Multiple sequence alignment - TraesCS2B01G117400

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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 TraesCS2B01G117400 chr2B 100.000 3689 0 0 1 3689 80539565 80535877 0.000000e+00 6813.0
1 TraesCS2B01G117400 chr2B 91.826 734 57 3 2956 3689 565058675 565057945 0.000000e+00 1020.0
2 TraesCS2B01G117400 chr2B 91.475 739 57 5 2953 3689 653894307 653895041 0.000000e+00 1011.0
3 TraesCS2B01G117400 chr2B 100.000 28 0 0 2925 2952 385089688 385089715 7.000000e-03 52.8
4 TraesCS2B01G117400 chr2D 93.632 1963 98 11 954 2908 42729563 42731506 0.000000e+00 2907.0
5 TraesCS2B01G117400 chr2D 92.979 1410 60 13 1540 2929 52025176 52023786 0.000000e+00 2019.0
6 TraesCS2B01G117400 chr2D 89.579 1353 57 30 161 1453 52026509 52025181 0.000000e+00 1640.0
7 TraesCS2B01G117400 chr2D 86.681 961 74 26 1 960 42727774 42728681 0.000000e+00 1016.0
8 TraesCS2B01G117400 chr2D 100.000 28 0 0 2925 2952 277960755 277960728 7.000000e-03 52.8
9 TraesCS2B01G117400 chr2A 90.893 2207 114 36 667 2856 53291476 53289340 0.000000e+00 2881.0
10 TraesCS2B01G117400 chr2A 86.347 271 20 8 383 650 53334236 53333980 2.810000e-71 279.0
11 TraesCS2B01G117400 chr2A 83.955 268 33 8 1 265 53383505 53383245 7.910000e-62 248.0
12 TraesCS2B01G117400 chr2A 91.304 138 12 0 2472 2609 53278321 53278184 4.860000e-44 189.0
13 TraesCS2B01G117400 chr2A 98.276 58 1 0 2839 2896 53289039 53288982 6.520000e-18 102.0
14 TraesCS2B01G117400 chr2A 100.000 28 0 0 2925 2952 724339054 724339081 7.000000e-03 52.8
15 TraesCS2B01G117400 chr1B 93.496 738 47 1 2953 3689 394894143 394894880 0.000000e+00 1096.0
16 TraesCS2B01G117400 chr1B 92.308 741 47 5 2953 3688 573066322 573065587 0.000000e+00 1044.0
17 TraesCS2B01G117400 chr1B 91.790 743 50 5 2953 3689 139087083 139086346 0.000000e+00 1024.0
18 TraesCS2B01G117400 chr5D 93.089 738 46 3 2953 3689 297122501 297123234 0.000000e+00 1075.0
19 TraesCS2B01G117400 chr5D 100.000 28 0 0 2925 2952 539718849 539718876 7.000000e-03 52.8
20 TraesCS2B01G117400 chr4B 92.276 738 53 3 2953 3689 1176983 1177717 0.000000e+00 1044.0
21 TraesCS2B01G117400 chr3B 92.287 739 51 6 2953 3689 225234088 225234822 0.000000e+00 1044.0
22 TraesCS2B01G117400 chr6B 91.667 744 51 5 2953 3689 132888640 132889379 0.000000e+00 1020.0
23 TraesCS2B01G117400 chr6B 92.500 40 0 2 2924 2960 203276366 203276405 2.000000e-03 54.7
24 TraesCS2B01G117400 chr3D 92.308 39 0 2 2925 2960 366227503 366227465 7.000000e-03 52.8


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 TraesCS2B01G117400 chr2B 80535877 80539565 3688 True 6813.0 6813 100.0000 1 3689 1 chr2B.!!$R1 3688
1 TraesCS2B01G117400 chr2B 565057945 565058675 730 True 1020.0 1020 91.8260 2956 3689 1 chr2B.!!$R2 733
2 TraesCS2B01G117400 chr2B 653894307 653895041 734 False 1011.0 1011 91.4750 2953 3689 1 chr2B.!!$F2 736
3 TraesCS2B01G117400 chr2D 42727774 42731506 3732 False 1961.5 2907 90.1565 1 2908 2 chr2D.!!$F1 2907
4 TraesCS2B01G117400 chr2D 52023786 52026509 2723 True 1829.5 2019 91.2790 161 2929 2 chr2D.!!$R2 2768
5 TraesCS2B01G117400 chr2A 53288982 53291476 2494 True 1491.5 2881 94.5845 667 2896 2 chr2A.!!$R4 2229
6 TraesCS2B01G117400 chr1B 394894143 394894880 737 False 1096.0 1096 93.4960 2953 3689 1 chr1B.!!$F1 736
7 TraesCS2B01G117400 chr1B 573065587 573066322 735 True 1044.0 1044 92.3080 2953 3688 1 chr1B.!!$R2 735
8 TraesCS2B01G117400 chr1B 139086346 139087083 737 True 1024.0 1024 91.7900 2953 3689 1 chr1B.!!$R1 736
9 TraesCS2B01G117400 chr5D 297122501 297123234 733 False 1075.0 1075 93.0890 2953 3689 1 chr5D.!!$F1 736
10 TraesCS2B01G117400 chr4B 1176983 1177717 734 False 1044.0 1044 92.2760 2953 3689 1 chr4B.!!$F1 736
11 TraesCS2B01G117400 chr3B 225234088 225234822 734 False 1044.0 1044 92.2870 2953 3689 1 chr3B.!!$F1 736
12 TraesCS2B01G117400 chr6B 132888640 132889379 739 False 1020.0 1020 91.6670 2953 3689 1 chr6B.!!$F1 736

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
57 58 0.027455 TGTCGTGAAGCTGCGTTTTG 59.973 50.0 0.0 0.0 0.0 2.44 F
105 106 0.329596 GGCCCTCTTCATGGAGTTGT 59.670 55.0 0.0 0.0 0.0 3.32 F
2017 2987 0.451783 GGATCAATCGTGTTGGTGGC 59.548 55.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 2995 0.729116 CAGGAAGTACGGCTGCAATG 59.271 55.0 0.50 0.0 0.00 2.82 R
2026 2996 1.026718 GCAGGAAGTACGGCTGCAAT 61.027 55.0 0.50 0.0 40.38 3.56 R
2929 4263 0.038166 TCACCCCATTGGAGTTGCTC 59.962 55.0 3.62 0.0 38.00 4.26 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
26 27 6.610075 TTCCCTACGTAATTACCAAACTCT 57.390 37.500 10.01 0.00 0.00 3.24
28 29 7.008021 TCCCTACGTAATTACCAAACTCTTT 57.992 36.000 10.01 0.00 0.00 2.52
57 58 0.027455 TGTCGTGAAGCTGCGTTTTG 59.973 50.000 0.00 0.00 0.00 2.44
77 78 1.805254 CCGCCTCTCCATTTTGCAG 59.195 57.895 0.00 0.00 0.00 4.41
79 80 1.138247 GCCTCTCCATTTTGCAGCG 59.862 57.895 0.00 0.00 0.00 5.18
99 100 1.695597 AGGAGGGCCCTCTTCATGG 60.696 63.158 43.34 0.00 43.31 3.66
105 106 0.329596 GGCCCTCTTCATGGAGTTGT 59.670 55.000 0.00 0.00 0.00 3.32
107 108 2.026262 GGCCCTCTTCATGGAGTTGTTA 60.026 50.000 0.00 0.00 0.00 2.41
112 113 4.556233 CTCTTCATGGAGTTGTTACGACA 58.444 43.478 5.46 0.00 0.00 4.35
115 116 4.594123 TCATGGAGTTGTTACGACAGAA 57.406 40.909 5.46 0.00 37.04 3.02
211 212 9.598517 TTAATACGTATTACCTCCGTTTCAAAT 57.401 29.630 24.16 0.00 36.12 2.32
227 228 9.543018 CCGTTTCAAATAGTTTGTCTTAGATTC 57.457 33.333 2.74 0.00 41.36 2.52
249 254 9.722056 GATTCAACTACAAATGGATGAATGTAC 57.278 33.333 3.76 0.00 37.56 2.90
250 255 8.862325 TTCAACTACAAATGGATGAATGTACT 57.138 30.769 0.00 0.00 0.00 2.73
252 257 9.952030 TCAACTACAAATGGATGAATGTACTAA 57.048 29.630 0.00 0.00 0.00 2.24
253 258 9.988350 CAACTACAAATGGATGAATGTACTAAC 57.012 33.333 0.00 0.00 0.00 2.34
254 259 9.733556 AACTACAAATGGATGAATGTACTAACA 57.266 29.630 0.00 0.00 40.69 2.41
255 260 9.162764 ACTACAAATGGATGAATGTACTAACAC 57.837 33.333 0.00 0.00 38.78 3.32
256 261 9.383519 CTACAAATGGATGAATGTACTAACACT 57.616 33.333 0.00 0.00 38.78 3.55
258 263 9.733556 ACAAATGGATGAATGTACTAACACTAA 57.266 29.630 0.00 0.00 38.78 2.24
262 267 9.959721 ATGGATGAATGTACTAACACTAAAAGT 57.040 29.630 0.00 0.00 38.78 2.66
273 278 7.624661 ACTAACACTAAAAGTCTAAAACGTGC 58.375 34.615 0.00 0.00 0.00 5.34
279 284 6.867293 ACTAAAAGTCTAAAACGTGCCTAGAG 59.133 38.462 0.00 0.00 0.00 2.43
280 285 3.870633 AGTCTAAAACGTGCCTAGAGG 57.129 47.619 0.00 0.00 38.53 3.69
300 333 5.041191 AGGCATTCGGATCTAGACAAATT 57.959 39.130 0.00 0.00 0.00 1.82
318 351 7.552330 AGACAAATTTAAAGCAAGCTTTTTGGA 59.448 29.630 23.25 4.64 42.93 3.53
319 352 7.471721 ACAAATTTAAAGCAAGCTTTTTGGAC 58.528 30.769 23.25 0.00 42.93 4.02
321 354 4.640789 TTAAAGCAAGCTTTTTGGACGA 57.359 36.364 23.25 2.89 42.93 4.20
326 359 1.953686 CAAGCTTTTTGGACGAAGGGA 59.046 47.619 0.00 0.00 0.00 4.20
327 360 1.897560 AGCTTTTTGGACGAAGGGAG 58.102 50.000 0.00 0.00 0.00 4.30
328 361 1.143073 AGCTTTTTGGACGAAGGGAGT 59.857 47.619 0.00 0.00 0.00 3.85
329 362 2.370849 AGCTTTTTGGACGAAGGGAGTA 59.629 45.455 0.00 0.00 0.00 2.59
330 363 3.009143 AGCTTTTTGGACGAAGGGAGTAT 59.991 43.478 0.00 0.00 0.00 2.12
331 364 3.756963 GCTTTTTGGACGAAGGGAGTATT 59.243 43.478 0.00 0.00 0.00 1.89
332 365 4.939439 GCTTTTTGGACGAAGGGAGTATTA 59.061 41.667 0.00 0.00 0.00 0.98
333 366 5.064834 GCTTTTTGGACGAAGGGAGTATTAG 59.935 44.000 0.00 0.00 0.00 1.73
334 367 4.748277 TTTGGACGAAGGGAGTATTAGG 57.252 45.455 0.00 0.00 0.00 2.69
335 368 2.037144 TGGACGAAGGGAGTATTAGGC 58.963 52.381 0.00 0.00 0.00 3.93
385 418 7.068226 GCACATTAAAACTGGGTAGGATGTTAT 59.932 37.037 0.00 0.00 0.00 1.89
440 473 9.932207 TTTGACAATCAATATGATTTTGCTCTT 57.068 25.926 2.93 0.00 44.03 2.85
459 518 5.457799 GCTCTTTACACATATCGAACGCTTA 59.542 40.000 0.00 0.00 0.00 3.09
492 551 2.622546 TCACGTCGTTGAATCGATGA 57.377 45.000 13.78 2.56 45.90 2.92
521 580 2.297701 AGTCGTGTTGTTTTCATGGCT 58.702 42.857 0.00 0.00 32.81 4.75
522 581 2.290641 AGTCGTGTTGTTTTCATGGCTC 59.709 45.455 0.00 0.00 32.26 4.70
525 584 3.496884 TCGTGTTGTTTTCATGGCTCTAC 59.503 43.478 0.00 0.00 0.00 2.59
568 627 1.539065 CCGTCGAGGAATCCAAGGATG 60.539 57.143 6.70 0.95 45.00 3.51
624 683 2.037136 CGTCCTCGTCGTAGGTGGT 61.037 63.158 9.58 0.00 37.91 4.16
693 752 3.124921 CCACGGGATGTTGACGCC 61.125 66.667 0.00 0.00 0.00 5.68
718 777 2.160417 CGGCTGAACTTTCACAGAATCC 59.840 50.000 0.00 0.00 36.38 3.01
1025 1987 1.936880 CGCTCGCAGATCTCGTGTC 60.937 63.158 12.27 7.31 33.89 3.67
1026 1988 1.936880 GCTCGCAGATCTCGTGTCG 60.937 63.158 12.27 3.87 33.89 4.35
1027 1989 1.425825 CTCGCAGATCTCGTGTCGT 59.574 57.895 12.27 0.00 33.89 4.34
1028 1990 0.859374 CTCGCAGATCTCGTGTCGTG 60.859 60.000 12.27 0.00 33.89 4.35
1155 2121 2.041265 TTCCTGGAGGAGAGCCCC 59.959 66.667 0.00 0.00 46.36 5.80
1319 2285 2.122167 CGAGGAGGAAGGAGGACGG 61.122 68.421 0.00 0.00 0.00 4.79
1465 2431 3.097728 CGTGTCCGTGTGCTCGAC 61.098 66.667 0.00 0.00 0.00 4.20
1845 2811 2.311854 CCACCTGGGCTCCTTCCAT 61.312 63.158 0.00 0.00 33.29 3.41
1848 2814 1.277580 ACCTGGGCTCCTTCCATCTG 61.278 60.000 0.00 0.00 33.29 2.90
1979 2949 5.528043 TCAGAGCTCTGGATTATTCTGAC 57.472 43.478 36.92 0.00 43.91 3.51
1994 2964 9.534565 GATTATTCTGACATGTACTTTCTGCTA 57.465 33.333 0.00 0.00 0.00 3.49
2003 2973 7.112122 ACATGTACTTTCTGCTAAATGGATCA 58.888 34.615 0.00 0.00 0.00 2.92
2008 2978 5.882557 ACTTTCTGCTAAATGGATCAATCGT 59.117 36.000 0.00 0.00 0.00 3.73
2011 2981 5.185454 TCTGCTAAATGGATCAATCGTGTT 58.815 37.500 0.00 0.00 0.00 3.32
2013 2983 4.096231 TGCTAAATGGATCAATCGTGTTGG 59.904 41.667 0.00 0.00 0.00 3.77
2014 2984 4.096382 GCTAAATGGATCAATCGTGTTGGT 59.904 41.667 0.00 0.00 0.00 3.67
2015 2985 4.439305 AAATGGATCAATCGTGTTGGTG 57.561 40.909 0.00 0.00 0.00 4.17
2016 2986 1.819928 TGGATCAATCGTGTTGGTGG 58.180 50.000 0.00 0.00 0.00 4.61
2017 2987 0.451783 GGATCAATCGTGTTGGTGGC 59.548 55.000 0.00 0.00 0.00 5.01
2018 2988 1.164411 GATCAATCGTGTTGGTGGCA 58.836 50.000 0.00 0.00 0.00 4.92
2019 2989 0.881118 ATCAATCGTGTTGGTGGCAC 59.119 50.000 9.70 9.70 0.00 5.01
2020 2990 0.464554 TCAATCGTGTTGGTGGCACA 60.465 50.000 20.82 2.61 36.71 4.57
2255 3225 7.864379 GGTAAGCGATCAAATCAAATCAATCAT 59.136 33.333 0.00 0.00 0.00 2.45
2291 3261 3.823281 ATCCAGAGCTCAGACATGAAG 57.177 47.619 17.77 0.00 34.23 3.02
2379 3360 2.207229 CGTGGTGAGGGACCTGACA 61.207 63.158 10.10 0.00 46.32 3.58
2629 3610 3.239627 TTCGGCAGGGAGGAGGAGT 62.240 63.158 0.00 0.00 0.00 3.85
2733 3714 0.095417 GAAGTCTCAAACGATGCCGC 59.905 55.000 0.00 0.00 39.95 6.53
2761 3770 6.374894 AGTCATAGTGTACAGAACTACAGGAC 59.625 42.308 0.00 4.42 33.11 3.85
2812 3827 0.618458 AGCGGGATTCTTGCTGGTAA 59.382 50.000 3.01 0.00 37.62 2.85
2818 3834 5.102313 CGGGATTCTTGCTGGTAATTTTTC 58.898 41.667 0.00 0.00 0.00 2.29
2902 4236 8.896744 CAAAATCATCCATTAGAGCTTCTACAA 58.103 33.333 0.00 0.00 0.00 2.41
2924 4258 2.487265 CCGGATATAGCAAAACCAGCCT 60.487 50.000 0.00 0.00 0.00 4.58
2929 4263 5.703130 GGATATAGCAAAACCAGCCTCTAAG 59.297 44.000 0.00 0.00 0.00 2.18
2930 4264 4.844349 ATAGCAAAACCAGCCTCTAAGA 57.156 40.909 0.00 0.00 0.00 2.10
2931 4265 3.064900 AGCAAAACCAGCCTCTAAGAG 57.935 47.619 0.00 0.00 0.00 2.85
2932 4266 1.470494 GCAAAACCAGCCTCTAAGAGC 59.530 52.381 0.00 0.00 0.00 4.09
2933 4267 2.783135 CAAAACCAGCCTCTAAGAGCA 58.217 47.619 0.00 0.00 0.00 4.26
2934 4268 3.149196 CAAAACCAGCCTCTAAGAGCAA 58.851 45.455 0.00 0.00 0.00 3.91
2935 4269 2.481289 AACCAGCCTCTAAGAGCAAC 57.519 50.000 0.00 0.00 0.00 4.17
2936 4270 1.650528 ACCAGCCTCTAAGAGCAACT 58.349 50.000 0.00 0.00 0.00 3.16
2937 4271 1.552792 ACCAGCCTCTAAGAGCAACTC 59.447 52.381 0.00 0.00 0.00 3.01
2938 4272 1.134551 CCAGCCTCTAAGAGCAACTCC 60.135 57.143 0.00 0.00 0.00 3.85
2939 4273 1.552337 CAGCCTCTAAGAGCAACTCCA 59.448 52.381 0.00 0.00 0.00 3.86
2940 4274 2.027745 CAGCCTCTAAGAGCAACTCCAA 60.028 50.000 0.00 0.00 0.00 3.53
2941 4275 2.843113 AGCCTCTAAGAGCAACTCCAAT 59.157 45.455 0.00 0.00 0.00 3.16
2942 4276 2.941720 GCCTCTAAGAGCAACTCCAATG 59.058 50.000 0.00 0.00 0.00 2.82
2943 4277 3.539604 CCTCTAAGAGCAACTCCAATGG 58.460 50.000 0.00 0.00 0.00 3.16
2944 4278 3.539604 CTCTAAGAGCAACTCCAATGGG 58.460 50.000 0.00 0.00 0.00 4.00
2945 4279 2.239654 TCTAAGAGCAACTCCAATGGGG 59.760 50.000 0.00 0.00 38.37 4.96
2946 4280 0.779997 AAGAGCAACTCCAATGGGGT 59.220 50.000 0.00 0.00 38.11 4.95
2947 4281 0.038744 AGAGCAACTCCAATGGGGTG 59.961 55.000 5.14 3.24 38.11 4.61
2948 4282 0.038166 GAGCAACTCCAATGGGGTGA 59.962 55.000 5.14 0.00 38.11 4.02
2949 4283 0.251341 AGCAACTCCAATGGGGTGAC 60.251 55.000 5.14 0.27 38.11 3.67
3014 4348 3.243771 CGTCCGCCCTCTTTTAGATATGT 60.244 47.826 0.00 0.00 0.00 2.29
3134 4480 7.254852 TCATTTTGGACGGAATAAAATAGCAC 58.745 34.615 0.00 0.00 33.59 4.40
3183 4529 9.624373 AATAAAAATGTCTCACATAGCTCTGAT 57.376 29.630 6.05 0.00 37.97 2.90
3184 4530 7.551035 AAAAATGTCTCACATAGCTCTGATC 57.449 36.000 6.05 0.00 37.97 2.92
3185 4531 4.870123 ATGTCTCACATAGCTCTGATCC 57.130 45.455 6.05 0.00 36.99 3.36
3294 4640 1.069227 GTGAGTTTCCCAATCACGCAC 60.069 52.381 0.00 0.00 34.55 5.34
3338 4684 1.003223 GTTCAAACGTTGCCGCTACTT 60.003 47.619 0.00 0.00 37.70 2.24
3450 4799 3.946606 TGATCACACAAGCAGTCATCAT 58.053 40.909 0.00 0.00 0.00 2.45
3555 4906 3.118000 TCGACATCCTTCCTAGCACTCTA 60.118 47.826 0.00 0.00 0.00 2.43
3567 4918 2.977772 GCACTCTATTGCTCCTGAGT 57.022 50.000 0.00 0.00 39.59 3.41
3593 4944 4.090090 TCTTTTCCTCTTCTCTCCGACAT 58.910 43.478 0.00 0.00 0.00 3.06
3616 4967 5.144100 TGGTTGGGTATTGTCTTGACAATT 58.856 37.500 27.05 15.13 40.42 2.32
3629 4980 2.571212 TGACAATTGTGGTCCACTGAC 58.429 47.619 22.56 13.11 40.98 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.101579 TCACGACACGACAGAGCAAA 59.898 50.000 0.00 0.00 0.00 3.68
28 29 0.317854 CTTCACGACACGACAGAGCA 60.318 55.000 0.00 0.00 0.00 4.26
57 58 3.068729 GCAAAATGGAGAGGCGGCC 62.069 63.158 12.11 12.11 0.00 6.13
99 100 4.483311 CCCTAGTTCTGTCGTAACAACTC 58.517 47.826 0.00 0.00 34.24 3.01
105 106 1.538047 ACGCCCTAGTTCTGTCGTAA 58.462 50.000 0.00 0.00 0.00 3.18
107 108 0.243095 GAACGCCCTAGTTCTGTCGT 59.757 55.000 2.95 0.00 45.07 4.34
112 113 3.015312 GCCCGAACGCCCTAGTTCT 62.015 63.158 8.02 0.00 46.00 3.01
227 228 9.988350 GTTAGTACATTCATCCATTTGTAGTTG 57.012 33.333 0.00 0.00 32.17 3.16
249 254 7.042254 AGGCACGTTTTAGACTTTTAGTGTTAG 60.042 37.037 0.00 0.00 0.00 2.34
250 255 6.762661 AGGCACGTTTTAGACTTTTAGTGTTA 59.237 34.615 0.00 0.00 0.00 2.41
252 257 5.121105 AGGCACGTTTTAGACTTTTAGTGT 58.879 37.500 0.00 0.00 0.00 3.55
253 258 5.668558 AGGCACGTTTTAGACTTTTAGTG 57.331 39.130 0.00 0.00 0.00 2.74
254 259 6.752168 TCTAGGCACGTTTTAGACTTTTAGT 58.248 36.000 0.00 0.00 0.00 2.24
255 260 6.310711 CCTCTAGGCACGTTTTAGACTTTTAG 59.689 42.308 0.00 0.00 0.00 1.85
256 261 6.161381 CCTCTAGGCACGTTTTAGACTTTTA 58.839 40.000 0.00 0.00 0.00 1.52
257 262 4.995487 CCTCTAGGCACGTTTTAGACTTTT 59.005 41.667 0.00 0.00 0.00 2.27
258 263 4.566987 CCTCTAGGCACGTTTTAGACTTT 58.433 43.478 0.00 0.00 0.00 2.66
259 264 4.189639 CCTCTAGGCACGTTTTAGACTT 57.810 45.455 0.00 0.00 0.00 3.01
260 265 3.870633 CCTCTAGGCACGTTTTAGACT 57.129 47.619 0.00 0.00 0.00 3.24
273 278 3.442273 GTCTAGATCCGAATGCCTCTAGG 59.558 52.174 0.00 0.00 38.37 3.02
279 284 5.757850 AAATTTGTCTAGATCCGAATGCC 57.242 39.130 0.00 0.00 0.00 4.40
280 285 7.377131 GCTTTAAATTTGTCTAGATCCGAATGC 59.623 37.037 0.00 0.00 0.00 3.56
287 292 9.631452 AAAGCTTGCTTTAAATTTGTCTAGATC 57.369 29.630 17.66 0.00 0.00 2.75
300 333 4.640789 TCGTCCAAAAAGCTTGCTTTAA 57.359 36.364 19.13 5.05 0.00 1.52
318 351 5.185442 GCTAATAGCCTAATACTCCCTTCGT 59.815 44.000 0.00 0.00 34.48 3.85
319 352 5.652518 GCTAATAGCCTAATACTCCCTTCG 58.347 45.833 0.00 0.00 34.48 3.79
334 367 7.533426 CAATTGATGGTATCTTGGCTAATAGC 58.467 38.462 3.17 3.17 41.46 2.97
335 368 7.175467 TGCAATTGATGGTATCTTGGCTAATAG 59.825 37.037 10.34 0.00 0.00 1.73
440 473 4.996344 TGGTAAGCGTTCGATATGTGTAA 58.004 39.130 0.00 0.00 0.00 2.41
459 518 2.095768 CGACGTGAATTGCTTCAATGGT 60.096 45.455 0.00 0.00 42.85 3.55
492 551 3.655276 AACAACACGACTAATCTCGGT 57.345 42.857 0.00 0.00 38.02 4.69
521 580 2.571231 TGCGCTCGTGCATGTAGA 59.429 55.556 9.73 0.00 40.62 2.59
568 627 3.501445 GCAGCATCTCCATTTCTACATCC 59.499 47.826 0.00 0.00 0.00 3.51
605 664 2.758089 CCACCTACGACGAGGACGG 61.758 68.421 16.88 13.01 44.46 4.79
624 683 1.005867 GGGCACGAACGTTCTGGTA 60.006 57.895 24.80 0.00 0.00 3.25
693 752 0.878523 TGTGAAAGTTCAGCCGTCCG 60.879 55.000 0.00 0.00 37.98 4.79
718 777 3.810373 CGATTCACCGGAAACTTTTCTG 58.190 45.455 9.46 3.85 41.99 3.02
753 812 2.604174 CGGAACCTTCACGTGTGCC 61.604 63.158 16.51 2.84 0.00 5.01
1465 2431 2.526304 TCTGTCAAGGACAAGAACGG 57.474 50.000 0.33 0.00 42.26 4.44
1499 2465 3.038946 GCACACACGCGGATAACTA 57.961 52.632 12.47 0.00 0.00 2.24
1702 2668 4.988598 CAGCCTGCGGTGGTTCGT 62.989 66.667 0.00 0.00 33.70 3.85
1902 2868 4.388499 ACCGATTTGACCCGCGCT 62.388 61.111 5.56 0.00 0.00 5.92
1968 2938 8.430801 AGCAGAAAGTACATGTCAGAATAATC 57.569 34.615 0.00 0.00 0.00 1.75
1979 2949 7.558161 TGATCCATTTAGCAGAAAGTACATG 57.442 36.000 0.00 0.00 0.00 3.21
1994 2964 3.193267 CCACCAACACGATTGATCCATTT 59.807 43.478 5.86 0.00 0.00 2.32
2003 2973 2.029743 GTGTGCCACCAACACGATT 58.970 52.632 0.00 0.00 41.03 3.34
2013 2983 4.722855 GCAATGCCGGTGTGCCAC 62.723 66.667 13.28 0.00 31.94 5.01
2015 2985 4.424566 CTGCAATGCCGGTGTGCC 62.425 66.667 19.20 6.28 37.48 5.01
2017 2987 4.424566 GGCTGCAATGCCGGTGTG 62.425 66.667 1.90 0.00 43.74 3.82
2024 2994 1.026718 AGGAAGTACGGCTGCAATGC 61.027 55.000 0.00 0.00 0.00 3.56
2025 2995 0.729116 CAGGAAGTACGGCTGCAATG 59.271 55.000 0.50 0.00 0.00 2.82
2026 2996 1.026718 GCAGGAAGTACGGCTGCAAT 61.027 55.000 0.50 0.00 40.38 3.56
2255 3225 8.027524 AGCTCTGGATTAATCTGAGTTAATCA 57.972 34.615 25.17 10.79 45.97 2.57
2291 3261 0.961019 TCCAGGCAAATGTGTTGCTC 59.039 50.000 10.58 2.05 44.36 4.26
2294 3264 3.087031 AGAGATCCAGGCAAATGTGTTG 58.913 45.455 0.00 0.00 0.00 3.33
2339 3309 2.202919 CCACGCCGCTGATGATGA 60.203 61.111 0.00 0.00 0.00 2.92
2341 3311 2.202932 GTCCACGCCGCTGATGAT 60.203 61.111 0.00 0.00 0.00 2.45
2379 3360 2.591715 GAGTGGTGCGTGTGCCTT 60.592 61.111 0.00 0.00 41.78 4.35
2523 3504 4.731612 CGGCTGCTGCACTCGACT 62.732 66.667 17.89 0.00 41.91 4.18
2629 3610 4.033776 CCGGAGCTCTTGGGCCAA 62.034 66.667 19.68 19.68 0.00 4.52
2683 3664 0.925558 TTCCCCAGCATCCATTAGCA 59.074 50.000 0.00 0.00 0.00 3.49
2733 3714 8.346300 CCTGTAGTTCTGTACACTATGACTATG 58.654 40.741 0.00 0.00 0.00 2.23
2761 3770 5.418310 ACAACATGTTTCCTACAGTTTCG 57.582 39.130 8.77 0.00 40.83 3.46
2812 3827 6.678900 GCGTGATGCCTTCATTCTAGAAAAAT 60.679 38.462 9.71 0.00 36.54 1.82
2902 4236 2.572290 GCTGGTTTTGCTATATCCGGT 58.428 47.619 0.00 0.00 0.00 5.28
2924 4258 2.239654 CCCCATTGGAGTTGCTCTTAGA 59.760 50.000 3.62 0.00 35.39 2.10
2929 4263 0.038166 TCACCCCATTGGAGTTGCTC 59.962 55.000 3.62 0.00 38.00 4.26
2930 4264 0.251341 GTCACCCCATTGGAGTTGCT 60.251 55.000 3.62 0.00 38.00 3.91
2931 4265 1.250840 GGTCACCCCATTGGAGTTGC 61.251 60.000 3.62 0.00 38.00 4.17
2932 4266 2.961424 GGTCACCCCATTGGAGTTG 58.039 57.895 3.62 0.00 38.00 3.16
2943 4277 2.387476 AAAACGGACGAGGGTCACCC 62.387 60.000 3.85 3.85 45.28 4.61
2944 4278 0.533531 AAAAACGGACGAGGGTCACC 60.534 55.000 0.00 0.00 45.28 4.02
2945 4279 2.996444 AAAAACGGACGAGGGTCAC 58.004 52.632 0.00 0.00 45.28 3.67
3002 4336 3.809832 CCCTGCCGACACATATCTAAAAG 59.190 47.826 0.00 0.00 0.00 2.27
3110 4455 7.032580 TGTGCTATTTTATTCCGTCCAAAATG 58.967 34.615 0.00 0.00 34.57 2.32
3111 4457 7.093945 ACTGTGCTATTTTATTCCGTCCAAAAT 60.094 33.333 0.00 0.00 36.25 1.82
3181 4527 7.810766 TTTATTCGATTTGCAAAACTGGATC 57.189 32.000 17.19 7.04 0.00 3.36
3183 4529 7.429633 TCTTTTATTCGATTTGCAAAACTGGA 58.570 30.769 17.19 4.64 0.00 3.86
3184 4530 7.636259 TCTTTTATTCGATTTGCAAAACTGG 57.364 32.000 17.19 2.02 0.00 4.00
3185 4531 8.967218 TCTTCTTTTATTCGATTTGCAAAACTG 58.033 29.630 17.19 9.02 0.00 3.16
3294 4640 4.216257 AGTTCACCCAATTTCATGAAGACG 59.784 41.667 8.41 1.00 31.94 4.18
3450 4799 2.133195 ACGCAGAAACTGTGGGAGA 58.867 52.632 15.06 0.00 45.11 3.71
3494 4843 1.971481 CAATCTCGATGGGGCATCAA 58.029 50.000 0.00 0.00 40.54 2.57
3495 4844 0.535780 GCAATCTCGATGGGGCATCA 60.536 55.000 0.00 0.00 40.54 3.07
3555 4906 6.488715 AGGAAAAGATTTACTCAGGAGCAAT 58.511 36.000 0.00 0.00 0.00 3.56
3562 4913 7.763985 GGAGAGAAGAGGAAAAGATTTACTCAG 59.236 40.741 15.46 0.00 30.96 3.35
3565 4916 6.437793 TCGGAGAGAAGAGGAAAAGATTTACT 59.562 38.462 0.00 0.00 0.00 2.24
3567 4918 6.210784 TGTCGGAGAGAAGAGGAAAAGATTTA 59.789 38.462 0.00 0.00 36.95 1.40
3593 4944 3.866703 TGTCAAGACAATACCCAACCA 57.133 42.857 0.00 0.00 38.56 3.67
3616 4967 2.209690 TCTATCGTCAGTGGACCACA 57.790 50.000 26.30 5.69 41.13 4.17
3629 4980 2.501261 TCTGGGTGACGGTATCTATCG 58.499 52.381 0.00 0.00 35.57 2.92


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

AutoCloner maintained by Alex Coulton.