Multiple sequence alignment - TraesCS5D01G509400

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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 TraesCS5D01G509400 chr5D 100.000 4511 0 0 1 4511 534576062 534571552 0.000000e+00 8331.0
1 TraesCS5D01G509400 chr5D 95.854 2822 76 19 442 3244 487950184 487952983 0.000000e+00 4525.0
2 TraesCS5D01G509400 chr5D 95.337 1201 46 6 3312 4511 487953005 487954196 0.000000e+00 1899.0
3 TraesCS5D01G509400 chr5D 97.817 229 5 0 177 405 487949959 487950187 3.270000e-106 396.0
4 TraesCS5D01G509400 chr5D 97.321 112 1 1 1 112 487949506 487949615 5.960000e-44 189.0
5 TraesCS5D01G509400 chr5D 72.500 400 95 14 1108 1501 445492366 445491976 1.030000e-21 115.0
6 TraesCS5D01G509400 chr5A 93.319 2874 103 22 873 3713 608653723 608656540 0.000000e+00 4161.0
7 TraesCS5D01G509400 chr5A 95.092 326 5 3 464 787 608653407 608653723 1.870000e-138 503.0
8 TraesCS5D01G509400 chr5A 96.026 151 6 0 3710 3860 608656833 608656983 3.490000e-61 246.0
9 TraesCS5D01G509400 chr5B 92.842 1425 42 15 825 2210 600548955 600550358 0.000000e+00 2012.0
10 TraesCS5D01G509400 chr5B 96.484 768 27 0 2452 3219 600550355 600551122 0.000000e+00 1269.0
11 TraesCS5D01G509400 chr5B 95.096 469 19 4 3392 3859 600551120 600551585 0.000000e+00 736.0
12 TraesCS5D01G509400 chr5B 93.871 310 11 4 378 686 600548654 600548956 1.140000e-125 460.0
13 TraesCS5D01G509400 chr5B 84.590 305 21 10 1 280 600545239 600545542 3.440000e-71 279.0
14 TraesCS5D01G509400 chrUn 83.528 1196 172 13 2003 3193 26487444 26486269 0.000000e+00 1094.0
15 TraesCS5D01G509400 chrUn 83.298 952 99 34 821 1733 26488653 26487723 0.000000e+00 822.0
16 TraesCS5D01G509400 chrUn 77.366 486 93 14 1124 1605 63573185 63572713 5.750000e-69 272.0
17 TraesCS5D01G509400 chrUn 77.366 486 93 14 1124 1605 411620758 411620286 5.750000e-69 272.0
18 TraesCS5D01G509400 chrUn 88.820 161 13 4 3238 3394 95996416 95996575 4.610000e-45 193.0
19 TraesCS5D01G509400 chrUn 90.909 88 8 0 193 280 238126117 238126204 7.930000e-23 119.0
20 TraesCS5D01G509400 chr6B 82.403 1182 168 21 2003 3178 82726898 82725751 0.000000e+00 994.0
21 TraesCS5D01G509400 chr6B 79.741 1160 190 26 1963 3110 2637501 2638627 0.000000e+00 798.0
22 TraesCS5D01G509400 chr6B 85.694 720 88 9 1022 1733 82727895 82727183 0.000000e+00 745.0
23 TraesCS5D01G509400 chr6B 83.901 646 74 18 1022 1639 2636474 2637117 1.400000e-164 590.0
24 TraesCS5D01G509400 chr6B 90.506 158 11 3 3240 3394 140859324 140859480 5.920000e-49 206.0
25 TraesCS5D01G509400 chr6B 79.181 293 34 14 1056 1338 718911614 718911889 1.290000e-40 178.0
26 TraesCS5D01G509400 chr6B 74.359 429 61 19 2005 2395 718916985 718917402 2.190000e-28 137.0
27 TraesCS5D01G509400 chr6B 95.745 47 2 0 1107 1153 716263200 716263246 4.840000e-10 76.8
28 TraesCS5D01G509400 chr6B 74.419 172 30 10 1657 1825 2637188 2637348 1.350000e-05 62.1
29 TraesCS5D01G509400 chr1D 82.131 1192 178 22 1998 3170 405056292 405057467 0.000000e+00 989.0
30 TraesCS5D01G509400 chr1D 86.066 732 84 9 1053 1771 405055313 405056039 0.000000e+00 771.0
31 TraesCS5D01G509400 chr6D 76.661 587 79 33 2043 2587 473277203 473276633 5.750000e-69 272.0
32 TraesCS5D01G509400 chr6D 96.226 53 2 0 123 175 63119719 63119667 2.240000e-13 87.9
33 TraesCS5D01G509400 chr4D 76.236 526 95 22 1108 1624 2110158 2110662 7.490000e-63 252.0
34 TraesCS5D01G509400 chr4D 71.429 259 67 7 1245 1501 2973696 2973949 1.350000e-05 62.1
35 TraesCS5D01G509400 chr7A 90.446 157 11 3 3240 3393 130229540 130229695 2.130000e-48 204.0
36 TraesCS5D01G509400 chr7A 81.034 174 31 2 2880 3052 719637762 719637590 2.190000e-28 137.0
37 TraesCS5D01G509400 chr7A 90.196 102 8 2 183 283 646477221 646477321 1.020000e-26 132.0
38 TraesCS5D01G509400 chr7A 90.909 88 8 0 193 280 85744177 85744264 7.930000e-23 119.0
39 TraesCS5D01G509400 chr7A 96.226 53 2 0 126 178 646477141 646477193 2.240000e-13 87.9
40 TraesCS5D01G509400 chr7A 85.484 62 4 3 847 903 709897718 709897657 4.870000e-05 60.2
41 TraesCS5D01G509400 chr7D 90.446 157 9 5 3241 3393 457148795 457148949 7.650000e-48 202.0
42 TraesCS5D01G509400 chr7D 78.531 177 38 0 2886 3062 174333115 174333291 2.850000e-22 117.0
43 TraesCS5D01G509400 chr7D 89.011 91 10 0 186 276 15501027 15500937 3.690000e-21 113.0
44 TraesCS5D01G509400 chr3D 89.091 165 13 4 3234 3394 300566847 300567010 2.750000e-47 200.0
45 TraesCS5D01G509400 chr3D 91.000 100 7 2 186 283 8382537 8382438 2.830000e-27 134.0
46 TraesCS5D01G509400 chr3D 91.667 60 5 0 123 182 8382623 8382564 2.890000e-12 84.2
47 TraesCS5D01G509400 chr3A 89.873 158 12 3 3240 3394 434850224 434850068 2.750000e-47 200.0
48 TraesCS5D01G509400 chr2D 89.241 158 13 3 3239 3393 86085961 86086117 1.280000e-45 195.0
49 TraesCS5D01G509400 chr2D 91.228 57 4 1 123 178 37471205 37471261 4.840000e-10 76.8
50 TraesCS5D01G509400 chr6A 78.621 290 41 9 2245 2513 616413864 616413575 6.000000e-39 172.0
51 TraesCS5D01G509400 chr2B 93.333 60 4 0 123 182 10603242 10603183 6.220000e-14 89.8
52 TraesCS5D01G509400 chr2A 85.714 56 4 3 123 177 42333384 42333436 6.300000e-04 56.5


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 TraesCS5D01G509400 chr5D 534571552 534576062 4510 True 8331.000000 8331 100.000000 1 4511 1 chr5D.!!$R2 4510
1 TraesCS5D01G509400 chr5D 487949506 487954196 4690 False 1752.250000 4525 96.582250 1 4511 4 chr5D.!!$F1 4510
2 TraesCS5D01G509400 chr5A 608653407 608656983 3576 False 1636.666667 4161 94.812333 464 3860 3 chr5A.!!$F1 3396
3 TraesCS5D01G509400 chr5B 600545239 600551585 6346 False 951.200000 2012 92.576600 1 3859 5 chr5B.!!$F1 3858
4 TraesCS5D01G509400 chrUn 26486269 26488653 2384 True 958.000000 1094 83.413000 821 3193 2 chrUn.!!$R3 2372
5 TraesCS5D01G509400 chr6B 82725751 82727895 2144 True 869.500000 994 84.048500 1022 3178 2 chr6B.!!$R1 2156
6 TraesCS5D01G509400 chr6B 2636474 2638627 2153 False 483.366667 798 79.353667 1022 3110 3 chr6B.!!$F5 2088
7 TraesCS5D01G509400 chr1D 405055313 405057467 2154 False 880.000000 989 84.098500 1053 3170 2 chr1D.!!$F1 2117
8 TraesCS5D01G509400 chr6D 473276633 473277203 570 True 272.000000 272 76.661000 2043 2587 1 chr6D.!!$R2 544
9 TraesCS5D01G509400 chr4D 2110158 2110662 504 False 252.000000 252 76.236000 1108 1624 1 chr4D.!!$F1 516

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
443 3800 0.101759 ATGCACATCATTTCAGCGCC 59.898 50.0 2.29 0.0 29.16 6.53 F
1562 5011 0.179124 GCTCTTCGTCTTCGGCATCT 60.179 55.0 0.00 0.0 37.69 2.90 F
2037 5639 0.393132 GTGGCCTTAGCTTCCCTGAC 60.393 60.0 3.32 0.0 39.73 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2355 5991 0.320421 GTGCCGTTGAACTAGCTCCA 60.320 55.000 8.35 0.0 0.0 3.86 R
3129 6791 0.459489 TGCTGTTGAAGTTTGGTGGC 59.541 50.000 0.00 0.0 0.0 5.01 R
3918 7882 1.008538 CAGCGTTCAACTTGCCCAC 60.009 57.895 0.00 0.0 0.0 4.61 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
42 43 0.537371 CCACTCTGACCCACCCAAAC 60.537 60.000 0.00 0.00 0.00 2.93
118 119 4.069869 CATTCATGCCGCCCTAGG 57.930 61.111 0.06 0.06 0.00 3.02
120 121 2.078665 ATTCATGCCGCCCTAGGGT 61.079 57.895 28.96 5.79 37.65 4.34
121 122 2.343475 ATTCATGCCGCCCTAGGGTG 62.343 60.000 31.45 31.45 44.81 4.61
178 179 1.230497 GAGGAGGATGAGGACCCGA 59.770 63.158 0.00 0.00 0.00 5.14
190 493 2.122989 ACCCGACACACTGGAGGT 60.123 61.111 0.00 0.00 0.00 3.85
347 1045 9.944663 GTAATTTAAGTTGTGTTCTGTTGATCA 57.055 29.630 0.00 0.00 0.00 2.92
405 3762 2.171237 CTCATGACCATAGTTCTGCCCA 59.829 50.000 0.00 0.00 0.00 5.36
406 3763 2.171237 TCATGACCATAGTTCTGCCCAG 59.829 50.000 0.00 0.00 0.00 4.45
407 3764 0.911769 TGACCATAGTTCTGCCCAGG 59.088 55.000 0.00 0.00 0.00 4.45
408 3765 0.464554 GACCATAGTTCTGCCCAGGC 60.465 60.000 0.38 0.38 42.35 4.85
409 3766 1.524621 CCATAGTTCTGCCCAGGCG 60.525 63.158 3.83 0.00 45.51 5.52
410 3767 2.182842 CATAGTTCTGCCCAGGCGC 61.183 63.158 0.00 0.00 45.51 6.53
411 3768 3.740128 ATAGTTCTGCCCAGGCGCG 62.740 63.158 0.00 0.00 45.51 6.86
441 3798 2.554806 ACATGCACATCATTTCAGCG 57.445 45.000 0.00 0.00 31.79 5.18
442 3799 1.197055 CATGCACATCATTTCAGCGC 58.803 50.000 0.00 0.00 31.79 5.92
443 3800 0.101759 ATGCACATCATTTCAGCGCC 59.898 50.000 2.29 0.00 29.16 6.53
444 3801 1.226773 GCACATCATTTCAGCGCCC 60.227 57.895 2.29 0.00 0.00 6.13
682 4041 7.734924 AAGCAGATAATTAAAGCATCGATGA 57.265 32.000 29.20 7.94 0.00 2.92
759 4118 7.486647 AGGCATGAAATCAAAAGCATTAGTAG 58.513 34.615 0.00 0.00 0.00 2.57
760 4119 6.698766 GGCATGAAATCAAAAGCATTAGTAGG 59.301 38.462 0.00 0.00 0.00 3.18
761 4120 7.416664 GGCATGAAATCAAAAGCATTAGTAGGA 60.417 37.037 0.00 0.00 0.00 2.94
762 4121 7.646922 GCATGAAATCAAAAGCATTAGTAGGAG 59.353 37.037 0.00 0.00 0.00 3.69
763 4122 8.680903 CATGAAATCAAAAGCATTAGTAGGAGT 58.319 33.333 0.00 0.00 0.00 3.85
764 4123 9.905713 ATGAAATCAAAAGCATTAGTAGGAGTA 57.094 29.630 0.00 0.00 0.00 2.59
871 4234 1.528542 CTAGGGGAGATGGCGTCGA 60.529 63.158 0.00 0.00 0.00 4.20
971 4338 0.372334 GGTGTTGCCGTATGTAAGCG 59.628 55.000 0.00 0.00 0.00 4.68
1322 4762 2.173669 CGCCATAAGCAGTGGACGG 61.174 63.158 6.26 0.00 44.04 4.79
1518 4967 4.736896 GTGGTGGTCCGGCGAGTC 62.737 72.222 9.30 0.00 36.30 3.36
1562 5011 0.179124 GCTCTTCGTCTTCGGCATCT 60.179 55.000 0.00 0.00 37.69 2.90
1741 5253 2.638719 GCGACAATGTGCACAGCA 59.361 55.556 25.84 1.00 35.60 4.41
1774 5286 1.550130 AAGCTGCTAACCCGCCTACA 61.550 55.000 0.90 0.00 0.00 2.74
2037 5639 0.393132 GTGGCCTTAGCTTCCCTGAC 60.393 60.000 3.32 0.00 39.73 3.51
2218 5846 2.381911 GGATGGCATGACATGGTTTCT 58.618 47.619 21.56 0.00 0.00 2.52
2310 5946 7.311092 TCGAATGTCTAATGGGGTATGTTAT 57.689 36.000 0.00 0.00 0.00 1.89
2355 5991 2.222027 GCCTGCAGCCTACGAAATTAT 58.778 47.619 8.66 0.00 34.35 1.28
2413 6055 4.184629 GGAAGACGTTCATAACTGATGCT 58.815 43.478 0.00 0.00 35.29 3.79
2428 6081 0.618680 ATGCTGCCACCTACAGGAGA 60.619 55.000 1.29 0.00 38.96 3.71
2449 6102 1.678635 CAGCGATTTCAGGGGCCAA 60.679 57.895 4.39 0.00 0.00 4.52
2545 6204 3.243873 TGCCATTCGACAGGAGTATCATC 60.244 47.826 6.51 0.00 36.25 2.92
2649 6311 2.789339 CGCAACGTAGTATGGAGATGTG 59.211 50.000 0.00 0.00 45.00 3.21
2817 6479 6.037786 TCAAGAGATTATTCAACAGACGGT 57.962 37.500 0.00 0.00 0.00 4.83
3225 6888 9.975218 ATGTGTTAAAAATGTATTACTCCCTCT 57.025 29.630 0.00 0.00 0.00 3.69
3245 6908 9.322769 TCCCTCTGTTTCCTAATATAATACTCC 57.677 37.037 0.00 0.00 0.00 3.85
3246 6909 8.541234 CCCTCTGTTTCCTAATATAATACTCCC 58.459 40.741 0.00 0.00 0.00 4.30
3249 6912 9.322769 TCTGTTTCCTAATATAATACTCCCTCC 57.677 37.037 0.00 0.00 0.00 4.30
3250 6913 8.130671 TGTTTCCTAATATAATACTCCCTCCG 57.869 38.462 0.00 0.00 0.00 4.63
3252 6915 7.951347 TTCCTAATATAATACTCCCTCCGTC 57.049 40.000 0.00 0.00 0.00 4.79
3253 6916 6.430007 TCCTAATATAATACTCCCTCCGTCC 58.570 44.000 0.00 0.00 0.00 4.79
3254 6917 5.597594 CCTAATATAATACTCCCTCCGTCCC 59.402 48.000 0.00 0.00 0.00 4.46
3255 6918 4.687262 ATATAATACTCCCTCCGTCCCA 57.313 45.455 0.00 0.00 0.00 4.37
3256 6919 3.562108 ATAATACTCCCTCCGTCCCAT 57.438 47.619 0.00 0.00 0.00 4.00
3257 6920 4.687262 ATAATACTCCCTCCGTCCCATA 57.313 45.455 0.00 0.00 0.00 2.74
3258 6921 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
3259 6922 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
3260 6923 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
3261 6924 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3262 6925 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3263 6926 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
3264 6927 5.600749 ACTCCCTCCGTCCCATAATATAAT 58.399 41.667 0.00 0.00 0.00 1.28
3265 6928 6.748969 ACTCCCTCCGTCCCATAATATAATA 58.251 40.000 0.00 0.00 0.00 0.98
3266 6929 7.194050 ACTCCCTCCGTCCCATAATATAATAA 58.806 38.462 0.00 0.00 0.00 1.40
3267 6930 7.125356 ACTCCCTCCGTCCCATAATATAATAAC 59.875 40.741 0.00 0.00 0.00 1.89
3268 6931 6.097270 TCCCTCCGTCCCATAATATAATAACG 59.903 42.308 0.00 0.00 0.00 3.18
3269 6932 6.127253 CCCTCCGTCCCATAATATAATAACGT 60.127 42.308 0.00 0.00 0.00 3.99
3270 6933 7.325694 CCTCCGTCCCATAATATAATAACGTT 58.674 38.462 5.88 5.88 0.00 3.99
3271 6934 7.820872 CCTCCGTCCCATAATATAATAACGTTT 59.179 37.037 5.91 0.00 0.00 3.60
3272 6935 9.211485 CTCCGTCCCATAATATAATAACGTTTT 57.789 33.333 5.91 3.53 0.00 2.43
3275 6938 9.962759 CGTCCCATAATATAATAACGTTTTAGC 57.037 33.333 5.91 0.00 0.00 3.09
3324 6987 9.944376 AGACACATTTTAGTATGTATGTTCACT 57.056 29.630 0.00 0.00 36.64 3.41
3326 6989 9.719355 ACACATTTTAGTATGTATGTTCACTCA 57.281 29.630 0.00 0.00 36.64 3.41
3343 7006 9.419297 TGTTCACTCATTTTAGTATGTACAGTC 57.581 33.333 0.33 0.00 0.00 3.51
3451 7116 3.834231 CCACCATGTTTCATTTCCTTCCT 59.166 43.478 0.00 0.00 0.00 3.36
3454 7119 5.186409 CACCATGTTTCATTTCCTTCCTCAT 59.814 40.000 0.00 0.00 0.00 2.90
3455 7120 5.781818 ACCATGTTTCATTTCCTTCCTCATT 59.218 36.000 0.00 0.00 0.00 2.57
3514 7179 6.585322 GCAATGAATTCTTCTTTCACCTGAAG 59.415 38.462 7.05 0.00 40.53 3.02
3516 7181 7.684937 ATGAATTCTTCTTTCACCTGAAGAG 57.315 36.000 7.05 0.00 46.01 2.85
3520 7185 6.927294 TTCTTCTTTCACCTGAAGAGAAAC 57.073 37.500 0.00 0.00 46.01 2.78
3600 7266 8.432110 AAATATGTGATGTAATGCGTCAGTTA 57.568 30.769 0.00 0.00 43.16 2.24
3802 7766 6.456795 AGGCTTCAGTTAATGGAATAAAGC 57.543 37.500 0.00 0.00 37.68 3.51
3918 7882 4.024048 ACTGACAATTAGTTTTGTGGCTCG 60.024 41.667 0.00 0.00 39.85 5.03
3934 7898 2.051345 CGTGGGCAAGTTGAACGC 60.051 61.111 7.16 3.96 0.00 4.84
3951 7915 0.671251 CGCTGGAGACTGGGATAGAC 59.329 60.000 0.00 0.00 43.59 2.59
4081 8045 2.820197 GGAAATTTTTGACGCTCCTCCT 59.180 45.455 0.00 0.00 0.00 3.69
4086 8050 0.973632 TTTGACGCTCCTCCTAAGCA 59.026 50.000 0.00 0.00 39.81 3.91
4087 8051 1.195115 TTGACGCTCCTCCTAAGCAT 58.805 50.000 0.00 0.00 39.81 3.79
4097 8061 2.486191 CCTCCTAAGCATGGCCTTACAG 60.486 54.545 3.32 0.00 0.00 2.74
4165 8129 4.536888 TCCCTATGTAACCTAGTTTTGCCA 59.463 41.667 0.00 0.00 0.00 4.92
4204 8168 1.597027 CCTCCGCCGAAACTGTTGT 60.597 57.895 0.00 0.00 0.00 3.32
4235 8199 1.774110 ATTGCCAAATCGCCCATACA 58.226 45.000 0.00 0.00 0.00 2.29
4264 8228 5.730550 TGCGTAGTAGACCAAATCTGAAAT 58.269 37.500 0.00 0.00 38.49 2.17
4277 8241 8.726870 CCAAATCTGAAATTGGCAATTTAGAT 57.273 30.769 31.80 29.76 40.97 1.98
4293 8257 6.645790 ATTTAGATTCCCATGTCTTGATGC 57.354 37.500 0.00 0.00 0.00 3.91
4297 8261 3.726557 TTCCCATGTCTTGATGCTCTT 57.273 42.857 0.00 0.00 0.00 2.85
4403 8367 1.815003 CAGCTCCAAGGGCACTTTTAG 59.185 52.381 0.00 0.00 33.81 1.85
4430 8394 7.532682 GTCTAGAAGGACATCTTGACAATTC 57.467 40.000 12.04 0.00 45.49 2.17
4483 8447 0.037512 CAAAAATCCATGGGTGCGCA 60.038 50.000 13.02 5.66 0.00 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.073199 GGGTGGGTCAGAGTGGTTG 59.927 63.158 0.00 0.00 0.00 3.77
118 119 4.899239 CCATCCCTCTCGCGCACC 62.899 72.222 8.75 0.00 0.00 5.01
347 1045 3.506810 CAAATTGGACGTGTTGTTGTGT 58.493 40.909 0.00 0.00 0.00 3.72
419 3776 3.972502 CGCTGAAATGATGTGCATGTATG 59.027 43.478 0.00 0.00 37.28 2.39
420 3777 3.549423 GCGCTGAAATGATGTGCATGTAT 60.549 43.478 0.00 0.00 37.28 2.29
421 3778 2.223317 GCGCTGAAATGATGTGCATGTA 60.223 45.455 0.00 0.00 37.28 2.29
422 3779 1.468565 GCGCTGAAATGATGTGCATGT 60.469 47.619 0.00 0.00 37.28 3.21
423 3780 1.197055 GCGCTGAAATGATGTGCATG 58.803 50.000 0.00 0.00 37.28 4.06
424 3781 0.101759 GGCGCTGAAATGATGTGCAT 59.898 50.000 7.64 0.00 38.76 3.96
425 3782 1.507630 GGCGCTGAAATGATGTGCA 59.492 52.632 7.64 0.00 38.76 4.57
426 3783 1.226773 GGGCGCTGAAATGATGTGC 60.227 57.895 7.64 0.00 36.59 4.57
427 3784 1.033746 AGGGGCGCTGAAATGATGTG 61.034 55.000 7.64 0.00 0.00 3.21
428 3785 0.323725 AAGGGGCGCTGAAATGATGT 60.324 50.000 7.64 0.00 0.00 3.06
429 3786 0.819582 AAAGGGGCGCTGAAATGATG 59.180 50.000 7.64 0.00 0.00 3.07
430 3787 1.106285 GAAAGGGGCGCTGAAATGAT 58.894 50.000 7.64 0.00 0.00 2.45
431 3788 0.251121 TGAAAGGGGCGCTGAAATGA 60.251 50.000 7.64 0.00 0.00 2.57
432 3789 0.819582 ATGAAAGGGGCGCTGAAATG 59.180 50.000 7.64 0.00 0.00 2.32
433 3790 1.106285 GATGAAAGGGGCGCTGAAAT 58.894 50.000 7.64 0.00 0.00 2.17
434 3791 0.038166 AGATGAAAGGGGCGCTGAAA 59.962 50.000 7.64 0.00 0.00 2.69
435 3792 0.908910 TAGATGAAAGGGGCGCTGAA 59.091 50.000 7.64 0.00 0.00 3.02
436 3793 0.465705 CTAGATGAAAGGGGCGCTGA 59.534 55.000 7.64 0.00 0.00 4.26
437 3794 0.465705 TCTAGATGAAAGGGGCGCTG 59.534 55.000 7.64 0.00 0.00 5.18
438 3795 0.755686 CTCTAGATGAAAGGGGCGCT 59.244 55.000 7.64 0.00 0.00 5.92
439 3796 0.466124 ACTCTAGATGAAAGGGGCGC 59.534 55.000 0.00 0.00 0.00 6.53
440 3797 2.288518 GCTACTCTAGATGAAAGGGGCG 60.289 54.545 0.00 0.00 0.00 6.13
441 3798 2.969262 AGCTACTCTAGATGAAAGGGGC 59.031 50.000 0.00 0.00 0.00 5.80
442 3799 4.479158 AGAGCTACTCTAGATGAAAGGGG 58.521 47.826 0.00 0.00 39.28 4.79
443 3800 5.136828 TGAGAGCTACTCTAGATGAAAGGG 58.863 45.833 12.45 0.00 41.35 3.95
444 3801 6.061441 TCTGAGAGCTACTCTAGATGAAAGG 58.939 44.000 12.45 0.00 41.35 3.11
682 4041 3.960102 TCTTGATGTTTGGCAAAACTCCT 59.040 39.130 15.29 2.82 45.01 3.69
759 4118 7.041098 CCTGCTATTGATGTTATTTGGTACTCC 60.041 40.741 0.00 0.00 0.00 3.85
760 4119 7.715249 TCCTGCTATTGATGTTATTTGGTACTC 59.285 37.037 0.00 0.00 0.00 2.59
761 4120 7.573710 TCCTGCTATTGATGTTATTTGGTACT 58.426 34.615 0.00 0.00 0.00 2.73
762 4121 7.801716 TCCTGCTATTGATGTTATTTGGTAC 57.198 36.000 0.00 0.00 0.00 3.34
763 4122 8.995027 ATTCCTGCTATTGATGTTATTTGGTA 57.005 30.769 0.00 0.00 0.00 3.25
764 4123 7.014615 GGATTCCTGCTATTGATGTTATTTGGT 59.985 37.037 0.00 0.00 0.00 3.67
871 4234 1.821136 GCTGCTCCTTGGCATAAACTT 59.179 47.619 0.00 0.00 41.63 2.66
971 4338 2.599082 CGTCTCCGTGCTTAAGATGTTC 59.401 50.000 6.67 0.00 0.00 3.18
1004 4400 4.084888 CGCCAACGGAAAGCGTCC 62.085 66.667 3.64 0.00 44.65 4.79
1562 5011 4.262549 CCATGGCTTGAGACCAAATTTCAA 60.263 41.667 0.00 0.00 41.49 2.69
1741 5253 2.641559 GCTTGTTGCTCGCAGCTT 59.358 55.556 7.25 0.00 42.97 3.74
1774 5286 3.623906 ATGTGTCTGACTGCTATTGCT 57.376 42.857 9.51 0.00 40.48 3.91
2054 5656 2.293122 TGCTGTTGTAACCATGCTTGTC 59.707 45.455 0.00 0.00 0.00 3.18
2283 5915 6.601332 ACATACCCCATTAGACATTCGAAAT 58.399 36.000 0.00 0.00 0.00 2.17
2284 5916 5.996644 ACATACCCCATTAGACATTCGAAA 58.003 37.500 0.00 0.00 0.00 3.46
2310 5946 4.331968 CTGCCTTACATACCAAACCTTGA 58.668 43.478 0.00 0.00 0.00 3.02
2355 5991 0.320421 GTGCCGTTGAACTAGCTCCA 60.320 55.000 8.35 0.00 0.00 3.86
2413 6055 1.833630 CTGAATCTCCTGTAGGTGGCA 59.166 52.381 0.00 0.00 36.34 4.92
2428 6081 0.753111 GGCCCCTGAAATCGCTGAAT 60.753 55.000 0.00 0.00 0.00 2.57
2449 6102 2.158385 ACTGAACCTCTCCAGAGTCAGT 60.158 50.000 17.93 17.93 45.61 3.41
2649 6311 3.978687 AGCAGGTATAACATGTAGTCGC 58.021 45.455 0.00 0.00 31.66 5.19
2817 6479 3.081710 TGTGAATCAGAGTACTCCCGA 57.918 47.619 19.38 16.05 0.00 5.14
3129 6791 0.459489 TGCTGTTGAAGTTTGGTGGC 59.541 50.000 0.00 0.00 0.00 5.01
3225 6888 7.731688 ACGGAGGGAGTATTATATTAGGAAACA 59.268 37.037 0.00 0.00 0.00 2.83
3240 6903 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
3244 6907 6.127253 ACGTTATTATATTATGGGACGGAGGG 60.127 42.308 0.00 0.00 33.95 4.30
3245 6908 6.870769 ACGTTATTATATTATGGGACGGAGG 58.129 40.000 0.00 0.00 33.95 4.30
3246 6909 8.767478 AAACGTTATTATATTATGGGACGGAG 57.233 34.615 0.00 0.00 33.95 4.63
3249 6912 9.962759 GCTAAAACGTTATTATATTATGGGACG 57.037 33.333 0.00 0.00 35.59 4.79
3263 6926 9.744468 ACAAATCAAGAAAAGCTAAAACGTTAT 57.256 25.926 0.00 0.00 0.00 1.89
3265 6928 9.744468 ATACAAATCAAGAAAAGCTAAAACGTT 57.256 25.926 0.00 0.00 0.00 3.99
3266 6929 9.180678 CATACAAATCAAGAAAAGCTAAAACGT 57.819 29.630 0.00 0.00 0.00 3.99
3267 6930 9.180678 ACATACAAATCAAGAAAAGCTAAAACG 57.819 29.630 0.00 0.00 0.00 3.60
3316 6979 9.944376 ACTGTACATACTAAAATGAGTGAACAT 57.056 29.630 0.00 0.00 0.00 2.71
3317 6980 9.419297 GACTGTACATACTAAAATGAGTGAACA 57.581 33.333 0.00 0.00 0.00 3.18
3318 6981 9.419297 TGACTGTACATACTAAAATGAGTGAAC 57.581 33.333 0.00 0.00 0.00 3.18
3319 6982 9.990360 TTGACTGTACATACTAAAATGAGTGAA 57.010 29.630 0.00 0.00 0.00 3.18
3365 7028 7.059202 TCCCTCCGTTTCTTAATATAAGACC 57.941 40.000 0.00 0.00 0.00 3.85
3379 7042 2.140839 AGATCGTACTCCCTCCGTTT 57.859 50.000 0.00 0.00 0.00 3.60
3386 7049 2.815478 CTCTTGCAAGATCGTACTCCC 58.185 52.381 28.57 0.00 33.93 4.30
3520 7185 4.050553 CAGCATACACACAACCTTTTTGG 58.949 43.478 0.00 0.00 42.93 3.28
3600 7266 3.181471 GCTAGCGGTGCCTATGATGATAT 60.181 47.826 0.00 0.00 0.00 1.63
3740 7703 2.165319 ACTTTTCCGTACTGCCAGTC 57.835 50.000 0.00 0.00 0.00 3.51
3802 7766 6.426633 TCATAATATTTGAGTATGGCACCGTG 59.573 38.462 0.00 0.00 36.85 4.94
3918 7882 1.008538 CAGCGTTCAACTTGCCCAC 60.009 57.895 0.00 0.00 0.00 4.61
3934 7898 2.035632 GTGGTCTATCCCAGTCTCCAG 58.964 57.143 0.00 0.00 34.43 3.86
3992 7956 9.087424 GCAAGACAAAGTTTTTCAAGAAATAGT 57.913 29.630 4.66 0.00 0.00 2.12
4030 7994 6.742559 AACTATTACCTACCATCGTGGATT 57.257 37.500 10.46 0.00 40.96 3.01
4115 8079 5.862678 TTTTTAGGGGAAGTTGTCCTTTG 57.137 39.130 0.00 0.00 46.92 2.77
4137 8101 6.947376 AAACTAGGTTACATAGGGAGTGTT 57.053 37.500 8.90 0.00 0.00 3.32
4165 8129 6.125589 AGGTGCATTTTGGTCCATTAATTT 57.874 33.333 0.00 0.00 0.00 1.82
4204 8168 4.380761 CGATTTGGCAATTTGAGGTCATGA 60.381 41.667 0.00 0.00 0.00 3.07
4235 8199 7.985184 TCAGATTTGGTCTACTACGCATAATTT 59.015 33.333 0.00 0.00 34.69 1.82
4271 8235 5.759059 AGCATCAAGACATGGGAATCTAAA 58.241 37.500 0.00 0.00 0.00 1.85
4277 8241 3.726557 AAGAGCATCAAGACATGGGAA 57.273 42.857 0.00 0.00 37.82 3.97
4293 8257 4.201950 CCAAAAATGCTCCCGTGATAAGAG 60.202 45.833 0.00 0.00 0.00 2.85
4297 8261 3.013921 GACCAAAAATGCTCCCGTGATA 58.986 45.455 0.00 0.00 0.00 2.15
4430 8394 1.069049 CACTTGAAAACAAGCAGGGGG 59.931 52.381 9.44 0.00 35.70 5.40


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

AutoCloner maintained by Alex Coulton.