Multiple sequence alignment - TraesCS6A01G234900

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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 TraesCS6A01G234900 chr6A 100.000 2802 0 0 1 2802 443423280 443420479 0.000000e+00 5175.0
1 TraesCS6A01G234900 chr6B 87.385 2608 172 66 1 2591 474438221 474435754 0.000000e+00 2848.0
2 TraesCS6A01G234900 chr6B 89.119 193 16 4 2588 2778 474435671 474435482 4.670000e-58 235.0
3 TraesCS6A01G234900 chr6D 90.183 2180 118 35 412 2568 307118735 307116629 0.000000e+00 2752.0
4 TraesCS6A01G234900 chr6D 84.795 342 31 11 1 337 307119201 307118876 9.680000e-85 324.0
5 TraesCS6A01G234900 chr6D 87.317 205 15 4 2588 2784 307116535 307116334 1.010000e-54 224.0
6 TraesCS6A01G234900 chr5B 91.667 48 4 0 355 402 595315130 595315083 1.800000e-07 67.6


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 TraesCS6A01G234900 chr6A 443420479 443423280 2801 True 5175.0 5175 100.000000 1 2802 1 chr6A.!!$R1 2801
1 TraesCS6A01G234900 chr6B 474435482 474438221 2739 True 1541.5 2848 88.252000 1 2778 2 chr6B.!!$R1 2777
2 TraesCS6A01G234900 chr6D 307116334 307119201 2867 True 1100.0 2752 87.431667 1 2784 3 chr6D.!!$R1 2783

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
896 998 0.587285 CTCGTCTATCCGTTCCTCCG 59.413 60.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2527 2657 1.068333 GTTGGCTCGCATTGTGATTGT 60.068 47.619 0.0 0.0 0.0 2.71 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
56 57 7.277174 ACAAAATGACTTCTCCTTTTGGTAG 57.723 36.000 12.73 0.00 42.17 3.18
87 88 0.981956 GCGTAGAATTGCAAAACCGC 59.018 50.000 1.71 9.75 0.00 5.68
90 91 2.656422 CGTAGAATTGCAAAACCGCTTG 59.344 45.455 1.71 0.00 0.00 4.01
136 139 7.712264 ATGTGTTTTGTTGTTGTGGATAATG 57.288 32.000 0.00 0.00 0.00 1.90
145 148 6.545666 TGTTGTTGTGGATAATGAAGTTCAGT 59.454 34.615 11.91 11.47 0.00 3.41
154 157 7.765819 TGGATAATGAAGTTCAGTATGTGTGAG 59.234 37.037 25.91 0.00 37.72 3.51
157 160 4.702831 TGAAGTTCAGTATGTGTGAGCAA 58.297 39.130 0.08 0.00 37.40 3.91
158 161 4.751600 TGAAGTTCAGTATGTGTGAGCAAG 59.248 41.667 0.08 0.00 37.40 4.01
181 184 7.440523 AGAACATGACAGGACAATTTCTTAC 57.559 36.000 0.00 0.00 0.00 2.34
185 188 4.651778 TGACAGGACAATTTCTTACCAGG 58.348 43.478 0.00 0.00 0.00 4.45
186 189 4.349636 TGACAGGACAATTTCTTACCAGGA 59.650 41.667 0.00 0.00 0.00 3.86
231 234 8.864069 ATATCTTCTCAAACTATTCACAGTCG 57.136 34.615 0.00 0.00 0.00 4.18
232 235 6.327279 TCTTCTCAAACTATTCACAGTCGA 57.673 37.500 0.00 0.00 0.00 4.20
233 236 6.150318 TCTTCTCAAACTATTCACAGTCGAC 58.850 40.000 7.70 7.70 0.00 4.20
234 237 5.447624 TCTCAAACTATTCACAGTCGACA 57.552 39.130 19.50 0.00 0.00 4.35
235 238 6.025749 TCTCAAACTATTCACAGTCGACAT 57.974 37.500 19.50 4.36 0.00 3.06
236 239 5.863935 TCTCAAACTATTCACAGTCGACATG 59.136 40.000 19.50 15.44 0.00 3.21
237 240 5.778862 TCAAACTATTCACAGTCGACATGA 58.221 37.500 19.50 17.56 0.00 3.07
238 241 5.863935 TCAAACTATTCACAGTCGACATGAG 59.136 40.000 19.50 11.48 0.00 2.90
239 242 3.775202 ACTATTCACAGTCGACATGAGC 58.225 45.455 19.50 0.00 0.00 4.26
240 243 3.445450 ACTATTCACAGTCGACATGAGCT 59.555 43.478 19.50 13.41 0.00 4.09
241 244 2.820059 TTCACAGTCGACATGAGCTT 57.180 45.000 19.50 0.00 0.00 3.74
242 245 3.934457 TTCACAGTCGACATGAGCTTA 57.066 42.857 19.50 3.30 0.00 3.09
243 246 3.934457 TCACAGTCGACATGAGCTTAA 57.066 42.857 19.50 0.00 0.00 1.85
247 250 4.686091 CACAGTCGACATGAGCTTAAGAAA 59.314 41.667 19.50 0.00 0.00 2.52
337 345 5.452078 TGTATTTGTTCTTGCCCTTTCAG 57.548 39.130 0.00 0.00 0.00 3.02
339 347 5.362430 TGTATTTGTTCTTGCCCTTTCAGTT 59.638 36.000 0.00 0.00 0.00 3.16
340 348 3.799281 TTGTTCTTGCCCTTTCAGTTG 57.201 42.857 0.00 0.00 0.00 3.16
341 349 1.408702 TGTTCTTGCCCTTTCAGTTGC 59.591 47.619 0.00 0.00 0.00 4.17
347 355 2.660572 TGCCCTTTCAGTTGCTTGTAA 58.339 42.857 0.00 0.00 0.00 2.41
348 356 3.027412 TGCCCTTTCAGTTGCTTGTAAA 58.973 40.909 0.00 0.00 0.00 2.01
349 357 3.640967 TGCCCTTTCAGTTGCTTGTAAAT 59.359 39.130 0.00 0.00 0.00 1.40
350 358 4.830046 TGCCCTTTCAGTTGCTTGTAAATA 59.170 37.500 0.00 0.00 0.00 1.40
351 359 5.480073 TGCCCTTTCAGTTGCTTGTAAATAT 59.520 36.000 0.00 0.00 0.00 1.28
352 360 6.014669 TGCCCTTTCAGTTGCTTGTAAATATT 60.015 34.615 0.00 0.00 0.00 1.28
353 361 6.531594 GCCCTTTCAGTTGCTTGTAAATATTC 59.468 38.462 0.00 0.00 0.00 1.75
354 362 7.601856 CCCTTTCAGTTGCTTGTAAATATTCA 58.398 34.615 0.00 0.00 0.00 2.57
355 363 7.542130 CCCTTTCAGTTGCTTGTAAATATTCAC 59.458 37.037 0.00 0.00 0.00 3.18
356 364 8.081633 CCTTTCAGTTGCTTGTAAATATTCACA 58.918 33.333 0.00 0.00 0.00 3.58
357 365 9.462174 CTTTCAGTTGCTTGTAAATATTCACAA 57.538 29.630 4.12 4.12 33.76 3.33
358 366 9.809096 TTTCAGTTGCTTGTAAATATTCACAAA 57.191 25.926 5.68 0.00 34.43 2.83
359 367 9.462174 TTCAGTTGCTTGTAAATATTCACAAAG 57.538 29.630 5.68 2.13 34.43 2.77
360 368 8.629158 TCAGTTGCTTGTAAATATTCACAAAGT 58.371 29.630 5.68 0.00 34.43 2.66
361 369 9.248291 CAGTTGCTTGTAAATATTCACAAAGTT 57.752 29.630 5.68 0.00 34.43 2.66
362 370 9.248291 AGTTGCTTGTAAATATTCACAAAGTTG 57.752 29.630 5.68 0.00 34.43 3.16
363 371 9.030301 GTTGCTTGTAAATATTCACAAAGTTGT 57.970 29.630 5.68 0.00 43.36 3.32
365 373 9.672086 TGCTTGTAAATATTCACAAAGTTGTAC 57.328 29.630 5.68 0.00 39.91 2.90
376 384 4.967575 CACAAAGTTGTACTAAAGCAACGG 59.032 41.667 0.00 0.00 46.66 4.44
407 415 3.031736 TGGATCGGAGGGAGTAGAAAAG 58.968 50.000 0.00 0.00 0.00 2.27
410 418 2.253610 TCGGAGGGAGTAGAAAAGCAA 58.746 47.619 0.00 0.00 0.00 3.91
480 572 8.538409 AAATGATTTTACAGCACTGGATTTTC 57.462 30.769 2.21 0.00 34.19 2.29
511 604 7.999679 TCCCAGATCAAAACATATGACATTTC 58.000 34.615 10.38 0.00 0.00 2.17
572 665 2.863658 GTCAGAAGACACGAACATGC 57.136 50.000 0.00 0.00 44.34 4.06
589 682 2.118228 TGCATGTTGTCAAACGAAGC 57.882 45.000 0.00 0.00 39.30 3.86
669 765 3.119531 TCACCCGCATGAATTTCACAATC 60.120 43.478 0.15 0.00 0.00 2.67
696 792 4.391830 TGCTTATGAATTTCACGGTCTGTC 59.608 41.667 0.15 0.00 0.00 3.51
751 848 1.668826 TGATAACAGCCCTGGGAAGT 58.331 50.000 19.27 11.01 34.19 3.01
752 849 1.281867 TGATAACAGCCCTGGGAAGTG 59.718 52.381 19.27 12.62 34.19 3.16
753 850 0.625849 ATAACAGCCCTGGGAAGTGG 59.374 55.000 19.27 2.35 34.19 4.00
754 851 1.497309 TAACAGCCCTGGGAAGTGGG 61.497 60.000 19.27 0.44 46.00 4.61
755 852 2.935481 CAGCCCTGGGAAGTGGGA 60.935 66.667 19.27 0.00 46.15 4.37
756 853 2.121506 AGCCCTGGGAAGTGGGAA 60.122 61.111 19.27 0.00 46.15 3.97
757 854 2.234296 AGCCCTGGGAAGTGGGAAG 61.234 63.158 19.27 0.00 46.15 3.46
758 855 2.539081 GCCCTGGGAAGTGGGAAGT 61.539 63.158 19.27 0.00 46.15 3.01
769 866 2.955614 AGTGGGAAGTTTACGATGACG 58.044 47.619 0.00 0.00 45.75 4.35
836 936 2.097466 ACCGAAAGCGCCAGAAATATTG 59.903 45.455 2.29 0.00 35.83 1.90
880 982 1.416813 GCACAATCCTCACTCGCTCG 61.417 60.000 0.00 0.00 0.00 5.03
896 998 0.587285 CTCGTCTATCCGTTCCTCCG 59.413 60.000 0.00 0.00 0.00 4.63
998 1100 3.134127 GCGCCCCACATTCCAGTC 61.134 66.667 0.00 0.00 0.00 3.51
999 1101 2.819595 CGCCCCACATTCCAGTCG 60.820 66.667 0.00 0.00 0.00 4.18
1000 1102 3.134127 GCCCCACATTCCAGTCGC 61.134 66.667 0.00 0.00 0.00 5.19
1412 1514 2.430921 CAGCTCACCGTCGACACC 60.431 66.667 17.16 0.00 0.00 4.16
1421 1523 2.112297 GTCGACACCCAGCCCAAA 59.888 61.111 11.55 0.00 0.00 3.28
1594 1698 3.255725 CGTGTGTATATTGTTCCGGTGT 58.744 45.455 0.00 0.00 0.00 4.16
1595 1699 3.061563 CGTGTGTATATTGTTCCGGTGTG 59.938 47.826 0.00 0.00 0.00 3.82
1596 1700 3.998341 GTGTGTATATTGTTCCGGTGTGT 59.002 43.478 0.00 0.00 0.00 3.72
1597 1701 3.997681 TGTGTATATTGTTCCGGTGTGTG 59.002 43.478 0.00 0.00 0.00 3.82
1598 1702 3.998341 GTGTATATTGTTCCGGTGTGTGT 59.002 43.478 0.00 0.00 0.00 3.72
1599 1703 3.997681 TGTATATTGTTCCGGTGTGTGTG 59.002 43.478 0.00 0.00 0.00 3.82
1600 1704 2.623878 TATTGTTCCGGTGTGTGTGT 57.376 45.000 0.00 0.00 0.00 3.72
1601 1705 1.021202 ATTGTTCCGGTGTGTGTGTG 58.979 50.000 0.00 0.00 0.00 3.82
1602 1706 0.321741 TTGTTCCGGTGTGTGTGTGT 60.322 50.000 0.00 0.00 0.00 3.72
1603 1707 1.021920 TGTTCCGGTGTGTGTGTGTG 61.022 55.000 0.00 0.00 0.00 3.82
1604 1708 1.022451 GTTCCGGTGTGTGTGTGTGT 61.022 55.000 0.00 0.00 0.00 3.72
1605 1709 1.021920 TTCCGGTGTGTGTGTGTGTG 61.022 55.000 0.00 0.00 0.00 3.82
1606 1710 1.743623 CCGGTGTGTGTGTGTGTGT 60.744 57.895 0.00 0.00 0.00 3.72
1607 1711 1.423450 CGGTGTGTGTGTGTGTGTG 59.577 57.895 0.00 0.00 0.00 3.82
1608 1712 1.295357 CGGTGTGTGTGTGTGTGTGT 61.295 55.000 0.00 0.00 0.00 3.72
1609 1713 0.167908 GGTGTGTGTGTGTGTGTGTG 59.832 55.000 0.00 0.00 0.00 3.82
1620 1724 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1846 1951 7.993101 TGATAATTTCATTCCAAGAGCTTCTG 58.007 34.615 0.00 0.00 0.00 3.02
1886 1991 6.899393 AATCACATTGTTGCTTCTAGGAAA 57.101 33.333 0.00 0.00 0.00 3.13
1887 1992 5.689383 TCACATTGTTGCTTCTAGGAAAC 57.311 39.130 0.00 0.00 0.00 2.78
1888 1993 4.213270 TCACATTGTTGCTTCTAGGAAACG 59.787 41.667 0.00 0.00 0.00 3.60
1889 1994 4.024048 CACATTGTTGCTTCTAGGAAACGT 60.024 41.667 0.00 0.00 0.00 3.99
1890 1995 4.024048 ACATTGTTGCTTCTAGGAAACGTG 60.024 41.667 0.00 0.00 0.00 4.49
1891 1996 3.188159 TGTTGCTTCTAGGAAACGTGT 57.812 42.857 0.00 0.00 0.00 4.49
1892 1997 3.128349 TGTTGCTTCTAGGAAACGTGTC 58.872 45.455 0.00 0.00 0.00 3.67
1893 1998 2.450609 TGCTTCTAGGAAACGTGTCC 57.549 50.000 17.70 17.70 38.03 4.02
1898 2003 1.897802 TCTAGGAAACGTGTCCCCTTC 59.102 52.381 21.62 3.90 38.59 3.46
1990 2095 4.211164 GGCAACAAGTATCTTGTTTTTGGC 59.789 41.667 20.48 19.29 40.30 4.52
2017 2123 8.380644 CAATACGATAAGTGTTTGGAGTGTAAG 58.619 37.037 0.00 0.00 31.52 2.34
2076 2191 6.053650 ACTGTAACCCTGTAAACTTGAACTC 58.946 40.000 0.00 0.00 0.00 3.01
2077 2192 5.991861 TGTAACCCTGTAAACTTGAACTCA 58.008 37.500 0.00 0.00 0.00 3.41
2106 2221 6.024049 GCTAAAGTTCGTCTGAATTTGGATG 58.976 40.000 0.00 0.00 34.65 3.51
2107 2222 5.376854 AAAGTTCGTCTGAATTTGGATGG 57.623 39.130 0.00 0.00 34.65 3.51
2108 2223 4.021102 AGTTCGTCTGAATTTGGATGGT 57.979 40.909 0.00 0.00 36.29 3.55
2109 2224 4.003648 AGTTCGTCTGAATTTGGATGGTC 58.996 43.478 0.00 0.00 36.29 4.02
2110 2225 3.981071 TCGTCTGAATTTGGATGGTCT 57.019 42.857 0.00 0.00 0.00 3.85
2111 2226 5.046591 AGTTCGTCTGAATTTGGATGGTCTA 60.047 40.000 0.00 0.00 36.29 2.59
2112 2227 5.614324 TCGTCTGAATTTGGATGGTCTAT 57.386 39.130 0.00 0.00 0.00 1.98
2113 2228 5.359756 TCGTCTGAATTTGGATGGTCTATG 58.640 41.667 0.00 0.00 0.00 2.23
2114 2229 5.104941 TCGTCTGAATTTGGATGGTCTATGT 60.105 40.000 0.00 0.00 0.00 2.29
2115 2230 5.586243 CGTCTGAATTTGGATGGTCTATGTT 59.414 40.000 0.00 0.00 0.00 2.71
2116 2231 6.457392 CGTCTGAATTTGGATGGTCTATGTTG 60.457 42.308 0.00 0.00 0.00 3.33
2117 2232 6.375455 GTCTGAATTTGGATGGTCTATGTTGT 59.625 38.462 0.00 0.00 0.00 3.32
2118 2233 7.552687 GTCTGAATTTGGATGGTCTATGTTGTA 59.447 37.037 0.00 0.00 0.00 2.41
2119 2234 8.274322 TCTGAATTTGGATGGTCTATGTTGTAT 58.726 33.333 0.00 0.00 0.00 2.29
2120 2235 9.559732 CTGAATTTGGATGGTCTATGTTGTATA 57.440 33.333 0.00 0.00 0.00 1.47
2121 2236 9.913310 TGAATTTGGATGGTCTATGTTGTATAA 57.087 29.630 0.00 0.00 0.00 0.98
2184 2307 6.156748 TGTAGAGTGAACAAACAGCTAAGA 57.843 37.500 0.00 0.00 0.00 2.10
2201 2324 5.826208 AGCTAAGACTCTAAGCTAGGTTCTC 59.174 44.000 11.11 2.37 44.55 2.87
2204 2327 3.054213 AGACTCTAAGCTAGGTTCTCGGT 60.054 47.826 11.11 6.35 0.00 4.69
2209 2332 1.926108 AGCTAGGTTCTCGGTTGACT 58.074 50.000 0.00 0.00 0.00 3.41
2210 2333 1.546476 AGCTAGGTTCTCGGTTGACTG 59.454 52.381 0.00 0.00 0.00 3.51
2217 2340 3.119566 GGTTCTCGGTTGACTGTAGGTAG 60.120 52.174 0.00 0.00 0.00 3.18
2245 2368 9.657419 CCTAAAATTTAGTTGCTTCCATTCATT 57.343 29.630 11.34 0.00 0.00 2.57
2324 2453 8.371699 AGTTCTTTATATCAGCTCATACTTCCC 58.628 37.037 0.00 0.00 0.00 3.97
2359 2488 2.957680 TGTGAAACAGCACATTGGACAT 59.042 40.909 0.00 0.00 45.67 3.06
2366 2495 5.484173 ACAGCACATTGGACATATTTACG 57.516 39.130 0.00 0.00 0.00 3.18
2465 2595 8.041323 CCCTACTACTTGGTGGCTTATTATATG 58.959 40.741 0.00 0.00 0.00 1.78
2468 2598 7.450903 ACTACTTGGTGGCTTATTATATGGAC 58.549 38.462 0.00 0.00 0.00 4.02
2573 2703 5.007682 GGCAATGTTGGGTTCTCTAACTAA 58.992 41.667 0.00 0.00 35.81 2.24
2574 2704 5.652452 GGCAATGTTGGGTTCTCTAACTAAT 59.348 40.000 0.00 0.00 35.81 1.73
2643 2941 7.716799 TCCATGCTCTTGGTTATAAACAAAT 57.283 32.000 16.44 5.04 38.01 2.32
2733 3031 8.682710 TGTGGCATTAAAGTTGAAATATAGTCC 58.317 33.333 0.00 0.00 0.00 3.85
2757 3055 6.481976 CCACAAGAGTACATGTGAACTGTTAA 59.518 38.462 21.14 0.00 44.99 2.01
2760 3058 8.774586 ACAAGAGTACATGTGAACTGTTAATTC 58.225 33.333 9.11 0.00 29.03 2.17
2762 3060 9.561069 AAGAGTACATGTGAACTGTTAATTCTT 57.439 29.630 9.11 0.15 28.36 2.52
2763 3061 9.209175 AGAGTACATGTGAACTGTTAATTCTTC 57.791 33.333 9.11 0.00 0.00 2.87
2764 3062 8.902540 AGTACATGTGAACTGTTAATTCTTCA 57.097 30.769 9.11 0.00 0.00 3.02
2765 3063 8.993121 AGTACATGTGAACTGTTAATTCTTCAG 58.007 33.333 9.11 0.00 35.60 3.02
2766 3064 7.807977 ACATGTGAACTGTTAATTCTTCAGT 57.192 32.000 0.00 4.86 43.04 3.41
2767 3065 8.902540 ACATGTGAACTGTTAATTCTTCAGTA 57.097 30.769 0.00 0.00 40.81 2.74
2768 3066 8.774586 ACATGTGAACTGTTAATTCTTCAGTAC 58.225 33.333 0.00 6.89 40.81 2.73
2785 3083 9.696572 TCTTCAGTACTAGTATGTACCATTTCT 57.303 33.333 5.75 0.00 42.58 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.988064 TGTAAACAAAGTGCAAAGAATTTACA 57.012 26.923 16.71 16.71 35.03 2.41
56 57 3.531262 ATTCTACGCCGAAACAAACAC 57.469 42.857 0.00 0.00 0.00 3.32
125 128 7.882791 ACACATACTGAACTTCATTATCCACAA 59.117 33.333 0.00 0.00 0.00 3.33
136 139 4.991056 TCTTGCTCACACATACTGAACTTC 59.009 41.667 0.00 0.00 0.00 3.01
145 148 4.640364 TGTCATGTTCTTGCTCACACATA 58.360 39.130 0.00 0.00 0.00 2.29
154 157 4.510038 AATTGTCCTGTCATGTTCTTGC 57.490 40.909 0.00 0.00 0.00 4.01
157 160 6.431234 GGTAAGAAATTGTCCTGTCATGTTCT 59.569 38.462 0.00 0.00 0.00 3.01
158 161 6.206634 TGGTAAGAAATTGTCCTGTCATGTTC 59.793 38.462 0.00 0.00 0.00 3.18
181 184 4.286297 TGTTCCTACAAATCAGTCCTGG 57.714 45.455 0.00 0.00 0.00 4.45
209 212 6.150318 GTCGACTGTGAATAGTTTGAGAAGA 58.850 40.000 8.70 0.00 0.00 2.87
210 213 5.920840 TGTCGACTGTGAATAGTTTGAGAAG 59.079 40.000 17.92 0.00 0.00 2.85
211 214 5.838529 TGTCGACTGTGAATAGTTTGAGAA 58.161 37.500 17.92 0.00 0.00 2.87
212 215 5.447624 TGTCGACTGTGAATAGTTTGAGA 57.552 39.130 17.92 0.00 0.00 3.27
214 217 5.778862 TCATGTCGACTGTGAATAGTTTGA 58.221 37.500 17.92 0.00 0.00 2.69
215 218 5.445142 GCTCATGTCGACTGTGAATAGTTTG 60.445 44.000 17.92 8.30 0.00 2.93
216 219 4.627467 GCTCATGTCGACTGTGAATAGTTT 59.373 41.667 17.92 0.00 0.00 2.66
217 220 4.081972 AGCTCATGTCGACTGTGAATAGTT 60.082 41.667 17.92 5.23 0.00 2.24
218 221 3.445450 AGCTCATGTCGACTGTGAATAGT 59.555 43.478 17.92 3.63 0.00 2.12
219 222 4.039151 AGCTCATGTCGACTGTGAATAG 57.961 45.455 17.92 10.15 0.00 1.73
220 223 4.456280 AAGCTCATGTCGACTGTGAATA 57.544 40.909 17.92 0.00 0.00 1.75
222 225 2.820059 AAGCTCATGTCGACTGTGAA 57.180 45.000 17.92 0.00 0.00 3.18
223 226 3.506067 TCTTAAGCTCATGTCGACTGTGA 59.494 43.478 17.92 18.35 0.00 3.58
224 227 3.838120 TCTTAAGCTCATGTCGACTGTG 58.162 45.455 17.92 15.17 0.00 3.66
225 228 4.521130 TTCTTAAGCTCATGTCGACTGT 57.479 40.909 17.92 2.41 0.00 3.55
226 229 6.312426 AGAATTTCTTAAGCTCATGTCGACTG 59.688 38.462 17.92 12.33 0.00 3.51
227 230 6.402222 AGAATTTCTTAAGCTCATGTCGACT 58.598 36.000 17.92 0.00 0.00 4.18
228 231 6.654793 AGAATTTCTTAAGCTCATGTCGAC 57.345 37.500 9.11 9.11 0.00 4.20
229 232 7.772166 TCTAGAATTTCTTAAGCTCATGTCGA 58.228 34.615 3.86 0.00 0.00 4.20
230 233 7.993821 TCTAGAATTTCTTAAGCTCATGTCG 57.006 36.000 3.86 0.00 0.00 4.35
247 250 8.547173 CCAGGAGCCATTTCTAATATCTAGAAT 58.453 37.037 0.00 0.00 34.02 2.40
322 330 1.683385 AGCAACTGAAAGGGCAAGAAC 59.317 47.619 0.00 0.00 40.29 3.01
329 337 7.542130 GTGAATATTTACAAGCAACTGAAAGGG 59.458 37.037 5.54 0.00 39.30 3.95
337 345 9.030301 ACAACTTTGTGAATATTTACAAGCAAC 57.970 29.630 20.88 0.00 40.49 4.17
339 347 9.672086 GTACAACTTTGTGAATATTTACAAGCA 57.328 29.630 20.88 10.36 42.31 3.91
340 348 9.893305 AGTACAACTTTGTGAATATTTACAAGC 57.107 29.630 20.88 10.01 42.31 4.01
348 356 9.893305 GTTGCTTTAGTACAACTTTGTGAATAT 57.107 29.630 4.82 0.00 42.27 1.28
349 357 8.065407 CGTTGCTTTAGTACAACTTTGTGAATA 58.935 33.333 4.82 0.00 43.14 1.75
350 358 6.910433 CGTTGCTTTAGTACAACTTTGTGAAT 59.090 34.615 4.82 0.00 43.14 2.57
351 359 6.252281 CGTTGCTTTAGTACAACTTTGTGAA 58.748 36.000 4.82 0.00 43.14 3.18
352 360 5.220700 CCGTTGCTTTAGTACAACTTTGTGA 60.221 40.000 4.82 0.00 43.14 3.58
353 361 4.967575 CCGTTGCTTTAGTACAACTTTGTG 59.032 41.667 4.82 0.00 43.14 3.33
354 362 4.496840 GCCGTTGCTTTAGTACAACTTTGT 60.497 41.667 0.00 0.00 43.14 2.83
355 363 3.972502 GCCGTTGCTTTAGTACAACTTTG 59.027 43.478 0.00 0.00 43.14 2.77
356 364 3.628487 TGCCGTTGCTTTAGTACAACTTT 59.372 39.130 0.00 0.00 43.14 2.66
357 365 3.207778 TGCCGTTGCTTTAGTACAACTT 58.792 40.909 0.00 0.00 43.14 2.66
358 366 2.841215 TGCCGTTGCTTTAGTACAACT 58.159 42.857 0.00 0.00 43.14 3.16
359 367 3.612472 TTGCCGTTGCTTTAGTACAAC 57.388 42.857 0.00 0.00 42.15 3.32
360 368 4.839668 AATTGCCGTTGCTTTAGTACAA 57.160 36.364 0.00 0.00 38.71 2.41
361 369 5.238868 TGTTAATTGCCGTTGCTTTAGTACA 59.761 36.000 0.00 0.00 38.71 2.90
362 370 5.691815 TGTTAATTGCCGTTGCTTTAGTAC 58.308 37.500 0.00 0.00 38.71 2.73
363 371 5.943706 TGTTAATTGCCGTTGCTTTAGTA 57.056 34.783 0.00 0.00 38.71 1.82
364 372 4.839668 TGTTAATTGCCGTTGCTTTAGT 57.160 36.364 0.00 0.00 38.71 2.24
365 373 4.562394 CCATGTTAATTGCCGTTGCTTTAG 59.438 41.667 0.00 0.00 38.71 1.85
373 381 1.946768 CCGATCCATGTTAATTGCCGT 59.053 47.619 0.00 0.00 0.00 5.68
376 384 2.554032 CCCTCCGATCCATGTTAATTGC 59.446 50.000 0.00 0.00 0.00 3.56
407 415 2.554032 AGCACAGGTCACAATACTTTGC 59.446 45.455 0.00 0.00 36.22 3.68
410 418 5.483685 TCTTAGCACAGGTCACAATACTT 57.516 39.130 0.00 0.00 0.00 2.24
490 582 7.972277 GCACAGAAATGTCATATGTTTTGATCT 59.028 33.333 1.90 0.00 0.00 2.75
549 642 3.793797 TGTTCGTGTCTTCTGACTGAA 57.206 42.857 0.00 0.00 43.29 3.02
572 665 2.772568 TGGCTTCGTTTGACAACATG 57.227 45.000 0.00 0.00 32.54 3.21
613 706 3.560068 CGCACTCAAACAGTAAAAGGAGT 59.440 43.478 0.00 0.00 36.12 3.85
656 752 7.894708 TCATAAGCAAAGGATTGTGAAATTCA 58.105 30.769 0.00 0.00 37.55 2.57
669 765 5.059404 ACCGTGAAATTCATAAGCAAAGG 57.941 39.130 0.00 0.00 0.00 3.11
713 810 3.664107 TCAATCTCAGAAAACGGTGGAG 58.336 45.455 0.00 0.00 0.00 3.86
715 812 5.411361 TGTTATCAATCTCAGAAAACGGTGG 59.589 40.000 0.00 0.00 0.00 4.61
751 848 1.894466 TCCGTCATCGTAAACTTCCCA 59.106 47.619 0.00 0.00 35.01 4.37
752 849 2.537401 CTCCGTCATCGTAAACTTCCC 58.463 52.381 0.00 0.00 35.01 3.97
753 850 1.925185 GCTCCGTCATCGTAAACTTCC 59.075 52.381 0.00 0.00 35.01 3.46
754 851 2.877335 AGCTCCGTCATCGTAAACTTC 58.123 47.619 0.00 0.00 35.01 3.01
755 852 3.192001 TGTAGCTCCGTCATCGTAAACTT 59.808 43.478 0.00 0.00 35.01 2.66
756 853 2.751259 TGTAGCTCCGTCATCGTAAACT 59.249 45.455 0.00 0.00 35.01 2.66
757 854 3.141002 TGTAGCTCCGTCATCGTAAAC 57.859 47.619 0.00 0.00 35.01 2.01
758 855 3.853831 TTGTAGCTCCGTCATCGTAAA 57.146 42.857 0.00 0.00 35.01 2.01
769 866 1.664151 CGTCCGGAATTTTGTAGCTCC 59.336 52.381 5.23 0.00 0.00 4.70
836 936 0.458716 GAGAGAGGGTTGCGTACTGC 60.459 60.000 3.22 3.22 46.70 4.40
849 949 0.869454 GATTGTGCGAGGCGAGAGAG 60.869 60.000 0.00 0.00 0.00 3.20
850 950 1.139734 GATTGTGCGAGGCGAGAGA 59.860 57.895 0.00 0.00 0.00 3.10
851 951 1.880340 GGATTGTGCGAGGCGAGAG 60.880 63.158 0.00 0.00 0.00 3.20
852 952 2.184322 GGATTGTGCGAGGCGAGA 59.816 61.111 0.00 0.00 0.00 4.04
880 982 1.108132 AGGCGGAGGAACGGATAGAC 61.108 60.000 0.00 0.00 0.00 2.59
1045 1147 3.077556 CGGAGGTGGAGGTGGAGG 61.078 72.222 0.00 0.00 0.00 4.30
1046 1148 3.775654 GCGGAGGTGGAGGTGGAG 61.776 72.222 0.00 0.00 0.00 3.86
1049 1151 3.775654 GAGGCGGAGGTGGAGGTG 61.776 72.222 0.00 0.00 0.00 4.00
1421 1523 1.289380 GACGAAGAGCTTGACCGGT 59.711 57.895 6.92 6.92 0.00 5.28
1471 1573 0.243907 ACAGTGGTCTCATTCGTCGG 59.756 55.000 0.00 0.00 0.00 4.79
1594 1698 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1595 1699 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1596 1700 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1597 1701 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1598 1702 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1599 1703 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1600 1704 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1601 1705 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1602 1706 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1603 1707 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1604 1708 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1605 1709 0.167908 CCACACACACACACACACAC 59.832 55.000 0.00 0.00 0.00 3.82
1606 1710 0.250510 ACCACACACACACACACACA 60.251 50.000 0.00 0.00 0.00 3.72
1607 1711 0.167908 CACCACACACACACACACAC 59.832 55.000 0.00 0.00 0.00 3.82
1608 1712 0.035458 TCACCACACACACACACACA 59.965 50.000 0.00 0.00 0.00 3.72
1609 1713 0.726827 CTCACCACACACACACACAC 59.273 55.000 0.00 0.00 0.00 3.82
1620 1724 1.279496 CCTTCATCCCTCTCACCACA 58.721 55.000 0.00 0.00 0.00 4.17
1790 1894 4.097589 GCTGCAAGGAAGAGCAAAATATCT 59.902 41.667 0.00 0.00 40.73 1.98
1830 1935 6.596888 TCAGATTAACAGAAGCTCTTGGAATG 59.403 38.462 0.00 0.00 0.00 2.67
1886 1991 4.295141 TCAATAAATGAAGGGGACACGT 57.705 40.909 0.00 0.00 34.30 4.49
1937 2042 7.041780 CCGAACTCCCTCATAAAAGAACATATG 60.042 40.741 0.00 0.00 0.00 1.78
1947 2052 3.118519 GCCTAACCGAACTCCCTCATAAA 60.119 47.826 0.00 0.00 0.00 1.40
1958 2063 4.251268 AGATACTTGTTGCCTAACCGAAC 58.749 43.478 0.00 0.00 35.92 3.95
1990 2095 5.642063 ACACTCCAAACACTTATCGTATTGG 59.358 40.000 0.00 0.00 40.50 3.16
2065 2180 6.064717 ACTTTAGCCATCTGAGTTCAAGTTT 58.935 36.000 0.00 0.00 0.00 2.66
2076 2191 3.849911 TCAGACGAACTTTAGCCATCTG 58.150 45.455 0.00 0.00 34.68 2.90
2077 2192 4.537135 TTCAGACGAACTTTAGCCATCT 57.463 40.909 0.00 0.00 0.00 2.90
2149 2264 5.215160 GTTCACTCTACAAGCCACAATTTG 58.785 41.667 0.00 0.00 0.00 2.32
2150 2265 4.887071 TGTTCACTCTACAAGCCACAATTT 59.113 37.500 0.00 0.00 0.00 1.82
2151 2266 4.460263 TGTTCACTCTACAAGCCACAATT 58.540 39.130 0.00 0.00 0.00 2.32
2184 2307 3.369242 ACCGAGAACCTAGCTTAGAGT 57.631 47.619 0.00 0.00 0.00 3.24
2201 2324 2.444421 AGGACTACCTACAGTCAACCG 58.556 52.381 5.69 0.00 45.64 4.44
2209 2332 8.599792 AGCAACTAAATTTTAGGACTACCTACA 58.400 33.333 18.05 0.00 46.97 2.74
2210 2333 9.445878 AAGCAACTAAATTTTAGGACTACCTAC 57.554 33.333 18.05 0.94 46.97 3.18
2217 2340 8.303876 TGAATGGAAGCAACTAAATTTTAGGAC 58.696 33.333 18.05 8.54 0.00 3.85
2341 2470 6.468956 CGTAAATATGTCCAATGTGCTGTTTC 59.531 38.462 0.00 0.00 0.00 2.78
2416 2546 1.208293 CCTCAGGCTCAGGGTAAGTTC 59.792 57.143 0.00 0.00 0.00 3.01
2465 2595 1.523758 ACCTTCGCATTGTCTTGTCC 58.476 50.000 0.00 0.00 0.00 4.02
2468 2598 1.393539 CGGTACCTTCGCATTGTCTTG 59.606 52.381 10.90 0.00 0.00 3.02
2506 2636 1.076906 ACTCTGCCTACCCACGTCT 59.923 57.895 0.00 0.00 0.00 4.18
2509 2639 2.125512 GCACTCTGCCTACCCACG 60.126 66.667 0.00 0.00 37.42 4.94
2511 2641 1.414866 TTGTGCACTCTGCCTACCCA 61.415 55.000 19.41 0.00 44.23 4.51
2527 2657 1.068333 GTTGGCTCGCATTGTGATTGT 60.068 47.619 0.00 0.00 0.00 2.71
2555 2685 5.546499 ACAGGATTAGTTAGAGAACCCAACA 59.454 40.000 0.00 0.00 36.08 3.33
2557 2687 6.697641 AACAGGATTAGTTAGAGAACCCAA 57.302 37.500 0.00 0.00 36.08 4.12
2559 2689 8.366401 GGTATAACAGGATTAGTTAGAGAACCC 58.634 40.741 0.00 0.00 36.08 4.11
2636 2934 7.761249 GCAAATCCTAGAACATGCTATTTGTTT 59.239 33.333 0.00 0.00 37.43 2.83
2639 2937 7.035840 AGCAAATCCTAGAACATGCTATTTG 57.964 36.000 10.15 0.00 41.92 2.32
2643 2941 5.070981 AGCTAGCAAATCCTAGAACATGCTA 59.929 40.000 18.83 15.01 43.33 3.49
2708 3006 8.682710 TGGACTATATTTCAACTTTAATGCCAC 58.317 33.333 0.00 0.00 0.00 5.01
2725 3023 7.898014 TCACATGTACTCTTGTGGACTATAT 57.102 36.000 17.94 0.00 44.50 0.86
2726 3024 7.544622 GTTCACATGTACTCTTGTGGACTATA 58.455 38.462 19.70 3.97 46.14 1.31
2733 3031 5.991328 AACAGTTCACATGTACTCTTGTG 57.009 39.130 14.25 14.25 45.21 3.33


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

AutoCloner maintained by Alex Coulton.