Multiple sequence alignment - TraesCS3B01G307500

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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 TraesCS3B01G307500 chr3B 100.000 3170 0 0 1 3170 493652255 493655424 0.000000e+00 5854
1 TraesCS3B01G307500 chr3D 94.294 2506 96 15 1 2503 378575478 378577939 0.000000e+00 3792
2 TraesCS3B01G307500 chr3D 93.023 430 25 4 2744 3170 378578204 378578631 9.660000e-175 623
3 TraesCS3B01G307500 chr3D 92.208 77 4 2 2656 2731 378578052 378578127 1.200000e-19 108
4 TraesCS3B01G307500 chr3A 91.573 2302 129 31 235 2509 502508325 502510588 0.000000e+00 3116
5 TraesCS3B01G307500 chr3A 88.339 566 30 13 2614 3170 502510624 502511162 0.000000e+00 647
6 TraesCS3B01G307500 chr3A 95.041 242 11 1 1 242 502508272 502508512 2.310000e-101 379


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 TraesCS3B01G307500 chr3B 493652255 493655424 3169 False 5854.000000 5854 100.000 1 3170 1 chr3B.!!$F1 3169
1 TraesCS3B01G307500 chr3D 378575478 378578631 3153 False 1507.666667 3792 93.175 1 3170 3 chr3D.!!$F1 3169
2 TraesCS3B01G307500 chr3A 502508272 502511162 2890 False 1380.666667 3116 91.651 1 3170 3 chr3A.!!$F1 3169

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
957 960 1.367471 GGCCTTTTGTGGGTTCTGC 59.633 57.895 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2537 2568 0.111878 CGTGTTGTTCGCGTGTAGTG 60.112 55.0 5.77 0.0 43.87 2.74 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
63 64 2.938956 AACAGCTAACAGGAAGCACT 57.061 45.000 0.00 0.00 42.62 4.40
169 170 5.667539 TGAATAGTGGGAAGAAGTCTCAG 57.332 43.478 0.00 0.00 37.43 3.35
191 192 1.450312 CCATCGAGGCACAGTTCCC 60.450 63.158 0.00 0.00 0.00 3.97
210 211 1.669115 CGATAGGCCAAGCATCCGG 60.669 63.158 5.01 0.00 0.00 5.14
279 281 7.345914 CCCCCTAATTTTCATGTAATAAACCCA 59.654 37.037 0.00 0.00 0.00 4.51
296 298 3.436243 ACCCACTTAGAGAGGAAGTCTG 58.564 50.000 0.00 0.00 34.90 3.51
345 347 9.230932 GAAGCTCATGATACTTTCTTAAATTGC 57.769 33.333 11.29 0.00 0.00 3.56
361 363 3.923017 ATTGCGGAAAGAAACCTCAAG 57.077 42.857 0.00 0.00 35.95 3.02
371 373 5.774498 AAGAAACCTCAAGTTCCATTGAC 57.226 39.130 0.00 0.00 37.88 3.18
391 393 3.472652 ACGCAGTTAATCAAACACCTCA 58.527 40.909 0.00 0.00 37.78 3.86
422 424 3.561503 CGACTATCCGCATTATCGTCAA 58.438 45.455 0.00 0.00 0.00 3.18
437 439 5.860941 ATCGTCAACCATCTAATCTCAGT 57.139 39.130 0.00 0.00 0.00 3.41
513 515 6.996509 AGCTCAATGGAAAATACAAATGTGT 58.003 32.000 0.00 0.00 42.09 3.72
703 705 2.685017 AGAGCATCAGGCCGACCA 60.685 61.111 0.00 0.00 46.50 4.02
859 861 3.918253 TAGGCCGCCTGTGCTTTGG 62.918 63.158 22.95 0.00 34.61 3.28
864 867 1.965930 CGCCTGTGCTTTGGTGCTA 60.966 57.895 0.00 0.00 34.43 3.49
891 894 3.059472 GATGTGAGCGTGTCGTGCG 62.059 63.158 0.00 0.00 37.44 5.34
957 960 1.367471 GGCCTTTTGTGGGTTCTGC 59.633 57.895 0.00 0.00 0.00 4.26
1209 1215 4.933064 GCCGTCCTCGCATCCTCG 62.933 72.222 0.00 0.00 35.54 4.63
1248 1254 4.214327 CGCCTCCTCTTCCCGCTC 62.214 72.222 0.00 0.00 0.00 5.03
1575 1581 1.745489 GGGCAACGACTCCATGGTC 60.745 63.158 12.58 1.45 37.60 4.02
2065 2071 0.182061 GGAGATGGGCATGCTCAGAA 59.818 55.000 26.87 1.68 0.00 3.02
2132 2138 2.501128 CGACGATGGCCTGGATGT 59.499 61.111 3.32 0.00 0.00 3.06
2139 2148 0.327924 ATGGCCTGGATGTTGACGAA 59.672 50.000 3.32 0.00 0.00 3.85
2148 2157 0.512952 ATGTTGACGAAAGCACGAGC 59.487 50.000 0.00 0.00 42.56 5.03
2178 2187 1.992170 GGCGACGATGACAAAGTAGT 58.008 50.000 0.00 0.00 0.00 2.73
2200 2209 3.988976 AGCAGAGAATTCAGCAGGTTA 57.011 42.857 8.44 0.00 38.22 2.85
2201 2210 4.500499 AGCAGAGAATTCAGCAGGTTAT 57.500 40.909 8.44 0.00 38.22 1.89
2202 2211 5.620738 AGCAGAGAATTCAGCAGGTTATA 57.379 39.130 8.44 0.00 38.22 0.98
2204 2213 6.229733 AGCAGAGAATTCAGCAGGTTATATC 58.770 40.000 8.44 0.00 38.22 1.63
2205 2214 6.043012 AGCAGAGAATTCAGCAGGTTATATCT 59.957 38.462 8.44 0.00 38.22 1.98
2206 2215 6.147492 GCAGAGAATTCAGCAGGTTATATCTG 59.853 42.308 8.44 8.16 36.02 2.90
2216 2225 5.139435 CAGGTTATATCTGCTTCGGATGA 57.861 43.478 0.00 0.00 31.33 2.92
2219 2233 4.021016 GGTTATATCTGCTTCGGATGAGGT 60.021 45.833 0.00 0.00 31.33 3.85
2224 2241 4.280436 TCTGCTTCGGATGAGGTTTTTA 57.720 40.909 0.00 0.00 0.00 1.52
2335 2352 9.646427 AATGAACAAGCACACTAAAACTAAAAA 57.354 25.926 0.00 0.00 0.00 1.94
2403 2431 0.610687 GTGGAGGGAGGAACAGAGTG 59.389 60.000 0.00 0.00 0.00 3.51
2463 2491 5.291371 TGAAAACGGATCGCGTAATTGAATA 59.709 36.000 5.77 0.00 0.00 1.75
2465 2493 5.917541 AACGGATCGCGTAATTGAATATT 57.082 34.783 5.77 0.00 0.00 1.28
2466 2494 7.410800 AAACGGATCGCGTAATTGAATATTA 57.589 32.000 5.77 0.00 0.00 0.98
2467 2495 6.627690 ACGGATCGCGTAATTGAATATTAG 57.372 37.500 5.77 0.00 0.00 1.73
2509 2540 7.759489 AGTGTCTTAAATTATCACCTGCAAA 57.241 32.000 0.00 0.00 0.00 3.68
2510 2541 8.177119 AGTGTCTTAAATTATCACCTGCAAAA 57.823 30.769 0.00 0.00 0.00 2.44
2511 2542 8.637986 AGTGTCTTAAATTATCACCTGCAAAAA 58.362 29.630 0.00 0.00 0.00 1.94
2512 2543 8.915654 GTGTCTTAAATTATCACCTGCAAAAAG 58.084 33.333 0.00 0.00 0.00 2.27
2513 2544 8.087750 TGTCTTAAATTATCACCTGCAAAAAGG 58.912 33.333 0.00 0.00 43.57 3.11
2514 2545 8.303876 GTCTTAAATTATCACCTGCAAAAAGGA 58.696 33.333 0.00 0.00 40.02 3.36
2515 2546 8.865090 TCTTAAATTATCACCTGCAAAAAGGAA 58.135 29.630 0.00 0.00 40.02 3.36
2516 2547 9.657419 CTTAAATTATCACCTGCAAAAAGGAAT 57.343 29.630 0.00 0.00 40.02 3.01
2519 2550 7.716799 ATTATCACCTGCAAAAAGGAATACA 57.283 32.000 0.00 0.00 40.02 2.29
2520 2551 5.649782 ATCACCTGCAAAAAGGAATACAG 57.350 39.130 0.00 0.00 40.02 2.74
2521 2552 4.469657 TCACCTGCAAAAAGGAATACAGT 58.530 39.130 0.00 0.00 40.02 3.55
2522 2553 5.626142 TCACCTGCAAAAAGGAATACAGTA 58.374 37.500 0.00 0.00 40.02 2.74
2523 2554 5.472137 TCACCTGCAAAAAGGAATACAGTAC 59.528 40.000 0.00 0.00 40.02 2.73
2524 2555 5.473504 CACCTGCAAAAAGGAATACAGTACT 59.526 40.000 0.00 0.00 40.02 2.73
2525 2556 6.653320 CACCTGCAAAAAGGAATACAGTACTA 59.347 38.462 0.00 0.00 40.02 1.82
2526 2557 7.336931 CACCTGCAAAAAGGAATACAGTACTAT 59.663 37.037 0.00 0.00 40.02 2.12
2527 2558 7.553044 ACCTGCAAAAAGGAATACAGTACTATC 59.447 37.037 0.00 0.00 40.02 2.08
2528 2559 7.770897 CCTGCAAAAAGGAATACAGTACTATCT 59.229 37.037 0.00 0.00 40.02 1.98
2529 2560 9.167311 CTGCAAAAAGGAATACAGTACTATCTT 57.833 33.333 0.00 0.00 0.00 2.40
2530 2561 8.946085 TGCAAAAAGGAATACAGTACTATCTTG 58.054 33.333 0.00 0.00 0.00 3.02
2531 2562 9.162764 GCAAAAAGGAATACAGTACTATCTTGA 57.837 33.333 0.00 0.00 0.00 3.02
2567 2598 3.244579 GCGAACAACACGTCTTCTAAACT 59.755 43.478 0.00 0.00 0.00 2.66
2580 2611 4.844085 TCTTCTAAACTCAGGGTGGAATGA 59.156 41.667 0.00 0.00 0.00 2.57
2581 2612 5.309543 TCTTCTAAACTCAGGGTGGAATGAA 59.690 40.000 0.00 0.00 0.00 2.57
2582 2613 5.576563 TCTAAACTCAGGGTGGAATGAAA 57.423 39.130 0.00 0.00 0.00 2.69
2583 2614 5.560724 TCTAAACTCAGGGTGGAATGAAAG 58.439 41.667 0.00 0.00 0.00 2.62
2584 2615 4.453480 AAACTCAGGGTGGAATGAAAGA 57.547 40.909 0.00 0.00 0.00 2.52
2585 2616 3.710209 ACTCAGGGTGGAATGAAAGAG 57.290 47.619 0.00 0.00 0.00 2.85
2586 2617 3.251484 ACTCAGGGTGGAATGAAAGAGA 58.749 45.455 0.00 0.00 0.00 3.10
2587 2618 3.008485 ACTCAGGGTGGAATGAAAGAGAC 59.992 47.826 0.00 0.00 0.00 3.36
2588 2619 2.978978 TCAGGGTGGAATGAAAGAGACA 59.021 45.455 0.00 0.00 0.00 3.41
2589 2620 3.077359 CAGGGTGGAATGAAAGAGACAC 58.923 50.000 0.00 0.00 0.00 3.67
2590 2621 2.040412 AGGGTGGAATGAAAGAGACACC 59.960 50.000 0.00 0.00 45.70 4.16
2591 2622 2.437413 GGTGGAATGAAAGAGACACCC 58.563 52.381 0.00 0.00 41.81 4.61
2592 2623 2.076863 GTGGAATGAAAGAGACACCCG 58.923 52.381 0.00 0.00 0.00 5.28
2593 2624 1.087501 GGAATGAAAGAGACACCCGC 58.912 55.000 0.00 0.00 0.00 6.13
2594 2625 1.610624 GGAATGAAAGAGACACCCGCA 60.611 52.381 0.00 0.00 0.00 5.69
2595 2626 2.151202 GAATGAAAGAGACACCCGCAA 58.849 47.619 0.00 0.00 0.00 4.85
2596 2627 2.270352 ATGAAAGAGACACCCGCAAA 57.730 45.000 0.00 0.00 0.00 3.68
2597 2628 2.045561 TGAAAGAGACACCCGCAAAA 57.954 45.000 0.00 0.00 0.00 2.44
2598 2629 1.946768 TGAAAGAGACACCCGCAAAAG 59.053 47.619 0.00 0.00 0.00 2.27
2599 2630 2.218603 GAAAGAGACACCCGCAAAAGA 58.781 47.619 0.00 0.00 0.00 2.52
2600 2631 2.341846 AAGAGACACCCGCAAAAGAA 57.658 45.000 0.00 0.00 0.00 2.52
2601 2632 2.341846 AGAGACACCCGCAAAAGAAA 57.658 45.000 0.00 0.00 0.00 2.52
2602 2633 2.650322 AGAGACACCCGCAAAAGAAAA 58.350 42.857 0.00 0.00 0.00 2.29
2603 2634 2.618709 AGAGACACCCGCAAAAGAAAAG 59.381 45.455 0.00 0.00 0.00 2.27
2604 2635 2.616842 GAGACACCCGCAAAAGAAAAGA 59.383 45.455 0.00 0.00 0.00 2.52
2605 2636 3.020984 AGACACCCGCAAAAGAAAAGAA 58.979 40.909 0.00 0.00 0.00 2.52
2606 2637 3.445805 AGACACCCGCAAAAGAAAAGAAA 59.554 39.130 0.00 0.00 0.00 2.52
2607 2638 4.081917 AGACACCCGCAAAAGAAAAGAAAA 60.082 37.500 0.00 0.00 0.00 2.29
2608 2639 4.570930 ACACCCGCAAAAGAAAAGAAAAA 58.429 34.783 0.00 0.00 0.00 1.94
2669 2752 5.175859 TGGCTAAATTCCTTGTTCTCGTAG 58.824 41.667 0.00 0.00 0.00 3.51
2731 2815 0.608130 AGAGCTATGCCGACACAACA 59.392 50.000 0.00 0.00 0.00 3.33
2733 2817 0.673644 AGCTATGCCGACACAACACC 60.674 55.000 0.00 0.00 0.00 4.16
2734 2818 0.673644 GCTATGCCGACACAACACCT 60.674 55.000 0.00 0.00 0.00 4.00
2735 2819 1.078709 CTATGCCGACACAACACCTG 58.921 55.000 0.00 0.00 0.00 4.00
2736 2820 0.953471 TATGCCGACACAACACCTGC 60.953 55.000 0.00 0.00 0.00 4.85
2737 2821 4.012895 GCCGACACAACACCTGCG 62.013 66.667 0.00 0.00 0.00 5.18
2738 2822 4.012895 CCGACACAACACCTGCGC 62.013 66.667 0.00 0.00 0.00 6.09
2739 2823 3.268603 CGACACAACACCTGCGCA 61.269 61.111 10.98 10.98 0.00 6.09
2740 2824 2.327940 GACACAACACCTGCGCAC 59.672 61.111 5.66 0.00 0.00 5.34
2741 2825 3.506312 GACACAACACCTGCGCACG 62.506 63.158 5.66 5.13 0.00 5.34
2742 2826 4.312231 CACAACACCTGCGCACGG 62.312 66.667 20.07 20.07 0.00 4.94
2805 2954 2.991250 ACAAGACTCGCAGGCAAATAT 58.009 42.857 0.00 0.00 0.00 1.28
2806 2955 4.137116 ACAAGACTCGCAGGCAAATATA 57.863 40.909 0.00 0.00 0.00 0.86
2812 2961 4.486090 ACTCGCAGGCAAATATAGTATCG 58.514 43.478 0.00 0.00 0.00 2.92
2840 2989 5.133221 CCTGCATATAGCTTGTACCCTTTT 58.867 41.667 0.00 0.00 45.94 2.27
2846 2995 9.720769 GCATATAGCTTGTACCCTTTTATCTTA 57.279 33.333 0.00 0.00 41.15 2.10
2939 3088 3.615849 AGACTTTTTCGCTCTTGCTTG 57.384 42.857 0.00 0.00 36.97 4.01
2950 3099 3.189287 CGCTCTTGCTTGGAATAAGTTGT 59.811 43.478 0.00 0.00 36.97 3.32
2964 3113 9.179909 TGGAATAAGTTGTTCTTACAAAGTTGA 57.820 29.630 11.56 0.00 45.33 3.18
3005 3154 4.446745 GGGGTAAGTCTACAACCAAAACCT 60.447 45.833 6.89 0.00 34.83 3.50
3018 3169 2.192624 CAAAACCTTGTTTGTCAGGCG 58.807 47.619 0.00 0.00 34.43 5.52
3102 3253 6.183360 ACCGTCTGTAATTTGCTTATTCTTCG 60.183 38.462 0.00 0.00 0.00 3.79
3113 3264 0.679505 TATTCTTCGGGCTGATCGGG 59.320 55.000 3.14 0.00 0.00 5.14
3159 3310 2.356125 GGTGGACATAGGCACAATCACT 60.356 50.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 6.552008 ACATGAAACTTAGGGGAAATGAGAA 58.448 36.000 0.00 0.00 0.00 2.87
169 170 1.936547 GAACTGTGCCTCGATGGAATC 59.063 52.381 5.24 0.00 40.89 2.52
191 192 1.669115 CGGATGCTTGGCCTATCGG 60.669 63.158 3.32 3.90 0.00 4.18
204 205 2.146342 GGTTGATGATAGTGCCGGATG 58.854 52.381 5.05 0.00 0.00 3.51
210 211 7.157347 TGAGATTAGATGGTTGATGATAGTGC 58.843 38.462 0.00 0.00 0.00 4.40
253 254 7.345914 TGGGTTTATTACATGAAAATTAGGGGG 59.654 37.037 0.00 0.00 0.00 5.40
272 274 5.480772 CAGACTTCCTCTCTAAGTGGGTTTA 59.519 44.000 0.00 0.00 37.31 2.01
274 276 3.835395 CAGACTTCCTCTCTAAGTGGGTT 59.165 47.826 0.00 0.00 37.31 4.11
279 281 3.761752 GCTCACAGACTTCCTCTCTAAGT 59.238 47.826 0.00 0.00 39.84 2.24
296 298 2.143925 GTTGTGTTCCAGTAGGCTCAC 58.856 52.381 0.00 0.00 38.10 3.51
345 347 3.211045 TGGAACTTGAGGTTTCTTTCCG 58.789 45.455 0.00 0.00 38.41 4.30
361 363 4.678509 TGATTAACTGCGTCAATGGAAC 57.321 40.909 0.00 0.00 0.00 3.62
371 373 4.437390 GGATGAGGTGTTTGATTAACTGCG 60.437 45.833 0.00 0.00 37.64 5.18
391 393 0.389391 CGGATAGTCGGCTTGTGGAT 59.611 55.000 0.00 0.00 0.00 3.41
422 424 5.854010 TTCGCTTACTGAGATTAGATGGT 57.146 39.130 0.00 0.00 0.00 3.55
437 439 7.644490 ACAGTTATGTTTGAATGTTTCGCTTA 58.356 30.769 0.00 0.00 35.63 3.09
584 586 2.032620 GAGATTCGTCTGCTAAGGGGA 58.967 52.381 0.00 0.00 0.00 4.81
625 627 3.626924 GTGTGACCTGGCCCTCGT 61.627 66.667 0.00 0.00 0.00 4.18
703 705 1.063942 GTAAGCCCTAACCCATTGCCT 60.064 52.381 0.00 0.00 0.00 4.75
768 770 0.905337 CGACTCCTCCACCTCCCTTT 60.905 60.000 0.00 0.00 0.00 3.11
859 861 3.002042 GCTCACATCACATCACATAGCAC 59.998 47.826 0.00 0.00 0.00 4.40
860 862 3.200483 GCTCACATCACATCACATAGCA 58.800 45.455 0.00 0.00 0.00 3.49
864 867 2.004733 CACGCTCACATCACATCACAT 58.995 47.619 0.00 0.00 0.00 3.21
957 960 0.249699 TGCAACACCAGTACAGTCCG 60.250 55.000 0.00 0.00 0.00 4.79
1061 1067 4.658786 AGGTGGCGAAGGGGAGGT 62.659 66.667 0.00 0.00 0.00 3.85
1156 1162 3.474570 GAGGGAGGCGATGGCAGT 61.475 66.667 1.01 0.00 42.47 4.40
1248 1254 3.077556 CCGAGGGAGTGGGTGAGG 61.078 72.222 0.00 0.00 0.00 3.86
1324 1330 3.391382 GTGGTAGAGCTGGGCGGT 61.391 66.667 0.00 0.00 0.00 5.68
1575 1581 3.531538 GGTGTCCATGTACATGTAGTGG 58.468 50.000 29.25 22.69 37.11 4.00
1803 1809 4.083862 AGCTCCCGGGCGTTCTTC 62.084 66.667 18.49 0.00 37.29 2.87
2004 2010 3.471806 GCGTCCTCCCTCTTCCCC 61.472 72.222 0.00 0.00 0.00 4.81
2094 2100 0.170561 CGTCCTCGTCGTCTTGGATT 59.829 55.000 0.00 0.00 0.00 3.01
2132 2138 2.307309 CCGCTCGTGCTTTCGTCAA 61.307 57.895 7.97 0.00 36.97 3.18
2139 2148 3.240134 ATCACCACCGCTCGTGCTT 62.240 57.895 7.97 0.00 41.53 3.91
2167 2176 7.441836 TGAATTCTCTGCTAACTACTTTGTCA 58.558 34.615 7.05 0.00 0.00 3.58
2178 2187 3.988976 ACCTGCTGAATTCTCTGCTAA 57.011 42.857 7.05 0.00 44.53 3.09
2200 2209 4.696479 AAACCTCATCCGAAGCAGATAT 57.304 40.909 0.00 0.00 0.00 1.63
2201 2210 4.487714 AAAACCTCATCCGAAGCAGATA 57.512 40.909 0.00 0.00 0.00 1.98
2202 2211 3.356529 AAAACCTCATCCGAAGCAGAT 57.643 42.857 0.00 0.00 0.00 2.90
2204 2213 5.567138 AATAAAAACCTCATCCGAAGCAG 57.433 39.130 0.00 0.00 0.00 4.24
2205 2214 5.975693 AAATAAAAACCTCATCCGAAGCA 57.024 34.783 0.00 0.00 0.00 3.91
2283 2300 7.811236 TCATTTCAATCCGACCGTAATCTATAC 59.189 37.037 0.00 0.00 0.00 1.47
2290 2307 5.179533 TCATTCATTTCAATCCGACCGTAA 58.820 37.500 0.00 0.00 0.00 3.18
2294 2311 5.309323 TGTTCATTCATTTCAATCCGACC 57.691 39.130 0.00 0.00 0.00 4.79
2295 2312 5.287035 GCTTGTTCATTCATTTCAATCCGAC 59.713 40.000 0.00 0.00 0.00 4.79
2297 2314 5.061311 GTGCTTGTTCATTCATTTCAATCCG 59.939 40.000 0.00 0.00 0.00 4.18
2466 2494 9.668497 AAGACACTTTAACTCTTCAAACTTACT 57.332 29.630 0.00 0.00 0.00 2.24
2486 2517 8.810652 TTTTTGCAGGTGATAATTTAAGACAC 57.189 30.769 0.00 0.00 0.00 3.67
2493 2524 8.592809 TGTATTCCTTTTTGCAGGTGATAATTT 58.407 29.630 0.00 0.00 35.15 1.82
2520 2551 8.903723 GCGTGTAGTGATAATTCAAGATAGTAC 58.096 37.037 0.00 0.00 32.48 2.73
2521 2552 7.801783 CGCGTGTAGTGATAATTCAAGATAGTA 59.198 37.037 0.00 0.00 32.48 1.82
2522 2553 6.637254 CGCGTGTAGTGATAATTCAAGATAGT 59.363 38.462 0.00 0.00 32.48 2.12
2523 2554 6.856426 TCGCGTGTAGTGATAATTCAAGATAG 59.144 38.462 5.77 0.00 33.87 2.08
2524 2555 6.731164 TCGCGTGTAGTGATAATTCAAGATA 58.269 36.000 5.77 0.00 33.87 1.98
2525 2556 5.588240 TCGCGTGTAGTGATAATTCAAGAT 58.412 37.500 5.77 0.00 33.87 2.40
2526 2557 4.989044 TCGCGTGTAGTGATAATTCAAGA 58.011 39.130 5.77 0.00 33.87 3.02
2527 2558 5.061684 TGTTCGCGTGTAGTGATAATTCAAG 59.938 40.000 5.77 0.00 39.39 3.02
2528 2559 4.924462 TGTTCGCGTGTAGTGATAATTCAA 59.076 37.500 5.77 0.00 39.39 2.69
2529 2560 4.487019 TGTTCGCGTGTAGTGATAATTCA 58.513 39.130 5.77 0.00 39.39 2.57
2530 2561 5.164031 TGTTGTTCGCGTGTAGTGATAATTC 60.164 40.000 5.77 0.00 39.39 2.17
2531 2562 4.687018 TGTTGTTCGCGTGTAGTGATAATT 59.313 37.500 5.77 0.00 39.39 1.40
2532 2563 4.090930 GTGTTGTTCGCGTGTAGTGATAAT 59.909 41.667 5.77 0.00 39.39 1.28
2533 2564 3.426191 GTGTTGTTCGCGTGTAGTGATAA 59.574 43.478 5.77 0.00 39.39 1.75
2534 2565 2.981805 GTGTTGTTCGCGTGTAGTGATA 59.018 45.455 5.77 0.00 39.39 2.15
2535 2566 1.790623 GTGTTGTTCGCGTGTAGTGAT 59.209 47.619 5.77 0.00 39.39 3.06
2536 2567 1.202203 GTGTTGTTCGCGTGTAGTGA 58.798 50.000 5.77 0.00 37.63 3.41
2537 2568 0.111878 CGTGTTGTTCGCGTGTAGTG 60.112 55.000 5.77 0.00 43.87 2.74
2538 2569 2.209872 CGTGTTGTTCGCGTGTAGT 58.790 52.632 5.77 0.00 43.87 2.73
2567 2598 2.978978 TGTCTCTTTCATTCCACCCTGA 59.021 45.455 0.00 0.00 0.00 3.86
2580 2611 2.341846 TCTTTTGCGGGTGTCTCTTT 57.658 45.000 0.00 0.00 0.00 2.52
2581 2612 2.341846 TTCTTTTGCGGGTGTCTCTT 57.658 45.000 0.00 0.00 0.00 2.85
2582 2613 2.341846 TTTCTTTTGCGGGTGTCTCT 57.658 45.000 0.00 0.00 0.00 3.10
2583 2614 2.616842 TCTTTTCTTTTGCGGGTGTCTC 59.383 45.455 0.00 0.00 0.00 3.36
2584 2615 2.650322 TCTTTTCTTTTGCGGGTGTCT 58.350 42.857 0.00 0.00 0.00 3.41
2585 2616 3.430333 TTCTTTTCTTTTGCGGGTGTC 57.570 42.857 0.00 0.00 0.00 3.67
2586 2617 3.878160 TTTCTTTTCTTTTGCGGGTGT 57.122 38.095 0.00 0.00 0.00 4.16
2608 2639 5.054477 TCGTCGTCTCTTTCATTCCTTTTT 58.946 37.500 0.00 0.00 0.00 1.94
2609 2640 4.628074 TCGTCGTCTCTTTCATTCCTTTT 58.372 39.130 0.00 0.00 0.00 2.27
2610 2641 4.252971 TCGTCGTCTCTTTCATTCCTTT 57.747 40.909 0.00 0.00 0.00 3.11
2611 2642 3.936372 TCGTCGTCTCTTTCATTCCTT 57.064 42.857 0.00 0.00 0.00 3.36
2612 2643 3.936372 TTCGTCGTCTCTTTCATTCCT 57.064 42.857 0.00 0.00 0.00 3.36
2613 2644 6.455246 GGTTTATTCGTCGTCTCTTTCATTCC 60.455 42.308 0.00 0.00 0.00 3.01
2614 2645 6.090358 TGGTTTATTCGTCGTCTCTTTCATTC 59.910 38.462 0.00 0.00 0.00 2.67
2615 2646 5.929992 TGGTTTATTCGTCGTCTCTTTCATT 59.070 36.000 0.00 0.00 0.00 2.57
2616 2647 5.475719 TGGTTTATTCGTCGTCTCTTTCAT 58.524 37.500 0.00 0.00 0.00 2.57
2617 2648 4.873817 TGGTTTATTCGTCGTCTCTTTCA 58.126 39.130 0.00 0.00 0.00 2.69
2618 2649 5.163982 CCTTGGTTTATTCGTCGTCTCTTTC 60.164 44.000 0.00 0.00 0.00 2.62
2629 2660 3.081804 AGCCAGTTCCTTGGTTTATTCG 58.918 45.455 0.00 0.00 40.49 3.34
2660 2691 2.503920 ACACACACCACTACGAGAAC 57.496 50.000 0.00 0.00 0.00 3.01
2669 2752 3.374058 GGTGCTCATATTACACACACCAC 59.626 47.826 0.00 0.00 44.32 4.16
2710 2793 2.194271 GTTGTGTCGGCATAGCTCTAC 58.806 52.381 0.00 0.00 0.00 2.59
2738 2822 3.129502 CAGCCACAGCCATCCGTG 61.130 66.667 0.00 0.00 41.25 4.94
2805 2954 5.886474 AGCTATATGCAGGTAAGCGATACTA 59.114 40.000 0.00 0.00 45.94 1.82
2806 2955 4.707448 AGCTATATGCAGGTAAGCGATACT 59.293 41.667 0.00 0.00 45.94 2.12
2812 2961 4.691216 GGTACAAGCTATATGCAGGTAAGC 59.309 45.833 0.00 0.00 45.94 3.09
2840 2989 6.869695 TGCACTAAAACCTCGTCATAAGATA 58.130 36.000 0.00 0.00 0.00 1.98
2846 2995 3.689649 GGATTGCACTAAAACCTCGTCAT 59.310 43.478 0.00 0.00 0.00 3.06
3005 3154 1.317613 AGAATGCGCCTGACAAACAA 58.682 45.000 4.18 0.00 0.00 2.83
3102 3253 4.918201 CTTCCGCCCGATCAGCCC 62.918 72.222 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.