Multiple sequence alignment - TraesCS7A01G384600

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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 TraesCS7A01G384600 chr7A 100.000 2396 0 0 1 2396 560882817 560880422 0.000000e+00 4425
1 TraesCS7A01G384600 chr7B 86.495 2451 143 80 2 2396 522815351 522813033 0.000000e+00 2519
2 TraesCS7A01G384600 chr7D 89.124 2078 90 53 359 2396 494970473 494968492 0.000000e+00 2460
3 TraesCS7A01G384600 chr7D 93.831 308 13 2 1 303 494970783 494970477 2.170000e-125 459


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 TraesCS7A01G384600 chr7A 560880422 560882817 2395 True 4425.0 4425 100.0000 1 2396 1 chr7A.!!$R1 2395
1 TraesCS7A01G384600 chr7B 522813033 522815351 2318 True 2519.0 2519 86.4950 2 2396 1 chr7B.!!$R1 2394
2 TraesCS7A01G384600 chr7D 494968492 494970783 2291 True 1459.5 2460 91.4775 1 2396 2 chr7D.!!$R1 2395

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
330 361 0.036388 AATGTGTACGCCAGTCCCAG 60.036 55.0 3.51 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2029 2138 0.182299 ATCCCTTGCAAGCTAGAGGC 59.818 55.0 21.43 0.0 42.19 4.7 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
111 130 2.224066 ACCAACCGAAGTGTCAAGAGAG 60.224 50.000 0.00 0.00 0.00 3.20
185 204 1.528076 TGCAACACACGGCATTCCT 60.528 52.632 0.00 0.00 34.58 3.36
212 231 0.108804 CTACACACACAGTAGCCCGG 60.109 60.000 0.00 0.00 33.32 5.73
256 282 1.128188 ATGCCCCTCTCCCCGTATTC 61.128 60.000 0.00 0.00 0.00 1.75
320 351 3.529634 TTTTCCGCAGAAATGTGTACG 57.470 42.857 0.00 0.00 41.55 3.67
321 352 0.793861 TTCCGCAGAAATGTGTACGC 59.206 50.000 0.00 0.00 0.00 4.42
322 353 1.017177 TCCGCAGAAATGTGTACGCC 61.017 55.000 3.51 0.00 0.00 5.68
323 354 1.295357 CCGCAGAAATGTGTACGCCA 61.295 55.000 3.51 0.00 0.00 5.69
324 355 0.095245 CGCAGAAATGTGTACGCCAG 59.905 55.000 3.51 0.00 0.00 4.85
325 356 1.156736 GCAGAAATGTGTACGCCAGT 58.843 50.000 3.51 0.00 0.00 4.00
326 357 1.128692 GCAGAAATGTGTACGCCAGTC 59.871 52.381 3.51 0.00 0.00 3.51
327 358 1.732259 CAGAAATGTGTACGCCAGTCC 59.268 52.381 3.51 0.00 0.00 3.85
328 359 1.084289 GAAATGTGTACGCCAGTCCC 58.916 55.000 3.51 0.00 0.00 4.46
329 360 0.398696 AAATGTGTACGCCAGTCCCA 59.601 50.000 3.51 0.00 0.00 4.37
330 361 0.036388 AATGTGTACGCCAGTCCCAG 60.036 55.000 3.51 0.00 0.00 4.45
331 362 2.434359 GTGTACGCCAGTCCCAGC 60.434 66.667 0.00 0.00 0.00 4.85
332 363 2.920384 TGTACGCCAGTCCCAGCA 60.920 61.111 0.00 0.00 0.00 4.41
333 364 2.290287 TGTACGCCAGTCCCAGCAT 61.290 57.895 0.00 0.00 0.00 3.79
357 388 6.370593 TGAGCTAGCAAAACGAAAACAATAG 58.629 36.000 18.83 0.00 0.00 1.73
376 407 9.565213 AACAATAGTAGTCACGTGTAGAATTAC 57.435 33.333 16.51 7.43 0.00 1.89
400 431 6.145535 CCTTATCTTGAGAAATAAATGCGCC 58.854 40.000 4.18 0.00 0.00 6.53
404 435 3.502191 TGAGAAATAAATGCGCCCAAC 57.498 42.857 4.18 0.00 0.00 3.77
454 496 9.715121 TCAACTAAATAAGCCCTAAATATACGG 57.285 33.333 0.00 0.00 0.00 4.02
475 517 2.681344 GGATCGGCGTAAAACAGGAAAT 59.319 45.455 6.85 0.00 0.00 2.17
476 518 3.486875 GGATCGGCGTAAAACAGGAAATG 60.487 47.826 6.85 0.00 0.00 2.32
477 519 1.198178 TCGGCGTAAAACAGGAAATGC 59.802 47.619 6.85 0.00 0.00 3.56
481 523 3.993736 GGCGTAAAACAGGAAATGCAAAT 59.006 39.130 0.00 0.00 0.00 2.32
538 580 0.648784 CACGAGATCATTTTCGCGCG 60.649 55.000 26.76 26.76 41.77 6.86
589 631 4.262036 GGGCAAAGATTTTCGATATTCCCC 60.262 45.833 0.00 0.00 0.00 4.81
591 633 4.274950 GCAAAGATTTTCGATATTCCCCGA 59.725 41.667 0.00 0.00 0.00 5.14
640 687 6.042143 GTGGAAAGATAAACGGAATACGGTA 58.958 40.000 0.00 0.00 45.59 4.02
657 704 1.153249 TATGGAAAAGGGAGCGGCG 60.153 57.895 0.51 0.51 0.00 6.46
774 821 2.588314 GCAGATCGAGGCAGGCAG 60.588 66.667 0.00 0.00 0.00 4.85
775 822 2.108566 CAGATCGAGGCAGGCAGG 59.891 66.667 0.00 0.00 0.00 4.85
776 823 3.859414 AGATCGAGGCAGGCAGGC 61.859 66.667 0.00 0.00 44.61 4.85
849 896 1.153429 CGCCACCAACCCTAGCTAC 60.153 63.158 0.00 0.00 0.00 3.58
863 926 4.189188 CTACCCAGTCGACGGCCG 62.189 72.222 26.86 26.86 40.25 6.13
983 1046 1.982958 CTTGGTACAGGGTAGGGTGTT 59.017 52.381 0.00 0.00 42.39 3.32
984 1047 1.354101 TGGTACAGGGTAGGGTGTTG 58.646 55.000 0.00 0.00 0.00 3.33
985 1048 1.355112 GGTACAGGGTAGGGTGTTGT 58.645 55.000 0.00 0.00 0.00 3.32
986 1049 1.002773 GGTACAGGGTAGGGTGTTGTG 59.997 57.143 0.00 0.00 0.00 3.33
987 1050 1.972795 GTACAGGGTAGGGTGTTGTGA 59.027 52.381 0.00 0.00 0.00 3.58
995 1058 4.003648 GGTAGGGTGTTGTGAAGATCAAG 58.996 47.826 0.00 0.00 0.00 3.02
1399 1462 0.179051 CTGCTTCAGGGCCTGAGATC 60.179 60.000 33.14 24.96 41.75 2.75
1400 1463 1.148048 GCTTCAGGGCCTGAGATCC 59.852 63.158 33.14 19.53 41.75 3.36
1401 1464 1.445095 CTTCAGGGCCTGAGATCCG 59.555 63.158 33.14 17.62 41.75 4.18
1402 1465 2.657102 CTTCAGGGCCTGAGATCCGC 62.657 65.000 33.14 0.00 41.75 5.54
1449 1512 3.991051 CGGCCGGATAGACGCCAT 61.991 66.667 20.10 0.00 32.72 4.40
1451 1514 2.048127 GCCGGATAGACGCCATCC 60.048 66.667 5.05 1.38 38.92 3.51
1452 1515 2.657237 CCGGATAGACGCCATCCC 59.343 66.667 0.00 0.00 39.08 3.85
1453 1516 2.657237 CGGATAGACGCCATCCCC 59.343 66.667 5.27 0.00 39.08 4.81
1454 1517 2.207229 CGGATAGACGCCATCCCCA 61.207 63.158 5.27 0.00 39.08 4.96
1455 1518 1.544825 CGGATAGACGCCATCCCCAT 61.545 60.000 5.27 0.00 39.08 4.00
1456 1519 0.036010 GGATAGACGCCATCCCCATG 60.036 60.000 0.15 0.00 36.69 3.66
1464 1527 3.754068 CATCCCCATGGACGCATG 58.246 61.111 15.22 5.58 45.58 4.06
1477 1540 4.881440 GCATGCATCTCCGGCCCA 62.881 66.667 14.21 0.00 0.00 5.36
1503 1566 7.116519 AGTCTCGTTGCTTTGTTAATTAGAGTC 59.883 37.037 0.00 0.00 0.00 3.36
1504 1567 7.116519 GTCTCGTTGCTTTGTTAATTAGAGTCT 59.883 37.037 0.00 0.00 0.00 3.24
1505 1568 8.301720 TCTCGTTGCTTTGTTAATTAGAGTCTA 58.698 33.333 0.00 0.00 0.00 2.59
1506 1569 8.462143 TCGTTGCTTTGTTAATTAGAGTCTAG 57.538 34.615 0.00 0.00 0.00 2.43
1507 1570 8.301720 TCGTTGCTTTGTTAATTAGAGTCTAGA 58.698 33.333 0.00 0.00 0.00 2.43
1620 1691 1.414181 ACACAGATGGATCATCCGGAC 59.586 52.381 6.12 0.00 41.36 4.79
1622 1693 1.967066 ACAGATGGATCATCCGGACTC 59.033 52.381 6.12 3.84 41.36 3.36
1625 1696 1.821061 ATGGATCATCCGGACTCCGC 61.821 60.000 6.12 0.00 46.86 5.54
1721 1801 1.343465 TGTTCTCGTGTCCCTTTCCTC 59.657 52.381 0.00 0.00 0.00 3.71
1776 1856 5.045869 TGGTTGGTAGTATTCTCTTTCCAGG 60.046 44.000 0.00 0.00 0.00 4.45
1827 1907 1.087202 TGGTTCATCCATACGCACGC 61.087 55.000 0.00 0.00 41.93 5.34
1836 1916 4.679955 TACGCACGCACGTACGCA 62.680 61.111 16.72 0.00 46.19 5.24
1867 1947 6.368791 GGGCCAAGAATTAATGAACAAACTTC 59.631 38.462 4.39 0.00 0.00 3.01
1893 1973 6.540914 TGAAGAACATTAAGTGGTTTCGAAGT 59.459 34.615 0.00 0.00 0.00 3.01
1899 1979 6.645415 ACATTAAGTGGTTTCGAAGTGAGTAG 59.355 38.462 0.00 0.00 0.00 2.57
1909 1991 3.057456 TCGAAGTGAGTAGCTCCAAGTTC 60.057 47.826 0.00 0.00 0.00 3.01
1911 1993 3.669251 AGTGAGTAGCTCCAAGTTCAC 57.331 47.619 0.00 0.00 36.17 3.18
1928 2037 7.257722 CAAGTTCACACACAATTAACTCCTTT 58.742 34.615 0.00 0.00 30.37 3.11
1979 2088 0.723981 CGAGCTAGCTTGCAAAGGAC 59.276 55.000 20.42 1.13 46.35 3.85
1981 2090 0.322906 AGCTAGCTTGCAAAGGACCC 60.323 55.000 22.05 0.00 46.35 4.46
1988 2097 2.676076 CTTGCAAAGGACCCATTTTCG 58.324 47.619 0.00 0.00 41.27 3.46
1991 2100 2.035321 TGCAAAGGACCCATTTTCGTTC 59.965 45.455 0.00 0.00 0.00 3.95
1992 2101 2.296190 GCAAAGGACCCATTTTCGTTCT 59.704 45.455 0.00 0.00 0.00 3.01
1993 2102 3.243737 GCAAAGGACCCATTTTCGTTCTT 60.244 43.478 0.00 0.00 28.55 2.52
1994 2103 4.739436 GCAAAGGACCCATTTTCGTTCTTT 60.739 41.667 0.00 0.00 38.15 2.52
1995 2104 4.848562 AAGGACCCATTTTCGTTCTTTC 57.151 40.909 0.00 0.00 0.00 2.62
1996 2105 4.100279 AGGACCCATTTTCGTTCTTTCT 57.900 40.909 0.00 0.00 0.00 2.52
1997 2106 4.470602 AGGACCCATTTTCGTTCTTTCTT 58.529 39.130 0.00 0.00 0.00 2.52
1998 2107 4.893524 AGGACCCATTTTCGTTCTTTCTTT 59.106 37.500 0.00 0.00 0.00 2.52
1999 2108 5.362717 AGGACCCATTTTCGTTCTTTCTTTT 59.637 36.000 0.00 0.00 0.00 2.27
2000 2109 6.548251 AGGACCCATTTTCGTTCTTTCTTTTA 59.452 34.615 0.00 0.00 0.00 1.52
2001 2110 7.068962 AGGACCCATTTTCGTTCTTTCTTTTAA 59.931 33.333 0.00 0.00 0.00 1.52
2002 2111 7.381408 GGACCCATTTTCGTTCTTTCTTTTAAG 59.619 37.037 0.00 0.00 0.00 1.85
2003 2112 7.207383 ACCCATTTTCGTTCTTTCTTTTAAGG 58.793 34.615 0.00 0.00 0.00 2.69
2004 2113 7.068962 ACCCATTTTCGTTCTTTCTTTTAAGGA 59.931 33.333 0.00 0.00 0.00 3.36
2005 2114 7.381408 CCCATTTTCGTTCTTTCTTTTAAGGAC 59.619 37.037 0.00 0.00 31.47 3.85
2006 2115 7.381408 CCATTTTCGTTCTTTCTTTTAAGGACC 59.619 37.037 0.00 0.00 31.12 4.46
2007 2116 7.634671 TTTTCGTTCTTTCTTTTAAGGACCT 57.365 32.000 0.00 0.00 31.12 3.85
2008 2117 6.856135 TTCGTTCTTTCTTTTAAGGACCTC 57.144 37.500 0.00 0.00 31.12 3.85
2009 2118 6.170846 TCGTTCTTTCTTTTAAGGACCTCT 57.829 37.500 0.00 0.00 31.12 3.69
2010 2119 7.294017 TCGTTCTTTCTTTTAAGGACCTCTA 57.706 36.000 0.00 0.00 31.12 2.43
2011 2120 7.376615 TCGTTCTTTCTTTTAAGGACCTCTAG 58.623 38.462 0.00 0.00 31.12 2.43
2029 2138 5.883115 CCTCTAGCTTTCTTTCTTTTAGGGG 59.117 44.000 0.00 0.00 0.00 4.79
2044 2153 1.452833 GGGGCCTCTAGCTTGCAAG 60.453 63.158 22.44 22.44 43.05 4.01
2090 2199 1.289231 TCCCATCTACTGTCTGCCTCT 59.711 52.381 0.00 0.00 0.00 3.69
2121 2230 0.783206 TCCCCAATCAAGCAAGGGAA 59.217 50.000 0.00 0.00 43.88 3.97
2134 2249 2.684927 GCAAGGGAATAGTGCTGGATGT 60.685 50.000 0.00 0.00 35.36 3.06
2162 2277 7.817962 AGTGGAGTACTATGTAAACATTCACAC 59.182 37.037 0.00 3.96 38.04 3.82
2193 2308 7.232534 ACTCATCAATATTCTCCTACTCCACTC 59.767 40.741 0.00 0.00 0.00 3.51
2194 2309 6.495181 TCATCAATATTCTCCTACTCCACTCC 59.505 42.308 0.00 0.00 0.00 3.85
2273 2388 1.412710 GGAATATCGAGGCACCTGTGA 59.587 52.381 0.51 0.00 0.00 3.58
2276 2391 1.103803 TATCGAGGCACCTGTGAGAC 58.896 55.000 0.51 0.00 0.00 3.36
2315 2430 0.979665 TCTTGTGGCAGAGGAGAAGG 59.020 55.000 0.00 0.00 0.00 3.46
2375 2490 2.557555 AGGATGGATGGAGTGAGACA 57.442 50.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.137872 CTAGAGCTTGGTGGGCACTAG 59.862 57.143 0.00 0.00 41.63 2.57
111 130 0.457166 TAGTGCCGTGTGTCGCATAC 60.457 55.000 0.00 0.00 38.35 2.39
165 184 0.456653 GGAATGCCGTGTGTTGCATC 60.457 55.000 0.00 0.00 46.97 3.91
185 204 0.033920 CTGTGTGTGTAGCAGCTGGA 59.966 55.000 17.12 0.00 0.00 3.86
212 231 2.685202 CCCCCAGGGTATAGCTAGC 58.315 63.158 6.62 6.62 38.25 3.42
303 334 1.017177 GGCGTACACATTTCTGCGGA 61.017 55.000 0.00 0.00 0.00 5.54
306 337 1.128692 GACTGGCGTACACATTTCTGC 59.871 52.381 0.00 0.00 0.00 4.26
307 338 1.732259 GGACTGGCGTACACATTTCTG 59.268 52.381 0.00 0.00 0.00 3.02
308 339 1.338769 GGGACTGGCGTACACATTTCT 60.339 52.381 0.00 0.00 0.00 2.52
309 340 1.084289 GGGACTGGCGTACACATTTC 58.916 55.000 0.00 0.00 0.00 2.17
310 341 0.398696 TGGGACTGGCGTACACATTT 59.601 50.000 0.00 0.00 0.00 2.32
311 342 0.036388 CTGGGACTGGCGTACACATT 60.036 55.000 0.00 0.00 0.00 2.71
312 343 1.596934 CTGGGACTGGCGTACACAT 59.403 57.895 0.00 0.00 0.00 3.21
313 344 3.056458 CTGGGACTGGCGTACACA 58.944 61.111 0.00 0.00 0.00 3.72
314 345 2.434359 GCTGGGACTGGCGTACAC 60.434 66.667 0.00 0.00 0.00 2.90
315 346 2.290287 ATGCTGGGACTGGCGTACA 61.290 57.895 0.00 0.00 0.00 2.90
316 347 1.815421 CATGCTGGGACTGGCGTAC 60.815 63.158 0.00 0.00 0.00 3.67
317 348 1.960040 CTCATGCTGGGACTGGCGTA 61.960 60.000 0.00 0.00 0.00 4.42
318 349 3.320879 CTCATGCTGGGACTGGCGT 62.321 63.158 0.00 0.00 0.00 5.68
319 350 2.513204 CTCATGCTGGGACTGGCG 60.513 66.667 0.00 0.00 0.00 5.69
320 351 2.827642 GCTCATGCTGGGACTGGC 60.828 66.667 0.00 0.00 36.03 4.85
330 361 2.900122 TTCGTTTTGCTAGCTCATGC 57.100 45.000 17.23 0.00 40.05 4.06
331 362 4.536065 TGTTTTCGTTTTGCTAGCTCATG 58.464 39.130 17.23 5.34 0.00 3.07
332 363 4.829064 TGTTTTCGTTTTGCTAGCTCAT 57.171 36.364 17.23 0.00 0.00 2.90
333 364 4.624336 TTGTTTTCGTTTTGCTAGCTCA 57.376 36.364 17.23 0.00 0.00 4.26
357 388 8.619546 AGATAAGGTAATTCTACACGTGACTAC 58.380 37.037 25.01 12.49 0.00 2.73
376 407 6.145535 GGCGCATTTATTTCTCAAGATAAGG 58.854 40.000 10.83 0.00 0.00 2.69
400 431 2.225068 ATCTTATCTCGCCGTGTTGG 57.775 50.000 0.00 0.00 42.50 3.77
404 435 2.727777 TCGAAATCTTATCTCGCCGTG 58.272 47.619 0.00 0.00 32.66 4.94
454 496 1.729284 TTCCTGTTTTACGCCGATCC 58.271 50.000 0.00 0.00 0.00 3.36
493 535 4.776795 ATCCCCACGTTTATTGTTCAAC 57.223 40.909 0.00 0.00 0.00 3.18
494 536 6.896021 TTAATCCCCACGTTTATTGTTCAA 57.104 33.333 0.00 0.00 0.00 2.69
538 580 1.207089 TGGCACAGTACTGCAGTATCC 59.793 52.381 28.37 21.75 39.08 2.59
599 641 7.439381 TCTTTCCACAAGGTATATCGATAACC 58.561 38.462 20.31 20.31 35.89 2.85
603 649 9.490379 GTTTATCTTTCCACAAGGTATATCGAT 57.510 33.333 2.16 2.16 35.89 3.59
615 661 4.871557 CCGTATTCCGTTTATCTTTCCACA 59.128 41.667 0.00 0.00 33.66 4.17
639 686 1.153249 CGCCGCTCCCTTTTCCATA 60.153 57.895 0.00 0.00 0.00 2.74
640 687 2.438434 CGCCGCTCCCTTTTCCAT 60.438 61.111 0.00 0.00 0.00 3.41
657 704 1.080569 CTGCGGTTTGTTGCCATCC 60.081 57.895 0.00 0.00 0.00 3.51
822 869 4.885270 TTGGTGGCGGTGGTGGTG 62.885 66.667 0.00 0.00 0.00 4.17
823 870 4.887190 GTTGGTGGCGGTGGTGGT 62.887 66.667 0.00 0.00 0.00 4.16
827 874 3.622060 CTAGGGTTGGTGGCGGTGG 62.622 68.421 0.00 0.00 0.00 4.61
832 879 1.223763 GGTAGCTAGGGTTGGTGGC 59.776 63.158 0.00 0.00 0.00 5.01
983 1046 5.012046 ACGCCCATATATCTTGATCTTCACA 59.988 40.000 0.00 0.00 0.00 3.58
984 1047 5.349817 CACGCCCATATATCTTGATCTTCAC 59.650 44.000 0.00 0.00 0.00 3.18
985 1048 5.245977 TCACGCCCATATATCTTGATCTTCA 59.754 40.000 0.00 0.00 0.00 3.02
986 1049 5.724328 TCACGCCCATATATCTTGATCTTC 58.276 41.667 0.00 0.00 0.00 2.87
987 1050 5.728471 CTCACGCCCATATATCTTGATCTT 58.272 41.667 0.00 0.00 0.00 2.40
1392 1455 3.209812 TCGACGGGCGGATCTCAG 61.210 66.667 2.16 0.00 41.33 3.35
1454 1517 1.596203 CGGAGATGCATGCGTCCAT 60.596 57.895 31.48 17.61 32.67 3.41
1455 1518 2.202919 CGGAGATGCATGCGTCCA 60.203 61.111 31.48 7.12 32.67 4.02
1456 1519 2.969238 CCGGAGATGCATGCGTCC 60.969 66.667 31.48 24.84 32.67 4.79
1457 1520 3.643978 GCCGGAGATGCATGCGTC 61.644 66.667 28.89 28.89 31.36 5.19
1460 1523 4.881440 TGGGCCGGAGATGCATGC 62.881 66.667 11.82 11.82 0.00 4.06
1461 1524 2.593725 CTGGGCCGGAGATGCATG 60.594 66.667 6.48 0.00 0.00 4.06
1462 1525 3.092511 ACTGGGCCGGAGATGCAT 61.093 61.111 21.81 0.00 0.00 3.96
1463 1526 3.785859 GACTGGGCCGGAGATGCA 61.786 66.667 21.81 0.00 0.00 3.96
1464 1527 3.453070 GAGACTGGGCCGGAGATGC 62.453 68.421 21.81 2.65 0.00 3.91
1477 1540 6.929606 ACTCTAATTAACAAAGCAACGAGACT 59.070 34.615 0.00 0.00 0.00 3.24
1503 1566 6.805760 CGATCATCACATACCTGACAATCTAG 59.194 42.308 0.00 0.00 0.00 2.43
1504 1567 6.490040 TCGATCATCACATACCTGACAATCTA 59.510 38.462 0.00 0.00 0.00 1.98
1505 1568 5.302823 TCGATCATCACATACCTGACAATCT 59.697 40.000 0.00 0.00 0.00 2.40
1506 1569 5.532557 TCGATCATCACATACCTGACAATC 58.467 41.667 0.00 0.00 0.00 2.67
1507 1570 5.535753 TCGATCATCACATACCTGACAAT 57.464 39.130 0.00 0.00 0.00 2.71
1509 1572 4.202151 CCTTCGATCATCACATACCTGACA 60.202 45.833 0.00 0.00 0.00 3.58
1539 1610 1.827969 CTAGCTAGCACTCAACCCACT 59.172 52.381 18.83 0.00 0.00 4.00
1560 1631 3.411351 CCGCAGACCCGAACAACG 61.411 66.667 0.00 0.00 42.18 4.10
1591 1662 4.326826 TGATCCATCTGTGTTTCCAAGTC 58.673 43.478 0.00 0.00 0.00 3.01
1620 1691 2.435586 CCACAAGCTGGAGCGGAG 60.436 66.667 0.00 0.00 43.95 4.63
1625 1696 0.463295 ATCATCGCCACAAGCTGGAG 60.463 55.000 0.00 0.00 43.95 3.86
1708 1788 4.828072 ATTCAGTAGAGGAAAGGGACAC 57.172 45.455 0.00 0.00 0.00 3.67
1796 1876 3.439825 TGGATGAACCATGATGAACAACG 59.560 43.478 0.00 0.00 44.64 4.10
1835 1915 0.391927 TAATTCTTGGCCCCGACGTG 60.392 55.000 0.00 0.00 0.00 4.49
1836 1916 0.325602 TTAATTCTTGGCCCCGACGT 59.674 50.000 0.00 0.00 0.00 4.34
1837 1917 1.333619 CATTAATTCTTGGCCCCGACG 59.666 52.381 0.00 0.00 0.00 5.12
1838 1918 2.650322 TCATTAATTCTTGGCCCCGAC 58.350 47.619 0.00 0.00 0.00 4.79
1839 1919 3.020984 GTTCATTAATTCTTGGCCCCGA 58.979 45.455 0.00 0.00 0.00 5.14
1840 1920 2.757868 TGTTCATTAATTCTTGGCCCCG 59.242 45.455 0.00 0.00 0.00 5.73
1844 1924 7.867403 TCAGAAGTTTGTTCATTAATTCTTGGC 59.133 33.333 0.00 0.00 0.00 4.52
1867 1947 6.539649 TCGAAACCACTTAATGTTCTTCAG 57.460 37.500 0.00 0.00 0.00 3.02
1893 1973 2.698274 TGTGTGAACTTGGAGCTACTCA 59.302 45.455 0.00 0.00 31.08 3.41
1899 1979 3.715628 AATTGTGTGTGAACTTGGAGC 57.284 42.857 0.00 0.00 0.00 4.70
1909 1991 6.636850 GCTTGTAAAGGAGTTAATTGTGTGTG 59.363 38.462 0.00 0.00 46.35 3.82
1911 1993 6.734137 TGCTTGTAAAGGAGTTAATTGTGTG 58.266 36.000 0.00 0.00 46.35 3.82
1946 2055 5.105752 AGCTAGCTCGACAGTTTCAATTAG 58.894 41.667 12.68 0.00 0.00 1.73
1948 2057 3.931578 AGCTAGCTCGACAGTTTCAATT 58.068 40.909 12.68 0.00 0.00 2.32
1949 2058 3.601443 AGCTAGCTCGACAGTTTCAAT 57.399 42.857 12.68 0.00 0.00 2.57
1979 2088 7.381408 GTCCTTAAAAGAAAGAACGAAAATGGG 59.619 37.037 0.00 0.00 0.00 4.00
1981 2090 8.135529 AGGTCCTTAAAAGAAAGAACGAAAATG 58.864 33.333 0.00 0.00 0.00 2.32
1988 2097 7.162761 AGCTAGAGGTCCTTAAAAGAAAGAAC 58.837 38.462 0.00 0.00 0.00 3.01
1991 2100 7.880713 AGAAAGCTAGAGGTCCTTAAAAGAAAG 59.119 37.037 0.00 0.00 0.00 2.62
1992 2101 7.746703 AGAAAGCTAGAGGTCCTTAAAAGAAA 58.253 34.615 0.00 0.00 0.00 2.52
1993 2102 7.317722 AGAAAGCTAGAGGTCCTTAAAAGAA 57.682 36.000 0.00 0.00 0.00 2.52
1994 2103 6.936968 AGAAAGCTAGAGGTCCTTAAAAGA 57.063 37.500 0.00 0.00 0.00 2.52
1995 2104 7.880713 AGAAAGAAAGCTAGAGGTCCTTAAAAG 59.119 37.037 0.00 0.00 0.00 2.27
1996 2105 7.746703 AGAAAGAAAGCTAGAGGTCCTTAAAA 58.253 34.615 0.00 0.00 0.00 1.52
1997 2106 7.317722 AGAAAGAAAGCTAGAGGTCCTTAAA 57.682 36.000 0.00 0.00 0.00 1.52
1998 2107 6.936968 AGAAAGAAAGCTAGAGGTCCTTAA 57.063 37.500 0.00 0.00 0.00 1.85
1999 2108 6.936968 AAGAAAGAAAGCTAGAGGTCCTTA 57.063 37.500 0.00 0.00 0.00 2.69
2000 2109 5.834281 AAGAAAGAAAGCTAGAGGTCCTT 57.166 39.130 0.00 0.00 0.00 3.36
2001 2110 5.834281 AAAGAAAGAAAGCTAGAGGTCCT 57.166 39.130 0.00 0.00 0.00 3.85
2002 2111 6.596106 CCTAAAAGAAAGAAAGCTAGAGGTCC 59.404 42.308 0.00 0.00 0.00 4.46
2003 2112 6.596106 CCCTAAAAGAAAGAAAGCTAGAGGTC 59.404 42.308 0.00 0.00 0.00 3.85
2004 2113 6.477253 CCCTAAAAGAAAGAAAGCTAGAGGT 58.523 40.000 0.00 0.00 0.00 3.85
2005 2114 5.883115 CCCCTAAAAGAAAGAAAGCTAGAGG 59.117 44.000 0.00 0.00 0.00 3.69
2006 2115 5.355630 GCCCCTAAAAGAAAGAAAGCTAGAG 59.644 44.000 0.00 0.00 0.00 2.43
2007 2116 5.254115 GCCCCTAAAAGAAAGAAAGCTAGA 58.746 41.667 0.00 0.00 0.00 2.43
2008 2117 4.399618 GGCCCCTAAAAGAAAGAAAGCTAG 59.600 45.833 0.00 0.00 0.00 3.42
2009 2118 4.044191 AGGCCCCTAAAAGAAAGAAAGCTA 59.956 41.667 0.00 0.00 0.00 3.32
2010 2119 3.165875 GGCCCCTAAAAGAAAGAAAGCT 58.834 45.455 0.00 0.00 0.00 3.74
2011 2120 3.165875 AGGCCCCTAAAAGAAAGAAAGC 58.834 45.455 0.00 0.00 0.00 3.51
2029 2138 0.182299 ATCCCTTGCAAGCTAGAGGC 59.818 55.000 21.43 0.00 42.19 4.70
2090 2199 7.911651 TGCTTGATTGGGGAAAATTAATGTAA 58.088 30.769 0.00 0.00 0.00 2.41
2121 2230 4.033709 ACTCCACTAACATCCAGCACTAT 58.966 43.478 0.00 0.00 0.00 2.12
2134 2249 9.865321 GTGAATGTTTACATAGTACTCCACTAA 57.135 33.333 0.00 0.00 43.00 2.24
2162 2277 9.853555 GAGTAGGAGAATATTGATGAGTACATG 57.146 37.037 0.00 0.00 36.82 3.21
2193 2308 7.464178 GCGTACACTTAATCTGTTGATTAGTGG 60.464 40.741 19.53 10.40 43.50 4.00
2194 2309 7.391786 GCGTACACTTAATCTGTTGATTAGTG 58.608 38.462 16.86 16.86 43.50 2.74
2273 2388 1.181741 TCTCAACGGCTGCAGAGTCT 61.182 55.000 20.43 4.97 0.00 3.24
2276 2391 2.099431 GCTCTCAACGGCTGCAGAG 61.099 63.158 20.43 13.14 34.76 3.35
2315 2430 5.355596 CCTGTCCTTTCAGATAGACATCAC 58.644 45.833 0.00 0.00 38.49 3.06
2351 2466 1.846439 TCACTCCATCCATCCTTTCCC 59.154 52.381 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.