Multiple sequence alignment - TraesCS5B01G097600

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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 TraesCS5B01G097600 chr5B 100.000 3298 0 0 1 3298 128856822 128853525 0.000000e+00 6091
1 TraesCS5B01G097600 chr5B 79.104 536 95 12 20 548 406886408 406885883 1.460000e-93 353
2 TraesCS5B01G097600 chr5B 77.547 530 102 14 25 545 466649774 466650295 1.490000e-78 303
3 TraesCS5B01G097600 chr5B 84.118 170 25 2 1038 1206 128853856 128853688 2.630000e-36 163
4 TraesCS5B01G097600 chr5B 84.118 170 25 2 2967 3135 128855785 128855617 2.630000e-36 163
5 TraesCS5B01G097600 chr5D 90.414 2848 156 40 514 3298 118007396 118010189 0.000000e+00 3639
6 TraesCS5B01G097600 chr5D 80.112 538 103 3 11 545 108092456 108091920 6.630000e-107 398
7 TraesCS5B01G097600 chr5D 82.990 388 64 2 11 396 509573045 509573432 1.880000e-92 350
8 TraesCS5B01G097600 chr5D 82.687 387 65 2 12 396 457402052 457401666 3.150000e-90 342
9 TraesCS5B01G097600 chr5D 84.118 170 25 2 2967 3135 118007904 118008072 2.630000e-36 163
10 TraesCS5B01G097600 chr5D 81.765 170 29 2 1038 1206 118009858 118010026 1.230000e-29 141
11 TraesCS5B01G097600 chr5A 87.534 1468 90 31 623 2051 127519373 127520786 0.000000e+00 1611
12 TraesCS5B01G097600 chr5A 88.870 1195 72 23 2137 3298 127532199 127533365 0.000000e+00 1413
13 TraesCS5B01G097600 chr5A 84.118 170 25 2 1038 1206 127533033 127533201 2.630000e-36 163
14 TraesCS5B01G097600 chr5A 83.429 175 26 3 2964 3135 127519779 127519953 3.410000e-35 159
15 TraesCS5B01G097600 chr6D 81.197 468 77 6 20 485 363322005 363321547 1.870000e-97 366
16 TraesCS5B01G097600 chr6D 82.169 415 69 5 12 423 56920494 56920082 5.240000e-93 351
17 TraesCS5B01G097600 chr7B 80.000 485 86 11 11 490 46810505 46810983 6.770000e-92 348
18 TraesCS5B01G097600 chr7D 77.944 535 101 11 12 543 606831682 606831162 5.310000e-83 318
19 TraesCS5B01G097600 chr7D 75.817 306 68 6 247 549 530334554 530334856 2.050000e-32 150
20 TraesCS5B01G097600 chrUn 74.009 454 104 12 105 545 79966253 79965801 4.380000e-39 172


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 TraesCS5B01G097600 chr5B 128853525 128856822 3297 True 2139.000000 6091 89.412000 1 3298 3 chr5B.!!$R2 3297
1 TraesCS5B01G097600 chr5B 406885883 406886408 525 True 353.000000 353 79.104000 20 548 1 chr5B.!!$R1 528
2 TraesCS5B01G097600 chr5B 466649774 466650295 521 False 303.000000 303 77.547000 25 545 1 chr5B.!!$F1 520
3 TraesCS5B01G097600 chr5D 118007396 118010189 2793 False 1314.333333 3639 85.432333 514 3298 3 chr5D.!!$F2 2784
4 TraesCS5B01G097600 chr5D 108091920 108092456 536 True 398.000000 398 80.112000 11 545 1 chr5D.!!$R1 534
5 TraesCS5B01G097600 chr5A 127519373 127520786 1413 False 885.000000 1611 85.481500 623 3135 2 chr5A.!!$F1 2512
6 TraesCS5B01G097600 chr5A 127532199 127533365 1166 False 788.000000 1413 86.494000 1038 3298 2 chr5A.!!$F2 2260
7 TraesCS5B01G097600 chr7D 606831162 606831682 520 True 318.000000 318 77.944000 12 543 1 chr7D.!!$R1 531

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
254 261 0.325933 CCACCACAGATGAGCTTGGA 59.674 55.0 6.87 0.0 32.50 3.53 F
426 436 0.970937 GAGGGATGTCGGTCAGTCCA 60.971 60.0 0.00 0.0 35.57 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1242 1277 0.168128 CGAACGCAGTCCCCAATTTC 59.832 55.0 0.0 0.0 45.0 2.17 R
2302 2381 0.176680 ACTAATCACTGAGCTGGGCG 59.823 55.0 0.0 0.0 0.0 6.13 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
45 46 1.608055 CCAGATCCATGCGCCATTTA 58.392 50.000 4.18 0.00 0.00 1.40
199 206 1.971357 GGTCTGAAGGTGAAGGACTCA 59.029 52.381 0.00 0.00 0.00 3.41
208 215 2.025155 GTGAAGGACTCAGATCCGCTA 58.975 52.381 0.00 0.00 44.22 4.26
209 216 2.625790 GTGAAGGACTCAGATCCGCTAT 59.374 50.000 0.00 0.00 44.22 2.97
221 228 4.662961 CGCTATCCGCCATGCCGA 62.663 66.667 0.00 0.00 34.21 5.54
229 236 2.125512 GCCATGCCGAAGACGTCT 60.126 61.111 13.58 13.58 37.88 4.18
245 252 1.913262 TCTGGACGCCACCACAGAT 60.913 57.895 0.00 0.00 35.24 2.90
254 261 0.325933 CCACCACAGATGAGCTTGGA 59.674 55.000 6.87 0.00 32.50 3.53
263 270 1.487976 GATGAGCTTGGATGGTGGAGA 59.512 52.381 0.00 0.00 0.00 3.71
264 271 1.361204 TGAGCTTGGATGGTGGAGAA 58.639 50.000 0.00 0.00 0.00 2.87
267 274 1.988107 AGCTTGGATGGTGGAGAAGAA 59.012 47.619 0.00 0.00 0.00 2.52
289 296 3.815809 TGAAGTGAAGTGGTTAGGGTTG 58.184 45.455 0.00 0.00 0.00 3.77
291 298 2.132686 AGTGAAGTGGTTAGGGTTGGT 58.867 47.619 0.00 0.00 0.00 3.67
297 305 1.073548 GGTTAGGGTTGGTTCGGCA 59.926 57.895 0.00 0.00 0.00 5.69
350 358 4.660938 GCCAGCTTGGACCGGGTT 62.661 66.667 6.32 0.00 40.96 4.11
396 404 4.441495 CGCTCCATATCCGCCTCATATTTA 60.441 45.833 0.00 0.00 0.00 1.40
426 436 0.970937 GAGGGATGTCGGTCAGTCCA 60.971 60.000 0.00 0.00 35.57 4.02
434 444 1.267806 GTCGGTCAGTCCAGACGTTTA 59.732 52.381 0.00 0.00 39.42 2.01
438 448 3.367087 CGGTCAGTCCAGACGTTTAAGAT 60.367 47.826 0.00 0.00 39.42 2.40
455 465 3.659089 ATCCGTTTGAGGCGTCCGG 62.659 63.158 14.10 14.10 39.98 5.14
456 466 4.675029 CCGTTTGAGGCGTCCGGT 62.675 66.667 12.60 0.00 34.10 5.28
507 518 3.461773 GCGGCTAGCCAGGACTGA 61.462 66.667 32.47 0.00 40.81 3.41
510 521 1.040646 CGGCTAGCCAGGACTGATTA 58.959 55.000 32.47 0.00 35.37 1.75
529 540 3.909651 GGAGGGTTTGGGGTGGCA 61.910 66.667 0.00 0.00 0.00 4.92
556 567 7.393234 GGATGTAGATGCTCTGAGTCTACTTAT 59.607 40.741 24.28 16.08 42.89 1.73
579 590 3.401033 ACGACAAGTGTGATCCATTGA 57.599 42.857 0.00 0.00 0.00 2.57
580 591 3.329386 ACGACAAGTGTGATCCATTGAG 58.671 45.455 0.00 0.00 0.00 3.02
581 592 2.674852 CGACAAGTGTGATCCATTGAGG 59.325 50.000 0.00 0.00 39.47 3.86
582 593 3.012518 GACAAGTGTGATCCATTGAGGG 58.987 50.000 0.00 0.00 38.24 4.30
583 594 2.376518 ACAAGTGTGATCCATTGAGGGT 59.623 45.455 0.00 0.00 38.24 4.34
584 595 3.181429 ACAAGTGTGATCCATTGAGGGTT 60.181 43.478 0.00 0.00 38.24 4.11
585 596 3.077484 AGTGTGATCCATTGAGGGTTG 57.923 47.619 0.00 0.00 38.24 3.77
661 672 3.428452 CGACTAAGTCCAAGTTGCCGATA 60.428 47.826 0.00 0.00 0.00 2.92
672 683 4.207891 AGTTGCCGATAAGTGATGAGTT 57.792 40.909 0.00 0.00 0.00 3.01
689 700 1.956477 AGTTAGCAACCACAGCTTTGG 59.044 47.619 17.55 17.55 43.25 3.28
776 792 2.358737 CCTCAACTGACGTGCCCC 60.359 66.667 0.00 0.00 0.00 5.80
778 794 3.220999 CTCAACTGACGTGCCCCGA 62.221 63.158 0.00 0.00 40.70 5.14
805 821 4.261238 CGAATCAGATCACGTAAGGTAGCT 60.261 45.833 0.00 0.00 46.39 3.32
806 822 4.839668 ATCAGATCACGTAAGGTAGCTC 57.160 45.455 0.00 0.00 46.39 4.09
913 929 4.752879 TACACGCCGCTGCCCTTC 62.753 66.667 0.00 0.00 0.00 3.46
918 934 3.521796 GCCGCTGCCCTTCCATTC 61.522 66.667 0.00 0.00 0.00 2.67
919 935 2.830370 CCGCTGCCCTTCCATTCC 60.830 66.667 0.00 0.00 0.00 3.01
920 936 2.045045 CGCTGCCCTTCCATTCCA 60.045 61.111 0.00 0.00 0.00 3.53
1014 1035 3.140814 GCCATGGCGGAGGAAACC 61.141 66.667 23.48 0.00 36.56 3.27
1167 1197 4.379143 CGCCTCGTCGTCGTCACA 62.379 66.667 1.33 0.00 38.33 3.58
1242 1277 2.845752 TTCCCTCCATCGCGTTTCCG 62.846 60.000 5.77 0.00 37.07 4.30
1243 1278 2.183300 CCTCCATCGCGTTTCCGA 59.817 61.111 5.77 0.00 41.98 4.55
1253 1288 0.109458 GCGTTTCCGAAATTGGGGAC 60.109 55.000 0.00 0.00 35.63 4.46
1254 1289 1.530323 CGTTTCCGAAATTGGGGACT 58.470 50.000 0.00 0.00 35.63 3.85
1258 1293 1.674322 CCGAAATTGGGGACTGCGT 60.674 57.895 0.00 0.00 0.00 5.24
1267 1302 2.582498 GGACTGCGTTCGATCGGG 60.582 66.667 16.41 6.33 0.00 5.14
1268 1303 3.255379 GACTGCGTTCGATCGGGC 61.255 66.667 16.41 16.33 0.00 6.13
1296 1331 5.835257 ACGGAGATTTATCGGTCGATTTTA 58.165 37.500 11.20 0.00 36.17 1.52
1300 1335 7.592533 CGGAGATTTATCGGTCGATTTTAACTA 59.407 37.037 11.20 0.00 36.17 2.24
1301 1336 8.697960 GGAGATTTATCGGTCGATTTTAACTAC 58.302 37.037 11.20 3.33 36.17 2.73
1315 1351 1.843368 AACTACTACTAGGTGCCGCA 58.157 50.000 0.00 0.00 0.00 5.69
1318 1354 1.604755 CTACTACTAGGTGCCGCAGAG 59.395 57.143 0.00 0.00 0.00 3.35
1508 1558 1.371389 GACGCGTATGATCCCGTCC 60.371 63.158 13.97 0.00 42.91 4.79
1510 1560 1.371758 CGCGTATGATCCCGTCCAG 60.372 63.158 0.00 0.00 0.00 3.86
1577 1627 7.534723 ACCACGTCTATATTATGCCTAAAGA 57.465 36.000 0.00 0.00 0.00 2.52
1608 1658 9.991906 TGTCTAACAATTATTATACCTACCAGC 57.008 33.333 0.00 0.00 0.00 4.85
1609 1659 9.991906 GTCTAACAATTATTATACCTACCAGCA 57.008 33.333 0.00 0.00 0.00 4.41
1674 1734 4.042398 CGAATCACACTTACCCTACATCG 58.958 47.826 0.00 0.00 0.00 3.84
1684 1748 0.676736 CCCTACATCGAGGAAGCTCC 59.323 60.000 3.06 0.00 39.15 4.70
1723 1787 1.102978 AATTTCCCCGCGGATGAAAG 58.897 50.000 31.85 16.53 38.24 2.62
1724 1788 0.254747 ATTTCCCCGCGGATGAAAGA 59.745 50.000 31.85 19.84 38.24 2.52
1725 1789 0.037017 TTTCCCCGCGGATGAAAGAA 59.963 50.000 30.73 15.76 38.24 2.52
1726 1790 0.037017 TTCCCCGCGGATGAAAGAAA 59.963 50.000 30.73 4.21 38.24 2.52
1737 1801 5.408604 GCGGATGAAAGAAAAGTCTAGTTGA 59.591 40.000 0.00 0.00 32.16 3.18
1739 1803 7.519970 GCGGATGAAAGAAAAGTCTAGTTGAAA 60.520 37.037 0.00 0.00 32.16 2.69
1782 1846 5.825507 ACTTGAGAATTGCTTGTCAGTTTC 58.174 37.500 0.00 0.00 36.18 2.78
1792 1869 2.048222 TCAGTTTCAGCGAGGGCG 60.048 61.111 0.00 0.00 46.35 6.13
2000 2078 0.764369 TGTGCTCTGTTCTCCCCTGT 60.764 55.000 0.00 0.00 0.00 4.00
2007 2085 0.823356 TGTTCTCCCCTGTTTGCAGC 60.823 55.000 0.00 0.00 41.26 5.25
2014 2092 2.019984 CCCCTGTTTGCAGCTTAGATC 58.980 52.381 0.00 0.00 41.26 2.75
2015 2093 1.667724 CCCTGTTTGCAGCTTAGATCG 59.332 52.381 0.00 0.00 41.26 3.69
2027 2105 2.487934 CTTAGATCGATGGCACCTTGG 58.512 52.381 0.54 0.00 0.00 3.61
2035 2113 4.492604 GGCACCTTGGCAGTGTTA 57.507 55.556 8.44 0.00 43.14 2.41
2036 2114 1.956802 GGCACCTTGGCAGTGTTAC 59.043 57.895 8.44 0.00 43.14 2.50
2037 2115 1.574428 GCACCTTGGCAGTGTTACG 59.426 57.895 8.44 0.00 37.56 3.18
2070 2149 4.223032 CACTCTCTCTAAGCCTAAAACCCA 59.777 45.833 0.00 0.00 0.00 4.51
2071 2150 4.844655 ACTCTCTCTAAGCCTAAAACCCAA 59.155 41.667 0.00 0.00 0.00 4.12
2101 2180 2.509166 TCCATGGACTAGTGTCGTCT 57.491 50.000 11.44 0.00 43.79 4.18
2120 2199 6.362820 GTCGTCTTCTTAGTTAAACACCTCTG 59.637 42.308 0.00 0.00 0.00 3.35
2122 2201 5.408909 GTCTTCTTAGTTAAACACCTCTGGC 59.591 44.000 0.00 0.00 0.00 4.85
2200 2279 5.765182 CCTGTGTTATCAACTTTCCTGAACT 59.235 40.000 0.00 0.00 0.00 3.01
2202 2281 7.259290 TGTGTTATCAACTTTCCTGAACTTC 57.741 36.000 0.00 0.00 0.00 3.01
2205 2284 2.218603 TCAACTTTCCTGAACTTCGCC 58.781 47.619 0.00 0.00 0.00 5.54
2310 2389 3.946201 ACTGAGCAACGCCCAGCT 61.946 61.111 0.00 0.00 45.25 4.24
2319 2416 0.613260 AACGCCCAGCTCAGTGATTA 59.387 50.000 0.00 0.00 0.00 1.75
2339 2436 6.649141 TGATTAGTATTTGAGCTTTCGTGTGT 59.351 34.615 0.00 0.00 0.00 3.72
2340 2437 7.815549 TGATTAGTATTTGAGCTTTCGTGTGTA 59.184 33.333 0.00 0.00 0.00 2.90
2341 2438 8.718102 ATTAGTATTTGAGCTTTCGTGTGTAT 57.282 30.769 0.00 0.00 0.00 2.29
2342 2439 9.811995 ATTAGTATTTGAGCTTTCGTGTGTATA 57.188 29.630 0.00 0.00 0.00 1.47
2349 2446 3.623060 AGCTTTCGTGTGTATAGCCAATG 59.377 43.478 0.00 0.00 32.36 2.82
2357 2454 3.377798 TGTGTATAGCCAATGTGTGCATG 59.622 43.478 0.00 0.00 35.15 4.06
2378 2475 4.657055 TGTTTGTGAATAAATGGATCGCG 58.343 39.130 0.00 0.00 0.00 5.87
2386 2483 1.299541 AAATGGATCGCGGATGTCAC 58.700 50.000 6.13 0.00 0.00 3.67
2388 2485 0.177836 ATGGATCGCGGATGTCACAA 59.822 50.000 6.13 0.00 0.00 3.33
2407 2512 5.466728 TCACAATTCACAACTTCAGAGTAGC 59.533 40.000 0.00 0.00 34.21 3.58
2422 2527 1.071605 GTAGCGAACTCCTGCAAGTG 58.928 55.000 0.00 0.00 0.00 3.16
2476 2591 7.496920 TGATTGAGATGGTGAATAACTGATGAC 59.503 37.037 0.00 0.00 0.00 3.06
2702 2824 2.725127 TAGCCACAGGACACGGAGGT 62.725 60.000 0.00 0.00 0.00 3.85
2817 2939 6.950041 TCCCTTCTTTTCTTGTTCATCATCAT 59.050 34.615 0.00 0.00 0.00 2.45
2818 2940 7.121759 TCCCTTCTTTTCTTGTTCATCATCATC 59.878 37.037 0.00 0.00 0.00 2.92
2819 2941 7.094075 CCCTTCTTTTCTTGTTCATCATCATCA 60.094 37.037 0.00 0.00 0.00 3.07
2834 2956 1.614903 TCATCAAAGCCAGCCAAGTTG 59.385 47.619 0.00 0.00 0.00 3.16
2847 2972 1.906574 CCAAGTTGAGGCCACTAGGTA 59.093 52.381 5.01 0.00 37.19 3.08
2848 2973 2.304761 CCAAGTTGAGGCCACTAGGTAA 59.695 50.000 5.01 0.00 37.19 2.85
2849 2974 3.335579 CAAGTTGAGGCCACTAGGTAAC 58.664 50.000 5.01 0.00 37.19 2.50
2850 2975 1.549170 AGTTGAGGCCACTAGGTAACG 59.451 52.381 5.01 0.00 46.39 3.18
2851 2976 0.899720 TTGAGGCCACTAGGTAACGG 59.100 55.000 5.01 0.00 46.39 4.44
2861 2986 1.822990 CTAGGTAACGGAACTGGCTCA 59.177 52.381 0.00 0.00 46.39 4.26
2865 2990 1.001633 GTAACGGAACTGGCTCAAGGA 59.998 52.381 0.00 0.00 0.00 3.36
2919 3044 1.379309 GGAGAGGGCAGAGACGTCT 60.379 63.158 20.18 20.18 38.60 4.18
2961 3086 1.740025 GAATCAGGAGCAAACGGGAAG 59.260 52.381 0.00 0.00 0.00 3.46
3219 3344 2.037136 CGACAAGGCCAAGGAGCAG 61.037 63.158 5.01 0.00 0.00 4.24
3236 3361 0.027194 CAGTGCTCACATGTATGCGC 59.973 55.000 21.02 21.02 36.34 6.09
3251 3376 2.892334 GCGCCGTGCTTTGTCAGAA 61.892 57.895 0.00 0.00 41.73 3.02
3258 3383 0.534203 TGCTTTGTCAGAACGGGGAC 60.534 55.000 0.00 0.00 34.63 4.46
3279 3405 2.096069 CGCAATCCTTATTGATCGCCAG 60.096 50.000 2.38 0.00 44.50 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.409055 GGCAGCCGTCATTGCATGA 61.409 57.895 0.00 0.00 42.02 3.07
3 4 2.269520 TAGGGCAGCCGTCATTGCAT 62.270 55.000 10.72 0.00 42.02 3.96
5 6 2.124736 TAGGGCAGCCGTCATTGC 60.125 61.111 10.72 0.00 39.56 3.56
6 7 2.182842 GCTAGGGCAGCCGTCATTG 61.183 63.158 10.72 1.16 45.23 2.82
7 8 2.190578 GCTAGGGCAGCCGTCATT 59.809 61.111 10.72 0.00 45.23 2.57
28 29 1.901591 CCTAAATGGCGCATGGATCT 58.098 50.000 10.83 0.00 0.00 2.75
45 46 0.749454 GGAATCCATTGCGTCTGCCT 60.749 55.000 0.00 0.00 41.78 4.75
49 50 1.740380 CGTCAGGAATCCATTGCGTCT 60.740 52.381 0.61 0.00 32.98 4.18
74 75 3.946201 ACGGCAGTGCTCAGGCTT 61.946 61.111 16.11 0.00 39.59 4.35
129 136 0.464735 CGAGGAGGAGATGGTCGTCT 60.465 60.000 0.00 0.00 39.60 4.18
180 187 2.894126 TCTGAGTCCTTCACCTTCAGAC 59.106 50.000 0.00 0.00 39.31 3.51
185 192 1.827969 CGGATCTGAGTCCTTCACCTT 59.172 52.381 0.00 0.00 36.07 3.50
208 215 2.203070 GTCTTCGGCATGGCGGAT 60.203 61.111 36.93 0.00 37.70 4.18
209 216 4.812476 CGTCTTCGGCATGGCGGA 62.812 66.667 36.93 30.37 36.16 5.54
227 234 1.913262 ATCTGTGGTGGCGTCCAGA 60.913 57.895 1.49 0.00 38.23 3.86
229 236 2.171209 CTCATCTGTGGTGGCGTCCA 62.171 60.000 0.00 0.00 34.85 4.02
235 242 0.325933 TCCAAGCTCATCTGTGGTGG 59.674 55.000 0.00 0.00 32.68 4.61
241 248 1.211212 TCCACCATCCAAGCTCATCTG 59.789 52.381 0.00 0.00 0.00 2.90
245 252 1.280133 CTTCTCCACCATCCAAGCTCA 59.720 52.381 0.00 0.00 0.00 4.26
254 261 4.916041 TCACTTCATTCTTCTCCACCAT 57.084 40.909 0.00 0.00 0.00 3.55
263 270 5.163088 ACCCTAACCACTTCACTTCATTCTT 60.163 40.000 0.00 0.00 0.00 2.52
264 271 4.351111 ACCCTAACCACTTCACTTCATTCT 59.649 41.667 0.00 0.00 0.00 2.40
267 274 4.398319 CAACCCTAACCACTTCACTTCAT 58.602 43.478 0.00 0.00 0.00 2.57
297 305 5.707298 CACATATATTTCTCCCCATTCGCTT 59.293 40.000 0.00 0.00 0.00 4.68
339 347 3.225798 ACGTCGAACCCGGTCCAA 61.226 61.111 0.00 0.00 36.24 3.53
376 384 7.016153 AGTTTAAATATGAGGCGGATATGGA 57.984 36.000 0.00 0.00 0.00 3.41
396 404 3.568853 CCGACATCCCTCGTATCTAGTTT 59.431 47.826 0.00 0.00 31.35 2.66
406 414 1.433879 GACTGACCGACATCCCTCG 59.566 63.158 0.00 0.00 0.00 4.63
415 425 1.608055 TAAACGTCTGGACTGACCGA 58.392 50.000 0.00 0.00 42.61 4.69
426 436 4.243270 CCTCAAACGGATCTTAAACGTCT 58.757 43.478 0.00 0.00 40.31 4.18
434 444 0.391263 GGACGCCTCAAACGGATCTT 60.391 55.000 0.00 0.00 34.00 2.40
455 465 4.408694 CGGTCATAAAATTTCGACCCAAC 58.591 43.478 20.39 3.80 44.20 3.77
456 466 3.440872 CCGGTCATAAAATTTCGACCCAA 59.559 43.478 20.39 0.00 44.20 4.12
496 507 2.122768 CCTCCTTAATCAGTCCTGGCT 58.877 52.381 0.00 0.00 0.00 4.75
500 511 3.267031 CCAAACCCTCCTTAATCAGTCCT 59.733 47.826 0.00 0.00 0.00 3.85
505 516 2.042433 CACCCCAAACCCTCCTTAATCA 59.958 50.000 0.00 0.00 0.00 2.57
506 517 2.623239 CCACCCCAAACCCTCCTTAATC 60.623 54.545 0.00 0.00 0.00 1.75
507 518 1.361197 CCACCCCAAACCCTCCTTAAT 59.639 52.381 0.00 0.00 0.00 1.40
510 521 3.160478 GCCACCCCAAACCCTCCTT 62.160 63.158 0.00 0.00 0.00 3.36
556 567 4.219725 TCAATGGATCACACTTGTCGTAGA 59.780 41.667 0.00 0.00 0.00 2.59
604 615 2.620251 TTGCCTCAATGGATCTACGG 57.380 50.000 0.00 0.00 38.35 4.02
661 672 4.067896 CTGTGGTTGCTAACTCATCACTT 58.932 43.478 0.00 0.00 0.00 3.16
672 683 0.467106 TGCCAAAGCTGTGGTTGCTA 60.467 50.000 24.24 3.57 41.12 3.49
689 700 2.214387 GGCTTTGCCTGTCATTATGC 57.786 50.000 0.73 0.00 46.69 3.14
776 792 1.105363 CGTGATCTGATTCGACGTCG 58.895 55.000 31.30 31.30 41.45 5.12
778 794 3.487042 CCTTACGTGATCTGATTCGACGT 60.487 47.826 19.98 19.98 44.79 4.34
873 889 6.831664 ACTCCTCATGAACCTTACCATAAT 57.168 37.500 0.00 0.00 0.00 1.28
878 894 4.677250 CGTGTACTCCTCATGAACCTTACC 60.677 50.000 0.00 0.00 0.00 2.85
909 925 3.640029 CTGGAATGGAATGGAATGGAAGG 59.360 47.826 0.00 0.00 0.00 3.46
911 927 4.280819 GTCTGGAATGGAATGGAATGGAA 58.719 43.478 0.00 0.00 0.00 3.53
912 928 3.373001 GGTCTGGAATGGAATGGAATGGA 60.373 47.826 0.00 0.00 0.00 3.41
913 929 2.961062 GGTCTGGAATGGAATGGAATGG 59.039 50.000 0.00 0.00 0.00 3.16
914 930 2.961062 GGGTCTGGAATGGAATGGAATG 59.039 50.000 0.00 0.00 0.00 2.67
915 931 2.423373 CGGGTCTGGAATGGAATGGAAT 60.423 50.000 0.00 0.00 0.00 3.01
916 932 1.064758 CGGGTCTGGAATGGAATGGAA 60.065 52.381 0.00 0.00 0.00 3.53
917 933 0.546122 CGGGTCTGGAATGGAATGGA 59.454 55.000 0.00 0.00 0.00 3.41
918 934 0.255890 ACGGGTCTGGAATGGAATGG 59.744 55.000 0.00 0.00 0.00 3.16
919 935 1.668419 GACGGGTCTGGAATGGAATG 58.332 55.000 0.00 0.00 0.00 2.67
920 936 0.178068 CGACGGGTCTGGAATGGAAT 59.822 55.000 0.00 0.00 0.00 3.01
1242 1277 0.168128 CGAACGCAGTCCCCAATTTC 59.832 55.000 0.00 0.00 45.00 2.17
1243 1278 0.250553 TCGAACGCAGTCCCCAATTT 60.251 50.000 0.00 0.00 45.00 1.82
1253 1288 2.956964 GAGCCCGATCGAACGCAG 60.957 66.667 18.66 4.35 0.00 5.18
1254 1289 4.847516 CGAGCCCGATCGAACGCA 62.848 66.667 18.66 0.00 45.56 5.24
1258 1293 2.711311 CGTACGAGCCCGATCGAA 59.289 61.111 18.66 0.00 45.56 3.71
1267 1302 2.031333 ACCGATAAATCTCCGTACGAGC 60.031 50.000 18.76 0.00 38.62 5.03
1268 1303 3.663754 CGACCGATAAATCTCCGTACGAG 60.664 52.174 18.76 12.27 40.30 4.18
1296 1331 1.749634 CTGCGGCACCTAGTAGTAGTT 59.250 52.381 0.00 0.00 0.00 2.24
1300 1335 1.038130 CCTCTGCGGCACCTAGTAGT 61.038 60.000 0.00 0.00 0.00 2.73
1301 1336 1.038130 ACCTCTGCGGCACCTAGTAG 61.038 60.000 0.00 0.00 35.61 2.57
1304 1339 2.185350 CACCTCTGCGGCACCTAG 59.815 66.667 0.00 0.00 35.61 3.02
1315 1351 3.165160 AACGAACGGCAGCACCTCT 62.165 57.895 0.00 0.00 35.61 3.69
1318 1354 2.954753 CTCAACGAACGGCAGCACC 61.955 63.158 0.00 0.00 0.00 5.01
1399 1435 6.532988 ACCAGAAGAGTAGTACAGAAATCC 57.467 41.667 2.52 0.00 0.00 3.01
1508 1558 3.250744 TCATACGCGTCCTTCTTTTCTG 58.749 45.455 18.63 0.00 0.00 3.02
1510 1560 4.113354 AGATCATACGCGTCCTTCTTTTC 58.887 43.478 18.63 3.40 0.00 2.29
1627 1677 8.411683 CGTCTTACAAACTCCTGTATATTAGGT 58.588 37.037 6.05 0.00 36.67 3.08
1628 1678 8.627403 TCGTCTTACAAACTCCTGTATATTAGG 58.373 37.037 0.69 0.69 36.63 2.69
1631 1681 9.530633 GATTCGTCTTACAAACTCCTGTATATT 57.469 33.333 0.00 0.00 31.96 1.28
1637 1687 4.988540 TGTGATTCGTCTTACAAACTCCTG 59.011 41.667 0.00 0.00 0.00 3.86
1650 1710 4.445452 TGTAGGGTAAGTGTGATTCGTC 57.555 45.455 0.00 0.00 0.00 4.20
1684 1748 8.064814 GGAAATTAGACAATTAAGCTAGCTTCG 58.935 37.037 32.51 20.67 37.47 3.79
1698 1762 0.614294 TCCGCGGGGAAATTAGACAA 59.386 50.000 27.83 0.00 40.15 3.18
1726 1790 9.736023 CAGCTTAAATTTGTTTCAACTAGACTT 57.264 29.630 0.00 0.00 0.00 3.01
1737 1801 3.572255 TCGAGCCCAGCTTAAATTTGTTT 59.428 39.130 0.00 0.00 39.88 2.83
1739 1803 2.488153 GTCGAGCCCAGCTTAAATTTGT 59.512 45.455 0.00 0.00 39.88 2.83
1771 1835 1.151668 CCCTCGCTGAAACTGACAAG 58.848 55.000 0.00 0.00 0.00 3.16
1792 1869 2.793278 ATGAGCAAAAACGGTTCACC 57.207 45.000 0.00 0.00 0.00 4.02
1902 1979 0.737367 TCTCTGCGTGATGCCTTTCG 60.737 55.000 0.00 0.00 45.60 3.46
2000 2078 1.942657 GCCATCGATCTAAGCTGCAAA 59.057 47.619 1.02 0.00 0.00 3.68
2007 2085 2.487934 CCAAGGTGCCATCGATCTAAG 58.512 52.381 0.00 0.00 0.00 2.18
2014 2092 2.360350 ACTGCCAAGGTGCCATCG 60.360 61.111 0.00 0.00 0.00 3.84
2015 2093 1.181098 AACACTGCCAAGGTGCCATC 61.181 55.000 0.00 0.00 38.14 3.51
2027 2105 2.287308 TGGCAATTGTTCGTAACACTGC 60.287 45.455 7.40 16.86 44.12 4.40
2029 2107 3.211045 AGTGGCAATTGTTCGTAACACT 58.789 40.909 7.40 7.62 41.97 3.55
2033 2111 3.994392 GAGAGAGTGGCAATTGTTCGTAA 59.006 43.478 7.40 0.00 0.00 3.18
2035 2113 2.037772 AGAGAGAGTGGCAATTGTTCGT 59.962 45.455 7.40 0.00 0.00 3.85
2036 2114 2.693069 AGAGAGAGTGGCAATTGTTCG 58.307 47.619 7.40 0.00 0.00 3.95
2037 2115 4.094146 GCTTAGAGAGAGTGGCAATTGTTC 59.906 45.833 7.40 0.75 0.00 3.18
2070 2149 8.116026 ACACTAGTCCATGGATTTATTTTCCTT 58.884 33.333 19.62 0.00 34.17 3.36
2071 2150 7.643123 ACACTAGTCCATGGATTTATTTTCCT 58.357 34.615 19.62 9.29 34.17 3.36
2088 2167 8.072567 TGTTTAACTAAGAAGACGACACTAGTC 58.927 37.037 0.00 0.00 41.46 2.59
2101 2180 5.298989 TGCCAGAGGTGTTTAACTAAGAA 57.701 39.130 0.00 0.00 0.00 2.52
2120 2199 5.812127 GGGAAGATATTTTGTGTTGAATGCC 59.188 40.000 0.00 0.00 0.00 4.40
2122 2201 7.605449 ACAGGGAAGATATTTTGTGTTGAATG 58.395 34.615 0.00 0.00 0.00 2.67
2161 2240 2.025605 ACACAGGTGAGCAATGATGGAT 60.026 45.455 6.40 0.00 0.00 3.41
2205 2284 1.580845 CTTCCAAGAACAGCCCTGCG 61.581 60.000 0.00 0.00 0.00 5.18
2258 2337 6.295249 TGGTTTCTTCACAATCATCACAGTA 58.705 36.000 0.00 0.00 0.00 2.74
2302 2381 0.176680 ACTAATCACTGAGCTGGGCG 59.823 55.000 0.00 0.00 0.00 6.13
2310 2389 7.063426 CACGAAAGCTCAAATACTAATCACTGA 59.937 37.037 0.00 0.00 0.00 3.41
2319 2416 6.255887 GCTATACACACGAAAGCTCAAATACT 59.744 38.462 0.00 0.00 0.00 2.12
2339 2436 4.462132 ACAAACATGCACACATTGGCTATA 59.538 37.500 0.00 0.00 32.87 1.31
2340 2437 3.258872 ACAAACATGCACACATTGGCTAT 59.741 39.130 0.00 0.00 32.87 2.97
2341 2438 2.627221 ACAAACATGCACACATTGGCTA 59.373 40.909 0.00 0.00 32.87 3.93
2342 2439 1.413445 ACAAACATGCACACATTGGCT 59.587 42.857 0.00 0.00 32.87 4.75
2349 2446 5.925397 TCCATTTATTCACAAACATGCACAC 59.075 36.000 0.00 0.00 0.00 3.82
2357 2454 4.035017 CCGCGATCCATTTATTCACAAAC 58.965 43.478 8.23 0.00 0.00 2.93
2378 2475 5.239306 TCTGAAGTTGTGAATTGTGACATCC 59.761 40.000 0.00 0.00 0.00 3.51
2386 2483 4.686091 TCGCTACTCTGAAGTTGTGAATTG 59.314 41.667 1.73 0.00 42.23 2.32
2388 2485 4.521130 TCGCTACTCTGAAGTTGTGAAT 57.479 40.909 1.73 0.00 42.23 2.57
2407 2512 2.328099 GGCCACTTGCAGGAGTTCG 61.328 63.158 1.40 0.00 43.89 3.95
2422 2527 3.149196 CACATGTAGGATATTGTGGGCC 58.851 50.000 0.00 0.00 35.31 5.80
2476 2591 1.073964 CACTGTTCTGATGAGGCACG 58.926 55.000 0.00 0.00 0.00 5.34
2753 2875 2.173143 ACGGTTTGTACCTCTGGGAAAA 59.827 45.455 0.00 0.00 42.66 2.29
2817 2939 1.321474 CTCAACTTGGCTGGCTTTGA 58.679 50.000 2.00 7.84 0.00 2.69
2818 2940 0.316204 CCTCAACTTGGCTGGCTTTG 59.684 55.000 2.00 3.86 0.00 2.77
2819 2941 1.466851 GCCTCAACTTGGCTGGCTTT 61.467 55.000 2.00 0.00 46.38 3.51
2834 2956 1.134877 GTTCCGTTACCTAGTGGCCTC 60.135 57.143 3.32 0.00 36.63 4.70
2847 2972 0.472471 TTCCTTGAGCCAGTTCCGTT 59.528 50.000 0.00 0.00 0.00 4.44
2848 2973 0.472471 TTTCCTTGAGCCAGTTCCGT 59.528 50.000 0.00 0.00 0.00 4.69
2849 2974 0.875059 GTTTCCTTGAGCCAGTTCCG 59.125 55.000 0.00 0.00 0.00 4.30
2850 2975 1.981256 TGTTTCCTTGAGCCAGTTCC 58.019 50.000 0.00 0.00 0.00 3.62
2851 2976 2.229784 CCATGTTTCCTTGAGCCAGTTC 59.770 50.000 0.00 0.00 0.00 3.01
2861 2986 3.061848 CCGCCGCCATGTTTCCTT 61.062 61.111 0.00 0.00 0.00 3.36
2936 3061 1.378514 TTTGCTCCTGATTCCGCCC 60.379 57.895 0.00 0.00 0.00 6.13
2938 3063 1.425428 CGTTTGCTCCTGATTCCGC 59.575 57.895 0.00 0.00 0.00 5.54
3219 3344 1.353103 GGCGCATACATGTGAGCAC 59.647 57.895 19.89 12.55 45.17 4.40


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

AutoCloner maintained by Alex Coulton.