Multiple sequence alignment - TraesCS4A01G178200

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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 TraesCS4A01G178200 chr4A 100.000 3809 0 0 1 3809 450761338 450765146 0.000000e+00 7035.0
1 TraesCS4A01G178200 chr4A 90.769 65 6 0 3745 3809 667005119 667005055 1.880000e-13 87.9
2 TraesCS4A01G178200 chr4B 89.179 2375 107 38 1514 3809 182258252 182260555 0.000000e+00 2824.0
3 TraesCS4A01G178200 chr4B 87.621 824 76 16 1 804 182256243 182257060 0.000000e+00 933.0
4 TraesCS4A01G178200 chr4B 92.214 411 11 6 880 1287 182257437 182257829 2.570000e-156 562.0
5 TraesCS4A01G178200 chr4B 93.750 256 7 6 1301 1555 182257885 182258132 3.590000e-100 375.0
6 TraesCS4A01G178200 chr4D 90.807 1153 44 7 1916 3022 119803766 119804902 0.000000e+00 1485.0
7 TraesCS4A01G178200 chr4D 94.007 851 29 10 2973 3809 119805010 119805852 0.000000e+00 1269.0
8 TraesCS4A01G178200 chr4D 92.444 622 21 11 1303 1907 119802864 119803476 0.000000e+00 865.0
9 TraesCS4A01G178200 chr4D 88.141 683 57 10 107 771 119801553 119802229 0.000000e+00 791.0
10 TraesCS4A01G178200 chr4D 94.321 405 13 6 893 1289 119802406 119802808 2.520000e-171 612.0
11 TraesCS4A01G178200 chr4D 86.408 103 5 3 1 103 119801273 119801366 1.870000e-18 104.0
12 TraesCS4A01G178200 chr7D 83.420 193 29 3 98 288 564374987 564375178 3.910000e-40 176.0
13 TraesCS4A01G178200 chr7A 76.730 318 64 9 98 410 733976195 733976507 6.540000e-38 169.0
14 TraesCS4A01G178200 chr7A 94.340 53 3 0 3757 3809 602227187 602227135 8.770000e-12 82.4
15 TraesCS4A01G178200 chr5B 80.000 210 42 0 3259 3468 288176222 288176431 5.090000e-34 156.0
16 TraesCS4A01G178200 chr5A 80.597 201 39 0 3268 3468 337943192 337942992 5.090000e-34 156.0
17 TraesCS4A01G178200 chr5A 81.928 166 29 1 98 262 504932925 504933090 5.130000e-29 139.0
18 TraesCS4A01G178200 chr5A 81.437 167 28 3 98 263 655873839 655873675 2.390000e-27 134.0
19 TraesCS4A01G178200 chr5A 84.615 104 16 0 1372 1475 338231758 338231655 1.870000e-18 104.0
20 TraesCS4A01G178200 chr5D 80.100 201 40 0 3268 3468 254588540 254588340 2.370000e-32 150.0
21 TraesCS4A01G178200 chr3A 92.308 65 5 0 3745 3809 625330585 625330521 4.050000e-15 93.5
22 TraesCS4A01G178200 chr2B 89.231 65 6 1 3745 3809 699180024 699179961 3.150000e-11 80.5
23 TraesCS4A01G178200 chr2B 78.899 109 18 3 3702 3806 224649786 224649679 6.830000e-08 69.4
24 TraesCS4A01G178200 chr2A 79.817 109 17 3 3702 3806 176671247 176671140 1.470000e-09 75.0
25 TraesCS4A01G178200 chr6B 100.000 29 0 0 693 721 695278978 695278950 2.000000e-03 54.7


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 TraesCS4A01G178200 chr4A 450761338 450765146 3808 False 7035.000000 7035 100.000000 1 3809 1 chr4A.!!$F1 3808
1 TraesCS4A01G178200 chr4B 182256243 182260555 4312 False 1173.500000 2824 90.691000 1 3809 4 chr4B.!!$F1 3808
2 TraesCS4A01G178200 chr4D 119801273 119805852 4579 False 854.333333 1485 91.021333 1 3809 6 chr4D.!!$F1 3808

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
609 820 0.323629 TGGTCTTACTCCCCGCAAAG 59.676 55.0 0.0 0.0 0.00 2.77 F
1873 2639 0.107017 AGATGGGTGAAATCCAGCGG 60.107 55.0 0.0 0.0 44.61 5.52 F
2161 3208 1.909700 TTTTCGCTTTGGCTCCATCT 58.090 45.0 0.0 0.0 36.09 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2307 3354 0.185901 TGGCTGCTTCAAAAGGGAGT 59.814 50.0 0.0 0.0 0.00 3.85 R
2782 3858 0.700564 AGGAATGGCACCTCACATGT 59.299 50.0 0.0 0.0 31.43 3.21 R
3010 4261 0.846427 ATTTCTCCACAGCCTCCCCA 60.846 55.0 0.0 0.0 0.00 4.96 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
61 71 2.828877 GGGTAGCATACACGCAATACA 58.171 47.619 0.00 0.00 45.43 2.29
62 72 2.542595 GGGTAGCATACACGCAATACAC 59.457 50.000 0.00 0.00 45.43 2.90
63 73 3.191669 GGTAGCATACACGCAATACACA 58.808 45.455 0.00 0.00 45.43 3.72
68 78 4.873259 AGCATACACGCAATACACACATAA 59.127 37.500 0.00 0.00 0.00 1.90
69 79 4.961551 GCATACACGCAATACACACATAAC 59.038 41.667 0.00 0.00 0.00 1.89
173 368 7.226720 ACAAGAATGAAAGTAAGATCAACGTGT 59.773 33.333 0.00 0.00 30.79 4.49
251 447 0.869454 GAGCCTCGACATTGAGCTCG 60.869 60.000 9.64 0.00 33.08 5.03
265 461 3.838120 TGAGCTCGTAAACTCATGACTG 58.162 45.455 9.64 0.00 37.99 3.51
266 462 3.182967 GAGCTCGTAAACTCATGACTGG 58.817 50.000 0.00 0.00 32.98 4.00
306 502 1.837439 ACCCGGACTGCTCATTGATTA 59.163 47.619 0.73 0.00 0.00 1.75
355 551 3.316308 GCGCTTCCTTGGTTGATATCATT 59.684 43.478 6.17 0.00 0.00 2.57
394 590 2.288642 AATGCCACATGGATCCGCCT 62.289 55.000 7.39 0.00 37.39 5.52
411 607 3.010420 CGCCTCTCGTATAGATCATCCA 58.990 50.000 0.00 0.00 32.41 3.41
458 654 0.380378 GTGCTTCAAGCGTTGTTGGA 59.620 50.000 4.57 0.00 46.26 3.53
465 674 4.377839 TCAAGCGTTGTTGGATCAAAAA 57.622 36.364 0.00 0.00 0.00 1.94
471 680 7.350110 AGCGTTGTTGGATCAAAAATAATTG 57.650 32.000 0.00 0.00 0.00 2.32
504 714 5.279910 CCAGATAAGACCCAAGATGATCTCC 60.280 48.000 0.00 0.00 0.00 3.71
563 773 6.255670 GTCGCATCAACATAGATCTTACACAA 59.744 38.462 0.00 0.00 0.00 3.33
604 815 3.560636 ATGATTTGGTCTTACTCCCCG 57.439 47.619 0.00 0.00 0.00 5.73
609 820 0.323629 TGGTCTTACTCCCCGCAAAG 59.676 55.000 0.00 0.00 0.00 2.77
610 821 0.611714 GGTCTTACTCCCCGCAAAGA 59.388 55.000 0.00 0.00 0.00 2.52
611 822 1.002773 GGTCTTACTCCCCGCAAAGAA 59.997 52.381 0.00 0.00 30.24 2.52
612 823 2.551504 GGTCTTACTCCCCGCAAAGAAA 60.552 50.000 0.00 0.00 30.24 2.52
640 854 1.334160 TGGTCTAACTGGAGCGACAA 58.666 50.000 0.00 0.00 36.62 3.18
643 857 2.094182 GGTCTAACTGGAGCGACAATGA 60.094 50.000 0.00 0.00 0.00 2.57
666 880 2.290960 GGTTGTATTGGAGGGCTTGTCT 60.291 50.000 0.00 0.00 0.00 3.41
677 891 4.876679 GGAGGGCTTGTCTACAATCTAAAC 59.123 45.833 0.00 0.00 35.02 2.01
682 896 6.116126 GGCTTGTCTACAATCTAAACATCCT 58.884 40.000 0.00 0.00 35.02 3.24
726 940 3.502123 TTGGTGGATATCGGGATTTCC 57.498 47.619 10.21 10.21 38.78 3.13
740 955 7.896383 TCGGGATTTCCAAAATATCTTCAAT 57.104 32.000 0.00 0.00 37.91 2.57
774 991 2.169769 CCTTGCTCCATACCGTCCTAAA 59.830 50.000 0.00 0.00 0.00 1.85
777 994 2.037144 GCTCCATACCGTCCTAAAGGA 58.963 52.381 0.00 0.00 43.08 3.36
838 1319 7.782049 TGAGACAACCTCCTAAACTATACATG 58.218 38.462 0.00 0.00 41.25 3.21
861 1342 4.503296 GCCGTACTTGAGTGGATCCAATAT 60.503 45.833 18.20 5.43 0.00 1.28
868 1349 4.568956 TGAGTGGATCCAATATACGCATG 58.431 43.478 18.20 0.00 0.00 4.06
872 1353 5.246203 AGTGGATCCAATATACGCATGTACT 59.754 40.000 18.20 0.48 32.26 2.73
873 1354 5.932303 GTGGATCCAATATACGCATGTACTT 59.068 40.000 18.20 0.00 32.26 2.24
875 1356 7.063074 GTGGATCCAATATACGCATGTACTTAC 59.937 40.741 18.20 0.00 32.26 2.34
880 1361 8.077991 TCCAATATACGCATGTACTTACTACAC 58.922 37.037 0.00 0.00 38.22 2.90
882 1363 9.240159 CAATATACGCATGTACTTACTACACAA 57.760 33.333 0.00 0.00 38.22 3.33
883 1364 9.976511 AATATACGCATGTACTTACTACACAAT 57.023 29.630 0.00 0.00 38.22 2.71
886 1367 5.747197 ACGCATGTACTTACTACACAATAGC 59.253 40.000 0.00 0.00 38.22 2.97
887 1368 5.175126 CGCATGTACTTACTACACAATAGCC 59.825 44.000 0.00 0.00 38.22 3.93
891 1372 7.655521 TGTACTTACTACACAATAGCCAGAT 57.344 36.000 0.00 0.00 29.73 2.90
949 1468 4.162320 TCACTTCTCTCTCTCTCTCTCTCC 59.838 50.000 0.00 0.00 0.00 3.71
969 1488 1.527433 CTCCAGCTGTCGTCTCCACA 61.527 60.000 13.81 0.00 0.00 4.17
970 1489 1.373497 CCAGCTGTCGTCTCCACAC 60.373 63.158 13.81 0.00 0.00 3.82
971 1490 1.363807 CAGCTGTCGTCTCCACACA 59.636 57.895 5.25 0.00 0.00 3.72
1061 1580 3.628646 GAGGGTTCGTGGCATGGCT 62.629 63.158 21.08 0.00 0.00 4.75
1112 1631 2.363306 TCACCAAGAACAAGCACCAT 57.637 45.000 0.00 0.00 0.00 3.55
1263 1788 1.057275 GGTCCATTCCTCCTCCTCCC 61.057 65.000 0.00 0.00 0.00 4.30
1289 1814 5.044558 CCTTCTTCCTCGTGATTAAGTAGC 58.955 45.833 0.00 0.00 0.00 3.58
1291 1816 4.279145 TCTTCCTCGTGATTAAGTAGCCT 58.721 43.478 0.00 0.00 0.00 4.58
1292 1817 4.338682 TCTTCCTCGTGATTAAGTAGCCTC 59.661 45.833 0.00 0.00 0.00 4.70
1293 1818 2.957006 TCCTCGTGATTAAGTAGCCTCC 59.043 50.000 0.00 0.00 0.00 4.30
1294 1819 2.693591 CCTCGTGATTAAGTAGCCTCCA 59.306 50.000 0.00 0.00 0.00 3.86
1295 1820 3.243569 CCTCGTGATTAAGTAGCCTCCAG 60.244 52.174 0.00 0.00 0.00 3.86
1328 1895 6.268617 TCACTCAAATCTTCTTTCCTCTCTCA 59.731 38.462 0.00 0.00 0.00 3.27
1331 1898 6.413052 TCAAATCTTCTTTCCTCTCTCATGG 58.587 40.000 0.00 0.00 0.00 3.66
1332 1899 6.013032 TCAAATCTTCTTTCCTCTCTCATGGT 60.013 38.462 0.00 0.00 0.00 3.55
1333 1900 5.612725 ATCTTCTTTCCTCTCTCATGGTC 57.387 43.478 0.00 0.00 0.00 4.02
1334 1901 3.445450 TCTTCTTTCCTCTCTCATGGTCG 59.555 47.826 0.00 0.00 0.00 4.79
1335 1902 2.808919 TCTTTCCTCTCTCATGGTCGT 58.191 47.619 0.00 0.00 0.00 4.34
1336 1903 2.493675 TCTTTCCTCTCTCATGGTCGTG 59.506 50.000 0.00 0.00 0.00 4.35
1337 1904 1.186200 TTCCTCTCTCATGGTCGTGG 58.814 55.000 0.00 0.00 0.00 4.94
1338 1905 0.684479 TCCTCTCTCATGGTCGTGGG 60.684 60.000 0.00 0.00 0.00 4.61
1339 1906 1.680522 CCTCTCTCATGGTCGTGGGG 61.681 65.000 0.00 0.00 0.00 4.96
1603 2329 6.049149 TCAACTCAAGAGATTTCAACGAGTT 58.951 36.000 3.73 8.33 38.12 3.01
1617 2343 0.921347 CGAGTTCGTAGGCAATTCCG 59.079 55.000 0.00 0.00 35.63 4.30
1628 2354 1.369091 GCAATTCCGTCATCCGCAGT 61.369 55.000 0.00 0.00 34.38 4.40
1630 2356 1.062587 CAATTCCGTCATCCGCAGTTC 59.937 52.381 0.00 0.00 34.38 3.01
1769 2535 4.516652 ATCTTTAGGCCTTCAGAGCAAT 57.483 40.909 12.58 0.00 0.00 3.56
1771 2537 2.315925 TTAGGCCTTCAGAGCAATCG 57.684 50.000 12.58 0.00 0.00 3.34
1873 2639 0.107017 AGATGGGTGAAATCCAGCGG 60.107 55.000 0.00 0.00 44.61 5.52
1959 3006 9.258826 CTTGTATTTTGTTTGAATGGTCATGAA 57.741 29.630 0.00 0.00 32.48 2.57
1960 3007 8.586570 TGTATTTTGTTTGAATGGTCATGAAC 57.413 30.769 2.98 2.98 32.48 3.18
1961 3008 8.420222 TGTATTTTGTTTGAATGGTCATGAACT 58.580 29.630 12.94 0.00 32.48 3.01
1962 3009 7.951530 ATTTTGTTTGAATGGTCATGAACTC 57.048 32.000 12.94 2.46 32.48 3.01
2059 3106 4.500035 GCCGTAGCTGCTCTTAAGAAGTAT 60.500 45.833 4.91 0.00 35.50 2.12
2159 3206 2.099756 GCTATTTTCGCTTTGGCTCCAT 59.900 45.455 0.00 0.00 36.09 3.41
2161 3208 1.909700 TTTTCGCTTTGGCTCCATCT 58.090 45.000 0.00 0.00 36.09 2.90
2210 3257 2.238898 AGGTTTGTAGCATCTACCCCAC 59.761 50.000 1.99 0.00 0.00 4.61
2264 3311 7.126421 ACAGTAGGACCTCAACATCATAGAAAT 59.874 37.037 0.00 0.00 0.00 2.17
2307 3354 5.128205 CAACATAGATGGGAGCTGAATTGA 58.872 41.667 0.00 0.00 0.00 2.57
2337 3384 4.672587 TGAAGCAGCCATAGGTAGTTAG 57.327 45.455 0.00 0.00 0.00 2.34
2340 3387 2.103263 AGCAGCCATAGGTAGTTAGCAC 59.897 50.000 0.00 0.00 0.00 4.40
2363 3410 6.523201 CACTATGTTAAAACTTCATTGCCGTC 59.477 38.462 0.00 0.00 0.00 4.79
2567 3638 2.367107 GAGGGAAGGGAGGGGGTC 60.367 72.222 0.00 0.00 0.00 4.46
2571 3642 3.090532 GAAGGGAGGGGGTCGCAT 61.091 66.667 0.00 0.00 40.67 4.73
2657 3728 3.870538 TCAGCTAAATGGATCTGGCAT 57.129 42.857 0.00 0.00 0.00 4.40
2661 3732 2.363038 GCTAAATGGATCTGGCATTGCA 59.637 45.455 11.39 0.00 0.00 4.08
2682 3753 4.778773 GCATTGCGTGTGTTCTTGTTTTTC 60.779 41.667 0.00 0.00 0.00 2.29
2782 3858 2.292192 GGGTGATGAAAATGGAGGGGAA 60.292 50.000 0.00 0.00 0.00 3.97
2810 3895 1.275856 GGTGCCATTCCTTCATTTGCA 59.724 47.619 0.00 0.00 0.00 4.08
2812 3897 3.602483 GTGCCATTCCTTCATTTGCAAT 58.398 40.909 0.00 0.00 0.00 3.56
2813 3898 4.382901 GGTGCCATTCCTTCATTTGCAATA 60.383 41.667 0.00 0.00 0.00 1.90
2835 3920 1.925888 CAGGAGGGAGGGAATTGGG 59.074 63.158 0.00 0.00 0.00 4.12
2849 3934 4.895297 GGGAATTGGGCTATTTGAGATGAA 59.105 41.667 0.00 0.00 0.00 2.57
2851 3936 6.127083 GGGAATTGGGCTATTTGAGATGAAAA 60.127 38.462 0.00 0.00 0.00 2.29
2982 4076 3.508845 TGAATTATTAGGGGAGGCTGC 57.491 47.619 0.00 0.00 0.00 5.25
2983 4077 2.224523 TGAATTATTAGGGGAGGCTGCG 60.225 50.000 0.00 0.00 0.00 5.18
3029 4294 0.846427 TGGGGAGGCTGTGGAGAAAT 60.846 55.000 0.00 0.00 0.00 2.17
3044 4309 9.877178 CTGTGGAGAAATTAGAGTTACAGTAAT 57.123 33.333 0.00 0.00 0.00 1.89
3106 4374 9.924010 AGTAGTAGCCCTAAATATATGGAGTAG 57.076 37.037 0.00 0.00 0.00 2.57
3128 4396 9.690913 AGTAGTATGTATAACTGGAGTGTACAA 57.309 33.333 0.00 0.00 35.25 2.41
3176 4444 7.012989 GGATCACTGTCATCATGAATCAATCAA 59.987 37.037 0.00 0.00 42.54 2.57
3240 4521 3.063084 GGCGTCAGTCGTCCCTCT 61.063 66.667 0.00 0.00 42.13 3.69
3241 4522 2.486042 GCGTCAGTCGTCCCTCTC 59.514 66.667 0.00 0.00 42.13 3.20
3242 4523 2.785921 CGTCAGTCGTCCCTCTCG 59.214 66.667 0.00 0.00 34.52 4.04
3243 4524 2.751913 CGTCAGTCGTCCCTCTCGG 61.752 68.421 0.00 0.00 34.52 4.63
3311 4592 3.056465 AGAAGACCTTGTCGATGTTCTCC 60.056 47.826 0.00 0.00 37.67 3.71
3650 4931 1.447838 CGTCGGGATGAACCTGGTG 60.448 63.158 0.00 0.00 44.73 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.682465 GGAGAATAGGGTTTAATGTACTTTTCT 57.318 33.333 0.00 0.00 33.97 2.52
105 298 7.440523 AATAAAAAGCTTCGTGAGATTGTCT 57.559 32.000 0.00 0.00 41.60 3.41
115 308 6.774354 TGACGAGTTAATAAAAAGCTTCGT 57.226 33.333 0.00 0.01 0.00 3.85
191 386 2.688958 TCTCTCTTTAAGGGCTAGTCGC 59.311 50.000 0.00 0.00 38.13 5.19
251 447 5.627499 TGCATTTCCAGTCATGAGTTTAC 57.373 39.130 0.00 0.00 0.00 2.01
288 484 4.212847 CAGATTAATCAATGAGCAGTCCGG 59.787 45.833 17.56 0.00 0.00 5.14
289 485 5.052481 TCAGATTAATCAATGAGCAGTCCG 58.948 41.667 17.56 0.00 0.00 4.79
328 524 0.102120 CAACCAAGGAAGCGCAACAA 59.898 50.000 11.47 0.00 0.00 2.83
355 551 7.123397 TGGCATTAGATTGCAAGGTTGTTATTA 59.877 33.333 4.94 0.00 44.59 0.98
394 590 4.202577 ACCTGGTGGATGATCTATACGAGA 60.203 45.833 0.00 0.00 36.37 4.04
430 626 1.136141 CGCTTGAAGCACTAGCAGTTG 60.136 52.381 18.22 0.00 44.96 3.16
471 680 2.099756 GGGTCTTATCTGGTGCATTTGC 59.900 50.000 0.00 0.00 42.50 3.68
504 714 1.399727 GGTTCAATTGGAGTTGTCGCG 60.400 52.381 5.42 0.00 0.00 5.87
563 773 3.243359 TGGCTTCACCCTCTGAAAATT 57.757 42.857 0.00 0.00 38.47 1.82
611 822 6.570378 CGCTCCAGTTAGACCAAATCATTTTT 60.570 38.462 0.00 0.00 0.00 1.94
612 823 5.106157 CGCTCCAGTTAGACCAAATCATTTT 60.106 40.000 0.00 0.00 0.00 1.82
640 854 1.408266 GCCCTCCAATACAACCGTCAT 60.408 52.381 0.00 0.00 0.00 3.06
643 857 0.696501 AAGCCCTCCAATACAACCGT 59.303 50.000 0.00 0.00 0.00 4.83
740 955 4.108570 TGGAGCAAGGAGGAAGGTTATAA 58.891 43.478 0.00 0.00 0.00 0.98
816 1033 5.758784 GGCATGTATAGTTTAGGAGGTTGTC 59.241 44.000 0.00 0.00 0.00 3.18
817 1034 5.681639 GGCATGTATAGTTTAGGAGGTTGT 58.318 41.667 0.00 0.00 0.00 3.32
819 1036 4.407945 ACGGCATGTATAGTTTAGGAGGTT 59.592 41.667 0.00 0.00 0.00 3.50
821 1038 4.602340 ACGGCATGTATAGTTTAGGAGG 57.398 45.455 0.00 0.00 0.00 4.30
822 1039 6.328641 AGTACGGCATGTATAGTTTAGGAG 57.671 41.667 0.00 0.00 35.02 3.69
824 1041 6.509656 TCAAGTACGGCATGTATAGTTTAGG 58.490 40.000 0.00 0.00 35.02 2.69
825 1042 7.167635 CACTCAAGTACGGCATGTATAGTTTAG 59.832 40.741 0.00 0.00 35.02 1.85
826 1043 6.976349 CACTCAAGTACGGCATGTATAGTTTA 59.024 38.462 0.00 0.00 35.02 2.01
827 1044 5.810587 CACTCAAGTACGGCATGTATAGTTT 59.189 40.000 0.00 0.00 35.02 2.66
829 1046 4.202121 CCACTCAAGTACGGCATGTATAGT 60.202 45.833 0.00 0.00 35.02 2.12
830 1047 4.037565 TCCACTCAAGTACGGCATGTATAG 59.962 45.833 0.00 0.00 35.02 1.31
832 1049 2.764010 TCCACTCAAGTACGGCATGTAT 59.236 45.455 0.00 0.00 35.02 2.29
834 1051 0.973632 TCCACTCAAGTACGGCATGT 59.026 50.000 0.00 0.00 0.00 3.21
838 1319 0.535335 TGGATCCACTCAAGTACGGC 59.465 55.000 11.44 0.00 0.00 5.68
861 1342 6.914215 GCTATTGTGTAGTAAGTACATGCGTA 59.086 38.462 0.00 0.00 43.70 4.42
868 1349 8.195436 TCAATCTGGCTATTGTGTAGTAAGTAC 58.805 37.037 11.25 0.00 37.94 2.73
872 1353 7.390823 TGTTCAATCTGGCTATTGTGTAGTAA 58.609 34.615 11.25 0.00 37.94 2.24
873 1354 6.941857 TGTTCAATCTGGCTATTGTGTAGTA 58.058 36.000 11.25 0.00 37.94 1.82
875 1356 6.741992 TTGTTCAATCTGGCTATTGTGTAG 57.258 37.500 11.25 0.00 37.94 2.74
880 1361 4.790766 GCCGATTGTTCAATCTGGCTATTG 60.791 45.833 30.00 14.42 41.34 1.90
882 1363 2.880890 GCCGATTGTTCAATCTGGCTAT 59.119 45.455 30.00 3.61 41.34 2.97
883 1364 2.288666 GCCGATTGTTCAATCTGGCTA 58.711 47.619 30.00 0.00 41.34 3.93
885 1366 0.101219 GGCCGATTGTTCAATCTGGC 59.899 55.000 29.76 29.76 42.53 4.85
886 1367 0.740737 GGGCCGATTGTTCAATCTGG 59.259 55.000 19.00 19.93 0.00 3.86
887 1368 1.462616 TGGGCCGATTGTTCAATCTG 58.537 50.000 19.00 14.98 0.00 2.90
891 1372 1.182385 GGGTTGGGCCGATTGTTCAA 61.182 55.000 0.00 0.00 38.44 2.69
949 1468 1.979155 TGGAGACGACAGCTGGAGG 60.979 63.158 19.93 9.00 0.00 4.30
969 1488 2.123468 GCTGTTGGGGTTGGGTGT 60.123 61.111 0.00 0.00 0.00 4.16
970 1489 2.917227 GGCTGTTGGGGTTGGGTG 60.917 66.667 0.00 0.00 0.00 4.61
971 1490 4.233558 GGGCTGTTGGGGTTGGGT 62.234 66.667 0.00 0.00 0.00 4.51
1041 1560 1.746615 CCATGCCACGAACCCTCAG 60.747 63.158 0.00 0.00 0.00 3.35
1248 1767 3.994000 GGGGGAGGAGGAGGAATG 58.006 66.667 0.00 0.00 0.00 2.67
1263 1788 0.912486 AATCACGAGGAAGAAGGGGG 59.088 55.000 0.00 0.00 0.00 5.40
1295 1820 3.501445 AGAAGATTTGAGTGAGCTGTTGC 59.499 43.478 0.00 0.00 40.05 4.17
1297 1822 5.240403 GGAAAGAAGATTTGAGTGAGCTGTT 59.760 40.000 0.00 0.00 0.00 3.16
1298 1823 4.759183 GGAAAGAAGATTTGAGTGAGCTGT 59.241 41.667 0.00 0.00 0.00 4.40
1513 2081 9.969001 AGTGCAGTTTTTAGGGATTATTAACTA 57.031 29.630 0.00 0.00 0.00 2.24
1515 2083 9.923143 AAAGTGCAGTTTTTAGGGATTATTAAC 57.077 29.630 13.86 0.00 0.00 2.01
1603 2329 1.202486 GGATGACGGAATTGCCTACGA 60.202 52.381 0.00 0.00 0.00 3.43
1610 2336 1.062587 GAACTGCGGATGACGGAATTG 59.937 52.381 0.00 0.00 44.20 2.32
1616 2342 1.156736 AAAAGGAACTGCGGATGACG 58.843 50.000 0.00 0.00 42.87 4.35
1638 2384 4.156556 TCAGTGAAGAATGCAAGCCATTAC 59.843 41.667 0.00 0.00 44.02 1.89
1640 2386 3.057033 GTCAGTGAAGAATGCAAGCCATT 60.057 43.478 0.00 0.00 46.57 3.16
1769 2535 5.123502 ACGATAAACAGAGAGAAGTTAGCGA 59.876 40.000 6.41 0.00 0.00 4.93
1771 2537 6.557110 AGACGATAAACAGAGAGAAGTTAGC 58.443 40.000 0.00 0.00 0.00 3.09
1873 2639 7.707035 CCACTCTTGTCATAGTTAATGGAGTAC 59.293 40.741 0.00 0.00 33.92 2.73
1959 3006 6.328410 TCCAGTAATGGAGATGAATCATGAGT 59.672 38.462 8.07 0.00 33.38 3.41
1960 3007 6.766429 TCCAGTAATGGAGATGAATCATGAG 58.234 40.000 8.07 0.00 33.38 2.90
1961 3008 6.752285 TCCAGTAATGGAGATGAATCATGA 57.248 37.500 8.07 0.00 33.38 3.07
1962 3009 7.395617 AGATCCAGTAATGGAGATGAATCATG 58.604 38.462 18.08 0.00 41.88 3.07
2059 3106 2.161410 GCCATCAAGATGCACGTTGTTA 59.839 45.455 4.53 0.00 37.49 2.41
2159 3206 4.166144 AGGAAAACTGAAGTTTCCAGGAGA 59.834 41.667 16.12 0.00 46.47 3.71
2161 3208 4.519906 AGGAAAACTGAAGTTTCCAGGA 57.480 40.909 16.12 0.00 46.47 3.86
2210 3257 9.533983 CAATATAAATAGTTTCTGCATAGCACG 57.466 33.333 0.00 0.00 33.79 5.34
2239 3286 6.471233 TTCTATGATGTTGAGGTCCTACTG 57.529 41.667 0.00 0.00 0.00 2.74
2240 3287 7.682787 ATTTCTATGATGTTGAGGTCCTACT 57.317 36.000 0.00 0.00 0.00 2.57
2241 3288 9.482627 CTTATTTCTATGATGTTGAGGTCCTAC 57.517 37.037 0.00 0.00 0.00 3.18
2242 3289 9.434275 TCTTATTTCTATGATGTTGAGGTCCTA 57.566 33.333 0.00 0.00 0.00 2.94
2243 3290 8.324191 TCTTATTTCTATGATGTTGAGGTCCT 57.676 34.615 0.00 0.00 0.00 3.85
2307 3354 0.185901 TGGCTGCTTCAAAAGGGAGT 59.814 50.000 0.00 0.00 0.00 3.85
2337 3384 5.286082 CGGCAATGAAGTTTTAACATAGTGC 59.714 40.000 0.00 0.00 32.61 4.40
2340 3387 6.842163 AGACGGCAATGAAGTTTTAACATAG 58.158 36.000 0.00 0.00 0.00 2.23
2479 3526 1.768684 GACCACTGAAGCCACCTCCA 61.769 60.000 0.00 0.00 0.00 3.86
2547 3618 4.806339 CCCCTCCCTTCCCTCGCT 62.806 72.222 0.00 0.00 0.00 4.93
2567 3638 0.449388 GCAGAAAGTTCCAGGATGCG 59.551 55.000 0.00 0.00 31.97 4.73
2571 3642 0.473755 TGCAGCAGAAAGTTCCAGGA 59.526 50.000 0.00 0.00 0.00 3.86
2657 3728 1.133982 ACAAGAACACACGCAATGCAA 59.866 42.857 5.91 0.00 0.00 4.08
2661 3732 4.562394 CAGAAAAACAAGAACACACGCAAT 59.438 37.500 0.00 0.00 0.00 3.56
2698 3774 9.316594 TCGTTATCCAATTAATATAGGTCAGGA 57.683 33.333 0.00 0.00 0.00 3.86
2720 3796 4.941263 TGCCAGTTTAGCATAAAGATCGTT 59.059 37.500 0.00 0.00 34.69 3.85
2782 3858 0.700564 AGGAATGGCACCTCACATGT 59.299 50.000 0.00 0.00 31.43 3.21
2810 3895 3.655972 TTCCCTCCCTCCTGCTATATT 57.344 47.619 0.00 0.00 0.00 1.28
2812 3897 3.251484 CAATTCCCTCCCTCCTGCTATA 58.749 50.000 0.00 0.00 0.00 1.31
2813 3898 2.061061 CAATTCCCTCCCTCCTGCTAT 58.939 52.381 0.00 0.00 0.00 2.97
2835 3920 8.805688 GCTTCAGAAATTTTCATCTCAAATAGC 58.194 33.333 11.53 3.80 0.00 2.97
2849 3934 9.635520 CTGAATGTGATTAAGCTTCAGAAATTT 57.364 29.630 13.18 0.00 43.40 1.82
2851 3936 7.395489 ACCTGAATGTGATTAAGCTTCAGAAAT 59.605 33.333 17.84 0.00 43.40 2.17
2862 3947 6.516527 GCCAAACAGAACCTGAATGTGATTAA 60.517 38.462 0.45 0.00 35.18 1.40
2863 3948 5.048083 GCCAAACAGAACCTGAATGTGATTA 60.048 40.000 0.45 0.00 35.18 1.75
2967 4061 2.516888 GCCGCAGCCTCCCCTAATA 61.517 63.158 0.00 0.00 0.00 0.98
2968 4062 3.878667 GCCGCAGCCTCCCCTAAT 61.879 66.667 0.00 0.00 0.00 1.73
2982 4076 1.026718 GTGGAGATCACCAAAGGCCG 61.027 60.000 13.92 0.00 41.87 6.13
2983 4077 2.873797 GTGGAGATCACCAAAGGCC 58.126 57.895 13.92 0.00 41.87 5.19
3010 4261 0.846427 ATTTCTCCACAGCCTCCCCA 60.846 55.000 0.00 0.00 0.00 4.96
3044 4309 6.619018 GCGTACGTGGAATGAGTTGATTTTTA 60.619 38.462 17.90 0.00 0.00 1.52
3045 4310 5.685841 CGTACGTGGAATGAGTTGATTTTT 58.314 37.500 7.22 0.00 0.00 1.94
3046 4311 4.378046 GCGTACGTGGAATGAGTTGATTTT 60.378 41.667 17.90 0.00 0.00 1.82
3047 4312 3.124636 GCGTACGTGGAATGAGTTGATTT 59.875 43.478 17.90 0.00 0.00 2.17
3048 4313 2.671396 GCGTACGTGGAATGAGTTGATT 59.329 45.455 17.90 0.00 0.00 2.57
3051 4316 1.126113 GTGCGTACGTGGAATGAGTTG 59.874 52.381 17.90 0.00 0.00 3.16
3101 4369 9.334947 TGTACACTCCAGTTATACATACTACTC 57.665 37.037 0.00 0.00 0.00 2.59
3446 4727 2.743928 GTGACGCTGCCCTTCCTG 60.744 66.667 0.00 0.00 0.00 3.86
3650 4931 4.021925 AAGGTGCTGGAGGCCGTC 62.022 66.667 0.00 0.00 40.92 4.79


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

AutoCloner maintained by Alex Coulton.