Multiple sequence alignment - TraesCS6D01G291600

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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 TraesCS6D01G291600 chr6D 100.000 2706 0 0 1 2706 402137377 402134672 0.000000e+00 4998.0
1 TraesCS6D01G291600 chr6D 100.000 53 0 0 3014 3066 402134364 402134312 7.000000e-17 99.0
2 TraesCS6D01G291600 chr6A 91.795 1231 65 22 1368 2569 548420372 548419149 0.000000e+00 1681.0
3 TraesCS6D01G291600 chr6A 91.384 1149 58 16 1 1122 548421814 548420680 0.000000e+00 1535.0
4 TraesCS6D01G291600 chr6B 91.974 922 46 13 1476 2374 602961864 602960948 0.000000e+00 1267.0
5 TraesCS6D01G291600 chr6B 90.643 855 41 12 587 1421 602962716 602961881 0.000000e+00 1099.0
6 TraesCS6D01G291600 chr6B 90.766 509 33 8 1 503 602963366 602962866 0.000000e+00 667.0
7 TraesCS6D01G291600 chr6B 90.043 231 15 6 2392 2615 602960897 602960668 2.990000e-75 292.0
8 TraesCS6D01G291600 chr6B 90.991 111 9 1 489 598 602962848 602962738 6.850000e-32 148.0
9 TraesCS6D01G291600 chr6B 75.346 361 51 25 1014 1346 502997653 502997303 4.120000e-29 139.0
10 TraesCS6D01G291600 chr6B 85.981 107 15 0 1014 1120 502998500 502998394 6.950000e-22 115.0
11 TraesCS6D01G291600 chr6B 85.047 107 16 0 1014 1120 502999136 502999030 3.230000e-20 110.0
12 TraesCS6D01G291600 chr6B 89.855 69 5 2 2567 2633 532385194 532385262 1.510000e-13 87.9
13 TraesCS6D01G291600 chr6B 95.238 42 2 0 2665 2706 602960662 602960621 1.970000e-07 67.6
14 TraesCS6D01G291600 chr1D 84.000 150 22 2 974 1122 249564435 249564287 3.190000e-30 143.0
15 TraesCS6D01G291600 chr1D 90.769 65 5 1 2570 2633 307215996 307215932 5.450000e-13 86.1
16 TraesCS6D01G291600 chr1B 79.058 191 31 6 934 1122 364915572 364915755 4.150000e-24 122.0
17 TraesCS6D01G291600 chr2D 94.444 54 3 0 2578 2631 5553673 5553620 1.960000e-12 84.2
18 TraesCS6D01G291600 chr2D 85.915 71 9 1 2568 2637 175594194 175594124 1.180000e-09 75.0
19 TraesCS6D01G291600 chr5A 86.486 74 7 2 2569 2639 607563342 607563269 9.110000e-11 78.7
20 TraesCS6D01G291600 chr5D 91.228 57 4 1 2578 2633 410642370 410642426 3.280000e-10 76.8
21 TraesCS6D01G291600 chr4A 88.889 63 5 2 2567 2627 19952456 19952394 3.280000e-10 76.8
22 TraesCS6D01G291600 chr4A 88.889 63 5 2 2567 2627 20001276 20001214 3.280000e-10 76.8


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 TraesCS6D01G291600 chr6D 402134312 402137377 3065 True 2548.5 4998 100.000000 1 3066 2 chr6D.!!$R1 3065
1 TraesCS6D01G291600 chr6A 548419149 548421814 2665 True 1608.0 1681 91.589500 1 2569 2 chr6A.!!$R1 2568
2 TraesCS6D01G291600 chr6B 602960621 602963366 2745 True 590.1 1267 91.609167 1 2706 6 chr6B.!!$R2 2705

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
578 620 0.401356 TGCACTCCTGGAATGCAGAA 59.599 50.0 27.19 6.64 44.17 3.02 F
1825 2006 0.170561 AGGTCGTCGAGGTCAATTCG 59.829 55.0 4.85 0.00 39.33 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1906 2102 0.316196 GCAGTCGCAACAACACAGTC 60.316 55.0 0.0 0.0 38.36 3.51 R
3022 3274 0.108804 GTCCGGTCATCACGATGTGT 60.109 55.0 0.0 0.0 39.72 3.72 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
66 67 7.933396 TGAATATTGTTCAACTATGAGGCATG 58.067 34.615 0.00 0.00 36.78 4.06
148 151 8.401046 TGTAAAATGCGCATATTTTAGGTTTC 57.599 30.769 25.61 13.45 40.94 2.78
204 208 6.090763 GCAACCCACTAACAAGCATTATTTTC 59.909 38.462 0.00 0.00 0.00 2.29
344 352 7.872483 AGTGTGTTTTCAAAAACTGTTCATCTT 59.128 29.630 16.77 0.00 46.37 2.40
385 394 0.664166 GTGCCAAACAGATGGTTGCG 60.664 55.000 5.05 0.63 41.22 4.85
578 620 0.401356 TGCACTCCTGGAATGCAGAA 59.599 50.000 27.19 6.64 44.17 3.02
626 701 1.373497 GTGAGGACACCGCTGACTG 60.373 63.158 0.00 0.00 40.74 3.51
894 987 2.205342 CCTTTTCCCTATCCTCCCACA 58.795 52.381 0.00 0.00 0.00 4.17
1151 1278 7.475840 CAATATGCTTCTCCTTTTTGGTAGAC 58.524 38.462 0.00 0.00 37.07 2.59
1152 1279 4.706842 TGCTTCTCCTTTTTGGTAGACT 57.293 40.909 0.00 0.00 37.07 3.24
1153 1280 5.818678 TGCTTCTCCTTTTTGGTAGACTA 57.181 39.130 0.00 0.00 37.07 2.59
1154 1281 6.182507 TGCTTCTCCTTTTTGGTAGACTAA 57.817 37.500 0.00 0.00 37.07 2.24
1156 1283 7.057894 TGCTTCTCCTTTTTGGTAGACTAAAA 58.942 34.615 0.31 0.31 35.08 1.52
1157 1284 7.012989 TGCTTCTCCTTTTTGGTAGACTAAAAC 59.987 37.037 3.69 0.00 36.31 2.43
1158 1285 7.486802 TTCTCCTTTTTGGTAGACTAAAACG 57.513 36.000 3.69 2.82 36.31 3.60
1182 1309 4.881273 TGTAGTGTGCAATGTTCTTGACTT 59.119 37.500 0.00 0.00 0.00 3.01
1188 1316 5.588246 TGTGCAATGTTCTTGACTTCTTGTA 59.412 36.000 0.00 0.00 0.00 2.41
1200 1328 5.305585 TGACTTCTTGTACATTCCAACTCC 58.694 41.667 0.00 0.00 0.00 3.85
1209 1337 1.466167 CATTCCAACTCCTTGCACTCG 59.534 52.381 0.00 0.00 0.00 4.18
1272 1401 3.560068 GCTGGTCCTTGTTGTTATATCCG 59.440 47.826 0.00 0.00 0.00 4.18
1280 1409 5.106948 CCTTGTTGTTATATCCGCTAGCATG 60.107 44.000 16.45 5.14 0.00 4.06
1286 1415 1.263356 TATCCGCTAGCATGTACCCC 58.737 55.000 16.45 0.00 0.00 4.95
1378 1557 1.134580 GCTCTGCTCAAGCTATGGTCA 60.135 52.381 3.32 0.00 42.66 4.02
1432 1612 9.387123 CTCTCTGAGCATTTTAAGTTTGTAAAC 57.613 33.333 0.00 0.00 39.17 2.01
1435 1615 8.462811 TCTGAGCATTTTAAGTTTGTAAACACA 58.537 29.630 9.85 0.00 41.30 3.72
1457 1637 6.480981 CACAGGCAGTTTCTTCAATGAAAATT 59.519 34.615 0.00 0.00 37.63 1.82
1638 1819 2.756760 CACTCCCTACATGCATGCTTTT 59.243 45.455 26.53 9.67 0.00 2.27
1670 1851 2.163412 TCCTGCGTCAATAACAATTGGC 59.837 45.455 10.83 1.24 33.13 4.52
1741 1922 2.526873 ACGAAGGTGAGCCAGGGT 60.527 61.111 0.00 0.00 37.19 4.34
1744 1925 3.260100 AAGGTGAGCCAGGGTGGG 61.260 66.667 0.00 0.00 38.19 4.61
1825 2006 0.170561 AGGTCGTCGAGGTCAATTCG 59.829 55.000 4.85 0.00 39.33 3.34
1843 2024 3.358076 GAAGCTGTCCGAGACCCCG 62.358 68.421 0.00 0.00 0.00 5.73
1883 2065 0.591741 CACCTCGCCTCGTCGATTAC 60.592 60.000 0.00 0.00 37.87 1.89
1891 2076 2.795470 GCCTCGTCGATTACAAATCCTC 59.205 50.000 0.00 0.00 0.00 3.71
1892 2077 3.381949 CCTCGTCGATTACAAATCCTCC 58.618 50.000 0.00 0.00 0.00 4.30
1893 2078 3.068307 CCTCGTCGATTACAAATCCTCCT 59.932 47.826 0.00 0.00 0.00 3.69
1895 2080 5.221185 CCTCGTCGATTACAAATCCTCCTAA 60.221 44.000 0.00 0.00 0.00 2.69
1896 2081 5.585390 TCGTCGATTACAAATCCTCCTAAC 58.415 41.667 0.00 0.00 0.00 2.34
1898 2083 6.543465 TCGTCGATTACAAATCCTCCTAACTA 59.457 38.462 0.00 0.00 0.00 2.24
1899 2084 7.067372 TCGTCGATTACAAATCCTCCTAACTAA 59.933 37.037 0.00 0.00 0.00 2.24
1900 2085 7.167136 CGTCGATTACAAATCCTCCTAACTAAC 59.833 40.741 0.00 0.00 0.00 2.34
1901 2086 7.977853 GTCGATTACAAATCCTCCTAACTAACA 59.022 37.037 0.00 0.00 0.00 2.41
1906 2102 6.653989 ACAAATCCTCCTAACTAACAGATGG 58.346 40.000 0.00 0.00 0.00 3.51
1922 2120 0.944386 ATGGACTGTGTTGTTGCGAC 59.056 50.000 0.00 0.00 0.00 5.19
2072 2271 3.372554 GACGCCCACTAGTGCTCCC 62.373 68.421 17.86 4.08 0.00 4.30
2076 2275 1.842381 GCCCACTAGTGCTCCCTTGT 61.842 60.000 17.86 0.00 0.00 3.16
2087 2286 2.290008 TGCTCCCTTGTTCGCTTATCAA 60.290 45.455 0.00 0.00 0.00 2.57
2095 2294 5.801947 CCTTGTTCGCTTATCAATCCTTTTG 59.198 40.000 0.00 0.00 0.00 2.44
2096 2295 4.732784 TGTTCGCTTATCAATCCTTTTGC 58.267 39.130 0.00 0.00 0.00 3.68
2111 2312 3.119531 CCTTTTGCTGCAACCATATCGAA 60.120 43.478 15.72 3.19 0.00 3.71
2177 2378 5.630680 CAGTTCATCGGTTCCAATTTTCTTG 59.369 40.000 0.00 0.00 0.00 3.02
2195 2396 2.098233 GTGTCGGTGTACATGGCGG 61.098 63.158 0.00 0.00 0.00 6.13
2257 2458 8.146053 TCAGAGATATGGGAAAGAGTTTGTAA 57.854 34.615 0.00 0.00 0.00 2.41
2266 2467 8.842358 TGGGAAAGAGTTTGTAAGTTATAGTG 57.158 34.615 0.00 0.00 0.00 2.74
2308 2509 7.342541 ACATTATCATCCACCAACAAATCATCA 59.657 33.333 0.00 0.00 0.00 3.07
2309 2510 7.901283 TTATCATCCACCAACAAATCATCAT 57.099 32.000 0.00 0.00 0.00 2.45
2374 2583 4.660789 AGAGCTTGTGCAAAGATTGTTT 57.339 36.364 11.34 0.00 42.74 2.83
2375 2584 5.014808 AGAGCTTGTGCAAAGATTGTTTT 57.985 34.783 11.34 0.00 42.74 2.43
2472 2721 6.505048 TGACAATCATTGGAGATGTCCTAT 57.495 37.500 10.72 5.16 44.30 2.57
2513 2762 5.860941 TTTTAGCCATGGAAAAGAACACA 57.139 34.783 18.40 0.00 0.00 3.72
2559 2810 8.078596 GGCAGATTAGTTTGAGCCAATTAATAG 58.921 37.037 0.00 0.00 41.63 1.73
2569 2820 5.104360 TGAGCCAATTAATAGCAGAGGTCTT 60.104 40.000 11.71 0.00 0.00 3.01
2570 2821 5.760131 AGCCAATTAATAGCAGAGGTCTTT 58.240 37.500 11.71 0.00 0.00 2.52
2600 2852 0.179026 GAGATAAAACCCCCGGCCTC 60.179 60.000 0.00 0.00 0.00 4.70
2634 2886 6.094193 TGATGCACACAACCATTTTTATCA 57.906 33.333 0.00 0.00 0.00 2.15
2635 2887 6.519382 TGATGCACACAACCATTTTTATCAA 58.481 32.000 0.00 0.00 0.00 2.57
2636 2888 7.160049 TGATGCACACAACCATTTTTATCAAT 58.840 30.769 0.00 0.00 0.00 2.57
2637 2889 8.309656 TGATGCACACAACCATTTTTATCAATA 58.690 29.630 0.00 0.00 0.00 1.90
2638 2890 8.706492 ATGCACACAACCATTTTTATCAATAG 57.294 30.769 0.00 0.00 0.00 1.73
2639 2891 6.589523 TGCACACAACCATTTTTATCAATAGC 59.410 34.615 0.00 0.00 0.00 2.97
2640 2892 6.589523 GCACACAACCATTTTTATCAATAGCA 59.410 34.615 0.00 0.00 0.00 3.49
2641 2893 7.117523 GCACACAACCATTTTTATCAATAGCAA 59.882 33.333 0.00 0.00 0.00 3.91
2642 2894 9.153721 CACACAACCATTTTTATCAATAGCAAT 57.846 29.630 0.00 0.00 0.00 3.56
2655 2907 6.741992 TCAATAGCAATATCTAATTGGGCG 57.258 37.500 0.38 0.00 0.00 6.13
2656 2908 5.647658 TCAATAGCAATATCTAATTGGGCGG 59.352 40.000 0.38 0.00 0.00 6.13
2657 2909 3.788227 AGCAATATCTAATTGGGCGGA 57.212 42.857 0.38 0.00 0.00 5.54
2658 2910 4.307032 AGCAATATCTAATTGGGCGGAT 57.693 40.909 0.38 0.00 0.00 4.18
2659 2911 4.012374 AGCAATATCTAATTGGGCGGATG 58.988 43.478 0.38 0.00 0.00 3.51
2660 2912 3.758554 GCAATATCTAATTGGGCGGATGT 59.241 43.478 0.38 0.00 0.00 3.06
2661 2913 4.379813 GCAATATCTAATTGGGCGGATGTG 60.380 45.833 0.38 0.00 0.00 3.21
2662 2914 1.609208 ATCTAATTGGGCGGATGTGC 58.391 50.000 0.00 0.00 0.00 4.57
2663 2915 0.813610 TCTAATTGGGCGGATGTGCG 60.814 55.000 0.00 0.00 35.06 5.34
2664 2916 1.078072 TAATTGGGCGGATGTGCGT 60.078 52.632 0.00 0.00 35.06 5.24
2665 2917 1.092921 TAATTGGGCGGATGTGCGTC 61.093 55.000 0.00 0.00 35.06 5.19
2666 2918 2.819984 AATTGGGCGGATGTGCGTCT 62.820 55.000 0.00 0.00 35.06 4.18
2667 2919 4.758251 TGGGCGGATGTGCGTCTG 62.758 66.667 0.00 0.00 35.06 3.51
2668 2920 4.451150 GGGCGGATGTGCGTCTGA 62.451 66.667 4.54 0.00 35.06 3.27
2669 2921 3.188786 GGCGGATGTGCGTCTGAC 61.189 66.667 4.54 0.00 35.06 3.51
2670 2922 2.432456 GCGGATGTGCGTCTGACA 60.432 61.111 8.73 0.00 0.00 3.58
3035 3287 4.819769 TCTTGATCAACACATCGTGATGA 58.180 39.130 16.33 9.14 46.16 2.92
3036 3288 4.627035 TCTTGATCAACACATCGTGATGAC 59.373 41.667 16.33 5.13 45.26 3.06
3037 3289 3.261580 TGATCAACACATCGTGATGACC 58.738 45.455 16.33 0.94 45.26 4.02
3038 3290 1.708822 TCAACACATCGTGATGACCG 58.291 50.000 16.33 6.93 39.68 4.79
3039 3291 0.721154 CAACACATCGTGATGACCGG 59.279 55.000 16.33 0.00 38.34 5.28
3040 3292 0.606096 AACACATCGTGATGACCGGA 59.394 50.000 9.46 0.00 41.20 5.14
3041 3293 0.108804 ACACATCGTGATGACCGGAC 60.109 55.000 9.46 1.07 41.20 4.79
3042 3294 0.173481 CACATCGTGATGACCGGACT 59.827 55.000 9.46 0.00 41.20 3.85
3043 3295 1.404035 CACATCGTGATGACCGGACTA 59.596 52.381 9.46 0.00 41.20 2.59
3044 3296 2.097036 ACATCGTGATGACCGGACTAA 58.903 47.619 9.46 0.00 41.20 2.24
3045 3297 2.494471 ACATCGTGATGACCGGACTAAA 59.506 45.455 9.46 0.00 41.20 1.85
3046 3298 3.132289 ACATCGTGATGACCGGACTAAAT 59.868 43.478 9.46 0.00 41.20 1.40
3047 3299 4.340097 ACATCGTGATGACCGGACTAAATA 59.660 41.667 9.46 0.00 41.20 1.40
3048 3300 4.987408 TCGTGATGACCGGACTAAATAA 57.013 40.909 9.46 0.00 0.00 1.40
3049 3301 5.524971 TCGTGATGACCGGACTAAATAAT 57.475 39.130 9.46 0.00 0.00 1.28
3050 3302 6.638096 TCGTGATGACCGGACTAAATAATA 57.362 37.500 9.46 0.00 0.00 0.98
3051 3303 7.223260 TCGTGATGACCGGACTAAATAATAT 57.777 36.000 9.46 0.00 0.00 1.28
3052 3304 8.339344 TCGTGATGACCGGACTAAATAATATA 57.661 34.615 9.46 0.00 0.00 0.86
3053 3305 8.963725 TCGTGATGACCGGACTAAATAATATAT 58.036 33.333 9.46 0.00 0.00 0.86
3054 3306 9.020813 CGTGATGACCGGACTAAATAATATATG 57.979 37.037 9.46 0.00 0.00 1.78
3055 3307 9.314321 GTGATGACCGGACTAAATAATATATGG 57.686 37.037 9.46 0.00 0.00 2.74
3056 3308 8.482943 TGATGACCGGACTAAATAATATATGGG 58.517 37.037 9.46 0.00 0.00 4.00
3057 3309 6.646267 TGACCGGACTAAATAATATATGGGC 58.354 40.000 9.46 0.00 0.00 5.36
3058 3310 5.997843 ACCGGACTAAATAATATATGGGCC 58.002 41.667 9.46 0.00 0.00 5.80
3059 3311 5.054477 CCGGACTAAATAATATATGGGCCG 58.946 45.833 0.00 0.00 0.00 6.13
3060 3312 5.163385 CCGGACTAAATAATATATGGGCCGA 60.163 44.000 12.67 0.00 36.21 5.54
3061 3313 5.983720 CGGACTAAATAATATATGGGCCGAG 59.016 44.000 0.00 0.00 36.21 4.63
3062 3314 5.758784 GGACTAAATAATATATGGGCCGAGC 59.241 44.000 0.00 0.00 0.00 5.03
3063 3315 6.308015 ACTAAATAATATATGGGCCGAGCA 57.692 37.500 0.00 0.00 0.00 4.26
3064 3316 6.349300 ACTAAATAATATATGGGCCGAGCAG 58.651 40.000 0.00 0.00 0.00 4.24
3065 3317 5.435686 AAATAATATATGGGCCGAGCAGA 57.564 39.130 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
181 184 7.539034 AGAAAATAATGCTTGTTAGTGGGTT 57.461 32.000 0.00 0.00 0.00 4.11
568 610 6.264841 AGAGAGAATTTGTTTCTGCATTCC 57.735 37.500 0.00 0.00 44.88 3.01
626 701 0.792640 CGCGTGGGCATATTCTCATC 59.207 55.000 0.00 0.00 39.92 2.92
894 987 2.832733 GTGGTAGTAGTGGAAAGAGGCT 59.167 50.000 0.00 0.00 0.00 4.58
1083 1176 4.215399 GTGGAGAAGTATCTGGAGATCGAG 59.785 50.000 0.00 0.00 35.54 4.04
1133 1259 7.226128 ACGTTTTAGTCTACCAAAAAGGAGAAG 59.774 37.037 13.46 0.00 41.22 2.85
1151 1278 5.090652 ACATTGCACACTACACGTTTTAG 57.909 39.130 0.00 0.00 0.00 1.85
1152 1279 5.294799 AGAACATTGCACACTACACGTTTTA 59.705 36.000 0.00 0.00 0.00 1.52
1153 1280 4.095782 AGAACATTGCACACTACACGTTTT 59.904 37.500 0.00 0.00 0.00 2.43
1154 1281 3.625764 AGAACATTGCACACTACACGTTT 59.374 39.130 0.00 0.00 0.00 3.60
1156 1283 2.833794 AGAACATTGCACACTACACGT 58.166 42.857 0.00 0.00 0.00 4.49
1157 1284 3.247411 TCAAGAACATTGCACACTACACG 59.753 43.478 0.00 0.00 0.00 4.49
1158 1285 4.273480 AGTCAAGAACATTGCACACTACAC 59.727 41.667 0.00 0.00 0.00 2.90
1182 1309 4.072131 GCAAGGAGTTGGAATGTACAAGA 58.928 43.478 0.00 0.00 33.87 3.02
1188 1316 2.508526 GAGTGCAAGGAGTTGGAATGT 58.491 47.619 0.00 0.00 35.52 2.71
1200 1328 3.002791 ACCACAATGTATCGAGTGCAAG 58.997 45.455 0.00 0.00 0.00 4.01
1246 1375 0.468029 AACAACAAGGACCAGCCCAG 60.468 55.000 0.00 0.00 37.37 4.45
1247 1376 0.847373 TAACAACAAGGACCAGCCCA 59.153 50.000 0.00 0.00 37.37 5.36
1272 1401 2.427095 CCTTTTTGGGGTACATGCTAGC 59.573 50.000 8.10 8.10 0.00 3.42
1280 1409 4.108501 TCTCCTTTCCTTTTTGGGGTAC 57.891 45.455 0.00 0.00 36.20 3.34
1378 1557 6.158598 CGGAGAAAACCATTCATTCAAACAT 58.841 36.000 0.00 0.00 0.00 2.71
1432 1612 4.572985 TTCATTGAAGAAACTGCCTGTG 57.427 40.909 0.00 0.00 0.00 3.66
1435 1615 6.819284 TCAATTTTCATTGAAGAAACTGCCT 58.181 32.000 0.00 0.00 44.89 4.75
1612 1793 1.521681 GCATGTAGGGAGTGCCGTC 60.522 63.158 0.00 0.00 33.56 4.79
1638 1819 3.817709 TGACGCAGGATTGACATATGA 57.182 42.857 10.38 0.00 0.00 2.15
1670 1851 4.864334 GAGATGGCCCTGCACCCG 62.864 72.222 0.00 0.00 0.00 5.28
1718 1899 4.681978 GCTCACCTTCGTGCCGGT 62.682 66.667 1.90 0.00 40.04 5.28
1822 2003 1.585006 GGTCTCGGACAGCTTCGAA 59.415 57.895 0.00 0.00 34.87 3.71
1825 2006 2.579738 GGGGTCTCGGACAGCTTC 59.420 66.667 6.41 0.00 33.68 3.86
1843 2024 2.175035 TTGCTGTACGTACCAGGCCC 62.175 60.000 22.43 8.27 0.00 5.80
1855 2036 0.320421 GAGGCGAGGTGTTTGCTGTA 60.320 55.000 0.00 0.00 36.37 2.74
1883 2065 6.763610 GTCCATCTGTTAGTTAGGAGGATTTG 59.236 42.308 0.00 0.00 0.00 2.32
1901 2086 1.202639 TCGCAACAACACAGTCCATCT 60.203 47.619 0.00 0.00 0.00 2.90
1906 2102 0.316196 GCAGTCGCAACAACACAGTC 60.316 55.000 0.00 0.00 38.36 3.51
1933 2132 0.391661 GGCTCGAGTTGATCTGCCAA 60.392 55.000 15.13 0.00 41.79 4.52
2072 2271 5.287035 GCAAAAGGATTGATAAGCGAACAAG 59.713 40.000 0.00 0.00 0.00 3.16
2076 2275 4.675146 GCAGCAAAAGGATTGATAAGCGAA 60.675 41.667 0.00 0.00 0.00 4.70
2087 2286 3.067180 CGATATGGTTGCAGCAAAAGGAT 59.933 43.478 10.11 1.39 0.00 3.24
2095 2294 4.310769 AGAGTATTCGATATGGTTGCAGC 58.689 43.478 0.00 0.00 0.00 5.25
2096 2295 5.755375 ACAAGAGTATTCGATATGGTTGCAG 59.245 40.000 0.00 0.00 0.00 4.41
2177 2378 2.098233 CCGCCATGTACACCGACAC 61.098 63.158 12.35 0.00 30.52 3.67
2195 2396 4.718940 AATGGTATAACAAAGTGCTGGC 57.281 40.909 0.00 0.00 0.00 4.85
2202 2403 6.148811 ACGGTCACTGAAATGGTATAACAAAG 59.851 38.462 0.00 0.00 0.00 2.77
2257 2458 9.269453 GTCTCTTTTTACCAACACACTATAACT 57.731 33.333 0.00 0.00 0.00 2.24
2262 2463 9.787435 ATAATGTCTCTTTTTACCAACACACTA 57.213 29.630 0.00 0.00 0.00 2.74
2263 2464 8.691661 ATAATGTCTCTTTTTACCAACACACT 57.308 30.769 0.00 0.00 0.00 3.55
2264 2465 8.564574 TGATAATGTCTCTTTTTACCAACACAC 58.435 33.333 0.00 0.00 0.00 3.82
2265 2466 8.684386 TGATAATGTCTCTTTTTACCAACACA 57.316 30.769 0.00 0.00 0.00 3.72
2266 2467 9.774742 GATGATAATGTCTCTTTTTACCAACAC 57.225 33.333 0.00 0.00 0.00 3.32
2349 2558 4.164294 CAATCTTTGCACAAGCTCTAAGC 58.836 43.478 0.00 0.00 42.84 3.09
2434 2681 5.590145 TGATTGTCAATTTTGTCACCTGTG 58.410 37.500 0.00 0.00 0.00 3.66
2435 2682 5.850557 TGATTGTCAATTTTGTCACCTGT 57.149 34.783 0.00 0.00 0.00 4.00
2535 2784 8.623903 TGCTATTAATTGGCTCAAACTAATCTG 58.376 33.333 12.22 5.93 0.00 2.90
2584 2836 1.613061 CAGAGGCCGGGGGTTTTAT 59.387 57.895 2.18 0.00 0.00 1.40
2586 2838 4.678743 GCAGAGGCCGGGGGTTTT 62.679 66.667 2.18 0.00 0.00 2.43
2615 2867 6.589523 TGCTATTGATAAAAATGGTTGTGTGC 59.410 34.615 0.00 0.00 0.00 4.57
2629 2881 8.892723 CGCCCAATTAGATATTGCTATTGATAA 58.107 33.333 0.00 0.00 0.00 1.75
2630 2882 7.498900 CCGCCCAATTAGATATTGCTATTGATA 59.501 37.037 0.00 0.00 0.00 2.15
2631 2883 6.319658 CCGCCCAATTAGATATTGCTATTGAT 59.680 38.462 0.00 0.00 0.00 2.57
2632 2884 5.647658 CCGCCCAATTAGATATTGCTATTGA 59.352 40.000 0.00 0.00 0.00 2.57
2633 2885 5.647658 TCCGCCCAATTAGATATTGCTATTG 59.352 40.000 0.00 0.00 0.00 1.90
2634 2886 5.815581 TCCGCCCAATTAGATATTGCTATT 58.184 37.500 0.00 0.00 0.00 1.73
2635 2887 5.435686 TCCGCCCAATTAGATATTGCTAT 57.564 39.130 0.00 0.00 0.00 2.97
2636 2888 4.901197 TCCGCCCAATTAGATATTGCTA 57.099 40.909 0.00 0.00 0.00 3.49
2637 2889 3.788227 TCCGCCCAATTAGATATTGCT 57.212 42.857 0.00 0.00 0.00 3.91
2638 2890 3.758554 ACATCCGCCCAATTAGATATTGC 59.241 43.478 0.00 0.00 0.00 3.56
2639 2891 4.379813 GCACATCCGCCCAATTAGATATTG 60.380 45.833 0.00 0.00 0.00 1.90
2640 2892 3.758554 GCACATCCGCCCAATTAGATATT 59.241 43.478 0.00 0.00 0.00 1.28
2641 2893 3.347216 GCACATCCGCCCAATTAGATAT 58.653 45.455 0.00 0.00 0.00 1.63
2642 2894 2.778299 GCACATCCGCCCAATTAGATA 58.222 47.619 0.00 0.00 0.00 1.98
2643 2895 1.609208 GCACATCCGCCCAATTAGAT 58.391 50.000 0.00 0.00 0.00 1.98
2644 2896 0.813610 CGCACATCCGCCCAATTAGA 60.814 55.000 0.00 0.00 0.00 2.10
2645 2897 1.095228 ACGCACATCCGCCCAATTAG 61.095 55.000 0.00 0.00 0.00 1.73
2646 2898 1.078072 ACGCACATCCGCCCAATTA 60.078 52.632 0.00 0.00 0.00 1.40
2647 2899 2.361104 ACGCACATCCGCCCAATT 60.361 55.556 0.00 0.00 0.00 2.32
2648 2900 2.824041 GACGCACATCCGCCCAAT 60.824 61.111 0.00 0.00 0.00 3.16
2649 2901 4.015406 AGACGCACATCCGCCCAA 62.015 61.111 0.00 0.00 0.00 4.12
2650 2902 4.758251 CAGACGCACATCCGCCCA 62.758 66.667 0.00 0.00 0.00 5.36
2651 2903 4.451150 TCAGACGCACATCCGCCC 62.451 66.667 0.00 0.00 0.00 6.13
2652 2904 3.188786 GTCAGACGCACATCCGCC 61.189 66.667 0.00 0.00 0.00 6.13
2653 2905 2.432456 TGTCAGACGCACATCCGC 60.432 61.111 0.00 0.00 0.00 5.54
2654 2906 0.799917 CTCTGTCAGACGCACATCCG 60.800 60.000 0.00 0.00 0.00 4.18
2655 2907 0.528017 TCTCTGTCAGACGCACATCC 59.472 55.000 0.00 0.00 0.00 3.51
2656 2908 2.191802 CATCTCTGTCAGACGCACATC 58.808 52.381 0.00 0.00 32.26 3.06
2657 2909 1.134877 CCATCTCTGTCAGACGCACAT 60.135 52.381 0.00 0.00 32.26 3.21
2658 2910 0.244721 CCATCTCTGTCAGACGCACA 59.755 55.000 0.00 0.00 32.26 4.57
2659 2911 0.528017 TCCATCTCTGTCAGACGCAC 59.472 55.000 0.00 0.00 32.26 5.34
2660 2912 0.813821 CTCCATCTCTGTCAGACGCA 59.186 55.000 0.00 0.00 32.26 5.24
2661 2913 1.098869 TCTCCATCTCTGTCAGACGC 58.901 55.000 0.00 0.00 32.26 5.19
2662 2914 2.479389 GCTTCTCCATCTCTGTCAGACG 60.479 54.545 0.00 0.00 32.26 4.18
2663 2915 2.760092 AGCTTCTCCATCTCTGTCAGAC 59.240 50.000 0.00 0.00 32.26 3.51
2664 2916 2.759535 CAGCTTCTCCATCTCTGTCAGA 59.240 50.000 1.78 1.78 34.78 3.27
2665 2917 2.759535 TCAGCTTCTCCATCTCTGTCAG 59.240 50.000 0.00 0.00 0.00 3.51
2666 2918 2.812658 TCAGCTTCTCCATCTCTGTCA 58.187 47.619 0.00 0.00 0.00 3.58
2667 2919 4.405116 AATCAGCTTCTCCATCTCTGTC 57.595 45.455 0.00 0.00 0.00 3.51
2668 2920 4.840716 AAATCAGCTTCTCCATCTCTGT 57.159 40.909 0.00 0.00 0.00 3.41
2669 2921 5.430007 AGAAAATCAGCTTCTCCATCTCTG 58.570 41.667 0.00 0.00 0.00 3.35
2670 2922 5.426185 AGAGAAAATCAGCTTCTCCATCTCT 59.574 40.000 8.44 8.33 46.70 3.10
3013 3265 4.627035 GTCATCACGATGTGTTGATCAAGA 59.373 41.667 8.80 4.42 41.95 3.02
3014 3266 4.201753 GGTCATCACGATGTGTTGATCAAG 60.202 45.833 8.80 0.00 41.95 3.02
3015 3267 3.684305 GGTCATCACGATGTGTTGATCAA 59.316 43.478 3.38 3.38 41.95 2.57
3016 3268 3.261580 GGTCATCACGATGTGTTGATCA 58.738 45.455 13.61 0.00 41.95 2.92
3017 3269 2.282555 CGGTCATCACGATGTGTTGATC 59.717 50.000 12.32 11.12 41.95 2.92
3018 3270 2.270923 CGGTCATCACGATGTGTTGAT 58.729 47.619 12.32 0.00 41.95 2.57
3019 3271 1.671556 CCGGTCATCACGATGTGTTGA 60.672 52.381 6.91 6.61 39.13 3.18
3020 3272 0.721154 CCGGTCATCACGATGTGTTG 59.279 55.000 6.91 2.38 39.72 3.33
3021 3273 0.606096 TCCGGTCATCACGATGTGTT 59.394 50.000 0.00 0.00 39.72 3.32
3022 3274 0.108804 GTCCGGTCATCACGATGTGT 60.109 55.000 0.00 0.00 39.72 3.72
3023 3275 0.173481 AGTCCGGTCATCACGATGTG 59.827 55.000 0.00 0.00 39.72 3.21
3024 3276 1.758936 TAGTCCGGTCATCACGATGT 58.241 50.000 0.00 0.00 39.72 3.06
3025 3277 2.863401 TTAGTCCGGTCATCACGATG 57.137 50.000 0.00 0.33 40.09 3.84
3026 3278 5.524971 TTATTTAGTCCGGTCATCACGAT 57.475 39.130 0.00 0.00 0.00 3.73
3027 3279 4.987408 TTATTTAGTCCGGTCATCACGA 57.013 40.909 0.00 0.00 0.00 4.35
3028 3280 9.020813 CATATATTATTTAGTCCGGTCATCACG 57.979 37.037 0.00 0.00 0.00 4.35
3029 3281 9.314321 CCATATATTATTTAGTCCGGTCATCAC 57.686 37.037 0.00 0.00 0.00 3.06
3030 3282 8.482943 CCCATATATTATTTAGTCCGGTCATCA 58.517 37.037 0.00 0.00 0.00 3.07
3031 3283 7.441458 GCCCATATATTATTTAGTCCGGTCATC 59.559 40.741 0.00 0.00 0.00 2.92
3032 3284 7.280356 GCCCATATATTATTTAGTCCGGTCAT 58.720 38.462 0.00 0.00 0.00 3.06
3033 3285 6.352394 GGCCCATATATTATTTAGTCCGGTCA 60.352 42.308 0.00 0.00 0.00 4.02
3034 3286 6.053650 GGCCCATATATTATTTAGTCCGGTC 58.946 44.000 0.00 0.00 0.00 4.79
3035 3287 5.395990 CGGCCCATATATTATTTAGTCCGGT 60.396 44.000 0.00 0.00 0.00 5.28
3036 3288 5.054477 CGGCCCATATATTATTTAGTCCGG 58.946 45.833 0.00 0.00 0.00 5.14
3037 3289 5.909477 TCGGCCCATATATTATTTAGTCCG 58.091 41.667 0.00 0.00 0.00 4.79
3038 3290 5.758784 GCTCGGCCCATATATTATTTAGTCC 59.241 44.000 0.00 0.00 0.00 3.85
3039 3291 6.346096 TGCTCGGCCCATATATTATTTAGTC 58.654 40.000 0.00 0.00 0.00 2.59
3040 3292 6.156256 TCTGCTCGGCCCATATATTATTTAGT 59.844 38.462 0.00 0.00 0.00 2.24
3041 3293 6.582636 TCTGCTCGGCCCATATATTATTTAG 58.417 40.000 0.00 0.00 0.00 1.85
3042 3294 6.553953 TCTGCTCGGCCCATATATTATTTA 57.446 37.500 0.00 0.00 0.00 1.40
3043 3295 5.435686 TCTGCTCGGCCCATATATTATTT 57.564 39.130 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.