Multiple sequence alignment - TraesCS5D01G046200

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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 TraesCS5D01G046200 chr5D 100.000 3491 0 0 1 3491 45138300 45141790 0.000000e+00 6447.0
1 TraesCS5D01G046200 chr5A 90.489 2166 135 34 923 3066 35803928 35806044 0.000000e+00 2793.0
2 TraesCS5D01G046200 chr5A 97.114 797 22 1 1 797 634149261 634148466 0.000000e+00 1343.0
3 TraesCS5D01G046200 chr5A 92.541 429 31 1 3063 3491 35806135 35806562 6.400000e-172 614.0
4 TraesCS5D01G046200 chr5B 93.129 1761 81 14 904 2655 45034956 45036685 0.000000e+00 2545.0
5 TraesCS5D01G046200 chr5B 92.541 429 29 2 3063 3491 45037172 45037597 2.300000e-171 612.0
6 TraesCS5D01G046200 chr5B 82.353 357 51 8 2718 3066 45036720 45037072 2.040000e-77 300.0
7 TraesCS5D01G046200 chr5B 100.000 28 0 0 856 883 45034938 45034965 6.000000e-03 52.8
8 TraesCS5D01G046200 chr2A 96.478 795 27 1 1 795 33551229 33552022 0.000000e+00 1312.0
9 TraesCS5D01G046200 chr4B 95.463 529 24 0 269 797 458932416 458931888 0.000000e+00 845.0
10 TraesCS5D01G046200 chr4B 83.042 802 126 9 1 798 630350578 630349783 0.000000e+00 719.0
11 TraesCS5D01G046200 chr4B 93.750 272 17 0 1 272 458936763 458936492 3.240000e-110 409.0
12 TraesCS5D01G046200 chr1D 83.333 798 125 8 1 795 314001294 314000502 0.000000e+00 730.0
13 TraesCS5D01G046200 chr1D 74.293 389 94 6 222 608 83816447 83816831 3.610000e-35 159.0
14 TraesCS5D01G046200 chr7A 75.547 274 64 3 336 608 436851947 436851676 7.860000e-27 132.0
15 TraesCS5D01G046200 chr6A 80.117 171 33 1 438 608 536794187 536794018 3.660000e-25 126.0
16 TraesCS5D01G046200 chr6A 80.117 171 33 1 438 608 536797787 536797618 3.660000e-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 TraesCS5D01G046200 chr5D 45138300 45141790 3490 False 6447.00 6447 100.00000 1 3491 1 chr5D.!!$F1 3490
1 TraesCS5D01G046200 chr5A 35803928 35806562 2634 False 1703.50 2793 91.51500 923 3491 2 chr5A.!!$F1 2568
2 TraesCS5D01G046200 chr5A 634148466 634149261 795 True 1343.00 1343 97.11400 1 797 1 chr5A.!!$R1 796
3 TraesCS5D01G046200 chr5B 45034938 45037597 2659 False 877.45 2545 92.00575 856 3491 4 chr5B.!!$F1 2635
4 TraesCS5D01G046200 chr2A 33551229 33552022 793 False 1312.00 1312 96.47800 1 795 1 chr2A.!!$F1 794
5 TraesCS5D01G046200 chr4B 458931888 458932416 528 True 845.00 845 95.46300 269 797 1 chr4B.!!$R1 528
6 TraesCS5D01G046200 chr4B 630349783 630350578 795 True 719.00 719 83.04200 1 798 1 chr4B.!!$R3 797
7 TraesCS5D01G046200 chr1D 314000502 314001294 792 True 730.00 730 83.33300 1 795 1 chr1D.!!$R1 794

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
407 408 0.040514 CGCAAATTCAGCCACGAACA 60.041 50.0 0.0 0.0 0.0 3.18 F
2289 2302 0.670546 ATGTTGCAGAGGGTTCGTCG 60.671 55.0 0.0 0.0 0.0 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2337 2350 0.179000 CCTCATTCCAGTCTTCCCCG 59.821 60.0 0.0 0.0 0.0 5.73 R
3396 3535 1.192146 TGGTACTCCAGAGGTGGCAC 61.192 60.0 9.7 9.7 44.6 5.01 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
26 27 2.110967 CGGCCACATGAGAAGCAGG 61.111 63.158 2.24 0.00 0.00 4.85
101 102 2.684881 GCCGATTCAATCACAATCCAGT 59.315 45.455 0.00 0.00 0.00 4.00
144 145 2.449518 TGTGACCCTGGCCCTCAA 60.450 61.111 0.00 0.00 0.00 3.02
157 158 2.356741 GGCCCTCAAGTAGCCATTAACA 60.357 50.000 0.00 0.00 46.34 2.41
384 385 4.933483 GCGATCGCGATCTCTCTT 57.067 55.556 37.76 11.76 40.82 2.85
407 408 0.040514 CGCAAATTCAGCCACGAACA 60.041 50.000 0.00 0.00 0.00 3.18
418 419 1.814248 GCCACGAACATATTCTCCCCC 60.814 57.143 0.00 0.00 32.12 5.40
490 491 4.272489 CATTGGTTATGGTCTGGATGTGT 58.728 43.478 0.00 0.00 0.00 3.72
539 540 2.281484 GCAACCACTTCTCCGGCA 60.281 61.111 0.00 0.00 0.00 5.69
712 713 4.749310 CAAGCCTGTCGCCTCGCT 62.749 66.667 0.00 0.00 38.78 4.93
764 765 1.064685 CCAAAACCCTAGATCGCCCTT 60.065 52.381 0.00 0.00 0.00 3.95
815 816 5.432885 AAAAATACCTGTTGAGTTGGACG 57.567 39.130 0.00 0.00 0.00 4.79
816 817 4.345859 AAATACCTGTTGAGTTGGACGA 57.654 40.909 0.00 0.00 0.00 4.20
817 818 4.345859 AATACCTGTTGAGTTGGACGAA 57.654 40.909 0.00 0.00 0.00 3.85
818 819 2.930826 ACCTGTTGAGTTGGACGAAT 57.069 45.000 0.00 0.00 0.00 3.34
819 820 5.670792 ATACCTGTTGAGTTGGACGAATA 57.329 39.130 0.00 0.00 0.00 1.75
820 821 4.345859 ACCTGTTGAGTTGGACGAATAA 57.654 40.909 0.00 0.00 0.00 1.40
821 822 4.710324 ACCTGTTGAGTTGGACGAATAAA 58.290 39.130 0.00 0.00 0.00 1.40
822 823 5.127491 ACCTGTTGAGTTGGACGAATAAAA 58.873 37.500 0.00 0.00 0.00 1.52
823 824 5.591067 ACCTGTTGAGTTGGACGAATAAAAA 59.409 36.000 0.00 0.00 0.00 1.94
839 840 3.544772 AAAAACTTGCCCCACCGG 58.455 55.556 0.00 0.00 0.00 5.28
850 851 4.524318 CCACCGGCGCCTATCGTT 62.524 66.667 26.68 0.00 41.07 3.85
851 852 3.261951 CACCGGCGCCTATCGTTG 61.262 66.667 26.68 5.84 41.07 4.10
901 902 9.175312 ACAGTATATGTACTCTCGAGAAAAAGA 57.825 33.333 17.36 3.70 41.60 2.52
908 909 8.744008 TGTACTCTCGAGAAAAAGAATTACAG 57.256 34.615 17.36 2.28 0.00 2.74
909 910 8.358148 TGTACTCTCGAGAAAAAGAATTACAGT 58.642 33.333 17.36 8.32 0.00 3.55
910 911 9.837525 GTACTCTCGAGAAAAAGAATTACAGTA 57.162 33.333 17.36 7.34 0.00 2.74
1019 1029 4.035102 GGCGCCTTCCACCCTCTT 62.035 66.667 22.15 0.00 0.00 2.85
1662 1675 2.087009 GGACGTCTTCACCTTCGCG 61.087 63.158 16.46 0.00 0.00 5.87
1848 1861 2.439701 CGGGACTACCTCCTGCGA 60.440 66.667 0.00 0.00 38.70 5.10
1986 1999 4.082523 CGGACGCTGGTGGACCAT 62.083 66.667 0.00 0.00 46.46 3.55
2167 2180 4.585216 TGGTTGGGAGGGACCGGT 62.585 66.667 6.92 6.92 38.81 5.28
2203 2216 2.354103 CGTGAGGGCAAGAAGATCAGAA 60.354 50.000 0.00 0.00 0.00 3.02
2210 2223 2.355513 GCAAGAAGATCAGAAGGGCTCA 60.356 50.000 0.00 0.00 0.00 4.26
2241 2254 1.201414 GTTTTTCCGGTTGATGGCGAT 59.799 47.619 0.00 0.00 0.00 4.58
2253 2266 2.560105 TGATGGCGATAGTGATGAGGAG 59.440 50.000 0.00 0.00 39.35 3.69
2289 2302 0.670546 ATGTTGCAGAGGGTTCGTCG 60.671 55.000 0.00 0.00 0.00 5.12
2310 2323 2.557452 GGAGGTGGATGGTGAATTTGGT 60.557 50.000 0.00 0.00 0.00 3.67
2325 2338 5.067674 TGAATTTGGTGACCTGTTTGAAGAG 59.932 40.000 2.11 0.00 0.00 2.85
2328 2341 2.507886 TGGTGACCTGTTTGAAGAGGAA 59.492 45.455 13.28 0.00 41.78 3.36
2335 2348 4.199310 CCTGTTTGAAGAGGAAAGTGTCA 58.801 43.478 0.81 0.00 41.78 3.58
2337 2350 3.945285 TGTTTGAAGAGGAAAGTGTCACC 59.055 43.478 0.00 0.00 0.00 4.02
2373 2386 4.489771 GTGGGTGATGGAGGCGGG 62.490 72.222 0.00 0.00 0.00 6.13
2389 2405 2.123812 GGATCGAGGGGGACGACT 60.124 66.667 0.00 0.00 42.37 4.18
2407 2423 4.580995 ACGACTACGAAGATGATCCTGAAT 59.419 41.667 0.00 0.00 42.66 2.57
2451 2467 1.296715 GAAGAAGGCTGCGGAGGAA 59.703 57.895 5.93 0.00 0.00 3.36
2513 2529 3.821600 GGAGTGTCGAGATGCTAGGATTA 59.178 47.826 0.00 0.00 0.00 1.75
2521 2537 4.006319 GAGATGCTAGGATTATTGCCCAC 58.994 47.826 0.00 0.00 0.00 4.61
2529 2545 2.685897 GGATTATTGCCCACGCTGTTAA 59.314 45.455 0.00 0.00 35.36 2.01
2530 2546 3.488553 GGATTATTGCCCACGCTGTTAAC 60.489 47.826 0.00 0.00 35.36 2.01
2540 2556 0.319211 CGCTGTTAACGAGGACCACA 60.319 55.000 0.26 0.00 0.00 4.17
2559 2575 4.142773 CCACAAATTGCTCAAATGCATTCC 60.143 41.667 13.38 2.62 42.96 3.01
2567 2583 2.358267 CTCAAATGCATTCCTCTCAGCC 59.642 50.000 13.38 0.00 0.00 4.85
2581 2597 0.833287 TCAGCCATCTTCAGTAGCCC 59.167 55.000 0.00 0.00 0.00 5.19
2586 2602 1.576356 CATCTTCAGTAGCCCGAAGC 58.424 55.000 0.00 0.00 38.80 3.86
2604 2623 5.393787 CCGAAGCTGTAGTACATAACTTGGA 60.394 44.000 17.12 0.00 39.80 3.53
2610 2629 6.036191 GCTGTAGTACATAACTTGGAAGCTTC 59.964 42.308 18.54 18.54 39.80 3.86
2615 2634 7.727181 AGTACATAACTTGGAAGCTTCGATAT 58.273 34.615 19.91 8.55 33.35 1.63
2655 2674 5.995897 AGGGTATGTTCTTGTTACTTGTGAC 59.004 40.000 0.00 0.00 0.00 3.67
2662 2688 1.860676 TGTTACTTGTGACGCTCACC 58.139 50.000 13.24 1.32 46.40 4.02
2667 2693 1.354337 CTTGTGACGCTCACCCATCG 61.354 60.000 13.24 0.00 46.40 3.84
2670 2696 1.080093 TGACGCTCACCCATCGAAC 60.080 57.895 0.00 0.00 0.00 3.95
2676 2702 1.204941 GCTCACCCATCGAACTGTACT 59.795 52.381 0.00 0.00 0.00 2.73
2678 2704 3.512680 CTCACCCATCGAACTGTACTTC 58.487 50.000 0.00 0.00 0.00 3.01
2679 2705 2.094906 TCACCCATCGAACTGTACTTCG 60.095 50.000 10.18 10.18 43.65 3.79
2686 2712 4.556942 TCGAACTGTACTTCGAAGAACA 57.443 40.909 31.08 12.81 46.88 3.18
2699 2725 7.470079 ACTTCGAAGAACAACTTTTACCTTTC 58.530 34.615 31.08 0.00 45.90 2.62
2705 2731 8.441312 AAGAACAACTTTTACCTTTCGATGTA 57.559 30.769 0.00 0.00 34.94 2.29
2719 2745 6.984474 CCTTTCGATGTATTAACCTTCTAGCA 59.016 38.462 0.00 0.00 0.00 3.49
2735 2761 6.127310 CCTTCTAGCATAACTTGTACTGACCT 60.127 42.308 0.00 0.00 0.00 3.85
2781 2811 4.625324 GCCTGTACATTGGACTGGTATCAA 60.625 45.833 21.97 0.00 38.00 2.57
2792 2822 6.288294 TGGACTGGTATCAATACAAGCATAC 58.712 40.000 4.73 0.00 37.75 2.39
2869 2901 6.454795 TGGTAATTCTTGCATTTTCCTTGTC 58.545 36.000 0.00 0.00 0.00 3.18
2874 2906 5.705609 TCTTGCATTTTCCTTGTCCTTAC 57.294 39.130 0.00 0.00 0.00 2.34
2888 2920 3.252215 TGTCCTTACAAGCCATGTTTTCG 59.748 43.478 0.00 0.00 43.63 3.46
2892 2924 4.679654 CCTTACAAGCCATGTTTTCGTTTC 59.320 41.667 0.00 0.00 43.63 2.78
2896 2928 2.582052 AGCCATGTTTTCGTTTCCTCA 58.418 42.857 0.00 0.00 0.00 3.86
2909 2941 6.737254 TCGTTTCCTCATTATGAGTTTTCC 57.263 37.500 19.37 4.33 42.80 3.13
2910 2942 6.472887 TCGTTTCCTCATTATGAGTTTTCCT 58.527 36.000 19.37 0.00 42.80 3.36
2911 2943 6.371548 TCGTTTCCTCATTATGAGTTTTCCTG 59.628 38.462 19.37 4.14 42.80 3.86
2912 2944 6.325596 GTTTCCTCATTATGAGTTTTCCTGC 58.674 40.000 19.37 0.34 42.80 4.85
2913 2945 5.178096 TCCTCATTATGAGTTTTCCTGCA 57.822 39.130 19.37 0.00 42.80 4.41
2915 2947 4.096984 CCTCATTATGAGTTTTCCTGCACC 59.903 45.833 19.37 0.00 42.80 5.01
2916 2948 4.922206 TCATTATGAGTTTTCCTGCACCT 58.078 39.130 0.00 0.00 0.00 4.00
2919 2951 6.945435 TCATTATGAGTTTTCCTGCACCTAAA 59.055 34.615 0.00 0.00 0.00 1.85
2920 2952 6.569179 TTATGAGTTTTCCTGCACCTAAAC 57.431 37.500 5.20 5.20 0.00 2.01
2926 2961 5.010012 AGTTTTCCTGCACCTAAACAATGAG 59.990 40.000 12.61 0.00 33.94 2.90
2931 2966 4.154918 CCTGCACCTAAACAATGAGTTCTC 59.845 45.833 0.00 0.00 40.26 2.87
2938 2973 5.853282 CCTAAACAATGAGTTCTCAAAAGCG 59.147 40.000 6.60 0.00 40.26 4.68
2953 2988 8.186178 TCTCAAAAGCGAAGTTCATAGTATTC 57.814 34.615 3.32 0.00 0.00 1.75
2965 3000 4.631131 TCATAGTATTCGCACAGGAATGG 58.369 43.478 0.00 0.00 37.24 3.16
2983 3018 1.876799 TGGAACATGCCTTGTAACACG 59.123 47.619 0.00 0.00 37.68 4.49
2993 3028 3.502920 CCTTGTAACACGTGCAACAAAA 58.497 40.909 26.65 13.44 35.74 2.44
3046 3081 7.597643 CGAACTTGTCGCTTAAATGTAAAAA 57.402 32.000 0.00 0.00 44.14 1.94
3092 3231 7.973048 ACTAGTCTATTAATTGTGTCCTCCA 57.027 36.000 0.00 0.00 0.00 3.86
3094 3233 8.993424 ACTAGTCTATTAATTGTGTCCTCCAAT 58.007 33.333 0.00 0.00 34.07 3.16
3180 3319 4.392754 CAGATTGTGTGCTGTGCTACATTA 59.607 41.667 0.00 0.00 0.00 1.90
3256 3395 6.239036 GGCATAAGTTTTCACTTTCCTCTGTT 60.239 38.462 0.00 0.00 40.66 3.16
3268 3407 1.487976 TCCTCTGTTCATGGAGGCATC 59.512 52.381 10.09 0.00 46.22 3.91
3270 3409 0.548031 TCTGTTCATGGAGGCATCCC 59.452 55.000 16.13 0.00 46.04 3.85
3342 3481 1.542030 CAAGGACGCTGTAGAGTCTGT 59.458 52.381 13.98 0.00 43.10 3.41
3396 3535 2.209273 TGGTCGTCAATATTGCATCCG 58.791 47.619 10.76 9.75 0.00 4.18
3410 3549 2.362369 ATCCGTGCCACCTCTGGAG 61.362 63.158 0.00 0.00 40.55 3.86
3415 3554 1.157513 TGCCACCTCTGGAGTACCA 59.842 57.895 0.00 0.00 44.76 3.25
3425 3564 4.938226 CCTCTGGAGTACCAAAATGAAGAC 59.062 45.833 0.00 0.00 46.32 3.01
3427 3566 4.597507 TCTGGAGTACCAAAATGAAGACCT 59.402 41.667 0.00 0.00 46.32 3.85
3428 3567 4.906618 TGGAGTACCAAAATGAAGACCTC 58.093 43.478 0.00 0.00 43.91 3.85
3431 3570 5.946377 GGAGTACCAAAATGAAGACCTCAAT 59.054 40.000 0.00 0.00 35.22 2.57
3458 3597 0.606604 TAAACCAGCACTCGAGGACC 59.393 55.000 18.41 4.23 0.00 4.46
3485 3624 2.357517 CCGCTCGTGAAAGCCTGT 60.358 61.111 0.00 0.00 39.17 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.101582 AGTATGAGAACATCCCGCACTC 59.898 50.000 0.00 0.00 37.87 3.51
144 145 5.918608 ACTTCGATCATGTTAATGGCTACT 58.081 37.500 0.00 0.00 34.30 2.57
157 158 5.046529 GCTACTGATGTGAACTTCGATCAT 58.953 41.667 0.00 0.71 0.00 2.45
384 385 0.040514 CGTGGCTGAATTTGCGAACA 60.041 50.000 0.00 0.00 0.00 3.18
407 408 5.732331 TTCAAATCTGTGGGGGAGAATAT 57.268 39.130 0.00 0.00 0.00 1.28
539 540 0.603569 GATGATGCGGACGAGGGTAT 59.396 55.000 0.00 0.00 0.00 2.73
649 650 1.904990 GACAGGGCAGAGGGAAGGAC 61.905 65.000 0.00 0.00 0.00 3.85
798 799 5.471556 TTATTCGTCCAACTCAACAGGTA 57.528 39.130 0.00 0.00 0.00 3.08
799 800 2.930826 ATTCGTCCAACTCAACAGGT 57.069 45.000 0.00 0.00 0.00 4.00
800 801 5.682943 TTTTATTCGTCCAACTCAACAGG 57.317 39.130 0.00 0.00 0.00 4.00
822 823 3.544772 CCGGTGGGGCAAGTTTTT 58.455 55.556 0.00 0.00 0.00 1.94
833 834 4.524318 AACGATAGGCGCCGGTGG 62.524 66.667 23.20 17.15 46.04 4.61
834 835 3.261951 CAACGATAGGCGCCGGTG 61.262 66.667 23.20 14.56 46.04 4.94
839 840 2.403378 TTTGGGCAACGATAGGCGC 61.403 57.895 0.00 0.00 46.04 6.53
840 841 6.041372 ATATTGTTTGGGCAACGATAGGCG 62.041 45.833 0.00 0.00 42.68 5.52
841 842 0.885196 TTGTTTGGGCAACGATAGGC 59.115 50.000 0.00 0.00 38.36 3.93
842 843 5.163561 ACAATATTGTTTGGGCAACGATAGG 60.164 40.000 15.47 2.73 42.68 2.57
843 844 5.743398 CACAATATTGTTTGGGCAACGATAG 59.257 40.000 18.50 0.00 42.68 2.08
844 845 5.416013 TCACAATATTGTTTGGGCAACGATA 59.584 36.000 18.50 1.41 43.30 2.92
845 846 4.219507 TCACAATATTGTTTGGGCAACGAT 59.780 37.500 18.50 0.00 41.71 3.73
846 847 3.570125 TCACAATATTGTTTGGGCAACGA 59.430 39.130 18.50 6.84 39.91 3.85
847 848 3.906998 TCACAATATTGTTTGGGCAACG 58.093 40.909 18.50 4.58 39.91 4.10
848 849 6.610741 TTTTCACAATATTGTTTGGGCAAC 57.389 33.333 18.50 0.00 39.91 4.17
849 850 7.814264 AATTTTCACAATATTGTTTGGGCAA 57.186 28.000 18.50 6.61 39.91 4.52
850 851 7.814264 AAATTTTCACAATATTGTTTGGGCA 57.186 28.000 18.50 1.87 39.91 5.36
851 852 8.778358 TGTAAATTTTCACAATATTGTTTGGGC 58.222 29.630 18.50 5.41 39.91 5.36
883 884 8.358148 ACTGTAATTCTTTTTCTCGAGAGTACA 58.642 33.333 15.94 10.99 0.00 2.90
884 885 8.745464 ACTGTAATTCTTTTTCTCGAGAGTAC 57.255 34.615 15.94 6.93 0.00 2.73
930 931 5.869344 CGATGGGATGCGAGATAAAAAGATA 59.131 40.000 0.00 0.00 0.00 1.98
1521 1534 4.335647 AGGAGGCGGTGCACCTTG 62.336 66.667 32.28 19.50 37.77 3.61
1662 1675 3.948719 TGGCCGTGGGAGGTGTTC 61.949 66.667 0.00 0.00 0.00 3.18
1848 1861 3.329889 TCGGGCAGGCTGTGGAAT 61.330 61.111 17.16 0.00 0.00 3.01
1986 1999 2.049156 CTGCGGAAGTGCGTGAGA 60.049 61.111 0.00 0.00 37.81 3.27
2067 2080 2.892425 CGGACGCCCTTGATGCTC 60.892 66.667 0.00 0.00 0.00 4.26
2167 2180 1.118965 TCACGGACAAGCTCCTCCAA 61.119 55.000 9.69 0.00 36.80 3.53
2184 2197 2.238144 CCTTCTGATCTTCTTGCCCTCA 59.762 50.000 0.00 0.00 0.00 3.86
2203 2216 0.853530 ACACCCTTCTTTTGAGCCCT 59.146 50.000 0.00 0.00 0.00 5.19
2210 2223 3.101437 ACCGGAAAAACACCCTTCTTTT 58.899 40.909 9.46 0.00 0.00 2.27
2241 2254 4.168871 TCTTCCTCATCCTCCTCATCACTA 59.831 45.833 0.00 0.00 0.00 2.74
2253 2266 5.766670 TGCAACATTATCATCTTCCTCATCC 59.233 40.000 0.00 0.00 0.00 3.51
2289 2302 2.102578 CCAAATTCACCATCCACCTCC 58.897 52.381 0.00 0.00 0.00 4.30
2310 2323 4.199310 CACTTTCCTCTTCAAACAGGTCA 58.801 43.478 0.00 0.00 0.00 4.02
2325 2338 0.605589 CTTCCCCGGTGACACTTTCC 60.606 60.000 5.39 0.00 0.00 3.13
2328 2341 0.763223 AGTCTTCCCCGGTGACACTT 60.763 55.000 5.39 0.00 33.56 3.16
2335 2348 0.546747 TCATTCCAGTCTTCCCCGGT 60.547 55.000 0.00 0.00 0.00 5.28
2337 2350 0.179000 CCTCATTCCAGTCTTCCCCG 59.821 60.000 0.00 0.00 0.00 5.73
2373 2386 1.505477 CGTAGTCGTCCCCCTCGATC 61.505 65.000 0.00 0.00 39.45 3.69
2389 2405 4.142038 TCCGATTCAGGATCATCTTCGTA 58.858 43.478 0.00 0.00 34.92 3.43
2407 2423 0.982852 AACTCCTCCATGGCATCCGA 60.983 55.000 6.96 0.00 35.26 4.55
2451 2467 2.839098 CCACTGTCAACCAGCCCT 59.161 61.111 0.00 0.00 45.68 5.19
2513 2529 0.604243 TCGTTAACAGCGTGGGCAAT 60.604 50.000 6.39 0.00 43.41 3.56
2521 2537 0.319211 TGTGGTCCTCGTTAACAGCG 60.319 55.000 6.39 0.00 0.00 5.18
2529 2545 3.725754 AGCAATTTGTGGTCCTCGT 57.274 47.368 0.00 0.00 29.87 4.18
2559 2575 2.224018 GGCTACTGAAGATGGCTGAGAG 60.224 54.545 0.00 0.00 0.00 3.20
2581 2597 5.647589 TCCAAGTTATGTACTACAGCTTCG 58.352 41.667 0.00 0.00 35.54 3.79
2586 2602 6.253727 CGAAGCTTCCAAGTTATGTACTACAG 59.746 42.308 20.62 0.00 35.54 2.74
2587 2603 6.071784 TCGAAGCTTCCAAGTTATGTACTACA 60.072 38.462 20.62 0.00 35.54 2.74
2588 2604 6.327934 TCGAAGCTTCCAAGTTATGTACTAC 58.672 40.000 20.62 0.00 35.54 2.73
2604 2623 4.446371 CCTCACCTTCAATATCGAAGCTT 58.554 43.478 0.00 0.00 40.94 3.74
2610 2629 3.819564 TCACCCTCACCTTCAATATCG 57.180 47.619 0.00 0.00 0.00 2.92
2615 2634 0.771127 CCCTTCACCCTCACCTTCAA 59.229 55.000 0.00 0.00 0.00 2.69
2655 2674 0.172578 TACAGTTCGATGGGTGAGCG 59.827 55.000 0.00 0.00 33.68 5.03
2667 2693 6.585389 AAGTTGTTCTTCGAAGTACAGTTC 57.415 37.500 28.73 23.17 37.56 3.01
2670 2696 7.224167 AGGTAAAAGTTGTTCTTCGAAGTACAG 59.776 37.037 28.73 6.25 37.56 2.74
2676 2702 6.313411 TCGAAAGGTAAAAGTTGTTCTTCGAA 59.687 34.615 0.00 0.00 35.02 3.71
2678 2704 6.039781 TCGAAAGGTAAAAGTTGTTCTTCG 57.960 37.500 0.00 0.00 35.02 3.79
2679 2705 7.415229 ACATCGAAAGGTAAAAGTTGTTCTTC 58.585 34.615 0.00 0.00 35.02 2.87
2680 2706 7.329588 ACATCGAAAGGTAAAAGTTGTTCTT 57.670 32.000 0.00 0.00 38.10 2.52
2681 2707 6.937436 ACATCGAAAGGTAAAAGTTGTTCT 57.063 33.333 0.00 0.00 0.00 3.01
2685 2711 9.550811 GGTTAATACATCGAAAGGTAAAAGTTG 57.449 33.333 0.00 0.00 0.00 3.16
2686 2712 9.511272 AGGTTAATACATCGAAAGGTAAAAGTT 57.489 29.630 0.00 0.00 0.00 2.66
2699 2725 9.477484 AAGTTATGCTAGAAGGTTAATACATCG 57.523 33.333 0.00 0.00 0.00 3.84
2705 2731 9.601217 CAGTACAAGTTATGCTAGAAGGTTAAT 57.399 33.333 0.00 0.00 0.00 1.40
2716 2742 4.891992 ACAGGTCAGTACAAGTTATGCT 57.108 40.909 0.00 0.00 0.00 3.79
2719 2745 9.841295 TTTCTTAAACAGGTCAGTACAAGTTAT 57.159 29.630 0.00 0.00 0.00 1.89
2722 2748 8.570068 TTTTTCTTAAACAGGTCAGTACAAGT 57.430 30.769 0.00 0.00 0.00 3.16
2757 2783 1.362224 ACCAGTCCAATGTACAGGCT 58.638 50.000 0.33 0.00 0.00 4.58
2758 2784 3.118408 TGATACCAGTCCAATGTACAGGC 60.118 47.826 0.33 0.00 0.00 4.85
2765 2791 5.589855 TGCTTGTATTGATACCAGTCCAATG 59.410 40.000 0.00 0.00 33.21 2.82
2768 2794 4.835284 TGCTTGTATTGATACCAGTCCA 57.165 40.909 4.71 0.00 30.93 4.02
2781 2811 8.630054 TTAACAAGAAACTGGTATGCTTGTAT 57.370 30.769 0.00 0.00 45.84 2.29
2792 2822 8.417884 TGGGAACTAAATTTAACAAGAAACTGG 58.582 33.333 0.00 0.00 0.00 4.00
2812 2843 5.659440 TGCAAGGATCTTATTTTGGGAAC 57.341 39.130 0.00 0.00 0.00 3.62
2821 2852 5.104193 AGAGGACAACATGCAAGGATCTTAT 60.104 40.000 0.00 0.00 0.00 1.73
2823 2854 3.009916 AGAGGACAACATGCAAGGATCTT 59.990 43.478 0.00 0.00 0.00 2.40
2830 2861 3.500448 TTACCAGAGGACAACATGCAA 57.500 42.857 0.00 0.00 0.00 4.08
2869 2901 3.915437 ACGAAAACATGGCTTGTAAGG 57.085 42.857 6.44 0.27 37.68 2.69
2874 2906 3.243367 TGAGGAAACGAAAACATGGCTTG 60.243 43.478 0.00 0.00 0.00 4.01
2896 2928 6.719370 TGTTTAGGTGCAGGAAAACTCATAAT 59.281 34.615 15.02 0.00 33.89 1.28
2909 2941 4.756642 TGAGAACTCATTGTTTAGGTGCAG 59.243 41.667 0.00 0.00 39.30 4.41
2910 2942 4.713553 TGAGAACTCATTGTTTAGGTGCA 58.286 39.130 0.00 0.00 39.30 4.57
2911 2943 5.689383 TTGAGAACTCATTGTTTAGGTGC 57.311 39.130 5.34 0.00 39.30 5.01
2912 2944 6.638468 GCTTTTGAGAACTCATTGTTTAGGTG 59.362 38.462 5.34 0.00 39.30 4.00
2913 2945 6.513393 CGCTTTTGAGAACTCATTGTTTAGGT 60.513 38.462 5.34 0.00 39.30 3.08
2915 2947 6.658831 TCGCTTTTGAGAACTCATTGTTTAG 58.341 36.000 5.34 0.09 39.30 1.85
2916 2948 6.612247 TCGCTTTTGAGAACTCATTGTTTA 57.388 33.333 5.34 0.00 39.30 2.01
2919 2951 4.576463 ACTTCGCTTTTGAGAACTCATTGT 59.424 37.500 5.34 0.00 39.64 2.71
2920 2952 5.100751 ACTTCGCTTTTGAGAACTCATTG 57.899 39.130 5.34 1.25 39.64 2.82
2926 2961 6.229561 ACTATGAACTTCGCTTTTGAGAAC 57.770 37.500 0.00 0.00 34.62 3.01
2938 2973 5.348986 TCCTGTGCGAATACTATGAACTTC 58.651 41.667 0.00 0.00 0.00 3.01
2953 2988 0.179156 GCATGTTCCATTCCTGTGCG 60.179 55.000 0.00 0.00 0.00 5.34
2965 3000 2.916111 CACGTGTTACAAGGCATGTTC 58.084 47.619 7.58 0.00 43.63 3.18
2997 3032 1.895131 CTGCCAACAAAGCCCATACTT 59.105 47.619 0.00 0.00 0.00 2.24
2998 3033 1.549203 CTGCCAACAAAGCCCATACT 58.451 50.000 0.00 0.00 0.00 2.12
2999 3034 0.532115 CCTGCCAACAAAGCCCATAC 59.468 55.000 0.00 0.00 0.00 2.39
3000 3035 0.407528 TCCTGCCAACAAAGCCCATA 59.592 50.000 0.00 0.00 0.00 2.74
3001 3036 0.252375 ATCCTGCCAACAAAGCCCAT 60.252 50.000 0.00 0.00 0.00 4.00
3002 3037 1.155859 ATCCTGCCAACAAAGCCCA 59.844 52.632 0.00 0.00 0.00 5.36
3005 3040 1.444895 CGCATCCTGCCAACAAAGC 60.445 57.895 0.00 0.00 41.12 3.51
3006 3041 0.597568 TTCGCATCCTGCCAACAAAG 59.402 50.000 0.00 0.00 41.12 2.77
3009 3044 0.537143 AAGTTCGCATCCTGCCAACA 60.537 50.000 11.24 0.00 44.96 3.33
3010 3045 0.109597 CAAGTTCGCATCCTGCCAAC 60.110 55.000 1.98 1.98 43.30 3.77
3023 3058 8.556517 AGTTTTTACATTTAAGCGACAAGTTC 57.443 30.769 0.00 0.00 0.00 3.01
3069 3208 9.838339 AATTGGAGGACACAATTAATAGACTAG 57.162 33.333 1.90 0.00 44.27 2.57
3094 3233 8.364142 CCACCAATATCAAAAAGACCTAAACAA 58.636 33.333 0.00 0.00 0.00 2.83
3100 3239 5.010708 ACCCACCAATATCAAAAAGACCT 57.989 39.130 0.00 0.00 0.00 3.85
3238 3377 5.299279 TCCATGAACAGAGGAAAGTGAAAAC 59.701 40.000 0.00 0.00 0.00 2.43
3242 3381 4.277515 CTCCATGAACAGAGGAAAGTGA 57.722 45.455 0.00 0.00 0.00 3.41
3268 3407 1.916181 ACATTGTTGTCCTAGAGGGGG 59.084 52.381 0.00 0.00 35.41 5.40
3320 3459 2.029828 CAGACTCTACAGCGTCCTTGTT 60.030 50.000 0.00 0.00 30.53 2.83
3342 3481 1.555075 GTAGCTTGGGAGTGGTCATCA 59.445 52.381 0.00 0.00 0.00 3.07
3396 3535 1.192146 TGGTACTCCAGAGGTGGCAC 61.192 60.000 9.70 9.70 44.60 5.01
3400 3539 4.286297 TCATTTTGGTACTCCAGAGGTG 57.714 45.455 0.00 0.00 45.22 4.00
3410 3549 6.208599 TCCAATTGAGGTCTTCATTTTGGTAC 59.791 38.462 18.72 0.00 43.36 3.34
3415 3554 7.365497 AGTTTCCAATTGAGGTCTTCATTTT 57.635 32.000 7.12 0.00 35.27 1.82
3425 3564 4.280677 TGCTGGTTTAGTTTCCAATTGAGG 59.719 41.667 7.12 0.00 33.06 3.86
3427 3566 4.892934 AGTGCTGGTTTAGTTTCCAATTGA 59.107 37.500 7.12 0.00 33.06 2.57
3428 3567 5.200368 AGTGCTGGTTTAGTTTCCAATTG 57.800 39.130 0.00 0.00 33.06 2.32
3431 3570 2.875933 CGAGTGCTGGTTTAGTTTCCAA 59.124 45.455 0.00 0.00 33.06 3.53
3458 3597 4.498520 ACGAGCGGTGATCCTGCG 62.499 66.667 0.00 0.00 37.94 5.18


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

AutoCloner maintained by Alex Coulton.