Multiple sequence alignment - TraesCS4A01G426300

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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 TraesCS4A01G426300 chr4A 100.000 3917 0 0 1 3917 697950818 697954734 0.000000e+00 7234
1 TraesCS4A01G426300 chr4A 92.498 1573 106 9 1899 3463 698040583 698042151 0.000000e+00 2241
2 TraesCS4A01G426300 chr4A 88.929 1680 140 9 2 1640 698038645 698040319 0.000000e+00 2030
3 TraesCS4A01G426300 chr4A 90.196 204 15 3 1703 1906 698040363 698040561 1.080000e-65 261
4 TraesCS4A01G426300 chr7A 90.386 3630 235 38 332 3917 31103424 31099865 0.000000e+00 4665
5 TraesCS4A01G426300 chr7A 90.066 302 27 1 33 334 31103803 31103505 4.750000e-104 388
6 TraesCS4A01G426300 chr7D 90.506 2212 133 35 1712 3917 30839837 30837697 0.000000e+00 2850
7 TraesCS4A01G426300 chr7D 90.627 1643 109 18 33 1673 30841438 30839839 0.000000e+00 2139
8 TraesCS4A01G426300 chr7D 92.793 555 33 4 3365 3917 30525234 30524685 0.000000e+00 797
9 TraesCS4A01G426300 chr3D 75.393 382 71 18 1105 1473 123517116 123516745 3.130000e-36 163
10 TraesCS4A01G426300 chr3B 73.600 500 100 25 1105 1582 176859970 176859481 3.130000e-36 163
11 TraesCS4A01G426300 chr3B 73.600 500 100 25 1105 1582 176879721 176879232 3.130000e-36 163
12 TraesCS4A01G426300 chr3B 75.131 382 69 20 1105 1473 176783459 176783091 5.240000e-34 156
13 TraesCS4A01G426300 chr3B 82.584 178 24 6 1105 1280 176636616 176636444 2.440000e-32 150
14 TraesCS4A01G426300 chr3A 73.936 376 75 20 1105 1473 131084031 131083672 3.180000e-26 130


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 TraesCS4A01G426300 chr4A 697950818 697954734 3916 False 7234.000000 7234 100.0000 1 3917 1 chr4A.!!$F1 3916
1 TraesCS4A01G426300 chr4A 698038645 698042151 3506 False 1510.666667 2241 90.5410 2 3463 3 chr4A.!!$F2 3461
2 TraesCS4A01G426300 chr7A 31099865 31103803 3938 True 2526.500000 4665 90.2260 33 3917 2 chr7A.!!$R1 3884
3 TraesCS4A01G426300 chr7D 30837697 30841438 3741 True 2494.500000 2850 90.5665 33 3917 2 chr7D.!!$R2 3884
4 TraesCS4A01G426300 chr7D 30524685 30525234 549 True 797.000000 797 92.7930 3365 3917 1 chr7D.!!$R1 552

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
75 88 0.107945 GAGCTCTTGTTGCCGGATCT 60.108 55.0 5.05 0.0 0.0 2.75 F
1014 1142 0.618458 TCAAGATGGGTAGTGGTGGC 59.382 55.0 0.00 0.0 0.0 5.01 F
2014 2187 0.970640 TCTTCGTGGGTGAATTCGGA 59.029 50.0 0.04 0.0 0.0 4.55 F
2291 2465 0.246635 CACCGATCCTCGTCACCTTT 59.753 55.0 0.00 0.0 38.4 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1291 1419 0.035176 GAGGGAGGCTGCTGATGATC 59.965 60.000 5.84 0.0 0.00 2.92 R
2037 2210 0.392193 CTGCATGCTCTTCTTCCCGT 60.392 55.000 20.33 0.0 0.00 5.28 R
2833 3010 1.295423 GGTAAGCTGCCTCCGTCAA 59.705 57.895 0.00 0.0 0.00 3.18 R
3315 3502 2.042831 AAGAGCAGACGCAATGGCC 61.043 57.895 0.00 0.0 42.27 5.36 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
20 21 1.735700 CGCCTGCTCTTATCGTCAACA 60.736 52.381 0.00 0.00 0.00 3.33
70 83 2.671177 CGTGGAGCTCTTGTTGCCG 61.671 63.158 14.64 2.14 0.00 5.69
75 88 0.107945 GAGCTCTTGTTGCCGGATCT 60.108 55.000 5.05 0.00 0.00 2.75
148 161 7.402811 TGTAAACGAGTTAATTGTCAGACAG 57.597 36.000 2.82 0.00 0.00 3.51
165 179 8.316946 TGTCAGACAGAATAAATGTTGATCTCT 58.683 33.333 0.00 0.00 0.00 3.10
168 182 9.985318 CAGACAGAATAAATGTTGATCTCTTTC 57.015 33.333 0.00 0.00 0.00 2.62
169 183 9.956640 AGACAGAATAAATGTTGATCTCTTTCT 57.043 29.630 0.00 0.00 0.00 2.52
172 186 9.784680 CAGAATAAATGTTGATCTCTTTCTTGG 57.215 33.333 0.00 0.00 0.00 3.61
173 187 9.745018 AGAATAAATGTTGATCTCTTTCTTGGA 57.255 29.630 0.00 0.00 0.00 3.53
178 192 3.238108 TGATCTCTTTCTTGGACTCGC 57.762 47.619 0.00 0.00 0.00 5.03
215 229 8.358148 GGATCAAGCAAATCTTATCACAATGAT 58.642 33.333 0.00 0.00 40.72 2.45
316 330 7.588169 AGCTAAATGGTGGTATATACCCAAAA 58.412 34.615 25.90 11.66 45.87 2.44
326 340 7.281549 GTGGTATATACCCAAAATTTCTGACGT 59.718 37.037 25.90 0.00 45.87 4.34
328 342 6.693315 ATATACCCAAAATTTCTGACGTGG 57.307 37.500 0.00 0.00 0.00 4.94
401 498 6.895782 TCTACCCAATGTATAAGGAAGGTTG 58.104 40.000 0.00 0.00 0.00 3.77
433 530 4.564821 CCTCTCAAAAAGGACGGATACCAA 60.565 45.833 0.00 0.00 35.83 3.67
475 576 0.877743 GAGCCAACTTCCTGCTGAAC 59.122 55.000 0.00 0.00 34.99 3.18
490 591 6.262273 TCCTGCTGAACTTTTAGTTGTAAAGG 59.738 38.462 0.00 0.50 38.80 3.11
639 740 1.225373 AGGCCAGCCATCCTATCAAA 58.775 50.000 12.03 0.00 38.92 2.69
648 749 3.960102 GCCATCCTATCAAATTTGTCCCA 59.040 43.478 17.47 0.00 0.00 4.37
771 898 9.950680 GGTTCCTTATATATGACACAACAATTG 57.049 33.333 3.24 3.24 0.00 2.32
791 918 7.989170 ACAATTGATCTACAGATTGTATGAGCA 59.011 33.333 13.59 0.00 37.86 4.26
793 920 7.958053 TTGATCTACAGATTGTATGAGCATG 57.042 36.000 0.00 0.00 31.69 4.06
860 987 1.669502 GCGATGCAAAGCCAACAATGA 60.670 47.619 5.56 0.00 0.00 2.57
864 991 2.768698 TGCAAAGCCAACAATGAATGG 58.231 42.857 5.67 5.67 39.80 3.16
915 1042 1.282570 CAACGTGCCAAATGCGACT 59.717 52.632 0.00 0.00 45.60 4.18
955 1082 4.562963 GGTGGAGGCTTCCCTATAAATACG 60.563 50.000 13.07 0.00 43.12 3.06
1014 1142 0.618458 TCAAGATGGGTAGTGGTGGC 59.382 55.000 0.00 0.00 0.00 5.01
1077 1205 4.100084 CACCCATCGGCTGAGGCA 62.100 66.667 6.86 0.00 40.87 4.75
1095 1223 3.717294 GCATCCCTCCGTGGTGGT 61.717 66.667 6.28 0.00 39.52 4.16
1228 1356 1.613630 ATGACCTCCTTCGGTGGCT 60.614 57.895 1.10 0.00 39.73 4.75
1229 1357 1.903877 ATGACCTCCTTCGGTGGCTG 61.904 60.000 1.10 0.00 39.73 4.85
1288 1416 7.808381 TCATCGACTTCATCGGTAATTAATCTC 59.192 37.037 0.00 0.00 44.39 2.75
1291 1419 7.555639 GACTTCATCGGTAATTAATCTCTCG 57.444 40.000 0.00 0.00 0.00 4.04
1300 1428 6.252441 CGGTAATTAATCTCTCGATCATCAGC 59.748 42.308 0.00 0.00 0.00 4.26
1312 1440 2.071262 CATCAGCAGCCTCCCTCCT 61.071 63.158 0.00 0.00 0.00 3.69
1316 1444 3.726144 GCAGCCTCCCTCCTTGCT 61.726 66.667 0.00 0.00 33.52 3.91
1318 1446 1.378250 CAGCCTCCCTCCTTGCTTG 60.378 63.158 0.00 0.00 30.08 4.01
1323 1451 2.172717 GCCTCCCTCCTTGCTTGTATAA 59.827 50.000 0.00 0.00 0.00 0.98
1324 1452 3.371595 GCCTCCCTCCTTGCTTGTATAAA 60.372 47.826 0.00 0.00 0.00 1.40
1326 1454 5.066593 CCTCCCTCCTTGCTTGTATAAATC 58.933 45.833 0.00 0.00 0.00 2.17
1327 1455 5.397899 CCTCCCTCCTTGCTTGTATAAATCA 60.398 44.000 0.00 0.00 0.00 2.57
1328 1456 6.266131 TCCCTCCTTGCTTGTATAAATCAT 57.734 37.500 0.00 0.00 0.00 2.45
1329 1457 6.299141 TCCCTCCTTGCTTGTATAAATCATC 58.701 40.000 0.00 0.00 0.00 2.92
1330 1458 5.180117 CCCTCCTTGCTTGTATAAATCATCG 59.820 44.000 0.00 0.00 0.00 3.84
1331 1459 5.180117 CCTCCTTGCTTGTATAAATCATCGG 59.820 44.000 0.00 0.00 0.00 4.18
1332 1460 5.680619 TCCTTGCTTGTATAAATCATCGGT 58.319 37.500 0.00 0.00 0.00 4.69
1335 1463 7.936847 TCCTTGCTTGTATAAATCATCGGTAAT 59.063 33.333 0.00 0.00 0.00 1.89
1336 1464 8.567948 CCTTGCTTGTATAAATCATCGGTAATT 58.432 33.333 0.00 0.00 0.00 1.40
1337 1465 9.599322 CTTGCTTGTATAAATCATCGGTAATTC 57.401 33.333 0.00 0.00 0.00 2.17
1343 1472 9.869757 TGTATAAATCATCGGTAATTCATCGAT 57.130 29.630 0.00 0.00 43.28 3.59
1385 1514 3.741476 GGCTTGCCTCTTGTGCCG 61.741 66.667 4.11 0.00 33.96 5.69
1414 1543 1.672356 CACACAAGGGGAGCTTCCG 60.672 63.158 4.51 0.00 37.43 4.30
1436 1565 3.723348 GGTGCCAACTTCGCCGTC 61.723 66.667 0.00 0.00 0.00 4.79
1442 1571 3.920196 AACTTCGCCGTCGGTGGT 61.920 61.111 23.98 12.50 33.43 4.16
1474 1603 1.876156 CAACTCCAGCTTCTTCCACAC 59.124 52.381 0.00 0.00 0.00 3.82
1520 1649 2.845345 CCCCCTCAACACCAGCCTT 61.845 63.158 0.00 0.00 0.00 4.35
1673 1812 1.703513 ACCTGGGTTTGGAGAAGTACC 59.296 52.381 0.00 0.00 0.00 3.34
1684 1823 3.508793 TGGAGAAGTACCGGTTAAGTCAG 59.491 47.826 15.04 0.00 0.00 3.51
1700 1839 4.399004 AGTCAGCTGATTATGGTCACTC 57.601 45.455 21.47 1.81 0.00 3.51
1925 2097 8.569641 GTTGTACCATTAACCAAACACTTGATA 58.430 33.333 0.00 0.00 34.14 2.15
1927 2099 9.961264 TGTACCATTAACCAAACACTTGATATA 57.039 29.630 0.00 0.00 34.14 0.86
1948 2121 9.680315 GATATACGTACATATAATCAAGAGGCC 57.320 37.037 0.00 0.00 0.00 5.19
1968 2141 3.863400 GCCAAATGCTTCATTGCAGAGTT 60.863 43.478 0.00 0.00 46.71 3.01
1984 2157 4.321527 GCAGAGTTCAAGGATTTCTTTGGG 60.322 45.833 3.02 0.00 34.22 4.12
2014 2187 0.970640 TCTTCGTGGGTGAATTCGGA 59.029 50.000 0.04 0.00 0.00 4.55
2035 2208 4.341099 GAATCAACGACTACCACTACTCG 58.659 47.826 0.00 0.00 0.00 4.18
2037 2210 3.925379 TCAACGACTACCACTACTCGTA 58.075 45.455 0.00 0.00 38.38 3.43
2056 2229 0.392193 ACGGGAAGAAGAGCATGCAG 60.392 55.000 21.98 0.34 0.00 4.41
2074 2247 2.031437 GCAGGAAATCAGAGCATTCGTC 59.969 50.000 0.00 0.00 0.00 4.20
2086 2259 2.437281 AGCATTCGTCCCAGATCTCATT 59.563 45.455 0.00 0.00 0.00 2.57
2096 2269 3.554544 CCCAGATCTCATTCAGACCATCG 60.555 52.174 0.00 0.00 32.26 3.84
2122 2295 2.435059 GCCGAGGCAAGACCACTC 60.435 66.667 9.58 0.00 43.14 3.51
2165 2338 4.757149 GTCACTACTGCCATTTTGAGTCTT 59.243 41.667 0.00 0.00 0.00 3.01
2166 2339 5.239525 GTCACTACTGCCATTTTGAGTCTTT 59.760 40.000 0.00 0.00 0.00 2.52
2291 2465 0.246635 CACCGATCCTCGTCACCTTT 59.753 55.000 0.00 0.00 38.40 3.11
2487 2661 1.535462 AGTCGCCTGAAAAATTCGGTG 59.465 47.619 7.65 7.65 36.15 4.94
2547 2721 2.223433 GCCCTGAGATTCATTTCGCTTG 60.223 50.000 0.00 0.00 0.00 4.01
2786 2963 4.063967 TGGTGACGAAGCCGCGAT 62.064 61.111 8.23 0.00 39.95 4.58
2854 3031 2.125106 CGGAGGCAGCTTACCACC 60.125 66.667 8.53 8.53 34.82 4.61
2918 3095 4.330347 GCCTACAACAGCTAGCTCTTAAAC 59.670 45.833 16.15 0.00 0.00 2.01
2941 3118 1.224075 CTGCCTATGTCTGAATGCGG 58.776 55.000 0.00 0.00 0.00 5.69
3113 3293 3.719816 AAAAAGGACGGTGGAGACC 57.280 52.632 0.00 0.00 39.14 3.85
3117 3297 1.777941 AAGGACGGTGGAGACCTATC 58.222 55.000 0.00 0.00 40.58 2.08
3190 3370 4.260784 GCACGCCATCGAGAAAATTTAGAT 60.261 41.667 0.00 0.00 39.41 1.98
3208 3388 2.968574 AGATCTACTTGGACGGCATCAT 59.031 45.455 0.00 0.00 0.00 2.45
3226 3406 7.011016 CGGCATCATGACACTTTTTAGTATGTA 59.989 37.037 0.00 0.00 0.00 2.29
3227 3407 8.840321 GGCATCATGACACTTTTTAGTATGTAT 58.160 33.333 0.00 0.00 0.00 2.29
3315 3502 2.097056 CGCATTACGCTCACTGATCATG 60.097 50.000 0.00 0.00 39.08 3.07
3339 3526 0.106708 TTGCGTCTGCTCTTGGAACT 59.893 50.000 0.00 0.00 43.34 3.01
3342 3529 0.601046 CGTCTGCTCTTGGAACTGCA 60.601 55.000 0.00 0.00 0.00 4.41
3347 3534 0.601311 GCTCTTGGAACTGCAGACGT 60.601 55.000 23.35 4.69 0.00 4.34
3424 3611 7.488187 TGAGCTACAGAAAAGATTATGCATC 57.512 36.000 0.19 0.00 30.83 3.91
3512 3700 1.028330 ATGGGCGTGCAAGTGAGATG 61.028 55.000 0.59 0.00 0.00 2.90
3521 3709 5.500931 GCGTGCAAGTGAGATGAGTATAAAC 60.501 44.000 0.59 0.00 0.00 2.01
3526 3714 8.289618 TGCAAGTGAGATGAGTATAAACAAAAC 58.710 33.333 0.00 0.00 0.00 2.43
3544 3732 3.735237 AACGTGAGAATATGATCCGCT 57.265 42.857 0.00 0.00 0.00 5.52
3555 3743 2.559698 TGATCCGCTCAAAAGGAACA 57.440 45.000 0.00 0.00 40.32 3.18
3596 3784 9.300681 ACAAAAGATTGATTCCTCACTATTGAA 57.699 29.630 0.00 0.00 38.94 2.69
3599 3787 9.690913 AAAGATTGATTCCTCACTATTGAATGA 57.309 29.630 0.00 0.00 0.00 2.57
3604 3792 9.551734 TTGATTCCTCACTATTGAATGATACAG 57.448 33.333 0.00 0.00 0.00 2.74
3607 3795 7.839680 TCCTCACTATTGAATGATACAGCTA 57.160 36.000 0.00 0.00 0.00 3.32
3614 3802 8.260818 ACTATTGAATGATACAGCTACAACACT 58.739 33.333 0.00 0.00 0.00 3.55
3617 3805 9.618890 ATTGAATGATACAGCTACAACACTATT 57.381 29.630 0.00 0.00 0.00 1.73
3618 3806 9.448438 TTGAATGATACAGCTACAACACTATTT 57.552 29.630 0.00 0.00 0.00 1.40
3669 3857 7.663081 CCACACTTCTGGTTAATCTATATGCAT 59.337 37.037 3.79 3.79 0.00 3.96
3723 3913 5.526479 GCACATAGTGATCATGACTTGATGT 59.474 40.000 8.47 1.96 45.29 3.06
3729 3919 6.705302 AGTGATCATGACTTGATGTACAACT 58.295 36.000 8.47 0.00 45.29 3.16
3732 3922 9.750125 GTGATCATGACTTGATGTACAACTATA 57.250 33.333 8.47 0.00 45.29 1.31
3830 4021 6.161855 TGGACCTATAAAGATACAGTGCAG 57.838 41.667 0.00 0.00 0.00 4.41
3910 4101 7.259088 ACCAAACCTAGTGATTCACTTCTAT 57.741 36.000 23.53 6.80 42.59 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.924090 GTTGACGATAAGAGCAGGCG 59.076 55.000 0.00 0.00 0.00 5.52
20 21 2.590821 AGCAGGCAACAAGAGTTTCAT 58.409 42.857 0.00 0.00 35.28 2.57
66 79 2.900273 GGTAGCACAGATCCGGCA 59.100 61.111 0.00 0.00 0.00 5.69
70 83 1.084370 GCACACGGTAGCACAGATCC 61.084 60.000 0.00 0.00 0.00 3.36
75 88 0.892063 TGATAGCACACGGTAGCACA 59.108 50.000 7.37 2.70 36.64 4.57
148 161 9.780413 GTCCAAGAAAGAGATCAACATTTATTC 57.220 33.333 0.00 0.00 0.00 1.75
165 179 2.358247 GGCCGCGAGTCCAAGAAA 60.358 61.111 8.23 0.00 0.00 2.52
178 192 4.161295 TTGATCCTCGCCAGGCCG 62.161 66.667 5.63 0.84 40.12 6.13
215 229 3.860641 TGCAGCAATTTCTACAGATCGA 58.139 40.909 0.00 0.00 0.00 3.59
401 498 3.267031 TCCTTTTTGAGAGGGGAAGATCC 59.733 47.826 0.00 0.00 34.93 3.36
475 576 8.126700 CGGGCATATTACCTTTACAACTAAAAG 58.873 37.037 0.00 0.00 34.40 2.27
490 591 4.377021 TGTGAGACATTCGGGCATATTAC 58.623 43.478 0.00 0.00 0.00 1.89
771 898 6.307558 CGACATGCTCATACAATCTGTAGATC 59.692 42.308 0.00 0.00 36.14 2.75
791 918 1.086067 CAATGCACCGAGAGCGACAT 61.086 55.000 0.00 0.00 40.82 3.06
793 920 1.014044 TTCAATGCACCGAGAGCGAC 61.014 55.000 0.00 0.00 40.82 5.19
860 987 1.656818 CTTTGTCGCGCCATCCCATT 61.657 55.000 0.00 0.00 0.00 3.16
864 991 1.353103 CATCTTTGTCGCGCCATCC 59.647 57.895 0.00 0.00 0.00 3.51
926 1053 2.032681 GAAGCCTCCACCAAGCGT 59.967 61.111 0.00 0.00 0.00 5.07
955 1082 4.036971 ACGTCCTTAGTGATGATGAGCTAC 59.963 45.833 0.00 0.00 0.00 3.58
1014 1142 2.730094 GCAGCCAACACCAACCTG 59.270 61.111 0.00 0.00 0.00 4.00
1077 1205 3.402681 CCACCACGGAGGGATGCT 61.403 66.667 1.11 0.00 43.89 3.79
1080 1208 3.009115 CCACCACCACGGAGGGAT 61.009 66.667 4.48 0.00 41.68 3.85
1098 1226 0.450583 CGAAGATGGAGTCGAACGGA 59.549 55.000 0.00 0.00 39.64 4.69
1288 1416 0.319727 GGAGGCTGCTGATGATCGAG 60.320 60.000 0.00 0.00 0.00 4.04
1291 1419 0.035176 GAGGGAGGCTGCTGATGATC 59.965 60.000 5.84 0.00 0.00 2.92
1300 1428 1.378250 CAAGCAAGGAGGGAGGCTG 60.378 63.158 0.00 0.00 36.58 4.85
1312 1440 9.114952 TGAATTACCGATGATTTATACAAGCAA 57.885 29.630 0.00 0.00 0.00 3.91
1316 1444 9.699703 TCGATGAATTACCGATGATTTATACAA 57.300 29.630 0.00 0.00 0.00 2.41
1327 1455 6.531503 AGGATACATCGATGAATTACCGAT 57.468 37.500 31.33 8.43 42.88 4.18
1328 1456 5.977489 AGGATACATCGATGAATTACCGA 57.023 39.130 31.33 6.47 41.41 4.69
1329 1457 7.170828 TGAAAAGGATACATCGATGAATTACCG 59.829 37.037 31.33 2.81 41.41 4.02
1330 1458 8.378172 TGAAAAGGATACATCGATGAATTACC 57.622 34.615 31.33 22.50 41.41 2.85
1331 1459 8.012241 GCTGAAAAGGATACATCGATGAATTAC 58.988 37.037 31.33 15.30 41.41 1.89
1332 1460 7.933577 AGCTGAAAAGGATACATCGATGAATTA 59.066 33.333 31.33 14.05 41.41 1.40
1335 1463 5.674525 AGCTGAAAAGGATACATCGATGAA 58.325 37.500 31.33 3.35 41.41 2.57
1336 1464 5.163416 TGAGCTGAAAAGGATACATCGATGA 60.163 40.000 31.33 15.26 41.41 2.92
1337 1465 5.052481 TGAGCTGAAAAGGATACATCGATG 58.948 41.667 23.68 23.68 41.41 3.84
1343 1472 3.347216 GCCTTGAGCTGAAAAGGATACA 58.653 45.455 19.09 0.00 44.93 2.29
1379 1508 4.367023 GACAGGTACGGCGGCACA 62.367 66.667 13.24 0.00 0.00 4.57
1385 1514 0.949105 CCTTGTGTGACAGGTACGGC 60.949 60.000 0.00 0.00 0.00 5.68
1442 1571 2.343758 GAGTTGAGAGCGGTGGCA 59.656 61.111 0.00 0.00 43.41 4.92
1673 1812 4.442706 ACCATAATCAGCTGACTTAACCG 58.557 43.478 20.97 11.74 0.00 4.44
1700 1839 1.115930 ATCCTACGCTGGCCTAGGTG 61.116 60.000 11.31 8.80 32.59 4.00
1736 1875 6.089920 TGTTCATCACGTTTGATATTCGTC 57.910 37.500 0.00 0.00 40.79 4.20
1737 1876 6.662414 ATGTTCATCACGTTTGATATTCGT 57.338 33.333 0.00 0.00 40.79 3.85
1738 1877 7.579093 GTGTATGTTCATCACGTTTGATATTCG 59.421 37.037 0.00 0.00 40.79 3.34
1925 2097 7.476540 TGGCCTCTTGATTATATGTACGTAT 57.523 36.000 12.18 12.18 0.00 3.06
1927 2099 5.801531 TGGCCTCTTGATTATATGTACGT 57.198 39.130 3.32 0.00 0.00 3.57
1948 2121 4.552355 TGAACTCTGCAATGAAGCATTTG 58.448 39.130 0.00 0.00 44.68 2.32
1968 2141 4.517285 CGATCTCCCAAAGAAATCCTTGA 58.483 43.478 0.00 0.00 37.61 3.02
1984 2157 1.535015 CCCACGAAGAAGAGCGATCTC 60.535 57.143 2.43 0.00 39.65 2.75
2014 2187 4.352600 CGAGTAGTGGTAGTCGTTGATT 57.647 45.455 2.18 0.00 44.08 2.57
2035 2208 1.291132 GCATGCTCTTCTTCCCGTAC 58.709 55.000 11.37 0.00 0.00 3.67
2037 2210 0.392193 CTGCATGCTCTTCTTCCCGT 60.392 55.000 20.33 0.00 0.00 5.28
2056 2229 1.943340 GGGACGAATGCTCTGATTTCC 59.057 52.381 0.00 0.00 0.00 3.13
2074 2247 3.554544 CGATGGTCTGAATGAGATCTGGG 60.555 52.174 0.00 0.00 32.29 4.45
2122 2295 1.039068 ATGAGGAGCAGGATGAGTCG 58.961 55.000 0.00 0.00 39.69 4.18
2193 2366 5.521372 CGATCACTCTCTTCATGTGCATTAA 59.479 40.000 0.00 0.00 0.00 1.40
2291 2465 3.699955 CGAAGCATCGGCGTCCTCA 62.700 63.158 6.85 0.00 44.36 3.86
2487 2661 9.209175 GAAGAACATATACACAGAATGATACCC 57.791 37.037 0.00 0.00 39.69 3.69
2547 2721 6.958296 TGTGCAATATGTTTGGACAAAACTCC 60.958 38.462 12.86 0.00 45.42 3.85
2606 2780 5.296813 ACCTTACGAATCAAGATTTGCAC 57.703 39.130 9.44 0.00 35.98 4.57
2643 2817 1.956477 ACTTCTGCAATGTTCACCACC 59.044 47.619 0.00 0.00 0.00 4.61
2786 2963 3.060000 ACGGATCCTCGCACGTCA 61.060 61.111 10.75 0.00 33.92 4.35
2833 3010 1.295423 GGTAAGCTGCCTCCGTCAA 59.705 57.895 0.00 0.00 0.00 3.18
2854 3031 2.490509 TGAGCCAATCTTCAGCAATGTG 59.509 45.455 0.00 0.00 0.00 3.21
2918 3095 2.133553 CATTCAGACATAGGCAGCTCG 58.866 52.381 0.00 0.00 0.00 5.03
2929 3106 2.028567 TGACATGTACCGCATTCAGACA 60.029 45.455 0.00 0.00 35.19 3.41
2941 3118 2.380084 ACCGTGTCCATGACATGTAC 57.620 50.000 14.26 9.32 45.07 2.90
3117 3297 8.763049 TGCTGAGATATCATAATTTTAGACCG 57.237 34.615 5.32 0.00 0.00 4.79
3190 3370 2.107366 TCATGATGCCGTCCAAGTAGA 58.893 47.619 0.00 0.00 0.00 2.59
3226 3406 8.044908 ACATACCGGTAAAACATCTAAACTCAT 58.955 33.333 20.22 0.00 0.00 2.90
3227 3407 7.388437 ACATACCGGTAAAACATCTAAACTCA 58.612 34.615 20.22 0.00 0.00 3.41
3315 3502 2.042831 AAGAGCAGACGCAATGGCC 61.043 57.895 0.00 0.00 42.27 5.36
3339 3526 3.378911 TGTGACAAATCTACGTCTGCA 57.621 42.857 0.00 0.00 33.18 4.41
3342 3529 4.330944 TGGTTGTGACAAATCTACGTCT 57.669 40.909 0.00 0.00 33.18 4.18
3347 3534 6.073276 CGTCTTCAATGGTTGTGACAAATCTA 60.073 38.462 0.00 0.00 36.13 1.98
3424 3611 3.282831 TGTATGCACGTATCGATCTGG 57.717 47.619 0.00 0.00 0.00 3.86
3454 3642 3.561143 TGACCAAGCTAAGAAAAAGCCA 58.439 40.909 0.00 0.00 41.02 4.75
3521 3709 4.271049 AGCGGATCATATTCTCACGTTTTG 59.729 41.667 0.00 0.00 0.00 2.44
3526 3714 3.288809 TGAGCGGATCATATTCTCACG 57.711 47.619 0.00 0.00 31.12 4.35
3540 3728 4.865776 TGTTTATTGTTCCTTTTGAGCGG 58.134 39.130 0.00 0.00 0.00 5.52
3544 3732 6.577103 TGTGCATGTTTATTGTTCCTTTTGA 58.423 32.000 0.00 0.00 0.00 2.69
3555 3743 9.107177 TCAATCTTTTGTTTGTGCATGTTTATT 57.893 25.926 0.00 0.00 34.32 1.40
3596 3784 7.224753 CCGAAAATAGTGTTGTAGCTGTATCAT 59.775 37.037 0.00 0.00 0.00 2.45
3597 3785 6.533723 CCGAAAATAGTGTTGTAGCTGTATCA 59.466 38.462 0.00 0.00 0.00 2.15
3598 3786 6.534079 ACCGAAAATAGTGTTGTAGCTGTATC 59.466 38.462 0.00 0.00 0.00 2.24
3599 3787 6.312918 CACCGAAAATAGTGTTGTAGCTGTAT 59.687 38.462 0.00 0.00 0.00 2.29
3604 3792 5.407387 TCTTCACCGAAAATAGTGTTGTAGC 59.593 40.000 0.00 0.00 35.45 3.58
3607 3795 4.210537 CGTCTTCACCGAAAATAGTGTTGT 59.789 41.667 0.00 0.00 35.45 3.32
3614 3802 5.001237 TCATAGCGTCTTCACCGAAAATA 57.999 39.130 0.00 0.00 0.00 1.40
3617 3805 2.991190 GTTCATAGCGTCTTCACCGAAA 59.009 45.455 0.00 0.00 0.00 3.46
3618 3806 2.230508 AGTTCATAGCGTCTTCACCGAA 59.769 45.455 0.00 0.00 0.00 4.30
3669 3857 9.964354 ATCTATTTATCTTGGCAGCATACATAA 57.036 29.630 0.00 0.00 0.00 1.90
3830 4021 5.106277 GGAAGAGCCACACCAGTAAATAAAC 60.106 44.000 0.00 0.00 36.34 2.01


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

AutoCloner maintained by Alex Coulton.