Multiple sequence alignment - TraesCS5A01G198500

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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 TraesCS5A01G198500 chr5A 100.000 3216 0 0 1 3216 403027353 403030568 0.000000e+00 5939.0
1 TraesCS5A01G198500 chr5D 90.378 2484 111 45 806 3216 309694364 309696792 0.000000e+00 3145.0
2 TraesCS5A01G198500 chr5D 86.509 845 55 25 1 808 309693518 309694340 0.000000e+00 874.0
3 TraesCS5A01G198500 chr5D 88.462 52 4 1 2382 2433 117066740 117066789 9.630000e-06 62.1
4 TraesCS5A01G198500 chr5B 90.319 2386 109 42 806 3113 355234558 355236899 0.000000e+00 3014.0
5 TraesCS5A01G198500 chr5B 84.442 842 51 36 1 808 355233738 355234533 0.000000e+00 756.0
6 TraesCS5A01G198500 chr5B 95.506 89 4 0 3128 3216 355237067 355237155 3.340000e-30 143.0
7 TraesCS5A01G198500 chr7A 81.071 280 35 9 1301 1580 83636049 83635788 1.170000e-49 207.0
8 TraesCS5A01G198500 chr7A 82.653 98 14 2 1934 2028 83635422 83635325 2.060000e-12 84.2
9 TraesCS5A01G198500 chr7D 80.488 287 36 11 1301 1580 80979980 80979707 5.440000e-48 202.0
10 TraesCS5A01G198500 chr7D 83.673 98 13 2 1934 2028 80979335 80979238 4.420000e-14 89.8
11 TraesCS5A01G198500 chr7D 97.143 35 1 0 2399 2433 537122855 537122889 3.460000e-05 60.2
12 TraesCS5A01G198500 chr7B 82.653 98 14 2 1934 2028 28505762 28505665 2.060000e-12 84.2
13 TraesCS5A01G198500 chr7B 84.058 69 10 1 2399 2466 310256689 310256757 7.450000e-07 65.8
14 TraesCS5A01G198500 chr7B 97.222 36 1 0 2402 2437 38557396 38557361 9.630000e-06 62.1
15 TraesCS5A01G198500 chr7B 94.737 38 2 0 2399 2436 219934505 219934468 3.460000e-05 60.2
16 TraesCS5A01G198500 chr6B 81.944 72 12 1 2402 2472 449057997 449057926 3.460000e-05 60.2
17 TraesCS5A01G198500 chr6B 81.944 72 12 1 2402 2472 449104143 449104072 3.460000e-05 60.2


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 TraesCS5A01G198500 chr5A 403027353 403030568 3215 False 5939.000000 5939 100.0000 1 3216 1 chr5A.!!$F1 3215
1 TraesCS5A01G198500 chr5D 309693518 309696792 3274 False 2009.500000 3145 88.4435 1 3216 2 chr5D.!!$F2 3215
2 TraesCS5A01G198500 chr5B 355233738 355237155 3417 False 1304.333333 3014 90.0890 1 3216 3 chr5B.!!$F1 3215

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
229 230 0.108585 GGCCCACGTCCATGTATGAT 59.891 55.0 0.0 0.0 0.0 2.45 F
755 804 0.317160 TACACAGCCCAACGAGACAG 59.683 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1641 1739 1.299321 GCTCCTGCTTCTGCTCCTT 59.701 57.895 0.00 0.0 40.48 3.36 R
2647 2798 0.250640 GACTCCATGGCCATGCTAGG 60.251 60.000 36.08 24.4 37.49 3.02 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
28 29 2.034066 CCAGATGGTTGGCCGTGT 59.966 61.111 0.00 0.00 37.67 4.49
29 30 1.298340 CCAGATGGTTGGCCGTGTA 59.702 57.895 0.00 0.00 37.67 2.90
103 104 1.414897 CGCTGTTACGCTCGGTTTC 59.585 57.895 0.00 0.00 0.00 2.78
107 108 1.193874 CTGTTACGCTCGGTTTCAACC 59.806 52.381 0.00 0.00 45.76 3.77
133 134 2.663196 GGAGTTCCCACGGGACAG 59.337 66.667 3.66 0.00 45.11 3.51
165 166 0.895559 CCTCCCTTGGCAGTTGGTTC 60.896 60.000 0.00 0.00 0.00 3.62
172 173 2.335011 GCAGTTGGTTCGTTGGCC 59.665 61.111 0.00 0.00 0.00 5.36
173 174 2.637025 CAGTTGGTTCGTTGGCCG 59.363 61.111 0.00 0.00 38.13 6.13
174 175 2.184167 CAGTTGGTTCGTTGGCCGT 61.184 57.895 0.00 0.00 37.94 5.68
175 176 1.452470 AGTTGGTTCGTTGGCCGTT 60.452 52.632 0.00 0.00 37.94 4.44
176 177 1.298788 GTTGGTTCGTTGGCCGTTG 60.299 57.895 0.00 0.00 37.94 4.10
177 178 2.482333 TTGGTTCGTTGGCCGTTGG 61.482 57.895 0.00 0.00 37.94 3.77
192 193 0.746923 GTTGGCACCCTCGTAATCCC 60.747 60.000 0.00 0.00 0.00 3.85
212 213 3.660111 AGAAAACACTGCCGCGGC 61.660 61.111 42.35 42.35 42.35 6.53
225 226 4.460683 GCGGCCCACGTCCATGTA 62.461 66.667 0.00 0.00 46.52 2.29
226 227 2.504032 CGGCCCACGTCCATGTAT 59.496 61.111 0.00 0.00 37.93 2.29
227 228 1.887242 CGGCCCACGTCCATGTATG 60.887 63.158 0.00 0.00 37.93 2.39
228 229 1.524961 GGCCCACGTCCATGTATGA 59.475 57.895 0.00 0.00 0.00 2.15
229 230 0.108585 GGCCCACGTCCATGTATGAT 59.891 55.000 0.00 0.00 0.00 2.45
267 275 1.145156 CGATGGTTGCCGATGGGTA 59.855 57.895 0.00 0.00 34.97 3.69
300 325 1.439693 GCTACGATCGAGCTCGCTC 60.440 63.158 30.97 28.24 42.35 5.03
408 433 1.213799 GTCCACGGGTCGAAGTACC 59.786 63.158 0.00 0.00 38.94 3.34
414 439 3.073101 GGTCGAAGTACCCCGGCT 61.073 66.667 0.00 0.00 33.02 5.52
415 440 2.493501 GTCGAAGTACCCCGGCTC 59.506 66.667 0.00 0.00 0.00 4.70
571 611 0.603975 AGGAAGAAGCTTCACGTGGC 60.604 55.000 27.57 12.35 0.00 5.01
594 634 1.831652 CGCCCAGGTATCCATCCTCC 61.832 65.000 0.00 0.00 32.37 4.30
749 798 2.223479 GCCAATAATACACAGCCCAACG 60.223 50.000 0.00 0.00 0.00 4.10
755 804 0.317160 TACACAGCCCAACGAGACAG 59.683 55.000 0.00 0.00 0.00 3.51
782 831 3.526534 GAAGATGGTCAAGTGAGTAGGC 58.473 50.000 0.00 0.00 0.00 3.93
917 996 2.743636 TCGTTCCACTCCAACTGATC 57.256 50.000 0.00 0.00 0.00 2.92
919 998 1.676014 CGTTCCACTCCAACTGATCCC 60.676 57.143 0.00 0.00 0.00 3.85
1041 1136 3.157252 GGAGGAGGAGCATGGCGA 61.157 66.667 0.00 0.00 0.00 5.54
1089 1184 3.154473 TCGGGCGGGAGATCAAGG 61.154 66.667 0.00 0.00 0.00 3.61
1245 1340 1.002257 TGCGGGTTGATGCACATCT 60.002 52.632 11.66 0.00 38.60 2.90
1998 2102 0.393537 GTCCAAGATCTGGCAGTGGG 60.394 60.000 18.57 12.28 45.98 4.61
2237 2341 9.860898 ATAAGCATTTCATGTTAAGAGTTTTCC 57.139 29.630 0.00 0.00 0.00 3.13
2238 2342 7.288810 AGCATTTCATGTTAAGAGTTTTCCA 57.711 32.000 0.00 0.00 0.00 3.53
2239 2343 7.899973 AGCATTTCATGTTAAGAGTTTTCCAT 58.100 30.769 0.00 0.00 0.00 3.41
2240 2344 7.816031 AGCATTTCATGTTAAGAGTTTTCCATG 59.184 33.333 0.00 0.00 0.00 3.66
2279 2383 4.057406 TCTTTTTGGGCAATGTTGAGTG 57.943 40.909 0.00 0.00 0.00 3.51
2309 2413 2.772739 CTCGGAAGTGGATGGCAAG 58.227 57.895 0.00 0.00 0.00 4.01
2315 2419 0.537143 AAGTGGATGGCAAGCGAACA 60.537 50.000 0.00 0.00 0.00 3.18
2326 2431 0.381801 AAGCGAACACACTTTGCTGG 59.618 50.000 0.00 0.00 35.77 4.85
2344 2449 0.584876 GGCAGTTTTAGTTGCGACGT 59.415 50.000 0.00 0.00 41.17 4.34
2358 2463 1.730121 GCGACGTGAGATCAAACGGTA 60.730 52.381 20.09 0.00 43.96 4.02
2360 2465 2.981805 CGACGTGAGATCAAACGGTAAA 59.018 45.455 20.09 0.00 43.96 2.01
2377 2509 8.446599 AACGGTAAATTTCTTCTTCTCAGAAA 57.553 30.769 0.00 0.00 42.93 2.52
2379 2511 8.507249 ACGGTAAATTTCTTCTTCTCAGAAATG 58.493 33.333 8.33 0.26 46.01 2.32
2380 2512 7.965107 CGGTAAATTTCTTCTTCTCAGAAATGG 59.035 37.037 8.33 0.00 46.01 3.16
2381 2513 8.246871 GGTAAATTTCTTCTTCTCAGAAATGGG 58.753 37.037 8.33 0.00 46.01 4.00
2382 2514 9.014297 GTAAATTTCTTCTTCTCAGAAATGGGA 57.986 33.333 8.33 0.00 46.01 4.37
2384 2516 8.482852 AATTTCTTCTTCTCAGAAATGGGAAA 57.517 30.769 8.33 0.00 46.01 3.13
2385 2517 8.661752 ATTTCTTCTTCTCAGAAATGGGAAAT 57.338 30.769 7.03 9.57 45.34 2.17
2386 2518 8.482852 TTTCTTCTTCTCAGAAATGGGAAATT 57.517 30.769 0.00 0.00 38.63 1.82
2388 2520 8.567285 TCTTCTTCTCAGAAATGGGAAATTAC 57.433 34.615 0.00 0.00 38.63 1.89
2390 2522 6.789268 TCTTCTCAGAAATGGGAAATTACCA 58.211 36.000 0.00 0.00 43.22 3.25
2441 2573 0.725117 CGTTCGCAAATACCACCCTC 59.275 55.000 0.00 0.00 0.00 4.30
2449 2581 0.537188 AATACCACCCTCGCAGTGAG 59.463 55.000 3.74 3.74 44.83 3.51
2460 2592 2.356313 CAGTGAGCGTTCGCCAGT 60.356 61.111 13.54 10.91 34.29 4.00
2531 2663 7.228108 ACAAGTACAACATCATCATCATCATCC 59.772 37.037 0.00 0.00 0.00 3.51
2588 2739 5.392380 GCATTGCTACATTTTGTACTGCTCT 60.392 40.000 0.16 0.00 28.91 4.09
2597 2748 6.372659 ACATTTTGTACTGCTCTACTGGAATG 59.627 38.462 0.00 0.00 0.00 2.67
2615 2766 4.638421 GGAATGTTCCGGTGTTTATCATCA 59.362 41.667 0.00 0.00 37.65 3.07
2619 2770 1.134220 TCCGGTGTTTATCATCAGCCC 60.134 52.381 0.00 0.00 0.00 5.19
2648 2799 3.847621 GCAGGGGCTAGCAAATCC 58.152 61.111 18.24 11.83 36.96 3.01
2696 2847 4.815108 GTGGCCCCGTCCCAATCC 62.815 72.222 0.00 0.00 33.39 3.01
2707 2858 1.149174 CCCAATCCGAGGTCCCATG 59.851 63.158 0.00 0.00 0.00 3.66
2744 2895 1.374252 CCACGTACAGGTGTCTGCC 60.374 63.158 0.00 0.00 44.59 4.85
2765 2916 3.844090 GGCGCCTCCTCAGTCCTC 61.844 72.222 22.15 0.00 0.00 3.71
2766 2917 4.200283 GCGCCTCCTCAGTCCTCG 62.200 72.222 0.00 0.00 0.00 4.63
2781 2932 1.153862 CTCGCTCACCTGTGCTCTC 60.154 63.158 0.00 0.00 32.84 3.20
2805 2956 1.199097 GCACCACCACCATTAAACTCG 59.801 52.381 0.00 0.00 0.00 4.18
2820 2971 3.447025 CTCGGGATCTGGGCCGTTC 62.447 68.421 0.00 0.00 0.00 3.95
2842 2993 2.649129 GGGCAGATTTGGGTGGCAC 61.649 63.158 9.70 9.70 40.92 5.01
2866 3017 1.660560 CTTGGCTTCTGGCGGGATTG 61.661 60.000 0.00 0.00 42.94 2.67
2906 3057 1.267574 ATGCGTGAGAGGTGTCCCAT 61.268 55.000 0.00 0.00 0.00 4.00
2936 3087 1.502231 CATCTACCGCCATTCTTCCG 58.498 55.000 0.00 0.00 0.00 4.30
2949 3100 3.950794 CTTCCGGCCGCAGCAACTA 62.951 63.158 22.85 0.00 42.56 2.24
2950 3101 3.950794 TTCCGGCCGCAGCAACTAG 62.951 63.158 22.85 2.11 42.56 2.57
2995 3160 2.553602 CTGCTGAATTGGTTGCACAGTA 59.446 45.455 0.00 0.00 0.00 2.74
2996 3161 2.553602 TGCTGAATTGGTTGCACAGTAG 59.446 45.455 0.00 0.00 0.00 2.57
2997 3162 2.095059 GCTGAATTGGTTGCACAGTAGG 60.095 50.000 0.00 0.00 0.00 3.18
2998 3163 3.411446 CTGAATTGGTTGCACAGTAGGA 58.589 45.455 0.00 0.00 0.00 2.94
2999 3164 3.411446 TGAATTGGTTGCACAGTAGGAG 58.589 45.455 0.00 0.00 0.00 3.69
3000 3165 3.181445 TGAATTGGTTGCACAGTAGGAGT 60.181 43.478 0.00 0.00 0.00 3.85
3042 3207 2.060567 ATCGGCACTGGGATCATGGG 62.061 60.000 0.00 0.00 0.00 4.00
3068 3234 2.486966 GCTTGGATGGAGCGTTGC 59.513 61.111 0.00 0.00 0.00 4.17
3079 3245 2.103538 GCGTTGCTGGGCATGATG 59.896 61.111 0.00 0.00 38.76 3.07
3080 3246 2.409055 GCGTTGCTGGGCATGATGA 61.409 57.895 0.00 0.00 38.76 2.92
3081 3247 1.731433 GCGTTGCTGGGCATGATGAT 61.731 55.000 0.00 0.00 38.76 2.45
3082 3248 0.309922 CGTTGCTGGGCATGATGATC 59.690 55.000 0.00 0.00 38.76 2.92
3083 3249 0.309922 GTTGCTGGGCATGATGATCG 59.690 55.000 0.00 0.00 38.76 3.69
3084 3250 0.820482 TTGCTGGGCATGATGATCGG 60.820 55.000 0.00 0.00 38.76 4.18
3085 3251 1.228063 GCTGGGCATGATGATCGGT 60.228 57.895 0.00 0.00 0.00 4.69
3086 3252 0.035317 GCTGGGCATGATGATCGGTA 59.965 55.000 0.00 0.00 0.00 4.02
3087 3253 1.943046 GCTGGGCATGATGATCGGTAG 60.943 57.143 0.00 0.00 0.00 3.18
3088 3254 0.686789 TGGGCATGATGATCGGTAGG 59.313 55.000 0.00 0.00 0.00 3.18
3089 3255 0.976641 GGGCATGATGATCGGTAGGA 59.023 55.000 0.00 0.00 0.00 2.94
3151 3473 4.563140 ACTTCCTTTATCGTTGGCCTTA 57.437 40.909 3.32 0.00 0.00 2.69
3168 3490 1.676006 CTTAATGGGCACGGTGATTCC 59.324 52.381 13.29 10.13 0.00 3.01
3198 3526 6.634805 TGATTCCTCTTCACTGTCAGTTATC 58.365 40.000 1.67 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 1.677966 TGGGAACTCCGGAGAGACG 60.678 63.158 37.69 12.68 43.39 4.18
133 134 2.416260 GGAGGACGGACGTATGCC 59.584 66.667 0.00 0.00 0.00 4.40
172 173 1.087771 GGATTACGAGGGTGCCAACG 61.088 60.000 0.00 0.00 0.00 4.10
173 174 0.746923 GGGATTACGAGGGTGCCAAC 60.747 60.000 0.00 0.00 0.00 3.77
174 175 1.605453 GGGATTACGAGGGTGCCAA 59.395 57.895 0.00 0.00 0.00 4.52
175 176 2.727392 CGGGATTACGAGGGTGCCA 61.727 63.158 0.00 0.00 35.47 4.92
176 177 2.108362 CGGGATTACGAGGGTGCC 59.892 66.667 0.00 0.00 35.47 5.01
177 178 2.588034 GCGGGATTACGAGGGTGC 60.588 66.667 0.00 0.00 35.47 5.01
178 179 1.227263 CTGCGGGATTACGAGGGTG 60.227 63.158 0.00 0.00 35.47 4.61
183 184 2.070783 GTGTTTTCTGCGGGATTACGA 58.929 47.619 0.00 0.00 35.47 3.43
212 213 2.917933 ACAATCATACATGGACGTGGG 58.082 47.619 0.00 0.00 0.00 4.61
222 223 7.286775 TCTGCTACCTGTACATACAATCATACA 59.713 37.037 0.00 0.00 35.50 2.29
223 224 7.595502 GTCTGCTACCTGTACATACAATCATAC 59.404 40.741 0.00 0.00 35.50 2.39
224 225 7.521585 CGTCTGCTACCTGTACATACAATCATA 60.522 40.741 0.00 0.00 35.50 2.15
225 226 6.516718 GTCTGCTACCTGTACATACAATCAT 58.483 40.000 0.00 0.00 35.50 2.45
226 227 5.449999 CGTCTGCTACCTGTACATACAATCA 60.450 44.000 0.00 0.00 35.50 2.57
227 228 4.976731 CGTCTGCTACCTGTACATACAATC 59.023 45.833 0.00 0.00 35.50 2.67
228 229 4.643334 TCGTCTGCTACCTGTACATACAAT 59.357 41.667 0.00 0.00 35.50 2.71
229 230 4.011698 TCGTCTGCTACCTGTACATACAA 58.988 43.478 0.00 0.00 35.50 2.41
398 423 2.493501 GAGCCGGGGTACTTCGAC 59.506 66.667 2.18 0.00 0.00 4.20
411 436 4.742201 TGGTTGAGCGAGCGAGCC 62.742 66.667 2.87 0.00 38.01 4.70
412 437 3.482783 GTGGTTGAGCGAGCGAGC 61.483 66.667 0.00 0.00 37.41 5.03
414 439 3.282745 GAGGTGGTTGAGCGAGCGA 62.283 63.158 0.00 0.00 0.00 4.93
415 440 2.811317 GAGGTGGTTGAGCGAGCG 60.811 66.667 0.00 0.00 0.00 5.03
500 525 2.125912 CAGTCGGGTTGAGGCTCG 60.126 66.667 10.42 0.00 0.00 5.03
545 585 3.595173 GTGAAGCTTCTTCCTCTTCCTC 58.405 50.000 26.09 0.00 36.34 3.71
546 586 2.028567 CGTGAAGCTTCTTCCTCTTCCT 60.029 50.000 26.09 0.00 36.34 3.36
547 587 2.289133 ACGTGAAGCTTCTTCCTCTTCC 60.289 50.000 26.09 0.00 36.34 3.46
548 588 2.734079 CACGTGAAGCTTCTTCCTCTTC 59.266 50.000 26.09 0.00 37.36 2.87
549 589 2.548920 CCACGTGAAGCTTCTTCCTCTT 60.549 50.000 26.09 2.23 0.00 2.85
550 590 1.001406 CCACGTGAAGCTTCTTCCTCT 59.999 52.381 26.09 1.45 0.00 3.69
724 773 2.546789 GGGCTGTGTATTATTGGCGTAC 59.453 50.000 0.00 0.00 0.00 3.67
725 774 2.170817 TGGGCTGTGTATTATTGGCGTA 59.829 45.455 0.00 0.00 0.00 4.42
726 775 1.065053 TGGGCTGTGTATTATTGGCGT 60.065 47.619 0.00 0.00 0.00 5.68
727 776 1.674359 TGGGCTGTGTATTATTGGCG 58.326 50.000 0.00 0.00 0.00 5.69
728 777 2.223479 CGTTGGGCTGTGTATTATTGGC 60.223 50.000 0.00 0.00 0.00 4.52
749 798 2.693074 GACCATCTTCCTCCTCTGTCTC 59.307 54.545 0.00 0.00 0.00 3.36
755 804 2.834549 TCACTTGACCATCTTCCTCCTC 59.165 50.000 0.00 0.00 0.00 3.71
782 831 5.020132 AGAATATTGTATCCTCCTCCTCCG 58.980 45.833 0.00 0.00 0.00 4.63
844 923 1.003718 GGTGAGGTCAACCGGGAAG 60.004 63.158 6.32 0.00 42.08 3.46
845 924 2.874664 CGGTGAGGTCAACCGGGAA 61.875 63.158 6.32 0.00 42.70 3.97
846 925 3.307906 CGGTGAGGTCAACCGGGA 61.308 66.667 6.32 0.00 42.70 5.14
917 996 2.907917 CTCTCGGTAGGCGGAGGG 60.908 72.222 0.00 0.00 40.93 4.30
919 998 0.606944 ATAGCTCTCGGTAGGCGGAG 60.607 60.000 0.00 0.00 41.63 4.63
1041 1136 4.954118 TGCCACCCTCCTCACCGT 62.954 66.667 0.00 0.00 0.00 4.83
1089 1184 2.671177 CGAATCCATCATCGCCGGC 61.671 63.158 19.07 19.07 31.71 6.13
1245 1340 4.760047 GAGGAAGAGCCGGCGCAA 62.760 66.667 32.12 0.00 43.43 4.85
1391 1486 3.955101 CCGGAGAGCTCGGCGTAG 61.955 72.222 8.37 4.28 41.07 3.51
1641 1739 1.299321 GCTCCTGCTTCTGCTCCTT 59.701 57.895 0.00 0.00 40.48 3.36
2051 2155 1.381872 CCACGGGAGGTCCTGATCT 60.382 63.158 12.04 0.00 45.36 2.75
2236 2340 3.254470 TCATCAAAAAGGCATGCATGG 57.746 42.857 27.34 9.48 0.00 3.66
2237 2341 5.116180 AGATTCATCAAAAAGGCATGCATG 58.884 37.500 22.70 22.70 0.00 4.06
2238 2342 5.353394 AGATTCATCAAAAAGGCATGCAT 57.647 34.783 21.36 10.32 0.00 3.96
2239 2343 4.811969 AGATTCATCAAAAAGGCATGCA 57.188 36.364 21.36 0.00 0.00 3.96
2240 2344 6.490566 AAAAGATTCATCAAAAAGGCATGC 57.509 33.333 9.90 9.90 0.00 4.06
2279 2383 1.145803 CTTCCGAGGAAACGTCAACC 58.854 55.000 6.01 0.00 33.34 3.77
2309 2413 1.658409 GCCAGCAAAGTGTGTTCGC 60.658 57.895 0.00 0.00 0.00 4.70
2315 2419 3.023832 ACTAAAACTGCCAGCAAAGTGT 58.976 40.909 0.00 0.00 0.00 3.55
2326 2431 1.259507 TCACGTCGCAACTAAAACTGC 59.740 47.619 0.00 0.00 35.14 4.40
2344 2449 7.979444 AGAAGAAATTTACCGTTTGATCTCA 57.021 32.000 0.00 0.00 0.00 3.27
2377 2509 8.677871 TCATATAGTTCCATGGTAATTTCCCAT 58.322 33.333 12.58 1.34 43.53 4.00
2379 2511 8.934023 TTCATATAGTTCCATGGTAATTTCCC 57.066 34.615 12.58 0.00 0.00 3.97
2380 2512 9.793259 TCTTCATATAGTTCCATGGTAATTTCC 57.207 33.333 12.58 0.00 0.00 3.13
2386 2518 9.066892 GCATTTTCTTCATATAGTTCCATGGTA 57.933 33.333 12.58 0.00 0.00 3.25
2388 2520 7.014518 TGGCATTTTCTTCATATAGTTCCATGG 59.985 37.037 4.97 4.97 0.00 3.66
2390 2522 7.255730 GCTGGCATTTTCTTCATATAGTTCCAT 60.256 37.037 0.00 0.00 0.00 3.41
2391 2523 6.039717 GCTGGCATTTTCTTCATATAGTTCCA 59.960 38.462 0.00 0.00 0.00 3.53
2392 2524 6.039717 TGCTGGCATTTTCTTCATATAGTTCC 59.960 38.462 0.00 0.00 0.00 3.62
2394 2526 7.408756 TTGCTGGCATTTTCTTCATATAGTT 57.591 32.000 0.00 0.00 0.00 2.24
2395 2527 7.408756 TTTGCTGGCATTTTCTTCATATAGT 57.591 32.000 0.00 0.00 0.00 2.12
2396 2528 8.598075 GTTTTTGCTGGCATTTTCTTCATATAG 58.402 33.333 0.00 0.00 0.00 1.31
2397 2529 7.275341 CGTTTTTGCTGGCATTTTCTTCATATA 59.725 33.333 0.00 0.00 0.00 0.86
2398 2530 6.091169 CGTTTTTGCTGGCATTTTCTTCATAT 59.909 34.615 0.00 0.00 0.00 1.78
2399 2531 5.404968 CGTTTTTGCTGGCATTTTCTTCATA 59.595 36.000 0.00 0.00 0.00 2.15
2449 2581 1.427819 CCCAATAACTGGCGAACGC 59.572 57.895 10.81 10.81 44.90 4.84
2456 2588 2.826674 ACATGGACCCCAATAACTGG 57.173 50.000 0.00 0.00 45.97 4.00
2597 2748 2.354821 GGCTGATGATAAACACCGGAAC 59.645 50.000 9.46 0.00 0.00 3.62
2615 2766 4.065281 GCTGTACGTGTCCGGGCT 62.065 66.667 7.97 0.00 38.78 5.19
2619 2770 2.126071 CCCTGCTGTACGTGTCCG 60.126 66.667 0.00 0.00 40.83 4.79
2644 2795 1.075050 CTCCATGGCCATGCTAGGATT 59.925 52.381 36.08 1.35 37.49 3.01
2646 2797 0.695462 ACTCCATGGCCATGCTAGGA 60.695 55.000 36.08 26.93 37.49 2.94
2647 2798 0.250640 GACTCCATGGCCATGCTAGG 60.251 60.000 36.08 24.40 37.49 3.02
2648 2799 0.250640 GGACTCCATGGCCATGCTAG 60.251 60.000 36.08 32.75 45.54 3.42
2686 2837 2.499685 GGACCTCGGATTGGGACG 59.500 66.667 0.00 0.00 0.00 4.79
2696 2847 2.821366 GCTGTGCATGGGACCTCG 60.821 66.667 0.00 0.00 0.00 4.63
2707 2858 3.113745 AGCGCCATTATGCTGTGC 58.886 55.556 2.29 0.00 40.62 4.57
2752 2903 1.379176 TGAGCGAGGACTGAGGAGG 60.379 63.158 0.00 0.00 0.00 4.30
2760 2911 2.433318 GCACAGGTGAGCGAGGAC 60.433 66.667 3.10 0.00 0.00 3.85
2761 2912 2.601666 AGCACAGGTGAGCGAGGA 60.602 61.111 3.10 0.00 36.73 3.71
2762 2913 2.125753 GAGCACAGGTGAGCGAGG 60.126 66.667 3.10 0.00 36.73 4.63
2763 2914 1.153862 GAGAGCACAGGTGAGCGAG 60.154 63.158 3.10 0.00 36.73 5.03
2764 2915 2.965783 GAGAGCACAGGTGAGCGA 59.034 61.111 3.10 0.00 36.73 4.93
2765 2916 2.505777 CGAGAGCACAGGTGAGCG 60.506 66.667 3.10 0.00 36.73 5.03
2781 2932 1.240641 TTAATGGTGGTGGTGCTGCG 61.241 55.000 0.00 0.00 0.00 5.18
2786 2937 1.810151 CCGAGTTTAATGGTGGTGGTG 59.190 52.381 0.00 0.00 0.00 4.17
2805 2956 2.808206 ATCGAACGGCCCAGATCCC 61.808 63.158 0.00 0.00 0.00 3.85
2820 2971 1.386525 CCACCCAAATCTGCCCATCG 61.387 60.000 0.00 0.00 0.00 3.84
2842 2993 2.037136 CGCCAGAAGCCAAGGACAG 61.037 63.158 0.00 0.00 38.78 3.51
2866 3017 3.127099 GCCATTAAGCCCCCTAACC 57.873 57.895 0.00 0.00 0.00 2.85
2885 3036 1.517257 GGACACCTCTCACGCATCG 60.517 63.158 0.00 0.00 0.00 3.84
2906 3057 2.236766 GCGGTAGATGGGTTAGCTAGA 58.763 52.381 0.00 0.00 0.00 2.43
2936 3087 1.811679 GTCTCTAGTTGCTGCGGCC 60.812 63.158 16.57 0.00 37.74 6.13
2947 3098 9.400638 CATAATTAAAGTCGGCTAAGTCTCTAG 57.599 37.037 0.00 0.00 0.00 2.43
2948 3099 7.866393 GCATAATTAAAGTCGGCTAAGTCTCTA 59.134 37.037 0.00 0.00 0.00 2.43
2949 3100 6.702282 GCATAATTAAAGTCGGCTAAGTCTCT 59.298 38.462 0.00 0.00 0.00 3.10
2950 3101 6.702282 AGCATAATTAAAGTCGGCTAAGTCTC 59.298 38.462 0.00 0.00 0.00 3.36
2995 3160 4.884744 CACTGCAGACTGTACTATACTCCT 59.115 45.833 23.35 0.00 0.00 3.69
2996 3161 4.036971 CCACTGCAGACTGTACTATACTCC 59.963 50.000 23.35 0.00 0.00 3.85
2997 3162 4.641094 ACCACTGCAGACTGTACTATACTC 59.359 45.833 23.35 0.00 0.00 2.59
2998 3163 4.601084 ACCACTGCAGACTGTACTATACT 58.399 43.478 23.35 0.00 0.00 2.12
2999 3164 4.496010 CGACCACTGCAGACTGTACTATAC 60.496 50.000 23.35 0.59 0.00 1.47
3000 3165 3.626217 CGACCACTGCAGACTGTACTATA 59.374 47.826 23.35 0.00 0.00 1.31
3068 3234 1.338484 CCTACCGATCATCATGCCCAG 60.338 57.143 0.00 0.00 0.00 4.45
3079 3245 3.256136 CCACTTGGATACTCCTACCGATC 59.744 52.174 0.00 0.00 37.46 3.69
3080 3246 3.231818 CCACTTGGATACTCCTACCGAT 58.768 50.000 0.00 0.00 37.46 4.18
3081 3247 2.662866 CCACTTGGATACTCCTACCGA 58.337 52.381 0.00 0.00 37.46 4.69
3082 3248 1.687123 CCCACTTGGATACTCCTACCG 59.313 57.143 0.00 0.00 37.46 4.02
3083 3249 2.047830 CCCCACTTGGATACTCCTACC 58.952 57.143 0.00 0.00 37.46 3.18
3084 3250 2.047830 CCCCCACTTGGATACTCCTAC 58.952 57.143 0.00 0.00 37.46 3.18
3085 3251 1.694693 GCCCCCACTTGGATACTCCTA 60.695 57.143 0.00 0.00 37.46 2.94
3086 3252 0.988678 GCCCCCACTTGGATACTCCT 60.989 60.000 0.00 0.00 37.46 3.69
3087 3253 1.532238 GCCCCCACTTGGATACTCC 59.468 63.158 0.00 0.00 37.39 3.85
3088 3254 1.146263 CGCCCCCACTTGGATACTC 59.854 63.158 0.00 0.00 37.39 2.59
3089 3255 2.375345 CCGCCCCCACTTGGATACT 61.375 63.158 0.00 0.00 37.39 2.12
3109 3275 5.551233 AGTAGAAAATGTTGTCTGCTAGCA 58.449 37.500 18.22 18.22 35.38 3.49
3151 3473 4.337013 GGAATCACCGTGCCCATT 57.663 55.556 0.00 0.00 0.00 3.16
3168 3490 4.753233 ACAGTGAAGAGGAATCAGAATCG 58.247 43.478 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.