Multiple sequence alignment - TraesCS5A01G180700

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 TraesCS5A01G180700 chr5A 100.000 2555 0 0 1 2555 379351559 379354113 0.000000e+00 4719
1 TraesCS5A01G180700 chr5A 87.611 113 10 3 1 110 295073338 295073227 7.420000e-26 128
2 TraesCS5A01G180700 chr5B 88.090 2544 147 61 105 2555 326570452 326572932 0.000000e+00 2876
3 TraesCS5A01G180700 chr5D 87.833 1726 101 42 105 1775 287439234 287440905 0.000000e+00 1923
4 TraesCS5A01G180700 chr5D 93.797 790 35 7 1777 2555 287441025 287441811 0.000000e+00 1175
5 TraesCS5A01G180700 chr3A 90.909 110 8 2 1 108 181108066 181107957 2.050000e-31 147
6 TraesCS5A01G180700 chr1D 90.909 110 7 2 1 107 199833840 199833949 7.370000e-31 145
7 TraesCS5A01G180700 chr4B 88.991 109 9 2 1 107 659399716 659399823 5.740000e-27 132
8 TraesCS5A01G180700 chr4B 88.889 108 9 2 1 106 659372337 659372443 2.060000e-26 130
9 TraesCS5A01G180700 chr1A 88.889 108 11 1 1 107 252279825 252279932 5.740000e-27 132
10 TraesCS5A01G180700 chr3D 87.719 114 11 3 1 111 559601028 559600915 2.060000e-26 130
11 TraesCS5A01G180700 chr3D 88.182 110 10 2 1 108 149766795 149766903 7.420000e-26 128
12 TraesCS5A01G180700 chr2D 87.500 112 13 1 1 111 633225216 633225327 7.420000e-26 128
13 TraesCS5A01G180700 chrUn 87.255 102 6 2 893 988 103504829 103504929 2.690000e-20 110


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 TraesCS5A01G180700 chr5A 379351559 379354113 2554 False 4719 4719 100.000 1 2555 1 chr5A.!!$F1 2554
1 TraesCS5A01G180700 chr5B 326570452 326572932 2480 False 2876 2876 88.090 105 2555 1 chr5B.!!$F1 2450
2 TraesCS5A01G180700 chr5D 287439234 287441811 2577 False 1549 1923 90.815 105 2555 2 chr5D.!!$F1 2450

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
95 96 0.043940 AGAGGCAGGGTCATCCTTCT 59.956 55.0 0.00 0.0 45.47 2.85 F
505 509 0.670706 TAGGCTGCTGCTATGACTCG 59.329 55.0 15.64 0.0 39.59 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1416 1475 0.740868 CGTTGTCGATGCCCATGAGT 60.741 55.0 0.00 0.0 39.71 3.41 R
2344 2552 2.492484 GAGAGACTTTAGGCCTCGACAA 59.508 50.0 9.68 0.0 32.52 3.18 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
36 37 9.787435 TGATGTATTACTTTGTAAGGTCTTTGT 57.213 29.630 0.00 0.00 0.00 2.83
38 39 9.787435 ATGTATTACTTTGTAAGGTCTTTGTGA 57.213 29.630 0.00 0.00 0.00 3.58
39 40 9.616156 TGTATTACTTTGTAAGGTCTTTGTGAA 57.384 29.630 0.00 0.00 0.00 3.18
58 59 7.979115 TGTGAATATTTAATAAAACGGCAGC 57.021 32.000 0.00 0.00 0.00 5.25
59 60 7.539436 TGTGAATATTTAATAAAACGGCAGCA 58.461 30.769 0.00 0.00 0.00 4.41
60 61 8.194104 TGTGAATATTTAATAAAACGGCAGCAT 58.806 29.630 0.00 0.00 0.00 3.79
61 62 8.479280 GTGAATATTTAATAAAACGGCAGCATG 58.521 33.333 0.00 0.00 40.87 4.06
72 73 3.057548 CAGCATGCACCGCCAAGA 61.058 61.111 21.98 0.00 0.00 3.02
73 74 2.044650 AGCATGCACCGCCAAGAT 60.045 55.556 21.98 0.00 0.00 2.40
74 75 2.103538 GCATGCACCGCCAAGATG 59.896 61.111 14.21 0.00 0.00 2.90
75 76 2.103538 CATGCACCGCCAAGATGC 59.896 61.111 0.00 0.00 40.76 3.91
77 78 3.057548 TGCACCGCCAAGATGCAG 61.058 61.111 0.00 0.00 46.39 4.41
78 79 2.747460 GCACCGCCAAGATGCAGA 60.747 61.111 0.00 0.00 39.86 4.26
79 80 2.758089 GCACCGCCAAGATGCAGAG 61.758 63.158 0.00 0.00 39.86 3.35
80 81 2.110967 CACCGCCAAGATGCAGAGG 61.111 63.158 0.00 0.00 0.00 3.69
81 82 3.207669 CCGCCAAGATGCAGAGGC 61.208 66.667 10.45 10.45 43.61 4.70
91 92 2.191641 GCAGAGGCAGGGTCATCC 59.808 66.667 0.00 0.00 40.72 3.51
93 94 1.919600 GCAGAGGCAGGGTCATCCTT 61.920 60.000 0.00 0.00 45.47 3.36
94 95 0.179936 CAGAGGCAGGGTCATCCTTC 59.820 60.000 0.00 0.00 45.47 3.46
95 96 0.043940 AGAGGCAGGGTCATCCTTCT 59.956 55.000 0.00 0.00 45.47 2.85
96 97 0.915364 GAGGCAGGGTCATCCTTCTT 59.085 55.000 0.00 0.00 45.47 2.52
97 98 1.283321 GAGGCAGGGTCATCCTTCTTT 59.717 52.381 0.00 0.00 45.47 2.52
98 99 1.713078 AGGCAGGGTCATCCTTCTTTT 59.287 47.619 0.00 0.00 45.47 2.27
99 100 2.919602 AGGCAGGGTCATCCTTCTTTTA 59.080 45.455 0.00 0.00 45.47 1.52
100 101 3.333680 AGGCAGGGTCATCCTTCTTTTAA 59.666 43.478 0.00 0.00 45.47 1.52
101 102 4.086457 GGCAGGGTCATCCTTCTTTTAAA 58.914 43.478 0.00 0.00 45.47 1.52
102 103 4.526650 GGCAGGGTCATCCTTCTTTTAAAA 59.473 41.667 0.00 0.00 45.47 1.52
103 104 5.011635 GGCAGGGTCATCCTTCTTTTAAAAA 59.988 40.000 1.66 0.00 45.47 1.94
183 184 3.694926 AGATTCTGCAGCTTTAAGCCTT 58.305 40.909 13.84 0.00 43.77 4.35
229 230 6.208644 TGAGCAACAGAAAAGCATTTAGTTC 58.791 36.000 2.79 0.00 37.28 3.01
251 252 8.842280 AGTTCTCATGTATTACAAAAACGGAAA 58.158 29.630 0.00 0.00 0.00 3.13
252 253 8.898792 GTTCTCATGTATTACAAAAACGGAAAC 58.101 33.333 0.00 0.00 0.00 2.78
257 258 7.988904 TGTATTACAAAAACGGAAACAAAGG 57.011 32.000 0.00 0.00 0.00 3.11
263 264 2.812358 AACGGAAACAAAGGAATGCC 57.188 45.000 0.00 0.00 0.00 4.40
288 289 6.774656 CAGAATTAGCCTGGGATTGTTCTTAT 59.225 38.462 0.00 0.00 0.00 1.73
289 290 7.939039 CAGAATTAGCCTGGGATTGTTCTTATA 59.061 37.037 0.00 0.00 0.00 0.98
290 291 8.673251 AGAATTAGCCTGGGATTGTTCTTATAT 58.327 33.333 0.00 0.00 0.00 0.86
318 319 4.096382 GGCCATATCATTTGAAGTCGTGTT 59.904 41.667 0.00 0.00 0.00 3.32
324 325 5.878332 TCATTTGAAGTCGTGTTATGCAT 57.122 34.783 3.79 3.79 0.00 3.96
326 327 7.552458 TCATTTGAAGTCGTGTTATGCATAT 57.448 32.000 7.36 0.00 0.00 1.78
327 328 8.655651 TCATTTGAAGTCGTGTTATGCATATA 57.344 30.769 7.36 0.00 0.00 0.86
328 329 8.547894 TCATTTGAAGTCGTGTTATGCATATAC 58.452 33.333 7.36 9.11 0.00 1.47
329 330 8.551205 CATTTGAAGTCGTGTTATGCATATACT 58.449 33.333 7.36 4.14 0.00 2.12
330 331 7.463469 TTGAAGTCGTGTTATGCATATACTG 57.537 36.000 7.36 7.06 0.00 2.74
336 337 8.141909 AGTCGTGTTATGCATATACTGTATGTT 58.858 33.333 7.36 0.00 32.00 2.71
339 340 7.383843 CGTGTTATGCATATACTGTATGTTCCA 59.616 37.037 7.36 4.30 32.00 3.53
350 351 6.045072 ACTGTATGTTCCAAGAAATACCGA 57.955 37.500 0.00 0.00 0.00 4.69
369 371 3.434637 CGACAAAAACTGTGGTTGAAGG 58.565 45.455 9.84 0.00 38.84 3.46
396 398 6.836242 TCTCTAGTTCTCAGAGATGCAGATA 58.164 40.000 0.00 0.00 42.79 1.98
404 406 6.286758 TCTCAGAGATGCAGATAAACATTCC 58.713 40.000 0.00 0.00 0.00 3.01
415 417 6.701400 GCAGATAAACATTCCAACAACAGTTT 59.299 34.615 0.00 0.00 34.11 2.66
422 424 2.557317 TCCAACAACAGTTTCGGACTC 58.443 47.619 0.00 0.00 36.10 3.36
423 425 2.093394 TCCAACAACAGTTTCGGACTCA 60.093 45.455 0.00 0.00 36.10 3.41
447 449 1.967319 ACCGCTGCTTTCTGAAGAAA 58.033 45.000 5.43 5.43 41.29 2.52
448 450 2.297701 ACCGCTGCTTTCTGAAGAAAA 58.702 42.857 6.92 0.00 42.72 2.29
449 451 2.291741 ACCGCTGCTTTCTGAAGAAAAG 59.708 45.455 6.92 4.07 42.72 2.27
450 452 2.549754 CCGCTGCTTTCTGAAGAAAAGA 59.450 45.455 6.92 0.00 42.72 2.52
451 453 3.003689 CCGCTGCTTTCTGAAGAAAAGAA 59.996 43.478 6.92 0.00 42.72 2.52
452 454 4.217497 CGCTGCTTTCTGAAGAAAAGAAG 58.783 43.478 6.92 6.46 42.72 2.85
453 455 4.024556 CGCTGCTTTCTGAAGAAAAGAAGA 60.025 41.667 7.61 0.00 42.72 2.87
505 509 0.670706 TAGGCTGCTGCTATGACTCG 59.329 55.000 15.64 0.00 39.59 4.18
507 511 2.243264 GCTGCTGCTATGACTCGGC 61.243 63.158 8.53 0.00 36.03 5.54
574 579 6.624352 TGTTCTCCAAAACAATCTTCAGAG 57.376 37.500 0.00 0.00 36.25 3.35
636 662 3.441101 TGTACTATGACTCAGGCCAAGT 58.559 45.455 5.01 8.24 0.00 3.16
652 678 3.796717 GCCAAGTAACTGTCACTTTTTGC 59.203 43.478 0.00 0.00 33.99 3.68
728 754 5.177326 AGCTTGTTTCAATCACTGCAAAAA 58.823 33.333 0.00 0.00 0.00 1.94
742 768 3.719924 TGCAAAAATTCTGCAACTCAGG 58.280 40.909 11.63 0.00 46.47 3.86
743 769 3.132646 TGCAAAAATTCTGCAACTCAGGT 59.867 39.130 11.63 0.00 46.47 4.00
744 770 3.737774 GCAAAAATTCTGCAACTCAGGTC 59.262 43.478 7.43 0.00 43.06 3.85
745 771 4.737352 GCAAAAATTCTGCAACTCAGGTCA 60.737 41.667 7.43 0.00 43.06 4.02
746 772 5.350633 CAAAAATTCTGCAACTCAGGTCAA 58.649 37.500 0.00 0.00 43.06 3.18
747 773 4.574599 AAATTCTGCAACTCAGGTCAAC 57.425 40.909 0.00 0.00 43.06 3.18
802 856 6.128445 GCATGATCAACCTATAAATCACTCCG 60.128 42.308 0.00 0.00 31.41 4.63
806 860 5.902681 TCAACCTATAAATCACTCCGACAG 58.097 41.667 0.00 0.00 0.00 3.51
932 988 2.141517 CAGATCATCATCCGCTCCAAC 58.858 52.381 0.00 0.00 0.00 3.77
966 1025 0.693049 AGCAGTCAGTAACCAAGGGG 59.307 55.000 0.00 0.00 41.29 4.79
1060 1119 3.388703 CTCCTCCTCCTGCTGCTGC 62.389 68.421 8.89 8.89 40.20 5.25
1082 1141 3.461773 CCTCATGCCGGACGAGGT 61.462 66.667 20.52 0.00 41.26 3.85
1203 1262 4.126390 CTGCTGCTCAACGCGTCG 62.126 66.667 14.44 0.00 43.27 5.12
1206 1265 3.470567 CTGCTCAACGCGTCGTCC 61.471 66.667 14.44 2.23 39.99 4.79
1344 1403 4.415150 CAGCACGGGGGCAGACAT 62.415 66.667 0.00 0.00 35.83 3.06
1348 1407 4.082523 ACGGGGGCAGACATGTCG 62.083 66.667 19.85 15.27 34.09 4.35
1710 1784 5.245075 CCCTCTCATGATTAGTAGGGAACTC 59.755 48.000 16.54 0.00 45.53 3.01
1711 1785 5.245075 CCTCTCATGATTAGTAGGGAACTCC 59.755 48.000 0.00 0.00 43.67 3.85
1726 1800 8.931568 GTAGGGAACTCCTTTTTCCACTATATA 58.068 37.037 3.64 0.00 45.47 0.86
1727 1801 8.582891 AGGGAACTCCTTTTTCCACTATATAT 57.417 34.615 3.64 0.00 45.47 0.86
1818 2012 3.957497 TCTGTTTGGTTTGGCAGTACAAT 59.043 39.130 0.00 0.00 0.00 2.71
1823 2017 7.103641 TGTTTGGTTTGGCAGTACAATTTTTA 58.896 30.769 0.00 0.00 0.00 1.52
1885 2079 4.937201 GGGCAATGACCCCTTTTTATAG 57.063 45.455 0.00 0.00 45.00 1.31
1889 2083 6.099701 GGGCAATGACCCCTTTTTATAGAAAT 59.900 38.462 0.00 0.00 45.00 2.17
1891 2085 8.360390 GGCAATGACCCCTTTTTATAGAAATAG 58.640 37.037 0.00 0.00 0.00 1.73
1892 2086 8.914011 GCAATGACCCCTTTTTATAGAAATAGT 58.086 33.333 0.66 0.00 0.00 2.12
1985 2185 1.606668 CAAACGCAGCCTTAACTTGGA 59.393 47.619 0.00 0.00 0.00 3.53
1986 2186 1.975660 AACGCAGCCTTAACTTGGAA 58.024 45.000 0.00 0.00 0.00 3.53
1997 2197 6.675303 AGCCTTAACTTGGAACCCTTAGTATA 59.325 38.462 0.00 0.00 0.00 1.47
2113 2313 5.888691 ACACATTATATTCGCACAAACCA 57.111 34.783 0.00 0.00 0.00 3.67
2215 2422 7.814587 AGATGATCATGTACATATTACACGGTG 59.185 37.037 14.30 6.58 0.00 4.94
2320 2528 2.810274 CACAAACTCACCCTGACATCTG 59.190 50.000 0.00 0.00 0.00 2.90
2323 2531 1.270907 ACTCACCCTGACATCTGTCC 58.729 55.000 7.81 0.00 44.15 4.02
2344 2552 5.048713 GTCCGAAAGATGAAAACCTCAATGT 60.049 40.000 0.00 0.00 37.67 2.71
2348 2556 6.360681 CGAAAGATGAAAACCTCAATGTTGTC 59.639 38.462 0.00 0.00 37.67 3.18
2361 2570 2.450609 TGTTGTCGAGGCCTAAAGTC 57.549 50.000 4.42 0.00 0.00 3.01
2416 2625 5.240844 CGAAACCTTCCCAATTAAGTTCTGT 59.759 40.000 0.00 0.00 0.00 3.41
2540 2749 2.634815 ACATATCTGCCAGCCTTGAG 57.365 50.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.787435 ACAAAGACCTTACAAAGTAATACATCA 57.213 29.630 0.00 0.00 0.00 3.07
12 13 9.787435 TCACAAAGACCTTACAAAGTAATACAT 57.213 29.630 0.00 0.00 0.00 2.29
13 14 9.616156 TTCACAAAGACCTTACAAAGTAATACA 57.384 29.630 0.00 0.00 0.00 2.29
32 33 8.865001 GCTGCCGTTTTATTAAATATTCACAAA 58.135 29.630 0.00 0.00 0.00 2.83
33 34 8.029522 TGCTGCCGTTTTATTAAATATTCACAA 58.970 29.630 0.00 0.00 0.00 3.33
34 35 7.539436 TGCTGCCGTTTTATTAAATATTCACA 58.461 30.769 0.00 0.00 0.00 3.58
35 36 7.979115 TGCTGCCGTTTTATTAAATATTCAC 57.021 32.000 0.00 0.00 0.00 3.18
36 37 7.168972 GCATGCTGCCGTTTTATTAAATATTCA 59.831 33.333 11.37 0.00 37.42 2.57
37 38 7.168972 TGCATGCTGCCGTTTTATTAAATATTC 59.831 33.333 20.33 0.00 44.23 1.75
38 39 6.983307 TGCATGCTGCCGTTTTATTAAATATT 59.017 30.769 20.33 0.00 44.23 1.28
39 40 6.420604 GTGCATGCTGCCGTTTTATTAAATAT 59.579 34.615 20.33 0.00 44.23 1.28
40 41 5.746245 GTGCATGCTGCCGTTTTATTAAATA 59.254 36.000 20.33 0.00 44.23 1.40
41 42 4.566360 GTGCATGCTGCCGTTTTATTAAAT 59.434 37.500 20.33 0.00 44.23 1.40
42 43 3.923461 GTGCATGCTGCCGTTTTATTAAA 59.077 39.130 20.33 0.00 44.23 1.52
43 44 3.506810 GTGCATGCTGCCGTTTTATTAA 58.493 40.909 20.33 0.00 44.23 1.40
44 45 2.159310 GGTGCATGCTGCCGTTTTATTA 60.159 45.455 20.33 0.00 44.23 0.98
45 46 1.404047 GGTGCATGCTGCCGTTTTATT 60.404 47.619 20.33 0.00 44.23 1.40
46 47 0.173255 GGTGCATGCTGCCGTTTTAT 59.827 50.000 20.33 0.00 44.23 1.40
47 48 1.583986 GGTGCATGCTGCCGTTTTA 59.416 52.632 20.33 0.00 44.23 1.52
48 49 2.339712 GGTGCATGCTGCCGTTTT 59.660 55.556 20.33 0.00 44.23 2.43
49 50 4.041917 CGGTGCATGCTGCCGTTT 62.042 61.111 31.62 0.00 44.23 3.60
54 55 4.789075 CTTGGCGGTGCATGCTGC 62.789 66.667 20.33 18.93 45.29 5.25
55 56 2.412323 ATCTTGGCGGTGCATGCTG 61.412 57.895 20.33 9.93 0.00 4.41
56 57 2.044650 ATCTTGGCGGTGCATGCT 60.045 55.556 20.33 0.00 0.00 3.79
57 58 2.103538 CATCTTGGCGGTGCATGC 59.896 61.111 11.82 11.82 0.00 4.06
58 59 2.103538 GCATCTTGGCGGTGCATG 59.896 61.111 0.00 0.00 38.68 4.06
59 60 2.361483 TGCATCTTGGCGGTGCAT 60.361 55.556 0.00 0.00 43.30 3.96
60 61 3.057548 CTGCATCTTGGCGGTGCA 61.058 61.111 0.44 0.44 45.69 4.57
61 62 2.747460 TCTGCATCTTGGCGGTGC 60.747 61.111 0.00 0.00 41.03 5.01
62 63 2.110967 CCTCTGCATCTTGGCGGTG 61.111 63.158 0.00 0.00 41.03 4.94
63 64 2.270205 CCTCTGCATCTTGGCGGT 59.730 61.111 0.00 0.00 41.03 5.68
64 65 3.207669 GCCTCTGCATCTTGGCGG 61.208 66.667 0.00 0.00 41.61 6.13
74 75 2.191641 GGATGACCCTGCCTCTGC 59.808 66.667 0.00 0.00 38.26 4.26
75 76 4.063335 AGGATGACCCTGCCTCTG 57.937 61.111 0.00 0.00 45.61 3.35
102 103 7.123247 CACCTCCTCCTGAATTCATATGTTTTT 59.877 37.037 8.96 0.00 0.00 1.94
103 104 6.604795 CACCTCCTCCTGAATTCATATGTTTT 59.395 38.462 8.96 0.00 0.00 2.43
113 114 2.800250 CAAAGCACCTCCTCCTGAATT 58.200 47.619 0.00 0.00 0.00 2.17
115 116 0.250901 GCAAAGCACCTCCTCCTGAA 60.251 55.000 0.00 0.00 0.00 3.02
151 152 8.517062 AAAGCTGCAGAATCTATATGTTCTTT 57.483 30.769 20.43 9.42 32.60 2.52
183 184 4.365514 TTTGCAGTGGTAAGGAATCTGA 57.634 40.909 0.00 0.00 0.00 3.27
229 230 8.789881 TTGTTTCCGTTTTTGTAATACATGAG 57.210 30.769 0.00 0.00 0.00 2.90
240 241 4.260579 GGCATTCCTTTGTTTCCGTTTTTG 60.261 41.667 0.00 0.00 0.00 2.44
243 244 2.432510 TGGCATTCCTTTGTTTCCGTTT 59.567 40.909 0.00 0.00 0.00 3.60
251 252 3.448660 GGCTAATTCTGGCATTCCTTTGT 59.551 43.478 0.00 0.00 0.00 2.83
252 253 3.703052 AGGCTAATTCTGGCATTCCTTTG 59.297 43.478 7.48 0.00 0.00 2.77
263 264 4.530875 AGAACAATCCCAGGCTAATTCTG 58.469 43.478 0.00 0.00 0.00 3.02
276 277 9.686683 ATATGGCCAACTATATAAGAACAATCC 57.313 33.333 10.96 0.00 0.00 3.01
288 289 7.387673 CGACTTCAAATGATATGGCCAACTATA 59.612 37.037 10.96 0.00 0.00 1.31
289 290 6.205464 CGACTTCAAATGATATGGCCAACTAT 59.795 38.462 10.96 3.44 0.00 2.12
290 291 5.527214 CGACTTCAAATGATATGGCCAACTA 59.473 40.000 10.96 0.00 0.00 2.24
306 307 7.039270 ACAGTATATGCATAACACGACTTCAA 58.961 34.615 11.13 0.00 0.00 2.69
324 325 8.916062 TCGGTATTTCTTGGAACATACAGTATA 58.084 33.333 0.00 0.00 39.30 1.47
326 327 7.037438 GTCGGTATTTCTTGGAACATACAGTA 58.963 38.462 0.00 0.00 39.30 2.74
327 328 5.873164 GTCGGTATTTCTTGGAACATACAGT 59.127 40.000 0.00 0.00 39.30 3.55
328 329 5.872617 TGTCGGTATTTCTTGGAACATACAG 59.127 40.000 0.00 0.00 39.30 2.74
329 330 5.795972 TGTCGGTATTTCTTGGAACATACA 58.204 37.500 0.00 0.00 39.30 2.29
330 331 6.730960 TTGTCGGTATTTCTTGGAACATAC 57.269 37.500 0.00 0.00 39.30 2.39
336 337 5.591067 ACAGTTTTTGTCGGTATTTCTTGGA 59.409 36.000 0.00 0.00 33.87 3.53
339 340 5.358725 ACCACAGTTTTTGTCGGTATTTCTT 59.641 36.000 0.00 0.00 38.55 2.52
350 351 3.576550 ACACCTTCAACCACAGTTTTTGT 59.423 39.130 0.00 0.00 41.94 2.83
396 398 4.158764 TCCGAAACTGTTGTTGGAATGTTT 59.841 37.500 6.28 0.00 36.39 2.83
404 406 2.675844 TGTGAGTCCGAAACTGTTGTTG 59.324 45.455 0.00 0.00 38.74 3.33
415 417 1.901948 AGCGGTTCTGTGAGTCCGA 60.902 57.895 6.63 0.00 44.86 4.55
422 424 0.236711 CAGAAAGCAGCGGTTCTGTG 59.763 55.000 23.79 9.11 43.74 3.66
423 425 2.621763 CAGAAAGCAGCGGTTCTGT 58.378 52.632 23.79 0.00 43.74 3.41
459 461 3.003689 CCTGAAATTTTGTGAGCGACTGT 59.996 43.478 0.00 0.00 0.00 3.55
461 463 3.476552 TCCTGAAATTTTGTGAGCGACT 58.523 40.909 0.00 0.00 0.00 4.18
462 464 3.896648 TCCTGAAATTTTGTGAGCGAC 57.103 42.857 0.00 0.00 0.00 5.19
505 509 2.812358 AAAAGTGATCGTTTTGGGCC 57.188 45.000 0.00 0.00 0.00 5.80
618 644 4.081420 CAGTTACTTGGCCTGAGTCATAGT 60.081 45.833 14.45 4.16 0.00 2.12
630 656 3.796717 GCAAAAAGTGACAGTTACTTGGC 59.203 43.478 11.30 11.43 38.32 4.52
636 662 2.920524 TCGGGCAAAAAGTGACAGTTA 58.079 42.857 0.00 0.00 36.72 2.24
652 678 4.039730 AGGACATGAGACTGATTTATCGGG 59.960 45.833 0.00 0.00 37.50 5.14
740 766 1.837439 TGACACTTGACCTGTTGACCT 59.163 47.619 0.00 0.00 0.00 3.85
741 767 2.325583 TGACACTTGACCTGTTGACC 57.674 50.000 0.00 0.00 0.00 4.02
742 768 3.063997 CAGTTGACACTTGACCTGTTGAC 59.936 47.826 0.00 0.00 0.00 3.18
743 769 3.270027 CAGTTGACACTTGACCTGTTGA 58.730 45.455 0.00 0.00 0.00 3.18
744 770 2.355756 CCAGTTGACACTTGACCTGTTG 59.644 50.000 0.00 0.00 0.00 3.33
745 771 2.026262 ACCAGTTGACACTTGACCTGTT 60.026 45.455 0.00 0.00 0.00 3.16
746 772 1.559682 ACCAGTTGACACTTGACCTGT 59.440 47.619 0.00 0.00 0.00 4.00
747 773 2.213499 GACCAGTTGACACTTGACCTG 58.787 52.381 0.00 0.00 0.00 4.00
773 827 6.860023 GTGATTTATAGGTTGATCATGCTTGC 59.140 38.462 0.00 0.00 31.85 4.01
802 856 1.447838 TTTGCGAGGCCGATCTGTC 60.448 57.895 0.00 0.00 38.22 3.51
932 988 4.695231 GCTGCTGCTGTGTTGGCG 62.695 66.667 8.53 0.00 36.03 5.69
1327 1386 4.415150 ATGTCTGCCCCCGTGCTG 62.415 66.667 0.00 0.00 0.00 4.41
1416 1475 0.740868 CGTTGTCGATGCCCATGAGT 60.741 55.000 0.00 0.00 39.71 3.41
1660 1734 7.701445 AGAGAAAAACATTCAGAACAGAAGTG 58.299 34.615 0.00 0.00 0.00 3.16
1662 1736 7.358830 GGAGAGAAAAACATTCAGAACAGAAG 58.641 38.462 0.00 0.00 0.00 2.85
1673 1747 6.131972 TCATGAGAGGGAGAGAAAAACATT 57.868 37.500 0.00 0.00 0.00 2.71
1677 1751 7.502060 ACTAATCATGAGAGGGAGAGAAAAA 57.498 36.000 0.09 0.00 0.00 1.94
1682 1756 5.016173 CCCTACTAATCATGAGAGGGAGAG 58.984 50.000 18.15 8.00 45.65 3.20
1727 1801 9.851686 AGAATGCCAAGTTCACTATTAATCATA 57.148 29.630 0.00 0.00 0.00 2.15
1780 1974 7.931275 ACCAAACAGACTGAAAGATAAGTTTC 58.069 34.615 10.08 0.00 37.43 2.78
1798 1992 4.744795 AATTGTACTGCCAAACCAAACA 57.255 36.364 0.00 0.00 0.00 2.83
1885 2079 9.677567 TGTTTAGCATCAACAAAGAACTATTTC 57.322 29.630 0.00 0.00 31.05 2.17
1889 2083 7.561021 TGTGTTTAGCATCAACAAAGAACTA 57.439 32.000 0.00 0.00 35.91 2.24
1891 2085 6.917477 TGATGTGTTTAGCATCAACAAAGAAC 59.083 34.615 5.62 0.00 46.49 3.01
1892 2086 7.036996 TGATGTGTTTAGCATCAACAAAGAA 57.963 32.000 5.62 0.00 46.49 2.52
1893 2087 6.631971 TGATGTGTTTAGCATCAACAAAGA 57.368 33.333 5.62 0.00 46.49 2.52
1985 2185 9.930158 TGCCATAATTTTTCTATACTAAGGGTT 57.070 29.630 0.00 0.00 0.00 4.11
1986 2186 9.930158 TTGCCATAATTTTTCTATACTAAGGGT 57.070 29.630 0.00 0.00 0.00 4.34
1997 2197 8.358582 AGTTCAGAGATTGCCATAATTTTTCT 57.641 30.769 0.00 0.00 0.00 2.52
2154 2354 7.658982 TCTGCTATGAAGTTCATAATGTCCATC 59.341 37.037 22.67 2.57 38.72 3.51
2155 2355 7.512130 TCTGCTATGAAGTTCATAATGTCCAT 58.488 34.615 22.67 1.62 38.72 3.41
2156 2356 6.888105 TCTGCTATGAAGTTCATAATGTCCA 58.112 36.000 22.67 14.40 38.72 4.02
2157 2357 7.976135 ATCTGCTATGAAGTTCATAATGTCC 57.024 36.000 22.67 11.47 38.72 4.02
2159 2359 8.969260 TGAATCTGCTATGAAGTTCATAATGT 57.031 30.769 22.67 4.33 38.72 2.71
2215 2422 7.609532 AGATTAATCTGGTTGAGCCTTATATGC 59.390 37.037 17.26 0.00 35.42 3.14
2251 2458 3.755112 TGTCGGAAATTGTACAGTCCA 57.245 42.857 17.59 6.70 0.00 4.02
2252 2459 5.427036 TTTTGTCGGAAATTGTACAGTCC 57.573 39.130 10.74 10.74 0.00 3.85
2320 2528 5.048713 ACATTGAGGTTTTCATCTTTCGGAC 60.049 40.000 0.00 0.00 35.27 4.79
2323 2531 6.208644 ACAACATTGAGGTTTTCATCTTTCG 58.791 36.000 0.00 0.00 35.27 3.46
2344 2552 2.492484 GAGAGACTTTAGGCCTCGACAA 59.508 50.000 9.68 0.00 32.52 3.18
2348 2556 3.547746 ACTAGAGAGACTTTAGGCCTCG 58.452 50.000 9.68 0.88 32.52 4.63
2361 2570 3.374367 TCGATGGAACGTGAACTAGAGAG 59.626 47.826 0.00 0.00 34.70 3.20
2416 2625 3.342377 TGCCAATGTTCGAGTTGGATA 57.658 42.857 22.74 12.17 46.15 2.59
2447 2656 2.673523 GGGCTGGCAGACATCAGT 59.326 61.111 24.18 0.00 33.81 3.41


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

AutoCloner maintained by Alex Coulton.