Multiple sequence alignment - TraesCS6D01G327300

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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 TraesCS6D01G327300 chr6D 100.000 4217 0 0 1 4217 432711580 432707364 0.000000e+00 7788.0
1 TraesCS6D01G327300 chr6D 83.333 444 57 16 3786 4217 143980771 143980333 1.100000e-105 394.0
2 TraesCS6D01G327300 chr6A 91.749 3454 126 66 390 3758 578888300 578884921 0.000000e+00 4652.0
3 TraesCS6D01G327300 chr6A 95.259 464 21 1 3755 4217 578884563 578884100 0.000000e+00 734.0
4 TraesCS6D01G327300 chr6A 80.879 387 45 10 1 360 578888793 578888409 1.150000e-70 278.0
5 TraesCS6D01G327300 chr6B 92.180 3312 133 64 389 3627 652631944 652628686 0.000000e+00 4566.0
6 TraesCS6D01G327300 chr6B 93.151 219 15 0 3973 4191 652619839 652619621 5.260000e-84 322.0
7 TraesCS6D01G327300 chr6B 78.427 445 57 29 3786 4217 697661268 697661686 1.950000e-63 254.0
8 TraesCS6D01G327300 chr6B 92.073 164 13 0 3758 3921 652627256 652627093 9.120000e-57 231.0
9 TraesCS6D01G327300 chr6B 100.000 50 0 0 3662 3711 652628689 652628640 4.490000e-15 93.5
10 TraesCS6D01G327300 chr1D 87.773 458 43 7 3763 4217 440872782 440873229 1.340000e-144 523.0
11 TraesCS6D01G327300 chr1D 83.333 444 58 15 3786 4217 90624126 90624565 3.060000e-106 396.0
12 TraesCS6D01G327300 chr1A 86.797 462 51 3 3748 4206 537154896 537154442 1.350000e-139 507.0
13 TraesCS6D01G327300 chr1A 87.770 139 17 0 1001 1139 444136354 444136492 3.370000e-36 163.0
14 TraesCS6D01G327300 chr1A 90.426 94 9 0 2383 2476 444136846 444136939 1.590000e-24 124.0
15 TraesCS6D01G327300 chr3B 84.953 319 40 4 3906 4217 480677199 480677516 2.450000e-82 316.0
16 TraesCS6D01G327300 chr7A 79.054 444 55 28 3786 4217 14838819 14839236 1.930000e-68 270.0
17 TraesCS6D01G327300 chr5B 90.141 142 14 0 998 1139 585835968 585835827 7.200000e-43 185.0
18 TraesCS6D01G327300 chr5D 90.071 141 14 0 999 1139 478222936 478222796 2.590000e-42 183.0
19 TraesCS6D01G327300 chr5A 88.732 142 16 0 998 1139 597330185 597330044 1.560000e-39 174.0
20 TraesCS6D01G327300 chr2D 89.394 132 12 2 1001 1131 28550792 28550922 9.380000e-37 165.0
21 TraesCS6D01G327300 chr2D 91.579 95 8 0 2382 2476 28552375 28552469 9.510000e-27 132.0
22 TraesCS6D01G327300 chr2D 91.954 87 7 0 2383 2469 424015075 424014989 5.730000e-24 122.0
23 TraesCS6D01G327300 chr2B 89.394 132 12 2 1001 1131 45736914 45736784 9.380000e-37 165.0
24 TraesCS6D01G327300 chr2B 91.954 87 7 0 2383 2469 498310555 498310469 5.730000e-24 122.0
25 TraesCS6D01G327300 chr2B 88.542 96 11 0 2381 2476 45735370 45735275 2.660000e-22 117.0
26 TraesCS6D01G327300 chr2A 89.394 132 12 2 1001 1131 30331905 30331775 9.380000e-37 165.0
27 TraesCS6D01G327300 chr2A 90.426 94 9 0 2383 2476 30330305 30330212 1.590000e-24 124.0
28 TraesCS6D01G327300 chr1B 89.362 94 10 0 2383 2476 466076234 466076141 7.410000e-23 119.0


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 TraesCS6D01G327300 chr6D 432707364 432711580 4216 True 7788.000000 7788 100.000000 1 4217 1 chr6D.!!$R2 4216
1 TraesCS6D01G327300 chr6A 578884100 578888793 4693 True 1888.000000 4652 89.295667 1 4217 3 chr6A.!!$R1 4216
2 TraesCS6D01G327300 chr6B 652627093 652631944 4851 True 1630.166667 4566 94.751000 389 3921 3 chr6B.!!$R2 3532

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
195 219 0.041312 ATGACGCGCACAAGAACAAC 60.041 50.000 5.73 0.0 0.0 3.32 F
1247 1381 0.169009 GACCTTTGATTGACCAGCGC 59.831 55.000 0.00 0.0 0.0 5.92 F
1945 2095 1.001974 TGCCTCTACAGTTTCGTGCAT 59.998 47.619 0.00 0.0 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1400 1540 0.263765 TATGGCTAGTTCCTCCGGGT 59.736 55.000 0.00 0.0 0.00 5.28 R
2093 2273 1.077930 GAGCCATCTCAGCCTGCAA 60.078 57.895 0.00 0.0 39.16 4.08 R
3717 3936 1.290134 GACCCATGGACTCCTCCTTT 58.710 55.000 15.22 0.0 37.48 3.11 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
23 24 6.049263 GCAGTAGAATAGTTTGGTGCATAC 57.951 41.667 0.00 0.00 0.00 2.39
40 41 6.255887 GGTGCATACAGTGACACTATAGTTTC 59.744 42.308 8.02 11.41 36.08 2.78
44 45 7.433719 GCATACAGTGACACTATAGTTTCAGAG 59.566 40.741 19.62 16.70 35.66 3.35
60 61 8.560124 AGTTTCAGAGTGAAATCCCTAGATAT 57.440 34.615 5.44 0.00 46.55 1.63
64 65 8.642935 TCAGAGTGAAATCCCTAGATATGTAG 57.357 38.462 0.00 0.00 30.42 2.74
69 70 8.811017 AGTGAAATCCCTAGATATGTAGATGTG 58.189 37.037 8.44 0.00 30.42 3.21
70 71 8.589338 GTGAAATCCCTAGATATGTAGATGTGT 58.411 37.037 8.44 0.00 30.42 3.72
82 84 5.027293 TGTAGATGTGTGGATGGATCAAG 57.973 43.478 0.00 0.00 0.00 3.02
93 95 6.612863 TGTGGATGGATCAAGAATAGAAGAGA 59.387 38.462 0.00 0.00 0.00 3.10
95 97 7.440856 GTGGATGGATCAAGAATAGAAGAGAAC 59.559 40.741 0.00 0.00 0.00 3.01
99 101 5.689961 GGATCAAGAATAGAAGAGAACGAGC 59.310 44.000 0.00 0.00 0.00 5.03
100 102 5.000012 TCAAGAATAGAAGAGAACGAGCC 58.000 43.478 0.00 0.00 0.00 4.70
102 104 4.911514 AGAATAGAAGAGAACGAGCCTC 57.088 45.455 0.00 0.00 0.00 4.70
103 105 3.634910 AGAATAGAAGAGAACGAGCCTCC 59.365 47.826 0.00 0.00 0.00 4.30
109 111 0.738389 GAGAACGAGCCTCCTCTCTG 59.262 60.000 10.01 0.00 35.90 3.35
130 132 1.568612 CGTGAAGGCGCTGTCATTGT 61.569 55.000 7.64 0.00 0.00 2.71
140 143 3.187700 CGCTGTCATTGTAGTAAGGTCC 58.812 50.000 0.00 0.00 0.00 4.46
152 155 6.258354 TGTAGTAAGGTCCTTGTTCTCCATA 58.742 40.000 14.84 0.00 0.00 2.74
163 166 5.770162 CCTTGTTCTCCATAGTGAAAACCTT 59.230 40.000 0.00 0.00 0.00 3.50
165 168 5.935945 TGTTCTCCATAGTGAAAACCTTCA 58.064 37.500 0.00 0.00 39.30 3.02
179 203 7.708752 GTGAAAACCTTCAATTGGTTACAATGA 59.291 33.333 5.42 0.00 46.25 2.57
195 219 0.041312 ATGACGCGCACAAGAACAAC 60.041 50.000 5.73 0.00 0.00 3.32
207 231 2.256117 AGAACAACGACCCCTTTCTG 57.744 50.000 0.00 0.00 0.00 3.02
210 234 1.963172 ACAACGACCCCTTTCTGAAC 58.037 50.000 0.00 0.00 0.00 3.18
256 280 4.567971 TCCGTTATTCGCTTTAGTTTGGA 58.432 39.130 0.00 0.00 38.35 3.53
257 281 5.180271 TCCGTTATTCGCTTTAGTTTGGAT 58.820 37.500 0.00 0.00 38.35 3.41
264 290 5.734855 TCGCTTTAGTTTGGATTAGATGC 57.265 39.130 0.00 0.00 0.00 3.91
270 296 2.420022 AGTTTGGATTAGATGCGTGTGC 59.580 45.455 0.00 0.00 43.20 4.57
282 308 2.131972 TGCGTGTGCTAGTTGTAACAG 58.868 47.619 0.00 0.00 43.34 3.16
285 311 2.155732 CGTGTGCTAGTTGTAACAGCAG 59.844 50.000 16.50 5.05 40.78 4.24
289 315 2.037121 TGCTAGTTGTAACAGCAGCTCA 59.963 45.455 13.82 0.00 37.78 4.26
290 316 3.265791 GCTAGTTGTAACAGCAGCTCAT 58.734 45.455 0.00 0.00 35.00 2.90
294 320 3.937706 AGTTGTAACAGCAGCTCATCATC 59.062 43.478 0.00 0.00 0.00 2.92
296 322 3.528532 TGTAACAGCAGCTCATCATCTG 58.471 45.455 0.00 0.00 0.00 2.90
300 326 3.418995 ACAGCAGCTCATCATCTGTTTT 58.581 40.909 0.00 0.00 34.69 2.43
302 328 4.082895 ACAGCAGCTCATCATCTGTTTTTC 60.083 41.667 0.00 0.00 34.69 2.29
305 331 5.942236 AGCAGCTCATCATCTGTTTTTCTTA 59.058 36.000 0.00 0.00 33.09 2.10
315 341 7.496747 TCATCTGTTTTTCTTAAAAGGGGTTG 58.503 34.615 0.00 0.00 34.08 3.77
317 343 6.869695 TCTGTTTTTCTTAAAAGGGGTTGAC 58.130 36.000 0.00 0.00 34.08 3.18
361 387 7.686438 TGATGCACACAACTATCTTTATTGT 57.314 32.000 0.00 0.00 37.02 2.71
362 388 8.785329 TGATGCACACAACTATCTTTATTGTA 57.215 30.769 0.00 0.00 34.84 2.41
363 389 9.394767 TGATGCACACAACTATCTTTATTGTAT 57.605 29.630 0.00 0.00 34.84 2.29
364 390 9.869844 GATGCACACAACTATCTTTATTGTATC 57.130 33.333 0.00 0.00 34.84 2.24
365 391 8.785329 TGCACACAACTATCTTTATTGTATCA 57.215 30.769 0.00 0.00 34.84 2.15
366 392 9.225436 TGCACACAACTATCTTTATTGTATCAA 57.775 29.630 0.00 0.00 34.84 2.57
367 393 9.708222 GCACACAACTATCTTTATTGTATCAAG 57.292 33.333 0.00 0.00 34.84 3.02
368 394 9.708222 CACACAACTATCTTTATTGTATCAAGC 57.292 33.333 0.00 0.00 34.84 4.01
369 395 9.448438 ACACAACTATCTTTATTGTATCAAGCA 57.552 29.630 0.00 0.00 34.84 3.91
407 512 1.039068 TCACACCAGCCAAACCAATG 58.961 50.000 0.00 0.00 0.00 2.82
429 534 1.488390 ACAATTCCCATGCCACCATC 58.512 50.000 0.00 0.00 0.00 3.51
435 541 1.288633 TCCCATGCCACCATCTCAAAT 59.711 47.619 0.00 0.00 0.00 2.32
445 551 4.441079 CCACCATCTCAAATGCCAAGATTC 60.441 45.833 0.00 0.00 0.00 2.52
638 751 1.308069 GGCAGCAACCGTCACATCAT 61.308 55.000 0.00 0.00 0.00 2.45
653 766 2.947938 ATCATAAGGCAAGGCGCGCT 62.948 55.000 32.29 14.46 43.84 5.92
654 767 3.204827 ATAAGGCAAGGCGCGCTG 61.205 61.111 32.29 23.29 43.84 5.18
724 850 3.492102 GCTATAAAGCTCCCCACATCA 57.508 47.619 0.00 0.00 45.85 3.07
812 938 4.077184 CCGCCCTAGTCCAACGCA 62.077 66.667 0.00 0.00 0.00 5.24
816 942 1.448540 CCCTAGTCCAACGCAGCTG 60.449 63.158 10.11 10.11 0.00 4.24
989 1118 4.707768 ACGACCGATCCCACCCCA 62.708 66.667 0.00 0.00 0.00 4.96
1047 1181 2.529389 ACGGTCAAGAAGGGGCCT 60.529 61.111 0.84 0.00 0.00 5.19
1247 1381 0.169009 GACCTTTGATTGACCAGCGC 59.831 55.000 0.00 0.00 0.00 5.92
1265 1399 4.157958 GCGCGCTCTTGCCTTGAG 62.158 66.667 26.67 0.00 35.36 3.02
1291 1425 5.930569 AGTCGAACCTAATCTTGTGGTTAAC 59.069 40.000 0.00 0.00 43.28 2.01
1469 1609 3.146066 CGTTTGGTCAATCTGAAAGGGA 58.854 45.455 0.00 0.00 0.00 4.20
1568 1708 6.061022 TCAATTATACACCTTGAGCCAGAA 57.939 37.500 0.00 0.00 0.00 3.02
1668 1808 4.880759 TGCAACCAATGGAATTACAGTTG 58.119 39.130 6.16 14.13 40.78 3.16
1687 1827 7.438564 ACAGTTGGTTGTTCTTAAACTTTTGT 58.561 30.769 0.00 0.00 36.30 2.83
1692 1832 7.616313 TGGTTGTTCTTAAACTTTTGTTGGAT 58.384 30.769 0.00 0.00 42.67 3.41
1706 1846 7.334671 ACTTTTGTTGGATAGAAAGCTAGCTAC 59.665 37.037 19.70 15.17 33.58 3.58
1777 1917 6.828273 AGATCTAGTTAGATGGGATCGATCAG 59.172 42.308 25.93 11.07 42.79 2.90
1869 2018 7.195374 AGTAAGAACATGTGATTAGGCCTTA 57.805 36.000 12.58 0.11 0.00 2.69
1916 2065 8.798859 ATAATTATTGTAGGGCATGTGATCTC 57.201 34.615 0.00 0.00 0.00 2.75
1930 2080 3.891977 TGTGATCTCCAGTACTATGCCTC 59.108 47.826 0.00 0.00 0.00 4.70
1931 2081 4.148838 GTGATCTCCAGTACTATGCCTCT 58.851 47.826 0.00 0.00 0.00 3.69
1932 2082 5.163088 TGTGATCTCCAGTACTATGCCTCTA 60.163 44.000 0.00 0.00 0.00 2.43
1933 2083 5.182380 GTGATCTCCAGTACTATGCCTCTAC 59.818 48.000 0.00 0.00 0.00 2.59
1934 2084 4.790718 TCTCCAGTACTATGCCTCTACA 57.209 45.455 0.00 0.00 0.00 2.74
1938 2088 5.269991 TCCAGTACTATGCCTCTACAGTTT 58.730 41.667 0.00 0.00 0.00 2.66
1940 2090 5.274718 CAGTACTATGCCTCTACAGTTTCG 58.725 45.833 0.00 0.00 0.00 3.46
1941 2091 4.948621 AGTACTATGCCTCTACAGTTTCGT 59.051 41.667 0.00 0.00 0.00 3.85
1945 2095 1.001974 TGCCTCTACAGTTTCGTGCAT 59.998 47.619 0.00 0.00 0.00 3.96
1946 2096 2.232696 TGCCTCTACAGTTTCGTGCATA 59.767 45.455 0.00 0.00 0.00 3.14
1991 2169 8.674263 TTTTGTACTGGCAATTCAATCATTTT 57.326 26.923 0.00 0.00 0.00 1.82
2052 2232 7.834068 TGCTAAATTGTCACTGAAGATCTAC 57.166 36.000 0.00 0.00 0.00 2.59
2093 2273 0.465460 TGAAGAGGTGCGGCAAAAGT 60.465 50.000 3.23 0.00 0.00 2.66
2189 2369 5.102953 TCATTTGCAGCCTCTACATTAGT 57.897 39.130 0.00 0.00 0.00 2.24
2232 2412 8.683615 CAATTAGTTACCTAACCTCAATTTCCC 58.316 37.037 0.00 0.00 36.03 3.97
2252 2432 1.442526 CTTCCTCATCGCATGCACCC 61.443 60.000 19.57 0.00 0.00 4.61
2269 2469 1.974343 CCCGTTCGCAAATTCCCCA 60.974 57.895 0.00 0.00 0.00 4.96
2271 2471 1.384525 CCGTTCGCAAATTCCCCATA 58.615 50.000 0.00 0.00 0.00 2.74
2281 2481 5.368145 GCAAATTCCCCATAAATTTCTCCC 58.632 41.667 0.00 0.00 34.84 4.30
2289 2489 5.280985 CCCCATAAATTTCTCCCGATCCATA 60.281 44.000 0.00 0.00 0.00 2.74
2293 2493 8.806146 CCATAAATTTCTCCCGATCCATAAAAT 58.194 33.333 0.00 0.00 0.00 1.82
2299 2499 8.988546 TTTCTCCCGATCCATAAAATTAATCA 57.011 30.769 0.00 0.00 0.00 2.57
2300 2500 7.979444 TCTCCCGATCCATAAAATTAATCAC 57.021 36.000 0.00 0.00 0.00 3.06
2301 2501 7.513856 TCTCCCGATCCATAAAATTAATCACA 58.486 34.615 0.00 0.00 0.00 3.58
2302 2502 8.163408 TCTCCCGATCCATAAAATTAATCACAT 58.837 33.333 0.00 0.00 0.00 3.21
2303 2503 8.335532 TCCCGATCCATAAAATTAATCACATC 57.664 34.615 0.00 0.00 0.00 3.06
2304 2504 7.119116 TCCCGATCCATAAAATTAATCACATCG 59.881 37.037 0.00 0.00 0.00 3.84
2344 2544 7.666388 CCTCTTAAGGCTAGCTAGATACACTAA 59.334 40.741 25.15 12.57 35.37 2.24
2351 2551 6.931840 GGCTAGCTAGATACACTAAAAATGCT 59.068 38.462 25.15 0.00 33.96 3.79
2366 2566 9.550811 ACTAAAAATGCTTACTAATTAACGCAC 57.449 29.630 0.00 0.00 31.10 5.34
2373 2574 5.176958 GCTTACTAATTAACGCACGATGGAT 59.823 40.000 0.00 0.00 0.00 3.41
3420 3639 7.857734 TGTGAGCTCGAATATTTATTTCCAA 57.142 32.000 9.64 0.00 0.00 3.53
3515 3734 7.833285 ACTGTTTACCTTGAATTACATTGGT 57.167 32.000 0.00 0.00 38.52 3.67
3637 3856 1.256376 GATGATGCAACGAGTACGCAG 59.744 52.381 0.00 0.00 43.96 5.18
3659 3878 7.641411 CGCAGGATAAAATGAACATTCTACAAG 59.359 37.037 0.45 0.00 0.00 3.16
3715 3934 6.702329 TCCACTCTTTCATTTTCTCTACTCC 58.298 40.000 0.00 0.00 0.00 3.85
3717 3936 7.674348 TCCACTCTTTCATTTTCTCTACTCCTA 59.326 37.037 0.00 0.00 0.00 2.94
3766 5322 3.119919 CGCTCGTTTGTTAGTACTCCTCT 60.120 47.826 0.00 0.00 0.00 3.69
3784 5340 2.616376 CTCTCATCGATCGACAGGACTT 59.384 50.000 22.06 0.00 0.00 3.01
3791 5347 0.041238 ATCGACAGGACTTCCCCTCA 59.959 55.000 0.00 0.00 33.38 3.86
3863 5419 7.986085 ATCCACCAATTTCTTTCCTATATCG 57.014 36.000 0.00 0.00 0.00 2.92
3887 5443 0.109504 ACGCAACGCAACACAAAACT 60.110 45.000 0.00 0.00 0.00 2.66
4008 5564 1.153369 CTTCATGCCCGACGTGGAT 60.153 57.895 0.00 0.00 42.00 3.41
4051 5607 1.141881 CCTGATCCTGTTCCGTCGG 59.858 63.158 4.39 4.39 0.00 4.79
4110 5666 0.668535 GTCAGACCACCAAGGCAAAC 59.331 55.000 0.00 0.00 43.14 2.93
4140 5697 2.427506 GCGAAGAGGGAACAAGAACAT 58.572 47.619 0.00 0.00 0.00 2.71
4143 5700 3.433615 CGAAGAGGGAACAAGAACATGAC 59.566 47.826 0.00 0.00 0.00 3.06
4152 5709 6.378280 GGGAACAAGAACATGACTTGGATAAT 59.622 38.462 26.89 15.25 45.92 1.28
4153 5710 7.253422 GGAACAAGAACATGACTTGGATAATG 58.747 38.462 26.89 12.14 45.92 1.90
4154 5711 6.764308 ACAAGAACATGACTTGGATAATGG 57.236 37.500 26.89 11.08 45.92 3.16
4212 5769 2.356278 GCCAATGGCCACTGAGGA 59.644 61.111 17.55 0.00 44.06 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.878406 GTGTCACTGTATGCACCAAACT 59.122 45.455 0.00 0.00 32.42 2.66
11 12 2.878406 AGTGTCACTGTATGCACCAAAC 59.122 45.455 4.21 0.00 36.54 2.93
19 20 8.462811 ACTCTGAAACTATAGTGTCACTGTATG 58.537 37.037 19.96 10.62 37.36 2.39
20 21 8.462811 CACTCTGAAACTATAGTGTCACTGTAT 58.537 37.037 19.96 4.67 37.36 2.29
23 24 6.914259 TCACTCTGAAACTATAGTGTCACTG 58.086 40.000 19.96 16.74 37.36 3.66
40 41 8.642935 TCTACATATCTAGGGATTTCACTCTG 57.357 38.462 0.00 0.00 33.71 3.35
44 45 8.589338 ACACATCTACATATCTAGGGATTTCAC 58.411 37.037 0.00 0.00 33.71 3.18
60 61 4.716287 TCTTGATCCATCCACACATCTACA 59.284 41.667 0.00 0.00 0.00 2.74
64 65 6.528321 TCTATTCTTGATCCATCCACACATC 58.472 40.000 0.00 0.00 0.00 3.06
69 70 7.060383 TCTCTTCTATTCTTGATCCATCCAC 57.940 40.000 0.00 0.00 0.00 4.02
70 71 7.504403 GTTCTCTTCTATTCTTGATCCATCCA 58.496 38.462 0.00 0.00 0.00 3.41
82 84 3.634910 AGGAGGCTCGTTCTCTTCTATTC 59.365 47.826 8.69 0.00 0.00 1.75
93 95 2.355193 GGCAGAGAGGAGGCTCGTT 61.355 63.158 11.50 0.00 39.87 3.85
95 97 3.898509 CGGCAGAGAGGAGGCTCG 61.899 72.222 8.69 0.00 39.87 5.03
99 101 1.515020 CTTCACGGCAGAGAGGAGG 59.485 63.158 0.00 0.00 0.00 4.30
100 102 1.515020 CCTTCACGGCAGAGAGGAG 59.485 63.158 0.00 0.00 0.00 3.69
121 123 5.794894 ACAAGGACCTTACTACAATGACAG 58.205 41.667 6.38 0.00 0.00 3.51
130 132 6.380274 CACTATGGAGAACAAGGACCTTACTA 59.620 42.308 6.38 0.00 0.00 1.82
140 143 6.486657 TGAAGGTTTTCACTATGGAGAACAAG 59.513 38.462 0.00 0.00 38.37 3.16
152 155 6.783708 TGTAACCAATTGAAGGTTTTCACT 57.216 33.333 7.12 0.00 46.85 3.41
163 166 2.413502 GCGCGTCATTGTAACCAATTGA 60.414 45.455 8.43 0.00 39.28 2.57
165 168 1.537638 TGCGCGTCATTGTAACCAATT 59.462 42.857 8.43 0.00 39.28 2.32
179 203 2.168503 TCGTTGTTCTTGTGCGCGT 61.169 52.632 8.43 0.00 0.00 6.01
195 219 2.185004 ACATGTTCAGAAAGGGGTCG 57.815 50.000 0.00 0.00 0.00 4.79
207 231 1.666888 CCGCAGAAGGCAAACATGTTC 60.667 52.381 12.39 0.00 45.17 3.18
210 234 1.213537 CCCGCAGAAGGCAAACATG 59.786 57.895 0.00 0.00 45.17 3.21
244 268 5.163754 ACACGCATCTAATCCAAACTAAAGC 60.164 40.000 0.00 0.00 0.00 3.51
245 269 6.250819 CACACGCATCTAATCCAAACTAAAG 58.749 40.000 0.00 0.00 0.00 1.85
256 280 3.861840 ACAACTAGCACACGCATCTAAT 58.138 40.909 0.00 0.00 42.27 1.73
257 281 3.313012 ACAACTAGCACACGCATCTAA 57.687 42.857 0.00 0.00 42.27 2.10
264 290 2.131972 TGCTGTTACAACTAGCACACG 58.868 47.619 12.25 0.00 37.78 4.49
270 296 4.498241 TGATGAGCTGCTGTTACAACTAG 58.502 43.478 7.01 0.00 0.00 2.57
282 308 4.698583 AGAAAAACAGATGATGAGCTGC 57.301 40.909 0.00 0.00 39.36 5.25
285 311 7.543520 CCCTTTTAAGAAAAACAGATGATGAGC 59.456 37.037 0.00 0.00 31.37 4.26
289 315 7.855784 ACCCCTTTTAAGAAAAACAGATGAT 57.144 32.000 0.00 0.00 31.37 2.45
290 316 7.343316 TCAACCCCTTTTAAGAAAAACAGATGA 59.657 33.333 0.00 0.00 31.37 2.92
294 320 6.046593 GGTCAACCCCTTTTAAGAAAAACAG 58.953 40.000 0.00 0.00 31.37 3.16
315 341 2.549754 CAATGATGCATAGAACGGGGTC 59.450 50.000 0.00 0.00 0.00 4.46
317 343 2.291465 CACAATGATGCATAGAACGGGG 59.709 50.000 0.00 0.00 0.00 5.73
319 345 4.779987 CATCACAATGATGCATAGAACGG 58.220 43.478 0.00 0.00 46.37 4.44
376 402 1.227853 GGTGTGACTTGCTCGGGTT 60.228 57.895 0.00 0.00 0.00 4.11
378 404 1.669115 CTGGTGTGACTTGCTCGGG 60.669 63.158 0.00 0.00 0.00 5.14
379 405 2.320587 GCTGGTGTGACTTGCTCGG 61.321 63.158 0.00 0.00 0.00 4.63
429 534 5.464168 AGAAAACGAATCTTGGCATTTGAG 58.536 37.500 0.00 0.00 0.00 3.02
435 541 3.186409 CGAGAAGAAAACGAATCTTGGCA 59.814 43.478 6.80 0.00 37.26 4.92
445 551 4.144731 GTGCATTTTGACGAGAAGAAAACG 59.855 41.667 0.00 0.00 0.00 3.60
724 850 0.114560 TGGGAAGAGACGAGGAAGGT 59.885 55.000 0.00 0.00 0.00 3.50
801 927 1.254975 TAGGCAGCTGCGTTGGACTA 61.255 55.000 35.82 24.07 43.26 2.59
812 938 1.006805 GCGATCGATGTAGGCAGCT 60.007 57.895 21.57 0.00 0.00 4.24
816 942 3.106407 GCGGCGATCGATGTAGGC 61.106 66.667 21.57 7.94 42.43 3.93
878 1005 5.139727 AGAAGAGATCGGAGATCAACTGAT 58.860 41.667 11.94 12.08 45.12 2.90
879 1006 4.531854 AGAAGAGATCGGAGATCAACTGA 58.468 43.478 11.94 0.00 45.12 3.41
880 1007 4.261572 GGAGAAGAGATCGGAGATCAACTG 60.262 50.000 11.94 0.00 45.12 3.16
881 1008 3.888930 GGAGAAGAGATCGGAGATCAACT 59.111 47.826 11.94 7.96 45.12 3.16
882 1009 3.304391 CGGAGAAGAGATCGGAGATCAAC 60.304 52.174 11.94 6.11 45.12 3.18
883 1010 2.881513 CGGAGAAGAGATCGGAGATCAA 59.118 50.000 11.94 0.00 45.12 2.57
884 1011 2.499197 CGGAGAAGAGATCGGAGATCA 58.501 52.381 11.94 0.00 45.12 2.92
974 1103 3.793888 GGTGGGGTGGGATCGGTC 61.794 72.222 0.00 0.00 0.00 4.79
1035 1169 1.675641 CGACCAAGGCCCCTTCTTG 60.676 63.158 0.00 0.00 40.75 3.02
1047 1181 4.689549 TCCTCCTCCGGCGACCAA 62.690 66.667 9.30 0.00 0.00 3.67
1265 1399 2.673368 CCACAAGATTAGGTTCGACTGC 59.327 50.000 0.00 0.00 0.00 4.40
1301 1435 3.020274 TGACCAAATCGAGGAGAGAGAG 58.980 50.000 0.00 0.00 0.00 3.20
1399 1539 1.338136 ATGGCTAGTTCCTCCGGGTG 61.338 60.000 0.00 0.00 0.00 4.61
1400 1540 0.263765 TATGGCTAGTTCCTCCGGGT 59.736 55.000 0.00 0.00 0.00 5.28
1668 1808 9.244799 CTATCCAACAAAAGTTTAAGAACAACC 57.755 33.333 0.00 0.00 38.26 3.77
1687 1827 5.302059 ACATCGTAGCTAGCTTTCTATCCAA 59.698 40.000 24.88 0.00 0.00 3.53
1692 1832 4.643334 TGGAACATCGTAGCTAGCTTTCTA 59.357 41.667 24.88 14.09 0.00 2.10
1777 1917 3.798878 GGAAAGTTGCTTCTTTGTCAAGC 59.201 43.478 10.41 0.00 45.59 4.01
1916 2065 5.593010 GAAACTGTAGAGGCATAGTACTGG 58.407 45.833 5.39 0.00 0.00 4.00
1940 2090 9.498307 AATTAATTAGCTGTTAAACGTATGCAC 57.502 29.630 0.00 0.00 0.00 4.57
1954 2104 8.755696 TTGCCAGTACAAAAATTAATTAGCTG 57.244 30.769 0.01 2.31 0.00 4.24
1955 2105 9.942850 AATTGCCAGTACAAAAATTAATTAGCT 57.057 25.926 0.01 0.00 32.27 3.32
2000 2178 9.941664 GAACACATCATTCAGGAAATTACATAG 57.058 33.333 0.00 0.00 0.00 2.23
2002 2180 8.585471 AGAACACATCATTCAGGAAATTACAT 57.415 30.769 0.00 0.00 0.00 2.29
2003 2181 8.298854 CAAGAACACATCATTCAGGAAATTACA 58.701 33.333 0.00 0.00 0.00 2.41
2004 2182 7.274250 GCAAGAACACATCATTCAGGAAATTAC 59.726 37.037 0.00 0.00 0.00 1.89
2006 2184 6.014840 AGCAAGAACACATCATTCAGGAAATT 60.015 34.615 0.00 0.00 0.00 1.82
2007 2185 5.479375 AGCAAGAACACATCATTCAGGAAAT 59.521 36.000 0.00 0.00 0.00 2.17
2008 2186 4.828939 AGCAAGAACACATCATTCAGGAAA 59.171 37.500 0.00 0.00 0.00 3.13
2009 2187 4.401022 AGCAAGAACACATCATTCAGGAA 58.599 39.130 0.00 0.00 0.00 3.36
2011 2189 5.885230 TTAGCAAGAACACATCATTCAGG 57.115 39.130 0.00 0.00 0.00 3.86
2012 2190 7.811236 ACAATTTAGCAAGAACACATCATTCAG 59.189 33.333 0.00 0.00 0.00 3.02
2013 2191 7.660112 ACAATTTAGCAAGAACACATCATTCA 58.340 30.769 0.00 0.00 0.00 2.57
2014 2192 7.809331 TGACAATTTAGCAAGAACACATCATTC 59.191 33.333 0.00 0.00 0.00 2.67
2015 2193 7.596248 GTGACAATTTAGCAAGAACACATCATT 59.404 33.333 0.00 0.00 0.00 2.57
2016 2194 7.040201 AGTGACAATTTAGCAAGAACACATCAT 60.040 33.333 0.00 0.00 0.00 2.45
2017 2195 6.262944 AGTGACAATTTAGCAAGAACACATCA 59.737 34.615 0.00 0.00 0.00 3.07
2052 2232 1.602668 CCCTGCACAACCAAACATTCG 60.603 52.381 0.00 0.00 0.00 3.34
2093 2273 1.077930 GAGCCATCTCAGCCTGCAA 60.078 57.895 0.00 0.00 39.16 4.08
2102 2282 3.554752 GCCTCAGATAGTTGAGCCATCTC 60.555 52.174 0.00 0.00 42.58 2.75
2189 2369 3.769739 ATTGATTACCTGCTGCCGATA 57.230 42.857 0.00 0.00 0.00 2.92
2232 2412 1.442526 GGTGCATGCGATGAGGAAGG 61.443 60.000 14.09 0.00 0.00 3.46
2252 2432 1.384525 TATGGGGAATTTGCGAACGG 58.615 50.000 0.00 0.00 0.00 4.44
2302 2502 7.042950 CCTTAAGAGGTCGATCTATCTATCGA 58.957 42.308 0.00 4.93 45.93 3.59
2303 2503 6.238266 GCCTTAAGAGGTCGATCTATCTATCG 60.238 46.154 0.00 0.00 44.93 2.92
2304 2504 6.826741 AGCCTTAAGAGGTCGATCTATCTATC 59.173 42.308 0.00 0.00 45.44 2.08
2307 2507 4.993028 AGCCTTAAGAGGTCGATCTATCT 58.007 43.478 0.00 0.00 45.44 1.98
2326 2526 6.931840 AGCATTTTTAGTGTATCTAGCTAGCC 59.068 38.462 16.35 6.89 0.00 3.93
2327 2527 7.954788 AGCATTTTTAGTGTATCTAGCTAGC 57.045 36.000 16.35 6.62 0.00 3.42
2338 2538 9.550811 GCGTTAATTAGTAAGCATTTTTAGTGT 57.449 29.630 0.00 0.00 0.00 3.55
2344 2544 6.833839 TCGTGCGTTAATTAGTAAGCATTTT 58.166 32.000 1.91 0.00 36.96 1.82
2351 2551 6.274579 TGATCCATCGTGCGTTAATTAGTAA 58.725 36.000 0.00 0.00 0.00 2.24
2366 2566 3.072211 CACCTGAATCCATGATCCATCG 58.928 50.000 0.00 0.00 0.00 3.84
2373 2574 1.567357 TCGACCACCTGAATCCATGA 58.433 50.000 0.00 0.00 0.00 3.07
3114 3315 3.003378 TCGTAGGAACATAGTGATCGCAG 59.997 47.826 9.33 0.47 0.00 5.18
3159 3360 2.563427 GAGTTTCCGCCTGCTTGC 59.437 61.111 0.00 0.00 0.00 4.01
3320 3537 8.877808 ACACTGAATCACATACATACATACAG 57.122 34.615 0.00 0.00 0.00 2.74
3522 3741 3.711704 CAGAGGCCAAGTTATCCTCCTTA 59.288 47.826 5.01 0.00 45.73 2.69
3637 3856 8.677300 TGCTCTTGTAGAATGTTCATTTTATCC 58.323 33.333 0.00 0.00 0.00 2.59
3659 3878 2.358898 TCTGTTTGCTGAAGGTTTGCTC 59.641 45.455 0.00 0.00 0.00 4.26
3715 3934 2.436173 GACCCATGGACTCCTCCTTTAG 59.564 54.545 15.22 0.00 37.48 1.85
3717 3936 1.290134 GACCCATGGACTCCTCCTTT 58.710 55.000 15.22 0.00 37.48 3.11
3728 3947 2.736682 GCGAACGAACGACCCATGG 61.737 63.158 4.14 4.14 35.09 3.66
3732 3951 3.170585 CGAGCGAACGAACGACCC 61.171 66.667 9.67 0.00 35.09 4.46
3766 5322 1.676529 GGAAGTCCTGTCGATCGATGA 59.323 52.381 22.50 15.10 0.00 2.92
3863 5419 4.544689 TGTTGCGTTGCGTGCACC 62.545 61.111 12.15 4.74 43.10 5.01
4110 5666 3.532155 CTCTTCGCCTCGAGGGGG 61.532 72.222 38.89 27.37 46.90 5.40
4140 5697 3.433598 GCTAGTGGCCATTATCCAAGTCA 60.434 47.826 9.72 0.00 35.01 3.41
4143 5700 2.146342 CGCTAGTGGCCATTATCCAAG 58.854 52.381 9.72 0.00 37.74 3.61


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

AutoCloner maintained by Alex Coulton.