Multiple sequence alignment - TraesCS3B01G048200

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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 TraesCS3B01G048200 chr3B 100.000 3167 0 0 1 3167 24411262 24408096 0.000000e+00 5849
1 TraesCS3B01G048200 chr3D 90.236 1823 61 40 584 2337 17012282 17010508 0.000000e+00 2272
2 TraesCS3B01G048200 chr3D 85.363 813 52 22 2377 3167 17010366 17009599 0.000000e+00 780
3 TraesCS3B01G048200 chr3D 85.664 565 50 8 1 563 17012804 17012269 1.650000e-157 566
4 TraesCS3B01G048200 chr3A 89.856 1528 55 34 590 2086 19862387 19863845 0.000000e+00 1871
5 TraesCS3B01G048200 chr3A 90.802 424 31 6 1 422 19861891 19862308 7.670000e-156 560
6 TraesCS3B01G048200 chr3A 86.364 308 21 11 2612 2905 19864451 19864751 1.830000e-82 316
7 TraesCS3B01G048200 chr3A 89.100 211 13 3 2127 2337 19863951 19864151 1.460000e-63 254
8 TraesCS3B01G048200 chr1D 75.630 952 189 28 935 1864 36315692 36316622 1.740000e-117 433
9 TraesCS3B01G048200 chr2D 88.579 359 32 3 1196 1554 12874389 12874738 8.120000e-116 427
10 TraesCS3B01G048200 chr1B 75.581 946 182 32 993 1915 56140812 56139893 3.780000e-114 422
11 TraesCS3B01G048200 chr1B 74.869 955 196 34 935 1867 55998392 55999324 8.230000e-106 394
12 TraesCS3B01G048200 chr1B 74.816 953 199 32 935 1867 56017044 56017975 2.960000e-105 392
13 TraesCS3B01G048200 chr1B 73.432 1148 226 58 749 1867 55976968 55978065 1.080000e-94 357
14 TraesCS3B01G048200 chr1A 75.196 895 184 29 992 1867 35536331 35537206 3.830000e-104 388
15 TraesCS3B01G048200 chr1A 73.754 903 193 32 986 1867 35486125 35487004 6.590000e-82 315


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 TraesCS3B01G048200 chr3B 24408096 24411262 3166 True 5849.00 5849 100.000000 1 3167 1 chr3B.!!$R1 3166
1 TraesCS3B01G048200 chr3D 17009599 17012804 3205 True 1206.00 2272 87.087667 1 3167 3 chr3D.!!$R1 3166
2 TraesCS3B01G048200 chr3A 19861891 19864751 2860 False 750.25 1871 89.030500 1 2905 4 chr3A.!!$F1 2904
3 TraesCS3B01G048200 chr1D 36315692 36316622 930 False 433.00 433 75.630000 935 1864 1 chr1D.!!$F1 929
4 TraesCS3B01G048200 chr1B 56139893 56140812 919 True 422.00 422 75.581000 993 1915 1 chr1B.!!$R1 922
5 TraesCS3B01G048200 chr1B 55998392 55999324 932 False 394.00 394 74.869000 935 1867 1 chr1B.!!$F2 932
6 TraesCS3B01G048200 chr1B 56017044 56017975 931 False 392.00 392 74.816000 935 1867 1 chr1B.!!$F3 932
7 TraesCS3B01G048200 chr1B 55976968 55978065 1097 False 357.00 357 73.432000 749 1867 1 chr1B.!!$F1 1118
8 TraesCS3B01G048200 chr1A 35536331 35537206 875 False 388.00 388 75.196000 992 1867 1 chr1A.!!$F2 875
9 TraesCS3B01G048200 chr1A 35486125 35487004 879 False 315.00 315 73.754000 986 1867 1 chr1A.!!$F1 881

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
875 905 0.816018 TCCTCGTCCATCTCGCTCTC 60.816 60.0 0.0 0.0 0.00 3.20 F
1881 1975 0.320596 CAATTGGTTGCCGCCATTGT 60.321 50.0 0.0 0.0 38.48 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 2009 0.190069 TCAGCCCGACCCTATATGGT 59.810 55.0 0.00 0.0 42.79 3.55 R
3075 3425 0.456653 CCGCGGCCAAAGAAATCAAG 60.457 55.0 14.67 0.0 0.00 3.02 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 8.938906 GGCATTTTAGTCATCAATTTGATTTGT 58.061 29.630 9.19 0.18 34.28 2.83
123 124 8.090831 TCTCTCTCCAATCCATATTAATCGTTG 58.909 37.037 0.00 0.00 0.00 4.10
223 247 9.412460 AGCAGATTCCAATACTATTTTTCATGA 57.588 29.630 0.00 0.00 0.00 3.07
255 279 5.918608 AGATATTTGTGTCAACCTCGCTAT 58.081 37.500 0.00 0.00 0.00 2.97
273 297 8.798153 CCTCGCTATTGAATTGTTTTAAATGTC 58.202 33.333 0.00 0.00 0.00 3.06
348 374 3.074094 ACATAGGTACTGCCTCTATCCGA 59.926 47.826 0.00 0.00 46.96 4.55
371 397 4.280929 AGTTTGTAAAGAGGGCATGGTTTC 59.719 41.667 0.00 0.00 0.00 2.78
384 410 4.646492 GGCATGGTTTCTTAGGTCATCAAT 59.354 41.667 0.00 0.00 0.00 2.57
410 436 3.871594 ACTAGCGAAATGTATGTTGCCTC 59.128 43.478 0.00 0.00 0.00 4.70
413 439 3.871594 AGCGAAATGTATGTTGCCTCTAC 59.128 43.478 0.00 0.00 0.00 2.59
418 444 7.466725 GCGAAATGTATGTTGCCTCTACAAATA 60.467 37.037 0.00 0.00 0.00 1.40
419 445 8.559536 CGAAATGTATGTTGCCTCTACAAATAT 58.440 33.333 0.00 0.00 0.00 1.28
427 453 9.797642 ATGTTGCCTCTACAAATATATCATTGA 57.202 29.630 4.50 0.00 0.00 2.57
428 454 9.797642 TGTTGCCTCTACAAATATATCATTGAT 57.202 29.630 4.28 4.28 0.00 2.57
478 504 7.076842 GTGTAGATGAACACTGCATTACATT 57.923 36.000 0.00 0.00 45.12 2.71
482 508 9.098355 GTAGATGAACACTGCATTACATTAAGA 57.902 33.333 0.00 0.00 0.00 2.10
567 595 8.599624 ACAATGAAACAGAATGATTTATCCCT 57.400 30.769 0.00 0.00 39.69 4.20
568 596 8.689972 ACAATGAAACAGAATGATTTATCCCTC 58.310 33.333 0.00 0.00 39.69 4.30
569 597 8.689061 CAATGAAACAGAATGATTTATCCCTCA 58.311 33.333 0.00 0.00 39.69 3.86
570 598 8.827832 ATGAAACAGAATGATTTATCCCTCAA 57.172 30.769 0.00 0.00 39.69 3.02
571 599 8.648698 TGAAACAGAATGATTTATCCCTCAAA 57.351 30.769 0.00 0.00 39.69 2.69
572 600 9.087871 TGAAACAGAATGATTTATCCCTCAAAA 57.912 29.630 0.00 0.00 39.69 2.44
573 601 9.927668 GAAACAGAATGATTTATCCCTCAAAAA 57.072 29.630 0.00 0.00 39.69 1.94
696 724 9.754382 CATCCCATTATAATCCACAAAGAAAAG 57.246 33.333 0.00 0.00 0.00 2.27
698 726 8.966868 TCCCATTATAATCCACAAAGAAAAGAC 58.033 33.333 0.00 0.00 0.00 3.01
699 727 8.748412 CCCATTATAATCCACAAAGAAAAGACA 58.252 33.333 0.00 0.00 0.00 3.41
787 817 2.051692 CCCCGATACTTATTCACCCCA 58.948 52.381 0.00 0.00 0.00 4.96
871 901 1.791103 CTCCTCCTCGTCCATCTCGC 61.791 65.000 0.00 0.00 0.00 5.03
872 902 1.826054 CCTCCTCGTCCATCTCGCT 60.826 63.158 0.00 0.00 0.00 4.93
873 903 1.652012 CTCCTCGTCCATCTCGCTC 59.348 63.158 0.00 0.00 0.00 5.03
874 904 0.817634 CTCCTCGTCCATCTCGCTCT 60.818 60.000 0.00 0.00 0.00 4.09
875 905 0.816018 TCCTCGTCCATCTCGCTCTC 60.816 60.000 0.00 0.00 0.00 3.20
1649 1707 3.073735 CCGTGCCTCCTCTGCTCT 61.074 66.667 0.00 0.00 0.00 4.09
1739 1812 1.742768 CCGTCCCCAGATGCTACTC 59.257 63.158 0.00 0.00 0.00 2.59
1881 1975 0.320596 CAATTGGTTGCCGCCATTGT 60.321 50.000 0.00 0.00 38.48 2.71
1882 1976 0.320596 AATTGGTTGCCGCCATTGTG 60.321 50.000 0.00 0.00 38.48 3.33
1883 1977 1.184322 ATTGGTTGCCGCCATTGTGA 61.184 50.000 0.00 0.00 38.48 3.58
1884 1978 1.804396 TTGGTTGCCGCCATTGTGAG 61.804 55.000 0.00 0.00 38.48 3.51
1885 1979 2.126346 GTTGCCGCCATTGTGAGC 60.126 61.111 0.00 0.00 0.00 4.26
1915 2009 9.453572 GCTCTACATAATCCATCCATTAATTGA 57.546 33.333 0.00 0.00 0.00 2.57
1936 2034 1.208052 CCATATAGGGTCGGGCTGATG 59.792 57.143 0.00 0.00 0.00 3.07
1956 2054 1.404391 GTGAATCCCAGCAGCATTCAG 59.596 52.381 6.20 0.00 37.24 3.02
1972 2070 4.532276 CATTCAGCTAGTAGTCGTAGCAG 58.468 47.826 5.01 0.00 44.62 4.24
1973 2071 1.941294 TCAGCTAGTAGTCGTAGCAGC 59.059 52.381 5.01 0.00 44.62 5.25
1974 2072 1.671328 CAGCTAGTAGTCGTAGCAGCA 59.329 52.381 5.01 0.00 44.62 4.41
1975 2073 1.944024 AGCTAGTAGTCGTAGCAGCAG 59.056 52.381 5.01 0.00 44.62 4.24
1976 2074 1.671845 GCTAGTAGTCGTAGCAGCAGT 59.328 52.381 0.00 0.00 42.21 4.40
1977 2075 2.871022 GCTAGTAGTCGTAGCAGCAGTA 59.129 50.000 0.00 0.00 42.21 2.74
1978 2076 3.059461 GCTAGTAGTCGTAGCAGCAGTAG 60.059 52.174 0.00 0.00 42.21 2.57
1979 2077 2.988570 AGTAGTCGTAGCAGCAGTAGT 58.011 47.619 0.00 0.00 0.00 2.73
1980 2078 2.678836 AGTAGTCGTAGCAGCAGTAGTG 59.321 50.000 0.00 0.00 0.00 2.74
1981 2079 0.811915 AGTCGTAGCAGCAGTAGTGG 59.188 55.000 0.00 0.00 0.00 4.00
1982 2080 0.526662 GTCGTAGCAGCAGTAGTGGT 59.473 55.000 0.00 0.00 33.53 4.16
1983 2081 1.741706 GTCGTAGCAGCAGTAGTGGTA 59.258 52.381 1.09 0.00 31.49 3.25
1984 2082 2.163010 GTCGTAGCAGCAGTAGTGGTAA 59.837 50.000 1.09 0.00 31.49 2.85
1985 2083 2.422479 TCGTAGCAGCAGTAGTGGTAAG 59.578 50.000 1.09 0.00 31.49 2.34
1986 2084 2.541556 GTAGCAGCAGTAGTGGTAAGC 58.458 52.381 1.09 3.00 31.49 3.09
1987 2085 0.976641 AGCAGCAGTAGTGGTAAGCA 59.023 50.000 12.85 0.00 31.49 3.91
2004 2102 3.786809 CAGCAAGTGCAAGTGATGG 57.213 52.632 6.00 0.00 45.16 3.51
2045 2146 1.453745 CCAGCAGTGGTGGTTGTGT 60.454 57.895 29.49 0.00 45.06 3.72
2110 2240 4.316446 CGCTCAGTACAATCGTTAACATCG 60.316 45.833 6.39 0.00 0.00 3.84
2122 2252 3.612423 CGTTAACATCGATCTCTGTTGCA 59.388 43.478 15.95 0.00 36.34 4.08
2123 2253 4.091365 CGTTAACATCGATCTCTGTTGCAA 59.909 41.667 15.95 0.00 36.34 4.08
2124 2254 5.389411 CGTTAACATCGATCTCTGTTGCAAA 60.389 40.000 15.95 4.37 36.34 3.68
2125 2255 6.546395 GTTAACATCGATCTCTGTTGCAAAT 58.454 36.000 15.95 0.00 36.34 2.32
2165 2331 5.221880 TCTTCTGTGCATGGAAATTTTTCG 58.778 37.500 0.00 0.00 38.06 3.46
2256 2433 1.971695 GAGGGGTTGCGTTTCTGGG 60.972 63.158 0.00 0.00 0.00 4.45
2397 2699 2.637025 CGTGCCCCAAGTTCGTTG 59.363 61.111 0.00 0.00 35.71 4.10
2406 2708 1.999823 CAAGTTCGTTGGTTCGTTCG 58.000 50.000 0.00 0.00 31.82 3.95
2407 2709 0.932399 AAGTTCGTTGGTTCGTTCGG 59.068 50.000 0.00 0.00 0.00 4.30
2408 2710 0.179103 AGTTCGTTGGTTCGTTCGGT 60.179 50.000 0.00 0.00 0.00 4.69
2409 2711 0.042794 GTTCGTTGGTTCGTTCGGTG 60.043 55.000 0.00 0.00 0.00 4.94
2410 2712 0.179116 TTCGTTGGTTCGTTCGGTGA 60.179 50.000 0.00 0.00 0.00 4.02
2411 2713 0.871163 TCGTTGGTTCGTTCGGTGAC 60.871 55.000 0.00 0.00 0.00 3.67
2487 2791 0.589729 CGTCCATGCACGCTTTATGC 60.590 55.000 0.00 0.00 43.68 3.14
2489 2793 0.394216 TCCATGCACGCTTTATGCCT 60.394 50.000 0.00 0.00 42.69 4.75
2491 2795 1.135024 CCATGCACGCTTTATGCCTTT 60.135 47.619 0.00 0.00 42.69 3.11
2493 2797 2.810439 TGCACGCTTTATGCCTTTTT 57.190 40.000 0.00 0.00 42.69 1.94
2516 2820 1.060937 CGTCTGCACGCTTTATGGC 59.939 57.895 0.00 0.00 39.69 4.40
2517 2821 1.361668 CGTCTGCACGCTTTATGGCT 61.362 55.000 0.00 0.00 39.69 4.75
2520 2824 1.996786 CTGCACGCTTTATGGCTGGG 61.997 60.000 0.00 0.00 0.00 4.45
2523 2850 0.392998 CACGCTTTATGGCTGGGAGT 60.393 55.000 0.00 0.00 0.00 3.85
2525 2852 1.134491 ACGCTTTATGGCTGGGAGTAC 60.134 52.381 0.00 0.00 0.00 2.73
2528 2855 2.822764 CTTTATGGCTGGGAGTACGTC 58.177 52.381 0.00 0.00 0.00 4.34
2544 2871 1.728426 GTCACGTTACGCGCTGAGT 60.728 57.895 5.73 0.00 46.11 3.41
2562 2889 2.671396 GAGTCGCCGTTATTTGTCATGT 59.329 45.455 0.00 0.00 0.00 3.21
2563 2890 2.415168 AGTCGCCGTTATTTGTCATGTG 59.585 45.455 0.00 0.00 0.00 3.21
2564 2891 1.129624 TCGCCGTTATTTGTCATGTGC 59.870 47.619 0.00 0.00 0.00 4.57
2565 2892 1.534028 GCCGTTATTTGTCATGTGCG 58.466 50.000 0.00 0.00 0.00 5.34
2566 2893 1.793714 GCCGTTATTTGTCATGTGCGG 60.794 52.381 0.00 0.00 40.72 5.69
2582 2909 5.957842 TGTGCGGAACATTTTTAATCTCT 57.042 34.783 0.00 0.00 32.36 3.10
2585 2912 7.877003 TGTGCGGAACATTTTTAATCTCTTTA 58.123 30.769 0.00 0.00 32.36 1.85
2588 2915 9.352784 TGCGGAACATTTTTAATCTCTTTATTG 57.647 29.630 0.00 0.00 0.00 1.90
2601 2928 6.687081 TCTCTTTATTGAACACCGTTTTGT 57.313 33.333 0.00 0.00 0.00 2.83
2603 2930 8.385898 TCTCTTTATTGAACACCGTTTTGTAT 57.614 30.769 0.00 0.00 0.00 2.29
2615 2942 5.062308 CACCGTTTTGTATAGCTCTGTTCTC 59.938 44.000 0.00 0.00 0.00 2.87
2649 2979 4.907582 CGAAAATCGTACTGTTTTGGAACC 59.092 41.667 9.06 0.00 34.72 3.62
2684 3014 7.637709 TCGAATCGTTATTAGTCCAATGATG 57.362 36.000 1.52 0.00 32.16 3.07
2727 3057 0.248702 GCTCTCCGAACCGTCTGATC 60.249 60.000 0.00 0.00 0.00 2.92
2801 3131 1.000938 CCTACCGTAGTTATGGGACGC 60.001 57.143 4.86 0.00 36.66 5.19
2910 3251 2.556622 CGGACCTATTTTGTGTTTGCCT 59.443 45.455 0.00 0.00 0.00 4.75
2920 3261 0.451783 GTGTTTGCCTATGCCTTCCG 59.548 55.000 0.00 0.00 36.33 4.30
2964 3305 4.203226 TGCCTTGTTGTTTATGTGTCTCA 58.797 39.130 0.00 0.00 0.00 3.27
2965 3306 4.036262 TGCCTTGTTGTTTATGTGTCTCAC 59.964 41.667 0.00 0.00 34.56 3.51
2980 3322 1.533033 TCACCCGAGACAGGCTGAA 60.533 57.895 23.66 0.00 0.00 3.02
2992 3342 0.400213 AGGCTGAAAATGGGTCGTGA 59.600 50.000 0.00 0.00 0.00 4.35
3036 3386 5.679734 ATATGGCTCGATTGATTTGTCAC 57.320 39.130 0.00 0.00 0.00 3.67
3046 3396 8.956533 TCGATTGATTTGTCACTCCATTAATA 57.043 30.769 0.00 0.00 0.00 0.98
3047 3397 9.389755 TCGATTGATTTGTCACTCCATTAATAA 57.610 29.630 0.00 0.00 0.00 1.40
3054 3404 9.872684 ATTTGTCACTCCATTAATAATGATCCT 57.127 29.630 14.10 0.00 41.46 3.24
3072 3422 9.584008 AATGATCCTGATCTTTACTATGCAAAT 57.416 29.630 8.50 0.00 38.60 2.32
3075 3425 5.466728 TCCTGATCTTTACTATGCAAATCGC 59.533 40.000 0.00 0.00 42.89 4.58
3083 3433 7.910162 TCTTTACTATGCAAATCGCTTGATTTC 59.090 33.333 0.00 0.00 46.79 2.17
3128 3478 4.673580 CGGATTATACGGATAACCCTGACG 60.674 50.000 9.24 1.85 29.53 4.35
3146 3496 3.196901 TGACGGTGCACCTATCATAGTTT 59.803 43.478 32.28 0.96 0.00 2.66
3148 3498 4.189231 ACGGTGCACCTATCATAGTTTTC 58.811 43.478 32.28 2.08 0.00 2.29
3164 3514 0.660488 TTTCGCACGCAACATTCACT 59.340 45.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.713967 GCCATGGCCGCTTCACAAT 61.714 57.895 27.24 0.00 34.56 2.71
103 104 6.545666 AGCAACAACGATTAATATGGATTGGA 59.454 34.615 0.00 0.00 0.00 3.53
104 105 6.738114 AGCAACAACGATTAATATGGATTGG 58.262 36.000 0.00 0.00 0.00 3.16
106 107 9.950680 CTAAAGCAACAACGATTAATATGGATT 57.049 29.630 0.00 0.00 0.00 3.01
119 120 5.106830 CCCCTTTAGTACTAAAGCAACAACG 60.107 44.000 35.17 24.23 46.46 4.10
123 124 4.586884 AGCCCCTTTAGTACTAAAGCAAC 58.413 43.478 35.17 27.42 46.46 4.17
225 249 8.450964 CGAGGTTGACACAAATATCTTTACATT 58.549 33.333 0.00 0.00 0.00 2.71
226 250 7.414098 GCGAGGTTGACACAAATATCTTTACAT 60.414 37.037 0.00 0.00 0.00 2.29
227 251 6.128391 GCGAGGTTGACACAAATATCTTTACA 60.128 38.462 0.00 0.00 0.00 2.41
228 252 6.092259 AGCGAGGTTGACACAAATATCTTTAC 59.908 38.462 0.00 0.00 0.00 2.01
229 253 6.170506 AGCGAGGTTGACACAAATATCTTTA 58.829 36.000 0.00 0.00 0.00 1.85
230 254 5.003804 AGCGAGGTTGACACAAATATCTTT 58.996 37.500 0.00 0.00 0.00 2.52
231 255 4.579869 AGCGAGGTTGACACAAATATCTT 58.420 39.130 0.00 0.00 0.00 2.40
232 256 4.207891 AGCGAGGTTGACACAAATATCT 57.792 40.909 0.00 0.00 0.00 1.98
233 257 6.257849 TCAATAGCGAGGTTGACACAAATATC 59.742 38.462 0.00 0.00 29.93 1.63
234 258 6.112734 TCAATAGCGAGGTTGACACAAATAT 58.887 36.000 0.00 0.00 29.93 1.28
235 259 5.483811 TCAATAGCGAGGTTGACACAAATA 58.516 37.500 0.00 0.00 29.93 1.40
236 260 4.323417 TCAATAGCGAGGTTGACACAAAT 58.677 39.130 0.00 0.00 29.93 2.32
237 261 3.734463 TCAATAGCGAGGTTGACACAAA 58.266 40.909 0.00 0.00 29.93 2.83
238 262 3.394674 TCAATAGCGAGGTTGACACAA 57.605 42.857 0.00 0.00 29.93 3.33
239 263 3.394674 TTCAATAGCGAGGTTGACACA 57.605 42.857 0.00 0.00 34.34 3.72
288 313 6.151691 TCATCGTAGTACTAAAACTTGCGTT 58.848 36.000 3.61 0.00 32.33 4.84
348 374 3.525800 ACCATGCCCTCTTTACAAACT 57.474 42.857 0.00 0.00 0.00 2.66
384 410 5.391523 GGCAACATACATTTCGCTAGTCAAA 60.392 40.000 0.00 0.00 0.00 2.69
437 463 9.778741 TCATCTACACATTAGAAACTTTGTTCT 57.221 29.630 0.00 0.00 40.89 3.01
490 516 6.588204 TGTTTCAGTGTACCTGTTTACATCT 58.412 36.000 10.08 0.00 42.19 2.90
491 517 6.854496 TGTTTCAGTGTACCTGTTTACATC 57.146 37.500 10.08 0.00 42.19 3.06
498 524 5.680619 TGAGAAATGTTTCAGTGTACCTGT 58.319 37.500 8.09 0.00 42.19 4.00
605 633 8.340618 TCCATTTCTCTTCGAATTTCTCATTT 57.659 30.769 0.00 0.00 0.00 2.32
696 724 5.857517 GCCGCTGATTTAGTACTACTATGTC 59.142 44.000 0.91 0.00 29.64 3.06
698 726 4.852104 CGCCGCTGATTTAGTACTACTATG 59.148 45.833 0.91 0.00 29.64 2.23
699 727 4.758674 TCGCCGCTGATTTAGTACTACTAT 59.241 41.667 0.91 0.00 29.64 2.12
700 728 4.129380 TCGCCGCTGATTTAGTACTACTA 58.871 43.478 0.91 0.00 0.00 1.82
701 729 2.947652 TCGCCGCTGATTTAGTACTACT 59.052 45.455 0.91 0.00 0.00 2.57
702 730 3.344904 TCGCCGCTGATTTAGTACTAC 57.655 47.619 0.91 0.00 0.00 2.73
787 817 6.919775 AAATAGATGGAATAGTAGGCGTCT 57.080 37.500 0.00 0.00 0.00 4.18
871 901 1.421646 GGAGAGGAGAGGAGAGGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
872 902 1.010793 AGGAGAGGAGAGGAGAGGAGA 59.989 57.143 0.00 0.00 0.00 3.71
873 903 1.421646 GAGGAGAGGAGAGGAGAGGAG 59.578 61.905 0.00 0.00 0.00 3.69
874 904 1.518367 GAGGAGAGGAGAGGAGAGGA 58.482 60.000 0.00 0.00 0.00 3.71
875 905 0.478507 GGAGGAGAGGAGAGGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
1603 1649 3.123620 GAGCTGCTTCTGCACGGG 61.124 66.667 2.53 0.00 45.31 5.28
1649 1707 2.922955 TGGAATGTAATGTGAGGGGGAA 59.077 45.455 0.00 0.00 0.00 3.97
1883 1977 4.222588 GGATGGATTATGTAGAGCTCAGCT 59.777 45.833 17.77 0.00 43.88 4.24
1884 1978 4.020751 TGGATGGATTATGTAGAGCTCAGC 60.021 45.833 17.77 8.55 0.00 4.26
1885 1979 5.735285 TGGATGGATTATGTAGAGCTCAG 57.265 43.478 17.77 0.00 0.00 3.35
1915 2009 0.190069 TCAGCCCGACCCTATATGGT 59.810 55.000 0.00 0.00 42.79 3.55
1916 2010 1.208052 CATCAGCCCGACCCTATATGG 59.792 57.143 0.00 0.00 0.00 2.74
1956 2054 1.671845 ACTGCTGCTACGACTACTAGC 59.328 52.381 0.00 0.00 37.68 3.42
1972 2070 1.734465 CTTGCTGCTTACCACTACTGC 59.266 52.381 0.00 0.00 0.00 4.40
1973 2071 2.738846 CACTTGCTGCTTACCACTACTG 59.261 50.000 0.00 0.00 0.00 2.74
1974 2072 2.872038 GCACTTGCTGCTTACCACTACT 60.872 50.000 0.00 0.00 43.33 2.57
1975 2073 1.464997 GCACTTGCTGCTTACCACTAC 59.535 52.381 0.00 0.00 43.33 2.73
1976 2074 1.808411 GCACTTGCTGCTTACCACTA 58.192 50.000 0.00 0.00 43.33 2.74
1977 2075 2.633860 GCACTTGCTGCTTACCACT 58.366 52.632 0.00 0.00 43.33 4.00
1986 2084 0.956633 ACCATCACTTGCACTTGCTG 59.043 50.000 2.33 0.00 42.66 4.41
1987 2085 1.610522 GAACCATCACTTGCACTTGCT 59.389 47.619 2.33 0.00 42.66 3.91
2004 2102 6.039616 GGAGAATCACTGACTAGTCATGAAC 58.960 44.000 27.05 23.70 36.29 3.18
2045 2146 3.121738 TCCGCTGATGATACTACGAGA 57.878 47.619 0.00 0.00 0.00 4.04
2088 2218 4.796830 TCGATGTTAACGATTGTACTGAGC 59.203 41.667 0.26 0.00 34.85 4.26
2122 2252 7.117812 CAGAAGAAGCATTGAGATTGCAAATTT 59.882 33.333 1.71 0.00 42.62 1.82
2123 2253 6.590292 CAGAAGAAGCATTGAGATTGCAAATT 59.410 34.615 1.71 0.00 42.62 1.82
2124 2254 6.100004 CAGAAGAAGCATTGAGATTGCAAAT 58.900 36.000 1.71 0.00 42.62 2.32
2125 2255 5.010314 ACAGAAGAAGCATTGAGATTGCAAA 59.990 36.000 1.71 0.00 42.62 3.68
2193 2359 2.020720 CACGGCCATTAGCACCAATAA 58.979 47.619 2.24 0.00 46.50 1.40
2194 2360 1.674359 CACGGCCATTAGCACCAATA 58.326 50.000 2.24 0.00 46.50 1.90
2195 2361 1.037030 CCACGGCCATTAGCACCAAT 61.037 55.000 2.24 0.00 46.50 3.16
2207 2373 1.215647 CTCACTACTCACCACGGCC 59.784 63.158 0.00 0.00 0.00 6.13
2345 2531 4.106925 CTGCCTCCCTCTGCCCAC 62.107 72.222 0.00 0.00 0.00 4.61
2397 2699 3.408851 GGCGTCACCGAACGAACC 61.409 66.667 8.76 0.00 45.37 3.62
2503 2807 1.718757 CTCCCAGCCATAAAGCGTGC 61.719 60.000 0.00 0.00 38.01 5.34
2504 2808 0.392998 ACTCCCAGCCATAAAGCGTG 60.393 55.000 0.00 0.00 38.01 5.34
2505 2809 1.134491 GTACTCCCAGCCATAAAGCGT 60.134 52.381 0.00 0.00 38.01 5.07
2506 2810 1.583054 GTACTCCCAGCCATAAAGCG 58.417 55.000 0.00 0.00 38.01 4.68
2507 2811 1.134491 ACGTACTCCCAGCCATAAAGC 60.134 52.381 0.00 0.00 0.00 3.51
2508 2812 2.167693 TGACGTACTCCCAGCCATAAAG 59.832 50.000 0.00 0.00 0.00 1.85
2509 2813 2.093869 GTGACGTACTCCCAGCCATAAA 60.094 50.000 0.00 0.00 0.00 1.40
2510 2814 1.479323 GTGACGTACTCCCAGCCATAA 59.521 52.381 0.00 0.00 0.00 1.90
2511 2815 1.108776 GTGACGTACTCCCAGCCATA 58.891 55.000 0.00 0.00 0.00 2.74
2512 2816 1.898154 GTGACGTACTCCCAGCCAT 59.102 57.895 0.00 0.00 0.00 4.40
2513 2817 2.632544 CGTGACGTACTCCCAGCCA 61.633 63.158 0.00 0.00 0.00 4.75
2514 2818 2.151049 AACGTGACGTACTCCCAGCC 62.151 60.000 12.37 0.00 39.99 4.85
2515 2819 0.523072 TAACGTGACGTACTCCCAGC 59.477 55.000 12.37 0.00 39.99 4.85
2516 2820 1.464687 CGTAACGTGACGTACTCCCAG 60.465 57.143 17.61 0.00 39.99 4.45
2517 2821 0.516877 CGTAACGTGACGTACTCCCA 59.483 55.000 17.61 0.00 39.99 4.37
2520 2824 1.714789 GCGCGTAACGTGACGTACTC 61.715 60.000 25.62 8.86 44.74 2.59
2523 2850 1.793223 CAGCGCGTAACGTGACGTA 60.793 57.895 25.62 0.00 44.74 3.57
2525 2852 2.764925 CTCAGCGCGTAACGTGACG 61.765 63.158 21.41 21.41 46.11 4.35
2528 2855 2.764925 CGACTCAGCGCGTAACGTG 61.765 63.158 8.43 0.00 46.11 4.49
2544 2871 1.129624 GCACATGACAAATAACGGCGA 59.870 47.619 16.62 0.00 0.00 5.54
2562 2889 9.352784 CAATAAAGAGATTAAAAATGTTCCGCA 57.647 29.630 0.00 0.00 0.00 5.69
2563 2890 9.567848 TCAATAAAGAGATTAAAAATGTTCCGC 57.432 29.630 0.00 0.00 0.00 5.54
2576 2903 7.712797 ACAAAACGGTGTTCAATAAAGAGATT 58.287 30.769 0.00 0.00 0.00 2.40
2578 2905 6.687081 ACAAAACGGTGTTCAATAAAGAGA 57.313 33.333 0.00 0.00 0.00 3.10
2579 2906 9.755064 CTATACAAAACGGTGTTCAATAAAGAG 57.245 33.333 0.00 0.00 32.75 2.85
2580 2907 8.231837 GCTATACAAAACGGTGTTCAATAAAGA 58.768 33.333 0.00 0.00 32.75 2.52
2581 2908 8.234546 AGCTATACAAAACGGTGTTCAATAAAG 58.765 33.333 0.00 0.00 32.75 1.85
2582 2909 8.101654 AGCTATACAAAACGGTGTTCAATAAA 57.898 30.769 0.00 0.00 32.75 1.40
2585 2912 5.938125 AGAGCTATACAAAACGGTGTTCAAT 59.062 36.000 0.00 0.00 32.75 2.57
2588 2915 4.689345 ACAGAGCTATACAAAACGGTGTTC 59.311 41.667 0.00 0.00 32.75 3.18
2595 2922 6.818644 TCCATGAGAACAGAGCTATACAAAAC 59.181 38.462 0.00 0.00 0.00 2.43
2601 2928 5.011431 CACCATCCATGAGAACAGAGCTATA 59.989 44.000 0.00 0.00 0.00 1.31
2603 2930 3.133542 CACCATCCATGAGAACAGAGCTA 59.866 47.826 0.00 0.00 0.00 3.32
2615 2942 1.401552 ACGATTTTCGCACCATCCATG 59.598 47.619 0.00 0.00 45.12 3.66
2684 3014 4.133078 GAGGACCAGGACAATTCATCATC 58.867 47.826 0.00 0.00 0.00 2.92
2743 3073 4.642542 GTACGAGCCGCCGATCCC 62.643 72.222 8.04 0.00 0.00 3.85
2752 3082 2.493501 GGGTTCTCCGTACGAGCC 59.506 66.667 18.76 12.08 38.62 4.70
2764 3094 1.600916 GGTGCACTGTCAGGGGTTC 60.601 63.158 17.98 0.00 0.00 3.62
2801 3131 2.371910 TGCATGCATGTCAATGTTGG 57.628 45.000 26.79 0.00 36.08 3.77
2832 3172 2.113774 TGGATCCGCCATCATGCC 59.886 61.111 7.39 0.00 43.33 4.40
2964 3305 0.693049 ATTTTCAGCCTGTCTCGGGT 59.307 50.000 0.00 0.00 34.51 5.28
2965 3306 1.089920 CATTTTCAGCCTGTCTCGGG 58.910 55.000 0.00 0.00 0.00 5.14
3002 3352 5.290493 TCGAGCCATATATTCCAAACAGT 57.710 39.130 0.00 0.00 0.00 3.55
3015 3365 4.769688 AGTGACAAATCAATCGAGCCATA 58.230 39.130 0.00 0.00 36.31 2.74
3046 3396 8.985315 TTTGCATAGTAAAGATCAGGATCATT 57.015 30.769 11.55 8.26 40.22 2.57
3047 3397 9.228949 GATTTGCATAGTAAAGATCAGGATCAT 57.771 33.333 11.55 0.00 40.22 2.45
3048 3398 7.386025 CGATTTGCATAGTAAAGATCAGGATCA 59.614 37.037 11.55 0.00 40.22 2.92
3049 3399 7.623089 GCGATTTGCATAGTAAAGATCAGGATC 60.623 40.741 0.95 0.95 45.45 3.36
3050 3400 6.148480 GCGATTTGCATAGTAAAGATCAGGAT 59.852 38.462 0.00 0.00 45.45 3.24
3051 3401 5.466728 GCGATTTGCATAGTAAAGATCAGGA 59.533 40.000 0.00 0.00 45.45 3.86
3052 3402 5.683859 GCGATTTGCATAGTAAAGATCAGG 58.316 41.667 0.00 0.00 45.45 3.86
3072 3422 0.521291 CGGCCAAAGAAATCAAGCGA 59.479 50.000 2.24 0.00 0.00 4.93
3075 3425 0.456653 CCGCGGCCAAAGAAATCAAG 60.457 55.000 14.67 0.00 0.00 3.02
3083 3433 3.508840 GTCCATCCGCGGCCAAAG 61.509 66.667 23.51 7.24 0.00 2.77
3128 3478 3.002348 GCGAAAACTATGATAGGTGCACC 59.998 47.826 29.22 29.22 0.00 5.01
3146 3496 0.660488 AAGTGAATGTTGCGTGCGAA 59.340 45.000 0.00 0.00 0.00 4.70
3148 3498 2.412900 CAAGTGAATGTTGCGTGCG 58.587 52.632 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.