Multiple sequence alignment - TraesCS7B01G437700

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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 TraesCS7B01G437700 chr7B 100.000 7227 0 0 1 7227 704086241 704093467 0.000000e+00 13346.0
1 TraesCS7B01G437700 chr7B 98.531 6127 54 13 343 6455 704151432 704157536 0.000000e+00 10783.0
2 TraesCS7B01G437700 chr7B 78.614 2352 366 76 1798 4088 639090322 639088047 0.000000e+00 1430.0
3 TraesCS7B01G437700 chr7B 92.351 706 20 12 6470 7151 704157777 704158472 0.000000e+00 974.0
4 TraesCS7B01G437700 chr7B 80.333 1022 104 45 5459 6448 639086753 639085797 0.000000e+00 684.0
5 TraesCS7B01G437700 chr7B 84.157 688 86 15 4075 4758 639087892 639087224 0.000000e+00 645.0
6 TraesCS7B01G437700 chr7B 83.285 347 41 11 4903 5244 639087147 639086813 3.280000e-78 303.0
7 TraesCS7B01G437700 chr7B 84.553 246 14 7 38 259 704151150 704151395 9.440000e-54 222.0
8 TraesCS7B01G437700 chr7B 72.691 758 134 45 1016 1752 639091037 639090332 1.240000e-42 185.0
9 TraesCS7B01G437700 chr7B 77.617 277 39 15 6681 6954 639085617 639085361 5.840000e-31 147.0
10 TraesCS7B01G437700 chr7A 93.003 5002 261 41 1078 6041 705135130 705140080 0.000000e+00 7215.0
11 TraesCS7B01G437700 chr7A 80.931 2837 417 76 1952 4751 667481019 667478270 0.000000e+00 2128.0
12 TraesCS7B01G437700 chr7A 84.254 978 94 26 123 1086 705132729 705133660 0.000000e+00 898.0
13 TraesCS7B01G437700 chr7A 94.550 422 14 3 6031 6448 705141577 705141993 1.700000e-180 643.0
14 TraesCS7B01G437700 chr7A 87.634 372 37 4 6681 7049 705142305 705142670 2.410000e-114 424.0
15 TraesCS7B01G437700 chr7A 80.551 581 56 29 5892 6448 667478230 667477683 1.890000e-105 394.0
16 TraesCS7B01G437700 chr7A 91.905 210 16 1 6469 6678 705141979 705142187 7.090000e-75 292.0
17 TraesCS7B01G437700 chr7A 76.098 205 29 10 6623 6818 667477274 667477081 9.990000e-14 89.8
18 TraesCS7B01G437700 chr7D 80.271 3031 438 92 1798 4758 576340137 576337197 0.000000e+00 2137.0
19 TraesCS7B01G437700 chr7D 80.607 1021 104 48 5459 6448 576336664 576335707 0.000000e+00 702.0
20 TraesCS7B01G437700 chr7D 84.058 345 40 10 4903 5244 576337118 576336786 1.170000e-82 318.0
21 TraesCS7B01G437700 chr7D 79.155 355 43 17 6616 6954 576335576 576335237 4.390000e-52 217.0
22 TraesCS7B01G437700 chr3D 83.202 1012 122 32 3788 4782 181109635 181108655 0.000000e+00 883.0
23 TraesCS7B01G437700 chr3D 80.355 677 60 29 5720 6372 181107811 181107184 5.140000e-121 446.0
24 TraesCS7B01G437700 chr3D 84.393 346 40 11 4903 5244 181108584 181108249 1.940000e-85 327.0
25 TraesCS7B01G437700 chr3D 82.692 104 6 8 6638 6729 181106509 181106406 1.670000e-11 82.4
26 TraesCS7B01G437700 chr3A 81.241 677 62 27 5720 6372 227919305 227919940 3.030000e-133 486.0
27 TraesCS7B01G437700 chr3A 82.022 445 64 13 4320 4757 227918107 227918542 1.480000e-96 364.0
28 TraesCS7B01G437700 chr3A 81.731 416 43 16 3895 4298 227917536 227917930 4.210000e-82 316.0
29 TraesCS7B01G437700 chr3A 82.571 350 45 10 4900 5244 227918613 227918951 1.970000e-75 294.0
30 TraesCS7B01G437700 chr3A 85.185 135 14 3 5721 5852 14856306 14856437 4.550000e-27 134.0
31 TraesCS7B01G437700 chr3A 84.270 89 14 0 5721 5809 227916230 227916318 3.590000e-13 87.9
32 TraesCS7B01G437700 chr3A 82.692 104 6 7 6638 6729 227920763 227920866 1.670000e-11 82.4
33 TraesCS7B01G437700 chr3B 74.725 364 53 22 6638 6966 259373024 259372665 7.610000e-25 126.0


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 TraesCS7B01G437700 chr7B 704086241 704093467 7226 False 13346.000000 13346 100.000000 1 7227 1 chr7B.!!$F1 7226
1 TraesCS7B01G437700 chr7B 704151150 704158472 7322 False 3993.000000 10783 91.811667 38 7151 3 chr7B.!!$F2 7113
2 TraesCS7B01G437700 chr7B 639085361 639091037 5676 True 565.666667 1430 79.449500 1016 6954 6 chr7B.!!$R1 5938
3 TraesCS7B01G437700 chr7A 705132729 705142670 9941 False 1894.400000 7215 90.269200 123 7049 5 chr7A.!!$F1 6926
4 TraesCS7B01G437700 chr7A 667477081 667481019 3938 True 870.600000 2128 79.193333 1952 6818 3 chr7A.!!$R1 4866
5 TraesCS7B01G437700 chr7D 576335237 576340137 4900 True 843.500000 2137 81.022750 1798 6954 4 chr7D.!!$R1 5156
6 TraesCS7B01G437700 chr3D 181106406 181109635 3229 True 434.600000 883 82.660500 3788 6729 4 chr3D.!!$R1 2941
7 TraesCS7B01G437700 chr3A 227916230 227920866 4636 False 271.716667 486 82.421167 3895 6729 6 chr3A.!!$F2 2834

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
256 280 0.033894 GGTATTTTTCCGGGGGCAGA 60.034 55.000 0.00 0.00 0.00 4.26 F
330 355 0.730494 GGTCCGTCCGTCGTACAAAG 60.730 60.000 0.00 0.00 37.94 2.77 F
638 673 1.002087 ACGAGCAGAACCCCTTACTTG 59.998 52.381 0.00 0.00 0.00 3.16 F
1183 2703 1.847328 TGTAGGAGAACATGCCTCGA 58.153 50.000 8.93 0.00 35.73 4.04 F
1199 2719 3.004524 GCCTCGACCTACCTACATTACAG 59.995 52.174 0.00 0.00 0.00 2.74 F
2944 4522 0.661483 GTCGCAAAGGTCAAAGCTGC 60.661 55.000 0.00 0.00 0.00 5.25 F
3270 4849 3.255642 ACTGGCTGTTTTTGAATGCGTAT 59.744 39.130 0.00 0.00 0.00 3.06 F
4769 6733 1.061887 GGATAATGCGCGCAAACGT 59.938 52.632 39.68 24.48 42.83 3.99 F
6022 8183 5.700832 TCTCGCAACAACTTATCAGTCAAAT 59.299 36.000 0.00 0.00 30.45 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1199 2719 1.202428 GGAACGGTGATGGACTAGCTC 60.202 57.143 0.00 0.0 0.00 4.09 R
1413 2933 1.579429 GGCTTTTGTCGCCATCGTT 59.421 52.632 0.00 0.0 46.77 3.85 R
2792 4368 2.432510 ACAAGAATAGGAAGCGAGGGAG 59.567 50.000 0.00 0.0 0.00 4.30 R
2924 4502 0.662619 CAGCTTTGACCTTTGCGACA 59.337 50.000 0.00 0.0 0.00 4.35 R
3228 4807 3.908103 AGTCAAAAGAACAGGTAGGGCTA 59.092 43.478 0.00 0.0 0.00 3.93 R
4759 6723 2.091588 ACTATCAGTTAACGTTTGCGCG 59.908 45.455 5.91 0.0 42.83 6.86 R
5388 7495 6.329496 AGTGTTTTTGATTTCGTGTGAATGT 58.671 32.000 0.00 0.0 33.20 2.71 R
6051 9719 1.818060 GAGCAACTGAGAGAGAGAGCA 59.182 52.381 0.00 0.0 0.00 4.26 R
7187 12152 0.031449 GAGATAGAGGCGCTCCACAC 59.969 60.000 7.64 0.0 33.74 3.82 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
19 20 4.767841 CTCGTCGCTGCTCGCACT 62.768 66.667 0.00 0.00 39.08 4.40
68 70 0.773305 ATCCATGGCCTATCCCTGCA 60.773 55.000 6.96 0.00 0.00 4.41
72 74 2.322658 CATGGCCTATCCCTGCATTTT 58.677 47.619 3.32 0.00 0.00 1.82
92 96 7.380870 GCATTTTCTTCTTGAGTTTCTCTTTCC 59.619 37.037 0.00 0.00 0.00 3.13
100 104 4.655963 TGAGTTTCTCTTTCCCATCTTGG 58.344 43.478 0.00 0.00 37.25 3.61
105 109 0.984230 TCTTTCCCATCTTGGCGAGT 59.016 50.000 0.77 0.00 35.79 4.18
184 204 2.384828 TCGTAGATCCAGCCAAGCTAA 58.615 47.619 0.00 0.00 36.40 3.09
249 273 1.296727 GGCTCTCGGTATTTTTCCGG 58.703 55.000 0.00 0.00 46.82 5.14
252 276 3.089788 CTCGGTATTTTTCCGGGGG 57.910 57.895 0.00 0.00 44.22 5.40
253 277 1.077572 TCGGTATTTTTCCGGGGGC 60.078 57.895 0.00 0.00 46.82 5.80
254 278 1.378778 CGGTATTTTTCCGGGGGCA 60.379 57.895 0.00 0.00 43.68 5.36
256 280 0.033894 GGTATTTTTCCGGGGGCAGA 60.034 55.000 0.00 0.00 0.00 4.26
258 282 2.384828 GTATTTTTCCGGGGGCAGAAT 58.615 47.619 0.00 0.00 0.00 2.40
259 283 1.485124 ATTTTTCCGGGGGCAGAATC 58.515 50.000 0.00 0.00 0.00 2.52
260 284 0.963355 TTTTTCCGGGGGCAGAATCG 60.963 55.000 0.00 0.00 0.00 3.34
262 286 2.530958 TTTCCGGGGGCAGAATCGAC 62.531 60.000 0.00 0.00 0.00 4.20
263 287 4.891727 CCGGGGGCAGAATCGACG 62.892 72.222 0.00 0.00 0.00 5.12
278 303 1.810030 GACGGATCGTGTGGCTTCC 60.810 63.158 0.00 0.00 41.37 3.46
307 332 3.751621 CGTTGGTTCATCTTCTTCATGC 58.248 45.455 0.00 0.00 0.00 4.06
329 354 1.285641 GGTCCGTCCGTCGTACAAA 59.714 57.895 0.00 0.00 37.94 2.83
330 355 0.730494 GGTCCGTCCGTCGTACAAAG 60.730 60.000 0.00 0.00 37.94 2.77
331 356 1.081242 TCCGTCCGTCGTACAAAGC 60.081 57.895 0.00 0.00 37.94 3.51
332 357 1.080974 CCGTCCGTCGTACAAAGCT 60.081 57.895 0.00 0.00 37.94 3.74
341 366 2.426381 GTCGTACAAAGCTAGCTAGGGT 59.574 50.000 19.70 17.91 0.00 4.34
356 381 2.195741 AGGGTTCGGGCTTTTAACTC 57.804 50.000 0.00 0.00 0.00 3.01
359 384 1.199327 GGTTCGGGCTTTTAACTCTGC 59.801 52.381 0.00 0.00 0.00 4.26
459 484 6.320926 TGGTTTGATGATGTGTTTCTTCTTCA 59.679 34.615 0.00 0.00 34.80 3.02
462 487 8.697067 GTTTGATGATGTGTTTCTTCTTCATTG 58.303 33.333 0.00 0.00 35.75 2.82
552 580 6.848069 TGGTTTCCGGATTCCTGATTATTAT 58.152 36.000 20.96 0.00 0.00 1.28
554 582 8.441572 TGGTTTCCGGATTCCTGATTATTATTA 58.558 33.333 20.96 0.00 0.00 0.98
601 632 6.668541 TTTCTTTGCTCCATCTAAATCTCG 57.331 37.500 0.00 0.00 0.00 4.04
609 640 3.007290 TCCATCTAAATCTCGCCTGGATG 59.993 47.826 0.00 0.00 0.00 3.51
631 666 3.132467 GGGATATATACGAGCAGAACCCC 59.868 52.174 0.00 0.00 0.00 4.95
638 673 1.002087 ACGAGCAGAACCCCTTACTTG 59.998 52.381 0.00 0.00 0.00 3.16
1183 2703 1.847328 TGTAGGAGAACATGCCTCGA 58.153 50.000 8.93 0.00 35.73 4.04
1199 2719 3.004524 GCCTCGACCTACCTACATTACAG 59.995 52.174 0.00 0.00 0.00 2.74
2845 4423 6.706270 TCAGTCTTTTGGTAGTCATGTCTTTC 59.294 38.462 0.00 0.00 0.00 2.62
2924 4502 7.309805 GCAAAGGTATAAAAGGTCTTTGTCCAT 60.310 37.037 13.32 0.00 43.40 3.41
2944 4522 0.661483 GTCGCAAAGGTCAAAGCTGC 60.661 55.000 0.00 0.00 0.00 5.25
3270 4849 3.255642 ACTGGCTGTTTTTGAATGCGTAT 59.744 39.130 0.00 0.00 0.00 3.06
4759 6723 2.173569 AGTTGTCCTCCTGGGATAATGC 59.826 50.000 0.00 0.00 44.86 3.56
4769 6733 1.061887 GGATAATGCGCGCAAACGT 59.938 52.632 39.68 24.48 42.83 3.99
4987 6971 6.039616 GCTGTCTAAGGAGTTCTATTGTCTG 58.960 44.000 0.00 0.00 0.00 3.51
5280 7282 7.147888 TCCCCCTGGTAACCTATATCTTTTAA 58.852 38.462 0.00 0.00 0.00 1.52
5285 7287 9.117183 CCTGGTAACCTATATCTTTTAACCAAC 57.883 37.037 0.00 0.00 0.00 3.77
5388 7495 7.275341 CGTTAGGTTGTTCCGTTTGTATATACA 59.725 37.037 11.62 11.62 41.99 2.29
5672 7820 5.921976 TGATTGTAATTCACTGCTTTGCAAG 59.078 36.000 0.00 0.00 38.41 4.01
6022 8183 5.700832 TCTCGCAACAACTTATCAGTCAAAT 59.299 36.000 0.00 0.00 30.45 2.32
6051 9719 4.404394 TGCATGGCTGATCATCTGATTTTT 59.596 37.500 0.00 0.00 34.37 1.94
6448 10312 4.042187 AGGACCTTAAACTCTGCTCATGTT 59.958 41.667 0.00 0.00 0.00 2.71
6455 10319 0.809241 CTCTGCTCATGTTCTCCCGC 60.809 60.000 0.00 0.00 0.00 6.13
6456 10320 1.078918 CTGCTCATGTTCTCCCGCA 60.079 57.895 0.00 0.00 0.00 5.69
6457 10321 0.674581 CTGCTCATGTTCTCCCGCAA 60.675 55.000 0.00 0.00 0.00 4.85
6458 10322 0.250684 TGCTCATGTTCTCCCGCAAA 60.251 50.000 0.00 0.00 0.00 3.68
6459 10323 0.881118 GCTCATGTTCTCCCGCAAAA 59.119 50.000 0.00 0.00 0.00 2.44
6460 10324 1.269448 GCTCATGTTCTCCCGCAAAAA 59.731 47.619 0.00 0.00 0.00 1.94
6511 10601 1.406341 CCAACGTATTCGGGGTGTCAT 60.406 52.381 0.00 0.00 41.85 3.06
6888 11832 5.012046 TCAGTGCAAAATACAGGAGAGAGAA 59.988 40.000 0.00 0.00 0.00 2.87
7011 11955 1.689243 CCGGTGGCCATCAGATCTGA 61.689 60.000 27.03 27.03 44.59 3.27
7040 11984 1.984570 CTGCCCCTCTCGGAGTTCA 60.985 63.158 4.69 0.00 0.00 3.18
7065 12030 0.166814 GATTGTGTGCTTGTCTCGGC 59.833 55.000 0.00 0.00 0.00 5.54
7067 12032 0.463654 TTGTGTGCTTGTCTCGGCTT 60.464 50.000 0.00 0.00 0.00 4.35
7084 12049 2.817470 CTTTGGGCGCCAATTGACGG 62.817 60.000 30.85 5.44 43.55 4.79
7139 12104 2.109126 GCTGCGCTAGTTGGGAAGG 61.109 63.158 9.73 0.00 35.02 3.46
7144 12109 1.885163 CGCTAGTTGGGAAGGTCGGT 61.885 60.000 0.00 0.00 0.00 4.69
7147 12112 0.688487 TAGTTGGGAAGGTCGGTTGG 59.312 55.000 0.00 0.00 0.00 3.77
7149 12114 3.501040 TTGGGAAGGTCGGTTGGCC 62.501 63.158 0.00 0.00 0.00 5.36
7178 12143 4.436998 GAGTGGACGGCGGGTCTG 62.437 72.222 13.24 0.00 45.35 3.51
7183 12148 4.736896 GACGGCGGGTCTGGTGAC 62.737 72.222 13.24 0.00 42.62 3.67
7185 12150 4.082523 CGGCGGGTCTGGTGACAT 62.083 66.667 0.00 0.00 44.61 3.06
7186 12151 2.125106 GGCGGGTCTGGTGACATC 60.125 66.667 0.00 0.00 44.61 3.06
7187 12152 2.509336 GCGGGTCTGGTGACATCG 60.509 66.667 0.00 0.00 44.61 3.84
7188 12153 2.970639 CGGGTCTGGTGACATCGT 59.029 61.111 0.00 0.00 44.61 3.73
7189 12154 1.446099 CGGGTCTGGTGACATCGTG 60.446 63.158 0.00 0.00 44.61 4.35
7190 12155 1.671742 GGGTCTGGTGACATCGTGT 59.328 57.895 0.00 0.00 44.61 4.49
7191 12156 0.670546 GGGTCTGGTGACATCGTGTG 60.671 60.000 0.00 0.00 44.61 3.82
7192 12157 0.670546 GGTCTGGTGACATCGTGTGG 60.671 60.000 0.00 0.00 44.61 4.17
7193 12158 0.317160 GTCTGGTGACATCGTGTGGA 59.683 55.000 0.00 0.00 42.48 4.02
7194 12159 0.603065 TCTGGTGACATCGTGTGGAG 59.397 55.000 0.00 0.00 41.51 3.86
7195 12160 1.005037 TGGTGACATCGTGTGGAGC 60.005 57.895 0.00 0.00 33.40 4.70
7196 12161 2.094659 GGTGACATCGTGTGGAGCG 61.095 63.158 0.00 0.00 0.00 5.03
7197 12162 2.432456 TGACATCGTGTGGAGCGC 60.432 61.111 0.00 0.00 0.00 5.92
7198 12163 3.188786 GACATCGTGTGGAGCGCC 61.189 66.667 2.29 0.00 0.00 6.53
7199 12164 3.649277 GACATCGTGTGGAGCGCCT 62.649 63.158 8.34 0.00 34.31 5.52
7200 12165 2.887568 CATCGTGTGGAGCGCCTC 60.888 66.667 8.34 4.55 34.31 4.70
7201 12166 3.071206 ATCGTGTGGAGCGCCTCT 61.071 61.111 8.34 0.00 34.31 3.69
7202 12167 1.753078 ATCGTGTGGAGCGCCTCTA 60.753 57.895 8.34 0.00 34.31 2.43
7203 12168 1.109920 ATCGTGTGGAGCGCCTCTAT 61.110 55.000 8.34 0.00 34.31 1.98
7204 12169 1.299468 CGTGTGGAGCGCCTCTATC 60.299 63.158 8.34 0.00 34.31 2.08
7205 12170 1.729470 CGTGTGGAGCGCCTCTATCT 61.729 60.000 8.34 0.00 34.31 1.98
7206 12171 0.031449 GTGTGGAGCGCCTCTATCTC 59.969 60.000 8.34 0.00 34.31 2.75
7207 12172 1.109920 TGTGGAGCGCCTCTATCTCC 61.110 60.000 8.34 2.61 45.02 3.71
7208 12173 0.825840 GTGGAGCGCCTCTATCTCCT 60.826 60.000 8.34 0.00 45.04 3.69
7209 12174 0.105964 TGGAGCGCCTCTATCTCCTT 60.106 55.000 8.34 0.00 45.04 3.36
7210 12175 1.044611 GGAGCGCCTCTATCTCCTTT 58.955 55.000 2.29 0.00 42.31 3.11
7211 12176 1.000394 GGAGCGCCTCTATCTCCTTTC 60.000 57.143 2.29 0.00 42.31 2.62
7212 12177 0.671251 AGCGCCTCTATCTCCTTTCG 59.329 55.000 2.29 0.00 0.00 3.46
7213 12178 0.386113 GCGCCTCTATCTCCTTTCGT 59.614 55.000 0.00 0.00 0.00 3.85
7214 12179 1.866063 GCGCCTCTATCTCCTTTCGTG 60.866 57.143 0.00 0.00 0.00 4.35
7215 12180 1.405821 CGCCTCTATCTCCTTTCGTGT 59.594 52.381 0.00 0.00 0.00 4.49
7216 12181 2.541999 CGCCTCTATCTCCTTTCGTGTC 60.542 54.545 0.00 0.00 0.00 3.67
7217 12182 2.691011 GCCTCTATCTCCTTTCGTGTCT 59.309 50.000 0.00 0.00 0.00 3.41
7218 12183 3.490078 GCCTCTATCTCCTTTCGTGTCTG 60.490 52.174 0.00 0.00 0.00 3.51
7219 12184 3.948473 CCTCTATCTCCTTTCGTGTCTGA 59.052 47.826 0.00 0.00 0.00 3.27
7220 12185 4.582656 CCTCTATCTCCTTTCGTGTCTGAT 59.417 45.833 0.00 0.00 0.00 2.90
7221 12186 5.765677 CCTCTATCTCCTTTCGTGTCTGATA 59.234 44.000 0.00 0.00 0.00 2.15
7222 12187 6.432783 CCTCTATCTCCTTTCGTGTCTGATAT 59.567 42.308 0.00 0.00 0.00 1.63
7223 12188 7.208225 TCTATCTCCTTTCGTGTCTGATATG 57.792 40.000 0.00 0.00 0.00 1.78
7224 12189 6.998673 TCTATCTCCTTTCGTGTCTGATATGA 59.001 38.462 0.00 0.00 0.00 2.15
7225 12190 5.914898 TCTCCTTTCGTGTCTGATATGAA 57.085 39.130 5.11 5.11 0.00 2.57
7226 12191 5.895928 TCTCCTTTCGTGTCTGATATGAAG 58.104 41.667 8.70 4.73 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.885644 CGATCGTCACCTTGGCCG 60.886 66.667 7.03 0.00 0.00 6.13
26 27 1.519455 CTCGATCGTCACCTTGGCC 60.519 63.158 15.94 0.00 0.00 5.36
27 28 2.167861 GCTCGATCGTCACCTTGGC 61.168 63.158 15.94 4.52 0.00 4.52
28 29 0.526524 GAGCTCGATCGTCACCTTGG 60.527 60.000 15.94 0.00 0.00 3.61
30 31 0.965866 TGGAGCTCGATCGTCACCTT 60.966 55.000 15.94 0.00 0.00 3.50
32 33 0.318275 GATGGAGCTCGATCGTCACC 60.318 60.000 20.98 15.52 0.00 4.02
33 34 0.318275 GGATGGAGCTCGATCGTCAC 60.318 60.000 26.35 13.03 32.72 3.67
35 36 0.600557 ATGGATGGAGCTCGATCGTC 59.399 55.000 26.35 16.94 32.72 4.20
36 37 0.316522 CATGGATGGAGCTCGATCGT 59.683 55.000 26.35 17.46 32.72 3.73
68 70 7.561356 TGGGAAAGAGAAACTCAAGAAGAAAAT 59.439 33.333 0.00 0.00 32.06 1.82
72 74 5.630415 TGGGAAAGAGAAACTCAAGAAGA 57.370 39.130 0.00 0.00 32.06 2.87
92 96 0.391130 TCCGAAACTCGCCAAGATGG 60.391 55.000 0.00 0.00 38.82 3.51
100 104 1.668151 AGCACCTTCCGAAACTCGC 60.668 57.895 0.00 0.00 38.82 5.03
105 109 1.021202 CAACACAGCACCTTCCGAAA 58.979 50.000 0.00 0.00 0.00 3.46
184 204 6.825213 TCGTATACCTAATACATACCAGCGAT 59.175 38.462 0.00 0.00 40.56 4.58
198 218 2.615447 CCAGCGAGTGTCGTATACCTAA 59.385 50.000 0.00 0.00 42.81 2.69
249 273 1.301009 GATCCGTCGATTCTGCCCC 60.301 63.158 0.00 0.00 0.00 5.80
250 274 4.345337 GATCCGTCGATTCTGCCC 57.655 61.111 0.00 0.00 0.00 5.36
260 284 1.810030 GGAAGCCACACGATCCGTC 60.810 63.158 0.00 0.00 38.32 4.79
290 315 3.067742 CCATGGCATGAAGAAGATGAACC 59.932 47.826 28.43 0.00 0.00 3.62
329 354 2.134933 GCCCGAACCCTAGCTAGCT 61.135 63.158 23.12 23.12 0.00 3.32
330 355 1.687297 AAGCCCGAACCCTAGCTAGC 61.687 60.000 15.74 6.62 34.49 3.42
331 356 0.831307 AAAGCCCGAACCCTAGCTAG 59.169 55.000 14.20 14.20 34.49 3.42
332 357 1.282382 AAAAGCCCGAACCCTAGCTA 58.718 50.000 0.00 0.00 34.49 3.32
341 366 1.153353 CGCAGAGTTAAAAGCCCGAA 58.847 50.000 0.00 0.00 0.00 4.30
356 381 2.998670 ACTGTTTCATCATCACTCGCAG 59.001 45.455 0.00 0.00 0.00 5.18
359 384 2.028523 GCGACTGTTTCATCATCACTCG 59.971 50.000 0.00 0.00 0.00 4.18
459 484 4.202182 TGCAGCAAGAAGAAGAAAAGCAAT 60.202 37.500 0.00 0.00 0.00 3.56
462 487 3.360249 TGCAGCAAGAAGAAGAAAAGC 57.640 42.857 0.00 0.00 0.00 3.51
601 632 3.243907 GCTCGTATATATCCCATCCAGGC 60.244 52.174 0.00 0.00 35.39 4.85
609 640 3.132467 GGGGTTCTGCTCGTATATATCCC 59.868 52.174 0.00 0.00 0.00 3.85
638 673 8.122472 TCCCACAAAGAAATTAAGGAGAAATC 57.878 34.615 0.00 0.00 0.00 2.17
668 703 2.482864 TGCTATGATGTATGCGTGGTG 58.517 47.619 0.00 0.00 0.00 4.17
990 1032 2.091885 AGTGTGGGACATTGGTGACTTT 60.092 45.455 0.00 0.00 44.52 2.66
1109 2629 3.433598 CCCAGAGACTTTGAAGTGGTTCA 60.434 47.826 0.30 0.00 41.13 3.18
1183 2703 6.015991 ACTAGCTCTGTAATGTAGGTAGGT 57.984 41.667 11.24 0.00 42.74 3.08
1199 2719 1.202428 GGAACGGTGATGGACTAGCTC 60.202 57.143 0.00 0.00 0.00 4.09
1413 2933 1.579429 GGCTTTTGTCGCCATCGTT 59.421 52.632 0.00 0.00 46.77 3.85
2792 4368 2.432510 ACAAGAATAGGAAGCGAGGGAG 59.567 50.000 0.00 0.00 0.00 4.30
2845 4423 5.051816 ACATGGAAATGAGCACACAAAAAG 58.948 37.500 0.00 0.00 0.00 2.27
2924 4502 0.662619 CAGCTTTGACCTTTGCGACA 59.337 50.000 0.00 0.00 0.00 4.35
3228 4807 3.908103 AGTCAAAAGAACAGGTAGGGCTA 59.092 43.478 0.00 0.00 0.00 3.93
4759 6723 2.091588 ACTATCAGTTAACGTTTGCGCG 59.908 45.455 5.91 0.00 42.83 6.86
4987 6971 6.954684 TCTCACTAACTCCATCCCTAATATCC 59.045 42.308 0.00 0.00 0.00 2.59
5280 7282 8.528044 TTTGAAAGAATGTAAAGGTAGTTGGT 57.472 30.769 0.00 0.00 0.00 3.67
5388 7495 6.329496 AGTGTTTTTGATTTCGTGTGAATGT 58.671 32.000 0.00 0.00 33.20 2.71
6022 8183 1.895231 GATCAGCCATGCATGCCGA 60.895 57.895 21.69 15.94 0.00 5.54
6051 9719 1.818060 GAGCAACTGAGAGAGAGAGCA 59.182 52.381 0.00 0.00 0.00 4.26
6148 9816 4.486503 GCAGCCTCAGCCTGGGAG 62.487 72.222 0.00 0.00 41.25 4.30
6385 10243 1.871080 ATTATTGCGAAGGAGCTCCG 58.129 50.000 26.95 16.25 42.08 4.63
6844 11780 9.132521 GCACTGATATGAATATTGCAAATTACC 57.867 33.333 1.71 0.00 29.09 2.85
6929 11873 8.190784 GGTGTAAATTGGAGTCAAAATATGAGG 58.809 37.037 0.00 0.00 39.19 3.86
7003 11947 2.943690 CAGGTCAAAGGCATCAGATCTG 59.056 50.000 17.07 17.07 33.44 2.90
7011 11955 2.037847 GGGGCAGGTCAAAGGCAT 59.962 61.111 0.00 0.00 0.00 4.40
7012 11956 3.185203 AGGGGCAGGTCAAAGGCA 61.185 61.111 0.00 0.00 0.00 4.75
7040 11984 3.290710 AGACAAGCACACAATCCAAGTT 58.709 40.909 0.00 0.00 0.00 2.66
7084 12049 0.890683 CTCTGCAACCCAAATCCCAC 59.109 55.000 0.00 0.00 0.00 4.61
7108 12073 3.863681 CGCAGCTCTAAGCCTCTAG 57.136 57.895 0.00 0.00 43.77 2.43
7161 12126 4.436998 CAGACCCGCCGTCCACTC 62.437 72.222 0.00 0.00 43.08 3.51
7166 12131 4.736896 GTCACCAGACCCGCCGTC 62.737 72.222 0.00 0.00 42.32 4.79
7168 12133 4.082523 ATGTCACCAGACCCGCCG 62.083 66.667 0.00 0.00 44.33 6.46
7169 12134 2.125106 GATGTCACCAGACCCGCC 60.125 66.667 0.00 0.00 44.33 6.13
7170 12135 2.509336 CGATGTCACCAGACCCGC 60.509 66.667 0.00 0.00 44.33 6.13
7171 12136 1.446099 CACGATGTCACCAGACCCG 60.446 63.158 0.00 0.00 44.33 5.28
7172 12137 0.670546 CACACGATGTCACCAGACCC 60.671 60.000 0.00 0.00 44.33 4.46
7173 12138 0.670546 CCACACGATGTCACCAGACC 60.671 60.000 0.00 0.00 44.33 3.85
7174 12139 0.317160 TCCACACGATGTCACCAGAC 59.683 55.000 0.00 0.00 45.19 3.51
7175 12140 0.603065 CTCCACACGATGTCACCAGA 59.397 55.000 0.00 0.00 0.00 3.86
7176 12141 1.016130 GCTCCACACGATGTCACCAG 61.016 60.000 0.00 0.00 0.00 4.00
7177 12142 1.005037 GCTCCACACGATGTCACCA 60.005 57.895 0.00 0.00 0.00 4.17
7178 12143 2.094659 CGCTCCACACGATGTCACC 61.095 63.158 0.00 0.00 0.00 4.02
7179 12144 2.730672 GCGCTCCACACGATGTCAC 61.731 63.158 0.00 0.00 0.00 3.67
7180 12145 2.432456 GCGCTCCACACGATGTCA 60.432 61.111 0.00 0.00 0.00 3.58
7181 12146 3.188786 GGCGCTCCACACGATGTC 61.189 66.667 7.64 0.00 0.00 3.06
7182 12147 3.649277 GAGGCGCTCCACACGATGT 62.649 63.158 7.64 0.00 33.74 3.06
7183 12148 2.004808 TAGAGGCGCTCCACACGATG 62.005 60.000 7.64 0.00 33.74 3.84
7184 12149 1.109920 ATAGAGGCGCTCCACACGAT 61.110 55.000 7.64 0.00 33.74 3.73
7185 12150 1.725557 GATAGAGGCGCTCCACACGA 61.726 60.000 7.64 0.00 33.74 4.35
7186 12151 1.299468 GATAGAGGCGCTCCACACG 60.299 63.158 7.64 0.00 33.74 4.49
7187 12152 0.031449 GAGATAGAGGCGCTCCACAC 59.969 60.000 7.64 0.00 33.74 3.82
7188 12153 1.109920 GGAGATAGAGGCGCTCCACA 61.110 60.000 7.64 0.00 45.89 4.17
7189 12154 1.663173 GGAGATAGAGGCGCTCCAC 59.337 63.158 7.64 0.00 45.89 4.02
7190 12155 4.182744 GGAGATAGAGGCGCTCCA 57.817 61.111 7.64 0.00 45.89 3.86
7191 12156 1.000394 GAAAGGAGATAGAGGCGCTCC 60.000 57.143 7.64 4.09 46.75 4.70
7192 12157 1.335506 CGAAAGGAGATAGAGGCGCTC 60.336 57.143 7.64 2.67 0.00 5.03
7193 12158 0.671251 CGAAAGGAGATAGAGGCGCT 59.329 55.000 7.64 0.00 0.00 5.92
7194 12159 0.386113 ACGAAAGGAGATAGAGGCGC 59.614 55.000 0.00 0.00 0.00 6.53
7195 12160 1.405821 ACACGAAAGGAGATAGAGGCG 59.594 52.381 0.00 0.00 0.00 5.52
7196 12161 2.691011 AGACACGAAAGGAGATAGAGGC 59.309 50.000 0.00 0.00 0.00 4.70
7197 12162 3.948473 TCAGACACGAAAGGAGATAGAGG 59.052 47.826 0.00 0.00 0.00 3.69
7198 12163 5.766150 ATCAGACACGAAAGGAGATAGAG 57.234 43.478 0.00 0.00 0.00 2.43
7199 12164 6.998673 TCATATCAGACACGAAAGGAGATAGA 59.001 38.462 0.00 0.00 0.00 1.98
7200 12165 7.208225 TCATATCAGACACGAAAGGAGATAG 57.792 40.000 0.00 0.00 0.00 2.08
7201 12166 7.582667 TTCATATCAGACACGAAAGGAGATA 57.417 36.000 0.00 0.00 0.00 1.98
7202 12167 6.471233 TTCATATCAGACACGAAAGGAGAT 57.529 37.500 0.00 0.00 0.00 2.75
7203 12168 5.895928 CTTCATATCAGACACGAAAGGAGA 58.104 41.667 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.