Multiple sequence alignment - TraesCS3D01G114200

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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 TraesCS3D01G114200 chr3D 100.000 2658 0 0 1 2658 67714848 67712191 0.000000e+00 4909
1 TraesCS3D01G114200 chr3A 93.581 1963 85 22 719 2658 79404003 79402059 0.000000e+00 2889
2 TraesCS3D01G114200 chr3B 90.287 1081 64 18 1604 2656 114143227 114144294 0.000000e+00 1376
3 TraesCS3D01G114200 chr3B 90.899 879 41 14 755 1633 114142387 114143226 0.000000e+00 1144
4 TraesCS3D01G114200 chr3B 81.902 652 88 16 2 627 114138733 114139380 8.430000e-145 523
5 TraesCS3D01G114200 chr2A 83.763 893 72 25 1697 2535 73554194 73555067 0.000000e+00 778
6 TraesCS3D01G114200 chr2B 85.904 752 46 20 1898 2608 113325565 113326297 0.000000e+00 747
7 TraesCS3D01G114200 chr2B 84.065 433 52 6 364 788 113323970 113324393 4.120000e-108 401
8 TraesCS3D01G114200 chr2B 92.000 100 5 2 789 886 113325480 113325578 1.280000e-28 137
9 TraesCS3D01G114200 chr2D 84.422 796 60 21 1902 2656 74279191 74279963 0.000000e+00 725
10 TraesCS3D01G114200 chr2D 86.544 327 20 8 551 877 74278887 74279189 3.280000e-89 339
11 TraesCS3D01G114200 chr7A 83.092 207 23 5 2424 2627 35157199 35157396 7.560000e-41 178


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 TraesCS3D01G114200 chr3D 67712191 67714848 2657 True 4909.000000 4909 100.000 1 2658 1 chr3D.!!$R1 2657
1 TraesCS3D01G114200 chr3A 79402059 79404003 1944 True 2889.000000 2889 93.581 719 2658 1 chr3A.!!$R1 1939
2 TraesCS3D01G114200 chr3B 114138733 114144294 5561 False 1014.333333 1376 87.696 2 2656 3 chr3B.!!$F1 2654
3 TraesCS3D01G114200 chr2A 73554194 73555067 873 False 778.000000 778 83.763 1697 2535 1 chr2A.!!$F1 838
4 TraesCS3D01G114200 chr2B 113323970 113326297 2327 False 428.333333 747 87.323 364 2608 3 chr2B.!!$F1 2244
5 TraesCS3D01G114200 chr2D 74278887 74279963 1076 False 532.000000 725 85.483 551 2656 2 chr2D.!!$F1 2105

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
663 697 0.035439 GAAACGGGATTCAGGCAGGA 60.035 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2217 6365 0.10412 TCACACACGGTCTTCCACTG 59.896 55.0 0.0 0.0 37.41 3.66 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
36 38 2.038863 TACATGTCCTTGTGGAGGGT 57.961 50.000 0.00 0.00 46.31 4.34
49 51 1.526575 GGAGGGTGCAACATGTGGTG 61.527 60.000 3.06 0.00 39.98 4.17
68 70 2.788786 GTGATGTTCACCAAAAAGTGCG 59.211 45.455 0.00 0.00 41.37 5.34
69 71 2.425312 TGATGTTCACCAAAAAGTGCGT 59.575 40.909 0.00 0.00 37.68 5.24
70 72 3.628032 TGATGTTCACCAAAAAGTGCGTA 59.372 39.130 0.00 0.00 37.68 4.42
95 97 4.586001 AGGTGTTAAAACTAGTCGACCTCA 59.414 41.667 13.01 0.00 0.00 3.86
103 105 4.640789 ACTAGTCGACCTCATTGATCAC 57.359 45.455 13.01 0.00 0.00 3.06
104 106 4.017126 ACTAGTCGACCTCATTGATCACA 58.983 43.478 13.01 0.00 0.00 3.58
109 111 4.207224 GTCGACCTCATTGATCACAATACG 59.793 45.833 3.51 0.00 43.76 3.06
110 112 3.060272 CGACCTCATTGATCACAATACGC 60.060 47.826 0.00 0.00 43.76 4.42
111 113 3.206150 ACCTCATTGATCACAATACGCC 58.794 45.455 0.00 0.00 43.76 5.68
115 117 3.308595 TCATTGATCACAATACGCCGTTC 59.691 43.478 0.00 0.00 43.76 3.95
117 119 3.786516 TGATCACAATACGCCGTTCTA 57.213 42.857 0.00 0.00 0.00 2.10
126 128 2.365408 ACGCCGTTCTAGGAAGAAAG 57.635 50.000 0.00 0.00 43.30 2.62
133 135 5.163540 GCCGTTCTAGGAAGAAAGTGAGATA 60.164 44.000 0.00 0.00 43.30 1.98
136 138 6.920758 CGTTCTAGGAAGAAAGTGAGATATGG 59.079 42.308 0.00 0.00 43.30 2.74
143 145 8.214364 AGGAAGAAAGTGAGATATGGGTTATTC 58.786 37.037 0.00 0.00 0.00 1.75
151 153 8.239478 AGTGAGATATGGGTTATTCTTAGGGTA 58.761 37.037 0.00 0.00 0.00 3.69
152 154 8.532819 GTGAGATATGGGTTATTCTTAGGGTAG 58.467 40.741 0.00 0.00 0.00 3.18
155 157 8.239478 AGATATGGGTTATTCTTAGGGTAGTCA 58.761 37.037 0.00 0.00 0.00 3.41
156 158 6.749036 ATGGGTTATTCTTAGGGTAGTCAG 57.251 41.667 0.00 0.00 0.00 3.51
159 161 5.163332 GGGTTATTCTTAGGGTAGTCAGTGG 60.163 48.000 0.00 0.00 0.00 4.00
162 164 3.116096 TCTTAGGGTAGTCAGTGGCAT 57.884 47.619 0.00 0.00 0.00 4.40
163 165 2.766263 TCTTAGGGTAGTCAGTGGCATG 59.234 50.000 0.00 0.00 0.00 4.06
167 169 1.026718 GGTAGTCAGTGGCATGGTGC 61.027 60.000 0.00 0.00 44.08 5.01
193 195 2.740055 GCACACGGAGCAGAGGTG 60.740 66.667 0.00 0.00 37.67 4.00
219 221 2.104170 AGTAGCTAGGAGACAGTTGGC 58.896 52.381 0.00 0.00 0.00 4.52
239 241 3.136763 GCGACATGGTTCATGAGATCAT 58.863 45.455 13.96 0.00 43.81 2.45
241 243 4.388165 GCGACATGGTTCATGAGATCATAG 59.612 45.833 13.96 0.76 43.81 2.23
246 248 5.798125 TGGTTCATGAGATCATAGGAGAC 57.202 43.478 0.00 0.00 34.26 3.36
249 251 5.279406 GGTTCATGAGATCATAGGAGACCAG 60.279 48.000 0.00 0.00 34.26 4.00
251 253 5.901598 TCATGAGATCATAGGAGACCAGAT 58.098 41.667 0.00 0.00 34.26 2.90
252 254 6.321321 TCATGAGATCATAGGAGACCAGATT 58.679 40.000 0.00 0.00 34.26 2.40
255 257 4.424842 AGATCATAGGAGACCAGATTCCC 58.575 47.826 0.00 0.00 33.83 3.97
297 313 7.411372 GGTTTCACAACAAATAACACACACAAG 60.411 37.037 0.00 0.00 34.15 3.16
302 318 6.806249 ACAACAAATAACACACACAAGAACTG 59.194 34.615 0.00 0.00 0.00 3.16
321 337 5.717119 ACTGGATTATACTTTGCCCTTCT 57.283 39.130 0.00 0.00 0.00 2.85
322 338 6.824958 ACTGGATTATACTTTGCCCTTCTA 57.175 37.500 0.00 0.00 0.00 2.10
327 343 3.771577 ATACTTTGCCCTTCTATCGGG 57.228 47.619 0.00 0.00 44.89 5.14
348 365 4.142227 GGGCTAGTCGAATGAACAAGACTA 60.142 45.833 0.00 13.13 42.99 2.59
355 372 5.740099 GTCGAATGAACAAGACTACTAGAGC 59.260 44.000 0.00 0.00 0.00 4.09
359 376 1.765230 ACAAGACTACTAGAGCGGGG 58.235 55.000 0.00 0.00 0.00 5.73
360 377 1.005687 ACAAGACTACTAGAGCGGGGT 59.994 52.381 0.00 0.00 0.00 4.95
361 378 2.240667 ACAAGACTACTAGAGCGGGGTA 59.759 50.000 0.00 0.00 0.00 3.69
362 379 2.879646 CAAGACTACTAGAGCGGGGTAG 59.120 54.545 0.00 0.00 38.89 3.18
381 398 1.971357 AGGGGATCGACGATTTGCTAT 59.029 47.619 12.40 0.00 0.00 2.97
384 401 4.223032 AGGGGATCGACGATTTGCTATTAT 59.777 41.667 12.40 0.00 0.00 1.28
387 404 4.929808 GGATCGACGATTTGCTATTATGGT 59.070 41.667 12.40 0.00 0.00 3.55
393 410 6.377327 ACGATTTGCTATTATGGTTGAAGG 57.623 37.500 0.00 0.00 0.00 3.46
402 419 5.841957 ATTATGGTTGAAGGCAGTTCATC 57.158 39.130 1.88 1.98 44.89 2.92
410 427 2.927553 AGGCAGTTCATCGAAAATGC 57.072 45.000 12.55 12.55 36.45 3.56
416 433 4.400845 CAGTTCATCGAAAATGCACTCTG 58.599 43.478 0.00 0.00 0.00 3.35
436 453 2.106338 TGCCATTTGTGAAGTCCAGAGA 59.894 45.455 0.00 0.00 0.00 3.10
440 457 3.475566 TTTGTGAAGTCCAGAGACCAG 57.524 47.619 0.00 0.00 44.72 4.00
443 460 1.068194 GTGAAGTCCAGAGACCAGTCG 60.068 57.143 0.00 0.00 44.72 4.18
444 461 1.249407 GAAGTCCAGAGACCAGTCGT 58.751 55.000 0.00 0.00 44.72 4.34
449 473 2.162008 GTCCAGAGACCAGTCGTAAGTC 59.838 54.545 0.00 0.00 37.00 3.01
450 474 2.160205 CCAGAGACCAGTCGTAAGTCA 58.840 52.381 0.00 0.00 39.48 3.41
474 499 2.223711 ACACGCCAGTTTTGATTCCAAC 60.224 45.455 0.00 0.00 30.88 3.77
485 510 6.310224 AGTTTTGATTCCAACGAAACAAAGTG 59.690 34.615 0.00 0.00 45.67 3.16
495 520 2.397549 GAAACAAAGTGCATGCCTCAC 58.602 47.619 16.68 6.91 34.80 3.51
531 565 0.827089 CATGGTGGACAAGGTGGCAA 60.827 55.000 0.00 0.00 0.00 4.52
543 577 3.477582 TGGCAACAGTCGGGATGA 58.522 55.556 0.00 0.00 46.17 2.92
596 630 2.296920 TCCAGGTTGGATTAGCGCT 58.703 52.632 17.26 17.26 42.67 5.92
613 647 2.910199 CGCTGAATCAAAGGGATCTCA 58.090 47.619 0.00 0.00 34.28 3.27
627 661 3.432378 GGATCTCACGTATGGGGAGTAT 58.568 50.000 0.00 0.00 0.00 2.12
638 672 1.764854 GGGAGTATGGAAGCGGGGA 60.765 63.158 0.00 0.00 0.00 4.81
639 673 1.342672 GGGAGTATGGAAGCGGGGAA 61.343 60.000 0.00 0.00 0.00 3.97
640 674 0.106894 GGAGTATGGAAGCGGGGAAG 59.893 60.000 0.00 0.00 0.00 3.46
641 675 0.106894 GAGTATGGAAGCGGGGAAGG 59.893 60.000 0.00 0.00 0.00 3.46
642 676 0.326238 AGTATGGAAGCGGGGAAGGA 60.326 55.000 0.00 0.00 0.00 3.36
643 677 0.179054 GTATGGAAGCGGGGAAGGAC 60.179 60.000 0.00 0.00 0.00 3.85
644 678 1.682451 TATGGAAGCGGGGAAGGACG 61.682 60.000 0.00 0.00 0.00 4.79
645 679 3.387947 GGAAGCGGGGAAGGACGA 61.388 66.667 0.00 0.00 0.00 4.20
646 680 2.660802 GAAGCGGGGAAGGACGAA 59.339 61.111 0.00 0.00 0.00 3.85
663 697 0.035439 GAAACGGGATTCAGGCAGGA 60.035 55.000 0.00 0.00 0.00 3.86
703 737 0.803768 CGTCACCGCTGATGGAAGAG 60.804 60.000 0.00 0.00 30.60 2.85
712 746 1.277273 CTGATGGAAGAGAGGCACACA 59.723 52.381 0.00 0.00 0.00 3.72
716 750 1.980765 TGGAAGAGAGGCACACAAGAT 59.019 47.619 0.00 0.00 0.00 2.40
717 751 2.289882 TGGAAGAGAGGCACACAAGATG 60.290 50.000 0.00 0.00 0.00 2.90
737 773 3.990092 TGAGAGCGAGCAAAGTTTCTAA 58.010 40.909 0.00 0.00 0.00 2.10
788 3734 3.191078 GCTGATTAGCCTCATGTGAGT 57.809 47.619 9.03 0.00 44.33 3.41
789 3735 2.871022 GCTGATTAGCCTCATGTGAGTG 59.129 50.000 9.03 2.50 44.33 3.51
790 3736 3.431346 GCTGATTAGCCTCATGTGAGTGA 60.431 47.826 9.03 0.00 44.33 3.41
844 4876 2.542595 CGCTTTCACGTGGTTTACTCTT 59.457 45.455 17.00 0.00 0.00 2.85
886 4920 7.924103 AAATTTTCGCAAAGTTAACTACAGG 57.076 32.000 8.92 0.21 28.44 4.00
887 4921 6.628919 ATTTTCGCAAAGTTAACTACAGGT 57.371 33.333 8.92 0.00 0.00 4.00
916 4980 3.878103 AGTGTAGAGTAGCCATAGACACG 59.122 47.826 0.00 0.00 40.42 4.49
917 4981 3.875727 GTGTAGAGTAGCCATAGACACGA 59.124 47.826 0.00 0.00 0.00 4.35
918 4982 4.024725 GTGTAGAGTAGCCATAGACACGAG 60.025 50.000 0.00 0.00 0.00 4.18
919 4983 1.950909 AGAGTAGCCATAGACACGAGC 59.049 52.381 0.00 0.00 0.00 5.03
920 4984 1.676529 GAGTAGCCATAGACACGAGCA 59.323 52.381 0.00 0.00 0.00 4.26
921 4985 2.294791 GAGTAGCCATAGACACGAGCAT 59.705 50.000 0.00 0.00 0.00 3.79
922 4986 3.487372 AGTAGCCATAGACACGAGCATA 58.513 45.455 0.00 0.00 0.00 3.14
923 4987 3.504134 AGTAGCCATAGACACGAGCATAG 59.496 47.826 0.00 0.00 0.00 2.23
924 4988 2.587522 AGCCATAGACACGAGCATAGA 58.412 47.619 0.00 0.00 0.00 1.98
925 4989 2.294791 AGCCATAGACACGAGCATAGAC 59.705 50.000 0.00 0.00 0.00 2.59
926 4990 2.034685 GCCATAGACACGAGCATAGACA 59.965 50.000 0.00 0.00 0.00 3.41
927 4991 3.633235 CCATAGACACGAGCATAGACAC 58.367 50.000 0.00 0.00 0.00 3.67
933 4997 3.082548 ACACGAGCATAGACACTGTAGT 58.917 45.455 0.00 0.00 0.00 2.73
976 5040 2.221299 AGCCAAACTAGCACCGGGA 61.221 57.895 6.32 0.00 0.00 5.14
977 5041 2.038837 GCCAAACTAGCACCGGGAC 61.039 63.158 6.32 0.00 0.00 4.46
1140 5204 3.702048 CCGGCCAAGGTCTTCCGA 61.702 66.667 2.24 0.00 44.23 4.55
1346 5410 0.394488 GAGCCCAAGGTAAAGGAGCC 60.394 60.000 0.00 0.00 0.00 4.70
1402 5466 2.868583 CGTGTGGATATTGCAGAAGGAG 59.131 50.000 0.00 0.00 0.00 3.69
1410 5474 0.250295 TTGCAGAAGGAGTTGACGGG 60.250 55.000 0.00 0.00 0.00 5.28
1415 5479 0.605589 GAAGGAGTTGACGGGTTGGG 60.606 60.000 0.00 0.00 0.00 4.12
1421 5485 1.064240 AGTTGACGGGTTGGGTTTTCT 60.064 47.619 0.00 0.00 0.00 2.52
1423 5487 1.394618 TGACGGGTTGGGTTTTCTTG 58.605 50.000 0.00 0.00 0.00 3.02
1483 5547 2.827190 ATCGTCGTCGGCCTGCTA 60.827 61.111 0.00 0.00 37.69 3.49
1511 5575 2.203337 TGTTGGCTGTGGTGGCTC 60.203 61.111 0.00 0.00 0.00 4.70
1656 5754 2.621998 GGAGCCGAGCTACTGTAATGTA 59.378 50.000 1.26 0.00 39.88 2.29
1657 5755 3.067742 GGAGCCGAGCTACTGTAATGTAA 59.932 47.826 1.26 0.00 39.88 2.41
1658 5756 4.262079 GGAGCCGAGCTACTGTAATGTAAT 60.262 45.833 1.26 0.00 39.88 1.89
1785 5887 5.953183 TGCTTCAACGCAAATAATCATCTT 58.047 33.333 0.00 0.00 36.89 2.40
1806 5908 7.894376 TCTTTGCTGATGAAATTTTCCATTC 57.106 32.000 6.68 2.65 0.00 2.67
1848 5950 5.459536 TCCATAATCATCTCTCAGAACCG 57.540 43.478 0.00 0.00 0.00 4.44
1934 6044 2.614057 CCTCGTCAAAACAGCTTTCAGT 59.386 45.455 0.00 0.00 0.00 3.41
2164 6312 3.764434 TCATTCAGTACTGGGTCTGAGTC 59.236 47.826 22.48 0.00 40.91 3.36
2277 6425 2.076100 TCACATCGGTCAGTGCAATTC 58.924 47.619 0.00 0.00 35.76 2.17
2278 6426 1.078709 ACATCGGTCAGTGCAATTCG 58.921 50.000 0.00 0.00 0.00 3.34
2299 6447 8.922058 ATTCGAATGATGAAGAAAAATCCTTG 57.078 30.769 10.50 0.00 0.00 3.61
2533 6707 9.268282 TCCTAAGGTCAAAGATTATAGTCAGTT 57.732 33.333 0.00 0.00 0.00 3.16
2564 6738 9.424319 ACGTTAAGGCATCTAGATTGTAATATG 57.576 33.333 1.33 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.467598 AGGACATGTATTACTACACAACTACTG 58.532 37.037 0.00 0.00 40.57 2.74
36 38 2.034432 GTGAACATCACCACATGTTGCA 59.966 45.455 0.00 0.00 45.23 4.08
49 51 3.078594 ACGCACTTTTTGGTGAACATC 57.921 42.857 0.00 0.00 39.34 3.06
62 64 5.823209 AGTTTTAACACCTTTACGCACTT 57.177 34.783 0.00 0.00 0.00 3.16
63 65 6.051074 ACTAGTTTTAACACCTTTACGCACT 58.949 36.000 0.00 0.00 0.00 4.40
65 67 5.175491 CGACTAGTTTTAACACCTTTACGCA 59.825 40.000 0.00 0.00 0.00 5.24
67 69 6.129088 GGTCGACTAGTTTTAACACCTTTACG 60.129 42.308 16.46 0.00 0.00 3.18
68 70 6.925718 AGGTCGACTAGTTTTAACACCTTTAC 59.074 38.462 16.46 0.00 0.00 2.01
69 71 7.054491 AGGTCGACTAGTTTTAACACCTTTA 57.946 36.000 16.46 0.00 0.00 1.85
70 72 5.922053 AGGTCGACTAGTTTTAACACCTTT 58.078 37.500 16.46 0.00 0.00 3.11
95 97 3.531538 AGAACGGCGTATTGTGATCAAT 58.468 40.909 15.20 0.00 45.00 2.57
103 105 3.431922 TCTTCCTAGAACGGCGTATTG 57.568 47.619 15.20 6.29 0.00 1.90
104 106 4.081807 ACTTTCTTCCTAGAACGGCGTATT 60.082 41.667 15.20 7.26 40.04 1.89
109 111 3.056749 TCTCACTTTCTTCCTAGAACGGC 60.057 47.826 0.00 0.00 40.04 5.68
110 112 4.785511 TCTCACTTTCTTCCTAGAACGG 57.214 45.455 0.00 0.00 40.04 4.44
111 113 6.920758 CCATATCTCACTTTCTTCCTAGAACG 59.079 42.308 0.00 0.00 40.04 3.95
115 117 6.739331 ACCCATATCTCACTTTCTTCCTAG 57.261 41.667 0.00 0.00 0.00 3.02
117 119 7.698163 ATAACCCATATCTCACTTTCTTCCT 57.302 36.000 0.00 0.00 0.00 3.36
126 128 7.317722 ACCCTAAGAATAACCCATATCTCAC 57.682 40.000 0.00 0.00 0.00 3.51
133 135 6.099845 CACTGACTACCCTAAGAATAACCCAT 59.900 42.308 0.00 0.00 0.00 4.00
136 138 5.684291 GCCACTGACTACCCTAAGAATAACC 60.684 48.000 0.00 0.00 0.00 2.85
143 145 2.158900 CCATGCCACTGACTACCCTAAG 60.159 54.545 0.00 0.00 0.00 2.18
146 148 0.547712 ACCATGCCACTGACTACCCT 60.548 55.000 0.00 0.00 0.00 4.34
159 161 2.652530 CAACACCTGGCACCATGC 59.347 61.111 0.00 0.00 44.08 4.06
181 183 0.529337 CTACATGCACCTCTGCTCCG 60.529 60.000 0.00 0.00 44.57 4.63
186 188 3.005261 CCTAGCTACTACATGCACCTCTG 59.995 52.174 0.00 0.00 0.00 3.35
193 195 3.886505 ACTGTCTCCTAGCTACTACATGC 59.113 47.826 0.00 0.00 0.00 4.06
219 221 4.928020 CCTATGATCTCATGAACCATGTCG 59.072 45.833 11.98 1.18 41.98 4.35
239 241 1.023719 TGGGGGAATCTGGTCTCCTA 58.976 55.000 0.00 0.00 38.36 2.94
241 243 0.475906 CATGGGGGAATCTGGTCTCC 59.524 60.000 0.00 0.00 37.45 3.71
246 248 1.202976 GGTCATCATGGGGGAATCTGG 60.203 57.143 0.00 0.00 0.00 3.86
249 251 0.250901 CGGGTCATCATGGGGGAATC 60.251 60.000 0.00 0.00 0.00 2.52
251 253 0.916845 TTCGGGTCATCATGGGGGAA 60.917 55.000 0.00 0.00 0.00 3.97
252 254 1.307430 TTCGGGTCATCATGGGGGA 60.307 57.895 0.00 0.00 0.00 4.81
255 257 4.885426 CCTTCGGGTCATCATGGG 57.115 61.111 0.00 0.00 0.00 4.00
283 299 6.959639 AATCCAGTTCTTGTGTGTGTTATT 57.040 33.333 0.00 0.00 0.00 1.40
297 313 6.122964 AGAAGGGCAAAGTATAATCCAGTTC 58.877 40.000 0.00 0.00 0.00 3.01
302 318 5.875359 CCGATAGAAGGGCAAAGTATAATCC 59.125 44.000 0.00 0.00 39.76 3.01
321 337 2.953648 TGTTCATTCGACTAGCCCGATA 59.046 45.455 8.38 2.01 35.84 2.92
322 338 1.754803 TGTTCATTCGACTAGCCCGAT 59.245 47.619 8.38 0.00 35.84 4.18
327 343 5.642686 AGTAGTCTTGTTCATTCGACTAGC 58.357 41.667 0.00 0.00 39.03 3.42
329 345 7.201626 GCTCTAGTAGTCTTGTTCATTCGACTA 60.202 40.741 0.00 0.00 37.80 2.59
332 349 5.447413 CGCTCTAGTAGTCTTGTTCATTCGA 60.447 44.000 0.00 0.00 0.00 3.71
348 365 1.369855 ATCCCCTACCCCGCTCTAGT 61.370 60.000 0.00 0.00 0.00 2.57
355 372 3.292936 CGTCGATCCCCTACCCCG 61.293 72.222 0.00 0.00 0.00 5.73
359 376 1.068741 AGCAAATCGTCGATCCCCTAC 59.931 52.381 8.45 0.00 0.00 3.18
360 377 1.410004 AGCAAATCGTCGATCCCCTA 58.590 50.000 8.45 0.00 0.00 3.53
361 378 1.410004 TAGCAAATCGTCGATCCCCT 58.590 50.000 8.45 7.35 0.00 4.79
362 379 2.457366 ATAGCAAATCGTCGATCCCC 57.543 50.000 8.45 0.00 0.00 4.81
381 398 3.689161 CGATGAACTGCCTTCAACCATAA 59.311 43.478 0.00 0.00 42.37 1.90
384 401 1.071542 TCGATGAACTGCCTTCAACCA 59.928 47.619 0.00 0.00 42.37 3.67
387 404 4.797471 CATTTTCGATGAACTGCCTTCAA 58.203 39.130 0.00 0.00 42.37 2.69
393 410 3.120060 AGAGTGCATTTTCGATGAACTGC 60.120 43.478 2.78 4.29 38.00 4.40
410 427 2.227388 GGACTTCACAAATGGCAGAGTG 59.773 50.000 9.62 9.62 0.00 3.51
416 433 2.485814 GTCTCTGGACTTCACAAATGGC 59.514 50.000 0.00 0.00 39.24 4.40
436 453 2.797087 CGTGTTGTGACTTACGACTGGT 60.797 50.000 0.00 0.00 43.04 4.00
440 457 0.505655 GGCGTGTTGTGACTTACGAC 59.494 55.000 10.05 4.42 42.95 4.34
443 460 1.578583 ACTGGCGTGTTGTGACTTAC 58.421 50.000 0.00 0.00 0.00 2.34
444 461 2.319136 AACTGGCGTGTTGTGACTTA 57.681 45.000 0.00 0.00 0.00 2.24
449 473 2.490328 ATCAAAACTGGCGTGTTGTG 57.510 45.000 10.62 8.87 39.05 3.33
450 474 2.223711 GGAATCAAAACTGGCGTGTTGT 60.224 45.455 10.62 0.00 39.05 3.32
474 499 1.001487 TGAGGCATGCACTTTGTTTCG 60.001 47.619 21.36 0.00 0.00 3.46
531 565 4.129737 CGCCGTCATCCCGACTGT 62.130 66.667 0.00 0.00 42.98 3.55
547 581 2.656651 CTCCAGATTCGCGGCTCG 60.657 66.667 6.13 0.00 40.15 5.03
596 630 3.981071 ACGTGAGATCCCTTTGATTCA 57.019 42.857 0.00 0.00 32.41 2.57
613 647 1.692519 GCTTCCATACTCCCCATACGT 59.307 52.381 0.00 0.00 0.00 3.57
627 661 3.702048 CGTCCTTCCCCGCTTCCA 61.702 66.667 0.00 0.00 0.00 3.53
638 672 1.338769 CCTGAATCCCGTTTCGTCCTT 60.339 52.381 0.00 0.00 0.00 3.36
639 673 0.249398 CCTGAATCCCGTTTCGTCCT 59.751 55.000 0.00 0.00 0.00 3.85
640 674 1.366854 GCCTGAATCCCGTTTCGTCC 61.367 60.000 0.00 0.00 0.00 4.79
641 675 0.672401 TGCCTGAATCCCGTTTCGTC 60.672 55.000 0.00 0.00 0.00 4.20
642 676 0.673644 CTGCCTGAATCCCGTTTCGT 60.674 55.000 0.00 0.00 0.00 3.85
643 677 1.369091 CCTGCCTGAATCCCGTTTCG 61.369 60.000 0.00 0.00 0.00 3.46
644 678 0.035439 TCCTGCCTGAATCCCGTTTC 60.035 55.000 0.00 0.00 0.00 2.78
645 679 0.625849 ATCCTGCCTGAATCCCGTTT 59.374 50.000 0.00 0.00 0.00 3.60
646 680 0.625849 AATCCTGCCTGAATCCCGTT 59.374 50.000 0.00 0.00 0.00 4.44
663 697 7.807907 GTGACGATTTGTTCTCAAACCATAAAT 59.192 33.333 0.00 0.00 44.69 1.40
703 737 1.367659 GCTCTCATCTTGTGTGCCTC 58.632 55.000 0.00 0.00 0.00 4.70
712 746 2.758736 ACTTTGCTCGCTCTCATCTT 57.241 45.000 0.00 0.00 0.00 2.40
716 750 2.533266 AGAAACTTTGCTCGCTCTCA 57.467 45.000 0.00 0.00 0.00 3.27
717 751 3.991121 AGTTAGAAACTTTGCTCGCTCTC 59.009 43.478 0.00 0.00 39.04 3.20
737 773 0.242286 CACGCTGCAGTCACTCTAGT 59.758 55.000 16.64 0.49 0.00 2.57
788 3734 2.526304 AGCGTGAAAGTGTAAGCTCA 57.474 45.000 0.00 0.00 0.00 4.26
789 3735 2.157863 GGAAGCGTGAAAGTGTAAGCTC 59.842 50.000 0.00 0.00 33.42 4.09
790 3736 2.143925 GGAAGCGTGAAAGTGTAAGCT 58.856 47.619 0.00 0.00 36.40 3.74
844 4876 8.058915 CGAAAATTTAAGCAATTTGAAACGGAA 58.941 29.630 0.00 0.00 43.20 4.30
886 4920 8.584157 TCTATGGCTACTCTACACTAGTACTAC 58.416 40.741 0.00 0.00 0.00 2.73
887 4921 8.584157 GTCTATGGCTACTCTACACTAGTACTA 58.416 40.741 1.89 1.89 0.00 1.82
916 4980 5.299531 TGGTGATACTACAGTGTCTATGCTC 59.700 44.000 0.00 0.00 37.13 4.26
917 4981 5.201243 TGGTGATACTACAGTGTCTATGCT 58.799 41.667 0.00 0.00 37.13 3.79
918 4982 5.067936 ACTGGTGATACTACAGTGTCTATGC 59.932 44.000 0.00 0.00 43.29 3.14
919 4983 6.701145 ACTGGTGATACTACAGTGTCTATG 57.299 41.667 0.00 0.00 43.29 2.23
920 4984 6.890268 TGAACTGGTGATACTACAGTGTCTAT 59.110 38.462 0.00 0.00 44.08 1.98
921 4985 6.150641 GTGAACTGGTGATACTACAGTGTCTA 59.849 42.308 0.00 0.00 44.08 2.59
922 4986 5.047943 GTGAACTGGTGATACTACAGTGTCT 60.048 44.000 0.00 0.00 44.08 3.41
923 4987 5.047943 AGTGAACTGGTGATACTACAGTGTC 60.048 44.000 0.00 0.00 44.08 3.67
924 4988 4.833380 AGTGAACTGGTGATACTACAGTGT 59.167 41.667 0.00 0.00 44.08 3.55
925 4989 5.164233 CAGTGAACTGGTGATACTACAGTG 58.836 45.833 2.35 0.00 44.08 3.66
926 4990 4.322049 GCAGTGAACTGGTGATACTACAGT 60.322 45.833 12.20 0.00 46.59 3.55
927 4991 4.177026 GCAGTGAACTGGTGATACTACAG 58.823 47.826 12.20 0.00 43.94 2.74
933 4997 0.320050 TGCGCAGTGAACTGGTGATA 59.680 50.000 5.66 0.00 43.94 2.15
1126 5190 1.521681 CCGATCGGAAGACCTTGGC 60.522 63.158 30.62 0.00 46.97 4.52
1210 5274 1.296715 GCTTGAAGGCGAAGAGGGA 59.703 57.895 0.00 0.00 0.00 4.20
1346 5410 3.051392 GCAAAACGGGCAGGGATCG 62.051 63.158 0.00 0.00 0.00 3.69
1381 5445 2.868583 CTCCTTCTGCAATATCCACACG 59.131 50.000 0.00 0.00 0.00 4.49
1385 5449 4.517285 GTCAACTCCTTCTGCAATATCCA 58.483 43.478 0.00 0.00 0.00 3.41
1402 5466 1.395635 AGAAAACCCAACCCGTCAAC 58.604 50.000 0.00 0.00 0.00 3.18
1410 5474 0.317519 CGCGACCAAGAAAACCCAAC 60.318 55.000 0.00 0.00 0.00 3.77
1415 5479 1.082104 CCTGCGCGACCAAGAAAAC 60.082 57.895 12.10 0.00 0.00 2.43
1496 5560 1.993701 TTGAGAGCCACCACAGCCAA 61.994 55.000 0.00 0.00 0.00 4.52
1501 5565 2.425592 CCGTTGAGAGCCACCACA 59.574 61.111 0.00 0.00 0.00 4.17
1658 5756 9.642343 TCTTGATAGTACAAAGGAGAGCTATTA 57.358 33.333 0.00 0.00 0.00 0.98
1741 5839 4.143263 GCAAACTGCACACATTTATTCTGC 60.143 41.667 0.00 0.00 44.26 4.26
1785 5887 6.023357 TCGAATGGAAAATTTCATCAGCAA 57.977 33.333 8.09 0.00 0.00 3.91
1792 5894 6.507958 TGCATACTCGAATGGAAAATTTCA 57.492 33.333 8.09 0.00 0.00 2.69
1806 5908 5.056480 TGGAATATGGAACTTGCATACTCG 58.944 41.667 5.22 0.00 33.52 4.18
1848 5950 5.708230 TGGTTGTAATGTATCTTGGTGTTCC 59.292 40.000 0.00 0.00 0.00 3.62
1948 6058 6.377146 GGCTTTCCTGATCTTATTTGGTTGTA 59.623 38.462 0.00 0.00 0.00 2.41
2217 6365 0.104120 TCACACACGGTCTTCCACTG 59.896 55.000 0.00 0.00 37.41 3.66
2277 6425 6.624423 ACCAAGGATTTTTCTTCATCATTCG 58.376 36.000 0.00 0.00 0.00 3.34
2278 6426 6.749118 CGACCAAGGATTTTTCTTCATCATTC 59.251 38.462 0.00 0.00 0.00 2.67
2322 6470 5.390991 GCTGCTGTTACCATTAAACTGAGTC 60.391 44.000 0.00 0.00 0.00 3.36
2533 6707 6.096423 ACAATCTAGATGCCTTAACGTGACTA 59.904 38.462 5.86 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.