Multiple sequence alignment - TraesCS6B01G348900

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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 TraesCS6B01G348900 chr6B 100.000 3261 0 0 1 3261 613575754 613572494 0.000000e+00 6023.0
1 TraesCS6B01G348900 chr6A 89.009 2593 134 63 1 2523 554694165 554691654 0.000000e+00 3070.0
2 TraesCS6B01G348900 chr6A 93.429 350 21 2 2912 3261 554691414 554691067 4.820000e-143 518.0
3 TraesCS6B01G348900 chr6A 95.652 184 8 0 2730 2913 595647018 595647201 2.460000e-76 296.0
4 TraesCS6B01G348900 chr6A 92.857 196 11 3 2518 2710 554691608 554691413 6.890000e-72 281.0
5 TraesCS6B01G348900 chr6A 91.579 190 15 1 1995 2183 554519279 554519090 8.970000e-66 261.0
6 TraesCS6B01G348900 chr6D 92.882 1419 74 9 479 1885 408896523 408895120 0.000000e+00 2036.0
7 TraesCS6B01G348900 chr6D 92.788 624 31 10 1898 2518 408894015 408893403 0.000000e+00 891.0
8 TraesCS6B01G348900 chr6D 89.597 471 22 10 1 449 408896985 408896520 1.010000e-159 573.0
9 TraesCS6B01G348900 chr6D 90.306 196 16 2 2518 2710 408893359 408893164 1.500000e-63 254.0
10 TraesCS6B01G348900 chr6D 80.233 258 24 13 1917 2153 408691057 408690806 5.600000e-38 169.0
11 TraesCS6B01G348900 chr1D 87.308 717 66 8 1027 1740 491685282 491685976 0.000000e+00 797.0
12 TraesCS6B01G348900 chr2B 95.676 185 8 0 2730 2914 16225462 16225278 6.840000e-77 298.0
13 TraesCS6B01G348900 chr7D 95.652 184 8 0 2730 2913 62255410 62255593 2.460000e-76 296.0
14 TraesCS6B01G348900 chr7D 98.077 52 0 1 1676 1727 426824434 426824384 4.480000e-14 89.8
15 TraesCS6B01G348900 chr7B 95.652 184 8 0 2730 2913 152487061 152486878 2.460000e-76 296.0
16 TraesCS6B01G348900 chr5B 95.652 184 8 0 2730 2913 36478163 36478346 2.460000e-76 296.0
17 TraesCS6B01G348900 chr5B 95.652 184 8 0 2730 2913 184284149 184283966 2.460000e-76 296.0
18 TraesCS6B01G348900 chr5B 93.750 64 4 0 1384 1447 447194410 447194473 2.680000e-16 97.1
19 TraesCS6B01G348900 chr2D 95.652 184 8 0 2730 2913 103731864 103732047 2.460000e-76 296.0
20 TraesCS6B01G348900 chr2A 95.652 184 8 0 2730 2913 763213638 763213821 2.460000e-76 296.0
21 TraesCS6B01G348900 chr3D 95.161 186 9 0 2730 2915 561707971 561708156 8.850000e-76 294.0


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 TraesCS6B01G348900 chr6B 613572494 613575754 3260 True 6023.000000 6023 100.00000 1 3261 1 chr6B.!!$R1 3260
1 TraesCS6B01G348900 chr6A 554691067 554694165 3098 True 1289.666667 3070 91.76500 1 3261 3 chr6A.!!$R2 3260
2 TraesCS6B01G348900 chr6D 408893164 408896985 3821 True 938.500000 2036 91.39325 1 2710 4 chr6D.!!$R2 2709
3 TraesCS6B01G348900 chr1D 491685282 491685976 694 False 797.000000 797 87.30800 1027 1740 1 chr1D.!!$F1 713

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
779 835 0.034896 GAGAGGCAAGGGACAAACGA 59.965 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2618 3857 0.035036 TCCCAACGTTGCGGATGTTA 59.965 50.0 25.45 10.63 35.73 2.41 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
51 52 4.213564 AGCCAGGAGTAGAGTGATTTTG 57.786 45.455 0.00 0.00 0.00 2.44
55 56 5.241728 GCCAGGAGTAGAGTGATTTTGTTTT 59.758 40.000 0.00 0.00 0.00 2.43
56 57 6.430000 GCCAGGAGTAGAGTGATTTTGTTTTA 59.570 38.462 0.00 0.00 0.00 1.52
57 58 7.121315 GCCAGGAGTAGAGTGATTTTGTTTTAT 59.879 37.037 0.00 0.00 0.00 1.40
285 298 8.017418 TGTCAAATTTTGGGATCAAACTAGTT 57.983 30.769 1.12 1.12 41.97 2.24
323 336 0.539051 CCCTTCTGCTCCGTGAGAAT 59.461 55.000 5.24 0.00 0.00 2.40
337 351 3.242413 CGTGAGAATAATTGGTCGCAAGG 60.242 47.826 0.00 0.00 38.47 3.61
379 403 0.828959 GTGTCGTTGTTTGCGTTTCG 59.171 50.000 0.00 0.00 0.00 3.46
390 414 6.627690 TGTTTGCGTTTCGTAAATTGAAAA 57.372 29.167 8.36 0.00 42.40 2.29
402 426 8.370493 TCGTAAATTGAAAATTTTGGCATGAA 57.630 26.923 8.47 0.00 0.00 2.57
501 527 3.057946 GGCAAGAGACATTCCAAGTGTTC 60.058 47.826 0.00 0.00 0.00 3.18
549 592 2.727798 AACGTGTGATAACGGTTTCTCG 59.272 45.455 0.00 3.89 41.71 4.04
552 595 2.340577 GTGTGATAACGGTTTCTCGACG 59.659 50.000 0.00 0.00 0.00 5.12
558 613 2.861006 GGTTTCTCGACGCCTTGC 59.139 61.111 0.00 0.00 0.00 4.01
559 614 1.959226 GGTTTCTCGACGCCTTGCA 60.959 57.895 0.00 0.00 0.00 4.08
560 615 1.298859 GGTTTCTCGACGCCTTGCAT 61.299 55.000 0.00 0.00 0.00 3.96
561 616 0.179215 GTTTCTCGACGCCTTGCATG 60.179 55.000 0.00 0.00 0.00 4.06
562 617 0.320334 TTTCTCGACGCCTTGCATGA 60.320 50.000 0.00 0.00 0.00 3.07
563 618 0.320334 TTCTCGACGCCTTGCATGAA 60.320 50.000 0.00 0.00 0.00 2.57
564 619 0.108186 TCTCGACGCCTTGCATGAAT 60.108 50.000 0.00 0.00 0.00 2.57
565 620 0.729116 CTCGACGCCTTGCATGAATT 59.271 50.000 0.00 0.00 0.00 2.17
566 621 1.933181 CTCGACGCCTTGCATGAATTA 59.067 47.619 0.00 0.00 0.00 1.40
567 622 1.663643 TCGACGCCTTGCATGAATTAC 59.336 47.619 0.00 0.00 0.00 1.89
568 623 1.396648 CGACGCCTTGCATGAATTACA 59.603 47.619 0.00 0.00 0.00 2.41
569 624 2.537529 CGACGCCTTGCATGAATTACAG 60.538 50.000 0.00 0.00 0.00 2.74
674 729 2.111384 AGTCACTGAACACCAGACAGT 58.889 47.619 0.00 0.00 45.78 3.55
714 769 2.584492 AAAACAGCCAGAAAGCACAC 57.416 45.000 0.00 0.00 34.23 3.82
715 770 0.381801 AAACAGCCAGAAAGCACACG 59.618 50.000 0.00 0.00 34.23 4.49
716 771 1.447317 AACAGCCAGAAAGCACACGG 61.447 55.000 0.00 0.00 34.23 4.94
717 772 1.597854 CAGCCAGAAAGCACACGGA 60.598 57.895 0.00 0.00 34.23 4.69
718 773 1.148273 AGCCAGAAAGCACACGGAA 59.852 52.632 0.00 0.00 34.23 4.30
719 774 0.465460 AGCCAGAAAGCACACGGAAA 60.465 50.000 0.00 0.00 34.23 3.13
752 807 3.728864 GCGAACGACTTTACCACGATCTA 60.729 47.826 0.00 0.00 0.00 1.98
764 819 0.465824 ACGATCTACCCCGTGGAGAG 60.466 60.000 0.00 0.00 37.64 3.20
779 835 0.034896 GAGAGGCAAGGGACAAACGA 59.965 55.000 0.00 0.00 0.00 3.85
780 836 0.693049 AGAGGCAAGGGACAAACGAT 59.307 50.000 0.00 0.00 0.00 3.73
960 1025 2.614057 GTTTCTTGCACCCCATAGATCG 59.386 50.000 0.00 0.00 0.00 3.69
966 1031 0.886490 CACCCCATAGATCGCTTGGC 60.886 60.000 6.20 0.00 0.00 4.52
974 1039 0.687757 AGATCGCTTGGCCTGGAGTA 60.688 55.000 3.32 0.00 0.00 2.59
1009 1074 0.935366 GATCGGTCGAATGGAGACGC 60.935 60.000 0.00 0.00 39.38 5.19
1010 1075 1.663379 ATCGGTCGAATGGAGACGCA 61.663 55.000 0.00 0.00 39.38 5.24
1059 1124 4.530857 CCCATGGACCCGCTCGTC 62.531 72.222 15.22 0.00 0.00 4.20
1844 1912 3.454573 CCGGCTGGCTGGTACGTA 61.455 66.667 11.97 0.00 37.68 3.57
1845 1913 2.202703 CGGCTGGCTGGTACGTAC 60.203 66.667 17.56 17.56 0.00 3.67
1871 1942 1.134946 CGTGCAATCCATTTCCTTCCC 59.865 52.381 0.00 0.00 0.00 3.97
1886 1961 5.924769 TCCTTCCCTCCTTAAGAAACTTT 57.075 39.130 3.36 0.00 0.00 2.66
2209 3376 3.175710 ACCGACTGGCCCAACCTT 61.176 61.111 0.00 0.00 39.70 3.50
2273 3440 3.730761 CTTGACCAGCAGCGGCAC 61.731 66.667 12.44 0.09 44.61 5.01
2286 3455 2.125673 GGCACGTACGTGGAGCAT 60.126 61.111 40.17 8.50 45.49 3.79
2304 3473 2.671396 GCATTTTTGGCTGATGCTCAAG 59.329 45.455 0.00 0.00 42.12 3.02
2331 3505 0.368227 GCACTCGATCGAGCAACTTG 59.632 55.000 38.12 29.32 45.54 3.16
2357 3538 7.980099 GCTGGTAATAGTGTATGTAAGTTCAGT 59.020 37.037 0.00 0.00 0.00 3.41
2383 3570 3.117888 ACAACAGAGTGGGAAGTTCACAT 60.118 43.478 11.79 0.28 37.58 3.21
2393 3580 5.590259 GTGGGAAGTTCACATGTTATGCTAT 59.410 40.000 11.79 0.00 29.44 2.97
2463 3650 3.488048 GCAGGCGTGTGCAAATTTA 57.512 47.368 8.40 0.00 45.35 1.40
2498 3685 5.308825 TCTTCAGAGAACCCAACAGATTTC 58.691 41.667 0.00 0.00 0.00 2.17
2502 3689 1.077169 AGAACCCAACAGATTTCCCCC 59.923 52.381 0.00 0.00 0.00 5.40
2523 3760 2.354203 CCTTCCCTGAGCAGTACAAGTC 60.354 54.545 0.00 0.00 0.00 3.01
2710 3952 3.874392 ATGAATTTGGGCAACAGCTAC 57.126 42.857 0.00 0.00 39.74 3.58
2711 3953 2.875296 TGAATTTGGGCAACAGCTACT 58.125 42.857 0.00 0.00 39.74 2.57
2712 3954 4.027674 TGAATTTGGGCAACAGCTACTA 57.972 40.909 0.00 0.00 39.74 1.82
2713 3955 3.756434 TGAATTTGGGCAACAGCTACTAC 59.244 43.478 0.00 0.00 39.74 2.73
2714 3956 2.194201 TTTGGGCAACAGCTACTACC 57.806 50.000 0.00 0.00 39.74 3.18
2715 3957 1.358152 TTGGGCAACAGCTACTACCT 58.642 50.000 0.00 0.00 39.74 3.08
2716 3958 0.902531 TGGGCAACAGCTACTACCTC 59.097 55.000 0.00 0.00 39.74 3.85
2717 3959 0.178301 GGGCAACAGCTACTACCTCC 59.822 60.000 0.00 0.00 39.74 4.30
2718 3960 0.179108 GGCAACAGCTACTACCTCCG 60.179 60.000 0.00 0.00 0.00 4.63
2719 3961 0.531200 GCAACAGCTACTACCTCCGT 59.469 55.000 0.00 0.00 0.00 4.69
2720 3962 1.469423 GCAACAGCTACTACCTCCGTC 60.469 57.143 0.00 0.00 0.00 4.79
2721 3963 2.093106 CAACAGCTACTACCTCCGTCT 58.907 52.381 0.00 0.00 0.00 4.18
2722 3964 2.041251 ACAGCTACTACCTCCGTCTC 57.959 55.000 0.00 0.00 0.00 3.36
2723 3965 0.938713 CAGCTACTACCTCCGTCTCG 59.061 60.000 0.00 0.00 0.00 4.04
2734 3976 3.888093 CCGTCTCGGTGAAAGTTCT 57.112 52.632 0.00 0.00 42.73 3.01
2736 3978 2.864968 CCGTCTCGGTGAAAGTTCTAG 58.135 52.381 0.00 0.00 42.73 2.43
2737 3979 2.415625 CCGTCTCGGTGAAAGTTCTAGG 60.416 54.545 0.00 0.00 42.73 3.02
2738 3980 2.228343 CGTCTCGGTGAAAGTTCTAGGT 59.772 50.000 0.00 0.00 0.00 3.08
2739 3981 3.305199 CGTCTCGGTGAAAGTTCTAGGTT 60.305 47.826 0.00 0.00 0.00 3.50
2740 3982 3.988517 GTCTCGGTGAAAGTTCTAGGTTG 59.011 47.826 0.00 0.00 0.00 3.77
2741 3983 3.893200 TCTCGGTGAAAGTTCTAGGTTGA 59.107 43.478 0.00 0.00 0.00 3.18
2742 3984 3.986277 TCGGTGAAAGTTCTAGGTTGAC 58.014 45.455 0.00 0.00 0.00 3.18
2743 3985 2.729882 CGGTGAAAGTTCTAGGTTGACG 59.270 50.000 0.00 0.00 0.00 4.35
2744 3986 3.551454 CGGTGAAAGTTCTAGGTTGACGA 60.551 47.826 0.00 0.00 0.00 4.20
2745 3987 4.566987 GGTGAAAGTTCTAGGTTGACGAT 58.433 43.478 0.00 0.00 0.00 3.73
2746 3988 4.995487 GGTGAAAGTTCTAGGTTGACGATT 59.005 41.667 0.00 0.00 0.00 3.34
2747 3989 5.469084 GGTGAAAGTTCTAGGTTGACGATTT 59.531 40.000 0.00 0.00 0.00 2.17
2748 3990 6.647895 GGTGAAAGTTCTAGGTTGACGATTTA 59.352 38.462 0.00 0.00 0.00 1.40
2749 3991 7.172019 GGTGAAAGTTCTAGGTTGACGATTTAA 59.828 37.037 0.00 0.00 0.00 1.52
2750 3992 8.008279 GTGAAAGTTCTAGGTTGACGATTTAAC 58.992 37.037 0.00 0.00 0.00 2.01
2751 3993 7.929785 TGAAAGTTCTAGGTTGACGATTTAACT 59.070 33.333 0.00 0.00 0.00 2.24
2752 3994 9.415544 GAAAGTTCTAGGTTGACGATTTAACTA 57.584 33.333 0.00 0.00 0.00 2.24
2753 3995 9.939802 AAAGTTCTAGGTTGACGATTTAACTAT 57.060 29.630 0.00 0.00 0.00 2.12
2754 3996 9.583765 AAGTTCTAGGTTGACGATTTAACTATC 57.416 33.333 0.00 0.00 0.00 2.08
2755 3997 8.968969 AGTTCTAGGTTGACGATTTAACTATCT 58.031 33.333 0.00 0.00 0.00 1.98
2874 4116 9.830975 TTTAATTCCTCAAATCGATGACATAGA 57.169 29.630 0.00 0.40 0.00 1.98
2875 4117 9.830975 TTAATTCCTCAAATCGATGACATAGAA 57.169 29.630 0.00 0.00 0.00 2.10
2876 4118 7.721286 ATTCCTCAAATCGATGACATAGAAC 57.279 36.000 0.00 0.00 0.00 3.01
2877 4119 6.471233 TCCTCAAATCGATGACATAGAACT 57.529 37.500 0.00 0.00 0.00 3.01
2878 4120 7.582667 TCCTCAAATCGATGACATAGAACTA 57.417 36.000 0.00 0.00 0.00 2.24
2879 4121 7.426410 TCCTCAAATCGATGACATAGAACTAC 58.574 38.462 0.00 0.00 0.00 2.73
2880 4122 6.360947 CCTCAAATCGATGACATAGAACTACG 59.639 42.308 0.00 0.00 0.00 3.51
2881 4123 5.685954 TCAAATCGATGACATAGAACTACGC 59.314 40.000 0.00 0.00 0.00 4.42
2882 4124 3.249013 TCGATGACATAGAACTACGCG 57.751 47.619 3.53 3.53 0.00 6.01
2883 4125 2.867975 TCGATGACATAGAACTACGCGA 59.132 45.455 15.93 0.00 0.00 5.87
2884 4126 3.310501 TCGATGACATAGAACTACGCGAA 59.689 43.478 15.93 0.00 0.00 4.70
2885 4127 4.024302 TCGATGACATAGAACTACGCGAAT 60.024 41.667 15.93 0.00 0.00 3.34
2886 4128 4.087225 CGATGACATAGAACTACGCGAATG 59.913 45.833 15.93 4.47 0.00 2.67
2887 4129 4.625972 TGACATAGAACTACGCGAATGA 57.374 40.909 15.93 0.00 0.00 2.57
2888 4130 4.348656 TGACATAGAACTACGCGAATGAC 58.651 43.478 15.93 0.66 0.00 3.06
2889 4131 4.095932 TGACATAGAACTACGCGAATGACT 59.904 41.667 15.93 9.07 0.00 3.41
2890 4132 4.995124 ACATAGAACTACGCGAATGACTT 58.005 39.130 15.93 0.00 0.00 3.01
2891 4133 6.127810 ACATAGAACTACGCGAATGACTTA 57.872 37.500 15.93 0.00 0.00 2.24
2892 4134 6.736123 ACATAGAACTACGCGAATGACTTAT 58.264 36.000 15.93 0.00 0.00 1.73
2893 4135 7.201145 ACATAGAACTACGCGAATGACTTATT 58.799 34.615 15.93 0.00 0.00 1.40
2894 4136 7.378995 ACATAGAACTACGCGAATGACTTATTC 59.621 37.037 15.93 3.24 41.46 1.75
2895 4137 5.647589 AGAACTACGCGAATGACTTATTCA 58.352 37.500 15.93 0.00 44.42 2.57
2896 4138 5.515626 AGAACTACGCGAATGACTTATTCAC 59.484 40.000 15.93 0.00 44.42 3.18
2897 4139 4.110482 ACTACGCGAATGACTTATTCACC 58.890 43.478 15.93 0.00 44.42 4.02
2898 4140 3.247006 ACGCGAATGACTTATTCACCT 57.753 42.857 15.93 0.00 44.42 4.00
2899 4141 4.380841 ACGCGAATGACTTATTCACCTA 57.619 40.909 15.93 0.00 44.42 3.08
2900 4142 4.360563 ACGCGAATGACTTATTCACCTAG 58.639 43.478 15.93 0.00 44.42 3.02
2901 4143 4.097437 ACGCGAATGACTTATTCACCTAGA 59.903 41.667 15.93 0.00 44.42 2.43
2902 4144 4.441415 CGCGAATGACTTATTCACCTAGAC 59.559 45.833 0.00 0.00 44.42 2.59
2903 4145 4.441415 GCGAATGACTTATTCACCTAGACG 59.559 45.833 0.00 0.00 44.42 4.18
2904 4146 4.976731 CGAATGACTTATTCACCTAGACGG 59.023 45.833 0.00 0.00 44.42 4.79
2905 4147 5.220989 CGAATGACTTATTCACCTAGACGGA 60.221 44.000 0.00 0.00 44.42 4.69
2906 4148 5.776173 ATGACTTATTCACCTAGACGGAG 57.224 43.478 0.00 0.00 36.92 4.63
2907 4149 3.952323 TGACTTATTCACCTAGACGGAGG 59.048 47.826 0.00 0.00 42.89 4.30
2908 4150 3.297736 ACTTATTCACCTAGACGGAGGG 58.702 50.000 5.42 0.00 41.36 4.30
2909 4151 3.053095 ACTTATTCACCTAGACGGAGGGA 60.053 47.826 5.42 0.00 41.36 4.20
2910 4152 2.074729 ATTCACCTAGACGGAGGGAG 57.925 55.000 5.42 0.00 41.36 4.30
2911 4153 0.702902 TTCACCTAGACGGAGGGAGT 59.297 55.000 5.42 0.00 41.36 3.85
2912 4154 1.588239 TCACCTAGACGGAGGGAGTA 58.412 55.000 5.42 0.00 41.36 2.59
2924 4166 3.108376 GGAGGGAGTATTCAGGACAAGT 58.892 50.000 0.00 0.00 0.00 3.16
2953 4195 2.739913 GGCAACAATACTTGAGTGCGTA 59.260 45.455 11.34 0.00 42.21 4.42
2961 4203 1.344763 ACTTGAGTGCGTAGGAGCTTT 59.655 47.619 0.00 0.00 38.13 3.51
2966 4208 2.413453 GAGTGCGTAGGAGCTTTTTCTG 59.587 50.000 0.00 0.00 38.13 3.02
2974 4216 6.203723 GCGTAGGAGCTTTTTCTGATGATTAT 59.796 38.462 0.00 0.00 0.00 1.28
3015 4257 2.747446 CCGGTTACAACAGATTCTTGGG 59.253 50.000 0.00 0.00 0.00 4.12
3038 4280 5.777732 GGGTTCATATCCTGATCACTCTACT 59.222 44.000 0.00 0.00 32.72 2.57
3191 4433 0.965363 TCGCCCCTTCCTGCAAATTC 60.965 55.000 0.00 0.00 0.00 2.17
3196 4438 2.373224 CCCTTCCTGCAAATTCTCTCC 58.627 52.381 0.00 0.00 0.00 3.71
3204 4446 4.082354 CCTGCAAATTCTCTCCCTTTGAAG 60.082 45.833 0.00 0.00 35.95 3.02
3220 4462 7.852971 CCTTTGAAGGGTATAACGTATTGAA 57.147 36.000 1.68 0.00 42.66 2.69
3230 4472 7.130269 GGTATAACGTATTGAATTTCTGTGGC 58.870 38.462 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.219115 CTCTACTCCTGGCTATTTCCTCA 58.781 47.826 0.00 0.00 0.00 3.86
55 56 8.322828 TGCCAACTAGTTTTACCAGAACATATA 58.677 33.333 5.07 0.00 0.00 0.86
56 57 7.172342 TGCCAACTAGTTTTACCAGAACATAT 58.828 34.615 5.07 0.00 0.00 1.78
57 58 6.535540 TGCCAACTAGTTTTACCAGAACATA 58.464 36.000 5.07 0.00 0.00 2.29
128 130 3.945981 TCTGTACACGCAAGACCAATA 57.054 42.857 0.00 0.00 43.62 1.90
130 132 2.831685 ATCTGTACACGCAAGACCAA 57.168 45.000 0.00 0.00 43.62 3.67
132 134 3.064207 TGAAATCTGTACACGCAAGACC 58.936 45.455 0.00 0.00 43.62 3.85
133 135 3.123621 CCTGAAATCTGTACACGCAAGAC 59.876 47.826 0.00 0.00 43.62 3.01
134 136 3.325870 CCTGAAATCTGTACACGCAAGA 58.674 45.455 0.00 0.00 43.62 3.02
253 266 4.478206 TCCCAAAATTTGACAAGTTGCA 57.522 36.364 7.37 0.00 0.00 4.08
285 298 3.394606 AGGGCTCTTTCCTTTACAGACAA 59.605 43.478 0.00 0.00 0.00 3.18
289 302 4.006319 CAGAAGGGCTCTTTCCTTTACAG 58.994 47.826 0.00 0.00 43.98 2.74
290 303 3.810743 GCAGAAGGGCTCTTTCCTTTACA 60.811 47.826 0.00 0.00 43.98 2.41
291 304 2.750166 GCAGAAGGGCTCTTTCCTTTAC 59.250 50.000 0.00 0.00 43.98 2.01
292 305 2.644798 AGCAGAAGGGCTCTTTCCTTTA 59.355 45.455 0.00 0.00 43.98 1.85
323 336 1.164411 CAGTGCCTTGCGACCAATTA 58.836 50.000 0.00 0.00 0.00 1.40
337 351 1.002033 CAGAAGCCAAGTGTTCAGTGC 60.002 52.381 0.00 0.00 0.00 4.40
390 414 5.389859 TCTTCACGAATTCATGCCAAAAT 57.610 34.783 6.22 0.00 0.00 1.82
428 452 0.031178 CCAGTTGTTTCTGCTGCACC 59.969 55.000 0.00 0.00 34.47 5.01
486 510 2.875933 TCAACCGAACACTTGGAATGTC 59.124 45.455 0.00 0.00 0.00 3.06
501 527 1.600023 TGGTTTTACAGCCTCAACCG 58.400 50.000 0.00 0.00 41.51 4.44
549 592 2.420022 ACTGTAATTCATGCAAGGCGTC 59.580 45.455 0.00 0.00 0.00 5.19
552 595 5.505173 ACATACTGTAATTCATGCAAGGC 57.495 39.130 0.00 0.00 0.00 4.35
580 635 7.206687 TGAATTGCCAGTCGTTTTAGAATTTT 58.793 30.769 0.00 0.00 0.00 1.82
637 692 2.565391 TGACTTATCCTTCGCTTGTGGA 59.435 45.455 0.00 0.00 0.00 4.02
674 729 2.184836 CCGCCGAACCGTGGATAA 59.815 61.111 0.00 0.00 0.00 1.75
714 769 0.453282 TCGCGACTCTACGTTTTCCG 60.453 55.000 3.71 0.00 44.03 4.30
715 770 1.384742 GTTCGCGACTCTACGTTTTCC 59.615 52.381 9.15 0.00 35.59 3.13
716 771 1.055476 CGTTCGCGACTCTACGTTTTC 59.945 52.381 19.83 0.00 44.71 2.29
717 772 1.047739 CGTTCGCGACTCTACGTTTT 58.952 50.000 19.83 0.00 44.71 2.43
718 773 0.235665 TCGTTCGCGACTCTACGTTT 59.764 50.000 24.99 0.00 45.62 3.60
719 774 1.862123 TCGTTCGCGACTCTACGTT 59.138 52.632 24.99 0.00 45.62 3.99
740 795 3.594453 ACGGGGTAGATCGTGGTAA 57.406 52.632 0.00 0.00 38.25 2.85
752 807 3.322466 CTTGCCTCTCCACGGGGT 61.322 66.667 2.12 0.00 34.93 4.95
764 819 1.644786 CCGATCGTTTGTCCCTTGCC 61.645 60.000 15.09 0.00 0.00 4.52
960 1025 1.451028 CAGCTACTCCAGGCCAAGC 60.451 63.158 5.01 3.73 0.00 4.01
966 1031 1.065854 CAGGGAAACAGCTACTCCAGG 60.066 57.143 9.46 0.00 0.00 4.45
974 1039 0.329596 GATCACCCAGGGAAACAGCT 59.670 55.000 14.54 0.00 0.00 4.24
1099 1164 4.456253 CTCGGTGGTCGACGACGG 62.456 72.222 25.48 25.48 43.74 4.79
1123 1191 1.153429 GTATCGTGGAGGTGGTGGC 60.153 63.158 0.00 0.00 0.00 5.01
1844 1912 2.380084 AATGGATTGCACGTCGTAGT 57.620 45.000 0.00 0.00 0.00 2.73
1845 1913 2.030457 GGAAATGGATTGCACGTCGTAG 59.970 50.000 0.00 0.00 0.00 3.51
1849 1920 2.159379 GGAAGGAAATGGATTGCACGTC 60.159 50.000 0.00 0.00 0.00 4.34
1858 1929 4.444611 TCTTAAGGAGGGAAGGAAATGGA 58.555 43.478 1.85 0.00 0.00 3.41
1886 1961 1.057636 CGCGTGCGTCTTCTTCTTAA 58.942 50.000 6.00 0.00 34.35 1.85
1912 3079 2.281070 ACTGCACCGACAGGCAAG 60.281 61.111 5.30 0.00 42.21 4.01
1916 3083 1.961277 GGAACACTGCACCGACAGG 60.961 63.158 5.30 0.00 42.21 4.00
2269 3436 1.296056 AAATGCTCCACGTACGTGCC 61.296 55.000 36.76 26.74 44.16 5.01
2270 3437 0.515564 AAAATGCTCCACGTACGTGC 59.484 50.000 36.76 27.70 44.16 5.34
2271 3438 2.570169 CAAAAATGCTCCACGTACGTG 58.430 47.619 35.57 35.57 45.02 4.49
2272 3439 1.533731 CCAAAAATGCTCCACGTACGT 59.466 47.619 16.72 16.72 0.00 3.57
2273 3440 1.727857 GCCAAAAATGCTCCACGTACG 60.728 52.381 15.01 15.01 0.00 3.67
2274 3441 1.539827 AGCCAAAAATGCTCCACGTAC 59.460 47.619 0.00 0.00 32.41 3.67
2275 3442 1.539388 CAGCCAAAAATGCTCCACGTA 59.461 47.619 0.00 0.00 36.81 3.57
2276 3443 0.314935 CAGCCAAAAATGCTCCACGT 59.685 50.000 0.00 0.00 36.81 4.49
2277 3444 0.597568 TCAGCCAAAAATGCTCCACG 59.402 50.000 0.00 0.00 36.81 4.94
2278 3445 2.613691 CATCAGCCAAAAATGCTCCAC 58.386 47.619 0.00 0.00 36.81 4.02
2279 3446 1.066716 GCATCAGCCAAAAATGCTCCA 60.067 47.619 0.00 0.00 41.95 3.86
2331 3505 7.980099 ACTGAACTTACATACACTATTACCAGC 59.020 37.037 0.00 0.00 0.00 4.85
2340 3521 8.853126 TGTTGTAGTACTGAACTTACATACACT 58.147 33.333 5.39 0.00 39.80 3.55
2357 3538 4.897076 TGAACTTCCCACTCTGTTGTAGTA 59.103 41.667 0.00 0.00 0.00 1.82
2358 3539 3.709653 TGAACTTCCCACTCTGTTGTAGT 59.290 43.478 0.00 0.00 0.00 2.73
2359 3540 4.058817 GTGAACTTCCCACTCTGTTGTAG 58.941 47.826 0.00 0.00 0.00 2.74
2428 3615 2.344950 CTGCATGAACAGAGTCCAGAC 58.655 52.381 0.00 0.00 40.25 3.51
2463 3650 6.783482 GGGTTCTCTGAAGATAGTAGGGTTAT 59.217 42.308 0.00 0.00 0.00 1.89
2502 3689 1.625818 ACTTGTACTGCTCAGGGAAGG 59.374 52.381 1.66 0.00 0.00 3.46
2523 3760 4.763279 TGTATCCATGCAGCATTTCTATGG 59.237 41.667 4.69 4.46 39.66 2.74
2558 3795 1.015607 CAAATGAGCAAAAGGCCGCC 61.016 55.000 0.00 0.00 46.50 6.13
2560 3797 0.037975 AGCAAATGAGCAAAAGGCCG 60.038 50.000 0.00 0.00 46.50 6.13
2618 3857 0.035036 TCCCAACGTTGCGGATGTTA 59.965 50.000 25.45 10.63 35.73 2.41
2717 3959 2.228343 ACCTAGAACTTTCACCGAGACG 59.772 50.000 0.00 0.00 0.00 4.18
2718 3960 3.938289 ACCTAGAACTTTCACCGAGAC 57.062 47.619 0.00 0.00 0.00 3.36
2719 3961 3.893200 TCAACCTAGAACTTTCACCGAGA 59.107 43.478 0.00 0.00 0.00 4.04
2720 3962 3.988517 GTCAACCTAGAACTTTCACCGAG 59.011 47.826 0.00 0.00 0.00 4.63
2721 3963 3.551454 CGTCAACCTAGAACTTTCACCGA 60.551 47.826 0.00 0.00 0.00 4.69
2722 3964 2.729882 CGTCAACCTAGAACTTTCACCG 59.270 50.000 0.00 0.00 0.00 4.94
2723 3965 3.986277 TCGTCAACCTAGAACTTTCACC 58.014 45.455 0.00 0.00 0.00 4.02
2724 3966 6.541111 AAATCGTCAACCTAGAACTTTCAC 57.459 37.500 0.00 0.00 0.00 3.18
2725 3967 7.929785 AGTTAAATCGTCAACCTAGAACTTTCA 59.070 33.333 0.00 0.00 0.00 2.69
2726 3968 8.307921 AGTTAAATCGTCAACCTAGAACTTTC 57.692 34.615 0.00 0.00 0.00 2.62
2727 3969 9.939802 ATAGTTAAATCGTCAACCTAGAACTTT 57.060 29.630 0.00 0.00 0.00 2.66
2728 3970 9.583765 GATAGTTAAATCGTCAACCTAGAACTT 57.416 33.333 0.00 0.00 0.00 2.66
2729 3971 8.968969 AGATAGTTAAATCGTCAACCTAGAACT 58.031 33.333 0.00 0.00 0.00 3.01
2848 4090 9.830975 TCTATGTCATCGATTTGAGGAATTAAA 57.169 29.630 0.00 0.00 39.46 1.52
2849 4091 9.830975 TTCTATGTCATCGATTTGAGGAATTAA 57.169 29.630 0.00 0.00 39.46 1.40
2850 4092 9.261180 GTTCTATGTCATCGATTTGAGGAATTA 57.739 33.333 0.00 0.00 39.46 1.40
2851 4093 7.989741 AGTTCTATGTCATCGATTTGAGGAATT 59.010 33.333 0.00 0.00 39.46 2.17
2852 4094 7.504403 AGTTCTATGTCATCGATTTGAGGAAT 58.496 34.615 0.00 0.00 39.46 3.01
2853 4095 6.878317 AGTTCTATGTCATCGATTTGAGGAA 58.122 36.000 0.00 0.00 39.46 3.36
2854 4096 6.471233 AGTTCTATGTCATCGATTTGAGGA 57.529 37.500 0.00 0.00 34.44 3.71
2855 4097 6.360947 CGTAGTTCTATGTCATCGATTTGAGG 59.639 42.308 0.00 0.00 0.00 3.86
2856 4098 6.129326 GCGTAGTTCTATGTCATCGATTTGAG 60.129 42.308 0.00 0.00 0.00 3.02
2857 4099 5.685954 GCGTAGTTCTATGTCATCGATTTGA 59.314 40.000 0.00 0.00 0.00 2.69
2858 4100 5.386424 CGCGTAGTTCTATGTCATCGATTTG 60.386 44.000 0.00 0.00 0.00 2.32
2859 4101 4.675565 CGCGTAGTTCTATGTCATCGATTT 59.324 41.667 0.00 0.00 0.00 2.17
2860 4102 4.024302 TCGCGTAGTTCTATGTCATCGATT 60.024 41.667 5.77 0.00 0.00 3.34
2861 4103 3.497262 TCGCGTAGTTCTATGTCATCGAT 59.503 43.478 5.77 0.00 0.00 3.59
2862 4104 2.867975 TCGCGTAGTTCTATGTCATCGA 59.132 45.455 5.77 0.00 0.00 3.59
2863 4105 3.249013 TCGCGTAGTTCTATGTCATCG 57.751 47.619 5.77 0.00 0.00 3.84
2864 4106 5.115773 GTCATTCGCGTAGTTCTATGTCATC 59.884 44.000 5.77 0.00 0.00 2.92
2865 4107 4.976731 GTCATTCGCGTAGTTCTATGTCAT 59.023 41.667 5.77 0.00 0.00 3.06
2866 4108 4.095932 AGTCATTCGCGTAGTTCTATGTCA 59.904 41.667 5.77 0.00 0.00 3.58
2867 4109 4.599047 AGTCATTCGCGTAGTTCTATGTC 58.401 43.478 5.77 0.00 0.00 3.06
2868 4110 4.634184 AGTCATTCGCGTAGTTCTATGT 57.366 40.909 5.77 0.00 0.00 2.29
2869 4111 7.378728 TGAATAAGTCATTCGCGTAGTTCTATG 59.621 37.037 5.77 0.44 45.25 2.23
2870 4112 7.378995 GTGAATAAGTCATTCGCGTAGTTCTAT 59.621 37.037 5.77 0.00 45.25 1.98
2871 4113 6.690098 GTGAATAAGTCATTCGCGTAGTTCTA 59.310 38.462 5.77 0.00 45.25 2.10
2872 4114 5.515626 GTGAATAAGTCATTCGCGTAGTTCT 59.484 40.000 5.77 0.00 45.25 3.01
2873 4115 5.715264 GTGAATAAGTCATTCGCGTAGTTC 58.285 41.667 5.77 0.29 45.25 3.01
2874 4116 5.697848 GTGAATAAGTCATTCGCGTAGTT 57.302 39.130 5.77 2.59 45.25 2.24
2881 4123 4.976731 CCGTCTAGGTGAATAAGTCATTCG 59.023 45.833 0.00 0.00 45.25 3.34
2882 4124 6.145338 TCCGTCTAGGTGAATAAGTCATTC 57.855 41.667 0.00 0.00 40.27 2.67
2883 4125 5.069251 CCTCCGTCTAGGTGAATAAGTCATT 59.931 44.000 0.00 0.00 38.90 2.57
2884 4126 4.585162 CCTCCGTCTAGGTGAATAAGTCAT 59.415 45.833 0.00 0.00 38.90 3.06
2885 4127 3.952323 CCTCCGTCTAGGTGAATAAGTCA 59.048 47.826 0.00 0.00 41.99 3.41
2886 4128 3.318557 CCCTCCGTCTAGGTGAATAAGTC 59.681 52.174 0.00 0.00 41.99 3.01
2887 4129 3.053095 TCCCTCCGTCTAGGTGAATAAGT 60.053 47.826 0.00 0.00 41.99 2.24
2888 4130 3.563223 TCCCTCCGTCTAGGTGAATAAG 58.437 50.000 0.00 0.00 41.99 1.73
2889 4131 3.053095 ACTCCCTCCGTCTAGGTGAATAA 60.053 47.826 0.00 0.00 41.99 1.40
2890 4132 2.512896 ACTCCCTCCGTCTAGGTGAATA 59.487 50.000 0.00 0.00 41.99 1.75
2891 4133 1.288335 ACTCCCTCCGTCTAGGTGAAT 59.712 52.381 0.00 0.00 41.99 2.57
2892 4134 0.702902 ACTCCCTCCGTCTAGGTGAA 59.297 55.000 0.00 0.00 41.99 3.18
2893 4135 1.588239 TACTCCCTCCGTCTAGGTGA 58.412 55.000 0.00 0.00 41.99 4.02
2894 4136 2.660670 ATACTCCCTCCGTCTAGGTG 57.339 55.000 0.00 0.00 41.99 4.00
2895 4137 2.512896 TGAATACTCCCTCCGTCTAGGT 59.487 50.000 0.00 0.00 41.99 3.08
2896 4138 3.150767 CTGAATACTCCCTCCGTCTAGG 58.849 54.545 0.00 0.00 42.97 3.02
2897 4139 3.150767 CCTGAATACTCCCTCCGTCTAG 58.849 54.545 0.00 0.00 0.00 2.43
2898 4140 2.781757 TCCTGAATACTCCCTCCGTCTA 59.218 50.000 0.00 0.00 0.00 2.59
2899 4141 1.569548 TCCTGAATACTCCCTCCGTCT 59.430 52.381 0.00 0.00 0.00 4.18
2900 4142 1.682323 GTCCTGAATACTCCCTCCGTC 59.318 57.143 0.00 0.00 0.00 4.79
2901 4143 1.006758 TGTCCTGAATACTCCCTCCGT 59.993 52.381 0.00 0.00 0.00 4.69
2902 4144 1.776662 TGTCCTGAATACTCCCTCCG 58.223 55.000 0.00 0.00 0.00 4.63
2903 4145 3.108376 ACTTGTCCTGAATACTCCCTCC 58.892 50.000 0.00 0.00 0.00 4.30
2904 4146 4.828072 AACTTGTCCTGAATACTCCCTC 57.172 45.455 0.00 0.00 0.00 4.30
2905 4147 6.893020 ATAAACTTGTCCTGAATACTCCCT 57.107 37.500 0.00 0.00 0.00 4.20
2906 4148 9.057089 CATTATAAACTTGTCCTGAATACTCCC 57.943 37.037 0.00 0.00 0.00 4.30
2907 4149 9.057089 CCATTATAAACTTGTCCTGAATACTCC 57.943 37.037 0.00 0.00 0.00 3.85
2908 4150 8.560374 GCCATTATAAACTTGTCCTGAATACTC 58.440 37.037 0.00 0.00 0.00 2.59
2909 4151 8.052748 TGCCATTATAAACTTGTCCTGAATACT 58.947 33.333 0.00 0.00 0.00 2.12
2910 4152 8.220755 TGCCATTATAAACTTGTCCTGAATAC 57.779 34.615 0.00 0.00 0.00 1.89
2911 4153 8.682710 GTTGCCATTATAAACTTGTCCTGAATA 58.317 33.333 0.00 0.00 0.00 1.75
2912 4154 7.178274 TGTTGCCATTATAAACTTGTCCTGAAT 59.822 33.333 0.00 0.00 0.00 2.57
2938 4180 2.761208 AGCTCCTACGCACTCAAGTATT 59.239 45.455 0.00 0.00 0.00 1.89
2946 4188 2.037251 TCAGAAAAAGCTCCTACGCACT 59.963 45.455 0.00 0.00 0.00 4.40
2949 4191 3.262420 TCATCAGAAAAAGCTCCTACGC 58.738 45.455 0.00 0.00 0.00 4.42
2953 4195 7.951347 AACATAATCATCAGAAAAAGCTCCT 57.049 32.000 0.00 0.00 0.00 3.69
3015 4257 6.266558 ACAGTAGAGTGATCAGGATATGAACC 59.733 42.308 0.00 0.00 42.53 3.62
3109 4351 1.004044 CCATCAGAGAACCAAGCACCT 59.996 52.381 0.00 0.00 0.00 4.00
3154 4396 4.424711 GGAATGCCACTGCCGGGA 62.425 66.667 2.18 0.00 36.33 5.14
3176 4418 2.373224 GGAGAGAATTTGCAGGAAGGG 58.627 52.381 0.00 0.00 0.00 3.95
3196 4438 7.852971 TTCAATACGTTATACCCTTCAAAGG 57.147 36.000 0.00 1.54 46.06 3.11
3204 4446 7.636326 CCACAGAAATTCAATACGTTATACCC 58.364 38.462 0.00 0.00 0.00 3.69
3213 4455 3.487544 GCTCCGCCACAGAAATTCAATAC 60.488 47.826 0.00 0.00 0.00 1.89
3220 4462 1.021390 CGAAGCTCCGCCACAGAAAT 61.021 55.000 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.