Multiple sequence alignment - TraesCS6D01G216400

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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 TraesCS6D01G216400 chr6D 100.000 4284 0 0 1 4284 306147035 306142752 0.000000e+00 7912.0
1 TraesCS6D01G216400 chr6B 93.565 3419 139 33 913 4284 473089054 473085670 0.000000e+00 5020.0
2 TraesCS6D01G216400 chr6B 80.934 792 106 22 1 791 473089854 473089107 6.170000e-163 584.0
3 TraesCS6D01G216400 chr6A 95.034 2517 80 19 1701 4209 441521746 441519267 0.000000e+00 3914.0
4 TraesCS6D01G216400 chr6A 94.945 811 26 8 902 1699 441523404 441522596 0.000000e+00 1256.0
5 TraesCS6D01G216400 chr6A 85.714 868 84 21 1 864 441524243 441523412 0.000000e+00 880.0
6 TraesCS6D01G216400 chr4D 95.918 49 0 2 3448 3495 14928716 14928763 1.280000e-10 78.7
7 TraesCS6D01G216400 chr3A 94.000 50 3 0 3439 3488 53028046 53027997 4.590000e-10 76.8
8 TraesCS6D01G216400 chr2A 90.164 61 2 4 3431 3490 615095337 615095280 4.590000e-10 76.8
9 TraesCS6D01G216400 chr3B 90.909 55 4 1 3446 3499 578594682 578594628 5.940000e-09 73.1
10 TraesCS6D01G216400 chr1D 89.655 58 4 2 3438 3495 10263558 10263503 5.940000e-09 73.1
11 TraesCS6D01G216400 chr7A 89.474 57 4 2 3448 3503 618680954 618680899 2.140000e-08 71.3
12 TraesCS6D01G216400 chr5A 86.567 67 4 4 3438 3503 656668298 656668360 7.690000e-08 69.4
13 TraesCS6D01G216400 chr3D 97.222 36 1 0 4232 4267 596846486 596846521 1.290000e-05 62.1
14 TraesCS6D01G216400 chr5D 100.000 28 0 0 4240 4267 495349717 495349690 8.000000e-03 52.8
15 TraesCS6D01G216400 chr5D 96.774 31 1 0 4233 4263 518763730 518763760 8.000000e-03 52.8


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 TraesCS6D01G216400 chr6D 306142752 306147035 4283 True 7912.000000 7912 100.000000 1 4284 1 chr6D.!!$R1 4283
1 TraesCS6D01G216400 chr6B 473085670 473089854 4184 True 2802.000000 5020 87.249500 1 4284 2 chr6B.!!$R1 4283
2 TraesCS6D01G216400 chr6A 441519267 441524243 4976 True 2016.666667 3914 91.897667 1 4209 3 chr6A.!!$R1 4208

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
875 897 0.030297 AGTCCATCCATCTGCTCCCT 60.030 55.0 0.0 0.0 0.00 4.20 F
880 902 0.188587 ATCCATCTGCTCCCTCCGTA 59.811 55.0 0.0 0.0 0.00 4.02 F
886 908 0.323629 CTGCTCCCTCCGTACCAAAA 59.676 55.0 0.0 0.0 0.00 2.44 F
887 909 0.988832 TGCTCCCTCCGTACCAAAAT 59.011 50.0 0.0 0.0 0.00 1.82 F
1399 1424 1.122849 GCTGTTTGTGTGCGTGAATG 58.877 50.0 0.0 0.0 0.00 2.67 F
3043 3954 1.481871 CATTTCAGGGCATGGAAGCT 58.518 50.0 0.0 0.0 26.83 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2193 3104 1.082104 GTGCTAAAAACTGCGCGCT 60.082 52.632 33.29 13.56 0.00 5.92 R
2473 3384 2.159382 CCTGACGCAACCACCTTTAAT 58.841 47.619 0.00 0.00 0.00 1.40 R
2731 3642 3.258123 TCAATGACACCAGAGATGACGAA 59.742 43.478 0.00 0.00 0.00 3.85 R
2973 3884 2.939103 ACATCAATAGCGGCAAGAAGTC 59.061 45.455 1.45 0.00 0.00 3.01 R
3216 4127 1.035139 AAAGTTCACCTTGCAGCCAG 58.965 50.000 0.00 0.00 32.32 4.85 R
4146 5068 2.268076 GCCACGGTGCCAATCTTGT 61.268 57.895 1.68 0.00 0.00 3.16 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
33 34 4.516321 TGTCTGTGTCAAATCATTGTCCAG 59.484 41.667 0.00 0.00 37.79 3.86
104 106 3.137544 TCCAAACCTTCTAGACAAAGGCA 59.862 43.478 8.62 0.00 46.03 4.75
153 155 1.246056 TGGAATGAGCAGCAGCCAAC 61.246 55.000 0.00 0.00 43.56 3.77
192 194 4.184629 CGTCTAGCAGCTGAGGTAAAAAT 58.815 43.478 20.43 0.00 0.00 1.82
236 238 1.808411 GAAGCGACCACTTCATTGGA 58.192 50.000 0.00 0.00 44.50 3.53
340 342 4.959399 GCCAGAGCTGCTCAAGAT 57.041 55.556 29.49 7.87 35.50 2.40
341 343 2.395651 GCCAGAGCTGCTCAAGATG 58.604 57.895 29.49 18.78 35.50 2.90
342 344 0.107800 GCCAGAGCTGCTCAAGATGA 60.108 55.000 29.49 0.00 35.50 2.92
343 345 1.475392 GCCAGAGCTGCTCAAGATGAT 60.475 52.381 29.49 5.97 35.50 2.45
344 346 2.485903 CCAGAGCTGCTCAAGATGATC 58.514 52.381 29.49 2.01 32.06 2.92
345 347 2.158943 CCAGAGCTGCTCAAGATGATCA 60.159 50.000 29.49 0.00 32.06 2.92
346 348 3.532542 CAGAGCTGCTCAAGATGATCAA 58.467 45.455 29.49 0.00 32.06 2.57
347 349 3.558006 CAGAGCTGCTCAAGATGATCAAG 59.442 47.826 29.49 0.00 32.06 3.02
369 371 1.003580 TCTTGGTCTGACATCCCTTGC 59.996 52.381 10.38 0.00 0.00 4.01
376 378 3.665675 GACATCCCTTGCGCGGTCT 62.666 63.158 8.83 0.00 0.00 3.85
452 454 2.948979 CAGCGGATGTAAAAGCCCATTA 59.051 45.455 0.00 0.00 0.00 1.90
462 464 1.609208 AAGCCCATTACATCGGATGC 58.391 50.000 17.61 2.12 0.00 3.91
463 465 0.767375 AGCCCATTACATCGGATGCT 59.233 50.000 17.61 4.50 0.00 3.79
472 474 5.722021 TTACATCGGATGCTGCTATTCTA 57.278 39.130 17.61 0.00 0.00 2.10
478 480 2.408050 GATGCTGCTATTCTACACCCG 58.592 52.381 0.00 0.00 0.00 5.28
479 481 0.464036 TGCTGCTATTCTACACCCGG 59.536 55.000 0.00 0.00 0.00 5.73
480 482 0.249911 GCTGCTATTCTACACCCGGG 60.250 60.000 22.25 22.25 0.00 5.73
481 483 0.249911 CTGCTATTCTACACCCGGGC 60.250 60.000 24.08 2.08 0.00 6.13
506 508 4.309950 ACGAGCCCGGGTGTGAAC 62.310 66.667 24.63 3.42 40.78 3.18
574 576 1.689984 TTTGTGGTGCAAGATGCTCA 58.310 45.000 3.78 0.02 45.31 4.26
578 580 1.400846 GTGGTGCAAGATGCTCATCTG 59.599 52.381 12.62 8.48 46.75 2.90
579 581 0.381089 GGTGCAAGATGCTCATCTGC 59.619 55.000 12.62 16.27 46.75 4.26
588 590 0.392060 TGCTCATCTGCGTGATTGCT 60.392 50.000 12.07 0.00 34.91 3.91
594 596 0.448990 TCTGCGTGATTGCTTGATGC 59.551 50.000 0.00 0.00 43.25 3.91
626 628 7.595819 AAATTTGGTAAAGTCTGGACATTCA 57.404 32.000 3.51 0.00 0.00 2.57
635 637 3.648067 AGTCTGGACATTCAAGGAGTTCA 59.352 43.478 3.51 0.00 0.00 3.18
706 708 5.531634 ACATTGTTCATGCTCGATTTTGTT 58.468 33.333 0.00 0.00 36.14 2.83
713 715 8.698854 TGTTCATGCTCGATTTTGTTTTATTTC 58.301 29.630 0.00 0.00 0.00 2.17
717 719 9.079833 CATGCTCGATTTTGTTTTATTTCTCAT 57.920 29.630 0.00 0.00 0.00 2.90
743 745 5.304101 AGCTTATCAAATGTCCAAACAACCA 59.696 36.000 0.00 0.00 39.30 3.67
828 850 0.874390 CTGTTCACCGGGTGTTGATG 59.126 55.000 25.53 10.48 34.79 3.07
832 854 3.256960 ACCGGGTGTTGATGGGCT 61.257 61.111 6.32 0.00 0.00 5.19
851 873 1.472480 CTGGGGCGTCGAATTGAATTT 59.528 47.619 0.00 0.00 0.00 1.82
853 875 2.094957 TGGGGCGTCGAATTGAATTTTC 60.095 45.455 0.00 0.00 0.00 2.29
864 886 3.848272 TTGAATTTTCGCAGTCCATCC 57.152 42.857 0.00 0.00 0.00 3.51
865 887 2.789213 TGAATTTTCGCAGTCCATCCA 58.211 42.857 0.00 0.00 0.00 3.41
866 888 3.355378 TGAATTTTCGCAGTCCATCCAT 58.645 40.909 0.00 0.00 0.00 3.41
868 890 2.787473 TTTTCGCAGTCCATCCATCT 57.213 45.000 0.00 0.00 0.00 2.90
869 891 2.028420 TTTCGCAGTCCATCCATCTG 57.972 50.000 0.00 0.00 0.00 2.90
873 895 3.702147 CAGTCCATCCATCTGCTCC 57.298 57.895 0.00 0.00 0.00 4.70
874 896 0.108207 CAGTCCATCCATCTGCTCCC 59.892 60.000 0.00 0.00 0.00 4.30
875 897 0.030297 AGTCCATCCATCTGCTCCCT 60.030 55.000 0.00 0.00 0.00 4.20
876 898 0.396060 GTCCATCCATCTGCTCCCTC 59.604 60.000 0.00 0.00 0.00 4.30
877 899 0.765903 TCCATCCATCTGCTCCCTCC 60.766 60.000 0.00 0.00 0.00 4.30
878 900 1.370437 CATCCATCTGCTCCCTCCG 59.630 63.158 0.00 0.00 0.00 4.63
879 901 1.074926 ATCCATCTGCTCCCTCCGT 60.075 57.895 0.00 0.00 0.00 4.69
880 902 0.188587 ATCCATCTGCTCCCTCCGTA 59.811 55.000 0.00 0.00 0.00 4.02
881 903 0.755698 TCCATCTGCTCCCTCCGTAC 60.756 60.000 0.00 0.00 0.00 3.67
882 904 1.742768 CATCTGCTCCCTCCGTACC 59.257 63.158 0.00 0.00 0.00 3.34
883 905 1.043116 CATCTGCTCCCTCCGTACCA 61.043 60.000 0.00 0.00 0.00 3.25
884 906 0.325296 ATCTGCTCCCTCCGTACCAA 60.325 55.000 0.00 0.00 0.00 3.67
885 907 0.543410 TCTGCTCCCTCCGTACCAAA 60.543 55.000 0.00 0.00 0.00 3.28
886 908 0.323629 CTGCTCCCTCCGTACCAAAA 59.676 55.000 0.00 0.00 0.00 2.44
887 909 0.988832 TGCTCCCTCCGTACCAAAAT 59.011 50.000 0.00 0.00 0.00 1.82
888 910 2.169769 CTGCTCCCTCCGTACCAAAATA 59.830 50.000 0.00 0.00 0.00 1.40
889 911 2.169769 TGCTCCCTCCGTACCAAAATAG 59.830 50.000 0.00 0.00 0.00 1.73
890 912 2.433239 GCTCCCTCCGTACCAAAATAGA 59.567 50.000 0.00 0.00 0.00 1.98
891 913 3.071167 GCTCCCTCCGTACCAAAATAGAT 59.929 47.826 0.00 0.00 0.00 1.98
892 914 4.799917 GCTCCCTCCGTACCAAAATAGATC 60.800 50.000 0.00 0.00 0.00 2.75
893 915 3.319972 TCCCTCCGTACCAAAATAGATCG 59.680 47.826 0.00 0.00 0.00 3.69
894 916 3.554337 CCCTCCGTACCAAAATAGATCGG 60.554 52.174 0.00 0.00 38.16 4.18
895 917 3.319972 CCTCCGTACCAAAATAGATCGGA 59.680 47.826 0.00 0.00 42.33 4.55
896 918 4.579454 TCCGTACCAAAATAGATCGGAG 57.421 45.455 0.00 0.00 40.28 4.63
897 919 3.319972 TCCGTACCAAAATAGATCGGAGG 59.680 47.826 0.00 0.00 40.28 4.30
898 920 3.554337 CCGTACCAAAATAGATCGGAGGG 60.554 52.174 0.00 0.00 38.96 4.30
899 921 3.319972 CGTACCAAAATAGATCGGAGGGA 59.680 47.826 0.00 0.00 0.00 4.20
900 922 4.558898 CGTACCAAAATAGATCGGAGGGAG 60.559 50.000 0.00 0.00 0.00 4.30
904 926 4.344102 CCAAAATAGATCGGAGGGAGTACA 59.656 45.833 0.00 0.00 0.00 2.90
919 941 2.091541 AGTACATTGCAAATGTCCCCG 58.908 47.619 14.94 0.00 33.76 5.73
966 991 4.575885 TGGACTGAAAACTAATCCCTTCG 58.424 43.478 0.00 0.00 0.00 3.79
1233 1258 2.279784 CCGGGCATTCTCGAGCTC 60.280 66.667 7.81 2.73 0.00 4.09
1326 1351 2.354805 GGGGTTCTGCAATCTACGAGTT 60.355 50.000 0.00 0.00 0.00 3.01
1399 1424 1.122849 GCTGTTTGTGTGCGTGAATG 58.877 50.000 0.00 0.00 0.00 2.67
1462 1496 8.096414 AGGATTTGTGATTTATTGGGTTTCTTG 58.904 33.333 0.00 0.00 0.00 3.02
1651 1685 3.609853 CAAATAGCCCAGACAGCTACAA 58.390 45.455 0.00 0.00 45.16 2.41
1927 2809 2.096019 CAGCTCCGAGAAAAAGTTCTGC 60.096 50.000 0.00 0.00 44.42 4.26
2224 3135 6.588756 CAGTTTTTAGCACGGACTGATACTTA 59.411 38.462 0.00 0.00 39.97 2.24
2660 3571 4.693283 TCTAGCCGATGGTTGTCATAAAG 58.307 43.478 0.00 0.00 35.97 1.85
2973 3884 4.122776 AGAAGTCTGTTGTGCAACTGTAG 58.877 43.478 14.97 5.77 41.67 2.74
3043 3954 1.481871 CATTTCAGGGCATGGAAGCT 58.518 50.000 0.00 0.00 26.83 3.74
3160 4071 4.192000 GAGTACCTCGACGTCCGA 57.808 61.111 10.58 9.76 46.35 4.55
3368 4279 3.963428 ACTGTAGAAAGTAGCACCAGG 57.037 47.619 0.00 0.00 0.00 4.45
3516 4427 1.266989 GCTTTCTGGGTATAATGGCGC 59.733 52.381 0.00 0.00 0.00 6.53
3521 4432 1.603802 CTGGGTATAATGGCGCTGTTG 59.396 52.381 7.64 0.00 0.00 3.33
3546 4457 6.699642 GTGTTGCTAAATGTTGTAAATGTGGT 59.300 34.615 0.00 0.00 0.00 4.16
3548 4459 8.580720 TGTTGCTAAATGTTGTAAATGTGGTAT 58.419 29.630 0.00 0.00 0.00 2.73
3621 4532 7.096558 CCAAAAACGCATCCAAAATTGAATTTG 60.097 33.333 3.62 0.00 39.47 2.32
3648 4559 5.584442 ACTTACAAAACGGTGGCTTAAAAG 58.416 37.500 0.00 0.00 0.00 2.27
3738 4651 5.935945 TGTCTCCCAGAATGAACAGTAAAA 58.064 37.500 0.00 0.00 39.69 1.52
3745 4658 8.573035 TCCCAGAATGAACAGTAAAACATAAAC 58.427 33.333 0.00 0.00 39.69 2.01
4007 4924 8.477419 AAAATTATTTTCCACCTGAGAGAACA 57.523 30.769 0.00 0.00 0.00 3.18
4011 4928 1.649321 TCCACCTGAGAGAACATGCT 58.351 50.000 0.00 0.00 0.00 3.79
4015 4932 3.057736 CCACCTGAGAGAACATGCTTTTG 60.058 47.826 0.00 0.00 0.00 2.44
4021 4938 7.147915 ACCTGAGAGAACATGCTTTTGTTTTTA 60.148 33.333 0.00 0.00 39.85 1.52
4055 4975 2.943036 TTGGAGTTTGGACTACCCAC 57.057 50.000 0.00 0.00 46.62 4.61
4146 5068 4.020543 GGTAGGGGTAATGTGAATTTGCA 58.979 43.478 0.00 0.00 0.00 4.08
4236 5159 8.947115 GTTGCCAAAATCAGTCTAGTACTAAAT 58.053 33.333 3.76 0.00 35.76 1.40
4266 5189 9.391006 ACTCTCTCCGTCTCATAATATAAGATC 57.609 37.037 0.00 0.00 0.00 2.75
4268 5191 7.496263 TCTCTCCGTCTCATAATATAAGATCGG 59.504 40.741 7.62 7.62 36.21 4.18
4278 5201 8.999431 TCATAATATAAGATCGGTTTTCAAGCC 58.001 33.333 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.132502 AGAACTGGACAATGATTTGACACA 58.867 37.500 0.00 0.00 36.64 3.72
53 54 1.523154 GGTTTCCTCACCGCATGCAA 61.523 55.000 19.57 0.00 0.00 4.08
104 106 2.093235 GCACCACATTCTAGAAGCCTCT 60.093 50.000 11.53 0.00 35.52 3.69
113 115 3.758023 CACATTTCCTGCACCACATTCTA 59.242 43.478 0.00 0.00 0.00 2.10
153 155 0.962356 ACGCTTGAAGGGATTGGCAG 60.962 55.000 16.51 0.00 31.91 4.85
185 187 1.785518 CGTGCGAGCGGTGATTTTTAC 60.786 52.381 0.00 0.00 0.00 2.01
192 194 2.809174 CAATCGTGCGAGCGGTGA 60.809 61.111 0.00 0.00 0.00 4.02
325 327 3.180891 TGATCATCTTGAGCAGCTCTG 57.819 47.619 23.15 15.35 37.93 3.35
339 341 3.262660 TGTCAGACCAAGAGCTTGATCAT 59.737 43.478 11.61 0.00 42.93 2.45
340 342 2.634453 TGTCAGACCAAGAGCTTGATCA 59.366 45.455 11.61 0.00 42.93 2.92
341 343 3.325293 TGTCAGACCAAGAGCTTGATC 57.675 47.619 11.61 4.11 42.93 2.92
342 344 3.370315 GGATGTCAGACCAAGAGCTTGAT 60.370 47.826 11.61 0.00 42.93 2.57
343 345 2.027745 GGATGTCAGACCAAGAGCTTGA 60.028 50.000 11.61 0.00 42.93 3.02
344 346 2.354259 GGATGTCAGACCAAGAGCTTG 58.646 52.381 3.27 3.27 40.13 4.01
345 347 1.280421 GGGATGTCAGACCAAGAGCTT 59.720 52.381 0.00 0.00 0.00 3.74
346 348 0.908198 GGGATGTCAGACCAAGAGCT 59.092 55.000 0.00 0.00 0.00 4.09
347 349 0.908198 AGGGATGTCAGACCAAGAGC 59.092 55.000 0.00 0.00 0.00 4.09
369 371 3.000322 GTGAGAATTGACAATAGACCGCG 60.000 47.826 0.00 0.00 0.00 6.46
376 378 5.945191 TCTTGGCATGTGAGAATTGACAATA 59.055 36.000 0.00 0.00 37.72 1.90
452 454 3.321968 TGTAGAATAGCAGCATCCGATGT 59.678 43.478 10.10 0.00 0.00 3.06
457 459 2.772287 GGGTGTAGAATAGCAGCATCC 58.228 52.381 0.00 0.00 35.09 3.51
462 464 0.249911 GCCCGGGTGTAGAATAGCAG 60.250 60.000 24.63 0.00 0.00 4.24
463 465 1.827394 GCCCGGGTGTAGAATAGCA 59.173 57.895 24.63 0.00 0.00 3.49
490 492 4.308458 TGTTCACACCCGGGCTCG 62.308 66.667 24.08 12.58 0.00 5.03
574 576 1.065102 GCATCAAGCAATCACGCAGAT 59.935 47.619 0.00 0.00 44.79 2.90
588 590 3.322254 ACCAAATTTTGTACGGGCATCAA 59.678 39.130 8.26 0.00 0.00 2.57
594 596 6.146898 CAGACTTTACCAAATTTTGTACGGG 58.853 40.000 8.26 0.00 0.00 5.28
693 695 8.296000 TCATGAGAAATAAAACAAAATCGAGCA 58.704 29.630 0.00 0.00 0.00 4.26
694 696 8.673626 TCATGAGAAATAAAACAAAATCGAGC 57.326 30.769 0.00 0.00 0.00 5.03
695 697 8.792538 GCTCATGAGAAATAAAACAAAATCGAG 58.207 33.333 27.04 0.00 0.00 4.04
713 715 6.688637 TTGGACATTTGATAAGCTCATGAG 57.311 37.500 18.84 18.84 32.72 2.90
717 719 6.446318 GTTGTTTGGACATTTGATAAGCTCA 58.554 36.000 0.00 0.00 35.29 4.26
752 754 4.201851 GCTCAAATGTGTGATATTCGTGCT 60.202 41.667 0.00 0.00 0.00 4.40
760 762 4.277921 TGCAAGTTGCTCAAATGTGTGATA 59.722 37.500 27.17 0.00 45.31 2.15
806 828 1.065345 TCAACACCCGGTGAACAGAAA 60.065 47.619 24.80 0.00 36.96 2.52
808 830 0.762418 ATCAACACCCGGTGAACAGA 59.238 50.000 24.80 14.80 36.96 3.41
828 850 4.796495 AATTCGACGCCCCAGCCC 62.796 66.667 0.00 0.00 34.57 5.19
832 854 1.540267 AAATTCAATTCGACGCCCCA 58.460 45.000 0.00 0.00 0.00 4.96
851 873 0.462581 GCAGATGGATGGACTGCGAA 60.463 55.000 0.00 0.00 45.25 4.70
853 875 3.728474 GCAGATGGATGGACTGCG 58.272 61.111 0.00 0.00 45.25 5.18
864 886 1.043116 TGGTACGGAGGGAGCAGATG 61.043 60.000 0.00 0.00 0.00 2.90
865 887 0.325296 TTGGTACGGAGGGAGCAGAT 60.325 55.000 0.00 0.00 0.00 2.90
866 888 0.543410 TTTGGTACGGAGGGAGCAGA 60.543 55.000 0.00 0.00 0.00 4.26
868 890 0.988832 ATTTTGGTACGGAGGGAGCA 59.011 50.000 0.00 0.00 0.00 4.26
869 891 2.433239 TCTATTTTGGTACGGAGGGAGC 59.567 50.000 0.00 0.00 0.00 4.70
871 893 3.319972 CGATCTATTTTGGTACGGAGGGA 59.680 47.826 0.00 0.00 0.00 4.20
872 894 3.554337 CCGATCTATTTTGGTACGGAGGG 60.554 52.174 0.00 0.00 41.09 4.30
873 895 3.319972 TCCGATCTATTTTGGTACGGAGG 59.680 47.826 0.00 0.00 42.14 4.30
874 896 4.579454 TCCGATCTATTTTGGTACGGAG 57.421 45.455 0.00 0.00 42.14 4.63
875 897 3.319972 CCTCCGATCTATTTTGGTACGGA 59.680 47.826 0.00 0.00 44.18 4.69
876 898 3.554337 CCCTCCGATCTATTTTGGTACGG 60.554 52.174 0.00 0.00 40.16 4.02
877 899 3.319972 TCCCTCCGATCTATTTTGGTACG 59.680 47.826 0.00 0.00 0.00 3.67
878 900 4.344390 ACTCCCTCCGATCTATTTTGGTAC 59.656 45.833 0.00 0.00 0.00 3.34
879 901 4.553678 ACTCCCTCCGATCTATTTTGGTA 58.446 43.478 0.00 0.00 0.00 3.25
880 902 3.385115 ACTCCCTCCGATCTATTTTGGT 58.615 45.455 0.00 0.00 0.00 3.67
881 903 4.344102 TGTACTCCCTCCGATCTATTTTGG 59.656 45.833 0.00 0.00 0.00 3.28
882 904 5.531122 TGTACTCCCTCCGATCTATTTTG 57.469 43.478 0.00 0.00 0.00 2.44
883 905 6.525629 CAATGTACTCCCTCCGATCTATTTT 58.474 40.000 0.00 0.00 0.00 1.82
884 906 5.511545 GCAATGTACTCCCTCCGATCTATTT 60.512 44.000 0.00 0.00 0.00 1.40
885 907 4.021016 GCAATGTACTCCCTCCGATCTATT 60.021 45.833 0.00 0.00 0.00 1.73
886 908 3.511934 GCAATGTACTCCCTCCGATCTAT 59.488 47.826 0.00 0.00 0.00 1.98
887 909 2.891580 GCAATGTACTCCCTCCGATCTA 59.108 50.000 0.00 0.00 0.00 1.98
888 910 1.689273 GCAATGTACTCCCTCCGATCT 59.311 52.381 0.00 0.00 0.00 2.75
889 911 1.412710 TGCAATGTACTCCCTCCGATC 59.587 52.381 0.00 0.00 0.00 3.69
890 912 1.496060 TGCAATGTACTCCCTCCGAT 58.504 50.000 0.00 0.00 0.00 4.18
891 913 1.271856 TTGCAATGTACTCCCTCCGA 58.728 50.000 0.00 0.00 0.00 4.55
892 914 2.107950 TTTGCAATGTACTCCCTCCG 57.892 50.000 0.00 0.00 0.00 4.63
893 915 3.356290 ACATTTGCAATGTACTCCCTCC 58.644 45.455 0.00 0.00 0.00 4.30
894 916 3.378427 GGACATTTGCAATGTACTCCCTC 59.622 47.826 13.73 3.16 30.35 4.30
895 917 3.356290 GGACATTTGCAATGTACTCCCT 58.644 45.455 13.73 0.00 30.35 4.20
896 918 2.427095 GGGACATTTGCAATGTACTCCC 59.573 50.000 17.96 16.49 33.46 4.30
897 919 2.427095 GGGGACATTTGCAATGTACTCC 59.573 50.000 17.96 14.69 33.46 3.85
898 920 2.097466 CGGGGACATTTGCAATGTACTC 59.903 50.000 17.96 15.05 33.46 2.59
899 921 2.091541 CGGGGACATTTGCAATGTACT 58.908 47.619 17.96 0.00 33.46 2.73
900 922 2.088423 TCGGGGACATTTGCAATGTAC 58.912 47.619 0.00 7.77 31.52 2.90
904 926 2.214376 TCTTCGGGGACATTTGCAAT 57.786 45.000 0.00 0.00 0.00 3.56
919 941 5.695851 TGCAATGGAGACTTCTTTTCTTC 57.304 39.130 0.00 0.00 0.00 2.87
976 1001 6.711277 TGACCGTAGTTAGAGTTAGGAGTAA 58.289 40.000 0.00 0.00 0.00 2.24
979 1004 5.589452 ACATGACCGTAGTTAGAGTTAGGAG 59.411 44.000 0.00 0.00 0.00 3.69
981 1006 5.589452 AGACATGACCGTAGTTAGAGTTAGG 59.411 44.000 0.00 0.00 0.00 2.69
982 1007 6.487960 CAGACATGACCGTAGTTAGAGTTAG 58.512 44.000 0.00 0.00 0.00 2.34
983 1008 5.163683 GCAGACATGACCGTAGTTAGAGTTA 60.164 44.000 0.00 0.00 0.00 2.24
984 1009 4.380655 GCAGACATGACCGTAGTTAGAGTT 60.381 45.833 0.00 0.00 0.00 3.01
985 1010 3.128938 GCAGACATGACCGTAGTTAGAGT 59.871 47.826 0.00 0.00 0.00 3.24
988 1013 3.503827 TGCAGACATGACCGTAGTTAG 57.496 47.619 0.00 0.00 0.00 2.34
989 1014 3.445805 TGATGCAGACATGACCGTAGTTA 59.554 43.478 0.00 0.00 36.35 2.24
991 1016 1.824852 TGATGCAGACATGACCGTAGT 59.175 47.619 0.00 0.00 36.35 2.73
992 1017 2.196749 GTGATGCAGACATGACCGTAG 58.803 52.381 0.00 0.00 34.66 3.51
993 1018 1.469079 CGTGATGCAGACATGACCGTA 60.469 52.381 0.00 0.00 37.12 4.02
994 1019 0.737367 CGTGATGCAGACATGACCGT 60.737 55.000 0.00 0.00 37.12 4.83
1233 1258 2.725008 GGCGACTGGGAGAGATCG 59.275 66.667 0.00 0.00 37.63 3.69
1326 1351 2.659016 CAGTTCTGCAGGGCGAGA 59.341 61.111 15.13 0.00 0.00 4.04
1366 1391 0.108186 AACAGCGCGAATGGATCAGA 60.108 50.000 12.10 0.00 0.00 3.27
1399 1424 1.125566 GAAAGCTTTCTGCATTTGCGC 59.874 47.619 28.16 0.00 45.94 6.09
1437 1469 7.148423 GCAAGAAACCCAATAAATCACAAATCC 60.148 37.037 0.00 0.00 0.00 3.01
1462 1496 2.119495 TCTCTCCCATCTTTGTAGGGC 58.881 52.381 0.00 0.00 42.52 5.19
1573 1607 8.889849 ACCAGTTCGTATTTCATTAAATTTCG 57.110 30.769 0.00 0.00 36.67 3.46
1651 1685 5.648526 TCTCACTTCGAATTAGAGCAGTAGT 59.351 40.000 13.66 0.00 0.00 2.73
1927 2809 7.364970 GGTTATTACCACAACAAAGTACCAAG 58.635 38.462 0.00 0.00 44.36 3.61
2166 3077 4.609691 CCAAAATGGCAATGAAAGATGC 57.390 40.909 0.00 0.00 41.82 3.91
2193 3104 1.082104 GTGCTAAAAACTGCGCGCT 60.082 52.632 33.29 13.56 0.00 5.92
2473 3384 2.159382 CCTGACGCAACCACCTTTAAT 58.841 47.619 0.00 0.00 0.00 1.40
2660 3571 7.459486 CATTTGCTTATGTCTAGTGACTTCAC 58.541 38.462 0.77 0.77 46.77 3.18
2731 3642 3.258123 TCAATGACACCAGAGATGACGAA 59.742 43.478 0.00 0.00 0.00 3.85
2973 3884 2.939103 ACATCAATAGCGGCAAGAAGTC 59.061 45.455 1.45 0.00 0.00 3.01
3043 3954 6.285224 TCTCAATTCCGACTGAAACAAGTTA 58.715 36.000 0.00 0.00 36.33 2.24
3160 4071 3.370953 GCCTTGTAACCTGAGGACATGAT 60.371 47.826 4.99 0.00 32.11 2.45
3216 4127 1.035139 AAAGTTCACCTTGCAGCCAG 58.965 50.000 0.00 0.00 32.32 4.85
3368 4279 6.369615 ACTTTTTCTTATTCATTGCATGTGCC 59.630 34.615 2.07 0.00 41.18 5.01
3419 4330 4.778842 AGTACATGCAATTCGATCGAAC 57.221 40.909 31.27 19.48 36.91 3.95
3516 4427 7.748031 TTTACAACATTTAGCAACACAACAG 57.252 32.000 0.00 0.00 0.00 3.16
3521 4432 6.699642 ACCACATTTACAACATTTAGCAACAC 59.300 34.615 0.00 0.00 0.00 3.32
3556 4467 8.770438 GCTTTAGCTATGCTCATTTAGTCTAT 57.230 34.615 10.78 0.00 40.44 1.98
3621 4532 4.556942 AGCCACCGTTTTGTAAGTAAAC 57.443 40.909 0.00 0.00 33.28 2.01
3648 4559 8.263940 TCTTTACAATCACCTATTTGTAGTGC 57.736 34.615 0.00 0.00 0.00 4.40
3776 4692 5.305569 GCACGATCATGCACAAAATAATG 57.694 39.130 9.26 0.00 45.39 1.90
3787 4703 2.565210 TGAAAATGGCACGATCATGC 57.435 45.000 4.90 4.90 45.34 4.06
3828 4744 0.458025 GCATTGAAGCTGCCAAGAGC 60.458 55.000 0.00 9.55 44.14 4.09
3943 4859 6.290605 AGGGAGGAATTTTTGTCAAACATTG 58.709 36.000 13.16 0.00 0.00 2.82
3946 4862 4.959210 TGAGGGAGGAATTTTTGTCAAACA 59.041 37.500 0.00 0.00 0.00 2.83
3987 4904 4.943705 GCATGTTCTCTCAGGTGGAAAATA 59.056 41.667 0.00 0.00 0.00 1.40
4007 4924 6.151817 TGCCCTTTTTGTAAAAACAAAAGCAT 59.848 30.769 17.73 0.00 46.19 3.79
4011 4928 6.004574 AGGTGCCCTTTTTGTAAAAACAAAA 58.995 32.000 11.31 11.31 44.71 2.44
4095 5017 2.682856 TGAAGTTTGAGCAAGTGTCACC 59.317 45.455 0.00 0.00 0.00 4.02
4146 5068 2.268076 GCCACGGTGCCAATCTTGT 61.268 57.895 1.68 0.00 0.00 3.16
4244 5167 7.110810 ACCGATCTTATATTATGAGACGGAGA 58.889 38.462 26.83 7.69 39.49 3.71


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

AutoCloner maintained by Alex Coulton.