Multiple sequence alignment - TraesCS1D01G212100

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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 TraesCS1D01G212100 chr1D 100.000 3197 0 0 1 3197 297999889 298003085 0.000000e+00 5904
1 TraesCS1D01G212100 chr1A 94.350 2124 72 10 420 2520 371075441 371077539 0.000000e+00 3214
2 TraesCS1D01G212100 chr1A 90.719 431 26 4 1 428 371074986 371075405 2.150000e-156 562
3 TraesCS1D01G212100 chr1A 89.028 319 30 3 2863 3180 371077825 371078139 1.080000e-104 390
4 TraesCS1D01G212100 chr1B 90.862 1729 105 24 1 1681 400571906 400573629 0.000000e+00 2268
5 TraesCS1D01G212100 chr1B 92.729 1114 56 12 1675 2774 400579629 400580731 0.000000e+00 1585
6 TraesCS1D01G212100 chr1B 89.644 309 26 2 2876 3180 400580734 400581040 3.870000e-104 388
7 TraesCS1D01G212100 chr1B 80.342 234 36 9 2361 2592 401442513 401442288 5.480000e-38 169


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 TraesCS1D01G212100 chr1D 297999889 298003085 3196 False 5904.000000 5904 100.000000 1 3197 1 chr1D.!!$F1 3196
1 TraesCS1D01G212100 chr1A 371074986 371078139 3153 False 1388.666667 3214 91.365667 1 3180 3 chr1A.!!$F1 3179
2 TraesCS1D01G212100 chr1B 400571906 400573629 1723 False 2268.000000 2268 90.862000 1 1681 1 chr1B.!!$F1 1680
3 TraesCS1D01G212100 chr1B 400579629 400581040 1411 False 986.500000 1585 91.186500 1675 3180 2 chr1B.!!$F2 1505

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
641 734 0.239879 GGGTCGCGAGCAATTTTTGA 59.76 50.0 35.8 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2603 2859 0.257039 CTCCACCCCAAGCAAGCTAT 59.743 55.0 0.0 0.0 0.0 2.97 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
65 66 7.065324 GGGACTATCATCGTGTTTAATCACAAA 59.935 37.037 15.19 4.80 38.12 2.83
121 122 5.936372 TCAGAGTGGTGATCAAAAGAGATTG 59.064 40.000 0.00 0.00 0.00 2.67
199 200 6.376299 TGACTCGAGGTAGCTAAATAAGAACA 59.624 38.462 18.41 0.00 0.00 3.18
264 265 4.398988 ACTTCATTTCGATTATGCCAGCAA 59.601 37.500 0.00 0.00 0.00 3.91
266 267 2.823196 TTTCGATTATGCCAGCAACG 57.177 45.000 0.00 1.31 0.00 4.10
368 373 5.069318 TCAACAAGCACATGTAATCTCCAA 58.931 37.500 0.00 0.00 32.02 3.53
383 388 8.912988 TGTAATCTCCAAACTTCAGACATTTTT 58.087 29.630 0.00 0.00 0.00 1.94
387 392 8.519799 TCTCCAAACTTCAGACATTTTTAACT 57.480 30.769 0.00 0.00 0.00 2.24
433 482 6.061022 TCTACATAATGCTTGAAACCTCCA 57.939 37.500 0.00 0.00 0.00 3.86
434 483 6.662755 TCTACATAATGCTTGAAACCTCCAT 58.337 36.000 0.00 0.00 0.00 3.41
484 577 7.569297 TGTAGTTAACGAATTTGTAGCAACTG 58.431 34.615 20.40 0.00 0.00 3.16
576 669 5.591472 GGGTTATGTAACATTACCCCTGTTC 59.409 44.000 14.89 0.00 42.13 3.18
614 707 0.745486 CAGCCGCTGGATGACATCAA 60.745 55.000 17.08 4.99 42.34 2.57
637 730 2.358247 ACGGGTCGCGAGCAATTT 60.358 55.556 35.80 16.17 0.00 1.82
638 731 1.908066 GACGGGTCGCGAGCAATTTT 61.908 55.000 35.80 16.80 0.00 1.82
639 732 1.209127 CGGGTCGCGAGCAATTTTT 59.791 52.632 35.80 0.00 0.00 1.94
640 733 1.065031 CGGGTCGCGAGCAATTTTTG 61.065 55.000 35.80 14.44 0.00 2.44
641 734 0.239879 GGGTCGCGAGCAATTTTTGA 59.760 50.000 35.80 0.00 0.00 2.69
642 735 1.606606 GGTCGCGAGCAATTTTTGAG 58.393 50.000 31.60 0.00 0.00 3.02
643 736 1.196808 GGTCGCGAGCAATTTTTGAGA 59.803 47.619 31.60 0.00 0.00 3.27
644 737 2.159517 GGTCGCGAGCAATTTTTGAGAT 60.160 45.455 31.60 0.00 0.00 2.75
645 738 3.063452 GGTCGCGAGCAATTTTTGAGATA 59.937 43.478 31.60 0.00 0.00 1.98
646 739 4.260784 GGTCGCGAGCAATTTTTGAGATAT 60.261 41.667 31.60 0.00 0.00 1.63
647 740 5.050363 GGTCGCGAGCAATTTTTGAGATATA 60.050 40.000 31.60 0.00 0.00 0.86
648 741 5.841296 GTCGCGAGCAATTTTTGAGATATAC 59.159 40.000 10.24 0.00 0.00 1.47
649 742 5.753438 TCGCGAGCAATTTTTGAGATATACT 59.247 36.000 3.71 0.00 0.00 2.12
650 743 5.842843 CGCGAGCAATTTTTGAGATATACTG 59.157 40.000 0.00 0.00 0.00 2.74
651 744 6.510157 CGCGAGCAATTTTTGAGATATACTGT 60.510 38.462 0.00 0.00 0.00 3.55
652 745 7.306574 CGCGAGCAATTTTTGAGATATACTGTA 60.307 37.037 0.00 0.00 0.00 2.74
653 746 7.794349 GCGAGCAATTTTTGAGATATACTGTAC 59.206 37.037 0.00 0.00 0.00 2.90
654 747 9.035607 CGAGCAATTTTTGAGATATACTGTACT 57.964 33.333 0.00 0.00 0.00 2.73
700 838 4.920927 CCGAAAACGCTCATAATTGGTTTT 59.079 37.500 0.37 0.37 41.82 2.43
789 929 3.172919 GCTGAAGCTGAAGACGCC 58.827 61.111 0.00 0.00 38.21 5.68
890 1033 7.648142 ACGAAATAAATCCGATGCATTTATGT 58.352 30.769 0.00 0.00 36.80 2.29
1293 1446 0.033796 AGTTCTACGACATCCCCGGA 60.034 55.000 0.73 0.00 0.00 5.14
1539 1692 3.358076 CTTCCTCGTCCTCGCCACC 62.358 68.421 0.00 0.00 36.96 4.61
2097 2250 2.346766 TGCTGGTGCTGAAGAAGAAA 57.653 45.000 0.00 0.00 40.48 2.52
2372 2528 1.805345 CTGAAAGCTCTGGTTCTGCAG 59.195 52.381 7.63 7.63 0.00 4.41
2394 2550 6.208204 GCAGCCTGTTCCTATATGATTCAAAT 59.792 38.462 0.00 0.00 0.00 2.32
2404 2560 7.171508 TCCTATATGATTCAAATGAGTTGCGAC 59.828 37.037 0.00 0.00 37.13 5.19
2419 2575 0.589729 GCGACGCAACCAGCAATATG 60.590 55.000 16.42 0.00 46.13 1.78
2422 2578 2.543848 CGACGCAACCAGCAATATGTAT 59.456 45.455 0.00 0.00 46.13 2.29
2449 2618 2.402305 GACAAATGTTGATTGCGCCAA 58.598 42.857 4.18 0.00 0.00 4.52
2452 2621 2.801679 CAAATGTTGATTGCGCCAAACT 59.198 40.909 4.18 0.00 0.00 2.66
2469 2638 4.343323 TGGGGTGTGATGCGTGGG 62.343 66.667 0.00 0.00 0.00 4.61
2486 2655 0.584876 GGGCATATACACGAAACGGC 59.415 55.000 0.00 0.00 0.00 5.68
2489 2658 1.790623 GCATATACACGAAACGGCGAT 59.209 47.619 16.62 0.00 34.83 4.58
2490 2659 2.220133 GCATATACACGAAACGGCGATT 59.780 45.455 16.62 8.47 34.83 3.34
2491 2660 3.302870 GCATATACACGAAACGGCGATTT 60.303 43.478 16.62 10.68 34.83 2.17
2520 2715 9.881529 TTTTTCATAATTCATTTTCAGCTTTGC 57.118 25.926 0.00 0.00 0.00 3.68
2521 2716 8.604640 TTTCATAATTCATTTTCAGCTTTGCA 57.395 26.923 0.00 0.00 0.00 4.08
2522 2717 7.821595 TCATAATTCATTTTCAGCTTTGCAG 57.178 32.000 0.00 0.00 0.00 4.41
2523 2718 7.604549 TCATAATTCATTTTCAGCTTTGCAGA 58.395 30.769 0.00 0.00 0.00 4.26
2524 2719 8.089597 TCATAATTCATTTTCAGCTTTGCAGAA 58.910 29.630 0.00 0.00 32.52 3.02
2525 2720 8.879759 CATAATTCATTTTCAGCTTTGCAGAAT 58.120 29.630 0.00 0.00 34.31 2.40
2526 2721 6.963049 ATTCATTTTCAGCTTTGCAGAATC 57.037 33.333 0.00 0.00 34.31 2.52
2527 2722 4.813027 TCATTTTCAGCTTTGCAGAATCC 58.187 39.130 0.00 0.00 34.31 3.01
2528 2723 4.525487 TCATTTTCAGCTTTGCAGAATCCT 59.475 37.500 0.00 0.00 34.31 3.24
2529 2724 5.711506 TCATTTTCAGCTTTGCAGAATCCTA 59.288 36.000 0.00 0.00 34.31 2.94
2530 2725 5.633830 TTTTCAGCTTTGCAGAATCCTAG 57.366 39.130 0.00 0.00 34.31 3.02
2531 2726 2.636830 TCAGCTTTGCAGAATCCTAGC 58.363 47.619 0.00 0.00 0.00 3.42
2532 2727 2.238144 TCAGCTTTGCAGAATCCTAGCT 59.762 45.455 0.00 0.00 39.38 3.32
2533 2728 3.452264 TCAGCTTTGCAGAATCCTAGCTA 59.548 43.478 0.00 0.00 36.88 3.32
2534 2729 4.080919 TCAGCTTTGCAGAATCCTAGCTAA 60.081 41.667 0.00 0.00 36.88 3.09
2535 2730 4.272991 CAGCTTTGCAGAATCCTAGCTAAG 59.727 45.833 0.00 0.00 41.69 2.18
2537 2732 3.845781 TTGCAGAATCCTAGCTAAGGG 57.154 47.619 0.00 0.00 46.55 3.95
2538 2733 3.046283 TGCAGAATCCTAGCTAAGGGA 57.954 47.619 4.31 4.31 46.55 4.20
2539 2734 2.700897 TGCAGAATCCTAGCTAAGGGAC 59.299 50.000 3.93 0.00 46.55 4.46
2540 2735 2.969262 GCAGAATCCTAGCTAAGGGACT 59.031 50.000 3.93 0.00 46.55 3.85
2541 2736 3.006430 GCAGAATCCTAGCTAAGGGACTC 59.994 52.174 3.93 3.43 46.55 3.36
2542 2737 4.479158 CAGAATCCTAGCTAAGGGACTCT 58.521 47.826 7.08 7.08 46.55 3.24
2543 2738 4.898861 CAGAATCCTAGCTAAGGGACTCTT 59.101 45.833 9.61 0.00 46.55 2.85
2544 2739 5.365314 CAGAATCCTAGCTAAGGGACTCTTT 59.635 44.000 9.61 0.00 46.55 2.52
2545 2740 5.365314 AGAATCCTAGCTAAGGGACTCTTTG 59.635 44.000 7.08 0.00 46.55 2.77
2616 2872 6.000219 AGTATTCATGTATAGCTTGCTTGGG 59.000 40.000 0.00 0.00 0.00 4.12
2625 2881 1.527433 GCTTGCTTGGGGTGGAGAAC 61.527 60.000 0.00 0.00 0.00 3.01
2628 2884 1.973812 GCTTGGGGTGGAGAACTGC 60.974 63.158 0.00 0.00 0.00 4.40
2647 2903 2.353269 TGCACACCGTAGACAGTTTTTG 59.647 45.455 0.00 0.00 0.00 2.44
2648 2904 2.353579 GCACACCGTAGACAGTTTTTGT 59.646 45.455 0.00 0.00 44.55 2.83
2649 2905 3.787476 GCACACCGTAGACAGTTTTTGTG 60.787 47.826 0.00 0.00 41.05 3.33
2650 2906 3.372822 CACACCGTAGACAGTTTTTGTGT 59.627 43.478 0.00 0.00 41.05 3.72
2651 2907 3.372822 ACACCGTAGACAGTTTTTGTGTG 59.627 43.478 0.00 0.00 41.05 3.82
2652 2908 3.372822 CACCGTAGACAGTTTTTGTGTGT 59.627 43.478 0.00 0.00 41.05 3.72
2653 2909 3.372822 ACCGTAGACAGTTTTTGTGTGTG 59.627 43.478 0.00 0.00 41.05 3.82
2663 2919 2.695613 TTTGTGTGTGTGTGTGTGTG 57.304 45.000 0.00 0.00 0.00 3.82
2669 2925 0.954452 TGTGTGTGTGTGTGTTTGCA 59.046 45.000 0.00 0.00 0.00 4.08
2670 2926 1.543358 TGTGTGTGTGTGTGTTTGCAT 59.457 42.857 0.00 0.00 0.00 3.96
2723 2979 6.648725 TCCACTTTACATGCAATTTTAAAGGC 59.351 34.615 17.23 2.67 35.25 4.35
2739 2996 8.744568 TTTTAAAGGCAAAAATTCCATTCAGT 57.255 26.923 0.00 0.00 0.00 3.41
2741 2998 5.813513 AAGGCAAAAATTCCATTCAGTCT 57.186 34.783 0.00 0.00 0.00 3.24
2744 3001 6.691508 AGGCAAAAATTCCATTCAGTCTAAC 58.308 36.000 0.00 0.00 0.00 2.34
2797 3054 2.886862 TGTTTCAACAACAGCCATGG 57.113 45.000 7.63 7.63 35.67 3.66
2798 3055 1.202510 TGTTTCAACAACAGCCATGGC 60.203 47.619 30.12 30.12 37.40 4.40
2799 3056 1.117994 TTTCAACAACAGCCATGGCA 58.882 45.000 37.18 12.49 44.88 4.92
2800 3057 1.340088 TTCAACAACAGCCATGGCAT 58.660 45.000 37.18 22.84 44.88 4.40
2801 3058 0.604073 TCAACAACAGCCATGGCATG 59.396 50.000 37.18 30.92 44.88 4.06
2802 3059 0.319083 CAACAACAGCCATGGCATGT 59.681 50.000 37.18 31.54 44.88 3.21
2803 3060 0.319083 AACAACAGCCATGGCATGTG 59.681 50.000 37.18 29.70 44.88 3.21
2804 3061 1.447140 CAACAGCCATGGCATGTGC 60.447 57.895 37.18 24.60 44.88 4.57
2805 3062 1.909287 AACAGCCATGGCATGTGCA 60.909 52.632 37.18 0.00 44.88 4.57
2806 3063 1.261938 AACAGCCATGGCATGTGCAT 61.262 50.000 37.18 19.45 44.88 3.96
2807 3064 1.227234 CAGCCATGGCATGTGCATG 60.227 57.895 37.18 21.23 44.88 4.06
2808 3065 2.108157 GCCATGGCATGTGCATGG 59.892 61.111 32.08 21.63 44.75 3.66
2809 3066 2.428085 GCCATGGCATGTGCATGGA 61.428 57.895 32.08 0.00 44.75 3.41
2810 3067 1.739667 CCATGGCATGTGCATGGAG 59.260 57.895 24.80 4.34 44.75 3.86
2811 3068 1.040893 CCATGGCATGTGCATGGAGT 61.041 55.000 24.80 0.00 44.75 3.85
2812 3069 1.682740 CATGGCATGTGCATGGAGTA 58.317 50.000 19.32 0.00 44.36 2.59
2813 3070 2.235891 CATGGCATGTGCATGGAGTAT 58.764 47.619 19.32 0.00 44.36 2.12
2814 3071 2.440517 TGGCATGTGCATGGAGTATT 57.559 45.000 13.28 0.00 44.36 1.89
2815 3072 2.737544 TGGCATGTGCATGGAGTATTT 58.262 42.857 13.28 0.00 44.36 1.40
2816 3073 2.427812 TGGCATGTGCATGGAGTATTTG 59.572 45.455 13.28 0.00 44.36 2.32
2817 3074 2.689471 GGCATGTGCATGGAGTATTTGA 59.311 45.455 13.28 0.00 44.36 2.69
2818 3075 3.243301 GGCATGTGCATGGAGTATTTGAG 60.243 47.826 13.28 0.00 44.36 3.02
2819 3076 3.628942 GCATGTGCATGGAGTATTTGAGA 59.371 43.478 13.28 0.00 41.59 3.27
2820 3077 4.096833 GCATGTGCATGGAGTATTTGAGAA 59.903 41.667 13.28 0.00 41.59 2.87
2821 3078 5.393352 GCATGTGCATGGAGTATTTGAGAAA 60.393 40.000 13.28 0.00 41.59 2.52
2822 3079 5.885230 TGTGCATGGAGTATTTGAGAAAG 57.115 39.130 0.00 0.00 0.00 2.62
2823 3080 4.156556 TGTGCATGGAGTATTTGAGAAAGC 59.843 41.667 0.00 0.00 0.00 3.51
2824 3081 4.156556 GTGCATGGAGTATTTGAGAAAGCA 59.843 41.667 0.00 0.00 0.00 3.91
2825 3082 4.951715 TGCATGGAGTATTTGAGAAAGCAT 59.048 37.500 0.00 0.00 0.00 3.79
2826 3083 5.163591 TGCATGGAGTATTTGAGAAAGCATG 60.164 40.000 0.00 0.00 0.00 4.06
2827 3084 4.970662 TGGAGTATTTGAGAAAGCATGC 57.029 40.909 10.51 10.51 0.00 4.06
2828 3085 4.592942 TGGAGTATTTGAGAAAGCATGCT 58.407 39.130 16.30 16.30 0.00 3.79
2829 3086 5.012239 TGGAGTATTTGAGAAAGCATGCTT 58.988 37.500 27.21 27.21 37.98 3.91
2830 3087 5.124457 TGGAGTATTTGAGAAAGCATGCTTC 59.876 40.000 32.01 23.41 34.84 3.86
2831 3088 5.356470 GGAGTATTTGAGAAAGCATGCTTCT 59.644 40.000 32.01 27.11 34.84 2.85
2832 3089 6.127786 GGAGTATTTGAGAAAGCATGCTTCTT 60.128 38.462 32.01 22.48 34.84 2.52
2833 3090 7.224522 AGTATTTGAGAAAGCATGCTTCTTT 57.775 32.000 32.01 17.90 36.55 2.52
2834 3091 7.311408 AGTATTTGAGAAAGCATGCTTCTTTC 58.689 34.615 32.01 24.69 45.87 2.62
2885 3142 8.454570 AAATATGCCATGAAATCAAATTTCCC 57.545 30.769 9.31 0.00 46.18 3.97
2895 3152 7.413446 TGAAATCAAATTTCCCAGTCCTATCT 58.587 34.615 9.31 0.00 46.18 1.98
2906 3163 7.324388 TCCCAGTCCTATCTTTTTAAGAACA 57.676 36.000 0.00 0.00 41.63 3.18
2934 3191 6.312918 AGAGGTGCACTTACAATGTAATAACG 59.687 38.462 17.98 0.00 0.00 3.18
2949 3206 8.873215 ATGTAATAACGTCTGATCCTTAGTTG 57.127 34.615 0.00 0.00 0.00 3.16
2962 3219 5.165961 TCCTTAGTTGGATGGAGTCTTTG 57.834 43.478 0.00 0.00 0.00 2.77
2973 3230 4.836125 TGGAGTCTTTGCTGTTTTGATC 57.164 40.909 0.00 0.00 0.00 2.92
2983 3240 2.879826 CTGTTTTGATCGGAATTGGCC 58.120 47.619 0.00 0.00 0.00 5.36
2984 3241 2.230992 CTGTTTTGATCGGAATTGGCCA 59.769 45.455 0.00 0.00 0.00 5.36
2985 3242 2.029470 TGTTTTGATCGGAATTGGCCAC 60.029 45.455 3.88 0.00 0.00 5.01
2986 3243 0.808125 TTTGATCGGAATTGGCCACG 59.192 50.000 3.88 5.91 0.00 4.94
2999 3256 1.202758 TGGCCACGTGTTCTCATTTCT 60.203 47.619 15.65 0.00 0.00 2.52
3004 3261 4.776743 CCACGTGTTCTCATTTCTGAAAG 58.223 43.478 15.65 1.82 0.00 2.62
3027 3284 7.492077 AGACCTAAACCCCCTATTTATATCG 57.508 40.000 0.00 0.00 0.00 2.92
3061 3318 5.848286 TGATAGGCCATATCCATTCACTT 57.152 39.130 5.01 0.00 39.78 3.16
3154 3416 9.836864 TCTAAATAGTCATGTGATATTTGTGCT 57.163 29.630 16.08 0.00 32.75 4.40
3155 3417 9.874215 CTAAATAGTCATGTGATATTTGTGCTG 57.126 33.333 16.08 0.00 32.75 4.41
3186 3448 9.816787 ACTCCCTACAATTATTTAAACAAGGAA 57.183 29.630 0.00 0.00 0.00 3.36
3189 3451 9.869757 CCCTACAATTATTTAAACAAGGAAAGG 57.130 33.333 0.00 0.00 0.00 3.11
3192 3454 8.601845 ACAATTATTTAAACAAGGAAAGGTGC 57.398 30.769 0.00 0.00 0.00 5.01
3193 3455 7.383843 ACAATTATTTAAACAAGGAAAGGTGCG 59.616 33.333 0.00 0.00 0.00 5.34
3194 3456 6.636562 TTATTTAAACAAGGAAAGGTGCGA 57.363 33.333 0.00 0.00 0.00 5.10
3195 3457 4.561735 TTTAAACAAGGAAAGGTGCGAG 57.438 40.909 0.00 0.00 0.00 5.03
3196 3458 1.318576 AAACAAGGAAAGGTGCGAGG 58.681 50.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 5.511373 GCAATCCTATTAAAGGGGAAATGGC 60.511 44.000 4.51 0.00 46.55 4.40
143 144 4.748102 CGGTGAAGTTAAACTCTACAAGCA 59.252 41.667 0.00 0.00 0.00 3.91
145 146 4.748102 TGCGGTGAAGTTAAACTCTACAAG 59.252 41.667 0.00 0.00 0.00 3.16
199 200 7.174772 TGCGCCATCACTATAAATATCACAAAT 59.825 33.333 4.18 0.00 0.00 2.32
218 219 0.670162 GCATGATAAACCTGCGCCAT 59.330 50.000 4.18 0.00 31.36 4.40
264 265 1.666872 GCTGGTGACCGTTTAGCGT 60.667 57.895 0.00 0.00 39.32 5.07
266 267 0.248289 TAGGCTGGTGACCGTTTAGC 59.752 55.000 3.27 3.27 0.00 3.09
273 274 2.364324 TCGTATTGATAGGCTGGTGACC 59.636 50.000 0.00 0.00 0.00 4.02
383 388 9.990360 TGATCTATGTTTGTGTCTTTGTAGTTA 57.010 29.630 0.00 0.00 0.00 2.24
433 482 5.299949 GCAAAACAAACATTTGAGAGGGAT 58.700 37.500 11.24 0.00 39.56 3.85
434 483 4.442753 GGCAAAACAAACATTTGAGAGGGA 60.443 41.667 11.24 0.00 39.56 4.20
484 577 6.628461 CCAACGATTCAAATTTTTGCTTGAAC 59.372 34.615 0.00 0.00 36.41 3.18
614 707 4.421479 CTCGCGACCCGTCAGCTT 62.421 66.667 3.71 0.00 38.35 3.74
641 734 9.257651 GCGTCCAAAATAAAGTACAGTATATCT 57.742 33.333 0.00 0.00 0.00 1.98
642 735 9.037737 TGCGTCCAAAATAAAGTACAGTATATC 57.962 33.333 0.00 0.00 0.00 1.63
643 736 8.951787 TGCGTCCAAAATAAAGTACAGTATAT 57.048 30.769 0.00 0.00 0.00 0.86
644 737 8.774890 TTGCGTCCAAAATAAAGTACAGTATA 57.225 30.769 0.00 0.00 0.00 1.47
645 738 7.675962 TTGCGTCCAAAATAAAGTACAGTAT 57.324 32.000 0.00 0.00 0.00 2.12
646 739 7.493743 TTTGCGTCCAAAATAAAGTACAGTA 57.506 32.000 0.00 0.00 37.97 2.74
647 740 6.380095 TTTGCGTCCAAAATAAAGTACAGT 57.620 33.333 0.00 0.00 37.97 3.55
648 741 7.081349 TCATTTGCGTCCAAAATAAAGTACAG 58.919 34.615 0.00 0.00 43.58 2.74
649 742 6.971602 TCATTTGCGTCCAAAATAAAGTACA 58.028 32.000 0.00 0.00 43.58 2.90
650 743 7.302524 TCTCATTTGCGTCCAAAATAAAGTAC 58.697 34.615 0.00 0.00 43.58 2.73
651 744 7.441890 TCTCATTTGCGTCCAAAATAAAGTA 57.558 32.000 0.00 0.00 43.58 2.24
652 745 6.325919 TCTCATTTGCGTCCAAAATAAAGT 57.674 33.333 0.00 0.00 43.58 2.66
653 746 6.089417 GGTTCTCATTTGCGTCCAAAATAAAG 59.911 38.462 0.00 0.00 43.58 1.85
654 747 5.923684 GGTTCTCATTTGCGTCCAAAATAAA 59.076 36.000 0.00 0.00 43.58 1.40
655 748 5.465935 GGTTCTCATTTGCGTCCAAAATAA 58.534 37.500 0.00 0.00 43.58 1.40
656 749 4.378978 CGGTTCTCATTTGCGTCCAAAATA 60.379 41.667 0.00 0.00 43.58 1.40
657 750 3.611530 CGGTTCTCATTTGCGTCCAAAAT 60.612 43.478 0.00 0.00 43.58 1.82
700 838 8.627403 CAATTCGTAGTAGTAGAACATAAGGGA 58.373 37.037 0.00 0.00 0.00 4.20
789 929 0.952497 AATGCATCCTATCGCCTGCG 60.952 55.000 4.92 4.92 37.44 5.18
1045 1192 1.378119 GGTTTTTCCCCGGATCGCT 60.378 57.895 0.73 0.00 0.00 4.93
1437 1590 1.300620 CTTGAACGGCCACGACAGA 60.301 57.895 2.24 0.00 44.60 3.41
1758 1911 4.397832 TGGCGCATGCTGCTCTCA 62.398 61.111 25.77 16.58 42.25 3.27
1971 2124 3.959975 GGCTGGTGCGCGAACAAA 61.960 61.111 21.02 5.54 40.82 2.83
2097 2250 2.990967 CCTTGCCGGTGGTGCATT 60.991 61.111 1.90 0.00 38.76 3.56
2127 2280 0.314302 AGAACCAGAACGAGTCACCG 59.686 55.000 0.00 0.00 0.00 4.94
2253 2406 8.871125 CCCATGGTTCTACACTATATCTTAGTT 58.129 37.037 11.73 0.00 0.00 2.24
2372 2528 7.446625 ACTCATTTGAATCATATAGGAACAGGC 59.553 37.037 0.00 0.00 0.00 4.85
2404 2560 6.303022 CGATAAAATACATATTGCTGGTTGCG 59.697 38.462 0.00 0.00 46.63 4.85
2419 2575 8.252454 CGCAATCAACATTTGTCGATAAAATAC 58.748 33.333 11.51 0.00 0.00 1.89
2422 2578 5.060323 GCGCAATCAACATTTGTCGATAAAA 59.940 36.000 11.51 5.13 0.00 1.52
2449 2618 1.600636 CACGCATCACACCCCAGTT 60.601 57.895 0.00 0.00 0.00 3.16
2452 2621 4.343323 CCCACGCATCACACCCCA 62.343 66.667 0.00 0.00 0.00 4.96
2469 2638 1.202203 TCGCCGTTTCGTGTATATGC 58.798 50.000 0.00 0.00 0.00 3.14
2520 2715 4.898861 AAGAGTCCCTTAGCTAGGATTCTG 59.101 45.833 20.90 0.00 45.54 3.02
2526 2721 5.129485 TGAATCAAAGAGTCCCTTAGCTAGG 59.871 44.000 0.00 0.00 44.33 3.02
2527 2722 6.227298 TGAATCAAAGAGTCCCTTAGCTAG 57.773 41.667 0.00 0.00 34.00 3.42
2528 2723 6.814954 ATGAATCAAAGAGTCCCTTAGCTA 57.185 37.500 0.00 0.00 34.00 3.32
2529 2724 5.707066 ATGAATCAAAGAGTCCCTTAGCT 57.293 39.130 0.00 0.00 34.00 3.32
2530 2725 9.732130 ATATTATGAATCAAAGAGTCCCTTAGC 57.268 33.333 0.00 0.00 34.00 3.09
2595 2851 4.147321 CCCCAAGCAAGCTATACATGAAT 58.853 43.478 0.00 0.00 0.00 2.57
2603 2859 0.257039 CTCCACCCCAAGCAAGCTAT 59.743 55.000 0.00 0.00 0.00 2.97
2616 2872 1.961277 CGGTGTGCAGTTCTCCACC 60.961 63.158 11.00 11.00 43.13 4.61
2625 2881 1.865865 AAACTGTCTACGGTGTGCAG 58.134 50.000 0.00 0.00 35.26 4.41
2628 2884 3.372822 ACACAAAAACTGTCTACGGTGTG 59.627 43.478 8.19 8.19 36.92 3.82
2630 2886 3.372822 ACACACAAAAACTGTCTACGGTG 59.627 43.478 0.00 0.00 35.47 4.94
2634 2890 5.086058 CACACACACACAAAAACTGTCTAC 58.914 41.667 0.00 0.00 35.47 2.59
2647 2903 2.315011 CAAACACACACACACACACAC 58.685 47.619 0.00 0.00 0.00 3.82
2648 2904 1.335415 GCAAACACACACACACACACA 60.335 47.619 0.00 0.00 0.00 3.72
2649 2905 1.335415 TGCAAACACACACACACACAC 60.335 47.619 0.00 0.00 0.00 3.82
2650 2906 0.954452 TGCAAACACACACACACACA 59.046 45.000 0.00 0.00 0.00 3.72
2651 2907 1.919263 CATGCAAACACACACACACAC 59.081 47.619 0.00 0.00 0.00 3.82
2652 2908 1.543358 ACATGCAAACACACACACACA 59.457 42.857 0.00 0.00 0.00 3.72
2653 2909 2.184448 GACATGCAAACACACACACAC 58.816 47.619 0.00 0.00 0.00 3.82
2723 2979 9.865321 ATGATGTTAGACTGAATGGAATTTTTG 57.135 29.630 0.00 0.00 36.07 2.44
2739 2996 8.927721 CATTGTGAAATTTTGCATGATGTTAGA 58.072 29.630 0.00 0.00 0.00 2.10
2741 2998 7.876582 TCCATTGTGAAATTTTGCATGATGTTA 59.123 29.630 0.00 0.00 0.00 2.41
2744 3001 6.729391 TCCATTGTGAAATTTTGCATGATG 57.271 33.333 0.00 0.00 0.00 3.07
2777 3034 2.741228 GCCATGGCTGTTGTTGAAACAA 60.741 45.455 29.98 4.52 41.13 2.83
2778 3035 1.202510 GCCATGGCTGTTGTTGAAACA 60.203 47.619 29.98 0.00 38.26 2.83
2779 3036 1.202510 TGCCATGGCTGTTGTTGAAAC 60.203 47.619 35.53 4.22 42.51 2.78
2780 3037 1.117994 TGCCATGGCTGTTGTTGAAA 58.882 45.000 35.53 10.21 42.51 2.69
2781 3038 1.001068 CATGCCATGGCTGTTGTTGAA 59.999 47.619 35.53 14.13 42.51 2.69
2782 3039 0.604073 CATGCCATGGCTGTTGTTGA 59.396 50.000 35.53 14.91 42.51 3.18
2783 3040 0.319083 ACATGCCATGGCTGTTGTTG 59.681 50.000 35.53 23.10 42.51 3.33
2784 3041 0.319083 CACATGCCATGGCTGTTGTT 59.681 50.000 35.53 17.40 42.51 2.83
2785 3042 1.969085 CACATGCCATGGCTGTTGT 59.031 52.632 35.53 29.60 42.51 3.32
2786 3043 1.447140 GCACATGCCATGGCTGTTG 60.447 57.895 35.53 29.01 42.51 3.33
2787 3044 1.261938 ATGCACATGCCATGGCTGTT 61.262 50.000 35.53 18.68 42.51 3.16
2788 3045 1.684391 ATGCACATGCCATGGCTGT 60.684 52.632 35.53 30.33 42.51 4.40
2789 3046 1.227234 CATGCACATGCCATGGCTG 60.227 57.895 35.53 29.73 42.51 4.85
2790 3047 2.431454 CCATGCACATGCCATGGCT 61.431 57.895 35.53 19.42 40.25 4.75
2791 3048 2.108157 CCATGCACATGCCATGGC 59.892 61.111 30.54 30.54 40.25 4.40
2792 3049 1.040893 ACTCCATGCACATGCCATGG 61.041 55.000 27.83 27.83 44.05 3.66
2793 3050 1.682740 TACTCCATGCACATGCCATG 58.317 50.000 16.17 16.17 41.18 3.66
2794 3051 2.670019 ATACTCCATGCACATGCCAT 57.330 45.000 5.06 0.00 41.18 4.40
2795 3052 2.427812 CAAATACTCCATGCACATGCCA 59.572 45.455 5.06 0.00 41.18 4.92
2796 3053 2.689471 TCAAATACTCCATGCACATGCC 59.311 45.455 5.06 0.00 41.18 4.40
2797 3054 3.628942 TCTCAAATACTCCATGCACATGC 59.371 43.478 5.06 0.00 37.49 4.06
2798 3055 5.823209 TTCTCAAATACTCCATGCACATG 57.177 39.130 3.56 3.56 38.51 3.21
2799 3056 5.163581 GCTTTCTCAAATACTCCATGCACAT 60.164 40.000 0.00 0.00 0.00 3.21
2800 3057 4.156556 GCTTTCTCAAATACTCCATGCACA 59.843 41.667 0.00 0.00 0.00 4.57
2801 3058 4.156556 TGCTTTCTCAAATACTCCATGCAC 59.843 41.667 0.00 0.00 0.00 4.57
2802 3059 4.334552 TGCTTTCTCAAATACTCCATGCA 58.665 39.130 0.00 0.00 0.00 3.96
2803 3060 4.970662 TGCTTTCTCAAATACTCCATGC 57.029 40.909 0.00 0.00 0.00 4.06
2804 3061 5.067413 AGCATGCTTTCTCAAATACTCCATG 59.933 40.000 16.30 0.00 0.00 3.66
2805 3062 5.198965 AGCATGCTTTCTCAAATACTCCAT 58.801 37.500 16.30 0.00 0.00 3.41
2806 3063 4.592942 AGCATGCTTTCTCAAATACTCCA 58.407 39.130 16.30 0.00 0.00 3.86
2807 3064 5.356470 AGAAGCATGCTTTCTCAAATACTCC 59.644 40.000 32.36 15.35 36.26 3.85
2808 3065 6.434018 AGAAGCATGCTTTCTCAAATACTC 57.566 37.500 32.36 15.89 36.26 2.59
2809 3066 6.830873 AAGAAGCATGCTTTCTCAAATACT 57.169 33.333 32.36 18.63 36.26 2.12
2842 3099 9.120538 GGCATATTTAATCCTACAAGAACTGAA 57.879 33.333 0.00 0.00 0.00 3.02
2843 3100 8.271458 TGGCATATTTAATCCTACAAGAACTGA 58.729 33.333 0.00 0.00 0.00 3.41
2844 3101 8.450578 TGGCATATTTAATCCTACAAGAACTG 57.549 34.615 0.00 0.00 0.00 3.16
2845 3102 9.071276 CATGGCATATTTAATCCTACAAGAACT 57.929 33.333 0.00 0.00 0.00 3.01
2846 3103 9.066892 TCATGGCATATTTAATCCTACAAGAAC 57.933 33.333 0.00 0.00 0.00 3.01
2847 3104 9.639563 TTCATGGCATATTTAATCCTACAAGAA 57.360 29.630 0.00 0.00 0.00 2.52
2848 3105 9.639563 TTTCATGGCATATTTAATCCTACAAGA 57.360 29.630 0.00 0.00 0.00 3.02
2851 3108 9.585369 TGATTTCATGGCATATTTAATCCTACA 57.415 29.630 0.00 0.00 0.00 2.74
2895 3152 6.930731 AGTGCACCTCTTTTGTTCTTAAAAA 58.069 32.000 14.63 0.00 0.00 1.94
2906 3163 6.952773 TTACATTGTAAGTGCACCTCTTTT 57.047 33.333 14.63 3.09 0.00 2.27
2934 3191 4.407296 ACTCCATCCAACTAAGGATCAGAC 59.593 45.833 0.00 0.00 45.16 3.51
2949 3206 3.569701 TCAAAACAGCAAAGACTCCATCC 59.430 43.478 0.00 0.00 0.00 3.51
2962 3219 2.262211 GCCAATTCCGATCAAAACAGC 58.738 47.619 0.00 0.00 0.00 4.40
2973 3230 1.209127 GAACACGTGGCCAATTCCG 59.791 57.895 21.57 9.96 0.00 4.30
2983 3240 5.435557 GTCTTTCAGAAATGAGAACACGTG 58.564 41.667 15.48 15.48 0.00 4.49
2984 3241 4.511826 GGTCTTTCAGAAATGAGAACACGT 59.488 41.667 0.00 0.00 0.00 4.49
2985 3242 4.752101 AGGTCTTTCAGAAATGAGAACACG 59.248 41.667 0.00 0.00 0.00 4.49
2986 3243 7.730364 TTAGGTCTTTCAGAAATGAGAACAC 57.270 36.000 0.00 0.00 0.00 3.32
2999 3256 5.871324 AAATAGGGGGTTTAGGTCTTTCA 57.129 39.130 0.00 0.00 0.00 2.69
3004 3261 7.250032 ACGATATAAATAGGGGGTTTAGGTC 57.750 40.000 0.00 0.00 0.00 3.85
3012 3269 3.446161 TCTGCGACGATATAAATAGGGGG 59.554 47.826 0.00 0.00 0.00 5.40
3027 3284 2.139118 GGCCTATCATTCTTCTGCGAC 58.861 52.381 0.00 0.00 0.00 5.19
3136 3398 8.400947 AGTATTTCAGCACAAATATCACATGAC 58.599 33.333 0.00 0.00 32.20 3.06
3150 3412 8.451908 AATAATTGTAGGGAGTATTTCAGCAC 57.548 34.615 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.