7.717436 CACCATCTTCTATGTGTAGAGACTAGA 59.283 40.741 0.00 0.00 38.17 2.43
208 209 7.717436 TCACCATCTTCTATGTGTAGAGACTAG 59.283 40.741 0.00 0.00 38.17 2.57
209 210 7.574607 TCACCATCTTCTATGTGTAGAGACTA 58.425 38.462 0.00 0.00 38.17 2.59
210 211 6.427441 TCACCATCTTCTATGTGTAGAGACT 58.573 40.000 0.00 0.00 38.17 3.24
211 212 6.701145 TCACCATCTTCTATGTGTAGAGAC 57.299 41.667 0.00 0.00 38.17 3.36
212 213 6.491745 GGATCACCATCTTCTATGTGTAGAGA 59.508 42.308 0.00 0.00 35.91 3.10
213 214 6.493115 AGGATCACCATCTTCTATGTGTAGAG 59.507 42.308 0.00 0.00 37.15 2.43
214 215 6.377080 AGGATCACCATCTTCTATGTGTAGA 58.623 40.000 0.00 0.00 38.94 2.59
225 226 5.163152 GGAAGTAATGGAGGATCACCATCTT 60.163 44.000 19.26 18.03 45.89 2.40
231 232 4.261825 CGAGAGGAAGTAATGGAGGATCAC 60.262 50.000 0.00 0.00 36.25 3.06
296 928 2.290093 CGAGTACACGTTAGATCCCTCC 59.710 54.545 4.40 0.00 0.00 4.30
339 971 4.025401 CCACAACCCAAGCGCGAC 62.025 66.667 12.10 0.04 0.00 5.19
355 987 5.465724 CGATGGTATAGAAGCAAGTAAACCC 59.534 44.000 0.00 0.00 39.48 4.11
374 1006 4.058721 TCATCAAGTGGTACATCGATGG 57.941 45.455 28.09 11.30 44.52 3.51
376 1008 7.415541 CCATTTTTCATCAAGTGGTACATCGAT 60.416 37.037 0.00 0.00 44.52 3.59
377 1009 6.128035 CCATTTTTCATCAAGTGGTACATCGA 60.128 38.462 0.00 0.00 44.52 3.59
400 1032 5.136828 TCCTCTTTTTCTGTTTGTATGCCA 58.863 37.500 0.00 0.00 0.00 4.92
401 1033 5.705609 TCCTCTTTTTCTGTTTGTATGCC 57.294 39.130 0.00 0.00 0.00 4.40
446 1078 2.137523 CTGAAGCCCAATTTGTGTTGC 58.862 47.619 0.00 0.00 0.00 4.17
494 1126 5.105675 GGCCTAAATTTTTGACCGACCAATA 60.106 40.000 0.00 0.00 0.00 1.90
561 1193 0.392336 TGCTTCAACATTTGTGCCCC 59.608 50.000 0.00 0.00 33.10 5.80
565 1197 6.642917 GTTGATTTCTGCTTCAACATTTGTG 58.357 36.000 10.11 0.00 46.95 3.33
625 1257 9.950680 GCATAGCAATTTAGCTGTATAAAGAAA 57.049 29.630 0.00 0.00 46.11 2.52
627 1259 8.908786 AGCATAGCAATTTAGCTGTATAAAGA 57.091 30.769 0.00 0.00 46.11 2.52
628 1260 8.997323 AGAGCATAGCAATTTAGCTGTATAAAG 58.003 33.333 0.00 0.00 46.11 1.85
629 1261 8.777413 CAGAGCATAGCAATTTAGCTGTATAAA 58.223 33.333 0.00 0.00 46.11 1.40
631 1263 6.369890 GCAGAGCATAGCAATTTAGCTGTATA 59.630 38.462 0.00 0.00 46.11 1.47
635 1273 3.314357 TGCAGAGCATAGCAATTTAGCTG 59.686 43.478 0.00 0.00 38.47 4.24
646 1284 2.282306 CACGTCGTGCAGAGCATAG 58.718 57.895 13.22 0.00 41.91 2.23
667 1305 4.203076 ATACAGGCGGACGGCGTC 62.203 66.667 30.72 30.72 44.92 5.19
670 1308 1.741327 TAAGGATACAGGCGGACGGC 61.741 60.000 10.47 10.47 39.75 5.68
671 1309 0.748450 TTAAGGATACAGGCGGACGG 59.252 55.000 0.00 0.00 41.41 4.79
672 1310 2.404215 CATTAAGGATACAGGCGGACG 58.596 52.381 0.00 0.00 41.41 4.79
673 1311 2.767505 CCATTAAGGATACAGGCGGAC 58.232 52.381 0.00 0.00 41.22 4.79
674 1312 1.071699 GCCATTAAGGATACAGGCGGA 59.928 52.381 0.00 0.00 41.22 5.54
675 1313 1.072331 AGCCATTAAGGATACAGGCGG 59.928 52.381 0.00 0.00 46.34 6.13
676 1314 2.417719 GAGCCATTAAGGATACAGGCG 58.582 52.381 0.00 0.00 46.34 5.52
677 1315 2.373502 AGGAGCCATTAAGGATACAGGC 59.626 50.000 0.00 0.00 39.95 4.85
678 1316 3.648067 TGAGGAGCCATTAAGGATACAGG 59.352 47.826 0.00 0.00 39.95 4.00
679 1317 4.963318 TGAGGAGCCATTAAGGATACAG 57.037 45.455 0.00 0.00 39.95 2.74
680 1318 4.505566 GCATGAGGAGCCATTAAGGATACA 60.506 45.833 0.00 0.00 39.95 2.29
681 1319 4.006319 GCATGAGGAGCCATTAAGGATAC 58.994 47.826 0.00 0.00 41.22 2.24
682 1320 3.912528 AGCATGAGGAGCCATTAAGGATA 59.087 43.478 0.00 0.00 41.22 2.59
683 1321 2.715336 AGCATGAGGAGCCATTAAGGAT 59.285 45.455 0.00 0.00 41.22 3.24
684 1322 2.130193 AGCATGAGGAGCCATTAAGGA 58.870 47.619 0.00 0.00 41.22 3.36
685 1323 2.653234 AGCATGAGGAGCCATTAAGG 57.347 50.000 0.00 0.00 41.84 2.69
686 1324 7.164122 TCTAATTAGCATGAGGAGCCATTAAG 58.836 38.462 7.67 0.00 0.00 1.85
687 1325 7.078249 TCTAATTAGCATGAGGAGCCATTAA 57.922 36.000 7.67 0.00 0.00 1.40
688 1326 6.686484 TCTAATTAGCATGAGGAGCCATTA 57.314 37.500 7.67 0.00 0.00 1.90
742 1380 2.101917 GGGCTACTAATCGTAAGTGCCA 59.898 50.000 18.74 0.00 40.19 4.92
827 1465 7.070322 TGTCATGTCCTAATTCAGAGATGATCA 59.930 37.037 15.98 0.00 42.58 2.92
885 1533 1.063266 AGGTAGCAGGAGAGGAGAAGG 60.063 57.143 0.00 0.00 0.00 3.46
899 1547 6.846325 ATTCAAGCGTTTATTCTAGGTAGC 57.154 37.500 0.00 0.00 0.00 3.58
915 1563 2.223665 GCCACCTGCAGATTATTCAAGC 60.224 50.000 17.39 0.87 40.77 4.01
968 1616 2.203938 AGGTGACGGGGTGGATGT 60.204 61.111 0.00 0.00 0.00 3.06
1040 1690 0.389948 TCGCTCTCTTTTTCCTCCGC 60.390 55.000 0.00 0.00 0.00 5.54
1041 1691 1.202582 TCTCGCTCTCTTTTTCCTCCG 59.797 52.381 0.00 0.00 0.00 4.63
1046 1696 6.456718 CCATTCAATCTCTCGCTCTCTTTTTC 60.457 42.308 0.00 0.00 0.00 2.29
1047 1697 5.353678 CCATTCAATCTCTCGCTCTCTTTTT 59.646 40.000 0.00 0.00 0.00 1.94
1049 1699 4.440880 CCATTCAATCTCTCGCTCTCTTT 58.559 43.478 0.00 0.00 0.00 2.52
1051 1701 2.364970 CCCATTCAATCTCTCGCTCTCT 59.635 50.000 0.00 0.00 0.00 3.10
1052 1702 2.102252 ACCCATTCAATCTCTCGCTCTC 59.898 50.000 0.00 0.00 0.00 3.20
1057 1707 2.939103 GTGGAACCCATTCAATCTCTCG 59.061 50.000 0.00 0.00 35.28 4.04
1187 1852 9.930693 AAAACGAAACCAGGCAAAATAATAATA 57.069 25.926 0.00 0.00 0.00 0.98
1220 1896 2.027192 GGAGTTGATCAACCCAGCACTA 60.027 50.000 30.34 0.00 42.06 2.74
1429 2109 0.392595 TTCAGATGCTCCAGCTGCAG 60.393 55.000 10.11 10.11 45.97 4.41
1443 2123 0.034767 CCTTGCCCATCTGCTTCAGA 60.035 55.000 0.00 0.00 44.99 3.27
1719 2427 4.362279 AGAAACAGCTTAAACGTACGTCA 58.638 39.130 23.05 10.06 0.00 4.35
1833 2541 1.839894 CAGGGCCCTCCTTGTATCC 59.160 63.158 25.77 0.00 45.47 2.59
1896 2604 6.041637 ACATAATAGGGTAGCAGATCGTTTGA 59.958 38.462 0.00 0.00 0.00 2.69
1940 2648 8.826765 TCTTATGGGTGAAAGAGAGTTTATTCT 58.173 33.333 0.00 0.00 0.00 2.40
1991 2699 0.673985 CTCTCCCGTTCGGCATATGA 59.326 55.000 6.97 0.00 0.00 2.15
2017 2725 0.537371 CTCTTTTGGCCTTGACGGGT 60.537 55.000 3.32 0.00 0.00 5.28
2020 2728 1.581447 GGCTCTTTTGGCCTTGACG 59.419 57.895 3.32 0.00 45.57 4.35
2062 2770 8.897752 GCAATTCAACACTCTAATCTTCCTATT 58.102 33.333 0.00 0.00 0.00 1.73
2075 2783 4.439305 TGGCATTAGCAATTCAACACTC 57.561 40.909 0.00 0.00 44.61 3.51
2122 2830 1.016627 GCAATGATGCGTTAGAGGCA 58.983 50.000 0.00 0.00 43.83 4.75
2149 2857 2.411628 TTGCGGCCTACATGTGTATT 57.588 45.000 9.11 0.00 0.00 1.89
2156 2864 1.065491 TGTCATCTTTGCGGCCTACAT 60.065 47.619 0.00 0.00 0.00 2.29
2157 2865 0.323302 TGTCATCTTTGCGGCCTACA 59.677 50.000 0.00 0.00 0.00 2.74
2164 2872 3.261580 TGATGGTAGTGTCATCTTTGCG 58.738 45.455 0.00 0.00 41.01 4.85
2177 2885 7.348080 TGGTACTAAGAAGACATGATGGTAG 57.652 40.000 0.00 0.00 0.00 3.18
2242 2950 1.058695 CAAGTTGCGTTATCGGTCGAC 59.941 52.381 7.13 7.13 37.56 4.20
2318 3026 5.890985 AGATGCTAGTGTAGTGTGAAGATCT 59.109 40.000 0.00 0.00 0.00 2.75
2320 3028 6.406400 GGAAGATGCTAGTGTAGTGTGAAGAT 60.406 42.308 0.00 0.00 0.00 2.40
2331 3039 4.713814 TCATCAAGAGGAAGATGCTAGTGT 59.286 41.667 0.00 0.00 41.02 3.55
2336 3044 4.040706 GGAGATCATCAAGAGGAAGATGCT 59.959 45.833 0.00 0.00 41.02 3.79
2346 3054 6.012337 ACTCTACAGAGGAGATCATCAAGA 57.988 41.667 10.86 0.00 46.13 3.02
2391 3099 7.012044 ACGACTACCTTCAAAATTATATGCACC 59.988 37.037 0.00 0.00 0.00 5.01
2435 3147 1.308047 CATGGCGCATGGTAAAGCTA 58.692 50.000 10.83 0.00 38.11 3.32
2437 3149 0.248621 GACATGGCGCATGGTAAAGC 60.249 55.000 10.83 0.00 45.16 3.51
2471 3183 7.665559 GCACCATAATGTTAATCTGGAGGATTA 59.334 37.037 0.00 0.00 43.59 1.75
2502 3214 4.745649 TGAATTGCAATGATGAAATGCGA 58.254 34.783 13.82 0.00 42.91 5.10
2547 3259 1.070758 CTGCTGCGGGATACAGGTAAT 59.929 52.381 0.00 0.00 35.62 1.89
2579 3291 1.344438 TGCGTTCAGTGTGGAATCTCT 59.656 47.619 0.00 0.00 0.00 3.10
2673 3385 3.634448 CCACTCGAGATACATGTCCTCTT 59.366 47.826 21.68 7.07 0.00 2.85
2699 3411 5.484173 TTCTTGCAAGAAATATAGGCACG 57.516 39.130 34.01 2.89 41.75 5.34
2777 3489 2.587522 GAGTTTGGGAAGCTCAGGTTT 58.412 47.619 0.00 0.00 0.00 3.27
2782 3494 1.302511 GGCGAGTTTGGGAAGCTCA 60.303 57.895 0.00 0.00 0.00 4.26
2787 3499 1.125093 TCTGGAGGCGAGTTTGGGAA 61.125 55.000 0.00 0.00 0.00 3.97
2793 3505 3.036429 GCCCATCTGGAGGCGAGTT 62.036 63.158 0.00 0.00 39.87 3.01
2822 3534 0.464373 CGCATCAAGTACCAGCCCAT 60.464 55.000 0.00 0.00 0.00 4.00
2852 3564 2.421424 GCAGTAGAGAACCAATTGGCAG 59.579 50.000 24.79 4.35 39.32 4.85
2880 3592 6.598753 TTGTTCACAGTTAAGAGTGCTTAC 57.401 37.500 3.01 2.83 36.37 2.34


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

AutoCloner maintained by Alex Coulton.