Multiple sequence alignment - TraesCS5B01G033800

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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 TraesCS5B01G033800 chr5B 100.000 3053 0 0 1 3053 36768664 36765612 0.000000e+00 5638
1 TraesCS5B01G033800 chr5B 94.084 2248 72 16 850 3053 36720316 36722546 0.000000e+00 3358
2 TraesCS5B01G033800 chr5B 92.629 2252 114 19 850 3053 535111109 535113356 0.000000e+00 3192
3 TraesCS5B01G033800 chr5B 89.889 633 57 7 74 700 526266707 526267338 0.000000e+00 808
4 TraesCS5B01G033800 chr5B 88.994 636 61 9 69 697 526247299 526247932 0.000000e+00 778
5 TraesCS5B01G033800 chr5D 94.996 2238 70 12 850 3053 42016671 42018900 0.000000e+00 3474
6 TraesCS5B01G033800 chr5D 93.126 2255 102 17 850 3053 440160192 440162444 0.000000e+00 3256
7 TraesCS5B01G033800 chr5D 91.088 1627 65 26 850 2434 42053506 42051918 0.000000e+00 2128
8 TraesCS5B01G033800 chr5A 93.139 2259 102 16 847 3053 30404336 30406593 0.000000e+00 3264
9 TraesCS5B01G033800 chr5A 93.108 2249 108 18 850 3053 555770539 555772785 0.000000e+00 3251
10 TraesCS5B01G033800 chr5A 98.667 75 1 0 1 75 296865856 296865782 1.910000e-27 134
11 TraesCS5B01G033800 chr5A 97.468 79 1 1 1 78 651108018 651108096 1.910000e-27 134
12 TraesCS5B01G033800 chr5A 98.649 74 1 0 1 74 35413951 35414024 6.870000e-27 132
13 TraesCS5B01G033800 chr6A 87.949 780 75 12 73 847 558111189 558110424 0.000000e+00 902
14 TraesCS5B01G033800 chr6A 98.701 77 0 1 1 76 601665818 601665894 5.310000e-28 135
15 TraesCS5B01G033800 chr2B 89.301 701 67 7 75 767 795990710 795990010 0.000000e+00 872
16 TraesCS5B01G033800 chr1A 86.462 783 93 8 69 848 516557265 516558037 0.000000e+00 846
17 TraesCS5B01G033800 chr2A 86.260 786 93 11 69 848 715992934 715993710 0.000000e+00 839
18 TraesCS5B01G033800 chr2A 86.300 781 90 13 69 843 715992107 715992876 0.000000e+00 833
19 TraesCS5B01G033800 chr2A 87.160 662 78 6 86 741 715989682 715990342 0.000000e+00 745
20 TraesCS5B01G033800 chr1B 85.897 780 76 18 69 821 570825879 570825107 0.000000e+00 800
21 TraesCS5B01G033800 chr6B 85.199 804 80 26 74 848 669398985 669399778 0.000000e+00 789
22 TraesCS5B01G033800 chr3D 86.774 310 30 7 542 848 18792017 18792318 4.880000e-88 335
23 TraesCS5B01G033800 chr4A 86.275 306 33 3 544 847 38664368 38664070 1.060000e-84 324
24 TraesCS5B01G033800 chr3A 86.039 308 32 9 544 847 128580527 128580227 1.370000e-83 320
25 TraesCS5B01G033800 chr3A 84.194 310 38 8 542 848 673436671 673436370 1.070000e-74 291
26 TraesCS5B01G033800 chr3A 97.468 79 1 1 1 79 523966282 523966205 1.910000e-27 134
27 TraesCS5B01G033800 chr3A 96.296 81 0 3 1 81 98274433 98274510 2.470000e-26 130
28 TraesCS5B01G033800 chr7A 98.667 75 0 1 1 74 525690324 525690398 6.870000e-27 132
29 TraesCS5B01G033800 chr7A 98.667 75 0 1 1 74 718140580 718140506 6.870000e-27 132
30 TraesCS5B01G033800 chr2D 88.660 97 7 4 1 95 463067841 463067935 6.920000e-22 115


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 TraesCS5B01G033800 chr5B 36765612 36768664 3052 True 5638.000000 5638 100.000000 1 3053 1 chr5B.!!$R1 3052
1 TraesCS5B01G033800 chr5B 36720316 36722546 2230 False 3358.000000 3358 94.084000 850 3053 1 chr5B.!!$F1 2203
2 TraesCS5B01G033800 chr5B 535111109 535113356 2247 False 3192.000000 3192 92.629000 850 3053 1 chr5B.!!$F4 2203
3 TraesCS5B01G033800 chr5B 526266707 526267338 631 False 808.000000 808 89.889000 74 700 1 chr5B.!!$F3 626
4 TraesCS5B01G033800 chr5B 526247299 526247932 633 False 778.000000 778 88.994000 69 697 1 chr5B.!!$F2 628
5 TraesCS5B01G033800 chr5D 42016671 42018900 2229 False 3474.000000 3474 94.996000 850 3053 1 chr5D.!!$F1 2203
6 TraesCS5B01G033800 chr5D 440160192 440162444 2252 False 3256.000000 3256 93.126000 850 3053 1 chr5D.!!$F2 2203
7 TraesCS5B01G033800 chr5D 42051918 42053506 1588 True 2128.000000 2128 91.088000 850 2434 1 chr5D.!!$R1 1584
8 TraesCS5B01G033800 chr5A 30404336 30406593 2257 False 3264.000000 3264 93.139000 847 3053 1 chr5A.!!$F1 2206
9 TraesCS5B01G033800 chr5A 555770539 555772785 2246 False 3251.000000 3251 93.108000 850 3053 1 chr5A.!!$F3 2203
10 TraesCS5B01G033800 chr6A 558110424 558111189 765 True 902.000000 902 87.949000 73 847 1 chr6A.!!$R1 774
11 TraesCS5B01G033800 chr2B 795990010 795990710 700 True 872.000000 872 89.301000 75 767 1 chr2B.!!$R1 692
12 TraesCS5B01G033800 chr1A 516557265 516558037 772 False 846.000000 846 86.462000 69 848 1 chr1A.!!$F1 779
13 TraesCS5B01G033800 chr2A 715989682 715993710 4028 False 805.666667 839 86.573333 69 848 3 chr2A.!!$F1 779
14 TraesCS5B01G033800 chr1B 570825107 570825879 772 True 800.000000 800 85.897000 69 821 1 chr1B.!!$R1 752
15 TraesCS5B01G033800 chr6B 669398985 669399778 793 False 789.000000 789 85.199000 74 848 1 chr6B.!!$F1 774

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
46 47 0.038709 GCAAAACTGGTGCGCCATTA 60.039 50.0 21.54 0.00 45.05 1.90 F
84 1717 0.039798 GTGCACCATTGTGTCAGCTG 60.040 55.0 7.63 7.63 44.65 4.24 F
959 4233 0.321298 GGCACACTCCGCTTTCCTAA 60.321 55.0 0.00 0.00 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 5087 0.767375 TCTCCTTGCACAAGAAGCCT 59.233 50.000 11.94 0.0 40.79 4.58 R
1846 5127 1.283029 CCTCATCCTCCCAAGCAAAGA 59.717 52.381 0.00 0.0 0.00 2.52 R
2096 5393 0.034767 ATCCATCCACCACTGCACTG 60.035 55.000 0.00 0.0 0.00 3.66 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
20 21 3.136123 GCACCAGTGATGCGCCAT 61.136 61.111 4.18 0.00 32.45 4.40
21 22 2.703798 GCACCAGTGATGCGCCATT 61.704 57.895 4.18 0.00 32.45 3.16
23 24 0.659427 CACCAGTGATGCGCCATTAG 59.341 55.000 4.18 0.00 0.00 1.73
25 26 1.484653 ACCAGTGATGCGCCATTAGTA 59.515 47.619 4.18 0.00 0.00 1.82
26 27 2.138320 CCAGTGATGCGCCATTAGTAG 58.862 52.381 4.18 0.00 0.00 2.57
27 28 2.138320 CAGTGATGCGCCATTAGTAGG 58.862 52.381 4.18 0.00 0.00 3.18
38 39 4.701956 CCATTAGTAGGCAAAACTGGTG 57.298 45.455 0.00 0.00 0.00 4.17
39 40 3.119495 CCATTAGTAGGCAAAACTGGTGC 60.119 47.826 0.00 0.00 41.45 5.01
40 41 1.803334 TAGTAGGCAAAACTGGTGCG 58.197 50.000 0.00 0.00 43.18 5.34
41 42 1.081442 GTAGGCAAAACTGGTGCGC 60.081 57.895 0.00 0.00 43.18 6.09
42 43 2.265182 TAGGCAAAACTGGTGCGCC 61.265 57.895 10.11 10.11 43.18 6.53
45 46 1.300853 GCAAAACTGGTGCGCCATT 60.301 52.632 21.54 12.16 45.05 3.16
46 47 0.038709 GCAAAACTGGTGCGCCATTA 60.039 50.000 21.54 0.00 45.05 1.90
48 49 1.269448 CAAAACTGGTGCGCCATTAGT 59.731 47.619 21.54 11.93 45.05 2.24
50 51 2.024176 AACTGGTGCGCCATTAGTAG 57.976 50.000 21.54 9.57 45.05 2.57
60 61 3.298686 GCCATTAGTAGGCCTTTTCCT 57.701 47.619 12.58 4.76 46.50 3.36
61 62 4.432980 GCCATTAGTAGGCCTTTTCCTA 57.567 45.455 12.58 3.66 46.50 2.94
62 63 4.390264 GCCATTAGTAGGCCTTTTCCTAG 58.610 47.826 12.58 0.00 46.50 3.02
64 65 5.071384 GCCATTAGTAGGCCTTTTCCTAGTA 59.929 44.000 12.58 0.00 46.50 1.82
65 66 6.741801 GCCATTAGTAGGCCTTTTCCTAGTAG 60.742 46.154 12.58 0.00 46.50 2.57
66 67 6.326843 CCATTAGTAGGCCTTTTCCTAGTAGT 59.673 42.308 12.58 0.00 42.48 2.73
67 68 6.786967 TTAGTAGGCCTTTTCCTAGTAGTG 57.213 41.667 12.58 0.00 42.48 2.74
69 70 2.266279 AGGCCTTTTCCTAGTAGTGCA 58.734 47.619 0.00 0.00 33.95 4.57
70 71 2.027100 AGGCCTTTTCCTAGTAGTGCAC 60.027 50.000 9.40 9.40 33.95 4.57
72 73 2.290071 GCCTTTTCCTAGTAGTGCACCA 60.290 50.000 14.63 0.00 0.00 4.17
83 1716 0.179009 AGTGCACCATTGTGTCAGCT 60.179 50.000 14.63 0.00 44.65 4.24
84 1717 0.039798 GTGCACCATTGTGTCAGCTG 60.040 55.000 7.63 7.63 44.65 4.24
89 1722 0.885879 CCATTGTGTCAGCTGTGCAT 59.114 50.000 14.67 0.00 0.00 3.96
92 1725 1.677942 TTGTGTCAGCTGTGCATCAA 58.322 45.000 14.67 15.70 0.00 2.57
155 1788 0.540597 GCTCTGCCCACTTTTCCCTT 60.541 55.000 0.00 0.00 0.00 3.95
207 1840 6.261826 GCCTCATAATTATATCTGGCATGGAC 59.738 42.308 17.70 0.00 37.11 4.02
217 1850 2.746904 TCTGGCATGGACAATTAACGTG 59.253 45.455 0.00 0.00 0.00 4.49
261 2620 4.553330 AACATCACTAGTTACTGTGGGG 57.447 45.455 12.43 8.83 35.15 4.96
271 2630 8.698210 CACTAGTTACTGTGGGGTTATTACATA 58.302 37.037 0.00 0.00 0.00 2.29
297 2658 1.062587 CCGCAGCCTCACTAAAAATCG 59.937 52.381 0.00 0.00 0.00 3.34
368 2729 5.754890 GTGTCTGAACTTTGCCATGAAAATT 59.245 36.000 0.00 0.00 0.00 1.82
538 2903 9.295825 TCATGACAAAGTTCATATACCAGTTTT 57.704 29.630 0.00 0.00 34.29 2.43
653 3846 4.080863 ACTTCCAACAACATAGGCTAGAGG 60.081 45.833 0.00 0.00 0.00 3.69
660 3855 7.220030 CAACAACATAGGCTAGAGGTAATCAT 58.780 38.462 0.00 0.00 0.00 2.45
663 3858 7.950684 ACAACATAGGCTAGAGGTAATCATAGA 59.049 37.037 0.00 0.00 0.00 1.98
709 3947 4.829064 AAAACGAATCTAGCAACAGCAA 57.171 36.364 0.00 0.00 0.00 3.91
738 3976 1.203187 ACTGGACAAGACTAGCCTGGA 60.203 52.381 0.00 0.00 0.00 3.86
741 3979 2.292521 TGGACAAGACTAGCCTGGATCT 60.293 50.000 0.00 0.00 0.00 2.75
744 3982 4.406003 GGACAAGACTAGCCTGGATCTTAA 59.594 45.833 0.00 0.00 30.28 1.85
751 3989 0.480252 GCCTGGATCTTAATGGGGCT 59.520 55.000 0.00 0.00 35.73 5.19
759 3997 4.141390 GGATCTTAATGGGGCTCTTCTCAA 60.141 45.833 0.00 0.00 0.00 3.02
768 4006 3.636764 GGGGCTCTTCTCAACTTTTTCAA 59.363 43.478 0.00 0.00 0.00 2.69
769 4007 4.099419 GGGGCTCTTCTCAACTTTTTCAAA 59.901 41.667 0.00 0.00 0.00 2.69
770 4008 5.221521 GGGGCTCTTCTCAACTTTTTCAAAT 60.222 40.000 0.00 0.00 0.00 2.32
771 4009 5.693555 GGGCTCTTCTCAACTTTTTCAAATG 59.306 40.000 0.00 0.00 0.00 2.32
772 4010 5.176406 GGCTCTTCTCAACTTTTTCAAATGC 59.824 40.000 0.00 0.00 0.00 3.56
773 4011 5.750067 GCTCTTCTCAACTTTTTCAAATGCA 59.250 36.000 0.00 0.00 0.00 3.96
774 4012 6.423001 GCTCTTCTCAACTTTTTCAAATGCAT 59.577 34.615 0.00 0.00 0.00 3.96
788 4026 2.333938 GCATCATGCATCGTGGGC 59.666 61.111 4.20 0.00 44.26 5.36
814 4052 4.203076 ACGGTGGAGATACGCGCC 62.203 66.667 5.73 0.00 36.92 6.53
848 4086 2.493278 CGAATGTGAATGCCTTTTCCCT 59.507 45.455 0.00 0.00 0.00 4.20
959 4233 0.321298 GGCACACTCCGCTTTCCTAA 60.321 55.000 0.00 0.00 0.00 2.69
960 4234 0.796927 GCACACTCCGCTTTCCTAAC 59.203 55.000 0.00 0.00 0.00 2.34
961 4235 1.439679 CACACTCCGCTTTCCTAACC 58.560 55.000 0.00 0.00 0.00 2.85
974 4251 2.156098 TCCTAACCACCAAACGCATTC 58.844 47.619 0.00 0.00 0.00 2.67
1036 4314 2.250924 CCAAAAACCCATTGCTCCTCT 58.749 47.619 0.00 0.00 0.00 3.69
1651 4932 0.669625 GCTTGAGTTTAGCGACCGGT 60.670 55.000 6.92 6.92 0.00 5.28
1740 5021 2.281761 AGGGTTGTTGAGGCGCTG 60.282 61.111 7.64 0.00 0.00 5.18
2096 5393 2.066262 CACCCTGATGTTGTGACGTAC 58.934 52.381 0.00 0.00 31.66 3.67
2105 5402 1.257936 GTTGTGACGTACAGTGCAGTG 59.742 52.381 20.11 20.11 41.10 3.66
2130 5427 0.396556 TGGATTCTGTCGGATCGGGA 60.397 55.000 0.00 0.00 0.00 5.14
2142 5439 4.095782 GTCGGATCGGGAAAATTGATCAAA 59.904 41.667 13.09 0.00 40.17 2.69
2234 5531 0.694771 ATGGTCTCTGCAAAGCTGGA 59.305 50.000 0.00 0.00 0.00 3.86
2283 5580 1.342074 CAACAGTGGAGAGGAGTGGA 58.658 55.000 0.00 0.00 0.00 4.02
2284 5581 1.001406 CAACAGTGGAGAGGAGTGGAC 59.999 57.143 0.00 0.00 0.00 4.02
2285 5582 0.485099 ACAGTGGAGAGGAGTGGACT 59.515 55.000 0.00 0.00 0.00 3.85
2286 5583 1.181786 CAGTGGAGAGGAGTGGACTC 58.818 60.000 0.00 0.00 42.14 3.36
2360 5659 6.268566 GGAAACTAAAGGAATCATGTGATGC 58.731 40.000 0.00 0.00 34.49 3.91
2385 5684 1.318158 CCCAGATGTTGCAGAAGGGC 61.318 60.000 0.00 0.00 0.00 5.19
2397 5696 0.405973 AGAAGGGCTTCTTTCCCACC 59.594 55.000 0.48 0.00 46.95 4.61
2421 5720 7.399191 ACCACTGTGGAGATTAACTTACTGATA 59.601 37.037 32.30 0.00 40.96 2.15
2546 5845 1.559219 TCATGGATTTTCTCGGCAGGA 59.441 47.619 0.00 0.00 0.00 3.86
2563 5862 1.561542 AGGAGGATTTGGAATCAGCGT 59.438 47.619 3.39 0.00 0.00 5.07
2758 6058 8.453681 TGATACATAGATACTGGAGAAGGGTAA 58.546 37.037 0.00 0.00 0.00 2.85
2862 6162 9.277783 AGAAGCTATGTGCATTAGGTAAAATAG 57.722 33.333 10.58 0.00 45.94 1.73
2886 6186 0.814457 AGCTTACAGTCTCCTCAGCG 59.186 55.000 0.00 0.00 32.31 5.18
2906 6206 1.133407 GAGGTACTGAGAACTGCCTCG 59.867 57.143 0.00 0.00 41.55 4.63
3009 6309 4.436584 CGTGCCAGATGTTTCAGAGAAATC 60.437 45.833 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.253044 ACTAATGGCGCATCACTGGT 59.747 50.000 10.83 0.00 0.00 4.00
6 7 2.138320 CTACTAATGGCGCATCACTGG 58.862 52.381 10.83 0.00 0.00 4.00
7 8 2.138320 CCTACTAATGGCGCATCACTG 58.862 52.381 10.83 0.00 0.00 3.66
8 9 1.541233 GCCTACTAATGGCGCATCACT 60.541 52.381 10.83 0.00 41.03 3.41
9 10 0.868406 GCCTACTAATGGCGCATCAC 59.132 55.000 10.83 0.00 41.03 3.06
10 11 3.305709 GCCTACTAATGGCGCATCA 57.694 52.632 10.83 0.00 41.03 3.07
17 18 3.119495 GCACCAGTTTTGCCTACTAATGG 60.119 47.826 0.00 0.00 33.58 3.16
18 19 3.426159 CGCACCAGTTTTGCCTACTAATG 60.426 47.826 0.00 0.00 36.57 1.90
19 20 2.747446 CGCACCAGTTTTGCCTACTAAT 59.253 45.455 0.00 0.00 36.57 1.73
20 21 2.147958 CGCACCAGTTTTGCCTACTAA 58.852 47.619 0.00 0.00 36.57 2.24
21 22 1.803334 CGCACCAGTTTTGCCTACTA 58.197 50.000 0.00 0.00 36.57 1.82
23 24 1.081442 GCGCACCAGTTTTGCCTAC 60.081 57.895 0.30 0.00 36.57 3.18
25 26 3.605664 GGCGCACCAGTTTTGCCT 61.606 61.111 10.83 0.00 42.44 4.75
26 27 3.910490 TGGCGCACCAGTTTTGCC 61.910 61.111 10.83 0.00 42.67 4.52
41 42 5.632034 ACTAGGAAAAGGCCTACTAATGG 57.368 43.478 5.16 0.00 39.50 3.16
42 43 7.210873 CACTACTAGGAAAAGGCCTACTAATG 58.789 42.308 5.16 0.00 39.50 1.90
45 46 4.648307 GCACTACTAGGAAAAGGCCTACTA 59.352 45.833 5.16 5.95 39.50 1.82
46 47 3.451540 GCACTACTAGGAAAAGGCCTACT 59.548 47.826 5.16 4.94 39.50 2.57
48 49 3.197116 GTGCACTACTAGGAAAAGGCCTA 59.803 47.826 5.16 0.00 39.50 3.93
50 51 2.357075 GTGCACTACTAGGAAAAGGCC 58.643 52.381 10.32 0.00 0.00 5.19
53 54 5.003804 ACAATGGTGCACTACTAGGAAAAG 58.996 41.667 17.98 0.00 0.00 2.27
54 55 4.759693 CACAATGGTGCACTACTAGGAAAA 59.240 41.667 17.98 0.00 38.37 2.29
56 57 3.937814 CACAATGGTGCACTACTAGGAA 58.062 45.455 17.98 0.00 38.37 3.36
57 58 3.610040 CACAATGGTGCACTACTAGGA 57.390 47.619 17.98 0.00 38.37 2.94
69 70 0.466007 TGCACAGCTGACACAATGGT 60.466 50.000 23.35 0.00 0.00 3.55
70 71 0.885879 ATGCACAGCTGACACAATGG 59.114 50.000 23.35 0.18 0.00 3.16
72 73 1.900245 TGATGCACAGCTGACACAAT 58.100 45.000 23.35 6.29 0.00 2.71
83 1716 2.368548 ACTAGTCTGTGGTTGATGCACA 59.631 45.455 0.00 0.00 0.00 4.57
84 1717 3.045601 ACTAGTCTGTGGTTGATGCAC 57.954 47.619 0.00 0.00 0.00 4.57
89 1722 7.482169 AATGAATCTACTAGTCTGTGGTTGA 57.518 36.000 0.00 0.00 0.00 3.18
92 1725 7.617723 AGAGAAATGAATCTACTAGTCTGTGGT 59.382 37.037 0.00 0.00 0.00 4.16
99 1732 9.515226 CCTAGCTAGAGAAATGAATCTACTAGT 57.485 37.037 22.70 0.00 33.54 2.57
143 1776 3.267031 AGGAGTATGGAAGGGAAAAGTGG 59.733 47.826 0.00 0.00 0.00 4.00
155 1788 3.178046 TGCCACTAAACAGGAGTATGGA 58.822 45.455 0.00 0.00 0.00 3.41
237 1871 6.899075 ACCCCACAGTAACTAGTGATGTTATA 59.101 38.462 0.00 0.00 37.97 0.98
261 2620 5.704053 AGGCTGCGGGTTAATATGTAATAAC 59.296 40.000 0.00 0.00 29.06 1.89
271 2630 1.200519 TAGTGAGGCTGCGGGTTAAT 58.799 50.000 0.00 0.00 0.00 1.40
279 2638 1.529826 CGCGATTTTTAGTGAGGCTGC 60.530 52.381 0.00 0.00 0.00 5.25
653 3846 8.021396 GGCCGTGGAATTAATTTCTATGATTAC 58.979 37.037 7.98 0.00 34.61 1.89
660 3855 3.118334 TCCGGCCGTGGAATTAATTTCTA 60.118 43.478 26.12 0.00 34.30 2.10
663 3858 2.021457 CTCCGGCCGTGGAATTAATTT 58.979 47.619 26.12 0.00 37.64 1.82
691 3887 2.480419 GTGTTGCTGTTGCTAGATTCGT 59.520 45.455 0.00 0.00 40.48 3.85
709 3947 4.115398 AGTCTTGTCCAGTAGTAGGTGT 57.885 45.455 0.00 0.00 0.00 4.16
738 3976 4.476479 AGTTGAGAAGAGCCCCATTAAGAT 59.524 41.667 0.00 0.00 0.00 2.40
741 3979 4.657814 AAGTTGAGAAGAGCCCCATTAA 57.342 40.909 0.00 0.00 0.00 1.40
744 3982 3.532641 AAAAGTTGAGAAGAGCCCCAT 57.467 42.857 0.00 0.00 0.00 4.00
751 3989 7.490840 TGATGCATTTGAAAAAGTTGAGAAGA 58.509 30.769 0.00 0.00 0.00 2.87
771 4009 2.333938 GCCCACGATGCATGATGC 59.666 61.111 11.12 11.12 45.29 3.91
772 4010 0.816421 TCTGCCCACGATGCATGATG 60.816 55.000 2.46 1.25 38.22 3.07
773 4011 0.109913 ATCTGCCCACGATGCATGAT 59.890 50.000 2.46 0.00 38.22 2.45
774 4012 0.107066 AATCTGCCCACGATGCATGA 60.107 50.000 2.46 0.00 38.22 3.07
783 4021 1.303317 ACCGTCCAAATCTGCCCAC 60.303 57.895 0.00 0.00 0.00 4.61
788 4026 2.698855 ATCTCCACCGTCCAAATCTG 57.301 50.000 0.00 0.00 0.00 2.90
814 4052 1.225368 CATTCGCGTTCCGTTCACG 60.225 57.895 5.77 0.00 40.75 4.35
834 4072 4.535526 TTTGCTAAGGGAAAAGGCATTC 57.464 40.909 0.00 0.00 32.87 2.67
848 4086 2.495669 GCCCATGTAGCCTTTTTGCTAA 59.504 45.455 0.00 0.00 44.92 3.09
874 4112 2.665185 GTGGGGTCACAGCGTCAC 60.665 66.667 0.00 0.00 43.13 3.67
943 4191 1.053424 TGGTTAGGAAAGCGGAGTGT 58.947 50.000 0.00 0.00 35.82 3.55
944 4192 1.439679 GTGGTTAGGAAAGCGGAGTG 58.560 55.000 0.00 0.00 35.82 3.51
945 4193 0.323957 GGTGGTTAGGAAAGCGGAGT 59.676 55.000 0.00 0.00 35.82 3.85
947 4195 0.766131 TTGGTGGTTAGGAAAGCGGA 59.234 50.000 0.00 0.00 35.82 5.54
948 4196 1.268625 GTTTGGTGGTTAGGAAAGCGG 59.731 52.381 0.00 0.00 35.82 5.52
959 4233 0.893727 GAGGGAATGCGTTTGGTGGT 60.894 55.000 0.00 0.00 0.00 4.16
960 4234 1.595093 GGAGGGAATGCGTTTGGTGG 61.595 60.000 0.00 0.00 0.00 4.61
961 4235 1.595093 GGGAGGGAATGCGTTTGGTG 61.595 60.000 0.00 0.00 0.00 4.17
1651 4932 2.589442 GACCCCAACACGTCGCAA 60.589 61.111 0.00 0.00 0.00 4.85
1717 4998 1.002134 CCTCAACAACCCTCCGCAT 60.002 57.895 0.00 0.00 0.00 4.73
1740 5021 1.069823 AGCATCACACCGATCATCTCC 59.930 52.381 0.00 0.00 29.21 3.71
1806 5087 0.767375 TCTCCTTGCACAAGAAGCCT 59.233 50.000 11.94 0.00 40.79 4.58
1845 5126 2.641305 CTCATCCTCCCAAGCAAAGAG 58.359 52.381 0.00 0.00 0.00 2.85
1846 5127 1.283029 CCTCATCCTCCCAAGCAAAGA 59.717 52.381 0.00 0.00 0.00 2.52
2096 5393 0.034767 ATCCATCCACCACTGCACTG 60.035 55.000 0.00 0.00 0.00 3.66
2105 5402 0.830648 TCCGACAGAATCCATCCACC 59.169 55.000 0.00 0.00 0.00 4.61
2142 5439 7.876936 ACATATGCTTCATCATCTTTCTTGT 57.123 32.000 1.58 0.00 0.00 3.16
2234 5531 3.312736 TCCCAAGCCTCTGAAGTTTTT 57.687 42.857 0.00 0.00 0.00 1.94
2283 5580 5.453903 GCTGTATGTGATATCACTTGGGAGT 60.454 44.000 30.67 13.68 46.55 3.85
2284 5581 4.993584 GCTGTATGTGATATCACTTGGGAG 59.006 45.833 30.67 21.62 46.55 4.30
2285 5582 4.501400 CGCTGTATGTGATATCACTTGGGA 60.501 45.833 30.67 14.86 46.55 4.37
2286 5583 3.742882 CGCTGTATGTGATATCACTTGGG 59.257 47.826 30.67 18.69 46.55 4.12
2307 5606 4.955925 TCTAAACCCATGCATTACAACG 57.044 40.909 0.00 0.00 0.00 4.10
2360 5659 2.203972 CTGCAACATCTGGGCAACGG 62.204 60.000 0.00 0.00 37.06 4.44
2397 5696 8.251026 TGTATCAGTAAGTTAATCTCCACAGTG 58.749 37.037 0.00 0.00 0.00 3.66
2522 5821 4.357142 CTGCCGAGAAAATCCATGAATTG 58.643 43.478 0.00 0.00 0.00 2.32
2546 5845 2.749621 GACAACGCTGATTCCAAATCCT 59.250 45.455 0.00 0.00 0.00 3.24
2563 5862 6.998074 AGATACAAGTCATCCAACAAAGACAA 59.002 34.615 0.00 0.00 33.56 3.18
2758 6058 7.416890 CCAGTAGATCGAGTAATTCTTCCACTT 60.417 40.741 0.00 0.00 0.00 3.16
2862 6162 4.681744 CTGAGGAGACTGTAAGCTTCATC 58.318 47.826 0.00 0.00 44.43 2.92
2886 6186 1.133407 CGAGGCAGTTCTCAGTACCTC 59.867 57.143 0.00 0.00 40.26 3.85
2906 6206 0.455410 ATGTCTGAGCGTCTCTCTGC 59.545 55.000 8.07 0.00 42.38 4.26
3026 6326 5.944013 TGATTGTCAACTTTTCGACACAAA 58.056 33.333 0.00 0.00 41.67 2.83


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

AutoCloner maintained by Alex Coulton.