Multiple sequence alignment - TraesCS2D01G539200

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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 TraesCS2D01G539200 chr2D 100.000 3448 0 0 1 3448 619704861 619708308 0.000000e+00 6368
1 TraesCS2D01G539200 chr2D 79.646 565 93 13 1079 1629 620640665 620640109 1.500000e-103 387
2 TraesCS2D01G539200 chr2D 93.077 260 15 3 2779 3036 619704986 619705244 9.030000e-101 377
3 TraesCS2D01G539200 chr2D 93.077 260 15 3 126 384 619707639 619707896 9.030000e-101 377
4 TraesCS2D01G539200 chr2D 80.124 483 44 23 529 983 620641227 620640769 2.580000e-81 313
5 TraesCS2D01G539200 chr2D 88.942 208 18 5 618 823 620741871 620742075 5.710000e-63 252
6 TraesCS2D01G539200 chr2B 89.958 1414 73 27 2058 3429 759445700 759447086 0.000000e+00 1760
7 TraesCS2D01G539200 chr2B 92.135 445 27 4 1 437 759442990 759443434 3.780000e-174 621
8 TraesCS2D01G539200 chr2B 90.667 450 21 8 1630 2058 218624454 218624005 2.310000e-161 579
9 TraesCS2D01G539200 chr2B 92.381 315 22 2 1316 1629 759445391 759445704 6.790000e-122 448
10 TraesCS2D01G539200 chr2B 92.440 291 21 1 126 416 759446412 759446701 6.880000e-112 414
11 TraesCS2D01G539200 chr2B 91.892 259 20 1 2779 3036 759443123 759443381 9.100000e-96 361
12 TraesCS2D01G539200 chr2B 81.191 319 52 6 1317 1629 761709355 761709671 2.050000e-62 250
13 TraesCS2D01G539200 chr2B 78.592 355 70 6 2058 2410 761707464 761707814 2.680000e-56 230
14 TraesCS2D01G539200 chr2B 76.751 357 71 10 2058 2411 761719077 761719424 4.540000e-44 189
15 TraesCS2D01G539200 chr2B 87.248 149 17 2 677 823 761699402 761699550 5.920000e-38 169
16 TraesCS2D01G539200 chr3B 93.561 497 20 6 750 1243 713760384 713759897 0.000000e+00 730
17 TraesCS2D01G539200 chr3B 90.606 330 18 4 436 756 713761333 713761008 3.180000e-115 425
18 TraesCS2D01G539200 chr3B 95.000 240 11 1 1630 1869 7250350 7250588 3.250000e-100 375
19 TraesCS2D01G539200 chr3B 82.178 303 24 14 3149 3432 713761838 713761547 2.070000e-57 233
20 TraesCS2D01G539200 chr2A 93.561 497 20 6 750 1243 751252588 751253075 0.000000e+00 730
21 TraesCS2D01G539200 chr2A 93.561 497 20 6 750 1243 751274674 751275161 0.000000e+00 730
22 TraesCS2D01G539200 chr2A 88.547 585 32 17 2849 3429 751379777 751380330 0.000000e+00 676
23 TraesCS2D01G539200 chr2A 95.696 395 12 5 1239 1629 751371482 751371875 6.280000e-177 630
24 TraesCS2D01G539200 chr2A 93.029 416 29 0 1 416 751240901 751241316 2.940000e-170 608
25 TraesCS2D01G539200 chr2A 92.788 416 30 0 1 416 751271480 751271895 1.370000e-168 603
26 TraesCS2D01G539200 chr2A 94.580 369 20 0 2058 2426 751371871 751372239 3.860000e-159 571
27 TraesCS2D01G539200 chr2A 90.663 332 18 4 436 758 751273725 751274052 2.460000e-116 429
28 TraesCS2D01G539200 chr2A 90.606 330 18 4 436 756 751251096 751251421 3.180000e-115 425
29 TraesCS2D01G539200 chr2A 90.262 267 24 2 2776 3040 751241022 751241288 7.080000e-92 348
30 TraesCS2D01G539200 chr2A 90.262 267 24 2 2776 3040 751271601 751271867 7.080000e-92 348
31 TraesCS2D01G539200 chr2A 82.723 382 36 14 3067 3429 751273138 751273508 2.580000e-81 313
32 TraesCS2D01G539200 chr2A 96.277 188 7 0 1868 2055 51595397 51595210 3.340000e-80 309
33 TraesCS2D01G539200 chr2A 88.492 252 20 6 2611 2854 751373966 751374216 2.600000e-76 296
34 TraesCS2D01G539200 chr2A 78.378 481 39 28 529 983 752298447 752298006 5.710000e-63 252
35 TraesCS2D01G539200 chr2A 81.818 319 27 15 3130 3429 751250573 751250879 4.450000e-59 239
36 TraesCS2D01G539200 chr2A 90.270 185 15 2 2430 2612 751373695 751373878 4.450000e-59 239
37 TraesCS2D01G539200 chr2A 87.500 216 16 1 201 416 751379782 751379986 4.450000e-59 239
38 TraesCS2D01G539200 chr2A 78.904 365 67 9 2058 2416 752297347 752296987 4.450000e-59 239
39 TraesCS2D01G539200 chr2A 75.362 345 72 9 2058 2391 752550023 752550365 1.660000e-33 154
40 TraesCS2D01G539200 chr2A 91.667 72 5 1 128 199 751374144 751374214 7.880000e-17 99
41 TraesCS2D01G539200 chr3D 91.982 449 15 1 1630 2057 449755421 449754973 8.180000e-171 610
42 TraesCS2D01G539200 chr1D 92.063 441 21 2 1630 2057 269822303 269822742 2.940000e-170 608
43 TraesCS2D01G539200 chr7D 91.275 447 18 6 1630 2055 102994092 102993646 1.070000e-164 590
44 TraesCS2D01G539200 chr7B 90.265 452 18 10 1630 2058 151621421 151620973 4.990000e-158 568
45 TraesCS2D01G539200 chr7B 95.789 190 8 0 1868 2057 726611723 726611534 1.200000e-79 307
46 TraesCS2D01G539200 chr5A 89.035 456 22 8 1630 2057 44340931 44340476 1.090000e-149 540
47 TraesCS2D01G539200 chr5A 96.667 240 8 0 1630 1869 631470537 631470298 1.930000e-107 399
48 TraesCS2D01G539200 chr5A 97.409 193 5 0 1868 2060 631470017 631469825 2.570000e-86 329
49 TraesCS2D01G539200 chr5A 79.935 309 43 14 2058 2358 691531250 691530953 3.490000e-50 209
50 TraesCS2D01G539200 chr1B 88.764 445 29 7 1638 2061 660415715 660416159 3.050000e-145 525
51 TraesCS2D01G539200 chr1B 95.789 190 8 0 1868 2057 600376230 600376419 1.200000e-79 307
52 TraesCS2D01G539200 chr5B 95.633 229 10 0 1630 1858 137655973 137655745 5.440000e-98 368
53 TraesCS2D01G539200 chr5B 96.316 190 7 0 1868 2057 137656088 137655899 2.580000e-81 313
54 TraesCS2D01G539200 chr1A 94.764 191 10 0 1868 2058 221666442 221666252 7.230000e-77 298
55 TraesCS2D01G539200 chr4B 80.528 303 52 6 2058 2358 653955609 653955312 3.460000e-55 226
56 TraesCS2D01G539200 chrUn 79.934 304 52 8 2058 2358 126691688 126691985 7.490000e-52 215


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 TraesCS2D01G539200 chr2D 619704861 619708308 3447 False 2374.000000 6368 95.384667 1 3448 3 chr2D.!!$F2 3447
1 TraesCS2D01G539200 chr2D 620640109 620641227 1118 True 350.000000 387 79.885000 529 1629 2 chr2D.!!$R1 1100
2 TraesCS2D01G539200 chr2B 759442990 759447086 4096 False 720.800000 1760 91.761200 1 3429 5 chr2B.!!$F3 3428
3 TraesCS2D01G539200 chr2B 761707464 761709671 2207 False 240.000000 250 79.891500 1317 2410 2 chr2B.!!$F4 1093
4 TraesCS2D01G539200 chr3B 713759897 713761838 1941 True 462.666667 730 88.781667 436 3432 3 chr3B.!!$R1 2996
5 TraesCS2D01G539200 chr2A 751271480 751275161 3681 False 484.600000 730 89.999400 1 3429 5 chr2A.!!$F4 3428
6 TraesCS2D01G539200 chr2A 751250573 751253075 2502 False 464.666667 730 88.661667 436 3429 3 chr2A.!!$F3 2993
7 TraesCS2D01G539200 chr2A 751379777 751380330 553 False 457.500000 676 88.023500 201 3429 2 chr2A.!!$F6 3228
8 TraesCS2D01G539200 chr2A 751371482 751374216 2734 False 367.000000 630 92.141000 128 2854 5 chr2A.!!$F5 2726
9 TraesCS2D01G539200 chr2A 752296987 752298447 1460 True 245.500000 252 78.641000 529 2416 2 chr2A.!!$R2 1887
10 TraesCS2D01G539200 chr5A 631469825 631470537 712 True 364.000000 399 97.038000 1630 2060 2 chr5A.!!$R3 430

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
640 2472 0.327867 TTGGCCCTCCTCCTCATCAT 60.328 55.000 0.0 0.0 0.0 2.45 F
641 2473 0.765903 TGGCCCTCCTCCTCATCATC 60.766 60.000 0.0 0.0 0.0 2.92 F
1669 5292 1.133945 CCCTCTCTCTCAGATCCGTCA 60.134 57.143 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 5839 0.249868 GCTATATGACGTGGGCAGCA 60.250 55.000 0.00 0.0 0.00 4.41 R
2400 6308 3.010138 TGAAACCAGGAAGGGGATACAAG 59.990 47.826 0.00 0.0 43.89 3.16 R
3331 8817 0.034089 GCTAGCACCCCATTTCCTGT 60.034 55.000 10.63 0.0 0.00 4.00 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
53 54 0.530431 GCACTTGCACCACCCTTTTG 60.530 55.000 0.00 0.00 41.59 2.44
106 107 9.453572 TCAGAGCAATAATCTTGAATTACACTT 57.546 29.630 0.00 0.00 0.00 3.16
110 119 7.761249 AGCAATAATCTTGAATTACACTTTGCC 59.239 33.333 0.00 0.00 0.00 4.52
140 149 5.910637 TGTGATCGTGTGGTTACTTTTAC 57.089 39.130 0.00 0.00 0.00 2.01
261 270 2.661675 CACGAGTTCGACCATTACACTG 59.338 50.000 8.72 0.00 43.02 3.66
306 315 2.224769 TGGTAGCTTTCAAAGAGGGTGG 60.225 50.000 0.00 0.00 0.00 4.61
315 324 2.106511 TCAAAGAGGGTGGAAACAGAGG 59.893 50.000 0.00 0.00 44.46 3.69
395 404 8.270799 TCTACGAAAAGTACACGATTTTCTTTG 58.729 33.333 13.18 7.56 41.24 2.77
396 405 6.196571 ACGAAAAGTACACGATTTTCTTTGG 58.803 36.000 13.18 4.09 41.24 3.28
452 2276 0.749454 CAGTGGATGGCCCTTGCTAC 60.749 60.000 0.00 0.00 37.74 3.58
455 2279 1.152881 GGATGGCCCTTGCTACCTG 60.153 63.158 0.00 0.00 37.74 4.00
474 2298 4.344865 GGAAGCGGGGGTGAAGCA 62.345 66.667 0.00 0.00 0.00 3.91
494 2326 4.335647 AGTGGTTCCAGGCAGCCG 62.336 66.667 5.55 0.53 0.00 5.52
550 2382 3.014623 GACAATAAAGCCTACCGCCTTT 58.985 45.455 0.00 0.00 38.78 3.11
597 2429 1.293924 GTCCGAGCATGAGTTGGATG 58.706 55.000 0.00 0.00 0.00 3.51
639 2471 1.082766 TTGGCCCTCCTCCTCATCA 59.917 57.895 0.00 0.00 0.00 3.07
640 2472 0.327867 TTGGCCCTCCTCCTCATCAT 60.328 55.000 0.00 0.00 0.00 2.45
641 2473 0.765903 TGGCCCTCCTCCTCATCATC 60.766 60.000 0.00 0.00 0.00 2.92
932 4013 4.320057 GGTGAACAAATTGCAGTCTCAGAG 60.320 45.833 0.00 0.00 0.00 3.35
941 4022 1.654317 CAGTCTCAGAGGAGCAATGC 58.346 55.000 0.00 0.00 41.13 3.56
1039 4129 5.936956 TGGCATGGATTATTTGTTTTTGGTC 59.063 36.000 0.00 0.00 0.00 4.02
1132 4246 1.539827 CCCCGATTGTGAGGAAACAAC 59.460 52.381 0.00 0.00 42.56 3.32
1299 4882 4.503007 AGCGTGTATCTACAATTTAGTGCG 59.497 41.667 0.00 0.00 38.04 5.34
1410 5029 3.834813 TGAATACCTTGCAGTCAGTCTCT 59.165 43.478 0.00 0.00 0.00 3.10
1665 5288 1.178534 CGGCCCTCTCTCTCAGATCC 61.179 65.000 0.00 0.00 0.00 3.36
1669 5292 1.133945 CCCTCTCTCTCAGATCCGTCA 60.134 57.143 0.00 0.00 0.00 4.35
1711 5334 3.185188 GCATGCACTTCTACATGGTATCG 59.815 47.826 14.21 0.00 43.13 2.92
1841 5464 4.022762 CGTATAATGTGCTGCCTAGTCTCT 60.023 45.833 0.00 0.00 0.00 3.10
1847 5470 2.093235 GTGCTGCCTAGTCTCTTCCATT 60.093 50.000 0.00 0.00 0.00 3.16
2393 6301 9.241317 CAATCTATATGGTTGCATCTTTTGTTC 57.759 33.333 0.00 0.00 0.00 3.18
2400 6308 5.517054 TGGTTGCATCTTTTGTTCGTAAAAC 59.483 36.000 0.00 0.00 0.00 2.43
2416 6325 4.634443 CGTAAAACTTGTATCCCCTTCCTG 59.366 45.833 0.00 0.00 0.00 3.86
2426 6335 5.435041 TGTATCCCCTTCCTGGTTTCATATT 59.565 40.000 0.00 0.00 0.00 1.28
2457 7818 0.179215 GCTCGTGTAGTTGCATGCAC 60.179 55.000 22.58 15.59 33.04 4.57
2470 7831 6.923012 AGTTGCATGCACATTTTTGTCTATA 58.077 32.000 22.58 0.00 0.00 1.31
2479 7840 7.975058 TGCACATTTTTGTCTATATTGTGATGG 59.025 33.333 4.47 0.00 36.06 3.51
2518 7879 3.988517 GTCGTTGTTGGACTTCTTCCTAG 59.011 47.826 0.00 0.00 46.10 3.02
2519 7880 2.737252 CGTTGTTGGACTTCTTCCTAGC 59.263 50.000 0.00 0.00 46.10 3.42
2527 7888 4.935808 TGGACTTCTTCCTAGCGAAATTTC 59.064 41.667 8.20 8.20 46.10 2.17
2533 7894 5.977635 TCTTCCTAGCGAAATTTCATCAGA 58.022 37.500 17.99 5.14 0.00 3.27
2608 7970 5.350914 GGCAGCAGCTCTGTTATTCTATATG 59.649 44.000 0.00 0.00 44.66 1.78
2612 8063 7.980662 CAGCAGCTCTGTTATTCTATATGCTAT 59.019 37.037 0.00 0.00 38.15 2.97
2641 8092 5.718649 TTATGCTTCGAGCTTATTGTGAC 57.281 39.130 8.07 0.00 42.97 3.67
2793 8252 9.887406 CGACTAAAAATGTGTGGTTACTTTTAT 57.113 29.630 0.00 0.00 30.59 1.40
2832 8291 5.422331 AGACGGAGAATCAAGATAAAGGTGA 59.578 40.000 0.00 0.00 36.25 4.02
2857 8316 3.386768 TTTCACTGTAGGTCTCTGCAC 57.613 47.619 0.00 0.00 32.30 4.57
2885 8344 4.458989 TGAAGTTGAACTTTGTCTTGCACT 59.541 37.500 12.37 0.00 38.80 4.40
2896 8355 1.461127 GTCTTGCACTCTGGCTTTACG 59.539 52.381 0.00 0.00 34.04 3.18
2913 8372 4.771590 TTACGAGTTCGACCATTACACT 57.228 40.909 8.72 0.00 43.02 3.55
2955 8414 2.047061 TGGTGGTAGCTTTCACAGAGT 58.953 47.619 17.17 0.00 35.74 3.24
2983 8442 9.487790 TGAAACAAGAGTCAAATTCAAAAGTTT 57.512 25.926 0.00 0.00 0.00 2.66
2984 8443 9.745323 GAAACAAGAGTCAAATTCAAAAGTTTG 57.255 29.630 0.00 0.00 39.48 2.93
3013 8472 7.038799 ACCAATTCTTTCTATGGCAAGAAACAT 60.039 33.333 7.88 10.75 41.28 2.71
3024 8483 4.100653 TGGCAAGAAACATGGTCAAATTCA 59.899 37.500 0.00 0.00 0.00 2.57
3025 8484 4.448732 GGCAAGAAACATGGTCAAATTCAC 59.551 41.667 0.00 0.00 0.00 3.18
3026 8485 4.148696 GCAAGAAACATGGTCAAATTCACG 59.851 41.667 0.00 0.00 0.00 4.35
3027 8486 5.518812 CAAGAAACATGGTCAAATTCACGA 58.481 37.500 0.00 0.00 0.00 4.35
3030 8514 4.909696 AACATGGTCAAATTCACGACAA 57.090 36.364 0.00 0.00 33.66 3.18
3039 8523 4.511454 TCAAATTCACGACAAGAACAGGAG 59.489 41.667 0.00 0.00 0.00 3.69
3063 8547 9.267084 GAGAAATCAGAGGTTCAACTTATATCC 57.733 37.037 0.00 0.00 0.00 2.59
3065 8549 9.566432 GAAATCAGAGGTTCAACTTATATCCAT 57.434 33.333 0.00 0.00 0.00 3.41
3067 8551 6.291377 TCAGAGGTTCAACTTATATCCATGC 58.709 40.000 0.00 0.00 0.00 4.06
3071 8555 4.024048 GGTTCAACTTATATCCATGCCACG 60.024 45.833 0.00 0.00 0.00 4.94
3097 8581 1.075601 TTGGTGGGCTGAGGAGAAAT 58.924 50.000 0.00 0.00 0.00 2.17
3141 8625 5.086104 TGCATCTCCTCCAAGTAGTTTAC 57.914 43.478 0.00 0.00 0.00 2.01
3201 8685 3.782523 ACCATCCCACTATGATGTTCAGT 59.217 43.478 0.00 0.00 38.32 3.41
3412 8898 1.000607 CAAGCTTCAGTGCTGCAACAT 60.001 47.619 2.77 0.00 43.24 2.71
3413 8899 2.189594 AGCTTCAGTGCTGCAACATA 57.810 45.000 2.77 0.00 42.33 2.29
3432 8918 6.550938 ACATATCAGTTGAGATTCAGGTGA 57.449 37.500 0.00 0.00 0.00 4.02
3433 8919 6.580788 ACATATCAGTTGAGATTCAGGTGAG 58.419 40.000 0.00 0.00 0.00 3.51
3434 8920 6.155910 ACATATCAGTTGAGATTCAGGTGAGT 59.844 38.462 0.00 0.00 0.00 3.41
3435 8921 4.963318 TCAGTTGAGATTCAGGTGAGTT 57.037 40.909 0.00 0.00 0.00 3.01
3436 8922 5.296151 TCAGTTGAGATTCAGGTGAGTTT 57.704 39.130 0.00 0.00 0.00 2.66
3437 8923 5.300752 TCAGTTGAGATTCAGGTGAGTTTC 58.699 41.667 0.00 0.00 0.00 2.78
3438 8924 5.059161 CAGTTGAGATTCAGGTGAGTTTCA 58.941 41.667 0.00 0.00 0.00 2.69
3439 8925 5.704515 CAGTTGAGATTCAGGTGAGTTTCAT 59.295 40.000 0.00 0.00 28.11 2.57
3440 8926 5.936956 AGTTGAGATTCAGGTGAGTTTCATC 59.063 40.000 0.00 0.00 28.11 2.92
3441 8927 4.498241 TGAGATTCAGGTGAGTTTCATCG 58.502 43.478 0.00 0.00 31.44 3.84
3442 8928 3.265791 AGATTCAGGTGAGTTTCATCGC 58.734 45.455 0.00 0.00 31.44 4.58
3443 8929 2.839486 TTCAGGTGAGTTTCATCGCT 57.161 45.000 0.00 0.00 31.44 4.93
3444 8930 2.839486 TCAGGTGAGTTTCATCGCTT 57.161 45.000 0.00 0.00 31.44 4.68
3445 8931 3.126001 TCAGGTGAGTTTCATCGCTTT 57.874 42.857 0.00 0.00 31.44 3.51
3446 8932 3.476552 TCAGGTGAGTTTCATCGCTTTT 58.523 40.909 0.00 0.00 31.44 2.27
3447 8933 4.637276 TCAGGTGAGTTTCATCGCTTTTA 58.363 39.130 0.00 0.00 31.44 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 107 1.340893 ACGATCACAATGGATGGGCAA 60.341 47.619 0.00 0.00 30.09 4.52
110 119 1.672363 CCACACGATCACAATGGATGG 59.328 52.381 0.00 0.00 31.69 3.51
140 149 5.734311 TCTTCGTCTTTTAAAAAGCACTCG 58.266 37.500 1.66 2.01 0.00 4.18
261 270 0.669625 GCACCTCAACACCCTACGTC 60.670 60.000 0.00 0.00 0.00 4.34
306 315 6.908870 AACTTTTGAATTTGCCTCTGTTTC 57.091 33.333 0.00 0.00 0.00 2.78
315 324 9.220635 GAATTGGTGTTAAACTTTTGAATTTGC 57.779 29.630 0.00 0.00 0.00 3.68
452 2276 4.101448 CACCCCCGCTTCCTCAGG 62.101 72.222 0.00 0.00 0.00 3.86
455 2279 2.269241 CTTCACCCCCGCTTCCTC 59.731 66.667 0.00 0.00 0.00 3.71
462 2286 4.335647 ACTGCTGCTTCACCCCCG 62.336 66.667 0.00 0.00 0.00 5.73
474 2298 2.433446 CTGCCTGGAACCACTGCT 59.567 61.111 0.00 0.00 0.00 4.24
494 2326 4.131088 GCTCTCCCGGTCCGACAC 62.131 72.222 14.39 0.00 0.00 3.67
517 2349 3.122948 GCTTTATTGTCTTTCAGTCGCGA 59.877 43.478 3.71 3.71 0.00 5.87
522 2354 4.935808 CGGTAGGCTTTATTGTCTTTCAGT 59.064 41.667 0.00 0.00 0.00 3.41
550 2382 2.959030 CCGTGGATGAATAGGAGTCTCA 59.041 50.000 1.47 0.00 0.00 3.27
597 2429 1.092345 GCTCTGGAATTGGAGTCGGC 61.092 60.000 0.00 0.00 32.67 5.54
640 2472 8.478066 CGACCATGGATCCAATAAGAATATAGA 58.522 37.037 20.67 0.00 0.00 1.98
641 2473 8.478066 TCGACCATGGATCCAATAAGAATATAG 58.522 37.037 20.67 1.90 0.00 1.31
789 3810 0.247736 GTGTAGGTGTCTCAGCCTGG 59.752 60.000 0.00 0.00 36.38 4.45
831 3855 6.626844 GCAGATTGAGTTGAGAGAGTGTATGA 60.627 42.308 0.00 0.00 0.00 2.15
914 3995 3.672808 CTCCTCTGAGACTGCAATTTGT 58.327 45.455 6.17 0.00 41.42 2.83
932 4013 2.496291 GCATCCCCAGCATTGCTCC 61.496 63.158 8.54 0.00 36.40 4.70
1039 4129 3.095332 TCTCCTTCACACAGATCCAGAG 58.905 50.000 0.00 0.00 0.00 3.35
1132 4246 1.901591 AGGCACTCACCACAATTCTG 58.098 50.000 0.00 0.00 0.00 3.02
1189 4303 6.757897 TGAGAACAATTCAAAACAGACACT 57.242 33.333 0.00 0.00 0.00 3.55
1299 4882 1.610522 GTTAGGGATCCATGCATGCAC 59.389 52.381 25.37 9.85 0.00 4.57
1410 5029 1.138069 TGAGCTCTTGAACCGACAACA 59.862 47.619 16.19 0.00 0.00 3.33
1665 5288 1.070038 GCCAATGCAACCAAATGACG 58.930 50.000 0.00 0.00 37.47 4.35
1669 5292 2.167075 GCTCTAGCCAATGCAACCAAAT 59.833 45.455 0.00 0.00 41.13 2.32
1748 5371 5.406649 CGAAAGTGGGCTGCAATTTAATTA 58.593 37.500 0.50 0.00 0.00 1.40
1797 5420 3.178540 AACACTCCCCCTCACGTGC 62.179 63.158 11.67 0.00 0.00 5.34
1799 5422 1.458777 TCAACACTCCCCCTCACGT 60.459 57.895 0.00 0.00 0.00 4.49
1847 5470 4.215109 TGTTCATCCATCAGACCGATCTA 58.785 43.478 0.00 0.00 32.25 1.98
1934 5839 0.249868 GCTATATGACGTGGGCAGCA 60.250 55.000 0.00 0.00 0.00 4.41
1942 5847 4.592485 CTCCTTTGGAGCTATATGACGT 57.408 45.455 0.27 0.00 43.29 4.34
2083 5988 3.119029 TCTGTATACTAACAACCACGGGC 60.119 47.826 4.17 0.00 0.00 6.13
2095 6000 6.592220 GCAGATCATCGAGACTCTGTATACTA 59.408 42.308 17.22 0.00 35.81 1.82
2351 6258 9.315525 CATATAGATTGATCAGTCCATAAGCAG 57.684 37.037 14.09 1.12 0.00 4.24
2358 6265 6.183361 TGCAACCATATAGATTGATCAGTCCA 60.183 38.462 14.09 1.54 0.00 4.02
2393 6301 4.634443 CAGGAAGGGGATACAAGTTTTACG 59.366 45.833 0.00 0.00 39.74 3.18
2400 6308 3.010138 TGAAACCAGGAAGGGGATACAAG 59.990 47.826 0.00 0.00 43.89 3.16
2457 7818 9.859427 AACACCATCACAATATAGACAAAAATG 57.141 29.630 0.00 0.00 0.00 2.32
2470 7831 7.230849 ACACATATGAAAACACCATCACAAT 57.769 32.000 10.38 0.00 0.00 2.71
2479 7840 6.884187 ACAACGACTACACATATGAAAACAC 58.116 36.000 10.38 0.00 0.00 3.32
2518 7879 8.719648 AGATATCAAGATCTGATGAAATTTCGC 58.280 33.333 13.34 8.53 44.84 4.70
2618 8069 5.817296 TGTCACAATAAGCTCGAAGCATAAT 59.183 36.000 9.09 0.00 45.56 1.28
2641 8092 0.390603 TGCGACCCGATTTACACCTG 60.391 55.000 0.00 0.00 0.00 4.00
2670 8121 6.489675 CATGATATCCTTGTTGTTACTGTGC 58.510 40.000 0.00 0.00 0.00 4.57
2793 8252 5.120399 TCTCCGTCTTTTAAAAAGCACTCA 58.880 37.500 1.66 0.00 0.00 3.41
2832 8291 5.181748 GCAGAGACCTACAGTGAAATTCAT 58.818 41.667 0.00 0.00 0.00 2.57
2857 8316 3.306166 AGACAAAGTTCAACTTCACGTCG 59.694 43.478 2.45 0.00 37.47 5.12
2885 8344 1.068055 GGTCGAACTCGTAAAGCCAGA 60.068 52.381 0.00 0.00 40.80 3.86
2896 8355 4.479619 ACGTTAGTGTAATGGTCGAACTC 58.520 43.478 0.33 0.00 0.00 3.01
2913 8372 1.337447 GCAGCTCAACACCCTACGTTA 60.337 52.381 0.00 0.00 0.00 3.18
2955 8414 8.087750 ACTTTTGAATTTGACTCTTGTTTCACA 58.912 29.630 0.00 0.00 0.00 3.58
2983 8442 4.661222 TGCCATAGAAAGAATTGGTGTCA 58.339 39.130 0.00 0.00 0.00 3.58
2984 8443 5.415701 TCTTGCCATAGAAAGAATTGGTGTC 59.584 40.000 0.00 0.00 29.59 3.67
3013 8472 3.942115 TGTTCTTGTCGTGAATTTGACCA 59.058 39.130 4.59 0.00 34.18 4.02
3024 8483 4.039245 TCTGATTTCTCCTGTTCTTGTCGT 59.961 41.667 0.00 0.00 0.00 4.34
3025 8484 4.560128 TCTGATTTCTCCTGTTCTTGTCG 58.440 43.478 0.00 0.00 0.00 4.35
3026 8485 4.934602 CCTCTGATTTCTCCTGTTCTTGTC 59.065 45.833 0.00 0.00 0.00 3.18
3027 8486 4.349342 ACCTCTGATTTCTCCTGTTCTTGT 59.651 41.667 0.00 0.00 0.00 3.16
3030 8514 4.594920 TGAACCTCTGATTTCTCCTGTTCT 59.405 41.667 0.00 0.00 33.74 3.01
3039 8523 8.964476 TGGATATAAGTTGAACCTCTGATTTC 57.036 34.615 0.00 0.00 0.00 2.17
3063 8547 0.680921 ACCAATTCTCCCGTGGCATG 60.681 55.000 0.00 0.00 35.72 4.06
3065 8549 1.303236 CACCAATTCTCCCGTGGCA 60.303 57.895 0.00 0.00 35.72 4.92
3067 8551 1.378514 CCCACCAATTCTCCCGTGG 60.379 63.158 0.00 0.00 44.47 4.94
3071 8555 0.394899 CTCAGCCCACCAATTCTCCC 60.395 60.000 0.00 0.00 0.00 4.30
3097 8581 5.622914 GCATGAACCGTGTAGGAGTACTTAA 60.623 44.000 0.00 0.00 45.00 1.85
3113 8597 2.295885 CTTGGAGGAGATGCATGAACC 58.704 52.381 2.46 4.51 0.00 3.62
3326 8812 1.341080 CACCCCATTTCCTGTGCTTT 58.659 50.000 0.00 0.00 0.00 3.51
3327 8813 3.056213 CACCCCATTTCCTGTGCTT 57.944 52.632 0.00 0.00 0.00 3.91
3329 8815 2.973082 GCACCCCATTTCCTGTGC 59.027 61.111 0.00 0.00 46.09 4.57
3330 8816 1.755179 CTAGCACCCCATTTCCTGTG 58.245 55.000 0.00 0.00 0.00 3.66
3331 8817 0.034089 GCTAGCACCCCATTTCCTGT 60.034 55.000 10.63 0.00 0.00 4.00
3332 8818 0.034186 TGCTAGCACCCCATTTCCTG 60.034 55.000 14.93 0.00 0.00 3.86
3334 8820 1.035139 CATGCTAGCACCCCATTTCC 58.965 55.000 22.07 0.00 0.00 3.13
3335 8821 0.386838 GCATGCTAGCACCCCATTTC 59.613 55.000 22.07 0.00 0.00 2.17
3339 8825 2.273123 CAGCATGCTAGCACCCCA 59.727 61.111 22.07 0.00 36.85 4.96
3363 8849 2.565210 TGCTGAGCACAACTGTTTTG 57.435 45.000 1.40 2.39 31.71 2.44
3412 8898 6.611613 AACTCACCTGAATCTCAACTGATA 57.388 37.500 0.00 0.00 0.00 2.15
3413 8899 5.495926 AACTCACCTGAATCTCAACTGAT 57.504 39.130 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.