Multiple sequence alignment - TraesCS5A01G436000

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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 TraesCS5A01G436000 chr5A 100.000 3359 0 0 1 3359 619100172 619096814 0.000000e+00 6204
1 TraesCS5A01G436000 chr5A 74.130 460 112 6 1788 2245 574785317 574785771 2.060000e-42 183
2 TraesCS5A01G436000 chr5D 93.153 2994 100 29 445 3359 495032551 495029584 0.000000e+00 4296
3 TraesCS5A01G436000 chr5D 88.670 203 5 10 2 186 495034640 495034438 7.250000e-57 231
4 TraesCS5A01G436000 chr5D 74.620 461 108 8 1788 2245 456751773 456752227 9.510000e-46 195
5 TraesCS5A01G436000 chr5B 91.099 3011 136 54 426 3359 611481913 611478958 0.000000e+00 3954
6 TraesCS5A01G436000 chr5B 83.088 408 15 12 2 381 611482294 611481913 4.180000e-84 322
7 TraesCS5A01G436000 chr5B 74.130 460 112 6 1788 2245 558687039 558687493 2.060000e-42 183
8 TraesCS5A01G436000 chr1D 77.941 340 56 17 1174 1504 119010744 119010415 9.510000e-46 195
9 TraesCS5A01G436000 chr1A 77.713 341 55 19 1174 1504 131521532 131521203 4.420000e-44 189
10 TraesCS5A01G436000 chr1B 76.696 339 62 15 1174 1504 181218219 181217890 4.460000e-39 172
11 TraesCS5A01G436000 chr7D 76.071 280 48 15 1251 1519 525774364 525774093 9.780000e-26 128
12 TraesCS5A01G436000 chr6B 75.986 279 50 13 1251 1519 134000202 133999931 9.780000e-26 128
13 TraesCS5A01G436000 chr7B 75.451 277 55 11 1251 1519 562409238 562408967 4.550000e-24 122
14 TraesCS5A01G436000 chr7A 75.269 279 52 12 1251 1519 606330896 606330625 2.120000e-22 117


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 TraesCS5A01G436000 chr5A 619096814 619100172 3358 True 6204.0 6204 100.0000 1 3359 1 chr5A.!!$R1 3358
1 TraesCS5A01G436000 chr5D 495029584 495034640 5056 True 2263.5 4296 90.9115 2 3359 2 chr5D.!!$R1 3357
2 TraesCS5A01G436000 chr5B 611478958 611482294 3336 True 2138.0 3954 87.0935 2 3359 2 chr5B.!!$R1 3357

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
31 32 0.035534 TCGTGCAGGCCACACATAAT 60.036 50.0 23.82 0.00 44.91 1.28 F
644 2382 0.036671 CTGAGTGCAGGCATCAGTCA 60.037 55.0 17.78 13.42 40.45 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 3828 1.070275 CTGCTCGAGGGCATGCATA 59.930 57.895 21.36 0.0 41.63 3.14 R
2619 4467 2.019156 GCATGGCCCCTCAACTAACTC 61.019 57.143 0.00 0.0 0.00 3.01 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
30 31 0.250510 TTCGTGCAGGCCACACATAA 60.251 50.000 23.82 15.98 44.91 1.90
31 32 0.035534 TCGTGCAGGCCACACATAAT 60.036 50.000 23.82 0.00 44.91 1.28
32 33 0.810648 CGTGCAGGCCACACATAATT 59.189 50.000 23.82 0.00 44.91 1.40
131 160 1.465777 CGACAAACACGGGGAATAACC 59.534 52.381 0.00 0.00 38.08 2.85
186 216 9.793252 CATGTTAAGTTAAAGGAAAGGATCATG 57.207 33.333 0.00 0.00 0.00 3.07
188 218 8.792633 TGTTAAGTTAAAGGAAAGGATCATGTG 58.207 33.333 0.00 0.00 0.00 3.21
191 221 8.567285 AAGTTAAAGGAAAGGATCATGTGTAG 57.433 34.615 0.00 0.00 0.00 2.74
192 222 7.918076 AGTTAAAGGAAAGGATCATGTGTAGA 58.082 34.615 0.00 0.00 0.00 2.59
193 223 8.043710 AGTTAAAGGAAAGGATCATGTGTAGAG 58.956 37.037 0.00 0.00 0.00 2.43
194 224 6.380079 AAAGGAAAGGATCATGTGTAGAGT 57.620 37.500 0.00 0.00 0.00 3.24
196 226 6.723298 AGGAAAGGATCATGTGTAGAGTAG 57.277 41.667 0.00 0.00 0.00 2.57
197 227 6.198639 AGGAAAGGATCATGTGTAGAGTAGT 58.801 40.000 0.00 0.00 0.00 2.73
198 228 7.355101 AGGAAAGGATCATGTGTAGAGTAGTA 58.645 38.462 0.00 0.00 0.00 1.82
199 229 7.285858 AGGAAAGGATCATGTGTAGAGTAGTAC 59.714 40.741 0.00 0.00 0.00 2.73
200 230 7.068348 GGAAAGGATCATGTGTAGAGTAGTACA 59.932 40.741 2.52 0.00 0.00 2.90
201 231 7.575414 AAGGATCATGTGTAGAGTAGTACAG 57.425 40.000 2.52 0.00 33.52 2.74
202 232 6.664714 AGGATCATGTGTAGAGTAGTACAGT 58.335 40.000 2.52 0.00 33.52 3.55
203 233 7.803131 AGGATCATGTGTAGAGTAGTACAGTA 58.197 38.462 2.52 0.00 33.52 2.74
204 234 8.441572 AGGATCATGTGTAGAGTAGTACAGTAT 58.558 37.037 2.52 0.00 33.52 2.12
205 235 9.722184 GGATCATGTGTAGAGTAGTACAGTATA 57.278 37.037 2.52 0.00 33.52 1.47
242 1962 1.959282 GGGGCAGGTCATCATTTGATC 59.041 52.381 0.00 0.00 36.54 2.92
270 1990 6.524586 GCACTAAAAGAACATGATTAGCACAC 59.475 38.462 0.00 0.00 0.00 3.82
303 2023 6.268158 AGACCGGCGAGATAGATAGATAGATA 59.732 42.308 9.30 0.00 0.00 1.98
304 2024 6.460781 ACCGGCGAGATAGATAGATAGATAG 58.539 44.000 9.30 0.00 0.00 2.08
305 2025 6.268158 ACCGGCGAGATAGATAGATAGATAGA 59.732 42.308 9.30 0.00 0.00 1.98
306 2026 7.038587 ACCGGCGAGATAGATAGATAGATAGAT 60.039 40.741 9.30 0.00 0.00 1.98
307 2027 8.471609 CCGGCGAGATAGATAGATAGATAGATA 58.528 40.741 9.30 0.00 0.00 1.98
308 2028 9.516314 CGGCGAGATAGATAGATAGATAGATAG 57.484 40.741 0.00 0.00 0.00 2.08
340 2060 4.823157 TCAACATCATTGCAAGGAAATGG 58.177 39.130 18.75 10.37 36.01 3.16
351 2071 2.988493 CAAGGAAATGGCGTTGTGAATG 59.012 45.455 0.00 0.00 0.00 2.67
381 2101 5.288472 GGATTTCCATTAACAAACACGATGC 59.712 40.000 0.00 0.00 35.64 3.91
382 2102 4.837896 TTCCATTAACAAACACGATGCA 57.162 36.364 0.00 0.00 0.00 3.96
383 2103 4.837896 TCCATTAACAAACACGATGCAA 57.162 36.364 0.00 0.00 0.00 4.08
385 2105 3.672867 CCATTAACAAACACGATGCAACC 59.327 43.478 0.00 0.00 0.00 3.77
386 2106 2.672188 TAACAAACACGATGCAACCG 57.328 45.000 9.84 9.84 0.00 4.44
387 2107 0.736053 AACAAACACGATGCAACCGT 59.264 45.000 11.07 11.07 41.36 4.83
400 2120 3.936902 GCAACCGTGCGAGATAAATAA 57.063 42.857 0.00 0.00 41.93 1.40
401 2121 3.861834 GCAACCGTGCGAGATAAATAAG 58.138 45.455 0.00 0.00 41.93 1.73
402 2122 3.554324 GCAACCGTGCGAGATAAATAAGA 59.446 43.478 0.00 0.00 41.93 2.10
403 2123 4.033587 GCAACCGTGCGAGATAAATAAGAA 59.966 41.667 0.00 0.00 41.93 2.52
404 2124 5.277345 GCAACCGTGCGAGATAAATAAGAAT 60.277 40.000 0.00 0.00 41.93 2.40
405 2125 6.355638 CAACCGTGCGAGATAAATAAGAATC 58.644 40.000 0.00 0.00 0.00 2.52
406 2126 5.844004 ACCGTGCGAGATAAATAAGAATCT 58.156 37.500 0.00 0.00 35.15 2.40
407 2127 6.978338 ACCGTGCGAGATAAATAAGAATCTA 58.022 36.000 0.00 0.00 32.60 1.98
408 2128 7.431249 ACCGTGCGAGATAAATAAGAATCTAA 58.569 34.615 0.00 0.00 32.60 2.10
409 2129 7.924412 ACCGTGCGAGATAAATAAGAATCTAAA 59.076 33.333 0.00 0.00 32.60 1.85
410 2130 8.926710 CCGTGCGAGATAAATAAGAATCTAAAT 58.073 33.333 0.00 0.00 32.60 1.40
411 2131 9.944941 CGTGCGAGATAAATAAGAATCTAAATC 57.055 33.333 0.00 0.00 32.60 2.17
422 2142 9.692325 AATAAGAATCTAAATCAGAAGGCAAGT 57.308 29.630 0.00 0.00 36.67 3.16
423 2143 9.692325 ATAAGAATCTAAATCAGAAGGCAAGTT 57.308 29.630 0.00 0.00 36.67 2.66
424 2144 7.388460 AGAATCTAAATCAGAAGGCAAGTTG 57.612 36.000 0.00 0.00 36.67 3.16
425 2145 6.376581 AGAATCTAAATCAGAAGGCAAGTTGG 59.623 38.462 4.75 0.00 36.67 3.77
426 2146 4.335416 TCTAAATCAGAAGGCAAGTTGGG 58.665 43.478 4.75 0.00 0.00 4.12
427 2147 1.928868 AATCAGAAGGCAAGTTGGGG 58.071 50.000 4.75 0.00 0.00 4.96
428 2148 0.613012 ATCAGAAGGCAAGTTGGGGC 60.613 55.000 4.75 0.00 0.00 5.80
434 2154 3.369921 GCAAGTTGGGGCCAGAAG 58.630 61.111 4.39 0.00 0.00 2.85
435 2155 1.531602 GCAAGTTGGGGCCAGAAGT 60.532 57.895 4.39 0.00 0.00 3.01
436 2156 1.809567 GCAAGTTGGGGCCAGAAGTG 61.810 60.000 4.39 0.00 0.00 3.16
437 2157 0.178992 CAAGTTGGGGCCAGAAGTGA 60.179 55.000 4.39 0.00 0.00 3.41
438 2158 0.111253 AAGTTGGGGCCAGAAGTGAG 59.889 55.000 4.39 0.00 0.00 3.51
439 2159 1.973812 GTTGGGGCCAGAAGTGAGC 60.974 63.158 4.39 0.00 0.00 4.26
440 2160 3.551496 TTGGGGCCAGAAGTGAGCG 62.551 63.158 4.39 0.00 0.00 5.03
442 2162 4.704833 GGGCCAGAAGTGAGCGCA 62.705 66.667 11.47 0.00 39.11 6.09
443 2163 3.123620 GGCCAGAAGTGAGCGCAG 61.124 66.667 11.47 0.00 0.00 5.18
468 2188 9.618890 AGTTAATGAATGAAGCTAAGCAATAGA 57.381 29.630 0.00 0.00 33.04 1.98
474 2194 7.279536 TGAATGAAGCTAAGCAATAGAAGACAG 59.720 37.037 0.00 0.00 33.04 3.51
495 2223 7.285401 AGACAGAGAGTTTTAAAGGAAATGCAA 59.715 33.333 0.00 0.00 0.00 4.08
509 2237 8.593492 AAGGAAATGCAAAACTTCATAAAGAC 57.407 30.769 0.00 0.00 36.30 3.01
522 2250 7.398024 ACTTCATAAAGACAAGGCATCTTACT 58.602 34.615 0.00 0.00 35.31 2.24
524 2252 9.553064 CTTCATAAAGACAAGGCATCTTACTAT 57.447 33.333 0.00 0.00 35.31 2.12
525 2253 8.893219 TCATAAAGACAAGGCATCTTACTATG 57.107 34.615 9.42 9.42 35.31 2.23
526 2254 8.486210 TCATAAAGACAAGGCATCTTACTATGT 58.514 33.333 12.60 0.00 35.31 2.29
527 2255 6.992063 AAAGACAAGGCATCTTACTATGTG 57.008 37.500 0.00 0.00 35.31 3.21
528 2256 4.446371 AGACAAGGCATCTTACTATGTGC 58.554 43.478 0.00 0.00 36.88 4.57
529 2257 4.080919 AGACAAGGCATCTTACTATGTGCA 60.081 41.667 0.00 0.00 39.27 4.57
530 2258 3.941483 ACAAGGCATCTTACTATGTGCAC 59.059 43.478 10.75 10.75 39.27 4.57
532 2260 5.104941 ACAAGGCATCTTACTATGTGCACTA 60.105 40.000 19.41 4.84 39.27 2.74
533 2261 5.614324 AGGCATCTTACTATGTGCACTAA 57.386 39.130 19.41 7.23 39.27 2.24
534 2262 6.179906 AGGCATCTTACTATGTGCACTAAT 57.820 37.500 19.41 6.65 39.27 1.73
535 2263 6.595682 AGGCATCTTACTATGTGCACTAATT 58.404 36.000 19.41 2.87 39.27 1.40
536 2264 7.056635 AGGCATCTTACTATGTGCACTAATTT 58.943 34.615 19.41 1.13 39.27 1.82
537 2265 7.227512 AGGCATCTTACTATGTGCACTAATTTC 59.772 37.037 19.41 0.00 39.27 2.17
538 2266 7.012327 GGCATCTTACTATGTGCACTAATTTCA 59.988 37.037 19.41 0.00 39.27 2.69
539 2267 8.562892 GCATCTTACTATGTGCACTAATTTCAT 58.437 33.333 19.41 3.58 37.52 2.57
551 2279 7.485913 GTGCACTAATTTCATCACCAATAACAG 59.514 37.037 10.32 0.00 0.00 3.16
557 2285 6.778834 TTTCATCACCAATAACAGATGCAT 57.221 33.333 0.00 0.00 38.15 3.96
584 2316 2.928801 TATGTGTGTGCTCTGTTGGT 57.071 45.000 0.00 0.00 0.00 3.67
603 2335 3.067833 GGTGCCACTAACTCTGAAGAAC 58.932 50.000 0.00 0.00 0.00 3.01
606 2338 3.067833 GCCACTAACTCTGAAGAACACC 58.932 50.000 0.00 0.00 0.00 4.16
644 2382 0.036671 CTGAGTGCAGGCATCAGTCA 60.037 55.000 17.78 13.42 40.45 3.41
678 2416 1.984570 CTCAGGGCCAAGGAGTCGA 60.985 63.158 6.18 0.00 0.00 4.20
679 2417 1.535444 TCAGGGCCAAGGAGTCGAA 60.535 57.895 6.18 0.00 0.00 3.71
754 2492 0.181350 GATCACCCATCACCCACTCC 59.819 60.000 0.00 0.00 0.00 3.85
755 2493 1.626356 ATCACCCATCACCCACTCCG 61.626 60.000 0.00 0.00 0.00 4.63
767 2505 2.033448 ACTCCGCCAAAATCCGCA 59.967 55.556 0.00 0.00 0.00 5.69
875 2630 9.118300 GGACATCATCATTAAACAAAGAGAGAT 57.882 33.333 0.00 0.00 0.00 2.75
893 2648 8.970859 AGAGAGATAGAGAGAGAGAAAGAAAG 57.029 38.462 0.00 0.00 0.00 2.62
894 2649 7.500559 AGAGAGATAGAGAGAGAGAAAGAAAGC 59.499 40.741 0.00 0.00 0.00 3.51
895 2650 6.260936 AGAGATAGAGAGAGAGAAAGAAAGCG 59.739 42.308 0.00 0.00 0.00 4.68
896 2651 3.866883 AGAGAGAGAGAAAGAAAGCGG 57.133 47.619 0.00 0.00 0.00 5.52
897 2652 3.426615 AGAGAGAGAGAAAGAAAGCGGA 58.573 45.455 0.00 0.00 0.00 5.54
944 2707 3.761752 CCAACGAACACCCAAGGAATAAT 59.238 43.478 0.00 0.00 0.00 1.28
953 2729 5.066593 CACCCAAGGAATAATAAGAGGAGC 58.933 45.833 0.00 0.00 0.00 4.70
1004 2780 1.089481 AACGCACGGCAGGACATATG 61.089 55.000 0.00 0.00 0.00 1.78
1008 2784 1.502231 CACGGCAGGACATATGCTAC 58.498 55.000 1.58 0.00 43.35 3.58
1017 2793 5.631026 CAGGACATATGCTACAACACAAAC 58.369 41.667 1.58 0.00 0.00 2.93
1348 3167 2.670148 GGCCTCCGTGGACCTCAAT 61.670 63.158 0.00 0.00 38.13 2.57
1522 3341 3.647771 ACCGGCAACTTCCCCTCC 61.648 66.667 0.00 0.00 0.00 4.30
1526 3345 2.539081 GGCAACTTCCCCTCCCAGT 61.539 63.158 0.00 0.00 0.00 4.00
1595 3414 5.294306 CGCATCATCATCATCATCATCATCA 59.706 40.000 0.00 0.00 0.00 3.07
1596 3415 6.017605 CGCATCATCATCATCATCATCATCAT 60.018 38.462 0.00 0.00 0.00 2.45
1597 3416 7.358830 GCATCATCATCATCATCATCATCATC 58.641 38.462 0.00 0.00 0.00 2.92
1598 3417 7.012704 GCATCATCATCATCATCATCATCATCA 59.987 37.037 0.00 0.00 0.00 3.07
1599 3418 9.064706 CATCATCATCATCATCATCATCATCAT 57.935 33.333 0.00 0.00 0.00 2.45
1600 3419 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
1601 3420 8.267183 TCATCATCATCATCATCATCATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
1602 3421 9.064706 CATCATCATCATCATCATCATCATCAT 57.935 33.333 0.00 0.00 0.00 2.45
1603 3422 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
2039 3858 3.482783 GAGCAGCTCAACGTCGCC 61.483 66.667 18.17 0.00 0.00 5.54
2051 3870 1.282570 CGTCGCCAACAACATGCTT 59.717 52.632 0.00 0.00 0.00 3.91
2354 4194 1.593196 CTTTGTGCCGTGAGAAAGGA 58.407 50.000 0.00 0.00 0.00 3.36
2363 4203 4.764823 TGCCGTGAGAAAGGATAAAAATGT 59.235 37.500 0.00 0.00 0.00 2.71
2494 4336 3.955650 TCTTTACCTGTTCCTTCCTCG 57.044 47.619 0.00 0.00 0.00 4.63
2531 4373 8.926710 CAATTGTTTAACAGTCTACTAGTCCTG 58.073 37.037 0.00 7.11 0.00 3.86
2542 4384 8.965819 CAGTCTACTAGTCCTGCATAATCATAT 58.034 37.037 0.00 0.00 0.00 1.78
2544 4386 8.194104 GTCTACTAGTCCTGCATAATCATATGG 58.806 40.741 0.00 0.00 39.49 2.74
2545 4387 5.738909 ACTAGTCCTGCATAATCATATGGC 58.261 41.667 2.13 0.00 39.49 4.40
2619 4467 1.696336 AGTTGGATCGATCTGGGATGG 59.304 52.381 23.96 0.00 0.00 3.51
2669 4517 8.778358 GTCAGAATTCAGTTCAGAATTAGTTGT 58.222 33.333 8.44 0.00 45.51 3.32
2710 4558 2.294449 AAAGTGGGAAAAGAGGGAGC 57.706 50.000 0.00 0.00 0.00 4.70
2711 4559 0.405973 AAGTGGGAAAAGAGGGAGCC 59.594 55.000 0.00 0.00 0.00 4.70
2750 4598 7.650903 TCTCTGTAAAGGTTTAAAAGACGACTC 59.349 37.037 0.00 0.00 0.00 3.36
2811 4659 5.423931 TGAACCCTGGGGATTTATAAAAAGC 59.576 40.000 18.88 0.00 38.96 3.51
2850 4698 1.230324 GGCAGCTCGGATATCAAACC 58.770 55.000 4.83 0.00 0.00 3.27
2935 4783 1.482593 AGAGGACGGAGCAAGTAATGG 59.517 52.381 0.00 0.00 0.00 3.16
3036 4886 6.183360 GCAATTGATAACGATTGGTCAGAGAA 60.183 38.462 10.34 0.00 44.01 2.87
3059 4909 8.890718 AGAAGAATTAATAAAAAGCGAGTACCC 58.109 33.333 0.00 0.00 0.00 3.69
3068 4918 0.968901 AGCGAGTACCCGTTCATGGA 60.969 55.000 0.00 0.00 0.00 3.41
3237 5087 2.425539 CCAACCCATGTGAATTTTGCC 58.574 47.619 0.00 0.00 0.00 4.52
3261 5111 0.940126 GACCTTGTCACACACAGCAG 59.060 55.000 0.00 0.00 35.97 4.24
3266 5116 1.091197 TGTCACACACAGCAGCACAG 61.091 55.000 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.061131 CCTGCACGAATGTTGACGATC 59.939 52.381 0.00 0.00 0.00 3.69
30 31 1.686355 TCAGCACAAACCACCGAAAT 58.314 45.000 0.00 0.00 0.00 2.17
31 32 1.686355 ATCAGCACAAACCACCGAAA 58.314 45.000 0.00 0.00 0.00 3.46
32 33 1.336440 CAATCAGCACAAACCACCGAA 59.664 47.619 0.00 0.00 0.00 4.30
197 227 9.316730 CCGGCAAAGTATTAGTTTTATACTGTA 57.683 33.333 0.00 0.00 38.48 2.74
198 228 7.281549 CCCGGCAAAGTATTAGTTTTATACTGT 59.718 37.037 0.00 0.00 38.48 3.55
199 229 7.255001 CCCCGGCAAAGTATTAGTTTTATACTG 60.255 40.741 0.00 0.00 38.48 2.74
200 230 6.769341 CCCCGGCAAAGTATTAGTTTTATACT 59.231 38.462 0.00 0.00 39.80 2.12
201 231 6.513884 GCCCCGGCAAAGTATTAGTTTTATAC 60.514 42.308 0.00 0.00 41.49 1.47
202 232 5.532032 GCCCCGGCAAAGTATTAGTTTTATA 59.468 40.000 0.00 0.00 41.49 0.98
203 233 4.340097 GCCCCGGCAAAGTATTAGTTTTAT 59.660 41.667 0.00 0.00 41.49 1.40
204 234 3.695556 GCCCCGGCAAAGTATTAGTTTTA 59.304 43.478 0.00 0.00 41.49 1.52
205 235 2.494471 GCCCCGGCAAAGTATTAGTTTT 59.506 45.455 0.00 0.00 41.49 2.43
206 236 2.097036 GCCCCGGCAAAGTATTAGTTT 58.903 47.619 0.00 0.00 41.49 2.66
207 237 1.758936 GCCCCGGCAAAGTATTAGTT 58.241 50.000 0.00 0.00 41.49 2.24
208 238 3.489391 GCCCCGGCAAAGTATTAGT 57.511 52.632 0.00 0.00 41.49 2.24
219 249 3.721370 AATGATGACCTGCCCCGGC 62.721 63.158 0.00 0.00 42.35 6.13
222 1942 1.959282 GATCAAATGATGACCTGCCCC 59.041 52.381 0.00 0.00 41.93 5.80
242 1962 6.127925 TGCTAATCATGTTCTTTTAGTGCTGG 60.128 38.462 0.00 0.00 0.00 4.85
270 1990 2.509052 TCTCGCCGGTCTTGATTATG 57.491 50.000 1.90 0.00 0.00 1.90
311 2031 8.929260 TTCCTTGCAATGATGTTGATATATCT 57.071 30.769 13.79 0.00 0.00 1.98
313 2033 9.923143 CATTTCCTTGCAATGATGTTGATATAT 57.077 29.630 5.20 0.00 34.05 0.86
314 2034 8.361889 CCATTTCCTTGCAATGATGTTGATATA 58.638 33.333 5.20 0.00 34.05 0.86
315 2035 7.214381 CCATTTCCTTGCAATGATGTTGATAT 58.786 34.615 5.20 0.00 34.05 1.63
316 2036 6.575267 CCATTTCCTTGCAATGATGTTGATA 58.425 36.000 5.20 0.00 34.05 2.15
317 2037 5.424757 CCATTTCCTTGCAATGATGTTGAT 58.575 37.500 5.20 0.00 34.05 2.57
318 2038 4.823157 CCATTTCCTTGCAATGATGTTGA 58.177 39.130 5.20 0.00 34.05 3.18
340 2060 0.605319 TCCTCACCCATTCACAACGC 60.605 55.000 0.00 0.00 0.00 4.84
351 2071 5.245075 TGTTTGTTAATGGAAATCCTCACCC 59.755 40.000 0.44 0.00 36.82 4.61
381 2101 5.712217 TTCTTATTTATCTCGCACGGTTG 57.288 39.130 0.00 0.00 0.00 3.77
382 2102 6.281405 AGATTCTTATTTATCTCGCACGGTT 58.719 36.000 0.00 0.00 0.00 4.44
383 2103 5.844004 AGATTCTTATTTATCTCGCACGGT 58.156 37.500 0.00 0.00 0.00 4.83
385 2105 9.944941 GATTTAGATTCTTATTTATCTCGCACG 57.055 33.333 0.00 0.00 33.38 5.34
396 2116 9.692325 ACTTGCCTTCTGATTTAGATTCTTATT 57.308 29.630 0.00 0.00 34.80 1.40
398 2118 8.950210 CAACTTGCCTTCTGATTTAGATTCTTA 58.050 33.333 0.00 0.00 34.80 2.10
399 2119 7.094032 CCAACTTGCCTTCTGATTTAGATTCTT 60.094 37.037 0.00 0.00 34.80 2.52
400 2120 6.376581 CCAACTTGCCTTCTGATTTAGATTCT 59.623 38.462 0.00 0.00 34.80 2.40
401 2121 6.405176 CCCAACTTGCCTTCTGATTTAGATTC 60.405 42.308 0.00 0.00 34.80 2.52
402 2122 5.420104 CCCAACTTGCCTTCTGATTTAGATT 59.580 40.000 0.00 0.00 34.80 2.40
403 2123 4.952335 CCCAACTTGCCTTCTGATTTAGAT 59.048 41.667 0.00 0.00 34.80 1.98
404 2124 4.335416 CCCAACTTGCCTTCTGATTTAGA 58.665 43.478 0.00 0.00 0.00 2.10
405 2125 3.445096 CCCCAACTTGCCTTCTGATTTAG 59.555 47.826 0.00 0.00 0.00 1.85
406 2126 3.430453 CCCCAACTTGCCTTCTGATTTA 58.570 45.455 0.00 0.00 0.00 1.40
407 2127 2.250924 CCCCAACTTGCCTTCTGATTT 58.749 47.619 0.00 0.00 0.00 2.17
408 2128 1.928868 CCCCAACTTGCCTTCTGATT 58.071 50.000 0.00 0.00 0.00 2.57
409 2129 0.613012 GCCCCAACTTGCCTTCTGAT 60.613 55.000 0.00 0.00 0.00 2.90
410 2130 1.228552 GCCCCAACTTGCCTTCTGA 60.229 57.895 0.00 0.00 0.00 3.27
411 2131 2.278330 GGCCCCAACTTGCCTTCTG 61.278 63.158 0.00 0.00 44.46 3.02
412 2132 2.118294 GGCCCCAACTTGCCTTCT 59.882 61.111 0.00 0.00 44.46 2.85
417 2137 1.531602 ACTTCTGGCCCCAACTTGC 60.532 57.895 0.00 0.00 0.00 4.01
418 2138 0.178992 TCACTTCTGGCCCCAACTTG 60.179 55.000 0.00 0.00 0.00 3.16
419 2139 0.111253 CTCACTTCTGGCCCCAACTT 59.889 55.000 0.00 0.00 0.00 2.66
420 2140 1.763770 CTCACTTCTGGCCCCAACT 59.236 57.895 0.00 0.00 0.00 3.16
421 2141 1.973812 GCTCACTTCTGGCCCCAAC 60.974 63.158 0.00 0.00 0.00 3.77
422 2142 2.436109 GCTCACTTCTGGCCCCAA 59.564 61.111 0.00 0.00 0.00 4.12
423 2143 4.020617 CGCTCACTTCTGGCCCCA 62.021 66.667 0.00 0.00 0.00 4.96
425 2145 4.704833 TGCGCTCACTTCTGGCCC 62.705 66.667 9.73 0.00 0.00 5.80
426 2146 3.123620 CTGCGCTCACTTCTGGCC 61.124 66.667 9.73 0.00 0.00 5.36
427 2147 0.670546 TAACTGCGCTCACTTCTGGC 60.671 55.000 9.73 0.00 0.00 4.85
428 2148 1.795768 TTAACTGCGCTCACTTCTGG 58.204 50.000 9.73 0.00 0.00 3.86
429 2149 2.995939 TCATTAACTGCGCTCACTTCTG 59.004 45.455 9.73 0.00 0.00 3.02
430 2150 3.319137 TCATTAACTGCGCTCACTTCT 57.681 42.857 9.73 0.00 0.00 2.85
431 2151 4.093408 TCATTCATTAACTGCGCTCACTTC 59.907 41.667 9.73 0.00 0.00 3.01
432 2152 4.002982 TCATTCATTAACTGCGCTCACTT 58.997 39.130 9.73 0.00 0.00 3.16
433 2153 3.599343 TCATTCATTAACTGCGCTCACT 58.401 40.909 9.73 0.00 0.00 3.41
434 2154 4.337763 CTTCATTCATTAACTGCGCTCAC 58.662 43.478 9.73 0.00 0.00 3.51
435 2155 3.181507 GCTTCATTCATTAACTGCGCTCA 60.182 43.478 9.73 0.00 0.00 4.26
436 2156 3.064545 AGCTTCATTCATTAACTGCGCTC 59.935 43.478 9.73 0.00 0.00 5.03
437 2157 3.012518 AGCTTCATTCATTAACTGCGCT 58.987 40.909 9.73 0.00 0.00 5.92
438 2158 3.411415 AGCTTCATTCATTAACTGCGC 57.589 42.857 0.00 0.00 0.00 6.09
439 2159 4.966366 GCTTAGCTTCATTCATTAACTGCG 59.034 41.667 0.00 0.00 0.00 5.18
440 2160 5.883661 TGCTTAGCTTCATTCATTAACTGC 58.116 37.500 5.60 0.00 0.00 4.40
441 2161 9.661187 CTATTGCTTAGCTTCATTCATTAACTG 57.339 33.333 5.60 0.00 0.00 3.16
442 2162 9.618890 TCTATTGCTTAGCTTCATTCATTAACT 57.381 29.630 5.60 0.00 0.00 2.24
468 2188 7.285401 TGCATTTCCTTTAAAACTCTCTGTCTT 59.715 33.333 0.00 0.00 0.00 3.01
474 2194 8.648557 AGTTTTGCATTTCCTTTAAAACTCTC 57.351 30.769 0.00 0.00 43.94 3.20
491 2219 5.163468 TGCCTTGTCTTTATGAAGTTTTGCA 60.163 36.000 0.00 0.00 34.41 4.08
495 2223 7.530426 AAGATGCCTTGTCTTTATGAAGTTT 57.470 32.000 0.00 0.00 32.17 2.66
509 2237 4.194640 AGTGCACATAGTAAGATGCCTTG 58.805 43.478 21.04 0.00 37.26 3.61
522 2250 7.643569 ATTGGTGATGAAATTAGTGCACATA 57.356 32.000 21.04 6.49 0.00 2.29
524 2252 5.981088 ATTGGTGATGAAATTAGTGCACA 57.019 34.783 21.04 0.00 0.00 4.57
525 2253 7.312154 TGTTATTGGTGATGAAATTAGTGCAC 58.688 34.615 9.40 9.40 0.00 4.57
526 2254 7.392953 TCTGTTATTGGTGATGAAATTAGTGCA 59.607 33.333 0.00 0.00 0.00 4.57
527 2255 7.761409 TCTGTTATTGGTGATGAAATTAGTGC 58.239 34.615 0.00 0.00 0.00 4.40
528 2256 9.726232 CATCTGTTATTGGTGATGAAATTAGTG 57.274 33.333 0.00 0.00 38.72 2.74
529 2257 8.408601 GCATCTGTTATTGGTGATGAAATTAGT 58.591 33.333 0.00 0.00 38.72 2.24
530 2258 8.407832 TGCATCTGTTATTGGTGATGAAATTAG 58.592 33.333 0.00 0.00 38.72 1.73
532 2260 7.172868 TGCATCTGTTATTGGTGATGAAATT 57.827 32.000 0.00 0.00 38.72 1.82
533 2261 6.778834 TGCATCTGTTATTGGTGATGAAAT 57.221 33.333 0.00 0.00 38.72 2.17
534 2262 6.778834 ATGCATCTGTTATTGGTGATGAAA 57.221 33.333 0.00 0.00 38.72 2.69
535 2263 7.878547 TTATGCATCTGTTATTGGTGATGAA 57.121 32.000 0.19 0.00 38.72 2.57
536 2264 9.002600 GTATTATGCATCTGTTATTGGTGATGA 57.997 33.333 0.19 0.00 38.72 2.92
537 2265 9.006839 AGTATTATGCATCTGTTATTGGTGATG 57.993 33.333 0.19 0.00 39.24 3.07
538 2266 9.578576 AAGTATTATGCATCTGTTATTGGTGAT 57.421 29.630 0.19 0.00 0.00 3.06
539 2267 8.978874 AAGTATTATGCATCTGTTATTGGTGA 57.021 30.769 0.19 0.00 0.00 4.02
557 2285 7.119116 CCAACAGAGCACACACATAAAGTATTA 59.881 37.037 0.00 0.00 0.00 0.98
568 2300 1.356624 GCACCAACAGAGCACACAC 59.643 57.895 0.00 0.00 0.00 3.82
572 2304 0.250295 TAGTGGCACCAACAGAGCAC 60.250 55.000 15.27 0.00 0.00 4.40
584 2316 3.494398 GGTGTTCTTCAGAGTTAGTGGCA 60.494 47.826 0.00 0.00 0.00 4.92
603 2335 1.535462 GACAAAATCCCACTGACGGTG 59.465 52.381 7.49 7.49 44.96 4.94
606 2338 2.494059 AGTGACAAAATCCCACTGACG 58.506 47.619 0.00 0.00 39.43 4.35
644 2382 1.341531 CTGAGGACACGGTCAAAGACT 59.658 52.381 6.41 0.00 33.68 3.24
678 2416 0.732571 CTGTCGTGTGCCTTTGTGTT 59.267 50.000 0.00 0.00 0.00 3.32
679 2417 1.714899 GCTGTCGTGTGCCTTTGTGT 61.715 55.000 0.00 0.00 0.00 3.72
703 2441 3.439857 TTCCTGCCTAGCAAATTGACT 57.560 42.857 0.00 0.00 38.41 3.41
728 2466 0.527817 GTGATGGGTGATCGTCCGTC 60.528 60.000 15.53 15.53 39.02 4.79
754 2492 1.013596 TCATACTGCGGATTTTGGCG 58.986 50.000 0.00 0.00 0.00 5.69
755 2493 2.163412 TGTTCATACTGCGGATTTTGGC 59.837 45.455 0.00 0.00 0.00 4.52
767 2505 2.222729 GCGACGCGATTTTGTTCATACT 60.223 45.455 15.93 0.00 0.00 2.12
822 2560 1.876497 ATTGGCGCGCATCCAAAACT 61.876 50.000 34.42 13.96 45.63 2.66
875 2630 4.396790 GTCCGCTTTCTTTCTCTCTCTCTA 59.603 45.833 0.00 0.00 0.00 2.43
883 2638 3.498397 TGTTCATGTCCGCTTTCTTTCTC 59.502 43.478 0.00 0.00 0.00 2.87
893 2648 1.882198 CATCGTTTGTTCATGTCCGC 58.118 50.000 0.00 0.00 0.00 5.54
894 2649 1.196581 TGCATCGTTTGTTCATGTCCG 59.803 47.619 0.00 0.00 0.00 4.79
895 2650 2.226437 AGTGCATCGTTTGTTCATGTCC 59.774 45.455 0.00 0.00 0.00 4.02
896 2651 3.482786 GAGTGCATCGTTTGTTCATGTC 58.517 45.455 0.00 0.00 0.00 3.06
897 2652 2.096268 CGAGTGCATCGTTTGTTCATGT 60.096 45.455 9.48 0.00 46.62 3.21
921 2684 1.104577 TTCCTTGGGTGTTCGTTGGC 61.105 55.000 0.00 0.00 0.00 4.52
944 2707 2.584608 GGCGCCTTGCTCCTCTTA 59.415 61.111 22.15 0.00 45.43 2.10
1004 2780 2.303175 TCTTGGGGTTTGTGTTGTAGC 58.697 47.619 0.00 0.00 0.00 3.58
1008 2784 4.464069 TCTTTTCTTGGGGTTTGTGTTG 57.536 40.909 0.00 0.00 0.00 3.33
1017 2793 1.271656 CTGCTGCTTCTTTTCTTGGGG 59.728 52.381 0.00 0.00 0.00 4.96
1165 2984 2.664851 TCCAGCCGCGAGTTGTTG 60.665 61.111 8.23 0.00 0.00 3.33
1522 3341 2.674220 GGGGAGGCAGAGGAACTGG 61.674 68.421 0.00 0.00 45.82 4.00
1526 3345 2.592993 CGTTGGGGAGGCAGAGGAA 61.593 63.158 0.00 0.00 0.00 3.36
1733 3552 1.592064 TGTTGTTGATGAAGAGCGCA 58.408 45.000 11.47 0.00 0.00 6.09
2009 3828 1.070275 CTGCTCGAGGGCATGCATA 59.930 57.895 21.36 0.00 41.63 3.14
2014 3833 2.663075 TTGAGCTGCTCGAGGGCAT 61.663 57.895 23.35 0.00 41.63 4.40
2015 3834 3.313524 TTGAGCTGCTCGAGGGCA 61.314 61.111 23.35 6.89 40.15 5.36
2039 3858 2.023223 GCCGGCAAGCATGTTGTTG 61.023 57.895 24.80 0.00 0.00 3.33
2494 4336 9.952341 GACTGTTAAACAATTGTTTCTTGAAAC 57.048 29.630 33.71 29.07 44.15 2.78
2531 4373 5.174398 GCGCATTATTGCCATATGATTATGC 59.826 40.000 0.30 9.93 46.57 3.14
2542 4384 3.715495 CCAAATTAGCGCATTATTGCCA 58.285 40.909 11.47 0.00 46.57 4.92
2544 4386 3.776043 GCCAAATTAGCGCATTATTGC 57.224 42.857 11.47 0.00 45.78 3.56
2619 4467 2.019156 GCATGGCCCCTCAACTAACTC 61.019 57.143 0.00 0.00 0.00 3.01
2669 4517 3.185880 AGCAGTGGTCCTAAGTCCTAA 57.814 47.619 0.00 0.00 0.00 2.69
2710 4558 7.661847 ACCTTTACAGAGAAAAACAGTGATAGG 59.338 37.037 0.00 0.00 0.00 2.57
2711 4559 8.608844 ACCTTTACAGAGAAAAACAGTGATAG 57.391 34.615 0.00 0.00 0.00 2.08
2750 4598 6.746745 TTGGGTTATTTAGTTTAGCCGAAG 57.253 37.500 0.00 0.00 0.00 3.79
2850 4698 1.475682 GAAATGGAGCTCTTTGGCAGG 59.524 52.381 14.64 0.00 34.17 4.85
3014 4864 6.878317 TCTTCTCTGACCAATCGTTATCAAT 58.122 36.000 0.00 0.00 0.00 2.57
3036 4886 6.820152 ACGGGTACTCGCTTTTTATTAATTCT 59.180 34.615 16.75 0.00 0.00 2.40
3059 4909 0.379669 GCAGCTGGAATCCATGAACG 59.620 55.000 17.12 0.00 30.82 3.95
3068 4918 0.324091 CCCCTCTTTGCAGCTGGAAT 60.324 55.000 22.04 0.00 0.00 3.01
3237 5087 0.304705 GTGTGTGACAAGGTCAAGCG 59.695 55.000 0.00 0.00 44.49 4.68
3261 5111 2.478134 CAGTTGTCTGAGCTTACTGTGC 59.522 50.000 0.00 0.00 43.76 4.57


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

AutoCloner maintained by Alex Coulton.