Multiple sequence alignment - TraesCS3B01G605300

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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 TraesCS3B01G605300 chr3B 100.000 2360 0 0 1 2360 823760895 823763254 0.000000e+00 4359
1 TraesCS3B01G605300 chr3B 86.826 167 16 6 2198 2360 225448200 225448036 5.180000e-42 182
2 TraesCS3B01G605300 chr2B 91.163 1754 95 18 9 1721 58075748 58074014 0.000000e+00 2326
3 TraesCS3B01G605300 chr2B 91.731 387 27 1 1811 2197 58073489 58073108 1.240000e-147 532
4 TraesCS3B01G605300 chr2B 93.277 238 15 1 1719 1955 58073982 58073745 1.340000e-92 350
5 TraesCS3B01G605300 chr2B 87.805 164 19 1 2196 2358 712952276 712952439 8.610000e-45 191
6 TraesCS3B01G605300 chr2B 91.667 120 10 0 2078 2197 58073735 58073616 1.450000e-37 167
7 TraesCS3B01G605300 chr3A 92.340 1449 77 17 301 1725 750617249 750618687 0.000000e+00 2030
8 TraesCS3B01G605300 chr3A 89.027 401 39 1 1735 2135 750631324 750631719 2.110000e-135 492
9 TraesCS3B01G605300 chr3A 88.997 309 19 6 1 304 750611134 750611432 3.710000e-98 368
10 TraesCS3B01G605300 chr3A 80.603 232 17 5 1480 1705 750619442 750619651 1.130000e-33 154
11 TraesCS3B01G605300 chr3A 97.333 75 1 1 1382 1456 750619376 750619449 2.460000e-25 126
12 TraesCS3B01G605300 chr2D 90.249 1405 85 21 340 1721 35082180 35080805 0.000000e+00 1788
13 TraesCS3B01G605300 chr2D 90.397 479 28 3 1719 2197 35080773 35080313 4.310000e-172 614
14 TraesCS3B01G605300 chr2D 92.386 197 11 2 4 196 35082556 35082360 6.420000e-71 278
15 TraesCS3B01G605300 chr2D 86.747 166 17 5 2198 2360 555729061 555728898 1.860000e-41 180
16 TraesCS3B01G605300 chr5D 88.824 170 15 3 2194 2360 361194208 361194376 3.070000e-49 206
17 TraesCS3B01G605300 chr5D 89.535 86 8 1 517 601 101454875 101454790 8.920000e-20 108
18 TraesCS3B01G605300 chr5D 89.412 85 8 1 518 601 68239690 68239774 3.210000e-19 106
19 TraesCS3B01G605300 chr5D 89.412 85 8 1 518 601 175636978 175637062 3.210000e-19 106
20 TraesCS3B01G605300 chr1B 88.554 166 15 3 2199 2360 25468786 25468621 5.140000e-47 198
21 TraesCS3B01G605300 chr1B 88.415 164 17 2 2198 2360 3567661 3567499 1.850000e-46 196
22 TraesCS3B01G605300 chr1B 87.117 163 19 2 2199 2360 66526903 66526742 1.440000e-42 183
23 TraesCS3B01G605300 chr1B 86.550 171 16 6 2196 2360 27730600 27730431 5.180000e-42 182
24 TraesCS3B01G605300 chr1D 86.667 165 18 3 2199 2360 281215232 281215395 1.860000e-41 180
25 TraesCS3B01G605300 chr1D 89.412 85 8 1 518 601 59557593 59557509 3.210000e-19 106
26 TraesCS3B01G605300 chr6A 91.250 80 6 1 518 596 153508462 153508541 8.920000e-20 108
27 TraesCS3B01G605300 chr4B 89.412 85 8 1 518 601 306583729 306583645 3.210000e-19 106


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 TraesCS3B01G605300 chr3B 823760895 823763254 2359 False 4359.000000 4359 100.000000 1 2360 1 chr3B.!!$F1 2359
1 TraesCS3B01G605300 chr2B 58073108 58075748 2640 True 843.750000 2326 91.959500 9 2197 4 chr2B.!!$R1 2188
2 TraesCS3B01G605300 chr3A 750617249 750619651 2402 False 770.000000 2030 90.092000 301 1725 3 chr3A.!!$F3 1424
3 TraesCS3B01G605300 chr2D 35080313 35082556 2243 True 893.333333 1788 91.010667 4 2197 3 chr2D.!!$R2 2193

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
965 1034 0.532573 TTCTCCTCACACTCGCATCC 59.467 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 2726 0.036022 AAGAGACCCAGCTGCTTGAC 59.964 55.0 8.66 0.0 0.0 3.18 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
106 111 8.970020 TGATAATGATAAATGGGATAATGCACC 58.030 33.333 0.00 0.00 0.00 5.01
132 140 4.911610 AGCGATTCGTTTTTGAGAATTGTG 59.088 37.500 8.03 0.00 39.34 3.33
158 166 8.229811 GTGATTTTGTTTTGGAAGAATATTGGC 58.770 33.333 0.00 0.00 0.00 4.52
269 277 7.636259 TTTTTCTAAATGAATTGAACCAGCG 57.364 32.000 0.00 0.00 34.24 5.18
289 297 2.275318 GACTACCAGAGCAAGCATCAC 58.725 52.381 0.00 0.00 0.00 3.06
293 301 1.241165 CCAGAGCAAGCATCACACAA 58.759 50.000 0.00 0.00 0.00 3.33
296 304 2.747989 CAGAGCAAGCATCACACAAGAT 59.252 45.455 0.00 0.00 0.00 2.40
318 327 3.052186 TCTCCCCCTTTAATTGGATTGGG 60.052 47.826 0.00 0.00 34.68 4.12
390 434 4.831107 AGGCGAAAATAAACCAATGCAAT 58.169 34.783 0.00 0.00 0.00 3.56
453 497 6.262273 GGCAAAAATAAACCAGGATATCGAGA 59.738 38.462 0.00 0.00 0.00 4.04
471 515 5.974108 TCGAGATACCAACTTCCCTTTTAG 58.026 41.667 0.00 0.00 0.00 1.85
472 516 5.718130 TCGAGATACCAACTTCCCTTTTAGA 59.282 40.000 0.00 0.00 0.00 2.10
473 517 6.043411 CGAGATACCAACTTCCCTTTTAGAG 58.957 44.000 0.00 0.00 0.00 2.43
474 518 6.351117 CGAGATACCAACTTCCCTTTTAGAGT 60.351 42.308 0.00 0.00 0.00 3.24
475 519 7.147949 CGAGATACCAACTTCCCTTTTAGAGTA 60.148 40.741 0.00 0.00 0.00 2.59
476 520 8.080363 AGATACCAACTTCCCTTTTAGAGTAG 57.920 38.462 0.00 0.00 0.00 2.57
477 521 7.899709 AGATACCAACTTCCCTTTTAGAGTAGA 59.100 37.037 0.00 0.00 0.00 2.59
478 522 6.361768 ACCAACTTCCCTTTTAGAGTAGAG 57.638 41.667 0.00 0.00 0.00 2.43
479 523 6.082707 ACCAACTTCCCTTTTAGAGTAGAGA 58.917 40.000 0.00 0.00 0.00 3.10
480 524 6.731448 ACCAACTTCCCTTTTAGAGTAGAGAT 59.269 38.462 0.00 0.00 0.00 2.75
481 525 7.899709 ACCAACTTCCCTTTTAGAGTAGAGATA 59.100 37.037 0.00 0.00 0.00 1.98
482 526 8.759782 CCAACTTCCCTTTTAGAGTAGAGATAA 58.240 37.037 0.00 0.00 0.00 1.75
515 571 8.074370 AGATTGATCAATGATAACTGATTTGCG 58.926 33.333 25.37 0.00 32.40 4.85
579 638 5.890334 TCAATTAATCTCGGCCATCAAAAC 58.110 37.500 2.24 0.00 0.00 2.43
711 771 5.728351 AATATCAACGTTCATTACCCGTG 57.272 39.130 0.00 0.00 34.62 4.94
712 772 2.529780 TCAACGTTCATTACCCGTGT 57.470 45.000 0.00 0.00 34.62 4.49
765 825 3.181537 GGTTATTGACGAACGCACACTAC 60.182 47.826 0.00 0.00 0.00 2.73
918 982 4.227864 CCAAGAGGCTAAGACTTCCATT 57.772 45.455 0.00 0.00 0.00 3.16
938 1002 9.899661 TTCCATTACTTGTATAAATAGCACTGT 57.100 29.630 0.00 0.00 0.00 3.55
939 1003 9.325198 TCCATTACTTGTATAAATAGCACTGTG 57.675 33.333 2.76 2.76 0.00 3.66
945 1014 8.668353 ACTTGTATAAATAGCACTGTGATGTTG 58.332 33.333 12.86 0.00 0.00 3.33
960 1029 2.509052 TGTTGTTCTCCTCACACTCG 57.491 50.000 0.00 0.00 0.00 4.18
965 1034 0.532573 TTCTCCTCACACTCGCATCC 59.467 55.000 0.00 0.00 0.00 3.51
1063 1132 0.182299 CCTGCTCCTCATTTCCTCCC 59.818 60.000 0.00 0.00 0.00 4.30
1102 1172 3.249320 CGGATCGTAGTACTGAATTCCGA 59.751 47.826 23.64 14.04 45.79 4.55
1164 1234 5.461032 TTTTCGGGTGCATCTGTAAATTT 57.539 34.783 5.52 0.00 0.00 1.82
1166 1236 5.461032 TTCGGGTGCATCTGTAAATTTTT 57.539 34.783 5.52 0.00 0.00 1.94
1194 1264 1.740025 GGCGCTAAGCTGAAAGATTGT 59.260 47.619 7.64 0.00 45.56 2.71
1377 1455 5.445964 TGTTAGATTTTATGGGCTTCCTCC 58.554 41.667 0.00 0.00 0.00 4.30
1380 1458 2.710096 TTTTATGGGCTTCCTCCTCG 57.290 50.000 0.00 0.00 0.00 4.63
1395 1473 6.117975 TCCTCCTCGTAAAATTGTAAACCT 57.882 37.500 0.00 0.00 0.00 3.50
1456 1541 4.415735 GCTCGAATTTGATTTCCTTGTCC 58.584 43.478 0.00 0.00 0.00 4.02
1481 1568 0.668096 GTGTGTACAACCGCGGATCA 60.668 55.000 35.90 18.85 0.00 2.92
1521 1608 3.389656 CCTTATGTCTTCCCCTTCCTCTC 59.610 52.174 0.00 0.00 0.00 3.20
1527 1614 2.383683 TCTTCCCCTTCCTCTCTTCTCA 59.616 50.000 0.00 0.00 0.00 3.27
1534 1636 4.541705 CCTTCCTCTCTTCTCATCCACTA 58.458 47.826 0.00 0.00 0.00 2.74
1606 1710 1.089481 AGACAGAGAGCGAGCGAGAG 61.089 60.000 0.00 0.00 0.00 3.20
1638 1742 0.685097 GACAGGCAGAGTGGTGGTAA 59.315 55.000 0.00 0.00 0.00 2.85
1667 1771 2.515057 GCGGAGAGCTCGAGGAGA 60.515 66.667 15.58 0.00 44.04 3.71
1694 1798 3.785859 GGCTGGGACGGAGATGCA 61.786 66.667 0.00 0.00 36.31 3.96
1705 1809 2.045926 AGATGCACACGAAGGGGC 60.046 61.111 0.00 0.00 0.00 5.80
1742 1888 0.459759 GTACTCCAACCGCTGGCTAC 60.460 60.000 0.00 0.00 45.98 3.58
1776 1922 3.198068 GTCAATCTAAAGCATCTCGCCA 58.802 45.455 0.00 0.00 44.04 5.69
1800 1946 2.756025 CCGGCGCGGCAAGATTTAA 61.756 57.895 32.60 0.00 41.17 1.52
1810 1956 2.887152 GGCAAGATTTAATGAGCGGGAT 59.113 45.455 0.00 0.00 0.00 3.85
1816 1962 2.509052 TTAATGAGCGGGATCGACAG 57.491 50.000 0.00 0.00 39.00 3.51
1887 2434 4.329545 GCGGAAGTGAGGGTGCCA 62.330 66.667 0.00 0.00 0.00 4.92
1937 2484 4.855715 TGGAGGAAGCATAGTAAGATCG 57.144 45.455 0.00 0.00 0.00 3.69
1955 2502 3.777465 TCGTCTGTAATTTAGCTCGCT 57.223 42.857 0.00 0.00 0.00 4.93
1962 2509 5.535030 TCTGTAATTTAGCTCGCTCCTGATA 59.465 40.000 0.00 0.00 0.00 2.15
1974 2521 3.440522 CGCTCCTGATATGATTCCGTCTA 59.559 47.826 0.00 0.00 0.00 2.59
1983 2530 6.264518 TGATATGATTCCGTCTACTGTTGCTA 59.735 38.462 0.00 0.00 0.00 3.49
1984 2531 4.371855 TGATTCCGTCTACTGTTGCTAG 57.628 45.455 0.00 0.00 0.00 3.42
1985 2532 2.649331 TTCCGTCTACTGTTGCTAGC 57.351 50.000 8.10 8.10 0.00 3.42
1986 2533 1.541379 TCCGTCTACTGTTGCTAGCA 58.459 50.000 14.93 14.93 0.00 3.49
1987 2534 1.472878 TCCGTCTACTGTTGCTAGCAG 59.527 52.381 18.45 9.26 39.67 4.24
2009 2556 1.863454 GCAGACATGATAGACTTGCCG 59.137 52.381 0.00 0.00 0.00 5.69
2044 2591 3.769844 TCAAGTTTCGCTTAGATCTCCCT 59.230 43.478 0.00 0.00 35.27 4.20
2076 2623 1.952296 AGCTAGCACCATAAGCATTGC 59.048 47.619 18.83 0.00 38.75 3.56
2099 2646 9.651913 TTGCTTCTTTTTCAACATTAACTTTCT 57.348 25.926 0.00 0.00 0.00 2.52
2152 2699 8.701908 ATGTTAATCAGAATTGCCTACATCAT 57.298 30.769 0.00 0.00 0.00 2.45
2175 2722 2.079925 AGCGTCCTTTCTGAATTCTGC 58.920 47.619 7.05 0.00 0.00 4.26
2179 2726 2.092838 GTCCTTTCTGAATTCTGCGACG 59.907 50.000 7.05 0.00 0.00 5.12
2197 2744 1.676384 GTCAAGCAGCTGGGTCTCT 59.324 57.895 17.12 0.00 0.00 3.10
2198 2745 0.036022 GTCAAGCAGCTGGGTCTCTT 59.964 55.000 17.12 6.78 0.00 2.85
2199 2746 0.767375 TCAAGCAGCTGGGTCTCTTT 59.233 50.000 17.12 0.00 0.00 2.52
2200 2747 1.143684 TCAAGCAGCTGGGTCTCTTTT 59.856 47.619 17.12 0.00 0.00 2.27
2201 2748 1.959282 CAAGCAGCTGGGTCTCTTTTT 59.041 47.619 17.12 0.00 0.00 1.94
2227 2774 2.684735 GGAGAGACTCCCCGACCT 59.315 66.667 6.54 0.00 44.36 3.85
2228 2775 1.454295 GGAGAGACTCCCCGACCTC 60.454 68.421 6.54 0.00 44.36 3.85
2229 2776 1.610873 GAGAGACTCCCCGACCTCT 59.389 63.158 0.00 0.00 38.57 3.69
2230 2777 0.750182 GAGAGACTCCCCGACCTCTG 60.750 65.000 0.00 0.00 36.25 3.35
2231 2778 2.363147 AGACTCCCCGACCTCTGC 60.363 66.667 0.00 0.00 0.00 4.26
2232 2779 2.680352 GACTCCCCGACCTCTGCA 60.680 66.667 0.00 0.00 0.00 4.41
2233 2780 2.039624 ACTCCCCGACCTCTGCAT 59.960 61.111 0.00 0.00 0.00 3.96
2234 2781 2.022240 GACTCCCCGACCTCTGCATC 62.022 65.000 0.00 0.00 0.00 3.91
2235 2782 1.760086 CTCCCCGACCTCTGCATCT 60.760 63.158 0.00 0.00 0.00 2.90
2236 2783 2.025767 CTCCCCGACCTCTGCATCTG 62.026 65.000 0.00 0.00 0.00 2.90
2241 2788 0.171231 CGACCTCTGCATCTGAACGA 59.829 55.000 0.00 0.00 0.00 3.85
2252 2799 4.201208 CATCTGAACGATGCATACAACC 57.799 45.455 0.00 0.00 42.75 3.77
2254 2801 3.000041 TCTGAACGATGCATACAACCAC 59.000 45.455 0.00 0.00 0.00 4.16
2257 2804 3.755905 TGAACGATGCATACAACCACATT 59.244 39.130 0.00 0.00 0.00 2.71
2260 2807 5.888691 ACGATGCATACAACCACATTTAA 57.111 34.783 0.00 0.00 0.00 1.52
2287 2834 9.838339 ATATAAATAGAGGTTCAACAAGGTCTG 57.162 33.333 0.00 0.00 0.00 3.51
2288 2835 5.825593 AATAGAGGTTCAACAAGGTCTGA 57.174 39.130 0.00 0.00 0.00 3.27
2290 2837 4.503714 AGAGGTTCAACAAGGTCTGAAA 57.496 40.909 0.00 0.00 33.52 2.69
2292 2839 4.080299 AGAGGTTCAACAAGGTCTGAAAGT 60.080 41.667 0.00 0.00 33.52 2.66
2303 2850 4.625972 GGTCTGAAAGTCCGAAAACAAA 57.374 40.909 0.00 0.00 31.17 2.83
2323 2870 2.857592 AAAACAGCAAGCTCACACAG 57.142 45.000 0.00 0.00 0.00 3.66
2324 2871 2.042686 AAACAGCAAGCTCACACAGA 57.957 45.000 0.00 0.00 0.00 3.41
2333 2880 2.229039 CTCACACAGAGCCACAACG 58.771 57.895 0.00 0.00 37.59 4.10
2335 2882 2.591715 ACACAGAGCCACAACGCC 60.592 61.111 0.00 0.00 0.00 5.68
2336 2883 2.591429 CACAGAGCCACAACGCCA 60.591 61.111 0.00 0.00 0.00 5.69
2337 2884 2.186160 CACAGAGCCACAACGCCAA 61.186 57.895 0.00 0.00 0.00 4.52
2340 2887 0.102120 CAGAGCCACAACGCCAAAAA 59.898 50.000 0.00 0.00 0.00 1.94
2341 2888 0.102300 AGAGCCACAACGCCAAAAAC 59.898 50.000 0.00 0.00 0.00 2.43
2342 2889 0.179124 GAGCCACAACGCCAAAAACA 60.179 50.000 0.00 0.00 0.00 2.83
2343 2890 0.179113 AGCCACAACGCCAAAAACAG 60.179 50.000 0.00 0.00 0.00 3.16
2344 2891 0.179124 GCCACAACGCCAAAAACAGA 60.179 50.000 0.00 0.00 0.00 3.41
2345 2892 1.737363 GCCACAACGCCAAAAACAGAA 60.737 47.619 0.00 0.00 0.00 3.02
2346 2893 2.192624 CCACAACGCCAAAAACAGAAG 58.807 47.619 0.00 0.00 0.00 2.85
2347 2894 2.192624 CACAACGCCAAAAACAGAAGG 58.807 47.619 0.00 0.00 0.00 3.46
2348 2895 1.208259 CAACGCCAAAAACAGAAGGC 58.792 50.000 0.00 0.00 43.61 4.35
2349 2896 0.104120 AACGCCAAAAACAGAAGGCC 59.896 50.000 0.00 0.00 44.18 5.19
2353 2900 1.134250 GCCAAAAACAGAAGGCCCAAA 60.134 47.619 0.00 0.00 41.25 3.28
2355 2902 3.205338 CCAAAAACAGAAGGCCCAAAAG 58.795 45.455 0.00 0.00 0.00 2.27
2356 2903 2.613595 CAAAAACAGAAGGCCCAAAAGC 59.386 45.455 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 92 4.331968 TCGGGTGCATTATCCCATTTATC 58.668 43.478 10.51 0.00 43.57 1.75
120 128 8.449397 CCAAAACAAAATCACACAATTCTCAAA 58.551 29.630 0.00 0.00 0.00 2.69
132 140 8.229811 GCCAATATTCTTCCAAAACAAAATCAC 58.770 33.333 0.00 0.00 0.00 3.06
204 212 7.455638 AGGAAATTCAGAATTCAGAAATCCCAA 59.544 33.333 27.26 6.81 34.73 4.12
250 258 5.551760 AGTCGCTGGTTCAATTCATTTAG 57.448 39.130 0.00 0.00 0.00 1.85
267 275 0.460987 ATGCTTGCTCTGGTAGTCGC 60.461 55.000 0.00 0.00 0.00 5.19
269 277 2.275318 GTGATGCTTGCTCTGGTAGTC 58.725 52.381 0.00 0.00 0.00 2.59
289 297 4.646492 CCAATTAAAGGGGGAGATCTTGTG 59.354 45.833 0.00 0.00 0.00 3.33
293 301 5.400653 CCAATCCAATTAAAGGGGGAGATCT 60.401 44.000 0.00 0.00 31.96 2.75
296 304 3.052186 CCCAATCCAATTAAAGGGGGAGA 60.052 47.826 0.00 0.00 36.40 3.71
318 327 8.083462 TGGATTTTTCTCCCGTACATTAAAAAC 58.917 33.333 0.00 0.00 34.12 2.43
329 338 2.042433 TCCCATTGGATTTTTCTCCCGT 59.958 45.455 3.62 0.00 35.03 5.28
390 434 1.296832 TCTAACCTCCCATCATCCCCA 59.703 52.381 0.00 0.00 0.00 4.96
453 497 7.899709 TCTCTACTCTAAAAGGGAAGTTGGTAT 59.100 37.037 0.00 0.00 0.00 2.73
733 793 6.292274 GCGTTCGTCAATAACCCGAATAAATA 60.292 38.462 0.00 0.00 41.90 1.40
750 810 1.081906 TCGGTAGTGTGCGTTCGTC 60.082 57.895 0.00 0.00 0.00 4.20
845 909 5.120519 GTGTATCAAAATGTTGCATGTTGGG 59.879 40.000 10.91 0.00 34.50 4.12
918 982 9.884636 AACATCACAGTGCTATTTATACAAGTA 57.115 29.630 0.00 0.00 0.00 2.24
937 1001 3.733337 AGTGTGAGGAGAACAACATCAC 58.267 45.455 0.00 0.00 40.49 3.06
938 1002 3.552890 CGAGTGTGAGGAGAACAACATCA 60.553 47.826 0.00 0.00 0.00 3.07
939 1003 2.989840 CGAGTGTGAGGAGAACAACATC 59.010 50.000 0.00 0.00 0.00 3.06
945 1014 1.634702 GATGCGAGTGTGAGGAGAAC 58.365 55.000 0.00 0.00 0.00 3.01
960 1029 3.891422 TGAAATTGTTGGATGGGATGC 57.109 42.857 0.00 0.00 0.00 3.91
1063 1132 1.135199 TCCGAGCCAGCTTAACTTACG 60.135 52.381 0.00 0.00 0.00 3.18
1164 1234 0.596082 GCTTAGCGCCTGAACCAAAA 59.404 50.000 2.29 0.00 0.00 2.44
1166 1236 0.955428 CAGCTTAGCGCCTGAACCAA 60.955 55.000 2.29 0.00 40.39 3.67
1194 1264 3.847671 TCACCAATATCAATACGGGCA 57.152 42.857 0.00 0.00 0.00 5.36
1377 1455 5.631929 GGGCAAAGGTTTACAATTTTACGAG 59.368 40.000 0.00 0.00 0.00 4.18
1380 1458 6.285224 ACAGGGCAAAGGTTTACAATTTTAC 58.715 36.000 0.00 0.00 0.00 2.01
1395 1473 7.398618 TGGATTTTTATTATCTGACAGGGCAAA 59.601 33.333 1.81 0.00 0.00 3.68
1456 1541 2.549282 GGTTGTACACACGCGCAG 59.451 61.111 5.73 0.55 0.00 5.18
1521 1608 8.141268 GGATTAGAGAAAGTAGTGGATGAGAAG 58.859 40.741 0.00 0.00 0.00 2.85
1527 1614 7.472100 CGGAATGGATTAGAGAAAGTAGTGGAT 60.472 40.741 0.00 0.00 0.00 3.41
1534 1636 3.433740 GGCCGGAATGGATTAGAGAAAGT 60.434 47.826 5.05 0.00 42.00 2.66
1607 1711 0.749818 TGCCTGTCTAGCTCCTCGAG 60.750 60.000 5.13 5.13 0.00 4.04
1608 1712 0.749818 CTGCCTGTCTAGCTCCTCGA 60.750 60.000 0.00 0.00 0.00 4.04
1609 1713 0.749818 TCTGCCTGTCTAGCTCCTCG 60.750 60.000 0.00 0.00 0.00 4.63
1610 1714 1.032014 CTCTGCCTGTCTAGCTCCTC 58.968 60.000 0.00 0.00 0.00 3.71
1620 1724 0.396811 GTTACCACCACTCTGCCTGT 59.603 55.000 0.00 0.00 0.00 4.00
1649 1753 3.947841 CTCCTCGAGCTCTCCGCG 61.948 72.222 12.85 0.00 45.59 6.46
1661 1765 1.227118 GCCGCTTGCTACTCTCCTC 60.227 63.158 0.00 0.00 36.87 3.71
1797 1943 1.538204 GCTGTCGATCCCGCTCATTAA 60.538 52.381 0.00 0.00 35.37 1.40
1800 1946 2.360949 CTGCTGTCGATCCCGCTCAT 62.361 60.000 0.00 0.00 35.37 2.90
1810 1956 2.917227 TCCACCAGCTGCTGTCGA 60.917 61.111 26.41 15.83 0.00 4.20
1855 2001 3.323136 CGCGAGATTTCGGCTCCG 61.323 66.667 0.00 1.14 46.76 4.63
1874 2421 0.400594 GTACCTTGGCACCCTCACTT 59.599 55.000 0.00 0.00 0.00 3.16
1937 2484 3.799420 CAGGAGCGAGCTAAATTACAGAC 59.201 47.826 0.00 0.00 0.00 3.51
1955 2502 5.386060 ACAGTAGACGGAATCATATCAGGA 58.614 41.667 0.00 0.00 0.00 3.86
1962 2509 3.895232 AGCAACAGTAGACGGAATCAT 57.105 42.857 0.00 0.00 0.00 2.45
1983 2530 3.298619 AGTCTATCATGTCTGCTCTGCT 58.701 45.455 0.00 0.00 0.00 4.24
1984 2531 3.731652 AGTCTATCATGTCTGCTCTGC 57.268 47.619 0.00 0.00 0.00 4.26
1985 2532 3.803231 GCAAGTCTATCATGTCTGCTCTG 59.197 47.826 0.00 0.00 0.00 3.35
1986 2533 3.181467 GGCAAGTCTATCATGTCTGCTCT 60.181 47.826 0.00 0.00 0.00 4.09
1987 2534 3.129871 GGCAAGTCTATCATGTCTGCTC 58.870 50.000 0.00 0.00 0.00 4.26
2026 2573 3.863041 ACAAGGGAGATCTAAGCGAAAC 58.137 45.455 0.00 0.00 0.00 2.78
2030 2577 4.130286 AGAAACAAGGGAGATCTAAGCG 57.870 45.455 0.00 0.00 0.00 4.68
2069 2616 7.712205 AGTTAATGTTGAAAAAGAAGCAATGCT 59.288 29.630 0.00 0.00 42.56 3.79
2073 2620 9.651913 AGAAAGTTAATGTTGAAAAAGAAGCAA 57.348 25.926 0.00 0.00 0.00 3.91
2097 2644 7.378181 GGGCATTTCTTAACAAAATCTGAAGA 58.622 34.615 0.00 0.00 0.00 2.87
2099 2646 6.155827 CGGGCATTTCTTAACAAAATCTGAA 58.844 36.000 0.00 0.00 0.00 3.02
2152 2699 1.806542 GAATTCAGAAAGGACGCTGCA 59.193 47.619 0.00 0.00 32.27 4.41
2175 2722 3.114616 CCCAGCTGCTTGACGTCG 61.115 66.667 8.66 0.00 0.00 5.12
2179 2726 0.036022 AAGAGACCCAGCTGCTTGAC 59.964 55.000 8.66 0.00 0.00 3.18
2211 2758 0.750182 CAGAGGTCGGGGAGTCTCTC 60.750 65.000 0.00 0.00 34.71 3.20
2212 2759 1.304952 CAGAGGTCGGGGAGTCTCT 59.695 63.158 0.00 0.00 37.09 3.10
2213 2760 2.419739 GCAGAGGTCGGGGAGTCTC 61.420 68.421 0.00 0.00 0.00 3.36
2214 2761 2.363147 GCAGAGGTCGGGGAGTCT 60.363 66.667 0.00 0.00 0.00 3.24
2215 2762 2.022240 GATGCAGAGGTCGGGGAGTC 62.022 65.000 0.00 0.00 0.00 3.36
2216 2763 2.039624 ATGCAGAGGTCGGGGAGT 59.960 61.111 0.00 0.00 0.00 3.85
2217 2764 1.760086 AGATGCAGAGGTCGGGGAG 60.760 63.158 0.00 0.00 0.00 4.30
2218 2765 2.060383 CAGATGCAGAGGTCGGGGA 61.060 63.158 0.00 0.00 0.00 4.81
2219 2766 1.617018 TTCAGATGCAGAGGTCGGGG 61.617 60.000 0.00 0.00 0.00 5.73
2220 2767 0.460987 GTTCAGATGCAGAGGTCGGG 60.461 60.000 0.00 0.00 0.00 5.14
2221 2768 0.803768 CGTTCAGATGCAGAGGTCGG 60.804 60.000 0.00 0.00 0.00 4.79
2222 2769 0.171231 TCGTTCAGATGCAGAGGTCG 59.829 55.000 0.00 0.00 0.00 4.79
2223 2770 2.593346 ATCGTTCAGATGCAGAGGTC 57.407 50.000 0.00 0.00 38.36 3.85
2232 2779 3.623060 GTGGTTGTATGCATCGTTCAGAT 59.377 43.478 0.19 0.00 41.01 2.90
2233 2780 3.000041 GTGGTTGTATGCATCGTTCAGA 59.000 45.455 0.19 0.00 0.00 3.27
2234 2781 2.741517 TGTGGTTGTATGCATCGTTCAG 59.258 45.455 0.19 0.00 0.00 3.02
2235 2782 2.772287 TGTGGTTGTATGCATCGTTCA 58.228 42.857 0.19 0.00 0.00 3.18
2236 2783 4.355543 AATGTGGTTGTATGCATCGTTC 57.644 40.909 0.19 0.00 0.00 3.95
2266 2813 5.825593 TCAGACCTTGTTGAACCTCTATT 57.174 39.130 0.00 0.00 0.00 1.73
2270 2817 4.200092 ACTTTCAGACCTTGTTGAACCTC 58.800 43.478 0.00 0.00 33.36 3.85
2272 2819 3.315470 GGACTTTCAGACCTTGTTGAACC 59.685 47.826 0.00 0.00 33.36 3.62
2273 2820 3.002348 CGGACTTTCAGACCTTGTTGAAC 59.998 47.826 0.00 0.00 33.36 3.18
2275 2822 2.432874 TCGGACTTTCAGACCTTGTTGA 59.567 45.455 0.00 0.00 0.00 3.18
2276 2823 2.833794 TCGGACTTTCAGACCTTGTTG 58.166 47.619 0.00 0.00 0.00 3.33
2278 2825 3.553828 TTTCGGACTTTCAGACCTTGT 57.446 42.857 0.00 0.00 0.00 3.16
2279 2826 3.625764 TGTTTTCGGACTTTCAGACCTTG 59.374 43.478 0.00 0.00 0.00 3.61
2280 2827 3.881220 TGTTTTCGGACTTTCAGACCTT 58.119 40.909 0.00 0.00 0.00 3.50
2282 2829 4.625972 TTTGTTTTCGGACTTTCAGACC 57.374 40.909 0.00 0.00 0.00 3.85
2303 2850 2.754552 TCTGTGTGAGCTTGCTGTTTTT 59.245 40.909 0.00 0.00 0.00 1.94
2306 2853 1.590932 CTCTGTGTGAGCTTGCTGTT 58.409 50.000 0.00 0.00 35.84 3.16
2307 2854 3.302375 CTCTGTGTGAGCTTGCTGT 57.698 52.632 0.00 0.00 35.84 4.40
2315 2862 1.835483 GCGTTGTGGCTCTGTGTGAG 61.835 60.000 0.00 0.00 45.33 3.51
2317 2864 2.633657 GCGTTGTGGCTCTGTGTG 59.366 61.111 0.00 0.00 0.00 3.82
2318 2865 2.591715 GGCGTTGTGGCTCTGTGT 60.592 61.111 0.00 0.00 40.72 3.72
2319 2866 1.723608 TTTGGCGTTGTGGCTCTGTG 61.724 55.000 0.00 0.00 45.14 3.66
2320 2867 1.034838 TTTTGGCGTTGTGGCTCTGT 61.035 50.000 0.00 0.00 45.14 3.41
2321 2868 0.102120 TTTTTGGCGTTGTGGCTCTG 59.898 50.000 0.00 0.00 45.14 3.35
2322 2869 0.102300 GTTTTTGGCGTTGTGGCTCT 59.898 50.000 0.00 0.00 45.14 4.09
2323 2870 0.179124 TGTTTTTGGCGTTGTGGCTC 60.179 50.000 0.00 0.00 45.14 4.70
2324 2871 0.179113 CTGTTTTTGGCGTTGTGGCT 60.179 50.000 0.00 0.00 45.14 4.75
2325 2872 0.179124 TCTGTTTTTGGCGTTGTGGC 60.179 50.000 0.00 0.00 45.12 5.01
2326 2873 2.192624 CTTCTGTTTTTGGCGTTGTGG 58.807 47.619 0.00 0.00 0.00 4.17
2327 2874 2.192624 CCTTCTGTTTTTGGCGTTGTG 58.807 47.619 0.00 0.00 0.00 3.33
2329 2876 1.208259 GCCTTCTGTTTTTGGCGTTG 58.792 50.000 0.00 0.00 35.79 4.10
2330 2877 0.104120 GGCCTTCTGTTTTTGGCGTT 59.896 50.000 0.00 0.00 45.75 4.84
2331 2878 1.739667 GGCCTTCTGTTTTTGGCGT 59.260 52.632 0.00 0.00 45.75 5.68
2332 2879 1.006220 GGGCCTTCTGTTTTTGGCG 60.006 57.895 0.84 0.00 45.75 5.69
2333 2880 0.467804 TTGGGCCTTCTGTTTTTGGC 59.532 50.000 4.53 0.00 44.22 4.52
2335 2882 2.613595 GCTTTTGGGCCTTCTGTTTTTG 59.386 45.455 4.53 0.00 0.00 2.44
2336 2883 2.917933 GCTTTTGGGCCTTCTGTTTTT 58.082 42.857 4.53 0.00 0.00 1.94
2337 2884 2.620251 GCTTTTGGGCCTTCTGTTTT 57.380 45.000 4.53 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.