Multiple sequence alignment - TraesCS6B01G260200

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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 TraesCS6B01G260200 chr6B 100.000 3921 0 0 1 3921 470803668 470799748 0.000000e+00 7241
1 TraesCS6B01G260200 chr6A 91.687 1251 64 16 2017 3232 440530223 440531468 0.000000e+00 1698
2 TraesCS6B01G260200 chr6A 91.709 1170 59 14 1131 2268 440529311 440530474 0.000000e+00 1589
3 TraesCS6B01G260200 chr6A 85.144 727 53 30 245 955 440528037 440528724 0.000000e+00 693
4 TraesCS6B01G260200 chr6A 92.537 201 14 1 1 201 440527829 440528028 1.780000e-73 287
5 TraesCS6B01G260200 chr6D 91.596 1059 49 15 2142 3164 306029845 306030899 0.000000e+00 1426
6 TraesCS6B01G260200 chr6D 83.681 1152 82 47 473 1610 306026941 306028000 0.000000e+00 989
7 TraesCS6B01G260200 chr6D 94.305 439 20 2 1 436 306026507 306026943 0.000000e+00 667
8 TraesCS6B01G260200 chr6D 87.834 337 30 7 1640 1969 306029002 306029334 6.150000e-103 385
9 TraesCS6B01G260200 chr3D 89.525 716 47 14 3226 3918 104206189 104206899 0.000000e+00 881
10 TraesCS6B01G260200 chr3D 85.135 518 50 16 3225 3720 599783539 599783027 4.520000e-139 505
11 TraesCS6B01G260200 chr3D 84.808 520 51 16 3225 3720 599689063 599689578 7.570000e-137 497
12 TraesCS6B01G260200 chr5A 89.193 694 46 13 3246 3916 6405997 6406684 0.000000e+00 839
13 TraesCS6B01G260200 chr1B 87.029 717 68 12 3224 3918 341394040 341394753 0.000000e+00 785
14 TraesCS6B01G260200 chr1B 87.685 609 52 10 3332 3918 341499321 341499928 0.000000e+00 688
15 TraesCS6B01G260200 chr2D 85.154 714 81 12 3226 3917 383863558 383864268 0.000000e+00 708
16 TraesCS6B01G260200 chr7D 81.579 722 99 20 3225 3921 202051880 202051168 2.040000e-157 566
17 TraesCS6B01G260200 chr5D 92.025 163 11 2 3225 3387 42806981 42806821 1.100000e-55 228
18 TraesCS6B01G260200 chr4B 91.447 152 10 2 3224 3375 645899555 645899703 5.140000e-49 206
19 TraesCS6B01G260200 chr1D 84.239 184 24 4 3225 3408 457218886 457218708 1.450000e-39 174


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 TraesCS6B01G260200 chr6B 470799748 470803668 3920 True 7241.00 7241 100.00000 1 3921 1 chr6B.!!$R1 3920
1 TraesCS6B01G260200 chr6A 440527829 440531468 3639 False 1066.75 1698 90.26925 1 3232 4 chr6A.!!$F1 3231
2 TraesCS6B01G260200 chr6D 306026507 306030899 4392 False 866.75 1426 89.35400 1 3164 4 chr6D.!!$F1 3163
3 TraesCS6B01G260200 chr3D 104206189 104206899 710 False 881.00 881 89.52500 3226 3918 1 chr3D.!!$F1 692
4 TraesCS6B01G260200 chr3D 599783027 599783539 512 True 505.00 505 85.13500 3225 3720 1 chr3D.!!$R1 495
5 TraesCS6B01G260200 chr3D 599689063 599689578 515 False 497.00 497 84.80800 3225 3720 1 chr3D.!!$F2 495
6 TraesCS6B01G260200 chr5A 6405997 6406684 687 False 839.00 839 89.19300 3246 3916 1 chr5A.!!$F1 670
7 TraesCS6B01G260200 chr1B 341394040 341394753 713 False 785.00 785 87.02900 3224 3918 1 chr1B.!!$F1 694
8 TraesCS6B01G260200 chr1B 341499321 341499928 607 False 688.00 688 87.68500 3332 3918 1 chr1B.!!$F2 586
9 TraesCS6B01G260200 chr2D 383863558 383864268 710 False 708.00 708 85.15400 3226 3917 1 chr2D.!!$F1 691
10 TraesCS6B01G260200 chr7D 202051168 202051880 712 True 566.00 566 81.57900 3225 3921 1 chr7D.!!$R1 696

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
930 958 0.036858 AAGAGCGAGAGGGCTTCAAC 60.037 55.0 0.00 0.00 44.93 3.18 F
966 994 0.040425 GCGCCGAGCTTTCAAAAGAA 60.040 50.0 6.67 0.00 44.04 2.52 F
1313 1784 0.917533 TAGACTACTCCGTGGAGCCT 59.082 55.0 15.80 10.07 45.54 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2305 4164 1.070445 AGCACATATCTGAGCCGGC 59.930 57.895 21.89 21.89 39.51 6.13 R
2364 4223 1.133575 CATGATGGGTGGCAAGAGGAT 60.134 52.381 0.00 0.00 0.00 3.24 R
2956 4817 2.069273 AGCTCTGGATCGACAAAAACG 58.931 47.619 0.00 0.00 0.00 3.60 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
73 74 8.766000 TGACACGACACTATTGTAATACATTT 57.234 30.769 0.00 0.00 35.47 2.32
74 75 9.210329 TGACACGACACTATTGTAATACATTTT 57.790 29.630 0.00 0.00 35.47 1.82
440 444 7.893302 AGGGAATATCACACAACCAATAGAAAA 59.107 33.333 0.00 0.00 0.00 2.29
442 446 8.739972 GGAATATCACACAACCAATAGAAAAGT 58.260 33.333 0.00 0.00 0.00 2.66
451 455 6.708054 ACAACCAATAGAAAAGTGAGAGACAG 59.292 38.462 0.00 0.00 0.00 3.51
460 464 4.696479 AAGTGAGAGACAGTTTCCACAT 57.304 40.909 12.33 1.99 38.83 3.21
553 558 4.684703 ACTGCGTGTACTTTGACTATGAAC 59.315 41.667 0.00 0.00 0.00 3.18
554 559 4.878439 TGCGTGTACTTTGACTATGAACT 58.122 39.130 0.00 0.00 0.00 3.01
557 562 6.924612 TGCGTGTACTTTGACTATGAACTTTA 59.075 34.615 0.00 0.00 0.00 1.85
636 641 7.623268 AAAATTTGAATAGAGTTGTTCACGC 57.377 32.000 0.00 0.00 34.65 5.34
637 642 5.940192 ATTTGAATAGAGTTGTTCACGCA 57.060 34.783 0.00 0.00 34.65 5.24
638 643 5.940192 TTTGAATAGAGTTGTTCACGCAT 57.060 34.783 0.00 0.00 34.65 4.73
639 644 7.609760 ATTTGAATAGAGTTGTTCACGCATA 57.390 32.000 0.00 0.00 34.65 3.14
640 645 7.609760 TTTGAATAGAGTTGTTCACGCATAT 57.390 32.000 0.00 0.00 34.65 1.78
641 646 7.609760 TTGAATAGAGTTGTTCACGCATATT 57.390 32.000 0.00 0.00 34.65 1.28
642 647 8.710835 TTGAATAGAGTTGTTCACGCATATTA 57.289 30.769 0.00 0.00 34.65 0.98
643 648 8.352752 TGAATAGAGTTGTTCACGCATATTAG 57.647 34.615 0.00 0.00 30.59 1.73
644 649 6.771188 ATAGAGTTGTTCACGCATATTAGC 57.229 37.500 0.00 0.00 0.00 3.09
645 650 4.503910 AGAGTTGTTCACGCATATTAGCA 58.496 39.130 0.00 0.00 0.00 3.49
646 651 4.935205 AGAGTTGTTCACGCATATTAGCAA 59.065 37.500 0.00 0.00 0.00 3.91
649 654 6.442952 AGTTGTTCACGCATATTAGCAAAAA 58.557 32.000 0.00 0.00 0.00 1.94
758 765 4.470334 AAGAGCAAAAGCAAAAACAGGA 57.530 36.364 0.00 0.00 0.00 3.86
759 766 4.470334 AGAGCAAAAGCAAAAACAGGAA 57.530 36.364 0.00 0.00 0.00 3.36
895 920 0.812811 GCAGGCTCGCATCATCAGAA 60.813 55.000 4.40 0.00 0.00 3.02
898 923 2.421073 CAGGCTCGCATCATCAGAAAAA 59.579 45.455 0.00 0.00 0.00 1.94
926 954 0.907230 AGGAAAGAGCGAGAGGGCTT 60.907 55.000 0.00 0.00 44.93 4.35
927 955 0.461163 GGAAAGAGCGAGAGGGCTTC 60.461 60.000 0.00 0.00 44.93 3.86
930 958 0.036858 AAGAGCGAGAGGGCTTCAAC 60.037 55.000 0.00 0.00 44.93 3.18
939 967 4.062991 GAGAGGGCTTCAACGAAGTAAAA 58.937 43.478 0.00 0.00 45.00 1.52
943 971 3.188667 GGGCTTCAACGAAGTAAAAGGAG 59.811 47.826 5.68 0.00 45.00 3.69
944 972 4.062991 GGCTTCAACGAAGTAAAAGGAGA 58.937 43.478 5.68 0.00 45.00 3.71
945 973 4.083961 GGCTTCAACGAAGTAAAAGGAGAC 60.084 45.833 5.68 0.00 45.00 3.36
946 974 4.750598 GCTTCAACGAAGTAAAAGGAGACT 59.249 41.667 5.68 0.00 45.00 3.24
947 975 5.333416 GCTTCAACGAAGTAAAAGGAGACTG 60.333 44.000 5.68 0.00 45.00 3.51
948 976 4.056050 TCAACGAAGTAAAAGGAGACTGC 58.944 43.478 0.00 0.00 45.00 4.40
950 978 1.390463 CGAAGTAAAAGGAGACTGCGC 59.610 52.381 0.00 0.00 42.68 6.09
951 979 1.732809 GAAGTAAAAGGAGACTGCGCC 59.267 52.381 4.18 0.00 42.68 6.53
952 980 0.389948 AGTAAAAGGAGACTGCGCCG 60.390 55.000 4.18 0.00 42.68 6.46
953 981 0.389426 GTAAAAGGAGACTGCGCCGA 60.389 55.000 4.18 0.00 42.68 5.54
954 982 0.108804 TAAAAGGAGACTGCGCCGAG 60.109 55.000 4.18 0.00 42.68 4.63
955 983 3.941657 AAAGGAGACTGCGCCGAGC 62.942 63.158 4.18 0.00 42.68 5.03
964 992 4.137145 GCGCCGAGCTTTCAAAAG 57.863 55.556 0.00 0.00 44.04 2.27
965 993 1.574428 GCGCCGAGCTTTCAAAAGA 59.426 52.632 6.67 0.00 44.04 2.52
966 994 0.040425 GCGCCGAGCTTTCAAAAGAA 60.040 50.000 6.67 0.00 44.04 2.52
967 995 1.599419 GCGCCGAGCTTTCAAAAGAAA 60.599 47.619 6.67 0.00 44.04 2.52
968 996 2.726633 CGCCGAGCTTTCAAAAGAAAA 58.273 42.857 6.67 0.00 38.28 2.29
969 997 3.112580 CGCCGAGCTTTCAAAAGAAAAA 58.887 40.909 6.67 0.00 38.28 1.94
970 998 3.180387 CGCCGAGCTTTCAAAAGAAAAAG 59.820 43.478 6.67 0.00 38.28 2.27
971 999 3.490896 GCCGAGCTTTCAAAAGAAAAAGG 59.509 43.478 6.67 3.46 38.28 3.11
972 1000 4.736464 GCCGAGCTTTCAAAAGAAAAAGGA 60.736 41.667 6.67 0.00 38.28 3.36
992 1020 2.202756 CTGCGCCGAGGAGTTACC 60.203 66.667 4.18 0.00 39.35 2.85
1044 1072 1.449353 GGAGAAGCAGCCGATGGAT 59.551 57.895 0.00 0.00 0.00 3.41
1313 1784 0.917533 TAGACTACTCCGTGGAGCCT 59.082 55.000 15.80 10.07 45.54 4.58
1343 1814 2.025727 CCCGCCGTAGACGATGTC 59.974 66.667 3.07 0.00 43.02 3.06
1382 1853 1.079057 GCAGAGGAAAGGACGGACC 60.079 63.158 0.00 0.00 39.35 4.46
1451 1922 4.465688 TGGATTCCCAGAGGTAATCCACC 61.466 52.174 16.35 0.00 45.29 4.61
1610 2081 7.322664 TCCTAATGGTGAAGATTGCATTTTTC 58.677 34.615 5.22 5.22 34.23 2.29
1617 3052 7.225145 TGGTGAAGATTGCATTTTTCTTCTTTG 59.775 33.333 20.50 0.00 43.64 2.77
1621 3056 9.252962 GAAGATTGCATTTTTCTTCTTTGAAGA 57.747 29.630 16.07 5.97 41.27 2.87
1685 3134 1.070275 TGCTGTGACTGCCTCTGTG 59.930 57.895 11.94 0.00 0.00 3.66
1706 3155 7.384932 TCTGTGAACATGTATAGGATAATTGCG 59.615 37.037 0.00 0.00 0.00 4.85
1716 3165 9.602568 TGTATAGGATAATTGCGTTAGTTTGAA 57.397 29.630 0.00 0.00 0.00 2.69
1727 3176 6.276847 TGCGTTAGTTTGAAAAATTCATGGT 58.723 32.000 0.00 0.00 39.84 3.55
1728 3177 7.426410 TGCGTTAGTTTGAAAAATTCATGGTA 58.574 30.769 0.00 0.00 39.84 3.25
1786 3235 5.014202 AGGGAAGTTGGCGTATTGTTAATT 58.986 37.500 0.00 0.00 0.00 1.40
1789 3238 5.106078 GGAAGTTGGCGTATTGTTAATTCCA 60.106 40.000 0.00 0.00 34.10 3.53
1874 3324 9.162764 TCAAGTGGCTGTAAGAAATAATAGAAC 57.837 33.333 0.00 0.00 34.07 3.01
1928 3378 4.686554 GTGTACAGCTCAGTTGTTCCTAAG 59.313 45.833 0.00 0.00 0.00 2.18
1971 3421 6.818644 TGTCTTTGCTTATGTGAGAGGTATTC 59.181 38.462 0.00 0.00 0.00 1.75
2030 3835 9.745018 CATGGGGAATCTATCTTACATAAATGT 57.255 33.333 0.63 0.63 44.48 2.71
2146 3978 4.759782 AGAATGAGAATCCCACAAGTACG 58.240 43.478 0.00 0.00 0.00 3.67
2214 4046 9.891828 TCTGATTAATTGTTGTATGTTGTGAAC 57.108 29.630 0.00 0.00 0.00 3.18
2291 4150 8.328146 CAAGATAACACAACTAACCGTGATATG 58.672 37.037 0.00 0.00 33.00 1.78
2298 4157 3.699067 ACTAACCGTGATATGTACGTGC 58.301 45.455 0.00 0.00 39.76 5.34
2305 4164 1.202521 TGATATGTACGTGCTGGCCTG 60.203 52.381 3.32 4.26 0.00 4.85
2364 4223 5.048364 AGCATGGTTACGTTCTTATTGCAAA 60.048 36.000 1.71 0.00 0.00 3.68
2399 4258 6.009589 ACCCATCATGTAATTGTCTGTTTCA 58.990 36.000 0.00 0.00 0.00 2.69
2493 4354 1.065564 GCACAGCTCCTTGAGGATTCT 60.066 52.381 0.00 0.00 44.46 2.40
2520 4381 1.882623 GCTTTCACTTCAGAACCCTGG 59.117 52.381 0.00 0.00 40.76 4.45
2535 4396 7.068593 TCAGAACCCTGGATGCTTTAAATATTG 59.931 37.037 0.00 0.00 40.76 1.90
2580 4441 9.174166 GATTGTTCACCTTTATATTGGTACTGT 57.826 33.333 0.00 0.00 34.79 3.55
2599 4460 9.821662 GGTACTGTTGACAATAGATTTTACAAC 57.178 33.333 17.76 0.00 37.31 3.32
2610 4471 9.885743 CAATAGATTTTACAACGCTTAAATTGC 57.114 29.630 0.00 0.00 0.00 3.56
2623 4484 9.646336 AACGCTTAAATTGCTATTTTATACGAG 57.354 29.630 11.32 3.10 35.61 4.18
2624 4485 8.823818 ACGCTTAAATTGCTATTTTATACGAGT 58.176 29.630 11.32 0.00 35.61 4.18
2625 4486 9.092322 CGCTTAAATTGCTATTTTATACGAGTG 57.908 33.333 11.32 4.49 35.61 3.51
2680 4541 3.880490 TGTTCAGGCACGAAAAGTATGTT 59.120 39.130 0.00 0.00 0.00 2.71
2805 4666 6.911250 TGATTCTACTACACCAGAAGTTGA 57.089 37.500 0.00 0.00 34.43 3.18
2991 4853 3.388308 CAGAGCTGATGTGGTAGTATGC 58.612 50.000 0.00 0.00 0.00 3.14
2994 4856 2.035193 AGCTGATGTGGTAGTATGCGAG 59.965 50.000 0.00 0.00 0.00 5.03
3000 4862 5.983118 TGATGTGGTAGTATGCGAGTTATTG 59.017 40.000 0.00 0.00 0.00 1.90
3033 4901 6.422333 TCATGATATCAAGTTAAACCTGCCA 58.578 36.000 9.99 0.00 0.00 4.92
3043 4911 2.905415 AAACCTGCCATCCTTCATGA 57.095 45.000 0.00 0.00 33.80 3.07
3066 4934 8.709272 TGAAAATTATATTCTGGCATCATGGA 57.291 30.769 0.00 0.00 0.00 3.41
3067 4935 8.799367 TGAAAATTATATTCTGGCATCATGGAG 58.201 33.333 0.00 0.00 0.00 3.86
3068 4936 8.945195 AAAATTATATTCTGGCATCATGGAGA 57.055 30.769 0.00 0.00 0.00 3.71
3077 4945 3.893200 TGGCATCATGGAGAATTTGGATC 59.107 43.478 0.00 0.00 0.00 3.36
3111 4979 5.896963 ACAGAATTTTCAGAGGGGAAGAAT 58.103 37.500 0.00 0.00 0.00 2.40
3114 4982 6.435277 CAGAATTTTCAGAGGGGAAGAATCAA 59.565 38.462 0.00 0.00 0.00 2.57
3115 4983 7.123847 CAGAATTTTCAGAGGGGAAGAATCAAT 59.876 37.037 0.00 0.00 0.00 2.57
3202 5071 5.814705 GCAGCATGTTACTATCTTCAAGTCT 59.185 40.000 0.00 0.00 39.31 3.24
3210 5079 8.540388 TGTTACTATCTTCAAGTCTTGGCTTAT 58.460 33.333 12.66 4.73 0.00 1.73
3222 5091 5.665812 AGTCTTGGCTTATAGGGAATGTGTA 59.334 40.000 0.00 0.00 0.00 2.90
3227 5096 6.727394 TGGCTTATAGGGAATGTGTACTTTT 58.273 36.000 0.00 0.00 0.00 2.27
3293 5167 6.539649 TCGTTTACAACTTGAGGAAGAATG 57.460 37.500 0.00 0.00 32.98 2.67
3299 5173 5.934781 ACAACTTGAGGAAGAATGAAGTCT 58.065 37.500 0.00 0.00 32.98 3.24
3306 5180 5.907662 TGAGGAAGAATGAAGTCTGGGATAT 59.092 40.000 0.00 0.00 0.00 1.63
3310 5184 6.652900 GGAAGAATGAAGTCTGGGATATTAGC 59.347 42.308 0.00 0.00 0.00 3.09
3311 5185 5.788450 AGAATGAAGTCTGGGATATTAGCG 58.212 41.667 0.00 0.00 0.00 4.26
3314 5188 4.215908 TGAAGTCTGGGATATTAGCGTCT 58.784 43.478 0.00 0.00 0.00 4.18
3363 5237 5.876357 AGGAGTGTTTGGCTAAACTATCAA 58.124 37.500 23.82 3.13 45.06 2.57
3413 5294 6.775629 AGAAATAGTAGCCAACACTTCCAAAA 59.224 34.615 0.00 0.00 0.00 2.44
3426 5307 4.090066 CACTTCCAAAACGAGATGAGTACG 59.910 45.833 0.00 0.00 0.00 3.67
3449 5330 2.461110 GCTAACACCGCCACATCCG 61.461 63.158 0.00 0.00 0.00 4.18
3497 5394 6.513180 GGTAACCGACTCATCAGATTCAATA 58.487 40.000 0.00 0.00 0.00 1.90
3561 5458 5.338708 CCATTCCGGATAGCATTTATCTCCT 60.339 44.000 4.15 0.00 36.56 3.69
3607 5506 0.751643 AAAACCCAAGTCGCAGCAGT 60.752 50.000 0.00 0.00 0.00 4.40
3655 5555 4.135153 CGCACCACTAGCTCCGCT 62.135 66.667 0.00 0.00 43.41 5.52
3801 5701 2.704572 CCAGAACCAGGATTGAGACAC 58.295 52.381 0.00 0.00 0.00 3.67
3824 5724 2.052690 GCGACTAGGCTCCTGGACA 61.053 63.158 6.28 0.00 0.00 4.02
3877 5777 6.615316 TGCCACCATATATACCACATAGCTAT 59.385 38.462 0.00 0.00 0.00 2.97
3918 5818 5.089970 TGGAAGTTCATCAATCATCTCGT 57.910 39.130 5.01 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.988293 TCCAAACGCATCCCAAAAGA 58.012 45.000 0.00 0.00 0.00 2.52
74 75 9.942850 TGTTCAGATGAATTTGAGACTATTACA 57.057 29.630 0.00 0.00 36.33 2.41
83 84 8.019669 ACTCGAAAATGTTCAGATGAATTTGAG 58.980 33.333 15.83 15.83 37.12 3.02
90 91 6.566564 GCTTCAACTCGAAAATGTTCAGATGA 60.567 38.462 0.00 1.19 32.89 2.92
253 257 2.767394 TCCATAGTTACCGCTTAAGGCA 59.233 45.455 4.29 0.00 41.91 4.75
386 390 5.846528 TTTGGCTTTACCCTTACTCCTAA 57.153 39.130 0.00 0.00 37.83 2.69
440 444 3.643320 TCATGTGGAAACTGTCTCTCACT 59.357 43.478 0.00 0.00 0.00 3.41
442 446 4.897509 ATCATGTGGAAACTGTCTCTCA 57.102 40.909 0.00 0.00 0.00 3.27
523 527 4.494410 GTCAAAGTACACGCAGTTTTTCAC 59.506 41.667 0.00 0.00 41.61 3.18
564 569 6.019318 CCACATGCAGAAACTTTTTCTTCAAG 60.019 38.462 5.33 4.18 0.00 3.02
611 616 7.704472 TGCGTGAACAACTCTATTCAAATTTTT 59.296 29.630 0.00 0.00 36.62 1.94
616 621 5.940192 ATGCGTGAACAACTCTATTCAAA 57.060 34.783 0.00 0.00 36.62 2.69
617 622 7.609760 AATATGCGTGAACAACTCTATTCAA 57.390 32.000 0.00 0.00 36.62 2.69
618 623 7.042725 GCTAATATGCGTGAACAACTCTATTCA 60.043 37.037 0.00 0.00 32.44 2.57
619 624 7.042725 TGCTAATATGCGTGAACAACTCTATTC 60.043 37.037 0.00 0.00 35.36 1.75
620 625 6.761242 TGCTAATATGCGTGAACAACTCTATT 59.239 34.615 0.00 0.00 35.36 1.73
621 626 6.280643 TGCTAATATGCGTGAACAACTCTAT 58.719 36.000 0.00 0.00 35.36 1.98
622 627 5.656480 TGCTAATATGCGTGAACAACTCTA 58.344 37.500 0.00 0.00 35.36 2.43
623 628 4.503910 TGCTAATATGCGTGAACAACTCT 58.496 39.130 0.00 0.00 35.36 3.24
624 629 4.857871 TGCTAATATGCGTGAACAACTC 57.142 40.909 0.00 0.00 35.36 3.01
625 630 5.621197 TTTGCTAATATGCGTGAACAACT 57.379 34.783 0.00 0.00 35.36 3.16
626 631 6.683090 TTTTTGCTAATATGCGTGAACAAC 57.317 33.333 0.00 0.00 35.36 3.32
646 651 7.715657 TCTAACATGCATGAACAACTCTTTTT 58.284 30.769 32.75 13.87 0.00 1.94
649 654 6.882610 TTCTAACATGCATGAACAACTCTT 57.117 33.333 32.75 15.76 0.00 2.85
836 843 2.095059 GCAAATCCTATATGCCGCCTTG 60.095 50.000 0.00 0.00 34.03 3.61
898 923 4.962155 TCTCGCTCTTTCCTCTTCTTTTT 58.038 39.130 0.00 0.00 0.00 1.94
926 954 4.056050 GCAGTCTCCTTTTACTTCGTTGA 58.944 43.478 0.00 0.00 0.00 3.18
927 955 3.120991 CGCAGTCTCCTTTTACTTCGTTG 60.121 47.826 0.00 0.00 29.57 4.10
930 958 1.390463 GCGCAGTCTCCTTTTACTTCG 59.610 52.381 0.30 0.00 35.82 3.79
943 971 1.841663 TTTGAAAGCTCGGCGCAGTC 61.842 55.000 10.83 1.77 42.61 3.51
944 972 1.444119 TTTTGAAAGCTCGGCGCAGT 61.444 50.000 10.83 0.00 42.61 4.40
945 973 0.727122 CTTTTGAAAGCTCGGCGCAG 60.727 55.000 10.83 5.07 42.61 5.18
946 974 1.163420 TCTTTTGAAAGCTCGGCGCA 61.163 50.000 10.83 0.00 42.61 6.09
947 975 0.040425 TTCTTTTGAAAGCTCGGCGC 60.040 50.000 0.00 0.00 35.17 6.53
948 976 2.399396 TTTCTTTTGAAAGCTCGGCG 57.601 45.000 0.00 0.00 42.84 6.46
956 984 5.339990 CGCAGTCTCCTTTTTCTTTTGAAA 58.660 37.500 0.00 0.00 45.65 2.69
957 985 4.733523 GCGCAGTCTCCTTTTTCTTTTGAA 60.734 41.667 0.30 0.00 36.52 2.69
958 986 3.243068 GCGCAGTCTCCTTTTTCTTTTGA 60.243 43.478 0.30 0.00 0.00 2.69
959 987 3.045688 GCGCAGTCTCCTTTTTCTTTTG 58.954 45.455 0.30 0.00 0.00 2.44
960 988 2.034685 GGCGCAGTCTCCTTTTTCTTTT 59.965 45.455 10.83 0.00 0.00 2.27
961 989 1.609072 GGCGCAGTCTCCTTTTTCTTT 59.391 47.619 10.83 0.00 0.00 2.52
962 990 1.239347 GGCGCAGTCTCCTTTTTCTT 58.761 50.000 10.83 0.00 0.00 2.52
963 991 0.951040 CGGCGCAGTCTCCTTTTTCT 60.951 55.000 10.83 0.00 0.00 2.52
964 992 0.949105 TCGGCGCAGTCTCCTTTTTC 60.949 55.000 10.83 0.00 0.00 2.29
965 993 0.951040 CTCGGCGCAGTCTCCTTTTT 60.951 55.000 10.83 0.00 0.00 1.94
966 994 1.374758 CTCGGCGCAGTCTCCTTTT 60.375 57.895 10.83 0.00 0.00 2.27
967 995 2.262915 CTCGGCGCAGTCTCCTTT 59.737 61.111 10.83 0.00 0.00 3.11
968 996 3.764466 CCTCGGCGCAGTCTCCTT 61.764 66.667 10.83 0.00 0.00 3.36
969 997 4.742649 TCCTCGGCGCAGTCTCCT 62.743 66.667 10.83 0.00 0.00 3.69
970 998 4.200283 CTCCTCGGCGCAGTCTCC 62.200 72.222 10.83 0.00 0.00 3.71
971 999 1.654954 TAACTCCTCGGCGCAGTCTC 61.655 60.000 10.83 0.00 0.00 3.36
972 1000 1.677966 TAACTCCTCGGCGCAGTCT 60.678 57.895 10.83 0.00 0.00 3.24
989 1017 1.140312 GGGCTCCATGAATCCTGGTA 58.860 55.000 4.52 0.00 35.19 3.25
990 1018 1.925888 GGGCTCCATGAATCCTGGT 59.074 57.895 4.52 0.00 35.19 4.00
991 1019 1.228063 CGGGCTCCATGAATCCTGG 60.228 63.158 0.00 0.00 34.93 4.45
992 1020 0.250209 CTCGGGCTCCATGAATCCTG 60.250 60.000 0.00 0.00 0.00 3.86
1205 1674 8.430801 AGAGCACTTATTAGAACATGATTCAC 57.569 34.615 0.00 0.00 0.00 3.18
1382 1853 2.505777 CTGAGCACGGCGTCAGAG 60.506 66.667 19.00 6.08 42.49 3.35
1453 1924 3.296854 ACGAGACCCTATGTGAAGCATA 58.703 45.455 0.00 0.00 38.94 3.14
1484 1955 0.909610 TAGTCCAAGAGCCCCCTGTG 60.910 60.000 0.00 0.00 0.00 3.66
1531 2002 8.288689 TCTTTGAAGCATAATAAAAGTACCCC 57.711 34.615 0.00 0.00 0.00 4.95
1564 2035 1.470098 AGAAGTATTGCTGCAAAGCCG 59.530 47.619 20.06 0.00 0.00 5.52
1583 2054 6.461110 AATGCAATCTTCACCATTAGGAAG 57.539 37.500 0.00 0.00 41.42 3.46
1610 2081 5.466728 TGTTCCGTCTTCATCTTCAAAGAAG 59.533 40.000 0.39 0.39 38.77 2.85
1617 3052 6.969828 ATAAGTTGTTCCGTCTTCATCTTC 57.030 37.500 0.00 0.00 0.00 2.87
1621 3056 7.556844 ACAGATATAAGTTGTTCCGTCTTCAT 58.443 34.615 0.00 0.00 0.00 2.57
1685 3134 9.204570 ACTAACGCAATTATCCTATACATGTTC 57.795 33.333 2.30 0.00 0.00 3.18
1874 3324 5.297776 CCTAGACAAATAAACCATGCAGAGG 59.702 44.000 6.44 6.44 0.00 3.69
1948 3398 7.187824 AGAATACCTCTCACATAAGCAAAGA 57.812 36.000 0.00 0.00 0.00 2.52
1971 3421 1.072965 AGTGGTTTCTGCTTCCAGGAG 59.927 52.381 0.00 0.00 39.61 3.69
2030 3835 8.121305 ACAAACAGGCACAATTAAGAATGATA 57.879 30.769 0.00 0.00 0.00 2.15
2146 3978 6.978080 ACTTCACAACATACACCAAACAAATC 59.022 34.615 0.00 0.00 0.00 2.17
2246 4078 4.694509 TCTTGTGCAAAGCAAAACAACATT 59.305 33.333 0.00 0.00 41.47 2.71
2305 4164 1.070445 AGCACATATCTGAGCCGGC 59.930 57.895 21.89 21.89 39.51 6.13
2364 4223 1.133575 CATGATGGGTGGCAAGAGGAT 60.134 52.381 0.00 0.00 0.00 3.24
2453 4314 5.236263 TGTGCAGTACAGTGACAACTTTATG 59.764 40.000 0.00 0.00 32.98 1.90
2493 4354 4.929808 GGTTCTGAAGTGAAAGCTTCGATA 59.070 41.667 0.00 0.00 45.67 2.92
2535 4396 7.308782 ACAATCAGAAAGACGGATAATTGAC 57.691 36.000 0.00 0.00 33.42 3.18
2545 4406 5.424121 AAAGGTGAACAATCAGAAAGACG 57.576 39.130 0.00 0.00 35.88 4.18
2599 4460 9.092322 CACTCGTATAAAATAGCAATTTAAGCG 57.908 33.333 0.00 0.00 34.12 4.68
2623 4484 6.042143 CCATCCACAATTTTAGTATTGGCAC 58.958 40.000 0.00 0.00 39.33 5.01
2624 4485 5.719085 ACCATCCACAATTTTAGTATTGGCA 59.281 36.000 0.00 0.00 39.33 4.92
2625 4486 6.220726 ACCATCCACAATTTTAGTATTGGC 57.779 37.500 0.00 0.00 39.33 4.52
2680 4541 2.843401 ACATTGCACGGTACTGGTTA 57.157 45.000 6.65 0.00 0.00 2.85
2710 4571 7.613022 AGAATCTGATTAATCTTGACCTTGCAA 59.387 33.333 16.24 0.00 0.00 4.08
2724 4585 3.901844 CCCCTCCCGTAGAATCTGATTAA 59.098 47.826 2.28 0.00 0.00 1.40
2726 4587 2.090719 TCCCCTCCCGTAGAATCTGATT 60.091 50.000 1.81 1.81 0.00 2.57
2805 4666 3.323691 GTGATAAACTGGCCCCTTGTTTT 59.676 43.478 15.07 3.15 35.77 2.43
2956 4817 2.069273 AGCTCTGGATCGACAAAAACG 58.931 47.619 0.00 0.00 0.00 3.60
3033 4901 9.370930 TGCCAGAATATAATTTTCATGAAGGAT 57.629 29.630 8.41 4.55 0.00 3.24
3043 4911 8.945195 TCTCCATGATGCCAGAATATAATTTT 57.055 30.769 0.00 0.00 0.00 1.82
3066 4934 7.832685 TCTGTCATTTCAGATGATCCAAATTCT 59.167 33.333 0.00 0.00 39.20 2.40
3067 4935 7.993101 TCTGTCATTTCAGATGATCCAAATTC 58.007 34.615 0.00 0.00 39.20 2.17
3068 4936 7.949690 TCTGTCATTTCAGATGATCCAAATT 57.050 32.000 0.00 0.00 39.20 1.82
3111 4979 4.502171 TGCTTCGATTTTGCAAGATTGA 57.498 36.364 14.39 14.39 33.48 2.57
3126 4995 4.944962 TCATGTTTATCCACTTGCTTCG 57.055 40.909 0.00 0.00 0.00 3.79
3181 5050 6.457528 GCCAAGACTTGAAGATAGTAACATGC 60.458 42.308 16.99 2.49 0.00 4.06
3202 5071 5.968676 AGTACACATTCCCTATAAGCCAA 57.031 39.130 0.00 0.00 0.00 4.52
3210 5079 7.940137 TGCTAAAAGAAAAGTACACATTCCCTA 59.060 33.333 0.00 0.00 0.00 3.53
3227 5096 9.691362 GGAAATAAAGTTGTTGATGCTAAAAGA 57.309 29.630 0.00 0.00 0.00 2.52
3293 5167 4.278669 TGAGACGCTAATATCCCAGACTTC 59.721 45.833 0.00 0.00 0.00 3.01
3299 5173 5.304357 TGAATTCTGAGACGCTAATATCCCA 59.696 40.000 7.05 0.00 0.00 4.37
3311 5185 6.025280 GTCTAGTTCGTCTGAATTCTGAGAC 58.975 44.000 14.63 13.97 36.29 3.36
3314 5188 5.959618 TGTCTAGTTCGTCTGAATTCTGA 57.040 39.130 10.68 10.68 36.29 3.27
3329 5203 5.013183 AGCCAAACACTCCTTTATGTCTAGT 59.987 40.000 0.00 0.00 0.00 2.57
3363 5237 6.376299 TGTTGCAGAGAAGCTAATTCAATCAT 59.624 34.615 0.00 0.00 40.67 2.45
3413 5294 2.085320 AGCTGAACGTACTCATCTCGT 58.915 47.619 0.00 0.00 39.49 4.18
3426 5307 0.882927 TGTGGCGGTGTTAGCTGAAC 60.883 55.000 0.00 0.00 38.65 3.18
3449 5330 5.105228 CCATGCAAATGATTATATGGGTCCC 60.105 44.000 0.00 0.00 32.01 4.46
3497 5394 2.584835 TAGGATGCAACAAGCTGGTT 57.415 45.000 0.00 0.00 45.94 3.67
3561 5458 4.218852 TCATGTTTGCAATGCTGAATCAGA 59.781 37.500 15.38 0.00 32.44 3.27
3654 5554 7.080724 GCATCTTTTCACCTTGAAACTCTTAG 58.919 38.462 0.78 0.00 45.03 2.18
3655 5555 6.545666 TGCATCTTTTCACCTTGAAACTCTTA 59.454 34.615 0.78 0.00 45.03 2.10
3738 5638 3.142951 CAACACCGAATCAACCTACCAA 58.857 45.455 0.00 0.00 0.00 3.67
3824 5724 4.757149 CGTCAAATTGGAAAAGGAGAGACT 59.243 41.667 0.00 0.00 0.00 3.24
3877 5777 3.264193 TCCAAAGGCAGAGCTAATCTTGA 59.736 43.478 0.00 0.00 35.47 3.02


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

AutoCloner maintained by Alex Coulton.