Multiple sequence alignment - TraesCS5B01G111800

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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 TraesCS5B01G111800 chr5B 100.000 2616 0 0 1 2616 169681062 169678447 0.000000e+00 4831
1 TraesCS5B01G111800 chr5A 94.109 1426 55 17 461 1882 208745919 208747319 0.000000e+00 2141
2 TraesCS5B01G111800 chr5A 91.006 467 37 3 1 467 208745126 208745587 2.210000e-175 625
3 TraesCS5B01G111800 chr5D 96.139 1269 42 5 617 1882 158803996 158805260 0.000000e+00 2065
4 TraesCS5B01G111800 chr5D 90.000 350 35 0 78 427 158778985 158779334 1.100000e-123 453
5 TraesCS5B01G111800 chr5D 86.800 250 22 6 1878 2125 473992287 473992527 4.290000e-68 268
6 TraesCS5B01G111800 chr5D 90.674 193 16 2 2272 2462 557160231 557160039 3.340000e-64 255
7 TraesCS5B01G111800 chr7B 85.930 398 45 10 1875 2265 746373249 746372856 5.210000e-112 414
8 TraesCS5B01G111800 chr7B 84.224 393 28 7 1883 2273 616393782 616393422 4.140000e-93 351
9 TraesCS5B01G111800 chr2A 84.826 402 42 8 1874 2273 224911423 224911039 1.140000e-103 387
10 TraesCS5B01G111800 chr3D 84.518 394 27 11 1874 2265 583388603 583388964 2.480000e-95 359
11 TraesCS5B01G111800 chr4D 84.536 388 27 13 1879 2264 461460107 461460463 1.150000e-93 353
12 TraesCS5B01G111800 chr4B 83.594 384 29 11 1883 2264 449104462 449104813 1.940000e-86 329
13 TraesCS5B01G111800 chr4B 81.365 381 37 8 1886 2264 449101836 449102184 1.980000e-71 279
14 TraesCS5B01G111800 chr7A 92.063 189 14 1 2272 2459 69838614 69838426 5.550000e-67 265
15 TraesCS5B01G111800 chr7D 91.979 187 14 1 2274 2459 449766237 449766051 7.180000e-66 261
16 TraesCS5B01G111800 chrUn 91.444 187 15 1 2274 2459 308016501 308016687 3.340000e-64 255
17 TraesCS5B01G111800 chrUn 91.444 187 15 1 2274 2459 308020615 308020801 3.340000e-64 255
18 TraesCS5B01G111800 chrUn 91.444 187 15 1 2274 2459 311192639 311192453 3.340000e-64 255
19 TraesCS5B01G111800 chr6A 91.444 187 15 1 2274 2459 31375893 31376079 3.340000e-64 255
20 TraesCS5B01G111800 chr1A 91.444 187 15 1 2274 2459 222517043 222516857 3.340000e-64 255
21 TraesCS5B01G111800 chr6B 88.208 212 20 5 2270 2479 16421638 16421846 5.590000e-62 248
22 TraesCS5B01G111800 chr6D 82.192 146 21 5 98 242 115632548 115632689 1.270000e-23 121


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 TraesCS5B01G111800 chr5B 169678447 169681062 2615 True 4831 4831 100.0000 1 2616 1 chr5B.!!$R1 2615
1 TraesCS5B01G111800 chr5A 208745126 208747319 2193 False 1383 2141 92.5575 1 1882 2 chr5A.!!$F1 1881
2 TraesCS5B01G111800 chr5D 158803996 158805260 1264 False 2065 2065 96.1390 617 1882 1 chr5D.!!$F2 1265
3 TraesCS5B01G111800 chr4B 449101836 449104813 2977 False 304 329 82.4795 1883 2264 2 chr4B.!!$F1 381
4 TraesCS5B01G111800 chrUn 308016501 308020801 4300 False 255 255 91.4440 2274 2459 2 chrUn.!!$F1 185

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
35 36 0.250234 TTGAGACCATCAAGCCCGAG 59.75 55.0 0.0 0.0 43.09 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2024 2370 0.248825 CGAGGAGAGGACAGCATTCG 60.249 60.0 0.0 0.0 0.0 3.34 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
35 36 0.250234 TTGAGACCATCAAGCCCGAG 59.750 55.000 0.00 0.00 43.09 4.63
76 77 4.098501 AGAACAACCCTTGCTTCTCTTTTG 59.901 41.667 0.00 0.00 30.59 2.44
79 80 1.133356 ACCCTTGCTTCTCTTTTGCCT 60.133 47.619 0.00 0.00 0.00 4.75
85 86 3.784338 TGCTTCTCTTTTGCCTTTGTTG 58.216 40.909 0.00 0.00 0.00 3.33
101 102 7.094377 TGCCTTTGTTGACCTTATATTCTTGTC 60.094 37.037 0.00 0.00 0.00 3.18
108 109 5.655090 TGACCTTATATTCTTGTCGACCTCA 59.345 40.000 14.12 0.00 0.00 3.86
114 115 2.724977 TCTTGTCGACCTCATGTGTC 57.275 50.000 14.12 7.73 0.00 3.67
117 118 0.603065 TGTCGACCTCATGTGTCTGG 59.397 55.000 14.12 4.11 0.00 3.86
135 136 5.061853 GTCTGGATATCTAGTGGACGTGTA 58.938 45.833 15.00 0.00 0.00 2.90
146 147 4.457466 AGTGGACGTGTAATTTGGACTTT 58.543 39.130 0.00 0.00 0.00 2.66
158 159 3.536956 TTGGACTTTCGTCTGAGTGTT 57.463 42.857 0.00 0.00 40.10 3.32
161 162 2.036089 GGACTTTCGTCTGAGTGTTCCT 59.964 50.000 0.00 0.00 40.10 3.36
163 164 3.458189 ACTTTCGTCTGAGTGTTCCTTG 58.542 45.455 0.00 0.00 0.00 3.61
174 175 4.044426 GAGTGTTCCTTGTTGTGATTTGC 58.956 43.478 0.00 0.00 0.00 3.68
214 215 3.287222 CCTCCAAGTTGTGAAAGACCAA 58.713 45.455 1.45 0.00 0.00 3.67
223 224 2.224523 TGTGAAAGACCAAGCCACCTAG 60.225 50.000 0.00 0.00 0.00 3.02
233 234 2.219027 GCCACCTAGGGTTCCTACC 58.781 63.158 14.81 0.00 44.22 3.18
274 275 5.587388 ACCATCATTCCAAATAAGCACAG 57.413 39.130 0.00 0.00 0.00 3.66
275 276 4.403432 ACCATCATTCCAAATAAGCACAGG 59.597 41.667 0.00 0.00 0.00 4.00
329 330 9.280174 CTAACCATACAGGAACTTTTTAGTGAA 57.720 33.333 0.00 0.00 41.22 3.18
365 366 4.047166 TCATCATAATGGGAGGTTGGAGT 58.953 43.478 0.00 0.00 33.42 3.85
366 367 5.223655 TCATCATAATGGGAGGTTGGAGTA 58.776 41.667 0.00 0.00 33.42 2.59
369 370 4.163458 TCATAATGGGAGGTTGGAGTACAC 59.837 45.833 0.00 0.00 0.00 2.90
370 371 2.038863 ATGGGAGGTTGGAGTACACA 57.961 50.000 0.00 0.00 0.00 3.72
375 376 2.288886 GGAGGTTGGAGTACACAGACAC 60.289 54.545 0.00 0.00 0.00 3.67
383 384 3.069729 GGAGTACACAGACACAAAGGAGT 59.930 47.826 0.00 0.00 0.00 3.85
388 389 5.489792 ACACAGACACAAAGGAGTGATAT 57.510 39.130 0.57 0.00 42.05 1.63
403 404 7.971201 AGGAGTGATATATCTTCAGAAATGCA 58.029 34.615 13.79 0.00 0.00 3.96
416 417 7.825761 TCTTCAGAAATGCAACTCAGAATATCA 59.174 33.333 0.00 0.00 0.00 2.15
417 418 7.549615 TCAGAAATGCAACTCAGAATATCAG 57.450 36.000 0.00 0.00 0.00 2.90
418 419 7.108194 TCAGAAATGCAACTCAGAATATCAGT 58.892 34.615 0.00 0.00 0.00 3.41
431 432 9.486497 CTCAGAATATCAGTAGTTGCATGTATT 57.514 33.333 0.00 0.00 0.00 1.89
444 445 4.037858 GCATGTATTGCCTCAAAGAAGG 57.962 45.455 0.00 0.00 46.15 3.46
446 447 4.439289 GCATGTATTGCCTCAAAGAAGGTC 60.439 45.833 0.00 0.00 46.15 3.85
458 459 7.164803 CCTCAAAGAAGGTCTGAAGTTATCTT 58.835 38.462 0.00 0.00 36.51 2.40
467 806 8.423906 AGGTCTGAAGTTATCTTGTCTTAGAA 57.576 34.615 0.00 0.00 33.64 2.10
479 818 5.468746 TCTTGTCTTAGAATGAAACAACCCG 59.531 40.000 0.00 0.00 0.00 5.28
503 843 3.701040 GGCAACCATATTCACACTTGGAT 59.299 43.478 0.00 0.00 33.36 3.41
505 845 5.359576 GGCAACCATATTCACACTTGGATTA 59.640 40.000 0.00 0.00 33.36 1.75
507 847 6.095440 GCAACCATATTCACACTTGGATTACT 59.905 38.462 0.00 0.00 33.36 2.24
509 849 9.173021 CAACCATATTCACACTTGGATTACTAA 57.827 33.333 0.00 0.00 33.36 2.24
563 903 1.280421 GTGTTGGCCAAGAGAGGAGAT 59.720 52.381 21.21 0.00 0.00 2.75
576 916 7.420680 CCAAGAGAGGAGATTGGGTAATTGTAT 60.421 40.741 0.00 0.00 39.87 2.29
577 917 7.698163 AGAGAGGAGATTGGGTAATTGTATT 57.302 36.000 0.00 0.00 0.00 1.89
578 918 8.107196 AGAGAGGAGATTGGGTAATTGTATTT 57.893 34.615 0.00 0.00 0.00 1.40
705 1045 4.721142 AGCAAACACAAAAACAAACATGC 58.279 34.783 0.00 0.00 0.00 4.06
722 1062 8.246180 ACAAACATGCTTCTTATAATCCAAGTG 58.754 33.333 0.00 0.00 0.00 3.16
805 1145 2.362369 CCACATGCGGAGGAGGAGT 61.362 63.158 0.00 0.00 31.22 3.85
838 1179 2.751436 CCACCTCACAATGCCCCG 60.751 66.667 0.00 0.00 0.00 5.73
936 1277 0.617820 TTTTCCCTCTCCTCTCCGGG 60.618 60.000 0.00 0.00 38.07 5.73
1023 1364 0.107312 CCTTGGAGACATGCCTCAGG 60.107 60.000 11.40 6.22 42.32 3.86
1152 1493 1.066143 CCATACAAGTCCGCTCTGGTT 60.066 52.381 0.00 0.00 39.52 3.67
1241 1582 2.090999 CCTTACCCCTCTCTCTAGGCTT 60.091 54.545 0.00 0.00 35.09 4.35
1260 1601 3.507622 GCTTGGTGAACAATAAAGGAGCT 59.492 43.478 0.00 0.00 38.65 4.09
1261 1602 4.379918 GCTTGGTGAACAATAAAGGAGCTC 60.380 45.833 4.71 4.71 38.65 4.09
1265 1606 4.096984 GGTGAACAATAAAGGAGCTCATGG 59.903 45.833 17.19 0.00 0.00 3.66
1591 1932 1.656587 AGACAACCCTCTGCACCATA 58.343 50.000 0.00 0.00 0.00 2.74
1658 1999 1.816863 AATCGAGGACGCACACACCT 61.817 55.000 0.00 0.00 39.58 4.00
1675 2016 2.096909 CACCTTTACTGTTCTGTTCGCG 60.097 50.000 0.00 0.00 0.00 5.87
1722 2063 0.723790 CGCGTATACGATCCACCGAC 60.724 60.000 28.66 6.57 43.02 4.79
1727 2068 1.481871 ATACGATCCACCGACCAGTT 58.518 50.000 0.00 0.00 0.00 3.16
1741 2082 4.321750 CCGACCAGTTGTGACTTGTACTAT 60.322 45.833 0.00 0.00 32.38 2.12
1847 2190 6.959639 TTCTGTAGCAAAGGACAAAAGATT 57.040 33.333 0.00 0.00 0.00 2.40
1856 2201 9.638176 AGCAAAGGACAAAAGATTCTGATATAT 57.362 29.630 0.00 0.00 0.00 0.86
1888 2233 9.696917 AAGAGCAAGTGATTAATTTTCGAAAAT 57.303 25.926 26.51 26.51 40.15 1.82
1905 2250 1.734163 AATACTAAGCCCACACGTGC 58.266 50.000 17.22 0.41 0.00 5.34
1923 2269 2.360475 GGGCTGAGACCACTTGCC 60.360 66.667 0.00 0.00 41.61 4.52
1925 2271 2.743928 GCTGAGACCACTTGCCCG 60.744 66.667 0.00 0.00 0.00 6.13
1929 2275 2.027625 GAGACCACTTGCCCGAACG 61.028 63.158 0.00 0.00 0.00 3.95
1936 2282 4.388499 TTGCCCGAACGCCCTCTC 62.388 66.667 0.00 0.00 0.00 3.20
1944 2290 2.221906 GAACGCCCTCTCTGCCGTTA 62.222 60.000 0.00 0.00 43.05 3.18
1950 2296 0.461548 CCTCTCTGCCGTTAGATGCA 59.538 55.000 0.00 0.00 35.86 3.96
1979 2325 2.472695 TCTTAAAGCAGGACGCACAT 57.527 45.000 0.00 0.00 46.13 3.21
1989 2335 2.738521 ACGCACATCCACGTCAGC 60.739 61.111 0.00 0.00 38.28 4.26
2051 2397 2.826287 CCTCTCCTCGCTCGCTCA 60.826 66.667 0.00 0.00 0.00 4.26
2056 2402 3.137459 CCTCGCTCGCTCACTCCT 61.137 66.667 0.00 0.00 0.00 3.69
2063 2409 2.022754 GCTCGCTCACTCCTACCCTTA 61.023 57.143 0.00 0.00 0.00 2.69
2065 2411 2.554893 CTCGCTCACTCCTACCCTTATC 59.445 54.545 0.00 0.00 0.00 1.75
2066 2412 1.267261 CGCTCACTCCTACCCTTATCG 59.733 57.143 0.00 0.00 0.00 2.92
2067 2413 2.308690 GCTCACTCCTACCCTTATCGT 58.691 52.381 0.00 0.00 0.00 3.73
2068 2414 2.694109 GCTCACTCCTACCCTTATCGTT 59.306 50.000 0.00 0.00 0.00 3.85
2069 2415 3.491104 GCTCACTCCTACCCTTATCGTTG 60.491 52.174 0.00 0.00 0.00 4.10
2070 2416 3.952323 CTCACTCCTACCCTTATCGTTGA 59.048 47.826 0.00 0.00 0.00 3.18
2076 2422 0.548197 ACCCTTATCGTTGACCCCCA 60.548 55.000 0.00 0.00 0.00 4.96
2083 2429 4.295199 GTTGACCCCCACCCCCAC 62.295 72.222 0.00 0.00 0.00 4.61
2095 2441 4.596585 CCCCACCCCCACACACAC 62.597 72.222 0.00 0.00 0.00 3.82
2096 2442 4.947147 CCCACCCCCACACACACG 62.947 72.222 0.00 0.00 0.00 4.49
2114 2460 2.202544 CGGAGCGAGTGAGCAGAC 60.203 66.667 0.00 0.00 40.15 3.51
2115 2461 2.202544 GGAGCGAGTGAGCAGACG 60.203 66.667 0.00 0.00 40.15 4.18
2123 2469 0.326595 AGTGAGCAGACGGAGAGAGA 59.673 55.000 0.00 0.00 0.00 3.10
2125 2471 0.393673 TGAGCAGACGGAGAGAGAGG 60.394 60.000 0.00 0.00 0.00 3.69
2133 2479 0.887387 CGGAGAGAGAGGATCCCGAC 60.887 65.000 8.55 0.17 39.31 4.79
2137 2483 1.144093 AGAGAGAGGATCCCGACGATT 59.856 52.381 8.55 0.00 33.66 3.34
2143 2489 0.315568 GGATCCCGACGATTGAGAGG 59.684 60.000 0.00 0.00 0.00 3.69
2151 2497 3.376540 CGACGATTGAGAGGGAAGATTC 58.623 50.000 0.00 0.00 0.00 2.52
2176 2522 4.736896 GTGAGGTGGCCGACGTCC 62.737 72.222 10.58 0.00 38.48 4.79
2177 2523 4.988716 TGAGGTGGCCGACGTCCT 62.989 66.667 10.58 12.20 38.48 3.85
2178 2524 4.131088 GAGGTGGCCGACGTCCTC 62.131 72.222 10.58 6.47 39.41 3.71
2218 2564 1.811025 AATTCCCCTTCACCCCCACC 61.811 60.000 0.00 0.00 0.00 4.61
2219 2565 3.759073 TTCCCCTTCACCCCCACCA 62.759 63.158 0.00 0.00 0.00 4.17
2223 2569 2.282462 CTTCACCCCCACCACAGC 60.282 66.667 0.00 0.00 0.00 4.40
2250 2596 2.482494 CTCCCCCAATACTCCTCACTT 58.518 52.381 0.00 0.00 0.00 3.16
2264 2610 2.376855 CCTCACTTTCTTCTCCCCCTTT 59.623 50.000 0.00 0.00 0.00 3.11
2265 2611 3.560239 CCTCACTTTCTTCTCCCCCTTTC 60.560 52.174 0.00 0.00 0.00 2.62
2266 2612 2.375509 TCACTTTCTTCTCCCCCTTTCC 59.624 50.000 0.00 0.00 0.00 3.13
2267 2613 2.108250 CACTTTCTTCTCCCCCTTTCCA 59.892 50.000 0.00 0.00 0.00 3.53
2268 2614 2.996742 ACTTTCTTCTCCCCCTTTCCAT 59.003 45.455 0.00 0.00 0.00 3.41
2269 2615 3.010696 ACTTTCTTCTCCCCCTTTCCATC 59.989 47.826 0.00 0.00 0.00 3.51
2270 2616 1.204146 TCTTCTCCCCCTTTCCATCG 58.796 55.000 0.00 0.00 0.00 3.84
2271 2617 0.464554 CTTCTCCCCCTTTCCATCGC 60.465 60.000 0.00 0.00 0.00 4.58
2272 2618 1.921869 TTCTCCCCCTTTCCATCGCC 61.922 60.000 0.00 0.00 0.00 5.54
2280 2626 1.340600 CCTTTCCATCGCCCAAGGTTA 60.341 52.381 0.00 0.00 32.49 2.85
2290 2636 2.483013 CGCCCAAGGTTATCAGAATCGA 60.483 50.000 0.00 0.00 0.00 3.59
2337 2683 4.476628 TTACGATCCAAACTAACCCCTC 57.523 45.455 0.00 0.00 0.00 4.30
2353 2699 5.437191 ACCCCTCTGATTCTACGATTTTT 57.563 39.130 0.00 0.00 0.00 1.94
2424 2771 2.853705 ACGATCCTACTACCAGAGCTC 58.146 52.381 5.27 5.27 0.00 4.09
2468 2815 0.457166 TGACAACCTTATCGTCGCCG 60.457 55.000 0.00 0.00 32.17 6.46
2480 2827 0.456142 CGTCGCCGAATCTGAAGACA 60.456 55.000 0.00 0.00 35.63 3.41
2484 2831 0.107945 GCCGAATCTGAAGACAGGCT 60.108 55.000 12.57 0.00 43.60 4.58
2542 2889 2.600731 GTGAGGTCGAGTCTCATTGTG 58.399 52.381 17.86 0.00 42.36 3.33
2544 2891 3.190744 GTGAGGTCGAGTCTCATTGTGTA 59.809 47.826 17.86 0.00 42.36 2.90
2546 2893 4.167268 GAGGTCGAGTCTCATTGTGTAAC 58.833 47.826 9.96 0.00 37.35 2.50
2547 2894 6.724290 TGAGGTCGAGTCTCATTGTGTAACA 61.724 44.000 12.72 0.00 39.79 2.41
2548 2895 8.656159 TGAGGTCGAGTCTCATTGTGTAACAC 62.656 46.154 12.72 0.00 40.64 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.392616 TCTTCCCAAATCCTATGGAGCTC 59.607 47.826 4.71 4.71 40.56 4.09
35 36 3.864789 TCTTCCCAAATCCTATGGAGC 57.135 47.619 0.00 0.00 40.56 4.70
43 44 2.889512 AGGGTTGTTCTTCCCAAATCC 58.110 47.619 3.04 0.00 45.64 3.01
76 77 7.158099 ACAAGAATATAAGGTCAACAAAGGC 57.842 36.000 0.00 0.00 0.00 4.35
79 80 7.118680 GGTCGACAAGAATATAAGGTCAACAAA 59.881 37.037 18.91 0.00 0.00 2.83
85 86 6.145338 TGAGGTCGACAAGAATATAAGGTC 57.855 41.667 18.91 0.00 0.00 3.85
101 102 3.571828 AGATATCCAGACACATGAGGTCG 59.428 47.826 0.00 3.87 40.20 4.79
108 109 4.520874 CGTCCACTAGATATCCAGACACAT 59.479 45.833 5.08 0.00 0.00 3.21
114 115 6.576662 ATTACACGTCCACTAGATATCCAG 57.423 41.667 0.00 0.00 0.00 3.86
117 118 7.381678 GTCCAAATTACACGTCCACTAGATATC 59.618 40.741 0.00 0.00 0.00 1.63
146 147 2.167693 ACAACAAGGAACACTCAGACGA 59.832 45.455 0.00 0.00 0.00 4.20
158 159 2.020720 ACACGCAAATCACAACAAGGA 58.979 42.857 0.00 0.00 0.00 3.36
161 162 2.425312 AGGAACACGCAAATCACAACAA 59.575 40.909 0.00 0.00 0.00 2.83
163 164 2.290641 AGAGGAACACGCAAATCACAAC 59.709 45.455 0.00 0.00 0.00 3.32
174 175 2.084546 GGGGAAATCAAGAGGAACACG 58.915 52.381 0.00 0.00 0.00 4.49
214 215 0.326332 GGTAGGAACCCTAGGTGGCT 60.326 60.000 8.29 0.00 40.21 4.75
233 234 2.874701 GGTATGCAAGCAGTGATGTAGG 59.125 50.000 0.00 0.00 0.00 3.18
274 275 6.834168 TTTCATCAAAGACAGAAATACCCC 57.166 37.500 0.00 0.00 0.00 4.95
303 304 8.842358 TCACTAAAAAGTTCCTGTATGGTTAG 57.158 34.615 0.00 0.00 37.07 2.34
305 306 8.528044 TTTCACTAAAAAGTTCCTGTATGGTT 57.472 30.769 0.00 0.00 37.07 3.67
329 330 9.197306 CCCATTATGATGATGTCCATATCAATT 57.803 33.333 0.00 0.00 40.21 2.32
354 355 1.968493 TGTCTGTGTACTCCAACCTCC 59.032 52.381 0.00 0.00 0.00 4.30
365 366 4.955811 ATCACTCCTTTGTGTCTGTGTA 57.044 40.909 0.00 0.00 38.90 2.90
366 367 3.845781 ATCACTCCTTTGTGTCTGTGT 57.154 42.857 0.00 0.00 38.90 3.72
369 370 8.200120 TGAAGATATATCACTCCTTTGTGTCTG 58.800 37.037 15.08 0.00 38.90 3.51
370 371 8.311395 TGAAGATATATCACTCCTTTGTGTCT 57.689 34.615 15.08 0.00 38.90 3.41
383 384 9.269453 CTGAGTTGCATTTCTGAAGATATATCA 57.731 33.333 15.08 0.00 0.00 2.15
388 389 9.842775 ATATTCTGAGTTGCATTTCTGAAGATA 57.157 29.630 17.87 11.28 33.99 1.98
403 404 7.334090 ACATGCAACTACTGATATTCTGAGTT 58.666 34.615 0.00 0.00 0.00 3.01
431 432 2.439507 ACTTCAGACCTTCTTTGAGGCA 59.560 45.455 0.00 0.00 40.65 4.75
444 445 9.862371 TCATTCTAAGACAAGATAACTTCAGAC 57.138 33.333 0.00 0.00 33.70 3.51
458 459 4.963373 TCGGGTTGTTTCATTCTAAGACA 58.037 39.130 0.00 0.00 0.00 3.41
467 806 0.958822 GTTGCCTCGGGTTGTTTCAT 59.041 50.000 0.00 0.00 0.00 2.57
475 814 0.916086 TGAATATGGTTGCCTCGGGT 59.084 50.000 0.00 0.00 0.00 5.28
479 818 3.129287 CCAAGTGTGAATATGGTTGCCTC 59.871 47.826 0.00 0.00 0.00 4.70
520 860 9.845740 ACACATTGTGGTATATAATCAAAGCTA 57.154 29.630 20.33 0.00 37.94 3.32
533 873 2.300956 TGGCCAACACATTGTGGTAT 57.699 45.000 20.33 4.20 37.94 2.73
541 881 1.004044 CTCCTCTCTTGGCCAACACAT 59.996 52.381 16.05 0.00 0.00 3.21
544 884 1.661463 ATCTCCTCTCTTGGCCAACA 58.339 50.000 16.05 2.93 0.00 3.33
705 1045 6.931840 GCTAGGGACACTTGGATTATAAGAAG 59.068 42.308 0.00 0.00 0.00 2.85
768 1108 3.084039 TGGATGAGGTGATTTTGCTGTC 58.916 45.455 0.00 0.00 0.00 3.51
770 1110 2.821378 TGTGGATGAGGTGATTTTGCTG 59.179 45.455 0.00 0.00 0.00 4.41
936 1277 0.321653 CTGGTTCCTGTGCCAGTACC 60.322 60.000 12.67 12.67 45.28 3.34
1241 1582 4.365514 TGAGCTCCTTTATTGTTCACCA 57.634 40.909 12.15 0.00 0.00 4.17
1260 1601 7.720957 CCATTATTAAGACCATTCTCACCATGA 59.279 37.037 0.00 0.00 0.00 3.07
1261 1602 7.522725 GCCATTATTAAGACCATTCTCACCATG 60.523 40.741 0.00 0.00 0.00 3.66
1265 1606 5.560953 GCGCCATTATTAAGACCATTCTCAC 60.561 44.000 0.00 0.00 0.00 3.51
1273 1614 2.293122 TGCATGCGCCATTATTAAGACC 59.707 45.455 14.09 0.00 37.32 3.85
1576 1917 1.837439 TCGATTATGGTGCAGAGGGTT 59.163 47.619 0.00 0.00 0.00 4.11
1591 1932 2.540515 CTGCCGATGTACTTGTCGATT 58.459 47.619 14.48 0.00 40.11 3.34
1658 1999 3.047796 GTCTCGCGAACAGAACAGTAAA 58.952 45.455 11.33 0.00 0.00 2.01
1704 2045 0.386478 GGTCGGTGGATCGTATACGC 60.386 60.000 20.42 7.35 39.60 4.42
1722 2063 8.827177 TTAAGAATAGTACAAGTCACAACTGG 57.173 34.615 0.00 0.00 35.36 4.00
1741 2082 9.985730 AGTTTTGATTTGCATCAGAATTAAGAA 57.014 25.926 0.00 0.00 40.66 2.52
1877 2222 6.617879 GTGTGGGCTTAGTATTTTCGAAAAT 58.382 36.000 32.16 32.16 41.24 1.82
1881 2226 3.255725 CGTGTGGGCTTAGTATTTTCGA 58.744 45.455 0.00 0.00 0.00 3.71
1882 2227 2.997986 ACGTGTGGGCTTAGTATTTTCG 59.002 45.455 0.00 0.00 0.00 3.46
1883 2228 3.425758 GCACGTGTGGGCTTAGTATTTTC 60.426 47.826 18.38 0.00 0.00 2.29
1884 2229 2.486592 GCACGTGTGGGCTTAGTATTTT 59.513 45.455 18.38 0.00 0.00 1.82
1885 2230 2.081462 GCACGTGTGGGCTTAGTATTT 58.919 47.619 18.38 0.00 0.00 1.40
1886 2231 1.734163 GCACGTGTGGGCTTAGTATT 58.266 50.000 18.38 0.00 0.00 1.89
1887 2232 0.459585 CGCACGTGTGGGCTTAGTAT 60.460 55.000 21.32 0.00 36.73 2.12
1888 2233 1.080366 CGCACGTGTGGGCTTAGTA 60.080 57.895 21.32 0.00 36.73 1.82
1889 2234 2.357034 CGCACGTGTGGGCTTAGT 60.357 61.111 21.32 0.00 36.73 2.24
1890 2235 3.118454 CCGCACGTGTGGGCTTAG 61.118 66.667 35.43 12.81 41.84 2.18
1905 2250 2.743928 GCAAGTGGTCTCAGCCCG 60.744 66.667 0.00 0.00 0.00 6.13
1923 2269 4.821589 GGCAGAGAGGGCGTTCGG 62.822 72.222 0.00 0.00 0.00 4.30
1929 2275 0.249657 CATCTAACGGCAGAGAGGGC 60.250 60.000 0.00 0.00 0.00 5.19
1932 2278 1.135915 AGTGCATCTAACGGCAGAGAG 59.864 52.381 0.00 0.00 41.35 3.20
1936 2282 1.020861 TGCAGTGCATCTAACGGCAG 61.021 55.000 15.37 0.00 42.53 4.85
1950 2296 4.397417 GTCCTGCTTTAAGATTGATGCAGT 59.603 41.667 17.91 0.00 40.78 4.40
1972 2318 2.738521 GCTGACGTGGATGTGCGT 60.739 61.111 0.00 0.00 44.50 5.24
1979 2325 2.566529 CGCTACTGCTGACGTGGA 59.433 61.111 0.00 0.00 36.97 4.02
1986 2332 3.181967 GCACGACCGCTACTGCTG 61.182 66.667 0.00 0.00 36.97 4.41
2024 2370 0.248825 CGAGGAGAGGACAGCATTCG 60.249 60.000 0.00 0.00 0.00 3.34
2028 2374 2.036414 AGCGAGGAGAGGACAGCA 59.964 61.111 0.00 0.00 0.00 4.41
2030 2376 3.106552 CGAGCGAGGAGAGGACAG 58.893 66.667 0.00 0.00 0.00 3.51
2051 2397 3.029570 GGTCAACGATAAGGGTAGGAGT 58.970 50.000 0.00 0.00 0.00 3.85
2056 2402 1.273724 TGGGGGTCAACGATAAGGGTA 60.274 52.381 0.00 0.00 0.00 3.69
2063 2409 3.335729 GGGGTGGGGGTCAACGAT 61.336 66.667 0.00 0.00 32.74 3.73
2066 2412 4.295199 GTGGGGGTGGGGGTCAAC 62.295 72.222 0.00 0.00 0.00 3.18
2096 2442 4.121669 TCTGCTCACTCGCTCCGC 62.122 66.667 0.00 0.00 0.00 5.54
2097 2443 2.202544 GTCTGCTCACTCGCTCCG 60.203 66.667 0.00 0.00 0.00 4.63
2110 2456 1.604604 GGATCCTCTCTCTCCGTCTG 58.395 60.000 3.84 0.00 0.00 3.51
2114 2460 0.887387 GTCGGGATCCTCTCTCTCCG 60.887 65.000 12.58 3.98 38.92 4.63
2115 2461 0.887387 CGTCGGGATCCTCTCTCTCC 60.887 65.000 12.58 0.00 0.00 3.71
2123 2469 1.323412 CTCTCAATCGTCGGGATCCT 58.677 55.000 12.58 0.00 33.02 3.24
2125 2471 0.315568 CCCTCTCAATCGTCGGGATC 59.684 60.000 0.00 0.00 37.05 3.36
2133 2479 2.546795 CCGGAATCTTCCCTCTCAATCG 60.547 54.545 0.00 0.00 44.67 3.34
2137 2483 0.325671 AGCCGGAATCTTCCCTCTCA 60.326 55.000 5.05 0.00 44.67 3.27
2143 2489 1.521681 CACGGAGCCGGAATCTTCC 60.522 63.158 5.05 2.23 44.69 3.46
2159 2505 4.736896 GGACGTCGGCCACCTCAC 62.737 72.222 13.76 0.00 0.00 3.51
2183 2529 2.817470 AATTGTGCCATCGCGGTTGC 62.817 55.000 8.75 8.75 38.08 4.17
2184 2530 0.798009 GAATTGTGCCATCGCGGTTG 60.798 55.000 6.13 4.44 38.08 3.77
2185 2531 1.506262 GAATTGTGCCATCGCGGTT 59.494 52.632 6.13 0.00 38.08 4.44
2225 2571 2.369706 AGTATTGGGGGAGGGGCC 60.370 66.667 0.00 0.00 0.00 5.80
2226 2572 2.461739 GGAGTATTGGGGGAGGGGC 61.462 68.421 0.00 0.00 0.00 5.80
2239 2585 3.442076 GGGGAGAAGAAAGTGAGGAGTA 58.558 50.000 0.00 0.00 0.00 2.59
2250 2596 1.559682 CGATGGAAAGGGGGAGAAGAA 59.440 52.381 0.00 0.00 0.00 2.52
2264 2610 1.140852 CTGATAACCTTGGGCGATGGA 59.859 52.381 8.43 0.00 0.00 3.41
2265 2611 1.140852 TCTGATAACCTTGGGCGATGG 59.859 52.381 0.00 0.00 0.00 3.51
2266 2612 2.620251 TCTGATAACCTTGGGCGATG 57.380 50.000 0.00 0.00 0.00 3.84
2267 2613 3.744660 GATTCTGATAACCTTGGGCGAT 58.255 45.455 0.00 0.00 0.00 4.58
2268 2614 2.483013 CGATTCTGATAACCTTGGGCGA 60.483 50.000 0.00 0.00 0.00 5.54
2269 2615 1.867233 CGATTCTGATAACCTTGGGCG 59.133 52.381 0.00 0.00 0.00 6.13
2270 2616 3.134458 CTCGATTCTGATAACCTTGGGC 58.866 50.000 0.00 0.00 0.00 5.36
2271 2617 4.672587 TCTCGATTCTGATAACCTTGGG 57.327 45.455 0.00 0.00 0.00 4.12
2272 2618 6.777526 GAATCTCGATTCTGATAACCTTGG 57.222 41.667 11.41 0.00 42.85 3.61
2290 2636 8.001881 AGTCGTAGAATCATACAACAGAATCT 57.998 34.615 0.00 0.00 39.69 2.40
2297 2643 7.959718 TCGTAAAGTCGTAGAATCATACAAC 57.040 36.000 0.00 0.00 39.69 3.32
2398 2745 5.474189 GCTCTGGTAGTAGGATCGTAAATCT 59.526 44.000 0.00 0.00 0.00 2.40
2404 2751 2.487625 GGAGCTCTGGTAGTAGGATCGT 60.488 54.545 14.64 0.00 0.00 3.73
2414 2761 0.110678 ATCGGATCGGAGCTCTGGTA 59.889 55.000 22.38 4.43 0.00 3.25
2416 2763 0.038709 GAATCGGATCGGAGCTCTGG 60.039 60.000 22.38 10.62 0.00 3.86
2442 2789 4.265556 CGACGATAAGGTTGTCAGAATCAC 59.734 45.833 0.00 0.00 40.69 3.06
2443 2790 4.421058 CGACGATAAGGTTGTCAGAATCA 58.579 43.478 0.00 0.00 40.69 2.57
2468 2815 1.377536 GGCAGCCTGTCTTCAGATTC 58.622 55.000 3.29 0.00 43.76 2.52
2472 2819 2.435586 CCGGCAGCCTGTCTTCAG 60.436 66.667 10.54 0.00 41.01 3.02
2519 2866 1.032657 ATGAGACTCGACCTCACCCG 61.033 60.000 13.20 0.00 42.68 5.28


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

AutoCloner maintained by Alex Coulton.