Multiple sequence alignment - TraesCS2B01G528500

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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 TraesCS2B01G528500 chr2B 100.000 2309 0 0 1 2309 722861712 722864020 0.000000e+00 4265.0
1 TraesCS2B01G528500 chr2D 90.599 2255 101 54 1 2189 595210800 595213009 0.000000e+00 2887.0
2 TraesCS2B01G528500 chr2D 91.176 68 6 0 1829 1896 595212531 595212598 2.440000e-15 93.5
3 TraesCS2B01G528500 chr2A 83.272 1094 85 61 502 1541 729346339 729347388 0.000000e+00 917.0
4 TraesCS2B01G528500 chr2A 87.800 459 45 7 1829 2279 729347618 729348073 5.650000e-146 527.0
5 TraesCS2B01G528500 chr2A 88.197 305 28 6 1484 1781 729347383 729347686 7.850000e-95 357.0


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 TraesCS2B01G528500 chr2B 722861712 722864020 2308 False 4265.000000 4265 100.0000 1 2309 1 chr2B.!!$F1 2308
1 TraesCS2B01G528500 chr2D 595210800 595213009 2209 False 1490.250000 2887 90.8875 1 2189 2 chr2D.!!$F1 2188
2 TraesCS2B01G528500 chr2A 729346339 729348073 1734 False 600.333333 917 86.4230 502 2279 3 chr2A.!!$F1 1777

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
395 412 0.032515 TTGACGCCTCCTCCCTCATA 60.033 55.0 0.0 0.0 0.0 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1419 1530 1.032657 TTCTTCTCCTCCTCCGCTCG 61.033 60.0 0.0 0.0 0.0 5.03 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
19 20 1.876664 GCAGGGACTTTCGAAAGCC 59.123 57.895 32.49 30.23 39.63 4.35
97 103 2.220133 CCACGTACTGACCAAACGAAAG 59.780 50.000 10.30 2.56 39.80 2.62
100 106 2.729882 CGTACTGACCAAACGAAAGGAG 59.270 50.000 0.00 0.00 38.89 3.69
112 118 6.909357 CCAAACGAAAGGAGTACTATACTACG 59.091 42.308 0.00 7.36 44.55 3.51
159 165 1.661821 CATACGCCGTCCAGCTAGC 60.662 63.158 6.62 6.62 0.00 3.42
164 170 2.202623 CCGTCCAGCTAGCGACAC 60.203 66.667 18.89 11.68 0.00 3.67
168 174 2.262603 CCAGCTAGCGACACTGCA 59.737 61.111 9.55 0.00 37.31 4.41
171 177 3.549150 GCTAGCGACACTGCAGCG 61.549 66.667 15.27 10.91 37.31 5.18
172 178 2.179267 CTAGCGACACTGCAGCGA 59.821 61.111 15.27 0.00 37.31 4.93
173 179 1.871345 CTAGCGACACTGCAGCGAG 60.871 63.158 15.27 6.75 37.31 5.03
174 180 3.971453 TAGCGACACTGCAGCGAGC 62.971 63.158 15.27 15.35 45.96 5.03
183 191 3.337889 GCAGCGAGCACACGACAA 61.338 61.111 0.00 0.00 44.79 3.18
190 198 2.472397 GCGAGCACACGACAATAAAGTC 60.472 50.000 0.00 0.00 35.09 3.01
202 210 0.175073 ATAAAGTCGACGACCTGGCC 59.825 55.000 23.76 0.00 32.18 5.36
218 228 4.344390 ACCTGGCCTAGTACTAAATGTAGC 59.656 45.833 3.32 0.93 0.00 3.58
246 260 3.704609 CGTGCGTTTTACGGGCGT 61.705 61.111 1.14 0.00 42.82 5.68
262 276 1.401552 GGCGTGCAGATAATTGCTTGA 59.598 47.619 0.00 0.00 44.38 3.02
279 296 3.067320 GCTTGATTAGCTTGATTGGGTCC 59.933 47.826 0.00 0.00 46.77 4.46
284 301 0.846427 AGCTTGATTGGGTCCTGGGA 60.846 55.000 0.00 0.00 0.00 4.37
303 320 2.373269 GAGCGTAGTACATGCACGTAG 58.627 52.381 0.00 0.00 42.04 3.51
393 410 2.119611 TTGACGCCTCCTCCCTCA 59.880 61.111 0.00 0.00 0.00 3.86
394 411 1.306141 TTGACGCCTCCTCCCTCAT 60.306 57.895 0.00 0.00 0.00 2.90
395 412 0.032515 TTGACGCCTCCTCCCTCATA 60.033 55.000 0.00 0.00 0.00 2.15
396 413 0.032515 TGACGCCTCCTCCCTCATAA 60.033 55.000 0.00 0.00 0.00 1.90
397 414 0.676736 GACGCCTCCTCCCTCATAAG 59.323 60.000 0.00 0.00 0.00 1.73
398 415 1.369321 CGCCTCCTCCCTCATAAGC 59.631 63.158 0.00 0.00 0.00 3.09
399 416 1.757949 GCCTCCTCCCTCATAAGCC 59.242 63.158 0.00 0.00 0.00 4.35
403 420 3.251484 CCTCCTCCCTCATAAGCCATAA 58.749 50.000 0.00 0.00 0.00 1.90
414 431 7.405292 CCTCATAAGCCATAATAATCCTTGGA 58.595 38.462 0.00 0.00 0.00 3.53
425 442 2.773525 ATCCTTGGAGAGAGAGAGGG 57.226 55.000 0.00 0.00 0.00 4.30
426 443 1.687492 TCCTTGGAGAGAGAGAGGGA 58.313 55.000 0.00 0.00 0.00 4.20
427 444 1.568597 TCCTTGGAGAGAGAGAGGGAG 59.431 57.143 0.00 0.00 0.00 4.30
428 445 1.568597 CCTTGGAGAGAGAGAGGGAGA 59.431 57.143 0.00 0.00 0.00 3.71
449 466 3.331150 AGAGACTAGACGAGTGTGAGTG 58.669 50.000 0.00 0.00 39.06 3.51
450 467 3.068560 GAGACTAGACGAGTGTGAGTGT 58.931 50.000 0.00 0.00 39.06 3.55
451 468 2.809119 AGACTAGACGAGTGTGAGTGTG 59.191 50.000 0.00 0.00 39.06 3.82
452 469 2.806818 GACTAGACGAGTGTGAGTGTGA 59.193 50.000 0.00 0.00 39.06 3.58
453 470 2.809119 ACTAGACGAGTGTGAGTGTGAG 59.191 50.000 0.00 0.00 36.87 3.51
454 471 1.681538 AGACGAGTGTGAGTGTGAGT 58.318 50.000 0.00 0.00 0.00 3.41
455 472 1.335182 AGACGAGTGTGAGTGTGAGTG 59.665 52.381 0.00 0.00 0.00 3.51
456 473 1.065701 GACGAGTGTGAGTGTGAGTGT 59.934 52.381 0.00 0.00 0.00 3.55
457 474 1.202302 ACGAGTGTGAGTGTGAGTGTG 60.202 52.381 0.00 0.00 0.00 3.82
458 475 1.065551 CGAGTGTGAGTGTGAGTGTGA 59.934 52.381 0.00 0.00 0.00 3.58
459 476 2.736978 GAGTGTGAGTGTGAGTGTGAG 58.263 52.381 0.00 0.00 0.00 3.51
460 477 2.099921 GAGTGTGAGTGTGAGTGTGAGT 59.900 50.000 0.00 0.00 0.00 3.41
461 478 2.159184 AGTGTGAGTGTGAGTGTGAGTG 60.159 50.000 0.00 0.00 0.00 3.51
470 487 0.882042 GAGTGTGAGTGTGCAGTGGG 60.882 60.000 0.00 0.00 0.00 4.61
474 491 0.106708 GTGAGTGTGCAGTGGGAGAA 59.893 55.000 0.00 0.00 0.00 2.87
561 584 3.055021 CCATCCATCCATCTGATCTGAGG 60.055 52.174 8.37 7.79 0.00 3.86
617 651 2.196749 CTCTGTGTGTGTGTGTGTCTC 58.803 52.381 0.00 0.00 0.00 3.36
623 657 1.001706 GTGTGTGTGTGTCTCTCGCTA 60.002 52.381 0.00 0.00 0.00 4.26
791 836 1.066071 CACCATTGCCATTGCCATTGA 60.066 47.619 0.00 0.00 36.33 2.57
831 885 2.197324 CTCCCGCTAGCCTCTCCT 59.803 66.667 9.66 0.00 0.00 3.69
865 920 0.679505 TCTTTGACTCCACTCCACCG 59.320 55.000 0.00 0.00 0.00 4.94
919 1005 4.206200 CACGCCAAAACATTCACTTGTTAC 59.794 41.667 0.00 0.00 38.85 2.50
925 1011 7.306574 GCCAAAACATTCACTTGTTACTTAAGC 60.307 37.037 1.29 0.00 38.85 3.09
926 1012 7.920682 CCAAAACATTCACTTGTTACTTAAGCT 59.079 33.333 1.29 0.00 38.85 3.74
927 1013 9.301153 CAAAACATTCACTTGTTACTTAAGCTT 57.699 29.630 3.48 3.48 38.85 3.74
948 1034 0.460722 TTGCTTGCTTGCTTGCTTGA 59.539 45.000 10.35 0.00 0.00 3.02
951 1037 1.767289 CTTGCTTGCTTGCTTGAGTG 58.233 50.000 3.47 0.00 0.00 3.51
1148 1245 3.168604 CGTGAGCGCTGACGACAG 61.169 66.667 40.19 14.30 42.67 3.51
1317 1428 2.592897 GCACAACAGATGAGTACGTACG 59.407 50.000 19.49 15.01 0.00 3.67
1319 1430 4.089341 CACAACAGATGAGTACGTACGAG 58.911 47.826 24.41 9.63 0.00 4.18
1320 1431 3.099362 CAACAGATGAGTACGTACGAGC 58.901 50.000 24.41 13.65 0.00 5.03
1385 1496 1.717791 CGTCGGTCCGTATACTGGCA 61.718 60.000 11.88 0.00 30.45 4.92
1439 1550 1.408969 GAGCGGAGGAGGAGAAGAAT 58.591 55.000 0.00 0.00 0.00 2.40
1568 1733 5.662456 ACTACTAGCTAGCTACCTTTTTGC 58.338 41.667 20.67 0.00 0.00 3.68
1598 1764 5.177511 GTCTTTTGCCCTTATTTTCTTGTGC 59.822 40.000 0.00 0.00 0.00 4.57
1602 1768 2.567169 GCCCTTATTTTCTTGTGCCCTT 59.433 45.455 0.00 0.00 0.00 3.95
1654 1820 6.404074 GCCATTCTGTTGGTTGAAAGAGATAG 60.404 42.308 0.00 0.00 39.11 2.08
1747 1917 2.559440 GATCTTGCCTCAGATCACACC 58.441 52.381 11.10 0.00 46.04 4.16
1755 1925 2.154462 CTCAGATCACACCCACCAAAC 58.846 52.381 0.00 0.00 0.00 2.93
1756 1926 1.202879 TCAGATCACACCCACCAAACC 60.203 52.381 0.00 0.00 0.00 3.27
1764 1934 0.185175 ACCCACCAAACCTTCACCTC 59.815 55.000 0.00 0.00 0.00 3.85
1768 1938 1.676006 CACCAAACCTTCACCTCACAC 59.324 52.381 0.00 0.00 0.00 3.82
1789 1959 3.056322 ACTGATTTTCCTTGCTGCATTCC 60.056 43.478 1.84 0.00 0.00 3.01
1792 1962 4.040706 TGATTTTCCTTGCTGCATTCCTTT 59.959 37.500 1.84 0.00 0.00 3.11
1824 1994 4.571984 TCTCCGCTTCATTATGTTGACATG 59.428 41.667 6.87 0.00 37.15 3.21
1826 1996 4.699735 TCCGCTTCATTATGTTGACATGTT 59.300 37.500 0.00 0.00 37.15 2.71
1828 1998 5.391843 CCGCTTCATTATGTTGACATGTTGA 60.392 40.000 0.00 6.76 37.15 3.18
1835 2005 8.764287 TCATTATGTTGACATGTTGACGATATC 58.236 33.333 0.00 0.00 37.15 1.63
1872 2042 2.414481 CTGAGATCACACGGAGCAAAAG 59.586 50.000 0.00 0.00 33.23 2.27
1887 2057 5.009610 GGAGCAAAAGTTCACCTTACATTGA 59.990 40.000 0.00 0.00 31.48 2.57
1933 2107 3.304458 GGCTGTAAAGTTGTTACCAGCAC 60.304 47.826 11.08 0.00 34.15 4.40
1974 2148 5.065474 TCTGTCAAACGTTTCCGAAGAAAAT 59.935 36.000 11.37 0.00 43.48 1.82
1978 2152 4.483476 AACGTTTCCGAAGAAAATGGAG 57.517 40.909 0.00 0.00 43.48 3.86
1982 2156 1.438651 TCCGAAGAAAATGGAGTGCG 58.561 50.000 0.00 0.00 0.00 5.34
2162 2341 4.684120 TGAACGCATCAATCGATCGATCG 61.684 47.826 35.91 35.91 42.57 3.69
2189 2368 3.716006 GCGAGCGCACTTTGAGCA 61.716 61.111 11.47 0.00 45.82 4.26
2190 2369 2.171940 CGAGCGCACTTTGAGCAC 59.828 61.111 11.47 0.00 45.82 4.40
2192 2371 1.008875 CGAGCGCACTTTGAGCACTA 61.009 55.000 11.47 0.00 45.82 2.74
2193 2372 1.148310 GAGCGCACTTTGAGCACTAA 58.852 50.000 11.47 0.00 45.82 2.24
2194 2373 1.531149 GAGCGCACTTTGAGCACTAAA 59.469 47.619 11.47 0.00 45.82 1.85
2198 2377 3.735746 GCGCACTTTGAGCACTAAATTTT 59.264 39.130 0.30 0.00 42.85 1.82
2203 2382 5.403466 CACTTTGAGCACTAAATTTTGGAGC 59.597 40.000 6.78 6.78 0.00 4.70
2217 2396 7.910441 AATTTTGGAGCACTATCATTTTTGG 57.090 32.000 0.00 0.00 0.00 3.28
2218 2397 5.404466 TTTGGAGCACTATCATTTTTGGG 57.596 39.130 0.00 0.00 0.00 4.12
2227 2409 6.572119 GCACTATCATTTTTGGGTTGTGATGA 60.572 38.462 0.00 0.00 32.31 2.92
2231 2413 5.468592 TCATTTTTGGGTTGTGATGATTCG 58.531 37.500 0.00 0.00 0.00 3.34
2233 2415 4.497473 TTTTGGGTTGTGATGATTCGTC 57.503 40.909 0.00 0.00 0.00 4.20
2236 2418 3.750371 TGGGTTGTGATGATTCGTCTTT 58.250 40.909 7.38 0.00 0.00 2.52
2237 2419 3.501828 TGGGTTGTGATGATTCGTCTTTG 59.498 43.478 7.38 0.00 0.00 2.77
2238 2420 3.751175 GGGTTGTGATGATTCGTCTTTGA 59.249 43.478 7.38 0.00 0.00 2.69
2245 2427 6.652900 TGTGATGATTCGTCTTTGAATTACCA 59.347 34.615 7.38 0.00 38.65 3.25
2249 2431 4.977741 TTCGTCTTTGAATTACCACGTC 57.022 40.909 0.00 0.00 0.00 4.34
2253 2435 4.446385 CGTCTTTGAATTACCACGTCTTCA 59.554 41.667 0.00 0.00 0.00 3.02
2257 2439 3.921677 TGAATTACCACGTCTTCACTCC 58.078 45.455 0.00 0.00 0.00 3.85
2279 2461 7.037586 ACTCCCATTTCTTCAGTACAATTCCTA 60.038 37.037 0.00 0.00 0.00 2.94
2280 2462 7.695055 TCCCATTTCTTCAGTACAATTCCTAA 58.305 34.615 0.00 0.00 0.00 2.69
2281 2463 7.829211 TCCCATTTCTTCAGTACAATTCCTAAG 59.171 37.037 0.00 0.00 0.00 2.18
2282 2464 7.611855 CCCATTTCTTCAGTACAATTCCTAAGT 59.388 37.037 0.00 0.00 0.00 2.24
2283 2465 9.014297 CCATTTCTTCAGTACAATTCCTAAGTT 57.986 33.333 0.00 0.00 0.00 2.66
2294 2476 9.473640 GTACAATTCCTAAGTTAGTATACTGCC 57.526 37.037 15.90 5.65 0.00 4.85
2295 2477 8.320338 ACAATTCCTAAGTTAGTATACTGCCT 57.680 34.615 15.90 7.86 0.00 4.75
2296 2478 8.769359 ACAATTCCTAAGTTAGTATACTGCCTT 58.231 33.333 15.90 17.00 0.00 4.35
2297 2479 9.614792 CAATTCCTAAGTTAGTATACTGCCTTT 57.385 33.333 15.90 7.19 0.00 3.11
2298 2480 9.833917 AATTCCTAAGTTAGTATACTGCCTTTC 57.166 33.333 15.90 0.21 0.00 2.62
2299 2481 7.035840 TCCTAAGTTAGTATACTGCCTTTCG 57.964 40.000 15.90 10.45 0.00 3.46
2300 2482 6.830324 TCCTAAGTTAGTATACTGCCTTTCGA 59.170 38.462 15.90 11.40 0.00 3.71
2301 2483 7.504911 TCCTAAGTTAGTATACTGCCTTTCGAT 59.495 37.037 15.90 0.00 0.00 3.59
2302 2484 8.790718 CCTAAGTTAGTATACTGCCTTTCGATA 58.209 37.037 15.90 1.77 0.00 2.92
2304 2486 8.868635 AAGTTAGTATACTGCCTTTCGATAAC 57.131 34.615 15.90 7.55 0.00 1.89
2305 2487 8.004087 AGTTAGTATACTGCCTTTCGATAACA 57.996 34.615 15.90 0.00 0.00 2.41
2306 2488 8.136165 AGTTAGTATACTGCCTTTCGATAACAG 58.864 37.037 15.90 0.00 0.00 3.16
2307 2489 6.710597 AGTATACTGCCTTTCGATAACAGA 57.289 37.500 4.10 0.00 32.67 3.41
2308 2490 6.740110 AGTATACTGCCTTTCGATAACAGAG 58.260 40.000 4.10 0.00 32.67 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.943653 GAGGCACGGTCAAAACGG 59.056 61.111 0.00 0.00 35.23 4.44
89 95 6.317391 AGCGTAGTATAGTACTCCTTTCGTTT 59.683 38.462 14.38 0.00 40.14 3.60
97 103 7.148885 CGTAACTGTAGCGTAGTATAGTACTCC 60.149 44.444 14.38 6.64 40.14 3.85
100 106 7.396190 ACGTAACTGTAGCGTAGTATAGTAC 57.604 40.000 7.56 7.56 37.07 2.73
112 118 1.262882 GCGGTGTACGTAACTGTAGC 58.737 55.000 0.00 0.00 46.52 3.58
168 174 1.726791 CTTTATTGTCGTGTGCTCGCT 59.273 47.619 0.00 0.00 0.00 4.93
180 186 2.929592 GCCAGGTCGTCGACTTTATTGT 60.930 50.000 23.69 0.00 32.47 2.71
183 191 0.175073 GGCCAGGTCGTCGACTTTAT 59.825 55.000 23.69 6.27 32.47 1.40
190 198 0.747283 AGTACTAGGCCAGGTCGTCG 60.747 60.000 5.01 0.00 0.00 5.12
195 203 4.344390 GCTACATTTAGTACTAGGCCAGGT 59.656 45.833 5.01 5.58 0.00 4.00
197 205 5.302059 TGAGCTACATTTAGTACTAGGCCAG 59.698 44.000 5.01 2.64 0.00 4.85
218 228 3.722555 AAAACGCACGATGTGTATGAG 57.277 42.857 0.00 0.00 40.68 2.90
262 276 2.091665 CCCAGGACCCAATCAAGCTAAT 60.092 50.000 0.00 0.00 0.00 1.73
279 296 0.459899 TGCATGTACTACGCTCCCAG 59.540 55.000 0.00 0.00 0.00 4.45
284 301 1.065102 CCTACGTGCATGTACTACGCT 59.935 52.381 14.85 4.16 41.19 5.07
303 320 5.768980 TGATTCTCCCCATGATCTATTCC 57.231 43.478 0.00 0.00 0.00 3.01
371 388 1.376037 GGAGGAGGCGTCAACTTGG 60.376 63.158 8.91 0.00 0.00 3.61
393 410 8.454859 TCTCTCCAAGGATTATTATGGCTTAT 57.545 34.615 0.00 0.00 32.87 1.73
394 411 7.734865 TCTCTCTCCAAGGATTATTATGGCTTA 59.265 37.037 0.00 0.00 32.87 3.09
395 412 6.560304 TCTCTCTCCAAGGATTATTATGGCTT 59.440 38.462 0.00 0.00 32.87 4.35
396 413 6.087456 TCTCTCTCCAAGGATTATTATGGCT 58.913 40.000 0.00 0.00 32.87 4.75
397 414 6.212388 TCTCTCTCTCCAAGGATTATTATGGC 59.788 42.308 0.00 0.00 32.87 4.40
398 415 7.093377 CCTCTCTCTCTCCAAGGATTATTATGG 60.093 44.444 0.00 0.00 0.00 2.74
399 416 7.093377 CCCTCTCTCTCTCCAAGGATTATTATG 60.093 44.444 0.00 0.00 0.00 1.90
403 420 4.421911 TCCCTCTCTCTCTCCAAGGATTAT 59.578 45.833 0.00 0.00 0.00 1.28
414 431 3.136641 AGTCTCTCTCCCTCTCTCTCT 57.863 52.381 0.00 0.00 0.00 3.10
425 442 3.852286 TCACACTCGTCTAGTCTCTCTC 58.148 50.000 0.00 0.00 35.76 3.20
426 443 3.259876 ACTCACACTCGTCTAGTCTCTCT 59.740 47.826 0.00 0.00 35.76 3.10
427 444 3.369756 CACTCACACTCGTCTAGTCTCTC 59.630 52.174 0.00 0.00 35.76 3.20
428 445 3.244284 ACACTCACACTCGTCTAGTCTCT 60.244 47.826 0.00 0.00 35.76 3.10
449 466 0.933097 CACTGCACACTCACACTCAC 59.067 55.000 0.00 0.00 0.00 3.51
450 467 0.179076 CCACTGCACACTCACACTCA 60.179 55.000 0.00 0.00 0.00 3.41
451 468 0.882042 CCCACTGCACACTCACACTC 60.882 60.000 0.00 0.00 0.00 3.51
452 469 1.146930 CCCACTGCACACTCACACT 59.853 57.895 0.00 0.00 0.00 3.55
453 470 0.882042 CTCCCACTGCACACTCACAC 60.882 60.000 0.00 0.00 0.00 3.82
454 471 1.048160 TCTCCCACTGCACACTCACA 61.048 55.000 0.00 0.00 0.00 3.58
455 472 0.106708 TTCTCCCACTGCACACTCAC 59.893 55.000 0.00 0.00 0.00 3.51
456 473 0.394192 CTTCTCCCACTGCACACTCA 59.606 55.000 0.00 0.00 0.00 3.41
457 474 0.681733 TCTTCTCCCACTGCACACTC 59.318 55.000 0.00 0.00 0.00 3.51
458 475 0.683973 CTCTTCTCCCACTGCACACT 59.316 55.000 0.00 0.00 0.00 3.55
459 476 0.952984 GCTCTTCTCCCACTGCACAC 60.953 60.000 0.00 0.00 0.00 3.82
460 477 1.372683 GCTCTTCTCCCACTGCACA 59.627 57.895 0.00 0.00 0.00 4.57
461 478 0.035630 ATGCTCTTCTCCCACTGCAC 60.036 55.000 0.00 0.00 33.16 4.57
470 487 1.868498 GCTCATGCTCATGCTCTTCTC 59.132 52.381 5.04 0.00 38.65 2.87
474 491 1.148723 GGGCTCATGCTCATGCTCT 59.851 57.895 5.04 0.00 40.03 4.09
561 584 4.103103 GCCGCCACGCTTTTCTCC 62.103 66.667 0.00 0.00 0.00 3.71
601 635 1.200483 CGAGAGACACACACACACAC 58.800 55.000 0.00 0.00 0.00 3.82
603 637 0.249073 AGCGAGAGACACACACACAC 60.249 55.000 0.00 0.00 0.00 3.82
617 651 1.950216 TGCTCACCTGTCTATAGCGAG 59.050 52.381 0.00 0.00 35.95 5.03
623 657 2.106566 CACCTCTGCTCACCTGTCTAT 58.893 52.381 0.00 0.00 0.00 1.98
631 671 0.108709 CTCAGCTCACCTCTGCTCAC 60.109 60.000 0.00 0.00 37.44 3.51
791 836 2.512476 GGATTTATGTAGGTGGGGGTGT 59.488 50.000 0.00 0.00 0.00 4.16
925 1011 1.137513 GCAAGCAAGCAAGCAAGAAG 58.862 50.000 3.19 0.00 36.85 2.85
926 1012 0.748450 AGCAAGCAAGCAAGCAAGAA 59.252 45.000 10.52 0.00 36.85 2.52
927 1013 0.748450 AAGCAAGCAAGCAAGCAAGA 59.252 45.000 10.52 0.00 36.85 3.02
1319 1430 3.063485 GGTGATTAGCAAGCTAGCTAGC 58.937 50.000 33.96 33.96 46.77 3.42
1320 1431 3.658709 GGGTGATTAGCAAGCTAGCTAG 58.341 50.000 19.70 16.84 46.77 3.42
1419 1530 1.032657 TTCTTCTCCTCCTCCGCTCG 61.033 60.000 0.00 0.00 0.00 5.03
1439 1550 3.116939 CCTATCCTCTCTTCTCCTTCCCA 60.117 52.174 0.00 0.00 0.00 4.37
1568 1733 4.525912 AATAAGGGCAAAAGACAAGCAG 57.474 40.909 0.00 0.00 0.00 4.24
1598 1764 3.243839 CCACTTCACAAACCAATCAAGGG 60.244 47.826 0.00 0.00 0.00 3.95
1602 1768 3.625853 TGTCCACTTCACAAACCAATCA 58.374 40.909 0.00 0.00 0.00 2.57
1747 1917 1.318576 GTGAGGTGAAGGTTTGGTGG 58.681 55.000 0.00 0.00 0.00 4.61
1755 1925 3.503748 GGAAAATCAGTGTGAGGTGAAGG 59.496 47.826 0.00 0.00 0.00 3.46
1756 1926 4.392940 AGGAAAATCAGTGTGAGGTGAAG 58.607 43.478 0.00 0.00 0.00 3.02
1764 1934 2.034939 TGCAGCAAGGAAAATCAGTGTG 59.965 45.455 0.00 0.00 0.00 3.82
1768 1938 3.194968 AGGAATGCAGCAAGGAAAATCAG 59.805 43.478 0.00 0.00 0.00 2.90
1792 1962 6.206634 ACATAATGAAGCGGAGAAGAACAAAA 59.793 34.615 0.00 0.00 0.00 2.44
1796 1966 5.351465 TCAACATAATGAAGCGGAGAAGAAC 59.649 40.000 0.00 0.00 0.00 3.01
1798 1968 4.870426 GTCAACATAATGAAGCGGAGAAGA 59.130 41.667 0.00 0.00 0.00 2.87
1799 1969 4.631377 TGTCAACATAATGAAGCGGAGAAG 59.369 41.667 0.00 0.00 0.00 2.85
1800 1970 4.574892 TGTCAACATAATGAAGCGGAGAA 58.425 39.130 0.00 0.00 0.00 2.87
1801 1971 4.200838 TGTCAACATAATGAAGCGGAGA 57.799 40.909 0.00 0.00 0.00 3.71
1806 1976 5.509272 CGTCAACATGTCAACATAATGAAGC 59.491 40.000 0.00 2.10 34.25 3.86
1811 1981 7.933577 AGGATATCGTCAACATGTCAACATAAT 59.066 33.333 0.00 0.00 34.26 1.28
1887 2057 6.466812 CCTTTGGCAGAACAATAAGGAAAAT 58.533 36.000 6.07 0.00 32.52 1.82
1923 2096 3.127425 AGGAAACTCAGTGCTGGTAAC 57.873 47.619 0.00 0.00 32.90 2.50
1982 2156 2.159627 CCACAGCCATTTTCGTACTCAC 59.840 50.000 0.00 0.00 0.00 3.51
2122 2301 5.518812 CGTTCATCATTCTTGTTTGAACCA 58.481 37.500 8.12 0.00 40.24 3.67
2192 2371 7.391275 CCCAAAAATGATAGTGCTCCAAAATTT 59.609 33.333 0.00 0.00 0.00 1.82
2193 2372 6.880529 CCCAAAAATGATAGTGCTCCAAAATT 59.119 34.615 0.00 0.00 0.00 1.82
2194 2373 6.013466 ACCCAAAAATGATAGTGCTCCAAAAT 60.013 34.615 0.00 0.00 0.00 1.82
2198 2377 4.046286 ACCCAAAAATGATAGTGCTCCA 57.954 40.909 0.00 0.00 0.00 3.86
2203 2382 6.923012 TCATCACAACCCAAAAATGATAGTG 58.077 36.000 0.00 0.00 0.00 2.74
2216 2395 3.751175 TCAAAGACGAATCATCACAACCC 59.249 43.478 0.00 0.00 0.00 4.11
2217 2396 5.356882 TTCAAAGACGAATCATCACAACC 57.643 39.130 0.00 0.00 0.00 3.77
2218 2397 7.481798 GGTAATTCAAAGACGAATCATCACAAC 59.518 37.037 0.00 0.00 34.49 3.32
2227 2409 5.235516 AGACGTGGTAATTCAAAGACGAAT 58.764 37.500 0.00 0.00 37.20 3.34
2231 2413 5.465724 AGTGAAGACGTGGTAATTCAAAGAC 59.534 40.000 0.00 0.00 33.74 3.01
2233 2415 5.107065 GGAGTGAAGACGTGGTAATTCAAAG 60.107 44.000 0.00 0.00 33.74 2.77
2236 2418 3.306502 GGGAGTGAAGACGTGGTAATTCA 60.307 47.826 0.00 0.00 0.00 2.57
2237 2419 3.259902 GGGAGTGAAGACGTGGTAATTC 58.740 50.000 0.00 0.00 0.00 2.17
2238 2420 2.635915 TGGGAGTGAAGACGTGGTAATT 59.364 45.455 0.00 0.00 0.00 1.40
2245 2427 3.071023 TGAAGAAATGGGAGTGAAGACGT 59.929 43.478 0.00 0.00 0.00 4.34
2249 2431 5.551233 TGTACTGAAGAAATGGGAGTGAAG 58.449 41.667 0.00 0.00 0.00 3.02
2253 2435 5.946377 GGAATTGTACTGAAGAAATGGGAGT 59.054 40.000 0.00 0.00 0.00 3.85
2257 2439 8.567285 ACTTAGGAATTGTACTGAAGAAATGG 57.433 34.615 0.00 0.00 0.00 3.16
2279 2461 8.472413 TGTTATCGAAAGGCAGTATACTAACTT 58.528 33.333 4.74 9.88 0.00 2.66
2280 2462 8.004087 TGTTATCGAAAGGCAGTATACTAACT 57.996 34.615 4.74 3.92 0.00 2.24
2281 2463 8.133627 TCTGTTATCGAAAGGCAGTATACTAAC 58.866 37.037 4.74 3.26 0.00 2.34
2282 2464 8.229253 TCTGTTATCGAAAGGCAGTATACTAA 57.771 34.615 4.74 0.00 0.00 2.24
2283 2465 7.812690 TCTGTTATCGAAAGGCAGTATACTA 57.187 36.000 4.74 0.00 0.00 1.82
2284 2466 6.710597 TCTGTTATCGAAAGGCAGTATACT 57.289 37.500 0.00 0.00 0.00 2.12
2285 2467 6.994868 CTCTGTTATCGAAAGGCAGTATAC 57.005 41.667 0.00 0.00 0.00 1.47


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

AutoCloner maintained by Alex Coulton.