Multiple sequence alignment - TraesCS2A01G267100

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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 TraesCS2A01G267100 chr2A 100.000 3071 0 0 1 3071 425808412 425811482 0.000000e+00 5672.0
1 TraesCS2A01G267100 chr2A 82.723 191 23 10 630 817 746983398 746983215 8.810000e-36 161.0
2 TraesCS2A01G267100 chr2B 92.694 2231 129 17 7 2219 379831347 379833561 0.000000e+00 3186.0
3 TraesCS2A01G267100 chr2B 87.681 276 29 3 2506 2781 737052518 737052788 1.780000e-82 316.0
4 TraesCS2A01G267100 chr2B 95.349 172 8 0 2338 2509 379833826 379833997 1.080000e-69 274.0
5 TraesCS2A01G267100 chr2B 76.109 293 56 11 2512 2798 326482903 326483187 1.150000e-29 141.0
6 TraesCS2A01G267100 chr2D 97.101 1311 32 3 912 2219 312064418 312063111 0.000000e+00 2206.0
7 TraesCS2A01G267100 chr2D 93.386 378 18 3 2 378 49248931 49248560 1.240000e-153 553.0
8 TraesCS2A01G267100 chr2D 86.127 519 38 14 2 518 312178912 312178426 2.100000e-146 529.0
9 TraesCS2A01G267100 chr2D 84.767 407 38 15 534 921 312065218 312064817 1.340000e-103 387.0
10 TraesCS2A01G267100 chr2D 90.698 172 5 1 2338 2509 312062846 312062686 5.160000e-53 219.0
11 TraesCS2A01G267100 chr5A 95.583 566 23 2 2507 3071 465113498 465112934 0.000000e+00 905.0
12 TraesCS2A01G267100 chrUn 93.122 378 18 4 2 378 237100792 237100422 5.790000e-152 547.0
13 TraesCS2A01G267100 chrUn 83.880 366 33 12 2512 2867 5466741 5466392 2.950000e-85 326.0
14 TraesCS2A01G267100 chrUn 89.773 88 7 2 2975 3062 5448869 5448784 9.000000e-21 111.0
15 TraesCS2A01G267100 chr7D 93.122 378 18 4 2 378 381901142 381900772 5.790000e-152 547.0
16 TraesCS2A01G267100 chr7D 82.209 163 23 5 655 813 173900777 173900937 5.340000e-28 135.0
17 TraesCS2A01G267100 chr4D 92.857 378 19 4 2 378 123636317 123636687 2.690000e-150 542.0
18 TraesCS2A01G267100 chr4D 90.526 95 4 1 246 340 336583856 336583767 1.500000e-23 121.0
19 TraesCS2A01G267100 chr1D 92.328 378 21 4 2 378 141328430 141328060 5.830000e-147 531.0
20 TraesCS2A01G267100 chr5B 88.480 408 39 5 2507 2908 166165495 166165900 1.280000e-133 486.0
21 TraesCS2A01G267100 chr5B 88.235 408 40 5 2507 2908 165774159 165774564 5.960000e-132 481.0
22 TraesCS2A01G267100 chr5B 87.047 193 21 3 631 821 710209689 710209879 6.670000e-52 215.0
23 TraesCS2A01G267100 chr6B 80.551 617 62 29 2512 3071 614723525 614724140 3.660000e-114 422.0
24 TraesCS2A01G267100 chr6A 92.810 153 10 1 2 154 256475177 256475026 1.430000e-53 220.0
25 TraesCS2A01G267100 chr1B 83.708 178 27 2 641 817 395260694 395260870 1.890000e-37 167.0
26 TraesCS2A01G267100 chr7B 76.846 298 54 13 2507 2798 417081487 417081199 1.470000e-33 154.0
27 TraesCS2A01G267100 chr3A 81.967 183 31 2 639 821 515951578 515951758 1.470000e-33 154.0
28 TraesCS2A01G267100 chr3B 86.861 137 15 2 644 778 613641334 613641199 1.910000e-32 150.0
29 TraesCS2A01G267100 chr4B 76.952 269 54 8 2512 2777 391560880 391561143 2.470000e-31 147.0
30 TraesCS2A01G267100 chr5D 83.226 155 23 3 640 792 461044009 461043856 4.130000e-29 139.0
31 TraesCS2A01G267100 chr6D 89.796 98 5 1 243 340 127339306 127339398 1.500000e-23 121.0
32 TraesCS2A01G267100 chr4A 95.745 47 2 0 2975 3021 22189932 22189886 3.280000e-10 76.8


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 TraesCS2A01G267100 chr2A 425808412 425811482 3070 False 5672.000000 5672 100.000000 1 3071 1 chr2A.!!$F1 3070
1 TraesCS2A01G267100 chr2B 379831347 379833997 2650 False 1730.000000 3186 94.021500 7 2509 2 chr2B.!!$F3 2502
2 TraesCS2A01G267100 chr2D 312062686 312065218 2532 True 937.333333 2206 90.855333 534 2509 3 chr2D.!!$R3 1975
3 TraesCS2A01G267100 chr5A 465112934 465113498 564 True 905.000000 905 95.583000 2507 3071 1 chr5A.!!$R1 564
4 TraesCS2A01G267100 chr6B 614723525 614724140 615 False 422.000000 422 80.551000 2512 3071 1 chr6B.!!$F1 559

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
87 88 0.319900 CATATCGGTCGGGGCTTCTG 60.320 60.0 0.0 0.0 0.00 3.02 F
375 377 0.902531 GGAAACTCGGATGAGGTGGA 59.097 55.0 0.0 0.0 42.87 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 2312 0.468226 ACTCAAGGAAAGACCGCACA 59.532 50.000 0.0 0.0 44.74 4.57 R
2330 2917 3.010624 TGGCACACACAAAATTGATCG 57.989 42.857 0.0 0.0 0.00 3.69 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
38 39 2.678336 GGGATTACTTTCGTTCCAGCAG 59.322 50.000 0.00 0.00 0.00 4.24
41 42 3.462483 TTACTTTCGTTCCAGCAGTCA 57.538 42.857 0.00 0.00 0.00 3.41
47 48 3.026630 TCGTTCCAGCAGTCACTTAAG 57.973 47.619 0.00 0.00 0.00 1.85
48 49 2.069273 CGTTCCAGCAGTCACTTAAGG 58.931 52.381 7.53 0.00 0.00 2.69
49 50 2.288825 CGTTCCAGCAGTCACTTAAGGA 60.289 50.000 7.53 0.00 0.00 3.36
50 51 3.617531 CGTTCCAGCAGTCACTTAAGGAT 60.618 47.826 7.53 0.00 0.00 3.24
51 52 3.616956 TCCAGCAGTCACTTAAGGATG 57.383 47.619 7.53 0.00 0.00 3.51
52 53 3.173151 TCCAGCAGTCACTTAAGGATGA 58.827 45.455 7.53 0.00 0.00 2.92
53 54 3.582647 TCCAGCAGTCACTTAAGGATGAA 59.417 43.478 7.53 0.00 0.00 2.57
54 55 4.041567 TCCAGCAGTCACTTAAGGATGAAA 59.958 41.667 7.53 0.00 0.00 2.69
55 56 4.394300 CCAGCAGTCACTTAAGGATGAAAG 59.606 45.833 7.53 0.48 0.00 2.62
74 75 9.743057 GATGAAAGGATAGGAATAGTCATATCG 57.257 37.037 16.02 0.00 44.78 2.92
87 88 0.319900 CATATCGGTCGGGGCTTCTG 60.320 60.000 0.00 0.00 0.00 3.02
90 91 0.974010 ATCGGTCGGGGCTTCTGTTA 60.974 55.000 0.00 0.00 0.00 2.41
96 97 2.036089 GTCGGGGCTTCTGTTAGATAGG 59.964 54.545 0.00 0.00 0.00 2.57
100 101 3.324268 GGGGCTTCTGTTAGATAGGGTAC 59.676 52.174 0.00 0.00 0.00 3.34
159 160 5.355467 TGTTCGTAACATGACGTAGTGTA 57.645 39.130 0.00 0.00 43.39 2.90
180 181 5.929992 TGTAATCACTCGAACCAAAAGTAGG 59.070 40.000 0.00 0.00 0.00 3.18
287 289 8.206325 TGCTAATTTCACTGAAAGATCTGATC 57.794 34.615 9.65 9.65 34.92 2.92
289 291 8.336806 GCTAATTTCACTGAAAGATCTGATCTG 58.663 37.037 20.20 10.48 40.13 2.90
299 301 8.327941 TGAAAGATCTGATCTGTTCGAATTTT 57.672 30.769 20.20 7.87 40.13 1.82
305 307 7.728847 TCTGATCTGTTCGAATTTTCTTTCA 57.271 32.000 0.00 0.00 0.00 2.69
309 311 9.748708 TGATCTGTTCGAATTTTCTTTCATTTT 57.251 25.926 0.00 0.00 0.00 1.82
344 346 4.640771 AAACTTCTCCTGTTGCTATGGA 57.359 40.909 0.00 0.00 0.00 3.41
353 355 3.055530 CCTGTTGCTATGGAGAAGTCACT 60.056 47.826 0.00 0.00 0.00 3.41
354 356 4.564406 CCTGTTGCTATGGAGAAGTCACTT 60.564 45.833 0.00 0.00 0.00 3.16
357 359 5.112686 GTTGCTATGGAGAAGTCACTTAGG 58.887 45.833 0.00 0.00 0.00 2.69
373 375 3.195825 ACTTAGGAAACTCGGATGAGGTG 59.804 47.826 0.00 0.00 42.87 4.00
375 377 0.902531 GGAAACTCGGATGAGGTGGA 59.097 55.000 0.00 0.00 42.87 4.02
378 380 3.408634 GAAACTCGGATGAGGTGGAAAA 58.591 45.455 0.00 0.00 42.87 2.29
405 407 5.092554 TCAAAAGTGACACTTACAGGTCA 57.907 39.130 20.85 0.00 37.47 4.02
408 410 6.704493 TCAAAAGTGACACTTACAGGTCATAC 59.296 38.462 20.85 0.00 44.94 2.39
426 428 5.795441 GTCATACGACAATTGCTTCTTTTCC 59.205 40.000 5.05 0.00 42.13 3.13
428 430 1.978782 CGACAATTGCTTCTTTTCCGC 59.021 47.619 5.05 0.00 0.00 5.54
429 431 2.604373 CGACAATTGCTTCTTTTCCGCA 60.604 45.455 5.05 0.00 0.00 5.69
470 472 6.816640 TCTTTAACAACTATCATACAAGCGCT 59.183 34.615 2.64 2.64 0.00 5.92
549 551 1.885049 ATGCTATGGTGTGTCCTCCT 58.115 50.000 0.00 0.00 37.07 3.69
561 563 3.076182 TGTGTCCTCCTCTCTAAGGTCTT 59.924 47.826 0.00 0.00 46.32 3.01
566 568 4.017407 TCCTCCTCTCTAAGGTCTTGCTTA 60.017 45.833 0.00 0.00 46.32 3.09
573 575 8.646900 CCTCTCTAAGGTCTTGCTTAGATAATT 58.353 37.037 0.00 0.00 40.19 1.40
579 581 6.587273 AGGTCTTGCTTAGATAATTGACTCC 58.413 40.000 0.00 0.00 34.79 3.85
582 584 7.654116 GGTCTTGCTTAGATAATTGACTCCTAC 59.346 40.741 0.00 0.00 34.79 3.18
845 869 4.183865 ACATCATGTGTGACAGTTATCGG 58.816 43.478 0.00 0.00 40.28 4.18
846 870 3.953712 TCATGTGTGACAGTTATCGGT 57.046 42.857 0.00 0.00 0.00 4.69
847 871 3.584834 TCATGTGTGACAGTTATCGGTG 58.415 45.455 0.00 0.00 0.00 4.94
848 872 3.006430 TCATGTGTGACAGTTATCGGTGT 59.994 43.478 0.00 0.00 0.00 4.16
849 873 4.218852 TCATGTGTGACAGTTATCGGTGTA 59.781 41.667 0.00 0.00 0.00 2.90
1202 1633 1.379642 GCGGCCTTTCTCCAATCTGG 61.380 60.000 0.00 0.00 39.43 3.86
1252 1683 1.006805 CTATCCAAGCTCGCCTCCG 60.007 63.158 0.00 0.00 0.00 4.63
1334 1765 4.077184 CTACGCCTCCGCCACCAA 62.077 66.667 0.00 0.00 38.22 3.67
1502 1933 2.965783 ATCGGCGGGATCATCGAG 59.034 61.111 7.21 5.05 35.07 4.04
1875 2306 3.379865 GACGGGCAGGGCGACATTA 62.380 63.158 0.00 0.00 0.00 1.90
1881 2312 1.826024 CAGGGCGACATTAGAGGCT 59.174 57.895 0.00 0.00 0.00 4.58
1902 2333 1.531578 GTGCGGTCTTTCCTTGAGTTC 59.468 52.381 0.00 0.00 0.00 3.01
1923 2354 2.113433 GCTGTGGAGGCTGCATGAG 61.113 63.158 13.12 12.42 34.18 2.90
1970 2401 2.401766 CGAGGGCTGGATTGTGTGC 61.402 63.158 0.00 0.00 0.00 4.57
2207 2641 9.695155 AATTTAACCCTGCATACAGTTTATAGT 57.305 29.630 0.00 0.00 42.81 2.12
2227 2661 7.672983 ATAGTAATTTCTGGCAATATCGGTG 57.327 36.000 0.00 0.00 0.00 4.94
2228 2662 5.680619 AGTAATTTCTGGCAATATCGGTGA 58.319 37.500 0.00 0.00 0.00 4.02
2230 2664 3.627395 TTTCTGGCAATATCGGTGAGT 57.373 42.857 0.00 0.00 0.00 3.41
2231 2665 3.627395 TTCTGGCAATATCGGTGAGTT 57.373 42.857 0.00 0.00 0.00 3.01
2233 2667 4.746535 TCTGGCAATATCGGTGAGTTTA 57.253 40.909 0.00 0.00 0.00 2.01
2236 2670 5.361571 TCTGGCAATATCGGTGAGTTTACTA 59.638 40.000 0.00 0.00 0.00 1.82
2237 2671 6.041637 TCTGGCAATATCGGTGAGTTTACTAT 59.958 38.462 0.00 0.00 0.00 2.12
2238 2672 7.231925 TCTGGCAATATCGGTGAGTTTACTATA 59.768 37.037 0.00 0.00 0.00 1.31
2239 2673 7.728148 TGGCAATATCGGTGAGTTTACTATAA 58.272 34.615 0.00 0.00 0.00 0.98
2240 2674 8.205512 TGGCAATATCGGTGAGTTTACTATAAA 58.794 33.333 0.00 0.00 0.00 1.40
2278 2712 9.667107 TTGGTAAGTTTAATCAGACTAGATTGG 57.333 33.333 0.00 0.00 38.60 3.16
2279 2713 8.822805 TGGTAAGTTTAATCAGACTAGATTGGT 58.177 33.333 0.00 0.00 38.60 3.67
2289 2723 9.668497 AATCAGACTAGATTGGTAAGTTTAACC 57.332 33.333 0.00 0.00 36.88 2.85
2290 2724 8.431910 TCAGACTAGATTGGTAAGTTTAACCT 57.568 34.615 0.00 0.00 37.91 3.50
2293 2727 8.657712 AGACTAGATTGGTAAGTTTAACCTTGT 58.342 33.333 0.00 0.00 37.91 3.16
2300 2887 8.578448 TTGGTAAGTTTAACCTTGTAAGTTGT 57.422 30.769 0.00 0.00 37.91 3.32
2302 2889 8.676401 TGGTAAGTTTAACCTTGTAAGTTGTTC 58.324 33.333 0.00 0.00 37.91 3.18
2312 2899 9.802039 AACCTTGTAAGTTGTTCATCCTTATAA 57.198 29.630 0.00 0.00 0.00 0.98
2313 2900 9.449719 ACCTTGTAAGTTGTTCATCCTTATAAG 57.550 33.333 5.43 5.43 38.53 1.73
2314 2901 9.449719 CCTTGTAAGTTGTTCATCCTTATAAGT 57.550 33.333 11.50 0.00 37.80 2.24
2322 2909 9.106070 GTTGTTCATCCTTATAAGTTTACCGAT 57.894 33.333 11.50 3.27 0.00 4.18
2373 2960 7.620188 GCCAACAGATTGATCGAGTAAATATCG 60.620 40.741 0.00 0.00 38.15 2.92
2426 3013 8.298729 TCTGTATGTACTGAAGAATCACTGAT 57.701 34.615 0.00 0.00 32.34 2.90
2476 3063 2.202946 GCCTGCCTCTAGTTCGCC 60.203 66.667 0.00 0.00 0.00 5.54
2493 3080 4.021102 TCGCCTTTTGAGGAATTCTTCT 57.979 40.909 17.42 1.62 0.00 2.85
2499 3086 6.461509 GCCTTTTGAGGAATTCTTCTGTTTCA 60.462 38.462 17.42 0.00 0.00 2.69
2502 3089 7.822161 TTTGAGGAATTCTTCTGTTTCATCA 57.178 32.000 17.42 0.00 38.11 3.07
2514 3101 9.268268 TCTTCTGTTTCATCACGTATTTAAACT 57.732 29.630 13.48 0.00 0.00 2.66
2641 3228 7.283625 TGACTGCATGGTAAATTTTGTTACT 57.716 32.000 0.00 0.00 34.88 2.24
2642 3229 7.721402 TGACTGCATGGTAAATTTTGTTACTT 58.279 30.769 0.00 0.00 34.88 2.24
2712 3300 3.443329 TGATTCGGTTGATTCATTGTGGG 59.557 43.478 0.00 0.00 31.41 4.61
2921 3554 3.739080 AATCCCCTCCTCCCGCCAT 62.739 63.158 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.716612 AGTAATCCCTTGAAGTTCAACAAAAG 58.283 34.615 14.35 4.47 32.21 2.27
1 2 7.654022 AGTAATCCCTTGAAGTTCAACAAAA 57.346 32.000 14.35 1.53 32.21 2.44
2 3 7.654022 AAGTAATCCCTTGAAGTTCAACAAA 57.346 32.000 14.35 3.23 32.21 2.83
3 4 7.468084 CGAAAGTAATCCCTTGAAGTTCAACAA 60.468 37.037 14.35 3.57 32.21 2.83
4 5 6.017440 CGAAAGTAATCCCTTGAAGTTCAACA 60.017 38.462 14.35 2.26 32.21 3.33
5 6 6.017357 ACGAAAGTAATCCCTTGAAGTTCAAC 60.017 38.462 14.35 3.98 46.88 3.18
38 39 7.125792 TCCTATCCTTTCATCCTTAAGTGAC 57.874 40.000 0.97 0.00 0.00 3.67
41 42 9.453830 ACTATTCCTATCCTTTCATCCTTAAGT 57.546 33.333 0.97 0.00 0.00 2.24
48 49 9.743057 CGATATGACTATTCCTATCCTTTCATC 57.257 37.037 0.00 0.00 29.71 2.92
49 50 8.700051 CCGATATGACTATTCCTATCCTTTCAT 58.300 37.037 0.00 0.00 29.71 2.57
50 51 7.674348 ACCGATATGACTATTCCTATCCTTTCA 59.326 37.037 0.00 0.00 29.71 2.69
51 52 8.068892 ACCGATATGACTATTCCTATCCTTTC 57.931 38.462 0.00 0.00 29.71 2.62
52 53 7.148052 CGACCGATATGACTATTCCTATCCTTT 60.148 40.741 0.00 0.00 29.71 3.11
53 54 6.319152 CGACCGATATGACTATTCCTATCCTT 59.681 42.308 0.00 0.00 29.71 3.36
54 55 5.823570 CGACCGATATGACTATTCCTATCCT 59.176 44.000 0.00 0.00 29.71 3.24
55 56 5.008811 CCGACCGATATGACTATTCCTATCC 59.991 48.000 0.00 0.00 29.71 2.59
73 74 1.153628 CTAACAGAAGCCCCGACCG 60.154 63.158 0.00 0.00 0.00 4.79
74 75 0.831307 ATCTAACAGAAGCCCCGACC 59.169 55.000 0.00 0.00 0.00 4.79
87 88 2.358898 TGGCGAACGTACCCTATCTAAC 59.641 50.000 0.00 0.00 0.00 2.34
90 91 1.700955 ATGGCGAACGTACCCTATCT 58.299 50.000 0.00 0.00 0.00 1.98
96 97 1.395954 GGAAGAAATGGCGAACGTACC 59.604 52.381 0.00 0.00 0.00 3.34
100 101 2.989422 AAAGGAAGAAATGGCGAACG 57.011 45.000 0.00 0.00 0.00 3.95
159 160 5.221661 ACTCCTACTTTTGGTTCGAGTGATT 60.222 40.000 0.00 0.00 35.31 2.57
260 262 8.206325 TCAGATCTTTCAGTGAAATTAGCATC 57.794 34.615 18.35 13.53 30.85 3.91
273 275 7.536895 AATTCGAACAGATCAGATCTTTCAG 57.463 36.000 22.19 17.58 37.58 3.02
277 279 8.558973 AAGAAAATTCGAACAGATCAGATCTT 57.441 30.769 10.51 0.00 37.58 2.40
279 281 8.446273 TGAAAGAAAATTCGAACAGATCAGATC 58.554 33.333 0.00 1.64 31.80 2.75
333 335 4.623932 AAGTGACTTCTCCATAGCAACA 57.376 40.909 0.00 0.00 0.00 3.33
337 339 5.599999 TTCCTAAGTGACTTCTCCATAGC 57.400 43.478 0.00 0.00 0.00 2.97
344 346 4.150359 TCCGAGTTTCCTAAGTGACTTCT 58.850 43.478 0.00 0.00 0.00 2.85
353 355 2.500098 CCACCTCATCCGAGTTTCCTAA 59.500 50.000 0.00 0.00 37.59 2.69
354 356 2.108168 CCACCTCATCCGAGTTTCCTA 58.892 52.381 0.00 0.00 37.59 2.94
357 359 2.762535 TTCCACCTCATCCGAGTTTC 57.237 50.000 0.00 0.00 37.59 2.78
393 395 5.445939 GCAATTGTCGTATGACCTGTAAGTG 60.446 44.000 12.54 10.04 44.86 3.16
394 396 4.630069 GCAATTGTCGTATGACCTGTAAGT 59.370 41.667 12.54 0.00 44.86 2.24
404 406 4.788100 CGGAAAAGAAGCAATTGTCGTATG 59.212 41.667 7.40 0.00 0.00 2.39
405 407 4.671766 GCGGAAAAGAAGCAATTGTCGTAT 60.672 41.667 7.40 0.00 0.00 3.06
408 410 1.978782 GCGGAAAAGAAGCAATTGTCG 59.021 47.619 7.40 0.00 0.00 4.35
470 472 8.348285 ACTTACAATAAGCCTAATCAAAGCAA 57.652 30.769 0.00 0.00 0.00 3.91
505 507 2.194859 TGGTAGACTAGACTCCGGAGT 58.805 52.381 36.89 36.89 45.84 3.85
561 563 6.238953 GGTCGTAGGAGTCAATTATCTAAGCA 60.239 42.308 0.00 0.00 0.00 3.91
566 568 4.341520 GTGGGTCGTAGGAGTCAATTATCT 59.658 45.833 0.00 0.00 0.00 1.98
573 575 0.178984 TGTGTGGGTCGTAGGAGTCA 60.179 55.000 0.00 0.00 0.00 3.41
579 581 1.890894 CCCTCTGTGTGGGTCGTAG 59.109 63.158 0.00 0.00 39.82 3.51
667 669 0.598065 AGTGTGGGCGAAATTGCTTC 59.402 50.000 0.00 0.00 34.52 3.86
727 731 6.138761 CAGAAAGTTAGACATGCTTCACAAC 58.861 40.000 0.00 0.00 0.00 3.32
742 746 7.639113 AACTTGTCATCCAAACAGAAAGTTA 57.361 32.000 0.00 0.00 40.26 2.24
817 825 3.255888 ACTGTCACACATGATGTAGACGT 59.744 43.478 18.96 16.82 40.64 4.34
818 826 3.838120 ACTGTCACACATGATGTAGACG 58.162 45.455 18.96 16.39 40.64 4.18
819 827 6.197282 CGATAACTGTCACACATGATGTAGAC 59.803 42.308 18.03 18.03 40.64 2.59
820 828 6.265577 CGATAACTGTCACACATGATGTAGA 58.734 40.000 0.00 0.00 40.64 2.59
823 842 4.183865 CCGATAACTGTCACACATGATGT 58.816 43.478 0.00 0.00 44.81 3.06
829 853 3.570975 ACTACACCGATAACTGTCACACA 59.429 43.478 0.00 0.00 0.00 3.72
860 884 7.607991 TGGGATGAGAGAAGTCTGTTTTAAATC 59.392 37.037 0.00 0.00 30.97 2.17
877 901 2.989639 CCTTGGCGTGGGATGAGA 59.010 61.111 0.00 0.00 0.00 3.27
1202 1633 1.139947 GTAGGCAGTGAGTCCGAGC 59.860 63.158 0.00 0.00 0.00 5.03
1334 1765 3.854669 CGCCTCCGGAAGCTGGAT 61.855 66.667 22.30 0.00 38.36 3.41
1449 1880 1.473434 GGGACAGAATAACAGGCGAGG 60.473 57.143 0.00 0.00 0.00 4.63
1501 1932 2.760385 GTCTACCCAGCTCGCCCT 60.760 66.667 0.00 0.00 0.00 5.19
1502 1933 4.208686 CGTCTACCCAGCTCGCCC 62.209 72.222 0.00 0.00 0.00 6.13
1875 2306 1.004440 GAAAGACCGCACAGCCTCT 60.004 57.895 0.00 0.00 0.00 3.69
1881 2312 0.468226 ACTCAAGGAAAGACCGCACA 59.532 50.000 0.00 0.00 44.74 4.57
1902 2333 4.994471 TGCAGCCTCCACAGCACG 62.994 66.667 0.00 0.00 31.05 5.34
1970 2401 4.202264 ACCTTTCGCTCATATACCTCAAGG 60.202 45.833 0.00 0.00 42.17 3.61
2083 2514 9.747293 GTTTCAGTATATTCTCTACCCAAGTAC 57.253 37.037 0.00 0.00 0.00 2.73
2084 2515 9.710818 AGTTTCAGTATATTCTCTACCCAAGTA 57.289 33.333 0.00 0.00 0.00 2.24
2085 2516 8.478877 CAGTTTCAGTATATTCTCTACCCAAGT 58.521 37.037 0.00 0.00 0.00 3.16
2128 2562 5.453198 CCAAACTTATTGTTTCTGTTGCCCT 60.453 40.000 0.00 0.00 46.11 5.19
2186 2620 9.695155 AAATTACTATAAACTGTATGCAGGGTT 57.305 29.630 15.65 10.81 46.62 4.11
2207 2641 5.680619 ACTCACCGATATTGCCAGAAATTA 58.319 37.500 0.00 0.00 0.00 1.40
2221 2655 9.578439 GTTACAGTTTATAGTAAACTCACCGAT 57.422 33.333 11.12 0.00 38.32 4.18
2223 2657 8.976986 AGTTACAGTTTATAGTAAACTCACCG 57.023 34.615 11.12 4.75 38.32 4.94
2252 2686 9.667107 CCAATCTAGTCTGATTAAACTTACCAA 57.333 33.333 0.00 0.00 35.18 3.67
2253 2687 8.822805 ACCAATCTAGTCTGATTAAACTTACCA 58.177 33.333 0.00 0.00 35.18 3.25
2263 2697 9.668497 GGTTAAACTTACCAATCTAGTCTGATT 57.332 33.333 0.00 0.00 37.16 2.57
2264 2698 9.047947 AGGTTAAACTTACCAATCTAGTCTGAT 57.952 33.333 0.00 0.00 38.16 2.90
2267 2701 8.657712 ACAAGGTTAAACTTACCAATCTAGTCT 58.342 33.333 5.20 0.00 38.16 3.24
2268 2702 8.843885 ACAAGGTTAAACTTACCAATCTAGTC 57.156 34.615 5.20 0.00 38.16 2.59
2272 2706 9.636789 AACTTACAAGGTTAAACTTACCAATCT 57.363 29.630 5.20 0.00 38.16 2.40
2274 2708 9.192642 ACAACTTACAAGGTTAAACTTACCAAT 57.807 29.630 5.20 0.00 38.16 3.16
2275 2709 8.578448 ACAACTTACAAGGTTAAACTTACCAA 57.422 30.769 5.20 0.00 38.16 3.67
2276 2710 8.578448 AACAACTTACAAGGTTAAACTTACCA 57.422 30.769 5.20 0.00 38.16 3.25
2277 2711 8.676401 TGAACAACTTACAAGGTTAAACTTACC 58.324 33.333 5.20 0.00 35.85 2.85
2280 2714 8.410912 GGATGAACAACTTACAAGGTTAAACTT 58.589 33.333 0.00 0.00 0.00 2.66
2281 2715 7.778382 AGGATGAACAACTTACAAGGTTAAACT 59.222 33.333 0.00 0.00 0.00 2.66
2282 2716 7.937649 AGGATGAACAACTTACAAGGTTAAAC 58.062 34.615 0.00 0.00 0.00 2.01
2283 2717 8.528044 AAGGATGAACAACTTACAAGGTTAAA 57.472 30.769 0.00 0.00 0.00 1.52
2284 2718 9.802039 ATAAGGATGAACAACTTACAAGGTTAA 57.198 29.630 0.00 0.00 30.33 2.01
2286 2720 9.802039 TTATAAGGATGAACAACTTACAAGGTT 57.198 29.630 0.00 0.00 30.33 3.50
2287 2721 9.449719 CTTATAAGGATGAACAACTTACAAGGT 57.550 33.333 4.42 0.00 31.14 3.50
2288 2722 9.449719 ACTTATAAGGATGAACAACTTACAAGG 57.550 33.333 16.73 8.43 36.20 3.61
2296 2883 8.483307 TCGGTAAACTTATAAGGATGAACAAC 57.517 34.615 16.73 3.69 0.00 3.32
2311 2898 9.760077 ATTGATCGAGTAAATATCGGTAAACTT 57.240 29.630 0.00 0.00 40.54 2.66
2312 2899 9.760077 AATTGATCGAGTAAATATCGGTAAACT 57.240 29.630 0.00 0.00 40.54 2.66
2317 2904 8.335356 CACAAAATTGATCGAGTAAATATCGGT 58.665 33.333 0.00 0.00 40.54 4.69
2319 2906 9.147364 CACACAAAATTGATCGAGTAAATATCG 57.853 33.333 0.00 0.00 41.50 2.92
2322 2909 7.748683 GCACACACAAAATTGATCGAGTAAATA 59.251 33.333 0.00 0.00 0.00 1.40
2323 2910 6.582295 GCACACACAAAATTGATCGAGTAAAT 59.418 34.615 0.00 0.00 0.00 1.40
2324 2911 5.912396 GCACACACAAAATTGATCGAGTAAA 59.088 36.000 0.00 0.00 0.00 2.01
2327 2914 3.304659 GGCACACACAAAATTGATCGAGT 60.305 43.478 0.00 0.00 0.00 4.18
2330 2917 3.010624 TGGCACACACAAAATTGATCG 57.989 42.857 0.00 0.00 0.00 3.69
2331 2918 4.118410 TGTTGGCACACACAAAATTGATC 58.882 39.130 0.00 0.00 39.29 2.92
2332 2919 4.121317 CTGTTGGCACACACAAAATTGAT 58.879 39.130 0.00 0.00 39.29 2.57
2333 2920 3.194329 TCTGTTGGCACACACAAAATTGA 59.806 39.130 0.00 0.00 39.29 2.57
2334 2921 3.519579 TCTGTTGGCACACACAAAATTG 58.480 40.909 0.00 0.00 39.29 2.32
2335 2922 3.883830 TCTGTTGGCACACACAAAATT 57.116 38.095 0.00 0.00 39.29 1.82
2336 2923 4.121317 CAATCTGTTGGCACACACAAAAT 58.879 39.130 0.00 0.00 39.29 1.82
2373 2960 8.911247 AAATGAAGAAACGCAAAATCTATACC 57.089 30.769 0.00 0.00 0.00 2.73
2426 3013 7.424803 CATTAACACCTTTGTCTGATTGTTCA 58.575 34.615 0.00 0.00 33.55 3.18
2514 3101 2.565834 GGGTCGGCTAGCATCCTTATAA 59.434 50.000 18.24 0.00 0.00 0.98
2550 3137 3.484742 GATCGATGCGCACGGGAGA 62.485 63.158 24.69 15.59 0.00 3.71
2761 3350 2.175530 GTCAGACGACTCATACACGG 57.824 55.000 0.00 0.00 39.22 4.94
2812 3408 4.796231 CGTCCTCTGGTTCCCGCG 62.796 72.222 0.00 0.00 0.00 6.46
2921 3554 1.005450 GGGAAGGGGATAGTGTTTGCA 59.995 52.381 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.