Multiple sequence alignment - TraesCS5A01G499000

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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 TraesCS5A01G499000 chr5A 100.000 3170 0 0 1 3170 665824604 665821435 0.000000e+00 5854
1 TraesCS5A01G499000 chr4D 92.466 1407 80 15 955 2339 484777457 484776055 0.000000e+00 1988
2 TraesCS5A01G499000 chr4D 90.920 837 52 10 2335 3170 484776018 484775205 0.000000e+00 1103
3 TraesCS5A01G499000 chr4D 85.914 717 40 22 1 697 484778505 484777830 0.000000e+00 708
4 TraesCS5A01G499000 chr4D 97.717 219 5 0 697 915 484777781 484777563 8.300000e-101 377
5 TraesCS5A01G499000 chr4B 90.704 1420 89 22 939 2339 617858481 617857086 0.000000e+00 1851
6 TraesCS5A01G499000 chr4B 90.647 278 8 9 434 697 617859203 617858930 1.400000e-93 353
7 TraesCS5A01G499000 chr4B 92.079 202 13 3 697 897 617858881 617858682 6.690000e-72 281
8 TraesCS5A01G499000 chr4B 91.457 199 17 0 186 384 617859402 617859204 1.120000e-69 274
9 TraesCS5A01G499000 chr4B 94.937 158 3 2 1 158 617859548 617859396 3.160000e-60 243
10 TraesCS5A01G499000 chr1A 82.057 1293 169 26 939 2176 54076470 54075186 0.000000e+00 1044
11 TraesCS5A01G499000 chr1D 81.839 1305 162 26 939 2176 55670414 55669118 0.000000e+00 1027
12 TraesCS5A01G499000 chr1B 81.811 1303 166 24 939 2176 90994092 90992796 0.000000e+00 1027


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 TraesCS5A01G499000 chr5A 665821435 665824604 3169 True 5854.0 5854 100.00000 1 3170 1 chr5A.!!$R1 3169
1 TraesCS5A01G499000 chr4D 484775205 484778505 3300 True 1044.0 1988 91.75425 1 3170 4 chr4D.!!$R1 3169
2 TraesCS5A01G499000 chr4B 617857086 617859548 2462 True 600.4 1851 91.96480 1 2339 5 chr4B.!!$R1 2338
3 TraesCS5A01G499000 chr1A 54075186 54076470 1284 True 1044.0 1044 82.05700 939 2176 1 chr1A.!!$R1 1237
4 TraesCS5A01G499000 chr1D 55669118 55670414 1296 True 1027.0 1027 81.83900 939 2176 1 chr1D.!!$R1 1237
5 TraesCS5A01G499000 chr1B 90992796 90994092 1296 True 1027.0 1027 81.81100 939 2176 1 chr1B.!!$R1 1237

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
464 473 0.109272 TCTGCGACCAGACGATCAAC 60.109 55.0 0.0 0.0 42.98 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2190 2503 0.247736 AGTGTAGGAAGCAAGCTCGG 59.752 55.0 0.0 0.0 0.0 4.63 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
36 37 9.539825 CGACATCTTAGTTTAGTAGGAGTAGTA 57.460 37.037 0.00 0.00 0.00 1.82
54 55 8.239998 GGAGTAGTAGTCGTTTACTTGTTGTAT 58.760 37.037 6.85 0.00 39.80 2.29
173 177 1.227586 CGATCTCCTCCCGACTCGA 60.228 63.158 0.00 0.00 0.00 4.04
174 178 0.604243 CGATCTCCTCCCGACTCGAT 60.604 60.000 0.00 0.00 0.00 3.59
184 188 1.586564 CGACTCGATTCGCTCCACC 60.587 63.158 12.37 0.00 31.03 4.61
229 233 4.514441 GGACAGATACTCATGATGCTTTGG 59.486 45.833 0.00 0.00 0.00 3.28
255 259 3.461773 TCCCACCGCTAGCTGCTC 61.462 66.667 13.93 0.00 40.11 4.26
327 331 2.022754 GCTCCAATCAGGCAATCAGCT 61.023 52.381 0.00 0.00 44.79 4.24
328 332 1.676529 CTCCAATCAGGCAATCAGCTG 59.323 52.381 7.63 7.63 44.79 4.24
331 335 1.134367 CAATCAGGCAATCAGCTGGTG 59.866 52.381 15.13 13.54 44.79 4.17
340 344 3.581755 CAATCAGCTGGTGTGATTTTGG 58.418 45.455 15.13 0.00 41.69 3.28
342 346 2.229792 TCAGCTGGTGTGATTTTGGAC 58.770 47.619 15.13 0.00 0.00 4.02
349 353 3.181477 TGGTGTGATTTTGGACTGCTTTG 60.181 43.478 0.00 0.00 0.00 2.77
351 355 4.044426 GTGTGATTTTGGACTGCTTTGTC 58.956 43.478 0.00 0.00 36.31 3.18
366 375 1.679139 TTGTCCCTGCAAGTGTTCAG 58.321 50.000 0.00 0.00 0.00 3.02
378 387 4.293415 CAAGTGTTCAGATTGGCAAAGAC 58.707 43.478 3.01 0.00 0.00 3.01
391 400 2.012051 GCAAAGACCTATCGTGGGGTG 61.012 57.143 0.00 0.00 35.77 4.61
393 402 0.981277 AAGACCTATCGTGGGGTGGG 60.981 60.000 0.00 0.00 35.77 4.61
401 410 1.000019 CGTGGGGTGGGACTAGAGA 60.000 63.158 0.00 0.00 0.00 3.10
405 414 1.982958 TGGGGTGGGACTAGAGAAAAC 59.017 52.381 0.00 0.00 0.00 2.43
406 415 1.982958 GGGGTGGGACTAGAGAAAACA 59.017 52.381 0.00 0.00 0.00 2.83
407 416 2.290134 GGGGTGGGACTAGAGAAAACAC 60.290 54.545 0.00 0.00 0.00 3.32
408 417 2.370849 GGGTGGGACTAGAGAAAACACA 59.629 50.000 0.00 0.00 0.00 3.72
409 418 3.181448 GGGTGGGACTAGAGAAAACACAA 60.181 47.826 0.00 0.00 0.00 3.33
410 419 4.506802 GGGTGGGACTAGAGAAAACACAAT 60.507 45.833 0.00 0.00 0.00 2.71
411 420 4.695928 GGTGGGACTAGAGAAAACACAATC 59.304 45.833 0.00 0.00 0.00 2.67
412 421 5.305585 GTGGGACTAGAGAAAACACAATCA 58.694 41.667 0.00 0.00 0.00 2.57
413 422 5.940470 GTGGGACTAGAGAAAACACAATCAT 59.060 40.000 0.00 0.00 0.00 2.45
414 423 6.431234 GTGGGACTAGAGAAAACACAATCATT 59.569 38.462 0.00 0.00 0.00 2.57
415 424 7.606456 GTGGGACTAGAGAAAACACAATCATTA 59.394 37.037 0.00 0.00 0.00 1.90
416 425 8.328758 TGGGACTAGAGAAAACACAATCATTAT 58.671 33.333 0.00 0.00 0.00 1.28
417 426 9.178758 GGGACTAGAGAAAACACAATCATTATT 57.821 33.333 0.00 0.00 0.00 1.40
422 431 8.452989 AGAGAAAACACAATCATTATTTTCGC 57.547 30.769 8.30 8.30 41.80 4.70
423 432 8.081633 AGAGAAAACACAATCATTATTTTCGCA 58.918 29.630 14.41 0.00 41.80 5.10
424 433 8.231304 AGAAAACACAATCATTATTTTCGCAG 57.769 30.769 0.00 0.00 41.80 5.18
464 473 0.109272 TCTGCGACCAGACGATCAAC 60.109 55.000 0.00 0.00 42.98 3.18
483 492 5.897050 TCAACGTTTTGTTTTGATTAGGCT 58.103 33.333 0.00 0.00 39.29 4.58
484 493 5.746245 TCAACGTTTTGTTTTGATTAGGCTG 59.254 36.000 0.00 0.00 39.29 4.85
485 494 5.257082 ACGTTTTGTTTTGATTAGGCTGT 57.743 34.783 0.00 0.00 0.00 4.40
486 495 5.040635 ACGTTTTGTTTTGATTAGGCTGTG 58.959 37.500 0.00 0.00 0.00 3.66
487 496 4.444056 CGTTTTGTTTTGATTAGGCTGTGG 59.556 41.667 0.00 0.00 0.00 4.17
488 497 3.658757 TTGTTTTGATTAGGCTGTGGC 57.341 42.857 0.00 0.00 37.82 5.01
781 853 7.577979 CGCTTAAGTTCTGTTAAACCAATACA 58.422 34.615 4.02 0.00 0.00 2.29
782 854 7.532884 CGCTTAAGTTCTGTTAAACCAATACAC 59.467 37.037 4.02 0.00 0.00 2.90
876 949 9.669887 TTACAAGTTTTACCTTTCACTTCTACA 57.330 29.630 0.00 0.00 0.00 2.74
933 1170 4.792521 TTTGCCACACTTTTACTTGTGT 57.207 36.364 1.39 0.00 46.79 3.72
934 1171 5.899120 TTTGCCACACTTTTACTTGTGTA 57.101 34.783 0.00 0.00 44.43 2.90
935 1172 6.458232 TTTGCCACACTTTTACTTGTGTAT 57.542 33.333 0.00 0.00 44.43 2.29
936 1173 6.458232 TTGCCACACTTTTACTTGTGTATT 57.542 33.333 0.00 0.00 44.43 1.89
937 1174 6.067263 TGCCACACTTTTACTTGTGTATTC 57.933 37.500 0.00 0.00 44.43 1.75
995 1242 1.334869 CTTCATTACCGCCCATGAAGC 59.665 52.381 12.83 0.00 45.78 3.86
1015 1262 2.662866 CAACAATGGGCATCTCATCCT 58.337 47.619 0.00 0.00 0.00 3.24
1016 1263 3.028850 CAACAATGGGCATCTCATCCTT 58.971 45.455 0.00 0.00 0.00 3.36
1017 1264 2.662866 ACAATGGGCATCTCATCCTTG 58.337 47.619 0.00 0.00 0.00 3.61
1070 1326 2.125912 CTTCGCCGACTCCACCAG 60.126 66.667 0.00 0.00 0.00 4.00
1093 1349 0.440371 CTCGAAAGACGCAAAGGAGC 59.560 55.000 0.00 0.00 42.26 4.70
1140 1396 2.583593 GCCGTGATCCTCTGCGTC 60.584 66.667 0.00 0.00 0.00 5.19
1230 1486 4.225340 CTCCTCTCGGACGTCGCG 62.225 72.222 17.01 17.01 39.05 5.87
1254 1510 3.826157 CCTTCGCCATATCTCTCTTCTCT 59.174 47.826 0.00 0.00 0.00 3.10
1398 1654 2.131183 GCTATCATGAGGCTCGTCAAC 58.869 52.381 6.18 0.00 0.00 3.18
1638 1930 1.833630 ACCGTCACCACTCATCATCAT 59.166 47.619 0.00 0.00 0.00 2.45
1653 1945 4.573021 TCATCATCCTCATTCAACCACA 57.427 40.909 0.00 0.00 0.00 4.17
1723 2036 1.279271 GTGCCAAGGAAGCTAAGGAGA 59.721 52.381 0.00 0.00 0.00 3.71
1899 2212 1.069090 GCTGTTCACCACGGTCAGA 59.931 57.895 7.42 0.00 33.70 3.27
2017 2330 2.747822 GCTGTCCATGAGCTGCACG 61.748 63.158 1.02 0.00 33.37 5.34
2097 2410 1.643832 GGACGCCGATCAAATGCTC 59.356 57.895 0.00 0.00 0.00 4.26
2151 2464 0.464373 ACATCGGCCATGTCACCATC 60.464 55.000 13.17 0.00 42.62 3.51
2163 2476 1.953138 CACCATCCAGATCGAGCGC 60.953 63.158 0.00 0.00 0.00 5.92
2180 2493 1.019278 CGCGAGTAAGGCCATTGTGT 61.019 55.000 5.01 0.00 0.00 3.72
2181 2494 1.165270 GCGAGTAAGGCCATTGTGTT 58.835 50.000 5.01 0.00 0.00 3.32
2182 2495 1.539827 GCGAGTAAGGCCATTGTGTTT 59.460 47.619 5.01 0.00 0.00 2.83
2183 2496 2.745281 GCGAGTAAGGCCATTGTGTTTA 59.255 45.455 5.01 0.00 0.00 2.01
2184 2497 3.377172 GCGAGTAAGGCCATTGTGTTTAT 59.623 43.478 5.01 0.00 0.00 1.40
2185 2498 4.730613 GCGAGTAAGGCCATTGTGTTTATG 60.731 45.833 5.01 0.00 0.00 1.90
2186 2499 4.394920 CGAGTAAGGCCATTGTGTTTATGT 59.605 41.667 5.01 0.00 0.00 2.29
2187 2500 5.640732 GAGTAAGGCCATTGTGTTTATGTG 58.359 41.667 5.01 0.00 0.00 3.21
2188 2501 5.076873 AGTAAGGCCATTGTGTTTATGTGT 58.923 37.500 5.01 0.00 0.00 3.72
2189 2502 3.940209 AGGCCATTGTGTTTATGTGTG 57.060 42.857 5.01 0.00 0.00 3.82
2190 2503 2.029110 AGGCCATTGTGTTTATGTGTGC 60.029 45.455 5.01 0.00 0.00 4.57
2191 2504 2.336667 GCCATTGTGTTTATGTGTGCC 58.663 47.619 0.00 0.00 0.00 5.01
2192 2505 2.594321 CCATTGTGTTTATGTGTGCCG 58.406 47.619 0.00 0.00 0.00 5.69
2193 2506 2.227626 CCATTGTGTTTATGTGTGCCGA 59.772 45.455 0.00 0.00 0.00 5.54
2194 2507 3.491356 CATTGTGTTTATGTGTGCCGAG 58.509 45.455 0.00 0.00 0.00 4.63
2195 2508 0.871722 TGTGTTTATGTGTGCCGAGC 59.128 50.000 0.00 0.00 0.00 5.03
2196 2509 1.156736 GTGTTTATGTGTGCCGAGCT 58.843 50.000 0.00 0.00 0.00 4.09
2197 2510 1.535462 GTGTTTATGTGTGCCGAGCTT 59.465 47.619 0.00 0.00 0.00 3.74
2198 2511 1.535028 TGTTTATGTGTGCCGAGCTTG 59.465 47.619 0.00 0.00 0.00 4.01
2227 2566 6.968904 CCTACACTTGAATATTGTGTGAATGC 59.031 38.462 16.36 0.00 43.61 3.56
2252 2591 1.952296 GGATTGGCAGTCATCATGGTC 59.048 52.381 12.30 0.00 0.00 4.02
2257 2596 0.543277 GCAGTCATCATGGTCCCTGA 59.457 55.000 5.73 0.00 0.00 3.86
2258 2597 1.065199 GCAGTCATCATGGTCCCTGAA 60.065 52.381 0.51 0.00 0.00 3.02
2261 2600 4.275810 CAGTCATCATGGTCCCTGAAAAT 58.724 43.478 0.51 0.00 0.00 1.82
2267 2606 0.958091 TGGTCCCTGAAAATTGCACG 59.042 50.000 0.00 0.00 0.00 5.34
2272 2611 0.597568 CCTGAAAATTGCACGGCTGA 59.402 50.000 0.00 0.00 0.00 4.26
2279 2618 0.608856 ATTGCACGGCTGATGGTTCA 60.609 50.000 0.00 0.00 0.00 3.18
2285 2625 0.606401 CGGCTGATGGTTCACCTTGT 60.606 55.000 0.00 0.00 36.82 3.16
2294 2634 2.901839 TGGTTCACCTTGTAGTAGTCCC 59.098 50.000 0.00 0.00 36.82 4.46
2299 2639 3.007614 TCACCTTGTAGTAGTCCCTTTGC 59.992 47.826 0.00 0.00 0.00 3.68
2311 2651 3.132824 AGTCCCTTTGCCAAAGTTTTCAG 59.867 43.478 15.61 0.00 36.77 3.02
2314 2654 2.170397 CCTTTGCCAAAGTTTTCAGGGT 59.830 45.455 15.61 0.00 36.77 4.34
2315 2655 3.386402 CCTTTGCCAAAGTTTTCAGGGTA 59.614 43.478 15.61 0.00 36.77 3.69
2333 2673 5.193679 AGGGTACTGAATATGCAAGGTTTC 58.806 41.667 0.00 0.00 0.00 2.78
2423 2805 3.244976 CAAATCGACCCAACTTCAATGC 58.755 45.455 0.00 0.00 0.00 3.56
2424 2806 2.198827 ATCGACCCAACTTCAATGCA 57.801 45.000 0.00 0.00 0.00 3.96
2425 2807 1.974265 TCGACCCAACTTCAATGCAA 58.026 45.000 0.00 0.00 0.00 4.08
2426 2808 2.302260 TCGACCCAACTTCAATGCAAA 58.698 42.857 0.00 0.00 0.00 3.68
2427 2809 2.034053 TCGACCCAACTTCAATGCAAAC 59.966 45.455 0.00 0.00 0.00 2.93
2428 2810 2.034558 CGACCCAACTTCAATGCAAACT 59.965 45.455 0.00 0.00 0.00 2.66
2485 2867 9.161629 CACCAAAATCATACTGTACTTCACATA 57.838 33.333 0.00 0.00 36.29 2.29
2522 2904 6.531948 GGAATTCGATTATCGGATCCTTGTAG 59.468 42.308 14.86 0.00 37.04 2.74
2526 2908 3.386768 TTATCGGATCCTTGTAGCTGC 57.613 47.619 10.75 0.00 0.00 5.25
2569 2951 3.603532 TGATCAGTTCCTTCAGCATGTC 58.396 45.455 0.00 0.00 37.40 3.06
2585 2967 4.079253 GCATGTCCCTTCTCCTTTTGTTA 58.921 43.478 0.00 0.00 0.00 2.41
2587 2969 5.185828 GCATGTCCCTTCTCCTTTTGTTAAT 59.814 40.000 0.00 0.00 0.00 1.40
2614 2996 3.076621 CTGCAGCAACAAGGTATCTCAA 58.923 45.455 0.00 0.00 0.00 3.02
2621 3003 6.036953 CAGCAACAAGGTATCTCAAGAGATTC 59.963 42.308 16.94 12.08 45.31 2.52
2636 3018 3.395470 ATTCGGCGCGTTTGGATGC 62.395 57.895 8.43 0.00 34.36 3.91
2657 3039 4.837298 TGCATAGCATTCAGATACCTCTCT 59.163 41.667 0.00 0.00 31.71 3.10
2661 3043 3.390639 AGCATTCAGATACCTCTCTTGGG 59.609 47.826 0.00 0.00 0.00 4.12
2682 3064 2.562298 GAGAAGAGCTCGATGATCCCAT 59.438 50.000 8.37 0.00 33.17 4.00
2701 3083 2.425143 TCCCTTCCATTCTCACATGC 57.575 50.000 0.00 0.00 0.00 4.06
2777 3159 2.340210 TCGAGCATCTCTAGCAGAGT 57.660 50.000 11.37 0.17 42.83 3.24
2779 3161 2.158827 TCGAGCATCTCTAGCAGAGTCT 60.159 50.000 11.37 0.00 42.83 3.24
2784 3166 5.005740 AGCATCTCTAGCAGAGTCTCTATG 58.994 45.833 0.94 2.32 42.83 2.23
2789 3171 2.428544 AGCAGAGTCTCTATGTCCGT 57.571 50.000 0.94 0.00 0.00 4.69
2790 3172 2.294074 AGCAGAGTCTCTATGTCCGTC 58.706 52.381 0.94 0.00 0.00 4.79
2792 3174 1.600013 CAGAGTCTCTATGTCCGTCCG 59.400 57.143 0.94 0.00 0.00 4.79
2795 3177 1.826921 TCTCTATGTCCGTCCGGCC 60.827 63.158 0.00 0.00 34.68 6.13
2797 3179 3.151710 CTATGTCCGTCCGGCCCA 61.152 66.667 0.00 0.65 34.68 5.36
2808 3190 0.112606 TCCGGCCCACAAAATAACCA 59.887 50.000 0.00 0.00 0.00 3.67
2809 3191 1.190643 CCGGCCCACAAAATAACCAT 58.809 50.000 0.00 0.00 0.00 3.55
2844 3226 3.313526 CCGATTAGGTACCGTATATCCGG 59.686 52.174 5.01 5.01 43.91 5.14
2861 3243 4.717629 GCCGGCCCGCAAAAGAAC 62.718 66.667 18.11 0.00 0.00 3.01
2862 3244 2.983592 CCGGCCCGCAAAAGAACT 60.984 61.111 0.00 0.00 0.00 3.01
2863 3245 2.561037 CCGGCCCGCAAAAGAACTT 61.561 57.895 0.00 0.00 0.00 2.66
2867 3249 0.869730 GCCCGCAAAAGAACTTACGA 59.130 50.000 0.00 0.00 0.00 3.43
2869 3251 1.868498 CCCGCAAAAGAACTTACGACA 59.132 47.619 0.00 0.00 0.00 4.35
2875 3257 4.554134 GCAAAAGAACTTACGACAACCTCC 60.554 45.833 0.00 0.00 0.00 4.30
2908 3290 7.712264 TTTATGCACATTGAACCTTTTTCAG 57.288 32.000 0.00 0.00 0.00 3.02
2922 3304 9.541143 GAACCTTTTTCAGATACAATTTTGGAA 57.459 29.630 0.00 0.00 0.00 3.53
3061 3446 7.112009 CGTGAACAATTCTTTAACTGTCATGTG 59.888 37.037 0.00 0.00 0.00 3.21
3108 3493 6.773976 AAATTTGTCCCGTGATCATATGTT 57.226 33.333 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 3.777910 GGGGAGCGAGGGCGTTTA 61.778 66.667 0.00 0.00 46.35 2.01
184 188 1.226323 CTTAGACTCCGTCGCACCG 60.226 63.158 0.00 0.00 37.67 4.94
193 197 6.153000 TGAGTATCTGTCCAAACTTAGACTCC 59.847 42.308 0.00 0.00 32.65 3.85
197 201 7.718334 TCATGAGTATCTGTCCAAACTTAGA 57.282 36.000 0.00 0.00 34.92 2.10
198 202 7.042187 GCATCATGAGTATCTGTCCAAACTTAG 60.042 40.741 0.09 0.00 34.92 2.18
229 233 4.222847 GCGGTGGGACGAGGGATC 62.223 72.222 0.00 0.00 35.47 3.36
255 259 2.408050 CAACGAAGTCACAGAAGGAGG 58.592 52.381 0.00 0.00 45.00 4.30
327 331 2.363306 AGCAGTCCAAAATCACACCA 57.637 45.000 0.00 0.00 0.00 4.17
328 332 3.181476 ACAAAGCAGTCCAAAATCACACC 60.181 43.478 0.00 0.00 0.00 4.16
340 344 0.595095 CTTGCAGGGACAAAGCAGTC 59.405 55.000 0.00 0.00 39.72 3.51
342 346 0.313043 CACTTGCAGGGACAAAGCAG 59.687 55.000 0.00 0.00 39.72 4.24
349 353 2.191128 ATCTGAACACTTGCAGGGAC 57.809 50.000 0.00 0.00 33.05 4.46
351 355 1.542915 CCAATCTGAACACTTGCAGGG 59.457 52.381 0.00 0.00 33.05 4.45
366 375 2.614057 CCACGATAGGTCTTTGCCAATC 59.386 50.000 0.00 0.00 43.77 2.67
378 387 0.105862 TAGTCCCACCCCACGATAGG 60.106 60.000 0.00 0.00 43.77 2.57
391 400 8.738645 ATAATGATTGTGTTTTCTCTAGTCCC 57.261 34.615 0.00 0.00 0.00 4.46
401 410 7.945033 ACTGCGAAAATAATGATTGTGTTTT 57.055 28.000 0.00 0.00 0.00 2.43
405 414 6.324819 AGGAACTGCGAAAATAATGATTGTG 58.675 36.000 0.00 0.00 37.18 3.33
406 415 6.515272 AGGAACTGCGAAAATAATGATTGT 57.485 33.333 0.00 0.00 37.18 2.71
423 432 1.238439 CAAATCACCGTGCAGGAACT 58.762 50.000 8.24 0.00 45.00 3.01
424 433 0.240945 CCAAATCACCGTGCAGGAAC 59.759 55.000 8.24 0.00 45.00 3.62
432 441 0.250124 TCGCAGAACCAAATCACCGT 60.250 50.000 0.00 0.00 0.00 4.83
458 467 6.640907 AGCCTAATCAAAACAAAACGTTGATC 59.359 34.615 0.00 0.00 40.28 2.92
464 473 4.444056 CCACAGCCTAATCAAAACAAAACG 59.556 41.667 0.00 0.00 0.00 3.60
483 492 1.068895 CAACTCAAGCAAATGGCCACA 59.931 47.619 8.16 0.00 46.50 4.17
484 493 1.340889 TCAACTCAAGCAAATGGCCAC 59.659 47.619 8.16 0.00 46.50 5.01
485 494 1.702182 TCAACTCAAGCAAATGGCCA 58.298 45.000 8.56 8.56 46.50 5.36
486 495 2.613691 CATCAACTCAAGCAAATGGCC 58.386 47.619 0.00 0.00 46.50 5.36
487 496 1.997606 GCATCAACTCAAGCAAATGGC 59.002 47.619 0.00 0.00 45.30 4.40
488 497 3.306917 TGCATCAACTCAAGCAAATGG 57.693 42.857 0.00 0.00 33.48 3.16
489 498 5.856126 AAATGCATCAACTCAAGCAAATG 57.144 34.783 0.00 0.00 40.76 2.32
490 499 6.147164 CAGAAAATGCATCAACTCAAGCAAAT 59.853 34.615 0.00 0.00 40.76 2.32
493 502 4.038282 ACAGAAAATGCATCAACTCAAGCA 59.962 37.500 0.00 0.00 41.73 3.91
494 503 4.553323 ACAGAAAATGCATCAACTCAAGC 58.447 39.130 0.00 0.00 0.00 4.01
665 688 5.123820 TGGCAAAGTCAACATTCAGCTATAC 59.876 40.000 0.00 0.00 0.00 1.47
666 689 5.252547 TGGCAAAGTCAACATTCAGCTATA 58.747 37.500 0.00 0.00 0.00 1.31
667 690 4.081406 TGGCAAAGTCAACATTCAGCTAT 58.919 39.130 0.00 0.00 0.00 2.97
668 691 3.485394 TGGCAAAGTCAACATTCAGCTA 58.515 40.909 0.00 0.00 0.00 3.32
781 853 3.053395 AGGGATATTTGCACATGACAGGT 60.053 43.478 0.00 0.00 0.00 4.00
782 854 3.559069 AGGGATATTTGCACATGACAGG 58.441 45.455 0.00 0.00 0.00 4.00
924 1161 7.833786 ACCGAGTCAATAGAATACACAAGTAA 58.166 34.615 0.00 0.00 33.13 2.24
933 1170 7.972832 AAACAACAACCGAGTCAATAGAATA 57.027 32.000 0.00 0.00 0.00 1.75
934 1171 6.877611 AAACAACAACCGAGTCAATAGAAT 57.122 33.333 0.00 0.00 0.00 2.40
935 1172 6.316640 TGAAAACAACAACCGAGTCAATAGAA 59.683 34.615 0.00 0.00 0.00 2.10
936 1173 5.818336 TGAAAACAACAACCGAGTCAATAGA 59.182 36.000 0.00 0.00 0.00 1.98
937 1174 6.018262 TCTGAAAACAACAACCGAGTCAATAG 60.018 38.462 0.00 0.00 0.00 1.73
947 1184 4.610945 CTGTCCATCTGAAAACAACAACC 58.389 43.478 0.00 0.00 0.00 3.77
973 1210 2.036958 TCATGGGCGGTAATGAAGTG 57.963 50.000 0.00 0.00 29.97 3.16
981 1221 0.250945 TTGTTGCTTCATGGGCGGTA 60.251 50.000 0.00 0.00 0.00 4.02
995 1242 2.662866 AGGATGAGATGCCCATTGTTG 58.337 47.619 0.00 0.00 0.00 3.33
1004 1251 0.533755 CCCGGACAAGGATGAGATGC 60.534 60.000 0.73 0.00 0.00 3.91
1015 1262 0.958091 CACATTTTGCTCCCGGACAA 59.042 50.000 0.73 0.90 0.00 3.18
1016 1263 2.639970 CACATTTTGCTCCCGGACA 58.360 52.632 0.73 0.00 0.00 4.02
1070 1326 0.110644 CTTTGCGTCTTTCGAGGTGC 60.111 55.000 0.00 0.00 42.86 5.01
1140 1396 2.291465 CACCTCAACCGCCATGAATATG 59.709 50.000 0.00 0.00 0.00 1.78
1524 1798 4.053983 CCGAGTTACCATGATCATGTGAG 58.946 47.826 29.23 18.75 37.11 3.51
1638 1930 2.054021 TGTCCTGTGGTTGAATGAGGA 58.946 47.619 0.00 0.00 0.00 3.71
1653 1945 1.340405 GCATCATCCTGGTGTTGTCCT 60.340 52.381 0.00 0.00 29.39 3.85
1723 2036 2.202703 GATGTTACGGCGGCGAGT 60.203 61.111 38.93 19.54 0.00 4.18
1899 2212 1.156736 CGAGCAAGTTCCGAACCATT 58.843 50.000 7.68 0.00 0.00 3.16
2017 2330 1.144057 CCACCGTGATAGCCCAGAC 59.856 63.158 0.00 0.00 0.00 3.51
2097 2410 2.465860 TGTACCCAATGACCTTGTCG 57.534 50.000 0.00 0.00 34.95 4.35
2151 2464 0.658829 CTTACTCGCGCTCGATCTGG 60.659 60.000 5.56 0.00 44.56 3.86
2163 2476 4.394920 ACATAAACACAATGGCCTTACTCG 59.605 41.667 3.32 0.00 0.00 4.18
2180 2493 0.521291 GCAAGCTCGGCACACATAAA 59.479 50.000 5.52 0.00 0.00 1.40
2181 2494 0.321564 AGCAAGCTCGGCACACATAA 60.322 50.000 12.27 0.00 0.00 1.90
2182 2495 0.321564 AAGCAAGCTCGGCACACATA 60.322 50.000 12.27 0.00 0.00 2.29
2183 2496 1.580845 GAAGCAAGCTCGGCACACAT 61.581 55.000 12.27 0.00 0.00 3.21
2184 2497 2.203195 AAGCAAGCTCGGCACACA 60.203 55.556 12.27 0.00 0.00 3.72
2185 2498 2.558313 GAAGCAAGCTCGGCACAC 59.442 61.111 12.27 0.76 0.00 3.82
2186 2499 1.826340 TAGGAAGCAAGCTCGGCACA 61.826 55.000 12.27 0.00 0.00 4.57
2187 2500 1.079127 TAGGAAGCAAGCTCGGCAC 60.079 57.895 12.27 6.17 0.00 5.01
2188 2501 1.079127 GTAGGAAGCAAGCTCGGCA 60.079 57.895 12.27 0.00 0.00 5.69
2189 2502 1.079127 TGTAGGAAGCAAGCTCGGC 60.079 57.895 2.25 2.25 0.00 5.54
2190 2503 0.247736 AGTGTAGGAAGCAAGCTCGG 59.752 55.000 0.00 0.00 0.00 4.63
2191 2504 1.728971 CAAGTGTAGGAAGCAAGCTCG 59.271 52.381 0.00 0.00 0.00 5.03
2192 2505 3.045601 TCAAGTGTAGGAAGCAAGCTC 57.954 47.619 0.00 0.00 0.00 4.09
2193 2506 3.492102 TTCAAGTGTAGGAAGCAAGCT 57.508 42.857 0.00 0.00 0.00 3.74
2194 2507 6.127897 ACAATATTCAAGTGTAGGAAGCAAGC 60.128 38.462 0.00 0.00 0.00 4.01
2195 2508 7.094634 ACACAATATTCAAGTGTAGGAAGCAAG 60.095 37.037 7.97 0.00 44.02 4.01
2196 2509 6.714810 ACACAATATTCAAGTGTAGGAAGCAA 59.285 34.615 7.97 0.00 44.02 3.91
2197 2510 6.149308 CACACAATATTCAAGTGTAGGAAGCA 59.851 38.462 9.10 0.00 44.02 3.91
2198 2511 6.371548 TCACACAATATTCAAGTGTAGGAAGC 59.628 38.462 9.10 0.00 44.02 3.86
2227 2566 0.729116 GATGACTGCCAATCCACACG 59.271 55.000 0.00 0.00 0.00 4.49
2252 2591 0.388907 CAGCCGTGCAATTTTCAGGG 60.389 55.000 10.36 10.36 41.14 4.45
2257 2596 0.968405 ACCATCAGCCGTGCAATTTT 59.032 45.000 0.00 0.00 0.00 1.82
2258 2597 0.968405 AACCATCAGCCGTGCAATTT 59.032 45.000 0.00 0.00 0.00 1.82
2261 2600 1.228094 TGAACCATCAGCCGTGCAA 60.228 52.632 0.00 0.00 0.00 4.08
2272 2611 3.518303 GGGACTACTACAAGGTGAACCAT 59.482 47.826 1.62 0.00 38.89 3.55
2279 2618 2.305052 GGCAAAGGGACTACTACAAGGT 59.695 50.000 0.00 0.00 38.49 3.50
2285 2625 4.717279 AACTTTGGCAAAGGGACTACTA 57.283 40.909 35.57 3.00 42.82 1.82
2294 2634 3.541996 ACCCTGAAAACTTTGGCAAAG 57.458 42.857 32.52 32.52 44.10 2.77
2311 2651 4.338400 GGAAACCTTGCATATTCAGTACCC 59.662 45.833 0.00 0.00 0.00 3.69
2314 2654 5.593909 CCATGGAAACCTTGCATATTCAGTA 59.406 40.000 5.56 0.00 39.89 2.74
2315 2655 4.403432 CCATGGAAACCTTGCATATTCAGT 59.597 41.667 5.56 0.00 39.89 3.41
2322 2662 4.041938 ACAAAATCCATGGAAACCTTGCAT 59.958 37.500 20.67 0.00 42.84 3.96
2333 2673 5.642919 CACCAAAACCATACAAAATCCATGG 59.357 40.000 4.97 4.97 44.04 3.66
2423 2805 1.159713 TGTCCAGTGCGAGCAGTTTG 61.160 55.000 2.19 0.47 0.00 2.93
2424 2806 0.463654 TTGTCCAGTGCGAGCAGTTT 60.464 50.000 2.19 0.00 0.00 2.66
2425 2807 0.882042 CTTGTCCAGTGCGAGCAGTT 60.882 55.000 2.19 0.00 0.00 3.16
2426 2808 1.301244 CTTGTCCAGTGCGAGCAGT 60.301 57.895 0.00 0.00 0.00 4.40
2427 2809 2.675056 GCTTGTCCAGTGCGAGCAG 61.675 63.158 0.00 0.00 41.68 4.24
2428 2810 2.665008 AAGCTTGTCCAGTGCGAGCA 62.665 55.000 0.00 0.00 43.83 4.26
2485 2867 1.347707 TCGAATTCCCAGAGTGCTTGT 59.652 47.619 0.00 0.00 0.00 3.16
2522 2904 1.524165 CCAGCAGGATCAGAGCAGC 60.524 63.158 0.00 0.00 36.89 5.25
2569 2951 6.648879 TTGTCATTAACAAAAGGAGAAGGG 57.351 37.500 0.00 0.00 44.83 3.95
2585 2967 2.223876 CCTTGTTGCTGCAGTTGTCATT 60.224 45.455 16.64 0.00 0.00 2.57
2587 2969 0.740149 CCTTGTTGCTGCAGTTGTCA 59.260 50.000 16.64 7.21 0.00 3.58
2614 2996 2.100631 CCAAACGCGCCGAATCTCT 61.101 57.895 5.73 0.00 0.00 3.10
2621 3003 2.700334 CTATGCATCCAAACGCGCCG 62.700 60.000 5.73 0.00 0.00 6.46
2636 3018 6.164876 CCAAGAGAGGTATCTGAATGCTATG 58.835 44.000 0.00 0.00 35.30 2.23
2654 3036 1.468985 TCGAGCTCTTCTCCCAAGAG 58.531 55.000 12.85 6.95 44.95 2.85
2655 3037 1.753649 CATCGAGCTCTTCTCCCAAGA 59.246 52.381 12.85 0.00 38.62 3.02
2657 3039 1.852633 TCATCGAGCTCTTCTCCCAA 58.147 50.000 12.85 0.00 38.62 4.12
2661 3043 1.959985 TGGGATCATCGAGCTCTTCTC 59.040 52.381 12.85 1.65 38.47 2.87
2682 3064 1.918262 AGCATGTGAGAATGGAAGGGA 59.082 47.619 0.00 0.00 0.00 4.20
2701 3083 4.190772 GGAGCCTCTTCATCTTCTTCAAG 58.809 47.826 0.00 0.00 0.00 3.02
2777 3159 1.826921 GGCCGGACGGACATAGAGA 60.827 63.158 15.99 0.00 44.50 3.10
2784 3166 3.981609 TATTTTGTGGGCCGGACGGAC 62.982 57.143 15.99 12.34 44.33 4.79
2789 3171 0.112606 TGGTTATTTTGTGGGCCGGA 59.887 50.000 5.05 0.00 0.00 5.14
2790 3172 1.136110 GATGGTTATTTTGTGGGCCGG 59.864 52.381 0.00 0.00 0.00 6.13
2792 3174 2.096248 TCGATGGTTATTTTGTGGGCC 58.904 47.619 0.00 0.00 0.00 5.80
2844 3226 4.717629 GTTCTTTTGCGGGCCGGC 62.718 66.667 29.48 27.27 0.00 6.13
2858 3240 4.995487 AGATTTGGAGGTTGTCGTAAGTTC 59.005 41.667 0.00 0.00 39.48 3.01
2861 3243 5.941948 AAAGATTTGGAGGTTGTCGTAAG 57.058 39.130 0.00 0.00 0.00 2.34
2862 3244 6.702716 AAAAAGATTTGGAGGTTGTCGTAA 57.297 33.333 0.00 0.00 0.00 3.18
2966 3351 9.273016 TGTAAAAAGGTTCATGTTGTTTGAAAA 57.727 25.926 0.00 0.00 35.03 2.29
2967 3352 8.833231 TGTAAAAAGGTTCATGTTGTTTGAAA 57.167 26.923 0.00 0.00 35.03 2.69
2968 3353 9.442047 AATGTAAAAAGGTTCATGTTGTTTGAA 57.558 25.926 0.00 0.00 0.00 2.69
2969 3354 8.877779 CAATGTAAAAAGGTTCATGTTGTTTGA 58.122 29.630 0.00 0.00 0.00 2.69
2970 3355 8.663911 ACAATGTAAAAAGGTTCATGTTGTTTG 58.336 29.630 0.00 0.00 0.00 2.93
2971 3356 8.785329 ACAATGTAAAAAGGTTCATGTTGTTT 57.215 26.923 0.00 0.00 0.00 2.83
3012 3397 8.376203 CACGTATTTCAAAAACATGTTCAAACA 58.624 29.630 12.39 0.00 44.06 2.83
3016 3401 7.755373 TGTTCACGTATTTCAAAAACATGTTCA 59.245 29.630 12.39 0.00 0.00 3.18
3017 3402 8.109843 TGTTCACGTATTTCAAAAACATGTTC 57.890 30.769 12.39 0.00 0.00 3.18
3034 3419 6.671614 TGACAGTTAAAGAATTGTTCACGT 57.328 33.333 0.00 0.00 35.79 4.49
3035 3420 7.112009 CACATGACAGTTAAAGAATTGTTCACG 59.888 37.037 0.00 0.00 35.79 4.35
3143 3528 0.179056 ATCGGTCACAAATAGCCCCG 60.179 55.000 0.00 0.00 36.83 5.73


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

AutoCloner maintained by Alex Coulton.