Multiple sequence alignment - TraesCS6B01G085000

Loading Multiple Alignment...

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 TraesCS6B01G085000 chr6B 100.000 2684 0 0 1 2684 62000284 62002967 0.000000e+00 4957.0
1 TraesCS6B01G085000 chr6B 82.905 1556 205 30 935 2469 95819067 95820582 0.000000e+00 1343.0
2 TraesCS6B01G085000 chr6B 86.036 845 83 20 1 830 61807180 61808004 0.000000e+00 874.0
3 TraesCS6B01G085000 chr6B 81.274 1036 150 23 886 1911 95722807 95723808 0.000000e+00 798.0
4 TraesCS6B01G085000 chr6B 86.190 630 68 13 1917 2544 95755896 95756508 0.000000e+00 664.0
5 TraesCS6B01G085000 chr6B 84.750 400 49 6 922 1313 61918590 61918985 9.010000e-105 390.0
6 TraesCS6B01G085000 chr6D 94.151 1590 71 11 968 2548 28683612 28682036 0.000000e+00 2401.0
7 TraesCS6B01G085000 chr6D 84.695 1555 171 37 940 2469 41545389 41543877 0.000000e+00 1491.0
8 TraesCS6B01G085000 chr6D 84.481 1205 150 22 902 2093 41596569 41595389 0.000000e+00 1155.0
9 TraesCS6B01G085000 chr6D 86.463 458 46 9 2090 2547 41583082 41582641 3.110000e-134 488.0
10 TraesCS6B01G085000 chr6D 92.857 140 7 2 2545 2684 28682006 28681870 1.630000e-47 200.0
11 TraesCS6B01G085000 chr6D 91.667 72 3 1 796 867 28683707 28683639 2.200000e-16 97.1
12 TraesCS6B01G085000 chr6A 92.539 1662 80 25 889 2547 33967032 33968652 0.000000e+00 2342.0
13 TraesCS6B01G085000 chr6A 86.008 1458 168 16 941 2384 52118816 52117381 0.000000e+00 1530.0
14 TraesCS6B01G085000 chr6A 83.812 1532 182 28 951 2469 52039104 52037626 0.000000e+00 1395.0
15 TraesCS6B01G085000 chr4D 75.290 1206 237 43 1030 2215 73997964 73996800 1.100000e-143 520.0


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 TraesCS6B01G085000 chr6B 62000284 62002967 2683 False 4957.000000 4957 100.000000 1 2684 1 chr6B.!!$F3 2683
1 TraesCS6B01G085000 chr6B 95819067 95820582 1515 False 1343.000000 1343 82.905000 935 2469 1 chr6B.!!$F6 1534
2 TraesCS6B01G085000 chr6B 61807180 61808004 824 False 874.000000 874 86.036000 1 830 1 chr6B.!!$F1 829
3 TraesCS6B01G085000 chr6B 95722807 95723808 1001 False 798.000000 798 81.274000 886 1911 1 chr6B.!!$F4 1025
4 TraesCS6B01G085000 chr6B 95755896 95756508 612 False 664.000000 664 86.190000 1917 2544 1 chr6B.!!$F5 627
5 TraesCS6B01G085000 chr6D 41543877 41545389 1512 True 1491.000000 1491 84.695000 940 2469 1 chr6D.!!$R1 1529
6 TraesCS6B01G085000 chr6D 41595389 41596569 1180 True 1155.000000 1155 84.481000 902 2093 1 chr6D.!!$R3 1191
7 TraesCS6B01G085000 chr6D 28681870 28683707 1837 True 899.366667 2401 92.891667 796 2684 3 chr6D.!!$R4 1888
8 TraesCS6B01G085000 chr6A 33967032 33968652 1620 False 2342.000000 2342 92.539000 889 2547 1 chr6A.!!$F1 1658
9 TraesCS6B01G085000 chr6A 52117381 52118816 1435 True 1530.000000 1530 86.008000 941 2384 1 chr6A.!!$R2 1443
10 TraesCS6B01G085000 chr6A 52037626 52039104 1478 True 1395.000000 1395 83.812000 951 2469 1 chr6A.!!$R1 1518
11 TraesCS6B01G085000 chr4D 73996800 73997964 1164 True 520.000000 520 75.290000 1030 2215 1 chr4D.!!$R1 1185

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
849 863 0.031721 CCCGCTATAGTCGAACCCAC 59.968 60.0 15.26 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2651 2786 0.465097 AACAGCAACAGCAGCAGACT 60.465 50.0 0.0 0.0 0.0 3.24 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
46 47 1.002033 GATGGCGCAGAATGACATTCC 60.002 52.381 21.89 9.71 39.69 3.01
49 50 0.804364 GCGCAGAATGACATTCCACA 59.196 50.000 21.89 0.00 39.69 4.17
50 51 1.199789 GCGCAGAATGACATTCCACAA 59.800 47.619 21.89 0.00 39.69 3.33
51 52 2.351641 GCGCAGAATGACATTCCACAAA 60.352 45.455 21.89 0.00 39.69 2.83
107 108 8.438513 CAGTCATAACAGTAGAATCAACACTTG 58.561 37.037 0.00 0.00 0.00 3.16
129 130 5.067273 TGAACCCAAGTTACACCATAACTG 58.933 41.667 0.28 0.00 37.77 3.16
134 135 4.263331 CCAAGTTACACCATAACTGAGGGT 60.263 45.833 0.28 0.00 45.37 4.34
135 136 5.046159 CCAAGTTACACCATAACTGAGGGTA 60.046 44.000 0.28 0.00 41.45 3.69
158 159 9.341899 GGTATTTCAGTCATTTCAACATGTTAC 57.658 33.333 11.53 4.76 0.00 2.50
164 165 4.917415 GTCATTTCAACATGTTACTGCACC 59.083 41.667 11.53 0.00 0.00 5.01
192 193 5.144359 GCAACTGTTACATCAAAACTACGG 58.856 41.667 0.00 0.00 0.00 4.02
220 221 1.471684 GCATCTCAGCTCCAACCTTTG 59.528 52.381 0.00 0.00 0.00 2.77
225 226 1.302832 AGCTCCAACCTTTGAGCCG 60.303 57.895 7.81 0.00 41.21 5.52
248 249 2.733517 GCTATCAGCTACAGTCGTTCC 58.266 52.381 0.00 0.00 38.45 3.62
249 250 2.359531 GCTATCAGCTACAGTCGTTCCT 59.640 50.000 0.00 0.00 38.45 3.36
250 251 3.181485 GCTATCAGCTACAGTCGTTCCTT 60.181 47.826 0.00 0.00 38.45 3.36
251 252 3.512033 ATCAGCTACAGTCGTTCCTTC 57.488 47.619 0.00 0.00 0.00 3.46
252 253 1.544691 TCAGCTACAGTCGTTCCTTCC 59.455 52.381 0.00 0.00 0.00 3.46
253 254 1.272490 CAGCTACAGTCGTTCCTTCCA 59.728 52.381 0.00 0.00 0.00 3.53
254 255 1.546476 AGCTACAGTCGTTCCTTCCAG 59.454 52.381 0.00 0.00 0.00 3.86
255 256 1.997669 CTACAGTCGTTCCTTCCAGC 58.002 55.000 0.00 0.00 0.00 4.85
256 257 0.606604 TACAGTCGTTCCTTCCAGCC 59.393 55.000 0.00 0.00 0.00 4.85
263 264 2.959484 TTCCTTCCAGCCGGAGCAG 61.959 63.158 5.05 0.00 44.10 4.24
282 283 3.426525 GCAGTTGTAGCTGTGAAATTTGC 59.573 43.478 0.00 0.00 38.65 3.68
296 297 5.961263 GTGAAATTTGCAGCTGAAACAAAAG 59.039 36.000 20.43 0.00 36.90 2.27
297 298 5.064962 TGAAATTTGCAGCTGAAACAAAAGG 59.935 36.000 20.43 0.00 36.90 3.11
326 327 1.810030 GGTTTACTCCTCTGCGCGG 60.810 63.158 10.86 10.86 0.00 6.46
333 335 3.458163 CCTCTGCGCGGGGTAAGA 61.458 66.667 16.51 3.84 0.00 2.10
340 342 0.179148 GCGCGGGGTAAGATTTTTGG 60.179 55.000 8.83 0.00 0.00 3.28
346 348 3.512496 GGGGTAAGATTTTTGGGGAACA 58.488 45.455 0.00 0.00 0.00 3.18
360 362 2.238395 GGGGAACAGAGAAGATGCTTCT 59.762 50.000 9.28 9.28 0.00 2.85
362 364 3.307339 GGGAACAGAGAAGATGCTTCTGT 60.307 47.826 13.88 7.64 42.62 3.41
377 379 2.812358 TCTGTGTATGCGTTGTGAGT 57.188 45.000 0.00 0.00 0.00 3.41
402 404 4.712122 TTTTGTTGAACTGTGGAGAACC 57.288 40.909 0.00 0.00 0.00 3.62
407 409 1.967779 TGAACTGTGGAGAACCGATCA 59.032 47.619 0.00 0.00 39.42 2.92
427 431 1.033574 ATAGCGGCTACTGAGGTGAC 58.966 55.000 12.67 0.00 0.00 3.67
428 432 1.374343 TAGCGGCTACTGAGGTGACG 61.374 60.000 5.42 0.00 0.00 4.35
429 433 2.697761 GCGGCTACTGAGGTGACGA 61.698 63.158 6.40 0.00 0.00 4.20
440 444 1.996191 GAGGTGACGAATCTTGTGCTC 59.004 52.381 0.00 0.00 0.00 4.26
446 450 1.344226 CGAATCTTGTGCTCGCGTCA 61.344 55.000 5.77 2.39 0.00 4.35
496 500 3.281240 GGTGCTAGACCGGTCGAA 58.719 61.111 28.26 19.28 34.02 3.71
497 501 1.588082 GGTGCTAGACCGGTCGAAA 59.412 57.895 28.26 16.80 34.02 3.46
504 508 0.466963 AGACCGGTCGAAACCAAAGT 59.533 50.000 28.26 4.27 46.86 2.66
505 509 1.134310 AGACCGGTCGAAACCAAAGTT 60.134 47.619 28.26 3.70 46.86 2.66
580 584 0.179145 CGAGGCCCGTATATAAGCGG 60.179 60.000 0.00 10.33 46.80 5.52
588 592 2.159517 CCGTATATAAGCGGGTCGTACC 60.160 54.545 9.64 0.00 43.85 3.34
629 633 4.189188 CGAGGCCCAGGTACGACG 62.189 72.222 0.00 0.00 0.00 5.12
647 651 1.752501 CGCATGAGCTAAACGGGTCG 61.753 60.000 0.00 0.00 39.10 4.79
731 735 2.203625 TTTGGGCTGCTTGTCCCC 60.204 61.111 0.00 0.00 40.46 4.81
734 738 3.971702 GGGCTGCTTGTCCCCTGT 61.972 66.667 0.00 0.00 36.50 4.00
773 787 2.480610 CCCATTTAGCCGTGCGCAT 61.481 57.895 15.91 0.00 41.38 4.73
789 803 3.731728 ATGTCACGGGCTGGGCAT 61.732 61.111 0.00 0.00 0.00 4.40
844 858 1.913778 TATGGCCCGCTATAGTCGAA 58.086 50.000 15.26 2.60 0.00 3.71
848 862 1.741327 GCCCGCTATAGTCGAACCCA 61.741 60.000 15.26 0.00 0.00 4.51
849 863 0.031721 CCCGCTATAGTCGAACCCAC 59.968 60.000 15.26 0.00 0.00 4.61
850 864 0.031721 CCGCTATAGTCGAACCCACC 59.968 60.000 15.26 0.00 0.00 4.61
851 865 0.742505 CGCTATAGTCGAACCCACCA 59.257 55.000 9.97 0.00 0.00 4.17
852 866 1.135527 CGCTATAGTCGAACCCACCAA 59.864 52.381 9.97 0.00 0.00 3.67
853 867 2.547826 GCTATAGTCGAACCCACCAAC 58.452 52.381 0.84 0.00 0.00 3.77
854 868 2.740904 GCTATAGTCGAACCCACCAACC 60.741 54.545 0.84 0.00 0.00 3.77
855 869 1.354101 ATAGTCGAACCCACCAACCA 58.646 50.000 0.00 0.00 0.00 3.67
856 870 1.129917 TAGTCGAACCCACCAACCAA 58.870 50.000 0.00 0.00 0.00 3.67
857 871 0.179029 AGTCGAACCCACCAACCAAG 60.179 55.000 0.00 0.00 0.00 3.61
858 872 0.464916 GTCGAACCCACCAACCAAGT 60.465 55.000 0.00 0.00 0.00 3.16
859 873 1.129917 TCGAACCCACCAACCAAGTA 58.870 50.000 0.00 0.00 0.00 2.24
860 874 1.071071 TCGAACCCACCAACCAAGTAG 59.929 52.381 0.00 0.00 0.00 2.57
861 875 1.244816 GAACCCACCAACCAAGTAGC 58.755 55.000 0.00 0.00 0.00 3.58
862 876 0.553819 AACCCACCAACCAAGTAGCA 59.446 50.000 0.00 0.00 0.00 3.49
863 877 0.110486 ACCCACCAACCAAGTAGCAG 59.890 55.000 0.00 0.00 0.00 4.24
864 878 0.400213 CCCACCAACCAAGTAGCAGA 59.600 55.000 0.00 0.00 0.00 4.26
865 879 1.611673 CCCACCAACCAAGTAGCAGAG 60.612 57.143 0.00 0.00 0.00 3.35
866 880 1.611673 CCACCAACCAAGTAGCAGAGG 60.612 57.143 0.00 0.00 0.00 3.69
867 881 1.072331 CACCAACCAAGTAGCAGAGGT 59.928 52.381 0.00 0.00 35.47 3.85
868 882 1.348036 ACCAACCAAGTAGCAGAGGTC 59.652 52.381 0.00 0.00 32.05 3.85
869 883 1.625818 CCAACCAAGTAGCAGAGGTCT 59.374 52.381 0.00 0.00 32.05 3.85
870 884 2.039084 CCAACCAAGTAGCAGAGGTCTT 59.961 50.000 0.00 0.00 32.05 3.01
871 885 3.496870 CCAACCAAGTAGCAGAGGTCTTT 60.497 47.826 0.00 0.00 32.05 2.52
872 886 3.686916 ACCAAGTAGCAGAGGTCTTTC 57.313 47.619 0.00 0.00 0.00 2.62
873 887 3.243724 ACCAAGTAGCAGAGGTCTTTCT 58.756 45.455 0.00 0.00 0.00 2.52
874 888 3.259625 ACCAAGTAGCAGAGGTCTTTCTC 59.740 47.826 0.00 0.00 0.00 2.87
875 889 3.259374 CCAAGTAGCAGAGGTCTTTCTCA 59.741 47.826 0.00 0.00 36.30 3.27
876 890 4.262635 CCAAGTAGCAGAGGTCTTTCTCAA 60.263 45.833 0.00 0.00 36.30 3.02
877 891 5.300752 CAAGTAGCAGAGGTCTTTCTCAAA 58.699 41.667 0.00 0.00 36.30 2.69
878 892 5.552870 AGTAGCAGAGGTCTTTCTCAAAA 57.447 39.130 0.00 0.00 36.30 2.44
879 893 5.930135 AGTAGCAGAGGTCTTTCTCAAAAA 58.070 37.500 0.00 0.00 36.30 1.94
921 935 2.737180 CCGTGTGTGGCTGTCTCT 59.263 61.111 0.00 0.00 0.00 3.10
922 936 1.665916 CCGTGTGTGGCTGTCTCTG 60.666 63.158 0.00 0.00 0.00 3.35
923 937 1.068083 CGTGTGTGGCTGTCTCTGT 59.932 57.895 0.00 0.00 0.00 3.41
932 948 2.033602 TGTCTCTGTCTCGCCCGA 59.966 61.111 0.00 0.00 0.00 5.14
935 951 3.827898 CTCTGTCTCGCCCGACCC 61.828 72.222 0.00 0.00 32.97 4.46
938 954 4.051167 TGTCTCGCCCGACCCCTA 62.051 66.667 0.00 0.00 32.97 3.53
948 964 1.110518 CCGACCCCTAGCTCCTCTTC 61.111 65.000 0.00 0.00 0.00 2.87
962 986 1.984288 CTCTTCCCCCATTCCGTCCC 61.984 65.000 0.00 0.00 0.00 4.46
985 1009 4.904590 CACCCAAACCCCACGCCA 62.905 66.667 0.00 0.00 0.00 5.69
986 1010 4.906537 ACCCAAACCCCACGCCAC 62.907 66.667 0.00 0.00 0.00 5.01
993 1017 4.814294 CCCCACGCCACGAGCTAC 62.814 72.222 0.00 0.00 40.39 3.58
1115 1154 2.125350 CCTCGTCTGCAAGCCCTC 60.125 66.667 0.00 0.00 0.00 4.30
1221 1263 3.461773 CAGGTCTGCGACGGGGAT 61.462 66.667 0.00 0.00 32.65 3.85
1562 1610 2.576317 GTACTCGTCGGCGACAGC 60.576 66.667 35.62 18.05 42.81 4.40
1798 1846 0.918983 CCCACCACCACCAGATACAT 59.081 55.000 0.00 0.00 0.00 2.29
1829 1877 0.902531 GGTTTCGTCTCCCTCATGGA 59.097 55.000 0.00 0.00 42.41 3.41
1863 1911 4.767255 CTGGGGCTCGCTGGTGTC 62.767 72.222 0.00 0.00 0.00 3.67
1930 1990 2.298729 GGAGCTGCAAAATGGGTACAAA 59.701 45.455 0.00 0.00 0.00 2.83
1989 2049 4.856801 CCCCGCGAAGGTGATGGG 62.857 72.222 8.23 2.27 38.74 4.00
2008 2068 2.175202 GGGCATATGTGGTTGGTTTCA 58.825 47.619 4.29 0.00 0.00 2.69
2079 2139 2.415608 CGAGCTCAAGTCCGGGCTA 61.416 63.158 10.18 0.00 35.01 3.93
2246 2341 4.640364 TGTGAACAGTCAGTCATATTGCA 58.360 39.130 0.00 0.00 33.27 4.08
2300 2395 8.602472 ATTCCTGTAAATACCTTGCCAAATTA 57.398 30.769 0.00 0.00 0.00 1.40
2304 2399 8.931775 CCTGTAAATACCTTGCCAAATTAAAAC 58.068 33.333 0.00 0.00 0.00 2.43
2346 2441 6.325919 ACGTAACATGTGACATTGGAAAAT 57.674 33.333 13.91 0.00 0.00 1.82
2398 2495 6.957984 CTGTTAAGGACCATGATGATATCG 57.042 41.667 0.00 0.00 0.00 2.92
2400 2497 7.244886 TGTTAAGGACCATGATGATATCGAT 57.755 36.000 2.16 2.16 0.00 3.59
2401 2498 8.361169 TGTTAAGGACCATGATGATATCGATA 57.639 34.615 7.75 7.75 0.00 2.92
2402 2499 8.251026 TGTTAAGGACCATGATGATATCGATAC 58.749 37.037 7.41 2.86 0.00 2.24
2403 2500 6.857437 AAGGACCATGATGATATCGATACA 57.143 37.500 7.41 8.54 0.00 2.29
2404 2501 6.214191 AGGACCATGATGATATCGATACAC 57.786 41.667 7.41 5.93 0.00 2.90
2405 2502 5.037385 GGACCATGATGATATCGATACACG 58.963 45.833 7.41 0.00 44.09 4.49
2484 2586 6.974965 ACCTTGCTTCAGACTTTCTAATTTG 58.025 36.000 0.00 0.00 0.00 2.32
2560 2695 5.248477 AGCTCAGTCTTACCAAAGTGGAATA 59.752 40.000 0.18 0.00 40.96 1.75
2604 2739 5.942872 AGTTTTCAGCATGGTATCTTTTCG 58.057 37.500 0.00 0.00 36.16 3.46
2617 2752 5.010012 GGTATCTTTTCGGATCATGGCATTT 59.990 40.000 0.00 0.00 0.00 2.32
2618 2753 5.603170 ATCTTTTCGGATCATGGCATTTT 57.397 34.783 0.00 0.00 0.00 1.82
2619 2754 4.746729 TCTTTTCGGATCATGGCATTTTG 58.253 39.130 0.00 0.00 0.00 2.44
2620 2755 4.462132 TCTTTTCGGATCATGGCATTTTGA 59.538 37.500 0.00 0.00 0.00 2.69
2661 2796 4.222588 ACTTGATCTCTTAAGTCTGCTGCT 59.777 41.667 1.63 0.00 31.88 4.24
2663 2798 3.513119 TGATCTCTTAAGTCTGCTGCTGT 59.487 43.478 1.63 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 8.438513 CAAGTGTTGATTCTACTGTTATGACTG 58.561 37.037 0.17 0.00 0.00 3.51
107 108 5.310451 TCAGTTATGGTGTAACTTGGGTTC 58.690 41.667 0.00 0.00 35.76 3.62
129 130 6.817765 TGTTGAAATGACTGAAATACCCTC 57.182 37.500 0.00 0.00 0.00 4.30
135 136 7.596248 GCAGTAACATGTTGAAATGACTGAAAT 59.404 33.333 28.63 3.13 35.75 2.17
148 149 3.631144 CAACTGGTGCAGTAACATGTTG 58.369 45.455 21.42 6.49 44.62 3.33
173 174 5.403166 TCGTTCCGTAGTTTTGATGTAACAG 59.597 40.000 0.00 0.00 0.00 3.16
181 182 2.129607 GCAGTCGTTCCGTAGTTTTGA 58.870 47.619 0.00 0.00 0.00 2.69
184 185 2.029290 AGATGCAGTCGTTCCGTAGTTT 60.029 45.455 0.00 0.00 0.00 2.66
192 193 1.276415 GAGCTGAGATGCAGTCGTTC 58.724 55.000 0.00 0.00 46.62 3.95
233 234 1.272490 TGGAAGGAACGACTGTAGCTG 59.728 52.381 0.00 0.00 0.00 4.24
234 235 1.546476 CTGGAAGGAACGACTGTAGCT 59.454 52.381 0.00 0.00 0.00 3.32
235 236 1.997669 CTGGAAGGAACGACTGTAGC 58.002 55.000 0.00 0.00 0.00 3.58
236 237 1.404315 GGCTGGAAGGAACGACTGTAG 60.404 57.143 0.00 0.00 0.00 2.74
237 238 0.606604 GGCTGGAAGGAACGACTGTA 59.393 55.000 0.00 0.00 0.00 2.74
238 239 1.371558 GGCTGGAAGGAACGACTGT 59.628 57.895 0.00 0.00 0.00 3.55
239 240 1.738099 CGGCTGGAAGGAACGACTG 60.738 63.158 0.00 0.00 0.00 3.51
240 241 2.657237 CGGCTGGAAGGAACGACT 59.343 61.111 0.00 0.00 0.00 4.18
241 242 2.434359 CCGGCTGGAAGGAACGAC 60.434 66.667 5.28 0.00 37.49 4.34
243 244 2.125512 CTCCGGCTGGAAGGAACG 60.126 66.667 16.91 0.00 45.87 3.95
244 245 2.436824 GCTCCGGCTGGAAGGAAC 60.437 66.667 16.91 0.00 45.87 3.62
245 246 2.927856 TGCTCCGGCTGGAAGGAA 60.928 61.111 16.91 0.00 45.87 3.36
246 247 3.393970 CTGCTCCGGCTGGAAGGA 61.394 66.667 16.91 10.11 45.87 3.36
247 248 3.259633 AACTGCTCCGGCTGGAAGG 62.260 63.158 16.91 10.78 45.87 3.46
248 249 2.037136 CAACTGCTCCGGCTGGAAG 61.037 63.158 16.91 13.71 45.87 3.46
249 250 1.476845 TACAACTGCTCCGGCTGGAA 61.477 55.000 16.91 0.00 45.87 3.53
250 251 1.888436 CTACAACTGCTCCGGCTGGA 61.888 60.000 15.16 15.16 43.88 3.86
251 252 1.448540 CTACAACTGCTCCGGCTGG 60.449 63.158 4.71 4.71 40.90 4.85
252 253 2.103042 GCTACAACTGCTCCGGCTG 61.103 63.158 0.00 0.00 42.04 4.85
253 254 2.266055 GCTACAACTGCTCCGGCT 59.734 61.111 0.00 0.00 39.59 5.52
254 255 2.103042 CAGCTACAACTGCTCCGGC 61.103 63.158 0.00 0.00 38.92 6.13
255 256 1.016130 CACAGCTACAACTGCTCCGG 61.016 60.000 0.00 0.00 41.60 5.14
256 257 0.038251 TCACAGCTACAACTGCTCCG 60.038 55.000 0.00 0.00 41.60 4.63
282 283 2.695147 AGGTTCCCTTTTGTTTCAGCTG 59.305 45.455 7.63 7.63 0.00 4.24
285 286 4.556699 CGCTAAGGTTCCCTTTTGTTTCAG 60.557 45.833 0.06 0.00 41.69 3.02
306 307 2.453638 GCGCAGAGGAGTAAACCGC 61.454 63.158 0.30 0.00 34.73 5.68
308 309 3.782042 CGCGCAGAGGAGTAAACC 58.218 61.111 8.75 0.00 0.00 3.27
319 320 0.808755 AAAAATCTTACCCCGCGCAG 59.191 50.000 8.75 0.00 0.00 5.18
326 327 4.412843 TCTGTTCCCCAAAAATCTTACCC 58.587 43.478 0.00 0.00 0.00 3.69
333 335 4.221482 GCATCTTCTCTGTTCCCCAAAAAT 59.779 41.667 0.00 0.00 0.00 1.82
340 342 3.269178 CAGAAGCATCTTCTCTGTTCCC 58.731 50.000 6.14 0.00 32.03 3.97
346 348 4.440880 GCATACACAGAAGCATCTTCTCT 58.559 43.478 6.14 0.00 32.03 3.10
360 362 4.624336 AAAAACTCACAACGCATACACA 57.376 36.364 0.00 0.00 0.00 3.72
392 394 2.481276 CGCTATTGATCGGTTCTCCACA 60.481 50.000 0.00 0.00 0.00 4.17
402 404 2.590073 CTCAGTAGCCGCTATTGATCG 58.410 52.381 21.83 10.71 33.46 3.69
407 409 1.409427 GTCACCTCAGTAGCCGCTATT 59.591 52.381 2.79 0.00 0.00 1.73
417 421 2.868044 GCACAAGATTCGTCACCTCAGT 60.868 50.000 0.00 0.00 0.00 3.41
418 422 1.728971 GCACAAGATTCGTCACCTCAG 59.271 52.381 0.00 0.00 0.00 3.35
419 423 1.344438 AGCACAAGATTCGTCACCTCA 59.656 47.619 0.00 0.00 0.00 3.86
427 431 1.341802 GACGCGAGCACAAGATTCG 59.658 57.895 15.93 0.00 37.40 3.34
428 432 0.368227 CTGACGCGAGCACAAGATTC 59.632 55.000 15.93 0.00 0.00 2.52
429 433 0.319900 ACTGACGCGAGCACAAGATT 60.320 50.000 15.93 0.00 0.00 2.40
440 444 2.946597 CGCTAGCAGACTGACGCG 60.947 66.667 16.45 3.53 34.03 6.01
521 525 3.436924 CGTTTAAGGGTGGGGCGC 61.437 66.667 0.00 0.00 0.00 6.53
559 563 1.467035 CGCTTATATACGGGCCTCGAC 60.467 57.143 18.74 0.00 42.43 4.20
621 625 1.587034 GTTTAGCTCATGCGTCGTACC 59.413 52.381 0.00 0.00 45.42 3.34
629 633 1.429148 CCGACCCGTTTAGCTCATGC 61.429 60.000 0.00 0.00 40.05 4.06
713 717 2.278330 GGGGACAAGCAGCCCAAAG 61.278 63.158 0.00 0.00 46.57 2.77
720 724 2.263741 GCACACAGGGGACAAGCAG 61.264 63.158 0.00 0.00 0.00 4.24
723 727 2.669569 CGGCACACAGGGGACAAG 60.670 66.667 0.00 0.00 0.00 3.16
754 758 4.552745 GCGCACGGCTAAATGGGC 62.553 66.667 0.30 0.00 45.81 5.36
758 762 1.024046 TGACATGCGCACGGCTAAAT 61.024 50.000 14.90 0.00 44.05 1.40
759 763 1.669437 TGACATGCGCACGGCTAAA 60.669 52.632 14.90 0.00 44.05 1.85
773 787 4.720902 CATGCCCAGCCCGTGACA 62.721 66.667 0.00 0.00 0.00 3.58
789 803 0.948678 GGCCAGTTTGTTAGAACGCA 59.051 50.000 0.00 0.00 34.74 5.24
794 808 0.759959 TCACGGGCCAGTTTGTTAGA 59.240 50.000 5.51 0.00 0.00 2.10
832 846 0.742505 TGGTGGGTTCGACTATAGCG 59.257 55.000 0.00 5.00 0.00 4.26
844 858 0.110486 CTGCTACTTGGTTGGTGGGT 59.890 55.000 0.00 0.00 0.00 4.51
848 862 1.348036 GACCTCTGCTACTTGGTTGGT 59.652 52.381 0.00 0.00 32.30 3.67
849 863 1.625818 AGACCTCTGCTACTTGGTTGG 59.374 52.381 0.00 0.00 32.30 3.77
850 864 3.409026 AAGACCTCTGCTACTTGGTTG 57.591 47.619 0.00 0.00 32.30 3.77
851 865 3.648545 AGAAAGACCTCTGCTACTTGGTT 59.351 43.478 0.00 0.00 32.30 3.67
852 866 3.243724 AGAAAGACCTCTGCTACTTGGT 58.756 45.455 0.00 0.00 35.23 3.67
853 867 3.259374 TGAGAAAGACCTCTGCTACTTGG 59.741 47.826 0.00 0.00 34.38 3.61
854 868 4.527509 TGAGAAAGACCTCTGCTACTTG 57.472 45.455 0.00 0.00 34.38 3.16
855 869 5.552870 TTTGAGAAAGACCTCTGCTACTT 57.447 39.130 0.00 0.00 34.38 2.24
856 870 5.552870 TTTTGAGAAAGACCTCTGCTACT 57.447 39.130 0.00 0.00 34.38 2.57
885 899 2.239400 GGCCTCTGCTACTTGGTTTTT 58.761 47.619 0.00 0.00 37.74 1.94
886 900 1.882352 CGGCCTCTGCTACTTGGTTTT 60.882 52.381 0.00 0.00 37.74 2.43
887 901 0.321653 CGGCCTCTGCTACTTGGTTT 60.322 55.000 0.00 0.00 37.74 3.27
921 935 4.051167 TAGGGGTCGGGCGAGACA 62.051 66.667 12.59 0.00 42.62 3.41
922 936 3.217743 CTAGGGGTCGGGCGAGAC 61.218 72.222 3.53 3.53 40.25 3.36
932 948 1.315216 GGGAAGAGGAGCTAGGGGT 59.685 63.158 0.00 0.00 0.00 4.95
935 951 0.104725 ATGGGGGAAGAGGAGCTAGG 60.105 60.000 0.00 0.00 0.00 3.02
938 954 0.990818 GGAATGGGGGAAGAGGAGCT 60.991 60.000 0.00 0.00 0.00 4.09
948 964 2.044352 GTTGGGACGGAATGGGGG 60.044 66.667 0.00 0.00 0.00 5.40
962 986 2.525629 GGGGTTTGGGTGGGGTTG 60.526 66.667 0.00 0.00 0.00 3.77
984 1008 4.873129 ATGGCGCGGTAGCTCGTG 62.873 66.667 8.83 4.15 42.32 4.35
985 1009 4.873129 CATGGCGCGGTAGCTCGT 62.873 66.667 8.83 0.00 42.32 4.18
1148 1190 4.832608 GGAAGGCGCGGTACTGGG 62.833 72.222 14.19 14.19 0.00 4.45
1534 1582 1.006571 ACGAGTACACGGTTGCCTG 60.007 57.895 16.97 0.00 37.61 4.85
1798 1846 2.622942 AGACGAAACCACCGTACACTTA 59.377 45.455 0.00 0.00 40.67 2.24
1829 1877 1.349026 CCAGTGAACTGTCCTCCATGT 59.651 52.381 9.49 0.00 42.27 3.21
1989 2049 2.560542 TGTGAAACCAACCACATATGCC 59.439 45.455 1.58 0.00 38.26 4.40
2008 2068 0.832135 ATGACACCGACACCCTCTGT 60.832 55.000 0.00 0.00 34.96 3.41
2079 2139 4.275936 CCAAATTCGTCAACCTTCTTCACT 59.724 41.667 0.00 0.00 0.00 3.41
2284 2379 7.990314 ACACAAGTTTTAATTTGGCAAGGTATT 59.010 29.630 0.00 0.20 30.79 1.89
2286 2381 6.879400 ACACAAGTTTTAATTTGGCAAGGTA 58.121 32.000 0.00 0.00 30.79 3.08
2360 2456 7.775561 GGTCCTTAACAGGTCAAATCTCATAAT 59.224 37.037 0.00 0.00 41.69 1.28
2397 2494 3.160545 GCAATTCAACCAACGTGTATCG 58.839 45.455 0.00 0.00 46.00 2.92
2398 2495 3.057876 TGGCAATTCAACCAACGTGTATC 60.058 43.478 0.00 0.00 31.46 2.24
2400 2497 2.298610 TGGCAATTCAACCAACGTGTA 58.701 42.857 0.00 0.00 31.46 2.90
2401 2498 1.107114 TGGCAATTCAACCAACGTGT 58.893 45.000 0.00 0.00 31.46 4.49
2402 2499 2.215907 TTGGCAATTCAACCAACGTG 57.784 45.000 0.00 0.00 40.98 4.49
2403 2500 2.969628 TTTGGCAATTCAACCAACGT 57.030 40.000 0.00 0.00 45.42 3.99
2404 2501 4.201705 GCATATTTGGCAATTCAACCAACG 60.202 41.667 0.00 0.00 45.42 4.10
2405 2502 4.694509 TGCATATTTGGCAATTCAACCAAC 59.305 37.500 0.00 0.00 45.42 3.77
2588 2723 4.422073 TGATCCGAAAAGATACCATGCT 57.578 40.909 0.00 0.00 0.00 3.79
2604 2739 3.569701 ACGGTATCAAAATGCCATGATCC 59.430 43.478 0.00 0.00 37.50 3.36
2617 2752 7.766738 TCAAGTAATATTTGCTGACGGTATCAA 59.233 33.333 0.00 0.00 36.69 2.57
2618 2753 7.269316 TCAAGTAATATTTGCTGACGGTATCA 58.731 34.615 0.00 0.00 35.45 2.15
2619 2754 7.709269 TCAAGTAATATTTGCTGACGGTATC 57.291 36.000 0.00 0.00 0.00 2.24
2620 2755 8.150945 AGATCAAGTAATATTTGCTGACGGTAT 58.849 33.333 0.00 0.00 0.00 2.73
2651 2786 0.465097 AACAGCAACAGCAGCAGACT 60.465 50.000 0.00 0.00 0.00 3.24
2658 2793 5.574891 TCTAAAAGAAAACAGCAACAGCA 57.425 34.783 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.