Multiple sequence alignment - TraesCS5B01G376500

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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 TraesCS5B01G376500 chr5B 100.000 3241 0 0 1 3241 554517585 554514345 0.000000e+00 5986.0
1 TraesCS5B01G376500 chr5B 84.277 477 71 4 2767 3241 33628672 33628198 2.280000e-126 462.0
2 TraesCS5B01G376500 chr5B 98.864 88 1 0 2668 2755 554514833 554514746 1.200000e-34 158.0
3 TraesCS5B01G376500 chr5B 98.864 88 1 0 2753 2840 554514918 554514831 1.200000e-34 158.0
4 TraesCS5B01G376500 chr5B 90.588 85 7 1 682 766 391148409 391148492 9.510000e-21 111.0
5 TraesCS5B01G376500 chr5B 90.698 86 5 3 682 766 393069275 393069192 9.510000e-21 111.0
6 TraesCS5B01G376500 chr5D 92.449 2119 96 22 254 2365 453819044 453816983 0.000000e+00 2968.0
7 TraesCS5B01G376500 chr5D 96.728 489 16 0 2753 3241 453816602 453816114 0.000000e+00 815.0
8 TraesCS5B01G376500 chr5D 94.960 377 12 3 2376 2752 453816887 453816518 4.660000e-163 584.0
9 TraesCS5B01G376500 chr5D 83.019 477 77 4 2767 3241 40091747 40092221 2.310000e-116 429.0
10 TraesCS5B01G376500 chr5D 84.956 113 8 6 676 787 528755099 528754995 4.420000e-19 106.0
11 TraesCS5B01G376500 chr5A 94.637 1734 77 6 569 2302 572842978 572841261 0.000000e+00 2673.0
12 TraesCS5B01G376500 chr5A 96.728 489 16 0 2753 3241 572840780 572840292 0.000000e+00 815.0
13 TraesCS5B01G376500 chr5A 91.681 601 26 6 1 590 572843741 572843154 0.000000e+00 811.0
14 TraesCS5B01G376500 chr5A 89.974 379 17 4 2376 2752 572841055 572840696 1.360000e-128 470.0
15 TraesCS5B01G376500 chr5A 83.925 479 73 4 2765 3241 28104117 28104593 3.810000e-124 455.0
16 TraesCS5B01G376500 chr5A 91.579 95 5 3 2273 2365 572841258 572841165 9.440000e-26 128.0
17 TraesCS5B01G376500 chr1A 92.941 85 5 1 682 766 568391202 568391285 4.390000e-24 122.0
18 TraesCS5B01G376500 chr2D 90.698 86 5 3 682 766 61023794 61023711 9.510000e-21 111.0
19 TraesCS5B01G376500 chr1D 90.698 86 5 3 682 766 10183703 10183786 9.510000e-21 111.0
20 TraesCS5B01G376500 chr1B 88.172 93 7 4 682 773 608052565 608052476 1.230000e-19 108.0
21 TraesCS5B01G376500 chr7D 89.362 47 5 0 490 536 36488403 36488357 3.490000e-05 60.2


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 TraesCS5B01G376500 chr5B 554514345 554517585 3240 True 2100.666667 5986 99.242667 1 3241 3 chr5B.!!$R3 3240
1 TraesCS5B01G376500 chr5D 453816114 453819044 2930 True 1455.666667 2968 94.712333 254 3241 3 chr5D.!!$R2 2987
2 TraesCS5B01G376500 chr5A 572840292 572843741 3449 True 979.400000 2673 92.919800 1 3241 5 chr5A.!!$R1 3240

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
23 24 0.766674 ATGCAGAGGCCGGGGTAATA 60.767 55.0 2.18 0.0 40.13 0.98 F
1200 1409 0.393944 GGTACTTAGCCCTGCCCAAC 60.394 60.0 0.00 0.0 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1742 1952 0.036732 AAGACGGCCATTGCAAGAGA 59.963 50.0 4.94 0.0 40.13 3.10 R
2734 3081 0.169009 GTCGCAACTTTGGAGGATGC 59.831 55.0 0.00 0.0 36.84 3.91 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
20 21 3.161450 GATGCAGAGGCCGGGGTA 61.161 66.667 2.18 0.00 40.13 3.69
23 24 0.766674 ATGCAGAGGCCGGGGTAATA 60.767 55.000 2.18 0.00 40.13 0.98
111 122 4.473520 CCCCTGCTAGCACACCCG 62.474 72.222 14.93 3.32 0.00 5.28
118 129 1.972198 CTAGCACACCCGAGAACCA 59.028 57.895 0.00 0.00 0.00 3.67
124 135 2.356135 CACACCCGAGAACCATTTAGG 58.644 52.381 0.00 0.00 45.67 2.69
133 144 4.686122 CGAGAACCATTTAGGCATAAGGGT 60.686 45.833 9.84 9.84 43.14 4.34
240 251 9.191995 GTGCTTAAATAACAATTGCTTGTAGTT 57.808 29.630 5.05 1.74 44.83 2.24
265 276 7.695480 TTTACCTAGCACATTAAAATCTGCA 57.305 32.000 5.86 0.00 33.44 4.41
421 432 8.186821 CCTAAGAAAATTCAGGAGCATTTGTAG 58.813 37.037 0.00 0.00 0.00 2.74
422 433 7.530426 AAGAAAATTCAGGAGCATTTGTAGT 57.470 32.000 0.00 0.00 0.00 2.73
423 434 7.530426 AGAAAATTCAGGAGCATTTGTAGTT 57.470 32.000 0.00 0.00 0.00 2.24
424 435 7.955918 AGAAAATTCAGGAGCATTTGTAGTTT 58.044 30.769 0.00 0.00 0.00 2.66
425 436 8.424133 AGAAAATTCAGGAGCATTTGTAGTTTT 58.576 29.630 0.00 0.00 0.00 2.43
426 437 7.951530 AAATTCAGGAGCATTTGTAGTTTTG 57.048 32.000 0.00 0.00 0.00 2.44
427 438 6.655078 ATTCAGGAGCATTTGTAGTTTTGT 57.345 33.333 0.00 0.00 0.00 2.83
469 480 3.953612 AGAATTTTCGCCTCATGCCAATA 59.046 39.130 0.00 0.00 36.24 1.90
516 528 3.327404 TGAAACCCCCGGCCTCTC 61.327 66.667 0.00 0.00 0.00 3.20
525 537 1.528824 CCGGCCTCTCCATCATTGT 59.471 57.895 0.00 0.00 34.01 2.71
662 871 4.202245 TCCTGTGTGGTAGTGAATTAGC 57.798 45.455 0.00 0.00 37.07 3.09
703 912 6.042093 TGTTACTCCCTCTGATCCATATTCAC 59.958 42.308 0.00 0.00 0.00 3.18
743 952 5.178809 ACAACTTTGTACTAAATCAGCGACC 59.821 40.000 0.00 0.00 40.16 4.79
815 1024 3.754965 TGCAAAATCCTGCTACTCTTGT 58.245 40.909 0.00 0.00 43.07 3.16
850 1059 4.199310 TCTCTCCAAAGAAAACCTGTGTG 58.801 43.478 0.00 0.00 0.00 3.82
882 1091 6.868339 CCTGTCCTTTATCAAACAAATTGTCC 59.132 38.462 0.00 0.00 40.11 4.02
895 1104 5.553123 ACAAATTGTCCATTGAATGTGCAT 58.447 33.333 4.27 0.00 0.00 3.96
999 1208 0.952497 ATTGTGACAGAGTGCTGCGG 60.952 55.000 0.00 0.00 46.26 5.69
1044 1253 1.003580 TCCTTCATTGCCACCAGAGTC 59.996 52.381 0.00 0.00 0.00 3.36
1137 1346 1.395635 TCGCTACGTGGTATGGTGAT 58.604 50.000 0.00 0.00 0.00 3.06
1200 1409 0.393944 GGTACTTAGCCCTGCCCAAC 60.394 60.000 0.00 0.00 0.00 3.77
1423 1633 1.153309 TGAGGCCATGAGCATGACG 60.153 57.895 5.01 0.00 46.50 4.35
1436 1646 1.733389 GCATGACGGCAAATTGTCTGG 60.733 52.381 0.00 0.00 36.10 3.86
1474 1684 7.770433 CAGTAATCTTGATTTCATCAGGTGGTA 59.230 37.037 0.95 0.00 40.94 3.25
1570 1780 2.409651 CTGAGCGGGCTAGTCGAC 59.590 66.667 7.70 7.70 0.00 4.20
1585 1795 2.022129 CGACGGACAGTGCCAGAAC 61.022 63.158 0.00 0.00 0.00 3.01
1651 1861 0.962356 CGAAACCTGGCCAAGCTGAT 60.962 55.000 7.01 0.00 0.00 2.90
1681 1891 1.669999 GCGCTGGCCTCATCCAAATT 61.670 55.000 3.32 0.00 35.36 1.82
1735 1945 8.258708 GGAACATATATAGGTCATGGTTACTCC 58.741 40.741 0.00 0.00 0.00 3.85
1742 1952 2.505819 GGTCATGGTTACTCCTCATGGT 59.494 50.000 0.00 0.00 38.87 3.55
1768 1978 3.616219 TGCAATGGCCGTCTTTTATAGT 58.384 40.909 0.00 0.00 40.13 2.12
1780 1990 6.645415 CCGTCTTTTATAGTCGCCATTAATCT 59.355 38.462 0.00 0.00 34.66 2.40
1783 1993 8.827677 GTCTTTTATAGTCGCCATTAATCTGTT 58.172 33.333 0.00 0.00 0.00 3.16
1796 2006 7.331687 GCCATTAATCTGTTGTGTTAGCATTTT 59.668 33.333 0.00 0.00 0.00 1.82
1799 2009 6.529463 AATCTGTTGTGTTAGCATTTTTGC 57.471 33.333 0.00 0.00 0.00 3.68
1943 2153 2.879070 CGACATCATGCAGAGCGGC 61.879 63.158 0.00 0.00 0.00 6.53
2005 2215 2.664851 CGCGGTGTGGAAGCTCAA 60.665 61.111 0.00 0.00 0.00 3.02
2006 2216 2.946762 GCGGTGTGGAAGCTCAAC 59.053 61.111 0.00 0.00 0.00 3.18
2219 2429 0.908198 ATCACCTCCTCCTGTTGCTC 59.092 55.000 0.00 0.00 0.00 4.26
2226 2436 1.310933 CCTCCTGTTGCTCATGGTGC 61.311 60.000 0.00 0.00 0.00 5.01
2246 2456 0.178995 TGTTCCAGCTGTGATGCCAA 60.179 50.000 13.81 0.00 0.00 4.52
2248 2458 0.609957 TTCCAGCTGTGATGCCAAGG 60.610 55.000 13.81 0.00 0.00 3.61
2251 2461 0.896940 CAGCTGTGATGCCAAGGGTT 60.897 55.000 5.25 0.00 0.00 4.11
2305 2547 0.827368 AGTGTAGCTTAGCCTGGAGC 59.173 55.000 0.00 0.00 44.25 4.70
2308 2550 0.391228 GTAGCTTAGCCTGGAGCCTC 59.609 60.000 0.00 0.00 45.47 4.70
2354 2601 0.969149 AAACCTTAAGCAGCTTGGCC 59.031 50.000 18.54 0.00 0.00 5.36
2411 2758 6.564709 TGTGACCAAGATGATCTTTCTTTG 57.435 37.500 4.67 8.06 33.78 2.77
2412 2759 6.298361 TGTGACCAAGATGATCTTTCTTTGA 58.702 36.000 4.67 0.00 33.78 2.69
2431 2778 6.820470 TTTGAAAGGCAAACAAAGATAACG 57.180 33.333 0.00 0.00 41.37 3.18
2537 2884 8.916654 GCATAATACAGTACAGTTATGTAGCTG 58.083 37.037 0.00 2.81 42.53 4.24
2606 2953 3.244078 ACAATGAACACCTCGCTACAAGA 60.244 43.478 0.00 0.00 0.00 3.02
2715 3062 2.625823 AACGGCGGCAACAATCTGG 61.626 57.895 13.24 0.00 0.00 3.86
2716 3063 3.814268 CGGCGGCAACAATCTGGG 61.814 66.667 10.53 0.00 0.00 4.45
2717 3064 4.133796 GGCGGCAACAATCTGGGC 62.134 66.667 3.07 0.00 0.00 5.36
2718 3065 3.372730 GCGGCAACAATCTGGGCA 61.373 61.111 0.00 0.00 0.00 5.36
2719 3066 2.879907 CGGCAACAATCTGGGCAG 59.120 61.111 0.00 0.00 0.00 4.85
2720 3067 2.703798 CGGCAACAATCTGGGCAGG 61.704 63.158 0.00 0.00 0.00 4.85
2721 3068 2.575461 GCAACAATCTGGGCAGGC 59.425 61.111 0.00 0.00 0.00 4.85
2722 3069 1.980772 GCAACAATCTGGGCAGGCT 60.981 57.895 0.00 0.00 0.00 4.58
2723 3070 1.888018 CAACAATCTGGGCAGGCTG 59.112 57.895 10.94 10.94 0.00 4.85
2724 3071 1.980772 AACAATCTGGGCAGGCTGC 60.981 57.895 30.93 30.93 44.08 5.25
2734 3081 3.716006 CAGGCTGCACGACGGTTG 61.716 66.667 0.00 0.00 0.00 3.77
2737 3084 3.726517 GCTGCACGACGGTTGCAT 61.727 61.111 12.80 0.00 37.95 3.96
2738 3085 2.476051 CTGCACGACGGTTGCATC 59.524 61.111 12.80 0.00 37.95 3.91
2739 3086 3.027170 CTGCACGACGGTTGCATCC 62.027 63.158 12.80 3.51 37.95 3.51
2740 3087 2.742372 GCACGACGGTTGCATCCT 60.742 61.111 11.96 0.00 0.00 3.24
2741 3088 2.740714 GCACGACGGTTGCATCCTC 61.741 63.158 11.96 7.51 0.00 3.71
2742 3089 2.100631 CACGACGGTTGCATCCTCC 61.101 63.158 11.96 2.79 0.00 4.30
2743 3090 2.264480 CGACGGTTGCATCCTCCA 59.736 61.111 11.96 0.00 0.00 3.86
2744 3091 1.375396 CGACGGTTGCATCCTCCAA 60.375 57.895 11.96 0.00 0.00 3.53
2745 3092 0.953471 CGACGGTTGCATCCTCCAAA 60.953 55.000 11.96 0.00 0.00 3.28
2746 3093 0.804989 GACGGTTGCATCCTCCAAAG 59.195 55.000 11.96 0.00 0.00 2.77
2747 3094 0.110486 ACGGTTGCATCCTCCAAAGT 59.890 50.000 11.96 0.00 0.00 2.66
2748 3095 1.247567 CGGTTGCATCCTCCAAAGTT 58.752 50.000 11.96 0.00 0.00 2.66
2749 3096 1.068333 CGGTTGCATCCTCCAAAGTTG 60.068 52.381 11.96 0.00 0.00 3.16
2750 3097 1.337167 GGTTGCATCCTCCAAAGTTGC 60.337 52.381 6.56 0.00 32.91 4.17
2751 3098 0.597568 TTGCATCCTCCAAAGTTGCG 59.402 50.000 0.00 0.00 34.24 4.85
2752 3099 0.250684 TGCATCCTCCAAAGTTGCGA 60.251 50.000 0.00 0.00 34.24 5.10
2753 3100 0.169009 GCATCCTCCAAAGTTGCGAC 59.831 55.000 0.00 0.00 0.00 5.19
2754 3101 1.522668 CATCCTCCAAAGTTGCGACA 58.477 50.000 6.90 0.00 0.00 4.35
2755 3102 1.466167 CATCCTCCAAAGTTGCGACAG 59.534 52.381 6.90 0.00 0.00 3.51
2756 3103 0.756294 TCCTCCAAAGTTGCGACAGA 59.244 50.000 6.90 0.00 0.00 3.41
2757 3104 1.347707 TCCTCCAAAGTTGCGACAGAT 59.652 47.619 6.90 0.00 0.00 2.90
2758 3105 1.466167 CCTCCAAAGTTGCGACAGATG 59.534 52.381 6.90 1.99 0.00 2.90
2759 3106 2.416747 CTCCAAAGTTGCGACAGATGA 58.583 47.619 6.90 0.00 0.00 2.92
2760 3107 3.005554 CTCCAAAGTTGCGACAGATGAT 58.994 45.455 6.90 0.00 0.00 2.45
2761 3108 2.743664 TCCAAAGTTGCGACAGATGATG 59.256 45.455 6.90 0.00 0.00 3.07
2762 3109 2.512885 CAAAGTTGCGACAGATGATGC 58.487 47.619 6.90 0.00 0.00 3.91
2763 3110 1.089920 AAGTTGCGACAGATGATGCC 58.910 50.000 6.90 0.00 0.00 4.40
2764 3111 0.745845 AGTTGCGACAGATGATGCCC 60.746 55.000 6.90 0.00 0.00 5.36
2765 3112 0.745845 GTTGCGACAGATGATGCCCT 60.746 55.000 0.00 0.00 0.00 5.19
2766 3113 0.829990 TTGCGACAGATGATGCCCTA 59.170 50.000 0.00 0.00 0.00 3.53
2767 3114 1.051008 TGCGACAGATGATGCCCTAT 58.949 50.000 0.00 0.00 0.00 2.57
2768 3115 1.417517 TGCGACAGATGATGCCCTATT 59.582 47.619 0.00 0.00 0.00 1.73
2769 3116 1.802960 GCGACAGATGATGCCCTATTG 59.197 52.381 0.00 0.00 0.00 1.90
2770 3117 2.420642 CGACAGATGATGCCCTATTGG 58.579 52.381 0.00 0.00 37.09 3.16
2788 3135 2.858729 GCATATTTGCTCAACGGCG 58.141 52.632 4.80 4.80 45.77 6.46
2789 3136 0.592247 GCATATTTGCTCAACGGCGG 60.592 55.000 13.24 0.00 45.77 6.13
2790 3137 0.592247 CATATTTGCTCAACGGCGGC 60.592 55.000 13.24 5.21 34.52 6.53
2791 3138 1.029408 ATATTTGCTCAACGGCGGCA 61.029 50.000 13.24 8.34 34.52 5.69
2792 3139 1.237954 TATTTGCTCAACGGCGGCAA 61.238 50.000 15.51 15.51 42.97 4.52
2793 3140 2.747507 ATTTGCTCAACGGCGGCAAC 62.748 55.000 18.39 1.93 44.08 4.17
2795 3142 3.959975 GCTCAACGGCGGCAACAA 61.960 61.111 13.24 0.00 0.00 2.83
2796 3143 2.953821 CTCAACGGCGGCAACAAT 59.046 55.556 13.24 0.00 0.00 2.71
2797 3144 1.154225 CTCAACGGCGGCAACAATC 60.154 57.895 13.24 0.00 0.00 2.67
2798 3145 1.577328 CTCAACGGCGGCAACAATCT 61.577 55.000 13.24 0.00 0.00 2.40
2799 3146 1.442520 CAACGGCGGCAACAATCTG 60.443 57.895 13.24 0.00 0.00 2.90
2839 3186 1.074775 ATCCTCCAAAGTTGCGGCA 59.925 52.632 0.00 0.00 0.00 5.69
2845 3192 1.139520 CAAAGTTGCGGCATAGGGC 59.860 57.895 2.28 0.00 43.74 5.19
2883 3230 2.215451 GACAGGCACATGATGGGGGT 62.215 60.000 0.00 0.00 0.00 4.95
3049 3396 3.116300 CGACCTAATGTCAATCACCTCG 58.884 50.000 0.00 0.00 44.71 4.63
3052 3399 2.485479 CCTAATGTCAATCACCTCGGGG 60.485 54.545 0.00 0.00 38.88 5.73
3187 3534 2.918549 GCATAGCGTGTACTCCTCATCG 60.919 54.545 0.00 0.00 0.00 3.84
3213 3560 6.264518 GGAATTTTCTCCTTCAGGTTGTACAA 59.735 38.462 3.59 3.59 36.34 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 9.868277 AACAAAAATTGTCTTAGACATTGTGAA 57.132 25.926 23.89 8.33 44.59 3.18
77 78 7.971368 AGCAGGGGTACATATAACAAAAATT 57.029 32.000 0.00 0.00 0.00 1.82
111 122 4.793201 ACCCTTATGCCTAAATGGTTCTC 58.207 43.478 0.00 0.00 38.35 2.87
118 129 8.552296 CATCTAGGATAACCCTTATGCCTAAAT 58.448 37.037 0.00 0.00 44.85 1.40
133 144 7.287696 TCTGTGTTATCACTGCATCTAGGATAA 59.712 37.037 5.57 0.00 44.14 1.75
230 241 5.369833 TGTGCTAGGTAAAAACTACAAGCA 58.630 37.500 6.94 6.94 36.38 3.91
265 276 8.827177 TCTGATACACTTAAAATGAAACGAGT 57.173 30.769 0.00 0.00 0.00 4.18
395 406 6.928520 ACAAATGCTCCTGAATTTTCTTAGG 58.071 36.000 0.00 0.00 29.22 2.69
525 537 1.913778 AAGAATGGCTGTGTGCATCA 58.086 45.000 0.00 0.00 45.15 3.07
636 845 4.336889 TTCACTACCACACAGGAAAGAG 57.663 45.455 0.00 0.00 41.22 2.85
637 846 4.974645 ATTCACTACCACACAGGAAAGA 57.025 40.909 0.00 0.00 41.22 2.52
638 847 5.122396 GCTAATTCACTACCACACAGGAAAG 59.878 44.000 0.00 0.00 41.22 2.62
639 848 5.001232 GCTAATTCACTACCACACAGGAAA 58.999 41.667 0.00 0.00 41.22 3.13
640 849 4.575885 GCTAATTCACTACCACACAGGAA 58.424 43.478 0.00 0.00 41.22 3.36
641 850 3.368013 CGCTAATTCACTACCACACAGGA 60.368 47.826 0.00 0.00 41.22 3.86
642 851 2.930040 CGCTAATTCACTACCACACAGG 59.070 50.000 0.00 0.00 45.67 4.00
662 871 5.516339 GGAGTAACAAAAATGGCATCAATCG 59.484 40.000 0.00 0.00 0.00 3.34
703 912 6.073765 ACAAAGTTGTACTAAATCAGCGACAG 60.074 38.462 0.00 0.00 40.16 3.51
743 952 2.094026 TCCGCTCCGATCCATATCAATG 60.094 50.000 0.00 0.00 31.93 2.82
815 1024 2.677914 TGGAGAGAGGACACACTGAAA 58.322 47.619 0.00 0.00 0.00 2.69
850 1059 3.492102 TGATAAAGGACAGGCCATAGC 57.508 47.619 5.01 0.00 40.02 2.97
912 1121 8.881262 GGAGGGAAGACAAATAGAGGAATAATA 58.119 37.037 0.00 0.00 0.00 0.98
913 1122 7.574372 AGGAGGGAAGACAAATAGAGGAATAAT 59.426 37.037 0.00 0.00 0.00 1.28
914 1123 6.909158 AGGAGGGAAGACAAATAGAGGAATAA 59.091 38.462 0.00 0.00 0.00 1.40
1021 1230 1.144708 TCTGGTGGCAATGAAGGACAA 59.855 47.619 0.00 0.00 0.00 3.18
1044 1253 3.125316 GGTGGAAGAGTGAAGCAATAACG 59.875 47.826 0.00 0.00 0.00 3.18
1187 1396 3.338250 CCAGGTTGGGCAGGGCTA 61.338 66.667 0.00 0.00 32.67 3.93
1200 1409 1.676006 ACTTCAAGTTCAAACGCCAGG 59.324 47.619 0.00 0.00 0.00 4.45
1423 1633 2.738314 GTCAAATGCCAGACAATTTGCC 59.262 45.455 0.00 0.00 34.88 4.52
1436 1646 8.922058 AATCAAGATTACTGAATGTCAAATGC 57.078 30.769 0.00 0.00 0.00 3.56
1474 1684 1.252904 AAGCTTGATTGCCACCGCAT 61.253 50.000 0.00 0.00 46.67 4.73
1570 1780 1.734477 CTCGTTCTGGCACTGTCCG 60.734 63.158 0.00 0.00 0.00 4.79
1681 1891 0.966875 ATGCGTACCGGGTGTACTGA 60.967 55.000 10.66 0.00 46.36 3.41
1735 1945 1.404391 GCCATTGCAAGAGACCATGAG 59.596 52.381 4.94 0.00 37.47 2.90
1742 1952 0.036732 AAGACGGCCATTGCAAGAGA 59.963 50.000 4.94 0.00 40.13 3.10
1768 1978 4.094294 GCTAACACAACAGATTAATGGCGA 59.906 41.667 0.00 0.00 0.00 5.54
1780 1990 4.118410 CAGGCAAAAATGCTAACACAACA 58.882 39.130 0.40 0.00 34.73 3.33
1783 1993 3.715495 CACAGGCAAAAATGCTAACACA 58.285 40.909 0.40 0.00 34.73 3.72
1799 2009 3.046087 CAGGTCACGCTGCACAGG 61.046 66.667 0.00 0.00 0.00 4.00
2003 2213 3.316573 GAGGGTGGAGCCGGAGTTG 62.317 68.421 5.05 0.00 38.44 3.16
2004 2214 3.003763 GAGGGTGGAGCCGGAGTT 61.004 66.667 5.05 0.00 38.44 3.01
2168 2378 1.437397 ACCTCCCTTCAAACCCGTAA 58.563 50.000 0.00 0.00 0.00 3.18
2246 2456 3.864789 ACATTCTCACAGAACAACCCT 57.135 42.857 0.00 0.00 37.00 4.34
2248 2458 4.083271 GGCTTACATTCTCACAGAACAACC 60.083 45.833 0.00 0.00 37.00 3.77
2251 2461 3.325870 CGGCTTACATTCTCACAGAACA 58.674 45.455 0.00 0.00 37.00 3.18
2305 2547 5.508153 CCATACTTACAGAGATTGTCCGAGG 60.508 48.000 0.00 0.00 41.29 4.63
2308 2550 5.263968 ACCATACTTACAGAGATTGTCCG 57.736 43.478 0.00 0.00 41.29 4.79
2345 2592 0.597568 TTGTTTGATCGGCCAAGCTG 59.402 50.000 2.24 0.00 36.06 4.24
2354 2601 3.501828 TCTCACCACCAATTGTTTGATCG 59.498 43.478 4.43 0.00 34.60 3.69
2411 2758 7.009723 TGTTTTCGTTATCTTTGTTTGCCTTTC 59.990 33.333 0.00 0.00 0.00 2.62
2412 2759 6.814146 TGTTTTCGTTATCTTTGTTTGCCTTT 59.186 30.769 0.00 0.00 0.00 3.11
2431 2778 5.008712 GGGCAAGGTATAGCTATGTGTTTTC 59.991 44.000 16.77 1.82 0.00 2.29
2537 2884 5.948992 ATTCCTGCTTGAGTTAACACTTC 57.051 39.130 8.61 0.00 31.22 3.01
2717 3064 3.716006 CAACCGTCGTGCAGCCTG 61.716 66.667 0.00 0.00 0.00 4.85
2723 3070 2.740714 GAGGATGCAACCGTCGTGC 61.741 63.158 7.44 1.11 42.55 5.34
2724 3071 2.100631 GGAGGATGCAACCGTCGTG 61.101 63.158 7.44 0.00 34.73 4.35
2725 3072 2.107041 TTGGAGGATGCAACCGTCGT 62.107 55.000 7.44 0.00 43.23 4.34
2726 3073 1.375396 TTGGAGGATGCAACCGTCG 60.375 57.895 7.44 0.00 43.23 5.12
2727 3074 4.713946 TTGGAGGATGCAACCGTC 57.286 55.556 7.44 5.73 43.23 4.79
2733 3080 0.250684 TCGCAACTTTGGAGGATGCA 60.251 50.000 0.00 0.00 38.81 3.96
2734 3081 0.169009 GTCGCAACTTTGGAGGATGC 59.831 55.000 0.00 0.00 36.84 3.91
2735 3082 1.466167 CTGTCGCAACTTTGGAGGATG 59.534 52.381 0.00 0.00 0.00 3.51
2736 3083 1.347707 TCTGTCGCAACTTTGGAGGAT 59.652 47.619 0.00 0.00 0.00 3.24
2737 3084 0.756294 TCTGTCGCAACTTTGGAGGA 59.244 50.000 0.00 0.00 0.00 3.71
2738 3085 1.466167 CATCTGTCGCAACTTTGGAGG 59.534 52.381 0.00 0.00 0.00 4.30
2739 3086 2.416747 TCATCTGTCGCAACTTTGGAG 58.583 47.619 0.00 0.00 0.00 3.86
2740 3087 2.542020 TCATCTGTCGCAACTTTGGA 57.458 45.000 0.00 0.00 0.00 3.53
2741 3088 2.730090 GCATCATCTGTCGCAACTTTGG 60.730 50.000 0.00 0.00 0.00 3.28
2742 3089 2.512885 GCATCATCTGTCGCAACTTTG 58.487 47.619 0.00 0.00 0.00 2.77
2743 3090 1.470098 GGCATCATCTGTCGCAACTTT 59.530 47.619 0.00 0.00 0.00 2.66
2744 3091 1.089920 GGCATCATCTGTCGCAACTT 58.910 50.000 0.00 0.00 0.00 2.66
2745 3092 0.745845 GGGCATCATCTGTCGCAACT 60.746 55.000 0.00 0.00 0.00 3.16
2746 3093 0.745845 AGGGCATCATCTGTCGCAAC 60.746 55.000 0.00 0.00 0.00 4.17
2747 3094 0.829990 TAGGGCATCATCTGTCGCAA 59.170 50.000 0.00 0.00 0.00 4.85
2748 3095 1.051008 ATAGGGCATCATCTGTCGCA 58.949 50.000 0.00 0.00 0.00 5.10
2749 3096 1.802960 CAATAGGGCATCATCTGTCGC 59.197 52.381 0.00 0.00 0.00 5.19
2750 3097 2.420642 CCAATAGGGCATCATCTGTCG 58.579 52.381 0.00 0.00 0.00 4.35
2771 3118 0.592247 GCCGCCGTTGAGCAAATATG 60.592 55.000 0.00 0.00 0.00 1.78
2772 3119 1.029408 TGCCGCCGTTGAGCAAATAT 61.029 50.000 0.00 0.00 32.56 1.28
2773 3120 1.237954 TTGCCGCCGTTGAGCAAATA 61.238 50.000 0.00 0.00 43.14 1.40
2774 3121 2.560119 TTGCCGCCGTTGAGCAAAT 61.560 52.632 0.00 0.00 43.14 2.32
2775 3122 3.212682 TTGCCGCCGTTGAGCAAA 61.213 55.556 0.00 0.00 43.14 3.68
2776 3123 3.959975 GTTGCCGCCGTTGAGCAA 61.960 61.111 0.00 0.00 43.83 3.91
2778 3125 3.267597 ATTGTTGCCGCCGTTGAGC 62.268 57.895 0.00 0.00 0.00 4.26
2779 3126 1.154225 GATTGTTGCCGCCGTTGAG 60.154 57.895 0.00 0.00 0.00 3.02
2780 3127 1.599518 AGATTGTTGCCGCCGTTGA 60.600 52.632 0.00 0.00 0.00 3.18
2781 3128 1.442520 CAGATTGTTGCCGCCGTTG 60.443 57.895 0.00 0.00 0.00 4.10
2782 3129 2.625823 CCAGATTGTTGCCGCCGTT 61.626 57.895 0.00 0.00 0.00 4.44
2783 3130 3.055719 CCAGATTGTTGCCGCCGT 61.056 61.111 0.00 0.00 0.00 5.68
2784 3131 3.814268 CCCAGATTGTTGCCGCCG 61.814 66.667 0.00 0.00 0.00 6.46
2785 3132 4.133796 GCCCAGATTGTTGCCGCC 62.134 66.667 0.00 0.00 0.00 6.13
2786 3133 3.346631 CTGCCCAGATTGTTGCCGC 62.347 63.158 0.00 0.00 0.00 6.53
2787 3134 2.703798 CCTGCCCAGATTGTTGCCG 61.704 63.158 0.00 0.00 0.00 5.69
2788 3135 3.010413 GCCTGCCCAGATTGTTGCC 62.010 63.158 0.00 0.00 0.00 4.52
2789 3136 1.980772 AGCCTGCCCAGATTGTTGC 60.981 57.895 0.00 0.00 0.00 4.17
2790 3137 1.888018 CAGCCTGCCCAGATTGTTG 59.112 57.895 0.00 0.00 0.00 3.33
2791 3138 1.980772 GCAGCCTGCCCAGATTGTT 60.981 57.895 5.06 0.00 37.42 2.83
2792 3139 2.362120 GCAGCCTGCCCAGATTGT 60.362 61.111 5.06 0.00 37.42 2.71
2793 3140 2.361992 TGCAGCCTGCCCAGATTG 60.362 61.111 15.29 0.00 44.23 2.67
2794 3141 2.362120 GTGCAGCCTGCCCAGATT 60.362 61.111 15.29 0.00 44.23 2.40
2795 3142 4.790962 CGTGCAGCCTGCCCAGAT 62.791 66.667 15.29 0.00 44.23 2.90
2818 3165 1.243342 CCGCAACTTTGGAGGATGCA 61.243 55.000 0.00 0.00 38.81 3.96
2839 3186 2.421739 GATGTGCCGACGCCCTAT 59.578 61.111 0.00 0.00 0.00 2.57
2845 3192 1.517257 GTCTCAGGATGTGCCGACG 60.517 63.158 0.00 0.00 43.43 5.12
2883 3230 2.972348 ACTTCTGGGACTACCTTGACA 58.028 47.619 0.00 0.00 41.11 3.58
3052 3399 2.140717 CTGGTGAACAAAGGGTACGAC 58.859 52.381 0.00 0.00 0.00 4.34
3172 3519 1.100510 TTCCCGATGAGGAGTACACG 58.899 55.000 0.00 0.00 45.00 4.49
3187 3534 4.152647 ACAACCTGAAGGAGAAAATTCCC 58.847 43.478 2.62 0.00 38.02 3.97


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

AutoCloner maintained by Alex Coulton.