Multiple sequence alignment - TraesCS1B01G079800

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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 TraesCS1B01G079800 chr1B 100.000 2877 0 0 1 2877 62283387 62286263 0.000000e+00 5313.0
1 TraesCS1B01G079800 chr1B 91.435 899 71 5 3 900 86678881 86679774 0.000000e+00 1229.0
2 TraesCS1B01G079800 chr1B 80.978 368 43 14 2516 2877 62003027 62003373 1.700000e-67 267.0
3 TraesCS1B01G079800 chr1A 94.616 1263 54 7 900 2152 41918969 41920227 0.000000e+00 1943.0
4 TraesCS1B01G079800 chr1A 87.597 774 91 5 129 900 172909594 172910364 0.000000e+00 893.0
5 TraesCS1B01G079800 chr1A 93.805 565 20 4 2313 2877 41920225 41920774 0.000000e+00 835.0
6 TraesCS1B01G079800 chr1A 90.811 185 16 1 2149 2332 74014405 74014221 2.210000e-61 246.0
7 TraesCS1B01G079800 chr1A 90.566 53 5 0 2389 2441 41907816 41907868 1.430000e-08 71.3
8 TraesCS1B01G079800 chr1D 92.087 1289 60 17 900 2152 41914549 41915831 0.000000e+00 1777.0
9 TraesCS1B01G079800 chr1D 91.325 415 33 1 2313 2724 41915829 41916243 5.380000e-157 564.0
10 TraesCS1B01G079800 chr1D 93.491 169 10 1 2146 2314 490423320 490423153 1.710000e-62 250.0
11 TraesCS1B01G079800 chr1D 94.631 149 8 0 2723 2871 41922043 41922191 6.200000e-57 231.0
12 TraesCS1B01G079800 chr1D 83.333 168 22 5 2494 2661 41863376 41863537 1.790000e-32 150.0
13 TraesCS1B01G079800 chr4A 92.905 902 59 5 1 901 713599333 713598436 0.000000e+00 1306.0
14 TraesCS1B01G079800 chrUn 92.376 905 60 7 1 900 381378551 381377651 0.000000e+00 1280.0
15 TraesCS1B01G079800 chrUn 92.537 670 42 6 236 900 193285143 193284477 0.000000e+00 953.0
16 TraesCS1B01G079800 chr4B 92.264 698 50 4 206 901 500107233 500106538 0.000000e+00 987.0
17 TraesCS1B01G079800 chr4B 94.643 168 8 1 1 168 500107583 500107417 2.840000e-65 259.0
18 TraesCS1B01G079800 chr6B 91.108 731 58 4 171 900 671579514 671578790 0.000000e+00 983.0
19 TraesCS1B01G079800 chr6B 91.603 131 8 3 1 131 157797238 157797365 8.190000e-41 178.0
20 TraesCS1B01G079800 chr5B 92.241 696 51 3 206 900 272828546 272827853 0.000000e+00 983.0
21 TraesCS1B01G079800 chr5B 93.333 300 18 1 1 300 272829166 272828869 2.630000e-120 442.0
22 TraesCS1B01G079800 chr5B 94.643 168 8 1 1 168 272828713 272828547 2.840000e-65 259.0
23 TraesCS1B01G079800 chr5A 88.486 773 84 5 129 900 685053198 685053966 0.000000e+00 929.0
24 TraesCS1B01G079800 chr5A 92.135 178 12 2 2138 2315 382564846 382565021 1.710000e-62 250.0
25 TraesCS1B01G079800 chr4D 95.294 170 7 1 2147 2316 470142618 470142786 4.730000e-68 268.0
26 TraesCS1B01G079800 chr4D 92.655 177 13 0 2144 2320 93338036 93338212 3.680000e-64 255.0
27 TraesCS1B01G079800 chr4D 93.103 174 11 1 2144 2316 93079375 93079202 1.320000e-63 254.0
28 TraesCS1B01G079800 chr2D 94.220 173 10 0 2145 2317 632423579 632423751 6.110000e-67 265.0
29 TraesCS1B01G079800 chr2D 93.642 173 11 0 2145 2317 632685870 632686042 2.840000e-65 259.0
30 TraesCS1B01G079800 chr7A 91.257 183 13 3 2136 2316 48903931 48903750 2.210000e-61 246.0
31 TraesCS1B01G079800 chr3A 93.846 130 6 1 1 130 343807005 343806878 8.130000e-46 195.0
32 TraesCS1B01G079800 chr7D 92.366 131 10 0 1 131 111289641 111289511 1.360000e-43 187.0


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 TraesCS1B01G079800 chr1B 62283387 62286263 2876 False 5313.000000 5313 100.000000 1 2877 1 chr1B.!!$F2 2876
1 TraesCS1B01G079800 chr1B 86678881 86679774 893 False 1229.000000 1229 91.435000 3 900 1 chr1B.!!$F3 897
2 TraesCS1B01G079800 chr1A 41918969 41920774 1805 False 1389.000000 1943 94.210500 900 2877 2 chr1A.!!$F3 1977
3 TraesCS1B01G079800 chr1A 172909594 172910364 770 False 893.000000 893 87.597000 129 900 1 chr1A.!!$F2 771
4 TraesCS1B01G079800 chr1D 41914549 41916243 1694 False 1170.500000 1777 91.706000 900 2724 2 chr1D.!!$F3 1824
5 TraesCS1B01G079800 chr4A 713598436 713599333 897 True 1306.000000 1306 92.905000 1 901 1 chr4A.!!$R1 900
6 TraesCS1B01G079800 chrUn 381377651 381378551 900 True 1280.000000 1280 92.376000 1 900 1 chrUn.!!$R2 899
7 TraesCS1B01G079800 chrUn 193284477 193285143 666 True 953.000000 953 92.537000 236 900 1 chrUn.!!$R1 664
8 TraesCS1B01G079800 chr4B 500106538 500107583 1045 True 623.000000 987 93.453500 1 901 2 chr4B.!!$R1 900
9 TraesCS1B01G079800 chr6B 671578790 671579514 724 True 983.000000 983 91.108000 171 900 1 chr6B.!!$R1 729
10 TraesCS1B01G079800 chr5B 272827853 272829166 1313 True 561.333333 983 93.405667 1 900 3 chr5B.!!$R1 899
11 TraesCS1B01G079800 chr5A 685053198 685053966 768 False 929.000000 929 88.486000 129 900 1 chr5A.!!$F2 771

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
385 954 1.070758 GACAAGACTCAAGGAGTGGCA 59.929 52.381 3.21 0.0 43.53 4.92 F
1099 1679 0.633921 TCTCCCTCCTTCTGCTAGCT 59.366 55.000 17.23 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 2145 1.103803 AATCTACCTCAGCGCGAGAA 58.896 50.0 24.28 14.03 45.45 2.87 R
2819 3434 0.511653 GGAAAGCGAAACAGACGTCC 59.488 55.0 13.01 0.00 0.00 4.79 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
99 101 5.565592 TCGAGCTAGAAAACCATACGTTA 57.434 39.130 0.00 0.00 33.05 3.18
153 155 5.395325 CATCGATGCACTTTAACTCGAAT 57.605 39.130 13.37 0.00 41.15 3.34
155 157 6.576021 CATCGATGCACTTTAACTCGAATAG 58.424 40.000 13.37 1.32 41.15 1.73
157 159 4.267690 CGATGCACTTTAACTCGAATAGCA 59.732 41.667 0.00 0.00 0.00 3.49
188 190 1.601419 CGAGCCCGAAACCCTAGACA 61.601 60.000 0.00 0.00 38.22 3.41
196 198 4.081309 CCCGAAACCCTAGACAGATGTAAA 60.081 45.833 0.00 0.00 0.00 2.01
201 349 7.496346 AAACCCTAGACAGATGTAAATCTCA 57.504 36.000 0.00 0.00 0.00 3.27
267 415 2.281761 CTCCCTTGCAGCAACCGT 60.282 61.111 2.83 0.00 0.00 4.83
363 932 4.858692 CACAATGCAAAGAAGATAAACGGG 59.141 41.667 0.00 0.00 0.00 5.28
385 954 1.070758 GACAAGACTCAAGGAGTGGCA 59.929 52.381 3.21 0.00 43.53 4.92
510 1082 7.413877 GGCAAGATCACACTCAGAAAAGATAAG 60.414 40.741 0.00 0.00 0.00 1.73
523 1095 6.690957 CAGAAAAGATAAGTTGTTTGACGCAA 59.309 34.615 0.00 0.00 0.00 4.85
528 1100 6.913170 AGATAAGTTGTTTGACGCAATCATT 58.087 32.000 4.83 1.86 37.11 2.57
638 1210 9.391006 CACTATAGTGTTTAGAAAAATGCCCTA 57.609 33.333 22.48 0.00 40.96 3.53
669 1241 5.413309 AACTTTGGTCCAAACACATGAAA 57.587 34.783 13.26 0.00 0.00 2.69
739 1312 2.289320 CCATCGCTAAGAGGCTTAGCAT 60.289 50.000 28.37 20.46 45.63 3.79
923 1497 1.395608 ACCAACACGACTTGTTCAACG 59.604 47.619 0.00 0.00 46.05 4.10
980 1556 4.081697 CGTCCATATATACACATCCAGGCA 60.082 45.833 0.00 0.00 0.00 4.75
999 1575 2.888447 GCTCAGGCCAGACCACACT 61.888 63.158 5.01 0.00 43.14 3.55
1022 1602 1.678101 AGTTGAAGAAACAGCACAGCC 59.322 47.619 0.00 0.00 41.61 4.85
1029 1609 2.040278 AGAAACAGCACAGCCCAAGATA 59.960 45.455 0.00 0.00 0.00 1.98
1099 1679 0.633921 TCTCCCTCCTTCTGCTAGCT 59.366 55.000 17.23 0.00 0.00 3.32
1283 1869 3.825833 GAGGAGTCGGCGCGTATGG 62.826 68.421 8.43 0.00 0.00 2.74
1302 1888 3.803082 CAGCATGTTCACCGGCGG 61.803 66.667 27.06 27.06 0.00 6.13
1365 1956 1.192428 GTACCCTCCTCACATCCGTT 58.808 55.000 0.00 0.00 0.00 4.44
1502 2102 3.718210 CTCGCCCGTCCAAGCCTAC 62.718 68.421 0.00 0.00 0.00 3.18
1545 2145 2.938428 AGAACCTGGAGGAGTCTCAT 57.062 50.000 0.00 0.00 41.69 2.90
1554 2154 1.034838 AGGAGTCTCATTCTCGCGCT 61.035 55.000 5.56 0.00 33.26 5.92
1586 2187 2.186903 CGACCGGCCTGCATTAGT 59.813 61.111 0.00 0.00 0.00 2.24
1853 2459 3.252974 AGTATCTCTGTTTCTTGCCCG 57.747 47.619 0.00 0.00 0.00 6.13
2135 2746 4.766404 AGAATTTTACGGGCTGTGAAAG 57.234 40.909 19.35 0.00 39.14 2.62
2152 2763 8.668510 CTGTGAAAGTCCAGCAAATATATACT 57.331 34.615 0.00 0.00 0.00 2.12
2153 2764 8.662781 TGTGAAAGTCCAGCAAATATATACTC 57.337 34.615 0.00 0.00 0.00 2.59
2154 2765 7.715249 TGTGAAAGTCCAGCAAATATATACTCC 59.285 37.037 0.00 0.00 0.00 3.85
2155 2766 7.173390 GTGAAAGTCCAGCAAATATATACTCCC 59.827 40.741 0.00 0.00 0.00 4.30
2156 2767 7.072454 TGAAAGTCCAGCAAATATATACTCCCT 59.928 37.037 0.00 0.00 0.00 4.20
2157 2768 6.613153 AGTCCAGCAAATATATACTCCCTC 57.387 41.667 0.00 0.00 0.00 4.30
2158 2769 5.485708 AGTCCAGCAAATATATACTCCCTCC 59.514 44.000 0.00 0.00 0.00 4.30
2159 2770 4.466370 TCCAGCAAATATATACTCCCTCCG 59.534 45.833 0.00 0.00 0.00 4.63
2160 2771 4.223032 CCAGCAAATATATACTCCCTCCGT 59.777 45.833 0.00 0.00 0.00 4.69
2161 2772 5.280011 CCAGCAAATATATACTCCCTCCGTT 60.280 44.000 0.00 0.00 0.00 4.44
2162 2773 6.231211 CAGCAAATATATACTCCCTCCGTTT 58.769 40.000 0.00 0.00 0.00 3.60
2163 2774 6.710744 CAGCAAATATATACTCCCTCCGTTTT 59.289 38.462 0.00 0.00 0.00 2.43
2164 2775 7.228706 CAGCAAATATATACTCCCTCCGTTTTT 59.771 37.037 0.00 0.00 0.00 1.94
2165 2776 8.434392 AGCAAATATATACTCCCTCCGTTTTTA 58.566 33.333 0.00 0.00 0.00 1.52
2166 2777 9.059260 GCAAATATATACTCCCTCCGTTTTTAA 57.941 33.333 0.00 0.00 0.00 1.52
2174 2785 7.770366 ACTCCCTCCGTTTTTAAATATTTGT 57.230 32.000 11.05 0.00 0.00 2.83
2175 2786 7.823665 ACTCCCTCCGTTTTTAAATATTTGTC 58.176 34.615 11.05 0.00 0.00 3.18
2176 2787 7.668469 ACTCCCTCCGTTTTTAAATATTTGTCT 59.332 33.333 11.05 0.00 0.00 3.41
2177 2788 8.411991 TCCCTCCGTTTTTAAATATTTGTCTT 57.588 30.769 11.05 0.00 0.00 3.01
2178 2789 8.862085 TCCCTCCGTTTTTAAATATTTGTCTTT 58.138 29.630 11.05 0.00 0.00 2.52
2179 2790 9.135843 CCCTCCGTTTTTAAATATTTGTCTTTC 57.864 33.333 11.05 0.00 0.00 2.62
2180 2791 9.908152 CCTCCGTTTTTAAATATTTGTCTTTCT 57.092 29.630 11.05 0.00 0.00 2.52
2196 2807 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
2197 2808 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
2198 2809 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
2199 2810 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
2200 2811 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
2201 2812 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
2202 2813 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
2203 2814 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
2204 2815 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
2206 2817 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
2207 2818 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
2208 2819 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
2209 2820 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
2210 2821 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2211 2822 5.010314 TTCAACAAGTGACTACATACGGAGT 59.990 40.000 0.00 0.00 39.84 3.85
2212 2823 6.207221 TTCAACAAGTGACTACATACGGAGTA 59.793 38.462 0.00 0.00 41.66 2.59
2213 2824 7.255555 TTCAACAAGTGACTACATACGGAGTAA 60.256 37.037 0.00 0.00 41.03 2.24
2229 2840 7.972832 ACGGAGTAAAATGAGTGAATTTACA 57.027 32.000 2.93 0.00 41.94 2.41
2230 2841 7.803724 ACGGAGTAAAATGAGTGAATTTACAC 58.196 34.615 2.93 0.00 41.94 2.90
2305 2916 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2306 2917 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2307 2918 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2308 2919 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2309 2920 6.555463 AGACAAATATTTAGGAACGGAGGA 57.445 37.500 0.00 0.00 0.00 3.71
2310 2921 6.954232 AGACAAATATTTAGGAACGGAGGAA 58.046 36.000 0.00 0.00 0.00 3.36
2311 2922 7.048512 AGACAAATATTTAGGAACGGAGGAAG 58.951 38.462 0.00 0.00 0.00 3.46
2387 3001 2.281761 AGTTGAGGCACGCCCAAG 60.282 61.111 3.95 0.00 36.58 3.61
2463 3077 3.427909 GCGCATCAAAAGGACATGAATCA 60.428 43.478 0.30 0.00 0.00 2.57
2473 3087 5.679734 AGGACATGAATCATAAACGATGC 57.320 39.130 0.00 0.00 35.29 3.91
2474 3088 4.212004 AGGACATGAATCATAAACGATGCG 59.788 41.667 0.00 0.00 35.29 4.73
2485 3099 1.560923 AACGATGCGCAGATCACTAC 58.439 50.000 18.32 0.00 0.00 2.73
2685 3300 3.818295 ATACAGGTAGCTAGGAGAGGG 57.182 52.381 0.00 0.00 0.00 4.30
2695 3310 3.105283 GCTAGGAGAGGGTTGGTTTAGA 58.895 50.000 0.00 0.00 0.00 2.10
2762 3377 5.702670 CCTCATGCTACAAATATCCACGAAT 59.297 40.000 0.00 0.00 0.00 3.34
2774 3389 7.730364 AATATCCACGAATAGCCTTTTACAG 57.270 36.000 0.00 0.00 0.00 2.74
2805 3420 6.112058 CCCCAAAAGAGAGATTTCTACTCTG 58.888 44.000 0.00 0.00 43.55 3.35
2848 3463 2.074547 TTCGCTTTCCAACTACTCCG 57.925 50.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 60 3.822167 TCGATGCATGCATATGTGGATTT 59.178 39.130 32.27 8.08 33.74 2.17
99 101 5.243283 ACTTGTAGTCCGTACTGAATTGTCT 59.757 40.000 0.00 0.00 36.36 3.41
153 155 1.864029 GCTCGATGCATGTACGTGCTA 60.864 52.381 33.63 22.80 45.27 3.49
155 157 1.273887 GCTCGATGCATGTACGTGC 59.726 57.895 29.29 29.29 45.25 5.34
157 159 1.227263 GGGCTCGATGCATGTACGT 60.227 57.895 2.46 0.00 45.15 3.57
188 190 2.420129 GGTGGCGGTGAGATTTACATCT 60.420 50.000 0.00 0.00 43.03 2.90
196 198 2.064581 GGTAGGGTGGCGGTGAGAT 61.065 63.158 0.00 0.00 0.00 2.75
201 349 3.007323 GGAAGGTAGGGTGGCGGT 61.007 66.667 0.00 0.00 0.00 5.68
234 382 1.071385 GGGAGCTCATCGTCCATGAAT 59.929 52.381 17.19 0.00 41.25 2.57
267 415 1.580942 GGACGCATTGCAGCTGAAA 59.419 52.632 20.43 15.35 0.00 2.69
337 906 5.630680 CGTTTATCTTCTTTGCATTGTGCTT 59.369 36.000 3.41 0.00 45.31 3.91
363 932 1.002544 CCACTCCTTGAGTCTTGTCCC 59.997 57.143 0.00 0.00 41.37 4.46
385 954 5.050091 CGACATTATTTCATCTTTAGCCGCT 60.050 40.000 0.00 0.00 0.00 5.52
528 1100 4.576873 GCGGACTGCTAGCTCTATCATATA 59.423 45.833 17.23 0.00 41.73 0.86
535 1107 2.835705 GCGCGGACTGCTAGCTCTA 61.836 63.158 17.23 0.00 43.27 2.43
555 1127 4.201724 GCGAAAGTCGATGCTAGACAATTT 60.202 41.667 1.05 2.97 43.74 1.82
589 1161 2.570365 GGCAGATGATGTGTGGCAA 58.430 52.632 0.00 0.00 44.87 4.52
638 1210 3.202829 TGGACCAAAGTTTCTTAGCGT 57.797 42.857 0.00 0.00 0.00 5.07
669 1241 7.042321 TGCTATAGCGTCTATTTAAAATGCGTT 60.042 33.333 19.55 0.00 45.83 4.84
739 1312 8.161425 GGGTATCCTCCATAGTTTTAAATAGCA 58.839 37.037 0.00 0.00 0.00 3.49
822 1396 3.053842 ACACGGTAAGATGGAGTCTCCTA 60.054 47.826 19.82 6.94 37.46 2.94
923 1497 0.247736 AGTGCTGCACTGCTAGTACC 59.752 55.000 32.54 2.88 43.63 3.34
980 1556 2.527624 TGTGGTCTGGCCTGAGCT 60.528 61.111 33.08 0.00 39.73 4.09
999 1575 3.181497 GCTGTGCTGTTTCTTCAACTGAA 60.181 43.478 0.00 0.00 36.63 3.02
1022 1602 4.142513 GCTTCTTTGGCAGACTTATCTTGG 60.143 45.833 0.00 0.00 30.42 3.61
1029 1609 2.936202 TCTTGCTTCTTTGGCAGACTT 58.064 42.857 0.00 0.00 40.90 3.01
1283 1869 2.870372 GCCGGTGAACATGCTGTC 59.130 61.111 1.90 0.00 0.00 3.51
1365 1956 7.066163 CAGAGCAAAATTCAGTATGTGGACATA 59.934 37.037 0.00 0.00 37.76 2.29
1500 2100 3.119280 TCTGCAGATCATCGTTTTCGGTA 60.119 43.478 13.74 0.00 44.25 4.02
1502 2102 2.270923 TCTGCAGATCATCGTTTTCGG 58.729 47.619 13.74 0.00 44.25 4.30
1545 2145 1.103803 AATCTACCTCAGCGCGAGAA 58.896 50.000 24.28 14.03 45.45 2.87
1554 2154 2.889045 CCGGTCGGATTAATCTACCTCA 59.111 50.000 25.13 3.18 37.50 3.86
1853 2459 8.660373 GTGACTTGCATATCACTTATATTAGGC 58.340 37.037 18.86 0.00 41.69 3.93
2135 2746 5.624738 CGGAGGGAGTATATATTTGCTGGAC 60.625 48.000 0.00 0.00 0.00 4.02
2149 2760 8.866970 ACAAATATTTAAAAACGGAGGGAGTA 57.133 30.769 0.00 0.00 0.00 2.59
2150 2761 7.668469 AGACAAATATTTAAAAACGGAGGGAGT 59.332 33.333 0.00 0.00 0.00 3.85
2151 2762 8.051901 AGACAAATATTTAAAAACGGAGGGAG 57.948 34.615 0.00 0.00 0.00 4.30
2152 2763 8.411991 AAGACAAATATTTAAAAACGGAGGGA 57.588 30.769 0.00 0.00 0.00 4.20
2153 2764 9.135843 GAAAGACAAATATTTAAAAACGGAGGG 57.864 33.333 0.00 0.00 0.00 4.30
2154 2765 9.908152 AGAAAGACAAATATTTAAAAACGGAGG 57.092 29.630 0.00 0.00 0.00 4.30
2170 2781 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
2171 2782 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
2172 2783 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
2173 2784 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
2174 2785 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
2175 2786 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
2176 2787 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
2177 2788 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
2178 2789 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
2179 2790 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
2180 2791 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
2181 2792 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
2182 2793 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
2183 2794 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
2184 2795 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
2185 2796 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
2186 2797 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
2187 2798 5.010314 ACTCCGTATGTAGTCACTTGTTGAA 59.990 40.000 0.00 0.00 35.39 2.69
2188 2799 4.521639 ACTCCGTATGTAGTCACTTGTTGA 59.478 41.667 0.00 0.00 0.00 3.18
2189 2800 4.806330 ACTCCGTATGTAGTCACTTGTTG 58.194 43.478 0.00 0.00 0.00 3.33
2190 2801 6.579666 TTACTCCGTATGTAGTCACTTGTT 57.420 37.500 0.00 0.00 0.00 2.83
2191 2802 6.579666 TTTACTCCGTATGTAGTCACTTGT 57.420 37.500 0.00 0.00 0.00 3.16
2192 2803 7.758076 TCATTTTACTCCGTATGTAGTCACTTG 59.242 37.037 0.00 0.00 0.00 3.16
2193 2804 7.833786 TCATTTTACTCCGTATGTAGTCACTT 58.166 34.615 0.00 0.00 0.00 3.16
2194 2805 7.122353 ACTCATTTTACTCCGTATGTAGTCACT 59.878 37.037 0.00 0.00 0.00 3.41
2195 2806 7.220300 CACTCATTTTACTCCGTATGTAGTCAC 59.780 40.741 0.00 0.00 0.00 3.67
2196 2807 7.121611 TCACTCATTTTACTCCGTATGTAGTCA 59.878 37.037 0.00 0.00 0.00 3.41
2197 2808 7.478322 TCACTCATTTTACTCCGTATGTAGTC 58.522 38.462 0.00 0.00 0.00 2.59
2198 2809 7.400599 TCACTCATTTTACTCCGTATGTAGT 57.599 36.000 0.00 0.00 0.00 2.73
2199 2810 8.873215 ATTCACTCATTTTACTCCGTATGTAG 57.127 34.615 0.00 0.00 0.00 2.74
2200 2811 9.661563 AAATTCACTCATTTTACTCCGTATGTA 57.338 29.630 0.00 0.00 0.00 2.29
2201 2812 8.561738 AAATTCACTCATTTTACTCCGTATGT 57.438 30.769 0.00 0.00 0.00 2.29
2202 2813 9.916397 GTAAATTCACTCATTTTACTCCGTATG 57.084 33.333 0.00 0.00 34.51 2.39
2203 2814 9.661563 TGTAAATTCACTCATTTTACTCCGTAT 57.338 29.630 0.00 0.00 36.96 3.06
2204 2815 8.928733 GTGTAAATTCACTCATTTTACTCCGTA 58.071 33.333 0.00 0.00 36.96 4.02
2205 2816 7.660208 AGTGTAAATTCACTCATTTTACTCCGT 59.340 33.333 0.00 0.00 44.07 4.69
2206 2817 8.029642 AGTGTAAATTCACTCATTTTACTCCG 57.970 34.615 0.00 0.00 44.07 4.63
2279 2890 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2280 2891 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2281 2892 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2282 2893 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2283 2894 7.551617 TCCTCCGTTCCTAAATATTTGTCTTTC 59.448 37.037 11.05 0.00 0.00 2.62
2284 2895 7.399634 TCCTCCGTTCCTAAATATTTGTCTTT 58.600 34.615 11.05 0.00 0.00 2.52
2285 2896 6.954232 TCCTCCGTTCCTAAATATTTGTCTT 58.046 36.000 11.05 0.00 0.00 3.01
2286 2897 6.555463 TCCTCCGTTCCTAAATATTTGTCT 57.445 37.500 11.05 0.00 0.00 3.41
2287 2898 6.822170 ACTTCCTCCGTTCCTAAATATTTGTC 59.178 38.462 11.05 0.00 0.00 3.18
2288 2899 6.718294 ACTTCCTCCGTTCCTAAATATTTGT 58.282 36.000 11.05 0.00 0.00 2.83
2289 2900 7.767198 TGTACTTCCTCCGTTCCTAAATATTTG 59.233 37.037 11.05 1.40 0.00 2.32
2290 2901 7.854337 TGTACTTCCTCCGTTCCTAAATATTT 58.146 34.615 5.89 5.89 0.00 1.40
2291 2902 7.427989 TGTACTTCCTCCGTTCCTAAATATT 57.572 36.000 0.00 0.00 0.00 1.28
2292 2903 7.427989 TTGTACTTCCTCCGTTCCTAAATAT 57.572 36.000 0.00 0.00 0.00 1.28
2293 2904 6.628844 GCTTGTACTTCCTCCGTTCCTAAATA 60.629 42.308 0.00 0.00 0.00 1.40
2294 2905 5.731591 CTTGTACTTCCTCCGTTCCTAAAT 58.268 41.667 0.00 0.00 0.00 1.40
2295 2906 4.562143 GCTTGTACTTCCTCCGTTCCTAAA 60.562 45.833 0.00 0.00 0.00 1.85
2296 2907 3.056322 GCTTGTACTTCCTCCGTTCCTAA 60.056 47.826 0.00 0.00 0.00 2.69
2297 2908 2.494870 GCTTGTACTTCCTCCGTTCCTA 59.505 50.000 0.00 0.00 0.00 2.94
2298 2909 1.275573 GCTTGTACTTCCTCCGTTCCT 59.724 52.381 0.00 0.00 0.00 3.36
2299 2910 1.275573 AGCTTGTACTTCCTCCGTTCC 59.724 52.381 0.00 0.00 0.00 3.62
2300 2911 2.745515 AGCTTGTACTTCCTCCGTTC 57.254 50.000 0.00 0.00 0.00 3.95
2301 2912 2.094130 GCTAGCTTGTACTTCCTCCGTT 60.094 50.000 7.70 0.00 0.00 4.44
2302 2913 1.477295 GCTAGCTTGTACTTCCTCCGT 59.523 52.381 7.70 0.00 0.00 4.69
2303 2914 1.751924 AGCTAGCTTGTACTTCCTCCG 59.248 52.381 12.68 0.00 0.00 4.63
2304 2915 3.700038 TGTAGCTAGCTTGTACTTCCTCC 59.300 47.826 24.88 0.00 0.00 4.30
2305 2916 4.985538 TGTAGCTAGCTTGTACTTCCTC 57.014 45.455 24.88 2.09 0.00 3.71
2306 2917 4.442192 GCATGTAGCTAGCTTGTACTTCCT 60.442 45.833 24.88 0.00 41.15 3.36
2307 2918 3.804873 GCATGTAGCTAGCTTGTACTTCC 59.195 47.826 24.88 0.00 41.15 3.46
2308 2919 4.433615 TGCATGTAGCTAGCTTGTACTTC 58.566 43.478 24.88 8.80 45.94 3.01
2309 2920 4.471904 TGCATGTAGCTAGCTTGTACTT 57.528 40.909 24.88 10.50 45.94 2.24
2310 2921 4.679373 ATGCATGTAGCTAGCTTGTACT 57.321 40.909 24.88 0.00 45.94 2.73
2311 2922 4.811024 TGAATGCATGTAGCTAGCTTGTAC 59.189 41.667 24.88 15.83 45.94 2.90
2387 3001 2.672961 TGGTGTGATCGATCAACTCC 57.327 50.000 28.83 26.79 38.75 3.85
2446 3060 7.680442 TCGTTTATGATTCATGTCCTTTTGA 57.320 32.000 9.46 0.00 0.00 2.69
2463 3077 2.826428 AGTGATCTGCGCATCGTTTAT 58.174 42.857 12.24 0.00 0.00 1.40
2473 3087 4.433615 AGGTACATTTGTAGTGATCTGCG 58.566 43.478 0.00 0.00 0.00 5.18
2474 3088 9.542462 TTTATAGGTACATTTGTAGTGATCTGC 57.458 33.333 0.00 0.00 0.00 4.26
2659 3274 5.378332 TCTCCTAGCTACCTGTATTGTCTC 58.622 45.833 0.00 0.00 0.00 3.36
2725 3340 2.289565 GCATGAGGCTTTGTACCTACC 58.710 52.381 0.00 0.00 37.77 3.18
2762 3377 2.420967 GGGGAATCGCTGTAAAAGGCTA 60.421 50.000 0.00 0.00 0.00 3.93
2774 3389 1.065418 TCTCTCTTTTGGGGGAATCGC 60.065 52.381 0.00 0.00 0.00 4.58
2805 3420 3.982058 CAGACGTCCTGTACTCTTGTTTC 59.018 47.826 13.01 0.00 38.10 2.78
2819 3434 0.511653 GGAAAGCGAAACAGACGTCC 59.488 55.000 13.01 0.00 0.00 4.79
2848 3463 1.330521 TCTGTTTGCTTGCTCGTCAAC 59.669 47.619 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.