Multiple sequence alignment - TraesCS1D01G289300

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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 TraesCS1D01G289300 chr1D 100.000 6008 0 0 1 6008 387422553 387428560 0.000000e+00 11095.0
1 TraesCS1D01G289300 chr1D 88.679 53 6 0 4111 4163 436190991 436190939 1.400000e-06 65.8
2 TraesCS1D01G289300 chr1B 94.511 6067 176 72 2 5971 520780441 520786447 0.000000e+00 9214.0
3 TraesCS1D01G289300 chr1B 88.046 435 48 4 4 435 573580019 573580452 4.150000e-141 512.0
4 TraesCS1D01G289300 chr1B 88.679 53 6 0 4111 4163 591111308 591111256 1.400000e-06 65.8
5 TraesCS1D01G289300 chr1A 95.662 4449 132 27 1614 6008 487089598 487094039 0.000000e+00 7090.0
6 TraesCS1D01G289300 chr1A 91.996 1062 39 22 555 1596 487088510 487089545 0.000000e+00 1448.0
7 TraesCS1D01G289300 chr1A 84.342 479 65 6 3992 4463 403390326 403390801 1.530000e-125 460.0
8 TraesCS1D01G289300 chr1A 88.679 53 6 0 4111 4163 533449243 533449191 1.400000e-06 65.8
9 TraesCS1D01G289300 chr7D 81.448 884 112 23 3992 4856 530712659 530713509 0.000000e+00 676.0
10 TraesCS1D01G289300 chr7D 86.207 435 52 5 5 433 186793338 186793770 1.180000e-126 464.0
11 TraesCS1D01G289300 chr7D 86.493 422 54 3 5 424 230998212 230998632 1.530000e-125 460.0
12 TraesCS1D01G289300 chr7B 81.215 889 115 25 3992 4860 570062779 570063635 0.000000e+00 669.0
13 TraesCS1D01G289300 chr7B 86.667 390 44 5 3992 4375 570173783 570174170 5.570000e-115 425.0
14 TraesCS1D01G289300 chr3D 85.912 433 60 1 6 437 501309194 501309626 1.530000e-125 460.0
15 TraesCS1D01G289300 chr7A 85.681 433 60 2 4 435 243855742 243856173 7.100000e-124 455.0
16 TraesCS1D01G289300 chr7A 81.405 242 31 7 4799 5029 610941685 610941923 1.030000e-42 185.0
17 TraesCS1D01G289300 chr6D 85.781 429 59 2 8 434 422193985 422194413 2.550000e-123 453.0
18 TraesCS1D01G289300 chr5D 85.169 445 63 3 5 446 543832896 543833340 2.550000e-123 453.0
19 TraesCS1D01G289300 chr6B 85.484 434 62 1 5 437 626461973 626461540 9.180000e-123 451.0
20 TraesCS1D01G289300 chr6B 94.444 36 2 0 4973 5008 39197852 39197887 8.410000e-04 56.5
21 TraesCS1D01G289300 chr4D 81.051 533 69 16 4337 4858 488358241 488357730 4.360000e-106 396.0
22 TraesCS1D01G289300 chr5A 79.888 537 71 22 4337 4858 670228542 670229056 5.730000e-95 359.0
23 TraesCS1D01G289300 chr5A 85.000 120 17 1 4345 4463 640561166 640561047 2.940000e-23 121.0
24 TraesCS1D01G289300 chr4B 80.738 488 57 15 4337 4795 624402876 624402397 4.460000e-91 346.0
25 TraesCS1D01G289300 chr3A 87.129 202 21 3 1200 1400 374728692 374728889 2.180000e-54 224.0
26 TraesCS1D01G289300 chr2B 85.437 103 11 3 4542 4640 289174835 289174733 2.960000e-18 104.0


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 TraesCS1D01G289300 chr1D 387422553 387428560 6007 False 11095 11095 100.000 1 6008 1 chr1D.!!$F1 6007
1 TraesCS1D01G289300 chr1B 520780441 520786447 6006 False 9214 9214 94.511 2 5971 1 chr1B.!!$F1 5969
2 TraesCS1D01G289300 chr1A 487088510 487094039 5529 False 4269 7090 93.829 555 6008 2 chr1A.!!$F2 5453
3 TraesCS1D01G289300 chr7D 530712659 530713509 850 False 676 676 81.448 3992 4856 1 chr7D.!!$F3 864
4 TraesCS1D01G289300 chr7B 570062779 570063635 856 False 669 669 81.215 3992 4860 1 chr7B.!!$F1 868
5 TraesCS1D01G289300 chr4D 488357730 488358241 511 True 396 396 81.051 4337 4858 1 chr4D.!!$R1 521
6 TraesCS1D01G289300 chr5A 670228542 670229056 514 False 359 359 79.888 4337 4858 1 chr5A.!!$F1 521

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
756 790 0.103755 TGCCACGCTCTCATCTCATC 59.896 55.0 0.00 0.0 0.00 2.92 F
757 791 0.103755 GCCACGCTCTCATCTCATCA 59.896 55.0 0.00 0.0 0.00 3.07 F
1992 2095 0.111253 CCTGCCCTTCTCCACAAAGT 59.889 55.0 0.00 0.0 0.00 2.66 F
2710 2818 0.530650 ACATCTTACCGGCATCTGCG 60.531 55.0 0.00 0.0 43.26 5.18 F
3927 4043 0.179081 AAGGCGCGGAAGAGAATACC 60.179 55.0 8.83 0.0 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1735 1834 1.376466 GGAGCTGCTCCTTGGTGAA 59.624 57.895 35.51 0.0 46.41 3.18 R
2643 2750 3.264706 TGGCACAAAGGCTATGTACCTTA 59.735 43.478 0.00 0.0 46.96 2.69 R
3906 4022 0.104304 TATTCTCTTCCGCGCCTTCC 59.896 55.000 0.00 0.0 0.00 3.46 R
4398 4516 0.108804 ACGGTTGAGCAGTACATCGG 60.109 55.000 0.00 0.0 0.00 4.18 R
5665 5823 0.343726 CCCTCCTCCCTTTCCTACCT 59.656 60.000 0.00 0.0 0.00 3.08 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
25 26 5.116069 ACTTCTTCTTCGAGTCAGTCTTC 57.884 43.478 0.00 0.00 0.00 2.87
46 47 0.676736 GGGCTCCGATACTCCTCAAG 59.323 60.000 0.00 0.00 0.00 3.02
100 101 0.249657 CGTAGATTCCTGCCAGCTCC 60.250 60.000 0.00 0.00 0.00 4.70
137 138 1.480954 AGGGTTTCTCGTCATGCGTAT 59.519 47.619 8.91 0.00 42.13 3.06
189 191 8.496707 TTCAGATCGATTCAAGAATTCAATGA 57.503 30.769 8.44 8.90 0.00 2.57
198 200 6.413018 TCAAGAATTCAATGACGATGACTG 57.587 37.500 8.44 0.00 0.00 3.51
228 230 0.694444 ACGATGGTCCTTAGGGGCAT 60.694 55.000 0.00 0.00 39.39 4.40
252 254 1.446272 CGAAGACTTCCCGGCTGTC 60.446 63.158 9.63 3.58 0.00 3.51
260 262 1.822114 TTCCCGGCTGTCATCGACAA 61.822 55.000 0.00 0.00 42.26 3.18
282 284 0.397957 TTAGGCTGGCTCCGGTATGA 60.398 55.000 7.13 0.00 0.00 2.15
295 297 1.546834 GGTATGAGAGCGACGACAAC 58.453 55.000 0.00 0.00 0.00 3.32
296 298 1.135489 GGTATGAGAGCGACGACAACA 60.135 52.381 0.00 0.00 0.00 3.33
297 299 2.592194 GTATGAGAGCGACGACAACAA 58.408 47.619 0.00 0.00 0.00 2.83
346 348 0.601841 ATGGTCGTTCGGTTGTCCAC 60.602 55.000 0.00 0.00 0.00 4.02
389 393 2.373335 TGTTTGGGGTGCATTGTACT 57.627 45.000 4.86 0.00 0.00 2.73
394 398 4.374689 TTGGGGTGCATTGTACTTTCTA 57.625 40.909 4.86 0.00 0.00 2.10
494 498 6.457159 TTTTGGGACAGAGGGAGTAAATTA 57.543 37.500 0.00 0.00 42.39 1.40
497 501 7.758820 TTGGGACAGAGGGAGTAAATTATTA 57.241 36.000 0.00 0.00 42.39 0.98
599 629 1.849829 CGTCCAAACGCTTTTTCCAAC 59.150 47.619 0.00 0.00 42.82 3.77
601 631 3.254892 GTCCAAACGCTTTTTCCAACAA 58.745 40.909 0.00 0.00 0.00 2.83
602 632 3.061563 GTCCAAACGCTTTTTCCAACAAC 59.938 43.478 0.00 0.00 0.00 3.32
680 714 2.029518 CACGTCTGGCTGTGCAGA 59.970 61.111 3.02 0.00 0.00 4.26
682 716 3.117171 CGTCTGGCTGTGCAGAGC 61.117 66.667 26.78 26.78 38.34 4.09
683 717 2.031616 GTCTGGCTGTGCAGAGCA 59.968 61.111 33.70 19.94 41.08 4.26
684 718 1.376942 GTCTGGCTGTGCAGAGCAT 60.377 57.895 33.70 0.00 41.91 3.79
685 719 1.078637 TCTGGCTGTGCAGAGCATC 60.079 57.895 33.70 19.70 41.91 3.91
686 720 2.435410 TGGCTGTGCAGAGCATCG 60.435 61.111 33.70 0.00 41.91 3.84
687 721 3.873883 GGCTGTGCAGAGCATCGC 61.874 66.667 33.70 15.29 41.91 4.58
688 722 3.122971 GCTGTGCAGAGCATCGCA 61.123 61.111 29.31 0.00 41.91 5.10
689 723 3.090656 CTGTGCAGAGCATCGCAG 58.909 61.111 0.00 0.00 43.07 5.18
690 724 2.435410 TGTGCAGAGCATCGCAGG 60.435 61.111 0.00 0.00 43.07 4.85
691 725 2.125391 GTGCAGAGCATCGCAGGA 60.125 61.111 0.00 0.00 43.07 3.86
755 789 0.179089 GTGCCACGCTCTCATCTCAT 60.179 55.000 0.00 0.00 0.00 2.90
756 790 0.103755 TGCCACGCTCTCATCTCATC 59.896 55.000 0.00 0.00 0.00 2.92
757 791 0.103755 GCCACGCTCTCATCTCATCA 59.896 55.000 0.00 0.00 0.00 3.07
758 792 1.868930 GCCACGCTCTCATCTCATCAG 60.869 57.143 0.00 0.00 0.00 2.90
759 793 1.269673 CCACGCTCTCATCTCATCAGG 60.270 57.143 0.00 0.00 0.00 3.86
760 794 1.408340 CACGCTCTCATCTCATCAGGT 59.592 52.381 0.00 0.00 0.00 4.00
761 795 1.680735 ACGCTCTCATCTCATCAGGTC 59.319 52.381 0.00 0.00 0.00 3.85
762 796 1.000385 CGCTCTCATCTCATCAGGTCC 60.000 57.143 0.00 0.00 0.00 4.46
763 797 2.037901 GCTCTCATCTCATCAGGTCCA 58.962 52.381 0.00 0.00 0.00 4.02
764 798 2.433604 GCTCTCATCTCATCAGGTCCAA 59.566 50.000 0.00 0.00 0.00 3.53
765 799 3.493002 GCTCTCATCTCATCAGGTCCAAG 60.493 52.174 0.00 0.00 0.00 3.61
766 800 2.433604 TCTCATCTCATCAGGTCCAAGC 59.566 50.000 0.00 0.00 0.00 4.01
767 801 2.169978 CTCATCTCATCAGGTCCAAGCA 59.830 50.000 0.00 0.00 0.00 3.91
768 802 2.573009 TCATCTCATCAGGTCCAAGCAA 59.427 45.455 0.00 0.00 0.00 3.91
1379 1432 2.113243 GACCGTCCTTGTTGCCTCCT 62.113 60.000 0.00 0.00 0.00 3.69
1406 1459 2.222976 CGCAATGTTGATGCTCTCTGAC 60.223 50.000 0.00 0.00 41.64 3.51
1500 1560 6.373005 TGTCAGATAGATTTTCAGGTTGGA 57.627 37.500 0.00 0.00 0.00 3.53
1514 1574 3.005684 CAGGTTGGACAGCAAAGCATTAA 59.994 43.478 0.00 0.00 0.00 1.40
1612 1676 5.972935 TGAATCTTAGGCTGTACGAATGAA 58.027 37.500 0.00 0.00 0.00 2.57
1693 1792 2.419620 TCGCAAGCGAGGTGTTCA 59.580 55.556 13.74 0.00 44.01 3.18
1735 1834 0.755686 GATCGACCCAGAGCAAGGAT 59.244 55.000 0.00 0.00 0.00 3.24
1794 1893 1.792367 TCTGACAACAACTTCGATGCG 59.208 47.619 0.00 0.00 0.00 4.73
1878 1977 2.034879 CACTGCCGGCGTCTTGATT 61.035 57.895 23.90 0.00 0.00 2.57
1879 1978 2.034879 ACTGCCGGCGTCTTGATTG 61.035 57.895 23.90 5.39 0.00 2.67
1955 2054 0.173708 GGTCAAGGAGGTCAGTAGCG 59.826 60.000 0.00 0.00 0.00 4.26
1992 2095 0.111253 CCTGCCCTTCTCCACAAAGT 59.889 55.000 0.00 0.00 0.00 2.66
2182 2289 3.908643 TCTCTTCTTCTGATGCAGCAT 57.091 42.857 7.91 7.91 0.00 3.79
2517 2624 3.512516 GTCTGCATCGCCAAGGGC 61.513 66.667 0.00 0.00 46.75 5.19
2608 2715 1.138459 CGATCGACTGCACTCAGCT 59.862 57.895 10.26 0.00 44.10 4.24
2643 2750 6.627395 TTTGACGACAACATAAACTTCCAT 57.373 33.333 0.00 0.00 35.63 3.41
2710 2818 0.530650 ACATCTTACCGGCATCTGCG 60.531 55.000 0.00 0.00 43.26 5.18
2860 2968 1.341482 TGCCCAAGTGACAAGTTCCAA 60.341 47.619 0.00 0.00 0.00 3.53
2912 3020 1.444933 ACCAACATGGGGAACTCTGA 58.555 50.000 12.15 0.00 43.37 3.27
2914 3022 2.379907 ACCAACATGGGGAACTCTGATT 59.620 45.455 12.15 0.00 43.37 2.57
2926 3034 1.144565 CTCTGATTGCGAGCACTCCG 61.145 60.000 11.91 6.72 0.00 4.63
3613 3727 2.212652 CCAAGGCTTTGGCTTCAAAAC 58.787 47.619 15.40 0.00 45.21 2.43
3797 3913 4.408276 ACTTGTGAGGAGCTTACACTCTA 58.592 43.478 15.82 5.32 36.87 2.43
3798 3914 5.020132 ACTTGTGAGGAGCTTACACTCTAT 58.980 41.667 15.82 2.26 36.87 1.98
3843 3959 9.748708 GAAAAAGTATAATAATTCATGCAGGCA 57.251 29.630 0.00 0.00 0.00 4.75
3906 4022 2.094494 ACTTGAGACCACAGTCATAGCG 60.094 50.000 0.00 0.00 46.15 4.26
3927 4043 0.179081 AAGGCGCGGAAGAGAATACC 60.179 55.000 8.83 0.00 0.00 2.73
3929 4045 0.461339 GGCGCGGAAGAGAATACCAA 60.461 55.000 8.83 0.00 0.00 3.67
3942 4058 9.699703 GAAGAGAATACCAAGTGATTATACCTC 57.300 37.037 0.00 0.00 0.00 3.85
4223 4339 3.875134 CTCATACATGAGTGCAGATGCAA 59.125 43.478 9.46 0.00 45.59 4.08
4398 4516 6.845302 TGAATGAAGTTGCTGAATGTGATAC 58.155 36.000 0.00 0.00 0.00 2.24
4455 4579 1.722011 CAACGTCCCACATAGTCCAC 58.278 55.000 0.00 0.00 0.00 4.02
4659 4799 5.888161 CCCTCTGTTACCTGCAATAAGATTT 59.112 40.000 0.00 0.00 0.00 2.17
4699 4841 2.154462 CTTTCCTGACCGCTGTTTCAT 58.846 47.619 0.00 0.00 0.00 2.57
4750 4892 5.580998 ACTGGAGAAAGGTGTACTCTGATA 58.419 41.667 0.00 0.00 0.00 2.15
5011 5158 5.855045 TCCACAAGGAGAACTTCTAACTTC 58.145 41.667 5.60 0.00 39.61 3.01
5058 5205 0.176680 AGCATCGGGTAGCAGTTCTG 59.823 55.000 0.00 0.00 0.00 3.02
5231 5379 8.321353 TGCTTCTTAGAATAATTCAGACCTTGA 58.679 33.333 0.00 0.00 0.00 3.02
5404 5554 3.442977 AGGAGCATTTCAAGTCAATCTGC 59.557 43.478 0.00 0.00 0.00 4.26
5407 5557 2.231964 GCATTTCAAGTCAATCTGCCCA 59.768 45.455 0.00 0.00 0.00 5.36
5436 5586 4.844998 TTCAATTTTGAACGATGCTCCA 57.155 36.364 1.66 0.00 41.88 3.86
5517 5667 4.439153 GCATTGCACACAAGCACATACTAT 60.439 41.667 3.15 0.00 45.61 2.12
5652 5802 5.662674 TGGGTAGTAAGAAGAGAAGAAGC 57.337 43.478 0.00 0.00 0.00 3.86
5653 5803 4.158025 TGGGTAGTAAGAAGAGAAGAAGCG 59.842 45.833 0.00 0.00 0.00 4.68
5656 5806 4.464069 AGTAAGAAGAGAAGAAGCGCAT 57.536 40.909 11.47 0.00 0.00 4.73
5659 5809 1.552337 AGAAGAGAAGAAGCGCATCCA 59.448 47.619 11.47 0.00 0.00 3.41
5660 5810 2.170187 AGAAGAGAAGAAGCGCATCCAT 59.830 45.455 11.47 0.00 0.00 3.41
5753 5920 1.251527 AAGCGACCAGGATCTGACGT 61.252 55.000 0.00 0.00 35.23 4.34
5796 5966 1.534729 CGTTAGGGGCTTTTGCTTCT 58.465 50.000 0.00 0.00 46.54 2.85
5797 5967 2.617021 CCGTTAGGGGCTTTTGCTTCTA 60.617 50.000 0.00 0.00 46.54 2.10
5809 5979 5.277538 GCTTTTGCTTCTAATATCAGGGACG 60.278 44.000 0.00 0.00 43.35 4.79
5833 6003 5.289434 GCTAGCTGTTTGATAAAATGCCAAC 59.711 40.000 7.70 0.00 0.00 3.77
5843 6021 2.014010 AAATGCCAACATGGACAGGT 57.986 45.000 0.00 0.00 40.96 4.00
5852 6030 2.050144 ACATGGACAGGTCAGTGAACT 58.950 47.619 4.37 4.37 0.00 3.01
5868 6054 2.017049 GAACTGGTGCAACAACACTCT 58.983 47.619 5.64 0.00 39.98 3.24
5909 6095 3.859386 GCATTTGCAGTTGTAAGCCATAC 59.141 43.478 0.00 0.00 41.59 2.39
5933 6119 6.925165 ACTTTGAGCCAAATACATGTGAAAAG 59.075 34.615 9.11 7.34 32.70 2.27
5935 6121 4.176271 GAGCCAAATACATGTGAAAAGGC 58.824 43.478 9.11 14.77 39.82 4.35
5943 6135 3.652274 ACATGTGAAAAGGCGGAATTTG 58.348 40.909 0.00 0.00 0.00 2.32
5945 6137 2.035632 TGTGAAAAGGCGGAATTTGGT 58.964 42.857 0.00 0.00 0.00 3.67
5978 6170 3.722147 CCTGTTCATAAGGTCTGGATCG 58.278 50.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.310451 AGACTGACTCGAAGAAGAAGTACT 58.690 41.667 0.00 0.00 34.09 2.73
3 4 4.022676 GGAAGACTGACTCGAAGAAGAAGT 60.023 45.833 0.00 0.00 34.09 3.01
37 38 2.470821 CGACAAACGAACTTGAGGAGT 58.529 47.619 0.00 0.00 45.77 3.85
46 47 0.595825 ACTCGTCCCGACAAACGAAC 60.596 55.000 0.00 0.00 46.17 3.95
108 109 0.459759 CGAGAAACCCTAACCTCGCC 60.460 60.000 0.00 0.00 41.31 5.54
137 138 9.997482 GAACCTAATTCAAATTTCGCTATTGTA 57.003 29.630 0.00 0.00 37.27 2.41
189 191 4.148825 GGGAGCCGCAGTCATCGT 62.149 66.667 0.00 0.00 0.00 3.73
212 214 0.552848 CACATGCCCCTAAGGACCAT 59.447 55.000 0.00 0.00 38.24 3.55
228 230 1.300620 CGGGAAGTCTTCGTGCACA 60.301 57.895 18.64 0.81 0.00 4.57
252 254 1.656652 CCAGCCTAACCTTGTCGATG 58.343 55.000 0.00 0.00 0.00 3.84
260 262 2.525284 TACCGGAGCCAGCCTAACCT 62.525 60.000 9.46 0.00 0.00 3.50
282 284 2.300787 GCGTTGTTGTCGTCGCTCT 61.301 57.895 0.00 0.00 44.28 4.09
601 631 1.142965 GCCGCACCCAACTTTTTGT 59.857 52.632 0.00 0.00 0.00 2.83
602 632 1.948635 CGCCGCACCCAACTTTTTG 60.949 57.895 0.00 0.00 0.00 2.44
680 714 4.479993 GCCCTGTCCTGCGATGCT 62.480 66.667 0.00 0.00 0.00 3.79
682 716 2.513204 CTGCCCTGTCCTGCGATG 60.513 66.667 0.00 0.00 0.00 3.84
683 717 2.685017 TCTGCCCTGTCCTGCGAT 60.685 61.111 0.00 0.00 0.00 4.58
684 718 3.695606 GTCTGCCCTGTCCTGCGA 61.696 66.667 0.00 0.00 0.00 5.10
685 719 3.655810 GAGTCTGCCCTGTCCTGCG 62.656 68.421 0.00 0.00 0.00 5.18
686 720 2.267324 GAGTCTGCCCTGTCCTGC 59.733 66.667 0.00 0.00 0.00 4.85
687 721 2.575993 CGAGTCTGCCCTGTCCTG 59.424 66.667 0.00 0.00 0.00 3.86
688 722 3.386237 GCGAGTCTGCCCTGTCCT 61.386 66.667 0.00 0.00 0.00 3.85
689 723 4.803426 CGCGAGTCTGCCCTGTCC 62.803 72.222 0.00 0.00 0.00 4.02
690 724 4.057428 ACGCGAGTCTGCCCTGTC 62.057 66.667 15.93 0.00 44.19 3.51
766 800 5.745769 GTGTCTCTTCTTCCTTTTGCTTTTG 59.254 40.000 0.00 0.00 0.00 2.44
767 801 5.449177 CGTGTCTCTTCTTCCTTTTGCTTTT 60.449 40.000 0.00 0.00 0.00 2.27
768 802 4.035675 CGTGTCTCTTCTTCCTTTTGCTTT 59.964 41.667 0.00 0.00 0.00 3.51
1092 1136 3.567797 GGCTGCTTCCGCATCGTC 61.568 66.667 0.00 0.00 46.74 4.20
1146 1190 2.982130 CGGAAGGAGGTCACCCTG 59.018 66.667 0.00 0.00 42.86 4.45
1391 1444 3.865011 TCAGAGTCAGAGAGCATCAAC 57.135 47.619 0.00 0.00 37.82 3.18
1393 1446 3.888323 GGTATCAGAGTCAGAGAGCATCA 59.112 47.826 4.69 0.00 37.82 3.07
1406 1459 3.549827 CGTCAAGCTAGCAGGTATCAGAG 60.550 52.174 18.83 0.00 0.00 3.35
1500 1560 1.273327 GGCTGGTTAATGCTTTGCTGT 59.727 47.619 0.00 0.00 0.00 4.40
1581 1645 6.313905 CGTACAGCCTAAGATTCAGTTTCAAT 59.686 38.462 0.00 0.00 0.00 2.57
1612 1676 5.215069 TCTGGGCTTAGAGATTCAGAGATT 58.785 41.667 0.00 0.00 0.00 2.40
1693 1792 2.374830 CTTCTCCTCGCCATCGCCAT 62.375 60.000 0.00 0.00 35.26 4.40
1735 1834 1.376466 GGAGCTGCTCCTTGGTGAA 59.624 57.895 35.51 0.00 46.41 3.18
1992 2095 8.884124 ATGAAAACCCTGAAATTTCATAGAGA 57.116 30.769 20.76 0.00 46.44 3.10
2517 2624 4.717629 TTGGTCGTCTCAGCGGCG 62.718 66.667 0.51 0.51 37.35 6.46
2643 2750 3.264706 TGGCACAAAGGCTATGTACCTTA 59.735 43.478 0.00 0.00 46.96 2.69
2860 2968 2.204213 AAGGGCCCCAGCTTCTCT 60.204 61.111 21.43 0.00 39.73 3.10
2912 3020 4.473520 CCCCGGAGTGCTCGCAAT 62.474 66.667 0.73 0.00 0.00 3.56
2926 3034 1.054978 GGAGGATACCAGTCCACCCC 61.055 65.000 0.00 0.00 41.56 4.95
3613 3727 3.719924 TGCCTGCAAACATTGAAGAAAG 58.280 40.909 0.00 0.00 38.71 2.62
3843 3959 8.924511 TCTTGGAATTTACTTCTTCTTCACAT 57.075 30.769 0.00 0.00 34.08 3.21
3906 4022 0.104304 TATTCTCTTCCGCGCCTTCC 59.896 55.000 0.00 0.00 0.00 3.46
3927 4043 7.856145 AGAAAGCTTGAGGTATAATCACTTG 57.144 36.000 0.00 0.00 0.00 3.16
3929 4045 9.606631 CTTAAGAAAGCTTGAGGTATAATCACT 57.393 33.333 0.00 0.00 34.92 3.41
4398 4516 0.108804 ACGGTTGAGCAGTACATCGG 60.109 55.000 0.00 0.00 0.00 4.18
4659 4799 1.378531 GAAGCAACCATGGCGTATCA 58.621 50.000 13.04 0.00 36.08 2.15
4699 4841 3.342377 TGCAAAATGTGTCCGGATCTA 57.658 42.857 7.81 0.00 0.00 1.98
4750 4892 3.118665 GCATTCTTGTGGGTATTTGCCAT 60.119 43.478 0.00 0.00 0.00 4.40
5011 5158 1.691196 TTTTGTTGGCCTGACCTCAG 58.309 50.000 3.32 0.00 43.40 3.35
5114 5261 7.859325 ATAACTAACGCCACATACTTTTCAT 57.141 32.000 0.00 0.00 0.00 2.57
5231 5379 3.578456 CGAGCCAATCGCCTGTTT 58.422 55.556 0.00 0.00 45.98 2.83
5422 5572 4.321156 CCAAGAAATTGGAGCATCGTTCAA 60.321 41.667 0.53 0.00 44.82 2.69
5436 5586 5.279685 TCCCAAATATCCAGCCAAGAAATT 58.720 37.500 0.00 0.00 0.00 1.82
5471 5621 7.620458 GCAAGGTGCTAGCTATATCCGTAGG 62.620 52.000 17.23 4.91 46.14 3.18
5473 5623 3.192844 GCAAGGTGCTAGCTATATCCGTA 59.807 47.826 17.23 0.00 40.96 4.02
5517 5667 5.068723 GGGATTCCTCTTCGTCTGTATGTAA 59.931 44.000 2.01 0.00 0.00 2.41
5622 5772 4.287552 TCTTCTTACTACCCATCCTGGAC 58.712 47.826 0.00 0.00 40.96 4.02
5652 5802 0.898320 CCTACCTCCCTATGGATGCG 59.102 60.000 0.00 0.00 40.80 4.73
5653 5803 2.327325 TCCTACCTCCCTATGGATGC 57.673 55.000 0.00 0.00 40.80 3.91
5656 5806 2.090153 CCCTTTCCTACCTCCCTATGGA 60.090 54.545 0.00 0.00 38.75 3.41
5659 5809 2.182536 CCTCCCTTTCCTACCTCCCTAT 59.817 54.545 0.00 0.00 0.00 2.57
5660 5810 1.579191 CCTCCCTTTCCTACCTCCCTA 59.421 57.143 0.00 0.00 0.00 3.53
5665 5823 0.343726 CCCTCCTCCCTTTCCTACCT 59.656 60.000 0.00 0.00 0.00 3.08
5729 5896 2.683933 ATCCTGGTCGCTTCCCGT 60.684 61.111 0.00 0.00 38.35 5.28
5743 5910 1.084370 CCGGCTTTCACGTCAGATCC 61.084 60.000 0.00 0.00 0.00 3.36
5796 5966 3.497332 ACAGCTAGCGTCCCTGATATTA 58.503 45.455 9.55 0.00 0.00 0.98
5797 5967 2.320781 ACAGCTAGCGTCCCTGATATT 58.679 47.619 9.55 0.00 0.00 1.28
5809 5979 4.997565 TGGCATTTTATCAAACAGCTAGC 58.002 39.130 6.62 6.62 0.00 3.42
5833 6003 2.420642 CAGTTCACTGACCTGTCCATG 58.579 52.381 0.14 0.00 46.59 3.66
5843 6021 1.742831 GTTGTTGCACCAGTTCACTGA 59.257 47.619 8.61 0.00 46.59 3.41
5852 6030 1.134250 TGCTAGAGTGTTGTTGCACCA 60.134 47.619 0.00 0.00 40.04 4.17
5853 6031 1.593196 TGCTAGAGTGTTGTTGCACC 58.407 50.000 0.00 0.00 40.04 5.01
5868 6054 7.519843 CAAATGCATACAAAAATTGCTTGCTA 58.480 30.769 0.00 6.18 40.47 3.49
5904 6090 6.095300 TCACATGTATTTGGCTCAAAGTATGG 59.905 38.462 0.00 10.66 36.76 2.74
5909 6095 6.366877 CCTTTTCACATGTATTTGGCTCAAAG 59.633 38.462 0.00 0.00 36.76 2.77
5933 6119 1.379527 CTAGGACACCAAATTCCGCC 58.620 55.000 0.00 0.00 36.95 6.13
5935 6121 2.629051 GTCCTAGGACACCAAATTCCG 58.371 52.381 32.91 0.00 44.02 4.30
5943 6135 1.542187 AACAGGCGTCCTAGGACACC 61.542 60.000 33.31 33.31 45.02 4.16
5945 6137 0.541063 TGAACAGGCGTCCTAGGACA 60.541 55.000 35.32 15.35 44.77 4.02
5978 6170 2.271944 ACTGGTTGGCTCAAACTACC 57.728 50.000 4.87 0.00 31.53 3.18


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

AutoCloner maintained by Alex Coulton.