Multiple sequence alignment - TraesCS1A01G200500

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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 TraesCS1A01G200500 chr1A 100.000 2876 0 0 1 2876 361175437 361172562 0.000000e+00 5312
1 TraesCS1A01G200500 chr1A 80.345 290 44 9 1079 1363 548789926 548790207 1.040000e-49 207
2 TraesCS1A01G200500 chr1D 91.351 2613 106 52 1 2517 288894139 288891551 0.000000e+00 3463
3 TraesCS1A01G200500 chr1D 88.593 263 21 8 2556 2810 288891553 288891292 7.740000e-81 311
4 TraesCS1A01G200500 chr1B 90.854 2471 90 56 137 2512 390382120 390379691 0.000000e+00 3186
5 TraesCS1A01G200500 chr1B 89.394 330 25 7 2557 2876 390379688 390379359 9.590000e-110 407
6 TraesCS1A01G200500 chr3D 81.000 300 38 14 1079 1376 362069952 362069670 1.340000e-53 220
7 TraesCS1A01G200500 chr3A 80.667 300 39 14 1079 1376 482184058 482183776 6.240000e-52 215
8 TraesCS1A01G200500 chr3A 79.720 286 44 11 1078 1362 30997360 30997632 8.130000e-46 195
9 TraesCS1A01G200500 chr5A 80.797 276 39 9 1088 1362 665079587 665079325 1.350000e-48 204
10 TraesCS1A01G200500 chr5A 81.500 200 32 5 1234 1432 685432556 685432751 2.970000e-35 159
11 TraesCS1A01G200500 chrUn 79.720 286 44 11 1078 1362 270382315 270382043 8.130000e-46 195


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 TraesCS1A01G200500 chr1A 361172562 361175437 2875 True 5312.0 5312 100.000 1 2876 1 chr1A.!!$R1 2875
1 TraesCS1A01G200500 chr1D 288891292 288894139 2847 True 1887.0 3463 89.972 1 2810 2 chr1D.!!$R1 2809
2 TraesCS1A01G200500 chr1B 390379359 390382120 2761 True 1796.5 3186 90.124 137 2876 2 chr1B.!!$R1 2739

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
104 105 0.179129 GACCATTTCCCGCAGCAATG 60.179 55.0 0.00 0.0 0.00 2.82 F
115 117 0.179189 GCAGCAATGCACGAGGTTAC 60.179 55.0 8.35 0.0 34.41 2.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1479 1593 0.438830 GGCGATGTGACAAAGACGAC 59.561 55.0 0.0 0.0 0.00 4.34 R
1927 2041 0.747283 GCATTGCCTCTCTGGACTGG 60.747 60.0 0.0 0.0 38.35 4.00 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
53 54 7.775093 CCACTTTTTCACCTCATATCCAGATTA 59.225 37.037 0.00 0.00 0.00 1.75
55 56 9.347240 ACTTTTTCACCTCATATCCAGATTATG 57.653 33.333 0.00 0.00 0.00 1.90
81 82 8.122952 GGACAACCAAATCTCAACGAAATATAG 58.877 37.037 0.00 0.00 35.97 1.31
85 86 6.129393 CCAAATCTCAACGAAATATAGTGCG 58.871 40.000 0.00 0.00 0.00 5.34
90 91 4.689071 TCAACGAAATATAGTGCGACCAT 58.311 39.130 7.72 0.00 0.00 3.55
103 104 1.656818 CGACCATTTCCCGCAGCAAT 61.657 55.000 0.00 0.00 0.00 3.56
104 105 0.179129 GACCATTTCCCGCAGCAATG 60.179 55.000 0.00 0.00 0.00 2.82
113 115 2.956987 GCAGCAATGCACGAGGTT 59.043 55.556 8.35 0.00 34.41 3.50
115 117 0.179189 GCAGCAATGCACGAGGTTAC 60.179 55.000 8.35 0.00 34.41 2.50
123 125 1.479323 TGCACGAGGTTACCCTATCAC 59.521 52.381 0.00 0.00 42.86 3.06
130 132 4.759183 CGAGGTTACCCTATCACCTAGTAC 59.241 50.000 0.00 0.00 42.86 2.73
131 133 5.072129 AGGTTACCCTATCACCTAGTACC 57.928 47.826 0.00 0.00 40.19 3.34
133 135 5.137429 AGGTTACCCTATCACCTAGTACCAT 59.863 44.000 0.00 0.00 40.19 3.55
134 136 5.245526 GGTTACCCTATCACCTAGTACCATG 59.754 48.000 0.00 0.00 0.00 3.66
135 137 4.554553 ACCCTATCACCTAGTACCATGT 57.445 45.455 0.00 0.00 0.00 3.21
136 138 5.674799 ACCCTATCACCTAGTACCATGTA 57.325 43.478 0.00 0.00 0.00 2.29
141 169 7.931948 CCCTATCACCTAGTACCATGTAAAAAG 59.068 40.741 0.00 0.00 0.00 2.27
195 223 9.837525 ATGAGATTTCTTTCTTTTTCAGAATCG 57.162 29.630 0.00 0.00 41.42 3.34
196 224 9.056005 TGAGATTTCTTTCTTTTTCAGAATCGA 57.944 29.630 0.00 0.00 41.42 3.59
197 225 9.540431 GAGATTTCTTTCTTTTTCAGAATCGAG 57.460 33.333 0.00 0.00 41.42 4.04
198 226 9.277783 AGATTTCTTTCTTTTTCAGAATCGAGA 57.722 29.630 0.00 0.00 41.42 4.04
220 248 9.208022 CGAGATTTCTTTTATATAGTGGATGCA 57.792 33.333 0.00 0.00 0.00 3.96
234 291 2.830923 TGGATGCAACCTATTTTGTGGG 59.169 45.455 14.77 0.00 33.95 4.61
252 309 3.998341 GTGGGAATACAACGCAACTCTTA 59.002 43.478 0.00 0.00 32.47 2.10
280 337 3.162666 CCAATCCCATGATTCATGAGGG 58.837 50.000 24.93 18.95 43.81 4.30
281 338 3.437491 CCAATCCCATGATTCATGAGGGT 60.437 47.826 24.93 17.77 43.81 4.34
289 346 4.146745 TGATTCATGAGGGTCTGTGATG 57.853 45.455 0.00 0.00 0.00 3.07
354 417 3.576550 TCGATCCATCCATTTCACCGATA 59.423 43.478 0.00 0.00 0.00 2.92
377 442 1.233950 CGTGCCAGTATGCCACACAA 61.234 55.000 0.00 0.00 34.06 3.33
378 443 0.958091 GTGCCAGTATGCCACACAAA 59.042 50.000 0.00 0.00 34.41 2.83
395 460 6.296017 ACACAAATTGTTAACCGAAGGGGC 62.296 45.833 2.48 0.00 46.59 5.80
467 535 1.073125 ACCGATCACACACAATTGGGA 59.927 47.619 16.31 1.66 32.02 4.37
546 614 2.035237 GACCCCACACGTCCTCACAA 62.035 60.000 0.00 0.00 0.00 3.33
554 622 0.608640 ACGTCCTCACAACCATCTCC 59.391 55.000 0.00 0.00 0.00 3.71
645 713 4.892934 TGCTTGTATTGTTCCTGACCTTTT 59.107 37.500 0.00 0.00 0.00 2.27
646 714 5.009610 TGCTTGTATTGTTCCTGACCTTTTC 59.990 40.000 0.00 0.00 0.00 2.29
676 746 9.268282 CCTACCTTATCCCATATACATACACTT 57.732 37.037 0.00 0.00 0.00 3.16
770 859 1.197721 CCGTTTCTGGCATCTGTTCAC 59.802 52.381 0.00 0.00 0.00 3.18
781 870 2.418368 TCTGTTCACCCATGGCATAC 57.582 50.000 6.09 1.90 0.00 2.39
851 958 7.291182 AGGCCCATATTATAGTAAGCTGATAGG 59.709 40.741 0.00 0.00 0.00 2.57
931 1038 2.224281 CGGCTCCCAGAAATAGCATACA 60.224 50.000 0.00 0.00 0.00 2.29
932 1039 3.744214 CGGCTCCCAGAAATAGCATACAA 60.744 47.826 0.00 0.00 0.00 2.41
933 1040 3.565902 GGCTCCCAGAAATAGCATACAAC 59.434 47.826 0.00 0.00 0.00 3.32
1339 1453 0.243907 CCGCTTCGTGAAGGAGAAGA 59.756 55.000 11.32 0.00 44.76 2.87
1470 1584 3.315949 ACCGTAGCTTTCCCGCCA 61.316 61.111 0.00 0.00 0.00 5.69
1587 1701 4.115199 GCTGCCTCGGGGTCCAAT 62.115 66.667 1.62 0.00 34.45 3.16
1767 1881 4.314440 GGCACCTGCGGAGTCACA 62.314 66.667 2.36 0.00 43.26 3.58
1904 2018 7.180408 TCAAGGCCAGATTAAAGACTAGTACTT 59.820 37.037 5.01 0.00 0.00 2.24
1926 2040 2.030185 AGTACTGACACGCGAACTTGAT 60.030 45.455 15.93 0.00 0.00 2.57
1927 2041 1.419374 ACTGACACGCGAACTTGATC 58.581 50.000 15.93 1.75 0.00 2.92
1928 2042 0.716108 CTGACACGCGAACTTGATCC 59.284 55.000 15.93 0.00 0.00 3.36
1929 2043 0.032815 TGACACGCGAACTTGATCCA 59.967 50.000 15.93 0.00 0.00 3.41
1930 2044 0.716108 GACACGCGAACTTGATCCAG 59.284 55.000 15.93 0.00 0.00 3.86
2116 2232 4.141274 TCTGAGTTTTCCCCTTGACAATGA 60.141 41.667 0.00 0.00 0.00 2.57
2168 2284 5.430007 TGCATCATGAGATACATTCACACA 58.570 37.500 0.09 0.00 37.07 3.72
2180 2296 5.571784 ACATTCACACAGATTATGGCTTG 57.428 39.130 0.00 0.00 0.00 4.01
2183 2299 7.056006 ACATTCACACAGATTATGGCTTGATA 58.944 34.615 0.00 0.00 0.00 2.15
2209 2326 5.420409 CCCCGTTCTATAGATTTATGGCTC 58.580 45.833 2.58 0.00 0.00 4.70
2219 2370 4.477249 AGATTTATGGCTCCCCTTCATTG 58.523 43.478 0.00 0.00 0.00 2.82
2220 2371 4.168675 AGATTTATGGCTCCCCTTCATTGA 59.831 41.667 0.00 0.00 0.00 2.57
2231 2382 6.160576 TCCCCTTCATTGACAAAAGAAAAG 57.839 37.500 1.86 0.91 0.00 2.27
2264 2415 9.918630 TCGCTTCCCTTTATATACTTATTACAC 57.081 33.333 0.00 0.00 0.00 2.90
2265 2416 9.924650 CGCTTCCCTTTATATACTTATTACACT 57.075 33.333 0.00 0.00 0.00 3.55
2324 2476 7.566760 TGATAACAATTAGCACCAATGTAGG 57.433 36.000 0.00 0.00 0.00 3.18
2325 2477 7.342581 TGATAACAATTAGCACCAATGTAGGA 58.657 34.615 0.00 0.00 0.00 2.94
2326 2478 7.498900 TGATAACAATTAGCACCAATGTAGGAG 59.501 37.037 0.00 0.00 0.00 3.69
2356 2508 2.224426 ACTCATGCTTGGGTACGTTTCA 60.224 45.455 2.71 0.00 33.71 2.69
2398 2550 2.097629 GTGTCGTTCTGGAGATCGATCA 59.902 50.000 26.47 6.64 44.66 2.92
2424 2576 2.955461 GCTCTCCTCCCTAAGCAAGGTA 60.955 54.545 4.59 0.00 44.90 3.08
2425 2577 2.962421 CTCTCCTCCCTAAGCAAGGTAG 59.038 54.545 4.59 0.00 44.90 3.18
2430 2582 2.621486 CCTAAGCAAGGTAGGGGCT 58.379 57.895 0.00 0.00 40.94 5.19
2431 2583 1.802553 CCTAAGCAAGGTAGGGGCTA 58.197 55.000 0.00 0.00 40.94 3.93
2445 2601 0.757561 GGGCTAGAGGAGGTCAGGTC 60.758 65.000 0.00 0.00 0.00 3.85
2446 2602 0.033011 GGCTAGAGGAGGTCAGGTCA 60.033 60.000 0.00 0.00 0.00 4.02
2474 2630 6.325286 GTCAGAACCTAATCCTTCTCCTACAT 59.675 42.308 0.00 0.00 0.00 2.29
2496 2652 4.010349 TGTACAGATATCCGCATCGATCT 58.990 43.478 0.00 0.00 0.00 2.75
2512 2668 4.044426 TCGATCTGCTATGAACATTGTCG 58.956 43.478 0.00 0.00 0.00 4.35
2513 2669 3.798878 CGATCTGCTATGAACATTGTCGT 59.201 43.478 0.00 0.00 0.00 4.34
2514 2670 4.317628 CGATCTGCTATGAACATTGTCGTG 60.318 45.833 0.00 0.00 0.00 4.35
2515 2671 2.672874 TCTGCTATGAACATTGTCGTGC 59.327 45.455 0.00 0.00 0.00 5.34
2516 2672 2.674852 CTGCTATGAACATTGTCGTGCT 59.325 45.455 0.00 0.00 0.00 4.40
2517 2673 3.855858 TGCTATGAACATTGTCGTGCTA 58.144 40.909 0.00 0.00 0.00 3.49
2518 2674 3.865164 TGCTATGAACATTGTCGTGCTAG 59.135 43.478 0.00 0.00 0.00 3.42
2519 2675 3.302740 GCTATGAACATTGTCGTGCTAGC 60.303 47.826 8.10 8.10 0.00 3.42
2520 2676 2.455674 TGAACATTGTCGTGCTAGCT 57.544 45.000 17.23 0.00 0.00 3.32
2521 2677 2.766313 TGAACATTGTCGTGCTAGCTT 58.234 42.857 17.23 0.00 0.00 3.74
2522 2678 2.736721 TGAACATTGTCGTGCTAGCTTC 59.263 45.455 17.23 8.33 0.00 3.86
2523 2679 2.751166 ACATTGTCGTGCTAGCTTCT 57.249 45.000 17.23 0.00 0.00 2.85
2524 2680 3.045601 ACATTGTCGTGCTAGCTTCTT 57.954 42.857 17.23 0.00 0.00 2.52
2525 2681 2.738846 ACATTGTCGTGCTAGCTTCTTG 59.261 45.455 17.23 7.07 0.00 3.02
2526 2682 1.795768 TTGTCGTGCTAGCTTCTTGG 58.204 50.000 17.23 0.00 0.00 3.61
2527 2683 0.037326 TGTCGTGCTAGCTTCTTGGG 60.037 55.000 17.23 0.00 0.00 4.12
2528 2684 0.037232 GTCGTGCTAGCTTCTTGGGT 60.037 55.000 17.23 0.00 0.00 4.51
2529 2685 0.685097 TCGTGCTAGCTTCTTGGGTT 59.315 50.000 17.23 0.00 0.00 4.11
2530 2686 0.798776 CGTGCTAGCTTCTTGGGTTG 59.201 55.000 17.23 0.00 0.00 3.77
2531 2687 1.168714 GTGCTAGCTTCTTGGGTTGG 58.831 55.000 17.23 0.00 0.00 3.77
2532 2688 0.771127 TGCTAGCTTCTTGGGTTGGT 59.229 50.000 17.23 0.00 0.00 3.67
2533 2689 1.144913 TGCTAGCTTCTTGGGTTGGTT 59.855 47.619 17.23 0.00 0.00 3.67
2534 2690 1.813178 GCTAGCTTCTTGGGTTGGTTC 59.187 52.381 7.70 0.00 0.00 3.62
2535 2691 2.553247 GCTAGCTTCTTGGGTTGGTTCT 60.553 50.000 7.70 0.00 0.00 3.01
2536 2692 2.278332 AGCTTCTTGGGTTGGTTCTC 57.722 50.000 0.00 0.00 0.00 2.87
2537 2693 0.875059 GCTTCTTGGGTTGGTTCTCG 59.125 55.000 0.00 0.00 0.00 4.04
2538 2694 1.814248 GCTTCTTGGGTTGGTTCTCGT 60.814 52.381 0.00 0.00 0.00 4.18
2539 2695 1.873591 CTTCTTGGGTTGGTTCTCGTG 59.126 52.381 0.00 0.00 0.00 4.35
2540 2696 0.534203 TCTTGGGTTGGTTCTCGTGC 60.534 55.000 0.00 0.00 0.00 5.34
2541 2697 1.841663 CTTGGGTTGGTTCTCGTGCG 61.842 60.000 0.00 0.00 0.00 5.34
2542 2698 3.723348 GGGTTGGTTCTCGTGCGC 61.723 66.667 0.00 0.00 0.00 6.09
2543 2699 2.970324 GGTTGGTTCTCGTGCGCA 60.970 61.111 5.66 5.66 0.00 6.09
2544 2700 2.539338 GGTTGGTTCTCGTGCGCAA 61.539 57.895 14.00 0.00 0.00 4.85
2545 2701 1.574428 GTTGGTTCTCGTGCGCAAT 59.426 52.632 14.00 0.00 0.00 3.56
2546 2702 0.040425 GTTGGTTCTCGTGCGCAATT 60.040 50.000 14.00 0.00 0.00 2.32
2547 2703 0.237235 TTGGTTCTCGTGCGCAATTC 59.763 50.000 14.00 0.00 0.00 2.17
2548 2704 0.602638 TGGTTCTCGTGCGCAATTCT 60.603 50.000 14.00 0.00 0.00 2.40
2549 2705 0.517316 GGTTCTCGTGCGCAATTCTT 59.483 50.000 14.00 0.00 0.00 2.52
2550 2706 1.069227 GGTTCTCGTGCGCAATTCTTT 60.069 47.619 14.00 0.00 0.00 2.52
2551 2707 2.234187 GTTCTCGTGCGCAATTCTTTC 58.766 47.619 14.00 0.00 0.00 2.62
2552 2708 0.796312 TCTCGTGCGCAATTCTTTCC 59.204 50.000 14.00 0.00 0.00 3.13
2553 2709 0.179189 CTCGTGCGCAATTCTTTCCC 60.179 55.000 14.00 0.00 0.00 3.97
2554 2710 0.886938 TCGTGCGCAATTCTTTCCCA 60.887 50.000 14.00 0.00 0.00 4.37
2555 2711 0.454957 CGTGCGCAATTCTTTCCCAG 60.455 55.000 14.00 0.00 0.00 4.45
2556 2712 0.733909 GTGCGCAATTCTTTCCCAGC 60.734 55.000 14.00 0.00 0.00 4.85
2557 2713 0.895100 TGCGCAATTCTTTCCCAGCT 60.895 50.000 8.16 0.00 0.00 4.24
2558 2714 0.457337 GCGCAATTCTTTCCCAGCTG 60.457 55.000 6.78 6.78 0.00 4.24
2559 2715 0.457337 CGCAATTCTTTCCCAGCTGC 60.457 55.000 8.66 0.00 0.00 5.25
2560 2716 0.108472 GCAATTCTTTCCCAGCTGCC 60.108 55.000 8.66 0.00 0.00 4.85
2561 2717 1.553706 CAATTCTTTCCCAGCTGCCT 58.446 50.000 8.66 0.00 0.00 4.75
2580 2736 3.661944 CCTCATGCATCTGATGTCTACC 58.338 50.000 18.19 2.79 0.00 3.18
2590 2746 5.250235 TCTGATGTCTACCGATTTCTGAC 57.750 43.478 0.00 0.00 0.00 3.51
2603 2759 0.032130 TTCTGACGCGCTTCTGACTT 59.968 50.000 20.48 0.00 0.00 3.01
2612 2768 2.378806 CGCTTCTGACTTTGTTTGCTG 58.621 47.619 0.00 0.00 0.00 4.41
2647 2803 2.517321 GCAAATCTCTGCAGTTCGTC 57.483 50.000 14.67 0.00 42.17 4.20
2656 2812 1.000283 CTGCAGTTCGTCCAAGACTCT 60.000 52.381 5.25 0.00 0.00 3.24
2671 2827 5.220739 CCAAGACTCTTCTGAAATTATGCCG 60.221 44.000 0.00 0.00 29.98 5.69
2698 2855 6.855836 TGCTTCAGCCTTGAAATTAATACTG 58.144 36.000 0.00 0.00 42.48 2.74
2707 2864 8.343366 GCCTTGAAATTAATACTGTTACTAGCC 58.657 37.037 0.00 0.00 0.00 3.93
2713 2870 6.494666 TTAATACTGTTACTAGCCAGCCAT 57.505 37.500 4.95 0.00 31.76 4.40
2716 2873 2.093447 ACTGTTACTAGCCAGCCATGTC 60.093 50.000 4.95 0.00 31.76 3.06
2717 2874 1.905894 TGTTACTAGCCAGCCATGTCA 59.094 47.619 0.00 0.00 0.00 3.58
2718 2875 2.304470 TGTTACTAGCCAGCCATGTCAA 59.696 45.455 0.00 0.00 0.00 3.18
2720 2877 0.987294 ACTAGCCAGCCATGTCAACT 59.013 50.000 0.00 0.00 0.00 3.16
2721 2878 1.339438 ACTAGCCAGCCATGTCAACTG 60.339 52.381 0.00 0.00 0.00 3.16
2724 2881 3.040965 CCAGCCATGTCAACTGGTT 57.959 52.632 11.29 0.00 44.91 3.67
2725 2882 0.599558 CCAGCCATGTCAACTGGTTG 59.400 55.000 7.10 7.10 44.91 3.77
2728 2885 1.133823 AGCCATGTCAACTGGTTGTGA 60.134 47.619 12.34 2.46 41.16 3.58
2729 2886 1.267806 GCCATGTCAACTGGTTGTGAG 59.732 52.381 12.34 3.28 41.16 3.51
2730 2887 2.849942 CCATGTCAACTGGTTGTGAGA 58.150 47.619 12.34 0.00 41.16 3.27
2732 2889 3.003689 CCATGTCAACTGGTTGTGAGAAC 59.996 47.826 12.34 4.78 41.16 3.01
2763 2929 8.268850 AGTAATACTGTTATGAAGCTTTGTGG 57.731 34.615 0.00 0.00 0.00 4.17
2828 2996 5.416952 AGTTCAAATATTCTTCAGGGCACAG 59.583 40.000 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 9.136323 GGATATGAGGTGAAAAAGTGGAAATAT 57.864 33.333 0.00 0.00 0.00 1.28
27 28 5.500234 TCTGGATATGAGGTGAAAAAGTGG 58.500 41.667 0.00 0.00 0.00 4.00
53 54 3.750371 TCGTTGAGATTTGGTTGTCCAT 58.250 40.909 0.00 0.00 43.91 3.41
55 56 4.561735 TTTCGTTGAGATTTGGTTGTCC 57.438 40.909 0.00 0.00 0.00 4.02
85 86 0.179129 CATTGCTGCGGGAAATGGTC 60.179 55.000 2.68 0.00 37.32 4.02
98 99 2.854522 GGTAACCTCGTGCATTGCT 58.145 52.632 10.49 0.00 0.00 3.91
113 115 5.674799 ACATGGTACTAGGTGATAGGGTA 57.325 43.478 0.00 0.00 35.63 3.69
115 117 6.989155 TTTACATGGTACTAGGTGATAGGG 57.011 41.667 6.80 0.00 35.63 3.53
123 125 8.385898 TGTGTTTCTTTTTACATGGTACTAGG 57.614 34.615 0.00 0.00 0.00 3.02
133 135 7.598278 ACACTCAACATGTGTTTCTTTTTACA 58.402 30.769 0.00 0.00 45.11 2.41
193 221 9.424319 GCATCCACTATATAAAAGAAATCTCGA 57.576 33.333 0.00 0.00 0.00 4.04
194 222 9.208022 TGCATCCACTATATAAAAGAAATCTCG 57.792 33.333 0.00 0.00 0.00 4.04
197 225 9.899226 GGTTGCATCCACTATATAAAAGAAATC 57.101 33.333 9.02 0.00 0.00 2.17
198 226 9.646522 AGGTTGCATCCACTATATAAAAGAAAT 57.353 29.630 16.12 0.00 0.00 2.17
214 242 3.096092 TCCCACAAAATAGGTTGCATCC 58.904 45.455 5.61 5.61 31.29 3.51
218 246 5.652994 TGTATTCCCACAAAATAGGTTGC 57.347 39.130 0.00 0.00 31.29 4.17
220 248 5.336134 GCGTTGTATTCCCACAAAATAGGTT 60.336 40.000 0.00 0.00 39.98 3.50
222 250 4.156922 TGCGTTGTATTCCCACAAAATAGG 59.843 41.667 0.00 0.00 39.98 2.57
228 285 2.550606 GAGTTGCGTTGTATTCCCACAA 59.449 45.455 0.00 0.00 36.08 3.33
234 291 4.927425 TGACCTAAGAGTTGCGTTGTATTC 59.073 41.667 0.00 0.00 0.00 1.75
252 309 3.464456 TGAATCATGGGATTGGATGACCT 59.536 43.478 0.00 0.00 43.69 3.85
280 337 9.928236 GATATTTTCTAGCTTTTCATCACAGAC 57.072 33.333 0.00 0.00 0.00 3.51
281 338 8.820933 CGATATTTTCTAGCTTTTCATCACAGA 58.179 33.333 0.00 0.00 0.00 3.41
289 346 5.505819 GGGGCACGATATTTTCTAGCTTTTC 60.506 44.000 0.00 0.00 0.00 2.29
354 417 2.187946 GGCATACTGGCACGAGCT 59.812 61.111 4.48 0.00 43.14 4.09
377 442 2.597578 AGCCCCTTCGGTTAACAATT 57.402 45.000 8.10 0.00 0.00 2.32
378 443 2.356432 GGTAGCCCCTTCGGTTAACAAT 60.356 50.000 8.10 0.00 35.15 2.71
395 460 2.472695 TGGTTTGCTAGCTGTGGTAG 57.527 50.000 17.23 0.03 36.79 3.18
467 535 0.247736 GAGCATGTCCCTCTCAACGT 59.752 55.000 0.00 0.00 0.00 3.99
546 614 1.629297 GAGGAGGGAGGGAGATGGT 59.371 63.158 0.00 0.00 0.00 3.55
554 622 3.700350 AGGTGGGGAGGAGGGAGG 61.700 72.222 0.00 0.00 0.00 4.30
645 713 7.599353 TGTATATGGGATAAGGTAGGAGAGA 57.401 40.000 0.00 0.00 0.00 3.10
646 714 9.357161 GTATGTATATGGGATAAGGTAGGAGAG 57.643 40.741 0.00 0.00 0.00 3.20
676 746 3.508426 TGGTGTGTGTGTAGTGGGTATA 58.492 45.455 0.00 0.00 0.00 1.47
770 859 2.093288 AGATATGCGAGTATGCCATGGG 60.093 50.000 15.13 0.00 0.00 4.00
781 870 5.991606 TGGAAAACTGGAATAGATATGCGAG 59.008 40.000 0.00 0.00 0.00 5.03
851 958 5.133221 TGGAGAAAAGAATTAGGGCTATGC 58.867 41.667 0.00 0.00 0.00 3.14
931 1038 1.212935 AGGTGCTGACTTTGACTGGTT 59.787 47.619 0.00 0.00 0.00 3.67
932 1039 0.839946 AGGTGCTGACTTTGACTGGT 59.160 50.000 0.00 0.00 0.00 4.00
933 1040 1.605710 CAAGGTGCTGACTTTGACTGG 59.394 52.381 0.00 0.00 40.72 4.00
961 1068 2.203938 TCCCAACCTCCCGAGCTT 60.204 61.111 0.00 0.00 0.00 3.74
1400 1514 0.739561 GAAGTCGATGTAGAGGCGGT 59.260 55.000 0.00 0.00 0.00 5.68
1441 1555 2.361483 TACGGTGGCGCTGTAGGA 60.361 61.111 15.47 0.00 37.88 2.94
1470 1584 3.969802 AAAGACGACGTCGCCGGT 61.970 61.111 35.92 18.32 44.43 5.28
1479 1593 0.438830 GGCGATGTGACAAAGACGAC 59.561 55.000 0.00 0.00 0.00 4.34
1587 1701 1.802508 CGCAGGAATAGCACATGACGA 60.803 52.381 0.00 0.00 0.00 4.20
1753 1867 2.088674 GTCTGTGTGACTCCGCAGGT 62.089 60.000 0.00 0.00 42.14 4.00
1767 1881 1.362717 CGTTGAGGTCACCGTCTGT 59.637 57.895 0.00 0.00 0.00 3.41
1904 2018 2.549329 TCAAGTTCGCGTGTCAGTACTA 59.451 45.455 5.77 0.00 0.00 1.82
1926 2040 0.907486 CATTGCCTCTCTGGACTGGA 59.093 55.000 0.00 0.00 38.35 3.86
1927 2041 0.747283 GCATTGCCTCTCTGGACTGG 60.747 60.000 0.00 0.00 38.35 4.00
1928 2042 1.088340 CGCATTGCCTCTCTGGACTG 61.088 60.000 2.41 0.00 38.35 3.51
1929 2043 1.220206 CGCATTGCCTCTCTGGACT 59.780 57.895 2.41 0.00 38.35 3.85
1930 2044 1.078848 ACGCATTGCCTCTCTGGAC 60.079 57.895 2.41 0.00 38.35 4.02
2103 2219 6.377996 TGATACATTCTTTCATTGTCAAGGGG 59.622 38.462 0.00 0.00 0.00 4.79
2116 2232 7.391833 GGTTCAGAGAGGTTTGATACATTCTTT 59.608 37.037 0.00 0.00 0.00 2.52
2180 2296 4.715527 AATCTATAGAACGGGGCGTATC 57.284 45.455 6.52 0.00 39.99 2.24
2183 2299 4.322499 CCATAAATCTATAGAACGGGGCGT 60.322 45.833 6.52 0.00 43.97 5.68
2209 2326 5.917462 ACTTTTCTTTTGTCAATGAAGGGG 58.083 37.500 0.00 0.01 30.09 4.79
2219 2370 9.062674 GGAAGCGATAAATACTTTTCTTTTGTC 57.937 33.333 0.00 0.00 0.00 3.18
2220 2371 8.027189 GGGAAGCGATAAATACTTTTCTTTTGT 58.973 33.333 0.00 0.00 0.00 2.83
2239 2390 9.924650 AGTGTAATAAGTATATAAAGGGAAGCG 57.075 33.333 0.00 0.00 0.00 4.68
2263 2414 3.501445 GGAACGAGACTGTACACTGTAGT 59.499 47.826 0.00 0.00 0.00 2.73
2264 2415 3.119919 GGGAACGAGACTGTACACTGTAG 60.120 52.174 0.00 0.00 0.00 2.74
2265 2416 2.816087 GGGAACGAGACTGTACACTGTA 59.184 50.000 0.00 0.00 0.00 2.74
2266 2417 1.612463 GGGAACGAGACTGTACACTGT 59.388 52.381 0.00 0.00 0.00 3.55
2267 2418 1.887198 AGGGAACGAGACTGTACACTG 59.113 52.381 0.00 0.00 0.00 3.66
2268 2419 1.887198 CAGGGAACGAGACTGTACACT 59.113 52.381 0.00 0.00 0.00 3.55
2269 2420 1.669211 GCAGGGAACGAGACTGTACAC 60.669 57.143 0.00 0.00 34.79 2.90
2270 2421 0.601558 GCAGGGAACGAGACTGTACA 59.398 55.000 0.00 0.00 34.79 2.90
2271 2422 0.889306 AGCAGGGAACGAGACTGTAC 59.111 55.000 0.00 0.00 34.79 2.90
2356 2508 5.183904 ACACTGCTTCAAGAAACTTGAAAGT 59.816 36.000 21.58 19.66 42.04 2.66
2424 2576 1.623625 CTGACCTCCTCTAGCCCCT 59.376 63.158 0.00 0.00 0.00 4.79
2425 2577 1.458588 CCTGACCTCCTCTAGCCCC 60.459 68.421 0.00 0.00 0.00 5.80
2428 2580 1.341581 ACTGACCTGACCTCCTCTAGC 60.342 57.143 0.00 0.00 0.00 3.42
2429 2581 2.291282 ACACTGACCTGACCTCCTCTAG 60.291 54.545 0.00 0.00 0.00 2.43
2430 2582 1.711375 ACACTGACCTGACCTCCTCTA 59.289 52.381 0.00 0.00 0.00 2.43
2431 2583 0.485099 ACACTGACCTGACCTCCTCT 59.515 55.000 0.00 0.00 0.00 3.69
2445 2601 5.413309 AGAAGGATTAGGTTCTGACACTG 57.587 43.478 0.00 0.00 31.63 3.66
2446 2602 4.468153 GGAGAAGGATTAGGTTCTGACACT 59.532 45.833 0.00 0.00 33.04 3.55
2474 2630 4.010349 AGATCGATGCGGATATCTGTACA 58.990 43.478 13.12 4.05 0.00 2.90
2496 2652 2.698803 AGCACGACAATGTTCATAGCA 58.301 42.857 0.00 0.00 0.00 3.49
2512 2668 1.168714 CCAACCCAAGAAGCTAGCAC 58.831 55.000 18.83 10.61 0.00 4.40
2513 2669 0.771127 ACCAACCCAAGAAGCTAGCA 59.229 50.000 18.83 0.00 0.00 3.49
2514 2670 1.813178 GAACCAACCCAAGAAGCTAGC 59.187 52.381 6.62 6.62 0.00 3.42
2515 2671 3.339141 GAGAACCAACCCAAGAAGCTAG 58.661 50.000 0.00 0.00 0.00 3.42
2516 2672 2.289444 CGAGAACCAACCCAAGAAGCTA 60.289 50.000 0.00 0.00 0.00 3.32
2517 2673 1.543429 CGAGAACCAACCCAAGAAGCT 60.543 52.381 0.00 0.00 0.00 3.74
2518 2674 0.875059 CGAGAACCAACCCAAGAAGC 59.125 55.000 0.00 0.00 0.00 3.86
2519 2675 1.873591 CACGAGAACCAACCCAAGAAG 59.126 52.381 0.00 0.00 0.00 2.85
2520 2676 1.961793 CACGAGAACCAACCCAAGAA 58.038 50.000 0.00 0.00 0.00 2.52
2521 2677 0.534203 GCACGAGAACCAACCCAAGA 60.534 55.000 0.00 0.00 0.00 3.02
2522 2678 1.841663 CGCACGAGAACCAACCCAAG 61.842 60.000 0.00 0.00 0.00 3.61
2523 2679 1.890041 CGCACGAGAACCAACCCAA 60.890 57.895 0.00 0.00 0.00 4.12
2524 2680 2.280524 CGCACGAGAACCAACCCA 60.281 61.111 0.00 0.00 0.00 4.51
2525 2681 3.723348 GCGCACGAGAACCAACCC 61.723 66.667 0.30 0.00 0.00 4.11
2526 2682 1.852067 ATTGCGCACGAGAACCAACC 61.852 55.000 11.12 0.00 0.00 3.77
2527 2683 0.040425 AATTGCGCACGAGAACCAAC 60.040 50.000 11.12 0.00 0.00 3.77
2528 2684 0.237235 GAATTGCGCACGAGAACCAA 59.763 50.000 11.12 0.00 0.00 3.67
2529 2685 0.602638 AGAATTGCGCACGAGAACCA 60.603 50.000 11.12 0.00 0.00 3.67
2530 2686 0.517316 AAGAATTGCGCACGAGAACC 59.483 50.000 11.12 0.00 0.00 3.62
2531 2687 2.234187 GAAAGAATTGCGCACGAGAAC 58.766 47.619 11.12 0.00 0.00 3.01
2532 2688 1.196808 GGAAAGAATTGCGCACGAGAA 59.803 47.619 11.12 0.00 0.00 2.87
2533 2689 0.796312 GGAAAGAATTGCGCACGAGA 59.204 50.000 11.12 0.00 0.00 4.04
2534 2690 0.179189 GGGAAAGAATTGCGCACGAG 60.179 55.000 11.12 0.00 0.00 4.18
2535 2691 0.886938 TGGGAAAGAATTGCGCACGA 60.887 50.000 11.12 0.00 0.00 4.35
2536 2692 0.454957 CTGGGAAAGAATTGCGCACG 60.455 55.000 11.12 0.00 0.00 5.34
2537 2693 0.733909 GCTGGGAAAGAATTGCGCAC 60.734 55.000 11.12 0.00 0.00 5.34
2538 2694 0.895100 AGCTGGGAAAGAATTGCGCA 60.895 50.000 5.66 5.66 0.00 6.09
2539 2695 0.457337 CAGCTGGGAAAGAATTGCGC 60.457 55.000 5.57 0.00 0.00 6.09
2540 2696 0.457337 GCAGCTGGGAAAGAATTGCG 60.457 55.000 17.12 0.00 0.00 4.85
2541 2697 0.108472 GGCAGCTGGGAAAGAATTGC 60.108 55.000 17.12 0.00 0.00 3.56
2542 2698 1.475682 GAGGCAGCTGGGAAAGAATTG 59.524 52.381 17.12 0.00 0.00 2.32
2543 2699 1.076024 TGAGGCAGCTGGGAAAGAATT 59.924 47.619 17.12 0.00 0.00 2.17
2544 2700 0.700564 TGAGGCAGCTGGGAAAGAAT 59.299 50.000 17.12 0.00 0.00 2.40
2545 2701 0.700564 ATGAGGCAGCTGGGAAAGAA 59.299 50.000 17.12 0.00 0.00 2.52
2546 2702 0.034767 CATGAGGCAGCTGGGAAAGA 60.035 55.000 17.12 0.00 0.00 2.52
2547 2703 1.664321 GCATGAGGCAGCTGGGAAAG 61.664 60.000 17.12 0.00 43.97 2.62
2548 2704 1.679977 GCATGAGGCAGCTGGGAAA 60.680 57.895 17.12 0.00 43.97 3.13
2549 2705 2.044650 GCATGAGGCAGCTGGGAA 60.045 61.111 17.12 0.00 43.97 3.97
2558 2714 2.257691 AGACATCAGATGCATGAGGC 57.742 50.000 2.46 0.00 45.13 4.70
2559 2715 3.661944 GGTAGACATCAGATGCATGAGG 58.338 50.000 2.46 1.32 37.04 3.86
2560 2716 3.005155 TCGGTAGACATCAGATGCATGAG 59.995 47.826 2.46 0.00 31.44 2.90
2561 2717 2.958355 TCGGTAGACATCAGATGCATGA 59.042 45.455 2.46 0.00 0.00 3.07
2580 2736 0.024238 CAGAAGCGCGTCAGAAATCG 59.976 55.000 24.95 1.04 0.00 3.34
2590 2746 1.388888 CAAACAAAGTCAGAAGCGCG 58.611 50.000 0.00 0.00 0.00 6.86
2647 2803 5.220739 CGGCATAATTTCAGAAGAGTCTTGG 60.221 44.000 10.90 2.35 28.78 3.61
2656 2812 1.405105 GCAGCCGGCATAATTTCAGAA 59.595 47.619 31.54 0.00 43.97 3.02
2698 2855 2.678336 GTTGACATGGCTGGCTAGTAAC 59.322 50.000 0.00 0.00 0.00 2.50
2707 2864 1.001048 CACAACCAGTTGACATGGCTG 60.001 52.381 17.06 1.05 42.93 4.85
2713 2870 3.055458 TCAGTTCTCACAACCAGTTGACA 60.055 43.478 17.06 2.34 42.93 3.58
2716 2873 3.797039 TCTCAGTTCTCACAACCAGTTG 58.203 45.455 8.95 8.95 45.58 3.16
2717 2874 4.080863 ACTTCTCAGTTCTCACAACCAGTT 60.081 41.667 0.00 0.00 0.00 3.16
2718 2875 3.452627 ACTTCTCAGTTCTCACAACCAGT 59.547 43.478 0.00 0.00 0.00 4.00
2720 2877 5.607939 TTACTTCTCAGTTCTCACAACCA 57.392 39.130 0.00 0.00 34.06 3.67
2721 2878 7.329717 CAGTATTACTTCTCAGTTCTCACAACC 59.670 40.741 0.00 0.00 34.06 3.77
2722 2879 7.868415 ACAGTATTACTTCTCAGTTCTCACAAC 59.132 37.037 0.00 0.00 34.06 3.32
2724 2881 7.526142 ACAGTATTACTTCTCAGTTCTCACA 57.474 36.000 0.00 0.00 34.06 3.58
2730 2887 9.372369 GCTTCATAACAGTATTACTTCTCAGTT 57.628 33.333 0.00 0.00 34.06 3.16
2732 2889 9.593134 AAGCTTCATAACAGTATTACTTCTCAG 57.407 33.333 0.00 0.00 0.00 3.35
2763 2929 1.794222 GGTGGTTGCACGATAGCAC 59.206 57.895 9.44 9.44 45.61 4.40
2797 2965 6.541641 CCTGAAGAATATTTGAACTGGAGAGG 59.458 42.308 0.00 0.00 0.00 3.69
2828 2996 8.148351 TGGACTGAAGGTGCTATATACAAATAC 58.852 37.037 0.00 0.00 37.18 1.89


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

AutoCloner maintained by Alex Coulton.