Multiple sequence alignment - TraesCS4B01G255200

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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 TraesCS4B01G255200 chr4B 100.000 2604 0 0 1 2604 520232655 520230052 0.000000e+00 4809
1 TraesCS4B01G255200 chr4B 87.640 356 36 6 2253 2604 520238866 520238515 8.680000e-110 407
2 TraesCS4B01G255200 chr4B 84.898 245 13 8 1913 2151 520239142 520238916 2.610000e-55 226
3 TraesCS4B01G255200 chr4D 93.936 874 33 8 784 1654 423886252 423885396 0.000000e+00 1303
4 TraesCS4B01G255200 chr4D 93.375 800 26 8 1806 2604 423881809 423881036 0.000000e+00 1158
5 TraesCS4B01G255200 chr4D 89.022 920 73 12 2 911 423892028 423891127 0.000000e+00 1114
6 TraesCS4B01G255200 chr4D 84.517 704 70 19 1911 2604 423908222 423907548 0.000000e+00 660
7 TraesCS4B01G255200 chr4D 90.583 223 12 4 1590 1804 423885398 423885177 1.180000e-73 287
8 TraesCS4B01G255200 chr4A 85.206 703 76 11 1908 2604 40435543 40436223 0.000000e+00 697
9 TraesCS4B01G255200 chr4A 85.470 351 49 2 2255 2604 40412462 40412811 5.300000e-97 364
10 TraesCS4B01G255200 chr2D 98.333 120 2 0 1438 1557 23549057 23548938 7.300000e-51 211
11 TraesCS4B01G255200 chr2D 93.506 77 4 1 330 405 39657491 39657415 2.120000e-21 113
12 TraesCS4B01G255200 chr2D 93.506 77 4 1 330 405 291452561 291452637 2.120000e-21 113
13 TraesCS4B01G255200 chr7B 94.805 77 3 1 330 405 33501610 33501534 4.550000e-23 119
14 TraesCS4B01G255200 chr7B 94.521 73 3 1 330 401 716785463 716785391 7.620000e-21 111
15 TraesCS4B01G255200 chr6B 93.506 77 4 1 330 405 388227304 388227380 2.120000e-21 113
16 TraesCS4B01G255200 chr1B 93.243 74 4 1 330 402 583560710 583560783 9.850000e-20 108
17 TraesCS4B01G255200 chrUn 93.151 73 4 1 330 401 378557395 378557323 3.540000e-19 106
18 TraesCS4B01G255200 chrUn 93.151 73 4 1 330 401 417899464 417899392 3.540000e-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 TraesCS4B01G255200 chr4B 520230052 520232655 2603 True 4809.0 4809 100.000000 1 2604 1 chr4B.!!$R1 2603
1 TraesCS4B01G255200 chr4B 520238515 520239142 627 True 316.5 407 86.269000 1913 2604 2 chr4B.!!$R2 691
2 TraesCS4B01G255200 chr4D 423891127 423892028 901 True 1114.0 1114 89.022000 2 911 1 chr4D.!!$R1 909
3 TraesCS4B01G255200 chr4D 423881036 423886252 5216 True 916.0 1303 92.631333 784 2604 3 chr4D.!!$R3 1820
4 TraesCS4B01G255200 chr4D 423907548 423908222 674 True 660.0 660 84.517000 1911 2604 1 chr4D.!!$R2 693
5 TraesCS4B01G255200 chr4A 40435543 40436223 680 False 697.0 697 85.206000 1908 2604 1 chr4A.!!$F2 696

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
772 782 0.039165 CTTTTGACTTTGCCGCCCTC 60.039 55.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2337 5817 1.180029 TAGCACCGGTGGACTTACTC 58.82 55.0 34.58 15.96 0.0 2.59 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
33 34 0.652592 CGACGACATTCTTCCATGCC 59.347 55.000 0.00 0.00 0.00 4.40
39 40 3.152341 GACATTCTTCCATGCCATAGGG 58.848 50.000 0.00 0.00 37.18 3.53
55 56 0.178953 AGGGCAAGCAACTCCATTGT 60.179 50.000 0.00 0.00 40.77 2.71
60 61 2.095059 GCAAGCAACTCCATTGTTCGAT 60.095 45.455 0.00 0.00 40.77 3.59
66 67 0.374758 CTCCATTGTTCGATGGTGCG 59.625 55.000 16.02 5.59 45.53 5.34
69 70 0.795698 CATTGTTCGATGGTGCGACA 59.204 50.000 0.00 0.00 40.42 4.35
70 71 1.398041 CATTGTTCGATGGTGCGACAT 59.602 47.619 0.00 0.00 40.42 3.06
86 87 2.120232 GACATATGTTCGAGCCAGACG 58.880 52.381 10.30 0.00 0.00 4.18
124 125 0.682855 TTGGGGATGGAAATGGACGC 60.683 55.000 0.00 0.00 0.00 5.19
127 128 1.133915 GGGGATGGAAATGGACGCTTA 60.134 52.381 0.00 0.00 0.00 3.09
137 138 0.174617 TGGACGCTTATGTCGCATCA 59.825 50.000 0.00 0.00 39.83 3.07
161 162 8.615211 TCATGATCCTCAATTGTTTTAAGATCG 58.385 33.333 5.13 0.15 33.25 3.69
173 174 1.131638 TAAGATCGCATGCCCTTCCT 58.868 50.000 13.15 0.00 0.00 3.36
175 176 0.257039 AGATCGCATGCCCTTCCTTT 59.743 50.000 13.15 0.00 0.00 3.11
197 198 0.673956 GGACGGGCTTTTCACCTCTC 60.674 60.000 0.00 0.00 0.00 3.20
201 202 0.321996 GGGCTTTTCACCTCTCGAGT 59.678 55.000 13.13 0.00 0.00 4.18
207 208 0.965866 TTCACCTCTCGAGTCGGCAT 60.966 55.000 13.54 0.00 0.00 4.40
215 216 0.965866 TCGAGTCGGCATGTTCCTCT 60.966 55.000 13.54 0.00 0.00 3.69
220 221 2.003301 GTCGGCATGTTCCTCTTCTTC 58.997 52.381 0.00 0.00 0.00 2.87
233 234 1.067974 TCTTCTTCGGTGCTTCGTTCA 59.932 47.619 0.00 0.00 0.00 3.18
236 237 0.934496 CTTCGGTGCTTCGTTCACAA 59.066 50.000 6.74 0.00 36.22 3.33
262 263 5.083533 AGATCTTAGTGTCTCCAAGCTTG 57.916 43.478 19.93 19.93 0.00 4.01
275 276 4.647424 CCAAGCTTGGTGTTTCTTGTTA 57.353 40.909 33.46 0.00 43.43 2.41
279 280 6.018832 CCAAGCTTGGTGTTTCTTGTTAATTG 60.019 38.462 33.46 4.92 43.43 2.32
345 346 3.583806 CGGCCTTATCACAATTTGCAAA 58.416 40.909 15.44 15.44 0.00 3.68
346 347 3.613737 CGGCCTTATCACAATTTGCAAAG 59.386 43.478 18.19 7.44 0.00 2.77
349 350 4.328169 GCCTTATCACAATTTGCAAAGCTC 59.672 41.667 18.19 0.00 0.00 4.09
350 351 4.560035 CCTTATCACAATTTGCAAAGCTCG 59.440 41.667 18.19 8.03 0.00 5.03
359 360 4.340894 TTTGCAAAGCTCGTCACATATC 57.659 40.909 8.05 0.00 0.00 1.63
362 363 2.677836 GCAAAGCTCGTCACATATCCAA 59.322 45.455 0.00 0.00 0.00 3.53
414 416 8.399529 TCAGGTATAGGTATAGGCTTTATGAGT 58.600 37.037 0.00 0.00 0.00 3.41
415 417 9.696572 CAGGTATAGGTATAGGCTTTATGAGTA 57.303 37.037 0.00 0.00 0.00 2.59
444 454 5.833082 TCTATTCAGATGTAAGAACTCCGC 58.167 41.667 0.00 0.00 0.00 5.54
478 488 1.366111 GCGCTTATCGGCAAGGTTGA 61.366 55.000 0.00 0.00 38.94 3.18
480 490 1.017387 GCTTATCGGCAAGGTTGAGG 58.983 55.000 0.00 0.00 0.00 3.86
582 592 8.293867 TCATTGTTGTACTTTGCCTTGTTATAC 58.706 33.333 0.00 0.00 0.00 1.47
586 596 7.932491 TGTTGTACTTTGCCTTGTTATACACTA 59.068 33.333 0.00 0.00 0.00 2.74
587 597 7.894376 TGTACTTTGCCTTGTTATACACTAC 57.106 36.000 0.00 0.00 0.00 2.73
588 598 6.587226 TGTACTTTGCCTTGTTATACACTACG 59.413 38.462 0.00 0.00 0.00 3.51
617 627 7.853524 TGTTTCTGTTGTTCGTCGTTATAAAT 58.146 30.769 0.00 0.00 0.00 1.40
619 629 6.636666 TCTGTTGTTCGTCGTTATAAATCC 57.363 37.500 0.00 0.00 0.00 3.01
621 631 7.537715 TCTGTTGTTCGTCGTTATAAATCCTA 58.462 34.615 0.00 0.00 0.00 2.94
625 635 5.975344 TGTTCGTCGTTATAAATCCTAGCTG 59.025 40.000 0.00 0.00 0.00 4.24
629 639 5.175126 CGTCGTTATAAATCCTAGCTGGTTG 59.825 44.000 0.00 0.00 37.07 3.77
632 642 8.086522 GTCGTTATAAATCCTAGCTGGTTGATA 58.913 37.037 0.00 0.00 37.07 2.15
638 648 7.814264 AAATCCTAGCTGGTTGATATCTTTG 57.186 36.000 3.98 0.00 37.07 2.77
658 668 5.957842 TTGTTAATTCAAATGCGGACTCT 57.042 34.783 0.00 0.00 0.00 3.24
688 698 6.827727 AGCCTTTGTTCTAGAAAACTCTGTA 58.172 36.000 6.78 0.00 0.00 2.74
691 701 7.226918 GCCTTTGTTCTAGAAAACTCTGTAAGT 59.773 37.037 6.78 0.00 41.10 2.24
700 710 2.770164 ACTCTGTAAGTCATGGCCAC 57.230 50.000 8.16 0.00 30.02 5.01
701 711 2.260822 ACTCTGTAAGTCATGGCCACT 58.739 47.619 8.16 0.00 30.02 4.00
704 714 1.003580 CTGTAAGTCATGGCCACTGGT 59.996 52.381 8.16 0.00 0.00 4.00
706 716 1.279271 GTAAGTCATGGCCACTGGTCT 59.721 52.381 8.16 0.58 0.00 3.85
772 782 0.039165 CTTTTGACTTTGCCGCCCTC 60.039 55.000 0.00 0.00 0.00 4.30
780 790 0.329931 TTTGCCGCCCTCCAGATAAA 59.670 50.000 0.00 0.00 0.00 1.40
781 791 0.329931 TTGCCGCCCTCCAGATAAAA 59.670 50.000 0.00 0.00 0.00 1.52
782 792 0.393808 TGCCGCCCTCCAGATAAAAC 60.394 55.000 0.00 0.00 0.00 2.43
796 806 6.486657 TCCAGATAAAACAACCAAACAGAGAG 59.513 38.462 0.00 0.00 0.00 3.20
812 822 4.404073 ACAGAGAGTGTTGACAGAGAAACT 59.596 41.667 0.00 0.00 34.94 2.66
834 844 2.618241 GAGAACATTCAGCAACACCACA 59.382 45.455 0.00 0.00 0.00 4.17
835 845 3.023119 AGAACATTCAGCAACACCACAA 58.977 40.909 0.00 0.00 0.00 3.33
869 879 0.107456 AGACCAACAGCTCAGTGTGG 59.893 55.000 0.00 0.00 0.00 4.17
916 926 0.250553 AGGCTCGATCGACTCCTAGG 60.251 60.000 24.81 11.90 0.00 3.02
920 930 1.071071 CTCGATCGACTCCTAGGTCCT 59.929 57.143 15.15 0.00 33.07 3.85
921 931 2.299582 CTCGATCGACTCCTAGGTCCTA 59.700 54.545 15.15 0.00 33.07 2.94
922 932 2.299582 TCGATCGACTCCTAGGTCCTAG 59.700 54.545 15.15 17.97 34.16 3.02
923 933 2.429478 GATCGACTCCTAGGTCCTAGC 58.571 57.143 19.30 5.89 33.12 3.42
924 934 0.473326 TCGACTCCTAGGTCCTAGCC 59.527 60.000 19.30 7.78 33.12 3.93
925 935 0.885596 CGACTCCTAGGTCCTAGCCG 60.886 65.000 19.30 13.95 33.12 5.52
926 936 1.152715 ACTCCTAGGTCCTAGCCGC 60.153 63.158 19.30 0.00 33.12 6.53
927 937 1.151908 CTCCTAGGTCCTAGCCGCT 59.848 63.158 19.30 0.00 33.12 5.52
928 938 0.400975 CTCCTAGGTCCTAGCCGCTA 59.599 60.000 19.30 0.00 33.12 4.26
929 939 0.400975 TCCTAGGTCCTAGCCGCTAG 59.599 60.000 19.30 19.03 33.12 3.42
930 940 1.245376 CCTAGGTCCTAGCCGCTAGC 61.245 65.000 20.33 4.06 44.25 3.42
952 962 3.884091 CGGCCCTATATATAGAGACGCTT 59.116 47.826 15.55 0.00 32.92 4.68
981 991 1.047002 CCCCAACAGCAAAACCATCA 58.953 50.000 0.00 0.00 0.00 3.07
998 1008 3.563508 CATCAAGAGACCGATCGATCAG 58.436 50.000 24.40 16.23 0.00 2.90
1188 1201 1.079503 GAGACCATCAACAAGACCGC 58.920 55.000 0.00 0.00 0.00 5.68
1443 1456 1.454847 GAACCCACAACACCAGGCA 60.455 57.895 0.00 0.00 0.00 4.75
1451 1464 0.107456 CAACACCAGGCAGTCTGACT 59.893 55.000 0.94 0.94 46.18 3.41
1557 1570 0.456221 ACGTACAAGATGGAGCTCCG 59.544 55.000 27.43 15.16 39.43 4.63
1588 1601 4.878682 CCGTACGCCCCTTACGCC 62.879 72.222 10.49 0.00 40.82 5.68
1638 1714 2.408368 CCGCTACATACATGCATGTACG 59.592 50.000 35.53 31.05 45.11 3.67
1641 1717 5.092781 CGCTACATACATGCATGTACGATA 58.907 41.667 35.53 25.67 45.11 2.92
1657 1733 1.745087 CGATAAAACCACTGCCAGCAT 59.255 47.619 0.00 0.00 0.00 3.79
1745 1825 7.545615 GCTTTTGTGGGGAATTGTTATTTCTAG 59.454 37.037 0.00 0.00 0.00 2.43
1749 1829 8.746052 TGTGGGGAATTGTTATTTCTAGTATG 57.254 34.615 0.00 0.00 0.00 2.39
1751 1831 9.057089 GTGGGGAATTGTTATTTCTAGTATGAG 57.943 37.037 0.00 0.00 0.00 2.90
1821 5267 2.370849 AGTGGAGTATGGGTTTCAACGT 59.629 45.455 0.00 0.00 0.00 3.99
1831 5277 4.487948 TGGGTTTCAACGTTAGATAGTCG 58.512 43.478 0.00 0.00 0.00 4.18
1845 5291 7.218583 CGTTAGATAGTCGAAACTTTCTCCTTC 59.781 40.741 2.45 0.00 41.26 3.46
1867 5313 5.755849 TCCTGAATCCAGTTTATCCTTTCC 58.244 41.667 0.00 0.00 38.74 3.13
1919 5365 2.038164 ACAGATGTCACAGAGCACACAT 59.962 45.455 0.00 0.00 32.02 3.21
1920 5366 2.671888 CAGATGTCACAGAGCACACATC 59.328 50.000 3.21 3.21 43.70 3.06
1957 5403 3.629087 AGAAATTCAGCATCTTCCCTGG 58.371 45.455 0.00 0.00 0.00 4.45
1962 5408 1.925255 TCAGCATCTTCCCTGGGAAAT 59.075 47.619 27.32 19.66 41.54 2.17
1963 5409 2.312741 TCAGCATCTTCCCTGGGAAATT 59.687 45.455 27.32 15.50 41.54 1.82
1964 5410 3.102204 CAGCATCTTCCCTGGGAAATTT 58.898 45.455 27.32 13.11 41.54 1.82
1965 5411 3.131755 CAGCATCTTCCCTGGGAAATTTC 59.868 47.826 27.32 16.78 41.54 2.17
1966 5412 3.099141 GCATCTTCCCTGGGAAATTTCA 58.901 45.455 27.32 10.66 41.54 2.69
1967 5413 3.131755 GCATCTTCCCTGGGAAATTTCAG 59.868 47.826 27.32 15.55 41.54 3.02
2031 5497 0.329261 TCCCAGCTTACATGCAGCTT 59.671 50.000 15.74 1.54 45.82 3.74
2337 5817 2.554032 GGTGGTCTTCTGGTTGAATGTG 59.446 50.000 0.00 0.00 33.71 3.21
2345 5825 6.146347 GTCTTCTGGTTGAATGTGAGTAAGTC 59.854 42.308 0.00 0.00 33.71 3.01
2356 5836 1.180029 GAGTAAGTCCACCGGTGCTA 58.820 55.000 29.75 16.32 0.00 3.49
2371 5851 3.909574 CGGTGCTAATTTTGTACAAACGG 59.090 43.478 20.43 11.41 0.00 4.44
2394 5874 2.105821 TCTTGTCCTCCCGTTTGTCAAT 59.894 45.455 0.00 0.00 0.00 2.57
2456 5936 2.838736 CATAGTCGGATTTCCAGTGGG 58.161 52.381 9.92 0.00 35.14 4.61
2593 6073 0.106868 CATCCTCCTCTGGCAATGCA 60.107 55.000 7.79 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.135199 GTCGTCGATAGGCTCCAACAA 60.135 52.381 0.00 0.00 39.78 2.83
17 18 2.810274 CCTATGGCATGGAAGAATGTCG 59.190 50.000 12.93 0.00 34.80 4.35
33 34 2.062971 ATGGAGTTGCTTGCCCTATG 57.937 50.000 0.00 0.00 0.00 2.23
39 40 1.266718 TCGAACAATGGAGTTGCTTGC 59.733 47.619 0.00 0.00 41.69 4.01
40 41 3.495193 CATCGAACAATGGAGTTGCTTG 58.505 45.455 0.00 0.00 41.69 4.01
55 56 2.595124 ACATATGTCGCACCATCGAA 57.405 45.000 1.41 0.00 40.43 3.71
60 61 1.921243 CTCGAACATATGTCGCACCA 58.079 50.000 9.23 0.00 0.00 4.17
66 67 2.120232 CGTCTGGCTCGAACATATGTC 58.880 52.381 9.23 2.22 0.00 3.06
69 70 1.338337 CCTCGTCTGGCTCGAACATAT 59.662 52.381 0.00 0.00 36.89 1.78
70 71 0.738975 CCTCGTCTGGCTCGAACATA 59.261 55.000 0.00 0.00 36.89 2.29
86 87 2.168458 AAGAAGGCCTCTACCTCCTC 57.832 55.000 5.23 0.00 39.93 3.71
124 125 4.563061 TGAGGATCATGATGCGACATAAG 58.437 43.478 19.97 0.00 42.56 1.73
160 161 1.213537 CACAAAGGAAGGGCATGCG 59.786 57.895 12.44 0.00 0.00 4.73
161 162 0.899717 TCCACAAAGGAAGGGCATGC 60.900 55.000 9.90 9.90 45.65 4.06
173 174 0.741915 GTGAAAAGCCCGTCCACAAA 59.258 50.000 0.00 0.00 0.00 2.83
175 176 1.527380 GGTGAAAAGCCCGTCCACA 60.527 57.895 0.00 0.00 0.00 4.17
197 198 0.108615 AAGAGGAACATGCCGACTCG 60.109 55.000 0.00 0.00 33.58 4.18
201 202 1.404181 CGAAGAAGAGGAACATGCCGA 60.404 52.381 0.00 0.00 0.00 5.54
207 208 1.048601 AGCACCGAAGAAGAGGAACA 58.951 50.000 0.00 0.00 0.00 3.18
215 216 1.214367 GTGAACGAAGCACCGAAGAA 58.786 50.000 4.78 0.00 0.00 2.52
220 221 1.329292 TCTTTTGTGAACGAAGCACCG 59.671 47.619 0.00 0.00 35.43 4.94
233 234 6.672266 TGGAGACACTAAGATCTCTTTTGT 57.328 37.500 0.00 2.70 41.05 2.83
236 237 5.483583 AGCTTGGAGACACTAAGATCTCTTT 59.516 40.000 0.00 0.00 42.67 2.52
262 263 9.093970 AGCTAAAAACAATTAACAAGAAACACC 57.906 29.630 0.00 0.00 0.00 4.16
275 276 7.983307 TCAAATGCAACAAGCTAAAAACAATT 58.017 26.923 0.00 0.00 45.94 2.32
279 280 5.558844 GCCTCAAATGCAACAAGCTAAAAAC 60.559 40.000 0.00 0.00 45.94 2.43
309 310 1.295423 GCCGCCAGAGAAACAGGTA 59.705 57.895 0.00 0.00 0.00 3.08
311 312 2.747855 GGCCGCCAGAGAAACAGG 60.748 66.667 3.91 0.00 0.00 4.00
314 315 1.300481 GATAAGGCCGCCAGAGAAAC 58.700 55.000 13.15 0.00 0.00 2.78
325 326 3.371898 GCTTTGCAAATTGTGATAAGGCC 59.628 43.478 13.23 0.00 0.00 5.19
345 346 4.471904 TTTCTTGGATATGTGACGAGCT 57.528 40.909 0.00 0.00 0.00 4.09
346 347 4.811024 TCATTTCTTGGATATGTGACGAGC 59.189 41.667 0.00 0.00 0.00 5.03
349 350 6.092670 ACAACTCATTTCTTGGATATGTGACG 59.907 38.462 6.90 0.00 0.00 4.35
350 351 7.246311 CACAACTCATTTCTTGGATATGTGAC 58.754 38.462 0.00 0.00 37.27 3.67
359 360 5.710513 TCAATCCACAACTCATTTCTTGG 57.289 39.130 0.00 0.00 0.00 3.61
362 363 7.954835 TGATTTTCAATCCACAACTCATTTCT 58.045 30.769 0.00 0.00 0.00 2.52
432 434 0.862283 CTCGCTCGCGGAGTTCTTAC 60.862 60.000 6.13 0.00 40.25 2.34
460 470 0.652592 CTCAACCTTGCCGATAAGCG 59.347 55.000 0.00 0.00 40.47 4.68
463 473 3.426787 TTTCCTCAACCTTGCCGATAA 57.573 42.857 0.00 0.00 0.00 1.75
475 485 2.071778 ACTTGCAGGCTTTTCCTCAA 57.928 45.000 0.00 0.00 45.52 3.02
480 490 3.258123 TCCCATTTACTTGCAGGCTTTTC 59.742 43.478 0.00 0.00 0.00 2.29
489 499 6.206829 ACACTAGAAACTTCCCATTTACTTGC 59.793 38.462 0.00 0.00 0.00 4.01
493 503 7.381408 GCAAAACACTAGAAACTTCCCATTTAC 59.619 37.037 0.00 0.00 0.00 2.01
494 504 7.286775 AGCAAAACACTAGAAACTTCCCATTTA 59.713 33.333 0.00 0.00 0.00 1.40
498 508 4.532834 AGCAAAACACTAGAAACTTCCCA 58.467 39.130 0.00 0.00 0.00 4.37
499 509 4.319549 CGAGCAAAACACTAGAAACTTCCC 60.320 45.833 0.00 0.00 0.00 3.97
567 577 6.476243 AACGTAGTGTATAACAAGGCAAAG 57.524 37.500 0.00 0.00 45.00 2.77
568 578 6.864360 AAACGTAGTGTATAACAAGGCAAA 57.136 33.333 0.00 0.00 45.00 3.68
569 579 6.260493 ACAAAACGTAGTGTATAACAAGGCAA 59.740 34.615 2.37 0.00 45.00 4.52
570 580 5.759273 ACAAAACGTAGTGTATAACAAGGCA 59.241 36.000 2.37 0.00 45.00 4.75
582 592 5.224313 CGAACAACAGAAACAAAACGTAGTG 59.776 40.000 0.00 0.00 45.00 2.74
586 596 4.149910 ACGAACAACAGAAACAAAACGT 57.850 36.364 0.00 0.00 0.00 3.99
587 597 3.234284 CGACGAACAACAGAAACAAAACG 59.766 43.478 0.00 0.00 0.00 3.60
588 598 4.153256 ACGACGAACAACAGAAACAAAAC 58.847 39.130 0.00 0.00 0.00 2.43
617 627 5.957771 ACAAAGATATCAACCAGCTAGGA 57.042 39.130 5.32 0.00 41.22 2.94
621 631 8.579850 TGAATTAACAAAGATATCAACCAGCT 57.420 30.769 5.32 0.00 0.00 4.24
629 639 8.958043 GTCCGCATTTGAATTAACAAAGATATC 58.042 33.333 0.00 0.00 41.87 1.63
632 642 6.924111 AGTCCGCATTTGAATTAACAAAGAT 58.076 32.000 0.00 0.00 41.87 2.40
638 648 6.183309 AGAAGAGTCCGCATTTGAATTAAC 57.817 37.500 0.00 0.00 0.00 2.01
658 668 8.747538 AGTTTTCTAGAACAAAGGCTTAAGAA 57.252 30.769 6.67 1.05 31.94 2.52
688 698 0.773644 AAGACCAGTGGCCATGACTT 59.226 50.000 9.72 10.09 0.00 3.01
691 701 2.380064 AAAAAGACCAGTGGCCATGA 57.620 45.000 9.72 0.00 0.00 3.07
741 751 7.011016 CGGCAAAGTCAAAAGGTCTTTTTAAAT 59.989 33.333 6.01 0.00 40.45 1.40
743 753 5.808030 CGGCAAAGTCAAAAGGTCTTTTTAA 59.192 36.000 6.01 0.00 40.45 1.52
759 769 1.271840 TATCTGGAGGGCGGCAAAGT 61.272 55.000 12.47 0.00 0.00 2.66
772 782 6.263168 ACTCTCTGTTTGGTTGTTTTATCTGG 59.737 38.462 0.00 0.00 0.00 3.86
780 790 4.156008 GTCAACACTCTCTGTTTGGTTGTT 59.844 41.667 0.00 0.00 41.50 2.83
781 791 3.689649 GTCAACACTCTCTGTTTGGTTGT 59.310 43.478 0.00 0.00 41.50 3.32
782 792 3.689161 TGTCAACACTCTCTGTTTGGTTG 59.311 43.478 0.00 0.00 41.50 3.77
796 806 4.870426 TGTTCTCAGTTTCTCTGTCAACAC 59.130 41.667 0.00 0.00 43.97 3.32
812 822 2.618241 GTGGTGTTGCTGAATGTTCTCA 59.382 45.455 0.00 0.00 0.00 3.27
834 844 3.314693 TGGTCTTGGTCCAAGTCTAGTT 58.685 45.455 27.29 0.00 41.66 2.24
835 845 2.972348 TGGTCTTGGTCCAAGTCTAGT 58.028 47.619 27.29 0.00 41.66 2.57
924 934 3.409570 TCTATATATAGGGCCGCTAGCG 58.590 50.000 29.93 29.93 45.17 4.26
925 935 4.456566 GTCTCTATATATAGGGCCGCTAGC 59.543 50.000 17.81 4.06 42.60 3.42
926 936 4.691685 CGTCTCTATATATAGGGCCGCTAG 59.308 50.000 17.81 7.70 30.80 3.42
927 937 4.639334 CGTCTCTATATATAGGGCCGCTA 58.361 47.826 17.81 0.00 30.80 4.26
928 938 3.478509 CGTCTCTATATATAGGGCCGCT 58.521 50.000 17.81 0.00 30.80 5.52
929 939 2.030981 GCGTCTCTATATATAGGGCCGC 60.031 54.545 26.67 26.67 35.03 6.53
930 940 3.478509 AGCGTCTCTATATATAGGGCCG 58.521 50.000 16.80 16.80 30.80 6.13
931 941 5.127356 ACAAAGCGTCTCTATATATAGGGCC 59.873 44.000 17.81 5.33 30.80 5.80
932 942 6.210287 ACAAAGCGTCTCTATATATAGGGC 57.790 41.667 17.81 15.27 30.80 5.19
952 962 0.035439 GCTGTTGGGGCTAGCTACAA 60.035 55.000 15.72 16.41 34.70 2.41
981 991 1.393603 TGCTGATCGATCGGTCTCTT 58.606 50.000 29.95 1.00 35.60 2.85
1063 1073 0.106708 AGAACAGCTTTGAGGTGCGA 59.893 50.000 7.02 0.00 46.94 5.10
1188 1201 1.063649 CCGTCGACGACCATGTAGG 59.936 63.158 37.65 14.70 43.02 3.18
1318 1331 2.494918 GTGATGGACGTCCCCTCG 59.505 66.667 31.19 0.00 32.84 4.63
1367 1380 0.617935 TGGATCGTGATCTTGGCCAA 59.382 50.000 19.25 19.25 37.92 4.52
1443 1456 4.436368 CCACCGGGTAGTCAGACT 57.564 61.111 6.32 8.50 0.00 3.24
1557 1570 2.292559 TACGGGGGCCAGTACAACC 61.293 63.158 4.39 0.00 0.00 3.77
1588 1601 2.125106 GGCTACTGCGGAGTTGGG 60.125 66.667 16.89 7.43 40.82 4.12
1619 1632 6.944557 TTATCGTACATGCATGTATGTAGC 57.055 37.500 38.96 26.66 45.77 3.58
1620 1633 8.221100 GGTTTTATCGTACATGCATGTATGTAG 58.779 37.037 38.96 29.03 45.77 2.74
1638 1714 5.334105 CGTATATGCTGGCAGTGGTTTTATC 60.334 44.000 17.16 0.00 0.00 1.75
1641 1717 2.682856 CGTATATGCTGGCAGTGGTTTT 59.317 45.455 17.16 0.00 0.00 2.43
1657 1733 4.819769 ACTGCTCCGTTTTAAACCGTATA 58.180 39.130 4.40 0.00 0.00 1.47
1745 1825 4.455606 AGCCCTTTACATTGCTCTCATAC 58.544 43.478 0.00 0.00 0.00 2.39
1749 1829 4.998033 GGTATAGCCCTTTACATTGCTCTC 59.002 45.833 0.00 0.00 35.34 3.20
1751 1831 4.714632 TGGTATAGCCCTTTACATTGCTC 58.285 43.478 0.00 0.00 35.34 4.26
1796 1876 4.927267 TGAAACCCATACTCCACTTCAT 57.073 40.909 0.00 0.00 0.00 2.57
1801 1881 2.774687 ACGTTGAAACCCATACTCCAC 58.225 47.619 0.00 0.00 0.00 4.02
1804 1884 7.263496 ACTATCTAACGTTGAAACCCATACTC 58.737 38.462 11.99 0.00 0.00 2.59
1811 5257 6.695292 TTTCGACTATCTAACGTTGAAACC 57.305 37.500 11.99 0.00 38.15 3.27
1821 5267 7.396623 AGGAAGGAGAAAGTTTCGACTATCTAA 59.603 37.037 9.91 0.00 34.02 2.10
1831 5277 5.316987 TGGATTCAGGAAGGAGAAAGTTTC 58.683 41.667 7.57 7.57 0.00 2.78
1845 5291 4.889995 GGGAAAGGATAAACTGGATTCAGG 59.110 45.833 5.84 0.00 44.99 3.86
1867 5313 4.552365 ATCATGGCGTGCTCCCGG 62.552 66.667 0.65 0.00 0.00 5.73
1919 5365 8.158025 TGAATTTCTTGGAAATACTAGAGGGA 57.842 34.615 0.00 0.00 0.00 4.20
1920 5366 7.012799 GCTGAATTTCTTGGAAATACTAGAGGG 59.987 40.741 0.00 0.00 0.00 4.30
1957 5403 6.454795 TGCAAATACAGTTCCTGAAATTTCC 58.545 36.000 15.48 0.00 32.74 3.13
1962 5408 5.620206 TCTCTGCAAATACAGTTCCTGAAA 58.380 37.500 0.00 0.00 38.84 2.69
1963 5409 5.012046 TCTCTCTGCAAATACAGTTCCTGAA 59.988 40.000 0.00 0.00 38.84 3.02
1964 5410 4.528206 TCTCTCTGCAAATACAGTTCCTGA 59.472 41.667 0.00 0.00 38.84 3.86
1965 5411 4.825422 TCTCTCTGCAAATACAGTTCCTG 58.175 43.478 0.00 0.00 38.84 3.86
1966 5412 5.426504 CATCTCTCTGCAAATACAGTTCCT 58.573 41.667 0.00 0.00 38.84 3.36
1967 5413 4.574013 CCATCTCTCTGCAAATACAGTTCC 59.426 45.833 0.00 0.00 38.84 3.62
1968 5414 4.034975 GCCATCTCTCTGCAAATACAGTTC 59.965 45.833 0.00 0.00 38.84 3.01
1969 5415 3.944015 GCCATCTCTCTGCAAATACAGTT 59.056 43.478 0.00 0.00 38.84 3.16
1970 5416 3.199508 AGCCATCTCTCTGCAAATACAGT 59.800 43.478 0.00 0.00 38.84 3.55
1971 5417 3.806380 AGCCATCTCTCTGCAAATACAG 58.194 45.455 0.00 0.00 39.12 2.74
1972 5418 3.920231 AGCCATCTCTCTGCAAATACA 57.080 42.857 0.00 0.00 0.00 2.29
1973 5419 4.314121 CCTAGCCATCTCTCTGCAAATAC 58.686 47.826 0.00 0.00 0.00 1.89
1974 5420 3.326006 CCCTAGCCATCTCTCTGCAAATA 59.674 47.826 0.00 0.00 0.00 1.40
1975 5421 2.106166 CCCTAGCCATCTCTCTGCAAAT 59.894 50.000 0.00 0.00 0.00 2.32
1976 5422 1.487976 CCCTAGCCATCTCTCTGCAAA 59.512 52.381 0.00 0.00 0.00 3.68
2031 5497 9.665719 TCATGTAAATAAACTGATTGTAGCAGA 57.334 29.630 0.00 0.00 36.86 4.26
2049 5515 6.208988 AGCTCTATTCTGTCGTCATGTAAA 57.791 37.500 0.00 0.00 0.00 2.01
2050 5516 5.836821 AGCTCTATTCTGTCGTCATGTAA 57.163 39.130 0.00 0.00 0.00 2.41
2051 5517 6.238676 GGTTAGCTCTATTCTGTCGTCATGTA 60.239 42.308 0.00 0.00 0.00 2.29
2052 5518 5.450688 GGTTAGCTCTATTCTGTCGTCATGT 60.451 44.000 0.00 0.00 0.00 3.21
2099 5565 7.995463 TTTTTGTTTTCTTGAACCTATTCCG 57.005 32.000 0.00 0.00 33.49 4.30
2194 5666 6.650427 TGAGCGTGACACCTCTTTATATAT 57.350 37.500 18.79 0.00 0.00 0.86
2195 5667 6.459670 TTGAGCGTGACACCTCTTTATATA 57.540 37.500 18.79 1.85 0.00 0.86
2196 5668 5.339008 TTGAGCGTGACACCTCTTTATAT 57.661 39.130 18.79 0.00 0.00 0.86
2197 5669 4.794278 TTGAGCGTGACACCTCTTTATA 57.206 40.909 18.79 2.89 0.00 0.98
2337 5817 1.180029 TAGCACCGGTGGACTTACTC 58.820 55.000 34.58 15.96 0.00 2.59
2345 5825 2.814919 TGTACAAAATTAGCACCGGTGG 59.185 45.455 34.58 18.07 0.00 4.61
2356 5836 6.443792 GGACAAGATCCGTTTGTACAAAATT 58.556 36.000 22.14 7.79 38.87 1.82
2371 5851 2.289444 TGACAAACGGGAGGACAAGATC 60.289 50.000 0.00 0.00 0.00 2.75
2394 5874 3.772025 GGAGAGAGATGGTCTTTTCCTGA 59.228 47.826 0.00 0.00 36.81 3.86
2444 5924 1.250840 GGTGCACCCCACTGGAAATC 61.251 60.000 26.31 0.00 44.08 2.17


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

AutoCloner maintained by Alex Coulton.