Multiple sequence alignment - TraesCS2B01G454300

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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 TraesCS2B01G454300 chr2B 100.000 3051 0 0 1 3051 648654804 648651754 0.000000e+00 5635.0
1 TraesCS2B01G454300 chr2D 90.957 2256 109 43 3 2200 543431122 543428904 0.000000e+00 2948.0
2 TraesCS2B01G454300 chr2D 86.875 640 24 21 2351 2965 543428781 543428177 0.000000e+00 662.0
3 TraesCS2B01G454300 chr2A 89.616 2263 137 55 5 2200 686216361 686214130 0.000000e+00 2787.0
4 TraesCS2B01G454300 chr2A 85.000 620 37 27 2357 2942 686214044 686213447 2.040000e-161 579.0
5 TraesCS2B01G454300 chr4A 85.897 234 30 2 1042 1275 494074879 494074649 2.350000e-61 246.0
6 TraesCS2B01G454300 chr3B 88.406 69 8 0 1661 1729 525242675 525242607 1.950000e-12 84.2
7 TraesCS2B01G454300 chr3B 90.566 53 3 2 1677 1728 507286712 507286763 5.460000e-08 69.4
8 TraesCS2B01G454300 chr3D 86.957 69 9 0 1661 1729 399380675 399380607 9.070000e-11 78.7
9 TraesCS2B01G454300 chr3A 86.957 69 9 0 1661 1729 518642918 518642850 9.070000e-11 78.7
10 TraesCS2B01G454300 chr3A 90.566 53 3 2 1677 1728 510664003 510664054 5.460000e-08 69.4


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 TraesCS2B01G454300 chr2B 648651754 648654804 3050 True 5635 5635 100.000 1 3051 1 chr2B.!!$R1 3050
1 TraesCS2B01G454300 chr2D 543428177 543431122 2945 True 1805 2948 88.916 3 2965 2 chr2D.!!$R1 2962
2 TraesCS2B01G454300 chr2A 686213447 686216361 2914 True 1683 2787 87.308 5 2942 2 chr2A.!!$R1 2937

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
671 692 0.179094 TTGTGCGACCTTCAGTTCGT 60.179 50.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2251 2354 0.036388 ACGATTTGCAGATCCGGTGT 60.036 50.0 11.36 1.17 0.0 4.16 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
193 194 2.677836 CAATATCATATCCCCAACGCGG 59.322 50.000 12.47 0.00 0.00 6.46
295 296 1.611977 TCATTATAGCCAGGACGTCCG 59.388 52.381 28.26 21.63 42.08 4.79
339 340 1.678101 ACTTTGAAGCCAAGACACAGC 59.322 47.619 0.00 0.00 33.23 4.40
372 376 9.800433 ACGCATATGATATTTTCTCTCTATCTG 57.200 33.333 6.97 0.00 0.00 2.90
373 377 8.754096 CGCATATGATATTTTCTCTCTATCTGC 58.246 37.037 6.97 0.00 0.00 4.26
499 508 0.596082 ACCGCATTGGGTCTTTTTCG 59.404 50.000 0.00 0.00 44.64 3.46
503 512 2.724174 CGCATTGGGTCTTTTTCGAAAC 59.276 45.455 10.79 0.00 0.00 2.78
573 582 7.958053 ACAGTAAACAACTAATCACTGTACC 57.042 36.000 3.50 0.00 43.43 3.34
574 583 6.932960 ACAGTAAACAACTAATCACTGTACCC 59.067 38.462 3.50 0.00 43.43 3.69
575 584 7.159372 CAGTAAACAACTAATCACTGTACCCT 58.841 38.462 0.00 0.00 35.76 4.34
576 585 7.117812 CAGTAAACAACTAATCACTGTACCCTG 59.882 40.741 0.00 0.00 35.76 4.45
577 586 5.562298 AACAACTAATCACTGTACCCTGT 57.438 39.130 0.00 0.00 0.00 4.00
578 587 6.675413 AACAACTAATCACTGTACCCTGTA 57.325 37.500 0.00 0.00 0.00 2.74
579 588 6.034161 ACAACTAATCACTGTACCCTGTAC 57.966 41.667 0.00 0.00 0.00 2.90
580 589 5.541101 ACAACTAATCACTGTACCCTGTACA 59.459 40.000 6.88 6.88 0.00 2.90
593 602 8.010733 TGTACCCTGTACAGTATACATAAACC 57.989 38.462 23.01 5.72 0.00 3.27
607 616 9.997482 GTATACATAAACCGCCATAAATATTGG 57.003 33.333 0.00 0.00 37.31 3.16
610 619 7.657336 ACATAAACCGCCATAAATATTGGAAG 58.343 34.615 0.00 0.00 36.26 3.46
671 692 0.179094 TTGTGCGACCTTCAGTTCGT 60.179 50.000 0.00 0.00 0.00 3.85
786 816 5.938125 GCTGACACTTTATAAAGAAGGACCA 59.062 40.000 27.92 17.03 39.31 4.02
792 822 4.855298 TTATAAAGAAGGACCAGTGGGG 57.145 45.455 15.21 0.00 44.81 4.96
793 823 5.281037 CTTTATAAAGAAGGACCAGTGGGGT 60.281 44.000 18.69 0.00 45.56 4.95
808 838 4.047166 AGTGGGGTCATATCTCCAATTCA 58.953 43.478 0.00 0.00 0.00 2.57
810 840 4.103153 GTGGGGTCATATCTCCAATTCAGA 59.897 45.833 0.00 0.00 0.00 3.27
811 841 4.915809 TGGGGTCATATCTCCAATTCAGAT 59.084 41.667 2.65 2.65 34.80 2.90
812 842 5.373555 TGGGGTCATATCTCCAATTCAGATT 59.626 40.000 2.42 0.00 32.61 2.40
828 858 5.901413 TCAGATTGAATTCAGGGAGCTAT 57.099 39.130 8.41 0.00 0.00 2.97
829 859 7.379059 TTCAGATTGAATTCAGGGAGCTATA 57.621 36.000 8.41 0.00 30.26 1.31
839 869 2.116238 AGGGAGCTATACCGAAAAGCA 58.884 47.619 0.00 0.00 38.75 3.91
1317 1347 4.354943 CCACCTCCTCCCCCACCT 62.355 72.222 0.00 0.00 0.00 4.00
1446 1521 2.494073 GACATCCACGTCCTTCTTCTCT 59.506 50.000 0.00 0.00 0.00 3.10
1751 1826 2.762535 TCTTTCCTCACCGATCCAAC 57.237 50.000 0.00 0.00 0.00 3.77
1753 1828 1.279271 CTTTCCTCACCGATCCAACCT 59.721 52.381 0.00 0.00 0.00 3.50
1774 1854 9.533253 CAACCTCAACAGAATAAACAAGATTTT 57.467 29.630 0.00 0.00 0.00 1.82
1777 1857 9.918630 CCTCAACAGAATAAACAAGATTTTGAT 57.081 29.630 2.48 0.00 37.73 2.57
1802 1882 7.604549 TCAACAATAGTCATGATGTTTGCAAT 58.395 30.769 9.23 0.00 33.97 3.56
1813 1893 6.335471 TGATGTTTGCAATGATCTGACTTT 57.665 33.333 15.53 0.00 0.00 2.66
1819 1899 4.300803 TGCAATGATCTGACTTTGTTTGC 58.699 39.130 0.00 0.00 38.85 3.68
1924 2004 2.046892 GCGATGCTGGTGGTGACT 60.047 61.111 0.00 0.00 0.00 3.41
2060 2146 3.675228 CGGGCACGTCTGACTTAGTTAAT 60.675 47.826 0.00 0.00 34.81 1.40
2105 2197 1.228154 GGGGTGCTTCGTTGGTTCT 60.228 57.895 0.00 0.00 0.00 3.01
2200 2293 7.595819 AGATTTTACTATCTCCAGACTCCAG 57.404 40.000 0.00 0.00 28.74 3.86
2202 2295 8.282982 AGATTTTACTATCTCCAGACTCCAGTA 58.717 37.037 0.00 0.00 28.74 2.74
2204 2297 6.578313 TTACTATCTCCAGACTCCAGTACT 57.422 41.667 0.00 0.00 0.00 2.73
2206 2299 6.578313 ACTATCTCCAGACTCCAGTACTTA 57.422 41.667 0.00 0.00 0.00 2.24
2207 2300 7.156694 ACTATCTCCAGACTCCAGTACTTAT 57.843 40.000 0.00 0.00 0.00 1.73
2208 2301 7.228590 ACTATCTCCAGACTCCAGTACTTATC 58.771 42.308 0.00 0.00 0.00 1.75
2209 2302 5.452341 TCTCCAGACTCCAGTACTTATCA 57.548 43.478 0.00 0.00 0.00 2.15
2232 2335 9.840427 ATCATTTTATTTGTTCGTCAAACCTAG 57.160 29.630 9.70 0.00 46.77 3.02
2237 2340 3.188159 TGTTCGTCAAACCTAGCAACT 57.812 42.857 0.00 0.00 37.03 3.16
2238 2341 2.869801 TGTTCGTCAAACCTAGCAACTG 59.130 45.455 0.00 0.00 37.03 3.16
2241 2344 7.692211 TGTTCGTCAAACCTAGCAACTGCTA 62.692 44.000 10.85 10.85 42.72 3.49
2242 2345 7.298182 GTTCGTCAAACCTAGCAACTGCTAC 62.298 48.000 7.34 0.00 46.89 3.58
2249 2352 3.876300 GCAACTGCTACCACTCCG 58.124 61.111 0.00 0.00 38.21 4.63
2251 2354 1.005037 CAACTGCTACCACTCCGCA 60.005 57.895 0.00 0.00 0.00 5.69
2252 2355 1.004918 AACTGCTACCACTCCGCAC 60.005 57.895 0.00 0.00 0.00 5.34
2253 2356 1.754380 AACTGCTACCACTCCGCACA 61.754 55.000 0.00 0.00 0.00 4.57
2254 2357 1.738099 CTGCTACCACTCCGCACAC 60.738 63.158 0.00 0.00 0.00 3.82
2255 2358 2.434359 GCTACCACTCCGCACACC 60.434 66.667 0.00 0.00 0.00 4.16
2256 2359 2.126071 CTACCACTCCGCACACCG 60.126 66.667 0.00 0.00 0.00 4.94
2272 2375 1.062587 CACCGGATCTGCAAATCGTTC 59.937 52.381 9.46 0.00 0.00 3.95
2274 2377 1.062587 CCGGATCTGCAAATCGTTCAC 59.937 52.381 0.00 0.00 0.00 3.18
2280 2383 4.630894 TCTGCAAATCGTTCACTTTGTT 57.369 36.364 0.00 0.00 35.33 2.83
2285 2388 5.061560 TGCAAATCGTTCACTTTGTTTGTTC 59.938 36.000 0.00 0.00 35.33 3.18
2288 2391 5.560966 ATCGTTCACTTTGTTTGTTCTGT 57.439 34.783 0.00 0.00 0.00 3.41
2293 2396 2.593775 CACTTTGTTTGTTCTGTGTGCG 59.406 45.455 0.00 0.00 0.00 5.34
2294 2397 2.184448 CTTTGTTTGTTCTGTGTGCGG 58.816 47.619 0.00 0.00 0.00 5.69
2295 2398 0.453793 TTGTTTGTTCTGTGTGCGGG 59.546 50.000 0.00 0.00 0.00 6.13
2296 2399 1.358759 GTTTGTTCTGTGTGCGGGG 59.641 57.895 0.00 0.00 0.00 5.73
2297 2400 1.077357 TTTGTTCTGTGTGCGGGGT 60.077 52.632 0.00 0.00 0.00 4.95
2298 2401 1.380403 TTTGTTCTGTGTGCGGGGTG 61.380 55.000 0.00 0.00 0.00 4.61
2299 2402 2.978010 GTTCTGTGTGCGGGGTGG 60.978 66.667 0.00 0.00 0.00 4.61
2307 2410 2.366837 TGCGGGGTGGATGGAGAT 60.367 61.111 0.00 0.00 0.00 2.75
2310 2413 0.036010 GCGGGGTGGATGGAGATATG 60.036 60.000 0.00 0.00 0.00 1.78
2315 2418 2.368875 GGGTGGATGGAGATATGTCGTT 59.631 50.000 0.00 0.00 0.00 3.85
2316 2419 3.555168 GGGTGGATGGAGATATGTCGTTC 60.555 52.174 0.00 0.00 0.00 3.95
2325 2428 4.985409 GGAGATATGTCGTTCCATGACTTC 59.015 45.833 0.00 0.00 35.24 3.01
2329 2432 1.611977 TGTCGTTCCATGACTTCGAGT 59.388 47.619 0.00 0.00 35.24 4.18
2337 2440 0.603569 ATGACTTCGAGTTGAGCGGT 59.396 50.000 0.00 0.00 0.00 5.68
2341 2444 0.784778 CTTCGAGTTGAGCGGTGTTC 59.215 55.000 0.00 0.00 0.00 3.18
2425 2552 4.677779 GCGGTTACAGTTAATAAGGACGGA 60.678 45.833 0.00 0.00 0.00 4.69
2426 2553 4.800471 CGGTTACAGTTAATAAGGACGGAC 59.200 45.833 0.00 0.00 0.00 4.79
2427 2554 4.800471 GGTTACAGTTAATAAGGACGGACG 59.200 45.833 0.00 0.00 0.00 4.79
2428 2555 3.515330 ACAGTTAATAAGGACGGACGG 57.485 47.619 0.00 0.00 0.00 4.79
2429 2556 3.091545 ACAGTTAATAAGGACGGACGGA 58.908 45.455 0.00 0.00 0.00 4.69
2430 2557 3.119352 ACAGTTAATAAGGACGGACGGAC 60.119 47.826 0.00 0.00 0.00 4.79
2431 2558 2.098117 AGTTAATAAGGACGGACGGACG 59.902 50.000 0.00 0.00 40.31 4.79
2432 2559 1.024271 TAATAAGGACGGACGGACGG 58.976 55.000 6.00 0.00 38.39 4.79
2433 2560 0.680921 AATAAGGACGGACGGACGGA 60.681 55.000 6.00 0.00 38.39 4.69
2434 2561 1.379642 ATAAGGACGGACGGACGGAC 61.380 60.000 6.00 0.00 38.39 4.79
2486 2619 4.716784 TCTCCATTGATTGCTACTGGTACT 59.283 41.667 0.00 0.00 0.00 2.73
2487 2620 4.769688 TCCATTGATTGCTACTGGTACTG 58.230 43.478 0.00 0.00 0.00 2.74
2510 2643 2.073816 ACAATACAGTGCGCCAACTAC 58.926 47.619 4.18 0.00 0.00 2.73
2528 2697 5.848833 ACTACAGTATAGAAAACTCGGGG 57.151 43.478 0.00 0.00 0.00 5.73
2530 2699 2.169978 ACAGTATAGAAAACTCGGGGGC 59.830 50.000 0.00 0.00 0.00 5.80
2611 2781 1.072489 TGAATACTTTGTCGTGGGGCA 59.928 47.619 0.00 0.00 0.00 5.36
2626 2796 3.721706 GCACCCTCCCCCTCTGTG 61.722 72.222 0.00 0.00 0.00 3.66
2689 2866 6.400579 TTGTTTGCGCCATTATTATTGTTG 57.599 33.333 4.18 0.00 0.00 3.33
2693 2870 7.598869 TGTTTGCGCCATTATTATTGTTGTTTA 59.401 29.630 4.18 0.00 0.00 2.01
2743 2922 3.623365 TCCATCTGGGTGAGGAGAG 57.377 57.895 0.00 0.00 38.11 3.20
2744 2923 0.031716 TCCATCTGGGTGAGGAGAGG 60.032 60.000 0.00 0.00 38.11 3.69
2745 2924 0.326048 CCATCTGGGTGAGGAGAGGT 60.326 60.000 0.00 0.00 0.00 3.85
2746 2925 0.829333 CATCTGGGTGAGGAGAGGTG 59.171 60.000 0.00 0.00 0.00 4.00
2747 2926 0.415429 ATCTGGGTGAGGAGAGGTGT 59.585 55.000 0.00 0.00 0.00 4.16
2748 2927 0.542938 TCTGGGTGAGGAGAGGTGTG 60.543 60.000 0.00 0.00 0.00 3.82
2749 2928 0.542938 CTGGGTGAGGAGAGGTGTGA 60.543 60.000 0.00 0.00 0.00 3.58
2750 2929 0.117140 TGGGTGAGGAGAGGTGTGAT 59.883 55.000 0.00 0.00 0.00 3.06
2761 2940 0.768221 AGGTGTGATGAGTGGTGGGT 60.768 55.000 0.00 0.00 0.00 4.51
2904 3087 1.375652 CCCAGCAGTGCAGTGAGAG 60.376 63.158 25.76 12.73 0.00 3.20
2905 3088 1.670015 CCAGCAGTGCAGTGAGAGA 59.330 57.895 25.76 0.00 0.00 3.10
2906 3089 0.390078 CCAGCAGTGCAGTGAGAGAG 60.390 60.000 25.76 8.63 0.00 3.20
2965 3149 5.105064 CGATCCTCCCACCTCTTTTACTTTA 60.105 44.000 0.00 0.00 0.00 1.85
2966 3150 6.408206 CGATCCTCCCACCTCTTTTACTTTAT 60.408 42.308 0.00 0.00 0.00 1.40
2967 3151 6.713731 TCCTCCCACCTCTTTTACTTTATT 57.286 37.500 0.00 0.00 0.00 1.40
2968 3152 7.098845 TCCTCCCACCTCTTTTACTTTATTT 57.901 36.000 0.00 0.00 0.00 1.40
2969 3153 8.222138 TCCTCCCACCTCTTTTACTTTATTTA 57.778 34.615 0.00 0.00 0.00 1.40
2970 3154 8.842764 TCCTCCCACCTCTTTTACTTTATTTAT 58.157 33.333 0.00 0.00 0.00 1.40
2971 3155 9.475620 CCTCCCACCTCTTTTACTTTATTTATT 57.524 33.333 0.00 0.00 0.00 1.40
3018 3202 4.725790 ATCAAATGAAAGTAAGGGCTGC 57.274 40.909 0.00 0.00 0.00 5.25
3019 3203 2.487762 TCAAATGAAAGTAAGGGCTGCG 59.512 45.455 0.00 0.00 0.00 5.18
3020 3204 1.463674 AATGAAAGTAAGGGCTGCGG 58.536 50.000 0.00 0.00 0.00 5.69
3021 3205 0.394352 ATGAAAGTAAGGGCTGCGGG 60.394 55.000 0.00 0.00 0.00 6.13
3022 3206 1.002502 GAAAGTAAGGGCTGCGGGT 60.003 57.895 0.00 0.00 0.00 5.28
3023 3207 1.303317 AAAGTAAGGGCTGCGGGTG 60.303 57.895 0.00 0.00 0.00 4.61
3024 3208 2.764637 AAAGTAAGGGCTGCGGGTGG 62.765 60.000 0.00 0.00 0.00 4.61
3025 3209 4.796495 GTAAGGGCTGCGGGTGGG 62.796 72.222 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.668632 GGCGTGATCAGGGGTTGA 59.331 61.111 16.66 0.00 40.85 3.18
1 2 2.819595 CGGCGTGATCAGGGGTTG 60.820 66.667 16.66 0.00 0.00 3.77
193 194 1.036707 CTCTCCCCTAGCAGCACTAC 58.963 60.000 0.00 0.00 0.00 2.73
231 232 4.892433 CCAAAACAAAGTTGGCCATGATA 58.108 39.130 6.09 0.00 39.21 2.15
295 296 1.488705 TATGGGGATGGATGGGCGAC 61.489 60.000 0.00 0.00 0.00 5.19
339 340 8.929746 AGAGAAAATATCATATGCGTATGTGTG 58.070 33.333 22.30 2.18 39.01 3.82
368 372 1.677966 CACAAGCAGGCAGGCAGAT 60.678 57.895 0.00 0.00 35.83 2.90
372 376 2.882876 CATCACAAGCAGGCAGGC 59.117 61.111 0.00 0.00 0.00 4.85
373 377 2.882876 GCATCACAAGCAGGCAGG 59.117 61.111 0.00 0.00 0.00 4.85
455 462 5.008415 GTGATAATGACATCTTCTTGGCCAG 59.992 44.000 5.11 0.00 0.00 4.85
512 521 4.130118 GGGTGTGATGGCATAGAAGTTAG 58.870 47.826 0.00 0.00 0.00 2.34
513 522 3.521531 TGGGTGTGATGGCATAGAAGTTA 59.478 43.478 0.00 0.00 0.00 2.24
515 524 1.915489 TGGGTGTGATGGCATAGAAGT 59.085 47.619 0.00 0.00 0.00 3.01
518 527 1.284313 TGTGGGTGTGATGGCATAGA 58.716 50.000 0.00 0.00 0.00 1.98
526 535 1.767692 GGGGACTTGTGGGTGTGAT 59.232 57.895 0.00 0.00 0.00 3.06
573 582 4.986659 GGCGGTTTATGTATACTGTACAGG 59.013 45.833 26.12 9.07 0.00 4.00
574 583 5.593968 TGGCGGTTTATGTATACTGTACAG 58.406 41.667 21.44 21.44 0.00 2.74
575 584 5.595257 TGGCGGTTTATGTATACTGTACA 57.405 39.130 4.17 0.00 0.00 2.90
576 585 8.592105 TTTATGGCGGTTTATGTATACTGTAC 57.408 34.615 4.17 0.00 0.00 2.90
578 587 9.953565 ATATTTATGGCGGTTTATGTATACTGT 57.046 29.630 4.17 0.00 0.00 3.55
581 590 9.997482 CCAATATTTATGGCGGTTTATGTATAC 57.003 33.333 0.00 0.00 0.00 1.47
582 591 9.961264 TCCAATATTTATGGCGGTTTATGTATA 57.039 29.630 0.00 0.00 37.88 1.47
583 592 8.871629 TCCAATATTTATGGCGGTTTATGTAT 57.128 30.769 0.00 0.00 37.88 2.29
584 593 8.693120 TTCCAATATTTATGGCGGTTTATGTA 57.307 30.769 0.00 0.00 37.88 2.29
585 594 7.286775 ACTTCCAATATTTATGGCGGTTTATGT 59.713 33.333 0.00 0.00 37.88 2.29
586 595 7.657336 ACTTCCAATATTTATGGCGGTTTATG 58.343 34.615 0.00 0.00 37.88 1.90
587 596 7.833285 ACTTCCAATATTTATGGCGGTTTAT 57.167 32.000 0.00 0.00 37.88 1.40
588 597 8.749026 TTACTTCCAATATTTATGGCGGTTTA 57.251 30.769 0.00 0.00 37.88 2.01
589 598 7.648039 TTACTTCCAATATTTATGGCGGTTT 57.352 32.000 0.00 0.00 37.88 3.27
590 599 7.648039 TTTACTTCCAATATTTATGGCGGTT 57.352 32.000 0.00 0.00 37.88 4.44
656 677 0.714439 GCTAACGAACTGAAGGTCGC 59.286 55.000 17.29 0.00 0.00 5.19
786 816 4.047166 TGAATTGGAGATATGACCCCACT 58.953 43.478 0.00 0.00 0.00 4.00
808 838 5.279708 CGGTATAGCTCCCTGAATTCAATCT 60.280 44.000 9.88 5.00 0.00 2.40
810 840 4.593206 TCGGTATAGCTCCCTGAATTCAAT 59.407 41.667 9.88 0.81 0.00 2.57
811 841 3.964688 TCGGTATAGCTCCCTGAATTCAA 59.035 43.478 9.88 0.00 0.00 2.69
812 842 3.572642 TCGGTATAGCTCCCTGAATTCA 58.427 45.455 8.12 8.12 0.00 2.57
817 847 2.102588 GCTTTTCGGTATAGCTCCCTGA 59.897 50.000 0.00 0.00 32.26 3.86
823 853 3.007635 GTGGTTGCTTTTCGGTATAGCT 58.992 45.455 0.00 0.00 35.93 3.32
828 858 2.156098 GATGGTGGTTGCTTTTCGGTA 58.844 47.619 0.00 0.00 0.00 4.02
829 859 0.958822 GATGGTGGTTGCTTTTCGGT 59.041 50.000 0.00 0.00 0.00 4.69
839 869 1.271325 TGCGAGTCAATGATGGTGGTT 60.271 47.619 0.00 0.00 0.00 3.67
1302 1332 1.852626 CAAAGGTGGGGGAGGAGGT 60.853 63.158 0.00 0.00 0.00 3.85
1305 1335 1.850755 GGTCAAAGGTGGGGGAGGA 60.851 63.158 0.00 0.00 0.00 3.71
1308 1338 2.448931 ACGGTCAAAGGTGGGGGA 60.449 61.111 0.00 0.00 0.00 4.81
1428 1503 2.164624 CGAAGAGAAGAAGGACGTGGAT 59.835 50.000 0.00 0.00 0.00 3.41
1751 1826 9.918630 ATCAAAATCTTGTTTATTCTGTTGAGG 57.081 29.630 0.00 0.00 33.94 3.86
1774 1854 7.094291 TGCAAACATCATGACTATTGTTGATCA 60.094 33.333 12.03 8.31 32.90 2.92
1777 1857 6.572167 TGCAAACATCATGACTATTGTTGA 57.428 33.333 12.03 0.00 32.90 3.18
1778 1858 7.542824 TCATTGCAAACATCATGACTATTGTTG 59.457 33.333 12.03 8.34 32.90 3.33
1782 1862 8.135529 CAGATCATTGCAAACATCATGACTATT 58.864 33.333 18.41 0.00 0.00 1.73
1783 1863 7.501225 TCAGATCATTGCAAACATCATGACTAT 59.499 33.333 18.41 0.00 0.00 2.12
1785 1865 5.650703 TCAGATCATTGCAAACATCATGACT 59.349 36.000 18.41 8.41 0.00 3.41
1795 1875 5.234757 GCAAACAAAGTCAGATCATTGCAAA 59.765 36.000 1.71 0.00 41.03 3.68
1796 1876 4.746115 GCAAACAAAGTCAGATCATTGCAA 59.254 37.500 0.00 0.00 41.03 4.08
1802 1882 4.274214 CAGACAGCAAACAAAGTCAGATCA 59.726 41.667 0.00 0.00 33.56 2.92
1813 1893 2.023673 CTGAAACCCAGACAGCAAACA 58.976 47.619 0.00 0.00 45.78 2.83
1819 1899 1.303643 GCCCCTGAAACCCAGACAG 60.304 63.158 0.00 0.00 45.78 3.51
1924 2004 4.124351 CGGTGCTCGCCCTCGTAA 62.124 66.667 0.00 0.00 36.96 3.18
2091 2177 2.807967 CAGATTGAGAACCAACGAAGCA 59.192 45.455 0.00 0.00 37.63 3.91
2105 2197 2.562738 ACACGGACATCAGACAGATTGA 59.437 45.455 0.00 0.00 33.72 2.57
2232 2335 2.391389 GCGGAGTGGTAGCAGTTGC 61.391 63.158 3.31 7.82 42.49 4.17
2237 2340 2.342279 GTGTGCGGAGTGGTAGCA 59.658 61.111 0.00 0.00 38.71 3.49
2238 2341 2.434359 GGTGTGCGGAGTGGTAGC 60.434 66.667 0.00 0.00 0.00 3.58
2242 2345 4.082523 ATCCGGTGTGCGGAGTGG 62.083 66.667 0.00 0.00 39.05 4.00
2243 2346 2.509336 GATCCGGTGTGCGGAGTG 60.509 66.667 0.00 0.00 39.05 3.51
2244 2347 2.680352 AGATCCGGTGTGCGGAGT 60.680 61.111 0.00 0.00 39.05 3.85
2246 2349 4.451150 GCAGATCCGGTGTGCGGA 62.451 66.667 0.00 0.00 37.36 5.54
2249 2352 0.099436 GATTTGCAGATCCGGTGTGC 59.901 55.000 15.90 15.90 46.68 4.57
2251 2354 0.036388 ACGATTTGCAGATCCGGTGT 60.036 50.000 11.36 1.17 0.00 4.16
2252 2355 1.062587 GAACGATTTGCAGATCCGGTG 59.937 52.381 11.36 0.00 0.00 4.94
2253 2356 1.338674 TGAACGATTTGCAGATCCGGT 60.339 47.619 11.36 5.61 0.00 5.28
2254 2357 1.062587 GTGAACGATTTGCAGATCCGG 59.937 52.381 11.36 0.00 0.00 5.14
2255 2358 2.002586 AGTGAACGATTTGCAGATCCG 58.997 47.619 11.36 9.04 0.00 4.18
2256 2359 4.161333 CAAAGTGAACGATTTGCAGATCC 58.839 43.478 11.36 0.00 30.37 3.36
2257 2360 4.787598 ACAAAGTGAACGATTTGCAGATC 58.212 39.130 7.16 7.16 39.49 2.75
2260 2363 4.562394 ACAAACAAAGTGAACGATTTGCAG 59.438 37.500 0.00 0.00 39.49 4.41
2261 2364 4.489810 ACAAACAAAGTGAACGATTTGCA 58.510 34.783 0.00 0.00 39.49 4.08
2262 2365 5.288472 AGAACAAACAAAGTGAACGATTTGC 59.712 36.000 0.00 0.00 39.49 3.68
2263 2366 6.307800 ACAGAACAAACAAAGTGAACGATTTG 59.692 34.615 0.00 0.00 41.22 2.32
2272 2375 2.593775 CGCACACAGAACAAACAAAGTG 59.406 45.455 0.00 0.00 0.00 3.16
2274 2377 2.184448 CCGCACACAGAACAAACAAAG 58.816 47.619 0.00 0.00 0.00 2.77
2280 2383 1.821759 CACCCCGCACACAGAACAA 60.822 57.895 0.00 0.00 0.00 2.83
2285 2388 2.747460 CATCCACCCCGCACACAG 60.747 66.667 0.00 0.00 0.00 3.66
2288 2391 3.716195 CTCCATCCACCCCGCACA 61.716 66.667 0.00 0.00 0.00 4.57
2293 2396 1.276421 CGACATATCTCCATCCACCCC 59.724 57.143 0.00 0.00 0.00 4.95
2294 2397 1.971357 ACGACATATCTCCATCCACCC 59.029 52.381 0.00 0.00 0.00 4.61
2295 2398 3.555168 GGAACGACATATCTCCATCCACC 60.555 52.174 0.00 0.00 0.00 4.61
2296 2399 3.069586 TGGAACGACATATCTCCATCCAC 59.930 47.826 0.00 0.00 31.12 4.02
2297 2400 3.304829 TGGAACGACATATCTCCATCCA 58.695 45.455 0.00 0.00 33.54 3.41
2298 2401 4.021104 TCATGGAACGACATATCTCCATCC 60.021 45.833 0.00 0.00 35.99 3.51
2299 2402 4.926238 GTCATGGAACGACATATCTCCATC 59.074 45.833 0.00 0.00 35.99 3.51
2307 2410 3.442625 ACTCGAAGTCATGGAACGACATA 59.557 43.478 0.00 0.00 35.77 2.29
2310 2413 2.349297 ACTCGAAGTCATGGAACGAC 57.651 50.000 0.00 0.00 0.00 4.34
2315 2418 1.402852 CGCTCAACTCGAAGTCATGGA 60.403 52.381 0.00 0.00 0.00 3.41
2316 2419 0.994995 CGCTCAACTCGAAGTCATGG 59.005 55.000 0.00 0.00 0.00 3.66
2321 2424 0.104304 AACACCGCTCAACTCGAAGT 59.896 50.000 0.00 0.00 0.00 3.01
2325 2428 2.372690 CGGAACACCGCTCAACTCG 61.373 63.158 0.00 0.00 40.29 4.18
2329 2432 0.948623 CACATCGGAACACCGCTCAA 60.949 55.000 3.67 0.00 45.52 3.02
2337 2440 5.290885 CGTTGAATCTTATCACATCGGAACA 59.709 40.000 0.00 0.00 0.00 3.18
2341 2444 3.059597 GGCGTTGAATCTTATCACATCGG 60.060 47.826 0.00 0.00 0.00 4.18
2425 2552 2.025418 GCATTTGTCGTCCGTCCGT 61.025 57.895 0.00 0.00 0.00 4.69
2426 2553 1.683790 GAGCATTTGTCGTCCGTCCG 61.684 60.000 0.00 0.00 0.00 4.79
2427 2554 1.359459 GGAGCATTTGTCGTCCGTCC 61.359 60.000 0.00 0.00 0.00 4.79
2428 2555 1.683790 CGGAGCATTTGTCGTCCGTC 61.684 60.000 1.43 0.00 45.62 4.79
2429 2556 1.736645 CGGAGCATTTGTCGTCCGT 60.737 57.895 1.43 0.00 45.62 4.69
2430 2557 3.081133 CGGAGCATTTGTCGTCCG 58.919 61.111 0.00 0.00 45.48 4.79
2431 2558 0.389948 AGTCGGAGCATTTGTCGTCC 60.390 55.000 0.00 0.00 0.00 4.79
2432 2559 1.429463 AAGTCGGAGCATTTGTCGTC 58.571 50.000 0.00 0.00 0.00 4.20
2433 2560 1.531149 CAAAGTCGGAGCATTTGTCGT 59.469 47.619 0.00 0.00 31.30 4.34
2434 2561 1.798223 TCAAAGTCGGAGCATTTGTCG 59.202 47.619 9.00 0.00 35.31 4.35
2435 2562 2.095718 GGTCAAAGTCGGAGCATTTGTC 60.096 50.000 9.00 5.24 35.31 3.18
2436 2563 1.880027 GGTCAAAGTCGGAGCATTTGT 59.120 47.619 9.00 0.00 35.31 2.83
2486 2619 0.321996 TGGCGCACTGTATTGTACCA 59.678 50.000 10.83 0.00 0.00 3.25
2487 2620 1.129811 GTTGGCGCACTGTATTGTACC 59.870 52.381 10.83 0.00 0.00 3.34
2510 2643 2.802057 CGCCCCCGAGTTTTCTATACTG 60.802 54.545 0.00 0.00 36.29 2.74
2528 2697 1.512156 TTGTTCTTTTCTCCGCCGCC 61.512 55.000 0.00 0.00 0.00 6.13
2530 2699 1.508632 TCTTGTTCTTTTCTCCGCCG 58.491 50.000 0.00 0.00 0.00 6.46
2611 2781 3.947041 AGCACAGAGGGGGAGGGT 61.947 66.667 0.00 0.00 0.00 4.34
2621 2791 1.368950 GACCTCTGCACAGCACAGA 59.631 57.895 0.00 0.00 41.78 3.41
2624 2794 1.233285 CCTTGACCTCTGCACAGCAC 61.233 60.000 0.00 0.00 33.79 4.40
2625 2795 1.071987 CCTTGACCTCTGCACAGCA 59.928 57.895 0.00 0.00 36.92 4.41
2626 2796 1.673665 CCCTTGACCTCTGCACAGC 60.674 63.158 0.00 0.00 0.00 4.40
2689 2866 3.613030 ACGGAGGAGAGAGAGAGTAAAC 58.387 50.000 0.00 0.00 0.00 2.01
2693 2870 0.544697 GGACGGAGGAGAGAGAGAGT 59.455 60.000 0.00 0.00 0.00 3.24
2725 2904 0.031716 CCTCTCCTCACCCAGATGGA 60.032 60.000 0.00 0.00 37.39 3.41
2728 2907 0.415429 ACACCTCTCCTCACCCAGAT 59.585 55.000 0.00 0.00 0.00 2.90
2740 2919 0.979665 CCACCACTCATCACACCTCT 59.020 55.000 0.00 0.00 0.00 3.69
2741 2920 0.036010 CCCACCACTCATCACACCTC 60.036 60.000 0.00 0.00 0.00 3.85
2742 2921 0.768221 ACCCACCACTCATCACACCT 60.768 55.000 0.00 0.00 0.00 4.00
2743 2922 0.321653 GACCCACCACTCATCACACC 60.322 60.000 0.00 0.00 0.00 4.16
2744 2923 0.321653 GGACCCACCACTCATCACAC 60.322 60.000 0.00 0.00 38.79 3.82
2745 2924 1.488705 GGGACCCACCACTCATCACA 61.489 60.000 5.33 0.00 41.20 3.58
2746 2925 1.299976 GGGACCCACCACTCATCAC 59.700 63.158 5.33 0.00 41.20 3.06
2747 2926 1.151921 TGGGACCCACCACTCATCA 60.152 57.895 9.95 0.00 41.20 3.07
2748 2927 3.820425 TGGGACCCACCACTCATC 58.180 61.111 9.95 0.00 41.20 2.92
2761 2940 3.224324 GGAGCCTATCGCGTGGGA 61.224 66.667 5.77 0.00 44.76 4.37
2805 2984 4.660938 GGGTGCAGGCCGGAAAGT 62.661 66.667 5.05 0.00 0.00 2.66
2858 3037 2.544694 GCGTGACGAGATGAGATTGGAT 60.545 50.000 10.10 0.00 0.00 3.41
2859 3038 1.202302 GCGTGACGAGATGAGATTGGA 60.202 52.381 10.10 0.00 0.00 3.53
2904 3087 2.440569 GCGCGCTCTCTGTGTTCTC 61.441 63.158 26.67 0.00 0.00 2.87
2905 3088 2.431601 GCGCGCTCTCTGTGTTCT 60.432 61.111 26.67 0.00 0.00 3.01
2906 3089 2.724708 CTGCGCGCTCTCTGTGTTC 61.725 63.158 33.29 0.00 0.00 3.18
2940 3124 1.952621 AAAAGAGGTGGGAGGATCGA 58.047 50.000 0.00 0.00 34.37 3.59
2941 3125 2.766828 AGTAAAAGAGGTGGGAGGATCG 59.233 50.000 0.00 0.00 34.37 3.69
2942 3126 4.846168 AAGTAAAAGAGGTGGGAGGATC 57.154 45.455 0.00 0.00 0.00 3.36
2943 3127 6.910259 ATAAAGTAAAAGAGGTGGGAGGAT 57.090 37.500 0.00 0.00 0.00 3.24
2992 3176 7.765819 GCAGCCCTTACTTTCATTTGATAATTT 59.234 33.333 0.00 0.00 0.00 1.82
2993 3177 7.267857 GCAGCCCTTACTTTCATTTGATAATT 58.732 34.615 0.00 0.00 0.00 1.40
2994 3178 6.460123 CGCAGCCCTTACTTTCATTTGATAAT 60.460 38.462 0.00 0.00 0.00 1.28
2995 3179 5.163663 CGCAGCCCTTACTTTCATTTGATAA 60.164 40.000 0.00 0.00 0.00 1.75
2996 3180 4.335315 CGCAGCCCTTACTTTCATTTGATA 59.665 41.667 0.00 0.00 0.00 2.15
2997 3181 3.129287 CGCAGCCCTTACTTTCATTTGAT 59.871 43.478 0.00 0.00 0.00 2.57
2998 3182 2.487762 CGCAGCCCTTACTTTCATTTGA 59.512 45.455 0.00 0.00 0.00 2.69
2999 3183 2.415893 CCGCAGCCCTTACTTTCATTTG 60.416 50.000 0.00 0.00 0.00 2.32
3000 3184 1.818674 CCGCAGCCCTTACTTTCATTT 59.181 47.619 0.00 0.00 0.00 2.32
3001 3185 1.463674 CCGCAGCCCTTACTTTCATT 58.536 50.000 0.00 0.00 0.00 2.57
3002 3186 0.394352 CCCGCAGCCCTTACTTTCAT 60.394 55.000 0.00 0.00 0.00 2.57
3003 3187 1.002624 CCCGCAGCCCTTACTTTCA 60.003 57.895 0.00 0.00 0.00 2.69
3004 3188 1.002502 ACCCGCAGCCCTTACTTTC 60.003 57.895 0.00 0.00 0.00 2.62
3005 3189 1.303317 CACCCGCAGCCCTTACTTT 60.303 57.895 0.00 0.00 0.00 2.66
3006 3190 2.351276 CACCCGCAGCCCTTACTT 59.649 61.111 0.00 0.00 0.00 2.24
3007 3191 3.717294 CCACCCGCAGCCCTTACT 61.717 66.667 0.00 0.00 0.00 2.24
3008 3192 4.796495 CCCACCCGCAGCCCTTAC 62.796 72.222 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.