Multiple sequence alignment - TraesCS3B01G175700

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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 TraesCS3B01G175700 chr3B 100.000 2162 0 0 1 2162 177849461 177851622 0.000000e+00 3993
1 TraesCS3B01G175700 chr3B 98.333 60 1 0 1 60 809252783 809252842 2.930000e-19 106
2 TraesCS3B01G175700 chr3B 98.305 59 1 0 1 59 91357116 91357058 1.060000e-18 104
3 TraesCS3B01G175700 chr3B 98.305 59 1 0 1 59 505761596 505761538 1.060000e-18 104
4 TraesCS3B01G175700 chr3B 96.721 61 2 0 1 61 481887789 481887849 3.800000e-18 102
5 TraesCS3B01G175700 chr1B 89.509 2116 199 11 55 2162 117373721 117375821 0.000000e+00 2656
6 TraesCS3B01G175700 chr1B 87.207 2048 250 10 118 2162 65746059 65744021 0.000000e+00 2320
7 TraesCS3B01G175700 chr2A 87.541 2111 247 14 59 2162 691688185 691690286 0.000000e+00 2427
8 TraesCS3B01G175700 chr5A 87.453 2112 250 14 59 2162 689877505 689875401 0.000000e+00 2418
9 TraesCS3B01G175700 chr2D 87.494 2087 246 11 80 2162 131527679 131525604 0.000000e+00 2394
10 TraesCS3B01G175700 chr4A 86.774 2117 261 14 59 2162 533022661 533020551 0.000000e+00 2340
11 TraesCS3B01G175700 chr6A 86.807 2092 265 7 74 2162 408866630 408868713 0.000000e+00 2324
12 TraesCS3B01G175700 chr6D 86.654 2098 266 13 72 2162 224571724 224569634 0.000000e+00 2311
13 TraesCS3B01G175700 chr7D 85.667 2107 286 13 61 2162 556869546 556867451 0.000000e+00 2204
14 TraesCS3B01G175700 chr7B 100.000 57 0 0 1 57 324532604 324532548 2.930000e-19 106
15 TraesCS3B01G175700 chr6B 100.000 57 0 0 1 57 151194799 151194743 2.930000e-19 106
16 TraesCS3B01G175700 chr6B 93.939 66 2 2 1 66 129377046 129376983 4.910000e-17 99
17 TraesCS3B01G175700 chr2B 100.000 57 0 0 1 57 176455458 176455514 2.930000e-19 106
18 TraesCS3B01G175700 chr2B 94.030 67 2 2 1 65 550314942 550314876 1.370000e-17 100


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 TraesCS3B01G175700 chr3B 177849461 177851622 2161 False 3993 3993 100.000 1 2162 1 chr3B.!!$F1 2161
1 TraesCS3B01G175700 chr1B 117373721 117375821 2100 False 2656 2656 89.509 55 2162 1 chr1B.!!$F1 2107
2 TraesCS3B01G175700 chr1B 65744021 65746059 2038 True 2320 2320 87.207 118 2162 1 chr1B.!!$R1 2044
3 TraesCS3B01G175700 chr2A 691688185 691690286 2101 False 2427 2427 87.541 59 2162 1 chr2A.!!$F1 2103
4 TraesCS3B01G175700 chr5A 689875401 689877505 2104 True 2418 2418 87.453 59 2162 1 chr5A.!!$R1 2103
5 TraesCS3B01G175700 chr2D 131525604 131527679 2075 True 2394 2394 87.494 80 2162 1 chr2D.!!$R1 2082
6 TraesCS3B01G175700 chr4A 533020551 533022661 2110 True 2340 2340 86.774 59 2162 1 chr4A.!!$R1 2103
7 TraesCS3B01G175700 chr6A 408866630 408868713 2083 False 2324 2324 86.807 74 2162 1 chr6A.!!$F1 2088
8 TraesCS3B01G175700 chr6D 224569634 224571724 2090 True 2311 2311 86.654 72 2162 1 chr6D.!!$R1 2090
9 TraesCS3B01G175700 chr7D 556867451 556869546 2095 True 2204 2204 85.667 61 2162 1 chr7D.!!$R1 2101

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
466 469 0.393077 GTACATCCACCATCCCCTCG 59.607 60.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1379 1394 0.394565 GAGTGGTGCACCTCTTCACT 59.605 55.0 34.4 28.36 39.71 3.41 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
22 23 3.367646 AGATCTTGGTGACTCGTAGGA 57.632 47.619 0.00 0.00 0.00 2.94
23 24 3.698289 AGATCTTGGTGACTCGTAGGAA 58.302 45.455 0.00 0.00 0.00 3.36
24 25 4.087182 AGATCTTGGTGACTCGTAGGAAA 58.913 43.478 0.00 0.00 0.00 3.13
25 26 4.527038 AGATCTTGGTGACTCGTAGGAAAA 59.473 41.667 0.00 0.00 0.00 2.29
26 27 4.884668 TCTTGGTGACTCGTAGGAAAAT 57.115 40.909 0.00 0.00 0.00 1.82
27 28 5.223449 TCTTGGTGACTCGTAGGAAAATT 57.777 39.130 0.00 0.00 0.00 1.82
28 29 5.617252 TCTTGGTGACTCGTAGGAAAATTT 58.383 37.500 0.00 0.00 0.00 1.82
29 30 6.059484 TCTTGGTGACTCGTAGGAAAATTTT 58.941 36.000 2.28 2.28 0.00 1.82
30 31 5.682943 TGGTGACTCGTAGGAAAATTTTG 57.317 39.130 8.47 0.00 0.00 2.44
31 32 5.369833 TGGTGACTCGTAGGAAAATTTTGA 58.630 37.500 8.47 0.00 0.00 2.69
32 33 5.823570 TGGTGACTCGTAGGAAAATTTTGAA 59.176 36.000 8.47 0.00 0.00 2.69
33 34 6.488683 TGGTGACTCGTAGGAAAATTTTGAAT 59.511 34.615 8.47 0.00 0.00 2.57
34 35 7.013846 TGGTGACTCGTAGGAAAATTTTGAATT 59.986 33.333 8.47 0.00 0.00 2.17
35 36 7.865889 GGTGACTCGTAGGAAAATTTTGAATTT 59.134 33.333 8.47 0.00 0.00 1.82
36 37 8.902735 GTGACTCGTAGGAAAATTTTGAATTTC 58.097 33.333 8.47 0.00 35.33 2.17
37 38 8.846211 TGACTCGTAGGAAAATTTTGAATTTCT 58.154 29.630 8.47 0.00 36.15 2.52
38 39 9.118236 GACTCGTAGGAAAATTTTGAATTTCTG 57.882 33.333 8.47 0.00 36.15 3.02
39 40 7.595130 ACTCGTAGGAAAATTTTGAATTTCTGC 59.405 33.333 8.47 0.00 36.15 4.26
40 41 7.657336 TCGTAGGAAAATTTTGAATTTCTGCT 58.343 30.769 8.47 0.00 36.15 4.24
41 42 8.788806 TCGTAGGAAAATTTTGAATTTCTGCTA 58.211 29.630 8.47 0.00 36.15 3.49
42 43 9.573133 CGTAGGAAAATTTTGAATTTCTGCTAT 57.427 29.630 8.47 0.00 36.15 2.97
45 46 9.783081 AGGAAAATTTTGAATTTCTGCTATGTT 57.217 25.926 8.47 0.00 36.15 2.71
48 49 8.552083 AAATTTTGAATTTCTGCTATGTTCCC 57.448 30.769 0.00 0.00 0.00 3.97
49 50 5.659440 TTTGAATTTCTGCTATGTTCCCC 57.341 39.130 0.00 0.00 0.00 4.81
50 51 4.314522 TGAATTTCTGCTATGTTCCCCA 57.685 40.909 0.00 0.00 0.00 4.96
51 52 4.671831 TGAATTTCTGCTATGTTCCCCAA 58.328 39.130 0.00 0.00 0.00 4.12
52 53 4.462483 TGAATTTCTGCTATGTTCCCCAAC 59.538 41.667 0.00 0.00 0.00 3.77
53 54 3.517296 TTTCTGCTATGTTCCCCAACA 57.483 42.857 0.00 0.00 46.71 3.33
54 55 2.787473 TCTGCTATGTTCCCCAACAG 57.213 50.000 0.00 0.00 45.85 3.16
55 56 1.985159 TCTGCTATGTTCCCCAACAGT 59.015 47.619 0.00 0.00 45.85 3.55
56 57 2.375174 TCTGCTATGTTCCCCAACAGTT 59.625 45.455 0.00 0.00 45.85 3.16
57 58 3.585289 TCTGCTATGTTCCCCAACAGTTA 59.415 43.478 0.00 0.00 45.85 2.24
96 97 2.124996 CCTCCCTTCCCCCTGTGA 59.875 66.667 0.00 0.00 0.00 3.58
111 112 2.323599 CTGTGATGATCCAGGAGGCTA 58.676 52.381 0.00 0.00 33.74 3.93
134 135 2.111613 CCTAGAGGTCATGGAGGAGGAT 59.888 54.545 0.00 0.00 0.00 3.24
138 139 3.051803 AGAGGTCATGGAGGAGGATGTTA 60.052 47.826 0.00 0.00 0.00 2.41
150 151 1.846439 AGGATGTTATGACTGTGGGGG 59.154 52.381 0.00 0.00 0.00 5.40
173 174 4.373116 GTGCGCCCCTCGTCTTCA 62.373 66.667 4.18 0.00 41.07 3.02
202 203 1.207791 CCTGGGATGGTCTGCTACTT 58.792 55.000 0.00 0.00 0.00 2.24
209 210 0.679505 TGGTCTGCTACTTGCGTTCT 59.320 50.000 0.00 0.00 46.63 3.01
274 277 2.656069 GCCTCCGCACTTGGACCTA 61.656 63.158 0.00 0.00 33.48 3.08
360 363 1.290324 GTCAGAGTGCGAGGCTCAA 59.710 57.895 15.95 0.00 35.55 3.02
364 367 1.301716 GAGTGCGAGGCTCAACCAA 60.302 57.895 15.95 0.00 43.14 3.67
387 390 2.365105 GGTCCTCCCGGATGGTCA 60.365 66.667 0.73 0.00 42.43 4.02
413 416 3.154473 CGATCCCGGAGAAGGCCA 61.154 66.667 5.01 0.00 0.00 5.36
451 454 0.601558 GCGACTTGTCCTCAGGTACA 59.398 55.000 0.00 0.00 34.06 2.90
466 469 0.393077 GTACATCCACCATCCCCTCG 59.607 60.000 0.00 0.00 0.00 4.63
504 507 0.944386 TCTCGGTTTTCTGTGCTTGC 59.056 50.000 0.00 0.00 0.00 4.01
517 520 3.028366 GCTTGCTTCCGCTCCGTTC 62.028 63.158 0.00 0.00 36.97 3.95
575 578 2.513259 TTTCGTGGCGAGAAGGGGT 61.513 57.895 0.00 0.00 37.14 4.95
618 621 0.613012 ATTTGCACCAAGGAGAGGCC 60.613 55.000 0.00 0.00 0.00 5.19
667 670 2.899838 GCTGCACGTGGTGAACCA 60.900 61.111 18.88 4.33 45.30 3.67
766 769 2.548547 GCCCCTTGAAGTTCCCCCT 61.549 63.158 0.00 0.00 0.00 4.79
831 844 4.003648 CCACTGAACACCAAATAGAGGTC 58.996 47.826 0.00 0.00 37.23 3.85
863 876 2.370445 CCAGGTCCGCTTCCCTCAT 61.370 63.158 0.00 0.00 0.00 2.90
931 944 2.616458 GGTGAAGGCATCCCCCTGT 61.616 63.158 0.00 0.00 34.80 4.00
935 948 3.908712 AAGGCATCCCCCTGTCCCA 62.909 63.158 0.00 0.00 34.80 4.37
992 1005 2.409570 GGCCTAGGGATTCCACTAAGT 58.590 52.381 11.72 0.00 34.83 2.24
1034 1047 3.161866 GTTGGAACATTAGGGGCTTTGA 58.838 45.455 0.00 0.00 39.30 2.69
1045 1058 1.073897 GGCTTTGACCTCACTGGCT 59.926 57.895 0.00 0.00 40.22 4.75
1093 1106 5.478407 TGCGACAAGAAGAGATTGACATTA 58.522 37.500 0.00 0.00 0.00 1.90
1117 1130 2.159043 GGACTTCAGGAGATGATTCGCA 60.159 50.000 0.00 0.00 37.89 5.10
1279 1293 2.235898 GAGTTCTTCCTGAGCATGTCCT 59.764 50.000 0.00 0.00 0.00 3.85
1285 1299 2.820178 TCCTGAGCATGTCCTTCACTA 58.180 47.619 0.00 0.00 0.00 2.74
1308 1323 1.739562 CGAGTTCACCTCAGCTGGC 60.740 63.158 15.13 0.00 40.48 4.85
1379 1394 3.823873 TCCTTGCCGAGCTGAAAAATAAA 59.176 39.130 0.00 0.00 0.00 1.40
1383 1398 3.818210 TGCCGAGCTGAAAAATAAAGTGA 59.182 39.130 0.00 0.00 0.00 3.41
1400 1415 0.764369 TGAAGAGGTGCACCACTCCT 60.764 55.000 36.39 21.74 45.09 3.69
1477 1493 0.744414 AATGTTGATCGGGTCCGCAG 60.744 55.000 4.27 0.00 39.59 5.18
1491 1507 0.739462 CCGCAGGCGTCTATTCAACA 60.739 55.000 13.07 0.00 46.14 3.33
1523 1541 1.016130 ACCTTGCGCTTCGTGAGATG 61.016 55.000 9.73 0.00 41.60 2.90
1594 1612 1.644786 CGGAGTGTTTTGGATCGGGC 61.645 60.000 0.00 0.00 0.00 6.13
1651 1669 0.909610 TTCTCCCTCAAGGCGGTCAT 60.910 55.000 0.00 0.00 34.51 3.06
1782 1801 4.452114 TCTTTGAGTTGGTTCGTGATCATG 59.548 41.667 8.74 8.74 0.00 3.07
1809 1828 4.003788 CTGTCGCGTCCCCACCTT 62.004 66.667 5.77 0.00 0.00 3.50
1826 1845 4.441356 CCACCTTGTGTGTTTTGTGCTATT 60.441 41.667 0.00 0.00 43.85 1.73
1894 1914 4.280019 GGGGGCGAACCTTGGTGT 62.280 66.667 0.00 0.00 40.03 4.16
1993 2013 4.279671 GTCTCGTGATGACTGGATTAGGAT 59.720 45.833 0.00 0.00 0.00 3.24
2033 2053 4.081697 TCGCTCATGGACATTTACAAGAGA 60.082 41.667 0.45 0.00 35.16 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.050126 TCCTACGAGTCACCAAGATCTAT 57.950 43.478 0.00 0.00 0.00 1.98
2 3 3.367646 TCCTACGAGTCACCAAGATCT 57.632 47.619 0.00 0.00 0.00 2.75
3 4 4.451629 TTTCCTACGAGTCACCAAGATC 57.548 45.455 0.00 0.00 0.00 2.75
4 5 4.884668 TTTTCCTACGAGTCACCAAGAT 57.115 40.909 0.00 0.00 0.00 2.40
5 6 4.884668 ATTTTCCTACGAGTCACCAAGA 57.115 40.909 0.00 0.00 0.00 3.02
6 7 5.941948 AAATTTTCCTACGAGTCACCAAG 57.058 39.130 0.00 0.00 0.00 3.61
7 8 5.823570 TCAAAATTTTCCTACGAGTCACCAA 59.176 36.000 0.00 0.00 0.00 3.67
8 9 5.369833 TCAAAATTTTCCTACGAGTCACCA 58.630 37.500 0.00 0.00 0.00 4.17
9 10 5.934935 TCAAAATTTTCCTACGAGTCACC 57.065 39.130 0.00 0.00 0.00 4.02
10 11 8.797266 AAATTCAAAATTTTCCTACGAGTCAC 57.203 30.769 0.00 0.00 0.00 3.67
11 12 8.846211 AGAAATTCAAAATTTTCCTACGAGTCA 58.154 29.630 0.00 0.00 33.30 3.41
12 13 9.118236 CAGAAATTCAAAATTTTCCTACGAGTC 57.882 33.333 0.00 0.00 33.30 3.36
13 14 7.595130 GCAGAAATTCAAAATTTTCCTACGAGT 59.405 33.333 0.00 0.00 33.30 4.18
14 15 7.809806 AGCAGAAATTCAAAATTTTCCTACGAG 59.190 33.333 0.00 0.00 33.30 4.18
15 16 7.657336 AGCAGAAATTCAAAATTTTCCTACGA 58.343 30.769 0.00 0.00 33.30 3.43
16 17 7.873739 AGCAGAAATTCAAAATTTTCCTACG 57.126 32.000 0.00 0.00 33.30 3.51
19 20 9.783081 AACATAGCAGAAATTCAAAATTTTCCT 57.217 25.926 0.00 0.86 33.30 3.36
22 23 9.002600 GGGAACATAGCAGAAATTCAAAATTTT 57.997 29.630 0.00 0.00 0.00 1.82
23 24 7.607607 GGGGAACATAGCAGAAATTCAAAATTT 59.392 33.333 0.00 0.00 0.00 1.82
24 25 7.105588 GGGGAACATAGCAGAAATTCAAAATT 58.894 34.615 0.00 0.00 0.00 1.82
25 26 6.213195 TGGGGAACATAGCAGAAATTCAAAAT 59.787 34.615 0.00 0.00 0.00 1.82
26 27 5.541868 TGGGGAACATAGCAGAAATTCAAAA 59.458 36.000 0.00 0.00 0.00 2.44
27 28 5.083122 TGGGGAACATAGCAGAAATTCAAA 58.917 37.500 0.00 0.00 0.00 2.69
28 29 4.671831 TGGGGAACATAGCAGAAATTCAA 58.328 39.130 0.00 0.00 0.00 2.69
29 30 4.314522 TGGGGAACATAGCAGAAATTCA 57.685 40.909 0.00 0.00 0.00 2.57
30 31 4.462483 TGTTGGGGAACATAGCAGAAATTC 59.538 41.667 0.00 0.00 0.00 2.17
31 32 4.415596 TGTTGGGGAACATAGCAGAAATT 58.584 39.130 0.00 0.00 0.00 1.82
32 33 4.019174 CTGTTGGGGAACATAGCAGAAAT 58.981 43.478 0.00 0.00 31.47 2.17
33 34 3.181434 ACTGTTGGGGAACATAGCAGAAA 60.181 43.478 0.00 0.00 32.05 2.52
34 35 2.375174 ACTGTTGGGGAACATAGCAGAA 59.625 45.455 0.00 0.00 32.05 3.02
35 36 1.985159 ACTGTTGGGGAACATAGCAGA 59.015 47.619 0.00 0.00 32.05 4.26
36 37 2.496899 ACTGTTGGGGAACATAGCAG 57.503 50.000 0.00 0.00 33.10 4.24
37 38 2.969821 AACTGTTGGGGAACATAGCA 57.030 45.000 0.00 0.00 31.47 3.49
38 39 3.279434 CCTAACTGTTGGGGAACATAGC 58.721 50.000 14.56 0.00 31.47 2.97
47 48 1.137594 TCCCACCCCTAACTGTTGGG 61.138 60.000 15.33 15.33 45.34 4.12
48 49 0.037734 GTCCCACCCCTAACTGTTGG 59.962 60.000 2.69 0.00 0.00 3.77
49 50 1.064825 AGTCCCACCCCTAACTGTTG 58.935 55.000 2.69 0.00 0.00 3.33
50 51 1.064825 CAGTCCCACCCCTAACTGTT 58.935 55.000 0.00 0.00 35.51 3.16
51 52 0.104620 ACAGTCCCACCCCTAACTGT 60.105 55.000 1.36 1.36 45.55 3.55
52 53 0.324943 CACAGTCCCACCCCTAACTG 59.675 60.000 0.00 0.00 43.69 3.16
53 54 0.840722 CCACAGTCCCACCCCTAACT 60.841 60.000 0.00 0.00 0.00 2.24
54 55 1.683441 CCACAGTCCCACCCCTAAC 59.317 63.158 0.00 0.00 0.00 2.34
55 56 2.228480 GCCACAGTCCCACCCCTAA 61.228 63.158 0.00 0.00 0.00 2.69
56 57 2.609610 GCCACAGTCCCACCCCTA 60.610 66.667 0.00 0.00 0.00 3.53
96 97 2.503869 AGGTTAGCCTCCTGGATCAT 57.496 50.000 0.00 0.00 42.67 2.45
123 124 4.102210 CACAGTCATAACATCCTCCTCCAT 59.898 45.833 0.00 0.00 0.00 3.41
134 135 0.695924 CCACCCCCACAGTCATAACA 59.304 55.000 0.00 0.00 0.00 2.41
138 139 1.925455 CCTCCACCCCCACAGTCAT 60.925 63.158 0.00 0.00 0.00 3.06
264 267 1.913762 ACCGCTGCTAGGTCCAAGT 60.914 57.895 0.00 0.00 37.44 3.16
274 277 2.352032 GGTAGGAGTCACCGCTGCT 61.352 63.158 0.00 0.00 44.74 4.24
360 363 4.171186 GGAGGACCCAGGATTGGT 57.829 61.111 0.00 0.00 43.40 3.67
387 390 3.224324 CCGGGATCGTCGGGACAT 61.224 66.667 15.67 0.00 43.45 3.06
413 416 1.680522 CGAGTAGCTGCCCTCATGGT 61.681 60.000 14.78 0.00 36.04 3.55
451 454 2.702771 TCCGAGGGGATGGTGGAT 59.297 61.111 0.00 0.00 37.43 3.41
466 469 4.202070 CGAGAACCAGAACTAGAAGGATCC 60.202 50.000 2.48 2.48 0.00 3.36
504 507 0.457851 ATGAGAGAACGGAGCGGAAG 59.542 55.000 0.00 0.00 0.00 3.46
575 578 4.718774 AGCAGAAATCTACTCAAGGATGGA 59.281 41.667 0.00 0.00 0.00 3.41
618 621 2.751436 CAGCCAACACCCCATCGG 60.751 66.667 0.00 0.00 37.81 4.18
766 769 4.434483 TCGCAGAGCCCTCACTAA 57.566 55.556 0.00 0.00 0.00 2.24
831 844 1.550976 GACCTGGAACTAGACCCACAG 59.449 57.143 0.00 0.00 0.00 3.66
863 876 2.656069 GCAACGGAGGCCTCTGGTA 61.656 63.158 38.61 0.00 40.22 3.25
888 901 0.258484 TCCATGTTGCCCCATGTAGG 59.742 55.000 10.67 0.00 40.50 3.18
889 902 1.958579 CATCCATGTTGCCCCATGTAG 59.041 52.381 10.67 0.00 40.50 2.74
890 903 1.287442 ACATCCATGTTGCCCCATGTA 59.713 47.619 10.67 0.00 40.50 2.29
893 906 0.397535 GGACATCCATGTTGCCCCAT 60.398 55.000 0.00 0.00 41.95 4.00
894 907 1.000233 GGACATCCATGTTGCCCCA 60.000 57.895 0.00 0.00 41.95 4.96
908 921 2.668632 GGATGCCTTCACCGGACA 59.331 61.111 9.46 0.00 0.00 4.02
935 948 0.107456 CTAGCCTGCCCATCAATCGT 59.893 55.000 0.00 0.00 0.00 3.73
992 1005 8.865090 TCCAACAAAGGAGCTTCATTTAATAAA 58.135 29.630 0.00 0.00 28.50 1.40
1062 1075 5.392767 TCTCTTCTTGTCGCAAATACTCT 57.607 39.130 0.00 0.00 0.00 3.24
1093 1106 3.070734 CGAATCATCTCCTGAAGTCCCAT 59.929 47.826 0.00 0.00 37.44 4.00
1117 1130 5.363939 GAGCTCATGCATACTAAAGTCCTT 58.636 41.667 9.40 0.00 42.74 3.36
1183 1197 1.486211 CCTCCAGATTGACCCGTAGT 58.514 55.000 0.00 0.00 0.00 2.73
1279 1293 2.620115 AGGTGAACTCGTCGTTAGTGAA 59.380 45.455 0.00 0.00 35.56 3.18
1308 1323 5.256474 AGGACCATAGACAAAAATCACCTG 58.744 41.667 0.00 0.00 0.00 4.00
1379 1394 0.394565 GAGTGGTGCACCTCTTCACT 59.605 55.000 34.40 28.36 39.71 3.41
1383 1398 1.556911 CATAGGAGTGGTGCACCTCTT 59.443 52.381 34.40 24.37 39.71 2.85
1400 1415 4.743125 TCCCCGGCCACCACCATA 62.743 66.667 2.24 0.00 0.00 2.74
1477 1493 1.804151 TGCAGTTGTTGAATAGACGCC 59.196 47.619 0.00 0.00 0.00 5.68
1491 1507 1.959085 CAAGGTCCGCAATGCAGTT 59.041 52.632 5.91 0.00 0.00 3.16
1523 1541 2.125106 CTAGCCCCAACGTGAGCC 60.125 66.667 0.00 0.00 0.00 4.70
1532 1550 0.548926 TCCATGTGAACCTAGCCCCA 60.549 55.000 0.00 0.00 0.00 4.96
1571 1589 2.159014 CCGATCCAAAACACTCCGGATA 60.159 50.000 3.57 0.00 38.38 2.59
1594 1612 0.518636 CCACTGAGCCGACACAAATG 59.481 55.000 0.00 0.00 0.00 2.32
1633 1651 0.909610 AATGACCGCCTTGAGGGAGA 60.910 55.000 0.00 0.00 37.02 3.71
1782 1801 4.577246 CGCGACAGCCTCTAGCCC 62.577 72.222 0.00 0.00 45.47 5.19
1809 1828 5.299028 AGACATCAATAGCACAAAACACACA 59.701 36.000 0.00 0.00 0.00 3.72
1975 1995 7.777095 GGAGTATATCCTAATCCAGTCATCAC 58.223 42.308 0.00 0.00 45.64 3.06
2033 2053 1.745141 CGCTGCCAAAATAGCTCCTCT 60.745 52.381 0.00 0.00 37.78 3.69
2075 2095 2.378547 AGTGTTTGCATCCCCCTTAAGA 59.621 45.455 3.36 0.00 0.00 2.10
2118 2139 0.947244 CATTTCCACCTGCGGCTATC 59.053 55.000 0.00 0.00 0.00 2.08


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

AutoCloner maintained by Alex Coulton.